Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth n_ref_count n_alt_count callers all_effects Allele Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation ALLELE_NUM DISTANCE STRAND_VEP SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP SWISSPROT TREMBL UNIPARC RefSeq SIFT PolyPhen EXON INTRON DOMAINS GMAF AFR_MAF AMR_MAF ASN_MAF EAS_MAF EUR_MAF SAS_MAF AA_MAF EA_MAF CLIN_SIG SOMATIC PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO MINIMISED ExAC_AF ExAC_AF_AFR ExAC_AF_AMR ExAC_AF_EAS ExAC_AF_FIN ExAC_AF_NFE ExAC_AF_OTH ExAC_AF_SAS GENE_PHENO FILTER flanking_bps variant_id variant_qual ExAC_AF_Adj ExAC_AC_AN_Adj ExAC_AC_AN ExAC_AC_AN_AFR ExAC_AC_AN_AMR ExAC_AC_AN_EAS ExAC_AC_AN_FIN ExAC_AC_AN_NFE ExAC_AC_AN_OTH ExAC_AC_AN_SAS ExAC_FILTER PoN_filtered_pon_total_counts_coverage_less_8 PoN_filtered_pon_total_counts_coverage_greater_8 PoN_filtered_pon_alt_count_greater1_af_greater_01percent PoN_filtered_pon_alt_count_greater2_af_greater_03percent PoN_filtered_pon_alt_count_greater3_af_greater_1percent PoN_filtered_pon_alt_count_greater3_af_greater_3percent PoN_filtered_pon_alt_count_greater3_af_greater_20percent PoN_filtered_pon_alt_count_greater10_af_greater_20percent PoN_filtered_pon_loglike PoN_filtered_pon_weight PoN_filtered_pon_pass_grid PoN_filtered_pon_pass_loglike PoN_filtered_pon_pass_weight PoN_filtered_pon_low_alt_count newbase effect_idx newbase_idx pat_idx start end tum_allele1 tum_allele2 is_coding is_flank is_indel is_ins is_del is_missense is_nonsense is_splice is_silent gene_idx context_and_effect context65 categ_idx trackpos categ gene chr pos type classification ref_allele patient DistBetween_Mutations Distance_to_LT_end Distance_to_RT_end Strain_Mutation_ID Dataset_Mutation_ID Complex_ID Complex_Size StrainCluster_ID Dataset_Cluster_ID Distance_Between_Clusters Cluster_Size_Mutations Cluster_Size_Complexes Cluster_Length Cluster_Coordination Content_of_non_coordinated_cluster Cluster_Pvalue NBPF6 0 . GRCh38 1 108452197 108452197 + Silent SNP A A G novel 11LU013_T 11LU013_N A A c.186A>G p.= p.E62E ENST00000495380 3/15 59 47 12 43 43 0 strelka-varscan-mutect NBPF6,synonymous_variant,p.=,ENST00000495380,NM_001143988.1;NBPF6,synonymous_variant,p.=,ENST00000294652,;NBPF6,synonymous_variant,p.=,ENST00000370040,NM_001143987.1;NBPF6,synonymous_variant,p.=,ENST00000531446,; G ENST00000495380 Transcript synonymous_variant 399/2494 186/1917 62/638 E gaA/gaG 1 1 NBPF6 HGNC HGNC:31988 protein_coding YES CCDS44184.1 ENSP00000417277 Q5VWK0 UPI0000160A67 NM_001143988.1 3/15 hmmpanther:PTHR14199 LOW 1 SNV 5 1 PASS . . 66 143 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 1 108452197 108452197 A G 1 0 0 0 0 0 0 0 1 10214 69 3 5 5 NBPF6 1 108452197 Silent SNP A 11LU013_T 108452197 140504225 1 1 PROK1 0 . GRCh38 1 110454043 110454043 + Missense_Mutation SNP C C T rs751951334 11LU013_T 11LU013_N C C c.155C>T p.Pro52Leu p.P52L ENST00000271331 2/3 319 291 28 360 360 0 strelka-varscan-mutect PROK1,missense_variant,p.Pro52Leu,ENST00000271331,NM_032414.2;RP11-470L19.5,downstream_gene_variant,,ENST00000481350,; T ENST00000271331 Transcript missense_variant 172/1338 155/318 52/105 P/L cCg/cTg rs751951334,COSM2118696 1 1 PROK1 HGNC HGNC:18454 protein_coding YES CCDS825.1 ENSP00000271331 P58294 A0A024R0B1 UPI0000034E3F NM_032414.2 deleterious(0) 2/3 hmmpanther:PTHR18821,hmmpanther:PTHR18821:SF7,Pfam_domain:PF06607,Gene3D:2.10.80.10,Superfamily_domains:SSF57190,PD059788 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751951334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 110454043 110454043 C T 1 0 0 0 0 1 0 0 0 12683 652 23 1 1 PROK1 1 110454043 Missense_Mutation SNP C 11LU013_T 2001846 110454043 138502379 2 2 UBAP2L 0 . GRCh38 1 154228721 154228721 + Missense_Mutation SNP A A G novel 11LU013_T 11LU013_N A A c.275A>G p.Asp92Gly p.D92G ENST00000428931 4/27 126 95 31 168 168 0 strelka-varscan-mutect UBAP2L,missense_variant,p.Asp92Gly,ENST00000271877,NM_001287816.1;UBAP2L,missense_variant,p.Asp92Gly,ENST00000428931,NM_014847.3;UBAP2L,missense_variant,p.Asp92Gly,ENST00000361546,;UBAP2L,missense_variant,p.Asp92Gly,ENST00000613315,NM_001287815.1;UBAP2L,missense_variant,p.Asp92Gly,ENST00000343815,NM_001127320.2;UBAP2L,missense_variant,p.Asp92Gly,ENST00000368504,;UBAP2L,missense_variant,p.Asp92Gly,ENST00000412596,;UBAP2L,missense_variant,p.Asp92Gly,ENST00000437652,;UBAP2L,missense_variant,p.Asp92Gly,ENST00000456325,;UBAP2L,missense_variant,p.Asp92Gly,ENST00000441890,; G ENST00000428931 Transcript missense_variant 442/3988 275/3264 92/1087 D/G gAc/gGc 1 1 UBAP2L HGNC HGNC:29877 protein_coding YES CCDS1063.1 ENSP00000389445 Q14157 UPI000013E257 NM_014847.3 deleterious(0) 4/27 hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF18,Superfamily_domains:SSF46934 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 1 154228721 154228721 A G 1 0 0 0 0 1 0 0 0 17360 289 10 5 5 UBAP2L 1 154228721 Missense_Mutation SNP A 11LU013_T 43774678 154228721 94727701 3 3 PEAR1 0 . GRCh38 1 156905362 156905362 + Missense_Mutation SNP C C T rs192672356 11LU013_T 11LU013_N C C c.245C>T p.Thr82Met p.T82M ENST00000338302 5/24 193 175 18 148 147 1 strelka-varscan-mutect PEAR1,missense_variant,p.Thr82Met,ENST00000338302,;PEAR1,missense_variant,p.Thr82Met,ENST00000292357,NM_001080471.1;PEAR1,missense_variant,p.Thr82Met,ENST00000455314,;PEAR1,3_prime_UTR_variant,,ENST00000444016,;PEAR1,upstream_gene_variant,,ENST00000469390,;PEAR1,upstream_gene_variant,,ENST00000482505,; T ENST00000338302 Transcript missense_variant 470/4970 245/3114 82/1037 T/M aCg/aTg rs192672356,COSM1162337 1 1 PEAR1 HGNC HGNC:33631 protein_coding YES CCDS30892.1 ENSP00000344465 Q5VY43 UPI000045889A tolerated(0.15) 5/24 PROSITE_profiles:PS51041,hmmpanther:PTHR24052,hmmpanther:PTHR24052:SF12 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs192672356 . 0 205 0 3 2 0 0 0 -7.149164 0.9397098 1 1 1 0 T 3 4 1 156905362 156905362 C T 1 0 0 0 0 1 0 0 0 11801 536 19 1 1 PEAR1 1 156905362 Missense_Mutation SNP C 11LU013_T 2676641 156905362 92051060 4 4 LMX1A 0 . GRCh38 1 165213729 165213729 + Missense_Mutation SNP C C T 11LU013_T 11LU013_N C C c.581G>A p.Arg194His p.R194H ENST00000342310 5/9 410 352 58 342 342 0 strelka-varscan-mutect LMX1A,missense_variant,p.Arg194His,ENST00000342310,NM_177398.3;LMX1A,missense_variant,p.Arg194His,ENST00000294816,NM_001174069.1;LMX1A,missense_variant,p.Arg194His,ENST00000367893,;RP11-38C18.2,downstream_gene_variant,,ENST00000457106,;RP11-38C18.3,upstream_gene_variant,,ENST00000441773,;RP11-38C18.3,upstream_gene_variant,,ENST00000426178,;LMX1A,upstream_gene_variant,,ENST00000489443,; T ENST00000342310 Transcript missense_variant 964/3545 581/1149 194/382 R/H cGc/cAc COSM2088818 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 deleterious(0) 5/9 PROSITE_profiles:PS50071,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 1 MODERATE 1 SNV 2 1 1 PASS rs909983869 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 165213729 165213729 C T 1 0 0 0 0 1 0 0 0 8788 768 27 1 1 LMX1A 1 165213729 Missense_Mutation SNP C 11LU013_T 8308367 165213729 83742693 5 5 TNR 0 . GRCh38 1 175365050 175365050 + Silent SNP G G A novel 11LU013_T 11LU013_N G G c.2547C>T p.= p.G849G ENST00000367674 12/23 116 101 15 87 87 0 strelka-varscan-mutect TNR,synonymous_variant,p.=,ENST00000367674,;TNR,synonymous_variant,p.=,ENST00000263525,NM_003285.2; A ENST00000367674 Transcript synonymous_variant 3256/12949 2547/4077 849/1358 G ggC/ggT 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 12/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 1 175365050 175365050 G A 1 0 0 0 0 0 0 0 1 16811 1306 46 3 3 TNR 1 175365050 Silent SNP G 11LU013_T 10151321 175365050 73591372 6 6 RNF2 0 . GRCh38 1 185093072 185093072 + Missense_Mutation SNP G G A novel 11LU013_T 11LU013_N G G c.260G>A p.Cys87Tyr p.C87Y ENST00000367510 4/7 103 93 10 218 217 1 strelka-varscan-mutect RNF2,missense_variant,p.Cys87Tyr,ENST00000367510,NM_007212.3;RNF2,missense_variant,p.Cys87Tyr,ENST00000453650,;RNF2,intron_variant,,ENST00000367509,;RNF2,downstream_gene_variant,,ENST00000498201,; A ENST00000367510 Transcript missense_variant 548/3606 260/1011 87/336 C/Y tGt/tAt 1 1 RNF2 HGNC HGNC:10061 protein_coding YES CCDS1365.1 ENSP00000356480 Q99496 UPI000007131D NM_007212.3 deleterious(0) 4/7 Gene3D:3.30.40.10,Pfam_domain:PF13923,PROSITE_profiles:PS50089,hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF41,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 185093072 185093072 G A 1 0 0 0 0 1 0 0 0 13650 1377 48 3 3 RNF2 1 185093072 Missense_Mutation SNP G 11LU013_T 9728022 185093072 63863350 7 7 SLC30A10 0 . GRCh38 1 219928165 219928165 + Silent SNP G G C novel 11LU013_T 11LU013_N G G c.276C>G p.= p.L92L ENST00000366926 1/4 641 594 47 475 475 0 strelka-varscan-mutect SLC30A10,synonymous_variant,p.=,ENST00000366926,NM_018713.2;SLC30A10,intron_variant,,ENST00000484239,;SLC30A10,synonymous_variant,p.=,ENST00000356609,; C ENST00000366926 Transcript synonymous_variant 438/1915 276/1458 92/485 L ctC/ctG 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 1/4 Superfamily_domains:0054606,Gene3D:3h90A01,Pfam_domain:PF01545,hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF14,TIGRFAM_domain:TIGR01297,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 1 219928165 219928165 G C 1 0 0 0 0 0 0 0 1 14824 929 33 4 4 SLC30A10 1 219928165 Silent SNP G 11LU013_T 34835093 219928165 29028257 8 8 MARCH4 0 . GRCh38 2 216277789 216277789 + Missense_Mutation SNP C C T rs367784136 11LU013_T 11LU013_N C C c.748G>A p.Ala250Thr p.A250T ENST00000273067 3/4 230 185 45 231 231 0 strelka-varscan MARCH4,missense_variant,p.Ala250Thr,ENST00000273067,NM_020814.2; T ENST00000273067 Transcript missense_variant 2515/4447 748/1233 250/410 A/T Gcc/Acc rs367784136,COSM1326434,COSM573605 1 -1 MARCH4 HGNC HGNC:29269 protein_coding YES CCDS33376.1 ENSP00000273067 Q9P2E8 UPI00001C1DB9 NM_020814.2 deleterious(0.03) 3/4 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF51,Transmembrane_helices:TMhelix 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 216277789 216277789 C T 1 0 0 0 0 1 0 0 0 9228 768 27 1 1 MARCH4 2 216277789 Missense_Mutation SNP C 11LU013_T 216277789 25915740 9 9 ANO7 0 . GRCh38 2 241203346 241203346 + Missense_Mutation SNP C C T rs374614039 11LU013_T 11LU013_N C C c.899C>T p.Thr300Met p.T300M ENST00000274979 9/25 53 32 21 66 66 0 strelka-varscan-mutect ANO7,missense_variant,p.Thr300Met,ENST00000274979,NM_001001891.3;ANO7,missense_variant,p.Thr299Met,ENST00000402430,;ANO7,downstream_gene_variant,,ENST00000475532,; T ENST00000274979 Transcript missense_variant 1002/4128 899/2802 300/933 T/M aCg/aTg rs374614039 1 1 ANO7 HGNC HGNC:31677 protein_coding YES CCDS33423.1 ENSP00000274979 Q6IWH7 UPI0000D612DB NM_001001891.3 tolerated(0.34) 9/25 hmmpanther:PTHR12308:SF22,hmmpanther:PTHR12308,Pfam_domain:PF16178 MODERATE 1 SNV 1 1 PASS rs374614039 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 241203346 241203346 C T 1 0 0 0 0 1 0 0 0 809 536 19 1 1 ANO7 2 241203346 Missense_Mutation SNP C 11LU013_T 24925557 241203346 990183 10 10 GOLGA4 0 . GRCh38 3 37295045 37295046 + In_Frame_Ins INS - - AAGATC novel 11LU013_T 11LU013_N - - c.717_722dupAGATCA p.Asp240_Gln241dup p.D240_Q241dup ENST00000356847 7/23 50 37 13 161 161 0 sindel-varindel GOLGA4,inframe_insertion,p.Asp218_Gln219dup,ENST00000361924,NM_002078.4;GOLGA4,inframe_insertion,p.Asp240_Gln241dup,ENST00000356847,NM_001172713.1;GOLGA4,inframe_insertion,p.Asp89_Gln90dup,ENST00000437131,;GOLGA4,inframe_insertion,p.Asp223_Gln224dup,ENST00000450863,;GOLGA4,inframe_insertion,p.Asp21_Gln22dup,ENST00000617480,;GOLGA4,intron_variant,,ENST00000429018,;GOLGA4,intron_variant,,ENST00000444882,;GOLGA4,non_coding_transcript_exon_variant,,ENST00000435830,;GOLGA4,non_coding_transcript_exon_variant,,ENST00000419177,; AAGATC ENST00000356847 Transcript inframe_insertion 1014-1015/7673 715-716/6732 239/2243 K/KDQ aaa/aAAGATCaa 1 1 GOLGA4 HGNC HGNC:4427 protein_coding YES CCDS54564.1 ENSP00000349305 Q13439 UPI000198C9CA NM_001172713.1 7/23 hmmpanther:PTHR19327 MODERATE 1 insertion 1 7 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 AAGATC 7 5 1 37295045 37295045 - AAGATC 1 0 1 1 0 0 0 0 0 6433 247 9 0 0 GOLGA4 3 37295045 In_Frame_Ins INS - 11LU013_T 37295045 161000514 11 11 ANO10 0 . GRCh38 3 43600486 43600486 + Missense_Mutation SNP T T A novel 11LU013_T 11LU013_N T T c.235A>T p.Met79Leu p.M79L ENST00000292246 3/13 140 112 28 346 346 0 strelka-varscan-mutect ANO10,missense_variant,p.Met79Leu,ENST00000292246,NM_018075.3;ANO10,missense_variant,p.Met79Leu,ENST00000414522,NM_001204831.1;ANO10,missense_variant,p.Met79Leu,ENST00000350459,NM_001204834.1;ANO10,missense_variant,p.Met79Leu,ENST00000427171,;ANO10,missense_variant,p.Met79Leu,ENST00000428831,;ANO10,missense_variant,p.Met79Leu,ENST00000444344,;ANO10,missense_variant,p.Met79Leu,ENST00000439141,;ANO10,missense_variant,p.Met79Leu,ENST00000456438,;ANO10,missense_variant,p.Met79Leu,ENST00000413397,;ANO10,intron_variant,,ENST00000396091,NM_001204832.1;ANO10,intron_variant,,ENST00000451430,NM_001204833.1;ANO10,intron_variant,,ENST00000428472,; A ENST00000292246 Transcript missense_variant 406/3212 235/1983 79/660 M/L Atg/Ttg 1 -1 ANO10 HGNC HGNC:25519 protein_coding YES CCDS2710.2 ENSP00000292246 Q9NW15 A0A024R2S0 UPI000020A59A NM_018075.3 tolerated(1) 3/13 hmmpanther:PTHR12308:SF40,hmmpanther:PTHR12308 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 43600486 43600486 T A 1 0 0 0 0 1 0 0 0 803 1493 52 4 4 ANO10 3 43600486 Missense_Mutation SNP T 11LU013_T 6305441 43600486 154695073 12 12 RBM15B 0 . GRCh38 3 51393138 51393138 + Missense_Mutation SNP C C A rs140480557 11LU013_T 11LU013_N C C c.1739C>A p.Ala580Glu p.A580E ENST00000563281 1/1 154 131 23 200 200 0 strelka-varscan-mutect RBM15B,missense_variant,p.Ala580Glu,ENST00000563281,NM_013286.4;DCAF1,downstream_gene_variant,,ENST00000504652,NM_001171904.1;DCAF1,downstream_gene_variant,,ENST00000423656,NM_014703.2;DCAF1,downstream_gene_variant,,ENST00000335891,;MANF,downstream_gene_variant,,ENST00000528157,NM_006010.5;MANF,downstream_gene_variant,,ENST00000470900,;MANF,downstream_gene_variant,,ENST00000446668,;MANF,downstream_gene_variant,,ENST00000482262,; A ENST00000563281 Transcript missense_variant 1871/6641 1739/2673 580/890 A/E gCa/gAa rs140480557 1 1 RBM15B HGNC HGNC:24303 protein_coding YES CCDS33764.1 ENSP00000454545 Q8NDT2 UPI0000160BDE NM_013286.4 tolerated(1) 1/1 hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF40 MODERATE SNV 1 PASS rs140480557 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 51393138 51393138 C A 1 0 0 0 0 1 0 0 0 13283 710 25 2 2 RBM15B 3 51393138 Missense_Mutation SNP C 11LU013_T 7792652 51393138 146902421 13 13 FGB 0 . GRCh38 4 154570631 154570631 + Missense_Mutation SNP C C T novel 11LU013_T 11LU013_N C C c.1457C>T p.Pro486Leu p.P486L ENST00000302068 8/8 399 370 29 567 566 1 strelka-varscan FGB,missense_variant,p.Pro486Leu,ENST00000302068,NM_005141.4,NM_001184741.1;FGB,missense_variant,p.Pro267Leu,ENST00000509493,;FGB,non_coding_transcript_exon_variant,,ENST00000502545,;FGB,downstream_gene_variant,,ENST00000498375,;FGB,downstream_gene_variant,,ENST00000473984,;FGB,downstream_gene_variant,,ENST00000497097,;FGB,downstream_gene_variant,,ENST00000425838,; T ENST00000302068 Transcript missense_variant 1520/1975 1457/1476 486/491 P/L cCc/cTc 1 1 FGB HGNC HGNC:3662 protein_coding YES CCDS3786.1 ENSP00000306099 P02675 V9HVY1 UPI000012A778 NM_005141.4,NM_001184741.1 deleterious(0) 8/8 Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF203,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 154570631 154570631 C T 1 0 0 0 0 1 0 0 0 5695 623 22 3 3 FGB 4 154570631 Missense_Mutation SNP C 11LU013_T 154570631 35643924 14 14 TRIML2 0 . GRCh38 4 188091633 188091633 + Missense_Mutation SNP G G T novel 11LU013_T 11LU013_N G G c.1054C>A p.Leu352Ile p.L352I ENST00000512729 7/7 121 91 30 101 99 2 strelka-varscan TRIML2,missense_variant,p.Leu352Ile,ENST00000512729,NM_173553.2;TRIML2,missense_variant,p.Leu337Ile,ENST00000326754,NM_001303419.1;TRIML2,3_prime_UTR_variant,,ENST00000503141,;TRIML2,3_prime_UTR_variant,,ENST00000503475,; T ENST00000512729 Transcript missense_variant 1279/1639 1054/1314 352/437 L/I Ctc/Atc 1 -1 TRIML2 HGNC HGNC:26378 protein_coding YES ENSP00000422581 Q8N7C3 UPI000020B818 NM_173553.2 deleterious(0.02) 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF347,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 188091633 188091633 G T 1 0 0 0 0 1 0 0 0 17048 942 33 2 2 TRIML2 4 188091633 Missense_Mutation SNP G 11LU013_T 33521002 188091633 2122922 15 15 NIM1K 0 . GRCh38 5 43280190 43280190 + Missense_Mutation SNP G G T 11LU013_T 11LU013_N G G c.772G>T p.Gly258Trp p.G258W ENST00000512796 4/4 242 227 15 179 179 0 strelka-varscan-mutect NIM1K,missense_variant,p.Gly258Trp,ENST00000512796,;NIM1K,missense_variant,p.Gly258Trp,ENST00000326035,NM_153361.3; T ENST00000512796 Transcript missense_variant 2271/2929 772/1311 258/436 G/W Ggg/Tgg COSM339195 1 1 NIM1K HGNC HGNC:28646 protein_coding YES CCDS3943.1 ENSP00000420849 Q8IY84 UPI0000035B5F deleterious(0) 4/4 PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF0,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 43280190 43280190 G T 1 0 0 0 0 1 0 0 0 10451 1232 43 2 2 NIM1K 5 43280190 Missense_Mutation SNP G 11LU013_T 43280190 138258069 16 16 PDE4D 0 . GRCh38 5 59893368 59893368 + Silent SNP C C T novel 11LU013_T 11LU013_N C C c.255G>A p.= p.P85P ENST00000340635 1/15 100 82 18 76 76 0 strelka-varscan-mutect PDE4D,synonymous_variant,p.=,ENST00000340635,NM_001104631.1;PDE4D,intron_variant,,ENST00000502484,NM_001165899.1;PDE4D,intron_variant,,ENST00000512069,;PDE4D,upstream_gene_variant,,ENST00000405053,;PDE4D,intron_variant,,ENST00000514231,; T ENST00000340635 Transcript synonymous_variant 431/8232 255/2430 85/809 P ccG/ccA 1 -1 PDE4D HGNC HGNC:8783 protein_coding YES CCDS47213.1 ENSP00000345502 Q08499 A0A140VJR0 UPI0000050EB1 NM_001104631.1 1/15 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1168292552 . 0 192 18 0 0 0 0 0 -20 0.9988739 1 1 1 0 T 2 4 1 59893368 59893368 C T 1 0 0 0 0 0 0 0 1 11730 755 27 1 1 PDE4D 5 59893368 Silent SNP C 11LU013_T 16613178 59893368 121644891 17 17 ENC1 0 . GRCh38 5 74634852 74634858 + Frame_Shift_Del DEL CCTCCAA CCTCCAA - novel 11LU013_T 11LU013_N CCTCCAA CCTCCAA c.1628_1634delTTGGAGG p.Val543AspfsTer18 p.V543Dfs*18 ENST00000618628 3/4 284 255 29 292 292 0 sindel-varindel-pindel ENC1,frameshift_variant,p.Val543AspfsTer18,ENST00000618628,NM_001256574.1;ENC1,frameshift_variant,p.Val543AspfsTer18,ENST00000302351,NM_003633.3,NM_001256575.1;ENC1,frameshift_variant,p.Val470AspfsTer18,ENST00000510316,NM_001256576.1;ENC1,frameshift_variant,p.Val543AspfsTer18,ENST00000537006,;ENC1,downstream_gene_variant,,ENST00000508331,;ENC1,downstream_gene_variant,,ENST00000509127,;ENC1,upstream_gene_variant,,ENST00000509284,; - ENST00000618628 Transcript frameshift_variant 2896-2902/5657 1628-1634/1770 543-545/589 VGG/X gTTGGAGGa/ga 1 -1 ENC1 HGNC HGNC:3345 protein_coding YES CCDS4021.1 ENSP00000479101 O14682 Q53XS2 UPI0000129EBB NM_001256574.1 3/4 hmmpanther:PTHR24410:SF5,hmmpanther:PTHR24410,PIRSF_domain:PIRSF037037,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,Superfamily_domains:0052715 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 1 74634852 74634852 CCTCCAA - 1 0 1 0 1 0 0 0 0 4955 855 30 0 0 ENC1 5 74634852 Frame_Shift_Del DEL CCTCCAA 11LU013_T 14741484 74634852 106903407 18 18 KDM3B 0 . GRCh38 5 138417573 138417573 + Missense_Mutation SNP C C T novel 11LU013_T 11LU013_N C C c.3398C>T p.Ser1133Phe p.S1133F ENST00000314358 13/24 185 171 14 175 175 0 strelka-varscan-mutect KDM3B,missense_variant,p.Ser1133Phe,ENST00000314358,NM_016604.3;KDM3B,missense_variant,p.Ser131Phe,ENST00000542866,;KDM3B,upstream_gene_variant,,ENST00000508386,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,3_prime_UTR_variant,,ENST00000507996,; T ENST00000314358 Transcript missense_variant 3598/6813 3398/5286 1133/1761 S/F tCt/tTt 1 1 KDM3B HGNC HGNC:1337 protein_coding YES CCDS34242.1 ENSP00000326563 Q7LBC6 UPI000020C6A8 NM_016604.3 tolerated(0.13) 13/24 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.38819 0.9999997 1 1 1 0 T 3 4 1 138417573 138417573 C T 1 0 0 0 0 1 0 0 0 8045 913 32 3 3 KDM3B 5 138417573 Missense_Mutation SNP C 11LU013_T 63782721 138417573 43120686 19 19 PCDHB15 0 . GRCh38 5 141247523 141247523 + Missense_Mutation SNP G G A novel 11LU013_T 11LU013_N G G c.1945G>A p.Glu649Lys p.E649K ENST00000231173 1/1 799 556 243 764 764 0 strelka-varscan-mutect PCDHB15,missense_variant,p.Glu649Lys,ENST00000231173,NM_018935.3;PCDHB15,downstream_gene_variant,,ENST00000623671,;CH17-140K24.8,downstream_gene_variant,,ENST00000624396,;CH17-140K24.2,upstream_gene_variant,,ENST00000624560,;PCDHB19P,downstream_gene_variant,,ENST00000625133,; A ENST00000231173 Transcript missense_variant 2175/4017 1945/2364 649/787 E/K Gag/Aag 1 1 PCDHB15 HGNC HGNC:8686 protein_coding YES CCDS4257.1 ENSP00000231173 Q9Y5E8 UPI00001273E8 NM_018935.3 deleterious_low_confidence(0.01) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF97,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 141247523 141247523 G A 1 0 0 0 0 1 0 0 0 11627 1059 37 1 1 PCDHB15 5 141247523 Missense_Mutation SNP G 11LU013_T 2829950 141247523 40290736 20 20 PCDHGA2 0 . GRCh38 5 141340924 141340924 + Missense_Mutation SNP G G T 11LU013_T 11LU013_N G G c.1953G>T p.Gln651His p.Q651H ENST00000394576 1/4 604 536 68 568 568 0 varscan-mutect PCDHGA2,missense_variant,p.Gln651His,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Gln651His,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; T ENST00000394576 Transcript missense_variant 1953/4605 1953/2799 651/932 Q/H caG/caT COSM590207,COSM590208 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 141340924 141340924 G T 1 0 0 0 0 1 0 0 0 11641 962 34 2 2 PCDHGA2 5 141340924 Missense_Mutation SNP G 11LU013_T 93401 141340924 40197335 21 21 ARAP3 0 . GRCh38 5 141673114 141673114 + Missense_Mutation SNP A A T novel 11LU013_T 11LU013_N A A c.992T>A p.Val331Glu p.V331E ENST00000239440 7/33 202 176 26 196 196 0 strelka-varscan-mutect ARAP3,missense_variant,p.Val331Glu,ENST00000239440,NM_022481.5;ARAP3,missense_variant,p.Val253Glu,ENST00000626478,;ARAP3,missense_variant,p.Val253Glu,ENST00000508305,;ARAP3,missense_variant,p.Val331Glu,ENST00000504448,;ARAP3,5_prime_UTR_variant,,ENST00000513878,;ARAP3,non_coding_transcript_exon_variant,,ENST00000524066,; T ENST00000239440 Transcript missense_variant 1058/5250 992/4635 331/1544 V/E gTg/gAg 1 -1 ARAP3 HGNC HGNC:24097 protein_coding YES CCDS4266.1 ENSP00000239440 Q8WWN8 UPI0000049886 NM_022481.5 deleterious(0) 7/33 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 1 141673114 141673114 A T 1 0 0 0 0 1 0 0 0 962 159 6 4 4 ARAP3 5 141673114 Missense_Mutation SNP A 11LU013_T 332190 141673114 39865145 22 22 PLA2G7 0 . GRCh38 6 46704694 46704694 + Missense_Mutation SNP G G A novel 11LU013_T 11LU013_N G G c.1192C>T p.Leu398Phe p.L398F ENST00000274793 12/12 49 41 8 146 146 0 strelka-varscan-mutect PLA2G7,missense_variant,p.Leu398Phe,ENST00000274793,NM_005084.3;PLA2G7,missense_variant,p.Leu398Phe,ENST00000537365,NM_001168357.1;TDRD6,downstream_gene_variant,,ENST00000544460,NM_001168359.1;TDRD6,downstream_gene_variant,,ENST00000316081,NM_001010870.2;TDRD6,downstream_gene_variant,,ENST00000450697,; A ENST00000274793 Transcript missense_variant,splice_region_variant 1389/1882 1192/1326 398/441 L/F Ctt/Ttt 1 -1 PLA2G7 HGNC HGNC:9040 protein_coding YES CCDS4917.1 ENSP00000274793 Q13093 UPI000002FED1 NM_005084.3 deleterious(0) 12/12 Gene3D:3.40.50.1820,Pfam_domain:PF03403,PIRSF_domain:PIRSF018169,hmmpanther:PTHR10272,hmmpanther:PTHR10272:SF12,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 46704694 46704694 G A 1 0 0 0 0 1 0 0 0 12105 1043 36 3 3 PLA2G7 6 46704694 Missense_Mutation SNP G 11LU013_T 46704694 124101285 23 23 FAM184A 0 . GRCh38 6 118960165 118960165 + Missense_Mutation SNP A A C novel 11LU013_T 11LU013_N A A c.3361T>G p.Ser1121Ala p.S1121A ENST00000338891 18/18 177 119 58 168 168 0 strelka-varscan-mutect FAM184A,missense_variant,p.Ser1121Ala,ENST00000338891,NM_024581.5;FAM184A,missense_variant,p.Ser1079Ala,ENST00000621231,;FAM184A,missense_variant,p.Ser952Ala,ENST00000352896,NM_001100411.2;FAM184A,missense_variant,p.Ser917Ala,ENST00000368475,NM_001288576.1;FAM184A,missense_variant,p.Ser1037Ala,ENST00000521531,;FAM184A,missense_variant,p.Ser249Ala,ENST00000521043,;FAM184A,missense_variant,p.Ser146Ala,ENST00000368472,;FAM184A,missense_variant,p.Ser55Ala,ENST00000481884,;FAM184A,missense_variant,p.Ser51Ala,ENST00000517987,;FAM184A,3_prime_UTR_variant,,ENST00000617072,;RP11-351A11.1,intron_variant,,ENST00000518570,;FAM184A,3_prime_UTR_variant,,ENST00000475529,;FAM184A,non_coding_transcript_exon_variant,,ENST00000482219,; C ENST00000338891 Transcript missense_variant 3805/4141 3361/3423 1121/1140 S/A Tct/Gct 1 -1 FAM184A HGNC HGNC:20991 protein_coding YES CCDS43499.1 ENSP00000342604 Q8NB25 UPI0000470B36 NM_024581.5 tolerated(0.22) 18/18 hmmpanther:PTHR18870:SF7,hmmpanther:PTHR18870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 1 118960165 118960165 A C 1 0 0 0 0 1 0 0 0 5358 246 9 5 5 FAM184A 6 118960165 Missense_Mutation SNP A 11LU013_T 72255471 118960165 51845814 24 24 FKBP9 0 . GRCh38 7 32976452 32976452 + Missense_Mutation SNP G G A rs781596802 11LU013_T 11LU013_N G G c.815G>A p.Arg272His p.R272H ENST00000538336 5/11 311 177 134 145 144 1 strelka-varscan FKBP9,missense_variant,p.Arg272His,ENST00000538336,NM_001284341.1;FKBP9,missense_variant,p.Arg219His,ENST00000242209,NM_007270.4;FKBP9,upstream_gene_variant,,ENST00000490776,NM_001284343.1;FKBP9,upstream_gene_variant,,ENST00000418354,;FKBP9,non_coding_transcript_exon_variant,,ENST00000489038,;FKBP9,non_coding_transcript_exon_variant,,ENST00000469202,;FKBP9,non_coding_transcript_exon_variant,,ENST00000472007,;FKBP9,downstream_gene_variant,,ENST00000464334,;FKBP9,upstream_gene_variant,,ENST00000463443,;FKBP9,non_coding_transcript_exon_variant,,ENST00000494374,;FKBP9,downstream_gene_variant,,ENST00000485309,; A ENST00000538336 Transcript missense_variant 985/3621 815/1872 272/623 R/H cGc/cAc rs781596802,COSM77722 1 1 FKBP9 HGNC HGNC:3725 protein_coding YES CCDS64622.1 ENSP00000439250 O95302 UPI0001914EC6 NM_001284341.1 deleterious(0) 5/11 PROSITE_profiles:PS50059,hmmpanther:PTHR10516:SF111,hmmpanther:PTHR10516,Pfam_domain:PF00254,Gene3D:3.10.50.40,Superfamily_domains:SSF54534 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 120 2 11 13 64 0 0 -19.88353 0 0 1 0 0 A 3 1 1 32976452 32976452 G A 1 0 0 0 0 1 0 0 0 5778 1087 38 1 1 FKBP9 7 32976452 Missense_Mutation SNP G 11LU013_T 32976452 126369521 25 25 EGFR 0 . GRCh38 7 55174774 55174791 + In_Frame_Del DEL AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT - rs121913422 11LU013_T 11LU013_N AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT c.2237_2254delAATTAAGAGAAGCAACAT p.Glu746_Ser752delinsAla p.E746_S752delinsA ENST00000275493 19/28 7272 441 6831 755 755 0 sindel-varindel EGFR,inframe_deletion,p.Glu746_Ser752delinsAla,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2414-2431/9821 2237-2254/3633 746-752/1210 ELREATS/A gAATTAAGAGAAGCAACATct/gct rs121913422,COSM12367 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 1 55174774 55174774 AATTAAGAGAAGCAACAT - 1 0 1 0 1 0 0 0 0 4803 246 9 0 0 EGFR 7 55174774 In_Frame_Del DEL AATTAAGAGAAGCAACAT 11LU013_T 22198322 55174774 104171199 26 26 HEPACAM2 0 . GRCh38 7 93215550 93215550 + Missense_Mutation SNP A A G novel 11LU013_T 11LU013_N A A c.635T>C p.Val212Ala p.V212A ENST00000453812 4/11 486 439 47 364 364 0 strelka-varscan HEPACAM2,missense_variant,p.Val189Ala,ENST00000394468,NM_001039372.2;HEPACAM2,missense_variant,p.Val177Ala,ENST00000341723,NM_198151.2;HEPACAM2,missense_variant,p.Val177Ala,ENST00000440868,NM_001288810.1;HEPACAM2,missense_variant,p.Val212Ala,ENST00000453812,NM_001288804.1; G ENST00000453812 Transcript missense_variant 658/1869 635/1458 212/485 V/A gTc/gCc 1 -1 HEPACAM2 HGNC HGNC:27364 protein_coding YES CCDS75632.1 ENSP00000390204 A8MVW5 UPI000198CEF3 NM_001288804.1 deleterious(0.01) 4/11 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 1 93215550 93215550 A G 1 0 0 0 0 1 0 0 0 6937 275 10 5 5 HEPACAM2 7 93215550 Missense_Mutation SNP A 11LU013_T 38040776 93215550 66130423 27 27 CPA1 0 . GRCh38 7 130381164 130381164 + Missense_Mutation SNP C C A novel 11LU013_T 11LU013_N C C c.132C>A p.Asp44Glu p.D44E ENST00000011292 2/10 226 177 49 183 183 0 strelka-varscan-mutect CPA1,missense_variant,p.Asp44Glu,ENST00000011292,NM_001868.3;CPA1,5_prime_UTR_variant,,ENST00000484324,;CPA1,5_prime_UTR_variant,,ENST00000476062,;CPA1,5_prime_UTR_variant,,ENST00000481342,;CPA1,intron_variant,,ENST00000604896,;CPA1,non_coding_transcript_exon_variant,,ENST00000491460,;CPA1,upstream_gene_variant,,ENST00000479106,;CPA1,upstream_gene_variant,,ENST00000478096,;CPA1,upstream_gene_variant,,ENST00000470838,; A ENST00000011292 Transcript missense_variant 282/1487 132/1260 44/419 D/E gaC/gaA 1 1 CPA1 HGNC HGNC:2296 protein_coding YES CCDS5820.1 ENSP00000011292 P15085 UPI000004D332 NM_001868.3 tolerated(0.91) 2/10 hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF74,Gene3D:3.30.70.340,Pfam_domain:PF02244,Superfamily_domains:SSF54897,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 130381164 130381164 C A 1 0 0 0 0 1 0 0 0 3583 506 18 2 2 CPA1 7 130381164 Missense_Mutation SNP C 11LU013_T 37165614 130381164 28964809 28 28 LRP12 0 . GRCh38 8 104498045 104498045 + Silent SNP A A G novel 11LU013_T 11LU013_N A A c.507T>C p.= p.D169D ENST00000276654 5/7 138 124 14 66 66 0 strelka-varscan-mutect LRP12,synonymous_variant,p.=,ENST00000276654,NM_013437.4;LRP12,synonymous_variant,p.=,ENST00000424843,NM_001135703.2;LRP12,upstream_gene_variant,,ENST00000523007,;LRP12,non_coding_transcript_exon_variant,,ENST00000520770,;LRP12,upstream_gene_variant,,ENST00000518375,;LRP12,upstream_gene_variant,,ENST00000522046,; G ENST00000276654 Transcript synonymous_variant 616/4112 507/2580 169/859 D gaT/gaC 1 -1 LRP12 HGNC HGNC:31708 protein_coding YES CCDS6303.1 ENSP00000276654 Q9Y561 UPI0000047A9F NM_013437.4 5/7 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF216,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 1 104498045 104498045 A G 1 0 0 0 0 0 0 0 1 8849 330 12 5 5 LRP12 8 104498045 Silent SNP A 11LU013_T 104498045 40640591 29 29 OXR1 0 . GRCh38 8 106706942 106706942 + Missense_Mutation SNP C C T novel 11LU013_T 11LU013_N C C c.1424C>T p.Ala475Val p.A475V ENST00000442977 8/16 348 315 33 277 277 0 strelka-varscan-mutect OXR1,missense_variant,p.Ala474Val,ENST00000517566,NM_001198533.1;OXR1,missense_variant,p.Ala467Val,ENST00000312046,NM_181354.4;OXR1,missense_variant,p.Ala474Val,ENST00000531443,NM_018002.3;OXR1,missense_variant,p.Ala475Val,ENST00000442977,NM_001198532.1;OXR1,missense_variant,p.Ala188Val,ENST00000519415,;OXR1,missense_variant,p.Ala407Val,ENST00000497705,;OXR1,downstream_gene_variant,,ENST00000517455,;OXR1,3_prime_UTR_variant,,ENST00000438229,;OXR1,intron_variant,,ENST00000435082,; T ENST00000442977 Transcript missense_variant 1523/2956 1424/2625 475/874 A/V gCa/gTa 1 1 OXR1 HGNC HGNC:15822 protein_coding YES CCDS56548.1 ENSP00000405424 Q8N573 UPI0001914BEA NM_001198532.1 tolerated(0.49) 8/16 hmmpanther:PTHR23354:SF69,hmmpanther:PTHR23354 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 106706942 106706942 C T 1 0 0 0 0 1 0 0 0 11407 710 25 3 3 OXR1 8 106706942 Missense_Mutation SNP C 11LU013_T 2208897 106706942 38431694 30 30 GTPBP4 0 . GRCh38 10 988526 988526 + Missense_Mutation SNP A A G rs201885506 11LU013_T 11LU013_N A A c.47A>G p.Lys16Arg p.K16R ENST00000360803 1/17 213 191 22 200 200 0 strelka-varscan-mutect GTPBP4,missense_variant,p.Lys16Arg,ENST00000360803,NM_012341.2;GTPBP4,upstream_gene_variant,,ENST00000360059,;RP11-363N22.3,upstream_gene_variant,,ENST00000381466,;GTPBP4,splice_region_variant,,ENST00000491635,;RP11-363N22.3,upstream_gene_variant,,ENST00000615314,; G ENST00000360803 Transcript missense_variant,splice_region_variant 508/5075 47/1905 16/634 K/R aAg/aGg rs201885506 1 1 GTPBP4 HGNC HGNC:21535 protein_coding YES CCDS31132.1 ENSP00000354040 Q9BZE4 D2CFK9 UPI000000D960 NM_012341.2 deleterious(0.03) 1/17 hmmpanther:PTHR11702:SF4,hmmpanther:PTHR11702,PIRSF_domain:PIRSF038919 MODERATE 1 SNV 1 1 PASS rs201885506 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 1 988526 988526 A G 1 0 0 0 0 1 0 0 0 6763 86 3 5 5 GTPBP4 10 988526 Missense_Mutation SNP A 11LU013_T 988526 132808896 31 31 MBL2 0 . GRCh38 10 52768158 52768158 + Silent SNP G G A rs139905034 11LU013_T 11LU013_N G G c.726C>T p.= p.A242A ENST00000373968 4/4 70 59 11 54 54 0 strelka-varscan-mutect MBL2,synonymous_variant,p.=,ENST00000373968,NM_000242.2; A ENST00000373968 Transcript synonymous_variant 791/3569 726/747 242/248 A gcC/gcT rs139905034 1 -1 MBL2 HGNC HGNC:6922 protein_coding YES CCDS7247.1 ENSP00000363079 P11226 UPI0000035011 NM_000242.2 4/4 PROSITE_profiles:PS50041,hmmpanther:PTHR24020,PROSITE_patterns:PS00615,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs139905034 . 0 203 7 0 0 0 0 0 -19.99998 0.9999996 1 1 1 0 A 2 1 1 52768158 52768158 G A 1 0 0 0 0 0 0 0 1 9282 1103 39 1 1 MBL2 10 52768158 Silent SNP G 11LU013_T 51779632 52768158 81029264 32 32 OR52A1 0 . GRCh38 11 5151676 5151676 + Missense_Mutation SNP G G T novel 11LU013_T 11LU013_N G G c.694C>A p.Pro232Thr p.P232T ENST00000380367 2/2 183 166 17 298 298 0 strelka-varscan-mutect OR52A1,missense_variant,p.Pro232Thr,ENST00000380367,;OR52A1,missense_variant,p.Pro232Thr,ENST00000328942,NM_012375.2; T ENST00000380367 Transcript missense_variant 1112/1779 694/939 232/312 P/T Ccc/Acc 1 -1 OR52A1 HGNC HGNC:8318 protein_coding YES CCDS31374.1 ENSP00000369725 Q9UKL2 UPI0000140B1E deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF98,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1434373052 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 5151676 5151676 G T 1 0 0 0 0 1 0 0 0 11182 1203 42 2 2 OR52A1 11 5151676 Missense_Mutation SNP G 11LU013_T 5151676 129934946 33 33 RAB30 0 . GRCh38 11 82987749 82987749 + Missense_Mutation SNP C C G novel 11LU013_T 11LU013_N C C c.199G>C p.Gly67Arg p.G67R ENST00000533486 5/6 168 156 12 143 143 0 strelka-varscan-mutect RAB30,missense_variant,p.Gly67Arg,ENST00000533486,NM_014488.4,NM_001286060.1;RAB30,missense_variant,p.Gly67Arg,ENST00000612684,NM_001286061.1;RAB30,missense_variant,p.Gly67Arg,ENST00000534141,;RAB30,missense_variant,p.Gly67Arg,ENST00000260056,NM_001286059.1;RAB30,missense_variant,p.Gly39Arg,ENST00000525117,;RAB30,missense_variant,p.Gly67Arg,ENST00000527633,;RAB30,missense_variant,p.Gly67Arg,ENST00000534103,;RAB30,missense_variant,p.Gly67Arg,ENST00000532548,;RAB30,missense_variant,p.Gly67Arg,ENST00000526205,;RAB30,missense_variant,p.Gly67Arg,ENST00000531021,;RAB30,missense_variant,p.Gly31Arg,ENST00000533014,;RAB30,missense_variant,p.Gly67Arg,ENST00000534301,;RAB30,missense_variant,p.Gly21Arg,ENST00000524635,;RAB30,downstream_gene_variant,,ENST00000530224,;RP11-659G9.3,intron_variant,,ENST00000527550,; G ENST00000533486 Transcript missense_variant 484/9929 199/612 67/203 G/R Ggt/Cgt 1 -1 RAB30 HGNC HGNC:9770 protein_coding YES CCDS8264.1 ENSP00000435189 Q15771 A8K5R1 UPI000002356C NM_014488.4,NM_001286060.1 deleterious(0) 5/6 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF408,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00176,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99673 1 1 1 1 0 G 3 3 1 82987749 82987749 C G 1 0 0 0 0 1 0 0 0 13078 681 24 4 4 RAB30 11 82987749 Missense_Mutation SNP C 11LU013_T 77836073 82987749 52098873 34 34 ROBO4 0 . GRCh38 11 124895457 124895457 + Missense_Mutation SNP C C G novel 11LU013_T 11LU013_N C C c.1036G>C p.Val346Leu p.V346L ENST00000306534 6/18 95 88 7 78 78 0 strelka-varscan-mutect ROBO4,missense_variant,p.Val346Leu,ENST00000306534,NM_019055.5;ROBO4,missense_variant,p.Val201Leu,ENST00000533054,NM_001301088.1;RP11-664I21.6,downstream_gene_variant,,ENST00000524433,;ROBO4,downstream_gene_variant,,ENST00000526899,;ROBO4,downstream_gene_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000529941,;ROBO4,upstream_gene_variant,,ENST00000534407,;ROBO4,upstream_gene_variant,,ENST00000532216,;ROBO4,upstream_gene_variant,,ENST00000525182,;ROBO4,downstream_gene_variant,,ENST00000533337,;ROBO4,downstream_gene_variant,,ENST00000532300,; G ENST00000306534 Transcript missense_variant,splice_region_variant 1522/4710 1036/3024 346/1007 V/L Gtg/Ctg 1 -1 ROBO4 HGNC HGNC:17985 protein_coding YES CCDS8455.1 ENSP00000304945 Q8WZ75 UPI000004A023 NM_019055.5 deleterious(0) 6/18 hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1281608574 . 0 191 12 6 0 0 0 0 -10.70637 0.8917082 1 1 1 0 G 3 3 1 124895457 124895457 C G 1 0 0 0 0 1 0 0 0 13694 695 24 4 4 ROBO4 11 124895457 Missense_Mutation SNP C 11LU013_T 41907708 124895457 10191165 35 35 CD163 0 . GRCh38 12 7485373 7485373 + Silent SNP G G A novel 11LU013_T 11LU013_N G G c.2502C>T p.= p.A834A ENST00000359156 11/17 280 227 53 157 157 0 strelka-varscan-mutect CD163,synonymous_variant,p.=,ENST00000359156,NM_004244.5;CD163,synonymous_variant,p.=,ENST00000396620,;CD163,synonymous_variant,p.=,ENST00000432237,NM_203416.3;CD163,synonymous_variant,p.=,ENST00000541972,;CD163,upstream_gene_variant,,ENST00000537626,;CD163,upstream_gene_variant,,ENST00000542280,;CD163,upstream_gene_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;CD163,non_coding_transcript_exon_variant,,ENST00000538840,; A ENST00000359156 Transcript synonymous_variant 2705/4268 2502/3471 834/1156 A gcC/gcT 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 11/17 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF324,SMART_domains:SM00202,Superfamily_domains:SSF56487 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 1 7485373 7485373 G A 1 0 0 0 0 0 0 0 1 2670 987 35 3 3 CD163 12 7485373 Silent SNP G 11LU013_T 7485373 125789936 36 36 CALCOCO1 0 . GRCh38 12 53714677 53714677 + Missense_Mutation SNP C C T novel 11LU013_T 11LU013_N C C c.1403G>A p.Ser468Asn p.S468N ENST00000550804 11/15 198 118 80 155 155 0 strelka-varscan-mutect CALCOCO1,missense_variant,p.Ser468Asn,ENST00000262059,;CALCOCO1,missense_variant,p.Ser468Asn,ENST00000548263,;CALCOCO1,missense_variant,p.Ser383Asn,ENST00000430117,NM_001143682.1;CALCOCO1,missense_variant,p.Ser468Asn,ENST00000550804,NM_020898.2;CALCOCO1,upstream_gene_variant,,ENST00000546443,;CALCOCO1,non_coding_transcript_exon_variant,,ENST00000549935,;CALCOCO1,non_coding_transcript_exon_variant,,ENST00000549613,;CALCOCO1,downstream_gene_variant,,ENST00000552282,; T ENST00000550804 Transcript missense_variant 1464/2291 1403/2076 468/691 S/N aGt/aAt 1 -1 CALCOCO1 HGNC HGNC:29306 protein_coding YES CCDS8864.1 ENSP00000449960 Q9P1Z2 A0A024RAZ1 UPI0000037D7A NM_020898.2 tolerated(0.26) 11/15 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF07888,hmmpanther:PTHR31915,hmmpanther:PTHR31915:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 53714677 53714677 C T 1 0 0 0 0 1 0 0 0 2267 565 20 3 3 CALCOCO1 12 53714677 Missense_Mutation SNP C 11LU013_T 46229304 53714677 79560632 37 37 CATSPERB 0 . GRCh38 14 91669841 91669841 + Missense_Mutation SNP G G T novel 11LU013_T 11LU013_N G G c.1260C>A p.Ser420Arg p.S420R ENST00000256343 14/27 84 60 24 99 99 0 strelka-varscan-mutect CATSPERB,missense_variant,p.Ser420Arg,ENST00000256343,NM_024764.3;CATSPERB,missense_variant,p.Ser30Arg,ENST00000557036,; T ENST00000256343 Transcript missense_variant 1417/3623 1260/3351 420/1116 S/R agC/agA 1 -1 CATSPERB HGNC HGNC:20500 protein_coding YES CCDS32142.1 ENSP00000256343 Q9H7T0 UPI0000418DA1 NM_024764.3 deleterious(0) 14/27 hmmpanther:PTHR14705 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 91669841 91669841 G T 1 0 0 0 0 1 0 0 0 2391 1194 42 2 2 CATSPERB 14 91669841 Missense_Mutation SNP G 11LU013_T 91669841 15373877 38 38 ARHGAP11A 0 . GRCh38 15 32623517 32623517 + Silent SNP T T C novel 11LU013_T 11LU013_N T T c.226T>C p.= p.L76L ENST00000361627 3/12 92 81 11 238 238 0 strelka-varscan-mutect ARHGAP11A,synonymous_variant,p.=,ENST00000361627,NM_014783.4;ARHGAP11A,synonymous_variant,p.=,ENST00000567348,NM_199357.1;ARHGAP11A,synonymous_variant,p.=,ENST00000563864,;ARHGAP11A,5_prime_UTR_variant,,ENST00000565905,NM_001286479.1;ARHGAP11A,5_prime_UTR_variant,,ENST00000543522,NM_001286480.1; C ENST00000361627 Transcript synonymous_variant 948/5898 226/3072 76/1023 L Tta/Cta 1 1 ARHGAP11A HGNC HGNC:15783 protein_coding YES CCDS10028.1 ENSP00000355090 Q6P4F7 UPI0000071553 NM_014783.4 3/12 PROSITE_profiles:PS50238,hmmpanther:PTHR15670:SF5,hmmpanther:PTHR15670,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 1 32623517 32623517 T C 1 0 0 0 0 0 0 0 1 987 1838 64 5 5 ARHGAP11A 15 32623517 Silent SNP T 11LU013_T 32623517 69367672 39 39 ERCC4 0 . GRCh38 16 13935451 13935451 + Nonsense_Mutation SNP G G T novel 11LU013_T 11LU013_N G G c.1519G>T p.Glu507Ter p.E507* ENST00000311895 8/11 165 151 14 211 211 0 strelka-varscan-mutect ERCC4,stop_gained,p.Glu507Ter,ENST00000311895,NM_005236.2;ERCC4,downstream_gene_variant,,ENST00000575156,;CTD-2135D7.2,non_coding_transcript_exon_variant,,ENST00000575137,;CTD-2135D7.2,non_coding_transcript_exon_variant,,ENST00000570663,;ERCC4,downstream_gene_variant,,ENST00000574781,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,upstream_gene_variant,,ENST00000462862,;ERCC4,downstream_gene_variant,,ENST00000574194,;ERCC4,downstream_gene_variant,,ENST00000573018,; T ENST00000311895 Transcript stop_gained 1528/6758 1519/2751 507/916 E/* Gaa/Taa 1 1 ERCC4 HGNC HGNC:3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 UPI0000161BBF NM_005236.2 8/11 hmmpanther:PTHR10150,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00596 HIGH 1 SNV 1 1 PASS rs1457367930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 1 13935451 13935451 G T 1 0 0 0 0 0 1 0 0 5064 1175 41 2 2 ERCC4 16 13935451 Nonsense_Mutation SNP G 11LU013_T 13935451 76402894 40 40 TP53 0 . GRCh38 17 7674221 7674221 + Missense_Mutation SNP G G A rs121912651 11LU013_T 11LU013_N G G c.742C>T p.Arg248Trp p.R248W ENST00000269305 7/11 266 191 75 340 340 0 strelka-varscan-mutect TP53,missense_variant,p.Arg248Trp,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg248Trp,ENST00000420246,;TP53,missense_variant,p.Arg209Trp,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg209Trp,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg248Trp,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg209Trp,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg248Trp,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg209Trp,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg248Trp,ENST00000445888,;TP53,missense_variant,p.Arg209Trp,ENST00000619485,;TP53,missense_variant,p.Arg116Trp,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg89Trp,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg116Trp,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg89Trp,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg116Trp,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg89Trp,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg248Trp,ENST00000359597,;TP53,missense_variant,p.Arg237Trp,ENST00000615910,;TP53,missense_variant,p.Arg248Trp,ENST00000413465,;TP53,missense_variant,p.Arg116Trp,ENST00000509690,;TP53,missense_variant,p.Arg155Trp,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg209Trp,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 932/2579 742/1182 248/393 R/W Cgg/Tgg rs121912651,CM010465,CM900211,TP53_g.13379C>G,TP53_g.13379C>T,TP53_g.13379C>A,TP53_g.13379del,COSM10656,COSM11564,COSM1189381,COSM1189382,COSM1189383,COSM120005,COSM120006,COSM120007,COSM1640831,COSM2744594,COSM3388183,COSM4271789,COSM44920,COSM45116 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 7674221 7674221 G A 1 0 0 0 0 1 0 0 0 16859 1115 39 1 1 TP53 17 7674221 Missense_Mutation SNP G 11LU013_T 7674221 75583220 41 41 DSC2 0 . GRCh38 18 31080241 31080242 + Frame_Shift_Ins INS - - A novel 11LU013_T 11LU013_N - - c.1374dupT p.Thr459TyrfsTer3 p.T459Yfs*3 ENST00000280904 10/16 331 306 25 348 348 0 sindel-varindel-pindel DSC2,frameshift_variant,p.Thr459TyrfsTer3,ENST00000280904,NM_024422.4;DSC2,frameshift_variant,p.Thr459TyrfsTer3,ENST00000251081,NM_004949.4; A ENST00000280904 Transcript frameshift_variant 1818-1819/12325 1374-1375/2706 458-459/901 -/X -/T 1 -1 DSC2 HGNC HGNC:3036 protein_coding YES CCDS11892.1 ENSP00000280904 Q02487 UPI00001298F9 NM_024422.4 10/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 1 31080241 31080241 - A 1 0 1 1 0 0 0 0 0 4587 1638 57 0 0 DSC2 18 31080241 Frame_Shift_Ins INS - 11LU013_T 31080241 49293044 42 42 WDR7 0 . GRCh38 18 56731520 56731520 + Missense_Mutation SNP G G A novel 11LU013_T 11LU013_N G G c.1912G>A p.Ala638Thr p.A638T ENST00000254442 14/28 146 124 22 222 222 0 strelka-varscan-mutect WDR7,missense_variant,p.Ala638Thr,ENST00000254442,NM_015285.2;WDR7,missense_variant,p.Ala638Thr,ENST00000357574,NM_052834.2;WDR7,intron_variant,,ENST00000615645,;WDR7,intron_variant,,ENST00000589935,;WDR7,non_coding_transcript_exon_variant,,ENST00000585824,;WDR7,non_coding_transcript_exon_variant,,ENST00000590557,;WDR7,non_coding_transcript_exon_variant,,ENST00000587403,; A ENST00000254442 Transcript missense_variant 2123/14083 1912/4473 638/1490 A/T Gct/Act 1 1 WDR7 HGNC HGNC:13490 protein_coding YES CCDS11962.1 ENSP00000254442 Q9Y4E6 UPI000013CE33 NM_015285.2 tolerated(0.22) 14/28 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF409 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 1 56731520 56731520 G A 1 0 0 0 0 1 0 0 0 17876 1319 46 3 3 WDR7 18 56731520 Missense_Mutation SNP G 11LU013_T 25651279 56731520 23641765 43 43 ADAT3 0 . GRCh38 19 1912953 1912953 + Silent SNP G G A novel 11LU013_T 11LU013_N G G c.906G>A p.= p.V302V ENST00000329478 2/2 649 583 66 672 670 2 strelka-varscan-mutect ADAT3,synonymous_variant,p.=,ENST00000329478,NM_138422.2;SCAMP4,intron_variant,,ENST00000316097,NM_079834.2;SCAMP4,intron_variant,,ENST00000409472,;SCAMP4,intron_variant,,ENST00000414057,;SCAMP4,intron_variant,,ENST00000411971,;SCAMP4,intron_variant,,ENST00000588907,;SCAMP4,upstream_gene_variant,,ENST00000621748,;ADAT3,downstream_gene_variant,,ENST00000454697,;SCAMP4,upstream_gene_variant,,ENST00000590266,;SCAMP4,intron_variant,,ENST00000489554,;SCAMP4,intron_variant,,ENST00000452128,;SCAMP4,intron_variant,,ENST00000460767,; A ENST00000329478 Transcript synonymous_variant 1126/1620 906/1104 302/367 V gtG/gtA 1 1 ADAT3 HGNC HGNC:25151 protein_coding YES CCDS12076.2 ENSP00000332448 D6W601 UPI00003749C2 NM_138422.2 2/2 Gene3D:3.40.140.10,Pfam_domain:PF00383,PROSITE_profiles:PS51747,hmmpanther:PTHR11079,hmmpanther:PTHR11079:SF3,Superfamily_domains:SSF53927 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 1 1912953 1912953 G A 1 0 0 0 0 0 0 0 1 330 1277 45 3 3 ADAT3 19 1912953 Silent SNP G 11LU013_T 1912953 56704663 44 44 KDM4B 0 . GRCh38 19 5039877 5039877 + Silent SNP T T C novel 11LU013_T 11LU013_N T T c.183T>C p.= p.D61D ENST00000159111 4/23 151 134 17 189 188 1 strelka-mutect KDM4B,synonymous_variant,p.=,ENST00000611640,;KDM4B,synonymous_variant,p.=,ENST00000159111,NM_015015.2;KDM4B,synonymous_variant,p.=,ENST00000536461,;KDM4B,synonymous_variant,p.=,ENST00000381759,;KDM4B,synonymous_variant,p.=,ENST00000588337,; C ENST00000159111 Transcript synonymous_variant 401/5593 183/3291 61/1096 D gaT/gaC 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 4/23 Low_complexity_(Seg):seg,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 1 5039877 5039877 T C 1 0 0 0 0 0 0 0 1 8047 1461 51 5 5 KDM4B 19 5039877 Silent SNP T 11LU013_T 3126924 5039877 53577739 45 45 MUC16 0 . GRCh38 19 8963173 8963173 + Missense_Mutation SNP G G T novel 11LU013_T 11LU013_N G G c.13597C>A p.Pro4533Thr p.P4533T ENST00000397910 3/84 155 124 31 131 131 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro4533Thr,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 13801/43816 13597/43524 4533/14507 P/T Cct/Act 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS rs1368136222 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 8963173 8963173 G T 1 0 0 0 0 1 0 0 0 9972 1174 41 2 2 MUC16 19 8963173 Missense_Mutation SNP G 11LU013_T 3923296 8963173 49654443 46 46 KLK8 0 . GRCh38 19 50996102 50996102 + Missense_Mutation SNP C C T rs371793414 11LU013_T 11LU013_N C C c.875G>A p.Arg292His p.R292H ENST00000391806 6/6 201 186 15 228 228 0 strelka-mutect KLK8,missense_variant,p.Arg247His,ENST00000600767,NM_007196.3;KLK8,missense_variant,p.Arg292His,ENST00000391806,NM_144505.2;KLK8,missense_variant,p.Arg126His,ENST00000291726,NM_001281431.1;KLK8,missense_variant,p.Arg106His,ENST00000347619,NM_144506.2;KLK8,3_prime_UTR_variant,,ENST00000320838,NM_144507.2;KLK8,3_prime_UTR_variant,,ENST00000593490,;KLK8,downstream_gene_variant,,ENST00000595238,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK8,non_coding_transcript_exon_variant,,ENST00000598195,;CTC-518B2.8,3_prime_UTR_variant,,ENST00000599166,;KLK8,non_coding_transcript_exon_variant,,ENST00000594914,;CTC-518B2.8,downstream_gene_variant,,ENST00000250366,;KLK8,downstream_gene_variant,,ENST00000599710,;KLK8,downstream_gene_variant,,ENST00000594669,; T ENST00000391806 Transcript missense_variant 956/1051 875/918 292/305 R/H cGc/cAc rs371793414,COSM999891 1 -1 KLK8 HGNC HGNC:6369 protein_coding YES CCDS42600.1 ENSP00000375682 O60259 UPI000002ACDB NM_144505.2 tolerated(0.35) 6/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF123,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371793414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 50996102 50996102 C T 1 0 0 0 0 1 0 0 0 8279 768 27 1 1 KLK8 19 50996102 Missense_Mutation SNP C 11LU013_T 42032929 50996102 7621514 47 47 ZBTB45 0 . GRCh38 19 58517618 58517618 + Missense_Mutation SNP A A T novel 11LU013_T 11LU013_N A A c.56T>A p.Leu19Gln p.L19Q ENST00000594051 2/3 236 188 48 259 259 0 strelka-varscan-mutect ZBTB45,missense_variant,p.Leu19Gln,ENST00000594051,NM_001316979.1;ZBTB45,missense_variant,p.Leu19Gln,ENST00000354590,NM_032792.2;ZBTB45,missense_variant,p.Leu19Gln,ENST00000600990,;ZBTB45,missense_variant,p.Leu19Gln,ENST00000600130,;ZBTB45,downstream_gene_variant,,ENST00000596739,; T ENST00000594051 Transcript missense_variant 537/2541 56/1536 19/511 L/Q cTg/cAg 1 -1 ZBTB45 HGNC HGNC:23715 protein_coding YES CCDS12984.1 ENSP00000469089 Q96K62 A0A024R4T8 UPI00000739B8 NM_001316979.1 deleterious(0) 2/3 Gene3D:3.30.710.10,Superfamily_domains:SSF54695 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 58517618 58517618 A T 1 0 0 0 0 1 0 0 0 18116 188 7 4 4 ZBTB45 19 58517618 Missense_Mutation SNP A 11LU013_T 7521516 58517618 99998 48 48 MYH9 0 . GRCh38 22 36341463 36341463 + Missense_Mutation SNP C C T novel 11LU013_T 11LU013_N C C c.397G>A p.Glu133Lys p.E133K ENST00000216181 3/41 494 427 67 701 701 0 strelka-varscan-mutect MYH9,missense_variant,p.Glu133Lys,ENST00000216181,NM_002473.5;MYH9,missense_variant,p.Glu133Lys,ENST00000401701,; T ENST00000216181 Transcript missense_variant 628/7501 397/5883 133/1960 E/K Gag/Aag 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 tolerated(1) 3/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF317,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 1 36341463 36341463 C T 1 0 0 0 0 1 0 0 0 10042 922 32 3 3 MYH9 22 36341463 Missense_Mutation SNP C 11LU013_T 36341463 14477005 49 49 CELSR1 0 . GRCh38 22 46366464 46366464 + Missense_Mutation SNP T T C rs753600009 11LU013_T 11LU013_N T T c.8222A>G p.Asn2741Ser p.N2741S ENST00000262738 30/35 277 242 35 298 298 0 strelka-varscan-mutect CELSR1,missense_variant,p.Asn2741Ser,ENST00000262738,NM_014246.1;CELSR1,upstream_gene_variant,,ENST00000473624,; C ENST00000262738 Transcript missense_variant 8222/11389 8222/9045 2741/3014 N/S aAc/aGc rs753600009 1 -1 CELSR1 HGNC HGNC:1850 protein_coding YES CCDS14076.1 ENSP00000262738 Q9NYQ6 UPI0000040648 NM_014246.1 deleterious(0.03) 30/35 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF36 MODERATE 1 SNV 1 1 PASS rs753600009 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 1 46366464 46366464 T C 1 0 0 0 0 1 0 0 0 2928 1725 60 5 5 CELSR1 22 46366464 Missense_Mutation SNP T 11LU013_T 10025001 46366464 4452004 50 50 COL4A5 0 . GRCh38 X 108692863 108692863 + Silent SNP A A G novel 11LU013_T 11LU013_N A A c.4644A>G p.= p.P1548P ENST00000328300 50/53 274 190 84 174 174 0 strelka-varscan-mutect COL4A5,synonymous_variant,p.=,ENST00000328300,NM_033380.2;COL4A5,synonymous_variant,p.=,ENST00000361603,NM_000495.4;COL4A5,synonymous_variant,p.=,ENST00000504541,;COL4A5,intron_variant,,ENST00000515658,; G ENST00000328300 Transcript synonymous_variant 4888/6483 4644/5076 1548/1691 P ccA/ccG 1 1 COL4A5 HGNC HGNC:2207 protein_coding YES CCDS35366.1 ENSP00000331902 P29400 UPI000002A538 NM_033380.2 50/53 PROSITE_profiles:PS51403,hmmpanther:PTHR24023:SF543,hmmpanther:PTHR24023,Gene3D:1t60D00,Pfam_domain:PF01413,SMART_domains:SM00111,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 1 108692863 108692863 A G 1 0 0 0 0 0 0 0 1 3483 175 7 5 5 COL4A5 23 108692863 Silent SNP A 11LU013_T 108692863 47348032 51 51 PGRMC1 0 . GRCh38 X 119236405 119236405 + Silent SNP C C T novel 11LU013_T 11LU013_N C C c.42C>T p.= p.S14S ENST00000217971 1/3 299 210 89 192 192 0 strelka-varscan-mutect PGRMC1,synonymous_variant,p.=,ENST00000217971,NM_006667.4;PGRMC1,synonymous_variant,p.=,ENST00000535419,NM_001282621.1; T ENST00000217971 Transcript synonymous_variant 153/1911 42/588 14/195 S agC/agT 1 1 PGRMC1 HGNC HGNC:16090 protein_coding YES CCDS14576.1 ENSP00000217971 O00264 Q6IB11 UPI000013C73E NM_006667.4 1/3 hmmpanther:PTHR10281,hmmpanther:PTHR10281:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 1 119236405 119236405 C T 1 0 0 0 0 0 0 0 1 11895 767 27 1 1 PGRMC1 23 119236405 Silent SNP C 11LU013_T 10543542 119236405 36804490 52 52 AGRN 0 . GRCh38 1 1047641 1047641 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.3585G>T p.= p.G1195G ENST00000379370 21/36 516 402 114 585 583 2 strelka-varscan-mutect AGRN,synonymous_variant,p.=,ENST00000620552,NM_001305275.1;AGRN,synonymous_variant,p.=,ENST00000379370,NM_198576.3;AGRN,upstream_gene_variant,,ENST00000419249,;AGRN,non_coding_transcript_exon_variant,,ENST00000466223,;AGRN,non_coding_transcript_exon_variant,,ENST00000478677,;AGRN,upstream_gene_variant,,ENST00000461111,;AGRN,upstream_gene_variant,,ENST00000492947,;AGRN,downstream_gene_variant,,ENST00000479707,; T ENST00000379370 Transcript synonymous_variant 3635/7323 3585/6138 1195/2045 G ggG/ggT 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 21/36 Superfamily_domains:0047452,Gene3D:1ivzA00,Pfam_domain:PF01390,PROSITE_profiles:PS50024,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288,SMART_domains:SM00200 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 1047641 1047641 G T 1 0 0 0 0 0 0 0 1 476 1190 42 2 2 AGRN 1 1047641 Silent SNP G 11LU016_T 1047641 247908781 1 53 CFAP74 0 . GRCh38 1 1955788 1955788 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2079G>T p.Glu693Asp p.E693D ENST00000493964 18/38 235 214 21 198 198 0 strelka-varscan-mutect CFAP74,missense_variant,p.Glu693Asp,ENST00000493964,NM_001304360.1;CFAP74,non_coding_transcript_exon_variant,,ENST00000270720,;CFAP74,non_coding_transcript_exon_variant,,ENST00000468610,;CFAP74,non_coding_transcript_exon_variant,,ENST00000493316,;CFAP74,non_coding_transcript_exon_variant,,ENST00000461752,; A ENST00000493964 Transcript missense_variant 2235/5247 2079/4755 693/1584 E/D gaG/gaT 1 -1 CFAP74 HGNC HGNC:29368 protein_coding YES ENSP00000417061 Q9C0B2 UPI0004620AE2 NM_001304360.1 tolerated(0.11) 18/38 hmmpanther:PTHR22538 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1955788 1955788 C A 1 0 0 0 0 1 0 0 0 3033 796 28 2 2 CFAP74 1 1955788 Missense_Mutation SNP C 11LU016_T 908147 1955788 247000634 2 54 ARHGEF16 0 . GRCh38 1 3473101 3473101 + Missense_Mutation SNP G G T rs536938385 11LU016_T 11LU016_N G G c.1046G>T p.Arg349Leu p.R349L ENST00000378378 7/15 82 63 19 130 130 0 strelka-varscan-mutect ARHGEF16,missense_variant,p.Arg349Leu,ENST00000378378,NM_014448.3;ARHGEF16,missense_variant,p.Arg61Leu,ENST00000378371,;ARHGEF16,missense_variant,p.Arg61Leu,ENST00000378373,;ARHGEF16,missense_variant,p.Arg61Leu,ENST00000445297,;ARHGEF16,missense_variant,p.Arg53Leu,ENST00000418137,;ARHGEF16,non_coding_transcript_exon_variant,,ENST00000485984,;ARHGEF16,non_coding_transcript_exon_variant,,ENST00000464620,; T ENST00000378378 Transcript missense_variant 1451/3061 1046/2130 349/709 R/L cGg/cTg rs536938385,COSM1146305,COSM681066,COSM681067 1 1 ARHGEF16 HGNC HGNC:15515 protein_coding YES CCDS46.2 ENSP00000367629 Q5VV41 UPI00002039A3 NM_014448.3 deleterious(0) 7/15 PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF3,hmmpanther:PTHR12845,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 0,1,1,1 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs536938385 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 3473101 3473101 G T 1 0 0 0 0 1 0 0 0 1029 1116 39 1 1 ARHGEF16 1 3473101 Missense_Mutation SNP G 11LU016_T 1517313 3473101 245483321 3 55 TP73 0 . GRCh38 1 3722162 3722162 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.571G>T p.Val191Leu p.V191L ENST00000378295 5/14 194 164 30 381 381 0 strelka-varscan-mutect TP73,missense_variant,p.Val191Leu,ENST00000378295,NM_005427.3,NM_001204185.1;TP73,missense_variant,p.Val142Leu,ENST00000378288,NM_001204191.1,NM_001126240.2,NM_001204190.1;TP73,missense_variant,p.Val191Leu,ENST00000357733,NM_001204187.1;TP73,missense_variant,p.Val191Leu,ENST00000346387,NM_001204188.1;TP73,missense_variant,p.Val191Leu,ENST00000604074,NM_001204189.1,NM_001204186.1;TP73,missense_variant,p.Val191Leu,ENST00000354437,NM_001204184.1;TP73,missense_variant,p.Val142Leu,ENST00000378285,NM_001126241.2;TP73,missense_variant,p.Val142Leu,ENST00000378280,NM_001126242.2;TP73,missense_variant,p.Val120Leu,ENST00000378290,NM_001204192.1;TP73,missense_variant,p.Val191Leu,ENST00000603362,;TP73,missense_variant,p.Val191Leu,ENST00000604479,;TP73,non_coding_transcript_exon_variant,,ENST00000603364,; T ENST00000378295 Transcript missense_variant 726/5188 571/1911 191/636 V/L Gtg/Ttg COSM3356580,COSM3356581 1 1 TP73 HGNC HGNC:12003 protein_coding YES CCDS49.1 ENSP00000367545 O15350 A0A024R4C3 UPI000002E988 NM_005427.3,NM_001204185.1 deleterious(0.04) 5/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF21,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 2 3722162 3722162 G T 1 0 0 0 0 1 0 0 0 16872 1145 40 1 1 TP73 1 3722162 Missense_Mutation SNP G 11LU016_T 249061 3722162 245234260 4 56 CHD5 0 . GRCh38 1 6125181 6125181 + Missense_Mutation SNP C C A rs866772665 11LU016_T 11LU016_N C C c.4313G>T p.Arg1438Leu p.R1438L ENST00000262450 29/42 134 117 17 159 159 0 strelka-varscan-mutect CHD5,missense_variant,p.Arg1438Leu,ENST00000262450,NM_015557.2;CHD5,missense_variant,p.Arg821Leu,ENST00000462991,;CHD5,3_prime_UTR_variant,,ENST00000377999,;CHD5,intron_variant,,ENST00000496404,;CHD5,downstream_gene_variant,,ENST00000491020,; A ENST00000262450 Transcript missense_variant 4413/9646 4313/5865 1438/1954 R/L cGc/cTc rs866772665 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 deleterious(0.01) 29/42 Pfam_domain:PF06461,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583,SMART_domains:SM01146 MODERATE 1 SNV 1 1 PASS rs866772665 . 0 204 2 4 0 0 0 0 -20 0.9996247 1 1 1 0 A 3 1 2 6125181 6125181 C A 1 0 0 0 0 1 0 0 0 3087 768 27 1 1 CHD5 1 6125181 Missense_Mutation SNP C 11LU016_T 2403019 6125181 242831241 5 57 PLEKHG5 0 . GRCh38 1 6470272 6470272 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.2001G>A p.= p.E667E ENST00000537245 17/22 142 109 33 170 170 0 strelka-varscan-mutect PLEKHG5,synonymous_variant,p.=,ENST00000377748,NM_198681.3;PLEKHG5,synonymous_variant,p.=,ENST00000537245,NM_001265592.1;PLEKHG5,synonymous_variant,p.=,ENST00000535355,NM_001265593.1;PLEKHG5,synonymous_variant,p.=,ENST00000340850,NM_001042664.1;PLEKHG5,synonymous_variant,p.=,ENST00000400913,NM_001042665.1;PLEKHG5,synonymous_variant,p.=,ENST00000377732,;PLEKHG5,synonymous_variant,p.=,ENST00000400915,NM_001042663.1;PLEKHG5,synonymous_variant,p.=,ENST00000377728,NM_020631.4;PLEKHG5,synonymous_variant,p.=,ENST00000377740,;PLEKHG5,synonymous_variant,p.=,ENST00000377725,NM_001265594.1;TNFRSF25,upstream_gene_variant,,ENST00000377782,NM_148965.1;TNFRSF25,upstream_gene_variant,,ENST00000356876,NM_003790.2;TNFRSF25,upstream_gene_variant,,ENST00000351959,NM_148966.1;TNFRSF25,upstream_gene_variant,,ENST00000348333,NM_148967.1;TNFRSF25,upstream_gene_variant,,ENST00000481401,;TNFRSF25,upstream_gene_variant,,ENST00000351748,NM_148970.1;TNFRSF25,upstream_gene_variant,,ENST00000461703,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000487949,;TNFRSF25,upstream_gene_variant,,ENST00000513135,;TNFRSF25,upstream_gene_variant,,ENST00000485036,;TNFRSF25,upstream_gene_variant,,ENST00000480393,;TNFRSF25,upstream_gene_variant,,ENST00000414040,;TNFRSF25,upstream_gene_variant,,ENST00000510563,;TNFRSF25,upstream_gene_variant,,ENST00000502588,;TNFRSF25,upstream_gene_variant,,ENST00000502730,;TNFRSF25,upstream_gene_variant,,ENST00000469691,;TNFRSF25,upstream_gene_variant,,ENST00000453341,;TNFRSF25,upstream_gene_variant,,ENST00000515145,; T ENST00000537245 Transcript synonymous_variant 2066/4794 2001/3258 667/1085 E gaG/gaA 1 -1 PLEKHG5 HGNC HGNC:29105 protein_coding YES CCDS57969.1 ENSP00000439625 O94827 UPI000206539E NM_001265592.1 17/22 PROSITE_profiles:PS50003,hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF9,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 6470272 6470272 C T 1 0 0 0 0 0 0 0 1 12166 680 24 3 3 PLEKHG5 1 6470272 Silent SNP C 11LU016_T 345091 6470272 242486150 6 58 SLC2A7 0 . GRCh38 1 9013599 9013599 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.940G>T p.Gly314Cys p.G314C ENST00000400906 8/12 149 119 30 160 159 1 strelka-varscan-mutect SLC2A7,missense_variant,p.Gly314Cys,ENST00000400906,NM_207420.2; A ENST00000400906 Transcript missense_variant 940/1539 940/1539 314/512 G/C Ggc/Tgc 1 -1 SLC2A7 HGNC HGNC:13445 protein_coding YES CCDS98.2 ENSP00000383698 Q6PXP3 UPI00001A73A8 NM_207420.2 deleterious(0) 8/12 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF30,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 9013599 9013599 C A 1 0 0 0 0 1 0 0 0 14820 623 22 2 2 SLC2A7 1 9013599 Missense_Mutation SNP C 11LU016_T 2543327 9013599 239942823 7 59 TMEM51 0 . GRCh38 1 15219518 15219518 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.537G>T p.= p.V179V ENST00000428417 3/3 239 190 49 201 201 0 strelka-varscan-mutect TMEM51,synonymous_variant,p.=,ENST00000428417,NM_001136217.1;TMEM51,synonymous_variant,p.=,ENST00000376008,NM_001319665.1,NM_001136218.1;TMEM51,synonymous_variant,p.=,ENST00000376014,NM_001136216.1;TMEM51,synonymous_variant,p.=,ENST00000400796,NM_018022.2;TMEM51,3_prime_UTR_variant,,ENST00000434578,;TMEM51,downstream_gene_variant,,ENST00000451326,; T ENST00000428417 Transcript synonymous_variant 983/1942 537/762 179/253 V gtG/gtT 1 1 TMEM51 HGNC HGNC:25488 protein_coding YES CCDS154.1 ENSP00000394899 Q9NW97 A0A024QZ97 UPI0000073712 NM_001136217.1 3/3 hmmpanther:PTHR16015,Pfam_domain:PF15345 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 15219518 15219518 G T 1 0 0 0 0 0 0 0 1 16652 1335 47 2 2 TMEM51 1 15219518 Silent SNP G 11LU016_T 6205919 15219518 233736904 8 60 CLCNKA 0 . GRCh38 1 16026547 16026547 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.510G>T p.= p.V170V ENST00000331433 6/20 715 576 139 891 890 1 strelka-varscan-mutect CLCNKA,synonymous_variant,p.=,ENST00000375692,NM_001042704.1;CLCNKA,synonymous_variant,p.=,ENST00000331433,NM_004070.3;CLCNKA,synonymous_variant,p.=,ENST00000439316,NM_001257139.1;CLCNKA,non_coding_transcript_exon_variant,,ENST00000464764,;CLCNKA,non_coding_transcript_exon_variant,,ENST00000495784,;CLCNKA,upstream_gene_variant,,ENST00000491433,;CLCNKA,downstream_gene_variant,,ENST00000477360,; T ENST00000331433 Transcript synonymous_variant 529/2475 510/2064 170/687 V gtG/gtT 1 1 CLCNKA HGNC HGNC:2026 protein_coding YES CCDS167.1 ENSP00000332771 P51800 UPI0000127993 NM_004070.3 6/20 Gene3D:1otsB00,Pfam_domain:PF00654,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF95,Superfamily_domains:SSF81340,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 16026547 16026547 G T 1 0 0 0 0 0 0 0 1 3233 1306 46 2 2 CLCNKA 1 16026547 Silent SNP G 11LU016_T 807029 16026547 232929875 9 61 HTR6 0 . GRCh38 1 19666051 19666051 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.298C>A p.Leu100Met p.L100M ENST00000289753 1/3 185 145 40 160 160 0 strelka-varscan-mutect HTR6,missense_variant,p.Leu100Met,ENST00000289753,NM_000871.2; A ENST00000289753 Transcript missense_variant 765/1984 298/1323 100/440 L/M Ctg/Atg 1 1 HTR6 HGNC HGNC:5301 protein_coding YES CCDS197.1 ENSP00000289753 P50406 UPI00000503E0 NM_000871.2 tolerated(0.12) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF114,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 19666051 19666051 C A 1 0 0 0 0 1 0 0 0 7347 680 24 2 2 HTR6 1 19666051 Missense_Mutation SNP C 11LU016_T 3639504 19666051 229290371 10 62 RUNX3 0 . GRCh38 1 24907382 24907382 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.622T>C p.Phe208Leu p.F208L ENST00000399916 5/6 153 134 19 166 166 0 strelka-varscan-mutect RUNX3,missense_variant,p.Phe208Leu,ENST00000399916,NM_001320672.1,NM_001031680.2;RUNX3,missense_variant,p.Phe194Leu,ENST00000308873,NM_004350.2;RUNX3,missense_variant,p.Phe208Leu,ENST00000338888,;RUNX3,non_coding_transcript_exon_variant,,ENST00000496967,; G ENST00000399916 Transcript missense_variant 1061/4340 622/1290 208/429 F/L Ttc/Ctc 1 -1 RUNX3 HGNC HGNC:10473 protein_coding YES CCDS30633.1 ENSP00000382800 Q13761 A0A024RAH4 UPI000002B2FF NM_001320672.1,NM_001031680.2 deleterious(0.01) 5/6 hmmpanther:PTHR11950,hmmpanther:PTHR11950:SF26 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 24907382 24907382 A G 1 0 0 0 0 1 0 0 0 14010 43 2 5 5 RUNX3 1 24907382 Missense_Mutation SNP A 11LU016_T 5241331 24907382 224049040 11 63 GMEB1 0 . GRCh38 1 28714431 28714431 + Silent SNP A A G novel 11LU016_T 11LU016_N A A c.1380A>G p.= p.P460P ENST00000294409 10/10 288 252 36 238 238 0 strelka-varscan-mutect GMEB1,synonymous_variant,p.=,ENST00000373816,NM_024482.2;GMEB1,synonymous_variant,p.=,ENST00000294409,NM_006582.3;GMEB1,synonymous_variant,p.=,ENST00000361872,;GMEB1,non_coding_transcript_exon_variant,,ENST00000480454,; G ENST00000294409 Transcript synonymous_variant 1470/1912 1380/1722 460/573 P ccA/ccG 1 1 GMEB1 HGNC HGNC:4370 protein_coding YES CCDS327.1 ENSP00000294409 Q9Y692 UPI000012B8AB NM_006582.3 10/10 hmmpanther:PTHR10417,hmmpanther:PTHR10417:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 28714431 28714431 A G 1 0 0 0 0 0 0 0 1 6366 175 7 5 5 GMEB1 1 28714431 Silent SNP A 11LU016_T 3807049 28714431 220241991 12 64 EPHA10 0 . GRCh38 1 37720038 37720038 + Silent SNP T T A rs768211661 11LU016_T 11LU016_N T T c.2433A>T p.= p.L811L ENST00000373048 14/17 239 184 55 339 339 0 strelka-varscan-mutect EPHA10,synonymous_variant,p.=,ENST00000373048,NM_001099439.1;EPHA10,synonymous_variant,p.=,ENST00000427468,;EPHA10,downstream_gene_variant,,ENST00000540011,;EPHA10,non_coding_transcript_exon_variant,,ENST00000446149,;EPHA10,synonymous_variant,p.=,ENST00000534097,;EPHA10,3_prime_UTR_variant,,ENST00000437645,;EPHA10,3_prime_UTR_variant,,ENST00000432874,;EPHA10,downstream_gene_variant,,ENST00000453577,; A ENST00000373048 Transcript synonymous_variant 2433/5425 2433/3027 811/1008 L ctA/ctT rs768211661 1 -1 EPHA10 HGNC HGNC:19987 protein_coding YES CCDS41305.1 ENSP00000362139 Q5JZY3 UPI00001A41BD NM_001099439.1 14/17 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF258,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS rs768211661 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 37720038 37720038 T A 1 0 0 0 0 0 0 0 1 5013 1393 49 4 4 EPHA10 1 37720038 Silent SNP T 11LU016_T 9005607 37720038 211236384 13 65 MACF1 0 . GRCh38 1 39429981 39429981 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.10857G>C p.Trp3619Cys p.W3619C ENST00000361689 59/93 299 277 22 328 328 0 strelka-varscan-mutect MACF1,missense_variant,p.Trp5681Cys,ENST00000564288,;MACF1,missense_variant,p.Trp5718Cys,ENST00000567887,;MACF1,missense_variant,p.Trp5577Cys,ENST00000372915,;MACF1,missense_variant,p.Trp4121Cys,ENST00000289893,;MACF1,missense_variant,p.Trp3619Cys,ENST00000361689,NM_012090.5;MACF1,missense_variant,p.Trp2623Cys,ENST00000372925,;MACF1,downstream_gene_variant,,ENST00000482035,;MACF1,upstream_gene_variant,,ENST00000473843,; C ENST00000361689 Transcript missense_variant 10909/17538 10857/16293 3619/5430 W/C tgG/tgC 1 1 MACF1 HGNC HGNC:13664 protein_coding YES CCDS435.1 ENSP00000354573 Q9UPN3 UPI00001B3DC6 NM_012090.5 deleterious(0) 59/93 Gene3D:1.20.58.60,SMART_domains:SM00150 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 39429981 39429981 G C 1 0 0 0 0 1 0 0 0 9060 1212 42 4 4 MACF1 1 39429981 Missense_Mutation SNP G 11LU016_T 1709943 39429981 209526441 14 66 CTPS1 0 . GRCh38 1 40991789 40991789 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.664C>G p.Leu222Val p.L222V ENST00000372621 7/19 195 172 23 193 193 0 strelka-varscan-mutect CTPS1,missense_variant,p.Leu222Val,ENST00000372621,NM_001905.3;CTPS1,missense_variant,p.Leu222Val,ENST00000372616,;CTPS1,non_coding_transcript_exon_variant,,ENST00000479480,;CTPS1,non_coding_transcript_exon_variant,,ENST00000480420,;CTPS1,upstream_gene_variant,,ENST00000463285,; G ENST00000372621 Transcript missense_variant 1172/3201 664/1776 222/591 L/V Ctt/Gtt 1 1 CTPS1 HGNC HGNC:2519 protein_coding YES CCDS459.1 ENSP00000361704 P17812 UPI0000132D63 NM_001905.3 tolerated(0.07) 7/19 HAMAP:MF_01227,hmmpanther:PTHR11550,hmmpanther:PTHR11550:SF8,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00337,Pfam_domain:PF06418,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 40991789 40991789 C G 1 0 0 0 0 1 0 0 0 3831 565 20 4 4 CTPS1 1 40991789 Missense_Mutation SNP C 11LU016_T 1561808 40991789 207964633 15 67 ERMAP 0 . GRCh38 1 42842537 42842537 + Missense_Mutation SNP G G A rs757264741 11LU016_T 11LU016_N G G c.733G>A p.Asp245Asn p.D245N ENST00000372517 12/12 84 76 8 99 99 0 strelka-varscan-mutect ERMAP,missense_variant,p.Asp155Asn,ENST00000328249,;ERMAP,missense_variant,p.Asp245Asn,ENST00000372517,NM_001017922.1;ERMAP,missense_variant,p.Asp245Asn,ENST00000372514,NM_018538.3;ZNF691,upstream_gene_variant,,ENST00000372504,;ZNF691,upstream_gene_variant,,ENST00000372502,NM_001242739.1;ZNF691,upstream_gene_variant,,ENST00000372506,;ZNF691,upstream_gene_variant,,ENST00000372507,;ZNF691,upstream_gene_variant,,ENST00000372508,NM_015911.3;RP11-342M1.3,intron_variant,,ENST00000416809,;RP11-342M1.3,intron_variant,,ENST00000444563,;RP11-342M1.3,intron_variant,,ENST00000425076,;RP11-342M1.3,intron_variant,,ENST00000414798,;ERMAP,non_coding_transcript_exon_variant,,ENST00000487556,; A ENST00000372517 Transcript missense_variant 977/3423 733/1428 245/475 D/N Gac/Aac rs757264741 1 1 ERMAP HGNC HGNC:15743 protein_coding YES CCDS475.1 ENSP00000361595 Q96PL5 UPI000007000D NM_001017922.1 tolerated(0.1) 12/12 Pfam_domain:PF13765,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF46,SMART_domains:SM00589,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs757264741 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 42842537 42842537 G A 1 0 0 0 0 1 0 0 0 5091 942 33 3 3 ERMAP 1 42842537 Missense_Mutation SNP G 11LU016_T 1850748 42842537 206113885 16 68 TTC22 0 . GRCh38 1 54787828 54787828 + Splice_Site SNP T T A rs868843299 11LU016_T 11LU016_N T T c.624-2A>T p.X208_splice ENST00000371276 161 136 25 190 190 0 strelka-varscan-mutect TTC22,splice_acceptor_variant,,ENST00000371276,NM_001114108.1;TTC22,splice_acceptor_variant,,ENST00000371274,NM_017904.3;TTC22,upstream_gene_variant,,ENST00000448308,;TTC22,non_coding_transcript_exon_variant,,ENST00000488771,;TTC22,non_coding_transcript_exon_variant,,ENST00000474654,; A ENST00000371276 Transcript splice_acceptor_variant -/3345 624/1710 208/569 rs868843299 1 -1 TTC22 HGNC HGNC:26067 protein_coding YES CCDS44152.1 ENSP00000360323 Q5TAA0 UPI0000470B73 NM_001114108.1 2/6 HIGH 1 SNV 5 1 PASS rs868843299 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 2 54787828 54787828 T A 1 0 0 0 0 0 0 1 0 17197 1594 55 4 4 TTC22 1 54787828 Splice_Site SNP T 11LU016_T 11945291 54787828 194168594 17 69 LRRC7 0 . GRCh38 1 70039739 70039739 + Silent SNP T T A novel 11LU016_T 11LU016_N T T c.3801T>A p.= p.P1267P ENST00000035383 19/25 62 55 7 74 74 0 strelka-varscan-mutect LRRC7,synonymous_variant,p.=,ENST00000310961,;LRRC7,synonymous_variant,p.=,ENST00000035383,NM_020794.2;LRRC7,synonymous_variant,p.=,ENST00000415775,; A ENST00000035383 Transcript synonymous_variant 3831/5000 3801/4614 1267/1537 P ccT/ccA 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 19/25 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -16.27822 1 1 1 1 0 A 2 1 2 70039739 70039739 T A 1 0 0 0 0 0 0 0 1 8916 1567 55 4 4 LRRC7 1 70039739 Silent SNP T 11LU016_T 15251911 70039739 178916683 18 70 LRRIQ3 0 . GRCh38 1 74041832 74041832 + Missense_Mutation SNP T T G rs769394699 11LU016_T 11LU016_N T T c.1099A>C p.Asn367His p.N367H ENST00000354431 7/8 147 129 18 97 97 0 strelka-varscan-mutect LRRIQ3,missense_variant,p.Asn367His,ENST00000354431,NM_001105659.1;LRRIQ3,missense_variant,p.Asn367His,ENST00000395089,;LRRIQ3,intron_variant,,ENST00000417067,;LRRIQ3,3_prime_UTR_variant,,ENST00000415760,; G ENST00000354431 Transcript missense_variant 1291/2849 1099/1875 367/624 N/H Aat/Cat rs769394699 1 -1 LRRIQ3 HGNC HGNC:28318 protein_coding YES CCDS41350.1 ENSP00000346414 A6PVS8 UPI000155D493 NM_001105659.1 tolerated(0.07) 7/8 MODERATE 1 SNV 5 1 PASS rs769394699 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 74041832 74041832 T G 1 0 0 0 0 1 0 0 0 8936 1754 61 5 5 LRRIQ3 1 74041832 Missense_Mutation SNP T 11LU016_T 4002093 74041832 174914590 19 71 WDR63 0 . GRCh38 1 85098619 85098619 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1440A>T p.Lys480Asn p.K480N ENST00000294664 13/23 173 163 10 204 204 0 strelka-varscan-mutect WDR63,missense_variant,p.Lys480Asn,ENST00000294664,NM_145172.4;WDR63,missense_variant,p.Lys441Asn,ENST00000370596,;WDR63,missense_variant,p.Lys441Asn,ENST00000326813,NM_001288563.1;WDR63,3_prime_UTR_variant,,ENST00000464801,; T ENST00000294664 Transcript missense_variant 1620/2995 1440/2676 480/891 K/N aaA/aaT 1 1 WDR63 HGNC HGNC:30711 protein_coding YES CCDS702.1 ENSP00000294664 Q8IWG1 A0A140VJZ8 UPI00000744F1 NM_145172.4 tolerated(0.18) 13/23 Gene3D:2.130.10.10,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF5,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 85098619 85098619 A T 1 0 0 0 0 1 0 0 0 17873 69 3 4 4 WDR63 1 85098619 Missense_Mutation SNP A 11LU016_T 11056787 85098619 163857803 20 72 COL24A1 0 . GRCh38 1 85734803 85734803 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.4944G>T p.Gln1648His p.Q1648H ENST00000370571 59/60 332 285 47 366 364 2 strelka-varscan-mutect COL24A1,missense_variant,p.Gln1648His,ENST00000370571,NM_152890.5;COL24A1,3_prime_UTR_variant,,ENST00000426639,;COL24A1,3_prime_UTR_variant,,ENST00000473734,; A ENST00000370571 Transcript missense_variant 5311/6825 4944/5145 1648/1714 Q/H caG/caT 1 -1 COL24A1 HGNC HGNC:20821 protein_coding YES CCDS41353.1 ENSP00000359603 Q17RW2 UPI000013E81F NM_152890.5 tolerated(0.09) 59/60 PD002078,Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF590,SMART_domains:SM00038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 85734803 85734803 C A 1 0 0 0 0 1 0 0 0 3471 912 32 2 2 COL24A1 1 85734803 Missense_Mutation SNP C 11LU016_T 636184 85734803 163221619 21 73 CLCA1 0 . GRCh38 1 86489124 86489124 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.1311G>T p.Leu437Phe p.L437F ENST00000234701 9/15 175 164 11 201 201 0 strelka-varscan-mutect CLCA1,missense_variant,p.Leu437Phe,ENST00000234701,;CLCA1,missense_variant,p.Leu437Phe,ENST00000394711,NM_001285.3; T ENST00000234701 Transcript missense_variant 1662/3310 1311/2745 437/914 L/F ttG/ttT COSM212036 1 1 CLCA1 HGNC HGNC:2015 protein_coding YES CCDS709.1 ENSP00000234701 A8K7I4 UPI00001AE689 deleterious(0.03) 9/15 PROSITE_profiles:PS50234,hmmpanther:PTHR10579:SF52,hmmpanther:PTHR10579,Gene3D:3.40.50.410,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434,SMART_domains:SM00327,Superfamily_domains:SSF53300 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 86489124 86489124 G T 1 0 0 0 0 1 0 0 0 3221 1339 47 2 2 CLCA1 1 86489124 Missense_Mutation SNP G 11LU016_T 754321 86489124 162467298 22 74 CLCA4 0 . GRCh38 1 86580010 86580010 + Nonsense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.2425C>T p.Gln809Ter p.Q809* ENST00000370563 14/14 107 91 16 107 107 0 strelka-varscan-mutect CLCA4,stop_gained,p.Gln809Ter,ENST00000370563,NM_012128.3;RP4-651E10.4,intron_variant,,ENST00000456587,; T ENST00000370563 Transcript stop_gained 2467/3211 2425/2760 809/919 Q/* Caa/Taa 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 14/14 hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 2 86580010 86580010 C T 1 0 0 0 0 0 1 0 0 3223 827 29 3 3 CLCA4 1 86580010 Nonsense_Mutation SNP C 11LU016_T 90886 86580010 162376412 23 75 ABCA4 0 . GRCh38 1 94048914 94048914 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.2697C>T p.= p.P899P ENST00000370225 18/50 353 325 28 326 326 0 strelka-varscan-mutect ABCA4,synonymous_variant,p.=,ENST00000370225,NM_000350.2;ABCA4,intron_variant,,ENST00000536513,; A ENST00000370225 Transcript synonymous_variant 2784/7309 2697/6822 899/2273 P ccC/ccT 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 18/50 Low_complexity_(Seg):seg,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF97,TIGRFAM_domain:TIGR01257 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 94048914 94048914 G A 1 0 0 0 0 0 0 0 1 38 1219 43 3 3 ABCA4 1 94048914 Silent SNP G 11LU016_T 7468904 94048914 154907508 24 76 COL11A1 0 . GRCh38 1 102995907 102995907 + Missense_Mutation SNP C C T 11LU016_T 11LU016_N C C c.2297G>A p.Gly766Glu p.G766E ENST00000370096 28/67 263 229 34 266 266 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly778Glu,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly766Glu,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly727Glu,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly650Glu,ENST00000512756,NM_080630.3;COL11A1,missense_variant,p.Gly539Glu,ENST00000635193,; T ENST00000370096 Transcript missense_variant,splice_region_variant 2610/7286 2297/5421 766/1806 G/E gGa/gAa COSM224805 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 28/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 102995907 102995907 C T 1 0 0 0 0 1 0 0 0 3455 869 30 3 3 COL11A1 1 102995907 Missense_Mutation SNP C 11LU016_T 8946993 102995907 145960515 25 77 AP4B1 0 . GRCh38 1 113895763 113895763 + Missense_Mutation SNP C C G rs190617142 11LU016_T 11LU016_N C C c.1786G>C p.Ala596Pro p.A596P ENST00000369569 9/10 155 143 12 170 170 0 strelka-varscan-mutect AP4B1,missense_variant,p.Ala596Pro,ENST00000369569,NM_001253852.1;AP4B1,missense_variant,p.Ala596Pro,ENST00000256658,NM_001253853.1,NM_006594.3;AP4B1,missense_variant,p.Ala428Pro,ENST00000369567,NM_001308312.1;AP4B1,downstream_gene_variant,,ENST00000369564,;AP4B1,downstream_gene_variant,,ENST00000369571,;AP4B1,downstream_gene_variant,,ENST00000432415,;AP4B1-AS1,intron_variant,,ENST00000419536,;AP4B1,non_coding_transcript_exon_variant,,ENST00000462591,;AP4B1,non_coding_transcript_exon_variant,,ENST00000479285,;AP4B1,downstream_gene_variant,,ENST00000489499,;AP4B1,downstream_gene_variant,,ENST00000484201,;AP4B1,downstream_gene_variant,,ENST00000489092,;AP4B1,downstream_gene_variant,,ENST00000472122,;AP4B1,downstream_gene_variant,,ENST00000479801,;AP4B1,downstream_gene_variant,,ENST00000460653,; G ENST00000369569 Transcript missense_variant 2067/2818 1786/2220 596/739 A/P Gca/Cca rs190617142 1 -1 AP4B1 HGNC HGNC:572 protein_coding YES CCDS865.1 ENSP00000358582 Q9Y6B7 A0A024R0D2 UPI0000072F63 NM_001253852.1 tolerated(0.27) 9/10 PIRSF_domain:PIRSF002291,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF4 MODERATE 1 SNV 1 1 PASS rs190617142 . 0 207 0 3 0 0 0 0 -16.32235 0.999975 1 1 1 0 G 3 3 2 113895763 113895763 C G 1 0 0 0 0 1 0 0 0 867 768 27 4 4 AP4B1 1 113895763 Missense_Mutation SNP C 11LU016_T 10899856 113895763 135060659 26 78 DENND2C 0 . GRCh38 1 114587742 114587742 + Missense_Mutation SNP C C A rs199932240 11LU016_T 11LU016_N C C c.2642G>T p.Arg881Leu p.R881L ENST00000393274 19/21 76 56 20 67 67 0 strelka-varscan-mutect DENND2C,missense_variant,p.Arg881Leu,ENST00000393274,NM_001256404.1;DENND2C,missense_variant,p.Arg824Leu,ENST00000393276,NM_198459.3;DENND2C,missense_variant,p.Arg881Leu,ENST00000393277,;DENND2C,non_coding_transcript_exon_variant,,ENST00000481894,;DENND2C,non_coding_transcript_exon_variant,,ENST00000495031,; A ENST00000393274 Transcript missense_variant 3268/6163 2642/2787 881/928 R/L cGa/cTa rs199932240 1 -1 DENND2C HGNC HGNC:24748 protein_coding YES CCDS58018.1 ENSP00000376955 Q68D51 UPI000048AF71 NM_001256404.1 deleterious(0) 19/21 PROSITE_profiles:PS50947,hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF6,Pfam_domain:PF03455,SMART_domains:SM00801 MODERATE 1 SNV 5 1 PASS rs199932240 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 114587742 114587742 C A 1 0 0 0 0 1 0 0 0 4234 884 31 1 1 DENND2C 1 114587742 Missense_Mutation SNP C 11LU016_T 691979 114587742 134368680 27 79 NOTCH2 0 . GRCh38 1 119969557 119969573 + Frame_Shift_Del DEL GATGCAGGTGGAGCCTG GATGCAGGTGGAGCCTG - novel 11LU016_T 11LU016_N GATGCAGGTGGAGCCTG GATGCAGGTGGAGCCTG c.1046_1062delCAGGCTCCACCTGCATC p.Pro349ArgfsTer23 p.P349Rfs*23 ENST00000256646 6/34 471 384 87 398 398 0 sindel-varindel-pindel NOTCH2,frameshift_variant,p.Pro349ArgfsTer23,ENST00000256646,NM_024408.3;NOTCH2,frameshift_variant,p.Pro310ArgfsTer23,ENST00000579475,;NOTCH2,non_coding_transcript_exon_variant,,ENST00000479412,; - ENST00000256646 Transcript frameshift_variant 1266-1282/11389 1046-1062/7416 349-354/2471 PGSTCI/X cCAGGCTCCACCTGCATC/c 1 -1 NOTCH2 HGNC HGNC:7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 UPI000013CF1D NM_024408.3 6/34 Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF66,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 2 -2.689072 0 0 1 0 0 - 7 5 2 119969557 119969557 GATGCAGGTGGAGCCTG - 1 0 1 0 1 0 0 0 0 10593 1048 37 0 0 NOTCH2 1 119969557 Frame_Shift_Del DEL GATGCAGGTGGAGCCTG 11LU016_T 5381815 119969557 128986865 28 80 POLR3GL 0 . GRCh38 1 145974907 145974907 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.42G>T p.Gln14His p.Q14H ENST00000369314 2/8 37 28 9 53 53 0 strelka-varscan-mutect POLR3GL,missense_variant,p.Gln14His,ENST00000369314,NM_032305.1;POLR3GL,missense_variant,p.Gln14His,ENST00000369313,;CH17-270A2.2,intron_variant,,ENST00000625258,;CH17-270A2.2,intron_variant,,ENST00000630636,;POLR3GL,non_coding_transcript_exon_variant,,ENST00000622508,;POLR3GL,non_coding_transcript_exon_variant,,ENST00000471706,; T ENST00000369314 Transcript missense_variant 149/1165 42/657 14/218 Q/H caG/caT 1 1 POLR3GL HGNC HGNC:28466 protein_coding YES CCDS72875.1 ENSP00000358320 Q9BT43 UPI000006F290 NM_032305.1 tolerated(0.09) 2/8 Pfam_domain:PF11705,hmmpanther:PTHR15367,hmmpanther:PTHR15367:SF4 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99952 1 1 1 1 0 T 3 4 2 145974907 145974907 G T 1 0 0 0 0 1 0 0 0 12346 1020 36 2 2 POLR3GL 1 145974907 Missense_Mutation SNP G 11LU016_T 26005350 145974907 102981515 29 81 HRNR 0 . GRCh38 1 152219536 152219536 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.2093C>A p.Ser698Tyr p.S698Y ENST00000368801 3/3 529 414 115 552 551 1 strelka-varscan-mutect HRNR,missense_variant,p.Ser698Tyr,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368801 Transcript missense_variant 2169/9623 2093/8553 698/2850 S/Y tCt/tAt COSM675375 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.05) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 152219536 152219536 G T 1 0 0 0 0 1 0 0 0 7254 942 33 2 2 HRNR 1 152219536 Missense_Mutation SNP G 11LU016_T 6244629 152219536 96736886 30 82 FLG 0 . GRCh38 1 152304935 152304935 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.9951C>T p.= p.G3317G ENST00000368799 3/3 566 476 90 496 496 0 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript synonymous_variant 9987/12747 9951/12186 3317/4061 G ggC/ggT 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 152304935 152304935 G A 1 0 0 0 0 0 0 0 1 5784 1306 46 3 3 FLG 1 152304935 Silent SNP G 11LU016_T 85399 152304935 96651487 31 83 C1orf68 0 . GRCh38 1 152720184 152720184 + Nonsense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.663T>A p.Cys221Ter p.C221* ENST00000368775 1/1 147 118 29 160 160 0 strelka-varscan-mutect C1orf68,stop_gained,p.Cys221Ter,ENST00000368775,NM_001024679.2; A ENST00000368775 Transcript stop_gained 663/949 663/753 221/250 C/* tgT/tgA 1 1 C1orf68 HGNC HGNC:29468 protein_coding YES CCDS44226.1 ENSP00000357764 Q5T750 UPI00001C1D9F NM_001024679.2 1/1 hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF4,Low_complexity_(Seg):seg HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 152720184 152720184 T A 1 0 0 0 0 0 1 0 0 1997 1702 59 4 4 C1orf68 1 152720184 Nonsense_Mutation SNP T 11LU016_T 415249 152720184 96236238 32 84 LCE1D 0 . GRCh38 1 152797907 152797907 + Missense_Mutation SNP C C A rs764963989 11LU016_T 11LU016_N C C c.113C>A p.Ser38Tyr p.S38Y ENST00000326233 2/2 623 520 103 513 512 1 strelka-varscan-mutect LCE1D,missense_variant,p.Ser38Tyr,ENST00000326233,NM_178352.2; A ENST00000326233 Transcript missense_variant 156/430 113/345 38/114 S/Y tCc/tAc rs764963989,COSM3474279 1 1 LCE1D HGNC HGNC:29465 protein_coding YES CCDS1025.1 ENSP00000316737 Q5T752 UPI0000192765 NM_178352.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs764963989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 152797907 152797907 C A 1 0 0 0 0 1 0 0 0 8567 855 30 2 2 LCE1D 1 152797907 Missense_Mutation SNP C 11LU016_T 77723 152797907 96158515 33 85 CHRNB2 0 . GRCh38 1 154571912 154571912 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.1089G>T p.= p.L363L ENST00000368476 5/6 482 333 149 660 659 1 strelka-varscan-mutect CHRNB2,synonymous_variant,p.=,ENST00000368476,NM_000748.2;CHRNB2,synonymous_variant,p.=,ENST00000637900,;CHRNB2,upstream_gene_variant,,ENST00000635876,;CHRNB2,synonymous_variant,p.=,ENST00000636034,;CHRNB2,downstream_gene_variant,,ENST00000636695,; T ENST00000368476 Transcript synonymous_variant 1353/5867 1089/1509 363/502 L ctG/ctT 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 5/6 Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF80,Low_complexity_(Seg):seg,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 LOW 1 SNV 1 1 PASS rs930562574 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 154571912 154571912 G T 1 0 0 0 0 0 0 0 1 3151 1306 46 2 2 CHRNB2 1 154571912 Silent SNP G 11LU016_T 1774005 154571912 94384510 34 86 MUC1 0 . GRCh38 1 155192238 155192238 + Missense_Mutation SNP T T A rs745939858 11LU016_T 11LU016_N T T c.131A>T p.Lys44Met p.K44M ENST00000612778 2/8 527 491 36 435 435 0 strelka-varscan-mutect MUC1,missense_variant,p.Lys35Met,ENST00000611571,;MUC1,missense_variant,p.Lys44Met,ENST00000612778,NM_001204286.1;MUC1,missense_variant,p.Lys35Met,ENST00000620103,NM_001204285.1;MUC1,missense_variant,p.Lys44Met,ENST00000462215,;MUC1,missense_variant,p.Lys44Met,ENST00000457295,;MUC1,missense_variant,p.Lys44Met,ENST00000338684,NM_001204289.1,NM_001204291.1;MUC1,missense_variant,p.Lys44Met,ENST00000610359,NM_001204292.1;MUC1,missense_variant,p.Lys44Met,ENST00000614519,;MUC1,missense_variant,p.Lys44Met,ENST00000368392,NM_001018016.2,NM_001204288.1;MUC1,missense_variant,p.Lys32Met,ENST00000611577,;MUC1,missense_variant,p.Lys44Met,ENST00000615517,NM_001204295.1;MUC1,missense_variant,p.Lys35Met,ENST00000368393,NM_001204293.1;MUC1,missense_variant,p.Lys35Met,ENST00000438413,NM_001204290.1;MUC1,missense_variant,p.Lys35Met,ENST00000337604,NM_001204287.1,NM_002456.5;MUC1,missense_variant,p.Lys35Met,ENST00000368390,NM_001018017.2;MUC1,missense_variant,p.Lys35Met,ENST00000368398,NM_001204294.1;MUC1,missense_variant,p.Lys35Met,ENST00000343256,NM_001044390.2,NM_001204296.1;MUC1,missense_variant,p.Lys35Met,ENST00000471283,NM_001044393.2;MUC1,missense_variant,p.Lys35Met,ENST00000368389,NM_001204297.1;MUC1,missense_variant,p.Lys44Met,ENST00000342482,;MUC1,missense_variant,p.Lys44Met,ENST00000368396,NM_001044392.2,NM_001044391.2;THBS3,downstream_gene_variant,,ENST00000541576,NM_001252607.1;THBS3,downstream_gene_variant,,ENST00000368378,NM_007112.4;THBS3,downstream_gene_variant,,ENST00000541990,;THBS3,downstream_gene_variant,,ENST00000457183,NM_001252608.1;MUC1,upstream_gene_variant,,ENST00000462317,;MUC1,upstream_gene_variant,,ENST00000485118,;AC234582.2,downstream_gene_variant,,ENST00000623940,;AC234582.1,downstream_gene_variant,,ENST00000624572,;MIR92B,upstream_gene_variant,,ENST00000607575,;MIR92B,upstream_gene_variant,,ENST00000447623,;MUC1,non_coding_transcript_exon_variant,,ENST00000466913,;MUC1,missense_variant,p.Lys35Met,ENST00000610468,;MUC1,missense_variant,p.Lys35Met,ENST00000498431,;MUC1,missense_variant,p.Lys44Met,ENST00000467134,;MUC1,non_coding_transcript_exon_variant,,ENST00000620770,;MUC1,upstream_gene_variant,,ENST00000468978,;THBS3,downstream_gene_variant,,ENST00000469769,;THBS3,downstream_gene_variant,,ENST00000498500,;RP11-201K10.3,upstream_gene_variant,,ENST00000473363,; A ENST00000612778 Transcript missense_variant 203/1836 131/1455 44/484 K/M aAg/aTg rs745939858 1 -1 MUC1 HGNC HGNC:7508 protein_coding YES CCDS72933.1 ENSP00000484824 A0A087X2A4 UPI000059C524 NM_001204286.1 tolerated(0.15) 2/8 hmmpanther:PTHR10006:SF8,hmmpanther:PTHR10006 MODERATE SNV 5 1 PASS rs745939858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 155192238 155192238 T A 1 0 0 0 0 1 0 0 0 9968 1609 56 4 4 MUC1 1 155192238 Missense_Mutation SNP T 11LU016_T 620326 155192238 93764184 35 87 FCRL1 0 . GRCh38 1 157796103 157796103 + Missense_Mutation SNP A A C novel 11LU016_T 11LU016_N A A c.1286T>G p.Met429Arg p.M429R ENST00000368176 11/11 144 114 30 142 142 0 strelka-varscan-mutect FCRL1,missense_variant,p.Met429Arg,ENST00000368176,NM_052938.4;FCRL1,missense_variant,p.Met428Arg,ENST00000491942,NM_001159398.1;FCRL1,3_prime_UTR_variant,,ENST00000358292,NM_001159397.1;FCRL1,non_coding_transcript_exon_variant,,ENST00000489998,;FCRL1,non_coding_transcript_exon_variant,,ENST00000368175,;FCRL1,non_coding_transcript_exon_variant,,ENST00000463001,;FCRL1,non_coding_transcript_exon_variant,,ENST00000495126,; C ENST00000368176 Transcript missense_variant 1354/2596 1286/1290 429/429 M/R aTg/aGg 1 -1 FCRL1 HGNC HGNC:18509 protein_coding YES CCDS1170.1 ENSP00000357158 Q96LA6 UPI000006E5BD NM_052938.4 deleterious(0) 11/11 MODERATE 1 SNV 1 1 PASS rs1425178243 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 157796103 157796103 A C 1 0 0 0 0 1 0 0 0 5657 217 8 5 5 FCRL1 1 157796103 Missense_Mutation SNP A 11LU016_T 2603865 157796103 91160319 36 88 OR10R2 0 . GRCh38 1 158480091 158480091 + Missense_Mutation SNP G G C rs775943308 11LU016_T 11LU016_N G G c.214G>C p.Asp72His p.D72H ENST00000368152 1/1 183 124 59 179 179 0 strelka-varscan-mutect OR10R2,missense_variant,p.Asp72His,ENST00000368152,NM_001004472.1;RP11-144L1.4,non_coding_transcript_exon_variant,,ENST00000419738,;RP11-144L1.4,intron_variant,,ENST00000426251,; C ENST00000368152 Transcript missense_variant 214/1008 214/1008 72/335 D/H Gat/Cat rs775943308 1 1 OR10R2 HGNC HGNC:14820 protein_coding YES CCDS30898.1 ENSP00000357134 Q8NGX6 UPI000004CA1C NM_001004472.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF42,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs775943308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 158480091 158480091 G C 1 0 0 0 0 1 0 0 0 10994 1174 41 4 4 OR10R2 1 158480091 Missense_Mutation SNP G 11LU016_T 683988 158480091 90476331 37 89 SPTA1 0 . GRCh38 1 158666373 158666373 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2163G>T p.Glu721Asp p.E721D ENST00000368147 16/52 430 341 89 292 291 1 strelka-varscan-mutect SPTA1,missense_variant,p.Glu721Asp,ENST00000368147,NM_003126.2; A ENST00000368147 Transcript missense_variant 2344/7999 2163/7260 721/2419 E/D gaG/gaT 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.76) 16/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 158666373 158666373 C A 1 0 0 0 0 1 0 0 0 15472 680 24 2 2 SPTA1 1 158666373 Missense_Mutation SNP C 11LU016_T 186282 158666373 90290049 38 90 MNDA 0 . GRCh38 1 158845887 158845887 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.871C>A p.Gln291Lys p.Q291K ENST00000368141 5/7 197 159 38 171 171 0 strelka-varscan-mutect MNDA,missense_variant,p.Gln291Lys,ENST00000368141,NM_002432.1;MNDA,upstream_gene_variant,,ENST00000438394,;MNDA,downstream_gene_variant,,ENST00000491210,; A ENST00000368141 Transcript missense_variant 1132/1752 871/1224 291/407 Q/K Caa/Aaa 1 1 MNDA HGNC HGNC:7183 protein_coding YES CCDS1177.1 ENSP00000357123 P41218 Q5VUU6 UPI0000001609 NM_002432.1 deleterious(0.04) 5/7 Gene3D:2.40.50.140,Pfam_domain:PF02760,PROSITE_profiles:PS50834,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF18,Superfamily_domains:SSF159141 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 158845887 158845887 C A 1 0 0 0 0 1 0 0 0 9640 827 29 2 2 MNDA 1 158845887 Missense_Mutation SNP C 11LU016_T 179514 158845887 90110535 39 91 F5 0 . GRCh38 1 169542877 169542877 + Nonsense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.2213C>G p.Ser738Ter p.S738* ENST00000367797 13/25 278 215 63 205 205 0 strelka-varscan F5,stop_gained,p.Ser743Ter,ENST00000367796,;F5,stop_gained,p.Ser738Ter,ENST00000367797,NM_000130.4; C ENST00000367797 Transcript stop_gained 2415/7024 2213/6675 738/2224 S/* tCa/tGa 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 13/25 PIRSF_domain:PIRSF000354 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 2 169542877 169542877 G C 1 0 0 0 0 0 1 0 0 5216 1294 45 4 4 F5 1 169542877 Nonsense_Mutation SNP G 11LU016_T 10696990 169542877 79413545 40 92 FMO1 0 . GRCh38 1 171278797 171278797 + Nonsense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.553A>T p.Lys185Ter p.K185* ENST00000617670 5/9 144 134 10 134 134 0 strelka-varscan FMO1,stop_gained,p.Lys185Ter,ENST00000617670,NM_001282693.1,NM_002021.2;FMO1,stop_gained,p.Lys185Ter,ENST00000354841,NM_001282692.1;FMO1,stop_gained,p.Lys185Ter,ENST00000367750,;FMO1,stop_gained,p.Lys122Ter,ENST00000402921,NM_001282694.1;FMO1,stop_gained,p.Lys185Ter,ENST00000433267,;FMO1,non_coding_transcript_exon_variant,,ENST00000469112,;FMO1,non_coding_transcript_exon_variant,,ENST00000472893,;FMO1,upstream_gene_variant,,ENST00000469711,; T ENST00000617670 Transcript stop_gained 712/2192 553/1599 185/532 K/* Aag/Tag 1 1 FMO1 HGNC HGNC:3769 protein_coding YES CCDS1294.1 ENSP00000481732 Q01740 A0A024R934 UPI000000DBBA NM_001282693.1,NM_002021.2 5/9 Gene3D:3.50.50.60,Pfam_domain:PF00743,PIRSF_domain:PIRSF000332,Prints_domain:PR00370,hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF84,Superfamily_domains:SSF51905 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.92787 0.9999997 1 1 1 0 T 4 4 2 171278797 171278797 A T 1 0 0 0 0 0 1 0 0 5810 131 5 4 4 FMO1 1 171278797 Nonsense_Mutation SNP A 11LU016_T 1735920 171278797 77677625 41 93 TNR 0 . GRCh38 1 175403333 175403333 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.783C>T p.= p.C261C ENST00000367674 4/23 372 315 57 294 294 0 strelka-varscan TNR,synonymous_variant,p.=,ENST00000367674,;TNR,synonymous_variant,p.=,ENST00000263525,NM_003285.2;TNR,intron_variant,,ENST00000422274,; A ENST00000367674 Transcript synonymous_variant 1492/12949 783/4077 261/1358 C tgC/tgT 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 4/23 Gene3D:2.10.25.10,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00181 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 175403333 175403333 G A 1 0 0 0 0 0 0 0 1 16811 1311 46 3 3 TNR 1 175403333 Silent SNP G 11LU016_T 4124536 175403333 73553089 42 94 PAPPA2 0 . GRCh38 1 176556694 176556694 + Missense_Mutation SNP G G T rs757885352 11LU016_T 11LU016_N G G c.372G>T p.Glu124Asp p.E124D ENST00000367662 2/23 196 147 49 158 158 0 strelka-varscan PAPPA2,missense_variant,p.Glu124Asp,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Glu124Asp,ENST00000367661,NM_021936.2;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,; T ENST00000367662 Transcript missense_variant 1536/9691 372/5376 124/1791 E/D gaG/gaT rs757885352,COSM3359466,COSM3359467 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated_low_confidence(0.22) 2/23 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 176556694 176556694 G T 1 0 0 0 0 1 0 0 0 11513 962 34 2 2 PAPPA2 1 176556694 Missense_Mutation SNP G 11LU016_T 1153361 176556694 72399728 43 95 AXDND1 0 . GRCh38 1 179528430 179528430 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.2714G>T p.Trp905Leu p.W905L ENST00000367618 23/26 137 125 12 110 110 0 strelka-varscan AXDND1,missense_variant,p.Trp905Leu,ENST00000367618,NM_144696.5;AXDND1,missense_variant,p.Trp765Leu,ENST00000434088,;AXDND1,splice_region_variant,,ENST00000617277,;AXDND1,splice_region_variant,,ENST00000484883,;AXDND1,splice_region_variant,,ENST00000511157,; T ENST00000367618 Transcript missense_variant,splice_region_variant 3101/3642 2714/3039 905/1012 W/L tGg/tTg COSM5689838 1 1 AXDND1 HGNC HGNC:26564 protein_coding YES CCDS30948.1 ENSP00000356590 Q5T1B0 UPI000022AC91 NM_144696.5 tolerated(0.51) 23/26 hmmpanther:PTHR23052 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 179528430 179528430 G T 1 0 0 0 0 1 0 0 0 1392 1362 47 2 2 AXDND1 1 179528430 Missense_Mutation SNP G 11LU016_T 2971736 179528430 69427992 44 96 LHX9 0 . GRCh38 1 197921653 197921653 + Missense_Mutation SNP A A C novel 11LU016_T 11LU016_N A A c.727A>C p.Asn243His p.N243H ENST00000367387 3/5 58 46 12 37 37 0 strelka-varscan LHX9,missense_variant,p.Asn243His,ENST00000367387,NM_020204.2;LHX9,missense_variant,p.Asn234His,ENST00000367390,NM_001014434.1;LHX9,missense_variant,p.Asn249His,ENST00000561173,;LHX9,missense_variant,p.Asn234His,ENST00000367391,;LHX9,downstream_gene_variant,,ENST00000367388,;LHX9,downstream_gene_variant,,ENST00000606127,;LHX9,downstream_gene_variant,,ENST00000475727,; C ENST00000367387 Transcript missense_variant 1152/7836 727/1194 243/397 N/H Aac/Cac 1 1 LHX9 HGNC HGNC:14222 protein_coding YES CCDS1393.1 ENSP00000356357 Q9NQ69 UPI00001B6453 NM_020204.2 deleterious(0.04) 3/5 hmmpanther:PTHR24208 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 197921653 197921653 A C 1 0 0 0 0 1 0 0 0 8686 130 5 5 5 LHX9 1 197921653 Missense_Mutation SNP A 11LU016_T 18393223 197921653 51034769 45 97 ESRRG 0 . GRCh38 1 216677146 216677146 + Silent SNP G G T rs553364135 11LU016_T 11LU016_N G G c.417C>A p.= p.I139I ENST00000366937 3/8 225 175 50 140 140 0 strelka-varscan ESRRG,synonymous_variant,p.=,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,synonymous_variant,p.=,ENST00000360012,NM_001243514.1;ESRRG,synonymous_variant,p.=,ENST00000366937,NM_001243518.1;ESRRG,synonymous_variant,p.=,ENST00000361525,NM_206594.2;ESRRG,synonymous_variant,p.=,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,synonymous_variant,p.=,ENST00000493603,NM_001243510.2;ESRRG,synonymous_variant,p.=,ENST00000366938,NM_001243513.1;ESRRG,synonymous_variant,p.=,ENST00000361395,;ESRRG,synonymous_variant,p.=,ENST00000408911,NM_001438.3;ESRRG,synonymous_variant,p.=,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,synonymous_variant,p.=,ENST00000616180,;ESRRG,synonymous_variant,p.=,ENST00000463665,NM_001243507.1;ESRRG,synonymous_variant,p.=,ENST00000487276,NM_001243512.1;ESRRG,synonymous_variant,p.=,ENST00000493748,NM_001243509.1;ESRRG,synonymous_variant,p.=,ENST00000475275,;ESRRG,downstream_gene_variant,,ENST00000481543,;ESRRG,downstream_gene_variant,,ENST00000469486,;ESRRG,downstream_gene_variant,,ENST00000459955,;ESRRG,intron_variant,,ENST00000586199,; T ENST00000366937 Transcript synonymous_variant 684/5365 417/1413 139/470 I atC/atA rs553364135,COSM234679 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 3/8 PROSITE_profiles:PS51030,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PROSITE_patterns:PS00031,PIRSF_domain:PIRSF500939,PIRSF_domain:PIRSF002527,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 216677146 216677146 G T 1 0 0 0 0 0 0 0 1 5124 1048 37 1 1 ESRRG 1 216677146 Silent SNP G 11LU016_T 18755493 216677146 32279276 46 98 RAB3GAP2 0 . GRCh38 1 220157336 220157336 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.3489C>T p.= p.S1163S ENST00000358951 31/35 416 393 23 329 329 0 strelka-varscan RAB3GAP2,synonymous_variant,p.=,ENST00000358951,NM_012414.3;RAB3GAP2,upstream_gene_variant,,ENST00000491005,;RAB3GAP2,upstream_gene_variant,,ENST00000474966,;RAB3GAP2,upstream_gene_variant,,ENST00000491305,; A ENST00000358951 Transcript synonymous_variant 3606/7257 3489/4182 1163/1393 S tcC/tcT 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 31/35 Pfam_domain:PF14656,hmmpanther:PTHR12472 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 220157336 220157336 G A 1 0 0 0 0 0 0 0 1 13095 1335 47 3 3 RAB3GAP2 1 220157336 Silent SNP G 11LU016_T 3480190 220157336 28799086 47 99 MARK1 0 . GRCh38 1 220650673 220650673 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1524A>T p.Glu508Asp p.E508D ENST00000611084 14/18 148 122 26 136 136 0 strelka-varscan MARK1,missense_variant,p.Glu508Asp,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Glu508Asp,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Glu486Asp,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Glu508Asp,ENST00000366917,NM_018650.4; T ENST00000611084 Transcript missense_variant 2164/5321 1524/2391 508/796 E/D gaA/gaT 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 tolerated(0.16) 14/18 hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 220650673 220650673 A T 1 0 0 0 0 1 0 0 0 9237 11 1 4 4 MARK1 1 220650673 Missense_Mutation SNP A 11LU016_T 493337 220650673 28305749 48 100 HIST3H2A 0 . GRCh38 1 228457437 228457437 + Silent SNP G G T rs866126653 11LU016_T 11LU016_N G G c.381C>A p.= p.A127A ENST00000366695 1/1 246 185 61 216 216 0 strelka-varscan HIST3H2A,synonymous_variant,p.=,ENST00000366695,NM_033445.2;HIST3H2BB,upstream_gene_variant,,ENST00000620438,NM_175055.2;MIR4666A,upstream_gene_variant,,ENST00000580160,; T ENST00000366695 Transcript synonymous_variant 437/895 381/393 127/130 A gcC/gcA rs866126653 1 -1 HIST3H2A HGNC HGNC:20507 protein_coding YES CCDS1573.1 ENSP00000355656 Q7L7L0 UPI0000073CEF NM_033445.2 1/1 hmmpanther:PTHR23430,Gene3D:1.10.20.10,Superfamily_domains:SSF47113 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 228457437 228457437 G T 1 0 0 0 0 0 0 0 1 7071 1335 47 2 2 HIST3H2A 1 228457437 Silent SNP G 11LU016_T 7806764 228457437 20498985 49 101 RGS7 0 . GRCh38 1 240801464 240801464 + Silent SNP T T C novel 11LU016_T 11LU016_N T T c.1404A>G p.= p.A468A ENST00000366565 17/18 354 335 19 250 250 0 strelka-varscan RGS7,synonymous_variant,p.=,ENST00000366565,NM_002924.5;RGS7,synonymous_variant,p.=,ENST00000440928,;RGS7,intron_variant,,ENST00000366564,NM_001282778.1;RGS7,intron_variant,,ENST00000366563,NM_001282775.1;RGS7,intron_variant,,ENST00000348120,NM_001282773.1; C ENST00000366565 Transcript synonymous_variant 1786/2494 1404/1464 468/487 A gcA/gcG 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 17/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 240801464 240801464 T C 1 0 0 0 0 0 0 0 1 13481 1683 59 5 5 RGS7 1 240801464 Silent SNP T 11LU016_T 12344027 240801464 8154958 50 102 CEP170 0 . GRCh38 1 243186381 243186381 + Missense_Mutation SNP C C A rs371580565 11LU016_T 11LU016_N C C c.1150G>T p.Ala384Ser p.A384S ENST00000366542 9/20 137 90 47 104 104 0 strelka-varscan CEP170,missense_variant,p.Ala384Ser,ENST00000366542,NM_014812.2;CEP170,missense_variant,p.Ala384Ser,ENST00000366544,NM_001042404.1;CEP170,missense_variant,p.Ala384Ser,ENST00000366543,NM_001042405.1;CEP170,missense_variant,p.Ala286Ser,ENST00000336415,;CEP170,missense_variant,p.Ala11Ser,ENST00000522895,;CEP170,non_coding_transcript_exon_variant,,ENST00000521911,;CEP170,upstream_gene_variant,,ENST00000461671,; A ENST00000366542 Transcript missense_variant 1202/6828 1150/4755 384/1584 A/S Gct/Tct rs371580565 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 tolerated(0.12) 9/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 243186381 243186381 C A 1 0 0 0 0 1 0 0 0 2964 768 27 1 1 CEP170 1 243186381 Missense_Mutation SNP C 11LU016_T 2384917 243186381 5770041 51 103 OR1C1 0 . GRCh38 1 247757853 247757853 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.554T>C p.Leu185Pro p.L185P ENST00000408896 1/1 269 219 50 235 235 0 strelka-varscan OR1C1,missense_variant,p.Leu185Pro,ENST00000408896,NM_012353.2; G ENST00000408896 Transcript missense_variant 554/945 554/945 185/314 L/P cTg/cCg 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 247757853 247757853 A G 1 0 0 0 0 1 0 0 0 11029 188 7 5 5 OR1C1 1 247757853 Missense_Mutation SNP A 11LU016_T 4571472 247757853 1198569 52 104 OR2AK2 0 . GRCh38 1 247965740 247965740 + Missense_Mutation SNP C C A rs764277744 11LU016_T 11LU016_N C C c.409C>A p.Arg137Ser p.R137S ENST00000366480 1/1 38 30 8 18 18 0 strelka-varscan OR2AK2,missense_variant,p.Arg137Ser,ENST00000366480,NM_001004491.1; A ENST00000366480 Transcript missense_variant 508/1107 409/1008 137/335 R/S Cgc/Agc rs764277744,COSM3486895 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 0,1 1 PASS . . 0 206 4 0 0 0 0 0 -19.85608 1 1 1 1 0 A 3 1 2 247965740 247965740 C A 1 0 0 0 0 1 0 0 0 11064 884 31 1 1 OR2AK2 1 247965740 Missense_Mutation SNP C 11LU016_T 207887 247965740 990682 53 105 ZNF672 0 . GRCh38 1 248848139 248848139 + Missense_Mutation SNP G G A 11LU016_T 11LU016_N G G c.865G>A p.Gly289Ser p.G289S ENST00000306562 4/4 168 155 13 138 138 0 strelka-varscan ZNF672,missense_variant,p.Gly289Ser,ENST00000306562,NM_024836.2;ZNF692,downstream_gene_variant,,ENST00000451251,NM_001136036.2;ZNF692,downstream_gene_variant,,ENST00000306601,NM_017865.3;ZNF692,downstream_gene_variant,,ENST00000366471,NM_001193328.1;ZNF692,downstream_gene_variant,,ENST00000476503,;ZNF672,downstream_gene_variant,,ENST00000428515,;ZNF672,downstream_gene_variant,,ENST00000423362,;ZNF672,downstream_gene_variant,,ENST00000505503,;ZNF672,downstream_gene_variant,,ENST00000502697,;ZNF672,downstream_gene_variant,,ENST00000510904,;ZNF672,downstream_gene_variant,,ENST00000515369,;ZNF692,downstream_gene_variant,,ENST00000463519,;ZNF692,downstream_gene_variant,,ENST00000533927,;ZNF692,downstream_gene_variant,,ENST00000412341,;ZNF692,downstream_gene_variant,,ENST00000470787,;ZNF692,downstream_gene_variant,,ENST00000477070,;ZNF692,downstream_gene_variant,,ENST00000474351,;ZNF692,downstream_gene_variant,,ENST00000482023,;ZNF692,downstream_gene_variant,,ENST00000462037,; A ENST00000306562 Transcript missense_variant 1611/2989 865/1359 289/452 G/S Ggc/Agc COSM4030813 1 1 ZNF672 HGNC HGNC:26179 protein_coding YES CCDS1638.1 ENSP00000421915 Q499Z4 UPI0000070D6C NM_024836.2 tolerated(0.09) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 248848139 248848139 G A 1 0 0 0 0 1 0 0 0 18653 1116 39 1 1 ZNF672 1 248848139 Missense_Mutation SNP G 11LU016_T 882399 248848139 108283 54 106 TPO 0 . GRCh38 2 1493962 1493962 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1929C>A p.Phe643Leu p.F643L ENST00000345913 11/17 596 481 115 567 565 2 strelka-varscan-mutect TPO,missense_variant,p.Phe572Leu,ENST00000422464,;TPO,missense_variant,p.Phe643Leu,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Phe643Leu,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Phe586Leu,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Phe643Leu,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Phe470Leu,ENST00000382198,NM_175722.3;TPO,missense_variant,p.Phe118Leu,ENST00000446278,;TPO,missense_variant,p.Phe117Leu,ENST00000469607,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,non_coding_transcript_exon_variant,,ENST00000462973,; A ENST00000345913 Transcript missense_variant 2020/3145 1929/2802 643/933 F/L ttC/ttA 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 tolerated(0.47) 11/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1493962 1493962 C A 1 0 0 0 0 1 0 0 0 16891 854 30 2 2 TPO 2 1493962 Missense_Mutation SNP C 11LU016_T 1493962 240699567 55 107 MYT1L 0 . GRCh38 2 1923115 1923115 + Silent SNP C C A 11LU016_T 11LU016_N C C c.654G>T p.= p.R218R ENST00000399161 10/25 427 351 76 362 360 2 strelka-varscan-mutect MYT1L,synonymous_variant,p.=,ENST00000399161,NM_001303052.1;MYT1L,synonymous_variant,p.=,ENST00000428368,NM_015025.3;MYT1L,upstream_gene_variant,,ENST00000602387,; A ENST00000399161 Transcript synonymous_variant 1402/7063 654/3561 218/1186 R cgG/cgT COSM1014217,COSM5312159,COSM5312160 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 10/25 hmmpanther:PTHR10816:SF11,hmmpanther:PTHR10816 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 1923115 1923115 C A 1 0 0 0 0 0 0 0 1 10106 610 22 2 2 MYT1L 2 1923115 Silent SNP C 11LU016_T 429153 1923115 240270414 56 108 NTSR2 0 . GRCh38 2 11661993 11661993 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.872G>T p.Ser291Ile p.S291I ENST00000306928 2/4 57 47 10 62 62 0 strelka-varscan-mutect NTSR2,missense_variant,p.Ser291Ile,ENST00000306928,NM_012344.3;AC110754.3,downstream_gene_variant,,ENST00000399740,; A ENST00000306928 Transcript missense_variant 907/1569 872/1233 291/410 S/I aGc/aTc 1 -1 NTSR2 HGNC HGNC:8040 protein_coding YES CCDS1681.1 ENSP00000303686 O95665 UPI000013EBAA NM_012344.3 deleterious(0.03) 2/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99977 1 1 1 1 0 A 3 1 2 11661993 11661993 C A 1 0 0 0 0 1 0 0 0 10777 797 28 2 2 NTSR2 2 11661993 Missense_Mutation SNP C 11LU016_T 9738878 11661993 230531536 57 109 FAM84A 0 . GRCh38 2 14634154 14634154 + Missense_Mutation SNP C C A rs777422351 11LU016_T 11LU016_N C C c.175C>A p.Pro59Thr p.P59T ENST00000295092 2/2 253 205 48 193 193 0 strelka-varscan-mutect FAM84A,missense_variant,p.Pro59Thr,ENST00000295092,NM_145175.2;FAM84A,missense_variant,p.Pro59Thr,ENST00000331243,;AC011897.2,downstream_gene_variant,,ENST00000450715,;AC011897.2,downstream_gene_variant,,ENST00000418481,;FAM84A,upstream_gene_variant,,ENST00000497769,;FAM84A,upstream_gene_variant,,ENST00000464947,; A ENST00000295092 Transcript missense_variant 463/6355 175/879 59/292 P/T Ccg/Acg rs777422351 1 1 FAM84A HGNC HGNC:20743 protein_coding YES CCDS1684.1 ENSP00000295092 Q96KN4 UPI000013E203 NM_145175.2 tolerated(0.22) 2/2 hmmpanther:PTHR13943:SF38,hmmpanther:PTHR13943 MODERATE 1 SNV 1 1 PASS rs777422351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 14634154 14634154 C A 1 0 0 0 0 1 0 0 0 5499 623 22 2 2 FAM84A 2 14634154 Missense_Mutation SNP C 11LU016_T 2972161 14634154 227559375 58 110 APOB 0 . GRCh38 2 21004383 21004383 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.11973G>A p.= p.Q3991Q ENST00000233242 28/29 331 277 54 295 295 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; T ENST00000233242 Transcript synonymous_variant 12101/14121 11973/13692 3991/4563 Q caG/caA 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 28/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 21004383 21004383 C T 1 0 0 0 0 0 0 0 1 907 912 32 3 3 APOB 2 21004383 Silent SNP C 11LU016_T 6370229 21004383 221189146 59 111 APOB 0 . GRCh38 2 21007461 21007461 + Missense_Mutation SNP C C A rs199590149 11LU016_T 11LU016_N C C c.9407G>T p.Arg3136Leu p.R3136L ENST00000233242 26/29 298 258 40 270 270 0 strelka-varscan-mutect APOB,missense_variant,p.Arg3136Leu,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript missense_variant 9535/14121 9407/13692 3136/4563 R/L cGt/cTt rs199590149,COSM318732 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.17) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199590149 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 21007461 21007461 C A 1 0 0 0 0 1 0 0 0 907 536 19 1 1 APOB 2 21007461 Missense_Mutation SNP C 11LU016_T 3078 21007461 221186068 60 112 TDRD15 0 . GRCh38 2 21138410 21138410 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.947delC p.Pro316GlnfsTer4 p.P316Qfs*4 ENST00000405799 4/4 70 57 13 90 90 0 sindel-varindel-pindel TDRD15,frameshift_variant,p.Pro316GlnfsTer4,ENST00000405799,;TDRD15,frameshift_variant,p.Pro316GlnfsTer4,ENST00000622654,; - ENST00000405799 Transcript frameshift_variant 1273/6135 943/5805 315/1934 P/X Ccc/cc 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 Gene3D:2.30.30.140,Pfam_domain:PF00567,PROSITE_profiles:PS50304,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,SMART_domains:SM00333,Superfamily_domains:SSF63748 HIGH 1 deletion 2 4 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 21138410 21138410 C - 1 0 1 0 1 0 0 0 0 16141 739 26 0 0 TDRD15 2 21138410 Frame_Shift_Del DEL C 11LU016_T 130949 21138410 221055119 61 113 ABHD1 0 . GRCh38 2 27130376 27130376 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.966C>T p.= p.L322L ENST00000316470 8/9 190 176 14 156 156 0 strelka-mutect ABHD1,synonymous_variant,p.=,ENST00000316470,NM_032604.3;PREB,downstream_gene_variant,,ENST00000260643,NM_013388.4;PREB,downstream_gene_variant,,ENST00000406567,;PREB,downstream_gene_variant,,ENST00000456259,;ABHD1,downstream_gene_variant,,ENST00000621324,;ABHD1,downstream_gene_variant,,ENST00000416071,;PREB,downstream_gene_variant,,ENST00000430533,;PREB,downstream_gene_variant,,ENST00000416802,;ABHD1,3_prime_UTR_variant,,ENST00000448950,;ABHD1,3_prime_UTR_variant,,ENST00000420647,;ABHD1,non_coding_transcript_exon_variant,,ENST00000489120,;ABHD1,non_coding_transcript_exon_variant,,ENST00000496739,;ABHD1,downstream_gene_variant,,ENST00000622011,;PREB,downstream_gene_variant,,ENST00000468045,;PREB,downstream_gene_variant,,ENST00000444452,;PREB,downstream_gene_variant,,ENST00000474802,;PREB,downstream_gene_variant,,ENST00000441451,; T ENST00000316470 Transcript synonymous_variant 1080/1400 966/1218 322/405 L ctC/ctT 1 1 ABHD1 HGNC HGNC:17553 protein_coding YES CCDS1736.1 ENSP00000326491 Q96SE0 A0A140VJD1 UPI000006D45E NM_032604.3 8/9 hmmpanther:PTHR10794,hmmpanther:PTHR10794:SF60,PROSITE_patterns:PS01133,PIRSF_domain:PIRSF005211,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS rs765048369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 27130376 27130376 C T 1 0 0 0 0 0 0 0 1 77 900 32 3 3 ABHD1 2 27130376 Silent SNP C 11LU016_T 5991966 27130376 215063153 62 114 PRR30 0 . GRCh38 2 27137093 27137093 + Nonstop_Mutation SNP A A T rs751384314 11LU016_T 11LU016_N A A c.1237T>A p.Ter413LysextTer31 p.*413Kext*31 ENST00000335524 3/3 96 73 23 96 96 0 strelka-varscan-mutect PRR30,stop_lost,p.Ter413LysextTer31,ENST00000335524,NM_178553.3;PREB,upstream_gene_variant,,ENST00000260643,NM_013388.4;PREB,upstream_gene_variant,,ENST00000406567,;PREB,upstream_gene_variant,,ENST00000456259,;PRR30,downstream_gene_variant,,ENST00000432962,;PREB,upstream_gene_variant,,ENST00000430533,;PREB,upstream_gene_variant,,ENST00000416802,;PREB,upstream_gene_variant,,ENST00000468045,;PREB,upstream_gene_variant,,ENST00000444452,;PREB,upstream_gene_variant,,ENST00000474802,;PREB,upstream_gene_variant,,ENST00000441451,; T ENST00000335524 Transcript stop_lost 1763/2008 1237/1239 413/412 */K Tag/Aag rs751384314 1 -1 PRR30 HGNC HGNC:28677 protein_coding YES CCDS1739.1 ENSP00000335017 Q53SZ7 UPI00001995FD NM_178553.3 3/3 HIGH 1 SNV 1 1 PASS rs751384314 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 27137093 27137093 A T 1 0 0 0 0 0 0 0 0 12737 433 15 4 4 PRR30 2 27137093 Nonstop_Mutation SNP A 11LU016_T 6717 27137093 215056436 63 115 C2orf71 0 . GRCh38 2 29071274 29071274 + Silent SNP G G T rs754342177 11LU016_T 11LU016_N G G c.2988C>A p.= p.P996P ENST00000331664 1/2 147 119 28 126 126 0 strelka-varscan-mutect C2orf71,synonymous_variant,p.=,ENST00000331664,NM_001029883.2; T ENST00000331664 Transcript synonymous_variant 2988/7044 2988/3867 996/1288 P ccC/ccA rs754342177 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 LOW 1 SNV 2 1 PASS rs754342177 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 29071274 29071274 G T 1 0 0 0 0 0 0 0 1 2045 1335 47 2 2 C2orf71 2 29071274 Silent SNP G 11LU016_T 1934181 29071274 213122255 64 116 STON1 0 . GRCh38 2 48581682 48581682 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1049A>T p.Glu350Val p.E350V ENST00000406226 3/5 122 112 10 105 105 0 strelka-varscan STON1,missense_variant,p.Glu350Val,ENST00000406226,NM_001198595.1;STON1,missense_variant,p.Glu350Val,ENST00000404752,NM_006873.3;STON1-GTF2A1L,missense_variant,p.Glu350Val,ENST00000394754,NM_172311.2;STON1-GTF2A1L,missense_variant,p.Glu350Val,ENST00000405008,;STON1-GTF2A1L,missense_variant,p.Glu350Val,ENST00000402114,NM_001198593.1;STON1-GTF2A1L,missense_variant,p.Glu350Val,ENST00000394751,NM_001198594.1;STON1,upstream_gene_variant,,ENST00000444932,; T ENST00000406226 Transcript missense_variant 1244/5614 1049/2208 350/735 E/V gAa/gTa 1 1 STON1 HGNC HGNC:17003 protein_coding YES CCDS1841.1 ENSP00000384615 Q9Y6Q2 UPI000006E627 NM_001198595.1 deleterious(0) 3/5 PROSITE_profiles:PS51070 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 48581682 48581682 A T 1 0 0 0 0 1 0 0 0 15695 246 9 4 4 STON1 2 48581682 Missense_Mutation SNP A 11LU016_T 19510408 48581682 193611847 65 117 GTF2A1L 0 . GRCh38 2 48647016 48647016 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.3064C>A p.Pro1022Thr p.P1022T ENST00000394754 8/11 69 55 14 55 55 0 strelka-varscan STON1-GTF2A1L,missense_variant,p.Pro1022Thr,ENST00000394754,NM_172311.2;STON1-GTF2A1L,missense_variant,p.Pro1022Thr,ENST00000405008,;STON1-GTF2A1L,missense_variant,p.Pro1022Thr,ENST00000402114,NM_001198593.1;STON1-GTF2A1L,missense_variant,p.Pro975Thr,ENST00000394751,NM_001198594.1;GTF2A1L,missense_variant,p.Pro318Thr,ENST00000403751,NM_006872.4;GTF2A1L,missense_variant,p.Pro284Thr,ENST00000430487,NM_001193487.2;GTF2A1L,missense_variant,p.Pro327Thr,ENST00000437125,;GTF2A1L,downstream_gene_variant,,ENST00000448460,;GTF2A1L,downstream_gene_variant,,ENST00000468326,;RP11-310N16.1,intron_variant,,ENST00000602369,;GTF2A1L,downstream_gene_variant,,ENST00000423675,; A ENST00000394754 Transcript missense_variant 3178/3824 3064/3549 1022/1182 P/T Ccc/Acc 1 1 STON1-GTF2A1L HGNC HGNC:30651 protein_coding YES CCDS1840.1 ENSP00000378236 Q53S48 UPI000013C976 NM_172311.2 tolerated(0.22) 8/11 hmmpanther:PTHR12694,hmmpanther:PTHR12694:SF9,Pfam_domain:PF03153,SMART_domains:SM01371 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.999999 1 1 1 0 A 3 1 2 48647016 48647016 C A 1 0 0 0 0 1 0 0 0 6735 507 18 2 2 GTF2A1L 2 48647016 Missense_Mutation SNP C 11LU016_T 65334 48647016 193546513 66 118 NRXN1 0 . GRCh38 2 49922162 49922162 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.4426G>T p.Gly1476Trp p.G1476W ENST00000404971 24/24 197 169 28 149 149 0 strelka-varscan NRXN1,missense_variant,p.Gly1406Trp,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Gly1425Trp,ENST00000625672,;NRXN1,missense_variant,p.Gly1476Trp,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Gly1436Trp,ENST00000401669,;NRXN1,missense_variant,p.Gly1424Trp,ENST00000405472,;NRXN1,missense_variant,p.Gly1428Trp,ENST00000630543,;NRXN1,missense_variant,p.Gly72Trp,ENST00000636345,;NRXN1,missense_variant,p.Gly371Trp,ENST00000342183,NM_138735.2;NRXN1,missense_variant,p.Gly401Trp,ENST00000401710,;NRXN1,missense_variant,p.Gly398Trp,ENST00000628364,;NRXN1,missense_variant,p.Gly68Trp,ENST00000412315,;NRXN1,missense_variant,p.Gly127Trp,ENST00000611589,;NRXN1,missense_variant,p.Gly71Trp,ENST00000378262,;NRXN1,missense_variant,p.Gly4Trp,ENST00000630656,;NRXN1,3_prime_UTR_variant,,ENST00000635519,;NRXN1,non_coding_transcript_exon_variant,,ENST00000634431,;NRXN1,non_coding_transcript_exon_variant,,ENST00000634764,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635164,;NRXN1,non_coding_transcript_exon_variant,,ENST00000634412,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,non_coding_transcript_exon_variant,,ENST00000484192,;NRXN1,non_coding_transcript_exon_variant,,ENST00000629717,;NRXN1,3_prime_UTR_variant,,ENST00000637906,; A ENST00000404971 Transcript missense_variant 5766/7578 4426/4644 1476/1547 G/W Ggg/Tgg 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 24/24 Pfam_domain:PF01034,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 49922162 49922162 C A 1 0 0 0 0 1 0 0 0 10724 594 21 2 2 NRXN1 2 49922162 Missense_Mutation SNP C 11LU016_T 1275146 49922162 192271367 67 119 GPR75 0 . GRCh38 2 53853511 53853511 + Missense_Mutation SNP C C T rs778576313 11LU016_T 11LU016_N C C c.1246G>A p.Glu416Lys p.E416K ENST00000394705 2/2 196 181 15 171 171 0 strelka-varscan GPR75,missense_variant,p.Glu416Lys,ENST00000394705,NM_006794.3;GPR75-ASB3,intron_variant,,ENST00000406625,NM_001164165.1;MIR3682,upstream_gene_variant,,ENST00000581338,;GPR75-ASB3,intron_variant,,ENST00000498475,;GPR75-ASB3,intron_variant,,ENST00000459916,; T ENST00000394705 Transcript missense_variant 1517/2115 1246/1623 416/540 E/K Gaa/Aaa rs778576313,COSM3426528 1 -1 GPR75 HGNC HGNC:4526 protein_coding YES CCDS1849.1 ENSP00000378195 O95800 UPI0000050454 NM_006794.3 deleterious(0.03) 2/2 hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF226 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 53853511 53853511 C T 1 0 0 0 0 1 0 0 0 6591 893 31 1 1 GPR75 2 53853511 Missense_Mutation SNP C 11LU016_T 3931349 53853511 188340018 68 120 EXOC6B 0 . GRCh38 2 72515119 72515119 + Missense_Mutation SNP C C T rs749620876 11LU016_T 11LU016_N C C c.923G>A p.Arg308Gln p.R308Q ENST00000272427 9/22 233 196 37 240 240 0 strelka-varscan EXOC6B,missense_variant,p.Arg308Gln,ENST00000272427,NM_001321729.1,NM_001321734.1,NM_015189.1;EXOC6B,missense_variant,p.Arg308Gln,ENST00000410104,;EXOC6B,missense_variant,p.Arg308Gln,ENST00000634650,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000485398,;EXOC6B,3_prime_UTR_variant,,ENST00000410112,; T ENST00000272427 Transcript missense_variant 1054/5918 923/2436 308/811 R/Q cGg/cAg rs749620876,COSM1022719 1 -1 EXOC6B HGNC HGNC:17085 protein_coding YES CCDS46333.1 ENSP00000272427 Q9Y2D4 UPI000046995C NM_001321729.1,NM_001321734.1,NM_015189.1 tolerated(0.11) 9/22 hmmpanther:PTHR12702:SF3,hmmpanther:PTHR12702,PIRSF_domain:PIRSF025007 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 72515119 72515119 C T 1 0 0 0 0 1 0 0 0 5177 652 23 1 1 EXOC6B 2 72515119 Missense_Mutation SNP C 11LU016_T 18661608 72515119 169678410 69 121 ALMS1 0 . GRCh38 2 73490887 73490887 + Silent SNP A A T rs373374154 11LU016_T 11LU016_N A A c.8928A>T p.= p.V2976V ENST00000613296 10/23 307 250 57 234 234 0 strelka-varscan ALMS1,synonymous_variant,p.=,ENST00000613296,NM_015120.4;ALMS1,synonymous_variant,p.=,ENST00000484298,;ALMS1,synonymous_variant,p.=,ENST00000614410,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,;ALMS1,intron_variant,,ENST00000423048,; T ENST00000613296 Transcript synonymous_variant 9039/12925 8928/12507 2976/4168 V gtA/gtT rs373374154 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 10/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 73490887 73490887 A T 1 0 0 0 0 0 0 0 1 635 407 15 4 4 ALMS1 2 73490887 Silent SNP A 11LU016_T 975768 73490887 168702642 70 122 ANAPC1 0 . GRCh38 2 111803769 111803769 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.3995G>T p.Gly1332Val p.G1332V ENST00000341068 31/48 238 201 37 220 220 0 strelka-varscan ANAPC1,missense_variant,p.Gly1332Val,ENST00000341068,NM_022662.3;ANAPC1,missense_variant,p.Gly867Val,ENST00000427997,;ANAPC1,non_coding_transcript_exon_variant,,ENST00000485325,; A ENST00000341068 Transcript missense_variant 4768/8262 3995/5835 1332/1944 G/V gGa/gTa 1 -1 ANAPC1 HGNC HGNC:19988 protein_coding YES CCDS2093.1 ENSP00000339109 Q9H1A4 UPI000006EC6E NM_022662.3 deleterious(0) 31/48 hmmpanther:PTHR12827 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 111803769 111803769 C A 1 0 0 0 0 1 0 0 0 695 855 30 2 2 ANAPC1 2 111803769 Missense_Mutation SNP C 11LU016_T 38312882 111803769 130389760 71 123 DDX18 0 . GRCh38 2 117830617 117830617 + Nonsense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1906G>T p.Gly636Ter p.G636* ENST00000263239 14/14 220 208 12 222 222 0 strelka-varscan DDX18,stop_gained,p.Gly636Ter,ENST00000263239,NM_006773.3;DDX18,downstream_gene_variant,,ENST00000415038,;AC009404.2,upstream_gene_variant,,ENST00000420330,;DDX18,non_coding_transcript_exon_variant,,ENST00000476149,;DDX18,downstream_gene_variant,,ENST00000461443,; T ENST00000263239 Transcript stop_gained 2034/3796 1906/2013 636/670 G/* Gga/Tga 1 1 DDX18 HGNC HGNC:2741 protein_coding YES CCDS2120.1 ENSP00000263239 Q9NVP1 A0A024RAH8 UPI000012907E NM_006773.3 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF301 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 117830617 117830617 G T 1 0 0 0 0 0 1 0 0 4148 1001 35 2 2 DDX18 2 117830617 Nonsense_Mutation SNP G 11LU016_T 6026848 117830617 124362912 72 124 CNTNAP5 0 . GRCh38 2 124763717 124763717 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.2277C>A p.= p.V759V ENST00000431078 15/24 195 184 11 174 173 1 strelka-varscan CNTNAP5,synonymous_variant,p.=,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript synonymous_variant 2641/5284 2277/3921 759/1306 V gtC/gtA 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 124763717 124763717 C A 1 0 0 0 0 0 0 0 1 3432 813 29 2 2 CNTNAP5 2 124763717 Silent SNP C 11LU016_T 6933100 124763717 117429812 73 125 POTEJ 0 . GRCh38 2 130657110 130657110 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2350C>A p.Gln784Lys p.Q784K ENST00000409602 15/15 188 160 28 224 224 0 strelka-varscan POTEJ,missense_variant,p.Gln784Lys,ENST00000409602,NM_001277083.1; A ENST00000409602 Transcript missense_variant 2402/3383 2350/3117 784/1038 Q/K Cag/Aag 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0.02) 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 130657110 130657110 C A 1 0 0 0 0 1 0 0 0 12383 595 21 2 2 POTEJ 2 130657110 Missense_Mutation SNP C 11LU016_T 5893393 130657110 111536419 74 126 R3HDM1 0 . GRCh38 2 135715689 135715689 + Missense_Mutation SNP G G T rs754207538 11LU016_T 11LU016_N G G c.2774G>T p.Gly925Val p.G925V ENST00000409606 23/26 81 75 6 85 85 0 strelka-varscan R3HDM1,missense_variant,p.Gly924Val,ENST00000264160,NM_015361.3;R3HDM1,missense_variant,p.Gly869Val,ENST00000410054,NM_001282800.1;R3HDM1,missense_variant,p.Gly796Val,ENST00000628915,;R3HDM1,missense_variant,p.Gly796Val,ENST00000409478,NM_001282799.1;R3HDM1,missense_variant,p.Gly925Val,ENST00000409606,NM_001282798.1;R3HDM1,missense_variant,p.Gly648Val,ENST00000429703,;R3HDM1,intron_variant,,ENST00000445855,; T ENST00000409606 Transcript missense_variant 3093/3673 2774/3303 925/1100 G/V gGg/gTg rs754207538 1 1 R3HDM1 HGNC HGNC:9757 protein_coding YES CCDS63025.1 ENSP00000387010 Q15032 UPI0001881805 NM_001282798.1 deleterious(0) 23/26 hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF12 MODERATE 1 SNV 2 1 PASS . . 0 199 10 0 0 0 0 0 -12.77073 0.9999246 1 1 1 0 T 3 4 2 135715689 135715689 G T 1 0 0 0 0 1 0 0 0 13044 1246 43 2 2 R3HDM1 2 135715689 Missense_Mutation SNP G 11LU016_T 5058579 135715689 106477840 75 127 LCT 0 . GRCh38 2 135804848 135804848 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.4383C>A p.= p.T1461T ENST00000264162 10/17 231 188 43 180 180 0 strelka-varscan LCT,synonymous_variant,p.=,ENST00000264162,NM_002299.2;LCT,synonymous_variant,p.=,ENST00000452974,; T ENST00000264162 Transcript synonymous_variant 4394/6279 4383/5784 1461/1927 T acC/acA 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 10/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 135804848 135804848 G T 1 0 0 0 0 0 0 0 1 8599 1335 47 2 2 LCT 2 135804848 Silent SNP G 11LU016_T 89159 135804848 106388681 76 128 LCT 0 . GRCh38 2 135808829 135808829 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.3518G>T p.Gly1173Val p.G1173V ENST00000264162 8/17 79 60 19 82 82 0 strelka-varscan LCT,missense_variant,p.Gly1173Val,ENST00000264162,NM_002299.2;Y_RNA,downstream_gene_variant,,ENST00000363794,;LCT,missense_variant,p.Gly605Val,ENST00000452974,; A ENST00000264162 Transcript missense_variant 3529/6279 3518/5784 1173/1927 G/V gGg/gTg 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 deleterious(0.02) 8/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 135808829 135808829 C A 1 0 0 0 0 1 0 0 0 8599 623 22 2 2 LCT 2 135808829 Missense_Mutation SNP C 11LU016_T 3981 135808829 106384700 77 129 LCT 0 . GRCh38 2 135817679 135817679 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1369T>A p.Trp457Arg p.W457R ENST00000264162 6/17 327 266 61 288 287 1 strelka-varscan LCT,missense_variant,p.Trp457Arg,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; T ENST00000264162 Transcript missense_variant 1380/6279 1369/5784 457/1927 W/R Tgg/Agg 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 deleterious(0) 6/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 135817679 135817679 A T 1 0 0 0 0 1 0 0 0 8599 188 7 4 4 LCT 2 135817679 Missense_Mutation SNP A 11LU016_T 8850 135817679 106375850 78 130 GTDC1 0 . GRCh38 2 143957328 143957328 + Nonsense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.997G>T p.Glu333Ter p.E333* ENST00000392869 8/11 77 62 15 61 60 1 strelka-varscan GTDC1,stop_gained,p.Glu333Ter,ENST00000392869,;GTDC1,stop_gained,p.Glu333Ter,ENST00000409214,NM_001006636.3;GTDC1,stop_gained,p.Glu333Ter,ENST00000542155,NM_001164629.3;GTDC1,stop_gained,p.Glu333Ter,ENST00000344850,;GTDC1,stop_gained,p.Glu301Ter,ENST00000618778,NM_001284238.1;GTDC1,stop_gained,p.Glu215Ter,ENST00000409298,;GTDC1,stop_gained,p.Glu204Ter,ENST00000463875,NM_001284234.1;GTDC1,intron_variant,,ENST00000392867,NM_024659.4;GTDC1,intron_variant,,ENST00000241391,NM_001284233.1;AC016910.1,intron_variant,,ENST00000422799,;GTDC1,3_prime_UTR_variant,,ENST00000415569,;GTDC1,intron_variant,,ENST00000392871,; A ENST00000392869 Transcript stop_gained 1150/10514 997/1377 333/458 E/* Gag/Tag COSM441193 1 -1 GTDC1 HGNC HGNC:20887 protein_coding YES CCDS33300.1 ENSP00000376608 Q4AE62 UPI000022BC3B 8/11 hmmpanther:PTHR13615,hmmpanther:PTHR13615:SF3,Pfam_domain:PF00534,Gene3D:3.40.50.2000,Superfamily_domains:SSF53756 1 HIGH SNV 5 1 1 PASS . . 0 187 21 0 0 0 0 0 -20 0.9972263 1 1 1 0 A 4 1 2 143957328 143957328 C A 1 0 0 0 0 0 1 0 0 6733 922 32 2 2 GTDC1 2 143957328 Nonsense_Mutation SNP C 11LU016_T 8139649 143957328 98236201 79 131 NEB 0 . GRCh38 2 151646138 151646138 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.7528A>C p.Thr2510Pro p.T2510P ENST00000618972 55/183 178 155 23 108 108 0 strelka-varscan NEB,missense_variant,p.Thr2510Pro,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Thr2510Pro,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Thr2510Pro,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Thr2510Pro,ENST00000603639,;NEB,missense_variant,p.Thr2510Pro,ENST00000604864,;NEB,missense_variant,p.Thr2510Pro,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Thr2510Pro,ENST00000172853,; G ENST00000618972 Transcript missense_variant 7731/26307 7528/25683 2510/8560 T/P Aca/Cca 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.21) 55/183 PROSITE_profiles:PS51216,Pfam_domain:PF00880,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 151646138 151646138 T G 1 0 0 0 0 1 0 0 0 10326 1696 59 5 5 NEB 2 151646138 Missense_Mutation SNP T 11LU016_T 7688810 151646138 90547391 80 132 KCNH7 0 . GRCh38 2 162400257 162400257 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.2339C>G p.Thr780Ser p.T780S ENST00000332142 10/16 317 255 62 290 290 0 strelka-varscan KCNH7,missense_variant,p.Thr780Ser,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Thr680Ser,ENST00000618399,; C ENST00000332142 Transcript missense_variant 2439/4113 2339/3591 780/1196 T/S aCt/aGt 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 tolerated(0.27) 10/16 PROSITE_profiles:PS50042,hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 162400257 162400257 G C 1 0 0 0 0 1 0 0 0 7953 1029 36 4 4 KCNH7 2 162400257 Missense_Mutation SNP G 11LU016_T 10754119 162400257 79793272 81 133 KCNH7 0 . GRCh38 2 162518043 162518043 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.579T>A p.Asp193Glu p.D193E ENST00000332142 4/16 334 314 20 264 264 0 strelka-varscan KCNH7,missense_variant,p.Asp193Glu,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Asp93Glu,ENST00000618399,;KCNH7,missense_variant,p.Asp193Glu,ENST00000328032,NM_173162.2;KCNH7,missense_variant,p.Asp91Glu,ENST00000621889,;KCNH7,non_coding_transcript_exon_variant,,ENST00000477019,; T ENST00000332142 Transcript missense_variant 679/4113 579/3591 193/1196 D/E gaT/gaA 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 tolerated(1) 4/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 162518043 162518043 A T 1 0 0 0 0 1 0 0 0 7953 98 4 4 4 KCNH7 2 162518043 Missense_Mutation SNP A 11LU016_T 117786 162518043 79675486 82 134 GRB14 0 . GRCh38 2 164522118 164522118 + Splice_Site SNP C C A novel 11LU016_T 11LU016_N C C c.679-1G>T p.X227_splice ENST00000263915 60 45 15 55 55 0 strelka-varscan GRB14,splice_acceptor_variant,,ENST00000263915,NM_004490.2;GRB14,splice_acceptor_variant,,ENST00000446413,;GRB14,downstream_gene_variant,,ENST00000424693,;GRB14,splice_acceptor_variant,,ENST00000488342,;GRB14,splice_acceptor_variant,,ENST00000469573,; A ENST00000263915 Transcript splice_acceptor_variant -/2382 679/1623 227/540 1 -1 GRB14 HGNC HGNC:4565 protein_coding YES CCDS2222.1 ENSP00000263915 Q14449 UPI000013D489 NM_004490.2 5/13 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 2 164522118 164522118 C A 1 0 0 0 0 0 0 1 0 6636 927 32 2 2 GRB14 2 164522118 Splice_Site SNP C 11LU016_T 2004075 164522118 77671411 83 135 XIRP2 0 . GRCh38 2 167245295 167245295 + Silent SNP T T A rs373942557 11LU016_T 11LU016_N T T c.3903T>A p.= p.T1301T ENST00000409195 9/11 138 128 10 130 130 0 strelka-varscan XIRP2,synonymous_variant,p.=,ENST00000409195,NM_152381.5;XIRP2,synonymous_variant,p.=,ENST00000409273,NM_001199144.1;XIRP2,synonymous_variant,p.=,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript synonymous_variant 3992/12675 3903/10650 1301/3549 T acT/acA rs373942557 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 167245295 167245295 T A 1 0 0 0 0 0 0 0 1 17989 1567 55 4 4 XIRP2 2 167245295 Silent SNP T 11LU016_T 2723177 167245295 74948234 84 136 TTN 0 . GRCh38 2 178558069 178558069 + Missense_Mutation SNP A A C 11LU016_T 11LU016_N A A c.87285T>G p.Ile29095Met p.I29095M ENST00000589042 328/363 279 220 59 248 248 0 strelka-varscan TTN,missense_variant,p.Ile29095Met,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ile27454Met,ENST00000591111,;TTN,missense_variant,p.Ile27454Met,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ile26527Met,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ile20030Met,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ile20222Met,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ile20155Met,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,non_coding_transcript_exon_variant,,ENST00000624360,; C ENST00000589042 Transcript missense_variant 87510/109224 87285/107976 29095/35991 I/M atT/atG COSM3798266,COSM3798267,COSM3798268,COSM3798269 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 328/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1 MODERATE SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 178558069 178558069 A C 1 0 0 0 0 1 0 0 0 17245 358 13 5 5 TTN 2 178558069 Missense_Mutation SNP A 11LU016_T 11312774 178558069 63635460 85 137 DNAJC10 0 . GRCh38 2 182741286 182741286 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1121G>A p.Gly374Glu p.G374E ENST00000264065 13/24 127 120 7 156 156 0 strelka-varscan DNAJC10,missense_variant,p.Gly374Glu,ENST00000264065,NM_018981.2;DNAJC10,missense_variant,p.Gly328Glu,ENST00000616986,NM_001271581.1;DNAJC10,intron_variant,,ENST00000613960,;DNAJC10,downstream_gene_variant,,ENST00000537515,;DNAJC10,3_prime_UTR_variant,,ENST00000418559,;DNAJC10,non_coding_transcript_exon_variant,,ENST00000491074,;DNAJC10,downstream_gene_variant,,ENST00000444005,; A ENST00000264065 Transcript missense_variant 1536/20129 1121/2382 374/793 G/E gGa/gAa 1 1 DNAJC10 HGNC HGNC:24637 protein_coding YES CCDS33345.1 ENSP00000264065 Q8IXB1 UPI000007376C NM_018981.2 deleterious(0.03) 13/24 hmmpanther:PTHR24078:SF235,hmmpanther:PTHR24078,Gene3D:3.40.30.10,PIRSF_domain:PIRSF037293,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 197 2 3 8 0 0 0 -2.820721 0.03906248 1 1 0 0 A 3 1 2 182741286 182741286 G A 1 0 0 0 0 1 0 0 0 4443 1174 41 3 3 DNAJC10 2 182741286 Missense_Mutation SNP G 11LU016_T 4183217 182741286 59452243 86 138 FAM171B 0 . GRCh38 2 186761718 186761718 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1376A>T p.Asp459Val p.D459V ENST00000304698 8/8 200 165 35 173 173 0 strelka-varscan FAM171B,missense_variant,p.Asp459Val,ENST00000304698,NM_177454.3; T ENST00000304698 Transcript missense_variant 1579/5826 1376/2481 459/826 D/V gAt/gTt 1 1 FAM171B HGNC HGNC:29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 UPI0000161631 NM_177454.3 deleterious(0.01) 8/8 hmmpanther:PTHR31626:SF2,hmmpanther:PTHR31626,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 186761718 186761718 A T 1 0 0 0 0 1 0 0 0 5339 333 12 4 4 FAM171B 2 186761718 Missense_Mutation SNP A 11LU016_T 4020432 186761718 55431811 87 139 CALCRL 0 . GRCh38 2 187359256 187359256 + Silent SNP A A T novel 11LU016_T 11LU016_N A A c.798T>A p.= p.P266P ENST00000409998 12/16 128 116 12 103 103 0 strelka-varscan CALCRL,synonymous_variant,p.=,ENST00000409998,;CALCRL,synonymous_variant,p.=,ENST00000392370,NM_005795.5;CALCRL,synonymous_variant,p.=,ENST00000410068,NM_001271751.1;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; T ENST00000409998 Transcript synonymous_variant 1580/5223 798/1386 266/461 P ccT/ccA 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF 12/16 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF67,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR01350,Prints_domain:PR00249 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 187359256 187359256 A T 1 0 0 0 0 0 0 0 1 2270 175 7 4 4 CALCRL 2 187359256 Silent SNP A 11LU016_T 597538 187359256 54834273 88 140 ERBB4 0 . GRCh38 2 211424271 211424271 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2750G>T p.Gly917Val p.G917V ENST00000342788 23/28 324 271 53 277 276 1 strelka-varscan ERBB4,missense_variant,p.Gly917Val,ENST00000342788,NM_005235.2;ERBB4,missense_variant,p.Gly917Val,ENST00000436443,NM_001042599.1;ERBB4,missense_variant,p.Gly891Val,ENST00000402597,; A ENST00000342788 Transcript missense_variant 3061/12136 2750/3927 917/1308 G/V gGa/gTa 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 deleterious(0) 23/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF90,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000619,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 211424271 211424271 C A 1 0 0 0 0 1 0 0 0 5057 855 30 2 2 ERBB4 2 211424271 Missense_Mutation SNP C 11LU016_T 24065015 211424271 30769258 89 141 ABCA12 0 . GRCh38 2 215019724 215019724 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1360C>A p.Gln454Lys p.Q454K ENST00000272895 12/53 485 409 76 377 376 1 strelka-varscan ABCA12,missense_variant,p.Gln454Lys,ENST00000272895,NM_173076.2;ABCA12,missense_variant,p.Gln136Lys,ENST00000389661,NM_015657.3;AC072062.3,intron_variant,,ENST00000617699,;AC072062.3,intron_variant,,ENST00000627811,;AC072062.3,upstream_gene_variant,,ENST00000437897,;AC072062.3,upstream_gene_variant,,ENST00000595058,;AC072062.3,upstream_gene_variant,,ENST00000419251,;AC072062.3,upstream_gene_variant,,ENST00000627336,;AC072062.3,upstream_gene_variant,,ENST00000615813,;AC072062.3,upstream_gene_variant,,ENST00000602182,; T ENST00000272895 Transcript missense_variant 1580/9100 1360/7788 454/2595 Q/K Cag/Aag 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 tolerated(0.18) 12/53 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 215019724 215019724 G T 1 0 0 0 0 1 0 0 0 34 1357 47 2 2 ABCA12 2 215019724 Missense_Mutation SNP G 11LU016_T 3595453 215019724 27173805 90 142 SP140 0 . GRCh38 2 230285769 230285769 + Missense_Mutation SNP G G T rs776385432 11LU016_T 11LU016_N G G c.1582G>T p.Gly528Cys p.G528C ENST00000392045 17/27 179 169 10 178 177 1 strelka-varscan SP140,missense_variant,p.Gly528Cys,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Gly501Cys,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Gly468Cys,ENST00000343805,NM_001278452.1;SP140,missense_variant,p.Gly414Cys,ENST00000417495,NM_001278453.1;SP140,non_coding_transcript_exon_variant,,ENST00000476126,; T ENST00000392045 Transcript missense_variant 1696/3246 1582/2604 528/867 G/C Ggc/Tgc rs776385432 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 deleterious(0) 17/27 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -12.90316 0.9999994 1 1 1 0 T 3 4 2 230285769 230285769 G T 1 0 0 0 0 1 0 0 0 15288 1116 39 1 1 SP140 2 230285769 Missense_Mutation SNP G 11LU016_T 15266045 230285769 11907760 91 143 NMUR1 0 . GRCh38 2 231525373 231525373 + Silent SNP G G C rs367827633 11LU016_T 11LU016_N G G c.951C>G p.= p.R317R ENST00000305141 3/3 122 101 21 135 135 0 strelka-varscan NMUR1,synonymous_variant,p.=,ENST00000305141,NM_006056.4; C ENST00000305141 Transcript synonymous_variant 1085/3298 951/1281 317/426 R cgC/cgG rs367827633 1 -1 NMUR1 HGNC HGNC:4518 protein_coding YES CCDS2486.1 ENSP00000305877 Q9HB89 UPI0000071CAE NM_006056.4 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF109,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01565,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 231525373 231525373 G C 1 0 0 0 0 0 0 0 1 10547 1074 38 4 4 NMUR1 2 231525373 Silent SNP G 11LU016_T 1239604 231525373 10668156 92 144 KIF1A 0 . GRCh38 2 240761268 240761268 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.2226C>A p.= p.L742L ENST00000498729 24/49 118 98 20 92 92 0 strelka-varscan KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,synonymous_variant,p.=,ENST00000404283,; T ENST00000498729 Transcript synonymous_variant 2473/9223 2226/5376 742/1791 L ctC/ctA 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 24/49 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 240761268 240761268 G T 1 0 0 0 0 0 0 0 1 8147 1277 45 2 2 KIF1A 2 240761268 Silent SNP G 11LU016_T 9235895 240761268 1432261 93 145 ANO7 0 . GRCh38 2 241199373 241199373 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.529G>T p.Ala177Ser p.A177S ENST00000274979 5/25 347 287 60 306 306 0 strelka-varscan ANO7,missense_variant,p.Ala177Ser,ENST00000274979,NM_001001891.3;ANO7,missense_variant,p.Ala176Ser,ENST00000402430,;ANO7,downstream_gene_variant,,ENST00000402530,NM_001001666.3;ANO7,non_coding_transcript_exon_variant,,ENST00000475532,; T ENST00000274979 Transcript missense_variant 632/4128 529/2802 177/933 A/S Gct/Tct 1 1 ANO7 HGNC HGNC:31677 protein_coding YES CCDS33423.1 ENSP00000274979 Q6IWH7 UPI0000D612DB NM_001001891.3 tolerated(0.73) 5/25 hmmpanther:PTHR12308:SF22,hmmpanther:PTHR12308,Pfam_domain:PF16178 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 241199373 241199373 G T 1 0 0 0 0 1 0 0 0 809 1203 42 2 2 ANO7 2 241199373 Missense_Mutation SNP G 11LU016_T 438105 241199373 994156 94 146 VHL 0 . GRCh38 3 10142151 10142151 + Missense_Mutation SNP C C T rs532018719 11LU016_T 11LU016_N C C c.304C>T p.Pro102Ser p.P102S ENST00000256474 1/3 331 310 21 394 394 0 strelka-varscan-mutect VHL,missense_variant,p.Pro102Ser,ENST00000256474,NM_000551.3;VHL,missense_variant,p.Pro102Ser,ENST00000345392,NM_198156.2;VHL,upstream_gene_variant,,ENST00000477538,; T ENST00000256474 Transcript missense_variant 1144/3737 304/642 102/213 P/S Ccg/Tcg rs532018719,COSM17734 1 1 VHL HGNC HGNC:12687 protein_coding YES CCDS2597.1 ENSP00000256474 P40337 A0A024R2F2 UPI0000035C95 NM_000551.3 tolerated(0.77) 1/3 Superfamily_domains:0040561,Gene3D:1lm8V02,PD035809,Pfam_domain:PF01847,hmmpanther:PTHR15160,hmmpanther:PTHR15160:SF5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs532018719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 10142151 10142151 C T 1 0 0 0 0 1 0 0 0 17708 739 26 3 3 VHL 3 10142151 Missense_Mutation SNP C 11LU016_T 10142151 188153408 95 147 SYN2 0 . GRCh38 3 12187401 12187401 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1402C>A p.Pro468Thr p.P468T ENST00000621198 12/13 94 75 19 85 85 0 strelka-varscan-mutect SYN2,missense_variant,p.Pro468Thr,ENST00000621198,NM_133625.4;SYN2,downstream_gene_variant,,ENST00000620175,NM_003178.5;SYN2,non_coding_transcript_exon_variant,,ENST00000439861,;SYN2,downstream_gene_variant,,ENST00000425297,; A ENST00000621198 Transcript missense_variant 1552/2674 1402/1749 468/582 P/T Cca/Aca 1 1 SYN2 HGNC HGNC:11495 protein_coding YES CCDS74900.1 ENSP00000480050 A0A087WW96 UPI0000167B8A NM_133625.4 tolerated(0.08) 12/13 Low_complexity_(Seg):seg,hmmpanther:PTHR10841:SF20,hmmpanther:PTHR10841 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 12187401 12187401 C A 1 0 0 0 0 1 0 0 0 15831 623 22 2 2 SYN2 3 12187401 Missense_Mutation SNP C 11LU016_T 2045250 12187401 186108158 96 148 NEK10 0 . GRCh38 3 27111303 27111303 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.3488G>T p.Trp1163Leu p.W1163L ENST00000429845 39/39 120 99 21 125 124 1 strelka-varscan-mutect NEK10,missense_variant,p.Trp1163Leu,ENST00000429845,NM_152534.4;NEK10,missense_variant,p.Trp475Leu,ENST00000295720,NM_001304384.1;NEK10,missense_variant,p.Trp465Leu,ENST00000383771,NM_001031741.3;NEK10,missense_variant,p.Trp409Leu,ENST00000383770,; A ENST00000429845 Transcript missense_variant 3851/4250 3488/3519 1163/1172 W/L tGg/tTg 1 -1 NEK10 HGNC HGNC:18592 protein_coding ENSP00000395849 Q6ZWH5 UPI0000EE2A86 NM_152534.4 tolerated_low_confidence(0.23) 39/39 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 27111303 27111303 C A 1 0 0 0 0 1 0 0 0 10350 595 21 2 2 NEK10 3 27111303 Missense_Mutation SNP C 11LU016_T 14923902 27111303 171184256 97 149 GOLGA4 0 . GRCh38 3 37315491 37315491 + Nonsense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.1372G>T p.Glu458Ter p.E458* ENST00000356847 12/23 230 186 44 200 200 0 strelka-varscan-mutect GOLGA4,stop_gained,p.Glu436Ter,ENST00000361924,NM_002078.4;GOLGA4,stop_gained,p.Glu458Ter,ENST00000356847,NM_001172713.1;GOLGA4,stop_gained,p.Glu307Ter,ENST00000437131,;GOLGA4,stop_gained,p.Glu441Ter,ENST00000450863,;GOLGA4,intron_variant,,ENST00000429018,;GOLGA4,intron_variant,,ENST00000444882,;GOLGA4,non_coding_transcript_exon_variant,,ENST00000435830,; T ENST00000356847 Transcript stop_gained 1671/7673 1372/6732 458/2243 E/* Gaa/Taa COSM446410 1 1 GOLGA4 HGNC HGNC:4427 protein_coding YES CCDS54564.1 ENSP00000349305 Q13439 UPI000198C9CA NM_001172713.1 12/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19327 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 37315491 37315491 G T 1 0 0 0 0 0 1 0 0 6433 943 33 2 2 GOLGA4 3 37315491 Nonsense_Mutation SNP G 11LU016_T 10204188 37315491 160980068 98 150 SCN11A 0 . GRCh38 3 38950211 38950211 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.152G>T p.Arg51Leu p.R51L ENST00000302328 1/26 345 319 26 344 344 0 strelka-varscan-mutect SCN11A,missense_variant,p.Arg51Leu,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,missense_variant,p.Arg51Leu,ENST00000444237,;SCN11A,missense_variant,p.Arg51Leu,ENST00000456224,; A ENST00000302328 Transcript missense_variant 351/6500 152/5376 51/1791 R/L cGg/cTg 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 deleterious(0) 1/26 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210 MODERATE 1 SNV 5 1 PASS rs1191368962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 38950211 38950211 C A 1 0 0 0 0 1 0 0 0 14182 652 23 1 1 SCN11A 3 38950211 Missense_Mutation SNP C 11LU016_T 1634720 38950211 159345348 99 151 MYRIP 0 . GRCh38 3 40182277 40182277 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.931G>C p.Glu311Gln p.E311Q ENST00000302541 9/17 116 109 7 135 135 0 strelka-varscan-mutect MYRIP,missense_variant,p.Glu311Gln,ENST00000302541,NM_015460.3;MYRIP,missense_variant,p.Glu222Gln,ENST00000396217,NM_001284425.1;MYRIP,missense_variant,p.Glu124Gln,ENST00000539167,NM_001284426.1;MYRIP,missense_variant,p.Glu311Gln,ENST00000425621,NM_001284424.1;MYRIP,missense_variant,p.Glu311Gln,ENST00000444716,NM_001284423.1;EIF1B-AS1,intron_variant,,ENST00000625390,;MYRIP,non_coding_transcript_exon_variant,,ENST00000459828,;MYRIP,missense_variant,p.Glu311Gln,ENST00000458292,;MYRIP,3_prime_UTR_variant,,ENST00000458441,; C ENST00000302541 Transcript missense_variant 1273/5077 931/2580 311/859 E/Q Gag/Cag 1 1 MYRIP HGNC HGNC:19156 protein_coding YES CCDS2689.1 ENSP00000301972 Q8NFW9 UPI0000074787 NM_015460.3 tolerated(0.05) 9/17 Pfam_domain:PF04698,hmmpanther:PTHR14555,hmmpanther:PTHR14555:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 40182277 40182277 G C 1 0 0 0 0 1 0 0 0 10103 1175 41 4 4 MYRIP 3 40182277 Missense_Mutation SNP G 11LU016_T 1232066 40182277 158113282 100 152 ELP6 0 . GRCh38 3 47501847 47501847 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.328G>C p.Ala110Pro p.A110P ENST00000296149 5/7 135 127 8 172 172 0 strelka-varscan-mutect ELP6,missense_variant,p.Ala110Pro,ENST00000296149,NM_001031703.2;ELP6,missense_variant,p.Ala37Pro,ENST00000444760,;ELP6,missense_variant,p.Ala37Pro,ENST00000446787,;ELP6,missense_variant,p.Ala37Pro,ENST00000439305,;ELP6,missense_variant,p.Ala37Pro,ENST00000412761,;ELP6,missense_variant,p.Ala37Pro,ENST00000425291,;ELP6,missense_variant,p.Ala37Pro,ENST00000449409,;ELP6,missense_variant,p.Ala37Pro,ENST00000414236,;BOLA2P2,downstream_gene_variant,,ENST00000604904,;ELP6,3_prime_UTR_variant,,ENST00000442215,;ELP6,3_prime_UTR_variant,,ENST00000445044,;ELP6,non_coding_transcript_exon_variant,,ENST00000461208,;ELP6,non_coding_transcript_exon_variant,,ENST00000494161,;ELP6,downstream_gene_variant,,ENST00000485029,;BOLA2P2,downstream_gene_variant,,ENST00000603861,; G ENST00000296149 Transcript missense_variant 499/1401 328/801 110/266 A/P Gct/Cct 1 -1 ELP6 HGNC HGNC:25976 protein_coding YES CCDS43082.1 ENSP00000296149 Q0PNE2 UPI000020A684 NM_001031703.2 tolerated(0.43) 5/7 Pfam_domain:PF09807,hmmpanther:PTHR16184 MODERATE 1 SNV 1 1 PASS rs1248103269 . 0 208 2 0 0 0 0 0 -15.54615 1 1 1 1 0 G 3 3 2 47501847 47501847 C G 1 0 0 0 0 1 0 0 0 4918 753 26 4 4 ELP6 3 47501847 Missense_Mutation SNP C 11LU016_T 7319570 47501847 150793712 101 153 WNT5A 0 . GRCh38 3 55470272 55470272 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.963G>C p.Gln321His p.Q321H ENST00000264634 5/5 218 174 44 215 214 1 strelka-varscan WNT5A,missense_variant,p.Gln321His,ENST00000264634,NM_003392.4;WNT5A,missense_variant,p.Gln321His,ENST00000474267,;WNT5A,missense_variant,p.Gln306His,ENST00000497027,NM_001256105.1;WNT5A,intron_variant,,ENST00000614415,;WNT5A,downstream_gene_variant,,ENST00000482079,;WNT5A,upstream_gene_variant,,ENST00000493406,; G ENST00000264634 Transcript missense_variant 1620/6176 963/1143 321/380 Q/H caG/caC 1 -1 WNT5A HGNC HGNC:12784 protein_coding YES CCDS46850.1 ENSP00000264634 P41221 UPI0000231C66 NM_003392.4 tolerated(0.13) 5/5 hmmpanther:PTHR12027:SF33,hmmpanther:PTHR12027,Pfam_domain:PF00110,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 55470272 55470272 C G 1 0 0 0 0 1 0 0 0 17947 680 24 4 4 WNT5A 3 55470272 Missense_Mutation SNP C 11LU016_T 7968425 55470272 142825287 102 154 ARHGEF3 0 . GRCh38 3 56729523 56729530 + Frame_Shift_Del DEL CAGTTAAG CAGTTAAG - novel 11LU016_T 11LU016_N CAGTTAAG CAGTTAAG c.1417_1424delCTTAACTG p.Leu473TyrfsTer19 p.L473Yfs*19 ENST00000338458 13/13 171 157 14 224 224 0 sindel-pindel ARHGEF3,frameshift_variant,p.Leu447TyrfsTer19,ENST00000413728,NM_001128616.1;ARHGEF3,frameshift_variant,p.Leu473TyrfsTer19,ENST00000338458,NM_001128615.1;ARHGEF3,frameshift_variant,p.Leu441TyrfsTer19,ENST00000296315,NM_019555.2;ARHGEF3,frameshift_variant,p.Leu412TyrfsTer19,ENST00000497267,;ARHGEF3,frameshift_variant,p.Leu447TyrfsTer19,ENST00000496106,NM_001289698.1;ARHGEF3,downstream_gene_variant,,ENST00000495373,;ARHGEF3,3_prime_UTR_variant,,ENST00000465659,; - ENST00000338458 Transcript frameshift_variant 1527-1534/3639 1417-1424/1677 473-475/558 LNC/X CTTAACTGt/t 1 -1 ARHGEF3 HGNC HGNC:683 protein_coding YES CCDS46854.1 ENSP00000341071 Q9NR81 UPI00001B3D98 NM_001128615.1 13/13 PROSITE_profiles:PS50003,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF139,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 56729523 56729523 CAGTTAAG - 1 0 1 0 1 0 0 0 0 1037 478 17 0 0 ARHGEF3 3 56729523 Frame_Shift_Del DEL CAGTTAAG 11LU016_T 1259251 56729523 141566036 103 155 GPR27 0 . GRCh38 3 71754977 71754977 + Missense_Mutation SNP G G T rs755213093 11LU016_T 11LU016_N G G c.928G>T p.Val310Leu p.V310L ENST00000304411 1/1 353 307 46 440 439 1 strelka-varscan GPR27,missense_variant,p.Val310Leu,ENST00000304411,NM_018971.1;EIF4E3,upstream_gene_variant,,ENST00000448225,NM_001134649.2;EIF4E3,upstream_gene_variant,,ENST00000295612,NM_001282886.1;EIF4E3,upstream_gene_variant,,ENST00000421769,NM_173359.4;EIF4E3,upstream_gene_variant,,ENST00000496214,; T ENST00000304411 Transcript missense_variant 928/2447 928/1128 310/375 V/L Gtg/Ttg rs755213093 1 1 GPR27 HGNC HGNC:4482 protein_coding YES CCDS2915.1 ENSP00000303149 Q9NS67 F1DAM3 UPI0000049802 NM_018971.1 tolerated(0.42) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF8,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 71754977 71754977 G T 1 0 0 0 0 1 0 0 0 6569 1261 44 2 2 GPR27 3 71754977 Missense_Mutation SNP G 11LU016_T 15025454 71754977 126540582 104 156 TBC1D23 0 . GRCh38 3 100320883 100320883 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.1930A>G p.Ile644Val p.I644V ENST00000394144 18/19 122 98 24 122 122 0 strelka-varscan-mutect TBC1D23,missense_variant,p.Ile644Val,ENST00000394144,NM_001199198.2;TBC1D23,missense_variant,p.Ile629Val,ENST00000344949,NM_018309.4;TBC1D23,missense_variant,p.Ile507Val,ENST00000475134,;TBC1D23,non_coding_transcript_exon_variant,,ENST00000486274,;TBC1D23,non_coding_transcript_exon_variant,,ENST00000471273,; G ENST00000394144 Transcript missense_variant 1937/3677 1930/2100 644/699 I/V Att/Gtt 1 1 TBC1D23 HGNC HGNC:25622 protein_coding YES CCDS56265.1 ENSP00000377700 Q9NUY8 UPI000013D5E5 NM_001199198.2 deleterious(0) 18/19 hmmpanther:PTHR13297 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 100320883 100320883 A G 1 0 0 0 0 1 0 0 0 16013 101 4 5 5 TBC1D23 3 100320883 Missense_Mutation SNP A 11LU016_T 28565906 100320883 97974676 105 157 BBX 0 . GRCh38 3 107774783 107774783 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1980G>T p.Trp660Cys p.W660C ENST00000325805 12/18 197 177 20 137 137 0 strelka-varscan-mutect BBX,missense_variant,p.Trp660Cys,ENST00000415149,NM_020235.6;BBX,missense_variant,p.Trp660Cys,ENST00000402543,;BBX,missense_variant,p.Trp660Cys,ENST00000406780,;BBX,missense_variant,p.Trp660Cys,ENST00000325805,NM_001142568.2;BBX,missense_variant,p.Gly324Val,ENST00000416476,NM_001276286.1;BBX,downstream_gene_variant,,ENST00000402163,;BBX,upstream_gene_variant,,ENST00000443253,;BBX,upstream_gene_variant,,ENST00000473542,;BBX,downstream_gene_variant,,ENST00000485939,;BBX,downstream_gene_variant,,ENST00000472032,; T ENST00000325805 Transcript missense_variant 2267/3517 1980/2826 660/941 W/C tgG/tgT 1 1 BBX HGNC HGNC:14422 protein_coding YES CCDS46881.1 ENSP00000319974 Q8WY36 UPI000007315E NM_001142568.2 deleterious(0.04) 12/18 hmmpanther:PTHR13059 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 107774783 107774783 G T 1 0 0 0 0 1 0 0 0 1490 1183 41 2 2 BBX 3 107774783 Missense_Mutation SNP G 11LU016_T 7453900 107774783 90520776 106 158 CD200R1L 0 . GRCh38 3 112827210 112827210 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.462G>T p.Arg154Ser p.R154S ENST00000398214 4/6 113 90 23 107 107 0 strelka-varscan-mutect CD200R1L,missense_variant,p.Arg133Ser,ENST00000488794,NM_001199215.1;CD200R1L,missense_variant,p.Arg154Ser,ENST00000398214,NM_001008784.2;CD200R1L,missense_variant,p.Arg139Ser,ENST00000617549,;CD200R1L,missense_variant,p.Arg133Ser,ENST00000448932,;CD200R1L,3_prime_UTR_variant,,ENST00000486723,; A ENST00000398214 Transcript missense_variant 688/1296 462/816 154/271 R/S agG/agT 1 -1 CD200R1L HGNC HGNC:24665 protein_coding YES CCDS43131.1 ENSP00000381272 Q6Q8B3 UPI000042263C NM_001008784.2 tolerated(0.4) 4/6 Gene3D:2.60.40.10,Pfam_domain:PF08205,PROSITE_profiles:PS50835,hmmpanther:PTHR21462,hmmpanther:PTHR21462:SF3,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 112827210 112827210 C A 1 0 0 0 0 1 0 0 0 2685 854 30 2 2 CD200R1L 3 112827210 Missense_Mutation SNP C 11LU016_T 5052427 112827210 85468349 107 159 GOLGB1 0 . GRCh38 3 121697669 121697669 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2854G>T p.Glu952Ter p.E952* ENST00000393667 13/22 112 89 23 95 95 0 strelka-varscan-mutect GOLGB1,stop_gained,p.Glu952Ter,ENST00000393667,NM_001256486.1;GOLGB1,stop_gained,p.Glu947Ter,ENST00000340645,NM_004487.4;GOLGB1,stop_gained,p.Glu872Ter,ENST00000614479,NM_001256488.1,NM_001256487.1;GOLGB1,stop_gained,p.Glu911Ter,ENST00000494517,;GOLGB1,stop_gained,p.Glu818Ter,ENST00000489400,;GOLGB1,3_prime_UTR_variant,,ENST00000482512,; A ENST00000393667 Transcript stop_gained 2965/11198 2854/9810 952/3269 E/* Gag/Tag 1 -1 GOLGB1 HGNC HGNC:4429 protein_coding YES CCDS58847.1 ENSP00000377275 Q14789 UPI0001AE7645 NM_001256486.1 13/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18887,hmmpanther:PTHR18887:SF2 HIGH 1 SNV 1 1 PASS rs774978171 . 0 204 2 4 0 0 0 0 -20 0.9998511 1 1 1 0 A 4 1 2 121697669 121697669 C A 1 0 0 0 0 0 1 0 0 6459 922 32 2 2 GOLGB1 3 121697669 Nonsense_Mutation SNP C 11LU016_T 8870459 121697669 76597890 108 160 CD86 0 . GRCh38 3 122103811 122103811 + Missense_Mutation SNP C C A rs770052627 11LU016_T 11LU016_N C C c.364C>A p.Arg122Ser p.R122S ENST00000330540 3/7 118 99 19 125 125 0 strelka-varscan-mutect CD86,missense_variant,p.Arg122Ser,ENST00000330540,NM_175862.4;CD86,missense_variant,p.Arg116Ser,ENST00000264468,NM_176892.1;CD86,missense_variant,p.Arg40Ser,ENST00000469710,NM_001206925.1;CD86,missense_variant,p.Arg116Ser,ENST00000393627,NM_006889.4;CD86,missense_variant,p.Arg118Ser,ENST00000478741,;CD86,missense_variant,p.Arg116Ser,ENST00000482356,;CD86,intron_variant,,ENST00000493101,NM_001206924.1;CD86,downstream_gene_variant,,ENST00000483949,; A ENST00000330540 Transcript missense_variant 480/2708 364/990 122/329 R/S Cgc/Agc rs770052627 1 1 CD86 HGNC HGNC:1705 protein_coding YES CCDS3009.1 ENSP00000332049 P42081 UPI00001AFC7C NM_175862.4 tolerated(0.46) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR25466,hmmpanther:PTHR25466:SF2,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs770052627 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 122103811 122103811 C A 1 0 0 0 0 1 0 0 0 2747 884 31 1 1 CD86 3 122103811 Missense_Mutation SNP C 11LU016_T 406142 122103811 76191748 109 161 HEG1 0 . GRCh38 3 125019592 125019592 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1258G>T p.Gly420Ter p.G420* ENST00000311127 5/17 119 97 22 107 107 0 strelka-varscan-mutect HEG1,stop_gained,p.Gly420Ter,ENST00000311127,NM_020733.1;HEG1,upstream_gene_variant,,ENST00000477536,; A ENST00000311127 Transcript stop_gained 1326/9156 1258/4146 420/1381 G/* Gga/Tga 1 -1 HEG1 HGNC HGNC:29227 protein_coding YES CCDS46898.1 ENSP00000311502 Q9ULI3 UPI00006C069B NM_020733.1 5/17 hmmpanther:PTHR24037:SF3,hmmpanther:PTHR24037 HIGH 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999888 1 1 1 0 A 4 1 2 125019592 125019592 C A 1 0 0 0 0 0 1 0 0 6926 608 21 2 2 HEG1 3 125019592 Nonsense_Mutation SNP C 11LU016_T 2915781 125019592 73275967 110 162 NMNAT3 0 . GRCh38 3 139599355 139599355 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.223T>A p.Cys75Ser p.C75S ENST00000514703 4/4 206 167 39 217 217 0 strelka-varscan-mutect NMNAT3,missense_variant,p.Cys75Ser,ENST00000514703,;NMNAT3,intron_variant,,ENST00000339837,NM_178177.3;NMNAT3,intron_variant,,ENST00000413939,NM_001200047.1;NMNAT3,intron_variant,,ENST00000296202,;NMNAT3,intron_variant,,ENST00000511444,;NMNAT3,intron_variant,,ENST00000512391,;NMNAT3,intron_variant,,ENST00000509291,;NMNAT3,intron_variant,,ENST00000506254,NM_001320513.1; T ENST00000514703 Transcript missense_variant 377/584 223/297 75/98 C/S Tgc/Agc 1 -1 NMNAT3 HGNC HGNC:20989 protein_coding ENSP00000426375 D6RGG8 UPI0000EE21AE tolerated(0.77) 4/4 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 139599355 139599355 A T 1 0 0 0 0 1 0 0 0 10539 159 6 4 4 NMNAT3 3 139599355 Missense_Mutation SNP A 11LU016_T 14579763 139599355 58696204 111 163 PLOD2 0 . GRCh38 3 146121180 146121180 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.270G>T p.= p.V90V ENST00000282903 3/20 343 275 68 260 260 0 strelka-varscan-mutect PLOD2,synonymous_variant,p.=,ENST00000282903,NM_182943.2;PLOD2,synonymous_variant,p.=,ENST00000360060,NM_000935.2;PLOD2,synonymous_variant,p.=,ENST00000494950,;PLOD2,synonymous_variant,p.=,ENST00000469350,;PLOD2,3_prime_UTR_variant,,ENST00000480704,; A ENST00000282903 Transcript synonymous_variant 448/3732 270/2277 90/758 V gtG/gtT 1 -1 PLOD2 HGNC HGNC:9082 protein_coding YES CCDS3132.1 ENSP00000282903 O00469 UPI0000049C44 NM_182943.2 3/20 hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 146121180 146121180 C A 1 0 0 0 0 0 0 0 1 12198 813 29 2 2 PLOD2 3 146121180 Silent SNP C 11LU016_T 6521825 146121180 52174379 112 164 GPR149 0 . GRCh38 3 154428881 154428881 + Silent SNP C C A rs754858826 11LU016_T 11LU016_N C C c.735G>T p.= p.A245A ENST00000389740 1/4 212 166 46 220 219 1 strelka-varscan-mutect GPR149,synonymous_variant,p.=,ENST00000389740,NM_001038705.1; A ENST00000389740 Transcript synonymous_variant 835/2323 735/2196 245/731 A gcG/gcT rs754858826 1 -1 GPR149 HGNC HGNC:23627 protein_coding YES CCDS43162.1 ENSP00000374390 Q86SP6 Q2MKA6 UPI00001AEEA9 NM_001038705.1 1/4 PROSITE_profiles:PS50262 LOW 1 SNV 1 1 PASS rs754858826 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 154428881 154428881 C A 1 0 0 0 0 0 0 0 1 6540 639 23 1 1 GPR149 3 154428881 Silent SNP C 11LU016_T 8307701 154428881 43866678 113 165 ZBBX 0 . GRCh38 3 167372871 167372871 + Missense_Mutation SNP A A G rs375762855 11LU016_T 11LU016_N A A c.31T>C p.Trp11Arg p.W11R ENST00000455345 3/21 74 65 9 99 99 0 strelka-varscan-mutect ZBBX,missense_variant,p.Trp11Arg,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Trp11Arg,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Trp11Arg,ENST00000307529,;ZBBX,missense_variant,p.Trp11Arg,ENST00000474464,;ZBBX,5_prime_UTR_variant,,ENST00000392767,;ZBBX,5_prime_UTR_variant,,ENST00000392764,NM_001199202.1;ZBBX,5_prime_UTR_variant,,ENST00000485651,;ZBBX,intron_variant,,ENST00000469220,;ZBBX,non_coding_transcript_exon_variant,,ENST00000473888,; G ENST00000455345 Transcript missense_variant 315/3185 31/2520 11/839 W/R Tgg/Cgg rs375762855,COSM3203221,COSM3203222 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 tolerated(0.08) 3/21 hmmpanther:PTHR28634 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs375762855 . 0 206 0 0 0 0 0 4 -3.020069 0 0 1 0 0 G 3 3 2 167372871 167372871 A G 1 0 0 0 0 1 0 0 0 18078 217 8 5 5 ZBBX 3 167372871 Missense_Mutation SNP A 11LU016_T 12943990 167372871 30922688 114 166 NLGN1 0 . GRCh38 3 174279235 174279235 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.1234G>C p.Asp412His p.D412H ENST00000457714 6/7 125 103 22 92 92 0 strelka-varscan-mutect NLGN1,missense_variant,p.Asp412His,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Asp412His,ENST00000361589,;NLGN1,missense_variant,p.Asp197His,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,non_coding_transcript_exon_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,;NLGN1,downstream_gene_variant,,ENST00000490929,; C ENST00000457714 Transcript missense_variant 1663/8242 1234/2472 412/823 D/H Gac/Cac 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 deleterious(0) 6/7 hmmpanther:PTHR11559:SF52,hmmpanther:PTHR11559,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs1470109013 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 174279235 174279235 G C 1 0 0 0 0 1 0 0 0 10498 1290 45 4 4 NLGN1 3 174279235 Missense_Mutation SNP G 11LU016_T 6906364 174279235 24016324 115 167 PIK3CA 0 . GRCh38 3 179203771 179203771 + Missense_Mutation SNP T T A 11LU016_T 11LU016_N T T c.1041T>A p.Asn347Lys p.N347K ENST00000263967 5/21 101 93 8 53 53 0 strelka-varscan-mutect PIK3CA,missense_variant,p.Asn347Lys,ENST00000263967,NM_006218.2;PIK3CA,downstream_gene_variant,,ENST00000468036,;PIK3CA,downstream_gene_variant,,ENST00000477735,; A ENST00000263967 Transcript missense_variant 1198/9093 1041/3207 347/1068 N/K aaT/aaA COSM5613054 1 1 PIK3CA HGNC HGNC:8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 UPI000013D494 NM_006218.2 deleterious(0.04) 5/21 Gene3D:2.60.40.150,PROSITE_profiles:PS51547,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF54,SMART_domains:SM00142,Superfamily_domains:SSF49562 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.69741 1 1 1 1 0 A 3 1 2 179203771 179203771 T A 1 0 0 0 0 1 0 0 0 12008 1403 49 4 4 PIK3CA 3 179203771 Missense_Mutation SNP T 11LU016_T 4924536 179203771 19091788 116 168 1 2 PIK3CA 0 . GRCh38 3 179203778 179203778 + Missense_Mutation SNP G G C 11LU016_T 11LU016_N G G c.1048G>C p.Asp350His p.D350H ENST00000263967 5/21 84 78 6 49 49 0 strelka-mutect PIK3CA,missense_variant,p.Asp350His,ENST00000263967,NM_006218.2;PIK3CA,downstream_gene_variant,,ENST00000468036,;PIK3CA,downstream_gene_variant,,ENST00000477735,; C ENST00000263967 Transcript missense_variant 1205/9093 1048/3207 350/1068 D/H Gac/Cac COSM1736106,COSM582510,COSM582511,COSM755 1 1 PIK3CA HGNC HGNC:8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 UPI000013D494 NM_006218.2 deleterious(0) 5/21 Gene3D:2.60.40.150,PROSITE_profiles:PS51547,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF54,SMART_domains:SM00142,Superfamily_domains:SSF49562 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS rs1064793349 . 0 204 6 0 0 0 0 0 -12.88034 0.9999997 1 1 1 0 C 3 2 2 179203778 179203778 G C 1 0 0 0 0 1 0 0 0 12008 942 33 4 4 PIK3CA 3 179203778 Missense_Mutation SNP G 11LU016_T 7 179203778 19091781 117 169 1 2 PEX5L 0 . GRCh38 3 179808399 179808399 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1391C>T p.Ala464Val p.A464V ENST00000467460 13/15 69 62 7 63 63 0 strelka-varscan-mutect PEX5L,missense_variant,p.Ala464Val,ENST00000467460,NM_016559.2;PEX5L,missense_variant,p.Ala356Val,ENST00000392649,;PEX5L,missense_variant,p.Ala429Val,ENST00000485199,NM_001256752.1;PEX5L,missense_variant,p.Ala462Val,ENST00000263962,NM_001256750.1;PEX5L,missense_variant,p.Ala421Val,ENST00000476138,NM_001256754.1;PEX5L,missense_variant,p.Ala272Val,ENST00000468741,NM_001256756.1;PEX5L,missense_variant,p.Ala405Val,ENST00000472994,NM_001256753.1;PEX5L,missense_variant,p.Ala440Val,ENST00000465751,NM_001256751.1;PEX5L,missense_variant,p.Ala356Val,ENST00000464614,NM_001256755.1;RP11-494H4.3,downstream_gene_variant,,ENST00000602704,;PEX5L,non_coding_transcript_exon_variant,,ENST00000467440,;PEX5L,downstream_gene_variant,,ENST00000461537,;PEX5L,downstream_gene_variant,,ENST00000477829,; A ENST00000467460 Transcript missense_variant 1722/9082 1391/1881 464/626 A/V gCt/gTt 1 -1 PEX5L HGNC HGNC:30024 protein_coding YES CCDS3236.1 ENSP00000419975 Q8IYB4 UPI0000049CE2 NM_016559.2 deleterious(0.03) 13/15 PROSITE_profiles:PS50293,hmmpanther:PTHR10130,hmmpanther:PTHR10130:SF1,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -15.41691 0.9999858 1 1 1 0 A 3 1 2 179808399 179808399 G A 1 0 0 0 0 1 0 0 0 11839 971 34 3 3 PEX5L 3 179808399 Missense_Mutation SNP G 11LU016_T 604621 179808399 18487160 118 170 ATP11B 0 . GRCh38 3 182873922 182873922 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.2159G>T p.Cys720Phe p.C720F ENST00000323116 19/30 324 259 65 333 333 0 strelka-varscan-mutect ATP11B,missense_variant,p.Cys720Phe,ENST00000323116,NM_014616.2;ATP11B,missense_variant,p.Cys521Phe,ENST00000498086,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,;ATP11B,upstream_gene_variant,,ENST00000466758,; T ENST00000323116 Transcript missense_variant 2419/7325 2159/3534 720/1177 C/F tGt/tTt 1 1 ATP11B HGNC HGNC:13553 protein_coding YES CCDS33896.1 ENSP00000321195 Q9Y2G3 UPI000004124E NM_014616.2 deleterious(0) 19/30 Gene3D:3.40.50.1000,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 182873922 182873922 G T 1 0 0 0 0 1 0 0 0 1272 1377 48 2 2 ATP11B 3 182873922 Missense_Mutation SNP G 11LU016_T 3065523 182873922 15421637 119 171 MAGEF1 0 . GRCh38 3 184710919 184710919 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.903G>T p.Arg301Ser p.R301S ENST00000317897 1/1 59 45 14 47 47 0 strelka-varscan MAGEF1,missense_variant,p.Arg301Ser,ENST00000317897,NM_022149.4; A ENST00000317897 Transcript missense_variant 1084/1636 903/924 301/307 R/S agG/agT 1 -1 MAGEF1 HGNC HGNC:29639 protein_coding YES CCDS3269.1 ENSP00000315064 Q9HAY2 UPI0000140198 NM_022149.4 deleterious_low_confidence(0.01) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF61 MODERATE 1 SNV 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999975 1 1 1 0 A 3 1 2 184710919 184710919 C A 1 0 0 0 0 1 0 0 0 9105 622 22 2 2 MAGEF1 3 184710919 Missense_Mutation SNP C 11LU016_T 1836997 184710919 13584640 120 172 TBCCD1 0 . GRCh38 3 186554562 186554562 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1236G>T p.Gln412His p.Q412H ENST00000424280 6/8 161 149 12 263 262 1 strelka-varscan-mutect TBCCD1,missense_variant,p.Gln412His,ENST00000424280,NM_001134415.1;TBCCD1,missense_variant,p.Gln412His,ENST00000338733,NM_018138.4;TBCCD1,missense_variant,p.Gln316His,ENST00000446782,NM_001286749.1;TBCCD1,downstream_gene_variant,,ENST00000413695,;TBCCD1,downstream_gene_variant,,ENST00000430560,;TBCCD1,upstream_gene_variant,,ENST00000479590,; A ENST00000424280 Transcript missense_variant 1716/3058 1236/1674 412/557 Q/H caG/caT 1 -1 TBCCD1 HGNC HGNC:25546 protein_coding YES CCDS3276.1 ENSP00000411253 Q9NVR7 UPI0000073055 NM_001134415.1 tolerated(0.11) 6/8 Gene3D:2.160.20.70,Pfam_domain:PF07986,PROSITE_profiles:PS51329,hmmpanther:PTHR16052,hmmpanther:PTHR16052:SF0 MODERATE 1 SNV 5 1 PASS rs1439973646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 186554562 186554562 C A 1 0 0 0 0 1 0 0 0 16037 912 32 2 2 TBCCD1 3 186554562 Missense_Mutation SNP C 11LU016_T 1843643 186554562 11740997 121 173 FETUB 0 . GRCh38 3 186652420 186652420 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.938A>T p.Lys313Ile p.K313I ENST00000265029 7/7 126 88 38 137 136 1 strelka-varscan-mutect FETUB,missense_variant,p.Lys313Ile,ENST00000265029,NM_014375.2;FETUB,missense_variant,p.Lys313Ile,ENST00000450521,;FETUB,missense_variant,p.Lys248Ile,ENST00000382134,NM_001308079.1;FETUB,missense_variant,p.Lys276Ile,ENST00000382136,;FETUB,downstream_gene_variant,,ENST00000431018,;RP11-573D15.8,intron_variant,,ENST00000630864,;RP11-573D15.8,intron_variant,,ENST00000625303,;RP11-573D15.8,intron_variant,,ENST00000629106,;RP11-573D15.8,intron_variant,,ENST00000630315,;RP11-573D15.8,intron_variant,,ENST00000628253,;RP11-573D15.8,intron_variant,,ENST00000630178,;RP11-573D15.8,intron_variant,,ENST00000628505,;RP11-573D15.8,intron_variant,,ENST00000625826,;RP11-573D15.8,intron_variant,,ENST00000626649,;RP11-573D15.8,intron_variant,,ENST00000625741,;RP11-573D15.8,intron_variant,,ENST00000626845,;RP11-573D15.8,intron_variant,,ENST00000629451,;RP11-573D15.8,intron_variant,,ENST00000627469,;RP11-573D15.8,intron_variant,,ENST00000428501,;RP11-573D15.8,intron_variant,,ENST00000628190,;RP11-573D15.8,intron_variant,,ENST00000625386,;RP11-573D15.8,intron_variant,,ENST00000630331,;RP11-573D15.8,intron_variant,,ENST00000626633,;RP11-573D15.8,intron_variant,,ENST00000455926,;RP11-573D15.8,intron_variant,,ENST00000630726,;FETUB,3_prime_UTR_variant,,ENST00000435961,;FETUB,3_prime_UTR_variant,,ENST00000420570,; T ENST00000265029 Transcript missense_variant 1039/1627 938/1149 313/382 K/I aAa/aTa 1 1 FETUB HGNC HGNC:3658 protein_coding YES CCDS3279.1 ENSP00000265029 Q9UGM5 UPI00000361F3 NM_014375.2 deleterious(0.01) 7/7 hmmpanther:PTHR13814,hmmpanther:PTHR13814:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 186652420 186652420 A T 1 0 0 0 0 1 0 0 0 5684 14 1 4 4 FETUB 3 186652420 Missense_Mutation SNP A 11LU016_T 97858 186652420 11643139 122 174 RUBCN 0 . GRCh38 3 197701820 197701820 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.615G>T p.Gln205His p.Q205H ENST00000296343 6/20 325 264 61 270 269 1 strelka-varscan-mutect RUBCN,missense_variant,p.Gln145His,ENST00000273582,NM_001145642.3;RUBCN,missense_variant,p.Gln184His,ENST00000413360,;RUBCN,missense_variant,p.Gln205His,ENST00000296343,NM_014687.2;RUBCN,missense_variant,p.Gln205His,ENST00000449205,;RUBCN,upstream_gene_variant,,ENST00000415452,;RUBCN,downstream_gene_variant,,ENST00000474214,;RUBCN,upstream_gene_variant,,ENST00000447048,;RUBCN,non_coding_transcript_exon_variant,,ENST00000467303,; A ENST00000296343 Transcript missense_variant 615/2919 615/2919 205/972 Q/H caG/caT 1 -1 RUBCN HGNC HGNC:28991 protein_coding YES CCDS43195.1 ENSP00000296343 Q92622 UPI00001C1DE4 NM_014687.2 tolerated(0.13) 6/20 hmmpanther:PTHR12326:SF11,hmmpanther:PTHR12326 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 197701820 197701820 C A 1 0 0 0 0 1 0 0 0 13999 912 32 2 2 RUBCN 3 197701820 Missense_Mutation SNP C 11LU016_T 11049400 197701820 593739 123 175 PIGG 0 . GRCh38 4 533841 533841 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.2595C>T p.= p.T865T ENST00000453061 12/13 121 112 9 131 131 0 strelka-varscan-mutect PIGG,synonymous_variant,p.=,ENST00000453061,NM_001127178.2;PIGG,synonymous_variant,p.=,ENST00000310340,NM_017733.4;PIGG,synonymous_variant,p.=,ENST00000504346,NM_001289051.1;PIGG,synonymous_variant,p.=,ENST00000383028,NM_001289052.1;PIGG,downstream_gene_variant,,ENST00000510235,;PIGG,non_coding_transcript_exon_variant,,ENST00000503261,;PIGG,non_coding_transcript_exon_variant,,ENST00000504879,;PIGG,upstream_gene_variant,,ENST00000515237,;PIGG,downstream_gene_variant,,ENST00000508562,;PIGG,upstream_gene_variant,,ENST00000505800,;PIGG,non_coding_transcript_exon_variant,,ENST00000513239,;PIGG,non_coding_transcript_exon_variant,,ENST00000513192,;PIGG,non_coding_transcript_exon_variant,,ENST00000508144,;PIGG,non_coding_transcript_exon_variant,,ENST00000511666,; T ENST00000453061 Transcript synonymous_variant 2701/3218 2595/2952 865/983 T acC/acT 1 1 PIGG HGNC HGNC:25985 protein_coding YES CCDS46992.1 ENSP00000415203 Q5H8A4 UPI00004C7A82 NM_001127178.2 12/13 hmmpanther:PTHR23072,hmmpanther:PTHR23072:SF0 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 533841 533841 C T 1 0 0 0 0 0 0 0 1 11982 639 23 1 1 PIGG 4 533841 Silent SNP C 11LU016_T 533841 189680714 124 176 ADD1 0 . GRCh38 4 2907805 2907805 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1569G>T p.Leu523Phe p.L523F ENST00000264758 11/15 237 211 26 223 223 0 strelka-varscan-mutect ADD1,missense_variant,p.Leu492Phe,ENST00000355842,NM_001286645.1;ADD1,missense_variant,p.Leu523Phe,ENST00000398125,NM_176801.2;ADD1,missense_variant,p.Leu523Phe,ENST00000264758,NM_014189.3;ADD1,missense_variant,p.Leu492Phe,ENST00000398129,NM_001119.4;ADD1,missense_variant,p.Leu523Phe,ENST00000503455,;ADD1,missense_variant,p.Leu492Phe,ENST00000513328,NM_014190.3;ADD1,missense_variant,p.Leu523Phe,ENST00000398123,;ADD1,missense_variant,p.Leu229Phe,ENST00000514940,;ADD1,3_prime_UTR_variant,,ENST00000446856,;ADD1,upstream_gene_variant,,ENST00000536424,;ADD1,non_coding_transcript_exon_variant,,ENST00000513762,;ADD1,non_coding_transcript_exon_variant,,ENST00000541051,;ADD1,non_coding_transcript_exon_variant,,ENST00000536078,;ADD1,downstream_gene_variant,,ENST00000506157,;ADD1,downstream_gene_variant,,ENST00000503169,; T ENST00000264758 Transcript missense_variant 1757/4045 1569/2307 523/768 L/F ttG/ttT 1 1 ADD1 HGNC HGNC:243 protein_coding YES CCDS3363.1 ENSP00000264758 P35611 UPI000002A35E NM_014189.3 deleterious(0) 11/15 hmmpanther:PTHR10672:SF4,hmmpanther:PTHR10672 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 2907805 2907805 G T 1 0 0 0 0 1 0 0 0 348 1281 45 2 2 ADD1 4 2907805 Missense_Mutation SNP G 11LU016_T 2373964 2907805 187306750 125 177 HTT 0 . GRCh38 4 3173130 3173130 + Nonsense_Mutation SNP G G T rs775338972 11LU016_T 11LU016_N G G c.4165G>T p.Gly1389Ter p.G1389* ENST00000355072 31/67 172 151 21 162 162 0 strelka-varscan-mutect HTT,stop_gained,p.Gly1389Ter,ENST00000355072,NM_002111.7;HTT,missense_variant,p.Gly112Trp,ENST00000509618,;HTT,splice_region_variant,,ENST00000510626,; T ENST00000355072 Transcript stop_gained,splice_region_variant 4310/13474 4165/9429 1389/3142 G/* Gga/Tga rs775338972 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 31/67 hmmpanther:PTHR10170,hmmpanther:PTHR10170:SF10 HIGH 1 SNV 1 1 PASS rs775338972 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 3173130 3173130 G T 1 0 0 0 0 0 1 0 0 7353 1246 43 2 2 HTT 4 3173130 Nonsense_Mutation SNP G 11LU016_T 265325 3173130 187041425 126 178 JAKMIP1 0 . GRCh38 4 6085456 6085456 + Silent SNP G G T rs139885716 11LU016_T 11LU016_N G G c.798C>A p.= p.P266P ENST00000409021 4/21 227 157 70 260 260 0 strelka-varscan-mutect JAKMIP1,synonymous_variant,p.=,ENST00000409021,NM_001099433.1;JAKMIP1,synonymous_variant,p.=,ENST00000282924,NM_144720.3;JAKMIP1,synonymous_variant,p.=,ENST00000409371,;JAKMIP1,synonymous_variant,p.=,ENST00000409831,NM_001306133.1;JAKMIP1,synonymous_variant,p.=,ENST00000410077,NM_001306134.1;JAKMIP1,non_coding_transcript_exon_variant,,ENST00000457227,;JAKMIP1,synonymous_variant,p.=,ENST00000473053,; T ENST00000409021 Transcript synonymous_variant 1248/2975 798/2496 266/831 P ccC/ccA rs139885716 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 4/21 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 LOW 1 SNV 1 1 PASS rs139885716 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 6085456 6085456 G T 1 0 0 0 0 0 0 0 1 7853 1103 39 1 1 JAKMIP1 4 6085456 Silent SNP G 11LU016_T 2912326 6085456 184129099 127 179 HTRA3 0 . GRCh38 4 8286646 8286646 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.571C>T p.His191Tyr p.H191Y ENST00000307358 3/9 315 231 84 324 324 0 strelka-varscan-mutect HTRA3,missense_variant,p.His191Tyr,ENST00000307358,NM_053044.4;HTRA3,missense_variant,p.His191Tyr,ENST00000382512,NM_001297559.1; T ENST00000307358 Transcript missense_variant 775/2541 571/1362 191/453 H/Y Cac/Tac 1 1 HTRA3 HGNC HGNC:30406 protein_coding YES CCDS3400.1 ENSP00000303766 P83110 UPI0000001647 NM_053044.4 deleterious(0.01) 3/9 hmmpanther:PTHR22939:SF14,hmmpanther:PTHR22939,Gene3D:2.40.10.10,Pfam_domain:PF13365,Superfamily_domains:SSF50494,Prints_domain:PR00834 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 8286646 8286646 C T 1 0 0 0 0 1 0 0 0 7351 594 21 3 3 HTRA3 4 8286646 Missense_Mutation SNP C 11LU016_T 2201190 8286646 181927909 128 180 CLNK 0 . GRCh38 4 10490534 10490534 + Missense_Mutation SNP C C A rs762033179 11LU016_T 11LU016_N C C c.1220G>T p.Gly407Val p.G407V ENST00000226951 19/19 284 262 22 239 237 2 strelka-varscan-mutect CLNK,missense_variant,p.Gly407Val,ENST00000226951,NM_052964.2;CLNK,missense_variant,p.Gly145Val,ENST00000515667,;CLNK,missense_variant,p.Gly407Val,ENST00000442825,; A ENST00000226951 Transcript missense_variant 1460/5599 1220/1287 407/428 G/V gGg/gTg rs762033179 1 -1 CLNK HGNC HGNC:17438 protein_coding YES CCDS47024.1 ENSP00000226951 Q7Z7G1 UPI000004A23A NM_052964.2 deleterious(0) 19/19 PROSITE_profiles:PS50001,hmmpanther:PTHR14098:SF2,hmmpanther:PTHR14098,Gene3D:3.30.505.10,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs762033179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 10490534 10490534 C A 1 0 0 0 0 1 0 0 0 3317 623 22 2 2 CLNK 4 10490534 Missense_Mutation SNP C 11LU016_T 2203888 10490534 179724021 129 181 ADGRL3 0 . GRCh38 4 61733215 61733215 + Frame_Shift_Del DEL G G - novel 11LU016_T 11LU016_N G G c.856delG p.Val286SerfsTer5 p.V286Sfs*5 ENST00000514591 7/25 256 225 31 300 300 0 sindel-varindel-pindel ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000512091,NM_001322246.1;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000514591,NM_015236.4;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000509896,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000511324,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000508693,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000507164,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000506720,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000506746,;ADGRL3,frameshift_variant,p.Val354SerfsTer5,ENST00000507625,;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000506700,;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000504896,;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000514157,;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000508946,;ADGRL3,frameshift_variant,p.Val286SerfsTer5,ENST00000514996,; - ENST00000514591 Transcript frameshift_variant 1185/6297 856/4410 286/1469 V/X Gtc/tc 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 7/25 PROSITE_profiles:PS51132,Pfam_domain:PF02191,SMART_domains:SM00284 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 61733215 61733215 G - 1 0 1 0 1 0 0 0 0 377 1377 48 0 0 ADGRL3 4 61733215 Frame_Shift_Del DEL G 11LU016_T 51242681 61733215 128481340 130 182 TECRL 0 . GRCh38 4 64314734 64314734 + Silent SNP C C A 11LU016_T 11LU016_N C C c.465G>T p.= p.L155L ENST00000381210 5/12 138 122 16 177 177 0 strelka-varscan-mutect TECRL,synonymous_variant,p.=,ENST00000381210,NM_001010874.4;TECRL,synonymous_variant,p.=,ENST00000507440,;TECRL,non_coding_transcript_exon_variant,,ENST00000513125,;TECRL,non_coding_transcript_exon_variant,,ENST00000511356,; A ENST00000381210 Transcript synonymous_variant 576/3573 465/1092 155/363 L ctG/ctT COSM347287 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 5/12 hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 2 0 0 0 -7.98617 0.9949798 1 1 1 0 A 2 1 2 64314734 64314734 C A 1 0 0 0 0 0 0 0 1 16157 697 25 2 2 TECRL 4 64314734 Silent SNP C 11LU016_T 2581519 64314734 125899821 131 183 EPHA5 0 . GRCh38 4 65351505 65351505 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.2395C>T p.His799Tyr p.H799Y ENST00000622150 14/18 296 266 30 278 278 0 strelka-varscan-mutect EPHA5,missense_variant,p.His799Tyr,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.His777Tyr,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.His798Tyr,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.His799Tyr,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.His635Tyr,ENST00000432638,;EPHA5,missense_variant,p.His776Tyr,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 3148/8421 2395/3117 799/1038 H/Y Cat/Tat 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 14/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Prints_domain:PR00109,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 65351505 65351505 G A 1 0 0 0 0 1 0 0 0 5017 1319 46 3 3 EPHA5 4 65351505 Missense_Mutation SNP G 11LU016_T 1036771 65351505 124863050 132 184 UGT2A1 0 . GRCh38 4 69647001 69647001 + Missense_Mutation SNP G G T rs149931914 11LU016_T 11LU016_N G G c.644C>A p.Ser215Tyr p.S215Y ENST00000514019 2/7 62 49 13 61 61 0 strelka-varscan-mutect UGT2A1,missense_variant,p.Ser215Tyr,ENST00000503640,NM_006798.4;UGT2A1,missense_variant,p.Ser215Tyr,ENST00000512704,NM_001301239.1;UGT2A1,missense_variant,p.Ser215Tyr,ENST00000514019,NM_001252274.2;UGT2A1,missense_variant,p.Ser215Tyr,ENST00000286604,NM_001252275.2;UGT2A1,downstream_gene_variant,,ENST00000505512,; T ENST00000514019 Transcript missense_variant 760/2376 644/2082 215/693 S/Y tCc/tAc rs149931914 1 -1 UGT2A1 HGNC HGNC:12542 protein_coding YES CCDS58902.1 ENSP00000425497 A0A140T9Z0 UPI0004620AF5 NM_001252274.2 tolerated(1) 2/7 Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 2 1 PASS rs149931914 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 69647001 69647001 G T 1 0 0 0 0 1 0 0 0 17478 1174 41 2 2 UGT2A1 4 69647001 Missense_Mutation SNP G 11LU016_T 4295496 69647001 120567554 133 185 NPFFR2 0 . GRCh38 4 72147320 72147320 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1077G>T p.Lys359Asn p.K359N ENST00000308744 4/4 239 165 74 263 263 0 strelka-varscan-mutect NPFFR2,missense_variant,p.Lys359Asn,ENST00000308744,NM_004885.2;NPFFR2,missense_variant,p.Lys260Asn,ENST00000395999,NM_001144756.1;NPFFR2,missense_variant,p.Lys257Asn,ENST00000358749,NM_053036.2;NPFFR2,3_prime_UTR_variant,,ENST00000344413,;NPFFR2,non_coding_transcript_exon_variant,,ENST00000506359,; T ENST00000308744 Transcript missense_variant 1175/1922 1077/1569 359/522 K/N aaG/aaT 1 1 NPFFR2 HGNC HGNC:4525 protein_coding YES CCDS3551.1 ENSP00000307822 Q9Y5X5 UPI000012FFBD NM_004885.2 tolerated(0.45) 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF3,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs898931282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 72147320 72147320 G T 1 0 0 0 0 1 0 0 0 10626 933 33 2 2 NPFFR2 4 72147320 Missense_Mutation SNP G 11LU016_T 2500319 72147320 118067235 134 186 ADAMTS3 0 . GRCh38 4 72548793 72548793 + Silent SNP C C A rs777768285 11LU016_T 11LU016_N C C c.189G>T p.= p.A63A ENST00000286657 3/22 261 226 35 189 189 0 strelka-varscan-mutect ADAMTS3,synonymous_variant,p.=,ENST00000286657,;ADAMTS3,synonymous_variant,p.=,ENST00000622135,NM_014243.2;ADAMTS3,non_coding_transcript_exon_variant,,ENST00000505193,; A ENST00000286657 Transcript synonymous_variant 813/6409 189/3618 63/1205 A gcG/gcT rs777768285 1 -1 ADAMTS3 HGNC HGNC:219 protein_coding YES CCDS3553.1 ENSP00000286657 O15072 UPI00001AEAEA 3/22 Pfam_domain:PF01562 LOW 1 SNV 1 1 PASS rs777768285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 72548793 72548793 C A 1 0 0 0 0 0 0 0 1 311 871 31 1 1 ADAMTS3 4 72548793 Silent SNP C 11LU016_T 401473 72548793 117665762 135 187 CENPE 0 . GRCh38 4 103159299 103159299 + Missense_Mutation SNP T T A rs774151339 11LU016_T 11LU016_N T T c.2312A>T p.His771Leu p.H771L ENST00000265148 22/49 37 33 4 35 35 0 strelka-mutect CENPE,missense_variant,p.His771Leu,ENST00000265148,NM_001813.2;CENPE,missense_variant,p.His771Leu,ENST00000611174,;CENPE,missense_variant,p.His746Leu,ENST00000380026,NM_001286734.1;CENPE,missense_variant,p.His771Leu,ENST00000503705,; A ENST00000265148 Transcript missense_variant 2402/8612 2312/8106 771/2701 H/L cAt/cTt rs774151339 1 -1 CENPE HGNC HGNC:1856 protein_coding YES CCDS34042.1 ENSP00000265148 Q02224 UPI000020B28A NM_001813.2 tolerated(0.64) 22/49 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF459,hmmpanther:PTHR24115 MODERATE 1 SNV 2 1 PASS rs774151339 . 2 205 3 0 0 0 0 0 -11.15639 1 1 1 1 0 A 3 1 2 103159299 103159299 T A 1 0 0 0 0 1 0 0 0 2938 1464 51 4 4 CENPE 4 103159299 Missense_Mutation SNP T 11LU016_T 30610506 103159299 87055256 136 188 EGF 0 . GRCh38 4 109969019 109969019 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1624G>T p.Asp542Tyr p.D542Y ENST00000265171 11/24 430 386 44 419 419 0 strelka-varscan-mutect EGF,missense_variant,p.Asp542Tyr,ENST00000265171,NM_001963.4;EGF,missense_variant,p.Asp500Tyr,ENST00000509793,NM_001178131.1;EGF,missense_variant,p.Asp542Tyr,ENST00000503392,NM_001178130.1;EGF,non_coding_transcript_exon_variant,,ENST00000502579,; T ENST00000265171 Transcript missense_variant 2069/4880 1624/3624 542/1207 D/Y Gat/Tat 1 1 EGF HGNC HGNC:3229 protein_coding YES CCDS3689.1 ENSP00000265171 P01133 UPI000013D5C8 NM_001963.4 deleterious(0) 11/24 Gene3D:2.120.10.30,Pfam_domain:PF00058,PIRSF_domain:PIRSF001778,PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF200,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 109969019 109969019 G T 1 0 0 0 0 1 0 0 0 4798 1174 41 2 2 EGF 4 109969019 Missense_Mutation SNP G 11LU016_T 6809720 109969019 80245536 137 189 ANK2 0 . GRCh38 4 113359225 113359225 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.10607G>A p.Arg3536Lys p.R3536K ENST00000357077 38/46 94 85 9 102 102 0 strelka-varscan-mutect ANK2,missense_variant,p.Arg3536Lys,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Arg3503Lys,ENST00000264366,;ANK2,missense_variant,p.Arg546Lys,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript missense_variant 10660/14196 10607/11874 3536/3957 R/K aGg/aAg 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated(0.06) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 113359225 113359225 G A 1 0 0 0 0 1 0 0 0 721 1000 35 3 3 ANK2 4 113359225 Missense_Mutation SNP G 11LU016_T 3390206 113359225 76855330 138 190 TRPC3 0 . GRCh38 4 121932479 121932479 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.779A>T p.Glu260Val p.E260V ENST00000379645 2/12 298 271 27 237 237 0 strelka-varscan-mutect TRPC3,missense_variant,p.Glu187Val,ENST00000264811,NM_003305.2;TRPC3,missense_variant,p.Glu260Val,ENST00000379645,NM_001130698.1;TRPC3,missense_variant,p.Glu187Val,ENST00000513531,;TRPC3,downstream_gene_variant,,ENST00000502968,;TRPC3,missense_variant,p.Glu187Val,ENST00000506449,; A ENST00000379645 Transcript missense_variant 853/3548 779/2766 260/921 E/V gAg/gTg 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 tolerated(0.07) 2/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 121932479 121932479 T A 1 0 0 0 0 1 0 0 0 17084 1551 54 4 4 TRPC3 4 121932479 Missense_Mutation SNP T 11LU016_T 8573254 121932479 68282076 139 191 SMARCA5 0 . GRCh38 4 143540487 143540487 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.1895T>G p.Ile632Ser p.I632S ENST00000283131 14/24 101 77 24 67 67 0 strelka-varscan-mutect SMARCA5,missense_variant,p.Ile632Ser,ENST00000283131,NM_003601.3;SMARCA5,upstream_gene_variant,,ENST00000515531,; G ENST00000283131 Transcript missense_variant 2357/7923 1895/3159 632/1052 I/S aTt/aGt 1 1 SMARCA5 HGNC HGNC:11101 protein_coding YES CCDS3761.1 ENSP00000283131 O60264 UPI000006E693 NM_003601.3 deleterious(0) 14/24 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF691,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 143540487 143540487 T G 1 0 0 0 0 1 0 0 0 15064 1493 52 5 5 SMARCA5 4 143540487 Missense_Mutation SNP T 11LU016_T 21608008 143540487 46674068 140 192 FREM3 0 . GRCh38 4 143699833 143699833 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.843C>A p.= p.S281S ENST00000329798 1/8 148 138 10 126 126 0 strelka-varscan-mutect FREM3,synonymous_variant,p.=,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; T ENST00000329798 Transcript synonymous_variant 843/6729 843/6420 281/2139 S tcC/tcA 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 1/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 LOW SNV 5 1 PASS rs1271605163 . 0 207 0 3 0 0 0 0 -13.62191 0.9999667 1 1 1 0 T 2 4 2 143699833 143699833 G T 1 0 0 0 0 0 0 0 1 5913 1103 39 1 1 FREM3 4 143699833 Silent SNP G 11LU016_T 159346 143699833 46514722 141 193 LRBA 0 . GRCh38 4 150828448 150828448 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.4903G>T p.Asp1635Tyr p.D1635Y ENST00000357115 30/58 263 229 34 283 283 0 strelka-varscan-mutect LRBA,missense_variant,p.Asp1635Tyr,ENST00000510413,NM_001199282.2;LRBA,missense_variant,p.Asp1635Tyr,ENST00000357115,NM_006726.4;LRBA,missense_variant,p.Asp1635Tyr,ENST00000507224,;LRBA,missense_variant,p.Asp288Tyr,ENST00000509835,; A ENST00000357115 Transcript missense_variant 5147/9899 4903/8592 1635/2863 D/Y Gat/Tat 1 -1 LRBA HGNC HGNC:1742 protein_coding YES CCDS3773.1 ENSP00000349629 P50851 UPI000013E35C NM_006726.4 deleterious(0) 30/58 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 150828448 150828448 C A 1 0 0 0 0 1 0 0 0 8825 913 32 2 2 LRBA 4 150828448 Missense_Mutation SNP C 11LU016_T 7128615 150828448 39386107 142 194 NPY2R 0 . GRCh38 4 155214547 155214547 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.608G>T p.Cys203Phe p.C203F ENST00000329476 2/2 296 271 25 240 240 0 strelka-varscan-mutect NPY2R,missense_variant,p.Cys203Phe,ENST00000329476,NM_000910.3;NPY2R,missense_variant,p.Cys203Phe,ENST00000506608,;AC097467.2,intron_variant,,ENST00000630664,; T ENST00000329476 Transcript missense_variant 1097/3626 608/1146 203/381 C/F tGt/tTt COSM5666029 1 1 NPY2R HGNC HGNC:7957 protein_coding YES CCDS3791.1 ENSP00000332591 P49146 UPI000003B342 NM_000910.3 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF42,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01014 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 155214547 155214547 G T 1 0 0 0 0 1 0 0 0 10664 1377 48 2 2 NPY2R 4 155214547 Missense_Mutation SNP G 11LU016_T 4386099 155214547 35000008 143 195 FSTL5 0 . GRCh38 4 161538177 161538177 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1301C>A p.Ala434Asp p.A434D ENST00000306100 10/16 137 108 29 103 103 0 strelka-varscan-mutect FSTL5,missense_variant,p.Ala434Asp,ENST00000306100,NM_020116.4;FSTL5,missense_variant,p.Ala433Asp,ENST00000379164,NM_001128427.2;FSTL5,missense_variant,p.Ala433Asp,ENST00000427802,NM_001128428.2;FSTL5,downstream_gene_variant,,ENST00000511170,; T ENST00000306100 Transcript missense_variant 1738/4831 1301/2544 434/847 A/D gCt/gAt 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 deleterious(0) 10/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 161538177 161538177 G T 1 0 0 0 0 1 0 0 0 5954 971 34 2 2 FSTL5 4 161538177 Missense_Mutation SNP G 11LU016_T 6323630 161538177 28676378 144 196 TENM3 0 . GRCh38 4 182754856 182754856 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.4489G>T p.Ala1497Ser p.A1497S ENST00000511685 22/28 283 263 20 289 287 2 strelka-varscan-mutect TENM3,missense_variant,p.Ala1497Ser,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,; T ENST00000511685 Transcript missense_variant 4612/10896 4489/8100 1497/2699 A/S Gct/Tct 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 tolerated(0.69) 22/28 Gene3D:2.120.10.30,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10,Superfamily_domains:SSF101898,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 182754856 182754856 G T 1 0 0 0 0 1 0 0 0 16173 1203 42 2 2 TENM3 4 182754856 Missense_Mutation SNP G 11LU016_T 21216679 182754856 7459699 145 197 FAM149A 0 . GRCh38 4 186167187 186167187 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1300G>T p.Asp434Tyr p.D434Y ENST00000227065 13/14 184 158 26 176 176 0 strelka-varscan-mutect FAM149A,missense_variant,p.Asp725Tyr,ENST00000356371,;FAM149A,missense_variant,p.Asp434Tyr,ENST00000227065,NM_015398.2,NM_001006655.2;FAM149A,missense_variant,p.Asp434Tyr,ENST00000514153,;FAM149A,missense_variant,p.Asp434Tyr,ENST00000503432,;FAM149A,missense_variant,p.Asp434Tyr,ENST00000502970,;FAM149A,missense_variant,p.Asp112Tyr,ENST00000510843,;FAM149A,missense_variant,p.Asp111Tyr,ENST00000512271,;FAM149A,3_prime_UTR_variant,,ENST00000389354,;FAM149A,upstream_gene_variant,,ENST00000502894,;FAM149A,non_coding_transcript_exon_variant,,ENST00000515078,;FAM149A,non_coding_transcript_exon_variant,,ENST00000514956,;ORAOV1P1,downstream_gene_variant,,ENST00000503108,; T ENST00000227065 Transcript missense_variant 1879/2708 1300/1449 434/482 D/Y Gat/Tat 1 1 FAM149A HGNC HGNC:24527 protein_coding YES CCDS34117.1 ENSP00000227065 A5PLN7 UPI00001C1E1F NM_015398.2,NM_001006655.2 deleterious(0) 13/14 hmmpanther:PTHR31997,hmmpanther:PTHR31997:SF2 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 186167187 186167187 G T 1 0 0 0 0 1 0 0 0 5304 1174 41 2 2 FAM149A 4 186167187 Missense_Mutation SNP G 11LU016_T 3412331 186167187 4047368 146 198 FAT1 0 . GRCh38 4 186618116 186618116 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.8470G>T p.Gly2824Trp p.G2824W ENST00000441802 10/27 157 133 24 198 198 0 strelka-varscan-mutect FAT1,missense_variant,p.Gly2824Trp,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Gly2826Trp,ENST00000614102,; A ENST00000441802 Transcript missense_variant 8680/14786 8470/13767 2824/4588 G/W Ggg/Tgg 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0.03) 10/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 186618116 186618116 C A 1 0 0 0 0 1 0 0 0 5549 681 24 2 2 FAT1 4 186618116 Missense_Mutation SNP C 11LU016_T 450929 186618116 3596439 147 199 SLC12A7 0 . GRCh38 5 1076774 1076774 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1668G>T p.Trp556Cys p.W556C ENST00000264930 13/24 209 176 33 224 223 1 strelka-varscan-mutect SLC12A7,missense_variant,p.Trp556Cys,ENST00000264930,NM_006598.2;SLC12A7,missense_variant,p.Trp457Cys,ENST00000634447,;SLC12A7,upstream_gene_variant,,ENST00000513223,;SLC12A7,missense_variant,p.Trp3Cys,ENST00000504576,;SLC12A7,downstream_gene_variant,,ENST00000510943,; A ENST00000264930 Transcript missense_variant 1712/5280 1668/3252 556/1083 W/C tgG/tgT 1 -1 SLC12A7 HGNC HGNC:10915 protein_coding YES CCDS34129.1 ENSP00000264930 Q9Y666 UPI0000141815 NM_006598.2 deleterious(0.02) 13/24 Pfam_domain:PF00324,Prints_domain:PR01081,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF47,TIGRFAM_domain:TIGR00930,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1076774 1076774 C A 1 0 0 0 0 1 0 0 0 14653 624 22 2 2 SLC12A7 5 1076774 Missense_Mutation SNP C 11LU016_T 1076774 180461485 148 200 ADCY2 0 . GRCh38 5 7766703 7766703 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2111C>A p.Ser704Ter p.S704* ENST00000338316 17/25 130 106 24 247 245 2 strelka-varscan-mutect ADCY2,stop_gained,p.Ser704Ter,ENST00000338316,NM_020546.2; A ENST00000338316 Transcript stop_gained 2200/6575 2111/3276 704/1091 S/* tCa/tAa 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 17/25 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 7766703 7766703 C A 1 0 0 0 0 0 1 0 0 338 838 29 2 2 ADCY2 5 7766703 Nonsense_Mutation SNP C 11LU016_T 6689929 7766703 173771556 149 201 DNAH5 0 . GRCh38 5 13735837 13735837 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.11551T>C p.Phe3851Leu p.F3851L ENST00000265104 67/79 616 487 129 461 461 0 strelka-varscan-mutect DNAH5,missense_variant,p.Phe3851Leu,ENST00000265104,NM_001369.2; G ENST00000265104 Transcript missense_variant 11656/15633 11551/13875 3851/4624 F/L Ttt/Ctt 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 67/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 13735837 13735837 A G 1 0 0 0 0 1 0 0 0 4419 101 4 5 5 DNAH5 5 13735837 Missense_Mutation SNP A 11LU016_T 5969134 13735837 167802422 150 202 ADAMTS12 0 . GRCh38 5 33561033 33561033 + Missense_Mutation SNP C C G 11LU016_T 11LU016_N C C c.4119G>C p.Trp1373Cys p.W1373C ENST00000504830 20/24 165 119 46 128 128 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Trp1373Cys,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Trp1288Cys,ENST00000352040,; G ENST00000504830 Transcript missense_variant 4455/8774 4119/4785 1373/1594 W/C tgG/tgC COSM3615474 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 20/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 33561033 33561033 C G 1 0 0 0 0 1 0 0 0 301 856 30 4 4 ADAMTS12 5 33561033 Missense_Mutation SNP C 11LU016_T 19825196 33561033 147977226 151 203 ADAMTS12 0 . GRCh38 5 33658278 33658278 + Missense_Mutation SNP G G C rs770463039 11LU016_T 11LU016_N G G c.1096C>G p.Leu366Val p.L366V ENST00000504830 7/24 279 242 37 217 217 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Leu366Val,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Leu366Val,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; C ENST00000504830 Transcript missense_variant 1432/8774 1096/4785 366/1594 L/V Ctt/Gtt rs770463039 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.69) 7/24 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs770463039 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 2 33658278 33658278 G C 1 0 0 0 0 1 0 0 0 301 1000 35 4 4 ADAMTS12 5 33658278 Missense_Mutation SNP G 11LU016_T 97245 33658278 147879981 152 204 CAPSL 0 . GRCh38 5 35910512 35910512 + Silent SNP G G T rs202156612 11LU016_T 11LU016_N G G c.169C>A p.= p.R57R ENST00000397367 3/5 115 96 19 66 66 0 strelka-varscan-mutect CAPSL,synonymous_variant,p.=,ENST00000397367,NM_144647.3;CAPSL,synonymous_variant,p.=,ENST00000397366,NM_001042625.1;CAPSL,synonymous_variant,p.=,ENST00000513623,;CAPSL,synonymous_variant,p.=,ENST00000514524,; T ENST00000397367 Transcript synonymous_variant 296/1004 169/627 57/208 R Cga/Aga rs202156612,COSM266185,COSM5102613 1 -1 CAPSL HGNC HGNC:28375 protein_coding YES CCDS3912.2 ENSP00000380524 Q8WWF8 UPI0000149B20 NM_144647.3 3/5 Gene3D:1.10.238.10,Pfam_domain:PF13499,PROSITE_patterns:PS00018,PROSITE_profiles:PS50222,hmmpanther:PTHR10891,hmmpanther:PTHR10891:SF551,SMART_domains:SM00054,Superfamily_domains:SSF47473 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs747567733 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 35910512 35910512 G T 1 0 0 0 0 0 0 0 1 2334 1066 37 1 1 CAPSL 5 35910512 Silent SNP G 11LU016_T 2252234 35910512 145627747 153 205 VCAN 0 . GRCh38 5 83519354 83519354 + Nonsense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1048G>T p.Glu350Ter p.E350* ENST00000265077 7/15 87 69 18 101 101 0 strelka-varscan VCAN,stop_gained,p.Glu350Ter,ENST00000265077,NM_004385.4;VCAN,stop_gained,p.Glu350Ter,ENST00000342785,NM_001164098.1;VCAN,stop_gained,p.Glu302Ter,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; T ENST00000265077 Transcript stop_gained 1613/12625 1048/10191 350/3396 E/* Gag/Tag 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6,Gene3D:3.10.100.10,Superfamily_domains:SSF56436 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 83519354 83519354 G T 1 0 0 0 0 0 1 0 0 17683 956 33 2 2 VCAN 5 83519354 Nonsense_Mutation SNP G 11LU016_T 47608842 83519354 98018905 154 206 RASA1 0 . GRCh38 5 87372193 87372193 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1774C>G p.Gln592Glu p.Q592E ENST00000274376 13/25 227 186 41 256 256 0 strelka-varscan RASA1,missense_variant,p.Gln415Glu,ENST00000456692,NM_022650.2;RASA1,missense_variant,p.Gln592Glu,ENST00000274376,NM_002890.2;RASA1,missense_variant,p.Gln425Glu,ENST00000512763,;RASA1,missense_variant,p.Gln426Glu,ENST00000506290,;CTC-428H11.2,downstream_gene_variant,,ENST00000607486,;RASA1,splice_region_variant,,ENST00000515800,;RASA1,downstream_gene_variant,,ENST00000509953,; G ENST00000274376 Transcript missense_variant,splice_region_variant 2338/3752 1774/3144 592/1047 Q/E Cag/Gag 1 1 RASA1 HGNC HGNC:9871 protein_coding YES CCDS34200.1 ENSP00000274376 P20936 UPI00001351F3 NM_002890.2 tolerated(0.65) 13/25 hmmpanther:PTHR10194:SF19,hmmpanther:PTHR10194,Gene3D:2.60.40.150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 87372193 87372193 C G 1 0 0 0 0 1 0 0 0 13219 840 29 4 4 RASA1 5 87372193 Missense_Mutation SNP C 11LU016_T 3852839 87372193 94166066 155 207 SLC27A6 0 . GRCh38 5 129029625 129029625 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1601C>A p.Thr534Lys p.T534K ENST00000262462 9/10 34 25 9 87 86 1 strelka-varscan SLC27A6,missense_variant,p.Thr534Lys,ENST00000262462,;SLC27A6,missense_variant,p.Thr534Lys,ENST00000395266,NM_014031.3,NM_001017372.1;SLC27A6,missense_variant,p.Thr534Lys,ENST00000506176,; A ENST00000262462 Transcript missense_variant 2611/3219 1601/1860 534/619 T/K aCa/aAa 1 1 SLC27A6 HGNC HGNC:11000 protein_coding YES CCDS4145.1 ENSP00000262462 Q9Y2P4 UPI0000038E83 tolerated(0.47) 9/10 hmmpanther:PTHR24096:SF98,hmmpanther:PTHR24096,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 129029625 129029625 C A 1 0 0 0 0 1 0 0 0 14800 478 17 2 2 SLC27A6 5 129029625 Missense_Mutation SNP C 11LU016_T 41657432 129029625 52508634 156 208 TRPC7 0 . GRCh38 5 136274727 136274727 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.1074C>A p.= p.V358V ENST00000513104 4/12 198 185 13 206 206 0 strelka-varscan TRPC7,synonymous_variant,p.=,ENST00000513104,NM_020389.2;TRPC7,synonymous_variant,p.=,ENST00000378459,NM_001167577.1;TRPC7,intron_variant,,ENST00000502753,;TRPC7,intron_variant,,ENST00000352189,NM_001167576.1;TRPC7,synonymous_variant,p.=,ENST00000503275,;TRPC7,intron_variant,,ENST00000514963,; T ENST00000513104 Transcript synonymous_variant 1357/2987 1074/2589 358/862 V gtC/gtA 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 4/12 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 136274727 136274727 G T 1 0 0 0 0 0 0 0 1 17090 929 33 2 2 TRPC7 5 136274727 Silent SNP G 11LU016_T 7245102 136274727 45263532 157 209 FAM196B 0 . GRCh38 5 169883691 169883691 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.208G>T p.Ala70Ser p.A70S ENST00000377365 2/4 51 46 5 55 55 0 strelka-varscan FAM196B,missense_variant,p.Ala70Ser,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; A ENST00000377365 Transcript missense_variant 1590/2999 208/1608 70/535 A/S Gca/Tca 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 tolerated(0.08) 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 MODERATE SNV 2 1 PASS . . 0 202 8 0 0 0 0 0 -12.12751 0.9999953 1 1 1 0 A 3 1 2 169883691 169883691 C A 1 0 0 0 0 1 0 0 0 5374 797 28 2 2 FAM196B 5 169883691 Missense_Mutation SNP C 11LU016_T 33608964 169883691 11654568 158 210 HRH2 0 . GRCh38 5 175683978 175683978 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.747delC p.Tyr250ThrfsTer10 p.Y250Tfs*10 ENST00000377291 2/3 319 284 35 393 392 1 sindel-varindel-pindel HRH2,frameshift_variant,p.Tyr250ThrfsTer10,ENST00000636584,;HRH2,frameshift_variant,p.Tyr250ThrfsTer10,ENST00000377291,NM_001131055.1;HRH2,frameshift_variant,p.Tyr250ThrfsTer10,ENST00000231683,NM_022304.2;HRH2,frameshift_variant,p.Tyr250ThrfsTer10,ENST00000624694,; - ENST00000377291 Transcript frameshift_variant 1396/2561 745/1194 249/397 P/X Ccc/cc 1 1 HRH2 HGNC HGNC:5183 protein_coding YES CCDS47344.1 ENSP00000366506 P25021 UPI00001B2326 NM_001131055.1 2/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF280,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 175683978 175683978 C - 1 0 1 0 1 0 0 0 0 7251 855 30 0 0 HRH2 5 175683978 Frame_Shift_Del DEL C 11LU016_T 5800287 175683978 5854281 159 211 UNC5A 0 . GRCh38 5 176878603 176878603 + Missense_Mutation SNP C C A rs750617210 11LU016_T 11LU016_N C C c.2148C>A p.Asp716Glu p.D716E ENST00000329542 13/15 100 71 29 116 116 0 strelka-varscan UNC5A,missense_variant,p.Asp716Glu,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000292432,NM_002115.2;UNC5A,downstream_gene_variant,,ENST00000509580,;HK3,downstream_gene_variant,,ENST00000514058,;HK3,downstream_gene_variant,,ENST00000506834,;UNC5A,downstream_gene_variant,,ENST00000513890,;HK3,downstream_gene_variant,,ENST00000514666,; A ENST00000329542 Transcript missense_variant 2422/3812 2148/2529 716/842 D/E gaC/gaA rs750617210 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 tolerated(1) 13/15 hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 176878603 176878603 C A 1 0 0 0 0 1 0 0 0 17515 535 19 1 1 UNC5A 5 176878603 Missense_Mutation SNP C 11LU016_T 1194625 176878603 4659656 160 212 SLC17A1 0 . GRCh38 6 25826478 25826478 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.190C>G p.Leu64Val p.L64V ENST00000244527 3/13 73 65 8 70 70 0 strelka-varscan-mutect SLC17A1,missense_variant,p.Leu64Val,ENST00000244527,NM_005074.3;SLC17A1,missense_variant,p.Leu64Val,ENST00000476801,;SLC17A1,missense_variant,p.Leu64Val,ENST00000468082,;SLC17A1,missense_variant,p.Leu64Val,ENST00000377886,; C ENST00000244527 Transcript missense_variant 306/1844 190/1404 64/467 L/V Ctc/Gtc 1 -1 SLC17A1 HGNC HGNC:10929 protein_coding YES CCDS4565.1 ENSP00000244527 Q14916 UPI00000719C0 NM_005074.3 tolerated(0.47) 3/13 Pfam_domain:PF07690,PROSITE_profiles:PS50850,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00894 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -17.82414 1 1 1 1 0 C 3 2 2 25826478 25826478 G C 1 0 0 0 0 1 0 0 0 14681 971 34 4 4 SLC17A1 6 25826478 Missense_Mutation SNP G 11LU016_T 25826478 144979501 161 213 SLC17A2 0 . GRCh38 6 25914666 25914666 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1216G>T p.Ala406Ser p.A406S ENST00000377850 11/12 141 110 31 109 109 0 strelka-varscan-mutect SLC17A2,missense_variant,p.Ala406Ser,ENST00000377850,NM_001286123.1;SLC17A2,missense_variant,p.Met356Ile,ENST00000360488,NM_005835.3,NM_001286125.1;SLC17A2,missense_variant,p.Ala406Ser,ENST00000265425,; A ENST00000377850 Transcript missense_variant 1749/2524 1216/1437 406/478 A/S Gca/Tca 1 -1 SLC17A2 HGNC HGNC:10930 protein_coding YES CCDS69060.1 ENSP00000367081 O00624 UPI000052BFEE NM_001286123.1 tolerated(0.94) 11/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF193,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 25914666 25914666 C A 1 0 0 0 0 1 0 0 0 14682 724 25 2 2 SLC17A2 6 25914666 Missense_Mutation SNP C 11LU016_T 88188 25914666 144891313 162 214 MOG 0 . GRCh38 6 29666195 29666195 + Frame_Shift_Del DEL G G - rs148630553 11LU016_T 11LU016_N G G c.481delG p.Val161CysfsTer22 p.V161Cfs*22 ENST00000376898 3/8 296 253 43 344 344 0 sindel-varindel-pindel MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000376894,;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000376917,NM_206809.3;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000431798,NM_206812.3;MOG,frameshift_variant,p.Val45CysfsTer22,ENST00000376888,NM_206814.5;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000376898,NM_002433.4;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000494692,NM_206811.3;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000396701,NM_206810.3;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000376891,NM_001008229.2;MOG,frameshift_variant,p.Val161CysfsTer22,ENST00000396704,NM_001008228.2;MOG,frameshift_variant,p.Val45CysfsTer22,ENST00000490427,NM_001170418.1;MOG,frameshift_variant,p.Val45CysfsTer22,ENST00000483013,;MOG,intron_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000469603,;MOG,downstream_gene_variant,,ENST00000476244,;MOG,3_prime_UTR_variant,,ENST00000376889,;MOG,3_prime_UTR_variant,,ENST00000485211,;MOG,3_prime_UTR_variant,,ENST00000376903,;MOG,upstream_gene_variant,,ENST00000485885,; - ENST00000376898 Transcript frameshift_variant 480/1027 480/759 160/252 A/X gcG/gc rs148630553,COSM168100,COSM4391093 1 1 MOG HGNC HGNC:7197 protein_coding YES CCDS4667.1 ENSP00000366095 Q16653 UPI00004573E8 NM_002433.4 3/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24100,PIRSF_domain:PIRSF016522 0,1,1 HIGH 1 deletion 1 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 29666195 29666195 G - 1 0 1 0 1 0 0 0 0 9656 1103 39 0 0 MOG 6 29666195 Frame_Shift_Del DEL G 11LU016_T 3751529 29666195 141139784 163 215 GTF2H4 0 . GRCh38 6 30913818 30913818 + Silent SNP G G A rs754410511 11LU016_T 11LU016_N G G c.1224G>A p.= p.L408L ENST00000259895 14/14 52 40 12 56 56 0 strelka-varscan-mutect GTF2H4,synonymous_variant,p.=,ENST00000259895,NM_001517.4;GTF2H4,synonymous_variant,p.=,ENST00000376316,;VARS2,upstream_gene_variant,,ENST00000321897,NM_020442.5;VARS2,upstream_gene_variant,,ENST00000542001,;VARS2,upstream_gene_variant,,ENST00000541562,NM_001167734.1;VARS2,upstream_gene_variant,,ENST00000625423,NM_001167733.2;VARS2,upstream_gene_variant,,ENST00000428017,;VARS2,upstream_gene_variant,,ENST00000421263,;VARS2,upstream_gene_variant,,ENST00000467717,;GTF2H4,downstream_gene_variant,,ENST00000453897,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;GTF2H4,non_coding_transcript_exon_variant,,ENST00000483318,;GTF2H4,non_coding_transcript_exon_variant,,ENST00000475845,;VARS2,upstream_gene_variant,,ENST00000469358,;GTF2H4,downstream_gene_variant,,ENST00000487746,;VARS2,upstream_gene_variant,,ENST00000490699,; A ENST00000259895 Transcript synonymous_variant 1447/1735 1224/1389 408/462 L ctG/ctA rs754410511 1 1 GTF2H4 HGNC HGNC:4658 protein_coding YES CCDS34386.1 ENSP00000259895 Q92759 UPI000000D741 NM_001517.4 14/14 hmmpanther:PTHR13152,TIGRFAM_domain:TIGR00625 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 30913818 30913818 G A 1 0 0 0 0 0 0 0 1 6746 1364 48 3 3 GTF2H4 6 30913818 Silent SNP G 11LU016_T 1247623 30913818 139892161 164 216 PRRT1 0 . GRCh38 6 32149222 32149222 + Nonstop_Mutation SNP T T G 11LU016_T 11LU016_N T T c.921A>C p.Ter307TyrextTer107 p.*307Yext*107 ENST00000211413 4/4 194 172 22 181 181 0 strelka-varscan-mutect PRRT1,stop_lost,p.Ter307TyrextTer107,ENST00000211413,NM_030651.3;PRRT1,stop_lost,p.Ter226TyrextTer107,ENST00000375150,;PPT2,upstream_gene_variant,,ENST00000395523,;PPT2,upstream_gene_variant,,ENST00000324816,NM_001204103.1,NM_005155.6;PPT2,upstream_gene_variant,,ENST00000375137,;PPT2,upstream_gene_variant,,ENST00000361568,NM_138717.2;PPT2,upstream_gene_variant,,ENST00000375143,;PPT2,upstream_gene_variant,,ENST00000414204,;PPT2,upstream_gene_variant,,ENST00000424499,;PRRT1,downstream_gene_variant,,ENST00000428778,;PRRT1,non_coding_transcript_exon_variant,,ENST00000467780,;PRRT1,non_coding_transcript_exon_variant,,ENST00000472641,;PPT2,upstream_gene_variant,,ENST00000493548,;PRRT1,downstream_gene_variant,,ENST00000486917,;PPT2,upstream_gene_variant,,ENST00000478521,;PRRT1,downstream_gene_variant,,ENST00000485392,;PRRT1,downstream_gene_variant,,ENST00000498575,;PRRT1,downstream_gene_variant,,ENST00000497552,;PRRT1,downstream_gene_variant,,ENST00000475826,;PRRT1,downstream_gene_variant,,ENST00000494332,;PRRT1,non_coding_transcript_exon_variant,,ENST00000495191,;PPT2-EGFL8,upstream_gene_variant,,ENST00000422437,;PPT2-EGFL8,upstream_gene_variant,,ENST00000428388,;PPT2-EGFL8,upstream_gene_variant,,ENST00000585246,; G ENST00000211413 Transcript stop_lost 1046/1909 921/921 307/306 */Y taA/taC COSM351385 1 -1 PRRT1 HGNC HGNC:13943 protein_coding YES CCDS4739.1 ENSP00000211413 Q99946 UPI000012FFED NM_030651.3 4/4 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 2 32149222 32149222 T G 1 0 0 0 0 0 0 0 0 12755 1848 64 5 5 PRRT1 6 32149222 Nonstop_Mutation SNP T 11LU016_T 1235404 32149222 138656757 165 217 BRPF3 0 . GRCh38 6 36214161 36214161 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.2764G>T p.Gly922Cys p.G922C ENST00000357641 8/13 149 111 38 150 150 0 strelka-varscan-mutect BRPF3,missense_variant,p.Gly922Cys,ENST00000357641,NM_015695.2;BRPF3,missense_variant,p.Gly922Cys,ENST00000534400,;BRPF3,intron_variant,,ENST00000339717,;BRPF3,intron_variant,,ENST00000534694,;BRPF3,missense_variant,p.Gly133Cys,ENST00000441730,;BRPF3,3_prime_UTR_variant,,ENST00000441123,;BRPF3,3_prime_UTR_variant,,ENST00000532330,;BRPF3,intron_variant,,ENST00000449261,;BRPF3,downstream_gene_variant,,ENST00000532538,; T ENST00000357641 Transcript missense_variant 3017/6052 2764/3618 922/1205 G/C Ggt/Tgt 1 1 BRPF3 HGNC HGNC:14256 protein_coding YES CCDS34437.1 ENSP00000350267 Q9ULD4 UPI00001C1E4C NM_015695.2 deleterious(0.01) 8/13 hmmpanther:PTHR13793:SF19,hmmpanther:PTHR13793 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 36214161 36214161 G T 1 0 0 0 0 1 0 0 0 1695 1348 47 2 2 BRPF3 6 36214161 Missense_Mutation SNP G 11LU016_T 4064939 36214161 134591818 166 218 KIF6 0 . GRCh38 6 39639643 39639643 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.366G>C p.Arg122Ser p.R122S ENST00000287152 4/23 98 80 18 82 82 0 strelka-varscan-mutect KIF6,missense_variant,p.Arg122Ser,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,missense_variant,p.Arg14Ser,ENST00000458470,;KIF6,5_prime_UTR_variant,,ENST00000538893,;KIF6,downstream_gene_variant,,ENST00000482238,; G ENST00000287152 Transcript missense_variant 461/9082 366/2445 122/814 R/S agG/agC 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 deleterious(0) 4/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 39639643 39639643 C G 1 0 0 0 0 1 0 0 0 8173 854 30 4 4 KIF6 6 39639643 Missense_Mutation SNP C 11LU016_T 3425482 39639643 131166336 167 219 SLC22A7 0 . GRCh38 6 43298512 43298512 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.154C>A p.Pro52Thr p.P52T ENST00000372585 1/11 207 196 11 268 268 0 strelka-mutect SLC22A7,missense_variant,p.Pro52Thr,ENST00000372585,NM_153320.2;SLC22A7,missense_variant,p.Pro52Thr,ENST00000372589,NM_006672.3;SLC22A7,missense_variant,p.Pro52Thr,ENST00000372574,;SLC22A7,missense_variant,p.Pro52Thr,ENST00000449231,;SLC22A7,intron_variant,,ENST00000451757,;SLC22A7,upstream_gene_variant,,ENST00000436107,;CRIP3,downstream_gene_variant,,ENST00000416431,;SLC22A7,intron_variant,,ENST00000487175,;SLC22A7,intron_variant,,ENST00000480882,;SLC22A7,missense_variant,p.Pro52Thr,ENST00000498232,; A ENST00000372585 Transcript missense_variant 249/2555 154/1647 52/548 P/T Ccg/Acg 1 1 SLC22A7 HGNC HGNC:10971 protein_coding YES CCDS4893.2 ENSP00000361666 Q9Y694 UPI000006F307 NM_153320.2 deleterious(0.03) 1/11 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF33,TIGRFAM_domain:TIGR00898 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 43298512 43298512 C A 1 0 0 0 0 1 0 0 0 14725 739 26 2 2 SLC22A7 6 43298512 Missense_Mutation SNP C 11LU016_T 3658869 43298512 127507467 168 220 TJAP1 0 . GRCh38 6 43501684 43501684 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.287G>T p.Arg96Leu p.R96L ENST00000372445 6/11 105 94 11 165 163 2 strelka-varscan-mutect TJAP1,missense_variant,p.Arg54Leu,ENST00000454762,;TJAP1,missense_variant,p.Arg96Leu,ENST00000372444,NM_001146018.1;TJAP1,missense_variant,p.Arg96Leu,ENST00000372445,NM_001146016.1;TJAP1,missense_variant,p.Arg96Leu,ENST00000259751,NM_080604.2;TJAP1,missense_variant,p.Arg96Leu,ENST00000438588,NM_001146017.1;TJAP1,missense_variant,p.Arg96Leu,ENST00000372449,;TJAP1,missense_variant,p.Arg96Leu,ENST00000372452,NM_001146019.1;TJAP1,missense_variant,p.Arg96Leu,ENST00000436109,NM_001146020.1;TJAP1,missense_variant,p.Arg96Leu,ENST00000442878,;TJAP1,missense_variant,p.Arg96Leu,ENST00000372454,;TJAP1,3_prime_UTR_variant,,ENST00000612912,;TJAP1,non_coding_transcript_exon_variant,,ENST00000483640,;TJAP1,non_coding_transcript_exon_variant,,ENST00000490050,;TJAP1,non_coding_transcript_exon_variant,,ENST00000478173,;TJAP1,non_coding_transcript_exon_variant,,ENST00000459851,; T ENST00000372445 Transcript missense_variant 663/2751 287/1674 96/557 R/L cGc/cTc COSM1444735,COSM5156444 1 1 TJAP1 HGNC HGNC:17949 protein_coding YES CCDS55004.1 ENSP00000361522 Q5JTD0 UPI00004A3A96 NM_001146016.1 deleterious(0.03) 6/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR28664,hmmpanther:PTHR28664:SF3 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1382952411 . 0 208 0 2 0 0 0 0 -17.06577 0.9999999 1 1 1 0 T 3 4 2 43501684 43501684 G T 1 0 0 0 0 1 0 0 0 16370 1101 38 1 1 TJAP1 6 43501684 Missense_Mutation SNP G 11LU016_T 203172 43501684 127304295 169 221 EEF1A1 0 . GRCh38 6 73519881 73519881 + Splice_Site SNP A A G novel 11LU016_T 11LU016_N A A c.144+2T>C p.X48_splice ENST00000316292 99 85 14 100 100 0 strelka-varscan-mutect EEF1A1,splice_donor_variant,,ENST00000316292,NM_001402.5;EEF1A1,splice_donor_variant,,ENST00000615060,;EEF1A1,splice_donor_variant,,ENST00000610520,;EEF1A1,splice_donor_variant,,ENST00000309268,;EEF1A1,splice_donor_variant,,ENST00000331523,;EEF1A1,splice_donor_variant,,ENST00000455918,;EEF1A1,splice_donor_variant,,ENST00000356303,;RP11-505P4.7,upstream_gene_variant,,ENST00000429386,;RP11-505P4.7,upstream_gene_variant,,ENST00000431108,;EEF1A1,upstream_gene_variant,,ENST00000491404,;EEF1A1,splice_donor_variant,,ENST00000490569,;EEF1A1,splice_donor_variant,,ENST00000495333,;EEF1A1,splice_donor_variant,,ENST00000488500,; G ENST00000316292 Transcript splice_donor_variant -/4441 144/1389 48/462 1 -1 EEF1A1 HGNC HGNC:3189 protein_coding YES CCDS4980.1 ENSP00000339063 P68104 Q6IPS9 UPI00000012CA NM_001402.5 1/6 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 2 73519881 73519881 A G 1 0 0 0 0 0 0 1 0 4752 405 14 5 5 EEF1A1 6 73519881 Splice_Site SNP A 11LU016_T 30018197 73519881 97286098 170 222 COL12A1 0 . GRCh38 6 75183249 75183249 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1692G>T p.= p.L564L ENST00000322507 10/66 230 210 20 231 231 0 strelka-varscan-mutect COL12A1,synonymous_variant,p.=,ENST00000322507,NM_004370.5;COL12A1,synonymous_variant,p.=,ENST00000483888,;COL12A1,synonymous_variant,p.=,ENST00000416123,;COL12A1,5_prime_UTR_variant,,ENST00000615798,;COL12A1,intron_variant,,ENST00000345356,NM_080645.2;COL12A1,non_coding_transcript_exon_variant,,ENST00000486533,; A ENST00000322507 Transcript synonymous_variant 2002/11723 1692/9192 564/3063 L ctG/ctT 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 10/66 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF106,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 75183249 75183249 C A 1 0 0 0 0 0 0 0 1 3457 813 29 2 2 COL12A1 6 75183249 Silent SNP C 11LU016_T 1663368 75183249 95622730 171 223 SNAP91 0 . GRCh38 6 83605727 83605727 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1099C>A p.Pro367Thr p.P367T ENST00000439399 14/30 147 133 14 158 158 0 strelka-varscan-mutect SNAP91,missense_variant,p.Pro367Thr,ENST00000521485,;SNAP91,missense_variant,p.Pro367Thr,ENST00000439399,NM_014841.2;SNAP91,missense_variant,p.Pro367Thr,ENST00000369694,NM_001242792.1;SNAP91,missense_variant,p.Pro367Thr,ENST00000195649,NM_001256718.1;SNAP91,missense_variant,p.Pro367Thr,ENST00000521743,;SNAP91,missense_variant,p.Pro365Thr,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,missense_variant,p.Pro351Thr,ENST00000520213,NM_001242794.1;SNAP91,missense_variant,p.Pro365Thr,ENST00000521931,;SNAP91,missense_variant,p.Pro27Thr,ENST00000369691,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,; T ENST00000439399 Transcript missense_variant 1416/4452 1099/2724 367/907 P/T Cca/Aca 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 tolerated(0.06) 14/30 Low_complexity_(Seg):seg,hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4 MODERATE 1 SNV 5 1 PASS rs956062773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 83605727 83605727 G T 1 0 0 0 0 1 0 0 0 15154 1261 44 2 2 SNAP91 6 83605727 Missense_Mutation SNP G 11LU016_T 8422478 83605727 87200252 172 224 CEP162 0 . GRCh38 6 84215902 84215902 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.193A>T p.Ser65Cys p.S65C ENST00000403245 4/27 56 49 7 90 90 0 strelka-varscan-mutect CEP162,missense_variant,p.Ser65Cys,ENST00000403245,NM_014895.3;CEP162,5_prime_UTR_variant,,ENST00000617909,;CEP162,5_prime_UTR_variant,,ENST00000257766,NM_001286206.1;CEP162,non_coding_transcript_exon_variant,,ENST00000497936,;CEP162,3_prime_UTR_variant,,ENST00000435955,; A ENST00000403245 Transcript missense_variant 308/5156 193/4212 65/1403 S/C Agc/Tgc 1 -1 CEP162 HGNC HGNC:21107 protein_coding YES CCDS34494.2 ENSP00000385215 Q5TB80 UPI0001533DAA NM_014895.3 deleterious(0) 4/27 hmmpanther:PTHR34031 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -16.8217 1 1 1 1 0 A 3 1 2 84215902 84215902 T A 1 0 0 0 0 1 0 0 0 2962 1551 54 4 4 CEP162 6 84215902 Missense_Mutation SNP T 11LU016_T 610175 84215902 86590077 173 225 QRSL1 0 . GRCh38 6 106652479 106652479 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.746G>T p.Gly249Val p.G249V ENST00000369046 7/11 118 97 21 119 119 0 strelka-varscan-mutect QRSL1,missense_variant,p.Gly249Val,ENST00000369046,NM_018292.4;QRSL1,missense_variant,p.Gly249Val,ENST00000369044,; T ENST00000369046 Transcript missense_variant 850/4106 746/1587 249/528 G/V gGa/gTa 1 1 QRSL1 HGNC HGNC:21020 protein_coding YES CCDS5057.1 ENSP00000358042 Q9H0R6 UPI0000047463 NM_018292.4 deleterious(0) 7/11 HAMAP:MF_00120,hmmpanther:PTHR11895:SF7,hmmpanther:PTHR11895,TIGRFAM_domain:TIGR00132,Gene3D:3.90.1300.10,Pfam_domain:PF01425,Superfamily_domains:SSF75304 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 106652479 106652479 G T 1 0 0 0 0 1 0 0 0 13036 1174 41 2 2 QRSL1 6 106652479 Missense_Mutation SNP G 11LU016_T 22436577 106652479 64153500 174 226 TBC1D32 0 . GRCh38 6 121160959 121160959 + Missense_Mutation SNP A A C 11LU016_T 11LU016_N A A c.2668T>G p.Leu890Val p.L890V ENST00000398212 23/32 188 174 14 278 278 0 strelka-varscan-mutect TBC1D32,missense_variant,p.Leu931Val,ENST00000275159,;TBC1D32,missense_variant,p.Leu890Val,ENST00000398212,NM_152730.5;TBC1D32,non_coding_transcript_exon_variant,,ENST00000398197,;TBC1D32,non_coding_transcript_exon_variant,,ENST00000523345,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,;TBC1D32,upstream_gene_variant,,ENST00000509492,; C ENST00000398212 Transcript missense_variant 2718/3824 2668/3774 890/1257 L/V Tta/Gta COSM4570368 1 -1 TBC1D32 HGNC HGNC:21485 protein_coding YES CCDS43501.1 ENSP00000381270 Q96NH3 UPI0000E67203 NM_152730.5 tolerated(0.87) 23/32 Pfam_domain:PF14961,hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 121160959 121160959 A C 1 0 0 0 0 1 0 0 0 16022 40 2 5 5 TBC1D32 6 121160959 Missense_Mutation SNP A 11LU016_T 14508480 121160959 49645020 175 227 TCF21 0 . GRCh38 6 133889563 133889563 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.166C>A p.Leu56Met p.L56M ENST00000367882 1/2 368 295 73 377 377 0 strelka-varscan-mutect TCF21,missense_variant,p.Leu56Met,ENST00000367882,NM_003206.3;TCF21,missense_variant,p.Leu56Met,ENST00000237316,NM_198392.2;TARID,intron_variant,,ENST00000630728,;TARID,intron_variant,,ENST00000607641,;TARID,intron_variant,,ENST00000630119,;TARID,intron_variant,,ENST00000626104,;TARID,intron_variant,,ENST00000631362,;TARID,intron_variant,,ENST00000607573,;TARID,upstream_gene_variant,,ENST00000607033,;TARID,upstream_gene_variant,,ENST00000606544,; A ENST00000367882 Transcript missense_variant 426/4551 166/540 56/179 L/M Ctg/Atg COSM740034 1 1 TCF21 HGNC HGNC:11632 protein_coding YES CCDS5167.1 ENSP00000356857 O43680 UPI0000001290 NM_003206.3 tolerated(0.22) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23349:SF67,hmmpanther:PTHR23349 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 133889563 133889563 C A 1 0 0 0 0 1 0 0 0 16098 680 24 2 2 TCF21 6 133889563 Missense_Mutation SNP C 11LU016_T 12728604 133889563 36916416 176 228 MYB 0 . GRCh38 6 135194406 135194406 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.894A>T p.Leu298Phe p.L298F ENST00000341911 8/16 93 84 9 158 158 0 strelka-varscan-mutect MYB,missense_variant,p.Leu298Phe,ENST00000341911,NM_001130173.1;MYB,missense_variant,p.Leu298Phe,ENST00000616088,;MYB,missense_variant,p.Leu298Phe,ENST00000316528,;MYB,missense_variant,p.Leu298Phe,ENST00000618728,;MYB,missense_variant,p.Leu298Phe,ENST00000442647,NM_001130172.1;MYB,missense_variant,p.Leu298Phe,ENST00000367814,NM_005375.2;MYB,missense_variant,p.Leu298Phe,ENST00000525369,NM_001161657.1;MYB,missense_variant,p.Leu298Phe,ENST00000527615,;MYB,missense_variant,p.Leu298Phe,ENST00000528774,NM_001161656.1;MYB,missense_variant,p.Leu298Phe,ENST00000534121,NM_001161658.1;MYB,missense_variant,p.Leu298Phe,ENST00000534044,NM_001161659.1;MYB,missense_variant,p.Leu274Phe,ENST00000420123,;MYB,missense_variant,p.Leu252Phe,ENST00000430686,;MYB,intron_variant,,ENST00000533624,NM_001161660.1;MYB-AS1,downstream_gene_variant,,ENST00000455534,;MYB,non_coding_transcript_exon_variant,,ENST00000531845,;MYB,missense_variant,p.Leu298Phe,ENST00000367812,;MYB,missense_variant,p.Leu298Phe,ENST00000533837,;MYB,missense_variant,p.Leu298Phe,ENST00000438901,;MYB,missense_variant,p.Leu298Phe,ENST00000525477,;MYB,missense_variant,p.Leu298Phe,ENST00000463282,;MYB,missense_variant,p.Leu298Phe,ENST00000339290,;MYB,missense_variant,p.Leu298Phe,ENST00000533808,;MYB,missense_variant,p.Leu298Phe,ENST00000525514,;MYB,missense_variant,p.Leu298Phe,ENST00000529586,;MYB,missense_variant,p.Leu298Phe,ENST00000526889,;MYB,missense_variant,p.Leu298Phe,ENST00000526320,;MYB,missense_variant,p.Leu298Phe,ENST00000531519,;MYB,missense_variant,p.Leu298Phe,ENST00000533384,;MYB,missense_variant,p.Leu298Phe,ENST00000531737,;MYB,missense_variant,p.Leu298Phe,ENST00000529262,;MYB,missense_variant,p.Leu298Phe,ENST00000526565,;MYB,missense_variant,p.Leu298Phe,ENST00000528015,;MYB,missense_variant,p.Leu298Phe,ENST00000526187,;MYB,missense_variant,p.Leu298Phe,ENST00000525002,;MYB,missense_variant,p.Leu298Phe,ENST00000528343,;MYB,missense_variant,p.Leu298Phe,ENST00000528140,;MYB,missense_variant,p.Leu274Phe,ENST00000528345,;MYB,missense_variant,p.Leu298Phe,ENST00000525940,;MYB,3_prime_UTR_variant,,ENST00000531634,;MYB,3_prime_UTR_variant,,ENST00000524588,;MYB,upstream_gene_variant,,ENST00000534736,; T ENST00000341911 Transcript missense_variant 1093/3672 894/2286 298/761 L/F ttA/ttT 1 1 MYB HGNC HGNC:7545 protein_coding YES CCDS47481.1 ENSP00000339992 P10242 UPI000002AE9A NM_001130173.1 deleterious(0) 8/16 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF07988,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.39329 0.9999998 1 1 1 0 T 3 4 2 135194406 135194406 A T 1 0 0 0 0 1 0 0 0 10007 417 15 4 4 MYB 6 135194406 Missense_Mutation SNP A 11LU016_T 1304843 135194406 35611573 177 229 HIVEP2 0 . GRCh38 6 142764910 142764910 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.5407G>T p.Glu1803Ter p.E1803* ENST00000367603 7/10 131 108 23 210 210 0 strelka-varscan-mutect HIVEP2,stop_gained,p.Glu1803Ter,ENST00000367603,NM_006734.3;HIVEP2,stop_gained,p.Glu1803Ter,ENST00000367604,;HIVEP2,stop_gained,p.Glu1803Ter,ENST00000012134,; A ENST00000367603 Transcript stop_gained 6150/9723 5407/7341 1803/2446 E/* Gaa/Taa 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 7/10 PROSITE_profiles:PS50157,hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 142764910 142764910 C A 1 0 0 0 0 0 1 0 0 7076 922 32 2 2 HIVEP2 6 142764910 Nonsense_Mutation SNP C 11LU016_T 7570504 142764910 28041069 178 230 EPM2A 0 . GRCh38 6 145625714 145625714 + Missense_Mutation SNP T T A rs757334796 11LU016_T 11LU016_N T T c.935A>T p.Gln312Leu p.Q312L ENST00000618445 5/5 338 272 66 290 290 0 strelka-varscan-mutect EPM2A,missense_variant,p.Gln312Leu,ENST00000618445,NM_001018041.1;EPM2A,missense_variant,p.Gln232Leu,ENST00000435470,;EPM2A,3_prime_UTR_variant,,ENST00000611340,;EPM2A,3_prime_UTR_variant,,ENST00000367519,NM_005670.3;EPM2A,intron_variant,,ENST00000450221,; A ENST00000618445 Transcript missense_variant 1292/1694 935/954 312/317 Q/L cAg/cTg rs757334796 1 -1 EPM2A HGNC HGNC:3413 protein_coding ENSP00000480339 O95278 UPI00003BF71F NM_001018041.1 deleterious_low_confidence(0.01) 5/5 hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF326 MODERATE SNV 1 1 PASS rs757334796 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 145625714 145625714 T A 1 0 0 0 0 1 0 0 0 5030 1580 55 4 4 EPM2A 6 145625714 Missense_Mutation SNP T 11LU016_T 2860804 145625714 25180265 179 231 PCMT1 0 . GRCh38 6 149749764 149749764 + Missense_Mutation SNP G G A rs778241850 11LU016_T 11LU016_N G G c.37G>A p.Gly13Ser p.G13S ENST00000367384 1/8 93 81 12 107 107 0 strelka-varscan-mutect PCMT1,missense_variant,p.Gly13Ser,ENST00000464889,NM_005389.2;PCMT1,missense_variant,p.Gly13Ser,ENST00000367384,NM_001252052.1,NM_001252049.1;PCMT1,missense_variant,p.Gly13Ser,ENST00000367380,NM_001252051.1;PCMT1,missense_variant,p.Gly13Ser,ENST00000544496,NM_001252050.1;PCMT1,missense_variant,p.Gly13Ser,ENST00000367378,NM_001252053.1;NUP43,upstream_gene_variant,,ENST00000340413,NM_198887.2;NUP43,upstream_gene_variant,,ENST00000367404,;NUP43,upstream_gene_variant,,ENST00000543637,;PCMT1,upstream_gene_variant,,ENST00000495487,;NUP43,upstream_gene_variant,,ENST00000463048,;PCMT1,missense_variant,p.Gly13Ser,ENST00000484601,;PCMT1,missense_variant,p.Gly13Ser,ENST00000494411,;PCMT1,missense_variant,p.Gly13Ser,ENST00000460828,;NUP43,upstream_gene_variant,,ENST00000403890,;NUP43,upstream_gene_variant,,ENST00000367402,;PCMT1,upstream_gene_variant,,ENST00000486585,; A ENST00000367384 Transcript missense_variant 322/1938 37/861 13/286 G/S Ggc/Agc rs778241850 1 1 PCMT1 HGNC HGNC:8728 protein_coding YES CCDS59041.1 ENSP00000356354 H7BY58 UPI0001B7942B NM_001252052.1,NM_001252049.1 deleterious_low_confidence(0) 1/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs778241850 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 149749764 149749764 G A 1 0 0 0 0 1 0 0 0 11673 1116 39 1 1 PCMT1 6 149749764 Missense_Mutation SNP G 11LU016_T 4124050 149749764 21056215 180 232 FNDC1 0 . GRCh38 6 159229834 159229834 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1200C>A p.= p.A400A ENST00000297267 10/23 75 69 6 84 83 1 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,intron_variant,,ENST00000329629,;FNDC1,downstream_gene_variant,,ENST00000480856,; A ENST00000297267 Transcript synonymous_variant 1400/6552 1200/5685 400/1894 A gcC/gcA 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 10/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.30978 1 1 1 1 0 A 2 1 2 159229834 159229834 C A 1 0 0 0 0 0 0 0 1 5824 610 22 2 2 FNDC1 6 159229834 Silent SNP C 11LU016_T 9480070 159229834 11576145 181 233 WTAP 0 . GRCh38 6 159755471 159755471 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.1051C>T p.His351Tyr p.H351Y ENST00000358372 8/8 252 238 14 273 273 0 strelka-varscan-mutect WTAP,missense_variant,p.His351Tyr,ENST00000358372,NM_004906.4;WTAP,missense_variant,p.His351Tyr,ENST00000621533,NM_001270531.1;SOD2,intron_variant,,ENST00000546087,NM_001322817.1;ACAT2,upstream_gene_variant,,ENST00000367048,NM_005891.2;SOD2,downstream_gene_variant,,ENST00000535372,; T ENST00000358372 Transcript missense_variant 2808/3656 1051/1191 351/396 H/Y Cac/Tac 1 1 WTAP HGNC HGNC:16846 protein_coding YES CCDS5266.1 ENSP00000351141 Q15007 UPI0000070280 NM_004906.4 deleterious_low_confidence(0.01) 8/8 hmmpanther:PTHR15217:SF0,hmmpanther:PTHR15217 MODERATE 1 SNV 1 1 PASS rs1347940126 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 159755471 159755471 C T 1 0 0 0 0 1 0 0 0 17966 478 17 3 3 WTAP 6 159755471 Missense_Mutation SNP C 11LU016_T 525637 159755471 11050508 182 234 PLG 0 . GRCh38 6 160706523 160706523 + Missense_Mutation SNP G G T rs770158666 11LU016_T 11LU016_N G G c.166G>T p.Asp56Tyr p.D56Y ENST00000308192 2/19 184 168 16 159 159 0 strelka-varscan-mutect PLG,missense_variant,p.Asp56Tyr,ENST00000308192,NM_000301.3;PLG,missense_variant,p.Asp56Tyr,ENST00000366924,NM_001168338.1;PLG,missense_variant,p.Asp56Tyr,ENST00000418964,;PLG,non_coding_transcript_exon_variant,,ENST00000462918,;PLG,non_coding_transcript_exon_variant,,ENST00000494325,;PLG,non_coding_transcript_exon_variant,,ENST00000483038,;PLG,intron_variant,,ENST00000297289,;PLG,non_coding_transcript_exon_variant,,ENST00000484367,;PLG,non_coding_transcript_exon_variant,,ENST00000471691,; T ENST00000308192 Transcript missense_variant 229/2741 166/2433 56/810 D/Y Gac/Tac rs770158666 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 deleterious(0) 2/19 Gene3D:3.50.4.10,Pfam_domain:PF00024,PIRSF_domain:PIRSF001150,PROSITE_profiles:PS50948,Low_complexity_(Seg):seg,SMART_domains:SM00473,Superfamily_domains:SSF57414 MODERATE 1 SNV 1 1 PASS rs770158666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 160706523 160706523 G T 1 0 0 0 0 1 0 0 0 12181 1174 41 2 2 PLG 6 160706523 Missense_Mutation SNP G 11LU016_T 951052 160706523 10099456 183 235 MAP3K4 0 . GRCh38 6 161048896 161048896 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.624A>T p.Arg208Ser p.R208S ENST00000392142 3/27 215 198 17 187 187 0 strelka-varscan-mutect MAP3K4,missense_variant,p.Arg208Ser,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,missense_variant,p.Arg208Ser,ENST00000366920,NM_001301072.1;MAP3K4,missense_variant,p.Arg208Ser,ENST00000366919,NM_006724.3;MAP3K4,missense_variant,p.Arg208Ser,ENST00000348824,;MAP3K4,downstream_gene_variant,,ENST00000446500,;MAP3K4,missense_variant,p.Arg208Ser,ENST00000490904,;MAP3K4,missense_variant,p.Arg208Ser,ENST00000544041,;MAP3K4,intron_variant,,ENST00000542952,; T ENST00000392142 Transcript missense_variant 772/5490 624/4827 208/1608 R/S agA/agT 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 deleterious(0) 3/27 MODERATE 1 SNV 1 1 PASS rs1205826086 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 161048896 161048896 A T 1 0 0 0 0 1 0 0 0 9175 272 10 4 4 MAP3K4 6 161048896 Missense_Mutation SNP A 11LU016_T 342373 161048896 9757083 184 236 MAP3K4 0 . GRCh38 6 161049811 161049811 + Silent SNP A A T rs770545383 11LU016_T 11LU016_N A A c.1539A>T p.= p.T513T ENST00000392142 3/27 171 157 14 149 149 0 strelka-varscan-mutect MAP3K4,synonymous_variant,p.=,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,synonymous_variant,p.=,ENST00000366920,NM_001301072.1;MAP3K4,synonymous_variant,p.=,ENST00000366919,NM_006724.3;MAP3K4,synonymous_variant,p.=,ENST00000348824,;MAP3K4,downstream_gene_variant,,ENST00000446500,;MAP3K4,synonymous_variant,p.=,ENST00000490904,;MAP3K4,synonymous_variant,p.=,ENST00000544041,;MAP3K4,intron_variant,,ENST00000542952,; T ENST00000392142 Transcript synonymous_variant 1687/5490 1539/4827 513/1608 T acA/acT rs770545383 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 3/27 LOW 1 SNV 1 1 PASS rs770545383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 161049811 161049811 A T 1 0 0 0 0 0 0 0 1 9175 175 7 4 4 MAP3K4 6 161049811 Silent SNP A 11LU016_T 915 161049811 9756168 185 237 GPR31 0 . GRCh38 6 167157006 167157006 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.826G>T p.Val276Leu p.V276L ENST00000366834 1/1 236 208 28 351 351 0 strelka-varscan-mutect GPR31,missense_variant,p.Val276Leu,ENST00000366834,NM_005299.2;TCP10L2,intron_variant,,ENST00000486697,;TCP10L2,intron_variant,,ENST00000539001,; A ENST00000366834 Transcript missense_variant 1324/2059 826/960 276/319 V/L Gtg/Ttg 1 -1 GPR31 HGNC HGNC:4486 protein_coding YES CCDS5299.1 ENSP00000355799 O00270 UPI000007390A NM_005299.2 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24231:SF37,hmmpanther:PTHR24231,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 167157006 167157006 C A 1 0 0 0 0 1 0 0 0 6571 478 17 2 2 GPR31 6 167157006 Missense_Mutation SNP C 11LU016_T 6107195 167157006 3648973 186 238 TTLL2 0 . GRCh38 6 167341545 167341545 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1645C>A p.Pro549Thr p.P549T ENST00000239587 3/3 313 290 23 360 359 1 strelka-varscan-mutect TTLL2,missense_variant,p.Pro549Thr,ENST00000239587,NM_031949.4;TTLL2,missense_variant,p.Pro549Thr,ENST00000515138,;TTLL2,downstream_gene_variant,,ENST00000512917,; A ENST00000239587 Transcript missense_variant 1733/2075 1645/1779 549/592 P/T Cca/Aca 1 1 TTLL2 HGNC HGNC:21211 protein_coding YES CCDS5301.1 ENSP00000239587 Q9BWV7 UPI00001A3A8B NM_031949.4 deleterious(0.02) 3/3 hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 167341545 167341545 C A 1 0 0 0 0 1 0 0 0 17238 855 30 2 2 TTLL2 6 167341545 Missense_Mutation SNP C 11LU016_T 184539 167341545 3464434 187 239 KIF25 0 . GRCh38 6 168040188 168040188 + Silent SNP A A G novel 11LU016_T 11LU016_N A A c.618A>G p.= p.L206L ENST00000443060 7/10 131 115 16 139 139 0 strelka-varscan-mutect KIF25,synonymous_variant,p.=,ENST00000443060,;KIF25,synonymous_variant,p.=,ENST00000354419,NM_030615.2;KIF25,synonymous_variant,p.=,ENST00000351261,NM_005355.3;KIF25,downstream_gene_variant,,ENST00000496008,;KIF25,downstream_gene_variant,,ENST00000504593,; G ENST00000443060 Transcript synonymous_variant 1009/1613 618/1155 206/384 L ctA/ctG 1 1 KIF25 HGNC HGNC:6390 protein_coding YES CCDS5305.1 ENSP00000388878 Q9UIL4 UPI000012DDAB 7/10 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF421,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 168040188 168040188 A G 1 0 0 0 0 0 0 0 1 8158 349 13 5 5 KIF25 6 168040188 Silent SNP A 11LU016_T 698643 168040188 2765791 188 240 DLL1 0 . GRCh38 6 170283431 170283431 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1848C>A p.Asn616Lys p.N616K ENST00000366756 9/11 595 541 54 722 722 0 strelka-varscan-mutect DLL1,missense_variant,p.Asn616Lys,ENST00000366756,NM_005618.3;LINC01624,downstream_gene_variant,,ENST00000607074,;LINC01624,downstream_gene_variant,,ENST00000438622,;LINC01624,downstream_gene_variant,,ENST00000422894,; T ENST00000366756 Transcript missense_variant 2182/3174 1848/2172 616/723 N/K aaC/aaA 1 -1 DLL1 HGNC HGNC:2908 protein_coding YES CCDS5313.1 ENSP00000355718 O00548 UPI000004C656 NM_005618.3 deleterious(0) 9/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 170283431 170283431 G T 1 0 0 0 0 1 0 0 0 4373 1368 48 2 2 DLL1 6 170283431 Missense_Mutation SNP G 11LU016_T 2243243 170283431 522548 189 241 PRKAR1B 0 . GRCh38 7 711475 711475 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.31G>T p.Glu11Ter p.E11* ENST00000406797 2/11 237 217 20 164 163 1 strelka-varscan-mutect PRKAR1B,stop_gained,p.Glu11Ter,ENST00000406797,NM_001164761.1;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000537384,NM_001164760.1;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000544935,NM_001164759.1,NM_001164762.1;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000360274,NM_002735.2;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000403562,NM_001164758.1;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000430040,;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000417852,;PRKAR1B,stop_gained,p.Glu11Ter,ENST00000456696,;PRKAR1B,non_coding_transcript_exon_variant,,ENST00000488474,; A ENST00000406797 Transcript stop_gained 206/2553 31/1146 11/381 E/* Gag/Tag 1 -1 PRKAR1B HGNC HGNC:9390 protein_coding YES CCDS34579.1 ENSP00000385749 P31321 UPI000021C478 NM_001164761.1 2/11 hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF126 HIGH 1 SNV 1 1 PASS rs954428465 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 711475 711475 C A 1 0 0 0 0 0 1 0 0 12637 864 30 2 2 PRKAR1B 7 711475 Nonsense_Mutation SNP C 11LU016_T 711475 158634498 190 242 UNCX 0 . GRCh38 7 1236526 1236526 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1145C>A p.Pro382His p.P382H ENST00000316333 3/3 160 117 43 173 173 0 strelka-varscan-mutect UNCX,missense_variant,p.Pro382His,ENST00000316333,NM_001080461.1; A ENST00000316333 Transcript missense_variant 1256/2048 1145/1596 382/531 P/H cCc/cAc 1 1 UNCX HGNC HGNC:33194 protein_coding YES CCDS34583.1 ENSP00000314480 A6NJT0 UPI0000D61BE6 NM_001080461.1 deleterious(0) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1236526 1236526 C A 1 0 0 0 0 1 0 0 0 17524 623 22 2 2 UNCX 7 1236526 Missense_Mutation SNP C 11LU016_T 525051 1236526 158109447 191 243 IQCE 0 . GRCh38 7 2594932 2594932 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.1396A>G p.Met466Val p.M466V ENST00000476665 16/21 291 266 25 148 148 0 strelka-varscan-mutect IQCE,missense_variant,p.Met466Val,ENST00000402050,NM_152558.4;IQCE,missense_variant,p.Met401Val,ENST00000623361,NM_001287501.1,NM_001287502.1;IQCE,missense_variant,p.Met466Val,ENST00000476665,NM_001287499.1;IQCE,missense_variant,p.Met450Val,ENST00000611775,NM_001287500.1;IQCE,missense_variant,p.Met401Val,ENST00000325979,;IQCE,missense_variant,p.Met450Val,ENST00000438376,;IQCE,missense_variant,p.Met415Val,ENST00000404984,;IQCE,upstream_gene_variant,,ENST00000423196,;IQCE,downstream_gene_variant,,ENST00000427817,;IQCE,upstream_gene_variant,,ENST00000486730,;IQCE,3_prime_UTR_variant,,ENST00000325997,;IQCE,non_coding_transcript_exon_variant,,ENST00000470731,;IQCE,non_coding_transcript_exon_variant,,ENST00000490913,; G ENST00000476665 Transcript missense_variant 1499/2400 1396/2109 466/702 M/V Atg/Gtg 1 1 IQCE HGNC HGNC:29171 protein_coding YES CCDS75559.1 ENSP00000480715 A0A087WX45 UPI0000EE76A1 NM_001287499.1 tolerated(0.35) 16/21 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22590 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 2594932 2594932 A G 1 0 0 0 0 1 0 0 0 7710 101 4 5 5 IQCE 7 2594932 Missense_Mutation SNP A 11LU016_T 1358406 2594932 156751041 192 244 TTYH3 0 . GRCh38 7 2658307 2658307 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1272G>T p.Glu424Asp p.E424D ENST00000258796 12/14 79 51 28 48 48 0 strelka-varscan-mutect TTYH3,missense_variant,p.Glu424Asp,ENST00000258796,NM_025250.2;TTYH3,missense_variant,p.Glu392Asp,ENST00000407643,;TTYH3,missense_variant,p.Glu253Asp,ENST00000403167,;TTYH3,missense_variant,p.Glu84Asp,ENST00000429448,;TTYH3,non_coding_transcript_exon_variant,,ENST00000498454,; T ENST00000258796 Transcript missense_variant 1477/4840 1272/1572 424/523 E/D gaG/gaT 1 1 TTYH3 HGNC HGNC:22222 protein_coding YES CCDS34588.1 ENSP00000258796 Q9C0H2 A0A024R816 UPI000020E9F9 NM_025250.2 tolerated(0.77) 12/14 Pfam_domain:PF04906,hmmpanther:PTHR12424,hmmpanther:PTHR12424:SF4 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 2658307 2658307 G T 1 0 0 0 0 1 0 0 0 17251 991 35 2 2 TTYH3 7 2658307 Missense_Mutation SNP G 11LU016_T 63375 2658307 156687666 193 245 SDK1 0 . GRCh38 7 3967409 3967409 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1521C>A p.= p.P507P ENST00000404826 10/45 218 190 28 175 175 0 strelka-varscan-mutect SDK1,synonymous_variant,p.=,ENST00000404826,NM_152744.3;SDK1,synonymous_variant,p.=,ENST00000615806,;SDK1,synonymous_variant,p.=,ENST00000389531,;SDK1,upstream_gene_variant,,ENST00000484011,; A ENST00000404826 Transcript synonymous_variant 1660/10397 1521/6642 507/2213 P ccC/ccA 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 10/45 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 3967409 3967409 C A 1 0 0 0 0 0 0 0 1 14243 581 21 2 2 SDK1 7 3967409 Silent SNP C 11LU016_T 1309102 3967409 155378564 194 246 SDK1 0 . GRCh38 7 4145863 4145863 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.4370G>T p.Arg1457Met p.R1457M ENST00000404826 29/45 173 143 30 173 173 0 strelka-varscan-mutect SDK1,missense_variant,p.Arg1457Met,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Arg1457Met,ENST00000615806,;SDK1,missense_variant,p.Arg1457Met,ENST00000389531,;SDK1,non_coding_transcript_exon_variant,,ENST00000476701,; T ENST00000404826 Transcript missense_variant 4509/10397 4370/6642 1457/2213 R/M aGg/aTg COSM5192792 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0) 29/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 4145863 4145863 G T 1 0 0 0 0 1 0 0 0 14243 1000 35 2 2 SDK1 7 4145863 Missense_Mutation SNP G 11LU016_T 178454 4145863 155200110 195 247 MMD2 0 . GRCh38 7 4911210 4911210 + Missense_Mutation SNP G G T rs770493219 11LU016_T 11LU016_N G G c.402C>A p.His134Gln p.H134Q ENST00000404774 5/7 337 287 50 210 210 0 strelka-varscan-mutect MMD2,missense_variant,p.His134Gln,ENST00000404774,NM_001100600.1;MMD2,missense_variant,p.His134Gln,ENST00000406755,NM_001270375.1;MMD2,missense_variant,p.His134Gln,ENST00000401401,NM_198403.3;MMD2,missense_variant,p.His134Gln,ENST00000612910,; T ENST00000404774 Transcript missense_variant 597/2415 402/813 134/270 H/Q caC/caA rs770493219 1 -1 MMD2 HGNC HGNC:30133 protein_coding YES CCDS47529.1 ENSP00000384690 Q8IY49 UPI000016199F NM_001100600.1 deleterious(0.05) 5/7 hmmpanther:PTHR20855:SF21,hmmpanther:PTHR20855,Pfam_domain:PF03006 MODERATE 1 SNV 1 1 PASS rs770493219 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 4911210 4911210 G T 1 0 0 0 0 1 0 0 0 9607 1368 48 2 2 MMD2 7 4911210 Missense_Mutation SNP G 11LU016_T 765347 4911210 154434763 196 248 MEOX2 0 . GRCh38 7 15686332 15686333 + Frame_Shift_Ins INS - - G novel 11LU016_T 11LU016_N - - c.70dupC p.Gln24ProfsTer11 p.Q24Pfs*11 ENST00000262041 1/3 247 230 17 154 153 1 varindel-pindel MEOX2,frameshift_variant,p.Gln24ProfsTer11,ENST00000262041,NM_005924.4;MEOX2-AS1,upstream_gene_variant,,ENST00000442176,;AC005550.5,downstream_gene_variant,,ENST00000438923,;AC005550.3,downstream_gene_variant,,ENST00000451240,; G ENST00000262041 Transcript frameshift_variant 480-481/2500 70-71/915 24/304 Q/PX caa/cCaa 1 -1 MEOX2 HGNC HGNC:7014 protein_coding YES CCDS34605.1 ENSP00000262041 P50222 UPI000013D247 NM_005924.4 1/3 hmmpanther:PTHR24328,hmmpanther:PTHR24328:SF1 HIGH 1 insertion 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.92061 0.9999996 1 1 1 0 G 7 5 2 15686332 15686332 - G 1 0 1 1 0 0 0 0 0 9419 1812 63 0 0 MEOX2 7 15686332 Frame_Shift_Ins INS - 11LU016_T 10775122 15686332 143659641 197 249 HDAC9 0 . GRCh38 7 18835473 18835473 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.2473C>T p.His825Tyr p.H825Y ENST00000441542 19/25 103 91 12 74 74 0 strelka-varscan-mutect HDAC9,missense_variant,p.His822Tyr,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.His781Tyr,ENST00000401921,;HDAC9,missense_variant,p.His825Tyr,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.His822Tyr,ENST00000432645,NM_058176.2;HDAC9,upstream_gene_variant,,ENST00000483142,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000490851,; T ENST00000441542 Transcript missense_variant 2473/3210 2473/3210 825/1069 H/Y Cac/Tac 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0) 19/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,Gene3D:3.40.800.20,Pfam_domain:PF00850,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768,Prints_domain:PR01270 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 2 18835473 18835473 C T 1 0 0 0 0 1 0 0 0 6901 826 29 3 3 HDAC9 7 18835473 Missense_Mutation SNP C 11LU016_T 3149141 18835473 140510500 198 250 ITGB8 0 . GRCh38 7 20379266 20379266 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.604A>G p.Ile202Val p.I202V ENST00000222573 4/14 180 149 31 118 116 2 strelka-varscan-mutect ITGB8,missense_variant,p.Ile202Val,ENST00000222573,NM_002214.2;ITGB8,missense_variant,p.Ile67Val,ENST00000537992,;SNORD56,downstream_gene_variant,,ENST00000363883,;ITGB8,non_coding_transcript_exon_variant,,ENST00000477859,;ITGB8,non_coding_transcript_exon_variant,,ENST00000478974,; G ENST00000222573 Transcript missense_variant 1288/8751 604/2310 202/769 I/V Atc/Gtc 1 1 ITGB8 HGNC HGNC:6163 protein_coding YES CCDS5370.1 ENSP00000222573 P26012 UPI000012DA14 NM_002214.2 tolerated(0.92) 4/14 hmmpanther:PTHR10082:SF9,hmmpanther:PTHR10082,Gene3D:3.40.50.410,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,SMART_domains:SM00187,Superfamily_domains:SSF53300,Prints_domain:PR01186 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 20379266 20379266 A G 1 0 0 0 0 1 0 0 0 7807 217 8 5 5 ITGB8 7 20379266 Missense_Mutation SNP A 11LU016_T 1543793 20379266 138966707 199 251 RAPGEF5 0 . GRCh38 7 22160606 22160606 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.979A>G p.Arg327Gly p.R327G ENST00000344041 14/26 96 75 21 66 66 0 strelka-varscan-mutect RAPGEF5,missense_variant,p.Arg327Gly,ENST00000344041,NM_012294.3;RAPGEF5,missense_variant,p.Arg177Gly,ENST00000401957,;RAPGEF5,missense_variant,p.Arg177Gly,ENST00000620335,;RAPGEF5,missense_variant,p.Arg65Gly,ENST00000458533,;RAPGEF5,3_prime_UTR_variant,,ENST00000451559,; C ENST00000344041 Transcript missense_variant 1292/6621 979/2193 327/730 R/G Agg/Ggg 1 -1 RAPGEF5 HGNC HGNC:16862 protein_coding YES CCDS55093.1 ENSP00000343656 A8MQ07 UPI0000EA87E4 NM_012294.3 tolerated(0.34) 14/26 PROSITE_profiles:PS50212,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF26,Gene3D:2ii0A01,SMART_domains:SM00229,Superfamily_domains:0041591 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 22160606 22160606 T C 1 0 0 0 0 1 0 0 0 13206 1521 53 5 5 RAPGEF5 7 22160606 Missense_Mutation SNP T 11LU016_T 1781340 22160606 137185367 200 252 IL6 0 . GRCh38 7 22729554 22729554 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.365T>C p.Phe122Ser p.F122S ENST00000404625 5/6 195 177 18 135 135 0 varscan-mutect IL6,missense_variant,p.Phe122Ser,ENST00000404625,;IL6,missense_variant,p.Phe122Ser,ENST00000258743,NM_000600.3;IL6,missense_variant,p.Phe46Ser,ENST00000407492,NM_001318095.1;IL6,missense_variant,p.Phe99Ser,ENST00000401630,;IL6,missense_variant,p.Phe122Ser,ENST00000406575,;IL6,missense_variant,p.Phe122Ser,ENST00000426291,;IL6,missense_variant,p.Phe46Ser,ENST00000401651,;AC073072.5,upstream_gene_variant,,ENST00000325042,;IL6,non_coding_transcript_exon_variant,,ENST00000485300,;IL6,non_coding_transcript_exon_variant,,ENST00000464710,; C ENST00000404625 Transcript missense_variant 824/1527 365/639 122/212 F/S tTt/tCt 1 1 IL6 HGNC HGNC:6018 protein_coding YES CCDS5375.1 ENSP00000385675 P05231 Q75MH2 UPI000002C4A6 deleterious(0) 5/6 hmmpanther:PTHR11457:SF0,hmmpanther:PTHR11457,PROSITE_patterns:PS00254,PIRSF_domain:PIRSF001935,Pfam_domain:PF00489,Gene3D:1.20.1250.10,SMART_domains:SM00126,Superfamily_domains:SSF47266,Prints_domain:PR00433,Prints_domain:PR00434 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 22729554 22729554 T C 1 0 0 0 0 1 0 0 0 7605 1841 64 5 5 IL6 7 22729554 Missense_Mutation SNP T 11LU016_T 568948 22729554 136616419 201 253 INMT 0 . GRCh38 7 30755589 30755589 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.530G>T p.Arg177Leu p.R177L ENST00000013222 3/3 299 239 60 202 202 0 strelka-varscan-mutect INMT,missense_variant,p.Arg177Leu,ENST00000013222,NM_006774.4;INMT,missense_variant,p.Arg176Leu,ENST00000409539,NM_001199219.1;INMT,non_coding_transcript_exon_variant,,ENST00000484180,;INMT-FAM188B,intron_variant,,ENST00000458257,;INMT-FAM188B,intron_variant,,ENST00000451002,; T ENST00000013222 Transcript missense_variant 546/2559 530/792 177/263 R/L cGc/cTc 1 1 INMT HGNC HGNC:6069 protein_coding YES CCDS5430.1 ENSP00000013222 O95050 UPI000013C526 NM_006774.4 deleterious(0.01) 3/3 Gene3D:3.40.50.150,Pfam_domain:PF01234,PIRSF_domain:PIRSF000384,PROSITE_profiles:PS51681,hmmpanther:PTHR10867,hmmpanther:PTHR10867:SF6,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS rs996421042 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 30755589 30755589 G T 1 0 0 0 0 1 0 0 0 7648 1087 38 1 1 INMT 7 30755589 Missense_Mutation SNP G 11LU016_T 8026035 30755589 128590384 202 254 PPP1R17 0 . GRCh38 7 31697072 31697072 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.343A>T p.Arg115Trp p.R115W ENST00000342032 4/5 245 207 38 149 149 0 strelka-varscan-mutect PPP1R17,missense_variant,p.Arg115Trp,ENST00000342032,NM_006658.4;PPP1R17,missense_variant,p.Arg64Trp,ENST00000409146,NM_001145123.2;PPP1R17,non_coding_transcript_exon_variant,,ENST00000498609,; T ENST00000342032 Transcript missense_variant 971/2268 343/468 115/155 R/W Agg/Tgg 1 1 PPP1R17 HGNC HGNC:16973 protein_coding YES CCDS5436.1 ENSP00000340125 O96001 A0A090N8N7 UPI000006D182 NM_006658.4 deleterious_low_confidence(0) 4/5 hmmpanther:PTHR15387,hmmpanther:PTHR15387:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 31697072 31697072 A T 1 0 0 0 0 1 0 0 0 12477 63 3 4 4 PPP1R17 7 31697072 Missense_Mutation SNP A 11LU016_T 941483 31697072 127648901 203 255 HERPUD2 0 . GRCh38 7 35634346 35634346 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1025G>T p.Gly342Val p.G342V ENST00000396081 7/8 238 196 42 124 124 0 strelka-varscan-mutect HERPUD2,missense_variant,p.Gly342Val,ENST00000396081,NM_022373.4;HERPUD2,missense_variant,p.Gly342Val,ENST00000311350,;HERPUD2,downstream_gene_variant,,ENST00000438224,;HERPUD2,downstream_gene_variant,,ENST00000413517,;HERPUD2,non_coding_transcript_exon_variant,,ENST00000426180,; A ENST00000396081 Transcript missense_variant 1830/3057 1025/1221 342/406 G/V gGg/gTg 1 -1 HERPUD2 HGNC HGNC:21915 protein_coding YES CCDS5446.1 ENSP00000379390 Q9BSE4 A0A024RA77 UPI000013F159 NM_022373.4 tolerated(0.32) 7/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12943,hmmpanther:PTHR12943:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 35634346 35634346 C A 1 0 0 0 0 1 0 0 0 6948 623 22 2 2 HERPUD2 7 35634346 Missense_Mutation SNP C 11LU016_T 3937274 35634346 123711627 204 256 AOAH 0 . GRCh38 7 36632080 36632080 + Silent SNP A A G novel 11LU016_T 11LU016_N A A c.477T>C p.= p.I159I ENST00000617267 6/22 155 108 47 138 138 0 strelka-varscan-mutect AOAH,synonymous_variant,p.=,ENST00000617267,NM_001177506.1;AOAH,synonymous_variant,p.=,ENST00000617537,NM_001637.3;AOAH,synonymous_variant,p.=,ENST00000612871,NM_001177507.1;AOAH,non_coding_transcript_exon_variant,,ENST00000543742,; G ENST00000617267 Transcript synonymous_variant 778/2398 477/2067 159/688 I atT/atC 1 -1 AOAH HGNC HGNC:548 protein_coding YES CCDS75584.1 ENSP00000479664 A0A087WVT3 UPI0001D043BB NM_001177506.1 6/22 hmmpanther:PTHR15010 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 36632080 36632080 A G 1 0 0 0 0 0 0 0 1 835 10 1 5 5 AOAH 7 36632080 Silent SNP A 11LU016_T 997734 36632080 122713893 205 257 DDX56 0 . GRCh38 7 44570807 44570807 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.961G>T p.Gly321Trp p.G321W ENST00000258772 7/14 223 158 65 197 197 0 strelka-varscan-mutect DDX56,missense_variant,p.Gly321Trp,ENST00000258772,NM_019082.3;DDX56,intron_variant,,ENST00000431640,NM_001257189.1;DDX56,upstream_gene_variant,,ENST00000448192,;DDX56,non_coding_transcript_exon_variant,,ENST00000485367,;DDX56,non_coding_transcript_exon_variant,,ENST00000467318,;DDX56,upstream_gene_variant,,ENST00000479602,;DDX56,missense_variant,p.Gly321Trp,ENST00000421223,;DDX56,missense_variant,p.Gly275Trp,ENST00000433257,;DDX56,3_prime_UTR_variant,,ENST00000446987,;DDX56,3_prime_UTR_variant,,ENST00000415758,;DDX56,downstream_gene_variant,,ENST00000479440,;DDX56,upstream_gene_variant,,ENST00000473924,; A ENST00000258772 Transcript missense_variant 1068/2336 961/1644 321/547 G/W Ggg/Tgg 1 -1 DDX56 HGNC HGNC:18193 protein_coding YES CCDS5492.1 ENSP00000258772 Q9NY93 UPI0000037BB1 NM_019082.3 deleterious(0.01) 7/14 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,SMART_domains:SM00490 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 44570807 44570807 C A 1 0 0 0 0 1 0 0 0 4177 623 22 2 2 DDX56 7 44570807 Missense_Mutation SNP C 11LU016_T 7938727 44570807 114775166 206 258 ZPBP 0 . GRCh38 7 50081807 50081807 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.301C>A p.Gln101Lys p.Q101K ENST00000046087 3/8 486 454 32 286 285 1 strelka-varscan-mutect ZPBP,missense_variant,p.Gln101Lys,ENST00000046087,NM_007009.2;ZPBP,missense_variant,p.Gln101Lys,ENST00000419417,NM_001159878.1;ZPBP,missense_variant,p.Gln62Lys,ENST00000450231,;ZPBP,downstream_gene_variant,,ENST00000413331,; T ENST00000046087 Transcript missense_variant 371/1213 301/1056 101/351 Q/K Caa/Aaa COSM3639470 1 -1 ZPBP HGNC HGNC:15662 protein_coding YES CCDS5509.1 ENSP00000046087 Q9BS86 UPI0000073BD0 NM_007009.2 tolerated(0.32) 3/8 Gene3D:2.60.40.10,Pfam_domain:PF07354,PROSITE_profiles:PS50835,hmmpanther:PTHR15443,hmmpanther:PTHR15443:SF5,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 50081807 50081807 G T 1 0 0 0 0 1 0 0 0 18811 1357 47 2 2 ZPBP 7 50081807 Missense_Mutation SNP G 11LU016_T 5511000 50081807 109264166 207 259 IKZF1 0 . GRCh38 7 50400527 50400527 + Missense_Mutation SNP G G A 11LU016_T 11LU016_N G G c.1460G>A p.Arg487His p.R487H ENST00000331340 8/8 281 186 95 322 321 1 strelka-varscan-mutect IKZF1,missense_variant,p.Arg487His,ENST00000331340,NM_006060.5;IKZF1,missense_variant,p.Arg400His,ENST00000343574,NM_001291839.1,NM_001220767.2,NM_001291841.1;IKZF1,missense_variant,p.Arg400His,ENST00000357364,NM_001220768.2;IKZF1,missense_variant,p.Arg344His,ENST00000349824,NM_001220771.2;IKZF1,missense_variant,p.Arg304His,ENST00000615491,;IKZF1,missense_variant,p.Arg262His,ENST00000440768,;IKZF1,missense_variant,p.Arg217His,ENST00000346667,;IKZF1,missense_variant,p.Arg445His,ENST00000439701,NM_001291837.1;IKZF1,missense_variant,p.Arg445His,ENST00000359197,NM_001220765.2;IKZF1,missense_variant,p.Arg400His,ENST00000438033,NM_001291838.1;IKZF1,missense_variant,p.Arg236His,ENST00000612658,;IKZF1,downstream_gene_variant,,ENST00000426121,;IKZF1,non_coding_transcript_exon_variant,,ENST00000471793,; A ENST00000331340 Transcript missense_variant 1615/6189 1460/1560 487/519 R/H cGt/cAt COSM5313026 1 1 IKZF1 HGNC HGNC:13176 protein_coding YES CCDS75596.1 ENSP00000331614 Q13422 UPI000012D465 NM_006060.5 deleterious(0.03) 8/8 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF36,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9992867 1 1 1 0 A 3 1 2 50400527 50400527 G A 1 0 0 0 0 1 0 0 0 7522 1145 40 1 1 IKZF1 7 50400527 Missense_Mutation SNP G 11LU016_T 318720 50400527 108945446 208 260 EGFR 0 . GRCh38 7 55174014 55174014 + Missense_Mutation SNP G G T rs28929495 11LU016_T 11LU016_N G G c.2155G>T p.Gly719Cys p.G719C ENST00000275493 18/28 483 321 162 368 367 1 strelka-varscan-mutect EGFR,missense_variant,p.Gly719Cys,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Gly674Cys,ENST00000454757,;EGFR,missense_variant,p.Gly674Cys,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1; T ENST00000275493 Transcript missense_variant 2332/9821 2155/3633 719/1210 G/C Ggc/Tgc rs28929495,COSM6252,COSM6253 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 18/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 likely_pathogenic,pathogenic,drug_response 0,1,1 1795663724712396 MODERATE 1 SNV 1 1,1,1 1 PASS rs28929495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 55174014 55174014 G T 1 0 0 0 0 1 0 0 0 4803 1232 43 2 2 EGFR 7 55174014 Missense_Mutation SNP G 11LU016_T 4773487 55174014 104171959 209 261 EGFR 0 . GRCh38 7 55181312 55181312 + Missense_Mutation SNP G G T rs121913465 11LU016_T 11LU016_N G G c.2303G>T p.Ser768Ile p.S768I ENST00000275493 20/28 344 241 103 244 243 1 strelka-varscan-mutect EGFR,missense_variant,p.Ser768Ile,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Ser723Ile,ENST00000454757,;EGFR,missense_variant,p.Ser723Ile,ENST00000455089,;EGFR-AS1,non_coding_transcript_exon_variant,,ENST00000442411,; T ENST00000275493 Transcript missense_variant 2480/9821 2303/3633 768/1210 S/I aGc/aTc rs121913465,COSM12989,COSM291998,COSM6241 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 20/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs146024686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 55181312 55181312 G T 1 0 0 0 0 1 0 0 0 4803 971 34 2 2 EGFR 7 55181312 Missense_Mutation SNP G 11LU016_T 7298 55181312 104164661 210 262 LANCL2 0 . GRCh38 7 55399978 55399978 + Silent SNP G G T rs532941386 11LU016_T 11LU016_N G G c.552G>T p.= p.S184S ENST00000254770 4/9 197 154 43 86 86 0 strelka-varscan-mutect LANCL2,synonymous_variant,p.=,ENST00000254770,NM_018697.3;LANCL2,non_coding_transcript_exon_variant,,ENST00000486376,;LANCL2,3_prime_UTR_variant,,ENST00000452107,; T ENST00000254770 Transcript synonymous_variant 1130/4353 552/1353 184/450 S tcG/tcT rs532941386 1 1 LANCL2 HGNC HGNC:6509 protein_coding YES CCDS5517.1 ENSP00000254770 Q9NS86 UPI000006F7D0 NM_018697.3 4/9 Superfamily_domains:0053930,Pfam_domain:PF05147,hmmpanther:PTHR12736,hmmpanther:PTHR12736:SF11,SMART_domains:SM01260 LOW 1 SNV 1 1 PASS rs532941386 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 55399978 55399978 G T 1 0 0 0 0 0 0 0 1 8531 1103 39 1 1 LANCL2 7 55399978 Silent SNP G 11LU016_T 218666 55399978 103945995 211 263 WBSCR28 0 . GRCh38 7 73865286 73865286 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.366G>T p.= p.L122L ENST00000320531 2/3 318 278 40 297 297 0 strelka-varscan-mutect WBSCR28,synonymous_variant,p.=,ENST00000320531,NM_182504.3;WBSCR28,3_prime_UTR_variant,,ENST00000426490,; T ENST00000320531 Transcript synonymous_variant 402/854 366/798 122/265 L ctG/ctT 1 1 WBSCR28 HGNC HGNC:23018 protein_coding YES CCDS43597.1 ENSP00000316775 Q6UE05 UPI00001408E5 NM_182504.3 2/3 hmmpanther:PTHR37369,Pfam_domain:PF15164 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 73865286 73865286 G T 1 0 0 0 0 0 0 0 1 17826 1364 48 2 2 WBSCR28 7 73865286 Silent SNP G 11LU016_T 18465308 73865286 85480687 212 264 PCLO 0 . GRCh38 7 82915481 82915481 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.12505C>A p.Leu4169Ile p.L4169I ENST00000333891 7/25 242 229 13 161 161 0 strelka-varscan-mutect PCLO,missense_variant,p.Leu4169Ile,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Leu4169Ile,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Leu889Ile,ENST00000437081,; T ENST00000333891 Transcript missense_variant 12843/20329 12505/15429 4169/5142 L/I Ctc/Atc COSM4828023,COSM4828024,COSM4828025 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.05) 7/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 82915481 82915481 G T 1 0 0 0 0 1 0 0 0 11671 1029 36 2 2 PCLO 7 82915481 Missense_Mutation SNP G 11LU016_T 9050195 82915481 76430492 213 265 PCLO 0 . GRCh38 7 82949643 82949643 + Missense_Mutation SNP C C A rs765735557 11LU016_T 11LU016_N C C c.10945G>T p.Asp3649Tyr p.D3649Y ENST00000333891 6/25 196 171 25 152 151 1 strelka-varscan-mutect PCLO,missense_variant,p.Asp3649Tyr,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Asp3649Tyr,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Asp369Tyr,ENST00000437081,; A ENST00000333891 Transcript missense_variant 11283/20329 10945/15429 3649/5142 D/Y Gat/Tat rs765735557 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.03) 6/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS rs765735557 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 82949643 82949643 C A 1 0 0 0 0 1 0 0 0 11671 826 29 2 2 PCLO 7 82949643 Missense_Mutation SNP C 11LU016_T 34162 82949643 76396330 214 266 SEMA3E 0 . GRCh38 7 83400114 83400114 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1280C>T p.Thr427Ile p.T427I ENST00000307792 11/17 562 516 46 388 388 0 strelka-varscan-mutect SEMA3E,missense_variant,p.Thr427Ile,ENST00000307792,NM_012431.2;SEMA3E,missense_variant,p.Thr367Ile,ENST00000427262,NM_001178129.1; A ENST00000307792 Transcript missense_variant 1748/6476 1280/2328 427/775 T/I aCa/aTa 1 -1 SEMA3E HGNC HGNC:10727 protein_coding YES CCDS34674.1 ENSP00000303212 O15041 UPI0000135A68 NM_012431.2 tolerated(0.17) 11/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 83400114 83400114 G A 1 0 0 0 0 1 0 0 0 14304 1377 48 3 3 SEMA3E 7 83400114 Missense_Mutation SNP G 11LU016_T 450471 83400114 75945859 215 267 KIAA1324L 0 . GRCh38 7 86897581 86897581 + Silent SNP C C T 11LU016_T 11LU016_N C C c.2610G>A p.= p.E870E ENST00000450689 19/22 216 160 56 167 167 0 strelka-varscan-mutect KIAA1324L,synonymous_variant,p.=,ENST00000450689,NM_001142749.2;KIAA1324L,synonymous_variant,p.=,ENST00000444627,;KIAA1324L,synonymous_variant,p.=,ENST00000416314,NM_152748.3,NM_001291990.1;KIAA1324L,synonymous_variant,p.=,ENST00000423294,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;KIAA1324L,upstream_gene_variant,,ENST00000480216,; T ENST00000450689 Transcript synonymous_variant 2796/6841 2610/3090 870/1029 E gaG/gaA COSM3641846,COSM3641847 1 -1 KIAA1324L HGNC HGNC:21945 protein_coding YES CCDS47632.1 ENSP00000413445 A8MWY0 UPI000173AA00 NM_001142749.2 19/22 hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Superfamily_domains:SSF50911 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 86897581 86897581 C T 1 0 0 0 0 0 0 0 1 8112 912 32 3 3 KIAA1324L 7 86897581 Silent SNP C 11LU016_T 3497467 86897581 72448392 216 268 ZNF804B 0 . GRCh38 7 89336851 89336851 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.3869C>G p.Ala1290Gly p.A1290G ENST00000333190 4/4 243 155 88 152 152 0 strelka-varscan-mutect ZNF804B,missense_variant,p.Ala1290Gly,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Ala1207Gly,ENST00000611114,; G ENST00000333190 Transcript missense_variant 4478/4659 3869/4050 1290/1349 A/G gCa/gGa 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 deleterious(0.01) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 89336851 89336851 C G 1 0 0 0 0 1 0 0 0 18756 710 25 4 4 ZNF804B 7 89336851 Missense_Mutation SNP C 11LU016_T 2439270 89336851 70009122 217 269 SLC25A13 0 . GRCh38 7 96193125 96193125 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.527G>T p.Gly176Val p.G176V ENST00000416240 6/18 323 291 32 218 218 0 strelka-varscan-mutect SLC25A13,missense_variant,p.Gly176Val,ENST00000416240,NM_001160210.1;SLC25A13,missense_variant,p.Gly176Val,ENST00000265631,NM_014251.2;SLC25A13,upstream_gene_variant,,ENST00000484495,;SLC25A13,downstream_gene_variant,,ENST00000472162,; A ENST00000416240 Transcript missense_variant 718/3192 527/2031 176/676 G/V gGg/gTg 1 -1 SLC25A13 HGNC HGNC:10983 protein_coding YES CCDS55130.1 ENSP00000400101 Q9UJS0 UPI0000001663 NM_001160210.1 deleterious(0) 6/18 PROSITE_profiles:PS50222,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 96193125 96193125 C A 1 0 0 0 0 1 0 0 0 14740 623 22 2 2 SLC25A13 7 96193125 Missense_Mutation SNP C 11LU016_T 6856274 96193125 63152848 218 270 TECPR1 0 . GRCh38 7 98236809 98236809 + Missense_Mutation SNP C C G rs757002726 11LU016_T 11LU016_N C C c.1148G>C p.Arg383Pro p.R383P ENST00000447648 10/26 241 225 16 221 221 0 strelka-varscan-mutect TECPR1,missense_variant,p.Arg383Pro,ENST00000447648,NM_015395.2;TECPR1,non_coding_transcript_exon_variant,,ENST00000471397,;TECPR1,upstream_gene_variant,,ENST00000490842,;TECPR1,downstream_gene_variant,,ENST00000463648,; G ENST00000447648 Transcript missense_variant 1448/6564 1148/3498 383/1165 R/P cGg/cCg rs757002726 1 -1 TECPR1 HGNC HGNC:22214 protein_coding YES CCDS47648.1 ENSP00000404923 Q7Z6L1 UPI0000161940 NM_015395.2 deleterious(0.02) 10/26 hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1 MODERATE 1 SNV 1 1 PASS rs757002726 . 0 206 0 0 3 0 0 0 -4.782559 0.8715059 1 1 1 0 G 3 3 2 98236809 98236809 C G 1 0 0 0 0 1 0 0 0 16154 652 23 4 4 TECPR1 7 98236809 Missense_Mutation SNP C 11LU016_T 2043684 98236809 61109164 219 271 ZAN 0 . GRCh38 7 100750707 100750707 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1332C>A p.= p.A444A ENST00000613979 12/48 339 305 34 293 293 0 strelka-varscan-mutect ZAN,synonymous_variant,p.=,ENST00000613979,NM_003386.2;ZAN,synonymous_variant,p.=,ENST00000618565,;ZAN,synonymous_variant,p.=,ENST00000620596,NM_173059.2;ZAN,synonymous_variant,p.=,ENST00000546292,;ZAN,synonymous_variant,p.=,ENST00000542585,;ZAN,synonymous_variant,p.=,ENST00000538115,;ZAN,synonymous_variant,p.=,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; A ENST00000613979 Transcript synonymous_variant 1497/8669 1332/8439 444/2812 A gcC/gcA 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 12/48 Pfam_domain:PF00629,PROSITE_patterns:PS00740,PROSITE_profiles:PS50060,SMART_domains:SM00137,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1438768116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 100750707 100750707 C A 1 0 0 0 0 0 0 0 1 18074 610 22 2 2 ZAN 7 100750707 Silent SNP C 11LU016_T 2513898 100750707 58595266 220 272 ZAN 0 . GRCh38 7 100773283 100773283 + Splice_Site SNP A A T novel 11LU016_T 11LU016_N A A c.5426-2A>T p.X1809_splice ENST00000613979 204 182 22 117 117 0 strelka-varscan-mutect ZAN,splice_acceptor_variant,,ENST00000613979,NM_003386.2;ZAN,splice_acceptor_variant,,ENST00000618565,;ZAN,splice_acceptor_variant,,ENST00000620596,NM_173059.2;ZAN,splice_acceptor_variant,,ENST00000546292,;ZAN,splice_acceptor_variant,,ENST00000620868,;ZAN,splice_acceptor_variant,,ENST00000542585,;ZAN,splice_acceptor_variant,,ENST00000538115,;ZAN,splice_acceptor_variant,,ENST00000546213,; T ENST00000613979 Transcript splice_acceptor_variant -/8669 5426/8439 1809/2812 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 29/47 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 2 100773283 100773283 A T 1 0 0 0 0 0 0 1 0 18074 434 15 4 4 ZAN 7 100773283 Splice_Site SNP A 11LU016_T 22576 100773283 58572690 221 273 SRPK2 0 . GRCh38 7 105143127 105143127 + Silent SNP T T A novel 11LU016_T 11LU016_N T T c.1017A>T p.= p.T339T ENST00000393651 10/16 279 225 54 133 132 1 strelka-varscan-mutect SRPK2,synonymous_variant,p.=,ENST00000357311,NM_182691.2;SRPK2,synonymous_variant,p.=,ENST00000393651,NM_182692.2;SRPK2,synonymous_variant,p.=,ENST00000489828,NM_001278273.1;SRPK2,upstream_gene_variant,,ENST00000477925,;SRPK2,intron_variant,,ENST00000485455,;SRPK2,non_coding_transcript_exon_variant,,ENST00000466917,; A ENST00000393651 Transcript synonymous_variant 1105/3650 1017/2100 339/699 T acA/acT 1 -1 SRPK2 HGNC HGNC:11306 protein_coding YES CCDS34724.1 ENSP00000377262 P78362 UPI00001A4785 NM_182692.2 10/16 PROSITE_profiles:PS50011,SMART_domains:SM00220 LOW 1 SNV 2 1 PASS rs1311516497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 105143127 105143127 T A 1 0 0 0 0 0 0 0 1 15521 1567 55 4 4 SRPK2 7 105143127 Silent SNP T 11LU016_T 4369844 105143127 54202846 222 274 COG5 0 . GRCh38 7 107548319 107548319 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.399G>T p.Met133Ile p.M133I ENST00000297135 4/22 593 498 95 433 433 0 strelka-varscan-mutect COG5,missense_variant,p.Met133Ile,ENST00000393603,NM_001161520.1;COG5,missense_variant,p.Met133Ile,ENST00000347053,NM_181733.2;COG5,missense_variant,p.Met133Ile,ENST00000297135,NM_006348.3;COG5,missense_variant,p.Met102Ile,ENST00000605888,;COG5,non_coding_transcript_exon_variant,,ENST00000475638,;COG5,non_coding_transcript_exon_variant,,ENST00000469503,; A ENST00000297135 Transcript missense_variant 924/4060 399/2583 133/860 M/I atG/atT COSM5288391 1 -1 COG5 HGNC HGNC:14857 protein_coding YES CCDS5742.1 ENSP00000297135 Q9UP83 UPI0000246D05 NM_006348.3 tolerated(0.22) 4/22 Pfam_domain:PF10392,hmmpanther:PTHR13228,hmmpanther:PTHR13228:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1267467691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 107548319 107548319 C A 1 0 0 0 0 1 0 0 0 3449 826 29 2 2 COG5 7 107548319 Missense_Mutation SNP C 11LU016_T 2405192 107548319 51797654 223 275 SLC26A4 0 . GRCh38 7 107674330 107674330 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.582G>T p.= p.L194L ENST00000265715 5/21 370 315 55 257 256 1 strelka-varscan-mutect SLC26A4,synonymous_variant,p.=,ENST00000265715,NM_000441.1;SLC26A4,downstream_gene_variant,,ENST00000440056,; T ENST00000265715 Transcript synonymous_variant 806/4930 582/2343 194/780 L ctG/ctT 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 5/21 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF33,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00815,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 107674330 107674330 G T 1 0 0 0 0 0 0 0 1 14789 1306 46 2 2 SLC26A4 7 107674330 Silent SNP G 11LU016_T 126011 107674330 51671643 224 276 SLC26A4 0 . GRCh38 7 107700160 107700180 + Splice_Site DEL ATGTATCAAGTCCACAGTAAG ATGTATCAAGTCCACAGTAAG - novel 11LU016_T 11LU016_N ATGTATCAAGTCCACAGTAAG ATGTATCAAGTCCACAGTAAG c.1692_1707+5delATGTATCAAGTCCACAGTAAG p.X564_splice ENST00000265715 15/21 353 328 25 273 273 0 sindel-pindel SLC26A4,splice_donor_variant,,ENST00000265715,NM_000441.1;SLC26A4,splice_donor_variant,,ENST00000480841,;SLC26A4,splice_donor_variant,,ENST00000492030,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000477350,;SLC26A4,downstream_gene_variant,,ENST00000460748,;SLC26A4,downstream_gene_variant,,ENST00000497446,; - ENST00000265715 Transcript splice_donor_variant,coding_sequence_variant,intron_variant 1916-?/4930 1692-?/2343 564-?/780 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 15/21 15/20 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 2 107700160 107700160 ATGTATCAAGTCCACAGTAAG - 1 0 1 0 1 0 0 1 0 14789 98 4 0 0 SLC26A4 7 107700160 Splice_Site DEL ATGTATCAAGTCCACAGTAAG 11LU016_T 25830 107700160 51645813 225 277 LAMB1 0 . GRCh38 7 107929412 107929412 + Missense_Mutation SNP C C T rs747370433 11LU016_T 11LU016_N C C c.4745G>A p.Ser1582Asn p.S1582N ENST00000222399 30/34 201 162 39 188 188 0 strelka-varscan-mutect LAMB1,missense_variant,p.Ser1606Asn,ENST00000393561,;LAMB1,missense_variant,p.Ser1582Asn,ENST00000222399,NM_002291.2;LAMB1,downstream_gene_variant,,ENST00000474380,;LAMB1,downstream_gene_variant,,ENST00000468518,;LAMB1,non_coding_transcript_exon_variant,,ENST00000472714,;DLD,intron_variant,,ENST00000417551,; T ENST00000222399 Transcript missense_variant,splice_region_variant 4976/5725 4745/5361 1582/1786 S/N aGc/aAc rs747370433 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 tolerated(0.19) 30/34 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF233,Superfamily_domains:SSF46579 MODERATE 1 SNV 1 1 PASS rs747370433 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 107929412 107929412 C T 1 0 0 0 0 1 0 0 0 8514 695 24 3 3 LAMB1 7 107929412 Missense_Mutation SNP C 11LU016_T 229252 107929412 51416561 226 278 HYAL4 0 . GRCh38 7 123868552 123868552 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.279C>A p.Asn93Lys p.N93K ENST00000223026 3/5 157 129 28 131 131 0 strelka-varscan-mutect HYAL4,missense_variant,p.Asn93Lys,ENST00000223026,NM_012269.2;HYAL4,missense_variant,p.Asn93Lys,ENST00000476325,;HYAL4,downstream_gene_variant,,ENST00000489978,;HYAL4,downstream_gene_variant,,ENST00000488323,;HYAL4,missense_variant,p.Asn93Lys,ENST00000483878,; A ENST00000223026 Transcript missense_variant 917/2407 279/1446 93/481 N/K aaC/aaA 1 1 HYAL4 HGNC HGNC:5323 protein_coding YES CCDS5789.1 ENSP00000223026 Q2M3T9 UPI000006F62B NM_012269.2 deleterious(0.01) 3/5 Gene3D:3.20.20.70,Pfam_domain:PF01630,PIRSF_domain:PIRSF038193,hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF7,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 123868552 123868552 C A 1 0 0 0 0 1 0 0 0 7362 477 17 2 2 HYAL4 7 123868552 Missense_Mutation SNP C 11LU016_T 15939140 123868552 35477421 227 279 PRRT4 0 . GRCh38 7 128352011 128352011 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.1545G>A p.= p.A515A ENST00000446477 6/6 52 48 4 59 59 0 strelka-mutect PRRT4,synonymous_variant,p.=,ENST00000446477,NM_001174164.1;PRRT4,synonymous_variant,p.=,ENST00000535159,;PRRT4,intron_variant,,ENST00000489835,NM_001114726.2;PRRT4,intron_variant,,ENST00000480290,;PRRT4,downstream_gene_variant,,ENST00000489517,; T ENST00000446477 Transcript synonymous_variant 1859/3544 1545/2700 515/899 A gcG/gcA 1 -1 PRRT4 HGNC HGNC:37280 protein_coding YES CCDS55160.1 ENSP00000415026 C9JH25 UPI0000DD7E1D NM_001174164.1 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR35578,hmmpanther:PTHR35578:SF1,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 202 7 0 0 0 0 0 -10.03666 0.9999981 1 1 1 0 T 2 4 2 128352011 128352011 C T 1 0 0 0 0 0 0 0 1 12758 755 27 1 1 PRRT4 7 128352011 Silent SNP C 11LU016_T 4483459 128352011 30993962 228 280 STRIP2 0 . GRCh38 7 129455339 129455339 + Nonsense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.802A>T p.Lys268Ter p.K268* ENST00000249344 8/21 161 150 11 123 123 0 strelka-varscan-mutect STRIP2,stop_gained,p.Lys268Ter,ENST00000249344,NM_020704.2;STRIP2,stop_gained,p.Lys268Ter,ENST00000435494,NM_001134336.1;STRIP2,upstream_gene_variant,,ENST00000465033,; T ENST00000249344 Transcript stop_gained 842/5115 802/2505 268/834 K/* Aag/Tag 1 1 STRIP2 HGNC HGNC:22209 protein_coding YES CCDS34752.1 ENSP00000249344 Q9ULQ0 UPI00001C1E68 NM_020704.2 8/21 Pfam_domain:PF07923,hmmpanther:PTHR13239,hmmpanther:PTHR13239:SF6,Low_complexity_(Seg):seg,SMART_domains:SM01292 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 129455339 129455339 A T 1 0 0 0 0 0 1 0 0 15711 247 9 4 4 STRIP2 7 129455339 Nonsense_Mutation SNP A 11LU016_T 1103328 129455339 29890634 229 281 PLXNA4 0 . GRCh38 7 132148554 132148554 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.4753G>A p.Ala1585Thr p.A1585T ENST00000359827 26/32 168 141 27 152 151 1 strelka-varscan-mutect PLXNA4,missense_variant,p.Ala1585Thr,ENST00000359827,;PLXNA4,missense_variant,p.Ala1585Thr,ENST00000321063,NM_020911.1;PLXNA4,upstream_gene_variant,,ENST00000496550,; T ENST00000359827 Transcript missense_variant 5716/13786 4753/5685 1585/1894 A/T Gcc/Acc 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B tolerated(0.08) 26/32 Gene3D:3.10.20.90,Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 132148554 132148554 C T 1 0 0 0 0 1 0 0 0 12228 739 26 3 3 PLXNA4 7 132148554 Missense_Mutation SNP C 11LU016_T 2693215 132148554 27197419 230 282 MGAM 0 . GRCh38 7 142008607 142008607 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.229G>T p.Asp77Tyr p.D77Y ENST00000549489 3/48 338 232 106 236 236 0 strelka-varscan-mutect MGAM,missense_variant,p.Asp77Tyr,ENST00000475668,;MGAM,missense_variant,p.Asp77Tyr,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Asp77Tyr,ENST00000620571,;MGAM,missense_variant,p.Asp77Tyr,ENST00000465654,;MGAM,missense_variant,p.Asp77Tyr,ENST00000497673,; T ENST00000549489 Transcript missense_variant 324/6525 229/5574 77/1857 D/Y Gat/Tat 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0.02) 3/48 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 142008607 142008607 G T 1 0 0 0 0 1 0 0 0 9499 942 33 2 2 MGAM 7 142008607 Missense_Mutation SNP G 11LU016_T 9860053 142008607 17337366 231 283 TRPV6 0 . GRCh38 7 142877281 142877281 + Splice_Site SNP T T C novel 11LU016_T 11LU016_N T T c.470-2A>G p.X157_splice ENST00000359396 112 91 21 88 88 0 strelka-varscan-mutect TRPV6,splice_acceptor_variant,,ENST00000359396,NM_018646.5;TRPV6,splice_acceptor_variant,,ENST00000431833,;TRPV6,intron_variant,,ENST00000436401,;RP11-114L10.2,intron_variant,,ENST00000438839,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000489123,;TRPV6,upstream_gene_variant,,ENST00000485138,;TRPV6,upstream_gene_variant,,ENST00000619250,;TRPV6,upstream_gene_variant,,ENST00000474388,; C ENST00000359396 Transcript splice_acceptor_variant -/2928 470/2298 157/765 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 3/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 2 142877281 142877281 T C 1 0 0 0 0 0 0 1 0 17106 1594 55 5 5 TRPV6 7 142877281 Splice_Site SNP T 11LU016_T 868674 142877281 16468692 232 284 TRPV5 0 . GRCh38 7 142929457 142929457 + Missense_Mutation SNP C C A rs192702809 11LU016_T 11LU016_N C C c.458G>T p.Arg153Leu p.R153L ENST00000265310 4/15 167 150 17 129 129 0 strelka-mutect TRPV5,missense_variant,p.Arg153Leu,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Arg153Leu,ENST00000442623,;TRPV5,missense_variant,p.Arg147Leu,ENST00000439304,; A ENST00000265310 Transcript missense_variant 807/2952 458/2190 153/729 R/L cGc/cTc rs192702809,COSM316219,COSM745233 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 tolerated(0.1) 4/15 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,Superfamily_domains:SSF48403,TIGRFAM_domain:TIGR00870 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs192702809 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 142929457 142929457 C A 1 0 0 0 0 1 0 0 0 17105 768 27 1 1 TRPV5 7 142929457 Missense_Mutation SNP C 11LU016_T 52176 142929457 16416516 233 285 CTAGE6 0 . GRCh38 7 143757005 143757005 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.654A>T p.Gln218His p.Q218H ENST00000470691 1/1 156 133 23 151 151 0 varscan-mutect CTAGE6,missense_variant,p.Gln218His,ENST00000470691,NM_178561.4;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,;RNU6-267P,upstream_gene_variant,,ENST00000516714,;RP11-61L23.2,downstream_gene_variant,,ENST00000491047,; A ENST00000470691 Transcript missense_variant 692/2608 654/2334 218/777 Q/H caA/caT 1 -1 CTAGE6 HGNC HGNC:28644 protein_coding YES CCDS64790.1 ENSP00000474388 Q86UF2 UPI0000199826 NM_178561.4 tolerated(0.48) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39 MODERATE 1 SNV 1 PASS rs905831435 . 10 199 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 143757005 143757005 T A 1 0 0 0 0 1 0 0 0 3800 1722 60 4 4 CTAGE6 7 143757005 Missense_Mutation SNP T 11LU016_T 827548 143757005 15588968 234 286 OR6B1 0 . GRCh38 7 144004123 144004123 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.127G>T p.Val43Leu p.V43L ENST00000408922 1/1 259 193 66 227 225 2 strelka-varscan-mutect OR6B1,missense_variant,p.Val43Leu,ENST00000408922,NM_001005281.1; T ENST00000408922 Transcript missense_variant 195/1055 127/936 43/311 V/L Gtg/Ttg 1 1 OR6B1 HGNC HGNC:8354 protein_coding YES CCDS43667.1 ENSP00000386151 O95007 UPI0000041B18 NM_001005281.1 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF284,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 144004123 144004123 G T 1 0 0 0 0 1 0 0 0 11255 1145 40 1 1 OR6B1 7 144004123 Missense_Mutation SNP G 11LU016_T 247118 144004123 15341850 235 287 SSPO 0 . GRCh38 7 149827817 149827817 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.14823G>A p.= p.G4941G ENST00000378016 102/107 106 69 37 64 64 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000492965,;SSPO,non_coding_transcript_exon_variant,,ENST00000488835,;SSPO,non_coding_transcript_exon_variant,,ENST00000461331,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,; A ENST00000378016 Transcript synonymous_variant 14823/15589 14823/15453 4941/5150 G ggG/ggA 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 102/107 Gene3D:2.10.25.10,Superfamily_domains:SSF57567 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 149827817 149827817 G A 1 0 0 0 0 0 0 0 1 15566 1190 42 3 3 SSPO 7 149827817 Silent SNP G 11LU016_T 5823694 149827817 9518156 236 288 HTR5A 0 . GRCh38 7 155071324 155071324 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.425C>A p.Ser142Tyr p.S142Y ENST00000287907 1/2 225 188 37 191 191 0 strelka-varscan-mutect HTR5A,missense_variant,p.Ser142Tyr,ENST00000287907,NM_024012.3;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000395731,;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000493904,;RP11-5C23.4,upstream_gene_variant,,ENST00000637588,; A ENST00000287907 Transcript missense_variant 1001/2912 425/1074 142/357 S/Y tCc/tAc 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 deleterious(0) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 155071324 155071324 C A 1 0 0 0 0 1 0 0 0 7346 855 30 2 2 HTR5A 7 155071324 Missense_Mutation SNP C 11LU016_T 5243507 155071324 4274649 237 289 EN2 0 . GRCh38 7 155458944 155458944 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.567C>A p.= p.G189G ENST00000297375 1/2 175 158 17 252 252 0 strelka-varscan-mutect EN2,synonymous_variant,p.=,ENST00000297375,NM_001427.3;AC008060.8,upstream_gene_variant,,ENST00000419225,; A ENST00000297375 Transcript synonymous_variant 816/3395 567/1002 189/333 G ggC/ggA 1 1 EN2 HGNC HGNC:3343 protein_coding YES CCDS5940.1 ENSP00000297375 P19622 UPI000012CA05 NM_001427.3 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24341:SF5,hmmpanther:PTHR24341 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 155458944 155458944 C A 1 0 0 0 0 0 0 0 1 4952 755 27 1 1 EN2 7 155458944 Silent SNP C 11LU016_T 387620 155458944 3887029 238 290 CSMD1 0 . GRCh38 8 3029334 3029334 + Missense_Mutation SNP T T A rs779259347 11LU016_T 11LU016_N T T c.7843A>T p.Arg2615Trp p.R2615W ENST00000520002 52/71 83 64 19 69 69 0 strelka-varscan-mutect CSMD1,missense_variant,p.Arg2476Trp,ENST00000537824,;CSMD1,missense_variant,p.Arg2032Trp,ENST00000335551,;CSMD1,missense_variant,p.Arg2615Trp,ENST00000520002,;CSMD1,missense_variant,p.Arg2615Trp,ENST00000602557,;CSMD1,missense_variant,p.Arg2614Trp,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Arg2615Trp,ENST00000400186,;CSMD1,missense_variant,p.Arg2615Trp,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000519623,; A ENST00000520002 Transcript missense_variant 8399/11740 7843/10698 2615/3565 R/W Agg/Tgg rs779259347 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.03) 52/71 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs779259347 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 3029334 3029334 T A 1 0 0 0 0 1 0 0 0 3745 1550 54 4 4 CSMD1 8 3029334 Missense_Mutation SNP T 11LU016_T 3029334 142109302 239 291 CSMD1 0 . GRCh38 8 3223759 3223759 + Missense_Mutation SNP G G T rs571113460 11LU016_T 11LU016_N G G c.4457C>A p.Pro1486Gln p.P1486Q ENST00000520002 29/71 215 203 12 177 176 1 strelka-mutect CSMD1,missense_variant,p.Pro1347Gln,ENST00000537824,;CSMD1,missense_variant,p.Pro966Gln,ENST00000335551,;CSMD1,missense_variant,p.Pro1486Gln,ENST00000520002,;CSMD1,missense_variant,p.Pro1486Gln,ENST00000602557,;CSMD1,missense_variant,p.Pro1485Gln,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Pro1486Gln,ENST00000400186,;CSMD1,missense_variant,p.Pro1486Gln,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; T ENST00000520002 Transcript missense_variant 5013/11740 4457/10698 1486/3565 P/Q cCg/cAg rs571113460,COSM383538,COSM383539,COSM4772151,COSM4772152,COSM4772153 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.01) 29/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1,1 1 PASS rs571113460 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 3223759 3223759 G T 1 0 0 0 0 1 0 0 0 3745 1116 39 1 1 CSMD1 8 3223759 Missense_Mutation SNP G 11LU016_T 194425 3223759 141914877 240 292 RP1L1 0 . GRCh38 8 10609234 10609234 + Missense_Mutation SNP G G A rs201695025 11LU016_T 11LU016_N G G c.4864C>T p.Arg1622Trp p.R1622W ENST00000382483 4/4 295 279 16 278 277 1 strelka-varscan-mutect RP1L1,missense_variant,p.Arg1622Trp,ENST00000382483,NM_178857.5; A ENST00000382483 Transcript missense_variant 5088/7973 4864/7203 1622/2400 R/W Cgg/Tgg rs201695025,COSM119889 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 deleterious(0) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201695025 . 0 208 0 0 0 0 0 2 -14.18881 0 0 1 0 0 A 3 1 2 10609234 10609234 G A 1 0 0 0 0 1 0 0 0 13773 1086 38 1 1 RP1L1 8 10609234 Missense_Mutation SNP G 11LU016_T 7385475 10609234 134529402 241 293 SLC39A14 0 . GRCh38 8 22408424 22408424 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.385G>T p.Ala129Ser p.A129S ENST00000359741 3/9 186 145 41 222 222 0 strelka-varscan-mutect SLC39A14,missense_variant,p.Ala129Ser,ENST00000359741,NM_015359.4;SLC39A14,missense_variant,p.Ala129Ser,ENST00000381237,NM_001128431.2;SLC39A14,missense_variant,p.Ala129Ser,ENST00000289952,NM_001135153.1;SLC39A14,missense_variant,p.Ala129Ser,ENST00000240095,NM_001135154.1;SLC39A14,missense_variant,p.Ala129Ser,ENST00000522881,;SLC39A14,upstream_gene_variant,,ENST00000517370,;SLC39A14,downstream_gene_variant,,ENST00000520832,;SLC39A14,downstream_gene_variant,,ENST00000517552,;SLC39A14,downstream_gene_variant,,ENST00000524285,;SLC39A14,downstream_gene_variant,,ENST00000519960,;SLC39A14,downstream_gene_variant,,ENST00000520644,; T ENST00000359741 Transcript missense_variant 560/4641 385/1479 129/492 A/S Gcc/Tcc 1 1 SLC39A14 HGNC HGNC:20858 protein_coding YES CCDS6030.1 ENSP00000352779 Q15043 UPI0000457680 NM_015359.4 tolerated(0.5) 3/9 hmmpanther:PTHR12191,hmmpanther:PTHR12191:SF5 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 22408424 22408424 G T 1 0 0 0 0 1 0 0 0 14895 1203 42 2 2 SLC39A14 8 22408424 Missense_Mutation SNP G 11LU016_T 11799190 22408424 122730212 242 294 DPYSL2 0 . GRCh38 8 26624194 26624194 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.365A>T p.Gln122Leu p.Q122L ENST00000311151 4/14 221 207 14 237 237 0 strelka-varscan-mutect DPYSL2,missense_variant,p.Gln227Leu,ENST00000521913,NM_001197293.2;DPYSL2,missense_variant,p.Gln122Leu,ENST00000311151,NM_001386.5;DPYSL2,missense_variant,p.Gln86Leu,ENST00000523027,NM_001244604.1;DPYSL2,upstream_gene_variant,,ENST00000521983,;DPYSL2,downstream_gene_variant,,ENST00000523690,;DPYSL2,non_coding_transcript_exon_variant,,ENST00000523093,; T ENST00000311151 Transcript missense_variant 777/4603 365/1719 122/572 Q/L cAg/cTg 1 1 DPYSL2 HGNC HGNC:3014 protein_coding YES CCDS6051.1 ENSP00000309539 Q16555 UPI0000129864 NM_001386.5 tolerated(0.05) 4/14 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF56,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 26624194 26624194 A T 1 0 0 0 0 1 0 0 0 4562 188 7 4 4 DPYSL2 8 26624194 Missense_Mutation SNP A 11LU016_T 4215770 26624194 118514442 243 295 NUGGC 0 . GRCh38 8 28029389 28029389 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.2031C>A p.= p.I677I ENST00000413272 17/19 180 147 33 123 122 1 strelka-varscan-mutect NUGGC,synonymous_variant,p.=,ENST00000413272,NM_001010906.1; T ENST00000413272 Transcript synonymous_variant 2174/3887 2031/2391 677/796 I atC/atA 1 -1 NUGGC HGNC HGNC:33550 protein_coding YES CCDS47833.1 ENSP00000408697 Q68CJ6 UPI0000237454 NM_001010906.1 17/19 LOW 1 SNV 2 1 PASS rs1222184266 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 28029389 28029389 G T 1 0 0 0 0 0 0 0 1 10814 1280 45 2 2 NUGGC 8 28029389 Silent SNP G 11LU016_T 1405195 28029389 117109247 244 296 ELP3 0 . GRCh38 8 28129592 28129592 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.708G>A p.= p.L236L ENST00000256398 8/15 285 243 42 241 241 0 strelka-varscan-mutect ELP3,synonymous_variant,p.=,ENST00000256398,NM_018091.5;ELP3,synonymous_variant,p.=,ENST00000521015,NM_001284222.1;ELP3,synonymous_variant,p.=,ENST00000380353,NM_001284226.1;ELP3,synonymous_variant,p.=,ENST00000537665,NM_001284225.1,NM_001284224.1;ELP3,synonymous_variant,p.=,ENST00000524103,NM_001284220.1;ELP3,non_coding_transcript_exon_variant,,ENST00000520110,;ELP3,3_prime_UTR_variant,,ENST00000518112,;ELP3,3_prime_UTR_variant,,ENST00000519261,;ELP3,3_prime_UTR_variant,,ENST00000523687,;ELP3,non_coding_transcript_exon_variant,,ENST00000520011,; A ENST00000256398 Transcript synonymous_variant 1085/3452 708/1644 236/547 L ttG/ttA 1 1 ELP3 HGNC HGNC:20696 protein_coding YES CCDS6065.1 ENSP00000256398 Q9H9T3 UPI000006F0B5 NM_018091.5 8/15 hmmpanther:PTHR11135,PIRSF_domain:PIRSF005669,TIGRFAM_domain:TIGR01211,Gene3D:2qgqB01,Pfam_domain:PF04055,SMART_domains:SM00729,Superfamily_domains:SSF102114 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 28129592 28129592 G A 1 0 0 0 0 0 0 0 1 4915 1281 45 3 3 ELP3 8 28129592 Silent SNP G 11LU016_T 100203 28129592 117009044 245 297 DCTN6 0 . GRCh38 8 30177139 30177139 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.208A>G p.Ile70Val p.I70V ENST00000221114 4/7 152 115 37 130 130 0 strelka-varscan-mutect DCTN6,missense_variant,p.Ile70Val,ENST00000221114,NM_006571.3;DCTN6,missense_variant,p.Ile70Val,ENST00000520829,;RP11-51J9.4,intron_variant,,ENST00000523733,;DCTN6,missense_variant,p.Ile34Met,ENST00000522141,;LEPROTL1,3_prime_UTR_variant,,ENST00000520739,;DCTN6,3_prime_UTR_variant,,ENST00000519830,;DCTN6,non_coding_transcript_exon_variant,,ENST00000522540,;DCTN6,intron_variant,,ENST00000523666,; G ENST00000221114 Transcript missense_variant 295/1127 208/573 70/190 I/V Atc/Gtc 1 1 DCTN6 HGNC HGNC:16964 protein_coding YES CCDS6076.1 ENSP00000221114 O00399 UPI0000138F9C NM_006571.3 tolerated(0.31) 4/7 Gene3D:2.160.10.10,hmmpanther:PTHR13072,Superfamily_domains:SSF51161 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 30177139 30177139 A G 1 0 0 0 0 1 0 0 0 4114 449 16 5 5 DCTN6 8 30177139 Missense_Mutation SNP A 11LU016_T 2047547 30177139 114961497 246 298 CHRNA6 0 . GRCh38 8 42756303 42756303 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.896T>A p.Val299Glu p.V299E ENST00000276410 5/6 227 214 13 226 226 0 strelka-varscan CHRNA6,missense_variant,p.Val299Glu,ENST00000276410,NM_004198.3;CHRNA6,missense_variant,p.Val284Glu,ENST00000534622,NM_001199279.1;CHRNA6,downstream_gene_variant,,ENST00000533810,;CHRNA6,downstream_gene_variant,,ENST00000530869,; T ENST00000276410 Transcript missense_variant 1252/2400 896/1485 299/494 V/E gTg/gAg 1 -1 CHRNA6 HGNC HGNC:15963 protein_coding YES CCDS6135.1 ENSP00000276410 Q15825 UPI0000061DF6 NM_004198.3 deleterious(0) 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF82,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 42756303 42756303 A T 1 0 0 0 0 1 0 0 0 3147 159 6 4 4 CHRNA6 8 42756303 Missense_Mutation SNP A 11LU016_T 12579164 42756303 102382333 247 299 XKR4 0 . GRCh38 8 55523345 55523345 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1071C>A p.= p.L357L ENST00000327381 3/3 111 85 26 140 140 0 strelka-varscan XKR4,synonymous_variant,p.=,ENST00000327381,NM_052898.1;XKR4,synonymous_variant,p.=,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; A ENST00000327381 Transcript synonymous_variant 1171/19880 1071/1953 357/650 L ctC/ctA 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 3/3 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14,Pfam_domain:PF09815 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 55523345 55523345 C A 1 0 0 0 0 0 0 0 1 17992 842 30 2 2 XKR4 8 55523345 Silent SNP C 11LU016_T 12767042 55523345 89615291 248 300 CSMD3 0 . GRCh38 8 112650185 112650185 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.3169A>T p.Ser1057Cys p.S1057C ENST00000297405 19/71 259 230 29 243 242 1 strelka-varscan-mutect CSMD3,missense_variant,p.Ser1057Cys,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser1017Cys,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser953Cys,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser397Cys,ENST00000339701,; A ENST00000297405 Transcript missense_variant 3414/13212 3169/11124 1057/3707 S/C Agt/Tgt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 19/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 112650185 112650185 T A 1 0 0 0 0 1 0 0 0 3747 1551 54 4 4 CSMD3 8 112650185 Missense_Mutation SNP T 11LU016_T 57126840 112650185 32488451 249 301 ASAP1 0 . GRCh38 8 130124106 130124106 + Splice_Site SNP T T A novel 11LU016_T 11LU016_N T T c.1516-2A>T p.X506_splice ENST00000518721 88 75 13 154 154 0 strelka-varscan-mutect ASAP1,splice_acceptor_variant,,ENST00000357668,NM_001247996.1;ASAP1,splice_acceptor_variant,,ENST00000518721,NM_018482.3;ASAP1,splice_acceptor_variant,,ENST00000524124,;ASAP1,splice_acceptor_variant,,ENST00000521075,; A ENST00000518721 Transcript splice_acceptor_variant -/5507 1516/3390 506/1129 1 -1 ASAP1 HGNC HGNC:2720 protein_coding YES CCDS6362.1 ENSP00000429900 Q9ULH1 UPI0000351D6E NM_018482.3 17/29 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 2 130124106 130124106 T A 1 0 0 0 0 0 0 1 0 1152 1594 55 4 4 ASAP1 8 130124106 Splice_Site SNP T 11LU016_T 17473921 130124106 15014530 250 302 ADCY8 0 . GRCh38 8 131039870 131039870 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.464C>A p.Pro155His p.P155H ENST00000286355 1/18 318 256 62 279 278 1 strelka-varscan-mutect ADCY8,missense_variant,p.Pro155His,ENST00000286355,NM_001115.2;ADCY8,missense_variant,p.Pro155His,ENST00000377928,; T ENST00000286355 Transcript missense_variant 2557/5938 464/3756 155/1251 P/H cCc/cAc 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 deleterious(0) 1/18 hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 131039870 131039870 G T 1 0 0 0 0 1 0 0 0 344 1232 43 2 2 ADCY8 8 131039870 Missense_Mutation SNP G 11LU016_T 915764 131039870 14098766 251 303 OC90 0 . GRCh38 8 132024709 132024709 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.1842C>A p.= p.T614T ENST00000262283 18/18 168 134 34 139 139 0 strelka-varscan-mutect RP11-240B13.2,synonymous_variant,p.=,ENST00000262283,;OC90,synonymous_variant,p.=,ENST00000254627,NM_001080399.2; T ENST00000262283 Transcript synonymous_variant 1942/2413 1842/2070 614/689 T acC/acA 1 -1 RP11-240B13.2 Clone_based_vega_gene protein_coding YES ENSP00000262283 I6L893 UPI0000E5AF6B 18/18 Gene3D:1.20.90.10,Pfam_domain:PF00068,hmmpanther:PTHR11716,hmmpanther:PTHR11716:SF1,SMART_domains:SM00085,Superfamily_domains:SSF48619 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 132024709 132024709 G T 1 0 0 0 0 0 0 0 1 10891 987 35 2 2 OC90 8 132024709 Silent SNP G 11LU016_T 984839 132024709 13113927 252 304 FAM135B 0 . GRCh38 8 138132672 138132672 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.4142C>A p.Ala1381Asp p.A1381D ENST00000395297 20/20 366 322 44 423 422 1 strelka-varscan FAM135B,missense_variant,p.Ala1381Asp,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,; T ENST00000395297 Transcript missense_variant 4313/6962 4142/4221 1381/1406 A/D gCc/gAc 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 20/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 138132672 138132672 G T 1 0 0 0 0 1 0 0 0 5299 1203 42 2 2 FAM135B 8 138132672 Missense_Mutation SNP G 11LU016_T 6107963 138132672 7005964 253 305 ADGRB1 0 . GRCh38 8 142481280 142481280 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1855G>T p.Asp619Tyr p.D619Y ENST00000517894 10/31 246 203 43 281 280 1 strelka-varscan ADGRB1,missense_variant,p.Asp619Tyr,ENST00000517894,;ADGRB1,missense_variant,p.Asp619Tyr,ENST00000323289,NM_001702.2;ADGRB1,missense_variant,p.Asp619Tyr,ENST00000521208,;ADGRB1,non_coding_transcript_exon_variant,,ENST00000518820,; T ENST00000517894 Transcript missense_variant 2749/6241 1855/4755 619/1584 D/Y Gac/Tac 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 deleterious(0) 10/31 PROSITE_profiles:PS50227,Pfam_domain:PF02793,SMART_domains:SM00008 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 142481280 142481280 G T 1 0 0 0 0 1 0 0 0 355 1174 41 2 2 ADGRB1 8 142481280 Missense_Mutation SNP G 11LU016_T 4348608 142481280 2657356 254 306 ARC 0 . GRCh38 8 142613254 142613254 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1018C>A p.Pro340Thr p.P340T ENST00000356613 1/3 186 175 11 202 202 0 strelka-varscan ARC,missense_variant,p.Pro340Thr,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; T ENST00000356613 Transcript missense_variant 1219/2948 1018/1191 340/396 P/T Ccc/Acc 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 tolerated(0.07) 1/3 hmmpanther:PTHR15962 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 142613254 142613254 G T 1 0 0 0 0 1 0 0 0 963 1232 43 2 2 ARC 8 142613254 Missense_Mutation SNP G 11LU016_T 131974 142613254 2525382 255 307 WDR97 0 . GRCh38 8 144110240 144110240 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1827C>A p.Asn609Lys p.N609K ENST00000323662 6/24 143 114 29 171 171 0 strelka-varscan WDR97,missense_variant,p.Asn609Lys,ENST00000323662,;MAF1,downstream_gene_variant,,ENST00000534585,;MAF1,downstream_gene_variant,,ENST00000322428,NM_032272.4;MAF1,downstream_gene_variant,,ENST00000532522,;MAF1,downstream_gene_variant,,ENST00000527058,;MAF1,downstream_gene_variant,,ENST00000527572,;MAF1,downstream_gene_variant,,ENST00000534811,;WDR97,non_coding_transcript_exon_variant,,ENST00000533108,;SHARPIN,upstream_gene_variant,,ENST00000533184,;WDR97,missense_variant,p.Asn609Lys,ENST00000534167,;WDR97,non_coding_transcript_exon_variant,,ENST00000528691,;WDR97,non_coding_transcript_exon_variant,,ENST00000525150,;WDR97,upstream_gene_variant,,ENST00000529209,; A ENST00000323662 Transcript missense_variant 1852/6916 1827/4869 609/1622 N/K aaC/aaA 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 deleterious(0.01) 6/24 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF497,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 144110240 144110240 C A 1 0 0 0 0 1 0 0 0 17897 477 17 2 2 WDR97 8 144110240 Missense_Mutation SNP C 11LU016_T 1496986 144110240 1028396 256 308 ZNF16 0 . GRCh38 8 144931312 144931312 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1475G>C p.Ser492Thr p.S492T ENST00000276816 4/4 121 108 13 125 125 0 strelka-varscan ZNF16,missense_variant,p.Ser492Thr,ENST00000276816,NM_001029976.2;ZNF16,missense_variant,p.Ser492Thr,ENST00000611477,NM_006958.2;ZNF16,missense_variant,p.Ser492Thr,ENST00000394909,;ZNF16,downstream_gene_variant,,ENST00000532351,;ZNF16,downstream_gene_variant,,ENST00000527811,;ZNF16,downstream_gene_variant,,ENST00000532811,;ZNF16,downstream_gene_variant,,ENST00000527512,; G ENST00000276816 Transcript missense_variant 1662/2616 1475/2049 492/682 S/T aGt/aCt 1 -1 ZNF16 HGNC HGNC:12947 protein_coding YES CCDS6437.1 ENSP00000276816 P17020 UPI00001E058F NM_001029976.2 tolerated(0.09) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF269,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 144931312 144931312 C G 1 0 0 0 0 1 0 0 0 18319 565 20 4 4 ZNF16 8 144931312 Missense_Mutation SNP C 11LU016_T 821072 144931312 207324 257 309 ZNF16 0 . GRCh38 8 144932090 144932090 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.697G>T p.Gly233Trp p.G233W ENST00000276816 4/4 257 222 35 321 321 0 strelka-varscan ZNF16,missense_variant,p.Gly233Trp,ENST00000276816,NM_001029976.2;ZNF16,missense_variant,p.Gly233Trp,ENST00000611477,NM_006958.2;ZNF16,missense_variant,p.Gly233Trp,ENST00000394909,;ZNF16,downstream_gene_variant,,ENST00000532351,;ZNF16,downstream_gene_variant,,ENST00000527811,;ZNF16,downstream_gene_variant,,ENST00000532811,;ZNF16,downstream_gene_variant,,ENST00000527512,; A ENST00000276816 Transcript missense_variant 884/2616 697/2049 233/682 G/W Ggg/Tgg COSM340294 1 -1 ZNF16 HGNC HGNC:12947 protein_coding YES CCDS6437.1 ENSP00000276816 P17020 UPI00001E058F NM_001029976.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF269,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 144932090 144932090 C A 1 0 0 0 0 1 0 0 0 18319 594 21 2 2 ZNF16 8 144932090 Missense_Mutation SNP C 11LU016_T 778 144932090 206546 258 310 IL33 0 . GRCh38 9 6253550 6253550 + Splice_Site SNP A A T novel 11LU016_T 11LU016_N A A c.470-2A>T p.X157_splice ENST00000381434 138 116 22 138 138 0 strelka-varscan-mutect IL33,splice_acceptor_variant,,ENST00000381434,NM_001314046.1,NM_001314047.1,NM_001314044.1,NM_001314045.1,NM_033439.3;IL33,splice_acceptor_variant,,ENST00000456383,NM_001199640.1;IL33,splice_acceptor_variant,,ENST00000417746,NM_001199641.1;IL33,splice_acceptor_variant,,ENST00000611532,; T ENST00000381434 Transcript splice_acceptor_variant -/2641 470/813 157/270 1 1 IL33 HGNC HGNC:16028 protein_coding YES CCDS6468.1 ENSP00000370842 O95760 UPI000000DBB2 NM_001314046.1,NM_001314047.1,NM_001314044.1,NM_001314045.1,NM_033439.3 4/6 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 2 6253550 6253550 A T 1 0 0 0 0 0 0 1 0 7592 202 7 4 4 IL33 9 6253550 Splice_Site SNP A 11LU016_T 6253550 132141167 259 311 PTPRD 0 . GRCh38 9 8633357 8633357 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.312G>A p.= p.V104V ENST00000381196 11/43 105 82 23 126 126 0 strelka-varscan-mutect PTPRD,synonymous_variant,p.=,ENST00000381196,NM_002839.3;PTPRD,synonymous_variant,p.=,ENST00000356435,;PTPRD,synonymous_variant,p.=,ENST00000355233,NM_130392.3;PTPRD,synonymous_variant,p.=,ENST00000397617,;PTPRD,synonymous_variant,p.=,ENST00000397611,NM_001040712.2;PTPRD,synonymous_variant,p.=,ENST00000537002,NM_130393.3;PTPRD,synonymous_variant,p.=,ENST00000540109,;PTPRD,synonymous_variant,p.=,ENST00000486161,NM_130391.3;PTPRD,synonymous_variant,p.=,ENST00000397606,NM_001171025.1;PTPRD,synonymous_variant,p.=,ENST00000463477,;PTPRD,downstream_gene_variant,,ENST00000481079,;PTPRD,non_coding_transcript_exon_variant,,ENST00000488774,; T ENST00000381196 Transcript synonymous_variant 856/9911 312/5739 104/1912 V gtG/gtA 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 11/43 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 8633357 8633357 C T 1 0 0 0 0 0 0 0 1 12953 581 21 3 3 PTPRD 9 8633357 Silent SNP C 11LU016_T 2379807 8633357 129761360 260 312 BNC2 0 . GRCh38 9 16437285 16437285 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.909C>A p.Asn303Lys p.N303K ENST00000380672 6/7 255 242 13 223 223 0 strelka-varscan-mutect BNC2,missense_variant,p.Asn303Lys,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Asn129Lys,ENST00000545497,;BNC2,missense_variant,p.Asn260Lys,ENST00000418777,;BNC2,missense_variant,p.Asn236Lys,ENST00000380667,;BNC2,missense_variant,p.Asn225Lys,ENST00000380666,;BNC2,missense_variant,p.Asn225Lys,ENST00000603713,;BNC2,upstream_gene_variant,,ENST00000411752,;BNC2,missense_variant,p.Asn303Lys,ENST00000484726,; T ENST00000380672 Transcript missense_variant 967/12844 909/3300 303/1099 N/K aaC/aaA 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 tolerated(1) 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 16437285 16437285 G T 1 0 0 0 0 1 0 0 0 1631 1368 48 2 2 BNC2 9 16437285 Missense_Mutation SNP G 11LU016_T 7803928 16437285 121957432 261 313 ADAMTSL1 0 . GRCh38 9 18777612 18777612 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.3386delC p.Pro1129GlnfsTer2 p.P1129Qfs*2 ENST00000380548 19/29 184 143 41 216 216 0 sindel-varindel-pindel ADAMTSL1,frameshift_variant,p.Pro1129GlnfsTer2,ENST00000380548,NM_001040272.5;ADAMTSL1,non_coding_transcript_exon_variant,,ENST00000380559,; - ENST00000380548 Transcript frameshift_variant 3722/8030 3383/5289 1128/1762 S/X tCc/tc 1 1 ADAMTSL1 HGNC HGNC:14632 protein_coding YES CCDS47954.1 ENSP00000369921 Q8N6G6 UPI000004FD83 NM_001040272.5 19/29 HIGH 1 deletion 5 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 18777612 18777612 C - 1 0 1 0 1 0 0 0 0 318 855 30 0 0 ADAMTSL1 9 18777612 Frame_Shift_Del DEL C 11LU016_T 2340327 18777612 119617105 262 314 HAUS6 0 . GRCh38 9 19058632 19058632 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.2135A>T p.Glu712Val p.E712V ENST00000380502 16/17 92 76 16 76 76 0 strelka-varscan-mutect HAUS6,missense_variant,p.Glu712Val,ENST00000380502,NM_001270890.1,NM_017645.4;HAUS6,missense_variant,p.Glu576Val,ENST00000380496,;HAUS6,downstream_gene_variant,,ENST00000415524,; A ENST00000380502 Transcript missense_variant 2603/6536 2135/2868 712/955 E/V gAg/gTg 1 -1 HAUS6 HGNC HGNC:25948 protein_coding YES CCDS6489.1 ENSP00000369871 Q7Z4H7 UPI00000740C7 NM_001270890.1,NM_017645.4 tolerated(0.06) 16/17 hmmpanther:PTHR16151 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 19058632 19058632 T A 1 0 0 0 0 1 0 0 0 6856 1551 54 4 4 HAUS6 9 19058632 Missense_Mutation SNP T 11LU016_T 281020 19058632 119336085 263 315 TAF1L 0 . GRCh38 9 32632190 32632190 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.3390G>C p.Lys1130Asn p.K1130N ENST00000242310 1/1 263 240 23 227 227 0 varscan-mutect TAF1L,missense_variant,p.Lys1130Asn,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; G ENST00000242310 Transcript missense_variant 3480/6216 3390/5481 1130/1826 K/N aaG/aaC 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 tolerated(0.13) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 32632190 32632190 C G 1 0 0 0 0 1 0 0 0 15919 912 32 4 4 TAF1L 9 32632190 Missense_Mutation SNP C 11LU016_T 13573558 32632190 105762527 264 316 TAF1L 0 . GRCh38 9 32632520 32632520 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.3060A>T p.Lys1020Asn p.K1020N ENST00000242310 1/1 439 383 56 371 371 0 strelka-varscan-mutect TAF1L,missense_variant,p.Lys1020Asn,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; A ENST00000242310 Transcript missense_variant 3150/6216 3060/5481 1020/1826 K/N aaA/aaT 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 tolerated(0.35) 1/1 Pfam_domain:PF12157,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 32632520 32632520 T A 1 0 0 0 0 1 0 0 0 15919 1838 64 4 4 TAF1L 9 32632520 Missense_Mutation SNP T 11LU016_T 330 32632520 105762197 265 317 CNTNAP3B 0 . GRCh38 9 41998501 41998501 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.642C>A p.= p.A214A ENST00000377561 5/24 132 110 22 92 92 0 strelka-varscan CNTNAP3B,synonymous_variant,p.=,ENST00000612828,;CNTNAP3B,synonymous_variant,p.=,ENST00000377561,NM_001201380.2;CNTNAP3B,synonymous_variant,p.=,ENST00000276974,;CNTNAP3B,synonymous_variant,p.=,ENST00000341990,;CNTNAP3B,synonymous_variant,p.=,ENST00000617422,;CNTNAP3B,synonymous_variant,p.=,ENST00000619138,;CNTNAP3B,synonymous_variant,p.=,ENST00000479351,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,; T ENST00000377561 Transcript synonymous_variant 1035/5379 642/3867 214/1288 A gcC/gcA 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 5/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 41998501 41998501 G T 1 0 0 0 0 0 0 0 1 3430 1335 47 2 2 CNTNAP3B 9 41998501 Silent SNP G 11LU016_T 9365981 41998501 96396216 266 318 SPATA31A3 0 . GRCh38 9 66987366 66987366 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.3132C>A p.His1044Gln p.H1044Q ENST00000428649 4/4 214 181 33 256 255 1 strelka-varscan SPATA31A3,missense_variant,p.His1044Gln,ENST00000428649,NM_001083124.1;RP11-395E19.2,non_coding_transcript_exon_variant,,ENST00000616253,; T ENST00000428649 Transcript missense_variant 3194/4256 3132/4044 1044/1347 H/Q caC/caA 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 tolerated(0.12) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 35 171 2 2 0 0 0 0 -20 0.9999889 1 1 1 0 T 3 4 2 66987366 66987366 G T 1 0 0 0 0 1 0 0 0 15344 1136 40 1 1 SPATA31A3 9 66987366 Missense_Mutation SNP G 11LU016_T 24988865 66987366 71407351 267 319 SPATA31D1 0 . GRCh38 9 81994082 81994083 + Frame_Shift_Ins INS - - T novel 11LU016_T 11LU016_N - - c.3614dupT p.Leu1205PhefsTer12 p.L1205Ffs*12 ENST00000344803 4/4 98 81 17 102 102 0 sindel-varindel-pindel SPATA31D1,frameshift_variant,p.Leu1205PhefsTer12,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; T ENST00000344803 Transcript frameshift_variant 3659-3660/4833 3612-3613/4731 1204-1205/1576 -/X -/T 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 4/4 hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859 HIGH 1 insertion 2 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 2 81994082 81994082 - T 1 0 1 1 0 0 0 0 0 15347 1377 48 0 0 SPATA31D1 9 81994082 Frame_Shift_Ins INS - 11LU016_T 15006716 81994082 56400635 268 320 SPATA31D1 0 . GRCh38 9 81995113 81995113 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.4643G>A p.Ser1548Asn p.S1548N ENST00000344803 4/4 146 122 24 127 127 0 strelka-varscan SPATA31D1,missense_variant,p.Ser1548Asn,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; A ENST00000344803 Transcript missense_variant 4690/4833 4643/4731 1548/1576 S/N aGc/aAc 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.25) 4/4 hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 81995113 81995113 G A 1 0 0 0 0 1 0 0 0 15347 971 34 3 3 SPATA31D1 9 81995113 Missense_Mutation SNP G 11LU016_T 1031 81995113 56399604 269 321 NTRK2 0 . GRCh38 9 84723572 84723572 + Splice_Site SNP G G T 11LU016_T 11LU016_N G G c.584-1G>T p.X195_splice ENST00000277120 387 304 83 300 300 0 strelka-varscan NTRK2,splice_acceptor_variant,,ENST00000277120,;NTRK2,splice_acceptor_variant,,ENST00000304053,NM_001018065.2;NTRK2,splice_acceptor_variant,,ENST00000376208,NM_001018066.2;NTRK2,splice_acceptor_variant,,ENST00000395882,NM_001291937.1,NM_001007097.2;NTRK2,splice_acceptor_variant,,ENST00000359847,;NTRK2,splice_acceptor_variant,,ENST00000376214,NM_006180.4;NTRK2,splice_acceptor_variant,,ENST00000376213,;NTRK2,splice_acceptor_variant,,ENST00000323115,NM_001018064.2; T ENST00000277120 Transcript splice_acceptor_variant -/8633 584/2517 195/838 COSM753996 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D 6/18 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 2 84723572 84723572 G T 1 0 0 0 0 0 0 1 0 10773 1014 35 2 2 NTRK2 9 84723572 Splice_Site SNP G 11LU016_T 2728459 84723572 53671145 270 322 COL15A1 0 . GRCh38 9 99000922 99000922 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.1036G>C p.Gly346Arg p.G346R ENST00000375001 7/42 130 105 25 191 191 0 strelka-varscan COL15A1,missense_variant,p.Gly346Arg,ENST00000375001,NM_001855.4;COL15A1,missense_variant,p.Gly332Arg,ENST00000610452,; C ENST00000375001 Transcript missense_variant 1459/5496 1036/4167 346/1388 G/R Ggg/Cgg 1 1 COL15A1 HGNC HGNC:2192 protein_coding YES CCDS35081.1 ENSP00000364140 P39059 UPI0000211506 NM_001855.4 tolerated_low_confidence(0.1) 7/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 99000922 99000922 G C 1 0 0 0 0 1 0 0 0 3460 1348 47 4 4 COL15A1 9 99000922 Missense_Mutation SNP G 11LU016_T 14277350 99000922 39393795 271 323 FKTN 0 . GRCh38 9 105601174 105601174 + Silent SNP A A T novel 11LU016_T 11LU016_N A A c.195A>T p.= p.T65T ENST00000223528 4/10 135 123 12 133 133 0 strelka-varscan FKTN,synonymous_variant,p.=,ENST00000223528,NM_006731.2;FKTN,synonymous_variant,p.=,ENST00000602661,NM_001079802.1;FKTN,synonymous_variant,p.=,ENST00000357998,;FKTN,synonymous_variant,p.=,ENST00000448551,NM_001198963.1;FKTN,synonymous_variant,p.=,ENST00000374705,;FKTN,downstream_gene_variant,,ENST00000490134,;FKTN,3_prime_UTR_variant,,ENST00000602526,; T ENST00000223528 Transcript synonymous_variant 319/7364 195/1386 65/461 T acA/acT 1 1 FKTN HGNC HGNC:3622 protein_coding YES CCDS6766.1 ENSP00000223528 O75072 UPI000012A5A6 NM_006731.2 4/10 hmmpanther:PTHR15407 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 105601174 105601174 A T 1 0 0 0 0 0 0 0 1 5781 204 8 4 4 FKTN 9 105601174 Silent SNP A 11LU016_T 6600252 105601174 32793543 272 324 TMEM245 0 . GRCh38 9 109091142 109091142 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.930G>T p.Arg310Ser p.R310S ENST00000374586 5/18 142 116 26 174 174 0 strelka-varscan TMEM245,missense_variant,p.Arg310Ser,ENST00000374586,NM_032012.3;TMEM245,upstream_gene_variant,,ENST00000413712,;TMEM245,missense_variant,p.Arg60Ser,ENST00000491854,; A ENST00000374586 Transcript missense_variant 962/7980 930/2640 310/879 R/S agG/agT 1 -1 TMEM245 HGNC HGNC:1363 protein_coding YES CCDS43858.1 ENSP00000363714 Q9H330 UPI000013C833 NM_032012.3 tolerated(0.86) 5/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 109091142 109091142 C A 1 0 0 0 0 1 0 0 0 16605 622 22 2 2 TMEM245 9 109091142 Missense_Mutation SNP C 11LU016_T 3489968 109091142 29303575 273 325 PAPPA 0 . GRCh38 9 116235506 116235506 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.2601C>A p.= p.A867A ENST00000328252 7/22 212 173 39 272 271 1 strelka-varscan PAPPA,synonymous_variant,p.=,ENST00000328252,NM_002581.3; A ENST00000328252 Transcript synonymous_variant 2970/10959 2601/4884 867/1627 A gcC/gcA 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 7/22 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 116235506 116235506 C A 1 0 0 0 0 0 0 0 1 11512 581 21 2 2 PAPPA 9 116235506 Silent SNP C 11LU016_T 7144364 116235506 22159211 274 326 COL5A1 0 . GRCh38 9 134731627 134731627 + Silent SNP G G T rs774882530 11LU016_T 11LU016_N G G c.1296G>T p.= p.P432P ENST00000371817 8/66 184 131 53 148 147 1 strelka-varscan COL5A1,synonymous_variant,p.=,ENST00000371817,NM_000093.4;COL5A1,synonymous_variant,p.=,ENST00000618395,NM_001278074.1;COL5A1,non_coding_transcript_exon_variant,,ENST00000469093,; T ENST00000371817 Transcript synonymous_variant 1710/8471 1296/5517 432/1838 P ccG/ccT rs774882530 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 8/66 LOW 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999759 1 1 1 0 T 2 4 2 134731627 134731627 G T 1 0 0 0 0 0 0 0 1 3485 1103 39 1 1 COL5A1 9 134731627 Silent SNP G 11LU016_T 18496121 134731627 3663090 275 327 FCN1 0 . GRCh38 9 134909401 134909401 + Silent SNP T T A novel 11LU016_T 11LU016_N T T c.852A>T p.= p.P284P ENST00000616356 8/8 288 229 59 313 313 0 strelka-varscan FCN1,synonymous_variant,p.=,ENST00000616356,;FCN1,downstream_gene_variant,,ENST00000371806,NM_002003.3; A ENST00000616356 Transcript synonymous_variant 858/4369 852/1083 284/360 P ccA/ccT 1 -1 FCN1 HGNC HGNC:3623 protein_coding ENSP00000479379 A0A087WVE2 UPI00015E02A0 8/8 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 134909401 134909401 T A 1 0 0 0 0 0 0 0 1 5654 1567 55 4 4 FCN1 9 134909401 Silent SNP T 11LU016_T 177774 134909401 3485316 276 328 OLFM1 0 . GRCh38 9 135119591 135119591 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.871T>C p.Ser291Pro p.S291P ENST00000371793 6/6 172 160 12 197 197 0 strelka-varscan OLFM1,missense_variant,p.Ser273Pro,ENST00000252854,NM_014279.4;OLFM1,missense_variant,p.Ser264Pro,ENST00000371796,NM_001282612.1;OLFM1,missense_variant,p.Ser291Pro,ENST00000371793,NM_001282611.1;OLFM1,missense_variant,p.Ser188Pro,ENST00000539877,;OLFM1,3_prime_UTR_variant,,ENST00000545657,;OLFM1,non_coding_transcript_exon_variant,,ENST00000483042,; C ENST00000371793 Transcript missense_variant 1122/2444 871/1458 291/485 S/P Tcc/Ccc 1 1 OLFM1 HGNC HGNC:17187 protein_coding YES CCDS65184.1 ENSP00000360858 Q99784 UPI000013DB05 NM_001282611.1 tolerated(0.08) 6/6 PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF34,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 135119591 135119591 T C 1 0 0 0 0 1 0 0 0 10927 1551 54 5 5 OLFM1 9 135119591 Missense_Mutation SNP T 11LU016_T 210190 135119591 3275126 277 329 PPP1R26 0 . GRCh38 9 135485205 135485205 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.695A>T p.Gln232Leu p.Q232L ENST00000356818 4/4 171 143 28 229 229 0 strelka-varscan PPP1R26,missense_variant,p.Gln232Leu,ENST00000356818,NM_014811.3;PPP1R26,missense_variant,p.Gln232Leu,ENST00000401470,;PPP1R26,missense_variant,p.Gln232Leu,ENST00000605286,;PPP1R26,missense_variant,p.Gln232Leu,ENST00000604351,;PPP1R26,missense_variant,p.Gln232Leu,ENST00000605660,;PPP1R26-AS1,upstream_gene_variant,,ENST00000455039,;PPP1R26-AS1,upstream_gene_variant,,ENST00000603893,;PPP1R26-AS1,upstream_gene_variant,,ENST00000605260,;PPP1R26,intron_variant,,ENST00000602993,; T ENST00000356818 Transcript missense_variant 1244/4932 695/3630 232/1209 Q/L cAg/cTg 1 1 PPP1R26 HGNC HGNC:29089 protein_coding YES CCDS6988.1 ENSP00000349274 Q5T8A7 UPI000013DB17 NM_014811.3 deleterious(0) 4/4 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15740,hmmpanther:PTHR15724 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 135485205 135485205 A T 1 0 0 0 0 1 0 0 0 12484 188 7 4 4 PPP1R26 9 135485205 Missense_Mutation SNP A 11LU016_T 365614 135485205 2909512 278 330 SEC16A 0 . GRCh38 9 136441819 136441819 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.7010delG p.Cys2337SerfsTer9 p.C2337Sfs*9 ENST00000313050 30/30 172 132 40 193 193 0 sindel-varindel-pindel SEC16A,frameshift_variant,p.Cys2314SerfsTer9,ENST00000290037,NM_001276418.1;SEC16A,frameshift_variant,p.Cys2337SerfsTer9,ENST00000313050,NM_014866.1;SEC16A,frameshift_variant,p.Cys2114SerfsTer9,ENST00000371706,;SEC16A,frameshift_variant,p.Cys2134SerfsTer9,ENST00000431893,;SEC16A,frameshift_variant,p.Cys1039SerfsTer9,ENST00000453963,;SEC16A,frameshift_variant,p.Cys731SerfsTer9,ENST00000277537,;SEC16A,frameshift_variant,p.Cys365SerfsTer9,ENST00000313084,;INPP5E,upstream_gene_variant,,ENST00000371712,NM_001318502.1,NM_019892.4;SEC16A,non_coding_transcript_exon_variant,,ENST00000467838,;INPP5E,upstream_gene_variant,,ENST00000635815,; - ENST00000313050 Transcript frameshift_variant 7084/8806 7010/7074 2337/2357 C/X tGc/tc 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 30/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 HIGH 1 deletion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999974 1 1 1 0 - 7 5 2 136441819 136441819 C - 1 0 1 0 1 0 0 0 0 14263 724 25 0 0 SEC16A 9 136441819 Frame_Shift_Del DEL C 11LU016_T 956614 136441819 1952898 279 331 SEC16A 0 . GRCh38 9 136474778 136474778 + Missense_Mutation SNP C C A rs763490788 11LU016_T 11LU016_N C C c.2838G>T p.Lys946Asn p.K946N ENST00000313050 1/30 178 168 10 171 170 1 strelka-varscan SEC16A,missense_variant,p.Lys946Asn,ENST00000290037,NM_001276418.1;SEC16A,missense_variant,p.Lys946Asn,ENST00000313050,NM_014866.1;SEC16A,missense_variant,p.Lys768Asn,ENST00000371706,;SEC16A,missense_variant,p.Lys768Asn,ENST00000431893,; A ENST00000313050 Transcript missense_variant 2912/8806 2838/7074 946/2357 K/N aaG/aaT rs763490788 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 tolerated(1) 1/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 136474778 136474778 C A 1 0 0 0 0 1 0 0 0 14263 680 24 2 2 SEC16A 9 136474778 Missense_Mutation SNP C 11LU016_T 32959 136474778 1919939 280 332 ANAPC2 0 . GRCh38 9 137183771 137183771 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.1069G>A p.Ala357Thr p.A357T ENST00000323927 5/13 117 97 20 132 132 0 strelka-varscan ANAPC2,missense_variant,p.Ala357Thr,ENST00000323927,NM_013366.3;SSNA1,upstream_gene_variant,,ENST00000322310,NM_003731.2;SSNA1,upstream_gene_variant,,ENST00000464553,;ANAPC2,upstream_gene_variant,,ENST00000483432,;ANAPC2,non_coding_transcript_exon_variant,,ENST00000495611,;ANAPC2,downstream_gene_variant,,ENST00000618649,;SSNA1,upstream_gene_variant,,ENST00000459860,;ANAPC2,upstream_gene_variant,,ENST00000471131,;SSNA1,upstream_gene_variant,,ENST00000463511,; T ENST00000323927 Transcript missense_variant 1074/2632 1069/2469 357/822 A/T Gcc/Acc 1 -1 ANAPC2 HGNC HGNC:19989 protein_coding YES CCDS7033.1 ENSP00000314004 Q9UJX6 UPI0000043E1B NM_013366.3 deleterious(0) 5/13 hmmpanther:PTHR11932:SF73,hmmpanther:PTHR11932 MODERATE 1 SNV 1 1 PASS . . 0 200 6 4 0 0 0 0 -20 0.9987606 1 1 1 0 T 3 4 2 137183771 137183771 C T 1 0 0 0 0 1 0 0 0 701 797 28 3 3 ANAPC2 9 137183771 Missense_Mutation SNP C 11LU016_T 708993 137183771 1210946 281 333 ADARB2 0 . GRCh38 10 1216995 1216995 + Silent SNP C C T rs142381078 11LU016_T 11LU016_N C C c.1638G>A p.= p.L546L ENST00000381312 7/10 240 194 46 350 349 1 strelka-varscan-mutect ADARB2,synonymous_variant,p.=,ENST00000381312,NM_018702.3;ADARB2,non_coding_transcript_exon_variant,,ENST00000469464,; T ENST00000381312 Transcript synonymous_variant 1964/8421 1638/2220 546/739 L ctG/ctA rs142381078 1 -1 ADARB2 HGNC HGNC:227 protein_coding YES CCDS7058.1 ENSP00000370713 Q9NS39 UPI0000071776 NM_018702.3 7/10 PROSITE_profiles:PS50141,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF17,Pfam_domain:PF02137,SMART_domains:SM00552 LOW 1 SNV 1 1 PASS rs142381078 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 1216995 1216995 C T 1 0 0 0 0 0 0 0 1 327 581 21 3 3 ADARB2 10 1216995 Silent SNP C 11LU016_T 1216995 132580427 282 334 AKR1C4 0 . GRCh38 10 5204433 5204433 + Frame_Shift_Del DEL G G - novel 11LU016_T 11LU016_N G G c.309delG p.Lys105AsnfsTer33 p.K105Nfs*33 ENST00000380448 5/11 145 134 11 159 159 0 sindel-varindel-pindel AKR1C4,frameshift_variant,p.Lys105AsnfsTer33,ENST00000380448,;AKR1C4,frameshift_variant,p.Lys105AsnfsTer33,ENST00000263126,NM_001818.3;RP11-445P17.6,upstream_gene_variant,,ENST00000441452,; - ENST00000380448 Transcript frameshift_variant 562/1414 309/972 103/323 L/X ctG/ct 1 1 AKR1C4 HGNC HGNC:387 protein_coding YES CCDS7064.1 ENSP00000369814 P17516 UPI000013D3B2 5/11 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF134,Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430,Prints_domain:PR00069 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 5204433 5204433 G - 1 0 1 0 1 0 0 0 0 556 1277 45 0 0 AKR1C4 10 5204433 Frame_Shift_Del DEL G 11LU016_T 3987438 5204433 128592989 283 335 SFMBT2 0 . GRCh38 10 7367766 7367766 + Missense_Mutation SNP G G T rs760397823 11LU016_T 11LU016_N G G c.319C>A p.Arg107Ser p.R107S ENST00000397167 4/21 338 305 33 386 386 0 strelka-varscan-mutect SFMBT2,missense_variant,p.Arg107Ser,ENST00000397167,NM_001029880.2;SFMBT2,missense_variant,p.Arg107Ser,ENST00000361972,NM_001018039.1;SFMBT2,missense_variant,p.Arg107Ser,ENST00000379713,;SFMBT2,missense_variant,p.Arg107Ser,ENST00000379711,; T ENST00000397167 Transcript missense_variant 512/8024 319/2685 107/894 R/S Cgc/Agc rs760397823,COSM1348973,COSM4015673,COSM4015674 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 deleterious(0) 4/21 PROSITE_profiles:PS51079,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF02820,Gene3D:2.30.30.160,SMART_domains:SM00561,Superfamily_domains:SSF63748 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs760397823 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 7367766 7367766 G T 1 0 0 0 0 1 0 0 0 14436 1087 38 1 1 SFMBT2 10 7367766 Missense_Mutation SNP G 11LU016_T 2163333 7367766 126429656 284 336 KIN 0 . GRCh38 10 7774878 7774878 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.621G>T p.Leu207Phe p.L207F ENST00000379562 7/13 134 123 11 143 143 0 strelka-varscan-mutect KIN,missense_variant,p.Leu207Phe,ENST00000379562,NM_012311.3;KIN,non_coding_transcript_exon_variant,,ENST00000460089,; A ENST00000379562 Transcript missense_variant 669/6348 621/1182 207/393 L/F ttG/ttT 1 -1 KIN HGNC HGNC:6327 protein_coding YES CCDS7080.1 ENSP00000368881 O60870 UPI00000315C2 NM_012311.3 tolerated(0.13) 7/13 hmmpanther:PTHR12805 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 7774878 7774878 C A 1 0 0 0 0 1 0 0 0 8180 825 29 2 2 KIN 10 7774878 Missense_Mutation SNP C 11LU016_T 407112 7774878 126022544 285 337 PIP4K2A 0 . GRCh38 10 22607927 22607927 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.339G>T p.Gln113His p.Q113H ENST00000376573 3/10 87 73 14 117 116 1 strelka-mutect PIP4K2A,missense_variant,p.Gln113His,ENST00000376573,NM_005028.4;PIP4K2A,missense_variant,p.Gln54His,ENST00000545335,;PIP4K2A,splice_region_variant,,ENST00000422321,;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000432610,; A ENST00000376573 Transcript missense_variant,splice_region_variant 568/3802 339/1221 113/406 Q/H caG/caT 1 -1 PIP4K2A HGNC HGNC:8997 protein_coding YES CCDS7141.1 ENSP00000365757 P48426 UPI0000001052 NM_005028.4 tolerated(0.51) 3/10 Gene3D:2gk9B01,PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF21,SMART_domains:SM00330,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 22607927 22607927 C A 1 0 0 0 0 1 0 0 0 12031 695 24 2 2 PIP4K2A 10 22607927 Missense_Mutation SNP C 11LU016_T 14833049 22607927 111189495 286 338 ITGB1 0 . GRCh38 10 32920355 32920355 + Missense_Mutation SNP C C A rs201962041 11LU016_T 11LU016_N C C c.1159G>T p.Gly387Cys p.G387C ENST00000396033 10/16 133 108 25 117 117 0 strelka-varscan-mutect ITGB1,missense_variant,p.Gly387Cys,ENST00000396033,NM_133376.2;ITGB1,missense_variant,p.Gly387Cys,ENST00000423113,NM_033668.2;ITGB1,missense_variant,p.Gly387Cys,ENST00000302278,NM_002211.3; A ENST00000396033 Transcript missense_variant 1295/3784 1159/2397 387/798 G/C Ggc/Tgc rs201962041 1 -1 ITGB1 HGNC HGNC:6153 protein_coding YES CCDS7174.1 ENSP00000379350 P05556 UPI0000070EEB NM_133376.2 deleterious(0) 10/16 Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF28,SMART_domains:SM00187,Superfamily_domains:SSF69179 MODERATE 1 SNV 5 1 PASS rs201962041 . 0 206 0 3 0 0 0 0 -20 0.9999958 1 1 1 0 A 3 1 2 32920355 32920355 C A 1 0 0 0 0 1 0 0 0 7797 652 23 1 1 ITGB1 10 32920355 Missense_Mutation SNP C 11LU016_T 10312428 32920355 100877067 287 339 ANXA8 0 . GRCh38 10 47475504 47475504 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.595T>C p.Cys199Arg p.C199R ENST00000611843 6/12 161 152 9 235 235 0 varscan-mutect ANXA8,missense_variant,p.Cys199Arg,ENST00000611843,NM_001271702.1;ANXA8,missense_variant,p.Cys161Arg,ENST00000585281,NM_001040084.2;ANXA8,missense_variant,p.Cys99Arg,ENST00000583911,NM_001271703.1;ANXA8,intron_variant,,ENST00000583448,;ANXA8,intron_variant,,ENST00000583874,;ANXA8,intron_variant,,ENST00000577813,;ANXA8,downstream_gene_variant,,ENST00000602877,; G ENST00000611843 Transcript missense_variant 820/2174 595/1098 199/365 C/R Tgc/Cgc 1 -1 ANXA8 HGNC HGNC:546 protein_coding YES CCDS73123.1 ENSP00000478026 A0A087WTN9 UPI000299A05A NM_001271702.1 deleterious(0.03) 6/12 hmmpanther:PTHR10502,PROSITE_patterns:PS00223,Gene3D:1.10.220.10,Pfam_domain:PF00191,SMART_domains:SM00335,Superfamily_domains:SSF47874 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 47475504 47475504 A G 1 0 0 0 0 1 0 0 0 832 159 6 5 5 ANXA8 10 47475504 Missense_Mutation SNP A 11LU016_T 14555149 47475504 86321918 288 340 WDFY4 0 . GRCh38 10 48731321 48731321 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.1341C>T p.= p.H447H ENST00000325239 8/61 231 194 37 281 280 1 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1;WDFY4,synonymous_variant,p.=,ENST00000360890,; T ENST00000325239 Transcript synonymous_variant 1341/9555 1341/9555 447/3184 H caC/caT 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 8/61 Gene3D:1.25.10.10,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,Superfamily_domains:SSF48371 LOW SNV 5 1 PASS rs1226797802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 48731321 48731321 C T 1 0 0 0 0 0 0 0 1 17831 564 20 3 3 WDFY4 10 48731321 Silent SNP C 11LU016_T 1255817 48731321 85066101 289 341 PCDH15 0 . GRCh38 10 54066854 54066854 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.2138C>G p.Thr713Arg p.T713R ENST00000373957 19/35 229 199 30 210 210 0 strelka-varscan-mutect PCDH15,missense_variant,p.Thr713Arg,ENST00000614895,;PCDH15,missense_variant,p.Thr708Arg,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Thr708Arg,ENST00000414778,;PCDH15,missense_variant,p.Thr713Arg,ENST00000617051,;PCDH15,missense_variant,p.Thr713Arg,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Thr708Arg,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Thr708Arg,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Thr686Arg,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Thr671Arg,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Thr708Arg,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Thr637Arg,ENST00000622048,;PCDH15,missense_variant,p.Thr637Arg,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Thr708Arg,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Thr720Arg,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Thr715Arg,ENST00000395445,;PCDH15,missense_variant,p.Thr708Arg,ENST00000616114,;PCDH15,missense_variant,p.Thr708Arg,ENST00000395438,;PCDH15,missense_variant,p.Thr720Arg,ENST00000612394,;PCDH15,missense_variant,p.Thr713Arg,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Thr319Arg,ENST00000409834,;PCDH15,missense_variant,p.Thr708Arg,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; C ENST00000373957 Transcript missense_variant 2533/7032 2138/5889 713/1962 T/R aCa/aGa 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.05) 19/35 Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,PROSITE_patterns:PS00232,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 5 1 PASS rs1181806436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 54066854 54066854 G C 1 0 0 0 0 1 0 0 0 11598 1377 48 4 4 PCDH15 10 54066854 Missense_Mutation SNP G 11LU016_T 5335533 54066854 79730568 290 342 PHYHIPL 0 . GRCh38 10 59238649 59238649 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.540G>A p.Met180Ile p.M180I ENST00000373880 4/5 154 145 9 153 153 0 strelka-varscan-mutect PHYHIPL,missense_variant,p.Met180Ile,ENST00000373880,NM_032439.3;PHYHIPL,missense_variant,p.Met154Ile,ENST00000373878,NM_001143774.1;PHYHIPL,non_coding_transcript_exon_variant,,ENST00000472199,;PHYHIPL,3_prime_UTR_variant,,ENST00000486074,; A ENST00000373880 Transcript missense_variant 804/3578 540/1131 180/376 M/I atG/atA 1 1 PHYHIPL HGNC HGNC:29378 protein_coding YES CCDS7254.1 ENSP00000362987 Q96FC7 UPI0000199879 NM_032439.3 deleterious(0.01) 4/5 hmmpanther:PTHR15698,hmmpanther:PTHR15698:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 59238649 59238649 G A 1 0 0 0 0 1 0 0 0 11955 1319 46 3 3 PHYHIPL 10 59238649 Missense_Mutation SNP G 11LU016_T 5171795 59238649 74558773 291 343 LIPK 0 . GRCh38 10 88743319 88743319 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.958C>A p.Gln320Lys p.Q320K ENST00000404190 8/9 168 148 20 192 192 0 strelka-varscan-mutect LIPK,missense_variant,p.Gln320Lys,ENST00000404190,NM_001080518.1; A ENST00000404190 Transcript missense_variant,splice_region_variant 958/1230 958/1200 320/399 Q/K Cag/Aag 1 1 LIPK HGNC HGNC:23444 protein_coding YES CCDS44455.1 ENSP00000383900 Q5VXJ0 UPI00000497BC NM_001080518.1 deleterious(0.01) 8/9 hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF45,PIRSF_domain:PIRSF000862,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 88743319 88743319 C A 1 0 0 0 0 1 0 0 0 8748 840 29 2 2 LIPK 10 88743319 Missense_Mutation SNP C 11LU016_T 29504670 88743319 45054103 292 344 HTR7 0 . GRCh38 10 90743625 90743625 + Missense_Mutation SNP A A T rs774014888 11LU016_T 11LU016_N A A c.1361T>A p.Leu454Gln p.L454Q ENST00000336152 3/4 221 195 26 274 274 0 strelka-mutect HTR7,missense_variant,p.Leu454Gln,ENST00000336152,NM_019859.3;HTR7,intron_variant,,ENST00000371719,NM_019860.3;HTR7,intron_variant,,ENST00000277874,NM_000872.4; T ENST00000336152 Transcript missense_variant 1388/3126 1361/1440 454/479 L/Q cTa/cAa rs774014888 1 -1 HTR7 HGNC HGNC:5302 protein_coding YES CCDS7408.1 ENSP00000337949 P34969 UPI0000049B68 NM_019859.3 tolerated_low_confidence(0.06) 3/4 MODERATE 1 SNV 1 1 PASS rs774014888 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 90743625 90743625 A T 1 0 0 0 0 1 0 0 0 7348 420 15 4 4 HTR7 10 90743625 Missense_Mutation SNP A 11LU016_T 2000306 90743625 43053797 293 345 HTR7 0 . GRCh38 10 90857445 90857445 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.227A>G p.Tyr76Cys p.Y76C ENST00000336152 1/4 182 158 24 269 269 0 strelka-varscan-mutect HTR7,missense_variant,p.Tyr76Cys,ENST00000336152,NM_019859.3;HTR7,missense_variant,p.Tyr76Cys,ENST00000371719,NM_019860.3;HTR7,missense_variant,p.Tyr76Cys,ENST00000277874,NM_000872.4; C ENST00000336152 Transcript missense_variant 254/3126 227/1440 76/479 Y/C tAc/tGc 1 -1 HTR7 HGNC HGNC:5302 protein_coding YES CCDS7408.1 ENSP00000337949 P34969 UPI0000049B68 NM_019859.3 deleterious(0.01) 1/4 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF116,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 90857445 90857445 T C 1 0 0 0 0 1 0 0 0 7348 1638 57 5 5 HTR7 10 90857445 Missense_Mutation SNP T 11LU016_T 113820 90857445 42939977 294 346 TLL2 0 . GRCh38 10 96376763 96376763 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.2377C>T p.Pro793Ser p.P793S ENST00000357947 18/21 39 35 4 61 61 0 strelka-varscan-mutect TLL2,missense_variant,p.Pro793Ser,ENST00000357947,NM_012465.3;TLL2,upstream_gene_variant,,ENST00000506028,; A ENST00000357947 Transcript missense_variant 2603/6756 2377/3048 793/1015 P/S Cct/Tct 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 deleterious(0) 18/21 PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF638,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -10.56241 0.9999861 1 1 1 0 A 3 1 2 96376763 96376763 G A 1 0 0 0 0 1 0 0 0 16392 1203 42 3 3 TLL2 10 96376763 Missense_Mutation SNP G 11LU016_T 5519318 96376763 37420659 295 347 PDZD7 0 . GRCh38 10 101010784 101010784 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.2105C>A p.Pro702Gln p.P702Q ENST00000619208 15/17 247 219 28 455 455 0 strelka-varscan-mutect PDZD7,missense_variant,p.Pro702Gln,ENST00000619208,NM_001195263.1;LZTS2,downstream_gene_variant,,ENST00000370220,;LZTS2,downstream_gene_variant,,ENST00000370223,NM_001318099.1,NM_032429.2;PDZD7,downstream_gene_variant,,ENST00000433616,;PDZD7,3_prime_UTR_variant,,ENST00000474125,; T ENST00000619208 Transcript missense_variant 2355/4135 2105/3102 702/1033 P/Q cCa/cAa 1 -1 PDZD7 HGNC HGNC:26257 protein_coding YES CCDS73182.1 ENSP00000480489 Q9H5P4 UPI0001D15DE5 NM_001195263.1 tolerated(0.6) 15/17 hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF29 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 101010784 101010784 G T 1 0 0 0 0 1 0 0 0 11792 1348 47 2 2 PDZD7 10 101010784 Missense_Mutation SNP G 11LU016_T 4634021 101010784 32786638 296 348 NEURL1 0 . GRCh38 10 103571760 103571760 + Missense_Mutation SNP C C A rs769464925 11LU016_T 11LU016_N C C c.587C>A p.Thr196Lys p.T196K ENST00000369780 3/6 132 123 9 171 171 0 strelka-varscan-mutect NEURL1,missense_variant,p.Thr196Lys,ENST00000369780,NM_004210.4;NEURL1,missense_variant,p.Thr179Lys,ENST00000437579,;NEURL1,downstream_gene_variant,,ENST00000455386,;NEURL1,non_coding_transcript_exon_variant,,ENST00000465048,; A ENST00000369780 Transcript missense_variant 996/4314 587/1725 196/574 T/K aCg/aAg rs769464925,COSM330211 1 1 NEURL1 HGNC HGNC:7761 protein_coding YES CCDS7551.1 ENSP00000358795 O76050 UPI0000073F46 NM_004210.4 deleterious(0.02) 3/6 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,hmmpanther:PTHR12429:SF13 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769464925 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 103571760 103571760 C A 1 0 0 0 0 1 0 0 0 10380 536 19 1 1 NEURL1 10 103571760 Missense_Mutation SNP C 11LU016_T 2560976 103571760 30225662 297 349 SORCS1 0 . GRCh38 10 107164249 107164249 + Missense_Mutation SNP C C A rs761794885 11LU016_T 11LU016_N C C c.278G>T p.Arg93Leu p.R93L ENST00000263054 1/26 166 136 30 170 170 0 strelka-varscan-mutect SORCS1,missense_variant,p.Arg93Leu,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1; A ENST00000263054 Transcript missense_variant 286/7272 278/3507 93/1168 R/L cGg/cTg rs761794885 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 tolerated_low_confidence(0.11) 1/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8 MODERATE 1 SNV 1 1 PASS rs761794885 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 107164249 107164249 C A 1 0 0 0 0 1 0 0 0 15252 652 23 1 1 SORCS1 10 107164249 Missense_Mutation SNP C 11LU016_T 3592489 107164249 26633173 298 350 BBIP1 0 . GRCh38 10 110907711 110907711 + Nonsense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.163A>T p.Lys55Ter p.K55* ENST00000454061 3/5 79 73 6 98 98 0 strelka-varscan-mutect BBIP1,stop_gained,p.Lys55Ter,ENST00000454061,NM_001195304.1;BBIP1,intron_variant,,ENST00000448814,NM_001195305.1;BBIP1,intron_variant,,ENST00000447005,NM_001243783.1;BBIP1,intron_variant,,ENST00000605742,NM_001195306.1;BBIP1,intron_variant,,ENST00000423273,NM_001195307.1;BBIP1,intron_variant,,ENST00000436562,;RP11-348N5.9,non_coding_transcript_exon_variant,,ENST00000619110,;RP11-348N5.7,upstream_gene_variant,,ENST00000603915,;BBIP1,upstream_gene_variant,,ENST00000605265,;BBIP1,non_coding_transcript_exon_variant,,ENST00000422050,;BBIP1,intron_variant,,ENST00000398289,; A ENST00000454061 Transcript stop_gained 300/812 163/312 55/103 K/* Aag/Tag 1 -1 BBIP1 HGNC HGNC:28093 protein_coding YES CCDS55728.1 ENSP00000433157 A8MTZ0 UPI0000251FC1 NM_001195304.1 3/5 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 110907711 110907711 T A 1 0 0 0 0 0 1 0 0 1479 1792 62 4 4 BBIP1 10 110907711 Nonsense_Mutation SNP T 11LU016_T 3743462 110907711 22889711 299 351 SHOC2 0 . GRCh38 10 111004691 111004691 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1058A>T p.Gln353Leu p.Q353L ENST00000369452 5/9 269 233 36 272 272 0 strelka-varscan-mutect SHOC2,missense_variant,p.Gln353Leu,ENST00000369452,NM_001324336.1,NM_001324337.1,NM_007373.3;SHOC2,missense_variant,p.Gln307Leu,ENST00000265277,NM_001269039.1;SHOC2,missense_variant,p.Gln143Leu,ENST00000451838,;SHOC2,non_coding_transcript_exon_variant,,ENST00000489390,; T ENST00000369452 Transcript missense_variant 1403/3943 1058/1749 353/582 Q/L cAg/cTg 1 1 SHOC2 HGNC HGNC:15454 protein_coding YES CCDS7568.1 ENSP00000358464 Q9UQ13 UPI0000135954 NM_001324336.1,NM_001324337.1,NM_007373.3 deleterious(0) 5/9 SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 111004691 111004691 A T 1 0 0 0 0 1 0 0 0 14550 188 7 4 4 SHOC2 10 111004691 Missense_Mutation SNP A 11LU016_T 96980 111004691 22792731 300 352 NRAP 0 . GRCh38 10 113597127 113597127 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.4390G>T p.Asp1464Tyr p.D1464Y ENST00000369358 37/42 170 153 17 257 257 0 strelka-varscan-mutect NRAP,missense_variant,p.Asp1464Tyr,ENST00000359988,NM_198060.3;NRAP,missense_variant,p.Asp1437Tyr,ENST00000369360,;NRAP,missense_variant,p.Asp1464Tyr,ENST00000369358,NM_001261463.1;NRAP,missense_variant,p.Asp1429Tyr,ENST00000360478,NM_006175.4; A ENST00000369358 Transcript missense_variant 4578/5534 4390/5196 1464/1731 D/Y Gac/Tac 1 -1 NRAP HGNC HGNC:7988 protein_coding YES CCDS73199.1 ENSP00000358365 A0A0A0MRM2 UPI000264ECBD NM_001261463.1 deleterious(0) 37/42 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,SMART_domains:SM00227 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 113597127 113597127 C A 1 0 0 0 0 1 0 0 0 10694 913 32 2 2 NRAP 10 113597127 Missense_Mutation SNP C 11LU016_T 2592436 113597127 20200295 301 353 DOCK1 0 . GRCh38 10 127403074 127403074 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.3947C>T p.Ala1316Val p.A1316V ENST00000623213 39/52 177 163 14 229 229 0 strelka-varscan-mutect DOCK1,missense_variant,p.Ala1295Val,ENST00000280333,NM_001380.4;DOCK1,missense_variant,p.Ala1316Val,ENST00000623213,NM_001290223.1; T ENST00000623213 Transcript missense_variant 4009/5761 3947/5661 1316/1886 A/V gCc/gTc 1 1 DOCK1 HGNC HGNC:2987 protein_coding YES CCDS76359.1 ENSP00000485033 A0A096LNH6 UPI0003EAEE97 NM_001290223.1 tolerated(0.28) 39/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF79,hmmpanther:PTHR23317,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 127403074 127403074 C T 1 0 0 0 0 1 0 0 0 4499 739 26 3 3 DOCK1 10 127403074 Missense_Mutation SNP C 11LU016_T 13805947 127403074 6394348 302 354 PWWP2B 0 . GRCh38 10 132406008 132406008 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1508G>T p.Trp503Leu p.W503L ENST00000305233 2/3 161 146 15 179 179 0 strelka-varscan-mutect PWWP2B,missense_variant,p.Trp503Leu,ENST00000305233,NM_138499.3;PWWP2B,intron_variant,,ENST00000631148,NM_001098637.1; T ENST00000305233 Transcript missense_variant 1567/2651 1508/1773 503/590 W/L tGg/tTg 1 1 PWWP2B HGNC HGNC:25150 protein_coding YES CCDS7667.2 ENSP00000306324 Q6NUJ5 UPI00001D7FE3 NM_138499.3 deleterious(0) 2/3 PROSITE_profiles:PS50812,hmmpanther:PTHR23068:SF6,hmmpanther:PTHR23068,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 132406008 132406008 G T 1 0 0 0 0 1 0 0 0 12999 1357 47 2 2 PWWP2B 10 132406008 Missense_Mutation SNP G 11LU016_T 5002934 132406008 1391414 303 355 KNDC1 0 . GRCh38 10 133198496 133198496 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.2066C>T p.Ala689Val p.A689V ENST00000304613 13/30 77 66 11 74 74 0 strelka-varscan-mutect KNDC1,missense_variant,p.Ala689Val,ENST00000304613,NM_152643.6;KNDC1,missense_variant,p.Ala624Val,ENST00000368571,; T ENST00000304613 Transcript missense_variant 2087/6793 2066/5250 689/1749 A/V gCc/gTc 1 1 KNDC1 HGNC HGNC:29374 protein_coding YES CCDS7674.1 ENSP00000304437 Q76NI1 UPI00003529F7 NM_152643.6 tolerated(0.07) 13/30 hmmpanther:PTHR21560,hmmpanther:PTHR21560:SF0 MODERATE 1 SNV 2 1 PASS . . 0 197 13 0 0 0 0 0 -19.99989 0.9998303 1 1 1 0 T 3 4 2 133198496 133198496 C T 1 0 0 0 0 1 0 0 0 8304 753 26 3 3 KNDC1 10 133198496 Missense_Mutation SNP C 11LU016_T 792488 133198496 598926 304 356 MUC6 0 . GRCh38 11 1017100 1017100 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.5701G>A p.Gly1901Arg p.G1901R ENST00000421673 31/33 816 753 63 928 927 1 varscan-mutect MUC6,missense_variant,p.Gly1901Arg,ENST00000421673,NM_005961.2;AP2A2,downstream_gene_variant,,ENST00000332231,NM_001242837.1;AP2A2,downstream_gene_variant,,ENST00000448903,NM_012305.3;MUC6,upstream_gene_variant,,ENST00000532016,;MUC6,downstream_gene_variant,,ENST00000527242,; T ENST00000421673 Transcript missense_variant 5752/8006 5701/7320 1901/2439 G/R Ggg/Agg 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 deleterious_low_confidence(0.01) 31/33 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS rs1479273032 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 1017100 1017100 C T 1 0 0 0 0 1 0 0 0 9980 594 21 3 3 MUC6 11 1017100 Missense_Mutation SNP C 11LU016_T 1017100 134069522 305 357 MUC5AC 0 . GRCh38 11 1188923 1188923 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.10778G>T p.Gly3593Val p.G3593V ENST00000621226 31/49 36 28 8 32 32 0 strelka-varscan-mutect MUC5AC,missense_variant,p.Gly3593Val,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript missense_variant 10825/17448 10778/16965 3593/5654 G/V gGc/gTc 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0) 31/49 Pfam_domain:PF13330 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -19.87076 1 1 1 1 0 T 3 4 2 1188923 1188923 G T 1 0 0 0 0 1 0 0 0 9978 1203 42 2 2 MUC5AC 11 1188923 Missense_Mutation SNP G 11LU016_T 171823 1188923 133897699 306 358 OSBPL5 0 . GRCh38 11 3122067 3122067 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.332A>T p.Lys111Met p.K111M ENST00000263650 5/22 260 245 15 319 319 0 strelka-varscan-mutect OSBPL5,missense_variant,p.Lys111Met,ENST00000263650,NM_020896.3;OSBPL5,missense_variant,p.Lys111Met,ENST00000389989,NM_145638.2,NM_001144063.1;OSBPL5,missense_variant,p.Lys111Met,ENST00000348039,;OSBPL5,missense_variant,p.Lys63Met,ENST00000525498,;OSBPL5,missense_variant,p.Lys111Met,ENST00000526122,;OSBPL5,missense_variant,p.Lys111Met,ENST00000533234,;OSBPL5,downstream_gene_variant,,ENST00000533721,;OSBPL5,downstream_gene_variant,,ENST00000534157,;OSBPL5,downstream_gene_variant,,ENST00000530372,;OSBPL5,missense_variant,p.Asn111Ile,ENST00000471998,;OSBPL5,non_coding_transcript_exon_variant,,ENST00000534491,;OSBPL5,non_coding_transcript_exon_variant,,ENST00000477622,;OSBPL5,non_coding_transcript_exon_variant,,ENST00000465323,;OSBPL5,non_coding_transcript_exon_variant,,ENST00000459995,;OSBPL5,upstream_gene_variant,,ENST00000532951,; A ENST00000263650 Transcript missense_variant 492/3889 332/2640 111/879 K/M aAg/aTg 1 -1 OSBPL5 HGNC HGNC:16392 protein_coding YES CCDS31344.1 ENSP00000263650 Q9H0X9 UPI000000D722 NM_020896.3 deleterious(0) 5/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10972:SF94,hmmpanther:PTHR10972 MODERATE 1 SNV 1 1 PASS rs1323154221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 3122067 3122067 T A 1 0 0 0 0 1 0 0 0 11346 1609 56 4 4 OSBPL5 11 3122067 Missense_Mutation SNP T 11LU016_T 1933144 3122067 131964555 307 359 OR51E1 0 . GRCh38 11 4652532 4652532 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.6G>T p.Met2Ile p.M2I ENST00000396952 2/2 48 28 20 77 77 0 strelka-varscan-mutect OR51E1,missense_variant,p.Met2Ile,ENST00000396952,NM_152430.3;OR51E1,missense_variant,p.Met2Ile,ENST00000530215,; T ENST00000396952 Transcript missense_variant 656/3612 6/957 2/318 M/I atG/atT 1 1 OR51E1 HGNC HGNC:15194 protein_coding YES CCDS31358.2 ENSP00000380155 Q8TCB6 A0A126GVF8 UPI000003ACE2 NM_152430.3 deleterious(0.03) 2/2 MODERATE 1 SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 4652532 4652532 G T 1 0 0 0 0 1 0 0 0 11168 1348 47 2 2 OR51E1 11 4652532 Missense_Mutation SNP G 11LU016_T 1530465 4652532 130434090 308 360 OR52J3 0 . GRCh38 11 5047134 5047134 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.609T>G p.Phe203Leu p.F203L ENST00000380370 1/1 201 158 43 230 230 0 strelka-varscan-mutect OR52J3,missense_variant,p.Phe203Leu,ENST00000380370,NM_001001916.2; G ENST00000380370 Transcript missense_variant 609/936 609/936 203/311 F/L ttT/ttG 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 tolerated(0.52) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 5047134 5047134 T G 1 0 0 0 0 1 0 0 0 11195 1809 63 5 5 OR52J3 11 5047134 Missense_Mutation SNP T 11LU016_T 394602 5047134 130039488 309 361 HBD 0 . GRCh38 11 5234192 5234192 + Missense_Mutation SNP C C G 11LU016_T 11LU016_N C C c.114G>C p.Trp38Cys p.W38C ENST00000380299 2/3 394 287 107 367 367 0 strelka-varscan-mutect HBD,missense_variant,p.Trp38Cys,ENST00000380299,NM_000519.3;HBD,missense_variant,p.Trp38Cys,ENST00000429817,;HBD,missense_variant,p.Trp38Cys,ENST00000292901,;HBD,intron_variant,,ENST00000417377,;HBB,upstream_gene_variant,,ENST00000380315,; G ENST00000380299 Transcript missense_variant 329/785 114/444 38/147 W/C tgG/tgC COSM1508721 1 -1 HBD HGNC HGNC:4829 protein_coding YES CCDS31376.1 ENSP00000369654 P02042 A0N071 UPI0000161DC2 NM_000519.3 deleterious(0) 2/3 PROSITE_profiles:PS01033,hmmpanther:PTHR11442:SF50,hmmpanther:PTHR11442,Pfam_domain:PF00042,Gene3D:1.10.490.10,Superfamily_domains:SSF46458,Prints_domain:PR00814 1 MODERATE 1 SNV 1 1 1 PASS rs1456294062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 5234192 5234192 C G 1 0 0 0 0 1 0 0 0 6865 856 30 4 4 HBD 11 5234192 Missense_Mutation SNP C 11LU016_T 187058 5234192 129852430 310 362 LMO1 0 . GRCh38 11 8230505 8230505 + Splice_Site SNP C C A novel 11LU016_T 11LU016_N C C c.26-1G>T p.X9_splice ENST00000335790 154 138 16 180 180 0 strelka-varscan-mutect LMO1,splice_acceptor_variant,,ENST00000335790,NM_002315.2;LMO1,splice_acceptor_variant,,ENST00000428101,NM_001270428.1;LMO1,splice_acceptor_variant,,ENST00000534484,;LMO1,splice_acceptor_variant,,ENST00000524379,; A ENST00000335790 Transcript splice_acceptor_variant -/1279 26/471 9/156 1 -1 LMO1 HGNC HGNC:6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 UPI0000133883 NM_002315.2 1/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 2 8230505 8230505 C A 1 0 0 0 0 0 0 1 0 8777 695 24 2 2 LMO1 11 8230505 Splice_Site SNP C 11LU016_T 2996313 8230505 126856117 311 363 ABCC8 0 . GRCh38 11 17460517 17460517 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.982G>T p.Gly328Trp p.G328W ENST00000302539 6/39 397 352 45 481 481 0 strelka-varscan-mutect ABCC8,missense_variant,p.Gly328Trp,ENST00000302539,NM_001287174.1;ABCC8,missense_variant,p.Gly328Trp,ENST00000389817,NM_000352.4;ABCC8,missense_variant,p.Gly328Trp,ENST00000527905,;ABCC8,non_coding_transcript_exon_variant,,ENST00000532728,;ABCC8,non_coding_transcript_exon_variant,,ENST00000635881,; A ENST00000302539 Transcript missense_variant 1051/4923 982/4749 328/1582 G/W Ggg/Tgg 1 -1 ABCC8 HGNC HGNC:59 protein_coding YES CCDS73264.1 ENSP00000303960 Q09428 UPI00015DFF64 NM_001287174.1 deleterious(0.02) 6/39 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF187,Superfamily_domains:SSF90123 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 17460517 17460517 C A 1 0 0 0 0 1 0 0 0 62 594 21 2 2 ABCC8 11 17460517 Missense_Mutation SNP C 11LU016_T 9230012 17460517 117626105 312 364 MYOD1 0 . GRCh38 11 17719984 17719984 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.202G>T p.Ala68Ser p.A68S ENST00000250003 1/3 152 142 10 151 151 0 strelka-varscan-mutect MYOD1,missense_variant,p.Ala68Ser,ENST00000250003,NM_002478.4; T ENST00000250003 Transcript missense_variant 417/1801 202/963 68/320 A/S Gcg/Tcg 1 1 MYOD1 HGNC HGNC:7611 protein_coding YES CCDS7826.1 ENSP00000250003 P15172 UPI000007280C NM_002478.4 tolerated(0.44) 1/3 Pfam_domain:PF01586,hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF2,SMART_domains:SM00520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 17719984 17719984 G T 1 0 0 0 0 1 0 0 0 10089 1203 42 2 2 MYOD1 11 17719984 Missense_Mutation SNP G 11LU016_T 259467 17719984 117366638 313 365 SLC6A5 0 . GRCh38 11 20601224 20601224 + Missense_Mutation SNP G G T rs547285018 11LU016_T 11LU016_N G G c.99G>T p.Arg33Ser p.R33S ENST00000525748 2/16 132 92 40 169 169 0 strelka-varscan-mutect SLC6A5,missense_variant,p.Arg33Ser,ENST00000525748,NM_004211.3;SLC6A5,missense_variant,p.Arg33Ser,ENST00000298923,; T ENST00000525748 Transcript missense_variant 372/7084 99/2394 33/797 R/S agG/agT rs547285018 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 tolerated_low_confidence(0.13) 2/16 MODERATE 1 SNV 1 1 PASS rs547285018 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 20601224 20601224 G T 1 0 0 0 0 1 0 0 0 14970 1165 41 2 2 SLC6A5 11 20601224 Missense_Mutation SNP G 11LU016_T 2881240 20601224 114485398 314 366 SLC5A12 0 . GRCh38 11 26671215 26671215 + Frame_Shift_Del DEL C C - 11LU016_T 11LU016_N C C c.1744delG p.Ala582LeufsTer43 p.A582Lfs*43 ENST00000396005 15/15 72 64 8 78 78 0 sindel-pindel SLC5A12,frameshift_variant,p.Ala582LeufsTer43,ENST00000396005,NM_178498.3;SLC5A12,3_prime_UTR_variant,,ENST00000527405,; - ENST00000396005 Transcript frameshift_variant 2054/6250 1744/1857 582/618 A/X Gct/ct COSM5672025 1 -1 SLC5A12 HGNC HGNC:28750 protein_coding YES CCDS7860.2 ENSP00000379326 Q1EHB4 UPI000003ED2C NM_178498.3 15/15 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF152 1 HIGH 1 deletion 1 1 1 PASS . . 0 199 8 3 0 0 0 0 -13.63891 0.9980933 1 1 1 0 - 7 5 2 26671215 26671215 C - 1 0 1 0 1 0 0 0 0 14947 739 26 0 0 SLC5A12 11 26671215 Frame_Shift_Del DEL C 11LU016_T 6069991 26671215 108415407 315 367 TCP11L1 0 . GRCh38 11 33061658 33061658 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.904G>T p.Val302Phe p.V302F ENST00000334274 7/10 152 143 9 98 98 0 strelka-varscan-mutect TCP11L1,missense_variant,p.Val302Phe,ENST00000334274,NM_018393.3;TCP11L1,missense_variant,p.Val302Phe,ENST00000432887,NM_001145541.1;TCP11L1,missense_variant,p.Val302Phe,ENST00000531632,;TCP11L1,downstream_gene_variant,,ENST00000530419,;TCP11L1,downstream_gene_variant,,ENST00000602733,;TCP11L1,downstream_gene_variant,,ENST00000530171,;TCP11L1,missense_variant,p.Val302Phe,ENST00000527661,;TCP11L1,3_prime_UTR_variant,,ENST00000528107,; T ENST00000334274 Transcript missense_variant 1304/2817 904/1530 302/509 V/F Gtt/Ttt 1 1 TCP11L1 HGNC HGNC:25655 protein_coding YES CCDS7882.1 ENSP00000335595 Q9NUJ3 UPI0000071A1F NM_018393.3 tolerated(0.13) 7/10 Pfam_domain:PF05794,hmmpanther:PTHR12832,hmmpanther:PTHR12832:SF15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 33061658 33061658 G T 1 0 0 0 0 1 0 0 0 16121 1377 48 2 2 TCP11L1 11 33061658 Missense_Mutation SNP G 11LU016_T 6390443 33061658 102024964 316 368 LMO2 0 . GRCh38 11 33864657 33864657 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.409G>T p.Gly137Trp p.G137W ENST00000257818 5/6 258 233 25 200 200 0 strelka-varscan-mutect LMO2,missense_variant,p.Gly137Trp,ENST00000257818,NM_005574.3;LMO2,missense_variant,p.Gly68Trp,ENST00000395833,NM_001142315.1,NM_001142316.1;LMO2,downstream_gene_variant,,ENST00000493667,;LMO2,3_prime_UTR_variant,,ENST00000411482,;LMO2,non_coding_transcript_exon_variant,,ENST00000464025,;LMO2,downstream_gene_variant,,ENST00000465614,; A ENST00000257818 Transcript missense_variant 1239/2294 409/684 137/227 G/W Ggg/Tgg 1 -1 LMO2 HGNC HGNC:6642 protein_coding YES CCDS7888.2 ENSP00000257818 P25791 UPI00001F9F84 NM_005574.3 deleterious(0) 5/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF109,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 33864657 33864657 C A 1 0 0 0 0 1 0 0 0 8778 623 22 2 2 LMO2 11 33864657 Missense_Mutation SNP C 11LU016_T 802999 33864657 101221965 317 369 LRRC4C 0 . GRCh38 11 40116052 40116052 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.241C>A p.Leu81Met p.L81M ENST00000278198 2/2 200 168 32 161 161 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Leu81Met,ENST00000278198,;LRRC4C,missense_variant,p.Leu81Met,ENST00000527150,;LRRC4C,missense_variant,p.Leu81Met,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Leu81Met,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Leu81Met,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript missense_variant 2205/4054 241/1923 81/640 L/M Ctg/Atg 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious(0) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 40116052 40116052 G T 1 0 0 0 0 1 0 0 0 8903 962 34 2 2 LRRC4C 11 40116052 Missense_Mutation SNP G 11LU016_T 6251395 40116052 94970570 318 370 OR4C5 0 . GRCh38 11 48366207 48366207 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.259T>A p.Phe87Ile p.F87I ENST00000319813 1/1 231 205 26 306 305 1 strelka-varscan-mutect OR4C5,missense_variant,p.Phe87Ile,ENST00000319813,; T ENST00000319813 Transcript missense_variant 259/981 259/981 87/326 F/I Ttt/Att 1 -1 OR4C5 HGNC HGNC:14702 protein_coding YES ENSP00000321338 Q8NGB2 UPI0000061EE9 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF9,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 48366207 48366207 A T 1 0 0 0 0 1 0 0 0 11128 72 3 4 4 OR4C5 11 48366207 Missense_Mutation SNP A 11LU016_T 8250155 48366207 86720415 319 371 OR4C12 0 . GRCh38 11 49982168 49982168 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.334C>A p.Leu112Met p.L112M ENST00000335238 1/1 177 145 32 131 130 1 strelka-varscan-mutect OR4C12,missense_variant,p.Leu112Met,ENST00000335238,NM_001005270.4; T ENST00000335238 Transcript missense_variant 368/1063 334/930 112/309 L/M Ctg/Atg 1 -1 OR4C12 HGNC HGNC:15168 protein_coding YES CCDS31496.1 ENSP00000334418 Q96R67 UPI0000041E30 NM_001005270.4 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF353,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1442841275 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 49982168 49982168 G T 1 0 0 0 0 1 0 0 0 11123 991 35 2 2 OR4C12 11 49982168 Missense_Mutation SNP G 11LU016_T 1615961 49982168 85104454 320 372 OR4C11 0 . GRCh38 11 55603623 55603623 + Missense_Mutation SNP G G C 11LU016_T 11LU016_N G G c.751C>G p.Pro251Ala p.P251A ENST00000302231 1/1 166 143 23 147 147 0 strelka-varscan-mutect OR4C11,missense_variant,p.Pro251Ala,ENST00000302231,NM_001004700.2; C ENST00000302231 Transcript missense_variant 776/1045 751/933 251/310 P/A Cca/Gca COSM3967582 1 -1 OR4C11 HGNC HGNC:15167 protein_coding YES CCDS31503.1 ENSP00000306651 Q6IEV9 A0A126GVN6 UPI000013E7AD NM_001004700.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF447,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 23 186 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 55603623 55603623 G C 1 0 0 0 0 1 0 0 0 11122 1232 43 4 4 OR4C11 11 55603623 Missense_Mutation SNP G 11LU016_T 5621455 55603623 79482999 321 373 OR5F1 0 . GRCh38 11 55994331 55994331 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.295C>T p.= p.L99L ENST00000278409 1/1 179 156 23 182 182 0 strelka-varscan-mutect OR5F1,synonymous_variant,p.=,ENST00000278409,NM_003697.1; A ENST00000278409 Transcript synonymous_variant 295/945 295/945 99/314 L Cta/Tta 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 55994331 55994331 G A 1 0 0 0 0 0 0 0 1 11228 991 35 3 3 OR5F1 11 55994331 Silent SNP G 11LU016_T 390708 55994331 79092291 322 374 OR8J3 0 . GRCh38 11 56137188 56137188 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.531T>A p.Phe177Leu p.F177L ENST00000301529 1/1 85 78 7 108 108 0 strelka-varscan-mutect OR8J3,missense_variant,p.Phe177Leu,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; T ENST00000301529 Transcript missense_variant 531/948 531/948 177/315 F/L ttT/ttA 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 56137188 56137188 A T 1 0 0 0 0 1 0 0 0 11310 11 1 4 4 OR8J3 11 56137188 Missense_Mutation SNP A 11LU016_T 142857 56137188 78949434 323 375 OR5T2 0 . GRCh38 11 56232375 56232375 + Missense_Mutation SNP C C T 11LU016_T 11LU016_N C C c.811G>A p.Glu271Lys p.E271K ENST00000313264 1/1 54 41 13 66 66 0 strelka-varscan-mutect OR5T2,missense_variant,p.Glu271Lys,ENST00000313264,NM_001004746.1; T ENST00000313264 Transcript missense_variant 811/1080 811/1080 271/359 E/K Gaa/Aaa COSM4641496,COSM5597271 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 56232375 56232375 C T 1 0 0 0 0 1 0 0 0 11250 835 29 3 3 OR5T2 11 56232375 Missense_Mutation SNP C 11LU016_T 95187 56232375 78854247 324 376 OR9G1 0 . GRCh38 11 56700759 56700759 + Silent SNP C C A rs753546668 11LU016_T 11LU016_N C C c.372C>A p.= p.A124A ENST00000312153 1/1 272 231 41 240 240 0 strelka-varscan-mutect OR9G1,synonymous_variant,p.=,ENST00000312153,NM_001005213.1; A ENST00000312153 Transcript synonymous_variant 372/918 372/918 124/305 A gcC/gcA rs753546668,COSM3359235 1 1 OR9G1 HGNC HGNC:15319 protein_coding YES CCDS31536.1 ENSP00000309012 Q8NH87 UPI0000061E7E NM_001005213.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF158,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW 1 SNV 0,1 1 PASS rs753546668 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 56700759 56700759 C A 1 0 0 0 0 0 0 0 1 11317 581 21 2 2 OR9G1 11 56700759 Silent SNP C 11LU016_T 468384 56700759 78385863 325 377 OR9G4 0 . GRCh38 11 56743274 56743274 + Missense_Mutation SNP G G A rs145468151 11LU016_T 11LU016_N G G c.538C>T p.Arg180Cys p.R180C ENST00000302957 1/1 317 300 17 319 319 0 strelka-varscan-mutect OR9G4,missense_variant,p.Arg180Cys,ENST00000302957,NM_001005284.1;MIR6128,upstream_gene_variant,,ENST00000615528,;OR9G3P,downstream_gene_variant,,ENST00000525553,; A ENST00000302957 Transcript missense_variant 538/985 538/984 180/327 R/C Cgc/Tgc rs145468151 1 -1 OR9G4 HGNC HGNC:15322 protein_coding YES CCDS31537.1 ENSP00000307515 Q8NGQ1 UPI00001D77DB NM_001005284.1 deleterious(0.05) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF141,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs145468151 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 56743274 56743274 G A 1 0 0 0 0 1 0 0 0 11318 1116 39 1 1 OR9G4 11 56743274 Missense_Mutation SNP G 11LU016_T 42515 56743274 78343348 326 378 BEST1 0 . GRCh38 11 61956947 61956947 + Silent SNP G G A rs776011957 11LU016_T 11LU016_N G G c.405G>A p.= p.A135A ENST00000449131 4/9 620 438 182 530 530 0 strelka-varscan-mutect BEST1,synonymous_variant,p.=,ENST00000449131,NM_001139443.1;BEST1,synonymous_variant,p.=,ENST00000378043,NM_004183.3,NM_001300787.1;BEST1,synonymous_variant,p.=,ENST00000526988,;BEST1,intron_variant,,ENST00000534553,;FTH1,downstream_gene_variant,,ENST00000530019,;FTH1,downstream_gene_variant,,ENST00000529191,;FTH1,downstream_gene_variant,,ENST00000529631,;BEST1,synonymous_variant,p.=,ENST00000524926,;BEST1,non_coding_transcript_exon_variant,,ENST00000524877,;BEST1,non_coding_transcript_exon_variant,,ENST00000529265,;BEST1,downstream_gene_variant,,ENST00000533521,; A ENST00000449131 Transcript synonymous_variant 491/4267 405/1815 135/604 A gcG/gcA rs776011957 1 1 BEST1 HGNC HGNC:12703 protein_coding YES CCDS44623.1 ENSP00000399709 O76090 UPI0000232791 NM_001139443.1 4/9 Pfam_domain:PF01062,hmmpanther:PTHR10736,hmmpanther:PTHR10736:SF4 LOW 1 SNV 1 1 PASS rs776011957 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 61956947 61956947 G A 1 0 0 0 0 0 0 0 1 1552 1132 40 1 1 BEST1 11 61956947 Silent SNP G 11LU016_T 5213673 61956947 73129675 327 379 EHD1 0 . GRCh38 11 64860216 64860216 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.665A>G p.Lys222Arg p.K222R ENST00000621096 4/6 353 314 39 388 388 0 strelka-varscan-mutect EHD1,missense_variant,p.Lys208Arg,ENST00000320631,NM_006795.3;EHD1,missense_variant,p.Lys208Arg,ENST00000359393,NM_001282444.1;EHD1,missense_variant,p.Lys222Arg,ENST00000621096,NM_001282445.1;EHD1,missense_variant,p.Lys222Arg,ENST00000433803,;EHD1,missense_variant,p.Lys72Arg,ENST00000421510,;EHD1,missense_variant,p.Lys72Arg,ENST00000455148,;EHD1,non_coding_transcript_exon_variant,,ENST00000466015,;EHD1,upstream_gene_variant,,ENST00000484846,;EHD1,upstream_gene_variant,,ENST00000498472,; C ENST00000621096 Transcript missense_variant 748/3336 665/1647 222/548 K/R aAg/aGg 1 -1 EHD1 HGNC HGNC:3242 protein_coding YES CCDS73315.1 ENSP00000479153 A0A024R571 UPI0000EE46CF NM_001282445.1 tolerated(0.86) 4/6 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51718,hmmpanther:PTHR11216:SF67,hmmpanther:PTHR11216,Gene3D:3.40.50.300,Pfam_domain:PF00350,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 64860216 64860216 T C 1 0 0 0 0 1 0 0 0 4813 1609 56 5 5 EHD1 11 64860216 Missense_Mutation SNP T 11LU016_T 2903269 64860216 70226406 328 380 ATG2A 0 . GRCh38 11 64910930 64910930 + Silent SNP C C G novel 11LU016_T 11LU016_N C C c.1491G>C p.= p.L497L ENST00000377264 11/41 328 271 57 386 386 0 strelka-varscan-mutect ATG2A,synonymous_variant,p.=,ENST00000377264,NM_015104.2;ATG2A,synonymous_variant,p.=,ENST00000418259,;ATG2A,intron_variant,,ENST00000421419,;ATG2A,downstream_gene_variant,,ENST00000461701,;ATG2A,downstream_gene_variant,,ENST00000461955,; G ENST00000377264 Transcript synonymous_variant 1604/6357 1491/5817 497/1938 L ctG/ctC 1 -1 ATG2A HGNC HGNC:29028 protein_coding YES CCDS31602.1 ENSP00000366475 Q2TAZ0 UPI00001C1F21 NM_015104.2 11/41 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF21 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 64910930 64910930 C G 1 0 0 0 0 0 0 0 1 1245 465 17 4 4 ATG2A 11 64910930 Silent SNP C 11LU016_T 50714 64910930 70175692 329 381 CDCA5 0 . GRCh38 11 65079437 65079437 + Silent SNP G G C novel 11LU016_T 11LU016_N G G c.594C>G p.= p.P198P ENST00000275517 5/6 328 266 62 248 247 1 strelka-varscan-mutect CDCA5,synonymous_variant,p.=,ENST00000275517,NM_080668.3;CDCA5,synonymous_variant,p.=,ENST00000404147,;ZFPL1,upstream_gene_variant,,ENST00000294258,NM_006782.3;CDCA5,upstream_gene_variant,,ENST00000529290,;ZFPL1,upstream_gene_variant,,ENST00000526334,;CDCA5,upstream_gene_variant,,ENST00000525464,;ZFPL1,upstream_gene_variant,,ENST00000526945,;ZFPL1,upstream_gene_variant,,ENST00000525509,;ZFPL1,upstream_gene_variant,,ENST00000526791,;CDCA5,missense_variant,p.Pro66Arg,ENST00000524733,;CDCA5,3_prime_UTR_variant,,ENST00000527430,;CDCA5,non_coding_transcript_exon_variant,,ENST00000479032,;CDCA5,non_coding_transcript_exon_variant,,ENST00000531401,;CDCA5,intron_variant,,ENST00000533015,;ZFPL1,upstream_gene_variant,,ENST00000533216,;ZFPL1,upstream_gene_variant,,ENST00000526289,;ZFPL1,upstream_gene_variant,,ENST00000526440,;ZFPL1,upstream_gene_variant,,ENST00000453524,;CDCA5,downstream_gene_variant,,ENST00000462902,;ZFPL1,upstream_gene_variant,,ENST00000531761,; C ENST00000275517 Transcript synonymous_variant 767/2587 594/759 198/252 P ccC/ccG 1 -1 CDCA5 HGNC HGNC:14626 protein_coding YES CCDS8091.1 ENSP00000275517 Q96FF9 A0A024R5D6 UPI000006E2A4 NM_080668.3 5/6 hmmpanther:PTHR31092,hmmpanther:PTHR31092:SF2,Pfam_domain:PF09666 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 65079437 65079437 G C 1 0 0 0 0 0 0 0 1 2792 987 35 4 4 CDCA5 11 65079437 Silent SNP G 11LU016_T 168507 65079437 70007185 330 382 SCYL1 0 . GRCh38 11 65537854 65537854 + Frame_Shift_Del DEL G G - rs371045520 11LU016_T 11LU016_N G G c.2009delG p.Gly670AlafsTer3 p.G670Afs*3 ENST00000270176 15/18 95 68 27 111 111 0 sindel-varindel-pindel SCYL1,frameshift_variant,p.Gly670AlafsTer3,ENST00000524944,;SCYL1,frameshift_variant,p.Gly670AlafsTer3,ENST00000270176,NM_020680.3;SCYL1,frameshift_variant,p.Gly527AlafsTer3,ENST00000527009,;SCYL1,frameshift_variant,p.Gly669AlafsTer3,ENST00000525364,;SCYL1,frameshift_variant,p.Gly653AlafsTer3,ENST00000420247,NM_001048218.1;SCYL1,frameshift_variant,p.Gly670AlafsTer3,ENST00000533862,;SCYL1,frameshift_variant,p.Gly142AlafsTer3,ENST00000528545,;SCYL1,3_prime_UTR_variant,,ENST00000279270,;LTBP3,downstream_gene_variant,,ENST00000301873,NM_001130144.2;LTBP3,downstream_gene_variant,,ENST00000322147,NM_001164266.1,NM_021070.4;LTBP3,downstream_gene_variant,,ENST00000530866,;LTBP3,downstream_gene_variant,,ENST00000532932,;LTBP3,downstream_gene_variant,,ENST00000526927,;LTBP3,downstream_gene_variant,,ENST00000530785,;LTBP3,downstream_gene_variant,,ENST00000529189,;LTBP3,downstream_gene_variant,,ENST00000532661,;LTBP3,downstream_gene_variant,,ENST00000529371,;SCYL1,non_coding_transcript_exon_variant,,ENST00000534462,;SCYL1,3_prime_UTR_variant,,ENST00000531601,;SCYL1,non_coding_transcript_exon_variant,,ENST00000532290,;LTBP3,downstream_gene_variant,,ENST00000528516,;LTBP3,downstream_gene_variant,,ENST00000525443,;LTBP3,downstream_gene_variant,,ENST00000529582,;SCYL1,downstream_gene_variant,,ENST00000526454,;SCYL1,downstream_gene_variant,,ENST00000524897,;SCYL1,downstream_gene_variant,,ENST00000529178,;LTBP3,downstream_gene_variant,,ENST00000530990,;SCYL1,downstream_gene_variant,,ENST00000529981,;LTBP3,downstream_gene_variant,,ENST00000526124,; - ENST00000270176 Transcript frameshift_variant 2082/2642 2005/2427 669/808 G/X Ggg/gg rs371045520 1 1 SCYL1 HGNC HGNC:14372 protein_coding YES CCDS41672.1 ENSP00000270176 Q96KG9 UPI0000035B94 NM_020680.3 15/18 hmmpanther:PTHR12984:SF3,hmmpanther:PTHR12984 HIGH 1 deletion 1 4 1 PASS . . 0 192 17 0 0 0 0 0 -20 0.9996589 1 1 1 0 - 7 5 2 65537854 65537854 G - 1 0 1 0 1 0 0 0 0 14219 1116 39 0 0 SCYL1 11 65537854 Frame_Shift_Del DEL G 11LU016_T 458417 65537854 69548768 331 383 GAL3ST3 0 . GRCh38 11 66043623 66043623 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.180C>A p.= p.R60R ENST00000312006 3/3 135 107 28 175 175 0 strelka-varscan-mutect GAL3ST3,synonymous_variant,p.=,ENST00000312006,NM_033036.2;GAL3ST3,synonymous_variant,p.=,ENST00000527878,;GAL3ST3,downstream_gene_variant,,ENST00000527048,; T ENST00000312006 Transcript synonymous_variant 462/2133 180/1296 60/431 R cgC/cgA 1 -1 GAL3ST3 HGNC HGNC:24144 protein_coding YES CCDS8128.1 ENSP00000308591 Q96A11 UPI0000071842 NM_033036.2 3/3 hmmpanther:PTHR14647:SF1,hmmpanther:PTHR14647,Gene3D:3.40.50.300,Pfam_domain:PF06990,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 66043623 66043623 G T 1 0 0 0 0 0 0 0 1 6067 1190 42 2 2 GAL3ST3 11 66043623 Silent SNP G 11LU016_T 505769 66043623 69042999 332 384 PPP1CA 0 . GRCh38 11 67400912 67400912 + Silent SNP T T A novel 11LU016_T 11LU016_N T T c.228A>T p.= p.I76I ENST00000312989 3/7 223 165 58 169 169 0 strelka-varscan-mutect PPP1CA,synonymous_variant,p.=,ENST00000376745,NM_002708.3;PPP1CA,synonymous_variant,p.=,ENST00000312989,NM_001008709.1;PPP1CA,synonymous_variant,p.=,ENST00000358239,NM_206873.1;PPP1CA,synonymous_variant,p.=,ENST00000527663,;PPP1CA,synonymous_variant,p.=,ENST00000542876,;PPP1CA,synonymous_variant,p.=,ENST00000546202,;RAD9A,downstream_gene_variant,,ENST00000307980,NM_004584.2;TBC1D10C,upstream_gene_variant,,ENST00000542590,NM_198517.3;TBC1D10C,upstream_gene_variant,,ENST00000526387,NM_001256508.1;TBC1D10C,upstream_gene_variant,,ENST00000312390,;RAD9A,downstream_gene_variant,,ENST00000544620,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000532446,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000537694,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000529724,;RAD9A,downstream_gene_variant,,ENST00000535644,;RAD9A,downstream_gene_variant,,ENST00000529100,;RAD9A,downstream_gene_variant,,ENST00000543808,;PPP1CA,upstream_gene_variant,,ENST00000532279,;PPP1CA,non_coding_transcript_exon_variant,,ENST00000526510,;TBC1D10C,upstream_gene_variant,,ENST00000526474,;TBC1D10C,upstream_gene_variant,,ENST00000529635,;RAD9A,downstream_gene_variant,,ENST00000530934,;TBC1D10C,upstream_gene_variant,,ENST00000530967,;RAD9A,downstream_gene_variant,,ENST00000538013,;TBC1D10C,upstream_gene_variant,,ENST00000529132,;TBC1D10C,upstream_gene_variant,,ENST00000533745,; A ENST00000312989 Transcript synonymous_variant 239/1389 228/1026 76/341 I atA/atT 1 -1 PPP1CA HGNC HGNC:9281 protein_coding YES CCDS31618.1 ENSP00000326031 P62136 A0A140VJS9 UPI0000070A42 NM_001008709.1 3/7 hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF255,Pfam_domain:PF00149,Gene3D:3.60.21.10,SMART_domains:SM00156,Superfamily_domains:SSF56300,Prints_domain:PR00114 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 67400912 67400912 T A 1 0 0 0 0 0 0 0 1 12459 1628 57 4 4 PPP1CA 11 67400912 Silent SNP T 11LU016_T 1357289 67400912 67685710 333 385 SHANK2 0 . GRCh38 11 70485908 70485908 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2621G>T p.Ser874Ile p.S874I ENST00000338508 10/11 684 581 103 606 604 2 strelka-varscan-mutect SHANK2,missense_variant,p.Ser866Ile,ENST00000409161,;SHANK2,missense_variant,p.Ser1462Ile,ENST00000601538,NM_012309.4;SHANK2,missense_variant,p.Ser874Ile,ENST00000449833,;SHANK2,missense_variant,p.Ser874Ile,ENST00000338508,NM_133266.4;SHANK2,missense_variant,p.Ser741Ile,ENST00000424924,;SHANK2,intron_variant,,ENST00000412252,;SHANK2,intron_variant,,ENST00000357171,;SHANK2,downstream_gene_variant,,ENST00000409530,;SHANK2,downstream_gene_variant,,ENST00000449116,; A ENST00000338508 Transcript missense_variant 2672/7271 2621/3786 874/1261 S/I aGc/aTc 1 -1 SHANK2 HGNC HGNC:14295 protein_coding YES CCDS76448.1 ENSP00000345193 A6NHU9 UPI0001B09234 NM_133266.4 tolerated(0.25) 10/11 hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 70485908 70485908 C A 1 0 0 0 0 1 0 0 0 14524 797 28 2 2 SHANK2 11 70485908 Missense_Mutation SNP C 11LU016_T 3084996 70485908 64600714 334 386 SHANK2 0 . GRCh38 11 70486707 70486707 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1822G>T p.Ala608Ser p.A608S ENST00000338508 10/11 388 324 64 526 525 1 strelka-varscan-mutect SHANK2,missense_variant,p.Ala600Ser,ENST00000409161,;SHANK2,missense_variant,p.Ala1196Ser,ENST00000601538,NM_012309.4;SHANK2,missense_variant,p.Ala608Ser,ENST00000449833,;SHANK2,missense_variant,p.Ala608Ser,ENST00000338508,NM_133266.4;SHANK2,missense_variant,p.Ala475Ser,ENST00000424924,;SHANK2,intron_variant,,ENST00000412252,;SHANK2,intron_variant,,ENST00000357171,;SHANK2,downstream_gene_variant,,ENST00000409530,;SHANK2,downstream_gene_variant,,ENST00000449116,; A ENST00000338508 Transcript missense_variant 1873/7271 1822/3786 608/1261 A/S Gcc/Tcc 1 -1 SHANK2 HGNC HGNC:14295 protein_coding YES CCDS76448.1 ENSP00000345193 A6NHU9 UPI0001B09234 NM_133266.4 tolerated(0.66) 10/11 Low_complexity_(Seg):seg,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF17 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 70486707 70486707 C A 1 0 0 0 0 1 0 0 0 14524 797 28 2 2 SHANK2 11 70486707 Missense_Mutation SNP C 11LU016_T 799 70486707 64599915 335 387 LRRC32 0 . GRCh38 11 76659895 76659895 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.1698C>A p.= p.L566L ENST00000407242 3/3 370 326 44 367 367 0 strelka-varscan-mutect LRRC32,synonymous_variant,p.=,ENST00000407242,NM_005512.2;LRRC32,synonymous_variant,p.=,ENST00000260061,NM_001128922.1;LRRC32,synonymous_variant,p.=,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,; T ENST00000407242 Transcript synonymous_variant 1941/4311 1698/1989 566/662 L ctC/ctA 1 -1 LRRC32 HGNC HGNC:4161 protein_coding YES CCDS8245.1 ENSP00000384126 Q14392 A0A024R5J7 UPI000012B0DF NM_005512.2 3/3 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF337,SMART_domains:SM00368,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 76659895 76659895 G T 1 0 0 0 0 0 0 0 1 8882 929 33 2 2 LRRC32 11 76659895 Silent SNP G 11LU016_T 6173188 76659895 58426727 336 388 MYO7A 0 . GRCh38 11 77198518 77198518 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.4465G>T p.Val1489Phe p.V1489F ENST00000409709 34/49 168 133 35 144 144 0 strelka-mutect MYO7A,missense_variant,p.Val1489Phe,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Val1489Phe,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Val1478Phe,ENST00000409619,;MYO7A,missense_variant,p.Val670Phe,ENST00000458169,;MYO7A,upstream_gene_variant,,ENST00000605744,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,; T ENST00000409709 Transcript missense_variant 4737/7462 4465/6648 1489/2215 V/F Gtc/Ttc COSM1492731 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.71) 34/49 PROSITE_profiles:PS50057 1 MODERATE 1 SNV 1 1 1 PASS rs1265094428 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 77198518 77198518 G T 1 0 0 0 0 1 0 0 0 10083 1145 40 1 1 MYO7A 11 77198518 Missense_Mutation SNP G 11LU016_T 538623 77198518 57888104 337 389 PCF11 0 . GRCh38 11 83164210 83164210 + Nonsense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.511G>T p.Glu171Ter p.E171* ENST00000298281 4/16 117 91 26 113 113 0 strelka-varscan-mutect PCF11,stop_gained,p.Glu171Ter,ENST00000298281,NM_015885.3;PCF11,stop_gained,p.Glu171Ter,ENST00000530660,;PCF11,stop_gained,p.Glu171Ter,ENST00000530304,;PCF11,downstream_gene_variant,,ENST00000533018,; T ENST00000298281 Transcript stop_gained 963/7677 511/4668 171/1555 E/* Gag/Tag 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 4/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 HIGH 1 SNV 1 1 PASS rs1391506247 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 2 83164210 83164210 G T 1 0 0 0 0 0 1 0 0 11661 1072 37 1 1 PCF11 11 83164210 Nonsense_Mutation SNP G 11LU016_T 5965692 83164210 51922412 338 390 ANKRD42 0 . GRCh38 11 83211411 83211411 + Missense_Mutation SNP C C G rs761893987 11LU016_T 11LU016_N C C c.567C>G p.Asp189Glu p.D189E ENST00000533342 5/11 255 236 19 206 206 0 strelka-varscan-mutect ANKRD42,missense_variant,p.Asp189Glu,ENST00000393389,NM_001300977.1;ANKRD42,missense_variant,p.Asp189Glu,ENST00000526731,NM_001300976.1;ANKRD42,missense_variant,p.Asp188Glu,ENST00000260047,NM_001300973.1;ANKRD42,missense_variant,p.Asp161Glu,ENST00000393392,NM_182603.3;ANKRD42,missense_variant,p.Asp189Glu,ENST00000533342,NM_001300975.1;ANKRD42,missense_variant,p.Asp189Glu,ENST00000531895,NM_001300972.1;ANKRD42,missense_variant,p.Asp76Glu,ENST00000528722,;RP11-727A23.7,intron_variant,,ENST00000531869,;RP11-727A23.1,upstream_gene_variant,,ENST00000463987,;RP11-727A23.8,downstream_gene_variant,,ENST00000533906,; G ENST00000533342 Transcript missense_variant 593/1949 567/1584 189/527 D/E gaC/gaG rs761893987 1 1 ANKRD42 HGNC HGNC:26752 protein_coding YES CCDS76459.1 ENSP00000435790 E9PIL2 UPI0001F781C9 NM_001300975.1 deleterious(0.02) 5/11 PROSITE_profiles:PS50297,hmmpanther:PTHR24201,hmmpanther:PTHR24201:SF2,Pfam_domain:PF13637,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs761893987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 83211411 83211411 C G 1 0 0 0 0 1 0 0 0 776 564 20 4 4 ANKRD42 11 83211411 Missense_Mutation SNP C 11LU016_T 47201 83211411 51875211 339 391 FAT3 0 . GRCh38 11 92857220 92857221 + Frame_Shift_Del DEL TG TG - novel 11LU016_T 11LU016_N TG TG c.10925_10926delGT p.Cys3642SerfsTer22 p.C3642Sfs*22 ENST00000525166 19/27 231 174 57 351 350 1 sindel-varindel-pindel FAT3,frameshift_variant,p.Cys3792SerfsTer22,ENST00000409404,NM_001008781.2;FAT3,frameshift_variant,p.Cys3642SerfsTer22,ENST00000525166,;FAT3,frameshift_variant,p.Cys127SerfsTer22,ENST00000533797,; - ENST00000525166 Transcript frameshift_variant 10944-10945/18699 10922-10923/13320 3641/4439 L/X cTG/c 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 19/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 HIGH 1 deletion 5 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 92857220 92857220 TG - 1 0 1 0 1 0 0 0 0 5551 1580 55 0 0 FAT3 11 92857220 Frame_Shift_Del DEL TG 11LU016_T 9645809 92857220 42229402 340 392 CWF19L2 0 . GRCh38 11 107416260 107416260 + Silent SNP T T G novel 11LU016_T 11LU016_N T T c.1566A>C p.= p.A522A ENST00000282251 10/18 115 96 19 88 88 0 strelka-varscan-mutect CWF19L2,synonymous_variant,p.=,ENST00000282251,NM_152434.2;CWF19L2,synonymous_variant,p.=,ENST00000431778,;CWF19L2,synonymous_variant,p.=,ENST00000532251,; G ENST00000282251 Transcript synonymous_variant 1594/3278 1566/2685 522/894 A gcA/gcC 1 -1 CWF19L2 HGNC HGNC:26508 protein_coding YES CCDS8336.2 ENSP00000282251 Q2TBE0 UPI00005A81B4 NM_152434.2 10/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12072,hmmpanther:PTHR12072:SF5 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 107416260 107416260 T G 1 0 0 0 0 0 0 0 1 3882 1799 63 5 5 CWF19L2 11 107416260 Silent SNP T 11LU016_T 14559040 107416260 27670362 341 393 JAML 0 . GRCh38 11 118210534 118210534 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.377T>A p.Val126Glu p.V126E ENST00000356289 4/10 231 161 70 215 215 0 strelka-varscan-mutect JAML,missense_variant,p.Val116Glu,ENST00000292067,NM_153206.2;JAML,missense_variant,p.Val126Glu,ENST00000356289,NM_001098526.1;JAML,missense_variant,p.Val126Glu,ENST00000533261,;JAML,missense_variant,p.Val87Glu,ENST00000526620,NM_001286571.1,NM_001286570.1;JAML,missense_variant,p.Val87Glu,ENST00000524477,;JAML,missense_variant,p.Val126Glu,ENST00000525565,;JAML,missense_variant,p.Val87Glu,ENST00000526595,;JAML,3_prime_UTR_variant,,ENST00000527877,;JAML,non_coding_transcript_exon_variant,,ENST00000534294,;JAML,non_coding_transcript_exon_variant,,ENST00000529164,;JAML,non_coding_transcript_exon_variant,,ENST00000531536,;HSPE1P18,upstream_gene_variant,,ENST00000517602,; T ENST00000356289 Transcript missense_variant 551/1944 377/1185 126/394 V/E gTg/gAg 1 -1 JAML HGNC HGNC:19084 protein_coding YES CCDS41723.1 ENSP00000348635 Q86YT9 UPI000000D82D NM_001098526.1 deleterious(0) 4/10 PROSITE_profiles:PS50835,hmmpanther:PTHR13869,hmmpanther:PTHR13869:SF22,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 118210534 118210534 A T 1 0 0 0 0 1 0 0 0 7858 159 6 4 4 JAML 11 118210534 Missense_Mutation SNP A 11LU016_T 10794274 118210534 16876088 342 394 SNX19 0 . GRCh38 11 130914528 130914528 + Missense_Mutation SNP C C A rs763675998 11LU016_T 11LU016_N C C c.1412G>T p.Gly471Val p.G471V ENST00000265909 1/11 161 108 53 178 176 2 strelka-varscan-mutect SNX19,missense_variant,p.Gly471Val,ENST00000265909,NM_014758.2;SNX19,missense_variant,p.Gly471Val,ENST00000533214,;SNX19,intron_variant,,ENST00000530356,;SNX19,intron_variant,,ENST00000528555,NM_001301089.1;SNX19,intron_variant,,ENST00000533318,;SNX19,upstream_gene_variant,,ENST00000524460,;SNX19,intron_variant,,ENST00000531608,; A ENST00000265909 Transcript missense_variant 1982/6535 1412/2979 471/992 G/V gGg/gTg rs763675998 1 -1 SNX19 HGNC HGNC:21532 protein_coding YES CCDS31721.1 ENSP00000265909 Q92543 UPI000013D6A5 NM_014758.2 tolerated(0.18) 1/11 hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF31 MODERATE 1 SNV 1 1 PASS rs763675998 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 130914528 130914528 C A 1 0 0 0 0 1 0 0 0 15211 623 22 2 2 SNX19 11 130914528 Missense_Mutation SNP C 11LU016_T 12703994 130914528 4172094 343 395 NCAPD3 0 . GRCh38 11 134158456 134158456 + Nonsense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.3907C>T p.Gln1303Ter p.Q1303* ENST00000534548 30/35 239 218 21 190 190 0 strelka-varscan-mutect NCAPD3,stop_gained,p.Gln1303Ter,ENST00000534548,NM_015261.2;NCAPD3,downstream_gene_variant,,ENST00000530396,;NCAPD3,downstream_gene_variant,,ENST00000527944,;NCAPD3,upstream_gene_variant,,ENST00000526787,;NCAPD3,3_prime_UTR_variant,,ENST00000534532,;NCAPD3,3_prime_UTR_variant,,ENST00000525964,;NCAPD3,upstream_gene_variant,,ENST00000525432,; A ENST00000534548 Transcript stop_gained 3972/5061 3907/4497 1303/1498 Q/* Caa/Taa 1 -1 NCAPD3 HGNC HGNC:28952 protein_coding YES CCDS31723.1 ENSP00000433681 P42695 UPI00001C1EFE NM_015261.2 30/35 PIRSF_domain:PIRSF036508 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 134158456 134158456 G A 1 0 0 0 0 0 1 0 0 10222 1357 47 3 3 NCAPD3 11 134158456 Nonsense_Mutation SNP G 11LU016_T 3243928 134158456 928166 344 396 WNK1 0 . GRCh38 12 900574 900574 + Frame_Shift_Del DEL C C - rs751969478 11LU016_T 11LU016_N C C c.7303delC p.Gln2435SerfsTer44 p.Q2435Sfs*44 ENST00000340908 26/28 335 318 17 404 403 1 varindel-pindel WNK1,frameshift_variant,p.Gln2596SerfsTer44,ENST00000530271,;WNK1,frameshift_variant,p.Gln2443SerfsTer44,ENST00000537687,NM_001184985.1;WNK1,frameshift_variant,p.Gln2435SerfsTer44,ENST00000340908,NM_213655.4;WNK1,frameshift_variant,p.Gln2183SerfsTer44,ENST00000315939,NM_018979.3;WNK1,frameshift_variant,p.Gln1935SerfsTer44,ENST00000535572,NM_014823.2;WNK1,upstream_gene_variant,,ENST00000544559,;WNK1,upstream_gene_variant,,ENST00000543065,;WNK1,non_coding_transcript_exon_variant,,ENST00000542424,;WNK1,non_coding_transcript_exon_variant,,ENST00000537603,; - ENST00000340908 Transcript frameshift_variant 7946/11208 7303/7905 2435/2634 Q/X Cag/ag rs751969478 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 26/28 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 900574 900574 C - 1 0 1 0 1 0 0 0 0 17933 479 17 0 0 WNK1 12 900574 Frame_Shift_Del DEL C 11LU016_T 900574 132374735 345 397 RP4-816N1.8 0 . GRCh38 12 2849291 2849291 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.858C>A p.= p.S286S ENST00000637658 3/3 117 91 26 158 158 0 strelka-varscan-mutect RP4-816N1.8,synonymous_variant,p.=,ENST00000637658,;ITFG2,intron_variant,,ENST00000537710,; T ENST00000637658 Transcript synonymous_variant 915/1167 858/918 286/305 S tcC/tcA 1 -1 RP4-816N1.8 Clone_based_vega_gene protein_coding YES ENSP00000489863 A6NCN8 UPI00017BE937 3/3 Pfam_domain:PF15046,hmmpanther:PTHR35156,hmmpanther:PTHR35156:SF1,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 2849291 2849291 G T 1 0 0 0 0 0 0 0 1 13779 1335 47 2 2 RP4-816N1.8 12 2849291 Silent SNP G 11LU016_T 1948717 2849291 130426018 346 398 PRMT8 0 . GRCh38 12 3592299 3592299 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.1048A>G p.Arg350Gly p.R350G ENST00000382622 9/10 40 31 9 142 142 0 strelka-varscan-mutect PRMT8,missense_variant,p.Arg350Gly,ENST00000382622,NM_019854.4;PRMT8,missense_variant,p.Arg341Gly,ENST00000452611,NM_001256536.1;PRMT8,non_coding_transcript_exon_variant,,ENST00000261252,;PRMT8,non_coding_transcript_exon_variant,,ENST00000543701,; G ENST00000382622 Transcript missense_variant 1438/2366 1048/1185 350/394 R/G Agg/Ggg 1 1 PRMT8 HGNC HGNC:5188 protein_coding YES CCDS8521.2 ENSP00000372067 Q9NR22 UPI00005B2E00 NM_019854.4 tolerated(0.1) 9/10 Gene3D:2.70.160.11,PROSITE_profiles:PS51678,hmmpanther:PTHR11006,hmmpanther:PTHR11006:SF47,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS rs1226553581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 3592299 3592299 A G 1 0 0 0 0 1 0 0 0 12673 295 11 5 5 PRMT8 12 3592299 Missense_Mutation SNP A 11LU016_T 743008 3592299 129683010 347 399 VWF 0 . GRCh38 12 5981937 5981937 + Missense_Mutation SNP C C T rs758156301 11LU016_T 11LU016_N C C c.7136G>A p.Arg2379His p.R2379H ENST00000261405 42/52 265 201 64 300 300 0 strelka-varscan-mutect VWF,missense_variant,p.Arg2379His,ENST00000261405,NM_000552.3; T ENST00000261405 Transcript missense_variant 7391/8838 7136/8442 2379/2813 R/H cGt/cAt rs758156301,COSM1363489 1 -1 VWF HGNC HGNC:12726 protein_coding YES CCDS8539.1 ENSP00000261405 P04275 UPI00001AE7EE NM_000552.3 deleterious(0) 42/52 PIRSF_domain:PIRSF002495 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758156301 . 0 205 0 2 3 0 0 0 -20 0.9646911 1 1 1 0 T 3 4 2 5981937 5981937 C T 1 0 0 0 0 1 0 0 0 17806 536 19 1 1 VWF 12 5981937 Missense_Mutation SNP C 11LU016_T 2389638 5981937 127293372 348 400 RECQL 0 . GRCh38 12 21490225 21490225 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.368A>T p.Tyr123Phe p.Y123F ENST00000444129 4/15 120 101 19 93 93 0 strelka-varscan-mutect RECQL,missense_variant,p.Tyr123Phe,ENST00000444129,NM_032941.2,NM_002907.3;RECQL,missense_variant,p.Tyr123Phe,ENST00000421138,;RECQL,missense_variant,p.Tyr123Phe,ENST00000314748,;RECQL,missense_variant,p.Tyr123Phe,ENST00000396093,;RECQL,missense_variant,p.Tyr123Phe,ENST00000542432,;RECQL,downstream_gene_variant,,ENST00000539672,;RECQL,downstream_gene_variant,,ENST00000536964,;RECQL,downstream_gene_variant,,ENST00000536240,; A ENST00000444129 Transcript missense_variant 837/3702 368/1950 123/649 Y/F tAc/tTc 1 -1 RECQL HGNC HGNC:9948 protein_coding YES CCDS31756.1 ENSP00000416739 P46063 A0A024RAV2 UPI0000167E2F NM_032941.2,NM_002907.3 tolerated(0.25) 4/15 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF72,SMART_domains:SM00487,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00614 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 21490225 21490225 T A 1 0 0 0 0 1 0 0 0 13371 1638 57 4 4 RECQL 12 21490225 Missense_Mutation SNP T 11LU016_T 15508288 21490225 111785084 349 401 SOX5 0 . GRCh38 12 23846186 23846186 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.278A>T p.Asp93Val p.D93V ENST00000451604 3/15 254 198 56 190 190 0 strelka-varscan-mutect SOX5,missense_variant,p.Asp80Val,ENST00000546136,NM_152989.3;SOX5,missense_variant,p.Asp93Val,ENST00000451604,NM_006940.4;SOX5,missense_variant,p.Asp80Val,ENST00000381381,;SOX5,missense_variant,p.Asp58Val,ENST00000537393,;SOX5,missense_variant,p.Asp83Val,ENST00000545921,NM_001261415.1;SOX5,missense_variant,p.Asp80Val,ENST00000541536,NM_001261414.1;SOX5,missense_variant,p.Asp83Val,ENST00000541847,;SOX5,missense_variant,p.Asp58Val,ENST00000441133,;SOX5,missense_variant,p.Asp80Val,ENST00000538083,;SOX5,missense_variant,p.Asp83Val,ENST00000367206,; A ENST00000451604 Transcript missense_variant 380/4261 278/2292 93/763 D/V gAt/gTt 1 -1 SOX5 HGNC HGNC:11201 protein_coding YES CCDS8699.1 ENSP00000398273 P35711 A0A024RB06 UPI000007405E NM_006940.4 deleterious(0) 3/15 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 23846186 23846186 T A 1 0 0 0 0 1 0 0 0 15280 1435 50 4 4 SOX5 12 23846186 Missense_Mutation SNP T 11LU016_T 2355961 23846186 109429123 350 402 OVCH1 0 . GRCh38 12 29477440 29477440 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.1147G>T p.Ala383Ser p.A383S ENST00000318184 11/28 356 283 73 215 215 0 strelka-varscan-mutect OVCH1,missense_variant,p.Ala383Ser,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; A ENST00000318184 Transcript missense_variant 1147/3405 1147/3405 383/1134 A/S Gca/Tca COSM332613 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 tolerated(0.08) 11/28 Gene3D:2.60.120.290,PROSITE_profiles:PS01180,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,Superfamily_domains:SSF49854 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 29477440 29477440 C A 1 0 0 0 0 1 0 0 0 11393 739 26 2 2 OVCH1 12 29477440 Missense_Mutation SNP C 11LU016_T 5631254 29477440 103797869 351 403 DENND5B 0 . GRCh38 12 31389403 31389403 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.3667T>A p.Tyr1223Asn p.Y1223N ENST00000536562 22/23 216 170 46 160 160 0 strelka-varscan-mutect DENND5B,missense_variant,p.Tyr1188Asn,ENST00000389082,NM_144973.3;DENND5B,missense_variant,p.Tyr1223Asn,ENST00000536562,NM_001308339.1; T ENST00000536562 Transcript missense_variant 3818/4291 3667/3930 1223/1309 Y/N Tac/Aac 1 -1 DENND5B HGNC HGNC:28338 protein_coding YES CCDS76542.1 ENSP00000444889 G3V1S3 UPI0000D621CB NM_001308339.1 deleterious(0) 22/23 PROSITE_profiles:PS50826,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF45,Pfam_domain:PF02759,Superfamily_domains:0052343 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 31389403 31389403 A T 1 0 0 0 0 1 0 0 0 4241 420 15 4 4 DENND5B 12 31389403 Missense_Mutation SNP A 11LU016_T 1911963 31389403 101885906 352 404 LRRK2 0 . GRCh38 12 40320135 40320135 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.4975G>T p.Ala1659Ser p.A1659S ENST00000298910 34/51 120 82 38 136 136 0 strelka-varscan-mutect LRRK2,missense_variant,p.Ala1659Ser,ENST00000298910,NM_198578.3;LRRK2,downstream_gene_variant,,ENST00000481256,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; T ENST00000298910 Transcript missense_variant 5033/9158 4975/7584 1659/2527 A/S Gct/Tct 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 tolerated(0.11) 34/51 Pfam_domain:PF16095 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 40320135 40320135 G T 1 0 0 0 0 1 0 0 0 8939 1319 46 2 2 LRRK2 12 40320135 Missense_Mutation SNP G 11LU016_T 8930732 40320135 92955174 353 405 LRRK2 0 . GRCh38 12 40335053 40335053 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.5844G>A p.= p.E1948E ENST00000298910 40/51 290 264 26 277 276 1 strelka-varscan-mutect LRRK2,synonymous_variant,p.=,ENST00000298910,NM_198578.3;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; A ENST00000298910 Transcript synonymous_variant 5902/9158 5844/7584 1948/2527 E gaG/gaA 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 40/51 PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF486,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 40335053 40335053 G A 1 0 0 0 0 0 0 0 1 8939 1020 36 3 3 LRRK2 12 40335053 Silent SNP G 11LU016_T 14918 40335053 92940256 354 406 TMEM117 0 . GRCh38 12 44211372 44211372 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.593G>A p.Arg198Lys p.R198K ENST00000266534 5/8 136 129 7 194 194 0 strelka-varscan-mutect TMEM117,missense_variant,p.Arg198Lys,ENST00000266534,NM_032256.2;TMEM117,missense_variant,p.Arg198Lys,ENST00000551577,NM_001286211.1;TMEM117,missense_variant,p.Arg54Lys,ENST00000550495,NM_001286213.1;TMEM117,non_coding_transcript_exon_variant,,ENST00000553253,;TMEM117,non_coding_transcript_exon_variant,,ENST00000550623,;TMEM117,3_prime_UTR_variant,,ENST00000546868,; A ENST00000266534 Transcript missense_variant 720/2758 593/1545 198/514 R/K aGg/aAg 1 1 TMEM117 HGNC HGNC:25308 protein_coding YES CCDS8745.1 ENSP00000266534 Q9H0C3 UPI0000037D18 NM_032256.2 deleterious(0.03) 5/8 Pfam_domain:PF15113,hmmpanther:PTHR31226 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 44211372 44211372 G A 1 0 0 0 0 1 0 0 0 16475 1000 35 3 3 TMEM117 12 44211372 Missense_Mutation SNP G 11LU016_T 3876319 44211372 89063937 355 407 PRPH 0 . GRCh38 12 49296233 49296233 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.601C>A p.Arg201Ser p.R201S ENST00000257860 2/9 343 280 63 340 340 0 strelka-varscan-mutect PRPH,missense_variant,p.Arg201Ser,ENST00000257860,NM_006262.3;PRPH,missense_variant,p.Arg88Ser,ENST00000451891,;PRPH,upstream_gene_variant,,ENST00000532332,;RP11-161H23.9,non_coding_transcript_exon_variant,,ENST00000553259,;PRPH,downstream_gene_variant,,ENST00000551194,;PRPH,non_coding_transcript_exon_variant,,ENST00000533401,;PRPH,non_coding_transcript_exon_variant,,ENST00000537252,;PRPH,upstream_gene_variant,,ENST00000530631,; A ENST00000257860 Transcript missense_variant 2100/3245 601/1413 201/470 R/S Cgc/Agc 1 1 PRPH HGNC HGNC:9461 protein_coding YES CCDS8783.1 ENSP00000257860 P41219 UPI000013CF92 NM_006262.3 deleterious(0) 2/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01248,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF29,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 49296233 49296233 C A 1 0 0 0 0 1 0 0 0 12712 666 23 1 1 PRPH 12 49296233 Missense_Mutation SNP C 11LU016_T 5084861 49296233 83979076 356 408 TROAP 0 . GRCh38 12 49330223 49330223 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1378G>T p.Gly460Cys p.G460C ENST00000257909 13/15 218 201 17 287 287 0 strelka-varscan-mutect TROAP,missense_variant,p.Gly460Cys,ENST00000551245,;TROAP,missense_variant,p.Gly460Cys,ENST00000257909,NM_005480.3;TROAP,missense_variant,p.Gly168Cys,ENST00000547923,;C1QL4,downstream_gene_variant,,ENST00000334221,NM_001008223.1;TROAP,downstream_gene_variant,,ENST00000547807,;TROAP,downstream_gene_variant,,ENST00000550346,;TROAP,downstream_gene_variant,,ENST00000551567,;TROAP,downstream_gene_variant,,ENST00000551192,;TROAP,downstream_gene_variant,,ENST00000546735,;TROAP,downstream_gene_variant,,ENST00000546776,;TROAP,downstream_gene_variant,,ENST00000549891,;TROAP,downstream_gene_variant,,ENST00000548817,; T ENST00000257909 Transcript missense_variant 1454/2527 1378/2337 460/778 G/C Ggc/Tgc 1 1 TROAP HGNC HGNC:12327 protein_coding YES CCDS8784.1 ENSP00000257909 Q12815 UPI000007108A NM_005480.3 deleterious(0) 13/15 hmmpanther:PTHR15289,hmmpanther:PTHR15289:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 49330223 49330223 G T 1 0 0 0 0 1 0 0 0 17080 1000 35 2 2 TROAP 12 49330223 Missense_Mutation SNP G 11LU016_T 33990 49330223 83945086 357 409 FMNL3 0 . GRCh38 12 49652103 49652103 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.1433T>C p.Leu478Pro p.L478P ENST00000335154 14/26 309 264 45 431 431 0 strelka-varscan-mutect FMNL3,missense_variant,p.Leu478Pro,ENST00000335154,NM_175736.4;FMNL3,missense_variant,p.Leu478Pro,ENST00000550488,;FMNL3,missense_variant,p.Leu427Pro,ENST00000352151,NM_198900.2;FMNL3,non_coding_transcript_exon_variant,,ENST00000549137,; G ENST00000335154 Transcript missense_variant 1667/12634 1433/3084 478/1027 L/P cTg/cCg 1 -1 FMNL3 HGNC HGNC:23698 protein_coding YES CCDS44874.1 ENSP00000335655 Q8IVF7 UPI00001FC1CB NM_175736.4 deleterious(0.03) 14/26 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF230 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 49652103 49652103 A G 1 0 0 0 0 1 0 0 0 5809 188 7 5 5 FMNL3 12 49652103 Missense_Mutation SNP A 11LU016_T 321880 49652103 83623206 358 410 KRT77 0 . GRCh38 12 52692801 52692801 + Missense_Mutation SNP C C A rs763066575 11LU016_T 11LU016_N C C c.1160G>T p.Arg387Leu p.R387L ENST00000341809 6/9 181 168 13 195 194 1 strelka-varscan-mutect KRT77,missense_variant,p.Arg387Leu,ENST00000341809,NM_175078.2;RP11-641A6.3,splice_region_variant,,ENST00000547533,;KRT77,3_prime_UTR_variant,,ENST00000553168,;KRT77,downstream_gene_variant,,ENST00000550823,; A ENST00000341809 Transcript missense_variant 1189/3305 1160/1737 387/578 R/L cGc/cTc rs763066575,COSM5083140 1 -1 KRT77 HGNC HGNC:20411 protein_coding YES CCDS8837.1 ENSP00000342710 Q7Z794 UPI00001D797A NM_175078.2 deleterious(0.02) 6/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF87,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763066575 . 0 208 0 2 0 0 0 0 -17.06748 0.9999997 1 1 1 0 A 3 1 2 52692801 52692801 C A 1 0 0 0 0 1 0 0 0 8372 768 27 1 1 KRT77 12 52692801 Missense_Mutation SNP C 11LU016_T 3040698 52692801 80582508 359 411 TAC3 0 . GRCh38 12 57012866 57012866 + Missense_Mutation SNP T T A rs143862988 11LU016_T 11LU016_N T T c.248A>T p.His83Leu p.H83L ENST00000615887 5/9 474 426 48 524 523 1 strelka-varscan-mutect TAC3,missense_variant,p.His83Leu,ENST00000615887,;TAC3,missense_variant,p.His83Leu,ENST00000458521,NM_013251.3;TAC3,missense_variant,p.His83Leu,ENST00000415231,;TAC3,intron_variant,,ENST00000441881,NM_001178054.1;TAC3,missense_variant,p.His83Leu,ENST00000393867,;TAC3,missense_variant,p.His83Leu,ENST00000300108,;TAC3,missense_variant,p.His83Leu,ENST00000438756,;TAC3,missense_variant,p.His83Leu,ENST00000357616,;TAC3,intron_variant,,ENST00000379411,;TAC3,intron_variant,,ENST00000423597,;TAC3,downstream_gene_variant,,ENST00000496757,; A ENST00000615887 Transcript missense_variant 387/1120 248/366 83/121 H/L cAt/cTt rs143862988 1 -1 TAC3 HGNC HGNC:11521 protein_coding YES CCDS8928.1 ENSP00000483110 Q9UHF0 A0A024RB47 UPI00000312E8 deleterious(0.01) 5/9 hmmpanther:PTHR15536,hmmpanther:PTHR15536:SF1,PIRSF_domain:PIRSF001843,Prints_domain:PR01828 likely_pathogenic MODERATE 1 SNV 2 1 1 PASS rs143862988 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 57012866 57012866 T A 1 0 0 0 0 1 0 0 0 15895 1464 51 4 4 TAC3 12 57012866 Missense_Mutation SNP T 11LU016_T 4320065 57012866 76262443 360 412 HELB 0 . GRCh38 12 66310358 66310358 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1430G>A p.Gly477Asp p.G477D ENST00000247815 4/13 361 332 29 263 263 0 strelka-varscan-mutect HELB,missense_variant,p.Gly477Asp,ENST00000247815,NM_033647.3;HELB,missense_variant,p.Gly477Asp,ENST00000545134,;HELB,missense_variant,p.Gly477Asp,ENST00000542394,;HELB,missense_variant,p.Gly477Asp,ENST00000440906,; A ENST00000247815 Transcript missense_variant 1489/12866 1430/3264 477/1087 G/D gGt/gAt 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 deleterious(0) 4/13 Gene3D:3.40.50.300,Pfam_domain:PF13604,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF135,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 66310358 66310358 G A 1 0 0 0 0 1 0 0 0 6927 1261 44 3 3 HELB 12 66310358 Missense_Mutation SNP G 11LU016_T 9297492 66310358 66964951 361 413 CAND1 0 . GRCh38 12 67281989 67281989 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.148G>C p.Val50Leu p.V50L ENST00000545606 2/15 88 78 10 148 148 0 strelka-varscan-mutect CAND1,missense_variant,p.Val50Leu,ENST00000545606,NM_018448.4;CAND1,missense_variant,p.Val26Leu,ENST00000540525,;CAND1,non_coding_transcript_exon_variant,,ENST00000539434,;CAND1,non_coding_transcript_exon_variant,,ENST00000541058,; C ENST00000545606 Transcript missense_variant 585/11251 148/3693 50/1230 V/L Gtg/Ctg 1 1 CAND1 HGNC HGNC:30688 protein_coding YES CCDS8977.1 ENSP00000442318 Q86VP6 UPI0000037CC5 NM_018448.4 deleterious(0) 2/15 hmmpanther:PTHR12696,hmmpanther:PTHR12696:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -16.30346 0.9999999 1 1 1 0 C 3 2 2 67281989 67281989 G C 1 0 0 0 0 1 0 0 0 2308 1029 36 4 4 CAND1 12 67281989 Missense_Mutation SNP G 11LU016_T 971631 67281989 65993320 362 414 FRS2 0 . GRCh38 12 69574285 69574285 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.857G>T p.Trp286Leu p.W286L ENST00000550389 7/7 188 164 24 202 202 0 strelka-varscan-mutect FRS2,missense_variant,p.Trp286Leu,ENST00000550389,NM_001278357.1;FRS2,missense_variant,p.Trp286Leu,ENST00000397997,;FRS2,missense_variant,p.Trp286Leu,ENST00000549921,NM_001278354.1,NM_001278356.1,NM_001278355.1,NM_001278351.1,NM_006654.4,NM_001042555.2,NM_001278353.1;FRS2,downstream_gene_variant,,ENST00000550937,;FRS2,downstream_gene_variant,,ENST00000551325,;FRS2,downstream_gene_variant,,ENST00000547219,;FRS2,downstream_gene_variant,,ENST00000548154,;FRS2,downstream_gene_variant,,ENST00000549092,;FRS2,downstream_gene_variant,,ENST00000547414,; T ENST00000550389 Transcript missense_variant 1103/6600 857/1527 286/508 W/L tGg/tTg 1 1 FRS2 HGNC HGNC:16971 protein_coding YES CCDS41809.1 ENSP00000447241 Q8WU20 L7RTG7 UPI000003F143 NM_001278357.1 tolerated(0.65) 7/7 hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF40 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 69574285 69574285 G T 1 0 0 0 0 1 0 0 0 5933 1357 47 2 2 FRS2 12 69574285 Missense_Mutation SNP G 11LU016_T 2292296 69574285 63701024 363 415 KCNC2 0 . GRCh38 12 75207659 75207659 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.325G>T p.Gly109Cys p.G109C ENST00000549446 2/5 262 191 71 259 259 0 strelka-mutect KCNC2,missense_variant,p.Gly109Cys,ENST00000549446,NM_139137.3;KCNC2,missense_variant,p.Gly109Cys,ENST00000298972,NM_139136.3;KCNC2,missense_variant,p.Gly109Cys,ENST00000350228,NM_153748.2;KCNC2,missense_variant,p.Gly109Cys,ENST00000548513,;KCNC2,missense_variant,p.Gly109Cys,ENST00000550433,NM_001260498.1;KCNC2,missense_variant,p.Gly109Cys,ENST00000393288,NM_001260497.1;KCNC2,missense_variant,p.Gly109Cys,ENST00000540018,NM_001260499.1; A ENST00000549446 Transcript missense_variant 1006/5625 325/1917 109/638 G/C Ggc/Tgc 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 deleterious(0) 2/5 Gene3D:3.30.710.10,Pfam_domain:PF02214,Prints_domain:PR00169,Prints_domain:PR01491,Prints_domain:PR01498,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 75207659 75207659 C A 1 0 0 0 0 1 0 0 0 7931 623 22 2 2 KCNC2 12 75207659 Missense_Mutation SNP C 11LU016_T 5633374 75207659 58067650 364 416 NAV3 0 . GRCh38 12 77968635 77968635 + Silent SNP C C A 11LU016_T 11LU016_N C C c.604C>A p.= p.R202R ENST00000397909 5/40 213 192 21 211 211 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,synonymous_variant,p.=,ENST00000550042,;NAV3,synonymous_variant,p.=,ENST00000550503,;NAV3,non_coding_transcript_exon_variant,,ENST00000547725,; A ENST00000397909 Transcript synonymous_variant 777/9821 604/7158 202/2385 R Cga/Aga COSM240824,COSM4924980,COSM4924981,COSM5173466 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 5/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784,Superfamily_domains:SSF47576 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS rs1480204948 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 2 77968635 77968635 C A 1 0 0 0 0 0 0 0 1 10194 760 27 1 1 NAV3 12 77968635 Silent SNP C 11LU016_T 2760976 77968635 55306674 365 417 PTPRQ 0 . GRCh38 12 80506098 80506098 + Missense_Mutation SNP C C A rs760006052 11LU016_T 11LU016_N C C c.2347C>A p.Pro783Thr p.P783T ENST00000614701 15/45 99 81 18 187 187 0 strelka-varscan-mutect PTPRQ,missense_variant,p.Pro783Thr,ENST00000614701,NM_001145026.1;PTPRQ,missense_variant,p.Pro825Thr,ENST00000616559,; A ENST00000614701 Transcript missense_variant 2525/8289 2347/6900 783/2299 P/T Cca/Aca rs760006052 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 deleterious(0) 15/45 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF414,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs760006052 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 80506098 80506098 C A 1 0 0 0 0 1 0 0 0 12964 623 22 2 2 PTPRQ 12 80506098 Missense_Mutation SNP C 11LU016_T 2537463 80506098 52769211 366 418 CFAP54 0 . GRCh38 12 96792415 96792415 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.8766G>T p.Met2922Ile p.M2922I ENST00000524981 63/68 186 156 30 175 175 0 strelka-varscan-mutect CFAP54,missense_variant,p.Met2922Ile,ENST00000524981,NM_001306084.1;CFAP54,missense_variant,p.Met1893Ile,ENST00000637336,; T ENST00000524981 Transcript missense_variant 8789/9766 8766/9291 2922/3096 M/I atG/atT 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 tolerated(0.57) 63/68 hmmpanther:PTHR33487,hmmpanther:PTHR33487:SF2 MODERATE 1 SNV 5 1 PASS rs906447863 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 96792415 96792415 G T 1 0 0 0 0 1 0 0 0 3025 1348 47 2 2 CFAP54 12 96792415 Missense_Mutation SNP G 11LU016_T 16286317 96792415 36482894 367 419 PAH 0 . GRCh38 12 102843737 102843737 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1108G>C p.Glu370Gln p.E370Q ENST00000553106 11/13 323 237 86 305 305 0 strelka-varscan-mutect PAH,missense_variant,p.Glu370Gln,ENST00000553106,NM_000277.1;PAH,missense_variant,p.Glu365Gln,ENST00000307000,;PAH,missense_variant,p.Glu72Gln,ENST00000635477,;PAH,non_coding_transcript_exon_variant,,ENST00000551114,;PAH,non_coding_transcript_exon_variant,,ENST00000549247,;PAH,non_coding_transcript_exon_variant,,ENST00000635528,; G ENST00000553106 Transcript missense_variant 1581/4122 1108/1359 370/452 E/Q Gag/Cag 1 -1 PAH HGNC HGNC:8582 protein_coding YES CCDS9092.1 ENSP00000448059 P00439 A0A024RBG4 UPI00001318A0 NM_000277.1 tolerated(0.1) 11/13 Low_complexity_(Seg):seg,PROSITE_profiles:PS51410,hmmpanther:PTHR11473,Gene3D:1.10.800.10,Pfam_domain:PF00351,PIRSF_domain:PIRSF000336,TIGRFAM_domain:TIGR01268,Superfamily_domains:SSF56534 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 102843737 102843737 C G 1 0 0 0 0 1 0 0 0 11474 864 30 4 4 PAH 12 102843737 Missense_Mutation SNP C 11LU016_T 6051322 102843737 30431572 368 420 C12orf42 0 . GRCh38 12 103302234 103302234 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.957C>A p.= p.S319S ENST00000378113 6/6 78 62 16 92 92 0 strelka-varscan-mutect C12orf42,synonymous_variant,p.=,ENST00000548048,;C12orf42,synonymous_variant,p.=,ENST00000378113,NM_001099336.2,NM_001278419.1;C12orf42,synonymous_variant,p.=,ENST00000548883,NM_198521.3;C12orf42,downstream_gene_variant,,ENST00000552578,;C12orf42,intron_variant,,ENST00000546526,;C12orf42,intron_variant,,ENST00000552977,;C12orf42,intron_variant,,ENST00000550650,;C12orf42,downstream_gene_variant,,ENST00000548789,;C12orf42,3_prime_UTR_variant,,ENST00000551134,;C12orf42,intron_variant,,ENST00000547347,; T ENST00000378113 Transcript synonymous_variant 1222/1513 957/1083 319/360 S tcC/tcA 1 -1 C12orf42 HGNC HGNC:24729 protein_coding YES CCDS44963.1 ENSP00000367353 Q96LP6 UPI00001D7906 NM_001099336.2,NM_001278419.1 6/6 Pfam_domain:PF15380,hmmpanther:PTHR40708,hmmpanther:PTHR40708:SF1 LOW 1 SNV 5 1 PASS rs1304578351 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 103302234 103302234 G T 1 0 0 0 0 0 0 0 1 1810 1335 47 2 2 C12orf42 12 103302234 Silent SNP G 11LU016_T 458497 103302234 29973075 369 421 STAB2 0 . GRCh38 12 103713739 103713739 + Missense_Mutation SNP G G C rs560420677 11LU016_T 11LU016_N G G c.4508G>C p.Gly1503Ala p.G1503A ENST00000388887 42/69 210 187 23 155 155 0 strelka-varscan-mutect STAB2,missense_variant,p.Gly1503Ala,ENST00000388887,NM_017564.9;STAB2,downstream_gene_variant,,ENST00000549798,; C ENST00000388887 Transcript missense_variant 4712/8251 4508/7656 1503/2551 G/A gGc/gCc rs560420677 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 deleterious(0) 42/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,PROSITE_patterns:PS01186,Gene3D:2.40.155.10,Pfam_domain:PF12947,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs560420677 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 103713739 103713739 G C 1 0 0 0 0 1 0 0 0 15616 1203 42 4 4 STAB2 12 103713739 Missense_Mutation SNP G 11LU016_T 411505 103713739 29561570 370 422 NOS1 0 . GRCh38 12 117234711 117234711 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.3191T>C p.Leu1064Pro p.L1064P ENST00000618760 22/30 130 103 27 93 93 0 strelka-varscan-mutect NOS1,missense_variant,p.Leu1064Pro,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Leu1030Pro,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Leu1064Pro,ENST00000338101,;NOS1,missense_variant,p.Leu1029Pro,ENST00000344089,; G ENST00000618760 Transcript missense_variant 3902/12283 3191/4407 1064/1468 L/P cTg/cCg 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 deleterious(0.04) 22/30 PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Gene3D:1.20.990.10,Pfam_domain:PF00667,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 117234711 117234711 A G 1 0 0 0 0 1 0 0 0 10586 188 7 5 5 NOS1 12 117234711 Missense_Mutation SNP A 11LU016_T 13520972 117234711 16040598 371 423 DNAH10 0 . GRCh38 12 123813283 123813283 + Silent SNP A A G novel 11LU016_T 11LU016_N A A c.2910A>G p.= p.E970E ENST00000638045 19/78 185 173 12 206 206 0 strelka-varscan-mutect DNAH10,synonymous_variant,p.=,ENST00000409039,;DNAH10,synonymous_variant,p.=,ENST00000638045,NM_207437.3;DNAH10,synonymous_variant,p.=,ENST00000614082,;DNAH10,non_coding_transcript_exon_variant,,ENST00000467219,;DNAH10,non_coding_transcript_exon_variant,,ENST00000447853,; G ENST00000638045 Transcript synonymous_variant 2935/13678 2910/13416 970/4471 E gaA/gaG 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 19/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 123813283 123813283 A G 1 0 0 0 0 0 0 0 1 4411 40 2 5 5 DNAH10 12 123813283 Silent SNP A 11LU016_T 6578572 123813283 9462026 372 424 TMEM132C 0 . GRCh38 12 128415372 128415372 + Silent SNP C C A 11LU016_T 11LU016_N C C c.726C>A p.= p.A242A ENST00000435159 2/9 52 45 7 65 65 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript synonymous_variant 726/4947 726/3327 242/1108 A gcC/gcA COSM3384138 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 1 LOW 1 SNV 5 1 1 PASS rs1242678522 . 0 198 11 0 0 0 0 0 -16.35051 0.999949 1 1 1 0 A 2 1 2 128415372 128415372 C A 1 0 0 0 0 0 0 0 1 16491 639 23 1 1 TMEM132C 12 128415372 Silent SNP C 11LU016_T 4602089 128415372 4859937 373 425 TMEM132C 0 . GRCh38 12 128669557 128669557 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1446C>G p.Ile482Met p.I482M ENST00000435159 5/9 88 77 11 85 85 0 strelka-mutect TMEM132C,missense_variant,p.Ile482Met,ENST00000435159,NM_001136103.2; G ENST00000435159 Transcript missense_variant 1446/4947 1446/3327 482/1108 I/M atC/atG 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0) 5/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 MODERATE 1 SNV 5 1 PASS rs1304277703 . 0 208 0 2 0 0 0 0 -18.00852 0.9999999 1 1 1 0 G 3 3 2 128669557 128669557 C G 1 0 0 0 0 1 0 0 0 16491 840 29 4 4 TMEM132C 12 128669557 Missense_Mutation SNP C 11LU016_T 254185 128669557 4605752 374 426 PIWIL1 0 . GRCh38 12 130355579 130355579 + Missense_Mutation SNP G G C rs552222799 11LU016_T 11LU016_N G G c.1316G>C p.Arg439Pro p.R439P ENST00000245255 12/21 207 186 21 229 229 0 strelka-varscan-mutect PIWIL1,missense_variant,p.Arg439Pro,ENST00000245255,NM_004764.4,NM_001190971.1;RP11-200K12.3,upstream_gene_variant,,ENST00000624997,; C ENST00000245255 Transcript missense_variant 1588/3897 1316/2586 439/861 R/P cGa/cCa rs552222799 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 deleterious(0.02) 12/21 hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF46,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS rs552222799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 130355579 130355579 G C 1 0 0 0 0 1 0 0 0 12053 1058 37 4 4 PIWIL1 12 130355579 Missense_Mutation SNP G 11LU016_T 1686022 130355579 2919730 375 427 EP400 0 . GRCh38 12 132043361 132043361 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.6265G>T p.Val2089Leu p.V2089L ENST00000389562 32/52 165 144 21 186 186 0 strelka-varscan-mutect EP400,missense_variant,p.Val2089Leu,ENST00000389562,;EP400,missense_variant,p.Val2089Leu,ENST00000389561,NM_015409.4;EP400,non_coding_transcript_exon_variant,,ENST00000611841,; T ENST00000389562 Transcript missense_variant 6300/12836 6265/9372 2089/3123 V/L Gtg/Ttg 1 1 EP400 HGNC HGNC:11958 protein_coding YES CCDS31929.2 ENSP00000374213 Q96L91 UPI00004566BC tolerated(0.26) 32/52 MODERATE 1 SNV 1 1 PASS rs916759408 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 132043361 132043361 G T 1 0 0 0 0 1 0 0 0 4995 1261 44 2 2 EP400 12 132043361 Missense_Mutation SNP G 11LU016_T 1687782 132043361 1231948 376 428 PSPC1 0 . GRCh38 13 19703194 19703194 + Missense_Mutation SNP T T A rs745410363 11LU016_T 11LU016_N T T c.1553A>T p.Asn518Ile p.N518I ENST00000338910 9/9 133 123 10 144 144 0 varscan-mutect PSPC1,missense_variant,p.Asn518Ile,ENST00000338910,;PSPC1,missense_variant,p.Asn518Ile,ENST00000619300,NM_001042414.2;PSPC1,intron_variant,,ENST00000492741,;PSPC1,intron_variant,,ENST00000471658,;PSPC1,intron_variant,,ENST00000635562,; A ENST00000338910 Transcript missense_variant 1713/2407 1553/1572 518/523 N/I aAt/aTt rs745410363 1 -1 PSPC1 HGNC HGNC:20320 protein_coding YES CCDS41870.1 ENSP00000343966 Q8WXF1 UPI000006F2BE deleterious(0) 9/9 hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF14 MODERATE 1 SNV 1 1 PASS rs745410363 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 19703194 19703194 T A 1 0 0 0 0 1 0 0 0 12868 1493 52 4 4 PSPC1 13 19703194 Missense_Mutation SNP T 11LU016_T 19703194 94661134 377 429 GJB6 0 . GRCh38 13 20223395 20223395 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.86T>C p.Phe29Ser p.F29S ENST00000356192 5/5 378 291 87 603 603 0 strelka-varscan-mutect GJB6,missense_variant,p.Phe29Ser,ENST00000356192,NM_001110219.2;GJB6,missense_variant,p.Phe29Ser,ENST00000400066,NM_001110220.2;GJB6,missense_variant,p.Phe29Ser,ENST00000636852,;GJB6,missense_variant,p.Phe29Ser,ENST00000241124,NM_006783.4;GJB6,missense_variant,p.Phe29Ser,ENST00000400065,NM_001110221.2; G ENST00000356192 Transcript missense_variant 707/2131 86/786 29/261 F/S tTt/tCt 1 -1 GJB6 HGNC HGNC:4288 protein_coding YES CCDS9291.1 ENSP00000348521 O95452 A0A024RDS4 UPI0000074737 NM_001110219.2 deleterious(0) 5/5 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF23,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 20223395 20223395 A G 1 0 0 0 0 1 0 0 0 6289 14 1 5 5 GJB6 13 20223395 Missense_Mutation SNP A 11LU016_T 520201 20223395 94140933 378 430 FRY 0 . GRCh38 13 32175550 32175550 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.2339A>T p.Asp780Val p.D780V ENST00000542859 20/61 353 289 64 400 400 0 strelka-varscan-mutect FRY,missense_variant,p.Asp780Val,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Asp780Val,ENST00000380250,; T ENST00000542859 Transcript missense_variant 2835/13200 2339/9042 780/3013 D/V gAc/gTc 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0.01) 20/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 32175550 32175550 A T 1 0 0 0 0 1 0 0 0 5935 289 10 4 4 FRY 13 32175550 Missense_Mutation SNP A 11LU016_T 11952155 32175550 82188778 379 431 SERTM1 0 . GRCh38 13 36695091 36695091 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.13G>A p.Asp5Asn p.D5N ENST00000315190 2/2 67 53 14 125 124 1 strelka-varscan-mutect SERTM1,missense_variant,p.Asp5Asn,ENST00000315190,NM_203451.2; A ENST00000315190 Transcript missense_variant 459/3207 13/324 5/107 D/N Gac/Aac 1 1 SERTM1 HGNC HGNC:33792 protein_coding YES CCDS9358.1 ENSP00000325776 A2A2V5 UPI00000306E4 NM_203451.2 tolerated_low_confidence(0.65) 2/2 hmmpanther:PTHR35660:SF1,hmmpanther:PTHR35660,Pfam_domain:PF15872 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 36695091 36695091 G A 1 0 0 0 0 1 0 0 0 14400 1290 45 3 3 SERTM1 13 36695091 Missense_Mutation SNP G 11LU016_T 4519541 36695091 77669237 380 432 POSTN 0 . GRCh38 13 37563351 37563351 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2493G>T p.Arg831Ser p.R831S ENST00000379747 23/23 76 62 14 104 104 0 strelka-varscan-mutect POSTN,missense_variant,p.Arg831Ser,ENST00000379747,NM_006475.2;POSTN,missense_variant,p.Arg776Ser,ENST00000541179,NM_001135936.1,NM_001135935.1;POSTN,missense_variant,p.Arg803Ser,ENST00000379749,;POSTN,missense_variant,p.Arg804Ser,ENST00000379743,NM_001286665.1;POSTN,missense_variant,p.Arg744Ser,ENST00000541481,NM_001286666.1,NM_001286667.1;POSTN,missense_variant,p.Arg774Ser,ENST00000379742,NM_001135934.1;POSTN,non_coding_transcript_exon_variant,,ENST00000478947,;POSTN,non_coding_transcript_exon_variant,,ENST00000473823,;POSTN,downstream_gene_variant,,ENST00000474646,; A ENST00000379747 Transcript missense_variant 2611/3373 2493/2511 831/836 R/S agG/agT 1 -1 POSTN HGNC HGNC:16953 protein_coding YES CCDS9364.1 ENSP00000369071 Q15063 A0A024RDS2 UPI000013CEB8 NM_006475.2 deleterious_low_confidence(0) 23/23 hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF12 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999882 1 1 1 0 A 3 1 2 37563351 37563351 C A 1 0 0 0 0 1 0 0 0 12373 622 22 2 2 POSTN 13 37563351 Missense_Mutation SNP C 11LU016_T 868260 37563351 76800977 381 433 RB1 0 . GRCh38 13 48364892 48364892 + Splice_Site SNP A A T novel 11LU016_T 11LU016_N A A c.862-2A>T p.X288_splice ENST00000267163 95 90 5 107 106 1 strelka-mutect RB1,splice_acceptor_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000525036,;RB1,downstream_gene_variant,,ENST00000467505,; T ENST00000267163 Transcript splice_acceptor_variant -/4840 862/2787 288/928 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 8/26 HIGH 1 SNV 1 1 PASS rs1131690914 . 0 200 8 2 0 0 0 0 -8.289673 0.9978406 1 1 1 0 T 5 4 2 48364892 48364892 A T 1 0 0 0 0 0 0 1 0 13259 202 7 4 4 RB1 13 48364892 Splice_Site SNP A 11LU016_T 10801541 48364892 65999436 382 434 RB1 0 . GRCh38 13 48373476 48373476 + Missense_Mutation SNP T T G 11LU016_T 11LU016_N T T c.1199T>G p.Leu400Arg p.L400R ENST00000267163 12/27 110 89 21 158 158 0 strelka-varscan-mutect RB1,missense_variant,p.Leu400Arg,ENST00000267163,NM_000321.2; G ENST00000267163 Transcript missense_variant 1337/4840 1199/2787 400/928 L/R cTg/cGg CD040609 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 deleterious(0) 12/27 Gene3D:1.10.472.10,Pfam_domain:PF01858,hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21,SMART_domains:SM01368,Superfamily_domains:SSF47954 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 48373476 48373476 T G 1 0 0 0 0 1 0 0 0 13259 1580 55 5 5 RB1 13 48373476 Missense_Mutation SNP T 11LU016_T 8584 48373476 65990852 383 435 PCDH8 0 . GRCh38 13 52846690 52846690 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1747G>T p.Asp583Tyr p.D583Y ENST00000377942 1/3 65 51 14 99 99 0 strelka-varscan-mutect PCDH8,missense_variant,p.Asp583Tyr,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Asp583Tyr,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; A ENST00000377942 Transcript missense_variant 1951/5088 1747/3213 583/1070 D/Y Gac/Tac 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 deleterious(0) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 52846690 52846690 C A 1 0 0 0 0 1 0 0 0 11604 884 31 1 1 PCDH8 13 52846690 Missense_Mutation SNP C 11LU016_T 4473214 52846690 61517638 384 436 DACH1 0 . GRCh38 13 71866134 71866134 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.636C>A p.= p.P212P ENST00000613252 1/11 103 81 22 123 123 0 strelka-varscan-mutect DACH1,synonymous_variant,p.=,ENST00000613252,NM_080759.5;DACH1,synonymous_variant,p.=,ENST00000611519,NM_080760.5;DACH1,synonymous_variant,p.=,ENST00000620444,NM_004392.6;DACH1,synonymous_variant,p.=,ENST00000619232,; T ENST00000613252 Transcript synonymous_variant 1059/5233 636/2121 212/706 P ccC/ccA 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 1/11 hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577,Pfam_domain:PF02437,Gene3D:3.10.260.20,Superfamily_domains:SSF46955 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 71866134 71866134 G T 1 0 0 0 0 0 0 0 1 4021 1219 43 2 2 DACH1 13 71866134 Silent SNP G 11LU016_T 19019444 71866134 42498194 385 437 DACH1 0 . GRCh38 13 71866224 71866224 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.546C>A p.= p.T182T ENST00000613252 1/11 112 95 17 110 109 1 strelka-varscan-mutect DACH1,synonymous_variant,p.=,ENST00000613252,NM_080759.5;DACH1,synonymous_variant,p.=,ENST00000611519,NM_080760.5;DACH1,synonymous_variant,p.=,ENST00000620444,NM_004392.6;DACH1,synonymous_variant,p.=,ENST00000619232,; T ENST00000613252 Transcript synonymous_variant 969/5233 546/2121 182/706 T acC/acA 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 1/11 hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577,Pfam_domain:PF02437 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 71866224 71866224 G T 1 0 0 0 0 0 0 0 1 4021 1219 43 2 2 DACH1 13 71866224 Silent SNP G 11LU016_T 90 71866224 42498104 386 438 MYCBP2 0 . GRCh38 13 77150879 77150879 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.6872A>T p.Gln2291Leu p.Q2291L ENST00000544440 47/83 284 245 39 226 226 0 strelka-varscan-mutect MYCBP2,missense_variant,p.Gln2291Leu,ENST00000357337,NM_015057.4;MYCBP2,missense_variant,p.Gln2291Leu,ENST00000544440,;MYCBP2,upstream_gene_variant,,ENST00000486679,; A ENST00000544440 Transcript missense_variant 6890/14664 6872/13923 2291/4640 Q/L cAa/cTa 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 deleterious(0.02) 47/83 Pfam_domain:PF00630 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 77150879 77150879 T A 1 0 0 0 0 1 0 0 0 10018 1812 63 4 4 MYCBP2 13 77150879 Missense_Mutation SNP T 11LU016_T 5284655 77150879 37213449 387 439 ZIC5 0 . GRCh38 13 99971125 99971125 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.551G>C p.Gly184Ala p.G184A ENST00000267294 1/2 75 64 11 166 165 1 strelka-varscan-mutect ZIC5,missense_variant,p.Gly184Ala,ENST00000267294,NM_033132.3; G ENST00000267294 Transcript missense_variant 785/4639 551/1992 184/663 G/A gGc/gCc 1 -1 ZIC5 HGNC HGNC:20322 protein_coding YES CCDS9494.2 ENSP00000267294 Q96T25 UPI0000458928 NM_033132.3 tolerated_low_confidence(0.33) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR19818 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 99971125 99971125 C G 1 0 0 0 0 1 0 0 0 18260 739 26 4 4 ZIC5 13 99971125 Missense_Mutation SNP C 11LU016_T 22820246 99971125 14393203 388 440 FGF14 0 . GRCh38 13 101916492 101916492 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.154C>A p.Arg52Ser p.R52S ENST00000376143 1/5 423 341 82 477 477 0 strelka-varscan-mutect FGF14,missense_variant,p.Arg52Ser,ENST00000376143,NM_004115.3;FGF14,intron_variant,,ENST00000376131,NM_175929.2; T ENST00000376143 Transcript missense_variant 154/744 154/744 52/247 R/S Cgc/Agc COSM4045739 1 -1 FGF14 HGNC HGNC:3671 protein_coding CCDS9501.1 ENSP00000365313 Q92915 UPI000003C0F2 NM_004115.3 deleterious(0.05) 1/5 hmmpanther:PTHR11486:SF18,hmmpanther:PTHR11486 1 MODERATE SNV 1 1 1 PASS rs987890018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 101916492 101916492 G T 1 0 0 0 0 1 0 0 0 5707 1087 38 1 1 FGF14 13 101916492 Missense_Mutation SNP G 11LU016_T 1945367 101916492 12447836 389 441 POTEG 0 . GRCh38 14 19428666 19428666 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.686G>C p.Gly229Ala p.G229A ENST00000547848 3/11 433 376 57 401 401 0 varscan-mutect POTEG,missense_variant,p.Gly229Ala,ENST00000547848,NM_001005356.2;RP11-244H18.1,downstream_gene_variant,,ENST00000621705,;POTEG,missense_variant,p.Gly229Ala,ENST00000547722,;POTEG,missense_variant,p.Gly229Ala,ENST00000622767,; G ENST00000547848 Transcript missense_variant 738/2204 686/1527 229/508 G/A gGc/gCc 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 deleterious(0) 3/11 PROSITE_profiles:PS50297,hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1375240293 . 25 184 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 19428666 19428666 C G 1 0 0 0 0 1 0 0 0 12380 739 26 4 4 POTEG 14 19428666 Missense_Mutation SNP C 11LU016_T 19428666 87615052 390 442 OR4K13 0 . GRCh38 14 20033988 20033988 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.771C>G p.Ile257Met p.I257M ENST00000315693 1/1 258 237 21 198 198 0 strelka-mutect OR4K13,missense_variant,p.Ile257Met,ENST00000315693,NM_001004714.1; C ENST00000315693 Transcript missense_variant 773/917 771/915 257/304 I/M atC/atG 1 -1 OR4K13 HGNC HGNC:15351 protein_coding YES CCDS32028.1 ENSP00000319322 Q8NH42 A0A126GVS2 UPI0000041CEB NM_001004714.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF123,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 20033988 20033988 G C 1 0 0 0 0 1 0 0 0 11145 932 33 4 4 OR4K13 14 20033988 Missense_Mutation SNP G 11LU016_T 605322 20033988 87009730 391 443 RNASE13 0 . GRCh38 14 21033978 21033978 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.311A>T p.Gln104Leu p.Q104L ENST00000382951 2/2 168 131 37 170 170 0 strelka-varscan-mutect RNASE13,missense_variant,p.Gln104Leu,ENST00000382951,NM_001012264.3;NDRG2,intron_variant,,ENST00000403829,NM_001282211.1;NDRG2,intron_variant,,ENST00000555026,;TPPP2,intron_variant,,ENST00000472458,;TPPP2,intron_variant,,ENST00000555751,;TPPP2,intron_variant,,ENST00000481535,;TPPP2,downstream_gene_variant,,ENST00000321760,NM_173846.4;TPPP2,downstream_gene_variant,,ENST00000530140,;TPPP2,downstream_gene_variant,,ENST00000460647,;AL161668.5,downstream_gene_variant,,ENST00000533984,;AL161668.5,downstream_gene_variant,,ENST00000532213,;RP11-998D10.1,downstream_gene_variant,,ENST00000531638,;TPPP2,intron_variant,,ENST00000495665,;TPPP2,intron_variant,,ENST00000529496,;TPPP2,downstream_gene_variant,,ENST00000534434,;TPPP2,downstream_gene_variant,,ENST00000533755,;TPPP2,downstream_gene_variant,,ENST00000525425,;TPPP2,downstream_gene_variant,,ENST00000532060,; A ENST00000382951 Transcript missense_variant 449/1607 311/471 104/156 Q/L cAg/cTg 1 -1 RNASE13 HGNC HGNC:25285 protein_coding YES CCDS32039.1 ENSP00000372410 Q5GAN3 V9HW52 UPI00001FCFB5 NM_001012264.3 deleterious(0.03) 2/2 Gene3D:3.10.130.10,PD000535,Pfam_domain:PF00074,hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF11,Superfamily_domains:SSF54076 MODERATE 1 SNV 1 1 PASS rs1213871966 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 21033978 21033978 T A 1 0 0 0 0 1 0 0 0 13582 1580 55 4 4 RNASE13 14 21033978 Missense_Mutation SNP T 11LU016_T 999990 21033978 86009740 392 444 CIDEB 0 . GRCh38 14 24306397 24306397 + Missense_Mutation SNP C C A rs773821735 11LU016_T 11LU016_N C C c.313G>T p.Gly105Cys p.G105C ENST00000336557 6/8 191 150 41 175 174 1 strelka-varscan-mutect CIDEB,missense_variant,p.Gly105Cys,ENST00000336557,NM_001318807.1;CIDEB,missense_variant,p.Gly105Cys,ENST00000258807,NM_014430.2;CIDEB,missense_variant,p.Gly105Cys,ENST00000554411,;CIDEB,missense_variant,p.Gly23Cys,ENST00000556756,;NOP9,3_prime_UTR_variant,,ENST00000267425,NM_174913.2;LTB4R2,intron_variant,,ENST00000527924,;NOP9,intron_variant,,ENST00000557362,;LTB4R2,upstream_gene_variant,,ENST00000528054,;NOP9,downstream_gene_variant,,ENST00000396802,NM_001286367.1;LTB4R2,upstream_gene_variant,,ENST00000543919,NM_001164692.2,NM_019839.4;LTB4R2,upstream_gene_variant,,ENST00000533293,;LTB4R2,upstream_gene_variant,,ENST00000530080,;CIDEB,downstream_gene_variant,,ENST00000555817,;CIDEB,downstream_gene_variant,,ENST00000555471,; A ENST00000336557 Transcript missense_variant 1616/2409 313/660 105/219 G/C Ggt/Tgt rs773821735 1 -1 CIDEB HGNC HGNC:1977 protein_coding YES CCDS32056.1 ENSP00000337731 Q9UHD4 UPI0000001BDD NM_001318807.1 deleterious(0.04) 6/8 PROSITE_profiles:PS51135,hmmpanther:PTHR12306:SF10,hmmpanther:PTHR12306,Pfam_domain:PF02017,Gene3D:3.10.20.10,SMART_domains:SM00266,Superfamily_domains:SSF54277 MODERATE SNV 2 1 PASS rs773821735 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 24306397 24306397 C A 1 0 0 0 0 1 0 0 0 3188 594 21 2 2 CIDEB 14 24306397 Missense_Mutation SNP C 11LU016_T 3272419 24306397 82737321 393 445 NYNRIN 0 . GRCh38 14 24409939 24409939 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.2145G>T p.Lys715Asn p.K715N ENST00000382554 4/9 210 195 15 257 256 1 strelka-varscan-mutect NYNRIN,missense_variant,p.Lys715Asn,ENST00000382554,NM_025081.2;NYNRIN,upstream_gene_variant,,ENST00000554505,; T ENST00000382554 Transcript missense_variant 2463/7857 2145/5697 715/1898 K/N aaG/aaT 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 deleterious_low_confidence(0) 4/9 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 24409939 24409939 G T 1 0 0 0 0 1 0 0 0 10874 991 35 2 2 NYNRIN 14 24409939 Missense_Mutation SNP G 11LU016_T 103542 24409939 82633779 394 446 HEATR5A 0 . GRCh38 14 31387131 31387131 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.1178A>G p.Lys393Arg p.K393R ENST00000543095 8/36 155 111 44 125 125 0 strelka-varscan-mutect HEATR5A,missense_variant,p.Lys393Arg,ENST00000543095,NM_015473.3;HEATR5A,missense_variant,p.Lys21Arg,ENST00000538864,;HEATR5A,missense_variant,p.Lys52Arg,ENST00000550366,;RP11-176H8.1,3_prime_UTR_variant,,ENST00000549185,; C ENST00000543095 Transcript missense_variant 1363/7840 1178/6141 393/2046 K/R aAg/aGg 1 -1 HEATR5A HGNC HGNC:20276 protein_coding YES ENSP00000437968 F5H619 UPI0001890E04 NM_015473.3 tolerated(0.26) 8/36 hmmpanther:PTHR21663,hmmpanther:PTHR21663:SF1,Gene3D:1.25.10.10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 31387131 31387131 T C 1 0 0 0 0 1 0 0 0 6913 1609 56 5 5 HEATR5A 14 31387131 Missense_Mutation SNP T 11LU016_T 6977192 31387131 75656587 395 447 NPAS3 0 . GRCh38 14 33799898 33799898 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.1591A>T p.Ser531Cys p.S531C ENST00000356141 12/12 365 283 82 512 511 1 strelka-varscan-mutect NPAS3,missense_variant,p.Ser499Cys,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Ser501Cys,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Ser536Cys,ENST00000551492,;NPAS3,missense_variant,p.Ser531Cys,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Ser518Cys,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Ser505Cys,ENST00000551634,; T ENST00000356141 Transcript missense_variant 1591/2802 1591/2802 531/933 S/C Agc/Tgc 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious(0.03) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 33799898 33799898 A T 1 0 0 0 0 1 0 0 0 10612 188 7 4 4 NPAS3 14 33799898 Missense_Mutation SNP A 11LU016_T 2412767 33799898 73243820 396 448 GEMIN2 0 . GRCh38 14 39136454 39136454 + Missense_Mutation SNP G G C rs751872461 11LU016_T 11LU016_N G G c.818G>C p.Arg273Pro p.R273P ENST00000308317 10/10 197 160 37 175 175 0 strelka-varscan-mutect GEMIN2,missense_variant,p.Arg273Pro,ENST00000308317,NM_003616.2;GEMIN2,missense_variant,p.Arg258Pro,ENST00000250379,NM_001009182.1;GEMIN2,3_prime_UTR_variant,,ENST00000396249,NM_001009183.1;GEMIN2,downstream_gene_variant,,ENST00000534684,;GEMIN2,downstream_gene_variant,,ENST00000524781,;GEMIN2,3_prime_UTR_variant,,ENST00000525153,;GEMIN2,3_prime_UTR_variant,,ENST00000412033,;GEMIN2,non_coding_transcript_exon_variant,,ENST00000524980,;GEMIN2,downstream_gene_variant,,ENST00000531684,;GEMIN2,downstream_gene_variant,,ENST00000529365,; C ENST00000308317 Transcript missense_variant 901/1420 818/843 273/280 R/P cGt/cCt rs751872461 1 1 GEMIN2 HGNC HGNC:10884 protein_coding YES CCDS9669.1 ENSP00000308533 O14893 UPI000012B3B7 NM_003616.2 tolerated(0.2) 10/10 PIRSF_domain:PIRSF038038,hmmpanther:PTHR12794 MODERATE 1 SNV 1 1 PASS rs751872461 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 39136454 39136454 G C 1 0 0 0 0 1 0 0 0 6203 1145 40 4 4 GEMIN2 14 39136454 Missense_Mutation SNP G 11LU016_T 5336556 39136454 67907264 397 449 FSCB 0 . GRCh38 14 44506453 44506453 + Nonsense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.535G>T p.Glu179Ter p.E179* ENST00000340446 1/1 158 132 26 174 174 0 strelka-varscan-mutect FSCB,stop_gained,p.Glu179Ter,ENST00000340446,NM_032135.3;RP11-163M18.1,upstream_gene_variant,,ENST00000557465,;RP11-163M18.1,upstream_gene_variant,,ENST00000556228,;RP11-163M18.1,upstream_gene_variant,,ENST00000555433,; A ENST00000340446 Transcript stop_gained 827/2938 535/2478 179/825 E/* Gaa/Taa COSM3886066 1 -1 FSCB HGNC HGNC:20494 protein_coding YES CCDS9679.1 ENSP00000344579 Q5H9T9 UPI00001FD466 NM_032135.3 1/1 hmmpanther:PTHR36135 1 HIGH SNV 1 1 PASS rs1436177188 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 44506453 44506453 C A 1 0 0 0 0 0 1 0 0 5939 864 30 2 2 FSCB 14 44506453 Nonsense_Mutation SNP C 11LU016_T 5369999 44506453 62537265 398 450 MDGA2 0 . GRCh38 14 46874062 46874062 + Missense_Mutation SNP C C A rs202047105 11LU016_T 11LU016_N C C c.2369G>T p.Arg790Leu p.R790L ENST00000399232 13/17 80 67 13 135 135 0 strelka-mutect MDGA2,missense_variant,p.Arg660Leu,ENST00000426342,;MDGA2,missense_variant,p.Arg790Leu,ENST00000399232,NM_001113498.2;MDGA2,missense_variant,p.Arg561Leu,ENST00000357362,NM_182830.4;MDGA2,3_prime_UTR_variant,,ENST00000557238,;MDGA2,non_coding_transcript_exon_variant,,ENST00000555521,;MDGA2,non_coding_transcript_exon_variant,,ENST00000557516,; A ENST00000399232 Transcript missense_variant 2734/5075 2369/2871 790/956 R/L cGt/cTt rs202047105,COSM5443980,COSM5443981,COSM5443982 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 tolerated(0.16) 13/17 Pfam_domain:PF00629,PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,SMART_domains:SM00137,Superfamily_domains:SSF49899 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs202047105 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 46874062 46874062 C A 1 0 0 0 0 1 0 0 0 9345 536 19 1 1 MDGA2 14 46874062 Missense_Mutation SNP C 11LU016_T 2367609 46874062 60169656 399 451 PTGDR 0 . GRCh38 14 52268339 52268339 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.525G>T p.= p.V175V ENST00000306051 1/2 440 329 111 348 347 1 strelka-varscan-mutect PTGDR,synonymous_variant,p.=,ENST00000306051,NM_000953.2;PTGDR,synonymous_variant,p.=,ENST00000553372,NM_001281469.1; T ENST00000306051 Transcript synonymous_variant 627/2942 525/1080 175/359 V gtG/gtT 1 1 PTGDR HGNC HGNC:9591 protein_coding YES CCDS9707.1 ENSP00000303424 Q13258 UPI000000D994 NM_000953.2 1/2 PROSITE_profiles:PS50262,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF14,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01788 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 52268339 52268339 G T 1 0 0 0 0 0 0 0 1 12894 1306 46 2 2 PTGDR 14 52268339 Silent SNP G 11LU016_T 5394277 52268339 54775379 400 452 SYNE2 0 . GRCh38 14 64016487 64016487 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.4743A>T p.Lys1581Asn p.K1581N ENST00000358025 33/116 130 97 33 123 123 0 strelka-varscan-mutect SYNE2,missense_variant,p.Lys1581Asn,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Lys1581Asn,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Lys1581Asn,ENST00000357395,;SYNE2,missense_variant,p.Lys1581Asn,ENST00000554584,;SYNE2,non_coding_transcript_exon_variant,,ENST00000557005,; T ENST00000358025 Transcript missense_variant 4955/21842 4743/20724 1581/6907 K/N aaA/aaT 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0) 33/116 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF317,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 64016487 64016487 A T 1 0 0 0 0 1 0 0 0 15838 69 3 4 4 SYNE2 14 64016487 Missense_Mutation SNP A 11LU016_T 11748148 64016487 43027231 401 453 PLEKHG3 0 . GRCh38 14 64741119 64741119 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1602C>G p.Asp534Glu p.D534E ENST00000247226 16/17 129 113 16 153 153 0 strelka-varscan-mutect PLEKHG3,missense_variant,p.Asp534Glu,ENST00000247226,NM_001308147.1;PLEKHG3,missense_variant,p.Asp478Glu,ENST00000394691,NM_015549.1;PLEKHG3,missense_variant,p.Asp67Glu,ENST00000471182,;PLEKHG3,missense_variant,p.Asp39Glu,ENST00000484731,;PLEKHG3,missense_variant,p.Asp478Glu,ENST00000634379,;PLEKHG3,upstream_gene_variant,,ENST00000492928,;PLEKHG3,non_coding_transcript_exon_variant,,ENST00000490180,; G ENST00000247226 Transcript missense_variant 1749/10351 1602/3660 534/1219 D/E gaC/gaG 1 1 PLEKHG3 HGNC HGNC:20364 protein_coding YES CCDS76690.1 ENSP00000247226 A1L390 UPI0000ECF248 NM_001308147.1 tolerated(0.18) 16/17 MODERATE 1 SNV 1 1 PASS rs1359668357 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 64741119 64741119 C G 1 0 0 0 0 1 0 0 0 12163 477 17 4 4 PLEKHG3 14 64741119 Missense_Mutation SNP C 11LU016_T 724632 64741119 42302599 402 454 EXD2 0 . GRCh38 14 69230547 69230547 + Silent SNP C C T novel 11LU016_T 11LU016_N C C c.666C>T p.= p.S222S ENST00000312994 4/9 153 128 25 103 103 0 strelka-varscan-mutect EXD2,synonymous_variant,p.=,ENST00000312994,NM_001193362.1,NM_001193363.1;EXD2,synonymous_variant,p.=,ENST00000409014,;EXD2,synonymous_variant,p.=,ENST00000409018,NM_001193361.1,NM_001193360.1;EXD2,synonymous_variant,p.=,ENST00000409675,NM_018199.3;EXD2,synonymous_variant,p.=,ENST00000409949,;EXD2,synonymous_variant,p.=,ENST00000409242,;EXD2,synonymous_variant,p.=,ENST00000413191,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,non_coding_transcript_exon_variant,,ENST00000489133,;EXD2,non_coding_transcript_exon_variant,,ENST00000494629,; T ENST00000312994 Transcript synonymous_variant 987/5107 666/1866 222/621 S tcC/tcT 1 1 EXD2 HGNC HGNC:20217 protein_coding YES CCDS53902.1 ENSP00000313140 Q9NVH0 UPI0000577ED7 NM_001193362.1,NM_001193363.1 4/9 Gene3D:3.30.420.10,Pfam_domain:PF01612,hmmpanther:PTHR13620,hmmpanther:PTHR13620:SF0,SMART_domains:SM00474,Superfamily_domains:SSF53098 LOW 1 SNV 2 1 PASS rs1020148139 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 69230547 69230547 C T 1 0 0 0 0 0 0 0 1 5165 610 22 3 3 EXD2 14 69230547 Silent SNP C 11LU016_T 4489428 69230547 37813171 403 455 YLPM1 0 . GRCh38 14 74797912 74797912 + Missense_Mutation SNP A A C novel 11LU016_T 11LU016_N A A c.2615A>C p.Asn872Thr p.N872T ENST00000325680 5/21 338 290 48 297 297 0 strelka-varscan-mutect YLPM1,missense_variant,p.Asn872Thr,ENST00000325680,NM_019589.2;YLPM1,intron_variant,,ENST00000552421,;YLPM1,missense_variant,p.Asn425Thr,ENST00000549293,; C ENST00000325680 Transcript missense_variant 2739/7108 2615/6441 872/2146 N/T aAc/aCc 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 deleterious_low_confidence(0) 5/21 hmmpanther:PTHR13413,hmmpanther:PTHR13413:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 74797912 74797912 A C 1 0 0 0 0 1 0 0 0 18048 43 2 5 5 YLPM1 14 74797912 Missense_Mutation SNP A 11LU016_T 5567365 74797912 32245806 404 456 2 2 YLPM1 0 . GRCh38 14 74797915 74797915 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.2618A>G p.Gln873Arg p.Q873R ENST00000325680 5/21 333 287 46 286 286 0 strelka-varscan-mutect YLPM1,missense_variant,p.Gln873Arg,ENST00000325680,NM_019589.2;YLPM1,intron_variant,,ENST00000552421,;YLPM1,missense_variant,p.Gln426Arg,ENST00000549293,; G ENST00000325680 Transcript missense_variant 2742/7108 2618/6441 873/2146 Q/R cAg/cGg 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 deleterious_low_confidence(0.03) 5/21 hmmpanther:PTHR13413,hmmpanther:PTHR13413:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 74797915 74797915 A G 1 0 0 0 0 1 0 0 0 18048 188 7 5 5 YLPM1 14 74797915 Missense_Mutation SNP A 11LU016_T 3 74797915 32245803 405 457 2 2 CEP128 0 . GRCh38 14 80743262 80743262 + Silent SNP T T C novel 11LU016_T 11LU016_N T T c.2619A>G p.= p.K873K ENST00000555265 19/25 242 178 64 212 212 0 strelka-varscan-mutect CEP128,synonymous_variant,p.=,ENST00000555265,;CEP128,synonymous_variant,p.=,ENST00000281129,NM_152446.3;CEP128,synonymous_variant,p.=,ENST00000554728,;CEP128,synonymous_variant,p.=,ENST00000554502,; C ENST00000555265 Transcript synonymous_variant 2995/4662 2619/3285 873/1094 K aaA/aaG 1 -1 CEP128 HGNC HGNC:20359 protein_coding YES CCDS32130.1 ENSP00000451162 Q6ZU80 UPI000022982E 19/25 hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF205 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 80743262 80743262 T C 1 0 0 0 0 0 0 0 1 2958 1739 60 5 5 CEP128 14 80743262 Silent SNP T 11LU016_T 5945347 80743262 26300456 406 458 TTC7B 0 . GRCh38 14 90644100 90644100 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1699G>T p.Asp567Tyr p.D567Y ENST00000328459 15/20 237 180 57 250 250 0 strelka-varscan-mutect TTC7B,missense_variant,p.Asp567Tyr,ENST00000328459,NM_001010854.1;TTC7B,missense_variant,p.Asp37Tyr,ENST00000553972,;RP11-1078H9.5,intron_variant,,ENST00000557007,;RP11-1078H9.5,intron_variant,,ENST00000553826,;TTC7B,non_coding_transcript_exon_variant,,ENST00000554654,;TTC7B,non_coding_transcript_exon_variant,,ENST00000556490,;TTC7B,missense_variant,p.Asp308Tyr,ENST00000555005,;TTC7B,3_prime_UTR_variant,,ENST00000555239,;TTC7B,downstream_gene_variant,,ENST00000556749,; A ENST00000328459 Transcript missense_variant 1821/19458 1699/2532 567/843 D/Y Gac/Tac 1 -1 TTC7B HGNC HGNC:19858 protein_coding YES CCDS32140.1 ENSP00000336127 Q86TV6 UPI00001FD9F0 NM_001010854.1 deleterious(0.03) 15/20 Gene3D:1.25.40.10,Pfam_domain:PF12895,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF365,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 90644100 90644100 C A 1 0 0 0 0 1 0 0 0 17223 826 29 2 2 TTC7B 14 90644100 Missense_Mutation SNP C 11LU016_T 9900838 90644100 16399618 407 459 UNC79 0 . GRCh38 14 93630880 93630880 + Silent SNP G G C rs778028999 11LU016_T 11LU016_N G G c.5157G>C p.= p.P1719P ENST00000256339 31/50 239 219 20 223 223 0 strelka-varscan-mutect UNC79,synonymous_variant,p.=,ENST00000553484,;UNC79,synonymous_variant,p.=,ENST00000555664,;UNC79,synonymous_variant,p.=,ENST00000256339,NM_020818.3;UNC79,synonymous_variant,p.=,ENST00000393151,;UNC79,synonymous_variant,p.=,ENST00000621021,; C ENST00000256339 Transcript synonymous_variant 5812/8400 5157/7377 1719/2458 P ccG/ccC rs778028999,COSM3386745,COSM3386746 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 31/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs778028999 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 93630880 93630880 G C 1 0 0 0 0 0 0 0 1 17520 1103 39 4 4 UNC79 14 93630880 Silent SNP G 11LU016_T 2986780 93630880 13412838 408 460 IFI27L1 0 . GRCh38 14 94101833 94101833 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.81G>T p.= p.V27V ENST00000555523 4/5 196 154 42 162 162 0 strelka-varscan-mutect IFI27L1,missense_variant,p.Ala50Ser,ENST00000553664,;IFI27L1,synonymous_variant,p.=,ENST00000556381,;IFI27L1,synonymous_variant,p.=,ENST00000555523,NM_206949.2;IFI27L1,synonymous_variant,p.=,ENST00000393115,NM_145249.2;IFI27L1,synonymous_variant,p.=,ENST00000555341,;IFI27L1,synonymous_variant,p.=,ENST00000554166,;IFI27L1,synonymous_variant,p.=,ENST00000554562,;IFI27L1,intron_variant,,ENST00000557066,;IFI27L1,intron_variant,,ENST00000557218,;IFI27L1,intron_variant,,ENST00000554544,;IFI27,upstream_gene_variant,,ENST00000614204,;IFI27L1,intron_variant,,ENST00000553350,;IFI27L1,downstream_gene_variant,,ENST00000557600,; T ENST00000555523 Transcript synonymous_variant 300/680 81/315 27/104 V gtG/gtT 1 1 IFI27L1 HGNC HGNC:19754 protein_coding YES CCDS9919.1 ENSP00000451851 Q96BM0 UPI000012A3C8 NM_206949.2 4/5 Pfam_domain:PF06140,hmmpanther:PTHR16932,hmmpanther:PTHR16932:SF22,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 94101833 94101833 G T 1 0 0 0 0 0 0 0 1 7414 1319 46 2 2 IFI27L1 14 94101833 Silent SNP G 11LU016_T 470953 94101833 12941885 409 461 SERPINA4 0 . GRCh38 14 94568206 94568206 + Missense_Mutation SNP C C A rs765511128 11LU016_T 11LU016_N C C c.1001C>A p.Pro334His p.P334H ENST00000557004 4/5 292 227 65 303 303 0 strelka-varscan-mutect SERPINA4,missense_variant,p.Pro334His,ENST00000557004,NM_006215.3;SERPINA4,missense_variant,p.Pro334His,ENST00000555095,NM_001289032.1;SERPINA4,missense_variant,p.Pro334His,ENST00000298841,NM_001289033.1;SERPINA5,intron_variant,,ENST00000553780,;SERPINA5,intron_variant,,ENST00000554220,; A ENST00000557004 Transcript missense_variant 1422/2012 1001/1284 334/427 P/H cCc/cAc rs765511128 1 1 SERPINA4 HGNC HGNC:8948 protein_coding YES CCDS9927.1 ENSP00000450838 P29622 A0A024R6I9 UPI000000CBEF NM_006215.3 deleterious(0.01) 4/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF194,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs765511128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 94568206 94568206 C A 1 0 0 0 0 1 0 0 0 14367 623 22 2 2 SERPINA4 14 94568206 Missense_Mutation SNP C 11LU016_T 466373 94568206 12475512 410 462 SERPINA5 0 . GRCh38 14 94592060 94592060 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1042G>T p.Val348Leu p.V348L ENST00000329597 6/6 82 75 7 78 78 0 strelka-varscan-mutect SERPINA5,missense_variant,p.Val348Leu,ENST00000329597,NM_000624.5;SERPINA5,missense_variant,p.Val348Leu,ENST00000554866,;SERPINA5,missense_variant,p.Val348Leu,ENST00000554276,;SERPINA5,missense_variant,p.Val348Leu,ENST00000553780,;SERPINA5,downstream_gene_variant,,ENST00000554760,;SERPINA5,downstream_gene_variant,,ENST00000556775,;SERPINA5,downstream_gene_variant,,ENST00000555681,;SERPINA5,downstream_gene_variant,,ENST00000557598,;SERPINA5,downstream_gene_variant,,ENST00000554220,;SERPINA5,downstream_gene_variant,,ENST00000553511,;SERPINA5,downstream_gene_variant,,ENST00000554633,;SERPINA5,downstream_gene_variant,,ENST00000556064,;SERPINA3,missense_variant,p.Val2Leu,ENST00000553947,;SERPINA5,downstream_gene_variant,,ENST00000556730,; T ENST00000329597 Transcript missense_variant 1277/2337 1042/1221 348/406 V/L Gtg/Ttg 1 1 SERPINA5 HGNC HGNC:8723 protein_coding YES CCDS9928.1 ENSP00000333203 P05154 A0A024R6N9 UPI000013E52C NM_000624.5 tolerated(0.13) 6/6 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF176,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -15.05623 1 1 1 1 0 T 3 4 2 94592060 94592060 G T 1 0 0 0 0 1 0 0 0 14368 1275 44 2 2 SERPINA5 14 94592060 Missense_Mutation SNP G 11LU016_T 23854 94592060 12451658 411 463 GSC 0 . GRCh38 14 94769209 94769209 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.364G>T p.Gly122Cys p.G122C ENST00000238558 2/3 128 111 17 119 119 0 strelka-mutect GSC,missense_variant,p.Gly122Cys,ENST00000238558,NM_173849.2; A ENST00000238558 Transcript missense_variant 579/1264 364/774 122/257 G/C Ggc/Tgc 1 -1 GSC HGNC HGNC:4612 protein_coding YES CCDS9930.1 ENSP00000238558 P56915 UPI000000D86A NM_173849.2 deleterious(0.02) 2/3 hmmpanther:PTHR24329:SF275,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS rs1317804947 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 94769209 94769209 C A 1 0 0 0 0 1 0 0 0 6696 623 22 2 2 GSC 14 94769209 Missense_Mutation SNP C 11LU016_T 177149 94769209 12274509 412 464 ATG2B 0 . GRCh38 14 96341690 96341690 + Silent SNP T T A novel 11LU016_T 11LU016_N T T c.756A>T p.= p.P252P ENST00000359933 6/42 78 73 5 66 66 0 strelka-varscan-mutect ATG2B,synonymous_variant,p.=,ENST00000359933,NM_018036.5; A ENST00000359933 Transcript synonymous_variant 1650/13684 756/6237 252/2078 P ccA/ccT 1 -1 ATG2B HGNC HGNC:20187 protein_coding YES CCDS9944.2 ENSP00000353010 Q96BY7 UPI000155D51F NM_018036.5 6/42 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF20 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -11.30334 1 1 1 1 0 A 2 1 2 96341690 96341690 T A 1 0 0 0 0 0 0 0 1 1246 1799 63 4 4 ATG2B 14 96341690 Silent SNP T 11LU016_T 1572481 96341690 10702028 413 465 HHIPL1 0 . GRCh38 14 99659704 99659704 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.1323G>A p.= p.A441A ENST00000330710 4/9 36 26 10 32 32 0 strelka-varscan-mutect HHIPL1,synonymous_variant,p.=,ENST00000330710,NM_001127258.1;HHIPL1,synonymous_variant,p.=,ENST00000357223,NM_032425.4; A ENST00000330710 Transcript synonymous_variant 1421/7390 1323/2349 441/782 A gcG/gcA 1 1 HHIPL1 HGNC HGNC:19710 protein_coding YES CCDS45162.1 ENSP00000330601 Q96JK4 F1T0G3 UPI000022988D NM_001127258.1 4/9 Superfamily_domains:0046203,Gene3D:2.120.10.30,Pfam_domain:PF07995,hmmpanther:PTHR19328,hmmpanther:PTHR19328:SF32 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 99659704 99659704 G A 1 0 0 0 0 0 0 0 1 6978 1074 38 1 1 HHIPL1 14 99659704 Silent SNP G 11LU016_T 3318014 99659704 7384014 414 466 BEGAIN 0 . GRCh38 14 100538690 100538690 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1061C>A p.Ala354Asp p.A354D ENST00000443071 6/6 221 172 49 233 233 0 strelka-varscan-mutect BEGAIN,missense_variant,p.Ala573Asp,ENST00000637716,;BEGAIN,missense_variant,p.Ala384Asp,ENST00000637646,;BEGAIN,missense_variant,p.Ala354Asp,ENST00000443071,NM_001159531.1;BEGAIN,missense_variant,p.Ala354Asp,ENST00000355173,NM_020836.3;BEGAIN,downstream_gene_variant,,ENST00000556188,;BEGAIN,downstream_gene_variant,,ENST00000553553,;BEGAIN,downstream_gene_variant,,ENST00000554356,;BEGAIN,downstream_gene_variant,,ENST00000557378,;BEGAIN,downstream_gene_variant,,ENST00000554140,;CTD-2062F14.3,upstream_gene_variant,,ENST00000553301,;BEGAIN,non_coding_transcript_exon_variant,,ENST00000556751,; T ENST00000443071 Transcript missense_variant 1207/2744 1061/1782 354/593 A/D gCc/gAc 1 -1 BEGAIN HGNC HGNC:24163 protein_coding YES CCDS9962.1 ENSP00000411124 Q9BUH8 UPI00000710B1 NM_001159531.1 deleterious(0.05) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR28664,hmmpanther:PTHR28664:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 100538690 100538690 G T 1 0 0 0 0 1 0 0 0 1545 1203 42 2 2 BEGAIN 14 100538690 Missense_Mutation SNP G 11LU016_T 878986 100538690 6505028 415 467 INF2 0 . GRCh38 14 104713483 104713483 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.2917A>T p.Ile973Phe p.I973F ENST00000392634 20/23 531 451 80 574 574 0 strelka-varscan-mutect INF2,missense_variant,p.Ile973Phe,ENST00000330634,NM_001031714.3;INF2,missense_variant,p.Ile973Phe,ENST00000392634,NM_022489.3;INF2,missense_variant,p.Ile441Phe,ENST00000252527,;INF2,5_prime_UTR_variant,,ENST00000617571,;INF2,upstream_gene_variant,,ENST00000481338,;INF2,non_coding_transcript_exon_variant,,ENST00000477497,;INF2,downstream_gene_variant,,ENST00000474229,;INF2,downstream_gene_variant,,ENST00000480763,; T ENST00000392634 Transcript missense_variant 3029/4672 2917/3750 973/1249 I/F Atc/Ttc 1 1 INF2 HGNC HGNC:23791 protein_coding YES CCDS9989.2 ENSP00000376410 Q27J81 UPI000156D0FB NM_022489.3 deleterious(0) 20/23 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF5,SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 104713483 104713483 A T 1 0 0 0 0 1 0 0 0 7636 217 8 4 4 INF2 14 104713483 Missense_Mutation SNP A 11LU016_T 4174793 104713483 2330235 416 468 AHNAK2 0 . GRCh38 14 104948606 104948606 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.6845C>A p.Pro2282His p.P2282H ENST00000333244 7/7 678 529 149 647 644 3 strelka-varscan-mutect AHNAK2,missense_variant,p.Pro2282His,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; T ENST00000333244 Transcript missense_variant 6965/18254 6845/17388 2282/5795 P/H cCc/cAc 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.08) 7/7 hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348 MODERATE 1 SNV 5 1 PASS rs1242845083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 104948606 104948606 G T 1 0 0 0 0 1 0 0 0 492 1232 43 2 2 AHNAK2 14 104948606 Missense_Mutation SNP G 11LU016_T 235123 104948606 2095112 417 469 GABRA5 0 . GRCh38 15 26937187 26937187 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.583G>T p.Ala195Ser p.A195S ENST00000335625 8/11 202 151 51 403 402 1 strelka-varscan-mutect GABRA5,missense_variant,p.Ala195Ser,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Ala195Ser,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Ala195Ser,ENST00000355395,;GABRA5,missense_variant,p.Ala163Ser,ENST00000555182,;GABRB3,intron_variant,,ENST00000541819,; T ENST00000335625 Transcript missense_variant,splice_region_variant 1471/3251 583/1389 195/462 A/S Gcg/Tcg 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0) 8/11 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 26937187 26937187 G T 1 0 0 0 0 1 0 0 0 6035 1333 46 2 2 GABRA5 15 26937187 Missense_Mutation SNP G 11LU016_T 26937187 75054002 418 470 SECISBP2L 0 . GRCh38 15 49016985 49016985 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.1282A>T p.Asn428Tyr p.N428Y ENST00000559471 10/18 133 98 35 109 109 0 strelka-varscan-mutect SECISBP2L,missense_variant,p.Asn428Tyr,ENST00000559471,NM_001193489.1;SECISBP2L,missense_variant,p.Asn383Tyr,ENST00000261847,NM_014701.3;SECISBP2L,missense_variant,p.Asn190Tyr,ENST00000380927,;SECISBP2L,missense_variant,p.Asn300Tyr,ENST00000559424,;SECISBP2L,non_coding_transcript_exon_variant,,ENST00000561203,;SECISBP2L,non_coding_transcript_exon_variant,,ENST00000557940,;SECISBP2L,non_coding_transcript_exon_variant,,ENST00000558461,;SECISBP2L,upstream_gene_variant,,ENST00000559198,; A ENST00000559471 Transcript missense_variant 1546/7176 1282/3306 428/1101 N/Y Aat/Tat 1 -1 SECISBP2L HGNC HGNC:28997 protein_coding YES CCDS53942.1 ENSP00000453854 Q93073 A0A024R5R0 UPI00001C1F8B NM_001193489.1 deleterious_low_confidence(0) 10/18 hmmpanther:PTHR13284:SF10,hmmpanther:PTHR13284 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 49016985 49016985 T A 1 0 0 0 0 1 0 0 0 14284 1812 63 4 4 SECISBP2L 15 49016985 Missense_Mutation SNP T 11LU016_T 22079798 49016985 52974204 419 471 SMAD6 0 . GRCh38 15 66781195 66781195 + Missense_Mutation SNP G G T rs748124400 11LU016_T 11LU016_N G G c.1151G>T p.Arg384Leu p.R384L ENST00000288840 4/4 319 227 92 316 315 1 strelka-varscan-mutect SMAD6,missense_variant,p.Arg384Leu,ENST00000288840,NM_005585.4;SMAD6,3_prime_UTR_variant,,ENST00000557916,;SMAD6,3_prime_UTR_variant,,ENST00000559931,; T ENST00000288840 Transcript missense_variant 2182/3835 1151/1491 384/496 R/L cGc/cTc rs748124400,COSM2257363 1 1 SMAD6 HGNC HGNC:6772 protein_coding YES CCDS10221.1 ENSP00000288840 O43541 UPI0000071360 NM_005585.4 deleterious(0) 4/4 PROSITE_profiles:PS51076,hmmpanther:PTHR13703,Pfam_domain:PF03166,Gene3D:2.60.200.10,SMART_domains:SM00524,Superfamily_domains:SSF49879 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748124400 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 66781195 66781195 G T 1 0 0 0 0 1 0 0 0 15055 1087 38 1 1 SMAD6 15 66781195 Missense_Mutation SNP G 11LU016_T 17764210 66781195 35209994 420 472 ISL2 0 . GRCh38 15 76340492 76340492 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.728G>A p.Arg243His p.R243H ENST00000290759 4/6 187 177 10 227 227 0 strelka-varscan-mutect ISL2,missense_variant,p.Arg243His,ENST00000290759,NM_145805.2;RP11-685G9.4,upstream_gene_variant,,ENST00000602530,;RP11-685G9.2,splice_region_variant,,ENST00000559539,;ISL2,synonymous_variant,p.=,ENST00000558656,;ISL2,downstream_gene_variant,,ENST00000558437,; A ENST00000290759 Transcript missense_variant 888/1881 728/1080 243/359 R/H cGc/cAc 1 1 ISL2 HGNC HGNC:18524 protein_coding YES CCDS10290.1 ENSP00000290759 Q96A47 UPI000012D8FC NM_145805.2 deleterious(0) 4/6 PROSITE_profiles:PS50071,hmmpanther:PTHR24204:SF2,hmmpanther:PTHR24204,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 76340492 76340492 G A 1 0 0 0 0 1 0 0 0 7764 1087 38 1 1 ISL2 15 76340492 Missense_Mutation SNP G 11LU016_T 9559297 76340492 25650697 421 473 MEX3B 0 . GRCh38 15 82044359 82044359 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.511G>T p.Val171Leu p.V171L ENST00000329713 2/2 79 62 17 116 116 0 strelka-varscan-mutect MEX3B,missense_variant,p.Val171Leu,ENST00000329713,NM_032246.4;MEX3B,3_prime_UTR_variant,,ENST00000558133,; A ENST00000329713 Transcript missense_variant 947/3528 511/1710 171/569 V/L Gtg/Ttg 1 -1 MEX3B HGNC HGNC:25297 protein_coding YES CCDS10319.1 ENSP00000329918 Q6ZN04 UPI00001982CC NM_032246.4 deleterious(0) 2/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS50084,hmmpanther:PTHR23285,hmmpanther:PTHR23285:SF5,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 82044359 82044359 C A 1 0 0 0 0 1 0 0 0 9463 536 19 1 1 MEX3B 15 82044359 Missense_Mutation SNP C 11LU016_T 5703867 82044359 19946830 422 474 C15orf40 0 . GRCh38 15 83011594 83011594 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.14G>T p.Arg5Leu p.R5L ENST00000451195 1/5 122 100 22 165 165 0 strelka-varscan-mutect C15orf40,missense_variant,p.Arg5Leu,ENST00000304177,NM_144597.2;C15orf40,missense_variant,p.Arg5Leu,ENST00000538348,NM_001160116.1;C15orf40,missense_variant,p.Arg5Leu,ENST00000565712,;C15orf40,missense_variant,p.Arg5Leu,ENST00000451195,NM_001160115.1;C15orf40,missense_variant,p.Arg4Leu,ENST00000510873,;BTBD1,downstream_gene_variant,,ENST00000261721,NM_025238.3;C15orf40,upstream_gene_variant,,ENST00000508990,NM_001160114.1;C15orf40,upstream_gene_variant,,ENST00000514272,;RP11-382A20.5,intron_variant,,ENST00000566841,;RP11-382A20.7,upstream_gene_variant,,ENST00000570202,;C15orf40,non_coding_transcript_exon_variant,,ENST00000505341,;C15orf40,non_coding_transcript_exon_variant,,ENST00000506912,;C15orf40,non_coding_transcript_exon_variant,,ENST00000565725,;C15orf40,upstream_gene_variant,,ENST00000512638,;C15orf40,upstream_gene_variant,,ENST00000563387,; A ENST00000451195 Transcript missense_variant 14/518 14/504 5/167 R/L cGc/cTc 1 -1 C15orf40 HGNC HGNC:28443 protein_coding YES CCDS53969.1 ENSP00000403987 Q8WUR7 UPI0001A48FB7 NM_001160115.1 tolerated_low_confidence(0.46) 1/5 MODERATE SNV 3 1 PASS . . 0 199 8 2 0 0 0 0 -20 0.9998024 1 1 1 0 A 3 1 2 83011594 83011594 C A 1 0 0 0 0 1 0 0 0 1844 768 27 1 1 C15orf40 15 83011594 Missense_Mutation SNP C 11LU016_T 967235 83011594 18979595 423 475 BNC1 0 . GRCh38 15 83264370 83264370 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.881C>A p.Ser294Tyr p.S294Y ENST00000345382 4/5 197 150 47 238 238 0 strelka-varscan-mutect BNC1,missense_variant,p.Ser294Tyr,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Ser287Tyr,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; T ENST00000345382 Transcript missense_variant 967/4610 881/2985 294/994 S/Y tCc/tAc 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 tolerated(0.05) 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 MODERATE 1 SNV 1 1 PASS rs1390936371 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 83264370 83264370 G T 1 0 0 0 0 1 0 0 0 1630 1174 41 2 2 BNC1 15 83264370 Missense_Mutation SNP G 11LU016_T 252776 83264370 18726819 424 476 NTRK3 0 . GRCh38 15 88137494 88137494 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.532G>A p.Gly178Arg p.G178R ENST00000360948 7/20 253 190 63 268 267 1 strelka-varscan-mutect NTRK3,missense_variant,p.Gly178Arg,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Gly178Arg,ENST00000558676,;NTRK3,missense_variant,p.Gly178Arg,ENST00000317501,;NTRK3,missense_variant,p.Gly178Arg,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Gly178Arg,ENST00000357724,;NTRK3,missense_variant,p.Gly178Arg,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Gly178Arg,ENST00000626019,;NTRK3,missense_variant,p.Gly178Arg,ENST00000629765,;NTRK3,missense_variant,p.Gly178Arg,ENST00000557856,;NTRK3,missense_variant,p.Gly80Arg,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Gly178Arg,ENST00000540489,NM_001007156.2;NTRK3,missense_variant,p.Gly80Arg,ENST00000559188,;NTRK3,upstream_gene_variant,,ENST00000560017,;NTRK3,upstream_gene_variant,,ENST00000559764,; T ENST00000360948 Transcript missense_variant 838/3004 532/2520 178/839 G/R Ggg/Agg 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0.02) 7/20 Gene3D:3.80.10.10,Pfam_domain:PF16920,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 88137494 88137494 C T 1 0 0 0 0 1 0 0 0 10774 623 22 3 3 NTRK3 15 88137494 Missense_Mutation SNP C 11LU016_T 4873124 88137494 13853695 425 477 MCTP2 0 . GRCh38 15 94385526 94385526 + Splice_Site SNP G G T rs200626556 11LU016_T 11LU016_N G G c.1788+1G>T p.X596_splice ENST00000357742 129 100 29 111 110 1 strelka-varscan-mutect MCTP2,splice_donor_variant,,ENST00000357742,NM_018349.3;MCTP2,splice_donor_variant,,ENST00000451018,NM_001159643.1;MCTP2,splice_donor_variant,,ENST00000557742,NM_001159644.1;MCTP2,splice_donor_variant,,ENST00000456504,; T ENST00000357742 Transcript splice_donor_variant -/7555 1788/2637 596/878 rs200626556,COSM1375577,COSM5101053 1 1 MCTP2 HGNC HGNC:25636 protein_coding YES CCDS32338.1 ENSP00000350377 Q6DN12 UPI0000D613A2 NM_018349.3 13/21 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs200626556 . 0 205 0 4 0 0 0 0 -20 0.9999613 1 1 1 0 T 5 4 2 94385526 94385526 G T 1 0 0 0 0 0 0 1 0 9337 1159 40 1 1 MCTP2 15 94385526 Splice_Site SNP G 11LU016_T 6248032 94385526 7605663 426 478 RPUSD1 0 . GRCh38 16 786125 786125 + Missense_Mutation SNP C C A rs771317301 11LU016_T 11LU016_N C C c.764G>T p.Arg255Leu p.R255L ENST00000561734 5/5 87 64 23 109 109 0 strelka-varscan-mutect RPUSD1,missense_variant,p.Arg255Leu,ENST00000561734,;RPUSD1,missense_variant,p.Arg255Leu,ENST00000007264,NM_001324415.1,NM_001324086.1,NM_058192.2;RPUSD1,missense_variant,p.Arg126Leu,ENST00000567114,NM_001324412.1;RPUSD1,missense_variant,p.Arg126Leu,ENST00000565377,;RPUSD1,missense_variant,p.Arg129Leu,ENST00000569601,;RPUSD1,3_prime_UTR_variant,,ENST00000565809,NM_001324411.1;CHTF18,upstream_gene_variant,,ENST00000631357,;CHTF18,upstream_gene_variant,,ENST00000455171,;CHTF18,upstream_gene_variant,,ENST00000262315,NM_022092.2;CHTF18,upstream_gene_variant,,ENST00000317063,;MSLNL,upstream_gene_variant,,ENST00000543963,;MSLNL,upstream_gene_variant,,ENST00000442466,;RPUSD1,downstream_gene_variant,,ENST00000562070,;CHTF18,upstream_gene_variant,,ENST00000426047,;RPUSD1,downstream_gene_variant,,ENST00000563560,;CHTF18,upstream_gene_variant,,ENST00000491530,;CHTF18,upstream_gene_variant,,ENST00000570058,;CHTF18,upstream_gene_variant,,ENST00000471202,;CHTF18,upstream_gene_variant,,ENST00000464728,;CHTF18,upstream_gene_variant,,ENST00000440239,;CHTF18,upstream_gene_variant,,ENST00000479976,;RPUSD1,downstream_gene_variant,,ENST00000567283,;CHTF18,upstream_gene_variant,,ENST00000569270,;CHTF18,upstream_gene_variant,,ENST00000567620,;CHTF18,upstream_gene_variant,,ENST00000563545,;CHTF18,upstream_gene_variant,,ENST00000484349,;RPUSD1,downstream_gene_variant,,ENST00000565503,; A ENST00000561734 Transcript missense_variant 1008/2159 764/939 255/312 R/L cGg/cTg rs771317301 1 -1 RPUSD1 HGNC HGNC:14173 protein_coding YES CCDS10426.1 ENSP00000455026 Q9UJJ7 UPI0000073C11 tolerated_low_confidence(0.25) 5/5 MODERATE 1 SNV 1 1 PASS rs771317301 . 0 200 10 0 0 0 0 0 -20 0.9999945 1 1 1 0 A 3 1 2 786125 786125 C A 1 0 0 0 0 1 0 0 0 13921 652 23 1 1 RPUSD1 16 786125 Missense_Mutation SNP C 11LU016_T 786125 89552220 427 479 BAIAP3 0 . GRCh38 16 1338593 1338593 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.149T>A p.Val50Glu p.V50E ENST00000324385 2/34 134 116 18 213 213 0 strelka-varscan-mutect BAIAP3,missense_variant,p.Val15Glu,ENST00000628027,;BAIAP3,missense_variant,p.Val50Glu,ENST00000324385,NM_003933.4;BAIAP3,missense_variant,p.Val15Glu,ENST00000397488,NM_001286464.1;BAIAP3,missense_variant,p.Val15Glu,ENST00000426824,NM_001199097.1;BAIAP3,missense_variant,p.Val15Glu,ENST00000421665,NM_001199096.1;BAIAP3,missense_variant,p.Val15Glu,ENST00000568887,NM_001199099.1;BAIAP3,missense_variant,p.Val15Glu,ENST00000562208,NM_001199098.1;BAIAP3,non_coding_transcript_exon_variant,,ENST00000567825,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000565665,;BAIAP3,upstream_gene_variant,,ENST00000568198,; A ENST00000324385 Transcript missense_variant 307/4678 149/3564 50/1187 V/E gTg/gAg 1 1 BAIAP3 HGNC HGNC:948 protein_coding YES CCDS10434.1 ENSP00000324510 O94812 UPI0000071E58 NM_003933.4 deleterious_low_confidence(0) 2/34 hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF65 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1338593 1338593 T A 1 0 0 0 0 1 0 0 0 1456 1696 59 4 4 BAIAP3 16 1338593 Missense_Mutation SNP T 11LU016_T 552468 1338593 88999752 428 480 UNKL 0 . GRCh38 16 1394146 1394146 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.922T>C p.Phe308Leu p.F308L ENST00000389221 7/15 180 139 41 216 216 0 strelka-varscan-mutect UNKL,missense_variant,p.Phe308Leu,ENST00000389221,NM_001193388.3;UNKL,missense_variant,p.Phe308Leu,ENST00000508903,;UNKL,downstream_gene_variant,,ENST00000301712,NM_001037125.3;UNKL,3_prime_UTR_variant,,ENST00000382757,;UNKL,downstream_gene_variant,,ENST00000502438,;UNKL,downstream_gene_variant,,ENST00000509981,; G ENST00000389221 Transcript missense_variant 951/5116 922/2052 308/683 F/L Ttt/Ctt 1 -1 UNKL HGNC HGNC:14184 protein_coding ENSP00000373873 A0A0A0MRZ1 UPI0002B3F787 NM_001193388.3 deleterious(0.01) 7/15 Gene3D:1m9oA00,Pfam_domain:PF00642,PROSITE_profiles:PS50103,hmmpanther:PTHR14493,hmmpanther:PTHR14493:SF37,SMART_domains:SM00356,Superfamily_domains:SSF90229 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 1394146 1394146 A G 1 0 0 0 0 1 0 0 0 17527 72 3 5 5 UNKL 16 1394146 Missense_Mutation SNP A 11LU016_T 55553 1394146 88944199 429 481 MAPK8IP3 0 . GRCh38 16 1748634 1748634 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1127G>A p.Gly376Asp p.G376D ENST00000250894 8/32 403 374 29 368 367 1 strelka-varscan-mutect MAPK8IP3,missense_variant,p.Gly376Asp,ENST00000250894,NM_001318852.1,NM_015133.3;MAPK8IP3,missense_variant,p.Gly377Asp,ENST00000610761,;MAPK8IP3,missense_variant,p.Gly376Asp,ENST00000356010,NM_001040439.1;LA16c-361A3.3,downstream_gene_variant,,ENST00000569670,;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000568271,;MAPK8IP3,3_prime_UTR_variant,,ENST00000567849,;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000568774,;MAPK8IP3,downstream_gene_variant,,ENST00000564098,;MAPK8IP3,downstream_gene_variant,,ENST00000561765,; A ENST00000250894 Transcript missense_variant 1284/5661 1127/4011 376/1336 G/D gGc/gAc 1 1 MAPK8IP3 HGNC HGNC:6884 protein_coding YES CCDS10442.2 ENSP00000250894 Q9UPT6 UPI000034ECA7 NM_001318852.1,NM_015133.3 tolerated(1) 8/32 hmmpanther:PTHR13886,hmmpanther:PTHR13886:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1748634 1748634 G A 1 0 0 0 0 1 0 0 0 9210 1203 42 3 3 MAPK8IP3 16 1748634 Missense_Mutation SNP G 11LU016_T 354488 1748634 88589711 430 482 PKD1 0 . GRCh38 16 2090437 2090437 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.12292G>T p.Ala4098Ser p.A4098S ENST00000262304 45/46 480 395 85 506 505 1 strelka-varscan-mutect PKD1,missense_variant,p.Ala4098Ser,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Ala4097Ser,ENST00000423118,NM_000296.3;TSC2,downstream_gene_variant,,ENST00000219476,NM_000548.3;TSC2,downstream_gene_variant,,ENST00000350773,NM_001114382.1;TSC2,downstream_gene_variant,,ENST00000568454,NM_001318832.1;TSC2,downstream_gene_variant,,ENST00000401874,NM_001077183.1;TSC2,downstream_gene_variant,,ENST00000439673,NM_001318827.1;TSC2,downstream_gene_variant,,ENST00000382538,NM_001318829.1;TSC2,downstream_gene_variant,,ENST00000569110,;MIR1225,upstream_gene_variant,,ENST00000408729,;RP11-304L19.1,upstream_gene_variant,,ENST00000570072,;RP11-304L19.3,downstream_gene_variant,,ENST00000565937,;RP11-304L19.1,upstream_gene_variant,,ENST00000563284,;PKD1,non_coding_transcript_exon_variant,,ENST00000472577,;PKD1,downstream_gene_variant,,ENST00000487932,;TSC2,downstream_gene_variant,,ENST00000439117,NM_001318831.1;TSC2,downstream_gene_variant,,ENST00000497886,;TSC2,downstream_gene_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000485120,;PKD1,downstream_gene_variant,,ENST00000561668,;PKD1,downstream_gene_variant,,ENST00000472659,;PKD1,downstream_gene_variant,,ENST00000562425,;PKD1,downstream_gene_variant,,ENST00000567355,;PKD1,downstream_gene_variant,,ENST00000564313,;PKD1,downstream_gene_variant,,ENST00000568796,; A ENST00000262304 Transcript missense_variant 12501/14138 12292/12912 4098/4303 A/S Gcc/Tcc COSM4059178 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 tolerated(0.06) 45/46 Pfam_domain:PF08016,Prints_domain:PR00500,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS rs1346816281 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 2090437 2090437 C A 1 0 0 0 0 1 0 0 0 12059 768 27 1 1 PKD1 16 2090437 Missense_Mutation SNP C 11LU016_T 341803 2090437 88247908 431 483 NTN3 0 . GRCh38 16 2472315 2472315 + Missense_Mutation SNP T T A rs370583910 11LU016_T 11LU016_N T T c.614T>A p.Leu205Gln p.L205Q ENST00000293973 1/6 100 72 28 106 106 0 strelka-varscan-mutect NTN3,missense_variant,p.Leu205Gln,ENST00000293973,NM_006181.2;TBC1D24,upstream_gene_variant,,ENST00000567020,NM_020705.2;TBC1D24,upstream_gene_variant,,ENST00000293970,NM_001199107.1;RP11-715J22.6,upstream_gene_variant,,ENST00000561847,;RP11-715J22.2,upstream_gene_variant,,ENST00000563775,;TBC1D24,upstream_gene_variant,,ENST00000630263,;TBC1D24,upstream_gene_variant,,ENST00000569874,; A ENST00000293973 Transcript missense_variant 817/1986 614/1743 205/580 L/Q cTg/cAg rs370583910 1 1 NTN3 HGNC HGNC:8030 protein_coding YES CCDS10469.1 ENSP00000293973 O00634 UPI000006ED30 NM_006181.2 deleterious(0) 1/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF292,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS rs370583910 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 2472315 2472315 T A 1 0 0 0 0 1 0 0 0 10766 1580 55 4 4 NTN3 16 2472315 Missense_Mutation SNP T 11LU016_T 381878 2472315 87866030 432 484 ERCC4 0 . GRCh38 16 13948145 13948145 + Missense_Mutation SNP A A T rs754705146 11LU016_T 11LU016_N A A c.2549A>T p.Asp850Val p.D850V ENST00000311895 11/11 282 263 19 231 231 0 strelka-varscan-mutect ERCC4,missense_variant,p.Asp850Val,ENST00000311895,NM_005236.2;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,downstream_gene_variant,,ENST00000462862,; T ENST00000311895 Transcript missense_variant 2558/6758 2549/2751 850/916 D/V gAc/gTc rs754705146 1 1 ERCC4 HGNC HGNC:3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 UPI0000161BBF NM_005236.2 deleterious(0) 11/11 hmmpanther:PTHR10150,Superfamily_domains:SSF47781,TIGRFAM_domain:TIGR00596 MODERATE 1 SNV 1 1 PASS rs754705146 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 13948145 13948145 A T 1 0 0 0 0 1 0 0 0 5064 275 10 4 4 ERCC4 16 13948145 Missense_Mutation SNP A 11LU016_T 11475830 13948145 76390200 433 485 ARL6IP1 0 . GRCh38 16 18793346 18793346 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.518G>T p.Gly173Val p.G173V ENST00000304414 6/6 62 42 20 140 140 0 strelka-varscan-mutect ARL6IP1,missense_variant,p.Gly173Val,ENST00000304414,NM_015161.1;ARL6IP1,missense_variant,p.Gly144Val,ENST00000546206,;ARL6IP1,missense_variant,p.Gly58Val,ENST00000562819,;RP11-1035H13.3,intron_variant,,ENST00000567078,;RPS15A,upstream_gene_variant,,ENST00000322989,NM_001019.4;RPS15A,upstream_gene_variant,,ENST00000576436,;RPS15A,upstream_gene_variant,,ENST00000569083,;RPS15A,upstream_gene_variant,,ENST00000565420,;RPS15A,upstream_gene_variant,,ENST00000563390,NM_001030009.1;ARL6IP1,downstream_gene_variant,,ENST00000562234,;RPS15A,upstream_gene_variant,,ENST00000573554,;ARL6IP1,3_prime_UTR_variant,,ENST00000563861,;ARL6IP1,downstream_gene_variant,,ENST00000566391,;RPS15A,upstream_gene_variant,,ENST00000572008,;ARL6IP1,downstream_gene_variant,,ENST00000569976,;RPS15A,upstream_gene_variant,,ENST00000576008,;ARL6IP1,downstream_gene_variant,,ENST00000567969,;RPS15A,upstream_gene_variant,,ENST00000569365,;RPS15A,upstream_gene_variant,,ENST00000562935,;RPS15A,upstream_gene_variant,,ENST00000574723,; A ENST00000304414 Transcript missense_variant 730/2409 518/612 173/203 G/V gGa/gTa 1 -1 ARL6IP1 HGNC HGNC:697 protein_coding YES CCDS10572.1 ENSP00000306788 Q15041 A0A024QYV7 UPI0000125D46 NM_015161.1 deleterious(0) 6/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR20952:SF3,hmmpanther:PTHR20952 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 2 18793346 18793346 C A 1 0 0 0 0 1 0 0 0 1082 855 30 2 2 ARL6IP1 16 18793346 Missense_Mutation SNP C 11LU016_T 4845201 18793346 71544999 434 486 ACSM1 0 . GRCh38 16 20685371 20685371 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.225G>T p.Trp75Cys p.W75C ENST00000307493 2/13 319 240 79 328 327 1 strelka-varscan-mutect ACSM1,missense_variant,p.Trp75Cys,ENST00000307493,NM_001318890.1,NM_052956.2;ACSM1,missense_variant,p.Trp75Cys,ENST00000520010,;ACSM1,missense_variant,p.Trp75Cys,ENST00000523065,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;ACSM3,downstream_gene_variant,,ENST00000614721,;ACSM1,missense_variant,p.Trp75Cys,ENST00000519745,; A ENST00000307493 Transcript missense_variant 293/2051 225/1734 75/577 W/C tgG/tgT 1 -1 ACSM1 HGNC HGNC:18049 protein_coding YES CCDS10587.1 ENSP00000301956 Q08AH1 UPI00000558D0 NM_001318890.1,NM_052956.2 deleterious(0) 2/13 hmmpanther:PTHR24095:SF150,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 20685371 20685371 C A 1 0 0 0 0 1 0 0 0 224 508 18 2 2 ACSM1 16 20685371 Missense_Mutation SNP C 11LU016_T 1892025 20685371 69652974 435 487 C16orf82 0 . GRCh38 16 27067044 27067044 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.238G>A p.Gly80Arg p.G80R ENST00000505035 1/1 416 351 65 411 411 0 strelka-varscan-mutect C16orf82,missense_variant,p.Gly80Arg,ENST00000505035,;C16orf82,missense_variant,p.Gly17Arg,ENST00000418886,NM_001145545.1;RP11-673P17.2,intron_variant,,ENST00000565783,; A ENST00000505035 Transcript missense_variant 338/2459 238/654 80/217 G/R Ggg/Agg 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 tolerated(0.12) 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 27067044 27067044 G A 1 0 0 0 0 1 0 0 0 1867 1000 35 3 3 C16orf82 16 27067044 Missense_Mutation SNP G 11LU016_T 6381673 27067044 63271301 436 488 IL21R 0 . GRCh38 16 27448875 27448875 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1209C>A p.Asp403Glu p.D403E ENST00000337929 9/9 110 82 28 96 96 0 strelka-varscan-mutect IL21R,missense_variant,p.Asp403Glu,ENST00000337929,NM_181078.2;IL21R,missense_variant,p.Asp403Glu,ENST00000564089,NM_181079.4;IL21R,missense_variant,p.Asp403Glu,ENST00000395754,NM_021798.3;IL21R-AS1,non_coding_transcript_exon_variant,,ENST00000563191,;IL21R,downstream_gene_variant,,ENST00000564583,;IL21R,downstream_gene_variant,,ENST00000561953,; A ENST00000337929 Transcript missense_variant 1682/4849 1209/1617 403/538 D/E gaC/gaA 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 deleterious(0.01) 9/9 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 27448875 27448875 C A 1 0 0 0 0 1 0 0 0 7574 506 18 2 2 IL21R 16 27448875 Missense_Mutation SNP C 11LU016_T 381831 27448875 62889470 437 489 SPNS1 0 . GRCh38 16 28983939 28983939 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1474G>T p.Ala492Ser p.A492S ENST00000311008 11/12 40 27 13 26 26 0 strelka-varscan-mutect SPNS1,missense_variant,p.Ala492Ser,ENST00000311008,NM_001142448.1,NM_032038.2;SPNS1,missense_variant,p.Ala419Ser,ENST00000323081,NM_001142450.1;SPNS1,missense_variant,p.Ala440Ser,ENST00000334536,NM_001142451.1;SPNS1,missense_variant,p.Ala537Ser,ENST00000565975,;SPNS1,missense_variant,p.Ala418Ser,ENST00000352260,NM_001142449.1;SPNS1,missense_variant,p.Ala258Ser,ENST00000564476,;SPNS1,missense_variant,p.Ala143Ser,ENST00000568829,;SPNS1,intron_variant,,ENST00000566059,;LAT,upstream_gene_variant,,ENST00000395456,NM_001014987.1;LAT,upstream_gene_variant,,ENST00000360872,NM_014387.3;LAT,upstream_gene_variant,,ENST00000395461,NM_001014989.1;LAT,upstream_gene_variant,,ENST00000454369,NM_001014988.1;LAT,upstream_gene_variant,,ENST00000564277,;SPNS1,downstream_gene_variant,,ENST00000567771,;LAT,upstream_gene_variant,,ENST00000566177,;SPNS1,downstream_gene_variant,,ENST00000568388,;LAT,upstream_gene_variant,,ENST00000570232,;LAT,upstream_gene_variant,,ENST00000630764,;RP11-264B17.3,upstream_gene_variant,,ENST00000354453,;LAT,upstream_gene_variant,,ENST00000563964,;SPNS1,downstream_gene_variant,,ENST00000561868,;RP11-264B17.3,non_coding_transcript_exon_variant,,ENST00000569969,;LAT,upstream_gene_variant,,ENST00000564447,;SPNS1,downstream_gene_variant,,ENST00000568900,;LAT,upstream_gene_variant,,ENST00000566270,;LAT,upstream_gene_variant,,ENST00000562701,;LAT,upstream_gene_variant,,ENST00000568899,;LAT,upstream_gene_variant,,ENST00000562472,;LAT,upstream_gene_variant,,ENST00000568440,; T ENST00000311008 Transcript missense_variant 1851/2208 1474/1587 492/528 A/S Gca/Tca 1 1 SPNS1 HGNC HGNC:30621 protein_coding YES CCDS10646.1 ENSP00000309945 Q9H2V7 UPI000004DB99 NM_001142448.1,NM_032038.2 deleterious(0) 11/12 hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF13 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 28983939 28983939 G T 1 0 0 0 0 1 0 0 0 15427 1203 42 2 2 SPNS1 16 28983939 Missense_Mutation SNP G 11LU016_T 1535064 28983939 61354406 438 490 ITGAX 0 . GRCh38 16 31363038 31363038 + Missense_Mutation SNP G G T rs151306268 11LU016_T 11LU016_N G G c.1463G>T p.Arg488Leu p.R488L ENST00000562522 13/31 101 84 17 136 136 0 strelka-varscan-mutect ITGAX,missense_variant,p.Arg488Leu,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Arg488Leu,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,; T ENST00000562522 Transcript missense_variant 1496/3990 1463/3510 488/1169 R/L cGa/cTa rs151306268 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.03) 13/31 Gene3D:3nigC00,Pfam_domain:PF01839,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS rs151306268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 31363038 31363038 G T 1 0 0 0 0 1 0 0 0 7796 1058 37 1 1 ITGAX 16 31363038 Missense_Mutation SNP G 11LU016_T 2379099 31363038 58975307 439 491 ITGAX 0 . GRCh38 16 31371678 31371678 + Missense_Mutation SNP G G T rs146647978 11LU016_T 11LU016_N G G c.2054G>T p.Arg685Leu p.R685L ENST00000562522 17/31 253 231 22 248 248 0 strelka-mutect ITGAX,missense_variant,p.Arg685Leu,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Arg685Leu,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,non_coding_transcript_exon_variant,,ENST00000562138,; T ENST00000562522 Transcript missense_variant 2087/3990 2054/3510 685/1169 R/L cGc/cTc rs146647978,COSM403529,COSM703158 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.03) 17/31 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69179 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs146647978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 31371678 31371678 G T 1 0 0 0 0 1 0 0 0 7796 1087 38 1 1 ITGAX 16 31371678 Missense_Mutation SNP G 11LU016_T 8640 31371678 58966667 440 492 MYLK3 0 . GRCh38 16 46709662 46709662 + Missense_Mutation SNP C C A rs756620434 11LU016_T 11LU016_N C C c.2277G>T p.Met759Ile p.M759I ENST00000394809 12/13 104 88 16 105 105 0 strelka-varscan-mutect MYLK3,missense_variant,p.Met759Ile,ENST00000394809,NM_182493.2;MYLK3,missense_variant,p.Met418Ile,ENST00000536476,NM_001308301.1;MYLK3,non_coding_transcript_exon_variant,,ENST00000562104,;MYLK3,non_coding_transcript_exon_variant,,ENST00000565182,; A ENST00000394809 Transcript missense_variant 2393/6911 2277/2460 759/819 M/I atG/atT rs756620434 1 -1 MYLK3 HGNC HGNC:29826 protein_coding YES CCDS10723.2 ENSP00000378288 Q32MK0 UPI000059D380 NM_182493.2 tolerated(0.15) 12/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF45,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs756620434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 46709662 46709662 C A 1 0 0 0 0 1 0 0 0 10058 826 29 2 2 MYLK3 16 46709662 Missense_Mutation SNP C 11LU016_T 15337984 46709662 43628683 441 493 MYLK3 0 . GRCh38 16 46729119 46729119 + Missense_Mutation SNP G G T rs150532170 11LU016_T 11LU016_N G G c.1677C>A p.Asn559Lys p.N559K ENST00000394809 7/13 180 151 29 227 226 1 strelka-varscan-mutect MYLK3,missense_variant,p.Asn559Lys,ENST00000394809,NM_182493.2;MYLK3,missense_variant,p.Asn218Lys,ENST00000536476,NM_001308301.1;MYLK3,non_coding_transcript_exon_variant,,ENST00000564731,;MYLK3,non_coding_transcript_exon_variant,,ENST00000569844,; T ENST00000394809 Transcript missense_variant 1793/6911 1677/2460 559/819 N/K aaC/aaA rs150532170 1 -1 MYLK3 HGNC HGNC:29826 protein_coding YES CCDS10723.2 ENSP00000378288 Q32MK0 UPI000059D380 NM_182493.2 deleterious(0) 7/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF45,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs150532170 . 0 208 0 0 2 0 0 0 -15.43348 0.9972718 1 1 1 0 T 3 4 2 46729119 46729119 G T 1 0 0 0 0 1 0 0 0 10058 1136 40 1 1 MYLK3 16 46729119 Missense_Mutation SNP G 11LU016_T 19457 46729119 43609226 442 494 C16orf87 0 . GRCh38 16 46824413 46824413 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.136C>T p.His46Tyr p.H46Y ENST00000285697 2/4 197 184 13 184 184 0 strelka-mutect C16orf87,missense_variant,p.His46Tyr,ENST00000394806,;C16orf87,missense_variant,p.His46Tyr,ENST00000285697,NM_001001436.2;C16orf87,missense_variant,p.His51Tyr,ENST00000565112,;C16orf87,non_coding_transcript_exon_variant,,ENST00000564250,; A ENST00000285697 Transcript missense_variant 398/1585 136/465 46/154 H/Y Cac/Tac 1 -1 C16orf87 HGNC HGNC:33754 protein_coding YES CCDS10724.1 ENSP00000285697 Q6PH81 UPI00001610B9 NM_001001436.2 tolerated(1) 2/4 hmmpanther:PTHR31101,hmmpanther:PTHR31101:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 46824413 46824413 G A 1 0 0 0 0 1 0 0 0 1869 1377 48 3 3 C16orf87 16 46824413 Missense_Mutation SNP G 11LU016_T 95294 46824413 43513932 443 495 ZNF423 0 . GRCh38 16 49638184 49638184 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.968A>G p.His323Arg p.H323R ENST00000561648 5/9 548 462 86 598 597 1 strelka-varscan-mutect ZNF423,missense_variant,p.His323Arg,ENST00000561648,;ZNF423,missense_variant,p.His263Arg,ENST00000563137,;ZNF423,missense_variant,p.His323Arg,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.His263Arg,ENST00000562871,;ZNF423,missense_variant,p.His206Arg,ENST00000535559,;ZNF423,missense_variant,p.His263Arg,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.His206Arg,ENST00000567169,; C ENST00000561648 Transcript missense_variant 1269/7907 968/3855 323/1284 H/R cAc/cGc 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC tolerated(0.1) 5/9 PROSITE_profiles:PS50157,SMART_domains:SM00355 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 49638184 49638184 T C 1 0 0 0 0 1 0 0 0 18470 1696 59 5 5 ZNF423 16 49638184 Missense_Mutation SNP T 11LU016_T 2813771 49638184 40700161 444 496 SNX20 0 . GRCh38 16 50677494 50677494 + Silent SNP G G C novel 11LU016_T 11LU016_N G G c.33C>G p.= p.G11G ENST00000330943 2/4 92 82 10 92 92 0 strelka-varscan-mutect SNX20,synonymous_variant,p.=,ENST00000300590,NM_153337.2;SNX20,synonymous_variant,p.=,ENST00000330943,NM_182854.2;SNX20,synonymous_variant,p.=,ENST00000423026,NM_001144972.1;SNX20,synonymous_variant,p.=,ENST00000610485,;SNX20,synonymous_variant,p.=,ENST00000568993,; C ENST00000330943 Transcript synonymous_variant 205/2904 33/951 11/316 G ggC/ggG 1 -1 SNX20 HGNC HGNC:30390 protein_coding YES CCDS10745.1 ENSP00000332062 Q7Z614 UPI000004348D NM_182854.2 2/4 hmmpanther:PTHR20939,hmmpanther:PTHR20939:SF1 LOW 1 SNV 1 1 PASS rs1177462840 . 0 206 4 0 0 0 0 0 -19.95557 1 1 1 1 0 C 2 2 2 50677494 50677494 G C 1 0 0 0 0 0 0 0 1 15213 958 34 4 4 SNX20 16 50677494 Silent SNP G 11LU016_T 1039310 50677494 39660851 445 497 RBL2 0 . GRCh38 16 53479159 53479168 + Frame_Shift_Del DEL AAAAGAAGAT AAAAGAAGAT - novel 11LU016_T 11LU016_N AAAAGAAGAT AAAAGAAGAT c.2711_2720delAAGAAGATAA p.Lys904SerfsTer25 p.K904Sfs*25 ENST00000262133 18/22 210 168 42 198 198 0 sindel-pindel RBL2,frameshift_variant,p.Lys904SerfsTer25,ENST00000262133,NM_001323611.1,NM_005611.3;RBL2,non_coding_transcript_exon_variant,,ENST00000379935,;RP11-44F14.7,non_coding_transcript_exon_variant,,ENST00000624289,;RBL2,upstream_gene_variant,,ENST00000564605,; - ENST00000262133 Transcript frameshift_variant 2846-2855/4906 2709-2718/3420 903-906/1139 TKED/X acAAAAGAAGAT/ac 1 1 RBL2 HGNC HGNC:9894 protein_coding YES CCDS10748.1 ENSP00000262133 Q08999 UPI000013D264 NM_001323611.1,NM_005611.3 18/22 hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF8,Gene3D:1.10.472.10,Pfam_domain:PF01857,SMART_domains:SM00385,Superfamily_domains:SSF47954 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 53479159 53479159 AAAAGAAGAT - 1 0 1 0 1 0 0 0 0 13276 144 5 0 0 RBL2 16 53479159 Frame_Shift_Del DEL AAAAGAAGAT 11LU016_T 2801665 53479159 36859186 446 498 IRX3 0 . GRCh38 16 54285099 54285099 + Missense_Mutation SNP C C A rs750442189 11LU016_T 11LU016_N C C c.782G>T p.Gly261Val p.G261V ENST00000329734 2/4 173 151 22 186 186 0 strelka-varscan-mutect IRX3,missense_variant,p.Gly261Val,ENST00000329734,NM_024336.2;IRX3,intron_variant,,ENST00000558054,;RP11-434E6.5,upstream_gene_variant,,ENST00000637770,;IRX3,non_coding_transcript_exon_variant,,ENST00000558180,; A ENST00000329734 Transcript missense_variant 1495/2601 782/1506 261/501 G/V gGc/gTc rs750442189 1 -1 IRX3 HGNC HGNC:14360 protein_coding YES CCDS10750.1 ENSP00000331608 P78415 UPI000019745F NM_024336.2 tolerated(0.11) 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11211:SF14,hmmpanther:PTHR11211 MODERATE 1 SNV 1 1 PASS rs750442189 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 54285099 54285099 C A 1 0 0 0 0 1 0 0 0 7753 739 26 2 2 IRX3 16 54285099 Missense_Mutation SNP C 11LU016_T 805940 54285099 36053246 447 499 LRRC36 0 . GRCh38 16 67378667 67378667 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1885G>A p.Gly629Ser p.G629S ENST00000329956 12/14 155 134 21 163 163 0 strelka-varscan-mutect LRRC36,missense_variant,p.Gly629Ser,ENST00000329956,NM_018296.5;LRRC36,missense_variant,p.Gly508Ser,ENST00000563189,NM_001161575.1;LRRC36,missense_variant,p.Gly404Ser,ENST00000435835,;LRRC36,3_prime_UTR_variant,,ENST00000567723,;LRRC36,3_prime_UTR_variant,,ENST00000565019,;LRRC36,3_prime_UTR_variant,,ENST00000568010,;LRRC36,3_prime_UTR_variant,,ENST00000567823,; A ENST00000329956 Transcript missense_variant 1904/2395 1885/2265 629/754 G/S Ggt/Agt 1 1 LRRC36 HGNC HGNC:25615 protein_coding YES CCDS32467.1 ENSP00000329943 Q1X8D7 UPI0000409634 NM_018296.5 tolerated(0.26) 12/14 hmmpanther:PTHR23311:SF6,hmmpanther:PTHR23311 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 2 67378667 67378667 G A 1 0 0 0 0 1 0 0 0 8884 1000 35 3 3 LRRC36 16 67378667 Missense_Mutation SNP G 11LU016_T 13093568 67378667 22959678 448 500 HSD11B2 0 . GRCh38 16 67436624 67436624 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.839A>T p.Lys280Met p.K280M ENST00000326152 5/5 428 401 27 331 331 0 strelka-varscan-mutect HSD11B2,missense_variant,p.Lys280Met,ENST00000326152,NM_000196.3;ATP6V0D1,downstream_gene_variant,,ENST00000290949,NM_004691.4;ATP6V0D1,downstream_gene_variant,,ENST00000602876,;ATP6V0D1,downstream_gene_variant,,ENST00000540149,;ATP6V0D1,downstream_gene_variant,,ENST00000565835,;ATP6V0D1,downstream_gene_variant,,ENST00000564615,;ATP6V0D1,downstream_gene_variant,,ENST00000567694,;HSD11B2,downstream_gene_variant,,ENST00000567684,;ATP6V0D1,downstream_gene_variant,,ENST00000568620,;ATP6V0D1,downstream_gene_variant,,ENST00000563305,;ATP6V0D1,downstream_gene_variant,,ENST00000426604,;ATP6V0D1,downstream_gene_variant,,ENST00000563064,;ATP6V0D1,downstream_gene_variant,,ENST00000564191,;ATP6V0D1,downstream_gene_variant,,ENST00000566322,;ATP6V0D1,downstream_gene_variant,,ENST00000561852,;HSD11B2,downstream_gene_variant,,ENST00000566606,;ATP6V0D1,downstream_gene_variant,,ENST00000567170,;ATP6V0D1,downstream_gene_variant,,ENST00000564788,;HSD11B2,downstream_gene_variant,,ENST00000569303,; T ENST00000326152 Transcript missense_variant 971/1900 839/1218 280/405 K/M aAg/aTg 1 1 HSD11B2 HGNC HGNC:5209 protein_coding YES CCDS10837.1 ENSP00000316786 P80365 UPI000014185A NM_000196.3 deleterious(0.04) 5/5 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 67436624 67436624 A T 1 0 0 0 0 1 0 0 0 7272 72 3 4 4 HSD11B2 16 67436624 Missense_Mutation SNP A 11LU016_T 57957 67436624 22901721 449 501 GFOD2 0 . GRCh38 16 67675915 67675915 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.398T>A p.Met133Lys p.M133K ENST00000268797 3/3 312 243 69 312 312 0 strelka-varscan-mutect GFOD2,missense_variant,p.Met133Lys,ENST00000268797,NM_030819.3;GFOD2,3_prime_UTR_variant,,ENST00000602377,;GFOD2,3_prime_UTR_variant,,ENST00000602627,;GFOD2,downstream_gene_variant,,ENST00000602279,NM_001243650.1;GFOD2,non_coding_transcript_exon_variant,,ENST00000602522,;GFOD2,downstream_gene_variant,,ENST00000602496,; T ENST00000268797 Transcript missense_variant 744/2126 398/1158 133/385 M/K aTg/aAg 1 -1 GFOD2 HGNC HGNC:28159 protein_coding YES CCDS10845.1 ENSP00000268797 Q3B7J2 UPI000013D7DD NM_030819.3 deleterious(0) 3/3 Gene3D:3.40.50.720,hmmpanther:PTHR22604,hmmpanther:PTHR22604:SF90,Superfamily_domains:SSF51735,Superfamily_domains:SSF55347 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 67675915 67675915 A T 1 0 0 0 0 1 0 0 0 6218 217 8 4 4 GFOD2 16 67675915 Missense_Mutation SNP A 11LU016_T 239291 67675915 22662430 450 502 DPEP3 0 . GRCh38 16 67980419 67980419 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.37C>A p.Leu13Met p.L13M ENST00000268793 1/10 21 17 4 38 38 0 strelka-varscan-mutect DPEP3,missense_variant,p.Leu13Met,ENST00000268793,NM_022357.3,NM_001129758.1;DPEP3,non_coding_transcript_exon_variant,,ENST00000574342,; T ENST00000268793 Transcript missense_variant 411/2018 37/1542 13/513 L/M Ctg/Atg 1 -1 DPEP3 HGNC HGNC:23029 protein_coding YES CCDS10856.1 ENSP00000268793 Q9H4B8 UPI000006F093 NM_022357.3,NM_001129758.1 tolerated_low_confidence(0.15) 1/10 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -12.12971 1 1 1 1 0 T 3 4 2 67980419 67980419 G T 1 0 0 0 0 1 0 0 0 4529 991 35 2 2 DPEP3 16 67980419 Missense_Mutation SNP G 11LU016_T 304504 67980419 22357926 451 503 SF3B3 0 . GRCh38 16 70568382 70568382 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.3052G>A p.Glu1018Lys p.E1018K ENST00000302516 22/26 399 329 70 287 285 2 strelka-varscan-mutect SF3B3,missense_variant,p.Glu1018Lys,ENST00000302516,NM_012426.4;SF3B3,downstream_gene_variant,,ENST00000563739,;SF3B3,upstream_gene_variant,,ENST00000565990,;SF3B3,downstream_gene_variant,,ENST00000562722,;SF3B3,downstream_gene_variant,,ENST00000568539,; A ENST00000302516 Transcript missense_variant 3263/9720 3052/3654 1018/1217 E/K Gaa/Aaa 1 1 SF3B3 HGNC HGNC:10770 protein_coding YES CCDS10894.1 ENSP00000305790 Q15393 UPI0000167878 NM_012426.4 deleterious(0.01) 22/26 hmmpanther:PTHR10644:SF1,hmmpanther:PTHR10644,Pfam_domain:PF03178,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 70568382 70568382 G A 1 0 0 0 0 1 0 0 0 14430 1291 45 3 3 SF3B3 16 70568382 Missense_Mutation SNP G 11LU016_T 2587963 70568382 19769963 452 504 DHX38 0 . GRCh38 16 72096184 72096184 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.27G>T p.= p.S9S ENST00000268482 2/27 91 72 19 81 81 0 strelka-varscan-mutect DHX38,synonymous_variant,p.=,ENST00000268482,NM_014003.3;DHX38,synonymous_variant,p.=,ENST00000566794,;DHX38,synonymous_variant,p.=,ENST00000566489,;TXNL4B,upstream_gene_variant,,ENST00000268483,NM_017853.2;TXNL4B,upstream_gene_variant,,ENST00000423037,NM_001142317.1;TXNL4B,upstream_gene_variant,,ENST00000426362,NM_001142318.1;TXNL4B,upstream_gene_variant,,ENST00000562153,;TXNL4B,upstream_gene_variant,,ENST00000569767,;DHX38,synonymous_variant,p.=,ENST00000579387,;DHX38,upstream_gene_variant,,ENST00000563650,;DHX38,upstream_gene_variant,,ENST00000564307,;TXNL4B,upstream_gene_variant,,ENST00000565171,;DHX38,upstream_gene_variant,,ENST00000566329,; T ENST00000268482 Transcript synonymous_variant 536/4608 27/3684 9/1227 S tcG/tcT 1 1 DHX38 HGNC HGNC:17211 protein_coding YES CCDS10907.1 ENSP00000268482 Q92620 UPI000002FBFE NM_014003.3 2/27 LOW 1 SNV 1 1 PASS rs985771779 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 72096184 72096184 G T 1 0 0 0 0 0 0 0 1 4315 1045 37 1 1 DHX38 16 72096184 Silent SNP G 11LU016_T 1527802 72096184 18242161 453 505 CNTNAP4 0 . GRCh38 16 76498673 76498673 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.2344C>T p.Pro782Ser p.P782S ENST00000611870 15/24 100 81 19 91 91 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Pro782Ser,ENST00000307431,;CNTNAP4,missense_variant,p.Pro782Ser,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Pro734Ser,ENST00000377504,;CNTNAP4,missense_variant,p.Pro785Ser,ENST00000476707,;CNTNAP4,missense_variant,p.Pro734Ser,ENST00000622250,;CNTNAP4,missense_variant,p.Pro709Ser,ENST00000478060,NM_138994.3;CNTNAP4,downstream_gene_variant,,ENST00000471618,; T ENST00000611870 Transcript missense_variant 2729/4867 2344/3927 782/1308 P/S Cct/Tct 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 tolerated(0.05) 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 MODERATE 1 SNV 1 1 PASS rs1273799729 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 76498673 76498673 C T 1 0 0 0 0 1 0 0 0 3431 739 26 3 3 CNTNAP4 16 76498673 Missense_Mutation SNP C 11LU016_T 4402489 76498673 13839672 454 506 SDR42E1 0 . GRCh38 16 81999281 81999281 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.1012G>C p.Ala338Pro p.A338P ENST00000328945 3/3 363 291 72 376 376 0 strelka-varscan-mutect SDR42E1,missense_variant,p.Ala338Pro,ENST00000328945,NM_145168.2;SDR42E1,downstream_gene_variant,,ENST00000532128,;SDR42E1,downstream_gene_variant,,ENST00000534209,; G ENST00000328945 Transcript missense_variant 1140/11566 1012/1182 338/393 A/P Gct/Cct 1 -1 SDR42E1 HGNC HGNC:29834 protein_coding YES CCDS42205.1 ENSP00000332407 Q8WUS8 UPI000003F552 NM_145168.2 tolerated(1) 3/3 hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF317,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 81999281 81999281 C G 1 0 0 0 0 1 0 0 0 14248 739 26 4 4 SDR42E1 16 81999281 Missense_Mutation SNP C 11LU016_T 5500608 81999281 8339064 455 507 IRF8 0 . GRCh38 16 85918702 85918702 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.887G>T p.Arg296Leu p.R296L ENST00000268638 7/9 258 224 34 309 308 1 strelka-varscan-mutect IRF8,missense_variant,p.Arg296Leu,ENST00000268638,NM_002163.2;IRF8,missense_variant,p.Arg296Leu,ENST00000564803,;IRF8,missense_variant,p.Arg92Leu,ENST00000562492,;IRF8,missense_variant,p.Arg92Leu,ENST00000569607,;IRF8,intron_variant,,ENST00000566369,;IRF8,downstream_gene_variant,,ENST00000569145,;MIR6774,downstream_gene_variant,,ENST00000614651,; T ENST00000268638 Transcript missense_variant 1309/3030 887/1281 296/426 R/L cGc/cTc 1 1 IRF8 HGNC HGNC:5358 protein_coding YES CCDS10956.1 ENSP00000268638 Q02556 UPI000012D188 NM_002163.2 deleterious(0) 7/9 hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF7,Gene3D:2.60.200.10,Pfam_domain:PF10401,SMART_domains:SM01243,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS rs1408985036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 85918702 85918702 G T 1 0 0 0 0 1 0 0 0 7743 1087 38 1 1 IRF8 16 85918702 Missense_Mutation SNP G 11LU016_T 3919421 85918702 4419643 456 508 FOXL1 0 . GRCh38 16 86579247 86579247 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.524G>T p.Gly175Val p.G175V ENST00000320241 1/1 51 40 11 103 103 0 strelka-varscan-mutect FOXL1,missense_variant,p.Gly175Val,ENST00000320241,NM_005250.2;FOXL1,downstream_gene_variant,,ENST00000593625,; T ENST00000320241 Transcript missense_variant 742/3655 524/1038 175/345 G/V gGg/gTg 1 1 FOXL1 HGNC HGNC:3817 protein_coding YES CCDS10959.1 ENSP00000326272 Q12952 UPI000012ADE2 NM_005250.2 tolerated(0.25) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF204 MODERATE 1 SNV 1 PASS rs1045302700 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 86579247 86579247 G T 1 0 0 0 0 1 0 0 0 5879 1232 43 2 2 FOXL1 16 86579247 Missense_Mutation SNP G 11LU016_T 660545 86579247 3759098 457 509 JPH3 0 . GRCh38 16 87690096 87690096 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1736C>A p.Pro579His p.P579H ENST00000284262 4/5 209 190 19 255 255 0 strelka-varscan-mutect JPH3,missense_variant,p.Pro579His,ENST00000284262,NM_020655.3;RP11-278A23.1,downstream_gene_variant,,ENST00000538868,;JPH3,non_coding_transcript_exon_variant,,ENST00000563609,;JPH3,non_coding_transcript_exon_variant,,ENST00000537256,; A ENST00000284262 Transcript missense_variant 1978/3985 1736/2247 579/748 P/H cCc/cAc 1 1 JPH3 HGNC HGNC:14203 protein_coding YES CCDS10962.1 ENSP00000284262 Q8WXH2 UPI000012DAC4 NM_020655.3 tolerated(0.36) 4/5 PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF7 MODERATE 1 SNV 1 1 PASS rs1466880630 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 87690096 87690096 C A 1 0 0 0 0 1 0 0 0 7874 623 22 2 2 JPH3 16 87690096 Missense_Mutation SNP C 11LU016_T 1110849 87690096 2648249 458 510 CBFA2T3 0 . GRCh38 16 88885223 88885223 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.940C>A p.Leu314Ile p.L314I ENST00000268679 7/12 53 48 5 49 49 0 strelka-varscan-mutect CBFA2T3,missense_variant,p.Leu314Ile,ENST00000268679,NM_005187.5;CBFA2T3,missense_variant,p.Leu228Ile,ENST00000327483,NM_175931.2;CBFA2T3,missense_variant,p.Leu253Ile,ENST00000569464,;RP11-830F9.5,intron_variant,,ENST00000565053,;RP11-830F9.5,downstream_gene_variant,,ENST00000569249,;RP11-830F9.5,downstream_gene_variant,,ENST00000562574,;RP11-830F9.5,downstream_gene_variant,,ENST00000562405,;CBFA2T3,upstream_gene_variant,,ENST00000563856,;CBFA2T3,upstream_gene_variant,,ENST00000566868,; T ENST00000268679 Transcript missense_variant 1337/4477 940/1962 314/653 L/I Ctc/Atc 1 -1 CBFA2T3 HGNC HGNC:1537 protein_coding YES CCDS10972.1 ENSP00000268679 O75081 UPI0000167F93 NM_005187.5 tolerated(0.37) 7/12 hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.62698 1 1 1 1 0 T 3 4 2 88885223 88885223 G T 1 0 0 0 0 1 0 0 0 2399 1000 35 2 2 CBFA2T3 16 88885223 Missense_Mutation SNP G 11LU016_T 1195127 88885223 1453122 459 511 PRDM7 0 . GRCh38 16 90060529 90060529 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1045C>A p.Pro349Thr p.P349T ENST00000449207 9/10 616 561 55 655 654 1 varscan-mutect PRDM7,missense_variant,p.Pro349Thr,ENST00000449207,NM_001098173.1;PRDM7,intron_variant,,ENST00000325921,;PRDM7,downstream_gene_variant,,ENST00000564210,;PRDM7,downstream_gene_variant,,ENST00000568473,; T ENST00000449207 Transcript missense_variant 1065/2008 1045/1479 349/492 P/T Cca/Aca 1 -1 PRDM7 HGNC HGNC:9351 protein_coding YES CCDS45557.1 ENSP00000396732 Q9NQW5 UPI00015294E9 NM_001098173.1 tolerated(0.07) 9/10 PROSITE_profiles:PS50280,hmmpanther:PTHR16515:SF10,hmmpanther:PTHR16515,Gene3D:2.170.270.10 MODERATE 1 SNV 1 1 PASS rs1173180580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 90060529 90060529 G T 1 0 0 0 0 1 0 0 0 12593 1203 42 2 2 PRDM7 16 90060529 Missense_Mutation SNP G 11LU016_T 1175306 90060529 277816 460 512 ABR 0 . GRCh38 17 1007171 1007171 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.2484G>T p.Met828Ile p.M828I ENST00000302538 22/23 76 64 12 88 88 0 strelka-varscan-mutect ABR,missense_variant,p.Met782Ile,ENST00000544583,NM_001159746.2;ABR,missense_variant,p.Met828Ile,ENST00000302538,NM_001322840.1,NM_021962.4;ABR,missense_variant,p.Met840Ile,ENST00000574437,;ABR,missense_variant,p.Met791Ile,ENST00000291107,NM_001092.4;ABR,missense_variant,p.Met610Ile,ENST00000536794,NM_001282149.1;ABR,missense_variant,p.Met279Ile,ENST00000543210,NM_001256847.2;ABR,missense_variant,p.Met153Ile,ENST00000571797,;ABR,intron_variant,,ENST00000572441,;TIMM22,downstream_gene_variant,,ENST00000327158,NM_013337.2;ABR,non_coding_transcript_exon_variant,,ENST00000573559,;ABR,downstream_gene_variant,,ENST00000577052,;ABR,downstream_gene_variant,,ENST00000571383,;ABR,downstream_gene_variant,,ENST00000571022,;ABR,non_coding_transcript_exon_variant,,ENST00000572585,;ABR,downstream_gene_variant,,ENST00000572152,;ABR,downstream_gene_variant,,ENST00000570688,;ABR,downstream_gene_variant,,ENST00000572650,;ABR,downstream_gene_variant,,ENST00000571120,; A ENST00000302538 Transcript missense_variant 2631/5289 2484/2580 828/859 M/I atG/atT 1 -1 ABR HGNC HGNC:81 protein_coding YES CCDS10999.1 ENSP00000303909 Q12979 UPI00001AED3D NM_001322840.1,NM_021962.4 deleterious(0.03) 22/23 PROSITE_profiles:PS50238,hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF5,SMART_domains:SM00324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 1007171 1007171 C A 1 0 0 0 0 1 0 0 0 108 594 21 2 2 ABR 17 1007171 Missense_Mutation SNP C 11LU016_T 1007171 82250270 461 513 TP53 0 . GRCh38 17 7674202 7674202 + Missense_Mutation SNP A A G 11LU016_T 11LU016_N A A c.761T>C p.Ile254Thr p.I254T ENST00000269305 7/11 262 201 61 256 255 1 strelka-varscan-mutect TP53,missense_variant,p.Ile254Thr,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Ile254Thr,ENST00000420246,;TP53,missense_variant,p.Ile215Thr,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Ile215Thr,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Ile254Thr,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Ile215Thr,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Ile254Thr,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Ile215Thr,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Ile254Thr,ENST00000445888,;TP53,missense_variant,p.Ile215Thr,ENST00000619485,;TP53,missense_variant,p.Ile122Thr,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Ile95Thr,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Ile122Thr,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Ile95Thr,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Ile122Thr,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Ile95Thr,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Ile254Thr,ENST00000359597,;TP53,missense_variant,p.Ile243Thr,ENST00000615910,;TP53,missense_variant,p.Ile254Thr,ENST00000413465,;TP53,missense_variant,p.Ile122Thr,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Ile215Thr,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 951/2579 761/1182 254/393 I/T aTc/aCc TP53_g.13398T>A,TP53_g.13398T>C,TP53_g.13398T>G,COSM1230106,COSM1230107,COSM1725383,COSM1725384,COSM1725385,COSM2744574,COSM3403259,COSM44058,COSM4423302,COSM4423303,COSM4423304,COSM4423305,COSM44535,COSM45035 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1330865474 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 7674202 7674202 A G 1 0 0 0 0 1 0 0 0 16859 333 12 5 5 TP53 17 7674202 Missense_Mutation SNP A 11LU016_T 6667031 7674202 75583239 462 514 MFSD6L 0 . GRCh38 17 8797618 8797618 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.1503delG p.Ser502ValfsTer14 p.S502Vfs*14 ENST00000329805 1/1 149 93 56 171 171 0 sindel-varindel MFSD6L,frameshift_variant,p.Ser502ValfsTer14,ENST00000329805,NM_152599.3; - ENST00000329805 Transcript frameshift_variant 1732/2188 1503/1761 501/586 G/X ggG/gg 1 -1 MFSD6L HGNC HGNC:26656 protein_coding YES CCDS11146.1 ENSP00000330051 Q8IWD5 UPI0000141B5F NM_152599.3 1/1 hmmpanther:PTHR16172:SF22,hmmpanther:PTHR16172,Pfam_domain:PF12832,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 HIGH 1 deletion 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 8797618 8797618 C - 1 0 1 0 1 0 0 0 0 9494 842 30 0 0 MFSD6L 17 8797618 Frame_Shift_Del DEL C 11LU016_T 1123416 8797618 74459823 463 515 MYH1 0 . GRCh38 17 10500646 10500646 + Missense_Mutation SNP G G A rs746118240 11LU016_T 11LU016_N G G c.3845C>T p.Ala1282Val p.A1282V ENST00000226207 28/40 167 126 41 198 198 0 strelka-varscan-mutect MYH1,missense_variant,p.Ala1282Val,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 3940/6024 3845/5820 1282/1939 A/V gCg/gTg rs746118240,COSM5525271 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 28/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 0,1 MODERATE SNV 5 0,1 1 PASS rs746118240 . 0 208 0 0 2 0 0 0 -20 0.9987339 1 1 1 0 A 3 1 2 10500646 10500646 G A 1 0 0 0 0 1 0 0 0 10029 1087 38 1 1 MYH1 17 10500646 Missense_Mutation SNP G 11LU016_T 1703028 10500646 72756795 464 516 TMEM199 0 . GRCh38 17 28359351 28359351 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.322A>G p.Ile108Val p.I108V ENST00000292114 3/6 225 178 47 201 201 0 strelka-varscan-mutect TMEM199,missense_variant,p.Ile108Val,ENST00000292114,NM_152464.2;TMEM199,5_prime_UTR_variant,,ENST00000395404,;POLDIP2,upstream_gene_variant,,ENST00000540200,NM_015584.4;POLDIP2,upstream_gene_variant,,ENST00000618887,NM_001290145.1;CTB-96E2.2,downstream_gene_variant,,ENST00000555059,;SEBOX,downstream_gene_variant,,ENST00000536498,NM_001080837.3;TMEM199,upstream_gene_variant,,ENST00000585070,;CTB-96E2.7,downstream_gene_variant,,ENST00000577850,;CTB-96E2.3,non_coding_transcript_exon_variant,,ENST00000591482,;TMEM199,non_coding_transcript_exon_variant,,ENST00000581386,;TMEM199,downstream_gene_variant,,ENST00000579762,;TMEM199,missense_variant,p.Ile108Val,ENST00000555264,;TMEM199,3_prime_UTR_variant,,ENST00000580868,;TMEM199,non_coding_transcript_exon_variant,,ENST00000483505,;TMEM199,non_coding_transcript_exon_variant,,ENST00000509083,;TMEM199,upstream_gene_variant,,ENST00000585027,; G ENST00000292114 Transcript missense_variant 412/3148 322/627 108/208 I/V Ata/Gta 1 1 TMEM199 HGNC HGNC:18085 protein_coding YES CCDS11228.1 ENSP00000292114 Q8N511 UPI0000039EBA NM_152464.2 tolerated(0.44) 3/6 hmmpanther:PTHR31394,hmmpanther:PTHR31394:SF1,Pfam_domain:PF11712 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 28359351 28359351 A G 1 0 0 0 0 1 0 0 0 16560 333 12 5 5 TMEM199 17 28359351 Missense_Mutation SNP A 11LU016_T 17858705 28359351 54898090 465 517 SEZ6 0 . GRCh38 17 28981424 28981424 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.671C>A p.Thr224Asn p.T224N ENST00000317338 2/17 83 59 24 72 72 0 strelka-varscan-mutect SEZ6,missense_variant,p.Thr224Asn,ENST00000317338,NM_178860.4;SEZ6,missense_variant,p.Thr224Asn,ENST00000360295,NM_001098635.1;SEZ6,missense_variant,p.Thr224Asn,ENST00000335960,;SEZ6,missense_variant,p.Thr224Asn,ENST00000442608,;SEZ6,missense_variant,p.Thr150Asn,ENST00000540632,NM_001290202.1;SEZ6,downstream_gene_variant,,ENST00000585644,;PIPOX,intron_variant,,ENST00000583215,;PIPOX,intron_variant,,ENST00000580241,;PIPOX,intron_variant,,ENST00000578748,;PIPOX,intron_variant,,ENST00000577182,;PIPOX,intron_variant,,ENST00000580383,;SEZ6,missense_variant,p.Thr57Asn,ENST00000540419,; T ENST00000317338 Transcript missense_variant 1100/4471 671/2985 224/994 T/N aCc/aAc 1 -1 SEZ6 HGNC HGNC:15955 protein_coding YES CCDS45639.1 ENSP00000312942 Q53EL9 UPI0000049D91 NM_178860.4 deleterious(0.01) 2/17 Low_complexity_(Seg):seg,hmmpanther:PTHR19325:SF92,hmmpanther:PTHR19325 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 28981424 28981424 G T 1 0 0 0 0 1 0 0 0 14421 1261 44 2 2 SEZ6 17 28981424 Missense_Mutation SNP G 11LU016_T 622073 28981424 54276017 466 518 SLC6A4 0 . GRCh38 17 30221876 30221876 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.83A>C p.Gln28Pro p.Q28P ENST00000261707 3/15 464 389 75 453 453 0 strelka-varscan-mutect SLC6A4,missense_variant,p.Gln28Pro,ENST00000261707,NM_001045.5;SLC6A4,missense_variant,p.Gln28Pro,ENST00000401766,;SLC6A4,missense_variant,p.Gln28Pro,ENST00000394821,; G ENST00000261707 Transcript missense_variant 659/6604 83/1893 28/630 Q/P cAg/cCg 1 -1 SLC6A4 HGNC HGNC:11050 protein_coding YES CCDS11256.1 ENSP00000261707 P31645 UPI0000135493 NM_001045.5 tolerated(0.25) 3/15 hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF105,Pfam_domain:PF03491,Prints_domain:PR01203 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 30221876 30221876 T G 1 0 0 0 0 1 0 0 0 14969 1580 55 5 5 SLC6A4 17 30221876 Missense_Mutation SNP T 11LU016_T 1240452 30221876 53035565 467 519 RHBDL3 0 . GRCh38 17 32294366 32294366 + Missense_Mutation SNP A A G rs767315929 11LU016_T 11LU016_N A A c.592A>G p.Lys198Glu p.K198E ENST00000269051 5/9 203 182 21 229 229 0 strelka-varscan-mutect RHBDL3,missense_variant,p.Lys198Glu,ENST00000269051,NM_138328.2;RHBDL3,missense_variant,p.Lys100Glu,ENST00000536287,;RHBDL3,missense_variant,p.Lys190Glu,ENST00000538145,;RHBDL3,missense_variant,p.Lys198Glu,ENST00000431505,;RHBDL3,3_prime_UTR_variant,,ENST00000578006,;RHBDL3,non_coding_transcript_exon_variant,,ENST00000582967,; G ENST00000269051 Transcript missense_variant 606/4661 592/1215 198/404 K/E Aag/Gag rs767315929,COSM5017202 1 1 RHBDL3 HGNC HGNC:16502 protein_coding YES CCDS32613.1 ENSP00000269051 P58872 UPI0000133858 NM_138328.2 tolerated(0.12) 5/9 hmmpanther:PTHR22936,hmmpanther:PTHR22936:SF14,Gene3D:2xovA00,PIRSF_domain:PIRSF037470,Superfamily_domains:SSF144091 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs767315929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 32294366 32294366 A G 1 0 0 0 0 1 0 0 0 13495 247 9 5 5 RHBDL3 17 32294366 Missense_Mutation SNP A 11LU016_T 2072490 32294366 50963075 468 520 SLFN14 0 . GRCh38 17 35549025 35549025 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1953G>T p.= p.G651G ENST00000415846 4/4 191 146 45 133 133 0 strelka-varscan-mutect SLFN14,synonymous_variant,p.=,ENST00000415846,NM_001129820.1;RP11-1094M14.12,upstream_gene_variant,,ENST00000588445,; A ENST00000415846 Transcript synonymous_variant 1989/2889 1953/2739 651/912 G ggG/ggT 1 -1 SLFN14 HGNC HGNC:32689 protein_coding YES CCDS45650.1 ENSP00000391101 P0C7P3 UPI000041A9FB NM_001129820.1 4/4 hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF30,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 35549025 35549025 C A 1 0 0 0 0 0 0 0 1 15026 610 22 2 2 SLFN14 17 35549025 Silent SNP C 11LU016_T 3254659 35549025 47708416 469 521 SLFN14 0 . GRCh38 17 35553355 35553355 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1279C>A p.Leu427Met p.L427M ENST00000415846 3/4 191 148 43 176 176 0 strelka-varscan-mutect SLFN14,missense_variant,p.Leu427Met,ENST00000415846,NM_001129820.1;RP11-1094M14.12,non_coding_transcript_exon_variant,,ENST00000588445,; T ENST00000415846 Transcript missense_variant 1315/2889 1279/2739 427/912 L/M Ctg/Atg 1 -1 SLFN14 HGNC HGNC:32689 protein_coding YES CCDS45650.1 ENSP00000391101 P0C7P3 UPI000041A9FB NM_001129820.1 deleterious(0.02) 3/4 hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF30 MODERATE 1 SNV 1 1 PASS rs1244556317 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 35553355 35553355 G T 1 0 0 0 0 1 0 0 0 15026 991 35 2 2 SLFN14 17 35553355 Missense_Mutation SNP G 11LU016_T 4330 35553355 47704086 470 522 ZPBP2 0 . GRCh38 17 39870727 39870727 + Missense_Mutation SNP C C A rs767043856 11LU016_T 11LU016_N C C c.152C>A p.Pro51Gln p.P51Q ENST00000348931 3/8 97 79 18 104 104 0 strelka-varscan-mutect ZPBP2,missense_variant,p.Pro29Gln,ENST00000377940,NM_198844.2;ZPBP2,missense_variant,p.Pro51Gln,ENST00000348931,NM_199321.2;ZPBP2,missense_variant,p.Pro51Gln,ENST00000584588,;ZPBP2,intron_variant,,ENST00000583811,; A ENST00000348931 Transcript missense_variant 343/1543 152/1017 51/338 P/Q cCa/cAa rs767043856 1 1 ZPBP2 HGNC HGNC:20678 protein_coding YES CCDS11352.1 ENSP00000335384 Q6X784 UPI00001D79E4 NM_199321.2 deleterious(0) 3/8 PROSITE_profiles:PS50835,hmmpanther:PTHR15443:SF4,hmmpanther:PTHR15443 MODERATE 1 SNV 1 1 PASS rs767043856 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 39870727 39870727 C A 1 0 0 0 0 1 0 0 0 18812 594 21 2 2 ZPBP2 17 39870727 Missense_Mutation SNP C 11LU016_T 4317372 39870727 43386714 471 523 MSL1 0 . GRCh38 17 40133593 40133593 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.827A>G p.Tyr276Cys p.Y276C ENST00000579565 8/10 141 122 19 115 115 0 strelka-varscan-mutect MSL1,missense_variant,p.Tyr539Cys,ENST00000398532,;MSL1,missense_variant,p.Tyr523Cys,ENST00000578648,;MSL1,missense_variant,p.Tyr276Cys,ENST00000579565,NM_001012241.1;MSL1,downstream_gene_variant,,ENST00000577454,;MSL1,downstream_gene_variant,,ENST00000582920,;MSL1,non_coding_transcript_exon_variant,,ENST00000339569,;MSL1,non_coding_transcript_exon_variant,,ENST00000580086,;MSL1,non_coding_transcript_exon_variant,,ENST00000583127,;MSL1,downstream_gene_variant,,ENST00000581246,;MSL1,downstream_gene_variant,,ENST00000582884,; G ENST00000579565 Transcript missense_variant 1091/1401 827/1056 276/351 Y/C tAt/tGt 1 1 MSL1 HGNC HGNC:27905 protein_coding YES CCDS45670.1 ENSP00000462945 Q68DK7 UPI0000DBE498 NM_001012241.1 tolerated(0.18) 8/10 Pfam_domain:PF15275,hmmpanther:PTHR21656,SMART_domains:SM01300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 40133593 40133593 A G 1 0 0 0 0 1 0 0 0 9860 449 16 5 5 MSL1 17 40133593 Missense_Mutation SNP A 11LU016_T 262866 40133593 43123848 472 524 KRT12 0 . GRCh38 17 40866633 40866633 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.554A>T p.Asp185Val p.D185V ENST00000251643 1/8 224 189 35 217 217 0 strelka-varscan-mutect KRT12,missense_variant,p.Asp185Val,ENST00000251643,NM_000223.3;RP5-1110E20.1,downstream_gene_variant,,ENST00000579136,; A ENST00000251643 Transcript missense_variant 578/1867 554/1485 185/494 D/V gAc/gTc 1 -1 KRT12 HGNC HGNC:6414 protein_coding YES CCDS11378.1 ENSP00000251643 Q99456 UPI000012DAE4 NM_000223.3 deleterious(0) 1/8 Gene3D:1.20.1270.60,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF115,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 40866633 40866633 T A 1 0 0 0 0 1 0 0 0 8331 1667 58 4 4 KRT12 17 40866633 Missense_Mutation SNP T 11LU016_T 733040 40866633 42390808 473 525 KRTAP9-7 0 . GRCh38 17 41276145 41276145 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.448T>G p.Cys150Gly p.C150G ENST00000391354 1/1 254 200 54 240 240 0 strelka-varscan-mutect KRTAP9-7,missense_variant,p.Cys150Gly,ENST00000391354,NM_001277332.1;KRTAP9-11P,downstream_gene_variant,,ENST00000431013,;KRTAP9-10P,upstream_gene_variant,,ENST00000435672,; G ENST00000391354 Transcript missense_variant 487/1039 448/510 150/169 C/G Tgc/Ggc 1 1 KRTAP9-7 HGNC HGNC:18915 protein_coding YES CCDS59287.1 ENSP00000375149 A8MTY7 UPI0000DD83F7 NM_001277332.1 deleterious(0.01) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF56,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 41276145 41276145 T G 1 0 0 0 0 1 0 0 0 8474 1580 55 5 5 KRTAP9-7 17 41276145 Missense_Mutation SNP T 11LU016_T 409512 41276145 41981296 474 526 KRT17 0 . GRCh38 17 41624459 41624459 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.51C>A p.= p.S17S ENST00000311208 1/8 189 174 15 236 236 0 varscan-mutect KRT17,synonymous_variant,p.=,ENST00000311208,NM_000422.2;KRT17,synonymous_variant,p.=,ENST00000577817,;KRT17,5_prime_UTR_variant,,ENST00000540235,;KRT17,intron_variant,,ENST00000463128,;KRT17,upstream_gene_variant,,ENST00000590038,;KRT42P,downstream_gene_variant,,ENST00000438131,;KRT42P,downstream_gene_variant,,ENST00000398469,;KRT17,non_coding_transcript_exon_variant,,ENST00000491673,;KRT17,upstream_gene_variant,,ENST00000493253,;KRT42P,downstream_gene_variant,,ENST00000587335,;KRT42P,downstream_gene_variant,,ENST00000458343,; T ENST00000311208 Transcript synonymous_variant 119/1524 51/1299 17/432 S tcC/tcA 1 -1 KRT17 HGNC HGNC:6427 protein_coding YES CCDS11402.1 ENSP00000308452 Q04695 UPI0000148FD6 NM_000422.2 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF180,hmmpanther:PTHR23239 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 41624459 41624459 G T 1 0 0 0 0 0 0 0 1 8336 987 35 2 2 KRT17 17 41624459 Silent SNP G 11LU016_T 348314 41624459 41632982 475 527 DHX58 0 . GRCh38 17 42103646 42103646 + Silent SNP C C A rs371461669 11LU016_T 11LU016_N C C c.1716G>T p.= p.V572V ENST00000251642 12/14 221 181 40 453 453 0 strelka-varscan-mutect DHX58,synonymous_variant,p.=,ENST00000251642,NM_024119.2;DHX58,downstream_gene_variant,,ENST00000413196,;DHX58,non_coding_transcript_exon_variant,,ENST00000586522,;DHX58,non_coding_transcript_exon_variant,,ENST00000590637,;DHX58,intron_variant,,ENST00000589979,;DHX58,upstream_gene_variant,,ENST00000592024,; A ENST00000251642 Transcript synonymous_variant 1939/2617 1716/2037 572/678 V gtG/gtT rs371461669 1 -1 DHX58 HGNC HGNC:29517 protein_coding YES CCDS11416.1 ENSP00000251642 Q96C10 A0A024R1Y5 UPI000006ED88 NM_024119.2 12/14 hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF7,Pfam_domain:PF11648 LOW 1 SNV 1 1 PASS rs371461669 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 42103646 42103646 C A 1 0 0 0 0 0 0 0 1 4318 581 21 2 2 DHX58 17 42103646 Silent SNP C 11LU016_T 479187 42103646 41153795 476 528 CCR10 0 . GRCh38 17 42680319 42680319 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.323T>A p.Leu108Gln p.L108Q ENST00000332438 2/2 199 186 13 212 212 0 strelka-varscan-mutect CCR10,missense_variant,p.Leu108Gln,ENST00000332438,NM_016602.2;CCR10,5_prime_UTR_variant,,ENST00000591765,;CCR10,5_prime_UTR_variant,,ENST00000591568,;CNTNAP1,upstream_gene_variant,,ENST00000264638,NM_003632.2;PLEKHH3,upstream_gene_variant,,ENST00000293349,;PLEKHH3,upstream_gene_variant,,ENST00000591022,NM_024927.4;PLEKHH3,upstream_gene_variant,,ENST00000587627,;CTD-3193K9.4,non_coding_transcript_exon_variant,,ENST00000593139,;CTD-3193K9.3,downstream_gene_variant,,ENST00000592440,;PLEKHH3,upstream_gene_variant,,ENST00000456950,;PLEKHH3,upstream_gene_variant,,ENST00000591544,;CNTNAP1,upstream_gene_variant,,ENST00000591662,;PLEKHH3,upstream_gene_variant,,ENST00000591490,;PLEKHH3,upstream_gene_variant,,ENST00000591196,; T ENST00000332438 Transcript missense_variant 343/1773 323/1089 108/362 L/Q cTg/cAg 1 -1 CCR10 HGNC HGNC:4474 protein_coding YES CCDS11435.1 ENSP00000332504 P46092 UPI0000212EE9 NM_016602.2 tolerated(0.06) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF726,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 42680319 42680319 A T 1 0 0 0 0 1 0 0 0 2640 188 7 4 4 CCR10 17 42680319 Missense_Mutation SNP A 11LU016_T 576673 42680319 40577122 477 529 FAM171A2 0 . GRCh38 17 44360018 44360018 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.233A>T p.Glu78Val p.E78V ENST00000293443 2/8 196 155 41 226 226 0 strelka-varscan-mutect FAM171A2,missense_variant,p.Glu78Val,ENST00000293443,NM_198475.2;FAM171A2,missense_variant,p.Glu78Val,ENST00000589407,;FAM171A2,missense_variant,p.Glu78Val,ENST00000588067,;FAM171A2,non_coding_transcript_exon_variant,,ENST00000592560,;RPL7L1P5,downstream_gene_variant,,ENST00000590816,; A ENST00000293443 Transcript missense_variant 394/3160 233/2481 78/826 E/V gAg/gTg 1 -1 FAM171A2 HGNC HGNC:30480 protein_coding YES CCDS45701.1 ENSP00000293443 A8MVW0 UPI0000E59FC0 NM_198475.2 deleterious(0) 2/8 Pfam_domain:PF10577,hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF3 MODERATE 1 SNV 1 1 PASS rs1222637343 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 44360018 44360018 T A 1 0 0 0 0 1 0 0 0 5338 1551 54 4 4 FAM171A2 17 44360018 Missense_Mutation SNP T 11LU016_T 1679699 44360018 38897423 478 530 SPPL2C 0 . GRCh38 17 45846906 45846906 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.2000A>T p.His667Leu p.H667L ENST00000329196 1/1 97 83 14 75 74 1 strelka-varscan-mutect SPPL2C,missense_variant,p.His667Leu,ENST00000329196,NM_175882.2;MAPT-AS1,intron_variant,,ENST00000634876,;MAPT-AS1,intron_variant,,ENST00000579599,;MAPT-AS1,intron_variant,,ENST00000579244,;MAPT-AS1,upstream_gene_variant,,ENST00000581125,; T ENST00000329196 Transcript missense_variant 2072/2238 2000/2055 667/684 H/L cAc/cTc 1 1 SPPL2C HGNC HGNC:28902 protein_coding YES CCDS32673.1 ENSP00000332488 Q8IUH8 UPI0000EE80B4 NM_175882.2 deleterious_low_confidence(0) 1/1 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 45846906 45846906 A T 1 0 0 0 0 1 0 0 0 15443 159 6 4 4 SPPL2C 17 45846906 Missense_Mutation SNP A 11LU016_T 1486888 45846906 37410535 479 531 HOXB13 0 . GRCh38 17 48728296 48728296 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.298T>A p.Cys100Ser p.C100S ENST00000290295 1/2 328 297 31 388 388 0 strelka-varscan-mutect HOXB13,missense_variant,p.Cys100Ser,ENST00000290295,NM_006361.5;PRAC2,downstream_gene_variant,,ENST00000422730,NM_001282275.1;PRAC2,downstream_gene_variant,,ENST00000432056,NM_001282276.1;CTD-2377D24.4,upstream_gene_variant,,ENST00000495536,;MIR3185,upstream_gene_variant,,ENST00000583892,;HOXB13-AS1_1,downstream_gene_variant,,ENST00000613209,;HOXB13-AS1_2,downstream_gene_variant,,ENST00000612962,; T ENST00000290295 Transcript missense_variant 883/3467 298/855 100/284 C/S Tgt/Agt 1 -1 HOXB13 HGNC HGNC:5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 tolerated(0.16) 1/2 hmmpanther:PTHR24326:SF47,hmmpanther:PTHR24326,Pfam_domain:PF12284 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 48728296 48728296 A T 1 0 0 0 0 1 0 0 0 7194 188 7 4 4 HOXB13 17 48728296 Missense_Mutation SNP A 11LU016_T 2881390 48728296 34529145 480 532 KAT7 0 . GRCh38 17 49821652 49821652 + Missense_Mutation SNP C C G rs763725929 11LU016_T 11LU016_N C C c.1248C>G p.Ile416Met p.I416M ENST00000259021 11/15 126 97 29 129 129 0 varscan-mutect KAT7,missense_variant,p.Ile416Met,ENST00000259021,NM_007067.4;KAT7,missense_variant,p.Ile230Met,ENST00000435742,;KAT7,missense_variant,p.Ile386Met,ENST00000424009,NM_001199155.1;KAT7,missense_variant,p.Ile277Met,ENST00000454930,NM_001199156.1;KAT7,missense_variant,p.Ile306Met,ENST00000509773,NM_001199157.1;KAT7,missense_variant,p.Ile247Met,ENST00000510819,NM_001199158.1;KAT7,splice_region_variant,,ENST00000513980,;KAT7,splice_region_variant,,ENST00000512616,;KAT7,splice_region_variant,,ENST00000513171,;KAT7,splice_region_variant,,ENST00000514540,;KAT7,splice_region_variant,,ENST00000508594,;KAT7,upstream_gene_variant,,ENST00000503101,;KAT7,non_coding_transcript_exon_variant,,ENST00000509794,;KAT7,upstream_gene_variant,,ENST00000503635,;KAT7,upstream_gene_variant,,ENST00000510426,;KAT7,upstream_gene_variant,,ENST00000513075,; G ENST00000259021 Transcript missense_variant,splice_region_variant 1528/9644 1248/1836 416/611 I/M atC/atG rs763725929 1 1 KAT7 HGNC HGNC:17016 protein_coding YES CCDS11554.1 ENSP00000259021 O95251 UPI000006D3D5 NM_007067.4 deleterious(0.01) 11/15 PROSITE_profiles:PS51726,hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF111,Pfam_domain:PF01853,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS rs763725929 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 49821652 49821652 C G 1 0 0 0 0 1 0 0 0 7900 927 32 4 4 KAT7 17 49821652 Missense_Mutation SNP C 11LU016_T 1093356 49821652 33435789 481 533 DLX3 0 . GRCh38 17 49993475 49993475 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.441C>A p.= p.R147R ENST00000434704 2/3 265 200 65 218 218 0 strelka-varscan-mutect DLX3,synonymous_variant,p.=,ENST00000434704,NM_005220.2;DLX3,synonymous_variant,p.=,ENST00000512495,;RP11-1094H24.3,upstream_gene_variant,,ENST00000511867,; T ENST00000434704 Transcript synonymous_variant 667/2602 441/864 147/287 R cgC/cgA 1 -1 DLX3 HGNC HGNC:2916 protein_coding YES CCDS11556.1 ENSP00000389870 O60479 UPI00001294B0 NM_005220.2 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF28,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 49993475 49993475 G T 1 0 0 0 0 0 0 0 1 4379 958 34 2 2 DLX3 17 49993475 Silent SNP G 11LU016_T 171823 49993475 33263966 482 534 CA10 0 . GRCh38 17 51747739 51747739 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.359G>T p.Gly120Val p.G120V ENST00000451037 4/9 164 134 30 189 189 0 strelka-varscan-mutect CA10,missense_variant,p.Gly120Val,ENST00000451037,NM_020178.4;CA10,missense_variant,p.Gly120Val,ENST00000442502,NM_001082534.1;CA10,missense_variant,p.Gly120Val,ENST00000285273,NM_001082533.1;CA10,missense_variant,p.Gly45Val,ENST00000570565,;CA10,missense_variant,p.Gly120Val,ENST00000575181,;CA10,missense_variant,p.Gly17Val,ENST00000575097,;CA10,non_coding_transcript_exon_variant,,ENST00000571918,;CA10,3_prime_UTR_variant,,ENST00000571371,; A ENST00000451037 Transcript missense_variant 1300/3189 359/987 120/328 G/V gGg/gTg COSM1630294 1 -1 CA10 HGNC HGNC:1369 protein_coding YES CCDS32684.1 ENSP00000405388 Q9NS85 UPI000000167C NM_020178.4 deleterious(0) 4/9 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 51747739 51747739 C A 1 0 0 0 0 1 0 0 0 2197 623 22 2 2 CA10 17 51747739 Missense_Mutation SNP C 11LU016_T 1754264 51747739 31509702 483 535 HELZ 0 . GRCh38 17 67078296 67078296 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.5785G>T p.Gly1929Trp p.G1929W ENST00000358691 33/33 286 230 56 245 245 0 strelka-varscan-mutect HELZ,missense_variant,p.Gly1929Trp,ENST00000358691,NM_014877.3;HELZ,missense_variant,p.Gly1930Trp,ENST00000580168,;HELZ,3_prime_UTR_variant,,ENST00000579953,; A ENST00000358691 Transcript missense_variant 5952/13810 5785/5829 1929/1942 G/W Ggg/Tgg 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 deleterious_low_confidence(0) 33/33 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 67078296 67078296 C A 1 0 0 0 0 1 0 0 0 6931 681 24 2 2 HELZ 17 67078296 Missense_Mutation SNP C 11LU016_T 15330557 67078296 16179145 484 536 ABCA10 0 . GRCh38 17 69152045 69152045 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.4395A>T p.Glu1465Asp p.E1465D ENST00000269081 37/40 69 50 19 53 53 0 strelka-varscan-mutect ABCA10,missense_variant,p.Glu1465Asp,ENST00000269081,NM_080282.3;ABCA10,upstream_gene_variant,,ENST00000521538,;ABCA10,upstream_gene_variant,,ENST00000522787,;ABCA10,splice_region_variant,,ENST00000519732,;ABCA10,splice_region_variant,,ENST00000522406,;ABCA10,splice_region_variant,,ENST00000518929,;ABCA10,splice_region_variant,,ENST00000523419,;ABCA10,upstream_gene_variant,,ENST00000524231,;ABCA10,upstream_gene_variant,,ENST00000588514,; A ENST00000269081 Transcript missense_variant,splice_region_variant 5305/6362 4395/4632 1465/1543 E/D gaA/gaT 1 -1 ABCA10 HGNC HGNC:30 protein_coding YES CCDS11684.1 ENSP00000269081 Q8WWZ4 UPI000013D7F6 NM_080282.3 tolerated(0.06) 37/40 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF140 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 69152045 69152045 T A 1 0 0 0 0 1 0 0 0 33 1855 64 4 4 ABCA10 17 69152045 Missense_Mutation SNP T 11LU016_T 2073749 69152045 14105396 485 537 SEC14L1 0 . GRCh38 17 77194898 77194898 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.696G>T p.= p.V232V ENST00000392476 9/20 187 145 42 153 152 1 strelka-varscan-mutect SEC14L1,synonymous_variant,p.=,ENST00000436233,NM_001143999.1,NM_003003.3,NM_001143998.1;SEC14L1,synonymous_variant,p.=,ENST00000430767,NM_001204410.1;SEC14L1,synonymous_variant,p.=,ENST00000392476,NM_001204408.1;SEC14L1,synonymous_variant,p.=,ENST00000443798,NM_001039573.2;SEC14L1,synonymous_variant,p.=,ENST00000591437,;SEC14L1,synonymous_variant,p.=,ENST00000585618,;SEC14L1,synonymous_variant,p.=,ENST00000431431,NM_001144001.1;SEC14L1,synonymous_variant,p.=,ENST00000589827,;SEC14L1,synonymous_variant,p.=,ENST00000589202,;SEC14L1,downstream_gene_variant,,ENST00000587820,;SEC14L1,downstream_gene_variant,,ENST00000588616,;SEC14L1,downstream_gene_variant,,ENST00000586429,;SEC14L1,downstream_gene_variant,,ENST00000590483,;SEC14L1,downstream_gene_variant,,ENST00000586390,;SEC14L1,downstream_gene_variant,,ENST00000591786,;CYCSP40,downstream_gene_variant,,ENST00000575927,; T ENST00000392476 Transcript synonymous_variant 1255/2957 696/2160 232/719 V gtG/gtT 1 1 SEC14L1 HGNC HGNC:10698 protein_coding YES CCDS42385.1 ENSP00000376268 Q92503 UPI00006AB82A NM_001204408.1 9/20 Superfamily_domains:SSF46938 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 77194898 77194898 G T 1 0 0 0 0 0 0 0 1 14257 1335 47 2 2 SEC14L1 17 77194898 Silent SNP G 11LU016_T 8042853 77194898 6062543 486 538 NOTUM 0 . GRCh38 17 81957060 81957060 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.710G>T p.Gly237Val p.G237V ENST00000409678 7/11 74 53 21 78 78 0 strelka-varscan-mutect NOTUM,missense_variant,p.Gly237Val,ENST00000409678,NM_178493.5;NOTUM,missense_variant,p.Gly237Val,ENST00000425009,;NOTUM,missense_variant,p.Gly95Val,ENST00000477214,;NOTUM,downstream_gene_variant,,ENST00000489218,; A ENST00000409678 Transcript missense_variant 1094/2329 710/1491 237/496 G/V gGg/gTg 1 -1 NOTUM HGNC HGNC:27106 protein_coding YES CCDS32771.2 ENSP00000387310 Q6P988 UPI000004EE80 NM_178493.5 deleterious(0) 7/11 Low_complexity_(Seg):seg,hmmpanther:PTHR21562,hmmpanther:PTHR21562:SF7,Pfam_domain:PF03283 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 81957060 81957060 C A 1 0 0 0 0 1 0 0 0 10598 623 22 2 2 NOTUM 17 81957060 Missense_Mutation SNP C 11LU016_T 4762162 81957060 1300381 487 539 ENOSF1 0 . GRCh38 18 690575 690575 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.655G>T p.Gly219Trp p.G219W ENST00000340116 8/15 245 196 49 342 341 1 strelka-varscan-mutect ENOSF1,missense_variant,p.Gly116Trp,ENST00000383578,NM_001318759.1,NM_001126123.3;ENOSF1,missense_variant,p.Gly198Trp,ENST00000251101,NM_017512.5;ENOSF1,missense_variant,p.Gly219Trp,ENST00000340116,NM_202758.3;ENOSF1,missense_variant,p.Gly122Trp,ENST00000580982,;ENOSF1,missense_variant,p.Gly96Trp,ENST00000583771,;ENOSF1,upstream_gene_variant,,ENST00000583973,;ENOSF1,downstream_gene_variant,,ENST00000580605,;ENOSF1,missense_variant,p.Trp198Cys,ENST00000581475,NM_001318760.1;ENOSF1,missense_variant,p.Trp173Cys,ENST00000584453,;ENOSF1,3_prime_UTR_variant,,ENST00000585128,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000584259,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000585004,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000579053,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000578651,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000577334,;ENOSF1,upstream_gene_variant,,ENST00000582745,;ENOSF1,upstream_gene_variant,,ENST00000578647,;ENOSF1,upstream_gene_variant,,ENST00000584706,; A ENST00000340116 Transcript missense_variant 693/1658 655/1353 219/450 G/W Ggg/Tgg 1 -1 ENOSF1 HGNC HGNC:30365 protein_coding YES CCDS11823.1 ENSP00000345974 Q7L5Y1 UPI0000252153 NM_202758.3 deleterious(0) 8/15 Gene3D:3.20.20.120,hmmpanther:PTHR13794,hmmpanther:PTHR13794:SF58,Superfamily_domains:SSF51604 MODERATE 1 SNV 5 1 PASS rs1417974536 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 690575 690575 C A 1 0 0 0 0 1 0 0 0 4970 623 22 2 2 ENOSF1 18 690575 Missense_Mutation SNP C 11LU016_T 690575 79682710 488 540 ARHGAP28 0 . GRCh38 18 6889968 6889968 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.1140G>C p.Met380Ile p.M380I ENST00000419673 12/17 359 330 29 299 299 0 strelka-varscan-mutect ARHGAP28,missense_variant,p.Met380Ile,ENST00000419673,NM_001010000.2;ARHGAP28,missense_variant,p.Met380Ile,ENST00000314319,;ARHGAP28,missense_variant,p.Met487Ile,ENST00000262227,;ARHGAP28,missense_variant,p.Met539Ile,ENST00000383472,;ARHGAP28,missense_variant,p.Met375Ile,ENST00000531294,;ARHGAP28,missense_variant,p.Met362Ile,ENST00000532996,;ARHGAP28,missense_variant,p.Met176Ile,ENST00000579689,; C ENST00000419673 Transcript missense_variant 1357/5492 1140/1713 380/570 M/I atG/atC 1 1 ARHGAP28 HGNC HGNC:25509 protein_coding YES CCDS32785.1 ENSP00000392660 Q9P2N2 UPI00004CEC5C NM_001010000.2 tolerated(0.06) 12/17 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF5,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 6889968 6889968 G C 1 0 0 0 0 1 0 0 0 1002 1348 47 4 4 ARHGAP28 18 6889968 Missense_Mutation SNP G 11LU016_T 6199393 6889968 73483317 489 541 PTPRM 0 . GRCh38 18 8384614 8384614 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.3972G>T p.Gln1324His p.Q1324H ENST00000580170 30/33 171 133 38 173 173 0 strelka-varscan-mutect PTPRM,missense_variant,p.Gln1311His,ENST00000332175,NM_002845.3;PTPRM,missense_variant,p.Gln1324His,ENST00000580170,NM_001105244.1;PTPRM,missense_variant,p.Gln1249His,ENST00000400053,;PTPRM,missense_variant,p.Gln138His,ENST00000400060,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,; T ENST00000580170 Transcript missense_variant 5009/5941 3972/4398 1324/1465 Q/H caG/caT 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 deleterious(0.02) 30/33 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 8384614 8384614 G T 1 0 0 0 0 1 0 0 0 12960 991 35 2 2 PTPRM 18 8384614 Missense_Mutation SNP G 11LU016_T 1494646 8384614 71988671 490 542 MC5R 0 . GRCh38 18 13826448 13826448 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.683C>A p.Ala228Glu p.A228E ENST00000324750 1/1 137 102 35 143 143 0 strelka-varscan-mutect MC5R,missense_variant,p.Ala228Glu,ENST00000324750,NM_005913.2;MC5R,downstream_gene_variant,,ENST00000589410,; A ENST00000324750 Transcript missense_variant 905/1200 683/978 228/325 A/E gCg/gAg COSM3403441 1 1 MC5R HGNC HGNC:6933 protein_coding YES CCDS11868.1 ENSP00000318077 P33032 UPI0000050405 NM_005913.2 tolerated(0.22) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF5,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01063 1 MODERATE 1 SNV 1 1 PASS rs1485593304 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 13826448 13826448 C A 1 0 0 0 0 1 0 0 0 9300 768 27 1 1 MC5R 18 13826448 Missense_Mutation SNP C 11LU016_T 5441834 13826448 66546837 491 543 ANKRD30B 0 . GRCh38 18 14752621 14752621 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.277G>T p.Val93Leu p.V93L ENST00000358984 2/36 108 93 15 149 149 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Val93Leu,ENST00000358984,NM_001145029.1;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Val93Leu,ENST00000580206,; T ENST00000358984 Transcript missense_variant 457/4359 277/4179 93/1392 V/L Gta/Tta 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.15) 2/36 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 14752621 14752621 G T 1 0 0 0 0 1 0 0 0 762 1261 44 2 2 ANKRD30B 18 14752621 Missense_Mutation SNP G 11LU016_T 926173 14752621 65620664 492 544 3 2 ANKRD30B 0 . GRCh38 18 14752628 14752628 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.284G>C p.Arg95Thr p.R95T ENST00000358984 2/36 112 97 15 150 150 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Arg95Thr,ENST00000358984,NM_001145029.1;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Arg95Thr,ENST00000580206,; C ENST00000358984 Transcript missense_variant 464/4359 284/4179 95/1392 R/T aGa/aCa 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 deleterious(0) 2/36 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99985 0.9999999 1 1 1 0 C 3 2 2 14752628 14752628 G C 1 0 0 0 0 1 0 0 0 762 942 33 4 4 ANKRD30B 18 14752628 Missense_Mutation SNP G 11LU016_T 7 14752628 65620657 493 545 3 2 CCDC178 0 . GRCh38 18 33397196 33397196 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.71A>T p.Gln24Leu p.Q24L ENST00000583930 3/23 101 86 15 137 137 0 strelka-varscan-mutect CCDC178,missense_variant,p.Gln24Leu,ENST00000383096,;CCDC178,missense_variant,p.Gln24Leu,ENST00000403303,NM_001105528.1;CCDC178,missense_variant,p.Gln24Leu,ENST00000583930,;CCDC178,missense_variant,p.Gln24Leu,ENST00000300227,NM_198995.2;CCDC178,missense_variant,p.Gln24Leu,ENST00000406524,;CCDC178,missense_variant,p.Gln24Leu,ENST00000579947,;CCDC178,missense_variant,p.Gln24Leu,ENST00000579916,;CCDC178,missense_variant,p.Gln24Leu,ENST00000577766,;CCDC178,missense_variant,p.Gln24Leu,ENST00000399177,; A ENST00000583930 Transcript missense_variant 150/3094 71/2676 24/891 Q/L cAg/cTg 1 -1 CCDC178 HGNC HGNC:29588 protein_coding YES CCDS77174.1 ENSP00000463254 F8W7A7 UPI00020655A5 tolerated_low_confidence(1) 3/23 hmmpanther:PTHR35088:SF1,hmmpanther:PTHR35088 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 33397196 33397196 T A 1 0 0 0 0 1 0 0 0 2493 1580 55 4 4 CCDC178 18 33397196 Missense_Mutation SNP T 11LU016_T 18644568 33397196 46976089 494 546 DTNA 0 . GRCh38 18 34875342 34875342 + Missense_Mutation SNP C C A rs199556035 11LU016_T 11LU016_N C C c.1586C>A p.Thr529Lys p.T529K ENST00000598334 16/20 393 277 116 316 316 0 strelka-varscan-mutect DTNA,missense_variant,p.Thr532Lys,ENST00000283365,NM_032975.3;DTNA,missense_variant,p.Thr536Lys,ENST00000399121,NM_001198939.1;DTNA,missense_variant,p.Thr589Lys,ENST00000444659,NM_001390.4;DTNA,missense_variant,p.Thr529Lys,ENST00000595022,NM_001198940.1;DTNA,missense_variant,p.Thr529Lys,ENST00000598334,NM_001198938.1;DTNA,missense_variant,p.Thr532Lys,ENST00000598142,;DTNA,missense_variant,p.Thr589Lys,ENST00000399113,;DTNA,missense_variant,p.Thr298Lys,ENST00000269192,NM_001198942.1;DTNA,missense_variant,p.Thr211Lys,ENST00000601125,NM_001198943.1;DTNA,missense_variant,p.Thr237Lys,ENST00000591182,NM_032980.3;DTNA,missense_variant,p.Thr241Lys,ENST00000556414,NM_001198944.1;DTNA,missense_variant,p.Thr15Lys,ENST00000590831,; A ENST00000598334 Transcript missense_variant 1912/3201 1586/2175 529/724 T/K aCg/aAg rs199556035,COSM4071971,COSM4071972,COSM4071973,COSM4071974 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 deleterious(0.03) 16/20 hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204 uncertain_significance 0,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs199556035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 34875342 34875342 C A 1 0 0 0 0 1 0 0 0 4611 536 19 1 1 DTNA 18 34875342 Missense_Mutation SNP C 11LU016_T 1478146 34875342 45497943 495 547 ALPK2 0 . GRCh38 18 58534987 58534987 + Silent SNP T T G novel 11LU016_T 11LU016_N T T c.5200A>C p.= p.R1734R ENST00000361673 5/13 194 162 32 246 246 0 strelka-varscan-mutect ALPK2,synonymous_variant,p.=,ENST00000361673,NM_052947.3;RP11-1151B14.4,upstream_gene_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; G ENST00000361673 Transcript synonymous_variant 5414/7303 5200/6513 1734/2170 R Agg/Cgg 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 5/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 58534987 58534987 T G 1 0 0 0 0 0 0 0 1 645 1579 55 5 5 ALPK2 18 58534987 Silent SNP T 11LU016_T 23659645 58534987 21838298 496 548 CDH20 0 . GRCh38 18 61554521 61554521 + Silent SNP C C G 11LU016_T 11LU016_N C C c.2232C>G p.= p.S744S ENST00000262717 12/12 285 210 75 260 260 0 strelka-varscan-mutect CDH20,synonymous_variant,p.=,ENST00000262717,;CDH20,synonymous_variant,p.=,ENST00000536675,NM_031891.2;CDH20,synonymous_variant,p.=,ENST00000538374,;CDH20,downstream_gene_variant,,ENST00000587582,; G ENST00000262717 Transcript synonymous_variant 2630/3882 2232/2406 744/801 S tcC/tcG COSM4478370 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D 12/12 hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 1 LOW 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 61554521 61554521 C G 1 0 0 0 0 0 0 0 1 2809 610 22 4 4 CDH20 18 61554521 Silent SNP C 11LU016_T 3019534 61554521 18818764 497 549 GALR1 0 . GRCh38 18 77268722 77268722 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.870C>A p.Cys290Ter p.C290* ENST00000299727 3/3 347 281 66 466 464 2 strelka-varscan-mutect GALR1,stop_gained,p.Cys290Ter,ENST00000299727,NM_001480.3; A ENST00000299727 Transcript stop_gained 870/10044 870/1050 290/349 C/* tgC/tgA 1 1 GALR1 HGNC HGNC:4132 protein_coding YES CCDS12012.1 ENSP00000299727 P47211 UPI000013E5DE NM_001480.3 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24230:SF31,hmmpanther:PTHR24230,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00663 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 77268722 77268722 C A 1 0 0 0 0 0 1 0 0 6095 747 26 2 2 GALR1 18 77268722 Nonsense_Mutation SNP C 11LU016_T 15714201 77268722 3104563 498 550 CDC34 0 . GRCh38 19 541390 541390 + Silent SNP G G T rs35573985 11LU016_T 11LU016_N G G c.549G>T p.= p.V183V ENST00000215574 5/5 207 168 39 213 213 0 strelka-varscan-mutect CDC34,synonymous_variant,p.=,ENST00000215574,NM_004359.1;CDC34,synonymous_variant,p.=,ENST00000607527,;CDC34,3_prime_UTR_variant,,ENST00000586283,;CDC34,3_prime_UTR_variant,,ENST00000606065,;GZMM,upstream_gene_variant,,ENST00000592501,NM_001258351.1;GZMM,upstream_gene_variant,,ENST00000264553,NM_005317.3;CDC34,non_coding_transcript_exon_variant,,ENST00000593036,;CDC34,non_coding_transcript_exon_variant,,ENST00000606400,;CDC34,downstream_gene_variant,,ENST00000586788,; T ENST00000215574 Transcript synonymous_variant 769/1471 549/711 183/236 V gtG/gtT rs35573985 1 1 CDC34 HGNC HGNC:1734 protein_coding YES CCDS12030.1 ENSP00000215574 P49427 A0A024R1Z1 UPI000013795A NM_004359.1 5/5 hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF135,Gene3D:3.10.110.10 LOW 1 SNV 1 1 PASS rs35573985 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 541390 541390 G T 1 0 0 0 0 0 0 0 1 2770 1306 46 2 2 CDC34 19 541390 Silent SNP G 11LU016_T 541390 58076226 499 551 ARHGAP45 0 . GRCh38 19 1073980 1073980 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.804G>T p.Glu268Asp p.E268D ENST00000539243 6/23 65 49 16 101 101 0 strelka-varscan-mutect ARHGAP45,missense_variant,p.Glu252Asp,ENST00000313093,NM_012292.4;ARHGAP45,missense_variant,p.Glu279Asp,ENST00000590214,;ARHGAP45,missense_variant,p.Glu268Asp,ENST00000539243,NM_001258328.2;ARHGAP45,missense_variant,p.Glu256Asp,ENST00000586866,;ARHGAP45,missense_variant,p.Glu135Asp,ENST00000543365,NM_001282335.1;ARHGAP45,upstream_gene_variant,,ENST00000590577,NM_001282334.1;ARHGAP45,downstream_gene_variant,,ENST00000587186,;ARHGAP45,downstream_gene_variant,,ENST00000592335,;ARHGAP45,3_prime_UTR_variant,,ENST00000587602,;ARHGAP45,non_coding_transcript_exon_variant,,ENST00000586033,;ARHGAP45,intron_variant,,ENST00000591293,; T ENST00000539243 Transcript missense_variant 907/4184 804/3459 268/1152 E/D gaG/gaT 1 1 ARHGAP45 HGNC HGNC:17102 protein_coding YES CCDS58637.1 ENSP00000439601 Q92619 UPI0001AE63E1 NM_001258328.2 tolerated(0.41) 6/23 hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF18 MODERATE 1 SNV 2 1 PASS rs1253632432 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 1073980 1073980 G T 1 0 0 0 0 1 0 0 0 1015 991 35 2 2 ARHGAP45 19 1073980 Missense_Mutation SNP G 11LU016_T 532590 1073980 57543636 500 552 KDM4B 0 . GRCh38 19 5134012 5134012 + Missense_Mutation SNP G G C rs757620888 11LU016_T 11LU016_N G G c.2036G>C p.Arg679Pro p.R679P ENST00000159111 14/23 115 92 23 162 162 0 strelka-varscan-mutect KDM4B,missense_variant,p.Arg713Pro,ENST00000611640,;KDM4B,missense_variant,p.Arg679Pro,ENST00000159111,NM_015015.2;KDM4B,missense_variant,p.Arg713Pro,ENST00000536461,;KDM4B,missense_variant,p.Arg425Pro,ENST00000588361,;KDM4B,upstream_gene_variant,,ENST00000588166,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,; C ENST00000159111 Transcript missense_variant 2254/5593 2036/3291 679/1096 R/P cGc/cCc rs757620888 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 tolerated(0.25) 14/23 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30 MODERATE 1 SNV 1 1 PASS rs757620888 . 0 199 7 4 0 0 0 0 -20 0.9986781 1 1 1 0 C 3 2 2 5134012 5134012 G C 1 0 0 0 0 1 0 0 0 8047 1087 38 4 4 KDM4B 19 5134012 Missense_Mutation SNP G 11LU016_T 4060032 5134012 53483604 501 553 ZNF557 0 . GRCh38 19 7083315 7083315 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.864G>T p.= p.G288G ENST00000252840 8/8 194 153 41 224 222 2 strelka-varscan-mutect ZNF557,synonymous_variant,p.=,ENST00000414706,NM_001044388.1;ZNF557,synonymous_variant,p.=,ENST00000252840,NM_024341.2,NM_001044387.1; T ENST00000252840 Transcript synonymous_variant 1365/2268 864/1293 288/430 G ggG/ggT 1 1 ZNF557 HGNC HGNC:28632 protein_coding YES CCDS42485.1 ENSP00000252840 Q8N988 UPI000020324B NM_024341.2,NM_001044387.1 8/8 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF145,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 7083315 7083315 G T 1 0 0 0 0 0 0 0 1 18562 1219 43 2 2 ZNF557 19 7083315 Silent SNP G 11LU016_T 1949303 7083315 51534301 502 554 FBN3 0 . GRCh38 19 8085540 8085540 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.6910G>T p.Val2304Leu p.V2304L ENST00000600128 56/64 84 71 13 86 86 0 strelka-varscan-mutect FBN3,missense_variant,p.Val2304Leu,ENST00000600128,;FBN3,missense_variant,p.Val2304Leu,ENST00000270509,NM_032447.3;FBN3,missense_variant,p.Val2304Leu,ENST00000601739,NM_001321431.1;FBN3,downstream_gene_variant,,ENST00000601281,;FBN3,upstream_gene_variant,,ENST00000595036,;FBN3,downstream_gene_variant,,ENST00000598269,; A ENST00000600128 Transcript missense_variant 7325/9362 6910/8430 2304/2809 V/L Gtg/Ttg 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F tolerated(0.19) 56/64 PROSITE_profiles:PS51364,hmmpanther:PTHR24039:SF0,hmmpanther:PTHR24039,PIRSF_domain:PIRSF036312,Gene3D:3.90.290.10,Superfamily_domains:SSF57581 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 8085540 8085540 C A 1 0 0 0 0 1 0 0 0 5567 507 18 2 2 FBN3 19 8085540 Missense_Mutation SNP C 11LU016_T 1002225 8085540 50532076 503 555 MUC16 0 . GRCh38 19 8953520 8953520 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.23250C>T p.= p.S7750S ENST00000397910 3/84 325 273 52 207 207 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript synonymous_variant 23454/43816 23250/43524 7750/14507 S tcC/tcT 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 8953520 8953520 G A 1 0 0 0 0 0 0 0 1 9972 1219 43 3 3 MUC16 19 8953520 Silent SNP G 11LU016_T 867980 8953520 49664096 504 556 OR7D2 0 . GRCh38 19 9186558 9186558 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.777C>G p.His259Gln p.H259Q ENST00000344248 1/1 154 146 8 140 140 0 strelka-mutect OR7D2,missense_variant,p.His259Gln,ENST00000344248,NM_175883.2;OR7E16P,upstream_gene_variant,,ENST00000592975,;TCEB1P29,upstream_gene_variant,,ENST00000588193,; G ENST00000344248 Transcript missense_variant 965/3224 777/939 259/312 H/Q caC/caG 1 1 OR7D2 HGNC HGNC:8378 protein_coding YES CCDS32900.1 ENSP00000345563 Q96RA2 UPI0000041C0C NM_175883.2 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF157,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs978622761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 9186558 9186558 C G 1 0 0 0 0 1 0 0 0 11289 564 20 4 4 OR7D2 19 9186558 Missense_Mutation SNP C 11LU016_T 233038 9186558 49431058 505 557 ZNF560 0 . GRCh38 19 9467157 9467157 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.1790A>T p.Glu597Val p.E597V ENST00000301480 10/10 291 237 54 238 238 0 strelka-varscan-mutect ZNF560,missense_variant,p.Glu597Val,ENST00000301480,NM_152476.2;ZNF560,downstream_gene_variant,,ENST00000585974,; A ENST00000301480 Transcript missense_variant 2004/2654 1790/2373 597/790 E/V gAg/gTg 1 -1 ZNF560 HGNC HGNC:26484 protein_coding YES CCDS12214.1 ENSP00000301480 Q96MR9 UPI000013E720 NM_152476.2 deleterious(0) 10/10 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF44,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1176509380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 9467157 9467157 T A 1 0 0 0 0 1 0 0 0 18565 1551 54 4 4 ZNF560 19 9467157 Missense_Mutation SNP T 11LU016_T 280599 9467157 49150459 506 558 C19orf38 0 . GRCh38 19 10850490 10850490 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.263G>T p.Cys88Phe p.C88F ENST00000397820 2/7 197 167 30 271 271 0 strelka-varscan-mutect C19orf38,missense_variant,p.Cys88Phe,ENST00000397820,NM_001136482.1;C19orf38,missense_variant,p.Cys88Phe,ENST00000592854,;C19orf38,non_coding_transcript_exon_variant,,ENST00000587494,; T ENST00000397820 Transcript missense_variant 370/1223 263/693 88/230 C/F tGc/tTc 1 1 C19orf38 HGNC HGNC:34073 protein_coding YES CCDS45970.1 ENSP00000380920 A8MVS5 UPI0000160991 NM_001136482.1 deleterious(0) 2/7 hmmpanther:PTHR36859,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 10850490 10850490 G T 1 0 0 0 0 1 0 0 0 1909 1319 46 2 2 C19orf38 19 10850490 Missense_Mutation SNP G 11LU016_T 1383333 10850490 47767126 507 559 ZNF442 0 . GRCh38 19 12353069 12353069 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.124G>T p.Glu42Ter p.E42* ENST00000242804 4/6 115 93 22 94 94 0 strelka-varscan-mutect ZNF442,stop_gained,p.Glu42Ter,ENST00000242804,NM_030824.2;ZNF442,stop_gained,p.Glu42Ter,ENST00000545749,;ZNF442,intron_variant,,ENST00000438182,;ZNF442,intron_variant,,ENST00000424168,;ZNF442,non_coding_transcript_exon_variant,,ENST00000462995,; A ENST00000242804 Transcript stop_gained 707/6219 124/1884 42/627 E/* Gag/Tag 1 -1 ZNF442 HGNC HGNC:20877 protein_coding YES CCDS12271.1 ENSP00000242804 Q9H7R0 UPI000006D14F NM_030824.2 4/6 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF6,SMART_domains:SM00349 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 12353069 12353069 C A 1 0 0 0 0 0 1 0 0 18486 922 32 2 2 ZNF442 19 12353069 Nonsense_Mutation SNP C 11LU016_T 1502579 12353069 46264547 508 560 GCDH 0 . GRCh38 19 12893483 12893483 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.335G>T p.Gly112Val p.G112V ENST00000222214 6/12 303 244 59 263 262 1 strelka-varscan-mutect GCDH,missense_variant,p.Gly112Val,ENST00000222214,NM_000159.3,NM_013976.3;GCDH,missense_variant,p.Gly112Val,ENST00000591470,;GCDH,missense_variant,p.Gly100Val,ENST00000588905,;GCDH,missense_variant,p.Gly91Val,ENST00000589039,;GCDH,missense_variant,p.Gly128Val,ENST00000587072,;GCDH,upstream_gene_variant,,ENST00000590472,;GCDH,upstream_gene_variant,,ENST00000591050,;GCDH,missense_variant,p.Arg130Ser,ENST00000590530,;GCDH,splice_region_variant,,ENST00000591043,;GCDH,splice_region_variant,,ENST00000585420,;GCDH,splice_region_variant,,ENST00000421816,;GCDH,splice_region_variant,,ENST00000590627,;GCDH,splice_region_variant,,ENST00000587832,;GCDH,downstream_gene_variant,,ENST00000590445,;GCDH,downstream_gene_variant,,ENST00000585760,;RPS6P25,upstream_gene_variant,,ENST00000464444,; T ENST00000222214 Transcript missense_variant,splice_region_variant 546/1956 335/1317 112/438 G/V gGa/gTa COSM1148084,COSM709902 1 1 GCDH HGNC HGNC:4189 protein_coding YES CCDS12286.1 ENSP00000222214 Q92947 A0A024R7F9 UPI000012B292 NM_000159.3,NM_013976.3 deleterious_low_confidence(0.01) 6/12 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF307,Pfam_domain:PF02771,Gene3D:1.10.540.10,Superfamily_domains:SSF56645 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 12893483 12893483 G T 1 0 0 0 0 1 0 0 0 6157 1188 41 2 2 GCDH 19 12893483 Missense_Mutation SNP G 11LU016_T 540414 12893483 45724133 509 561 ZNF333 0 . GRCh38 19 14718943 14718943 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1616G>A p.Cys539Tyr p.C539Y ENST00000292530 12/12 134 111 23 122 122 0 strelka-varscan-mutect ZNF333,missense_variant,p.Cys539Tyr,ENST00000292530,NM_032433.2;ZNF333,intron_variant,,ENST00000540689,NM_001300912.1;ZNF333,3_prime_UTR_variant,,ENST00000598161,;ZNF333,downstream_gene_variant,,ENST00000597301,;ZNF333,downstream_gene_variant,,ENST00000597007,; A ENST00000292530 Transcript missense_variant 1707/4672 1616/1998 539/665 C/Y tGc/tAc 1 1 ZNF333 HGNC HGNC:15624 protein_coding YES CCDS12316.1 ENSP00000292530 Q96JL9 UPI000013C35C NM_032433.2 deleterious(0) 12/12 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF183,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,SMART_domains:SM00614 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 14718943 14718943 G A 1 0 0 0 0 1 0 0 0 18422 1319 46 3 3 ZNF333 19 14718943 Missense_Mutation SNP G 11LU016_T 1825460 14718943 43898673 510 562 BRD4 0 . GRCh38 19 15255567 15255567 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.1777A>G p.Ser593Gly p.S593G ENST00000263377 10/20 110 103 7 100 100 0 strelka-varscan-mutect BRD4,missense_variant,p.Ser593Gly,ENST00000263377,NM_058243.2;BRD4,missense_variant,p.Ser593Gly,ENST00000371835,NM_014299.2;BRD4,missense_variant,p.Ser593Gly,ENST00000360016,;BRD4,downstream_gene_variant,,ENST00000594841,;BRD4,downstream_gene_variant,,ENST00000602230,;BRD4,upstream_gene_variant,,ENST00000595926,;BRD4,downstream_gene_variant,,ENST00000594842,; C ENST00000263377 Transcript missense_variant 1999/7169 1777/4089 593/1362 S/G Agc/Ggc 1 -1 BRD4 HGNC HGNC:13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 UPI0000126ACE NM_058243.2 tolerated(0.24) 10/20 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF143 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.11496 1 1 1 1 0 C 3 2 2 15255567 15255567 T C 1 0 0 0 0 1 0 0 0 1674 1551 54 5 5 BRD4 19 15255567 Missense_Mutation SNP T 11LU016_T 536624 15255567 43362049 511 563 PGLYRP2 0 . GRCh38 19 15475841 15475841 + Missense_Mutation SNP G G T rs201701673 11LU016_T 11LU016_N G G c.829C>A p.Leu277Met p.L277M ENST00000340880 2/5 308 240 68 321 321 0 strelka-varscan-mutect PGLYRP2,missense_variant,p.Leu277Met,ENST00000292609,;PGLYRP2,missense_variant,p.Leu277Met,ENST00000340880,NM_052890.3;PGLYRP2,downstream_gene_variant,,ENST00000594637,;PGLYRP2,downstream_gene_variant,,ENST00000601792,; T ENST00000340880 Transcript missense_variant 1310/2230 829/1731 277/576 L/M Ctg/Atg rs201701673 1 -1 PGLYRP2 HGNC HGNC:30013 protein_coding YES CCDS12330.2 ENSP00000345968 Q96PD5 UPI000004EEA6 NM_052890.3 tolerated(0.29) 2/5 hmmpanther:PTHR11022,hmmpanther:PTHR11022:SF43 MODERATE 1 SNV 1 1 PASS rs201701673 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 15475841 15475841 G T 1 0 0 0 0 1 0 0 0 11883 991 35 2 2 PGLYRP2 19 15475841 Missense_Mutation SNP G 11LU016_T 220274 15475841 43141775 512 564 OR10H2 0 . GRCh38 19 15728487 15728487 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.444C>A p.= p.S148S ENST00000305899 1/1 80 59 21 87 87 0 strelka-varscan-mutect OR10H2,synonymous_variant,p.=,ENST00000305899,NM_013939.2; A ENST00000305899 Transcript synonymous_variant 468/1041 444/948 148/315 S tcC/tcA 1 1 OR10H2 HGNC HGNC:8173 protein_coding YES CCDS12333.1 ENSP00000306095 O60403 A0A126GWJ7 UPI000004CA3E NM_013939.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF111,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 15728487 15728487 C A 1 0 0 0 0 0 0 0 1 10983 668 24 2 2 OR10H2 19 15728487 Silent SNP C 11LU016_T 252646 15728487 42889129 513 565 OR10H3 0 . GRCh38 19 15741973 15741973 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.581C>A p.Thr194Lys p.T194K ENST00000305892 1/1 501 407 94 369 369 0 strelka-varscan-mutect OR10H3,missense_variant,p.Thr194Lys,ENST00000305892,NM_013938.1; A ENST00000305892 Transcript missense_variant 581/951 581/951 194/316 T/K aCa/aAa 1 1 OR10H3 HGNC HGNC:8174 protein_coding YES CCDS12334.1 ENSP00000307130 O60404 A0A126GW93 UPI0000041DB5 NM_013938.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF78,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 15741973 15741973 C A 1 0 0 0 0 1 0 0 0 10984 478 17 2 2 OR10H3 19 15741973 Missense_Mutation SNP C 11LU016_T 13486 15741973 42875643 514 566 FAM129C 0 . GRCh38 19 17553553 17553553 + Missense_Mutation SNP C C T novel 11LU016_T 11LU016_N C C c.2084C>T p.Pro695Leu p.P695L ENST00000335393 16/16 181 144 37 198 198 0 strelka-varscan-mutect FAM129C,missense_variant,p.Pro695Leu,ENST00000335393,NM_001321826.1,NM_173544.4;FAM129C,missense_variant,p.Pro664Leu,ENST00000601861,;FAM129C,missense_variant,p.Pro421Leu,ENST00000449408,;COLGALT1,upstream_gene_variant,,ENST00000252599,NM_024656.2;FAM129C,downstream_gene_variant,,ENST00000595684,;FAM129C,downstream_gene_variant,,ENST00000332386,NM_001098524.1;FAM129C,downstream_gene_variant,,ENST00000599164,NM_001321827.1;FAM129C,downstream_gene_variant,,ENST00000599124,;FAM129C,downstream_gene_variant,,ENST00000600871,;COLGALT1,upstream_gene_variant,,ENST00000600474,;FAM129C,3_prime_UTR_variant,,ENST00000600519,; T ENST00000335393 Transcript missense_variant 2222/2508 2084/2094 695/697 P/L cCa/cTa 1 1 FAM129C HGNC HGNC:24130 protein_coding YES CCDS12362.1 ENSP00000335040 Q86XR2 UPI0000246FFF NM_001321826.1,NM_173544.4 deleterious_low_confidence(0) 16/16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 17553553 17553553 C T 1 0 0 0 0 1 0 0 0 5288 594 21 3 3 FAM129C 19 17553553 Missense_Mutation SNP C 11LU016_T 1811580 17553553 41064063 515 567 ZNF85 0 . GRCh38 19 20948981 20948981 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.467A>T p.His156Leu p.H156L ENST00000328178 4/4 133 108 25 135 135 0 strelka-varscan-mutect ZNF85,missense_variant,p.His156Leu,ENST00000328178,NM_003429.4;ZNF85,missense_variant,p.His123Leu,ENST00000345030,;ZNF85,missense_variant,p.His104Leu,ENST00000596534,;ZNF85,missense_variant,p.His79Leu,ENST00000599064,;ZNF85,missense_variant,p.His104Leu,ENST00000595742,;ZNF85,missense_variant,p.His79Leu,ENST00000598862,;ZNF85,missense_variant,p.His92Leu,ENST00000599885,;ZNF85,downstream_gene_variant,,ENST00000597314,;ZNF85,downstream_gene_variant,,ENST00000595854,;ZNF85,downstream_gene_variant,,ENST00000601924,;ZNF85,downstream_gene_variant,,ENST00000601284,NM_001256171.1;ZNF85,non_coding_transcript_exon_variant,,ENST00000601023,; T ENST00000328178 Transcript missense_variant 580/2296 467/1788 156/595 H/L cAt/cTt 1 1 ZNF85 HGNC HGNC:13160 protein_coding YES CCDS32977.1 ENSP00000329793 Q03923 UPI0000203897 NM_003429.4 deleterious(0.05) 4/4 Gene3D:3.30.160.60,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF88 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 20948981 20948981 A T 1 0 0 0 0 1 0 0 0 18781 217 8 4 4 ZNF85 19 20948981 Missense_Mutation SNP A 11LU016_T 3395428 20948981 37668635 516 568 ZNF729 0 . GRCh38 19 22314477 22314477 + Missense_Mutation SNP G G A 11LU016_T 11LU016_N G G c.1060G>A p.Gly354Ser p.G354S ENST00000601693 4/4 256 211 45 273 272 1 strelka-varscan-mutect ZNF729,missense_variant,p.Gly354Ser,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript missense_variant 1178/3877 1060/3759 354/1252 G/S Ggc/Agc COSM5691960 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0.03) 4/4 PROSITE_profiles:PS50157,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS rs1157399199 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 22314477 22314477 G A 1 0 0 0 0 1 0 0 0 18703 1348 47 3 3 ZNF729 19 22314477 Missense_Mutation SNP G 11LU016_T 1365496 22314477 36303139 517 569 ZNF492 0 . GRCh38 19 22665197 22665197 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.1528T>A p.Cys510Ser p.C510S ENST00000456783 4/4 83 70 13 108 108 0 strelka-varscan-mutect ZNF492,missense_variant,p.Cys510Ser,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; A ENST00000456783 Transcript missense_variant 1772/4245 1528/1596 510/531 C/S Tgt/Agt 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.01) 4/4 Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 22665197 22665197 T A 1 0 0 0 0 1 0 0 0 18516 1812 63 4 4 ZNF492 19 22665197 Missense_Mutation SNP T 11LU016_T 350720 22665197 35952419 518 570 ZNF585A 0 . GRCh38 19 37155879 37155879 + Missense_Mutation SNP C C T rs374585649 11LU016_T 11LU016_N C C c.278G>A p.Arg93His p.R93H ENST00000292841 4/5 223 210 13 235 235 0 varscan-mutect ZNF585A,missense_variant,p.Arg93His,ENST00000292841,NM_001288800.1;ZNF585A,missense_variant,p.Arg38His,ENST00000356958,NM_152655.3;ZNF585A,missense_variant,p.Arg38His,ENST00000392157,NM_199126.2;CTC-454I21.3,missense_variant,p.Arg81His,ENST00000588873,;ZNF585A,non_coding_transcript_exon_variant,,ENST00000588723,;ZNF585A,missense_variant,p.Arg93His,ENST00000587817,;CTC-454I21.3,downstream_gene_variant,,ENST00000590245,; T ENST00000292841 Transcript missense_variant 537/8618 278/2310 93/769 R/H cGt/cAt rs374585649,COSM1325303 1 -1 ZNF585A HGNC HGNC:26305 protein_coding YES CCDS74353.1 ENSP00000292841 Q6P3V2 UPI00002021E7 NM_001288800.1 tolerated(0.19) 4/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF105 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374585649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 37155879 37155879 C T 1 0 0 0 0 1 0 0 0 18591 536 19 1 1 ZNF585A 19 37155879 Missense_Mutation SNP C 11LU016_T 14490682 37155879 21461737 519 571 RYR1 0 . GRCh38 19 38519298 38519298 + Frame_Shift_Del DEL G G - novel 11LU016_T 11LU016_N G G c.10105delG p.Ala3369GlnfsTer56 p.A3369Qfs*56 ENST00000359596 67/106 360 262 98 327 327 0 sindel-varindel-pindel RYR1,frameshift_variant,p.Ala3369GlnfsTer56,ENST00000355481,NM_001042723.1;RYR1,frameshift_variant,p.Ala3369GlnfsTer56,ENST00000359596,NM_000540.2;RYR1,frameshift_variant,p.Ala305GlnfsTer56,ENST00000599547,;RYR1,3_prime_UTR_variant,,ENST00000594335,;RYR1,upstream_gene_variant,,ENST00000600337,; - ENST00000359596 Transcript frameshift_variant 10103/15117 10103/15117 3368/5038 R/X aGg/ag 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 67/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 HIGH 1 deletion 5 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 38519298 38519298 G - 1 0 1 0 1 0 0 0 0 14028 1000 35 0 0 RYR1 19 38519298 Frame_Shift_Del DEL G 11LU016_T 1363419 38519298 20098318 520 572 MAP4K1 0 . GRCh38 19 38612708 38612708 + Nonsense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.568G>T p.Gly190Ter p.G190* ENST00000591517 9/32 170 124 46 153 153 0 strelka-varscan-mutect MAP4K1,stop_gained,p.Gly190Ter,ENST00000591517,NM_007181.5;MAP4K1,stop_gained,p.Gly186Ter,ENST00000589130,;MAP4K1,stop_gained,p.Gly190Ter,ENST00000396857,NM_001042600.2;MAP4K1,stop_gained,p.Gly190Ter,ENST00000586296,;MAP4K1,upstream_gene_variant,,ENST00000591921,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000589002,;MAP4K1,stop_gained,p.Gly29Ter,ENST00000585583,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000591707,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000592888,;MAP4K1,downstream_gene_variant,,ENST00000592225,;MAP4K1,downstream_gene_variant,,ENST00000588083,;MAP4K1,downstream_gene_variant,,ENST00000587300,; A ENST00000591517 Transcript stop_gained 597/2700 568/2502 190/833 G/* Gga/Tga 1 -1 MAP4K1 HGNC HGNC:6863 protein_coding YES CCDS59385.1 ENSP00000465039 Q92918 UPI00000747ED NM_007181.5 9/32 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF88,hmmpanther:PTHR24361,Pfam_domain:PF00069,PIRSF_domain:PIRSF038172,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 38612708 38612708 C A 1 0 0 0 0 0 1 0 0 9183 632 22 2 2 MAP4K1 19 38612708 Nonsense_Mutation SNP C 11LU016_T 93410 38612708 20004908 521 573 FCGBP 0 . GRCh38 19 39894323 39894323 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.5438G>T p.Gly1813Val p.G1813V ENST00000616721 12/28 902 671 231 944 943 1 strelka-varscan-mutect FCGBP,missense_variant,p.Gly1813Val,ENST00000616721,NM_003890.2;FCGBP,missense_variant,p.Gly678Val,ENST00000620799,; A ENST00000616721 Transcript missense_variant 5446/12787 5438/12615 1813/4204 G/V gGg/gTg 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 deleterious(0) 12/28 Pfam_domain:PF00094,PROSITE_profiles:PS51233,SMART_domains:SM00216 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 39894323 39894323 C A 1 0 0 0 0 1 0 0 0 5641 623 22 2 2 FCGBP 19 39894323 Missense_Mutation SNP C 11LU016_T 1281615 39894323 18723293 522 574 HNRNPUL1 0 . GRCh38 19 41276174 41276174 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.662A>T p.His221Leu p.H221L ENST00000392006 5/15 264 197 67 368 368 0 strelka-varscan-mutect HNRNPUL1,missense_variant,p.His221Leu,ENST00000392006,NM_007040.4;HNRNPUL1,missense_variant,p.His121Leu,ENST00000352456,;HNRNPUL1,missense_variant,p.His132Leu,ENST00000263367,;HNRNPUL1,missense_variant,p.His221Leu,ENST00000602130,;HNRNPUL1,missense_variant,p.His178Leu,ENST00000378215,;HNRNPUL1,missense_variant,p.His121Leu,ENST00000595018,NM_144732.3;HNRNPUL1,missense_variant,p.His121Leu,ENST00000593587,;HNRNPUL1,missense_variant,p.His70Leu,ENST00000599614,;HNRNPUL1,missense_variant,p.His121Leu,ENST00000599719,;HNRNPUL1,missense_variant,p.His121Leu,ENST00000601336,;HNRNPUL1,missense_variant,p.His81Leu,ENST00000597725,;HNRNPUL1,intron_variant,,ENST00000617305,;HNRNPUL1,intron_variant,,ENST00000617774,;HNRNPUL1,downstream_gene_variant,,ENST00000601309,;HNRNPUL1,downstream_gene_variant,,ENST00000595336,;HNRNPUL1,non_coding_transcript_exon_variant,,ENST00000594207,;HNRNPUL1,missense_variant,p.His14Leu,ENST00000600596,;HNRNPUL1,3_prime_UTR_variant,,ENST00000595196,;HNRNPUL1,upstream_gene_variant,,ENST00000600332,;HNRNPUL1,downstream_gene_variant,,ENST00000599521,; T ENST00000392006 Transcript missense_variant 835/3555 662/2571 221/856 H/L cAc/cTc 1 1 HNRNPUL1 HGNC HGNC:17011 protein_coding YES CCDS12576.1 ENSP00000375863 Q9BUJ2 UPI000013D3F4 NM_007040.4 deleterious(0) 5/15 PROSITE_profiles:PS50188,hmmpanther:PTHR12381,hmmpanther:PTHR12381:SF41,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 41276174 41276174 A T 1 0 0 0 0 1 0 0 0 7169 159 6 4 4 HNRNPUL1 19 41276174 Missense_Mutation SNP A 11LU016_T 1381851 41276174 17341442 523 575 PTGIR 0 . GRCh38 19 46623830 46623830 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.396G>T p.= p.G132G ENST00000291294 2/3 165 119 46 200 200 0 strelka-varscan-mutect PTGIR,synonymous_variant,p.=,ENST00000291294,NM_000960.3;PTGIR,synonymous_variant,p.=,ENST00000596260,;PTGIR,intron_variant,,ENST00000597185,;PTGIR,intron_variant,,ENST00000598865,;PTGIR,intron_variant,,ENST00000594275,;PTGIR,non_coding_transcript_exon_variant,,ENST00000595460,; A ENST00000291294 Transcript synonymous_variant 530/2107 396/1161 132/386 G ggG/ggT 1 -1 PTGIR HGNC HGNC:9602 protein_coding YES CCDS12686.1 ENSP00000291294 P43119 UPI000005042B NM_000960.3 2/3 PROSITE_profiles:PS50262,hmmpanther:PTHR11866:SF7,hmmpanther:PTHR11866,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00856 LOW 1 SNV 1 1 PASS rs1473002305 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 46623830 46623830 C A 1 0 0 0 0 0 0 0 1 12907 726 26 2 2 PTGIR 19 46623830 Silent SNP C 11LU016_T 5347656 46623830 11993786 524 576 IZUMO2 0 . GRCh38 19 50159552 50159552 + Silent SNP G G A novel 11LU016_T 11LU016_N G G c.336C>T p.= p.T112T ENST00000293405 3/7 126 89 37 157 157 0 strelka-varscan-mutect IZUMO2,synonymous_variant,p.=,ENST00000600293,;IZUMO2,synonymous_variant,p.=,ENST00000293405,NM_152358.2;IZUMO2,3_prime_UTR_variant,,ENST00000486050,;IZUMO2,downstream_gene_variant,,ENST00000594854,; A ENST00000293405 Transcript synonymous_variant 337/728 336/666 112/221 T acC/acT 1 -1 IZUMO2 HGNC HGNC:28518 protein_coding YES CCDS12792.2 ENSP00000293405 Q6UXV1 UPI00001D6939 NM_152358.2 3/7 hmmpanther:PTHR26374:SF183,hmmpanther:PTHR26374,Pfam_domain:PF15005 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 50159552 50159552 G A 1 0 0 0 0 0 0 0 1 7841 1219 43 3 3 IZUMO2 19 50159552 Silent SNP G 11LU016_T 3535722 50159552 8458064 525 577 SIGLEC9 0 . GRCh38 19 51125692 51125692 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.517G>T p.Gly173Trp p.G173W ENST00000440804 2/7 137 93 44 245 245 0 strelka-varscan-mutect SIGLEC9,missense_variant,p.Gly173Trp,ENST00000440804,NM_001198558.1;SIGLEC9,missense_variant,p.Gly173Trp,ENST00000250360,NM_014441.2;SIGLEC9,upstream_gene_variant,,ENST00000599948,;SIGLEC18P,downstream_gene_variant,,ENST00000602271,; T ENST00000440804 Transcript missense_variant 584/1960 517/1440 173/479 G/W Ggg/Tgg 1 1 SIGLEC9 HGNC HGNC:10878 protein_coding YES CCDS56100.1 ENSP00000413861 Q9Y336 UPI00017A75A8 NM_001198558.1 deleterious(0) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF43,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 51125692 51125692 G T 1 0 0 0 0 1 0 0 0 14579 1232 43 2 2 SIGLEC9 19 51125692 Missense_Mutation SNP G 11LU016_T 966140 51125692 7491924 526 578 VN1R4 0 . GRCh38 19 53267168 53267168 + Nonsense_Mutation SNP G G C 11LU016_T 11LU016_N G G c.498C>G p.Tyr166Ter p.Y166* ENST00000311170 1/1 88 55 33 96 96 0 strelka-varscan-mutect VN1R4,stop_gained,p.Tyr166Ter,ENST00000311170,NM_173857.2;CTD-2245F17.9,downstream_gene_variant,,ENST00000599803,; C ENST00000311170 Transcript stop_gained 556/1048 498/906 166/301 Y/* taC/taG COSM5338137 1 -1 VN1R4 HGNC HGNC:19871 protein_coding YES CCDS33099.1 ENSP00000310856 Q7Z5H5 UPI000004B23A NM_173857.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF03402,PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF80,Superfamily_domains:SSF81321 1 HIGH SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 2 53267168 53267168 G C 1 0 0 0 0 0 1 0 0 17728 1024 36 4 4 VN1R4 19 53267168 Nonsense_Mutation SNP G 11LU016_T 2141476 53267168 5350448 527 579 PRKCG 0 . GRCh38 19 53891806 53891806 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.662C>A p.Pro221His p.P221H ENST00000263431 6/18 448 302 146 461 461 0 strelka-varscan-mutect PRKCG,missense_variant,p.Pro221His,ENST00000263431,NM_002739.3;PRKCG,missense_variant,p.Pro93His,ENST00000474397,;PRKCG,downstream_gene_variant,,ENST00000479081,;PRKCG,downstream_gene_variant,,ENST00000419486,; A ENST00000263431 Transcript missense_variant 944/3133 662/2094 221/697 P/H cCt/cAt 1 1 PRKCG HGNC HGNC:9402 protein_coding YES CCDS12867.1 ENSP00000263431 P05129 UPI000000DC69 NM_002739.3 deleterious(0.01) 6/18 PROSITE_profiles:PS50004,hmmpanther:PTHR24356:SF162,hmmpanther:PTHR24356,PIRSF_domain:PIRSF000550,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562,Prints_domain:PR00360 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 53891806 53891806 C A 1 0 0 0 0 1 0 0 0 12645 681 24 2 2 PRKCG 19 53891806 Missense_Mutation SNP C 11LU016_T 624638 53891806 4725810 528 580 SBK2 0 . GRCh38 19 55531229 55531229 + Missense_Mutation SNP C C A rs575501741 11LU016_T 11LU016_N C C c.370G>T p.Gly124Cys p.G124C ENST00000413299 3/4 526 462 64 467 467 0 strelka-varscan-mutect SBK2,missense_variant,p.Gly124Cys,ENST00000413299,NM_001101401.2;SBK2,missense_variant,p.Gly124Cys,ENST00000344158,; A ENST00000413299 Transcript missense_variant 408/1085 370/1047 124/348 G/C Ggc/Tgc rs575501741 1 -1 SBK2 HGNC HGNC:34416 protein_coding YES CCDS42631.1 ENSP00000389015 P0C263 UPI00015DFA43 NM_001101401.2 deleterious(0) 3/4 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF167,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs575501741 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 55531229 55531229 C A 1 0 0 0 0 1 0 0 0 14125 652 23 1 1 SBK2 19 55531229 Missense_Mutation SNP C 11LU016_T 1639423 55531229 3086387 529 581 PEG3 0 . GRCh38 19 56816882 56816882 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1560G>T p.Leu520Phe p.L520F ENST00000326441 10/10 138 93 45 149 148 1 strelka-varscan-mutect PEG3,missense_variant,p.Leu520Phe,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Leu396Phe,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Leu520Phe,ENST00000599534,;PEG3,missense_variant,p.Leu520Phe,ENST00000599577,;PEG3,missense_variant,p.Leu394Phe,ENST00000593695,NM_001146185.1;PEG3,missense_variant,p.Leu365Phe,ENST00000600833,;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 1924/8723 1560/4767 520/1588 L/F ttG/ttT 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 tolerated(0.07) 10/10 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs757748874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 56816882 56816882 C A 1 0 0 0 0 1 0 0 0 11808 593 21 2 2 PEG3 19 56816882 Missense_Mutation SNP C 11LU016_T 1285653 56816882 1800734 530 582 ZSCAN4 0 . GRCh38 19 57676509 57676509 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.364C>A p.Leu122Met p.L122M ENST00000318203 3/5 70 47 23 76 76 0 strelka-varscan-mutect ZSCAN4,missense_variant,p.Leu122Met,ENST00000318203,NM_152677.2;ZSCAN4,missense_variant,p.Leu122Met,ENST00000612521,; A ENST00000318203 Transcript missense_variant 1061/2246 364/1302 122/433 L/M Ctg/Atg COSM714164 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 deleterious(0) 3/5 Pfam_domain:PF02023,PROSITE_profiles:PS50804,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,SMART_domains:SM00431,Superfamily_domains:SSF47353 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 57676509 57676509 C A 1 0 0 0 0 1 0 0 0 18836 680 24 2 2 ZSCAN4 19 57676509 Missense_Mutation SNP C 11LU016_T 859627 57676509 941107 531 583 ANKEF1 0 . GRCh38 20 10044523 10044523 + Missense_Mutation SNP G G T rs755799255 11LU016_T 11LU016_N G G c.676G>T p.Ala226Ser p.A226S ENST00000378380 4/10 160 132 28 118 116 2 strelka-varscan-mutect ANKEF1,missense_variant,p.Ala226Ser,ENST00000378380,NM_198798.2,NM_001303472.1;ANKEF1,missense_variant,p.Ala226Ser,ENST00000378392,NM_022096.5;SNAP25-AS1,intron_variant,,ENST00000603542,;SNAP25-AS1,intron_variant,,ENST00000421143,;ANKEF1,non_coding_transcript_exon_variant,,ENST00000488991,;ANKEF1,downstream_gene_variant,,ENST00000437504,; T ENST00000378380 Transcript missense_variant 1005/5303 676/2331 226/776 A/S Gct/Tct rs755799255 1 1 ANKEF1 HGNC HGNC:15803 protein_coding YES CCDS13108.1 ENSP00000367631 Q9NU02 UPI0000125B51 NM_198798.2,NM_001303472.1 tolerated(0.09) 4/10 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR24127,hmmpanther:PTHR24127:SF1,Low_complexity_(Seg):seg,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs755799255 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 10044523 10044523 G T 1 0 0 0 0 1 0 0 0 726 1319 46 2 2 ANKEF1 20 10044523 Missense_Mutation SNP G 11LU016_T 10044523 54399644 532 584 PAX1 0 . GRCh38 20 21706539 21706539 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.388G>T p.Gly130Cys p.G130C ENST00000398485 2/5 250 202 48 249 249 0 strelka-varscan-mutect PAX1,missense_variant,p.Gly130Cys,ENST00000613128,NM_001257096.1;PAX1,missense_variant,p.Gly130Cys,ENST00000398485,NM_006192.4;PAX1,missense_variant,p.Gly106Cys,ENST00000444366,;RP5-1065O2.4,upstream_gene_variant,,ENST00000624692,;PAX1,intron_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,; T ENST00000398485 Transcript missense_variant 442/2838 388/1605 130/534 G/C Ggc/Tgc 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious(0) 2/5 Gene3D:1.10.10.10,Pfam_domain:PF00292,Prints_domain:PR00027,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF262,SMART_domains:SM00351,Superfamily_domains:SSF46689 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 21706539 21706539 G T 1 0 0 0 0 1 0 0 0 11563 1232 43 2 2 PAX1 20 21706539 Missense_Mutation SNP G 11LU016_T 11662016 21706539 42737628 533 585 TTLL9 0 . GRCh38 20 31871139 31871139 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.13A>T p.Arg5Trp p.R5W ENST00000535842 1/14 243 228 15 173 173 0 strelka-mutect TTLL9,missense_variant,p.Arg5Trp,ENST00000535842,;TTLL9,missense_variant,p.Arg5Trp,ENST00000375938,NM_001008409.2;DUSP15,upstream_gene_variant,,ENST00000278979,NM_001320479.1;DUSP15,upstream_gene_variant,,ENST00000486996,;DUSP15,upstream_gene_variant,,ENST00000339738,NM_080611.3;DUSP15,upstream_gene_variant,,ENST00000398084,NM_177991.1;DUSP15,upstream_gene_variant,,ENST00000398083,NM_001012644.1;DUSP15,upstream_gene_variant,,ENST00000375966,NM_001320478.1;DUSP15,upstream_gene_variant,,ENST00000428829,;TTLL9,intron_variant,,ENST00000375922,;DUSP15,upstream_gene_variant,,ENST00000493115,;DUSP15,upstream_gene_variant,,ENST00000459848,;TTLL9,missense_variant,p.Arg5Trp,ENST00000375921,;TTLL9,missense_variant,p.Arg5Trp,ENST00000310998,; T ENST00000535842 Transcript missense_variant 13/3261 13/1320 5/439 R/W Agg/Tgg 1 1 TTLL9 HGNC HGNC:16118 protein_coding YES CCDS42863.1 ENSP00000442515 Q3SXZ7 UPI00001998D0 deleterious_low_confidence(0.01) 1/14 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 31871139 31871139 A T 1 0 0 0 0 1 0 0 0 17244 179 7 4 4 TTLL9 20 31871139 Missense_Mutation SNP A 11LU016_T 10164600 31871139 32573028 534 586 CEP250 0 . GRCh38 20 35475593 35475593 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.1663G>A p.Glu555Lys p.E555K ENST00000397527 15/35 212 187 25 204 204 0 strelka-varscan-mutect CEP250,missense_variant,p.Glu555Lys,ENST00000397527,NM_007186.4;CEP250,missense_variant,p.Glu554Lys,ENST00000425934,;CEP250,missense_variant,p.Glu69Lys,ENST00000425096,;RP3-477O4.14,downstream_gene_variant,,ENST00000453914,;RP3-477O4.14,downstream_gene_variant,,ENST00000416260,;RP3-477O4.14,downstream_gene_variant,,ENST00000444933,;CEP250,intron_variant,,ENST00000461386,;CEP250,downstream_gene_variant,,ENST00000474829,; A ENST00000397527 Transcript missense_variant 2383/15703 1663/7329 555/2442 E/K Gaa/Aaa 1 1 CEP250 HGNC HGNC:1859 protein_coding YES CCDS13255.1 ENSP00000380661 Q9BV73 UPI000006FE8F NM_007186.4 deleterious(0.01) 15/35 hmmpanther:PTHR23159:SF1,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 35475593 35475593 G A 1 0 0 0 0 1 0 0 0 2968 1175 41 3 3 CEP250 20 35475593 Missense_Mutation SNP G 11LU016_T 3604454 35475593 28968574 535 587 PTPRT 0 . GRCh38 20 42106867 42106867 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.3366G>T p.Met1122Ile p.M1122I ENST00000373198 25/32 165 134 31 178 178 0 strelka-varscan-mutect PTPRT,missense_variant,p.Met1122Ile,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Met1125Ile,ENST00000373193,;PTPRT,missense_variant,p.Met1093Ile,ENST00000373201,;PTPRT,missense_variant,p.Met1102Ile,ENST00000373190,;PTPRT,missense_variant,p.Met1113Ile,ENST00000373184,;PTPRT,missense_variant,p.Met1112Ile,ENST00000356100,;PTPRT,missense_variant,p.Met1103Ile,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Met721Ile,ENST00000612229,;PTPRT,missense_variant,p.Met738Ile,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 3602/12746 3366/4383 1122/1460 M/I atG/atT 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 25/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 42106867 42106867 C A 1 0 0 0 0 1 0 0 0 12967 594 21 2 2 PTPRT 20 42106867 Missense_Mutation SNP C 11LU016_T 6631274 42106867 22337300 536 588 R3HDML 0 . GRCh38 20 44341217 44341217 + Missense_Mutation SNP A A T novel 11LU016_T 11LU016_N A A c.283A>T p.Arg95Trp p.R95W ENST00000217043 2/5 96 68 28 97 97 0 strelka-varscan-mutect R3HDML,missense_variant,p.Arg95Trp,ENST00000217043,NM_178491.3;Y_RNA,upstream_gene_variant,,ENST00000364493,; T ENST00000217043 Transcript missense_variant 455/1377 283/762 95/253 R/W Agg/Tgg 1 1 R3HDML HGNC HGNC:16249 protein_coding YES CCDS13329.1 ENSP00000217043 Q9H3Y0 UPI00000422F8 NM_178491.3 deleterious(0.04) 2/5 Gene3D:3.40.33.10,Pfam_domain:PF00188,Prints_domain:PR00837,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF62,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 2 44341217 44341217 A T 1 0 0 0 0 1 0 0 0 13047 179 7 4 4 R3HDML 20 44341217 Missense_Mutation SNP A 11LU016_T 2234350 44341217 20102950 537 589 NEURL2 0 . GRCh38 20 45890671 45890671 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.321G>T p.= p.L107L ENST00000372518 1/2 260 207 53 279 279 0 strelka-varscan-mutect NEURL2,synonymous_variant,p.=,ENST00000372518,NM_080749.3;CTSA,upstream_gene_variant,,ENST00000372484,NM_000308.2;CTSA,upstream_gene_variant,,ENST00000372459,;CTSA,upstream_gene_variant,,ENST00000191018,NM_001127695.1;CTSA,upstream_gene_variant,,ENST00000354880,NM_001167594.1;SPATA25,upstream_gene_variant,,ENST00000372519,NM_080608.3;CTSA,upstream_gene_variant,,ENST00000419493,;NEURL2,upstream_gene_variant,,ENST00000545238,;CTSA,upstream_gene_variant,,ENST00000607482,;RP3-337O18.9,downstream_gene_variant,,ENST00000607703,;CTSA,5_prime_UTR_variant,,ENST00000606788,;CTSA,upstream_gene_variant,,ENST00000493522,;CTSA,upstream_gene_variant,,ENST00000485627,;CTSA,upstream_gene_variant,,ENST00000606066,;CTSA,upstream_gene_variant,,ENST00000607212,;CTSA,upstream_gene_variant,,ENST00000606394,;CTSA,upstream_gene_variant,,ENST00000607814,;CTSA,upstream_gene_variant,,ENST00000606782,;CTSA,upstream_gene_variant,,ENST00000607841,;CTSA,upstream_gene_variant,,ENST00000480961,; A ENST00000372518 Transcript synonymous_variant 617/1278 321/858 107/285 L ctG/ctT 1 -1 NEURL2 HGNC HGNC:16156 protein_coding YES CCDS13384.1 ENSP00000361596 Q9BR09 UPI000003499E NM_080749.3 1/2 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,SMART_domains:SM00588 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 45890671 45890671 C A 1 0 0 0 0 0 0 0 1 10382 581 21 2 2 NEURL2 20 45890671 Silent SNP C 11LU016_T 1549454 45890671 18553496 538 590 SPATA2 0 . GRCh38 20 49906166 49906166 + Missense_Mutation SNP G G C novel 11LU016_T 11LU016_N G G c.1016C>G p.Thr339Arg p.T339R ENST00000422556 3/3 46 41 5 45 45 0 strelka-varscan-mutect SPATA2,missense_variant,p.Thr339Arg,ENST00000422556,NM_001135773.1;SPATA2,missense_variant,p.Thr339Arg,ENST00000289431,NM_006038.3; C ENST00000422556 Transcript missense_variant 1366/4138 1016/1563 339/520 T/R aCa/aGa 1 -1 SPATA2 HGNC HGNC:14681 protein_coding YES CCDS13422.1 ENSP00000416799 Q9UM82 UPI000013557F NM_001135773.1 deleterious(0) 3/3 hmmpanther:PTHR15326,hmmpanther:PTHR15326:SF8 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -12.70452 1 1 1 1 0 C 3 2 2 49906166 49906166 G C 1 0 0 0 0 1 0 0 0 15335 1377 48 4 4 SPATA2 20 49906166 Missense_Mutation SNP G 11LU016_T 4015495 49906166 14538001 539 591 CASS4 0 . GRCh38 20 56458612 56458612 + Missense_Mutation SNP C C A rs767407539 11LU016_T 11LU016_N C C c.2226C>A p.Ser742Arg p.S742R ENST00000360314 7/7 193 177 16 209 208 1 strelka-varscan-mutect CASS4,missense_variant,p.Ser305Arg,ENST00000434344,NM_001164115.1;CASS4,missense_variant,p.Ser742Arg,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,downstream_gene_variant,,ENST00000497244,;RPL39P,downstream_gene_variant,,ENST00000450188,; A ENST00000360314 Transcript missense_variant 2451/2619 2226/2361 742/786 S/R agC/agA rs767407539 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0.01) 7/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654,Pfam_domain:PF12026 MODERATE 1 SNV 1 1 PASS rs767407539 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 56458612 56458612 C A 1 0 0 0 0 1 0 0 0 2382 738 26 2 2 CASS4 20 56458612 Missense_Mutation SNP C 11LU016_T 6552446 56458612 7985555 540 592 C20orf85 0 . GRCh38 20 58155543 58155543 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.226G>T p.Val76Leu p.V76L ENST00000371168 3/4 224 209 15 238 236 2 strelka-varscan-mutect C20orf85,missense_variant,p.Val76Leu,ENST00000371168,NM_178456.2; T ENST00000371168 Transcript missense_variant 287/803 226/414 76/137 V/L Gtg/Ttg 1 1 C20orf85 HGNC HGNC:16216 protein_coding YES CCDS13465.1 ENSP00000360210 Q9H1P6 UPI00001285EF NM_178456.2 tolerated(0.1) 3/4 PD297655,Pfam_domain:PF14945,hmmpanther:PTHR31909,hmmpanther:PTHR31909:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 58155543 58155543 G T 1 0 0 0 0 1 0 0 0 2010 1261 44 2 2 C20orf85 20 58155543 Missense_Mutation SNP G 11LU016_T 1696931 58155543 6288624 541 593 CDH4 0 . GRCh38 20 61928338 61928338 + Silent SNP C C A rs371805176 11LU016_T 11LU016_N C C c.1920C>A p.= p.V640V ENST00000614565 12/16 591 490 101 480 480 0 strelka-varscan-mutect CDH4,synonymous_variant,p.=,ENST00000614565,NM_001794.4;CDH4,synonymous_variant,p.=,ENST00000611855,;CDH4,synonymous_variant,p.=,ENST00000543233,NM_001252338.2,NM_001252339.2; A ENST00000614565 Transcript synonymous_variant 2008/6513 1920/2751 640/916 V gtC/gtA rs371805176 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 12/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs371805176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 61928338 61928338 C A 1 0 0 0 0 0 0 0 1 2815 871 31 1 1 CDH4 20 61928338 Silent SNP C 11LU016_T 3772795 61928338 2515829 542 594 HELZ2 0 . GRCh38 20 63566892 63566892 + Missense_Mutation SNP C C G rs200398296 11LU016_T 11LU016_N C C c.2466G>C p.Trp822Cys p.W822C ENST00000467148 6/19 102 81 21 99 99 0 strelka-varscan-mutect HELZ2,missense_variant,p.Trp822Cys,ENST00000467148,NM_001037335.2;HELZ2,missense_variant,p.Trp253Cys,ENST00000427522,NM_033405.3;HELZ2,downstream_gene_variant,,ENST00000479540,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,downstream_gene_variant,,ENST00000370082,; G ENST00000467148 Transcript missense_variant 2536/8064 2466/7950 822/2649 W/C tgG/tgC rs200398296 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 deleterious(0) 6/19 Pfam_domain:PF13087,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs200398296 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 63566892 63566892 C G 1 0 0 0 0 1 0 0 0 6932 624 22 4 4 HELZ2 20 63566892 Missense_Mutation SNP C 11LU016_T 1638554 63566892 877275 543 595 NPBWR2 0 . GRCh38 20 64106520 64106520 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.312G>T p.Glu104Asp p.E104D ENST00000369768 1/1 187 147 40 192 192 0 strelka-varscan-mutect NPBWR2,missense_variant,p.Glu104Asp,ENST00000369768,NM_005286.2; A ENST00000369768 Transcript missense_variant 652/1352 312/1002 104/333 E/D gaG/gaT 1 -1 NPBWR2 HGNC HGNC:4530 protein_coding YES CCDS13557.1 ENSP00000358783 P48146 UPI000013CBB3 NM_005286.2 tolerated(0.81) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF18,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01855 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 64106520 64106520 C A 1 0 0 0 0 1 0 0 0 10617 796 28 2 2 NPBWR2 20 64106520 Missense_Mutation SNP C 11LU016_T 539628 64106520 337647 544 596 GART 0 . GRCh38 21 33534679 33534679 + Missense_Mutation SNP T T A rs755704506 11LU016_T 11LU016_N T T c.316A>T p.Ser106Cys p.S106C ENST00000381831 4/22 98 86 12 124 124 0 strelka-varscan-mutect GART,missense_variant,p.Ser106Cys,ENST00000381831,NM_001136005.1;GART,missense_variant,p.Ser106Cys,ENST00000381839,NM_001136006.1;GART,missense_variant,p.Ser106Cys,ENST00000381815,NM_000819.4;GART,missense_variant,p.Ser106Cys,ENST00000361093,NM_175085.2;GART,missense_variant,p.Ser106Cys,ENST00000430874,;GART,missense_variant,p.Ser106Cys,ENST00000426819,;GART,missense_variant,p.Ser106Cys,ENST00000441403,;GART,missense_variant,p.Ser106Cys,ENST00000438059,;GART,non_coding_transcript_exon_variant,,ENST00000497313,;GART,missense_variant,p.Ser106Cys,ENST00000424203,;GART,non_coding_transcript_exon_variant,,ENST00000476524,;GART,upstream_gene_variant,,ENST00000366093,;GART,upstream_gene_variant,,ENST00000488791,;GART,upstream_gene_variant,,ENST00000466882,; A ENST00000381831 Transcript missense_variant 580/3490 316/3033 106/1010 S/C Agc/Tgc rs755704506 1 -1 GART HGNC HGNC:4163 protein_coding YES CCDS13627.1 ENSP00000371253 P22102 UPI0000132A2A NM_001136005.1 deleterious(0) 4/22 HAMAP:MF_00138,hmmpanther:PTHR10520:SF38,hmmpanther:PTHR10520,TIGRFAM_domain:TIGR00877,Pfam_domain:PF01071,SMART_domains:SM01209,Superfamily_domains:SSF56059 MODERATE 1 SNV 1 1 PASS rs755704506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 33534679 33534679 T A 1 0 0 0 0 1 0 0 0 6113 1580 55 4 4 GART 21 33534679 Missense_Mutation SNP T 11LU016_T 33534679 13175304 545 597 COL18A1 0 . GRCh38 21 45455962 45455962 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.432C>A p.= p.V144V ENST00000359759 1/41 293 243 50 291 291 0 strelka-varscan-mutect COL18A1,synonymous_variant,p.=,ENST00000359759,NM_130444.2;COL18A1,synonymous_variant,p.=,ENST00000355480,NM_030582.3;COL18A1,intron_variant,,ENST00000400337,NM_130445.3; A ENST00000359759 Transcript synonymous_variant 432/6586 432/5265 144/1754 V gtC/gtA 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 1/41 Pfam_domain:PF06121 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 45455962 45455962 C A 1 0 0 0 0 0 0 0 1 3463 842 30 2 2 COL18A1 21 45455962 Silent SNP C 11LU016_T 11921283 45455962 1254021 546 598 GAB4 0 . GRCh38 22 16964839 16964839 + Missense_Mutation SNP G G T rs769919538 11LU016_T 11LU016_N G G c.1403C>A p.Ser468Tyr p.S468Y ENST00000400588 8/10 109 102 7 133 133 0 strelka-varscan-mutect GAB4,missense_variant,p.Ser468Tyr,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,downstream_gene_variant,,ENST00000523144,;GAB4,downstream_gene_variant,,ENST00000520505,;GAB4,3_prime_UTR_variant,,ENST00000465611,; T ENST00000400588 Transcript missense_variant 1511/2630 1403/1725 468/574 S/Y tCc/tAc rs769919538 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 tolerated(0.1) 8/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs769919538 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 16964839 16964839 G T 1 0 0 0 0 1 0 0 0 6022 1174 41 2 2 GAB4 22 16964839 Missense_Mutation SNP G 11LU016_T 16964839 33853629 547 599 MICAL3 0 . GRCh38 22 17818128 17818128 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.4533G>T p.Lys1511Asn p.K1511N ENST00000441493 26/32 395 332 63 364 364 0 strelka-varscan-mutect MICAL3,missense_variant,p.Lys1511Asn,ENST00000441493,NM_015241.2;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,; A ENST00000441493 Transcript missense_variant 4886/9445 4533/6009 1511/2002 K/N aaG/aaT 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 deleterious_low_confidence(0) 26/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF239 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 17818128 17818128 C A 1 0 0 0 0 1 0 0 0 9528 564 20 2 2 MICAL3 22 17818128 Missense_Mutation SNP C 11LU016_T 853289 17818128 33000340 548 600 DGCR2 0 . GRCh38 22 19068165 19068165 + Missense_Mutation SNP C C A rs759947288 11LU016_T 11LU016_N C C c.263G>T p.Arg88Leu p.R88L ENST00000263196 3/10 71 62 9 107 107 0 strelka-varscan-mutect DGCR2,missense_variant,p.Arg88Leu,ENST00000545799,;DGCR2,missense_variant,p.Arg88Leu,ENST00000263196,NM_005137.2,NM_001184781.1;DGCR2,missense_variant,p.Arg47Leu,ENST00000537045,NM_001173534.1,NM_001173533.1;DGCR2,upstream_gene_variant,,ENST00000473832,;DGCR2,upstream_gene_variant,,ENST00000608548,;DGCR2,5_prime_UTR_variant,,ENST00000389262,; A ENST00000263196 Transcript missense_variant 511/4480 263/1653 88/550 R/L cGg/cTg rs759947288 1 -1 DGCR2 HGNC HGNC:2845 protein_coding YES CCDS33598.1 ENSP00000263196 P98153 UPI0000001613 NM_005137.2,NM_001184781.1 deleterious_low_confidence(0.01) 3/10 hmmpanther:PTHR15256 MODERATE 1 SNV 1 1 PASS rs759947288 . 0 204 5 0 0 0 0 0 -19.65625 1 1 1 1 0 A 3 1 2 19068165 19068165 C A 1 0 0 0 0 1 0 0 0 4268 652 23 1 1 DGCR2 22 19068165 Missense_Mutation SNP C 11LU016_T 1250037 19068165 31750303 549 601 AIFM3 0 . GRCh38 22 20976262 20976262 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.855C>A p.= p.G285G ENST00000399167 10/21 266 252 14 358 358 0 strelka-varscan-mutect AIFM3,synonymous_variant,p.=,ENST00000399167,NM_144704.2;AIFM3,synonymous_variant,p.=,ENST00000440238,;AIFM3,synonymous_variant,p.=,ENST00000405089,NM_001146288.1;AIFM3,synonymous_variant,p.=,ENST00000399163,NM_001018060.2;AIFM3,downstream_gene_variant,,ENST00000434714,;AIFM3,downstream_gene_variant,,ENST00000441376,;AIFM3,non_coding_transcript_exon_variant,,ENST00000465606,;AIFM3,non_coding_transcript_exon_variant,,ENST00000483107,;LZTR1,upstream_gene_variant,,ENST00000479606,;AIFM3,downstream_gene_variant,,ENST00000468124,;AIFM3,downstream_gene_variant,,ENST00000496097,;AIFM3,upstream_gene_variant,,ENST00000486003,;AIFM3,downstream_gene_variant,,ENST00000417515,;AIFM3,downstream_gene_variant,,ENST00000484206,;AIFM3,downstream_gene_variant,,ENST00000472575,;AIFM3,downstream_gene_variant,,ENST00000467926,;AIFM3,downstream_gene_variant,,ENST00000426113,; A ENST00000399167 Transcript synonymous_variant 1095/2387 855/1818 285/605 G ggC/ggA 1 1 AIFM3 HGNC HGNC:26398 protein_coding YES CCDS13786.1 ENSP00000382120 Q96NN9 UPI0000071A61 NM_144704.2 10/21 Gene3D:3.50.50.60,Pfam_domain:PF07992,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF174,Superfamily_domains:SSF51905 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 20976262 20976262 C A 1 0 0 0 0 0 0 0 1 505 784 28 2 2 AIFM3 22 20976262 Silent SNP C 11LU016_T 1908097 20976262 29842206 550 602 PRAME 0 . GRCh38 22 22548152 22548152 + Missense_Mutation SNP A A C 11LU016_T 11LU016_N A A c.1445T>G p.Leu482Arg p.L482R ENST00000543184 5/5 161 147 14 237 237 0 strelka-mutect PRAME,missense_variant,p.Leu482Arg,ENST00000543184,NM_206953.2;PRAME,missense_variant,p.Leu482Arg,ENST00000398741,NM_206955.2;PRAME,missense_variant,p.Leu482Arg,ENST00000398743,NM_206954.2,NM_001291715.1,NM_006115.4;PRAME,missense_variant,p.Leu482Arg,ENST00000405655,NM_206956.2,NM_001291716.1;PRAME,missense_variant,p.Leu482Arg,ENST00000402697,;PRAME,downstream_gene_variant,,ENST00000439106,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000420709,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,downstream_gene_variant,,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000485532,;PRAME,downstream_gene_variant,,ENST00000476336,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,; C ENST00000543184 Transcript missense_variant 2308/2758 1445/1530 482/509 L/R cTt/cGt COSM5172792 1 -1 PRAME HGNC HGNC:9336 protein_coding YES CCDS13801.1 ENSP00000445675 P78395 A0A024R1E6 UPI0000000DDA NM_206953.2 deleterious(0) 5/5 hmmpanther:PTHR14224:SF4,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 22548152 22548152 A C 1 0 0 0 0 1 0 0 0 12553 72 3 5 5 PRAME 22 22548152 Missense_Mutation SNP A 11LU016_T 1571890 22548152 28270316 551 603 SEZ6L 0 . GRCh38 22 26299066 26299066 + Silent SNP C C A novel 11LU016_T 11LU016_N C C c.1245C>A p.= p.A415A ENST00000248933 5/17 69 62 7 102 102 0 strelka-varscan-mutect SEZ6L,synonymous_variant,p.=,ENST00000529632,NM_001184775.1;SEZ6L,synonymous_variant,p.=,ENST00000360929,NM_001184776.1;SEZ6L,synonymous_variant,p.=,ENST00000404234,NM_001184773.1;SEZ6L,synonymous_variant,p.=,ENST00000402979,;SEZ6L,synonymous_variant,p.=,ENST00000248933,NM_021115.4;SEZ6L,synonymous_variant,p.=,ENST00000629590,NM_001184774.1;SEZ6L,synonymous_variant,p.=,ENST00000403121,;SEZ6L,synonymous_variant,p.=,ENST00000343706,NM_001184777.1; A ENST00000248933 Transcript synonymous_variant 1340/3248 1245/3075 415/1024 A gcC/gcA 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 5/17 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.67218 1 1 1 1 0 A 2 1 2 26299066 26299066 C A 1 0 0 0 0 0 0 0 1 14422 610 22 2 2 SEZ6L 22 26299066 Silent SNP C 11LU016_T 3750914 26299066 24519402 552 604 SLC5A4 0 . GRCh38 22 32255291 32255291 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.39C>A p.= p.T13T ENST00000266086 1/15 174 156 18 196 196 0 strelka-varscan-mutect SLC5A4,synonymous_variant,p.=,ENST00000266086,NM_014227.2;RP1-90G24.10,intron_variant,,ENST00000434942,; T ENST00000266086 Transcript synonymous_variant 51/2030 39/1980 13/659 T acC/acA 1 -1 SLC5A4 HGNC HGNC:11039 protein_coding YES CCDS13903.1 ENSP00000266086 Q9NY91 UPI00001359F4 NM_014227.2 1/15 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 2 32255291 32255291 G T 1 0 0 0 0 0 0 0 1 14950 1219 43 2 2 SLC5A4 22 32255291 Silent SNP G 11LU016_T 5956225 32255291 18563177 553 605 RFPL3 0 . GRCh38 22 32358126 32358126 + Missense_Mutation SNP C C A rs775799598 11LU016_T 11LU016_N C C c.55C>A p.Leu19Ile p.L19I ENST00000249007 1/2 128 112 16 179 179 0 strelka-varscan-mutect RFPL3,missense_variant,p.Leu19Ile,ENST00000249007,NM_001098535.1;RFPL3,intron_variant,,ENST00000397468,NM_006604.2;RFPL3S,downstream_gene_variant,,ENST00000400234,;RFPL3S,downstream_gene_variant,,ENST00000382084,;RFPL3S,downstream_gene_variant,,ENST00000577714,;RFPL3S,downstream_gene_variant,,ENST00000382086,;RFPL3S,downstream_gene_variant,,ENST00000621921,;RFPL3-AS1_1,upstream_gene_variant,,ENST00000617561,;RFPL3S,downstream_gene_variant,,ENST00000461833,;IGLCOR22-2,upstream_gene_variant,,ENST00000605398,; A ENST00000249007 Transcript missense_variant 260/1488 55/954 19/317 L/I Ctt/Att rs775799598 1 1 RFPL3 HGNC HGNC:9980 protein_coding YES CCDS43011.1 ENSP00000249007 O75679 UPI000013CC68 NM_001098535.1 tolerated_low_confidence(0.35) 1/2 MODERATE 1 SNV 1 1 PASS rs775799598 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 32358126 32358126 C A 1 0 0 0 0 1 0 0 0 13426 913 32 2 2 RFPL3 22 32358126 Missense_Mutation SNP C 11LU016_T 102835 32358126 18460342 554 606 PLA2G6 0 . GRCh38 22 38148550 38148551 + Frame_Shift_Ins INS - - A novel 11LU016_T 11LU016_N - - c.282dupT p.Pro95SerfsTer20 p.P95Sfs*20 ENST00000435484 3/4 150 129 21 235 235 0 sindel-varindel PLA2G6,frameshift_variant,p.Pro95SerfsTer20,ENST00000435484,;PLA2G6,frameshift_variant,p.Pro95SerfsTer20,ENST00000447598,;PLA2G6,frameshift_variant,p.Pro95SerfsTer20,ENST00000417303,;PLA2G6,intron_variant,,ENST00000332509,NM_003560.2;PLA2G6,intron_variant,,ENST00000335539,NM_001004426.1;PLA2G6,intron_variant,,ENST00000402064,NM_001199562.1;PLA2G6,intron_variant,,ENST00000430886,;PLA2G6,intron_variant,,ENST00000436218,;PLA2G6,intron_variant,,ENST00000455341,;PLA2G6,upstream_gene_variant,,ENST00000427114,;CTA-228A9.4,non_coding_transcript_exon_variant,,ENST00000624072,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000420435,;PLA2G6,intron_variant,,ENST00000479641,;PLA2G6,intron_variant,,ENST00000445591,;PLA2G6,intron_variant,,ENST00000452972,;PLA2G6,intron_variant,,ENST00000426674,;PLA2G6,intron_variant,,ENST00000471636,; A ENST00000435484 Transcript frameshift_variant 492-493/612 282-283/300 94-95/99 -/X -/T 1 -1 PLA2G6 HGNC HGNC:9039 protein_coding ENSP00000413597 F2Z3G2 UPI000173A307 3/4 Low_complexity_(Seg):seg HIGH insertion 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 2 38148550 38148550 - A 1 0 1 1 0 0 0 0 0 12104 1174 41 0 0 PLA2G6 22 38148550 Frame_Shift_Ins INS - 11LU016_T 5790424 38148550 12669918 555 607 TTLL1 0 . GRCh38 22 43051831 43051831 + Silent SNP G G A rs756215079 11LU016_T 11LU016_N G G c.948C>T p.= p.I316I ENST00000266254 9/11 237 207 30 264 264 0 strelka-varscan-mutect TTLL1,synonymous_variant,p.=,ENST00000266254,NM_012263.4;TTLL1,intron_variant,,ENST00000331018,;AL022476.2,intron_variant,,ENST00000443063,;TTLL1,3_prime_UTR_variant,,ENST00000440761,;TTLL1,3_prime_UTR_variant,,ENST00000439248,; A ENST00000266254 Transcript synonymous_variant 1189/1645 948/1272 316/423 I atC/atT rs756215079,COSM1495272 1 -1 TTLL1 HGNC HGNC:1312 protein_coding YES CCDS14043.1 ENSP00000266254 O95922 A0A024R4U6 UPI00001377A7 NM_012263.4 9/11 Pfam_domain:PF03133,PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF31,Superfamily_domains:SSF56059 0,1 LOW 1 SNV 1 0,1 1 PASS rs756215079 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 2 43051831 43051831 G A 1 0 0 0 0 0 0 0 1 17234 1048 37 1 1 TTLL1 22 43051831 Silent SNP G 11LU016_T 4903281 43051831 7766637 556 608 EFCAB6 0 . GRCh38 22 43683749 43683749 + Missense_Mutation SNP T T A 11LU016_T 11LU016_N T T c.1249A>T p.Thr417Ser p.T417S ENST00000262726 12/32 95 79 16 83 83 0 strelka-varscan-mutect EFCAB6,missense_variant,p.Thr417Ser,ENST00000262726,NM_022785.3;EFCAB6,missense_variant,p.Thr265Ser,ENST00000396231,NM_198856.2;EFCAB6,non_coding_transcript_exon_variant,,ENST00000404038,; A ENST00000262726 Transcript missense_variant,splice_region_variant 1503/4869 1249/4506 417/1501 T/S Act/Tct COSM244204 1 -1 EFCAB6 HGNC HGNC:24204 protein_coding YES CCDS14049.1 ENSP00000262726 Q5THR3 UPI0000225CD7 NM_022785.3 tolerated(0.74) 12/32 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,Superfamily_domains:SSF47473 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 43683749 43683749 T A 1 0 0 0 0 1 0 0 0 4773 1710 59 4 4 EFCAB6 22 43683749 Missense_Mutation SNP T 11LU016_T 631918 43683749 7134719 557 609 PNPLA5 0 . GRCh38 22 43891107 43891107 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.381C>A p.= p.R127R ENST00000216177 2/9 76 68 8 106 106 0 strelka-varscan-mutect PNPLA5,synonymous_variant,p.=,ENST00000216177,NM_138814.3;PNPLA5,synonymous_variant,p.=,ENST00000597664,;PNPLA5,synonymous_variant,p.=,ENST00000438734,;PNPLA5,intron_variant,,ENST00000593866,NM_001177675.1;PNPLA5,intron_variant,,ENST00000381198,; T ENST00000216177 Transcript synonymous_variant 514/2539 381/1290 127/429 R cgC/cgA 1 -1 PNPLA5 HGNC HGNC:24888 protein_coding YES CCDS14053.1 ENSP00000216177 Q7Z6Z6 UPI000006D0C8 NM_138814.3 2/9 Pfam_domain:PF01734,hmmpanther:PTHR12406,hmmpanther:PTHR12406:SF4,Superfamily_domains:SSF52151 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.44094 1 1 1 1 0 T 2 4 2 43891107 43891107 G T 1 0 0 0 0 0 0 0 1 12276 1306 46 2 2 PNPLA5 22 43891107 Silent SNP G 11LU016_T 207358 43891107 6927361 558 610 PHF21B 0 . GRCh38 22 44920399 44920399 + Missense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.212A>C p.Gln71Pro p.Q71P ENST00000313237 3/13 65 57 8 124 124 0 strelka-varscan-mutect PHF21B,missense_variant,p.Gln71Pro,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Gln59Pro,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Gln71Pro,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Gln59Pro,ENST00000420689,;PHF21B,splice_region_variant,,ENST00000403565,NM_001284296.1;PHF21B,intron_variant,,ENST00000414269,;PHF21B,splice_region_variant,,ENST00000490679,;PHF21B,splice_region_variant,,ENST00000460507,;PHF21B,splice_region_variant,,ENST00000474327,; G ENST00000313237 Transcript missense_variant,splice_region_variant 363/3671 212/1596 71/531 Q/P cAg/cCg 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious_low_confidence(0) 3/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -17.86982 0.9999971 1 1 1 0 G 3 3 2 44920399 44920399 T G 1 0 0 0 0 1 0 0 0 11920 1594 55 5 5 PHF21B 22 44920399 Missense_Mutation SNP T 11LU016_T 1029292 44920399 5898069 559 611 GTSE1 0 . GRCh38 22 46297445 46297445 + Silent SNP A A C novel 11LU016_T 11LU016_N A A c.45A>C p.= p.A15A ENST00000454366 2/12 124 110 14 192 192 0 strelka-varscan-mutect GTSE1,synonymous_variant,p.=,ENST00000454366,NM_016426.6;TTC38,downstream_gene_variant,,ENST00000381031,NM_017931.2;GTSE1-AS1,upstream_gene_variant,,ENST00000623117,;GTSE1-AS1,upstream_gene_variant,,ENST00000617229,;TTC38,downstream_gene_variant,,ENST00000451998,; C ENST00000454366 Transcript synonymous_variant 257/3112 45/2220 15/739 A gcA/gcC 1 1 GTSE1 HGNC HGNC:13698 protein_coding YES CCDS14074.2 ENSP00000415430 Q9NYZ3 UPI000021D19B NM_016426.6 2/12 hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF10 LOW 1 SNV 1 1 PASS rs1037278148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 2 46297445 46297445 A C 1 0 0 0 0 0 0 0 1 6766 175 7 5 5 GTSE1 22 46297445 Silent SNP A 11LU016_T 1377046 46297445 4521023 560 612 MXRA5 0 . GRCh38 X 3320296 3320296 + Nonsense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.5389G>T p.Gly1797Ter p.G1797* ENST00000217939 5/7 121 103 18 82 82 0 strelka-varscan-mutect MXRA5,stop_gained,p.Gly1797Ter,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript stop_gained 5544/9793 5389/8487 1797/2828 G/* Gga/Tga COSM3973609,COSM3973610 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 2 3320296 3320296 C A 1 0 0 0 0 0 1 0 0 10002 632 22 2 2 MXRA5 23 3320296 Nonsense_Mutation SNP C 11LU016_T 3320296 152720599 561 613 GPR143 0 . GRCh38 X 9765638 9765638 + Frame_Shift_Del DEL G G - novel 11LU016_T 11LU016_N G G c.180delC p.Ala61ArgfsTer26 p.A61Rfs*26 ENST00000467482 1/9 15 6 9 15 15 0 sindel-varindel GPR143,frameshift_variant,p.Ala61ArgfsTer26,ENST00000467482,NM_000273.2;GPR143,intron_variant,,ENST00000447366,;GPR143,intron_variant,,ENST00000431126,; - ENST00000467482 Transcript frameshift_variant 327/1762 180/1215 60/404 P/X ccC/cc 1 -1 GPR143 HGNC HGNC:20145 protein_coding YES CCDS14134.2 ENSP00000417161 P51810 UPI0000130B4E NM_000273.2 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR15177,hmmpanther:PTHR15177:SF2,Pfam_domain:PF02101 HIGH 1 deletion 1 1 PASS . . 1 200 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 - 7 5 2 9765638 9765638 G - 1 0 1 0 1 0 0 0 0 6537 1103 39 0 0 GPR143 23 9765638 Frame_Shift_Del DEL G 11LU016_T 6445342 9765638 146275257 562 614 VEGFD 0 . GRCh38 X 15346161 15346161 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.1037A>T p.Gln346Leu p.Q346L ENST00000297904 7/7 109 103 6 94 94 0 strelka-mutect VEGFD,missense_variant,p.Gln346Leu,ENST00000297904,NM_004469.4;VEGFD,non_coding_transcript_exon_variant,,ENST00000488351,; A ENST00000297904 Transcript missense_variant 1467/2037 1037/1065 346/354 Q/L cAg/cTg 1 -1 VEGFD HGNC HGNC:3708 protein_coding YES CCDS14166.1 ENSP00000297904 O43915 UPI00000012B2 NM_004469.4 tolerated_low_confidence(0.05) 7/7 hmmpanther:PTHR12025,hmmpanther:PTHR12025:SF11 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.55759 1 1 1 1 0 A 3 1 2 15346161 15346161 T A 1 0 0 0 0 1 0 0 0 17698 1580 55 4 4 VEGFD 23 15346161 Missense_Mutation SNP T 11LU016_T 5580523 15346161 140694734 563 615 MBTPS2 0 . GRCh38 X 21882614 21882614 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1519G>T p.Ala507Ser p.A507S ENST00000379484 11/11 225 124 101 165 165 0 strelka-varscan-mutect MBTPS2,missense_variant,p.Ala507Ser,ENST00000379484,NM_015884.3; T ENST00000379484 Transcript missense_variant 1618/4428 1519/1560 507/519 A/S Gcc/Tcc 1 1 MBTPS2 HGNC HGNC:15455 protein_coding YES CCDS14201.1 ENSP00000368798 O43462 UPI000012F5A0 NM_015884.3 tolerated(0.13) 11/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR13325:SF3,hmmpanther:PTHR13325 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 21882614 21882614 G T 1 0 0 0 0 1 0 0 0 9295 1319 46 2 2 MBTPS2 23 21882614 Missense_Mutation SNP G 11LU016_T 6536453 21882614 134158281 564 616 MAGEB5 0 . GRCh38 X 26218093 26218093 + Silent SNP C C G novel 11LU016_T 11LU016_N C C c.792C>G p.= p.L264L ENST00000602297 2/2 64 41 23 52 52 0 strelka-varscan-mutect MAGEB5,synonymous_variant,p.=,ENST00000602297,NM_001271752.1; G ENST00000602297 Transcript synonymous_variant 1039/1216 792/828 264/275 L ctC/ctG 1 1 MAGEB5 HGNC HGNC:23795 protein_coding YES CCDS65233.1 ENSP00000473493 Q9BZ81 UPI0000237754 NM_001271752.1 2/2 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF35 LOW 1 SNV 3 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 26218093 26218093 C G 1 0 0 0 0 0 0 0 1 9095 813 29 4 4 MAGEB5 23 26218093 Silent SNP C 11LU016_T 4335479 26218093 129822802 565 617 MAGEB2 0 . GRCh38 X 30218928 30218928 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.348G>T p.= p.G116G ENST00000378988 2/2 166 111 55 128 128 0 strelka-varscan-mutect MAGEB2,synonymous_variant,p.=,ENST00000378988,NM_002364.4; T ENST00000378988 Transcript synonymous_variant 449/1610 348/960 116/319 G ggG/ggT 1 1 MAGEB2 HGNC HGNC:6809 protein_coding YES CCDS14219.1 ENSP00000368273 O15479 UPI000013C683 NM_002364.4 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF22 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 30218928 30218928 G T 1 0 0 0 0 0 0 0 1 9092 1248 44 2 2 MAGEB2 23 30218928 Silent SNP G 11LU016_T 4000835 30218928 125821967 566 618 FAM47C 0 . GRCh38 X 37009148 37009148 + Silent SNP C C G novel 11LU016_T 11LU016_N C C c.738C>G p.= p.L246L ENST00000358047 1/1 272 159 113 229 229 0 strelka-varscan-mutect FAM47C,synonymous_variant,p.=,ENST00000358047,NM_001013736.2; G ENST00000358047 Transcript synonymous_variant 752/3270 738/3108 246/1035 L ctC/ctG 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 1/1 Pfam_domain:PF14642,Pfam_domain:PF14642 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 2 37009148 37009148 C G 1 0 0 0 0 0 0 0 1 5449 842 30 4 4 FAM47C 23 37009148 Silent SNP C 11LU016_T 6790220 37009148 119031747 567 619 SYTL5 0 . GRCh38 X 38120413 38120413 + Nonsense_Mutation SNP T T G novel 11LU016_T 11LU016_N T T c.1718T>G p.Leu573Ter p.L573* ENST00000456733 14/17 126 103 23 104 104 0 strelka-varscan-mutect SYTL5,stop_gained,p.Leu551Ter,ENST00000297875,NM_138780.2,NM_001163335.1;SYTL5,stop_gained,p.Leu573Ter,ENST00000456733,NM_001163334.1;RP5-972B16.2,intron_variant,,ENST00000465127,; G ENST00000456733 Transcript stop_gained 2074/4704 1718/2259 573/752 L/* tTa/tGa 1 1 SYTL5 HGNC HGNC:15589 protein_coding YES CCDS55399.1 ENSP00000395220 Q8TDW5 UPI0000F0599F NM_001163334.1 14/17 Gene3D:2.60.40.150,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF13,Superfamily_domains:SSF49562 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 2 38120413 38120413 T G 1 0 0 0 0 0 1 0 0 15880 1764 61 5 5 SYTL5 23 38120413 Nonsense_Mutation SNP T 11LU016_T 1111265 38120413 117920482 568 620 SLC9A7 0 . GRCh38 X 46648768 46648768 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1380C>A p.His460Gln p.H460Q ENST00000616978 11/17 132 86 46 140 140 0 strelka-varscan-mutect SLC9A7,missense_variant,p.His460Gln,ENST00000616978,NM_001257291.1;SLC9A7,missense_variant,p.His459Gln,ENST00000328306,NM_032591.2;SLC9A7,intron_variant,,ENST00000489574,;PGAM1P7,upstream_gene_variant,,ENST00000413837,; T ENST00000616978 Transcript missense_variant 1523/10024 1380/2181 460/726 H/Q caC/caA 1 -1 SLC9A7 HGNC HGNC:17123 protein_coding YES CCDS75967.1 ENSP00000480916 A0A087WXD1 UPI000258D161 NM_001257291.1 deleterious(0) 11/17 Pfam_domain:PF00999,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF62,TIGRFAM_domain:TIGR00840,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 46648768 46648768 G T 1 0 0 0 0 1 0 0 0 15001 1368 48 2 2 SLC9A7 23 46648768 Missense_Mutation SNP G 11LU016_T 8528355 46648768 109392127 569 621 AR 0 . GRCh38 X 67680735 67680735 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.1784A>G p.Asn595Ser p.N595S ENST00000612010 3/6 84 76 8 65 65 0 strelka-varscan-mutect AR,missense_variant,p.Asn595Ser,ENST00000612010,;AR,intron_variant,,ENST00000612452,;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000504326,;AR,intron_variant,,ENST00000613054,;AR,intron_variant,,ENST00000396043,NM_001011645.2;AR,intron_variant,,ENST00000513847,;AR,missense_variant,p.Asn595Ser,ENST00000514029,; G ENST00000612010 Transcript missense_variant 2111/3896 1784/1929 595/642 N/S aAc/aGc 1 1 AR HGNC HGNC:644 protein_coding ENSP00000482407 A0A087WZ66 UPI0004E4CA27 deleterious_low_confidence(0.04) 3/6 SMART_domains:SM00399 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 67680735 67680735 A G 1 0 0 0 0 1 0 0 0 958 43 2 5 5 AR 23 67680735 Missense_Mutation SNP A 11LU016_T 21031967 67680735 88360160 570 622 CHIC1 0 . GRCh38 X 73584504 73584504 + Missense_Mutation SNP T T C novel 11LU016_T 11LU016_N T T c.439T>C p.Cys147Arg p.C147R ENST00000373502 3/6 139 131 8 75 75 0 strelka-varscan-mutect CHIC1,missense_variant,p.Cys147Arg,ENST00000373504,NM_001300884.1;CHIC1,missense_variant,p.Cys147Arg,ENST00000373502,NM_001039840.2;CHIC1,missense_variant,p.Cys140Arg,ENST00000498407,;CHIC1,3_prime_UTR_variant,,ENST00000498318,; C ENST00000373502 Transcript missense_variant 516/4158 439/675 147/224 C/R Tgt/Cgt 1 1 CHIC1 HGNC HGNC:1934 protein_coding YES CCDS35335.2 ENSP00000362601 Q5VXU3 UPI0000160F74 NM_001039840.2 deleterious(0) 3/6 Pfam_domain:PF10256,hmmpanther:PTHR13005,hmmpanther:PTHR13005:SF2,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 2 73584504 73584504 T C 1 0 0 0 0 1 0 0 0 3102 1696 59 5 5 CHIC1 23 73584504 Missense_Mutation SNP T 11LU016_T 5903769 73584504 82456391 571 623 UPRT 0 . GRCh38 X 75274348 75274348 + Frame_Shift_Del DEL G G - novel 11LU016_T 11LU016_N G G c.95delG p.Gly32AlafsTer3 p.G32Afs*3 ENST00000373383 1/7 87 71 16 73 73 0 sindel-varindel-pindel UPRT,frameshift_variant,p.Gly32AlafsTer3,ENST00000373379,NM_001307944.1;UPRT,frameshift_variant,p.Gly32AlafsTer3,ENST00000373383,NM_145052.3;UPRT,upstream_gene_variant,,ENST00000530743,;UPRT,non_coding_transcript_exon_variant,,ENST00000531704,;UPRT,frameshift_variant,p.Gly32AlafsTer3,ENST00000462237,;UPRT,frameshift_variant,p.Gly32AlafsTer3,ENST00000373373,; - ENST00000373383 Transcript frameshift_variant 261/2186 94/930 32/309 G/X Ggc/gc 1 1 UPRT HGNC HGNC:28334 protein_coding YES CCDS14429.1 ENSP00000362481 Q96BW1 A8KAF9 UPI000004B62E NM_145052.3 1/7 HIGH 1 deletion 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 75274348 75274348 G - 1 0 1 0 1 0 0 0 0 17540 1348 47 0 0 UPRT 23 75274348 Frame_Shift_Del DEL G 11LU016_T 1689844 75274348 80766547 572 624 PCDH11X 0 . GRCh38 X 91877916 91877916 + Missense_Mutation SNP G G T 11LU016_T 11LU016_N G G c.1676G>T p.Ser559Ile p.S559I ENST00000373094 2/7 296 277 19 218 218 0 varscan-mutect PCDH11X,missense_variant,p.Ser559Ile,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Ser559Ile,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Ser559Ile,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Ser559Ile,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Ser559Ile,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Ser559Ile,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Ser559Ile,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 2521/9179 1676/4044 559/1347 S/I aGc/aTc COSM125152,COSM125153 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 tolerated(0.09) 2/7 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 91877916 91877916 G T 1 0 0 0 0 1 0 0 0 11595 971 34 2 2 PCDH11X 23 91877916 Missense_Mutation SNP G 11LU016_T 16603568 91877916 64162979 573 625 TRPC5 0 . GRCh38 X 111847421 111847421 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.1393C>A p.Pro465Thr p.P465T ENST00000262839 6/11 69 47 22 56 56 0 strelka-varscan-mutect TRPC5,missense_variant,p.Pro465Thr,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript missense_variant 2312/5839 1393/2922 465/973 P/T Cca/Aca 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 deleterious(0.01) 6/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 111847421 111847421 G T 1 0 0 0 0 1 0 0 0 17087 1174 41 2 2 TRPC5 23 111847421 Missense_Mutation SNP G 11LU016_T 19969505 111847421 44193474 574 626 TRPC5 0 . GRCh38 X 111912741 111912741 + Silent SNP G G A 11LU016_T 11LU016_N G G c.450C>T p.= p.A150A ENST00000262839 3/11 113 104 9 57 57 0 strelka-mutect TRPC5,synonymous_variant,p.=,ENST00000262839,NM_012471.2; A ENST00000262839 Transcript synonymous_variant 1369/5839 450/2922 150/973 A gcC/gcT COSM5513851 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 3/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,SMART_domains:SM00248,Superfamily_domains:SSF48403 1 LOW 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.0484 1 1 1 1 0 A 2 1 2 111912741 111912741 G A 1 0 0 0 0 0 0 0 1 17087 1219 43 3 3 TRPC5 23 111912741 Silent SNP G 11LU016_T 65320 111912741 44128154 575 627 HTR2C 0 . GRCh38 X 114731420 114731420 + Frame_Shift_Del DEL C C - novel 11LU016_T 11LU016_N C C c.162delC p.Trp55GlyfsTer9 p.W55Gfs*9 ENST00000276198 4/6 148 75 73 143 143 0 sindel-varindel-pindel HTR2C,frameshift_variant,p.Trp55GlyfsTer9,ENST00000276198,NM_000868.3;HTR2C,frameshift_variant,p.Trp55GlyfsTer9,ENST00000371950,NM_001256761.2;HTR2C,frameshift_variant,p.Trp55GlyfsTer9,ENST00000371951,NM_001256760.2; - ENST00000276198 Transcript frameshift_variant 890/4751 162/1377 54/458 N/X aaC/aa 1 1 HTR2C HGNC HGNC:5295 protein_coding YES CCDS14564.1 ENSP00000276198 P28335 UPI000014653A NM_000868.3 4/6 Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,hmmpanther:PTHR24247:SF32,hmmpanther:PTHR24247 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 2 114731420 114731420 C - 1 0 1 0 1 0 0 0 0 7339 564 20 0 0 HTR2C 23 114731420 Frame_Shift_Del DEL C 11LU016_T 2818679 114731420 41309475 576 628 NKAP 0 . GRCh38 X 119930139 119930139 + Missense_Mutation SNP T T A novel 11LU016_T 11LU016_N T T c.950A>T p.Glu317Val p.E317V ENST00000371410 8/9 74 65 9 68 68 0 strelka-varscan-mutect NKAP,missense_variant,p.Glu317Val,ENST00000371410,NM_024528.3;NKAP,non_coding_transcript_exon_variant,,ENST00000477789,;NKAP,non_coding_transcript_exon_variant,,ENST00000482407,; A ENST00000371410 Transcript missense_variant 1117/5963 950/1248 317/415 E/V gAa/gTa 1 -1 NKAP HGNC HGNC:29873 protein_coding YES CCDS14592.1 ENSP00000360464 Q8N5F7 UPI000004A07B NM_024528.3 deleterious(0) 8/9 Pfam_domain:PF06047,hmmpanther:PTHR13087,hmmpanther:PTHR13087:SF2 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.49047 0.9999999 1 1 1 0 A 3 1 2 119930139 119930139 T A 1 0 0 0 0 1 0 0 0 10474 1783 62 4 4 NKAP 23 119930139 Missense_Mutation SNP T 11LU016_T 5198719 119930139 36110756 577 629 SH2D1A 0 . GRCh38 X 124346667 124346667 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.25G>T p.Gly9Cys p.G9C ENST00000371139 1/4 345 168 177 241 240 1 strelka-varscan-mutect SH2D1A,missense_variant,p.Gly9Cys,ENST00000371139,NM_002351.4;SH2D1A,missense_variant,p.Gly9Cys,ENST00000360027,NM_001114937.2;SH2D1A,missense_variant,p.Gly9Cys,ENST00000477673,;SH2D1A,non_coding_transcript_exon_variant,,ENST00000491950,;SH2D1A,non_coding_transcript_exon_variant,,ENST00000494073,;SH2D1A,intron_variant,,ENST00000635645,;STAG2,intron_variant,,ENST00000469481,; T ENST00000371139 Transcript missense_variant 324/2450 25/387 9/128 G/C Ggc/Tgc 1 1 SH2D1A HGNC HGNC:10820 protein_coding YES CCDS14608.1 ENSP00000360181 O60880 UPI0000000D0B NM_002351.4 deleterious(0) 1/4 PROSITE_profiles:PS50001,hmmpanther:PTHR11200,Pfam_domain:PF00017,Gene3D:3.30.505.10,PIRSF_domain:PIRSF037828,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 124346667 124346667 G T 1 0 0 0 0 1 0 0 0 14488 1348 47 2 2 SH2D1A 23 124346667 Missense_Mutation SNP G 11LU016_T 4416528 124346667 31694228 578 630 TEX13C 0 . GRCh38 X 125322229 125322229 + Missense_Mutation SNP C C G novel 11LU016_T 11LU016_N C C c.2110C>G p.Pro704Ala p.P704A ENST00000632600 1/1 302 150 152 261 261 0 strelka-varscan-mutect TEX13C,missense_variant,p.Pro704Ala,ENST00000632600,NM_001195272.1;RP13-147D17.1,downstream_gene_variant,,ENST00000394467,; G ENST00000632600 Transcript missense_variant 2110/5095 2110/2982 704/993 P/A Ccc/Gcc 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 deleterious(0.04) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 125322229 125322229 C G 1 0 0 0 0 1 0 0 0 16199 623 22 4 4 TEX13C 23 125322229 Missense_Mutation SNP C 11LU016_T 975562 125322229 30718666 579 631 SMARCA1 0 . GRCh38 X 129448317 129448317 + Missense_Mutation SNP A A G novel 11LU016_T 11LU016_N A A c.3157T>C p.Phe1053Leu p.F1053L ENST00000371122 24/25 82 60 22 53 53 0 strelka-varscan-mutect SMARCA1,missense_variant,p.Phe1053Leu,ENST00000371122,NM_003069.4;SMARCA1,intron_variant,,ENST00000371123,NM_001282875.1;SMARCA1,intron_variant,,ENST00000371121,NM_001282874.1;SMARCA1,non_coding_transcript_exon_variant,,ENST00000617310,; G ENST00000371122 Transcript missense_variant 3287/4099 3157/3165 1053/1054 F/L Ttt/Ctt 1 -1 SMARCA1 HGNC HGNC:11097 protein_coding CCDS14612.1 ENSP00000360163 P28370 UPI0000161FA6 NM_003069.4 tolerated_low_confidence(0.68) 24/25 MODERATE SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 2 129448317 129448317 A G 1 0 0 0 0 1 0 0 0 15061 101 4 5 5 SMARCA1 23 129448317 Missense_Mutation SNP A 11LU016_T 4126088 129448317 26592578 580 632 MCF2 0 . GRCh38 X 139588359 139588359 + Splice_Site SNP C C A novel 11LU016_T 11LU016_N C C c.2677+1G>T p.X893_splice ENST00000519895 80 33 47 43 43 0 strelka-varscan-mutect MCF2,splice_donor_variant,,ENST00000520602,;MCF2,splice_donor_variant,,ENST00000414978,NM_001099855.1;MCF2,splice_donor_variant,,ENST00000370576,NM_005369.4;MCF2,splice_donor_variant,,ENST00000536274,NM_001171877.1;MCF2,splice_donor_variant,,ENST00000519895,NM_001171876.1;MCF2,splice_donor_variant,,ENST00000338585,NM_001171879.1;MCF2,splice_donor_variant,,ENST00000370573,NM_001171878.1;MCF2,splice_donor_variant,,ENST00000437564,;MCF2,splice_donor_variant,,ENST00000446225,; A ENST00000519895 Transcript splice_donor_variant -/3346 2677/3006 893/1001 1 -1 MCF2 HGNC HGNC:6940 protein_coding YES CCDS55517.1 ENSP00000430276 P10911 UPI0001C33995 NM_001171876.1 25/28 HIGH 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 2 139588359 139588359 C A 1 0 0 0 0 0 0 1 0 9309 521 18 2 2 MCF2 23 139588359 Splice_Site SNP C 11LU016_T 10140042 139588359 16452536 581 633 PDZD4 0 . GRCh38 X 153804577 153804577 + Missense_Mutation SNP C C A novel 11LU016_T 11LU016_N C C c.1104G>T p.Glu368Asp p.E368D ENST00000393758 8/8 142 134 8 108 108 0 strelka-varscan-mutect PDZD4,missense_variant,p.Glu368Asp,ENST00000393758,NM_001303515.1,NM_001303513.1,NM_001303512.1;PDZD4,missense_variant,p.Glu362Asp,ENST00000164640,NM_001303516.1,NM_032512.3;PDZD4,missense_variant,p.Glu253Asp,ENST00000544474,NM_001303514.1;PDZD4,downstream_gene_variant,,ENST00000475140,;PDZD4,downstream_gene_variant,,ENST00000483693,;PDZD4,downstream_gene_variant,,ENST00000484792,;PDZD4,downstream_gene_variant,,ENST00000468491,;PDZD4,downstream_gene_variant,,ENST00000480418,;PDZD4,downstream_gene_variant,,ENST00000480650,; A ENST00000393758 Transcript missense_variant 1354/3763 1104/2328 368/775 E/D gaG/gaT 1 -1 PDZD4 HGNC HGNC:21167 protein_coding YES CCDS78518.1 ENSP00000377355 Q17RL8 UPI0000211CB2 NM_001303515.1,NM_001303513.1,NM_001303512.1 deleterious(0.04) 8/8 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -15.34685 1 1 1 1 0 A 3 1 2 153804577 153804577 C A 1 0 0 0 0 1 0 0 0 11791 912 32 2 2 PDZD4 23 153804577 Missense_Mutation SNP C 11LU016_T 14216218 153804577 2236318 582 634 RPL10 0 . GRCh38 X 154399883 154399883 + Missense_Mutation SNP C C A 11LU016_T 11LU016_N C C c.271C>A p.Leu91Ile p.L91I ENST00000424325 5/7 301 268 33 242 242 0 varscan-mutect RPL10,missense_variant,p.Leu91Ile,ENST00000424325,NM_001303625.1,NM_006013.4;RPL10,missense_variant,p.Leu91Ile,ENST00000344746,NM_001303624.1,NM_001303626.1;RPL10,missense_variant,p.Leu55Ile,ENST00000618723,NM_001256580.2;RPL10,missense_variant,p.Leu91Ile,ENST00000369817,;RPL10,missense_variant,p.Leu40Ile,ENST00000406022,;RPL10,missense_variant,p.Leu74Ile,ENST00000451365,;RPL10,missense_variant,p.Leu91Ile,ENST00000436473,;RPL10,missense_variant,p.Leu1Ile,ENST00000449494,;RPL10,missense_variant,p.Leu91Ile,ENST00000458500,NM_001256577.2;RPL10,missense_variant,p.Leu1Ile,ENST00000427682,;RPL10,missense_variant,p.Leu1Ile,ENST00000428169,;DNASE1L1,downstream_gene_variant,,ENST00000369809,NM_001009932.2;DNASE1L1,downstream_gene_variant,,ENST00000369808,NM_006730.3;DNASE1L1,downstream_gene_variant,,ENST00000393638,NM_001009934.2;DNASE1L1,downstream_gene_variant,,ENST00000014935,;DNASE1L1,downstream_gene_variant,,ENST00000309585,NM_001009933.2;DNASE1L1,downstream_gene_variant,,ENST00000369807,NM_001303620.1;DNASE1L1,downstream_gene_variant,,ENST00000424626,;DNASE1L1,downstream_gene_variant,,ENST00000451865,;DNASE1L1,downstream_gene_variant,,ENST00000447892,;DNASE1L1,downstream_gene_variant,,ENST00000412184,;SNORA70,upstream_gene_variant,,ENST00000384436,;XX-FW83563B9.5,upstream_gene_variant,,ENST00000624054,;RPL10,downstream_gene_variant,,ENST00000479366,;RPL10,non_coding_transcript_exon_variant,,ENST00000482732,;RPL10,non_coding_transcript_exon_variant,,ENST00000492572,;RPL10,non_coding_transcript_exon_variant,,ENST00000489200,;RPL10,non_coding_transcript_exon_variant,,ENST00000491035,;RPL10,non_coding_transcript_exon_variant,,ENST00000485196,;RPL10,non_coding_transcript_exon_variant,,ENST00000467168,;DNASE1L1,downstream_gene_variant,,ENST00000497242,; A ENST00000424325 Transcript missense_variant 459/2318 271/645 91/214 L/I Ctc/Atc COSM1117995 1 1 RPL10 HGNC HGNC:10298 protein_coding YES CCDS14746.1 ENSP00000413436 P27635 X5D2T3 UPI0000144CE2 NM_001303625.1,NM_006013.4 tolerated(0.15) 5/7 Gene3D:3.90.1170.10,Pfam_domain:PF00252,PIRSF_domain:PIRSF005590,hmmpanther:PTHR11726,Superfamily_domains:SSF54686,TIGRFAM_domain:TIGR00279 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 154399883 154399883 C A 1 0 0 0 0 1 0 0 0 13806 797 28 2 2 RPL10 23 154399883 Missense_Mutation SNP C 11LU016_T 595306 154399883 1641012 583 635 USP9Y 0 . GRCh38 Y 12757278 12757278 + Silent SNP G G T novel 11LU016_T 11LU016_N G G c.1509G>T p.= p.V503V ENST00000338981 13/46 210 185 25 203 203 0 strelka-varscan-mutect USP9Y,synonymous_variant,p.=,ENST00000338981,NM_004654.3;USP9Y,non_coding_transcript_exon_variant,,ENST00000426564,; T ENST00000338981 Transcript synonymous_variant 2454/10036 1509/7668 503/2555 V gtG/gtT 1 1 USP9Y HGNC HGNC:12633 protein_coding YES CCDS14781.1 ENSP00000342812 O00507 UPI00001AE67D NM_004654.3 13/46 Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 2 12757278 12757278 G T 1 0 0 0 0 0 0 0 1 17634 1277 45 2 2 USP9Y 24 12757278 Silent SNP G 11LU016_T 12757278 44470137 584 636 TMSB4Y 0 . GRCh38 Y 13704360 13704360 + Missense_Mutation SNP G G A novel 11LU016_T 11LU016_N G G c.25G>A p.Glu9Lys p.E9K ENST00000284856 1/2 119 107 12 129 129 0 strelka-varscan-mutect TMSB4Y,missense_variant,p.Glu9Lys,ENST00000284856,NM_004202.2; A ENST00000284856 Transcript missense_variant 794/1669 25/135 9/44 E/K Gag/Aag 1 1 TMSB4Y HGNC HGNC:11882 protein_coding YES CCDS14786.1 ENSP00000284856 O14604 UPI0000001073 NM_004202.2 deleterious(0.04) 1/2 Gene3D:1hj0A00,PD005116,Pfam_domain:PF01290,PIRSF_domain:PIRSF001828,hmmpanther:PTHR12021,hmmpanther:PTHR12021:SF13,SMART_domains:SM00152 MODERATE 1 SNV 1 1 PASS . . 72 136 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 2 13704360 13704360 G A 1 0 0 0 0 1 0 0 0 16733 1291 45 3 3 TMSB4Y 24 13704360 Missense_Mutation SNP G 11LU016_T 947082 13704360 43523055 585 637 RPS4Y2 0 . GRCh38 Y 20759897 20759897 + Missense_Mutation SNP G G T novel 11LU016_T 11LU016_N G G c.111G>T p.Lys37Asn p.K37N ENST00000629237 3/7 115 72 43 168 168 0 strelka-varscan-mutect RPS4Y2,missense_variant,p.Lys37Asn,ENST00000629237,NM_001039567.2; T ENST00000629237 Transcript missense_variant 111/792 111/792 37/263 K/N aaG/aaT 1 1 RPS4Y2 HGNC HGNC:18501 protein_coding YES CCDS44028.1 ENSP00000486252 Q8TD47 UPI000016788E NM_001039567.2 deleterious(0) 3/7 HAMAP:MF_00485,Pfam_domain:PF08071,PIRSF_domain:PIRSF002116,hmmpanther:PTHR11581,hmmpanther:PTHR11581:SF7 MODERATE 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 2 20759897 20759897 G T 1 0 0 0 0 1 0 0 0 13902 962 34 2 2 RPS4Y2 24 20759897 Missense_Mutation SNP G 11LU016_T 7055537 20759897 36467518 586 638 PLCH2 0 . GRCh38 1 2484610 2484610 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.808G>T p.Glu270Ter p.E270* ENST00000378486 5/22 102 83 19 207 205 2 strelka-varscan-mutect PLCH2,stop_gained,p.Glu243Ter,ENST00000449969,NM_001303012.1;PLCH2,stop_gained,p.Glu270Ter,ENST00000378486,NM_014638.3,NM_001303013.1;PLCH2,stop_gained,p.Glu270Ter,ENST00000419816,;PLCH2,stop_gained,p.Glu129Ter,ENST00000278878,;PLCH2,downstream_gene_variant,,ENST00000609981,;PLCH2,non_coding_transcript_exon_variant,,ENST00000343889,; T ENST00000378486 Transcript stop_gained 1082/4837 808/4251 270/1416 E/* Gag/Tag 1 1 PLCH2 HGNC HGNC:29037 protein_coding YES CCDS59959.1 ENSP00000367747 O75038 UPI00005B72F8 NM_014638.3,NM_001303013.1 5/22 Gene3D:1.10.238.10,Pfam_domain:PF09279,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF21,Superfamily_domains:SSF47473 HIGH 1 SNV 1 1 PASS rs969425551 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 2484610 2484610 G T 1 0 0 0 0 0 1 0 0 12132 1175 41 2 2 PLCH2 1 2484610 Nonsense_Mutation SNP G 11LU022_T 2484610 246471812 1 639 CASZ1 0 . GRCh38 1 10665208 10665208 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.380A>T p.Gln127Leu p.Q127L ENST00000377022 5/21 26 21 5 51 51 0 strelka-varscan-mutect CASZ1,missense_variant,p.Gln127Leu,ENST00000377022,NM_001079843.2;CASZ1,missense_variant,p.Gln127Leu,ENST00000344008,NM_017766.4;CASZ1,non_coding_transcript_exon_variant,,ENST00000478728,;CASZ1,non_coding_transcript_exon_variant,,ENST00000496432,;CASZ1,upstream_gene_variant,,ENST00000492173,; A ENST00000377022 Transcript missense_variant 698/7936 380/5280 127/1759 Q/L cAg/cTg 1 -1 CASZ1 HGNC HGNC:26002 protein_coding YES CCDS41246.1 ENSP00000366221 Q86V15 UPI0000EBB7D6 NM_001079843.2 deleterious_low_confidence(0) 5/21 hmmpanther:PTHR12451,hmmpanther:PTHR12451:SF0 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.25667 1 1 1 1 0 A 3 1 3 10665208 10665208 T A 1 0 0 0 0 1 0 0 0 2384 1580 55 4 4 CASZ1 1 10665208 Missense_Mutation SNP T 11LU022_T 8180598 10665208 238291214 2 640 DISP3 0 . GRCh38 1 11535632 11535632 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.3804C>A p.= p.P1268P ENST00000294484 20/21 54 50 4 83 83 0 varscan-mutect DISP3,missense_variant,p.Pro155Thr,ENST00000304391,;DISP3,synonymous_variant,p.=,ENST00000294484,NM_020780.1; A ENST00000294484 Transcript synonymous_variant 3942/5215 3804/4179 1268/1392 P ccC/ccA 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 20/21 hmmpanther:PTHR10796:SF125,hmmpanther:PTHR10796,Gene3D:2j8sB01,Pfam_domain:PF03176,Superfamily_domains:SSF82866 LOW 1 SNV 1 1 PASS rs1039143602 . 0 203 6 0 0 0 0 0 -10.02074 0.9999997 1 1 1 0 A 2 1 3 11535632 11535632 C A 1 0 0 0 0 0 0 0 1 4347 623 22 2 2 DISP3 1 11535632 Silent SNP C 11LU022_T 870424 11535632 237420790 3 641 PRAMEF2 0 . GRCh38 1 12860087 12860087 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.682C>A p.Leu228Met p.L228M ENST00000240189 3/4 144 128 16 216 214 2 strelka-varscan-mutect PRAMEF2,missense_variant,p.Leu228Met,ENST00000240189,NM_023014.1; A ENST00000240189 Transcript missense_variant 769/1642 682/1425 228/474 L/M Ctg/Atg 1 1 PRAMEF2 HGNC HGNC:28841 protein_coding YES CCDS149.1 ENSP00000240189 O60811 UPI0000139EF9 NM_023014.1 deleterious(0) 3/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF20,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs1264719576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 12860087 12860087 C A 1 0 0 0 0 1 0 0 0 12562 680 24 2 2 PRAMEF2 1 12860087 Missense_Mutation SNP C 11LU022_T 1324455 12860087 236096335 4 642 IGSF21 0 . GRCh38 1 18365684 18365684 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.1002A>T p.= p.A334A ENST00000251296 6/10 59 50 9 139 139 0 strelka-varscan-mutect IGSF21,synonymous_variant,p.=,ENST00000251296,NM_032880.4;IGSF21,non_coding_transcript_exon_variant,,ENST00000412684,;IGSF21,non_coding_transcript_exon_variant,,ENST00000497331,; T ENST00000251296 Transcript synonymous_variant 1385/1943 1002/1404 334/467 A gcA/gcT 1 1 IGSF21 HGNC HGNC:28246 protein_coding YES CCDS184.1 ENSP00000251296 Q96ID5 UPI000006FCF2 NM_032880.4 6/10 hmmpanther:PTHR10489:SF442,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.97118 1 1 1 1 0 T 2 4 3 18365684 18365684 A T 1 0 0 0 0 0 0 0 1 7506 175 7 4 4 IGSF21 1 18365684 Silent SNP A 11LU022_T 5505597 18365684 230590738 5 643 HSPG2 0 . GRCh38 1 21838885 21838885 + Missense_Mutation SNP G G T rs755855793 11LU022_T 11LU022_N G G c.10090C>A p.Arg3364Ser p.R3364S ENST00000374695 74/97 135 112 23 236 236 0 strelka-varscan-mutect HSPG2,missense_variant,p.Arg3364Ser,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,missense_variant,p.Arg42Ser,ENST00000374676,;HSPG2,upstream_gene_variant,,ENST00000471322,; T ENST00000374695 Transcript missense_variant 10170/14327 10090/13176 3364/4391 R/S Cgc/Agc rs755855793 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 tolerated(0.07) 74/97 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF273,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs755855793 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 21838885 21838885 G T 1 0 0 0 0 1 0 0 0 7326 1116 39 1 1 HSPG2 1 21838885 Missense_Mutation SNP G 11LU022_T 3473201 21838885 227117537 6 644 SRRM1 0 . GRCh38 1 24649029 24649029 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.405G>T p.Gln135His p.Q135H ENST00000323848 4/17 78 60 18 180 180 0 strelka-varscan-mutect SRRM1,missense_variant,p.Gln135His,ENST00000323848,NM_005839.3;SRRM1,missense_variant,p.Gln135His,ENST00000447431,;SRRM1,missense_variant,p.Gln135His,ENST00000374389,NM_001303448.1,NM_001303449.1;SRRM1,missense_variant,p.Gln96His,ENST00000596378,;SRRM1,missense_variant,p.Gln96His,ENST00000593639,;SRRM1,splice_region_variant,,ENST00000479034,;SRRM1,splice_region_variant,,ENST00000468822,;SRRM1,splice_region_variant,,ENST00000490543,;SRRM1,splice_region_variant,,ENST00000495561,;SRRM1,splice_region_variant,,ENST00000478890,;SRRM1,upstream_gene_variant,,ENST00000496882,;SRRM1,downstream_gene_variant,,ENST00000466910,;SRRM1,upstream_gene_variant,,ENST00000470243,;SRRM1,upstream_gene_variant,,ENST00000485441,;SRRM1,splice_region_variant,,ENST00000462710,;SRRM1,splice_region_variant,,ENST00000494934,;SRRM1,downstream_gene_variant,,ENST00000600523,; T ENST00000323848 Transcript missense_variant,splice_region_variant 720/4011 405/2715 135/904 Q/H caG/caT 1 1 SRRM1 HGNC HGNC:16638 protein_coding YES CCDS255.1 ENSP00000326261 Q8IYB3 A0A0S2Z4W1 UPI000013EBEB NM_005839.3 deleterious_low_confidence(0) 4/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23148 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 24649029 24649029 G T 1 0 0 0 0 1 0 0 0 15529 1014 35 2 2 SRRM1 1 24649029 Missense_Mutation SNP G 11LU022_T 2810144 24649029 224307393 7 645 ARID1A 0 . GRCh38 1 26761433 26761433 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2211G>T p.Met737Ile p.M737I ENST00000324856 6/20 135 124 11 240 240 0 strelka-varscan-mutect ARID1A,missense_variant,p.Met737Ile,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Met356Ile,ENST00000636219,;ARID1A,missense_variant,p.Met354Ile,ENST00000430799,;ARID1A,missense_variant,p.Met354Ile,ENST00000374152,;ARID1A,missense_variant,p.Met737Ile,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Met354Ile,ENST00000615191,;ARID1A,non_coding_transcript_exon_variant,,ENST00000636958,;ARID1A,upstream_gene_variant,,ENST00000636422,;ARID1A,upstream_gene_variant,,ENST00000430291,; T ENST00000324856 Transcript missense_variant 2582/8577 2211/6858 737/2285 M/I atG/atT 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 tolerated(0.38) 6/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 26761433 26761433 G T 1 0 0 0 0 1 0 0 0 1049 1319 46 2 2 ARID1A 1 26761433 Missense_Mutation SNP G 11LU022_T 2112404 26761433 222194989 8 646 KIAA0319L 0 . GRCh38 1 35474875 35474875 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.945G>T p.Glu315Asp p.E315D ENST00000325722 5/21 95 63 32 130 130 0 strelka-varscan-mutect KIAA0319L,missense_variant,p.Glu315Asp,ENST00000325722,NM_024874.4;KIAA0319L,missense_variant,p.Glu315Asp,ENST00000426982,;KIAA0319L,missense_variant,p.Glu315Asp,ENST00000440579,;KIAA0319L,intron_variant,,ENST00000431916,;KIAA0319L,downstream_gene_variant,,ENST00000469892,;KIAA0319L,non_coding_transcript_exon_variant,,ENST00000492888,;KIAA0319L,upstream_gene_variant,,ENST00000485551,;KIAA0319L,missense_variant,p.Glu315Asp,ENST00000482929,;KIAA0319L,missense_variant,p.Glu315Asp,ENST00000478463,;KIAA0319L,3_prime_UTR_variant,,ENST00000470388,; A ENST00000325722 Transcript missense_variant 1180/4789 945/3150 315/1049 E/D gaG/gaT 1 -1 KIAA0319L HGNC HGNC:30071 protein_coding YES CCDS390.1 ENSP00000318406 Q8IZA0 UPI000003F081 NM_024874.4 tolerated(1) 5/21 hmmpanther:PTHR10083:SF166,hmmpanther:PTHR10083,SMART_domains:SM00089 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 35474875 35474875 C A 1 0 0 0 0 1 0 0 0 8081 912 32 2 2 KIAA0319L 1 35474875 Missense_Mutation SNP C 11LU022_T 8713442 35474875 213481547 9 647 ERI3 0 . GRCh38 1 44284896 44284896 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.770A>T p.Gln257Leu p.Q257L ENST00000372257 7/9 208 140 68 222 222 0 strelka-varscan-mutect ERI3,missense_variant,p.Gln257Leu,ENST00000372257,NM_001301698.1,NM_024066.2;ERI3,missense_variant,p.Gln142Leu,ENST00000372259,;ERI3,missense_variant,p.Gln96Leu,ENST00000456170,;ERI3,missense_variant,p.Gln139Leu,ENST00000452396,;ERI3,non_coding_transcript_exon_variant,,ENST00000495828,; A ENST00000372257 Transcript missense_variant 952/1684 770/1014 257/337 Q/L cAg/cTg 1 -1 ERI3 HGNC HGNC:17276 protein_coding YES CCDS30696.1 ENSP00000361331 O43414 UPI00001C1D9B NM_001301698.1,NM_024066.2 deleterious(0) 7/9 Gene3D:3.30.420.10,Pfam_domain:PF00929,hmmpanther:PTHR23044,SMART_domains:SM00479,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 44284896 44284896 T A 1 0 0 0 0 1 0 0 0 5080 1580 55 4 4 ERI3 1 44284896 Missense_Mutation SNP T 11LU022_T 8810021 44284896 204671526 10 648 MKNK1 0 . GRCh38 1 46568460 46568460 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.655T>G p.Cys219Gly p.C219G ENST00000371946 9/14 245 159 86 270 270 0 strelka-varscan-mutect MKNK1,missense_variant,p.Cys219Gly,ENST00000371946,NM_003684.5;MKNK1,missense_variant,p.Cys178Gly,ENST00000371945,NM_001135553.2;MKNK1,missense_variant,p.Cys83Gly,ENST00000341183,;MKNK1,missense_variant,p.Cys178Gly,ENST00000428112,NM_198973.3;MKNK1,missense_variant,p.Cys178Gly,ENST00000496619,;MKNK1,upstream_gene_variant,,ENST00000524749,;MKNK1-AS1,intron_variant,,ENST00000602433,;MKNK1,non_coding_transcript_exon_variant,,ENST00000342571,;MKNK1,non_coding_transcript_exon_variant,,ENST00000532783,;MKNK1,non_coding_transcript_exon_variant,,ENST00000460098,;MKNK1,upstream_gene_variant,,ENST00000470237,;MKNK1,downstream_gene_variant,,ENST00000528237,;MKNK1,3_prime_UTR_variant,,ENST00000528077,;MKNK1,3_prime_UTR_variant,,ENST00000531355,;MKNK1,non_coding_transcript_exon_variant,,ENST00000532897,;MKNK1,downstream_gene_variant,,ENST00000526513,;MKNK1,upstream_gene_variant,,ENST00000524417,; C ENST00000371946 Transcript missense_variant 819/2719 655/1398 219/465 C/G Tgt/Ggt 1 -1 MKNK1 HGNC HGNC:7110 protein_coding YES CCDS538.1 ENSP00000361014 Q9BUB5 UPI0000073749 NM_003684.5 deleterious(0) 9/14 PROSITE_profiles:PS50011,hmmpanther:PTHR24349:SF114,hmmpanther:PTHR24349,PROSITE_patterns:PS00108,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 46568460 46568460 A C 1 0 0 0 0 1 0 0 0 9571 159 6 5 5 MKNK1 1 46568460 Missense_Mutation SNP A 11LU022_T 2283564 46568460 202387962 11 649 GLIS1 0 . GRCh38 1 53520712 53520712 + Nonsense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.1123C>T p.Gln375Ter p.Q375* ENST00000312233 6/10 135 79 56 143 143 0 strelka-varscan-mutect GLIS1,stop_gained,p.Gln375Ter,ENST00000312233,NM_147193.2;GLIS1,stop_gained,p.Gln550Ter,ENST00000628545,; A ENST00000312233 Transcript stop_gained 1690/2812 1123/1863 375/620 Q/* Cag/Tag 1 -1 GLIS1 HGNC HGNC:29525 protein_coding YES CCDS582.1 ENSP00000309653 Q8NBF1 UPI000013F293 NM_147193.2 6/10 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF93 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 53520712 53520712 G A 1 0 0 0 0 0 1 0 0 6323 1328 46 3 3 GLIS1 1 53520712 Nonsense_Mutation SNP G 11LU022_T 6952252 53520712 195435710 12 650 FOXD3 0 . GRCh38 1 63323414 63323414 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.356G>T p.Gly119Val p.G119V ENST00000371116 1/1 84 49 35 123 123 0 strelka-varscan-mutect FOXD3,missense_variant,p.Gly119Val,ENST00000371116,NM_012183.2;MIR6068,downstream_gene_variant,,ENST00000615405,;FOXD3-AS1,intron_variant,,ENST00000431294,;FOXD3-AS1,intron_variant,,ENST00000427268,;FOXD3-AS1,upstream_gene_variant,,ENST00000418244,;FOXD3-AS1,upstream_gene_variant,,ENST00000449386,;FOXD3-AS1,upstream_gene_variant,,ENST00000426393,; T ENST00000371116 Transcript missense_variant 374/2086 356/1437 119/478 G/V gGg/gTg 1 1 FOXD3 HGNC HGNC:3804 protein_coding YES CCDS624.1 ENSP00000360157 Q9UJU5 UPI000012ADCB NM_012183.2 tolerated(0.06) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF162,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 63323414 63323414 G T 1 0 0 0 0 1 0 0 0 5858 1232 43 2 2 FOXD3 1 63323414 Missense_Mutation SNP G 11LU022_T 9802702 63323414 185633008 13 651 DNAJC6 0 . GRCh38 1 65392690 65392690 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.1728C>A p.= p.T576T ENST00000371069 12/19 87 46 41 73 73 0 strelka-varscan-mutect DNAJC6,synonymous_variant,p.=,ENST00000263441,NM_001256865.1;DNAJC6,synonymous_variant,p.=,ENST00000395325,NM_014787.3;DNAJC6,synonymous_variant,p.=,ENST00000371069,NM_001256864.1;DNAJC6,downstream_gene_variant,,ENST00000494710,;DNAJC6,downstream_gene_variant,,ENST00000498720,; A ENST00000371069 Transcript synonymous_variant 1929/5365 1728/2913 576/970 T acC/acA 1 1 DNAJC6 HGNC HGNC:15469 protein_coding YES CCDS58004.1 ENSP00000360108 O75061 UPI000022AE8A NM_001256864.1 12/19 hmmpanther:PTHR23172:SF4,hmmpanther:PTHR23172 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 65392690 65392690 C A 1 0 0 0 0 0 0 0 1 4466 581 21 2 2 DNAJC6 1 65392690 Silent SNP C 11LU022_T 2069276 65392690 183563732 14 652 PDE4B 0 . GRCh38 1 66363518 66363518 + Missense_Mutation SNP G G T rs752353754 11LU022_T 11LU022_N G G c.1231G>T p.Ala411Ser p.A411S ENST00000329654 12/17 103 68 35 105 105 0 strelka-varscan-mutect PDE4B,missense_variant,p.Ala396Ser,ENST00000423207,NM_001037340.2;PDE4B,missense_variant,p.Ala411Ser,ENST00000329654,NM_001297440.1,NM_001037341.1,NM_001297441.1;PDE4B,missense_variant,p.Ala239Ser,ENST00000371045,NM_001037339.2;PDE4B,missense_variant,p.Ala411Ser,ENST00000341517,NM_002600.3;PDE4B,missense_variant,p.Ala178Ser,ENST00000480109,NM_001297442.1;PDE4B,downstream_gene_variant,,ENST00000531025,;PDE4B,downstream_gene_variant,,ENST00000526197,;PDE4B,downstream_gene_variant,,ENST00000528771,;PDE4B,downstream_gene_variant,,ENST00000524999,;PDE4B,downstream_gene_variant,,ENST00000534463,;PDE4B,upstream_gene_variant,,ENST00000483863,; T ENST00000329654 Transcript missense_variant 1418/3998 1231/2211 411/736 A/S Gct/Tct rs752353754 1 1 PDE4B HGNC HGNC:8781 protein_coding YES CCDS632.1 ENSP00000332116 Q07343 X5DNX5 UPI0000127BF6 NM_001297440.1,NM_001037341.1,NM_001297441.1 deleterious(0.02) 12/17 hmmpanther:PTHR11347:SF108,hmmpanther:PTHR11347,Pfam_domain:PF00233,Gene3D:1.10.1300.10,SMART_domains:SM00471,Superfamily_domains:SSF109604,Prints_domain:PR00387 MODERATE 1 SNV 1 1 PASS rs752353754 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 66363518 66363518 G T 1 0 0 0 0 1 0 0 0 11728 1087 38 1 1 PDE4B 1 66363518 Missense_Mutation SNP G 11LU022_T 970828 66363518 182592904 15 653 MSH4 0 . GRCh38 1 75899635 75899635 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2548G>T p.Val850Leu p.V850L ENST00000263187 19/20 84 58 26 112 111 1 strelka-varscan-mutect MSH4,missense_variant,p.Val850Leu,ENST00000263187,NM_002440.3; T ENST00000263187 Transcript missense_variant 2652/3266 2548/2811 850/936 V/L Gtg/Ttg 1 1 MSH4 HGNC HGNC:7327 protein_coding YES CCDS670.1 ENSP00000263187 O15457 UPI000006D934 NM_002440.3 tolerated(0.74) 19/20 Gene3D:3.40.50.300,Pfam_domain:PF00488,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF21,SMART_domains:SM00534,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 75899635 75899635 G T 1 0 0 0 0 1 0 0 0 9855 1261 44 2 2 MSH4 1 75899635 Missense_Mutation SNP G 11LU022_T 9536117 75899635 173056787 16 654 ST6GALNAC5 0 . GRCh38 1 77044469 77044469 + Missense_Mutation SNP A A T rs372192396 11LU022_T 11LU022_N A A c.527A>T p.Tyr176Phe p.Y176F ENST00000477717 3/5 104 69 35 116 116 0 strelka-varscan-mutect ST6GALNAC5,missense_variant,p.Tyr176Phe,ENST00000477717,NM_030965.1;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000488940,;ST6GALNAC5,missense_variant,p.Tyr176Phe,ENST00000318803,; T ENST00000477717 Transcript missense_variant 762/3751 527/1011 176/336 Y/F tAc/tTc rs372192396 1 1 ST6GALNAC5 HGNC HGNC:19342 protein_coding YES CCDS673.1 ENSP00000417583 Q9BVH7 UPI0000001C9F NM_030965.1 3/5 Pfam_domain:PF00777,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF33 MODERATE 1 SNV 1 1 PASS rs372192396 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 77044469 77044469 A T 1 0 0 0 0 1 0 0 0 15605 391 14 4 4 ST6GALNAC5 1 77044469 Missense_Mutation SNP A 11LU022_T 1144834 77044469 171911953 17 655 ADGRL2 0 . GRCh38 1 81968030 81968030 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.2303A>G p.Asp768Gly p.D768G ENST00000319517 12/20 188 109 79 181 181 0 strelka-varscan-mutect ADGRL2,missense_variant,p.Asp781Gly,ENST00000370728,;ADGRL2,missense_variant,p.Asp781Gly,ENST00000370730,;ADGRL2,missense_variant,p.Asp781Gly,ENST00000370717,;ADGRL2,missense_variant,p.Asp781Gly,ENST00000627151,;ADGRL2,missense_variant,p.Asp768Gly,ENST00000370715,NM_001297705.1;ADGRL2,missense_variant,p.Asp768Gly,ENST00000319517,NM_012302.3;ADGRL2,missense_variant,p.Asp768Gly,ENST00000370713,NM_001297706.1;ADGRL2,missense_variant,p.Asp781Gly,ENST00000370725,;ADGRL2,missense_variant,p.Asp768Gly,ENST00000370723,;ADGRL2,missense_variant,p.Asp781Gly,ENST00000370727,;ADGRL2,missense_variant,p.Asp706Gly,ENST00000370721,;ADGRL2,missense_variant,p.Asp768Gly,ENST00000359929,NM_001297704.1;ADGRL2,missense_variant,p.Asp649Gly,ENST00000449420,;ADGRL2,intron_variant,,ENST00000469377,;ADGRL2,downstream_gene_variant,,ENST00000468283,; G ENST00000319517 Transcript missense_variant 2519/5479 2303/4212 768/1403 D/G gAc/gGc 1 1 ADGRL2 HGNC HGNC:18582 protein_coding YES CCDS689.1 ENSP00000322270 O95490 UPI000005046B NM_012302.3 deleterious(0) 12/20 hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 81968030 81968030 A G 1 0 0 0 0 1 0 0 0 376 289 10 5 5 ADGRL2 1 81968030 Missense_Mutation SNP A 11LU022_T 4923561 81968030 166988392 18 656 NTNG1 0 . GRCh38 1 107430870 107430870 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1208A>G p.Tyr403Cys p.Y403C ENST00000370068 6/8 107 88 19 129 129 0 strelka-varscan-mutect NTNG1,missense_variant,p.Tyr403Cys,ENST00000370068,;NTNG1,missense_variant,p.Tyr403Cys,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Tyr403Cys,ENST00000370065,;NTNG1,intron_variant,,ENST00000370067,;NTNG1,intron_variant,,ENST00000370071,NM_001113228.1;NTNG1,intron_variant,,ENST00000370074,NM_014917.2;NTNG1,intron_variant,,ENST00000370066,; G ENST00000370068 Transcript missense_variant 2054/4034 1208/1620 403/539 Y/C tAc/tGc 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0.02) 6/8 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 107430870 107430870 A G 1 0 0 0 0 1 0 0 0 10769 391 14 5 5 NTNG1 1 107430870 Missense_Mutation SNP A 11LU022_T 25462840 107430870 141525552 19 657 KCNC4 0 . GRCh38 1 110223760 110223760 + Missense_Mutation SNP G G C rs140378578 11LU022_T 11LU022_N G G c.1475G>C p.Arg492Pro p.R492P ENST00000369787 2/4 131 96 35 169 169 0 strelka-varscan-mutect KCNC4,missense_variant,p.Arg492Pro,ENST00000369787,NM_004978.4;KCNC4,missense_variant,p.Arg492Pro,ENST00000413138,;KCNC4,missense_variant,p.Arg492Pro,ENST00000438661,NM_001039574.2;KCNC4,upstream_gene_variant,,ENST00000636402,;KCNC4,intron_variant,,ENST00000412512,;KCNC4,missense_variant,p.Arg492Pro,ENST00000469655,;KCNC4,non_coding_transcript_exon_variant,,ENST00000459877,;KCNC4,non_coding_transcript_exon_variant,,ENST00000489935,; C ENST00000369787 Transcript missense_variant 1502/18750 1475/1908 492/635 R/P cGg/cCg rs140378578,COSM1134396,COSM458738 1 1 KCNC4 HGNC HGNC:6236 protein_coding YES CCDS821.1 ENSP00000358802 Q03721 UPI000013CAC8 NM_004978.4 deleterious(0.01) 2/4 Prints_domain:PR01498,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF48 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs140378578 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 110223760 110223760 G C 1 0 0 0 0 1 0 0 0 7933 1116 39 4 4 KCNC4 1 110223760 Missense_Mutation SNP G 11LU022_T 2792890 110223760 138732662 20 658 KCNC4 0 . GRCh38 1 110223791 110223791 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1506G>T p.= p.L502L ENST00000369787 2/4 74 58 16 104 104 0 strelka-varscan-mutect KCNC4,synonymous_variant,p.=,ENST00000369787,NM_004978.4;KCNC4,synonymous_variant,p.=,ENST00000413138,;KCNC4,synonymous_variant,p.=,ENST00000438661,NM_001039574.2;KCNC4,upstream_gene_variant,,ENST00000636402,;KCNC4,intron_variant,,ENST00000412512,;KCNC4,synonymous_variant,p.=,ENST00000469655,;KCNC4,non_coding_transcript_exon_variant,,ENST00000459877,;KCNC4,non_coding_transcript_exon_variant,,ENST00000489935,; T ENST00000369787 Transcript synonymous_variant 1533/18750 1506/1908 502/635 L ctG/ctT 1 1 KCNC4 HGNC HGNC:6236 protein_coding YES CCDS821.1 ENSP00000358802 Q03721 UPI000013CAC8 NM_004978.4 2/4 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF48 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 110223791 110223791 G T 1 0 0 0 0 0 0 0 1 7933 1335 47 2 2 KCNC4 1 110223791 Silent SNP G 11LU022_T 31 110223791 138732631 21 659 CD101 0 . GRCh38 1 117011558 117011558 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.433G>C p.Asp145His p.D145H ENST00000369470 3/10 60 38 22 76 76 0 strelka-varscan-mutect CD101,missense_variant,p.Asp145His,ENST00000369470,NM_001256109.2,NM_001256106.2,NM_004258.5,NM_001256111.2;CD101,missense_variant,p.Asp145His,ENST00000256652,; C ENST00000369470 Transcript missense_variant 439/3324 433/3066 145/1021 D/H Gat/Cat 1 1 CD101 HGNC HGNC:5949 protein_coding YES CCDS891.1 ENSP00000358482 Q93033 UPI000013CF1F NM_001256109.2,NM_001256106.2,NM_004258.5,NM_001256111.2 deleterious(0) 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR12207:SF25,hmmpanther:PTHR12207,Gene3D:2.60.40.10 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 117011558 117011558 G C 1 0 0 0 0 1 0 0 0 2665 942 33 4 4 CD101 1 117011558 Missense_Mutation SNP G 11LU022_T 6787767 117011558 131944864 22 660 ADAM30 0 . GRCh38 1 119894489 119894489 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.1848G>T p.= p.R616R ENST00000369400 1/1 190 160 30 189 189 0 strelka-varscan-mutect ADAM30,synonymous_variant,p.=,ENST00000369400,NM_021794.3; A ENST00000369400 Transcript synonymous_variant 2007/2963 1848/2373 616/790 R cgG/cgT 1 -1 ADAM30 HGNC HGNC:208 protein_coding YES CCDS907.1 ENSP00000358407 Q9UKF2 UPI000004C638 NM_021794.3 1/1 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF148,SMART_domains:SM00608 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 119894489 119894489 C A 1 0 0 0 0 0 0 0 1 292 610 22 2 2 ADAM30 1 119894489 Silent SNP C 11LU022_T 2882931 119894489 129061933 23 661 NOTCH2 0 . GRCh38 1 119925738 119925738 + Missense_Mutation SNP T T A rs76636885 11LU022_T 11LU022_N T T c.4078A>T p.Thr1360Ser p.T1360S ENST00000256646 25/34 61 47 14 102 102 0 strelka-varscan-mutect NOTCH2,missense_variant,p.Thr1360Ser,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; A ENST00000256646 Transcript missense_variant 4298/11389 4078/7416 1360/2471 T/S Acc/Tcc rs76636885 1 -1 NOTCH2 HGNC HGNC:7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 UPI000013CF1D NM_024408.3 tolerated(0.68) 25/34 PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF66,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs76636885 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 119925738 119925738 T A 1 0 0 0 0 1 0 0 0 10593 1696 59 4 4 NOTCH2 1 119925738 Missense_Mutation SNP T 11LU022_T 31249 119925738 129030684 24 662 ADAMTSL4 0 . GRCh38 1 150556662 150556662 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1687T>C p.Trp563Arg p.W563R ENST00000369039 11/20 323 212 111 336 336 0 strelka-varscan-mutect ADAMTSL4,missense_variant,p.Trp563Arg,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,missense_variant,p.Trp540Arg,ENST00000271643,NM_019032.5;ADAMTSL4,missense_variant,p.Trp540Arg,ENST00000369038,;ADAMTSL4,missense_variant,p.Trp540Arg,ENST00000369041,NM_025008.4;MIR4257,downstream_gene_variant,,ENST00000581735,;RP11-54A4.2,non_coding_transcript_exon_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;ADAMTSL4,downstream_gene_variant,,ENST00000483335,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,;ADAMTSL4,upstream_gene_variant,,ENST00000489159,; C ENST00000369039 Transcript missense_variant 1976/4319 1687/3294 563/1097 W/R Tgg/Cgg 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 deleterious(0) 11/20 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144,Pfam_domain:PF05986 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 150556662 150556662 T C 1 0 0 0 0 1 0 0 0 321 1580 55 5 5 ADAMTSL4 1 150556662 Missense_Mutation SNP T 11LU022_T 30630924 150556662 98399760 25 663 BNIPL 0 . GRCh38 1 151043671 151043671 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.795G>T p.Arg265Ser p.R265S ENST00000368931 7/10 207 162 45 146 145 1 strelka-varscan-mutect BNIPL,missense_variant,p.Arg183Ser,ENST00000295294,NM_001159642.1;BNIPL,missense_variant,p.Arg265Ser,ENST00000368931,NM_138278.3;BNIPL,missense_variant,p.Arg249Ser,ENST00000361277,;C1orf56,upstream_gene_variant,,ENST00000368926,NM_017860.3;BNIPL,downstream_gene_variant,,ENST00000392802,;C1orf56,upstream_gene_variant,,ENST00000465135,;BNIPL,upstream_gene_variant,,ENST00000491386,;C1orf56,upstream_gene_variant,,ENST00000473308,;BNIPL,missense_variant,p.Arg183Ser,ENST00000485855,; T ENST00000368931 Transcript missense_variant 951/2143 795/1074 265/357 R/S agG/agT 1 1 BNIPL HGNC HGNC:16976 protein_coding YES CCDS978.2 ENSP00000357927 Q7Z465 UPI00001B94EF NM_138278.3 deleterious(0) 7/10 Gene3D:3.40.525.10,Pfam_domain:PF13716,PROSITE_profiles:PS50191,hmmpanther:PTHR12112,hmmpanther:PTHR12112:SF21,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 151043671 151043671 G T 1 0 0 0 0 1 0 0 0 1636 1223 43 2 2 BNIPL 1 151043671 Missense_Mutation SNP G 11LU022_T 487009 151043671 97912751 26 664 CELF3 0 . GRCh38 1 151707867 151707867 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.555G>A p.= p.Q185Q ENST00000290583 6/13 240 165 75 205 204 1 strelka-varscan-mutect CELF3,synonymous_variant,p.=,ENST00000290583,NM_001291106.1,NM_001172648.3,NM_007185.6,NM_001291107.1;CELF3,synonymous_variant,p.=,ENST00000420342,;CELF3,synonymous_variant,p.=,ENST00000290585,NM_001172649.3;RIIAD1,upstream_gene_variant,,ENST00000326413,;RP11-98D18.1,intron_variant,,ENST00000457548,;CELF3,non_coding_transcript_exon_variant,,ENST00000470688,;CELF3,non_coding_transcript_exon_variant,,ENST00000479893,;CELF3,downstream_gene_variant,,ENST00000478829,;CELF3,non_coding_transcript_exon_variant,,ENST00000419910,; T ENST00000290583 Transcript synonymous_variant 1349/3246 555/1398 185/465 Q caG/caA 1 -1 CELF3 HGNC HGNC:11967 protein_coding YES CCDS1002.1 ENSP00000290583 Q5SZQ8 UPI000013F059 NM_001291106.1,NM_001172648.3,NM_007185.6,NM_001291107.1 6/13 Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 151707867 151707867 C T 1 0 0 0 0 0 0 0 1 2924 796 28 3 3 CELF3 1 151707867 Silent SNP C 11LU022_T 664196 151707867 97248555 27 665 HRNR 0 . GRCh38 1 152220317 152220317 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1312A>T p.Ser438Cys p.S438C ENST00000368801 3/3 537 420 117 460 460 0 strelka-varscan-mutect HRNR,missense_variant,p.Ser438Cys,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368801 Transcript missense_variant 1388/9623 1312/8553 438/2850 S/C Agc/Tgc 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.11) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 152220317 152220317 T A 1 0 0 0 0 1 0 0 0 7254 1580 55 4 4 HRNR 1 152220317 Missense_Mutation SNP T 11LU022_T 512450 152220317 96736105 28 666 FLG 0 . GRCh38 1 152303351 152303351 + Silent SNP G G A rs564072147 11LU022_T 11LU022_N G G c.11535C>T p.= p.S3845S ENST00000368799 3/3 725 566 159 576 575 1 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript synonymous_variant 11571/12747 11535/12186 3845/4061 S tcC/tcT rs564072147,COSM896083 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 0,1 LOW 1 SNV 1 0,1 1 PASS rs564072147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 152303351 152303351 G A 1 0 0 0 0 0 0 0 1 5784 1103 39 1 1 FLG 1 152303351 Silent SNP G 11LU022_T 83034 152303351 96653071 29 667 FLG 0 . GRCh38 1 152311163 152311163 + Silent SNP G G T 11LU022_T 11LU022_N G G c.3723C>A p.= p.A1241A ENST00000368799 3/3 567 444 123 468 468 0 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript synonymous_variant 3759/12747 3723/12186 1241/4061 A gcC/gcA COSM3474046 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 Pfam_domain:PF03516 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 152311163 152311163 G T 1 0 0 0 0 0 0 0 1 5784 987 35 2 2 FLG 1 152311163 Silent SNP G 11LU022_T 7812 152311163 96645259 30 668 LCE3A 0 . GRCh38 1 152622922 152622922 + Missense_Mutation SNP C C A rs547378092 11LU022_T 11LU022_N C C c.182G>T p.Arg61Leu p.R61L ENST00000335674 1/1 484 408 76 349 349 0 strelka-varscan-mutect LCE3A,missense_variant,p.Arg61Leu,ENST00000335674,NM_178431.1; A ENST00000335674 Transcript missense_variant 182/270 182/270 61/89 R/L cGt/cTt rs547378092 1 -1 LCE3A HGNC HGNC:29461 protein_coding YES CCDS1017.1 ENSP00000335006 Q5TA76 UPI00001927D2 NM_178431.1 tolerated_low_confidence(0.09) 1/1 Pfam_domain:PF14672,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF54,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs547378092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 152622922 152622922 C A 1 0 0 0 0 1 0 0 0 8574 536 19 1 1 LCE3A 1 152622922 Missense_Mutation SNP C 11LU022_T 311759 152622922 96333500 31 669 LCE1E 0 . GRCh38 1 152787528 152787528 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.229C>A p.Leu77Met p.L77M ENST00000368770 2/2 351 314 37 287 287 0 strelka-varscan-mutect LCE1E,missense_variant,p.Leu77Met,ENST00000368770,NM_178353.1;LCE1E,missense_variant,p.Leu77Met,ENST00000368771,;LCE1E,missense_variant,p.Leu47Met,ENST00000619588,; A ENST00000368770 Transcript missense_variant 282/1180 229/357 77/118 L/M Ctg/Atg COSM5377693 1 1 LCE1E HGNC HGNC:29466 protein_coding YES CCDS1024.1 ENSP00000357759 Q5T753 UPI0000161050 NM_178353.1 deleterious_low_confidence(0) 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 152787528 152787528 C A 1 0 0 0 0 1 0 0 0 8568 680 24 2 2 LCE1E 1 152787528 Missense_Mutation SNP C 11LU022_T 164606 152787528 96168894 32 670 IVL 0 . GRCh38 1 152910502 152910502 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.705C>T p.= p.L235L ENST00000368764 2/2 73 53 20 57 57 0 strelka-varscan-mutect IVL,synonymous_variant,p.=,ENST00000368764,NM_005547.2; T ENST00000368764 Transcript synonymous_variant 769/2153 705/1758 235/585 L ctC/ctT 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 2/2 Pfam_domain:PF00904,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 152910502 152910502 C T 1 0 0 0 0 0 0 0 1 7835 842 30 3 3 IVL 1 152910502 Silent SNP C 11LU022_T 122974 152910502 96045920 33 671 ATP8B2 0 . GRCh38 1 154348487 154348487 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.3342G>A p.= p.V1114V ENST00000368489 27/28 216 199 17 186 186 0 strelka-varscan-mutect ATP8B2,synonymous_variant,p.=,ENST00000368489,NM_020452.3;ATP8B2,non_coding_transcript_exon_variant,,ENST00000505882,; A ENST00000368489 Transcript synonymous_variant 3342/5861 3342/3672 1114/1223 V gtG/gtA 1 1 ATP8B2 HGNC HGNC:13534 protein_coding YES CCDS1066.1 ENSP00000357475 P98198 UPI00001B92AB NM_020452.3 27/28 Superfamily_domains:0049473,Pfam_domain:PF16212,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF46,TIGRFAM_domain:TIGR01652,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 154348487 154348487 G A 1 0 0 0 0 0 0 0 1 1348 1335 47 3 3 ATP8B2 1 154348487 Silent SNP G 11LU022_T 1437985 154348487 94607935 34 672 DCST2 0 . GRCh38 1 155026684 155026684 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.1374T>A p.= p.G458G ENST00000368424 9/15 340 247 93 263 263 0 strelka-varscan-mutect DCST2,synonymous_variant,p.=,ENST00000368424,NM_144622.2;DCST2,synonymous_variant,p.=,ENST00000485982,;DCST2,non_coding_transcript_exon_variant,,ENST00000368423,;DCST2,non_coding_transcript_exon_variant,,ENST00000498036,;DCST2,upstream_gene_variant,,ENST00000467991,; T ENST00000368424 Transcript synonymous_variant 1433/2392 1374/2322 458/773 G ggT/ggA 1 -1 DCST2 HGNC HGNC:26562 protein_coding YES CCDS1082.2 ENSP00000357409 Q5T1A1 UPI0000D959B3 NM_144622.2 9/15 hmmpanther:PTHR21041:SF6,hmmpanther:PTHR21041,Pfam_domain:PF07782 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 155026684 155026684 A T 1 0 0 0 0 0 0 0 1 4105 378 14 4 4 DCST2 1 155026684 Silent SNP A 11LU022_T 678197 155026684 93929738 35 673 TTC24 0 . GRCh38 1 156581757 156581757 + Silent SNP C C A rs373435186 11LU022_T 11LU022_N C C c.393C>A p.= p.G131G ENST00000368236 2/11 444 299 145 356 355 1 strelka-varscan-mutect TTC24,synonymous_variant,p.=,ENST00000368236,NM_001105669.2;TTC24,synonymous_variant,p.=,ENST00000368237,;TTC24,upstream_gene_variant,,ENST00000478081,;TTC24,upstream_gene_variant,,ENST00000413282,;TTC24,upstream_gene_variant,,ENST00000495690,;TTC24,upstream_gene_variant,,ENST00000462049,; A ENST00000368236 Transcript synonymous_variant 429/2005 393/1749 131/582 G ggC/ggA rs373435186 1 1 TTC24 HGNC HGNC:32348 protein_coding YES CCDS53379.1 ENSP00000357219 A2A3L6 UPI0000418EC1 NM_001105669.2 2/11 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR10098,hmmpanther:PTHR10098:SF112,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452,Superfamily_domains:SSF48452 LOW 1 SNV 5 1 PASS rs373435186 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 156581757 156581757 C A 1 0 0 0 0 0 0 0 1 17200 755 27 1 1 TTC24 1 156581757 Silent SNP C 11LU022_T 1555073 156581757 92374665 36 674 HAPLN2 0 . GRCh38 1 156623958 156623958 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.237G>T p.= p.R79R ENST00000255039 4/7 116 92 24 98 97 1 strelka-varscan-mutect HAPLN2,synonymous_variant,p.=,ENST00000255039,NM_021817.2;HAPLN2,synonymous_variant,p.=,ENST00000456112,;HAPLN2,upstream_gene_variant,,ENST00000494218,;HAPLN2,downstream_gene_variant,,ENST00000487988,;HAPLN2,downstream_gene_variant,,ENST00000482204,; T ENST00000255039 Transcript synonymous_variant 644/1771 237/1023 79/340 R cgG/cgT 1 1 HAPLN2 HGNC HGNC:17410 protein_coding YES CCDS1148.1 ENSP00000255039 Q9GZV7 UPI00000012E0 NM_021817.2 4/7 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR22804,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1484729971 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 3 156623958 156623958 G T 1 0 0 0 0 0 0 0 1 6841 1219 43 2 2 HAPLN2 1 156623958 Silent SNP G 11LU022_T 42201 156623958 92332464 37 675 INSRR 0 . GRCh38 1 156858544 156858544 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.78A>T p.= p.T26T ENST00000368195 1/22 280 216 64 262 262 0 strelka-varscan-mutect INSRR,synonymous_variant,p.=,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,upstream_gene_variant,,ENST00000368196,NM_001012331.1;NTRK1,upstream_gene_variant,,ENST00000358660,;NTRK1,upstream_gene_variant,,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,upstream_gene_variant,,ENST00000533630,; A ENST00000368195 Transcript synonymous_variant 475/5101 78/3894 26/1297 T acA/acT 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 1/22 hmmpanther:PTHR24416:SF338,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 156858544 156858544 T A 1 0 0 0 0 0 0 0 1 7676 1567 55 4 4 INSRR 1 156858544 Silent SNP T 11LU022_T 234586 156858544 92097878 38 676 NTRK1 0 . GRCh38 1 156868219 156868219 + Missense_Mutation SNP C C A rs755312547 11LU022_T 11LU022_N C C c.544C>A p.Pro182Thr p.P182T ENST00000524377 5/17 376 293 83 316 316 0 strelka-varscan-mutect NTRK1,missense_variant,p.Pro182Thr,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Pro152Thr,ENST00000392302,NM_001007792.1;NTRK1,missense_variant,p.Pro182Thr,ENST00000358660,;NTRK1,missense_variant,p.Pro182Thr,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,missense_variant,p.Pro152Thr,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,downstream_gene_variant,,ENST00000533630,; A ENST00000524377 Transcript missense_variant 585/2432 544/2391 182/796 P/T Ccc/Acc rs755312547 1 1 NTRK1 HGNC HGNC:8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 tolerated(0.19) 5/17 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF370,Gene3D:3.80.10.10,Pfam_domain:PF16920,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs755312547 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 156868219 156868219 C A 1 0 0 0 0 1 0 0 0 10772 739 26 2 2 NTRK1 1 156868219 Missense_Mutation SNP C 11LU022_T 9675 156868219 92088203 39 677 FCRL5 0 . GRCh38 1 157544390 157544390 + Missense_Mutation SNP C C G rs756175836 11LU022_T 11LU022_N C C c.716G>C p.Trp239Ser p.W239S ENST00000361835 5/17 619 461 158 484 484 0 strelka-varscan-mutect FCRL5,missense_variant,p.Trp239Ser,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,missense_variant,p.Trp239Ser,ENST00000368189,;FCRL5,missense_variant,p.Trp239Ser,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000481082,; G ENST00000361835 Transcript missense_variant 874/5390 716/2934 239/977 W/S tGg/tCg rs756175836 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(0.75) 5/17 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF68,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs756175836 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 157544390 157544390 C G 1 0 0 0 0 1 0 0 0 5660 595 21 4 4 FCRL5 1 157544390 Missense_Mutation SNP C 11LU022_T 676171 157544390 91412032 40 678 CD1A 0 . GRCh38 1 158255082 158255082 + Splice_Site SNP A A T rs763962809 11LU022_T 11LU022_N A A c.59-2A>T p.X20_splice ENST00000289429 144 113 31 128 128 0 strelka-varscan-mutect CD1A,splice_acceptor_variant,,ENST00000289429,NM_001763.2; T ENST00000289429 Transcript splice_acceptor_variant -/2096 59/984 20/327 rs763962809 1 1 CD1A HGNC HGNC:1634 protein_coding YES CCDS1174.1 ENSP00000289429 P06126 UPI0000161A54 NM_001763.2 1/5 HIGH 1 SNV 1 1 PASS rs763962809 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 3 158255082 158255082 A T 1 0 0 0 0 0 0 1 0 2677 202 7 4 4 CD1A 1 158255082 Splice_Site SNP A 11LU022_T 710692 158255082 90701340 41 679 CD1E 0 . GRCh38 1 158355957 158355957 + Silent SNP G G T rs775039422 11LU022_T 11LU022_N G G c.756G>T p.= p.R252R ENST00000368167 4/6 235 148 87 128 128 0 strelka-varscan-mutect CD1E,synonymous_variant,p.=,ENST00000444681,NM_001185114.1;CD1E,synonymous_variant,p.=,ENST00000368160,NM_001042583.2;CD1E,synonymous_variant,p.=,ENST00000368161,NM_001042584.2;CD1E,synonymous_variant,p.=,ENST00000368167,NM_030893.3;CD1E,synonymous_variant,p.=,ENST00000368166,NM_001042586.2;CD1E,synonymous_variant,p.=,ENST00000368165,NM_001185107.1;CD1E,synonymous_variant,p.=,ENST00000368162,;CD1E,synonymous_variant,p.=,ENST00000368164,NM_001042587.2;CD1E,synonymous_variant,p.=,ENST00000368156,NM_001185115.1;CD1E,synonymous_variant,p.=,ENST00000452291,NM_001185112.1;CD1E,intron_variant,,ENST00000368163,NM_001042585.2;CD1E,intron_variant,,ENST00000368155,NM_001185108.1;CD1E,intron_variant,,ENST00000368154,NM_001185113.1;CD1E,intron_variant,,ENST00000368157,NM_001185110.1;CD1E,downstream_gene_variant,,ENST00000464822,; T ENST00000368167 Transcript synonymous_variant 995/1458 756/1167 252/388 R cgG/cgT rs775039422 1 1 CD1E HGNC HGNC:1638 protein_coding YES CCDS41417.1 ENSP00000357149 P15812 UPI000046F8C2 NM_030893.3 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF146,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs775039422 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 158355957 158355957 G T 1 0 0 0 0 0 0 0 1 2681 1219 43 2 2 CD1E 1 158355957 Silent SNP G 11LU022_T 100875 158355957 90600465 42 680 CD1E 0 . GRCh38 1 158356813 158356813 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1084C>A p.His362Asn p.H362N ENST00000368167 6/6 242 175 67 195 194 1 strelka-varscan-mutect CD1E,missense_variant,p.His263Asn,ENST00000444681,NM_001185114.1;CD1E,missense_variant,p.His350Asn,ENST00000368160,NM_001042583.2;CD1E,missense_variant,p.His295Asn,ENST00000368163,NM_001042585.2;CD1E,missense_variant,p.His362Asn,ENST00000368167,NM_030893.3;CD1E,missense_variant,p.His161Asn,ENST00000368166,NM_001042586.2;CD1E,missense_variant,p.His272Asn,ENST00000368165,NM_001185107.1;CD1E,missense_variant,p.His260Asn,ENST00000368156,NM_001185115.1;CD1E,missense_variant,p.His173Asn,ENST00000452291,NM_001185112.1;CD1E,missense_variant,p.His205Asn,ENST00000368155,NM_001185108.1;CD1E,missense_variant,p.His118Asn,ENST00000368154,NM_001185113.1;CD1E,missense_variant,p.His106Asn,ENST00000368157,NM_001185110.1;CD1E,3_prime_UTR_variant,,ENST00000368161,NM_001042584.2;CD1E,3_prime_UTR_variant,,ENST00000368162,;CD1E,3_prime_UTR_variant,,ENST00000368164,NM_001042587.2;CD1E,downstream_gene_variant,,ENST00000464822,; A ENST00000368167 Transcript missense_variant 1323/1458 1084/1167 362/388 H/N Cat/Aat 1 1 CD1E HGNC HGNC:1638 protein_coding YES CCDS41417.1 ENSP00000357149 P15812 UPI000046F8C2 NM_030893.3 tolerated(0.16) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 158356813 158356813 C A 1 0 0 0 0 1 0 0 0 2681 478 17 2 2 CD1E 1 158356813 Missense_Mutation SNP C 11LU022_T 856 158356813 90599609 43 681 SPTA1 0 . GRCh38 1 158645365 158645365 + Silent SNP C C T 11LU022_T 11LU022_N C C c.4017G>A p.= p.E1339E ENST00000368147 29/52 269 178 91 235 234 1 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000465741,; T ENST00000368147 Transcript synonymous_variant 4198/7999 4017/7260 1339/2419 E gaG/gaA COSM3476222,COSM676104 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 29/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 158645365 158645365 C T 1 0 0 0 0 0 0 0 1 15472 680 24 3 3 SPTA1 1 158645365 Silent SNP C 11LU022_T 288552 158645365 90311057 44 682 NCSTN 0 . GRCh38 1 160357066 160357066 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1820G>T p.Gly607Val p.G607V ENST00000294785 16/17 604 409 195 459 458 1 strelka-varscan-mutect NCSTN,missense_variant,p.Gly587Val,ENST00000368063,NM_001290184.1;NCSTN,missense_variant,p.Gly607Val,ENST00000294785,NM_001290186.1,NM_015331.2;NCSTN,downstream_gene_variant,,ENST00000424645,;NCSTN,downstream_gene_variant,,ENST00000435149,;NCSTN,downstream_gene_variant,,ENST00000421914,;NCSTN,downstream_gene_variant,,ENST00000424754,;NCSTN,non_coding_transcript_exon_variant,,ENST00000469159,;NCSTN,downstream_gene_variant,,ENST00000459963,;NCSTN,downstream_gene_variant,,ENST00000491390,; T ENST00000294785 Transcript missense_variant 1945/2936 1820/2130 607/709 G/V gGc/gTc 1 1 NCSTN HGNC HGNC:17091 protein_coding YES CCDS1203.1 ENSP00000294785 Q92542 UPI0000042050 NM_001290186.1,NM_015331.2 deleterious(0) 16/17 hmmpanther:PTHR21092:SF0,hmmpanther:PTHR21092 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 160357066 160357066 G T 1 0 0 0 0 1 0 0 0 10261 1203 42 2 2 NCSTN 1 160357066 Missense_Mutation SNP G 11LU022_T 1711701 160357066 88599356 45 683 SLAMF1 0 . GRCh38 1 160619843 160619843 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.797C>T p.Thr266Met p.T266M ENST00000302035 5/7 260 205 55 202 202 0 strelka-varscan-mutect SLAMF1,stop_gained,p.Arg294Ter,ENST00000538290,;SLAMF1,missense_variant,p.Thr266Met,ENST00000302035,NM_003037.3;SLAMF1,intron_variant,,ENST00000235739,; A ENST00000302035 Transcript missense_variant 1147/4006 797/1008 266/335 T/M aCg/aTg 1 -1 SLAMF1 HGNC HGNC:10903 protein_coding YES CCDS1207.1 ENSP00000306190 Q13291 UPI0000047630 NM_003037.3 deleterious(0.03) 5/7 hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF49 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 160619843 160619843 G A 1 0 0 0 0 1 0 0 0 14632 1145 40 1 1 SLAMF1 1 160619843 Missense_Mutation SNP G 11LU022_T 262777 160619843 88336579 46 684 ITLN1 0 . GRCh38 1 160881274 160881274 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.444C>T p.= p.G148G ENST00000326245 5/8 77 44 33 42 42 0 strelka-varscan-mutect ITLN1,synonymous_variant,p.=,ENST00000326245,NM_017625.2;ITLN1,non_coding_transcript_exon_variant,,ENST00000487531,;ITLN1,non_coding_transcript_exon_variant,,ENST00000464077,; A ENST00000326245 Transcript synonymous_variant 560/1183 444/942 148/313 G ggC/ggT 1 -1 ITLN1 HGNC HGNC:18259 protein_coding YES CCDS1211.1 ENSP00000323587 Q8WWA0 UPI0000032AA3 NM_017625.2 5/8 hmmpanther:PTHR16146,hmmpanther:PTHR16146:SF38,Superfamily_domains:SSF56496 LOW 1 SNV 1 1 PASS rs781141336 . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 160881274 160881274 G A 1 0 0 0 0 0 0 0 1 7816 1306 46 3 3 ITLN1 1 160881274 Silent SNP G 11LU022_T 261431 160881274 88075148 47 685 NECTIN4 0 . GRCh38 1 161072685 161072685 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1509C>A p.= p.I503I ENST00000368012 9/9 544 359 185 445 445 0 strelka-varscan-mutect NECTIN4,synonymous_variant,p.=,ENST00000368012,NM_030916.2;ARHGAP30,upstream_gene_variant,,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,upstream_gene_variant,,ENST00000368015,NM_001287602.1;ARHGAP30,upstream_gene_variant,,ENST00000368016,NM_181720.2;NECTIN4,non_coding_transcript_exon_variant,,ENST00000486694,;ARHGAP30,upstream_gene_variant,,ENST00000461003,;ARHGAP30,upstream_gene_variant,,ENST00000490279,;ARHGAP30,upstream_gene_variant,,ENST00000368018,;ARHGAP30,upstream_gene_variant,,ENST00000471492,; T ENST00000368012 Transcript synonymous_variant 1812/3502 1509/1533 503/510 I atC/atA 1 -1 NECTIN4 HGNC HGNC:19688 protein_coding YES CCDS1216.1 ENSP00000356991 Q96NY8 K4PZ75 UPI000006F072 NM_030916.2 9/9 hmmpanther:PTHR23277:SF11,hmmpanther:PTHR23277 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 161072685 161072685 G T 1 0 0 0 0 0 0 0 1 10336 1280 45 2 2 NECTIN4 1 161072685 Silent SNP G 11LU022_T 191411 161072685 87883737 48 686 DDR2 0 . GRCh38 1 162775687 162775687 + Missense_Mutation SNP G G T rs779963287 11LU022_T 11LU022_N G G c.1892G>T p.Arg631Leu p.R631L ENST00000367922 16/19 452 330 122 343 343 0 strelka-varscan-mutect DDR2,missense_variant,p.Arg631Leu,ENST00000367922,NM_001014796.1;DDR2,missense_variant,p.Arg631Leu,ENST00000367921,NM_006182.2;DDR2,downstream_gene_variant,,ENST00000433757,;DDR2,downstream_gene_variant,,ENST00000458105,;RN7SL861P,upstream_gene_variant,,ENST00000473793,; T ENST00000367922 Transcript missense_variant 2330/10160 1892/2568 631/855 R/L cGg/cTg rs779963287,COSM1335765,COSM1335766 1 1 DDR2 HGNC HGNC:2731 protein_coding YES CCDS1241.1 ENSP00000356899 Q16832 A0A024R906 UPI000013E1B4 NM_001014796.1 deleterious(0) 16/19 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF295,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs779963287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 162775687 162775687 G T 1 0 0 0 0 1 0 0 0 4141 1116 39 1 1 DDR2 1 162775687 Missense_Mutation SNP G 11LU022_T 1703002 162775687 86180735 49 687 LMX1A 0 . GRCh38 1 165249425 165249425 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.479C>G p.Pro160Arg p.P160R ENST00000342310 4/9 180 157 23 171 171 0 strelka-varscan-mutect LMX1A,missense_variant,p.Pro160Arg,ENST00000342310,NM_177398.3;LMX1A,missense_variant,p.Pro160Arg,ENST00000294816,NM_001174069.1;LMX1A,missense_variant,p.Pro160Arg,ENST00000367893,; C ENST00000342310 Transcript missense_variant 862/3545 479/1149 160/382 P/R cCa/cGa 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 deleterious(0.01) 4/9 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 165249425 165249425 G C 1 0 0 0 0 1 0 0 0 8788 1348 47 4 4 LMX1A 1 165249425 Missense_Mutation SNP G 11LU022_T 2473738 165249425 83706997 50 688 LRRC52 0 . GRCh38 1 165563747 165563747 + Frame_Shift_Del DEL G G - rs150359687 11LU022_T 11LU022_N G G c.867delG p.Thr290LeufsTer60 p.T290Lfs*60 ENST00000294818 2/2 327 218 109 317 317 0 sindel-varindel-pindel LRRC52,frameshift_variant,p.Thr290LeufsTer60,ENST00000294818,NM_001005214.3;RP11-280O1.2,intron_variant,,ENST00000438275,;RP11-280O1.2,intron_variant,,ENST00000421273,;RP11-280O1.2,intron_variant,,ENST00000416424,; - ENST00000294818 Transcript frameshift_variant 1155/1369 865/942 289/313 G/X Ggg/gg rs150359687,COSM4024732 1 1 LRRC52 HGNC HGNC:32156 protein_coding YES CCDS30930.1 ENSP00000294818 Q8N7C0 UPI000013E1BE NM_001005214.3 2/2 0,1 HIGH 1 deletion 1 2 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 165563747 165563747 G - 1 0 1 0 1 0 0 0 0 8904 1116 39 0 0 LRRC52 1 165563747 Frame_Shift_Del DEL G 11LU022_T 314322 165563747 83392675 51 689 ILDR2 0 . GRCh38 1 166922719 166922719 + Missense_Mutation SNP G G A rs765518152 11LU022_T 11LU022_N G G c.1085C>T p.Pro362Leu p.P362L ENST00000271417 8/10 627 532 95 464 463 1 strelka-varscan-mutect ILDR2,missense_variant,p.Pro362Leu,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Pro343Leu,ENST00000529071,;ILDR2,missense_variant,p.Pro303Leu,ENST00000528703,;ILDR2,missense_variant,p.Pro254Leu,ENST00000526687,;ILDR2,missense_variant,p.Pro235Leu,ENST00000525740,;ILDR2,missense_variant,p.Pro362Leu,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; A ENST00000271417 Transcript missense_variant 1141/13140 1085/1920 362/639 P/L cCt/cTt rs765518152 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 deleterious(0) 8/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0 MODERATE 1 SNV 1 1 PASS rs765518152 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 166922719 166922719 G A 1 0 0 0 0 1 0 0 0 7613 1000 35 3 3 ILDR2 1 166922719 Missense_Mutation SNP G 11LU022_T 1358972 166922719 82033703 52 690 MPC2 0 . GRCh38 1 167935814 167935814 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.28C>G p.Arg10Gly p.R10G ENST00000367846 1/5 189 177 12 158 158 0 strelka-varscan-mutect MPC2,missense_variant,p.Arg10Gly,ENST00000367846,NM_015415.3;MPC2,missense_variant,p.Arg10Gly,ENST00000271373,NM_001143674.3;MPC2,missense_variant,p.Arg10Gly,ENST00000458574,;DCAF6,upstream_gene_variant,,ENST00000432587,NM_001198957.1;DCAF6,upstream_gene_variant,,ENST00000367840,NM_001198956.1;DCAF6,upstream_gene_variant,,ENST00000367843,NM_018442.3;DCAF6,upstream_gene_variant,,ENST00000312263,NM_001017977.2;DCAF6,non_coding_transcript_exon_variant,,ENST00000450548,;DCAF6,upstream_gene_variant,,ENST00000470919,;DCAF6,upstream_gene_variant,,ENST00000455334,;DCAF6,upstream_gene_variant,,ENST00000470721,; C ENST00000367846 Transcript missense_variant 227/2177 28/384 10/127 R/G Cgg/Ggg 1 -1 MPC2 HGNC HGNC:24515 protein_coding YES CCDS1266.1 ENSP00000356820 O95563 A0A024R8Z5 UPI0000044E0B NM_015415.3 deleterious(0.04) 1/5 hmmpanther:PTHR14154,hmmpanther:PTHR14154:SF2 MODERATE 1 SNV 1 1 PASS . . 0 202 0 7 0 0 0 0 -14.84152 0.9784345 1 1 1 0 C 3 2 3 167935814 167935814 G C 1 0 0 0 0 1 0 0 0 9685 1086 38 4 4 MPC2 1 167935814 Missense_Mutation SNP G 11LU022_T 1013095 167935814 81020608 53 691 TNR 0 . GRCh38 1 175386121 175386121 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1688C>A p.Ala563Asp p.A563D ENST00000367674 8/23 177 156 21 148 148 0 strelka-varscan-mutect TNR,missense_variant,p.Ala563Asp,ENST00000367674,;TNR,missense_variant,p.Ala563Asp,ENST00000263525,NM_003285.2; T ENST00000367674 Transcript missense_variant 2397/12949 1688/4077 563/1358 A/D gCc/gAc 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C tolerated(0.66) 8/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 3 175386121 175386121 G T 1 0 0 0 0 1 0 0 0 16811 1203 42 2 2 TNR 1 175386121 Missense_Mutation SNP G 11LU022_T 7450307 175386121 73570301 54 692 RFWD2 0 . GRCh38 1 176081282 176081282 + Missense_Mutation SNP T T A 11LU022_T 11LU022_N T T c.1147A>T p.Ser383Cys p.S383C ENST00000367669 11/20 81 61 20 79 79 0 strelka-varscan-mutect RFWD2,missense_variant,p.Ser383Cys,ENST00000367669,NM_022457.6,NM_001286644.1;RFWD2,missense_variant,p.Ser359Cys,ENST00000308769,NM_001001740.3;RFWD2,missense_variant,p.Ser218Cys,ENST00000367666,;RFWD2,missense_variant,p.Ser103Cys,ENST00000459744,;RFWD2,downstream_gene_variant,,ENST00000498306,;RFWD2,3_prime_UTR_variant,,ENST00000367667,;RFWD2,upstream_gene_variant,,ENST00000461830,; A ENST00000367669 Transcript missense_variant 1662/3033 1147/2196 383/731 S/C Agt/Tgt COSM1295522 1 -1 RFWD2 HGNC HGNC:17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 UPI0000061E51 NM_022457.6,NM_001286644.1 tolerated(0.05) 11/20 hmmpanther:PTHR22847:SF451,hmmpanther:PTHR22847 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999937 1 1 1 0 A 3 1 3 176081282 176081282 T A 1 0 0 0 0 1 0 0 0 13434 1594 55 4 4 RFWD2 1 176081282 Missense_Mutation SNP T 11LU022_T 695161 176081282 72875140 55 693 RFWD2 0 . GRCh38 1 176085821 176085821 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1096G>T p.Asp366Tyr p.D366Y ENST00000367669 10/20 133 89 44 140 140 0 strelka-varscan-mutect RFWD2,missense_variant,p.Asp366Tyr,ENST00000367669,NM_022457.6,NM_001286644.1;RFWD2,missense_variant,p.Asp342Tyr,ENST00000308769,NM_001001740.3;RFWD2,missense_variant,p.Asp201Tyr,ENST00000367666,;RFWD2,missense_variant,p.Asp86Tyr,ENST00000459744,;RFWD2,downstream_gene_variant,,ENST00000498306,;RFWD2,3_prime_UTR_variant,,ENST00000367667,;RFWD2,upstream_gene_variant,,ENST00000461830,; A ENST00000367669 Transcript missense_variant 1611/3033 1096/2196 366/731 D/Y Gac/Tac 1 -1 RFWD2 HGNC HGNC:17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 UPI0000061E51 NM_022457.6,NM_001286644.1 deleterious(0) 10/20 hmmpanther:PTHR22847:SF451,hmmpanther:PTHR22847 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 176085821 176085821 C A 1 0 0 0 0 1 0 0 0 13434 913 32 2 2 RFWD2 1 176085821 Missense_Mutation SNP C 11LU022_T 4539 176085821 72870601 56 694 PAPPA2 0 . GRCh38 1 176595136 176595136 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.1532C>T p.Ser511Phe p.S511F ENST00000367662 3/23 355 242 113 371 371 0 strelka-varscan-mutect PAPPA2,missense_variant,p.Ser511Phe,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Ser511Phe,ENST00000367661,NM_021936.2; T ENST00000367662 Transcript missense_variant 2696/9691 1532/5376 511/1791 S/F tCc/tTc COSM390712,COSM390713,COSM4900732,COSM4900733 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated(0.24) 3/23 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 176595136 176595136 C T 1 0 0 0 0 1 0 0 0 11513 855 30 3 3 PAPPA2 1 176595136 Missense_Mutation SNP C 11LU022_T 509315 176595136 72361286 57 695 PAPPA2 0 . GRCh38 1 176771154 176771154 + Silent SNP A A C novel 11LU022_T 11LU022_N A A c.4689A>C p.= p.A1563A ENST00000367662 17/23 278 177 101 257 257 0 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2; C ENST00000367662 Transcript synonymous_variant 5853/9691 4689/5376 1563/1791 A gcA/gcC 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 17/23 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 176771154 176771154 A C 1 0 0 0 0 0 0 0 1 11513 175 7 5 5 PAPPA2 1 176771154 Silent SNP A 11LU022_T 176018 176771154 72185268 58 696 ASTN1 0 . GRCh38 1 176888081 176888081 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.3064C>A p.Pro1022Thr p.P1022T ENST00000361833 18/23 189 127 62 168 168 0 strelka-varscan-mutect ASTN1,missense_variant,p.Pro1022Thr,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Pro1022Thr,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Pro1022Thr,ENST00000424564,NM_207108.2; T ENST00000361833 Transcript missense_variant 3078/7116 3064/3885 1022/1294 P/T Cca/Aca 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious(0.01) 18/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 176888081 176888081 G T 1 0 0 0 0 1 0 0 0 1211 1232 43 2 2 ASTN1 1 176888081 Missense_Mutation SNP G 11LU022_T 116927 176888081 72068341 59 697 SEC16B 0 . GRCh38 1 177958892 177958892 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1082G>T p.Arg361Ile p.R361I ENST00000308284 9/26 209 129 80 172 172 0 strelka-varscan-mutect SEC16B,missense_variant,p.Arg361Ile,ENST00000308284,NM_033127.2;SEC16B,missense_variant,p.Arg362Ile,ENST00000464631,;SEC16B,missense_variant,p.Arg5Ile,ENST00000527976,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000354921,;SEC16B,3_prime_UTR_variant,,ENST00000528461,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000466953,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,;SEC16B,upstream_gene_variant,,ENST00000526773,; A ENST00000308284 Transcript missense_variant 1172/3985 1082/3183 361/1060 R/I aGa/aTa 1 -1 SEC16B HGNC HGNC:30301 protein_coding YES CCDS44281.1 ENSP00000308339 Q96JE7 UPI0000203C4D NM_033127.2 deleterious(0) 9/26 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF11,Pfam_domain:PF12932 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 177958892 177958892 C A 1 0 0 0 0 1 0 0 0 14264 913 32 2 2 SEC16B 1 177958892 Missense_Mutation SNP C 11LU022_T 1070811 177958892 70997530 60 698 NPHS2 0 . GRCh38 1 179551314 179551314 + Silent SNP A A T rs781246634 11LU022_T 11LU022_N A A c.1011T>A p.= p.T337T ENST00000367615 8/8 364 309 55 316 316 0 strelka-varscan-mutect NPHS2,synonymous_variant,p.=,ENST00000367615,NM_014625.3;NPHS2,synonymous_variant,p.=,ENST00000367616,NM_001297575.1;AXDND1,intron_variant,,ENST00000367618,NM_144696.5;AXDND1,intron_variant,,ENST00000617277,;AXDND1,intron_variant,,ENST00000434088,;RP11-545A16.1,upstream_gene_variant,,ENST00000569644,;AXDND1,non_coding_transcript_exon_variant,,ENST00000489080,;AXDND1,intron_variant,,ENST00000484883,;AXDND1,intron_variant,,ENST00000484455,;AXDND1,intron_variant,,ENST00000511157,; T ENST00000367615 Transcript synonymous_variant 1080/1855 1011/1152 337/383 T acT/acA rs781246634 1 -1 NPHS2 HGNC HGNC:13394 protein_coding YES CCDS1331.1 ENSP00000356587 Q9NP85 UPI000003F549 NM_014625.3 8/8 hmmpanther:PTHR10264:SF23,hmmpanther:PTHR10264 LOW 1 SNV 1 1 PASS rs781246634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 179551314 179551314 A T 1 0 0 0 0 0 0 0 1 10631 175 7 4 4 NPHS2 1 179551314 Silent SNP A 11LU022_T 1592422 179551314 69405108 61 699 CACNA1E 0 . GRCh38 1 181798429 181798429 + Frame_Shift_Del DEL G G - rs375338599 11LU022_T 11LU022_N G G c.6539delG p.Gly2180AlafsTer16 p.G2180Afs*16 ENST00000367573 48/48 253 217 36 239 239 0 sindel-varindel-pindel CACNA1E,frameshift_variant,p.Gly2118AlafsTer16,ENST00000621791,NM_001205294.1;CACNA1E,frameshift_variant,p.Gly2180AlafsTer16,ENST00000621551,;CACNA1E,frameshift_variant,p.Gly2137AlafsTer16,ENST00000367567,;CACNA1E,frameshift_variant,p.Gly2118AlafsTer16,ENST00000358338,;CACNA1E,frameshift_variant,p.Gly2137AlafsTer16,ENST00000367570,NM_000721.3;CACNA1E,frameshift_variant,p.Gly2180AlafsTer16,ENST00000367573,NM_001205293.1;CACNA1E,frameshift_variant,p.Gly2179AlafsTer16,ENST00000357570,;CACNA1E,frameshift_variant,p.Gly2161AlafsTer16,ENST00000360108,; - ENST00000367573 Transcript frameshift_variant 6537/7067 6537/6942 2179/2313 A/X gcG/gc rs375338599,COSM3671541,COSM3671542,COSM3671543,COSM414272 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 48/48 0,1,1,1,1 HIGH 1 deletion 1 2 0,1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 181798429 181798429 G - 1 0 1 0 1 0 0 0 0 2230 1103 39 0 0 CACNA1E 1 181798429 Frame_Shift_Del DEL G 11LU022_T 2247115 181798429 67157993 62 700 LAMC2 0 . GRCh38 1 183220917 183220917 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.596C>T p.Ser199Phe p.S199F ENST00000264144 5/23 393 370 23 341 341 0 strelka-varscan-mutect LAMC2,missense_variant,p.Ser199Phe,ENST00000264144,NM_005562.2;LAMC2,missense_variant,p.Ser199Phe,ENST00000493293,NM_018891.2; T ENST00000264144 Transcript missense_variant 661/5147 596/3582 199/1193 S/F tCt/tTt 1 1 LAMC2 HGNC HGNC:6493 protein_coding YES CCDS1352.1 ENSP00000264144 Q13753 UPI000013D4CA NM_005562.2 deleterious(0) 5/23 hmmpanther:PTHR10574:SF270,hmmpanther:PTHR10574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 183220917 183220917 C T 1 0 0 0 0 1 0 0 0 8519 913 32 3 3 LAMC2 1 183220917 Missense_Mutation SNP C 11LU022_T 1422488 183220917 65735505 63 701 CDC73 0 . GRCh38 1 193147882 193147882 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.745A>T p.Ile249Phe p.I249F ENST00000367435 8/17 397 341 56 324 324 0 strelka-varscan-mutect CDC73,missense_variant,p.Ile249Phe,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000635846,; T ENST00000367435 Transcript missense_variant 929/4969 745/1596 249/531 I/F Att/Ttt 1 1 CDC73 HGNC HGNC:16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 deleterious(0) 8/17 Pfam_domain:PF16050,hmmpanther:PTHR12466,hmmpanther:PTHR12466:SF8 MODERATE 1 SNV 1 1 PASS rs1250821112 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 193147882 193147882 A T 1 0 0 0 0 1 0 0 0 2788 217 8 4 4 CDC73 1 193147882 Missense_Mutation SNP A 11LU022_T 9926965 193147882 55808540 64 702 CFHR4 0 . GRCh38 1 196907418 196907418 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.716G>T p.Cys239Phe p.C239F ENST00000367416 5/10 423 400 23 314 313 1 strelka-varscan-mutect CFHR4,missense_variant,p.Cys239Phe,ENST00000367416,NM_001201551.1,NM_001201550.2;CFHR4,intron_variant,,ENST00000608469,;CFHR4,intron_variant,,ENST00000251424,NM_006684.4;CFHR4,intron_variant,,ENST00000367418,;RP4-608O15.3,intron_variant,,ENST00000367421,; T ENST00000367416 Transcript missense_variant 853/2178 716/1734 239/577 C/F tGc/tTc 1 1 CFHR4 HGNC HGNC:16979 protein_coding YES CCDS55671.1 ENSP00000356386 Q92496 UPI0001F6C576 NM_001201551.1,NM_001201550.2 deleterious(0) 5/10 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF366,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE SNV 2 1 PASS rs1161123780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 196907418 196907418 G T 1 0 0 0 0 1 0 0 0 3045 1319 46 2 2 CFHR4 1 196907418 Missense_Mutation SNP G 11LU022_T 3759536 196907418 52049004 65 703 ASPM 0 . GRCh38 1 197102859 197102859 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.6392A>T p.Gln2131Leu p.Q2131L ENST00000367409 18/28 306 261 45 249 249 0 strelka-varscan-mutect ASPM,missense_variant,p.Gln2131Leu,ENST00000367409,NM_018136.4;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000612785,;ASPM,intron_variant,,ENST00000367408,; A ENST00000367409 Transcript missense_variant 6649/10887 6392/10434 2131/3477 Q/L cAg/cTg 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.2) 18/28 PROSITE_profiles:PS50096,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 197102859 197102859 T A 1 0 0 0 0 1 0 0 0 1203 1580 55 4 4 ASPM 1 197102859 Missense_Mutation SNP T 11LU022_T 195441 197102859 51853563 66 704 ASPM 0 . GRCh38 1 197124109 197124109 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.3390+1G>T p.X1130_splice ENST00000367409 190 163 27 201 200 1 strelka-varscan-mutect ASPM,splice_donor_variant,,ENST00000367409,NM_018136.4;ASPM,splice_donor_variant,,ENST00000294732,NM_001206846.1;ASPM,splice_donor_variant,,ENST00000367408,;ASPM,intron_variant,,ENST00000612785,; A ENST00000367409 Transcript splice_donor_variant -/10887 3390/10434 1130/3477 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 13/27 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 197124109 197124109 C A 1 0 0 0 0 0 0 1 0 1203 521 18 2 2 ASPM 1 197124109 Splice_Site SNP C 11LU022_T 21250 197124109 51832313 67 705 CRB1 0 . GRCh38 1 197421438 197421438 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1610T>A p.Leu537Gln p.L537Q ENST00000367400 6/12 391 337 54 270 270 0 strelka-varscan-mutect CRB1,missense_variant,p.Leu468Gln,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Leu537Gln,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Leu425Gln,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Leu537Gln,ENST00000538660,NM_001257966.1;CRB1,5_prime_UTR_variant,,ENST00000367397,;CRB1,non_coding_transcript_exon_variant,,ENST00000476483,;CRB1,upstream_gene_variant,,ENST00000480086,;CRB1,missense_variant,p.Leu537Gln,ENST00000484075,; A ENST00000367400 Transcript missense_variant 1745/4932 1610/4221 537/1406 L/Q cTg/cAg 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0) 6/12 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24049,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 197421438 197421438 T A 1 0 0 0 0 1 0 0 0 3648 1580 55 4 4 CRB1 1 197421438 Missense_Mutation SNP T 11LU022_T 297329 197421438 51534984 68 706 CACNA1S 0 . GRCh38 1 201078028 201078028 + Missense_Mutation SNP C C A rs373712202 11LU022_T 11LU022_N C C c.1470G>T p.Gln490His p.Q490H ENST00000362061 11/44 517 315 202 451 451 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Gln490His,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Gln490His,ENST00000367338,; A ENST00000362061 Transcript missense_variant 1697/6166 1470/5622 490/1873 Q/H caG/caT rs373712202 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 deleterious(0.03) 11/44 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs373712202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 201078028 201078028 C A 1 0 0 0 0 1 0 0 0 2235 564 20 2 2 CACNA1S 1 201078028 Missense_Mutation SNP C 11LU022_T 3656590 201078028 47878394 69 707 IGFN1 0 . GRCh38 1 201206425 201206425 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1532A>T p.Glu511Val p.E511V ENST00000335211 12/24 272 172 100 233 233 0 strelka-varscan-mutect IGFN1,missense_variant,p.Glu511Val,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,non_coding_transcript_exon_variant,,ENST00000444705,;IGFN1,intron_variant,,ENST00000437879,; T ENST00000335211 Transcript missense_variant 1662/11810 1532/11127 511/3708 E/V gAg/gTg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 201206425 201206425 A T 1 0 0 0 0 1 0 0 0 7497 304 11 4 4 IGFN1 1 201206425 Missense_Mutation SNP A 11LU022_T 128397 201206425 47749997 70 708 ADORA1 0 . GRCh38 1 203165549 203165549 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.630G>T p.Gln210His p.Q210H ENST00000367236 3/3 103 71 32 77 77 0 strelka-varscan ADORA1,missense_variant,p.Gln210His,ENST00000367236,NM_001048230.1;ADORA1,missense_variant,p.Gln210His,ENST00000337894,NM_000674.2;ADORA1,missense_variant,p.Gln210His,ENST00000309502,;ADORA1,missense_variant,p.Gln94His,ENST00000618295,;ADORA1,3_prime_UTR_variant,,ENST00000367235,;MYBPH,downstream_gene_variant,,ENST00000255416,NM_004997.2;MYBPH,downstream_gene_variant,,ENST00000621380,;ADORA1,non_coding_transcript_exon_variant,,ENST00000472535,;ADORA1,non_coding_transcript_exon_variant,,ENST00000467253,;ADORA1,non_coding_transcript_exon_variant,,ENST00000464019,; T ENST00000367236 Transcript missense_variant 1551/3407 630/981 210/326 Q/H caG/caT 1 1 ADORA1 HGNC HGNC:262 protein_coding YES CCDS1434.1 ENSP00000356205 P30542 UPI00000503E1 NM_001048230.1 deleterious(0.03) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24246,hmmpanther:PTHR24246:SF1,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 203165549 203165549 G T 1 0 0 0 0 1 0 0 0 401 962 34 2 2 ADORA1 1 203165549 Missense_Mutation SNP G 11LU022_T 1959124 203165549 45790873 71 709 CHIT1 0 . GRCh38 1 203217054 203217054 + Frame_Shift_Del DEL G G - 11LU022_T 11LU022_N G G c.1236delC p.Ser413AlafsTer65 p.S413Afs*65 ENST00000367229 11/11 363 296 67 288 288 0 sindel-varindel-pindel CHIT1,frameshift_variant,p.Ser413AlafsTer65,ENST00000367229,NM_001270509.1,NM_003465.2;CHIT1,frameshift_variant,p.Ser394AlafsTer65,ENST00000255427,NM_001256125.1;CHIT1,intron_variant,,ENST00000484834,;CHIT1,intron_variant,,ENST00000479483,;CHIT1,downstream_gene_variant,,ENST00000506427,;CHIT1,3_prime_UTR_variant,,ENST00000491855,;CHIT1,3_prime_UTR_variant,,ENST00000503786,; - ENST00000367229 Transcript frameshift_variant 1271/2246 1236/1401 412/466 P/X ccC/cc COSM255941 1 -1 CHIT1 HGNC HGNC:1936 protein_coding YES CCDS1436.1 ENSP00000356198 Q13231 UPI00000399C1 NM_001270509.1,NM_003465.2 11/11 hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF211 1 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 203217054 203217054 G - 1 0 1 0 1 0 0 0 0 3105 1335 47 0 0 CHIT1 1 203217054 Frame_Shift_Del DEL G 11LU022_T 51505 203217054 45739368 72 710 AVPR1B 0 . GRCh38 1 206115970 206115970 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.921C>A p.Asp307Glu p.D307E ENST00000367126 1/2 59 28 31 48 48 0 strelka-varscan AVPR1B,missense_variant,p.Asp307Glu,ENST00000367126,NM_000707.3;RP11-38J22.3,upstream_gene_variant,,ENST00000425896,;AVPR1B,intron_variant,,ENST00000612906,; T ENST00000367126 Transcript missense_variant 1386/2237 921/1275 307/424 D/E gaC/gaA 1 -1 AVPR1B HGNC HGNC:896 protein_coding YES CCDS73015.1 ENSP00000356094 P47901 UPI000005043A NM_000707.3 deleterious(0.01) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00896,Prints_domain:PR00897,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF18,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 206115970 206115970 G T 1 0 0 0 0 1 0 0 0 1388 1368 48 2 2 AVPR1B 1 206115970 Missense_Mutation SNP G 11LU022_T 2898916 206115970 42840452 73 711 CR1 0 . GRCh38 1 207616689 207616689 + Missense_Mutation SNP G G T rs777865155 11LU022_T 11LU022_N G G c.6776G>T p.Arg2259Ile p.R2259I ENST00000367049 41/47 313 240 73 228 228 0 strelka-varscan CR1,missense_variant,p.Arg2259Ile,ENST00000367049,NM_000651.4;CR1,missense_variant,p.Arg1809Ile,ENST00000367051,;CR1,missense_variant,p.Arg1809Ile,ENST00000367052,;CR1,missense_variant,p.Arg1809Ile,ENST00000367053,;CR1,missense_variant,p.Arg1809Ile,ENST00000400960,NM_000573.3;CR1,missense_variant,p.Arg432Ile,ENST00000529814,; T ENST00000367049 Transcript missense_variant 6776/7470 6776/7470 2259/2489 R/I aGa/aTa rs777865155 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 deleterious(0.03) 41/47 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF354,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 207616689 207616689 G T 1 0 0 0 0 1 0 0 0 3638 942 33 2 2 CR1 1 207616689 Missense_Mutation SNP G 11LU022_T 1500719 207616689 41339733 74 712 TRAF3IP3 0 . GRCh38 1 209781452 209781453 + Frame_Shift_Ins INS - - C novel 11LU022_T 11LU022_N - - c.1560dupC p.Arg521GlnfsTer26 p.R521Qfs*26 ENST00000367024 16/17 148 86 62 144 144 0 sindel-varindel-pindel TRAF3IP3,frameshift_variant,p.Arg521GlnfsTer26,ENST00000367024,NM_001320143.1;TRAF3IP3,frameshift_variant,p.Arg521GlnfsTer26,ENST00000367025,NM_025228.3;TRAF3IP3,frameshift_variant,p.Arg501GlnfsTer26,ENST00000367026,NM_001320144.1;C1orf74,3_prime_UTR_variant,,ENST00000294811,NM_152485.2;TRAF3IP3,intron_variant,,ENST00000477431,;IRF6,downstream_gene_variant,,ENST00000367021,NM_006147.3;IRF6,downstream_gene_variant,,ENST00000542854,NM_001206696.1;TRAF3IP3,downstream_gene_variant,,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000367023,NM_001287754.1;TRAF3IP3,downstream_gene_variant,,ENST00000487271,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000467830,;TRAF3IP3,downstream_gene_variant,,ENST00000488702,;TRAF3IP3,3_prime_UTR_variant,,ENST00000471368,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000460314,;TRAF3IP3,downstream_gene_variant,,ENST00000476050,;TRAF3IP3,downstream_gene_variant,,ENST00000478359,;TRAF3IP3,downstream_gene_variant,,ENST00000474496,; C ENST00000367024 Transcript frameshift_variant 2073-2074/2331 1557-1558/1656 519-520/551 -/X -/C 1 1 TRAF3IP3 HGNC HGNC:30766 protein_coding YES CCDS1490.2 ENSP00000355991 Q9Y228 UPI00005190E1 NM_001320143.1 16/17 hmmpanther:PTHR15715:SF21,hmmpanther:PTHR15715 HIGH insertion 2 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 7 5 3 209781452 209781452 - C 1 0 1 1 0 0 0 0 0 16925 1538 54 0 0 TRAF3IP3 1 209781452 Frame_Shift_Ins INS - 11LU022_T 2164763 209781452 39174970 75 713 PTPN14 0 . GRCh38 1 214393744 214393744 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.880T>C p.= p.L294L ENST00000366956 10/19 349 330 19 281 281 0 strelka-varscan PTPN14,synonymous_variant,p.=,ENST00000366956,NM_005401.4;PTPN14,3_prime_UTR_variant,,ENST00000543945,; G ENST00000366956 Transcript synonymous_variant 1075/12985 880/3564 294/1187 L Ttg/Ctg 1 -1 PTPN14 HGNC HGNC:9647 protein_coding YES CCDS1514.1 ENSP00000355923 Q15678 UPI000013DCA6 NM_005401.4 10/19 PROSITE_profiles:PS50057,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,Pfam_domain:PF09380,PIRSF_domain:PIRSF000934,Gene3D:2.30.29.30,SMART_domains:SM01196,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 214393744 214393744 A G 1 0 0 0 0 0 0 0 1 12936 40 2 5 5 PTPN14 1 214393744 Silent SNP A 11LU022_T 4612292 214393744 34562678 76 714 KCNK2 0 . GRCh38 1 215086437 215086437 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.116C>T p.Thr39Met p.T39M ENST00000444842 2/7 280 248 32 215 214 1 strelka-varscan KCNK2,missense_variant,p.Thr39Met,ENST00000444842,NM_001017425.2;KCNK2,missense_variant,p.Thr24Met,ENST00000391894,NM_014217.3;KCNK2,missense_variant,p.Thr35Met,ENST00000391895,NM_001017424.2;KCNK2,5_prime_UTR_variant,,ENST00000457122,;KCNK2,5_prime_UTR_variant,,ENST00000478774,;KCNK2,missense_variant,p.Thr35Met,ENST00000486921,;KCNK2,missense_variant,p.Thr35Met,ENST00000467031,;KCNK2,missense_variant,p.Thr24Met,ENST00000474771,;KCNK2,missense_variant,p.Thr39Met,ENST00000470177,; T ENST00000444842 Transcript missense_variant 266/3379 116/1281 39/426 T/M aCg/aTg COSM1639719,COSM1639720,COSM5461139 1 1 KCNK2 HGNC HGNC:6277 protein_coding YES CCDS41467.1 ENSP00000394033 O95069 UPI000013D4B8 NM_001017425.2 deleterious_low_confidence(0) 2/7 hmmpanther:PTHR11003:SF21,hmmpanther:PTHR11003 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 215086437 215086437 C T 1 0 0 0 0 1 0 0 0 7983 536 19 1 1 KCNK2 1 215086437 Missense_Mutation SNP C 11LU022_T 692693 215086437 33869985 77 715 USH2A 0 . GRCh38 1 215838095 215838095 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.9267C>A p.= p.V3089V ENST00000307340 47/72 327 297 30 280 279 1 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript synonymous_variant 9654/18883 9267/15609 3089/5202 V gtC/gtA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 47/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 215838095 215838095 G T 1 0 0 0 0 0 0 0 1 17570 929 33 2 2 USH2A 1 215838095 Silent SNP G 11LU022_T 751658 215838095 33118327 78 716 ESRRG 0 . GRCh38 1 216519299 216519299 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1021G>T p.Asp341Tyr p.D341Y ENST00000366937 7/8 440 399 41 331 331 0 strelka-varscan ESRRG,missense_variant,p.Asp306Tyr,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000360012,NM_001243514.1;ESRRG,missense_variant,p.Asp341Tyr,ENST00000366937,NM_001243518.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000361525,NM_206594.2;ESRRG,missense_variant,p.Asp306Tyr,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,missense_variant,p.Asp306Tyr,ENST00000493603,NM_001243510.2;ESRRG,missense_variant,p.Asp306Tyr,ENST00000366938,NM_001243513.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000361395,;ESRRG,missense_variant,p.Asp329Tyr,ENST00000408911,NM_001438.3;ESRRG,missense_variant,p.Asp306Tyr,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000616180,;ESRRG,missense_variant,p.Asp267Tyr,ENST00000463665,NM_001243507.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000487276,NM_001243512.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000493748,NM_001243509.1;ESRRG,missense_variant,p.Asp306Tyr,ENST00000475275,; A ENST00000366937 Transcript missense_variant 1288/5365 1021/1413 341/470 D/Y Gat/Tat 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 deleterious(0) 7/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PIRSF_domain:PIRSF500939,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 216519299 216519299 C A 1 0 0 0 0 1 0 0 0 5124 884 31 1 1 ESRRG 1 216519299 Missense_Mutation SNP C 11LU022_T 681204 216519299 32437123 79 717 EPRS 0 . GRCh38 1 220032386 220032386 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.528+1G>T p.X176_splice ENST00000366923 157 145 12 162 161 1 strelka-varscan EPRS,splice_donor_variant,,ENST00000366923,NM_004446.2;EPRS,splice_donor_variant,,ENST00000609181,;EPRS,splice_donor_variant,,ENST00000477030,; A ENST00000366923 Transcript splice_donor_variant -/5014 528/4539 176/1512 1 -1 EPRS HGNC HGNC:3418 protein_coding YES CCDS31027.1 ENSP00000355890 P07814 UPI0000205E8C NM_004446.2 5/31 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 220032386 220032386 C A 1 0 0 0 0 0 0 1 0 5039 521 18 2 2 EPRS 1 220032386 Splice_Site SNP C 11LU022_T 3513087 220032386 28924036 80 718 RAB3GAP2 0 . GRCh38 1 220167534 220167534 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2948C>A p.Ser983Ter p.S983* ENST00000358951 25/35 453 415 38 395 395 0 strelka-varscan RAB3GAP2,stop_gained,p.Ser983Ter,ENST00000358951,NM_012414.3; T ENST00000358951 Transcript stop_gained 3065/7257 2948/4182 983/1393 S/* tCa/tAa 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 25/35 Pfam_domain:PF14656,hmmpanther:PTHR12472 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 220167534 220167534 G T 1 0 0 0 0 0 1 0 0 13095 1294 45 2 2 RAB3GAP2 1 220167534 Nonsense_Mutation SNP G 11LU022_T 135148 220167534 28788888 81 719 DISP1 0 . GRCh38 1 223004128 223004128 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.2731G>T p.Gly911Trp p.G911W ENST00000284476 8/8 229 123 106 235 235 0 strelka-varscan DISP1,missense_variant,p.Gly911Trp,ENST00000284476,NM_032890.3; T ENST00000284476 Transcript missense_variant 2895/4762 2731/4575 911/1524 G/W Ggg/Tgg COSM358333 1 1 DISP1 HGNC HGNC:19711 protein_coding YES CCDS1536.1 ENSP00000284476 Q96F81 UPI000016069D NM_032890.3 deleterious(0) 8/8 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF115 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 223004128 223004128 G T 1 0 0 0 0 1 0 0 0 4345 1000 35 2 2 DISP1 1 223004128 Missense_Mutation SNP G 11LU022_T 2836594 223004128 25952294 82 720 DNAH14 0 . GRCh38 1 224964549 224964549 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.438A>G p.= p.L146L ENST00000400952 5/11 194 112 82 179 179 0 strelka-varscan DNAH14,synonymous_variant,p.=,ENST00000430092,NM_001373.1;DNAH14,synonymous_variant,p.=,ENST00000439375,;DNAH14,synonymous_variant,p.=,ENST00000445597,;DNAH14,synonymous_variant,p.=,ENST00000366849,;DNAH14,synonymous_variant,p.=,ENST00000400952,NM_001145154.1;DNAH14,synonymous_variant,p.=,ENST00000366850,NM_144989.2;DNAH14,synonymous_variant,p.=,ENST00000366848,;DNAH14,synonymous_variant,p.=,ENST00000433124,;DNAH14,downstream_gene_variant,,ENST00000498360,;DNAH14,upstream_gene_variant,,ENST00000453375,;DNAH14,non_coding_transcript_exon_variant,,ENST00000486657,;DNAH14,upstream_gene_variant,,ENST00000474127,; G ENST00000400952 Transcript synonymous_variant 640/1984 438/1362 146/453 L ttA/ttG 1 1 DNAH14 HGNC HGNC:2945 protein_coding YES CCDS44322.1 ENSP00000383737 Q0VDD8 UPI0000203FC8 NM_001145154.1 5/11 hmmpanther:PTHR22645,hmmpanther:PTHR22645:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 224964549 224964549 A G 1 0 0 0 0 0 0 0 1 4415 388 14 5 5 DNAH14 1 224964549 Silent SNP A 11LU022_T 1960421 224964549 23991873 83 721 GJC2 0 . GRCh38 1 228158689 228158689 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.931C>A p.Pro311Thr p.P311T ENST00000366714 2/2 56 50 6 59 59 0 strelka-varscan GJC2,missense_variant,p.Pro311Thr,ENST00000366714,NM_020435.3; A ENST00000366714 Transcript missense_variant 1106/2243 931/1320 311/439 P/T Ccc/Acc 1 1 GJC2 HGNC HGNC:17494 protein_coding YES CCDS1569.1 ENSP00000355675 Q5T442 UPI000034ECE8 NM_020435.3 deleterious(0.05) 2/2 hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF52,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.14083 0.9999999 1 1 1 0 A 3 1 3 228158689 228158689 C A 1 0 0 0 0 1 0 0 0 6292 623 22 2 2 GJC2 1 228158689 Missense_Mutation SNP C 11LU022_T 3194140 228158689 20797733 84 722 PGBD5 0 . GRCh38 1 230337208 230337208 + Silent SNP C C A rs73119536 11LU022_T 11LU022_N C C c.975G>T p.= p.V325V ENST00000391860 4/7 255 163 92 219 218 1 strelka-varscan PGBD5,synonymous_variant,p.=,ENST00000391860,NM_001258311.1;PGBD5,synonymous_variant,p.=,ENST00000525115,;PGBD5,upstream_gene_variant,,ENST00000530424,; A ENST00000391860 Transcript synonymous_variant 1418/10961 975/1575 325/524 V gtG/gtT rs73119536 1 -1 PGBD5 HGNC HGNC:19405 protein_coding YES ENSP00000375733 A0A0A0MS21 UPI000004EBDA NM_001258311.1 4/7 hmmpanther:PTHR28576,hmmpanther:PTHR28576:SF2,Pfam_domain:PF13843 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 230337208 230337208 C A 1 0 0 0 0 0 0 0 1 11874 581 21 2 2 PGBD5 1 230337208 Silent SNP C 11LU022_T 2178519 230337208 18619214 85 723 SIPA1L2 0 . GRCh38 1 232483885 232483885 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1888G>T p.Ala630Ser p.A630S ENST00000366630 5/22 327 205 122 249 249 0 strelka-varscan SIPA1L2,missense_variant,p.Ala630Ser,ENST00000366630,;SIPA1L2,missense_variant,p.Ala630Ser,ENST00000262861,NM_020808.3; A ENST00000366630 Transcript missense_variant 2247/6690 1888/5169 630/1722 A/S Gcg/Tcg 1 -1 SIPA1L2 HGNC HGNC:23800 protein_coding YES CCDS41474.1 ENSP00000355589 Q9P2F8 UPI00001D7D6A deleterious(0) 5/22 PROSITE_profiles:PS50085,hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711,Pfam_domain:PF02145,Superfamily_domains:0043732 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 232483885 232483885 C A 1 0 0 0 0 1 0 0 0 14593 739 26 2 2 SIPA1L2 1 232483885 Missense_Mutation SNP C 11LU022_T 2146677 232483885 16472537 86 724 HEATR1 0 . GRCh38 1 236571671 236571671 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3723G>T p.Leu1241Phe p.L1241F ENST00000366582 27/45 291 251 40 226 226 0 strelka-varscan-mutect HEATR1,missense_variant,p.Leu1241Phe,ENST00000366582,NM_018072.5;HEATR1,missense_variant,p.Leu1160Phe,ENST00000366581,;HEATR1,downstream_gene_variant,,ENST00000490339,; A ENST00000366582 Transcript missense_variant 3838/8447 3723/6435 1241/2144 L/F ttG/ttT 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 tolerated(0.14) 27/45 Gene3D:1.25.10.10,hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs887404006 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 3 236571671 236571671 C A 1 0 0 0 0 1 0 0 0 6910 709 25 2 2 HEATR1 1 236571671 Missense_Mutation SNP C 11LU022_T 4087786 236571671 12384751 87 725 ACTN2 0 . GRCh38 1 236762604 236762604 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.2670G>T p.= p.G890G ENST00000542672 21/21 724 614 110 525 525 0 strelka-varscan-mutect ACTN2,synonymous_variant,p.=,ENST00000546208,NM_001278344.1;ACTN2,synonymous_variant,p.=,ENST00000542672,NM_001278343.1;ACTN2,synonymous_variant,p.=,ENST00000366578,NM_001103.3;ACTN2,downstream_gene_variant,,ENST00000461367,; T ENST00000542672 Transcript synonymous_variant 2890/4906 2670/2685 890/894 G ggG/ggT 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 21/21 Gene3D:1.10.238.10,Pfam_domain:PF08726,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM01184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 236762604 236762604 G T 1 0 0 0 0 0 0 0 1 249 1219 43 2 2 ACTN2 1 236762604 Silent SNP G 11LU022_T 190933 236762604 12193818 88 726 RYR2 0 . GRCh38 1 237640940 237640940 + Missense_Mutation SNP G G T rs794728753 11LU022_T 11LU022_N G G c.7159G>T p.Ala2387Ser p.A2387S ENST00000366574 47/105 138 99 39 117 117 0 strelka-varscan-mutect RYR2,missense_variant,p.Ala2387Ser,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ala2371Ser,ENST00000360064,; T ENST00000366574 Transcript missense_variant 7476/16562 7159/14904 2387/4967 A/S Gcg/Tcg rs794728753,CM056386,HM030024 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.08) 47/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 pathogenic MODERATE 1 SNV 1 1,1,1 1 PASS rs794728753 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 237640940 237640940 G T 1 0 0 0 0 1 0 0 0 14029 1087 38 1 1 RYR2 1 237640940 Missense_Mutation SNP G 11LU022_T 878336 237640940 11315482 89 727 RYR2 0 . GRCh38 1 237678104 237678104 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.8887T>A p.Phe2963Ile p.F2963I ENST00000366574 61/105 169 106 63 147 147 0 strelka-varscan-mutect RYR2,missense_variant,p.Phe2963Ile,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Phe2947Ile,ENST00000360064,;RYR2,intron_variant,,ENST00000609119,; A ENST00000366574 Transcript missense_variant 9204/16562 8887/14904 2963/4967 F/I Ttt/Att 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 61/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 237678104 237678104 T A 1 0 0 0 0 1 0 0 0 14029 1609 56 4 4 RYR2 1 237678104 Missense_Mutation SNP T 11LU022_T 37164 237678104 11278318 90 728 RYR2 0 . GRCh38 1 237709035 237709035 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.10079C>A p.Thr3360Asn p.T3360N ENST00000366574 69/105 116 97 19 107 107 0 strelka-varscan-mutect RYR2,missense_variant,p.Thr3360Asn,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Thr3344Asn,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript missense_variant 10396/16562 10079/14904 3360/4967 T/N aCc/aAc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.09) 69/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS rs924056885 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 237709035 237709035 C A 1 0 0 0 0 1 0 0 0 14029 507 18 2 2 RYR2 1 237709035 Missense_Mutation SNP C 11LU022_T 30931 237709035 11247387 91 729 RYR2 0 . GRCh38 1 237727182 237727182 + Silent SNP C C T rs780588693 11LU022_T 11LU022_N C C c.10821C>T p.= p.P3607P ENST00000366574 76/105 89 84 5 55 55 0 strelka-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;RYR2,downstream_gene_variant,,ENST00000609253,; T ENST00000366574 Transcript synonymous_variant 11138/16562 10821/14904 3607/4967 P ccC/ccT rs780588693,COSM679865 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 76/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 0,1 LOW 1 SNV 1 0,1 1 PASS rs780588693 . 0 208 2 0 0 0 0 0 -11.25823 1 1 1 1 0 T 2 4 3 237727182 237727182 C T 1 0 0 0 0 0 0 0 1 14029 668 24 3 3 RYR2 1 237727182 Silent SNP C 11LU022_T 18147 237727182 11229240 92 730 FMN2 0 . GRCh38 1 240207396 240207396 + Frame_Shift_Del DEL C C - rs759245231 11LU022_T 11LU022_N C C c.2585delC p.Pro862LeufsTer25 p.P862Lfs*25 ENST00000319653 5/18 210 190 20 175 175 0 sindel-varindel-pindel FMN2,frameshift_variant,p.Pro862LeufsTer25,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; - ENST00000319653 Transcript frameshift_variant 2814/6434 2584/5169 862/1722 P/X Cct/ct rs759245231 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 5/18 SMART_domains:SM00498 HIGH 1 deletion 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 240207396 240207396 C - 1 0 1 0 1 0 0 0 0 5806 739 26 0 0 FMN2 1 240207396 Frame_Shift_Del DEL C 11LU022_T 2480214 240207396 8749026 93 731 OPN3 0 . GRCh38 1 241597985 241597985 + Frame_Shift_Del DEL C C - rs776170535 11LU022_T 11LU022_N C C c.706delG p.Glu236LysfsTer8 p.E236Kfs*8 ENST00000366554 3/4 119 95 24 121 121 0 sindel-varindel-pindel OPN3,frameshift_variant,p.Glu236LysfsTer8,ENST00000366554,NM_014322.2;KMO,downstream_gene_variant,,ENST00000366559,NM_003679.4;KMO,downstream_gene_variant,,ENST00000366557,;KMO,downstream_gene_variant,,ENST00000366555,;OPN3,non_coding_transcript_exon_variant,,ENST00000463155,;OPN3,non_coding_transcript_exon_variant,,ENST00000462265,;OPN3,non_coding_transcript_exon_variant,,ENST00000635737,;OPN3,frameshift_variant,p.Trp182Ter,ENST00000469376,;OPN3,frameshift_variant,p.Gly129GlufsTer168,ENST00000490673,;OPN3,3_prime_UTR_variant,,ENST00000478849,; - ENST00000366554 Transcript frameshift_variant 813/2620 706/1209 236/402 E/X Gaa/aa rs776170535 1 -1 OPN3 HGNC HGNC:14007 protein_coding YES CCDS31072.1 ENSP00000355512 Q9H1Y3 UPI000000165B NM_014322.2 3/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24240:SF62,hmmpanther:PTHR24240,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 241597985 241597985 C - 1 0 1 0 1 0 0 0 0 10957 864 30 0 0 OPN3 1 241597985 Frame_Shift_Del DEL C 11LU022_T 1390589 241597985 7358437 94 732 C1orf101 0 . GRCh38 1 244560969 244560969 + Missense_Mutation SNP G G T rs376436911 11LU022_T 11LU022_N G G c.1331G>T p.Ser444Ile p.S444I ENST00000366534 10/22 392 235 157 316 316 0 strelka-varscan-mutect C1orf101,missense_variant,p.Ser444Ile,ENST00000366534,NM_001130957.1;C1orf101,missense_variant,p.Ser293Ile,ENST00000366531,NM_001242340.1;C1orf101,missense_variant,p.Ser444Ile,ENST00000366533,NM_173807.4;C1orf101,missense_variant,p.Ser364Ile,ENST00000428042,;C1orf101,non_coding_transcript_exon_variant,,ENST00000473875,; T ENST00000366534 Transcript missense_variant 1385/3333 1331/2856 444/951 S/I aGt/aTt rs376436911 1 1 C1orf101 HGNC HGNC:28491 protein_coding YES CCDS44340.1 ENSP00000355492 Q5SY80 UPI00004701CD NM_001130957.1 deleterious(0.02) 10/22 hmmpanther:PTHR33722:SF3,hmmpanther:PTHR33722 MODERATE 1 SNV 2 1 PASS rs376436911 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 244560969 244560969 G T 1 0 0 0 0 1 0 0 0 1954 1029 36 2 2 C1orf101 1 244560969 Missense_Mutation SNP G 11LU022_T 2962984 244560969 4395453 95 733 KIF26B 0 . GRCh38 1 245685542 245685542 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2559C>A p.Asp853Glu p.D853E ENST00000407071 12/15 257 237 20 228 228 0 strelka-varscan-mutect KIF26B,missense_variant,p.Asp472Glu,ENST00000366518,;KIF26B,missense_variant,p.Asp853Glu,ENST00000407071,NM_018012.3;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,; A ENST00000407071 Transcript missense_variant 2999/7287 2559/6327 853/2108 D/E gaC/gaA 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 tolerated(0.12) 12/15 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 245685542 245685542 C A 1 0 0 0 0 1 0 0 0 8160 564 20 2 2 KIF26B 1 245685542 Missense_Mutation SNP C 11LU022_T 1124573 245685542 3270880 96 734 KIF26B 0 . GRCh38 1 245685832 245685832 + Missense_Mutation SNP T T G rs751705273 11LU022_T 11LU022_N T T c.2849T>G p.Leu950Arg p.L950R ENST00000407071 12/15 112 103 9 91 91 0 strelka-varscan-mutect KIF26B,missense_variant,p.Leu569Arg,ENST00000366518,;KIF26B,missense_variant,p.Leu950Arg,ENST00000407071,NM_018012.3;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,; G ENST00000407071 Transcript missense_variant 3289/7287 2849/6327 950/2108 L/R cTg/cGg rs751705273 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 tolerated(0.59) 12/15 MODERATE 1 SNV 1 1 PASS rs751705273 . 0 206 4 0 0 0 0 0 -17.9638 1 1 1 1 0 G 3 3 3 245685832 245685832 T G 1 0 0 0 0 1 0 0 0 8160 1580 55 5 5 KIF26B 1 245685832 Missense_Mutation SNP T 11LU022_T 290 245685832 3270590 97 735 ZNF695 0 . GRCh38 1 246987674 246987674 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.841T>A p.Ser281Thr p.S281T ENST00000339986 4/4 77 70 7 57 57 0 strelka-varscan-mutect ZNF695,missense_variant,p.Ser281Thr,ENST00000339986,NM_020394.4;ZNF695,intron_variant,,ENST00000487338,NM_001204221.1;ZNF695,intron_variant,,ENST00000498046,;ZNF670-ZNF695,intron_variant,,ENST00000474541,;ZNF670-ZNF695,intron_variant,,ENST00000465049,;ZNF695,intron_variant,,ENST00000479214,;ZNF695,intron_variant,,ENST00000366504,;ZNF695,intron_variant,,ENST00000491337,; T ENST00000339986 Transcript missense_variant 989/3340 841/1548 281/515 S/T Tca/Aca 1 -1 ZNF695 HGNC HGNC:30954 protein_coding YES CCDS44344.1 ENSP00000341236 Q8IW36 UPI0000F734A8 NM_020394.4 tolerated(0.07) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF119,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -15.67811 1 1 1 1 0 T 3 4 3 246987674 246987674 A T 1 0 0 0 0 1 0 0 0 18671 304 11 4 4 ZNF695 1 246987674 Missense_Mutation SNP A 11LU022_T 1301842 246987674 1968748 98 736 OR2C3 0 . GRCh38 1 247531767 247531767 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.745G>T p.Val249Leu p.V249L ENST00000366487 2/2 451 427 24 413 413 0 strelka-varscan-mutect OR2C3,missense_variant,p.Val249Leu,ENST00000366487,NM_198074.4;OR2C3,missense_variant,p.Val249Leu,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; A ENST00000366487 Transcript missense_variant 1107/2742 745/963 249/320 V/L Gtg/Ttg 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 247531767 247531767 C A 1 0 0 0 0 1 0 0 0 11072 507 18 2 2 OR2C3 1 247531767 Missense_Mutation SNP C 11LU022_T 544093 247531767 1424655 99 737 OR2C3 0 . GRCh38 1 247532415 247532415 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.97T>C p.= p.L33L ENST00000366487 2/2 290 270 20 269 269 0 strelka-varscan-mutect OR2C3,synonymous_variant,p.=,ENST00000366487,NM_198074.4;OR2C3,synonymous_variant,p.=,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; G ENST00000366487 Transcript synonymous_variant 459/2742 97/963 33/320 L Ttg/Ctg 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 2/2 hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 247532415 247532415 A G 1 0 0 0 0 0 0 0 1 11072 69 3 5 5 OR2C3 1 247532415 Silent SNP A 11LU022_T 648 247532415 1424007 100 738 OR2G3 0 . GRCh38 1 247605949 247605949 + Silent SNP C C A rs747428945 11LU022_T 11LU022_N C C c.364C>A p.= p.R122R ENST00000320002 1/1 155 79 76 151 151 0 strelka-varscan-mutect OR2G3,synonymous_variant,p.=,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000320002 Transcript synonymous_variant 364/930 364/930 122/309 R Cgg/Agg rs747428945,COSM3486735 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW SNV 0,1 1 PASS rs747428945 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 247605949 247605949 C A 1 0 0 0 0 0 0 0 1 11077 875 31 1 1 OR2G3 1 247605949 Silent SNP C 11LU022_T 73534 247605949 1350473 101 739 OR6F1 0 . GRCh38 1 247712117 247712117 + Silent SNP G G T 11LU022_T 11LU022_N G G c.639C>A p.= p.I213I ENST00000302084 1/1 245 224 21 222 222 0 strelka-varscan-mutect OR6F1,synonymous_variant,p.=,ENST00000302084,NM_001005286.1;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; T ENST00000302084 Transcript synonymous_variant 639/927 639/927 213/308 I atC/atA COSM121420,COSM4143634 1 -1 OR6F1 HGNC HGNC:15027 protein_coding YES CCDS31095.1 ENSP00000305640 Q8NGZ6 A0A126GV68 UPI0000041CD7 NM_001005286.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF12,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1,1 LOW SNV 1,1 1 PASS rs1391430766 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 247712117 247712117 G T 1 0 0 0 0 0 0 0 1 11269 1280 45 2 2 OR6F1 1 247712117 Silent SNP G 11LU022_T 106168 247712117 1244305 102 740 TRIM58 0 . GRCh38 1 247864703 247864703 + Splice_Site SNP A A T novel 11LU022_T 11LU022_N A A c.517-2A>T p.X173_splice ENST00000366481 160 147 13 178 178 0 strelka-varscan-mutect TRIM58,splice_acceptor_variant,,ENST00000366481,NM_015431.3; T ENST00000366481 Transcript splice_acceptor_variant -/3225 517/1461 173/486 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 2/5 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99998 1 1 1 1 0 T 5 4 3 247864703 247864703 A T 1 0 0 0 0 0 0 1 0 17024 202 7 4 4 TRIM58 1 247864703 Splice_Site SNP A 11LU022_T 152586 247864703 1091719 103 741 TRIM58 0 . GRCh38 1 247864827 247864827 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.639G>C p.Gln213His p.Q213H ENST00000366481 3/6 504 289 215 419 419 0 strelka-varscan-mutect TRIM58,missense_variant,p.Gln213His,ENST00000366481,NM_015431.3; C ENST00000366481 Transcript missense_variant 687/3225 639/1461 213/486 Q/H caG/caC 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0.03) 3/6 Low_complexity_(Seg):seg,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 247864827 247864827 G C 1 0 0 0 0 1 0 0 0 17024 933 33 4 4 TRIM58 1 247864827 Missense_Mutation SNP G 11LU022_T 124 247864827 1091595 104 742 OR2L13 0 . GRCh38 1 248100031 248100031 + Missense_Mutation SNP G G T rs755310143 11LU022_T 11LU022_N G G c.656G>T p.Arg219Leu p.R219L ENST00000358120 2/2 345 291 54 308 306 2 strelka-varscan-mutect OR2L13,missense_variant,p.Arg219Leu,ENST00000358120,NM_001304535.1,NM_175911.3; T ENST00000358120 Transcript missense_variant 801/1692 656/939 219/312 R/L cGa/cTa rs755310143,COSM1341087,COSM1341088 1 1 OR2L13 HGNC HGNC:19578 protein_coding YES CCDS1637.1 ENSP00000350836 Q8N349 A0A126GW96 UPI0000043517 NM_001304535.1,NM_175911.3 tolerated(0.3) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF102,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs755310143 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 248100031 248100031 G T 1 0 0 0 0 1 0 0 0 11084 1058 37 1 1 OR2L13 1 248100031 Missense_Mutation SNP G 11LU022_T 235204 248100031 856391 105 743 OR2T10 0 . GRCh38 1 248593013 248593013 + Nonsense_Mutation SNP A A T rs758843051 11LU022_T 11LU022_N A A c.756T>A p.Tyr252Ter p.Y252* ENST00000330500 1/1 118 70 48 95 95 0 strelka-varscan-mutect OR2T10,stop_gained,p.Tyr252Ter,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; T ENST00000330500 Transcript stop_gained 756/939 756/939 252/312 Y/* taT/taA rs758843051 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS rs758843051 . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 248593013 248593013 A T 1 0 0 0 0 0 1 0 0 11095 224 8 4 4 OR2T10 1 248593013 Nonsense_Mutation SNP A 11LU022_T 492982 248593013 363409 106 744 OR2T10 0 . GRCh38 1 248593332 248593332 + Nonsense_Mutation SNP G G T rs200418834 11LU022_T 11LU022_N G G c.437C>A p.Ser146Ter p.S146* ENST00000330500 1/1 450 408 42 354 354 0 strelka-varscan-mutect OR2T10,stop_gained,p.Ser146Ter,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; T ENST00000330500 Transcript stop_gained 437/939 437/939 146/312 S/* tCa/tAa rs200418834,COSM4829138 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 HIGH 1 SNV 0,1 1 PASS rs200418834 . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 248593332 248593332 G T 1 0 0 0 0 0 1 0 0 11095 1294 45 2 2 OR2T10 1 248593332 Nonsense_Mutation SNP G 11LU022_T 319 248593332 363090 107 745 OR2T27 0 . GRCh38 1 248650433 248650433 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.452G>T p.Gly151Val p.G151V ENST00000344889 1/1 362 302 60 291 291 0 strelka-varscan-mutect OR2T27,missense_variant,p.Gly151Val,ENST00000344889,NM_001001824.1; A ENST00000344889 Transcript missense_variant 452/954 452/954 151/317 G/V gGa/gTa 1 -1 OR2T27 HGNC HGNC:31252 protein_coding YES CCDS31124.1 ENSP00000342008 Q8NH04 UPI000004F239 NM_001001824.1 tolerated(0.21) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF78,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 248650433 248650433 C A 1 0 0 0 0 1 0 0 0 11098 855 30 2 2 OR2T27 1 248650433 Missense_Mutation SNP C 11LU022_T 57101 248650433 305989 108 746 TPO 0 . GRCh38 2 1453728 1453728 + Missense_Mutation SNP C C A rs764723379 11LU022_T 11LU022_N C C c.517C>A p.Leu173Met p.L173M ENST00000345913 6/17 489 393 96 512 512 0 strelka-varscan-mutect TPO,missense_variant,p.Leu102Met,ENST00000422464,;TPO,missense_variant,p.Leu173Met,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Leu173Met,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Leu173Met,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Leu173Met,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Leu173Met,ENST00000382198,NM_175722.3;TPO,downstream_gene_variant,,ENST00000423320,;TPO,intron_variant,,ENST00000497517,; A ENST00000345913 Transcript missense_variant 608/3145 517/2802 173/933 L/M Ctg/Atg rs764723379,COSM401920 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 deleterious(0) 6/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764723379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 1453728 1453728 C A 1 0 0 0 0 1 0 0 0 16891 680 24 2 2 TPO 2 1453728 Missense_Mutation SNP C 11LU022_T 1453728 240739801 109 747 RNF144A 0 . GRCh38 2 7020649 7020649 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.478A>G p.Met160Val p.M160V ENST00000320892 6/9 241 188 53 268 268 0 strelka-varscan-mutect RNF144A,missense_variant,p.Met160Val,ENST00000320892,NM_014746.4;RNF144A,missense_variant,p.Met156Val,ENST00000432850,;RNF144A,non_coding_transcript_exon_variant,,ENST00000467276,;RNF144A,non_coding_transcript_exon_variant,,ENST00000480970,;RNF144A,downstream_gene_variant,,ENST00000471060,; G ENST00000320892 Transcript missense_variant 920/5743 478/879 160/292 M/V Atg/Gtg 1 1 RNF144A HGNC HGNC:20457 protein_coding YES CCDS1657.1 ENSP00000321330 P50876 UPI00001E058A NM_014746.4 tolerated(0.5) 6/9 hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF99 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 7020649 7020649 A G 1 0 0 0 0 1 0 0 0 13623 217 8 5 5 RNF144A 2 7020649 Missense_Mutation SNP A 11LU022_T 5566921 7020649 235172880 110 748 LDAH 0 . GRCh38 2 20685580 20685580 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.1052A>C p.Glu351Ala p.E351A ENST00000381090 8/9 181 146 35 153 153 0 strelka-varscan-mutect LDAH,missense_variant,p.Glu351Ala,ENST00000381090,;LDAH,missense_variant,p.Glu221Ala,ENST00000403006,;LDAH,3_prime_UTR_variant,,ENST00000435420,NM_001282724.1,NM_001282719.1;LDAH,3_prime_UTR_variant,,ENST00000541941,NM_001282721.1;LDAH,3_prime_UTR_variant,,ENST00000440866,NM_001282723.1;LDAH,3_prime_UTR_variant,,ENST00000619656,NM_001282722.1;LDAH,3_prime_UTR_variant,,ENST00000237822,NM_021925.3;LDAH,downstream_gene_variant,,ENST00000626491,NM_001282720.1;LDAH,non_coding_transcript_exon_variant,,ENST00000470099,; G ENST00000381090 Transcript missense_variant 1132/2045 1052/1113 351/370 E/A gAa/gCa 1 -1 LDAH HGNC HGNC:26145 protein_coding ENSP00000370480 B5MDU6 UPI0000208B2E 8/9 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 20685580 20685580 T G 1 0 0 0 0 1 0 0 0 8601 1783 62 5 5 LDAH 2 20685580 Missense_Mutation SNP T 11LU022_T 13664931 20685580 221507949 111 749 ADCY3 0 . GRCh38 2 24839900 24839900 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1328A>G p.Asn443Ser p.N443S ENST00000260600 6/21 355 292 63 381 381 0 strelka-varscan-mutect ADCY3,missense_variant,p.Asn443Ser,ENST00000260600,NM_004036.3;ADCY3,missense_variant,p.Asn443Ser,ENST00000405392,NM_001320613.1;ADCY3,missense_variant,p.Asn114Ser,ENST00000606682,;ADCY3,missense_variant,p.Asn393Ser,ENST00000435135,;ADCY3,missense_variant,p.Asn199Ser,ENST00000427849,;ADCY3,downstream_gene_variant,,ENST00000433852,;ADCY3,non_coding_transcript_exon_variant,,ENST00000454027,;ADCY3,downstream_gene_variant,,ENST00000479517,; C ENST00000260600 Transcript missense_variant 2180/5050 1328/3435 443/1144 N/S aAc/aGc 1 -1 ADCY3 HGNC HGNC:234 protein_coding YES CCDS1715.1 ENSP00000260600 O60266 UPI000013D0ED NM_004036.3 tolerated(0.05) 6/21 PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF291,PROSITE_patterns:PS00452,Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 24839900 24839900 T C 1 0 0 0 0 1 0 0 0 339 1725 60 5 5 ADCY3 2 24839900 Missense_Mutation SNP T 11LU022_T 4154320 24839900 217353629 112 750 EPT1 0 . GRCh38 2 26364875 26364875 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.170G>T p.Gly57Val p.G57V ENST00000260585 3/10 249 214 35 234 234 0 strelka-varscan-mutect EPT1,missense_variant,p.Gly57Val,ENST00000613142,;EPT1,missense_variant,p.Gly57Val,ENST00000260585,NM_033505.2;EPT1,missense_variant,p.Gly57Val,ENST00000447170,;EPT1,missense_variant,p.Gly25Val,ENST00000442141,; T ENST00000260585 Transcript missense_variant 289/8101 170/1194 57/397 G/V gGc/gTc 1 1 EPT1 HGNC HGNC:29361 protein_coding YES CCDS46240.1 ENSP00000260585 Q9C0D9 UPI00003CE422 NM_033505.2 deleterious(0) 3/10 Pfam_domain:PF01066,PIRSF_domain:PIRSF015665,hmmpanther:PTHR10414,hmmpanther:PTHR10414:SF47,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 26364875 26364875 G T 1 0 0 0 0 1 0 0 0 5047 1203 42 2 2 EPT1 2 26364875 Missense_Mutation SNP G 11LU022_T 1524975 26364875 215828654 113 751 C2orf71 0 . GRCh38 2 29071086 29071086 + Missense_Mutation SNP G G A 11LU022_T 11LU022_N G G c.3176C>T p.Pro1059Leu p.P1059L ENST00000331664 1/2 37 29 8 74 74 0 strelka-varscan-mutect C2orf71,missense_variant,p.Pro1059Leu,ENST00000331664,NM_001029883.2; A ENST00000331664 Transcript missense_variant 3176/7044 3176/3867 1059/1288 P/L cCt/cTt COSM353126 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.07) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 2 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.9112 1 1 1 1 0 A 3 1 3 29071086 29071086 G A 1 0 0 0 0 1 0 0 0 2045 1000 35 3 3 C2orf71 2 29071086 Missense_Mutation SNP G 11LU022_T 2706211 29071086 213122443 114 752 LBH 0 . GRCh38 2 30323535 30323535 + Nonstop_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.146A>G p.Ter49TrpextTer12 p.*49Wext*12 ENST00000404397 3/3 126 107 19 140 140 0 strelka-varscan-mutect LBH,stop_lost,p.Ter49TrpextTer12,ENST00000404397,; G ENST00000404397 Transcript stop_lost 348/543 146/147 49/48 */W tAg/tGg 1 1 LBH HGNC HGNC:29532 protein_coding ENSP00000384443 B5MC28 UPI000173A44E 3/3 HIGH 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 3 30323535 30323535 A G 1 0 0 0 0 0 0 0 0 8555 433 15 5 5 LBH 2 30323535 Nonstop_Mutation SNP A 11LU022_T 1252449 30323535 211869994 115 753 XDH 0 . GRCh38 2 31401277 31401277 + Frame_Shift_Del DEL A A - novel 11LU022_T 11LU022_N A A c.249delT p.Ala84GlnfsTer2 p.A84Qfs*2 ENST00000379416 4/36 512 407 105 544 544 0 sindel-varindel-pindel XDH,frameshift_variant,p.Ala84GlnfsTer2,ENST00000379416,NM_000379.3; - ENST00000379416 Transcript frameshift_variant 298/5688 249/4002 83/1333 V/X gtT/gt 1 -1 XDH HGNC HGNC:12805 protein_coding YES CCDS1775.1 ENSP00000368727 P47989 UPI0000036BC9 NM_000379.3 4/36 PROSITE_profiles:PS51085,hmmpanther:PTHR11908:SF78,hmmpanther:PTHR11908,Gene3D:3.10.20.30,TIGRFAM_domain:TIGR02963,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF54292 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 31401277 31401277 A - 1 0 1 0 1 0 0 0 0 17985 117 5 0 0 XDH 2 31401277 Frame_Shift_Del DEL A 11LU022_T 1077742 31401277 210792252 116 754 NLRC4 0 . GRCh38 2 32249806 32249806 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.2058T>A p.= p.S686S ENST00000404025 5/10 183 143 40 166 166 0 strelka-varscan-mutect NLRC4,synonymous_variant,p.=,ENST00000404025,;NLRC4,synonymous_variant,p.=,ENST00000360906,NM_001199139.1,NM_021209.4;NLRC4,synonymous_variant,p.=,ENST00000402280,NM_001199138.1;NLRC4,intron_variant,,ENST00000342905,NM_001302504.1; T ENST00000404025 Transcript synonymous_variant 2547/3581 2058/3075 686/1024 S tcT/tcA 1 -1 NLRC4 HGNC HGNC:16412 protein_coding YES CCDS33174.1 ENSP00000385090 Q9NPP4 UPI0000126FAD 5/10 hmmpanther:PTHR10044:SF104,hmmpanther:PTHR10044,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 32249806 32249806 A T 1 0 0 0 0 0 0 0 1 10506 175 7 4 4 NLRC4 2 32249806 Silent SNP A 11LU022_T 848529 32249806 209943723 117 755 TTC27 0 . GRCh38 2 32812580 32812580 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.2273A>T p.Lys758Met p.K758M ENST00000317907 18/20 166 138 28 197 197 0 strelka-varscan-mutect TTC27,missense_variant,p.Lys758Met,ENST00000317907,NM_017735.4,NM_001193509.1;TTC27,3_prime_UTR_variant,,ENST00000428527,; T ENST00000317907 Transcript missense_variant 2504/2876 2273/2532 758/843 K/M aAg/aTg 1 1 TTC27 HGNC HGNC:25986 protein_coding YES CCDS33176.1 ENSP00000313953 Q6P3X3 UPI0000208226 NM_017735.4,NM_001193509.1 deleterious(0.02) 18/20 hmmpanther:PTHR16193 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 32812580 32812580 A T 1 0 0 0 0 1 0 0 0 17203 72 3 4 4 TTC27 2 32812580 Missense_Mutation SNP A 11LU022_T 562774 32812580 209380949 118 756 LTBP1 0 . GRCh38 2 33222100 33222100 + Missense_Mutation SNP A A C rs751289584 11LU022_T 11LU022_N A A c.1825A>C p.Met609Leu p.M609L ENST00000404816 9/34 197 173 24 198 197 1 strelka-mutect LTBP1,missense_variant,p.Met609Leu,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Met283Leu,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Met283Leu,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Met283Leu,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Met283Leu,ENST00000402934,; C ENST00000404816 Transcript missense_variant 2178/6333 1825/5166 609/1721 M/L Atg/Ctg rs751289584 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 tolerated(0.36) 9/34 Gene3D:3.90.290.10,Pfam_domain:PF00683,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS rs751289584 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 33222100 33222100 A C 1 0 0 0 0 1 0 0 0 8979 101 4 5 5 LTBP1 2 33222100 Missense_Mutation SNP A 11LU022_T 409520 33222100 208971429 119 757 CRIM1 0 . GRCh38 2 36479607 36479607 + Missense_Mutation SNP G G T rs757223335 11LU022_T 11LU022_N G G c.1285G>T p.Gly429Cys p.G429C ENST00000280527 7/17 487 372 115 402 401 1 strelka-varscan-mutect CRIM1,missense_variant,p.Gly429Cys,ENST00000280527,NM_016441.2;CRIM1,non_coding_transcript_exon_variant,,ENST00000481321,; T ENST00000280527 Transcript missense_variant 1652/5912 1285/3111 429/1036 G/C Ggt/Tgt rs757223335 1 1 CRIM1 HGNC HGNC:2359 protein_coding YES CCDS1783.1 ENSP00000280527 Q9NZV1 UPI000004C628 NM_016441.2 deleterious(0) 7/17 Gene3D:2.10.70.10,Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11339,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS rs757223335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 36479607 36479607 G T 1 0 0 0 0 1 0 0 0 3674 1116 39 1 1 CRIM1 2 36479607 Missense_Mutation SNP G 11LU022_T 3257507 36479607 205713922 120 758 THADA 0 . GRCh38 2 43574737 43574737 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1328G>T p.Ser443Ile p.S443I ENST00000405006 11/38 195 161 34 217 217 0 strelka-varscan-mutect THADA,missense_variant,p.Ser443Ile,ENST00000403856,;THADA,missense_variant,p.Ser443Ile,ENST00000405006,NM_001083953.1;THADA,missense_variant,p.Ser443Ile,ENST00000405975,NM_022065.4;THADA,missense_variant,p.Ser443Ile,ENST00000404790,NM_001271644.1;THADA,missense_variant,p.Ser443Ile,ENST00000402360,NM_001271643.1;THADA,upstream_gene_variant,,ENST00000407351,;THADA,missense_variant,p.Ser26Ile,ENST00000402796,;THADA,3_prime_UTR_variant,,ENST00000398653,;THADA,3_prime_UTR_variant,,ENST00000408045,;THADA,intron_variant,,ENST00000474159,; A ENST00000405006 Transcript missense_variant 1680/6310 1328/5862 443/1953 S/I aGt/aTt 1 -1 THADA HGNC HGNC:19217 protein_coding YES CCDS46268.1 ENSP00000385995 Q6YHU6 UPI00001C0473 NM_001083953.1 deleterious(0.02) 11/38 hmmpanther:PTHR14387,hmmpanther:PTHR14387:SF2,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 43574737 43574737 C A 1 0 0 0 0 1 0 0 0 16272 565 20 2 2 THADA 2 43574737 Missense_Mutation SNP C 11LU022_T 7095130 43574737 198618792 121 759 PRKCE 0 . GRCh38 2 46010709 46010709 + Missense_Mutation SNP G G T rs774288612 11LU022_T 11LU022_N G G c.632G>T p.Cys211Phe p.C211F ENST00000394874 6/6 238 193 45 261 261 0 strelka-varscan-mutect PRKCE,missense_variant,p.Cys211Phe,ENST00000394874,;PRKCE,intron_variant,,ENST00000306156,NM_005400.2; T ENST00000394874 Transcript missense_variant 741/996 632/660 211/219 C/F tGt/tTt rs774288612 1 1 PRKCE HGNC HGNC:9401 protein_coding ENSP00000378341 E9PBI2 UPI0000E5A258 deleterious_low_confidence(0) 6/6 PROSITE_profiles:PS50011 MODERATE SNV 3 1 PASS rs774288612 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 46010709 46010709 G T 1 0 0 0 0 1 0 0 0 12644 1377 48 2 2 PRKCE 2 46010709 Missense_Mutation SNP G 11LU022_T 2435972 46010709 196182820 122 760 ATP6V1E2 0 . GRCh38 2 46512186 46512186 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.526A>G p.Asn176Asp p.N176D ENST00000306448 2/2 148 113 35 163 163 0 strelka-varscan-mutect ATP6V1E2,missense_variant,p.Asn176Asp,ENST00000306448,NM_080653.3;ATP6V1E2,missense_variant,p.Asn176Asp,ENST00000522587,NM_001318063.1;ATP6V1E2,intron_variant,,ENST00000524249,; C ENST00000306448 Transcript missense_variant 1640/1979 526/681 176/226 N/D Aat/Gat 1 -1 ATP6V1E2 HGNC HGNC:18125 protein_coding YES CCDS1826.1 ENSP00000304891 Q96A05 A0A140VKA8 UPI0000073C6E NM_080653.3 tolerated(1) 2/2 Superfamily_domains:0053834,HAMAP:MF_00311,Pfam_domain:PF01991,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF20 MODERATE 1 SNV 1 1 PASS rs1014102434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 46512186 46512186 T C 1 0 0 0 0 1 0 0 0 1337 1783 62 5 5 ATP6V1E2 2 46512186 Missense_Mutation SNP T 11LU022_T 501477 46512186 195681343 123 761 ASB3 0 . GRCh38 2 53670616 53670616 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1444G>T p.Asp482Tyr p.D482Y ENST00000263634 10/10 208 174 34 251 251 0 strelka-varscan-mutect ASB3,missense_variant,p.Asp482Tyr,ENST00000263634,NM_016115.4;ASB3,missense_variant,p.Asp409Tyr,ENST00000406687,NM_001201965.1;GPR75-ASB3,missense_variant,p.Asp520Tyr,ENST00000406625,NM_001164165.1;ASB3,missense_variant,p.Asp409Tyr,ENST00000394717,NM_145863.2;ASB3,intron_variant,,ENST00000406053,;ASB3,non_coding_transcript_exon_variant,,ENST00000482829,;ASB3,non_coding_transcript_exon_variant,,ENST00000470707,; A ENST00000263634 Transcript missense_variant 1579/2214 1444/1557 482/518 D/Y Gac/Tac 1 -1 ASB3 HGNC HGNC:16013 protein_coding YES CCDS1846.1 ENSP00000263634 Q9Y575 A0A0A6YY97 UPI00001260E7 NM_016115.4 deleterious(0) 10/10 PROSITE_profiles:PS50225,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF39,Pfam_domain:PF07525,SMART_domains:SM00969,Superfamily_domains:SSF158235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 53670616 53670616 C A 1 0 0 0 0 1 0 0 0 1166 826 29 2 2 ASB3 2 53670616 Missense_Mutation SNP C 11LU022_T 7158430 53670616 188522913 124 762 SPTBN1 0 . GRCh38 2 54649153 54649153 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.5165G>T p.Gly1722Val p.G1722V ENST00000356805 25/36 72 61 11 104 104 0 strelka-varscan-mutect SPTBN1,missense_variant,p.Gly1724Val,ENST00000615901,;SPTBN1,missense_variant,p.Gly1709Val,ENST00000333896,NM_178313.2;SPTBN1,missense_variant,p.Gly1722Val,ENST00000356805,NM_003128.2;SPTBN1,upstream_gene_variant,,ENST00000496323,; T ENST00000356805 Transcript missense_variant 5446/8482 5165/7095 1722/2364 G/V gGg/gTg 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 deleterious(0) 25/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.99997 0.9999996 1 1 1 0 T 3 4 3 54649153 54649153 G T 1 0 0 0 0 1 0 0 0 15475 1232 43 2 2 SPTBN1 2 54649153 Missense_Mutation SNP G 11LU022_T 978537 54649153 187544376 125 763 SPTBN1 0 . GRCh38 2 54655977 54655977 + Nonsense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.6025C>T p.Arg2009Ter p.R2009* ENST00000356805 29/36 117 105 12 147 147 0 strelka-varscan-mutect SPTBN1,stop_gained,p.Arg2011Ter,ENST00000615901,;SPTBN1,stop_gained,p.Arg1996Ter,ENST00000333896,NM_178313.2;SPTBN1,stop_gained,p.Arg2009Ter,ENST00000356805,NM_003128.2;SPTBN1,non_coding_transcript_exon_variant,,ENST00000496323,; T ENST00000356805 Transcript stop_gained 6306/8482 6025/7095 2009/2364 R/* Cga/Tga 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 29/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.09785 0.9999998 1 1 1 0 T 4 4 3 54655977 54655977 C T 1 0 0 0 0 0 1 0 0 15475 644 23 1 1 SPTBN1 2 54655977 Nonsense_Mutation SNP C 11LU022_T 6824 54655977 187537552 126 764 CLHC1 0 . GRCh38 2 55180697 55180697 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.1197G>T p.Glu399Asp p.E399D ENST00000401408 11/13 157 145 12 173 173 0 strelka-varscan-mutect CLHC1,missense_variant,p.Glu399Asp,ENST00000401408,NM_152385.2;CLHC1,missense_variant,p.Glu399Asp,ENST00000407122,;CLHC1,missense_variant,p.Glu277Asp,ENST00000406076,NM_001135598.1;CLHC1,non_coding_transcript_exon_variant,,ENST00000487320,;CLHC1,intron_variant,,ENST00000494539,;CLHC1,3_prime_UTR_variant,,ENST00000428621,;CLHC1,intron_variant,,ENST00000411884,; A ENST00000401408 Transcript missense_variant 1543/2248 1197/1761 399/586 E/D gaG/gaT COSM4624831,COSM4624832 1 -1 CLHC1 HGNC HGNC:26453 protein_coding YES CCDS33201.1 ENSP00000384869 Q8NHS4 UPI00004DEC65 NM_152385.2 deleterious(0.01) 11/13 Gene3D:1bpoA02,PIRSF_domain:PIRSF037469,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF11,Superfamily_domains:SSF48371 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 55180697 55180697 C A 1 0 0 0 0 1 0 0 0 3293 680 24 2 2 CLHC1 2 55180697 Missense_Mutation SNP C 11LU022_T 524720 55180697 187012832 127 765 MTIF2 0 . GRCh38 2 55237325 55237329 + Frame_Shift_Del DEL TTTTT TTTTT - novel 11LU022_T 11LU022_N TTTTT TTTTT c.1970_1974delAAAAA p.Lys657IlefsTer2 p.K657Ifs*2 ENST00000263629 15/16 113 87 26 120 120 0 sindel-varindel-pindel MTIF2,frameshift_variant,p.Lys657IlefsTer2,ENST00000263629,NM_001321001.1,NM_001005369.1,NM_002453.2;MTIF2,frameshift_variant,p.Lys657IlefsTer2,ENST00000403721,NM_001321002.1;MTIF2,frameshift_variant,p.Lys657IlefsTer2,ENST00000394600,;CLHC1,upstream_gene_variant,,ENST00000406076,NM_001135598.1;RPS27A,downstream_gene_variant,,ENST00000272317,NM_002954.5;MTIF2,downstream_gene_variant,,ENST00000418823,;RPS27A,downstream_gene_variant,,ENST00000404735,NM_001177413.1;RPS27A,downstream_gene_variant,,ENST00000402285,NM_001135592.2;CLHC1,upstream_gene_variant,,ENST00000451916,;RPS27A,downstream_gene_variant,,ENST00000449323,;CLHC1,upstream_gene_variant,,ENST00000487320,;RPS27A,downstream_gene_variant,,ENST00000495843,;RPS27A,downstream_gene_variant,,ENST00000468810,;RPS27A,downstream_gene_variant,,ENST00000463185,;RPS27A,downstream_gene_variant,,ENST00000478196,;RPS27A,downstream_gene_variant,,ENST00000471772,;RPS27A,downstream_gene_variant,,ENST00000494756,; - ENST00000263629 Transcript frameshift_variant 2286-2290/2528 1970-1974/2184 657-658/727 KK/X aAAAAA/a 1 -1 MTIF2 HGNC HGNC:7441 protein_coding YES CCDS1853.1 ENSP00000263629 P46199 UPI000013D42F NM_001321001.1,NM_001005369.1,NM_002453.2 15/16 HAMAP:MF_00100_B,hmmpanther:PTHR23115:SF184,hmmpanther:PTHR23115,Gene3D:2.40.30.10,Superfamily_domains:SSF50447 HIGH 1 deletion 1 1 PASS . . 0 145 3 32 29 0 0 0 -17.03963 0 0 1 0 0 - 7 5 3 55237325 55237325 TTTTT - 1 0 1 0 1 0 0 0 0 9923 1490 52 0 0 MTIF2 2 55237325 Frame_Shift_Del DEL TTTTT 11LU022_T 56628 55237325 186956204 128 766 PNPT1 0 . GRCh38 2 55667095 55667095 + Splice_Site SNP T T C novel 11LU022_T 11LU022_N T T c.1074-2A>G p.X358_splice ENST00000447944 180 139 41 173 173 0 strelka-varscan-mutect PNPT1,splice_acceptor_variant,,ENST00000447944,NM_033109.4;PNPT1,splice_acceptor_variant,,ENST00000260604,;PNPT1,splice_acceptor_variant,,ENST00000415374,;PNPT1,splice_acceptor_variant,,ENST00000415489,; C ENST00000447944 Transcript splice_acceptor_variant -/4411 1074/2352 358/783 1 -1 PNPT1 HGNC HGNC:23166 protein_coding YES CCDS1856.1 ENSP00000400646 Q8TCS8 UPI000020848E NM_033109.4 12/27 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 3 55667095 55667095 T C 1 0 0 0 0 0 0 1 0 12281 1536 53 5 5 PNPT1 2 55667095 Splice_Site SNP T 11LU022_T 429770 55667095 186526434 129 767 DCTN1 0 . GRCh38 2 74371048 74371048 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.774G>T p.= p.V258V ENST00000361874 9/32 314 226 88 372 372 0 strelka-varscan-mutect DCTN1,synonymous_variant,p.=,ENST00000361874,NM_004082.4;DCTN1,synonymous_variant,p.=,ENST00000628224,;DCTN1,synonymous_variant,p.=,ENST00000394003,NM_001190837.1;DCTN1,synonymous_variant,p.=,ENST00000409240,NM_001190836.1;DCTN1,synonymous_variant,p.=,ENST00000409868,;DCTN1,synonymous_variant,p.=,ENST00000633691,NM_023019.3;DCTN1,synonymous_variant,p.=,ENST00000409438,NM_001135041.2;DCTN1,synonymous_variant,p.=,ENST00000409567,NM_001135040.2;DCTN1,downstream_gene_variant,,ENST00000458655,;DCTN1,non_coding_transcript_exon_variant,,ENST00000463583,;DCTN1,upstream_gene_variant,,ENST00000495643,;DCTN1,upstream_gene_variant,,ENST00000497666,;DCTN1,synonymous_variant,p.=,ENST00000434055,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,;DCTN1,non_coding_transcript_exon_variant,,ENST00000470351,;DCTN1,downstream_gene_variant,,ENST00000477966,;DCTN1,upstream_gene_variant,,ENST00000495895,;DCTN1,downstream_gene_variant,,ENST00000462813,; A ENST00000361874 Transcript synonymous_variant 1092/4500 774/3837 258/1278 V gtG/gtT 1 -1 DCTN1 HGNC HGNC:2711 protein_coding YES CCDS1939.1 ENSP00000354791 Q14203 UPI0000129A25 NM_004082.4 9/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF40 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 74371048 74371048 C A 1 0 0 0 0 0 0 0 1 4109 697 25 2 2 DCTN1 2 74371048 Silent SNP C 11LU022_T 18703953 74371048 167822481 130 768 SEMA4F 0 . GRCh38 2 74654476 74654476 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.100G>T p.Gly34Cys p.G34C ENST00000357877 1/14 102 84 18 112 111 1 strelka-varscan-mutect SEMA4F,missense_variant,p.Gly34Cys,ENST00000611975,NM_001271662.1;SEMA4F,missense_variant,p.Gly34Cys,ENST00000357877,NM_004263.4;SEMA4F,missense_variant,p.Gly34Cys,ENST00000339773,NM_001271661.1;SEMA4F,missense_variant,p.Gly34Cys,ENST00000453930,;SEMA4F,missense_variant,p.Gly34Cys,ENST00000434486,;SEMA4F,missense_variant,p.Gly34Cys,ENST00000446927,;SEMA4F,missense_variant,p.Gly34Cys,ENST00000420077,;SEMA4F,missense_variant,p.Gly34Cys,ENST00000458114,;SEMA4F,missense_variant,p.Gly34Cys,ENST00000416236,; T ENST00000357877 Transcript missense_variant 249/4312 100/2313 34/770 G/C Ggc/Tgc 1 1 SEMA4F HGNC HGNC:10734 protein_coding YES CCDS1955.1 ENSP00000350547 O95754 UPI0000001BF5 NM_004263.4 deleterious_low_confidence(0.01) 1/14 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF72 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 74654476 74654476 G T 1 0 0 0 0 1 0 0 0 14311 1116 39 1 1 SEMA4F 2 74654476 Missense_Mutation SNP G 11LU022_T 283428 74654476 167539053 131 769 CTNNA2 0 . GRCh38 2 79858062 79858062 + Silent SNP G G T rs759308198 11LU022_T 11LU022_N G G c.348G>T p.= p.S116S ENST00000402739 3/18 157 121 36 148 148 0 strelka-varscan-mutect CTNNA2,synonymous_variant,p.=,ENST00000466387,;CTNNA2,synonymous_variant,p.=,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,synonymous_variant,p.=,ENST00000402739,NM_001282597.2;CTNNA2,synonymous_variant,p.=,ENST00000629316,NM_001164883.1;CTNNA2,synonymous_variant,p.=,ENST00000409971,; T ENST00000402739 Transcript synonymous_variant 353/3684 348/2862 116/953 S tcG/tcT rs759308198,COSM3963124,COSM3963126 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 3/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,Prints_domain:PR00805,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs759308198 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 79858062 79858062 G T 1 0 0 0 0 0 0 0 1 3822 1132 40 1 1 CTNNA2 2 79858062 Silent SNP G 11LU022_T 5203586 79858062 162335467 132 770 LRRTM1 0 . GRCh38 2 80302576 80302576 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1244G>T p.Gly415Val p.G415V ENST00000295057 2/2 142 122 20 196 196 0 strelka-varscan-mutect LRRTM1,missense_variant,p.Gly415Val,ENST00000295057,;LRRTM1,missense_variant,p.Gly415Val,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Gly415Val,ENST00000433224,;LRRTM1,missense_variant,p.Gly415Val,ENST00000417012,; A ENST00000295057 Transcript missense_variant 1901/2599 1244/1569 415/522 G/V gGc/gTc 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE tolerated(0.28) 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 80302576 80302576 C A 1 0 0 0 0 1 0 0 0 8945 739 26 2 2 LRRTM1 2 80302576 Missense_Mutation SNP C 11LU022_T 444514 80302576 161890953 133 771 POLR1A 0 . GRCh38 2 86028653 86028653 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4838G>T p.Gly1613Val p.G1613V ENST00000263857 32/34 284 216 68 328 326 2 strelka-varscan-mutect POLR1A,missense_variant,p.Gly1613Val,ENST00000263857,NM_015425.3;POLR1A,missense_variant,p.Gly1552Val,ENST00000409681,;POLR1A,non_coding_transcript_exon_variant,,ENST00000471427,;POLR1A,downstream_gene_variant,,ENST00000492034,;POLR1A,downstream_gene_variant,,ENST00000496892,; A ENST00000263857 Transcript missense_variant 5217/12749 4838/5163 1613/1720 G/V gGc/gTc 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 deleterious(0) 32/34 hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF11,Pfam_domain:PF04998,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS rs1436454276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 86028653 86028653 C A 1 0 0 0 0 1 0 0 0 12319 739 26 2 2 POLR1A 2 86028653 Missense_Mutation SNP C 11LU022_T 5726077 86028653 156164876 134 772 POLR1A 0 . GRCh38 2 86054228 86054228 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2120G>T p.Gly707Val p.G707V ENST00000263857 15/34 239 213 26 276 276 0 strelka-varscan-mutect POLR1A,missense_variant,p.Gly707Val,ENST00000263857,NM_015425.3;POLR1A,missense_variant,p.Gly707Val,ENST00000409681,;POLR1A,non_coding_transcript_exon_variant,,ENST00000483538,; A ENST00000263857 Transcript missense_variant 2499/12749 2120/5163 707/1720 G/V gGa/gTa 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 deleterious(0) 15/34 hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF11,Pfam_domain:PF04983,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 86054228 86054228 C A 1 0 0 0 0 1 0 0 0 12319 855 30 2 2 POLR1A 2 86054228 Missense_Mutation SNP C 11LU022_T 25575 86054228 156139301 135 773 AFF3 0 . GRCh38 2 99593774 99593774 + Silent SNP G G C rs746466474 11LU022_T 11LU022_N G G c.1962C>G p.= p.P654P ENST00000409579 15/25 139 108 31 146 146 0 strelka-varscan-mutect AFF3,synonymous_variant,p.=,ENST00000409236,;AFF3,synonymous_variant,p.=,ENST00000317233,NM_002285.2;AFF3,synonymous_variant,p.=,ENST00000409579,NM_001025108.1; C ENST00000409579 Transcript synonymous_variant 2195/4342 1962/3756 654/1251 P ccC/ccG rs746466474,COSM3564243 1 -1 AFF3 HGNC HGNC:6473 protein_coding YES CCDS33258.1 ENSP00000386834 P51826 UPI0000545269 NM_001025108.1 15/25 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110 0,1 LOW 1 SNV 5 0,1 1 PASS rs746466474 . 0 206 0 3 0 0 0 0 -20 0.999997 1 1 1 0 C 2 2 3 99593774 99593774 G C 1 0 0 0 0 0 0 0 1 435 987 35 4 4 AFF3 2 99593774 Silent SNP G 11LU022_T 13539546 99593774 142599755 136 774 IL18RAP 0 . GRCh38 2 102452037 102452037 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1656G>T p.Trp552Cys p.W552C ENST00000264260 12/12 217 178 39 236 236 0 strelka-varscan-mutect IL18RAP,missense_variant,p.Trp552Cys,ENST00000264260,NM_003853.3;IL18RAP,missense_variant,p.Trp410Cys,ENST00000409369,; T ENST00000264260 Transcript missense_variant 2245/2773 1656/1800 552/599 W/C tgG/tgT 1 1 IL18RAP HGNC HGNC:5989 protein_coding YES CCDS2061.1 ENSP00000264260 O95256 UPI0000071CAF NM_003853.3 deleterious(0) 12/12 Gene3D:3.40.50.10140,Pfam_domain:PF01582,Prints_domain:PR01537,PROSITE_profiles:PS50104,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF23,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 102452037 102452037 G T 1 0 0 0 0 1 0 0 0 7556 1241 43 2 2 IL18RAP 2 102452037 Missense_Mutation SNP G 11LU022_T 2858263 102452037 139741492 137 775 FBLN7 0 . GRCh38 2 112187387 112187387 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1201A>G p.Asn401Asp p.N401D ENST00000331203 8/8 256 208 48 277 277 0 strelka-varscan-mutect FBLN7,missense_variant,p.Asn401Asp,ENST00000331203,NM_153214.2;FBLN7,missense_variant,p.Asn223Asp,ENST00000272559,;FBLN7,missense_variant,p.Asn355Asp,ENST00000409450,NM_001128165.1;FBLN7,missense_variant,p.Asn267Asp,ENST00000409667,;FBLN7,splice_region_variant,p.=,ENST00000409903,;FBLN7,downstream_gene_variant,,ENST00000441565,;RP11-399B17.1,upstream_gene_variant,,ENST00000624058,; G ENST00000331203 Transcript missense_variant 1472/2301 1201/1320 401/439 N/D Aac/Gac 1 1 FBLN7 HGNC HGNC:26740 protein_coding YES CCDS2095.1 ENSP00000331411 Q53RD9 UPI000004E556 NM_153214.2 deleterious(0.01) 8/8 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF287 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 112187387 112187387 A G 1 0 0 0 0 1 0 0 0 5564 260 9 5 5 FBLN7 2 112187387 Missense_Mutation SNP A 11LU022_T 9735350 112187387 130006142 138 776 PSD4 0 . GRCh38 2 113193119 113193119 + Missense_Mutation SNP G G T rs45487591 11LU022_T 11LU022_N G G c.1910G>T p.Arg637Leu p.R637L ENST00000245796 7/17 80 57 23 75 75 0 strelka-varscan-mutect PSD4,missense_variant,p.Arg609Leu,ENST00000441564,;PSD4,missense_variant,p.Arg637Leu,ENST00000245796,NM_012455.2;PSD4,upstream_gene_variant,,ENST00000409378,;PSD4,3_prime_UTR_variant,,ENST00000409656,;PSD4,non_coding_transcript_exon_variant,,ENST00000418251,;PSD4,upstream_gene_variant,,ENST00000460725,;PSD4,upstream_gene_variant,,ENST00000487574,;PSD4,upstream_gene_variant,,ENST00000493329,;PSD4,upstream_gene_variant,,ENST00000465592,; T ENST00000245796 Transcript missense_variant 2105/5188 1910/3171 637/1056 R/L cGa/cTa rs45487591 1 1 PSD4 HGNC HGNC:19096 protein_coding YES CCDS33276.1 ENSP00000245796 Q8NDX1 UPI00004A0748 NM_012455.2 deleterious(0.04) 7/17 Gene3D:1.10.1000.11,Pfam_domain:PF01369,PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF135,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 1 1 PASS rs45487591 . 0 204 4 2 0 0 0 0 -20 0.9999953 1 1 1 0 T 3 4 3 113193119 113193119 G T 1 0 0 0 0 1 0 0 0 12800 1058 37 1 1 PSD4 2 113193119 Missense_Mutation SNP G 11LU022_T 1005732 113193119 129000410 139 777 POTEJ 0 . GRCh38 2 130611659 130611659 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.127G>T p.Val43Leu p.V43L ENST00000409602 1/15 541 496 45 715 715 0 varscan-mutect POTEJ,missense_variant,p.Val43Leu,ENST00000409602,NM_001277083.1; T ENST00000409602 Transcript missense_variant 179/3383 127/3117 43/1038 V/L Gtg/Ttg 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0) 1/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50 MODERATE 1 SNV 5 1 PASS rs1168552300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 130611659 130611659 G T 1 0 0 0 0 1 0 0 0 12383 1145 40 1 1 POTEJ 2 130611659 Missense_Mutation SNP G 11LU022_T 17418540 130611659 111581870 140 778 POTEJ 0 . GRCh38 2 130657106 130657106 + Missense_Mutation SNP G G T rs766525244 11LU022_T 11LU022_N G G c.2346G>T p.Met782Ile p.M782I ENST00000409602 15/15 355 312 43 459 459 0 varscan-mutect POTEJ,missense_variant,p.Met782Ile,ENST00000409602,NM_001277083.1; T ENST00000409602 Transcript missense_variant 2398/3383 2346/3117 782/1038 M/I atG/atT rs766525244 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0.01) 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 5 1 PASS rs766525244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 130657106 130657106 G T 1 0 0 0 0 1 0 0 0 12383 1290 45 2 2 POTEJ 2 130657106 Missense_Mutation SNP G 11LU022_T 45447 130657106 111536423 141 779 POTEE 0 . GRCh38 2 131264302 131264302 + Silent SNP C C G novel 11LU022_T 11LU022_N C C c.2847C>G p.= p.T949T ENST00000356920 15/15 649 606 43 719 719 0 varscan-mutect POTEE,synonymous_variant,p.=,ENST00000356920,NM_001083538.1;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000613282,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; G ENST00000356920 Transcript synonymous_variant 3183/4159 2847/3228 949/1075 T acC/acG 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 15/15 Pfam_domain:PF00022,Gene3D:3.90.640.10,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 131264302 131264302 C G 1 0 0 0 0 0 0 0 1 12378 581 21 4 4 POTEE 2 131264302 Silent SNP C 11LU022_T 607196 131264302 110929227 142 780 LCT 0 . GRCh38 2 135823948 135823948 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.860C>A p.Pro287His p.P287H ENST00000264162 4/17 459 359 100 510 508 2 strelka-varscan-mutect LCT,missense_variant,p.Pro287His,ENST00000264162,NM_002299.2;AC011893.3,downstream_gene_variant,,ENST00000437007,; T ENST00000264162 Transcript missense_variant 871/6279 860/5784 287/1927 P/H cCc/cAc 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 tolerated(0.17) 4/17 Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 135823948 135823948 G T 1 0 0 0 0 1 0 0 0 8599 1232 43 2 2 LCT 2 135823948 Missense_Mutation SNP G 11LU022_T 4559646 135823948 106369581 143 781 LRP1B 0 . GRCh38 2 141188460 141188460 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.974T>A p.Leu325His p.L325H ENST00000389484 7/91 295 274 21 241 241 0 strelka-varscan-mutect LRP1B,missense_variant,p.Leu325His,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; T ENST00000389484 Transcript missense_variant 1946/16535 974/13800 325/4599 L/H cTt/cAt 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 7/91 PROSITE_profiles:PS51120,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 141188460 141188460 A T 1 0 0 0 0 1 0 0 0 8850 72 3 4 4 LRP1B 2 141188460 Missense_Mutation SNP A 11LU022_T 5364512 141188460 101005069 144 782 KIF5C 0 . GRCh38 2 149000780 149000780 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2371G>T p.Val791Leu p.V791L ENST00000435030 21/26 126 102 24 116 116 0 strelka-varscan-mutect KIF5C,missense_variant,p.Val791Leu,ENST00000435030,NM_004522.2;KIF5C,splice_region_variant,,ENST00000464066,;KIF5C,splice_region_variant,,ENST00000482151,;KIF5C,downstream_gene_variant,,ENST00000460377,; T ENST00000435030 Transcript missense_variant,splice_region_variant 2739/6931 2371/2874 791/957 V/L Gtg/Ttg 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 deleterious(0) 21/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380 MODERATE 1 SNV 1 1 PASS rs918375830 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 149000780 149000780 G T 1 0 0 0 0 1 0 0 0 8172 1043 36 2 2 KIF5C 2 149000780 Missense_Mutation SNP G 11LU022_T 7812320 149000780 93192749 145 783 RIF1 0 . GRCh38 2 151443601 151443601 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.1878C>G p.Asp626Glu p.D626E ENST00000243326 17/35 95 75 20 120 120 0 strelka-varscan-mutect RIF1,missense_variant,p.Asp626Glu,ENST00000243326,;RIF1,missense_variant,p.Asp626Glu,ENST00000453091,NM_001177663.1;RIF1,missense_variant,p.Asp626Glu,ENST00000430328,NM_001177665.1;RIF1,missense_variant,p.Asp626Glu,ENST00000444746,NM_018151.4;RIF1,missense_variant,p.Asp626Glu,ENST00000428287,NM_001177664.1;RIF1,missense_variant,p.Asp618Glu,ENST00000414861,; G ENST00000243326 Transcript missense_variant 2361/15003 1878/7419 626/2472 D/E gaC/gaG 1 1 RIF1 HGNC HGNC:23207 protein_coding YES CCDS2194.1 ENSP00000243326 Q5UIP0 UPI000023729F tolerated(1) 17/35 hmmpanther:PTHR22928 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 151443601 151443601 C G 1 0 0 0 0 1 0 0 0 13533 564 20 4 4 RIF1 2 151443601 Missense_Mutation SNP C 11LU022_T 2442821 151443601 90749928 146 784 NEB 0 . GRCh38 2 151667866 151667866 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4657G>T p.Asp1553Tyr p.D1553Y ENST00000618972 40/183 180 152 28 192 192 0 strelka-varscan-mutect NEB,missense_variant,p.Asp1553Tyr,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Asp1553Tyr,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Asp1553Tyr,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Asp1553Tyr,ENST00000603639,;NEB,missense_variant,p.Asp1553Tyr,ENST00000604864,;NEB,missense_variant,p.Asp1553Tyr,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Asp1553Tyr,ENST00000172853,;NEB,non_coding_transcript_exon_variant,,ENST00000484968,; A ENST00000618972 Transcript missense_variant 4860/26307 4657/25683 1553/8560 D/Y Gat/Tat 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.06) 40/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 151667866 151667866 C A 1 0 0 0 0 1 0 0 0 10326 826 29 2 2 NEB 2 151667866 Missense_Mutation SNP C 11LU022_T 224265 151667866 90525663 147 785 GALNT5 0 . GRCh38 2 157258861 157258861 + Missense_Mutation SNP C C G rs757149965 11LU022_T 11LU022_N C C c.779C>G p.Thr260Ser p.T260S ENST00000259056 1/10 20 17 3 23 23 0 strelka-mutect GALNT5,missense_variant,p.Thr260Ser,ENST00000259056,NM_014568.1; G ENST00000259056 Transcript missense_variant 1264/6171 779/2823 260/940 T/S aCt/aGt rs757149965 1 1 GALNT5 HGNC HGNC:4127 protein_coding YES CCDS2203.1 ENSP00000259056 Q7Z7M9 UPI000019AD19 NM_014568.1 tolerated(0.25) 1/10 MODERATE 1 SNV 1 1 PASS rs757149965 . 0 206 4 0 0 0 0 0 -9.949002 1 1 1 1 0 G 3 3 3 157258861 157258861 C G 1 0 0 0 0 1 0 0 0 6087 565 20 4 4 GALNT5 2 157258861 Missense_Mutation SNP C 11LU022_T 5590995 157258861 84934668 148 786 UPP2 0 . GRCh38 2 157995221 157995221 + Nonsense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.23T>A p.Leu8Ter p.L8* ENST00000605860 2/10 191 153 38 229 229 0 strelka-varscan-mutect UPP2,stop_gained,p.Leu8Ter,ENST00000605860,NM_001135098.1; A ENST00000605860 Transcript stop_gained 69/2435 23/1125 8/374 L/* tTg/tAg 1 1 UPP2 HGNC HGNC:23061 protein_coding YES CCDS46435.1 ENSP00000474090 O95045 UPI0000EE2DE7 NM_001135098.1 2/10 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 157995221 157995221 T A 1 0 0 0 0 0 1 0 0 17539 1821 63 4 4 UPP2 2 157995221 Nonsense_Mutation SNP T 11LU022_T 736360 157995221 84198308 149 787 COBLL1 0 . GRCh38 2 164695609 164695609 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1897A>T p.Ser633Cys p.S633C ENST00000342193 12/14 157 120 37 158 157 1 strelka-varscan-mutect COBLL1,missense_variant,p.Ser671Cys,ENST00000392717,;COBLL1,missense_variant,p.Ser595Cys,ENST00000375458,NM_001278461.1;COBLL1,missense_variant,p.Ser633Cys,ENST00000342193,NM_014900.4;COBLL1,missense_variant,p.Ser635Cys,ENST00000409184,NM_001278460.1;COBLL1,missense_variant,p.Ser700Cys,ENST00000629362,NM_001278458.1;COBLL1,downstream_gene_variant,,ENST00000491126,;COBLL1,upstream_gene_variant,,ENST00000493713,;COBLL1,upstream_gene_variant,,ENST00000495084,;COBLL1,non_coding_transcript_exon_variant,,ENST00000493868,;COBLL1,non_coding_transcript_exon_variant,,ENST00000489955,;COBLL1,downstream_gene_variant,,ENST00000456171,; A ENST00000342193 Transcript missense_variant 2113/4898 1897/3501 633/1166 S/C Agt/Tgt 1 -1 COBLL1 HGNC HGNC:23571 protein_coding YES CCDS2223.2 ENSP00000341360 Q53SF7 UPI000007132B NM_014900.4 deleterious(0.01) 12/14 hmmpanther:PTHR21557,hmmpanther:PTHR21557:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 164695609 164695609 T A 1 0 0 0 0 1 0 0 0 3443 1580 55 4 4 COBLL1 2 164695609 Missense_Mutation SNP T 11LU022_T 6700388 164695609 77497920 150 788 SCN3A 0 . GRCh38 2 165090801 165090801 + Silent SNP G G T rs75324726 11LU022_T 11LU022_N G G c.5352C>A p.= p.P1784P ENST00000283254 28/28 484 405 79 406 405 1 strelka-varscan-mutect SCN3A,synonymous_variant,p.=,ENST00000360093,;SCN3A,synonymous_variant,p.=,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,synonymous_variant,p.=,ENST00000409101,NM_001081677.1;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000431341,;AC013463.2,upstream_gene_variant,,ENST00000625505,;SCN3A,downstream_gene_variant,,ENST00000465043,;SCN3A,downstream_gene_variant,,ENST00000471697,; T ENST00000283254 Transcript synonymous_variant 5820/9091 5352/6003 1784/2000 P ccC/ccA rs75324726 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 28/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 LOW 1 SNV 1 1 PASS rs75324726 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 165090801 165090801 G T 1 0 0 0 0 0 0 0 1 14187 1219 43 2 2 SCN3A 2 165090801 Silent SNP G 11LU022_T 395192 165090801 77102728 151 789 SCN3A 0 . GRCh38 2 165140852 165140852 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1818C>A p.Ser606Arg p.S606R ENST00000283254 13/28 330 266 64 310 309 1 strelka-varscan-mutect SCN3A,missense_variant,p.Ser606Arg,ENST00000360093,;SCN3A,missense_variant,p.Ser606Arg,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Ser606Arg,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Ser606Arg,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,; T ENST00000283254 Transcript missense_variant 2286/9091 1818/6003 606/2000 S/R agC/agA 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0.01) 13/28 Pfam_domain:PF11933,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 165140852 165140852 G T 1 0 0 0 0 1 0 0 0 14187 1310 46 2 2 SCN3A 2 165140852 Missense_Mutation SNP G 11LU022_T 50051 165140852 77052677 152 790 GALNT3 0 . GRCh38 2 165765002 165765002 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.570A>T p.= p.I190I ENST00000392701 3/11 354 274 80 325 325 0 strelka-varscan-mutect GALNT3,synonymous_variant,p.=,ENST00000392701,NM_004482.3;GALNT3,synonymous_variant,p.=,ENST00000412248,;GALNT3,upstream_gene_variant,,ENST00000409882,;GALNT3,upstream_gene_variant,,ENST00000437849,;GALNT3,upstream_gene_variant,,ENST00000463254,; A ENST00000392701 Transcript synonymous_variant 1346/3868 570/1902 190/633 I atA/atT 1 -1 GALNT3 HGNC HGNC:4125 protein_coding YES CCDS2226.1 ENSP00000376465 Q14435 UPI000013C989 NM_004482.3 3/11 hmmpanther:PTHR11675:SF33,hmmpanther:PTHR11675,Gene3D:3.90.550.10,Pfam_domain:PF00535,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 165765002 165765002 T A 1 0 0 0 0 0 0 0 1 6085 1744 61 4 4 GALNT3 2 165765002 Silent SNP T 11LU022_T 624150 165765002 76428527 153 791 MYO3B 0 . GRCh38 2 170200258 170200258 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.295G>T p.Gly99Trp p.G99W ENST00000408978 3/35 157 121 36 119 119 0 strelka-varscan-mutect MYO3B,missense_variant,p.Gly99Trp,ENST00000408978,NM_138995.4;MYO3B,missense_variant,p.Gly99Trp,ENST00000409044,NM_001083615.3;MYO3B,missense_variant,p.Gly108Trp,ENST00000484338,;MYO3B,missense_variant,p.Gly99Trp,ENST00000442690,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,missense_variant,p.Gly99Trp,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; T ENST00000408978 Transcript missense_variant 438/5529 295/4026 99/1341 G/W Ggg/Tgg 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 deleterious(0) 3/35 PROSITE_profiles:PS50011,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 170200258 170200258 G T 1 0 0 0 0 1 0 0 0 10078 1000 35 2 2 MYO3B 2 170200258 Missense_Mutation SNP G 11LU022_T 4435256 170200258 71993271 154 792 CHRNA1 0 . GRCh38 2 174759509 174759509 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.168G>T p.Gln56His p.Q56H ENST00000261007 2/10 557 438 119 597 597 0 strelka-varscan-mutect CHRNA1,missense_variant,p.Gln56His,ENST00000348749,NM_000079.3;CHRNA1,missense_variant,p.Gln56His,ENST00000261007,NM_001039523.2;CHRNA1,missense_variant,p.Gln69His,ENST00000636168,;CHRNA1,missense_variant,p.Gln56His,ENST00000409323,;CHRNA1,missense_variant,p.Gln56His,ENST00000409219,;CHRNA1,missense_variant,p.Gln56His,ENST00000409542,;AC018890.6,intron_variant,,ENST00000442996,;CHRNA1,missense_variant,p.Gln56His,ENST00000435083,; A ENST00000261007 Transcript missense_variant 235/1980 168/1449 56/482 Q/H caG/caT 1 -1 CHRNA1 HGNC HGNC:1955 protein_coding YES CCDS33331.1 ENSP00000261007 P02708 UPI000012524E NM_001039523.2 deleterious(0.01) 2/10 hmmpanther:PTHR18945:SF74,hmmpanther:PTHR18945,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 174759509 174759509 C A 1 0 0 0 0 1 0 0 0 3141 796 28 2 2 CHRNA1 2 174759509 Missense_Mutation SNP C 11LU022_T 4559251 174759509 67434020 155 793 TTN 0 . GRCh38 2 178611400 178611400 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.50829T>A p.= p.S16943S ENST00000589042 269/363 441 343 98 340 340 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000627527,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript synonymous_variant 51054/109224 50829/107976 16943/35991 S tcT/tcA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 269/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 178611400 178611400 A T 1 0 0 0 0 0 0 0 1 17245 175 7 4 4 TTN 2 178611400 Silent SNP A 11LU022_T 3851891 178611400 63582129 156 794 TTN 0 . GRCh38 2 178634453 178634453 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.42328G>T p.Val14110Phe p.V14110F ENST00000589042 230/363 265 207 58 238 238 0 strelka-varscan-mutect TTN,missense_variant,p.Val14110Phe,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Val12469Phe,ENST00000591111,;TTN,missense_variant,p.Val12469Phe,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Val11542Phe,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Val5045Phe,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Val5237Phe,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Val5170Phe,ENST00000359218,NM_133432.3;TTN,downstream_gene_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000626954,;TTN-AS1,upstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000418062,;TTN-AS1,downstream_gene_variant,,ENST00000628296,; A ENST00000589042 Transcript missense_variant 42553/109224 42328/107976 14110/35991 V/F Gtt/Ttt 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 230/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1230881799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 178634453 178634453 C A 1 0 0 0 0 1 0 0 0 17245 478 17 2 2 TTN 2 178634453 Missense_Mutation SNP C 11LU022_T 23053 178634453 63559076 157 795 TTN 0 . GRCh38 2 178689298 178689298 + Missense_Mutation SNP G G T rs753808404 11LU022_T 11LU022_N G G c.32003C>A p.Pro10668Gln p.P10668Q ENST00000589042 124/363 66 50 16 76 76 0 strelka-varscan-mutect TTN,missense_variant,p.Pro10668Gln,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro10351Gln,ENST00000591111,;TTN,missense_variant,p.Pro10351Gln,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro9424Gln,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Pro546Gln,ENST00000414766,;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 32228/109224 32003/107976 10668/35991 P/Q cCa/cAa rs753808404 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 124/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE 1 SNV 5 1 PASS rs753808404 . 0 202 6 2 0 0 0 0 -20 0.9999678 1 1 1 0 T 3 4 3 178689298 178689298 G T 1 0 0 0 0 1 0 0 0 17245 1348 47 2 2 TTN 2 178689298 Missense_Mutation SNP G 11LU022_T 54845 178689298 63504231 158 796 TTN 0 . GRCh38 2 178800576 178800576 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.402G>T p.= p.V134V ENST00000589042 4/363 75 59 16 88 88 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN,synonymous_variant,p.=,ENST00000360870,NM_133379.4;TTN,downstream_gene_variant,,ENST00000412264,;TTN,non_coding_transcript_exon_variant,,ENST00000470257,; A ENST00000589042 Transcript synonymous_variant 627/109224 402/107976 134/35991 V gtG/gtT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 4/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 178800576 178800576 C A 1 0 0 0 0 0 0 0 1 17245 581 21 2 2 TTN 2 178800576 Silent SNP C 11LU022_T 111278 178800576 63392953 159 797 ITGA4 0 . GRCh38 2 181457711 181457711 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.57G>T p.= p.T19T ENST00000397033 1/28 269 215 54 264 263 1 strelka-varscan-mutect ITGA4,synonymous_variant,p.=,ENST00000397033,NM_000885.4;ITGA4,synonymous_variant,p.=,ENST00000233573,;ITGA4,synonymous_variant,p.=,ENST00000339307,;ITGA4,upstream_gene_variant,,ENST00000478440,;ITGA4,non_coding_transcript_exon_variant,,ENST00000476089,;ITGA4,non_coding_transcript_exon_variant,,ENST00000465522,;ITGA4,upstream_gene_variant,,ENST00000484404,; T ENST00000397033 Transcript synonymous_variant 487/4189 57/3099 19/1032 T acG/acT 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 1/28 hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs1401307012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 181457711 181457711 G T 1 0 0 0 0 0 0 0 1 7785 1103 39 1 1 ITGA4 2 181457711 Silent SNP G 11LU022_T 2657135 181457711 60735818 160 798 ZNF804A 0 . GRCh38 2 184938285 184938285 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.2889G>T p.Gln963His p.Q963H ENST00000302277 4/4 130 106 24 122 122 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Gln963His,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Gln878His,ENST00000613975,; T ENST00000302277 Transcript missense_variant 3483/4690 2889/3630 963/1209 Q/H caG/caT COSM1013743 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.12) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 184938285 184938285 G T 1 0 0 0 0 1 0 0 0 18755 1020 36 2 2 ZNF804A 2 184938285 Missense_Mutation SNP G 11LU022_T 3480574 184938285 57255244 161 799 FSIP2 0 . GRCh38 2 185797360 185797360 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.10491T>C p.= p.S3497S ENST00000343098 16/23 131 98 33 114 114 0 strelka-varscan-mutect FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,synonymous_variant,p.=,ENST00000415915,; C ENST00000343098 Transcript synonymous_variant 10491/21054 10491/20991 3497/6996 S tcT/tcC 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 185797360 185797360 T C 1 0 0 0 0 0 0 0 1 5949 1596 56 5 5 FSIP2 2 185797360 Silent SNP T 11LU022_T 859075 185797360 56396169 162 800 TMEFF2 0 . GRCh38 2 192191942 192191942 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.220T>A p.Cys74Ser p.C74S ENST00000272771 2/10 190 157 33 172 171 1 strelka-varscan-mutect TMEFF2,missense_variant,p.Cys74Ser,ENST00000409056,;TMEFF2,missense_variant,p.Cys74Ser,ENST00000392314,NM_001305134.1;TMEFF2,missense_variant,p.Cys74Ser,ENST00000272771,NM_016192.2; T ENST00000272771 Transcript missense_variant 1405/2604 220/1125 74/374 C/S Tgt/Agt 1 -1 TMEFF2 HGNC HGNC:11867 protein_coding YES CCDS2314.1 ENSP00000272771 Q9UIK5 UPI0000048F19 NM_016192.2 deleterious(0) 2/10 Gene3D:3.30.60.30,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF88,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 192191942 192191942 A T 1 0 0 0 0 1 0 0 0 16458 188 7 4 4 TMEFF2 2 192191942 Missense_Mutation SNP A 11LU022_T 6394582 192191942 50001587 163 801 HECW2 0 . GRCh38 2 196307997 196307997 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.2523C>A p.= p.P841P ENST00000260983 11/29 98 78 20 96 96 0 strelka-varscan-mutect HECW2,synonymous_variant,p.=,ENST00000260983,NM_020760.2;HECW2,synonymous_variant,p.=,ENST00000409111,NM_001304840.1; T ENST00000260983 Transcript synonymous_variant 2706/11809 2523/4719 841/1572 P ccC/ccA 1 -1 HECW2 HGNC HGNC:29853 protein_coding YES CCDS33354.1 ENSP00000260983 Q9P2P5 UPI00001A75E8 NM_020760.2 11/29 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF127,Superfamily_domains:SSF51045 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 196307997 196307997 G T 1 0 0 0 0 0 0 0 1 6925 1219 43 2 2 HECW2 2 196307997 Silent SNP G 11LU022_T 4116055 196307997 45885532 164 802 MARS2 0 . GRCh38 2 197707051 197707051 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.1646G>T p.Gly549Val p.G549V ENST00000282276 1/1 389 298 91 387 386 1 strelka-varscan-mutect MARS2,missense_variant,p.Gly549Val,ENST00000282276,NM_138395.3;AC011997.1,intron_variant,,ENST00000409845,; T ENST00000282276 Transcript missense_variant 1683/3019 1646/1782 549/593 G/V gGa/gTa COSM1014554 1 1 MARS2 HGNC HGNC:25133 protein_coding YES CCDS33358.1 ENSP00000282276 Q96GW9 UPI00000492CE NM_138395.3 tolerated(0.23) 1/1 Gene3D:1.10.730.10,hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF88,Superfamily_domains:SSF47323 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 197707051 197707051 G T 1 0 0 0 0 1 0 0 0 9242 1174 41 2 2 MARS2 2 197707051 Missense_Mutation SNP G 11LU022_T 1399054 197707051 44486478 165 803 CD28 0 . GRCh38 2 203706575 203706575 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.52G>T p.Val18Leu p.V18L ENST00000458610 1/4 206 161 45 208 207 1 strelka-varscan-mutect CD28,missense_variant,p.Val18Leu,ENST00000458610,;CD28,5_prime_UTR_variant,,ENST00000324106,NM_006139.3;CD28,5_prime_UTR_variant,,ENST00000374481,NM_001243078.1; T ENST00000458610 Transcript missense_variant 52/705 52/705 18/234 V/L Gtg/Ttg 1 1 CD28 HGNC HGNC:1653 protein_coding ENSP00000393648 P10747 UPI00001BE8E0 tolerated_low_confidence(1) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11494,hmmpanther:PTHR11494:SF7 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 203706575 203706575 G T 1 0 0 0 0 1 0 0 0 2697 1261 44 2 2 CD28 2 203706575 Missense_Mutation SNP G 11LU022_T 5999524 203706575 38486954 166 804 PARD3B 0 . GRCh38 2 205301644 205301644 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.2573A>T p.Glu858Val p.E858V ENST00000406610 18/23 242 202 40 238 238 0 strelka-varscan-mutect PARD3B,missense_variant,p.Glu858Val,ENST00000406610,NM_001302769.1;PARD3B,missense_variant,p.Glu722Val,ENST00000613457,;PARD3B,missense_variant,p.Glu715Val,ENST00000614500,;PARD3B,missense_variant,p.Glu784Val,ENST00000622699,;PARD3B,missense_variant,p.Glu796Val,ENST00000358768,NM_152526.5;PARD3B,missense_variant,p.Glu789Val,ENST00000351153,NM_057177.6;PARD3B,missense_variant,p.Glu858Val,ENST00000349953,NM_205863.3;PARD3B,missense_variant,p.Glu858Val,ENST00000462231,;PARD3B,downstream_gene_variant,,ENST00000465890,; T ENST00000406610 Transcript missense_variant 2780/8174 2573/3618 858/1205 E/V gAg/gTg 1 1 PARD3B HGNC HGNC:14446 protein_coding YES CCDS77511.1 ENSP00000385848 Q8TEW8 UPI0000070178 NM_001302769.1 deleterious(0) 18/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 205301644 205301644 A T 1 0 0 0 0 1 0 0 0 11524 304 11 4 4 PARD3B 2 205301644 Missense_Mutation SNP A 11LU022_T 1595069 205301644 36891885 167 805 UNC80 0 . GRCh38 2 209829341 209829341 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.2588A>T p.His863Leu p.H863L ENST00000439458 15/64 176 138 38 142 142 0 strelka-varscan-mutect UNC80,missense_variant,p.His863Leu,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.His858Leu,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; T ENST00000439458 Transcript missense_variant 2668/13562 2588/9777 863/3258 H/L cAt/cTt 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0) 15/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS rs1031704064 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 209829341 209829341 A T 1 0 0 0 0 1 0 0 0 17521 217 8 4 4 UNC80 2 209829341 Missense_Mutation SNP A 11LU022_T 4527697 209829341 32364188 168 806 UNC80 0 . GRCh38 2 209993321 209993321 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.9205C>A p.Arg3069Ser p.R3069S ENST00000439458 62/64 114 87 27 98 98 0 strelka-mutect UNC80,missense_variant,p.Arg3069Ser,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Arg3045Ser,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,; A ENST00000439458 Transcript missense_variant 9285/13562 9205/9777 3069/3258 R/S Cgt/Agt 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious_low_confidence(0) 62/64 Low_complexity_(Seg):seg,hmmpanther:PTHR31781:SF1,hmmpanther:PTHR31781 MODERATE 1 SNV 5 1 PASS rs1401772812 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 209993321 209993321 C A 1 0 0 0 0 1 0 0 0 17521 536 19 1 1 UNC80 2 209993321 Missense_Mutation SNP C 11LU022_T 163980 209993321 32200208 169 807 IGFBP5 0 . GRCh38 2 216676802 216676802 + Nonsense_Mutation SNP G G T rs77515024 11LU022_T 11LU022_N G G c.768C>A p.Tyr256Ter p.Y256* ENST00000233813 4/4 205 175 30 242 240 2 strelka-varscan-mutect IGFBP5,stop_gained,p.Tyr256Ter,ENST00000233813,NM_000599.3;IGFBP5,downstream_gene_variant,,ENST00000449583,;IGFBP5,downstream_gene_variant,,ENST00000486341,; T ENST00000233813 Transcript stop_gained 1518/6215 768/819 256/272 Y/* taC/taA rs77515024 1 -1 IGFBP5 HGNC HGNC:5474 protein_coding YES CCDS2405.1 ENSP00000233813 P24593 A0A024R433 UPI000004E58C NM_000599.3 4/4 PROSITE_profiles:PS51162,hmmpanther:PTHR11551:SF4,hmmpanther:PTHR11551,Pfam_domain:PF00086,SMART_domains:SM00211,Superfamily_domains:SSF57610,Prints_domain:PR01981 HIGH 1 SNV 1 1 PASS rs77515024 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 216676802 216676802 G T 1 0 0 0 0 0 1 0 0 7488 1140 40 1 1 IGFBP5 2 216676802 Nonsense_Mutation SNP G 11LU022_T 6683481 216676802 25516727 170 808 USP37 0 . GRCh38 2 218488394 218488394 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.1500A>G p.= p.E500E ENST00000258399 15/26 141 114 27 145 145 0 strelka-varscan-mutect USP37,synonymous_variant,p.=,ENST00000258399,NM_020935.2;USP37,synonymous_variant,p.=,ENST00000454775,;USP37,synonymous_variant,p.=,ENST00000415516,;USP37,synonymous_variant,p.=,ENST00000418019,;USP37,upstream_gene_variant,,ENST00000475553,; C ENST00000258399 Transcript synonymous_variant 1913/8032 1500/2940 500/979 E gaA/gaG 1 -1 USP37 HGNC HGNC:20063 protein_coding YES CCDS2418.1 ENSP00000258399 Q86T82 UPI0000160023 NM_020935.2 15/26 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF125,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 218488394 218488394 T C 1 0 0 0 0 0 0 0 1 17610 1722 60 5 5 USP37 2 218488394 Silent SNP T 11LU022_T 1811592 218488394 23705135 171 809 PTPRN 0 . GRCh38 2 219299358 219299358 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1550G>A p.Arg517His p.R517H ENST00000295718 11/23 254 233 21 336 336 0 strelka-varscan-mutect PTPRN,missense_variant,p.Arg517His,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Arg488His,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Arg427His,ENST00000423636,NM_001199764.1;PTPRN,upstream_gene_variant,,ENST00000443981,;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,upstream_gene_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,non_coding_transcript_exon_variant,,ENST00000489650,;PTPRN,non_coding_transcript_exon_variant,,ENST00000486480,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,; T ENST00000295718 Transcript missense_variant 1791/3784 1550/2940 517/979 R/H cGc/cAc 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 deleterious(0) 11/23 Pfam_domain:PF11548,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2 MODERATE 1 SNV 1 1 PASS rs910099933 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 219299358 219299358 C T 1 0 0 0 0 1 0 0 0 12961 768 27 1 1 PTPRN 2 219299358 Missense_Mutation SNP C 11LU022_T 810964 219299358 22894171 172 810 SPEG 0 . GRCh38 2 219449053 219449053 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1895A>G p.Glu632Gly p.E632G ENST00000312358 4/41 79 65 14 91 91 0 strelka-varscan-mutect SPEG,missense_variant,p.Glu632Gly,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Glu528Gly,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; G ENST00000312358 Transcript missense_variant 2027/10782 1895/9804 632/3267 E/G gAg/gGg 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0.03) 4/41 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 219449053 219449053 A G 1 0 0 0 0 1 0 0 0 15387 304 11 5 5 SPEG 2 219449053 Missense_Mutation SNP A 11LU022_T 149695 219449053 22744476 173 811 SLC4A3 0 . GRCh38 2 219636317 219636317 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2288G>T p.Gly763Val p.G763V ENST00000273063 15/23 275 224 51 373 373 0 strelka-varscan-mutect SLC4A3,missense_variant,p.Gly736Val,ENST00000358055,NM_005070.3;SLC4A3,missense_variant,p.Gly763Val,ENST00000273063,NM_001326559.1,NM_201574.2;SLC4A3,missense_variant,p.Gly736Val,ENST00000373760,;SLC4A3,missense_variant,p.Gly736Val,ENST00000317151,;SLC4A3,downstream_gene_variant,,ENST00000413743,;SLC4A3,downstream_gene_variant,,ENST00000497589,;SLC4A3,3_prime_UTR_variant,,ENST00000425141,;SLC4A3,3_prime_UTR_variant,,ENST00000416910,;SLC4A3,downstream_gene_variant,,ENST00000444906,; T ENST00000273063 Transcript missense_variant 2502/4246 2288/3780 763/1259 G/V gGg/gTg 1 1 SLC4A3 HGNC HGNC:11029 protein_coding YES CCDS2446.1 ENSP00000273063 P48751 UPI000022BE50 NM_001326559.1,NM_201574.2 deleterious(0) 15/23 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF15,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 219636317 219636317 G T 1 0 0 0 0 1 0 0 0 14932 1232 43 2 2 SLC4A3 2 219636317 Missense_Mutation SNP G 11LU022_T 187264 219636317 22557212 174 812 CUL3 0 . GRCh38 2 224503726 224503726 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1303C>G p.His435Asp p.H435D ENST00000264414 9/16 49 41 8 92 92 0 strelka-varscan-mutect CUL3,missense_variant,p.His435Asp,ENST00000264414,NM_003590.4;CUL3,missense_variant,p.His369Asp,ENST00000344951,NM_001257197.1;CUL3,missense_variant,p.His411Asp,ENST00000409777,;CUL3,missense_variant,p.His411Asp,ENST00000409096,NM_001257198.1;CUL3,missense_variant,p.Asn9Lys,ENST00000617432,;CUL3,non_coding_transcript_exon_variant,,ENST00000481135,;CUL3,upstream_gene_variant,,ENST00000487558,;CUL3,downstream_gene_variant,,ENST00000484081,;AC073052.1,upstream_gene_variant,,ENST00000440417,; C ENST00000264414 Transcript missense_variant 1642/6741 1303/2307 435/768 H/D Cac/Gac 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 deleterious(0) 9/16 PROSITE_profiles:PS50069,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.20.1310.10,SMART_domains:SM00182,Superfamily_domains:SSF75632 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 224503726 224503726 G C 1 0 0 0 0 1 0 0 0 3866 1377 48 4 4 CUL3 2 224503726 Missense_Mutation SNP G 11LU022_T 4867409 224503726 17689803 175 813 DOCK10 0 . GRCh38 2 224862689 224862689 + Missense_Mutation SNP G G T rs750806425 11LU022_T 11LU022_N G G c.1660C>A p.Arg554Ser p.R554S ENST00000258390 14/56 178 142 36 147 147 0 strelka-varscan-mutect DOCK10,missense_variant,p.Arg548Ser,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Arg554Ser,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,; T ENST00000258390 Transcript missense_variant 1728/7260 1660/6561 554/2186 R/S Cgt/Agt rs750806425,COSM3962452,COSM3962453 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 deleterious(0.01) 14/56 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs750806425 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 224862689 224862689 G T 1 0 0 0 0 1 0 0 0 4500 1116 39 1 1 DOCK10 2 224862689 Missense_Mutation SNP G 11LU022_T 358963 224862689 17330840 176 814 MFF 0 . GRCh38 2 227330821 227330821 + Missense_Mutation SNP A A T rs138259047 11LU022_T 11LU022_N A A c.234A>T p.Gln78His p.Q78H ENST00000353339 4/11 228 171 57 244 244 0 strelka-varscan-mutect MFF,missense_variant,p.Gln78His,ENST00000353339,NM_001277061.1,NM_020194.5;MFF,missense_variant,p.Gln52His,ENST00000304593,NM_001277062.1,NM_001277068.1;MFF,missense_variant,p.Gln52His,ENST00000337110,NM_001277063.1;MFF,missense_variant,p.Gln52His,ENST00000349901,NM_001277064.1;MFF,missense_variant,p.Gln2His,ENST00000392059,NM_001277067.1;MFF,missense_variant,p.Gln52His,ENST00000409565,NM_001277066.1;MFF,missense_variant,p.Gln52His,ENST00000409616,;MFF,missense_variant,p.Gln52His,ENST00000354503,NM_001277065.1;MFF,missense_variant,p.Gln52His,ENST00000452930,;MFF,missense_variant,p.Gln52His,ENST00000418961,;MFF,missense_variant,p.Gln52His,ENST00000525195,;MFF,intron_variant,,ENST00000524634,;MFF,intron_variant,,ENST00000531278,;MFF,intron_variant,,ENST00000534203,;MFF,intron_variant,,ENST00000530359,;MFF,downstream_gene_variant,,ENST00000423098,;MFF,downstream_gene_variant,,ENST00000443428,;MFF,downstream_gene_variant,,ENST00000436237,;MFF,non_coding_transcript_exon_variant,,ENST00000436791,;MFF,intron_variant,,ENST00000476924,;MFF,non_coding_transcript_exon_variant,,ENST00000460756,;MFF,non_coding_transcript_exon_variant,,ENST00000489696,;MFF,intron_variant,,ENST00000470090,; T ENST00000353339 Transcript missense_variant 675/2186 234/1029 78/342 Q/H caA/caT rs138259047 1 1 MFF HGNC HGNC:24858 protein_coding YES CCDS2465.1 ENSP00000302037 Q9GZY8 A0A024R491 UPI0000072C36 NM_001277061.1,NM_020194.5 tolerated(0.11) 4/11 Pfam_domain:PF05644,hmmpanther:PTHR16501 MODERATE 1 SNV 5 1 PASS rs138259047 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 227330821 227330821 A T 1 0 0 0 0 1 0 0 0 9472 69 3 4 4 MFF 2 227330821 Missense_Mutation SNP A 11LU022_T 2468132 227330821 14862708 177 815 ECEL1 0 . GRCh38 2 232481091 232481091 + Missense_Mutation SNP G G T rs201375083 11LU022_T 11LU022_N G G c.2055C>A p.His685Gln p.H685Q ENST00000304546 15/18 228 185 43 240 240 0 strelka-varscan-mutect ECEL1,missense_variant,p.His685Gln,ENST00000304546,NM_004826.3;ECEL1,missense_variant,p.His683Gln,ENST00000409941,NM_001290787.1;ECEL1,intron_variant,,ENST00000411860,;ECEL1,splice_region_variant,,ENST00000482346,; T ENST00000304546 Transcript missense_variant,splice_region_variant 2266/2865 2055/2328 685/775 H/Q caC/caA rs201375083 1 -1 ECEL1 HGNC HGNC:3147 protein_coding YES CCDS2493.1 ENSP00000302051 O95672 UPI000013E997 NM_004826.3 deleterious(0.01) 15/18 Gene3D:3.40.390.10,Pfam_domain:PF01431,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF108,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs201375083 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 232481091 232481091 G T 1 0 0 0 0 1 0 0 0 4717 1159 40 1 1 ECEL1 2 232481091 Missense_Mutation SNP G 11LU022_T 5150270 232481091 9712438 178 816 ATG16L1 0 . GRCh38 2 233256115 233256115 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.129G>T p.= p.L43L ENST00000392017 2/18 195 155 40 238 237 1 strelka-varscan-mutect ATG16L1,synonymous_variant,p.=,ENST00000392017,NM_001190266.1,NM_001190267.1,NM_030803.6;ATG16L1,synonymous_variant,p.=,ENST00000392018,;ATG16L1,synonymous_variant,p.=,ENST00000392020,NM_017974.3;ATG16L1,synonymous_variant,p.=,ENST00000347464,NM_198890.2;ATG16L1,synonymous_variant,p.=,ENST00000373525,;ATG16L1,synonymous_variant,p.=,ENST00000444735,;ATG16L1,synonymous_variant,p.=,ENST00000417017,;ATG16L1,synonymous_variant,p.=,ENST00000419681,;ATG16L1,5_prime_UTR_variant,,ENST00000431917,;ATG16L1,3_prime_UTR_variant,,ENST00000392021,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000474148,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000479942,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000485623,; T ENST00000392017 Transcript synonymous_variant 386/3405 129/1824 43/607 L ctG/ctT 1 1 ATG16L1 HGNC HGNC:21498 protein_coding YES CCDS2503.2 ENSP00000375872 Q676U5 UPI0000208D0D NM_001190266.1,NM_001190267.1,NM_030803.6 2/18 hmmpanther:PTHR19878:SF6,hmmpanther:PTHR19878,Pfam_domain:PF08614 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 233256115 233256115 G T 1 0 0 0 0 0 0 0 1 1243 1335 47 2 2 ATG16L1 2 233256115 Silent SNP G 11LU022_T 775024 233256115 8937414 179 817 ATG16L1 0 . GRCh38 2 233265087 233265087 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.585G>T p.Met195Ile p.M195I ENST00000392017 5/18 374 288 86 361 360 1 strelka-varscan-mutect ATG16L1,missense_variant,p.Met195Ile,ENST00000392017,NM_001190266.1,NM_001190267.1,NM_030803.6;ATG16L1,missense_variant,p.Met195Ile,ENST00000392018,;ATG16L1,missense_variant,p.Met195Ile,ENST00000392020,NM_017974.3;ATG16L1,intron_variant,,ENST00000347464,NM_198890.2;ATG16L1,intron_variant,,ENST00000373525,;ATG16L1,intron_variant,,ENST00000444735,;ATG16L1,intron_variant,,ENST00000417017,;ATG16L1,intron_variant,,ENST00000419681,;ATG16L1,downstream_gene_variant,,ENST00000431917,;ATG16L1,upstream_gene_variant,,ENST00000498620,;ATG16L1,3_prime_UTR_variant,,ENST00000392021,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000474148,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000479942,;ATG16L1,downstream_gene_variant,,ENST00000485623,; T ENST00000392017 Transcript missense_variant 842/3405 585/1824 195/607 M/I atG/atT 1 1 ATG16L1 HGNC HGNC:21498 protein_coding YES CCDS2503.2 ENSP00000375872 Q676U5 UPI0000208D0D NM_001190266.1,NM_001190267.1,NM_030803.6 tolerated(0.09) 5/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19878:SF6,hmmpanther:PTHR19878,Pfam_domain:PF08614 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 233265087 233265087 G T 1 0 0 0 0 1 0 0 0 1243 1348 47 2 2 ATG16L1 2 233265087 Missense_Mutation SNP G 11LU022_T 8972 233265087 8928442 180 818 KIF1A 0 . GRCh38 2 240719164 240719164 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.5056C>A p.Leu1686Met p.L1686M ENST00000498729 47/49 153 127 26 169 168 1 strelka-varscan-mutect KIF1A,missense_variant,p.Leu1686Met,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Leu1585Met,ENST00000320389,NM_004321.6;KIF1A,downstream_gene_variant,,ENST00000404283,;KIF1A,downstream_gene_variant,,ENST00000431776,;KIF1A,non_coding_transcript_exon_variant,,ENST00000460788,;KIF1A,non_coding_transcript_exon_variant,,ENST00000492812,;KIF1A,non_coding_transcript_exon_variant,,ENST00000488776,;KIF1A,downstream_gene_variant,,ENST00000465813,; T ENST00000498729 Transcript missense_variant 5303/9223 5056/5376 1686/1791 L/M Ctg/Atg 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 tolerated(0.1) 47/49 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1015341506 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 240719164 240719164 G T 1 0 0 0 0 1 0 0 0 8147 991 35 2 2 KIF1A 2 240719164 Missense_Mutation SNP G 11LU022_T 7454077 240719164 1474365 181 819 CROCC2 0 . GRCh38 2 240931060 240931060 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.879G>T p.= p.R293R ENST00000443866 7/32 207 170 37 240 240 0 strelka-varscan-mutect CROCC2,synonymous_variant,p.=,ENST00000443866,;CROCC2,upstream_gene_variant,,ENST00000477311,; T ENST00000443866 Transcript synonymous_variant 1063/5382 879/4968 293/1655 R cgG/cgT 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A 7/32 hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 240931060 240931060 G T 1 0 0 0 0 0 0 0 1 3695 1219 43 2 2 CROCC2 2 240931060 Silent SNP G 11LU022_T 211896 240931060 1262469 182 820 GRM7 0 . GRCh38 3 6861853 6861853 + Silent SNP G G T 11LU022_T 11LU022_N G G c.465G>T p.= p.G155G ENST00000357716 1/10 106 79 27 157 155 2 strelka-varscan-mutect GRM7,synonymous_variant,p.=,ENST00000486284,NM_181874.2;GRM7,synonymous_variant,p.=,ENST00000357716,NM_000844.3;GRM7,synonymous_variant,p.=,ENST00000389336,;GRM7,intron_variant,,ENST00000448328,;GRM7,synonymous_variant,p.=,ENST00000467425,;GRM7,synonymous_variant,p.=,ENST00000440923,;GRM7,synonymous_variant,p.=,ENST00000389335,;GRM7,intron_variant,,ENST00000443259,;GRM7,upstream_gene_variant,,ENST00000435689,; T ENST00000357716 Transcript synonymous_variant 739/4127 465/2748 155/915 G ggG/ggT COSM4549135,COSM4549136,COSM4549137 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00248 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999978 1 1 1 0 T 2 4 3 6861853 6861853 G T 1 0 0 0 0 0 0 0 1 6684 1219 43 2 2 GRM7 3 6861853 Silent SNP G 11LU022_T 6861853 191433706 183 821 GRM7 0 . GRCh38 3 7298784 7298784 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.837C>A p.Asn279Lys p.N279K ENST00000357716 3/10 191 146 45 226 226 0 strelka-varscan-mutect GRM7,missense_variant,p.Asn279Lys,ENST00000486284,NM_181874.2;GRM7,missense_variant,p.Asn279Lys,ENST00000357716,NM_000844.3;GRM7,missense_variant,p.Asn279Lys,ENST00000389336,;GRM7,missense_variant,p.Asn34Lys,ENST00000402647,;GRM7,missense_variant,p.Asn71Lys,ENST00000448328,;GRM7,missense_variant,p.Asn279Lys,ENST00000467425,;GRM7,missense_variant,p.Asn279Lys,ENST00000440923,;GRM7,missense_variant,p.Asn279Lys,ENST00000389335,;GRM7,3_prime_UTR_variant,,ENST00000435689,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,;GRM7,non_coding_transcript_exon_variant,,ENST00000461677,; A ENST00000357716 Transcript missense_variant 1111/4127 837/2748 279/915 N/K aaC/aaA COSM3767546,COSM3767547,COSM3767548 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 deleterious(0.05) 3/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00593 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 7298784 7298784 C A 1 0 0 0 0 1 0 0 0 6684 564 20 2 2 GRM7 3 7298784 Missense_Mutation SNP C 11LU022_T 436931 7298784 190996775 184 822 SETD5 0 . GRCh38 3 9473296 9473296 + Nonsense_Mutation SNP G G T rs745536349 11LU022_T 11LU022_N G G c.3256G>T p.Gly1086Ter p.G1086* ENST00000402198 20/23 172 126 46 233 233 0 strelka-varscan-mutect SETD5,stop_gained,p.Gly1086Ter,ENST00000402198,NM_001080517.2;SETD5,stop_gained,p.Gly1086Ter,ENST00000406341,;SETD5,stop_gained,p.Gly1105Ter,ENST00000407969,;SETD5,stop_gained,p.Gly988Ter,ENST00000302463,NM_001292043.1;SETD5,stop_gained,p.Gly754Ter,ENST00000399686,;SETD5,stop_gained,p.Gly417Ter,ENST00000421188,;SETD5,upstream_gene_variant,,ENST00000479538,;SETD5,3_prime_UTR_variant,,ENST00000413704,;SETD5,non_coding_transcript_exon_variant,,ENST00000493918,;SETD5,non_coding_transcript_exon_variant,,ENST00000466242,;SETD5,non_coding_transcript_exon_variant,,ENST00000486465,;SETD5,non_coding_transcript_exon_variant,,ENST00000492939,;SETD5,upstream_gene_variant,,ENST00000459941,;SETD5,upstream_gene_variant,,ENST00000466826,; T ENST00000402198 Transcript stop_gained 3691/6827 3256/4329 1086/1442 G/* Gga/Tga rs745536349 1 1 SETD5 HGNC HGNC:25566 protein_coding YES CCDS46741.1 ENSP00000385852 Q9C0A6 UPI0000411FEE NM_001080517.2 20/23 Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS rs745536349 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 9473296 9473296 G T 1 0 0 0 0 0 1 0 0 14412 1233 43 2 2 SETD5 3 9473296 Nonsense_Mutation SNP G 11LU022_T 2174512 9473296 188822263 185 823 NEK10 0 . GRCh38 3 27162563 27162563 + Missense_Mutation SNP G G T rs773747733 11LU022_T 11LU022_N G G c.2908C>A p.His970Asn p.H970N ENST00000429845 32/39 161 119 42 164 164 0 strelka-varscan-mutect NEK10,missense_variant,p.His970Asn,ENST00000429845,NM_152534.4;NEK10,missense_variant,p.His282Asn,ENST00000295720,NM_001304384.1;NEK10,missense_variant,p.His282Asn,ENST00000383771,NM_001031741.3;NEK10,intron_variant,,ENST00000383770,;NEK10,intron_variant,,ENST00000498182,;NEK10,non_coding_transcript_exon_variant,,ENST00000574215,; T ENST00000429845 Transcript missense_variant 3271/4250 2908/3519 970/1172 H/N Cac/Aac rs773747733 1 -1 NEK10 HGNC HGNC:18592 protein_coding ENSP00000395849 Q6ZWH5 UPI0000EE2A86 NM_152534.4 tolerated(0.31) 32/39 MODERATE SNV 5 1 PASS rs773747733 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 27162563 27162563 G T 1 0 0 0 0 1 0 0 0 10350 1348 47 2 2 NEK10 3 27162563 Missense_Mutation SNP G 11LU022_T 17689267 27162563 171132996 186 824 EOMES 0 . GRCh38 3 27721848 27721848 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.447C>A p.= p.P149P ENST00000449599 1/6 131 99 32 172 172 0 strelka-varscan-mutect EOMES,synonymous_variant,p.=,ENST00000295743,NM_005442.3;EOMES,synonymous_variant,p.=,ENST00000449599,NM_001278182.1;EOMES,intron_variant,,ENST00000461503,NM_001278183.1; T ENST00000449599 Transcript synonymous_variant 465/2829 447/2118 149/705 P ccC/ccA 1 -1 EOMES HGNC HGNC:3372 protein_coding YES CCDS63585.1 ENSP00000388620 O95936 UPI00004DEF82 NM_001278182.1 1/6 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF13 LOW 1 SNV 1 1 PASS rs1455492414 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 27721848 27721848 G T 1 0 0 0 0 0 0 0 1 4993 1103 39 1 1 EOMES 3 27721848 Silent SNP G 11LU022_T 559285 27721848 170573711 187 825 GADL1 0 . GRCh38 3 30850041 30850041 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.606G>T p.Lys202Asn p.K202N ENST00000282538 6/15 148 114 34 235 235 0 strelka-varscan-mutect GADL1,missense_variant,p.Lys202Asn,ENST00000454381,;GADL1,missense_variant,p.Lys202Asn,ENST00000282538,NM_207359.2; A ENST00000282538 Transcript missense_variant 757/3759 606/1566 202/521 K/N aaG/aaT 1 -1 GADL1 HGNC HGNC:27949 protein_coding YES CCDS2649.2 ENSP00000282538 Q6ZQY3 UPI000022BF90 NM_207359.2 tolerated(0.1) 6/15 hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF95,Gene3D:3.40.640.10,Pfam_domain:PF00282,Superfamily_domains:SSF53383 MODERATE 1 SNV 5 1 PASS rs1241661514 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 30850041 30850041 C A 1 0 0 0 0 1 0 0 0 6056 680 24 2 2 GADL1 3 30850041 Missense_Mutation SNP C 11LU022_T 3128193 30850041 167445518 188 826 SCN11A 0 . GRCh38 3 38910180 38910180 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.987G>T p.Lys329Asn p.K329N ENST00000302328 8/26 88 69 19 112 112 0 strelka-mutect SCN11A,missense_variant,p.Lys329Asn,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,missense_variant,p.Lys329Asn,ENST00000444237,;SCN11A,missense_variant,p.Lys329Asn,ENST00000456224,; A ENST00000302328 Transcript missense_variant 1186/6500 987/5376 329/1791 K/N aaG/aaT 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 tolerated(0.69) 8/26 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 38910180 38910180 C A 1 0 0 0 0 1 0 0 0 14182 796 28 2 2 SCN11A 3 38910180 Missense_Mutation SNP C 11LU022_T 8060139 38910180 159385379 189 827 CACNA2D2 0 . GRCh38 3 50367444 50367444 + Missense_Mutation SNP C C A rs779297579 11LU022_T 11LU022_N C C c.2372G>T p.Arg791Leu p.R791L ENST00000479441 28/39 225 163 62 389 389 0 strelka-varscan-mutect CACNA2D2,missense_variant,p.Arg784Leu,ENST00000266039,NM_001005505.2;CACNA2D2,missense_variant,p.Arg791Leu,ENST00000423994,;CACNA2D2,missense_variant,p.Arg784Leu,ENST00000429770,;CACNA2D2,missense_variant,p.Arg715Leu,ENST00000360963,NM_001291101.1;CACNA2D2,missense_variant,p.Arg784Leu,ENST00000424201,NM_006030.3;CACNA2D2,missense_variant,p.Arg791Leu,ENST00000479441,NM_001174051.2;XXcos-LUCA11.5,intron_variant,,ENST00000606589,;CYB561D2,non_coding_transcript_exon_variant,,ENST00000607583,;CYB561D2,intron_variant,,ENST00000607121,;CYB561D2,intron_variant,,ENST00000606665,;CYB561D2,intron_variant,,ENST00000606259,;CYB561D2,intron_variant,,ENST00000607088,;CYB561D2,upstream_gene_variant,,ENST00000607362,;CACNA2D2,upstream_gene_variant,,ENST00000483620,; A ENST00000479441 Transcript missense_variant 2372/3453 2372/3453 791/1150 R/L cGc/cTc rs779297579 1 -1 CACNA2D2 HGNC HGNC:1400 protein_coding YES CCDS54588.1 ENSP00000418081 Q9NY47 UPI0000E5A6AF NM_001174051.2 deleterious(0) 28/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF7 MODERATE 1 SNV 1 1 PASS rs779297579 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 50367444 50367444 C A 1 0 0 0 0 1 0 0 0 2237 768 27 1 1 CACNA2D2 3 50367444 Missense_Mutation SNP C 11LU022_T 11457264 50367444 147928115 190 828 C3orf14 0 . GRCh38 3 62320475 62320475 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.4A>G p.Thr2Ala p.T2A ENST00000494481 3/6 71 57 14 158 158 0 strelka-mutect C3orf14,missense_variant,p.Thr2Ala,ENST00000494481,NM_020685.4;C3orf14,missense_variant,p.Thr2Ala,ENST00000542214,;C3orf14,missense_variant,p.Thr2Ala,ENST00000232519,NM_001291942.1;C3orf14,missense_variant,p.Thr2Ala,ENST00000462069,NM_001291941.1;C3orf14,missense_variant,p.Thr2Ala,ENST00000465142,;PTPRG-AS1,intron_variant,,ENST00000490916,;PTPRG-AS1,intron_variant,,ENST00000495542,;PTPRG-AS1,upstream_gene_variant,,ENST00000474795,;PTPRG-AS1,upstream_gene_variant,,ENST00000462497,;PTPRG-AS1,upstream_gene_variant,,ENST00000466893,;PTPRG-AS1,upstream_gene_variant,,ENST00000475371,;PTPRG-AS1,upstream_gene_variant,,ENST00000479018,;PTPRG-AS1,upstream_gene_variant,,ENST00000498655,;C3orf14,non_coding_transcript_exon_variant,,ENST00000486169,;C3orf14,non_coding_transcript_exon_variant,,ENST00000491323,;PTPRG-AS1,upstream_gene_variant,,ENST00000479588,; G ENST00000494481 Transcript missense_variant 318/3525 4/387 2/128 T/A Act/Gct 1 1 C3orf14 HGNC HGNC:25024 protein_coding YES CCDS2896.1 ENSP00000418086 Q9HBI5 A0A024R330 UPI00000729BA NM_020685.4 tolerated(0.58) 3/6 hmmpanther:PTHR14286,Pfam_domain:PF15134 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 62320475 62320475 A G 1 0 0 0 0 1 0 0 0 2059 275 10 5 5 C3orf14 3 62320475 Missense_Mutation SNP A 11LU022_T 11953031 62320475 135975084 191 829 PRICKLE2 0 . GRCh38 3 64099472 64099472 + Missense_Mutation SNP C C T rs760877594 11LU022_T 11LU022_N C C c.2114G>A p.Arg705His p.R705H ENST00000295902 8/8 25 21 4 49 49 0 strelka-varscan-mutect PRICKLE2,missense_variant,p.Arg705His,ENST00000295902,NM_198859.3;PRICKLE2,missense_variant,p.Arg761His,ENST00000564377,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000476308,;PRICKLE2-AS2,upstream_gene_variant,,ENST00000484703,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,; T ENST00000295902 Transcript missense_variant 2700/8305 2114/2535 705/844 R/H cGc/cAc rs760877594 1 -1 PRICKLE2 HGNC HGNC:20340 protein_coding YES CCDS2902.1 ENSP00000295902 Q7Z3G6 A0A024R368 UPI0000160A8B NM_198859.3 deleterious(0) 8/8 hmmpanther:PTHR24211:SF18,hmmpanther:PTHR24211 MODERATE 1 SNV 1 1 PASS rs760877594 . 0 199 11 0 0 0 0 0 -11.47033 0.9999652 1 1 1 0 T 3 4 3 64099472 64099472 C T 1 0 0 0 0 1 0 0 0 12619 768 27 1 1 PRICKLE2 3 64099472 Missense_Mutation SNP C 11LU022_T 1778997 64099472 134196087 192 830 LMOD3 0 . GRCh38 3 69118697 69118697 + Splice_Site SNP A A G novel 11LU022_T 11LU022_N A A c.1656+2T>C p.X552_splice ENST00000420581 38 28 10 60 60 0 strelka-varscan-mutect LMOD3,splice_donor_variant,,ENST00000420581,;LMOD3,splice_donor_variant,,ENST00000475434,;LMOD3,splice_donor_variant,,ENST00000489031,NM_001304418.1,NM_198271.4; G ENST00000420581 Transcript splice_donor_variant -/4086 1656/1683 552/560 1 -1 LMOD3 HGNC HGNC:6649 protein_coding YES CCDS46862.1 ENSP00000414670 Q0VAK6 UPI00001612AC 2/2 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 3 69118697 69118697 A G 1 0 0 0 0 0 0 1 0 8785 405 14 5 5 LMOD3 3 69118697 Splice_Site SNP A 11LU022_T 5019225 69118697 129176862 193 831 PDZRN3 0 . GRCh38 3 73383425 73383425 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.3141C>A p.= p.G1047G ENST00000263666 10/10 83 62 21 127 127 0 strelka-varscan-mutect PDZRN3,synonymous_variant,p.=,ENST00000263666,NM_015009.2;PDZRN3,synonymous_variant,p.=,ENST00000462146,NM_001303141.1;PDZRN3,synonymous_variant,p.=,ENST00000479530,NM_001303142.1;PDZRN3,synonymous_variant,p.=,ENST00000466780,NM_001303140.1;PDZRN3,synonymous_variant,p.=,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000492909,NM_001303139.1;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,; T ENST00000263666 Transcript synonymous_variant 3256/4248 3141/3201 1047/1066 G ggC/ggA 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 10/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 73383425 73383425 G T 1 0 0 0 0 0 0 0 1 11797 1306 46 2 2 PDZRN3 3 73383425 Silent SNP G 11LU022_T 4264728 73383425 124912134 194 832 GBE1 0 . GRCh38 3 81642857 81642857 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.916A>G p.Thr306Ala p.T306A ENST00000429644 7/16 166 118 48 220 220 0 strelka-varscan-mutect GBE1,missense_variant,p.Thr306Ala,ENST00000429644,NM_000158.3;GBE1,missense_variant,p.Thr265Ala,ENST00000489715,;GBE1,non_coding_transcript_exon_variant,,ENST00000498468,; C ENST00000429644 Transcript missense_variant 1560/3461 916/2109 306/702 T/A Aca/Gca 1 -1 GBE1 HGNC HGNC:4180 protein_coding YES CCDS54612.1 ENSP00000410833 Q04446 UPI0000209A24 NM_000158.3 deleterious(0.02) 7/16 Gene3D:3.20.20.80,PIRSF_domain:PIRSF000463,hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF146,SMART_domains:SM00642,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 81642857 81642857 T C 1 0 0 0 0 1 0 0 0 6141 1667 58 5 5 GBE1 3 81642857 Missense_Mutation SNP T 11LU022_T 8259432 81642857 116652702 195 833 OR5K1 0 . GRCh38 3 98469811 98469811 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.235C>A p.Pro79Thr p.P79T ENST00000332650 1/1 189 98 91 179 179 0 strelka-varscan-mutect OR5K1,missense_variant,p.Pro79Thr,ENST00000332650,NM_001004736.2; A ENST00000332650 Transcript missense_variant 332/1097 235/927 79/308 P/T Ccc/Acc 1 1 OR5K1 HGNC HGNC:8349 protein_coding YES CCDS43115.1 ENSP00000373193 Q8NHB7 A0A126GWC1 UPI000013F5A3 NM_001004736.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF311,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 98469811 98469811 C A 1 0 0 0 0 1 0 0 0 11236 623 22 2 2 OR5K1 3 98469811 Missense_Mutation SNP C 11LU022_T 16826954 98469811 99825748 196 834 USF3 0 . GRCh38 3 113660447 113660447 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.1235C>T p.Ser412Leu p.S412L ENST00000316407 7/7 270 212 58 253 252 1 strelka-varscan-mutect USF3,missense_variant,p.Ser412Leu,ENST00000316407,NM_001009899.3;USF3,missense_variant,p.Ser412Leu,ENST00000478658,;USF3,intron_variant,,ENST00000491165,;USF3,non_coding_transcript_exon_variant,,ENST00000496826,; A ENST00000316407 Transcript missense_variant 1646/13708 1235/6738 412/2245 S/L tCa/tTa 1 -1 USF3 HGNC HGNC:30494 protein_coding YES CCDS43133.1 ENSP00000320794 Q68DE3 UPI0004438052 NM_001009899.3 deleterious_low_confidence(0.01) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 113660447 113660447 G A 1 0 0 0 0 1 0 0 0 17567 1294 45 3 3 USF3 3 113660447 Missense_Mutation SNP G 11LU022_T 15190636 113660447 84635112 197 835 CASR 0 . GRCh38 3 122262210 122262210 + Missense_Mutation SNP G G A 11LU022_T 11LU022_N G G c.1175G>A p.Arg392Gln p.R392Q ENST00000498619 4/7 277 245 32 252 252 0 strelka-varscan-mutect CASR,missense_variant,p.Arg392Gln,ENST00000498619,NM_001178065.1;CASR,missense_variant,p.Arg392Gln,ENST00000490131,NM_000388.3; A ENST00000498619 Transcript missense_variant 1613/5011 1175/3267 392/1088 R/Q cGa/cAa COSM3121267 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 tolerated(0.14) 4/7 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF358,Superfamily_domains:SSF53822 1 MODERATE 1 SNV 1 1 1 PASS rs1287075426 . 0 208 0 0 2 0 0 0 -12.55295 0.9949457 1 1 1 0 A 3 1 3 122262210 122262210 G A 1 0 0 0 0 1 0 0 0 2381 1058 37 1 1 CASR 3 122262210 Missense_Mutation SNP G 11LU022_T 8601763 122262210 76033349 198 836 SLC12A8 0 . GRCh38 3 125088310 125088310 + Missense_Mutation SNP C C A rs747266705 11LU022_T 11LU022_N C C c.1982G>T p.Arg661Met p.R661M ENST00000393469 12/13 190 91 99 178 177 1 strelka-varscan-mutect SLC12A8,missense_variant,p.Arg661Met,ENST00000393469,NM_001195483.1;SLC12A8,missense_variant,p.Arg661Met,ENST00000469902,NM_024628.5;SLC12A8,missense_variant,p.Arg462Met,ENST00000430155,;SLC12A8,splice_acceptor_variant,,ENST00000461616,;SLC12A8,splice_region_variant,,ENST00000479352,;SLC12A8,splice_region_variant,,ENST00000483944,;SLC12A8,intron_variant,,ENST00000465475,;SLC12A8,splice_region_variant,,ENST00000473262,; A ENST00000393469 Transcript missense_variant,splice_region_variant 2032/3447 1982/2145 661/714 R/M aGg/aTg rs747266705 1 -1 SLC12A8 HGNC HGNC:15595 protein_coding YES CCDS43143.1 ENSP00000377112 A0AV02 UPI0004620A0B NM_001195483.1 deleterious(0.01) 12/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs747266705 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 125088310 125088310 C A 1 0 0 0 0 1 0 0 0 14654 695 24 2 2 SLC12A8 3 125088310 Missense_Mutation SNP C 11LU022_T 2826100 125088310 73207249 199 837 ZNF148 0 . GRCh38 3 125288173 125288173 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.389A>G p.Asp130Gly p.D130G ENST00000360647 5/9 161 103 58 182 182 0 strelka-varscan-mutect ZNF148,missense_variant,p.Asp130Gly,ENST00000360647,NM_021964.2;ZNF148,missense_variant,p.Asp130Gly,ENST00000485866,;ZNF148,missense_variant,p.Asp130Gly,ENST00000484491,;ZNF148,missense_variant,p.Asp130Gly,ENST00000492394,;ZNF148,intron_variant,,ENST00000468369,;ZNF148,non_coding_transcript_exon_variant,,ENST00000497929,; C ENST00000360647 Transcript missense_variant 875/9651 389/2385 130/794 D/G gAc/gGc 1 -1 ZNF148 HGNC HGNC:12933 protein_coding YES CCDS3031.1 ENSP00000353863 Q9UQR1 UPI000013C2FF NM_021964.2 tolerated(0.21) 5/9 hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF65 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 125288173 125288173 T C 1 0 0 0 0 1 0 0 0 18315 1667 58 5 5 ZNF148 3 125288173 Missense_Mutation SNP T 11LU022_T 199863 125288173 73007386 200 838 GP9 0 . GRCh38 3 129061818 129061818 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.79C>A p.Arg27Ser p.R27S ENST00000307395 3/3 307 163 144 350 350 0 strelka-varscan-mutect GP9,missense_variant,p.Arg27Ser,ENST00000307395,NM_000174.4; A ENST00000307395 Transcript missense_variant 301/889 79/534 27/177 R/S Cgc/Agc 1 1 GP9 HGNC HGNC:4444 protein_coding YES CCDS3055.1 ENSP00000303942 P14770 UPI000012B9D4 NM_000174.4 deleterious(0.03) 3/3 Pfam_domain:PF01462,hmmpanther:PTHR22650,hmmpanther:PTHR22650:SF6,SMART_domains:SM00013 MODERATE 1 SNV 1 1 PASS rs1394132097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 129061818 129061818 C A 1 0 0 0 0 1 0 0 0 6480 652 23 1 1 GP9 3 129061818 Missense_Mutation SNP C 11LU022_T 3773645 129061818 69233741 201 839 NCK1 0 . GRCh38 3 136928202 136928202 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.201T>G p.Ile67Met p.I67M ENST00000481752 2/4 174 91 83 155 155 0 strelka-varscan-mutect NCK1,missense_variant,p.Ile67Met,ENST00000481752,NM_001291999.1;NCK1,missense_variant,p.Ile67Met,ENST00000288986,NM_006153.5;NCK1,missense_variant,p.Ile67Met,ENST00000491539,;NCK1,missense_variant,p.Ile67Met,ENST00000485096,;NCK1,missense_variant,p.Ile67Met,ENST00000476286,;NCK1,missense_variant,p.Ile67Met,ENST00000488930,;NCK1,missense_variant,p.Ile55Met,ENST00000496489,;NCK1,upstream_gene_variant,,ENST00000469404,NM_001190796.2;NCK1,upstream_gene_variant,,ENST00000467911,;NCK1,non_coding_transcript_exon_variant,,ENST00000478862,;NCK1,non_coding_transcript_exon_variant,,ENST00000460960,; G ENST00000481752 Transcript missense_variant 365/1971 201/1134 67/377 I/M atT/atG 1 1 NCK1 HGNC HGNC:7664 protein_coding YES CCDS3092.1 ENSP00000417273 P16333 A0A0S2Z4Y3 UPI000012FE3E NM_001291999.1 tolerated(0.07) 2/4 PIRSF_domain:PIRSF037874,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF159 MODERATE 1 SNV 5 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999907 1 1 1 0 G 3 3 3 136928202 136928202 T G 1 0 0 0 0 1 0 0 0 10237 1800 63 5 5 NCK1 3 136928202 Missense_Mutation SNP T 11LU022_T 7866384 136928202 61367357 202 840 TRIM42 0 . GRCh38 3 140682854 140682854 + Missense_Mutation SNP G G C rs142526494 11LU022_T 11LU022_N G G c.734G>C p.Arg245Pro p.R245P ENST00000286349 2/5 215 131 84 228 228 0 strelka-varscan-mutect TRIM42,missense_variant,p.Arg245Pro,ENST00000286349,NM_152616.4; C ENST00000286349 Transcript missense_variant 925/2539 734/2172 245/723 R/P cGc/cCc rs142526494 1 1 TRIM42 HGNC HGNC:19014 protein_coding YES CCDS3113.1 ENSP00000286349 Q8IWZ5 UPI00001AEAE0 NM_152616.4 deleterious(0) 2/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF269,SMART_domains:SM00336 MODERATE 1 SNV 1 1 PASS rs142526494 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 140682854 140682854 G C 1 0 0 0 0 1 0 0 0 17007 1087 38 4 4 TRIM42 3 140682854 Missense_Mutation SNP G 11LU022_T 3754652 140682854 57612705 203 841 C3orf58 0 . GRCh38 3 143972461 143972461 + Silent SNP A A G rs778973713 11LU022_T 11LU022_N A A c.129A>G p.= p.E43E ENST00000315691 1/3 47 26 21 50 50 0 strelka-varscan-mutect C3orf58,synonymous_variant,p.=,ENST00000315691,NM_173552.3;C3orf58,upstream_gene_variant,,ENST00000441925,;C3orf58,upstream_gene_variant,,ENST00000495414,NM_001134470.1;C3orf58,upstream_gene_variant,,ENST00000492452,;C3orf58,upstream_gene_variant,,ENST00000493396,;C3orf58,upstream_gene_variant,,ENST00000491798,;C3orf58,upstream_gene_variant,,ENST00000483808,; G ENST00000315691 Transcript synonymous_variant 664/4346 129/1293 43/430 E gaA/gaG rs778973713 1 1 C3orf58 HGNC HGNC:28490 protein_coding YES CCDS3130.1 ENSP00000320081 Q8NDZ4 UPI000006EE5C NM_173552.3 1/3 PD307452,hmmpanther:PTHR32073,hmmpanther:PTHR32073:SF6 LOW 1 SNV 1 1 PASS rs778973713 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 143972461 143972461 A G 1 0 0 0 0 0 0 0 1 2069 40 2 5 5 C3orf58 3 143972461 Silent SNP A 11LU022_T 3289607 143972461 54323098 204 842 ZIC1 0 . GRCh38 3 147410131 147410131 + Missense_Mutation SNP C C A rs769500554 11LU022_T 11LU022_N C C c.19C>A p.Pro7Thr p.P7T ENST00000282928 1/3 87 58 29 88 88 0 strelka-varscan-mutect ZIC1,missense_variant,p.Pro7Thr,ENST00000282928,NM_003412.3;ZIC1,intron_variant,,ENST00000488404,;ZIC4,upstream_gene_variant,,ENST00000383075,NM_032153.5;ZIC4,upstream_gene_variant,,ENST00000425731,NM_001168379.1;ZIC4,upstream_gene_variant,,ENST00000473123,;ZIC4,upstream_gene_variant,,ENST00000462748,;ZIC4,upstream_gene_variant,,ENST00000491672,NM_001243256.1;ZIC4,upstream_gene_variant,,ENST00000463250,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,upstream_gene_variant,,ENST00000464144,; A ENST00000282928 Transcript missense_variant 748/5241 19/1344 7/447 P/T Ccc/Acc rs769500554 1 1 ZIC1 HGNC HGNC:12872 protein_coding YES CCDS3136.1 ENSP00000282928 Q15915 UPI000013DD09 NM_003412.3 deleterious_low_confidence(0.02) 1/3 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26 MODERATE 1 SNV 1 1 PASS rs769500554 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 3 147410131 147410131 C A 1 0 0 0 0 1 0 0 0 18257 623 22 2 2 ZIC1 3 147410131 Missense_Mutation SNP C 11LU022_T 3437670 147410131 50885428 205 843 P2RY13 0 . GRCh38 3 151328836 151328836 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.220A>T p.Ser74Cys p.S74C ENST00000325602 2/2 253 135 118 191 191 0 strelka-varscan-mutect P2RY13,missense_variant,p.Ser74Cys,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; A ENST00000325602 Transcript missense_variant 240/2764 220/1065 74/354 S/C Agc/Tgc 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 151328836 151328836 T A 1 0 0 0 0 1 0 0 0 11423 1580 55 4 4 P2RY13 3 151328836 Missense_Mutation SNP T 11LU022_T 3918705 151328836 46966723 206 844 P2RY12 0 . GRCh38 3 151338027 151338027 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.819A>G p.= p.E273E ENST00000302632 3/3 149 84 65 154 154 0 strelka-varscan-mutect P2RY12,synonymous_variant,p.=,ENST00000302632,NM_176876.2,NM_022788.4;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,downstream_gene_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,;P2RY12,downstream_gene_variant,,ENST00000468596,; C ENST00000302632 Transcript synonymous_variant 1119/1766 819/1029 273/342 E gaA/gaG 1 -1 P2RY12 HGNC HGNC:18124 protein_coding YES CCDS3159.1 ENSP00000307259 Q9H244 UPI0000001662 NM_176876.2,NM_022788.4 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF0,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 151338027 151338027 T C 1 0 0 0 0 0 0 0 1 11422 1838 64 5 5 P2RY12 3 151338027 Silent SNP T 11LU022_T 9191 151338027 46957532 207 845 LEKR1 0 . GRCh38 3 156829347 156829347 + Silent SNP C C T 11LU022_T 11LU022_N C C c.18C>T p.= p.P6P ENST00000491763 2/5 106 95 11 94 94 0 strelka-varscan-mutect LEKR1,synonymous_variant,p.=,ENST00000356539,NM_001004316.2;LEKR1,synonymous_variant,p.=,ENST00000491763,NM_001193283.1;LEKR1,synonymous_variant,p.=,ENST00000477399,;LEKR1,synonymous_variant,p.=,ENST00000498839,;LEKR1,synonymous_variant,p.=,ENST00000483177,;LEKR1,5_prime_UTR_variant,,ENST00000470811,;LEKR1,non_coding_transcript_exon_variant,,ENST00000489350,;LEKR1,non_coding_transcript_exon_variant,,ENST00000485017,;LEKR1,non_coding_transcript_exon_variant,,ENST00000465728,;LEKR1,non_coding_transcript_exon_variant,,ENST00000467376,; T ENST00000491763 Transcript synonymous_variant 813/1940 18/399 6/132 P ccC/ccT COSM5601731 1 1 LEKR1 HGNC HGNC:33765 protein_coding YES CCDS54660.1 ENSP00000474182 D3DNK7 UPI00006C06BC NM_001193283.1 2/5 hmmpanther:PTHR34251 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 156829347 156829347 C T 1 0 0 0 0 0 0 0 1 8625 581 21 3 3 LEKR1 3 156829347 Silent SNP C 11LU022_T 5491320 156829347 41466212 208 846 LEKR1 0 . GRCh38 3 156920657 156920657 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.346G>T p.Glu116Ter p.E116* ENST00000491763 4/5 89 61 28 105 105 0 strelka-varscan-mutect LEKR1,stop_gained,p.Glu116Ter,ENST00000356539,NM_001004316.2;LEKR1,stop_gained,p.Glu116Ter,ENST00000491763,NM_001193283.1;LEKR1,stop_gained,p.Glu116Ter,ENST00000477399,;LEKR1,5_prime_UTR_variant,,ENST00000470811,;LEKR1,non_coding_transcript_exon_variant,,ENST00000489350,;LEKR1,non_coding_transcript_exon_variant,,ENST00000467376,;LEKR1,upstream_gene_variant,,ENST00000495252,; T ENST00000491763 Transcript stop_gained 1141/1940 346/399 116/132 E/* Gag/Tag 1 1 LEKR1 HGNC HGNC:33765 protein_coding YES CCDS54660.1 ENSP00000474182 D3DNK7 UPI00006C06BC NM_001193283.1 4/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR34251 HIGH 1 SNV 1 1 PASS . . 0 204 2 3 0 0 0 0 -20 0.9999903 1 1 1 0 T 4 4 3 156920657 156920657 G T 1 0 0 0 0 0 1 0 0 8625 1291 45 2 2 LEKR1 3 156920657 Nonsense_Mutation SNP G 11LU022_T 91310 156920657 41374902 209 847 ZBBX 0 . GRCh38 3 167360721 167360721 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.276T>A p.Phe92Leu p.F92L ENST00000455345 6/21 44 32 12 53 53 0 strelka-varscan-mutect ZBBX,missense_variant,p.Phe92Leu,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Phe92Leu,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Phe92Leu,ENST00000307529,;ZBBX,missense_variant,p.Phe63Leu,ENST00000392767,;ZBBX,missense_variant,p.Phe63Leu,ENST00000392764,NM_001199202.1;ZBBX,missense_variant,p.Phe92Leu,ENST00000474464,;ZBBX,intron_variant,,ENST00000469220,; T ENST00000455345 Transcript missense_variant,splice_region_variant 560/3185 276/2520 92/839 F/L ttT/ttA 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 tolerated(1) 6/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 2 205 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 167360721 167360721 A T 1 0 0 0 0 1 0 0 0 18078 28 1 4 4 ZBBX 3 167360721 Missense_Mutation SNP A 11LU022_T 10440064 167360721 30934838 210 848 FNDC3B 0 . GRCh38 3 172112581 172112581 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.102A>T p.= p.A34A ENST00000336824 2/26 247 145 102 206 206 0 strelka-varscan-mutect FNDC3B,synonymous_variant,p.=,ENST00000336824,NM_001135095.1;FNDC3B,synonymous_variant,p.=,ENST00000415807,NM_022763.3;FNDC3B,synonymous_variant,p.=,ENST00000416957,;FNDC3B,synonymous_variant,p.=,ENST00000421757,;FNDC3B,synonymous_variant,p.=,ENST00000423424,;FNDC3B,non_coding_transcript_exon_variant,,ENST00000469491,; T ENST00000336824 Transcript synonymous_variant 201/7904 102/3615 34/1204 A gcA/gcT 1 1 FNDC3B HGNC HGNC:24670 protein_coding YES CCDS3217.1 ENSP00000338523 Q53EP0 UPI00001AE8B2 NM_001135095.1 2/26 LOW 1 SNV 1 1 PASS rs1444315410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 172112581 172112581 A T 1 0 0 0 0 0 0 0 1 5827 175 7 4 4 FNDC3B 3 172112581 Silent SNP A 11LU022_T 4751860 172112581 26182978 211 849 USP13 0 . GRCh38 3 179720003 179720003 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.869A>T p.His290Leu p.H290L ENST00000263966 7/21 208 140 68 211 211 0 strelka-varscan-mutect USP13,missense_variant,p.His290Leu,ENST00000263966,NM_003940.2;USP13,missense_variant,p.His225Leu,ENST00000496897,;USP13,upstream_gene_variant,,ENST00000497155,;USP13,non_coding_transcript_exon_variant,,ENST00000482333,; T ENST00000263966 Transcript missense_variant 1340/8323 869/2592 290/863 H/L cAt/cTt 1 1 USP13 HGNC HGNC:12611 protein_coding YES CCDS3235.1 ENSP00000263966 Q92995 A0A0A6YZ17 UPI000006DC10 NM_003940.2 deleterious(0) 7/21 Gene3D:3.30.40.10,PIRSF_domain:PIRSF016308,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 179720003 179720003 A T 1 0 0 0 0 1 0 0 0 17578 217 8 4 4 USP13 3 179720003 Missense_Mutation SNP A 11LU022_T 7607422 179720003 18575556 212 850 EPHB3 0 . GRCh38 3 184581079 184581079 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2646G>T p.Arg882Ser p.R882S ENST00000330394 14/16 207 124 83 276 276 0 strelka-varscan-mutect EPHB3,missense_variant,p.Arg882Ser,ENST00000330394,NM_004443.3;EPHB3,downstream_gene_variant,,ENST00000473079,;EPHB3,downstream_gene_variant,,ENST00000482987,; T ENST00000330394 Transcript missense_variant 3098/4236 2646/2997 882/998 R/S agG/agT 1 1 EPHB3 HGNC HGNC:3394 protein_coding YES CCDS3268.1 ENSP00000332118 P54753 UPI0000161C94 NM_004443.3 deleterious(0) 14/16 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF120,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 184581079 184581079 G T 1 0 0 0 0 1 0 0 0 5023 1194 42 2 2 EPHB3 3 184581079 Missense_Mutation SNP G 11LU022_T 4861076 184581079 13714480 213 851 TRMT44 0 . GRCh38 4 8446520 8446520 + Missense_Mutation SNP G G A rs746519271 11LU022_T 11LU022_N G G c.664G>A p.Asp222Asn p.D222N ENST00000389737 2/11 189 176 13 219 219 0 strelka-mutect TRMT44,missense_variant,p.Asp222Asn,ENST00000389737,NM_152544.2;TRMT44,5_prime_UTR_variant,,ENST00000513449,;TRMT44,intron_variant,,ENST00000504134,;TRMT44,non_coding_transcript_exon_variant,,ENST00000528167,; A ENST00000389737 Transcript missense_variant 664/2799 664/2274 222/757 D/N Gat/Aat rs746519271 1 1 TRMT44 HGNC HGNC:26653 protein_coding YES CCDS3402.2 ENSP00000374387 Q8IYL2 UPI0000DE1FA2 NM_152544.2 tolerated(0.17) 2/11 hmmpanther:PTHR21210:SF0,hmmpanther:PTHR21210 MODERATE 1 SNV 5 1 PASS rs746519271 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 8446520 8446520 G A 1 0 0 0 0 1 0 0 0 17071 1290 45 3 3 TRMT44 4 8446520 Missense_Mutation SNP G 11LU022_T 8446520 181768035 214 852 GPR78 0 . GRCh38 4 8581478 8581478 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.496C>G p.Arg166Gly p.R166G ENST00000382487 1/3 181 145 36 178 178 0 strelka-varscan-mutect GPR78,missense_variant,p.Arg166Gly,ENST00000382487,NM_080819.4;GPR78,intron_variant,,ENST00000509216,;GPR78,upstream_gene_variant,,ENST00000504255,;GPR78,downstream_gene_variant,,ENST00000503448,;GPR78,downstream_gene_variant,,ENST00000503981,;GPR78,missense_variant,p.Arg166Gly,ENST00000514302,; G ENST00000382487 Transcript missense_variant 913/1694 496/1092 166/363 R/G Cgt/Ggt 1 1 GPR78 HGNC HGNC:4528 protein_coding YES CCDS3403.1 ENSP00000371927 Q96P69 B2R7M4 UPI0000037A5F NM_080819.4 tolerated(0.26) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF7,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs1003441060 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 8581478 8581478 C G 1 0 0 0 0 1 0 0 0 6592 768 27 4 4 GPR78 4 8581478 Missense_Mutation SNP C 11LU022_T 134958 8581478 181633077 215 853 HS3ST1 0 . GRCh38 4 11399703 11399703 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.303C>T p.= p.G101G ENST00000002596 2/2 284 240 44 242 242 0 strelka-varscan-mutect HS3ST1,synonymous_variant,p.=,ENST00000002596,NM_005114.2;HS3ST1,downstream_gene_variant,,ENST00000510712,;HS3ST1,downstream_gene_variant,,ENST00000514690,; A ENST00000002596 Transcript synonymous_variant 1478/8031 303/924 101/307 G ggC/ggT 1 -1 HS3ST1 HGNC HGNC:5194 protein_coding YES CCDS3408.1 ENSP00000002596 O14792 A0A024R9R4 UPI0000072A23 NM_005114.2 2/2 hmmpanther:PTHR10605:SF16,hmmpanther:PTHR10605,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 11399703 11399703 G A 1 0 0 0 0 0 0 0 1 7257 958 34 3 3 HS3ST1 4 11399703 Silent SNP G 11LU022_T 2818225 11399703 178814852 216 854 SLIT2 0 . GRCh38 4 20617003 20617003 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.3941A>T p.Asn1314Ile p.N1314I ENST00000504154 35/37 287 242 45 228 228 0 strelka-varscan-mutect SLIT2,missense_variant,p.Asn1314Ile,ENST00000504154,NM_004787.2;SLIT2,missense_variant,p.Asn1224Ile,ENST00000622093,;SLIT2,missense_variant,p.Asn1306Ile,ENST00000503823,NM_001289136.1;SLIT2,missense_variant,p.Asn1327Ile,ENST00000273739,;SLIT2,missense_variant,p.Asn1310Ile,ENST00000503837,NM_001289135.1;SLIT2,intron_variant,,ENST00000512993,;SLIT2,non_coding_transcript_exon_variant,,ENST00000508541,; T ENST00000504154 Transcript missense_variant 4193/6390 3941/4590 1314/1529 N/I aAc/aTc 1 1 SLIT2 HGNC HGNC:11086 protein_coding YES CCDS3426.1 ENSP00000422591 O94813 UPI00000747E4 NM_004787.2 deleterious(0) 35/37 PROSITE_profiles:PS50025,hmmpanther:PTHR24373:SF107,hmmpanther:PTHR24373,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 20617003 20617003 A T 1 0 0 0 0 1 0 0 0 15031 43 2 4 4 SLIT2 4 20617003 Missense_Mutation SNP A 11LU022_T 9217300 20617003 169597552 217 855 ZCCHC4 0 . GRCh38 4 25365085 25365085 + Missense_Mutation SNP A A T rs368159327 11LU022_T 11LU022_N A A c.1325A>T p.Lys442Ile p.K442I ENST00000302874 12/13 243 201 42 237 237 0 strelka-varscan-mutect ZCCHC4,missense_variant,p.Lys442Ile,ENST00000302874,NM_024936.2;ZCCHC4,intron_variant,,ENST00000505412,;ZCCHC4,3_prime_UTR_variant,,ENST00000507760,;ZCCHC4,non_coding_transcript_exon_variant,,ENST00000508058,; T ENST00000302874 Transcript missense_variant 1349/2785 1325/1542 442/513 K/I aAa/aTa rs368159327 1 1 ZCCHC4 HGNC HGNC:22917 protein_coding YES CCDS43218.1 ENSP00000303468 Q9H5U6 UPI0000251F28 NM_024936.2 tolerated(0.15) 12/13 hmmpanther:PTHR13493,hmmpanther:PTHR13493:SF3 MODERATE 1 SNV 1 1 PASS rs368159327 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 25365085 25365085 A T 1 0 0 0 0 1 0 0 0 18165 14 1 4 4 ZCCHC4 4 25365085 Missense_Mutation SNP A 11LU022_T 4748082 25365085 164849470 218 856 RBPJ 0 . GRCh38 4 26406236 26406236 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.160A>G p.Lys54Glu p.K54E ENST00000342295 4/12 133 114 19 156 156 0 strelka-varscan-mutect RBPJ,missense_variant,p.Lys40Glu,ENST00000355476,NM_203284.2;RBPJ,missense_variant,p.Lys54Glu,ENST00000342295,NM_005349.3;RBPJ,missense_variant,p.Lys40Glu,ENST00000342320,;RBPJ,missense_variant,p.Lys41Glu,ENST00000348160,NM_015874.4;RBPJ,missense_variant,p.Lys54Glu,ENST00000361572,;RBPJ,missense_variant,p.Lys19Glu,ENST00000507561,;RBPJ,missense_variant,p.Lys39Glu,ENST00000345843,NM_203283.2;RBPJ,missense_variant,p.Lys40Glu,ENST00000504907,;RBPJ,missense_variant,p.Lys54Glu,ENST00000512671,;RBPJ,missense_variant,p.Lys19Glu,ENST00000504938,;RBPJ,missense_variant,p.Lys77Glu,ENST00000510778,;RBPJ,missense_variant,p.Lys19Glu,ENST00000515573,;RBPJ,missense_variant,p.Lys40Glu,ENST00000512351,;RBPJ,missense_variant,p.Lys19Glu,ENST00000507574,;RBPJ,missense_variant,p.Lys40Glu,ENST00000514675,;RBPJ,missense_variant,p.Lys40Glu,ENST00000511546,;RBPJ,missense_variant,p.Lys40Glu,ENST00000514730,;RBPJ,missense_variant,p.Lys40Glu,ENST00000506956,;RBPJ,missense_variant,p.Lys40Glu,ENST00000509158,;RBPJ,missense_variant,p.Lys40Glu,ENST00000514807,;RBPJ,downstream_gene_variant,,ENST00000505958,;RBPJ,non_coding_transcript_exon_variant,,ENST00000511401,;RBPJ,non_coding_transcript_exon_variant,,ENST00000515023,;RBPJ,missense_variant,p.Lys41Glu,ENST00000513182,;RBPJ,non_coding_transcript_exon_variant,,ENST00000514380,;RBPJ,non_coding_transcript_exon_variant,,ENST00000511451,; G ENST00000342295 Transcript missense_variant 396/5860 160/1503 54/500 K/E Aaa/Gaa 1 1 RBPJ HGNC HGNC:5724 protein_coding YES CCDS3437.1 ENSP00000345206 Q06330 UPI000020BDF1 NM_005349.3 deleterious(0) 4/12 hmmpanther:PTHR10665:SF3,hmmpanther:PTHR10665,Gene3D:2.60.40.1450,Pfam_domain:PF09271,SMART_domains:SM01267,Superfamily_domains:SSF49417 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 26406236 26406236 A G 1 0 0 0 0 1 0 0 0 13329 15 1 5 5 RBPJ 4 26406236 Missense_Mutation SNP A 11LU022_T 1041151 26406236 163808319 219 857 CCKAR 0 . GRCh38 4 26485819 26485819 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.444G>T p.Gln148His p.Q148H ENST00000295589 3/5 348 249 99 347 347 0 strelka-varscan-mutect CCKAR,missense_variant,p.Gln148His,ENST00000295589,NM_000730.2; A ENST00000295589 Transcript missense_variant 639/1720 444/1287 148/428 Q/H caG/caT 1 -1 CCKAR HGNC HGNC:1570 protein_coding YES CCDS3438.1 ENSP00000295589 P32238 UPI00000503F3 NM_000730.2 tolerated(0.08) 3/5 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01822,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF76,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 26485819 26485819 C A 1 0 0 0 0 1 0 0 0 2578 564 20 2 2 CCKAR 4 26485819 Missense_Mutation SNP C 11LU022_T 79583 26485819 163728736 220 858 PCDH7 0 . GRCh38 4 30721735 30721735 + Missense_Mutation SNP G G A rs745604162 11LU022_T 11LU022_N G G c.313G>A p.Glu105Lys p.E105K ENST00000543491 1/1 238 202 36 243 243 0 strelka-varscan-mutect PCDH7,missense_variant,p.Glu105Lys,ENST00000361762,NM_002589.2;PCDH7,missense_variant,p.Glu105Lys,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; A ENST00000543491 Transcript missense_variant 883/4457 313/3219 105/1072 E/K Gag/Aag rs745604162 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 tolerated(0.07) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF321,Pfam_domain:PF08266,SMART_domains:SM00112 MODERATE 1 SNV 1 PASS rs745604162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 30721735 30721735 G A 1 0 0 0 0 1 0 0 0 11603 1059 37 1 1 PCDH7 4 30721735 Missense_Mutation SNP G 11LU022_T 4235916 30721735 159492820 221 859 DTHD1 0 . GRCh38 4 36306315 36306315 + Missense_Mutation SNP G G T rs373949236 11LU022_T 11LU022_N G G c.1393G>T p.Gly465Cys p.G465C ENST00000456874 5/9 117 95 22 115 115 0 strelka-varscan-mutect DTHD1,missense_variant,p.Gly465Cys,ENST00000456874,NM_001170700.2;DTHD1,missense_variant,p.Gly300Cys,ENST00000357504,NM_001136536.4;DTHD1,missense_variant,p.Gly505Cys,ENST00000507598,;RP11-431M7.2,downstream_gene_variant,,ENST00000504344,; T ENST00000456874 Transcript missense_variant 1451/3365 1393/2346 465/781 G/C Ggc/Tgc rs373949236 1 1 DTHD1 HGNC HGNC:37261 protein_coding YES CCDS54754.1 ENSP00000401597 Q6ZMT9 UPI00006C079E NM_001170700.2 deleterious(0) 5/9 hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF47 MODERATE 1 SNV 1 1 PASS rs373949236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 36306315 36306315 G T 1 0 0 0 0 1 0 0 0 4609 1116 39 1 1 DTHD1 4 36306315 Missense_Mutation SNP G 11LU022_T 5584580 36306315 153908240 222 860 CHRNA9 0 . GRCh38 4 40335874 40335874 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.112C>A p.Leu38Ile p.L38I ENST00000310169 2/5 141 118 23 132 132 0 strelka-varscan-mutect CHRNA9,missense_variant,p.Leu38Ile,ENST00000310169,NM_017581.3;CHRNA9,upstream_gene_variant,,ENST00000502377,; A ENST00000310169 Transcript missense_variant 251/2276 112/1440 38/479 L/I Ctt/Att 1 1 CHRNA9 HGNC HGNC:14079 protein_coding YES CCDS3459.1 ENSP00000312663 Q9UGM1 UPI000013EFB8 NM_017581.3 deleterious(0) 2/5 hmmpanther:PTHR18945:SF546,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS rs1417338116 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 40335874 40335874 C A 1 0 0 0 0 1 0 0 0 3149 681 24 2 2 CHRNA9 4 40335874 Missense_Mutation SNP C 11LU022_T 4029559 40335874 149878681 223 861 SLAIN2 0 . GRCh38 4 48420179 48420179 + Missense_Mutation SNP G G T rs548702021 11LU022_T 11LU022_N G G c.1415G>T p.Arg472Leu p.R472L ENST00000264313 7/8 186 149 37 181 181 0 varscan-mutect SLAIN2,missense_variant,p.Arg472Leu,ENST00000264313,NM_020846.1;SLAIN2,missense_variant,p.Arg305Leu,ENST00000512093,;SLAIN2,missense_variant,p.Arg81Leu,ENST00000510595,; T ENST00000264313 Transcript missense_variant 1833/6299 1415/1746 472/581 R/L cGg/cTg rs548702021 1 1 SLAIN2 HGNC HGNC:29282 protein_coding YES CCDS47051.1 ENSP00000264313 Q9P270 A0A024R9T6 UPI0000074559 NM_020846.1 deleterious(0) 7/8 hmmpanther:PTHR22406:SF4,hmmpanther:PTHR22406,Pfam_domain:PF15301 MODERATE 1 SNV 1 1 PASS rs548702021 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 48420179 48420179 G T 1 0 0 0 0 1 0 0 0 14631 1116 39 1 1 SLAIN2 4 48420179 Missense_Mutation SNP G 11LU022_T 8084305 48420179 141794376 224 862 DCUN1D4 0 . GRCh38 4 51863704 51863704 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.263A>G p.Gln88Arg p.Q88R ENST00000451288 3/11 100 80 20 141 141 0 strelka-varscan-mutect DCUN1D4,missense_variant,p.Gln44Arg,ENST00000334635,NM_001287757.1,NM_001040402.2;DCUN1D4,missense_variant,p.Gln88Arg,ENST00000451288,NM_001287755.1;DCUN1D4,missense_variant,p.Gln44Arg,ENST00000381441,NM_015115.3;DCUN1D4,missense_variant,p.Gln88Arg,ENST00000505403,;DCUN1D4,non_coding_transcript_exon_variant,,ENST00000513800,;DCUN1D4,non_coding_transcript_exon_variant,,ENST00000504113,;DCUN1D4,non_coding_transcript_exon_variant,,ENST00000504661,;DCUN1D4,missense_variant,p.Gln44Arg,ENST00000477560,;DCUN1D4,missense_variant,p.Gln88Arg,ENST00000509068,;DCUN1D4,3_prime_UTR_variant,,ENST00000507741,;DCUN1D4,3_prime_UTR_variant,,ENST00000506673,;DCUN1D4,non_coding_transcript_exon_variant,,ENST00000511675,;DCUN1D4,intron_variant,,ENST00000509376,;DCUN1D4,intron_variant,,ENST00000502930,;DUTP7,downstream_gene_variant,,ENST00000507982,; G ENST00000451288 Transcript missense_variant 270/4269 263/1011 88/336 Q/R cAa/cGa 1 1 DCUN1D4 HGNC HGNC:28998 protein_coding YES CCDS75123.1 ENSP00000389900 Q92564 UPI00017A6FA4 NM_001287755.1 tolerated_low_confidence(0.07) 3/11 hmmpanther:PTHR12281,hmmpanther:PTHR12281:SF8 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 51863704 51863704 A G 1 0 0 0 0 1 0 0 0 4119 144 5 5 5 DCUN1D4 4 51863704 Missense_Mutation SNP A 11LU022_T 3443525 51863704 138350851 225 863 KIAA1211 0 . GRCh38 4 56314897 56314897 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1395G>T p.Gln465His p.Q465H ENST00000504228 6/9 277 214 63 213 213 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Gln465His,ENST00000504228,;KIAA1211,missense_variant,p.Gln458His,ENST00000541073,;KIAA1211,missense_variant,p.Gln465His,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; T ENST00000504228 Transcript missense_variant 1500/4628 1395/3702 465/1233 Q/H caG/caT 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 deleterious(0.03) 6/9 MODERATE 1 SNV 5 1 PASS rs892624885 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 56314897 56314897 G T 1 0 0 0 0 1 0 0 0 8107 991 35 2 2 KIAA1211 4 56314897 Missense_Mutation SNP G 11LU022_T 4451193 56314897 133899658 226 864 ADGRL3 0 . GRCh38 4 62031506 62031506 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.3283A>T p.Met1095Leu p.M1095L ENST00000514591 22/25 134 115 19 130 130 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Met1095Leu,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.Met1095Leu,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Met1163Leu,ENST00000509896,;ADGRL3,missense_variant,p.Met1154Leu,ENST00000511324,;ADGRL3,missense_variant,p.Met1163Leu,ENST00000508693,;ADGRL3,missense_variant,p.Met1154Leu,ENST00000507164,;ADGRL3,missense_variant,p.Met1163Leu,ENST00000506720,;ADGRL3,missense_variant,p.Met1154Leu,ENST00000506746,;ADGRL3,missense_variant,p.Met1154Leu,ENST00000507625,;ADGRL3,missense_variant,p.Met1086Leu,ENST00000506700,;ADGRL3,missense_variant,p.Met1095Leu,ENST00000504896,;ADGRL3,missense_variant,p.Met1086Leu,ENST00000514157,;ADGRL3,missense_variant,p.Met1095Leu,ENST00000508946,;ADGRL3,missense_variant,p.Met1086Leu,ENST00000514996,;ADGRL3,missense_variant,p.Met544Leu,ENST00000502815,; T ENST00000514591 Transcript missense_variant 3612/6297 3283/4410 1095/1469 M/L Atg/Ttg 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 tolerated(1) 22/25 PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs1228441734 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 62031506 62031506 A T 1 0 0 0 0 1 0 0 0 377 217 8 4 4 ADGRL3 4 62031506 Missense_Mutation SNP A 11LU022_T 5716609 62031506 128183049 227 865 TMPRSS11A 0 . GRCh38 4 67911458 67911458 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1150T>A p.Trp384Arg p.W384R ENST00000334830 10/10 133 107 26 165 164 1 strelka-varscan-mutect TMPRSS11A,missense_variant,p.Trp381Arg,ENST00000508048,NM_001114387.1;TMPRSS11A,missense_variant,p.Trp384Arg,ENST00000334830,NM_182606.3;TMPRSS11A,missense_variant,p.Trp348Arg,ENST00000513536,;UBA6-AS1,intron_variant,,ENST00000500538,; T ENST00000334830 Transcript missense_variant 1897/3054 1150/1266 384/421 W/R Tgg/Agg 1 -1 TMPRSS11A HGNC HGNC:27954 protein_coding YES CCDS3519.1 ENSP00000334611 A0A0A0MR82 UPI0000457217 NM_182606.3 deleterious(0) 10/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF37,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF037941,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 67911458 67911458 A T 1 0 0 0 0 1 0 0 0 16715 159 6 4 4 TMPRSS11A 4 67911458 Missense_Mutation SNP A 11LU022_T 5879952 67911458 122303097 228 866 UGT2B7 0 . GRCh38 4 69098660 69098660 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.842A>T p.His281Leu p.H281L ENST00000305231 2/6 207 163 44 198 198 0 strelka-varscan-mutect UGT2B7,missense_variant,p.His281Leu,ENST00000305231,NM_001074.2;UGT2B7,missense_variant,p.His281Leu,ENST00000508661,;UGT2B7,missense_variant,p.His281Leu,ENST00000622664,;UGT2B7,missense_variant,p.His32Leu,ENST00000502942,;UGT2B7,non_coding_transcript_exon_variant,,ENST00000509763,; T ENST00000305231 Transcript missense_variant 888/1887 842/1590 281/529 H/L cAc/cTc 1 1 UGT2B7 HGNC HGNC:12554 protein_coding YES CCDS3526.1 ENSP00000304811 P16662 UPI00000015EC NM_001074.2 deleterious(0.01) 2/6 hmmpanther:PTHR11926:SF382,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 69098660 69098660 A T 1 0 0 0 0 1 0 0 0 17486 159 6 4 4 UGT2B7 4 69098660 Missense_Mutation SNP A 11LU022_T 1187202 69098660 121115895 229 867 UGT2B7 0 . GRCh38 4 69112584 69112584 + Missense_Mutation SNP G G T rs780707514 11LU022_T 11LU022_N G G c.1438G>T p.Ala480Ser p.A480S ENST00000305231 6/6 277 225 52 305 305 0 strelka-varscan-mutect UGT2B7,missense_variant,p.Ala480Ser,ENST00000305231,NM_001074.2;UGT2B7,3_prime_UTR_variant,,ENST00000508661,;UGT2B7,3_prime_UTR_variant,,ENST00000622664,;UGT2B7,downstream_gene_variant,,ENST00000502942,;UGT2B7,downstream_gene_variant,,ENST00000509763,; T ENST00000305231 Transcript missense_variant 1484/1887 1438/1590 480/529 A/S Gcc/Tcc rs780707514 1 1 UGT2B7 HGNC HGNC:12554 protein_coding YES CCDS3526.1 ENSP00000304811 P16662 UPI00000015EC NM_001074.2 tolerated(0.24) 6/6 hmmpanther:PTHR11926:SF382,hmmpanther:PTHR11926,Pfam_domain:PF00201 MODERATE 1 SNV 1 1 PASS rs780707514 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 69112584 69112584 G T 1 0 0 0 0 1 0 0 0 17486 971 34 2 2 UGT2B7 4 69112584 Missense_Mutation SNP G 11LU022_T 13924 69112584 121101971 230 868 MUC7 0 . GRCh38 4 70481451 70481451 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.707C>A p.Ala236Asp p.A236D ENST00000413702 4/4 310 282 28 359 358 1 varscan-mutect MUC7,missense_variant,p.Ala236Asp,ENST00000413702,NM_001145006.1;MUC7,missense_variant,p.Ala236Asp,ENST00000456088,NM_001145007.1;MUC7,missense_variant,p.Ala236Asp,ENST00000304887,NM_152291.2;MUC7,downstream_gene_variant,,ENST00000505411,;MUC7,downstream_gene_variant,,ENST00000514512,;MUC7,downstream_gene_variant,,ENST00000504482,; A ENST00000413702 Transcript missense_variant 995/2540 707/1134 236/377 A/D gCt/gAt 1 1 MUC7 HGNC HGNC:7518 protein_coding YES CCDS3541.1 ENSP00000407422 Q8TAX7 UPI000013E9DD NM_001145006.1 tolerated(0.07) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR41683:SF1,hmmpanther:PTHR41683 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 70481451 70481451 C A 1 0 0 0 0 1 0 0 0 9981 797 28 2 2 MUC7 4 70481451 Missense_Mutation SNP C 11LU022_T 1368867 70481451 119733104 231 869 MUC7 0 . GRCh38 4 70481520 70481520 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.776C>A p.Ala259Asp p.A259D ENST00000413702 4/4 317 263 54 342 342 0 strelka-varscan-mutect MUC7,missense_variant,p.Ala259Asp,ENST00000413702,NM_001145006.1;MUC7,missense_variant,p.Ala259Asp,ENST00000456088,NM_001145007.1;MUC7,missense_variant,p.Ala259Asp,ENST00000304887,NM_152291.2;MUC7,downstream_gene_variant,,ENST00000505411,;MUC7,downstream_gene_variant,,ENST00000514512,;MUC7,downstream_gene_variant,,ENST00000504482,; A ENST00000413702 Transcript missense_variant 1064/2540 776/1134 259/377 A/D gCt/gAt 1 1 MUC7 HGNC HGNC:7518 protein_coding YES CCDS3541.1 ENSP00000407422 Q8TAX7 UPI000013E9DD NM_001145006.1 tolerated(0.39) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR41683:SF1,hmmpanther:PTHR41683 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 70481520 70481520 C A 1 0 0 0 0 1 0 0 0 9981 797 28 2 2 MUC7 4 70481520 Missense_Mutation SNP C 11LU022_T 69 70481520 119733035 232 870 GC 0 . GRCh38 4 71756711 71756711 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.1091+1G>T p.X364_splice ENST00000504199 137 111 26 143 143 0 strelka-varscan-mutect GC,splice_donor_variant,,ENST00000273951,NM_000583.3,NM_001204306.1;GC,splice_donor_variant,,ENST00000504199,NM_001204307.1;GC,splice_donor_variant,,ENST00000513476,;RNA5SP163,downstream_gene_variant,,ENST00000410304,;GC,splice_donor_variant,,ENST00000503472,;GC,upstream_gene_variant,,ENST00000503364,;GC,splice_donor_variant,,ENST00000509740,; A ENST00000504199 Transcript splice_donor_variant -/1777 1091/1482 364/493 1 -1 GC HGNC HGNC:4187 protein_coding YES CCDS56332.1 ENSP00000421725 P02774 UPI0001D3B4EE NM_001204307.1 9/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 71756711 71756711 C A 1 0 0 0 0 0 0 1 0 6152 579 20 2 2 GC 4 71756711 Splice_Site SNP C 11LU022_T 1275191 71756711 118457844 233 871 AFP 0 . GRCh38 4 73452556 73452556 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1584T>A p.Asp528Glu p.D528E ENST00000395792 12/15 295 222 73 325 325 0 strelka-varscan-mutect AFP,missense_variant,p.Asp528Glu,ENST00000395792,NM_001134.2;AFP,missense_variant,p.Asp528Glu,ENST00000226359,;AFP,upstream_gene_variant,,ENST00000506820,;AFP,non_coding_transcript_exon_variant,,ENST00000508838,;AFP,non_coding_transcript_exon_variant,,ENST00000514279,; A ENST00000395792 Transcript missense_variant 1684/2484 1584/1830 528/609 D/E gaT/gaA 1 1 AFP HGNC HGNC:317 protein_coding YES CCDS3556.1 ENSP00000379138 P02771 UPI00000012A9 NM_001134.2 tolerated(0.11) 12/15 Gene3D:1.10.246.10,Pfam_domain:PF00273,PIRSF_domain:PIRSF002520,PROSITE_profiles:PS51438,hmmpanther:PTHR11385,hmmpanther:PTHR11385:SF7,SMART_domains:SM00103,Superfamily_domains:SSF48552 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 73452556 73452556 T A 1 0 0 0 0 1 0 0 0 440 1461 51 4 4 AFP 4 73452556 Missense_Mutation SNP T 11LU022_T 1695845 73452556 116761999 234 872 CXCL1 0 . GRCh38 4 73869732 73869732 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.164A>T p.Lys55Met p.K55M ENST00000395761 2/4 219 183 36 246 246 0 strelka-varscan-mutect CXCL1,missense_variant,p.Lys55Met,ENST00000395761,NM_001511.3;CXCL1,non_coding_transcript_exon_variant,,ENST00000509101,; T ENST00000395761 Transcript missense_variant 231/1097 164/324 55/107 K/M aAg/aTg 1 1 CXCL1 HGNC HGNC:4602 protein_coding YES CCDS47074.1 ENSP00000379110 P09341 UPI0000047AA6 NM_001511.3 deleterious(0) 2/4 hmmpanther:PTHR10179,hmmpanther:PTHR10179:SF48,PROSITE_patterns:PS00471,Pfam_domain:PF00048,Gene3D:2.40.50.40,SMART_domains:SM00199,Superfamily_domains:SSF54117,Prints_domain:PR00436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 73869732 73869732 A T 1 0 0 0 0 1 0 0 0 3887 72 3 4 4 CXCL1 4 73869732 Missense_Mutation SNP A 11LU022_T 417176 73869732 116344823 235 873 CDKL2 0 . GRCh38 4 75581885 75581885 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1430C>A p.Pro477His p.P477H ENST00000429927 11/12 155 127 28 138 138 0 strelka-varscan-mutect CDKL2,missense_variant,p.Pro477His,ENST00000429927,NM_003948.3;CDKL2,missense_variant,p.Pro554His,ENST00000307465,; T ENST00000429927 Transcript missense_variant 2134/3383 1430/1482 477/493 P/H cCc/cAc 1 -1 CDKL2 HGNC HGNC:1782 protein_coding YES CCDS3570.1 ENSP00000412365 Q92772 A0A140VJG1 UPI000006D070 NM_003948.3 deleterious_low_confidence(0.02) 11/12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 75581885 75581885 G T 1 0 0 0 0 1 0 0 0 2858 1232 43 2 2 CDKL2 4 75581885 Missense_Mutation SNP G 11LU022_T 1712153 75581885 114632670 236 874 CCDC158 0 . GRCh38 4 76362177 76362177 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1969C>A p.Gln657Lys p.Q657K ENST00000388914 12/24 124 95 29 137 137 0 strelka-mutect CCDC158,missense_variant,p.Gln657Lys,ENST00000388914,NM_001042784.1;CCDC158,non_coding_transcript_exon_variant,,ENST00000504667,; T ENST00000388914 Transcript missense_variant 2122/3663 1969/3342 657/1113 Q/K Caa/Aaa 1 -1 CCDC158 HGNC HGNC:26374 protein_coding YES CCDS43242.1 ENSP00000373566 Q5M9N0 UPI00004DF23B NM_001042784.1 deleterious(0.04) 12/24 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15921,hmmpanther:PTHR13140 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 76362177 76362177 G T 1 0 0 0 0 1 0 0 0 2478 1299 45 2 2 CCDC158 4 76362177 Missense_Mutation SNP G 11LU022_T 780292 76362177 113852378 237 875 DSPP 0 . GRCh38 4 87615160 87615160 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2498G>T p.Ser833Ile p.S833I ENST00000399271 5/5 561 500 61 595 595 0 strelka-varscan-mutect DSPP,missense_variant,p.Ser833Ile,ENST00000399271,NM_014208.3;DSPP,missense_variant,p.Ser833Ile,ENST00000282478,;RP11-742B18.1,intron_variant,,ENST00000506480,; T ENST00000399271 Transcript missense_variant 2618/4331 2498/3906 833/1301 S/I aGc/aTc 1 1 DSPP HGNC HGNC:3054 protein_coding YES CCDS43248.1 ENSP00000382213 Q9NZW4 UPI00006BFF57 NM_014208.3 deleterious_low_confidence(0.01) 5/5 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 87615160 87615160 G T 1 0 0 0 0 1 0 0 0 4603 971 34 2 2 DSPP 4 87615160 Missense_Mutation SNP G 11LU022_T 11252983 87615160 102599395 238 876 MMRN1 0 . GRCh38 4 89935505 89935505 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1825G>T p.Asp609Tyr p.D609Y ENST00000394980 7/9 85 62 23 94 94 0 strelka-varscan-mutect MMRN1,missense_variant,p.Asp609Tyr,ENST00000394980,;MMRN1,missense_variant,p.Asp609Tyr,ENST00000264790,NM_007351.2;MMRN1,missense_variant,p.Asp351Tyr,ENST00000508372,; T ENST00000394980 Transcript missense_variant 2144/5217 1825/3687 609/1228 D/Y Gac/Tac 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 deleterious(0.01) 7/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 89935505 89935505 G T 1 0 0 0 0 1 0 0 0 9633 1174 41 2 2 MMRN1 4 89935505 Missense_Mutation SNP G 11LU022_T 2320345 89935505 100279050 239 877 MMRN1 0 . GRCh38 4 89936476 89936476 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.2796C>T p.= p.H932H ENST00000394980 7/9 150 132 18 127 127 0 strelka-varscan-mutect MMRN1,synonymous_variant,p.=,ENST00000394980,;MMRN1,synonymous_variant,p.=,ENST00000264790,NM_007351.2;MMRN1,synonymous_variant,p.=,ENST00000508372,; T ENST00000394980 Transcript synonymous_variant 3115/5217 2796/3687 932/1228 H caC/caT 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 7/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 89936476 89936476 C T 1 0 0 0 0 0 0 0 1 9633 477 17 3 3 MMRN1 4 89936476 Silent SNP C 11LU022_T 971 89936476 100278079 240 878 GRID2 0 . GRCh38 4 93395644 93395644 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1283C>A p.Ser428Ter p.S428* ENST00000282020 9/16 106 99 7 100 100 0 strelka-varscan-mutect GRID2,stop_gained,p.Ser428Ter,ENST00000282020,NM_001510.3;GRID2,stop_gained,p.Ser347Ter,ENST00000611049,;GRID2,stop_gained,p.Ser333Ter,ENST00000510992,NM_001286838.1; A ENST00000282020 Transcript stop_gained 2318/6117 1283/3024 428/1007 S/* tCa/tAa 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 9/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:3.40.190.10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 93395644 93395644 C A 1 0 0 0 0 0 1 0 0 6652 838 29 2 2 GRID2 4 93395644 Nonsense_Mutation SNP C 11LU022_T 3459168 93395644 96818911 241 879 GRID2 0 . GRCh38 4 93772377 93772377 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.2903G>A p.Arg968Lys p.R968K ENST00000282020 16/16 164 135 29 160 160 0 strelka-varscan-mutect GRID2,missense_variant,p.Arg968Lys,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Arg887Lys,ENST00000611049,;GRID2,missense_variant,p.Arg873Lys,ENST00000510992,NM_001286838.1;GRID2,intron_variant,,ENST00000637838,; A ENST00000282020 Transcript missense_variant 3938/6117 2903/3024 968/1007 R/K aGg/aAg 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 deleterious_low_confidence(0) 16/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 93772377 93772377 G A 1 0 0 0 0 1 0 0 0 6652 1000 35 3 3 GRID2 4 93772377 Missense_Mutation SNP G 11LU022_T 376733 93772377 96442178 242 880 ADH1A 0 . GRCh38 4 99276642 99276642 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.1110T>A p.= p.R370R ENST00000209668 9/9 195 178 17 206 206 0 strelka-varscan-mutect ADH1A,synonymous_variant,p.=,ENST00000209668,NM_000667.3;RP11-696N14.1,intron_variant,,ENST00000500358,;RP11-696N14.1,intron_variant,,ENST00000506160,;RP11-696N14.1,downstream_gene_variant,,ENST00000509295,;RP11-696N14.1,downstream_gene_variant,,ENST00000510764,; T ENST00000209668 Transcript synonymous_variant 1224/1499 1110/1128 370/375 R cgT/cgA 1 -1 ADH1A HGNC HGNC:249 protein_coding YES CCDS3648.1 ENSP00000209668 P07327 UPI0000062219 NM_000667.3 9/9 hmmpanther:PTHR11695:SF527,hmmpanther:PTHR11695,SMART_domains:SM00829,Superfamily_domains:SSF50129 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 99276642 99276642 A T 1 0 0 0 0 0 0 0 1 380 378 14 4 4 ADH1A 4 99276642 Silent SNP A 11LU022_T 5504265 99276642 90937913 243 881 ADH1B 0 . GRCh38 4 99314024 99314024 + Missense_Mutation SNP C C A rs371001544 11LU022_T 11LU022_N C C c.625G>T p.Val209Phe p.V209F ENST00000305046 6/9 293 256 37 306 305 1 strelka-varscan-mutect ADH1B,missense_variant,p.Val209Phe,ENST00000305046,NM_000668.5;ADH1B,missense_variant,p.Val169Phe,ENST00000625860,;ADH1B,missense_variant,p.Val169Phe,ENST00000506651,NM_001286650.1;ADH1B,non_coding_transcript_exon_variant,,ENST00000632775,;ADH1B,non_coding_transcript_exon_variant,,ENST00000515694,;ADH1B,downstream_gene_variant,,ENST00000504498,; A ENST00000305046 Transcript missense_variant 693/4072 625/1128 209/375 V/F Gtt/Ttt rs371001544 1 -1 ADH1B HGNC HGNC:250 protein_coding YES CCDS34033.1 ENSP00000306606 P00325 V9HW50 UPI00001699B5 NM_000668.5 deleterious(0) 6/9 hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF527,Pfam_domain:PF00107,Gene3D:3.40.50.720,SMART_domains:SM00829,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs371001544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 99314024 99314024 C A 1 0 0 0 0 1 0 0 0 381 478 17 2 2 ADH1B 4 99314024 Missense_Mutation SNP C 11LU022_T 37382 99314024 90900531 244 882 ALPK1 0 . GRCh38 4 112431186 112431186 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1639G>T p.Val547Phe p.V547F ENST00000458497 11/16 120 92 28 149 149 0 strelka-varscan-mutect ALPK1,missense_variant,p.Val547Phe,ENST00000458497,NM_025144.3,NM_001102406.1;ALPK1,missense_variant,p.Val469Phe,ENST00000504176,NM_001253884.1;ALPK1,missense_variant,p.Val547Phe,ENST00000177648,;ALPK1,downstream_gene_variant,,ENST00000508589,;ALPK1,3_prime_UTR_variant,,ENST00000509722,;ALPK1,non_coding_transcript_exon_variant,,ENST00000504745,;ALPK1,intron_variant,,ENST00000505127,;ALPK1,downstream_gene_variant,,ENST00000512847,; T ENST00000458497 Transcript missense_variant 1918/5410 1639/3735 547/1244 V/F Gtc/Ttc 1 1 ALPK1 HGNC HGNC:20917 protein_coding YES CCDS3697.1 ENSP00000398048 Q96QP1 UPI000045725F NM_025144.3,NM_001102406.1 tolerated(0.09) 11/16 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 112431186 112431186 G T 1 0 0 0 0 1 0 0 0 644 1029 36 2 2 ALPK1 4 112431186 Missense_Mutation SNP G 11LU022_T 13117162 112431186 77783369 245 883 ANK2 0 . GRCh38 4 113353551 113353551 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.4933A>T p.Asn1645Tyr p.N1645Y ENST00000357077 38/46 271 206 65 384 384 0 strelka-varscan-mutect ANK2,missense_variant,p.Asn1645Tyr,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Asn1612Tyr,ENST00000264366,;ANK2,missense_variant,p.Asn1660Tyr,ENST00000504454,;ANK2,missense_variant,p.Asn1558Tyr,ENST00000503423,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; T ENST00000357077 Transcript missense_variant 4986/14196 4933/11874 1645/3957 N/Y Aat/Tat 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious(0.01) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 113353551 113353551 A T 1 0 0 0 0 1 0 0 0 721 246 9 4 4 ANK2 4 113353551 Missense_Mutation SNP A 11LU022_T 922365 113353551 76861004 246 884 ANK2 0 . GRCh38 4 113357609 113357609 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.8991C>T p.= p.S2997S ENST00000357077 38/46 350 308 42 397 397 0 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; T ENST00000357077 Transcript synonymous_variant 9044/14196 8991/11874 2997/3957 S tcC/tcT 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 113357609 113357609 C T 1 0 0 0 0 0 0 0 1 721 610 22 3 3 ANK2 4 113357609 Silent SNP C 11LU022_T 4058 113357609 76856946 247 885 ANK2 0 . GRCh38 4 113367838 113367838 + Nonsense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.11305C>T p.Gln3769Ter p.Q3769* ENST00000357077 42/46 173 151 22 196 196 0 strelka-varscan-mutect ANK2,stop_gained,p.Gln3769Ter,ENST00000357077,NM_001148.4;ANK2,stop_gained,p.Gln3736Ter,ENST00000264366,;ANK2,stop_gained,p.Gln1675Ter,ENST00000506722,NM_001127493.1;ANK2,stop_gained,p.Gln1684Ter,ENST00000394537,NM_020977.3;ANK2,stop_gained,p.Gln779Ter,ENST00000505342,;ANK2,stop_gained,p.Gln686Ter,ENST00000514960,;ANK2,stop_gained,p.Gln860Ter,ENST00000509550,;ANK2,stop_gained,p.Gln336Ter,ENST00000510275,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,downstream_gene_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000508007,; T ENST00000357077 Transcript stop_gained 11358/14196 11305/11874 3769/3957 Q/* Cag/Tag 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 42/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 113367838 113367838 C T 1 0 0 0 0 0 1 0 0 721 827 29 3 3 ANK2 4 113367838 Nonsense_Mutation SNP C 11LU022_T 10229 113367838 76846717 248 886 NDST4 0 . GRCh38 4 114848214 114848214 + Splice_Site DEL C C - novel 11LU022_T 11LU022_N C C c.1940+1delG p.X647_splice ENST00000264363 40 37 3 70 70 0 varindel-pindel NDST4,splice_donor_variant,,ENST00000613194,;NDST4,splice_donor_variant,,ENST00000264363,NM_022569.1;NDST4,splice_donor_variant,,ENST00000504854,; - ENST00000264363 Transcript splice_donor_variant -/3351 1940/2619 647/872 1 -1 NDST4 HGNC HGNC:20779 protein_coding YES CCDS3706.1 ENSP00000264363 Q9H3R1 UPI000006CED7 NM_022569.1 9/13 HIGH 1 deletion 1 1 PASS . . 0 203 7 0 0 0 0 0 -8.484493 0.9999981 1 1 1 0 - 8 5 3 114848214 114848214 C - 1 0 1 0 1 0 0 1 0 10279 521 18 0 0 NDST4 4 114848214 Splice_Site DEL C 11LU022_T 1480376 114848214 75366341 249 887 FAT4 0 . GRCh38 4 125490400 125490400 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.13578T>C p.= p.C4526C ENST00000394329 17/17 312 261 51 308 308 0 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,synonymous_variant,p.=,ENST00000335110,; C ENST00000394329 Transcript synonymous_variant 13591/16123 13578/14946 4526/4981 C tgT/tgC 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 17/17 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 125490400 125490400 T C 1 0 0 0 0 0 0 0 1 5552 1644 57 5 5 FAT4 4 125490400 Silent SNP T 11LU022_T 10642186 125490400 64724155 250 888 DCHS2 0 . GRCh38 4 154391234 154391234 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.64C>A p.Gln22Lys p.Q22K ENST00000623607 1/25 82 64 18 135 135 0 strelka-varscan-mutect DCHS2,missense_variant,p.Gln22Lys,ENST00000357232,;DCHS2,missense_variant,p.Gln22Lys,ENST00000623607,NM_017639.3;DCHS2,intron_variant,,ENST00000339452,NM_001142552.1; T ENST00000623607 Transcript missense_variant 64/8912 64/8751 22/2916 Q/K Cag/Aag 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 tolerated_low_confidence(0.14) 1/25 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 154391234 154391234 G T 1 0 0 0 0 1 0 0 0 4091 1328 46 2 2 DCHS2 4 154391234 Missense_Mutation SNP G 11LU022_T 28900834 154391234 35823321 251 889 GRIA2 0 . GRCh38 4 157336458 157336458 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1555C>T p.Leu519Phe p.L519F ENST00000296526 11/16 54 50 4 58 58 0 strelka-varscan-mutect GRIA2,missense_variant,p.Leu519Phe,ENST00000296526,NM_000826.3;GRIA2,missense_variant,p.Leu472Phe,ENST00000393815,NM_001083620.1;GRIA2,missense_variant,p.Leu519Phe,ENST00000264426,NM_001083619.1;GRIA2,missense_variant,p.Leu472Phe,ENST00000507898,;GRIA2,upstream_gene_variant,,ENST00000510854,;GRIA2,missense_variant,p.Leu472Phe,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; T ENST00000296526 Transcript missense_variant 1880/5621 1555/2652 519/883 L/F Ctc/Ttc 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 deleterious(0) 11/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -10.02074 0.9999997 1 1 1 0 T 3 4 3 157336458 157336458 C T 1 0 0 0 0 1 0 0 0 6648 681 24 3 3 GRIA2 4 157336458 Missense_Mutation SNP C 11LU022_T 2945224 157336458 32878097 252 890 TLL1 0 . GRCh38 4 166003451 166003451 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.693C>A p.Asn231Lys p.N231K ENST00000061240 6/21 269 240 29 297 297 0 strelka-varscan-mutect TLL1,missense_variant,p.Asn231Lys,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Asn231Lys,ENST00000507499,;TLL1,missense_variant,p.Asn231Lys,ENST00000513213,NM_001204760.1;TLL1,3_prime_UTR_variant,,ENST00000509505,; A ENST00000061240 Transcript missense_variant 1340/6708 693/3042 231/1013 N/K aaC/aaA 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 deleterious(0) 6/21 Gene3D:3.40.390.10,Pfam_domain:PF01400,PIRSF_domain:PIRSF001199,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 166003451 166003451 C A 1 0 0 0 0 1 0 0 0 16391 564 20 2 2 TLL1 4 166003451 Missense_Mutation SNP C 11LU022_T 8666993 166003451 24211104 253 891 SPOCK3 0 . GRCh38 4 166742004 166742004 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.996G>T p.Lys332Asn p.K332N ENST00000357154 10/12 156 125 31 163 163 0 strelka-varscan-mutect SPOCK3,missense_variant,p.Lys281Asn,ENST00000421836,NM_001204352.1;SPOCK3,missense_variant,p.Lys332Asn,ENST00000357154,NM_016950.2;SPOCK3,missense_variant,p.Lys332Asn,ENST00000506886,;SPOCK3,missense_variant,p.Lys329Asn,ENST00000357545,NM_001040159.1;SPOCK3,missense_variant,p.Lys332Asn,ENST00000511531,;SPOCK3,missense_variant,p.Lys329Asn,ENST00000504953,;SPOCK3,missense_variant,p.Lys212Asn,ENST00000541354,NM_001204355.1,NM_001204353.1;SPOCK3,missense_variant,p.Lys332Asn,ENST00000502330,;SPOCK3,missense_variant,p.Lys240Asn,ENST00000535728,NM_001204354.1;SPOCK3,missense_variant,p.Lys289Asn,ENST00000510741,NM_001204356.1;SPOCK3,missense_variant,p.Lys329Asn,ENST00000511269,;SPOCK3,missense_variant,p.Lys234Asn,ENST00000512681,NM_001251967.1;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,; A ENST00000357154 Transcript missense_variant 1134/2986 996/1311 332/436 K/N aaG/aaT 1 -1 SPOCK3 HGNC HGNC:13565 protein_coding YES CCDS54817.1 ENSP00000349677 Q9BQ16 UPI000004BA60 NM_016950.2 tolerated(0.06) 10/12 PROSITE_profiles:PS51162,hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF10,Gene3D:4.10.800.10,Pfam_domain:PF00086,Superfamily_domains:SSF57610 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 166742004 166742004 C A 1 0 0 0 0 1 0 0 0 15434 796 28 2 2 SPOCK3 4 166742004 Missense_Mutation SNP C 11LU022_T 738553 166742004 23472551 254 892 DDX60 0 . GRCh38 4 168237764 168237764 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.4196C>T p.Ser1399Phe p.S1399F ENST00000393743 31/38 107 97 10 130 130 0 strelka-varscan-mutect DDX60,missense_variant,p.Ser1399Phe,ENST00000393743,NM_017631.5;DDX60,upstream_gene_variant,,ENST00000511317,;DDX60,upstream_gene_variant,,ENST00000507815,; A ENST00000393743 Transcript missense_variant 4488/6071 4196/5139 1399/1712 S/F tCc/tTc 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 deleterious(0.02) 31/38 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 168237764 168237764 G A 1 0 0 0 0 1 0 0 0 4181 1174 41 3 3 DDX60 4 168237764 Missense_Mutation SNP G 11LU022_T 1495760 168237764 21976791 255 893 DDX60L 0 . GRCh38 4 168472694 168472694 + Splice_Site SNP A A T rs756236304 11LU022_T 11LU022_N A A c.4+2T>A p.X2_splice ENST00000260184 122 98 24 154 154 0 strelka-varscan-mutect DDX60L,splice_donor_variant,,ENST00000511577,;DDX60L,splice_donor_variant,,ENST00000260184,NM_001012967.2;DDX60L,splice_donor_variant,,ENST00000505890,NM_001291510.1;DDX60L,splice_donor_variant,,ENST00000514748,;DDX60L,splice_donor_variant,,ENST00000505696,;DDX60L,splice_donor_variant,,ENST00000512371,;SNORA51,downstream_gene_variant,,ENST00000384442,;DDX60L,splice_donor_variant,,ENST00000515088,;DDX60L,splice_donor_variant,,ENST00000513901,;DDX60L,downstream_gene_variant,,ENST00000505150,; T ENST00000260184 Transcript splice_donor_variant -/6754 4/5121 2/1706 rs756236304 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 2/37 HIGH 1 SNV 5 1 PASS rs756236304 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 3 168472694 168472694 A T 1 0 0 0 0 0 0 1 0 4182 405 14 4 4 DDX60L 4 168472694 Splice_Site SNP A 11LU022_T 234930 168472694 21741861 256 894 PALLD 0 . GRCh38 4 168690669 168690669 + Frame_Shift_Del DEL C C - novel 11LU022_T 11LU022_N C C c.1406delC p.Pro469LeufsTer38 p.P469Lfs*38 ENST00000505667 7/22 352 267 85 391 391 0 sindel-varindel-pindel PALLD,frameshift_variant,p.Pro469LeufsTer38,ENST00000261509,NM_016081.3;PALLD,frameshift_variant,p.Pro469LeufsTer38,ENST00000505667,NM_001166108.1;PALLD,frameshift_variant,p.Pro87LeufsTer38,ENST00000512127,NM_001166109.1;PALLD,frameshift_variant,p.Pro448LeufsTer41,ENST00000508898,;PALLD,frameshift_variant,p.Pro87LeufsTer?,ENST00000503457,;PALLD,downstream_gene_variant,,ENST00000504519,;PALLD,downstream_gene_variant,,ENST00000513245,;RNU6-1336P,upstream_gene_variant,,ENST00000383886,; - ENST00000505667 Transcript frameshift_variant 1575/3637 1402/3372 468/1123 P/X Ccc/cc 1 1 PALLD HGNC HGNC:17068 protein_coding YES CCDS54818.1 ENSP00000425556 Q8WX93 UPI000189A85C NM_001166108.1 7/22 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF741,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 168690669 168690669 C - 1 0 1 0 1 0 0 0 0 11487 507 18 0 0 PALLD 4 168690669 Frame_Shift_Del DEL C 11LU022_T 217975 168690669 21523886 257 895 CENPU 0 . GRCh38 4 184710164 184710164 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.705G>T p.= p.V235V ENST00000281453 8/13 111 98 13 132 132 0 strelka-varscan-mutect CENPU,synonymous_variant,p.=,ENST00000281453,NM_024629.3;CENPU,non_coding_transcript_exon_variant,,ENST00000506535,;CENPU,synonymous_variant,p.=,ENST00000510146,; A ENST00000281453 Transcript synonymous_variant 776/1998 705/1257 235/418 V gtG/gtT 1 -1 CENPU HGNC HGNC:21348 protein_coding YES CCDS3838.1 ENSP00000281453 Q71F23 UPI00001BFAF6 NM_024629.3 8/13 hmmpanther:PTHR32222:SF1,hmmpanther:PTHR32222,Pfam_domain:PF13097 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.73716 0.9999999 1 1 1 0 A 2 1 3 184710164 184710164 C A 1 0 0 0 0 0 0 0 1 2951 697 25 2 2 CENPU 4 184710164 Silent SNP C 11LU022_T 16019495 184710164 5504391 258 896 FAT1 0 . GRCh38 4 186708895 186708895 + Silent SNP C C G novel 11LU022_T 11LU022_N C C c.933G>C p.= p.G311G ENST00000441802 2/27 129 101 28 198 198 0 strelka-varscan-mutect FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,;FAT1,synonymous_variant,p.=,ENST00000509647,; G ENST00000441802 Transcript synonymous_variant 1143/14786 933/13767 311/4588 G ggG/ggC 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 2/27 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 186708895 186708895 C G 1 0 0 0 0 0 0 0 1 5549 842 30 4 4 FAT1 4 186708895 Silent SNP C 11LU022_T 1998731 186708895 3505660 259 897 ADAMTS16 0 . GRCh38 5 5222835 5222835 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1652A>T p.Glu551Val p.E551V ENST00000274181 11/23 229 193 36 192 191 1 strelka-varscan-mutect ADAMTS16,missense_variant,p.Glu551Val,ENST00000274181,NM_139056.2;ADAMTS16,missense_variant,p.Glu551Val,ENST00000511368,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 1790/4979 1652/3675 551/1224 E/V gAg/gTg 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 tolerated(0.14) 11/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 5222835 5222835 A T 1 0 0 0 0 1 0 0 0 305 304 11 4 4 ADAMTS16 5 5222835 Missense_Mutation SNP A 11LU022_T 5222835 176315424 260 898 ICE1 0 . GRCh38 5 5443244 5443244 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.386A>T p.Gln129Leu p.Q129L ENST00000296564 6/19 92 85 7 101 101 0 strelka-varscan-mutect ICE1,missense_variant,p.Gln129Leu,ENST00000296564,NM_015325.2;ICE1,missense_variant,p.Gln52Leu,ENST00000512608,; T ENST00000296564 Transcript missense_variant,splice_region_variant 608/7927 386/6801 129/2266 Q/L cAg/cTg 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0.03) 6/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 5443244 5443244 A T 1 0 0 0 0 1 0 0 0 7384 202 7 4 4 ICE1 5 5443244 Missense_Mutation SNP A 11LU022_T 220409 5443244 176095015 261 899 ADCY2 0 . GRCh38 5 7773078 7773078 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2361C>A p.Asp787Glu p.D787E ENST00000338316 18/25 171 136 35 112 112 0 strelka-varscan-mutect ADCY2,missense_variant,p.Asp787Glu,ENST00000338316,NM_020546.2;ADCY2,missense_variant,p.Asp4Glu,ENST00000493243,; A ENST00000338316 Transcript missense_variant 2450/6575 2361/3276 787/1091 D/E gaC/gaA 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 tolerated(1) 18/25 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 7773078 7773078 C A 1 0 0 0 0 1 0 0 0 338 564 20 2 2 ADCY2 5 7773078 Missense_Mutation SNP C 11LU022_T 2329834 7773078 173765181 262 900 SEMA5A 0 . GRCh38 5 9051944 9051944 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.2774C>T p.Pro925Leu p.P925L ENST00000382496 20/23 297 275 22 192 192 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Pro925Leu,ENST00000382496,NM_003966.2;MIR4636,downstream_gene_variant,,ENST00000582271,; A ENST00000382496 Transcript missense_variant 3440/11762 2774/3225 925/1074 P/L cCc/cTc 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0.04) 20/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 9051944 9051944 G A 1 0 0 0 0 1 0 0 0 14313 1232 43 3 3 SEMA5A 5 9051944 Missense_Mutation SNP G 11LU022_T 1278866 9051944 172486315 263 901 FBXL7 0 . GRCh38 5 15928297 15928297 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.535C>A p.Gln179Lys p.Q179K ENST00000504595 3/4 638 600 38 490 490 0 strelka-varscan-mutect FBXL7,missense_variant,p.Gln179Lys,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Gln137Lys,ENST00000329673,;FBXL7,missense_variant,p.Gln132Lys,ENST00000510662,NM_001278317.1; A ENST00000504595 Transcript missense_variant 1016/4562 535/1476 179/491 Q/K Cag/Aag 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.39) 3/4 Gene3D:3.80.10.10,hmmpanther:PTHR24006,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 15928297 15928297 C A 1 0 0 0 0 1 0 0 0 5587 595 21 2 2 FBXL7 5 15928297 Missense_Mutation SNP C 11LU022_T 6876353 15928297 165609962 264 902 CDH12 0 . GRCh38 5 21755648 21755648 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1828G>A p.Val610Ile p.V610I ENST00000382254 14/15 294 253 41 203 203 0 strelka-varscan-mutect CDH12,missense_variant,p.Val610Ile,ENST00000382254,NM_004061.3;CDH12,missense_variant,p.Val610Ile,ENST00000504376,;CDH12,missense_variant,p.Val570Ile,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript missense_variant 2915/4164 1828/2385 610/794 V/I Gta/Ata 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 tolerated(0.15) 14/15 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 21755648 21755648 C T 1 0 0 0 0 1 0 0 0 2801 478 17 3 3 CDH12 5 21755648 Missense_Mutation SNP C 11LU022_T 5827351 21755648 159782611 265 903 PDZD2 0 . GRCh38 5 32087325 32087325 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.3877G>A p.Gly1293Arg p.G1293R ENST00000438447 20/25 226 108 118 140 140 0 strelka-varscan-mutect PDZD2,missense_variant,p.Gly1293Arg,ENST00000438447,NM_178140.2;PDZD2,downstream_gene_variant,,ENST00000503961,; A ENST00000438447 Transcript missense_variant 4265/11704 3877/8520 1293/2839 G/R Ggg/Agg 1 1 PDZD2 HGNC HGNC:18486 protein_coding YES CCDS34137.1 ENSP00000402033 O15018 A0A024RE15 UPI000069648B NM_178140.2 tolerated(0.83) 20/25 hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF16 MODERATE 1 SNV 1 1 PASS rs1407081973 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 32087325 32087325 G A 1 0 0 0 0 1 0 0 0 11789 1232 43 3 3 PDZD2 5 32087325 Missense_Mutation SNP G 11LU022_T 10331677 32087325 149450934 266 904 NPR3 0 . GRCh38 5 32712159 32712159 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.383C>A p.Pro128Gln p.P128Q ENST00000265074 1/8 258 212 46 193 193 0 strelka-varscan-mutect NPR3,missense_variant,p.Pro128Gln,ENST00000265074,NM_001204375.1;NPR3,missense_variant,p.Pro128Gln,ENST00000415167,NM_000908.3;NPR3,intron_variant,,ENST00000326958,NM_001204376.1;NPR3,intron_variant,,ENST00000434067,;NPR3,intron_variant,,ENST00000509104,;NPR3,upstream_gene_variant,,ENST00000507141,;NPR3,intron_variant,,ENST00000506712,; A ENST00000265074 Transcript missense_variant 726/7344 383/1626 128/541 P/Q cCa/cAa 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 deleterious(0.01) 1/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 32712159 32712159 C A 1 0 0 0 0 1 0 0 0 10652 594 21 2 2 NPR3 5 32712159 Missense_Mutation SNP C 11LU022_T 624834 32712159 148826100 267 905 ADAMTS12 0 . GRCh38 5 33588761 33588761 + Missense_Mutation SNP G G T rs754083071 11LU022_T 11LU022_N G G c.2703C>A p.His901Gln p.H901Q ENST00000504830 18/24 239 185 54 216 216 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.His901Gln,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.His816Gln,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 3039/8774 2703/4785 901/1594 H/Q caC/caA rs754083071,COSM5521258 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.54) 18/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754083071 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 33588761 33588761 G T 1 0 0 0 0 1 0 0 0 301 1136 40 1 1 ADAMTS12 5 33588761 Missense_Mutation SNP G 11LU022_T 876602 33588761 147949498 268 906 ADAMTS12 0 . GRCh38 5 33683941 33683941 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.749C>A p.Thr250Lys p.T250K ENST00000504830 4/24 116 81 35 66 66 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Thr250Lys,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Thr250Lys,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 1085/8774 749/4785 250/1594 T/K aCa/aAa 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 4/24 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 33683941 33683941 G T 1 0 0 0 0 1 0 0 0 301 1377 48 2 2 ADAMTS12 5 33683941 Missense_Mutation SNP G 11LU022_T 95180 33683941 147854318 269 907 NIPBL 0 . GRCh38 5 36985957 36985957 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2777G>T p.Ser926Ile p.S926I ENST00000282516 10/47 262 193 69 280 280 0 strelka-varscan-mutect NIPBL,missense_variant,p.Ser926Ile,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Ser926Ile,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,; T ENST00000282516 Transcript missense_variant 3276/10435 2777/8415 926/2804 S/I aGt/aTt 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated_low_confidence(0.38) 10/47 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 36985957 36985957 G T 1 0 0 0 0 1 0 0 0 10463 1029 36 2 2 NIPBL 5 36985957 Missense_Mutation SNP G 11LU022_T 3302016 36985957 144552302 270 908 C5orf42 0 . GRCh38 5 37165662 37165662 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.7410A>T p.Arg2470Ser p.R2470S ENST00000425232 36/52 108 85 23 88 88 0 strelka-varscan-mutect C5orf42,missense_variant,p.Arg2470Ser,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Arg2470Ser,ENST00000508244,;C5orf42,missense_variant,p.Arg1518Ser,ENST00000514429,;C5orf42,missense_variant,p.Arg161Ser,ENST00000511824,;C5orf42,upstream_gene_variant,,ENST00000511210,;C5orf42,missense_variant,p.Arg1474Ser,ENST00000509849,;C5orf42,downstream_gene_variant,,ENST00000511781,;C5orf42,upstream_gene_variant,,ENST00000510830,; A ENST00000425232 Transcript missense_variant 7641/11199 7410/9594 2470/3197 R/S agA/agT 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0.03) 36/52 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 37165662 37165662 T A 1 0 0 0 0 1 0 0 0 2100 1780 62 4 4 C5orf42 5 37165662 Missense_Mutation SNP T 11LU022_T 179705 37165662 144372597 271 909 MRPS30 0 . GRCh38 5 44809134 44809134 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.172G>T p.Ala58Ser p.A58S ENST00000507110 1/5 284 234 50 275 275 0 strelka-varscan-mutect MRPS30,missense_variant,p.Ala58Ser,ENST00000507110,NM_016640.3;RP11-53O19.1,upstream_gene_variant,,ENST00000503179,;RP11-53O19.1,upstream_gene_variant,,ENST00000503452,;RP11-53O19.1,upstream_gene_variant,,ENST00000505401,;RP11-53O19.1,upstream_gene_variant,,ENST00000514597,;RP11-53O19.1,upstream_gene_variant,,ENST00000508123,;RP11-53O19.1,upstream_gene_variant,,ENST00000505302,;RP11-53O19.1,upstream_gene_variant,,ENST00000508945,;RP11-53O19.1,upstream_gene_variant,,ENST00000505637,;MRPS30,upstream_gene_variant,,ENST00000515647,;MRPS30,upstream_gene_variant,,ENST00000508129,; T ENST00000507110 Transcript missense_variant 210/1678 172/1320 58/439 A/S Gca/Tca 1 1 MRPS30 HGNC HGNC:8769 protein_coding YES CCDS3951.1 ENSP00000424328 Q9NP92 UPI000013C944 NM_016640.3 deleterious(0) 1/5 hmmpanther:PTHR13014,Pfam_domain:PF07147 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 44809134 44809134 G T 1 0 0 0 0 1 0 0 0 9817 1319 46 2 2 MRPS30 5 44809134 Missense_Mutation SNP G 11LU022_T 7643472 44809134 136729125 272 910 HCN1 0 . GRCh38 5 45262454 45262454 + Missense_Mutation SNP C C A rs775543627 11LU022_T 11LU022_N C C c.2140G>T p.Ala714Ser p.A714S ENST00000303230 8/8 133 115 18 132 132 0 strelka-varscan-mutect HCN1,missense_variant,p.Ala714Ser,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; A ENST00000303230 Transcript missense_variant 2381/9885 2140/2673 714/890 A/S Gct/Tct rs775543627,COSM738675 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated_low_confidence(0.85) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775543627 . 0 205 3 2 0 0 0 0 -20 0.9999922 1 1 1 0 A 3 1 3 45262454 45262454 C A 1 0 0 0 0 1 0 0 0 6883 768 27 1 1 HCN1 5 45262454 Missense_Mutation SNP C 11LU022_T 453320 45262454 136275805 273 911 ISL1 0 . GRCh38 5 51391292 51391292 + Missense_Mutation SNP G G C 11LU022_T 11LU022_N G G c.784G>C p.Gly262Arg p.G262R ENST00000230658 5/6 109 98 11 162 162 0 strelka-varscan-mutect ISL1,missense_variant,p.Gly262Arg,ENST00000230658,NM_002202.2;ISL1,intron_variant,,ENST00000511384,;ISL1,non_coding_transcript_exon_variant,,ENST00000505475,; C ENST00000230658 Transcript missense_variant 1065/2459 784/1050 262/349 G/R Gga/Cga COSM3855461 1 1 ISL1 HGNC HGNC:6132 protein_coding YES CCDS43314.1 ENSP00000230658 P61371 UPI0000023E3A NM_002202.2 deleterious(0.02) 5/6 hmmpanther:PTHR24204 1 MODERATE 1 SNV 1 1 1 PASS rs1235320706 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 51391292 51391292 G C 1 0 0 0 0 1 0 0 0 7763 1001 35 4 4 ISL1 5 51391292 Missense_Mutation SNP G 11LU022_T 6128838 51391292 130146967 274 912 SNX18 0 . GRCh38 5 54518460 54518460 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.508G>T p.Ala170Ser p.A170S ENST00000343017 1/1 163 114 49 167 167 0 strelka-varscan-mutect SNX18,missense_variant,p.Ala170Ser,ENST00000381410,NM_001102575.1;SNX18,missense_variant,p.Ala170Ser,ENST00000343017,NM_052870.2;SNX18,missense_variant,p.Ala170Ser,ENST00000326277,NM_001145427.1; T ENST00000343017 Transcript missense_variant 596/3140 508/1887 170/628 A/S Gct/Tct 1 1 SNX18 HGNC HGNC:19245 protein_coding YES CCDS3962.1 ENSP00000342276 Q96RF0 UPI00001418B0 NM_052870.2 tolerated(0.24) 1/1 hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF13,PIRSF_domain:PIRSF027744 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 54518460 54518460 G T 1 0 0 0 0 1 0 0 0 15210 1087 38 1 1 SNX18 5 54518460 Missense_Mutation SNP G 11LU022_T 3127168 54518460 127019799 275 913 NDUFAF2 0 . GRCh38 5 61073192 61073192 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.195G>T p.= p.G65G ENST00000296597 2/4 155 137 18 293 292 1 strelka-varscan-mutect NDUFAF2,synonymous_variant,p.=,ENST00000296597,NM_174889.4;NDUFAF2,synonymous_variant,p.=,ENST00000502658,;NDUFAF2,intron_variant,,ENST00000511107,;NDUFAF2,non_coding_transcript_exon_variant,,ENST00000512623,; T ENST00000296597 Transcript synonymous_variant 322/719 195/510 65/169 G ggG/ggT 1 1 NDUFAF2 HGNC HGNC:28086 protein_coding YES CCDS3979.1 ENSP00000296597 Q8N183 A0A0S2Z5U1 UPI000006D648 NM_174889.4 2/4 Pfam_domain:PF05071,hmmpanther:PTHR32470,hmmpanther:PTHR32470:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 61073192 61073192 G T 1 0 0 0 0 0 0 0 1 10296 1219 43 2 2 NDUFAF2 5 61073192 Silent SNP G 11LU022_T 6554732 61073192 120465067 276 914 HTR1A 0 . GRCh38 5 63961321 63961321 + Missense_Mutation SNP G G T rs753948744 11LU022_T 11LU022_N G G c.399C>A p.Asp133Glu p.D133E ENST00000323865 1/1 181 163 18 269 269 0 strelka-varscan-mutect HTR1A,missense_variant,p.Asp133Glu,ENST00000323865,NM_000524.3;HTR1A,downstream_gene_variant,,ENST00000506598,;RP11-158J3.2,intron_variant,,ENST00000502882,; T ENST00000323865 Transcript missense_variant 813/1778 399/1269 133/422 D/E gaC/gaA rs753948744 1 -1 HTR1A HGNC HGNC:5286 protein_coding YES CCDS34168.1 ENSP00000316244 P08908 Q5ZGX3 UPI0000124F1A NM_000524.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF20,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS rs753948744 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 63961321 63961321 G T 1 0 0 0 0 1 0 0 0 7332 1368 48 2 2 HTR1A 5 63961321 Missense_Mutation SNP G 11LU022_T 2888129 63961321 117576938 277 915 MAST4 0 . GRCh38 5 67145294 67145294 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.3009G>A p.= p.K1003K ENST00000403625 23/29 336 296 40 314 314 0 strelka-varscan-mutect MAST4,synonymous_variant,p.=,ENST00000403625,NM_001164664.1;MAST4,synonymous_variant,p.=,ENST00000405643,NM_001290226.1;MAST4,synonymous_variant,p.=,ENST00000261569,NM_001290227.1,NM_001297651.1;MAST4,synonymous_variant,p.=,ENST00000403666,NM_015183.2;MAST4,synonymous_variant,p.=,ENST00000443808,;MAST4,downstream_gene_variant,,ENST00000485768,; A ENST00000403625 Transcript synonymous_variant 3304/10711 3009/7872 1003/2623 K aaG/aaA 1 1 MAST4 HGNC HGNC:19037 protein_coding YES CCDS54861.1 ENSP00000385727 J3QT34 UPI000173A2B0 NM_001164664.1 23/29 hmmpanther:PTHR24356:SF224,hmmpanther:PTHR24356 LOW 1 SNV 5 1 PASS rs934000304 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 67145294 67145294 G A 1 0 0 0 0 0 0 0 1 9253 962 34 3 3 MAST4 5 67145294 Silent SNP G 11LU022_T 3183973 67145294 114392965 278 916 PIK3R1 0 . GRCh38 5 68280949 68280949 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.859A>T p.Ile287Leu p.I287L ENST00000521381 7/16 61 48 13 92 92 0 strelka-varscan-mutect PIK3R1,missense_variant,p.Ile287Leu,ENST00000521381,NM_181523.2;PIK3R1,missense_variant,p.Ile287Leu,ENST00000521657,;PIK3R1,missense_variant,p.Ile17Leu,ENST00000522084,;PIK3R1,missense_variant,p.Ile17Leu,ENST00000523807,;PIK3R1,downstream_gene_variant,,ENST00000520675,; T ENST00000521381 Transcript missense_variant 1475/7011 859/2175 287/724 I/L Ata/Tta 1 1 PIK3R1 HGNC HGNC:8979 protein_coding YES CCDS3993.1 ENSP00000428056 P27986 UPI000013D9FF NM_181523.2 tolerated(0.34) 7/16 PROSITE_profiles:PS50238,hmmpanther:PTHR10155:SF3,hmmpanther:PTHR10155,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 68280949 68280949 A T 1 0 0 0 0 1 0 0 0 12013 217 8 4 4 PIK3R1 5 68280949 Missense_Mutation SNP A 11LU022_T 1135655 68280949 113257310 279 917 AK6 0 . GRCh38 5 69355715 69355715 + Missense_Mutation SNP C C A rs560641299 11LU022_T 11LU022_N C C c.260G>T p.Arg87Leu p.R87L ENST00000380822 4/5 85 69 16 112 112 0 strelka-varscan-mutect AK6,missense_variant,p.Arg87Leu,ENST00000380822,NM_016283.4;AK6,missense_variant,p.Arg84Leu,ENST00000380818,NM_001015891.1;AK6,missense_variant,p.Arg56Leu,ENST00000512561,;AK6,missense_variant,p.Arg87Leu,ENST00000618980,;AK6,intron_variant,,ENST00000502819,; A ENST00000380822 Transcript missense_variant 312/1648 260/519 87/172 R/L cGc/cTc rs560641299 1 -1 AK6 HGNC HGNC:49151 protein_coding YES CCDS4001.1 ENSP00000370201 Q9Y3D8 UPI0000037723 NM_016283.4 deleterious(0) 4/5 HAMAP:MF_00039,hmmpanther:PTHR12595,hmmpanther:PTHR12595:SF0,Gene3D:3.40.50.300,Pfam_domain:PF13238,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs560641299 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 69355715 69355715 C A 1 0 0 0 0 1 0 0 0 523 768 27 1 1 AK6 5 69355715 Missense_Mutation SNP C 11LU022_T 1074766 69355715 112182544 280 918 TAF9 0 . GRCh38 5 69365653 69365653 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.85A>G p.Thr29Ala p.T29A ENST00000328663 3/3 38 34 4 57 57 0 strelka-varscan-mutect TAF9,missense_variant,p.Thr29Ala,ENST00000328663,NM_001015892.1;TAF9,missense_variant,p.Thr29Ala,ENST00000506736,;TAF9,missense_variant,p.Thr29Ala,ENST00000217893,NM_003187.4;TAF9,missense_variant,p.Thr29Ala,ENST00000508954,;TAF9,missense_variant,p.Thr29Ala,ENST00000503245,;TAF9,missense_variant,p.Thr29Ala,ENST00000509462,;TAF9,missense_variant,p.Thr29Ala,ENST00000504109,;TAF9,missense_variant,p.Thr29Ala,ENST00000512152,;AK6,intron_variant,,ENST00000380822,NM_016283.4;AK6,intron_variant,,ENST00000380818,NM_001015891.1;AK6,intron_variant,,ENST00000502819,;AK6,intron_variant,,ENST00000512561,;AK6,intron_variant,,ENST00000618980,;RAD17,upstream_gene_variant,,ENST00000509734,;RAD17,upstream_gene_variant,,ENST00000354868,NM_133338.2;RAD17,upstream_gene_variant,,ENST00000616683,NM_001278622.1;RAD17,upstream_gene_variant,,ENST00000361732,NM_133343.1;RAD17,upstream_gene_variant,,ENST00000354312,NM_133342.2;RAD17,upstream_gene_variant,,ENST00000345306,NM_133344.2;RAD17,upstream_gene_variant,,ENST00000521422,;RAD17,upstream_gene_variant,,ENST00000512785,;RAD17,upstream_gene_variant,,ENST00000506564,;RAD17,upstream_gene_variant,,ENST00000507927,;RAD17,upstream_gene_variant,,ENST00000504177,;RAD17,upstream_gene_variant,,ENST00000511349,;RAD17,upstream_gene_variant,,ENST00000514066,; C ENST00000328663 Transcript missense_variant 552/1461 85/795 29/264 T/A Aca/Gca 1 -1 TAF9 HGNC HGNC:11542 protein_coding YES CCDS4002.1 ENSP00000370193 Q16594 UPI000000D8A6 NM_001015892.1 tolerated(0.13) 3/3 Gene3D:1.10.20.10,Pfam_domain:PF02291,hmmpanther:PTHR12595,hmmpanther:PTHR12595:SF8,Superfamily_domains:SSF47113 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -10.97223 1 1 1 1 0 C 3 2 3 69365653 69365653 T C 1 0 0 0 0 1 0 0 0 15931 1638 57 5 5 TAF9 5 69365653 Missense_Mutation SNP T 11LU022_T 9938 69365653 112172606 281 919 BTF3 0 . GRCh38 5 73502521 73502521 + Nonsense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.235A>T p.Arg79Ter p.R79* ENST00000380591 3/6 82 64 18 110 110 0 strelka-varscan-mutect BTF3,stop_gained,p.Arg79Ter,ENST00000380591,NM_001037637.1;BTF3,stop_gained,p.Arg35Ter,ENST00000335895,NM_001207.4;BTF3,intron_variant,,ENST00000507081,;BTF3,upstream_gene_variant,,ENST00000509708,;RP11-79P5.9,upstream_gene_variant,,ENST00000607001,;BTF3,non_coding_transcript_exon_variant,,ENST00000514505,;BTF3,non_coding_transcript_exon_variant,,ENST00000514360,;BTF3,non_coding_transcript_exon_variant,,ENST00000508901,;BTF3,non_coding_transcript_exon_variant,,ENST00000510787,;BTF3,downstream_gene_variant,,ENST00000512257,; T ENST00000380591 Transcript stop_gained 454/1237 235/621 79/206 R/* Aga/Tga 1 1 BTF3 HGNC HGNC:1125 protein_coding YES CCDS34185.1 ENSP00000369965 P20290 UPI0000049C1C NM_001037637.1 3/6 hmmpanther:PTHR10351 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 73502521 73502521 A T 1 0 0 0 0 0 1 0 0 1727 412 15 4 4 BTF3 5 73502521 Nonsense_Mutation SNP A 11LU022_T 4136868 73502521 108035738 282 920 SV2C 0 . GRCh38 5 76285858 76285858 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.1125G>A p.= p.E375E ENST00000502798 6/13 121 108 13 110 110 0 strelka-varscan-mutect SV2C,synonymous_variant,p.=,ENST00000502798,NM_014979.3;SV2C,synonymous_variant,p.=,ENST00000322285,NM_001297716.1;RP11-466P24.6,non_coding_transcript_exon_variant,,ENST00000502589,;PDCD5P2,downstream_gene_variant,,ENST00000507570,; A ENST00000502798 Transcript synonymous_variant 1567/11035 1125/2184 375/727 E gaG/gaA 1 1 SV2C HGNC HGNC:30670 protein_coding YES CCDS43331.1 ENSP00000423541 Q496J9 UPI000011DDBB NM_014979.3 6/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23511:SF6,hmmpanther:PTHR23511,TIGRFAM_domain:TIGR01299 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 76285858 76285858 G A 1 0 0 0 0 0 0 0 1 15803 933 33 3 3 SV2C 5 76285858 Silent SNP G 11LU022_T 2783337 76285858 105252401 283 921 F2RL2 0 . GRCh38 5 76618404 76618404 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.303C>T p.= p.Y101Y ENST00000296641 2/2 278 242 36 360 359 1 strelka-varscan-mutect F2RL2,synonymous_variant,p.=,ENST00000296641,NM_004101.3;F2RL2,synonymous_variant,p.=,ENST00000504899,NM_001256566.1;IQGAP2,intron_variant,,ENST00000274364,NM_006633.3;IQGAP2,intron_variant,,ENST00000379730,NM_001285460.1;IQGAP2,intron_variant,,ENST00000505766,;IQGAP2,intron_variant,,ENST00000502745,NM_001285462.1;IQGAP2,intron_variant,,ENST00000396234,NM_001285461.1;IQGAP2,intron_variant,,ENST00000514350,;IQGAP2,intron_variant,,ENST00000514001,;IQGAP2,intron_variant,,ENST00000509074,;IQGAP2,intron_variant,,ENST00000515505,;IQGAP2,intron_variant,,ENST00000504254,;IQGAP2,intron_variant,,ENST00000513534,; A ENST00000296641 Transcript synonymous_variant 507/3429 303/1125 101/374 Y taC/taT 1 -1 F2RL2 HGNC HGNC:3539 protein_coding YES CCDS4031.1 ENSP00000296641 O00254 UPI0000050431 NM_004101.3 2/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,Prints_domain:PR01428,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF0,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 76618404 76618404 G A 1 0 0 0 0 0 0 0 1 5213 1256 44 3 3 F2RL2 5 76618404 Silent SNP G 11LU022_T 332546 76618404 104919855 284 922 F2R 0 . GRCh38 5 76732740 76732740 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.515C>A p.Ser172Tyr p.S172Y ENST00000319211 2/2 440 350 90 507 506 1 strelka-varscan-mutect F2R,missense_variant,p.Ser172Tyr,ENST00000319211,NM_001992.3; A ENST00000319211 Transcript missense_variant 780/3821 515/1278 172/425 S/Y tCt/tAt 1 1 F2R HGNC HGNC:3537 protein_coding YES CCDS4032.1 ENSP00000321326 P25116 A0A024RAP7 UPI0000131312 NM_001992.3 deleterious(0.03) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF20,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01428 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 76732740 76732740 C A 1 0 0 0 0 1 0 0 0 5211 913 32 2 2 F2R 5 76732740 Missense_Mutation SNP C 11LU022_T 114336 76732740 104805519 285 923 AP3B1 0 . GRCh38 5 78128077 78128077 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1921G>T p.Glu641Ter p.E641* ENST00000255194 17/27 326 297 29 331 331 0 strelka-varscan-mutect AP3B1,stop_gained,p.Glu641Ter,ENST00000255194,NM_003664.4;AP3B1,stop_gained,p.Glu592Ter,ENST00000519295,NM_001271769.1;AP3B1,non_coding_transcript_exon_variant,,ENST00000517561,; A ENST00000255194 Transcript stop_gained 2097/5838 1921/3285 641/1094 E/* Gag/Tag 1 -1 AP3B1 HGNC HGNC:566 protein_coding YES CCDS4041.1 ENSP00000255194 O00203 A0A0S2Z5J4 UPI00001AE77D NM_003664.4 17/27 Gene3D:1.25.10.10,PIRSF_domain:PIRSF037096,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 78128077 78128077 C A 1 0 0 0 0 0 1 0 0 860 922 32 2 2 AP3B1 5 78128077 Nonsense_Mutation SNP C 11LU022_T 1395337 78128077 103410182 286 924 THBS4 0 . GRCh38 5 80059757 80059757 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.839C>T p.Pro280Leu p.P280L ENST00000350881 7/22 154 123 31 177 177 0 strelka-varscan-mutect THBS4,missense_variant,p.Pro280Leu,ENST00000350881,NM_001306213.1,NM_003248.4;THBS4,missense_variant,p.Pro189Leu,ENST00000511733,NM_001306212.1,NM_001306214.1;CTD-2201I18.1,intron_variant,,ENST00000503007,;THBS4,downstream_gene_variant,,ENST00000513310,;THBS4,downstream_gene_variant,,ENST00000510218,; T ENST00000350881 Transcript missense_variant 1029/3222 839/2886 280/961 P/L cCt/cTt 1 1 THBS4 HGNC HGNC:11788 protein_coding YES CCDS4049.1 ENSP00000339730 P35443 UPI000013D591 NM_001306213.1,NM_003248.4 tolerated(0.35) 7/22 Low_complexity_(Seg):seg,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF92 MODERATE 1 SNV 1 1 PASS rs1332467099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 80059757 80059757 C T 1 0 0 0 0 1 0 0 0 16289 681 24 3 3 THBS4 5 80059757 Missense_Mutation SNP C 11LU022_T 1931680 80059757 101478502 287 925 VCAN 0 . GRCh38 5 83522184 83522184 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3878C>A p.Pro1293Gln p.P1293Q ENST00000265077 7/15 72 66 6 117 117 0 strelka-varscan-mutect VCAN,missense_variant,p.Pro1293Gln,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Pro1293Gln,ENST00000342785,NM_001164098.1;VCAN,missense_variant,p.Pro1245Gln,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 4443/12625 3878/10191 1293/3396 P/Q cCa/cAa 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 deleterious(0.04) 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 83522184 83522184 C A 1 0 0 0 0 1 0 0 0 17683 594 21 2 2 VCAN 5 83522184 Missense_Mutation SNP C 11LU022_T 3462427 83522184 98016075 288 926 EDIL3 0 . GRCh38 5 83963282 83963282 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1216G>T p.Gly406Cys p.G406C ENST00000296591 10/11 130 108 22 131 131 0 strelka-varscan-mutect EDIL3,missense_variant,p.Gly406Cys,ENST00000296591,NM_005711.4;EDIL3,missense_variant,p.Gly396Cys,ENST00000380138,NM_001278642.1; A ENST00000296591 Transcript missense_variant 1635/4727 1216/1443 406/480 G/C Ggc/Tgc 1 -1 EDIL3 HGNC HGNC:3173 protein_coding YES CCDS4062.1 ENSP00000296591 O43854 UPI000004D126 NM_005711.4 deleterious(0) 10/11 PROSITE_profiles:PS50022,hmmpanther:PTHR10127:SF29,hmmpanther:PTHR10127,Gene3D:2.60.120.260,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 83963282 83963282 C A 1 0 0 0 0 1 0 0 0 4743 594 21 2 2 EDIL3 5 83963282 Missense_Mutation SNP C 11LU022_T 441098 83963282 97574977 289 927 KIAA0825 0 . GRCh38 5 94403773 94403773 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2683G>T p.Glu895Ter p.E895* ENST00000513200 15/20 144 125 19 158 158 0 strelka-varscan-mutect KIAA0825,stop_gained,p.Glu895Ter,ENST00000513200,NM_001145678.1; A ENST00000513200 Transcript stop_gained 2756/4942 2683/3828 895/1275 E/* Gag/Tag 1 -1 KIAA0825 HGNC HGNC:28532 protein_coding ENSP00000424618 A0A088AWM3 UPI0001D3B505 NM_001145678.1 15/20 hmmpanther:PTHR33960:SF1,hmmpanther:PTHR33960 HIGH 1 SNV 5 1 PASS rs1253398964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 94403773 94403773 C A 1 0 0 0 0 0 1 0 0 8091 893 31 1 1 KIAA0825 5 94403773 Nonsense_Mutation SNP C 11LU022_T 10440491 94403773 87134486 290 928 LIX1 0 . GRCh38 5 97094809 97094809 + Frame_Shift_Del DEL G G - novel 11LU022_T 11LU022_N G G c.788delC p.Pro263LeufsTer11 p.P263Lfs*11 ENST00000274382 6/6 136 111 25 201 201 0 sindel-varindel-pindel LIX1,frameshift_variant,p.Pro263LeufsTer11,ENST00000274382,NM_153234.4;CTD-2215E18.1,intron_variant,,ENST00000504578,; - ENST00000274382 Transcript frameshift_variant 1084/4026 788/849 263/282 P/X cCt/ct 1 -1 LIX1 HGNC HGNC:18581 protein_coding YES CCDS4088.1 ENSP00000274382 Q8N485 UPI000007388A NM_153234.4 6/6 hmmpanther:PTHR31139,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 97094809 97094809 G - 1 0 1 0 1 0 0 0 0 8754 1000 35 0 0 LIX1 5 97094809 Frame_Shift_Del DEL G 11LU022_T 2691036 97094809 84443450 291 929 SLCO6A1 0 . GRCh38 5 102459697 102459697 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.980G>T p.Cys327Phe p.C327F ENST00000506729 5/14 125 105 20 134 134 0 strelka-varscan-mutect SLCO6A1,missense_variant,p.Cys327Phe,ENST00000506729,NM_001289002.1,NM_173488.4;SLCO6A1,missense_variant,p.Cys327Phe,ENST00000379807,;SLCO6A1,missense_variant,p.Cys265Phe,ENST00000389019,NM_001289004.1;SLCO6A1,intron_variant,,ENST00000513675,NM_001308014.1;SLCO6A1,non_coding_transcript_exon_variant,,ENST00000514551,;SLCO6A1,intron_variant,,ENST00000505739,; A ENST00000506729 Transcript missense_variant 1152/2689 980/2160 327/719 C/F tGt/tTt 1 -1 SLCO6A1 HGNC HGNC:23613 protein_coding YES CCDS34206.1 ENSP00000421339 Q86UG4 A0A140VJU7 UPI000020C392 NM_001289002.1,NM_173488.4 tolerated(0.12) 5/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR11388:SF95,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Pfam_domain:PF03137,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.999928 1 1 1 0 A 3 1 3 102459697 102459697 C A 1 0 0 0 0 1 0 0 0 15019 478 17 2 2 SLCO6A1 5 102459697 Missense_Mutation SNP C 11LU022_T 5364888 102459697 79078562 292 930 SLC25A46 0 . GRCh38 5 110742046 110742046 + Splice_Site SNP G G T novel 11LU022_T 11LU022_N G G c.284-1G>T p.X95_splice ENST00000355943 81 74 7 142 142 0 strelka-varscan-mutect SLC25A46,splice_acceptor_variant,,ENST00000355943,NM_138773.2;SLC25A46,splice_acceptor_variant,,ENST00000447245,NM_001303249.1;SLC25A46,splice_acceptor_variant,,ENST00000513807,NM_001303250.1;SLC25A46,5_prime_UTR_variant,,ENST00000504098,;TMEM232,upstream_gene_variant,,ENST00000515278,;TMEM232,upstream_gene_variant,,ENST00000512886,;SLC25A46,splice_acceptor_variant,,ENST00000508781,;TMEM232,upstream_gene_variant,,ENST00000503527,;SLC25A46,upstream_gene_variant,,ENST00000502462,; T ENST00000355943 Transcript splice_acceptor_variant -/2385 284/1257 95/418 1 1 SLC25A46 HGNC HGNC:25198 protein_coding YES CCDS4100.1 ENSP00000348211 Q96AG3 UPI00000711AA NM_138773.2 1/7 HIGH 1 SNV 1 1 PASS . . 0 204 3 0 2 0 0 0 -4.508653 0.9795034 1 1 1 0 T 5 4 3 110742046 110742046 G T 1 0 0 0 0 0 0 1 0 14776 956 33 2 2 SLC25A46 5 110742046 Splice_Site SNP G 11LU022_T 8282349 110742046 70796213 293 931 YTHDC2 0 . GRCh38 5 113535641 113535641 + Splice_Site SNP G G C novel 11LU022_T 11LU022_N G G c.946-1G>C p.X316_splice ENST00000161863 43 34 9 69 69 0 strelka-varscan-mutect YTHDC2,splice_acceptor_variant,,ENST00000161863,NM_022828.3;YTHDC2,splice_acceptor_variant,,ENST00000515883,;YTHDC2,splice_acceptor_variant,,ENST00000503857,; C ENST00000161863 Transcript splice_acceptor_variant -/6316 946/4293 316/1430 1 1 YTHDC2 HGNC HGNC:24721 protein_coding YES CCDS4113.1 ENSP00000161863 Q9H6S0 UPI0000367311 NM_022828.3 6/29 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99851 1 1 1 1 0 C 5 2 3 113535641 113535641 G C 1 0 0 0 0 0 0 1 0 18058 1014 35 4 4 YTHDC2 5 113535641 Splice_Site SNP G 11LU022_T 2793595 113535641 68002618 294 932 HSD17B4 0 . GRCh38 5 119529909 119529909 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.1858G>T p.Asp620Tyr p.D620Y ENST00000504811 22/25 220 174 46 287 287 0 strelka-varscan-mutect HSD17B4,missense_variant,p.Asp620Tyr,ENST00000504811,NM_001199291.2;HSD17B4,missense_variant,p.Asp595Tyr,ENST00000256216,NM_000414.3;HSD17B4,missense_variant,p.Asp571Tyr,ENST00000510025,NM_001292027.1;HSD17B4,missense_variant,p.Asp455Tyr,ENST00000414835,NM_001292028.1;HSD17B4,missense_variant,p.Asp577Tyr,ENST00000515320,NM_001199292.1;HSD17B4,missense_variant,p.Asp333Tyr,ENST00000509514,;HSD17B4,missense_variant,p.Asp458Tyr,ENST00000513628,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000522415,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000509951,;HSD17B4,downstream_gene_variant,,ENST00000518349,;HSD17B4,downstream_gene_variant,,ENST00000520244,;HSD17B4,3_prime_UTR_variant,,ENST00000442060,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000515235,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000509606,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000507353,; T ENST00000504811 Transcript missense_variant 2042/2740 1858/2286 620/761 D/Y Gac/Tac COSM297575 1 1 HSD17B4 HGNC HGNC:5213 protein_coding YES CCDS56379.1 ENSP00000420914 P51659 UPI0001AE7403 NM_001199291.2 deleterious(0.01) 22/25 Gene3D:3.10.129.10,Pfam_domain:PF01575,hmmpanther:PTHR13078,hmmpanther:PTHR13078:SF53,Superfamily_domains:SSF54637 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 119529909 119529909 G T 1 0 0 0 0 1 0 0 0 7281 942 33 2 2 HSD17B4 5 119529909 Missense_Mutation SNP G 11LU022_T 5994268 119529909 62008350 295 933 FTMT 0 . GRCh38 5 121852095 121852095 + Silent SNP C C A rs750748977 11LU022_T 11LU022_N C C c.132C>A p.= p.A44A ENST00000321339 1/1 89 74 15 116 116 0 strelka-varscan-mutect FTMT,synonymous_variant,p.=,ENST00000321339,NM_177478.1; A ENST00000321339 Transcript synonymous_variant 141/879 132/729 44/242 A gcC/gcA rs750748977 1 1 FTMT HGNC HGNC:17345 protein_coding YES CCDS4128.1 ENSP00000313691 Q8N4E7 UPI000006F87E NM_177478.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11431:SF30,hmmpanther:PTHR11431 LOW 1 SNV 1 PASS rs750748977 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 121852095 121852095 C A 1 0 0 0 0 0 0 0 1 5959 610 22 2 2 FTMT 5 121852095 Silent SNP C 11LU022_T 2322186 121852095 59686164 296 934 MEGF10 0 . GRCh38 5 127438453 127438453 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2119C>A p.His707Asn p.H707N ENST00000274473 18/26 127 108 19 148 147 1 strelka-varscan-mutect MEGF10,missense_variant,p.His707Asn,ENST00000274473,NM_032446.2;MEGF10,missense_variant,p.His707Asn,ENST00000503335,NM_001256545.1;MEGF10,non_coding_transcript_exon_variant,,ENST00000506709,; A ENST00000274473 Transcript missense_variant 2386/7594 2119/3423 707/1140 H/N Cac/Aac 1 1 MEGF10 HGNC HGNC:29634 protein_coding YES CCDS4142.1 ENSP00000274473 Q96KG7 UPI000006F868 NM_032446.2 tolerated(0.19) 18/26 PD936484,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999936 1 1 1 0 A 3 1 3 127438453 127438453 C A 1 0 0 0 0 1 0 0 0 9400 594 21 2 2 MEGF10 5 127438453 Missense_Mutation SNP C 11LU022_T 5586358 127438453 54099806 297 935 FBN2 0 . GRCh38 5 128345529 128345529 + Silent SNP G G A rs371640952 11LU022_T 11LU022_N G G c.3045C>T p.= p.P1015P ENST00000508053 30/71 452 372 80 543 542 1 strelka-varscan-mutect FBN2,synonymous_variant,p.=,ENST00000508053,;FBN2,synonymous_variant,p.=,ENST00000262464,NM_001999.3;FBN2,synonymous_variant,p.=,ENST00000619499,;FBN2,synonymous_variant,p.=,ENST00000508989,; A ENST00000508053 Transcript synonymous_variant 4020/11132 3045/8739 1015/2912 P ccC/ccT rs371640952,COSM4776000,COSM4776001 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 30/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 benign 0,1,1 LOW 1 SNV 5 1,1,1 1 PASS rs371640952 . 0 208 0 0 0 0 0 2 -2.954124 0 0 1 0 0 A 2 1 3 128345529 128345529 G A 1 0 0 0 0 0 0 0 1 5566 1103 39 1 1 FBN2 5 128345529 Silent SNP G 11LU022_T 907076 128345529 53192730 298 936 SAR1B 0 . GRCh38 5 134606975 134606975 + Missense_Mutation SNP C C A rs200409139 11LU022_T 11LU022_N C C c.572G>T p.Arg191Leu p.R191L ENST00000402673 7/7 348 310 38 411 411 0 strelka-varscan-mutect SAR1B,missense_variant,p.Arg191Leu,ENST00000402673,NM_016103.3;SAR1B,missense_variant,p.Arg123Leu,ENST00000507419,;SAR1B,missense_variant,p.Arg191Leu,ENST00000439578,NM_001033503.2;SAR1B,missense_variant,p.Arg123Leu,ENST00000502539,;SAR1B,missense_variant,p.Arg123Leu,ENST00000509937,;SAR1B,downstream_gene_variant,,ENST00000505758,;SAR1B,downstream_gene_variant,,ENST00000502286,;SAR1B,downstream_gene_variant,,ENST00000509730,;SAR1B,non_coding_transcript_exon_variant,,ENST00000508363,;SAR1B,downstream_gene_variant,,ENST00000503318,; A ENST00000402673 Transcript missense_variant 851/6682 572/597 191/198 R/L cGc/cTc rs200409139 1 -1 SAR1B HGNC HGNC:10535 protein_coding YES CCDS4177.1 ENSP00000385432 Q9Y6B6 UPI0000135569 NM_016103.3 deleterious(0.02) 7/7 PROSITE_profiles:PS51422,hmmpanther:PTHR11711:SF133,hmmpanther:PTHR11711,Pfam_domain:PF00025,Gene3D:3.40.50.300,SMART_domains:SM00178,SMART_domains:SM00177,Superfamily_domains:SSF52540,Prints_domain:PR00328 MODERATE 1 SNV 1 1 PASS rs200409139 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 134606975 134606975 C A 1 0 0 0 0 1 0 0 0 14100 768 27 1 1 SAR1B 5 134606975 Missense_Mutation SNP C 11LU022_T 6261446 134606975 46931284 299 937 NRG2 0 . GRCh38 5 139887412 139887412 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.800C>A p.Ser267Tyr p.S267Y ENST00000361474 2/10 200 157 43 255 255 0 strelka-varscan-mutect NRG2,missense_variant,p.Ser267Tyr,ENST00000541337,NM_001184935.1;NRG2,missense_variant,p.Ser267Tyr,ENST00000361474,NM_004883.2;NRG2,missense_variant,p.Ser267Tyr,ENST00000289422,NM_013982.2;NRG2,missense_variant,p.Ser267Tyr,ENST00000358522,NM_013983.2;NRG2,missense_variant,p.Ser267Tyr,ENST00000289409,NM_013981.3;NRG2,missense_variant,p.Ser64Tyr,ENST00000340391,;NRG2,non_coding_transcript_exon_variant,,ENST00000518130,;NRG2,missense_variant,p.Ser267Tyr,ENST00000378238,; T ENST00000361474 Transcript missense_variant 1025/3020 800/2553 267/850 S/Y tCc/tAc 1 -1 NRG2 HGNC HGNC:7998 protein_coding YES CCDS4217.1 ENSP00000354910 O14511 UPI0000130507 NM_004883.2 deleterious(0) 2/10 PROSITE_profiles:PS50835,hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF20,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 139887412 139887412 G T 1 0 0 0 0 1 0 0 0 10706 1174 41 2 2 NRG2 5 139887412 Missense_Mutation SNP G 11LU022_T 5280437 139887412 41650847 300 938 PCDHA1 0 . GRCh38 5 140788417 140788417 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2127C>A p.Ser709Arg p.S709R ENST00000504120 1/4 391 295 96 433 433 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Ser709Arg,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Ser709Arg,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript missense_variant 2127/5263 2127/2853 709/950 S/R agC/agA 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 deleterious_low_confidence(0.01) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 140788417 140788417 C A 1 0 0 0 0 1 0 0 0 11606 738 26 2 2 PCDHA1 5 140788417 Missense_Mutation SNP C 11LU022_T 901005 140788417 40749842 301 939 PCDHA11 0 . GRCh38 5 140870536 140870536 + Missense_Mutation SNP C C A rs782205013 11LU022_T 11LU022_N C C c.1433C>A p.Ala478Glu p.A478E ENST00000398640 1/4 680 604 76 862 861 1 strelka-varscan-mutect PCDHA11,missense_variant,p.Ala478Glu,ENST00000398640,NM_018902.4;PCDHA11,missense_variant,p.Ala478Glu,ENST00000616325,NM_031861.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA10,downstream_gene_variant,,ENST00000562220,NM_031859.2;PCDHA12,upstream_gene_variant,,ENST00000398631,NM_018903.3;PCDHA12,upstream_gene_variant,,ENST00000613593,NM_031864.2;PCDHA11,upstream_gene_variant,,ENST00000617408,;AC005609.18,downstream_gene_variant,,ENST00000624566,;AC005609.20,upstream_gene_variant,,ENST00000625071,; A ENST00000398640 Transcript missense_variant 2291/6115 1433/2850 478/949 A/E gCg/gAg rs782205013 1 1 PCDHA11 HGNC HGNC:8665 protein_coding YES CCDS47284.1 ENSP00000381636 Q9Y5I1 UPI00001273D4 NM_018902.4 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF68,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs782205013 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 140870536 140870536 C A 1 0 0 0 0 1 0 0 0 11608 768 27 1 1 PCDHA11 5 140870536 Missense_Mutation SNP C 11LU022_T 82119 140870536 40667723 302 940 PCDHB7 0 . GRCh38 5 141174974 141174974 + Silent SNP G G A rs146189351 11LU022_T 11LU022_N G G c.2139G>A p.= p.R713R ENST00000231137 1/1 363 309 54 434 434 0 strelka-varscan-mutect PCDHB7,synonymous_variant,p.=,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; A ENST00000231137 Transcript synonymous_variant 2356/3765 2139/2382 713/793 R agG/agA rs146189351,COSM5201049 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69 0,1 LOW SNV 0,1 1 PASS rs146189351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 141174974 141174974 G A 1 0 0 0 0 0 0 0 1 11634 1165 41 3 3 PCDHB7 5 141174974 Silent SNP G 11LU022_T 304438 141174974 40363285 303 941 PCDHB9 0 . GRCh38 5 141189218 141189218 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1900G>C p.Asp634His p.D634H ENST00000316105 1/1 552 479 73 768 768 0 varscan-mutect PCDHB9,missense_variant,p.Asp634His,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; C ENST00000316105 Transcript missense_variant 2092/4415 1900/2394 634/797 D/H Gac/Cac 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 141189218 141189218 G C 1 0 0 0 0 1 0 0 0 11636 1058 37 4 4 PCDHB9 5 141189218 Missense_Mutation SNP G 11LU022_T 14244 141189218 40349041 304 942 PCDHGA7 0 . GRCh38 5 141383017 141383017 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.118G>T p.Asp40Tyr p.D40Y ENST00000518325 1/4 140 124 16 194 194 0 strelka-varscan-mutect PCDHGA7,missense_variant,p.Asp40Tyr,ENST00000518325,NM_018920.3;PCDHGA7,missense_variant,p.Asp40Tyr,ENST00000617050,NM_032087.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,downstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGB4,upstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB4,upstream_gene_variant,,ENST00000519479,NM_003736.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000518325 Transcript missense_variant 118/4605 118/2799 40/932 D/Y Gac/Tac 1 1 PCDHGA7 HGNC HGNC:8705 protein_coding YES CCDS54927.1 ENSP00000430024 Q9Y5G6 UPI000007146F NM_018920.3 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 141383017 141383017 G T 1 0 0 0 0 1 0 0 0 11646 1174 41 2 2 PCDHGA7 5 141383017 Missense_Mutation SNP G 11LU022_T 193799 141383017 40155242 305 943 PCDHGB4 0 . GRCh38 5 141389888 141389888 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.2004G>T p.Glu668Asp p.E668D ENST00000519479 1/4 257 218 39 311 311 0 strelka-varscan-mutect PCDHGB4,missense_variant,p.Glu668Asp,ENST00000615384,NM_032098.1;PCDHGB4,missense_variant,p.Glu668Asp,ENST00000519479,NM_003736.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000519479 Transcript missense_variant 2004/4578 2004/2772 668/923 E/D gaG/gaT COSM1063196 1 1 PCDHGB4 HGNC HGNC:8711 protein_coding YES CCDS54928.1 ENSP00000428288 Q9UN71 UPI000006F773 NM_003736.2 tolerated(0.22) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF117,hmmpanther:PTHR24028,SMART_domains:SM00112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 141389888 141389888 G T 1 0 0 0 0 1 0 0 0 11652 991 35 2 2 PCDHGB4 5 141389888 Missense_Mutation SNP G 11LU022_T 6871 141389888 40148371 306 944 PCDHGA8 0 . GRCh38 5 141394457 141394457 + Silent SNP G G T rs375756271 11LU022_T 11LU022_N G G c.1644G>T p.= p.L548L ENST00000398604 1/4 440 348 92 617 617 0 strelka-varscan-mutect PCDHGA8,synonymous_variant,p.=,ENST00000610569,NM_014004.2;PCDHGA8,synonymous_variant,p.=,ENST00000398604,NM_032088.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB4,downstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB5,upstream_gene_variant,,ENST00000617380,NM_018925.2;PCDHGB5,upstream_gene_variant,,ENST00000621169,NM_032099.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398604 Transcript synonymous_variant 1644/4605 1644/2799 548/932 L ctG/ctT rs375756271 1 1 PCDHGA8 HGNC HGNC:8706 protein_coding YES CCDS47291.1 ENSP00000381605 Q9Y5G5 UPI000006FC06 NM_032088.1 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF72,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs375756271 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 141394457 141394457 G T 1 0 0 0 0 0 0 0 1 11647 1277 45 2 2 PCDHGA8 5 141394457 Silent SNP G 11LU022_T 4569 141394457 40143802 307 945 ARHGAP26 0 . GRCh38 5 143041816 143041816 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1211G>T p.Gly404Val p.G404V ENST00000274498 14/23 176 159 17 182 181 1 strelka-varscan-mutect ARHGAP26,missense_variant,p.Gly404Val,ENST00000378004,NM_001135608.1;ARHGAP26,missense_variant,p.Gly404Val,ENST00000274498,NM_015071.4;ARHGAP26,missense_variant,p.Gly23Val,ENST00000443674,;ARHGAP26,downstream_gene_variant,,ENST00000451259,;ARHGAP26,splice_region_variant,,ENST00000469396,;ARHGAP26,downstream_gene_variant,,ENST00000470032,;ARHGAP26,splice_region_variant,,ENST00000469131,; T ENST00000274498 Transcript missense_variant,splice_region_variant 1589/6862 1211/2445 404/814 G/V gGg/gTg 1 1 ARHGAP26 HGNC HGNC:17073 protein_coding YES CCDS4277.1 ENSP00000274498 Q9UNA1 UPI0000130D6B NM_015071.4 deleterious(0) 14/23 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF4,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 143041816 143041816 G T 1 0 0 0 0 1 0 0 0 1000 1246 43 2 2 ARHGAP26 5 143041816 Missense_Mutation SNP G 11LU022_T 1647359 143041816 38496443 308 946 LARS 0 . GRCh38 5 146131035 146131035 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2471G>T p.Gly824Val p.G824V ENST00000394434 24/32 71 54 17 102 102 0 strelka-mutect LARS,missense_variant,p.Gly824Val,ENST00000394434,NM_001317965.1,NM_020117.9;LARS,missense_variant,p.Gly770Val,ENST00000510191,;LARS,missense_variant,p.Gly133Val,ENST00000274562,;LARS,downstream_gene_variant,,ENST00000512412,;LARS,non_coding_transcript_exon_variant,,ENST00000506231,;LARS,upstream_gene_variant,,ENST00000508709,;LARS,upstream_gene_variant,,ENST00000504611,; A ENST00000394434 Transcript missense_variant 2638/4766 2471/3531 824/1176 G/V gGg/gTg 1 -1 LARS HGNC HGNC:6512 protein_coding YES CCDS34265.1 ENSP00000377954 Q9P2J5 UPI0000037316 NM_001317965.1,NM_020117.9 tolerated(0.08) 24/32 hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF51,Pfam_domain:PF08264,Gene3D:1.10.730.10,TIGRFAM_domain:TIGR00395,Superfamily_domains:SSF47323 MODERATE 1 SNV 1 1 PASS rs1441508981 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 146131035 146131035 C A 1 0 0 0 0 1 0 0 0 8545 623 22 2 2 LARS 5 146131035 Missense_Mutation SNP C 11LU022_T 3089219 146131035 35407224 309 947 SLC6A7 0 . GRCh38 5 150199349 150199349 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.706G>C p.Val236Leu p.V236L ENST00000230671 5/14 72 63 9 90 90 0 strelka-varscan-mutect SLC6A7,missense_variant,p.Val236Leu,ENST00000230671,NM_014228.3;SLC6A7,missense_variant,p.Val236Leu,ENST00000524041,;SLC6A7,downstream_gene_variant,,ENST00000513403,; C ENST00000230671 Transcript missense_variant 1077/3739 706/1911 236/636 V/L Gtg/Ctg 1 1 SLC6A7 HGNC HGNC:11054 protein_coding YES CCDS4305.1 ENSP00000230671 Q99884 UPI000013C93C NM_014228.3 deleterious(0.01) 5/14 PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF35,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.73561 1 1 1 1 0 C 3 2 3 150199349 150199349 G C 1 0 0 0 0 1 0 0 0 14972 1377 48 4 4 SLC6A7 5 150199349 Missense_Mutation SNP G 11LU022_T 4068314 150199349 31338910 310 948 SLC36A1 0 . GRCh38 5 151479476 151479476 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1146G>T p.= p.L382L ENST00000243389 10/11 99 67 32 103 103 0 strelka-varscan-mutect SLC36A1,synonymous_variant,p.=,ENST00000243389,NM_078483.2;SLC36A1,synonymous_variant,p.=,ENST00000520701,;SLC36A1,synonymous_variant,p.=,ENST00000521925,;SLC36A1,synonymous_variant,p.=,ENST00000616007,;SLC36A1,synonymous_variant,p.=,ENST00000517628,;RNA5SP197,upstream_gene_variant,,ENST00000363357,;SLC36A1,3_prime_UTR_variant,,ENST00000522185,; T ENST00000243389 Transcript synonymous_variant 1369/5781 1146/1431 382/476 L ctG/ctT 1 1 SLC36A1 HGNC HGNC:18761 protein_coding YES CCDS4316.1 ENSP00000243389 Q7Z2H8 UPI00001A9D3C NM_078483.2 10/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF188,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 151479476 151479476 G T 1 0 0 0 0 0 0 0 1 14871 1335 47 2 2 SLC36A1 5 151479476 Silent SNP G 11LU022_T 1280127 151479476 30058783 311 949 TIMD4 0 . GRCh38 5 156926293 156926293 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.864T>A p.= p.P288P ENST00000274532 6/9 194 155 39 250 250 0 strelka-varscan-mutect TIMD4,synonymous_variant,p.=,ENST00000274532,NM_138379.2;TIMD4,synonymous_variant,p.=,ENST00000407087,NM_001146726.1;TIMD4,5_prime_UTR_variant,,ENST00000406964,;APOOP1,downstream_gene_variant,,ENST00000604695,; T ENST00000274532 Transcript synonymous_variant 921/1369 864/1137 288/378 P ccT/ccA 1 -1 TIMD4 HGNC HGNC:25132 protein_coding YES CCDS4332.1 ENSP00000274532 Q96H15 UPI000013DA13 NM_138379.2 6/9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 156926293 156926293 A T 1 0 0 0 0 0 0 0 1 16341 175 7 4 4 TIMD4 5 156926293 Silent SNP A 11LU022_T 5446817 156926293 24611966 312 950 ITK 0 . GRCh38 5 157222982 157222982 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.615G>C p.Glu205Asp p.E205D ENST00000422843 6/17 363 316 47 441 441 0 strelka-varscan-mutect ITK,missense_variant,p.Glu205Asp,ENST00000422843,NM_005546.3;ITK,downstream_gene_variant,,ENST00000521769,;CTB-4E7.1,intron_variant,,ENST00000519375,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,non_coding_transcript_exon_variant,,ENST00000519759,; C ENST00000422843 Transcript missense_variant 767/4528 615/1863 205/620 E/D gaG/gaC 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 tolerated(1) 6/17 PROSITE_profiles:PS50002,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Gene3D:2.30.30.40,Pfam_domain:PF00018,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 157222982 157222982 G C 1 0 0 0 0 1 0 0 0 7815 933 33 4 4 ITK 5 157222982 Missense_Mutation SNP G 11LU022_T 296689 157222982 24315277 313 951 CYFIP2 0 . GRCh38 5 157285425 157285425 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.64C>A p.Leu22Ile p.L22I ENST00000616178 2/32 208 173 35 201 201 0 strelka-varscan-mutect CYFIP2,missense_variant,p.Leu22Ile,ENST00000521420,NM_001291721.1;CYFIP2,missense_variant,p.Leu22Ile,ENST00000618329,NM_014376.3;CYFIP2,missense_variant,p.Leu22Ile,ENST00000616178,NM_001291722.1;CYFIP2,missense_variant,p.Leu22Ile,ENST00000620254,NM_001037333.2;CYFIP2,missense_variant,p.Leu22Ile,ENST00000435847,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000522463,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000611075,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000617629,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000611925,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000621516,;CYFIP2,missense_variant,p.Leu22Ile,ENST00000522637,;CYFIP2,non_coding_transcript_exon_variant,,ENST00000622696,; A ENST00000616178 Transcript missense_variant 204/4210 64/3837 22/1278 L/I Ctc/Atc 1 1 CYFIP2 HGNC HGNC:13760 protein_coding YES CCDS78077.1 ENSP00000479719 Q96F07 UPI0000DC89D8 NM_001291722.1 tolerated(0.08) 2/32 hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 157285425 157285425 C A 1 0 0 0 0 1 0 0 0 3941 681 24 2 2 CYFIP2 5 157285425 Missense_Mutation SNP C 11LU022_T 62443 157285425 24252834 314 952 ADAM19 0 . GRCh38 5 157481888 157481888 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2606G>T p.Gly869Val p.G869V ENST00000257527 22/23 126 109 17 145 145 0 strelka-varscan-mutect ADAM19,missense_variant,p.Gly869Val,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Gly869Val,ENST00000517905,;ADAM19,missense_variant,p.Gly440Val,ENST00000517374,;ADAM19,intron_variant,,ENST00000517951,; A ENST00000257527 Transcript missense_variant 2685/6481 2606/2757 869/918 G/V gGc/gTc 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 deleterious(0.05) 22/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 157481888 157481888 C A 1 0 0 0 0 1 0 0 0 284 739 26 2 2 ADAM19 5 157481888 Missense_Mutation SNP C 11LU022_T 196463 157481888 24056371 315 953 ATP10B 0 . GRCh38 5 160606798 160606798 + Missense_Mutation SNP G G C rs748360139 11LU022_T 11LU022_N G G c.3127C>G p.Arg1043Gly p.R1043G ENST00000327245 19/26 139 117 22 187 187 0 strelka-varscan-mutect ATP10B,missense_variant,p.Arg1043Gly,ENST00000327245,NM_025153.2;ATP10B,upstream_gene_variant,,ENST00000523758,;ATP10B,downstream_gene_variant,,ENST00000522169,;ATP10B,non_coding_transcript_exon_variant,,ENST00000517815,; C ENST00000327245 Transcript missense_variant 3974/7566 3127/4386 1043/1461 R/G Cga/Gga rs748360139,COSM1486558 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0.02) 19/26 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF79,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF56784 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748360139 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 160606798 160606798 G C 1 0 0 0 0 1 0 0 0 1269 1095 38 4 4 ATP10B 5 160606798 Missense_Mutation SNP G 11LU022_T 3124910 160606798 20931461 316 954 GABRA1 0 . GRCh38 5 161897311 161897311 + Missense_Mutation SNP C C A rs760920254 11LU022_T 11LU022_N C C c.1260C>A p.Asp420Glu p.D420E ENST00000393943 10/10 230 204 26 261 261 0 strelka-varscan-mutect GABRA1,missense_variant,p.Asp420Glu,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Asp420Glu,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Asp435Glu,ENST00000638159,;GABRA1,missense_variant,p.Asp420Glu,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Asp420Glu,ENST00000638112,;GABRA1,missense_variant,p.Asp420Glu,ENST00000636573,;GABRA1,missense_variant,p.Asp420Glu,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Asp420Glu,ENST00000637827,;GABRA1,missense_variant,p.Asp420Glu,ENST00000635880,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,; A ENST00000393943 Transcript missense_variant 2043/4686 1260/1371 420/456 D/E gaC/gaA rs760920254 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 deleterious(0.01) 10/10 Gene3D:1.20.58.390,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS rs760920254 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 161897311 161897311 C A 1 0 0 0 0 1 0 0 0 6031 506 18 2 2 GABRA1 5 161897311 Missense_Mutation SNP C 11LU022_T 1290513 161897311 19640948 317 955 WWC1 0 . GRCh38 5 168409940 168409940 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.886A>G p.Asn296Asp p.N296D ENST00000521089 8/23 218 177 41 268 268 0 strelka-varscan-mutect WWC1,missense_variant,p.Asn296Asp,ENST00000265293,NM_015238.2;WWC1,missense_variant,p.Asn258Asp,ENST00000393895,;WWC1,missense_variant,p.Asn296Asp,ENST00000521089,NM_001161662.1,NM_001161661.1;WWC1,missense_variant,p.Asn73Asp,ENST00000524228,;WWC1,non_coding_transcript_exon_variant,,ENST00000517425,;WWC1,non_coding_transcript_exon_variant,,ENST00000517646,;WWC1,upstream_gene_variant,,ENST00000624315,;WWC1,downstream_gene_variant,,ENST00000523043,;WWC1,non_coding_transcript_exon_variant,,ENST00000519659,;WWC1,upstream_gene_variant,,ENST00000518334,; G ENST00000521089 Transcript missense_variant 889/3562 886/3360 296/1119 N/D Aat/Gat 1 1 WWC1 HGNC HGNC:29435 protein_coding YES CCDS54945.1 ENSP00000427772 Q8IX03 UPI00017A7149 NM_001161662.1,NM_001161661.1 deleterious(0.01) 8/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14791,hmmpanther:PTHR14791:SF22 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 168409940 168409940 A G 1 0 0 0 0 1 0 0 0 17969 130 5 5 5 WWC1 5 168409940 Missense_Mutation SNP A 11LU022_T 6512629 168409940 13128319 318 956 FBLL1 0 . GRCh38 5 168530431 168530431 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.927G>T p.= p.L309L ENST00000338333 1/1 234 180 54 274 274 0 strelka-varscan-mutect FBLL1,synonymous_variant,p.=,ENST00000338333,; T ENST00000338333 Transcript synonymous_variant 1316/1519 927/1005 309/334 L ctG/ctT 1 1 FBLL1 HGNC HGNC:35458 protein_coding YES ENSP00000473383 A6NHQ2 UPI00006C099E 1/1 Gene3D:3.40.50.150,HAMAP:MF_00351,Pfam_domain:PF01269,Prints_domain:PR00052,hmmpanther:PTHR10335,hmmpanther:PTHR10335:SF6,SMART_domains:SM01206,Superfamily_domains:SSF53335 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 168530431 168530431 G T 1 0 0 0 0 0 0 0 1 5560 1277 45 2 2 FBLL1 5 168530431 Silent SNP G 11LU022_T 120491 168530431 13007828 319 957 SLIT3 0 . GRCh38 5 168708049 168708049 + Missense_Mutation SNP G G T rs781009300 11LU022_T 11LU022_N G G c.2792C>A p.Pro931Gln p.P931Q ENST00000332966 26/36 263 229 34 295 295 0 strelka-varscan-mutect SLIT3,missense_variant,p.Pro924Gln,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Pro794Gln,ENST00000404867,;SLIT3,missense_variant,p.Pro931Gln,ENST00000332966,NM_001271946.1;CTC-558O2.1,non_coding_transcript_exon_variant,,ENST00000522615,;CTC-558O2.1,intron_variant,,ENST00000521870,; T ENST00000332966 Transcript missense_variant 2865/4895 2792/4593 931/1530 P/Q cCg/cAg rs781009300,COSM1542863,COSM5302883,COSM5403046,COSM5403047 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 deleterious(0) 26/36 PROSITE_profiles:PS50026,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs781009300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 168708049 168708049 G T 1 0 0 0 0 1 0 0 0 15032 1116 39 1 1 SLIT3 5 168708049 Missense_Mutation SNP G 11LU022_T 177618 168708049 12830210 320 958 DOCK2 0 . GRCh38 5 169718769 169718769 + Silent SNP C C A rs748633577 11LU022_T 11LU022_N C C c.2245C>A p.= p.R749R ENST00000256935 22/52 129 103 26 124 124 0 strelka-varscan-mutect DOCK2,synonymous_variant,p.=,ENST00000256935,NM_004946.2;DOCK2,synonymous_variant,p.=,ENST00000520908,;DOCK2,intron_variant,,ENST00000540750,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520836,;DOCK2,synonymous_variant,p.=,ENST00000524185,; A ENST00000256935 Transcript synonymous_variant 2325/6097 2245/5493 749/1830 R Cgg/Agg rs748633577,COSM1696721 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 22/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Superfamily_domains:SSF48371 0,1 LOW 1 SNV 1 0,1 1 PASS rs748633577 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 169718769 169718769 C A 1 0 0 0 0 0 0 0 1 4502 875 31 1 1 DOCK2 5 169718769 Silent SNP C 11LU022_T 1010720 169718769 11819490 321 959 FAM196B 0 . GRCh38 5 169883091 169883091 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.808G>T p.Gly270Cys p.G270C ENST00000377365 2/4 144 114 30 171 170 1 strelka-varscan-mutect FAM196B,missense_variant,p.Gly270Cys,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; A ENST00000377365 Transcript missense_variant 2190/2999 808/1608 270/535 G/C Ggc/Tgc 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 tolerated(0.07) 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 169883091 169883091 C A 1 0 0 0 0 1 0 0 0 5374 681 24 2 2 FAM196B 5 169883091 Missense_Mutation SNP C 11LU022_T 164322 169883091 11655168 322 960 DOCK2 0 . GRCh38 5 170019066 170019066 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3339C>A p.Asp1113Glu p.D1113E ENST00000256935 33/52 202 171 31 218 217 1 strelka-varscan-mutect DOCK2,missense_variant,p.Asp1113Glu,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Asp605Glu,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,3_prime_UTR_variant,,ENST00000433448,; A ENST00000256935 Transcript missense_variant 3419/6097 3339/5493 1113/1830 D/E gaC/gaA 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0) 33/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 170019066 170019066 C A 1 0 0 0 0 1 0 0 0 4502 477 17 2 2 DOCK2 5 170019066 Missense_Mutation SNP C 11LU022_T 135975 170019066 11519193 323 961 DOCK2 0 . GRCh38 5 170079135 170079135 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.5155G>T p.Asp1719Tyr p.D1719Y ENST00000256935 49/52 126 109 17 117 117 0 strelka-varscan-mutect DOCK2,missense_variant,p.Asp1719Tyr,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Asp1211Tyr,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000519868,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520450,; T ENST00000256935 Transcript missense_variant 5235/6097 5155/5493 1719/1830 D/Y Gac/Tac 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious_low_confidence(0.01) 49/52 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 170079135 170079135 G T 1 0 0 0 0 1 0 0 0 4502 1174 41 2 2 DOCK2 5 170079135 Missense_Mutation SNP G 11LU022_T 60069 170079135 11459124 324 962 NEURL1B 0 . GRCh38 5 172669926 172669926 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.173G>T p.Arg58Leu p.R58L ENST00000369800 2/5 74 60 14 75 75 0 strelka-varscan-mutect NEURL1B,missense_variant,p.Arg58Leu,ENST00000369800,NM_001142651.1;NEURL1B,missense_variant,p.Arg58Leu,ENST00000520919,NM_001308178.1;NEURL1B,intron_variant,,ENST00000522853,; T ENST00000369800 Transcript missense_variant 314/6424 173/1668 58/555 R/L cGg/cTg 1 1 NEURL1B HGNC HGNC:35422 protein_coding YES CCDS47342.1 ENSP00000358815 A8MQ27 UPI0000D6E5EA NM_001142651.1 tolerated(0.07) 2/5 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,Pfam_domain:PF07177,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 172669926 172669926 G T 1 0 0 0 0 1 0 0 0 10381 1116 39 1 1 NEURL1B 5 172669926 Missense_Mutation SNP G 11LU022_T 2590791 172669926 8868333 325 963 UNC5A 0 . GRCh38 5 176868854 176868854 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.611A>G p.His204Arg p.H204R ENST00000329542 5/15 94 87 7 161 161 0 strelka-varscan-mutect UNC5A,missense_variant,p.His204Arg,ENST00000329542,NM_133369.2;UNC5A,missense_variant,p.His170Arg,ENST00000509580,;UNC5A,3_prime_UTR_variant,,ENST00000513890,; G ENST00000329542 Transcript missense_variant 885/3812 611/2529 204/842 H/R cAc/cGc 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 tolerated(0.15) 5/15 PROSITE_profiles:PS50835,hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.97001 1 1 1 1 0 G 3 3 3 176868854 176868854 A G 1 0 0 0 0 1 0 0 0 17515 159 6 5 5 UNC5A 5 176868854 Missense_Mutation SNP A 11LU022_T 4198928 176868854 4669405 326 964 DDX41 0 . GRCh38 5 177513388 177513388 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.1195G>T p.Gly399Trp p.G399W ENST00000507955 11/17 224 174 50 309 309 0 strelka-varscan-mutect DDX41,missense_variant,p.Gly399Trp,ENST00000507955,NM_016222.2;DDX41,missense_variant,p.Gly417Trp,ENST00000330503,;DOK3,upstream_gene_variant,,ENST00000312943,NM_001144875.1;DOK3,upstream_gene_variant,,ENST00000377112,NM_001144876.1;DOK3,upstream_gene_variant,,ENST00000501403,NM_001308236.1,NM_001308235.1;DOK3,upstream_gene_variant,,ENST00000357198,NM_024872.2;DOK3,upstream_gene_variant,,ENST00000510380,;DDX41,downstream_gene_variant,,ENST00000629036,;DOK3,upstream_gene_variant,,ENST00000509310,;DOK3,upstream_gene_variant,,ENST00000506493,;DOK3,upstream_gene_variant,,ENST00000502885,;DOK3,upstream_gene_variant,,ENST00000510389,;DOK3,upstream_gene_variant,,ENST00000510898,;DDX41,downstream_gene_variant,,ENST00000625286,;DDX41,downstream_gene_variant,,ENST00000506965,;DDX41,non_coding_transcript_exon_variant,,ENST00000505081,;DDX41,non_coding_transcript_exon_variant,,ENST00000503078,;DDX41,non_coding_transcript_exon_variant,,ENST00000507900,;DDX41,non_coding_transcript_exon_variant,,ENST00000504807,;DDX41,non_coding_transcript_exon_variant,,ENST00000511040,;DDX41,non_coding_transcript_exon_variant,,ENST00000512027,;DOK3,upstream_gene_variant,,ENST00000500323,;DDX41,downstream_gene_variant,,ENST00000515562,;DOK3,upstream_gene_variant,,ENST00000502380,;DDX41,downstream_gene_variant,,ENST00000512431,;DDX41,downstream_gene_variant,,ENST00000509576,;DDX41,downstream_gene_variant,,ENST00000508279,;DDX41,upstream_gene_variant,,ENST00000512334,;DDX41,downstream_gene_variant,,ENST00000504781,;DDX41,downstream_gene_variant,,ENST00000510171,;DOK3,upstream_gene_variant,,ENST00000512660,;DDX41,downstream_gene_variant,,ENST00000513562,; A ENST00000507955 Transcript missense_variant 1719/2607 1195/1869 399/622 G/W Ggg/Tgg COSM591522 1 -1 DDX41 HGNC HGNC:18674 protein_coding YES CCDS4427.1 ENSP00000422753 Q9UJV9 UPI0000125164 NM_016222.2 deleterious(0) 11/17 hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF20,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 177513388 177513388 C A 1 0 0 0 0 1 0 0 0 4164 623 22 2 2 DDX41 5 177513388 Missense_Mutation SNP C 11LU022_T 644534 177513388 4024871 327 965 GRM6 0 . GRCh38 5 178989337 178989337 + Missense_Mutation SNP A A T rs769552577 11LU022_T 11LU022_N A A c.1081T>A p.Trp361Arg p.W361R ENST00000231188 5/10 252 209 43 427 427 0 strelka-varscan-mutect GRM6,missense_variant,p.Trp361Arg,ENST00000231188,NM_000843.3;GRM6,missense_variant,p.Trp361Arg,ENST00000517717,;RP11-281O15.4,intron_variant,,ENST00000519491,;GRM6,upstream_gene_variant,,ENST00000518082,;GRM6,upstream_gene_variant,,ENST00000519003,; T ENST00000231188 Transcript missense_variant 1260/6143 1081/2634 361/877 W/R Tgg/Agg rs769552577,COSM4585759 1 -1 GRM6 HGNC HGNC:4598 protein_coding YES CCDS4442.1 ENSP00000231188 O15303 UPI000013C947 NM_000843.3 deleterious(0) 5/10 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF24,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs769552577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 178989337 178989337 A T 1 0 0 0 0 1 0 0 0 6683 188 7 4 4 GRM6 5 178989337 Missense_Mutation SNP A 11LU022_T 1475949 178989337 2548922 328 966 MAK 0 . GRCh38 6 10802041 10802041 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.682T>A p.Tyr228Asn p.Y228N ENST00000354489 8/15 160 145 15 166 166 0 strelka-varscan-mutect MAK,missense_variant,p.Tyr228Asn,ENST00000313243,;MAK,missense_variant,p.Tyr228Asn,ENST00000354489,NM_001242957.1;MAK,missense_variant,p.Tyr228Asn,ENST00000474039,NM_005906.4;MAK,missense_variant,p.Tyr228Asn,ENST00000536370,NM_001242385.1;MAK,missense_variant,p.Tyr228Asn,ENST00000538030,;TMEM14B,intron_variant,,ENST00000489137,;TMEM14B,intron_variant,,ENST00000463448,;RP11-637O19.3,intron_variant,,ENST00000480294,;TMEM14B,intron_variant,,ENST00000473166,;TMEM14B,intron_variant,,ENST00000460341,;TMEM14B,intron_variant,,ENST00000473807,;TMEM14B,intron_variant,,ENST00000463100,;TMEM14B,intron_variant,,ENST00000467229,;TMEM14B,intron_variant,,ENST00000478732,; T ENST00000354489 Transcript missense_variant 964/3941 682/1947 228/648 Y/N Tac/Aac 1 -1 MAK HGNC HGNC:6816 protein_coding YES CCDS75399.1 ENSP00000346484 P20794 UPI000217CBBA NM_001242957.1 deleterious(0) 8/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF194,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 10802041 10802041 A T 1 0 0 0 0 1 0 0 0 9116 449 16 4 4 MAK 6 10802041 Missense_Mutation SNP A 11LU022_T 10802041 160003938 329 967 RBM24 0 . GRCh38 6 17292041 17292041 + Silent SNP C C A rs552546103 11LU022_T 11LU022_N C C c.633C>A p.= p.A211A ENST00000379052 4/4 90 84 6 64 64 0 strelka-mutect RBM24,synonymous_variant,p.=,ENST00000379052,NM_001143942.1;RBM24,synonymous_variant,p.=,ENST00000318204,NM_153020.2;RBM24,synonymous_variant,p.=,ENST00000425446,NM_001143941.1;RBM24,synonymous_variant,p.=,ENST00000503965,;RBM24,3_prime_UTR_variant,,ENST00000509686,;RBM24,non_coding_transcript_exon_variant,,ENST00000508508,;RBM24,non_coding_transcript_exon_variant,,ENST00000510826,;RBM24,non_coding_transcript_exon_variant,,ENST00000504055,; A ENST00000379052 Transcript synonymous_variant 869/2703 633/711 211/236 A gcC/gcA rs552546103,COSM4625725,COSM4625726 1 1 RBM24 HGNC HGNC:21539 protein_coding YES CCDS47378.1 ENSP00000368341 Q9BX46 A8KAI7 UPI000006E912 NM_001143942.1 4/4 Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs552546103 . 0 204 6 0 0 0 0 0 -12.66782 0.9999996 1 1 1 0 A 2 1 3 17292041 17292041 C A 1 0 0 0 0 0 0 0 1 13290 639 23 1 1 RBM24 6 17292041 Silent SNP C 11LU022_T 6490000 17292041 153513938 330 968 ZSCAN9 0 . GRCh38 6 28227861 28227861 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.592G>T p.Val198Phe p.V198F ENST00000527436 3/3 166 152 14 168 168 0 strelka-varscan-mutect ZSCAN9,missense_variant,p.Val198Phe,ENST00000527436,;ZSCAN9,3_prime_UTR_variant,,ENST00000531981,;ZSCAN9,intron_variant,,ENST00000425468,NM_001199479.1;ZSCAN9,intron_variant,,ENST00000252207,NM_006299.4;ZSCAN9,intron_variant,,ENST00000531979,NM_001199480.1;ZSCAN9,intron_variant,,ENST00000527844,;ZSCAN9,intron_variant,,ENST00000526391,;ZSCAN9,downstream_gene_variant,,ENST00000531941,; T ENST00000527436 Transcript missense_variant 693/2062 592/786 198/261 V/F Gtt/Ttt 1 1 ZSCAN9 HGNC HGNC:12984 protein_coding ENSP00000433468 A0A0B4J224 UPI000035DB52 tolerated(0.06) 3/3 MODERATE SNV 1 1 PASS rs1212777180 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 28227861 28227861 G T 1 0 0 0 0 1 0 0 0 18840 1377 48 2 2 ZSCAN9 6 28227861 Missense_Mutation SNP G 11LU022_T 10935820 28227861 142578118 331 969 NKAPL 0 . GRCh38 6 28259551 28259551 + Frame_Shift_Del DEL G G - novel 11LU022_T 11LU022_N G G c.182delG p.Gly61AlafsTer62 p.G61Afs*62 ENST00000343684 1/1 125 113 12 116 116 0 sindel-varindel-pindel NKAPL,frameshift_variant,p.Gly61AlafsTer62,ENST00000343684,NM_001007531.2; - ENST00000343684 Transcript frameshift_variant 232/1639 180/1209 60/402 V/X gtG/gt 1 1 NKAPL HGNC HGNC:21584 protein_coding YES CCDS34353.1 ENSP00000345716 Q5M9Q1 UPI0000072A86 NM_001007531.2 1/1 hmmpanther:PTHR13087,hmmpanther:PTHR13087:SF3 HIGH 1 deletion 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.99984 1 1 1 1 0 - 7 5 3 28259551 28259551 G - 1 0 1 0 1 0 0 0 0 10475 1335 47 0 0 NKAPL 6 28259551 Frame_Shift_Del DEL G 11LU022_T 31690 28259551 142546428 332 970 OR14J1 0 . GRCh38 6 29307470 29307470 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.781C>A p.Pro261Thr p.P261T ENST00000377160 1/1 206 186 20 186 186 0 strelka-varscan-mutect OR14J1,missense_variant,p.Pro261Thr,ENST00000377160,NM_030946.1; A ENST00000377160 Transcript missense_variant 781/966 781/966 261/321 P/T Cct/Act 1 1 OR14J1 HGNC HGNC:13971 protein_coding YES CCDS34362.1 ENSP00000366365 Q9UGF5 A0A126GW10 UPI0000041CEC NM_030946.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF42,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs948194645 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 29307470 29307470 C A 1 0 0 0 0 1 0 0 0 11025 739 26 2 2 OR14J1 6 29307470 Missense_Mutation SNP C 11LU022_T 1047919 29307470 141498509 333 971 OR10C1 0 . GRCh38 6 29440811 29440811 + Missense_Mutation SNP G G T rs754635593 11LU022_T 11LU022_N G G c.796G>T p.Asp266Tyr p.D266Y ENST00000444197 1/1 341 311 30 253 253 0 strelka-varscan-mutect OR10C1,missense_variant,p.Asp266Tyr,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Asp268Tyr,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript missense_variant 1506/1649 796/939 266/312 D/Y Gat/Tat rs754635593,COSM595728 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs754635593 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 29440811 29440811 G T 1 0 0 0 0 1 0 0 0 10973 1058 37 1 1 OR10C1 6 29440811 Missense_Mutation SNP G 11LU022_T 133341 29440811 141365168 334 972 MAS1L 0 . GRCh38 6 29487806 29487806 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.97A>T p.Ser33Cys p.S33C ENST00000377127 1/1 190 130 60 216 216 0 strelka-varscan-mutect MAS1L,missense_variant,p.Ser33Cys,ENST00000377127,NM_052967.1;RPS17P1,downstream_gene_variant,,ENST00000396783,; A ENST00000377127 Transcript missense_variant 151/1260 97/1137 33/378 S/C Agt/Tgt 1 -1 MAS1L HGNC HGNC:13961 protein_coding YES CCDS4661.1 ENSP00000366331 P35410 W8W3J1 UPI000003B44C NM_052967.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF12 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 29487806 29487806 T A 1 0 0 0 0 1 0 0 0 9247 1580 55 4 4 MAS1L 6 29487806 Missense_Mutation SNP T 11LU022_T 46995 29487806 141318173 335 973 PBX2 0 . GRCh38 6 32187244 32187244 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.1022C>T p.Ala341Val p.A341V ENST00000375050 6/9 137 99 38 166 166 0 strelka-varscan-mutect PBX2,missense_variant,p.Ala341Val,ENST00000375050,NM_002586.4;AGER,upstream_gene_variant,,ENST00000375069,NM_001206929.1;AGER,upstream_gene_variant,,ENST00000438221,NM_001206934.1;AGER,upstream_gene_variant,,ENST00000375076,NM_001206932.1,NM_001136.4;GPSM3,downstream_gene_variant,,ENST00000375040,NM_001276501.1;AGER,upstream_gene_variant,,ENST00000375070,;GPSM3,downstream_gene_variant,,ENST00000487761,;GPSM3,downstream_gene_variant,,ENST00000375043,NM_022107.1;AGER,upstream_gene_variant,,ENST00000375055,NM_001206936.1,NM_001206954.1,NM_001206966.1,NM_001206940.1;AGER,upstream_gene_variant,,ENST00000375067,NM_172197.2;GPSM3,downstream_gene_variant,,ENST00000619085,;AGER,upstream_gene_variant,,ENST00000620802,;AGER,upstream_gene_variant,,ENST00000450110,;AGER,upstream_gene_variant,,ENST00000375056,;AGER,upstream_gene_variant,,ENST00000375065,;AGER,upstream_gene_variant,,ENST00000538695,;XXbac-BPG300A18.13,upstream_gene_variant,,ENST00000559458,;PBX2,splice_region_variant,,ENST00000495300,;PBX2,non_coding_transcript_exon_variant,,ENST00000478678,;PBX2,non_coding_transcript_exon_variant,,ENST00000496171,;AGER,upstream_gene_variant,,ENST00000484849,;GPSM3,downstream_gene_variant,,ENST00000472768,;AGER,upstream_gene_variant,,ENST00000473619,;AGER,upstream_gene_variant,,ENST00000488669,;PBX2,downstream_gene_variant,,ENST00000480254,; A ENST00000375050 Transcript missense_variant,splice_region_variant 1293/3205 1022/1293 341/430 A/V gCa/gTa 1 -1 PBX2 HGNC HGNC:8633 protein_coding YES CCDS4748.1 ENSP00000364190 P40425 A0A024RCR3 UPI00001313B2 NM_002586.4 tolerated(0.12) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF50 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 32187244 32187244 G A 1 0 0 0 0 1 0 0 0 11580 1333 46 3 3 PBX2 6 32187244 Missense_Mutation SNP G 11LU022_T 2699438 32187244 138618735 336 974 COL11A2 0 . GRCh38 6 33170822 33170822 + Silent SNP G G C novel 11LU022_T 11LU022_N G G c.3204C>G p.= p.P1068P ENST00000374708 44/64 371 245 126 486 486 0 strelka-varscan-mutect COL11A2,synonymous_variant,p.=,ENST00000341947,NM_080680.2;COL11A2,synonymous_variant,p.=,ENST00000374708,NM_080681.2;COL11A2,synonymous_variant,p.=,ENST00000361917,NM_080679.2;COL11A2,intron_variant,,ENST00000477772,; C ENST00000374708 Transcript synonymous_variant 3463/6209 3204/4953 1068/1650 P ccC/ccG 1 -1 COL11A2 HGNC HGNC:2187 protein_coding YES CCDS43452.1 ENSP00000363840 Q4VXY6 UPI000013E9A5 NM_080681.2 44/64 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF509,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 33170822 33170822 G C 1 0 0 0 0 0 0 0 1 3456 1335 47 4 4 COL11A2 6 33170822 Silent SNP G 11LU022_T 983578 33170822 137635157 337 975 ITPR3 0 . GRCh38 6 33680652 33680652 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.4448C>T p.Pro1483Leu p.P1483L ENST00000374316 34/59 135 93 42 154 154 0 strelka-varscan-mutect ITPR3,missense_variant,p.Pro1483Leu,ENST00000374316,;ITPR3,missense_variant,p.Pro1483Leu,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript missense_variant 5508/9870 4448/8016 1483/2671 P/L cCa/cTa 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 deleterious(0) 34/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 33680652 33680652 C T 1 0 0 0 0 1 0 0 0 7828 594 21 3 3 ITPR3 6 33680652 Missense_Mutation SNP C 11LU022_T 509830 33680652 137125327 338 976 C6orf106 0 . GRCh38 6 34606585 34606585 + Silent SNP T T G novel 11LU022_T 11LU022_N T T c.831A>C p.= p.A277A ENST00000374023 4/5 142 123 19 139 139 0 strelka-varscan-mutect C6orf106,synonymous_variant,p.=,ENST00000374023,NM_024294.3;C6orf106,synonymous_variant,p.=,ENST00000374026,NM_022758.5;C6orf106,synonymous_variant,p.=,ENST00000374021,; G ENST00000374023 Transcript synonymous_variant 1075/4418 831/897 277/298 A gcA/gcC 1 -1 C6orf106 HGNC HGNC:21215 protein_coding YES CCDS4796.1 ENSP00000363135 Q9H6K1 A0A024RCW2 UPI000006F934 NM_024294.3 4/5 hmmpanther:PTHR20930 LOW 1 SNV 1 1 PASS rs1188129162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 34606585 34606585 T G 1 0 0 0 0 0 0 0 1 2114 1799 63 5 5 C6orf106 6 34606585 Silent SNP T 11LU022_T 925933 34606585 136199394 339 977 GUCA1A 0 . GRCh38 6 42178427 42178427 + Nonsense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.349C>T p.Gln117Ter p.Q117* ENST00000394237 4/6 238 185 53 299 299 0 strelka-varscan-mutect GUCA1A,stop_gained,p.Gln117Ter,ENST00000394237,NM_001319061.1;GUCA1A,stop_gained,p.Gln113Ter,ENST00000541991,;GUCA1A,stop_gained,p.Gln117Ter,ENST00000053469,NM_000409.3;GUCA1A,stop_gained,p.Gln117Ter,ENST00000372958,;GUCA1A,downstream_gene_variant,,ENST00000418175,; T ENST00000394237 Transcript stop_gained,splice_region_variant 1325/2233 349/606 117/201 Q/* Cag/Tag 1 1 GUCA1A HGNC HGNC:4678 protein_coding YES CCDS4864.1 ENSP00000377784 P43080 UPI0000001C22 NM_001319061.1 4/6 PROSITE_profiles:PS50222,hmmpanther:PTHR23055:SF13,hmmpanther:PTHR23055,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473,Prints_domain:PR00450 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 42178427 42178427 C T 1 0 0 0 0 0 1 0 0 6769 608 21 3 3 GUCA1A 6 42178427 Nonsense_Mutation SNP C 11LU022_T 7571842 42178427 128627552 340 978 TMEM151B 0 . GRCh38 6 44275796 44275796 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.970T>A p.Tyr324Asn p.Y324N ENST00000451188 3/3 84 64 20 133 133 0 strelka-varscan-mutect TMEM151B,missense_variant,p.Tyr324Asn,ENST00000451188,NM_001137560.1;TMEM151B,intron_variant,,ENST00000438774,;TCTE1,downstream_gene_variant,,ENST00000371505,NM_182539.3;TCTE1,downstream_gene_variant,,ENST00000371504,;RP11-444E17.6,intron_variant,,ENST00000505802,; A ENST00000451188 Transcript missense_variant 1247/4895 970/1701 324/566 Y/N Tac/Aac 1 1 TMEM151B HGNC HGNC:21315 protein_coding YES CCDS47437.1 ENSP00000393161 Q8IW70 UPI00006C0A4E NM_001137560.1 tolerated(0.08) 3/3 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF4 MODERATE SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 44275796 44275796 T A 1 0 0 0 0 1 0 0 0 16513 1522 53 4 4 TMEM151B 6 44275796 Missense_Mutation SNP T 11LU022_T 2097369 44275796 126530183 341 979 AL161905.1 0 . GRCh38 6 44953368 44953368 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.776G>C p.Gly259Ala p.G259A ENST00000371460 11/13 179 147 32 229 229 0 strelka-varscan-mutect SUPT3H,missense_variant,p.Gly215Ala,ENST00000306867,;SUPT3H,missense_variant,p.Gly259Ala,ENST00000371460,NM_181356.2;SUPT3H,missense_variant,p.Gly248Ala,ENST00000371459,NM_003599.3;SUPT3H,missense_variant,p.Gly186Ala,ENST00000637480,;SUPT3H,missense_variant,p.Gly31Ala,ENST00000371458,;AL161905.1,missense_variant,p.Gly96Ala,ENST00000637763,NM_001261823.1;SUPT3H,missense_variant,p.Gly248Ala,ENST00000475057,; G ENST00000371460 Transcript missense_variant 1094/2389 776/987 259/328 G/A gGg/gCg 1 -1 SUPT3H HGNC HGNC:11466 protein_coding YES CCDS34466.1 ENSP00000360515 O75486 UPI000018CE7C NM_181356.2 deleterious(0.05) 11/13 hmmpanther:PTHR11380:SF3,hmmpanther:PTHR11380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 44953368 44953368 C G 1 0 0 0 0 1 0 0 0 574 623 22 4 4 AL161905.1 6 44953368 Missense_Mutation SNP C 11LU022_T 677572 44953368 125852611 342 980 PTCHD4 0 . GRCh38 6 47879722 47879722 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.1122T>A p.= p.S374S ENST00000339488 3/3 184 164 20 185 185 0 strelka-varscan-mutect PTCHD4,synonymous_variant,p.=,ENST00000339488,NM_001013732.3; T ENST00000339488 Transcript synonymous_variant 1156/2850 1122/2541 374/846 S tcT/tcA 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 3/3 Gene3D:2j8sB01,Pfam_domain:PF02460,PROSITE_profiles:PS50156,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15,Superfamily_domains:SSF82866,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 47879722 47879722 A T 1 0 0 0 0 0 0 0 1 12887 407 15 4 4 PTCHD4 6 47879722 Silent SNP A 11LU022_T 2926354 47879722 122926257 343 981 MUT 0 . GRCh38 6 49451672 49451672 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1126G>T p.Ala376Ser p.A376S ENST00000274813 6/13 248 218 30 260 260 0 strelka-varscan-mutect MUT,missense_variant,p.Ala376Ser,ENST00000274813,NM_000255.3; A ENST00000274813 Transcript missense_variant 1254/3749 1126/2253 376/750 A/S Gca/Tca 1 -1 MUT HGNC HGNC:7526 protein_coding YES CCDS4924.1 ENSP00000274813 P22033 A0A024RD82 UPI000013DA28 NM_000255.3 tolerated_low_confidence(0.09) 6/13 hmmpanther:PTHR23408,hmmpanther:PTHR23408:SF1,Gene3D:3.20.20.240,TIGRFAM_domain:TIGR00641,Pfam_domain:PF01642,Superfamily_domains:SSF51703 MODERATE 1 SNV 1 1 PASS rs1369851738 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49451672 49451672 C A 1 0 0 0 0 1 0 0 0 9989 739 26 2 2 MUT 6 49451672 Missense_Mutation SNP C 11LU022_T 1571950 49451672 121354307 344 982 RHAG 0 . GRCh38 6 49614804 49614804 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.690T>A p.= p.A230A ENST00000371175 5/10 387 305 82 442 442 0 strelka-varscan-mutect RHAG,synonymous_variant,p.=,ENST00000371175,NM_000324.2;RHAG,synonymous_variant,p.=,ENST00000229810,;RHAG,synonymous_variant,p.=,ENST00000618248,; T ENST00000371175 Transcript synonymous_variant 717/1912 690/1230 230/409 A gcT/gcA 1 -1 RHAG HGNC HGNC:10006 protein_coding YES CCDS4927.1 ENSP00000360217 Q02094 UPI000006D18F NM_000324.2 5/10 hmmpanther:PTHR11730:SF32,hmmpanther:PTHR11730,Pfam_domain:PF00909,Gene3D:1.10.3430.10,Superfamily_domains:0044218 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 49614804 49614804 A T 1 0 0 0 0 0 0 0 1 13487 175 7 4 4 RHAG 6 49614804 Silent SNP A 11LU022_T 163132 49614804 121191175 345 983 PGK2 0 . GRCh38 6 49786992 49786992 + Silent SNP G G T rs570804051 11LU022_T 11LU022_N G G c.196C>A p.= p.R66R ENST00000304801 1/1 148 128 20 130 130 0 strelka-varscan-mutect PGK2,synonymous_variant,p.=,ENST00000304801,NM_138733.4; T ENST00000304801 Transcript synonymous_variant 316/1657 196/1254 66/417 R Cgg/Agg rs570804051 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 1/1 Gene3D:3.40.50.1260,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 LOW 1 SNV 1 PASS rs570804051 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 49786992 49786992 G T 1 0 0 0 0 0 0 0 1 11880 1057 37 1 1 PGK2 6 49786992 Silent SNP G 11LU022_T 172188 49786992 121018987 346 984 DEFB113 0 . GRCh38 6 49968799 49968799 + Nonsense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.127A>T p.Lys43Ter p.K43* ENST00000398718 2/2 196 180 16 164 164 0 strelka-varscan-mutect DEFB113,stop_gained,p.Lys43Ter,ENST00000398718,NM_001037729.1;DEFB114,upstream_gene_variant,,ENST00000322066,NM_001037499.1; A ENST00000398718 Transcript stop_gained 127/249 127/249 43/82 K/* Aag/Tag 1 -1 DEFB113 HGNC HGNC:18094 protein_coding YES CCDS43472.1 ENSP00000381703 Q30KQ7 UPI00005E4A72 NM_001037729.1 2/2 hmmpanther:PTHR39411:SF1,hmmpanther:PTHR39411,Pfam_domain:PF13841 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 49968799 49968799 T A 1 0 0 0 0 0 1 0 0 4205 1821 63 4 4 DEFB113 6 49968799 Nonsense_Mutation SNP T 11LU022_T 181807 49968799 120837180 347 985 TFAP2B 0 . GRCh38 6 50823449 50823449 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.124C>A p.Gln42Lys p.Q42K ENST00000393655 2/7 262 235 27 279 279 0 strelka-varscan-mutect TFAP2B,missense_variant,p.Gln42Lys,ENST00000393655,NM_003221.3;TFAP2B,missense_variant,p.Gln40Lys,ENST00000344788,;TFAP2B,non_coding_transcript_exon_variant,,ENST00000489228,; A ENST00000393655 Transcript missense_variant 293/5773 124/1383 42/460 Q/K Cag/Aag 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 tolerated(0.07) 2/7 Prints_domain:PR01750,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 50823449 50823449 C A 1 0 0 0 0 1 0 0 0 16221 595 21 2 2 TFAP2B 6 50823449 Missense_Mutation SNP C 11LU022_T 854650 50823449 119982530 348 986 PKHD1 0 . GRCh38 6 52050221 52050221 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2215C>A p.Pro739Thr p.P739T ENST00000371117 22/67 456 405 51 538 538 0 strelka-varscan-mutect PKHD1,missense_variant,p.Pro739Thr,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Pro739Thr,ENST00000340994,NM_170724.2; T ENST00000371117 Transcript missense_variant 2491/16282 2215/12225 739/4074 P/T Ccg/Acg 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.01) 22/67 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 52050221 52050221 G T 1 0 0 0 0 1 0 0 0 12067 1174 41 2 2 PKHD1 6 52050221 Missense_Mutation SNP G 11LU022_T 1226772 52050221 118755758 349 987 IL17A 0 . GRCh38 6 52189068 52189068 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.244C>A p.Pro82Thr p.P82T ENST00000340057 3/3 189 136 53 168 168 0 strelka-varscan-mutect IL17A,missense_variant,p.Pro82Thr,ENST00000340057,NM_002190.2; A ENST00000340057 Transcript missense_variant 289/1859 244/468 82/155 P/T Cct/Act 1 1 IL17A HGNC HGNC:5981 protein_coding YES CCDS4937.1 ENSP00000344192 Q16552 UPI0000047D95 NM_002190.2 deleterious(0.02) 3/3 hmmpanther:PTHR21295:SF2,hmmpanther:PTHR21295,Pfam_domain:PF06083,Gene3D:2.10.90.10,Superfamily_domains:SSF57501,Prints_domain:PR01932 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 52189068 52189068 C A 1 0 0 0 0 1 0 0 0 7542 623 22 2 2 IL17A 6 52189068 Missense_Mutation SNP C 11LU022_T 138847 52189068 118616911 350 988 GCM1 0 . GRCh38 6 53130918 53130918 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.455A>G p.His152Arg p.H152R ENST00000259803 5/6 123 113 10 159 159 0 strelka-mutect GCM1,missense_variant,p.His152Arg,ENST00000259803,NM_003643.3;RP11-506E9.3,upstream_gene_variant,,ENST00000566420,; C ENST00000259803 Transcript missense_variant 667/2765 455/1311 152/436 H/R cAt/cGt 1 -1 GCM1 HGNC HGNC:4197 protein_coding YES CCDS4950.1 ENSP00000259803 Q9NP62 UPI0000073F99 NM_003643.3 deleterious(0) 5/6 Superfamily_domains:0041800,PD014393,Pfam_domain:PF03615,PROSITE_profiles:PS50807,hmmpanther:PTHR12414,hmmpanther:PTHR12414:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 53130918 53130918 T C 1 0 0 0 0 1 0 0 0 6167 1464 51 5 5 GCM1 6 53130918 Missense_Mutation SNP T 11LU022_T 941850 53130918 117675061 351 989 HCRTR2 0 . GRCh38 6 55263727 55263727 + Missense_Mutation SNP T T A 11LU022_T 11LU022_N T T c.667T>A p.Tyr223Asn p.Y223N ENST00000615358 5/8 132 115 17 180 180 0 strelka-varscan-mutect HCRTR2,missense_variant,p.Tyr223Asn,ENST00000615358,;HCRTR2,missense_variant,p.Tyr223Asn,ENST00000370862,NM_001526.3; A ENST00000615358 Transcript missense_variant 1130/1936 667/1335 223/444 Y/N Tac/Aac COSM1080418 1 1 HCRTR2 HGNC HGNC:4849 protein_coding YES CCDS4956.1 ENSP00000477548 O43614 S4X0W3 UPI000013D07A deleterious(0) 5/8 PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF75,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01064,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 55263727 55263727 T A 1 0 0 0 0 1 0 0 0 6889 1638 57 4 4 HCRTR2 6 55263727 Missense_Mutation SNP T 11LU022_T 2132809 55263727 115542252 352 990 KIAA1586 0 . GRCh38 6 57054306 57054306 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1807A>T p.Arg603Trp p.R603W ENST00000370733 4/4 29 23 6 42 42 0 strelka-varscan-mutect KIAA1586,missense_variant,p.Arg603Trp,ENST00000370733,NM_001286276.1,NM_020931.3,NM_001286275.1;KIAA1586,missense_variant,p.Arg576Trp,ENST00000545356,NM_001286274.1;KIAA1586,downstream_gene_variant,,ENST00000488682,; T ENST00000370733 Transcript missense_variant 2014/2933 1807/2364 603/787 R/W Agg/Tgg 1 1 KIAA1586 HGNC HGNC:21360 protein_coding YES CCDS34480.1 ENSP00000359768 Q9HCI6 UPI0000074573 NM_001286276.1,NM_020931.3,NM_001286275.1 tolerated(0.06) 4/4 hmmpanther:PTHR23232,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -16.72097 1 1 1 1 0 T 3 4 3 57054306 57054306 A T 1 0 0 0 0 1 0 0 0 8123 411 15 4 4 KIAA1586 6 57054306 Missense_Mutation SNP A 11LU022_T 1790579 57054306 113751673 353 991 ADGRB3 0 . GRCh38 6 68936617 68936617 + Missense_Mutation SNP G G C rs754128610 11LU022_T 11LU022_N G G c.967G>C p.Gly323Arg p.G323R ENST00000370598 5/32 176 116 60 155 155 0 strelka-varscan-mutect ADGRB3,missense_variant,p.Gly323Arg,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Gly323Arg,ENST00000546190,; C ENST00000370598 Transcript missense_variant 1788/6010 967/4569 323/1522 G/R Ggg/Cgg rs754128610,COSM5046629 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 deleterious(0.02) 5/32 PROSITE_profiles:PS50092,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754128610 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 68936617 68936617 G C 1 0 0 0 0 1 0 0 0 357 1116 39 4 4 ADGRB3 6 68936617 Missense_Mutation SNP G 11LU022_T 11882311 68936617 101869362 354 992 ADGRB3 0 . GRCh38 6 69018456 69018456 + Silent SNP G G T 11LU022_T 11LU022_N G G c.2064G>T p.= p.G688G ENST00000370598 13/32 60 45 15 120 120 0 strelka-varscan-mutect ADGRB3,synonymous_variant,p.=,ENST00000370598,NM_001704.2;ADGRB3,synonymous_variant,p.=,ENST00000546190,; T ENST00000370598 Transcript synonymous_variant 2885/6010 2064/4569 688/1522 G ggG/ggT COSM4851449 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 13/32 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF16489 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 69018456 69018456 G T 1 0 0 0 0 0 0 0 1 357 1161 41 2 2 ADGRB3 6 69018456 Silent SNP G 11LU022_T 81839 69018456 101787523 355 993 ADGRB3 0 . GRCh38 6 69339009 69339009 + Silent SNP C C T rs138734026 11LU022_T 11LU022_N C C c.3282C>T p.= p.N1094N ENST00000370598 25/32 196 179 17 210 209 1 strelka-varscan-mutect ADGRB3,synonymous_variant,p.=,ENST00000370598,NM_001704.2;ADGRB3,synonymous_variant,p.=,ENST00000546190,;ADGRB3,synonymous_variant,p.=,ENST00000238918,; T ENST00000370598 Transcript synonymous_variant 4103/6010 3282/4569 1094/1522 N aaC/aaT rs138734026,COSM3928577 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 25/32 Low_complexity_(Seg):seg,PROSITE_profiles:PS50261,Pfam_domain:PF00002 0,1 LOW 1 SNV 1 0,1 1 PASS rs138734026 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 69339009 69339009 C T 1 0 0 0 0 0 0 0 1 357 550 19 1 1 ADGRB3 6 69339009 Silent SNP C 11LU022_T 320553 69339009 101466970 356 994 COL19A1 0 . GRCh38 6 70207238 70207238 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.3393T>A p.= p.P1131P ENST00000620364 51/51 138 97 41 114 114 0 strelka-varscan-mutect COL19A1,synonymous_variant,p.=,ENST00000620364,NM_001858.5; A ENST00000620364 Transcript synonymous_variant 3495/6233 3393/3429 1131/1142 P ccT/ccA 1 1 COL19A1 HGNC HGNC:2196 protein_coding YES CCDS4970.1 ENSP00000480474 Q14993 UPI000004F1E3 NM_001858.5 51/51 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 70207238 70207238 T A 1 0 0 0 0 0 0 0 1 3464 1567 55 4 4 COL19A1 6 70207238 Silent SNP T 11LU022_T 868229 70207238 100598741 357 995 KCNQ5 0 . GRCh38 6 73194499 73194499 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.1941A>G p.= p.Q647Q ENST00000342056 15/15 107 94 13 97 97 0 strelka-varscan-mutect KCNQ5,synonymous_variant,p.=,ENST00000342056,NM_001160132.1,NM_001160133.1;KCNQ5,synonymous_variant,p.=,ENST00000355635,;KCNQ5,synonymous_variant,p.=,ENST00000402622,;KCNQ5,synonymous_variant,p.=,ENST00000355194,;KCNQ5,synonymous_variant,p.=,ENST00000403813,;KCNQ5,synonymous_variant,p.=,ENST00000370398,NM_019842.3;KCNQ5,synonymous_variant,p.=,ENST00000414165,;KCNQ5,synonymous_variant,p.=,ENST00000628967,NM_001160134.1;KCNQ5,synonymous_variant,p.=,ENST00000629977,NM_001160130.1; G ENST00000342056 Transcript synonymous_variant 2339/6688 1941/2856 647/951 Q caA/caG 1 1 KCNQ5 HGNC HGNC:6299 protein_coding YES CCDS55034.1 ENSP00000345055 Q9NR82 UPI000155D644 NM_001160132.1,NM_001160133.1 15/15 Pfam_domain:PF03520 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 73194499 73194499 A G 1 0 0 0 0 0 0 0 1 8002 40 2 5 5 KCNQ5 6 73194499 Silent SNP A 11LU022_T 2987261 73194499 97611480 358 996 TTK 0 . GRCh38 6 80011517 80011517 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.697G>T p.Gly233Ter p.G233* ENST00000369798 6/22 116 89 27 95 95 0 strelka-varscan-mutect TTK,stop_gained,p.Gly233Ter,ENST00000509894,;TTK,stop_gained,p.Gly233Ter,ENST00000230510,NM_001166691.1;TTK,stop_gained,p.Gly233Ter,ENST00000369798,NM_003318.4;TTK,downstream_gene_variant,,ENST00000504040,;TTK,downstream_gene_variant,,ENST00000511260,;TTK,downstream_gene_variant,,ENST00000502580,;TTK,downstream_gene_variant,,ENST00000627129,;TTK,upstream_gene_variant,,ENST00000515751,;TTK,non_coding_transcript_exon_variant,,ENST00000430061,;TTK,downstream_gene_variant,,ENST00000509313,; T ENST00000369798 Transcript stop_gained 808/3010 697/2574 233/857 G/* Gga/Tga 1 1 TTK HGNC HGNC:12401 protein_coding YES CCDS4993.1 ENSP00000358813 P33981 UPI0000073C7B NM_003318.4 6/22 hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 80011517 80011517 G T 1 0 0 0 0 0 1 0 0 17232 1001 35 2 2 TTK 6 80011517 Nonsense_Mutation SNP G 11LU022_T 6817018 80011517 90794462 359 997 SNAP91 0 . GRCh38 6 83641164 83641164 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.697G>T p.Ala233Ser p.A233S ENST00000439399 8/30 55 38 17 79 79 0 strelka-varscan-mutect SNAP91,missense_variant,p.Ala233Ser,ENST00000521485,;SNAP91,missense_variant,p.Ala233Ser,ENST00000439399,NM_014841.2;SNAP91,missense_variant,p.Ala233Ser,ENST00000369694,NM_001242792.1;SNAP91,missense_variant,p.Ala233Ser,ENST00000195649,NM_001256718.1;SNAP91,missense_variant,p.Ala233Ser,ENST00000521743,;SNAP91,missense_variant,p.Ala233Ser,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,missense_variant,p.Ala233Ser,ENST00000520213,NM_001242794.1;SNAP91,missense_variant,p.Ala233Ser,ENST00000521931,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,; A ENST00000439399 Transcript missense_variant 1014/4452 697/2724 233/907 A/S Gct/Tct 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 deleterious(0.05) 8/30 hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4,Gene3D:1hf8A02,Pfam_domain:PF07651,Superfamily_domains:SSF89009 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 83641164 83641164 C A 1 0 0 0 0 1 0 0 0 15154 710 25 2 2 SNAP91 6 83641164 Missense_Mutation SNP C 11LU022_T 3629647 83641164 87164815 360 998 CEP162 0 . GRCh38 6 84155511 84155511 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.2782-1G>T p.X928_splice ENST00000403245 107 71 36 110 110 0 strelka-varscan-mutect CEP162,splice_acceptor_variant,,ENST00000403245,NM_014895.3;CEP162,splice_acceptor_variant,,ENST00000617909,;CEP162,splice_acceptor_variant,,ENST00000257766,NM_001286206.1;CEP162,splice_acceptor_variant,,ENST00000461137,;CEP162,non_coding_transcript_exon_variant,,ENST00000487999,; A ENST00000403245 Transcript splice_acceptor_variant -/5156 2782/4212 928/1403 1 -1 CEP162 HGNC HGNC:21107 protein_coding YES CCDS34494.2 ENSP00000385215 Q5TB80 UPI0001533DAA NM_014895.3 21/26 HIGH 1 SNV 5 1 PASS rs1190048850 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 84155511 84155511 C A 1 0 0 0 0 0 0 1 0 2962 695 24 2 2 CEP162 6 84155511 Splice_Site SNP C 11LU022_T 514347 84155511 86650468 361 999 HTR1E 0 . GRCh38 6 87015403 87015403 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.69G>T p.Met23Ile p.M23I ENST00000305344 2/2 68 44 24 34 34 0 strelka-varscan-mutect HTR1E,missense_variant,p.Met23Ile,ENST00000305344,NM_000865.2; T ENST00000305344 Transcript missense_variant 772/2052 69/1098 23/365 M/I atG/atT 1 1 HTR1E HGNC HGNC:5291 protein_coding YES CCDS5006.1 ENSP00000307766 P28566 UPI000000126D NM_000865.2 tolerated(1) 2/2 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF33,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999988 1 1 1 0 T 3 4 3 87015403 87015403 G T 1 0 0 0 0 1 0 0 0 7335 1319 46 2 2 HTR1E 6 87015403 Missense_Mutation SNP G 11LU022_T 2859892 87015403 83790576 362 1000 MDN1 0 . GRCh38 6 89718412 89718412 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.6537G>T p.Leu2179Phe p.L2179F ENST00000369393 43/102 108 94 14 133 133 0 strelka-varscan-mutect MDN1,missense_variant,p.Leu2179Phe,ENST00000369393,NM_014611.2;MDN1,missense_variant,p.Leu2179Phe,ENST00000629399,; A ENST00000369393 Transcript missense_variant 6653/18413 6537/16791 2179/5596 L/F ttG/ttT 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 tolerated(0.11) 43/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64,SMART_domains:SM00382 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 89718412 89718412 C A 1 0 0 0 0 1 0 0 0 9353 709 25 2 2 MDN1 6 89718412 Missense_Mutation SNP C 11LU022_T 2703009 89718412 81087567 363 1001 UFL1 0 . GRCh38 6 96549579 96549579 + Splice_Site SNP G G C novel 11LU022_T 11LU022_N G G c.1687+1G>C p.X563_splice ENST00000369278 94 78 16 96 96 0 strelka-varscan-mutect UFL1,splice_donor_variant,,ENST00000369278,NM_015323.4; C ENST00000369278 Transcript splice_donor_variant -/4224 1687/2385 563/794 1 1 UFL1 HGNC HGNC:23039 protein_coding YES CCDS5034.1 ENSP00000358283 O94874 UPI0000072D61 NM_015323.4 14/18 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999985 1 1 1 0 C 5 2 3 96549579 96549579 G C 1 0 0 0 0 0 0 1 0 17460 1275 44 4 4 UFL1 6 96549579 Splice_Site SNP G 11LU022_T 6831167 96549579 74256400 364 1002 ASCC3 0 . GRCh38 6 100516306 100516306 + Missense_Mutation SNP C C A rs754980276 11LU022_T 11LU022_N C C c.5949G>T p.Lys1983Asn p.K1983N ENST00000369162 39/42 283 247 36 344 344 0 strelka-varscan-mutect ASCC3,missense_variant,p.Lys1983Asn,ENST00000369162,NM_006828.3; A ENST00000369162 Transcript missense_variant 6294/8146 5949/6609 1983/2202 K/N aaG/aaT rs754980276 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 tolerated(0.28) 39/42 hmmpanther:PTHR24075,hmmpanther:PTHR24075:SF0,Pfam_domain:PF02889,PIRSF_domain:PIRSF039073,SMART_domains:SM00973,Superfamily_domains:SSF158702 MODERATE 1 SNV 5 1 PASS rs754980276 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 100516306 100516306 C A 1 0 0 0 0 1 0 0 0 1175 680 24 2 2 ASCC3 6 100516306 Missense_Mutation SNP C 11LU022_T 3966727 100516306 70289673 365 1003 LIN28B 0 . GRCh38 6 105078620 105078620 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.590G>T p.Gly197Val p.G197V ENST00000345080 4/4 167 134 33 179 179 0 strelka-varscan-mutect LIN28B,missense_variant,p.Gly197Val,ENST00000345080,NM_001004317.3;LIN28B,missense_variant,p.Gly205Val,ENST00000637759,;LIN28B,downstream_gene_variant,,ENST00000635857,; T ENST00000345080 Transcript missense_variant 793/5505 590/753 197/250 G/V gGc/gTc 1 1 LIN28B HGNC HGNC:32207 protein_coding YES CCDS34504.1 ENSP00000344401 Q6ZN17 UPI000035E7BD NM_001004317.3 tolerated_low_confidence(0.2) 4/4 hmmpanther:PTHR11544:SF32,hmmpanther:PTHR11544 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 105078620 105078620 G T 1 0 0 0 0 1 0 0 0 8714 1203 42 2 2 LIN28B 6 105078620 Missense_Mutation SNP G 11LU022_T 4562314 105078620 65727359 366 1004 SEC63 0 . GRCh38 6 107908927 107908927 + Missense_Mutation SNP G G T rs754604388 11LU022_T 11LU022_N G G c.733C>A p.Arg245Ser p.R245S ENST00000369002 8/21 155 135 20 218 218 0 strelka-varscan-mutect SEC63,missense_variant,p.Arg245Ser,ENST00000369002,NM_007214.4;SEC63,downstream_gene_variant,,ENST00000429168,;SEC63,splice_region_variant,,ENST00000489455,;SEC63,downstream_gene_variant,,ENST00000484803,; T ENST00000369002 Transcript missense_variant,splice_region_variant 913/6411 733/2283 245/760 R/S Cgt/Agt rs754604388 1 -1 SEC63 HGNC HGNC:21082 protein_coding YES CCDS5061.1 ENSP00000357998 Q9UGP8 A0A0S2Z5M1 UPI000000DBBB NM_007214.4 deleterious(0) 8/21 Gene3D:2q0zX01,Pfam_domain:PF02889,hmmpanther:PTHR24075,SMART_domains:SM00973,Superfamily_domains:SSF158702 MODERATE 1 SNV 1 1 PASS rs754604388 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 107908927 107908927 G T 1 0 0 0 0 1 0 0 0 14282 1159 40 1 1 SEC63 6 107908927 Missense_Mutation SNP G 11LU022_T 2830307 107908927 62897052 367 1005 AK9 0 . GRCh38 6 109497498 109497498 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.5282G>A p.Cys1761Tyr p.C1761Y ENST00000424296 38/41 116 96 20 184 184 0 strelka-varscan-mutect AK9,missense_variant,p.Cys1761Tyr,ENST00000424296,NM_001145128.2;AK9,missense_variant,p.Cys599Tyr,ENST00000470564,;AK9,missense_variant,p.Cys162Tyr,ENST00000490722,;RP5-919F19.5,intron_variant,,ENST00000423747,; T ENST00000424296 Transcript missense_variant 5359/6326 5282/5736 1761/1911 C/Y tGt/tAt 1 -1 AK9 HGNC HGNC:33814 protein_coding YES CCDS55048.1 ENSP00000410186 Q5TCS8 UPI0001A48FC8 NM_001145128.2 tolerated(0.47) 38/41 hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF96 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 109497498 109497498 C T 1 0 0 0 0 1 0 0 0 526 478 17 3 3 AK9 6 109497498 Missense_Mutation SNP C 11LU022_T 1588571 109497498 61308481 368 1006 AK9 0 . GRCh38 6 109506414 109506414 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.4762A>T p.Ser1588Cys p.S1588C ENST00000424296 35/41 245 217 28 340 340 0 strelka-varscan-mutect AK9,missense_variant,p.Ser1588Cys,ENST00000424296,NM_001145128.2;AK9,missense_variant,p.Ser426Cys,ENST00000470564,;AK9,missense_variant,p.Ser3Cys,ENST00000490722,;RP5-919F19.5,intron_variant,,ENST00000423747,; A ENST00000424296 Transcript missense_variant 4839/6326 4762/5736 1588/1911 S/C Agc/Tgc 1 -1 AK9 HGNC HGNC:33814 protein_coding YES CCDS55048.1 ENSP00000410186 Q5TCS8 UPI0001A48FC8 NM_001145128.2 deleterious(0) 35/41 Gene3D:3.40.50.300,hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF96,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 109506414 109506414 T A 1 0 0 0 0 1 0 0 0 526 1580 55 4 4 AK9 6 109506414 Missense_Mutation SNP T 11LU022_T 8916 109506414 61299565 369 1007 SLC22A16 0 . GRCh38 6 110442436 110442436 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.991C>A p.Gln331Lys p.Q331K ENST00000368919 4/8 251 210 41 282 282 0 strelka-varscan-mutect SLC22A16,missense_variant,p.Gln297Lys,ENST00000330550,;SLC22A16,missense_variant,p.Gln331Lys,ENST00000368919,NM_033125.3;SLC22A16,missense_variant,p.Gln248Lys,ENST00000451557,;SLC22A16,missense_variant,p.Gln288Lys,ENST00000437378,;SLC22A16,missense_variant,p.Gln161Lys,ENST00000434949,;SLC22A16,downstream_gene_variant,,ENST00000424139,;RN7SL617P,upstream_gene_variant,,ENST00000485298,; T ENST00000368919 Transcript missense_variant 1058/1987 991/1734 331/577 Q/K Caa/Aaa 1 -1 SLC22A16 HGNC HGNC:20302 protein_coding YES CCDS5084.1 ENSP00000357915 Q86VW1 A0A0K0K1K9 UPI000000DC13 NM_033125.3 tolerated(0.48) 4/8 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF186,Pfam_domain:PF00083,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs916105839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 110442436 110442436 G T 1 0 0 0 0 1 0 0 0 14713 1386 48 2 2 SLC22A16 6 110442436 Missense_Mutation SNP G 11LU022_T 936022 110442436 60363543 370 1008 TUBE1 0 . GRCh38 6 112075982 112075982 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.767A>C p.Asp256Ala p.D256A ENST00000368662 8/12 71 61 10 101 101 0 strelka-varscan-mutect TUBE1,missense_variant,p.Asp256Ala,ENST00000368662,NM_016262.4;TUBE1,non_coding_transcript_exon_variant,,ENST00000604814,;TUBE1,downstream_gene_variant,,ENST00000441191,;TUBE1,3_prime_UTR_variant,,ENST00000605457,;TUBE1,3_prime_UTR_variant,,ENST00000604743,;TUBE1,non_coding_transcript_exon_variant,,ENST00000604689,;TUBE1,downstream_gene_variant,,ENST00000368657,;TUBE1,downstream_gene_variant,,ENST00000604967,;TUBE1,upstream_gene_variant,,ENST00000603651,; G ENST00000368662 Transcript missense_variant 846/2142 767/1428 256/475 D/A gAt/gCt 1 -1 TUBE1 HGNC HGNC:20775 protein_coding YES CCDS5100.1 ENSP00000357651 Q9UJT0 UPI0000136A4E NM_016262.4 deleterious(0) 8/12 hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF13,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 112075982 112075982 T G 1 0 0 0 0 1 0 0 0 17273 1435 50 5 5 TUBE1 6 112075982 Missense_Mutation SNP T 11LU022_T 1633546 112075982 58729997 371 1009 HS3ST5 0 . GRCh38 6 114058117 114058117 + Missense_Mutation SNP G G T rs777952604 11LU022_T 11LU022_N G G c.181C>A p.Leu61Met p.L61M ENST00000312719 5/5 149 122 27 178 177 1 strelka-varscan-mutect HS3ST5,missense_variant,p.Leu61Met,ENST00000312719,;HS3ST5,missense_variant,p.Leu61Met,ENST00000411826,NM_153612.3;RP3-399L15.3,intron_variant,,ENST00000519104,;RP3-399L15.3,intron_variant,,ENST00000519270,;RP3-399L15.3,intron_variant,,ENST00000523087,; T ENST00000312719 Transcript missense_variant 1370/3901 181/1041 61/346 L/M Ctg/Atg rs777952604 1 -1 HS3ST5 HGNC HGNC:19419 protein_coding YES CCDS34517.1 ENSP00000427888 Q8IZT8 UPI00000740A8 deleterious(0.02) 5/5 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF46 MODERATE SNV 2 1 PASS rs777952604 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 114058117 114058117 G T 1 0 0 0 0 1 0 0 0 7262 991 35 2 2 HS3ST5 6 114058117 Missense_Mutation SNP G 11LU022_T 1982135 114058117 56747862 372 1010 DSE 0 . GRCh38 6 116435765 116435765 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1297A>G p.Arg433Gly p.R433G ENST00000452085 6/6 189 162 27 205 205 0 strelka-varscan-mutect DSE,missense_variant,p.Arg433Gly,ENST00000452085,NM_001080976.1;DSE,missense_variant,p.Arg433Gly,ENST00000331677,;DSE,missense_variant,p.Arg433Gly,ENST00000359564,NM_013352.2;DSE,non_coding_transcript_exon_variant,,ENST00000606712,; G ENST00000452085 Transcript missense_variant 1491/10586 1297/2877 433/958 R/G Aga/Gga 1 1 DSE HGNC HGNC:21144 protein_coding YES CCDS5107.1 ENSP00000404049 Q9UL01 UPI0000073CB8 NM_001080976.1 tolerated(0.28) 6/6 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 116435765 116435765 A G 1 0 0 0 0 1 0 0 0 4595 180 7 5 5 DSE 6 116435765 Missense_Mutation SNP A 11LU022_T 2377648 116435765 54370214 373 1011 FAM26D 0 . GRCh38 6 116558149 116558149 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.454G>A p.Gly152Arg p.G152R ENST00000405399 4/4 118 106 12 125 125 0 strelka-varscan-mutect FAM26D,missense_variant,p.Gly295Arg,ENST00000368596,;FAM26D,missense_variant,p.Gly109Arg,ENST00000368597,NM_001256889.1,NM_153036.3;FAM26D,missense_variant,p.Gly152Arg,ENST00000405399,NM_001256887.1;FAM26D,missense_variant,p.Gly151Arg,ENST00000628083,NM_001256888.1;FAM26D,missense_variant,p.Gly109Arg,ENST00000452373,; A ENST00000405399 Transcript missense_variant 739/1165 454/516 152/171 G/R Gga/Aga 1 1 FAM26D HGNC HGNC:21094 protein_coding YES CCDS59032.1 ENSP00000385836 Q5JW98 UPI000056D4A2 NM_001256887.1 tolerated(0.2) 4/4 hmmpanther:PTHR32261,hmmpanther:PTHR32261:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 116558149 116558149 G A 1 0 0 0 0 1 0 0 0 5431 1349 47 3 3 FAM26D 6 116558149 Missense_Mutation SNP G 11LU022_T 122384 116558149 54247830 374 1012 GPRC6A 0 . GRCh38 6 116792889 116792889 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2034G>T p.Leu678Phe p.L678F ENST00000310357 6/6 191 154 37 182 182 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Leu678Phe,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Leu607Phe,ENST00000368549,NM_001286355.1;GPRC6A,missense_variant,p.Leu503Phe,ENST00000530250,NM_001286354.1; A ENST00000310357 Transcript missense_variant 2056/2860 2034/2781 678/926 L/F ttG/ttT 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated(0.06) 6/6 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF00003,Prints_domain:PR00248 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 116792889 116792889 C A 1 0 0 0 0 1 0 0 0 6607 825 29 2 2 GPRC6A 6 116792889 Missense_Mutation SNP C 11LU022_T 234740 116792889 54013090 375 1013 RFX6 0 . GRCh38 6 116928935 116928935 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.2575A>G p.Thr859Ala p.T859A ENST00000332958 18/19 269 234 35 347 346 1 strelka-varscan-mutect RFX6,missense_variant,p.Thr859Ala,ENST00000332958,NM_173560.3; G ENST00000332958 Transcript missense_variant 2591/3460 2575/2787 859/928 T/A Aca/Gca 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 tolerated_low_confidence(0.61) 18/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 116928935 116928935 A G 1 0 0 0 0 1 0 0 0 13441 159 6 5 5 RFX6 6 116928935 Missense_Mutation SNP A 11LU022_T 136046 116928935 53877044 376 1014 MOXD1 0 . GRCh38 6 132324034 132324034 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1010G>T p.Gly337Val p.G337V ENST00000367963 7/12 151 138 13 206 206 0 strelka-mutect MOXD1,missense_variant,p.Gly337Val,ENST00000367963,NM_015529.3;MOXD1,missense_variant,p.Gly269Val,ENST00000336749,;MOXD1,non_coding_transcript_exon_variant,,ENST00000489128,; A ENST00000367963 Transcript missense_variant 1129/3059 1010/1842 337/613 G/V gGg/gTg 1 -1 MOXD1 HGNC HGNC:21063 protein_coding YES CCDS5152.2 ENSP00000356940 Q6UVY6 UPI000003F04F NM_015529.3 deleterious(0) 7/12 hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF28,Pfam_domain:PF03712,Superfamily_domains:SSF49742,Prints_domain:PR00767 MODERATE 1 SNV 1 1 PASS rs1226979129 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 132324034 132324034 C A 1 0 0 0 0 1 0 0 0 9682 623 22 2 2 MOXD1 6 132324034 Missense_Mutation SNP C 11LU022_T 15395099 132324034 38481945 377 1015 MOXD1 0 . GRCh38 6 132324098 132324098 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.947-1G>T p.X316_splice ENST00000367963 152 139 13 243 243 0 strelka-mutect MOXD1,splice_acceptor_variant,,ENST00000367963,NM_015529.3;MOXD1,splice_acceptor_variant,,ENST00000336749,;MOXD1,splice_acceptor_variant,,ENST00000489128,; A ENST00000367963 Transcript splice_acceptor_variant -/3059 947/1842 316/613 1 -1 MOXD1 HGNC HGNC:21063 protein_coding YES CCDS5152.2 ENSP00000356940 Q6UVY6 UPI000003F04F NM_015529.3 6/11 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 132324098 132324098 C A 1 0 0 0 0 0 0 1 0 9682 695 24 2 2 MOXD1 6 132324098 Splice_Site SNP C 11LU022_T 64 132324098 38481881 378 1016 HBS1L 0 . GRCh38 6 134982473 134982473 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1582A>T p.Thr528Ser p.T528S ENST00000367837 13/18 86 78 8 105 105 0 strelka-mutect HBS1L,missense_variant,p.Thr528Ser,ENST00000367837,NM_006620.3;HBS1L,missense_variant,p.Thr486Ser,ENST00000367826,NM_001145158.1;HBS1L,missense_variant,p.Thr463Ser,ENST00000415177,;HBS1L,missense_variant,p.Thr364Ser,ENST00000527578,;HBS1L,missense_variant,p.Thr398Ser,ENST00000533274,;HBS1L,missense_variant,p.Thr152Ser,ENST00000529169,;MIR3662,upstream_gene_variant,,ENST00000637030,;HBS1L,3_prime_UTR_variant,,ENST00000526100,;HBS1L,non_coding_transcript_exon_variant,,ENST00000527005,; A ENST00000367837 Transcript missense_variant 1789/7163 1582/2055 528/684 T/S Act/Tct 1 -1 HBS1L HGNC HGNC:4834 protein_coding YES CCDS5173.1 ENSP00000356811 Q9Y450 D9YZV0 UPI00000372EA NM_006620.3 tolerated(0.39) 13/18 Gene3D:2.40.30.10,Pfam_domain:PF03144,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF188,Superfamily_domains:SSF50447 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.10856 0.9999998 1 1 1 0 A 3 1 3 134982473 134982473 T A 1 0 0 0 0 1 0 0 0 6873 1725 60 4 4 HBS1L 6 134982473 Missense_Mutation SNP T 11LU022_T 2658375 134982473 35823506 379 1017 SYNE1 0 . GRCh38 6 152321729 152321729 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.16075G>T p.Glu5359Ter p.E5359* ENST00000367255 83/146 188 166 22 295 295 0 strelka-mutect SYNE1,stop_gained,p.Glu5359Ter,ENST00000367255,NM_182961.3;SYNE1,stop_gained,p.Glu5288Ter,ENST00000423061,NM_033071.3;SYNE1,stop_gained,p.Glu5015Ter,ENST00000341594,;SYNE1,stop_gained,p.Glu53Ter,ENST00000448038,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,;SYNE1,upstream_gene_variant,,ENST00000367256,; A ENST00000367255 Transcript stop_gained 16677/27748 16075/26394 5359/8797 E/* Gaa/Taa 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 83/146 Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 152321729 152321729 C A 1 0 0 0 0 0 1 0 0 15837 922 32 2 2 SYNE1 6 152321729 Nonsense_Mutation SNP C 11LU022_T 17339256 152321729 18484250 380 1018 SYNE1 0 . GRCh38 6 152526104 152526104 + Silent SNP C C A 11LU022_T 11LU022_N C C c.201G>T p.= p.L67L ENST00000367255 5/146 298 265 33 333 333 0 strelka-varscan-mutect SYNE1,synonymous_variant,p.=,ENST00000367255,NM_182961.3;SYNE1,synonymous_variant,p.=,ENST00000423061,NM_033071.3;SYNE1,synonymous_variant,p.=,ENST00000341594,;SYNE1,synonymous_variant,p.=,ENST00000367248,;SYNE1,synonymous_variant,p.=,ENST00000367253,;SYNE1,synonymous_variant,p.=,ENST00000413186,;SYNE1,synonymous_variant,p.=,ENST00000537750,;SYNE1,synonymous_variant,p.=,ENST00000466159,;SYNE1,synonymous_variant,p.=,ENST00000610489,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; A ENST00000367255 Transcript synonymous_variant 803/27748 201/26394 67/8797 L ctG/ctT COSM5439181,COSM5439182,COSM5439183,COSM5439184,COSM5439185 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 5/146 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00033,Superfamily_domains:SSF47576 1,1,1,1,1 LOW 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 152526104 152526104 C A 1 0 0 0 0 0 0 0 1 15837 581 21 2 2 SYNE1 6 152526104 Silent SNP C 11LU022_T 204375 152526104 18279875 381 1019 FNDC1 0 . GRCh38 6 159233970 159233970 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.3458G>T p.Arg1153Met p.R1153M ENST00000297267 11/23 150 117 33 175 175 0 strelka-varscan-mutect FNDC1,missense_variant,p.Arg1153Met,ENST00000297267,NM_032532.2;FNDC1,missense_variant,p.Arg1049Met,ENST00000329629,; T ENST00000297267 Transcript missense_variant 3658/6552 3458/5685 1153/1894 R/M aGg/aTg COSM5255741 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 deleterious_low_confidence(0.02) 11/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 159233970 159233970 G T 1 0 0 0 0 1 0 0 0 5824 1000 35 2 2 FNDC1 6 159233970 Missense_Mutation SNP G 11LU022_T 6707866 159233970 11572009 382 1020 LPA 0 . GRCh38 6 160585155 160585155 + Nonsense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.4180C>T p.Gln1394Ter p.Q1394* ENST00000316300 26/39 187 151 36 280 280 0 strelka-varscan-mutect LPA,stop_gained,p.Gln1394Ter,ENST00000316300,NM_005577.2;LPA,downstream_gene_variant,,ENST00000447678,; A ENST00000316300 Transcript stop_gained 4225/6414 4180/6123 1394/2040 Q/* Cag/Tag 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 26/39 Gene3D:2.40.20.10,Pfam_domain:PF00051,Prints_domain:PR00018,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 160585155 160585155 G A 1 0 0 0 0 0 1 0 0 8806 1386 48 3 3 LPA 6 160585155 Nonsense_Mutation SNP G 11LU022_T 1351185 160585155 10220824 383 1021 LPA 0 . GRCh38 6 160599567 160599567 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.3220A>T p.Thr1074Ser p.T1074S ENST00000316300 20/39 387 328 59 435 435 0 strelka-varscan-mutect LPA,missense_variant,p.Thr1074Ser,ENST00000316300,NM_005577.2;LPA,missense_variant,p.Thr321Ser,ENST00000447678,; A ENST00000316300 Transcript missense_variant 3265/6414 3220/6123 1074/2040 T/S Act/Tct 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 tolerated(0.29) 20/39 Gene3D:2.40.20.10,Pfam_domain:PF00051,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 160599567 160599567 T A 1 0 0 0 0 1 0 0 0 8806 1725 60 4 4 LPA 6 160599567 Missense_Mutation SNP T 11LU022_T 14412 160599567 10206412 384 1022 PLG 0 . GRCh38 6 160752238 160752238 + Missense_Mutation SNP C C A rs138277465 11LU022_T 11LU022_N C C c.2249C>A p.Ala750Asp p.A750D ENST00000308192 18/19 248 221 27 333 333 0 strelka-varscan-mutect PLG,missense_variant,p.Ala750Asp,ENST00000308192,NM_000301.3;PLG,non_coding_transcript_exon_variant,,ENST00000461414,;PLG,non_coding_transcript_exon_variant,,ENST00000467466,;RP1-81D8.5,downstream_gene_variant,,ENST00000612111,; A ENST00000308192 Transcript missense_variant 2312/2741 2249/2433 750/810 A/D gCc/gAc rs138277465,COSM108513 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 tolerated(0.37) 18/19 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001150,PROSITE_profiles:PS50240,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00020,Superfamily_domains:SSF50494 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs138277465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 160752238 160752238 C A 1 0 0 0 0 1 0 0 0 12181 739 26 2 2 PLG 6 160752238 Missense_Mutation SNP C 11LU022_T 152671 160752238 10053741 385 1023 ELFN1 0 . GRCh38 7 1746493 1746493 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1897G>T p.Ala633Ser p.A633S ENST00000424383 3/3 106 83 23 118 118 0 strelka-varscan-mutect ELFN1,missense_variant,p.Ala633Ser,ENST00000424383,;ELFN1,missense_variant,p.Ala633Ser,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; T ENST00000424383 Transcript missense_variant 2384/3845 1897/2487 633/828 A/S Gcc/Tcc 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 tolerated(0.16) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24367:SF34,hmmpanther:PTHR24367 MODERATE SNV 5 1 PASS rs1301121297 . 0 196 11 3 0 0 0 0 -20 0.9984166 1 1 1 0 T 3 4 3 1746493 1746493 G T 1 0 0 0 0 1 0 0 0 4891 1087 38 1 1 ELFN1 7 1746493 Missense_Mutation SNP G 11LU022_T 1746493 157599480 386 1024 SNX8 0 . GRCh38 7 2256873 2256873 + Splice_Site SNP C C A 11LU022_T 11LU022_N C C c.1284+1G>T p.X428_splice ENST00000222990 82 54 28 73 73 0 strelka-varscan-mutect SNX8,splice_donor_variant,,ENST00000222990,NM_013321.3;SNX8,downstream_gene_variant,,ENST00000617724,;SNX8,splice_donor_variant,,ENST00000480807,;SNX8,downstream_gene_variant,,ENST00000479689,; A ENST00000222990 Transcript splice_donor_variant -/4727 1284/1398 428/465 COSM746422 1 -1 SNX8 HGNC HGNC:14972 protein_coding YES CCDS5331.1 ENSP00000222990 Q9Y5X2 UPI0000135B46 NM_013321.3 10/10 1 HIGH 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 5 1 3 2256873 2256873 C A 1 0 0 0 0 0 0 1 0 15229 521 18 2 2 SNX8 7 2256873 Splice_Site SNP C 11LU022_T 510380 2256873 157089100 387 1025 BRAT1 0 . GRCh38 7 2544971 2544971 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.368G>T p.Trp123Leu p.W123L ENST00000340611 4/14 185 120 65 159 159 0 strelka-varscan-mutect BRAT1,missense_variant,p.Trp123Leu,ENST00000340611,NM_152743.3;BRAT1,upstream_gene_variant,,ENST00000473879,;BRAT1,non_coding_transcript_exon_variant,,ENST00000469750,;BRAT1,non_coding_transcript_exon_variant,,ENST00000467558,;BRAT1,intron_variant,,ENST00000421712,;BRAT1,upstream_gene_variant,,ENST00000493232,; A ENST00000340611 Transcript missense_variant 625/2915 368/2466 123/821 W/L tGg/tTg 1 -1 BRAT1 HGNC HGNC:21701 protein_coding YES CCDS5334.1 ENSP00000339637 Q6PJG6 UPI00001AEB20 NM_152743.3 deleterious(0) 4/14 hmmpanther:PTHR21331,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 2544971 2544971 C A 1 0 0 0 0 1 0 0 0 1667 595 21 2 2 BRAT1 7 2544971 Missense_Mutation SNP C 11LU022_T 288098 2544971 156801002 388 1026 TNRC18 0 . GRCh38 7 5345754 5345754 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.5527A>T p.Ser1843Cys p.S1843C ENST00000430969 18/30 273 217 56 244 244 0 strelka-varscan-mutect TNRC18,missense_variant,p.Ser1843Cys,ENST00000399537,;TNRC18,missense_variant,p.Ser1843Cys,ENST00000430969,NM_001080495.2; A ENST00000430969 Transcript missense_variant 5876/10562 5527/8907 1843/2968 S/C Agc/Tgc 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious(0.02) 18/30 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 5345754 5345754 T A 1 0 0 0 0 1 0 0 0 16812 1580 55 4 4 TNRC18 7 5345754 Missense_Mutation SNP T 11LU022_T 2800783 5345754 154000219 389 1027 PHF14 0 . GRCh38 7 11038856 11038856 + Splice_Site SNP G G T novel 11LU022_T 11LU022_N G G c.2076+1G>T p.X692_splice ENST00000403050 128 109 19 84 84 0 strelka-varscan-mutect PHF14,splice_donor_variant,,ENST00000403050,NM_014660.3;PHF14,splice_donor_variant,,ENST00000634607,;PHF14,upstream_gene_variant,,ENST00000481418,;PHF14,splice_donor_variant,,ENST00000490957,;PHF14,splice_donor_variant,,ENST00000423760,;PHF14,splice_donor_variant,,ENST00000521747,;PHF14,downstream_gene_variant,,ENST00000497851,; T ENST00000403050 Transcript splice_donor_variant -/4276 2076/2667 692/888 1 1 PHF14 HGNC HGNC:22203 protein_coding YES CCDS47542.1 ENSP00000385795 O94880 UPI000020EB41 NM_014660.3 11/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 3 11038856 11038856 G T 1 0 0 0 0 0 0 1 0 11914 1275 44 2 2 PHF14 7 11038856 Splice_Site SNP G 11LU022_T 5693102 11038856 148307117 390 1028 INHBA 0 . GRCh38 7 41690126 41690126 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.805G>T p.Gly269Trp p.G269W ENST00000242208 3/3 205 154 51 220 218 2 strelka-varscan INHBA,missense_variant,p.Gly269Trp,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Gly269Trp,ENST00000638023,;INHBA,missense_variant,p.Gly269Trp,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript missense_variant 1052/6064 805/1281 269/426 G/W Ggg/Tgg 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious_low_confidence(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00688,Prints_domain:PR00670 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 41690126 41690126 C A 1 0 0 0 0 1 0 0 0 7643 681 24 2 2 INHBA 7 41690126 Missense_Mutation SNP C 11LU022_T 30651270 41690126 117655847 391 1029 GCK 0 . GRCh38 7 44145261 44145261 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1276G>A p.Ala426Thr p.A426T ENST00000345378 10/10 291 231 60 297 296 1 strelka-varscan GCK,missense_variant,p.Ala425Thr,ENST00000403799,NM_000162.3;GCK,missense_variant,p.Ala424Thr,ENST00000395796,NM_033508.1;GCK,missense_variant,p.Ala426Thr,ENST00000345378,NM_033507.1;GCK,missense_variant,p.Ala424Thr,ENST00000616242,;GCK,missense_variant,p.Ala408Thr,ENST00000437084,;GCK,missense_variant,p.Ala109Thr,ENST00000336642,;MYL7,upstream_gene_variant,,ENST00000458240,;MYL7,upstream_gene_variant,,ENST00000457314,;MYL7,upstream_gene_variant,,ENST00000223364,NM_021223.2;MYL7,upstream_gene_variant,,ENST00000447951,;MYL7,upstream_gene_variant,,ENST00000446581,;MYL7,upstream_gene_variant,,ENST00000431007,;MYL7,upstream_gene_variant,,ENST00000434895,;GCK,downstream_gene_variant,,ENST00000473353,;GCK,non_coding_transcript_exon_variant,,ENST00000459642,;MYL7,upstream_gene_variant,,ENST00000457910,;MYL7,upstream_gene_variant,,ENST00000431289,;MYL7,upstream_gene_variant,,ENST00000476118,; T ENST00000345378 Transcript missense_variant 1438/2421 1276/1401 426/466 A/T Gcc/Acc 1 -1 GCK HGNC HGNC:4195 protein_coding YES CCDS5480.1 ENSP00000223366 P35557 UPI000002AB76 NM_033507.1 tolerated(0.34) 10/10 Gene3D:3.40.367.20,Pfam_domain:PF03727,PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF3,Superfamily_domains:SSF53067 MODERATE SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 44145261 44145261 C T 1 0 0 0 0 1 0 0 0 6163 710 25 3 3 GCK 7 44145261 Missense_Mutation SNP C 11LU022_T 2455135 44145261 115200712 392 1030 NUDCD3 0 . GRCh38 7 44404536 44404536 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.690G>A p.= p.E230E ENST00000355451 4/6 130 108 22 139 139 0 strelka-varscan NUDCD3,synonymous_variant,p.=,ENST00000355451,NM_015332.3;NUDCD3,non_coding_transcript_exon_variant,,ENST00000460110,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000493613,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000472246,;NUDCD3,upstream_gene_variant,,ENST00000338427,;NUDCD3,upstream_gene_variant,,ENST00000487118,;NUDCD3,non_coding_transcript_exon_variant,,ENST00000464812,; T ENST00000355451 Transcript synonymous_variant 970/8256 690/1086 230/361 E gaG/gaA 1 -1 NUDCD3 HGNC HGNC:22208 protein_coding YES CCDS5490.2 ENSP00000347626 Q8IVD9 UPI000020EEEB NM_015332.3 4/6 Gene3D:2.60.40.790,Pfam_domain:PF04969,PROSITE_profiles:PS51203,hmmpanther:PTHR12356,hmmpanther:PTHR12356:SF19,Superfamily_domains:SSF49764 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 44404536 44404536 C T 1 0 0 0 0 0 0 0 1 10790 680 24 3 3 NUDCD3 7 44404536 Silent SNP C 11LU022_T 259275 44404536 114941437 393 1031 ABCA13 0 . GRCh38 7 48275947 48275947 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.6281T>C p.Leu2094Pro p.L2094P ENST00000435803 17/62 252 201 51 256 256 0 strelka-varscan ABCA13,missense_variant,p.Leu2094Pro,ENST00000435803,NM_152701.4;ABCA13,upstream_gene_variant,,ENST00000544596,;ABCA13,upstream_gene_variant,,ENST00000611776,;ABCA13,downstream_gene_variant,,ENST00000417403,; C ENST00000435803 Transcript missense_variant 6305/17184 6281/15177 2094/5058 L/P cTt/cCt 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.2) 17/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 48275947 48275947 T C 1 0 0 0 0 1 0 0 0 35 1609 56 5 5 ABCA13 7 48275947 Missense_Mutation SNP T 11LU022_T 3871411 48275947 111070026 394 1032 VWC2 0 . GRCh38 7 49775657 49775657 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.222G>T p.= p.R74R ENST00000340652 2/4 135 110 25 168 168 0 strelka-varscan VWC2,synonymous_variant,p.=,ENST00000340652,NM_198570.3; T ENST00000340652 Transcript synonymous_variant 778/11299 222/978 74/325 R cgG/cgT 1 1 VWC2 HGNC HGNC:30200 protein_coding YES CCDS5508.1 ENSP00000341819 Q2TAL6 UPI00002373A5 NM_198570.3 2/4 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 49775657 49775657 G T 1 0 0 0 0 0 0 0 1 17802 1219 43 2 2 VWC2 7 49775657 Silent SNP G 11LU022_T 1499710 49775657 109570316 395 1033 VWC2 0 . GRCh38 7 49775989 49775989 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.554C>A p.Pro185Gln p.P185Q ENST00000340652 2/4 311 246 65 408 407 1 strelka-varscan VWC2,missense_variant,p.Pro185Gln,ENST00000340652,NM_198570.3; A ENST00000340652 Transcript missense_variant 1110/11299 554/978 185/325 P/Q cCg/cAg 1 1 VWC2 HGNC HGNC:30200 protein_coding YES CCDS5508.1 ENSP00000341819 Q2TAL6 UPI00002373A5 NM_198570.3 deleterious(0) 2/4 hmmpanther:PTHR11339,SMART_domains:SM00214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49775989 49775989 C A 1 0 0 0 0 1 0 0 0 17802 652 23 1 1 VWC2 7 49775989 Missense_Mutation SNP C 11LU022_T 332 49775989 109569984 396 1034 POM121L12 0 . GRCh38 7 53036449 53036449 + Missense_Mutation SNP G G A rs202031574 11LU022_T 11LU022_N G G c.778G>A p.Ala260Thr p.A260T ENST00000408890 1/1 165 141 24 147 146 1 strelka-varscan POM121L12,missense_variant,p.Ala260Thr,ENST00000408890,NM_182595.3; A ENST00000408890 Transcript missense_variant 808/1283 778/891 260/296 A/T Gcc/Acc rs202031574,COSM1090729 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated_low_confidence(0.53) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 0,1 MODERATE 1 SNV 0,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 3 53036449 53036449 G A 1 0 0 0 0 1 0 0 0 12352 1087 38 1 1 POM121L12 7 53036449 Missense_Mutation SNP G 11LU022_T 3260460 53036449 106309524 397 1035 CALN1 0 . GRCh38 7 72278798 72278798 + Silent SNP C C A rs749576958 11LU022_T 11LU022_N C C c.132G>T p.= p.P44P ENST00000395275 3/7 164 123 41 169 169 0 strelka-varscan CALN1,synonymous_variant,p.=,ENST00000395275,NM_031468.3;CALN1,synonymous_variant,p.=,ENST00000329008,NM_001017440.2;CALN1,synonymous_variant,p.=,ENST00000395276,;CALN1,synonymous_variant,p.=,ENST00000431984,;CALN1,synonymous_variant,p.=,ENST00000446128,; A ENST00000395275 Transcript synonymous_variant 521/9459 132/786 44/261 P ccG/ccT rs749576958 1 -1 CALN1 HGNC HGNC:13248 protein_coding YES CCDS47603.1 ENSP00000378690 Q9BXU9 UPI0000D4B903 NM_031468.3 3/7 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 72278798 72278798 C A 1 0 0 0 0 0 0 0 1 2282 523 19 1 1 CALN1 7 72278798 Silent SNP C 11LU022_T 19242349 72278798 87067175 398 1036 DNAJC30 0 . GRCh38 7 73682889 73682889 + Frame_Shift_Del DEL C C - novel 11LU022_T 11LU022_N C C c.535delG p.Glu179AsnfsTer4 p.E179Nfs*4 ENST00000395176 1/1 222 181 41 239 239 0 sindel-varindel-pindel DNAJC30,frameshift_variant,p.Glu179AsnfsTer4,ENST00000395176,NM_032317.2;WBSCR22,upstream_gene_variant,,ENST00000265758,NM_017528.4;WBSCR22,upstream_gene_variant,,ENST00000423497,NM_001202560.2;WBSCR22,upstream_gene_variant,,ENST00000441822,;WBSCR22,upstream_gene_variant,,ENST00000421304,;WBSCR22,upstream_gene_variant,,ENST00000464615,;WBSCR22,upstream_gene_variant,,ENST00000436944,;WBSCR22,upstream_gene_variant,,ENST00000463307,;WBSCR22,upstream_gene_variant,,ENST00000430270,;WBSCR22,upstream_gene_variant,,ENST00000432522,;WBSCR22,upstream_gene_variant,,ENST00000421744,;WBSCR22,upstream_gene_variant,,ENST00000430446,;WBSCR22,upstream_gene_variant,,ENST00000487006,;WBSCR22,upstream_gene_variant,,ENST00000428163,;WBSCR22,upstream_gene_variant,,ENST00000478670,;WBSCR22,upstream_gene_variant,,ENST00000496153,; - ENST00000395176 Transcript frameshift_variant 565/2485 535/681 179/226 E/X Gaa/aa 1 -1 DNAJC30 HGNC HGNC:16410 protein_coding YES CCDS5556.1 ENSP00000378605 Q96LL9 UPI00000375B0 NM_032317.2 1/1 Low_complexity_(Seg):seg HIGH deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 73682889 73682889 C - 1 0 1 0 1 0 0 0 0 4461 864 30 0 0 DNAJC30 7 73682889 Frame_Shift_Del DEL C 11LU022_T 1404091 73682889 85663084 399 1037 PCLO 0 . GRCh38 7 82952975 82952975 + Nonsense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.7978C>T p.Gln2660Ter p.Q2660* ENST00000333891 5/25 168 143 25 153 153 0 strelka-varscan PCLO,stop_gained,p.Gln2660Ter,ENST00000333891,NM_033026.5;PCLO,stop_gained,p.Gln2660Ter,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript stop_gained 8316/20329 7978/15429 2660/5142 Q/* Caa/Taa 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 82952975 82952975 G A 1 0 0 0 0 0 1 0 0 11671 1299 45 3 3 PCLO 7 82952975 Nonsense_Mutation SNP G 11LU022_T 9270086 82952975 76392998 400 1038 SEMA3A 0 . GRCh38 7 84011204 84011204 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.904G>C p.Asp302His p.D302H ENST00000265362 8/17 128 102 26 140 140 0 strelka-varscan SEMA3A,missense_variant,p.Asp302His,ENST00000265362,NM_006080.2;SEMA3A,missense_variant,p.Asp302His,ENST00000436949,; G ENST00000265362 Transcript missense_variant 1219/8225 904/2316 302/771 D/H Gac/Cac 1 -1 SEMA3A HGNC HGNC:10723 protein_coding YES CCDS5599.1 ENSP00000265362 Q14563 UPI0000135A60 NM_006080.2 deleterious(0) 8/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF23,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 84011204 84011204 C G 1 0 0 0 0 1 0 0 0 14300 826 29 4 4 SEMA3A 7 84011204 Missense_Mutation SNP C 11LU022_T 1058229 84011204 75334769 401 1039 DLX6 0 . GRCh38 7 97006408 97006409 + Frame_Shift_Del DEL AC AC - novel 11LU022_T 11LU022_N AC AC c.434_435delCA p.Thr145ArgfsTer9 p.T145Rfs*9 ENST00000518156 1/3 21 15 6 42 42 0 sindel-varindel-pindel DLX6,frameshift_variant,p.Thr145ArgfsTer9,ENST00000518156,NM_005222.3;DLX6,upstream_gene_variant,,ENST00000555308,;DLX6-AS1,intron_variant,,ENST00000430027,;DLX6-AS1,intron_variant,,ENST00000605417,;DLX6-AS1,intron_variant,,ENST00000437331,;DLX6-AS1,intron_variant,,ENST00000452769,;DLX6-AS1,intron_variant,,ENST00000458352,;DLX6-AS1,intron_variant,,ENST00000430404,;DLX6-AS1,intron_variant,,ENST00000437541,;DLX6-AS1,upstream_gene_variant,,ENST00000431497,;DLX6,upstream_gene_variant,,ENST00000493273,; - ENST00000518156 Transcript frameshift_variant 861-862/2304 431-432/882 144/293 D/X gAC/g 1 1 DLX6 HGNC HGNC:2919 protein_coding YES CCDS47647.2 ENSP00000428480 P56179 UPI0000EE57E0 NM_005222.3 1/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF26 HIGH 1 deletion 1 3 1 PASS . . 0 205 5 0 0 0 0 0 -17.39603 1 1 1 1 0 - 7 5 3 97006408 97006408 AC - 1 0 1 0 1 0 0 0 0 4382 289 10 0 0 DLX6 7 97006408 Frame_Shift_Del DEL AC 11LU022_T 12995204 97006408 62339565 402 1040 CYP3A5 0 . GRCh38 7 99679853 99679853 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.44T>G p.Leu15Arg p.L15R ENST00000222982 1/13 288 223 65 279 279 0 strelka-varscan CYP3A5,missense_variant,p.Leu15Arg,ENST00000339843,;CYP3A5,missense_variant,p.Leu15Arg,ENST00000222982,NM_000777.4,NM_001291829.1,NM_001291830.1;CYP3A5,missense_variant,p.Leu15Arg,ENST00000439761,NM_001190484.2;CYP3A5,non_coding_transcript_exon_variant,,ENST00000480723,;CYP3A5,missense_variant,p.Leu15Arg,ENST00000456417,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000481825,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000461920,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000463364,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000463907,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000466061,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000489231,;CYP3A5,non_coding_transcript_exon_variant,,ENST00000469622,;CYP3A5,upstream_gene_variant,,ENST00000469887,; C ENST00000222982 Transcript missense_variant 144/1720 44/1509 15/502 L/R cTg/cGg 1 -1 CYP3A5 HGNC HGNC:2638 protein_coding YES CCDS5672.1 ENSP00000222982 P20815 UPI000000163D NM_000777.4,NM_001291829.1,NM_001291830.1 deleterious(0) 1/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24302:SF11,hmmpanther:PTHR24302,Prints_domain:PR01689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 99679853 99679853 A C 1 0 0 0 0 1 0 0 0 3983 188 7 5 5 CYP3A5 7 99679853 Missense_Mutation SNP A 11LU022_T 2673445 99679853 59666120 403 1041 ZAN 0 . GRCh38 7 100753229 100753229 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.3124G>T p.Glu1042Ter p.E1042* ENST00000613979 14/48 59 47 12 74 74 0 strelka-varscan ZAN,stop_gained,p.Glu1042Ter,ENST00000613979,NM_003386.2;ZAN,stop_gained,p.Glu1042Ter,ENST00000618565,;ZAN,stop_gained,p.Glu1042Ter,ENST00000620596,NM_173059.2;ZAN,stop_gained,p.Glu1042Ter,ENST00000546292,;ZAN,stop_gained,p.Glu1042Ter,ENST00000542585,;ZAN,stop_gained,p.Glu1042Ter,ENST00000538115,;ZAN,stop_gained,p.Glu1042Ter,ENST00000546213,;ZAN,splice_region_variant,,ENST00000620868,; T ENST00000613979 Transcript stop_gained,splice_region_variant 3289/8669 3124/8439 1042/2812 E/* Gag/Tag 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 14/48 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221 HIGH 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999549 1 1 1 0 T 4 4 3 100753229 100753229 G T 1 0 0 0 0 0 1 0 0 18074 1014 35 2 2 ZAN 7 100753229 Nonsense_Mutation SNP G 11LU022_T 1073376 100753229 58592744 404 1042 MUC12 0 . GRCh38 7 101002741 101002741 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.12178C>G p.His4060Asp p.H4060D ENST00000536621 2/12 648 528 120 835 835 0 strelka-varscan MUC12,missense_variant,p.His4203Asp,ENST00000379442,;MUC12,missense_variant,p.His4060Asp,ENST00000536621,NM_001164462.1; G ENST00000536621 Transcript missense_variant 12178/16321 12178/16008 4060/5335 H/D Cac/Gac 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 tolerated(0.31) 2/12 hmmpanther:PTHR32093,hmmpanther:PTHR32093:SF39,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 101002741 101002741 C G 1 0 0 0 0 1 0 0 0 9969 478 17 4 4 MUC12 7 101002741 Missense_Mutation SNP C 11LU022_T 249512 101002741 58343232 405 1043 MUC17 0 . GRCh38 7 101032951 101032951 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1535C>A p.Pro512Gln p.P512Q ENST00000306151 3/13 221 185 36 232 232 0 strelka-varscan MUC17,missense_variant,p.Pro512Gln,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Pro512Gln,ENST00000379439,; A ENST00000306151 Transcript missense_variant 1599/14247 1535/13482 512/4493 P/Q cCa/cAa 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 101032951 101032951 C A 1 0 0 0 0 1 0 0 0 9973 594 21 2 2 MUC17 7 101032951 Missense_Mutation SNP C 11LU022_T 30210 101032951 58313022 406 1044 MUC17 0 . GRCh38 7 101038509 101038509 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.7093A>C p.Thr2365Pro p.T2365P ENST00000306151 3/13 92 68 24 110 110 0 strelka-varscan MUC17,missense_variant,p.Thr2365Pro,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Thr2365Pro,ENST00000379439,; C ENST00000306151 Transcript missense_variant 7157/14247 7093/13482 2365/4493 T/P Acc/Ccc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 101038509 101038509 A C 1 0 0 0 0 1 0 0 0 9973 159 6 5 5 MUC17 7 101038509 Missense_Mutation SNP A 11LU022_T 5558 101038509 58307464 407 1045 PIK3CG 0 . GRCh38 7 106869019 106869019 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1458G>C p.Gln486His p.Q486H ENST00000359195 2/11 181 143 38 175 175 0 strelka-varscan PIK3CG,missense_variant,p.Gln486His,ENST00000359195,NM_002649.3;PIK3CG,missense_variant,p.Gln486His,ENST00000496166,NM_001282426.1;PIK3CG,missense_variant,p.Gln486His,ENST00000440650,NM_001282427.1;PIK3CG,intron_variant,,ENST00000473541,; C ENST00000359195 Transcript missense_variant 1768/5377 1458/3309 486/1102 Q/H caG/caC 1 1 PIK3CG HGNC HGNC:8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 A0A024R720 UPI00000746B8 NM_002649.3 deleterious(0.01) 2/11 PROSITE_profiles:PS51547,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34,Pfam_domain:PF00792,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 106869019 106869019 G C 1 0 0 0 0 1 0 0 0 12011 933 33 4 4 PIK3CG 7 106869019 Missense_Mutation SNP G 11LU022_T 5830510 106869019 52476954 408 1046 NRCAM 0 . GRCh38 7 108189669 108189669 + Missense_Mutation SNP C C A rs140011491 11LU022_T 11LU022_N C C c.2011G>T p.Asp671Tyr p.D671Y ENST00000379028 20/33 214 171 43 169 169 0 strelka-varscan NRCAM,missense_variant,p.Asp671Tyr,ENST00000379028,;NRCAM,missense_variant,p.Asp671Tyr,ENST00000413765,NM_001193582.1;NRCAM,missense_variant,p.Asp655Tyr,ENST00000351718,NM_005010.4;NRCAM,missense_variant,p.Asp652Tyr,ENST00000379024,NM_001193583.1,NM_001193584.1;NRCAM,missense_variant,p.Asp671Tyr,ENST00000425651,NM_001037132.2;NRCAM,missense_variant,p.Asp666Tyr,ENST00000379022,;NRCAM,missense_variant,p.Asp655Tyr,ENST00000613830,; A ENST00000379028 Transcript missense_variant 2497/6685 2011/3915 671/1304 D/Y Gat/Tat rs140011491 1 -1 NRCAM HGNC HGNC:7994 protein_coding YES CCDS47686.1 ENSP00000368314 Q92823 UPI00005E2661 deleterious(0.01) 20/33 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 108189669 108189669 C A 1 0 0 0 0 1 0 0 0 10700 884 31 1 1 NRCAM 7 108189669 Missense_Mutation SNP C 11LU022_T 1320650 108189669 51156304 409 1047 PNPLA8 0 . GRCh38 7 108497495 108497495 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1441G>T p.Gly481Cys p.G481C ENST00000422087 7/12 97 77 20 143 143 0 strelka-varscan PNPLA8,missense_variant,p.Gly481Cys,ENST00000426128,NM_001256009.1;PNPLA8,missense_variant,p.Gly481Cys,ENST00000422087,NM_015723.3;PNPLA8,missense_variant,p.Gly481Cys,ENST00000257694,NM_001256007.1;PNPLA8,missense_variant,p.Gly481Cys,ENST00000436062,NM_001256008.1;PNPLA8,missense_variant,p.Gly381Cys,ENST00000453144,NM_001256011.1,NM_001256010.1;PNPLA8,missense_variant,p.Gly381Cys,ENST00000453085,;PNPLA8,non_coding_transcript_exon_variant,,ENST00000483879,;PNPLA8,non_coding_transcript_exon_variant,,ENST00000476592,;PNPLA8,non_coding_transcript_exon_variant,,ENST00000489738,;PNPLA8,non_coding_transcript_exon_variant,,ENST00000462466,; A ENST00000422087 Transcript missense_variant 1848/3530 1441/2349 481/782 G/C Ggt/Tgt 1 -1 PNPLA8 HGNC HGNC:28900 protein_coding YES CCDS34733.1 ENSP00000410804 Q9NP80 A0A024R746 UPI0000073D34 NM_015723.3 deleterious(0) 7/12 hmmpanther:PTHR24185,Gene3D:3.40.1090.10,Pfam_domain:PF01734,Superfamily_domains:SSF52151 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 108497495 108497495 C A 1 0 0 0 0 1 0 0 0 12279 594 21 2 2 PNPLA8 7 108497495 Missense_Mutation SNP C 11LU022_T 307826 108497495 50848478 410 1048 DOCK4 0 . GRCh38 7 111834687 111834687 + Splice_Site SNP C C T novel 11LU022_T 11LU022_N C C c.2737-1G>A p.X913_splice ENST00000437633 92 77 15 88 88 0 strelka-varscan DOCK4,splice_acceptor_variant,,ENST00000428084,;DOCK4,splice_acceptor_variant,,ENST00000423057,;DOCK4,splice_acceptor_variant,,ENST00000437633,NM_014705.3;DOCK4,splice_acceptor_variant,,ENST00000445943,;DOCK4,splice_acceptor_variant,,ENST00000494651,; T ENST00000437633 Transcript splice_acceptor_variant -/6212 2737/5901 913/1966 1 -1 DOCK4 HGNC HGNC:19192 protein_coding YES CCDS47688.1 ENSP00000404179 Q8N1I0 UPI0000D5BB0D NM_014705.3 25/51 HIGH 1 SNV 1 1 PASS . . 0 187 12 9 2 0 0 0 -9.76032 0.5870143 0 1 1 0 T 5 4 3 111834687 111834687 C T 1 0 0 0 0 0 0 1 0 4504 695 24 3 3 DOCK4 7 111834687 Splice_Site SNP C 11LU022_T 3337192 111834687 47511286 411 1049 GPR85 0 . GRCh38 7 113083801 113083801 + Nonsense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.921G>A p.Trp307Ter p.W307* ENST00000297146 3/3 153 121 32 193 193 0 strelka-varscan GPR85,stop_gained,p.Trp307Ter,ENST00000297146,NM_001146265.1,NM_018970.6;GPR85,stop_gained,p.Trp307Ter,ENST00000424100,NM_001146267.1;GPR85,stop_gained,p.Trp307Ter,ENST00000449591,NM_001146266.1;GPR85,downstream_gene_variant,,ENST00000438062,;GPR85,downstream_gene_variant,,ENST00000449735,;GPR85,downstream_gene_variant,,ENST00000487573,;GPR85,stop_gained,p.Trp307Ter,ENST00000610164,; T ENST00000297146 Transcript stop_gained 1525/5079 921/1113 307/370 W/* tgG/tgA 1 -1 GPR85 HGNC HGNC:4536 protein_coding YES CCDS5758.1 ENSP00000297146 P60893 A4D0T8 UPI0000004048 NM_001146265.1,NM_018970.6 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 113083801 113083801 C T 1 0 0 0 0 0 1 0 0 6596 856 30 3 3 GPR85 7 113083801 Nonsense_Mutation SNP C 11LU022_T 1249114 113083801 46262172 412 1050 CTTNBP2 0 . GRCh38 7 117791589 117791589 + Missense_Mutation SNP C C A rs772434465 11LU022_T 11LU022_N C C c.1607G>T p.Arg536Leu p.R536L ENST00000160373 4/23 239 196 43 274 274 0 strelka-varscan CTTNBP2,missense_variant,p.Arg536Leu,ENST00000160373,NM_033427.2;CTTNBP2,missense_variant,p.Arg65Leu,ENST00000446636,;CTTNBP2,downstream_gene_variant,,ENST00000434890,;CTTNBP2,downstream_gene_variant,,ENST00000454375,;CTTNBP2,downstream_gene_variant,,ENST00000487820,;CTTNBP2,missense_variant,p.Arg536Leu,ENST00000441556,; A ENST00000160373 Transcript missense_variant 1699/5970 1607/4992 536/1663 R/L cGa/cTa rs772434465,COSM3374464 1 -1 CTTNBP2 HGNC HGNC:15679 protein_coding YES CCDS5774.1 ENSP00000160373 Q8WZ74 Q20BG9 UPI000006E94A NM_033427.2 deleterious(0) 4/23 hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF27 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 117791589 117791589 C A 1 0 0 0 0 1 0 0 0 3854 884 31 1 1 CTTNBP2 7 117791589 Missense_Mutation SNP C 11LU022_T 4707788 117791589 41554384 413 1051 ING3 0 . GRCh38 7 120953327 120953327 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.124A>G p.Arg42Gly p.R42G ENST00000315870 3/12 135 109 26 155 155 0 strelka-varscan ING3,missense_variant,p.Arg42Gly,ENST00000315870,NM_019071.2;ING3,missense_variant,p.Arg42Gly,ENST00000445699,;ING3,missense_variant,p.Arg27Gly,ENST00000431467,;ING3,missense_variant,p.Arg42Gly,ENST00000339121,NM_198267.1;ING3,missense_variant,p.Arg42Gly,ENST00000427726,; G ENST00000315870 Transcript missense_variant 272/3777 124/1257 42/418 R/G Aga/Gga 1 1 ING3 HGNC HGNC:14587 protein_coding YES CCDS5778.1 ENSP00000320566 Q9NXR8 UPI00000373B3 NM_019071.2 deleterious(0) 3/12 hmmpanther:PTHR10333:SF65,hmmpanther:PTHR10333,Pfam_domain:PF12998,SMART_domains:SM01408 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 120953327 120953327 A G 1 0 0 0 0 1 0 0 0 7639 64 3 5 5 ING3 7 120953327 Missense_Mutation SNP A 11LU022_T 3161738 120953327 38392646 414 1052 PTPRZ1 0 . GRCh38 7 121976788 121976788 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.556G>T p.Gly186Trp p.G186W ENST00000393386 6/30 141 118 23 112 112 0 strelka-varscan PTPRZ1,missense_variant,p.Gly186Trp,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.Gly186Trp,ENST00000449182,NM_001206839.1; T ENST00000393386 Transcript missense_variant 967/8175 556/6948 186/2315 G/W Ggg/Tgg 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0) 6/30 PROSITE_profiles:PS51144,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF214,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.999928 1 1 1 0 T 3 4 3 121976788 121976788 G T 1 0 0 0 0 1 0 0 0 12969 1362 47 2 2 PTPRZ1 7 121976788 Missense_Mutation SNP G 11LU022_T 1023461 121976788 37369185 415 1053 AASS 0 . GRCh38 7 122126438 122126438 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.409G>T p.Glu137Ter p.E137* ENST00000393376 3/23 376 317 59 347 347 0 strelka-varscan AASS,stop_gained,p.Glu137Ter,ENST00000393376,;AASS,stop_gained,p.Glu137Ter,ENST00000417368,NM_005763.3;AASS,intron_variant,,ENST00000473553,;AASS,stop_gained,p.Glu137Ter,ENST00000358954,;AASS,stop_gained,p.Glu137Ter,ENST00000431170,; A ENST00000393376 Transcript stop_gained 505/3233 409/2781 137/926 E/* Gag/Tag 1 -1 AASS HGNC HGNC:17366 protein_coding YES CCDS5783.1 ENSP00000377040 Q9UDR5 A4D0W4 UPI000004A105 3/23 hmmpanther:PTHR11133:SF14,hmmpanther:PTHR11133,Gene3D:3.40.50.1770,Pfam_domain:PF05222,SMART_domains:SM01003,Superfamily_domains:SSF52283 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 122126438 122126438 C A 1 0 0 0 0 0 1 0 0 28 835 29 2 2 AASS 7 122126438 Nonsense_Mutation SNP C 11LU022_T 149650 122126438 37219535 416 1054 GRM8 0 . GRCh38 7 126439134 126439134 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2712C>A p.Ser904Arg p.S904R ENST00000339582 11/11 100 82 18 128 128 0 strelka-varscan GRM8,missense_variant,p.Ser904Arg,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Ser412Arg,ENST00000444921,;GRM8,3_prime_UTR_variant,,ENST00000358373,NM_001127323.1;GRM8,non_coding_transcript_exon_variant,,ENST00000489939,;GRM8,non_coding_transcript_exon_variant,,ENST00000495315,;GRM8,3_prime_UTR_variant,,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; T ENST00000339582 Transcript missense_variant 3521/4057 2712/2727 904/908 S/R agC/agA 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious_low_confidence(0.01) 11/11 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 126439134 126439134 G T 1 0 0 0 0 1 0 0 0 6685 1310 46 2 2 GRM8 7 126439134 Missense_Mutation SNP G 11LU022_T 4312696 126439134 32906839 417 1055 PAX4 0 . GRCh38 7 127611194 127611194 + Frame_Shift_Del DEL G G - rs764742580 11LU022_T 11LU022_N G G c.902delC p.Pro301HisfsTer105 p.P301Hfs*105 ENST00000341640 9/9 285 236 49 316 316 0 sindel-varindel-pindel PAX4,frameshift_variant,p.Pro301HisfsTer105,ENST00000341640,NM_006193.2;PAX4,frameshift_variant,p.Pro299HisfsTer?,ENST00000463946,;PAX4,intron_variant,,ENST00000378740,;PAX4,intron_variant,,ENST00000338516,;PAX4,downstream_gene_variant,,ENST00000611453,;PAX4,intron_variant,,ENST00000483494,;PAX4,downstream_gene_variant,,ENST00000477423,; - ENST00000341640 Transcript frameshift_variant 1108/2010 902/1032 301/343 P/X cCa/ca rs764742580,COSM5026820 1 -1 PAX4 HGNC HGNC:8618 protein_coding YES CCDS5797.1 ENSP00000339906 O43316 UPI000013C824 NM_006193.2 9/9 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 127611194 127611194 G - 1 0 1 0 1 0 0 0 0 11566 1348 47 0 0 PAX4 7 127611194 Frame_Shift_Del DEL G 11LU022_T 1172060 127611194 31734779 418 1056 KCP 0 . GRCh38 7 128877579 128877579 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.4523C>T p.Ser1508Phe p.S1508F ENST00000610776 39/40 473 373 100 625 624 1 strelka-varscan KCP,missense_variant,p.Ser1508Phe,ENST00000610776,;KCP,missense_variant,p.Ser1448Phe,ENST00000613019,;KCP,missense_variant,p.Ser1384Phe,ENST00000620378,NM_001135914.1;KCP,3_prime_UTR_variant,,ENST00000611280,;KCP,intron_variant,,ENST00000492679,;KCP,intron_variant,,ENST00000460528,; A ENST00000610776 Transcript missense_variant 4566/5108 4523/4887 1508/1628 S/F tCc/tTc 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 deleterious(0.01) 39/40 hmmpanther:PTHR11339:SF280,hmmpanther:PTHR11339,SMART_domains:SM00832 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 128877579 128877579 G A 1 0 0 0 0 1 0 0 0 8012 1174 41 3 3 KCP 7 128877579 Missense_Mutation SNP G 11LU022_T 1266385 128877579 30468394 419 1057 CPA2 0 . GRCh38 7 130276687 130276687 + Silent SNP C C A rs754244605 11LU022_T 11LU022_N C C c.645C>A p.= p.I215I ENST00000222481 7/11 144 113 31 158 158 0 strelka-varscan CPA2,synonymous_variant,p.=,ENST00000222481,NM_001869.2;CPA2,3_prime_UTR_variant,,ENST00000416698,;CPA2,non_coding_transcript_exon_variant,,ENST00000487259,;CPA2,downstream_gene_variant,,ENST00000480781,; A ENST00000222481 Transcript synonymous_variant 700/1366 645/1260 215/419 I atC/atA rs754244605 1 1 CPA2 HGNC HGNC:2297 protein_coding YES CCDS5817.2 ENSP00000222481 P48052 UPI00005A7711 NM_001869.2 7/11 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF71,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 130276687 130276687 C A 1 0 0 0 0 0 0 0 1 3584 903 32 2 2 CPA2 7 130276687 Silent SNP C 11LU022_T 1399108 130276687 29069286 420 1058 PLXNA4 0 . GRCh38 7 132146543 132146543 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.5022T>A p.= p.S1674S ENST00000359827 28/32 533 439 94 576 576 0 strelka-varscan PLXNA4,synonymous_variant,p.=,ENST00000359827,;PLXNA4,synonymous_variant,p.=,ENST00000321063,NM_020911.1;PLXNA4,upstream_gene_variant,,ENST00000496550,; T ENST00000359827 Transcript synonymous_variant 5985/13786 5022/5685 1674/1894 S tcT/tcA 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 28/32 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 132146543 132146543 A T 1 0 0 0 0 0 0 0 1 12228 175 7 4 4 PLXNA4 7 132146543 Silent SNP A 11LU022_T 1869856 132146543 27199430 421 1059 CALD1 0 . GRCh38 7 134928818 134928818 + Silent SNP C C A 11LU022_T 11LU022_N C C c.136C>A p.= p.R46R ENST00000361675 4/15 139 111 28 131 131 0 strelka-varscan CALD1,synonymous_variant,p.=,ENST00000393118,NM_033139.3;CALD1,synonymous_variant,p.=,ENST00000361901,NM_004342.6;CALD1,synonymous_variant,p.=,ENST00000361675,NM_033138.3;CALD1,synonymous_variant,p.=,ENST00000422748,NM_033157.3;CALD1,synonymous_variant,p.=,ENST00000495522,;CALD1,synonymous_variant,p.=,ENST00000424922,NM_033140.3;CALD1,synonymous_variant,p.=,ENST00000417172,;CALD1,synonymous_variant,p.=,ENST00000436461,;CALD1,synonymous_variant,p.=,ENST00000454108,;CALD1,synonymous_variant,p.=,ENST00000445569,;CALD1,synonymous_variant,p.=,ENST00000435928,;CALD1,non_coding_transcript_exon_variant,,ENST00000496024,;CALD1,synonymous_variant,p.=,ENST00000443197,;CALD1,synonymous_variant,p.=,ENST00000430085,;CALD1,non_coding_transcript_exon_variant,,ENST00000482470,; A ENST00000361675 Transcript synonymous_variant 365/3612 136/2382 46/793 R Cga/Aga COSM4465168,COSM4465169 1 1 CALD1 HGNC HGNC:1441 protein_coding YES CCDS5835.1 ENSP00000354826 Q05682 UPI0000140A64 NM_033138.3 4/15 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF02029,hmmpanther:PTHR18949,hmmpanther:PTHR18949:SF0,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 134928818 134928818 C A 1 0 0 0 0 0 0 0 1 2271 644 23 1 1 CALD1 7 134928818 Silent SNP C 11LU022_T 2782275 134928818 24417155 422 1060 HIPK2 0 . GRCh38 7 139626759 139626759 + Silent SNP C C G novel 11LU022_T 11LU022_N C C c.1461G>C p.= p.G487G ENST00000406875 6/15 155 105 50 160 160 0 strelka-varscan HIPK2,synonymous_variant,p.=,ENST00000406875,NM_022740.4;HIPK2,synonymous_variant,p.=,ENST00000428878,NM_001113239.2;HIPK2,synonymous_variant,p.=,ENST00000342645,; G ENST00000406875 Transcript synonymous_variant 1556/15049 1461/3597 487/1198 G ggG/ggC 1 -1 HIPK2 HGNC HGNC:14402 protein_coding YES CCDS75667.1 ENSP00000385571 Q9H2X6 UPI000012C71E NM_022740.4 6/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF53,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 139626759 139626759 C G 1 0 0 0 0 0 0 0 1 7005 842 30 4 4 HIPK2 7 139626759 Silent SNP C 11LU022_T 4697941 139626759 19719214 423 1061 PARP12 0 . GRCh38 7 140026295 140026295 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1682A>T p.Gln561Leu p.Q561L ENST00000263549 11/12 255 204 51 255 255 0 strelka-varscan PARP12,missense_variant,p.Gln561Leu,ENST00000263549,NM_022750.3;PARP12,missense_variant,p.Gln33Leu,ENST00000484111,;PARP12,synonymous_variant,p.=,ENST00000489809,;PARP12,3_prime_UTR_variant,,ENST00000473341,;PARP12,3_prime_UTR_variant,,ENST00000491598,;PARP12,non_coding_transcript_exon_variant,,ENST00000488726,;PARP12,non_coding_transcript_exon_variant,,ENST00000496624,;PARP12,non_coding_transcript_exon_variant,,ENST00000489383,;PARP12,downstream_gene_variant,,ENST00000466597,; A ENST00000263549 Transcript missense_variant 2556/3796 1682/2106 561/701 Q/L cAg/cTg 1 -1 PARP12 HGNC HGNC:21919 protein_coding YES CCDS5857.1 ENSP00000263549 Q9H0J9 A4D1T0 UPI000006F644 NM_022750.3 tolerated(0.64) 11/12 Gene3D:3.90.228.10,Pfam_domain:PF00644,PROSITE_profiles:PS51059,hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF15,Superfamily_domains:SSF56399 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 140026295 140026295 T A 1 0 0 0 0 1 0 0 0 11537 1580 55 4 4 PARP12 7 140026295 Missense_Mutation SNP T 11LU022_T 399536 140026295 19319678 424 1062 MGAM 0 . GRCh38 7 142034280 142034280 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1688T>A p.Leu563Gln p.L563Q ENST00000549489 15/48 173 138 35 162 162 0 strelka-varscan MGAM,missense_variant,p.Leu563Gln,ENST00000475668,;MGAM,missense_variant,p.Leu563Gln,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Leu563Gln,ENST00000620571,;MGAM,downstream_gene_variant,,ENST00000495045,;MGAM,upstream_gene_variant,,ENST00000490593,; A ENST00000549489 Transcript missense_variant 1783/6525 1688/5574 563/1857 L/Q cTg/cAg 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 15/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 142034280 142034280 T A 1 0 0 0 0 1 0 0 0 9499 1580 55 4 4 MGAM 7 142034280 Missense_Mutation SNP T 11LU022_T 2007985 142034280 17311693 425 1063 MGAM 0 . GRCh38 7 142034731 142034731 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.1849G>T p.Gly617Cys p.G617C ENST00000549489 16/48 129 115 14 120 119 1 strelka-varscan MGAM,missense_variant,p.Gly617Cys,ENST00000475668,;MGAM,missense_variant,p.Gly617Cys,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Gly617Cys,ENST00000620571,;MGAM,downstream_gene_variant,,ENST00000495045,;MGAM,upstream_gene_variant,,ENST00000490593,; T ENST00000549489 Transcript missense_variant 1944/6525 1849/5574 617/1857 G/C Ggc/Tgc COSM321674,COSM321675 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 16/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055,Superfamily_domains:SSF51445 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 142034731 142034731 G T 1 0 0 0 0 1 0 0 0 9499 1232 43 2 2 MGAM 7 142034731 Missense_Mutation SNP G 11LU022_T 451 142034731 17311242 426 1064 MGAM2 0 . GRCh38 7 142170085 142170085 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.3038C>T p.Pro1013Leu p.P1013L ENST00000477922 27/48 75 53 22 84 84 0 strelka-varscan MGAM2,missense_variant,p.Pro1013Leu,ENST00000477922,NM_001293626.1;MGAM2,upstream_gene_variant,,ENST00000496337,; T ENST00000477922 Transcript missense_variant 3092/7867 3038/7548 1013/2515 P/L cCc/cTc 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.01) 27/48 Pfam_domain:PF16863,Superfamily_domains:SSF74650 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 3 142170085 142170085 C T 1 0 0 0 0 1 0 0 0 9500 623 22 3 3 MGAM2 7 142170085 Missense_Mutation SNP C 11LU022_T 135354 142170085 17175888 427 1065 MGAM2 0 . GRCh38 7 142198652 142198652 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.4961T>A p.Leu1654Gln p.L1654Q ENST00000477922 44/48 188 141 47 197 197 0 strelka-varscan MGAM2,missense_variant,p.Leu1654Gln,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript missense_variant 5015/7867 4961/7548 1654/2515 L/Q cTg/cAg 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 44/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51011 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 142198652 142198652 T A 1 0 0 0 0 1 0 0 0 9500 1580 55 4 4 MGAM2 7 142198652 Missense_Mutation SNP T 11LU022_T 28567 142198652 17147321 428 1066 EPHB6 0 . GRCh38 7 142864043 142864043 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.243T>A p.= p.P81P ENST00000619012 7/20 302 246 56 395 395 0 strelka-varscan EPHB6,synonymous_variant,p.=,ENST00000619012,;EPHB6,synonymous_variant,p.=,ENST00000422643,NM_004445.5;EPHB6,5_prime_UTR_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000497095,;EPHB6,synonymous_variant,p.=,ENST00000611578,;EPHB6,3_prime_UTR_variant,,ENST00000614832,;EPHB6,non_coding_transcript_exon_variant,,ENST00000616380,;EPHB6,upstream_gene_variant,,ENST00000486511,; A ENST00000619012 Transcript synonymous_variant 995/4011 243/3069 81/1022 P ccT/ccA 1 1 EPHB6 HGNC HGNC:3396 protein_coding YES CCDS5873.2 ENSP00000481994 F8WCM8 UPI0003EAF8C7 7/20 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF326,hmmpanther:PTHR24416,Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 142864043 142864043 T A 1 0 0 0 0 0 0 0 1 5025 1538 54 4 4 EPHB6 7 142864043 Silent SNP T 11LU022_T 665391 142864043 16481930 429 1067 TRPV6 0 . GRCh38 7 142885556 142885556 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.81G>T p.Trp27Cys p.W27C ENST00000359396 1/15 45 32 13 38 38 0 strelka-varscan TRPV6,missense_variant,p.Trp27Cys,ENST00000359396,NM_018646.5;TRPV6,intron_variant,,ENST00000436401,;RP11-114L10.2,intron_variant,,ENST00000438839,;TRPV6,upstream_gene_variant,,ENST00000615386,; A ENST00000359396 Transcript missense_variant 207/2928 81/2298 27/765 W/C tgG/tgT 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 deleterious_low_confidence(0.03) 1/15 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 142885556 142885556 C A 1 0 0 0 0 1 0 0 0 17106 740 26 2 2 TRPV6 7 142885556 Missense_Mutation SNP C 11LU022_T 21513 142885556 16460417 430 1068 TRPV5 0 . GRCh38 7 142928155 142928155 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.842C>A p.Thr281Lys p.T281K ENST00000265310 7/15 226 184 42 220 220 0 strelka-varscan TRPV5,missense_variant,p.Thr281Lys,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Thr281Lys,ENST00000442623,;TRPV5,intron_variant,,ENST00000439304,; T ENST00000265310 Transcript missense_variant 1191/2952 842/2190 281/729 T/K aCg/aAg 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 deleterious(0) 7/15 hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 142928155 142928155 G T 1 0 0 0 0 1 0 0 0 17105 1145 40 1 1 TRPV5 7 142928155 Missense_Mutation SNP G 11LU022_T 42599 142928155 16417818 431 1069 TAS2R39 0 . GRCh38 7 143184106 143184106 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.688C>A p.Leu230Met p.L230M ENST00000446620 1/1 219 165 54 195 194 1 strelka-varscan TAS2R39,missense_variant,p.Leu230Met,ENST00000446620,NM_176881.2; A ENST00000446620 Transcript missense_variant 688/1017 688/1017 230/338 L/M Ctg/Atg 1 1 TAS2R39 HGNC HGNC:18886 protein_coding YES CCDS47729.1 ENSP00000405095 P59534 UPI00000620BE NM_176881.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR11394:SF67,hmmpanther:PTHR11394,Pfam_domain:PF05296,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 143184106 143184106 C A 1 0 0 0 0 1 0 0 0 15975 680 24 2 2 TAS2R39 7 143184106 Missense_Mutation SNP C 11LU022_T 255951 143184106 16161867 432 1070 FAM131B 0 . GRCh38 7 143358890 143358890 + Missense_Mutation SNP G G T rs148056886 11LU022_T 11LU022_N G G c.403C>A p.Arg135Ser p.R135S ENST00000443739 5/7 298 267 31 414 413 1 strelka-varscan FAM131B,missense_variant,p.Arg107Ser,ENST00000409408,;FAM131B,missense_variant,p.Arg135Ser,ENST00000443739,NM_001031690.2,NM_001278297.1;FAM131B,missense_variant,p.Arg107Ser,ENST00000409346,;FAM131B,missense_variant,p.Arg123Ser,ENST00000409578,;FAM131B,missense_variant,p.Arg107Ser,ENST00000409222,NM_014690.4;FAM131B,3_prime_UTR_variant,,ENST00000410085,;FAM131B,3_prime_UTR_variant,,ENST00000521347,;FAM131B,3_prime_UTR_variant,,ENST00000519279,;FAM131B,non_coding_transcript_exon_variant,,ENST00000519161,; T ENST00000443739 Transcript missense_variant 552/4382 403/1083 135/360 R/S Cgc/Agc rs148056886 1 -1 FAM131B HGNC HGNC:22202 protein_coding YES CCDS47734.1 ENSP00000410603 Q86XD5 UPI0001633639 NM_001031690.2,NM_001278297.1 tolerated(0.13) 5/7 hmmpanther:PTHR15736,hmmpanther:PTHR15736:SF9,Pfam_domain:PF15010 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 143358890 143358890 G T 1 0 0 0 0 1 0 0 0 5290 1087 38 1 1 FAM131B 7 143358890 Missense_Mutation SNP G 11LU022_T 174784 143358890 15987083 433 1071 NOBOX 0 . GRCh38 7 144410200 144410200 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.28C>A p.Pro10Thr p.P10T ENST00000467773 1/10 153 118 35 165 165 0 strelka-varscan NOBOX,missense_variant,p.Pro10Thr,ENST00000467773,NM_001080413.3;NOBOX,missense_variant,p.Pro10Thr,ENST00000483238,; T ENST00000467773 Transcript missense_variant 28/2076 28/2076 10/691 P/T Cca/Aca 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 tolerated_low_confidence(0.28) 1/10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 144410200 144410200 G T 1 0 0 0 0 1 0 0 0 10554 1261 44 2 2 NOBOX 7 144410200 Missense_Mutation SNP G 11LU022_T 1051310 144410200 14935773 434 1072 GIMAP8 0 . GRCh38 7 150474236 150474236 + Missense_Mutation SNP G G A 11LU022_T 11LU022_N G G c.907G>A p.Ala303Thr p.A303T ENST00000307271 4/5 263 211 52 250 250 0 strelka-varscan GIMAP8,missense_variant,p.Ala303Thr,ENST00000307271,NM_175571.3; A ENST00000307271 Transcript missense_variant 1481/4184 907/1998 303/665 A/T Gct/Act COSM1285157 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 tolerated(1) 4/5 PROSITE_profiles:PS51720,Gene3D:3.40.50.300,Pfam_domain:PF04548,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 150474236 150474236 G A 1 0 0 0 0 1 0 0 0 6265 1319 46 3 3 GIMAP8 7 150474236 Missense_Mutation SNP G 11LU022_T 6064036 150474236 8871737 435 1073 HTR5A 0 . GRCh38 7 155071408 155071408 + Missense_Mutation SNP C C A rs185184389 11LU022_T 11LU022_N C C c.509C>A p.Ala170Asp p.A170D ENST00000287907 1/2 386 291 95 417 417 0 strelka-varscan HTR5A,missense_variant,p.Ala170Asp,ENST00000287907,NM_024012.3;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000395731,;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000493904,;RP11-5C23.4,upstream_gene_variant,,ENST00000637588,; A ENST00000287907 Transcript missense_variant 1085/2912 509/1074 170/357 A/D gCt/gAt rs185184389 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 deleterious(0.04) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 155071408 155071408 C A 1 0 0 0 0 1 0 0 0 7346 797 28 2 2 HTR5A 7 155071408 Missense_Mutation SNP C 11LU022_T 4597172 155071408 4274565 436 1074 HTR5A 0 . GRCh38 7 155084240 155084240 + Missense_Mutation SNP G G T rs770383539 11LU022_T 11LU022_N G G c.827G>T p.Arg276Leu p.R276L ENST00000287907 2/2 223 179 44 217 217 0 strelka-varscan HTR5A,missense_variant,p.Arg276Leu,ENST00000287907,NM_024012.3;HTR5A,non_coding_transcript_exon_variant,,ENST00000486819,; T ENST00000287907 Transcript missense_variant 1403/2912 827/1074 276/357 R/L cGg/cTg rs770383539,COSM1087806 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 deleterious(0.03) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 155084240 155084240 G T 1 0 0 0 0 1 0 0 0 7346 1116 39 1 1 HTR5A 7 155084240 Missense_Mutation SNP G 11LU022_T 12832 155084240 4261733 437 1075 DLGAP2 0 . GRCh38 8 1697208 1697208 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.2576A>C p.Gln859Pro p.Q859P ENST00000612087 10/11 130 92 38 95 95 0 strelka-varscan-mutect DLGAP2,missense_variant,p.Gln859Pro,ENST00000612087,NM_001277161.1;DLGAP2,missense_variant,p.Gln876Pro,ENST00000520901,;DLGAP2,missense_variant,p.Gln953Pro,ENST00000637795,;DLGAP2,missense_variant,p.Gln952Pro,ENST00000421627,;DLGAP2,missense_variant,p.Gln873Pro,ENST00000637152,NM_004745.4; C ENST00000612087 Transcript missense_variant 2710/10088 2576/2886 859/961 Q/P cAg/cCg 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 deleterious(0) 10/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3,Pfam_domain:PF03359 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 1697208 1697208 A C 1 0 0 0 0 1 0 0 0 4367 188 7 5 5 DLGAP2 8 1697208 Missense_Mutation SNP A 11LU022_T 1697208 143441428 438 1076 CSMD1 0 . GRCh38 8 2973246 2973246 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.8797C>A p.Leu2933Ile p.L2933I ENST00000520002 58/71 220 200 20 189 189 0 strelka-varscan-mutect CSMD1,missense_variant,p.Leu2794Ile,ENST00000537824,;CSMD1,missense_variant,p.Leu2350Ile,ENST00000335551,;CSMD1,missense_variant,p.Leu2933Ile,ENST00000520002,;CSMD1,missense_variant,p.Leu2933Ile,ENST00000602557,;CSMD1,missense_variant,p.Leu2932Ile,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Leu2875Ile,ENST00000400186,;CSMD1,missense_variant,p.Leu2875Ile,ENST00000602723,; T ENST00000520002 Transcript missense_variant 9353/11740 8797/10698 2933/3565 L/I Ctt/Att 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.24) 58/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 2973246 2973246 G T 1 0 0 0 0 1 0 0 0 3745 971 34 2 2 CSMD1 8 2973246 Missense_Mutation SNP G 11LU022_T 1276038 2973246 142165390 439 1077 CSMD1 0 . GRCh38 8 3000120 3000120 + Missense_Mutation SNP C C A rs757892398 11LU022_T 11LU022_N C C c.8044G>T p.Gly2682Cys p.G2682C ENST00000520002 54/71 106 61 45 87 87 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly2543Cys,ENST00000537824,;CSMD1,missense_variant,p.Gly2099Cys,ENST00000335551,;CSMD1,missense_variant,p.Gly2682Cys,ENST00000520002,;CSMD1,missense_variant,p.Gly2682Cys,ENST00000602557,;CSMD1,missense_variant,p.Gly2681Cys,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly2624Cys,ENST00000400186,;CSMD1,missense_variant,p.Gly2624Cys,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000519623,; A ENST00000520002 Transcript missense_variant 8600/11740 8044/10698 2682/3565 G/C Ggt/Tgt rs757892398,COSM211431,COSM211432 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 54/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs757892398 . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 3000120 3000120 C A 1 0 0 0 0 1 0 0 0 3745 652 23 1 1 CSMD1 8 3000120 Missense_Mutation SNP C 11LU022_T 26874 3000120 142138516 440 1078 CSMD1 0 . GRCh38 8 3359271 3359271 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3188G>T p.Gly1063Val p.G1063V ENST00000520002 22/71 182 155 27 170 170 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly924Val,ENST00000537824,;CSMD1,missense_variant,p.Gly543Val,ENST00000335551,;CSMD1,missense_variant,p.Gly1063Val,ENST00000520002,;CSMD1,missense_variant,p.Gly1063Val,ENST00000602557,;CSMD1,missense_variant,p.Gly1062Val,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly1063Val,ENST00000400186,;CSMD1,missense_variant,p.Gly1063Val,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; A ENST00000520002 Transcript missense_variant 3744/11740 3188/10698 1063/3565 G/V gGt/gTt 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.01) 22/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 3359271 3359271 C A 1 0 0 0 0 1 0 0 0 3745 507 18 2 2 CSMD1 8 3359271 Missense_Mutation SNP C 11LU022_T 359151 3359271 141779365 441 1079 PRSS55 0 . GRCh38 8 10529563 10529563 + Missense_Mutation SNP G G A rs779594803 11LU022_T 11LU022_N G G c.211G>A p.Gly71Arg p.G71R ENST00000328655 2/5 341 304 37 373 371 2 strelka-varscan-mutect PRSS55,missense_variant,p.Gly71Arg,ENST00000328655,NM_198464.3;PRSS55,missense_variant,p.Gly71Arg,ENST00000522210,NM_001197020.1;PRSS51,intron_variant,,ENST00000637190,;PRSS55,missense_variant,p.Gly52Arg,ENST00000518641,;PRSS51,intron_variant,,ENST00000523024,; A ENST00000328655 Transcript missense_variant 251/1124 211/1059 71/352 G/R Ggg/Agg rs779594803 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 deleterious(0.04) 2/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF191,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs779594803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 10529563 10529563 G A 1 0 0 0 0 1 0 0 0 12783 1232 43 3 3 PRSS55 8 10529563 Missense_Mutation SNP G 11LU022_T 7170292 10529563 134609073 442 1080 PRSS55 0 . GRCh38 8 10529591 10529591 + Missense_Mutation SNP C C A rs550455663 11LU022_T 11LU022_N C C c.239C>A p.Pro80Gln p.P80Q ENST00000328655 2/5 316 292 24 325 325 0 strelka-varscan-mutect PRSS55,missense_variant,p.Pro80Gln,ENST00000328655,NM_198464.3;PRSS55,missense_variant,p.Pro80Gln,ENST00000522210,NM_001197020.1;PRSS51,intron_variant,,ENST00000637190,;PRSS55,missense_variant,p.Pro61Gln,ENST00000518641,;PRSS51,intron_variant,,ENST00000523024,; A ENST00000328655 Transcript missense_variant 279/1124 239/1059 80/352 P/Q cCg/cAg rs550455663,COSM1094442 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 deleterious(0) 2/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF191,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs550455663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 10529591 10529591 C A 1 0 0 0 0 1 0 0 0 12783 652 23 1 1 PRSS55 8 10529591 Missense_Mutation SNP C 11LU022_T 28 10529591 134609045 443 1081 SLC35G5 0 . GRCh38 8 11331654 11331654 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.548G>A p.Gly183Glu p.G183E ENST00000382435 1/1 281 255 26 322 322 0 varscan-mutect SLC35G5,missense_variant,p.Gly183Glu,ENST00000382435,NM_054028.1;MTMR9,downstream_gene_variant,,ENST00000221086,NM_015458.3; A ENST00000382435 Transcript missense_variant 767/1321 548/1017 183/338 G/E gGg/gAg 1 1 SLC35G5 HGNC HGNC:15546 protein_coding YES CCDS5980.1 ENSP00000371872 Q96KT7 UPI0000071B8F NM_054028.1 tolerated(0.11) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR22911:SF32,hmmpanther:PTHR22911 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 11331654 11331654 G A 1 0 0 0 0 1 0 0 0 14869 1232 43 3 3 SLC35G5 8 11331654 Missense_Mutation SNP G 11LU022_T 802063 11331654 133806982 444 1082 DMTN 0 . GRCh38 8 22070185 22070185 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.455C>T p.Ser152Phe p.S152F ENST00000523266 8/16 40 32 8 50 50 0 strelka-varscan-mutect DMTN,missense_variant,p.Ser152Phe,ENST00000358242,;DMTN,missense_variant,p.Ser152Phe,ENST00000523266,NM_001978.3;DMTN,missense_variant,p.Ser152Phe,ENST00000519907,NM_001302816.1;DMTN,missense_variant,p.Ser152Phe,ENST00000381470,NM_001323384.1,NM_001323385.1,NM_001114137.2;DMTN,missense_variant,p.Ser152Phe,ENST00000265800,NM_001323378.1,NM_001323380.1,NM_001323381.1,NM_001114136.2,NM_001114135.3;DMTN,missense_variant,p.Ser152Phe,ENST00000517305,;DMTN,missense_variant,p.Ser152Phe,ENST00000432128,;DMTN,missense_variant,p.Ser127Phe,ENST00000443491,NM_001323387.1,NM_001114139.2;DMTN,missense_variant,p.Ser152Phe,ENST00000415253,NM_001114138.2;DMTN,missense_variant,p.Ser127Phe,ENST00000523782,;DMTN,missense_variant,p.Ser112Phe,ENST00000517600,NM_001302817.1;DMTN,missense_variant,p.Ser127Phe,ENST00000520174,;DMTN,missense_variant,p.Ser152Phe,ENST00000517418,;DMTN,missense_variant,p.Ser152Phe,ENST00000517804,;DMTN,missense_variant,p.Ser127Phe,ENST00000523300,;DMTN,missense_variant,p.Ser127Phe,ENST00000523623,;DMTN,downstream_gene_variant,,ENST00000522148,;DMTN,downstream_gene_variant,,ENST00000522340,;DMTN,downstream_gene_variant,,ENST00000519850,;DMTN,downstream_gene_variant,,ENST00000519333,;DMTN,non_coding_transcript_exon_variant,,ENST00000518816,;DMTN,downstream_gene_variant,,ENST00000520856,;DMTN,downstream_gene_variant,,ENST00000519959,; T ENST00000523266 Transcript missense_variant 917/2735 455/1218 152/405 S/F tCc/tTc COSM4162896,COSM4162897,COSM4495530,COSM4495531 1 1 DMTN HGNC HGNC:3382 protein_coding YES CCDS6020.1 ENSP00000427866 Q08495 UPI0000129189 NM_001978.3 deleterious(0.01) 8/16 Pfam_domain:PF16182,hmmpanther:PTHR24213 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs1464049702 . 0 208 2 0 0 0 0 0 -19.87805 1 1 1 1 0 T 3 4 3 22070185 22070185 C T 1 0 0 0 0 1 0 0 0 4401 869 30 3 3 DMTN 8 22070185 Missense_Mutation SNP C 11LU022_T 10738531 22070185 123068451 445 1083 HR 0 . GRCh38 8 22127692 22127692 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.750G>T p.Gln250His p.Q250H ENST00000381418 3/19 200 153 47 339 339 0 strelka-varscan-mutect HR,missense_variant,p.Gln250His,ENST00000381418,NM_005144.4;HR,missense_variant,p.Gln250His,ENST00000312841,NM_018411.4;HR,non_coding_transcript_exon_variant,,ENST00000519619,;HR,downstream_gene_variant,,ENST00000518377,;HR,downstream_gene_variant,,ENST00000522759,;HR,upstream_gene_variant,,ENST00000517699,; A ENST00000381418 Transcript missense_variant 2231/6336 750/3570 250/1189 Q/H caG/caT 1 -1 HR HGNC HGNC:5172 protein_coding YES CCDS6022.1 ENSP00000370826 O43593 UPI000013EB0B NM_005144.4 tolerated(0.15) 3/19 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 22127692 22127692 C A 1 0 0 0 0 1 0 0 0 7242 912 32 2 2 HR 8 22127692 Missense_Mutation SNP C 11LU022_T 57507 22127692 123010944 446 1084 EBF2 0 . GRCh38 8 25861152 25861152 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.1239A>T p.= p.P413P ENST00000520164 13/16 149 133 16 173 173 0 strelka-varscan EBF2,synonymous_variant,p.=,ENST00000520164,NM_022659.3;EBF2,synonymous_variant,p.=,ENST00000408929,;EBF2,synonymous_variant,p.=,ENST00000535548,; A ENST00000520164 Transcript synonymous_variant 1777/5145 1239/1728 413/575 P ccA/ccT 1 -1 EBF2 HGNC HGNC:19090 protein_coding YES CCDS43726.1 ENSP00000430241 Q9HAK2 UPI0000DD7EC9 NM_022659.3 13/16 Low_complexity_(Seg):seg,hmmpanther:PTHR10747 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 25861152 25861152 T A 1 0 0 0 0 0 0 0 1 4705 1567 55 4 4 EBF2 8 25861152 Silent SNP T 11LU022_T 3733460 25861152 119277484 447 1085 KCNU1 0 . GRCh38 8 36922538 36922538 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2645G>T p.Gly882Val p.G882V ENST00000399881 24/27 110 88 22 144 144 0 strelka-varscan KCNU1,missense_variant,p.Gly882Val,ENST00000399881,NM_001031836.2;KCNU1,missense_variant,p.Gly882Val,ENST00000522372,; T ENST00000399881 Transcript missense_variant 2682/3695 2645/3450 882/1149 G/V gGg/gTg 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 deleterious(0.04) 24/27 hmmpanther:PTHR10027:SF23,hmmpanther:PTHR10027 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 36922538 36922538 G T 1 0 0 0 0 1 0 0 0 8009 1232 43 2 2 KCNU1 8 36922538 Missense_Mutation SNP G 11LU022_T 11061386 36922538 108216098 448 1086 KCNU1 0 . GRCh38 8 36935556 36935556 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.3086C>T p.Pro1029Leu p.P1029L ENST00000399881 27/27 53 43 10 69 69 0 strelka-varscan KCNU1,missense_variant,p.Pro1029Leu,ENST00000399881,NM_001031836.2;KCNU1,downstream_gene_variant,,ENST00000518904,;KCNU1,3_prime_UTR_variant,,ENST00000522372,; T ENST00000399881 Transcript missense_variant 3123/3695 3086/3450 1029/1149 P/L cCt/cTt COSM4486655,COSM4486656 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 deleterious(0.04) 27/27 hmmpanther:PTHR10027:SF23,hmmpanther:PTHR10027 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 T 3 4 3 36935556 36935556 C T 1 0 0 0 0 1 0 0 0 8009 681 24 3 3 KCNU1 8 36935556 Missense_Mutation SNP C 11LU022_T 13018 36935556 108203080 449 1087 ADGRA2 0 . GRCh38 8 37837773 37837773 + Missense_Mutation SNP C C T rs575195976 11LU022_T 11LU022_N C C c.2093C>T p.Ser698Leu p.S698L ENST00000412232 14/19 141 107 34 170 170 0 strelka-varscan ADGRA2,missense_variant,p.Ser698Leu,ENST00000412232,NM_032777.9;ADGRA2,intron_variant,,ENST00000315215,; T ENST00000412232 Transcript missense_variant 2106/5651 2093/4017 698/1338 S/L tCg/tTg rs575195976,COSM4476753 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 deleterious(0.01) 14/19 hmmpanther:PTHR12011:SF33,hmmpanther:PTHR12011 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 37837773 37837773 C T 1 0 0 0 0 1 0 0 0 353 893 31 1 1 ADGRA2 8 37837773 Missense_Mutation SNP C 11LU022_T 902217 37837773 107300863 450 1088 4 2 ADGRA2 0 . GRCh38 8 37837780 37837780 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.2100G>T p.= p.R700R ENST00000412232 14/19 121 92 29 148 148 0 strelka-varscan ADGRA2,synonymous_variant,p.=,ENST00000412232,NM_032777.9;ADGRA2,intron_variant,,ENST00000315215,; T ENST00000412232 Transcript synonymous_variant 2113/5651 2100/4017 700/1338 R cgG/cgT 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 14/19 hmmpanther:PTHR12011:SF33,hmmpanther:PTHR12011 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 37837780 37837780 G T 1 0 0 0 0 0 0 0 1 353 1190 42 2 2 ADGRA2 8 37837780 Silent SNP G 11LU022_T 7 37837780 107300856 451 1089 4 2 RAB11FIP1 0 . GRCh38 8 37870408 37870408 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.1299G>A p.= p.L433L ENST00000524118 3/3 108 87 21 109 109 0 strelka-varscan RAB11FIP1,synonymous_variant,p.=,ENST00000524118,;RAB11FIP1,intron_variant,,ENST00000330843,NM_001002814.2;RAB11FIP1,intron_variant,,ENST00000287263,NM_025151.4;RAB11FIP1,intron_variant,,ENST00000522727,;RAB11FIP1,intron_variant,,ENST00000523182,;RAB11FIP1,intron_variant,,ENST00000522774,; T ENST00000524118 Transcript synonymous_variant 1938/1959 1299/1320 433/439 L ctG/ctA 1 -1 RAB11FIP1 HGNC HGNC:30265 protein_coding ENSP00000430680 Q6WKZ4 UPI000050AAED 3/3 LOW SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 37870408 37870408 C T 1 0 0 0 0 0 0 0 1 13051 813 29 3 3 RAB11FIP1 8 37870408 Silent SNP C 11LU022_T 32628 37870408 107268228 452 1090 OPRK1 0 . GRCh38 8 53234922 53234922 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.447G>T p.Leu149Phe p.L149F ENST00000265572 3/4 228 197 31 252 252 0 strelka-varscan OPRK1,missense_variant,p.Leu60Phe,ENST00000612786,NM_001282904.1;OPRK1,missense_variant,p.Leu149Phe,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,missense_variant,p.Leu135Phe,ENST00000613482,;OPRK1,missense_variant,p.Leu149Phe,ENST00000520287,;OPRK1,missense_variant,p.Leu60Phe,ENST00000524278,;RP11-162D9.3,intron_variant,,ENST00000524425,;OPRK1,3_prime_UTR_variant,,ENST00000522508,; A ENST00000265572 Transcript missense_variant 745/5014 447/1143 149/380 L/F ttG/ttT COSM1755744 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 deleterious(0) 3/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00384,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF1,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 53234922 53234922 C A 1 0 0 0 0 1 0 0 0 10961 825 29 2 2 OPRK1 8 53234922 Missense_Mutation SNP C 11LU022_T 15364514 53234922 91903714 453 1091 XKR4 0 . GRCh38 8 55524160 55524160 + Missense_Mutation SNP C C T rs745961938 11LU022_T 11LU022_N C C c.1886C>T p.Pro629Leu p.P629L ENST00000327381 3/3 141 120 21 158 158 0 strelka-varscan XKR4,missense_variant,p.Pro629Leu,ENST00000327381,NM_052898.1;XKR4,missense_variant,p.Pro629Leu,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; T ENST00000327381 Transcript missense_variant 1986/19880 1886/1953 629/650 P/L cCt/cTt rs745961938,COSM3649917 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 deleterious(0.01) 3/3 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 55524160 55524160 C T 1 0 0 0 0 1 0 0 0 17992 681 24 3 3 XKR4 8 55524160 Missense_Mutation SNP C 11LU022_T 2289238 55524160 89614476 454 1092 CLVS1 0 . GRCh38 8 61300085 61300085 + Missense_Mutation SNP C C G 11LU022_T 11LU022_N C C c.258C>G p.His86Gln p.H86Q ENST00000519846 3/7 168 149 19 201 200 1 strelka-varscan CLVS1,missense_variant,p.His86Gln,ENST00000519846,;CLVS1,missense_variant,p.His86Gln,ENST00000325897,NM_173519.2;CLVS1,intron_variant,,ENST00000518592,;CLVS1,downstream_gene_variant,,ENST00000523868,;CLVS1,downstream_gene_variant,,ENST00000522621,;RP11-787D18.1,downstream_gene_variant,,ENST00000518064,;RP11-787D18.1,downstream_gene_variant,,ENST00000521801,;CLVS1,non_coding_transcript_exon_variant,,ENST00000521189,; G ENST00000519846 Transcript missense_variant 730/3622 258/1065 86/354 H/Q caC/caG COSM5475190 1 1 CLVS1 HGNC HGNC:23139 protein_coding YES CCDS6176.1 ENSP00000428402 Q8IUQ0 UPI000007472D tolerated(0.12) 3/7 Gene3D:3.40.525.10,Pfam_domain:PF03765,Prints_domain:PR00180,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF72,SMART_domains:SM01100,Superfamily_domains:SSF46938 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 61300085 61300085 C G 1 0 0 0 0 1 0 0 0 3344 506 18 4 4 CLVS1 8 61300085 Missense_Mutation SNP C 11LU022_T 5775925 61300085 83838551 455 1093 XKR9 0 . GRCh38 8 70734395 70734395 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1093T>C p.Cys365Arg p.C365R ENST00000408926 5/5 40 32 8 83 83 0 strelka-varscan XKR9,missense_variant,p.Cys365Arg,ENST00000408926,NM_001287258.1,NM_001011720.1,NM_001287260.1;XKR9,missense_variant,p.Cys365Arg,ENST00000520030,NM_001287259.1;XKR9,intron_variant,,ENST00000520273,;XKR9,3_prime_UTR_variant,,ENST00000520092,; C ENST00000408926 Transcript missense_variant 1627/3174 1093/1122 365/373 C/R Tgt/Cgt 1 1 XKR9 HGNC HGNC:20937 protein_coding YES CCDS34905.1 ENSP00000386141 Q5GH70 UPI00004C7A9F NM_001287258.1,NM_001011720.1,NM_001287260.1 tolerated(0.34) 5/5 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF6 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.67067 0.9999998 1 1 1 0 C 3 2 3 70734395 70734395 T C 1 0 0 0 0 1 0 0 0 17997 1464 51 5 5 XKR9 8 70734395 Missense_Mutation SNP T 11LU022_T 9434310 70734395 74404241 456 1094 ZFHX4 0 . GRCh38 8 76852635 76852635 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.5714G>T p.Arg1905Ile p.R1905I ENST00000521891 10/11 218 119 99 184 184 0 strelka-varscan ZFHX4,missense_variant,p.Arg1905Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Arg1879Ile,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; T ENST00000521891 Transcript missense_variant 6162/14019 5714/10851 1905/3616 R/I aGa/aTa 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 76852635 76852635 G T 1 0 0 0 0 1 0 0 0 18213 942 33 2 2 ZFHX4 8 76852635 Missense_Mutation SNP G 11LU022_T 6118240 76852635 68286001 457 1095 ZFHX4 0 . GRCh38 8 76852957 76852957 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.6036G>A p.= p.L2012L ENST00000521891 10/11 149 139 10 132 132 0 strelka-varscan ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; A ENST00000521891 Transcript synonymous_variant 6484/14019 6036/10851 2012/3616 L ttG/ttA 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -13.76611 0.9999662 1 1 1 0 A 2 1 3 76852957 76852957 G A 1 0 0 0 0 0 0 0 1 18213 1310 46 3 3 ZFHX4 8 76852957 Silent SNP G 11LU022_T 322 76852957 68285679 458 1096 PSKH2 0 . GRCh38 8 86064504 86064504 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.313T>A p.Cys105Ser p.C105S ENST00000276616 2/3 498 454 44 410 410 0 strelka-varscan PSKH2,missense_variant,p.Cys105Ser,ENST00000276616,NM_033126.1;ATP6V0D2,intron_variant,,ENST00000521564,;PSKH2,non_coding_transcript_exon_variant,,ENST00000517981,;PSKH2,non_coding_transcript_exon_variant,,ENST00000523010,; T ENST00000276616 Transcript missense_variant 388/1322 313/1158 105/385 C/S Tgc/Agc 1 -1 PSKH2 HGNC HGNC:18997 protein_coding YES CCDS6240.1 ENSP00000276616 Q96QS6 UPI000006F951 NM_033126.1 tolerated(0.45) 2/3 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF255,Pfam_domain:PF00069,Gene3D:3.30.200.20,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 86064504 86064504 A T 1 0 0 0 0 1 0 0 0 12816 159 6 4 4 PSKH2 8 86064504 Missense_Mutation SNP A 11LU022_T 9211547 86064504 59074132 459 1097 PSKH2 0 . GRCh38 8 86069451 86069451 + Silent SNP G G T 11LU022_T 11LU022_N G G c.172C>A p.= p.R58R ENST00000276616 1/3 68 59 9 44 44 0 strelka-varscan PSKH2,synonymous_variant,p.=,ENST00000276616,NM_033126.1;ATP6V0D2,intron_variant,,ENST00000521564,;ATP6V0D2,upstream_gene_variant,,ENST00000523635,;PSKH2,intron_variant,,ENST00000517981,;PSKH2,intron_variant,,ENST00000523010,; T ENST00000276616 Transcript synonymous_variant 247/1322 172/1158 58/385 R Cgg/Agg COSM5512509 1 -1 PSKH2 HGNC HGNC:18997 protein_coding YES CCDS6240.1 ENSP00000276616 Q96QS6 UPI000006F951 NM_033126.1 1/3 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF255,Gene3D:3.30.200.20,Superfamily_domains:SSF56112 1 LOW 1 SNV 1 1 1 PASS . . 0 198 11 0 0 0 0 0 -19.57056 0.9999472 1 1 1 0 T 2 4 3 86069451 86069451 G T 1 0 0 0 0 0 0 0 1 12816 1115 39 1 1 PSKH2 8 86069451 Silent SNP G 11LU022_T 4947 86069451 59069185 460 1098 WWP1 0 . GRCh38 8 86425279 86425279 + Missense_Mutation SNP G G C rs267602027 11LU022_T 11LU022_N G G c.1118G>C p.Arg373Pro p.R373P ENST00000517970 10/25 192 157 35 169 169 0 strelka-varscan WWP1,missense_variant,p.Arg373Pro,ENST00000517970,NM_007013.3;WWP1,missense_variant,p.Arg373Pro,ENST00000265428,;WWP1,non_coding_transcript_exon_variant,,ENST00000520374,;WWP1,non_coding_transcript_exon_variant,,ENST00000521079,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,; C ENST00000517970 Transcript missense_variant 1425/4686 1118/2769 373/922 R/P cGa/cCa rs267602027,COSM170354 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 deleterious(0.01) 10/25 PROSITE_profiles:PS50020,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,PROSITE_patterns:PS01159,Gene3D:2.20.70.10,Pfam_domain:PF00397,PIRSF_domain:PIRSF001569,SMART_domains:SM00456,Superfamily_domains:SSF51045 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 86425279 86425279 G C 1 0 0 0 0 1 0 0 0 17973 1058 37 4 4 WWP1 8 86425279 Missense_Mutation SNP G 11LU022_T 355828 86425279 58713357 461 1099 RUNX1T1 0 . GRCh38 8 91975971 91975971 + Missense_Mutation SNP C C G rs747964791 11LU022_T 11LU022_N C C c.1459G>C p.Ala487Pro p.A487P ENST00000436581 10/12 162 118 44 121 121 0 strelka-varscan RUNX1T1,missense_variant,p.Ala428Pro,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.Ala428Pro,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.Ala428Pro,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.Ala428Pro,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.Ala487Pro,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.Ala401Pro,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.Ala408Pro,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.Ala428Pro,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.Ala401Pro,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.Ala401Pro,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.Ala391Pro,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.Ala391Pro,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.Ala439Pro,ENST00000520724,NM_001198634.1;GS1-5L10.1,non_coding_transcript_exon_variant,,ENST00000522980,;RUNX1T1,splice_region_variant,,ENST00000520978,;RUNX1T1,splice_region_variant,,ENST00000521751,;RUNX1T1,upstream_gene_variant,,ENST00000521078,; G ENST00000436581 Transcript missense_variant,splice_region_variant 1646/7454 1459/1992 487/663 A/P Gcg/Ccg rs747964791,COSM3358285,COSM3358286,COSM3358287 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 tolerated(0.11) 10/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,Prints_domain:PR01876 0,1,1,1 MODERATE SNV 5 0,1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 91975971 91975971 C G 1 0 0 0 0 1 0 0 0 14008 782 27 4 4 RUNX1T1 8 91975971 Missense_Mutation SNP C 11LU022_T 5550692 91975971 53162665 462 1100 KIAA1429 0 . GRCh38 8 94511515 94511515 + Silent SNP G G C 11LU022_T 11LU022_N G G c.3060C>G p.= p.L1020L ENST00000297591 13/24 342 261 81 267 267 0 strelka-varscan KIAA1429,synonymous_variant,p.=,ENST00000297591,NM_015496.4;KIAA1429,synonymous_variant,p.=,ENST00000421249,NM_183009.2;KIAA1429,non_coding_transcript_exon_variant,,ENST00000523405,;KIAA1429,synonymous_variant,p.=,ENST00000522263,;KIAA1429,non_coding_transcript_exon_variant,,ENST00000521080,; C ENST00000297591 Transcript synonymous_variant 3136/6528 3060/5439 1020/1812 L ctC/ctG COSM4403812,COSM4403813 1 -1 KIAA1429 HGNC HGNC:24500 protein_coding YES CCDS34923.1 ENSP00000297591 Q69YN4 UPI00001BBB23 NM_015496.4 13/24 hmmpanther:PTHR23185,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 94511515 94511515 G C 1 0 0 0 0 0 0 0 1 8114 1161 41 4 4 KIAA1429 8 94511515 Silent SNP G 11LU022_T 2535544 94511515 50627121 463 1101 UBR5 0 . GRCh38 8 102346959 102346959 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.520A>T p.Ser174Cys p.S174C ENST00000520539 6/59 180 154 26 116 116 0 strelka-varscan UBR5,missense_variant,p.Ser174Cys,ENST00000520539,NM_015902.5;UBR5,missense_variant,p.Ser174Cys,ENST00000220959,NM_001282873.1;UBR5,missense_variant,p.Ser174Cys,ENST00000521922,;UBR5,non_coding_transcript_exon_variant,,ENST00000518145,; A ENST00000520539 Transcript missense_variant 1127/10297 520/8400 174/2799 S/C Agt/Tgt 1 -1 UBR5 HGNC HGNC:16806 protein_coding YES CCDS34933.1 ENSP00000429084 O95071 UPI0000129BCB NM_015902.5 deleterious(0.02) 6/59 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF337 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 102346959 102346959 T A 1 0 0 0 0 1 0 0 0 17429 1580 55 4 4 UBR5 8 102346959 Missense_Mutation SNP T 11LU022_T 7835444 102346959 42791677 464 1102 RIMS2 0 . GRCh38 8 103961122 103961122 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2759G>T p.Gly920Val p.G920V ENST00000504942 15/24 127 106 21 132 132 0 strelka-varscan RIMS2,missense_variant,p.Gly712Val,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Gly698Val,ENST00000436393,;RIMS2,missense_variant,p.Gly920Val,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Gly862Val,ENST00000626043,;RIMS2,missense_variant,p.Gly712Val,ENST00000408894,;RIMS2,missense_variant,p.Gly759Val,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Gly908Val,ENST00000632716,;RIMS2,missense_variant,p.Gly314Val,ENST00000507677,; T ENST00000504942 Transcript missense_variant 2898/4228 2759/4050 920/1349 G/V gGt/gTt 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0.01) 15/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 103961122 103961122 G T 1 0 0 0 0 1 0 0 0 13543 1261 44 2 2 RIMS2 8 103961122 Missense_Mutation SNP G 11LU022_T 1614163 103961122 41177514 465 1103 RIMS2 0 . GRCh38 8 104251135 104251135 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.3803A>T p.Glu1268Val p.E1268V ENST00000504942 23/24 150 98 52 100 100 0 strelka-varscan RIMS2,missense_variant,p.Glu1082Val,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Glu1286Val,ENST00000436393,;RIMS2,missense_variant,p.Glu1268Val,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Glu1107Val,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Glu204Val,ENST00000339750,NM_001282882.1;RIMS2,missense_variant,p.Glu204Val,ENST00000523362,;RIMS2,downstream_gene_variant,,ENST00000626043,;RIMS2,downstream_gene_variant,,ENST00000408894,; T ENST00000504942 Transcript missense_variant 3942/4228 3803/4050 1268/1349 E/V gAa/gTa 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 23/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 104251135 104251135 A T 1 0 0 0 0 1 0 0 0 13543 246 9 4 4 RIMS2 8 104251135 Missense_Mutation SNP A 11LU022_T 290013 104251135 40887501 466 1104 DCSTAMP 0 . GRCh38 8 104349405 104349405 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.853C>T p.Pro285Ser p.P285S ENST00000297581 2/4 254 196 58 227 227 0 strelka-varscan DCSTAMP,missense_variant,p.Pro285Ser,ENST00000297581,NM_030788.3;DCSTAMP,intron_variant,,ENST00000622554,NM_001257317.1;DCSTAMP,intron_variant,,ENST00000517991,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,downstream_gene_variant,,ENST00000518023,;DCSTAMP,upstream_gene_variant,,ENST00000518051,;DCSTAMP,downstream_gene_variant,,ENST00000517364,;DCSTAMP,downstream_gene_variant,,ENST00000519562,; T ENST00000297581 Transcript missense_variant 902/1953 853/1413 285/470 P/S Ccg/Tcg COSM1094634 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 deleterious(0) 2/4 Pfam_domain:PF07782,hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 104349405 104349405 C T 1 0 0 0 0 1 0 0 0 4106 739 26 3 3 DCSTAMP 8 104349405 Missense_Mutation SNP C 11LU022_T 98270 104349405 40789231 467 1105 LRP12 0 . GRCh38 8 104588887 104588887 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.11G>C p.Arg4Pro p.R4P ENST00000276654 1/7 266 194 72 189 189 0 strelka-varscan LRP12,missense_variant,p.Arg4Pro,ENST00000276654,NM_013437.4;LRP12,missense_variant,p.Arg4Pro,ENST00000424843,NM_001135703.2;LRP12,non_coding_transcript_exon_variant,,ENST00000520770,;ZFPM2,upstream_gene_variant,,ENST00000521923,;LRP12,non_coding_transcript_exon_variant,,ENST00000519675,; G ENST00000276654 Transcript missense_variant 120/4112 11/2580 4/859 R/P cGc/cCc 1 -1 LRP12 HGNC HGNC:31708 protein_coding YES CCDS6303.1 ENSP00000276654 Q9Y561 UPI0000047A9F NM_013437.4 tolerated_low_confidence(0.2) 1/7 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 104588887 104588887 C G 1 0 0 0 0 1 0 0 0 8849 768 27 4 4 LRP12 8 104588887 Missense_Mutation SNP C 11LU022_T 239482 104588887 40549749 468 1106 OXR1 0 . GRCh38 8 106702973 106702973 + Missense_Mutation SNP C C T rs750085755 11LU022_T 11LU022_N C C c.746C>T p.Pro249Leu p.P249L ENST00000442977 7/16 191 140 51 176 176 0 strelka-varscan OXR1,missense_variant,p.Pro248Leu,ENST00000517566,NM_001198533.1;OXR1,missense_variant,p.Pro241Leu,ENST00000312046,NM_181354.4;OXR1,missense_variant,p.Pro248Leu,ENST00000531443,NM_018002.3;OXR1,missense_variant,p.Pro249Leu,ENST00000442977,NM_001198532.1;OXR1,missense_variant,p.Pro181Leu,ENST00000497705,;OXR1,upstream_gene_variant,,ENST00000519415,;OXR1,non_coding_transcript_exon_variant,,ENST00000517455,;OXR1,3_prime_UTR_variant,,ENST00000438229,;OXR1,intron_variant,,ENST00000435082,;TAGLN2P1,upstream_gene_variant,,ENST00000524097,; T ENST00000442977 Transcript missense_variant 845/2956 746/2625 249/874 P/L cCt/cTt rs750085755 1 1 OXR1 HGNC HGNC:15822 protein_coding YES CCDS56548.1 ENSP00000405424 Q8N573 UPI0001914BEA NM_001198532.1 deleterious(0.04) 7/16 hmmpanther:PTHR23354:SF69,hmmpanther:PTHR23354 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 106702973 106702973 C T 1 0 0 0 0 1 0 0 0 11407 681 24 3 3 OXR1 8 106702973 Missense_Mutation SNP C 11LU022_T 2114086 106702973 38435663 469 1107 TMEM74 0 . GRCh38 8 108784459 108784459 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.640A>G p.Met214Val p.M214V ENST00000297459 2/2 339 240 99 232 231 1 strelka-varscan TMEM74,missense_variant,p.Met214Val,ENST00000297459,NM_153015.1;TMEM74,intron_variant,,ENST00000518838,; C ENST00000297459 Transcript missense_variant 819/1741 640/918 214/305 M/V Atg/Gtg 1 -1 TMEM74 HGNC HGNC:26409 protein_coding YES CCDS6310.1 ENSP00000297459 Q96NL1 A0A024R9D4 UPI000006E80B NM_153015.1 deleterious(0) 2/2 hmmpanther:PTHR16125,hmmpanther:PTHR16125:SF3,Pfam_domain:PF14927 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 108784459 108784459 T C 1 0 0 0 0 1 0 0 0 16677 1435 50 5 5 TMEM74 8 108784459 Missense_Mutation SNP T 11LU022_T 2081486 108784459 36354177 470 1108 CSMD3 0 . GRCh38 8 112685705 112685705 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.2183C>G p.Pro728Arg p.P728R ENST00000297405 15/71 193 180 13 196 196 0 strelka-varscan CSMD3,missense_variant,p.Pro728Arg,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro688Arg,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro624Arg,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Pro68Arg,ENST00000339701,; C ENST00000297405 Transcript missense_variant 2428/13212 2183/11124 728/3707 P/R cCa/cGa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.1) 15/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 112685705 112685705 G C 1 0 0 0 0 1 0 0 0 3747 1348 47 4 4 CSMD3 8 112685705 Missense_Mutation SNP G 11LU022_T 3901246 112685705 32452931 471 1109 TNFRSF11B 0 . GRCh38 8 118924436 118924436 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.1144C>A p.Gln382Lys p.Q382K ENST00000297350 5/5 157 144 13 179 179 0 strelka-varscan TNFRSF11B,missense_variant,p.Gln382Lys,ENST00000297350,NM_002546.3;TNFRSF11B,downstream_gene_variant,,ENST00000517352,;TNFRSF11B,downstream_gene_variant,,ENST00000521597,; T ENST00000297350 Transcript missense_variant 1523/2402 1144/1206 382/401 Q/K Cag/Aag COSM5563658,COSM5563659 1 -1 TNFRSF11B HGNC HGNC:11909 protein_coding YES CCDS6326.1 ENSP00000297350 O00300 UPI0000157F05 NM_002546.3 deleterious(0.01) 5/5 hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF90,PIRSF_domain:PIRSF038065,Prints_domain:PR01975 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 3 118924436 118924436 G T 1 0 0 0 0 1 0 0 0 16759 1299 45 2 2 TNFRSF11B 8 118924436 Missense_Mutation SNP G 11LU022_T 6238731 118924436 26214200 472 1110 ENPP2 0 . GRCh38 8 119570816 119570816 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.1962T>C p.= p.P654P ENST00000259486 21/26 176 118 58 154 154 0 strelka-varscan ENPP2,synonymous_variant,p.=,ENST00000427067,;ENPP2,synonymous_variant,p.=,ENST00000259486,NM_006209.4;ENPP2,synonymous_variant,p.=,ENST00000522826,NM_001130863.2;ENPP2,synonymous_variant,p.=,ENST00000075322,NM_001040092.2;ENPP2,synonymous_variant,p.=,ENST00000522167,;ENPP2,downstream_gene_variant,,ENST00000518109,;ENPP2,non_coding_transcript_exon_variant,,ENST00000523861,; G ENST00000259486 Transcript synonymous_variant 2012/3233 1962/2748 654/915 P ccT/ccC 1 -1 ENPP2 HGNC HGNC:3357 protein_coding YES CCDS6329.1 ENSP00000259486 Q13822 UPI000013C57A NM_006209.4 21/26 hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF21,Superfamily_domains:SSF54060 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 119570816 119570816 A G 1 0 0 0 0 0 0 0 1 4975 175 7 5 5 ENPP2 8 119570816 Silent SNP A 11LU022_T 646380 119570816 25567820 473 1111 ADCY8 0 . GRCh38 8 130867855 130867855 + Missense_Mutation SNP G G T rs755996379 11LU022_T 11LU022_N G G c.2201C>A p.Pro734His p.P734H ENST00000286355 9/18 91 84 7 114 113 1 strelka-varscan ADCY8,missense_variant,p.Pro734His,ENST00000286355,NM_001115.2;ADCY8,intron_variant,,ENST00000377928,; T ENST00000286355 Transcript missense_variant 4294/5938 2201/3756 734/1251 P/H cCt/cAt rs755996379,COSM140612 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 deleterious(0) 9/18 hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 208 2 0 0 0 0 0 -15.08475 1 1 1 1 0 T 3 4 3 130867855 130867855 G T 1 0 0 0 0 1 0 0 0 344 1000 35 2 2 ADCY8 8 130867855 Missense_Mutation SNP G 11LU022_T 11297039 130867855 14270781 474 1112 TG 0 . GRCh38 8 132887195 132887195 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1823G>T p.Cys608Phe p.C608F ENST00000220616 9/48 95 88 7 121 120 1 strelka-varscan TG,missense_variant,p.Cys608Phe,ENST00000220616,NM_003235.4;TG,downstream_gene_variant,,ENST00000520769,; T ENST00000220616 Transcript missense_variant 1863/8450 1823/8307 608/2768 C/F tGt/tTt 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 deleterious(0) 9/48 PROSITE_profiles:PS51162,hmmpanther:PTHR14093:SF16,hmmpanther:PTHR14093,Pfam_domain:PF00086,PIRSF_domain:PIRSF001831,Gene3D:4.10.800.10 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.75652 1 1 1 1 0 T 3 4 3 132887195 132887195 G T 1 0 0 0 0 1 0 0 0 16246 1377 48 2 2 TG 8 132887195 Missense_Mutation SNP G 11LU022_T 2019340 132887195 12251441 475 1113 TG 0 . GRCh38 8 133113604 133113604 + Splice_Site SNP G G T 11LU022_T 11LU022_N G G c.7754+1G>T p.X2585_splice ENST00000220616 175 125 50 183 182 1 strelka-varscan TG,splice_donor_variant,,ENST00000220616,NM_003235.4;TG,splice_donor_variant,,ENST00000519178,;TG,splice_donor_variant,,ENST00000519543,;TG,splice_donor_variant,,ENST00000521107,;TG,splice_donor_variant,,ENST00000523756,;TG,non_coding_transcript_exon_variant,,ENST00000522809,;TG,downstream_gene_variant,,ENST00000522996,; T ENST00000220616 Transcript splice_donor_variant -/8450 7754/8307 2585/2768 COSM3924673 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 44/47 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 3 133113604 133113604 G T 1 0 0 0 0 0 0 1 0 16246 1275 44 2 2 TG 8 133113604 Splice_Site SNP G 11LU022_T 226409 133113604 12025032 476 1114 FAM135B 0 . GRCh38 8 138243038 138243038 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.573T>C p.= p.L191L ENST00000395297 7/20 123 69 54 135 135 0 strelka-varscan FAM135B,synonymous_variant,p.=,ENST00000395297,NM_015912.3;FAM135B,synonymous_variant,p.=,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; G ENST00000395297 Transcript synonymous_variant 744/6962 573/4221 191/1406 L ctT/ctC 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 7/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 138243038 138243038 A G 1 0 0 0 0 0 0 0 1 5299 117 5 5 5 FAM135B 8 138243038 Silent SNP A 11LU022_T 5129434 138243038 6895598 477 1115 COL22A1 0 . GRCh38 8 138807768 138807768 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1494G>T p.Lys498Asn p.K498N ENST00000303045 10/65 186 127 59 239 237 2 strelka-varscan COL22A1,missense_variant,p.Lys498Asn,ENST00000303045,NM_152888.2;COL22A1,intron_variant,,ENST00000435777,; A ENST00000303045 Transcript missense_variant,splice_region_variant 1941/6346 1494/4881 498/1626 K/N aaG/aaT 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 deleterious(0.02) 10/65 hmmpanther:PTHR24023 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 138807768 138807768 C A 1 0 0 0 0 1 0 0 0 3469 695 24 2 2 COL22A1 8 138807768 Missense_Mutation SNP C 11LU022_T 564730 138807768 6330868 478 1116 CCDC166 0 . GRCh38 8 143707372 143707372 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.642G>T p.= p.V214V ENST00000542437 2/2 54 29 25 65 65 0 strelka-varscan CCDC166,synonymous_variant,p.=,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; A ENST00000542437 Transcript synonymous_variant 642/1320 642/1320 214/439 V gtG/gtT 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 2/2 Pfam_domain:PF14988,hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 143707372 143707372 C A 1 0 0 0 0 0 0 0 1 2482 581 21 2 2 CCDC166 8 143707372 Silent SNP C 11LU022_T 4899604 143707372 1431264 479 1117 OPLAH 0 . GRCh38 8 144053346 144053346 + Nonsense_Mutation SNP C C A rs550610840 11LU022_T 11LU022_N C C c.2734G>T p.Gly912Ter p.G912* ENST00000618853 20/27 117 67 50 165 165 0 strelka-varscan OPLAH,stop_gained,p.Gly912Ter,ENST00000618853,NM_017570.4;MIR6846,downstream_gene_variant,,ENST00000613469,;SMPD5,downstream_gene_variant,,ENST00000528912,;SMPD5,downstream_gene_variant,,ENST00000561181,;OPLAH,non_coding_transcript_exon_variant,,ENST00000527993,;OPLAH,non_coding_transcript_exon_variant,,ENST00000531027,; A ENST00000618853 Transcript stop_gained 2838/4031 2734/3867 912/1288 G/* Gga/Tga rs550610840 1 -1 OPLAH HGNC HGNC:8149 protein_coding YES CCDS75802.1 ENSP00000480476 O14841 UPI000035154E NM_017570.4 20/27 Pfam_domain:PF02538,hmmpanther:PTHR11365,hmmpanther:PTHR11365:SF2 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 144053346 144053346 C A 1 0 0 0 0 0 1 0 0 10953 661 23 1 1 OPLAH 8 144053346 Nonsense_Mutation SNP C 11LU022_T 345974 144053346 1085290 480 1118 ZNF251 0 . GRCh38 8 144754236 144754236 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.119A>T p.Tyr40Phe p.Y40F ENST00000292562 3/5 162 135 27 150 150 0 strelka-varscan ZNF251,missense_variant,p.Tyr40Phe,ENST00000292562,NM_138367.1;ZNF251,missense_variant,p.Tyr78Phe,ENST00000525191,;ZNF251,non_coding_transcript_exon_variant,,ENST00000524394,;ZNF251,non_coding_transcript_exon_variant,,ENST00000530353,; A ENST00000292562 Transcript missense_variant 395/2807 119/2016 40/671 Y/F tAc/tTc 1 -1 ZNF251 HGNC HGNC:13045 protein_coding YES CCDS47944.1 ENSP00000292562 Q9BRH9 UPI0000160D9A NM_138367.1 tolerated(0.27) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF202,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 144754236 144754236 T A 1 0 0 0 0 1 0 0 0 18372 1638 57 4 4 ZNF251 8 144754236 Missense_Mutation SNP T 11LU022_T 700890 144754236 384400 481 1119 FREM1 0 . GRCh38 9 14801827 14801827 + Silent SNP A A C novel 11LU022_T 11LU022_N A A c.3519T>G p.= p.A1173A ENST00000422223 21/38 129 92 37 151 151 0 strelka-varscan-mutect FREM1,synonymous_variant,p.=,ENST00000422223,NM_144966.5;FREM1,synonymous_variant,p.=,ENST00000380880,;FREM1,synonymous_variant,p.=,ENST00000380875,; C ENST00000422223 Transcript synonymous_variant 4335/10086 3519/6540 1173/2179 A gcT/gcG 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 21/38 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 14801827 14801827 A C 1 0 0 0 0 0 0 0 1 5911 175 7 5 5 FREM1 9 14801827 Silent SNP A 11LU022_T 14801827 123592890 482 1120 FOCAD 0 . GRCh38 9 20740255 20740255 + Nonsense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.307A>T p.Lys103Ter p.K103* ENST00000380249 7/46 62 51 11 68 67 1 strelka-varscan-mutect FOCAD,stop_gained,p.Lys103Ter,ENST00000380249,NM_017794.4;FOCAD,stop_gained,p.Lys103Ter,ENST00000338382,;FOCAD,non_coding_transcript_exon_variant,,ENST00000604103,;FOCAD,non_coding_transcript_exon_variant,,ENST00000605031,; T ENST00000380249 Transcript stop_gained 671/6096 307/5406 103/1801 K/* Aaa/Taa 1 1 FOCAD HGNC HGNC:23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 UPI0000EE4244 NM_017794.4 7/46 hmmpanther:PTHR16212,hmmpanther:PTHR16212:SF4 HIGH 1 SNV 1 1 PASS rs1245631784 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 20740255 20740255 A T 1 0 0 0 0 0 1 0 0 5839 15 1 4 4 FOCAD 9 20740255 Nonsense_Mutation SNP A 11LU022_T 5938428 20740255 117654462 483 1121 PRSS3 0 . GRCh38 9 33750662 33750662 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.146C>A p.Pro49Gln p.P49Q ENST00000361005 1/5 41 31 10 43 43 0 strelka-varscan-mutect PRSS3,missense_variant,p.Pro49Gln,ENST00000361005,NM_007343.3;PRSS3,5_prime_UTR_variant,,ENST00000342836,NM_001197097.2;PRSS3,upstream_gene_variant,,ENST00000429677,NM_001197098.1;PRSS3,upstream_gene_variant,,ENST00000457896,;PRSS3,upstream_gene_variant,,ENST00000468152,; A ENST00000361005 Transcript missense_variant 146/966 146/915 49/304 P/Q cCg/cAg 1 1 PRSS3 HGNC HGNC:9486 protein_coding YES CCDS47958.1 ENSP00000354280 P35030 UPI000013C519 NM_007343.3 deleterious_low_confidence(0) 1/5 hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF23 MODERATE 1 SNV 1 1 PASS rs1340722501 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 33750662 33750662 C A 1 0 0 0 0 1 0 0 0 12769 652 23 1 1 PRSS3 9 33750662 Missense_Mutation SNP C 11LU022_T 13010407 33750662 104644055 484 1122 PRSS3 0 . GRCh38 9 33750682 33750682 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.166T>A p.Trp56Arg p.W56R ENST00000361005 1/5 38 30 8 23 23 0 strelka-varscan-mutect PRSS3,missense_variant,p.Trp56Arg,ENST00000361005,NM_007343.3;PRSS3,5_prime_UTR_variant,,ENST00000342836,NM_001197097.2;PRSS3,upstream_gene_variant,,ENST00000429677,NM_001197098.1;PRSS3,upstream_gene_variant,,ENST00000457896,;PRSS3,non_coding_transcript_exon_variant,,ENST00000468152,; A ENST00000361005 Transcript missense_variant 166/966 166/915 56/304 W/R Tgg/Agg 1 1 PRSS3 HGNC HGNC:9486 protein_coding YES CCDS47958.1 ENSP00000354280 P35030 UPI000013C519 NM_007343.3 tolerated_low_confidence(0.39) 1/5 hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF23 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -19.72492 0.9999968 1 1 1 0 A 3 1 3 33750682 33750682 T A 1 0 0 0 0 1 0 0 0 12769 1812 63 4 4 PRSS3 9 33750682 Missense_Mutation SNP T 11LU022_T 20 33750682 104644035 485 1123 FAM205A 0 . GRCh38 9 34725929 34725929 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.1311T>A p.= p.P437P ENST00000378788 4/4 173 152 21 197 197 0 varscan-mutect FAM205A,synonymous_variant,p.=,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript synonymous_variant 1351/4225 1311/4008 437/1335 P ccT/ccA 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859,Pfam_domain:PF14650 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 34725929 34725929 A T 1 0 0 0 0 0 0 0 1 5386 59 3 4 4 FAM205A 9 34725929 Silent SNP A 11LU022_T 975247 34725929 103668788 486 1124 FAM205A 0 . GRCh38 9 34726945 34726945 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.295T>A p.Cys99Ser p.C99S ENST00000378788 4/4 138 111 27 122 122 0 strelka-varscan-mutect FAM205A,missense_variant,p.Cys99Ser,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript missense_variant 335/4225 295/4008 99/1335 C/S Tgt/Agt 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 deleterious(0.01) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859,Pfam_domain:PF15371 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 34726945 34726945 A T 1 0 0 0 0 1 0 0 0 5386 159 6 4 4 FAM205A 9 34726945 Missense_Mutation SNP A 11LU022_T 1016 34726945 103667772 487 1125 ZBTB5 0 . GRCh38 9 37441749 37441749 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.803A>G p.Glu268Gly p.E268G ENST00000307750 2/2 122 104 18 170 170 0 strelka-varscan-mutect ZBTB5,missense_variant,p.Glu268Gly,ENST00000307750,NM_014872.2;GRHPR,downstream_gene_variant,,ENST00000318158,NM_012203.1;GRHPR,downstream_gene_variant,,ENST00000460882,;GRHPR,downstream_gene_variant,,ENST00000497693,;GRHPR,downstream_gene_variant,,ENST00000480596,;GRHPR,downstream_gene_variant,,ENST00000494290,; C ENST00000307750 Transcript missense_variant 992/4627 803/2034 268/677 E/G gAa/gGa 1 -1 ZBTB5 HGNC HGNC:23836 protein_coding YES CCDS6610.1 ENSP00000307604 O15062 Q5T942 UPI000006FAE2 NM_014872.2 deleterious_low_confidence(0) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 37441749 37441749 T C 1 0 0 0 0 1 0 0 0 18121 1783 62 5 5 ZBTB5 9 37441749 Missense_Mutation SNP T 11LU022_T 2714804 37441749 100952968 488 1126 FP325317.1 0 . GRCh38 9 43111383 43111383 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.13G>T p.Val5Leu p.V5L ENST00000539936 4/7 57 53 4 78 78 0 varscan-mutect FP325317.1,missense_variant,p.Val5Leu,ENST00000539936,; A ENST00000539936 Transcript missense_variant 345/1681 13/498 5/165 V/L Gtg/Ttg 1 -1 FP325317.1 Clone_based_ensembl_gene protein_coding YES ENSP00000439534 F6QWF9 UPI000514C5D5 tolerated(0.06) 4/7 Gene3D:1.20.1080.10,Pfam_domain:PF00230,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF16,Superfamily_domains:SSF81338 MODERATE 1 SNV 5 1 PASS . . 0 202 6 2 0 0 0 0 -8.028138 0.9996264 1 1 1 0 A 3 1 3 43111383 43111383 C A 1 0 0 0 0 1 0 0 0 5901 478 17 2 2 FP325317.1 9 43111383 Missense_Mutation SNP C 11LU022_T 5669634 43111383 95283334 489 1127 TRPM6 0 . GRCh38 9 74755370 74755370 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.4889C>G p.Ser1630Cys p.S1630C ENST00000360774 28/39 371 265 106 337 337 0 strelka-varscan-mutect TRPM6,missense_variant,p.Ser1630Cys,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Ser1625Cys,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Ser1625Cys,ENST00000449912,NM_001177310.1; C ENST00000360774 Transcript missense_variant 5127/8425 4889/6069 1630/2022 S/C tCc/tGc 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 deleterious_low_confidence(0) 28/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 74755370 74755370 G C 1 0 0 0 0 1 0 0 0 17096 1174 41 4 4 TRPM6 9 74755370 Missense_Mutation SNP G 11LU022_T 31643987 74755370 63639347 490 1128 PRUNE2 0 . GRCh38 9 76711267 76711267 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1007A>G p.Glu336Gly p.E336G ENST00000376718 8/19 222 168 54 200 199 1 strelka-varscan-mutect PRUNE2,missense_variant,p.Glu336Gly,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Glu336Gly,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,5_prime_UTR_variant,,ENST00000428286,;PRUNE2,upstream_gene_variant,,ENST00000426088,; C ENST00000376718 Transcript missense_variant 1131/12584 1007/9267 336/3088 E/G gAg/gGg 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 deleterious(0) 8/19 Pfam_domain:PF02833,SMART_domains:SM01131 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 76711267 76711267 T C 1 0 0 0 0 1 0 0 0 12791 1551 54 5 5 PRUNE2 9 76711267 Missense_Mutation SNP T 11LU022_T 1955897 76711267 61683450 491 1129 SPATA31D1 0 . GRCh38 9 81991512 81991512 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1042C>A p.His348Asn p.H348N ENST00000344803 4/4 388 350 38 473 471 2 strelka-varscan-mutect SPATA31D1,missense_variant,p.His348Asn,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; A ENST00000344803 Transcript missense_variant 1089/4833 1042/4731 348/1576 H/N Cat/Aat 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.19) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12 MODERATE 1 SNV 2 1 PASS rs1428932337 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 81991512 81991512 C A 1 0 0 0 0 1 0 0 0 15347 594 21 2 2 SPATA31D1 9 81991512 Missense_Mutation SNP C 11LU022_T 5280245 81991512 56403205 492 1130 GAS1 0 . GRCh38 9 86945816 86945816 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.964G>T p.Gly322Cys p.G322C ENST00000298743 1/1 244 177 67 267 267 0 strelka-varscan-mutect GAS1,missense_variant,p.Gly322Cys,ENST00000298743,NM_002048.2;GAS1RR,upstream_gene_variant,,ENST00000415801,; A ENST00000298743 Transcript missense_variant 1374/2827 964/1038 322/345 G/C Ggc/Tgc 1 -1 GAS1 HGNC HGNC:4165 protein_coding YES CCDS6674.1 ENSP00000298743 P54826 UPI0000140B67 NM_002048.2 tolerated_low_confidence(0.18) 1/1 hmmpanther:PTHR16840,hmmpanther:PTHR16840:SF3,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs1347299119 . 0 174 23 10 3 0 0 0 -20 0.4514865 0 1 0 0 A 3 1 3 86945816 86945816 C A 1 0 0 0 0 1 0 0 0 6114 652 23 1 1 GAS1 9 86945816 Missense_Mutation SNP C 11LU022_T 4954304 86945816 51448901 493 1131 WNK2 0 . GRCh38 9 93289364 93289364 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.4721G>C p.Gly1574Ala p.G1574A ENST00000297954 20/30 127 112 15 150 150 0 strelka-mutect WNK2,missense_variant,p.Gly1533Ala,ENST00000432730,;WNK2,missense_variant,p.Gly1574Ala,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Gly1537Ala,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Gly1141Ala,ENST00000411624,;WNK2,missense_variant,p.Gly334Ala,ENST00000448251,;WNK2,missense_variant,p.Gly60Ala,ENST00000453718,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000474009,;WNK2,upstream_gene_variant,,ENST00000479696,; C ENST00000297954 Transcript missense_variant 4721/7138 4721/6894 1574/2297 G/A gGg/gCg 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0) 20/30 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF10 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999723 1 1 1 0 C 3 2 3 93289364 93289364 G C 1 0 0 0 0 1 0 0 0 17934 1232 43 4 4 WNK2 9 93289364 Missense_Mutation SNP G 11LU022_T 6343548 93289364 45105353 494 1132 GABBR2 0 . GRCh38 9 98708654 98708654 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.84G>T p.= p.L28L ENST00000259455 1/19 30 21 9 29 29 0 strelka-mutect GABBR2,synonymous_variant,p.=,ENST00000259455,NM_005458.7;GABBR2,upstream_gene_variant,,ENST00000637717,; A ENST00000259455 Transcript synonymous_variant 544/5788 84/2826 28/941 L ctG/ctT 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 1/19 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs1213177596 . 1 204 5 0 0 0 0 0 -19.99996 1 1 1 1 0 A 2 1 3 98708654 98708654 C A 1 0 0 0 0 0 0 0 1 6027 697 25 2 2 GABBR2 9 98708654 Silent SNP C 11LU022_T 5419290 98708654 39686063 495 1133 TMEFF1 0 . GRCh38 9 100550099 100550099 + Silent SNP A A T 11LU022_T 11LU022_N A A c.714A>T p.= p.T238T ENST00000374879 7/10 80 59 21 75 75 0 strelka-varscan-mutect TMEFF1,synonymous_variant,p.=,ENST00000374879,NM_003692.4;MSANTD3-TMEFF1,synonymous_variant,p.=,ENST00000502978,NM_001198812.1; T ENST00000374879 Transcript synonymous_variant 1146/2611 714/1143 238/380 T acA/acT COSM1314320 1 1 TMEFF1 HGNC HGNC:11866 protein_coding YES CCDS6750.1 ENSP00000364013 Q8IYR6 UPI000004ECA5 NM_003692.4 7/10 hmmpanther:PTHR10574 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 100550099 100550099 A T 1 0 0 0 0 0 0 0 1 16457 202 7 4 4 TMEFF1 9 100550099 Silent SNP A 11LU022_T 1841445 100550099 37844618 496 1134 ABCA1 0 . GRCh38 9 104837043 104837043 + Nonsense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.1248G>A p.Trp416Ter p.W416* ENST00000374736 11/50 150 93 57 157 157 0 strelka-varscan-mutect ABCA1,stop_gained,p.Trp416Ter,ENST00000374736,NM_005502.3; T ENST00000374736 Transcript stop_gained 1643/10494 1248/6786 416/2261 W/* tgG/tgA COSM1243856 1 -1 ABCA1 HGNC HGNC:29 protein_coding YES CCDS6762.1 ENSP00000363868 O95477 UPI000013E441 NM_005502.3 11/50 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF34 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 104837043 104837043 C T 1 0 0 0 0 0 1 0 0 32 624 22 3 3 ABCA1 9 104837043 Nonsense_Mutation SNP C 11LU022_T 4286944 104837043 33557674 497 1135 ZNF462 0 . GRCh38 9 106932476 106932476 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.6043G>T p.Ala2015Ser p.A2015S ENST00000277225 5/13 343 231 112 321 321 0 strelka-varscan-mutect ZNF462,missense_variant,p.Ala2015Ser,ENST00000277225,NM_021224.4;ZNF462,missense_variant,p.Ala958Ser,ENST00000374686,;ZNF462,missense_variant,p.Ala921Ser,ENST00000441147,;ZNF462,downstream_gene_variant,,ENST00000472574,;ZNF462,non_coding_transcript_exon_variant,,ENST00000497489,;ZNF462,upstream_gene_variant,,ENST00000479166,;ZNF462,upstream_gene_variant,,ENST00000469433,;ZNF462,upstream_gene_variant,,ENST00000471032,;ZNF462,downstream_gene_variant,,ENST00000480607,; T ENST00000277225 Transcript missense_variant 6332/10414 6043/7521 2015/2506 A/S Gcc/Tcc 1 1 ZNF462 HGNC HGNC:21684 protein_coding YES CCDS35096.1 ENSP00000277225 Q96JM2 UPI0000470106 NM_021224.4 tolerated(0.09) 5/13 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF216 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 106932476 106932476 G T 1 0 0 0 0 1 0 0 0 18497 1203 42 2 2 ZNF462 9 106932476 Missense_Mutation SNP G 11LU022_T 2095433 106932476 31462241 498 1136 ACTL7B 0 . GRCh38 9 108855742 108855742 + Nonsense_Mutation SNP G G T rs770078766 11LU022_T 11LU022_N G G c.189C>A p.Cys63Ter p.C63* ENST00000374667 1/1 136 117 19 143 143 0 strelka-varscan-mutect ACTL7B,stop_gained,p.Cys63Ter,ENST00000374667,NM_006686.3; T ENST00000374667 Transcript stop_gained 1226/2379 189/1248 63/415 C/* tgC/tgA rs770078766 1 -1 ACTL7B HGNC HGNC:162 protein_coding YES CCDS6771.1 ENSP00000363799 Q9Y614 A0A140VKC6 UPI0000125053 NM_006686.3 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF59,SMART_domains:SM00268,Superfamily_domains:SSF53067 HIGH 1 SNV 1 PASS rs770078766 . 0 204 2 4 0 0 0 0 -20 0.9996887 1 1 1 0 T 4 4 3 108855742 108855742 G T 1 0 0 0 0 0 1 0 0 245 1079 38 1 1 ACTL7B 9 108855742 Nonsense_Mutation SNP G 11LU022_T 1923266 108855742 29538975 499 1137 FRRS1L 0 . GRCh38 9 109141542 109141542 + Silent SNP G G T 11LU022_T 11LU022_N G G c.663C>A p.= p.V221V ENST00000561981 4/5 205 185 20 225 225 0 strelka-varscan-mutect FRRS1L,synonymous_variant,p.=,ENST00000561981,NM_014334.2; T ENST00000561981 Transcript synonymous_variant 663/8197 663/1035 221/344 V gtC/gtA COSM3925862 1 -1 FRRS1L HGNC HGNC:1362 protein_coding YES CCDS35098.1 ENSP00000477141 Q9P0K9 UPI000013D040 NM_014334.2 4/5 PROSITE_profiles:PS50836,hmmpanther:PTHR23130,hmmpanther:PTHR23130:SF65,Pfam_domain:PF03351,SMART_domains:SM00664 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 109141542 109141542 G T 1 0 0 0 0 0 0 0 1 5932 1161 41 2 2 FRRS1L 9 109141542 Silent SNP G 11LU022_T 285800 109141542 29253175 500 1138 SVEP1 0 . GRCh38 9 110407442 110407442 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.8158C>A p.Pro2720Thr p.P2720T ENST00000374469 38/48 259 177 82 274 274 0 strelka-varscan-mutect SVEP1,missense_variant,p.Pro2723Thr,ENST00000401783,;SVEP1,missense_variant,p.Pro2720Thr,ENST00000374469,NM_153366.3; T ENST00000374469 Transcript missense_variant 8353/12194 8158/10716 2720/3571 P/T Cct/Act 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 deleterious(0.02) 38/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs1370243351 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 110407442 110407442 G T 1 0 0 0 0 1 0 0 0 15805 1203 42 2 2 SVEP1 9 110407442 Missense_Mutation SNP G 11LU022_T 1265900 110407442 27987275 501 1139 ASTN2 0 . GRCh38 9 116725903 116725903 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.2521G>A p.Glu841Lys p.E841K ENST00000361209 15/22 130 105 25 125 125 0 strelka-varscan-mutect ASTN2,missense_variant,p.Glu892Lys,ENST00000313400,;ASTN2,missense_variant,p.Glu841Lys,ENST00000361209,NM_014010.4;ASTN2,missense_variant,p.Glu615Lys,ENST00000373986,;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; T ENST00000361209 Transcript missense_variant 2653/4622 2521/3867 841/1288 E/K Gag/Aag COSM4538242,COSM4538243 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 deleterious(0) 15/22 Pfam_domain:PF01823,hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2,SMART_domains:SM00457 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 116725903 116725903 C T 1 0 0 0 0 1 0 0 0 1212 864 30 3 3 ASTN2 9 116725903 Missense_Mutation SNP C 11LU022_T 6318461 116725903 21668814 502 1140 TLR4 0 . GRCh38 9 117713650 117713650 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.1522C>G p.Leu508Val p.L508V ENST00000355622 3/3 245 214 31 211 211 0 strelka-varscan-mutect TLR4,missense_variant,p.Leu508Val,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Leu468Val,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; G ENST00000355622 Transcript missense_variant 1623/4844 1522/2520 508/839 L/V Ctg/Gtg 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 tolerated(0.08) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 117713650 117713650 C G 1 0 0 0 0 1 0 0 0 16399 564 20 4 4 TLR4 9 117713650 Missense_Mutation SNP C 11LU022_T 987747 117713650 20681067 503 1141 TLR4 0 . GRCh38 9 117713903 117713903 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1775A>T p.Gln592Leu p.Q592L ENST00000355622 3/3 157 144 13 198 198 0 strelka-varscan-mutect TLR4,missense_variant,p.Gln592Leu,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Gln552Leu,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; T ENST00000355622 Transcript missense_variant 1876/4844 1775/2520 592/839 Q/L cAa/cTa 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 tolerated(0.17) 3/3 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,SMART_domains:SM00082 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 117713903 117713903 A T 1 0 0 0 0 1 0 0 0 16399 130 5 4 4 TLR4 9 117713903 Missense_Mutation SNP A 11LU022_T 253 117713903 20680814 504 1142 MEGF9 0 . GRCh38 9 120612533 120612533 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.950G>T p.Cys317Phe p.C317F ENST00000373930 4/6 67 60 7 82 82 0 strelka-varscan-mutect MEGF9,missense_variant,p.Cys317Phe,ENST00000373930,NM_001080497.2; A ENST00000373930 Transcript missense_variant 1062/6298 950/1809 317/602 C/F tGt/tTt 1 -1 MEGF9 HGNC HGNC:3234 protein_coding YES CCDS48010.2 ENSP00000363040 Q9H1U4 UPI000045779F NM_001080497.2 deleterious(0) 4/6 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -15.99946 1 1 1 1 0 A 3 1 3 120612533 120612533 C A 1 0 0 0 0 1 0 0 0 9404 478 17 2 2 MEGF9 9 120612533 Missense_Mutation SNP C 11LU022_T 2898630 120612533 17782184 505 1143 OR1N1 0 . GRCh38 9 122526580 122526580 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.714C>A p.= p.T238T ENST00000304880 1/1 76 50 26 85 85 0 varscan-mutect OR1N1,synonymous_variant,p.=,ENST00000619659,;OR1N1,synonymous_variant,p.=,ENST00000304880,NM_012363.1; T ENST00000304880 Transcript synonymous_variant 714/936 714/936 238/311 T acC/acA 1 -1 OR1N1 HGNC HGNC:8221 protein_coding YES CCDS6844.1 ENSP00000306974 Q8NGS0 A0A126GW31 UPI0000041D08 NM_012363.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF218,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 122526580 122526580 G T 1 0 0 0 0 0 0 0 1 11047 987 35 2 2 OR1N1 9 122526580 Silent SNP G 11LU022_T 1914047 122526580 15868137 506 1144 OR1N2 0 . GRCh38 9 122553553 122553553 + Missense_Mutation SNP C C A rs778235748 11LU022_T 11LU022_N C C c.384C>A p.Asp128Glu p.D128E ENST00000373688 1/1 154 139 15 154 154 0 strelka-varscan-mutect OR1N2,missense_variant,p.Asp128Glu,ENST00000373688,NM_001004457.1;OR1N2,missense_variant,p.Asp110Glu,ENST00000616791,; A ENST00000373688 Transcript missense_variant 442/1103 384/993 128/330 D/E gaC/gaA rs778235748 1 1 OR1N2 HGNC HGNC:15111 protein_coding YES CCDS35123.1 ENSP00000362792 Q8NGR9 UPI000004618C NM_001004457.1 tolerated(0.12) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF156,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs778235748 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 122553553 122553553 C A 1 0 0 0 0 1 0 0 0 11048 477 17 2 2 OR1N2 9 122553553 Missense_Mutation SNP C 11LU022_T 26973 122553553 15841164 507 1145 OR5C1 0 . GRCh38 9 122789563 122789563 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.631C>A p.Gln211Lys p.Q211K ENST00000373680 1/1 52 35 17 69 69 0 strelka-varscan-mutect OR5C1,missense_variant,p.Gln211Lys,ENST00000373680,NM_001001923.1; A ENST00000373680 Transcript missense_variant 631/963 631/963 211/320 Q/K Cag/Aag 1 1 OR5C1 HGNC HGNC:8331 protein_coding YES CCDS35131.1 ENSP00000362784 Q8NGR4 A0A126GW42 UPI0000061E7B NM_001001923.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF119,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 122789563 122789563 C A 1 0 0 0 0 1 0 0 0 11224 595 21 2 2 OR5C1 9 122789563 Missense_Mutation SNP C 11LU022_T 236010 122789563 15605154 508 1146 HSPA5 0 . GRCh38 9 125238621 125238621 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1203G>T p.Gln401His p.Q401H ENST00000324460 6/8 144 129 15 165 165 0 strelka-varscan-mutect HSPA5,missense_variant,p.Gln401His,ENST00000324460,NM_005347.4;RABEPK,downstream_gene_variant,,ENST00000628863,;RABEPK,downstream_gene_variant,,ENST00000373538,NM_005833.3;RABEPK,downstream_gene_variant,,ENST00000394125,NM_001174152.1;RABEPK,downstream_gene_variant,,ENST00000259460,NM_001174153.1;RP11-65N13.8,upstream_gene_variant,,ENST00000468244,; A ENST00000324460 Transcript missense_variant 1407/3908 1203/1965 401/654 Q/H caG/caT 1 -1 HSPA5 HGNC HGNC:5238 protein_coding YES CCDS6863.1 ENSP00000324173 P11021 V9HWB4 UPI0000001061 NM_005347.4 deleterious_low_confidence(0) 6/8 Pfam_domain:PF00012,Prints_domain:PR00301,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF157,Low_complexity_(Seg):seg,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 125238621 125238621 C A 1 0 0 0 0 1 0 0 0 7310 680 24 2 2 HSPA5 9 125238621 Missense_Mutation SNP C 11LU022_T 2449058 125238621 13156096 509 1147 LMX1B 0 . GRCh38 9 126696393 126696393 + Missense_Mutation SNP G G T rs143906016 11LU022_T 11LU022_N G G c.1163G>T p.Arg388Leu p.R388L ENST00000355497 8/8 255 173 82 305 305 0 strelka-varscan-mutect LMX1B,missense_variant,p.Arg388Leu,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Arg384Leu,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Arg365Leu,ENST00000561065,;LMX1B,missense_variant,p.Arg377Leu,ENST00000526117,NM_002316.3; T ENST00000355497 Transcript missense_variant 1170/5809 1163/1221 388/406 R/L cGc/cTc rs143906016 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 deleterious(0.04) 8/8 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96 MODERATE 1 SNV 1 1 PASS rs143906016 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 126696393 126696393 G T 1 0 0 0 0 1 0 0 0 8789 1087 38 1 1 LMX1B 9 126696393 Missense_Mutation SNP G 11LU022_T 1457772 126696393 11698324 510 1148 FNBP1 0 . GRCh38 9 129900053 129900053 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1599G>T p.Lys533Asn p.K533N ENST00000446176 15/17 60 42 18 61 60 1 strelka-varscan-mutect FNBP1,missense_variant,p.Lys528Asn,ENST00000420781,;FNBP1,missense_variant,p.Lys533Asn,ENST00000446176,NM_015033.2;FNBP1,missense_variant,p.Lys467Asn,ENST00000443566,;FNBP1,missense_variant,p.Lys480Asn,ENST00000449089,;FNBP1,missense_variant,p.Lys504Asn,ENST00000355681,;FNBP1,non_coding_transcript_exon_variant,,ENST00000478129,;FNBP1,non_coding_transcript_exon_variant,,ENST00000462766,; A ENST00000446176 Transcript missense_variant 1786/5393 1599/1854 533/617 K/N aaG/aaT 1 -1 FNBP1 HGNC HGNC:17069 protein_coding YES CCDS48040.1 ENSP00000413625 Q96RU3 UPI000022408C NM_015033.2 tolerated(0.12) 15/17 hmmpanther:PTHR10663:SF157,hmmpanther:PTHR10663 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 129900053 129900053 C A 1 0 0 0 0 1 0 0 0 5821 680 24 2 2 FNBP1 9 129900053 Missense_Mutation SNP C 11LU022_T 3203660 129900053 8494664 511 1149 FNBP1 0 . GRCh38 9 129900074 129900074 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1578G>T p.Gln526His p.Q526H ENST00000446176 15/17 55 51 4 53 53 0 strelka-varscan-mutect FNBP1,missense_variant,p.Gln521His,ENST00000420781,;FNBP1,missense_variant,p.Gln526His,ENST00000446176,NM_015033.2;FNBP1,missense_variant,p.Gln460His,ENST00000443566,;FNBP1,missense_variant,p.Gln473His,ENST00000449089,;FNBP1,missense_variant,p.Gln497His,ENST00000355681,;FNBP1,non_coding_transcript_exon_variant,,ENST00000478129,;FNBP1,non_coding_transcript_exon_variant,,ENST00000462766,; A ENST00000446176 Transcript missense_variant 1765/5393 1578/1854 526/617 Q/H caG/caT 1 -1 FNBP1 HGNC HGNC:17069 protein_coding YES CCDS48040.1 ENSP00000413625 Q96RU3 UPI000022408C NM_015033.2 tolerated(0.18) 15/17 hmmpanther:PTHR10663:SF157,hmmpanther:PTHR10663 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.15657 1 1 1 1 0 A 3 1 3 129900074 129900074 C A 1 0 0 0 0 1 0 0 0 5821 912 32 2 2 FNBP1 9 129900074 Missense_Mutation SNP C 11LU022_T 21 129900074 8494643 512 1150 FUBP3 0 . GRCh38 9 130622755 130622755 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.819G>T p.= p.G273G ENST00000319725 10/19 88 61 27 114 114 0 strelka-varscan-mutect FUBP3,synonymous_variant,p.=,ENST00000319725,NM_003934.1;MIR6856,upstream_gene_variant,,ENST00000613330,;FUBP3,non_coding_transcript_exon_variant,,ENST00000487406,; T ENST00000319725 Transcript synonymous_variant 894/3124 819/1719 273/572 G ggG/ggT 1 1 FUBP3 HGNC HGNC:4005 protein_coding YES CCDS43893.1 ENSP00000318177 Q96I24 A0A024R8A7 UPI00001C1EAA NM_003934.1 10/19 PROSITE_profiles:PS50084,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF100,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 LOW 1 SNV 1 1 PASS rs1351653122 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 130622755 130622755 G T 1 0 0 0 0 0 0 0 1 5964 1219 43 2 2 FUBP3 9 130622755 Silent SNP G 11LU022_T 722681 130622755 7771962 513 1151 FUBP3 0 . GRCh38 9 130631569 130631569 + Nonsense_Mutation SNP G G T rs549143328 11LU022_T 11LU022_N G G c.1291G>T p.Gly431Ter p.G431* ENST00000319725 14/19 170 156 14 184 184 0 strelka-varscan-mutect FUBP3,stop_gained,p.Gly431Ter,ENST00000319725,NM_003934.1;FUBP3,non_coding_transcript_exon_variant,,ENST00000487406,;FUBP3,upstream_gene_variant,,ENST00000492199,;FUBP3,upstream_gene_variant,,ENST00000472006,; T ENST00000319725 Transcript stop_gained 1366/3124 1291/1719 431/572 G/* Gga/Tga rs549143328 1 1 FUBP3 HGNC HGNC:4005 protein_coding YES CCDS43893.1 ENSP00000318177 Q96I24 A0A024R8A7 UPI00001C1EAA NM_003934.1 14/19 hmmpanther:PTHR10288:SF100,hmmpanther:PTHR10288 HIGH 1 SNV 1 1 PASS rs549143328 . 0 208 0 2 0 0 0 0 -18.91395 0.9999998 1 1 1 0 T 4 4 3 130631569 130631569 G T 1 0 0 0 0 0 1 0 0 5964 1117 39 1 1 FUBP3 9 130631569 Nonsense_Mutation SNP G 11LU022_T 8814 130631569 7763148 514 1152 PRRC2B 0 . GRCh38 9 131474473 131474473 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.2344G>A p.Ala782Thr p.A782T ENST00000357304 15/31 67 58 9 103 103 0 strelka-varscan-mutect PRRC2B,missense_variant,p.Ala782Thr,ENST00000357304,NM_013318.3;PRRC2B,missense_variant,p.Ala51Thr,ENST00000456307,;PRRC2B,intron_variant,,ENST00000405995,;PRRC2B,upstream_gene_variant,,ENST00000451855,;PRRC2B,downstream_gene_variant,,ENST00000422467,; A ENST00000357304 Transcript missense_variant 2399/11042 2344/6690 782/2229 A/T Gcc/Acc 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 tolerated(0.14) 15/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -19.81663 1 1 1 1 0 A 3 1 3 131474473 131474473 G A 1 0 0 0 0 1 0 0 0 12749 1319 46 3 3 PRRC2B 9 131474473 Missense_Mutation SNP G 11LU022_T 842904 131474473 6920244 515 1153 CEL 0 . GRCh38 9 133062007 133062007 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.14G>T p.Gly5Val p.G5V ENST00000372080 1/11 228 190 38 253 253 0 strelka-varscan-mutect CEL,missense_variant,p.Gly5Val,ENST00000372080,NM_001807.4;CEL,missense_variant,p.Gly5Val,ENST00000621209,;GTF3C5,downstream_gene_variant,,ENST00000372097,NM_012087.3;GTF3C5,downstream_gene_variant,,ENST00000372108,NM_001122823.1;GTF3C5,downstream_gene_variant,,ENST00000372099,NM_001286709.1;GTF3C5,downstream_gene_variant,,ENST00000342018,;GTF3C5,downstream_gene_variant,,ENST00000489842,; T ENST00000372080 Transcript missense_variant 30/2384 14/2271 5/756 G/V gGg/gTg 1 1 CEL HGNC HGNC:1848 protein_coding YES CCDS43896.1 ENSP00000361151 X6R868 UPI000013E8C6 NM_001807.4 deleterious(0) 1/11 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139 MODERATE SNV 5 1 PASS rs1243599392 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 133062007 133062007 G T 1 0 0 0 0 1 0 0 0 2916 1232 43 2 2 CEL 9 133062007 Missense_Mutation SNP G 11LU022_T 1587534 133062007 5332710 516 1154 SLC2A6 0 . GRCh38 9 133478398 133478398 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.111G>T p.Arg37Ser p.R37S ENST00000371899 2/10 102 75 27 181 181 0 strelka-varscan-mutect SLC2A6,missense_variant,p.Arg37Ser,ENST00000371899,NM_017585.3;SLC2A6,missense_variant,p.Arg37Ser,ENST00000371897,NM_001145099.1;SLC2A6,missense_variant,p.Arg37Ser,ENST00000432868,;SLC2A6,intron_variant,,ENST00000414172,;SLC2A6,non_coding_transcript_exon_variant,,ENST00000485978,; A ENST00000371899 Transcript missense_variant 189/2528 111/1524 37/507 R/S agG/agT 1 -1 SLC2A6 HGNC HGNC:11011 protein_coding YES CCDS6975.1 ENSP00000360966 Q9UGQ3 UPI0000001BE8 NM_017585.3 deleterious(0.01) 2/10 hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF111,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00879,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 133478398 133478398 C A 1 0 0 0 0 1 0 0 0 14819 622 22 2 2 SLC2A6 9 133478398 Missense_Mutation SNP C 11LU022_T 416391 133478398 4916319 517 1155 TMEM8C 0 . GRCh38 9 133520240 133520240 + Missense_Mutation SNP G G T rs758679039 11LU022_T 11LU022_N G G c.184C>A p.Arg62Ser p.R62S ENST00000339996 2/5 178 124 54 260 260 0 strelka-varscan-mutect TMEM8C,missense_variant,p.Arg62Ser,ENST00000339996,NM_001080483.2;TMEM8C,non_coding_transcript_exon_variant,,ENST00000413714,; T ENST00000339996 Transcript missense_variant 286/818 184/666 62/221 R/S Cgt/Agt rs758679039,COSM1229761 1 -1 TMEM8C HGNC HGNC:33778 protein_coding YES CCDS35170.1 ENSP00000419712 A6NI61 UPI00003676C5 NM_001080483.2 tolerated(0.54) 2/5 hmmpanther:PTHR14319,hmmpanther:PTHR14319:SF5,Pfam_domain:PF12036 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs758679039 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 133520240 133520240 G T 1 0 0 0 0 1 0 0 0 16693 1087 38 1 1 TMEM8C 9 133520240 Missense_Mutation SNP G 11LU022_T 41842 133520240 4874477 518 1156 COL5A1 0 . GRCh38 9 134730298 134730298 + Missense_Mutation SNP G G T rs769516996 11LU022_T 11LU022_N G G c.987G>T p.Lys329Asn p.K329N ENST00000371817 7/66 508 462 46 653 653 0 strelka-varscan-mutect COL5A1,missense_variant,p.Lys329Asn,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Lys329Asn,ENST00000618395,NM_001278074.1;COL5A1,upstream_gene_variant,,ENST00000469093,; T ENST00000371817 Transcript missense_variant 1401/8471 987/5517 329/1838 K/N aaG/aaT rs769516996 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 tolerated(0.48) 7/66 MODERATE 1 SNV 1 1 PASS rs769516996 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 134730298 134730298 G T 1 0 0 0 0 1 0 0 0 3485 991 35 2 2 COL5A1 9 134730298 Missense_Mutation SNP G 11LU022_T 1210058 134730298 3664419 519 1157 COL5A1 0 . GRCh38 9 134763712 134763712 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.2009G>T p.Gly670Val p.G670V ENST00000371817 20/66 182 166 16 245 245 0 strelka-varscan-mutect COL5A1,missense_variant,p.Gly670Val,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly670Val,ENST00000618395,NM_001278074.1; T ENST00000371817 Transcript missense_variant 2423/8471 2009/5517 670/1838 G/V gGg/gTg COSM239410 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0.02) 20/66 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS rs1025918128 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 134763712 134763712 G T 1 0 0 0 0 1 0 0 0 3485 1232 43 2 2 COL5A1 9 134763712 Missense_Mutation SNP G 11LU022_T 33414 134763712 3631005 520 1158 SOHLH1 0 . GRCh38 9 135699456 135699456 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.12G>T p.= p.R4R ENST00000425225 1/8 475 321 154 621 621 0 strelka-varscan-mutect SOHLH1,synonymous_variant,p.=,ENST00000298466,NM_001012415.2;SOHLH1,synonymous_variant,p.=,ENST00000425225,NM_001101677.1;KCNT1,upstream_gene_variant,,ENST00000628528,NM_001272003.1;KCNT1,upstream_gene_variant,,ENST00000371757,NM_020822.2;KCNT1,upstream_gene_variant,,ENST00000487664,;KCNT1,upstream_gene_variant,,ENST00000636274,;KCNT1,upstream_gene_variant,,ENST00000636613,;KCNT1,upstream_gene_variant,,ENST00000460750,; A ENST00000425225 Transcript synonymous_variant 73/1411 12/1164 4/387 R cgG/cgT 1 -1 SOHLH1 HGNC HGNC:27845 protein_coding YES CCDS48054.1 ENSP00000404438 Q5JUK2 UPI0001AE6F1C NM_001101677.1 1/8 PROSITE_profiles:PS51257,hmmpanther:PTHR16223,hmmpanther:PTHR16223:SF14 LOW SNV 5 1 PASS rs1195631243 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 135699456 135699456 C A 1 0 0 0 0 0 0 0 1 15246 494 18 2 2 SOHLH1 9 135699456 Silent SNP C 11LU022_T 935744 135699456 2695261 521 1159 CAMSAP1 0 . GRCh38 9 135821370 135821370 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.3291G>T p.= p.R1097R ENST00000389532 11/17 86 59 27 144 144 0 strelka-varscan-mutect CAMSAP1,synonymous_variant,p.=,ENST00000389532,NM_015447.3;CAMSAP1,synonymous_variant,p.=,ENST00000312405,;CAMSAP1,synonymous_variant,p.=,ENST00000409386,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,;CAMSAP1,upstream_gene_variant,,ENST00000493088,;CAMSAP1,upstream_gene_variant,,ENST00000482664,;CAMSAP1,upstream_gene_variant,,ENST00000487868,; A ENST00000389532 Transcript synonymous_variant 3356/7696 3291/4809 1097/1602 R cgG/cgT 1 -1 CAMSAP1 HGNC HGNC:19946 protein_coding YES CCDS35176.2 ENSP00000374183 Q5T5Y3 UPI0000EDA283 NM_015447.3 11/17 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 135821370 135821370 C A 1 0 0 0 0 0 0 0 1 2303 842 30 2 2 CAMSAP1 9 135821370 Silent SNP C 11LU022_T 121914 135821370 2573347 522 1160 C9orf69 0 . GRCh38 9 136116525 136116525 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.376G>T p.Val126Phe p.V126F ENST00000418388 2/2 109 99 10 171 171 0 strelka-varscan-mutect C9orf69,missense_variant,p.Val126Phe,ENST00000418388,NM_152833.2;C9orf69,missense_variant,p.Val126Phe,ENST00000561457,NM_001256526.1;C9orf69,downstream_gene_variant,,ENST00000447934,;C9orf69,downstream_gene_variant,,ENST00000448040,;C9orf69,missense_variant,p.Val126Phe,ENST00000557985,; A ENST00000418388 Transcript missense_variant 879/2823 376/420 126/139 V/F Gtc/Ttc 1 -1 C9orf69 HGNC HGNC:31009 protein_coding YES CCDS59155.1 ENSP00000453019 H0YL14 UPI0000210F31 NM_152833.2 deleterious(0.01) 2/2 hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF59,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 136116525 136116525 C A 1 0 0 0 0 1 0 0 0 2189 507 18 2 2 C9orf69 9 136116525 Missense_Mutation SNP C 11LU022_T 295155 136116525 2278192 523 1161 CACNA1B 0 . GRCh38 9 138053909 138053909 + Missense_Mutation SNP C C T 11LU022_T 11LU022_N C C c.3871C>T p.Leu1291Phe p.L1291F ENST00000371372 26/47 153 115 38 179 179 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Leu1291Phe,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Leu1291Phe,ENST00000371363,;CACNA1B,missense_variant,p.Leu1292Phe,ENST00000371355,;CACNA1B,missense_variant,p.Leu1292Phe,ENST00000371357,;CACNA1B,missense_variant,p.Leu1291Phe,ENST00000277549,;CACNA1B,missense_variant,p.Leu1291Phe,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 4016/9790 3871/7020 1291/2339 L/F Ctc/Ttc COSM3906204 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 tolerated(0.05) 26/47 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 138053909 138053909 C T 1 0 0 0 0 1 0 0 0 2227 797 28 3 3 CACNA1B 9 138053909 Missense_Mutation SNP C 11LU022_T 1937384 138053909 340808 524 1162 FBXO18 0 . GRCh38 10 5903154 5903154 + Nonsense_Mutation SNP A A T 11LU022_T 11LU022_N A A c.289A>T p.Arg97Ter p.R97* ENST00000379999 3/22 90 73 17 90 90 0 strelka-varscan-mutect FBXO18,stop_gained,p.Arg97Ter,ENST00000379999,NM_032807.4;FBXO18,stop_gained,p.Arg46Ter,ENST00000362091,NM_178150.2;FBXO18,5_prime_UTR_variant,,ENST00000397269,NM_001258452.1,NM_001258453.1;FBXO18,non_coding_transcript_exon_variant,,ENST00000462507,;FBXO18,intron_variant,,ENST00000470089,;FBXO18,upstream_gene_variant,,ENST00000469009,;FBXO18,upstream_gene_variant,,ENST00000494526,; T ENST00000379999 Transcript stop_gained 393/3702 289/3285 97/1094 R/* Aga/Tga COSM4918230 1 1 FBXO18 HGNC HGNC:13620 protein_coding YES CCDS7073.1 ENSP00000369335 Q8NFZ0 UPI000019AB6F NM_032807.4 3/22 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 5903154 5903154 A T 1 0 0 0 0 0 1 0 0 5594 296 11 4 4 FBXO18 10 5903154 Nonsense_Mutation SNP A 11LU022_T 5903154 127894268 525 1163 SFMBT2 0 . GRCh38 10 7172565 7172565 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.2081G>T p.Arg694Leu p.R694L ENST00000397167 18/21 229 194 35 270 270 0 strelka-varscan-mutect SFMBT2,missense_variant,p.Arg694Leu,ENST00000397167,NM_001029880.2;SFMBT2,missense_variant,p.Arg694Leu,ENST00000361972,NM_001018039.1; A ENST00000397167 Transcript missense_variant 2274/8024 2081/2685 694/894 R/L cGa/cTa COSM5066782 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 deleterious(0) 18/21 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS rs1415368617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 7172565 7172565 C A 1 0 0 0 0 1 0 0 0 14436 884 31 1 1 SFMBT2 10 7172565 Missense_Mutation SNP C 11LU022_T 1269411 7172565 126624857 526 1164 FRMD4A 0 . GRCh38 10 13740214 13740214 + Missense_Mutation SNP C C A rs376633724 11LU022_T 11LU022_N C C c.652G>T p.Val218Phe p.V218F ENST00000357447 11/25 179 159 20 148 148 0 strelka-varscan-mutect FRMD4A,missense_variant,p.Val218Phe,ENST00000357447,NM_001318336.1,NM_018027.3;FRMD4A,missense_variant,p.Val251Phe,ENST00000264546,;RP11-353M9.1,intron_variant,,ENST00000449462,;FRMD4A,non_coding_transcript_exon_variant,,ENST00000342409,; A ENST00000357447 Transcript missense_variant 1021/6821 652/3120 218/1039 V/F Gtt/Ttt rs376633724 1 -1 FRMD4A HGNC HGNC:25491 protein_coding YES CCDS7101.1 ENSP00000350032 Q9P2Q2 UPI0000366665 NM_001318336.1,NM_018027.3 deleterious(0) 11/25 PROSITE_profiles:PS50057,hmmpanther:PTHR23281:SF12,hmmpanther:PTHR23281,PROSITE_patterns:PS00661,Pfam_domain:PF00373,Gene3D:2.30.29.30,SMART_domains:SM00295,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs376633724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 13740214 13740214 C A 1 0 0 0 0 1 0 0 0 5921 507 18 2 2 FRMD4A 10 13740214 Missense_Mutation SNP C 11LU022_T 6567649 13740214 120057208 527 1165 NMT2 0 . GRCh38 10 15133365 15133365 + Splice_Site SNP T T G novel 11LU022_T 11LU022_N T T c.392-2A>C p.X131_splice ENST00000378165 127 93 34 145 145 0 strelka-varscan-mutect NMT2,splice_acceptor_variant,,ENST00000378165,NM_004808.2;NMT2,splice_acceptor_variant,,ENST00000378150,NM_001308295.1;NMT2,splice_acceptor_variant,,ENST00000478580,;RPP38,intron_variant,,ENST00000451677,; G ENST00000378165 Transcript splice_acceptor_variant -/2907 392/1497 131/498 1 -1 NMT2 HGNC HGNC:7858 protein_coding YES CCDS7109.1 ENSP00000367407 O60551 UPI0000130278 NM_004808.2 3/11 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 3 15133365 15133365 T G 1 0 0 0 0 0 0 1 0 10545 1594 55 5 5 NMT2 10 15133365 Splice_Site SNP T 11LU022_T 1393151 15133365 118664057 528 1166 ITGA8 0 . GRCh38 10 15575496 15575496 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.2471T>A p.Ile824Asn p.I824N ENST00000378076 24/30 134 122 12 148 148 0 strelka-varscan-mutect ITGA8,missense_variant,p.Ile824Asn,ENST00000378076,NM_003638.2,NM_001291494.1; T ENST00000378076 Transcript missense_variant 2825/6755 2471/3192 824/1063 I/N aTt/aAt 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 deleterious(0) 24/30 Gene3D:1jv2A04,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 15575496 15575496 A T 1 0 0 0 0 1 0 0 0 7789 101 4 4 4 ITGA8 10 15575496 Missense_Mutation SNP A 11LU022_T 442131 15575496 118221926 529 1167 ARHGAP21 0 . GRCh38 10 24633440 24633440 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.402C>T p.= p.G134G ENST00000396432 6/26 105 97 8 153 153 0 strelka-varscan-mutect ARHGAP21,synonymous_variant,p.=,ENST00000396432,NM_020824.3;ARHGAP21,synonymous_variant,p.=,ENST00000612832,;ARHGAP21,synonymous_variant,p.=,ENST00000320481,;ARHGAP21,synonymous_variant,p.=,ENST00000446003,;ARHGAP21,synonymous_variant,p.=,ENST00000376410,;ARHGAP21,synonymous_variant,p.=,ENST00000416305,;ARHGAP21,synonymous_variant,p.=,ENST00000636842,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000476499,; A ENST00000396432 Transcript synonymous_variant 889/7167 402/5877 134/1958 G ggC/ggT 1 -1 ARHGAP21 HGNC HGNC:23725 protein_coding YES CCDS7144.2 ENSP00000379709 Q5T5U3 UPI0001639C78 NM_020824.3 6/26 PROSITE_profiles:PS50106,hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 24633440 24633440 G A 1 0 0 0 0 0 0 0 1 995 1306 46 3 3 ARHGAP21 10 24633440 Silent SNP G 11LU022_T 9057944 24633440 109163982 530 1168 ZEB1 0 . GRCh38 10 31521771 31521771 + Silent SNP C C T 11LU022_T 11LU022_N C C c.2439C>T p.= p.P813P ENST00000361642 7/9 112 91 21 114 114 0 strelka-varscan-mutect ZEB1,synonymous_variant,p.=,ENST00000446923,NM_001323656.1,NM_001323664.1,NM_001323657.1,NM_001323650.1,NM_001128128.2,NM_001174094.1;ZEB1,synonymous_variant,p.=,ENST00000361642,NM_001174096.1;ZEB1,synonymous_variant,p.=,ENST00000320985,NM_030751.5;ZEB1,synonymous_variant,p.=,ENST00000560721,NM_001174093.1;ZEB1,synonymous_variant,p.=,ENST00000542815,NM_001174095.1;ZEB1,downstream_gene_variant,,ENST00000561212,;ZEB1,downstream_gene_variant,,ENST00000559476,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,downstream_gene_variant,,ENST00000558440,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,NM_001323663.1,NM_001323661.1,NM_001323644.1,NM_001323649.1,NM_001323659.1,NM_001323652.1,NM_001323673.1,NM_001323662.1,NM_001323676.1,NM_001323653.1,NM_001323655.1,NM_001323645.1,NM_001323647.1,NM_001323660.1,NM_001323671.1,NM_001323638.1,NM_001323665.1,NM_001323643.1,NM_001323677.1,NM_001323641.1,NM_001323642.1,NM_001323658.1,NM_001323651.1,NM_001323672.1,NM_001323654.1;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;ZEB1,downstream_gene_variant,,ENST00000558863,; T ENST00000361642 Transcript synonymous_variant 2502/5990 2439/3378 813/1125 P ccC/ccT COSM393174 1 1 ZEB1 HGNC HGNC:11642 protein_coding YES CCDS53505.1 ENSP00000354487 P37275 UPI000068F51D NM_001174096.1 7/9 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF17 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 31521771 31521771 C T 1 0 0 0 0 0 0 0 1 18199 581 21 3 3 ZEB1 10 31521771 Silent SNP C 11LU022_T 6888331 31521771 102275651 531 1169 ITGB1 0 . GRCh38 10 32912115 32912115 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1479A>T p.Glu493Asp p.E493D ENST00000396033 12/16 60 52 8 66 66 0 strelka-varscan-mutect ITGB1,missense_variant,p.Glu493Asp,ENST00000396033,NM_133376.2;ITGB1,missense_variant,p.Glu493Asp,ENST00000423113,NM_033668.2;ITGB1,missense_variant,p.Glu493Asp,ENST00000302278,NM_002211.3;ITGB1,upstream_gene_variant,,ENST00000488427,;ITGB1,upstream_gene_variant,,ENST00000494395,; A ENST00000396033 Transcript missense_variant 1615/3784 1479/2397 493/798 E/D gaA/gaT 1 -1 ITGB1 HGNC HGNC:6153 protein_coding YES CCDS7174.1 ENSP00000379350 P05556 UPI0000070EEB NM_133376.2 tolerated(0.43) 12/16 PIRSF_domain:PIRSF002512,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF28 MODERATE 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -18.31621 0.9999999 1 1 1 0 A 3 1 3 32912115 32912115 T A 1 0 0 0 0 1 0 0 0 7797 1606 56 4 4 ITGB1 10 32912115 Missense_Mutation SNP T 11LU022_T 1390344 32912115 100885307 532 1170 ANKRD30A 0 . GRCh38 10 37130357 37130357 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.321A>T p.= p.A107A ENST00000361713 3/36 111 99 12 139 139 0 strelka-varscan-mutect ANKRD30A,synonymous_variant,p.=,ENST00000374660,;ANKRD30A,synonymous_variant,p.=,ENST00000611781,;ANKRD30A,synonymous_variant,p.=,ENST00000602533,;ANKRD30A,synonymous_variant,p.=,ENST00000361713,NM_052997.2;RNU6-811P,upstream_gene_variant,,ENST00000384069,; T ENST00000361713 Transcript synonymous_variant 420/4405 321/4026 107/1341 A gcA/gcT 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 3/36 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF00023,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 37130357 37130357 A T 1 0 0 0 0 0 0 0 1 761 175 7 4 4 ANKRD30A 10 37130357 Silent SNP A 11LU022_T 4218242 37130357 96667065 533 1171 WDFY4 0 . GRCh38 10 48776913 48776913 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.3027C>A p.= p.R1009R ENST00000325239 15/61 230 189 41 256 256 0 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1; A ENST00000325239 Transcript synonymous_variant 3027/9555 3027/9555 1009/3184 R cgC/cgA 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 15/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 48776913 48776913 C A 1 0 0 0 0 0 0 0 1 17831 697 25 2 2 WDFY4 10 48776913 Silent SNP C 11LU022_T 11646556 48776913 85020509 534 1172 C10orf71 0 . GRCh38 10 49324178 49324178 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.1633C>A p.Pro545Thr p.P545T ENST00000374144 3/3 140 120 20 197 197 0 strelka-varscan-mutect C10orf71,missense_variant,p.Pro545Thr,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript missense_variant 1921/5230 1633/4308 545/1435 P/T Ccc/Acc COSM3747190,COSM3747191 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0.01) 3/3 hmmpanther:PTHR33775 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49324178 49324178 C A 1 0 0 0 0 1 0 0 0 1769 623 22 2 2 C10orf71 10 49324178 Missense_Mutation SNP C 11LU022_T 547265 49324178 84473244 535 1173 OGDHL 0 . GRCh38 10 49737958 49737958 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.2506T>G p.Phe836Val p.F836V ENST00000374103 19/23 178 159 19 206 205 1 strelka-varscan-mutect OGDHL,missense_variant,p.Phe836Val,ENST00000374103,NM_018245.2;OGDHL,missense_variant,p.Phe779Val,ENST00000419399,NM_001143996.1;OGDHL,missense_variant,p.Phe627Val,ENST00000432695,NM_001143997.1;OGDHL,non_coding_transcript_exon_variant,,ENST00000490844,; C ENST00000374103 Transcript missense_variant 2592/3704 2506/3033 836/1010 F/V Ttc/Gtc 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 deleterious(0) 19/23 Gene3D:3.40.50.970,Pfam_domain:PF02779,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,SMART_domains:SM00861,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 49737958 49737958 A C 1 0 0 0 0 1 0 0 0 10914 72 3 5 5 OGDHL 10 49737958 Missense_Mutation SNP A 11LU022_T 413780 49737958 84059464 536 1174 PARG 0 . GRCh38 10 49885244 49885244 + Missense_Mutation SNP T T A rs782572864 11LU022_T 11LU022_N T T c.1789A>T p.Met597Leu p.M597L ENST00000402038 9/19 306 246 60 310 310 0 strelka-varscan-mutect PARG,missense_variant,p.Met597Leu,ENST00000402038,NM_001324381.1;PARG,missense_variant,p.Met597Leu,ENST00000616448,NM_001303487.1,NM_003631.3,NM_001303486.1,NM_001303489.1;PARG,non_coding_transcript_exon_variant,,ENST00000611974,;PARG,3_prime_UTR_variant,,ENST00000614063,;PARG,intron_variant,,ENST00000610922,; A ENST00000402038 Transcript missense_variant 1925/4128 1789/2931 597/976 M/L Atg/Ttg rs782572864 1 -1 PARG HGNC HGNC:8605 protein_coding YES CCDS73130.1 ENSP00000384408 Q86W56 UPI000018CEA9 NM_001324381.1 tolerated(0.06) 9/19 Pfam_domain:PF05028,hmmpanther:PTHR12837 MODERATE 1 SNV 5 1 PASS rs782572864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49885244 49885244 T A 1 0 0 0 0 1 0 0 0 11528 1406 49 4 4 PARG 10 49885244 Missense_Mutation SNP T 11LU022_T 147286 49885244 83912178 537 1175 PRKG1 0 . GRCh38 10 51153237 51153237 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.385G>T p.Glu129Ter p.E129* ENST00000373980 2/18 138 109 29 159 159 0 strelka-varscan-mutect PRKG1,stop_gained,p.Glu129Ter,ENST00000373980,NM_006258.3;PRKG1,stop_gained,p.Glu114Ter,ENST00000373985,NM_001098512.2;PRKG1,upstream_gene_variant,,ENST00000373976,; T ENST00000373980 Transcript stop_gained 802/6928 385/2061 129/686 E/* Gag/Tag 1 1 PRKG1 HGNC HGNC:9414 protein_coding YES CCDS7244.1 ENSP00000363092 Q13976 UPI000012DDCD NM_006258.3 2/18 Gene3D:2.60.120.10,PIRSF_domain:PIRSF000559,PROSITE_profiles:PS50042,hmmpanther:PTHR24353,hmmpanther:PTHR24353:SF68,SMART_domains:SM00100,Superfamily_domains:SSF51206 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 51153237 51153237 G T 1 0 0 0 0 0 1 0 0 12655 1175 41 2 2 PRKG1 10 51153237 Nonsense_Mutation SNP G 11LU022_T 1267993 51153237 82644185 538 1176 PCDH15 0 . GRCh38 10 53806750 53806750 + Silent SNP C C A rs572313030 11LU022_T 11LU022_N C C c.4875G>T p.= p.A1625A ENST00000614895 35/35 498 403 95 598 597 1 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000614895,;PCDH15,synonymous_variant,p.=,ENST00000373965,NM_001142772.1;PCDH15,synonymous_variant,p.=,ENST00000414778,;PCDH15,synonymous_variant,p.=,ENST00000616114,;PCDH15,synonymous_variant,p.=,ENST00000621708,NM_001142771.1;PCDH15,synonymous_variant,p.=,ENST00000495484,;PCDH15,synonymous_variant,p.=,ENST00000618301,;PCDH15,downstream_gene_variant,,ENST00000617271,NM_001142770.1;PCDH15,downstream_gene_variant,,ENST00000613657,NM_001142769.1;PCDH15,downstream_gene_variant,,ENST00000395445,;PCDH15,downstream_gene_variant,,ENST00000395438,;PCDH15,downstream_gene_variant,,ENST00000612394,;PCDH15,downstream_gene_variant,,ENST00000409834,;PCDH15,downstream_gene_variant,,ENST00000395446,;PCDH15,downstream_gene_variant,,ENST00000395440,;PCDH15,downstream_gene_variant,,ENST00000395442,;PCDH15,downstream_gene_variant,,ENST00000615043,;PCDH15,downstream_gene_variant,,ENST00000414367,;PCDH15,downstream_gene_variant,,ENST00000476074,; A ENST00000614895 Transcript synonymous_variant 5270/9249 4875/5046 1625/1681 A gcG/gcT rs572313030,COSM1348209 1 -1 PCDH15 HGNC HGNC:14674 protein_coding ENSP00000478512 A0A087WUA8 UPI0004E4CB60 35/35 0,1 LOW SNV 5 0,1 1 PASS rs572313030 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 53806750 53806750 C A 1 0 0 0 0 0 0 0 1 11598 639 23 1 1 PCDH15 10 53806750 Silent SNP C 11LU022_T 2653513 53806750 79990672 539 1177 PCDH15 0 . GRCh38 10 53807025 53807025 + Missense_Mutation SNP G G C 11LU022_T 11LU022_N G G c.4600C>G p.Pro1534Ala p.P1534A ENST00000614895 35/35 146 138 8 153 153 0 strelka-varscan-mutect PCDH15,missense_variant,p.Pro1534Ala,ENST00000614895,;PCDH15,missense_variant,p.Pro1530Ala,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Pro1529Ala,ENST00000414778,;PCDH15,missense_variant,p.Pro1528Ala,ENST00000616114,;PCDH15,missense_variant,p.Pro1535Ala,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Pro269Ala,ENST00000495484,;PCDH15,missense_variant,p.Pro313Ala,ENST00000618301,;PCDH15,downstream_gene_variant,,ENST00000617271,NM_001142770.1;PCDH15,downstream_gene_variant,,ENST00000613657,NM_001142769.1;PCDH15,downstream_gene_variant,,ENST00000395445,;PCDH15,downstream_gene_variant,,ENST00000395438,;PCDH15,downstream_gene_variant,,ENST00000612394,;PCDH15,downstream_gene_variant,,ENST00000409834,;PCDH15,downstream_gene_variant,,ENST00000395446,;PCDH15,downstream_gene_variant,,ENST00000395440,;PCDH15,downstream_gene_variant,,ENST00000395442,;PCDH15,downstream_gene_variant,,ENST00000615043,;PCDH15,non_coding_transcript_exon_variant,,ENST00000476074,;PCDH15,downstream_gene_variant,,ENST00000414367,; C ENST00000614895 Transcript missense_variant 4995/9249 4600/5046 1534/1681 P/A Cct/Gct COSM1505283 1 -1 PCDH15 HGNC HGNC:14674 protein_coding ENSP00000478512 A0A087WUA8 UPI0004E4CB60 tolerated_low_confidence(1) 35/35 1 MODERATE SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -11.05123 0.9999994 1 1 1 0 C 3 2 3 53807025 53807025 G C 1 0 0 0 0 1 0 0 0 11598 1174 41 4 4 PCDH15 10 53807025 Missense_Mutation SNP G 11LU022_T 275 53807025 79990397 540 1178 PCDH15 0 . GRCh38 10 53809142 53809142 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4923G>T p.Glu1641Asp p.E1641D ENST00000613657 37/37 356 306 50 407 407 0 strelka-varscan-mutect PCDH15,missense_variant,p.Glu1641Asp,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Glu1634Asp,ENST00000395445,;PCDH15,missense_variant,p.Glu1640Asp,ENST00000612394,;PCDH15,missense_variant,p.Glu832Asp,ENST00000395446,;PCDH15,missense_variant,p.Glu570Asp,ENST00000395440,;PCDH15,missense_variant,p.Glu501Asp,ENST00000395442,;PCDH15,3_prime_UTR_variant,,ENST00000617271,NM_001142770.1;PCDH15,3_prime_UTR_variant,,ENST00000395438,;PCDH15,3_prime_UTR_variant,,ENST00000409834,;PCDH15,3_prime_UTR_variant,,ENST00000615043,;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,3_prime_UTR_variant,,ENST00000414367,;PCDH15,intron_variant,,ENST00000476074,; A ENST00000613657 Transcript missense_variant 5318/6329 4923/5373 1641/1790 E/D gaG/gaT 1 -1 PCDH15 HGNC HGNC:14674 protein_coding CCDS73138.1 ENSP00000482794 A0A087WZN9 UPI0001884905 NM_001142769.1 tolerated_low_confidence(0.16) 37/37 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 53809142 53809142 C A 1 0 0 0 0 1 0 0 0 11598 912 32 2 2 PCDH15 10 53809142 Missense_Mutation SNP C 11LU022_T 2117 53809142 79988280 541 1179 PCDH15 0 . GRCh38 10 53809455 53809455 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.4610C>T p.Ala1537Val p.A1537V ENST00000613657 37/37 297 239 58 376 375 1 strelka-varscan-mutect PCDH15,missense_variant,p.Ala1537Val,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Ala1530Val,ENST00000395445,;PCDH15,missense_variant,p.Ala1536Val,ENST00000612394,;PCDH15,missense_variant,p.Ala728Val,ENST00000395446,;PCDH15,missense_variant,p.Ala466Val,ENST00000395440,;PCDH15,missense_variant,p.Ala397Val,ENST00000395442,;PCDH15,3_prime_UTR_variant,,ENST00000617271,NM_001142770.1;PCDH15,3_prime_UTR_variant,,ENST00000395438,;PCDH15,3_prime_UTR_variant,,ENST00000409834,;PCDH15,3_prime_UTR_variant,,ENST00000615043,;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,3_prime_UTR_variant,,ENST00000414367,;PCDH15,intron_variant,,ENST00000476074,; A ENST00000613657 Transcript missense_variant 5005/6329 4610/5373 1537/1790 A/V gCa/gTa 1 -1 PCDH15 HGNC HGNC:14674 protein_coding CCDS73138.1 ENSP00000482794 A0A087WZN9 UPI0001884905 NM_001142769.1 tolerated_low_confidence(0.16) 37/37 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 53809455 53809455 G A 1 0 0 0 0 1 0 0 0 11598 1319 46 3 3 PCDH15 10 53809455 Missense_Mutation SNP G 11LU022_T 313 53809455 79987967 542 1180 PCDH15 0 . GRCh38 10 54195830 54195830 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.1173G>T p.= p.L391L ENST00000373957 12/35 340 270 70 404 403 1 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000614895,;PCDH15,synonymous_variant,p.=,ENST00000373965,NM_001142772.1;PCDH15,synonymous_variant,p.=,ENST00000414778,;PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,synonymous_variant,p.=,ENST00000617271,NM_001142770.1;PCDH15,synonymous_variant,p.=,ENST00000613657,NM_001142769.1;PCDH15,synonymous_variant,p.=,ENST00000395445,;PCDH15,synonymous_variant,p.=,ENST00000616114,;PCDH15,synonymous_variant,p.=,ENST00000395438,;PCDH15,synonymous_variant,p.=,ENST00000612394,;PCDH15,synonymous_variant,p.=,ENST00000621708,NM_001142771.1;PCDH15,synonymous_variant,p.=,ENST00000373955,;PCDH15,synonymous_variant,p.=,ENST00000395446,;PCDH15,synonymous_variant,p.=,ENST00000395440,;PCDH15,5_prime_UTR_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,synonymous_variant,p.=,ENST00000448885,;PCDH15,synonymous_variant,p.=,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript synonymous_variant 1568/7032 1173/5889 391/1962 L ctG/ctT 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 12/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS rs1397995581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 54195830 54195830 C A 1 0 0 0 0 0 0 0 1 11598 581 21 2 2 PCDH15 10 54195830 Silent SNP C 11LU022_T 386375 54195830 79601592 543 1181 PCDH15 0 . GRCh38 10 54317438 54317438 + Missense_Mutation SNP G G T rs200798008 11LU022_T 11LU022_N G G c.724C>A p.Arg242Ser p.R242S ENST00000373957 9/35 422 376 46 474 469 5 strelka-varscan-mutect PCDH15,missense_variant,p.Arg242Ser,ENST00000614895,;PCDH15,missense_variant,p.Arg237Ser,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000414778,;PCDH15,missense_variant,p.Arg242Ser,ENST00000617051,;PCDH15,missense_variant,p.Arg242Ser,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Arg215Ser,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Arg200Ser,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Arg237Ser,ENST00000622048,;PCDH15,missense_variant,p.Arg237Ser,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Arg242Ser,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000395445,;PCDH15,missense_variant,p.Arg237Ser,ENST00000616114,;PCDH15,missense_variant,p.Arg237Ser,ENST00000395438,;PCDH15,missense_variant,p.Arg242Ser,ENST00000612394,;PCDH15,missense_variant,p.Arg242Ser,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Arg237Ser,ENST00000373955,;PCDH15,missense_variant,p.Arg237Ser,ENST00000395446,;PCDH15,missense_variant,p.Arg237Ser,ENST00000395440,;PCDH15,missense_variant,p.Arg237Ser,ENST00000395442,;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Arg237Ser,ENST00000448885,;PCDH15,missense_variant,p.Arg237Ser,ENST00000373956,;PCDH15,missense_variant,p.Arg237Ser,ENST00000414367,; T ENST00000373957 Transcript missense_variant 1119/7032 724/5889 242/1962 R/S Cgt/Agt rs200798008 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 deleterious(0) 9/35 PROSITE_profiles:PS50268,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 uncertain_significance MODERATE 1 SNV 5 1 1 PASS rs200798008 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 54317438 54317438 G T 1 0 0 0 0 1 0 0 0 11598 1130 39 1 1 PCDH15 10 54317438 Missense_Mutation SNP G 11LU022_T 121608 54317438 79479984 544 1182 ANK3 0 . GRCh38 10 60198475 60198475 + Silent SNP C C G novel 11LU022_T 11LU022_N C C c.1554G>C p.= p.L518L ENST00000280772 14/44 366 307 59 414 414 0 strelka-varscan-mutect ANK3,synonymous_variant,p.=,ENST00000280772,NM_020987.3;ANK3,synonymous_variant,p.=,ENST00000373827,NM_001204403.1;ANK3,synonymous_variant,p.=,ENST00000503366,NM_001204404.1;ANK3,3_prime_UTR_variant,,ENST00000622427,; G ENST00000280772 Transcript synonymous_variant 1746/16874 1554/13134 518/4377 L ctG/ctC 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 14/44 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 60198475 60198475 C G 1 0 0 0 0 0 0 0 1 722 465 17 4 4 ANK3 10 60198475 Silent SNP C 11LU022_T 5881037 60198475 73598947 545 1183 SIRT1 0 . GRCh38 10 67916505 67916505 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.2156C>T p.Thr719Ile p.T719I ENST00000212015 9/9 171 162 9 248 248 0 strelka-mutect SIRT1,missense_variant,p.Thr719Ile,ENST00000212015,NM_012238.4;SIRT1,missense_variant,p.Thr424Ile,ENST00000432464,NM_001142498.1;SIRT1,missense_variant,p.Thr416Ile,ENST00000403579,;SIRT1,missense_variant,p.Thr416Ile,ENST00000406900,NM_001314049.1; T ENST00000212015 Transcript missense_variant 2209/4094 2156/2244 719/747 T/I aCt/aTt 1 1 SIRT1 HGNC HGNC:14929 protein_coding YES CCDS7273.1 ENSP00000212015 Q96EB6 A0A024QZQ1 UPI0000073E1A NM_012238.4 tolerated_low_confidence(0.24) 9/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 67916505 67916505 C T 1 0 0 0 0 1 0 0 0 14600 565 20 3 3 SIRT1 10 67916505 Missense_Mutation SNP C 11LU022_T 7718030 67916505 65880917 546 1184 TET1 0 . GRCh38 10 68573293 68573293 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.955G>T p.Gly319Trp p.G319W ENST00000373644 2/12 196 166 30 235 235 0 strelka-varscan-mutect TET1,missense_variant,p.Gly319Trp,ENST00000373644,NM_030625.2; T ENST00000373644 Transcript missense_variant 1164/9288 955/6411 319/2136 G/W Ggg/Tgg 1 1 TET1 HGNC HGNC:29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 deleterious(0) 2/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 68573293 68573293 G T 1 0 0 0 0 1 0 0 0 16190 1348 47 2 2 TET1 10 68573293 Missense_Mutation SNP G 11LU022_T 656788 68573293 65224129 547 1185 PALD1 0 . GRCh38 10 70566700 70566700 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2538C>A p.Ser846Arg p.S846R ENST00000263563 20/20 148 104 44 151 151 0 strelka-varscan-mutect PALD1,missense_variant,p.Ser846Arg,ENST00000263563,NM_014431.2; A ENST00000263563 Transcript missense_variant 2806/4555 2538/2571 846/856 S/R agC/agA 1 1 PALD1 HGNC HGNC:23530 protein_coding YES CCDS31215.1 ENSP00000263563 Q9ULE6 A0A024QZM5 UPI00001C1EDC NM_014431.2 tolerated_low_confidence(0.15) 20/20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 70566700 70566700 C A 1 0 0 0 0 1 0 0 0 11486 738 26 2 2 PALD1 10 70566700 Missense_Mutation SNP C 11LU022_T 1993407 70566700 63230722 548 1186 CHST3 0 . GRCh38 10 72008200 72008200 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1169G>T p.Gly390Val p.G390V ENST00000373115 3/3 141 124 17 211 211 0 strelka-varscan-mutect CHST3,missense_variant,p.Gly390Val,ENST00000373115,NM_004273.4; T ENST00000373115 Transcript missense_variant 1606/6970 1169/1440 390/479 G/V gGc/gTc 1 1 CHST3 HGNC HGNC:1971 protein_coding YES CCDS7312.1 ENSP00000362207 Q7LGC8 UPI000013CB04 NM_004273.4 deleterious(0) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF38,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1035424190 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 3 72008200 72008200 G T 1 0 0 0 0 1 0 0 0 3165 1203 42 2 2 CHST3 10 72008200 Missense_Mutation SNP G 11LU022_T 1441500 72008200 61789222 549 1187 CHCHD1 0 . GRCh38 10 73782093 73782093 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.18G>T p.= p.L6L ENST00000372833 1/3 168 127 41 193 193 0 strelka-varscan-mutect CHCHD1,synonymous_variant,p.=,ENST00000372837,;CHCHD1,synonymous_variant,p.=,ENST00000372833,NM_203298.2;ZSWIM8,upstream_gene_variant,,ENST00000604729,;ZSWIM8,upstream_gene_variant,,ENST00000398706,NM_015037.3;ZSWIM8,upstream_gene_variant,,ENST00000605216,NM_001242487.1;ZSWIM8,upstream_gene_variant,,ENST00000603114,NM_001242488.1;ZSWIM8,upstream_gene_variant,,ENST00000604524,;FUT11,downstream_gene_variant,,ENST00000489264,;ZSWIM8,upstream_gene_variant,,ENST00000433366,;ZSWIM8,upstream_gene_variant,,ENST00000446546,; T ENST00000372833 Transcript synonymous_variant 31/835 18/357 6/118 L ctG/ctT 1 1 CHCHD1 HGNC HGNC:23518 protein_coding YES CCDS7334.1 ENSP00000361923 Q96BP2 UPI000006CC90 NM_203298.2 1/3 hmmpanther:PTHR31278 LOW 1 SNV 1 1 PASS rs1216640252 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 73782093 73782093 G T 1 0 0 0 0 0 0 0 1 3074 1306 46 2 2 CHCHD1 10 73782093 Silent SNP G 11LU022_T 1773893 73782093 60015329 550 1188 NUTM2E 0 . GRCh38 10 79850261 79850261 + Silent SNP C C G novel 11LU022_T 11LU022_N C C c.2292C>G p.= p.L764L ENST00000429984 7/7 95 74 21 190 190 0 varscan-mutect NUTM2E,synonymous_variant,p.=,ENST00000429984,;NUTM2E,3_prime_UTR_variant,,ENST00000602967,; G ENST00000429984 Transcript synonymous_variant 2675/3292 2292/2637 764/878 L ctC/ctG 1 1 NUTM2E HGNC HGNC:23448 protein_coding YES ENSP00000407521 B1AL46 UPI0001A5E5A7 7/7 Pfam_domain:PF12881,hmmpanther:PTHR22879 LOW 1 SNV 5 1 PASS . . 34 175 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 79850261 79850261 C G 1 0 0 0 0 0 0 0 1 10850 900 32 4 4 NUTM2E 10 79850261 Silent SNP C 11LU022_T 6068168 79850261 53947161 551 1189 OPN4 0 . GRCh38 10 86660046 86660046 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.985G>T p.Val329Leu p.V329L ENST00000372071 7/11 125 115 10 141 141 0 strelka-varscan-mutect OPN4,missense_variant,p.Val329Leu,ENST00000372071,NM_001030015.2;OPN4,missense_variant,p.Val318Leu,ENST00000241891,NM_033282.3;OPN4,missense_variant,p.Val329Leu,ENST00000443292,; T ENST00000372071 Transcript missense_variant 1212/2401 985/1470 329/489 V/L Gtg/Ttg 1 1 OPN4 HGNC HGNC:14449 protein_coding YES CCDS31237.1 ENSP00000361141 Q9UHM6 UPI00001544ED NM_001030015.2 tolerated(0.17) 7/11 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24240,hmmpanther:PTHR24240:SF72,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 86660046 86660046 G T 1 0 0 0 0 1 0 0 0 10958 1261 44 2 2 OPN4 10 86660046 Missense_Mutation SNP G 11LU022_T 6809785 86660046 47137376 552 1190 MMRN2 0 . GRCh38 10 86943014 86943014 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1770C>A p.= p.R590R ENST00000372027 6/7 61 46 15 63 63 0 strelka-varscan-mutect MMRN2,synonymous_variant,p.=,ENST00000372027,NM_024756.2;MMRN2,downstream_gene_variant,,ENST00000610081,;MMRN2,downstream_gene_variant,,ENST00000609457,;MMRN2,downstream_gene_variant,,ENST00000474994,;MMRN2,downstream_gene_variant,,ENST00000488950,;MMRN2,downstream_gene_variant,,ENST00000608090,;MMRN2,downstream_gene_variant,,ENST00000608753,; T ENST00000372027 Transcript synonymous_variant 2092/4375 1770/2850 590/949 R cgC/cgA 1 -1 MMRN2 HGNC HGNC:19888 protein_coding YES CCDS7379.1 ENSP00000361097 Q9H8L6 UPI000013F046 NM_024756.2 6/7 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF6 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 86943014 86943014 G T 1 0 0 0 0 0 0 0 1 9634 1190 42 2 2 MMRN2 10 86943014 Silent SNP G 11LU022_T 282968 86943014 46854408 553 1191 LIPM 0 . GRCh38 10 88803008 88803008 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.112A>T p.Thr38Ser p.T38S ENST00000404743 1/9 204 156 48 192 192 0 strelka-varscan-mutect LIPM,missense_variant,p.Thr38Ser,ENST00000404743,NM_001128215.1;LIPM,upstream_gene_variant,,ENST00000539337,; T ENST00000404743 Transcript missense_variant 279/1439 112/1272 38/423 T/S Act/Tct 1 1 LIPM HGNC HGNC:23455 protein_coding YES CCDS44457.1 ENSP00000383901 Q5VYY2 UPI00004B21B5 NM_001128215.1 tolerated(0.71) 1/9 Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000862,hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF12 MODERATE 1 SNV 1 1 PASS rs1373700038 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 88803008 88803008 A T 1 0 0 0 0 1 0 0 0 8749 43 2 4 4 LIPM 10 88803008 Missense_Mutation SNP A 11LU022_T 1859994 88803008 44994414 554 1192 KIF11 0 . GRCh38 10 92649869 92649869 + Silent SNP A A T rs774863991 11LU022_T 11LU022_N A A c.2805A>T p.= p.P935P ENST00000260731 20/22 130 105 25 156 156 0 strelka-varscan-mutect KIF11,synonymous_variant,p.=,ENST00000260731,NM_004523.3; T ENST00000260731 Transcript synonymous_variant 2895/4860 2805/3171 935/1056 P ccA/ccT rs774863991 1 1 KIF11 HGNC HGNC:6388 protein_coding YES CCDS7422.1 ENSP00000260731 P52732 UPI000013D0FC NM_004523.3 20/22 Pfam_domain:PF13931,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF105 LOW 1 SNV 1 1 PASS rs774863991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 92649869 92649869 A T 1 0 0 0 0 0 0 0 1 8136 204 8 4 4 KIF11 10 92649869 Silent SNP A 11LU022_T 3846861 92649869 41147553 555 1193 CYP2C18 0 . GRCh38 10 94733431 94733431 + Frame_Shift_Del DEL C C - 11LU022_T 11LU022_N C C c.1284delC p.Ser429GlnfsTer21 p.S429Qfs*21 ENST00000285979 8/9 80 66 14 86 86 0 sindel-pindel CYP2C18,frameshift_variant,p.Ser429GlnfsTer21,ENST00000285979,NM_000772.2;CYP2C18,frameshift_variant,p.Ser370GlnfsTer21,ENST00000339022,NM_001128925.1;RP11-400G3.5,frameshift_variant,p.Ser309GlnfsTer437,ENST00000464755,; - ENST00000285979 Transcript frameshift_variant 1483/2418 1284/1473 428/490 F/X ttC/tt COSM3441923 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 8/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,PROSITE_patterns:PS00086,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463,Prints_domain:PR00385 1 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 94733431 94733431 C - 1 0 1 0 1 0 0 0 0 3968 912 32 0 0 CYP2C18 10 94733431 Frame_Shift_Del DEL C 11LU022_T 2083562 94733431 39063991 556 1194 C10orf2 0 . GRCh38 10 100989450 100989450 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1240A>T p.Thr414Ser p.T414S ENST00000311916 1/5 492 373 119 695 695 0 strelka-varscan-mutect C10orf2,missense_variant,p.Thr414Ser,ENST00000370228,NM_001163812.1;C10orf2,missense_variant,p.Thr414Ser,ENST00000311916,NM_021830.4;SEMA4G,downstream_gene_variant,,ENST00000210633,NM_017893.3;SEMA4G,downstream_gene_variant,,ENST00000370250,;SEMA4G,downstream_gene_variant,,ENST00000517724,NM_001203244.1;MRPL43,upstream_gene_variant,,ENST00000318325,NM_176792.2;SEMA4G,downstream_gene_variant,,ENST00000613292,;MRPL43,upstream_gene_variant,,ENST00000318364,NM_032112.2;MRPL43,upstream_gene_variant,,ENST00000477279,;MRPL43,upstream_gene_variant,,ENST00000342071,NM_176794.1;MRPL43,upstream_gene_variant,,ENST00000370242,;MRPL43,upstream_gene_variant,,ENST00000370236,;MRPL43,upstream_gene_variant,,ENST00000523148,;MRPL43,upstream_gene_variant,,ENST00000370241,;MRPL43,upstream_gene_variant,,ENST00000370234,NM_001308396.1;MRPL43,upstream_gene_variant,,ENST00000299179,NM_176793.1;MRPL43,upstream_gene_variant,,ENST00000448244,;SEMA4G,downstream_gene_variant,,ENST00000476171,;RP11-108L7.4,upstream_gene_variant,,ENST00000447344,;C10orf2,intron_variant,,ENST00000473656,;C10orf2,intron_variant,,ENST00000476766,;C10orf2,intron_variant,,ENST00000459764,;MRPL43,upstream_gene_variant,,ENST00000493646,;SEMA4G,downstream_gene_variant,,ENST00000484128,;MRPL43,upstream_gene_variant,,ENST00000476012,;SEMA4G,downstream_gene_variant,,ENST00000521006,;MRPL43,upstream_gene_variant,,ENST00000487059,; T ENST00000311916 Transcript missense_variant 1425/3131 1240/2055 414/684 T/S Aca/Tca 1 1 C10orf2 HGNC HGNC:1160 protein_coding YES CCDS7506.1 ENSP00000309595 Q96RR1 E5KSY5 UPI000006D9D6 NM_021830.4 deleterious(0.01) 1/5 Gene3D:3.40.50.300,Pfam_domain:PF13481,PROSITE_profiles:PS51199,hmmpanther:PTHR12873,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 100989450 100989450 A T 1 0 0 0 0 1 0 0 0 1762 173 6 4 4 C10orf2 10 100989450 Missense_Mutation SNP A 11LU022_T 6256019 100989450 32807972 557 1195 LZTS2 0 . GRCh38 10 101003968 101003969 + Frame_Shift_Ins INS - - G novel 11LU022_T 11LU022_N - - c.876dupG p.Leu293AlafsTer11 p.L293Afs*11 ENST00000370220 2/4 64 44 20 97 97 0 sindel-varindel-pindel LZTS2,frameshift_variant,p.Leu293AlafsTer11,ENST00000370220,;LZTS2,frameshift_variant,p.Leu293AlafsTer11,ENST00000370223,NM_001318099.1,NM_032429.2;PDZD7,downstream_gene_variant,,ENST00000619208,NM_001195263.1;LZTS2,downstream_gene_variant,,ENST00000426584,;LZTS2,downstream_gene_variant,,ENST00000454422,;LZTS2,downstream_gene_variant,,ENST00000481129,;LZTS2,downstream_gene_variant,,ENST00000429732,;PDZD7,downstream_gene_variant,,ENST00000474125,;LZTS2,downstream_gene_variant,,ENST00000489526,; G ENST00000370220 Transcript frameshift_variant 3933-3934/5741 870-871/2010 290-291/669 -/X -/G 1 1 LZTS2 HGNC HGNC:29381 protein_coding YES CCDS7507.1 ENSP00000359240 Q9BRK4 UPI00001BD944 2/4 HAMAP:MF_03026,hmmpanther:PTHR19354,hmmpanther:PTHR19354:SF4,Low_complexity_(Seg):seg HIGH 1 insertion 1 6 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 7 5 3 101003968 101003968 - G 1 0 1 1 0 0 0 0 0 9052 1567 55 0 0 LZTS2 10 101003968 Frame_Shift_Ins INS - 11LU022_T 14518 101003968 32793454 558 1196 ARL3 0 . GRCh38 10 102685871 102685871 + Missense_Mutation SNP C C A rs770782663 11LU022_T 11LU022_N C C c.446G>T p.Arg149Leu p.R149L ENST00000260746 5/6 127 96 31 137 136 1 strelka-varscan-mutect ARL3,missense_variant,p.Arg149Leu,ENST00000260746,NM_004311.3; A ENST00000260746 Transcript missense_variant 578/3844 446/549 149/182 R/L cGc/cTc rs770782663,COSM1675524 1 -1 ARL3 HGNC HGNC:694 protein_coding YES CCDS7538.1 ENSP00000260746 P36405 UPI0000125EE4 NM_004311.3 deleterious(0.01) 5/6 PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF166,Pfam_domain:PF00025,Gene3D:3.40.50.300,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770782663 . 0 206 0 4 0 0 0 0 -20 0.9999683 1 1 1 0 A 3 1 3 102685871 102685871 C A 1 0 0 0 0 1 0 0 0 1074 768 27 1 1 ARL3 10 102685871 Missense_Mutation SNP C 11LU022_T 1681903 102685871 31111551 559 1197 PDCD11 0 . GRCh38 10 103440492 103440492 + Nonsense_Mutation SNP G G T rs763863942 11LU022_T 11LU022_N G G c.4351G>T p.Glu1451Ter p.E1451* ENST00000369797 29/36 231 173 58 287 287 0 strelka-varscan-mutect PDCD11,stop_gained,p.Glu1451Ter,ENST00000369797,NM_014976.1;PDCD11,upstream_gene_variant,,ENST00000478543,; T ENST00000369797 Transcript stop_gained 4445/6453 4351/5616 1451/1871 E/* Gag/Tag rs763863942 1 1 PDCD11 HGNC HGNC:13408 protein_coding YES CCDS31276.1 ENSP00000358812 Q14690 UPI00001C1ED1 NM_014976.1 29/36 hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF10 HIGH 1 SNV 1 1 PASS rs763863942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 103440492 103440492 G T 1 0 0 0 0 0 1 0 0 11705 1175 41 2 2 PDCD11 10 103440492 Nonsense_Mutation SNP G 11LU022_T 754621 103440492 30356930 560 1198 CFAP43 0 . GRCh38 10 104225543 104225543 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.334G>A p.Asp112Asn p.D112N ENST00000357060 3/38 117 90 27 158 158 0 strelka-varscan-mutect CFAP43,missense_variant,p.Asp112Asn,ENST00000357060,NM_025145.5;CFAP43,missense_variant,p.Asp42Asn,ENST00000278064,;CFAP43,missense_variant,p.Asp42Asn,ENST00000369720,;CFAP43,missense_variant,p.Asp42Asn,ENST00000369719,; T ENST00000357060 Transcript missense_variant 450/5365 334/4998 112/1665 D/N Gac/Aac 1 -1 CFAP43 HGNC HGNC:26684 protein_coding YES CCDS31281.1 ENSP00000349568 Q8NDM7 UPI0000D60FC7 NM_025145.5 deleterious(0.02) 3/38 hmmpanther:PTHR14885,hmmpanther:PTHR14885:SF1,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 104225543 104225543 C T 1 0 0 0 0 1 0 0 0 3018 855 30 3 3 CFAP43 10 104225543 Missense_Mutation SNP C 11LU022_T 785051 104225543 29571879 561 1199 SORCS1 0 . GRCh38 10 106677375 106677375 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.1770C>T p.= p.Y590Y ENST00000263054 13/26 175 143 32 170 170 0 strelka-varscan-mutect SORCS1,synonymous_variant,p.=,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,synonymous_variant,p.=,ENST00000612154,;SORCS1,synonymous_variant,p.=,ENST00000622431,;SORCS1,synonymous_variant,p.=,ENST00000344440,;SORCS1,synonymous_variant,p.=,ENST00000369698,;SORCS1,upstream_gene_variant,,ENST00000472196,; A ENST00000263054 Transcript synonymous_variant 1778/7272 1770/3507 590/1168 Y taC/taT 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 13/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8,Gene3D:2.130.10.140,Pfam_domain:PF15902,SMART_domains:SM00602,Superfamily_domains:SSF110296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 106677375 106677375 G A 1 0 0 0 0 0 0 0 1 15252 1256 44 3 3 SORCS1 10 106677375 Silent SNP G 11LU022_T 2451832 106677375 27120047 562 1200 CASP7 0 . GRCh38 10 113725511 113725511 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.781G>T p.Glu261Ter p.E261* ENST00000369321 5/7 44 29 15 70 70 0 strelka-varscan-mutect CASP7,stop_gained,p.Glu176Ter,ENST00000345633,NM_033339.4;CASP7,stop_gained,p.Glu261Ter,ENST00000369321,NM_001267057.1;CASP7,stop_gained,p.Glu176Ter,ENST00000621345,NM_001267056.1;CASP7,stop_gained,p.Glu176Ter,ENST00000369315,;CASP7,stop_gained,p.Glu209Ter,ENST00000621607,NM_033338.5;CASP7,stop_gained,p.Glu176Ter,ENST00000369318,NM_001227.4;CASP7,stop_gained,p.Glu151Ter,ENST00000452490,NM_001267058.1;CASP7,stop_gained,p.Glu176Ter,ENST00000429617,;CASP7,intron_variant,,ENST00000614447,;CASP7,intron_variant,,ENST00000369331,NM_033340.3;CASP7,downstream_gene_variant,,ENST00000468790,;CASP7,non_coding_transcript_exon_variant,,ENST00000487232,; T ENST00000369321 Transcript stop_gained 867/2620 781/1167 261/388 E/* Gag/Tag 1 1 CASP7 HGNC HGNC:1508 protein_coding YES CCDS73200.1 ENSP00000358327 A0A0A0MRL7 UPI000264F484 NM_001267057.1 5/7 PROSITE_profiles:PS50208,hmmpanther:PTHR10454,Gene3D:3.40.50.1460,Pfam_domain:PF00656,SMART_domains:SM00115,Superfamily_domains:SSF52129,Prints_domain:PR00376 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 113725511 113725511 G T 1 0 0 0 0 0 1 0 0 2376 943 33 2 2 CASP7 10 113725511 Nonsense_Mutation SNP G 11LU022_T 7048136 113725511 20071911 563 1201 ABLIM1 0 . GRCh38 10 114453436 114453436 + Missense_Mutation SNP C C G 11LU022_T 11LU022_N C C c.1489G>C p.Asp497His p.D497H ENST00000277895 13/23 89 68 21 129 129 0 strelka-varscan-mutect ABLIM1,missense_variant,p.Asp465His,ENST00000369252,NM_001322882.1;ABLIM1,missense_variant,p.Asp437His,ENST00000533213,;ABLIM1,missense_variant,p.Asp437His,ENST00000392955,NM_001003407.1;ABLIM1,missense_variant,p.Asp465His,ENST00000369256,NM_001003408.1;ABLIM1,missense_variant,p.Asp497His,ENST00000277895,NM_002313.5;ABLIM1,intron_variant,,ENST00000392952,NM_001322893.1,NM_001322896.1,NM_001322890.1,NM_001322891.1,NM_001322892.1,NM_006720.3;ABLIM1,intron_variant,,ENST00000369253,;ABLIM1,intron_variant,,ENST00000369266,;ABLIM1,intron_variant,,ENST00000428430,;ABLIM1,intron_variant,,ENST00000440467,; G ENST00000277895 Transcript missense_variant 1587/2657 1489/2337 497/778 D/H Gac/Cac COSM5696369,COSM5696370,COSM5696371 1 -1 ABLIM1 HGNC HGNC:78 protein_coding YES CCDS7590.1 ENSP00000277895 O14639 UPI0000418D06 NM_002313.5 deleterious(0.01) 13/23 hmmpanther:PTHR24213,hmmpanther:PTHR24213:SF18,Pfam_domain:PF16182 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs1377619838 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 114453436 114453436 C G 1 0 0 0 0 1 0 0 0 104 913 32 4 4 ABLIM1 10 114453436 Missense_Mutation SNP C 11LU022_T 727925 114453436 19343986 564 1202 ATRNL1 0 . GRCh38 10 115165609 115165609 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.1056T>A p.= p.P352P ENST00000355044 7/29 117 88 29 125 125 0 strelka-varscan-mutect ATRNL1,synonymous_variant,p.=,ENST00000355044,NM_207303.4;ATRNL1,synonymous_variant,p.=,ENST00000609571,NM_001276282.3;ATRNL1,intron_variant,,ENST00000527407,;ATRNL1,3_prime_UTR_variant,,ENST00000616894,; A ENST00000355044 Transcript synonymous_variant 1182/8479 1056/4140 352/1379 P ccT/ccA 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 7/29 hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,Pfam_domain:PF13854,Superfamily_domains:0052715 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999993 1 1 1 0 A 2 1 3 115165609 115165609 T A 1 0 0 0 0 0 0 0 1 1360 1538 54 4 4 ATRNL1 10 115165609 Silent SNP T 11LU022_T 712173 115165609 18631813 565 1203 SFXN4 0 . GRCh38 10 119162351 119162351 + Frame_Shift_Del DEL C C - novel 11LU022_T 11LU022_N C C c.241delG p.Ala81ArgfsTer23 p.A81Rfs*23 ENST00000355697 3/14 159 142 17 251 251 0 sindel-varindel-pindel SFXN4,frameshift_variant,p.Ala81ArgfsTer23,ENST00000355697,NM_213649.1;SFXN4,5_prime_UTR_variant,,ENST00000369131,;SFXN4,5_prime_UTR_variant,,ENST00000419372,;SFXN4,non_coding_transcript_exon_variant,,ENST00000461438,;SFXN4,non_coding_transcript_exon_variant,,ENST00000466218,;SFXN4,non_coding_transcript_exon_variant,,ENST00000462913,; - ENST00000355697 Transcript frameshift_variant 261/1363 241/1014 81/337 A/X Gcg/cg 1 -1 SFXN4 HGNC HGNC:16088 protein_coding YES CCDS7610.1 ENSP00000347924 Q6P4A7 UPI000004D333 NM_213649.1 3/14 Pfam_domain:PF03820,hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF3 HIGH 1 deletion 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.99996 0.9999867 1 1 1 0 - 7 5 3 119162351 119162351 C - 1 0 1 0 1 0 0 0 0 14457 739 26 0 0 SFXN4 10 119162351 Frame_Shift_Del DEL C 11LU022_T 3996742 119162351 14635071 566 1204 TACC2 0 . GRCh38 10 122087104 122087104 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.4604G>T p.Gly1535Val p.G1535V ENST00000369005 4/23 87 75 12 109 108 1 strelka-varscan-mutect TACC2,missense_variant,p.Gly1535Val,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Gly1535Val,ENST00000334433,;TACC2,missense_variant,p.Gly1535Val,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Gly1535Val,ENST00000453444,;TACC2,missense_variant,p.Gly1535Val,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; T ENST00000369005 Transcript missense_variant 4944/9673 4604/8847 1535/2948 G/V gGg/gTg 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious_low_confidence(0) 4/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 3 122087104 122087104 G T 1 0 0 0 0 1 0 0 0 15898 1232 43 2 2 TACC2 10 122087104 Missense_Mutation SNP G 11LU022_T 2924753 122087104 11710318 567 1205 EBF3 0 . GRCh38 10 129867829 129867829 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.838T>C p.Phe280Leu p.F280L ENST00000368648 9/16 157 128 29 215 215 0 strelka-varscan-mutect EBF3,missense_variant,p.Phe280Leu,ENST00000368648,NM_001005463.2;EBF3,missense_variant,p.Phe289Leu,ENST00000355311,; G ENST00000368648 Transcript missense_variant 911/4375 838/1656 280/551 F/L Ttt/Ctt 1 -1 EBF3 HGNC HGNC:19087 protein_coding YES CCDS31314.1 ENSP00000357637 Q9H4W6 UPI000002A6FB NM_001005463.2 deleterious(0) 9/16 Gene3D:2.60.40.10,Pfam_domain:PF01833,hmmpanther:PTHR10747,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 129867829 129867829 A G 1 0 0 0 0 1 0 0 0 4706 72 3 5 5 EBF3 10 129867829 Missense_Mutation SNP A 11LU022_T 7780725 129867829 3929593 568 1206 DPYSL4 0 . GRCh38 10 132196910 132196910 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.528C>A p.Cys176Ter p.C176* ENST00000338492 5/14 196 162 34 324 323 1 strelka-varscan-mutect DPYSL4,stop_gained,p.Cys176Ter,ENST00000338492,NM_006426.2;DPYSL4,stop_gained,p.Cys99Ter,ENST00000368627,;DPYSL4,downstream_gene_variant,,ENST00000493882,;DPYSL4,downstream_gene_variant,,ENST00000493927,; A ENST00000338492 Transcript stop_gained 692/2729 528/1719 176/572 C/* tgC/tgA 1 1 DPYSL4 HGNC HGNC:3016 protein_coding YES CCDS7665.1 ENSP00000339850 O14531 UPI000013DC70 NM_006426.2 5/14 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF55,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02033 HIGH 1 SNV 1 1 PASS rs1276846407 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 132196910 132196910 C A 1 0 0 0 0 0 1 0 0 4564 718 25 2 2 DPYSL4 10 132196910 Nonsense_Mutation SNP C 11LU022_T 2329081 132196910 1600512 569 1207 CALY 0 . GRCh38 10 133326935 133326935 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.303C>A p.= p.I101I ENST00000252939 4/6 193 173 20 295 295 0 strelka-varscan-mutect CALY,synonymous_variant,p.=,ENST00000252939,NM_015722.3;CALY,synonymous_variant,p.=,ENST00000368558,;ZNF511-PRAP1,intron_variant,,ENST00000368554,;CALY,downstream_gene_variant,,ENST00000368555,;CALY,upstream_gene_variant,,ENST00000467611,;CALY,upstream_gene_variant,,ENST00000467433,; T ENST00000252939 Transcript synonymous_variant 397/2271 303/654 101/217 I atC/atA 1 -1 CALY HGNC HGNC:17938 protein_coding YES CCDS7678.1 ENSP00000252939 Q9NYX4 UPI0000001C76 NM_015722.3 4/6 Pfam_domain:PF06387,PIRSF_domain:PIRSF002383,hmmpanther:PTHR28546,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 133326935 133326935 G T 1 0 0 0 0 0 0 0 1 2286 1280 45 2 2 CALY 10 133326935 Silent SNP G 11LU022_T 1130025 133326935 470487 570 1208 MUC5AC 0 . GRCh38 11 1162110 1162110 + Nonsense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.415A>T p.Lys139Ter p.K139* ENST00000621226 4/49 191 137 54 307 307 0 strelka-varscan-mutect MUC5AC,stop_gained,p.Lys139Ter,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript stop_gained 462/17448 415/16965 139/5654 K/* Aag/Tag 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 4/49 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,SMART_domains:SM00216 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 1162110 1162110 A T 1 0 0 0 0 0 1 0 0 9978 247 9 4 4 MUC5AC 11 1162110 Nonsense_Mutation SNP A 11LU022_T 1162110 133924512 571 1209 OR51V1 0 . GRCh38 11 5200231 5200231 + Missense_Mutation SNP A A G 11LU022_T 11LU022_N A A c.470T>C p.Ile157Thr p.I157T ENST00000321255 1/1 184 127 57 251 251 0 strelka-varscan-mutect OR51V1,missense_variant,p.Ile157Thr,ENST00000321255,NM_001004760.2;AC104389.16,upstream_gene_variant,,ENST00000418080,; G ENST00000321255 Transcript missense_variant 470/966 470/966 157/321 I/T aTa/aCa COSM4193468 1 -1 OR51V1 HGNC HGNC:19597 protein_coding YES CCDS31375.1 ENSP00000321729 Q9H2C8 UPI0000140ADA NM_001004760.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF67,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 5200231 5200231 A G 1 0 0 0 0 1 0 0 0 11181 449 16 5 5 OR51V1 11 5200231 Missense_Mutation SNP A 11LU022_T 4038121 5200231 129886391 572 1210 OR51B6 0 . GRCh38 11 5351851 5351851 + Missense_Mutation SNP C C G rs751155441 11LU022_T 11LU022_N C C c.344C>G p.Ala115Gly p.A115G ENST00000380219 1/1 116 97 19 171 171 0 strelka-varscan-mutect OR51B6,missense_variant,p.Ala115Gly,ENST00000380219,NM_001004750.1;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;AC104389.31,upstream_gene_variant,,ENST00000450768,; G ENST00000380219 Transcript missense_variant 344/939 344/939 115/312 A/G gCc/gGc rs751155441 1 1 OR51B6 HGNC HGNC:19600 protein_coding YES CCDS31379.1 ENSP00000369568 Q9H340 UPI000014017D NM_001004750.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF22,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs751155441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 5351851 5351851 C G 1 0 0 0 0 1 0 0 0 11166 739 26 4 4 OR51B6 11 5351851 Missense_Mutation SNP C 11LU022_T 151620 5351851 129734771 573 1211 TRIM6 0 . GRCh38 11 5611341 5611341 + Nonstop_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1550G>T p.Ter517LeuextTer19 p.*517Lext*19 ENST00000380097 8/8 36 28 8 51 51 0 strelka-varscan-mutect TRIM6,stop_lost,p.Ter517LeuextTer19,ENST00000380097,NM_001003818.2;TRIM6,stop_lost,p.Ter489LeuextTer19,ENST00000278302,NM_058166.4;TRIM6,stop_lost,p.Ter463LeuextTer19,ENST00000621176,;TRIM6,stop_lost,p.Ter314LeuextTer19,ENST00000445329,;TRIM6,stop_lost,p.Ter463LeuextTer19,ENST00000380107,;TRIM6,stop_lost,p.Ter314LeuextTer19,ENST00000507320,;TRIM6,stop_lost,p.Ter314LeuextTer19,ENST00000506134,NM_001198644.1;TRIM6,stop_lost,p.Ter314LeuextTer?,ENST00000515022,NM_001198645.1;TRIM6-TRIM34,intron_variant,,ENST00000354852,NM_001003819.3;HBG2,intron_variant,,ENST00000380259,;TRIM6,downstream_gene_variant,,ENST00000424369,;AC015691.13,intron_variant,,ENST00000394793,;TRIM6,non_coding_transcript_exon_variant,,ENST00000481603,;TRIM6,downstream_gene_variant,,ENST00000511284,;TRIM6,downstream_gene_variant,,ENST00000469187,; T ENST00000380097 Transcript stop_lost 1792/3403 1550/1551 517/516 */L tGa/tTa 1 1 TRIM6 HGNC HGNC:16277 protein_coding YES CCDS31389.1 ENSP00000369440 Q9C030 UPI000041A255 NM_001003818.2 8/8 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.90972 1 1 1 1 0 T 4 4 3 5611341 5611341 G T 1 0 0 0 0 0 0 0 0 17026 1285 45 2 2 TRIM6 11 5611341 Nonstop_Mutation SNP G 11LU022_T 259490 5611341 129475281 574 1212 APBB1 0 . GRCh38 11 6403187 6403187 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1062G>T p.Glu354Asp p.E354D ENST00000609360 6/15 43 35 8 100 99 1 strelka-varscan-mutect APBB1,missense_variant,p.Glu354Asp,ENST00000389906,;APBB1,missense_variant,p.Glu354Asp,ENST00000609360,NM_001164.4;APBB1,missense_variant,p.Glu354Asp,ENST00000299402,;APBB1,missense_variant,p.Glu354Asp,ENST00000311051,NM_145689.2;APBB1,missense_variant,p.Glu95Asp,ENST00000610474,;APBB1,missense_variant,p.Glu95Asp,ENST00000608394,NM_001257321.2;APBB1,missense_variant,p.Glu95Asp,ENST00000618005,;APBB1,missense_variant,p.Glu95Asp,ENST00000608704,NM_001257320.2;APBB1,missense_variant,p.Glu95Asp,ENST00000608645,NM_001257326.2;APBB1,missense_variant,p.Glu134Asp,ENST00000608655,NM_001257319.2;APBB1,missense_variant,p.Glu119Asp,ENST00000621678,;APBB1,missense_variant,p.Glu134Asp,ENST00000530885,NM_001257323.2;APBB1,missense_variant,p.Glu119Asp,ENST00000609331,NM_001257325.2;APBB1,missense_variant,p.Glu95Asp,ENST00000529890,;APBB1,intron_variant,,ENST00000529519,;APBB1,downstream_gene_variant,,ENST00000532020,;APBB1,missense_variant,p.Glu354Asp,ENST00000608435,;APBB1,non_coding_transcript_exon_variant,,ENST00000533407,;APBB1,non_coding_transcript_exon_variant,,ENST00000526925,;APBB1,non_coding_transcript_exon_variant,,ENST00000534188,;APBB1,non_coding_transcript_exon_variant,,ENST00000533139,;APBB1,upstream_gene_variant,,ENST00000524626,;APBB1,upstream_gene_variant,,ENST00000529778,; A ENST00000609360 Transcript missense_variant 1162/2642 1062/2133 354/710 E/D gaG/gaT 1 -1 APBB1 HGNC HGNC:581 protein_coding YES CCDS66018.1 ENSP00000477213 O00213 UPI000012510B NM_001164.4 tolerated(0.35) 6/15 hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF5,Low_complexity_(Seg):seg,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.70304 1 1 1 1 0 A 3 1 3 6403187 6403187 C A 1 0 0 0 0 1 0 0 0 879 680 24 2 2 APBB1 11 6403187 Missense_Mutation SNP C 11LU022_T 791846 6403187 128683435 575 1213 DCHS1 0 . GRCh38 11 6623267 6623267 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.8409G>T p.= p.V2803V ENST00000299441 21/21 159 112 47 256 255 1 strelka-varscan-mutect DCHS1,synonymous_variant,p.=,ENST00000299441,NM_003737.3;TPP1,upstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,upstream_gene_variant,,ENST00000533371,;TPP1,upstream_gene_variant,,ENST00000528657,;TPP1,upstream_gene_variant,,ENST00000436873,;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.9,downstream_gene_variant,,ENST00000545572,;TPP1,upstream_gene_variant,,ENST00000534644,;TPP1,upstream_gene_variant,,ENST00000524903,;TPP1,upstream_gene_variant,,ENST00000530040,;TPP1,upstream_gene_variant,,ENST00000428886,;TPP1,upstream_gene_variant,,ENST00000531754,;TPP1,upstream_gene_variant,,ENST00000528571,;TPP1,upstream_gene_variant,,ENST00000528917,; A ENST00000299441 Transcript synonymous_variant 8821/10765 8409/9897 2803/3298 V gtG/gtT 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 21/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,Low_complexity_(Seg):seg,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs1204674858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 6623267 6623267 C A 1 0 0 0 0 0 0 0 1 4090 813 29 2 2 DCHS1 11 6623267 Silent SNP C 11LU022_T 220080 6623267 128463355 576 1214 SYT9 0 . GRCh38 11 7418128 7418128 + Missense_Mutation SNP G G T rs761794324 11LU022_T 11LU022_N G G c.1337G>T p.Arg446Leu p.R446L ENST00000318881 5/7 70 57 13 93 93 0 strelka-varscan-mutect SYT9,missense_variant,p.Arg446Leu,ENST00000318881,NM_175733.3;SYT9,splice_region_variant,,ENST00000532592,;SYT9,splice_region_variant,,ENST00000524820,; T ENST00000318881 Transcript missense_variant,splice_region_variant 1574/3955 1337/1476 446/491 R/L cGt/cTt rs761794324 1 1 SYT9 HGNC HGNC:19265 protein_coding YES CCDS7778.1 ENSP00000324419 Q86SS6 UPI000000DB7B NM_175733.3 tolerated(0.33) 5/7 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF180,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs761794324 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 7418128 7418128 G T 1 0 0 0 0 1 0 0 0 15875 1130 39 1 1 SYT9 11 7418128 Missense_Mutation SNP G 11LU022_T 794861 7418128 127668494 577 1215 NLRP10 0 . GRCh38 11 7959662 7959662 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.1950A>T p.= p.P650P ENST00000328600 2/2 46 27 19 57 57 0 strelka-varscan-mutect NLRP10,synonymous_variant,p.=,ENST00000328600,NM_176821.3;NLRP10,downstream_gene_variant,,ENST00000526590,; A ENST00000328600 Transcript synonymous_variant 2112/2350 1950/1968 650/655 P ccA/ccT 1 -1 NLRP10 HGNC HGNC:21464 protein_coding YES CCDS7784.1 ENSP00000327763 Q86W26 UPI0000167F6C NM_176821.3 2/2 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 7959662 7959662 T A 1 0 0 0 0 0 0 0 1 10509 1799 63 4 4 NLRP10 11 7959662 Silent SNP T 11LU022_T 541534 7959662 127126960 578 1216 PIK3C2A 0 . GRCh38 11 17168897 17168897 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.845A>T p.Asp282Val p.D282V ENST00000265970 1/32 130 95 35 185 185 0 strelka-varscan-mutect PIK3C2A,missense_variant,p.Asp282Val,ENST00000265970,NM_001321378.1,NM_002645.2;PIK3C2A,downstream_gene_variant,,ENST00000532035,;PIK3C2A,intron_variant,,ENST00000531428,;PIK3C2A,missense_variant,p.Asp282Val,ENST00000533645,; A ENST00000265970 Transcript missense_variant 845/8227 845/5061 282/1686 D/V gAt/gTt 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 deleterious_low_confidence(0) 1/32 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF28 MODERATE 1 SNV 1 1 PASS rs1293039936 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 17168897 17168897 T A 1 0 0 0 0 1 0 0 0 12004 1435 50 4 4 PIK3C2A 11 17168897 Missense_Mutation SNP T 11LU022_T 9209235 17168897 117917725 579 1217 OTOG 0 . GRCh38 11 17573207 17573207 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.2246T>A p.Leu749Gln p.L749Q ENST00000399391 18/55 162 120 42 166 166 0 strelka-varscan-mutect OTOG,missense_variant,p.Leu737Gln,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Leu749Gln,ENST00000399391,NM_001277269.1;OTOG,downstream_gene_variant,,ENST00000498332,; A ENST00000399391 Transcript missense_variant 2246/8778 2246/8778 749/2925 L/Q cTg/cAg 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 18/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Pfam_domain:PF08742,SMART_domains:SM00832 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 17573207 17573207 T A 1 0 0 0 0 1 0 0 0 11370 1580 55 4 4 OTOG 11 17573207 Missense_Mutation SNP T 11LU022_T 404310 17573207 117513415 580 1218 LDHA 0 . GRCh38 11 18402992 18402992 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.658G>T p.Gly220Trp p.G220W ENST00000540430 5/8 255 183 72 309 307 2 strelka-varscan-mutect LDHA,missense_variant,p.Gly191Trp,ENST00000422447,NM_005566.3;LDHA,missense_variant,p.Gly220Trp,ENST00000540430,NM_001165414.1;LDHA,missense_variant,p.Gly191Trp,ENST00000379412,;LDHA,missense_variant,p.Gly191Trp,ENST00000227157,NM_001165416.1;LDHA,missense_variant,p.Gly191Trp,ENST00000396222,NM_001165415.1;LDHA,missense_variant,p.Gly133Trp,ENST00000430553,NM_001135239.1;LDHA,missense_variant,p.Gly191Trp,ENST00000542179,;LDHA,downstream_gene_variant,,ENST00000478970,;LDHA,downstream_gene_variant,,ENST00000495052,;LDHA,downstream_gene_variant,,ENST00000543445,;LDHA,downstream_gene_variant,,ENST00000535451,;LDHA,downstream_gene_variant,,ENST00000625635,;AC084117.3,upstream_gene_variant,,ENST00000496975,;LDHA,3_prime_UTR_variant,,ENST00000545215,;LDHA,3_prime_UTR_variant,,ENST00000486690,;LDHA,3_prime_UTR_variant,,ENST00000543695,;LDHA,3_prime_UTR_variant,,ENST00000536528,;LDHA,non_coding_transcript_exon_variant,,ENST00000375710,;LDHA,non_coding_transcript_exon_variant,,ENST00000537296,;LDHA,non_coding_transcript_exon_variant,,ENST00000538451,;LDHA,non_coding_transcript_exon_variant,,ENST00000460405,;LDHA,intron_variant,,ENST00000541097,;LDHA,downstream_gene_variant,,ENST00000494573,;LDHA,downstream_gene_variant,,ENST00000545467,;LDHA,downstream_gene_variant,,ENST00000539814,; T ENST00000540430 Transcript missense_variant 940/2305 658/1086 220/361 G/W Ggg/Tgg 1 1 LDHA HGNC HGNC:6535 protein_coding YES CCDS53609.1 ENSP00000445175 P00338 UPI0001914F68 NM_001165414.1 deleterious(0) 5/8 HAMAP:MF_00488,hmmpanther:PTHR11540:SF17,hmmpanther:PTHR11540,PROSITE_patterns:PS00064,Gene3D:3.90.110.10,Pfam_domain:PF02866,TIGRFAM_domain:TIGR01771,PIRSF_domain:PIRSF000102,Superfamily_domains:SSF56327,Prints_domain:PR00086 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 18402992 18402992 G T 1 0 0 0 0 1 0 0 0 8605 1348 47 2 2 LDHA 11 18402992 Missense_Mutation SNP G 11LU022_T 829785 18402992 116683630 581 1219 PTPN5 0 . GRCh38 11 18733360 18733360 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1093G>T p.Glu365Ter p.E365* ENST00000358540 11/15 171 149 22 175 175 0 strelka-mutect PTPN5,stop_gained,p.Glu333Ter,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,stop_gained,p.Glu365Ter,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,stop_gained,p.Glu169Ter,ENST00000477854,;PTPN5,stop_gained,p.Glu341Ter,ENST00000396168,NM_001278238.1,NM_001278239.1;PTPN5,upstream_gene_variant,,ENST00000396166,;RP11-1081L13.4,intron_variant,,ENST00000527285,; A ENST00000358540 Transcript stop_gained 1524/3135 1093/1698 365/565 E/* Gag/Tag 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 11/15 PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF40,Pfam_domain:PF00102,Gene3D:3.90.190.10,PIRSF_domain:PIRSF001997,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR01778 HIGH 1 SNV 1 1 PASS rs1384350284 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 18733360 18733360 C A 1 0 0 0 0 0 1 0 0 12945 864 30 2 2 PTPN5 11 18733360 Nonsense_Mutation SNP C 11LU022_T 330368 18733360 116353262 582 1220 FIBIN 0 . GRCh38 11 26994888 26994888 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.362G>T p.Arg121Leu p.R121L ENST00000318627 1/1 55 49 6 68 68 0 strelka-varscan-mutect FIBIN,missense_variant,p.Arg121Leu,ENST00000318627,NM_203371.1; T ENST00000318627 Transcript missense_variant 705/1938 362/636 121/211 R/L cGg/cTg 1 1 FIBIN HGNC HGNC:33747 protein_coding YES CCDS7861.1 ENSP00000321962 Q8TAL6 UPI000003B0F4 NM_203371.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR31185:SF0,hmmpanther:PTHR31185,Pfam_domain:PF15819 MODERATE 1 SNV 1 PASS rs902469109 . 0 203 7 0 0 0 0 0 -14.13041 0.9999991 1 1 1 0 T 3 4 3 26994888 26994888 G T 1 0 0 0 0 1 0 0 0 5750 1116 39 1 1 FIBIN 11 26994888 Missense_Mutation SNP G 11LU022_T 8261528 26994888 108091734 583 1221 BBOX1 0 . GRCh38 11 27093267 27093267 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.434A>G p.Lys145Arg p.K145R ENST00000263182 5/9 239 210 29 234 234 0 strelka-varscan-mutect BBOX1,missense_variant,p.Lys145Arg,ENST00000263182,NM_003986.2;BBOX1,missense_variant,p.Lys145Arg,ENST00000529202,;BBOX1,missense_variant,p.Lys145Arg,ENST00000528583,;BBOX1,missense_variant,p.Lys145Arg,ENST00000525090,;BBOX1-AS1,intron_variant,,ENST00000530430,;BBOX1-AS1,intron_variant,,ENST00000525302,;BBOX1-AS1,intron_variant,,ENST00000526061,;BBOX1,intron_variant,,ENST00000527505,; G ENST00000263182 Transcript missense_variant 802/1886 434/1164 145/387 K/R aAg/aGg 1 1 BBOX1 HGNC HGNC:964 protein_coding YES CCDS7862.1 ENSP00000263182 O75936 UPI0000126A4C NM_003986.2 tolerated(0.99) 5/9 hmmpanther:PTHR10696:SF33,hmmpanther:PTHR10696,TIGRFAM_domain:TIGR02409,Gene3D:3.60.130.10,Pfam_domain:PF02668,Superfamily_domains:SSF51197 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 27093267 27093267 A G 1 0 0 0 0 1 0 0 0 1481 72 3 5 5 BBOX1 11 27093267 Missense_Mutation SNP A 11LU022_T 98379 27093267 107993355 584 1222 FSHB 0 . GRCh38 11 30233711 30233711 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.301C>A p.His101Asn p.H101N ENST00000417547 3/3 392 309 83 381 381 0 strelka-varscan-mutect FSHB,missense_variant,p.His101Asn,ENST00000417547,NM_001018080.1;FSHB,missense_variant,p.His101Asn,ENST00000254122,NM_000510.2;FSHB,missense_variant,p.His101Asn,ENST00000533718,; A ENST00000417547 Transcript missense_variant 340/1890 301/390 101/129 H/N Cac/Aac 1 1 FSHB HGNC HGNC:3964 protein_coding YES CCDS7868.1 ENSP00000416606 P01225 A0A0F7RQE8 UPI000003FF95 NM_001018080.1 deleterious(0.01) 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00007,PROSITE_patterns:PS00689,hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF17,SMART_domains:SM00068,Superfamily_domains:SSF57501 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 30233711 30233711 C A 1 0 0 0 0 1 0 0 0 5946 826 29 2 2 FSHB 11 30233711 Missense_Mutation SNP C 11LU022_T 3140444 30233711 104852911 585 1223 KIAA1549L 0 . GRCh38 11 33591404 33591404 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.3843C>A p.= p.S1281S ENST00000321505 11/20 75 52 23 108 108 0 strelka-varscan-mutect KIAA1549L,synonymous_variant,p.=,ENST00000321505,NM_012194.2;KIAA1549L,synonymous_variant,p.=,ENST00000526400,;KIAA1549L,intron_variant,,ENST00000265654,; A ENST00000321505 Transcript synonymous_variant 4023/11678 3843/5550 1281/1849 S tcC/tcA 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 11/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3,Pfam_domain:PF12877 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 33591404 33591404 C A 1 0 0 0 0 0 0 0 1 8121 581 21 2 2 KIAA1549L 11 33591404 Silent SNP C 11LU022_T 3357693 33591404 101495218 586 1224 LDLRAD3 0 . GRCh38 11 36227192 36227192 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.562G>T p.Ala188Ser p.A188S ENST00000315571 5/6 192 163 29 229 229 0 strelka-varscan-mutect LDLRAD3,missense_variant,p.Ala188Ser,ENST00000315571,NM_174902.3;LDLRAD3,missense_variant,p.Ala178Ser,ENST00000524419,;LDLRAD3,missense_variant,p.Ala139Ser,ENST00000528989,NM_001304263.1;LDLRAD3,non_coding_transcript_exon_variant,,ENST00000529759,;LDLRAD3,non_coding_transcript_exon_variant,,ENST00000534091,;LDLRAD3,intron_variant,,ENST00000532490,; T ENST00000315571 Transcript missense_variant 583/3798 562/1038 188/345 A/S Gcc/Tcc 1 1 LDLRAD3 HGNC HGNC:27046 protein_coding YES CCDS31462.1 ENSP00000318607 Q86YD5 UPI000003B0FB NM_174902.3 deleterious(0.03) 5/6 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 36227192 36227192 G T 1 0 0 0 0 1 0 0 0 8614 1203 42 2 2 LDLRAD3 11 36227192 Missense_Mutation SNP G 11LU022_T 2635788 36227192 98859430 587 1225 LRRC4C 0 . GRCh38 11 40115884 40115884 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.409A>G p.Thr137Ala p.T137A ENST00000278198 2/2 172 149 23 191 191 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Thr137Ala,ENST00000278198,;LRRC4C,missense_variant,p.Thr137Ala,ENST00000527150,;LRRC4C,missense_variant,p.Thr137Ala,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Thr137Ala,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Thr137Ala,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; C ENST00000278198 Transcript missense_variant 2373/4054 409/1923 137/640 T/A Act/Gct 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious(0.02) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Gene3D:3.80.10.10,Pfam_domain:PF13306,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 40115884 40115884 T C 1 0 0 0 0 1 0 0 0 8903 1638 57 5 5 LRRC4C 11 40115884 Missense_Mutation SNP T 11LU022_T 3888692 40115884 94970738 588 1226 OR4C6 0 . GRCh38 11 55665808 55665808 + Silent SNP G G T rs201210743 11LU022_T 11LU022_N G G c.642G>T p.= p.A214A ENST00000314259 1/1 285 240 45 275 275 0 strelka-varscan-mutect OR4C6,synonymous_variant,p.=,ENST00000314259,NM_001004704.1; T ENST00000314259 Transcript synonymous_variant 642/930 642/930 214/309 A gcG/gcT rs201210743 1 1 OR4C6 HGNC HGNC:14743 protein_coding YES CCDS31506.1 ENSP00000324769 Q8NH72 A0A126GVN0 UPI0000041868 NM_001004704.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF80,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs201210743 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 55665808 55665808 G T 1 0 0 0 0 0 0 0 1 11129 1132 40 1 1 OR4C6 11 55665808 Silent SNP G 11LU022_T 15549924 55665808 79420814 589 1227 OR5F1 0 . GRCh38 11 55994172 55994172 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.454G>T p.Gly152Trp p.G152W ENST00000278409 1/1 183 144 39 187 187 0 strelka-varscan-mutect OR5F1,missense_variant,p.Gly152Trp,ENST00000278409,NM_003697.1; A ENST00000278409 Transcript missense_variant 454/945 454/945 152/314 G/W Ggg/Tgg 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 deleterious(0) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1360255369 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 55994172 55994172 C A 1 0 0 0 0 1 0 0 0 11228 681 24 2 2 OR5F1 11 55994172 Missense_Mutation SNP C 11LU022_T 328364 55994172 79092450 590 1228 OR8I2 0 . GRCh38 11 56094082 56094082 + Missense_Mutation SNP T T A rs781609430 11LU022_T 11LU022_N T T c.775T>A p.Leu259Met p.L259M ENST00000302124 1/1 103 91 12 115 115 0 strelka-varscan-mutect OR8I2,missense_variant,p.Leu259Met,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; A ENST00000302124 Transcript missense_variant 775/933 775/933 259/310 L/M Ttg/Atg rs781609430 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs781609430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56094082 56094082 T A 1 0 0 0 0 1 0 0 0 11308 1838 64 4 4 OR8I2 11 56094082 Missense_Mutation SNP T 11LU022_T 99910 56094082 78992540 591 1229 OR8H2 0 . GRCh38 11 56105956 56105956 + Missense_Mutation SNP T T G rs763111162 11LU022_T 11LU022_N T T c.914T>G p.Met305Arg p.M305R ENST00000313503 1/1 42 35 7 50 50 0 strelka-varscan-mutect OR8H2,missense_variant,p.Met304Arg,ENST00000618136,;OR8H2,missense_variant,p.Met305Arg,ENST00000313503,NM_001005200.1; G ENST00000313503 Transcript missense_variant 914/939 914/939 305/312 M/R aTg/aGg rs763111162 1 1 OR8H2 HGNC HGNC:15308 protein_coding YES CCDS31518.1 ENSP00000323982 Q8N162 UPI0000041D0C NM_001005200.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs763111162 . 1 204 5 0 0 0 0 0 -17.47407 1 1 1 1 0 G 3 3 3 56105956 56105956 T G 1 0 0 0 0 1 0 0 0 11306 1464 51 5 5 OR8H2 11 56105956 Missense_Mutation SNP T 11LU022_T 11874 56105956 78980666 592 1230 OR8H3 0 . GRCh38 11 56123214 56123214 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.842T>A p.Val281Glu p.V281E ENST00000313472 1/1 124 103 21 142 142 0 strelka-varscan-mutect OR8H3,missense_variant,p.Val281Glu,ENST00000313472,NM_001005201.1; A ENST00000313472 Transcript missense_variant 842/939 842/939 281/312 V/E gTg/gAg 1 1 OR8H3 HGNC HGNC:15309 protein_coding YES CCDS31519.1 ENSP00000323928 Q8N146 UPI0000041D25 NM_001005201.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56123214 56123214 T A 1 0 0 0 0 1 0 0 0 11307 1696 59 4 4 OR8H3 11 56123214 Missense_Mutation SNP T 11LU022_T 17258 56123214 78963408 593 1231 OR5M10 0 . GRCh38 11 56577208 56577208 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.514C>A p.Leu172Ile p.L172I ENST00000526812 1/1 136 99 37 153 153 0 strelka-varscan-mutect OR5M10,missense_variant,p.Leu172Ile,ENST00000526812,NM_001004741.1; T ENST00000526812 Transcript missense_variant 514/948 514/948 172/315 L/I Ctt/Att 1 -1 OR5M10 HGNC HGNC:15290 protein_coding YES CCDS53630.1 ENSP00000436004 Q6IEU7 UPI0000041BEE NM_001004741.1 tolerated(0.08) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF98,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 56577208 56577208 G T 1 0 0 0 0 1 0 0 0 11242 1000 35 2 2 OR5M10 11 56577208 Missense_Mutation SNP G 11LU022_T 453994 56577208 78509414 594 1232 OR9G1 0 . GRCh38 11 56700516 56700516 + Silent SNP C C A 11LU022_T 11LU022_N C C c.129C>A p.= p.T43T ENST00000312153 1/1 520 487 33 500 500 0 varscan-mutect OR9G1,synonymous_variant,p.=,ENST00000312153,NM_001005213.1; A ENST00000312153 Transcript synonymous_variant 129/918 129/918 43/305 T acC/acA COSM344021 1 1 OR9G1 HGNC HGNC:15319 protein_coding YES CCDS31536.1 ENSP00000309012 Q8NH87 UPI0000061E7E NM_001005213.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF158,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 56700516 56700516 C A 1 0 0 0 0 0 0 0 1 11317 610 22 2 2 OR9G1 11 56700516 Silent SNP C 11LU022_T 123308 56700516 78386106 595 1233 SMTNL1 0 . GRCh38 11 57546585 57546585 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1273T>A p.Phe425Ile p.F425I ENST00000527972 6/7 277 238 39 302 302 0 strelka-varscan-mutect SMTNL1,missense_variant,p.Phe425Ile,ENST00000527972,NM_001105565.2;SMTNL1,missense_variant,p.Phe388Ile,ENST00000399154,; A ENST00000527972 Transcript missense_variant 1275/1649 1273/1485 425/494 F/I Ttt/Att 1 1 SMTNL1 HGNC HGNC:32394 protein_coding YES ENSP00000432651 E9PPJ3 UPI0000D6C18B NM_001105565.2 deleterious(0) 6/7 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF215,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 57546585 57546585 T A 1 0 0 0 0 1 0 0 0 15136 1609 56 4 4 SMTNL1 11 57546585 Missense_Mutation SNP T 11LU022_T 846069 57546585 77540037 596 1234 SMTNL1 0 . GRCh38 11 57546597 57546597 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1285G>C p.Glu429Gln p.E429Q ENST00000527972 6/7 251 213 38 285 285 0 strelka-varscan-mutect SMTNL1,missense_variant,p.Glu429Gln,ENST00000527972,NM_001105565.2;SMTNL1,missense_variant,p.Glu392Gln,ENST00000399154,; C ENST00000527972 Transcript missense_variant 1287/1649 1285/1485 429/494 E/Q Gag/Cag 1 1 SMTNL1 HGNC HGNC:32394 protein_coding YES ENSP00000432651 E9PPJ3 UPI0000D6C18B NM_001105565.2 tolerated(0.25) 6/7 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF215,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 57546597 57546597 G C 1 0 0 0 0 1 0 0 0 15136 943 33 4 4 SMTNL1 11 57546597 Missense_Mutation SNP G 11LU022_T 12 57546597 77540025 597 1235 MS4A6A 0 . GRCh38 11 60175497 60175497 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.538G>T p.Asp180Tyr p.D180Y ENST00000426738 6/7 219 183 36 276 274 2 strelka-varscan-mutect MS4A6A,missense_variant,p.Asp152Tyr,ENST00000528851,NM_022349.3;MS4A6A,missense_variant,p.Asp180Tyr,ENST00000426738,NM_001247999.1;MS4A6A,missense_variant,p.Asp152Tyr,ENST00000530839,NM_152852.2;MS4A6A,missense_variant,p.Asp180Tyr,ENST00000412309,;MS4A6A,missense_variant,p.Asp180Tyr,ENST00000529054,;MS4A6A,intron_variant,,ENST00000420732,NM_152851.2;MS4A6A,intron_variant,,ENST00000533023,;MS4A6A,intron_variant,,ENST00000533989,;MS4A6A,downstream_gene_variant,,ENST00000532169,;MS4A6A,downstream_gene_variant,,ENST00000534596,;MS4A6A,downstream_gene_variant,,ENST00000529906,;MS4A6A,3_prime_UTR_variant,,ENST00000527254,;MS4A6A,non_coding_transcript_exon_variant,,ENST00000531914,;MS4A6A,downstream_gene_variant,,ENST00000526677,;MS4A6A,downstream_gene_variant,,ENST00000525549,;MS4A6A,downstream_gene_variant,,ENST00000530179,; A ENST00000426738 Transcript missense_variant 1011/1736 538/762 180/253 D/Y Gac/Tac 1 -1 MS4A6A HGNC HGNC:13375 protein_coding YES CCDS58134.1 ENSP00000392770 Q9H2W1 UPI0001F77AB4 NM_001247999.1 deleterious(0) 6/7 hmmpanther:PTHR23320:SF46,hmmpanther:PTHR23320,Pfam_domain:PF04103 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 60175497 60175497 C A 1 0 0 0 0 1 0 0 0 9843 855 30 2 2 MS4A6A 11 60175497 Missense_Mutation SNP C 11LU022_T 2628900 60175497 74911125 598 1236 MS4A7 0 . GRCh38 11 60383235 60383235 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.94C>A p.Gln32Lys p.Q32K ENST00000300184 2/7 126 115 11 119 119 0 strelka-varscan-mutect MS4A7,missense_variant,p.Gln32Lys,ENST00000358246,NM_206940.1,NM_206938.1;MS4A7,missense_variant,p.Gln32Lys,ENST00000300184,NM_021201.4,NM_206939.1;MS4A7,missense_variant,p.Gln32Lys,ENST00000534016,;MS4A7,missense_variant,p.Gln32Lys,ENST00000530234,;MS4A7,missense_variant,p.Gln32Lys,ENST00000530614,;MS4A7,missense_variant,p.Gln32Lys,ENST00000530027,;MS4A7,missense_variant,p.Gln3Lys,ENST00000528215,;MS4A14,intron_variant,,ENST00000531787,;MS4A7,non_coding_transcript_exon_variant,,ENST00000528808,;MS4A7,non_coding_transcript_exon_variant,,ENST00000528500,;MS4A6E,intron_variant,,ENST00000532756,;MS4A7,upstream_gene_variant,,ENST00000534310,; A ENST00000300184 Transcript missense_variant 290/1869 94/723 32/240 Q/K Caa/Aaa 1 1 MS4A7 HGNC HGNC:13378 protein_coding YES CCDS7985.1 ENSP00000300184 Q9GZW8 A0A024R556 UPI0000043671 NM_021201.4,NM_206939.1 tolerated(0.14) 2/7 hmmpanther:PTHR23320:SF8,hmmpanther:PTHR23320 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 60383235 60383235 C A 1 0 0 0 0 1 0 0 0 9845 595 21 2 2 MS4A7 11 60383235 Missense_Mutation SNP C 11LU022_T 207738 60383235 74703387 599 1237 TMEM109 0 . GRCh38 11 60922123 60922123 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.690G>T p.Gln230His p.Q230H ENST00000227525 4/4 115 86 29 198 197 1 strelka-varscan-mutect TMEM109,missense_variant,p.Gln230His,ENST00000227525,NM_024092.2;TMEM109,missense_variant,p.Gln230His,ENST00000536171,;TMEM132A,upstream_gene_variant,,ENST00000005286,NM_017870.3;TMEM132A,upstream_gene_variant,,ENST00000453848,NM_178031.2;TMEM132A,upstream_gene_variant,,ENST00000544065,;RP11-881M11.4,intron_variant,,ENST00000543907,;TMEM132A,upstream_gene_variant,,ENST00000543732,;TMEM109,upstream_gene_variant,,ENST00000540280,;TMEM132A,upstream_gene_variant,,ENST00000540276,;TMEM132A,upstream_gene_variant,,ENST00000537110,;TMEM132A,upstream_gene_variant,,ENST00000537065,;TMEM132A,upstream_gene_variant,,ENST00000544098,;TMEM132A,upstream_gene_variant,,ENST00000534983,; T ENST00000227525 Transcript missense_variant 1093/2413 690/732 230/243 Q/H caG/caT COSM5089759,COSM5517423 1 1 TMEM109 HGNC HGNC:28771 protein_coding YES CCDS7996.1 ENSP00000227525 Q9BVC6 UPI0000072CF3 NM_024092.2 deleterious(0) 4/4 hmmpanther:PTHR14550,hmmpanther:PTHR14550:SF2,Pfam_domain:PF14965,PD178468 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 60922123 60922123 G T 1 0 0 0 0 1 0 0 0 16469 933 33 2 2 TMEM109 11 60922123 Missense_Mutation SNP G 11LU022_T 538888 60922123 74164499 600 1238 CD6 0 . GRCh38 11 61017895 61017895 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1719C>A p.Cys573Ter p.C573* ENST00000313421 11/13 499 437 62 564 564 0 strelka-varscan-mutect CD6,stop_gained,p.Cys573Ter,ENST00000313421,NM_006725.4;CD6,stop_gained,p.Cys541Ter,ENST00000352009,NM_001254750.1;CD6,stop_gained,p.Cys532Ter,ENST00000452451,NM_001254751.1;CD6,downstream_gene_variant,,ENST00000433107,;CD6,downstream_gene_variant,,ENST00000542157,;CD6,downstream_gene_variant,,ENST00000538611,;CD6,downstream_gene_variant,,ENST00000545105,;CD6,3_prime_UTR_variant,,ENST00000344931,;CD6,non_coding_transcript_exon_variant,,ENST00000505761,;CD6,downstream_gene_variant,,ENST00000419282,; A ENST00000313421 Transcript stop_gained 1905/3252 1719/2007 573/668 C/* tgC/tgA 1 1 CD6 HGNC HGNC:1691 protein_coding YES CCDS7999.1 ENSP00000323280 P30203 UPI000013F532 NM_006725.4 11/13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 61017895 61017895 C A 1 0 0 0 0 0 1 0 0 2732 718 25 2 2 CD6 11 61017895 Nonsense_Mutation SNP C 11LU022_T 95772 61017895 74068727 601 1239 STX5 0 . GRCh38 11 62825473 62825473 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.490A>T p.Ser164Cys p.S164C ENST00000294179 6/11 209 173 36 254 254 0 strelka-varscan-mutect STX5,missense_variant,p.Ser164Cys,ENST00000294179,NM_003164.4;STX5,missense_variant,p.Ser164Cys,ENST00000377897,NM_001244666.1;STX5,missense_variant,p.Ser110Cys,ENST00000394690,;STX5,missense_variant,p.Ser19Cys,ENST00000431400,;STX5,missense_variant,p.Ser164Cys,ENST00000491231,;STX5,3_prime_UTR_variant,,ENST00000492066,;STX5,downstream_gene_variant,,ENST00000488303,;STX5,downstream_gene_variant,,ENST00000486437,; A ENST00000294179 Transcript missense_variant 644/1794 490/1068 164/355 S/C Agt/Tgt 1 -1 STX5 HGNC HGNC:11440 protein_coding YES CCDS8038.2 ENSP00000294179 Q13190 UPI00001FA9B0 NM_003164.4 deleterious(0.02) 6/11 hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF3,Gene3D:1.20.58.70,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 62825473 62825473 T A 1 0 0 0 0 1 0 0 0 15732 1551 54 4 4 STX5 11 62825473 Missense_Mutation SNP T 11LU022_T 1807578 62825473 72261149 602 1240 SLC22A6 0 . GRCh38 11 62983581 62983581 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.584C>A p.Ser195Ter p.S195* ENST00000377871 3/10 245 212 33 308 308 0 strelka-varscan-mutect SLC22A6,stop_gained,p.Ser195Ter,ENST00000377871,NM_004790.4;SLC22A6,stop_gained,p.Ser195Ter,ENST00000360421,NM_153276.2;SLC22A6,stop_gained,p.Ser195Ter,ENST00000421062,NM_153278.2;SLC22A6,stop_gained,p.Ser195Ter,ENST00000458333,NM_153277.2;SLC22A6,non_coding_transcript_exon_variant,,ENST00000537349,;SLC22A6,synonymous_variant,p.=,ENST00000540654,; T ENST00000377871 Transcript stop_gained 851/2151 584/1692 195/563 S/* tCg/tAg 1 -1 SLC22A6 HGNC HGNC:10970 protein_coding YES CCDS31591.1 ENSP00000367102 Q4U2R8 UPI00000747EC NM_004790.4 3/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF231,Gene3D:1.20.1250.20,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473 HIGH 1 SNV 1 1 PASS rs1249164896 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 62983581 62983581 G T 1 0 0 0 0 0 1 0 0 14724 1059 37 1 1 SLC22A6 11 62983581 Nonsense_Mutation SNP G 11LU022_T 158108 62983581 72103041 603 1241 STIP1 0 . GRCh38 11 64203153 64203153 + Silent SNP G G T rs2070232 11LU022_T 11LU022_N G G c.1452G>T p.= p.A484A ENST00000358794 12/14 250 223 27 331 331 0 strelka-varscan-mutect STIP1,synonymous_variant,p.=,ENST00000358794,NM_001282652.1;STIP1,synonymous_variant,p.=,ENST00000305218,NM_006819.2;STIP1,synonymous_variant,p.=,ENST00000538945,NM_001282653.1;STIP1,synonymous_variant,p.=,ENST00000540887,;FERMT3,upstream_gene_variant,,ENST00000279227,NM_178443.2;FERMT3,upstream_gene_variant,,ENST00000345728,NM_031471.5;FERMT3,upstream_gene_variant,,ENST00000544997,;FERMT3,upstream_gene_variant,,ENST00000541252,;STIP1,downstream_gene_variant,,ENST00000537479,;STIP1,intron_variant,,ENST00000536973,;STIP1,downstream_gene_variant,,ENST00000538497,;STIP1,downstream_gene_variant,,ENST00000355603,; T ENST00000358794 Transcript synonymous_variant 2005/2743 1452/1773 484/590 A gcG/gcT rs2070232 1 1 STIP1 HGNC HGNC:11387 protein_coding YES CCDS60827.1 ENSP00000351646 P31948 UPI00001FAA4C NM_001282652.1 12/14 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR22904:SF371,hmmpanther:PTHR22904,Gene3D:1.25.40.10,Pfam_domain:PF13181,SMART_domains:SM00028,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS rs2070232 . 0 184 0 0 0 0 0 26 -5.092205 0 0 1 0 0 T 2 4 3 64203153 64203153 G T 1 0 0 0 0 0 0 0 1 15662 1074 38 1 1 STIP1 11 64203153 Silent SNP G 11LU022_T 1219572 64203153 70883469 604 1242 GPR137 0 . GRCh38 11 64284685 64284685 + Silent SNP C C A rs558907072 11LU022_T 11LU022_N C C c.81C>A p.= p.P27P ENST00000411458 2/9 131 92 39 167 167 0 strelka-varscan-mutect GPR137,synonymous_variant,p.=,ENST00000411458,NM_001170726.1;GPR137,intron_variant,,ENST00000546139,;GPR137,intron_variant,,ENST00000538244,;GPR137,upstream_gene_variant,,ENST00000539851,NM_001177358.1;GPR137,upstream_gene_variant,,ENST00000438980,NM_001170880.1;GPR137,upstream_gene_variant,,ENST00000313074,NM_020155.3;GPR137,upstream_gene_variant,,ENST00000377702,NM_001170881.1;BAD,upstream_gene_variant,,ENST00000394532,NM_004322.3;GPR137,upstream_gene_variant,,ENST00000539833,;BAD,upstream_gene_variant,,ENST00000309032,NM_032989.2;GPR137,upstream_gene_variant,,ENST00000543383,;GPR137,upstream_gene_variant,,ENST00000536667,;BAD,upstream_gene_variant,,ENST00000394531,;GPR137,upstream_gene_variant,,ENST00000538032,;GPR137,upstream_gene_variant,,ENST00000535675,;GPR137,upstream_gene_variant,,ENST00000540370,;BAD,upstream_gene_variant,,ENST00000544785,;GPR137,upstream_gene_variant,,ENST00000541952,;GPR137,upstream_gene_variant,,ENST00000542190,;GPR137,upstream_gene_variant,,ENST00000536282,;BAD,non_coding_transcript_exon_variant,,ENST00000544271,;GPR137,upstream_gene_variant,,ENST00000536017,;GPR137,upstream_gene_variant,,ENST00000546201,;GPR137,upstream_gene_variant,,ENST00000545366,; A ENST00000411458 Transcript synonymous_variant 109/1495 81/1428 27/475 P ccC/ccA rs558907072 1 1 GPR137 HGNC HGNC:24300 protein_coding YES CCDS53655.1 ENSP00000411827 Q96N19 UPI00017A7FAD NM_001170726.1 2/9 LOW SNV 2 1 PASS rs558907072 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 64284685 64284685 C A 1 0 0 0 0 0 0 0 1 6531 637 22 2 2 GPR137 11 64284685 Silent SNP C 11LU022_T 81532 64284685 70801937 605 1243 MAP4K2 0 . GRCh38 11 64801125 64801125 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.516T>C p.= p.I172I ENST00000294066 8/32 207 156 51 305 305 0 strelka-varscan-mutect MAP4K2,synonymous_variant,p.=,ENST00000294066,NM_004579.3;MAP4K2,synonymous_variant,p.=,ENST00000377350,NM_001307990.1;MAP4K2,synonymous_variant,p.=,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000337652,NM_130803.2;MEN1,downstream_gene_variant,,ENST00000394374,NM_000244.3,NM_130801.2,NM_130800.2,NM_130802.2;MEN1,downstream_gene_variant,,ENST00000377326,;MEN1,downstream_gene_variant,,ENST00000315422,;MEN1,downstream_gene_variant,,ENST00000394376,NM_130804.2;MEN1,downstream_gene_variant,,ENST00000377316,;MEN1,downstream_gene_variant,,ENST00000312049,NM_130799.2;MEN1,downstream_gene_variant,,ENST00000377321,;MEN1,downstream_gene_variant,,ENST00000377313,;MAP4K2,non_coding_transcript_exon_variant,,ENST00000468062,;MAP4K2,non_coding_transcript_exon_variant,,ENST00000482314,;MEN1,downstream_gene_variant,,ENST00000487019,;MAP4K2,3_prime_UTR_variant,,ENST00000435926,;MAP4K2,3_prime_UTR_variant,,ENST00000433890,;MAP4K2,non_coding_transcript_exon_variant,,ENST00000493428,;MAP4K2,upstream_gene_variant,,ENST00000470088,;MAP4K2,upstream_gene_variant,,ENST00000489952,;MEN1,downstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000424945,;MAP4K2,upstream_gene_variant,,ENST00000467689,;MAP4K2,downstream_gene_variant,,ENST00000444560,; G ENST00000294066 Transcript synonymous_variant 608/7178 516/2463 172/820 I atT/atC 1 -1 MAP4K2 HGNC HGNC:6864 protein_coding YES CCDS8082.1 ENSP00000294066 Q12851 A0A024R567 UPI000013E13D NM_004579.3 8/32 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF392,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF038172,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs1242795941 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 64801125 64801125 A G 1 0 0 0 0 0 0 0 1 9184 126 5 5 5 MAP4K2 11 64801125 Silent SNP A 11LU022_T 516440 64801125 70285497 606 1244 CDC42BPG 0 . GRCh38 11 64829608 64829608 + Missense_Mutation SNP C C A rs571011118 11LU022_T 11LU022_N C C c.3830G>T p.Gly1277Val p.G1277V ENST00000342711 30/37 460 402 58 594 594 0 strelka-varscan-mutect CDC42BPG,missense_variant,p.Gly1277Val,ENST00000342711,NM_017525.2;CDC42BPG,downstream_gene_variant,,ENST00000491280,;CDC42BPG,downstream_gene_variant,,ENST00000468512,;CDC42BPG,downstream_gene_variant,,ENST00000480767,; A ENST00000342711 Transcript missense_variant 3830/5742 3830/4656 1277/1551 G/V gGt/gTt rs571011118 1 -1 CDC42BPG HGNC HGNC:29829 protein_coding YES CCDS31601.1 ENSP00000345133 Q6DT37 UPI000047C9E2 NM_017525.2 tolerated(0.1) 30/37 Low_complexity_(Seg):seg,PROSITE_profiles:PS50219,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS rs571011118 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 64829608 64829608 C A 1 0 0 0 0 1 0 0 0 2777 507 18 2 2 CDC42BPG 11 64829608 Missense_Mutation SNP C 11LU022_T 28483 64829608 70257014 607 1245 5 2 CDC42BPG 0 . GRCh38 11 64829615 64829615 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3823G>T p.Gly1275Cys p.G1275C ENST00000342711 30/37 491 429 62 621 620 1 strelka-varscan-mutect CDC42BPG,missense_variant,p.Gly1275Cys,ENST00000342711,NM_017525.2;CDC42BPG,downstream_gene_variant,,ENST00000491280,;CDC42BPG,downstream_gene_variant,,ENST00000468512,;CDC42BPG,downstream_gene_variant,,ENST00000480767,; A ENST00000342711 Transcript missense_variant 3823/5742 3823/4656 1275/1551 G/C Ggc/Tgc 1 -1 CDC42BPG HGNC HGNC:29829 protein_coding YES CCDS31601.1 ENSP00000345133 Q6DT37 UPI000047C9E2 NM_017525.2 tolerated(0.11) 30/37 Low_complexity_(Seg):seg,PROSITE_profiles:PS50219,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 64829615 64829615 C A 1 0 0 0 0 1 0 0 0 2777 623 22 2 2 CDC42BPG 11 64829615 Missense_Mutation SNP C 11LU022_T 7 64829615 70257007 608 1246 5 2 TSGA10IP 0 . GRCh38 11 65959301 65959301 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1534C>A p.Pro512Thr p.P512T ENST00000532620 7/8 123 110 13 162 162 0 strelka-varscan-mutect TSGA10IP,missense_variant,p.Pro512Thr,ENST00000532620,NM_152762.2;SART1,upstream_gene_variant,,ENST00000312397,NM_005146.4;SART1,upstream_gene_variant,,ENST00000528573,;TSGA10IP,3_prime_UTR_variant,,ENST00000608857,;TSGA10IP,3_prime_UTR_variant,,ENST00000534740,;SART1,upstream_gene_variant,,ENST00000529532,;SART1,upstream_gene_variant,,ENST00000532333,;SART1,upstream_gene_variant,,ENST00000530251,; A ENST00000532620 Transcript missense_variant 1765/1925 1534/1671 512/556 P/T Ccc/Acc 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 tolerated(0.1) 7/8 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 65959301 65959301 C A 1 0 0 0 0 1 0 0 0 17124 623 22 2 2 TSGA10IP 11 65959301 Missense_Mutation SNP C 11LU022_T 1129686 65959301 69127321 609 1247 CATSPER1 0 . GRCh38 11 66026228 66026228 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.152C>T p.Pro51Leu p.P51L ENST00000312106 1/12 106 88 18 175 175 0 strelka-varscan-mutect CATSPER1,missense_variant,p.Pro51Leu,ENST00000312106,NM_053054.3; A ENST00000312106 Transcript missense_variant 290/2619 152/2343 51/780 P/L cCc/cTc 1 -1 CATSPER1 HGNC HGNC:17116 protein_coding YES CCDS8127.1 ENSP00000309052 Q8NEC5 UPI000045651C NM_053054.3 tolerated(0.28) 1/12 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 66026228 66026228 G A 1 0 0 0 0 1 0 0 0 2387 1232 43 3 3 CATSPER1 11 66026228 Missense_Mutation SNP G 11LU022_T 66927 66026228 69060394 610 1248 IGHMBP2 0 . GRCh38 11 68911464 68911464 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.572G>T p.Cys191Phe p.C191F ENST00000255078 5/15 341 263 78 452 451 1 strelka-varscan-mutect IGHMBP2,missense_variant,p.Cys191Phe,ENST00000255078,NM_002180.2;IGHMBP2,synonymous_variant,p.=,ENST00000539224,;IGHMBP2,3_prime_UTR_variant,,ENST00000544541,;IGHMBP2,downstream_gene_variant,,ENST00000545146,; T ENST00000255078 Transcript missense_variant 683/3961 572/2982 191/993 C/F tGc/tTc 1 1 IGHMBP2 HGNC HGNC:5542 protein_coding YES CCDS8187.1 ENSP00000255078 P38935 UPI000013CE82 NM_002180.2 deleterious(0) 5/15 Gene3D:3.40.50.300,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF375,SMART_domains:SM00487,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00376 MODERATE 1 SNV 1 1 PASS rs1242233592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 68911464 68911464 G T 1 0 0 0 0 1 0 0 0 7498 1319 46 2 2 IGHMBP2 11 68911464 Missense_Mutation SNP G 11LU022_T 2885236 68911464 66175158 611 1249 NUMA1 0 . GRCh38 11 72004639 72004639 + Splice_Site DEL C C - novel 11LU022_T 11LU022_N C C c.6006+1delG p.X2002_splice ENST00000393695 98 71 27 104 104 0 sindel-varindel-pindel NUMA1,splice_donor_variant,,ENST00000393695,NM_006185.3;NUMA1,splice_donor_variant,,ENST00000358965,NM_001286561.1;NUMA1,splice_donor_variant,,ENST00000620566,;NUMA1,splice_donor_variant,,ENST00000616538,;NUMA1,splice_donor_variant,,ENST00000613205,;NUMA1,splice_donor_variant,,ENST00000351960,;NUMA1,splice_donor_variant,,ENST00000541584,;IL18BP,downstream_gene_variant,,ENST00000497194,NM_005699.3;IL18BP,downstream_gene_variant,,ENST00000404792,NM_173042.2;IL18BP,downstream_gene_variant,,ENST00000393703,NM_001039660.1;IL18BP,downstream_gene_variant,,ENST00000337131,;IL18BP,downstream_gene_variant,,ENST00000620017,NM_173044.2;IL18BP,downstream_gene_variant,,ENST00000393705,NM_001039659.1;IL18BP,downstream_gene_variant,,ENST00000260049,NM_001145057.1;IL18BP,downstream_gene_variant,,ENST00000393707,NM_001145055.1;IL18BP,downstream_gene_variant,,ENST00000531053,;NUMA1,downstream_gene_variant,,ENST00000541262,;IL18BP,downstream_gene_variant,,ENST00000525932,;IL18BP,downstream_gene_variant,,ENST00000531777,;IL18BP,downstream_gene_variant,,ENST00000414358,;NUMA1,splice_donor_variant,,ENST00000540626,;IL18BP,intron_variant,,ENST00000343898,;NUMA1,downstream_gene_variant,,ENST00000545721,;IL18BP,downstream_gene_variant,,ENST00000534583,;NUMA1,downstream_gene_variant,,ENST00000546036,; - ENST00000393695 Transcript splice_donor_variant -/7343 6006/6348 2002/2115 1 -1 NUMA1 HGNC HGNC:8059 protein_coding YES CCDS31633.1 ENSP00000377298 Q14980 UPI000013DB8B NM_006185.3 24/26 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 3 72004639 72004639 C - 1 0 1 0 1 0 0 1 0 10815 521 18 0 0 NUMA1 11 72004639 Splice_Site DEL C 11LU022_T 3093175 72004639 63081983 612 1250 USP35 0 . GRCh38 11 78210632 78210632 + Missense_Mutation SNP G G T rs771087419 11LU022_T 11LU022_N G G c.2777G>T p.Arg926Leu p.R926L ENST00000529308 10/11 70 59 11 93 93 0 strelka-varscan-mutect USP35,missense_variant,p.Arg926Leu,ENST00000529308,NM_020798.2;USP35,missense_variant,p.Arg657Leu,ENST00000526425,;USP35,missense_variant,p.Arg494Leu,ENST00000530267,;GAB2,downstream_gene_variant,,ENST00000361507,NM_080491.2;GAB2,downstream_gene_variant,,ENST00000340149,NM_012296.3;USP35,downstream_gene_variant,,ENST00000528910,;USP35,non_coding_transcript_exon_variant,,ENST00000530535,;USP35,3_prime_UTR_variant,,ENST00000530546,;USP35,downstream_gene_variant,,ENST00000530521,; T ENST00000529308 Transcript missense_variant 3038/4216 2777/3057 926/1018 R/L cGg/cTg rs771087419,COSM4979159,COSM4979160 1 1 USP35 HGNC HGNC:20061 protein_coding YES CCDS41693.1 ENSP00000431876 Q9P2H5 UPI0000456553 NM_020798.2 deleterious(0.04) 10/11 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF500,hmmpanther:PTHR24006,Superfamily_domains:SSF54001 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs771087419 . 0 203 6 0 0 0 0 0 -19.99998 0.9999999 1 1 1 0 T 3 4 3 78210632 78210632 G T 1 0 0 0 0 1 0 0 0 17608 1116 39 1 1 USP35 11 78210632 Missense_Mutation SNP G 11LU022_T 6205993 78210632 56875990 613 1251 TENM4 0 . GRCh38 11 78891238 78891238 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.848G>T p.Gly283Val p.G283V ENST00000278550 8/34 107 71 36 128 128 0 strelka-varscan-mutect TENM4,missense_variant,p.Gly283Val,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Gly128Val,ENST00000533074,;TENM4,splice_region_variant,,ENST00000533013,; A ENST00000278550 Transcript missense_variant,splice_region_variant 1311/14000 848/8310 283/2769 G/V gGg/gTg 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 tolerated_low_confidence(0.09) 8/34 Pfam_domain:PF06484,PROSITE_profiles:PS51361 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 78891238 78891238 C A 1 0 0 0 0 1 0 0 0 16174 637 22 2 2 TENM4 11 78891238 Missense_Mutation SNP C 11LU022_T 680606 78891238 56195384 614 1252 PRSS23 0 . GRCh38 11 86808302 86808302 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.659A>T p.Gln220Leu p.Q220L ENST00000280258 2/2 182 164 18 198 198 0 strelka-varscan-mutect PRSS23,missense_variant,p.Gln220Leu,ENST00000280258,NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1;PRSS23,intron_variant,,ENST00000533902,;PRSS23,downstream_gene_variant,,ENST00000527521,;PRSS23,intron_variant,,ENST00000531475,;PRSS23,intron_variant,,ENST00000533880,;PRSS23,intron_variant,,ENST00000532234,; T ENST00000280258 Transcript missense_variant 1084/4015 659/1152 220/383 Q/L cAg/cTg 1 1 PRSS23 HGNC HGNC:14370 protein_coding YES CCDS8278.1 ENSP00000280258 O95084 UPI0000048EBC NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1 deleterious(0.01) 2/2 Gene3D:2.40.10.10,Pfam_domain:PF00089,hmmpanther:PTHR15462,hmmpanther:PTHR15462:SF10,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 86808302 86808302 A T 1 0 0 0 0 1 0 0 0 12767 188 7 4 4 PRSS23 11 86808302 Missense_Mutation SNP A 11LU022_T 7917064 86808302 48278320 615 1253 GRM5 0 . GRCh38 11 88850136 88850136 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.681G>A p.= p.G227G ENST00000305447 2/9 139 94 45 155 155 0 strelka-varscan-mutect GRM5,synonymous_variant,p.=,ENST00000455756,NM_000842.4;GRM5,synonymous_variant,p.=,ENST00000305447,NM_001143831.2;GRM5,synonymous_variant,p.=,ENST00000305432,; T ENST00000305447 Transcript synonymous_variant 831/4571 681/3639 227/1212 G ggG/ggA 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 2/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 88850136 88850136 C T 1 0 0 0 0 0 0 0 1 6682 842 30 3 3 GRM5 11 88850136 Silent SNP C 11LU022_T 2041834 88850136 46236486 616 1254 FAT3 0 . GRCh38 11 92836598 92836598 + Missense_Mutation SNP C C A rs140093319 11LU022_T 11LU022_N C C c.9669C>A p.Asn3223Lys p.N3223K ENST00000525166 15/27 105 57 48 98 98 0 strelka-varscan-mutect FAT3,missense_variant,p.Asn3373Lys,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Asn3223Lys,ENST00000525166,; A ENST00000525166 Transcript missense_variant 9691/18699 9669/13320 3223/4439 N/K aaC/aaA rs140093319 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 15/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs140093319 . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 92836598 92836598 C A 1 0 0 0 0 1 0 0 0 5551 535 19 1 1 FAT3 11 92836598 Missense_Mutation SNP C 11LU022_T 3986462 92836598 42250024 617 1255 MTNR1B 0 . GRCh38 11 92982056 92982056 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.833C>A p.Pro278His p.P278H ENST00000257068 2/2 299 182 117 310 310 0 strelka-varscan-mutect MTNR1B,missense_variant,p.Pro278His,ENST00000257068,NM_005959.3;MTNR1B,intron_variant,,ENST00000528076,;MTNR1B,3_prime_UTR_variant,,ENST00000532482,; A ENST00000257068 Transcript missense_variant 839/1565 833/1089 278/362 P/H cCc/cAc COSM545530 1 1 MTNR1B HGNC HGNC:7464 protein_coding YES CCDS8290.1 ENSP00000257068 P49286 UPI0000050408 NM_005959.3 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF262,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00857,Prints_domain:PR01149 1 MODERATE 1 SNV 1 1 1 PASS rs1349971000 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 92982056 92982056 C A 1 0 0 0 0 1 0 0 0 9939 623 22 2 2 MTNR1B 11 92982056 Missense_Mutation SNP C 11LU022_T 145458 92982056 42104566 618 1256 MMP3 0 . GRCh38 11 102842733 102842733 + Missense_Mutation SNP C C A rs547601378 11LU022_T 11LU022_N C C c.289G>T p.Val97Phe p.V97F ENST00000299855 2/10 251 164 87 233 232 1 strelka-mutect MMP3,missense_variant,p.Val97Phe,ENST00000299855,NM_002422.3;MMP3,upstream_gene_variant,,ENST00000434103,;MMP3,3_prime_UTR_variant,,ENST00000524478,; A ENST00000299855 Transcript missense_variant 546/2016 289/1434 97/477 V/F Gtt/Ttt rs547601378 1 -1 MMP3 HGNC HGNC:7173 protein_coding YES CCDS8323.1 ENSP00000299855 P08254 UPI00000422BF NM_002422.3 deleterious(0.01) 2/10 hmmpanther:PTHR10201:SF164,hmmpanther:PTHR10201,PROSITE_patterns:PS00546,PIRSF_domain:PIRSF001191,Gene3D:3.40.390.10,Superfamily_domains:SSF47090,Prints_domain:PR00138 MODERATE 1 SNV 1 1 PASS rs547601378 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 102842733 102842733 C A 1 0 0 0 0 1 0 0 0 9629 478 17 2 2 MMP3 11 102842733 Missense_Mutation SNP C 11LU022_T 9860677 102842733 32243889 619 1257 GRIA4 0 . GRCh38 11 105972018 105972018 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2399C>A p.Ser800Tyr p.S800Y ENST00000282499 15/17 142 92 50 135 134 1 strelka-varscan-mutect GRIA4,missense_variant,p.Ser800Tyr,ENST00000282499,NM_000829.3;GRIA4,missense_variant,p.Ser800Tyr,ENST00000530497,;GRIA4,intron_variant,,ENST00000393127,NM_001077243.2;GRIA4,intron_variant,,ENST00000525187,;RNU6-277P,downstream_gene_variant,,ENST00000516272,;GRIA4,intron_variant,,ENST00000533094,;GRIA4,3_prime_UTR_variant,,ENST00000525942,; A ENST00000282499 Transcript missense_variant 2845/5508 2399/2709 800/902 S/Y tCt/tAt 1 1 GRIA4 HGNC HGNC:4574 protein_coding YES CCDS8333.1 ENSP00000282499 P48058 UPI000013DCE6 NM_000829.3 deleterious(0.03) 15/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF100,Pfam_domain:PF00060 MODERATE 1 SNV 5 1 PASS rs1490238236 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 105972018 105972018 C A 1 0 0 0 0 1 0 0 0 6650 913 32 2 2 GRIA4 11 105972018 Missense_Mutation SNP C 11LU022_T 3129285 105972018 29114604 620 1258 NPAT 0 . GRCh38 11 108173234 108173234 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1750G>T p.Val584Leu p.V584L ENST00000278612 13/18 136 90 46 240 240 0 strelka-varscan-mutect NPAT,missense_variant,p.Val584Leu,ENST00000278612,NM_001321307.1,NM_002519.2;NPAT,non_coding_transcript_exon_variant,,ENST00000610253,;NPAT,upstream_gene_variant,,ENST00000530859,; A ENST00000278612 Transcript missense_variant 1856/6117 1750/4284 584/1427 V/L Gtg/Ttg 1 -1 NPAT HGNC HGNC:7896 protein_coding YES CCDS41710.1 ENSP00000278612 Q14207 UPI00001FA306 NM_001321307.1,NM_002519.2 tolerated(0.3) 13/18 hmmpanther:PTHR15087,hmmpanther:PTHR15087:SF16 MODERATE 1 SNV 1 1 PASS rs899972140 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 108173234 108173234 C A 1 0 0 0 0 1 0 0 0 10614 478 17 2 2 NPAT 11 108173234 Missense_Mutation SNP C 11LU022_T 2201216 108173234 26913388 621 1259 C11orf87 0 . GRCh38 11 109424031 109424031 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.398G>T p.Arg133Met p.R133M ENST00000327419 2/2 189 141 48 245 244 1 strelka-varscan-mutect C11orf87,missense_variant,p.Arg133Met,ENST00000327419,NM_207645.3;RP11-708B6.2,intron_variant,,ENST00000532929,;RP11-708B6.2,intron_variant,,ENST00000532992,; T ENST00000327419 Transcript missense_variant 801/5884 398/594 133/197 R/M aGg/aTg COSM1676430 1 1 C11orf87 HGNC HGNC:33788 protein_coding YES CCDS31672.1 ENSP00000331581 Q6NUJ2 A0A158RFU1 UPI000013E5BC NM_207645.3 deleterious(0) 2/2 hmmpanther:PTHR31870,hmmpanther:PTHR31870:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 109424031 109424031 G T 1 0 0 0 0 1 0 0 0 1799 1000 35 2 2 C11orf87 11 109424031 Missense_Mutation SNP G 11LU022_T 1250797 109424031 25662591 622 1260 TTC12 0 . GRCh38 11 113339406 113339406 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.758C>T p.Ser253Phe p.S253F ENST00000529221 10/22 140 125 15 196 196 0 strelka-varscan-mutect TTC12,missense_variant,p.Ser253Phe,ENST00000393020,;TTC12,missense_variant,p.Ser253Phe,ENST00000314756,;TTC12,missense_variant,p.Ser253Phe,ENST00000529221,NM_001318533.1,NM_017868.3;TTC12,missense_variant,p.Ser259Phe,ENST00000483239,;TTC12,missense_variant,p.Ser209Phe,ENST00000525965,;TTC12,missense_variant,p.Ser79Phe,ENST00000524580,;TTC12,downstream_gene_variant,,ENST00000442859,;TTC12,downstream_gene_variant,,ENST00000529850,;TTC12,downstream_gene_variant,,ENST00000531164,;TTC12,upstream_gene_variant,,ENST00000478125,;TTC12,missense_variant,p.Ser253Phe,ENST00000494714,;TTC12,3_prime_UTR_variant,,ENST00000464224,;TTC12,non_coding_transcript_exon_variant,,ENST00000534793,;TTC12,intron_variant,,ENST00000527362,;TTC12,downstream_gene_variant,,ENST00000525989,; T ENST00000529221 Transcript missense_variant 863/2315 758/2118 253/705 S/F tCc/tTc 1 1 TTC12 HGNC HGNC:23700 protein_coding YES CCDS8360.2 ENSP00000433757 Q9H892 A8K8G6 UPI000013F914 NM_001318533.1,NM_017868.3 deleterious(0) 10/22 hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF330 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 113339406 113339406 C T 1 0 0 0 0 1 0 0 0 17189 855 30 3 3 TTC12 11 113339406 Missense_Mutation SNP C 11LU022_T 3915375 113339406 21747216 623 1261 CLDN25 0 . GRCh38 11 113780430 113780430 + Missense_Mutation SNP A A T rs761672821 11LU022_T 11LU022_N A A c.635A>T p.Glu212Val p.E212V ENST00000453129 1/1 130 92 38 174 174 0 strelka-varscan-mutect CLDN25,missense_variant,p.Glu212Val,ENST00000453129,NM_001101389.1; T ENST00000453129 Transcript missense_variant 684/754 635/690 212/229 E/V gAg/gTg rs761672821 1 1 CLDN25 HGNC HGNC:37218 protein_coding YES CCDS44736.1 ENSP00000396304 C9JDP6 UPI00000495B4 NM_001101389.1 deleterious(0.01) 1/1 hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF87 MODERATE 1 SNV 1 PASS rs761672821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 113780430 113780430 A T 1 0 0 0 0 1 0 0 0 3250 304 11 4 4 CLDN25 11 113780430 Missense_Mutation SNP A 11LU022_T 441024 113780430 21306192 624 1262 DSCAML1 0 . GRCh38 11 117432433 117432433 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.5278A>G p.Thr1760Ala p.T1760A ENST00000321322 30/33 154 124 30 274 274 0 strelka-varscan-mutect DSCAML1,missense_variant,p.Thr1760Ala,ENST00000321322,NM_020693.3;DSCAML1,missense_variant,p.Thr1490Ala,ENST00000527706,; C ENST00000321322 Transcript missense_variant 5280/6899 5278/6342 1760/2113 T/A Act/Gct 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 tolerated(0.2) 30/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 117432433 117432433 T C 1 0 0 0 0 1 0 0 0 4590 1638 57 5 5 DSCAML1 11 117432433 Missense_Mutation SNP T 11LU022_T 3652003 117432433 17654189 625 1263 IL10RA 0 . GRCh38 11 117998929 117998929 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1025C>A p.Pro342His p.P342H ENST00000227752 7/7 79 52 27 97 97 0 strelka-mutect IL10RA,missense_variant,p.Pro342His,ENST00000227752,NM_001558.3;TMPRSS4-AS1,downstream_gene_variant,,ENST00000636151,;IL10RA,non_coding_transcript_exon_variant,,ENST00000533700,;IL10RA,3_prime_UTR_variant,,ENST00000534574,;IL10RA,3_prime_UTR_variant,,ENST00000526544,;IL10RA,non_coding_transcript_exon_variant,,ENST00000529924,;IL10RA,non_coding_transcript_exon_variant,,ENST00000530761,;IL10RA,non_coding_transcript_exon_variant,,ENST00000525467,;IL10RA,non_coding_transcript_exon_variant,,ENST00000530178,;IL10RA,downstream_gene_variant,,ENST00000532009,; A ENST00000227752 Transcript missense_variant 1145/3695 1025/1737 342/578 P/H cCc/cAc 1 1 IL10RA HGNC HGNC:5964 protein_coding YES CCDS8388.1 ENSP00000227752 Q13651 UPI000013C8BF NM_001558.3 deleterious(0.01) 7/7 hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF43 MODERATE 1 SNV 1 1 PASS rs1185279086 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 117998929 117998929 C A 1 0 0 0 0 1 0 0 0 7528 623 22 2 2 IL10RA 11 117998929 Missense_Mutation SNP C 11LU022_T 566496 117998929 17087693 626 1264 KMT2A 0 . GRCh38 11 118505254 118505254 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.9362A>G p.Asn3121Ser p.N3121S ENST00000534358 27/36 185 131 54 239 239 0 strelka-varscan-mutect KMT2A,missense_variant,p.Asn3121Ser,ENST00000534358,NM_001197104.1;KMT2A,missense_variant,p.Asn3118Ser,ENST00000389506,NM_005933.3;KMT2A,downstream_gene_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534678,;KMT2A,upstream_gene_variant,,ENST00000534085,; G ENST00000534358 Transcript missense_variant 9385/16602 9362/11919 3121/3972 N/S aAt/aGt 1 1 KMT2A HGNC HGNC:7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 UPI0001E5E732 NM_001197104.1 tolerated_low_confidence(0.57) 27/36 PIRSF_domain:PIRSF010354 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 118505254 118505254 A G 1 0 0 0 0 1 0 0 0 8295 101 4 5 5 KMT2A 11 118505254 Missense_Mutation SNP A 11LU022_T 506325 118505254 16581368 627 1265 GRIK4 0 . GRCh38 11 120874216 120874216 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1057A>T p.Met353Leu p.M353L ENST00000527524 10/21 109 70 39 111 111 0 strelka-varscan-mutect GRIK4,missense_variant,p.Met353Leu,ENST00000527524,NM_014619.4;GRIK4,missense_variant,p.Met353Leu,ENST00000438375,NM_001282473.2,NM_001282470.2;RP11-640N11.2,intron_variant,,ENST00000505153,;GRIK4,splice_region_variant,,ENST00000533291,; T ENST00000527524 Transcript missense_variant,splice_region_variant 1344/5802 1057/2871 353/956 M/L Atg/Ttg 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 tolerated(0.42) 10/21 hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE SNV 2 1 PASS rs1487896652 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 120874216 120874216 A T 1 0 0 0 0 1 0 0 0 6658 231 8 4 4 GRIK4 11 120874216 Missense_Mutation SNP A 11LU022_T 2368962 120874216 14212406 628 1266 TECTA 0 . GRCh38 11 121130086 121130086 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.2816G>A p.Cys939Tyr p.C939Y ENST00000392793 10/24 173 151 22 240 240 0 strelka-varscan-mutect TECTA,missense_variant,p.Cys939Tyr,ENST00000392793,;TECTA,missense_variant,p.Cys939Tyr,ENST00000264037,NM_005422.2; A ENST00000392793 Transcript missense_variant 3087/7426 2816/6468 939/2155 C/Y tGc/tAc 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D deleterious(0) 10/24 Pfam_domain:PF08742,SMART_domains:SM00832 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999973 1 1 1 0 A 3 1 3 121130086 121130086 G A 1 0 0 0 0 1 0 0 0 16158 1319 46 3 3 TECTA 11 121130086 Missense_Mutation SNP G 11LU022_T 255870 121130086 13956536 629 1267 SPATA19 0 . GRCh38 11 133845439 133845439 + Missense_Mutation SNP A A T rs756056484 11LU022_T 11LU022_N A A c.8T>A p.Ile3Asn p.I3N ENST00000299140 1/7 85 73 12 167 167 0 strelka-varscan-mutect SPATA19,missense_variant,p.Ile3Asn,ENST00000299140,NM_001291992.1,NM_174927.2;SPATA19,missense_variant,p.Ile3Asn,ENST00000532889,; T ENST00000299140 Transcript missense_variant 63/861 8/504 3/167 I/N aTt/aAt rs756056484 1 -1 SPATA19 HGNC HGNC:30614 protein_coding YES CCDS8493.1 ENSP00000299140 Q7Z5L4 A0A140VKB6 UPI000007021D NM_001291992.1,NM_174927.2 deleterious(0) 1/7 hmmpanther:PTHR36468 MODERATE 1 SNV 1 1 PASS rs756056484 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 133845439 133845439 A T 1 0 0 0 0 1 0 0 0 15334 101 4 4 4 SPATA19 11 133845439 Missense_Mutation SNP A 11LU022_T 12715353 133845439 1241183 630 1268 WNK1 0 . GRCh38 12 868017 868017 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.2546C>G p.Ser849Cys p.S849C ENST00000340908 10/28 307 239 68 347 347 0 strelka-varscan-mutect WNK1,missense_variant,p.Ser764Cys,ENST00000530271,;WNK1,missense_variant,p.Ser764Cys,ENST00000537687,NM_001184985.1;WNK1,missense_variant,p.Ser849Cys,ENST00000340908,NM_213655.4;WNK1,missense_variant,p.Ser63Cys,ENST00000574564,;WNK1,intron_variant,,ENST00000315939,NM_018979.3;WNK1,intron_variant,,ENST00000535572,NM_014823.2;WNK1,intron_variant,,ENST00000535698,;WNK1,intron_variant,,ENST00000544965,;WNK1,intron_variant,,ENST00000545285,;WNK1,upstream_gene_variant,,ENST00000574679,; G ENST00000340908 Transcript missense_variant 3189/11208 2546/7905 849/2634 S/C tCc/tGc 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 deleterious_low_confidence(0) 10/28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 868017 868017 C G 1 0 0 0 0 1 0 0 0 17933 855 30 4 4 WNK1 12 868017 Missense_Mutation SNP C 11LU022_T 868017 132407292 631 1269 GALNT8 0 . GRCh38 12 4811308 4811308 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1267G>T p.Val423Leu p.V423L ENST00000280684 1/1 159 130 29 209 209 0 strelka-varscan-mutect GALNT8,missense_variant,p.Val423Leu,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Val423Leu,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; T ENST00000280684 Transcript missense_variant 2133/4237 1267/1590 423/529 V/L Gta/Tta 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD deleterious(0) 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104,Superfamily_domains:SSF81324 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 4811308 4811308 G T 1 0 0 0 0 1 0 0 0 6090 1261 44 2 2 GALNT8 12 4811308 Missense_Mutation SNP G 11LU022_T 3943291 4811308 128464001 632 1270 KCNA1 0 . GRCh38 12 4912137 4912137 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.759C>T p.= p.I253I ENST00000382545 2/2 497 408 89 683 683 0 strelka-varscan-mutect KCNA1,synonymous_variant,p.=,ENST00000382545,NM_000217.2;KCNA1,intron_variant,,ENST00000543874,;KCNA1,intron_variant,,ENST00000541095,; T ENST00000382545 Transcript synonymous_variant 1866/7976 759/1488 253/495 I atC/atT 1 1 KCNA1 HGNC HGNC:6218 protein_coding YES CCDS8535.1 ENSP00000371985 Q09470 UPI000013C8E0 NM_000217.2 2/2 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF24,Superfamily_domains:SSF81324 LOW 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 4912137 4912137 C T 1 0 0 0 0 0 0 0 1 7917 816 29 3 3 KCNA1 12 4912137 Silent SNP C 11LU022_T 100829 4912137 128363172 633 1271 KCNA5 0 . GRCh38 12 5045632 5045632 + Missense_Mutation SNP C C G rs764615241 11LU022_T 11LU022_N C C c.1485C>G p.Ile495Met p.I495M ENST00000252321 1/1 187 134 53 284 284 0 strelka-varscan-mutect KCNA5,missense_variant,p.Ile495Met,ENST00000252321,NM_002234.3; G ENST00000252321 Transcript missense_variant 1644/2800 1485/1842 495/613 I/M atC/atG rs764615241,COSM1512302 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 tolerated(0.17) 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs764615241 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 5045632 5045632 C G 1 0 0 0 0 1 0 0 0 7922 874 31 4 4 KCNA5 12 5045632 Missense_Mutation SNP C 11LU022_T 133495 5045632 128229677 634 1272 CD163 0 . GRCh38 12 7496921 7496921 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.991G>A p.Asp331Asn p.D331N ENST00000359156 5/17 237 210 27 304 304 0 strelka-varscan-mutect CD163,missense_variant,p.Asp331Asn,ENST00000359156,NM_004244.5;CD163,missense_variant,p.Asp331Asn,ENST00000396620,;CD163,missense_variant,p.Asp331Asn,ENST00000432237,NM_203416.3;CD163,missense_variant,p.Asp319Asn,ENST00000541972,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,; T ENST00000359156 Transcript missense_variant 1194/4268 991/3471 331/1156 D/N Gac/Aac 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 deleterious(0.03) 5/17 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF324,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS rs1460117132 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 7496921 7496921 C T 1 0 0 0 0 1 0 0 0 2670 826 29 3 3 CD163 12 7496921 Missense_Mutation SNP C 11LU022_T 2451289 7496921 125778388 635 1273 NANOGNB 0 . GRCh38 12 7773805 7773805 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.521G>A p.Arg174Lys p.R174K ENST00000382119 4/4 69 60 9 82 82 0 strelka-varscan-mutect NANOGNB,missense_variant,p.Arg174Lys,ENST00000382119,NM_001145465.1; A ENST00000382119 Transcript missense_variant 591/907 521/567 174/188 R/K aGa/aAa 1 1 NANOGNB HGNC HGNC:24958 protein_coding YES CCDS44826.1 ENSP00000371553 Q7Z5D8 UPI00001B3DAD NM_001145465.1 tolerated_low_confidence(0.99) 4/4 hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -19.55459 0.9999764 1 1 1 0 A 3 1 3 7773805 7773805 G A 1 0 0 0 0 1 0 0 0 10158 956 33 3 3 NANOGNB 12 7773805 Missense_Mutation SNP G 11LU022_T 276884 7773805 125501504 636 1274 GRIN2B 0 . GRCh38 12 13753422 13753422 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.905C>A p.Thr302Asn p.T302N ENST00000609686 3/13 196 161 35 289 289 0 strelka-varscan-mutect GRIN2B,missense_variant,p.Thr302Asn,ENST00000609686,NM_000834.3; T ENST00000609686 Transcript missense_variant 1359/30355 905/4455 302/1484 T/N aCt/aAt COSM1511568,COSM468068 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 tolerated(0.14) 3/13 Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF192,Superfamily_domains:SSF53822 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1321033549 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 13753422 13753422 G T 1 0 0 0 0 1 0 0 0 6662 1029 36 2 2 GRIN2B 12 13753422 Missense_Mutation SNP G 11LU022_T 5979617 13753422 119521887 637 1275 SLC15A5 0 . GRCh38 12 16216895 16216895 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1481A>T p.Asp494Val p.D494V ENST00000344941 7/9 57 49 8 91 91 0 strelka-varscan-mutect SLC15A5,missense_variant,p.Asp494Val,ENST00000344941,NM_001170798.1; A ENST00000344941 Transcript missense_variant,splice_region_variant 1481/2923 1481/1740 494/579 D/V gAt/gTt 1 -1 SLC15A5 HGNC HGNC:33455 protein_coding YES ENSP00000340402 A6NIM6 UPI0000DD8132 NM_001170798.1 deleterious(0.02) 7/9 hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF91,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 16216895 16216895 T A 1 0 0 0 0 1 0 0 0 14667 1449 50 4 4 SLC15A5 12 16216895 Missense_Mutation SNP T 11LU022_T 2463473 16216895 117058414 638 1276 SLCO1B7 0 . GRCh38 12 21019324 21019324 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.162T>C p.= p.C54C ENST00000421593 2/13 103 91 12 130 130 0 strelka-varscan-mutect SLCO1B7,synonymous_variant,p.=,ENST00000421593,NM_001009562.4;RP11-545J16.1,intron_variant,,ENST00000540229,;RP11-545J16.1,intron_variant,,ENST00000381541,; C ENST00000421593 Transcript synonymous_variant 162/1923 162/1923 54/640 C tgT/tgC 1 1 SLCO1B7 HGNC HGNC:32934 protein_coding YES CCDS44843.1 ENSP00000394168 G3V0H7 UPI0000E5E120 NM_001009562.4 2/13 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 21019324 21019324 T C 1 0 0 0 0 0 0 0 1 15011 1731 60 5 5 SLCO1B7 12 21019324 Silent SNP T 11LU022_T 4802429 21019324 112255985 639 1277 SLCO1A2 0 . GRCh38 12 21318793 21318793 + Missense_Mutation SNP C C A rs747052121 11LU022_T 11LU022_N C C c.191G>T p.Ser64Ile p.S64I ENST00000307378 4/16 57 47 10 116 116 0 strelka-varscan-mutect SLCO1A2,missense_variant,p.Ser64Ile,ENST00000307378,NM_021094.3,NM_134431.3;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000453443,;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000422327,;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000450590,;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000435179,;SLCO1A2,missense_variant,p.Ser62Ile,ENST00000445053,;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000421294,;SLCO1A2,intron_variant,,ENST00000458504,;SLCO1A2,intron_variant,,ENST00000413682,;SLCO1A2,downstream_gene_variant,,ENST00000421287,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000473830,;SLCO1A2,missense_variant,p.Ser64Ile,ENST00000544290,;SLCO1A2,missense_variant,p.Ser62Ile,ENST00000544020,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000463718,; A ENST00000307378 Transcript missense_variant 912/7682 191/2013 64/670 S/I aGc/aTc rs747052121,COSM1646483,COSM692807 1 -1 SLCO1A2 HGNC HGNC:10956 protein_coding YES CCDS8686.1 ENSP00000305974 P46721 A0A024RAT5 UPI0000037575 NM_021094.3,NM_134431.3 deleterious(0) 4/16 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF16,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747052121 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 21318793 21318793 C A 1 0 0 0 0 1 0 0 0 15008 797 28 2 2 SLCO1A2 12 21318793 Missense_Mutation SNP C 11LU022_T 299469 21318793 111956516 640 1278 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 11LU022_T 11LU022_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 425 228 197 350 349 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C 11LU022_T 3926558 25245351 108029958 641 1279 LMNTD1 0 . GRCh38 12 25546545 25546545 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.320C>A p.Pro107His p.P107H ENST00000458174 4/10 73 67 6 48 48 0 strelka-varscan-mutect LMNTD1,missense_variant,p.Pro86His,ENST00000282881,NM_152590.3;LMNTD1,missense_variant,p.Pro107His,ENST00000458174,NM_001145728.2;LMNTD1,missense_variant,p.Pro107His,ENST00000413632,NM_001145729.1;LMNTD1,missense_variant,p.Pro23His,ENST00000445693,NM_001145727.2;LMNTD1,missense_variant,p.Pro61His,ENST00000538178,;LMNTD1,missense_variant,p.Pro61His,ENST00000540106,;LMNTD1,missense_variant,p.Pro61His,ENST00000542224,;LMNTD1,5_prime_UTR_variant,,ENST00000539744,NM_001256266.1;LMNTD1,intron_variant,,ENST00000545543,; T ENST00000458174 Transcript missense_variant 565/1677 320/1230 107/409 P/H cCc/cAc 1 -1 LMNTD1 HGNC HGNC:26683 protein_coding YES CCDS44849.1 ENSP00000407353 Q8N9Z9 UPI0000E004B3 NM_001145728.2 tolerated(0.08) 4/10 MODERATE 1 SNV 2 1 PASS rs1394341088 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 25546545 25546545 G T 1 0 0 0 0 1 0 0 0 8775 1232 43 2 2 LMNTD1 12 25546545 Missense_Mutation SNP G 11LU022_T 301194 25546545 107728764 642 1280 KIF21A 0 . GRCh38 12 39331689 39331689 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.3153+1G>T p.X1051_splice ENST00000361418 233 211 22 306 305 1 strelka-varscan-mutect KIF21A,splice_donor_variant,,ENST00000361961,NM_017641.3;KIF21A,splice_donor_variant,,ENST00000636569,;KIF21A,splice_donor_variant,,ENST00000361418,NM_001173464.1;KIF21A,splice_donor_variant,,ENST00000544797,NM_001173463.1;KIF21A,splice_donor_variant,,ENST00000541463,NM_001173465.1;KIF21A,splice_donor_variant,,ENST00000552961,;KIF21A,splice_donor_variant,,ENST00000551264,;KIF21A,splice_donor_variant,,ENST00000551066,;KIF21A,splice_donor_variant,,ENST00000552475,;KIF21A,splice_donor_variant,,ENST00000547108,;KIF21A,downstream_gene_variant,,ENST00000546817,; A ENST00000361418 Transcript splice_donor_variant -/5044 3153/5025 1051/1674 1 -1 KIF21A HGNC HGNC:19349 protein_coding YES CCDS53776.1 ENSP00000354878 Q7Z4S6 UPI0000212ED9 NM_001173464.1 22/37 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 39331689 39331689 C A 1 0 0 0 0 0 0 1 0 8153 521 18 2 2 KIF21A 12 39331689 Splice_Site SNP C 11LU022_T 13785144 39331689 93943620 643 1281 PDZRN4 0 . GRCh38 12 41573316 41573316 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.2537A>T p.His846Leu p.H846L ENST00000402685 10/10 208 175 33 247 247 0 strelka-varscan-mutect PDZRN4,missense_variant,p.His586Leu,ENST00000298919,;PDZRN4,missense_variant,p.His846Leu,ENST00000402685,NM_001164595.1;PDZRN4,missense_variant,p.His588Leu,ENST00000539469,NM_013377.3;PDZRN4,non_coding_transcript_exon_variant,,ENST00000548316,; T ENST00000402685 Transcript missense_variant 2545/3347 2537/3111 846/1036 H/L cAc/cTc 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 deleterious(0.02) 10/10 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF6 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 41573316 41573316 A T 1 0 0 0 0 1 0 0 0 11798 159 6 4 4 PDZRN4 12 41573316 Missense_Mutation SNP A 11LU022_T 2241627 41573316 91701993 644 1282 DBX2 0 . GRCh38 12 45016391 45016391 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.915G>T p.Glu305Asp p.E305D ENST00000332700 4/4 119 104 15 115 115 0 strelka-varscan-mutect DBX2,missense_variant,p.Glu305Asp,ENST00000332700,NM_001004329.2; A ENST00000332700 Transcript missense_variant 1087/2806 915/1020 305/339 E/D gaG/gaT 1 -1 DBX2 HGNC HGNC:33186 protein_coding YES CCDS31781.1 ENSP00000331470 Q6ZNG2 UPI000041A784 NM_001004329.2 deleterious_low_confidence(0.03) 4/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 45016391 45016391 C A 1 0 0 0 0 1 0 0 0 4060 912 32 2 2 DBX2 12 45016391 Missense_Mutation SNP C 11LU022_T 3443075 45016391 88258918 645 1283 KMT2D 0 . GRCh38 12 49042178 49042178 + Missense_Mutation SNP T T A rs587783722 11LU022_T 11LU022_N T T c.6020A>T p.Glu2007Val p.E2007V ENST00000301067 28/54 243 200 43 289 289 0 strelka-varscan-mutect KMT2D,missense_variant,p.Glu2007Val,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000550356,; A ENST00000301067 Transcript missense_variant 6020/19419 6020/16614 2007/5537 E/V gAg/gTg rs587783722 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 deleterious(0) 28/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF380 likely_benign MODERATE 1 SNV 5 1 1 PASS rs587783722 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49042178 49042178 T A 1 0 0 0 0 1 0 0 0 8298 1551 54 4 4 KMT2D 12 49042178 Missense_Mutation SNP T 11LU022_T 4025787 49042178 84233131 646 1284 AQP6 0 . GRCh38 12 49973421 49973421 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.248C>A p.Pro83His p.P83H ENST00000615425 1/5 206 160 46 244 243 1 strelka-varscan-mutect AQP6,missense_variant,p.Pro83His,ENST00000615425,NM_001652.3;AQP6,missense_variant,p.Pro83His,ENST00000315520,;AQP6,missense_variant,p.Pro83His,ENST00000618286,;AQP6,intron_variant,,ENST00000551733,;RACGAP1,downstream_gene_variant,,ENST00000548961,;AQP6,non_coding_transcript_exon_variant,,ENST00000489786,; A ENST00000615425 Transcript missense_variant 248/2245 248/849 83/282 P/H cCc/cAc 1 1 AQP6 HGNC HGNC:639 protein_coding YES CCDS31798.1 ENSP00000477688 Q13520 UPI000013EBD8 NM_001652.3 deleterious(0) 1/5 Gene3D:1.20.1080.10,Pfam_domain:PF00230,Prints_domain:PR00783,PROSITE_patterns:PS00221,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF113,Superfamily_domains:SSF81338,TIGRFAM_domain:TIGR00861 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49973421 49973421 C A 1 0 0 0 0 1 0 0 0 953 623 22 2 2 AQP6 12 49973421 Missense_Mutation SNP C 11LU022_T 931243 49973421 83301888 647 1285 ANKRD33 0 . GRCh38 12 51891115 51891115 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1169G>T p.Arg390Met p.R390M ENST00000301190 5/5 234 209 25 350 350 0 strelka-varscan-mutect ANKRD33,missense_variant,p.Arg390Met,ENST00000301190,NM_182608.3;ANKRD33,intron_variant,,ENST00000340970,NM_001130015.1;ANKRD33,non_coding_transcript_exon_variant,,ENST00000547119,;ANKRD33,downstream_gene_variant,,ENST00000549316,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548526,;ANKRD33,intron_variant,,ENST00000548383,;ANKRD33,intron_variant,,ENST00000549751,;ANKRD33,intron_variant,,ENST00000550652,; T ENST00000301190 Transcript missense_variant 1396/1935 1169/1359 390/452 R/M aGg/aTg 1 1 ANKRD33 HGNC HGNC:13788 protein_coding YES CCDS8815.1 ENSP00000301190 Q7Z3H0 UPI00003668C0 NM_182608.3 deleterious(0) 5/5 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF29 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 51891115 51891115 G T 1 0 0 0 0 1 0 0 0 765 1000 35 2 2 ANKRD33 12 51891115 Missense_Mutation SNP G 11LU022_T 1917694 51891115 81384194 648 1286 NR4A1 0 . GRCh38 12 52054918 52054918 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.752G>T p.Gly251Val p.G251V ENST00000545748 3/8 183 164 19 242 242 0 strelka-varscan-mutect NR4A1,missense_variant,p.Gly251Val,ENST00000545748,NM_001202234.1;NR4A1,missense_variant,p.Gly197Val,ENST00000243050,NM_002135.4;NR4A1,missense_variant,p.Gly197Val,ENST00000394824,;NR4A1,missense_variant,p.Gly210Val,ENST00000360284,NM_001202233.1;NR4A1,missense_variant,p.Gly197Val,ENST00000394825,NM_173157.2;NR4A1,missense_variant,p.Gly210Val,ENST00000550082,;NR4A1,missense_variant,p.Gly210Val,ENST00000546842,;NR4A1,missense_variant,p.Gly197Val,ENST00000548232,;NR4A1,intron_variant,,ENST00000550763,;NR4A1,downstream_gene_variant,,ENST00000562373,;NR4A1,upstream_gene_variant,,ENST00000550582,;NR4A1,downstream_gene_variant,,ENST00000548977,;RP11-1100L3.8,downstream_gene_variant,,ENST00000564363,;RP11-1100L3.8,downstream_gene_variant,,ENST00000564531,;NR4A1,intron_variant,,ENST00000548733,;NR4A1,downstream_gene_variant,,ENST00000547206,;NR4A1,non_coding_transcript_exon_variant,,ENST00000550557,;NR4A1,non_coding_transcript_exon_variant,,ENST00000478250,;NR4A1,upstream_gene_variant,,ENST00000564201,;NR4A1,upstream_gene_variant,,ENST00000565848,;NR4A1,upstream_gene_variant,,ENST00000567890,;NR4A1,downstream_gene_variant,,ENST00000549102,;NR4A1,upstream_gene_variant,,ENST00000550339,; T ENST00000545748 Transcript missense_variant 1747/3511 752/1959 251/652 G/V gGc/gTc 1 1 NR4A1 HGNC HGNC:7980 protein_coding YES CCDS73471.1 ENSP00000440864 F5GXF0 UPI0000D621F3 NM_001202234.1 tolerated(0.14) 3/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24085:SF1,hmmpanther:PTHR24085,Prints_domain:PR01285 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 52054918 52054918 G T 1 0 0 0 0 1 0 0 0 10688 1203 42 2 2 NR4A1 12 52054918 Missense_Mutation SNP G 11LU022_T 163803 52054918 81220391 649 1287 KRT5 0 . GRCh38 12 52515166 52515166 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1549G>T p.Gly517Cys p.G517C ENST00000252242 9/9 379 312 67 434 434 0 strelka-varscan-mutect KRT5,missense_variant,p.Gly517Cys,ENST00000252242,NM_000424.3;KRT5,downstream_gene_variant,,ENST00000548409,;KRT5,downstream_gene_variant,,ENST00000549420,;KRT5,downstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000546577,;KRT5,downstream_gene_variant,,ENST00000551275,;KRT5,non_coding_transcript_exon_variant,,ENST00000549511,;KRT5,non_coding_transcript_exon_variant,,ENST00000552952,;KRT5,downstream_gene_variant,,ENST00000552629,;KRT5,downstream_gene_variant,,ENST00000551013,;KRT5,downstream_gene_variant,,ENST00000547890,; A ENST00000252242 Transcript missense_variant 1940/2531 1549/1773 517/590 G/C Ggc/Tgc 1 -1 KRT5 HGNC HGNC:6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 UPI000013CD4B NM_000424.3 deleterious(0.05) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF205,hmmpanther:PTHR23239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 52515166 52515166 C A 1 0 0 0 0 1 0 0 0 8361 594 21 2 2 KRT5 12 52515166 Missense_Mutation SNP C 11LU022_T 460248 52515166 80760143 650 1288 KRT73 0 . GRCh38 12 52613726 52613726 + Missense_Mutation SNP T T C rs559245335 11LU022_T 11LU022_N T T c.946A>G p.Lys316Glu p.K316E ENST00000305748 5/9 154 112 42 180 180 0 strelka-varscan-mutect KRT73,missense_variant,p.Lys316Glu,ENST00000305748,NM_175068.2;KRT73,missense_variant,p.Lys61Glu,ENST00000552855,;KRT73-AS1,non_coding_transcript_exon_variant,,ENST00000552364,;KRT73-AS1,non_coding_transcript_exon_variant,,ENST00000549180,;KRT73-AS1,downstream_gene_variant,,ENST00000551089,;KRT73,non_coding_transcript_exon_variant,,ENST00000546934,; C ENST00000305748 Transcript missense_variant 981/2284 946/1623 316/540 K/E Aag/Gag rs559245335 1 -1 KRT73 HGNC HGNC:28928 protein_coding YES CCDS8834.1 ENSP00000307014 Q86Y46 UPI000000DCB8 NM_175068.2 deleterious(0) 5/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF85,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs559245335 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 52613726 52613726 T C 1 0 0 0 0 1 0 0 0 8368 1792 62 5 5 KRT73 12 52613726 Missense_Mutation SNP T 11LU022_T 98560 52613726 80661583 651 1289 KRT73 0 . GRCh38 12 52616198 52616198 + Missense_Mutation SNP G G C rs116369374 11LU022_T 11LU022_N G G c.630C>G p.Ser210Arg p.S210R ENST00000305748 2/9 247 192 55 285 285 0 strelka-varscan-mutect KRT73,missense_variant,p.Ser210Arg,ENST00000305748,NM_175068.2;KRT73,upstream_gene_variant,,ENST00000552855,;KRT73-AS1,downstream_gene_variant,,ENST00000552364,;KRT73-AS1,downstream_gene_variant,,ENST00000549180,;KRT73-AS1,downstream_gene_variant,,ENST00000551089,;KRT73,non_coding_transcript_exon_variant,,ENST00000546934,; C ENST00000305748 Transcript missense_variant 665/2284 630/1623 210/540 S/R agC/agG rs116369374,COSM4042893,COSM694176 1 -1 KRT73 HGNC HGNC:28928 protein_coding YES CCDS8834.1 ENSP00000307014 Q86Y46 UPI000000DCB8 NM_175068.2 deleterious(0.04) 2/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF85,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593,Prints_domain:PR01276 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs116369374 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 52616198 52616198 G C 1 0 0 0 0 1 0 0 0 8368 1078 38 4 4 KRT73 12 52616198 Missense_Mutation SNP G 11LU022_T 2472 52616198 80659111 652 1290 KRT1 0 . GRCh38 12 52680004 52680004 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.345G>T p.= p.G115G ENST00000252244 1/9 236 181 55 329 327 2 strelka-varscan-mutect KRT1,synonymous_variant,p.=,ENST00000252244,NM_006121.3;KRT1,upstream_gene_variant,,ENST00000548765,; A ENST00000252244 Transcript synonymous_variant 404/2451 345/1935 115/644 G ggG/ggT 1 -1 KRT1 HGNC HGNC:6412 protein_coding YES CCDS8836.1 ENSP00000252244 P04264 UPI000013CD4D NM_006121.3 1/9 Low_complexity_(Seg):seg,Pfam_domain:PF16208 LOW 1 SNV 1 1 PASS rs1184390394 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 52680004 52680004 C A 1 0 0 0 0 0 0 0 1 8329 610 22 2 2 KRT1 12 52680004 Silent SNP C 11LU022_T 63806 52680004 80595305 653 1291 HOXC10 0 . GRCh38 12 53985861 53985861 + Frame_Shift_Del DEL C C - rs778861177 11LU022_T 11LU022_N C C c.606delC p.Lys203SerfsTer51 p.K203Sfs*51 ENST00000303460 1/2 124 83 41 150 150 0 sindel-varindel-pindel HOXC10,frameshift_variant,p.Lys203SerfsTer51,ENST00000303460,NM_017409.3;RP11-834C11.12,frameshift_variant,p.Lys8SerfsTer83,ENST00000513209,;HOXC10,frameshift_variant,p.Lys91SerfsTer?,ENST00000515593,;HOXC6,upstream_gene_variant,,ENST00000504315,;HOXC-AS3,upstream_gene_variant,,ENST00000509870,;HOXC-AS3,upstream_gene_variant,,ENST00000513165,;HOXC-AS3,upstream_gene_variant,,ENST00000514702,;HOXC10,upstream_gene_variant,,ENST00000511575,;HOXC10,upstream_gene_variant,,ENST00000513413,;HOXC10,upstream_gene_variant,,ENST00000514415,;HOXC-AS3,upstream_gene_variant,,ENST00000567780,; - ENST00000303460 Transcript frameshift_variant 676/1936 602/1029 201/342 T/X aCc/ac rs778861177 1 1 HOXC10 HGNC HGNC:5122 protein_coding YES CCDS8868.1 ENSP00000307321 Q9NYD6 Q53XI4 UPI000012CF7C NM_017409.3 1/2 hmmpanther:PTHR24326:SF135,hmmpanther:PTHR24326 HIGH 1 deletion 1 4 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 - 7 5 3 53985861 53985861 C - 1 0 1 0 1 0 0 0 0 7203 507 18 0 0 HOXC10 12 53985861 Frame_Shift_Del DEL C 11LU022_T 1305857 53985861 79289448 654 1292 OR10P1 0 . GRCh38 12 55636911 55636911 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.20C>A p.Thr7Asn p.T7N ENST00000309675 1/1 77 70 7 101 101 0 strelka-varscan-mutect OR10P1,missense_variant,p.Thr7Asn,ENST00000309675,NM_206899.1;RP11-644F5.16,downstream_gene_variant,,ENST00000556606,; A ENST00000309675 Transcript missense_variant 52/995 20/942 7/313 T/N aCt/aAt 1 1 OR10P1 HGNC HGNC:15378 protein_coding YES CCDS31828.1 ENSP00000308082 Q8NGE3 UPI0000061E9C NM_206899.1 deleterious(0) 1/1 hmmpanther:PTHR26453:SF194,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -15.67811 1 1 1 1 0 A 3 1 3 55636911 55636911 C A 1 0 0 0 0 1 0 0 0 10992 565 20 2 2 OR10P1 12 55636911 Missense_Mutation SNP C 11LU022_T 1651050 55636911 77638398 655 1293 TIMELESS 0 . GRCh38 12 56421015 56421015 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.2988G>T p.Gln996His p.Q996H ENST00000553532 24/29 250 211 39 297 297 0 strelka-varscan-mutect TIMELESS,missense_variant,p.Gln996His,ENST00000553532,NM_003920.3;TIMELESS,missense_variant,p.Gln995His,ENST00000229201,;TIMELESS,non_coding_transcript_exon_variant,,ENST00000557589,;TIMELESS,non_coding_transcript_exon_variant,,ENST00000553314,;TIMELESS,downstream_gene_variant,,ENST00000555808,; A ENST00000553532 Transcript missense_variant 3139/5121 2988/3627 996/1208 Q/H caG/caT COSM4043615 1 -1 TIMELESS HGNC HGNC:11813 protein_coding YES CCDS8918.1 ENSP00000450607 Q9UNS1 UPI000013C8EA NM_003920.3 tolerated(0.26) 24/29 hmmpanther:PTHR22940,hmmpanther:PTHR22940:SF4,Pfam_domain:PF05029 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56421015 56421015 C A 1 0 0 0 0 1 0 0 0 16342 680 24 2 2 TIMELESS 12 56421015 Missense_Mutation SNP C 11LU022_T 784104 56421015 76854294 656 1294 GLI1 0 . GRCh38 12 57470567 57470567 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1827G>T p.= p.L609L ENST00000228682 12/12 167 138 29 222 222 0 strelka-varscan-mutect GLI1,synonymous_variant,p.=,ENST00000228682,NM_005269.2;GLI1,synonymous_variant,p.=,ENST00000546141,NM_001167609.1;GLI1,synonymous_variant,p.=,ENST00000543426,NM_001160045.1;GLI1,synonymous_variant,p.=,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,downstream_gene_variant,,ENST00000548139,;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;MARS,upstream_gene_variant,,ENST00000549133,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;GLI1,downstream_gene_variant,,ENST00000527742,;ARHGAP9,downstream_gene_variant,,ENST00000546704,; T ENST00000228682 Transcript synonymous_variant 1918/3613 1827/3321 609/1106 L ctG/ctT 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 12/12 hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 57470567 57470567 G T 1 0 0 0 0 0 0 0 1 6315 1335 47 2 2 GLI1 12 57470567 Silent SNP G 11LU022_T 1049552 57470567 75804742 657 1295 KIF5A 0 . GRCh38 12 57569334 57569334 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.898A>T p.Met300Leu p.M300L ENST00000455537 10/29 524 462 62 606 605 1 strelka-varscan-mutect KIF5A,missense_variant,p.Met300Leu,ENST00000455537,NM_004984.2;KIF5A,missense_variant,p.Met211Leu,ENST00000286452,; T ENST00000455537 Transcript missense_variant 1172/5824 898/3099 300/1032 M/L Atg/Ttg 1 1 KIF5A HGNC HGNC:6323 protein_coding YES CCDS8945.1 ENSP00000408979 Q12840 UPI000013DE4C NM_004984.2 tolerated(0.37) 10/29 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF317,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 57569334 57569334 A T 1 0 0 0 0 1 0 0 0 8170 449 16 4 4 KIF5A 12 57569334 Missense_Mutation SNP A 11LU022_T 98767 57569334 75705975 658 1296 METTL21B 0 . GRCh38 12 57773129 57773129 + Splice_Site SNP G G C rs766086319 11LU022_T 11LU022_N G G c.289+1G>C p.X97_splice ENST00000300209 115 90 25 154 154 0 strelka-varscan-mutect METTL21B,splice_donor_variant,,ENST00000333012,NM_206914.1;METTL21B,splice_donor_variant,,ENST00000300209,NM_015433.2;METTL21B,splice_donor_variant,,ENST00000551420,;METTL21B,splice_donor_variant,,ENST00000548256,;RP11-571M6.15,splice_donor_variant,,ENST00000546504,;METTL1,upstream_gene_variant,,ENST00000324871,NM_005371.5;METTL1,upstream_gene_variant,,ENST00000257848,NM_023033.3;METTL1,upstream_gene_variant,,ENST00000547653,;CYP27B1,upstream_gene_variant,,ENST00000546609,;METTL1,upstream_gene_variant,,ENST00000548504,;RP11-571M6.15,splice_donor_variant,,ENST00000553083,;METTL21B,intron_variant,,ENST00000552307,;METTL1,upstream_gene_variant,,ENST00000548681,;RP11-571M6.15,splice_donor_variant,,ENST00000471530,;METTL1,upstream_gene_variant,,ENST00000553125,;METTL1,upstream_gene_variant,,ENST00000549773,;METTL1,upstream_gene_variant,,ENST00000551117,; C ENST00000300209 Transcript splice_donor_variant -/2563 289/681 97/226 rs766086319 1 1 METTL21B HGNC HGNC:24936 protein_coding YES CCDS8957.1 ENSP00000300209 Q96AZ1 UPI000006CEB5 NM_015433.2 2/2 HIGH 1 SNV 1 1 PASS rs766086319 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 3 57773129 57773129 G C 1 0 0 0 0 0 0 1 0 9446 1275 44 4 4 METTL21B 12 57773129 Splice_Site SNP G 11LU022_T 203795 57773129 75502180 659 1297 C12orf66 0 . GRCh38 12 64194179 64194179 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1001A>T p.His334Leu p.H334L ENST00000311915 3/4 177 153 24 205 205 0 strelka-varscan-mutect C12orf66,missense_variant,p.His334Leu,ENST00000398055,NM_152440.4;C12orf66,missense_variant,p.His334Leu,ENST00000311915,NM_001300940.1;C12orf66,missense_variant,p.His281Leu,ENST00000544871,NM_001300941.1; A ENST00000311915 Transcript missense_variant 1029/2698 1001/1407 334/468 H/L cAt/cTt 1 -1 C12orf66 HGNC HGNC:26517 protein_coding YES CCDS73490.1 ENSP00000311486 J3KNH0 UPI0003EAEA9B NM_001300940.1 tolerated(0.19) 3/4 Superfamily_domains:0053960,Pfam_domain:PF09404,hmmpanther:PTHR31581,hmmpanther:PTHR31581:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 64194179 64194179 T A 1 0 0 0 0 1 0 0 0 1820 1464 51 4 4 C12orf66 12 64194179 Missense_Mutation SNP T 11LU022_T 6421050 64194179 69081130 660 1298 GNS 0 . GRCh38 12 64744864 64744864 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.569G>T p.Gly190Val p.G190V ENST00000258145 5/14 301 266 35 331 330 1 strelka-varscan-mutect GNS,missense_variant,p.Gly190Val,ENST00000258145,NM_002076.3;GNS,missense_variant,p.Gly134Val,ENST00000418919,;GNS,missense_variant,p.Gly222Val,ENST00000543646,;GNS,missense_variant,p.Gly170Val,ENST00000542058,;GNS,missense_variant,p.Gly10Val,ENST00000540196,;GNS,missense_variant,p.Gly114Val,ENST00000545273,;GNS,non_coding_transcript_exon_variant,,ENST00000541781,; A ENST00000258145 Transcript missense_variant 740/5122 569/1659 190/552 G/V gGg/gTg 1 -1 GNS HGNC HGNC:4422 protein_coding YES CCDS8970.1 ENSP00000258145 P15586 A0A024RBC5 UPI0000000CC8 NM_002076.3 deleterious(0) 5/14 Gene3D:3.40.720.10,Pfam_domain:PF00884,PIRSF_domain:PIRSF036666,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF212,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 64744864 64744864 C A 1 0 0 0 0 1 0 0 0 6429 623 22 2 2 GNS 12 64744864 Missense_Mutation SNP C 11LU022_T 550685 64744864 68530445 661 1299 TBC1D30 0 . GRCh38 12 64870674 64870674 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1364G>T p.Arg455Leu p.R455L ENST00000539867 11/12 240 216 24 283 283 0 strelka-mutect TBC1D30,missense_variant,p.Arg341Leu,ENST00000542120,;TBC1D30,missense_variant,p.Arg455Leu,ENST00000539867,NM_015279.1;RPL7P39,upstream_gene_variant,,ENST00000481157,; T ENST00000539867 Transcript missense_variant 1672/2594 1364/2286 455/761 R/L cGa/cTa 1 1 TBC1D30 HGNC HGNC:29164 protein_coding YES CCDS53813.1 ENSP00000440207 Q9Y2I9 UPI000013F308 NM_015279.1 deleterious(0) 11/12 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF291 MODERATE 1 SNV 1 1 PASS rs1238599234 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 64870674 64870674 G T 1 0 0 0 0 1 0 0 0 16020 1058 37 1 1 TBC1D30 12 64870674 Missense_Mutation SNP G 11LU022_T 125810 64870674 68404635 662 1300 GRIP1 0 . GRCh38 12 66392790 66392790 + Missense_Mutation SNP C C A rs762131350 11LU022_T 11LU022_N C C c.2000G>T p.Arg667Leu p.R667L ENST00000398016 17/24 368 319 49 416 415 1 strelka-varscan-mutect GRIP1,missense_variant,p.Arg719Leu,ENST00000359742,;GRIP1,missense_variant,p.Arg667Leu,ENST00000398016,NM_021150.3;GRIP1,missense_variant,p.Arg667Leu,ENST00000538211,NM_001178074.1;GRIP1,missense_variant,p.Arg534Leu,ENST00000538164,;GRIP1,missense_variant,p.Arg611Leu,ENST00000540433,;GRIP1,missense_variant,p.Arg559Leu,ENST00000536215,;GRIP1,intron_variant,,ENST00000540854,;GRIP1,downstream_gene_variant,,ENST00000542021,;GRIP1,upstream_gene_variant,,ENST00000541299,; A ENST00000398016 Transcript missense_variant 2069/4888 2000/3231 667/1076 R/L cGa/cTa rs762131350 1 -1 GRIP1 HGNC HGNC:18708 protein_coding YES CCDS41807.1 ENSP00000381098 Q9Y3R0 UPI0000DD8148 NM_021150.3 deleterious(0) 17/24 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF39,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs762131350 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 66392790 66392790 C A 1 0 0 0 0 1 0 0 0 6668 884 31 1 1 GRIP1 12 66392790 Missense_Mutation SNP C 11LU022_T 1522116 66392790 66882519 663 1301 CAND1 0 . GRCh38 12 67305715 67305715 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2047G>T p.Asp683Tyr p.D683Y ENST00000545606 10/15 117 102 15 153 153 0 strelka-varscan-mutect CAND1,missense_variant,p.Asp683Tyr,ENST00000545606,NM_018448.4;CAND1,missense_variant,p.Asp223Tyr,ENST00000544619,;CAND1,intron_variant,,ENST00000540319,; T ENST00000545606 Transcript missense_variant 2484/11251 2047/3693 683/1230 D/Y Gac/Tac 1 1 CAND1 HGNC HGNC:30688 protein_coding YES CCDS8977.1 ENSP00000442318 Q86VP6 UPI0000037CC5 NM_018448.4 deleterious(0.04) 10/15 hmmpanther:PTHR12696,hmmpanther:PTHR12696:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 67305715 67305715 G T 1 0 0 0 0 1 0 0 0 2308 1290 45 2 2 CAND1 12 67305715 Missense_Mutation SNP G 11LU022_T 912925 67305715 65969594 664 1302 RAB3IP 0 . GRCh38 12 69795215 69795215 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.807G>T p.Gln269His p.Q269H ENST00000550536 6/11 192 174 18 225 225 0 strelka-varscan-mutect RAB3IP,missense_variant,p.Gln269His,ENST00000550536,NM_175623.3;RAB3IP,missense_variant,p.Gln253His,ENST00000247833,NM_022456.4;RAB3IP,missense_variant,p.Gln47His,ENST00000551641,NM_001024647.3;RAB3IP,missense_variant,p.Gln47His,ENST00000553099,NM_001278402.1;RAB3IP,missense_variant,p.Gln253His,ENST00000378815,;RAB3IP,missense_variant,p.Gln269His,ENST00000362025,NM_175625.3;RAB3IP,missense_variant,p.Gln253His,ENST00000483530,NM_175624.3;RAB3IP,missense_variant,p.Gln143His,ENST00000550647,;RAB3IP,upstream_gene_variant,,ENST00000526994,;RAB3IP,upstream_gene_variant,,ENST00000550847,;RAB3IP,missense_variant,p.Gln269His,ENST00000378809,;RAB3IP,missense_variant,p.Gln269His,ENST00000552199,;RAB3IP,missense_variant,p.Gln253His,ENST00000417413,;RAB3IP,3_prime_UTR_variant,,ENST00000547591,; T ENST00000550536 Transcript missense_variant 1264/9646 807/1431 269/476 Q/H caG/caT 1 1 RAB3IP HGNC HGNC:16508 protein_coding YES CCDS8993.1 ENSP00000447300 Q96QF0 UPI000006EB02 NM_175623.3 tolerated(0.17) 6/11 hmmpanther:PTHR14430,hmmpanther:PTHR14430:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 69795215 69795215 G T 1 0 0 0 0 1 0 0 0 13097 991 35 2 2 RAB3IP 12 69795215 Missense_Mutation SNP G 11LU022_T 2489500 69795215 63480094 665 1303 NAV3 0 . GRCh38 12 78006500 78006500 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.962C>G p.Ser321Cys p.S321C ENST00000397909 8/40 187 163 24 176 176 0 strelka-varscan-mutect NAV3,missense_variant,p.Ser321Cys,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Ser321Cys,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Ser321Cys,ENST00000549464,;NAV3,missense_variant,p.Ser264Cys,ENST00000550042,;NAV3,missense_variant,p.Ser145Cys,ENST00000550503,;NAV3,non_coding_transcript_exon_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,; G ENST00000397909 Transcript missense_variant 1135/9821 962/7158 321/2385 S/C tCt/tGt 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 8/40 Low_complexity_(Seg):seg,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 78006500 78006500 C G 1 0 0 0 0 1 0 0 0 10194 913 32 4 4 NAV3 12 78006500 Missense_Mutation SNP C 11LU022_T 8211285 78006500 55268809 666 1304 NAV3 0 . GRCh38 12 78051011 78051011 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.2380G>A p.Gly794Arg p.G794R ENST00000397909 11/40 245 226 19 245 245 0 strelka-varscan-mutect NAV3,missense_variant,p.Gly794Arg,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Gly794Arg,ENST00000536525,NM_014903.5;NAV3,downstream_gene_variant,,ENST00000549464,;RP11-136F16.1,downstream_gene_variant,,ENST00000549103,; A ENST00000397909 Transcript missense_variant 2553/9821 2380/7158 794/2385 G/R Gga/Aga 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0.02) 11/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 78051011 78051011 G A 1 0 0 0 0 1 0 0 0 10194 1233 43 3 3 NAV3 12 78051011 Missense_Mutation SNP G 11LU022_T 44511 78051011 55224298 667 1305 OTOGL 0 . GRCh38 12 80219862 80219862 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.257G>T p.Gly86Val p.G86V ENST00000458043 5/58 181 156 25 214 214 0 strelka-varscan-mutect OTOGL,missense_variant,p.Gly86Val,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Gly86Val,ENST00000547103,; T ENST00000458043 Transcript missense_variant 263/8083 257/7035 86/2344 G/V gGa/gTa 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0.01) 5/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 80219862 80219862 G T 1 0 0 0 0 1 0 0 0 11371 1174 41 2 2 OTOGL 12 80219862 Missense_Mutation SNP G 11LU022_T 2168851 80219862 53055447 668 1306 OTOGL 0 . GRCh38 12 80353392 80353392 + Silent SNP G G C novel 11LU022_T 11LU022_N G G c.5448G>C p.= p.L1816L ENST00000458043 45/58 112 89 23 129 129 0 strelka-varscan-mutect OTOGL,synonymous_variant,p.=,ENST00000458043,NM_173591.3;OTOGL,synonymous_variant,p.=,ENST00000547103,;OTOGL,synonymous_variant,p.=,ENST00000298820,;OTOGL,upstream_gene_variant,,ENST00000550182,;OTOGL,upstream_gene_variant,,ENST00000546620,;OTOGL,upstream_gene_variant,,ENST00000551340,; C ENST00000458043 Transcript synonymous_variant 5454/8083 5448/7035 1816/2344 L ctG/ctC 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 45/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Pfam_domain:PF01826,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 LOW 1 SNV 5 1 PASS rs1303304737 . 0 206 0 3 0 0 0 0 -20 0.9999965 1 1 1 0 C 2 2 3 80353392 80353392 G C 1 0 0 0 0 0 0 0 1 11371 1277 45 4 4 OTOGL 12 80353392 Silent SNP G 11LU022_T 133530 80353392 52921917 669 1307 MYF6 0 . GRCh38 12 80708099 80708099 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.380G>C p.Arg127Thr p.R127T ENST00000228641 1/3 305 273 32 373 373 0 strelka-varscan-mutect MYF6,missense_variant,p.Arg127Thr,ENST00000228641,NM_002469.2; C ENST00000228641 Transcript missense_variant 602/1465 380/729 127/242 R/T aGg/aCg 1 1 MYF6 HGNC HGNC:7566 protein_coding YES CCDS9019.1 ENSP00000228641 P23409 UPI0000001050 NM_002469.2 deleterious(0) 1/3 PROSITE_profiles:PS50888,hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4,Gene3D:4.10.280.10,Pfam_domain:PF00010,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 80708099 80708099 G C 1 0 0 0 0 1 0 0 0 10028 1000 35 4 4 MYF6 12 80708099 Missense_Mutation SNP G 11LU022_T 354707 80708099 52567210 670 1308 PPFIA2 0 . GRCh38 12 81358209 81358209 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1646T>C p.Leu549Pro p.L549P ENST00000549396 16/33 217 180 37 199 199 0 strelka-varscan-mutect PPFIA2,missense_variant,p.Leu450Pro,ENST00000333447,NM_001220478.2;PPFIA2,missense_variant,p.Leu549Pro,ENST00000550584,NM_001220473.2;PPFIA2,missense_variant,p.Leu549Pro,ENST00000549396,NM_003625.4;PPFIA2,missense_variant,p.Leu531Pro,ENST00000549325,NM_001220474.2;PPFIA2,missense_variant,p.Leu549Pro,ENST00000548586,NM_001220476.2;PPFIA2,missense_variant,p.Leu549Pro,ENST00000552948,NM_001220475.2;PPFIA2,missense_variant,p.Leu475Pro,ENST00000407050,NM_001220477.2;PPFIA2,missense_variant,p.Leu396Pro,ENST00000550359,NM_001282536.1;PPFIA2,missense_variant,p.Leu450Pro,ENST00000443686,;PPFIA2,missense_variant,p.Leu116Pro,ENST00000541570,NM_001220479.2;PPFIA2,missense_variant,p.Leu130Pro,ENST00000553058,;PPFIA2,missense_variant,p.Leu116Pro,ENST00000548670,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,NM_001220480.2;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,; G ENST00000549396 Transcript missense_variant 1807/5363 1646/3774 549/1257 L/P cTa/cCa 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 tolerated(0.11) 16/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 81358209 81358209 A G 1 0 0 0 0 1 0 0 0 12419 420 15 5 5 PPFIA2 12 81358209 Missense_Mutation SNP A 11LU022_T 650110 81358209 51917100 671 1309 SLC6A15 0 . GRCh38 12 84891887 84891887 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.234T>A p.= p.S78S ENST00000266682 2/12 143 112 31 147 147 0 strelka-varscan-mutect SLC6A15,synonymous_variant,p.=,ENST00000266682,NM_182767.5;SLC6A15,synonymous_variant,p.=,ENST00000450363,NM_018057.6;SLC6A15,synonymous_variant,p.=,ENST00000549540,;SLC6A15,intron_variant,,ENST00000552192,NM_001146335.2;SLC6A15,intron_variant,,ENST00000551612,;SLC6A15,downstream_gene_variant,,ENST00000551010,;SLC6A15,intron_variant,,ENST00000551388,;SLC6A15,intron_variant,,ENST00000547240,; T ENST00000266682 Transcript synonymous_variant 776/4879 234/2193 78/730 S tcT/tcA 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 2/12 Superfamily_domains:0053687,Pfam_domain:PF00209,Prints_domain:PR00176,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 84891887 84891887 A T 1 0 0 0 0 0 0 0 1 14961 175 7 4 4 SLC6A15 12 84891887 Silent SNP A 11LU022_T 3533678 84891887 48383422 672 1310 LRRIQ1 0 . GRCh38 12 85229612 85229612 + Frame_Shift_Del DEL G G - 11LU022_T 11LU022_N G G c.4921delG p.Val1641PhefsTer10 p.V1641Ffs*10 ENST00000393217 25/27 157 121 36 206 206 0 sindel-varindel-pindel LRRIQ1,frameshift_variant,p.Val1641PhefsTer10,ENST00000393217,NM_001079910.1;LRRIQ1,frameshift_variant,p.Val62PhefsTer10,ENST00000526363,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000528777,; - ENST00000393217 Transcript frameshift_variant 4979/5394 4918/5169 1640/1722 G/X Ggg/gg COSM375589 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 25/27 1 HIGH 1 deletion 5 3 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 85229612 85229612 G - 1 0 1 0 1 0 0 0 0 8935 1348 47 0 0 LRRIQ1 12 85229612 Frame_Shift_Del DEL G 11LU022_T 337725 85229612 48045697 673 1311 NEDD1 0 . GRCh38 12 96935122 96935122 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.657C>T p.= p.I219I ENST00000557644 6/15 313 280 33 331 331 0 strelka-varscan-mutect NEDD1,synonymous_variant,p.=,ENST00000266742,NM_152905.3;NEDD1,synonymous_variant,p.=,ENST00000429527,NM_001135176.1;NEDD1,synonymous_variant,p.=,ENST00000457368,;NEDD1,synonymous_variant,p.=,ENST00000411739,NM_001135177.1;NEDD1,synonymous_variant,p.=,ENST00000557644,NM_001135175.1;NEDD1,synonymous_variant,p.=,ENST00000553609,;NEDD1,downstream_gene_variant,,ENST00000557478,;NEDD1,non_coding_transcript_exon_variant,,ENST00000555114,;NEDD1,non_coding_transcript_exon_variant,,ENST00000557454,;NEDD1,intron_variant,,ENST00000555806,; T ENST00000557644 Transcript synonymous_variant 803/2367 657/2004 219/667 I atC/atT 1 1 NEDD1 HGNC HGNC:7723 protein_coding YES CCDS44955.1 ENSP00000451211 Q8NHV4 UPI000004D249 NM_001135175.1 6/15 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF450,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 96935122 96935122 C T 1 0 0 0 0 0 0 0 1 10337 903 32 3 3 NEDD1 12 96935122 Silent SNP C 11LU022_T 11705510 96935122 36340187 674 1312 UHRF1BP1L 0 . GRCh38 12 100057674 100057674 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.3321C>T p.= p.S1107S ENST00000279907 15/21 177 156 21 240 240 0 strelka-varscan-mutect UHRF1BP1L,synonymous_variant,p.=,ENST00000279907,NM_015054.1;UHRF1BP1L,synonymous_variant,p.=,ENST00000545232,; A ENST00000279907 Transcript synonymous_variant 3534/5168 3321/4395 1107/1464 S agC/agT 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 15/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 100057674 100057674 G A 1 0 0 0 0 0 0 0 1 17493 962 34 3 3 UHRF1BP1L 12 100057674 Silent SNP G 11LU022_T 3122552 100057674 33217635 675 1313 OAS3 0 . GRCh38 12 112969638 112969638 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.3135A>T p.= p.T1045T ENST00000228928 15/16 222 162 60 256 256 0 strelka-varscan-mutect OAS3,synonymous_variant,p.=,ENST00000228928,NM_006187.3;OAS3,downstream_gene_variant,,ENST00000546973,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS3,non_coding_transcript_exon_variant,,ENST00000549918,; T ENST00000228928 Transcript synonymous_variant 3314/6719 3135/3264 1045/1087 T acA/acT 1 1 OAS3 HGNC HGNC:8088 protein_coding YES CCDS44981.1 ENSP00000228928 Q9Y6K5 UPI000034ECD3 NM_006187.3 15/16 hmmpanther:PTHR11258:SF4,hmmpanther:PTHR11258,PROSITE_patterns:PS00833,Gene3D:1px5A02,Pfam_domain:PF10421,Superfamily_domains:SSF81631 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 112969638 112969638 A T 1 0 0 0 0 0 0 0 1 10880 175 7 4 4 OAS3 12 112969638 Silent SNP A 11LU022_T 12911964 112969638 20305671 676 1314 NOS1 0 . GRCh38 12 117242655 117242655 + Missense_Mutation SNP G G T rs758653629 11LU022_T 11LU022_N G G c.3115C>A p.Arg1039Ser p.R1039S ENST00000618760 21/30 183 159 24 239 239 0 strelka-varscan-mutect NOS1,missense_variant,p.Arg1039Ser,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Arg1005Ser,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Arg1039Ser,ENST00000338101,;NOS1,missense_variant,p.Arg1004Ser,ENST00000344089,;TCEB1P32,downstream_gene_variant,,ENST00000548625,; T ENST00000618760 Transcript missense_variant 3826/12283 3115/4407 1039/1468 R/S Cgt/Agt rs758653629,COSM4641624 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 tolerated(0.11) 21/30 PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Pfam_domain:PF00667,Gene3D:2.40.30.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs758653629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 117242655 117242655 G T 1 0 0 0 0 1 0 0 0 10586 1116 39 1 1 NOS1 12 117242655 Missense_Mutation SNP G 11LU022_T 4273017 117242655 16032654 677 1315 GCN1 0 . GRCh38 12 120137954 120137954 + Missense_Mutation SNP G G C 11LU022_T 11LU022_N G G c.6340C>G p.Pro2114Ala p.P2114A ENST00000300648 48/58 165 122 43 201 201 0 strelka-varscan-mutect GCN1,missense_variant,p.Pro2114Ala,ENST00000300648,NM_006836.1;GCN1,upstream_gene_variant,,ENST00000549815,;GCN1,downstream_gene_variant,,ENST00000547263,; C ENST00000300648 Transcript missense_variant 6353/8675 6340/8016 2114/2671 P/A Cca/Gca COSM5613499 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 deleterious(0) 48/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 120137954 120137954 G C 1 0 0 0 0 1 0 0 0 6169 1232 43 4 4 GCN1 12 120137954 Missense_Mutation SNP G 11LU022_T 2895299 120137954 13137355 678 1316 P2RX7 0 . GRCh38 12 121166124 121166124 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.681C>T p.= p.P227P ENST00000328963 7/13 148 138 10 174 174 0 strelka-varscan-mutect P2RX7,synonymous_variant,p.=,ENST00000328963,NM_002562.5;P2RX7,synonymous_variant,p.=,ENST00000535250,;P2RX7,synonymous_variant,p.=,ENST00000541564,;P2RX7,3_prime_UTR_variant,,ENST00000261826,;P2RX7,3_prime_UTR_variant,,ENST00000537312,;P2RX7,3_prime_UTR_variant,,ENST00000539606,;P2RX7,3_prime_UTR_variant,,ENST00000538011,;P2RX7,3_prime_UTR_variant,,ENST00000541716,;P2RX7,3_prime_UTR_variant,,ENST00000541022,;P2RX7,3_prime_UTR_variant,,ENST00000545434,;P2RX7,non_coding_transcript_exon_variant,,ENST00000539695,;P2RX7,intron_variant,,ENST00000535600,;P2RX7,downstream_gene_variant,,ENST00000535928,; T ENST00000328963 Transcript synonymous_variant 824/5161 681/1788 227/595 P ccC/ccT 1 1 P2RX7 HGNC HGNC:8537 protein_coding YES CCDS9213.1 ENSP00000330696 Q99572 UPI0001DB9556 NM_002562.5 7/13 hmmpanther:PTHR10125,hmmpanther:PTHR10125:SF13,Pfam_domain:PF00864,TIGRFAM_domain:TIGR00863,Gene3D:3h9vA02 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 121166124 121166124 C T 1 0 0 0 0 0 0 0 1 11418 581 21 3 3 P2RX7 12 121166124 Silent SNP C 11LU022_T 1028170 121166124 12109185 679 1317 DNAH10 0 . GRCh38 12 123918768 123918768 + Silent SNP C C A 11LU022_T 11LU022_N C C c.10971C>A p.= p.I3657I ENST00000638045 64/78 73 54 19 72 72 0 varscan-mutect DNAH10,synonymous_variant,p.=,ENST00000409039,;DNAH10,synonymous_variant,p.=,ENST00000638045,NM_207437.3;DNAH10,downstream_gene_variant,,ENST00000540041,;CCDC92,non_coding_transcript_exon_variant,,ENST00000542348,;CCDC92,downstream_gene_variant,,ENST00000544798,; A ENST00000638045 Transcript synonymous_variant 10996/13678 10971/13416 3657/4471 I atC/atA COSM1718630,COSM1718631 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 64/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676 1,1 LOW 1 SNV 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 123918768 123918768 C A 1 0 0 0 0 0 0 0 1 4411 845 30 2 2 DNAH10 12 123918768 Silent SNP C 11LU022_T 2752644 123918768 9356541 680 1318 PIWIL1 0 . GRCh38 12 130357064 130357064 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1551A>T p.Lys517Asn p.K517N ENST00000245255 13/21 79 65 14 113 113 0 strelka-varscan-mutect PIWIL1,missense_variant,p.Lys517Asn,ENST00000245255,NM_004764.4,NM_001190971.1; T ENST00000245255 Transcript missense_variant 1823/3897 1551/2586 517/861 K/N aaA/aaT 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 deleterious(0) 13/21 Gene3D:3.40.50.2300,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF46,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 130357064 130357064 A T 1 0 0 0 0 1 0 0 0 12053 69 3 4 4 PIWIL1 12 130357064 Missense_Mutation SNP A 11LU022_T 6438296 130357064 2918245 681 1319 ANHX 0 . GRCh38 12 133226349 133226349 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.808G>T p.Asp270Tyr p.D270Y ENST00000545940 5/8 270 235 35 352 352 0 strelka-varscan-mutect ANHX,missense_variant,p.Asp270Tyr,ENST00000545940,;ANHX,missense_variant,p.Asp270Tyr,ENST00000419717,NM_001191054.1; A ENST00000545940 Transcript missense_variant 2547/3452 808/1140 270/379 D/Y Gat/Tat 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 deleterious(0.01) 5/8 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 133226349 133226349 C A 1 0 0 0 0 1 0 0 0 719 913 32 2 2 ANHX 12 133226349 Missense_Mutation SNP C 11LU022_T 2869285 133226349 48960 682 1320 AMER2 0 . GRCh38 13 25170339 25170339 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.1281C>T p.= p.S427S ENST00000515384 1/1 97 65 32 194 193 1 strelka-varscan-mutect AMER2,synonymous_variant,p.=,ENST00000357816,NM_199138.2;AMER2,synonymous_variant,p.=,ENST00000515384,NM_152704.3;LINC00463,downstream_gene_variant,,ENST00000413501,; A ENST00000515384 Transcript synonymous_variant 1949/3197 1281/2016 427/671 S agC/agT 1 -1 AMER2 HGNC HGNC:26360 protein_coding YES CCDS53859.1 ENSP00000426528 Q8N7J2 UPI0000231C76 NM_152704.3 1/1 hmmpanther:PTHR22237:SF1,hmmpanther:PTHR22237,Pfam_domain:PF09422 LOW SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 25170339 25170339 G A 1 0 0 0 0 0 0 0 1 668 1194 42 3 3 AMER2 13 25170339 Silent SNP G 11LU022_T 25170339 89193989 683 1321 CDK8 0 . GRCh38 13 26353880 26353880 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.456G>T p.Leu152Phe p.L152F ENST00000381527 4/13 190 146 44 241 241 0 strelka-varscan-mutect CDK8,missense_variant,p.Leu152Phe,ENST00000381527,NM_001318368.1,NM_001260.1;CDK8,missense_variant,p.Leu152Phe,ENST00000536792,; T ENST00000381527 Transcript missense_variant,splice_region_variant 959/3055 456/1395 152/464 L/F ttG/ttT 1 1 CDK8 HGNC HGNC:1779 protein_coding YES CCDS9317.1 ENSP00000370938 P49336 UPI000002E531 NM_001318368.1,NM_001260.1 deleterious(0.02) 4/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF131,PROSITE_patterns:PS00108,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 26353880 26353880 G T 1 0 0 0 0 1 0 0 0 2854 1362 47 2 2 CDK8 13 26353880 Missense_Mutation SNP G 11LU022_T 1183541 26353880 88010448 684 1322 FLT3 0 . GRCh38 13 28028226 28028226 + Nonsense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.2005G>T p.Gly669Ter p.G669* ENST00000241453 16/24 169 125 44 225 225 0 strelka-varscan-mutect FLT3,stop_gained,p.Gly669Ter,ENST00000241453,NM_004119.2;FLT3,stop_gained,p.Gly669Ter,ENST00000380987,; A ENST00000241453 Transcript stop_gained 2087/3842 2005/2982 669/993 G/* Gga/Tga COSM4533690 1 -1 FLT3 HGNC HGNC:3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 16/24 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF356,PROSITE_patterns:PS00240,Pfam_domain:PF07714,Gene3D:3.30.200.20,SMART_domains:SM00219,Superfamily_domains:SSF56112 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 28028226 28028226 C A 1 0 0 0 0 0 1 0 0 5798 632 22 2 2 FLT3 13 28028226 Nonsense_Mutation SNP C 11LU022_T 1674346 28028226 86336102 685 1323 MTUS2 0 . GRCh38 13 29480218 29480218 + Nonsense_Mutation SNP G G T rs776367111 11LU022_T 11LU022_N G G c.3283G>T p.Glu1095Ter p.E1095* ENST00000612955 10/16 133 92 41 153 153 0 strelka-varscan-mutect MTUS2,stop_gained,p.Glu1095Ter,ENST00000612955,NM_001033602.2;MTUS2,stop_gained,p.Glu64Ter,ENST00000380808,NM_015233.5;MTUS2,5_prime_UTR_variant,,ENST00000542829,;MTUS2-AS1,intron_variant,,ENST00000323380,;MTUS2-AS1,intron_variant,,ENST00000587588,;MTUS2-AS1,downstream_gene_variant,,ENST00000626029,; T ENST00000612955 Transcript stop_gained 3832/7430 3283/4140 1095/1379 E/* Gag/Tag rs776367111 1 1 MTUS2 HGNC HGNC:20595 protein_coding YES CCDS45022.1 ENSP00000483729 J3KQA9 UPI0000F734AC NM_001033602.2 10/16 Low_complexity_(Seg):seg,hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200,Coiled-coils_(Ncoils):Coil HIGH 1 SNV 5 1 PASS rs776367111 . 0 206 0 4 0 0 0 0 -20 0.9999797 1 1 1 0 T 4 4 3 29480218 29480218 G T 1 0 0 0 0 0 1 0 0 9964 1059 37 1 1 MTUS2 13 29480218 Nonsense_Mutation SNP G 11LU022_T 1451992 29480218 84884110 686 1324 NBEA 0 . GRCh38 13 35109363 35109363 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1754C>A p.Ser585Tyr p.S585Y ENST00000400445 12/58 96 73 23 122 122 0 strelka-varscan-mutect NBEA,missense_variant,p.Ser585Tyr,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Ser585Tyr,ENST00000310336,;NBEA,missense_variant,p.Ser585Tyr,ENST00000629018,;NBEA,missense_variant,p.Ser585Tyr,ENST00000379939,; A ENST00000400445 Transcript missense_variant 2288/11119 1754/8841 585/2946 S/Y tCt/tAt 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 tolerated(0.27) 12/58 Pfam_domain:PF15787,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF62,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 35109363 35109363 C A 1 0 0 0 0 1 0 0 0 10198 913 32 2 2 NBEA 13 35109363 Missense_Mutation SNP C 11LU022_T 5629145 35109363 79254965 687 1325 POSTN 0 . GRCh38 13 37598657 37598657 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.70C>A p.His24Asn p.H24N ENST00000379747 1/23 111 76 35 170 170 0 strelka-varscan-mutect POSTN,missense_variant,p.His24Asn,ENST00000379747,NM_006475.2;POSTN,missense_variant,p.His24Asn,ENST00000541179,NM_001135936.1,NM_001135935.1;POSTN,missense_variant,p.His24Asn,ENST00000379749,;POSTN,missense_variant,p.His24Asn,ENST00000379743,NM_001286665.1;POSTN,missense_variant,p.His24Asn,ENST00000541481,NM_001286666.1,NM_001286667.1;POSTN,missense_variant,p.His24Asn,ENST00000379742,NM_001135934.1; T ENST00000379747 Transcript missense_variant 188/3373 70/2511 24/836 H/N Cat/Aat COSM4506062 1 -1 POSTN HGNC HGNC:16953 protein_coding YES CCDS9364.1 ENSP00000369071 Q15063 A0A024RDS2 UPI000013CEB8 NM_006475.2 tolerated(0.23) 1/23 PIRSF_domain:PIRSF016553,hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF12 1 MODERATE 1 SNV 1 1 1 PASS rs996691431 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 37598657 37598657 G T 1 0 0 0 0 1 0 0 0 12373 1290 45 2 2 POSTN 13 37598657 Missense_Mutation SNP G 11LU022_T 2489294 37598657 76765671 688 1326 SPERT 0 . GRCh38 13 45713231 45713231 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.206C>T p.Pro69Leu p.P69L ENST00000310521 3/3 80 55 25 85 85 0 strelka-varscan-mutect SPERT,missense_variant,p.Pro33Leu,ENST00000378966,;SPERT,missense_variant,p.Pro69Leu,ENST00000310521,NM_152719.2;SPERT,missense_variant,p.Pro33Leu,ENST00000610924,NM_001286342.1;SPERT,missense_variant,p.Pro42Leu,ENST00000533564,; T ENST00000310521 Transcript missense_variant 286/1613 206/1347 69/448 P/L cCt/cTt 1 1 SPERT HGNC HGNC:30720 protein_coding YES CCDS9399.1 ENSP00000309189 Q8NA61 A0A140VJV5 UPI0000070F5F NM_152719.2 deleterious_low_confidence(0) 3/3 hmmpanther:PTHR21533,hmmpanther:PTHR21533:SF13 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 45713231 45713231 C T 1 0 0 0 0 1 0 0 0 15390 681 24 3 3 SPERT 13 45713231 Missense_Mutation SNP C 11LU022_T 8114574 45713231 68651097 689 1327 RB1 0 . GRCh38 13 48381444 48381444 + Splice_Site SNP G G T rs587778857 11LU022_T 11LU022_N G G c.1695+1G>T p.X565_splice ENST00000267163 123 94 29 123 123 0 strelka-varscan-mutect RB1,splice_donor_variant,,ENST00000267163,NM_000321.2; T ENST00000267163 Transcript splice_donor_variant -/4840 1695/2787 565/928 rs587778857,CS051701,COSM1756815,COSM254916,COSM5027769,COSM5027770 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 17/26 pathogenic 0,0,1,1,1,1 HIGH 1 SNV 1 1,1,1,1,1,1 1 PASS rs587778857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 3 48381444 48381444 G T 1 0 0 0 0 0 0 1 0 13259 1043 36 2 2 RB1 13 48381444 Splice_Site SNP G 11LU022_T 2668213 48381444 65982884 690 1328 MYCBP2 0 . GRCh38 13 77088837 77088837 + Missense_Mutation SNP T T A 11LU022_T 11LU022_N T T c.10606A>T p.Met3536Leu p.M3536L ENST00000544440 61/83 156 95 61 162 162 0 strelka-varscan-mutect MYCBP2,missense_variant,p.Met3536Leu,ENST00000357337,NM_015057.4;MYCBP2,missense_variant,p.Met3536Leu,ENST00000544440,;RP11-226E21.4,intron_variant,,ENST00000638101,;MYCBP2,upstream_gene_variant,,ENST00000429715,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2-AS1,intron_variant,,ENST00000629771,;MYCBP2-AS1,intron_variant,,ENST00000627409,;MYCBP2-AS1,intron_variant,,ENST00000630676,;MYCBP2-AS1,downstream_gene_variant,,ENST00000422231,;MYCBP2-AS1,downstream_gene_variant,,ENST00000450627,;MYCBP2-AS1,downstream_gene_variant,,ENST00000448470,;MYCBP2,downstream_gene_variant,,ENST00000485061,;RP11-226E21.4,intron_variant,,ENST00000637192,; A ENST00000544440 Transcript missense_variant 10624/14664 10606/13923 3536/4640 M/L Atg/Ttg COSM1607226,COSM1607227 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 tolerated(0.17) 61/83 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1219177871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 77088837 77088837 T A 1 0 0 0 0 1 0 0 0 10018 1420 49 4 4 MYCBP2 13 77088837 Missense_Mutation SNP T 11LU022_T 28707393 77088837 37275491 691 1329 DZIP1 0 . GRCh38 13 95593959 95593959 + Silent SNP G G C novel 11LU022_T 11LU022_N G G c.1665C>G p.= p.T555T ENST00000347108 14/21 87 57 30 146 146 0 strelka-varscan-mutect DZIP1,synonymous_variant,p.=,ENST00000361396,NM_014934.4;DZIP1,synonymous_variant,p.=,ENST00000347108,;DZIP1,synonymous_variant,p.=,ENST00000361156,;DZIP1,synonymous_variant,p.=,ENST00000376829,NM_198968.3; C ENST00000347108 Transcript synonymous_variant 2098/7068 1665/2604 555/867 T acC/acG 1 -1 DZIP1 HGNC HGNC:20908 protein_coding YES CCDS9478.1 ENSP00000257312 Q86YF9 UPI000000D9B8 14/21 hmmpanther:PTHR21502,hmmpanther:PTHR21502:SF5 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 95593959 95593959 G C 1 0 0 0 0 0 0 0 1 4687 987 35 4 4 DZIP1 13 95593959 Silent SNP G 11LU022_T 18505122 95593959 18770369 692 1330 CLYBL 0 . GRCh38 13 99866283 99866283 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.678G>T p.= p.R226R ENST00000376355 6/8 291 191 100 291 291 0 strelka-varscan-mutect CLYBL,synonymous_variant,p.=,ENST00000376355,;CLYBL,synonymous_variant,p.=,ENST00000339105,NM_206808.3;CLYBL,synonymous_variant,p.=,ENST00000376354,;CLYBL,downstream_gene_variant,,ENST00000416504,;CLYBL,downstream_gene_variant,,ENST00000443887,;CLYBL,upstream_gene_variant,,ENST00000425186,;CLYBL,upstream_gene_variant,,ENST00000419700,; T ENST00000376355 Transcript synonymous_variant 705/6771 678/1023 226/340 R cgG/cgT 1 1 CLYBL HGNC HGNC:18355 protein_coding YES CCDS32002.1 ENSP00000365533 Q8N0X4 UPI0000071ADE 6/8 hmmpanther:PTHR11105:SF0,hmmpanther:PTHR11105,PIRSF_domain:PIRSF015582,Gene3D:3.20.20.60,Pfam_domain:PF03328,Superfamily_domains:SSF51621 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 99866283 99866283 G T 1 0 0 0 0 0 0 0 1 3346 1190 42 2 2 CLYBL 13 99866283 Silent SNP G 11LU022_T 4272324 99866283 14498045 693 1331 ZIC5 0 . GRCh38 13 99971120 99971120 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.556G>T p.Gly186Cys p.G186C ENST00000267294 1/2 147 102 45 213 212 1 strelka-varscan-mutect ZIC5,missense_variant,p.Gly186Cys,ENST00000267294,NM_033132.3; A ENST00000267294 Transcript missense_variant 790/4639 556/1992 186/663 G/C Ggc/Tgc 1 -1 ZIC5 HGNC HGNC:20322 protein_coding YES CCDS9494.2 ENSP00000267294 Q96T25 UPI0000458928 NM_033132.3 deleterious_low_confidence(0.03) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR19818 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 99971120 99971120 C A 1 0 0 0 0 1 0 0 0 18260 652 23 1 1 ZIC5 13 99971120 Missense_Mutation SNP C 11LU022_T 104837 99971120 14393208 694 1332 CCDC168 0 . GRCh38 13 102732325 102732325 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.18372G>T p.Glu6124Asp p.E6124D ENST00000322527 4/4 126 73 53 145 143 2 strelka-varscan-mutect CCDC168,missense_variant,p.Glu6124Asp,ENST00000322527,NM_001146197.1; A ENST00000322527 Transcript missense_variant 18510/21466 18372/21246 6124/7081 E/D gaG/gaT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.01) 4/4 hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 102732325 102732325 C A 1 0 0 0 0 1 0 0 0 2484 564 20 2 2 CCDC168 13 102732325 Missense_Mutation SNP C 11LU022_T 2761205 102732325 11632003 695 1333 COL4A1 0 . GRCh38 13 110174686 110174686 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.3262G>C p.Gly1088Arg p.G1088R ENST00000375820 38/52 421 272 149 578 578 0 strelka-varscan-mutect COL4A1,missense_variant,p.Gly1088Arg,ENST00000375820,NM_001845.5; G ENST00000375820 Transcript missense_variant 3384/6532 3262/5010 1088/1669 G/R Ggg/Cgg 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0) 38/52 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 110174686 110174686 C G 1 0 0 0 0 1 0 0 0 3478 594 21 4 4 COL4A1 13 110174686 Missense_Mutation SNP C 11LU022_T 7442361 110174686 4189642 696 1334 POTEM 0 . GRCh38 14 18976098 18976098 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.860T>A p.Val287Glu p.V287E ENST00000547889 4/11 37 18 19 30 30 0 strelka-varscan-mutect POTEM,missense_variant,p.Val287Glu,ENST00000547889,NM_001145442.1;RNU6-1239P,upstream_gene_variant,,ENST00000391310,;CTD-2311B13.5,downstream_gene_variant,,ENST00000613990,;POTEM,missense_variant,p.Val287Glu,ENST00000616847,;POTEM,3_prime_UTR_variant,,ENST00000552966,; A ENST00000547889 Transcript missense_variant 912/1817 860/1527 287/508 V/E gTg/gAg 1 1 POTEM HGNC HGNC:37096 protein_coding YES CCDS73609.1 ENSP00000448062 A6NI47 UPI00006C1407 NM_001145442.1 deleterious(0) 4/11 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 95 114 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 18976098 18976098 T A 1 0 0 0 0 1 0 0 0 12384 1696 59 4 4 POTEM 14 18976098 Missense_Mutation SNP T 11LU022_T 18976098 88067620 697 1335 OR4N2 0 . GRCh38 14 19828019 19828019 + Missense_Mutation SNP G G T rs200471583 11LU022_T 11LU022_N G G c.571G>T p.Asp191Tyr p.D191Y ENST00000315947 1/1 409 348 61 412 410 2 strelka-varscan-mutect OR4N2,missense_variant,p.Asp191Tyr,ENST00000315947,NM_001004723.2;OR4N2,downstream_gene_variant,,ENST00000557414,;OR4N2,downstream_gene_variant,,ENST00000557677,; T ENST00000315947 Transcript missense_variant 571/924 571/924 191/307 D/Y Gac/Tac rs200471583 1 1 OR4N2 HGNC HGNC:14742 protein_coding YES CCDS32022.1 ENSP00000319601 Q8NGD1 A0A126GVT2 UPI000004A5DF NM_001004723.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF439,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs200471583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 19828019 19828019 G T 1 0 0 0 0 1 0 0 0 11153 1058 37 1 1 OR4N2 14 19828019 Missense_Mutation SNP G 11LU022_T 851921 19828019 87215699 698 1336 TEP1 0 . GRCh38 14 20380943 20380943 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.4750C>G p.His1584Asp p.H1584D ENST00000262715 33/55 184 151 33 208 208 0 strelka-varscan-mutect TEP1,missense_variant,p.His1584Asp,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.His1476Asp,ENST00000556935,;TEP1,missense_variant,p.His927Asp,ENST00000555008,;TEP1,3_prime_UTR_variant,,ENST00000555727,;TEP1,3_prime_UTR_variant,,ENST00000557314,;TEP1,upstream_gene_variant,,ENST00000556488,;TEP1,upstream_gene_variant,,ENST00000471684,; C ENST00000262715 Transcript missense_variant 4791/10695 4750/7884 1584/2627 H/D Cat/Gat 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 deleterious(0.01) 33/55 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF448 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 20380943 20380943 G C 1 0 0 0 0 1 0 0 0 16175 1348 47 4 4 TEP1 14 20380943 Missense_Mutation SNP G 11LU022_T 552924 20380943 86662775 699 1337 TEP1 0 . GRCh38 14 20387906 20387906 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2683G>T p.Gly895Ter p.G895* ENST00000262715 18/55 101 80 21 158 157 1 strelka-varscan-mutect TEP1,stop_gained,p.Gly895Ter,ENST00000262715,NM_007110.4;TEP1,stop_gained,p.Gly787Ter,ENST00000556935,;TEP1,stop_gained,p.Gly895Ter,ENST00000555727,;TEP1,stop_gained,p.Gly245Ter,ENST00000555008,; A ENST00000262715 Transcript stop_gained,splice_region_variant 2724/10695 2683/7884 895/2627 G/* Gga/Tga 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 18/55 HIGH 1 SNV 1 1 PASS rs1168035545 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 20387906 20387906 C A 1 0 0 0 0 0 1 0 0 16175 695 24 2 2 TEP1 14 20387906 Nonsense_Mutation SNP C 11LU022_T 6963 20387906 86655812 700 1338 6 2 TEP1 0 . GRCh38 14 20387908 20387908 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.2681A>C p.Gln894Pro p.Q894P ENST00000262715 18/55 102 82 20 155 155 0 strelka-varscan-mutect TEP1,missense_variant,p.Gln894Pro,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Gln786Pro,ENST00000556935,;TEP1,missense_variant,p.Gln894Pro,ENST00000555727,;TEP1,missense_variant,p.Gln244Pro,ENST00000555008,; G ENST00000262715 Transcript missense_variant 2722/10695 2681/7884 894/2627 Q/P cAa/cCa 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 tolerated(0.12) 18/55 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 20387908 20387908 T G 1 0 0 0 0 1 0 0 0 16175 1826 63 5 5 TEP1 14 20387908 Missense_Mutation SNP T 11LU022_T 2 20387908 86655810 701 1339 6 2 OR6J1 0 . GRCh38 14 22633798 22633798 + Silent SNP T T C novel 11LU022_T 11LU022_N T T c.1014A>G p.= p.P338P ENST00000540461 1/1 63 52 11 55 55 0 strelka-varscan-mutect OR6J1,synonymous_variant,p.=,ENST00000540461,;AC243945.1,downstream_gene_variant,,ENST00000623775,; C ENST00000540461 Transcript synonymous_variant 1014/1044 1014/1044 338/347 P ccA/ccG 1 -1 OR6J1 HGNC HGNC:14707 protein_coding YES ENSP00000437629 Q8NGC5 UPI000462094B 1/1 LOW 1 SNV 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 22633798 22633798 T C 1 0 0 0 0 0 0 0 1 11270 1451 51 5 5 OR6J1 14 22633798 Silent SNP T 11LU022_T 2245890 22633798 84409920 702 1340 MYH7 0 . GRCh38 14 23424137 23424137 + Missense_Mutation SNP G G T rs727504407 11LU022_T 11LU022_N G G c.2692C>A p.Leu898Met p.L898M ENST00000355349 23/40 175 137 38 219 219 0 strelka-varscan-mutect MYH7,missense_variant,p.Leu898Met,ENST00000355349,NM_000257.3; T ENST00000355349 Transcript missense_variant 2855/6087 2692/5808 898/1935 L/M Ctg/Atg rs727504407 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 deleterious(0.01) 23/40 Gene3D:1.20.5.340,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,Superfamily_domains:SSF90257 uncertain_significance,likely_pathogenic MODERATE 1 SNV 1 1 1 PASS rs727504407 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 23424137 23424137 G T 1 0 0 0 0 1 0 0 0 10039 991 35 2 2 MYH7 14 23424137 Missense_Mutation SNP G 11LU022_T 790339 23424137 83619581 703 1341 NYNRIN 0 . GRCh38 14 24407949 24407949 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.279G>T p.= p.G93G ENST00000382554 3/9 242 184 58 276 276 0 strelka-varscan-mutect NYNRIN,synonymous_variant,p.=,ENST00000382554,NM_025081.2;NYNRIN,upstream_gene_variant,,ENST00000554505,; T ENST00000382554 Transcript synonymous_variant 597/7857 279/5697 93/1898 G ggG/ggT 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 3/9 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 24407949 24407949 G T 1 0 0 0 0 0 0 0 1 10874 1219 43 2 2 NYNRIN 14 24407949 Silent SNP G 11LU022_T 983812 24407949 82635769 704 1342 GZMH 0 . GRCh38 14 24607226 24607226 + Missense_Mutation SNP G G T rs149372387 11LU022_T 11LU022_N G G c.520C>A p.Arg174Ser p.R174S ENST00000216338 4/5 173 135 38 174 174 0 strelka-varscan-mutect GZMH,missense_variant,p.Arg174Ser,ENST00000216338,NM_001270780.1,NM_033423.4;GZMH,intron_variant,,ENST00000382548,NM_001270781.1;GZMH,intron_variant,,ENST00000557220,;RP11-104E19.1,intron_variant,,ENST00000557736,;RP11-104E19.1,intron_variant,,ENST00000555300,; T ENST00000216338 Transcript missense_variant 565/909 520/741 174/246 R/S Cgt/Agt rs149372387,COSM1515288 1 -1 GZMH HGNC HGNC:4710 protein_coding YES CCDS9632.1 ENSP00000216338 P20718 UPI00000012B3 NM_001270780.1,NM_033423.4 tolerated(1) 4/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF15,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs149372387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 24607226 24607226 G T 1 0 0 0 0 1 0 0 0 6799 1145 40 1 1 GZMH 14 24607226 Missense_Mutation SNP G 11LU022_T 199277 24607226 82436492 705 1343 NPAS3 0 . GRCh38 14 33800626 33800626 + Frame_Shift_Del DEL G G - novel 11LU022_T 11LU022_N G G c.2324delG p.Gly775AlafsTer35 p.G775Afs*35 ENST00000356141 12/12 69 55 14 86 86 0 sindel-varindel-pindel NPAS3,frameshift_variant,p.Gly743AlafsTer35,ENST00000346562,NM_022123.2;NPAS3,frameshift_variant,p.Gly745AlafsTer35,ENST00000548645,NM_001165893.1;NPAS3,frameshift_variant,p.Gly780AlafsTer35,ENST00000551492,;NPAS3,frameshift_variant,p.Gly775AlafsTer35,ENST00000356141,NM_001164749.1;NPAS3,frameshift_variant,p.Gly762AlafsTer35,ENST00000357798,NM_173159.2;NPAS3,frameshift_variant,p.Gly749AlafsTer35,ENST00000551634,; - ENST00000356141 Transcript frameshift_variant 2319/2802 2319/2802 773/933 A/X gcG/gc 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 HIGH 1 deletion 1 5 1 PASS . . 0 178 28 3 0 0 0 0 -19.99999 0.9451988 0 1 1 0 - 7 5 3 33800626 33800626 G - 1 0 1 0 1 0 0 0 0 10612 1103 39 0 0 NPAS3 14 33800626 Frame_Shift_Del DEL G 11LU022_T 9193400 33800626 73243092 706 1344 LRFN5 0 . GRCh38 14 41887080 41887080 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.455T>A p.Leu152Gln p.L152Q ENST00000298119 3/6 175 140 35 190 190 0 strelka-varscan-mutect LRFN5,missense_variant,p.Leu152Gln,ENST00000554171,;LRFN5,missense_variant,p.Leu152Gln,ENST00000298119,NM_152447.3;LRFN5,missense_variant,p.Leu152Gln,ENST00000554120,; A ENST00000298119 Transcript missense_variant 1644/3723 455/2160 152/719 L/Q cTg/cAg 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0) 3/6 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,Pfam_domain:PF13306,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 41887080 41887080 T A 1 0 0 0 0 1 0 0 0 8835 1580 55 4 4 LRFN5 14 41887080 Missense_Mutation SNP T 11LU022_T 8086454 41887080 65156638 707 1345 C14orf28 0 . GRCh38 14 44905498 44905498 + Missense_Mutation SNP C C A rs769577214 11LU022_T 11LU022_N C C c.881C>A p.Pro294Gln p.P294Q ENST00000325192 5/5 112 102 10 116 116 0 strelka-varscan-mutect C14orf28,missense_variant,p.Pro294Gln,ENST00000325192,NM_001017923.1;C14orf28,missense_variant,p.Pro264Gln,ENST00000557112,;RP11-857B24.5,intron_variant,,ENST00000555157,;C14orf28,downstream_gene_variant,,ENST00000553841,;C14orf28,non_coding_transcript_exon_variant,,ENST00000555826,; A ENST00000325192 Transcript missense_variant 1156/2915 881/933 294/310 P/Q cCa/cAa rs769577214,COSM395546 1 1 C14orf28 HGNC HGNC:19834 protein_coding YES CCDS32069.1 ENSP00000326846 Q4W4Y0 UPI000015FBE3 NM_001017923.1 deleterious_low_confidence(0) 5/5 hmmpanther:PTHR35350 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769577214 . 0 206 2 2 0 0 0 0 -15.13026 0.9999943 1 1 1 0 A 3 1 3 44905498 44905498 C A 1 0 0 0 0 1 0 0 0 1837 594 21 2 2 C14orf28 14 44905498 Missense_Mutation SNP C 11LU022_T 3018418 44905498 62138220 708 1346 PYGL 0 . GRCh38 14 50914816 50914816 + Splice_Site SNP C C A rs750567664 11LU022_T 11LU022_N C C c.1404-1G>T p.X468_splice ENST00000216392 417 327 90 428 428 0 strelka-varscan-mutect PYGL,splice_acceptor_variant,,ENST00000216392,NM_002863.4;PYGL,splice_acceptor_variant,,ENST00000532462,;PYGL,splice_acceptor_variant,,ENST00000544180,NM_001163940.1;RP11-218E20.5,downstream_gene_variant,,ENST00000557343,;PYGL,downstream_gene_variant,,ENST00000553872,;PYGL,upstream_gene_variant,,ENST00000532107,;PYGL,downstream_gene_variant,,ENST00000528757,; A ENST00000216392 Transcript splice_acceptor_variant -/3048 1404/2544 468/847 rs750567664 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 11/19 HIGH 1 SNV 1 1 PASS rs750567664 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 50914816 50914816 C A 1 0 0 0 0 0 0 1 0 13015 927 32 2 2 PYGL 14 50914816 Splice_Site SNP C 11LU022_T 6009318 50914816 56128902 709 1347 NID2 0 . GRCh38 14 52007808 52007808 + Splice_Site SNP A A G novel 11LU022_T 11LU022_N A A c.3880+2T>C p.X1294_splice ENST00000216286 179 152 27 197 196 1 strelka-mutect NID2,splice_donor_variant,,ENST00000216286,NM_007361.3;NID2,splice_donor_variant,,ENST00000617139,;NID2,splice_donor_variant,,ENST00000556572,;C14orf166,3_prime_UTR_variant,,ENST00000261700,NM_016039.2;C14orf166,downstream_gene_variant,,ENST00000556760,;C14orf166,downstream_gene_variant,,ENST00000553362,;NID2,splice_donor_variant,,ENST00000556686,;NID2,splice_donor_variant,,ENST00000555310,;NID2,downstream_gene_variant,,ENST00000553297,;C14orf166,downstream_gene_variant,,ENST00000553479,; G ENST00000216286 Transcript splice_donor_variant -/4811 3880/4128 1294/1375 1 -1 NID2 HGNC HGNC:13389 protein_coding YES CCDS9706.1 ENSP00000216286 Q14112 UPI000013C6E1 NM_007361.3 19/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 3 52007808 52007808 A G 1 0 0 0 0 0 0 1 0 10448 405 14 5 5 NID2 14 52007808 Splice_Site SNP A 11LU022_T 1092992 52007808 55035910 710 1348 ATG14 0 . GRCh38 14 55386096 55386096 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.410A>G p.Asn137Ser p.N137S ENST00000247178 5/10 57 46 11 68 68 0 strelka-varscan-mutect ATG14,missense_variant,p.Asn137Ser,ENST00000247178,NM_014924.4;ATG14,splice_region_variant,,ENST00000558189,; C ENST00000247178 Transcript missense_variant,splice_region_variant 446/4742 410/1479 137/492 N/S aAt/aGt 1 -1 ATG14 HGNC HGNC:19962 protein_coding YES CCDS32087.1 ENSP00000247178 Q6ZNE5 UPI00001FD5B2 NM_014924.4 tolerated(0.42) 5/10 Pfam_domain:PF10186,hmmpanther:PTHR13664,hmmpanther:PTHR13664:SF0 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 55386096 55386096 T C 1 0 0 0 0 1 0 0 0 1242 1449 50 5 5 ATG14 14 55386096 Missense_Mutation SNP T 11LU022_T 3378288 55386096 51657622 711 1349 SGPP1 0 . GRCh38 14 63686524 63686524 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.907G>T p.Gly303Trp p.G303W ENST00000247225 3/3 258 213 45 301 301 0 strelka-varscan-mutect SGPP1,missense_variant,p.Gly303Trp,ENST00000247225,NM_030791.3; A ENST00000247225 Transcript missense_variant 1002/3312 907/1326 303/441 G/W Ggg/Tgg 1 -1 SGPP1 HGNC HGNC:17720 protein_coding YES CCDS9760.1 ENSP00000247225 Q9BX95 UPI000006DEB2 NM_030791.3 deleterious(0) 3/3 hmmpanther:PTHR14969,hmmpanther:PTHR14969:SF16,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 63686524 63686524 C A 1 0 0 0 0 1 0 0 0 14477 623 22 2 2 SGPP1 14 63686524 Missense_Mutation SNP C 11LU022_T 8300428 63686524 43357194 712 1350 SYNE2 0 . GRCh38 14 64053149 64053149 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.9236G>T p.Ser3079Ile p.S3079I ENST00000358025 48/116 214 162 52 258 258 0 strelka-varscan-mutect SYNE2,missense_variant,p.Ser3079Ile,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Ser3079Ile,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Ser3112Ile,ENST00000357395,;SYNE2,missense_variant,p.Ser3112Ile,ENST00000554584,;SYNE2,downstream_gene_variant,,ENST00000557005,; T ENST00000358025 Transcript missense_variant 9448/21842 9236/20724 3079/6907 S/I aGc/aTc COSM5687436 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0.02) 48/116 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 64053149 64053149 G T 1 0 0 0 0 1 0 0 0 15838 971 34 2 2 SYNE2 14 64053149 Missense_Mutation SNP G 11LU022_T 366625 64053149 42990569 713 1351 MAP3K9 0 . GRCh38 14 70734420 70734420 + Silent SNP C C A rs555483404 11LU022_T 11LU022_N C C c.1992G>T p.= p.P664P ENST00000555993 10/13 234 176 58 251 250 1 strelka-varscan-mutect MAP3K9,synonymous_variant,p.=,ENST00000554752,NM_001284230.1;MAP3K9,synonymous_variant,p.=,ENST00000611979,NM_001284231.1;MAP3K9,synonymous_variant,p.=,ENST00000555993,NM_033141.3;MAP3K9,synonymous_variant,p.=,ENST00000381250,;MAP3K9,synonymous_variant,p.=,ENST00000553414,NM_001284232.1;MAP3K9,synonymous_variant,p.=,ENST00000554146,; A ENST00000555993 Transcript synonymous_variant 2355/4449 1992/3357 664/1118 P ccG/ccT rs555483404 1 -1 MAP3K9 HGNC HGNC:6861 protein_coding YES CCDS32112.1 ENSP00000451263 P80192 UPI00001D7B5C NM_033141.3 10/13 hmmpanther:PTHR23257:SF401,hmmpanther:PTHR23257,PIRSF_domain:PIRSF000556 LOW 1 SNV 1 1 PASS rs555483404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 70734420 70734420 C A 1 0 0 0 0 0 0 0 1 9181 639 23 1 1 MAP3K9 14 70734420 Silent SNP C 11LU022_T 6681271 70734420 36309298 714 1352 MAP3K9 0 . GRCh38 14 70742436 70742436 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1482G>T p.Glu494Asp p.E494D ENST00000555993 6/13 271 221 50 286 285 1 strelka-varscan-mutect MAP3K9,missense_variant,p.Glu494Asp,ENST00000554752,NM_001284230.1;MAP3K9,missense_variant,p.Glu231Asp,ENST00000611979,NM_001284231.1;MAP3K9,missense_variant,p.Glu494Asp,ENST00000555993,NM_033141.3;MAP3K9,missense_variant,p.Glu494Asp,ENST00000381250,;MAP3K9,missense_variant,p.Glu188Asp,ENST00000553414,NM_001284232.1;MAP3K9,missense_variant,p.Glu231Asp,ENST00000554146,; A ENST00000555993 Transcript missense_variant 1845/4449 1482/3357 494/1118 E/D gaG/gaT 1 -1 MAP3K9 HGNC HGNC:6861 protein_coding YES CCDS32112.1 ENSP00000451263 P80192 UPI00001D7B5C NM_033141.3 tolerated(0.18) 6/13 hmmpanther:PTHR23257:SF401,hmmpanther:PTHR23257,PIRSF_domain:PIRSF000556 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 70742436 70742436 C A 1 0 0 0 0 1 0 0 0 9181 912 32 2 2 MAP3K9 14 70742436 Missense_Mutation SNP C 11LU022_T 8016 70742436 36301282 715 1353 ESRRB 0 . GRCh38 14 76499955 76499955 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1389C>A p.Ser463Arg p.S463R ENST00000509242 8/9 441 373 68 561 561 0 strelka-varscan-mutect ESRRB,missense_variant,p.Ser463Arg,ENST00000509242,;ESRRB,missense_variant,p.Ser463Arg,ENST00000380887,NM_004452.3;ESRRB,missense_variant,p.Ser468Arg,ENST00000512784,;ESRRB,downstream_gene_variant,,ENST00000556177,;RP11-187O7.3,intron_variant,,ENST00000554926,;ESRRB,3_prime_UTR_variant,,ENST00000505752,;ESRRB,non_coding_transcript_exon_variant,,ENST00000611036,; A ENST00000509242 Transcript missense_variant 1597/2849 1389/1527 463/508 S/R agC/agA 1 1 ESRRB HGNC HGNC:3473 protein_coding YES CCDS9850.2 ENSP00000422488 O95718 UPI000003157B tolerated_low_confidence(0.06) 8/9 PIRSF_domain:PIRSF002527 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 76499955 76499955 C A 1 0 0 0 0 1 0 0 0 5123 709 25 2 2 ESRRB 14 76499955 Missense_Mutation SNP C 11LU022_T 5757519 76499955 30543763 716 1354 ISM2 0 . GRCh38 14 77484438 77484438 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.512C>A p.Thr171Asn p.T171N ENST00000342219 3/7 69 58 11 75 75 0 strelka-varscan-mutect ISM2,missense_variant,p.Thr171Asn,ENST00000342219,NM_199296.2;ISM2,missense_variant,p.Thr171Asn,ENST00000493585,NM_182509.3;ISM2,intron_variant,,ENST00000554801,;ISM2,3_prime_UTR_variant,,ENST00000216481,;ISM2,3_prime_UTR_variant,,ENST00000480979,;ISM2,3_prime_UTR_variant,,ENST00000471734,;ISM2,non_coding_transcript_exon_variant,,ENST00000472744,;ISM2,upstream_gene_variant,,ENST00000487738,; T ENST00000342219 Transcript missense_variant 569/2971 512/1716 171/571 T/N aCc/aAc 1 -1 ISM2 HGNC HGNC:23176 protein_coding YES CCDS9864.1 ENSP00000341490 Q6H9L7 UPI000019950C NM_199296.2 tolerated(0.05) 3/7 hmmpanther:PTHR10239:SF28,hmmpanther:PTHR10239 MODERATE 1 SNV 1 1 PASS rs1271612638 . 0 200 10 0 0 0 0 0 -19.99998 0.9999849 1 1 1 0 T 3 4 3 77484438 77484438 G T 1 0 0 0 0 1 0 0 0 7768 1261 44 2 2 ISM2 14 77484438 Missense_Mutation SNP G 11LU022_T 984483 77484438 29559280 717 1355 STON2 0 . GRCh38 14 81278474 81278474 + Silent SNP G G C novel 11LU022_T 11LU022_N G G c.837C>G p.= p.P279P ENST00000555447 6/8 179 141 38 170 170 0 strelka-varscan-mutect STON2,synonymous_variant,p.=,ENST00000555447,NM_001256430.1;STON2,synonymous_variant,p.=,ENST00000267540,NM_033104.3;STON2,synonymous_variant,p.=,ENST00000614646,;STON2,upstream_gene_variant,,ENST00000553821,;STON2,downstream_gene_variant,,ENST00000556280,;STON2,non_coding_transcript_exon_variant,,ENST00000555284,; C ENST00000555447 Transcript synonymous_variant 1250/4302 837/2763 279/920 P ccC/ccG 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 6/8 PIRSF_domain:PIRSF037099,Pfam_domain:PF12016 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 81278474 81278474 G C 1 0 0 0 0 0 0 0 1 15696 1335 47 4 4 STON2 14 81278474 Silent SNP G 11LU022_T 3794036 81278474 25765244 718 1356 UNC79 0 . GRCh38 14 93688769 93688769 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.6600C>A p.Asn2200Lys p.N2200K ENST00000256339 45/50 209 194 15 183 183 0 strelka-varscan-mutect UNC79,missense_variant,p.Asn2399Lys,ENST00000553484,;UNC79,missense_variant,p.Asn2338Lys,ENST00000555664,;UNC79,missense_variant,p.Asn2200Lys,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Asn2377Lys,ENST00000393151,;UNC79,missense_variant,p.Asn2200Lys,ENST00000621021,;UNC79,upstream_gene_variant,,ENST00000554549,; A ENST00000256339 Transcript missense_variant 7255/8400 6600/7377 2200/2458 N/K aaC/aaA 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious(0) 45/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 93688769 93688769 C A 1 0 0 0 0 1 0 0 0 17520 506 18 2 2 UNC79 14 93688769 Missense_Mutation SNP C 11LU022_T 12410295 93688769 13354949 719 1357 SERPINA3 0 . GRCh38 14 94619448 94619448 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.897G>C p.Trp299Cys p.W299C ENST00000467132 3/5 341 286 55 402 402 0 strelka-varscan-mutect SERPINA3,missense_variant,p.Trp299Cys,ENST00000467132,;SERPINA3,missense_variant,p.Trp81Cys,ENST00000482740,;SERPINA3,missense_variant,p.Trp299Cys,ENST00000393078,NM_001085.4;SERPINA3,missense_variant,p.Trp299Cys,ENST00000393080,;SERPINA3,missense_variant,p.Trp299Cys,ENST00000555820,;SERPINA3,missense_variant,p.Trp39Cys,ENST00000621603,;SERPINA3,intron_variant,,ENST00000556388,;SERPINA3,3_prime_UTR_variant,,ENST00000553947,;SERPINA3,intron_variant,,ENST00000556968,; C ENST00000467132 Transcript missense_variant 2045/2660 897/1272 299/423 W/C tgG/tgC 1 1 SERPINA3 HGNC HGNC:16 protein_coding YES CCDS32150.1 ENSP00000450540 P01011 A0A024R6P0 UPI000012509B deleterious(0) 3/5 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF145,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 94619448 94619448 G C 1 0 0 0 0 1 0 0 0 14366 1183 41 4 4 SERPINA3 14 94619448 Missense_Mutation SNP G 11LU022_T 930679 94619448 12424270 720 1358 DICER1 0 . GRCh38 14 95129491 95129491 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.715G>T p.Asp239Tyr p.D239Y ENST00000526495 8/29 225 185 40 165 165 0 strelka-varscan-mutect DICER1,missense_variant,p.Asp239Tyr,ENST00000526495,NM_030621.4,NM_001291628.1;DICER1,missense_variant,p.Asp239Tyr,ENST00000343455,NM_177438.2;DICER1,missense_variant,p.Asp239Tyr,ENST00000393063,;DICER1,missense_variant,p.Asp239Tyr,ENST00000527414,NM_001271282.2;DICER1,missense_variant,p.Asp239Tyr,ENST00000541352,NM_001195573.1;DICER1,downstream_gene_variant,,ENST00000531162,;DICER1,downstream_gene_variant,,ENST00000529720,;DICER1,non_coding_transcript_exon_variant,,ENST00000529206,; A ENST00000526495 Transcript missense_variant 1007/10331 715/5769 239/1922 D/Y Gac/Tac 1 -1 DICER1 HGNC HGNC:17098 protein_coding YES CCDS9931.1 ENSP00000437256 Q9UPY3 UPI0000168662 NM_030621.4,NM_001291628.1 deleterious(0) 8/29 hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF26,SMART_domains:SM00487 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 95129491 95129491 C A 1 0 0 0 0 1 0 0 0 4325 826 29 2 2 DICER1 14 95129491 Missense_Mutation SNP C 11LU022_T 510043 95129491 11914227 721 1359 ATG2B 0 . GRCh38 14 96315520 96315520 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3425G>T p.Trp1142Leu p.W1142L ENST00000359933 22/42 262 231 31 215 215 0 strelka-varscan-mutect ATG2B,missense_variant,p.Trp1142Leu,ENST00000359933,NM_018036.5;ATG2B,upstream_gene_variant,,ENST00000261834,;ATG2B,downstream_gene_variant,,ENST00000473234,;ATG2B,downstream_gene_variant,,ENST00000488421,; A ENST00000359933 Transcript missense_variant 4319/13684 3425/6237 1142/2078 W/L tGg/tTg 1 -1 ATG2B HGNC HGNC:20187 protein_coding YES CCDS9944.2 ENSP00000353010 Q96BY7 UPI000155D51F NM_018036.5 tolerated(0.18) 22/42 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF20 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 96315520 96315520 C A 1 0 0 0 0 1 0 0 0 1246 595 21 2 2 ATG2B 14 96315520 Missense_Mutation SNP C 11LU022_T 1186029 96315520 10728198 722 1360 GSKIP 0 . GRCh38 14 96385529 96385529 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.265G>A p.Gly89Ser p.G89S ENST00000556095 4/4 101 82 19 95 95 0 strelka-varscan-mutect GSKIP,missense_variant,p.Gly89Ser,ENST00000556095,NM_001271904.1;GSKIP,missense_variant,p.Gly89Ser,ENST00000555181,NM_016472.4,NM_001271905.1;GSKIP,missense_variant,p.Gly89Ser,ENST00000438650,NM_001271906.1;GSKIP,missense_variant,p.Gly89Ser,ENST00000554182,;GSKIP,missense_variant,p.Gly89Ser,ENST00000555757,;GSKIP,downstream_gene_variant,,ENST00000553699,;RNU2-33P,downstream_gene_variant,,ENST00000410344,; A ENST00000556095 Transcript missense_variant 2077/3834 265/420 89/139 G/S Ggc/Agc 1 1 GSKIP HGNC HGNC:20343 protein_coding YES CCDS32153.1 ENSP00000451188 Q9P0R6 A0A024R6P6 UPI0000034E26 NM_001271904.1 tolerated(0.24) 4/4 Superfamily_domains:0049393,PD080843,Pfam_domain:PF05303,hmmpanther:PTHR12490 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 96385529 96385529 G A 1 0 0 0 0 1 0 0 0 6709 1000 35 3 3 GSKIP 14 96385529 Missense_Mutation SNP G 11LU022_T 70009 96385529 10658189 723 1361 SETD3 0 . GRCh38 14 99410190 99410190 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.875C>A p.Ala292Asp p.A292D ENST00000329331 9/9 120 111 9 108 108 0 strelka-varscan-mutect SETD3,missense_variant,p.Ala292Asp,ENST00000329331,NM_199123.1;SETD3,3_prime_UTR_variant,,ENST00000630307,;SETD3,intron_variant,,ENST00000331768,NM_032233.2;SETD3,downstream_gene_variant,,ENST00000436070,;SETD3,intron_variant,,ENST00000446066,;SETD3,intron_variant,,ENST00000453764,;SETD3,intron_variant,,ENST00000489770,;SETD3,downstream_gene_variant,,ENST00000357563,; T ENST00000329331 Transcript missense_variant 944/1330 875/891 292/296 A/D gCt/gAt 1 -1 SETD3 HGNC HGNC:20493 protein_coding CCDS9952.1 ENSP00000327910 Q86TU7 UPI000000CC6C NM_199123.1 tolerated_low_confidence(0.15) 9/9 PROSITE_profiles:PS50280 MODERATE SNV 1 1 PASS rs1157085823 . 0 208 2 0 0 0 0 0 -17.95887 1 1 1 1 0 T 3 4 3 99410190 99410190 G T 1 0 0 0 0 1 0 0 0 14410 971 34 2 2 SETD3 14 99410190 Missense_Mutation SNP G 11LU022_T 3024661 99410190 7633528 724 1362 RTL1 0 . GRCh38 14 100882420 100882420 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.2369A>G p.Asn790Ser p.N790S ENST00000534062 1/1 243 225 18 279 278 1 strelka-varscan-mutect RTL1,missense_variant,p.Asn790Ser,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; C ENST00000534062 Transcript missense_variant 2428/4193 2369/4077 790/1358 N/S aAc/aGc 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 tolerated(0.11) 1/1 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF9,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 100882420 100882420 T C 1 0 0 0 0 1 0 0 0 13984 1725 60 5 5 RTL1 14 100882420 Missense_Mutation SNP T 11LU022_T 1472230 100882420 6161298 725 1363 DIO3 0 . GRCh38 14 101561776 101561776 + Missense_Mutation SNP C C T rs368850596 11LU022_T 11LU022_N C C c.280C>T p.Pro94Ser p.P94S ENST00000510508 1/1 321 220 101 329 328 1 strelka-varscan-mutect DIO3,missense_variant,p.Pro94Ser,ENST00000510508,NM_001362.3;DIO3OS,upstream_gene_variant,,ENST00000554735,;DIO3OS,upstream_gene_variant,,ENST00000557661,;DIO3OS,upstream_gene_variant,,ENST00000555174,;DIO3OS,upstream_gene_variant,,ENST00000554441,;DIO3OS,upstream_gene_variant,,ENST00000554694,;DIO3OS,upstream_gene_variant,,ENST00000555882,;DIO3OS,upstream_gene_variant,,ENST00000557532,;DIO3OS,upstream_gene_variant,,ENST00000557109,;DIO3OS,upstream_gene_variant,,ENST00000553729,;DIO3OS,upstream_gene_variant,,ENST00000556266,;DIO3OS,upstream_gene_variant,,ENST00000408206,; T ENST00000510508 Transcript missense_variant 426/2102 280/915 94/304 P/S Cct/Tct rs368850596 1 1 DIO3 HGNC HGNC:2885 protein_coding YES CCDS41992.2 ENSP00000427336 P55073 UPI0001B1A4B2 NM_001362.3 tolerated_low_confidence(0.32) 1/1 Pfam_domain:PF00837,PIRSF_domain:PIRSF001330,PIRSF_domain:PIRSF500144,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF4 MODERATE SNV 1 PASS rs368850596 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 101561776 101561776 C T 1 0 0 0 0 1 0 0 0 4331 739 26 3 3 DIO3 14 101561776 Missense_Mutation SNP C 11LU022_T 679356 101561776 5481942 726 1364 TDRD9 0 . GRCh38 14 103970545 103970545 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.770A>G p.His257Arg p.H257R ENST00000409874 6/36 127 82 45 120 120 0 strelka-varscan-mutect TDRD9,missense_variant,p.His257Arg,ENST00000409874,NM_153046.2;TDRD9,upstream_gene_variant,,ENST00000339063,;TDRD9,upstream_gene_variant,,ENST00000557332,;TDRD9,downstream_gene_variant,,ENST00000554571,; G ENST00000409874 Transcript missense_variant 818/4782 770/4149 257/1382 H/R cAc/cGc 1 1 TDRD9 HGNC HGNC:20122 protein_coding YES CCDS9987.2 ENSP00000387303 Q8NDG6 UPI0001642306 NM_153046.2 deleterious(0) 6/36 PROSITE_profiles:PS51192,hmmpanther:PTHR18934:SF113,hmmpanther:PTHR18934,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 103970545 103970545 A G 1 0 0 0 0 1 0 0 0 16146 173 6 5 5 TDRD9 14 103970545 Missense_Mutation SNP A 11LU022_T 2408769 103970545 3073173 727 1365 AKT1 0 . GRCh38 14 104775690 104775690 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.397G>A p.Glu133Lys p.E133K ENST00000554581 4/13 230 203 27 251 251 0 strelka-mutect AKT1,missense_variant,p.Glu133Lys,ENST00000554581,;AKT1,missense_variant,p.Glu133Lys,ENST00000402615,;AKT1,missense_variant,p.Glu133Lys,ENST00000555528,NM_005163.2;AKT1,missense_variant,p.Glu133Lys,ENST00000349310,NM_001014432.1;AKT1,missense_variant,p.Glu133Lys,ENST00000407796,NM_001014431.1;AKT1,missense_variant,p.Glu133Lys,ENST00000554848,;AKT1,upstream_gene_variant,,ENST00000554192,;AKT1,upstream_gene_variant,,ENST00000555458,;AKT1,downstream_gene_variant,,ENST00000555926,;AKT1,non_coding_transcript_exon_variant,,ENST00000544168,;AKT1,non_coding_transcript_exon_variant,,ENST00000555380,;AKT1,non_coding_transcript_exon_variant,,ENST00000557552,;AKT1,non_coding_transcript_exon_variant,,ENST00000554826,;AKT1,upstream_gene_variant,,ENST00000610370,;AKT1,upstream_gene_variant,,ENST00000553506,;AKT1,upstream_gene_variant,,ENST00000554585,;AKT1,upstream_gene_variant,,ENST00000556836,; T ENST00000554581 Transcript missense_variant 1878/3916 397/1443 133/480 E/K Gag/Aag 1 -1 AKT1 HGNC HGNC:391 protein_coding YES CCDS9994.1 ENSP00000451828 P31749 B0LPE5 UPI0000070813 tolerated(0.21) 4/13 hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 104775690 104775690 C T 1 0 0 0 0 1 0 0 0 561 922 32 3 3 AKT1 14 104775690 Missense_Mutation SNP C 11LU022_T 805145 104775690 2268028 728 1366 CRIP2 0 . GRCh38 14 105478285 105478285 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.285G>T p.= p.L95L ENST00000483017 2/8 164 151 13 200 200 0 strelka-varscan-mutect CRIP2,synonymous_variant,p.=,ENST00000329146,NM_001312.3;CRIP2,synonymous_variant,p.=,ENST00000483017,NM_001270837.1;CRIP2,intron_variant,,ENST00000538259,;CRIP2,intron_variant,,ENST00000550577,NM_001270841.1;CRIP2,non_coding_transcript_exon_variant,,ENST00000548989,;CRIP2,non_coding_transcript_exon_variant,,ENST00000548309,;CRIP2,non_coding_transcript_exon_variant,,ENST00000548923,;CRIP2,non_coding_transcript_exon_variant,,ENST00000552643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000547643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000551836,;CRIP2,upstream_gene_variant,,ENST00000551738,; T ENST00000483017 Transcript synonymous_variant 571/1176 285/849 95/282 L ctG/ctT 1 1 CRIP2 HGNC HGNC:2361 protein_coding YES CCDS59246.1 ENSP00000426119 P52943 UPI0001914E41 NM_001270837.1 2/8 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132 LOW 1 SNV 2 1 PASS . . 0 203 2 5 0 0 0 0 -17.26841 0.9963449 1 1 1 0 T 2 4 3 105478285 105478285 G T 1 0 0 0 0 0 0 0 1 3676 1335 47 2 2 CRIP2 14 105478285 Silent SNP G 11LU022_T 702595 105478285 1565433 729 1367 MAGEL2 0 . GRCh38 15 23644086 23644086 + Silent SNP C C T rs140288382 11LU022_T 11LU022_N C C c.3657G>A p.= p.A1219A ENST00000532292 1/1 93 78 15 101 101 0 strelka-varscan-mutect MAGEL2,synonymous_variant,p.=,ENST00000532292,NM_019066.4; T ENST00000532292 Transcript synonymous_variant 3756/4298 3657/3750 1219/1249 A gcG/gcA rs140288382,COSM1147457 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 1/1 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66 0,1 LOW 1 SNV 0,1 1 PASS rs140288382 . 0 208 0 2 0 0 0 0 -19.99999 0.9999999 1 1 1 0 T 2 4 3 23644086 23644086 C T 1 0 0 0 0 0 0 0 1 9107 755 27 1 1 MAGEL2 15 23644086 Silent SNP C 11LU022_T 23644086 78347103 730 1368 NPAP1 0 . GRCh38 15 24676945 24676945 + Missense_Mutation SNP C C A rs866655136 11LU022_T 11LU022_N C C c.1078C>A p.Leu360Met p.L360M ENST00000329468 1/1 85 64 21 131 131 0 strelka-varscan-mutect NPAP1,missense_variant,p.Leu360Met,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1078/7526 1078/3471 360/1156 L/M Ctg/Atg rs866655136 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.34) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229 MODERATE 1 SNV 1 PASS rs866655136 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 24676945 24676945 C A 1 0 0 0 0 1 0 0 0 10609 680 24 2 2 NPAP1 15 24676945 Missense_Mutation SNP C 11LU022_T 1032859 24676945 77314244 731 1369 UBE3A 0 . GRCh38 15 25370993 25370993 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1190A>G p.Asp397Gly p.D397G ENST00000397954 7/14 154 117 37 173 173 0 strelka-varscan-mutect UBE3A,missense_variant,p.Asp374Gly,ENST00000635914,;UBE3A,missense_variant,p.Asp374Gly,ENST00000638155,;UBE3A,missense_variant,p.Asp374Gly,ENST00000438097,;UBE3A,missense_variant,p.Asp374Gly,ENST00000638011,;UBE3A,missense_variant,p.Asp394Gly,ENST00000614096,NM_130839.2;UBE3A,missense_variant,p.Asp394Gly,ENST00000637886,;UBE3A,missense_variant,p.Asp374Gly,ENST00000630424,;UBE3A,missense_variant,p.Asp374Gly,ENST00000232165,NM_130838.1;UBE3A,missense_variant,p.Asp374Gly,ENST00000625778,;UBE3A,missense_variant,p.Asp374Gly,ENST00000566215,;UBE3A,missense_variant,p.Asp374Gly,ENST00000428984,;UBE3A,missense_variant,p.Asp397Gly,ENST00000397954,NM_000462.3;UBE3A,downstream_gene_variant,,ENST00000630607,;UBE3A,downstream_gene_variant,,ENST00000629252,;UBE3A,downstream_gene_variant,,ENST00000630907,;UBE3A,downstream_gene_variant,,ENST00000628267,;UBE3A,downstream_gene_variant,,ENST00000626068,;UBE3A,downstream_gene_variant,,ENST00000628733,;UBE3A,downstream_gene_variant,,ENST00000629886,;UBE3A,downstream_gene_variant,,ENST00000628890,;SNHG14,intron_variant,,ENST00000453082,;SNHG14,intron_variant,,ENST00000554726,;UBE3A,downstream_gene_variant,,ENST00000626793,; C ENST00000397954 Transcript missense_variant 1435/2873 1190/2628 397/875 D/G gAt/gGt 1 -1 UBE3A HGNC HGNC:12496 protein_coding YES CCDS45192.1 ENSP00000381045 Q05086 UPI0000161F3B NM_000462.3 tolerated(0.06) 7/14 Low_complexity_(Seg):seg,hmmpanther:PTHR11254,PIRSF_domain:PIRSF037201 MODERATE 1 SNV 5 1 PASS rs1452945833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 25370993 25370993 T C 1 0 0 0 0 1 0 0 0 17402 1435 50 5 5 UBE3A 15 25370993 Missense_Mutation SNP T 11LU022_T 694048 25370993 76620196 732 1370 GABRG3 0 . GRCh38 15 27527497 27527497 + Silent SNP G G A 11LU022_T 11LU022_N G G c.930G>A p.= p.V310V ENST00000615808 8/10 142 112 30 188 188 0 strelka-varscan-mutect GABRG3,synonymous_variant,p.=,ENST00000615808,NM_033223.4;GABRG3,synonymous_variant,p.=,ENST00000333743,;GABRG3,synonymous_variant,p.=,ENST00000554696,;GABRG3,synonymous_variant,p.=,ENST00000451330,;RP11-100M12.3,intron_variant,,ENST00000556642,; A ENST00000615808 Transcript synonymous_variant 1184/10768 930/1404 310/467 V gtG/gtA COSM5664415 1 1 GABRG3 HGNC HGNC:4088 protein_coding YES CCDS45195.1 ENSP00000479113 Q99928 UPI000012AFCB NM_033223.4 8/10 Gene3D:1.20.58.390,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF195,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 1 LOW 1 SNV 1 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999581 1 1 1 0 A 2 1 3 27527497 27527497 G A 1 0 0 0 0 0 0 0 1 6044 1364 48 3 3 GABRG3 15 27527497 Silent SNP G 11LU022_T 2156504 27527497 74463692 733 1371 TRPM1 0 . GRCh38 15 31060593 31060593 + Missense_Mutation SNP C C A rs767403814 11LU022_T 11LU022_N C C c.1265G>T p.Arg422Leu p.R422L ENST00000542188 10/27 406 294 112 539 539 0 strelka-varscan-mutect TRPM1,missense_variant,p.Arg422Leu,ENST00000542188,NM_001252020.1;TRPM1,missense_variant,p.Arg383Leu,ENST00000397795,NM_002420.5;TRPM1,missense_variant,p.Arg405Leu,ENST00000256552,NM_001252024.1;TRPM1,missense_variant,p.Arg306Leu,ENST00000558768,;TRPM1,missense_variant,p.Arg383Leu,ENST00000558445,;TRPM1,intron_variant,,ENST00000559177,;MIR211,downstream_gene_variant,,ENST00000384969,;TRPM1,3_prime_UTR_variant,,ENST00000560801,;TRPM1,3_prime_UTR_variant,,ENST00000560658,;TRPM1,non_coding_transcript_exon_variant,,ENST00000558070,; A ENST00000542188 Transcript missense_variant 1579/6004 1265/4929 422/1642 R/L cGc/cTc rs767403814 1 -1 TRPM1 HGNC HGNC:7146 protein_coding YES CCDS58347.1 ENSP00000437849 Q7Z4N2 UPI0001DBB3A9 NM_001252020.1 deleterious(0) 10/27 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF13 MODERATE 1 SNV 1 1 PASS rs767403814 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 31060593 31060593 C A 1 0 0 0 0 1 0 0 0 17091 768 27 1 1 TRPM1 15 31060593 Missense_Mutation SNP C 11LU022_T 3533096 31060593 70930596 734 1372 UBR1 0 . GRCh38 15 42970577 42970577 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4400G>T p.Ser1467Ile p.S1467I ENST00000290650 40/47 271 197 74 325 325 0 strelka-varscan-mutect UBR1,missense_variant,p.Ser1467Ile,ENST00000290650,NM_174916.2; A ENST00000290650 Transcript missense_variant 4479/7761 4400/5250 1467/1749 S/I aGt/aTt 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 tolerated(0.16) 40/47 Low_complexity_(Seg):seg,hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 42970577 42970577 C A 1 0 0 0 0 1 0 0 0 17425 565 20 2 2 UBR1 15 42970577 Missense_Mutation SNP C 11LU022_T 11909984 42970577 59020612 735 1373 EPB42 0 . GRCh38 15 43215308 43215308 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.307A>C p.Asn103His p.N103H ENST00000300215 3/13 232 168 64 339 338 1 strelka-varscan-mutect EPB42,missense_variant,p.Asn103His,ENST00000300215,NM_000119.2;EPB42,missense_variant,p.Asn73His,ENST00000441366,NM_001114134.1;EPB42,missense_variant,p.Asn73His,ENST00000622454,;EPB42,missense_variant,p.Asn26His,ENST00000568508,;EPB42,intron_variant,,ENST00000540029,;EPB42,upstream_gene_variant,,ENST00000569204,; G ENST00000300215 Transcript missense_variant 765/4553 307/2166 103/721 N/H Aac/Cac 1 -1 EPB42 HGNC HGNC:3381 protein_coding YES CCDS10093.1 ENSP00000300215 P16452 UPI000013E639 NM_000119.2 deleterious(0.01) 3/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF44,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000459,Pfam_domain:PF00868,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 43215308 43215308 T G 1 0 0 0 0 1 0 0 0 5005 1812 63 5 5 EPB42 15 43215308 Missense_Mutation SNP T 11LU022_T 244731 43215308 58775881 736 1374 TGM7 0 . GRCh38 15 43279794 43279794 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1509C>A p.= p.G503G ENST00000452443 10/13 281 198 83 292 291 1 strelka-varscan-mutect TGM7,synonymous_variant,p.=,ENST00000452443,NM_052955.2;TGM7,upstream_gene_variant,,ENST00000562372,; T ENST00000452443 Transcript synonymous_variant 1514/2313 1509/2133 503/710 G ggC/ggA 1 -1 TGM7 HGNC HGNC:30790 protein_coding YES CCDS32213.1 ENSP00000389466 Q96PF1 UPI0000049F68 NM_052955.2 10/13 hmmpanther:PTHR11590:SF41,hmmpanther:PTHR11590,PIRSF_domain:PIRSF000459,Gene3D:2.60.40.10,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS rs1397260275 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 43279794 43279794 G T 1 0 0 0 0 0 0 0 1 16268 1190 42 2 2 TGM7 15 43279794 Silent SNP G 11LU022_T 64486 43279794 58711395 737 1375 HYPK 0 . GRCh38 15 43801748 43801748 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.332G>A p.Arg111His p.R111H ENST00000406925 5/5 207 181 26 279 278 1 strelka-varscan-mutect HYPK,missense_variant,p.Arg111His,ENST00000406925,;HYPK,missense_variant,p.Arg111His,ENST00000442995,NM_016400.3;HYPK,3_prime_UTR_variant,,ENST00000458412,;SERINC4,upstream_gene_variant,,ENST00000319327,NM_001258031.1,NM_001258032.1;SERINC4,upstream_gene_variant,,ENST00000299969,;MFAP1,downstream_gene_variant,,ENST00000267812,NM_005926.2;SERF2,downstream_gene_variant,,ENST00000630046,;SERF2,downstream_gene_variant,,ENST00000409291,;SERF2,downstream_gene_variant,,ENST00000409646,;SERF2,downstream_gene_variant,,ENST00000430901,;HYPK,non_coding_transcript_exon_variant,,ENST00000497142,;HYPK,downstream_gene_variant,,ENST00000498605,;SERF2,3_prime_UTR_variant,,ENST00000448830,;SERF2,3_prime_UTR_variant,,ENST00000409617,;SERINC4,upstream_gene_variant,,ENST00000457418,;RP11-296A16.1,upstream_gene_variant,,ENST00000417761,;SERINC4,upstream_gene_variant,,ENST00000448553,;SERINC4,upstream_gene_variant,,ENST00000412697,;SERINC4,upstream_gene_variant,,ENST00000476490,;MFAP1,downstream_gene_variant,,ENST00000484386,; A ENST00000406925 Transcript missense_variant 4443/4777 332/390 111/129 R/H cGc/cAc 1 1 HYPK HGNC HGNC:18418 protein_coding YES CCDS10104.1 ENSP00000384474 Q9NX55 A0A024R5Q1 UPI000000D937 deleterious(0.01) 5/5 hmmpanther:PTHR31184:SF2,hmmpanther:PTHR31184,Gene3D:1.10.8.10 MODERATE SNV 2 1 PASS rs1440063953 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 43801748 43801748 G A 1 0 0 0 0 1 0 0 0 7368 1087 38 1 1 HYPK 15 43801748 Missense_Mutation SNP G 11LU022_T 521954 43801748 58189441 738 1376 CEP152 0 . GRCh38 15 48760219 48760219 + Silent SNP T T C rs774120199 11LU022_T 11LU022_N T T c.2610A>G p.= p.L870L ENST00000380950 19/27 318 243 75 442 442 0 strelka-varscan-mutect CEP152,synonymous_variant,p.=,ENST00000380950,NM_001194998.1;CEP152,synonymous_variant,p.=,ENST00000399334,NM_014985.3;CEP152,synonymous_variant,p.=,ENST00000325747,; C ENST00000380950 Transcript synonymous_variant 2798/5635 2610/5133 870/1710 L ctA/ctG rs774120199 1 -1 CEP152 HGNC HGNC:29298 protein_coding YES CCDS58361.1 ENSP00000370337 O94986 UPI00002378C4 NM_001194998.1 19/27 hmmpanther:PTHR10337,hmmpanther:PTHR10337:SF6 LOW 1 SNV 1 1 PASS rs774120199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 48760219 48760219 T C 1 0 0 0 0 0 0 0 1 2961 1625 57 5 5 CEP152 15 48760219 Silent SNP T 11LU022_T 4958471 48760219 53230970 739 1377 MYO1E 0 . GRCh38 15 59214307 59214307 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1196G>T p.Gly399Val p.G399V ENST00000288235 12/28 93 78 15 162 162 0 strelka-mutect MYO1E,missense_variant,p.Gly399Val,ENST00000288235,NM_004998.3;MYO1E,missense_variant,p.Gly119Val,ENST00000559489,;MYO1E,intron_variant,,ENST00000559269,;RNU4-80P,upstream_gene_variant,,ENST00000363200,; A ENST00000288235 Transcript missense_variant 1596/8673 1196/3327 399/1108 G/V gGc/gTc 1 -1 MYO1E HGNC HGNC:7599 protein_coding YES CCDS32254.1 ENSP00000288235 Q12965 Q4KMR3 UPI00001FE590 NM_004998.3 deleterious(0) 12/28 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF288,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 59214307 59214307 C A 1 0 0 0 0 1 0 0 0 10073 739 26 2 2 MYO1E 15 59214307 Missense_Mutation SNP C 11LU022_T 10454088 59214307 42776882 740 1378 IL16 0 . GRCh38 15 81282667 81282667 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1110G>T p.= p.L370L ENST00000302987 8/18 185 136 49 240 240 0 strelka-varscan-mutect IL16,synonymous_variant,p.=,ENST00000394660,NM_001172128.1;IL16,synonymous_variant,p.=,ENST00000302987,NM_172217.3;IL16,synonymous_variant,p.=,ENST00000559383,;IL16,synonymous_variant,p.=,ENST00000360547,;IL16,synonymous_variant,p.=,ENST00000560115,;IL16,synonymous_variant,p.=,ENST00000560241,; T ENST00000302987 Transcript synonymous_variant 1110/3999 1110/3999 370/1332 L ctG/ctT 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 8/18 PROSITE_profiles:PS50106,hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 1 1 PASS rs1216124210 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 81282667 81282667 G T 1 0 0 0 0 0 0 0 1 7541 1364 48 2 2 IL16 15 81282667 Silent SNP G 11LU022_T 22068360 81282667 20708522 741 1379 RPS17 0 . GRCh38 15 82540029 82540029 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.107A>T p.Glu36Val p.E36V ENST00000330244 2/5 892 689 203 1146 1145 1 strelka-varscan-mutect RPS17,missense_variant,p.Glu36Val,ENST00000561157,;RPS17,missense_variant,p.Glu36Val,ENST00000330244,NM_001021.4;CPEB1,downstream_gene_variant,,ENST00000614918,;CPEB1,downstream_gene_variant,,ENST00000611031,;CPEB1,downstream_gene_variant,,ENST00000617958,;CPEB1,downstream_gene_variant,,ENST00000618449,NM_001079533.1;CPEB1,downstream_gene_variant,,ENST00000620182,NM_001288819.1;CPEB1,downstream_gene_variant,,ENST00000617522,;CPEB1,downstream_gene_variant,,ENST00000615198,NM_030594.4;CPEB1,downstream_gene_variant,,ENST00000617462,NM_001079535.1;CPEB1,downstream_gene_variant,,ENST00000616959,;CPEB1,downstream_gene_variant,,ENST00000611163,NM_001079534.1,NM_001288820.1;RP11-152F13.10,downstream_gene_variant,,ENST00000562833,;RP11-379H8.1,upstream_gene_variant,,ENST00000621893,;RPS17,missense_variant,p.Glu36Val,ENST00000558397,;RPS17,missense_variant,p.Glu35Val,ENST00000561068,;RPS17,non_coding_transcript_exon_variant,,ENST00000561440,;RPS17,non_coding_transcript_exon_variant,,ENST00000560612,;RPS17,non_coding_transcript_exon_variant,,ENST00000560639,;RPS17,non_coding_transcript_exon_variant,,ENST00000560229,;RPS17,non_coding_transcript_exon_variant,,ENST00000559776,;RPS17,non_coding_transcript_exon_variant,,ENST00000559273,;CPEB1,downstream_gene_variant,,ENST00000618698,;CPEB1,downstream_gene_variant,,ENST00000614977,; A ENST00000330244 Transcript missense_variant 243/592 107/408 36/135 E/V gAg/gTg 1 -1 RPS17 HGNC HGNC:10397 protein_coding YES CCDS10320.1 ENSP00000346046 P08708 UPI0000167B0C NM_001021.4 deleterious(0.02) 2/5 HAMAP:MF_00511,hmmpanther:PTHR10732,Gene3D:1rq6A00,Pfam_domain:PF00833,Superfamily_domains:0049231 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 82540029 82540029 T A 1 0 0 0 0 1 0 0 0 13882 1551 54 4 4 RPS17 15 82540029 Missense_Mutation SNP T 11LU022_T 1257362 82540029 19451160 742 1380 AP3B2 0 . GRCh38 15 82663165 82663165 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2566G>T p.Glu856Ter p.E856* ENST00000535359 22/27 336 267 69 455 455 0 strelka-varscan-mutect AP3B2,stop_gained,p.Glu837Ter,ENST00000261722,;AP3B2,stop_gained,p.Glu837Ter,ENST00000620652,NM_004644.4;AP3B2,stop_gained,p.Glu856Ter,ENST00000535359,NM_001278512.1;AP3B2,stop_gained,p.Glu805Ter,ENST00000535348,NM_001278511.1;CPEB1-AS1,intron_variant,,ENST00000560650,;AP3B2,3_prime_UTR_variant,,ENST00000538592,;AP3B2,non_coding_transcript_exon_variant,,ENST00000543938,;AP3B2,non_coding_transcript_exon_variant,,ENST00000545315,;AP3B2,upstream_gene_variant,,ENST00000537735,; A ENST00000535359 Transcript stop_gained 2639/3402 2566/3306 856/1101 E/* Gag/Tag 1 -1 AP3B2 HGNC HGNC:567 protein_coding YES CCDS61737.1 ENSP00000440984 Q13367 UPI0001917049 NM_001278512.1 22/27 Pfam_domain:PF14796,PIRSF_domain:PIRSF037096,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF11,SMART_domains:SM01355 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 82663165 82663165 C A 1 0 0 0 0 0 1 0 0 861 864 30 2 2 AP3B2 15 82663165 Nonsense_Mutation SNP C 11LU022_T 123136 82663165 19328024 743 1381 AP3B2 0 . GRCh38 15 82663180 82663180 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.2551C>G p.Leu851Val p.L851V ENST00000535359 22/27 358 287 71 465 465 0 strelka-varscan-mutect AP3B2,missense_variant,p.Leu832Val,ENST00000261722,;AP3B2,missense_variant,p.Leu832Val,ENST00000620652,NM_004644.4;AP3B2,missense_variant,p.Leu851Val,ENST00000535359,NM_001278512.1;AP3B2,missense_variant,p.Leu800Val,ENST00000535348,NM_001278511.1;CPEB1-AS1,intron_variant,,ENST00000560650,;AP3B2,3_prime_UTR_variant,,ENST00000538592,;AP3B2,non_coding_transcript_exon_variant,,ENST00000543938,;AP3B2,non_coding_transcript_exon_variant,,ENST00000545315,;AP3B2,upstream_gene_variant,,ENST00000537735,; C ENST00000535359 Transcript missense_variant 2624/3402 2551/3306 851/1101 L/V Ctg/Gtg 1 -1 AP3B2 HGNC HGNC:567 protein_coding YES CCDS61737.1 ENSP00000440984 Q13367 UPI0001917049 NM_001278512.1 tolerated(0.09) 22/27 Pfam_domain:PF14796,PIRSF_domain:PIRSF037096,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF11,SMART_domains:SM01355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 82663180 82663180 G C 1 0 0 0 0 1 0 0 0 861 933 33 4 4 AP3B2 15 82663180 Missense_Mutation SNP G 11LU022_T 15 82663180 19328009 744 1382 BNC1 0 . GRCh38 15 83257595 83257595 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2832G>T p.Arg944Ser p.R944S ENST00000345382 5/5 313 282 31 351 350 1 strelka-varscan-mutect BNC1,missense_variant,p.Arg944Ser,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Arg937Ser,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; A ENST00000345382 Transcript missense_variant 2918/4610 2832/2985 944/994 R/S agG/agT 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1,PROSITE_patterns:PS00028,Pfam_domain:PF12874,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS rs1375578583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 83257595 83257595 C A 1 0 0 0 0 1 0 0 0 1630 622 22 2 2 BNC1 15 83257595 Missense_Mutation SNP C 11LU022_T 594415 83257595 18733594 745 1383 BNC1 0 . GRCh38 15 83268142 83268142 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.190G>T p.Val64Leu p.V64L ENST00000345382 2/5 177 139 38 192 191 1 strelka-varscan-mutect BNC1,missense_variant,p.Val64Leu,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Val57Leu,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; A ENST00000345382 Transcript missense_variant 276/4610 190/2985 64/994 V/L Gtg/Ttg 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0) 2/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 83268142 83268142 C A 1 0 0 0 0 1 0 0 0 1630 507 18 2 2 BNC1 15 83268142 Missense_Mutation SNP C 11LU022_T 10547 83268142 18723047 746 1384 ZNF592 0 . GRCh38 15 84799210 84799210 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.3137G>T p.Gly1046Val p.G1046V ENST00000560079 9/11 456 395 61 568 567 1 strelka-varscan-mutect ZNF592,missense_variant,p.Gly1046Val,ENST00000560079,NM_014630.2;ZNF592,missense_variant,p.Gly1046Val,ENST00000299927,;ZNF592,upstream_gene_variant,,ENST00000618477,;ZNF592,splice_region_variant,,ENST00000559607,; T ENST00000560079 Transcript missense_variant,splice_region_variant 3425/8131 3137/3804 1046/1267 G/V gGg/gTg 1 1 ZNF592 HGNC HGNC:28986 protein_coding YES CCDS32317.1 ENSP00000452877 Q92610 UPI000013E5FC NM_014630.2 tolerated(0.26) 9/11 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF209,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 84799210 84799210 G T 1 0 0 0 0 1 0 0 0 18597 1246 43 2 2 ZNF592 15 84799210 Missense_Mutation SNP G 11LU022_T 1531068 84799210 17191979 747 1385 NTRK3 0 . GRCh38 15 87880333 87880333 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.2271G>T p.= p.G757G ENST00000360948 19/20 392 359 33 430 430 0 strelka-varscan-mutect NTRK3,synonymous_variant,p.=,ENST00000394480,NM_002530.3;NTRK3,synonymous_variant,p.=,ENST00000360948,NM_001012338.2;NTRK3,synonymous_variant,p.=,ENST00000357724,;NTRK3,synonymous_variant,p.=,ENST00000355254,NM_001243101.1;NTRK3,synonymous_variant,p.=,ENST00000626019,;NTRK3,synonymous_variant,p.=,ENST00000629765,;NTRK3,synonymous_variant,p.=,ENST00000557856,; A ENST00000360948 Transcript synonymous_variant 2577/3004 2271/2520 757/839 G ggG/ggT 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 19/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 87880333 87880333 C A 1 0 0 0 0 0 0 0 1 10774 610 22 2 2 NTRK3 15 87880333 Silent SNP C 11LU022_T 3081123 87880333 14110856 748 1386 ACAN 0 . GRCh38 15 88840024 88840024 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.467A>T p.His156Leu p.H156L ENST00000439576 4/18 125 100 25 162 162 0 strelka-varscan-mutect ACAN,missense_variant,p.His156Leu,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.His156Leu,ENST00000617301,;ACAN,missense_variant,p.His156Leu,ENST00000559004,;ACAN,missense_variant,p.His156Leu,ENST00000561243,;ACAN,missense_variant,p.His156Leu,ENST00000352105,NM_001135.3;ACAN,missense_variant,p.His156Leu,ENST00000558207,; T ENST00000439576 Transcript missense_variant 841/8840 467/7593 156/2530 H/L cAt/cTt 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0) 4/18 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 88840024 88840024 A T 1 0 0 0 0 1 0 0 0 160 217 8 4 4 ACAN 15 88840024 Missense_Mutation SNP A 11LU022_T 959691 88840024 13151165 749 1387 ACAN 0 . GRCh38 15 88872063 88872063 + Missense_Mutation SNP G G T rs368833137 11LU022_T 11LU022_N G G c.7166G>T p.Arg2389Leu p.R2389L ENST00000439576 15/18 141 113 28 197 197 0 strelka-varscan-mutect ACAN,missense_variant,p.Arg2389Leu,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Arg2332Leu,ENST00000617301,;ACAN,missense_variant,p.Arg2351Leu,ENST00000559004,;ACAN,missense_variant,p.Arg2389Leu,ENST00000561243,;ACAN,missense_variant,p.Arg2351Leu,ENST00000352105,NM_001135.3;ACAN,upstream_gene_variant,,ENST00000558704,;ACAN,downstream_gene_variant,,ENST00000560601,;ACAN,upstream_gene_variant,,ENST00000558604,; T ENST00000439576 Transcript missense_variant 7540/8840 7166/7593 2389/2530 R/L cGc/cTc rs368833137 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0) 15/18 PROSITE_profiles:PS50041,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 5 1 PASS rs368833137 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 88872063 88872063 G T 1 0 0 0 0 1 0 0 0 160 1087 38 1 1 ACAN 15 88872063 Missense_Mutation SNP G 11LU022_T 32039 88872063 13119126 750 1388 TICRR 0 . GRCh38 15 89585853 89585853 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1322G>T p.Ser441Ile p.S441I ENST00000268138 4/22 267 236 31 269 269 0 strelka-varscan-mutect TICRR,missense_variant,p.Ser441Ile,ENST00000268138,NM_152259.3;TICRR,missense_variant,p.Ser440Ile,ENST00000560985,NM_001308025.1;RP11-429B14.1,intron_variant,,ENST00000559041,;RP11-429B14.3,upstream_gene_variant,,ENST00000560477,; T ENST00000268138 Transcript missense_variant 1427/6775 1322/5733 441/1910 S/I aGc/aTc 1 1 TICRR HGNC HGNC:28704 protein_coding YES CCDS10352.2 ENSP00000268138 Q7Z2Z1 UPI0000D61399 NM_152259.3 deleterious(0.02) 4/22 hmmpanther:PTHR21556,Pfam_domain:PF15292 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 89585853 89585853 G T 1 0 0 0 0 1 0 0 0 16328 971 34 2 2 TICRR 15 89585853 Missense_Mutation SNP G 11LU022_T 713790 89585853 12405336 751 1389 ANPEP 0 . GRCh38 15 89803443 89803443 + Missense_Mutation SNP G G T rs139342584 11LU022_T 11LU022_N G G c.1502C>A p.Ala501Glu p.A501E ENST00000300060 9/21 174 164 10 219 218 1 strelka-varscan-mutect ANPEP,missense_variant,p.Ala501Glu,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,missense_variant,p.Arg109Ser,ENST00000560030,;ANPEP,downstream_gene_variant,,ENST00000560028,;ANPEP,downstream_gene_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000559761,; T ENST00000300060 Transcript missense_variant,splice_region_variant 1816/3678 1502/2904 501/967 A/E gCg/gAg rs139342584 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 tolerated(0.45) 9/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs139342584 . 0 207 2 0 0 0 0 0 -18.14738 1 1 1 1 0 T 3 4 3 89803443 89803443 G T 1 0 0 0 0 1 0 0 0 817 1101 38 1 1 ANPEP 15 89803443 Missense_Mutation SNP G 11LU022_T 217590 89803443 12187746 752 1390 CRTC3 0 . GRCh38 15 90604448 90604448 + Splice_Site SNP G G A novel 11LU022_T 11LU022_N G G c.476+1G>A p.X159_splice ENST00000268184 112 92 20 154 154 0 strelka-varscan-mutect CRTC3,splice_donor_variant,,ENST00000420329,NM_001042574.2;CRTC3,splice_donor_variant,,ENST00000268184,NM_022769.4;CRTC3,splice_donor_variant,,ENST00000558005,;CRTC3,downstream_gene_variant,,ENST00000560098,;CTD-3065B20.3,non_coding_transcript_exon_variant,,ENST00000559839,;CRTC3,splice_donor_variant,,ENST00000558619,;CRTC3,splice_donor_variant,,ENST00000561255,;CRTC3,downstream_gene_variant,,ENST00000561218,;CRTC3,downstream_gene_variant,,ENST00000558496,;CRTC3,splice_donor_variant,,ENST00000561119,; A ENST00000268184 Transcript splice_donor_variant -/2537 476/1860 159/619 1 1 CRTC3 HGNC HGNC:26148 protein_coding YES CCDS32331.1 ENSP00000268184 Q6UUV7 UPI00001FEB98 NM_022769.4 5/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 90604448 90604448 G A 1 0 0 0 0 0 0 1 0 3703 1275 44 3 3 CRTC3 15 90604448 Splice_Site SNP G 11LU022_T 801005 90604448 11386741 753 1391 FES 0 . GRCh38 15 90890419 90890419 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1255G>T p.Gly419Ter p.G419* ENST00000328850 10/19 132 95 37 194 194 0 strelka-varscan-mutect FES,stop_gained,p.Gly419Ter,ENST00000328850,NM_002005.3;FES,stop_gained,p.Gly361Ter,ENST00000414248,NM_001143785.1;FES,stop_gained,p.Gly361Ter,ENST00000394300,NM_001143783.1;FES,stop_gained,p.Gly419Ter,ENST00000444422,NM_001143784.1;FES,stop_gained,p.Gly361Ter,ENST00000394302,;FES,downstream_gene_variant,,ENST00000452243,;FES,downstream_gene_variant,,ENST00000559355,;FES,downstream_gene_variant,,ENST00000443697,;FES,non_coding_transcript_exon_variant,,ENST00000448367,;FES,stop_gained,p.Gly419Ter,ENST00000464684,;FES,non_coding_transcript_exon_variant,,ENST00000496379,;FES,non_coding_transcript_exon_variant,,ENST00000462476,;FES,downstream_gene_variant,,ENST00000470152,;FES,downstream_gene_variant,,ENST00000481665,;FES,downstream_gene_variant,,ENST00000497945,;FES,downstream_gene_variant,,ENST00000494259,; T ENST00000328850 Transcript stop_gained 1397/2829 1255/2469 419/822 G/* Gga/Tga 1 1 FES HGNC HGNC:3657 protein_coding YES CCDS10365.1 ENSP00000331504 P07332 A0A024RC92 UPI0000001C30 NM_002005.3 10/19 hmmpanther:PTHR24418:SF197,hmmpanther:PTHR24418,PIRSF_domain:PIRSF000632 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 90890419 90890419 G T 1 0 0 0 0 0 1 0 0 5683 1233 43 2 2 FES 15 90890419 Nonsense_Mutation SNP G 11LU022_T 285971 90890419 11100770 754 1392 LRRK1 0 . GRCh38 15 101027646 101027646 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.2535G>T p.Arg845Ser p.R845S ENST00000388948 19/34 288 224 64 348 348 0 strelka-varscan-mutect LRRK1,missense_variant,p.Arg845Ser,ENST00000388948,NM_024652.4;LRRK1,3_prime_UTR_variant,,ENST00000525284,;LRRK1,3_prime_UTR_variant,,ENST00000531270,;LRRK1,downstream_gene_variant,,ENST00000525617,;LRRK1,downstream_gene_variant,,ENST00000538064,; T ENST00000388948 Transcript missense_variant 2894/7671 2535/6048 845/2015 R/S agG/agT 1 1 LRRK1 HGNC HGNC:18608 protein_coding YES CCDS42086.1 ENSP00000373600 Q38SD2 UPI0000D4FE63 NM_024652.4 deleterious(0.01) 19/34 Pfam_domain:PF16095 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 101027646 101027646 G T 1 0 0 0 0 1 0 0 0 8938 1165 41 2 2 LRRK1 15 101027646 Missense_Mutation SNP G 11LU022_T 10137227 101027646 963543 755 1393 AXIN1 0 . GRCh38 16 293519 293519 + Missense_Mutation SNP T T G novel 11LU022_T 11LU022_N T T c.2155A>C p.Lys719Gln p.K719Q ENST00000262320 8/11 141 124 17 229 229 0 strelka-varscan-mutect AXIN1,missense_variant,p.Lys719Gln,ENST00000262320,NM_003502.3;AXIN1,missense_variant,p.Lys719Gln,ENST00000354866,NM_181050.2;AXIN1,missense_variant,p.Lys7Gln,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; G ENST00000262320 Transcript missense_variant 2527/3643 2155/2589 719/862 K/Q Aag/Cag 1 -1 AXIN1 HGNC HGNC:903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 A0A0S2Z4R0 UPI000012669E NM_003502.3 deleterious(0.01) 8/11 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 293519 293519 T G 1 0 0 0 0 1 0 0 0 1393 1850 64 5 5 AXIN1 16 293519 Missense_Mutation SNP T 11LU022_T 293519 90044826 756 1394 MAPK8IP3 0 . GRCh38 16 1743356 1743356 + Silent SNP G G T 11LU022_T 11LU022_N G G c.624G>T p.= p.L208L ENST00000250894 5/32 89 73 16 168 168 0 strelka-varscan-mutect MAPK8IP3,synonymous_variant,p.=,ENST00000250894,NM_001318852.1,NM_015133.3;MAPK8IP3,synonymous_variant,p.=,ENST00000610761,;MAPK8IP3,synonymous_variant,p.=,ENST00000356010,NM_001040439.1;MAPK8IP3,upstream_gene_variant,,ENST00000568271,;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000564098,;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000561765,;MAPK8IP3,upstream_gene_variant,,ENST00000567849,;MAPK8IP3,upstream_gene_variant,,ENST00000568774,; T ENST00000250894 Transcript synonymous_variant 781/5661 624/4011 208/1336 L ctG/ctT COSM4826669,COSM4826670 1 1 MAPK8IP3 HGNC HGNC:6884 protein_coding YES CCDS10442.2 ENSP00000250894 Q9UPT6 UPI000034ECA7 NM_001318852.1,NM_015133.3 5/32 hmmpanther:PTHR13886,hmmpanther:PTHR13886:SF3 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 1743356 1743356 G T 1 0 0 0 0 0 0 0 1 9210 1277 45 2 2 MAPK8IP3 16 1743356 Silent SNP G 11LU022_T 1449837 1743356 88594989 757 1395 PKD1 0 . GRCh38 16 2116856 2116856 + Missense_Mutation SNP T T C rs750798165 11LU022_T 11LU022_N T T c.1583A>G p.Tyr528Cys p.Y528C ENST00000262304 7/46 420 359 61 609 609 0 strelka-varscan-mutect PKD1,missense_variant,p.Tyr528Cys,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Tyr528Cys,ENST00000423118,NM_000296.3;PKD1,intron_variant,,ENST00000488185,;PKD1,upstream_gene_variant,,ENST00000483024,;RP11-304L19.2,upstream_gene_variant,,ENST00000562027,;RP11-304L19.4,downstream_gene_variant,,ENST00000568795,;PKD1,intron_variant,,ENST00000570150,;PKD1,upstream_gene_variant,,ENST00000468674,;PKD1,missense_variant,p.Thr172Ala,ENST00000568591,;PKD1,upstream_gene_variant,,ENST00000483731,;PKD1,upstream_gene_variant,,ENST00000415938,;PKD1,upstream_gene_variant,,ENST00000565639,;PKD1,upstream_gene_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000469241,; C ENST00000262304 Transcript missense_variant 1792/14138 1583/12912 528/4303 Y/C tAc/tGc rs750798165,CM074432 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 deleterious(0) 7/46 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143,SMART_domains:SM00034,Superfamily_domains:SSF56436,TIGRFAM_domain:TIGR00864 MODERATE 1 SNV 1 0,1 1 PASS rs750798165 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 2116856 2116856 T C 1 0 0 0 0 1 0 0 0 12059 1638 57 5 5 PKD1 16 2116856 Missense_Mutation SNP T 11LU022_T 373500 2116856 88221489 758 1396 NLRC3 0 . GRCh38 16 3563415 3563415 + Missense_Mutation SNP C C T rs773631921 11LU022_T 11LU022_N C C c.1522G>A p.Gly508Arg p.G508R ENST00000359128 5/20 135 113 22 176 176 0 strelka-varscan-mutect NLRC3,missense_variant,p.Gly508Arg,ENST00000359128,NM_178844.3;NLRC3,missense_variant,p.Gly555Arg,ENST00000324659,;NLRC3,downstream_gene_variant,,ENST00000603055,;NLRC3,missense_variant,p.Gly508Arg,ENST00000615877,; T ENST00000359128 Transcript missense_variant 1933/6401 1522/3198 508/1065 G/R Ggg/Agg rs773631921,COSM1301949,COSM4812622 1 -1 NLRC3 HGNC HGNC:29889 protein_coding YES CCDS73817.1 ENSP00000352039 Q7RTR2 C3VPR7 UPI00004CE17D NM_178844.3 tolerated(0.09) 5/20 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF127 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs773631921 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 3563415 3563415 C T 1 0 0 0 0 1 0 0 0 10505 652 23 1 1 NLRC3 16 3563415 Missense_Mutation SNP C 11LU022_T 1446559 3563415 86774930 759 1397 CREBBP 0 . GRCh38 16 3728306 3728306 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.6741G>T p.Gln2247His p.Q2247H ENST00000262367 31/31 100 87 13 204 204 0 strelka-varscan-mutect CREBBP,missense_variant,p.Gln2247His,ENST00000262367,NM_004380.2;CREBBP,missense_variant,p.Gln2209His,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000637492,;CREBBP,downstream_gene_variant,,ENST00000576720,;CREBBP,downstream_gene_variant,,ENST00000571763,; A ENST00000262367 Transcript missense_variant 7551/10803 6741/7329 2247/2442 Q/H caG/caT 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 deleterious_low_confidence(0.03) 31/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 3728306 3728306 C A 1 0 0 0 0 1 0 0 0 3661 796 28 2 2 CREBBP 16 3728306 Missense_Mutation SNP C 11LU022_T 164891 3728306 86610039 760 1398 SEPT12 0 . GRCh38 16 4784001 4784001 + Missense_Mutation SNP T T A rs757367193 11LU022_T 11LU022_N T T c.442A>T p.Thr148Ser p.T148S ENST00000268231 5/10 196 174 22 309 309 0 strelka-varscan-mutect SEPT12,missense_variant,p.Thr148Ser,ENST00000268231,NM_144605.4;SEPT12,intron_variant,,ENST00000396693,NM_001154458.2;SMIM22,upstream_gene_variant,,ENST00000615889,NM_001253791.1;SMIM22,upstream_gene_variant,,ENST00000615471,;SMIM22,upstream_gene_variant,,ENST00000589721,NM_001253790.1;SMIM22,upstream_gene_variant,,ENST00000589327,;SEPT12,downstream_gene_variant,,ENST00000591624,;SEPT12,downstream_gene_variant,,ENST00000591861,;SEPT12,missense_variant,p.Thr148Ser,ENST00000587603,;SEPT12,3_prime_UTR_variant,,ENST00000590741,;SEPT12,intron_variant,,ENST00000588241,;SMIM22,upstream_gene_variant,,ENST00000591004,;SEPT12,downstream_gene_variant,,ENST00000590303,; A ENST00000268231 Transcript missense_variant 706/1469 442/1077 148/358 T/S Acc/Tcc rs757367193 1 -1 SEPT12 HGNC HGNC:26348 protein_coding YES CCDS10522.1 ENSP00000268231 Q8IYM1 UPI000007422A NM_144605.4 tolerated(0.26) 5/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF66,Pfam_domain:PF00735,Gene3D:3.40.50.300,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs757367193 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 4784001 4784001 T A 1 0 0 0 0 1 0 0 0 14338 1696 59 4 4 SEPT12 16 4784001 Missense_Mutation SNP T 11LU022_T 1055695 4784001 85554344 761 1399 SOCS1 0 . GRCh38 16 11254991 11254991 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.488G>T p.Gly163Val p.G163V ENST00000332029 2/2 200 161 39 272 270 2 strelka-varscan-mutect SOCS1,missense_variant,p.Gly163Val,ENST00000332029,NM_003745.1;RMI2,intron_variant,,ENST00000572173,;RMI2,intron_variant,,ENST00000573910,; A ENST00000332029 Transcript missense_variant 639/1225 488/636 163/211 G/V gGg/gTg 1 -1 SOCS1 HGNC HGNC:19383 protein_coding YES CCDS10546.1 ENSP00000329418 O15524 Q4JHT5 UPI0000033166 NM_003745.1 tolerated(0.39) 2/2 PROSITE_profiles:PS50001,PROSITE_profiles:PS50225,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF72,Gene3D:3.30.505.10,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs1412108457 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 11254991 11254991 C A 1 0 0 0 0 1 0 0 0 15234 623 22 2 2 SOCS1 16 11254991 Missense_Mutation SNP C 11LU022_T 6470990 11254991 79083354 762 1400 MKL2 0 . GRCh38 16 14240442 14240442 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1037A>T p.Lys346Met p.K346M ENST00000571589 10/17 151 129 22 179 179 0 strelka-varscan-mutect MKL2,missense_variant,p.Lys346Met,ENST00000571589,NM_001308142.1;MKL2,missense_variant,p.Lys346Met,ENST00000318282,;MKL2,missense_variant,p.Lys346Met,ENST00000574045,NM_014048.3;MKL2,missense_variant,p.Lys335Met,ENST00000572567,;MKL2,missense_variant,p.Lys295Met,ENST00000573051,; T ENST00000571589 Transcript missense_variant 1209/8799 1037/3300 346/1099 K/M aAg/aTg 1 1 MKL2 HGNC HGNC:29819 protein_coding YES CCDS76823.1 ENSP00000459626 Q9ULH7 UPI00001FEE5A NM_001308142.1 deleterious(0) 10/17 Low_complexity_(Seg):seg,hmmpanther:PTHR22793:SF5,hmmpanther:PTHR22793 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 14240442 14240442 A T 1 0 0 0 0 1 0 0 0 9569 72 3 4 4 MKL2 16 14240442 Missense_Mutation SNP A 11LU022_T 2985451 14240442 76097903 763 1401 XYLT1 0 . GRCh38 16 17134617 17134617 + Frame_Shift_Del DEL C C - rs775575069 11LU022_T 11LU022_N C C c.1883delG p.Arg628ProfsTer17 p.R628Pfs*17 ENST00000261381 9/12 302 252 50 430 430 0 sindel-varindel-pindel XYLT1,frameshift_variant,p.Arg628ProfsTer17,ENST00000261381,NM_022166.3;CTD-2576D5.4,intron_variant,,ENST00000567344,; - ENST00000261381 Transcript frameshift_variant 1968/9891 1883/2880 628/959 R/X cGc/cc rs775575069,COSM2127790 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 9/12 Pfam_domain:PF12529 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 17134617 17134617 C - 1 0 1 0 1 0 0 0 0 18022 768 27 0 0 XYLT1 16 17134617 Frame_Shift_Del DEL C 11LU022_T 2894175 17134617 73203728 764 1402 SMG1 0 . GRCh38 16 18847876 18847876 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.5781G>T p.Gln1927His p.Q1927H ENST00000446231 37/63 235 211 24 293 292 1 strelka-varscan-mutect SMG1,missense_variant,p.Gln1927His,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Gln1817His,ENST00000565324,;SMG1,non_coding_transcript_exon_variant,,ENST00000563448,;SMG1,non_coding_transcript_exon_variant,,ENST00000562668,; A ENST00000446231 Transcript missense_variant 6194/16115 5781/10986 1927/3661 Q/H caG/caT 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 deleterious(0.03) 37/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF71,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 18847876 18847876 C A 1 0 0 0 0 1 0 0 0 15089 680 24 2 2 SMG1 16 18847876 Missense_Mutation SNP C 11LU022_T 1713259 18847876 71490469 765 1403 DNAH3 0 . GRCh38 16 20959311 20959311 + Missense_Mutation SNP A A C rs150878924 11LU022_T 11LU022_N A A c.10694T>G p.Met3565Arg p.M3565R ENST00000261383 54/62 381 344 37 422 421 1 strelka-varscan-mutect DNAH3,missense_variant,p.Met3565Arg,ENST00000261383,NM_017539.2; C ENST00000261383 Transcript missense_variant 10694/12394 10694/12351 3565/4116 M/R aTg/aGg rs150878924 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0) 54/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS rs150878924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 20959311 20959311 A C 1 0 0 0 0 1 0 0 0 4418 217 8 5 5 DNAH3 16 20959311 Missense_Mutation SNP A 11LU022_T 2111435 20959311 69379034 766 1404 VWA3A 0 . GRCh38 16 22110896 22110896 + Silent SNP C C T rs776374263 11LU022_T 11LU022_N C C c.591C>T p.= p.I197I ENST00000389398 8/34 107 89 18 103 103 0 strelka-mutect VWA3A,synonymous_variant,p.=,ENST00000389398,NM_173615.4;VWA3A,synonymous_variant,p.=,ENST00000568328,;VWA3A,synonymous_variant,p.=,ENST00000567131,;VWA3A,non_coding_transcript_exon_variant,,ENST00000566668,;VWA3A,non_coding_transcript_exon_variant,,ENST00000562340,; T ENST00000389398 Transcript synonymous_variant 687/4600 591/3555 197/1184 I atC/atT rs776374263,COSM1478629 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 8/34 hmmpanther:PTHR10338:SF95,hmmpanther:PTHR10338,Pfam_domain:PF13768,Superfamily_domains:SSF53300 0,1 LOW 1 SNV 5 0,1 1 PASS rs776374263 . 0 204 4 2 0 0 0 0 -20 0.9999865 1 1 1 0 T 2 4 3 22110896 22110896 C T 1 0 0 0 0 0 0 0 1 17794 874 31 1 1 VWA3A 16 22110896 Silent SNP C 11LU022_T 1151585 22110896 68227449 767 1405 COG7 0 . GRCh38 16 23403767 23403767 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1730A>T p.Gln577Leu p.Q577L ENST00000307149 13/17 384 336 48 539 539 0 strelka-varscan-mutect COG7,missense_variant,p.Gln577Leu,ENST00000307149,NM_153603.3;COG7,non_coding_transcript_exon_variant,,ENST00000567821,; A ENST00000307149 Transcript missense_variant 1916/2926 1730/2313 577/770 Q/L cAg/cTg 1 -1 COG7 HGNC HGNC:18622 protein_coding YES CCDS10610.1 ENSP00000305442 P83436 A0A0S2Z652 UPI0000127E42 NM_153603.3 tolerated(0.19) 13/17 hmmpanther:PTHR21443,Pfam_domain:PF10191 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 23403767 23403767 T A 1 0 0 0 0 1 0 0 0 3451 1580 55 4 4 COG7 16 23403767 Missense_Mutation SNP T 11LU022_T 1292871 23403767 66934578 768 1406 KIAA0556 0 . GRCh38 16 27775070 27775070 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.4435A>G p.Ile1479Val p.I1479V ENST00000261588 24/28 192 151 41 236 236 0 strelka-varscan-mutect KIAA0556,missense_variant,p.Ile1479Val,ENST00000261588,NM_015202.2;KIAA0556,upstream_gene_variant,,ENST00000568622,; G ENST00000261588 Transcript missense_variant 4454/6616 4435/4857 1479/1618 I/V Atc/Gtc 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 tolerated(0.59) 24/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534,Pfam_domain:PF14652 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 27775070 27775070 A G 1 0 0 0 0 1 0 0 0 8088 217 8 5 5 KIAA0556 16 27775070 Missense_Mutation SNP A 11LU022_T 4371303 27775070 62563275 769 1407 APOBR 0 . GRCh38 16 28497873 28497873 + Missense_Mutation SNP G G T rs751700329 11LU022_T 11LU022_N G G c.2832G>T p.Arg944Ser p.R944S ENST00000564831 2/4 222 160 62 240 240 0 strelka-varscan-mutect APOBR,missense_variant,p.Arg944Ser,ENST00000564831,NM_018690.3;APOBR,missense_variant,p.Arg935Ser,ENST00000431282,;CLN3,upstream_gene_variant,,ENST00000569430,;IL27,downstream_gene_variant,,ENST00000356897,NM_145659.3;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566472,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,;CLN3,upstream_gene_variant,,ENST00000563874,; T ENST00000564831 Transcript missense_variant 2865/3792 2832/3294 944/1097 R/S agG/agT rs751700329 1 1 APOBR HGNC HGNC:24087 protein_coding YES CCDS58442.1 ENSP00000457539 Q0VD83 UPI000013EFFC NM_018690.3 tolerated(0.27) 2/4 hmmpanther:PTHR15964:SF0,hmmpanther:PTHR15964 MODERATE 1 SNV 1 1 PASS rs751700329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 28497873 28497873 G T 1 0 0 0 0 1 0 0 0 918 1223 43 2 2 APOBR 16 28497873 Missense_Mutation SNP G 11LU022_T 722803 28497873 61840472 770 1408 SH2B1 0 . GRCh38 16 28871811 28871811 + Frame_Shift_Del DEL G G - rs529774248 11LU022_T 11LU022_N G G c.1342delG p.Ala448HisfsTer95 p.A448Hfs*95 ENST00000322610 8/11 169 148 21 194 194 0 sindel-varindel-pindel SH2B1,frameshift_variant,p.Ala448HisfsTer95,ENST00000337120,NM_001145796.1,NM_001145812.1,NM_015503.2;SH2B1,frameshift_variant,p.Ala448HisfsTer95,ENST00000322610,NM_001308293.1;SH2B1,frameshift_variant,p.Ala448HisfsTer95,ENST00000359285,NM_001145797.1;SH2B1,frameshift_variant,p.Ala448HisfsTer95,ENST00000618521,NM_001145795.1;SH2B1,frameshift_variant,p.Ala448HisfsTer95,ENST00000395532,;SH2B1,frameshift_variant,p.Ala112HisfsTer95,ENST00000538342,NM_001308294.1;SH2B1,frameshift_variant,p.Ala138HisfsTer95,ENST00000545570,;SH2B1,frameshift_variant,p.Ala89HisfsTer?,ENST00000561629,;SH2B1,frameshift_variant,p.Ala135HisfsTer?,ENST00000566176,;SH2B1,upstream_gene_variant,,ENST00000569651,;SH2B1,downstream_gene_variant,,ENST00000567536,;SH2B1,upstream_gene_variant,,ENST00000568868,;SH2B1,intron_variant,,ENST00000563674,;SH2B1,non_coding_transcript_exon_variant,,ENST00000569471,; - ENST00000322610 Transcript frameshift_variant 1780/3095 1341/2271 447/756 S/X tcG/tc rs529774248 1 1 SH2B1 HGNC HGNC:30417 protein_coding YES CCDS53996.1 ENSP00000321221 Q9NRF2 A0A024QZD2 UPI00001AF36C NM_001308293.1 8/11 hmmpanther:PTHR10872,hmmpanther:PTHR10872:SF3,Low_complexity_(Seg):seg HIGH 1 deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 28871811 28871811 G - 1 0 1 0 1 0 0 0 0 14485 1103 39 0 0 SH2B1 16 28871811 Frame_Shift_Del DEL G 11LU022_T 373938 28871811 61466534 771 1409 QPRT 0 . GRCh38 16 29697341 29697341 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.824C>A p.Ala275Glu p.A275E ENST00000395384 4/4 168 138 30 195 194 1 strelka-varscan-mutect QPRT,missense_variant,p.Ala275Glu,ENST00000395384,NM_014298.3;QPRT,missense_variant,p.Ala127Glu,ENST00000562473,;AC009133.22,downstream_gene_variant,,ENST00000449759,;QPRT,non_coding_transcript_exon_variant,,ENST00000219771,;QPRT,non_coding_transcript_exon_variant,,ENST00000564967,; A ENST00000395384 Transcript missense_variant 985/2343 824/894 275/297 A/E gCg/gAg 1 1 QPRT HGNC HGNC:9755 protein_coding YES CCDS10651.1 ENSP00000378782 Q15274 UPI000013C78C NM_014298.3 deleterious(0) 4/4 hmmpanther:PTHR32179,PIRSF_domain:PIRSF006250,TIGRFAM_domain:TIGR00078,Pfam_domain:PF01729,Superfamily_domains:SSF51690 MODERATE 1 SNV 1 1 PASS rs1375163461 . 0 203 0 6 0 0 0 0 -20 0.9988204 1 1 1 0 A 3 1 3 29697341 29697341 C A 1 0 0 0 0 1 0 0 0 13031 768 27 1 1 QPRT 16 29697341 Missense_Mutation SNP C 11LU022_T 825530 29697341 60641004 772 1410 ALDOA 0 . GRCh38 16 30067584 30067584 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.409A>G p.Thr137Ala p.T137A ENST00000395248 10/16 334 268 66 444 444 0 strelka-varscan-mutect ALDOA,missense_variant,p.Thr83Ala,ENST00000566897,;ALDOA,missense_variant,p.Thr137Ala,ENST00000395248,;ALDOA,missense_variant,p.Thr83Ala,ENST00000627059,;ALDOA,missense_variant,p.Thr83Ala,ENST00000338110,NM_000034.3;ALDOA,missense_variant,p.Thr83Ala,ENST00000564546,NM_184041.2;ALDOA,missense_variant,p.Thr137Ala,ENST00000564595,NM_001243177.1;ALDOA,missense_variant,p.Thr83Ala,ENST00000412304,NM_001127617.2;ALDOA,missense_variant,p.Thr83Ala,ENST00000563060,NM_184043.2;ALDOA,missense_variant,p.Thr83Ala,ENST00000569798,;ALDOA,missense_variant,p.Thr83Ala,ENST00000395240,;ALDOA,missense_variant,p.Thr83Ala,ENST00000569545,;ALDOA,missense_variant,p.Thr137Ala,ENST00000562679,;ALDOA,missense_variant,p.Thr72Ala,ENST00000562168,;ALDOA,missense_variant,p.Thr28Ala,ENST00000564688,;ALDOA,missense_variant,p.Thr83Ala,ENST00000563987,;ALDOA,missense_variant,p.Thr72Ala,ENST00000566846,;ALDOA,downstream_gene_variant,,ENST00000568435,;ALDOA,upstream_gene_variant,,ENST00000565355,;ALDOA,downstream_gene_variant,,ENST00000636698,;CTD-2515O10.5,upstream_gene_variant,,ENST00000617969,;ALDOA,non_coding_transcript_exon_variant,,ENST00000566012,;ALDOA,downstream_gene_variant,,ENST00000575627,;ALDOA,downstream_gene_variant,,ENST00000562240,;ALDOA,non_coding_transcript_exon_variant,,ENST00000564521,;ALDOA,non_coding_transcript_exon_variant,,ENST00000567555,;ALDOA,upstream_gene_variant,,ENST00000566130,;ALDOA,downstream_gene_variant,,ENST00000562302,;ALDOA,upstream_gene_variant,,ENST00000566146,; G ENST00000395248 Transcript missense_variant 1391/2447 409/1257 137/418 T/A Aca/Gca 1 1 ALDOA HGNC HGNC:414 protein_coding YES CCDS58450.1 ENSP00000378669 P04075 UPI0000E59D76 deleterious(0.01) 10/16 hmmpanther:PTHR11627,Gene3D:3.20.20.70,Pfam_domain:PF00274,Superfamily_domains:SSF51569 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 30067584 30067584 A G 1 0 0 0 0 1 0 0 0 607 275 10 5 5 ALDOA 16 30067584 Missense_Mutation SNP A 11LU022_T 370243 30067584 60270761 773 1411 SEPT1 0 . GRCh38 16 30378689 30378689 + Missense_Mutation SNP C C G rs147923586 11LU022_T 11LU022_N C C c.1079G>C p.Arg360Pro p.R360P ENST00000321367 11/12 96 71 25 113 113 0 strelka-varscan-mutect SEPT1,missense_variant,p.Arg360Pro,ENST00000321367,NM_052838.4;ZNF48,intron_variant,,ENST00000528032,;ZNF48,intron_variant,,ENST00000495929,;MYLPF,downstream_gene_variant,,ENST00000322861,NM_013292.3;MYLPF,downstream_gene_variant,,ENST00000568749,;MYLPF,downstream_gene_variant,,ENST00000566955,;MYLPF,downstream_gene_variant,,ENST00000563718,;SEPT1,downstream_gene_variant,,ENST00000570039,;SEPT1,downstream_gene_variant,,ENST00000567783,;RP11-297C4.6,downstream_gene_variant,,ENST00000624127,;SEPT1,3_prime_UTR_variant,,ENST00000572252,;SEPT1,non_coding_transcript_exon_variant,,ENST00000563957,;SEPT1,non_coding_transcript_exon_variant,,ENST00000573615,;SEPT1,non_coding_transcript_exon_variant,,ENST00000566517,;SEPT1,downstream_gene_variant,,ENST00000568577,;SEPT1,downstream_gene_variant,,ENST00000563743,;SEPT1,downstream_gene_variant,,ENST00000562152,;MYLPF,downstream_gene_variant,,ENST00000563728,; G ENST00000321367 Transcript missense_variant 1125/1592 1079/1245 360/414 R/P cGc/cCc rs147923586 1 -1 SEPT1 HGNC HGNC:2879 protein_coding YES CCDS10678.3 ENSP00000324511 J3KNL2 UPI000066D948 NM_052838.4 tolerated(0.09) 11/12 hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF6,PIRSF_domain:PIRSF006698 MODERATE SNV 5 1 PASS rs147923586 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 30378689 30378689 C G 1 0 0 0 0 1 0 0 0 14335 768 27 4 4 SEPT1 16 30378689 Missense_Mutation SNP C 11LU022_T 311105 30378689 59959656 774 1412 ZNF646 0 . GRCh38 16 31079668 31079668 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.3344C>T p.Pro1115Leu p.P1115L ENST00000300850 2/3 113 86 27 153 153 0 strelka-varscan-mutect ZNF646,missense_variant,p.Pro1115Leu,ENST00000394979,;ZNF646,missense_variant,p.Pro1115Leu,ENST00000300850,NM_014699.3;PRSS53,downstream_gene_variant,,ENST00000280606,NM_001039503.2;ZNF646,downstream_gene_variant,,ENST00000428260,;ZNF646,downstream_gene_variant,,ENST00000564189,;PRSS53,downstream_gene_variant,,ENST00000486499,;RP11-196G11.1,downstream_gene_variant,,ENST00000533518,; T ENST00000300850 Transcript missense_variant 3633/6892 3344/5499 1115/1832 P/L cCa/cTa 1 1 ZNF646 HGNC HGNC:29004 protein_coding YES CCDS10702.1 ENSP00000300850 O15015 UPI00001FFF54 NM_014699.3 deleterious(0.01) 2/3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 31079668 31079668 C T 1 0 0 0 0 1 0 0 0 18635 594 21 3 3 ZNF646 16 31079668 Missense_Mutation SNP C 11LU022_T 700979 31079668 59258677 775 1413 ITGAX 0 . GRCh38 16 31357295 31357295 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.361T>A p.Tyr121Asn p.Y121N ENST00000562522 5/31 122 106 16 136 136 0 strelka-varscan-mutect ITGAX,missense_variant,p.Tyr121Asn,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Tyr121Asn,ENST00000562522,NM_001286375.1;ITGAX,intron_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000567409,;ITGAX,upstream_gene_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000564308,;RP11-120K18.3,downstream_gene_variant,,ENST00000561830,; A ENST00000562522 Transcript missense_variant 394/3990 361/3510 121/1169 Y/N Tac/Aac 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.01) 5/31 PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF53300,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 31357295 31357295 T A 1 0 0 0 0 1 0 0 0 7796 1638 57 4 4 ITGAX 16 31357295 Missense_Mutation SNP T 11LU022_T 277627 31357295 58981050 776 1414 ITGAD 0 . GRCh38 16 31426109 31426109 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3467C>A p.Pro1156Gln p.P1156Q ENST00000389202 30/30 214 175 39 283 283 0 strelka-varscan-mutect ITGAD,missense_variant,p.Pro1156Gln,ENST00000389202,NM_001318185.1,NM_005353.2;COX6A2,downstream_gene_variant,,ENST00000287490,NM_005205.3;RP11-452L6.8,upstream_gene_variant,,ENST00000615068,;ITGAD,downstream_gene_variant,,ENST00000567308,;COX6A2,downstream_gene_variant,,ENST00000565462,; A ENST00000389202 Transcript missense_variant 3516/3912 3467/3486 1156/1161 P/Q cCa/cAa 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 deleterious_low_confidence(0) 30/30 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 31426109 31426109 C A 1 0 0 0 0 1 0 0 0 7791 594 21 2 2 ITGAD 16 31426109 Missense_Mutation SNP C 11LU022_T 68814 31426109 58912236 777 1415 VPS35 0 . GRCh38 16 46677353 46677353 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.766G>T p.Ala256Ser p.A256S ENST00000299138 7/17 187 149 38 322 322 0 strelka-varscan-mutect VPS35,missense_variant,p.Ala256Ser,ENST00000299138,NM_018206.4;VPS35,non_coding_transcript_exon_variant,,ENST00000568642,;RP11-93O14.3,upstream_gene_variant,,ENST00000623850,;VPS35,3_prime_UTR_variant,,ENST00000568784,;VPS35,non_coding_transcript_exon_variant,,ENST00000569950,;VPS35,non_coding_transcript_exon_variant,,ENST00000565228,;VPS35,downstream_gene_variant,,ENST00000563884,;VPS35,downstream_gene_variant,,ENST00000568612,;VPS35,downstream_gene_variant,,ENST00000561713,;VPS35,downstream_gene_variant,,ENST00000568191,; A ENST00000299138 Transcript missense_variant 825/6790 766/2391 256/796 A/S Gct/Tct 1 -1 VPS35 HGNC HGNC:13487 protein_coding YES CCDS10721.1 ENSP00000299138 Q96QK1 UPI0000138BEF NM_018206.4 tolerated(0.33) 7/17 Pfam_domain:PF03635,hmmpanther:PTHR11099,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 46677353 46677353 C A 1 0 0 0 0 1 0 0 0 17749 710 25 2 2 VPS35 16 46677353 Missense_Mutation SNP C 11LU022_T 15251244 46677353 43660992 778 1416 CHD9 0 . GRCh38 16 53286226 53286226 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.5072G>C p.Gly1691Ala p.G1691A ENST00000447540 26/39 45 35 10 80 80 0 strelka-varscan-mutect CHD9,missense_variant,p.Gly1691Ala,ENST00000566029,NM_025134.4;CHD9,missense_variant,p.Gly1691Ala,ENST00000447540,NM_001308319.1;CHD9,missense_variant,p.Gly1691Ala,ENST00000564845,;CHD9,missense_variant,p.Gly1691Ala,ENST00000398510,;CHD9,missense_variant,p.Gly59Ala,ENST00000615216,;CHD9,missense_variant,p.Gly59Ala,ENST00000622617,;CHD9,splice_region_variant,,ENST00000219084,; C ENST00000447540 Transcript missense_variant,splice_region_variant 5281/11509 5072/8694 1691/2897 G/A gGa/gCa 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 deleterious(0) 26/39 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -19.99998 0.9999998 1 1 1 0 C 3 2 3 53286226 53286226 G C 1 0 0 0 0 1 0 0 0 3091 1188 41 4 4 CHD9 16 53286226 Missense_Mutation SNP G 11LU022_T 6608873 53286226 37052119 779 1417 CNOT1 0 . GRCh38 16 58556846 58556846 + Splice_Site SNP C C A novel 11LU022_T 11LU022_N C C c.2479+1G>T p.X827_splice ENST00000317147 74 50 24 99 99 0 strelka-varscan-mutect CNOT1,splice_donor_variant,,ENST00000317147,NM_016284.4;CNOT1,splice_donor_variant,,ENST00000441024,NM_206999.2;CNOT1,splice_donor_variant,,ENST00000569882,;CNOT1,splice_donor_variant,,ENST00000562046,;CNOT1,intron_variant,,ENST00000569240,NM_001265612.1;AC010287.1,downstream_gene_variant,,ENST00000623879,;SNORA50A,downstream_gene_variant,,ENST00000629536,;SNORA50A,downstream_gene_variant,,ENST00000384225,;CNOT1,intron_variant,,ENST00000569732,;CNOT1,intron_variant,,ENST00000567188,; A ENST00000317147 Transcript splice_donor_variant -/8471 2479/7131 827/2376 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 19/48 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 3 58556846 58556846 C A 1 0 0 0 0 0 0 1 0 3396 492 17 2 2 CNOT1 16 58556846 Splice_Site SNP C 11LU022_T 5270620 58556846 31781499 780 1418 CMTM1 0 . GRCh38 16 66566559 66566559 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.46G>T p.Gly16Trp p.G16W ENST00000379500 1/4 105 76 29 156 156 0 strelka-varscan-mutect CMTM1,missense_variant,p.Gly16Trp,ENST00000379500,NM_052999.3;CMTM1,missense_variant,p.Gly16Trp,ENST00000328020,NM_181268.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000533953,;CMTM1,missense_variant,p.Gly16Trp,ENST00000457188,NM_181269.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000528324,NM_181270.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000332695,NM_181271.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000336328,NM_181272.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000531885,NM_181283.2;CMTM1,missense_variant,p.Gly16Trp,ENST00000533666,NM_181296.2;CMTM1,5_prime_UTR_variant,,ENST00000529506,;CKLF-CMTM1,intron_variant,,ENST00000616804,NM_001204099.1;CKLF-CMTM1,intron_variant,,ENST00000527729,NM_001202509.1;CKLF-CMTM1,intron_variant,,ENST00000529718,;CKLF-CMTM1,intron_variant,,ENST00000615332,NM_001204098.1;CKLF,downstream_gene_variant,,ENST00000264001,NM_016951.3;CKLF,downstream_gene_variant,,ENST00000417030,NM_001040138.2;CKLF-CMTM1,downstream_gene_variant,,ENST00000532838,;CKLF,downstream_gene_variant,,ENST00000345436,NM_181641.2;CKLF,downstream_gene_variant,,ENST00000351137,NM_181640.2;CKLF,downstream_gene_variant,,ENST00000362093,NM_016326.3;RP11-403P17.6,upstream_gene_variant,,ENST00000612427,;CKLF,downstream_gene_variant,,ENST00000563092,;CMTM1,missense_variant,p.Gly16Trp,ENST00000529386,;CMTM1,missense_variant,p.Gly16Trp,ENST00000533915,;CMTM1,missense_variant,p.Gly16Trp,ENST00000333001,;CMTM1,missense_variant,p.Gly16Trp,ENST00000528484,;CMTM1,missense_variant,p.Gly16Trp,ENST00000533078,;CKLF-CMTM1,intron_variant,,ENST00000527845,;CMTM1,upstream_gene_variant,,ENST00000479381,;CMTM1,upstream_gene_variant,,ENST00000528441,;CMTM1,upstream_gene_variant,,ENST00000530141,;CMTM1,upstream_gene_variant,,ENST00000465057,;CMTM1,upstream_gene_variant,,ENST00000534143,;CKLF,downstream_gene_variant,,ENST00000534692,; T ENST00000379500 Transcript missense_variant 113/1064 46/861 16/286 G/W Ggg/Tgg COSM1609491,COSM1609492 1 1 CMTM1 HGNC HGNC:19172 protein_coding YES CCDS10812.2 ENSP00000368814 Q8IZ96 UPI000056D4A6 NM_052999.3 deleterious(0.01) 1/4 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 66566559 66566559 G T 1 0 0 0 0 1 0 0 0 3358 1000 35 2 2 CMTM1 16 66566559 Missense_Mutation SNP G 11LU022_T 8009713 66566559 23771786 781 1419 KCTD19 0 . GRCh38 16 67320834 67320834 + Missense_Mutation SNP C C A rs761287238 11LU022_T 11LU022_N C C c.55G>T p.Val19Leu p.V19L ENST00000304372 2/16 133 101 32 158 158 0 strelka-varscan-mutect KCTD19,missense_variant,p.Val19Leu,ENST00000304372,NM_001100915.1;KCTD19,missense_variant,p.Val14Leu,ENST00000567976,;KCTD19,missense_variant,p.Val14Leu,ENST00000566295,;RN7SKP118,downstream_gene_variant,,ENST00000364331,;KCTD19,non_coding_transcript_exon_variant,,ENST00000561625,;KCTD19,upstream_gene_variant,,ENST00000562860,;KCTD19,synonymous_variant,p.=,ENST00000562721,;KCTD19,non_coding_transcript_exon_variant,,ENST00000569333,;KCTD19,non_coding_transcript_exon_variant,,ENST00000570049,;KCTD19,non_coding_transcript_exon_variant,,ENST00000566392,;KCTD19,non_coding_transcript_exon_variant,,ENST00000568736,; A ENST00000304372 Transcript missense_variant 111/2958 55/2781 19/926 V/L Gta/Tta rs761287238 1 -1 KCTD19 HGNC HGNC:24753 protein_coding YES CCDS42179.1 ENSP00000305702 Q17RG1 UPI00001D7875 NM_001100915.1 deleterious(0) 2/16 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF20,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS rs761287238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 67320834 67320834 C A 1 0 0 0 0 1 0 0 0 8023 536 19 1 1 KCTD19 16 67320834 Missense_Mutation SNP C 11LU022_T 754275 67320834 23017511 782 1420 ACD 0 . GRCh38 16 67660323 67660323 + Silent SNP G G C rs765151223 11LU022_T 11LU022_N G G c.156C>G p.= p.L52L ENST00000620338 1/12 160 97 63 294 294 0 strelka-varscan-mutect ACD,synonymous_variant,p.=,ENST00000620338,NM_001082486.1;ACD,synonymous_variant,p.=,ENST00000219251,NM_001082487.1,NM_022914.2;ACD,synonymous_variant,p.=,ENST00000393919,;CARMIL2,downstream_gene_variant,,ENST00000334583,NM_001013838.1;CARMIL2,downstream_gene_variant,,ENST00000545661,NM_001317026.1;ENKD1,downstream_gene_variant,,ENST00000243878,NM_032140.1;ACD,upstream_gene_variant,,ENST00000620761,;ACD,upstream_gene_variant,,ENST00000602320,;ENKD1,downstream_gene_variant,,ENST00000602644,;PARD6A,upstream_gene_variant,,ENST00000458121,NM_001037281.1;PARD6A,upstream_gene_variant,,ENST00000219255,NM_016948.2;PARD6A,upstream_gene_variant,,ENST00000602551,;ACD,upstream_gene_variant,,ENST00000602382,;ENKD1,downstream_gene_variant,,ENST00000602409,;ENKD1,downstream_gene_variant,,ENST00000602415,;ACD,upstream_gene_variant,,ENST00000602622,;ACD,upstream_gene_variant,,ENST00000602860,;PARD6A,upstream_gene_variant,,ENST00000602727,;ENKD1,downstream_gene_variant,,ENST00000602942,;ACD,upstream_gene_variant,,ENST00000602519,;CARMIL2,downstream_gene_variant,,ENST00000602368,;ENKD1,downstream_gene_variant,,ENST00000602531,;ACD,upstream_gene_variant,,ENST00000602850,;ACD,upstream_gene_variant,,ENST00000602945,;ACD,upstream_gene_variant,,ENST00000602656,;CARMIL2,downstream_gene_variant,,ENST00000602705,;ACD,upstream_gene_variant,,ENST00000602780,;ACD,upstream_gene_variant,,ENST00000602821,;ENKD1,downstream_gene_variant,,ENST00000602642,;ACD,upstream_gene_variant,,ENST00000602423,; C ENST00000620338 Transcript synonymous_variant 493/2065 156/1635 52/544 L ctC/ctG rs765151223 1 -1 ACD HGNC HGNC:25070 protein_coding YES CCDS42181.1 ENSP00000483117 Q96AP0 UPI0000246BB2 NM_001082486.1 1/12 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs765151223 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 67660323 67660323 G C 1 0 0 0 0 0 0 0 1 173 1161 41 4 4 ACD 16 67660323 Silent SNP G 11LU022_T 339489 67660323 22678022 783 1421 TMEM231 0 . GRCh38 16 75540165 75540165 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.780A>T p.= p.P260P ENST00000258173 7/7 46 31 15 53 53 0 strelka-varscan-mutect TMEM231,synonymous_variant,p.=,ENST00000258173,NM_001077418.2;TMEM231,synonymous_variant,p.=,ENST00000568377,NM_001077416.2;TMEM231,synonymous_variant,p.=,ENST00000565067,;CHST5,upstream_gene_variant,,ENST00000336257,NM_024533.4;CHST5,upstream_gene_variant,,ENST00000565039,;TMEM231,non_coding_transcript_exon_variant,,ENST00000569294,;RP11-77K12.8,downstream_gene_variant,,ENST00000564489,;TMEM231,downstream_gene_variant,,ENST00000564576,;TMEM231,3_prime_UTR_variant,,ENST00000562410,;TMEM231,3_prime_UTR_variant,,ENST00000570006,;TMEM231,non_coding_transcript_exon_variant,,ENST00000564318,;RP11-77K12.7,intron_variant,,ENST00000460606,; A ENST00000258173 Transcript synonymous_variant 857/4278 780/951 260/316 P ccA/ccT 1 -1 TMEM231 HGNC HGNC:37234 protein_coding YES CCDS45530.1 ENSP00000258173 Q9H6L2 UPI00000704D8 NM_001077418.2 7/7 hmmpanther:PTHR14605,hmmpanther:PTHR14605:SF1,Pfam_domain:PF10149 LOW 1 SNV 1 1 PASS rs1412070252 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 75540165 75540165 T A 1 0 0 0 0 0 0 0 1 16592 1567 55 4 4 TMEM231 16 75540165 Silent SNP T 11LU022_T 7879842 75540165 14798180 784 1422 C16orf46 0 . GRCh38 16 81061466 81061466 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.883G>T p.Glu295Ter p.E295* ENST00000299578 4/4 112 81 31 164 164 0 strelka-varscan-mutect C16orf46,stop_gained,p.Glu295Ter,ENST00000378611,NM_001100873.1;C16orf46,stop_gained,p.Glu295Ter,ENST00000299578,NM_152337.2;C16orf46,downstream_gene_variant,,ENST00000565253,;RP11-303E16.8,intron_variant,,ENST00000564536,;C16orf46,downstream_gene_variant,,ENST00000444657,; A ENST00000299578 Transcript stop_gained 1119/1605 883/1188 295/395 E/* Gag/Tag 1 -1 C16orf46 HGNC HGNC:26525 protein_coding YES CCDS10932.1 ENSP00000299578 Q6P387 UPI000013E5BE NM_152337.2 4/4 hmmpanther:PTHR36869:SF1,hmmpanther:PTHR36869,Pfam_domain:PF15032 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 81061466 81061466 C A 1 0 0 0 0 0 1 0 0 1856 864 30 2 2 C16orf46 16 81061466 Nonsense_Mutation SNP C 11LU022_T 5521301 81061466 9276879 785 1423 CDH13 0 . GRCh38 16 83217436 83217436 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.716A>T p.Glu239Val p.E239V ENST00000268613 6/15 140 108 32 152 152 0 strelka-varscan-mutect CDH13,missense_variant,p.Glu192Val,ENST00000567109,NM_001220490.1,NM_001257.4;CDH13,missense_variant,p.Glu239Val,ENST00000268613,NM_001220488.1;CDH13,missense_variant,p.Glu153Val,ENST00000428848,NM_001220489.1;CDH13,non_coding_transcript_exon_variant,,ENST00000569454,;CDH13,3_prime_UTR_variant,,ENST00000539548,; T ENST00000268613 Transcript missense_variant 809/2722 716/2283 239/760 E/V gAg/gTg 1 1 CDH13 HGNC HGNC:1753 protein_coding YES CCDS58485.1 ENSP00000268613 P55290 UPI00020E71A6 NM_001220488.1 deleterious(0.04) 6/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF80,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 83217436 83217436 A T 1 0 0 0 0 1 0 0 0 2802 304 11 4 4 CDH13 16 83217436 Missense_Mutation SNP A 11LU022_T 2155970 83217436 7120909 786 1424 TRPV3 0 . GRCh38 17 3530082 3530082 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1187A>T p.Asp396Val p.D396V ENST00000301365 9/18 120 92 28 179 179 0 strelka-varscan-mutect TRPV3,missense_variant,p.Asp380Val,ENST00000616411,;TRPV3,missense_variant,p.Asp396Val,ENST00000301365,NM_001258205.1;TRPV3,missense_variant,p.Asp396Val,ENST00000572519,;TRPV3,missense_variant,p.Asp396Val,ENST00000576742,NM_145068.3;TRPV3,missense_variant,p.Asp170Val,ENST00000381913,;TRPV3,3_prime_UTR_variant,,ENST00000573539,;TRPV3,3_prime_UTR_variant,,ENST00000571139,;TRPV3,non_coding_transcript_exon_variant,,ENST00000575865,;TRPV3,non_coding_transcript_exon_variant,,ENST00000571005,;TRPV3,upstream_gene_variant,,ENST00000577016,; A ENST00000301365 Transcript missense_variant 1319/3235 1187/2376 396/791 D/V gAc/gTc 1 -1 TRPV3 HGNC HGNC:18084 protein_coding YES CCDS58500.1 ENSP00000301365 Q8NET8 UPI0000200627 NM_001258205.1 deleterious(0) 9/18 hmmpanther:PTHR10582:SF6,hmmpanther:PTHR10582 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 3530082 3530082 T A 1 0 0 0 0 1 0 0 0 17103 1667 58 4 4 TRPV3 17 3530082 Missense_Mutation SNP T 11LU022_T 3530082 79727359 787 1425 TP53 0 . GRCh38 17 7670709 7670709 + Missense_Mutation SNP C C A rs730882028 11LU022_T 11LU022_N C C c.1000G>T p.Gly334Trp p.G334W ENST00000269305 10/11 181 145 36 285 285 0 strelka-varscan-mutect TP53,missense_variant,p.Gly295Trp,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly334Trp,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly295Trp,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly334Trp,ENST00000445888,;TP53,missense_variant,p.Gly295Trp,ENST00000619485,;TP53,missense_variant,p.Gly202Trp,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly175Trp,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly323Trp,ENST00000615910,;TP53,3_prime_UTR_variant,,ENST00000617185,NM_001126114.2;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000622645,NM_001276696.1;TP53,3_prime_UTR_variant,,ENST00000455263,NM_001126113.2;TP53,3_prime_UTR_variant,,ENST00000610538,NM_001276695.1;TP53,3_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,3_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,3_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,3_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly295Trp,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 1190/2579 1000/1182 334/393 G/W Ggg/Tgg rs730882028,TP53_g.16891del,TP53_g.16891G>T,COSM1386569,COSM48816 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 10/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:1olgA00,Pfam_domain:PF07710,Superfamily_domains:SSF47719,Prints_domain:PR00386 uncertain_significance 0,0,0,1,1 MODERATE 1 SNV 1 1,0,0,1,1 1 PASS rs730882028 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 7670709 7670709 C A 1 0 0 0 0 1 0 0 0 16859 594 21 2 2 TP53 17 7670709 Missense_Mutation SNP C 11LU022_T 4140627 7670709 75586732 788 1426 PER1 0 . GRCh38 17 8149817 8149817 + Missense_Mutation SNP T T G rs144669833 11LU022_T 11LU022_N T T c.589A>C p.Met197Leu p.M197L ENST00000317276 5/23 235 184 51 361 361 0 strelka-varscan-mutect PER1,missense_variant,p.Met197Leu,ENST00000317276,NM_002616.2;PER1,missense_variant,p.Met197Leu,ENST00000581082,;PER1,missense_variant,p.Met181Leu,ENST00000354903,;PER1,downstream_gene_variant,,ENST00000577253,;PER1,downstream_gene_variant,,ENST00000584202,;PER1,downstream_gene_variant,,ENST00000581703,;PER1,upstream_gene_variant,,ENST00000583559,;RP11-599B13.6,downstream_gene_variant,,ENST00000498285,;PER1,upstream_gene_variant,,ENST00000614952,;PER1,upstream_gene_variant,,ENST00000578089,;PER1,missense_variant,p.Met197Leu,ENST00000582719,;PER1,missense_variant,p.Met197Leu,ENST00000581395,;PER1,non_coding_transcript_exon_variant,,ENST00000579065,;PER1,upstream_gene_variant,,ENST00000578223,;PER1,upstream_gene_variant,,ENST00000585095,;PER1,upstream_gene_variant,,ENST00000577424,;PER1,upstream_gene_variant,,ENST00000579203,;PER1,upstream_gene_variant,,ENST00000578950,; G ENST00000317276 Transcript missense_variant 827/4707 589/3873 197/1290 M/L Atg/Ctg rs144669833 1 -1 PER1 HGNC HGNC:8845 protein_coding YES CCDS11131.1 ENSP00000314420 O15534 UPI000013FFF5 NM_002616.2 tolerated(0.36) 5/23 hmmpanther:PTHR11269:SF8,hmmpanther:PTHR11269 MODERATE 1 SNV 1 1 PASS rs144669833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 8149817 8149817 T G 1 0 0 0 0 1 0 0 0 11817 1464 51 5 5 PER1 17 8149817 Missense_Mutation SNP T 11LU022_T 479108 8149817 75107624 789 1427 MYH1 0 . GRCh38 17 10496264 10496264 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.4942A>T p.Arg1648Trp p.R1648W ENST00000226207 34/40 117 103 14 173 173 0 strelka-mutect MYH1,missense_variant,p.Arg1648Trp,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 5037/6024 4942/5820 1648/1939 R/W Agg/Tgg 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 34/40 Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 10496264 10496264 T A 1 0 0 0 0 1 0 0 0 10029 1521 53 4 4 MYH1 17 10496264 Missense_Mutation SNP T 11LU022_T 2346447 10496264 72761177 790 1428 MYH1 0 . GRCh38 17 10508391 10508391 + Silent SNP G G C rs370081195 11LU022_T 11LU022_N G G c.1869C>G p.= p.L623L ENST00000226207 16/40 63 52 11 123 122 1 strelka-varscan-mutect MYH1,synonymous_variant,p.=,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; C ENST00000226207 Transcript synonymous_variant 1964/6024 1869/5820 623/1939 L ctC/ctG rs370081195,COSM5543160 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 16/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1 LOW SNV 5 0,1 1 PASS rs370081195 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 10508391 10508391 G C 1 0 0 0 0 0 0 0 1 10029 929 33 4 4 MYH1 17 10508391 Silent SNP G 11LU022_T 12127 10508391 72749050 791 1429 MYH2 0 . GRCh38 17 10542937 10542937 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.842A>T p.Lys281Met p.K281M ENST00000245503 10/40 120 84 36 216 216 0 strelka-varscan-mutect MYH2,missense_variant,p.Lys281Met,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.Lys281Met,ENST00000397183,NM_001100112.1;MYH2,missense_variant,p.Lys281Met,ENST00000532183,;MYH2,missense_variant,p.Lys281Met,ENST00000622564,;MYH2,downstream_gene_variant,,ENST00000420805,;MYH2,downstream_gene_variant,,ENST00000578017,;MYHAS,intron_variant,,ENST00000587182,; A ENST00000245503 Transcript missense_variant 1227/6339 842/5826 281/1941 K/M aAg/aTg 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 deleterious(0.02) 10/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 10542937 10542937 T A 1 0 0 0 0 1 0 0 0 10035 1609 56 4 4 MYH2 17 10542937 Missense_Mutation SNP T 11LU022_T 34546 10542937 72714504 792 1430 MYH3 0 . GRCh38 17 10642529 10642529 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.1776A>T p.= p.S592S ENST00000583535 16/41 263 214 49 437 437 0 strelka-varscan-mutect MYH3,synonymous_variant,p.=,ENST00000583535,NM_002470.3; A ENST00000583535 Transcript synonymous_variant 1864/6037 1776/5823 592/1940 S tcA/tcT 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 16/41 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF427,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs1331409157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 10642529 10642529 T A 1 0 0 0 0 0 0 0 1 10036 1567 55 4 4 MYH3 17 10642529 Silent SNP T 11LU022_T 99592 10642529 72614912 793 1431 NCOR1 0 . GRCh38 17 16186599 16186599 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.197G>T p.Arg66Leu p.R66L ENST00000268712 3/46 185 134 51 211 211 0 strelka-varscan-mutect NCOR1,missense_variant,p.Arg66Leu,ENST00000268712,NM_006311.3;NCOR1,missense_variant,p.Arg66Leu,ENST00000395851,NM_001190440.1;NCOR1,missense_variant,p.Arg66Leu,ENST00000436828,;NCOR1,missense_variant,p.Arg66Leu,ENST00000411510,;NCOR1,missense_variant,p.Arg66Leu,ENST00000582357,;NCOR1,missense_variant,p.Arg66Leu,ENST00000430577,;NCOR1,intron_variant,,ENST00000395857,;NCOR1,intron_variant,,ENST00000395848,NM_001190438.1;NCOR1,missense_variant,p.Arg66Leu,ENST00000460276,;NCOR1,non_coding_transcript_exon_variant,,ENST00000585296,;NCOR1,intron_variant,,ENST00000579974,; A ENST00000268712 Transcript missense_variant 455/10720 197/7323 66/2440 R/L cGa/cTa COSM254840,COSM4874523 1 -1 NCOR1 HGNC HGNC:7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 A0A024RD47 UPI000013D7D5 NM_006311.3 tolerated(0.09) 3/46 Low_complexity_(Seg):seg,hmmpanther:PTHR13992:SF5,hmmpanther:PTHR13992 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 16186599 16186599 C A 1 0 0 0 0 1 0 0 0 10254 884 31 1 1 NCOR1 17 16186599 Missense_Mutation SNP C 11LU022_T 5544070 16186599 67070842 794 1432 MYO15A 0 . GRCh38 17 18119931 18119931 + Silent SNP C C A rs779206128 11LU022_T 11LU022_N C C c.1131C>A p.= p.T377T ENST00000205890 2/66 464 332 132 678 678 0 strelka-varscan-mutect MYO15A,synonymous_variant,p.=,ENST00000205890,NM_016239.3;MYO15A,synonymous_variant,p.=,ENST00000615845,;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,; A ENST00000205890 Transcript synonymous_variant 1469/11863 1131/10593 377/3530 T acC/acA rs779206128,COSM3514858 1 1 MYO15A HGNC HGNC:7594 protein_coding YES CCDS42271.1 ENSP00000205890 Q9UKN7 UPI0000E59E6E NM_016239.3 2/66 0,1 LOW 1 SNV 5 0,1 1 PASS rs779206128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 18119931 18119931 C A 1 0 0 0 0 0 0 0 1 10063 639 23 1 1 MYO15A 17 18119931 Silent SNP C 11LU022_T 1933332 18119931 65137510 795 1433 CDRT15L2 0 . GRCh38 17 20579888 20579888 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.145C>A p.Gln49Lys p.Q49K ENST00000399044 1/2 188 142 46 308 308 0 strelka-varscan-mutect CDRT15L2,missense_variant,p.Gln49Lys,ENST00000399044,NM_001190790.1;RP11-434D2.12,upstream_gene_variant,,ENST00000580931,;ZSWIM5P2,downstream_gene_variant,,ENST00000420212,; A ENST00000399044 Transcript missense_variant 165/1048 145/846 49/281 Q/K Cag/Aag 1 1 CDRT15L2 HGNC HGNC:34075 protein_coding YES CCDS54096.1 ENSP00000382000 A8MXV6 UPI00001D7A81 NM_001190790.1 deleterious_low_confidence(0.03) 1/2 hmmpanther:PTHR16471,hmmpanther:PTHR16471:SF0 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 20579888 20579888 C A 1 0 0 0 0 1 0 0 0 2881 479 17 2 2 CDRT15L2 17 20579888 Missense_Mutation SNP C 11LU022_T 2459957 20579888 62677553 796 1434 USP22 0 . GRCh38 17 21015848 21015848 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.742G>C p.Val248Leu p.V248L ENST00000261497 6/13 223 169 54 301 301 0 strelka-varscan-mutect USP22,missense_variant,p.Val248Leu,ENST00000261497,NM_015276.1;USP22,missense_variant,p.Val236Leu,ENST00000537526,;USP22,intron_variant,,ENST00000582335,;USP22,downstream_gene_variant,,ENST00000476111,;USP22,downstream_gene_variant,,ENST00000584538,;USP22,non_coding_transcript_exon_variant,,ENST00000577610,;USP22,intron_variant,,ENST00000455117,;USP22,3_prime_UTR_variant,,ENST00000579645,;USP22,non_coding_transcript_exon_variant,,ENST00000578446,;USP22,upstream_gene_variant,,ENST00000478443,; G ENST00000261497 Transcript missense_variant 946/5220 742/1578 248/525 V/L Gtg/Ctg 1 -1 USP22 HGNC HGNC:12621 protein_coding YES CCDS42285.1 ENSP00000261497 Q9UPT9 UPI00001C1FC6 NM_015276.1 deleterious(0.01) 6/13 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF448,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 21015848 21015848 C G 1 0 0 0 0 1 0 0 0 17595 507 18 4 4 USP22 17 21015848 Missense_Mutation SNP C 11LU022_T 435960 21015848 62241593 797 1435 NOS2 0 . GRCh38 17 27772380 27772380 + Silent SNP C C A rs775135778 11LU022_T 11LU022_N C C c.1632G>T p.= p.A544A ENST00000313735 14/27 264 194 70 387 387 0 strelka-varscan-mutect NOS2,synonymous_variant,p.=,ENST00000313735,NM_000625.4;NOS2,synonymous_variant,p.=,ENST00000621962,; A ENST00000313735 Transcript synonymous_variant 1866/4176 1632/3462 544/1153 A gcG/gcT rs775135778 1 -1 NOS2 HGNC HGNC:7873 protein_coding YES CCDS11223.1 ENSP00000327251 P35228 UPI000011D645 NM_000625.4 14/27 PROSITE_profiles:PS50902,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF56,Pfam_domain:PF00258,Gene3D:3.40.50.360,Superfamily_domains:SSF52218,Prints_domain:PR00369 LOW 1 SNV 1 1 PASS rs775135778 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 27772380 27772380 C A 1 0 0 0 0 0 0 0 1 10588 871 31 1 1 NOS2 17 27772380 Silent SNP C 11LU022_T 6756532 27772380 55485061 798 1436 NF1 0 . GRCh38 17 31336712 31336712 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.6225G>T p.Trp2075Cys p.W2075C ENST00000358273 42/58 187 124 63 197 197 0 strelka-varscan-mutect NF1,missense_variant,p.Trp2075Cys,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Trp2054Cys,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Trp1720Cys,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000479536,;NF1,downstream_gene_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; T ENST00000358273 Transcript missense_variant 6608/12425 6225/8520 2075/2839 W/C tgG/tgT 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0) 42/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 31336712 31336712 G T 1 0 0 0 0 1 0 0 0 10393 1241 43 2 2 NF1 17 31336712 Missense_Mutation SNP G 11LU022_T 3564332 31336712 51920729 799 1437 NF1 0 . GRCh38 17 31337851 31337851 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.6675G>T p.Trp2225Cys p.W2225C ENST00000358273 44/58 368 262 106 348 346 2 strelka-varscan-mutect NF1,missense_variant,p.Trp2225Cys,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Trp2204Cys,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Trp1870Cys,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,missense_variant,p.Ala13Ser,ENST00000471572,;NF1,missense_variant,p.Ala13Ser,ENST00000581790,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000584328,;NF1,downstream_gene_variant,,ENST00000479536,;NF1,upstream_gene_variant,,ENST00000582892,; T ENST00000358273 Transcript missense_variant 7058/12425 6675/8520 2225/2839 W/C tgG/tgT COSM1520754,COSM1520755,COSM5274341 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0) 44/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,Superfamily_domains:SSF48371 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 31337851 31337851 G T 1 0 0 0 0 1 0 0 0 10393 1212 42 2 2 NF1 17 31337851 Missense_Mutation SNP G 11LU022_T 1139 31337851 51919590 800 1438 UNC45B 0 . GRCh38 17 35155349 35155349 + Silent SNP C C A rs565375347 11LU022_T 11LU022_N C C c.693C>A p.= p.A231A ENST00000268876 7/20 144 133 11 130 129 1 strelka-varscan-mutect UNC45B,synonymous_variant,p.=,ENST00000268876,NM_173167.2;UNC45B,synonymous_variant,p.=,ENST00000394570,NM_001267052.1,NM_001033576.1;UNC45B,synonymous_variant,p.=,ENST00000591048,NM_001308281.1; A ENST00000268876 Transcript synonymous_variant 790/5679 693/2796 231/931 A gcC/gcA rs565375347,COSM1382422 1 1 UNC45B HGNC HGNC:14304 protein_coding YES CCDS11292.1 ENSP00000268876 Q8IWX7 UPI0000074455 NM_173167.2 7/20 Gene3D:1.25.10.10,Superfamily_domains:SSF48371 0,1 LOW 1 SNV 5 0,1 1 PASS rs565375347 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 35155349 35155349 C A 1 0 0 0 0 0 0 0 1 17513 639 23 1 1 UNC45B 17 35155349 Silent SNP C 11LU022_T 3817498 35155349 48102092 801 1439 CCL5 0 . GRCh38 17 35878581 35878581 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.135C>A p.= p.A45A ENST00000603197 2/3 143 105 38 134 134 0 strelka-varscan-mutect CCL5,synonymous_variant,p.=,ENST00000603197,NM_002985.2;CCL5,synonymous_variant,p.=,ENST00000605140,;CCL5,synonymous_variant,p.=,ENST00000605509,NM_001278736.1;AC015849.2,intron_variant,,ENST00000605548,; T ENST00000603197 Transcript synonymous_variant 338/1365 135/276 45/91 A gcC/gcA 1 -1 CCL5 HGNC HGNC:10632 protein_coding YES CCDS11300.1 ENSP00000474412 P13501 UPI000004A187 NM_002985.2 2/3 Gene3D:2.40.50.40,Pfam_domain:PF00048,PROSITE_patterns:PS00472,hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF82,SMART_domains:SM00199,Superfamily_domains:SSF54117 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 35878581 35878581 G T 1 0 0 0 0 0 0 0 1 2603 1219 43 2 2 CCL5 17 35878581 Silent SNP G 11LU022_T 723232 35878581 47378860 802 1440 TBC1D3B 0 . GRCh38 17 36167629 36167629 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.996G>T p.Trp332Cys p.W332C ENST00000611257 13/14 38 34 4 44 44 0 varscan-mutect TBC1D3B,missense_variant,p.Trp332Cys,ENST00000611257,NM_001001417.6;TBC1D3B,downstream_gene_variant,,ENST00000616006,;CTB-91J4.1,intron_variant,,ENST00000617914,;TBC1D3B,downstream_gene_variant,,ENST00000622280,;RP11-428O23.1,downstream_gene_variant,,ENST00000633081,; A ENST00000611257 Transcript missense_variant 1113/2081 996/1650 332/549 W/C tgG/tgT 1 -1 TBC1D3B HGNC HGNC:27011 protein_coding YES CCDS42300.1 ENSP00000478473 A6NDS4 UPI000292EEF0 NM_001001417.6 deleterious(0) 13/14 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF233 MODERATE 1 SNV 1 1 PASS . . 34 171 5 0 0 0 0 0 -10.87532 0.9999999 1 1 1 0 A 3 1 3 36167629 36167629 C A 1 0 0 0 0 1 0 0 0 16023 624 22 2 2 TBC1D3B 17 36167629 Missense_Mutation SNP C 11LU022_T 289048 36167629 47089812 803 1441 KRT24 0 . GRCh38 17 40703153 40703153 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.541C>A p.Pro181Thr p.P181T ENST00000264651 1/8 145 91 54 155 155 0 strelka-varscan-mutect KRT24,missense_variant,p.Pro181Thr,ENST00000264651,NM_019016.2; T ENST00000264651 Transcript missense_variant 598/1881 541/1578 181/525 P/T Cct/Act 1 -1 KRT24 HGNC HGNC:18527 protein_coding YES CCDS11372.1 ENSP00000264651 Q2M2I5 UPI000013D54D NM_019016.2 tolerated(0.06) 1/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF207,Low_complexity_(Seg):seg,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 40703153 40703153 G T 1 0 0 0 0 1 0 0 0 8343 1203 42 2 2 KRT24 17 40703153 Missense_Mutation SNP G 11LU022_T 4535524 40703153 42554288 804 1442 KRTAP16-1 0 . GRCh38 17 41307730 41307730 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1524G>T p.Gln508His p.Q508H ENST00000391352 1/1 59 40 19 55 55 0 strelka-varscan-mutect KRTAP16-1,missense_variant,p.Gln508His,ENST00000391352,NM_001146182.1;KRTAP29-1,upstream_gene_variant,,ENST00000391353,NM_001257309.1; A ENST00000391352 Transcript missense_variant 1524/1554 1524/1554 508/517 Q/H caG/caT 1 -1 KRTAP16-1 HGNC HGNC:18916 protein_coding YES CCDS56032.1 ENSP00000375147 A8MUX0 UPI000015FD61 NM_001146182.1 tolerated_low_confidence(0.06) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs1489250395 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 41307730 41307730 C A 1 0 0 0 0 1 0 0 0 8410 796 28 2 2 KRTAP16-1 17 41307730 Missense_Mutation SNP C 11LU022_T 604577 41307730 41949711 805 1443 KRT15 0 . GRCh38 17 41516230 41516230 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.774G>T p.Gln258His p.Q258H ENST00000254043 4/8 101 65 36 126 126 0 strelka-mutect KRT15,missense_variant,p.Gln258His,ENST00000254043,NM_002275.3;KRT15,missense_variant,p.Gln93His,ENST00000393974,;KRT15,missense_variant,p.Gln258His,ENST00000393976,;KRT15,missense_variant,p.Gln93His,ENST00000458290,;KRT15,downstream_gene_variant,,ENST00000613845,;KRT15,3_prime_UTR_variant,,ENST00000497016,;KRT15,non_coding_transcript_exon_variant,,ENST00000474031,;KRT15,non_coding_transcript_exon_variant,,ENST00000463447,;KRT15,downstream_gene_variant,,ENST00000470004,;KRT15,upstream_gene_variant,,ENST00000586794,; A ENST00000254043 Transcript missense_variant 4360/5237 774/1371 258/456 Q/H caG/caT 1 -1 KRT15 HGNC HGNC:6421 protein_coding YES CCDS11398.1 ENSP00000254043 P19012 UPI000013CE0E NM_002275.3 tolerated(0.06) 4/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF164,SMART_domains:SM01391,Superfamily_domains:SSF46579 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 41516230 41516230 C A 1 0 0 0 0 1 0 0 0 8334 680 24 2 2 KRT15 17 41516230 Missense_Mutation SNP C 11LU022_T 208500 41516230 41741211 806 1444 GHDC 0 . GRCh38 17 42192633 42192633 + Nonsense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.497G>A p.Trp166Ter p.W166* ENST00000301671 4/9 100 89 11 131 131 0 strelka-varscan-mutect GHDC,stop_gained,p.Trp166Ter,ENST00000301671,;GHDC,stop_gained,p.Trp166Ter,ENST00000428494,;GHDC,stop_gained,p.Trp166Ter,ENST00000414034,NM_001142623.1;GHDC,stop_gained,p.Trp166Ter,ENST00000587427,NM_032484.4;GHDC,stop_gained,p.Trp166Ter,ENST00000593209,;GHDC,downstream_gene_variant,,ENST00000590249,;GHDC,downstream_gene_variant,,ENST00000588352,;GHDC,downstream_gene_variant,,ENST00000590520,;GHDC,downstream_gene_variant,,ENST00000586692,;GHDC,3_prime_UTR_variant,,ENST00000588762,;GHDC,upstream_gene_variant,,ENST00000585735,;GHDC,downstream_gene_variant,,ENST00000585375,; T ENST00000301671 Transcript stop_gained 939/2650 497/1593 166/530 W/* tGg/tAg 1 -1 GHDC HGNC HGNC:24438 protein_coding YES CCDS11422.1 ENSP00000301671 Q8N2G8 A0A024R1Y7 UPI000006E533 4/9 hmmpanther:PTHR31901,hmmpanther:PTHR31901:SF5 HIGH 1 SNV 2 1 PASS rs1428122427 . 0 205 4 0 0 0 0 0 -19.99909 1 1 1 1 0 T 4 4 3 42192633 42192633 C T 1 0 0 0 0 0 1 0 0 6247 595 21 3 3 GHDC 17 42192633 Nonsense_Mutation SNP C 11LU022_T 676403 42192633 41064808 807 1445 ATP6V0A1 0 . GRCh38 17 42480680 42480680 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.668A>G p.His223Arg p.H223R ENST00000264649 8/21 136 121 15 115 115 0 strelka-varscan-mutect ATP6V0A1,missense_variant,p.His216Arg,ENST00000343619,NM_001130021.1;ATP6V0A1,missense_variant,p.His223Arg,ENST00000264649,NM_001130020.1;ATP6V0A1,missense_variant,p.His216Arg,ENST00000393829,NM_005177.3;ATP6V0A1,missense_variant,p.His173Arg,ENST00000537728,;ATP6V0A1,missense_variant,p.His173Arg,ENST00000585525,;ATP6V0A1,missense_variant,p.His157Arg,ENST00000589727,;ATP6V0A1,missense_variant,p.His183Arg,ENST00000592324,;ATP6V0A1,intron_variant,,ENST00000544137,;ATP6V0A1,upstream_gene_variant,,ENST00000589759,;ATP6V0A1,non_coding_transcript_exon_variant,,ENST00000587882,;ATP6V0A1,non_coding_transcript_exon_variant,,ENST00000587375,;ATP6V0A1,downstream_gene_variant,,ENST00000588901,;ATP6V0A1,downstream_gene_variant,,ENST00000586001,; G ENST00000264649 Transcript missense_variant 799/4110 668/2517 223/838 H/R cAc/cGc 1 1 ATP6V0A1 HGNC HGNC:865 protein_coding YES CCDS45683.1 ENSP00000264649 Q93050 UPI0000E59F9E NM_001130020.1 tolerated(0.31) 8/21 hmmpanther:PTHR11629:SF68,hmmpanther:PTHR11629,PIRSF_domain:PIRSF001293,Pfam_domain:PF01496 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 42480680 42480680 A G 1 0 0 0 0 1 0 0 0 1321 159 6 5 5 ATP6V0A1 17 42480680 Missense_Mutation SNP A 11LU022_T 288047 42480680 40776761 808 1446 MEOX1 0 . GRCh38 17 43661134 43661134 + Missense_Mutation SNP T T A rs767408491 11LU022_T 11LU022_N T T c.401A>T p.Tyr134Phe p.Y134F ENST00000318579 1/3 29 22 7 33 33 0 strelka-varscan-mutect MEOX1,missense_variant,p.Tyr134Phe,ENST00000318579,NM_004527.3;MEOX1,missense_variant,p.Tyr134Phe,ENST00000329168,NM_013999.3;MEOX1,missense_variant,p.Tyr19Phe,ENST00000393661,NM_001040002.1;MEOX1,missense_variant,p.Thr105Ser,ENST00000549132,; A ENST00000318579 Transcript missense_variant 821/2707 401/765 134/254 Y/F tAc/tTc rs767408491 1 -1 MEOX1 HGNC HGNC:7013 protein_coding YES CCDS11466.1 ENSP00000321684 P50221 UPI000012F410 NM_004527.3 tolerated(0.41) 1/3 hmmpanther:PTHR24328:SF8,hmmpanther:PTHR24328 MODERATE 1 SNV 1 1 PASS rs767408491 . 0 206 4 0 0 0 0 0 -18.92327 1 1 1 1 0 A 3 1 3 43661134 43661134 T A 1 0 0 0 0 1 0 0 0 9418 1638 57 4 4 MEOX1 17 43661134 Missense_Mutation SNP T 11LU022_T 1180454 43661134 39596307 809 1447 FZD2 0 . GRCh38 17 44557758 44557758 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.70C>A p.Gln24Lys p.Q24K ENST00000315323 1/1 234 205 29 248 248 0 strelka-varscan-mutect FZD2,missense_variant,p.Gln24Lys,ENST00000315323,NM_001466.3; A ENST00000315323 Transcript missense_variant 300/2112 70/1698 24/565 Q/K Cag/Aag 1 1 FZD2 HGNC HGNC:4040 protein_coding YES CCDS11484.1 ENSP00000323901 Q14332 UPI0000050444 NM_001466.3 deleterious(0.04) 1/1 hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF34 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 44557758 44557758 C A 1 0 0 0 0 1 0 0 0 6001 595 21 2 2 FZD2 17 44557758 Missense_Mutation SNP C 11LU022_T 896624 44557758 38699683 810 1448 CACNA1G 0 . GRCh38 17 50618776 50618776 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.5549T>C p.Leu1850Pro p.L1850P ENST00000359106 33/38 313 283 30 377 377 0 strelka-varscan-mutect CACNA1G,missense_variant,p.Leu1816Pro,ENST00000354983,NM_198396.2;CACNA1G,missense_variant,p.Leu1816Pro,ENST00000352832,NM_198387.2;CACNA1G,missense_variant,p.Leu1850Pro,ENST00000359106,NM_018896.4;CACNA1G,missense_variant,p.Leu1827Pro,ENST00000360761,NM_198382.2;CACNA1G,missense_variant,p.Leu1809Pro,ENST00000442258,NM_198388.2;CACNA1G,missense_variant,p.Leu1832Pro,ENST00000429973,NM_198386.2;CACNA1G,missense_variant,p.Leu1839Pro,ENST00000507336,NM_198377.2;CACNA1G,missense_variant,p.Leu1816Pro,ENST00000358244,NM_198376.2;CACNA1G,missense_variant,p.Leu1850Pro,ENST00000507510,NM_198385.2;CACNA1G,missense_variant,p.Leu1839Pro,ENST00000515765,NM_198380.2;CACNA1G,missense_variant,p.Leu1832Pro,ENST00000515411,NM_001256324.1;CACNA1G,missense_variant,p.Leu1827Pro,ENST00000502264,NM_198383.2;CACNA1G,missense_variant,p.Leu1816Pro,ENST00000510115,NM_198379.2;CACNA1G,missense_variant,p.Leu1857Pro,ENST00000514079,NM_001256325.1;CACNA1G,missense_variant,p.Leu1805Pro,ENST00000513689,NM_001256326.1;CACNA1G,missense_variant,p.Leu1850Pro,ENST00000515165,NM_198384.2;CACNA1G,missense_variant,p.Leu1843Pro,ENST00000507609,NM_001256327.1;CACNA1G,missense_variant,p.Leu1839Pro,ENST00000512389,NM_198378.2;CACNA1G,missense_variant,p.Leu1825Pro,ENST00000514181,NM_001256328.1;CACNA1G,missense_variant,p.Leu1816Pro,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,missense_variant,p.Leu1805Pro,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,missense_variant,p.Leu1798Pro,ENST00000510366,NM_001256331.1;CACNA1G,missense_variant,p.Leu1793Pro,ENST00000514717,NM_001256332.1;CACNA1G,missense_variant,p.Leu1850Pro,ENST00000505165,NM_001256333.1;CACNA1G,missense_variant,p.Leu1839Pro,ENST00000507896,NM_001256334.1;CACNA1G,3_prime_UTR_variant,,ENST00000506406,;CACNA1G,3_prime_UTR_variant,,ENST00000504076,;CACNA1G,3_prime_UTR_variant,,ENST00000511765,;CACNA1G,3_prime_UTR_variant,,ENST00000503436,;CACNA1G,3_prime_UTR_variant,,ENST00000511768,;CACNA1G,3_prime_UTR_variant,,ENST00000503607,; C ENST00000359106 Transcript missense_variant 5549/7648 5549/7134 1850/2377 L/P cTg/cCg 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 deleterious(0) 33/38 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 50618776 50618776 T C 1 0 0 0 0 1 0 0 0 2232 1580 55 5 5 CACNA1G 17 50618776 Missense_Mutation SNP T 11LU022_T 6061018 50618776 32638665 811 1449 MSI2 0 . GRCh38 17 57675020 57675020 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.839G>T p.Gly280Val p.G280V ENST00000284073 12/14 191 169 22 183 183 0 strelka-varscan-mutect MSI2,missense_variant,p.Gly280Val,ENST00000284073,NM_138962.2;MSI2,missense_variant,p.Gly276Val,ENST00000416426,;MSI2,missense_variant,p.Gly219Val,ENST00000442934,;MSI2,non_coding_transcript_exon_variant,,ENST00000579505,;MSI2,non_coding_transcript_exon_variant,,ENST00000579466,; T ENST00000284073 Transcript missense_variant 1048/6364 839/987 280/328 G/V gGa/gTa 1 1 MSI2 HGNC HGNC:18585 protein_coding YES CCDS11596.1 ENSP00000284073 Q96DH6 UPI0000070D73 NM_138962.2 deleterious(0) 12/14 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF476 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999891 1 1 1 0 T 3 4 3 57675020 57675020 G T 1 0 0 0 0 1 0 0 0 9859 1174 41 2 2 MSI2 17 57675020 Missense_Mutation SNP G 11LU022_T 7056244 57675020 25582421 812 1450 MPO 0 . GRCh38 17 58279524 58279524 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.547A>G p.Arg183Gly p.R183G ENST00000225275 4/12 280 264 16 303 303 0 strelka-varscan-mutect MPO,missense_variant,p.Arg183Gly,ENST00000225275,NM_000250.1;MPO,upstream_gene_variant,,ENST00000578493,;MPO,downstream_gene_variant,,ENST00000580005,;MPO,upstream_gene_variant,,ENST00000581022,; C ENST00000225275 Transcript missense_variant,splice_region_variant 724/3215 547/2238 183/745 R/G Aga/Gga 1 -1 MPO HGNC HGNC:7218 protein_coding YES CCDS11604.1 ENSP00000225275 P05164 UPI0000131634 NM_000250.1 deleterious(0.01) 4/12 PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 58279524 58279524 T C 1 0 0 0 0 1 0 0 0 9698 1594 55 5 5 MPO 17 58279524 Missense_Mutation SNP T 11LU022_T 604504 58279524 24977917 813 1451 TSPOAP1 0 . GRCh38 17 58308904 58308904 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4368G>T p.Glu1456Asp p.E1456D ENST00000343736 22/32 63 39 24 60 60 0 strelka-varscan-mutect TSPOAP1,missense_variant,p.Glu1396Asp,ENST00000268893,NM_024418.2;TSPOAP1,missense_variant,p.Glu1456Asp,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1,intron_variant,,ENST00000582679,;TSPOAP1,upstream_gene_variant,,ENST00000581675,;TSPOAP1,upstream_gene_variant,,ENST00000580669,;TSPOAP1,upstream_gene_variant,,ENST00000581692,;TSPOAP1,upstream_gene_variant,,ENST00000578511,;TSPOAP1,upstream_gene_variant,,ENST00000577871,;TSPOAP1,upstream_gene_variant,,ENST00000578486,;TSPOAP1,downstream_gene_variant,,ENST00000585149,; A ENST00000343736 Transcript missense_variant 4532/5947 4368/5574 1456/1857 E/D gaG/gaT 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 tolerated(0.1) 22/32 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20 MODERATE 1 SNV 1 1 PASS rs1184635786 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 58308904 58308904 C A 1 0 0 0 0 1 0 0 0 17163 680 24 2 2 TSPOAP1 17 58308904 Missense_Mutation SNP C 11LU022_T 29380 58308904 24948537 814 1452 NACA2 0 . GRCh38 17 61591075 61591075 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.106C>A p.Pro36Thr p.P36T ENST00000521764 1/1 396 358 38 352 351 1 strelka-varscan-mutect NACA2,missense_variant,p.Pro36Thr,ENST00000521764,NM_199290.3; T ENST00000521764 Transcript missense_variant 128/777 106/648 36/215 P/T Cca/Aca 1 -1 NACA2 HGNC HGNC:23290 protein_coding YES CCDS11630.1 ENSP00000427802 Q9H009 UPI0000070B04 NM_199290.3 deleterious(0.01) 1/1 hmmpanther:PTHR21713,hmmpanther:PTHR21713:SF2,PIRSF_domain:PIRSF015901 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 61591075 61591075 G T 1 0 0 0 0 1 0 0 0 10140 1261 44 2 2 NACA2 17 61591075 Missense_Mutation SNP G 11LU022_T 3282171 61591075 21666366 815 1453 BRIP1 0 . GRCh38 17 61776532 61776532 + Nonsense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1966A>T p.Lys656Ter p.K656* ENST00000259008 14/20 319 274 45 289 289 0 strelka-varscan-mutect BRIP1,stop_gained,p.Lys656Ter,ENST00000259008,NM_032043.2;BRIP1,stop_gained,p.Lys656Ter,ENST00000577598,;BRIP1,upstream_gene_variant,,ENST00000584322,;BRIP1,non_coding_transcript_exon_variant,,ENST00000583837,;BRIP1,3_prime_UTR_variant,,ENST00000579028,; A ENST00000259008 Transcript stop_gained 2234/6048 1966/3750 656/1249 K/* Aag/Tag 1 -1 BRIP1 HGNC HGNC:20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 A0A024QZ45 UPI000013D01F NM_032043.2 14/20 hmmpanther:PTHR11472:SF6,hmmpanther:PTHR11472,TIGRFAM_domain:TIGR00604,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 61776532 61776532 T A 1 0 0 0 0 0 1 0 0 1688 1821 63 4 4 BRIP1 17 61776532 Nonsense_Mutation SNP T 11LU022_T 185457 61776532 21480909 816 1454 INTS2 0 . GRCh38 17 61867595 61867595 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3577G>T p.Val1193Leu p.V1193L ENST00000444766 25/25 84 52 32 104 104 0 strelka-varscan-mutect INTS2,missense_variant,p.Val1193Leu,ENST00000444766,NM_020748.2;INTS2,missense_variant,p.Val1193Leu,ENST00000617492,;INTS2,missense_variant,p.Val1185Leu,ENST00000251334,;BRIP1,upstream_gene_variant,,ENST00000259008,NM_032043.2;BRIP1,upstream_gene_variant,,ENST00000577913,;INTS2,downstream_gene_variant,,ENST00000583822,; A ENST00000444766 Transcript missense_variant 3653/5878 3577/3615 1193/1204 V/L Gta/Tta 1 -1 INTS2 HGNC HGNC:29241 protein_coding YES CCDS45750.1 ENSP00000414237 Q9H0H0 UPI0000E5A03A NM_020748.2 tolerated_low_confidence(0.21) 25/25 hmmpanther:PTHR28608 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 61867595 61867595 C A 1 0 0 0 0 1 0 0 0 7680 565 20 2 2 INTS2 17 61867595 Missense_Mutation SNP C 11LU022_T 91063 61867595 21389846 817 1455 1 1 3 3 405 N T_C 8.648087e-05 INTS2 0 . GRCh38 17 61867705 61867705 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.3467A>G p.Lys1156Arg p.K1156R ENST00000444766 25/25 59 51 8 72 72 0 strelka-varscan-mutect INTS2,missense_variant,p.Lys1156Arg,ENST00000444766,NM_020748.2;INTS2,missense_variant,p.Lys1156Arg,ENST00000617492,;INTS2,missense_variant,p.Lys1148Arg,ENST00000251334,;BRIP1,upstream_gene_variant,,ENST00000259008,NM_032043.2;BRIP1,upstream_gene_variant,,ENST00000577913,;INTS2,downstream_gene_variant,,ENST00000583822,; C ENST00000444766 Transcript missense_variant 3543/5878 3467/3615 1156/1204 K/R aAa/aGa 1 -1 INTS2 HGNC HGNC:29241 protein_coding YES CCDS45750.1 ENSP00000414237 Q9H0H0 UPI0000E5A03A NM_020748.2 tolerated_low_confidence(0.09) 25/25 hmmpanther:PTHR28608 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.67426 1 1 1 1 0 C 3 2 3 61867705 61867705 T C 1 0 0 0 0 1 0 0 0 7680 1841 64 5 5 INTS2 17 61867705 Missense_Mutation SNP T 11LU022_T 110 61867705 21389736 818 1456 1 1 3 3 405 N T_C 8.648087e-05 INTS2 0 . GRCh38 17 61867999 61867999 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3279G>T p.Gln1093His p.Q1093H ENST00000444766 24/25 79 51 28 62 62 0 strelka-varscan-mutect INTS2,missense_variant,p.Gln1093His,ENST00000444766,NM_020748.2;INTS2,missense_variant,p.Gln1093His,ENST00000617492,;INTS2,missense_variant,p.Gln1085His,ENST00000251334,;BRIP1,upstream_gene_variant,,ENST00000259008,NM_032043.2;BRIP1,upstream_gene_variant,,ENST00000577913,;INTS2,downstream_gene_variant,,ENST00000583822,; A ENST00000444766 Transcript missense_variant 3355/5878 3279/3615 1093/1204 Q/H caG/caT 1 -1 INTS2 HGNC HGNC:29241 protein_coding YES CCDS45750.1 ENSP00000414237 Q9H0H0 UPI0000E5A03A NM_020748.2 deleterious(0.02) 24/25 Pfam_domain:PF14750,hmmpanther:PTHR28608 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 61867999 61867999 C A 1 0 0 0 0 1 0 0 0 7680 680 24 2 2 INTS2 17 61867999 Missense_Mutation SNP C 11LU022_T 294 61867999 21389442 819 1457 1 1 3 3 405 N T_C 8.648087e-05 MED13 0 . GRCh38 17 61961080 61961080 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.5267G>C p.Cys1756Ser p.C1756S ENST00000397786 23/30 181 110 71 173 173 0 strelka-varscan-mutect MED13,missense_variant,p.Cys1756Ser,ENST00000397786,NM_005121.2; G ENST00000397786 Transcript missense_variant 5344/10465 5267/6525 1756/2174 C/S tGt/tCt 1 -1 MED13 HGNC HGNC:22474 protein_coding YES CCDS42366.1 ENSP00000380888 Q9UHV7 A0A024QZ75 UPI0000D7D6F6 NM_005121.2 tolerated(0.76) 23/30 hmmpanther:PTHR10791:SF51,hmmpanther:PTHR10791,Pfam_domain:PF06333 MODERATE 1 SNV 1 1 PASS rs1366271673 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 61961080 61961080 C G 1 0 0 0 0 1 0 0 0 9369 478 17 4 4 MED13 17 61961080 Missense_Mutation SNP C 11LU022_T 93081 61961080 21296361 820 1458 MED13 0 . GRCh38 17 62033946 62033946 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.655G>C p.Gly219Arg p.G219R ENST00000397786 5/30 212 137 75 220 220 0 strelka-varscan-mutect MED13,missense_variant,p.Gly219Arg,ENST00000397786,NM_005121.2;MED13,upstream_gene_variant,,ENST00000583958,;Y_RNA,upstream_gene_variant,,ENST00000363972,;MED13,upstream_gene_variant,,ENST00000580896,;MED13,upstream_gene_variant,,ENST00000581994,;MED13,upstream_gene_variant,,ENST00000578132,; G ENST00000397786 Transcript missense_variant 732/10465 655/6525 219/2174 G/R Gga/Cga 1 -1 MED13 HGNC HGNC:22474 protein_coding YES CCDS42366.1 ENSP00000380888 Q9UHV7 A0A024QZ75 UPI0000D7D6F6 NM_005121.2 deleterious(0) 5/30 hmmpanther:PTHR10791:SF51,hmmpanther:PTHR10791,Pfam_domain:PF11597 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 62033946 62033946 C G 1 0 0 0 0 1 0 0 0 9369 690 24 4 4 MED13 17 62033946 Missense_Mutation SNP C 11LU022_T 72866 62033946 21223495 821 1459 MAP3K3 0 . GRCh38 17 63692381 63692381 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1707G>T p.= p.V569V ENST00000361357 16/17 165 147 18 166 166 0 strelka-varscan-mutect MAP3K3,synonymous_variant,p.=,ENST00000361357,NM_203351.1;MAP3K3,synonymous_variant,p.=,ENST00000361733,NM_002401.3;MAP3K3,synonymous_variant,p.=,ENST00000579585,;MAP3K3,synonymous_variant,p.=,ENST00000584573,;MAP3K3,synonymous_variant,p.=,ENST00000577395,;LIMD2,downstream_gene_variant,,ENST00000259006,NM_030576.3;MAP3K3,downstream_gene_variant,,ENST00000577784,;MAP3K3,3_prime_UTR_variant,,ENST00000577597,;MAP3K3,downstream_gene_variant,,ENST00000585302,;MAP3K3,downstream_gene_variant,,ENST00000577839,;MAP3K3,downstream_gene_variant,,ENST00000581732,;MAP3K3,downstream_gene_variant,,ENST00000578622,; T ENST00000361357 Transcript synonymous_variant 2025/4818 1707/1974 569/657 V gtG/gtT 1 1 MAP3K3 HGNC HGNC:6855 protein_coding YES CCDS32701.1 ENSP00000354927 Q99759 UPI0000074003 NM_203351.1 16/17 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF350,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 63692381 63692381 G T 1 0 0 0 0 0 0 0 1 9174 1277 45 2 2 MAP3K3 17 63692381 Silent SNP G 11LU022_T 1658435 63692381 19565060 822 1460 HELZ 0 . GRCh38 17 67136164 67136164 + Silent SNP T T G novel 11LU022_T 11LU022_N T T c.2988A>C p.= p.V996V ENST00000358691 23/33 144 130 14 152 152 0 strelka-varscan-mutect HELZ,synonymous_variant,p.=,ENST00000358691,NM_014877.3;HELZ,synonymous_variant,p.=,ENST00000580168,;HELZ,synonymous_variant,p.=,ENST00000579953,; G ENST00000358691 Transcript synonymous_variant 3155/13810 2988/5829 996/1942 V gtA/gtC 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 23/33 Gene3D:3.40.50.300,Pfam_domain:PF13087,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 67136164 67136164 T G 1 0 0 0 0 0 0 0 1 6931 1625 57 5 5 HELZ 17 67136164 Silent SNP T 11LU022_T 3443783 67136164 16121277 823 1461 BPTF 0 . GRCh38 17 67854647 67854647 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1321G>C p.Gly441Arg p.G441R ENST00000306378 2/28 263 236 27 267 267 0 strelka-varscan-mutect BPTF,missense_variant,p.Gly441Arg,ENST00000321892,NM_004459.6;BPTF,missense_variant,p.Gly441Arg,ENST00000306378,NM_182641.3;BPTF,missense_variant,p.Gly302Arg,ENST00000424123,;BPTF,missense_variant,p.Gly441Arg,ENST00000544778,;BPTF,missense_variant,p.Gly302Arg,ENST00000335221,; C ENST00000306378 Transcript missense_variant 1381/9688 1321/8763 441/2920 G/R Ggt/Cgt 1 1 BPTF HGNC HGNC:3581 protein_coding YES CCDS11673.1 ENSP00000307208 Q12830 UPI00002263BF NM_182641.3 deleterious(0) 2/28 Gene3D:3.30.40.10,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF5,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 67854647 67854647 G C 1 0 0 0 0 1 0 0 0 1664 1348 47 4 4 BPTF 17 67854647 Missense_Mutation SNP G 11LU022_T 718483 67854647 15402794 824 1462 KIF19 0 . GRCh38 17 74347812 74347812 + Silent SNP C C T rs766695819 11LU022_T 11LU022_N C C c.960C>T p.= p.I320I ENST00000389916 9/20 173 150 23 230 230 0 strelka-varscan-mutect KIF19,synonymous_variant,p.=,ENST00000389916,NM_153209.3;KIF19,synonymous_variant,p.=,ENST00000551294,;KIF19,non_coding_transcript_exon_variant,,ENST00000547389,;KIF19,non_coding_transcript_exon_variant,,ENST00000359939,;KIF19,upstream_gene_variant,,ENST00000549637,; T ENST00000389916 Transcript synonymous_variant 1098/3643 960/2997 320/998 I atC/atT rs766695819 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 9/20 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF434,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs766695819 . 0 207 0 3 0 0 0 0 -20 0.9999919 1 1 1 0 T 2 4 3 74347812 74347812 C T 1 0 0 0 0 0 0 0 1 8146 874 31 1 1 KIF19 17 74347812 Silent SNP C 11LU022_T 6493165 74347812 8909629 825 1463 KIF19 0 . GRCh38 17 74347859 74347859 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.1007C>A p.Thr336Asn p.T336N ENST00000389916 9/20 173 128 45 239 238 1 strelka-varscan-mutect KIF19,missense_variant,p.Thr336Asn,ENST00000389916,NM_153209.3;KIF19,missense_variant,p.Thr294Asn,ENST00000551294,;KIF19,non_coding_transcript_exon_variant,,ENST00000547389,;KIF19,non_coding_transcript_exon_variant,,ENST00000359939,;KIF19,upstream_gene_variant,,ENST00000549637,; A ENST00000389916 Transcript missense_variant 1145/3643 1007/2997 336/998 T/N aCc/aAc COSM1710734 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 deleterious(0) 9/20 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF434,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 74347859 74347859 C A 1 0 0 0 0 1 0 0 0 8146 507 18 2 2 KIF19 17 74347859 Missense_Mutation SNP C 11LU022_T 47 74347859 8909582 826 1464 KIF19 0 . GRCh38 17 74354302 74354302 + Nonsense_Mutation SNP G G T rs771403100 11LU022_T 11LU022_N G G c.2449G>T p.Glu817Ter p.E817* ENST00000389916 18/20 177 161 16 222 221 1 strelka-varscan-mutect KIF19,stop_gained,p.Glu817Ter,ENST00000389916,NM_153209.3;KIF19,downstream_gene_variant,,ENST00000551294,;BTBD17,downstream_gene_variant,,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000547389,;KIF19,downstream_gene_variant,,ENST00000359939,;KIF19,downstream_gene_variant,,ENST00000549637,; T ENST00000389916 Transcript stop_gained 2587/3643 2449/2997 817/998 E/* Gag/Tag rs771403100 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 18/20 HIGH SNV 5 1 PASS rs771403100 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 74354302 74354302 G T 1 0 0 0 0 0 1 0 0 8146 1059 37 1 1 KIF19 17 74354302 Nonsense_Mutation SNP G 11LU022_T 6443 74354302 8903139 827 1465 USH1G 0 . GRCh38 17 74919512 74919512 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1324G>T p.Ala442Ser p.A442S ENST00000614341 2/3 155 99 56 223 220 3 strelka-varscan-mutect USH1G,missense_variant,p.Ala442Ser,ENST00000614341,NM_001282489.2,NM_173477.4;OTOP2,upstream_gene_variant,,ENST00000331427,NM_178160.2;USH1G,3_prime_UTR_variant,,ENST00000579243,;OTOP2,upstream_gene_variant,,ENST00000584711,; A ENST00000614341 Transcript missense_variant 1507/3558 1324/1386 442/461 A/S Gcc/Tcc 1 -1 USH1G HGNC HGNC:16356 protein_coding YES CCDS32725.1 ENSP00000480279 Q495M9 UPI00001BC010 NM_001282489.2,NM_173477.4 deleterious(0.02) 2/3 hmmpanther:PTHR24161:SF24,hmmpanther:PTHR24161,Gene3D:1.10.150.50,Pfam_domain:PF00536,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 74919512 74919512 C A 1 0 0 0 0 1 0 0 0 17569 739 26 2 2 USH1G 17 74919512 Missense_Mutation SNP C 11LU022_T 565210 74919512 8337929 828 1466 CDR2L 0 . GRCh38 17 75001380 75001380 + Missense_Mutation SNP G G C rs764486501 11LU022_T 11LU022_N G G c.232G>C p.Glu78Gln p.E78Q ENST00000337231 3/5 92 64 28 113 113 0 strelka-varscan-mutect CDR2L,missense_variant,p.Glu78Gln,ENST00000337231,NM_014603.2; C ENST00000337231 Transcript missense_variant 644/3536 232/1398 78/465 E/Q Gag/Cag rs764486501,COSM5528510 1 1 CDR2L HGNC HGNC:29999 protein_coding YES CCDS11710.2 ENSP00000336587 Q86X02 A0A024R8R6 UPI00005AE46D NM_014603.2 deleterious(0.01) 3/5 hmmpanther:PTHR19232:SF10,hmmpanther:PTHR19232 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764486501 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 75001380 75001380 G C 1 0 0 0 0 1 0 0 0 2878 1059 37 4 4 CDR2L 17 75001380 Missense_Mutation SNP G 11LU022_T 81868 75001380 8256061 829 1467 SEPT9 0 . GRCh38 17 77475598 77475598 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.80G>T p.Gly27Val p.G27V ENST00000427180 1/10 313 206 107 361 361 0 strelka-varscan-mutect SEPT9,missense_variant,p.Gly27Val,ENST00000427180,NM_001113495.1;SEPT9,intron_variant,,ENST00000329047,NM_006640.4;SEPT9,intron_variant,,ENST00000431235,;SEPT9,intron_variant,,ENST00000449803,NM_001113492.1;SEPT9,intron_variant,,ENST00000423034,NM_001113493.1;SEPT9,intron_variant,,ENST00000427674,NM_001113494.1;SEPT9,intron_variant,,ENST00000427177,NM_001113491.1;SEPT9,intron_variant,,ENST00000541152,NM_001113496.1;SEPT9,intron_variant,,ENST00000588690,;SEPT9,intron_variant,,ENST00000590294,;SEPT9,intron_variant,,ENST00000592420,;SEPT9,intron_variant,,ENST00000591198,NM_001293695.1;SEPT9,intron_variant,,ENST00000592951,NM_001293698.1;SEPT9,intron_variant,,ENST00000591088,NM_001293697.1;SEPT9,intron_variant,,ENST00000585930,NM_001293696.1;SEPT9,intron_variant,,ENST00000585929,;SEPT9,intron_variant,,ENST00000588958,;SEPT9,intron_variant,,ENST00000593189,;SEPT9,intron_variant,,ENST00000586128,;SEPT9,intron_variant,,ENST00000591704,;SEPT9,intron_variant,,ENST00000590059,;SEPT9,intron_variant,,ENST00000590938,;SEPT9,intron_variant,,ENST00000586521,;SEPT9,intron_variant,,ENST00000591020,;SEPT9,intron_variant,,ENST00000586433,;SEPT9,intron_variant,,ENST00000591472,;SEPT9,intron_variant,,ENST00000590917,;RP11-75C10.9,upstream_gene_variant,,ENST00000591110,;RP11-75C10.7,downstream_gene_variant,,ENST00000585369,;SEPT9,intron_variant,,ENST00000592481,;SEPT9,intron_variant,,ENST00000588575,; T ENST00000427180 Transcript missense_variant 356/3635 80/1425 27/474 G/V gGg/gTg 1 1 SEPT9 HGNC HGNC:7323 protein_coding CCDS45794.1 ENSP00000415624 Q9UHD8 UPI0000E5A0D3 NM_001113495.1 1/10 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 77475598 77475598 G T 1 0 0 0 0 1 0 0 0 14347 1232 43 2 2 SEPT9 17 77475598 Missense_Mutation SNP G 11LU022_T 2474218 77475598 5781843 830 1468 SEPT9 0 . GRCh38 17 77497345 77497345 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.1604A>G p.Tyr535Cys p.Y535C ENST00000427177 11/12 383 355 28 429 429 0 strelka-varscan-mutect SEPT9,missense_variant,p.Tyr517Cys,ENST00000329047,NM_006640.4;SEPT9,missense_variant,p.Tyr371Cys,ENST00000431235,;SEPT9,missense_variant,p.Tyr371Cys,ENST00000449803,NM_001113492.1;SEPT9,missense_variant,p.Tyr528Cys,ENST00000423034,NM_001113493.1;SEPT9,missense_variant,p.Tyr371Cys,ENST00000427674,NM_001113494.1;SEPT9,missense_variant,p.Tyr535Cys,ENST00000427177,NM_001113491.1;SEPT9,missense_variant,p.Tyr423Cys,ENST00000427180,NM_001113495.1;SEPT9,missense_variant,p.Tyr284Cys,ENST00000541152,NM_001113496.1;SEPT9,missense_variant,p.Tyr371Cys,ENST00000588690,;SEPT9,missense_variant,p.Tyr517Cys,ENST00000590294,;SEPT9,missense_variant,p.Tyr516Cys,ENST00000591198,NM_001293695.1;SEPT9,missense_variant,p.Tyr284Cys,ENST00000592951,NM_001293698.1;SEPT9,missense_variant,p.Tyr284Cys,ENST00000591088,NM_001293697.1;SEPT9,missense_variant,p.Tyr311Cys,ENST00000585930,NM_001293696.1;SEPT9,downstream_gene_variant,,ENST00000592481,;SEPT9,non_coding_transcript_exon_variant,,ENST00000589246,;SEPT9,non_coding_transcript_exon_variant,,ENST00000586456,;SEPT9,downstream_gene_variant,,ENST00000589250,; G ENST00000427177 Transcript missense_variant 1730/3821 1604/1761 535/586 Y/C tAc/tGc 1 1 SEPT9 HGNC HGNC:7323 protein_coding YES CCDS45790.1 ENSP00000391249 Q9UHD8 UPI00001AF955 NM_001113491.1 deleterious(0.01) 11/12 PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF47,Pfam_domain:PF00735,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 77497345 77497345 A G 1 0 0 0 0 1 0 0 0 14347 391 14 5 5 SEPT9 17 77497345 Missense_Mutation SNP A 11LU022_T 21747 77497345 5760096 831 1469 DNAH17 0 . GRCh38 17 78525138 78525138 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.3735G>T p.Met1245Ile p.M1245I ENST00000389840 25/81 137 83 54 143 143 0 strelka-varscan-mutect DNAH17,missense_variant,p.Met1245Ile,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Met1242Ile,ENST00000585328,;RP11-559N14.6,downstream_gene_variant,,ENST00000587621,; A ENST00000389840 Transcript missense_variant 3860/13723 3735/13389 1245/4462 M/I atG/atT 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 tolerated(0.12) 25/81 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 78525138 78525138 C A 1 0 0 0 0 1 0 0 0 4416 594 21 2 2 DNAH17 17 78525138 Missense_Mutation SNP C 11LU022_T 1027793 78525138 4732303 832 1470 DNAH17 0 . GRCh38 17 78571629 78571629 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.693G>C p.Trp231Cys p.W231C ENST00000389840 4/81 313 293 20 311 311 0 strelka-varscan-mutect DNAH17,missense_variant,p.Trp231Cys,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Trp231Cys,ENST00000585328,;DNAH17,upstream_gene_variant,,ENST00000589793,; G ENST00000389840 Transcript missense_variant 818/13723 693/13389 231/4462 W/C tgG/tgC 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 4/81 Pfam_domain:PF08385,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 78571629 78571629 C G 1 0 0 0 0 1 0 0 0 4416 624 22 4 4 DNAH17 17 78571629 Missense_Mutation SNP C 11LU022_T 46491 78571629 4685812 833 1471 CCDC40 0 . GRCh38 17 80099558 80099558 + Missense_Mutation SNP G G T rs142135083 11LU022_T 11LU022_N G G c.3212G>T p.Arg1071Leu p.R1071L ENST00000397545 20/20 419 388 31 457 457 0 strelka-varscan-mutect CCDC40,missense_variant,p.Arg1071Leu,ENST00000397545,NM_017950.3;GAA,upstream_gene_variant,,ENST00000302262,NM_000152.3;GAA,upstream_gene_variant,,ENST00000390015,NM_001079803.1,NM_001079804.1;GAA,upstream_gene_variant,,ENST00000570803,;GAA,upstream_gene_variant,,ENST00000577106,;MIR1268B,downstream_gene_variant,,ENST00000579691,;GAA,upstream_gene_variant,,ENST00000574376,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;CCDC40,downstream_gene_variant,,ENST00000572253,;CCDC40,downstream_gene_variant,,ENST00000575431,; T ENST00000397545 Transcript missense_variant 3239/4294 3212/3429 1071/1142 R/L cGc/cTc rs142135083 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 deleterious(0) 20/20 hmmpanther:PTHR16275 MODERATE SNV 5 1 PASS rs142135083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 80099558 80099558 G T 1 0 0 0 0 1 0 0 0 2521 1087 38 1 1 CCDC40 17 80099558 Missense_Mutation SNP G 11LU022_T 1527929 80099558 3157883 834 1472 RNF213 0 . GRCh38 17 80393354 80393357 + Frame_Shift_Del DEL CACT CACT - novel 11LU022_T 11LU022_N CACT CACT c.15481_15484delACTC p.Thr5161SerfsTer2 p.T5161Sfs*2 ENST00000582970 68/68 365 327 38 458 458 0 sindel-varindel-pindel RNF213,frameshift_variant,p.Thr5161SerfsTer2,ENST00000582970,NM_001256071.2;RNF213,frameshift_variant,p.Thr5210SerfsTer2,ENST00000508628,;CTD-2047H16.4,intron_variant,,ENST00000575034,;CTD-2047H16.4,intron_variant,,ENST00000572151,;CTD-2047H16.4,intron_variant,,ENST00000573394,;RNF213,non_coding_transcript_exon_variant,,ENST00000427003,;RNF213,non_coding_transcript_exon_variant,,ENST00000411702,;RNF213,non_coding_transcript_exon_variant,,ENST00000560083,;RNF213,downstream_gene_variant,,ENST00000573919,; - ENST00000582970 Transcript frameshift_variant 15623-15626/21055 15480-15483/15624 5160-5161/5207 DT/X gaCACT/ga 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 68/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 80393354 80393354 CACT - 1 0 1 0 1 0 0 0 0 13656 477 17 0 0 RNF213 17 80393354 Frame_Shift_Del DEL CACT 11LU022_T 293796 80393354 2864087 835 1473 BAHCC1 0 . GRCh38 17 81452729 81452729 + Missense_Mutation SNP C C A rs782729211 11LU022_T 11LU022_N C C c.4416C>A p.Asp1472Glu p.D1472E ENST00000584436 15/29 111 103 8 140 140 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Asp1472Glu,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Asp1441Glu,ENST00000307745,;MIR3186,upstream_gene_variant,,ENST00000577404,;BAHCC1,upstream_gene_variant,,ENST00000584330,; A ENST00000584436 Transcript missense_variant 4783/10801 4416/7920 1472/2639 D/E gaC/gaA rs782729211 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 tolerated(1) 15/29 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 MODERATE 1 SNV 5 1 PASS rs782729211 . 0 201 8 0 0 0 0 0 -15.71943 0.9999905 1 1 1 0 A 3 1 3 81452729 81452729 C A 1 0 0 0 0 1 0 0 0 1451 535 19 1 1 BAHCC1 17 81452729 Missense_Mutation SNP C 11LU022_T 1059375 81452729 1804712 836 1474 FASN 0 . GRCh38 17 82080192 82080192 + Missense_Mutation SNP G G T rs775705403 11LU022_T 11LU022_N G G c.7094C>A p.Thr2365Lys p.T2365K ENST00000306749 41/43 412 368 44 480 480 0 strelka-varscan-mutect FASN,missense_variant,p.Thr2365Lys,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Thr2363Lys,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000636628,;FASN,3_prime_UTR_variant,,ENST00000580382,;FASN,non_coding_transcript_exon_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,downstream_gene_variant,,ENST00000579410,; T ENST00000306749 Transcript missense_variant 7313/8565 7094/7536 2365/2511 T/K aCg/aAg rs775705403 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 deleterious(0.01) 41/43 Gene3D:2px6A02,Pfam_domain:PF00975,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs775705403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 82080192 82080192 G T 1 0 0 0 0 1 0 0 0 5543 1145 40 1 1 FASN 17 82080192 Missense_Mutation SNP G 11LU022_T 627463 82080192 1177249 837 1475 LAMA1 0 . GRCh38 18 6982586 6982586 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.5801C>T p.Ser1934Leu p.S1934L ENST00000389658 41/63 522 478 44 491 491 0 strelka-varscan-mutect LAMA1,missense_variant,p.Ser1934Leu,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript missense_variant 5895/9657 5801/9228 1934/3075 S/L tCa/tTa 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 tolerated(0.1) 41/63 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 6982586 6982586 G A 1 0 0 0 0 1 0 0 0 8509 1304 45 3 3 LAMA1 18 6982586 Missense_Mutation SNP G 11LU022_T 6982586 73390699 838 1476 LAMA1 0 . GRCh38 18 7002287 7002287 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.4359C>A p.= p.A1453A ENST00000389658 30/63 422 377 45 388 388 0 strelka-varscan-mutect LAMA1,synonymous_variant,p.=,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; T ENST00000389658 Transcript synonymous_variant 4453/9657 4359/9228 1453/3075 A gcC/gcA 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 30/63 Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 7002287 7002287 G T 1 0 0 0 0 0 0 0 1 8509 987 35 2 2 LAMA1 18 7002287 Silent SNP G 11LU022_T 19701 7002287 73370998 839 1477 SLC35G4 0 . GRCh38 18 11609705 11609705 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.110C>A p.Thr37Asn p.T37N ENST00000636911 1/2 105 82 23 175 175 0 strelka-varscan-mutect SLC35G4,missense_variant,p.Thr37Asn,ENST00000636911,;SLC35G4,missense_variant,p.Thr37Asn,ENST00000588001,NM_001282300.1; A ENST00000636911 Transcript missense_variant 231/1201 110/1017 37/338 T/N aCc/aAc 1 1 SLC35G4 HGNC HGNC:31043 protein_coding YES ENSP00000489773 UPI0001AE65E0 deleterious(0.02) 1/2 hmmpanther:PTHR22911,hmmpanther:PTHR22911:SF32,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 11609705 11609705 C A 1 0 0 0 0 1 0 0 0 14868 507 18 2 2 SLC35G4 18 11609705 Missense_Mutation SNP C 11LU022_T 4607418 11609705 68763580 840 1478 CIDEA 0 . GRCh38 18 12277264 12277264 + Nonsense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.654T>A p.Cys218Ter p.C218* ENST00000320477 5/5 112 77 35 143 143 0 strelka-varscan-mutect CIDEA,stop_gained,p.Cys218Ter,ENST00000320477,NM_001279.3;CIDEA,non_coding_transcript_exon_variant,,ENST00000521296,;CIDEA,non_coding_transcript_exon_variant,,ENST00000520620,;RP11-64C12.1,upstream_gene_variant,,ENST00000623093,;CIDEA,3_prime_UTR_variant,,ENST00000522713,; A ENST00000320477 Transcript stop_gained 719/828 654/660 218/219 C/* tgT/tgA 1 1 CIDEA HGNC HGNC:1976 protein_coding YES CCDS11856.1 ENSP00000320209 O60543 UPI0000049059 NM_001279.3 5/5 hmmpanther:PTHR12306,hmmpanther:PTHR12306:SF8 HIGH 1 SNV 1 1 PASS rs1325278992 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 12277264 12277264 T A 1 0 0 0 0 0 1 0 0 3187 1702 59 4 4 CIDEA 18 12277264 Nonsense_Mutation SNP T 11LU022_T 667559 12277264 68096021 841 1479 PRELID3A 0 . GRCh38 18 12420480 12420480 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.188G>T p.Ser63Ile p.S63I ENST00000440960 2/7 122 107 15 99 99 0 strelka-varscan-mutect PRELID3A,missense_variant,p.Ser42Ile,ENST00000592149,NM_001142406.1;PRELID3A,missense_variant,p.Ser63Ile,ENST00000440960,NM_001142405.1;PRELID3A,missense_variant,p.Ser63Ile,ENST00000336990,NM_006553.3;PRELID3A,missense_variant,p.Ser84Ile,ENST00000587862,;PRELID3A,missense_variant,p.Ser110Ile,ENST00000588729,;PRELID3A,missense_variant,p.Ser42Ile,ENST00000589952,;PRELID3A,intron_variant,,ENST00000590956,;PRELID3A,upstream_gene_variant,,ENST00000587735,;PRELID3A,intron_variant,,ENST00000589565,; T ENST00000440960 Transcript missense_variant 268/1716 188/519 63/172 S/I aGc/aTc 1 1 PRELID3A HGNC HGNC:24639 protein_coding YES CCDS11860.1 ENSP00000404700 Q96N28 UPI0000070E6F NM_001142405.1 deleterious(0.03) 2/7 PROSITE_profiles:PS50904,hmmpanther:PTHR11158:SF23,hmmpanther:PTHR11158,Pfam_domain:PF04707 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 12420480 12420480 G T 1 0 0 0 0 1 0 0 0 12605 971 34 2 2 PRELID3A 18 12420480 Missense_Mutation SNP G 11LU022_T 143216 12420480 67952805 842 1480 CEP192 0 . GRCh38 18 13049562 13049562 + Missense_Mutation SNP G G T rs759830148 11LU022_T 11LU022_N G G c.2771G>T p.Cys924Phe p.C924F ENST00000506447 16/45 154 141 13 176 175 1 strelka-varscan-mutect CEP192,missense_variant,p.Cys924Phe,ENST00000506447,NM_032142.3;CEP192,missense_variant,p.Cys449Phe,ENST00000325971,;CEP192,missense_variant,p.Cys463Phe,ENST00000511820,;CEP192,missense_variant,p.Cys665Phe,ENST00000589596,;CEP192,missense_variant,p.Cys524Phe,ENST00000510237,;CEP192,3_prime_UTR_variant,,ENST00000513432,; T ENST00000506447 Transcript missense_variant 2851/7960 2771/7614 924/2537 C/F tGt/tTt rs759830148 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 tolerated(0.66) 16/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 MODERATE 1 SNV 5 1 PASS rs759830148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 13049562 13049562 G T 1 0 0 0 0 1 0 0 0 2967 1377 48 2 2 CEP192 18 13049562 Missense_Mutation SNP G 11LU022_T 629082 13049562 67323723 843 1481 POTEC 0 . GRCh38 18 14524970 14524970 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1140G>T p.Lys380Asn p.K380N ENST00000358970 7/11 39 32 7 54 54 0 strelka-varscan-mutect POTEC,missense_variant,p.Lys380Asn,ENST00000358970,NM_001137671.1;POTEC,downstream_gene_variant,,ENST00000620346,;POTEC,downstream_gene_variant,,ENST00000389891,;POTEC,intron_variant,,ENST00000511306,; A ENST00000358970 Transcript missense_variant 1140/1629 1140/1629 380/542 K/N aaG/aaT 1 -1 POTEC HGNC HGNC:33894 protein_coding YES CCDS45835.1 ENSP00000351856 B2RU33 UPI0000197B83 NM_001137671.1 deleterious(0.02) 7/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38 MODERATE 1 SNV 1 1 PASS rs1452011480 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 14524970 14524970 C A 1 0 0 0 0 1 0 0 0 12376 796 28 2 2 POTEC 18 14524970 Missense_Mutation SNP C 11LU022_T 1475408 14524970 65848315 844 1482 POTEC 0 . GRCh38 18 14542810 14542810 + Missense_Mutation SNP C C A rs113041483 11LU022_T 11LU022_N C C c.337G>T p.Gly113Cys p.G113C ENST00000358970 1/11 542 474 68 619 619 0 strelka-varscan-mutect POTEC,missense_variant,p.Gly113Cys,ENST00000620346,;POTEC,missense_variant,p.Gly113Cys,ENST00000358970,NM_001137671.1;POTEC,non_coding_transcript_exon_variant,,ENST00000389891,;POTEC,missense_variant,p.Gly113Cys,ENST00000511306,; A ENST00000358970 Transcript missense_variant 337/1629 337/1629 113/542 G/C Ggc/Tgc rs113041483,COSM2884384 1 -1 POTEC HGNC HGNC:33894 protein_coding YES CCDS45835.1 ENSP00000351856 B2RU33 UPI0000197B83 NM_001137671.1 deleterious(0.01) 1/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs113041483 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 14542810 14542810 C A 1 0 0 0 0 1 0 0 0 12376 652 23 1 1 POTEC 18 14542810 Missense_Mutation SNP C 11LU022_T 17840 14542810 65830475 845 1483 LAMA3 0 . GRCh38 18 23864837 23864837 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.4637C>A p.Pro1546His p.P1546H ENST00000313654 36/75 303 230 73 362 362 0 strelka-varscan-mutect LAMA3,missense_variant,p.Pro1546His,ENST00000313654,NM_198129.2;LAMA3,missense_variant,p.Pro1546His,ENST00000399516,NM_001127717.2; A ENST00000313654 Transcript missense_variant 4878/10661 4637/10002 1546/3333 P/H cCt/cAt 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 deleterious(0) 36/75 Pfam_domain:PF00052,PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285,SMART_domains:SM00281 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 23864837 23864837 C A 1 0 0 0 0 1 0 0 0 8511 681 24 2 2 LAMA3 18 23864837 Missense_Mutation SNP C 11LU022_T 9322027 23864837 56508448 846 1484 ZNF521 0 . GRCh38 18 25227574 25227574 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.344G>C p.Gly115Ala p.G115A ENST00000361524 4/8 214 189 25 270 270 0 strelka-varscan-mutect ZNF521,missense_variant,p.Gly115Ala,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Gly115Ala,ENST00000538137,;ZNF521,missense_variant,p.Gly115Ala,ENST00000577801,;ZNF521,missense_variant,p.Gly115Ala,ENST00000580488,;ZNF521,5_prime_UTR_variant,,ENST00000584787,NM_001308225.1;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,non_coding_transcript_exon_variant,,ENST00000577720,;ZNF521,non_coding_transcript_exon_variant,,ENST00000581869,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,missense_variant,p.Gly115Ala,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; G ENST00000361524 Transcript missense_variant 493/4871 344/3936 115/1311 G/A gGg/gCg 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 deleterious(0) 4/8 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF222 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 25227574 25227574 C G 1 0 0 0 0 1 0 0 0 18537 623 22 4 4 ZNF521 18 25227574 Missense_Mutation SNP C 11LU022_T 1362737 25227574 55145711 847 1485 DSC3 0 . GRCh38 18 31022440 31022440 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.838C>A p.Leu280Met p.L280M ENST00000360428 7/16 284 243 41 396 396 0 strelka-varscan-mutect DSC3,missense_variant,p.Leu280Met,ENST00000434452,NM_024423.3;DSC3,missense_variant,p.Leu280Met,ENST00000360428,NM_001941.4; T ENST00000360428 Transcript missense_variant 919/6939 838/2691 280/896 L/M Ctg/Atg COSM5239060,COSM5239061 1 -1 DSC3 HGNC HGNC:3037 protein_coding YES CCDS32810.1 ENSP00000353608 Q14574 UPI000004CAAD NM_001941.4 deleterious(0) 7/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF12,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 31022440 31022440 G T 1 0 0 0 0 1 0 0 0 4588 991 35 2 2 DSC3 18 31022440 Missense_Mutation SNP G 11LU022_T 5794866 31022440 49350845 848 1486 DSG2 0 . GRCh38 18 31546727 31546727 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.3341A>T p.Gln1114Leu p.Q1114L ENST00000261590 15/15 397 355 42 434 434 0 strelka-varscan-mutect DSG2,missense_variant,p.Gln1114Leu,ENST00000261590,NM_001943.3;DSG2-AS1,intron_variant,,ENST00000583706,;DSG2-AS1,downstream_gene_variant,,ENST00000579251,; T ENST00000261590 Transcript missense_variant 3550/5831 3341/3357 1114/1118 Q/L cAg/cTg 1 1 DSG2 HGNC HGNC:3049 protein_coding YES CCDS42423.1 ENSP00000261590 Q14126 UPI0000048E38 NM_001943.3 deleterious(0) 15/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 31546727 31546727 A T 1 0 0 0 0 1 0 0 0 4598 188 7 4 4 DSG2 18 31546727 Missense_Mutation SNP A 11LU022_T 524287 31546727 48826558 849 1487 ASXL3 0 . GRCh38 18 33745966 33745966 + Missense_Mutation SNP C C A rs760150086 11LU022_T 11LU022_N C C c.6118C>A p.Pro2040Thr p.P2040T ENST00000269197 12/12 108 91 17 110 110 0 strelka-varscan-mutect ASXL3,missense_variant,p.Pro2040Thr,ENST00000269197,NM_030632.1;ASXL3,downstream_gene_variant,,ENST00000592288,; A ENST00000269197 Transcript missense_variant 6173/11399 6118/6747 2040/2248 P/T Ccg/Acg rs760150086 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 deleterious_low_confidence(0) 12/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs760150086 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 33745966 33745966 C A 1 0 0 0 0 1 0 0 0 1216 855 30 2 2 ASXL3 18 33745966 Missense_Mutation SNP C 11LU022_T 2199239 33745966 46627319 850 1488 NOL4 0 . GRCh38 18 34093597 34093597 + Missense_Mutation SNP C C A rs868184130 11LU022_T 11LU022_N C C c.640G>T p.Asp214Tyr p.D214Y ENST00000261592 5/11 63 56 7 68 68 0 strelka-varscan-mutect NOL4,missense_variant,p.Asp214Tyr,ENST00000261592,NM_003787.4;NOL4,missense_variant,p.Asp214Tyr,ENST00000589544,NM_001198548.1;NOL4,missense_variant,p.Asp140Tyr,ENST00000538587,NM_001198547.1;NOL4,missense_variant,p.Asp198Tyr,ENST00000590712,NM_001198546.1;NOL4,splice_region_variant,,ENST00000588280,;NOL4,splice_region_variant,,ENST00000586314,; A ENST00000261592 Transcript missense_variant,splice_region_variant 938/3957 640/1917 214/638 D/Y Gat/Tat rs868184130 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 deleterious(0) 5/11 Low_complexity_(Seg):seg,hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 MODERATE 1 SNV 1 1 PASS rs868184130 . 0 199 11 0 0 0 0 0 -15.6564 0.999928 1 1 1 0 A 3 1 3 34093597 34093597 C A 1 0 0 0 0 1 0 0 0 10567 869 30 2 2 NOL4 18 34093597 Missense_Mutation SNP C 11LU022_T 347631 34093597 46279688 851 1489 TPGS2 0 . GRCh38 18 36828755 36828755 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.13G>T p.Ala5Ser p.A5S ENST00000590842 1/7 161 139 22 216 216 0 strelka-varscan-mutect TPGS2,missense_variant,p.Ala5Ser,ENST00000334295,NM_015476.3;TPGS2,missense_variant,p.Ala5Ser,ENST00000593035,NM_001271949.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000383056,NM_001271950.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000610723,NM_001271955.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000614939,NM_001271956.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000590842,NM_001271951.1,NM_001271953.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000589049,NM_001271954.1;TPGS2,missense_variant,p.Ala5Ser,ENST00000587129,;TPGS2,missense_variant,p.Ala5Ser,ENST00000590337,;TPGS2,missense_variant,p.Ala5Ser,ENST00000588909,;KIAA1328,upstream_gene_variant,,ENST00000591619,;KIAA1328,upstream_gene_variant,,ENST00000280020,NM_020776.1;KIAA1328,upstream_gene_variant,,ENST00000587139,;TPGS2,upstream_gene_variant,,ENST00000587382,;KIAA1328,upstream_gene_variant,,ENST00000592521,;TPGS2,missense_variant,p.Ala5Ser,ENST00000585635,;TPGS2,missense_variant,p.Ala5Ser,ENST00000591823,;TPGS2,missense_variant,p.Ala5Ser,ENST00000587207,;TPGS2,missense_variant,p.Ala5Ser,ENST00000590692,;TPGS2,non_coding_transcript_exon_variant,,ENST00000591648,;TPGS2,non_coding_transcript_exon_variant,,ENST00000587511,;KIAA1328,upstream_gene_variant,,ENST00000590617,;KIAA1328,upstream_gene_variant,,ENST00000592611,; A ENST00000590842 Transcript missense_variant 88/1239 13/915 5/304 A/S Gca/Tca 1 -1 TPGS2 HGNC HGNC:24561 protein_coding YES CCDS62424.1 ENSP00000464780 Q68CL5 UPI0002840E1A NM_001271951.1,NM_001271953.1 tolerated_low_confidence(0.21) 1/7 hmmpanther:PTHR31854 MODERATE SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 3 36828755 36828755 C A 1 0 0 0 0 1 0 0 0 16881 739 26 2 2 TPGS2 18 36828755 Missense_Mutation SNP C 11LU022_T 2735158 36828755 43544530 852 1490 SETBP1 0 . GRCh38 18 44952226 44952226 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.2886C>T p.= p.T962T ENST00000282030 4/6 452 400 52 610 610 0 strelka-varscan-mutect SETBP1,synonymous_variant,p.=,ENST00000282030,NM_015559.2; T ENST00000282030 Transcript synonymous_variant 3182/9899 2886/4791 962/1596 T acC/acT 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 44952226 44952226 C T 1 0 0 0 0 0 0 0 1 14406 581 21 3 3 SETBP1 18 44952226 Silent SNP C 11LU022_T 8123471 44952226 35421059 853 1491 MAPK4 0 . GRCh38 18 50664036 50664036 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.78G>T p.= p.L26L ENST00000400384 2/6 182 144 38 239 239 0 strelka-varscan-mutect MAPK4,synonymous_variant,p.=,ENST00000400384,NM_002747.3;MAPK4,synonymous_variant,p.=,ENST00000592595,NM_001292040.1;MAPK4,synonymous_variant,p.=,ENST00000588540,;MAPK4,intron_variant,,ENST00000540640,NM_001292039.1;MAPK4,upstream_gene_variant,,ENST00000587823,;MAPK4,downstream_gene_variant,,ENST00000586735,; T ENST00000400384 Transcript synonymous_variant 1114/4770 78/1764 26/587 L ctG/ctT 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 2/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF25,hmmpanther:PTHR24055,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 50664036 50664036 G T 1 0 0 0 0 0 0 0 1 9204 1335 47 2 2 MAPK4 18 50664036 Silent SNP G 11LU022_T 5711810 50664036 29709249 854 1492 MAPK4 0 . GRCh38 18 50729809 50729809 + Silent SNP T T A novel 11LU022_T 11LU022_N T T c.1719T>A p.= p.P573P ENST00000400384 6/6 121 105 16 124 124 0 strelka-varscan-mutect MAPK4,synonymous_variant,p.=,ENST00000400384,NM_002747.3;MAPK4,synonymous_variant,p.=,ENST00000540640,NM_001292039.1;MAPK4,3_prime_UTR_variant,,ENST00000592595,NM_001292040.1; A ENST00000400384 Transcript synonymous_variant 2755/4770 1719/1764 573/587 P ccT/ccA 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 6/6 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 50729809 50729809 T A 1 0 0 0 0 0 0 0 1 9204 1567 55 4 4 MAPK4 18 50729809 Silent SNP T 11LU022_T 65773 50729809 29643476 855 1493 SMAD4 0 . GRCh38 18 51054953 51054953 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.627C>T p.= p.T209T ENST00000342988 5/12 265 238 27 324 324 0 strelka-varscan-mutect SMAD4,synonymous_variant,p.=,ENST00000342988,NM_005359.5;SMAD4,synonymous_variant,p.=,ENST00000398417,;SMAD4,synonymous_variant,p.=,ENST00000588745,;SMAD4,non_coding_transcript_exon_variant,,ENST00000592911,;SMAD4,synonymous_variant,p.=,ENST00000592186,;RP11-729L2.2,3_prime_UTR_variant,,ENST00000590722,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,upstream_gene_variant,,ENST00000611848,;SMAD4,downstream_gene_variant,,ENST00000585448,; T ENST00000342988 Transcript synonymous_variant 1165/8769 627/1659 209/552 T acC/acT 1 1 SMAD4 HGNC HGNC:6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 A0A024R274 UPI0000053431 NM_005359.5 5/12 LOW SNV 5 1 PASS rs905151346 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 51054953 51054953 C T 1 0 0 0 0 0 0 0 1 15053 581 21 3 3 SMAD4 18 51054953 Silent SNP C 11LU022_T 325144 51054953 29318332 856 1494 DCC 0 . GRCh38 18 53215551 53215551 + Missense_Mutation SNP C C G 11LU022_T 11LU022_N C C c.1865C>G p.Pro622Arg p.P622R ENST00000442544 12/29 303 267 36 422 422 0 strelka-varscan-mutect DCC,missense_variant,p.Pro622Arg,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Pro599Arg,ENST00000412726,;DCC,missense_variant,p.Pro277Arg,ENST00000581580,;DCC,missense_variant,p.Pro556Arg,ENST00000304775,; G ENST00000442544 Transcript missense_variant 2481/10206 1865/4344 622/1447 P/R cCa/cGa COSM709366 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 deleterious(0) 12/29 Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 53215551 53215551 C G 1 0 0 0 0 1 0 0 0 4084 608 21 4 4 DCC 18 53215551 Missense_Mutation SNP C 11LU022_T 2160598 53215551 27157734 857 1495 MBD2 0 . GRCh38 18 54203056 54203056 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.749G>T p.Arg250Ile p.R250I ENST00000583046 3/3 172 152 20 201 201 0 strelka-varscan-mutect MBD2,missense_variant,p.Arg250Ile,ENST00000583046,NM_015832.4;MBD2,3_prime_UTR_variant,,ENST00000398398,;MBD2,intron_variant,,ENST00000256429,NM_003927.4;MBD2,intron_variant,,ENST00000578272,; A ENST00000583046 Transcript missense_variant 807/1182 749/909 250/302 R/I aGa/aTa 1 -1 MBD2 HGNC HGNC:6917 protein_coding CCDS45871.1 ENSP00000464554 Q9UBB5 A0A024R2B8 UPI000006E78C NM_015832.4 deleterious_low_confidence(0) 3/3 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 54203056 54203056 C A 1 0 0 0 0 1 0 0 0 9272 913 32 2 2 MBD2 18 54203056 Missense_Mutation SNP C 11LU022_T 987505 54203056 26170229 858 1496 NEDD4L 0 . GRCh38 18 58325157 58325157 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.675C>T p.= p.S225S ENST00000400345 9/31 116 104 12 118 118 0 strelka-varscan-mutect NEDD4L,synonymous_variant,p.=,ENST00000456986,NM_001144964.1,NM_001144965.1;NEDD4L,synonymous_variant,p.=,ENST00000382850,NM_015277.5;NEDD4L,synonymous_variant,p.=,ENST00000456173,NM_001144970.2;NEDD4L,synonymous_variant,p.=,ENST00000635997,;NEDD4L,synonymous_variant,p.=,ENST00000400345,NM_001144967.2;NEDD4L,synonymous_variant,p.=,ENST00000357895,NM_001144968.1;NEDD4L,synonymous_variant,p.=,ENST00000435432,NM_001144971.1;NEDD4L,synonymous_variant,p.=,ENST00000586263,NM_001144969.1;NEDD4L,synonymous_variant,p.=,ENST00000431212,NM_001144966.2;NEDD4L,synonymous_variant,p.=,ENST00000356462,NM_001243960.1;NEDD4L,synonymous_variant,p.=,ENST00000256830,;NEDD4L,synonymous_variant,p.=,ENST00000587881,;NEDD4L,synonymous_variant,p.=,ENST00000586268,;NEDD4L,intron_variant,,ENST00000589054,;NEDD4L,downstream_gene_variant,,ENST00000587190,;NEDD4L,downstream_gene_variant,,ENST00000588494,;NEDD4L,downstream_gene_variant,,ENST00000592846,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000592601,;NEDD4L,downstream_gene_variant,,ENST00000587634,;NEDD4L,downstream_gene_variant,,ENST00000588066,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000590020,; T ENST00000400345 Transcript synonymous_variant 958/3647 675/2928 225/975 S agC/agT 1 1 NEDD4L HGNC HGNC:7728 protein_coding YES CCDS45872.1 ENSP00000383199 Q96PU5 UPI000058E3AE NM_001144967.2 9/31 Gene3D:2.20.70.10,PROSITE_profiles:PS50020,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF310,SMART_domains:SM00456,Superfamily_domains:SSF51045 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.14668 0.9999999 1 1 1 0 T 2 4 3 58325157 58325157 C T 1 0 0 0 0 0 0 0 1 10339 753 26 3 3 NEDD4L 18 58325157 Silent SNP C 11LU022_T 4122101 58325157 22048128 859 1497 ALPK2 0 . GRCh38 18 58503977 58503977 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.6201G>T p.Trp2067Cys p.W2067C ENST00000361673 11/13 105 88 17 139 139 0 strelka-varscan-mutect ALPK2,missense_variant,p.Trp2067Cys,ENST00000361673,NM_052947.3; A ENST00000361673 Transcript missense_variant 6415/7303 6201/6513 2067/2170 W/C tgG/tgT 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0) 11/13 Pfam_domain:PF02816,PROSITE_profiles:PS51158,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,SMART_domains:SM00811,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 58503977 58503977 C A 1 0 0 0 0 1 0 0 0 645 624 22 2 2 ALPK2 18 58503977 Missense_Mutation SNP C 11LU022_T 178820 58503977 21869308 860 1498 ZNF532 0 . GRCh38 18 58984336 58984336 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.3776G>T p.Gly1259Val p.G1259V ENST00000336078 11/11 306 267 39 321 321 0 strelka-varscan-mutect ZNF532,missense_variant,p.Gly1259Val,ENST00000336078,NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4;ZNF532,missense_variant,p.Gly1259Val,ENST00000589288,;ZNF532,missense_variant,p.Gly1259Val,ENST00000591083,;ZNF532,missense_variant,p.Gly1259Val,ENST00000591808,;ZNF532,missense_variant,p.Gly1259Val,ENST00000591230,;ZNF532,downstream_gene_variant,,ENST00000586997,;ZNF532,non_coding_transcript_exon_variant,,ENST00000588956,;ZNF532,non_coding_transcript_exon_variant,,ENST00000592249,;ZNF532,downstream_gene_variant,,ENST00000589131,;ZNF532,non_coding_transcript_exon_variant,,ENST00000590442,;ZNF532,downstream_gene_variant,,ENST00000585662,;ZNF532,downstream_gene_variant,,ENST00000586723,; T ENST00000336078 Transcript missense_variant 4552/6696 3776/3906 1259/1301 G/V gGc/gTc 1 1 ZNF532 HGNC HGNC:30940 protein_coding YES CCDS11969.1 ENSP00000338217 Q9HCE3 A0A024R283 UPI000013D30C NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4 tolerated(0.07) 11/11 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF204 MODERATE 1 SNV 1 1 PASS rs1486486746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 58984336 58984336 G T 1 0 0 0 0 1 0 0 0 18545 1203 42 2 2 ZNF532 18 58984336 Missense_Mutation SNP G 11LU022_T 480359 58984336 21388949 861 1499 ZNF516 0 . GRCh38 18 76442300 76442300 + Missense_Mutation SNP A A G novel 11LU022_T 11LU022_N A A c.755T>C p.Val252Ala p.V252A ENST00000443185 3/7 246 210 36 278 278 0 strelka-varscan-mutect ZNF516,missense_variant,p.Val252Ala,ENST00000443185,NM_014643.3;ZNF516,downstream_gene_variant,,ENST00000532857,; G ENST00000443185 Transcript missense_variant 1073/8118 755/3492 252/1163 V/A gTg/gCg 1 -1 ZNF516 HGNC HGNC:28990 protein_coding YES CCDS74234.1 ENSP00000394757 Q92618 UPI00001394A1 NM_014643.3 deleterious(0.02) 3/7 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 76442300 76442300 A G 1 0 0 0 0 1 0 0 0 18532 159 6 5 5 ZNF516 18 76442300 Missense_Mutation SNP A 11LU022_T 17457964 76442300 3930985 862 1500 GALR1 0 . GRCh38 18 77256223 77256223 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.732G>T p.Lys244Asn p.K244N ENST00000299727 2/3 86 77 9 133 132 1 strelka-varscan-mutect GALR1,missense_variant,p.Lys244Asn,ENST00000299727,NM_001480.3;GALR1,downstream_gene_variant,,ENST00000582943,; T ENST00000299727 Transcript missense_variant,splice_region_variant 732/10044 732/1050 244/349 K/N aaG/aaT 1 1 GALR1 HGNC HGNC:4132 protein_coding YES CCDS12012.1 ENSP00000299727 P47211 UPI000013E5DE NM_001480.3 deleterious(0) 2/3 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24230:SF31,hmmpanther:PTHR24230,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs747931381 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 77256223 77256223 G T 1 0 0 0 0 1 0 0 0 6095 1014 35 2 2 GALR1 18 77256223 Missense_Mutation SNP G 11LU022_T 813923 77256223 3117062 863 1501 SALL3 0 . GRCh38 18 78995287 78995287 + Missense_Mutation SNP C C A rs752632478 11LU022_T 11LU022_N C C c.3296C>A p.Ala1099Glu p.A1099E ENST00000537592 2/3 146 120 26 186 186 0 strelka-varscan-mutect SALL3,missense_variant,p.Ala1099Glu,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Ala894Glu,ENST00000536229,;SALL3,missense_variant,p.Ala1027Glu,ENST00000575389,;SALL3,missense_variant,p.Ala759Glu,ENST00000616649,;SALL3,missense_variant,p.Ala92Glu,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; A ENST00000537592 Transcript missense_variant 3296/6555 3296/3903 1099/1300 A/E gCg/gAg rs752632478,COSM1130036 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 tolerated(0.09) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs752632478 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 78995287 78995287 C A 1 0 0 0 0 1 0 0 0 14071 768 27 1 1 SALL3 18 78995287 Missense_Mutation SNP C 11LU022_T 1739064 78995287 1377998 864 1502 HCN2 0 . GRCh38 19 616454 616454 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2650C>A p.Arg884Ser p.R884S ENST00000251287 8/8 34 24 10 65 65 0 strelka-varscan-mutect HCN2,missense_variant,p.Arg884Ser,ENST00000251287,NM_001194.3;POLRMT,downstream_gene_variant,,ENST00000588649,NM_005035.3;POLRMT,downstream_gene_variant,,ENST00000590336,;POLRMT,downstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000589961,;POLRMT,downstream_gene_variant,,ENST00000592633,; A ENST00000251287 Transcript missense_variant 2703/3408 2650/2670 884/889 R/S Cgc/Agc 1 1 HCN2 HGNC HGNC:4846 protein_coding YES CCDS12035.1 ENSP00000251287 Q9UL51 UPI000013CCF6 NM_001194.3 deleterious_low_confidence(0) 8/8 MODERATE 1 SNV 1 1 PASS rs1344385887 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 616454 616454 C A 1 0 0 0 0 1 0 0 0 6884 768 27 1 1 HCN2 19 616454 Missense_Mutation SNP C 11LU022_T 616454 58001162 865 1503 PALM 0 . GRCh38 19 746736 746736 + Silent SNP G G T rs752701541 11LU022_T 11LU022_N G G c.1086G>T p.= p.A362A ENST00000338448 9/9 227 162 65 283 283 0 strelka-varscan-mutect PALM,synonymous_variant,p.=,ENST00000264560,NM_001040134.1;PALM,synonymous_variant,p.=,ENST00000338448,NM_002579.2;PALM,synonymous_variant,p.=,ENST00000592155,;PALM,synonymous_variant,p.=,ENST00000590161,;MISP,upstream_gene_variant,,ENST00000215582,NM_173481.2;PALM,non_coding_transcript_exon_variant,,ENST00000593172,;PALM,non_coding_transcript_exon_variant,,ENST00000587513,;PALM,non_coding_transcript_exon_variant,,ENST00000633534,; T ENST00000338448 Transcript synonymous_variant 1132/2725 1086/1164 362/387 A gcG/gcT rs752701541,COSM3541226 1 1 PALM HGNC HGNC:8594 protein_coding YES CCDS32857.1 ENSP00000341911 O75781 A0A024R1Y6 UPI0000001616 NM_002579.2 9/9 Pfam_domain:PF03285,hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF6 0,1 LOW 1 SNV 1 0,1 1 PASS rs752701541 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 746736 746736 G T 1 0 0 0 0 0 0 0 1 11488 1103 39 1 1 PALM 19 746736 Silent SNP G 11LU022_T 130282 746736 57870880 866 1504 ZFR2 0 . GRCh38 19 3827534 3827534 + Nonsense_Mutation SNP G G T rs773842233 11LU022_T 11LU022_N G G c.972C>A p.Cys324Ter p.C324* ENST00000262961 6/19 154 105 49 233 233 0 strelka-varscan-mutect ZFR2,stop_gained,p.Cys324Ter,ENST00000262961,NM_015174.1;ZFR2,downstream_gene_variant,,ENST00000591965,;ZFR2,stop_gained,p.Cys324Ter,ENST00000438164,; T ENST00000262961 Transcript stop_gained 983/4756 972/2820 324/939 C/* tgC/tgA rs773842233 1 -1 ZFR2 HGNC HGNC:29189 protein_coding YES CCDS45921.1 ENSP00000262961 Q9UPR6 UPI0000DD84BE NM_015174.1 6/19 hmmpanther:PTHR10910:SF85,hmmpanther:PTHR10910,PROSITE_patterns:PS00028,Pfam_domain:PF12874,SMART_domains:SM00355,SMART_domains:SM00451,Superfamily_domains:SSF57667 HIGH 1 SNV 5 1 PASS rs773842233 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 3827534 3827534 G T 1 0 0 0 0 0 1 0 0 18238 1079 38 1 1 ZFR2 19 3827534 Nonsense_Mutation SNP G 11LU022_T 3080798 3827534 54790082 867 1505 FUT3 0 . GRCh38 19 5843958 5843958 + Silent SNP G G A rs778985 11LU022_T 11LU022_N G G c.882C>T p.= p.D294D ENST00000303225 3/3 304 221 83 563 563 0 strelka-varscan FUT3,synonymous_variant,p.=,ENST00000303225,NM_000149.3;FUT3,synonymous_variant,p.=,ENST00000589620,NM_001097639.1;FUT3,synonymous_variant,p.=,ENST00000589918,NM_001097640.1;FUT3,synonymous_variant,p.=,ENST00000458379,NM_001097641.1;FUT6,upstream_gene_variant,,ENST00000318336,NM_000150.2;FUT6,upstream_gene_variant,,ENST00000286955,NM_001040701.1;FUT6,upstream_gene_variant,,ENST00000524754,;FUT3,downstream_gene_variant,,ENST00000585715,;FUT3,downstream_gene_variant,,ENST00000587183,;FUT3,downstream_gene_variant,,ENST00000587048,;FUT3,downstream_gene_variant,,ENST00000589714,;AC024592.9,upstream_gene_variant,,ENST00000589276,;FUT3,downstream_gene_variant,,ENST00000593144,;FUT3,downstream_gene_variant,,ENST00000588539,;FUT6,upstream_gene_variant,,ENST00000591079,; A ENST00000303225 Transcript synonymous_variant 1517/2584 882/1086 294/361 D gaC/gaT rs778985 1 -1 FUT3 HGNC HGNC:4014 protein_coding YES CCDS12153.1 ENSP00000305603 P21217 UPI000013E879 NM_000149.3 3/3 hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF150,Pfam_domain:PF00852,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 28 0 0 96 85 0 0 -3.417876 0 0 1 0 0 A 2 1 3 5843958 5843958 G A 1 0 0 0 0 0 0 0 1 5977 1136 40 1 1 FUT3 19 5843958 Silent SNP G 11LU022_T 2016424 5843958 52773658 868 1506 SLC25A23 0 . GRCh38 19 6444193 6444193 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1180A>T p.Ser394Cys p.S394C ENST00000301454 9/10 60 41 19 93 93 0 strelka-varscan-mutect SLC25A23,missense_variant,p.Ser394Cys,ENST00000301454,NM_024103.2;SLC25A23,missense_variant,p.Ser394Cys,ENST00000334510,;SLC25A23,missense_variant,p.Ser162Cys,ENST00000600682,;SLC25A23,missense_variant,p.Ser126Cys,ENST00000598908,;SLC25A23,missense_variant,p.Ser157Cys,ENST00000593600,;SLC25A23,missense_variant,p.Ser103Cys,ENST00000595810,;SLC25A23,missense_variant,p.Ser55Cys,ENST00000601322,;SLC25A23,non_coding_transcript_exon_variant,,ENST00000601760,;SLC25A23,missense_variant,p.Ser441Cys,ENST00000264088,;SLC25A23,missense_variant,p.Ser63Cys,ENST00000598704,;SLC25A23,non_coding_transcript_exon_variant,,ENST00000597039,; A ENST00000301454 Transcript missense_variant 1287/3425 1180/1407 394/468 S/C Agt/Tgt 1 -1 SLC25A23 HGNC HGNC:19375 protein_coding YES CCDS32882.1 ENSP00000301454 Q9BV35 UPI0000049FAD NM_024103.2 deleterious(0) 9/10 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF196,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588,Prints_domain:PR00926 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 6444193 6444193 T A 1 0 0 0 0 1 0 0 0 14751 1580 55 4 4 SLC25A23 19 6444193 Missense_Mutation SNP T 11LU022_T 600235 6444193 52173423 869 1507 FBN3 0 . GRCh38 19 8096521 8096521 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.5462G>C p.Cys1821Ser p.C1821S ENST00000600128 44/64 111 90 21 156 156 0 strelka-varscan-mutect FBN3,missense_variant,p.Cys1821Ser,ENST00000600128,;FBN3,missense_variant,p.Cys1821Ser,ENST00000270509,NM_032447.3;FBN3,missense_variant,p.Cys1821Ser,ENST00000601739,NM_001321431.1;FBN3,missense_variant,p.Cys82Ser,ENST00000602121,; G ENST00000600128 Transcript missense_variant 5877/9362 5462/8430 1821/2809 C/S tGc/tCc 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F deleterious(0) 44/64 PROSITE_profiles:PS50026,hmmpanther:PTHR24039:SF0,hmmpanther:PTHR24039,PROSITE_patterns:PS00010,PIRSF_domain:PIRSF036312,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 8096521 8096521 C G 1 0 0 0 0 1 0 0 0 5567 710 25 4 4 FBN3 19 8096521 Missense_Mutation SNP C 11LU022_T 1652328 8096521 50521095 870 1508 MUC16 0 . GRCh38 19 8903520 8903520 + Missense_Mutation SNP G G T rs267605781 11LU022_T 11LU022_N G G c.38452C>A p.His12818Asn p.H12818N ENST00000397910 32/84 83 55 28 115 115 0 strelka-varscan-mutect MUC16,missense_variant,p.His12818Asn,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 38656/43816 38452/43524 12818/14507 H/N Cat/Aat rs267605781,COSM341173 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 32/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Superfamily_domains:0047452 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs267605781 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 8903520 8903520 G T 1 0 0 0 0 1 0 0 0 9972 1348 47 2 2 MUC16 19 8903520 Missense_Mutation SNP G 11LU022_T 806999 8903520 49714096 871 1509 OLFM2 0 . GRCh38 19 9854589 9854589 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.962C>A p.Ser321Tyr p.S321Y ENST00000264833 6/6 177 112 65 263 262 1 strelka-varscan-mutect OLFM2,missense_variant,p.Ser321Tyr,ENST00000264833,NM_058164.3;OLFM2,missense_variant,p.Ser243Tyr,ENST00000590841,NM_001304348.1;OLFM2,downstream_gene_variant,,ENST00000593091,NM_001304347.1;PIN1,downstream_gene_variant,,ENST00000247970,NM_006221.3;PIN1,downstream_gene_variant,,ENST00000588695,;PIN1,downstream_gene_variant,,ENST00000380889,;PIN1,downstream_gene_variant,,ENST00000590540,;OLFM2,3_prime_UTR_variant,,ENST00000592448,;PIN1,downstream_gene_variant,,ENST00000586025,;OLFM2,downstream_gene_variant,,ENST00000590410,;PIN1,downstream_gene_variant,,ENST00000591777,; T ENST00000264833 Transcript missense_variant 1148/2019 962/1365 321/454 S/Y tCc/tAc 1 -1 OLFM2 HGNC HGNC:17189 protein_coding YES CCDS12221.1 ENSP00000264833 O95897 UPI000013D57B NM_058164.3 deleterious(0) 6/6 PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF27,Pfam_domain:PF02191,SMART_domains:SM00284 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 9854589 9854589 G T 1 0 0 0 0 1 0 0 0 10928 1174 41 2 2 OLFM2 19 9854589 Missense_Mutation SNP G 11LU022_T 951069 9854589 48763027 872 1510 CALR 0 . GRCh38 19 12940618 12940618 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.780G>T p.Glu260Asp p.E260D ENST00000316448 6/9 436 313 123 674 674 0 strelka-varscan-mutect CALR,missense_variant,p.Glu260Asp,ENST00000316448,NM_004343.3;CALR,missense_variant,p.Glu45Asp,ENST00000586760,;CALR,missense_variant,p.Glu192Asp,ENST00000588454,;MIR6515,downstream_gene_variant,,ENST00000619843,;CTC-425F1.4,downstream_gene_variant,,ENST00000589120,;CALR,downstream_gene_variant,,ENST00000587486,;CALR,downstream_gene_variant,,ENST00000590325,;CALR,upstream_gene_variant,,ENST00000586803,;CALR,upstream_gene_variant,,ENST00000586967,; T ENST00000316448 Transcript missense_variant 853/1903 780/1254 260/417 E/D gaG/gaT 1 1 CALR HGNC HGNC:1455 protein_coding YES CCDS12288.1 ENSP00000320866 P27797 V9HW88 UPI000004CEC9 NM_004343.3 deleterious(0.03) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11073:SF16,hmmpanther:PTHR11073,PIRSF_domain:PIRSF002356,Pfam_domain:PF00262,Superfamily_domains:SSF63887,Prints_domain:PR00626 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 12940618 12940618 G T 1 0 0 0 0 1 0 0 0 2283 1020 36 2 2 CALR 19 12940618 Missense_Mutation SNP G 11LU022_T 3086029 12940618 45676998 873 1511 TMEM38A 0 . GRCh38 19 16680421 16680421 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.306G>T p.= p.L102L ENST00000187762 3/6 119 79 40 142 142 0 strelka-varscan-mutect TMEM38A,synonymous_variant,p.=,ENST00000187762,NM_024074.1;TMEM38A,synonymous_variant,p.=,ENST00000599479,;TMEM38A,non_coding_transcript_exon_variant,,ENST00000595452,; T ENST00000187762 Transcript synonymous_variant 397/2649 306/900 102/299 L ctG/ctT 1 1 TMEM38A HGNC HGNC:28462 protein_coding YES CCDS12349.1 ENSP00000187762 Q9H6F2 UPI000006E0B9 NM_024074.1 3/6 Pfam_domain:PF05197,hmmpanther:PTHR12454,hmmpanther:PTHR12454:SF3,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 16680421 16680421 G T 1 0 0 0 0 0 0 0 1 16636 1335 47 2 2 TMEM38A 19 16680421 Silent SNP G 11LU022_T 3739803 16680421 41937195 874 1512 SLC5A5 0 . GRCh38 19 17888422 17888422 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1618G>T p.Val540Leu p.V540L ENST00000222248 13/15 438 326 112 596 595 1 strelka-varscan-mutect SLC5A5,missense_variant,p.Val540Leu,ENST00000222248,NM_000453.2;SLC5A5,downstream_gene_variant,,ENST00000597109,; T ENST00000222248 Transcript missense_variant 1965/3576 1618/1932 540/643 V/L Gtg/Ttg 1 1 SLC5A5 HGNC HGNC:11040 protein_coding YES CCDS12368.1 ENSP00000222248 Q92911 UPI00001359F6 NM_000453.2 tolerated(0.24) 13/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 17888422 17888422 G T 1 0 0 0 0 1 0 0 0 14951 1377 48 2 2 SLC5A5 19 17888422 Missense_Mutation SNP G 11LU022_T 1208001 17888422 40729194 875 1513 CERS1 0 . GRCh38 19 18895987 18895987 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.86G>T p.Ser29Ile p.S29I ENST00000623882 1/8 24 18 6 29 29 0 strelka-varscan-mutect CERS1,missense_variant,p.Ser29Ile,ENST00000623882,NM_021267.4;CERS1,missense_variant,p.Ser29Ile,ENST00000429504,NM_198207.2;CERS1,5_prime_UTR_variant,,ENST00000623927,NM_001492.5;GDF1,5_prime_UTR_variant,,ENST00000247005,;CERS1,intron_variant,,ENST00000542296,NM_001290265.1;COPE,downstream_gene_variant,,ENST00000600932,;COPE,downstream_gene_variant,,ENST00000262812,NM_007263.3;COPE,downstream_gene_variant,,ENST00000349893,NM_199444.1;COPE,downstream_gene_variant,,ENST00000351079,NM_199442.1;COPE,downstream_gene_variant,,ENST00000598969,;COPE,downstream_gene_variant,,ENST00000595984,;COPE,downstream_gene_variant,,ENST00000600528,;COPE,downstream_gene_variant,,ENST00000593827,; A ENST00000623882 Transcript missense_variant 110/2517 86/1053 29/350 S/I aGc/aTc 1 -1 CERS1 HGNC HGNC:14253 protein_coding CCDS46020.1 ENSP00000485308 P27544 UPI000012E98A NM_021267.4 tolerated(0.16) 1/8 hmmpanther:PTHR12560,hmmpanther:PTHR12560:SF20 MODERATE SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 18895987 18895987 C A 1 0 0 0 0 1 0 0 0 2995 797 28 2 2 CERS1 19 18895987 Missense_Mutation SNP C 11LU022_T 1007565 18895987 39721629 876 1514 GATAD2A 0 . GRCh38 19 19465392 19465392 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.47A>T p.Glu16Val p.E16V ENST00000404158 4/14 166 110 56 249 249 0 strelka-varscan-mutect GATAD2A,missense_variant,p.Glu16Val,ENST00000404158,NM_001300946.1;GATAD2A,missense_variant,p.Glu16Val,ENST00000360315,NM_017660.3;GATAD2A,missense_variant,p.Glu16Val,ENST00000358713,;GATAD2A,missense_variant,p.Glu16Val,ENST00000457895,;GATAD2A,missense_variant,p.Glu16Val,ENST00000417582,;GATAD2A,missense_variant,p.Glu16Val,ENST00000494516,;GATAD2A,missense_variant,p.Glu16Val,ENST00000432704,;GATAD2A,missense_variant,p.Glu16Val,ENST00000444839,;GATAD2A,missense_variant,p.Glu16Val,ENST00000429242,;GATAD2A,missense_variant,p.Glu16Val,ENST00000418032,;GATAD2A,missense_variant,p.Glu16Val,ENST00000609040,; T ENST00000404158 Transcript missense_variant 465/5776 47/1905 16/634 E/V gAa/gTa 1 1 GATAD2A HGNC HGNC:29989 protein_coding YES CCDS77270.1 ENSP00000384899 Q86YP4 A0A024R7M6 UPI0000203849 NM_001300946.1 deleterious(0) 4/14 hmmpanther:PTHR13455,hmmpanther:PTHR13455:SF3 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 19465392 19465392 A T 1 0 0 0 0 1 0 0 0 6130 246 9 4 4 GATAD2A 19 19465392 Missense_Mutation SNP A 11LU022_T 569405 19465392 39152224 877 1515 CILP2 0 . GRCh38 19 19545935 19545935 + Silent SNP C C T novel 11LU022_T 11LU022_N C C c.3390C>T p.= p.R1130R ENST00000291495 8/8 36 23 13 78 78 0 strelka-varscan-mutect CILP2,synonymous_variant,p.=,ENST00000586018,;CILP2,synonymous_variant,p.=,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; T ENST00000291495 Transcript synonymous_variant 3475/4199 3390/3471 1130/1156 R cgC/cgT 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 19545935 19545935 C T 1 0 0 0 0 0 0 0 1 3192 697 25 3 3 CILP2 19 19545935 Silent SNP C 11LU022_T 80543 19545935 39071681 878 1516 ZNF208 0 . GRCh38 19 21972370 21972370 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.2664C>A p.= p.P888P ENST00000397126 4/4 154 123 31 260 260 0 strelka-varscan-mutect ZNF208,synonymous_variant,p.=,ENST00000397126,NM_007153.3;ZNF208,synonymous_variant,p.=,ENST00000609966,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,;AC003973.3,upstream_gene_variant,,ENST00000624863,; T ENST00000397126 Transcript synonymous_variant 2813/3992 2664/3843 888/1280 P ccC/ccA 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 3 1 PASS rs1226235737 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 21972370 21972370 G T 1 0 0 0 0 0 0 0 1 18343 987 35 2 2 ZNF208 19 21972370 Silent SNP G 11LU022_T 2426435 21972370 36645246 879 1517 ZNF98 0 . GRCh38 19 22391988 22391988 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1247G>T p.Ser416Ile p.S416I ENST00000357774 4/4 41 33 8 89 89 0 strelka-varscan-mutect ZNF98,missense_variant,p.Ser416Ile,ENST00000357774,NM_001098626.1;ZNF98,downstream_gene_variant,,ENST00000593657,; A ENST00000357774 Transcript missense_variant 1369/2338 1247/1719 416/572 S/I aGc/aTc 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 tolerated(0.1) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 207 3 0 0 0 0 0 -19.79093 1 1 1 1 0 A 3 1 3 22391988 22391988 C A 1 0 0 0 0 1 0 0 0 18796 797 28 2 2 ZNF98 19 22391988 Missense_Mutation SNP C 11LU022_T 419618 22391988 36225628 880 1518 ZNF536 0 . GRCh38 19 30548155 30548155 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2536C>A p.Pro846Thr p.P846T ENST00000355537 4/5 179 143 36 213 213 0 strelka-varscan-mutect ZNF536,missense_variant,p.Pro846Thr,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Pro846Thr,ENST00000585628,;ZNF536,upstream_gene_variant,,ENST00000592773,; A ENST00000355537 Transcript missense_variant 2683/4945 2536/3903 846/1300 P/T Cct/Act 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated(0.11) 4/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 30548155 30548155 C A 1 0 0 0 0 1 0 0 0 18547 623 22 2 2 ZNF536 19 30548155 Missense_Mutation SNP C 11LU022_T 8156167 30548155 28069461 881 1519 ANKRD27 0 . GRCh38 19 32649694 32649694 + Silent SNP G G A novel 11LU022_T 11LU022_N G G c.201C>T p.= p.T67T ENST00000306065 3/29 146 112 34 188 188 0 strelka-varscan-mutect ANKRD27,synonymous_variant,p.=,ENST00000306065,NM_032139.2;ANKRD27,synonymous_variant,p.=,ENST00000587352,;ANKRD27,synonymous_variant,p.=,ENST00000590519,;ANKRD27,synonymous_variant,p.=,ENST00000586693,;ANKRD27,5_prime_UTR_variant,,ENST00000586463,;ANKRD27,synonymous_variant,p.=,ENST00000588700,; A ENST00000306065 Transcript synonymous_variant 360/4450 201/3153 67/1050 T acC/acT 1 -1 ANKRD27 HGNC HGNC:25310 protein_coding YES CCDS32986.1 ENSP00000304292 Q96NW4 UPI000004FDE9 NM_032139.2 3/29 hmmpanther:PTHR24170,hmmpanther:PTHR24170:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 32649694 32649694 G A 1 0 0 0 0 0 0 0 1 758 987 35 3 3 ANKRD27 19 32649694 Silent SNP G 11LU022_T 2101539 32649694 25967922 882 1520 WTIP 0 . GRCh38 19 34493581 34493581 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.990G>T p.= p.V330V ENST00000590071 5/8 169 122 47 215 215 0 strelka-varscan-mutect WTIP,synonymous_variant,p.=,ENST00000590071,NM_001080436.1;WTIP,synonymous_variant,p.=,ENST00000585928,; T ENST00000590071 Transcript synonymous_variant 1327/13665 990/1293 330/430 V gtG/gtT 1 1 WTIP HGNC HGNC:20964 protein_coding YES CCDS59375.1 ENSP00000466953 A6NIX2 UPI00006C19C5 NM_001080436.1 5/8 PROSITE_profiles:PS50023,hmmpanther:PTHR24219,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 34493581 34493581 G T 1 0 0 0 0 0 0 0 1 17968 1335 47 2 2 WTIP 19 34493581 Silent SNP G 11LU022_T 1843887 34493581 24124035 883 1521 HPN 0 . GRCh38 19 35060417 35060417 + Silent SNP G G C rs35890010 11LU022_T 11LU022_N G G c.525G>C p.= p.P175P ENST00000262626 8/13 327 259 68 380 380 0 strelka-varscan-mutect HPN,synonymous_variant,p.=,ENST00000262626,NM_182983.2;HPN,synonymous_variant,p.=,ENST00000392226,NM_002151.2;HPN,intron_variant,,ENST00000597419,;HPN,downstream_gene_variant,,ENST00000600390,;HPN-AS1,intron_variant,,ENST00000392227,;HPN,downstream_gene_variant,,ENST00000600675,;HPN,non_coding_transcript_exon_variant,,ENST00000593305,;HPN,non_coding_transcript_exon_variant,,ENST00000599363,;HPN,non_coding_transcript_exon_variant,,ENST00000541345,;HPN,downstream_gene_variant,,ENST00000596662,; C ENST00000262626 Transcript synonymous_variant 1350/2363 525/1254 175/417 P ccG/ccC rs35890010 1 1 HPN HGNC HGNC:5155 protein_coding YES CCDS32993.1 ENSP00000262626 P05981 A0A140VJK9 UPI000003FE67 NM_182983.2 8/13 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF130,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS rs35890010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 35060417 35060417 G C 1 0 0 0 0 0 0 0 1 7231 1132 40 4 4 HPN 19 35060417 Silent SNP G 11LU022_T 566836 35060417 23557199 884 1522 FFAR1 0 . GRCh38 19 35351639 35351639 + Missense_Mutation SNP G G C rs867765877 11LU022_T 11LU022_N G G c.88G>C p.Ala30Pro p.A30P ENST00000246553 1/1 146 112 34 196 196 0 strelka-varscan-mutect FFAR1,missense_variant,p.Ala30Pro,ENST00000246553,NM_005303.2;CD22,downstream_gene_variant,,ENST00000085219,NM_001771.3;CD22,downstream_gene_variant,,ENST00000536635,NM_001185099.1;CD22,downstream_gene_variant,,ENST00000341773,NM_001185101.1;CD22,downstream_gene_variant,,ENST00000544992,NM_001185100.1;CD22,downstream_gene_variant,,ENST00000419549,NM_001278417.1;CD22,downstream_gene_variant,,ENST00000594250,;CD22,downstream_gene_variant,,ENST00000601769,; C ENST00000246553 Transcript missense_variant 88/2311 88/903 30/300 A/P Gcg/Ccg rs867765877 1 1 FFAR1 HGNC HGNC:4498 protein_coding YES CCDS12458.1 ENSP00000246553 O14842 UPI000005045B NM_005303.2 tolerated(0.2) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF33,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs867765877 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 35351639 35351639 G C 1 0 0 0 0 1 0 0 0 5690 1087 38 4 4 FFAR1 19 35351639 Missense_Mutation SNP G 11LU022_T 291222 35351639 23265977 885 1523 ATP4A 0 . GRCh38 19 35560549 35560549 + Frame_Shift_Del DEL G G - novel 11LU022_T 11LU022_N G G c.601delC p.Leu201TrpfsTer4 p.L201Wfs*4 ENST00000262623 6/22 168 146 22 260 260 0 sindel-varindel-pindel ATP4A,frameshift_variant,p.Leu201TrpfsTer4,ENST00000262623,NM_000704.2;ATP4A,upstream_gene_variant,,ENST00000592131,;ATP4A,upstream_gene_variant,,ENST00000592767,;ATP4A,downstream_gene_variant,,ENST00000590916,; - ENST00000262623 Transcript frameshift_variant 630/3709 601/3108 201/1035 L/X Ctg/tg 1 -1 ATP4A HGNC HGNC:819 protein_coding YES CCDS12467.1 ENSP00000262623 P20648 UPI000016A49B NM_000704.2 6/22 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF251,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01106,Gene3D:2.70.150.10,Superfamily_domains:0049471 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 35560549 35560549 G - 1 0 1 0 1 0 0 0 0 1298 991 35 0 0 ATP4A 19 35560549 Frame_Shift_Del DEL G 11LU022_T 208910 35560549 23057067 886 1524 PRODH2 0 . GRCh38 19 35800073 35800073 + Silent SNP G G T rs752268187 11LU022_T 11LU022_N G G c.1576C>A p.= p.R526R ENST00000301175 11/11 109 86 23 121 121 0 strelka-varscan-mutect PRODH2,synonymous_variant,p.=,ENST00000301175,NM_021232.1;PRODH2,3_prime_UTR_variant,,ENST00000588266,;PRODH2,downstream_gene_variant,,ENST00000589835,;LINC01529,upstream_gene_variant,,ENST00000433059,;LINC01529,upstream_gene_variant,,ENST00000637365,;LINC01529,upstream_gene_variant,,ENST00000564335,;LINC01529,upstream_gene_variant,,ENST00000637448,;LINC01529,upstream_gene_variant,,ENST00000567313,;PRODH2,non_coding_transcript_exon_variant,,ENST00000587695,;PRODH2,non_coding_transcript_exon_variant,,ENST00000587808,;LINC01529,upstream_gene_variant,,ENST00000636474,; T ENST00000301175 Transcript synonymous_variant 1594/1677 1576/1611 526/536 R Cgg/Agg rs752268187 1 -1 PRODH2 HGNC HGNC:17325 protein_coding YES CCDS12478.1 ENSP00000301175 Q9UF12 UPI000006EE59 NM_021232.1 11/11 hmmpanther:PTHR13914,hmmpanther:PTHR13914:SF5,Gene3D:3.20.20.220,Superfamily_domains:SSF51730 LOW 1 SNV 1 1 PASS rs752268187 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 3 35800073 35800073 G T 1 0 0 0 0 0 0 0 1 12682 1086 38 1 1 PRODH2 19 35800073 Silent SNP G 11LU022_T 239524 35800073 22817543 887 1525 APLP1 0 . GRCh38 19 35872509 35872509 + Missense_Mutation SNP G G C rs775640224 11LU022_T 11LU022_N G G c.877G>C p.Gly293Arg p.G293R ENST00000221891 7/17 114 104 10 135 135 0 strelka-varscan-mutect APLP1,missense_variant,p.Gly293Arg,ENST00000221891,NM_005166.3,NM_001024807.1;APLP1,missense_variant,p.Gly254Arg,ENST00000537454,;APLP1,missense_variant,p.Gly287Arg,ENST00000586861,;APLP1,missense_variant,p.Gly196Arg,ENST00000592316,;APLP1,upstream_gene_variant,,ENST00000587274,;APLP1,upstream_gene_variant,,ENST00000588808,;APLP1,downstream_gene_variant,,ENST00000589743,;NPHS1,upstream_gene_variant,,ENST00000591817,;APLP1,upstream_gene_variant,,ENST00000589298,;APLP1,3_prime_UTR_variant,,ENST00000590561,; C ENST00000221891 Transcript missense_variant 1069/2495 877/1956 293/651 G/R Ggt/Cgt rs775640224,COSM3783228 1 1 APLP1 HGNC HGNC:597 protein_coding YES CCDS32997.1 ENSP00000221891 P51693 UPI000020215E NM_005166.3,NM_001024807.1 tolerated(0.09) 7/17 hmmpanther:PTHR23103,Pfam_domain:PF12925,Superfamily_domains:0043391 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775640224 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 35872509 35872509 G C 1 0 0 0 0 1 0 0 0 900 1116 39 4 4 APLP1 19 35872509 Missense_Mutation SNP G 11LU022_T 72436 35872509 22745107 888 1526 SYNE4 0 . GRCh38 19 36006865 36006865 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.503G>C p.Ser168Thr p.S168T ENST00000324444 4/8 166 148 18 203 203 0 strelka-varscan-mutect SYNE4,missense_variant,p.Ser168Thr,ENST00000324444,NM_001039876.1;SYNE4,missense_variant,p.Ser168Thr,ENST00000490730,;SYNE4,intron_variant,,ENST00000340477,NM_001297735.1;SYNE4,intron_variant,,ENST00000503121,;SYNE4,intron_variant,,ENST00000397428,;ALKBH6,downstream_gene_variant,,ENST00000486389,;ALKBH6,downstream_gene_variant,,ENST00000378875,NM_032878.3,NM_198867.1;ALKBH6,downstream_gene_variant,,ENST00000485128,;ALKBH6,downstream_gene_variant,,ENST00000252984,NM_001297701.1;ALKBH6,downstream_gene_variant,,ENST00000495116,;SYNE4,non_coding_transcript_exon_variant,,ENST00000465425,;SYNE4,intron_variant,,ENST00000505054,;ALKBH6,downstream_gene_variant,,ENST00000471323,;AC002116.8,downstream_gene_variant,,ENST00000473572,;ALKBH6,downstream_gene_variant,,ENST00000392183,;ALKBH6,downstream_gene_variant,,ENST00000490986,;ALKBH6,downstream_gene_variant,,ENST00000490483,;ALKBH6,downstream_gene_variant,,ENST00000468004,;ALKBH6,downstream_gene_variant,,ENST00000461668,;ALKBH6,downstream_gene_variant,,ENST00000497999,;ALKBH6,downstream_gene_variant,,ENST00000462793,;ALKBH6,downstream_gene_variant,,ENST00000475223,;ALKBH6,downstream_gene_variant,,ENST00000466196,;ALKBH6,downstream_gene_variant,,ENST00000481257,;ALKBH6,downstream_gene_variant,,ENST00000592353,;ALKBH6,downstream_gene_variant,,ENST00000590666,; G ENST00000324444 Transcript missense_variant 615/1354 503/1215 168/404 S/T aGt/aCt 1 -1 SYNE4 HGNC HGNC:26703 protein_coding YES CCDS42553.1 ENSP00000316130 Q8N205 UPI00006CA35A NM_001039876.1 tolerated(0.05) 4/8 hmmpanther:PTHR21640,hmmpanther:PTHR21640:SF1 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 36006865 36006865 C G 1 0 0 0 0 1 0 0 0 15840 565 20 4 4 SYNE4 19 36006865 Missense_Mutation SNP C 11LU022_T 134356 36006865 22610751 889 1527 ZNF382 0 . GRCh38 19 36627539 36627539 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.1642G>A p.Gly548Arg p.G548R ENST00000292928 5/5 73 66 7 96 96 0 strelka-varscan-mutect ZNF382,missense_variant,p.Gly548Arg,ENST00000292928,NM_032825.4;ZNF382,missense_variant,p.Gly547Arg,ENST00000435416,;ZNF382,missense_variant,p.Gly547Arg,ENST00000439428,NM_001256838.1;ZNF382,missense_variant,p.Gly499Arg,ENST00000423582,;ZNF382,downstream_gene_variant,,ENST00000590785,;ZNF382,upstream_gene_variant,,ENST00000585467,; A ENST00000292928 Transcript missense_variant 1755/8329 1642/1653 548/550 G/R Gga/Aga 1 1 ZNF382 HGNC HGNC:17409 protein_coding YES CCDS33004.1 ENSP00000292928 Q96SR6 UPI000013E0E2 NM_032825.4 tolerated_low_confidence(0.8) 5/5 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF22 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.47056 1 1 1 1 0 A 3 1 3 36627539 36627539 G A 1 0 0 0 0 1 0 0 0 18445 1233 43 3 3 ZNF382 19 36627539 Missense_Mutation SNP G 11LU022_T 620674 36627539 21990077 890 1528 DLL3 0 . GRCh38 19 39507928 39507928 + Missense_Mutation SNP T T A 11LU022_T 11LU022_N T T c.1772T>A p.Leu591His p.L591H ENST00000205143 8/8 269 194 75 350 350 0 strelka-varscan-mutect DLL3,missense_variant,p.Leu591His,ENST00000205143,NM_016941.3;DLL3,intron_variant,,ENST00000356433,NM_203486.2;DLL3,downstream_gene_variant,,ENST00000596614,;DLL3,downstream_gene_variant,,ENST00000600437,; A ENST00000205143 Transcript missense_variant 1779/2332 1772/1857 591/618 L/H cTt/cAt COSM5056639 1 1 DLL3 HGNC HGNC:2909 protein_coding YES CCDS12538.1 ENSP00000205143 Q9NYJ7 UPI0000051041 NM_016941.3 tolerated(0.24) 8/8 1 MODERATE 1 SNV 1 1 1 PASS rs1164056815 . 0 204 0 0 6 0 0 0 -20 0.7620864 1 1 1 0 A 3 1 3 39507928 39507928 T A 1 0 0 0 0 1 0 0 0 4374 1609 56 4 4 DLL3 19 39507928 Missense_Mutation SNP T 11LU022_T 2880389 39507928 19109688 891 1529 ZNF780A 0 . GRCh38 19 40081883 40081883 + Silent SNP C C A rs150224403 11LU022_T 11LU022_N C C c.171G>T p.= p.T57T ENST00000455521 5/6 190 177 13 206 206 0 strelka-varscan-mutect ZNF780A,synonymous_variant,p.=,ENST00000450241,;ZNF780A,synonymous_variant,p.=,ENST00000340963,NM_001010880.2,NM_001142578.1;ZNF780A,synonymous_variant,p.=,ENST00000455521,NM_001142577.1;ZNF780A,synonymous_variant,p.=,ENST00000595687,;ZNF780A,synonymous_variant,p.=,ENST00000414720,NM_001142579.1;ZNF780A,synonymous_variant,p.=,ENST00000594395,;ZNF780A,synonymous_variant,p.=,ENST00000595773,;ZNF780A,synonymous_variant,p.=,ENST00000599972,;AC005614.5,non_coding_transcript_exon_variant,,ENST00000595508,;ZNF780A,synonymous_variant,p.=,ENST00000599368,;ZNF780A,synonymous_variant,p.=,ENST00000601688,;ZNF780A,synonymous_variant,p.=,ENST00000601715,; A ENST00000455521 Transcript synonymous_variant 319/3600 171/1929 57/642 T acG/acT rs150224403 1 -1 ZNF780A HGNC HGNC:27603 protein_coding YES CCDS46079.1 ENSP00000400997 O75290 UPI0001881B53 NM_001142577.1 5/6 Superfamily_domains:0044637,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF313,SMART_domains:SM00349 LOW 1 SNV 5 1 PASS rs150224403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 40081883 40081883 C A 1 0 0 0 0 0 0 0 1 18735 523 19 1 1 ZNF780A 19 40081883 Silent SNP C 11LU022_T 573955 40081883 18535733 892 1530 PSG3 0 . GRCh38 19 42729238 42729238 + Silent SNP T T C rs146855604 11LU022_T 11LU022_N T T c.1128A>G p.= p.G376G ENST00000327495 5/7 334 290 44 369 369 0 strelka-varscan-mutect PSG3,synonymous_variant,p.=,ENST00000327495,NM_021016.3;PSG3,synonymous_variant,p.=,ENST00000595140,;PSG3,synonymous_variant,p.=,ENST00000614582,;PSG3,downstream_gene_variant,,ENST00000490592,;PSG3,intron_variant,,ENST00000594378,;PSG3,downstream_gene_variant,,ENST00000597009,; C ENST00000327495 Transcript synonymous_variant 1313/1961 1128/1287 376/428 G ggA/ggG rs146855604 1 -1 PSG3 HGNC HGNC:9520 protein_coding YES CCDS12611.1 ENSP00000332215 Q16557 UPI0000073DC1 NM_021016.3 5/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs146855604 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 42729238 42729238 T C 1 0 0 0 0 0 0 0 1 12807 1654 58 5 5 PSG3 19 42729238 Silent SNP T 11LU022_T 2647355 42729238 15888378 893 1531 PSG11 0 . GRCh38 19 43024794 43024794 + Missense_Mutation SNP G G C 11LU022_T 11LU022_N G G c.327C>G p.Ile109Met p.I109M ENST00000320078 2/6 114 85 29 163 163 0 strelka-varscan-mutect PSG11,missense_variant,p.Ile109Met,ENST00000320078,NM_002785.2;PSG11,missense_variant,p.Ile109Met,ENST00000598133,;PSG11,intron_variant,,ENST00000403486,NM_203287.1,NM_001113410.1;PSG11,intron_variant,,ENST00000306322,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG11,missense_variant,p.Ile73Met,ENST00000593983,;PSG11,non_coding_transcript_exon_variant,,ENST00000595138,;PSG11,non_coding_transcript_exon_variant,,ENST00000594655,;PSG11,non_coding_transcript_exon_variant,,ENST00000597093,;PSG11,non_coding_transcript_exon_variant,,ENST00000599245,;PSG11,intron_variant,,ENST00000488205,; C ENST00000320078 Transcript missense_variant 467/1575 327/1008 109/335 I/M atC/atG COSM3288540 1 -1 PSG11 HGNC HGNC:9516 protein_coding YES CCDS12614.2 ENSP00000319140 Q9UQ72 UPI000004EE8C NM_002785.2 deleterious(0.05) 2/6 hmmpanther:PTHR10489:SF615,hmmpanther:PTHR10489,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 2 1 1 PASS rs1341871273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 43024794 43024794 G C 1 0 0 0 0 1 0 0 0 12805 1164 41 4 4 PSG11 19 43024794 Missense_Mutation SNP G 11LU022_T 295556 43024794 15592822 894 1532 PSG5 0 . GRCh38 19 43184977 43184977 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.235A>G p.Ile79Val p.I79V ENST00000366175 2/6 180 135 45 231 230 1 strelka-varscan-mutect PSG5,missense_variant,p.Ile79Val,ENST00000404580,;PSG5,missense_variant,p.Ile79Val,ENST00000599812,;PSG5,missense_variant,p.Ile79Val,ENST00000366175,;PSG5,missense_variant,p.Ile79Val,ENST00000342951,NM_001130014.1,NM_002781.3;PSG5,missense_variant,p.Ile79Val,ENST00000407356,;PSG5,missense_variant,p.Ile79Val,ENST00000407568,;PSG5,non_coding_transcript_exon_variant,,ENST00000401992,;PSG5,upstream_gene_variant,,ENST00000489220,;PSG5,non_coding_transcript_exon_variant,,ENST00000600817,; C ENST00000366175 Transcript missense_variant 366/1766 235/1008 79/335 I/V Att/Gtt 1 -1 PSG5 HGNC HGNC:9522 protein_coding YES CCDS12617.1 ENSP00000382334 Q15238 A0A024R0S1 UPI000013C7B9 deleterious(0.03) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 43184977 43184977 T C 1 0 0 0 0 1 0 0 0 12809 1464 51 5 5 PSG5 19 43184977 Missense_Mutation SNP T 11LU022_T 160183 43184977 15432639 895 1533 PHLDB3 0 . GRCh38 19 43501751 43501751 + Missense_Mutation SNP G G A rs148749895 11LU022_T 11LU022_N G G c.517C>T p.Arg173Cys p.R173C ENST00000292140 4/16 268 207 61 306 306 0 strelka-varscan-mutect PHLDB3,missense_variant,p.Arg173Cys,ENST00000292140,NM_198850.3;PHLDB3,missense_variant,p.Arg173Cys,ENST00000599242,;ETHE1,downstream_gene_variant,,ENST00000292147,NM_014297.3;PHLDB3,upstream_gene_variant,,ENST00000600660,;PHLDB3,downstream_gene_variant,,ENST00000594808,;PHLDB3,downstream_gene_variant,,ENST00000601646,;PHLDB3,non_coding_transcript_exon_variant,,ENST00000596902,; A ENST00000292140 Transcript missense_variant 878/2591 517/1923 173/640 R/C Cgc/Tgc rs148749895,COSM3692835,COSM3692836 1 -1 PHLDB3 HGNC HGNC:30499 protein_coding YES CCDS12621.2 ENSP00000292140 Q6NSJ2 UPI00015C725F NM_198850.3 tolerated(0.06) 4/16 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12156:SF22,hmmpanther:PTHR12156 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs148749895 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 43501751 43501751 G A 1 0 0 0 0 1 0 0 0 11941 1116 39 1 1 PHLDB3 19 43501751 Missense_Mutation SNP G 11LU022_T 316774 43501751 15115865 896 1534 ZNF226 0 . GRCh38 19 44176619 44176619 + Missense_Mutation SNP G G T rs548204072 11LU022_T 11LU022_N G G c.1357G>T p.Gly453Cys p.G453C ENST00000590089 7/7 135 119 16 160 160 0 strelka-varscan-mutect ZNF226,missense_variant,p.Gly453Cys,ENST00000590089,NM_016444.2;ZNF226,missense_variant,p.Gly453Cys,ENST00000454662,NM_001319090.1,NM_001319089.1,NM_001319088.1,NM_001032372.1;ZNF226,missense_variant,p.Gly453Cys,ENST00000337433,NM_001032373.1;ZNF226,3_prime_UTR_variant,,ENST00000588883,;ZNF226,downstream_gene_variant,,ENST00000300823,NM_015919.3;ZNF226,downstream_gene_variant,,ENST00000413984,NM_001032374.1;ZNF226,downstream_gene_variant,,ENST00000589160,;ZNF226,downstream_gene_variant,,ENST00000588795,;ZNF226,downstream_gene_variant,,ENST00000590524,;ZNF226,downstream_gene_variant,,ENST00000585678,;ZNF226,downstream_gene_variant,,ENST00000586914,;ZNF226,downstream_gene_variant,,ENST00000588127,;ZNF226,downstream_gene_variant,,ENST00000586203,;ZNF226,downstream_gene_variant,,ENST00000590578,;ZNF226,downstream_gene_variant,,ENST00000590467,;ZNF226,downstream_gene_variant,,ENST00000586286,;ZNF226,downstream_gene_variant,,ENST00000585560,;ZNF226,downstream_gene_variant,,ENST00000588742,NM_001146220.2;ZNF226,downstream_gene_variant,,ENST00000590759,; T ENST00000590089 Transcript missense_variant 1724/2788 1357/2412 453/803 G/C Ggt/Tgt rs548204072 1 1 ZNF226 HGNC HGNC:13019 protein_coding YES CCDS46102.1 ENSP00000465121 Q9NYT6 A0A024R0P4 UPI000013C32A NM_016444.2 deleterious(0) 7/7 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF177,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs548204072 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 44176619 44176619 G T 1 0 0 0 0 1 0 0 0 18357 1348 47 2 2 ZNF226 19 44176619 Missense_Mutation SNP G 11LU022_T 674868 44176619 14440997 897 1535 APOE 0 . GRCh38 19 44909068 44909068 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.772C>A p.Arg258Ser p.R258S ENST00000252486 4/4 396 309 87 452 452 0 strelka-varscan-mutect APOE,missense_variant,p.Arg258Ser,ENST00000252486,NM_000041.3,NM_001302691.1,NM_001302689.1,NM_001302690.1;APOE,downstream_gene_variant,,ENST00000425718,;APOE,downstream_gene_variant,,ENST00000434152,NM_001302688.1;APOE,downstream_gene_variant,,ENST00000446996,;CTB-129P6.7,upstream_gene_variant,,ENST00000623895,;APOE,downstream_gene_variant,,ENST00000485628,; A ENST00000252486 Transcript missense_variant 883/1208 772/954 258/317 R/S Cgc/Agc 1 1 APOE HGNC HGNC:613 protein_coding YES CCDS12647.1 ENSP00000252486 P02649 A0A0S2Z3D5 UPI0000044948 NM_000041.3,NM_001302691.1,NM_001302689.1,NM_001302690.1 deleterious(0) 4/4 Superfamily_domains:0053393,Gene3D:1.20.120.20,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01442,hmmpanther:PTHR18976,hmmpanther:PTHR18976:SF2 MODERATE 1 SNV 1 1 PASS rs1003367097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 44909068 44909068 C A 1 0 0 0 0 1 0 0 0 924 768 27 1 1 APOE 19 44909068 Missense_Mutation SNP C 11LU022_T 732449 44909068 13708548 898 1536 CKM 0 . GRCh38 19 45311897 45311897 + Missense_Mutation SNP A A T rs746579943 11LU022_T 11LU022_N A A c.505T>A p.Phe169Ile p.F169I ENST00000221476 5/8 354 315 39 432 432 0 strelka-varscan-mutect CKM,missense_variant,p.Phe169Ile,ENST00000221476,NM_001824.4; T ENST00000221476 Transcript missense_variant 680/1657 505/1146 169/381 F/I Ttc/Atc rs746579943 1 -1 CKM HGNC HGNC:1994 protein_coding YES CCDS12659.1 ENSP00000221476 P06732 UPI000012DCC3 NM_001824.4 deleterious(0) 5/8 PROSITE_profiles:PS51510,hmmpanther:PTHR11547:SF31,hmmpanther:PTHR11547,Gene3D:3.30.590.10,Pfam_domain:PF00217,Superfamily_domains:SSF55931 MODERATE 1 SNV 1 1 PASS rs746579943 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 45311897 45311897 A T 1 0 0 0 0 1 0 0 0 3211 43 2 4 4 CKM 19 45311897 Missense_Mutation SNP A 11LU022_T 402829 45311897 13305719 899 1537 NANOS2 0 . GRCh38 19 45914399 45914399 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.295C>G p.Pro99Ala p.P99A ENST00000341294 1/1 213 190 23 266 266 0 strelka-varscan-mutect NANOS2,missense_variant,p.Pro99Ala,ENST00000341294,NM_001029861.2; C ENST00000341294 Transcript missense_variant 472/1657 295/417 99/138 P/A Ccc/Gcc 1 -1 NANOS2 HGNC HGNC:23292 protein_coding YES CCDS33056.1 ENSP00000341021 P60321 UPI00001984F7 NM_001029861.2 deleterious(0) 1/1 PROSITE_profiles:PS51522,hmmpanther:PTHR12887,hmmpanther:PTHR12887:SF7,Pfam_domain:PF05741 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 45914399 45914399 G C 1 0 0 0 0 1 0 0 0 10161 1174 41 4 4 NANOS2 19 45914399 Missense_Mutation SNP G 11LU022_T 602502 45914399 12703217 900 1538 SULT2B1 0 . GRCh38 19 48587237 48587237 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.223T>A p.Trp75Arg p.W75R ENST00000201586 3/7 72 63 9 96 96 0 strelka-varscan-mutect SULT2B1,missense_variant,p.Trp60Arg,ENST00000323090,NM_004605.2;SULT2B1,missense_variant,p.Trp75Arg,ENST00000201586,NM_177973.1;SULT2B1,upstream_gene_variant,,ENST00000594274,; A ENST00000201586 Transcript missense_variant 401/1295 223/1098 75/365 W/R Tgg/Agg 1 1 SULT2B1 HGNC HGNC:11459 protein_coding YES CCDS12723.1 ENSP00000201586 O00204 UPI0000073F98 NM_177973.1 deleterious(0) 3/7 hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF9,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 48587237 48587237 T A 1 0 0 0 0 1 0 0 0 15768 1580 55 4 4 SULT2B1 19 48587237 Missense_Mutation SNP T 11LU022_T 2672838 48587237 10030379 901 1539 SLC6A16 0 . GRCh38 19 49310469 49310469 + Missense_Mutation SNP C C A rs765324085 11LU022_T 11LU022_N C C c.457G>T p.Gly153Trp p.G153W ENST00000335875 3/12 198 133 65 230 230 0 strelka-varscan-mutect SLC6A16,missense_variant,p.Gly153Trp,ENST00000454748,;SLC6A16,missense_variant,p.Gly153Trp,ENST00000335875,NM_014037.2;SLC6A16,intron_variant,,ENST00000598828,;SLC6A16,upstream_gene_variant,,ENST00000597969,;SLC6A16,upstream_gene_variant,,ENST00000594180,;SLC6A16,upstream_gene_variant,,ENST00000594917,;MIR4324,upstream_gene_variant,,ENST00000584846,;SLC6A16,intron_variant,,ENST00000598221,; A ENST00000335875 Transcript missense_variant 699/2938 457/2211 153/736 G/W Ggg/Tgg rs765324085,COSM5471079 1 -1 SLC6A16 HGNC HGNC:13622 protein_coding YES CCDS42590.1 ENSP00000338627 Q9GZN6 UPI00001305CE NM_014037.2 deleterious(0) 3/12 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF113,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs765324085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 49310469 49310469 C A 1 0 0 0 0 1 0 0 0 14962 652 23 1 1 SLC6A16 19 49310469 Missense_Mutation SNP C 11LU022_T 723232 49310469 9307147 902 1540 BCL2L12 0 . GRCh38 19 49670248 49670248 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.714G>T p.= p.L238L ENST00000616144 6/7 603 415 188 707 707 0 strelka-varscan-mutect BCL2L12,synonymous_variant,p.=,ENST00000616144,NM_138639.1;BCL2L12,synonymous_variant,p.=,ENST00000246785,;BCL2L12,synonymous_variant,p.=,ENST00000441864,NM_001040668.1;BCL2L12,synonymous_variant,p.=,ENST00000246784,;BCL2L12,intron_variant,,ENST00000619007,NM_001282520.1,NM_001282516.1,NM_001282519.1;BCL2L12,intron_variant,,ENST00000614495,NM_001282521.1;BCL2L12,intron_variant,,ENST00000611631,;BCL2L12,intron_variant,,ENST00000600947,;BCL2L12,intron_variant,,ENST00000594157,NM_001282517.1;BCL2L12,intron_variant,,ENST00000598306,;IRF3,upstream_gene_variant,,ENST00000597198,;IRF3,upstream_gene_variant,,ENST00000377139,NM_001571.5;IRF3,upstream_gene_variant,,ENST00000601291,NM_001197122.1;IRF3,upstream_gene_variant,,ENST00000593922,NM_001197123.1;IRF3,upstream_gene_variant,,ENST00000598808,;IRF3,upstream_gene_variant,,ENST00000377135,NM_001197125.1;IRF3,upstream_gene_variant,,ENST00000598108,;IRF3,upstream_gene_variant,,ENST00000599144,NM_001197126.1;IRF3,upstream_gene_variant,,ENST00000599223,NM_001197124.1;IRF3,upstream_gene_variant,,ENST00000596756,;IRF3,upstream_gene_variant,,ENST00000593818,;IRF3,upstream_gene_variant,,ENST00000600022,NM_001197127.1;IRF3,upstream_gene_variant,,ENST00000596822,;IRF3,upstream_gene_variant,,ENST00000601809,;IRF3,upstream_gene_variant,,ENST00000595034,;IRF3,upstream_gene_variant,,ENST00000596765,NM_001197128.1;IRF3,upstream_gene_variant,,ENST00000600453,;IRF3,upstream_gene_variant,,ENST00000601373,;IRF3,upstream_gene_variant,,ENST00000593337,;BCL2L12,upstream_gene_variant,,ENST00000594793,;IRF3,upstream_gene_variant,,ENST00000597180,;BCL2L12,3_prime_UTR_variant,,ENST00000598979,;IRF3,upstream_gene_variant,,ENST00000597636,;IRF3,upstream_gene_variant,,ENST00000594387,;BCL2L12,downstream_gene_variant,,ENST00000601168,; T ENST00000616144 Transcript synonymous_variant 1396/1854 714/1005 238/334 L ctG/ctT 1 1 BCL2L12 HGNC HGNC:13787 protein_coding YES CCDS12776.1 ENSP00000482218 Q9HB09 UPI00001267BC NM_138639.1 6/7 hmmpanther:PTHR14965 LOW 1 SNV 1 1 PASS rs1457903134 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 49670248 49670248 G T 1 0 0 0 0 0 0 0 1 1517 1335 47 2 2 BCL2L12 19 49670248 Silent SNP G 11LU022_T 359779 49670248 8947368 903 1541 MYBPC2 0 . GRCh38 19 50435187 50435187 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.46G>T p.Asp16Tyr p.D16Y ENST00000357701 2/28 218 192 26 259 259 0 strelka-varscan-mutect MYBPC2,missense_variant,p.Asp16Tyr,ENST00000357701,NM_004533.3;SPIB,downstream_gene_variant,,ENST00000595883,NM_001244000.1,NM_003121.4;SPIB,downstream_gene_variant,,ENST00000439922,NM_001243998.1; T ENST00000357701 Transcript missense_variant 97/3593 46/3426 16/1141 D/Y Gat/Tat 1 1 MYBPC2 HGNC HGNC:7550 protein_coding YES CCDS46152.1 ENSP00000350332 Q14324 A0A140VJQ0 UPI000013C628 NM_004533.3 deleterious(0.01) 2/28 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 50435187 50435187 G T 1 0 0 0 0 1 0 0 0 10012 942 33 2 2 MYBPC2 19 50435187 Missense_Mutation SNP G 11LU022_T 764939 50435187 8182429 904 1542 KLK2 0 . GRCh38 19 50874817 50874817 + Missense_Mutation SNP C C A rs758680373 11LU022_T 11LU022_N C C c.143C>A p.Ala48Glu p.A48E ENST00000325321 2/5 115 106 9 123 122 1 strelka-varscan-mutect KLK2,missense_variant,p.Ala48Glu,ENST00000325321,NM_005551.4;KLK2,missense_variant,p.Ala48Glu,ENST00000358049,NM_001002231.2;KLK2,missense_variant,p.Ala48Glu,ENST00000600690,;KLK2,5_prime_UTR_variant,,ENST00000593493,;KLK2,intron_variant,,ENST00000391810,NM_001256080.1;KLK2,upstream_gene_variant,,ENST00000599568,;KLK2,non_coding_transcript_exon_variant,,ENST00000597509,;KLK2,intron_variant,,ENST00000596950,;KLK2,missense_variant,p.Ala48Glu,ENST00000597439,;KLK2,missense_variant,p.Ala48Glu,ENST00000594174,;KLK2,non_coding_transcript_exon_variant,,ENST00000600755,;KLK2,non_coding_transcript_exon_variant,,ENST00000595375,;KLK2,intron_variant,,ENST00000600866,;KLK2,intron_variant,,ENST00000599280,;KLK2,intron_variant,,ENST00000599121,;KLK2,intron_variant,,ENST00000595316,;KLK2,intron_variant,,ENST00000597727,;KLK2,upstream_gene_variant,,ENST00000595173,;KLK2,downstream_gene_variant,,ENST00000601743,;KLK2,upstream_gene_variant,,ENST00000601114,;KLK2,upstream_gene_variant,,ENST00000597461,;KLK2,upstream_gene_variant,,ENST00000595050,;KLK2,upstream_gene_variant,,ENST00000597911,; A ENST00000325321 Transcript missense_variant 368/3019 143/786 48/261 A/E gCa/gAa rs758680373 1 1 KLK2 HGNC HGNC:6363 protein_coding YES CCDS12808.1 ENSP00000313581 P20151 A0A024R4J4 UPI000004CA0C NM_005551.4 tolerated(0.1) 2/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF139,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs758680373 . 0 206 0 3 0 0 0 0 -13.28792 0.9999745 1 1 1 0 A 3 1 3 50874817 50874817 C A 1 0 0 0 0 1 0 0 0 8273 710 25 2 2 KLK2 19 50874817 Missense_Mutation SNP C 11LU022_T 439630 50874817 7742799 905 1543 KLK8 0 . GRCh38 19 50996124 50996124 + Missense_Mutation SNP C C A 11LU022_T 11LU022_N C C c.853G>T p.Gly285Cys p.G285C ENST00000391806 6/6 202 155 47 223 223 0 strelka-varscan-mutect KLK8,missense_variant,p.Gly240Cys,ENST00000600767,NM_007196.3;KLK8,missense_variant,p.Gly285Cys,ENST00000391806,NM_144505.2;KLK8,missense_variant,p.Gly119Cys,ENST00000291726,NM_001281431.1;KLK8,missense_variant,p.Gly99Cys,ENST00000347619,NM_144506.2;KLK8,3_prime_UTR_variant,,ENST00000320838,NM_144507.2;KLK8,3_prime_UTR_variant,,ENST00000593490,;KLK8,downstream_gene_variant,,ENST00000595238,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK8,non_coding_transcript_exon_variant,,ENST00000598195,;CTC-518B2.8,3_prime_UTR_variant,,ENST00000599166,;KLK8,non_coding_transcript_exon_variant,,ENST00000594914,;CTC-518B2.8,downstream_gene_variant,,ENST00000250366,;KLK8,downstream_gene_variant,,ENST00000599710,;KLK8,downstream_gene_variant,,ENST00000594669,; A ENST00000391806 Transcript missense_variant 934/1051 853/918 285/305 G/C Ggc/Tgc COSM3938231 1 -1 KLK8 HGNC HGNC:6369 protein_coding YES CCDS42600.1 ENSP00000375682 O60259 UPI000002ACDB NM_144505.2 deleterious(0) 6/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF123,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 1 MODERATE 1 SNV 1 1 1 PASS rs1402731016 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 50996124 50996124 C A 1 0 0 0 0 1 0 0 0 8279 594 21 2 2 KLK8 19 50996124 Missense_Mutation SNP C 11LU022_T 121307 50996124 7621492 906 1544 C19orf84 0 . GRCh38 19 51389194 51389194 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.351G>T p.Trp117Cys p.W117C ENST00000574814 2/2 118 107 11 156 156 0 strelka-mutect C19orf84,missense_variant,p.Trp117Cys,ENST00000574814,NM_001193623.1;C19orf84,5_prime_UTR_variant,,ENST00000570516,;LIM2,upstream_gene_variant,,ENST00000221973,NM_030657.3;LIM2,upstream_gene_variant,,ENST00000596399,NM_001161748.1; A ENST00000574814 Transcript missense_variant 413/1318 351/561 117/186 W/C tgG/tgT 1 -1 C19orf84 HGNC HGNC:27112 protein_coding YES CCDS58676.1 ENSP00000458772 I3L1E1 UPI0000161964 NM_001193623.1 deleterious(0.02) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 51389194 51389194 C A 1 0 0 0 0 1 0 0 0 1927 624 22 2 2 C19orf84 19 51389194 Missense_Mutation SNP C 11LU022_T 393070 51389194 7228422 907 1545 SIGLEC8 0 . GRCh38 19 51454269 51454269 + Missense_Mutation SNP C C A rs771308591 11LU022_T 11LU022_N C C c.1195G>T p.Gly399Trp p.G399W ENST00000321424 6/7 299 266 33 322 322 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Gly399Trp,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Gly290Trp,ENST00000430817,;SIGLEC8,missense_variant,p.Gly306Trp,ENST00000340550,;SIGLEC8,downstream_gene_variant,,ENST00000597352,; A ENST00000321424 Transcript missense_variant 1262/2949 1195/1500 399/499 G/W Ggg/Tgg rs771308591 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 deleterious(0.03) 6/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36 MODERATE 1 SNV 1 1 PASS rs771308591 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 51454269 51454269 C A 1 0 0 0 0 1 0 0 0 14578 623 22 2 2 SIGLEC8 19 51454269 Missense_Mutation SNP C 11LU022_T 65075 51454269 7163347 908 1546 SIGLEC12 0 . GRCh38 19 51501539 51501539 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.195G>T p.= p.R65R ENST00000291707 1/8 315 286 29 381 381 0 strelka-varscan-mutect SIGLEC12,synonymous_variant,p.=,ENST00000291707,NM_053003.3;SIGLEC12,upstream_gene_variant,,ENST00000598614,NM_033329.2;SIGLEC12,synonymous_variant,p.=,ENST00000596742,;CTD-3073N11.7,downstream_gene_variant,,ENST00000594712,; A ENST00000291707 Transcript synonymous_variant 251/2121 195/1788 65/595 R cgG/cgT 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 1/8 PROSITE_profiles:PS50835,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 51501539 51501539 C A 1 0 0 0 0 0 0 0 1 14572 610 22 2 2 SIGLEC12 19 51501539 Silent SNP C 11LU022_T 47270 51501539 7116077 909 1547 SIGLEC6 0 . GRCh38 19 51520182 51520182 + Missense_Mutation SNP T T A rs779618834 11LU022_T 11LU022_N T T c.1262A>T p.Glu421Val p.E421V ENST00000425629 8/8 181 157 24 196 196 0 strelka-varscan-mutect SIGLEC6,missense_variant,p.Glu405Val,ENST00000346477,NM_198845.4;SIGLEC6,missense_variant,p.Glu421Val,ENST00000425629,NM_001245.5;SIGLEC6,missense_variant,p.Glu369Val,ENST00000436458,NM_001177547.1;SIGLEC6,3_prime_UTR_variant,,ENST00000359982,NM_001177548.1;SIGLEC6,3_prime_UTR_variant,,ENST00000343300,NM_198846.4;SIGLEC6,3_prime_UTR_variant,,ENST00000391797,NM_001177549.1;CTD-3073N11.9,non_coding_transcript_exon_variant,,ENST00000598220,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000474054,; A ENST00000425629 Transcript missense_variant 1417/1852 1262/1362 421/453 E/V gAg/gTg rs779618834 1 -1 SIGLEC6 HGNC HGNC:10875 protein_coding YES CCDS12834.3 ENSP00000401502 O43699 A0A024R4K4 UPI0000223FFD NM_001245.5 deleterious(0) 8/8 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF52 MODERATE 1 SNV 2 1 PASS rs779618834 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 51520182 51520182 T A 1 0 0 0 0 1 0 0 0 14576 1551 54 4 4 SIGLEC6 19 51520182 Missense_Mutation SNP T 11LU022_T 18643 51520182 7097434 910 1548 PPP2R1A 0 . GRCh38 19 52212976 52212976 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.673G>T p.Val225Leu p.V225L ENST00000322088 6/15 63 55 8 63 63 0 strelka-varscan-mutect PPP2R1A,missense_variant,p.Val225Leu,ENST00000322088,NM_014225.5;PPP2R1A,missense_variant,p.Val46Leu,ENST00000462990,;PPP2R1A,missense_variant,p.Val265Leu,ENST00000454220,;PPP2R1A,downstream_gene_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000473820,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000462047,;PPP2R1A,downstream_gene_variant,,ENST00000468280,;PPP2R1A,downstream_gene_variant,,ENST00000490868,; T ENST00000322088 Transcript missense_variant 731/5380 673/1770 225/589 V/L Gtg/Ttg 1 1 PPP2R1A HGNC HGNC:9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 A8K7B7 UPI000006EB9C NM_014225.5 deleterious(0) 6/15 PROSITE_profiles:PS50077,hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Gene3D:1.25.10.10,Pfam_domain:PF13646,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.11984 0.9999999 1 1 1 0 T 3 4 3 52212976 52212976 G T 1 0 0 0 0 1 0 0 0 12505 1261 44 2 2 PPP2R1A 19 52212976 Missense_Mutation SNP G 11LU022_T 692794 52212976 6404640 911 1549 PPP2R1A 0 . GRCh38 19 52213110 52213110 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.807G>T p.Glu269Asp p.E269D ENST00000322088 6/15 38 21 17 42 42 0 strelka-varscan-mutect PPP2R1A,missense_variant,p.Glu269Asp,ENST00000322088,NM_014225.5;PPP2R1A,missense_variant,p.Glu90Asp,ENST00000462990,;PPP2R1A,missense_variant,p.Glu309Asp,ENST00000454220,;PPP2R1A,downstream_gene_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,splice_region_variant,,ENST00000473820,;PPP2R1A,splice_region_variant,,ENST00000462047,;PPP2R1A,downstream_gene_variant,,ENST00000468280,;PPP2R1A,downstream_gene_variant,,ENST00000490868,; T ENST00000322088 Transcript missense_variant,splice_region_variant 865/5380 807/1770 269/589 E/D gaG/gaT 1 1 PPP2R1A HGNC HGNC:9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 A8K7B7 UPI000006EB9C NM_014225.5 tolerated(0.24) 6/15 PROSITE_profiles:PS50077,hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 52213110 52213110 G T 1 0 0 0 0 1 0 0 0 12505 1014 35 2 2 PPP2R1A 19 52213110 Missense_Mutation SNP G 11LU022_T 134 52213110 6404506 912 1550 ZNF415 0 . GRCh38 19 53109266 53109266 + Missense_Mutation SNP G G C rs373210709 11LU022_T 11LU022_N G G c.779C>G p.Ala260Gly p.A260G ENST00000500065 4/4 247 220 27 247 247 0 strelka-varscan-mutect ZNF415,missense_variant,p.Ala260Gly,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Ala260Gly,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Ala260Gly,ENST00000243643,NM_018355.3;ZNF415,missense_variant,p.Ala30Gly,ENST00000601493,;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; C ENST00000500065 Transcript missense_variant 1113/2496 779/1668 260/555 A/G gCg/gGg rs373210709 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,SMART_domains:SM00614,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS rs373210709 . 0 208 0 0 2 0 0 0 -10.58472 0.9943953 1 1 1 0 C 3 2 3 53109266 53109266 G C 1 0 0 0 0 1 0 0 0 18464 1087 38 4 4 ZNF415 19 53109266 Missense_Mutation SNP G 11LU022_T 896156 53109266 5508350 913 1551 ZNF813 0 . GRCh38 19 53491382 53491382 + Nonsense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.1150A>T p.Lys384Ter p.K384* ENST00000396403 4/4 264 186 78 249 249 0 strelka-varscan-mutect ZNF813,stop_gained,p.Lys384Ter,ENST00000396403,NM_001004301.3;ZNF813,downstream_gene_variant,,ENST00000490956,;ZNF813,downstream_gene_variant,,ENST00000468450,;CTD-2224J9.4,upstream_gene_variant,,ENST00000483735,; T ENST00000396403 Transcript stop_gained 1278/6151 1150/1854 384/617 K/* Aag/Tag 1 1 ZNF813 HGNC HGNC:33257 protein_coding YES CCDS46172.1 ENSP00000379684 Q6ZN06 UPI000040C511 NM_001004301.3 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 3 1 PASS rs1434894125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 53491382 53491382 A T 1 0 0 0 0 0 1 0 0 18761 363 13 4 4 ZNF813 19 53491382 Nonsense_Mutation SNP A 11LU022_T 382116 53491382 5126234 914 1552 CACNG8 0 . GRCh38 19 53978208 53978208 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.346G>T p.Asp116Tyr p.D116Y ENST00000270458 2/4 135 125 10 151 151 0 strelka-varscan-mutect CACNG8,missense_variant,p.Asp116Tyr,ENST00000270458,NM_031895.5;CACNG8,upstream_gene_variant,,ENST00000401179,; T ENST00000270458 Transcript missense_variant 449/8747 346/1278 116/425 D/Y Gac/Tac 1 1 CACNG8 HGNC HGNC:13628 protein_coding YES CCDS33104.1 ENSP00000270458 Q8WXS5 UPI000013D88B NM_031895.5 deleterious(0) 2/4 hmmpanther:PTHR12107:SF2,hmmpanther:PTHR12107,Pfam_domain:PF00822 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 53978208 53978208 G T 1 0 0 0 0 1 0 0 0 2251 1058 37 1 1 CACNG8 19 53978208 Missense_Mutation SNP G 11LU022_T 486826 53978208 4639408 915 1553 LILRB5 0 . GRCh38 19 54256696 54256696 + Nonsense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.148C>T p.Gln50Ter p.Q50* ENST00000449561 3/13 353 317 36 404 404 0 strelka-varscan-mutect LILRB5,stop_gained,p.Gln50Ter,ENST00000316219,NM_006840.4;LILRB5,stop_gained,p.Gln50Ter,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,stop_gained,p.Gln50Ter,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000621581,;LILRB5,intron_variant,,ENST00000615654,; A ENST00000449561 Transcript stop_gained 219/2137 148/1776 50/591 Q/* Cag/Tag 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 3/13 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 54256696 54256696 G A 1 0 0 0 0 0 1 0 0 8702 1299 45 3 3 LILRB5 19 54256696 Nonsense_Mutation SNP G 11LU022_T 278488 54256696 4360920 916 1554 LAIR1 0 . GRCh38 19 54355377 54355377 + Missense_Mutation SNP G G C rs376569529 11LU022_T 11LU022_N G G c.755C>G p.Ala252Gly p.A252G ENST00000391742 10/10 108 74 34 102 102 0 strelka-varscan-mutect LAIR1,missense_variant,p.Ala252Gly,ENST00000391742,NM_002287.5;LAIR1,missense_variant,p.Ala234Gly,ENST00000391743,NM_001289026.2,NM_001289027.2;LAIR1,missense_variant,p.Ala251Gly,ENST00000434277,NM_001289025.2;LAIR1,missense_variant,p.Ala235Gly,ENST00000348231,NM_021706.4;LAIR1,missense_variant,p.Ala234Gly,ENST00000474878,NM_001289023.2;LAIR1,downstream_gene_variant,,ENST00000622064,;LAIR1,non_coding_transcript_exon_variant,,ENST00000440716,;LAIR1,downstream_gene_variant,,ENST00000463489,;LAIR1,downstream_gene_variant,,ENST00000468656,;LAIR1,3_prime_UTR_variant,,ENST00000391741,;LAIR1,non_coding_transcript_exon_variant,,ENST00000475389,;LAIR1,non_coding_transcript_exon_variant,,ENST00000467269,;LAIR1,non_coding_transcript_exon_variant,,ENST00000498511,;LAIR1,downstream_gene_variant,,ENST00000460312,;LAIR1,downstream_gene_variant,,ENST00000418556,;LAIR1,downstream_gene_variant,,ENST00000436513,;LAIR1,downstream_gene_variant,,ENST00000420483,; C ENST00000391742 Transcript missense_variant 908/4901 755/864 252/287 A/G gCt/gGt rs376569529 1 -1 LAIR1 HGNC HGNC:6477 protein_coding YES CCDS12891.1 ENSP00000375622 Q6GTX8 UPI00034F23B9 NM_002287.5 deleterious(0.01) 10/10 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF122 MODERATE 1 SNV 1 1 PASS rs376569529 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 54355377 54355377 G C 1 0 0 0 0 1 0 0 0 8506 971 34 4 4 LAIR1 19 54355377 Missense_Mutation SNP G 11LU022_T 98681 54355377 4262239 917 1555 LILRB1 0 . GRCh38 19 54636530 54636530 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1690T>A p.Tyr564Asn p.Y564N ENST00000324602 14/15 177 166 11 192 192 0 varscan-mutect LILRB1,missense_variant,p.Tyr562Asn,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Tyr563Asn,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Tyr563Asn,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Tyr564Asn,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Tyr613Asn,ENST00000427581,;LILRB1,missense_variant,p.Tyr564Asn,ENST00000396315,;LILRB1,missense_variant,p.Tyr546Asn,ENST00000396317,NM_001278398.2;AC009892.10,intron_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,3_prime_UTR_variant,,ENST00000421584,;LILRB1,downstream_gene_variant,,ENST00000480375,;LILRB1,downstream_gene_variant,,ENST00000487425,; A ENST00000324602 Transcript missense_variant 1855/2774 1690/1959 564/652 Y/N Tat/Aat 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 deleterious(0.03) 14/15 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 54636530 54636530 T A 1 0 0 0 0 1 0 0 0 8698 1638 57 4 4 LILRB1 19 54636530 Missense_Mutation SNP T 11LU022_T 281153 54636530 3981086 918 1556 NCR1 0 . GRCh38 19 54909345 54909345 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.456G>C p.Met152Ile p.M152I ENST00000291890 4/7 294 269 25 270 269 1 strelka-varscan-mutect NCR1,missense_variant,p.Met152Ile,ENST00000594765,NM_001145457.2;NCR1,missense_variant,p.Met152Ile,ENST00000291890,NM_004829.6;NCR1,missense_variant,p.Met140Ile,ENST00000598576,;NCR1,missense_variant,p.Met152Ile,ENST00000338835,NM_001145458.2,NM_001242357.2;NCR1,missense_variant,p.Met57Ile,ENST00000350790,NM_001242356.2;NCR1,missense_variant,p.Met45Ile,ENST00000357397,;NCR1,non_coding_transcript_exon_variant,,ENST00000601137,;NCR1,downstream_gene_variant,,ENST00000601903,; C ENST00000291890 Transcript missense_variant 494/1155 456/915 152/304 M/I atG/atC 1 1 NCR1 HGNC HGNC:6731 protein_coding YES CCDS12911.1 ENSP00000291890 A0A0A0MQZ0 UPI00034F23C0 NM_004829.6 tolerated(0.07) 4/7 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF14,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 54909345 54909345 G C 1 0 0 0 0 1 0 0 0 10256 1377 48 4 4 NCR1 19 54909345 Missense_Mutation SNP G 11LU022_T 272815 54909345 3708271 919 1557 NLRP2 0 . GRCh38 19 54982463 54982463 + Silent SNP G G T rs151132029 11LU022_T 11LU022_N G G c.765G>T p.= p.P255P ENST00000543010 6/13 448 408 40 464 464 0 strelka-varscan-mutect NLRP2,synonymous_variant,p.=,ENST00000543010,NM_001174081.1;NLRP2,synonymous_variant,p.=,ENST00000448584,NM_017852.3;NLRP2,synonymous_variant,p.=,ENST00000537859,NM_001174082.1;NLRP2,synonymous_variant,p.=,ENST00000263437,;NLRP2,synonymous_variant,p.=,ENST00000339757,;NLRP2,synonymous_variant,p.=,ENST00000391721,;NLRP2,synonymous_variant,p.=,ENST00000427260,NM_001174083.1;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000588107,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; T ENST00000543010 Transcript synonymous_variant 908/3576 765/3189 255/1062 P ccG/ccT rs151132029 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 6/13 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs151132029 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 54982463 54982463 G T 1 0 0 0 0 0 0 0 1 10514 1132 40 1 1 NLRP2 19 54982463 Silent SNP G 11LU022_T 73118 54982463 3635153 920 1558 NLRP2 0 . GRCh38 19 54982613 54982613 + Nonsense_Mutation SNP C C A rs370946962 11LU022_T 11LU022_N C C c.915C>A p.Cys305Ter p.C305* ENST00000543010 6/13 233 155 78 270 270 0 strelka-varscan-mutect NLRP2,stop_gained,p.Cys305Ter,ENST00000543010,NM_001174081.1;NLRP2,stop_gained,p.Cys305Ter,ENST00000448584,NM_017852.3;NLRP2,stop_gained,p.Cys283Ter,ENST00000537859,NM_001174082.1;NLRP2,stop_gained,p.Cys302Ter,ENST00000263437,;NLRP2,stop_gained,p.Cys283Ter,ENST00000339757,;NLRP2,stop_gained,p.Cys281Ter,ENST00000391721,;NLRP2,stop_gained,p.Cys282Ter,ENST00000427260,NM_001174083.1;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000588107,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; A ENST00000543010 Transcript stop_gained 1058/3576 915/3189 305/1062 C/* tgC/tgA rs370946962,COSM1564215 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 6/13 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729 0,1 HIGH 1 SNV 1 0,1 1 PASS rs370946962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 54982613 54982613 C A 1 0 0 0 0 0 1 0 0 10514 776 27 1 1 NLRP2 19 54982613 Nonsense_Mutation SNP C 11LU022_T 150 54982613 3635003 921 1559 EPN1 0 . GRCh38 19 55689950 55689950 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1020G>T p.Glu340Asp p.E340D ENST00000411543 6/11 121 110 11 171 171 0 strelka-varscan-mutect EPN1,missense_variant,p.Glu254Asp,ENST00000270460,NM_001130072.1;EPN1,missense_variant,p.Glu340Asp,ENST00000411543,NM_001130071.1;EPN1,missense_variant,p.Glu229Asp,ENST00000085079,NM_013333.3;EPN1,upstream_gene_variant,,ENST00000589704,;AC010525.4,downstream_gene_variant,,ENST00000585559,;EPN1,downstream_gene_variant,,ENST00000591743,;EPN1,upstream_gene_variant,,ENST00000586194,; T ENST00000411543 Transcript missense_variant,splice_region_variant 1567/2621 1020/1989 340/662 E/D gaG/gaT 1 1 EPN1 HGNC HGNC:21604 protein_coding YES CCDS46198.1 ENSP00000406209 Q9Y6I3 UPI000059D7B7 NM_001130071.1 deleterious(0.02) 6/11 hmmpanther:PTHR12276,hmmpanther:PTHR12276:SF48 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 55689950 55689950 G T 1 0 0 0 0 1 0 0 0 5032 1014 35 2 2 EPN1 19 55689950 Missense_Mutation SNP G 11LU022_T 707337 55689950 2927666 922 1560 NLRP5 0 . GRCh38 19 56027098 56027098 + Nonsense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.865G>T p.Gly289Ter p.G289* ENST00000390649 7/15 185 129 56 213 213 0 strelka-varscan-mutect NLRP5,stop_gained,p.Gly289Ter,ENST00000390649,NM_153447.4;NLRP5,stop_gained,p.Gly289Ter,ENST00000621651,; T ENST00000390649 Transcript stop_gained 865/3888 865/3603 289/1200 G/* Gga/Tga 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 7/15 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 56027098 56027098 G T 1 0 0 0 0 0 1 0 0 10518 1001 35 2 2 NLRP5 19 56027098 Nonsense_Mutation SNP G 11LU022_T 337148 56027098 2590518 923 1561 ZNF787 0 . GRCh38 19 56088615 56088615 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.557G>T p.Gly186Val p.G186V ENST00000610935 3/3 119 75 44 146 146 0 strelka-varscan-mutect ZNF787,missense_variant,p.Gly186Val,ENST00000610935,NM_001002836.3;ZNF787,downstream_gene_variant,,ENST00000586787,; A ENST00000610935 Transcript missense_variant 676/1925 557/1149 186/382 G/V gGc/gTc 1 -1 ZNF787 HGNC HGNC:26998 protein_coding YES CCDS42634.1 ENSP00000478557 A0A087WUD1 UPI0001596896 NM_001002836.3 deleterious(0.01) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24408:SF1,hmmpanther:PTHR24408,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56088615 56088615 C A 1 0 0 0 0 1 0 0 0 18743 739 26 2 2 ZNF787 19 56088615 Missense_Mutation SNP C 11LU022_T 61517 56088615 2529001 924 1562 ZNF787 0 . GRCh38 19 56088874 56088874 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.298G>T p.Gly100Cys p.G100C ENST00000610935 3/3 96 67 29 156 156 0 strelka-varscan-mutect ZNF787,missense_variant,p.Gly100Cys,ENST00000610935,NM_001002836.3;ZNF787,downstream_gene_variant,,ENST00000586787,; A ENST00000610935 Transcript missense_variant 417/1925 298/1149 100/382 G/C Ggc/Tgc 1 -1 ZNF787 HGNC HGNC:26998 protein_coding YES CCDS42634.1 ENSP00000478557 A0A087WUD1 UPI0001596896 NM_001002836.3 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24408:SF1,hmmpanther:PTHR24408,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56088874 56088874 C A 1 0 0 0 0 1 0 0 0 18743 652 23 1 1 ZNF787 19 56088874 Missense_Mutation SNP C 11LU022_T 259 56088874 2528742 925 1563 ZNF582 0 . GRCh38 19 56385174 56385174 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.243C>A p.= p.S81S ENST00000301310 5/5 72 67 5 68 68 0 strelka-varscan-mutect ZNF582,synonymous_variant,p.=,ENST00000301310,;ZNF582,synonymous_variant,p.=,ENST00000619584,NM_144690.1;ZNF582,synonymous_variant,p.=,ENST00000586929,;ZNF582,intron_variant,,ENST00000589143,;ZNF582,downstream_gene_variant,,ENST00000589895,;AC006116.12,upstream_gene_variant,,ENST00000589671,;ZNF582,synonymous_variant,p.=,ENST00000587778,;ZNF582,synonymous_variant,p.=,ENST00000593145,;SLC25A36P1,upstream_gene_variant,,ENST00000590111,; T ENST00000301310 Transcript synonymous_variant 402/2824 243/1554 81/517 S tcC/tcA 1 -1 ZNF582 HGNC HGNC:26421 protein_coding YES CCDS33121.1 ENSP00000301310 Q96NG8 A0A024R4P7 UPI000006D278 5/5 hmmpanther:PTHR24381:SF115,hmmpanther:PTHR24381 LOW 1 SNV 1 1 PASS rs1034688442 . 0 203 7 0 0 0 0 0 -11.27102 0.9999977 1 1 1 0 T 2 4 3 56385174 56385174 G T 1 0 0 0 0 0 0 0 1 18588 1335 47 2 2 ZNF582 19 56385174 Silent SNP G 11LU022_T 296300 56385174 2232442 926 1564 ZNF667 0 . GRCh38 19 56441869 56441869 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1126C>A p.His376Asn p.H376N ENST00000504904 7/7 103 76 27 128 128 0 strelka-varscan-mutect ZNF667,missense_variant,p.His376Asn,ENST00000504904,NM_001321356.1;ZNF667,missense_variant,p.His376Asn,ENST00000292069,NM_022103.3;ZNF667,missense_variant,p.His158Asn,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; T ENST00000504904 Transcript missense_variant 1846/4390 1126/1833 376/610 H/N Cat/Aat 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 56441869 56441869 G T 1 0 0 0 0 1 0 0 0 18648 1319 46 2 2 ZNF667 19 56441869 Missense_Mutation SNP G 11LU022_T 56695 56441869 2175747 927 1565 PEG3 0 . GRCh38 19 56815279 56815279 + Nonsense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.3163C>T p.Gln1055Ter p.Q1055* ENST00000326441 10/10 130 84 46 132 132 0 strelka-varscan-mutect PEG3,stop_gained,p.Gln1055Ter,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,stop_gained,p.Gln931Ter,ENST00000598410,NM_001146187.1;PEG3,stop_gained,p.Gln1055Ter,ENST00000599534,;PEG3,stop_gained,p.Gln1055Ter,ENST00000599577,;PEG3,stop_gained,p.Gln929Ter,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript stop_gained 3527/8723 3163/4767 1055/1588 Q/* Caa/Taa 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 10/10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 56815279 56815279 G A 1 0 0 0 0 0 1 0 0 11808 1357 47 3 3 PEG3 19 56815279 Nonsense_Mutation SNP G 11LU022_T 373410 56815279 1802337 928 1566 PEG3 0 . GRCh38 19 56817019 56817019 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.1423A>G p.Thr475Ala p.T475A ENST00000326441 10/10 159 116 43 179 179 0 strelka-varscan-mutect PEG3,missense_variant,p.Thr475Ala,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Thr351Ala,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Thr475Ala,ENST00000599534,;PEG3,missense_variant,p.Thr475Ala,ENST00000599577,;PEG3,missense_variant,p.Thr349Ala,ENST00000593695,NM_001146185.1;PEG3,missense_variant,p.Thr320Ala,ENST00000600833,;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; C ENST00000326441 Transcript missense_variant 1787/8723 1423/4767 475/1588 T/A Act/Gct 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0.01) 10/10 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 56817019 56817019 T C 1 0 0 0 0 1 0 0 0 11808 1638 57 5 5 PEG3 19 56817019 Missense_Mutation SNP T 11LU022_T 1740 56817019 1800597 929 1567 PEG3 0 . GRCh38 19 56817535 56817535 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.907G>T p.Gly303Trp p.G303W ENST00000326441 10/10 36 21 15 44 44 0 strelka-varscan-mutect PEG3,missense_variant,p.Gly303Trp,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Gly179Trp,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Gly303Trp,ENST00000599534,;PEG3,missense_variant,p.Gly303Trp,ENST00000599577,;PEG3,missense_variant,p.Gly177Trp,ENST00000593695,NM_001146185.1;PEG3,missense_variant,p.Gly148Trp,ENST00000600833,;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,downstream_gene_variant,,ENST00000593931,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 1271/8723 907/4767 303/1588 G/W Ggg/Tgg 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0) 10/10 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56817535 56817535 C A 1 0 0 0 0 1 0 0 0 11808 623 22 2 2 PEG3 19 56817535 Missense_Mutation SNP C 11LU022_T 516 56817535 1800081 930 1568 ZNF606 0 . GRCh38 19 57979550 57979550 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1130G>T p.Trp377Leu p.W377L ENST00000341164 7/7 100 65 35 118 118 0 strelka-varscan-mutect ZNF606,missense_variant,p.Trp377Leu,ENST00000341164,NM_025027.3;ZNF606,missense_variant,p.Trp377Leu,ENST00000551380,;ZNF606,3_prime_UTR_variant,,ENST00000550599,; A ENST00000341164 Transcript missense_variant 1751/4248 1130/2379 377/792 W/L tGg/tTg 1 -1 ZNF606 HGNC HGNC:25879 protein_coding YES CCDS12968.1 ENSP00000343617 Q8WXB4 A0A024R4S7 UPI000013C35B NM_025027.3 deleterious(0.03) 7/7 hmmpanther:PTHR24377:SF305,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999924 1 1 1 0 A 3 1 3 57979550 57979550 C A 1 0 0 0 0 1 0 0 0 18607 595 21 2 2 ZNF606 19 57979550 Missense_Mutation SNP C 11LU022_T 1162015 57979550 638066 931 1569 A1BG 0 . GRCh38 19 58351638 58351638 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.663C>A p.= p.V221V ENST00000263100 5/8 333 265 68 379 379 0 strelka-varscan-mutect A1BG,synonymous_variant,p.=,ENST00000263100,NM_130786.3;A1BG,synonymous_variant,p.=,ENST00000600966,;ZNF497,downstream_gene_variant,,ENST00000311044,NM_198458.2;ZNF497,downstream_gene_variant,,ENST00000425453,NM_001207009.1;A1BG-AS1,intron_variant,,ENST00000594950,;A1BG-AS1,intron_variant,,ENST00000600686,;A1BG-AS1,intron_variant,,ENST00000593960,;A1BG-AS1,intron_variant,,ENST00000593374,;A1BG-AS1,intron_variant,,ENST00000600379,;A1BG-AS1,intron_variant,,ENST00000599728,;A1BG-AS1,upstream_gene_variant,,ENST00000595302,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000599109,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000600123,;CTD-2619J13.5,non_coding_transcript_exon_variant,,ENST00000623509,;A1BG,upstream_gene_variant,,ENST00000596924,;CTD-2619J13.8,downstream_gene_variant,,ENST00000596636,;A1BG,non_coding_transcript_exon_variant,,ENST00000595014,;A1BG,upstream_gene_variant,,ENST00000598345,; T ENST00000263100 Transcript synonymous_variant 725/1722 663/1488 221/495 V gtC/gtA 1 -1 A1BG HGNC HGNC:5 protein_coding YES CCDS12976.1 ENSP00000263100 P04217 V9HWD8 UPI0000167B10 NM_130786.3 5/8 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,PROSITE_profiles:PS50835,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 58351638 58351638 G T 1 0 0 0 0 0 0 0 1 1 1161 41 2 2 A1BG 19 58351638 Silent SNP G 11LU022_T 372088 58351638 265978 932 1570 ZNF324 0 . GRCh38 19 58471530 58471530 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1038C>A p.Cys346Ter p.C346* ENST00000536459 4/4 84 79 5 84 84 0 varscan-mutect ZNF324,stop_gained,p.Cys346Ter,ENST00000536459,;ZNF324,stop_gained,p.Cys346Ter,ENST00000196482,NM_014347.2;ZNF324,stop_gained,p.Cys205Ter,ENST00000593925,;ZNF446,upstream_gene_variant,,ENST00000596341,;ZNF446,upstream_gene_variant,,ENST00000594369,NM_017908.3;ZNF446,upstream_gene_variant,,ENST00000335841,;ZNF446,upstream_gene_variant,,ENST00000622313,;ZNF446,upstream_gene_variant,,ENST00000610298,;ZNF324,downstream_gene_variant,,ENST00000535298,;ZNF446,upstream_gene_variant,,ENST00000600013,;CTD-2619J13.23,downstream_gene_variant,,ENST00000598051,;ZNF446,upstream_gene_variant,,ENST00000391694,;ZNF446,upstream_gene_variant,,ENST00000594468,; A ENST00000536459 Transcript stop_gained 1747/5653 1038/1662 346/553 C/* tgC/tgA 1 1 ZNF324 HGNC HGNC:14096 protein_coding YES CCDS12981.1 ENSP00000444812 O75467 A0A024R4R8 UPI000013C359 4/4 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF159,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH SNV 2 1 PASS rs1163674696 . 0 206 4 0 0 0 0 0 -11.10873 1 1 1 1 0 A 4 1 3 58471530 58471530 C A 1 0 0 0 0 0 1 0 0 18416 776 27 1 1 ZNF324 19 58471530 Nonsense_Mutation SNP C 11LU022_T 119892 58471530 146086 933 1571 HSPA12B 0 . GRCh38 20 3746001 3746001 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.645C>A p.= p.A215A ENST00000254963 7/13 202 145 57 307 307 0 strelka-mutect HSPA12B,synonymous_variant,p.=,ENST00000254963,NM_052970.4,NM_001197327.1;HSPA12B,synonymous_variant,p.=,ENST00000399701,NM_001318322.1; A ENST00000254963 Transcript synonymous_variant 790/3151 645/2061 215/686 A gcC/gcA 1 1 HSPA12B HGNC HGNC:16193 protein_coding YES CCDS13061.1 ENSP00000254963 Q96MM6 UPI00001285E5 NM_052970.4,NM_001197327.1 7/13 Gene3D:3.30.420.40,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF39,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 3746001 3746001 C A 1 0 0 0 0 0 0 0 1 7301 581 21 2 2 HSPA12B 20 3746001 Silent SNP C 11LU022_T 3746001 60698166 934 1572 RASSF2 0 . GRCh38 20 4790471 4790471 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.517G>T p.Gly173Cys p.G173C ENST00000379400 7/12 26 21 5 26 26 0 strelka-varscan-mutect RASSF2,missense_variant,p.Gly173Cys,ENST00000379400,NM_014737.2;RASSF2,missense_variant,p.Gly173Cys,ENST00000379376,NM_170774.1;RASSF2,non_coding_transcript_exon_variant,,ENST00000478553,; A ENST00000379400 Transcript missense_variant 713/5427 517/981 173/326 G/C Ggc/Tgc 1 -1 RASSF2 HGNC HGNC:9883 protein_coding YES CCDS13083.1 ENSP00000368710 P50749 UPI0000001C0A NM_014737.2 deleterious(0) 7/12 hmmpanther:PTHR22738,hmmpanther:PTHR22738:SF14 MODERATE 1 SNV 1 1 PASS rs1048112272 . 0 205 5 0 0 0 0 0 -14.15976 1 1 1 1 0 A 3 1 3 4790471 4790471 C A 1 0 0 0 0 1 0 0 0 13247 652 23 1 1 RASSF2 20 4790471 Missense_Mutation SNP C 11LU022_T 1044470 4790471 59653696 935 1573 CHGB 0 . GRCh38 20 5923566 5923566 + Nonsense_Mutation SNP C C A rs774814252 11LU022_T 11LU022_N C C c.1422C>A p.Tyr474Ter p.Y474* ENST00000378961 4/5 107 78 29 154 154 0 strelka-varscan-mutect CHGB,stop_gained,p.Tyr474Ter,ENST00000378961,NM_001819.2;CHGB,downstream_gene_variant,,ENST00000455042,;RP5-967N21.2,downstream_gene_variant,,ENST00000400619,; A ENST00000378961 Transcript stop_gained 1626/2550 1422/2034 474/677 Y/* taC/taA rs774814252,COSM2152052 1 1 CHGB HGNC HGNC:1930 protein_coding YES CCDS13092.1 ENSP00000368244 P05060 UPI000013C63D NM_001819.2 4/5 Pfam_domain:PF01271,hmmpanther:PTHR10583,hmmpanther:PTHR10583:SF4 0,1 HIGH 1 SNV 1 0,1 1 PASS rs774814252 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 5923566 5923566 C A 1 0 0 0 0 0 1 0 0 3098 547 19 1 1 CHGB 20 5923566 Nonsense_Mutation SNP C 11LU022_T 1133095 5923566 58520601 936 1574 PAX1 0 . GRCh38 20 21714632 21714632 + Silent SNP G G T rs780673145 11LU022_T 11LU022_N G G c.1434G>T p.= p.A478A ENST00000398485 5/5 170 137 33 258 258 0 strelka-varscan-mutect PAX1,synonymous_variant,p.=,ENST00000398485,NM_006192.4;PAX1,3_prime_UTR_variant,,ENST00000613128,NM_001257096.1;PAX1,3_prime_UTR_variant,,ENST00000444366,; T ENST00000398485 Transcript synonymous_variant 1488/2838 1434/1605 478/534 A gcG/gcT rs780673145,COSM3389630,COSM3389631 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 5/5 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs780673145 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 21714632 21714632 G T 1 0 0 0 0 0 0 0 1 11563 1103 39 1 1 PAX1 20 21714632 Silent SNP G 11LU022_T 15791066 21714632 42729535 937 1575 PAX1 0 . GRCh38 20 21714663 21714663 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.1465G>A p.Gly489Arg p.G489R ENST00000398485 5/5 186 143 43 296 296 0 strelka-varscan-mutect PAX1,missense_variant,p.Gly489Arg,ENST00000398485,NM_006192.4;PAX1,3_prime_UTR_variant,,ENST00000613128,NM_001257096.1;PAX1,3_prime_UTR_variant,,ENST00000444366,; A ENST00000398485 Transcript missense_variant 1519/2838 1465/1605 489/534 G/R Gga/Aga 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious_low_confidence(0.05) 5/5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 21714663 21714663 G A 1 0 0 0 0 1 0 0 0 11563 1001 35 3 3 PAX1 20 21714663 Missense_Mutation SNP G 11LU022_T 31 21714663 42729504 938 1576 XKR7 0 . GRCh38 20 31997127 31997127 + Silent SNP G G T rs746729361 11LU022_T 11LU022_N G G c.1410G>T p.= p.T470T ENST00000562532 3/3 326 274 52 301 301 0 strelka-varscan-mutect XKR7,synonymous_variant,p.=,ENST00000562532,NM_001011718.1; T ENST00000562532 Transcript synonymous_variant 1584/7844 1410/1740 470/579 T acG/acT rs746729361,COSM5327885 1 1 XKR7 HGNC HGNC:23062 protein_coding YES CCDS33459.1 ENSP00000477059 Q5GH72 UPI00004C7A9E NM_001011718.1 3/3 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF9 0,1 LOW 1 SNV 1 0,1 1 PASS rs746729361 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 31997127 31997127 G T 1 0 0 0 0 0 0 0 1 17995 1045 37 1 1 XKR7 20 31997127 Silent SNP G 11LU022_T 10282464 31997127 32447040 939 1577 BPIFB2 0 . GRCh38 20 33008628 33008628 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.54C>A p.= p.V18V ENST00000170150 2/16 201 182 19 165 164 1 strelka-varscan-mutect BPIFB2,synonymous_variant,p.=,ENST00000170150,NM_025227.2;SUN5,upstream_gene_variant,,ENST00000356173,NM_080675.3;SUN5,upstream_gene_variant,,ENST00000375523,;SUN5,upstream_gene_variant,,ENST00000420875,;SUN5,upstream_gene_variant,,ENST00000375519,; A ENST00000170150 Transcript synonymous_variant 249/1898 54/1377 18/458 V gtC/gtA 1 1 BPIFB2 HGNC HGNC:16177 protein_coding YES CCDS13210.1 ENSP00000170150 Q8N4F0 UPI00000377B0 NM_025227.2 2/16 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10504:SF92,hmmpanther:PTHR10504,PIRSF_domain:PIRSF002417 LOW 1 SNV 1 1 PASS rs1380855534 . 0 204 3 2 0 0 0 0 -20 0.9999828 1 1 1 0 A 2 1 3 33008628 33008628 C A 1 0 0 0 0 0 0 0 1 1658 871 31 1 1 BPIFB2 20 33008628 Silent SNP C 11LU022_T 1011501 33008628 31435539 940 1578 AHCY 0 . GRCh38 20 34290427 34290427 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.877G>A p.Asp293Asn p.D293N ENST00000217426 8/10 678 630 48 606 605 1 strelka-varscan-mutect AHCY,missense_variant,p.Asp265Asn,ENST00000538132,NM_001161766.1;AHCY,missense_variant,p.Asp293Asn,ENST00000217426,NM_000687.2;CTD-3216D2.5,upstream_gene_variant,,ENST00000609218,;AHCY,downstream_gene_variant,,ENST00000468908,;AHCY,non_coding_transcript_exon_variant,,ENST00000480653,;AHCY,downstream_gene_variant,,ENST00000606061,; T ENST00000217426 Transcript missense_variant 955/2143 877/1299 293/432 D/N Gat/Aat 1 -1 AHCY HGNC HGNC:343 protein_coding YES CCDS13233.1 ENSP00000217426 P23526 UPI00001354F1 NM_000687.2 tolerated_low_confidence(0.06) 8/10 HAMAP:MF_00563,hmmpanther:PTHR23420,Pfam_domain:PF00670,PIRSF_domain:PIRSF001109,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR00936,SMART_domains:SM00996,SMART_domains:SM00997,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 34290427 34290427 C T 1 0 0 0 0 1 0 0 0 486 826 29 3 3 AHCY 20 34290427 Missense_Mutation SNP C 11LU022_T 1281799 34290427 30153740 941 1579 PTPRT 0 . GRCh38 20 42106831 42106831 + Nonsense_Mutation SNP G G T rs189118400 11LU022_T 11LU022_N G G c.3402C>A p.Cys1134Ter p.C1134* ENST00000373198 25/32 198 169 29 181 181 0 strelka-varscan-mutect PTPRT,stop_gained,p.Cys1134Ter,ENST00000373198,NM_133170.3;PTPRT,stop_gained,p.Cys1137Ter,ENST00000373193,;PTPRT,stop_gained,p.Cys1105Ter,ENST00000373201,;PTPRT,stop_gained,p.Cys1114Ter,ENST00000373190,;PTPRT,stop_gained,p.Cys1125Ter,ENST00000373184,;PTPRT,stop_gained,p.Cys1124Ter,ENST00000356100,;PTPRT,stop_gained,p.Cys1115Ter,ENST00000373187,NM_007050.5;PTPRT,stop_gained,p.Cys733Ter,ENST00000612229,;PTPRT,stop_gained,p.Cys750Ter,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript stop_gained 3638/12746 3402/4383 1134/1460 C/* tgC/tgA rs189118400,COSM3291841,COSM4098494 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 25/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 0,1,1 HIGH 1 SNV 2 0,1,1 1 PASS rs189118400 . 0 204 0 4 0 0 0 2 -3.537056 0 0 1 0 0 T 4 4 3 42106831 42106831 G T 1 0 0 0 0 0 1 0 0 12967 1079 38 1 1 PTPRT 20 42106831 Nonsense_Mutation SNP G 11LU022_T 7816404 42106831 22337336 942 1580 PTPRT 0 . GRCh38 20 42161451 42161451 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.2640C>A p.= p.P880P ENST00000373198 18/32 241 201 40 175 175 0 strelka-varscan-mutect PTPRT,synonymous_variant,p.=,ENST00000373198,NM_133170.3;PTPRT,synonymous_variant,p.=,ENST00000373193,;PTPRT,synonymous_variant,p.=,ENST00000373201,;PTPRT,synonymous_variant,p.=,ENST00000373190,;PTPRT,synonymous_variant,p.=,ENST00000373184,;PTPRT,synonymous_variant,p.=,ENST00000356100,;PTPRT,synonymous_variant,p.=,ENST00000373187,NM_007050.5;PTPRT,synonymous_variant,p.=,ENST00000612229,;PTPRT,synonymous_variant,p.=,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript synonymous_variant 2876/12746 2640/4383 880/1460 P ccC/ccA 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 18/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 42161451 42161451 G T 1 0 0 0 0 0 0 0 1 12967 1219 43 2 2 PTPRT 20 42161451 Silent SNP G 11LU022_T 54620 42161451 22282716 943 1581 HNF4A 0 . GRCh38 20 44413776 44413776 + Silent SNP G G T rs764197818 11LU022_T 11LU022_N G G c.468G>T p.= p.L156L ENST00000316099 4/10 603 388 215 533 533 0 strelka-varscan-mutect HNF4A,synonymous_variant,p.=,ENST00000316099,NM_001258355.1,NM_000457.4;HNF4A,synonymous_variant,p.=,ENST00000619550,NM_001287182.1,NM_001287183.1;HNF4A,synonymous_variant,p.=,ENST00000415691,NM_178849.2;HNF4A,synonymous_variant,p.=,ENST00000443598,NM_178850.2;HNF4A,synonymous_variant,p.=,ENST00000316673,NM_175914.4;HNF4A,synonymous_variant,p.=,ENST00000457232,NM_001030003.2;HNF4A,synonymous_variant,p.=,ENST00000609795,NM_001030004.2,NM_001287184.1;HNF4A,3_prime_UTR_variant,,ENST00000372920,; T ENST00000316099 Transcript synonymous_variant 557/6445 468/1425 156/474 L ctG/ctT rs764197818 1 1 HNF4A HGNC HGNC:5024 protein_coding YES CCDS13330.1 ENSP00000312987 P41235 F1D8T1 UPI000016A0BA NM_001258355.1,NM_000457.4 4/10 hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF41,Gene3D:1.10.565.10,Superfamily_domains:SSF48508 LOW 1 SNV 1 1 PASS rs764197818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 44413776 44413776 G T 1 0 0 0 0 0 0 0 1 7144 1306 46 2 2 HNF4A 20 44413776 Silent SNP G 11LU022_T 2252325 44413776 20030391 944 1582 ZNF334 0 . GRCh38 20 46502557 46502557 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.782G>T p.Gly261Val p.G261V ENST00000347606 5/5 89 54 35 77 77 0 strelka-varscan-mutect ZNF334,missense_variant,p.Gly261Val,ENST00000347606,NM_018102.4;ZNF334,missense_variant,p.Gly260Val,ENST00000615481,;ZNF334,missense_variant,p.Gly223Val,ENST00000457685,;ZNF334,missense_variant,p.Gly284Val,ENST00000593880,;ZNF334,missense_variant,p.Gly260Val,ENST00000625284,NM_001270497.1;ZNF334,downstream_gene_variant,,ENST00000596323,; A ENST00000347606 Transcript missense_variant 965/3890 782/2043 261/680 G/V gGg/gTg 1 -1 ZNF334 HGNC HGNC:15806 protein_coding YES CCDS33480.1 ENSP00000255129 Q9HCZ1 UPI000004A0FE NM_018102.4 deleterious(0.03) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF116,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 46502557 46502557 C A 1 0 0 0 0 1 0 0 0 18423 623 22 2 2 ZNF334 20 46502557 Missense_Mutation SNP C 11LU022_T 2088781 46502557 17941610 945 1583 PREX1 0 . GRCh38 20 48632501 48632501 + Missense_Mutation SNP G G A rs558809203 11LU022_T 11LU022_N G G c.4406C>T p.Thr1469Met p.T1469M ENST00000371941 34/40 364 248 116 398 397 1 strelka-varscan-mutect PREX1,missense_variant,p.Thr1469Met,ENST00000371941,NM_020820.3;PREX1,missense_variant,p.Thr791Met,ENST00000482556,; A ENST00000371941 Transcript missense_variant 4429/6636 4406/4980 1469/1659 T/M aCg/aTg rs558809203,COSM3389808,COSM3389809 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 deleterious(0.02) 34/40 hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs558809203 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 48632501 48632501 G A 1 0 0 0 0 1 0 0 0 12610 1159 40 1 1 PREX1 20 48632501 Missense_Mutation SNP G 11LU022_T 2129944 48632501 15811666 946 1584 CEBPB 0 . GRCh38 20 50191890 50191890 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.857G>A p.Arg286His p.R286H ENST00000303004 1/1 886 581 305 854 854 0 strelka-varscan-mutect CEBPB,missense_variant,p.Arg286His,ENST00000303004,NM_001285879.1,NM_005194.3,NM_001285878.1;CEBPB-AS1,upstream_gene_variant,,ENST00000613921,; A ENST00000303004 Transcript missense_variant 1157/1956 857/1038 286/345 R/H cGc/cAc 1 1 CEBPB HGNC HGNC:1834 protein_coding YES CCDS13429.1 ENSP00000305422 P17676 UPI000000D8BA NM_001285879.1,NM_005194.3,NM_001285878.1 deleterious(0) 1/1 PROSITE_profiles:PS50217,hmmpanther:PTHR23334:SF21,hmmpanther:PTHR23334,PIRSF_domain:PIRSF005879,Pfam_domain:PF07716,SMART_domains:SM00338,Superfamily_domains:SSF57959 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 50191890 50191890 G A 1 0 0 0 0 1 0 0 0 2906 1087 38 1 1 CEBPB 20 50191890 Missense_Mutation SNP G 11LU022_T 1559389 50191890 14252277 947 1585 DOK5 0 . GRCh38 20 54610442 54610442 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.654C>A p.= p.A218A ENST00000262593 6/8 92 84 8 80 80 0 strelka-varscan-mutect DOK5,synonymous_variant,p.=,ENST00000262593,NM_018431.4;DOK5,synonymous_variant,p.=,ENST00000395939,NM_177959.2; A ENST00000262593 Transcript synonymous_variant 1004/1963 654/921 218/306 A gcC/gcA 1 1 DOK5 HGNC HGNC:16173 protein_coding YES CCDS13446.1 ENSP00000262593 Q9P104 UPI00001296AB NM_018431.4 6/8 Gene3D:2.30.29.30,Pfam_domain:PF02174,PROSITE_profiles:PS51064,hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF45,SMART_domains:SM00310,SMART_domains:SM01244,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -17.07041 1 1 1 1 0 A 2 1 3 54610442 54610442 C A 1 0 0 0 0 0 0 0 1 4515 581 21 2 2 DOK5 20 54610442 Silent SNP C 11LU022_T 4418552 54610442 9833725 948 1586 MC3R 0 . GRCh38 20 56248859 56248859 + Missense_Mutation SNP T T A 11LU022_T 11LU022_N T T c.16T>A p.Cys6Ser p.C6S ENST00000243911 1/1 213 146 67 171 171 0 strelka-varscan-mutect MC3R,missense_variant,p.Cys6Ser,ENST00000243911,NM_019888.3; A ENST00000243911 Transcript missense_variant 128/1084 16/972 6/323 C/S Tgc/Agc COSM4581899 1 1 MC3R HGNC HGNC:6931 protein_coding YES CCDS13449.2 ENSP00000243911 P41968 UPI0000E5A34B NM_019888.3 tolerated_low_confidence(0.4) 1/1 Prints_domain:PR01061,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF4 1 MODERATE 1 SNV 1 1 PASS rs1275101116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 56248859 56248859 T A 1 0 0 0 0 1 0 0 0 9298 1580 55 4 4 MC3R 20 56248859 Missense_Mutation SNP T 11LU022_T 1638417 56248859 8195308 949 1587 CSTF1 0 . GRCh38 20 56403470 56403470 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.1039G>C p.Ala347Pro p.A347P ENST00000217109 6/6 139 120 19 107 107 0 strelka-varscan-mutect CSTF1,missense_variant,p.Ala347Pro,ENST00000217109,NM_001033521.1,NM_001324.2,NM_001033522.1;CSTF1,downstream_gene_variant,,ENST00000415828,;CSTF1,downstream_gene_variant,,ENST00000452950,;CSTF1,splice_region_variant,,ENST00000493039,;CSTF1,downstream_gene_variant,,ENST00000490539,; C ENST00000217109 Transcript missense_variant,splice_region_variant 1391/4290 1039/1296 347/431 A/P Gcg/Ccg 1 1 CSTF1 HGNC HGNC:2483 protein_coding YES CCDS13452.1 ENSP00000217109 Q05048 UPI0000000C1E NM_001033521.1,NM_001324.2,NM_001033522.1 deleterious(0.05) 6/6 PROSITE_profiles:PS50294,hmmpanther:PTHR22840,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1182787727 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 56403470 56403470 G C 1 0 0 0 0 1 0 0 0 3783 1101 38 4 4 CSTF1 20 56403470 Missense_Mutation SNP G 11LU022_T 154611 56403470 8040697 950 1588 BMP7 0 . GRCh38 20 57265931 57265931 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.192G>T p.Leu64Phe p.L64F ENST00000395863 1/7 284 181 103 297 297 0 strelka-varscan-mutect BMP7,missense_variant,p.Leu64Phe,ENST00000395863,NM_001719.2;BMP7,missense_variant,p.Leu64Phe,ENST00000450594,;BMP7,missense_variant,p.Leu64Phe,ENST00000395864,;BMP7,upstream_gene_variant,,ENST00000433911,;RP4-813D12.3,upstream_gene_variant,,ENST00000412321,;RP4-813D12.3,upstream_gene_variant,,ENST00000426580,; A ENST00000395863 Transcript missense_variant 698/4013 192/1296 64/431 L/F ttG/ttT 1 -1 BMP7 HGNC HGNC:1074 protein_coding YES CCDS13455.1 ENSP00000379204 P18075 A8K571 UPI00000349AD NM_001719.2 deleterious(0) 1/7 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF135 MODERATE 1 SNV 1 1 PASS rs1377688221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 57265931 57265931 C A 1 0 0 0 0 1 0 0 0 1620 709 25 2 2 BMP7 20 57265931 Missense_Mutation SNP C 11LU022_T 862461 57265931 7178236 951 1589 CDH26 0 . GRCh38 20 59958756 59958756 + Silent SNP G G T 11LU022_T 11LU022_N G G c.30G>T p.= p.S10S ENST00000348616 1/18 251 209 42 182 182 0 strelka-varscan-mutect CDH26,synonymous_variant,p.=,ENST00000348616,NM_177980.2; T ENST00000348616 Transcript synonymous_variant 330/3182 30/2499 10/832 S tcG/tcT COSM1028655,COSM1028656 1 1 CDH26 HGNC HGNC:15902 protein_coding YES CCDS13485.1 ENSP00000339390 Q8IXH8 UPI000013CB55 NM_177980.2 1/18 Cleavage_site_(Signalp):SignalP-noTM 1,1 LOW 1 SNV 2 1,1 1 PASS rs928943004 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 59958756 59958756 G T 1 0 0 0 0 0 0 0 1 2813 1074 38 1 1 CDH26 20 59958756 Silent SNP G 11LU022_T 2692825 59958756 4485411 952 1590 NTSR1 0 . GRCh38 20 62709239 62709239 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.32C>A p.Pro11Gln p.P11Q ENST00000370501 1/4 103 61 42 110 110 0 strelka-varscan-mutect NTSR1,missense_variant,p.Pro11Gln,ENST00000370501,NM_002531.2; A ENST00000370501 Transcript missense_variant 403/4132 32/1257 11/418 P/Q cCg/cAg 1 1 NTSR1 HGNC HGNC:8039 protein_coding YES CCDS13502.1 ENSP00000359532 P30989 UPI000013D6CF NM_002531.2 tolerated_low_confidence(0.43) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF9 MODERATE 1 SNV 1 1 PASS rs1470757486 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 62709239 62709239 C A 1 0 0 0 0 1 0 0 0 10776 652 23 1 1 NTSR1 20 62709239 Missense_Mutation SNP C 11LU022_T 2750483 62709239 1734928 953 1591 CHRNA4 0 . GRCh38 20 63350532 63350532 + Silent SNP G G T rs371527699 11LU022_T 11LU022_N G G c.879C>A p.= p.T293T ENST00000370263 5/6 752 425 327 1068 1068 0 strelka-varscan-mutect CHRNA4,synonymous_variant,p.=,ENST00000615287,;CHRNA4,synonymous_variant,p.=,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,non_coding_transcript_exon_variant,,ENST00000463705,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,downstream_gene_variant,,ENST00000628665,;CHRNA4,downstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000637628,;CHRNA4,downstream_gene_variant,,ENST00000637243,;CHRNA4,3_prime_UTR_variant,,ENST00000627000,;CHRNA4,3_prime_UTR_variant,,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000630240,;CHRNA4,upstream_gene_variant,,ENST00000631289,; T ENST00000370263 Transcript synonymous_variant 1057/5577 879/1884 293/627 T acC/acA rs371527699 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,Low_complexity_(Seg):seg,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs371527699 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 63350532 63350532 G T 1 0 0 0 0 0 0 0 1 3145 1103 39 1 1 CHRNA4 20 63350532 Silent SNP G 11LU022_T 641293 63350532 1093635 954 1592 TPTE 0 . GRCh38 21 10542426 10542426 + Nonsense_Mutation SNP G G T rs751216471 11LU022_T 11LU022_N G G c.97G>T p.Glu33Ter p.E33* ENST00000618007 6/24 178 163 15 255 255 0 strelka-varscan-mutect TPTE,stop_gained,p.Glu33Ter,ENST00000622113,NM_199259.3;TPTE,stop_gained,p.Glu33Ter,ENST00000618007,NM_199261.3;TPTE,stop_gained,p.Glu33Ter,ENST00000427445,NM_199260.3;TPTE,intron_variant,,ENST00000612746,NM_001290224.1;TPTE,intron_variant,,ENST00000612957,;AL078471.5,non_coding_transcript_exon_variant,,ENST00000612267,; T ENST00000618007 Transcript stop_gained 427/2150 97/1656 33/551 E/* Gag/Tag rs751216471 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 6/24 HIGH 1 SNV 1 1 PASS rs751216471 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 10542426 10542426 G T 1 0 0 0 0 0 1 0 0 16911 1059 37 1 1 TPTE 21 10542426 Nonsense_Mutation SNP G 11LU022_T 10542426 36167557 955 1593 CYYR1 0 . GRCh38 21 26566329 26566334 + In_Frame_Del DEL TAAGAT TAAGAT - novel 11LU022_T 11LU022_N TAAGAT TAAGAT c.108_113delATCTTA p.Lys36_Tyr38delinsAsn p.K36_Y38delinsN ENST00000299340 2/4 101 77 24 191 191 0 sindel-varindel-pindel CYYR1,inframe_deletion,p.Lys36_Tyr38delinsAsn,ENST00000299340,NM_001320768.1,NM_052954.2;CYYR1,inframe_deletion,p.Lys36_Tyr38delinsAsn,ENST00000400043,;CYYR1-AS1,intron_variant,,ENST00000357401,; - ENST00000299340 Transcript inframe_deletion 452-457/3101 108-113/465 36-38/154 KSY/N aaATCTTAc/aac 1 -1 CYYR1 HGNC HGNC:16274 protein_coding YES CCDS13578.1 ENSP00000299340 Q96J86 UPI0000128D80 NM_001320768.1,NM_052954.2 2/4 hmmpanther:PTHR38490,Pfam_domain:PF10873,PD588499 MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 3 26566329 26566329 TAAGAT - 1 0 1 0 1 0 0 0 0 4014 1638 57 0 0 CYYR1 21 26566329 In_Frame_Del DEL TAAGAT 11LU022_T 16023903 26566329 20143654 956 1594 ADAMTS5 0 . GRCh38 21 26965451 26965451 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.941C>A p.Ala314Asp p.A314D ENST00000284987 1/8 213 160 53 314 314 0 strelka-varscan-mutect ADAMTS5,missense_variant,p.Ala314Asp,ENST00000284987,NM_007038.3; T ENST00000284987 Transcript missense_variant 1063/9056 941/2793 314/930 A/D gCc/gAc 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 deleterious(0) 1/8 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 26965451 26965451 G T 1 0 0 0 0 1 0 0 0 313 1203 42 2 2 ADAMTS5 21 26965451 Missense_Mutation SNP G 11LU022_T 399122 26965451 19744532 957 1595 KRTAP13-4 0 . GRCh38 21 30430503 30430503 + Silent SNP C C A novel 11LU022_T 11LU022_N C C c.228C>A p.= p.P76P ENST00000334068 1/1 122 83 39 160 160 0 strelka-varscan-mutect KRTAP13-4,synonymous_variant,p.=,ENST00000334068,NM_181600.1;KRTAP13-3,upstream_gene_variant,,ENST00000390690,NM_181622.1; A ENST00000334068 Transcript synonymous_variant 274/797 228/483 76/160 P ccC/ccA 1 1 KRTAP13-4 HGNC HGNC:18926 protein_coding YES CCDS13592.1 ENSP00000334834 Q3LI77 UPI000003B46D NM_181600.1 1/1 Pfam_domain:PF05287,hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF10 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 30430503 30430503 C A 1 0 0 0 0 0 0 0 1 8408 668 24 2 2 KRTAP13-4 21 30430503 Silent SNP C 11LU022_T 3465052 30430503 16279480 958 1596 KRTAP13-4 0 . GRCh38 21 30430656 30430656 + Nonsense_Mutation SNP C C A rs776369477 11LU022_T 11LU022_N C C c.381C>A p.Tyr127Ter p.Y127* ENST00000334068 1/1 129 97 32 184 184 0 strelka-varscan-mutect KRTAP13-4,stop_gained,p.Tyr127Ter,ENST00000334068,NM_181600.1;KRTAP13-3,upstream_gene_variant,,ENST00000390690,NM_181622.1; A ENST00000334068 Transcript stop_gained 427/797 381/483 127/160 Y/* taC/taA rs776369477,COSM261727 1 1 KRTAP13-4 HGNC HGNC:18926 protein_coding YES CCDS13592.1 ENSP00000334834 Q3LI77 UPI000003B46D NM_181600.1 1/1 Pfam_domain:PF05287,hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF10 0,1 HIGH 1 SNV 0,1 1 PASS rs776369477 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 30430656 30430656 C A 1 0 0 0 0 0 1 0 0 8408 547 19 1 1 KRTAP13-4 21 30430656 Nonsense_Mutation SNP C 11LU022_T 153 30430656 16279327 959 1597 CLDN14 0 . GRCh38 21 36461680 36461680 + Missense_Mutation SNP C C A rs202117396 11LU022_T 11LU022_N C C c.16G>T p.Val6Leu p.V6L ENST00000399137 3/3 166 122 44 219 219 0 strelka-varscan-mutect CLDN14,missense_variant,p.Val6Leu,ENST00000399137,NM_144492.2;CLDN14,missense_variant,p.Val6Leu,ENST00000399135,NM_001146079.1;CLDN14,missense_variant,p.Val6Leu,ENST00000342108,NM_001146077.1;CLDN14,missense_variant,p.Val6Leu,ENST00000399136,NM_001146078.2;CLDN14,missense_variant,p.Val6Leu,ENST00000399139,NM_012130.3;AP000695.6,intron_variant,,ENST00000429588,;AP000695.4,intron_variant,,ENST00000428667,;AP000695.4,downstream_gene_variant,,ENST00000454980,; A ENST00000399137 Transcript missense_variant 883/1942 16/720 6/239 V/L Gtg/Ttg rs202117396 1 -1 CLDN14 HGNC HGNC:2035 protein_coding YES CCDS13645.1 ENSP00000382090 O95500 UPI0000048F0B NM_144492.2 tolerated(1) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR12002:SF99,hmmpanther:PTHR12002,Pfam_domain:PF00822 MODERATE 1 SNV 1 1 PASS rs202117396 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 36461680 36461680 C A 1 0 0 0 0 1 0 0 0 3239 536 19 1 1 CLDN14 21 36461680 Missense_Mutation SNP C 11LU022_T 6031024 36461680 10248303 960 1598 AIRE 0 . GRCh38 21 44289676 44289676 + Silent SNP C C A rs200611273 11LU022_T 11LU022_N C C c.672C>A p.= p.I224I ENST00000291582 6/14 131 97 34 240 239 1 strelka-varscan-mutect AIRE,synonymous_variant,p.=,ENST00000291582,NM_000383.3;AIRE,non_coding_transcript_exon_variant,,ENST00000530812,;AIRE,non_coding_transcript_exon_variant,,ENST00000527919,;AIRE,upstream_gene_variant,,ENST00000337909,;AIRE,upstream_gene_variant,,ENST00000397994,; A ENST00000291582 Transcript synonymous_variant 799/2257 672/1638 224/545 I atC/atA rs200611273 1 1 AIRE HGNC HGNC:360 protein_coding YES CCDS13706.1 ENSP00000291582 O43918 UPI0000030FA6 NM_000383.3 6/14 Gene3D:3.10.390.10,Pfam_domain:PF01342,Prints_domain:PR01711,PROSITE_profiles:PS50864,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF15,SMART_domains:SM00258,Superfamily_domains:SSF63763 LOW 1 SNV 1 1 PASS rs200611273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 44289676 44289676 C A 1 0 0 0 0 0 0 0 1 514 845 30 2 2 AIRE 21 44289676 Silent SNP C 11LU022_T 7827996 44289676 2420307 961 1599 CCT8L2 0 . GRCh38 22 16591185 16591185 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1366G>T p.Ala456Ser p.A456S ENST00000359963 1/1 265 202 63 435 433 2 strelka-varscan-mutect CCT8L2,missense_variant,p.Ala456Ser,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; A ENST00000359963 Transcript missense_variant 1626/2060 1366/1674 456/557 A/S Gca/Tca 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 tolerated(0.32) 1/1 Gene3D:1.10.560.10,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100,Superfamily_domains:SSF48592 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 16591185 16591185 C A 1 0 0 0 0 1 0 0 0 2662 710 25 2 2 CCT8L2 22 16591185 Missense_Mutation SNP C 11LU022_T 16591185 34227283 962 1600 CCT8L2 0 . GRCh38 22 16591349 16591349 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.1202A>T p.Gln401Leu p.Q401L ENST00000359963 1/1 279 211 68 458 458 0 strelka-varscan-mutect CCT8L2,missense_variant,p.Gln401Leu,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; A ENST00000359963 Transcript missense_variant 1462/2060 1202/1674 401/557 Q/L cAg/cTg 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 tolerated(0.33) 1/1 Gene3D:3.30.260.10,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100,Superfamily_domains:SSF54849 MODERATE 1 SNV 1 PASS rs1318404497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 16591349 16591349 T A 1 0 0 0 0 1 0 0 0 2662 1580 55 4 4 CCT8L2 22 16591349 Missense_Mutation SNP T 11LU022_T 164 16591349 34227119 963 1601 MICAL3 0 . GRCh38 22 17817392 17817392 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.5269G>C p.Asp1757His p.D1757H ENST00000441493 26/32 244 156 88 354 354 0 strelka-varscan-mutect MICAL3,missense_variant,p.Asp1757His,ENST00000441493,NM_015241.2;MICAL3,missense_variant,p.Asp34His,ENST00000577821,;MICAL3,missense_variant,p.Asp12His,ENST00000579997,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000580469,; G ENST00000441493 Transcript missense_variant 5622/9445 5269/6009 1757/2002 D/H Gac/Cac 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 tolerated_low_confidence(0.16) 26/32 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1006225019 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 17817392 17817392 C G 1 0 0 0 0 1 0 0 0 9528 884 31 4 4 MICAL3 22 17817392 Missense_Mutation SNP C 11LU022_T 1226043 17817392 33001076 964 1602 SDF2L1 0 . GRCh38 22 21643965 21643965 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.456G>T p.Gln152His p.Q152H ENST00000248958 3/3 314 211 103 459 459 0 strelka-varscan-mutect SDF2L1,missense_variant,p.Gln152His,ENST00000248958,NM_022044.2;KB-1440D3.14,downstream_gene_variant,,ENST00000609038,;SDF2L1,downstream_gene_variant,,ENST00000466935,; T ENST00000248958 Transcript missense_variant 532/865 456/666 152/221 Q/H caG/caT 1 1 SDF2L1 HGNC HGNC:10676 protein_coding YES CCDS13792.1 ENSP00000248958 Q9HCN8 UPI0000048F31 NM_022044.2 deleterious(0.04) 3/3 Gene3D:2.80.10.50,Pfam_domain:PF02815,PROSITE_profiles:PS50919,hmmpanther:PTHR10050,hmmpanther:PTHR10050:SF9,SMART_domains:SM00472,Superfamily_domains:SSF82109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 21643965 21643965 G T 1 0 0 0 0 1 0 0 0 14233 962 34 2 2 SDF2L1 22 21643965 Missense_Mutation SNP G 11LU022_T 3826573 21643965 29174503 965 1603 ZNF280A 0 . GRCh38 22 22515117 22515117 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.514G>A p.Asp172Asn p.D172N ENST00000302097 2/2 226 162 64 273 273 0 strelka-varscan-mutect ZNF280A,missense_variant,p.Asp172Asn,ENST00000302097,NM_080740.4; T ENST00000302097 Transcript missense_variant 767/2148 514/1629 172/542 D/N Gat/Aat 1 -1 ZNF280A HGNC HGNC:18597 protein_coding YES CCDS13800.1 ENSP00000302855 P59817 UPI000011B50C NM_080740.4 tolerated(0.07) 2/2 Pfam_domain:PF13836 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 22515117 22515117 C T 1 0 0 0 0 1 0 0 0 18390 913 32 3 3 ZNF280A 22 22515117 Missense_Mutation SNP C 11LU022_T 871152 22515117 28303351 966 1604 ZNF280A 0 . GRCh38 22 22515326 22515326 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.305C>A p.Pro102Gln p.P102Q ENST00000302097 2/2 270 206 64 336 334 2 strelka-varscan-mutect ZNF280A,missense_variant,p.Pro102Gln,ENST00000302097,NM_080740.4; T ENST00000302097 Transcript missense_variant 558/2148 305/1629 102/542 P/Q cCg/cAg 1 -1 ZNF280A HGNC HGNC:18597 protein_coding YES CCDS13800.1 ENSP00000302855 P59817 UPI000011B50C NM_080740.4 deleterious(0) 2/2 Pfam_domain:PF13836 MODERATE 1 SNV 1 1 PASS rs1480649395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 22515326 22515326 G T 1 0 0 0 0 1 0 0 0 18390 1116 39 1 1 ZNF280A 22 22515326 Missense_Mutation SNP G 11LU022_T 209 22515326 28303142 967 1605 SYN3 0 . GRCh38 22 32596718 32596718 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.730C>A p.Pro244Thr p.P244T ENST00000358763 7/14 120 92 28 171 171 0 strelka-varscan-mutect SYN3,missense_variant,p.Pro244Thr,ENST00000358763,NM_001135774.1,NM_003490.3,NM_133633.2; T ENST00000358763 Transcript missense_variant 973/3126 730/1743 244/580 P/T Ccg/Acg 1 -1 SYN3 HGNC HGNC:11496 protein_coding YES CCDS13908.1 ENSP00000351614 O14994 A0A024R1I8 UPI00001365D3 NM_001135774.1,NM_003490.3,NM_133633.2 deleterious(0) 7/14 hmmpanther:PTHR10841,Pfam_domain:PF02750,Gene3D:3.30.1490.20,Superfamily_domains:SSF56059 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 32596718 32596718 G T 1 0 0 0 0 1 0 0 0 15832 1232 43 2 2 SYN3 22 32596718 Missense_Mutation SNP G 11LU022_T 10081392 32596718 18221750 968 1606 ISX 0 . GRCh38 22 35085659 35085659 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.704C>A p.Pro235His p.P235H ENST00000308700 4/4 250 183 67 330 330 0 strelka-varscan-mutect ISX,missense_variant,p.Pro235His,ENST00000308700,;ISX,missense_variant,p.Pro235His,ENST00000404699,NM_001303508.1; A ENST00000308700 Transcript missense_variant 1656/3384 704/738 235/245 P/H cCc/cAc 1 1 ISX HGNC HGNC:28084 protein_coding YES CCDS33640.1 ENSP00000311492 Q2M1V0 UPI00001BE8E5 deleterious(0) 4/4 hmmpanther:PTHR24329:SF362,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS rs1357492807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 35085659 35085659 C A 1 0 0 0 0 1 0 0 0 7773 623 22 2 2 ISX 22 35085659 Missense_Mutation SNP C 11LU022_T 2488941 35085659 15732809 969 1607 APOL5 0 . GRCh38 22 35726820 35726820 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.752C>T p.Ser251Phe p.S251F ENST00000249044 3/5 163 117 46 257 257 0 strelka-varscan-mutect APOL5,missense_variant,p.Ser251Phe,ENST00000249044,NM_030642.1; T ENST00000249044 Transcript missense_variant 752/1438 752/1302 251/433 S/F tCc/tTc 1 1 APOL5 HGNC HGNC:14869 protein_coding YES CCDS13920.1 ENSP00000249044 Q9BWW9 UPI0000125C99 NM_030642.1 deleterious(0.01) 3/5 hmmpanther:PTHR14096:SF6,hmmpanther:PTHR14096,Pfam_domain:PF05461 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 35726820 35726820 C T 1 0 0 0 0 1 0 0 0 931 855 30 3 3 APOL5 22 35726820 Missense_Mutation SNP C 11LU022_T 641161 35726820 15091648 970 1608 CYTH4 0 . GRCh38 22 37311028 37311028 + Silent SNP G G C novel 11LU022_T 11LU022_N G G c.849G>C p.= p.L283L ENST00000248901 10/13 116 87 29 177 177 0 strelka-varscan-mutect CYTH4,synonymous_variant,p.=,ENST00000248901,NM_001318024.1,NM_013385.3;CYTH4,synonymous_variant,p.=,ENST00000446506,;CYTH4,non_coding_transcript_exon_variant,,ENST00000462927,; C ENST00000248901 Transcript synonymous_variant 1036/3206 849/1185 283/394 L ctG/ctC 1 1 CYTH4 HGNC HGNC:9505 protein_coding YES CCDS13946.1 ENSP00000248901 Q9UIA0 UPI000000D99D NM_001318024.1,NM_013385.3 10/13 PROSITE_profiles:PS50003,hmmpanther:PTHR10663,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 3 37311028 37311028 G C 1 0 0 0 0 0 0 0 1 4011 1277 45 4 4 CYTH4 22 37311028 Silent SNP G 11LU022_T 1584208 37311028 13507440 971 1609 ELFN2 0 . GRCh38 22 37374724 37374724 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.811G>T p.Glu271Ter p.E271* ENST00000402918 3/3 158 106 52 223 223 0 strelka-varscan-mutect ELFN2,stop_gained,p.Glu271Ter,ENST00000402918,NM_052906.4;ELFN2,stop_gained,p.Glu271Ter,ENST00000613079,;ELFN2,intron_variant,,ENST00000430883,;ELFN2,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000451509,;ELFN2,downstream_gene_variant,,ENST00000424973,; A ENST00000402918 Transcript stop_gained 1597/8361 811/2463 271/820 E/* Gag/Tag 1 -1 ELFN2 HGNC HGNC:29396 protein_coding YES CCDS33642.1 ENSP00000385277 Q5R3F8 UPI000004E87D NM_052906.4 3/3 hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367 HIGH SNV 4 1 PASS rs1432979878 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 37374724 37374724 C A 1 0 0 0 0 0 1 0 0 4892 893 31 1 1 ELFN2 22 37374724 Nonsense_Mutation SNP C 11LU022_T 63696 37374724 13443744 972 1610 PICK1 0 . GRCh38 22 38072533 38072533 + Nonsense_Mutation SNP G G T rs200906170 11LU022_T 11LU022_N G G c.613G>T p.Glu205Ter p.E205* ENST00000404072 9/13 217 160 57 397 397 0 strelka-varscan-mutect PICK1,stop_gained,p.Glu205Ter,ENST00000404072,NM_001039584.1,NM_001039583.1;PICK1,stop_gained,p.Glu205Ter,ENST00000356976,NM_012407.3;PICK1,stop_gained,p.Glu205Ter,ENST00000424694,;PICK1,downstream_gene_variant,,ENST00000435166,;PICK1,downstream_gene_variant,,ENST00000437453,;RP5-1039K5.13,intron_variant,,ENST00000445483,;PICK1,downstream_gene_variant,,ENST00000468288,;PICK1,non_coding_transcript_exon_variant,,ENST00000484021,;PICK1,non_coding_transcript_exon_variant,,ENST00000494434,;PICK1,downstream_gene_variant,,ENST00000466374,;PICK1,downstream_gene_variant,,ENST00000432756,;PICK1,downstream_gene_variant,,ENST00000426258,;PICK1,downstream_gene_variant,,ENST00000472724,; T ENST00000404072 Transcript stop_gained 960/2164 613/1248 205/415 E/* Gag/Tag rs200906170,COSM580036 1 1 PICK1 HGNC HGNC:9394 protein_coding YES CCDS13965.1 ENSP00000385205 Q9NRD5 A0A024R1J5 UPI0000131A98 NM_001039584.1,NM_001039583.1 9/13 PROSITE_profiles:PS50870,hmmpanther:PTHR12141:SF1,hmmpanther:PTHR12141,Pfam_domain:PF06456,Gene3D:1.20.1270.60,SMART_domains:SM01015,Superfamily_domains:SSF103657 0,1 HIGH 1 SNV 2 0,1 1 PASS rs200906170 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 38072533 38072533 G T 1 0 0 0 0 0 1 0 0 11971 1059 37 1 1 PICK1 22 38072533 Nonsense_Mutation SNP G 11LU022_T 697809 38072533 12745935 973 1611 ENTHD1 0 . GRCh38 22 39765483 39765483 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.959A>G p.Gln320Arg p.Q320R ENST00000325157 6/7 170 125 45 217 217 0 strelka-varscan-mutect ENTHD1,missense_variant,p.Gln320Arg,ENST00000325157,NM_152512.3; C ENST00000325157 Transcript missense_variant 1210/2710 959/1824 320/607 Q/R cAa/cGa 1 -1 ENTHD1 HGNC HGNC:26352 protein_coding YES CCDS13998.1 ENSP00000317431 Q8IYW4 UPI00000741D2 NM_152512.3 deleterious(0.01) 6/7 hmmpanther:PTHR12276:SF57,hmmpanther:PTHR12276 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 39765483 39765483 T C 1 0 0 0 0 1 0 0 0 4982 1812 63 5 5 ENTHD1 22 39765483 Missense_Mutation SNP T 11LU022_T 1692950 39765483 11052985 974 1612 EFCAB6 0 . GRCh38 22 43671986 43671986 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1627G>A p.Ala543Thr p.A543T ENST00000262726 15/32 73 48 25 101 101 0 strelka-varscan-mutect EFCAB6,missense_variant,p.Ala543Thr,ENST00000262726,NM_022785.3;EFCAB6,missense_variant,p.Ala391Thr,ENST00000396231,NM_198856.2;EFCAB6,non_coding_transcript_exon_variant,,ENST00000468552,; T ENST00000262726 Transcript missense_variant 1881/4869 1627/4506 543/1501 A/T Gca/Aca 1 -1 EFCAB6 HGNC HGNC:24204 protein_coding YES CCDS14049.1 ENSP00000262726 Q5THR3 UPI0000225CD7 NM_022785.3 deleterious(0.02) 15/32 Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 2 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999834 1 1 1 0 T 3 4 3 43671986 43671986 C T 1 0 0 0 0 1 0 0 0 4773 710 25 3 3 EFCAB6 22 43671986 Missense_Mutation SNP C 11LU022_T 3906503 43671986 7146482 975 1613 PHF21B 0 . GRCh38 22 44920484 44920484 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.127G>A p.Gly43Arg p.G43R ENST00000313237 3/13 115 87 28 201 201 0 strelka-varscan-mutect PHF21B,missense_variant,p.Gly43Arg,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Gly31Arg,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Gly43Arg,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Gly31Arg,ENST00000420689,;PHF21B,5_prime_UTR_variant,,ENST00000403565,NM_001284296.1;PHF21B,intron_variant,,ENST00000414269,;PHF21B,non_coding_transcript_exon_variant,,ENST00000490679,;PHF21B,non_coding_transcript_exon_variant,,ENST00000460507,;PHF21B,non_coding_transcript_exon_variant,,ENST00000474327,; T ENST00000313237 Transcript missense_variant 278/3671 127/1596 43/531 G/R Gga/Aga 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious(0) 3/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 44920484 44920484 C T 1 0 0 0 0 1 0 0 0 11920 632 22 3 3 PHF21B 22 44920484 Missense_Mutation SNP C 11LU022_T 1248498 44920484 5897984 976 1614 EGFL6 0 . GRCh38 X 13633024 13633024 + Nonsense_Mutation SNP G G T rs774018380 11LU022_T 11LU022_N G G c.1594G>T p.Glu532Ter p.E532* ENST00000380602 12/12 111 66 45 106 106 0 strelka-varscan-mutect EGFL6,stop_gained,p.Glu531Ter,ENST00000361306,NM_015507.3;EGFL6,stop_gained,p.Glu532Ter,ENST00000380602,NM_001167890.1; T ENST00000380602 Transcript stop_gained 1834/2385 1594/1665 532/554 E/* Gaa/Taa rs774018380,COSM4529206,COSM4529207 1 1 EGFL6 HGNC HGNC:3235 protein_coding YES CCDS55370.1 ENSP00000369976 Q8IUX8 UPI0000034CAE NM_001167890.1 12/12 Pfam_domain:PF00629,PROSITE_profiles:PS50060,hmmpanther:PTHR24050,hmmpanther:PTHR24050:SF18,SMART_domains:SM00137,Superfamily_domains:SSF49899 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs774018380 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 3 13633024 13633024 G T 1 0 0 0 0 0 1 0 0 4799 1059 37 1 1 EGFL6 23 13633024 Nonsense_Mutation SNP G 11LU022_T 13633024 142407871 977 1615 BEND2 0 . GRCh38 X 18171016 18171016 + Missense_Mutation SNP T T C novel 11LU022_T 11LU022_N T T c.2170A>G p.Ile724Val p.I724V ENST00000380033 13/14 150 88 62 145 145 0 strelka-varscan-mutect BEND2,missense_variant,p.Ile724Val,ENST00000380033,NM_153346.4;BEND2,missense_variant,p.Ile633Val,ENST00000380030,NM_001184767.1; C ENST00000380033 Transcript missense_variant 2303/4611 2170/2400 724/799 I/V Att/Gtt 1 -1 BEND2 HGNC HGNC:28509 protein_coding YES CCDS14184.1 ENSP00000369372 Q8NDZ0 UPI000013FE0F NM_153346.4 deleterious(0.01) 13/14 PROSITE_profiles:PS51457,hmmpanther:PTHR16213:SF35,hmmpanther:PTHR16213,Pfam_domain:PF10523,SMART_domains:SM01025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 18171016 18171016 T C 1 0 0 0 0 1 0 0 0 1546 1435 50 5 5 BEND2 23 18171016 Missense_Mutation SNP T 11LU022_T 4537992 18171016 137869879 978 1616 ZFX 0 . GRCh38 X 24208347 24208347 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.1070C>T p.Pro357Leu p.P357L ENST00000379177 9/11 112 90 22 115 115 0 strelka-varscan-mutect ZFX,missense_variant,p.Pro357Leu,ENST00000379177,NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3;ZFX,missense_variant,p.Pro396Leu,ENST00000379188,;ZFX,missense_variant,p.Pro128Leu,ENST00000539115,NM_001178086.1;ZFX,missense_variant,p.Pro357Leu,ENST00000304543,;ZFX,missense_variant,p.Pro307Leu,ENST00000338565,;ZFX,intron_variant,,ENST00000459724,; T ENST00000379177 Transcript missense_variant 1497/7558 1070/2418 357/805 P/L cCg/cTg 1 1 ZFX HGNC HGNC:12869 protein_coding YES CCDS14211.1 ENSP00000368475 P17010 A0A024RC04 UPI000013C504 NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3 tolerated(0.06) 9/11 hmmpanther:PTHR24387:SF222,hmmpanther:PTHR24387,Pfam_domain:PF04704 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 24208347 24208347 C T 1 0 0 0 0 1 0 0 0 18239 652 23 1 1 ZFX 23 24208347 Missense_Mutation SNP C 11LU022_T 6037331 24208347 131832548 979 1617 FAM47A 0 . GRCh38 X 34130820 34130820 + Silent SNP G G T 11LU022_T 11LU022_N G G c.1459C>A p.= p.R487R ENST00000346193 1/1 31 22 9 30 30 0 strelka-varscan-mutect FAM47A,synonymous_variant,p.=,ENST00000346193,NM_203408.3;FAM47A,synonymous_variant,p.=,ENST00000613251,; T ENST00000346193 Transcript synonymous_variant 1492/2556 1459/2376 487/791 R Cgg/Agg COSM5587775 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 Pfam_domain:PF14642 1 LOW 1 SNV 1 1 PASS rs1173809696 . 0 207 3 0 0 0 0 0 -19.99996 1 1 1 1 0 T 2 4 3 34130820 34130820 G T 1 0 0 0 0 0 0 0 1 5447 1057 37 1 1 FAM47A 23 34130820 Silent SNP G 11LU022_T 9922473 34130820 121910075 980 1618 MAGEB16 0 . GRCh38 X 35802456 35802456 + Missense_Mutation SNP C C G novel 11LU022_T 11LU022_N C C c.260C>G p.Ser87Cys p.S87C ENST00000399989 2/2 60 33 27 67 67 0 strelka-varscan-mutect MAGEB16,missense_variant,p.Ser87Cys,ENST00000399989,NM_001099921.1;MAGEB16,missense_variant,p.Ser87Cys,ENST00000399987,;MAGEB16,missense_variant,p.Ser119Cys,ENST00000399992,;MAGEB16,missense_variant,p.Ser87Cys,ENST00000399988,;MAGEB16,missense_variant,p.Ser87Cys,ENST00000399985,; G ENST00000399989 Transcript missense_variant 539/1818 260/975 87/324 S/C tCc/tGc 1 1 MAGEB16 HGNC HGNC:21188 protein_coding YES CCDS43927.1 ENSP00000382871 A2A368 UPI00006C1BC1 NM_001099921.1 deleterious(0) 2/2 Pfam_domain:PF12440,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF24,Low_complexity_(Seg):seg,SMART_domains:SM01392 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 3 35802456 35802456 C G 1 0 0 0 0 1 0 0 0 9089 855 30 4 4 MAGEB16 23 35802456 Missense_Mutation SNP C 11LU022_T 1671636 35802456 120238439 981 1619 FAM47C 0 . GRCh38 X 37008981 37008981 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.571C>A p.Pro191Thr p.P191T ENST00000358047 1/1 84 42 42 100 100 0 strelka-varscan-mutect FAM47C,missense_variant,p.Pro191Thr,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript missense_variant 585/3270 571/3108 191/1035 P/T Ccc/Acc 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0.04) 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 37008981 37008981 C A 1 0 0 0 0 1 0 0 0 5449 855 30 2 2 FAM47C 23 37008981 Missense_Mutation SNP C 11LU022_T 1206525 37008981 119031914 982 1620 MED14 0 . GRCh38 X 40712280 40712280 + Missense_Mutation SNP C C A rs759299724 11LU022_T 11LU022_N C C c.795G>T p.Leu265Phe p.L265F ENST00000324817 7/31 64 33 31 67 67 0 strelka-varscan-mutect MED14,missense_variant,p.Leu265Phe,ENST00000324817,NM_004229.3;MED14,downstream_gene_variant,,ENST00000492219,;MED14,downstream_gene_variant,,ENST00000482034,; A ENST00000324817 Transcript missense_variant 914/7984 795/4365 265/1454 L/F ttG/ttT rs759299724 1 -1 MED14 HGNC HGNC:2370 protein_coding YES CCDS14254.1 ENSP00000323720 O60244 UPI00001414B1 NM_004229.3 deleterious(0) 7/31 hmmpanther:PTHR12809 MODERATE 1 SNV 1 1 PASS rs759299724 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 40712280 40712280 C A 1 0 0 0 0 1 0 0 0 9371 593 21 2 2 MED14 23 40712280 Missense_Mutation SNP C 11LU022_T 3703299 40712280 115328615 983 1621 NYX 0 . GRCh38 X 41474012 41474012 + Missense_Mutation SNP G G T 11LU022_T 11LU022_N G G c.559G>T p.Ala187Ser p.A187S ENST00000342595 2/2 88 43 45 52 52 0 strelka-varscan-mutect NYX,missense_variant,p.Ala187Ser,ENST00000342595,NM_022567.2;NYX,missense_variant,p.Ala187Ser,ENST00000378220,;NYX,downstream_gene_variant,,ENST00000486842,;RP1-169I5.4,upstream_gene_variant,,ENST00000451718,; T ENST00000342595 Transcript missense_variant 1015/2713 559/1446 187/481 A/S Gcg/Tcg CP005303 1 1 NYX HGNC HGNC:8082 protein_coding YES CCDS14256.1 ENSP00000340328 Q9GZU5 UPI0000130B37 NM_022567.2 deleterious(0.01) 2/2 Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 41474012 41474012 G T 1 0 0 0 0 1 0 0 0 10875 1087 38 1 1 NYX 23 41474012 Missense_Mutation SNP G 11LU022_T 761732 41474012 114566883 984 1622 SSX5 0 . GRCh38 X 48187675 48187675 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.646G>T p.Val216Leu p.V216L ENST00000311798 8/9 101 65 36 121 121 0 strelka-varscan-mutect SSX5,missense_variant,p.Val216Leu,ENST00000311798,NM_021015.3;SSX5,missense_variant,p.Val175Leu,ENST00000347757,NM_175723.1;SSX5,missense_variant,p.Val175Leu,ENST00000376923,;SSX5,missense_variant,p.Val115Leu,ENST00000403001,; A ENST00000311798 Transcript missense_variant 699/1384 646/690 216/229 V/L Gtg/Ttg 1 -1 SSX5 HGNC HGNC:11339 protein_coding YES CCDS14288.1 ENSP00000312415 O60225 UPI000013F201 NM_021015.3 deleterious(0.01) 8/9 hmmpanther:PTHR14112:SF9,hmmpanther:PTHR14112,Pfam_domain:PF09514 MODERATE 1 SNV 5 1 PASS . . 1 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 48187675 48187675 C A 1 0 0 0 0 1 0 0 0 15586 507 18 2 2 SSX5 23 48187675 Missense_Mutation SNP C 11LU022_T 6713663 48187675 107853220 985 1623 SLC38A5 0 . GRCh38 X 48461728 48461728 + Nonsense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.841G>T p.Glu281Ter p.E281* ENST00000595796 11/16 55 30 25 36 36 0 strelka-mutect SLC38A5,stop_gained,p.Glu281Ter,ENST00000595796,;SLC38A5,stop_gained,p.Glu230Ter,ENST00000619100,;SLC38A5,stop_gained,p.Glu147Ter,ENST00000622196,;SLC38A5,stop_gained,p.Glu281Ter,ENST00000620913,NM_033518.3;SLC38A5,downstream_gene_variant,,ENST00000440085,;SLC38A5,downstream_gene_variant,,ENST00000441948,;SLC38A5,downstream_gene_variant,,ENST00000413668,;SLC38A5,downstream_gene_variant,,ENST00000416711,;SLC38A5,downstream_gene_variant,,ENST00000429543,;SLC38A5,downstream_gene_variant,,ENST00000488083,;SLC38A5,intron_variant,,ENST00000497336,;SLC38A5,3_prime_UTR_variant,,ENST00000494034,;SLC38A5,upstream_gene_variant,,ENST00000480105,;SLC38A5,upstream_gene_variant,,ENST00000615300,; A ENST00000595796 Transcript stop_gained 1685/2659 841/1419 281/472 E/* Gag/Tag 1 -1 SLC38A5 HGNC HGNC:18070 protein_coding YES CCDS14293.1 ENSP00000471683 Q8WUX1 A0A024QYY0 UPI000004F5E1 11/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR22950:SF74,hmmpanther:PTHR22950,Pfam_domain:PF01490 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 3 48461728 48461728 C A 1 0 0 0 0 0 1 0 0 14885 864 30 2 2 SLC38A5 23 48461728 Nonsense_Mutation SNP C 11LU022_T 274053 48461728 107579167 986 1624 FTSJ1 0 . GRCh38 X 48481306 48481306 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.432A>G p.= p.T144T ENST00000348411 7/13 312 182 130 404 404 0 strelka-varscan-mutect FTSJ1,synonymous_variant,p.=,ENST00000019019,NM_177439.2;FTSJ1,synonymous_variant,p.=,ENST00000348411,NM_012280.3;FTSJ1,synonymous_variant,p.=,ENST00000396894,NM_001282157.1;FTSJ1,non_coding_transcript_exon_variant,,ENST00000496365,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000490202,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000466371,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000473235,;FTSJ1,intron_variant,,ENST00000492562,;FTSJ1,downstream_gene_variant,,ENST00000487353,;FTSJ1,upstream_gene_variant,,ENST00000467954,;FTSJ1,upstream_gene_variant,,ENST00000489599,;FTSJ1,upstream_gene_variant,,ENST00000475806,;FTSJ1,downstream_gene_variant,,ENST00000485486,; G ENST00000348411 Transcript synonymous_variant 755/1892 432/990 144/329 T acA/acG 1 1 FTSJ1 HGNC HGNC:13254 protein_coding YES CCDS14294.1 ENSP00000326948 Q9UET6 A0A024QYX5 UPI0000001C19 NM_012280.3 7/13 Gene3D:3.40.50.150,HAMAP:MF_01547,HAMAP:MF_03162,Pfam_domain:PF01728,hmmpanther:PTHR10920,hmmpanther:PTHR10920:SF12,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 48481306 48481306 A G 1 0 0 0 0 0 0 0 1 5961 146 6 5 5 FTSJ1 23 48481306 Silent SNP A 11LU022_T 19578 48481306 107559589 987 1625 SYP 0 . GRCh38 X 49191630 49191630 + Missense_Mutation SNP T T A novel 11LU022_T 11LU022_N T T c.749A>T p.Tyr250Phe p.Y250F ENST00000263233 6/7 100 47 53 106 106 0 strelka-varscan-mutect SYP,missense_variant,p.Tyr250Phe,ENST00000263233,NM_003179.2;SYP,missense_variant,p.Tyr250Phe,ENST00000479808,;SYP,missense_variant,p.Tyr140Phe,ENST00000472598,;SYP,3_prime_UTR_variant,,ENST00000376303,;SYP,downstream_gene_variant,,ENST00000469389,;SYP,downstream_gene_variant,,ENST00000466635,; A ENST00000263233 Transcript missense_variant 822/2498 749/942 250/313 Y/F tAc/tTc 1 -1 SYP HGNC HGNC:11506 protein_coding YES CCDS14321.1 ENSP00000263233 P08247 UPI0000117AEC NM_003179.2 tolerated(0.21) 6/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 200 7 2 0 0 0 0 -20 0.9999852 1 1 1 0 A 3 1 3 49191630 49191630 T A 1 0 0 0 0 1 0 0 0 15855 1638 57 4 4 SYP 23 49191630 Missense_Mutation SNP T 11LU022_T 710324 49191630 106849265 988 1626 PHF8 0 . GRCh38 X 53985064 53985064 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.2401G>A p.Val801Met p.V801M ENST00000357988 18/22 132 78 54 120 120 0 strelka-varscan-mutect PHF8,missense_variant,p.Val765Met,ENST00000338154,NM_015107.2;PHF8,missense_variant,p.Val801Met,ENST00000357988,NM_001184896.1;PHF8,missense_variant,p.Val664Met,ENST00000338946,NM_001184897.1;PHF8,missense_variant,p.Val669Met,ENST00000396282,;PHF8,missense_variant,p.Val748Met,ENST00000322659,NM_001184898.1;PHF8,missense_variant,p.Val529Met,ENST00000443302,;PHF8,downstream_gene_variant,,ENST00000494928,; T ENST00000357988 Transcript missense_variant 2760/6024 2401/3183 801/1060 V/M Gtg/Atg 1 -1 PHF8 HGNC HGNC:20672 protein_coding YES CCDS55420.1 ENSP00000350676 Q9UPP1 UPI00001C2071 NM_001184896.1 tolerated(0.12) 18/22 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 53985064 53985064 C T 1 0 0 0 0 1 0 0 0 11927 565 20 3 3 PHF8 23 53985064 Missense_Mutation SNP C 11LU022_T 4793434 53985064 102055831 989 1627 ITIH6 0 . GRCh38 X 54751272 54751272 + Missense_Mutation SNP G G A novel 11LU022_T 11LU022_N G G c.3461C>T p.Ala1154Val p.A1154V ENST00000218436 12/13 141 89 52 164 164 0 strelka-varscan-mutect ITIH6,missense_variant,p.Ala1154Val,ENST00000218436,NM_198510.2; A ENST00000218436 Transcript missense_variant 3491/4968 3461/3942 1154/1313 A/V gCc/gTc 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 tolerated(0.09) 12/13 Pfam_domain:PF06668,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 54751272 54751272 G A 1 0 0 0 0 1 0 0 0 7814 1203 42 3 3 ITIH6 23 54751272 Missense_Mutation SNP G 11LU022_T 766208 54751272 101289623 990 1628 ZXDB 0 . GRCh38 X 57592500 57592500 + Missense_Mutation SNP C C T novel 11LU022_T 11LU022_N C C c.452C>T p.Pro151Leu p.P151L ENST00000374888 1/1 116 106 10 120 120 0 varscan-mutect ZXDB,missense_variant,p.Pro151Leu,ENST00000374888,NM_007157.3; T ENST00000374888 Transcript missense_variant 849/5894 452/2412 151/803 P/L cCc/cTc 1 1 ZXDB HGNC HGNC:13199 protein_coding YES CCDS35313.1 ENSP00000364023 P98169 UPI000013C495 NM_007157.3 tolerated_low_confidence(0.06) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF85 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -19.60213 1 1 1 1 0 T 3 4 3 57592500 57592500 C T 1 0 0 0 0 1 0 0 0 18854 623 22 3 3 ZXDB 23 57592500 Missense_Mutation SNP C 11LU022_T 2841228 57592500 98448395 991 1629 STARD8 0 . GRCh38 X 68718070 68718070 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1156G>T p.Ala386Ser p.A386S ENST00000374599 6/15 122 53 69 129 127 2 strelka-varscan-mutect STARD8,missense_variant,p.Ala306Ser,ENST00000252336,NM_014725.4;STARD8,missense_variant,p.Ala386Ser,ENST00000374599,NM_001142503.2;STARD8,missense_variant,p.Ala306Ser,ENST00000374597,NM_001142504.2;STARD8,3_prime_UTR_variant,,ENST00000523864,; T ENST00000374599 Transcript missense_variant 1271/4841 1156/3312 386/1103 A/S Gct/Tct 1 1 STARD8 HGNC HGNC:19161 protein_coding YES CCDS48134.1 ENSP00000363727 Q92502 UPI00002122B9 NM_001142503.2 tolerated(0.1) 6/15 hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF3 MODERATE 1 SNV 1 1 PASS rs1314566732 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 68718070 68718070 G T 1 0 0 0 0 1 0 0 0 15638 1319 46 2 2 STARD8 23 68718070 Missense_Mutation SNP G 11LU022_T 11125570 68718070 87322825 992 1630 DGAT2L6 0 . GRCh38 X 70204405 70204406 + Frame_Shift_Ins INS - - A novel 11LU022_T 11LU022_N - - c.749dupA p.Asp251GlyfsTer47 p.D251Gfs*47 ENST00000333026 6/7 202 80 122 194 194 0 sindel-varindel-pindel DGAT2L6,frameshift_variant,p.Asp251GlyfsTer47,ENST00000333026,NM_198512.2; A ENST00000333026 Transcript frameshift_variant 848-849/1553 748-749/1014 250/337 Q/QX cag/cAag 1 1 DGAT2L6 HGNC HGNC:23250 protein_coding YES CCDS14397.1 ENSP00000328036 Q6ZPD8 UPI00001C10BF NM_198512.2 6/7 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF19 HIGH 1 insertion 2 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 7 5 3 70204405 70204405 - A 1 0 1 1 0 0 0 0 0 4266 595 21 0 0 DGAT2L6 23 70204405 Frame_Shift_Ins INS - 11LU022_T 1486335 70204405 85836490 993 1631 MED12 0 . GRCh38 X 71121762 71121762 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1047G>T p.= p.L349L ENST00000374080 7/45 75 62 13 83 83 0 strelka-varscan-mutect MED12,synonymous_variant,p.=,ENST00000333646,;MED12,synonymous_variant,p.=,ENST00000374102,;MED12,synonymous_variant,p.=,ENST00000374080,NM_005120.2;MED12,downstream_gene_variant,,ENST00000429213,;MED12,upstream_gene_variant,,ENST00000462984,;MED12,upstream_gene_variant,,ENST00000471663,; T ENST00000374080 Transcript synonymous_variant 1079/6795 1047/6534 349/2177 L ctG/ctT 1 1 MED12 HGNC HGNC:11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 UPI00004257E2 NM_005120.2 7/45 Pfam_domain:PF12145,hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF24 LOW 1 SNV 1 1 PASS rs990639258 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 71121762 71121762 G T 1 0 0 0 0 0 0 0 1 9367 1306 46 2 2 MED12 23 71121762 Silent SNP G 11LU022_T 917357 71121762 84919133 994 1632 ITGB1BP2 0 . GRCh38 X 71305047 71305047 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.899G>T p.Trp300Leu p.W300L ENST00000373829 11/11 168 74 94 152 152 0 strelka-varscan-mutect ITGB1BP2,missense_variant,p.Trp282Leu,ENST00000538820,;ITGB1BP2,missense_variant,p.Trp300Leu,ENST00000373829,NM_012278.2;NONO,downstream_gene_variant,,ENST00000535149,NM_001145410.1;NONO,downstream_gene_variant,,ENST00000276079,NM_007363.4;NONO,downstream_gene_variant,,ENST00000373841,NM_001145409.1;NONO,downstream_gene_variant,,ENST00000373856,NM_001145408.1;NONO,downstream_gene_variant,,ENST00000490044,;NONO,downstream_gene_variant,,ENST00000473525,;ITGB1BP2,downstream_gene_variant,,ENST00000465388,;NONO,downstream_gene_variant,,ENST00000474431,;ITGB1BP2,downstream_gene_variant,,ENST00000475413,;ITGB1BP2,downstream_gene_variant,,ENST00000483897,;NONO,downstream_gene_variant,,ENST00000472185,; T ENST00000373829 Transcript missense_variant 972/1296 899/1044 300/347 W/L tGg/tTg 1 1 ITGB1BP2 HGNC HGNC:6154 protein_coding YES CCDS14411.1 ENSP00000362935 Q9UKP3 UPI000000103C NM_012278.2 deleterious(0) 11/11 PROSITE_profiles:PS51203,hmmpanther:PTHR12621:SF8,hmmpanther:PTHR12621,Gene3D:2.60.40.790,Superfamily_domains:SSF49764 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 71305047 71305047 G T 1 0 0 0 0 1 0 0 0 7799 1357 47 2 2 ITGB1BP2 23 71305047 Missense_Mutation SNP G 11LU022_T 183285 71305047 84735848 995 1633 P2RY10 0 . GRCh38 X 78961212 78961212 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.692C>A p.Ala231Asp p.A231D ENST00000171757 4/4 146 55 91 106 106 0 strelka-varscan-mutect P2RY10,missense_variant,p.Ala231Asp,ENST00000171757,NM_014499.2;P2RY10,missense_variant,p.Ala231Asp,ENST00000544091,NM_198333.1;P2RY10,downstream_gene_variant,,ENST00000475374,;P2RY10,downstream_gene_variant,,ENST00000461541,; A ENST00000171757 Transcript missense_variant 972/1714 692/1020 231/339 A/D gCt/gAt 1 1 P2RY10 HGNC HGNC:19906 protein_coding YES CCDS14442.1 ENSP00000171757 O00398 UPI0000050471 NM_014499.2 tolerated(0.32) 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF47,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 78961212 78961212 C A 1 0 0 0 0 1 0 0 0 11420 797 28 2 2 P2RY10 23 78961212 Missense_Mutation SNP C 11LU022_T 7656165 78961212 77079683 996 1634 KLHL4 0 . GRCh38 X 87632383 87632383 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.1498G>T p.Gly500Cys p.G500C ENST00000373114 7/11 50 25 25 48 48 0 strelka-varscan-mutect KLHL4,missense_variant,p.Gly500Cys,ENST00000373119,NM_019117.4;KLHL4,missense_variant,p.Gly500Cys,ENST00000373114,NM_057162.2; T ENST00000373114 Transcript missense_variant 1578/2445 1498/2163 500/720 G/C Ggc/Tgc 1 1 KLHL4 HGNC HGNC:6355 protein_coding YES CCDS14456.1 ENSP00000362206 Q9C0H6 UPI000002ACC4 NM_057162.2 deleterious(0.02) 7/11 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF74,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 87632383 87632383 G T 1 0 0 0 0 1 0 0 0 8257 1348 47 2 2 KLHL4 23 87632383 Missense_Mutation SNP G 11LU022_T 8671171 87632383 68408512 997 1635 PCDH11X 0 . GRCh38 X 92618580 92618580 + Silent SNP T T A 11LU022_T 11LU022_N T T c.3684T>A p.= p.A1228A ENST00000373094 7/7 499 268 231 480 480 0 strelka-varscan-mutect PCDH11X,synonymous_variant,p.=,ENST00000373094,NM_032968.4;PCDH11X,synonymous_variant,p.=,ENST00000373097,NM_032969.4;PCDH11X,synonymous_variant,p.=,ENST00000406881,NM_001168360.1;PCDH11X,synonymous_variant,p.=,ENST00000361655,NM_001168363.1;PCDH11X,synonymous_variant,p.=,ENST00000373088,NM_001168362.1;PCDH11X,3_prime_UTR_variant,,ENST00000504220,NM_001168361.1; A ENST00000373094 Transcript synonymous_variant 4529/9179 3684/4044 1228/1347 A gcT/gcA COSM1636633 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 7/7 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 3 92618580 92618580 T A 1 0 0 0 0 0 0 0 1 11595 1509 53 4 4 PCDH11X 23 92618580 Silent SNP T 11LU022_T 4986197 92618580 63422315 998 1636 BHLHB9 0 . GRCh38 X 102749106 102749106 + Silent SNP A A T novel 11LU022_T 11LU022_N A A c.111A>T p.= p.V37V ENST00000372735 4/4 122 57 65 98 98 0 strelka-varscan-mutect BHLHB9,synonymous_variant,p.=,ENST00000372735,;BHLHB9,synonymous_variant,p.=,ENST00000457056,NM_001142528.1,NM_001142527.1,NM_001142525.1,NM_001142526.1,NM_001142524.1;BHLHB9,synonymous_variant,p.=,ENST00000447531,NM_001142529.1;BHLHB9,synonymous_variant,p.=,ENST00000361229,NM_030639.2;BHLHB9,synonymous_variant,p.=,ENST00000448867,NM_001142530.1;BHLHB9,downstream_gene_variant,,ENST00000483294,;BHLHB9,downstream_gene_variant,,ENST00000486988,; T ENST00000372735 Transcript synonymous_variant 696/5130 111/1644 37/547 V gtA/gtT 1 1 BHLHB9 HGNC HGNC:29353 protein_coding YES CCDS14502.1 ENSP00000361820 Q6PI77 UPI00001C1D50 4/4 hmmpanther:PTHR15712:SF18,hmmpanther:PTHR15712 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 102749106 102749106 A T 1 0 0 0 0 0 0 0 1 1568 407 15 4 4 BHLHB9 23 102749106 Silent SNP A 11LU022_T 10130526 102749106 53291789 999 1637 NRK 0 . GRCh38 X 105898624 105898624 + Silent SNP A A G novel 11LU022_T 11LU022_N A A c.621A>G p.= p.G207G ENST00000243300 8/29 93 76 17 76 76 0 strelka-varscan-mutect NRK,synonymous_variant,p.=,ENST00000243300,NM_198465.3;NRK,downstream_gene_variant,,ENST00000536164,;NRK,synonymous_variant,p.=,ENST00000428173,; G ENST00000243300 Transcript synonymous_variant 924/8062 621/4749 207/1582 G ggA/ggG 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 8/29 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF417,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 3 105898624 105898624 A G 1 0 0 0 0 0 0 0 1 10713 233 9 5 5 NRK 23 105898624 Silent SNP A 11LU022_T 3149518 105898624 50142271 1000 1638 ATG4A 0 . GRCh38 X 108150189 108150189 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.852G>T p.Gln284His p.Q284H ENST00000372232 10/13 90 78 12 83 83 0 strelka-varscan-mutect ATG4A,missense_variant,p.Gln284His,ENST00000372232,NM_001321288.1,NM_052936.3;ATG4A,missense_variant,p.Gln222His,ENST00000345734,NM_178270.2;ATG4A,missense_variant,p.Gln257His,ENST00000394892,;ATG4A,downstream_gene_variant,,ENST00000457035,;ATG4A,non_coding_transcript_exon_variant,,ENST00000489247,;ATG4A,non_coding_transcript_exon_variant,,ENST00000474825,;ATG4A,missense_variant,p.Arg207Ile,ENST00000343524,;ATG4A,3_prime_UTR_variant,,ENST00000372246,NM_178271.2,NM_001321290.1; T ENST00000372232 Transcript missense_variant 1011/2315 852/1197 284/398 Q/H caG/caT 1 1 ATG4A HGNC HGNC:16489 protein_coding YES CCDS14538.1 ENSP00000361306 Q8WYN0 UPI000000DCAF NM_001321288.1,NM_052936.3 deleterious(0) 10/13 Pfam_domain:PF03416,hmmpanther:PTHR22624,hmmpanther:PTHR22624:SF35,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 108150189 108150189 G T 1 0 0 0 0 1 0 0 0 1248 933 33 2 2 ATG4A 23 108150189 Missense_Mutation SNP G 11LU022_T 2251565 108150189 47890706 1001 1639 ALG13 0 . GRCh38 X 111727657 111727657 + Missense_Mutation SNP G G C rs769342903 11LU022_T 11LU022_N G G c.2134G>C p.Glu712Gln p.E712Q ENST00000394780 18/27 55 28 27 56 56 0 strelka-varscan-mutect ALG13,missense_variant,p.Glu634Gln,ENST00000610588,NM_001257231.1;ALG13,missense_variant,p.Glu712Gln,ENST00000394780,NM_001099922.2;ALG13,missense_variant,p.Glu608Gln,ENST00000251943,NM_001324292.1,NM_001257237.1;ALG13,missense_variant,p.Glu608Gln,ENST00000621367,NM_001257230.1,NM_001257234.1;ALG13,missense_variant,p.Glu608Gln,ENST00000436609,;ALG13,missense_variant,p.Glu308Gln,ENST00000623622,;ALG13,non_coding_transcript_exon_variant,,ENST00000486578,;ALG13,non_coding_transcript_exon_variant,,ENST00000460092,;ALG13,downstream_gene_variant,,ENST00000490774,;ALG13,upstream_gene_variant,,ENST00000635824,;ALG13,3_prime_UTR_variant,,ENST00000624161,;ALG13,3_prime_UTR_variant,,ENST00000623144,;ALG13,3_prime_UTR_variant,,ENST00000623148,;ALG13,3_prime_UTR_variant,,ENST00000636363,;ALG13,3_prime_UTR_variant,,ENST00000495283,;ALG13,3_prime_UTR_variant,,ENST00000470971,; C ENST00000394780 Transcript missense_variant 2203/4133 2134/3414 712/1137 E/Q Gag/Cag rs769342903 1 1 ALG13 HGNC HGNC:30881 protein_coding YES CCDS55477.1 ENSP00000378260 Q9NP73 UPI0000E5AFF9 NM_001099922.2 deleterious(0.02) 18/27 hmmpanther:PTHR12867,hmmpanther:PTHR12867:SF5 MODERATE 1 SNV 2 1 PASS rs769342903 . 0 205 3 2 0 0 0 0 -20 0.9999994 1 1 1 0 C 3 2 3 111727657 111727657 G C 1 0 0 0 0 1 0 0 0 615 1175 41 4 4 ALG13 23 111727657 Missense_Mutation SNP G 11LU022_T 3577468 111727657 44313238 1002 1640 DCAF12L1 0 . GRCh38 X 126551325 126551325 + Silent SNP G G T novel 11LU022_T 11LU022_N G G c.1284C>A p.= p.P428P ENST00000371126 1/2 118 72 46 144 144 0 strelka-varscan-mutect DCAF12L1,synonymous_variant,p.=,ENST00000371126,NM_178470.4; T ENST00000371126 Transcript synonymous_variant 1527/3382 1284/1392 428/463 P ccC/ccA 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 1/2 hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 3 126551325 126551325 G T 1 0 0 0 0 0 0 0 1 4065 1335 47 2 2 DCAF12L1 23 126551325 Silent SNP G 11LU022_T 14823668 126551325 29489570 1003 1641 ARHGAP36 0 . GRCh38 X 131081871 131081871 + Missense_Mutation SNP A A C novel 11LU022_T 11LU022_N A A c.206A>C p.His69Pro p.H69P ENST00000276211 2/12 143 126 17 119 119 0 strelka-varscan-mutect ARHGAP36,missense_variant,p.His69Pro,ENST00000276211,NM_144967.3;ARHGAP36,missense_variant,p.His57Pro,ENST00000370922,NM_001282607.1;ARHGAP36,missense_variant,p.His38Pro,ENST00000412432,;ARHGAP36,missense_variant,p.His21Pro,ENST00000423277,;ARHGAP36,upstream_gene_variant,,ENST00000370921,; C ENST00000276211 Transcript missense_variant 551/3083 206/1644 69/547 H/P cAc/cCc 1 1 ARHGAP36 HGNC HGNC:26388 protein_coding YES CCDS14628.1 ENSP00000276211 Q6ZRI8 UPI0000041347 NM_144967.3 tolerated(0.07) 2/12 hmmpanther:PTHR12635 MODERATE 1 SNV 2 1 PASS rs1438016907 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 131081871 131081871 A C 1 0 0 0 0 1 0 0 0 1009 159 6 5 5 ARHGAP36 23 131081871 Missense_Mutation SNP A 11LU022_T 4530546 131081871 24959024 1004 1642 MAP7D3 0 . GRCh38 X 136231684 136231684 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1273G>T p.Ala425Ser p.A425S ENST00000316077 8/19 138 47 91 115 115 0 strelka-varscan-mutect MAP7D3,missense_variant,p.Ala425Ser,ENST00000316077,NM_024597.3;MAP7D3,missense_variant,p.Ala407Ser,ENST00000370663,NM_001173516.1;MAP7D3,missense_variant,p.Ala390Ser,ENST00000370661,NM_001173517.1;MAP7D3,missense_variant,p.Ala384Ser,ENST00000370660,;MAP7D3,upstream_gene_variant,,ENST00000495432,;MAP7D3,upstream_gene_variant,,ENST00000477124,;MAP7D3,upstream_gene_variant,,ENST00000489788,; A ENST00000316077 Transcript missense_variant 1494/4567 1273/2631 425/876 A/S Gcc/Tcc 1 -1 MAP7D3 HGNC HGNC:25742 protein_coding YES CCDS44004.1 ENSP00000318086 Q8IWC1 UPI00001C207C NM_024597.3 tolerated(1) 8/19 hmmpanther:PTHR15073,hmmpanther:PTHR15073:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 136231684 136231684 C A 1 0 0 0 0 1 0 0 0 9193 797 28 2 2 MAP7D3 23 136231684 Missense_Mutation SNP C 11LU022_T 5149813 136231684 19809211 1005 1643 MAP7D3 0 . GRCh38 X 136246134 136246134 + Missense_Mutation SNP T T C rs754689236 11LU022_T 11LU022_N T T c.184A>G p.Met62Val p.M62V ENST00000316077 3/19 97 60 37 94 94 0 strelka-varscan-mutect MAP7D3,missense_variant,p.Met62Val,ENST00000316077,NM_024597.3;MAP7D3,missense_variant,p.Met44Val,ENST00000370663,NM_001173516.1;MAP7D3,missense_variant,p.Met62Val,ENST00000370661,NM_001173517.1;MAP7D3,missense_variant,p.Met62Val,ENST00000370660,; C ENST00000316077 Transcript missense_variant 405/4567 184/2631 62/876 M/V Atg/Gtg rs754689236 1 -1 MAP7D3 HGNC HGNC:25742 protein_coding YES CCDS44004.1 ENSP00000318086 Q8IWC1 UPI00001C207C NM_024597.3 tolerated(1) 3/19 hmmpanther:PTHR15073,hmmpanther:PTHR15073:SF5 MODERATE 1 SNV 1 1 PASS rs754689236 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 136246134 136246134 T C 1 0 0 0 0 1 0 0 0 9193 1464 51 5 5 MAP7D3 23 136246134 Missense_Mutation SNP T 11LU022_T 14450 136246134 19794761 1006 1644 ADGRG4 0 . GRCh38 X 136348153 136348153 + Missense_Mutation SNP G G T rs747707709 11LU022_T 11LU022_N G G c.4447G>T p.Asp1483Tyr p.D1483Y ENST00000394143 6/26 132 111 21 80 80 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Asp1483Tyr,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Asp1483Tyr,ENST00000370652,;ADGRG4,missense_variant,p.Asp1278Tyr,ENST00000394141,; T ENST00000394143 Transcript missense_variant 4738/9931 4447/9243 1483/3080 D/Y Gac/Tac rs747707709,COSM3231487,COSM611198 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 6/26 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747707709 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 136348153 136348153 G T 1 0 0 0 0 1 0 0 0 371 1058 37 1 1 ADGRG4 23 136348153 Missense_Mutation SNP G 11LU022_T 102019 136348153 19692742 1007 1645 F9 0 . GRCh38 X 139561671 139561671 + Missense_Mutation SNP G G C novel 11LU022_T 11LU022_N G G c.986G>C p.Ser329Thr p.S329T ENST00000218099 8/8 86 48 38 79 79 0 strelka-varscan-mutect F9,missense_variant,p.Ser329Thr,ENST00000218099,NM_000133.3;F9,missense_variant,p.Ser291Thr,ENST00000394090,; C ENST00000218099 Transcript missense_variant 993/2780 986/1386 329/461 S/T aGc/aCc 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 tolerated(0.2) 8/8 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001143,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF135,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 3 139561671 139561671 G C 1 0 0 0 0 1 0 0 0 5220 971 34 4 4 F9 23 139561671 Missense_Mutation SNP G 11LU022_T 3213518 139561671 16479224 1008 1646 SPANXN2 0 . GRCh38 X 143712337 143712337 + Missense_Mutation SNP C C A rs782507654 11LU022_T 11LU022_N C C c.241G>T p.Val81Phe p.V81F ENST00000598475 2/2 452 384 68 462 462 0 strelka-varscan-mutect SPANXN2,missense_variant,p.Val81Phe,ENST00000598475,NM_001009615.2; A ENST00000598475 Transcript missense_variant 996/1378 241/543 81/180 V/F Gtc/Ttc rs782507654,COSM2150022,COSM2150023 1 -1 SPANXN2 HGNC HGNC:33175 protein_coding YES CCDS35419.1 ENSP00000470584 Q5MJ10 UPI000049D98C NM_001009615.2 deleterious(0.02) 2/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF5 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782507654 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 143712337 143712337 C A 1 0 0 0 0 1 0 0 0 15322 565 20 2 2 SPANXN2 23 143712337 Missense_Mutation SNP C 11LU022_T 4150666 143712337 12328558 1009 1647 SLITRK2 0 . GRCh38 X 145824592 145824592 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2167C>A p.Leu723Met p.L723M ENST00000370490 1/1 98 80 18 94 93 1 strelka-varscan SLITRK2,missense_variant,p.Leu723Met,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,missense_variant,p.Leu723Met,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; A ENST00000370490 Transcript missense_variant 6422/7672 2167/2538 723/845 L/M Ctg/Atg 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 tolerated(0.19) 1/1 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 145824592 145824592 C A 1 0 0 0 0 1 0 0 0 15034 680 24 2 2 SLITRK2 23 145824592 Missense_Mutation SNP C 11LU022_T 2112255 145824592 10216303 1010 1648 GABRE 0 . GRCh38 X 151955372 151955372 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.1133G>T p.Arg378Leu p.R378L ENST00000370328 8/9 106 60 46 143 143 0 strelka-varscan-mutect GABRE,missense_variant,p.Arg378Leu,ENST00000370328,NM_004961.3;GABRE,downstream_gene_variant,,ENST00000385020,;GABRE,downstream_gene_variant,,ENST00000384889,;GABRE,non_coding_transcript_exon_variant,,ENST00000483564,;GABRE,downstream_gene_variant,,ENST00000462018,;GABRE,non_coding_transcript_exon_variant,,ENST00000486255,;GABRE,non_coding_transcript_exon_variant,,ENST00000489333,;GABRE,intron_variant,,ENST00000495862,;GABRE,downstream_gene_variant,,ENST00000441219,;GABRE,downstream_gene_variant,,ENST00000476016,; A ENST00000370328 Transcript missense_variant 1187/3152 1133/1521 378/506 R/L cGc/cTc 1 -1 GABRE HGNC HGNC:4085 protein_coding YES CCDS14703.1 ENSP00000359353 P78334 UPI00000307E6 NM_004961.3 deleterious(0.04) 8/9 hmmpanther:PTHR18945:SF397,hmmpanther:PTHR18945,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR01723 MODERATE 1 SNV 1 1 PASS rs1337854518 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 151955372 151955372 C A 1 0 0 0 0 1 0 0 0 6041 782 27 1 1 GABRE 23 151955372 Missense_Mutation SNP C 11LU022_T 6130780 151955372 4085523 1011 1649 ZNF275 0 . GRCh38 X 153347413 153347413 + Missense_Mutation SNP G G T novel 11LU022_T 11LU022_N G G c.728G>T p.Ser243Ile p.S243I ENST00000370251 4/5 85 45 40 85 85 0 strelka-mutect ZNF275,missense_variant,p.Ser243Ile,ENST00000370251,NM_001080485.3;ZNF275,missense_variant,p.Ser190Ile,ENST00000370249,;ZNF275,upstream_gene_variant,,ENST00000438239,; T ENST00000370251 Transcript missense_variant 905/6320 728/990 243/329 S/I aGc/aTc 1 1 ZNF275 HGNC HGNC:13069 protein_coding YES ENSP00000359271 A6NFS0 UPI000059DBB5 NM_001080485.3 deleterious(0.01) 4/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF340,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999993 1 1 1 0 T 3 4 3 153347413 153347413 G T 1 0 0 0 0 1 0 0 0 18386 971 34 2 2 ZNF275 23 153347413 Missense_Mutation SNP G 11LU022_T 1392041 153347413 2693482 1012 1650 ATP2B3 0 . GRCh38 X 153558219 153558219 + Missense_Mutation SNP C C A novel 11LU022_T 11LU022_N C C c.2541C>A p.Asp847Glu p.D847E ENST00000263519 15/20 122 103 19 127 127 0 strelka-varscan-mutect ATP2B3,missense_variant,p.Asp833Glu,ENST00000370186,;ATP2B3,missense_variant,p.Asp847Glu,ENST00000263519,NM_001001344.2;ATP2B3,missense_variant,p.Asp847Glu,ENST00000349466,;ATP2B3,missense_variant,p.Asp847Glu,ENST00000359149,NM_021949.3;ATP2B3,missense_variant,p.Asp833Glu,ENST00000393842,;ATP2B3,non_coding_transcript_exon_variant,,ENST00000460549,; A ENST00000263519 Transcript missense_variant 2667/6420 2541/3663 847/1220 D/E gaC/gaA 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 deleterious(0) 15/20 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,TIGRFAM_domain:TIGR01494,Superfamily_domains:0049473,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 3 153558219 153558219 C A 1 0 0 0 0 1 0 0 0 1294 477 17 2 2 ATP2B3 23 153558219 Missense_Mutation SNP C 11LU022_T 210806 153558219 2482676 1013 1651 FAM50A 0 . GRCh38 X 154444287 154444287 + Missense_Mutation SNP A A T novel 11LU022_T 11LU022_N A A c.52A>T p.Met18Leu p.M18L ENST00000393600 1/13 231 196 35 185 185 0 strelka-varscan-mutect FAM50A,missense_variant,p.Met18Leu,ENST00000393600,NM_004699.3;GDI1,downstream_gene_variant,,ENST00000447750,NM_001493.2;FAM50A,upstream_gene_variant,,ENST00000158526,;GDI1,downstream_gene_variant,,ENST00000630693,;GDI1,downstream_gene_variant,,ENST00000465640,;GDI1,downstream_gene_variant,,ENST00000471972,;FAM50A,non_coding_transcript_exon_variant,,ENST00000464419,;FAM50A,non_coding_transcript_exon_variant,,ENST00000481619,;GDI1,downstream_gene_variant,,ENST00000491154,;GDI1,downstream_gene_variant,,ENST00000468483,;GDI1,downstream_gene_variant,,ENST00000476540,;GDI1,downstream_gene_variant,,ENST00000481304,;GDI1,downstream_gene_variant,,ENST00000489589,;GDI1,downstream_gene_variant,,ENST00000434049,;FAM50A,upstream_gene_variant,,ENST00000478509,;GDI1,downstream_gene_variant,,ENST00000445564,;GDI1,downstream_gene_variant,,ENST00000460984,;FAM50A,upstream_gene_variant,,ENST00000490480,; T ENST00000393600 Transcript missense_variant 162/1352 52/1020 18/339 M/L Atg/Ttg 1 1 FAM50A HGNC HGNC:18786 protein_coding YES CCDS14751.1 ENSP00000377225 Q14320 UPI0000138FCD NM_004699.3 tolerated(0.65) 1/13 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12722,hmmpanther:PTHR12722:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 3 154444287 154444287 A T 1 0 0 0 0 1 0 0 0 5453 333 12 4 4 FAM50A 23 154444287 Missense_Mutation SNP A 11LU022_T 886068 154444287 1596608 1014 1652 GPN2 0 . GRCh38 1 26890067 26890067 + Silent SNP G G A 11LU035_T 11LU035_N G G c.30C>T p.= p.F10F ENST00000374135 1/5 28 25 3 65 65 0 strelka-mutect GPN2,synonymous_variant,p.=,ENST00000374135,NM_018066.3;GPN2,synonymous_variant,p.=,ENST00000431781,;GPATCH3,downstream_gene_variant,,ENST00000361720,NM_022078.2;GPN2,upstream_gene_variant,,ENST00000374133,;GPATCH3,downstream_gene_variant,,ENST00000445019,;GPATCH3,downstream_gene_variant,,ENST00000450844,;GPN2,upstream_gene_variant,,ENST00000461282,;GPN2,upstream_gene_variant,,ENST00000477418,; A ENST00000374135 Transcript synonymous_variant 231/4678 30/933 10/310 F ttC/ttT COSM3804827 1 -1 GPN2 HGNC HGNC:25513 protein_coding YES CCDS289.1 ENSP00000363250 Q9H9Y4 UPI0000071F43 NM_018066.3 1/5 hmmpanther:PTHR21231:SF3,hmmpanther:PTHR21231 1 LOW 1 SNV 1 1 1 PASS rs1225759168 . 0 207 3 0 0 0 0 0 -9.478102 1 1 1 1 0 A 2 1 4 26890067 26890067 G A 1 0 0 0 0 0 0 0 1 6520 1049 37 1 1 GPN2 1 26890067 Silent SNP G 11LU035_T 26890067 222066355 1 1653 KIAA0319L 0 . GRCh38 1 35434933 35434933 + Silent SNP G G A 11LU035_T 11LU035_N G G c.3111C>T p.= p.T1037T ENST00000325722 21/21 133 108 25 220 220 0 strelka-varscan-mutect KIAA0319L,synonymous_variant,p.=,ENST00000325722,NM_024874.4;KIAA0319L,synonymous_variant,p.=,ENST00000373266,;KIAA0319L,downstream_gene_variant,,ENST00000426982,;KIAA0319L,downstream_gene_variant,,ENST00000485551,;KIAA0319L,downstream_gene_variant,,ENST00000461312,; A ENST00000325722 Transcript synonymous_variant 3346/4789 3111/3150 1037/1049 T acC/acT COSM3488908 1 -1 KIAA0319L HGNC HGNC:30071 protein_coding YES CCDS390.1 ENSP00000318406 Q8IZA0 UPI000003F081 NM_024874.4 21/21 hmmpanther:PTHR10083:SF166,hmmpanther:PTHR10083 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 35434933 35434933 G A 1 0 0 0 0 0 0 0 1 8081 1219 43 3 3 KIAA0319L 1 35434933 Silent SNP G 11LU035_T 8544866 35434933 213521489 2 1654 PPCS 0 . GRCh38 1 42456883 42456883 + Silent SNP G G T novel 11LU035_T 11LU035_N G G c.318G>T p.= p.R106R ENST00000372561 1/3 317 274 43 445 444 1 strelka-varscan-mutect PPCS,synonymous_variant,p.=,ENST00000372561,NM_024664.3;PPCS,synonymous_variant,p.=,ENST00000372560,;PPCS,intron_variant,,ENST00000372556,;PPCS,intron_variant,,ENST00000372562,NM_001287506.1,NM_001287509.1,NM_001287508.1,NM_001287510.1,NM_001077447.2;ZMYND12,upstream_gene_variant,,ENST00000372565,NM_001146192.1,NM_032257.4;PPCS,non_coding_transcript_exon_variant,,ENST00000472013,;PPCS,non_coding_transcript_exon_variant,,ENST00000471420,;PPCS,upstream_gene_variant,,ENST00000469615,;PPCS,upstream_gene_variant,,ENST00000482168,;ZMYND12,upstream_gene_variant,,ENST00000611861,;ZMYND12,upstream_gene_variant,,ENST00000461083,; T ENST00000372561 Transcript synonymous_variant 325/1431 318/936 106/311 R cgG/cgT 1 1 PPCS HGNC HGNC:25686 protein_coding YES CCDS41311.1 ENSP00000361642 Q9HAB8 UPI000035B21F NM_024664.3 1/3 hmmpanther:PTHR12290,hmmpanther:PTHR12290:SF2,Gene3D:3.40.50.10300,Superfamily_domains:SSF102645 LOW 1 SNV 1 1 PASS rs753011525 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 42456883 42456883 G T 1 0 0 0 0 0 0 0 1 12414 1190 42 2 2 PPCS 1 42456883 Silent SNP G 11LU035_T 7021950 42456883 206499539 3 1655 KTI12 0 . GRCh38 1 52032840 52032840 + Missense_Mutation SNP G G C novel 11LU035_T 11LU035_N G G c.922C>G p.Arg308Gly p.R308G ENST00000371614 1/1 163 139 24 287 287 0 strelka-varscan-mutect KTI12,missense_variant,p.Arg308Gly,ENST00000371614,NM_138417.2;TXNDC12,intron_variant,,ENST00000371626,NM_015913.3;TXNDC12,downstream_gene_variant,,ENST00000610127,;RP11-91A18.4,upstream_gene_variant,,ENST00000425802,;TXNDC12,intron_variant,,ENST00000472624,; C ENST00000371614 Transcript missense_variant 977/1714 922/1065 308/354 R/G Cgg/Ggg 1 -1 KTI12 HGNC HGNC:25160 protein_coding YES CCDS562.1 ENSP00000360676 Q96EK9 UPI000007168B NM_138417.2 tolerated(0.2) 1/1 hmmpanther:PTHR12435:SF2,hmmpanther:PTHR12435,Pfam_domain:PF08433 MODERATE SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 4 52032840 52032840 G C 1 0 0 0 0 1 0 0 0 8482 1086 38 4 4 KTI12 1 52032840 Missense_Mutation SNP G 11LU035_T 9575957 52032840 196923582 4 1656 CTSK 0 . GRCh38 1 150804183 150804183 + Silent SNP G G C 11LU035_T 11LU035_N G G c.456C>G p.= p.L152L ENST00000271651 5/8 429 330 99 558 558 0 strelka-varscan-mutect CTSK,synonymous_variant,p.=,ENST00000271651,NM_000396.3;CTSK,synonymous_variant,p.=,ENST00000443913,;CTSK,non_coding_transcript_exon_variant,,ENST00000480670,;UBE2D3P3,downstream_gene_variant,,ENST00000426992,; C ENST00000271651 Transcript synonymous_variant 567/1692 456/990 152/329 L ctC/ctG COSM4495574,COSM4495575 1 -1 CTSK HGNC HGNC:2536 protein_coding YES CCDS969.1 ENSP00000271651 P43235 UPI0000000DFB NM_000396.3 5/8 hmmpanther:PTHR12411:SF55,hmmpanther:PTHR12411,Pfam_domain:PF00112,Gene3D:3.90.70.10,SMART_domains:SM00645,Superfamily_domains:SSF54001 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 4 150804183 150804183 G C 1 0 0 0 0 0 0 0 1 3846 1277 45 4 4 CTSK 1 150804183 Silent SNP G 11LU035_T 98771343 150804183 98152239 5 1657 RABGAP1L 0 . GRCh38 1 174702208 174702208 + Missense_Mutation SNP G G C 11LU035_T 11LU035_N G G c.2121G>C p.Lys707Asn p.K707N ENST00000251507 17/21 190 135 55 201 201 0 strelka-varscan RABGAP1L,missense_variant,p.Lys707Asn,ENST00000251507,NM_014857.4;RABGAP1L,missense_variant,p.Lys14Asn,ENST00000325589,;RABGAP1L,missense_variant,p.Lys33Asn,ENST00000367687,;RABGAP1L,missense_variant,p.Lys34Asn,ENST00000347255,;RABGAP1L,missense_variant,p.Lys136Asn,ENST00000474375,;RABGAP1L,missense_variant,p.Lys14Asn,ENST00000529145,;RABGAP1L,missense_variant,p.Lys14Asn,ENST00000469553,; C ENST00000251507 Transcript missense_variant 2295/2899 2121/2448 707/815 K/N aaG/aaC COSM4431252,COSM4431253,COSM4431254 1 1 RABGAP1L HGNC HGNC:24663 protein_coding YES CCDS1314.1 ENSP00000251507 Q5R372 F1LJ00 UPI0000458A9F NM_014857.4 deleterious(0) 17/21 Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF205,SMART_domains:SM00164,Superfamily_domains:SSF47923 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 174702208 174702208 G C 1 0 0 0 0 1 0 0 0 13124 1020 36 4 4 RABGAP1L 1 174702208 Missense_Mutation SNP G 11LU035_T 23898025 174702208 74254214 6 1658 KIAA1614 0 . GRCh38 1 180916566 180916566 + Missense_Mutation SNP A A T rs749727539 11LU035_T 11LU035_N A A c.463A>T p.Ser155Cys p.S155C ENST00000367588 2/9 56 47 9 103 103 0 strelka-varscan KIAA1614,missense_variant,p.Ser155Cys,ENST00000367588,NM_020950.1;KIAA1614,downstream_gene_variant,,ENST00000496210,; T ENST00000367588 Transcript missense_variant 518/9654 463/3573 155/1190 S/C Agc/Tgc rs749727539 1 1 KIAA1614 HGNC HGNC:29327 protein_coding YES CCDS41442.1 ENSP00000356560 Q5VZ46 UPI00001C1D75 NM_020950.1 deleterious(0.04) 2/9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 180916566 180916566 A T 1 0 0 0 0 1 0 0 0 8124 188 7 4 4 KIAA1614 1 180916566 Missense_Mutation SNP A 11LU035_T 6214358 180916566 68039856 7 1659 B3GALT2 0 . GRCh38 1 193180615 193180615 + Silent SNP A A T novel 11LU035_T 11LU035_N A A c.948T>A p.= p.G316G ENST00000367434 2/2 226 199 27 301 300 1 strelka-varscan B3GALT2,synonymous_variant,p.=,ENST00000367434,NM_003783.3;CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000635846,; T ENST00000367434 Transcript synonymous_variant 1704/3274 948/1269 316/422 G ggT/ggA 1 -1 B3GALT2 HGNC HGNC:917 protein_coding YES CCDS1383.1 ENSP00000356404 O43825 UPI0000073BFF NM_003783.3 2/2 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF19,Pfam_domain:PF01762 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 193180615 193180615 A T 1 0 0 0 0 0 0 0 1 1405 30 2 4 4 B3GALT2 1 193180615 Silent SNP A 11LU035_T 12264049 193180615 55775807 8 1660 PPFIA4 0 . GRCh38 1 203049699 203049699 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.1455G>A p.= p.E485E ENST00000447715 17/35 67 49 18 90 90 0 strelka-varscan PPFIA4,synonymous_variant,p.=,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,synonymous_variant,p.=,ENST00000447715,;PPFIA4,synonymous_variant,p.=,ENST00000600426,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;PPFIA4,upstream_gene_variant,,ENST00000272198,;PPFIA4,upstream_gene_variant,,ENST00000599966,;PPFIA4,upstream_gene_variant,,ENST00000599514,;PPFIA4,downstream_gene_variant,,ENST00000601609,;PPFIA4,upstream_gene_variant,,ENST00000600447,; A ENST00000447715 Transcript synonymous_variant 1896/6349 1455/3558 485/1185 E gaG/gaA 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 17/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 203049699 203049699 G A 1 0 0 0 0 0 0 0 1 12421 933 33 3 3 PPFIA4 1 203049699 Silent SNP G 11LU035_T 9869084 203049699 45906723 9 1661 DNAH14 0 . GRCh38 1 225192898 225192898 + Missense_Mutation SNP C C T novel 11LU035_T 11LU035_N C C c.5807C>T p.Ser1936Leu p.S1936L ENST00000430092 37/84 94 68 26 38 38 0 strelka-varscan DNAH14,missense_variant,p.Ser1936Leu,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Ser1936Leu,ENST00000439375,;DNAH14,missense_variant,p.Ser1531Leu,ENST00000445597,; T ENST00000430092 Transcript missense_variant 6022/13763 5807/13548 1936/4515 S/L tCa/tTa 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 tolerated(0.09) 37/84 SMART_domains:SM00382 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 225192898 225192898 C T 1 0 0 0 0 1 0 0 0 4415 838 29 3 3 DNAH14 1 225192898 Missense_Mutation SNP C 11LU035_T 22143199 225192898 23763524 10 1662 RYR2 0 . GRCh38 1 237589875 237589875 + Frame_Shift_Del DEL C C - novel 11LU035_T 11LU035_N C C c.3681delC p.Phe1227LeufsTer25 p.F1227Lfs*25 ENST00000366574 30/105 365 323 42 496 496 0 sindel-varindel-pindel RYR2,frameshift_variant,p.Phe1227LeufsTer25,ENST00000366574,NM_001035.2;RYR2,frameshift_variant,p.Phe1211LeufsTer25,ENST00000360064,; - ENST00000366574 Transcript frameshift_variant 3998/16562 3681/14904 1227/4967 F/X ttC/tt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 30/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 4 237589875 237589875 C - 1 0 1 0 1 0 0 0 0 14029 825 29 0 0 RYR2 1 237589875 Frame_Shift_Del DEL C 11LU035_T 12396977 237589875 11366547 11 1663 OR2T10 0 . GRCh38 1 248593050 248593050 + Missense_Mutation SNP G G T rs774284253 11LU035_T 11LU035_N G G c.719C>A p.Thr240Asn p.T240N ENST00000330500 1/1 109 81 28 169 169 0 strelka-varscan OR2T10,missense_variant,p.Thr240Asn,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; T ENST00000330500 Transcript missense_variant 719/939 719/939 240/312 T/N aCc/aAc rs774284253,COSM4911295 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 MODERATE 1 SNV 0,1 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 248593050 248593050 G T 1 0 0 0 0 1 0 0 0 11095 1261 44 2 2 OR2T10 1 248593050 Missense_Mutation SNP G 11LU035_T 11003175 248593050 363372 12 1664 TPO 0 . GRCh38 2 1477203 1477203 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.937C>A p.Pro313Thr p.P313T ENST00000345913 8/17 441 406 35 676 675 1 strelka-varscan-mutect TPO,missense_variant,p.Pro242Thr,ENST00000422464,;TPO,missense_variant,p.Pro313Thr,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Pro313Thr,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Pro313Thr,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Pro313Thr,ENST00000346956,NM_175721.3;TPO,intron_variant,,ENST00000382198,NM_175722.3;TPO,intron_variant,,ENST00000497517,; A ENST00000345913 Transcript missense_variant 1028/3145 937/2802 313/933 P/T Ccg/Acg 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 deleterious(0.04) 8/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS rs917619265 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 1477203 1477203 C A 1 0 0 0 0 1 0 0 0 16891 623 22 2 2 TPO 2 1477203 Missense_Mutation SNP C 11LU035_T 1477203 240716326 13 1665 PXDN 0 . GRCh38 2 1648428 1648428 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.3352C>T p.Leu1118Phe p.L1118F ENST00000252804 17/23 602 475 127 870 869 1 strelka-varscan-mutect PXDN,missense_variant,p.Leu1118Phe,ENST00000252804,NM_012293.2;PXDN,downstream_gene_variant,,ENST00000433670,;PXDN,upstream_gene_variant,,ENST00000477093,;PXDN,downstream_gene_variant,,ENST00000465809,;PXDN,intron_variant,,ENST00000478155,;PXDN,downstream_gene_variant,,ENST00000493779,;PXDN,upstream_gene_variant,,ENST00000453308,; A ENST00000252804 Transcript missense_variant 3403/6808 3352/4440 1118/1479 L/F Ctc/Ttc 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 deleterious(0) 17/23 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF75,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 1648428 1648428 G A 1 0 0 0 0 1 0 0 0 13001 942 33 3 3 PXDN 2 1648428 Missense_Mutation SNP G 11LU035_T 171225 1648428 240545101 14 1666 PXDN 0 . GRCh38 2 1648614 1648614 + Missense_Mutation SNP C C A rs759881927 11LU035_T 11LU035_N C C c.3166G>T p.Gly1056Cys p.G1056C ENST00000252804 17/23 367 254 113 785 784 1 strelka-varscan-mutect PXDN,missense_variant,p.Gly1056Cys,ENST00000252804,NM_012293.2;PXDN,downstream_gene_variant,,ENST00000433670,;PXDN,upstream_gene_variant,,ENST00000477093,;PXDN,downstream_gene_variant,,ENST00000465809,;PXDN,intron_variant,,ENST00000478155,;PXDN,downstream_gene_variant,,ENST00000493779,; A ENST00000252804 Transcript missense_variant 3217/6808 3166/4440 1056/1479 G/C Ggc/Tgc rs759881927 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 deleterious(0) 17/23 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF75,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS rs759881927 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 1648614 1648614 C A 1 0 0 0 0 1 0 0 0 13001 652 23 1 1 PXDN 2 1648614 Missense_Mutation SNP C 11LU035_T 186 1648614 240544915 15 1667 PPP1R21 0 . GRCh38 2 48440993 48440993 + Missense_Mutation SNP G G C rs770557645 11LU035_T 11LU035_N G G c.40G>C p.Ala14Pro p.A14P ENST00000294952 1/22 149 127 22 347 347 0 strelka-varscan PPP1R21,missense_variant,p.Ala14Pro,ENST00000294952,NM_001135629.2;PPP1R21,missense_variant,p.Ala14Pro,ENST00000281394,NM_152994.4;PPP1R21,missense_variant,p.Ala14Pro,ENST00000449090,NM_001193475.1;PPP1R21,upstream_gene_variant,,ENST00000421486,;RP11-191L17.1,upstream_gene_variant,,ENST00000609028,;PPP1R21,missense_variant,p.Ala14Pro,ENST00000416913,;PPP1R21,intron_variant,,ENST00000431614,; C ENST00000294952 Transcript missense_variant 197/3142 40/2343 14/780 A/P Gct/Cct rs770557645 1 1 PPP1R21 HGNC HGNC:30595 protein_coding YES CCDS46278.1 ENSP00000294952 Q6ZMI0 UPI000015C523 NM_001135629.2 deleterious(0) 1/22 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10205,hmmpanther:PTHR21448,SMART_domains:SM01254 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 4 48440993 48440993 G C 1 0 0 0 0 1 0 0 0 12483 1203 42 4 4 PPP1R21 2 48440993 Missense_Mutation SNP G 11LU035_T 46792379 48440993 193752536 16 1668 AFF3 0 . GRCh38 2 100006768 100006768 + Missense_Mutation SNP T T C novel 11LU035_T 11LU035_N T T c.812A>G p.Asp271Gly p.D271G ENST00000409579 7/25 233 219 14 278 278 0 strelka-varscan-mutect AFF3,missense_variant,p.Asp246Gly,ENST00000409236,;AFF3,missense_variant,p.Asp246Gly,ENST00000317233,NM_002285.2;AFF3,missense_variant,p.Asp271Gly,ENST00000409579,NM_001025108.1;AFF3,downstream_gene_variant,,ENST00000423966,;AFF3,downstream_gene_variant,,ENST00000440445,;AFF3,downstream_gene_variant,,ENST00000415384,;AFF3,downstream_gene_variant,,ENST00000432037,;AFF3,downstream_gene_variant,,ENST00000424600,;AFF3,downstream_gene_variant,,ENST00000416492,;AFF3,downstream_gene_variant,,ENST00000441400,;AFF3,missense_variant,p.Asp27Gly,ENST00000430789,;AFF3,non_coding_transcript_exon_variant,,ENST00000498090,; C ENST00000409579 Transcript missense_variant 1045/4342 812/3756 271/1251 D/G gAt/gGt 1 -1 AFF3 HGNC HGNC:6473 protein_coding YES CCDS33258.1 ENSP00000386834 P51826 UPI0000545269 NM_001025108.1 deleterious(0.03) 7/25 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 100006768 100006768 T C 1 0 0 0 0 1 0 0 0 435 1435 50 5 5 AFF3 2 100006768 Missense_Mutation SNP T 11LU035_T 51565775 100006768 142186761 17 1669 LRP1B 0 . GRCh38 2 140335831 140335831 + Missense_Mutation SNP T T C novel 11LU035_T 11LU035_N T T c.11900A>G p.Glu3967Gly p.E3967G ENST00000389484 78/91 175 163 12 211 211 0 strelka-varscan-mutect LRP1B,missense_variant,p.Glu3967Gly,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Glu199Gly,ENST00000437977,; C ENST00000389484 Transcript missense_variant 12872/16535 11900/13800 3967/4599 E/G gAa/gGa 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(1) 78/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 140335831 140335831 T C 1 0 0 0 0 1 0 0 0 8850 1783 62 5 5 LRP1B 2 140335831 Missense_Mutation SNP T 11LU035_T 40329063 140335831 101857698 18 1670 LRP1B 0 . GRCh38 2 140350800 140350800 + Missense_Mutation SNP C C G novel 11LU035_T 11LU035_N C C c.11889G>C p.Leu3963Phe p.L3963F ENST00000389484 77/91 108 81 27 165 165 0 strelka-varscan-mutect LRP1B,missense_variant,p.Leu3963Phe,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Leu195Phe,ENST00000437977,; G ENST00000389484 Transcript missense_variant 12861/16535 11889/13800 3963/4599 L/F ttG/ttC 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.07) 77/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 4 140350800 140350800 C G 1 0 0 0 0 1 0 0 0 8850 840 29 4 4 LRP1B 2 140350800 Missense_Mutation SNP C 11LU035_T 14969 140350800 101842729 19 1671 COL3A1 0 . GRCh38 2 189004317 189004317 + Missense_Mutation SNP C C T novel 11LU035_T 11LU035_N C C c.2884C>T p.Pro962Ser p.P962S ENST00000304636 40/51 239 218 21 315 314 1 strelka-varscan-mutect COL3A1,missense_variant,p.Pro962Ser,ENST00000304636,NM_000090.3;COL3A1,intron_variant,,ENST00000317840,;COL3A1,upstream_gene_variant,,ENST00000487010,;COL3A1,downstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript missense_variant 3054/5543 2884/4401 962/1466 P/S Cca/Tca 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0.04) 40/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 189004317 189004317 C T 1 0 0 0 0 1 0 0 0 3477 507 18 3 3 COL3A1 2 189004317 Missense_Mutation SNP C 11LU035_T 48653517 189004317 53189212 20 1672 COL5A2 0 . GRCh38 2 189043227 189043227 + Missense_Mutation SNP T T A rs781112304 11LU035_T 11LU035_N T T c.3395A>T p.Asp1132Val p.D1132V ENST00000374866 48/54 214 202 12 269 269 0 strelka-varscan-mutect COL5A2,missense_variant,p.Asp1132Val,ENST00000374866,NM_000393.3;COL5A2,missense_variant,p.Asp745Val,ENST00000618828,; A ENST00000374866 Transcript missense_variant 3670/6949 3395/4500 1132/1499 D/V gAt/gTt rs781112304 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 tolerated(0.13) 48/54 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF539,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs781112304 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 189043227 189043227 T A 1 0 0 0 0 1 0 0 0 3486 1435 50 4 4 COL5A2 2 189043227 Missense_Mutation SNP T 11LU035_T 38910 189043227 53150302 21 1673 C2orf66 0 . GRCh38 2 196807516 196807516 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.281C>T p.Ser94Leu p.S94L ENST00000342506 2/3 228 177 51 428 427 1 strelka-varscan-mutect C2orf66,missense_variant,p.Ser94Leu,ENST00000342506,NM_213608.2; A ENST00000342506 Transcript missense_variant 1170/1669 281/354 94/117 S/L tCa/tTa 1 -1 C2orf66 HGNC HGNC:33809 protein_coding YES CCDS2317.1 ENSP00000339384 Q6UXQ4 UPI00001602CE NM_213608.2 tolerated(0.22) 2/3 Pfam_domain:PF15846,hmmpanther:PTHR15495,hmmpanther:PTHR15495:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 196807516 196807516 G A 1 0 0 0 0 1 0 0 0 2041 1294 45 3 3 C2orf66 2 196807516 Missense_Mutation SNP G 11LU035_T 7764289 196807516 45386013 22 1674 TOPAZ1 0 . GRCh38 3 44244285 44244285 + Silent SNP T T C novel 11LU035_T 11LU035_N T T c.1779T>C p.= p.D593D ENST00000309765 2/20 128 93 35 123 123 0 strelka-varscan TOPAZ1,synonymous_variant,p.=,ENST00000309765,NM_001145030.1; C ENST00000309765 Transcript synonymous_variant 1947/5334 1779/5079 593/1692 D gaT/gaC 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 2/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 4 44244285 44244285 T C 1 0 0 0 0 0 0 0 1 16845 1403 49 5 5 TOPAZ1 3 44244285 Silent SNP T 11LU035_T 44244285 154051274 23 1675 EXOSC7 0 . GRCh38 3 44997097 44997097 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.265G>A p.Ala89Thr p.A89T ENST00000265564 4/8 121 112 9 176 176 0 strelka-varscan EXOSC7,missense_variant,p.Ala89Thr,ENST00000265564,NM_015004.3;EXOSC7,non_coding_transcript_exon_variant,,ENST00000461361,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000491476,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000468667,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000481405,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000482004,;CLEC3B,upstream_gene_variant,,ENST00000490386,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000467846,; A ENST00000265564 Transcript missense_variant 313/1055 265/876 89/291 A/T Gct/Act 1 1 EXOSC7 HGNC HGNC:28112 protein_coding YES CCDS2725.1 ENSP00000265564 Q15024 A0A024R2P7 UPI000020A5E9 NM_015004.3 deleterious(0) 4/8 Pfam_domain:PF01138,hmmpanther:PTHR11097,hmmpanther:PTHR11097:SF8,Superfamily_domains:SSF54211 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.24334 0.9999997 1 1 1 0 A 3 1 4 44997097 44997097 G A 1 0 0 0 0 1 0 0 0 5187 1319 46 3 3 EXOSC7 3 44997097 Missense_Mutation SNP G 11LU035_T 752812 44997097 153298462 24 1676 LSAMP 0 . GRCh38 3 115842517 115842517 + Silent SNP G G C novel 11LU035_T 11LU035_N G G c.711C>G p.= p.L237L ENST00000490035 5/7 221 153 68 327 327 0 strelka-varscan LSAMP,synonymous_variant,p.=,ENST00000490035,NM_002338.3;LSAMP,synonymous_variant,p.=,ENST00000539563,;LSAMP,synonymous_variant,p.=,ENST00000333617,;RN7SL815P,downstream_gene_variant,,ENST00000470970,;LSAMP,non_coding_transcript_exon_variant,,ENST00000498645,;LSAMP,upstream_gene_variant,,ENST00000475403,;LSAMP,non_coding_transcript_exon_variant,,ENST00000473171,; C ENST00000490035 Transcript synonymous_variant 1211/9446 711/1017 237/338 L ctC/ctG 1 -1 LSAMP HGNC HGNC:6705 protein_coding YES CCDS2982.1 ENSP00000419000 Q13449 UPI00000746A0 NM_002338.3 5/7 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF118,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 4 115842517 115842517 G C 1 0 0 0 0 0 0 0 1 8954 1277 45 4 4 LSAMP 3 115842517 Silent SNP G 11LU035_T 70845420 115842517 82453042 25 1677 ATP11B 0 . GRCh38 3 182867413 182867413 + Missense_Mutation SNP A A G rs759009161 11LU035_T 11LU035_N A A c.1657A>G p.Met553Val p.M553V ENST00000323116 15/30 104 60 44 94 94 0 strelka-varscan ATP11B,missense_variant,p.Met553Val,ENST00000323116,NM_014616.2;ATP11B,missense_variant,p.Met354Val,ENST00000498086,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,; G ENST00000323116 Transcript missense_variant 1917/7325 1657/3534 553/1177 M/V Atg/Gtg rs759009161,COSM1617245 1 1 ATP11B HGNC HGNC:13553 protein_coding YES CCDS33896.1 ENSP00000321195 Q9Y2G3 UPI000004124E NM_014616.2 tolerated(0.06) 15/30 Gene3D:3.40.1110.10,Pfam_domain:PF13246,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,Superfamily_domains:SSF81660,TIGRFAM_domain:TIGR01652 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 4 182867413 182867413 A G 1 0 0 0 0 1 0 0 0 1272 449 16 5 5 ATP11B 3 182867413 Missense_Mutation SNP A 11LU035_T 67024896 182867413 15428146 26 1678 ZNF721 0 . GRCh38 4 442175 442175 + Missense_Mutation SNP C C G novel 11LU035_T 11LU035_N C C c.2292G>C p.Gln764His p.Q764H ENST00000511833 3/3 139 127 12 201 201 0 strelka-varscan-mutect ZNF721,missense_variant,p.Gln752His,ENST00000338977,;ZNF721,missense_variant,p.Gln764His,ENST00000511833,NM_133474.3;ZNF721,intron_variant,,ENST00000506646,;ZNF721,downstream_gene_variant,,ENST00000505900,;RP11-2H3.7,intron_variant,,ENST00000631198,;ABCA11P,intron_variant,,ENST00000451020,;ABCA11P,intron_variant,,ENST00000507854,;ABCA11P,intron_variant,,ENST00000514396,;ZNF721,intron_variant,,ENST00000507078,;ZNF721,intron_variant,,ENST00000515578,; G ENST00000511833 Transcript missense_variant 2486/2966 2292/2772 764/923 Q/H caG/caC 1 -1 ZNF721 HGNC HGNC:29425 protein_coding YES CCDS46991.1 ENSP00000428878 Q8TF20 UPI0000E9B4A9 NM_133474.3 tolerated(0.55) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF20,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 4 442175 442175 C G 1 0 0 0 0 1 0 0 0 18698 564 20 4 4 ZNF721 4 442175 Missense_Mutation SNP C 11LU035_T 442175 189772380 27 1679 GAK 0 . GRCh38 4 867169 867169 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.2659C>T p.His887Tyr p.H887Y ENST00000314167 21/28 49 38 11 148 148 0 strelka-varscan-mutect GAK,missense_variant,p.His887Tyr,ENST00000314167,NM_005255.2;GAK,missense_variant,p.His808Tyr,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,missense_variant,p.His18Tyr,ENST00000510799,;GAK,intron_variant,,ENST00000618573,;GAK,upstream_gene_variant,,ENST00000511980,;GAK,non_coding_transcript_exon_variant,,ENST00000509566,;GAK,non_coding_transcript_exon_variant,,ENST00000515868,; A ENST00000314167 Transcript missense_variant 2770/4442 2659/3936 887/1311 H/Y Cac/Tac 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 tolerated(0.06) 21/28 hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 867169 867169 G A 1 0 0 0 0 1 0 0 0 6063 1319 46 3 3 GAK 4 867169 Missense_Mutation SNP G 11LU035_T 424994 867169 189347386 28 1680 GABRA4 0 . GRCh38 4 46977485 46977485 + Missense_Mutation SNP G G C 11LU035_T 11LU035_N G G c.419C>G p.Ser140Cys p.S140C ENST00000264318 4/9 209 194 15 166 166 0 strelka-varscan GABRA4,missense_variant,p.Ser140Cys,ENST00000264318,NM_000809.3,NM_001204266.1;GABRA4,3_prime_UTR_variant,,ENST00000508560,;GABRA4,3_prime_UTR_variant,,ENST00000511523,;GABRA4,3_prime_UTR_variant,,ENST00000502874,; C ENST00000264318 Transcript missense_variant 1402/11973 419/1665 140/554 S/C tCt/tGt COSM2848555 1 -1 GABRA4 HGNC HGNC:4078 protein_coding YES CCDS3473.1 ENSP00000264318 P48169 X5D7F5 UPI0000074200 NM_000809.3,NM_001204266.1 deleterious(0) 4/9 hmmpanther:PTHR18945:SF393,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 46977485 46977485 G C 1 0 0 0 0 1 0 0 0 6034 942 33 4 4 GABRA4 4 46977485 Missense_Mutation SNP G 11LU035_T 46110316 46977485 143237070 29 1681 UNC5C 0 . GRCh38 4 95301648 95301648 + Missense_Mutation SNP C C T rs149754110 11LU035_T 11LU035_N C C c.448G>A p.Ala150Thr p.A150T ENST00000453304 3/16 248 220 28 302 302 0 strelka-varscan UNC5C,missense_variant,p.Ala150Thr,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Ala109Thr,ENST00000610318,;UNC5C,missense_variant,p.Ala150Thr,ENST00000513796,;UNC5C,missense_variant,p.Ala150Thr,ENST00000506749,;UNC5C,missense_variant,p.Ala150Thr,ENST00000504962,; T ENST00000453304 Transcript missense_variant 797/9875 448/2796 150/931 A/T Gcg/Acg rs149754110,COSM5645887 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 tolerated(0.23) 3/16 Gene3D:2.60.40.10,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 95301648 95301648 C T 1 0 0 0 0 1 0 0 0 17517 768 27 1 1 UNC5C 4 95301648 Missense_Mutation SNP C 11LU035_T 48324163 95301648 94912907 30 1682 SLC45A2 0 . GRCh38 5 33944735 33944735 + Silent SNP C C A novel 11LU035_T 11LU035_N C C c.1506G>T p.= p.G502G ENST00000296589 7/7 1064 693 371 864 864 0 strelka-varscan SLC45A2,synonymous_variant,p.=,ENST00000296589,NM_016180.4;SLC45A2,downstream_gene_variant,,ENST00000382102,NM_001012509.3;SLC45A2,downstream_gene_variant,,ENST00000510600,; A ENST00000296589 Transcript synonymous_variant 1653/1772 1506/1593 502/530 G ggG/ggT 1 -1 SLC45A2 HGNC HGNC:16472 protein_coding YES CCDS3901.1 ENSP00000296589 Q9UMX9 A0A076YIB8 UPI00001AEC19 NM_016180.4 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF34,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 33944735 33944735 C A 1 0 0 0 0 0 0 0 1 14918 842 30 2 2 SLC45A2 5 33944735 Silent SNP C 11LU035_T 33944735 147593524 31 1683 FBN2 0 . GRCh38 5 128350888 128350888 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.2792C>T p.Pro931Leu p.P931L ENST00000508053 27/71 564 404 160 657 655 2 strelka-varscan FBN2,missense_variant,p.Pro931Leu,ENST00000508053,;FBN2,missense_variant,p.Pro931Leu,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Pro930Leu,ENST00000619499,;FBN2,missense_variant,p.Pro898Leu,ENST00000508989,; A ENST00000508053 Transcript missense_variant 3767/11132 2792/8739 931/2912 P/L cCc/cTc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 27/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 128350888 128350888 G A 1 0 0 0 0 1 0 0 0 5566 1232 43 3 3 FBN2 5 128350888 Missense_Mutation SNP G 11LU035_T 94406153 128350888 53187371 32 1684 DST 0 . GRCh38 6 56594134 56594134 + Silent SNP T T G novel 11LU035_T 11LU035_N T T c.5484A>C p.= p.A1828A ENST00000312431 40/95 37 32 5 49 49 0 strelka-varscan-mutect DST,synonymous_variant,p.=,ENST00000361203,;DST,synonymous_variant,p.=,ENST00000421834,NM_183380.3;DST,synonymous_variant,p.=,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,synonymous_variant,p.=,ENST00000370788,;DST,synonymous_variant,p.=,ENST00000244364,NM_015548.4;DST,synonymous_variant,p.=,ENST00000518398,; G ENST00000312431 Transcript synonymous_variant 5610/17756 5484/16614 1828/5537 A gcA/gcC 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 40/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 LOW 1 SNV 5 1 PASS rs1014197241 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 4 56594134 56594134 T G 1 0 0 0 0 0 0 0 1 4604 1683 59 5 5 DST 6 56594134 Silent SNP T 11LU035_T 56594134 114211845 33 1685 PRDM1 0 . GRCh38 6 106107121 106107121 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.2113C>A p.His705Asn p.H705N ENST00000369096 7/7 111 83 28 204 204 0 strelka-varscan-mutect PRDM1,missense_variant,p.His705Asn,ENST00000369096,NM_001198.3;PRDM1,missense_variant,p.His571Asn,ENST00000369089,NM_182907.2;PRDM1,missense_variant,p.His669Asn,ENST00000369091,;ATG5,intron_variant,,ENST00000636437,;PRDM1,downstream_gene_variant,,ENST00000450060,;ATG5,intron_variant,,ENST00000636335,; A ENST00000369096 Transcript missense_variant 2347/5164 2113/2478 705/825 H/N Cac/Aac 1 1 PRDM1 HGNC HGNC:9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 UPI0000D49069 NM_001198.3 deleterious(0) 7/7 Gene3D:3.30.160.60,PIRSF_domain:PIRSF013212,hmmpanther:PTHR24409,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1190911457 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 106107121 106107121 C A 1 0 0 0 0 1 0 0 0 12581 826 29 2 2 PRDM1 6 106107121 Missense_Mutation SNP C 11LU035_T 49512987 106107121 64698858 34 1686 RAET1G 0 . GRCh38 6 149919070 149919070 + Missense_Mutation SNP C C A rs377738718 11LU035_T 11LU035_N C C c.604G>T p.Asp202Tyr p.D202Y ENST00000367360 3/5 205 170 35 418 418 0 strelka-varscan-mutect RAET1G,missense_variant,p.Asp202Tyr,ENST00000367360,NM_001001788.3;RAET1G,missense_variant,p.Asp202Tyr,ENST00000479265,;RAET1E-AS1,intron_variant,,ENST00000606915,;RAET1E-AS1,intron_variant,,ENST00000446954,;RAET1E-AS1,intron_variant,,ENST00000605899,;RAET1G,missense_variant,p.Asp202Tyr,ENST00000367361,; A ENST00000367360 Transcript missense_variant 672/1107 604/1005 202/334 D/Y Gac/Tac rs377738718 1 -1 RAET1G HGNC HGNC:16795 protein_coding YES CCDS43514.1 ENSP00000356329 Q6H3X3 UPI00003B0CBD NM_001001788.3 deleterious(0) 3/5 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF148 MODERATE 1 SNV 1 1 PASS rs377738718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 149919070 149919070 C A 1 0 0 0 0 1 0 0 0 13161 855 30 2 2 RAET1G 6 149919070 Missense_Mutation SNP C 11LU035_T 43811949 149919070 20886909 35 1687 TWIST1 0 . GRCh38 7 19116782 19116782 + Missense_Mutation SNP G G T novel 11LU035_T 11LU035_N G G c.540C>A p.His180Gln p.H180Q ENST00000242261 1/2 318 263 55 331 331 0 strelka-varscan-mutect TWIST1,missense_variant,p.His180Gln,ENST00000242261,NM_000474.3;AC003986.6,downstream_gene_variant,,ENST00000419944,;AC003986.7,upstream_gene_variant,,ENST00000417460,;TWIST1,missense_variant,p.His113Gln,ENST00000354571,;TWIST1,missense_variant,p.His48Gln,ENST00000443687,; T ENST00000242261 Transcript missense_variant 891/1666 540/609 180/202 H/Q caC/caA 1 -1 TWIST1 HGNC HGNC:12428 protein_coding YES CCDS5367.1 ENSP00000242261 Q15672 UPI00001377DC NM_000474.3 tolerated(0.09) 1/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF64,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 19116782 19116782 G T 1 0 0 0 0 1 0 0 0 17298 1136 40 1 1 TWIST1 7 19116782 Missense_Mutation SNP G 11LU035_T 19116782 140229191 36 1688 GLI3 0 . GRCh38 7 41965020 41965020 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.4053C>T p.= p.T1351T ENST00000395925 15/15 905 798 107 865 865 0 strelka-varscan-mutect GLI3,synonymous_variant,p.=,ENST00000395925,NM_000168.5;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,; A ENST00000395925 Transcript synonymous_variant 4138/8208 4053/4743 1351/1580 T acC/acT 1 -1 GLI3 HGNC HGNC:4319 protein_coding YES CCDS5465.1 ENSP00000379258 P10071 UPI000020EE4C NM_000168.5 15/15 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF5 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 41965020 41965020 G A 1 0 0 0 0 0 0 0 1 6317 987 35 3 3 GLI3 7 41965020 Silent SNP G 11LU035_T 22848238 41965020 117380953 37 1689 LAMB4 0 . GRCh38 7 108078263 108078263 + Silent SNP C C T novel 11LU035_T 11LU035_N C C c.1941G>A p.= p.E647E ENST00000388781 16/34 322 262 60 293 293 0 strelka-varscan-mutect LAMB4,synonymous_variant,p.=,ENST00000388781,NM_007356.2;LAMB4,synonymous_variant,p.=,ENST00000205386,NM_001318046.1;LAMB4,synonymous_variant,p.=,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; T ENST00000388781 Transcript synonymous_variant 2025/5858 1941/5286 647/1761 E gaG/gaA 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 16/34 PROSITE_profiles:PS51116,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 108078263 108078263 C T 1 0 0 0 0 0 0 0 1 8517 796 28 3 3 LAMB4 7 108078263 Silent SNP C 11LU035_T 66113243 108078263 51267710 38 1690 SORBS3 0 . GRCh38 8 22571780 22571780 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.1806G>A p.= p.L602L ENST00000240123 19/21 196 172 24 347 347 0 strelka-varscan-mutect SORBS3,synonymous_variant,p.=,ENST00000240123,NM_005775.4;SORBS3,synonymous_variant,p.=,ENST00000523965,NM_001018003.2;SORBS3,synonymous_variant,p.=,ENST00000517962,;SORBS3,synonymous_variant,p.=,ENST00000523348,;SORBS3,downstream_gene_variant,,ENST00000523900,;SORBS3,downstream_gene_variant,,ENST00000522721,;RP11-582J16.3,upstream_gene_variant,,ENST00000517384,;SORBS3,non_coding_transcript_exon_variant,,ENST00000521554,;SORBS3,downstream_gene_variant,,ENST00000523740,;SORBS3,downstream_gene_variant,,ENST00000521787,;SORBS3,upstream_gene_variant,,ENST00000519127,;SORBS3,non_coding_transcript_exon_variant,,ENST00000517535,;SORBS3,non_coding_transcript_exon_variant,,ENST00000520207,;SORBS3,downstream_gene_variant,,ENST00000522315,;SORBS3,downstream_gene_variant,,ENST00000519453,; A ENST00000240123 Transcript synonymous_variant 2189/3459 1806/2016 602/671 L ctG/ctA 1 1 SORBS3 HGNC HGNC:30907 protein_coding YES CCDS6031.1 ENSP00000240123 O60504 UPI00001AE6B5 NM_005775.4 19/21 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF204 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 22571780 22571780 G A 1 0 0 0 0 0 0 0 1 15251 1335 47 3 3 SORBS3 8 22571780 Silent SNP G 11LU035_T 22571780 122566856 39 1691 KIF13B 0 . GRCh38 8 29099170 29099170 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.4287C>T p.= p.L1429L ENST00000524189 36/40 205 178 27 296 296 0 strelka-varscan-mutect KIF13B,synonymous_variant,p.=,ENST00000524189,NM_015254.3;KIF13B,synonymous_variant,p.=,ENST00000523130,; A ENST00000524189 Transcript synonymous_variant 4326/8745 4287/5481 1429/1826 L ctC/ctT 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 36/40 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 29099170 29099170 G A 1 0 0 0 0 0 0 0 1 8139 929 33 3 3 KIF13B 8 29099170 Silent SNP G 11LU035_T 6527390 29099170 116039466 40 1692 CNBD1 0 . GRCh38 8 87206075 87206075 + Missense_Mutation SNP G G C rs745548588 11LU035_T 11LU035_N G G c.514G>C p.Asp172His p.D172H ENST00000518476 5/11 107 100 7 116 116 0 strelka-varscan-mutect CNBD1,missense_variant,p.Asp172His,ENST00000518476,NM_173538.2;CNBD1,missense_variant,p.Asp28His,ENST00000620844,;CNBD1,non_coding_transcript_exon_variant,,ENST00000522427,;CNBD1,non_coding_transcript_exon_variant,,ENST00000522105,; C ENST00000518476 Transcript missense_variant 565/1594 514/1311 172/436 D/H Gat/Cat rs745548588,COSM1102238,COSM1102239 1 1 CNBD1 HGNC HGNC:26663 protein_coding YES CCDS55259.1 ENSP00000430073 Q8NA66 UPI000006EA68 NM_173538.2 deleterious(0.03) 5/11 hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF142,Gene3D:2.60.120.10,Superfamily_domains:SSF51206 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs745548588 . 0 204 6 0 0 0 0 0 -14.03609 0.9999996 1 1 1 0 C 3 2 4 87206075 87206075 G C 1 0 0 0 0 1 0 0 0 3369 1290 45 4 4 CNBD1 8 87206075 Missense_Mutation SNP G 11LU035_T 58106905 87206075 57932561 41 1693 CDK5RAP2 0 . GRCh38 9 120402852 120402855 + Frame_Shift_Del DEL TGAA TGAA - novel 11LU035_T 11LU035_N TGAA TGAA c.5258_5261delTTCA p.Ile1753LysfsTer23 p.I1753Kfs*23 ENST00000349780 34/38 141 98 43 190 190 0 sindel-varindel CDK5RAP2,frameshift_variant,p.Ile1753LysfsTer23,ENST00000349780,NM_018249.5;CDK5RAP2,frameshift_variant,p.Ile1674LysfsTer23,ENST00000360190,NM_001011649.2;CDK5RAP2,frameshift_variant,p.Ile1523LysfsTer23,ENST00000360822,NM_001272039.1;CDK5RAP2,frameshift_variant,p.Ile1147LysfsTer23,ENST00000416449,;CDK5RAP2,frameshift_variant,p.Ile763LysfsTer23,ENST00000425647,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000480467,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000433194,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000484546,;CDK5RAP2,downstream_gene_variant,,ENST00000483412,;CDK5RAP2,upstream_gene_variant,,ENST00000474262,; - ENST00000349780 Transcript frameshift_variant 5438-5441/6228 5258-5261/5682 1753-1754/1893 IQ/X aTTCAa/aa 1 -1 CDK5RAP2 HGNC HGNC:18672 protein_coding YES CCDS6823.1 ENSP00000343818 Q96SN8 UPI0000367673 NM_018249.5 34/38 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 4 120402852 120402852 TGAA - 1 0 1 0 1 0 0 0 0 2850 1812 63 0 0 CDK5RAP2 9 120402852 Frame_Shift_Del DEL TGAA 11LU035_T 120402852 17991865 42 1694 SLC2A8 0 . GRCh38 9 127404018 127404018 + Silent SNP G G T rs747262285 11LU035_T 11LU035_N G G c.927G>T p.= p.A309A ENST00000373371 7/10 87 81 6 221 221 0 strelka-varscan-mutect SLC2A8,synonymous_variant,p.=,ENST00000373371,NM_014580.4;SLC2A8,synonymous_variant,p.=,ENST00000373360,NM_001271711.1;SLC2A8,synonymous_variant,p.=,ENST00000610552,NM_001271712.1;SLC2A8,synonymous_variant,p.=,ENST00000430147,;SLC2A8,synonymous_variant,p.=,ENST00000451404,;SLC2A8,synonymous_variant,p.=,ENST00000423934,;SLC2A8,synonymous_variant,p.=,ENST00000373352,;SLC2A8,synonymous_variant,p.=,ENST00000439597,;SLC2A8,synonymous_variant,p.=,ENST00000419917,;SLC2A8,downstream_gene_variant,,ENST00000419132,;SLC2A8,non_coding_transcript_exon_variant,,ENST00000489239,;SLC2A8,upstream_gene_variant,,ENST00000485806,;SLC2A8,upstream_gene_variant,,ENST00000477027,;SLC2A8,downstream_gene_variant,,ENST00000484617,;SLC2A8,upstream_gene_variant,,ENST00000484208,; T ENST00000373371 Transcript synonymous_variant 1016/2172 927/1434 309/477 A gcG/gcT rs747262285 1 1 SLC2A8 HGNC HGNC:13812 protein_coding YES CCDS6870.1 ENSP00000362469 Q9NY64 A0A024R871 UPI000003E7A8 NM_014580.4 7/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF157,PROSITE_patterns:PS00216,TIGRFAM_domain:TIGR00879,Gene3D:1.20.1250.20,Pfam_domain:PF00083,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS rs747262285 . 0 206 3 0 0 0 0 0 -13.07321 1 1 1 1 0 T 2 4 4 127404018 127404018 G T 1 0 0 0 0 0 0 0 1 14821 1103 39 1 1 SLC2A8 9 127404018 Silent SNP G 11LU035_T 7001166 127404018 10990699 43 1695 INPP5E 0 . GRCh38 9 136431958 136431958 + Missense_Mutation SNP A A G novel 11LU035_T 11LU035_N A A c.1415T>C p.Val472Ala p.V472A ENST00000371712 7/10 412 309 103 702 700 2 strelka-varscan-mutect INPP5E,missense_variant,p.Val472Ala,ENST00000371712,NM_001318502.1,NM_019892.4;INPP5E,downstream_gene_variant,,ENST00000635815,; G ENST00000371712 Transcript missense_variant 1818/3394 1415/1935 472/644 V/A gTg/gCg 1 -1 INPP5E HGNC HGNC:21474 protein_coding YES CCDS7000.1 ENSP00000360777 Q9NRR6 UPI000014053C NM_001318502.1,NM_019892.4 deleterious(0) 7/10 hmmpanther:PTHR11200:SF165,hmmpanther:PTHR11200,Gene3D:3.60.10.10,Pfam_domain:PF03372,SMART_domains:SM00128,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 4 136431958 136431958 A G 1 0 0 0 0 1 0 0 0 7660 159 6 5 5 INPP5E 9 136431958 Missense_Mutation SNP A 11LU035_T 9027940 136431958 1962759 44 1696 OR5P3 0 . GRCh38 11 7825399 7825399 + Missense_Mutation SNP C C A 11LU035_T 11LU035_N C C c.574G>T p.Asp192Tyr p.D192Y ENST00000328375 1/1 229 216 13 275 275 0 strelka-varscan-mutect OR5P3,missense_variant,p.Asp192Tyr,ENST00000328375,NM_153445.1;RP11-35J10.5,intron_variant,,ENST00000527565,;RP11-494M8.4,intron_variant,,ENST00000529488,; A ENST00000328375 Transcript missense_variant 574/936 574/936 192/311 D/Y Gat/Tat COSM1703551 1 -1 OR5P3 HGNC HGNC:14784 protein_coding YES CCDS7783.1 ENSP00000332068 Q8WZ94 A0A126GVE6 UPI000004B1F2 NM_153445.1 tolerated(0.19) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF310,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 7825399 7825399 C A 1 0 0 0 0 1 0 0 0 11248 826 29 2 2 OR5P3 11 7825399 Missense_Mutation SNP C 11LU035_T 7825399 127261223 45 1697 SAA2 0 . GRCh38 11 18245478 18245478 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.268G>T p.Gly90Cys p.G90C ENST00000526900 4/4 188 134 54 244 244 0 strelka-varscan-mutect SAA2,missense_variant,p.Gly90Cys,ENST00000526900,;SAA2,missense_variant,p.Gly90Cys,ENST00000529528,;SAA2,missense_variant,p.Gly90Cys,ENST00000256733,NM_030754.4;SAA2,intron_variant,,ENST00000414546,NM_001127380.2;SAA2,intron_variant,,ENST00000528349,;SAA2-SAA4,intron_variant,,ENST00000524555,NM_001199744.1;SAA2,intron_variant,,ENST00000530400,;RNA5SP333,downstream_gene_variant,,ENST00000363466,; A ENST00000526900 Transcript missense_variant 452/687 268/369 90/122 G/C Ggt/Tgt 1 -1 SAA2 HGNC HGNC:10514 protein_coding YES CCDS7833.1 ENSP00000436126 P0DJI9 UPI000016A553 deleterious(0) 4/4 hmmpanther:PTHR23424:SF7,hmmpanther:PTHR23424,PIRSF_domain:PIRSF002472,Pfam_domain:PF00277,SMART_domains:SM00197 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 18245478 18245478 C A 1 0 0 0 0 1 0 0 0 14058 594 21 2 2 SAA2 11 18245478 Missense_Mutation SNP C 11LU035_T 10420079 18245478 116841144 46 1698 PCF11 0 . GRCh38 11 83168681 83168681 + Silent SNP A A T novel 11LU035_T 11LU035_N A A c.2346A>T p.= p.G782G ENST00000298281 8/16 401 319 82 586 585 1 strelka-varscan-mutect PCF11,synonymous_variant,p.=,ENST00000298281,NM_015885.3;PCF11,synonymous_variant,p.=,ENST00000530660,;PCF11,synonymous_variant,p.=,ENST00000530304,;PCF11,upstream_gene_variant,,ENST00000530906,;PCF11,downstream_gene_variant,,ENST00000533018,; T ENST00000298281 Transcript synonymous_variant 2798/7677 2346/4668 782/1555 G ggA/ggT 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 8/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 83168681 83168681 A T 1 0 0 0 0 0 0 0 1 11661 262 10 4 4 PCF11 11 83168681 Silent SNP A 11LU035_T 64923203 83168681 51917941 47 1699 ARID2 0 . GRCh38 12 45811549 45811550 + Frame_Shift_Ins INS - - G novel 11LU035_T 11LU035_N - - c.418+1dupG ENST00000334344 4/21 99 68 31 131 131 0 sindel-pindel ARID2,frameshift_variant,,ENST00000334344,NM_152641.2;ARID2,splice_region_variant,,ENST00000422737,; G ENST00000334344 Transcript frameshift_variant,splice_region_variant 588-589/8642 416-417/5508 139/1835 S/SX tcg/tcGg 1 1 ARID2 HGNC HGNC:18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 UPI00001D7973 NM_152641.2 4/21 hmmpanther:PTHR22970,hmmpanther:PTHR22970:SF14 HIGH 1 insertion 1 3 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 G 7 5 4 45811549 45811549 - G 1 0 1 1 0 0 0 0 0 1051 898 31 0 0 ARID2 12 45811549 Frame_Shift_Ins INS - 11LU035_T 45811549 87463760 48 1700 E2F7 0 . GRCh38 12 77046314 77046314 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.553C>T p.Arg185Cys p.R185C ENST00000322886 5/13 124 85 39 135 135 0 strelka-varscan-mutect E2F7,missense_variant,p.Arg185Cys,ENST00000322886,NM_203394.2;E2F7,missense_variant,p.Arg185Cys,ENST00000416496,;E2F7,missense_variant,p.Arg185Cys,ENST00000550669,;E2F7,missense_variant,p.Arg63Cys,ENST00000551058,;E2F7,missense_variant,p.Arg61Cys,ENST00000552907,;E2F7,non_coding_transcript_exon_variant,,ENST00000551558,; A ENST00000322886 Transcript missense_variant 789/5740 553/2736 185/911 R/C Cgc/Tgc 1 -1 E2F7 HGNC HGNC:23820 protein_coding YES CCDS9016.1 ENSP00000323246 Q96AV8 UPI00001B64A1 NM_203394.2 deleterious(0) 5/13 Gene3D:1.10.10.10,Pfam_domain:PF02319,hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF25,SMART_domains:SM01372,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 77046314 77046314 G A 1 0 0 0 0 1 0 0 0 4696 1145 40 1 1 E2F7 12 77046314 Missense_Mutation SNP G 11LU035_T 31234765 77046314 56228995 49 1701 SLC5A8 0 . GRCh38 12 101166540 101166540 + Nonsense_Mutation SNP C C A 11LU035_T 11LU035_N C C c.1480G>T p.Glu494Ter p.E494* ENST00000536262 12/15 146 116 30 212 210 2 strelka-mutect SLC5A8,stop_gained,p.Glu494Ter,ENST00000536262,NM_145913.3; A ENST00000536262 Transcript stop_gained 2039/4178 1480/1833 494/610 E/* Gaa/Taa COSM1706091,COSM933899 1 -1 SLC5A8 HGNC HGNC:19119 protein_coding YES CCDS9080.1 ENSP00000445340 Q8N695 UPI000004DAF6 NM_145913.3 12/15 1,1 HIGH 1 SNV 1 1,1 1 PASS rs1176077061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 4 101166540 101166540 C A 1 0 0 0 0 0 1 0 0 14954 922 32 2 2 SLC5A8 12 101166540 Nonsense_Mutation SNP C 11LU035_T 24120226 101166540 32108769 50 1702 CCDC53 0 . GRCh38 12 102025977 102025977 + Missense_Mutation SNP A A G novel 11LU035_T 11LU035_N A A c.497T>C p.Leu166Pro p.L166P ENST00000240079 6/7 70 42 28 24 24 0 strelka-varscan-mutect CCDC53,missense_variant,p.Leu166Pro,ENST00000240079,NM_016053.3;CCDC53,missense_variant,p.Leu165Pro,ENST00000545679,NM_001301107.1;CCDC53,missense_variant,p.Leu79Pro,ENST00000542923,;CCDC53,non_coding_transcript_exon_variant,,ENST00000539515,;CCDC53,missense_variant,p.Leu165Pro,ENST00000544341,;CCDC53,missense_variant,p.Leu166Pro,ENST00000540536,;CCDC53,3_prime_UTR_variant,,ENST00000535501,;CCDC53,3_prime_UTR_variant,,ENST00000538761,;CCDC53,non_coding_transcript_exon_variant,,ENST00000536197,;CCDC53,non_coding_transcript_exon_variant,,ENST00000541569,; G ENST00000240079 Transcript missense_variant 659/916 497/585 166/194 L/P cTt/cCt 1 -1 CCDC53 HGNC HGNC:24256 protein_coding YES CCDS44959.1 ENSP00000240079 Q9Y3C0 UPI00001254D2 NM_016053.3 deleterious(0.03) 6/7 hmmpanther:PTHR13015,hmmpanther:PTHR13015:SF0,Pfam_domain:PF10152 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 4 102025977 102025977 A G 1 0 0 0 0 1 0 0 0 2527 86 3 5 5 CCDC53 12 102025977 Missense_Mutation SNP A 11LU035_T 859437 102025977 31249332 51 1703 TBX5 0 . GRCh38 12 114399581 114399581 + Silent SNP C C T rs769736865 11LU035_T 11LU035_N C C c.294G>A p.= p.T98T ENST00000310346 4/9 522 382 140 911 911 0 strelka-varscan-mutect TBX5,synonymous_variant,p.=,ENST00000310346,NM_000192.3;TBX5,synonymous_variant,p.=,ENST00000349716,NM_080717.2;TBX5,synonymous_variant,p.=,ENST00000405440,NM_181486.2;TBX5,synonymous_variant,p.=,ENST00000526441,;TBX5,non_coding_transcript_exon_variant,,ENST00000552726,; T ENST00000310346 Transcript synonymous_variant 961/3825 294/1557 98/518 T acG/acA rs769736865,COSM1146914,COSM691954 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 4/9 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28,Gene3D:1h6fA00,Pfam_domain:PF00907,SMART_domains:SM00425,Superfamily_domains:SSF49417 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs769736865 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 114399581 114399581 C T 1 0 0 0 0 0 0 0 1 16065 871 31 1 1 TBX5 12 114399581 Silent SNP C 11LU035_T 12373604 114399581 18875728 52 1704 SLC46A3 0 . GRCh38 13 28717885 28717885 + Missense_Mutation SNP G G C novel 11LU035_T 11LU035_N G G c.114C>G p.Asn38Lys p.N38K ENST00000380814 2/7 174 158 16 236 236 0 strelka-varscan-mutect SLC46A3,missense_variant,p.Asn38Lys,ENST00000266943,NM_181785.3;SLC46A3,missense_variant,p.Asn38Lys,ENST00000380814,NM_001135919.1;CYP51A1P2,downstream_gene_variant,,ENST00000419457,; C ENST00000380814 Transcript missense_variant 613/2121 114/1392 38/463 N/K aaC/aaG 1 -1 SLC46A3 HGNC HGNC:27501 protein_coding YES CCDS45021.1 ENSP00000370192 Q7Z3Q1 UPI0000199D25 NM_001135919.1 deleterious(0) 2/7 Pfam_domain:PF07690,hmmpanther:PTHR23507,hmmpanther:PTHR23507:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 28717885 28717885 G C 1 0 0 0 0 1 0 0 0 14923 1020 36 4 4 SLC46A3 13 28717885 Missense_Mutation SNP G 11LU035_T 28717885 85646443 53 1705 RYR3 0 . GRCh38 15 33742376 33742376 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.7831C>A p.Pro2611Thr p.P2611T ENST00000634891 52/104 176 146 30 219 218 1 strelka-mutect RYR3,missense_variant,p.Pro2611Thr,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Pro2611Thr,ENST00000622037,;RYR3,missense_variant,p.Pro2611Thr,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Pro2610Thr,ENST00000389232,;RYR3,missense_variant,p.Pro2610Thr,ENST00000634418,;RYR3,missense_variant,p.Pro316Thr,ENST00000635790,; A ENST00000634891 Transcript missense_variant 7932/15591 7831/14613 2611/4870 P/T Cct/Act 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.09) 52/104 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 33742376 33742376 C A 1 0 0 0 0 1 0 0 0 14030 739 26 2 2 RYR3 15 33742376 Missense_Mutation SNP C 11LU035_T 33742376 68248813 54 1706 BUB1B 0 . GRCh38 15 40170575 40170575 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.278G>A p.Gly93Glu p.G93E ENST00000287598 4/23 372 265 107 404 404 0 strelka-varscan-mutect BUB1B,missense_variant,p.Gly93Glu,ENST00000287598,NM_001211.5;BUB1B,missense_variant,p.Gly107Glu,ENST00000412359,;BUB1B,splice_region_variant,,ENST00000559414,;BUB1B,non_coding_transcript_exon_variant,,ENST00000560120,;BUB1B,3_prime_UTR_variant,,ENST00000558715,; A ENST00000287598 Transcript missense_variant 473/3725 278/3153 93/1050 G/E gGg/gAg 1 1 BUB1B HGNC HGNC:1149 protein_coding YES CCDS10053.1 ENSP00000287598 O60566 UPI000006E699 NM_001211.5 deleterious(0) 4/23 PROSITE_profiles:PS51489,hmmpanther:PTHR14030:SF4,hmmpanther:PTHR14030,Pfam_domain:PF08311,SMART_domains:SM00777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 40170575 40170575 G A 1 0 0 0 0 1 0 0 0 1747 1232 43 3 3 BUB1B 15 40170575 Missense_Mutation SNP G 11LU035_T 6428199 40170575 61820614 55 1707 FBN1 0 . GRCh38 15 48463972 48463972 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.4992C>T p.= p.Y1664Y ENST00000316623 41/66 411 353 58 527 527 0 strelka-varscan-mutect FBN1,synonymous_variant,p.=,ENST00000316623,NM_000138.4;FBN1,synonymous_variant,p.=,ENST00000559133,;FBN1,3_prime_UTR_variant,,ENST00000537463,; A ENST00000316623 Transcript synonymous_variant 5448/11756 4992/8616 1664/2871 Y taC/taT 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 41/66 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 48463972 48463972 G A 1 0 0 0 0 0 0 0 1 5565 1372 48 3 3 FBN1 15 48463972 Silent SNP G 11LU035_T 8293397 48463972 53527217 56 1708 AP4E1 0 . GRCh38 15 50997788 50997788 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.2809G>A p.Asp937Asn p.D937N ENST00000261842 18/21 45 37 8 64 64 0 strelka-varscan-mutect AP4E1,missense_variant,p.Asp937Asn,ENST00000261842,NM_007347.4;AP4E1,missense_variant,p.Asp862Asn,ENST00000560508,NM_001252127.1;AP4E1,non_coding_transcript_exon_variant,,ENST00000561397,;AP4E1,3_prime_UTR_variant,,ENST00000558439,;AP4E1,3_prime_UTR_variant,,ENST00000561393,; A ENST00000261842 Transcript missense_variant 2915/6758 2809/3414 937/1137 D/N Gat/Aat 1 1 AP4E1 HGNC HGNC:573 protein_coding YES CCDS32240.1 ENSP00000261842 Q9UPM8 UPI00001D89D8 NM_007347.4 tolerated(0.06) 18/21 PIRSF_domain:PIRSF037097 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.45134 1 1 1 1 0 A 3 1 4 50997788 50997788 G A 1 0 0 0 0 1 0 0 0 868 942 33 3 3 AP4E1 15 50997788 Missense_Mutation SNP G 11LU035_T 2533816 50997788 50993401 57 1709 IQCH 0 . GRCh38 15 67388913 67388913 + Silent SNP A A G novel 11LU035_T 11LU035_N A A c.1539A>G p.= p.L513L ENST00000335894 12/21 209 175 34 209 208 1 strelka-varscan-mutect IQCH,synonymous_variant,p.=,ENST00000335894,NM_001031715.2;IQCH,synonymous_variant,p.=,ENST00000546225,NM_001284347.1;IQCH,synonymous_variant,p.=,ENST00000358767,NM_001284348.1;IQCH,synonymous_variant,p.=,ENST00000561357,;IQCH,3_prime_UTR_variant,,ENST00000514049,; G ENST00000335894 Transcript synonymous_variant 1605/4208 1539/3084 513/1027 L ctA/ctG 1 1 IQCH HGNC HGNC:25721 protein_coding YES CCDS32273.1 ENSP00000336861 Q86VS3 UPI000013CCE9 NM_001031715.2 12/21 hmmpanther:PTHR14465:SF0,hmmpanther:PTHR14465 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 4 67388913 67388913 A G 1 0 0 0 0 0 0 0 1 7717 378 14 5 5 IQCH 15 67388913 Silent SNP A 11LU035_T 16391125 67388913 34602276 58 1710 BNC1 0 . GRCh38 15 83264551 83264551 + Nonsense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.700G>T p.Glu234Ter p.E234* ENST00000345382 4/5 151 112 39 287 286 1 strelka-varscan-mutect BNC1,stop_gained,p.Glu234Ter,ENST00000345382,NM_001717.3;BNC1,stop_gained,p.Glu227Ter,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; A ENST00000345382 Transcript stop_gained 786/4610 700/2985 234/994 E/* Gag/Tag 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 4 83264551 83264551 C A 1 0 0 0 0 0 1 0 0 1630 835 29 2 2 BNC1 15 83264551 Nonsense_Mutation SNP C 11LU035_T 15875638 83264551 18726638 59 1711 SEPT1 0 . GRCh38 16 30378455 30378455 + Silent SNP G G A rs779596462 11LU035_T 11LU035_N G G c.1224C>T p.= p.G408G ENST00000321367 12/12 22 16 6 114 114 0 strelka-varscan-mutect SEPT1,synonymous_variant,p.=,ENST00000321367,NM_052838.4;ZNF48,intron_variant,,ENST00000528032,;ZNF48,intron_variant,,ENST00000495929,;MYLPF,downstream_gene_variant,,ENST00000322861,NM_013292.3;MYLPF,downstream_gene_variant,,ENST00000568749,;MYLPF,downstream_gene_variant,,ENST00000566955,;MYLPF,downstream_gene_variant,,ENST00000563718,;SEPT1,downstream_gene_variant,,ENST00000570039,;SEPT1,downstream_gene_variant,,ENST00000567783,;RP11-297C4.6,downstream_gene_variant,,ENST00000624127,;SEPT1,3_prime_UTR_variant,,ENST00000572252,;SEPT1,non_coding_transcript_exon_variant,,ENST00000563957,;SEPT1,non_coding_transcript_exon_variant,,ENST00000573615,;SEPT1,downstream_gene_variant,,ENST00000566517,;SEPT1,downstream_gene_variant,,ENST00000568577,;SEPT1,downstream_gene_variant,,ENST00000563743,;SEPT1,downstream_gene_variant,,ENST00000562152,;MYLPF,downstream_gene_variant,,ENST00000563728,; A ENST00000321367 Transcript synonymous_variant 1270/1592 1224/1245 408/414 G ggC/ggT rs779596462,COSM4623311 1 -1 SEPT1 HGNC HGNC:2879 protein_coding YES CCDS10678.3 ENSP00000324511 J3KNL2 UPI000066D948 NM_052838.4 12/12 Low_complexity_(Seg):seg,PIRSF_domain:PIRSF006698 0,1 LOW SNV 5 0,1 1 PASS rs779596462 . 0 205 5 0 0 0 0 0 -17.23913 1 1 1 1 0 A 2 1 4 30378455 30378455 G A 1 0 0 0 0 0 0 0 1 14335 1074 38 1 1 SEPT1 16 30378455 Silent SNP G 11LU035_T 30378455 59959890 60 1712 TP53 0 . GRCh38 17 7670699 7670699 + Missense_Mutation SNP C C A rs121912664 11LU035_T 11LU035_N C C c.1010G>T p.Arg337Leu p.R337L ENST00000269305 10/11 242 194 48 502 502 0 strelka-varscan-mutect TP53,missense_variant,p.Arg298Leu,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg337Leu,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg298Leu,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg337Leu,ENST00000445888,;TP53,missense_variant,p.Arg298Leu,ENST00000619485,;TP53,missense_variant,p.Arg205Leu,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg178Leu,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg326Leu,ENST00000615910,;TP53,3_prime_UTR_variant,,ENST00000617185,NM_001126114.2;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000622645,NM_001276696.1;TP53,3_prime_UTR_variant,,ENST00000455263,NM_001126113.2;TP53,3_prime_UTR_variant,,ENST00000610538,NM_001276695.1;TP53,3_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,3_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,3_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,3_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg298Leu,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 1200/2579 1010/1182 337/393 R/L cGc/cTc rs121912664,CM012663,CM104660,TP53_g.16901G>A,TP53_g.16901G>T,TP53_g.16901G>C,COSM11411,COSM131485,COSM220135,COSM378685,COSM378686,COSM43882 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.01) 10/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:1olgA00,Pfam_domain:PF07710,Superfamily_domains:SSF47719,Prints_domain:PR00386 likely_pathogenic,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1 2303263727081505 MODERATE 1 SNV 1 1,1,1,0,0,0,1,1,1,1,1,1 1 PASS rs121912664 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 7670699 7670699 C A 1 0 0 0 0 1 0 0 0 16859 768 27 1 1 TP53 17 7670699 Missense_Mutation SNP C 11LU035_T 7670699 75586742 61 1713 MYH13 0 . GRCh38 17 10345294 10345294 + Missense_Mutation SNP G G T novel 11LU035_T 11LU035_N G G c.1492C>A p.Leu498Met p.L498M ENST00000418404 14/41 479 434 45 848 847 1 varscan-mutect MYH13,missense_variant,p.Leu498Met,ENST00000418404,;MYH13,missense_variant,p.Leu498Met,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Leu498Met,ENST00000621918,;RP11-401O9.3,downstream_gene_variant,,ENST00000577743,; T ENST00000418404 Transcript missense_variant 1656/6296 1492/5817 498/1938 L/M Ctg/Atg 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0) 14/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 10345294 10345294 G T 1 0 0 0 0 1 0 0 0 10032 962 34 2 2 MYH13 17 10345294 Missense_Mutation SNP G 11LU035_T 2674595 10345294 72912147 62 1714 KRT26 0 . GRCh38 17 40771731 40771731 + Missense_Mutation SNP C C T rs764983838 11LU035_T 11LU035_N C C c.383G>A p.Arg128Gln p.R128Q ENST00000335552 1/8 213 117 96 213 213 0 strelka-varscan-mutect KRT26,missense_variant,p.Arg128Gln,ENST00000335552,NM_181539.4; T ENST00000335552 Transcript missense_variant 432/1733 383/1407 128/468 R/Q cGg/cAg rs764983838,COSM5055454 1 -1 KRT26 HGNC HGNC:30840 protein_coding YES CCDS11374.1 ENSP00000334798 Q7Z3Y9 UPI0000200C8F NM_181539.4 tolerated(0.07) 1/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF162,SMART_domains:SM01391 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764983838 . 0 206 0 4 0 0 0 0 -20 0.9999901 1 1 1 0 T 3 4 4 40771731 40771731 C T 1 0 0 0 0 1 0 0 0 8345 652 23 1 1 KRT26 17 40771731 Missense_Mutation SNP C 11LU035_T 30426437 40771731 42485710 63 1715 BAHCC1 0 . GRCh38 17 81443430 81443430 + Missense_Mutation SNP G G T 11LU035_T 11LU035_N G G c.2081G>T p.Gly694Val p.G694V ENST00000584436 5/29 113 56 57 187 187 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Gly694Val,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Gly694Val,ENST00000307745,;BAHCC1,upstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 2448/10801 2081/7920 694/2639 G/V gGc/gTc COSM4447924 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 tolerated(0.08) 5/29 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22 1 MODERATE 1 SNV 5 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 81443430 81443430 G T 1 0 0 0 0 1 0 0 0 1451 1203 42 2 2 BAHCC1 17 81443430 Missense_Mutation SNP G 11LU035_T 40671699 81443430 1814011 64 1716 PIEZO2 0 . GRCh38 18 10715800 10715800 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.4932G>T p.Arg1644Ser p.R1644S ENST00000503781 35/52 78 73 5 97 97 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Arg1595Ser,ENST00000383408,;PIEZO2,missense_variant,p.Arg1644Ser,ENST00000302079,;PIEZO2,missense_variant,p.Arg1669Ser,ENST00000580640,;PIEZO2,missense_variant,p.Arg1644Ser,ENST00000503781,NM_022068.3;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; A ENST00000503781 Transcript missense_variant 4932/8259 4932/8259 1644/2752 R/S agG/agT 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 35/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.30334 1 1 1 1 0 A 3 1 4 10715800 10715800 C A 1 0 0 0 0 1 0 0 0 11975 854 30 2 2 PIEZO2 18 10715800 Missense_Mutation SNP C 11LU035_T 10715800 69657485 65 1717 ZNF729 0 . GRCh38 19 22315931 22315931 + Silent SNP C C A novel 11LU035_T 11LU035_N C C c.2514C>A p.= p.A838A ENST00000601693 4/4 257 216 41 372 371 1 strelka-varscan-mutect ZNF729,synonymous_variant,p.=,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript synonymous_variant 2632/3877 2514/3759 838/1252 A gcC/gcA 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 4 22315931 22315931 C A 1 0 0 0 0 0 0 0 1 18703 610 22 2 2 ZNF729 19 22315931 Silent SNP C 11LU035_T 22315931 36301685 66 1718 TSHZ3 0 . GRCh38 19 31278897 31278897 + Missense_Mutation SNP T T A novel 11LU035_T 11LU035_N T T c.896A>T p.His299Leu p.H299L ENST00000240587 2/2 204 164 40 340 340 0 strelka-varscan-mutect TSHZ3,missense_variant,p.His299Leu,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; A ENST00000240587 Transcript missense_variant 1224/5176 896/3246 299/1081 H/L cAc/cTc 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 31278897 31278897 T A 1 0 0 0 0 1 0 0 0 17130 1696 59 4 4 TSHZ3 19 31278897 Missense_Mutation SNP T 11LU035_T 8962966 31278897 27338719 67 1719 MAP3K10 0 . GRCh38 19 40198492 40198492 + Missense_Mutation SNP A A G novel 11LU035_T 11LU035_N A A c.800A>G p.Tyr267Cys p.Y267C ENST00000253055 2/10 127 97 30 258 258 0 strelka-varscan-mutect MAP3K10,missense_variant,p.Tyr267Cys,ENST00000253055,NM_002446.3;MAP3K10,non_coding_transcript_exon_variant,,ENST00000593906,;MAP3K10,missense_variant,p.Tyr17Cys,ENST00000597986,;MAP3K10,missense_variant,p.Tyr33Cys,ENST00000594951,;MAP3K10,synonymous_variant,p.=,ENST00000593502,; G ENST00000253055 Transcript missense_variant 1088/3436 800/2865 267/954 Y/C tAc/tGc 1 1 MAP3K10 HGNC HGNC:6849 protein_coding YES CCDS12549.1 ENSP00000253055 Q02779 UPI000013CDAC NM_002446.3 deleterious(0) 2/10 PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF515,Pfam_domain:PF07714,PIRSF_domain:PIRSF000556,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999931 1 1 1 0 G 3 3 4 40198492 40198492 A G 1 0 0 0 0 1 0 0 0 9166 391 14 5 5 MAP3K10 19 40198492 Missense_Mutation SNP A 11LU035_T 8919595 40198492 18419124 68 1720 ERVV-2 0 . GRCh38 19 53050087 53050088 + Frame_Shift_Ins INS - - T novel 11LU035_T 11LU035_N - - c.837dupT p.Val280CysfsTer9 p.V280Cfs*9 ENST00000601417 2/2 377 287 90 790 788 2 sindel-varindel-pindel ERVV-2,frameshift_variant,p.Val280CysfsTer9,ENST00000601417,NM_001191055.1; T ENST00000601417 Transcript frameshift_variant 1442-1443/2431 836-837/1608 279/535 P/PX cct/ccTt 1 1 ERVV-2 HGNC HGNC:39051 protein_coding YES CCDS59420.1 ENSP00000472919 B6SEH9 M9QSX5 UPI00018258B9 NM_001191055.1 2/2 hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF8 HIGH 1 insertion 4 1 1 PASS . . 1 179 0 2 25 3 0 0 -3.372078 0 0 1 0 0 T 7 5 4 53050087 53050087 - T 1 0 1 1 0 0 0 0 0 5107 681 24 0 0 ERVV-2 19 53050087 Frame_Shift_Ins INS - 11LU035_T 12851595 53050087 5567529 69 1721 RFPL4A 0 . GRCh38 19 55762942 55762942 + Missense_Mutation SNP C C T novel 11LU035_T 11LU035_N C C c.631C>T p.Pro211Ser p.P211S ENST00000434937 3/3 852 777 75 1183 1183 0 varscan-mutect RFPL4A,missense_variant,p.Pro211Ser,ENST00000434937,NM_001145014.1; T ENST00000434937 Transcript missense_variant 802/1035 631/864 211/287 P/S Ccc/Tcc 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 tolerated(0.06) 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 5 1 PASS rs1225164085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 55762942 55762942 C T 1 0 0 0 0 1 0 0 0 13428 855 30 3 3 RFPL4A 19 55762942 Missense_Mutation SNP C 11LU035_T 2712855 55762942 2854674 70 1722 ZSCAN1 0 . GRCh38 19 58037930 58037930 + Missense_Mutation SNP A A G novel 11LU035_T 11LU035_N A A c.94A>G p.Arg32Gly p.R32G ENST00000282326 3/6 117 85 32 226 226 0 strelka-varscan-mutect ZSCAN1,missense_variant,p.Arg32Gly,ENST00000282326,NM_182572.3;ZSCAN1,missense_variant,p.Arg32Gly,ENST00000391700,;ZSCAN1,missense_variant,p.Arg32Gly,ENST00000601162,; G ENST00000282326 Transcript missense_variant 341/2054 94/1227 32/408 R/G Agg/Ggg 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 tolerated(1) 3/6 hmmpanther:PTHR10032:SF187,hmmpanther:PTHR10032,Superfamily_domains:SSF47353 MODERATE 1 SNV 2 1 PASS . . 0 204 2 4 0 0 0 0 -20 0.9999133 1 1 1 0 G 3 3 4 58037930 58037930 A G 1 0 0 0 0 1 0 0 0 18820 179 7 5 5 ZSCAN1 19 58037930 Missense_Mutation SNP A 11LU035_T 2274988 58037930 579686 71 1723 HAO1 0 . GRCh38 20 7934534 7934534 + Missense_Mutation SNP G G A rs758462740 11LU035_T 11LU035_N G G c.239C>T p.Thr80Met p.T80M ENST00000378789 2/8 180 168 12 286 285 1 strelka-varscan-mutect HAO1,missense_variant,p.Thr80Met,ENST00000378789,NM_017545.2; A ENST00000378789 Transcript missense_variant 291/1777 239/1113 80/370 T/M aCg/aTg rs758462740,COSM4689467 1 -1 HAO1 HGNC HGNC:4809 protein_coding YES CCDS13100.1 ENSP00000368066 Q9UJM8 A8K058 UPI000012C08B NM_017545.2 deleterious(0.01) 2/8 PROSITE_profiles:PS51349,hmmpanther:PTHR10578,Gene3D:3.20.20.70,PIRSF_domain:PIRSF000138,Pfam_domain:PF01070,Superfamily_domains:SSF51395 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758462740 . 0 205 0 2 3 0 0 0 -4.308678 0.7369527 1 1 1 0 A 3 1 4 7934534 7934534 G A 1 0 0 0 0 1 0 0 0 6837 1145 40 1 1 HAO1 20 7934534 Missense_Mutation SNP G 11LU035_T 7934534 56509633 72 1724 SLC9A8 0 . GRCh38 20 49883952 49883952 + Silent SNP C C T novel 11LU035_T 11LU035_N C C c.1425C>T p.= p.T475T ENST00000417961 14/16 359 328 31 690 690 0 strelka-varscan-mutect SLC9A8,synonymous_variant,p.=,ENST00000417961,NM_001260491.1;SLC9A8,synonymous_variant,p.=,ENST00000361573,NM_015266.2;SLC9A8,upstream_gene_variant,,ENST00000490250,; T ENST00000417961 Transcript synonymous_variant 1635/6309 1425/1794 475/597 T acC/acT 1 1 SLC9A8 HGNC HGNC:20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 UPI00017A7E08 NM_001260491.1 14/16 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF122,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 4 49883952 49883952 C T 1 0 0 0 0 0 0 0 1 15002 581 21 3 3 SLC9A8 20 49883952 Silent SNP C 11LU035_T 41949418 49883952 14560215 73 1725 PRELID3B 0 . GRCh38 20 59038608 59038608 + Missense_Mutation SNP G G A novel 11LU035_T 11LU035_N G G c.59C>T p.Ala20Val p.A20V ENST00000355937 2/6 113 107 6 146 145 1 varscan-mutect PRELID3B,missense_variant,p.Ala20Val,ENST00000355937,NM_016045.2;PRELID3B,missense_variant,p.Ala20Val,ENST00000371033,NM_001256403.1;PRELID3B,missense_variant,p.Ala20Val,ENST00000463057,;PRELID3B,non_coding_transcript_exon_variant,,ENST00000466051,; A ENST00000355937 Transcript missense_variant 238/2626 59/585 20/194 A/V gCt/gTt 1 -1 PRELID3B HGNC HGNC:15892 protein_coding YES CCDS42893.1 ENSP00000348206 Q9Y3B1 UPI00001285DF NM_016045.2 deleterious(0.03) 2/6 PROSITE_profiles:PS50904,hmmpanther:PTHR11158:SF22,hmmpanther:PTHR11158,Pfam_domain:PF04707 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -9.189111 0.9999993 1 1 1 0 A 3 1 4 59038608 59038608 G A 1 0 0 0 0 1 0 0 0 12606 971 34 3 3 PRELID3B 20 59038608 Missense_Mutation SNP G 11LU035_T 9154656 59038608 5405559 74 1726 KRTAP13-4 0 . GRCh38 21 30430332 30430332 + Silent SNP G G A novel 11LU035_T 11LU035_N G G c.57G>A p.= p.L19L ENST00000334068 1/1 105 96 9 157 157 0 strelka-varscan-mutect KRTAP13-4,synonymous_variant,p.=,ENST00000334068,NM_181600.1;KRTAP13-3,upstream_gene_variant,,ENST00000390690,NM_181622.1; A ENST00000334068 Transcript synonymous_variant 103/797 57/483 19/160 L ctG/ctA 1 1 KRTAP13-4 HGNC HGNC:18926 protein_coding YES CCDS13592.1 ENSP00000334834 Q3LI77 UPI000003B46D NM_181600.1 1/1 hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF10,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 206 2 2 0 0 0 0 -13.86056 0.9999938 1 1 1 0 A 2 1 4 30430332 30430332 G A 1 0 0 0 0 0 0 0 1 8408 1364 48 3 3 KRTAP13-4 21 30430332 Silent SNP G 11LU035_T 30430332 16279651 75 1727 KRTAP10-4 0 . GRCh38 21 44574309 44574309 + Missense_Mutation SNP G G T novel 11LU035_T 11LU035_N G G c.551G>T p.Ser184Ile p.S184I ENST00000400374 1/1 782 729 53 1415 1414 1 varscan-mutect KRTAP10-4,missense_variant,p.Ser184Ile,ENST00000400374,NM_198687.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,upstream_gene_variant,,ENST00000397916,; T ENST00000400374 Transcript missense_variant 581/1643 551/1206 184/401 S/I aGc/aTc 1 1 KRTAP10-4 HGNC HGNC:20521 protein_coding YES CCDS42957.1 ENSP00000383225 P60372 UPI00003D4D6E NM_198687.2 tolerated(0.09) 1/1 Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 44574309 44574309 G T 1 0 0 0 0 1 0 0 0 8394 971 34 2 2 KRTAP10-4 21 44574309 Missense_Mutation SNP G 11LU035_T 14143977 44574309 2135674 76 1728 KRTAP10-6 0 . GRCh38 21 44591934 44591934 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.551G>T p.Ser184Ile p.S184I ENST00000400368 1/1 540 483 57 977 976 1 varscan-mutect KRTAP10-6,missense_variant,p.Ser184Ile,ENST00000400368,NM_198688.3;KRTAP10-6,missense_variant,p.Ser179Ile,ENST00000622352,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; A ENST00000400368 Transcript missense_variant 572/1238 551/1098 184/365 S/I aGc/aTc 1 -1 KRTAP10-6 HGNC HGNC:20523 protein_coding YES CCDS42959.1 ENSP00000383219 P60371 UPI000021C43D NM_198688.3 tolerated(0.08) 1/1 Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 44591934 44591934 C A 1 0 0 0 0 1 0 0 0 8396 797 28 2 2 KRTAP10-6 21 44591934 Missense_Mutation SNP C 11LU035_T 17625 44591934 2118049 77 1729 ARFGAP3 0 . GRCh38 22 42817234 42817234 + Missense_Mutation SNP C C A novel 11LU035_T 11LU035_N C C c.972G>T p.Met324Ile p.M324I ENST00000263245 11/16 185 130 55 243 242 1 strelka-varscan-mutect ARFGAP3,missense_variant,p.Met324Ile,ENST00000263245,NM_014570.4;ARFGAP3,missense_variant,p.Met280Ile,ENST00000437119,NM_001142293.1;ARFGAP3,missense_variant,p.Met171Ile,ENST00000453516,; A ENST00000263245 Transcript missense_variant 1192/2857 972/1551 324/516 M/I atG/atT 1 -1 ARFGAP3 HGNC HGNC:661 protein_coding YES CCDS14042.1 ENSP00000263245 Q9NP61 A0A024R4U0 UPI0000125DF8 NM_014570.4 deleterious(0) 11/16 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF208 MODERATE 1 SNV 1 1 PASS rs1265101470 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 4 42817234 42817234 C A 1 0 0 0 0 1 0 0 0 974 710 25 2 2 ARFGAP3 22 42817234 Missense_Mutation SNP C 11LU035_T 42817234 8001234 78 1730 FAM155B 0 . GRCh38 X 69505769 69505769 + Missense_Mutation SNP G G A rs770211531 11LU035_T 11LU035_N G G c.487G>A p.Ala163Thr p.A163T ENST00000252338 1/3 115 69 46 223 223 0 strelka-varscan-mutect FAM155B,missense_variant,p.Ala163Thr,ENST00000252338,NM_015686.2; A ENST00000252338 Transcript missense_variant 529/4013 487/1419 163/472 A/T Gcc/Acc rs770211531,COSM4682634 1 1 FAM155B HGNC HGNC:30701 protein_coding YES CCDS35317.1 ENSP00000252338 O75949 UPI0000070EAA NM_015686.2 tolerated(0.25) 1/3 hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF8,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770211531 . 0 194 7 8 0 0 0 0 -20 0.9927766 1 1 1 0 A 3 1 4 69505769 69505769 G A 1 0 0 0 0 1 0 0 0 5314 1203 42 3 3 FAM155B 23 69505769 Missense_Mutation SNP G 11LU035_T 69505769 86535126 79 1731 ARMCX4 0 . GRCh38 X 101493421 101493421 + Missense_Mutation SNP G G C novel 11LU035_T 11LU035_N G G c.4832G>C p.Trp1611Ser p.W1611S ENST00000423738 2/2 111 67 44 164 164 0 strelka-varscan-mutect ARMCX4,missense_variant,p.Trp1611Ser,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; C ENST00000423738 Transcript missense_variant 5034/7424 4832/6873 1611/2290 W/S tGg/tCg 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 deleterious(0) 2/2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 4 101493421 101493421 G C 1 0 0 0 0 1 0 0 0 1102 1357 47 4 4 ARMCX4 23 101493421 Missense_Mutation SNP G 11LU035_T 31987652 101493421 54547474 80 1732 BCORL1 0 . GRCh38 X 130037366 130037366 + Splice_Site SNP G G T novel 11LU035_T 11LU035_N G G c.4306-1G>T p.X1436_splice ENST00000540052 158 106 52 291 290 1 strelka-varscan-mutect BCORL1,splice_acceptor_variant,,ENST00000540052,NM_021946.4;BCORL1,splice_acceptor_variant,,ENST00000218147,;BCORL1,splice_acceptor_variant,,ENST00000456822,; T ENST00000540052 Transcript splice_acceptor_variant -/7127 4306/5136 1436/1711 1 1 BCORL1 HGNC HGNC:25657 protein_coding YES CCDS14616.1 ENSP00000437775 Q5H9F3 UPI0001D3414A NM_021946.4 7/11 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 4 130037366 130037366 G T 1 0 0 0 0 0 0 1 0 1534 1014 35 2 2 BCORL1 23 130037366 Splice_Site SNP G 11LU035_T 28543945 130037366 26003529 81 1733 RAP2C 0 . GRCh38 X 132214438 132214438 + Frame_Shift_Del DEL C C - 11LU035_T 11LU035_N C C c.282delG p.Lys94AsnfsTer3 p.K94Nfs*3 ENST00000342983 3/4 51 37 14 67 67 0 sindel-varindel-pindel RAP2C,frameshift_variant,p.Lys94AsnfsTer3,ENST00000342983,NM_021183.4;RAP2C,frameshift_variant,p.Lys28AsnfsTer3,ENST00000620646,NM_001271187.1;RAP2C,frameshift_variant,p.Lys94AsnfsTer3,ENST00000370874,NM_001271186.1;RAP2C-AS1,upstream_gene_variant,,ENST00000441399,;RAP2C-AS1,upstream_gene_variant,,ENST00000421483,;RAP2C,non_coding_transcript_exon_variant,,ENST00000460462,;RAP2C,downstream_gene_variant,,ENST00000490400,; - ENST00000342983 Transcript frameshift_variant 1029/3896 282/552 94/183 K/X aaG/aa COSM121706 1 -1 RAP2C HGNC HGNC:21165 protein_coding YES CCDS14632.1 ENSP00000340274 Q9Y3L5 UPI00000236AB NM_021183.4 3/4 PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF200,hmmpanther:PTHR24070,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00173,SMART_domains:SM00175,SMART_domains:SM00174,Superfamily_domains:SSF52540 1 HIGH 1 deletion 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 4 132214438 132214438 C - 1 0 1 0 1 0 0 0 0 13201 796 28 0 0 RAP2C 23 132214438 Frame_Shift_Del DEL C 11LU035_T 2177072 132214438 23826457 82 1734 FLNA 0 . GRCh38 X 154368034 154368034 + Missense_Mutation SNP G G T novel 11LU035_T 11LU035_N G G c.430C>A p.Leu144Met p.L144M ENST00000369850 3/48 211 198 13 377 377 0 strelka-varscan-mutect FLNA,missense_variant,p.Leu144Met,ENST00000422373,NM_001456.3;FLNA,missense_variant,p.Leu144Met,ENST00000369850,NM_001110556.1;FLNA,missense_variant,p.Leu144Met,ENST00000360319,;FLNA,missense_variant,p.Leu117Met,ENST00000369856,;FLNA,missense_variant,p.Leu144Met,ENST00000344736,;FLNA,missense_variant,p.Leu117Met,ENST00000610817,;FLNA,missense_variant,p.Leu130Met,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000465144,; T ENST00000369850 Transcript missense_variant 667/8382 430/7944 144/2647 L/M Ctg/Atg 1 -1 FLNA HGNC HGNC:3754 protein_coding YES CCDS48194.1 ENSP00000358866 P21333 UPI000013C596 NM_001110556.1 deleterious(0) 3/48 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF173,PROSITE_patterns:PS00020,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 4 154368034 154368034 G T 1 0 0 0 0 1 0 0 0 5789 991 35 2 2 FLNA 23 154368034 Missense_Mutation SNP G 11LU035_T 22153596 154368034 1672861 83 1735 FBXO42 0 . GRCh38 1 16251086 16251086 + Missense_Mutation SNP G G C C3L-00001_T C3L-00001_N G G c.1738C>G p.Pro580Ala p.P580A ENST00000375592 10/10 184 136 48 121 121 0 strelka-varscan-mutect FBXO42,missense_variant,p.Pro580Ala,ENST00000375592,NM_018994.2;FBXO42,missense_variant,p.Pro298Ala,ENST00000456164,;FBXO42,missense_variant,p.Pro298Ala,ENST00000444116,; C ENST00000375592 Transcript missense_variant 1955/6202 1738/2154 580/717 P/A Cct/Gct COSM4471727 1 -1 FBXO42 HGNC HGNC:29249 protein_coding YES CCDS30613.1 ENSP00000364742 Q6P3S6 A0A024QZB0 UPI0000161A51 NM_018994.2 tolerated_low_confidence(0.41) 10/10 hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF316,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 16251086 16251086 G C 1 0 0 0 0 1 0 0 0 5614 1174 41 4 4 FBXO42 1 16251086 Missense_Mutation SNP G C3L-00001_T 16251086 232705336 1 1736 RRAGC 0 . GRCh38 1 38851634 38851634 + Missense_Mutation SNP C C A novel C3L-00001_T C3L-00001_N C C c.880G>T p.Asp294Tyr p.D294Y ENST00000373001 5/7 42 37 5 56 56 0 strelka-varscan-mutect RRAGC,missense_variant,p.Asp294Tyr,ENST00000373001,NM_022157.3,NM_001271851.1;RP5-864K19.7,non_coding_transcript_exon_variant,,ENST00000622355,;RRAGC,non_coding_transcript_exon_variant,,ENST00000493015,;RRAGC,non_coding_transcript_exon_variant,,ENST00000496778,;RRAGC,upstream_gene_variant,,ENST00000474456,; A ENST00000373001 Transcript missense_variant 1057/2732 880/1200 294/399 D/Y Gat/Tat 1 -1 RRAGC HGNC HGNC:19902 protein_coding YES CCDS430.1 ENSP00000362092 Q9HB90 UPI00000372EF NM_022157.3,NM_001271851.1 deleterious(0) 5/7 hmmpanther:PTHR11259,hmmpanther:PTHR11259:SF6 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -12.64783 0.9999967 1 1 1 0 A 3 1 5 38851634 38851634 C A 1 0 0 0 0 1 0 0 0 13928 826 29 2 2 RRAGC 1 38851634 Missense_Mutation SNP C C3L-00001_T 22600548 38851634 210104788 2 1737 NFIA 0 . GRCh38 1 61088636 61088636 + Missense_Mutation SNP T T C novel C3L-00001_T C3L-00001_N T T c.650T>C p.Val217Ala p.V217A ENST00000371189 3/12 109 93 16 78 78 0 strelka-varscan-mutect NFIA,missense_variant,p.Val172Ala,ENST00000403491,NM_001134673.3;NFIA,missense_variant,p.Val172Ala,ENST00000371187,NM_005595.4;NFIA,missense_variant,p.Val164Ala,ENST00000407417,NM_001145511.1;NFIA,missense_variant,p.Val217Ala,ENST00000371189,NM_001145512.1;NFIA,missense_variant,p.Val195Ala,ENST00000371191,;NFIA,missense_variant,p.Val172Ala,ENST00000371185,;NFIA,missense_variant,p.Val172Ala,ENST00000485903,;NFIA,missense_variant,p.Val172Ala,ENST00000371184,;NFIA,missense_variant,p.Val125Ala,ENST00000476646,;NFIA,missense_variant,p.Val76Ala,ENST00000496712,;NFIA,intron_variant,,ENST00000479364,; C ENST00000371189 Transcript missense_variant 732/1989 650/1665 217/554 V/A gTt/gCt 1 1 NFIA HGNC HGNC:7784 protein_coding YES CCDS53322.1 ENSP00000360231 Q12857 UPI000194EC2E NM_001145512.1 deleterious(0) 3/12 PROSITE_profiles:PS51080,hmmpanther:PTHR11492,SMART_domains:SM00523 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 61088636 61088636 T C 1 0 0 0 0 1 0 0 0 10407 1725 60 5 5 NFIA 1 61088636 Missense_Mutation SNP T C3L-00001_T 22237002 61088636 187867786 3 1738 OR6P1 0 . GRCh38 1 158563034 158563034 + Missense_Mutation SNP C C G novel C3L-00001_T C3L-00001_N C C c.571G>C p.Asp191His p.D191H ENST00000334632 1/1 364 326 38 248 248 0 strelka-varscan-mutect OR6P1,missense_variant,p.Asp191His,ENST00000334632,NM_001160325.1; G ENST00000334632 Transcript missense_variant 571/954 571/954 191/317 D/H Gac/Cac 1 -1 OR6P1 HGNC HGNC:15036 protein_coding YES CCDS53391.1 ENSP00000334721 Q8NGX9 A0A126GV72 UPI000004B1FF NM_001160325.1 tolerated(0.1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 5 158563034 158563034 C G 1 0 0 0 0 1 0 0 0 11277 826 29 4 4 OR6P1 1 158563034 Missense_Mutation SNP C C3L-00001_T 97474398 158563034 90393388 4 1739 SPTA1 0 . GRCh38 1 158645347 158645347 + Silent SNP G G A novel C3L-00001_T C3L-00001_N G G c.4035C>T p.= p.F1345F ENST00000368147 29/52 303 284 19 218 218 0 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000465741,; A ENST00000368147 Transcript synonymous_variant 4216/7999 4035/7260 1345/2419 F ttC/ttT 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 29/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 5 158645347 158645347 G A 1 0 0 0 0 0 0 0 1 15472 1165 41 3 3 SPTA1 1 158645347 Silent SNP G C3L-00001_T 82313 158645347 90311075 5 1740 FCGR3A 0 . GRCh38 1 161548469 161548469 + Missense_Mutation SNP T T G novel C3L-00001_T C3L-00001_N T T c.379A>C p.Thr127Pro p.T127P ENST00000367969 3/5 1226 1156 70 894 893 1 varscan-mutect FCGR3A,missense_variant,p.Thr127Pro,ENST00000367969,NM_001127592.1,NM_000569.6;FCGR3A,missense_variant,p.Thr91Pro,ENST00000443193,;FCGR3A,missense_variant,p.Thr91Pro,ENST00000436743,NM_001127595.1,NM_001127596.1,NM_001127593.1;FCGR3A,missense_variant,p.Thr91Pro,ENST00000367967,;FCGR3A,missense_variant,p.Thr108Pro,ENST00000426740,;FCGR3A,missense_variant,p.Thr90Pro,ENST00000442336,;FCGR3A,non_coding_transcript_exon_variant,,ENST00000476031,;RP11-25K21.6,intron_variant,,ENST00000537821,; G ENST00000367969 Transcript missense_variant 563/2310 379/873 127/290 T/P Aca/Cca 1 -1 FCGR3A HGNC HGNC:3619 protein_coding YES CCDS1232.1 ENSP00000356946 M9MML0 UPI000013E1BC NM_001127592.1,NM_000569.6 deleterious(0) 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF14,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 5 161548469 161548469 T G 1 0 0 0 0 1 0 0 0 5646 1667 58 5 5 FCGR3A 1 161548469 Missense_Mutation SNP T C3L-00001_T 2903122 161548469 87407953 6 1741 ASTN1 0 . GRCh38 1 176934301 176934301 + Missense_Mutation SNP G G T rs140709411 C3L-00001_T C3L-00001_N G G c.2522C>A p.Ser841Tyr p.S841Y ENST00000361833 16/23 165 152 13 84 84 0 strelka-varscan-mutect ASTN1,missense_variant,p.Ser841Tyr,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Ser841Tyr,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Ser841Tyr,ENST00000424564,NM_207108.2;ASTN1,downstream_gene_variant,,ENST00000281881,; T ENST00000361833 Transcript missense_variant 2536/7116 2522/3885 841/1294 S/Y tCt/tAt rs140709411 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious(0) 16/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS rs140709411 . 0 203 7 0 0 0 0 0 -19.9999 0.9999983 1 1 1 0 T 3 4 5 176934301 176934301 G T 1 0 0 0 0 1 0 0 0 1211 942 33 2 2 ASTN1 1 176934301 Missense_Mutation SNP G C3L-00001_T 15385832 176934301 72022121 7 1742 KDM3A 0 . GRCh38 2 86474798 86474798 + Missense_Mutation SNP G G T novel C3L-00001_T C3L-00001_N G G c.1747G>T p.Val583Leu p.V583L ENST00000409556 13/27 181 163 18 136 136 0 strelka-varscan KDM3A,missense_variant,p.Val583Leu,ENST00000409556,;KDM3A,missense_variant,p.Val583Leu,ENST00000312912,NM_018433.5;KDM3A,missense_variant,p.Val583Leu,ENST00000409064,NM_001146688.1;KDM3A,missense_variant,p.Val583Leu,ENST00000542128,;KDM3A,non_coding_transcript_exon_variant,,ENST00000485171,;KDM3A,missense_variant,p.Val583Leu,ENST00000441719,; T ENST00000409556 Transcript missense_variant 2112/4928 1747/3966 583/1321 V/L Gtg/Ttg 1 1 KDM3A HGNC HGNC:20815 protein_coding YES CCDS1990.1 ENSP00000386660 Q9Y4C1 UPI0000161FAE tolerated(0.18) 13/27 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF7 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 86474798 86474798 G T 1 0 0 0 0 1 0 0 0 8044 1377 48 2 2 KDM3A 2 86474798 Missense_Mutation SNP G C3L-00001_T 86474798 155718731 8 1743 XIRP2 0 . GRCh38 2 167239888 167239888 + Missense_Mutation SNP A A G novel C3L-00001_T C3L-00001_N A A c.892A>G p.Arg298Gly p.R298G ENST00000409195 6/11 276 230 46 233 232 1 strelka-varscan XIRP2,missense_variant,p.Arg298Gly,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Arg76Gly,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Arg123Gly,ENST00000628543,;XIRP2,missense_variant,p.Arg331Gly,ENST00000409728,NM_001199143.1;XIRP2,missense_variant,p.Arg298Gly,ENST00000409043,NM_001079810.3;XIRP2,missense_variant,p.Arg76Gly,ENST00000409605,NM_001199145.1; G ENST00000409195 Transcript missense_variant 981/12675 892/10650 298/3549 R/G Aga/Gga 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.27) 6/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 5 167239888 167239888 A G 1 0 0 0 0 1 0 0 0 17989 64 3 5 5 XIRP2 2 167239888 Missense_Mutation SNP A C3L-00001_T 80765090 167239888 74953641 9 1744 TTN 0 . GRCh38 2 178739284 178739289 + In_Frame_Del DEL AACTTT AACTTT - novel C3L-00001_T C3L-00001_N AACTTT AACTTT c.13944_13949delAAAGTT p.Glu4648_Phe4650delinsAsp p.E4648_F4650delinsD ENST00000589042 48/363 65 47 18 93 93 0 sindel-varindel-pindel TTN,inframe_deletion,p.Glu4648_Phe4650delinsAsp,ENST00000589042,NM_001267550.2;TTN,inframe_deletion,p.Glu4331_Phe4333delinsAsp,ENST00000591111,;TTN,inframe_deletion,p.Glu4331_Phe4333delinsAsp,ENST00000615779,NM_001256850.1;TTN,inframe_deletion,p.Glu4285_Phe4287delinsAsp,ENST00000460472,NM_003319.4;TTN,inframe_deletion,p.Glu4477_Phe4479delinsAsp,ENST00000342175,NM_133437.4;TTN,inframe_deletion,p.Glu4410_Phe4412delinsAsp,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000342992,NM_133378.4;TTN-AS1,intron_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000627661,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000631319,;TTN-AS1,downstream_gene_variant,,ENST00000625480,; - ENST00000589042 Transcript inframe_deletion 14169-14174/109224 13944-13949/107976 4648-4650/35991 EKF/D gaAAAGTTc/gac 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 48/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 deletion 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 5 178739284 178739284 AACTTT - 1 0 1 0 1 0 0 0 0 17245 246 9 0 0 TTN 2 178739284 In_Frame_Del DEL AACTTT C3L-00001_T 11499396 178739284 63454245 10 1745 MAP2 0 . GRCh38 2 209693503 209693503 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.1333G>A p.Glu445Lys p.E445K ENST00000360351 7/15 99 85 14 81 81 0 strelka-varscan MAP2,missense_variant,p.Glu445Lys,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Glu441Lys,ENST00000447185,;MAP2,missense_variant,p.Glu527Lys,ENST00000445941,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; A ENST00000360351 Transcript missense_variant 1839/9711 1333/5484 445/1827 E/K Gaa/Aaa 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0) 7/15 Low_complexity_(Seg):seg,hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 195 3 11 0 0 0 0 -19.99354 0.9134869 1 1 1 0 A 3 1 5 209693503 209693503 G A 1 0 0 0 0 1 0 0 0 9157 1291 45 3 3 MAP2 2 209693503 Missense_Mutation SNP G C3L-00001_T 30954219 209693503 32500026 11 1746 IQCA1 0 . GRCh38 2 236380595 236380595 + Silent SNP C C T novel C3L-00001_T C3L-00001_N C C c.1476G>A p.= p.K492K ENST00000431676 12/19 194 174 20 182 182 0 strelka-varscan-mutect IQCA1,synonymous_variant,p.=,ENST00000409907,NM_024726.4;IQCA1,synonymous_variant,p.=,ENST00000309507,NM_001270584.1;IQCA1,synonymous_variant,p.=,ENST00000431676,NM_001270585.1;IQCA1,synonymous_variant,p.=,ENST00000418802,;IQCA1,downstream_gene_variant,,ENST00000467572,;IQCA1,synonymous_variant,p.=,ENST00000254653,; T ENST00000431676 Transcript synonymous_variant 1511/3069 1476/2493 492/830 K aaG/aaA 1 -1 IQCA1 HGNC HGNC:26195 protein_coding YES CCDS74677.1 ENSP00000407213 A0A0A0MSY6 UPI0001AE77A0 NM_001270585.1 12/19 hmmpanther:PTHR14690,hmmpanther:PTHR14690:SF8,Low_complexity_(Seg):seg,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 5 236380595 236380595 C T 1 0 0 0 0 0 0 0 1 7705 912 32 3 3 IQCA1 2 236380595 Silent SNP C C3L-00001_T 26687092 236380595 5812934 12 1747 ELP6 0 . GRCh38 3 47496158 47496158 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.712C>T p.His238Tyr p.H238Y ENST00000296149 7/7 213 171 42 206 206 0 strelka-varscan-mutect ELP6,missense_variant,p.His238Tyr,ENST00000296149,NM_001031703.2;ELP6,missense_variant,p.His165Tyr,ENST00000446787,;ELP6,missense_variant,p.His165Tyr,ENST00000439305,;ELP6,downstream_gene_variant,,ENST00000444760,;ELP6,downstream_gene_variant,,ENST00000412761,;BOLA2P2,upstream_gene_variant,,ENST00000604904,;ELP6,3_prime_UTR_variant,,ENST00000442215,;ELP6,downstream_gene_variant,,ENST00000445044,;BOLA2P2,upstream_gene_variant,,ENST00000603861,; A ENST00000296149 Transcript missense_variant 883/1401 712/801 238/266 H/Y Cac/Tac 1 -1 ELP6 HGNC HGNC:25976 protein_coding YES CCDS43082.1 ENSP00000296149 Q0PNE2 UPI000020A684 NM_001031703.2 deleterious(0) 7/7 Pfam_domain:PF09807,hmmpanther:PTHR16184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 47496158 47496158 G A 1 0 0 0 0 1 0 0 0 4918 1348 47 3 3 ELP6 3 47496158 Missense_Mutation SNP G C3L-00001_T 47496158 150799401 13 1748 FAM19A4 0 . GRCh38 3 68752906 68752906 + Silent SNP T T C rs746821600 C3L-00001_T C3L-00001_N T T c.243A>G p.= p.G81G ENST00000295569 4/6 421 372 49 382 382 0 strelka-varscan-mutect FAM19A4,synonymous_variant,p.=,ENST00000295569,NM_001005527.2,NM_182522.4;FAM19A4,downstream_gene_variant,,ENST00000634242,;FAM19A4,downstream_gene_variant,,ENST00000495737,; C ENST00000295569 Transcript synonymous_variant 736/2292 243/423 81/140 G ggA/ggG rs746821600 1 -1 FAM19A4 HGNC HGNC:21591 protein_coding YES CCDS2907.1 ENSP00000295569 Q96LR4 A0A024R369 UPI0000071129 NM_001005527.2,NM_182522.4 4/6 PD298472,Pfam_domain:PF12020,hmmpanther:PTHR31770,hmmpanther:PTHR31770:SF7 LOW 1 SNV 1 1 PASS rs746821600 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 5 68752906 68752906 T C 1 0 0 0 0 0 0 0 1 5381 1654 58 5 5 FAM19A4 3 68752906 Silent SNP T C3L-00001_T 21256748 68752906 129542653 14 1749 IFT122 0 . GRCh38 3 129478032 129478032 + Silent SNP A A G novel C3L-00001_T C3L-00001_N A A c.1317A>G p.= p.K439K ENST00000296266 13/31 232 206 26 287 287 0 strelka-varscan-mutect IFT122,synonymous_variant,p.=,ENST00000431818,NM_001280545.1;IFT122,synonymous_variant,p.=,ENST00000296266,NM_052985.3;IFT122,synonymous_variant,p.=,ENST00000440957,NM_001280546.1;IFT122,synonymous_variant,p.=,ENST00000348417,NM_052989.2;IFT122,synonymous_variant,p.=,ENST00000347300,NM_018262.3;IFT122,synonymous_variant,p.=,ENST00000507564,NM_001280541.1;IFT122,synonymous_variant,p.=,ENST00000349441,NM_052990.2;IFT122,synonymous_variant,p.=,ENST00000504021,;IFT122,synonymous_variant,p.=,ENST00000515783,;IFT122,upstream_gene_variant,,ENST00000509522,;IFT122,downstream_gene_variant,,ENST00000512157,;IFT122,downstream_gene_variant,,ENST00000511498,;IFT122,downstream_gene_variant,,ENST00000509815,;IFT122,3_prime_UTR_variant,,ENST00000512220,;IFT122,non_coding_transcript_exon_variant,,ENST00000506507,;IFT122,non_coding_transcript_exon_variant,,ENST00000508654,;IFT122,upstream_gene_variant,,ENST00000513891,;IFT122,upstream_gene_variant,,ENST00000448668,;IFT122,upstream_gene_variant,,ENST00000512814,; G ENST00000296266 Transcript synonymous_variant 1509/4151 1317/3879 439/1292 K aaA/aaG 1 1 IFT122 HGNC HGNC:13556 protein_coding YES CCDS3060.1 ENSP00000296266 Q9HBG6 UPI0000141042 NM_052985.3 13/31 hmmpanther:PTHR12764,hmmpanther:PTHR12764:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 5 129478032 129478032 A G 1 0 0 0 0 0 0 0 1 7459 69 3 5 5 IFT122 3 129478032 Silent SNP A C3L-00001_T 60725126 129478032 68817527 15 1750 COL6A5 0 . GRCh38 3 130455494 130455494 + Silent SNP T T C novel C3L-00001_T C3L-00001_N T T c.6606T>C p.= p.N2202N ENST00000265379 38/43 117 86 31 217 217 0 strelka-varscan-mutect COL6A5,synonymous_variant,p.=,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,synonymous_variant,p.=,ENST00000512836,;COL6A5,synonymous_variant,p.=,ENST00000512482,;COL6A5,synonymous_variant,p.=,ENST00000373157,;COL6A5,synonymous_variant,p.=,ENST00000312481,; C ENST00000265379 Transcript synonymous_variant 7100/9214 6606/7836 2202/2611 N aaT/aaC 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 38/43 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 5 130455494 130455494 T C 1 0 0 0 0 0 0 0 1 3491 1461 51 5 5 COL6A5 3 130455494 Silent SNP T C3L-00001_T 977462 130455494 67840065 16 1751 ADCY2 0 . GRCh38 5 7709248 7709248 + Missense_Mutation SNP G G A C3L-00001_T C3L-00001_N G G c.1439G>A p.Arg480His p.R480H ENST00000338316 10/25 76 68 8 58 58 0 strelka-varscan-mutect ADCY2,missense_variant,p.Arg480His,ENST00000338316,NM_020546.2;RP11-711G10.1,intron_variant,,ENST00000514105,; A ENST00000338316 Transcript missense_variant 1528/6575 1439/3276 480/1091 R/H cGc/cAc COSM1757139,COSM254508 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0.01) 10/25 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1410091098 . 0 204 6 0 0 0 0 0 -17.36196 0.9999999 1 1 1 0 A 3 1 5 7709248 7709248 G A 1 0 0 0 0 1 0 0 0 338 1087 38 1 1 ADCY2 5 7709248 Missense_Mutation SNP G C3L-00001_T 7709248 173829011 17 1752 CDH12 0 . GRCh38 5 21760607 21760607 + Silent SNP T T C novel C3L-00001_T C3L-00001_N T T c.1584A>G p.= p.L528L ENST00000382254 13/15 218 199 19 162 162 0 strelka-varscan-mutect CDH12,synonymous_variant,p.=,ENST00000382254,NM_004061.3;CDH12,synonymous_variant,p.=,ENST00000504376,;CDH12,synonymous_variant,p.=,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; C ENST00000382254 Transcript synonymous_variant 2671/4164 1584/2385 528/794 L ttA/ttG 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 13/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 5 21760607 21760607 T C 1 0 0 0 0 0 0 0 1 2801 1403 49 5 5 CDH12 5 21760607 Silent SNP T C3L-00001_T 14051359 21760607 159777652 18 1753 OSMR 0 . GRCh38 5 38921644 38921644 + Missense_Mutation SNP A A C novel C3L-00001_T C3L-00001_N A A c.1615A>C p.Thr539Pro p.T539P ENST00000274276 12/18 225 203 22 227 227 0 strelka-varscan-mutect OSMR,missense_variant,p.Thr539Pro,ENST00000274276,NM_001323505.1,NM_001323506.1,NM_003999.2;OSMR,downstream_gene_variant,,ENST00000513831,; C ENST00000274276 Transcript missense_variant 2017/5539 1615/2940 539/979 T/P Aca/Cca 1 1 OSMR HGNC HGNC:8507 protein_coding YES CCDS3928.1 ENSP00000274276 Q99650 UPI000004CAC3 NM_001323505.1,NM_001323506.1,NM_003999.2 deleterious(0) 12/18 Pfam_domain:PF00041,PROSITE_patterns:PS01353,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF95,SMART_domains:SM00060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 38921644 38921644 A C 1 0 0 0 0 1 0 0 0 11359 159 6 5 5 OSMR 5 38921644 Missense_Mutation SNP A C3L-00001_T 17161037 38921644 142616615 19 1754 F2RL2 0 . GRCh38 5 76618513 76618513 + Missense_Mutation SNP G G C novel C3L-00001_T C3L-00001_N G G c.194C>G p.Thr65Ser p.T65S ENST00000296641 2/2 484 433 51 375 375 0 strelka-varscan-mutect F2RL2,missense_variant,p.Thr65Ser,ENST00000296641,NM_004101.3;F2RL2,missense_variant,p.Thr43Ser,ENST00000504899,NM_001256566.1;IQGAP2,intron_variant,,ENST00000274364,NM_006633.3;IQGAP2,intron_variant,,ENST00000379730,NM_001285460.1;IQGAP2,intron_variant,,ENST00000505766,;IQGAP2,intron_variant,,ENST00000502745,NM_001285462.1;IQGAP2,intron_variant,,ENST00000396234,NM_001285461.1;IQGAP2,intron_variant,,ENST00000514350,;IQGAP2,intron_variant,,ENST00000514001,;IQGAP2,intron_variant,,ENST00000509074,;IQGAP2,intron_variant,,ENST00000515505,;IQGAP2,splice_acceptor_variant,,ENST00000504254,;IQGAP2,intron_variant,,ENST00000513534,; C ENST00000296641 Transcript missense_variant 398/3429 194/1125 65/374 T/S aCt/aGt 1 -1 F2RL2 HGNC HGNC:3539 protein_coding YES CCDS4031.1 ENSP00000296641 O00254 UPI0000050431 NM_004101.3 tolerated(0.57) 2/2 Prints_domain:PR01429,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 76618513 76618513 G C 1 0 0 0 0 1 0 0 0 5213 1029 36 4 4 F2RL2 5 76618513 Missense_Mutation SNP G C3L-00001_T 37696869 76618513 104919746 20 1755 STK10 0 . GRCh38 5 172083082 172083082 + Missense_Mutation SNP C C T rs550965424 C3L-00001_T C3L-00001_N C C c.1688G>A p.Arg563His p.R563H ENST00000176763 11/19 453 402 51 297 297 0 strelka-varscan-mutect STK10,missense_variant,p.Arg563His,ENST00000176763,NM_005990.3;STK10,upstream_gene_variant,,ENST00000522879,; T ENST00000176763 Transcript missense_variant,splice_region_variant 2032/6060 1688/2907 563/968 R/H cGc/cAc rs550965424,COSM3410144 1 -1 STK10 HGNC HGNC:11388 protein_coding YES CCDS34290.1 ENSP00000176763 O94804 UPI0000136104 NM_005990.3 deleterious(0) 11/19 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs550965424 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 172083082 172083082 C T 1 0 0 0 0 1 0 0 0 15663 782 27 1 1 STK10 5 172083082 Missense_Mutation SNP C C3L-00001_T 95464569 172083082 9455177 21 1756 NT5E 0 . GRCh38 6 85467263 85467263 + Silent SNP C C A novel C3L-00001_T C3L-00001_N C C c.543C>A p.= p.T181T ENST00000257770 2/9 187 177 10 337 337 0 strelka-varscan NT5E,synonymous_variant,p.=,ENST00000369651,NM_001204813.1;NT5E,synonymous_variant,p.=,ENST00000257770,NM_002526.3;NT5E,synonymous_variant,p.=,ENST00000369646,;NT5E,upstream_gene_variant,,ENST00000416334,; A ENST00000257770 Transcript synonymous_variant 592/3548 543/1725 181/574 T acC/acA 1 1 NT5E HGNC HGNC:8021 protein_coding YES CCDS5002.1 ENSP00000257770 P21589 UPI0000124F48 NM_002526.3 2/9 hmmpanther:PTHR11575,hmmpanther:PTHR11575:SF25,Pfam_domain:PF00149,Gene3D:3.60.21.10,Superfamily_domains:SSF56300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 5 85467263 85467263 C A 1 0 0 0 0 0 0 0 1 10757 610 22 2 2 NT5E 6 85467263 Silent SNP C C3L-00001_T 85467263 85338716 22 1757 SLC16A10 0 . GRCh38 6 111206653 111206653 + Missense_Mutation SNP T T C novel C3L-00001_T C3L-00001_N T T c.1004T>C p.Ile335Thr p.I335T ENST00000368851 4/6 191 163 28 210 210 0 strelka-varscan SLC16A10,missense_variant,p.Ile21Thr,ENST00000368850,;SLC16A10,missense_variant,p.Ile335Thr,ENST00000368851,NM_018593.4; C ENST00000368851 Transcript missense_variant 1179/2508 1004/1548 335/515 I/T aTt/aCt 1 1 SLC16A10 HGNC HGNC:17027 protein_coding YES CCDS5089.1 ENSP00000357844 Q8TF71 UPI00000497DB NM_018593.4 tolerated(0.06) 4/6 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF119,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 111206653 111206653 T C 1 0 0 0 0 1 0 0 0 14669 1493 52 5 5 SLC16A10 6 111206653 Missense_Mutation SNP T C3L-00001_T 25739390 111206653 59599326 23 1758 HOXA3 0 . GRCh38 7 27108343 27108343 + Frame_Shift_Del DEL G G - novel C3L-00001_T C3L-00001_N G G c.904delC p.Gln302ArgfsTer74 p.Q302Rfs*74 ENST00000612286 4/4 20 16 4 11 11 0 sindel-pindel HOXA3,frameshift_variant,p.Gln302ArgfsTer74,ENST00000612286,NM_153631.2;HOXA3,frameshift_variant,p.Gln302ArgfsTer74,ENST00000396352,NM_030661.4;HOXA3,frameshift_variant,p.Gln302ArgfsTer74,ENST00000317201,;HOXA3,downstream_gene_variant,,ENST00000522788,;HOXA3,downstream_gene_variant,,ENST00000522456,;HOXA-AS2,intron_variant,,ENST00000518088,;HOXA3,downstream_gene_variant,,ENST00000521401,; - ENST00000612286 Transcript frameshift_variant 1243/3396 904/1332 302/443 Q/X Cag/ag 1 -1 HOXA3 HGNC HGNC:5104 protein_coding YES CCDS5404.1 ENSP00000484411 O43365 A0A024RA33 UPI000012CF22 NM_153631.2 4/4 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF137 HIGH 1 deletion 2 1 PASS . . 1 188 19 2 0 0 0 0 -10.3291 0.9927573 1 1 1 0 - 7 5 5 27108343 27108343 G - 1 0 1 0 1 0 0 0 0 7187 1357 47 0 0 HOXA3 7 27108343 Frame_Shift_Del DEL G C3L-00001_T 27108343 132237630 24 1759 AVL9 0 . GRCh38 7 32580232 32580232 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.1702G>A p.Gly568Ser p.G568S ENST00000318709 14/16 76 70 6 99 99 0 strelka-varscan AVL9,missense_variant,p.Gly568Ser,ENST00000318709,NM_015060.2;AVL9,intron_variant,,ENST00000446718,;AVL9,intron_variant,,ENST00000409301,;AVL9,non_coding_transcript_exon_variant,,ENST00000470500,;AVL9,upstream_gene_variant,,ENST00000497020,;AVL9,upstream_gene_variant,,ENST00000467779,;DPY19L1P1,downstream_gene_variant,,ENST00000417811,; A ENST00000318709 Transcript missense_variant 1923/6982 1702/1947 568/648 G/S Ggc/Agc 1 1 AVL9 HGNC HGNC:28994 protein_coding YES CCDS34613.1 ENSP00000315568 Q8NBF6 A0A024RA36 UPI0000049D97 NM_015060.2 deleterious(0) 14/16 hmmpanther:PTHR31017 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 32580232 32580232 G A 1 0 0 0 0 1 0 0 0 1384 1000 35 3 3 AVL9 7 32580232 Missense_Mutation SNP G C3L-00001_T 5471889 32580232 126765741 25 1760 URGCP 0 . GRCh38 7 43879256 43879256 + Missense_Mutation SNP C C G novel C3L-00001_T C3L-00001_N C C c.207G>C p.Glu69Asp p.E69D ENST00000453200 6/6 124 113 11 58 58 0 strelka-varscan URGCP,missense_variant,p.Glu26Asp,ENST00000336086,;URGCP,missense_variant,p.Glu69Asp,ENST00000453200,NM_001077663.2;URGCP,missense_variant,p.Glu26Asp,ENST00000443736,NM_001077664.2,NM_001290075.1,NM_001290076.1;URGCP,missense_variant,p.Glu60Asp,ENST00000402306,NM_017920.4;URGCP,missense_variant,p.Glu26Asp,ENST00000426198,;URGCP,missense_variant,p.Glu26Asp,ENST00000439702,;URGCP,missense_variant,p.Glu26Asp,ENST00000455877,;URGCP-MRPS24,intron_variant,,ENST00000603700,NM_001204871.1;URGCP,downstream_gene_variant,,ENST00000446958,;URGCP,non_coding_transcript_exon_variant,,ENST00000497914,;URGCP,non_coding_transcript_exon_variant,,ENST00000467410,;URGCP,non_coding_transcript_exon_variant,,ENST00000474376,; G ENST00000453200 Transcript missense_variant 701/4042 207/2796 69/931 E/D gaG/gaC 1 -1 URGCP HGNC HGNC:30890 protein_coding YES CCDS47578.1 ENSP00000396918 Q8TCY9 UPI000020EE9D NM_001077663.2 deleterious(0.02) 6/6 hmmpanther:PTHR22796 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99026 1 1 1 1 0 G 3 3 5 43879256 43879256 C G 1 0 0 0 0 1 0 0 0 17556 927 32 4 4 URGCP 7 43879256 Missense_Mutation SNP C C3L-00001_T 11299024 43879256 115466717 26 1761 ABCB1 0 . GRCh38 7 87600138 87600138 + Missense_Mutation SNP A A C novel C3L-00001_T C3L-00001_N A A c.47T>G p.Phe16Cys p.F16C ENST00000622132 2/28 241 151 90 188 187 1 strelka-varscan ABCB1,missense_variant,p.Phe16Cys,ENST00000622132,;ABCB1,missense_variant,p.Phe16Cys,ENST00000265724,NM_000927.4;ABCB1,missense_variant,p.Phe16Cys,ENST00000543898,;ABCB1,missense_variant,p.Phe16Cys,ENST00000416177,;ABCB1,downstream_gene_variant,,ENST00000476862,; C ENST00000622132 Transcript missense_variant 372/4778 47/3843 16/1280 F/C tTt/tGt 1 -1 ABCB1 HGNC HGNC:40 protein_coding YES CCDS5608.1 ENSP00000478255 P08183 A4D1D2 UPI000013D66C tolerated(0.18) 2/28 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 87600138 87600138 A C 1 0 0 0 0 1 0 0 0 44 14 1 5 5 ABCB1 7 87600138 Missense_Mutation SNP A C3L-00001_T 43720882 87600138 71745835 27 1762 TAC1 0 . GRCh38 7 97734259 97734259 + Missense_Mutation SNP G G C C3L-00001_T C3L-00001_N G G c.232G>C p.Glu78Gln p.E78Q ENST00000319273 4/7 98 86 12 130 130 0 strelka-varscan TAC1,missense_variant,p.Glu78Gln,ENST00000319273,NM_003182.2;TAC1,missense_variant,p.Glu78Gln,ENST00000350485,NM_013996.2;TAC1,intron_variant,,ENST00000346867,NM_013997.2;TAC1,non_coding_transcript_exon_variant,,ENST00000491437,;TAC1,downstream_gene_variant,,ENST00000495916,; C ENST00000319273 Transcript missense_variant 529/1239 232/390 78/129 E/Q Gaa/Caa COSM4394069 1 1 TAC1 HGNC HGNC:11517 protein_coding YES CCDS5649.1 ENSP00000321106 P20366 UPI000002C712 NM_003182.2 tolerated_low_confidence(0.35) 4/7 hmmpanther:PTHR11250:SF0,hmmpanther:PTHR11250 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -18.91772 0.9999904 1 1 1 0 C 3 2 5 97734259 97734259 G C 1 0 0 0 0 1 0 0 0 15894 1291 45 4 4 TAC1 7 97734259 Missense_Mutation SNP G C3L-00001_T 10134121 97734259 61611714 28 1763 DPP6 0 . GRCh38 7 154772888 154772888 + Nonsense_Mutation SNP T T A novel C3L-00001_T C3L-00001_N T T c.1082T>A p.Leu361Ter p.L361* ENST00000377770 10/26 121 103 18 101 101 0 strelka-varscan DPP6,stop_gained,p.Leu297Ter,ENST00000404039,NM_001039350.2;DPP6,stop_gained,p.Leu299Ter,ENST00000332007,NM_001936.4;DPP6,stop_gained,p.Leu361Ter,ENST00000377770,NM_130797.3;DPP6,stop_gained,p.Leu254Ter,ENST00000427557,NM_001290252.1; A ENST00000377770 Transcript stop_gained 1223/3710 1082/2598 361/865 L/* tTa/tAa 1 1 DPP6 HGNC HGNC:3010 protein_coding YES CCDS75683.1 ENSP00000367001 P42658 UPI00001AE746 NM_130797.3 10/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999936 1 1 1 0 A 4 1 5 154772888 154772888 T A 1 0 0 0 0 0 1 0 0 4545 1764 61 4 4 DPP6 7 154772888 Nonsense_Mutation SNP T C3L-00001_T 57038629 154772888 4573085 29 1764 CSMD1 0 . GRCh38 8 3110284 3110284 + Missense_Mutation SNP C C A novel C3L-00001_T C3L-00001_N C C c.6485G>T p.Gly2162Val p.G2162V ENST00000520002 44/71 106 90 16 107 107 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly2023Val,ENST00000537824,;CSMD1,missense_variant,p.Gly1642Val,ENST00000335551,;CSMD1,missense_variant,p.Gly2162Val,ENST00000520002,;CSMD1,missense_variant,p.Gly2162Val,ENST00000602557,;CSMD1,missense_variant,p.Gly2161Val,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly2162Val,ENST00000400186,;CSMD1,missense_variant,p.Gly2162Val,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000520561,;CSMD1,upstream_gene_variant,,ENST00000523062,; A ENST00000520002 Transcript missense_variant 7041/11740 6485/10698 2162/3565 G/V gGc/gTc 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 44/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 3110284 3110284 C A 1 0 0 0 0 1 0 0 0 3745 739 26 2 2 CSMD1 8 3110284 Missense_Mutation SNP C C3L-00001_T 3110284 142028352 30 1765 FBXO10 0 . GRCh38 9 37541626 37541626 + Missense_Mutation SNP A A T novel C3L-00001_T C3L-00001_N A A c.143T>A p.Leu48Gln p.L48Q ENST00000432825 2/11 153 139 14 135 135 0 strelka-varscan-mutect FBXO10,missense_variant,p.Leu48Gln,ENST00000432825,NM_012166.2;FBXO10,missense_variant,p.Leu48Gln,ENST00000541607,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000544475,;RP11-613M10.8,intron_variant,,ENST00000541804,;FBXO10,missense_variant,p.Leu48Gln,ENST00000276960,;RP11-613M10.8,3_prime_UTR_variant,,ENST00000537239,; T ENST00000432825 Transcript missense_variant 192/4575 143/2871 48/956 L/Q cTg/cAg 1 -1 FBXO10 HGNC HGNC:13589 protein_coding YES CCDS47966.1 ENSP00000403802 Q9UK96 UPI00001C1EC6 NM_012166.2 deleterious(0) 2/11 PROSITE_profiles:PS50181,hmmpanther:PTHR22990:SF19,hmmpanther:PTHR22990,Gene3D:1.20.1280.50,Pfam_domain:PF12937,SMART_domains:SM00256,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 37541626 37541626 A T 1 0 0 0 0 1 0 0 0 5589 188 7 4 4 FBXO10 9 37541626 Missense_Mutation SNP A C3L-00001_T 37541626 100853091 31 1766 SLC28A3 0 . GRCh38 9 84313383 84313383 + Silent SNP G G A novel C3L-00001_T C3L-00001_N G G c.132C>T p.= p.S44S ENST00000376238 2/18 112 99 13 113 113 0 strelka-varscan-mutect SLC28A3,synonymous_variant,p.=,ENST00000376238,NM_022127.2,NM_001199633.1;SLC28A3,non_coding_transcript_exon_variant,,ENST00000495823,; A ENST00000376238 Transcript synonymous_variant 182/4887 132/2076 44/691 S agC/agT 1 -1 SLC28A3 HGNC HGNC:16484 protein_coding YES CCDS6670.1 ENSP00000365413 Q9HAS3 UPI000006F5A6 NM_022127.2,NM_001199633.1 2/18 hmmpanther:PTHR10590,hmmpanther:PTHR10590:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 5 84313383 84313383 G A 1 0 0 0 0 0 0 0 1 14803 1310 46 3 3 SLC28A3 9 84313383 Silent SNP G C3L-00001_T 46771757 84313383 54081334 32 1767 WAPL 0 . GRCh38 10 86473887 86473888 + Frame_Shift_Ins INS - - T novel C3L-00001_T C3L-00001_N - - c.1730dupA p.Ser578GlufsTer16 p.S578Efs*16 ENST00000298767 5/19 81 73 8 130 130 0 sindel-pindel WAPL,frameshift_variant,p.Ser578GlufsTer16,ENST00000298767,NM_001318328.1,NM_015045.2;WAPL,frameshift_variant,p.Ser578GlufsTer16,ENST00000618527,;WAPL,5_prime_UTR_variant,,ENST00000263070,;WAPL,upstream_gene_variant,,ENST00000489996,; T ENST00000298767 Transcript frameshift_variant 2203-2204/6333 1730-1731/3573 577/1190 Q/QX cag/caAg 1 -1 WAPL HGNC HGNC:23293 protein_coding YES CCDS7375.1 ENSP00000298767 Q7Z5K2 UPI00001AE41A NM_001318328.1,NM_015045.2 5/19 hmmpanther:PTHR22100:SF13,hmmpanther:PTHR22100 HIGH 1 insertion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 5 86473887 86473887 - T 1 0 1 1 0 0 0 0 0 17808 912 32 0 0 WAPL 10 86473887 Frame_Shift_Ins INS - C3L-00001_T 86473887 47323535 33 1768 TRIM51 0 . GRCh38 11 55885522 55885522 + Missense_Mutation SNP C C A novel C3L-00001_T C3L-00001_N C C c.94C>A p.His32Asn p.H32N ENST00000449290 2/7 377 335 42 221 221 0 varscan-mutect TRIM51,missense_variant,p.His32Asn,ENST00000449290,NM_032681.3;TRIM51,upstream_gene_variant,,ENST00000244891,;RP11-738O11.9,downstream_gene_variant,,ENST00000533247,; A ENST00000449290 Transcript missense_variant 186/1629 94/1359 32/452 H/N Cac/Aac 1 1 TRIM51 HGNC HGNC:19023 protein_coding YES ENSP00000395086 Q9BSJ1 UPI0000DFFA1E NM_032681.3 deleterious(0.01) 2/7 PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF302,hmmpanther:PTHR24103,PROSITE_patterns:PS00518,Pfam_domain:PF15227,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 55885522 55885522 C A 1 0 0 0 0 1 0 0 0 17019 710 25 2 2 TRIM51 11 55885522 Missense_Mutation SNP C C3L-00001_T 55885522 79201100 34 1769 CD248 0 . GRCh38 11 66315059 66315059 + Missense_Mutation SNP G G C novel C3L-00001_T C3L-00001_N G G c.1969C>G p.Leu657Val p.L657V ENST00000311330 1/1 35 18 17 21 21 0 strelka-varscan-mutect CD248,missense_variant,p.Leu657Val,ENST00000311330,NM_020404.2;RP11-867G23.13,intron_variant,,ENST00000534065,; C ENST00000311330 Transcript missense_variant 1986/2558 1969/2274 657/757 L/V Ctg/Gtg 1 -1 CD248 HGNC HGNC:18219 protein_coding YES CCDS8134.1 ENSP00000308117 Q9HCU0 UPI0000049803 NM_020404.2 tolerated(1) 1/1 Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 66315059 66315059 G C 1 0 0 0 0 1 0 0 0 2693 991 35 4 4 CD248 11 66315059 Missense_Mutation SNP G C3L-00001_T 10429537 66315059 68771563 35 1770 DIXDC1 0 . GRCh38 11 111996144 111996144 + Nonsense_Mutation SNP C C G novel C3L-00001_T C3L-00001_N C C c.1754C>G p.Ser585Ter p.S585* ENST00000440460 17/20 169 156 13 141 141 0 varscan-mutect DIXDC1,stop_gained,p.Ser585Ter,ENST00000440460,NM_001037954.3;DIXDC1,stop_gained,p.Ser374Ter,ENST00000615255,NM_033425.4;DIXDC1,splice_region_variant,,ENST00000618522,;DIXDC1,splice_region_variant,,ENST00000526500,;DIXDC1,non_coding_transcript_exon_variant,,ENST00000530645,; G ENST00000440460 Transcript stop_gained,splice_region_variant 2051/5897 1754/2052 585/683 S/* tCa/tGa 1 1 DIXDC1 HGNC HGNC:23695 protein_coding YES CCDS73381.1 ENSP00000394352 Q155Q3 UPI000066DA69 NM_001037954.3 17/20 hmmpanther:PTHR10878,hmmpanther:PTHR10878:SF22 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 5 111996144 111996144 C G 1 0 0 0 0 0 1 0 0 4348 840 29 4 4 DIXDC1 11 111996144 Nonsense_Mutation SNP C C3L-00001_T 45681085 111996144 23090478 36 1771 PRB1 0 . GRCh38 12 11353891 11353891 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.212C>T p.Pro71Leu p.P71L ENST00000500254 3/5 247 229 18 128 128 0 varscan-mutect PRB1,missense_variant,p.Pro71Leu,ENST00000546254,;PRB1,missense_variant,p.Pro71Leu,ENST00000500254,NM_005039.3,NM_199353.2;PRB1,missense_variant,p.Pro71Leu,ENST00000545626,NM_199354.2;PRB1,missense_variant,p.Pro71Leu,ENST00000240636,; A ENST00000500254 Transcript missense_variant 250/775 212/597 71/198 P/L cCc/cTc 1 -1 PRB1 HGNC HGNC:9337 protein_coding YES CCDS8642.1 ENSP00000420826 G5E9X6 UPI00002371B8 NM_005039.3,NM_199353.2 deleterious_low_confidence(0.04) 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR23203:SF2,hmmpanther:PTHR23203,Pfam_domain:PF15240,SMART_domains:SM01412 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 11353891 11353891 G A 1 0 0 0 0 1 0 0 0 12573 1232 43 3 3 PRB1 12 11353891 Missense_Mutation SNP G C3L-00001_T 11353891 121921418 37 1772 RAN 0 . GRCh38 12 130872839 130872839 + Missense_Mutation SNP G G C novel C3L-00001_T C3L-00001_N G G c.40G>C p.Val14Leu p.V14L ENST00000543796 3/7 194 163 31 198 198 0 strelka-varscan-mutect RAN,missense_variant,p.Val14Leu,ENST00000543796,NM_006325.4;RAN,missense_variant,p.Val32Leu,ENST00000448750,;RAN,missense_variant,p.Val14Leu,ENST00000392369,;RAN,missense_variant,p.Val14Leu,ENST00000392367,;RAN,missense_variant,p.Val10Leu,ENST00000535090,;RAN,5_prime_UTR_variant,,ENST00000541630,NM_001300796.1,NM_001300797.1;RAN,intron_variant,,ENST00000541679,;RNU6-1077P,upstream_gene_variant,,ENST00000410506,;RAN,missense_variant,p.Val29Leu,ENST00000536606,;RAN,non_coding_transcript_exon_variant,,ENST00000537745,;RAN,non_coding_transcript_exon_variant,,ENST00000477395,;RAN,non_coding_transcript_exon_variant,,ENST00000464211,;RAN,upstream_gene_variant,,ENST00000539498,; C ENST00000543796 Transcript missense_variant 298/2661 40/651 14/216 V/L Gta/Cta 1 1 RAN HGNC HGNC:9846 protein_coding YES CCDS9271.1 ENSP00000446215 P62826 UPI0000000DE2 NM_006325.4 tolerated(0.23) 3/7 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51418,hmmpanther:PTHR24071,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 130872839 130872839 G C 1 0 0 0 0 1 0 0 0 13183 1391 48 4 4 RAN 12 130872839 Missense_Mutation SNP G C3L-00001_T 119518948 130872839 2402470 38 1773 KIAA0226L 0 . GRCh38 13 46359522 46359522 + Missense_Mutation SNP C C A novel C3L-00001_T C3L-00001_N C C c.1229G>T p.Arg410Ile p.R410I ENST00000429979 9/15 72 62 10 115 115 0 strelka-varscan-mutect KIAA0226L,missense_variant,p.Arg410Ile,ENST00000429979,NM_025113.3;KIAA0226L,missense_variant,p.Arg410Ile,ENST00000389908,NM_001286761.1;KIAA0226L,missense_variant,p.Arg253Ile,ENST00000378781,NM_001286765.1;KIAA0226L,missense_variant,p.Arg195Ile,ENST00000378797,NM_001286766.1;KIAA0226L,missense_variant,p.Arg253Ile,ENST00000409879,;KIAA0226L,missense_variant,p.Arg410Ile,ENST00000378787,NM_001286762.1;KIAA0226L,missense_variant,p.Arg343Ile,ENST00000378784,NM_001286763.1;KIAA0226L,missense_variant,p.Arg275Ile,ENST00000631139,NM_001286764.1;KIAA0226L,3_prime_UTR_variant,,ENST00000441284,; A ENST00000429979 Transcript missense_variant 1834/3979 1229/1989 410/662 R/I aGa/aTa 1 -1 KIAA0226L HGNC HGNC:20420 protein_coding YES CCDS31970.2 ENSP00000396935 Q9H714 UPI00001FCD59 NM_025113.3 deleterious(0) 9/15 hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF14 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -17.29484 0.9999999 1 1 1 0 A 3 1 5 46359522 46359522 C A 1 0 0 0 0 1 0 0 0 8078 913 32 2 2 KIAA0226L 13 46359522 Missense_Mutation SNP C C3L-00001_T 46359522 68004806 39 1774 SPRED1 0 . GRCh38 15 38351313 38351313 + Silent SNP G G A novel C3L-00001_T C3L-00001_N G G c.984G>A p.= p.E328E ENST00000299084 7/7 341 286 55 417 417 0 strelka-varscan-mutect SPRED1,synonymous_variant,p.=,ENST00000299084,NM_152594.2; A ENST00000299084 Transcript synonymous_variant 1844/7780 984/1335 328/444 E gaG/gaA 1 1 SPRED1 HGNC HGNC:20249 protein_coding YES CCDS32193.1 ENSP00000299084 Q7Z699 UPI0000072FBD NM_152594.2 7/7 hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 5 38351313 38351313 G A 1 0 0 0 0 0 0 0 1 15446 991 35 3 3 SPRED1 15 38351313 Silent SNP G C3L-00001_T 38351313 63639876 40 1775 DET1 0 . GRCh38 15 88530849 88530849 + Missense_Mutation SNP G G A C3L-00001_T C3L-00001_N G G c.890C>T p.Pro297Leu p.P297L ENST00000564406 3/6 77 64 13 62 62 0 strelka-varscan-mutect DET1,missense_variant,p.Pro297Leu,ENST00000564406,NM_001321596.1,NM_017996.3;DET1,missense_variant,p.Pro286Leu,ENST00000268148,NM_001321596.1,NM_001144074.1;DET1,missense_variant,p.Pro297Leu,ENST00000444300,NM_001321596.1;DET1,3_prime_UTR_variant,,ENST00000558413,;DET1,downstream_gene_variant,,ENST00000559656,;DET1,3_prime_UTR_variant,,ENST00000557842,;DET1,3_prime_UTR_variant,,ENST00000557837,; A ENST00000564406 Transcript missense_variant 1051/2315 890/1686 297/561 P/L cCc/cTc COSM3505064 1 -1 DET1 HGNC HGNC:25477 protein_coding YES CCDS45343.1 ENSP00000456340 Q7L5Y6 UPI00001A8183 NM_001321596.1,NM_017996.3 deleterious(0.04) 3/6 hmmpanther:PTHR13374,Pfam_domain:PF09737 1 MODERATE 1 SNV 2 1 1 PASS rs1321259346 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 88530849 88530849 G A 1 0 0 0 0 1 0 0 0 4258 1232 43 3 3 DET1 15 88530849 Missense_Mutation SNP G C3L-00001_T 50179536 88530849 13460340 41 1776 ZNF423 0 . GRCh38 16 49636578 49636578 + Silent SNP C C G rs773540555 C3L-00001_T C3L-00001_N C C c.2574G>C p.= p.L858L ENST00000561648 5/9 183 157 26 141 140 1 strelka-varscan-mutect ZNF423,synonymous_variant,p.=,ENST00000561648,;ZNF423,synonymous_variant,p.=,ENST00000563137,;ZNF423,synonymous_variant,p.=,ENST00000262383,NM_015069.3;ZNF423,synonymous_variant,p.=,ENST00000562871,;ZNF423,synonymous_variant,p.=,ENST00000535559,;ZNF423,synonymous_variant,p.=,ENST00000562520,NM_001271620.1;ZNF423,synonymous_variant,p.=,ENST00000567169,; G ENST00000561648 Transcript synonymous_variant 2875/7907 2574/3855 858/1284 L ctG/ctC rs773540555 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC 5/9 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 LOW 1 SNV 5 1 PASS rs773540555 . 0 207 0 3 0 0 0 0 -20 0.9999929 1 1 1 0 G 2 3 5 49636578 49636578 C G 1 0 0 0 0 0 0 0 1 18470 697 25 4 4 ZNF423 16 49636578 Silent SNP C C3L-00001_T 49636578 40701767 42 1777 EXOC3L1 0 . GRCh38 16 67187125 67187125 + Missense_Mutation SNP C C T novel C3L-00001_T C3L-00001_N C C c.1054G>A p.Gly352Arg p.G352R ENST00000314586 6/14 156 85 71 99 99 0 strelka-varscan-mutect EXOC3L1,missense_variant,p.Gly352Arg,ENST00000314586,NM_178516.3;EXOC3L1,missense_variant,p.Gly291Arg,ENST00000545725,;EXOC3L1,missense_variant,p.Gly296Arg,ENST00000563889,;KIAA0895L,upstream_gene_variant,,ENST00000290881,;KIAA0895L,upstream_gene_variant,,ENST00000561621,;KIAA0895L,upstream_gene_variant,,ENST00000563902,NM_001040715.1;EXOC3L1,downstream_gene_variant,,ENST00000564418,;EXOC3L1,non_coding_transcript_exon_variant,,ENST00000562887,;KIAA0895L,upstream_gene_variant,,ENST00000563831,;KIAA0895L,upstream_gene_variant,,ENST00000564423,;EXOC3L1,missense_variant,p.Gly74Glu,ENST00000564324,;EXOC3L1,upstream_gene_variant,,ENST00000563536,; T ENST00000314586 Transcript missense_variant 1295/2510 1054/2241 352/746 G/R Ggg/Agg 1 -1 EXOC3L1 HGNC HGNC:27540 protein_coding YES CCDS10832.1 ENSP00000325674 Q86VI1 A0A024R6U6 UPI000013F886 NM_178516.3 deleterious(0) 6/14 hmmpanther:PTHR21292:SF12,hmmpanther:PTHR21292,Pfam_domain:PF06046 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 67187125 67187125 C T 1 0 0 0 0 1 0 0 0 5171 623 22 3 3 EXOC3L1 16 67187125 Missense_Mutation SNP C C3L-00001_T 17550547 67187125 23151220 43 1778 CTNS 0 . GRCh38 17 3648865 3648865 + Silent SNP C C T rs769818124 C3L-00001_T C3L-00001_N C C c.159C>T p.= p.T53T ENST00000381870 5/13 367 262 105 429 428 1 strelka-varscan-mutect CTNS,synonymous_variant,p.=,ENST00000046640,NM_004937.2;CTNS,synonymous_variant,p.=,ENST00000381870,NM_001031681.2;CTNS,synonymous_variant,p.=,ENST00000399306,;CTNS,synonymous_variant,p.=,ENST00000452111,;CTNS,synonymous_variant,p.=,ENST00000576979,;CTNS,intron_variant,,ENST00000574218,;CTNS,intron_variant,,ENST00000574776,;CTNS,non_coding_transcript_exon_variant,,ENST00000488623,;CTNS,intron_variant,,ENST00000467663,;CTNS,downstream_gene_variant,,ENST00000495445,; T ENST00000381870 Transcript synonymous_variant 618/2470 159/1203 53/400 T acC/acT rs769818124 1 1 CTNS HGNC HGNC:2518 protein_coding YES CCDS32530.1 ENSP00000371294 O60931 A0A0S2Z3I9 UPI0000366B8B NM_001031681.2 5/13 hmmpanther:PTHR13131,hmmpanther:PTHR13131:SF9 LOW 1 SNV 1 1 PASS rs769818124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 5 3648865 3648865 C T 1 0 0 0 0 0 0 0 1 3830 610 22 3 3 CTNS 17 3648865 Silent SNP C C3L-00001_T 3648865 79608576 44 1779 CACNB1 0 . GRCh38 17 39183814 39183814 + Nonsense_Mutation SNP G G A rs370280712 C3L-00001_T C3L-00001_N G G c.949C>T p.Gln317Ter p.Q317* ENST00000394303 11/14 122 105 17 72 72 0 strelka-varscan-mutect CACNB1,stop_gained,p.Gln317Ter,ENST00000394303,NM_000723.4;CACNB1,stop_gained,p.Gln362Ter,ENST00000344140,NM_199247.2;CACNB1,stop_gained,p.Gln317Ter,ENST00000394310,NM_199248.2;CACNB1,3_prime_UTR_variant,,ENST00000622445,;CACNB1,downstream_gene_variant,,ENST00000582877,;CACNB1,downstream_gene_variant,,ENST00000492737,;CACNB1,downstream_gene_variant,,ENST00000577582,;CACNB1,non_coding_transcript_exon_variant,,ENST00000539338,;CACNB1,downstream_gene_variant,,ENST00000536613,; A ENST00000394303 Transcript stop_gained 1157/3742 949/1797 317/598 Q/* Cag/Tag rs370280712 1 -1 CACNB1 HGNC HGNC:1401 protein_coding YES CCDS42311.1 ENSP00000377840 Q02641 UPI0000127290 NM_000723.4 11/14 Gene3D:3.40.50.300,Pfam_domain:PF00625,Prints_domain:PR01626,hmmpanther:PTHR11824,hmmpanther:PTHR11824:SF6,SMART_domains:SM00072,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS rs370280712 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 5 39183814 39183814 G A 1 0 0 0 0 0 1 0 0 2240 1299 45 3 3 CACNB1 17 39183814 Nonsense_Mutation SNP G C3L-00001_T 35534949 39183814 44073627 45 1780 SMARCA4 0 . GRCh38 19 11041529 11041529 + Missense_Mutation SNP A A G novel C3L-00001_T C3L-00001_N A A c.4393A>G p.Ile1465Val p.I1465V ENST00000429416 31/36 212 174 38 153 153 0 strelka-varscan-mutect SMARCA4,missense_variant,p.Ile1465Val,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Ile1499Val,ENST00000413806,;SMARCA4,missense_variant,p.Ile1497Val,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.Ile1465Val,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Ile1432Val,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.Ile1435Val,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.Ile1435Val,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.Ile1432Val,ENST00000444061,NM_001128848.1;SMARCA4,downstream_gene_variant,,ENST00000592158,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000538456,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,; G ENST00000429416 Transcript missense_variant 4674/5691 4393/4944 1465/1647 I/V Att/Gtt 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 tolerated(0.14) 31/36 Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 5 11041529 11041529 A G 1 0 0 0 0 1 0 0 0 15063 333 12 5 5 SMARCA4 19 11041529 Missense_Mutation SNP A C3L-00001_T 11041529 47576087 46 1781 PSG5 0 . GRCh38 19 43175449 43175449 + Missense_Mutation SNP T T A novel C3L-00001_T C3L-00001_N T T c.730A>T p.Ile244Phe p.I244F ENST00000366175 4/6 69 60 9 58 58 0 strelka-varscan-mutect PSG5,missense_variant,p.Ile244Phe,ENST00000404580,;PSG5,missense_variant,p.Ile337Phe,ENST00000599812,;PSG5,missense_variant,p.Ile244Phe,ENST00000366175,;PSG5,missense_variant,p.Ile244Phe,ENST00000342951,NM_001130014.1,NM_002781.3;PSG5,missense_variant,p.Ile244Phe,ENST00000407356,;PSG5,intron_variant,,ENST00000407568,;CTC-490G23.6,downstream_gene_variant,,ENST00000635495,;PSG5,downstream_gene_variant,,ENST00000489220,;PSG5,downstream_gene_variant,,ENST00000600817,;PSG5,upstream_gene_variant,,ENST00000401942,;PSG5,upstream_gene_variant,,ENST00000599214,; A ENST00000366175 Transcript missense_variant 861/1766 730/1008 244/335 I/F Att/Ttt 1 -1 PSG5 HGNC HGNC:9522 protein_coding YES CCDS12617.1 ENSP00000382334 Q15238 A0A024R0S1 UPI000013C7B9 deleterious(0.01) 4/6 Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF615 MODERATE 1 SNV 5 1 PASS rs963405808 . 0 207 3 0 0 0 0 0 -19.81343 1 1 1 1 0 A 3 1 5 43175449 43175449 T A 1 0 0 0 0 1 0 0 0 12809 1464 51 4 4 PSG5 19 43175449 Missense_Mutation SNP T C3L-00001_T 32133920 43175449 15442167 47 1782 ZNF611 0 . GRCh38 19 52705306 52705306 + Nonsense_Mutation SNP G G T C3L-00001_T C3L-00001_N G G c.1749C>A p.Cys583Ter p.C583* ENST00000543227 6/6 172 163 9 155 154 1 varscan-mutect ZNF611,stop_gained,p.Cys583Ter,ENST00000543227,NM_001161499.1;ZNF611,stop_gained,p.Cys583Ter,ENST00000540744,NM_001161500.1;ZNF611,stop_gained,p.Cys514Ter,ENST00000453741,NM_001161501.1;ZNF611,stop_gained,p.Cys514Ter,ENST00000602162,;ZNF611,stop_gained,p.Cys583Ter,ENST00000319783,NM_030972.3;ZNF611,stop_gained,p.Cys514Ter,ENST00000595798,;ZNF611,downstream_gene_variant,,ENST00000600943,;ZNF611,downstream_gene_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000601643,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,3_prime_UTR_variant,,ENST00000601249,;ZNF611,downstream_gene_variant,,ENST00000597343,;ZNF611,downstream_gene_variant,,ENST00000598639,;ZNF611,downstream_gene_variant,,ENST00000598723,; T ENST00000543227 Transcript stop_gained 2024/4517 1749/2118 583/705 C/* tgC/tgA COSM567649 1 -1 ZNF611 HGNC HGNC:28766 protein_coding YES CCDS12855.1 ENSP00000437616 Q8N823 UPI00001406C1 NM_001161499.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF375,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 HIGH 1 SNV 4 1 1 PASS . . 0 194 0 7 9 0 0 0 -2.801624 0.01801933 1 1 0 0 T 4 4 5 52705306 52705306 G T 1 0 0 0 0 0 1 0 0 18612 1195 42 2 2 ZNF611 19 52705306 Nonsense_Mutation SNP G C3L-00001_T 9529857 52705306 5912310 48 1783 ZNF320 0 . GRCh38 19 52881956 52881956 + Missense_Mutation SNP G G T novel C3L-00001_T C3L-00001_N G G c.170C>A p.Thr57Lys p.T57K ENST00000595635 8/8 32 21 11 46 46 0 strelka-varscan-mutect ZNF320,missense_variant,p.Thr57Lys,ENST00000595635,;ZNF320,missense_variant,p.Thr57Lys,ENST00000391781,NM_207333.2;CTD-2331H12.8,missense_variant,p.Thr57Lys,ENST00000634278,;ZNF320,missense_variant,p.Thr57Lys,ENST00000593618,;ZNF320,missense_variant,p.Thr57Lys,ENST00000594741,;ZNF320,missense_variant,p.Thr57Lys,ENST00000597265,;ZNF320,intron_variant,,ENST00000597091,;ZNF320,intron_variant,,ENST00000597909,;ZNF320,intron_variant,,ENST00000600930,;ZNF320,upstream_gene_variant,,ENST00000598199,; T ENST00000595635 Transcript missense_variant 672/6448 170/1530 57/509 T/K aCa/aAa 1 -1 ZNF320 HGNC HGNC:13842 protein_coding YES CCDS33095.1 ENSP00000473091 A2RRD8 UPI00004EC06C tolerated(0.63) 8/8 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF197,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS rs996721800 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 52881956 52881956 G T 1 0 0 0 0 1 0 0 0 18414 1377 48 2 2 ZNF320 19 52881956 Missense_Mutation SNP G C3L-00001_T 176650 52881956 5735660 49 1784 CCDC106 0 . GRCh38 19 55652580 55652580 + Missense_Mutation SNP C C G rs755935967 C3L-00001_T C3L-00001_N C C c.677C>G p.Ala226Gly p.A226G ENST00000586790 5/5 456 388 68 298 298 0 strelka-varscan-mutect CCDC106,missense_variant,p.Ala226Gly,ENST00000586790,;CCDC106,missense_variant,p.Ala226Gly,ENST00000591578,;CCDC106,missense_variant,p.Ala226Gly,ENST00000308964,NM_013301.2;CCDC106,missense_variant,p.Ala226Gly,ENST00000588740,;CCDC106,missense_variant,p.Ala191Gly,ENST00000591241,;U2AF2,upstream_gene_variant,,ENST00000450554,NM_001012478.1;U2AF2,upstream_gene_variant,,ENST00000308924,NM_007279.2;CCDC106,downstream_gene_variant,,ENST00000592996,;CCDC106,downstream_gene_variant,,ENST00000587213,;CCDC106,downstream_gene_variant,,ENST00000593069,;U2AF2,upstream_gene_variant,,ENST00000587196,;CCDC106,downstream_gene_variant,,ENST00000586864,;U2AF2,upstream_gene_variant,,ENST00000588850,; G ENST00000586790 Transcript missense_variant 1581/2162 677/843 226/280 A/G gCc/gGc rs755935967 1 1 CCDC106 HGNC HGNC:30181 protein_coding YES CCDS33118.1 ENSP00000465757 Q9BWC9 UPI0000072074 tolerated(0.13) 5/5 Pfam_domain:PF15794,hmmpanther:PTHR16477,hmmpanther:PTHR16477:SF2 MODERATE 1 SNV 1 1 PASS rs755935967 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 5 55652580 55652580 C G 1 0 0 0 0 1 0 0 0 2438 739 26 4 4 CCDC106 19 55652580 Missense_Mutation SNP C C3L-00001_T 2770624 55652580 2965036 50 1785 ABCG1 0 . GRCh38 21 42259371 42259371 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.442G>A p.Val148Met p.V148M ENST00000398437 2/16 97 85 12 52 52 0 strelka-mutect ABCG1,missense_variant,p.Val148Met,ENST00000398437,;ABCG1,intron_variant,,ENST00000398457,NM_207627.1,NM_207628.1;ABCG1,intron_variant,,ENST00000343687,NM_207174.1;ABCG1,intron_variant,,ENST00000361802,NM_004915.3;ABCG1,intron_variant,,ENST00000398449,NM_016818.2;ABCG1,intron_variant,,ENST00000347800,NM_207629.1;ABCG1,intron_variant,,ENST00000450121,;ABCG1,intron_variant,,ENST00000462050,; A ENST00000398437 Transcript missense_variant 590/3475 442/2475 148/824 V/M Gtg/Atg 1 1 ABCG1 HGNC HGNC:73 protein_coding ENSP00000381464 E9PGV9 UPI000035AC75 2/16 MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 42259371 42259371 G A 1 0 0 0 0 1 0 0 0 72 1029 36 3 3 ABCG1 21 42259371 Missense_Mutation SNP G C3L-00001_T 42259371 4450612 51 1786 SCUBE1 0 . GRCh38 22 43262809 43262809 + Missense_Mutation SNP G G A novel C3L-00001_T C3L-00001_N G G c.521C>T p.Ala174Val p.A174V ENST00000360835 5/22 180 164 16 169 168 1 strelka-varscan-mutect SCUBE1,missense_variant,p.Ala174Val,ENST00000360835,NM_173050.3;SCUBE1,missense_variant,p.Ala174Val,ENST00000290460,;SCUBE1,missense_variant,p.Ala174Val,ENST00000615096,;SCUBE1,upstream_gene_variant,,ENST00000449304,; A ENST00000360835 Transcript missense_variant 648/9808 521/2967 174/988 A/V gCc/gTc 1 -1 SCUBE1 HGNC HGNC:13441 protein_coding YES CCDS14048.1 ENSP00000354080 Q8IWY4 UPI000020790F NM_173050.3 tolerated(0.1) 5/22 Gene3D:2.10.25.10,hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF4,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 43262809 43262809 G A 1 0 0 0 0 1 0 0 0 14215 1203 42 3 3 SCUBE1 22 43262809 Missense_Mutation SNP G C3L-00001_T 43262809 7555659 52 1787 MAPK12 0 . GRCh38 22 50255504 50255504 + Missense_Mutation SNP C C T rs774930213 C3L-00001_T C3L-00001_N C C c.799G>A p.Glu267Lys p.E267K ENST00000215659 10/12 159 145 14 130 129 1 strelka-varscan-mutect MAPK12,missense_variant,p.Glu267Lys,ENST00000215659,NM_002969.4;MAPK12,missense_variant,p.Glu257Lys,ENST00000622558,NM_001303252.1;MAPK12,missense_variant,p.Glu177Lys,ENST00000395780,;HDAC10,upstream_gene_variant,,ENST00000216271,NM_032019.5;HDAC10,upstream_gene_variant,,ENST00000626012,;HDAC10,upstream_gene_variant,,ENST00000448072,;HDAC10,upstream_gene_variant,,ENST00000349505,NM_001159286.1;MAPK12,downstream_gene_variant,,ENST00000395778,;MAPK12,non_coding_transcript_exon_variant,,ENST00000497036,;HDAC10,upstream_gene_variant,,ENST00000498366,;HDAC10,upstream_gene_variant,,ENST00000483222,;HDAC10,upstream_gene_variant,,ENST00000470965,;HDAC10,upstream_gene_variant,,ENST00000489424,;HDAC10,upstream_gene_variant,,ENST00000496909,;HDAC10,upstream_gene_variant,,ENST00000497483,;MAPK12,downstream_gene_variant,,ENST00000492218,;MAPK12,non_coding_transcript_exon_variant,,ENST00000496942,;MAPK12,non_coding_transcript_exon_variant,,ENST00000482969,;MAPK12,non_coding_transcript_exon_variant,,ENST00000497738,;MAPK12,non_coding_transcript_exon_variant,,ENST00000467891,;MAPK12,non_coding_transcript_exon_variant,,ENST00000488504,;HDAC10,upstream_gene_variant,,ENST00000415993,;HDAC10,upstream_gene_variant,,ENST00000454936,;HDAC10,upstream_gene_variant,,ENST00000429374,;HDAC10,upstream_gene_variant,,ENST00000482213,; T ENST00000215659 Transcript missense_variant 1115/1918 799/1104 267/367 E/K Gaa/Aaa rs774930213,COSM1417054,COSM1417055 1 -1 MAPK12 HGNC HGNC:6874 protein_coding YES CCDS14089.1 ENSP00000215659 P53778 UPI000012F180 NM_002969.4 tolerated(1) 10/12 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF146,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs774930213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 50255504 50255504 C T 1 0 0 0 0 1 0 0 0 9198 893 31 1 1 MAPK12 22 50255504 Missense_Mutation SNP C C3L-00001_T 6992695 50255504 562964 53 1788 AKAP4 0 . GRCh38 X 50193296 50193296 + Missense_Mutation SNP C C T novel C3L-00001_T C3L-00001_N C C c.1417G>A p.Glu473Lys p.E473K ENST00000358526 5/6 225 201 24 196 196 0 strelka-varscan-mutect AKAP4,missense_variant,p.Glu473Lys,ENST00000358526,NM_003886.2;AKAP4,missense_variant,p.Glu464Lys,ENST00000376064,NM_139289.1;AKAP4,intron_variant,,ENST00000448865,;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,; T ENST00000358526 Transcript missense_variant 1541/2881 1417/2565 473/854 E/K Gaa/Aaa 1 -1 AKAP4 HGNC HGNC:374 protein_coding YES CCDS14329.1 ENSP00000351327 Q5JQC9 UPI000013DA96 NM_003886.2 deleterious(0.04) 5/6 hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 5 50193296 50193296 C T 1 0 0 0 0 1 0 0 0 537 835 29 3 3 AKAP4 23 50193296 Missense_Mutation SNP C C3L-00001_T 50193296 105847599 54 1789 GLRA4 0 . GRCh38 X 103728191 103728191 + Missense_Mutation SNP C C A novel C3L-00001_T C3L-00001_N C C c.13G>T p.Val5Phe p.V5F ENST00000372617 1/9 224 207 17 165 164 1 strelka-varscan-mutect GLRA4,missense_variant,p.Val5Phe,ENST00000372617,NM_001024452.2;GLRA4,missense_variant,p.Val5Phe,ENST00000436213,;GLRA4,non_coding_transcript_exon_variant,,ENST00000480725,; A ENST00000372617 Transcript missense_variant 434/1795 13/1254 5/417 V/F Gtt/Ttt 1 -1 GLRA4 HGNC HGNC:31715 protein_coding YES CCDS43980.2 ENSP00000361700 Q5JXX5 UPI000188140C NM_001024452.2 tolerated_low_confidence(0.1) 1/9 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 5 103728191 103728191 C A 1 0 0 0 0 1 0 0 0 6336 478 17 2 2 GLRA4 23 103728191 Missense_Mutation SNP C C3L-00001_T 53534895 103728191 52312704 55 1790 AF011889.5 0 . GRCh38 X 149483000 149483000 + Missense_Mutation SNP G G T novel C3L-00001_T C3L-00001_N G G c.1399C>A p.Pro467Thr p.P467T ENST00000340855 9/9 142 128 14 129 129 0 strelka-varscan-mutect IDS,missense_variant,p.Pro467Thr,ENST00000340855,NM_001166550.2,NM_000202.6;AF011889.5,missense_variant,p.Pro256Thr,ENST00000422081,;IDS,downstream_gene_variant,,ENST00000370441,NM_006123.4;IDS,downstream_gene_variant,,ENST00000490775,;AF011889.5,downstream_gene_variant,,ENST00000441880,;IDS,downstream_gene_variant,,ENST00000466323,;IDS,downstream_gene_variant,,ENST00000464251,; T ENST00000340855 Transcript missense_variant 1609/7619 1399/1653 467/550 P/T Ccc/Acc 1 -1 IDS HGNC HGNC:5389 protein_coding YES CCDS14685.1 ENSP00000339801 P22304 UPI000012D213 NM_001166550.2,NM_000202.6 deleterious(0) 9/9 hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF207 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 5 149483000 149483000 G T 1 0 0 0 0 1 0 0 0 428 1174 41 2 2 AF011889.5 23 149483000 Missense_Mutation SNP G C3L-00001_T 45754809 149483000 6557895 56 1791 ZFP92 0 . GRCh38 X 153421328 153421328 + Missense_Mutation SNP G G C novel C3L-00001_T C3L-00001_N G G c.951G>C p.Glu317Asp p.E317D ENST00000338647 4/4 252 193 59 140 140 0 strelka-varscan-mutect ZFP92,missense_variant,p.Glu317Asp,ENST00000338647,NM_001136273.1; C ENST00000338647 Transcript missense_variant 952/6105 951/1251 317/416 E/D gaG/gaC 1 1 ZFP92 HGNC HGNC:12865 protein_coding YES CCDS59177.1 ENSP00000462054 A6NM28 UPI000052B478 NM_001136273.1 tolerated(0.16) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF167,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 5 153421328 153421328 G C 1 0 0 0 0 1 0 0 0 18233 962 34 4 4 ZFP92 23 153421328 Missense_Mutation SNP G C3L-00001_T 3938328 153421328 2619567 57 1792 MEGF6 0 . GRCh38 1 3499160 3499160 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.3072G>C p.Trp1024Cys p.W1024C ENST00000356575 24/37 275 239 36 352 352 0 strelka-varscan-mutect MEGF6,missense_variant,p.Trp1024Cys,ENST00000356575,NM_001409.3;MEGF6,intron_variant,,ENST00000294599,;MEGF6,upstream_gene_variant,,ENST00000491842,;MEGF6,missense_variant,p.Trp1031Cys,ENST00000485002,;MEGF6,upstream_gene_variant,,ENST00000475790,;MEGF6,upstream_gene_variant,,ENST00000461795,; G ENST00000356575 Transcript missense_variant 3299/5455 3072/4626 1024/1541 W/C tgG/tgC 1 -1 MEGF6 HGNC HGNC:3232 protein_coding YES CCDS41237.1 ENSP00000348982 O75095 UPI0000DACACB NM_001409.3 deleterious(0) 24/37 PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF106,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00180,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs1182548009 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 3499160 3499160 C G 1 0 0 0 0 1 0 0 0 9402 856 30 4 4 MEGF6 1 3499160 Missense_Mutation SNP C C3L-00009_T 3499160 245457262 1 1793 CAMTA1 0 . GRCh38 1 7738280 7738280 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.3980A>T p.Tyr1327Phe p.Y1327F ENST00000303635 16/23 270 249 21 366 366 0 strelka-varscan-mutect CAMTA1,missense_variant,p.Tyr1327Phe,ENST00000303635,NM_015215.3;CAMTA1,missense_variant,p.Tyr284Phe,ENST00000495233,; T ENST00000303635 Transcript missense_variant 4187/8444 3980/5022 1327/1673 Y/F tAc/tTc 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 tolerated_low_confidence(0.28) 16/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 7738280 7738280 A T 1 0 0 0 0 1 0 0 0 2306 391 14 4 4 CAMTA1 1 7738280 Missense_Mutation SNP A C3L-00009_T 4239120 7738280 241218142 2 1794 CLSTN1 0 . GRCh38 1 9733422 9733422 + Silent SNP G G A rs372309624 C3L-00009_T C3L-00009_N G G c.2406C>T p.= p.I802I ENST00000377298 16/19 221 206 15 310 310 0 strelka-varscan-mutect CLSTN1,synonymous_variant,p.=,ENST00000377298,NM_001302883.1,NM_001009566.2;CLSTN1,synonymous_variant,p.=,ENST00000361311,NM_014944.4;CLSTN1,synonymous_variant,p.=,ENST00000435891,;PIK3CD,downstream_gene_variant,,ENST00000536656,;PIK3CD,downstream_gene_variant,,ENST00000628140,;PIK3CD,downstream_gene_variant,,ENST00000377346,NM_005026.3;CLSTN1,non_coding_transcript_exon_variant,,ENST00000477264,; A ENST00000377298 Transcript synonymous_variant 3199/5221 2406/2946 802/981 I atC/atT rs372309624 1 -1 CLSTN1 HGNC HGNC:17447 protein_coding YES CCDS30580.1 ENSP00000366513 O94985 UPI0000127B95 NM_001302883.1,NM_001009566.2 16/19 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4 LOW 1 SNV 1 1 PASS rs372309624 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 9733422 9733422 G A 1 0 0 0 0 0 0 0 1 3333 1280 45 3 3 CLSTN1 1 9733422 Silent SNP G C3L-00009_T 1995142 9733422 239223000 3 1795 MAD2L2 0 . GRCh38 1 11675117 11675117 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.559A>G p.Ile187Val p.I187V ENST00000235310 10/11 45 37 8 83 83 0 strelka-mutect MAD2L2,missense_variant,p.Ile187Val,ENST00000235310,;MAD2L2,missense_variant,p.Ile187Val,ENST00000376692,NM_006341.3;MAD2L2,missense_variant,p.Ile200Val,ENST00000376672,;MAD2L2,missense_variant,p.Ile187Val,ENST00000376667,NM_001127325.1;MAD2L2,missense_variant,p.Ile200Val,ENST00000376669,;FBXO6,downstream_gene_variant,,ENST00000376753,NM_018438.5;MAD2L2,downstream_gene_variant,,ENST00000456915,;FBXO6,downstream_gene_variant,,ENST00000449067,;MAD2L2,downstream_gene_variant,,ENST00000445656,;MAD2L2,downstream_gene_variant,,ENST00000376655,;MAD2L2,downstream_gene_variant,,ENST00000376664,;FBXO6,downstream_gene_variant,,ENST00000474239,; C ENST00000235310 Transcript missense_variant 1488/1860 559/636 187/211 I/V Ata/Gta 1 -1 MAD2L2 HGNC HGNC:6764 protein_coding YES CCDS134.1 ENSP00000235310 Q9UI95 A0A024R4I4 UPI0000000DF1 tolerated(0.59) 10/11 PROSITE_profiles:PS50815,hmmpanther:PTHR11842,hmmpanther:PTHR11842:SF10,Gene3D:1go4B00 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 11675117 11675117 T C 1 0 0 0 0 1 0 0 0 9066 1435 50 5 5 MAD2L2 1 11675117 Missense_Mutation SNP T C3L-00009_T 1941695 11675117 237281305 4 1796 CROCC 0 . GRCh38 1 16922734 16922734 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.132C>T p.= p.I44I ENST00000375541 2/37 121 100 21 139 139 0 strelka-varscan-mutect CROCC,synonymous_variant,p.=,ENST00000375541,NM_014675.4;CROCC,upstream_gene_variant,,ENST00000445545,;CROCC,upstream_gene_variant,,ENST00000467938,;CROCC,intron_variant,,ENST00000466256,; T ENST00000375541 Transcript synonymous_variant 201/6656 132/6054 44/2017 I atC/atT 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 2/37 LOW 1 SNV 5 1 PASS rs1200846158 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 16922734 16922734 C T 1 0 0 0 0 0 0 0 1 3694 816 29 3 3 CROCC 1 16922734 Silent SNP C C3L-00009_T 5247617 16922734 232033688 5 1797 UBXN11 0 . GRCh38 1 26282874 26282874 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.1141G>A p.Glu381Lys p.E381K ENST00000374222 14/16 223 174 49 335 335 0 strelka-varscan-mutect UBXN11,missense_variant,p.Glu261Lys,ENST00000314675,NM_001077262.1;UBXN11,missense_variant,p.Glu381Lys,ENST00000374222,;UBXN11,missense_variant,p.Glu348Lys,ENST00000374217,NM_145345.2;UBXN11,missense_variant,p.Glu381Lys,ENST00000374221,NM_183008.2;UBXN11,missense_variant,p.Glu348Lys,ENST00000357089,;UBXN11,missense_variant,p.Glu138Lys,ENST00000374223,;CEP85,downstream_gene_variant,,ENST00000451429,NM_001281517.1;CEP85,downstream_gene_variant,,ENST00000252992,NM_001319944.1,NM_022778.3;CEP85,downstream_gene_variant,,ENST00000453146,;SH3BGRL3,downstream_gene_variant,,ENST00000270792,NM_031286.3;UBXN11,downstream_gene_variant,,ENST00000374215,;UBXN11,downstream_gene_variant,,ENST00000452980,;SH3BGRL3,downstream_gene_variant,,ENST00000319041,;UBXN11,downstream_gene_variant,,ENST00000442942,;CEP85,downstream_gene_variant,,ENST00000469609,;UBXN11,non_coding_transcript_exon_variant,,ENST00000472155,;UBXN11,non_coding_transcript_exon_variant,,ENST00000475591,;UBXN11,non_coding_transcript_exon_variant,,ENST00000496466,;UBXN11,non_coding_transcript_exon_variant,,ENST00000494942,;CEP85,downstream_gene_variant,,ENST00000476272,; T ENST00000374222 Transcript missense_variant 1606/2043 1141/1563 381/520 E/K Gag/Aag COSM5417883 1 -1 UBXN11 HGNC HGNC:30600 protein_coding YES CCDS41288.1 ENSP00000363339 Q5T124 UPI00004700E1 tolerated(0.15) 14/16 hmmpanther:PTHR23333,hmmpanther:PTHR23333:SF4,Gene3D:3.10.20.90,Superfamily_domains:SSF54236 1 MODERATE SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 26282874 26282874 C T 1 0 0 0 0 1 0 0 0 17437 835 29 3 3 UBXN11 1 26282874 Missense_Mutation SNP C C3L-00009_T 9360140 26282874 222673548 6 1798 CSF3R 0 . GRCh38 1 36466703 36466703 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.2246C>A p.Thr749Asn p.T749N ENST00000373103 17/17 264 244 20 319 319 0 strelka-varscan-mutect CSF3R,missense_variant,p.Thr749Asn,ENST00000373103,NM_156039.3;CSF3R,missense_variant,p.Thr722Asn,ENST00000373106,NM_000760.3;CSF3R,missense_variant,p.Thr722Asn,ENST00000373104,NM_172313.2;CSF3R,missense_variant,p.Thr722Asn,ENST00000361632,;CSF3R,missense_variant,p.Thr722Asn,ENST00000331941,;CSF3R,missense_variant,p.Thr274Asn,ENST00000464465,;MRPS15,upstream_gene_variant,,ENST00000373116,NM_031280.3;CSF3R,non_coding_transcript_exon_variant,,ENST00000487540,;MRPS15,upstream_gene_variant,,ENST00000462067,;CSF3R,non_coding_transcript_exon_variant,,ENST00000480825,;CSF3R,non_coding_transcript_exon_variant,,ENST00000484762,;CSF3R,downstream_gene_variant,,ENST00000464365,;CSF3R,downstream_gene_variant,,ENST00000466138,; T ENST00000373103 Transcript missense_variant 2794/3454 2246/2592 749/863 T/N aCt/aAt 1 -1 CSF3R HGNC HGNC:2439 protein_coding YES CCDS414.1 ENSP00000362195 Q99062 UPI000002AA5A NM_156039.3 deleterious(0.03) 17/17 hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF103 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 36466703 36466703 G T 1 0 0 0 0 1 0 0 0 3738 1029 36 2 2 CSF3R 1 36466703 Missense_Mutation SNP G C3L-00009_T 10183829 36466703 212489719 7 1799 YRDC 0 . GRCh38 1 37807111 37807111 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.494C>G p.Pro165Arg p.P165R ENST00000373044 2/5 185 173 12 242 242 0 strelka-varscan-mutect YRDC,missense_variant,p.Pro165Arg,ENST00000373044,NM_024640.3;C1orf122,5_prime_UTR_variant,,ENST00000373043,;MTF1,downstream_gene_variant,,ENST00000373036,NM_005955.2;C1orf122,upstream_gene_variant,,ENST00000468084,NM_001142726.1;C1orf122,upstream_gene_variant,,ENST00000373042,NM_198446.2;C1orf122,upstream_gene_variant,,ENST00000419397,; C ENST00000373044 Transcript missense_variant 499/1826 494/840 165/279 P/R cCt/cGt 1 -1 YRDC HGNC HGNC:28905 protein_coding YES CCDS30675.1 ENSP00000362135 Q86U90 UPI000019A401 NM_024640.3 deleterious(0) 2/5 Gene3D:3.90.870.10,Pfam_domain:PF01300,PROSITE_profiles:PS51163,hmmpanther:PTHR17490,Superfamily_domains:SSF55821,TIGRFAM_domain:TIGR00057 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 37807111 37807111 G C 1 0 0 0 0 1 0 0 0 18056 1000 35 4 4 YRDC 1 37807111 Missense_Mutation SNP G C3L-00009_T 1340408 37807111 211149311 8 1800 PTPRF 0 . GRCh38 1 43598002 43598002 + Missense_Mutation SNP G G T rs761857102 C3L-00009_T C3L-00009_N G G c.2068G>T p.Val690Leu p.V690L ENST00000359947 12/34 45 39 6 61 61 0 strelka-varscan-mutect PTPRF,missense_variant,p.Val690Leu,ENST00000359947,NM_002840.3;PTPRF,missense_variant,p.Val690Leu,ENST00000438120,NM_130440.2;PTPRF,missense_variant,p.Val347Leu,ENST00000429895,;PTPRF,intron_variant,,ENST00000414879,;PTPRF,intron_variant,,ENST00000412568,;PTPRF,upstream_gene_variant,,ENST00000372407,;PTPRF,upstream_gene_variant,,ENST00000496447,; T ENST00000359947 Transcript missense_variant 2408/7727 2068/5724 690/1907 V/L Gtg/Ttg rs761857102 1 1 PTPRF HGNC HGNC:9670 protein_coding YES CCDS489.2 ENSP00000353030 P10586 UPI0000470154 NM_002840.3 tolerated(0.07) 12/34 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs761857102 . 0 206 4 0 0 0 0 0 -15.00642 1 1 1 1 0 T 3 4 6 43598002 43598002 G T 1 0 0 0 0 1 0 0 0 12955 1145 40 1 1 PTPRF 1 43598002 Missense_Mutation SNP G C3L-00009_T 5790891 43598002 205358420 9 1801 PTPRF 0 . GRCh38 1 43620519 43620519 + Silent SNP G G A rs200215132 C3L-00009_T C3L-00009_N G G c.5304G>A p.= p.P1768P ENST00000359947 31/34 133 125 8 194 194 0 strelka-varscan-mutect PTPRF,synonymous_variant,p.=,ENST00000359947,NM_002840.3;PTPRF,synonymous_variant,p.=,ENST00000438120,NM_130440.2;PTPRF,synonymous_variant,p.=,ENST00000429895,;PTPRF,synonymous_variant,p.=,ENST00000414879,;PTPRF,synonymous_variant,p.=,ENST00000372407,;PTPRF,synonymous_variant,p.=,ENST00000412568,;PTPRF,non_coding_transcript_exon_variant,,ENST00000496447,;PTPRF,non_coding_transcript_exon_variant,,ENST00000477970,; A ENST00000359947 Transcript synonymous_variant 5644/7727 5304/5724 1768/1907 P ccG/ccA rs200215132,COSM5666964,COSM5666965 1 1 PTPRF HGNC HGNC:9670 protein_coding YES CCDS489.2 ENSP00000353030 P10586 UPI0000470154 NM_002840.3 31/34 PROSITE_profiles:PS50055,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs200215132 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 43620519 43620519 G A 1 0 0 0 0 0 0 0 1 12955 1045 37 1 1 PTPRF 1 43620519 Silent SNP G C3L-00009_T 22517 43620519 205335903 10 1802 CC2D1B 0 . GRCh38 1 52360443 52360443 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.584G>T p.Arg195Leu p.R195L ENST00000371586 6/24 112 101 11 157 157 0 strelka-mutect CC2D1B,missense_variant,p.Arg195Leu,ENST00000371586,NM_032449.2;CC2D1B,missense_variant,p.Arg195Leu,ENST00000284376,;CC2D1B,missense_variant,p.Arg36Leu,ENST00000450942,;CC2D1B,upstream_gene_variant,,ENST00000438021,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000460261,;CC2D1B,upstream_gene_variant,,ENST00000494789,;CC2D1B,non_coding_transcript_exon_variant,,ENST00000491136,;CC2D1B,upstream_gene_variant,,ENST00000460370,;CC2D1B,upstream_gene_variant,,ENST00000485966,; A ENST00000371586 Transcript missense_variant 723/5642 584/2577 195/858 R/L cGc/cTc 1 -1 CC2D1B HGNC HGNC:29386 protein_coding YES CCDS30714.1 ENSP00000360642 Q5T0F9 UPI00001609B7 NM_032449.2 deleterious(0) 6/24 hmmpanther:PTHR13076,hmmpanther:PTHR13076:SF5,Low_complexity_(Seg):seg,SMART_domains:SM00685 MODERATE 1 SNV 5 1 PASS rs1181517830 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 52360443 52360443 C A 1 0 0 0 0 1 0 0 0 2428 768 27 1 1 CC2D1B 1 52360443 Missense_Mutation SNP C C3L-00009_T 8739924 52360443 196595979 11 1803 MROH7 0 . GRCh38 1 54652961 54652961 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.35A>T p.His12Leu p.H12L ENST00000421030 3/24 68 61 7 88 88 0 strelka-varscan-mutect MROH7,missense_variant,p.His12Leu,ENST00000421030,NM_001039464.3;MROH7,missense_variant,p.His12Leu,ENST00000339553,;MROH7,missense_variant,p.His12Leu,ENST00000395690,;MROH7,intron_variant,,ENST00000409996,NM_001291332.1;MROH7,non_coding_transcript_exon_variant,,ENST00000472987,;MROH7,intron_variant,,ENST00000478097,;MROH7-TTC4,missense_variant,p.His12Leu,ENST00000425300,;MROH7-TTC4,missense_variant,p.His12Leu,ENST00000414150,;MROH7-TTC4,missense_variant,p.His12Leu,ENST00000606515,;MROH7,missense_variant,p.His12Leu,ENST00000413188,;MROH7,missense_variant,p.His12Leu,ENST00000422659,;MROH7,missense_variant,p.His12Leu,ENST00000440047,;MROH7,missense_variant,p.His12Leu,ENST00000438846,;MROH7,upstream_gene_variant,,ENST00000440217,; T ENST00000421030 Transcript missense_variant 320/4329 35/3972 12/1323 H/L cAt/cTt 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 tolerated_low_confidence(0.77) 3/24 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -15.7245 1 1 1 1 0 T 3 4 6 54652961 54652961 A T 1 0 0 0 0 1 0 0 0 9747 217 8 4 4 MROH7 1 54652961 Missense_Mutation SNP A C3L-00009_T 2292518 54652961 194303461 12 1804 CTH 0 . GRCh38 1 70432222 70432222 + Missense_Mutation SNP G G T rs368097625 C3L-00009_T C3L-00009_N G G c.864G>T p.Lys288Asn p.K288N ENST00000370938 8/12 237 220 17 319 319 0 strelka-mutect CTH,missense_variant,p.Lys256Asn,ENST00000411986,NM_001190463.1;CTH,missense_variant,p.Lys288Asn,ENST00000370938,NM_001902.5;CTH,missense_variant,p.Lys244Asn,ENST00000346806,NM_153742.4;Metazoa_SRP,downstream_gene_variant,,ENST00000612213,;CTH,downstream_gene_variant,,ENST00000464926,;CTH,upstream_gene_variant,,ENST00000482383,; T ENST00000370938 Transcript missense_variant 1008/1805 864/1218 288/405 K/N aaG/aaT rs368097625 1 1 CTH HGNC HGNC:2501 protein_coding YES CCDS650.1 ENSP00000359976 P32929 UPI00001275DE NM_001902.5 deleterious(0.03) 8/12 Gene3D:3.90.1150.10,Pfam_domain:PF01053,PIRSF_domain:PIRSF001434,hmmpanther:PTHR11808,hmmpanther:PTHR11808:SF15,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs368097625 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 70432222 70432222 G T 1 0 0 0 0 1 0 0 0 3817 991 35 2 2 CTH 1 70432222 Missense_Mutation SNP G C3L-00009_T 15779261 70432222 178524200 13 1805 ERICH3 0 . GRCh38 1 74572812 74572812 + Silent SNP T T C novel C3L-00009_T C3L-00009_N T T c.2898A>G p.= p.R966R ENST00000326665 14/15 311 278 33 530 530 0 strelka-varscan-mutect ERICH3,synonymous_variant,p.=,ENST00000326665,NM_001002912.4;ERICH3-AS1,upstream_gene_variant,,ENST00000612390,;ERICH3,non_coding_transcript_exon_variant,,ENST00000433746,;ERICH3,downstream_gene_variant,,ENST00000614534,; C ENST00000326665 Transcript synonymous_variant 3117/7159 2898/4593 966/1530 R agA/agG 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 14/15 hmmpanther:PTHR23034 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 74572812 74572812 T C 1 0 0 0 0 0 0 0 1 5083 1548 54 5 5 ERICH3 1 74572812 Silent SNP T C3L-00009_T 4140590 74572812 174383610 14 1806 AP4B1 0 . GRCh38 1 113901294 113901294 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.559C>T p.= p.L187L ENST00000369569 4/10 333 260 73 375 375 0 strelka-varscan-mutect AP4B1,synonymous_variant,p.=,ENST00000369569,NM_001253852.1;AP4B1,synonymous_variant,p.=,ENST00000256658,NM_001253853.1,NM_006594.3;AP4B1,synonymous_variant,p.=,ENST00000369564,;AP4B1,synonymous_variant,p.=,ENST00000369571,;AP4B1,intron_variant,,ENST00000369567,NM_001308312.1;AP4B1,intron_variant,,ENST00000432415,;DCLRE1B,upstream_gene_variant,,ENST00000369563,NM_022836.3;AP4B1-AS1,downstream_gene_variant,,ENST00000419536,;AP4B1,non_coding_transcript_exon_variant,,ENST00000484201,;AP4B1,non_coding_transcript_exon_variant,,ENST00000489092,;AP4B1,non_coding_transcript_exon_variant,,ENST00000472122,;AP4B1,intron_variant,,ENST00000489499,;DCLRE1B,upstream_gene_variant,,ENST00000466480,;AP4B1,upstream_gene_variant,,ENST00000462591,;AP4B1,upstream_gene_variant,,ENST00000479285,;AP4B1,upstream_gene_variant,,ENST00000479801,;AP4B1,upstream_gene_variant,,ENST00000460653,; A ENST00000369569 Transcript synonymous_variant 840/2818 559/2220 187/739 L Ctg/Ttg 1 -1 AP4B1 HGNC HGNC:572 protein_coding YES CCDS865.1 ENSP00000358582 Q9Y6B7 A0A024R0D2 UPI0000072F63 NM_001253852.1 4/10 Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF002291,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF4,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs1192505486 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 113901294 113901294 G A 1 0 0 0 0 0 0 0 1 867 933 33 3 3 AP4B1 1 113901294 Silent SNP G C3L-00009_T 39328482 113901294 135055128 15 1807 FAM72C 0 . GRCh38 1 143964980 143964980 + Splice_Site SNP C C A rs782189336 C3L-00009_T C3L-00009_N C C c.231-1G>T p.X77_splice ENST00000584486 170 149 21 230 230 0 varscan-mutect FAM72C,splice_acceptor_variant,,ENST00000584486,NM_001287385.1;FAM72C,intron_variant,,ENST00000369175,; A ENST00000584486 Transcript splice_acceptor_variant -/2297 231/450 77/149 rs782189336 1 -1 FAM72C HGNC HGNC:30602 protein_coding YES CCDS72850.1 ENSP00000463032 H0Y354 UPI0002742DFA NM_001287385.1 2/3 HIGH 1 SNV 1 1 PASS rs782189336 . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 6 143964980 143964980 C A 1 0 0 0 0 0 0 1 0 5481 579 20 2 2 FAM72C 1 143964980 Splice_Site SNP C C3L-00009_T 30063686 143964980 104991442 16 1808 PI4KB 0 . GRCh38 1 151307711 151307711 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.1081A>T p.Thr361Ser p.T361S ENST00000368875 5/13 496 463 33 604 604 0 strelka-varscan-mutect PI4KB,missense_variant,p.Thr361Ser,ENST00000368875,NM_002651.2;PI4KB,missense_variant,p.Thr334Ser,ENST00000368874,NM_001198774.1;PI4KB,missense_variant,p.Thr349Ser,ENST00000368873,;PI4KB,missense_variant,p.Thr334Ser,ENST00000368872,NM_001198773.1;PI4KB,missense_variant,p.Thr17Ser,ENST00000529142,NM_001198775.1;PI4KB,missense_variant,p.Thr17Ser,ENST00000430800,;PI4KB,missense_variant,p.Thr17Ser,ENST00000489223,;PI4KB,upstream_gene_variant,,ENST00000460323,; A ENST00000368875 Transcript missense_variant 1662/3983 1081/2487 361/828 T/S Aca/Tca 1 -1 PI4KB HGNC HGNC:8984 protein_coding YES CCDS993.1 ENSP00000357869 A0A0B4J1S8 UPI000007161F NM_002651.2 tolerated(0.07) 5/13 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF22,Gene3D:3.30.1010.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 151307711 151307711 T A 1 0 0 0 0 1 0 0 0 11963 1725 60 4 4 PI4KB 1 151307711 Missense_Mutation SNP T C3L-00009_T 7342731 151307711 97648711 17 1809 ARHGEF11 0 . GRCh38 1 156947809 156947809 + Silent SNP C C G novel C3L-00009_T C3L-00009_N C C c.2301G>C p.= p.G767G ENST00000368194 25/41 164 148 16 184 184 0 strelka-varscan-mutect ARHGEF11,synonymous_variant,p.=,ENST00000368194,NM_198236.2;ARHGEF11,synonymous_variant,p.=,ENST00000361409,NM_014784.3;ARHGEF11,upstream_gene_variant,,ENST00000487682,;ARHGEF11,upstream_gene_variant,,ENST00000461678,; G ENST00000368194 Transcript synonymous_variant 3341/6889 2301/4689 767/1562 G ggG/ggC 1 -1 ARHGEF11 HGNC HGNC:14580 protein_coding YES CCDS1163.1 ENSP00000357177 O15085 UPI00001D62A7 NM_198236.2 25/41 hmmpanther:PTHR12673:SF111,hmmpanther:PTHR12673,Gene3D:1.20.900.10,Superfamily_domains:SSF48065 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99791 0.9999998 1 1 1 0 G 2 3 6 156947809 156947809 C G 1 0 0 0 0 0 0 0 1 1026 726 26 4 4 ARHGEF11 1 156947809 Silent SNP C C3L-00009_T 5640098 156947809 92008613 18 1810 OR10J1 0 . GRCh38 1 159440069 159440069 + Nonsense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.311C>G p.Ser104Ter p.S104* ENST00000423932 1/1 240 211 29 333 333 0 strelka-varscan-mutect OR10J1,stop_gained,p.Ser104Ter,ENST00000423932,NM_012351.2;RP11-550P17.5,intron_variant,,ENST00000431862,; G ENST00000423932 Transcript stop_gained 348/1090 311/963 104/320 S/* tCa/tGa 1 1 OR10J1 HGNC HGNC:8175 protein_coding YES CCDS1185.1 ENSP00000399078 P30954 UPI000013E7DA NM_012351.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF417,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 6 159440069 159440069 C G 1 0 0 0 0 0 1 0 0 10987 838 29 4 4 OR10J1 1 159440069 Nonsense_Mutation SNP C C3L-00009_T 2492260 159440069 89516353 19 1811 SLAMF9 0 . GRCh38 1 159953615 159953615 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.85G>A p.Glu29Lys p.E29K ENST00000368093 2/4 101 93 8 151 151 0 strelka-varscan-mutect SLAMF9,missense_variant,p.Glu29Lys,ENST00000368093,NM_033438.3;SLAMF9,missense_variant,p.Glu29Lys,ENST00000368092,NM_001146172.1;SLAMF9,non_coding_transcript_exon_variant,,ENST00000489098,;SLAMF9,upstream_gene_variant,,ENST00000466773,; T ENST00000368093 Transcript missense_variant 202/1156 85/870 29/289 E/K Gaa/Aaa COSM3476710 1 -1 SLAMF9 HGNC HGNC:18430 protein_coding YES CCDS1191.1 ENSP00000357072 Q96A28 UPI000013E1B2 NM_033438.3 deleterious(0.02) 2/4 Gene3D:2.60.40.10,hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF18,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.39649 1 1 1 1 0 T 3 4 6 159953615 159953615 C T 1 0 0 0 0 1 0 0 0 14636 864 30 3 3 SLAMF9 1 159953615 Missense_Mutation SNP C C3L-00009_T 513546 159953615 89002807 20 1812 ARHGAP30 0 . GRCh38 1 161051605 161051605 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.1129G>A p.Glu377Lys p.E377K ENST00000368013 10/12 214 202 12 288 288 0 strelka-varscan-mutect ARHGAP30,missense_variant,p.Glu377Lys,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,missense_variant,p.Glu200Lys,ENST00000368015,NM_001287602.1;ARHGAP30,missense_variant,p.Glu377Lys,ENST00000368016,NM_181720.2;ARHGAP30,3_prime_UTR_variant,,ENST00000490279,;ARHGAP30,non_coding_transcript_exon_variant,,ENST00000461003,;ARHGAP30,downstream_gene_variant,,ENST00000368018,;ARHGAP30,downstream_gene_variant,,ENST00000471492,; T ENST00000368013 Transcript missense_variant 1450/4394 1129/3306 377/1101 E/K Gaa/Aaa 1 -1 ARHGAP30 HGNC HGNC:27414 protein_coding YES CCDS30918.1 ENSP00000356992 Q7Z6I6 UPI0000160677 NM_001287600.1,NM_001025598.1 deleterious(0) 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15729:SF12,hmmpanther:PTHR15729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 161051605 161051605 C T 1 0 0 0 0 1 0 0 0 1004 922 32 3 3 ARHGAP30 1 161051605 Missense_Mutation SNP C C3L-00009_T 1097990 161051605 87904817 21 1813 OLFML2B 0 . GRCh38 1 162020045 162020045 + Silent SNP G G T rs778879566 C3L-00009_T C3L-00009_N G G c.312C>A p.= p.T104T ENST00000367940 2/8 525 477 48 605 604 1 strelka-varscan-mutect OLFML2B,synonymous_variant,p.=,ENST00000294794,NM_015441.2;OLFML2B,synonymous_variant,p.=,ENST00000367940,NM_001297713.1; T ENST00000367940 Transcript synonymous_variant 522/2685 312/2256 104/751 T acC/acA rs778879566 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 2/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37 LOW 1 SNV 2 1 PASS rs778879566 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 162020045 162020045 G T 1 0 0 0 0 0 0 0 1 10933 1103 39 1 1 OLFML2B 1 162020045 Silent SNP G C3L-00009_T 968440 162020045 86936377 22 1814 RXRG 0 . GRCh38 1 165401287 165401287 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.1368G>T p.Leu456Phe p.L456F ENST00000359842 10/10 183 144 39 232 231 1 strelka-varscan-mutect RXRG,missense_variant,p.Leu333Phe,ENST00000619224,NM_001256570.1,NM_001256571.1;RXRG,missense_variant,p.Leu456Phe,ENST00000359842,NM_006917.4; A ENST00000359842 Transcript missense_variant 1671/2041 1368/1392 456/463 L/F ttG/ttT 1 -1 RXRG HGNC HGNC:10479 protein_coding YES CCDS1248.1 ENSP00000352900 P48443 F1D8Q7 UPI000004989F NM_006917.4 deleterious(0.01) 10/10 hmmpanther:PTHR24083:SF95,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 165401287 165401287 C A 1 0 0 0 0 1 0 0 0 14026 593 21 2 2 RXRG 1 165401287 Missense_Mutation SNP C C3L-00009_T 3381242 165401287 83555135 23 1815 LRRC52 0 . GRCh38 1 165563789 165563789 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.907A>T p.Thr303Ser p.T303S ENST00000294818 2/2 200 185 15 283 283 0 strelka-varscan-mutect LRRC52,missense_variant,p.Thr303Ser,ENST00000294818,NM_001005214.3;RP11-280O1.2,intron_variant,,ENST00000438275,;RP11-280O1.2,intron_variant,,ENST00000421273,;RP11-280O1.2,intron_variant,,ENST00000416424,; T ENST00000294818 Transcript missense_variant 1197/1369 907/942 303/313 T/S Acg/Tcg 1 1 LRRC52 HGNC HGNC:32156 protein_coding YES CCDS30930.1 ENSP00000294818 Q8N7C0 UPI000013E1BE NM_001005214.3 tolerated_low_confidence(0.88) 2/2 MODERATE 1 SNV 1 1 PASS rs1238352948 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 165563789 165563789 A T 1 0 0 0 0 1 0 0 0 8904 275 10 4 4 LRRC52 1 165563789 Missense_Mutation SNP A C3L-00009_T 162502 165563789 83392633 24 1816 DUSP27 0 . GRCh38 1 167119267 167119267 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.456G>T p.Lys152Asn p.K152N ENST00000361200 5/6 312 264 48 465 465 0 strelka-varscan-mutect DUSP27,missense_variant,p.Lys152Asn,ENST00000361200,;DUSP27,missense_variant,p.Lys152Asn,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Lys152Asn,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,; T ENST00000361200 Transcript missense_variant 622/4164 456/3477 152/1158 K/N aaG/aaT 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 5/6 PROSITE_profiles:PS50054,hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159,Gene3D:3.90.190.10,Pfam_domain:PF00782,SMART_domains:SM00195,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 167119267 167119267 G T 1 0 0 0 0 1 0 0 0 4646 991 35 2 2 DUSP27 1 167119267 Missense_Mutation SNP G C3L-00009_T 1555478 167119267 81837155 25 1817 DUSP27 0 . GRCh38 1 167125843 167125843 + Missense_Mutation SNP G G C rs748897144 C3L-00009_T C3L-00009_N G G c.712G>C p.Ala238Pro p.A238P ENST00000361200 6/6 137 113 24 141 141 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ala238Pro,ENST00000361200,;DUSP27,missense_variant,p.Ala238Pro,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ala238Pro,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,upstream_gene_variant,,ENST00000485151,; C ENST00000361200 Transcript missense_variant 878/4164 712/3477 238/1158 A/P Gcc/Ccc rs748897144 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 6/6 PROSITE_profiles:PS50056,PROSITE_profiles:PS50054,hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159,Gene3D:3.90.190.10,Pfam_domain:PF00782,SMART_domains:SM00195,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS rs748897144 . 0 197 10 3 0 0 0 0 -20 0.9983136 1 1 1 0 C 3 2 6 167125843 167125843 G C 1 0 0 0 0 1 0 0 0 4646 1087 38 4 4 DUSP27 1 167125843 Missense_Mutation SNP G C3L-00009_T 6576 167125843 81830579 26 1818 SUCO 0 . GRCh38 1 172600104 172600104 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.3407A>G p.Gln1136Arg p.Q1136R ENST00000367723 19/23 213 168 45 277 277 0 strelka-varscan-mutect SUCO,missense_variant,p.Gln1136Arg,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Gln1136Arg,ENST00000608151,;SUCO,missense_variant,p.Gln985Arg,ENST00000263688,NM_014283.4;SUCO,missense_variant,p.Gln422Arg,ENST00000616058,NM_001282751.1;SUCO,missense_variant,p.Gln614Arg,ENST00000610051,NM_001282750.1;SUCO,upstream_gene_variant,,ENST00000486569,; G ENST00000367723 Transcript missense_variant 3531/5916 3407/4218 1136/1405 Q/R cAg/cGg 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 deleterious(0.05) 19/23 hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 172600104 172600104 A G 1 0 0 0 0 1 0 0 0 15751 188 7 5 5 SUCO 1 172600104 Missense_Mutation SNP A C3L-00009_T 5474261 172600104 76356318 27 1819 SERPINC1 0 . GRCh38 1 173909726 173909726 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.979G>C p.Val327Leu p.V327L ENST00000367698 5/7 266 227 39 329 329 0 strelka-varscan-mutect SERPINC1,missense_variant,p.Val327Leu,ENST00000367698,NM_000488.3;SERPINC1,intron_variant,,ENST00000617423,;SERPINC1,downstream_gene_variant,,ENST00000494024,;SERPINC1,downstream_gene_variant,,ENST00000487183,; G ENST00000367698 Transcript missense_variant 1098/1594 979/1395 327/464 V/L Gta/Cta 1 -1 SERPINC1 HGNC HGNC:775 protein_coding YES CCDS1313.1 ENSP00000356671 P01008 A0A024R944 UPI000002C0C1 NM_000488.3 tolerated(0.49) 5/7 hmmpanther:PTHR11461:SF53,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 173909726 173909726 C G 1 0 0 0 0 1 0 0 0 14385 507 18 4 4 SERPINC1 1 173909726 Missense_Mutation SNP C C3L-00009_T 1309622 173909726 75046696 28 1820 CFHR4 0 . GRCh38 1 196918336 196918336 + Missense_Mutation SNP C C A rs576733857 C3L-00009_T C3L-00009_N C C c.1664C>A p.Ala555Glu p.A555E ENST00000367416 10/10 306 262 44 429 429 0 strelka-varscan-mutect CFHR4,missense_variant,p.Ala555Glu,ENST00000367416,NM_001201551.1,NM_001201550.2;CFHR4,missense_variant,p.Ala179Glu,ENST00000608469,;CFHR4,missense_variant,p.Ala309Glu,ENST00000251424,NM_006684.4;CFHR4,missense_variant,p.Ala309Glu,ENST00000367418,;RP4-608O15.3,intron_variant,,ENST00000367421,; A ENST00000367416 Transcript missense_variant 1801/2178 1664/1734 555/577 A/E gCg/gAg rs576733857,COSM1200895,COSM1200896 1 1 CFHR4 HGNC HGNC:16979 protein_coding YES CCDS55671.1 ENSP00000356386 Q92496 UPI0001F6C576 NM_001201551.1,NM_001201550.2 tolerated(1) 10/10 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF366,Superfamily_domains:SSF57535 0,1,1 MODERATE SNV 2 0,1,1 1 PASS rs576733857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 196918336 196918336 C A 1 0 0 0 0 1 0 0 0 3045 768 27 1 1 CFHR4 1 196918336 Missense_Mutation SNP C C3L-00009_T 23008610 196918336 52038086 29 1821 NR5A2 0 . GRCh38 1 200039729 200039729 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.136G>C p.Glu46Gln p.E46Q ENST00000367362 2/8 354 328 26 392 392 0 strelka-varscan-mutect NR5A2,missense_variant,p.Glu46Gln,ENST00000367362,NM_205860.2;NR5A2,missense_variant,p.Glu59Gln,ENST00000447034,;NR5A2,intron_variant,,ENST00000236914,NM_003822.4;NR5A2,upstream_gene_variant,,ENST00000544748,NM_001276464.1;NR5A2,upstream_gene_variant,,ENST00000367357,;NR5A2,intron_variant,,ENST00000474307,; C ENST00000367362 Transcript missense_variant 382/5086 136/1626 46/541 E/Q Gag/Cag 1 1 NR5A2 HGNC HGNC:7984 protein_coding YES CCDS1401.1 ENSP00000356331 O00482 UPI0000130482 NM_205860.2 tolerated_low_confidence(0.15) 2/8 hmmpanther:PTHR24086,hmmpanther:PTHR24086:SF18,PIRSF_domain:PIRSF002530 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 200039729 200039729 G C 1 0 0 0 0 1 0 0 0 10692 1175 41 4 4 NR5A2 1 200039729 Missense_Mutation SNP G C3L-00009_T 3121393 200039729 48916693 30 1822 TNNI1 0 . GRCh38 1 201411440 201411440 + Missense_Mutation SNP G G A rs757767988 C3L-00009_T C3L-00009_N G G c.373C>T p.Arg125Trp p.R125W ENST00000361379 7/9 362 312 50 410 410 0 strelka-varscan-mutect TNNI1,missense_variant,p.Arg125Trp,ENST00000622580,;TNNI1,missense_variant,p.Arg125Trp,ENST00000361379,NM_003281.3;TNNI1,missense_variant,p.Arg125Trp,ENST00000336092,;TNNI1,missense_variant,p.Arg125Trp,ENST00000367312,;TNNI1,missense_variant,p.Arg125Trp,ENST00000556362,;TNNI1,missense_variant,p.Arg104Trp,ENST00000555340,;TNNI1,intron_variant,,ENST00000555948,; A ENST00000361379 Transcript missense_variant 466/5413 373/564 125/187 R/W Cgg/Tgg rs757767988,COSM1295685 1 -1 TNNI1 HGNC HGNC:11945 protein_coding YES CCDS1411.1 ENSP00000354488 P19237 UPI0000000CCA NM_003281.3 deleterious(0) 7/9 hmmpanther:PTHR13738:SF9,hmmpanther:PTHR13738,Pfam_domain:PF00992,Gene3D:1.20.5.350,Superfamily_domains:SSF90250 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs757767988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 201411440 201411440 G A 1 0 0 0 0 1 0 0 0 16799 1115 39 1 1 TNNI1 1 201411440 Missense_Mutation SNP G C3L-00009_T 1371711 201411440 47544982 31 1823 NAV1 0 . GRCh38 1 201790765 201790765 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.3320A>G p.Asn1107Ser p.N1107S ENST00000367296 13/30 223 210 13 328 328 0 strelka-varscan-mutect NAV1,missense_variant,p.Asn1107Ser,ENST00000367296,NM_020443.4;NAV1,missense_variant,p.Asn716Ser,ENST00000367295,NM_001167738.1;NAV1,missense_variant,p.Asn1063Ser,ENST00000367302,;NAV1,missense_variant,p.Asn657Ser,ENST00000430015,;NAV1,missense_variant,p.Asn90Ser,ENST00000438083,;IPO9-AS1,intron_variant,,ENST00000413035,;NAV1,splice_region_variant,,ENST00000469130,;NAV1,splice_region_variant,,ENST00000490213,;NAV1,3_prime_UTR_variant,,ENST00000477118,; G ENST00000367296 Transcript missense_variant,splice_region_variant 3740/13091 3320/5634 1107/1877 N/S aAt/aGt 1 1 NAV1 HGNC HGNC:15989 protein_coding YES CCDS1414.2 ENSP00000356265 Q8NEY1 UPI00004562D4 NM_020443.4 deleterious(0) 13/30 hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 201790765 201790765 A G 1 0 0 0 0 1 0 0 0 10192 115 4 5 5 NAV1 1 201790765 Missense_Mutation SNP A C3L-00009_T 379325 201790765 47165657 32 1824 KCNH1 0 . GRCh38 1 210683964 210683964 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.2287G>A p.Asp763Asn p.D763N ENST00000271751 11/11 38 33 5 73 73 0 strelka-varscan-mutect KCNH1,missense_variant,p.Asp763Asn,ENST00000271751,NM_172362.2;KCNH1,missense_variant,p.Asp736Asn,ENST00000367007,NM_002238.3;RP11-75I2.3,downstream_gene_variant,,ENST00000625140,; T ENST00000271751 Transcript missense_variant 2315/7964 2287/2970 763/989 D/N Gac/Aac 1 -1 KCNH1 HGNC HGNC:6250 protein_coding YES CCDS1496.1 ENSP00000271751 O95259 UPI000003230D NM_172362.2 tolerated_low_confidence(0.24) 11/11 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -13.04279 0.9999999 1 1 1 0 T 3 4 6 210683964 210683964 C T 1 0 0 0 0 1 0 0 0 7947 826 29 3 3 KCNH1 1 210683964 Missense_Mutation SNP C C3L-00009_T 8893199 210683964 38272458 33 1825 USH2A 0 . GRCh38 1 215680324 215680324 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.12119G>T p.Arg4040Leu p.R4040L ENST00000307340 62/72 210 167 43 293 293 0 strelka-varscan-mutect USH2A,missense_variant,p.Arg4040Leu,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 12506/18883 12119/15609 4040/5202 R/L cGc/cTc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.09) 62/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1238450377 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 215680324 215680324 C A 1 0 0 0 0 1 0 0 0 17570 768 27 1 1 USH2A 1 215680324 Missense_Mutation SNP C C3L-00009_T 4996360 215680324 33276098 34 1826 USH2A 0 . GRCh38 1 215867107 215867107 + Silent SNP T T C novel C3L-00009_T C3L-00009_N T T c.8745A>G p.= p.E2915E ENST00000307340 44/72 360 307 53 488 488 0 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; C ENST00000307340 Transcript synonymous_variant 9132/18883 8745/15609 2915/5202 E gaA/gaG 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 44/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 215867107 215867107 T C 1 0 0 0 0 0 0 0 1 17570 1606 56 5 5 USH2A 1 215867107 Silent SNP T C3L-00009_T 186783 215867107 33089315 35 1827 USH2A 0 . GRCh38 1 216046515 216046515 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.6241G>C p.Ala2081Pro p.A2081P ENST00000307340 32/72 318 296 22 316 316 0 strelka-varscan-mutect USH2A,missense_variant,p.Ala2081Pro,ENST00000307340,NM_206933.2; G ENST00000307340 Transcript missense_variant 6628/18883 6241/15609 2081/5202 A/P Gca/Cca 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(1) 32/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 216046515 216046515 C G 1 0 0 0 0 1 0 0 0 17570 739 26 4 4 USH2A 1 216046515 Missense_Mutation SNP C C3L-00009_T 179408 216046515 32909907 36 1828 MARK1 0 . GRCh38 1 220632222 220632222 + Missense_Mutation SNP T T G novel C3L-00009_T C3L-00009_N T T c.1031T>G p.Phe344Cys p.F344C ENST00000611084 11/18 104 96 8 126 126 0 strelka-varscan-mutect MARK1,missense_variant,p.Phe344Cys,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Phe344Cys,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Phe322Cys,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Phe344Cys,ENST00000366917,NM_018650.4;HDAC1P2,downstream_gene_variant,,ENST00000602936,;HDAC1P2,downstream_gene_variant,,ENST00000453661,; G ENST00000611084 Transcript missense_variant 1671/5321 1031/2391 344/796 F/C tTt/tGt 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 deleterious(0) 11/18 PROSITE_profiles:PS50030,hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21,Pfam_domain:PF00627,Gene3D:1.10.8.10,SMART_domains:SM00165 MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -16.5807 1 1 1 1 0 G 3 3 6 220632222 220632222 T G 1 0 0 0 0 1 0 0 0 9237 1841 64 5 5 MARK1 1 220632222 Missense_Mutation SNP T C3L-00009_T 4585707 220632222 28324200 37 1829 DNAH14 0 . GRCh38 1 224923323 224923323 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.151C>T p.= p.L51L ENST00000445597 2/61 221 208 13 288 288 0 strelka-varscan-mutect DNAH14,synonymous_variant,p.=,ENST00000445597,; T ENST00000445597 Transcript synonymous_variant 151/10524 151/10524 51/3507 L Ctg/Ttg 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000409472 Q0VDD8 UPI0001642868 2/61 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 224923323 224923323 C T 1 0 0 0 0 0 0 0 1 4415 912 32 3 3 DNAH14 1 224923323 Silent SNP C C3L-00009_T 4291101 224923323 24033099 38 1830 H3F3A 0 . GRCh38 1 226064403 226064403 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.52A>G p.Arg18Gly p.R18G ENST00000366813 1/3 244 225 19 346 346 0 varscan-mutect H3F3A,missense_variant,p.Arg18Gly,ENST00000366814,;H3F3A,missense_variant,p.Arg18Gly,ENST00000366813,;H3F3A,missense_variant,p.Arg18Gly,ENST00000366815,NM_002107.4;H3F3A,missense_variant,p.Arg18Gly,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; G ENST00000366813 Transcript missense_variant 427/1308 52/411 18/136 R/G Agg/Ggg 1 1 H3F3A HGNC HGNC:4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 B2R4P9 UPI00000007B0 deleterious_low_confidence(0.02) 1/3 hmmpanther:PTHR11426,PROSITE_patterns:PS00322,Pfam_domain:PF00125,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 226064403 226064403 A G 1 0 0 0 0 1 0 0 0 6815 179 7 5 5 H3F3A 1 226064403 Missense_Mutation SNP A C3L-00009_T 1141080 226064403 22892019 39 1831 TRIM17 0 . GRCh38 1 228411114 228411114 + Silent SNP C C G novel C3L-00009_T C3L-00009_N C C c.588G>C p.= p.L196L ENST00000366697 3/6 159 146 13 186 186 0 strelka-varscan-mutect TRIM17,synonymous_variant,p.=,ENST00000366697,;TRIM17,synonymous_variant,p.=,ENST00000366698,NM_016102.3;TRIM17,synonymous_variant,p.=,ENST00000456946,NM_001134855.1;TRIM17,synonymous_variant,p.=,ENST00000295033,NM_001024940.2;TRIM17,synonymous_variant,p.=,ENST00000479800,;TRIM11,upstream_gene_variant,,ENST00000284551,NM_145214.2;TRIM11,upstream_gene_variant,,ENST00000366699,;TRIM17,downstream_gene_variant,,ENST00000355586,;TRIM11,upstream_gene_variant,,ENST00000602582,;TRIM11,upstream_gene_variant,,ENST00000602308,;TRIM17,downstream_gene_variant,,ENST00000457345,;TRIM17,downstream_gene_variant,,ENST00000520264,;RP11-245P10.4,downstream_gene_variant,,ENST00000436779,; G ENST00000366697 Transcript synonymous_variant 1545/2652 588/1434 196/477 L ctG/ctC 1 -1 TRIM17 HGNC HGNC:13430 protein_coding YES CCDS1571.1 ENSP00000355658 Q9Y577 A0A024R3T1 UPI000000163B 3/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF397 LOW SNV 2 1 PASS rs1158150851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 228411114 228411114 C G 1 0 0 0 0 0 0 0 1 16982 581 21 4 4 TRIM17 1 228411114 Silent SNP C C3L-00009_T 2346711 228411114 20545308 40 1832 RYR2 0 . GRCh38 1 237783820 237783820 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.12108C>A p.Asp4036Glu p.D4036E ENST00000366574 90/105 390 336 54 579 578 1 strelka-varscan-mutect RYR2,missense_variant,p.Asp4036Glu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp4020Glu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript missense_variant 12425/16562 12108/14904 4036/4967 D/E gaC/gaA 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.07) 90/105 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 237783820 237783820 C A 1 0 0 0 0 1 0 0 0 14029 506 18 2 2 RYR2 1 237783820 Missense_Mutation SNP C C3L-00009_T 9372706 237783820 11172602 41 1833 FMN2 0 . GRCh38 1 240092475 240092475 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.366C>G p.Ser122Arg p.S122R ENST00000319653 1/18 221 194 27 365 365 0 strelka-varscan-mutect FMN2,missense_variant,p.Ser122Arg,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,intron_variant,,ENST00000447095,; G ENST00000319653 Transcript missense_variant 596/6434 366/5169 122/1722 S/R agC/agG 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious(0.05) 1/18 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 240092475 240092475 C G 1 0 0 0 0 1 0 0 0 5806 738 26 4 4 FMN2 1 240092475 Missense_Mutation SNP C C3L-00009_T 2308655 240092475 8863947 42 1834 FMN2 0 . GRCh38 1 240207250 240207250 + Missense_Mutation SNP C C A rs750017017 C3L-00009_T C3L-00009_N C C c.2438C>A p.Pro813His p.P813H ENST00000319653 5/18 188 161 27 286 286 0 strelka-varscan-mutect FMN2,missense_variant,p.Pro813His,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; A ENST00000319653 Transcript missense_variant 2668/6434 2438/5169 813/1722 P/H cCt/cAt rs750017017 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious_low_confidence(0) 5/18 Low_complexity_(Seg):seg,SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS rs750017017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 240207250 240207250 C A 1 0 0 0 0 1 0 0 0 5806 681 24 2 2 FMN2 1 240207250 Missense_Mutation SNP C C3L-00009_T 114775 240207250 8749172 43 1835 EXO1 0 . GRCh38 1 241879173 241879173 + Missense_Mutation SNP A A C novel C3L-00009_T C3L-00009_N A A c.1939A>C p.Asn647His p.N647H ENST00000366548 13/16 77 67 10 116 116 0 strelka-varscan-mutect EXO1,missense_variant,p.Asn647His,ENST00000366548,NM_130398.3;EXO1,missense_variant,p.Asn647His,ENST00000348581,NM_001319224.1,NM_006027.4;EXO1,missense_variant,p.Asn647His,ENST00000518483,NM_003686.4;EXO1,missense_variant,p.Asn46His,ENST00000521202,; C ENST00000366548 Transcript missense_variant 2532/3473 1939/2541 647/846 N/H Aat/Cat 1 1 EXO1 HGNC HGNC:3511 protein_coding YES CCDS1620.1 ENSP00000355506 Q9UQ84 UPI000013DDA8 NM_130398.3 tolerated(0.09) 13/16 hmmpanther:PTHR11081:SF8,hmmpanther:PTHR11081 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99399 1 1 1 1 0 C 3 2 6 241879173 241879173 A C 1 0 0 0 0 1 0 0 0 5167 362 13 5 5 EXO1 1 241879173 Missense_Mutation SNP A C3L-00009_T 1671923 241879173 7077249 44 1836 KIF26B 0 . GRCh38 1 245156652 245156652 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.434G>T p.Arg145Met p.R145M ENST00000407071 2/15 260 212 48 306 306 0 strelka-varscan-mutect KIF26B,missense_variant,p.Arg145Met,ENST00000407071,NM_018012.3; T ENST00000407071 Transcript missense_variant 874/7287 434/6327 145/2108 R/M aGg/aTg 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 deleterious(0) 2/15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 245156652 245156652 G T 1 0 0 0 0 1 0 0 0 8160 1000 35 2 2 KIF26B 1 245156652 Missense_Mutation SNP G C3L-00009_T 3277479 245156652 3799770 45 1837 OR2M7 0 . GRCh38 1 248323961 248323961 + Missense_Mutation SNP C C A rs555916714 C3L-00009_T C3L-00009_N C C c.608G>T p.Cys203Phe p.C203F ENST00000317965 1/1 384 318 66 549 549 0 strelka-varscan-mutect OR2M7,missense_variant,p.Cys203Phe,ENST00000317965,NM_001004691.1; A ENST00000317965 Transcript missense_variant 608/939 608/939 203/312 C/F tGt/tTt rs555916714 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs555916714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 248323961 248323961 C A 1 0 0 0 0 1 0 0 0 11092 478 17 2 2 OR2M7 1 248323961 Missense_Mutation SNP C C3L-00009_T 3167309 248323961 632461 46 1838 OR2T2 0 . GRCh38 1 248453659 248453659 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.862C>T p.Pro288Ser p.P288S ENST00000342927 1/1 297 278 19 473 473 0 varscan-mutect OR2T2,missense_variant,p.Pro288Ser,ENST00000342927,NM_001004136.1; T ENST00000342927 Transcript missense_variant 862/975 862/975 288/324 P/S Cca/Tca 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1482568720 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 248453659 248453659 C T 1 0 0 0 0 1 0 0 0 11097 623 22 3 3 OR2T2 1 248453659 Missense_Mutation SNP C C3L-00009_T 129698 248453659 502763 47 1839 TPO 0 . GRCh38 2 1493920 1493920 + Silent SNP T T A novel C3L-00009_T C3L-00009_N T T c.1887T>A p.= p.P629P ENST00000345913 11/17 587 543 44 803 803 0 strelka-varscan-mutect TPO,synonymous_variant,p.=,ENST00000422464,;TPO,synonymous_variant,p.=,ENST00000345913,NM_000547.5;TPO,synonymous_variant,p.=,ENST00000329066,NM_001206744.1;TPO,synonymous_variant,p.=,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,synonymous_variant,p.=,ENST00000346956,NM_175721.3;TPO,synonymous_variant,p.=,ENST00000382198,NM_175722.3;TPO,synonymous_variant,p.=,ENST00000446278,;TPO,synonymous_variant,p.=,ENST00000469607,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,non_coding_transcript_exon_variant,,ENST00000462973,; A ENST00000345913 Transcript synonymous_variant 1978/3145 1887/2802 629/933 P ccT/ccA 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 11/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 1493920 1493920 T A 1 0 0 0 0 0 0 0 1 16891 1567 55 4 4 TPO 2 1493920 Silent SNP T C3L-00009_T 1493920 240699609 48 1840 WDCP 0 . GRCh38 2 24037696 24037696 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.1799A>G p.Tyr600Cys p.Y600C ENST00000295148 2/4 49 38 11 67 67 0 strelka-varscan-mutect WDCP,missense_variant,p.Tyr600Cys,ENST00000295148,NM_025203.2;WDCP,missense_variant,p.Tyr600Cys,ENST00000406895,NM_001142319.1;WDCP,downstream_gene_variant,,ENST00000443232,;MFSD2B,intron_variant,,ENST00000453731,; C ENST00000295148 Transcript missense_variant 1857/3817 1799/2166 600/721 Y/C tAt/tGt 1 -1 WDCP HGNC HGNC:26157 protein_coding YES CCDS1705.1 ENSP00000295148 Q9H6R7 UPI0000070788 NM_025203.2 deleterious(0.04) 2/4 Pfam_domain:PF15390,hmmpanther:PTHR14897,hmmpanther:PTHR14897:SF5 MODERATE 1 SNV 2 1 PASS rs756155854 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 24037696 24037696 T C 1 0 0 0 0 1 0 0 0 17827 1406 49 5 5 WDCP 2 24037696 Missense_Mutation SNP T C3L-00009_T 22543776 24037696 218155833 49 1841 ITSN2 0 . GRCh38 2 24204259 24204259 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.4922A>T p.Gln1641Leu p.Q1641L ENST00000355123 39/40 227 199 28 261 261 0 strelka-varscan-mutect ITSN2,missense_variant,p.Gln1641Leu,ENST00000355123,NM_006277.2;ITSN2,missense_variant,p.Gln1614Leu,ENST00000361999,NM_019595.3;ITSN2,missense_variant,p.Gln1624Leu,ENST00000622089,;FAM228A,downstream_gene_variant,,ENST00000415196,;AC008073.9,upstream_gene_variant,,ENST00000429717,;ITSN2,3_prime_UTR_variant,,ENST00000427234,;ITSN2,non_coding_transcript_exon_variant,,ENST00000478720,;ITSN2,downstream_gene_variant,,ENST00000479575,;ITSN2,downstream_gene_variant,,ENST00000449392,; A ENST00000355123 Transcript missense_variant 5366/6300 4922/5094 1641/1697 Q/L cAg/cTg 1 -1 ITSN2 HGNC HGNC:6184 protein_coding YES CCDS1710.2 ENSP00000347244 Q9NZM3 UPI000013D415 NM_006277.2 tolerated(0.21) 39/40 PROSITE_profiles:PS50004,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 24204259 24204259 T A 1 0 0 0 0 1 0 0 0 7833 1580 55 4 4 ITSN2 2 24204259 Missense_Mutation SNP T C3L-00009_T 166563 24204259 217989270 50 1842 MEMO1 0 . GRCh38 2 31963221 31963221 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.21C>G p.Asp7Glu p.D7E ENST00000379383 1/9 80 75 5 108 108 0 strelka-varscan-mutect MEMO1,missense_variant,p.Asp7Glu,ENST00000379383,;MEMO1,intron_variant,,ENST00000295065,NM_015955.3;MEMO1,intron_variant,,ENST00000404530,NM_001301833.1;MEMO1,intron_variant,,ENST00000426310,NM_001137602.2;MEMO1,intron_variant,,ENST00000407893,;DPY30,intron_variant,,ENST00000446765,;MEMO1,intron_variant,,ENST00000490459,;MEMO1,intron_variant,,ENST00000413686,; C ENST00000379383 Transcript missense_variant 78/1498 21/903 7/300 D/E gaC/gaG 1 -1 MEMO1 HGNC HGNC:14014 protein_coding ENSP00000368691 Q9Y316 UPI00004906CE tolerated_low_confidence(1) 1/9 MODERATE SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -10.99377 0.9999971 1 1 1 0 C 3 2 6 31963221 31963221 G C 1 0 0 0 0 1 0 0 0 9416 1368 48 4 4 MEMO1 2 31963221 Missense_Mutation SNP G C3L-00009_T 7758962 31963221 210230308 51 1843 PPP1R21 0 . GRCh38 2 48510060 48510060 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.2131G>C p.Glu711Gln p.E711Q ENST00000294952 20/22 148 123 25 165 165 0 strelka-varscan-mutect PPP1R21,missense_variant,p.Glu711Gln,ENST00000294952,NM_001135629.2;PPP1R21,missense_variant,p.Glu700Gln,ENST00000281394,NM_152994.4;PPP1R21,missense_variant,p.Glu669Gln,ENST00000449090,NM_001193475.1;PPP1R21,non_coding_transcript_exon_variant,,ENST00000476199,;PPP1R21,3_prime_UTR_variant,,ENST00000416913,;PPP1R21,3_prime_UTR_variant,,ENST00000431614,; C ENST00000294952 Transcript missense_variant 2288/3142 2131/2343 711/780 E/Q Gaa/Caa 1 1 PPP1R21 HGNC HGNC:30595 protein_coding YES CCDS46278.1 ENSP00000294952 Q6ZMI0 UPI000015C523 NM_001135629.2 tolerated(0.14) 20/22 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10212,hmmpanther:PTHR21448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 48510060 48510060 G C 1 0 0 0 0 1 0 0 0 12483 1175 41 4 4 PPP1R21 2 48510060 Missense_Mutation SNP G C3L-00009_T 16546839 48510060 193683469 52 1844 ETAA1 0 . GRCh38 2 67403607 67403607 + Missense_Mutation SNP A A C rs773474602 C3L-00009_T C3L-00009_N A A c.925A>C p.Ser309Arg p.S309R ENST00000272342 5/6 131 104 27 179 178 1 strelka-varscan-mutect ETAA1,missense_variant,p.Ser309Arg,ENST00000272342,NM_019002.3;ETAA1,intron_variant,,ENST00000462772,; C ENST00000272342 Transcript missense_variant 1055/3418 925/2781 309/926 S/R Agt/Cgt rs773474602 1 1 ETAA1 HGNC HGNC:24648 protein_coding YES CCDS1882.1 ENSP00000272342 Q9NY74 UPI00001414BC NM_019002.3 deleterious(0.04) 5/6 Pfam_domain:PF15350,hmmpanther:PTHR16434 MODERATE 1 SNV 1 1 PASS rs773474602 . 0 206 2 2 0 0 0 0 -20 0.999999 1 1 1 0 C 3 2 6 67403607 67403607 A C 1 0 0 0 0 1 0 0 0 5129 188 7 5 5 ETAA1 2 67403607 Missense_Mutation SNP A C3L-00009_T 18893547 67403607 174789922 53 1845 ADD2 0 . GRCh38 2 70706308 70706308 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.101T>A p.Leu34His p.L34H ENST00000264436 3/16 230 197 33 326 326 0 strelka-varscan-mutect ADD2,missense_variant,p.Leu34His,ENST00000264436,NM_001617.3;ADD2,missense_variant,p.Leu34His,ENST00000413157,NM_017482.3;ADD2,missense_variant,p.Leu34His,ENST00000407644,NM_001185054.1;ADD2,missense_variant,p.Leu34His,ENST00000355733,NM_017488.3;ADD2,missense_variant,p.Leu50His,ENST00000430656,NM_001185055.1;ADD2,missense_variant,p.Leu34His,ENST00000456320,;ADD2,missense_variant,p.Leu34His,ENST00000415348,;ADD2,missense_variant,p.Leu34His,ENST00000522886,;ADD2,missense_variant,p.Leu34His,ENST00000425976,;ADD2,downstream_gene_variant,,ENST00000447731,;ADD2,downstream_gene_variant,,ENST00000473232,;ADD2,missense_variant,p.Leu34His,ENST00000403045,; T ENST00000264436 Transcript missense_variant 546/9267 101/2181 34/726 L/H cTt/cAt 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 deleterious(0.05) 3/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 70706308 70706308 A T 1 0 0 0 0 1 0 0 0 349 72 3 4 4 ADD2 2 70706308 Missense_Mutation SNP A C3L-00009_T 3302701 70706308 171487221 54 1846 REG1B 0 . GRCh38 2 79086854 79086854 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.141C>G p.Cys47Trp p.C47W ENST00000305089 3/6 350 304 46 387 387 0 strelka-varscan-mutect REG1B,missense_variant,p.Cys47Trp,ENST00000305089,NM_006507.3;REG1B,upstream_gene_variant,,ENST00000454188,;REG1B,non_coding_transcript_exon_variant,,ENST00000479258,;REG1B,non_coding_transcript_exon_variant,,ENST00000476554,;REG1B,downstream_gene_variant,,ENST00000469052,; C ENST00000305089 Transcript missense_variant 222/767 141/501 47/166 C/W tgC/tgG 1 -1 REG1B HGNC HGNC:9952 protein_coding YES CCDS1963.1 ENSP00000303206 P48304 Q6ICS1 UPI00000012AB NM_006507.3 deleterious(0) 3/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF55,hmmpanther:PTHR22801,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 79086854 79086854 G C 1 0 0 0 0 1 0 0 0 13381 963 34 4 4 REG1B 2 79086854 Missense_Mutation SNP G C3L-00009_T 8380546 79086854 163106675 55 1847 TEX37 0 . GRCh38 2 88526455 88526455 + Missense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.78G>T p.Gln26His p.Q26H ENST00000303254 3/4 250 215 35 253 253 0 strelka-varscan-mutect TEX37,missense_variant,p.Gln26His,ENST00000303254,NM_152670.2; T ENST00000303254 Transcript missense_variant 220/795 78/543 26/180 Q/H caG/caT COSM1023582 1 1 TEX37 HGNC HGNC:26341 protein_coding YES CCDS2003.1 ENSP00000307142 Q96LM6 A0A140VK60 UPI0000072E9C NM_152670.2 deleterious_low_confidence(0.01) 3/4 hmmpanther:PTHR36882,hmmpanther:PTHR36882:SF1,Pfam_domain:PF15217 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 88526455 88526455 G T 1 0 0 0 0 1 0 0 0 16213 962 34 2 2 TEX37 2 88526455 Missense_Mutation SNP G C3L-00009_T 9439601 88526455 153667074 56 1848 ZC3H6 0 . GRCh38 2 112331715 112331715 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.2797G>A p.Ala933Thr p.A933T ENST00000409871 12/12 124 101 23 179 179 0 strelka-varscan-mutect ZC3H6,missense_variant,p.Ala933Thr,ENST00000409871,NM_198581.2;ZC3H6,missense_variant,p.Ala933Thr,ENST00000343936,;ZC3H6,upstream_gene_variant,,ENST00000502881,; A ENST00000409871 Transcript missense_variant 3198/11542 2797/3570 933/1189 A/T Gca/Aca 1 1 ZC3H6 HGNC HGNC:24762 protein_coding YES CCDS46393.1 ENSP00000386764 P61129 UPI00004215E8 NM_198581.2 deleterious(0.01) 12/12 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF22 MODERATE 1 SNV 2 1 PASS rs1301571839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 112331715 112331715 G A 1 0 0 0 0 1 0 0 0 18146 971 34 3 3 ZC3H6 2 112331715 Missense_Mutation SNP G C3L-00009_T 23805260 112331715 129861814 57 1849 TMEM185B 0 . GRCh38 2 120222604 120222604 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.373G>T p.Val125Leu p.V125L ENST00000426077 1/1 289 238 51 378 378 0 strelka-varscan-mutect TMEM185B,missense_variant,p.Val125Leu,ENST00000426077,NM_024121.2; A ENST00000426077 Transcript missense_variant 805/2131 373/1053 125/350 V/L Gtg/Ttg 1 -1 TMEM185B HGNC HGNC:18896 protein_coding YES CCDS58722.1 ENSP00000453399 Q9H7F4 UPI0000074167 NM_024121.2 tolerated(0.19) 1/1 Pfam_domain:PF10269,hmmpanther:PTHR13568,hmmpanther:PTHR13568:SF5,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 120222604 120222604 C A 1 0 0 0 0 1 0 0 0 16551 536 19 1 1 TMEM185B 2 120222604 Missense_Mutation SNP C C3L-00009_T 7890889 120222604 121970925 58 1850 CNTNAP5 0 . GRCh38 2 124790083 124790083 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.2931C>A p.His977Gln p.H977Q ENST00000431078 18/24 213 185 28 276 276 0 strelka-varscan-mutect CNTNAP5,missense_variant,p.His977Gln,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 3295/5284 2931/3921 977/1306 H/Q caC/caA 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 tolerated(0.41) 18/24 PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 124790083 124790083 C A 1 0 0 0 0 1 0 0 0 3432 477 17 2 2 CNTNAP5 2 124790083 Missense_Mutation SNP C C3L-00009_T 4567479 124790083 117403446 59 1851 POTEI 0 . GRCh38 2 130508776 130508776 + Nonsense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.460A>T p.Arg154Ter p.R154* ENST00000451531 1/15 97 83 14 185 185 0 varscan-mutect POTEI,stop_gained,p.Arg154Ter,ENST00000451531,NM_001277406.1;POTEI,stop_gained,p.Arg154Ter,ENST00000631234,;POTEI,stop_gained,p.Arg154Ter,ENST00000615053,; A ENST00000451531 Transcript stop_gained 891/7020 460/3228 154/1075 R/* Aga/Tga 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 1/15 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS . . 3 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 130508776 130508776 T A 1 0 0 0 0 0 1 0 0 12382 1588 55 4 4 POTEI 2 130508776 Nonsense_Mutation SNP T C3L-00009_T 5718693 130508776 111684753 60 1852 PLEKHB2 0 . GRCh38 2 131146773 131146773 + Nonstop_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.711G>T p.Ter237TyrextTer11 p.*237Yext*11 ENST00000403716 9/9 84 78 6 94 94 0 strelka-varscan-mutect PLEKHB2,stop_lost,p.Ter237TyrextTer11,ENST00000403716,NM_001267063.1,NM_001267062.1;PLEKHB2,stop_lost,p.Ter222TyrextTer11,ENST00000234115,NM_017958.2;PLEKHB2,stop_lost,p.Ter223TyrextTer11,ENST00000409279,;PLEKHB2,stop_lost,p.Ter231TyrextTer11,ENST00000409158,NM_001267065.1,NM_001267064.1;PLEKHB2,stop_lost,p.Ter223TyrextTer11,ENST00000409612,NM_001100623.1;PLEKHB2,3_prime_UTR_variant,,ENST00000439822,NM_001267067.1;PLEKHB2,3_prime_UTR_variant,,ENST00000438882,NM_001267066.1;PLEKHB2,3_prime_UTR_variant,,ENST00000628582,NM_001267068.1;PLEKHB2,intron_variant,,ENST00000404460,; T ENST00000403716 Transcript stop_lost 1271/4349 711/711 237/236 */Y taG/taT 1 1 PLEKHB2 HGNC HGNC:19236 protein_coding YES CCDS74576.1 ENSP00000385892 A0A0A0MSE9 UPI000264F47A NM_001267063.1,NM_001267062.1 9/9 HIGH 1 SNV 3 1 PASS . . 0 201 9 0 0 0 0 0 -12.70425 0.9999704 1 1 1 0 T 4 4 6 131146773 131146773 G T 1 0 0 0 0 0 0 0 0 12157 995 35 2 2 PLEKHB2 2 131146773 Nonstop_Mutation SNP G C3L-00009_T 637997 131146773 111046756 61 1853 NCKAP5 0 . GRCh38 2 132784366 132784366 + Missense_Mutation SNP T T G rs776322123 C3L-00009_T C3L-00009_N T T c.2445A>C p.Lys815Asn p.K815N ENST00000409261 14/20 197 176 21 218 217 1 strelka-varscan-mutect NCKAP5,missense_variant,p.Lys815Asn,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Lys815Asn,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; G ENST00000409261 Transcript missense_variant 2819/7594 2445/5730 815/1909 K/N aaA/aaC rs776322123 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 tolerated(0.06) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 MODERATE 1 SNV 5 1 PASS rs776322123 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 132784366 132784366 T G 1 0 0 0 0 1 0 0 0 10241 1722 60 5 5 NCKAP5 2 132784366 Missense_Mutation SNP T C3L-00009_T 1637593 132784366 109409163 62 1854 LRP1B 0 . GRCh38 2 140442606 140442606 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.10312C>A p.Pro3438Thr p.P3438T ENST00000389484 66/91 186 151 35 231 231 0 strelka-varscan-mutect LRP1B,missense_variant,p.Pro3438Thr,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript missense_variant 11284/16535 10312/13800 3438/4599 P/T Cca/Aca 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.03) 66/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 140442606 140442606 G T 1 0 0 0 0 1 0 0 0 8850 1174 41 2 2 LRP1B 2 140442606 Missense_Mutation SNP G C3L-00009_T 7658240 140442606 101750923 63 1855 PLA2R1 0 . GRCh38 2 159945053 159945053 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.3997C>G p.Pro1333Ala p.P1333A ENST00000283243 28/30 160 129 31 197 197 0 strelka-varscan-mutect PLA2R1,missense_variant,p.Pro1333Ala,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,downstream_gene_variant,,ENST00000392771,NM_001007267.2;PLA2R1,upstream_gene_variant,,ENST00000460710,; C ENST00000283243 Transcript missense_variant 4204/14371 3997/4392 1333/1463 P/A Ccc/Gcc 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 tolerated(0.08) 28/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 159945053 159945053 G C 1 0 0 0 0 1 0 0 0 12106 1174 41 4 4 PLA2R1 2 159945053 Missense_Mutation SNP G C3L-00009_T 19502447 159945053 82248476 64 1856 SCN7A 0 . GRCh38 2 166432446 166432446 + Nonsense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.2464G>T p.Glu822Ter p.E822* ENST00000409855 15/25 343 309 34 402 402 0 strelka-varscan-mutect SCN7A,stop_gained,p.Glu822Ter,ENST00000619410,;SCN7A,stop_gained,p.Glu822Ter,ENST00000621965,;SCN7A,stop_gained,p.Glu822Ter,ENST00000409855,NM_002976.3;SCN7A,stop_gained,p.Glu822Ter,ENST00000419992,;SCN7A,3_prime_UTR_variant,,ENST00000424326,; A ENST00000409855 Transcript stop_gained 2591/7183 2464/5049 822/1682 E/* Gag/Tag 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 15/25 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF06512 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 166432446 166432446 C A 1 0 0 0 0 0 1 0 0 14192 835 29 2 2 SCN7A 2 166432446 Nonsense_Mutation SNP C C3L-00009_T 6487393 166432446 75761083 65 1857 ZNF385B 0 . GRCh38 2 179483311 179483311 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.631T>A p.Ser211Thr p.S211T ENST00000410066 6/10 262 222 40 278 278 0 strelka-varscan-mutect ZNF385B,missense_variant,p.Ser211Thr,ENST00000410066,NM_152520.4;ZNF385B,missense_variant,p.Ser135Thr,ENST00000409343,NM_001113397.1;ZNF385B,missense_variant,p.Ser109Thr,ENST00000336917,NM_001113398.1;ZNF385B,missense_variant,p.Ser109Thr,ENST00000409692,NM_001282725.1;ZNF385B,missense_variant,p.Ser109Thr,ENST00000457304,;ZNF385B,downstream_gene_variant,,ENST00000439340,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000466398,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000495289,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000475539,;ZNF385B,intron_variant,,ENST00000469551,; T ENST00000410066 Transcript missense_variant 1235/3288 631/1416 211/471 S/T Tcc/Acc 1 -1 ZNF385B HGNC HGNC:26332 protein_coding YES CCDS33339.1 ENSP00000386845 Q569K4 UPI00004F9C24 NM_152520.4 tolerated(0.6) 6/10 hmmpanther:PTHR23067:SF8,hmmpanther:PTHR23067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 179483311 179483311 A T 1 0 0 0 0 1 0 0 0 18449 304 11 4 4 ZNF385B 2 179483311 Missense_Mutation SNP A C3L-00009_T 13050865 179483311 62710218 66 1858 ZNF804A 0 . GRCh38 2 184937846 184937846 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.2450G>T p.Gly817Val p.G817V ENST00000302277 4/4 236 206 30 326 325 1 strelka-varscan-mutect ZNF804A,missense_variant,p.Gly817Val,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Gly732Val,ENST00000613975,; T ENST00000302277 Transcript missense_variant 3044/4690 2450/3630 817/1209 G/V gGc/gTc 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 deleterious(0.02) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 184937846 184937846 G T 1 0 0 0 0 1 0 0 0 18755 1203 42 2 2 ZNF804A 2 184937846 Missense_Mutation SNP G C3L-00009_T 5454535 184937846 57255683 67 1859 FSIP2 0 . GRCh38 2 185804745 185804745 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.15706G>C p.Asp5236His p.D5236H ENST00000343098 17/23 110 93 17 150 150 0 strelka-varscan-mutect FSIP2,missense_variant,p.Asp5236His,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Asp5147His,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; C ENST00000343098 Transcript missense_variant 15706/21054 15706/20991 5236/6996 D/H Gat/Cat 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 17/23 Pfam_domain:PF15783,Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 185804745 185804745 G C 1 0 0 0 0 1 0 0 0 5949 1174 41 4 4 FSIP2 2 185804745 Missense_Mutation SNP G C3L-00009_T 866899 185804745 56388784 68 1860 NDUFS1 0 . GRCh38 2 206127946 206127946 + Missense_Mutation SNP T T A rs770664540 C3L-00009_T C3L-00009_N T T c.1777A>T p.Ile593Leu p.I593L ENST00000455934 16/19 414 362 52 525 525 0 strelka-varscan-mutect NDUFS1,missense_variant,p.Ile579Leu,ENST00000233190,NM_005006.6;NDUFS1,missense_variant,p.Ile593Leu,ENST00000455934,NM_001199984.1;NDUFS1,missense_variant,p.Ile522Leu,ENST00000423725,NM_001199983.1;NDUFS1,missense_variant,p.Ile543Leu,ENST00000440274,NM_001199981.1;NDUFS1,missense_variant,p.Ile579Leu,ENST00000449699,;NDUFS1,missense_variant,p.Ile463Leu,ENST00000457011,;NDUFS1,missense_variant,p.Ile468Leu,ENST00000432169,NM_001199982.1;NDUFS1,non_coding_transcript_exon_variant,,ENST00000498520,; A ENST00000455934 Transcript missense_variant 1838/3361 1777/2226 593/741 I/L Ata/Tta rs770664540 1 -1 NDUFS1 HGNC HGNC:7707 protein_coding YES CCDS56165.1 ENSP00000392709 P28331 UPI0000EE3600 NM_001199984.1 tolerated(0.66) 16/19 hmmpanther:PTHR11615:SF115,hmmpanther:PTHR11615,Gene3D:3.40.50.740,Pfam_domain:PF00384,TIGRFAM_domain:TIGR01973,Superfamily_domains:SSF53706 MODERATE 1 SNV 2 1 PASS rs770664540 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 206127946 206127946 T A 1 0 0 0 0 1 0 0 0 10315 1464 51 4 4 NDUFS1 2 206127946 Missense_Mutation SNP T C3L-00009_T 20323201 206127946 36065583 69 1861 FZD5 0 . GRCh38 2 207767750 207767750 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.990C>T p.= p.S330S ENST00000295417 2/2 355 305 50 491 490 1 strelka-varscan-mutect FZD5,synonymous_variant,p.=,ENST00000295417,NM_003468.3; A ENST00000295417 Transcript synonymous_variant 1544/6708 990/1758 330/585 S tcC/tcT 1 -1 FZD5 HGNC HGNC:4043 protein_coding YES CCDS33366.1 ENSP00000354607 Q13467 UPI000013E255 NM_003468.3 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF91,Pfam_domain:PF01534,SMART_domains:SM01330,Prints_domain:PR00489 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 207767750 207767750 G A 1 0 0 0 0 0 0 0 1 6004 1335 47 3 3 FZD5 2 207767750 Silent SNP G C3L-00009_T 1639804 207767750 34425779 70 1862 UNC80 0 . GRCh38 2 209912598 209912598 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.4623G>C p.Lys1541Asn p.K1541N ENST00000439458 29/64 204 177 27 218 218 0 strelka-varscan-mutect UNC80,missense_variant,p.Lys1541Asn,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Lys1536Asn,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; C ENST00000439458 Transcript missense_variant 4703/13562 4623/9777 1541/3258 K/N aaG/aaC 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0.03) 29/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 209912598 209912598 G C 1 0 0 0 0 1 0 0 0 17521 933 33 4 4 UNC80 2 209912598 Missense_Mutation SNP G C3L-00009_T 2144848 209912598 32280931 71 1863 ABCB6 0 . GRCh38 2 219216446 219216446 + Missense_Mutation SNP C C A rs759835717 C3L-00009_T C3L-00009_N C C c.888G>T p.Lys296Asn p.K296N ENST00000265316 4/19 284 245 39 381 381 0 strelka-varscan-mutect ABCB6,missense_variant,p.Lys296Asn,ENST00000265316,NM_005689.2;ABCB6,missense_variant,p.Lys144Asn,ENST00000295750,;ATG9A,downstream_gene_variant,,ENST00000409618,;ATG9A,downstream_gene_variant,,ENST00000396761,NM_024085.4;ATG9A,downstream_gene_variant,,ENST00000361242,NM_001077198.2;ATG9A,downstream_gene_variant,,ENST00000409422,;ATG9A,downstream_gene_variant,,ENST00000429920,;ATG9A,3_prime_UTR_variant,,ENST00000446716,;ABCB6,3_prime_UTR_variant,,ENST00000417678,;ABCB6,3_prime_UTR_variant,,ENST00000452545,;ABCB6,intron_variant,,ENST00000448398,;ATG9A,downstream_gene_variant,,ENST00000409033,;ABCB6,upstream_gene_variant,,ENST00000497882,;ATG9A,downstream_gene_variant,,ENST00000475339,;ABCB6,upstream_gene_variant,,ENST00000492543,;ABCB6,upstream_gene_variant,,ENST00000496984,;ABCB6,upstream_gene_variant,,ENST00000492953,;ABCB6,upstream_gene_variant,,ENST00000494639,; A ENST00000265316 Transcript missense_variant 1205/3016 888/2529 296/842 K/N aaG/aaT rs759835717 1 -1 ABCB6 HGNC HGNC:47 protein_coding YES CCDS2436.1 ENSP00000265316 Q9NP58 UPI000004C4BA NM_005689.2 tolerated(0.5) 4/19 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF18,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS rs759835717 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 219216446 219216446 C A 1 0 0 0 0 1 0 0 0 49 680 24 2 2 ABCB6 2 219216446 Missense_Mutation SNP C C3L-00009_T 9303848 219216446 22977083 72 1864 DOCK10 0 . GRCh38 2 224876098 224876098 + Missense_Mutation SNP T T C rs773654651 C3L-00009_T C3L-00009_N T T c.871A>G p.Ile291Val p.I291V ENST00000258390 8/56 203 168 35 248 248 0 strelka-mutect DOCK10,missense_variant,p.Ile285Val,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Ile291Val,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,;DOCK10,non_coding_transcript_exon_variant,,ENST00000543715,; C ENST00000258390 Transcript missense_variant 939/7260 871/6561 291/2186 I/V Atc/Gtc rs773654651 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 tolerated(0.16) 8/56 Gene3D:2.30.29.30,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71,SMART_domains:SM00233 MODERATE 1 SNV 5 1 PASS rs773654651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 224876098 224876098 T C 1 0 0 0 0 1 0 0 0 4500 1493 52 5 5 DOCK10 2 224876098 Missense_Mutation SNP T C3L-00009_T 5659652 224876098 17317431 73 1865 DNER 0 . GRCh38 2 229407292 229407292 + Missense_Mutation SNP C C G C3L-00009_T C3L-00009_N C C c.1663G>C p.Gly555Arg p.G555R ENST00000341772 10/13 148 129 19 195 195 0 strelka-varscan-mutect DNER,missense_variant,p.Gly555Arg,ENST00000341772,NM_139072.3; G ENST00000341772 Transcript missense_variant 1798/3260 1663/2214 555/737 G/R Gga/Cga COSM720317 1 -1 DNER HGNC HGNC:24456 protein_coding YES CCDS33390.1 ENSP00000345229 Q8NFT8 UPI0000048EB8 NM_139072.3 tolerated(0.09) 10/13 PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF275,hmmpanther:PTHR24044,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,Superfamily_domains:SSF57184 1 MODERATE 1 SNV 1 1 1 PASS rs1360082276 . 0 205 3 2 0 0 0 0 -20 0.9999913 1 1 1 0 G 3 3 6 229407292 229407292 C G 1 0 0 0 0 1 0 0 0 4480 661 23 4 4 DNER 2 229407292 Missense_Mutation SNP C C3L-00009_T 4531194 229407292 12786237 74 1866 AGXT 0 . GRCh38 2 240878040 240878040 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.961G>T p.Val321Phe p.V321F ENST00000307503 10/11 262 229 33 321 321 0 strelka-varscan-mutect AGXT,missense_variant,p.Val321Phe,ENST00000307503,NM_000030.2;AGXT,non_coding_transcript_exon_variant,,ENST00000470255,;AGXT,downstream_gene_variant,,ENST00000472436,;AGXT,downstream_gene_variant,,ENST00000476698,; T ENST00000307503 Transcript missense_variant 1348/1865 961/1179 321/392 V/F Gtc/Ttc 1 1 AGXT HGNC HGNC:341 protein_coding YES CCDS2543.1 ENSP00000302620 P21549 UPI0000135E9B NM_000030.2 deleterious(0) 10/11 Gene3D:3.90.1150.10,Pfam_domain:PF00266,PIRSF_domain:PIRSF000524,hmmpanther:PTHR21152,hmmpanther:PTHR21152:SF22,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 240878040 240878040 G T 1 0 0 0 0 1 0 0 0 483 1029 36 2 2 AGXT 2 240878040 Missense_Mutation SNP G C3L-00009_T 11470748 240878040 1315489 75 1867 ATP2B2 0 . GRCh38 3 10329026 10329026 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.3520C>G p.Arg1174Gly p.R1174G ENST00000360273 23/23 238 204 34 357 357 0 strelka-varscan-mutect ATP2B2,missense_variant,p.Arg1129Gly,ENST00000397077,;ATP2B2,missense_variant,p.Arg1174Gly,ENST00000360273,NM_001001331.2;ATP2B2,missense_variant,p.Arg1129Gly,ENST00000383800,NM_001683.3;ATP2B2,missense_variant,p.Arg1174Gly,ENST00000352432,;ATP2B2,missense_variant,p.Arg1030Gly,ENST00000452124,;MIR378B,upstream_gene_variant,,ENST00000578876,;ATP2B2,non_coding_transcript_exon_variant,,ENST00000467702,;ATP2B2,non_coding_transcript_exon_variant,,ENST00000468426,;ATP2B2,3_prime_UTR_variant,,ENST00000460129,; C ENST00000360273 Transcript missense_variant 3959/8962 3520/3732 1174/1243 R/G Cgg/Ggg 1 -1 ATP2B2 HGNC HGNC:815 protein_coding YES CCDS33701.1 ENSP00000353414 Q01814 A0A024R2K6 UPI00001261EF NM_001001331.2 tolerated_low_confidence(0.43) 23/23 MODERATE 1 SNV 5 1 PASS rs1453823607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 10329026 10329026 G C 1 0 0 0 0 1 0 0 0 1293 1115 39 4 4 ATP2B2 3 10329026 Missense_Mutation SNP G C3L-00009_T 10329026 187966533 76 1868 RAF1 0 . GRCh38 3 12604272 12604272 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.698C>G p.Ser233Cys p.S233C ENST00000251849 7/17 349 283 66 518 518 0 strelka-varscan-mutect RAF1,missense_variant,p.Ser233Cys,ENST00000251849,NM_002880.3;RAF1,missense_variant,p.Ser233Cys,ENST00000442415,;RAF1,missense_variant,p.Ser112Cys,ENST00000432427,;RAF1,3_prime_UTR_variant,,ENST00000423275,;RAF1,3_prime_UTR_variant,,ENST00000416093,;RAF1,non_coding_transcript_exon_variant,,ENST00000491290,;RAF1,upstream_gene_variant,,ENST00000465826,;RAF1,downstream_gene_variant,,ENST00000492690,;RAF1,upstream_gene_variant,,ENST00000460610,; C ENST00000251849 Transcript missense_variant 1138/3300 698/1947 233/648 S/C tCt/tGt 1 -1 RAF1 HGNC HGNC:9829 protein_coding YES CCDS2612.1 ENSP00000251849 P04049 L7RRS6 UPI0000049CFC NM_002880.3 deleterious(0.04) 7/17 hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 12604272 12604272 G C 1 0 0 0 0 1 0 0 0 13163 942 33 4 4 RAF1 3 12604272 Missense_Mutation SNP G C3L-00009_T 2275246 12604272 185691287 77 1869 DAZL 0 . GRCh38 3 16605202 16605202 + Splice_Site SNP C C A novel C3L-00009_T C3L-00009_N C C c.3+1G>T p.X1_splice ENST00000399444 365 306 59 545 545 0 strelka-varscan-mutect DAZL,splice_donor_variant,,ENST00000399444,NM_001351.3;DAZL,intron_variant,,ENST00000454457,;DAZL,upstream_gene_variant,,ENST00000250863,NM_001190811.1; A ENST00000399444 Transcript splice_donor_variant -/3050 3/888 1/295 1 -1 DAZL HGNC HGNC:2685 protein_coding CCDS43059.1 ENSP00000382373 Q92904 A0A140VK77 UPI0000128EDB NM_001351.3 1/10 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 6 16605202 16605202 C A 1 0 0 0 0 0 0 1 0 4047 521 18 2 2 DAZL 3 16605202 Splice_Site SNP C C3L-00009_T 4000930 16605202 181690357 78 1870 DNAH1 0 . GRCh38 3 52347874 52347874 + Missense_Mutation SNP G G T rs371417245 C3L-00009_T C3L-00009_N G G c.2006G>T p.Gly669Val p.G669V ENST00000420323 12/78 116 88 28 178 178 0 strelka-varscan-mutect DNAH1,missense_variant,p.Gly669Val,ENST00000420323,NM_015512.4;DNAH1,non_coding_transcript_exon_variant,,ENST00000486752,;DNAH1,non_coding_transcript_exon_variant,,ENST00000497875,; T ENST00000420323 Transcript missense_variant 2267/13104 2006/12798 669/4265 G/V gGg/gTg rs371417245 1 1 DNAH1 HGNC HGNC:2940 protein_coding YES CCDS46842.1 ENSP00000401514 Q9P2D7 A0A140VJI6 UPI00017EE9F6 NM_015512.4 deleterious(0.04) 12/78 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF137 MODERATE 1 SNV 1 1 PASS rs371417245 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 52347874 52347874 G T 1 0 0 0 0 1 0 0 0 4410 1232 43 2 2 DNAH1 3 52347874 Missense_Mutation SNP G C3L-00009_T 35742672 52347874 145947685 79 1871 PBRM1 0 . GRCh38 3 52662162 52662162 + Nonsense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.499C>T p.Gln167Ter p.Q167* ENST00000394830 5/30 196 152 44 199 199 0 strelka-varscan-mutect PBRM1,stop_gained,p.Gln167Ter,ENST00000356770,;PBRM1,stop_gained,p.Gln167Ter,ENST00000296302,;PBRM1,stop_gained,p.Gln167Ter,ENST00000394830,NM_018313.4;PBRM1,stop_gained,p.Gln167Ter,ENST00000409114,;PBRM1,stop_gained,p.Gln167Ter,ENST00000409057,;PBRM1,stop_gained,p.Gln167Ter,ENST00000410007,;PBRM1,stop_gained,p.Gln167Ter,ENST00000409767,;PBRM1,stop_gained,p.Gln167Ter,ENST00000337303,;PBRM1,stop_gained,p.Gln167Ter,ENST00000423351,;PBRM1,stop_gained,p.Gln111Ter,ENST00000446103,;PBRM1,stop_gained,p.Gln167Ter,ENST00000431678,;PBRM1,downstream_gene_variant,,ENST00000420148,;PBRM1,stop_gained,p.Gln167Ter,ENST00000412587,; A ENST00000394830 Transcript stop_gained 599/5071 499/4749 167/1582 Q/* Caa/Taa 1 -1 PBRM1 HGNC HGNC:30064 protein_coding YES CCDS43099.1 ENSP00000378307 Q86U86 UPI000013E31E NM_018313.4 5/30 hmmpanther:PTHR16062,hmmpanther:PTHR16062:SF11,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 52662162 52662162 G A 1 0 0 0 0 0 1 0 0 11578 1328 46 3 3 PBRM1 3 52662162 Nonsense_Mutation SNP G C3L-00009_T 314288 52662162 145633397 80 1872 GABRR3 0 . GRCh38 3 97986835 97986835 + Missense_Mutation SNP C C A rs748321383 C3L-00009_T C3L-00009_N C C c.1252G>T p.Asp418Tyr p.D418Y ENST00000621172 10/10 363 332 31 496 496 0 strelka-varscan-mutect GABRR3,missense_variant,p.Asp418Tyr,ENST00000621172,NM_001105580.2;GABRR3,missense_variant,p.Asp418Tyr,ENST00000472788,; A ENST00000621172 Transcript missense_variant 1369/1521 1252/1404 418/467 D/Y Gat/Tat rs748321383 1 -1 GABRR3 HGNC HGNC:17969 protein_coding YES CCDS54617.1 ENSP00000481321 A8MPY1 UPI000003F558 NM_001105580.2 deleterious(0.01) 10/10 TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 MODERATE 1 SNV 5 1 PASS rs748321383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 97986835 97986835 C A 1 0 0 0 0 1 0 0 0 6049 884 31 1 1 GABRR3 3 97986835 Missense_Mutation SNP C C3L-00009_T 45324673 97986835 100308724 81 1873 KIAA1257 0 . GRCh38 3 128987712 128987712 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.571C>T p.Leu191Phe p.L191F ENST00000265068 4/8 261 225 36 325 325 0 strelka-varscan-mutect KIAA1257,missense_variant,p.Leu191Phe,ENST00000265068,NM_020741.2;KIAA1257,missense_variant,p.Leu191Phe,ENST00000511438,;KIAA1257,missense_variant,p.Leu79Phe,ENST00000515659,;KIAA1257,non_coding_transcript_exon_variant,,ENST00000510149,; A ENST00000265068 Transcript missense_variant 739/6034 571/1230 191/409 L/F Ctc/Ttc 1 -1 KIAA1257 HGNC HGNC:29231 protein_coding YES CCDS46905.1 ENSP00000265068 Q9ULG3 UPI00001C1DE3 NM_020741.2 deleterious(0.02) 4/8 hmmpanther:PTHR33667:SF1,hmmpanther:PTHR33667,Pfam_domain:PF15084 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 128987712 128987712 G A 1 0 0 0 0 1 0 0 0 8110 971 34 3 3 KIAA1257 3 128987712 Missense_Mutation SNP G C3L-00009_T 31000877 128987712 69307847 82 1874 ACAD11 0 . GRCh38 3 132630435 132630435 + Splice_Site SNP A A T novel C3L-00009_T C3L-00009_N A A c.963+2T>A p.X321_splice ENST00000264990 66 57 9 84 84 0 strelka-varscan-mutect ACAD11,splice_donor_variant,,ENST00000264990,NM_032169.4;ACAD11,splice_donor_variant,,ENST00000481970,;ACAD11,downstream_gene_variant,,ENST00000489991,;NPHP3-ACAD11,splice_donor_variant,,ENST00000471702,;ACAD11,splice_donor_variant,,ENST00000496418,;ACAD11,splice_donor_variant,,ENST00000469042,;ACAD11,splice_donor_variant,,ENST00000485198,;ACAD11,upstream_gene_variant,,ENST00000487024,; T ENST00000264990 Transcript splice_donor_variant -/4142 963/2343 321/780 1 -1 ACAD11 HGNC HGNC:30211 protein_coding YES CCDS3074.1 ENSP00000264990 Q709F0 UPI0000223E4E NM_032169.4 7/19 HIGH 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -15.92306 0.9999923 1 1 1 0 T 5 4 6 132630435 132630435 A T 1 0 0 0 0 0 0 1 0 152 405 14 4 4 ACAD11 3 132630435 Splice_Site SNP A C3L-00009_T 3642723 132630435 65665124 83 1875 SPATA16 0 . GRCh38 3 173019513 173019513 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.821G>A p.Cys274Tyr p.C274Y ENST00000351008 4/11 431 384 47 484 483 1 strelka-varscan-mutect SPATA16,missense_variant,p.Cys274Tyr,ENST00000351008,NM_031955.5; T ENST00000351008 Transcript missense_variant 1005/2106 821/1710 274/569 C/Y tGt/tAt 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 tolerated(0.33) 4/11 Gene3D:1.25.40.10,Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 173019513 173019513 C T 1 0 0 0 0 1 0 0 0 15331 478 17 3 3 SPATA16 3 173019513 Missense_Mutation SNP C C3L-00009_T 40389078 173019513 25276046 84 1876 NLGN1 0 . GRCh38 3 174279179 174279179 + Nonsense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.1178T>A p.Leu393Ter p.L393* ENST00000457714 6/7 164 130 34 183 183 0 strelka-varscan-mutect NLGN1,stop_gained,p.Leu393Ter,ENST00000457714,NM_014932.3;NLGN1,stop_gained,p.Leu393Ter,ENST00000361589,;NLGN1,stop_gained,p.Leu178Ter,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,non_coding_transcript_exon_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,;NLGN1,downstream_gene_variant,,ENST00000490929,; A ENST00000457714 Transcript stop_gained 1607/8242 1178/2472 393/823 L/* tTa/tAa 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 6/7 hmmpanther:PTHR11559:SF52,hmmpanther:PTHR11559,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 174279179 174279179 T A 1 0 0 0 0 0 1 0 0 10498 1764 61 4 4 NLGN1 3 174279179 Nonsense_Mutation SNP T C3L-00009_T 1259666 174279179 24016380 85 1877 HTR3D 0 . GRCh38 3 184032917 184032917 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.87C>T p.= p.I29I ENST00000382489 1/8 322 261 61 349 349 0 strelka-varscan-mutect HTR3D,synonymous_variant,p.=,ENST00000382489,NM_001163646.1;HTR3D,intron_variant,,ENST00000334128,NM_182537.2;HTR3D,intron_variant,,ENST00000428798,NM_001145143.1;HTR3D,upstream_gene_variant,,ENST00000453435,; T ENST00000382489 Transcript synonymous_variant 87/1674 87/1365 29/454 I atC/atT 1 1 HTR3D HGNC HGNC:24004 protein_coding YES CCDS54685.1 ENSP00000371929 Q70Z44 UPI000024209D NM_001163646.1 1/8 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF409 LOW 1 SNV 1 1 PASS rs926622209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 184032917 184032917 C T 1 0 0 0 0 0 0 0 1 7343 816 29 3 3 HTR3D 3 184032917 Silent SNP C C3L-00009_T 9753738 184032917 14262642 86 1878 EIF4G1 0 . GRCh38 3 184323594 184323594 + Splice_Site SNP G G T novel C3L-00009_T C3L-00009_N G G c.2295+1G>T p.X765_splice ENST00000424196 437 332 105 518 518 0 strelka-varscan-mutect EIF4G1,splice_donor_variant,,ENST00000342981,NM_182917.4;EIF4G1,splice_donor_variant,,ENST00000424196,;EIF4G1,splice_donor_variant,,ENST00000414031,NM_001291157.1;EIF4G1,splice_donor_variant,,ENST00000346169,NM_198241.2;EIF4G1,splice_donor_variant,,ENST00000352767,NM_001194947.1;EIF4G1,splice_donor_variant,,ENST00000392537,NM_198244.2;EIF4G1,splice_donor_variant,,ENST00000382330,NM_001194946.1;EIF4G1,splice_donor_variant,,ENST00000427845,;EIF4G1,splice_donor_variant,,ENST00000434061,NM_004953.4;EIF4G1,splice_donor_variant,,ENST00000350481,NM_198242.2;EIF4G1,splice_donor_variant,,ENST00000411531,;EIF4G1,splice_donor_variant,,ENST00000435046,;EIF4G1,splice_donor_variant,,ENST00000441154,;EIF4G1,splice_donor_variant,,ENST00000426123,;EIF4G1,splice_donor_variant,,ENST00000421110,;EIF4G1,splice_donor_variant,,ENST00000450424,;EIF4G1,splice_donor_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000457456,;EIF4G1,downstream_gene_variant,,ENST00000427141,;EIF4G1,downstream_gene_variant,,ENST00000456033,;EIF4G1,upstream_gene_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000440448,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000428387,;SNORD66,upstream_gene_variant,,ENST00000390856,;EIF4G1,splice_donor_variant,,ENST00000442406,;EIF4G1,splice_donor_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,upstream_gene_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000493299,;EIF4G1,upstream_gene_variant,,ENST00000482303,; T ENST00000424196 Transcript splice_donor_variant -/5653 2295/4821 765/1606 1 1 EIF4G1 HGNC HGNC:3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 14/31 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 6 184323594 184323594 G T 1 0 0 0 0 0 0 1 0 4870 1275 44 2 2 EIF4G1 3 184323594 Splice_Site SNP G C3L-00009_T 290677 184323594 13971965 87 1879 MUC4 0 . GRCh38 3 195786878 195786878 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.4702C>A p.Pro1568Thr p.P1568T ENST00000463781 2/25 759 684 75 918 917 1 varscan-mutect MUC4,missense_variant,p.Pro1568Thr,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Pro1568Thr,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Pro1568Thr,ENST00000478156,;MUC4,missense_variant,p.Pro1568Thr,ENST00000466475,;MUC4,missense_variant,p.Pro1568Thr,ENST00000477756,;MUC4,missense_variant,p.Pro1568Thr,ENST00000477086,;MUC4,missense_variant,p.Pro1568Thr,ENST00000480843,;MUC4,missense_variant,p.Pro1568Thr,ENST00000462323,;MUC4,missense_variant,p.Pro1568Thr,ENST00000470451,;MUC4,missense_variant,p.Pro1568Thr,ENST00000479406,; T ENST00000463781 Transcript missense_variant 5162/17110 4702/16239 1568/5412 P/T Cct/Act 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 deleterious_low_confidence(0) 2/25 MODERATE 1 SNV 5 1 PASS rs1451574334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 195786878 195786878 G T 1 0 0 0 0 1 0 0 0 9977 1232 43 2 2 MUC4 3 195786878 Missense_Mutation SNP G C3L-00009_T 11463284 195786878 2508681 88 1880 IQCG 0 . GRCh38 3 197889716 197889716 + Splice_Site SNP T T C novel C3L-00009_T C3L-00009_N T T c.1198-2A>G p.X400_splice ENST00000265239 167 126 41 177 177 0 strelka-varscan-mutect IQCG,splice_acceptor_variant,,ENST00000265239,NM_001323029.1,NM_032263.3;IQCG,splice_acceptor_variant,,ENST00000455191,NM_001134435.2;LRCH3,downstream_gene_variant,,ENST00000438796,;RNU6-858P,upstream_gene_variant,,ENST00000362436,;IQCG,splice_acceptor_variant,,ENST00000485787,;IQCG,splice_acceptor_variant,,ENST00000490748,;IQCG,splice_acceptor_variant,,ENST00000478903,; C ENST00000265239 Transcript splice_acceptor_variant -/2262 1198/1332 400/443 1 -1 IQCG HGNC HGNC:25251 protein_coding YES CCDS3331.1 ENSP00000265239 Q9H095 UPI0000037D68 NM_001323029.1,NM_032263.3 11/11 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 5 2 6 197889716 197889716 T C 1 0 0 0 0 0 0 1 0 7716 1594 55 5 5 IQCG 3 197889716 Splice_Site SNP T C3L-00009_T 2102838 197889716 405843 89 1881 IQCG 0 . GRCh38 3 197943780 197943780 + Missense_Mutation SNP C C T rs146833269 C3L-00009_T C3L-00009_N C C c.280G>A p.Val94Met p.V94M ENST00000265239 4/12 163 115 48 210 210 0 strelka-varscan-mutect IQCG,missense_variant,p.Val94Met,ENST00000265239,NM_001323029.1,NM_032263.3;IQCG,missense_variant,p.Val94Met,ENST00000455191,NM_001134435.2;IQCG,missense_variant,p.Val94Met,ENST00000453254,NM_001323030.1;IQCG,missense_variant,p.Val75Met,ENST00000416896,;IQCG,downstream_gene_variant,,ENST00000452735,;IQCG,splice_region_variant,,ENST00000480302,;IQCG,non_coding_transcript_exon_variant,,ENST00000463651,;IQCG,upstream_gene_variant,,ENST00000490748,; T ENST00000265239 Transcript missense_variant,splice_region_variant 705/2262 280/1332 94/443 V/M Gtg/Atg rs146833269,COSM236140 1 -1 IQCG HGNC HGNC:25251 protein_coding YES CCDS3331.1 ENSP00000265239 Q9H095 UPI0000037D68 NM_001323029.1,NM_032263.3 tolerated(0.56) 4/12 hmmpanther:PTHR14871:SF1,hmmpanther:PTHR14871 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs146833269 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 197943780 197943780 C T 1 0 0 0 0 1 0 0 0 7716 550 19 1 1 IQCG 3 197943780 Missense_Mutation SNP C C3L-00009_T 54064 197943780 351779 90 1882 LMLN 0 . GRCh38 3 197960268 197960268 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.47G>A p.Gly16Glu p.G16E ENST00000420910 1/17 137 129 8 170 170 0 strelka-varscan-mutect LMLN,missense_variant,p.Gly16Glu,ENST00000330198,NM_033029.3;LMLN,missense_variant,p.Gly16Glu,ENST00000420910,NM_001136049.2;LMLN,synonymous_variant,p.=,ENST00000482695,;LMLN,synonymous_variant,p.=,ENST00000332636,;LMLN,intron_variant,,ENST00000419117,;IQCG,upstream_gene_variant,,ENST00000265239,NM_001323029.1,NM_032263.3;RPL35A,downstream_gene_variant,,ENST00000464167,;IQCG,upstream_gene_variant,,ENST00000416896,;RPL35A,downstream_gene_variant,,ENST00000448864,NM_001316311.1,NM_000996.2;IQCG,upstream_gene_variant,,ENST00000480302,;LMLN,non_coding_transcript_exon_variant,,ENST00000451139,;IQCG,upstream_gene_variant,,ENST00000493624,;RPL35A,downstream_gene_variant,,ENST00000474640,;RPL35A,downstream_gene_variant,,ENST00000439255,;RPL35A,downstream_gene_variant,,ENST00000429437,; A ENST00000420910 Transcript missense_variant 47/2423 47/2079 16/692 G/E gGa/gAa 1 1 LMLN HGNC HGNC:15991 protein_coding YES CCDS46988.1 ENSP00000410926 Q96KR4 UPI000192C367 NM_001136049.2 tolerated_low_confidence(0.49) 1/17 Low_complexity_(Seg):seg,hmmpanther:PTHR10942,hmmpanther:PTHR10942:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 197960268 197960268 G A 1 0 0 0 0 1 0 0 0 8771 1174 41 3 3 LMLN 3 197960268 Missense_Mutation SNP G C3L-00009_T 16488 197960268 335291 91 1883 PDE6B 0 . GRCh38 4 625978 625978 + Missense_Mutation SNP G G A rs201253138 C3L-00009_T C3L-00009_N G G c.352G>A p.Val118Ile p.V118I ENST00000496514 1/22 70 56 14 95 95 0 strelka-varscan-mutect PDE6B,missense_variant,p.Val118Ile,ENST00000255622,NM_001145291.1;PDE6B,missense_variant,p.Val118Ile,ENST00000496514,NM_000283.3; A ENST00000496514 Transcript missense_variant 373/3232 352/2565 118/854 V/I Gtc/Atc rs201253138,COSM3409389 1 1 PDE6B HGNC HGNC:8786 protein_coding YES CCDS33932.1 ENSP00000420295 P35913 UPI0000DBEE72 NM_000283.3 tolerated(0.17) 1/22 Gene3D:3.30.450.40,Pfam_domain:PF01590,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF73,SMART_domains:SM00065,Superfamily_domains:SSF55781 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201253138 . 0 199 11 0 0 0 0 0 -20 0.9999776 1 1 1 0 A 3 1 6 625978 625978 G A 1 0 0 0 0 1 0 0 0 11734 1145 40 1 1 PDE6B 4 625978 Missense_Mutation SNP G C3L-00009_T 625978 189588577 92 1884 ZFYVE28 0 . GRCh38 4 2305124 2305124 + Missense_Mutation SNP C C A rs779341433 C3L-00009_T C3L-00009_N C C c.1216G>T p.Val406Leu p.V406L ENST00000290974 8/13 46 29 17 70 70 0 strelka-varscan-mutect ZFYVE28,missense_variant,p.Val406Leu,ENST00000290974,NM_020972.2;ZFYVE28,missense_variant,p.Val376Leu,ENST00000511071,NM_001172656.1;ZFYVE28,missense_variant,p.Val336Leu,ENST00000515312,NM_001172659.1;RP11-478C1.7,intron_variant,,ENST00000510632,; A ENST00000290974 Transcript missense_variant 1556/4131 1216/2664 406/887 V/L Gtg/Ttg rs779341433,COSM4742759 1 -1 ZFYVE28 HGNC HGNC:29334 protein_coding YES CCDS33942.1 ENSP00000290974 Q9HCC9 UPI00001C1E08 NM_020972.2 tolerated_low_confidence(0.64) 8/13 hmmpanther:PTHR22835:SF41,hmmpanther:PTHR22835 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779341433 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 2305124 2305124 C A 1 0 0 0 0 1 0 0 0 18247 536 19 1 1 ZFYVE28 4 2305124 Missense_Mutation SNP C C3L-00009_T 1679146 2305124 187909431 93 1885 JAKMIP1 0 . GRCh38 4 6036059 6036059 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.2224C>T p.Pro742Ser p.P742S ENST00000409021 19/21 197 184 13 264 263 1 strelka-varscan-mutect JAKMIP1,missense_variant,p.Pro742Ser,ENST00000409021,NM_001099433.1;JAKMIP1,missense_variant,p.Pro557Ser,ENST00000409371,;JAKMIP1,missense_variant,p.Pro310Ser,ENST00000637373,; A ENST00000409021 Transcript missense_variant 2674/2975 2224/2496 742/831 P/S Ccg/Tcg 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 tolerated(0.34) 19/21 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 6036059 6036059 G A 1 0 0 0 0 1 0 0 0 7853 1203 42 3 3 JAKMIP1 4 6036059 Missense_Mutation SNP G C3L-00009_T 3730935 6036059 184178496 94 1886 ZNF518B 0 . GRCh38 4 10445067 10445067 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.1262T>C p.Phe421Ser p.F421S ENST00000326756 3/3 151 141 10 184 184 0 strelka-varscan-mutect ZNF518B,missense_variant,p.Phe421Ser,ENST00000326756,NM_053042.2;ZNF518B,downstream_gene_variant,,ENST00000507515,; G ENST00000326756 Transcript missense_variant 1701/6894 1262/3225 421/1074 F/S tTt/tCt 1 -1 ZNF518B HGNC HGNC:29365 protein_coding YES CCDS33960.1 ENSP00000317614 Q9C0D4 UPI0000160B97 NM_053042.2 deleterious(0) 3/3 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 10445067 10445067 A G 1 0 0 0 0 1 0 0 0 18535 14 1 5 5 ZNF518B 4 10445067 Missense_Mutation SNP A C3L-00009_T 4409008 10445067 179769488 95 1887 AASDH 0 . GRCh38 4 56353409 56353409 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1571C>A p.Ser524Tyr p.S524Y ENST00000205214 9/15 89 81 8 98 98 0 strelka-varscan-mutect AASDH,missense_variant,p.Ser524Tyr,ENST00000205214,NM_181806.3;AASDH,missense_variant,p.Ser371Tyr,ENST00000602986,NM_001286669.1;AASDH,missense_variant,p.Ser424Tyr,ENST00000513376,NM_001286668.1;AASDH,missense_variant,p.Ser524Tyr,ENST00000451613,NM_001286671.1;AASDH,missense_variant,p.Ser524Tyr,ENST00000502617,NM_001286672.1;AASDH,downstream_gene_variant,,ENST00000510762,;AASDH,3_prime_UTR_variant,,ENST00000514745,NM_001286670.1;AASDH,3_prime_UTR_variant,,ENST00000503808,;RPL7AP31,upstream_gene_variant,,ENST00000470544,; T ENST00000205214 Transcript missense_variant 1752/3590 1571/3297 524/1098 S/Y tCc/tAc 1 -1 AASDH HGNC HGNC:23993 protein_coding YES CCDS3504.1 ENSP00000205214 Q4L235 UPI000020B8EF NM_181806.3 tolerated(0.08) 9/15 hmmpanther:PTHR24095:SF185,hmmpanther:PTHR24095,Gene3D:3.30.300.30,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -16.90251 1 1 1 1 0 T 3 4 6 56353409 56353409 G T 1 0 0 0 0 1 0 0 0 26 1188 41 2 2 AASDH 4 56353409 Missense_Mutation SNP G C3L-00009_T 45908342 56353409 133861146 96 1888 EPHA5 0 . GRCh38 4 65404455 65404455 + Missense_Mutation SNP C C A C3L-00009_T C3L-00009_N C C c.1712G>T p.Ser571Ile p.S571I ENST00000622150 8/18 157 135 22 227 227 0 strelka-varscan-mutect EPHA5,missense_variant,p.Ser571Ile,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Ser571Ile,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Ser570Ile,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Ser571Ile,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Ser407Ile,ENST00000432638,;EPHA5,missense_variant,p.Ser570Ile,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 2465/8421 1712/3117 571/1038 S/I aGc/aTc COSM4530565 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.09) 8/18 PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 65404455 65404455 C A 1 0 0 0 0 1 0 0 0 5017 797 28 2 2 EPHA5 4 65404455 Missense_Mutation SNP C C3L-00009_T 9051046 65404455 124810100 97 1889 ANKRD17 0 . GRCh38 4 73092288 73092288 + Silent SNP T T C novel C3L-00009_T C3L-00009_N T T c.5340A>G p.= p.E1780E ENST00000358602 29/34 135 100 35 167 167 0 strelka-varscan-mutect ANKRD17,synonymous_variant,p.=,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,synonymous_variant,p.=,ENST00000558247,;ANKRD17,synonymous_variant,p.=,ENST00000509867,NM_001286771.1;ANKRD17,synonymous_variant,p.=,ENST00000330838,NM_198889.1; C ENST00000358602 Transcript synonymous_variant 5457/10784 5340/7812 1780/2603 E gaA/gaG 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 29/34 PROSITE_profiles:PS50084,hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 73092288 73092288 T C 1 0 0 0 0 0 0 0 1 747 1490 52 5 5 ANKRD17 4 73092288 Silent SNP T C3L-00009_T 7687833 73092288 117122267 98 1890 GK2 0 . GRCh38 4 79407786 79407786 + Missense_Mutation SNP A A G rs777425846 C3L-00009_T C3L-00009_N A A c.415T>C p.Ser139Pro p.S139P ENST00000358842 1/1 198 147 51 292 292 0 strelka-varscan-mutect GK2,missense_variant,p.Ser139Pro,ENST00000358842,NM_033214.2; G ENST00000358842 Transcript missense_variant 508/1942 415/1662 139/553 S/P Tct/Cct rs777425846 1 -1 GK2 HGNC HGNC:4291 protein_coding YES CCDS3585.1 ENSP00000351706 Q14410 A0A140VKG0 UPI000011E629 NM_033214.2 tolerated(0.95) 1/1 hmmpanther:PTHR10196:SF46,hmmpanther:PTHR10196,TIGRFAM_domain:TIGR01311,Pfam_domain:PF00370,Gene3D:3.30.420.40,PIRSF_domain:PIRSF000538,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS rs777425846 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 79407786 79407786 A G 1 0 0 0 0 1 0 0 0 6299 275 10 5 5 GK2 4 79407786 Missense_Mutation SNP A C3L-00009_T 6315498 79407786 110806769 99 1891 TIGD2 0 . GRCh38 4 89113239 89113239 + Nonsense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.265C>T p.Gln89Ter p.Q89* ENST00000603357 2/2 254 208 46 383 383 0 strelka-varscan-mutect TIGD2,stop_gained,p.Gln89Ter,ENST00000603357,;TIGD2,stop_gained,p.Gln89Ter,ENST00000317005,NM_145715.2;FAM13A,upstream_gene_variant,,ENST00000502459,; T ENST00000603357 Transcript stop_gained 1557/3217 265/1578 89/525 Q/* Caa/Taa 1 1 TIGD2 HGNC HGNC:18333 protein_coding YES CCDS3633.1 ENSP00000486687 Q4W5G0 V9HWD1 UPI000013FF3C 2/2 PROSITE_profiles:PS51253,hmmpanther:PTHR19303:SF220,hmmpanther:PTHR19303,Pfam_domain:PF03221,Gene3D:1.10.10.60,SMART_domains:SM00674,Superfamily_domains:SSF46689 HIGH 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 6 89113239 89113239 C T 1 0 0 0 0 0 1 0 0 16334 595 21 3 3 TIGD2 4 89113239 Nonsense_Mutation SNP C C3L-00009_T 9705453 89113239 101101316 100 1892 SMARCAD1 0 . GRCh38 4 94208473 94208473 + Missense_Mutation SNP C C A rs748529019 C3L-00009_T C3L-00009_N C C c.79C>A p.Pro27Thr p.P27T ENST00000359052 2/24 345 281 64 522 521 1 strelka-varscan-mutect SMARCAD1,missense_variant,p.Pro27Thr,ENST00000359052,NM_001128430.1;SMARCAD1,missense_variant,p.Pro27Thr,ENST00000354268,NM_020159.4;SMARCAD1,missense_variant,p.Pro27Thr,ENST00000457823,NM_001128429.2;RP11-363G15.2,upstream_gene_variant,,ENST00000501965,;SMARCAD1,missense_variant,p.Pro27Thr,ENST00000394961,;SMARCAD1,missense_variant,p.Pro27Thr,ENST00000510105,; A ENST00000359052 Transcript missense_variant 253/5017 79/3087 27/1028 P/T Cct/Act rs748529019 1 1 SMARCAD1 HGNC HGNC:18398 protein_coding YES CCDS47101.1 ENSP00000351947 Q9H4L7 UPI000020B1CF NM_001128430.1 tolerated_low_confidence(0.17) 2/24 Low_complexity_(Seg):seg,hmmpanther:PTHR10799 MODERATE 1 SNV 1 1 PASS rs748529019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 94208473 94208473 C A 1 0 0 0 0 1 0 0 0 15065 507 18 2 2 SMARCAD1 4 94208473 Missense_Mutation SNP C C3L-00009_T 5095234 94208473 96006082 101 1893 NPY5R 0 . GRCh38 4 163351002 163351002 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.729C>A p.= p.S243S ENST00000515560 4/4 141 93 48 217 216 1 strelka-varscan-mutect NPY5R,synonymous_variant,p.=,ENST00000515560,NM_001317091.1;NPY5R,synonymous_variant,p.=,ENST00000338566,NM_006174.2;NPY5R,synonymous_variant,p.=,ENST00000506953,; A ENST00000515560 Transcript synonymous_variant 2251/3183 729/1338 243/445 S tcC/tcA 1 1 NPY5R HGNC HGNC:7958 protein_coding YES CCDS3804.1 ENSP00000423917 Q15761 UPI000000D9D7 NM_001317091.1 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF217,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 163351002 163351002 C A 1 0 0 0 0 0 0 0 1 10666 581 21 2 2 NPY5R 4 163351002 Silent SNP C C3L-00009_T 69142529 163351002 26863553 102 1894 TENM3 0 . GRCh38 4 182324163 182324163 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.143A>T p.Lys48Ile p.K48I ENST00000511685 2/28 530 490 40 809 809 0 strelka-varscan-mutect TENM3,missense_variant,p.Lys48Ile,ENST00000511685,NM_001080477.2;TENM3,missense_variant,p.Lys48Ile,ENST00000512480,;TENM3,non_coding_transcript_exon_variant,,ENST00000513201,; T ENST00000511685 Transcript missense_variant 266/10896 143/8100 48/2699 K/I aAa/aTa 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 deleterious_low_confidence(0.01) 2/28 Pfam_domain:PF06484,PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 182324163 182324163 A T 1 0 0 0 0 1 0 0 0 16173 14 1 4 4 TENM3 4 182324163 Missense_Mutation SNP A C3L-00009_T 18973161 182324163 7890392 103 1895 SEMA5A 0 . GRCh38 5 9154612 9154612 + Nonsense_Mutation SNP C C A C3L-00009_T C3L-00009_N C C c.1357G>T p.Glu453Ter p.E453* ENST00000382496 12/23 466 363 103 545 545 0 strelka-varscan-mutect SEMA5A,stop_gained,p.Glu453Ter,ENST00000382496,NM_003966.2; A ENST00000382496 Transcript stop_gained 2023/11762 1357/3225 453/1074 E/* Gag/Tag COSM345780 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 12/23 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 9154612 9154612 C A 1 0 0 0 0 0 1 0 0 14313 835 29 2 2 SEMA5A 5 9154612 Nonsense_Mutation SNP C C3L-00009_T 9154612 172383647 104 1896 CDH18 0 . GRCh38 5 19473400 19473400 + Missense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.2199C>A p.Asp733Glu p.D733E ENST00000507958 15/15 445 356 89 479 479 0 strelka-varscan-mutect CDH18,missense_variant,p.Asp733Glu,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Asp733Glu,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Asp733Glu,ENST00000274170,;CDH18,downstream_gene_variant,,ENST00000506372,NM_001291957.1;CDH18,downstream_gene_variant,,ENST00000502796,NM_001167667.1;CDH18,downstream_gene_variant,,ENST00000515257,;CDH18,non_coding_transcript_exon_variant,,ENST00000510297,; T ENST00000507958 Transcript missense_variant 3190/3542 2199/2373 733/790 D/E gaC/gaA COSM5403265,COSM5403266 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 15/15 hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1439870841 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 19473400 19473400 G T 1 0 0 0 0 1 0 0 0 2806 1020 36 2 2 CDH18 5 19473400 Missense_Mutation SNP G C3L-00009_T 10318788 19473400 162064859 105 1897 CDH9 0 . GRCh38 5 26902534 26902534 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.1195G>A p.Gly399Ser p.G399S ENST00000231021 7/12 244 227 17 290 290 0 strelka-varscan-mutect CDH9,missense_variant,p.Gly399Ser,ENST00000231021,NM_016279.3;CDH9,downstream_gene_variant,,ENST00000505045,; T ENST00000231021 Transcript missense_variant 1368/3079 1195/2370 399/789 G/S Ggc/Agc COSM4347552 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0.04) 7/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 26902534 26902534 C T 1 0 0 0 0 1 0 0 0 2820 623 22 3 3 CDH9 5 26902534 Missense_Mutation SNP C C3L-00009_T 7429134 26902534 154635725 106 1898 FYB 0 . GRCh38 5 39134910 39134910 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.1650C>T p.= p.I550I ENST00000512982 8/19 224 184 40 210 210 0 strelka-varscan-mutect FYB,synonymous_variant,p.=,ENST00000351578,NM_199335.3;FYB,synonymous_variant,p.=,ENST00000505428,NM_001465.4;FYB,synonymous_variant,p.=,ENST00000512982,NM_001243093.1;FYB,synonymous_variant,p.=,ENST00000515010,; A ENST00000512982 Transcript synonymous_variant 1736/2747 1650/2520 550/839 I atC/atT 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 8/19 Gene3D:2.30.30.40,Pfam_domain:PF07653,hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF13,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 39134910 39134910 G A 1 0 0 0 0 0 0 0 1 5995 1164 41 3 3 FYB 5 39134910 Silent SNP G C3L-00009_T 12232376 39134910 142403349 107 1899 CCDC152 0 . GRCh38 5 42779512 42779512 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.317C>A p.Ser106Tyr p.S106Y ENST00000361970 5/9 105 89 16 139 139 0 strelka-varscan-mutect CCDC152,missense_variant,p.Ser106Tyr,ENST00000361970,NM_001134848.1;CCDC152,intron_variant,,ENST00000388827,; A ENST00000361970 Transcript missense_variant 404/3431 317/765 106/254 S/Y tCt/tAt 1 1 CCDC152 HGNC HGNC:34438 protein_coding YES CCDS47203.1 ENSP00000354888 Q4G0S7 A0A024R043 UPI0000160C50 NM_001134848.1 tolerated(0.12) 5/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR35253,hmmpanther:PTHR35253:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 42779512 42779512 C A 1 0 0 0 0 1 0 0 0 2473 913 32 2 2 CCDC152 5 42779512 Missense_Mutation SNP C C3L-00009_T 3644602 42779512 138758747 108 1900 ANKDD1B 0 . GRCh38 5 75635835 75635835 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.751G>A p.Val251Met p.V251M ENST00000601380 7/14 182 140 42 221 221 0 strelka-varscan-mutect ANKDD1B,missense_variant,p.Val251Met,ENST00000601380,NM_001276713.1;ANKDD1B,intron_variant,,ENST00000506596,;ANKDD1B,non_coding_transcript_exon_variant,,ENST00000594319,;ANKDD1B,non_coding_transcript_exon_variant,,ENST00000504514,; A ENST00000601380 Transcript missense_variant 927/2569 751/1587 251/528 V/M Gtg/Atg 1 1 ANKDD1B HGNC HGNC:32525 protein_coding YES CCDS64180.1 ENSP00000471417 A6NHY2 UPI0002A4709F NM_001276713.1 deleterious(0.01) 7/14 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24125,hmmpanther:PTHR24125:SF1,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 75635835 75635835 G A 1 0 0 0 0 1 0 0 0 725 1029 36 3 3 ANKDD1B 5 75635835 Missense_Mutation SNP G C3L-00009_T 32856323 75635835 105902424 109 1901 ADGRV1 0 . GRCh38 5 90778972 90778973 + Frame_Shift_Ins INS - - G novel C3L-00009_T C3L-00009_N - - c.12961dupG p.Glu4321GlyfsTer5 p.E4321Gfs*5 ENST00000405460 64/90 203 154 49 312 312 0 sindel-varindel-pindel ADGRV1,frameshift_variant,p.Glu4321GlyfsTer5,ENST00000405460,NM_032119.3;ADGRV1,upstream_gene_variant,,ENST00000425867,; G ENST00000405460 Transcript frameshift_variant 13053-13054/19338 12957-12958/18921 4319-4320/6306 -/X -/G 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 64/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,SMART_domains:SM00237,Superfamily_domains:SSF141072 HIGH 1 insertion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 6 90778972 90778972 - G 1 0 1 1 0 0 0 0 0 379 175 7 0 0 ADGRV1 5 90778972 Frame_Shift_Ins INS - C3L-00009_T 15143137 90778972 90759287 110 1902 FTMT 0 . GRCh38 5 121852599 121852599 + Silent SNP G G T novel C3L-00009_T C3L-00009_N G G c.636G>T p.= p.V212V ENST00000321339 1/1 281 232 49 421 420 1 strelka-varscan-mutect FTMT,synonymous_variant,p.=,ENST00000321339,NM_177478.1; T ENST00000321339 Transcript synonymous_variant 645/879 636/729 212/242 V gtG/gtT 1 1 FTMT HGNC HGNC:17345 protein_coding YES CCDS4128.1 ENSP00000313691 Q8N4E7 UPI000006F87E NM_177478.1 1/1 PROSITE_profiles:PS50905,hmmpanther:PTHR11431:SF30,hmmpanther:PTHR11431,Pfam_domain:PF00210,Gene3D:1.20.1260.10,Superfamily_domains:SSF47240 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 121852599 121852599 G T 1 0 0 0 0 0 0 0 1 5959 1306 46 2 2 FTMT 5 121852599 Silent SNP G C3L-00009_T 31073627 121852599 59685660 111 1903 FBN2 0 . GRCh38 5 128305902 128305902 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.5469G>T p.= p.V1823V ENST00000508053 49/71 365 293 72 566 566 0 strelka-varscan-mutect FBN2,synonymous_variant,p.=,ENST00000508053,;FBN2,synonymous_variant,p.=,ENST00000262464,NM_001999.3;FBN2,synonymous_variant,p.=,ENST00000619499,; A ENST00000508053 Transcript synonymous_variant 6444/11132 5469/8739 1823/2912 V gtG/gtT 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 49/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 128305902 128305902 C A 1 0 0 0 0 0 0 0 1 5566 465 17 2 2 FBN2 5 128305902 Silent SNP C C3L-00009_T 6453303 128305902 53232357 112 1904 PCDHB6 0 . GRCh38 5 141151198 141151198 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.941A>G p.Asp314Gly p.D314G ENST00000231136 1/1 254 203 51 369 368 1 strelka-varscan-mutect PCDHB6,missense_variant,p.Asp314Gly,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Asp178Gly,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; G ENST00000231136 Transcript missense_variant 1177/3266 941/2385 314/794 D/G gAc/gGc 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 tolerated_low_confidence(0.07) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 141151198 141151198 A G 1 0 0 0 0 1 0 0 0 11633 275 10 5 5 PCDHB6 5 141151198 Missense_Mutation SNP A C3L-00009_T 12845296 141151198 40387061 113 1905 PCDHGB1 0 . GRCh38 5 141352377 141352377 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.2117C>T p.Ala706Val p.A706V ENST00000523390 1/4 321 254 67 536 536 0 strelka-varscan-mutect PCDHGB1,missense_variant,p.Ala706Val,ENST00000523390,NM_018922.2;PCDHGB1,missense_variant,p.Ala706Val,ENST00000611598,NM_032095.1;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA4,upstream_gene_variant,,ENST00000571252,NM_018917.3;PCDHGA4,upstream_gene_variant,,ENST00000612927,NM_032053.2;AC005618.8,upstream_gene_variant,,ENST00000625053,;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000523390 Transcript missense_variant 2117/4590 2117/2784 706/927 A/V gCg/gTg COSM1063066,COSM1595001 1 1 PCDHGB1 HGNC HGNC:8708 protein_coding YES CCDS54923.1 ENSP00000429273 Q9Y5G3 UPI0000073588 NM_018922.2 tolerated(0.34) 1/4 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1324121719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 141352377 141352377 C T 1 0 0 0 0 1 0 0 0 11649 768 27 1 1 PCDHGB1 5 141352377 Missense_Mutation SNP C C3L-00009_T 201179 141352377 40185882 114 1906 HAVCR1 0 . GRCh38 5 157055528 157055528 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.52G>T p.Val18Leu p.V18L ENST00000625904 2/7 27 21 6 60 60 0 strelka-varscan-mutect HAVCR1,missense_variant,p.Val18Leu,ENST00000339252,NM_001099414.1,NM_012206.2;HAVCR1,missense_variant,p.Val18Leu,ENST00000625904,;HAVCR1,missense_variant,p.Val18Leu,ENST00000522693,NM_001308156.1;HAVCR1,missense_variant,p.Val18Leu,ENST00000523175,NM_001173393.1;HAVCR1,missense_variant,p.Val18Leu,ENST00000518745,; A ENST00000625904 Transcript missense_variant 585/1807 52/1206 18/401 V/L Gta/Tta 1 -1 HAVCR1 HGNC HGNC:17866 protein_coding YES CCDS78076.1 ENSP00000487363 E9PFX0 UPI000020C020 deleterious(0.01) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR15498,hmmpanther:PTHR15498:SF8,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -16.77945 1 1 1 1 0 A 3 1 6 157055528 157055528 C A 1 0 0 0 0 1 0 0 0 6859 492 17 2 2 HAVCR1 5 157055528 Missense_Mutation SNP C C3L-00009_T 15703151 157055528 24482731 115 1907 TLX3 0 . GRCh38 5 171310368 171310368 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.640T>A p.Phe214Ile p.F214I ENST00000296921 2/3 209 194 15 286 286 0 strelka-varscan-mutect TLX3,missense_variant,p.Phe214Ile,ENST00000296921,NM_021025.2;RP11-546B8.6,upstream_gene_variant,,ENST00000619056,; A ENST00000296921 Transcript missense_variant 722/1493 640/876 214/291 F/I Ttc/Atc 1 1 TLX3 HGNC HGNC:13532 protein_coding YES CCDS34288.1 ENSP00000296921 O43711 UPI000013E3AA NM_021025.2 deleterious(0) 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,Prints_domain:PR00024,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF154,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 171310368 171310368 T A 1 0 0 0 0 1 0 0 0 16407 1725 60 4 4 TLX3 5 171310368 Missense_Mutation SNP T C3L-00009_T 14254840 171310368 10227891 116 1908 ZNF454 0 . GRCh38 5 178964742 178964742 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.338G>T p.Arg113Ile p.R113I ENST00000320129 5/5 164 151 13 247 246 1 strelka-varscan-mutect ZNF454,missense_variant,p.Arg113Ile,ENST00000320129,NM_001178090.1,NM_182594.2;ZNF454,missense_variant,p.Arg113Ile,ENST00000519564,NM_001178089.1;RP11-281O15.4,upstream_gene_variant,,ENST00000519491,; T ENST00000320129 Transcript missense_variant 641/2332 338/1569 113/522 R/I aGa/aTa 1 1 ZNF454 HGNC HGNC:21200 protein_coding YES CCDS4441.1 ENSP00000326249 Q8N9F8 UPI00001407C7 NM_001178090.1,NM_182594.2 tolerated(0.24) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF274 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 178964742 178964742 G T 1 0 0 0 0 1 0 0 0 18494 942 33 2 2 ZNF454 5 178964742 Missense_Mutation SNP G C3L-00009_T 7654374 178964742 2573517 117 1909 ZSCAN9 0 . GRCh38 6 28232791 28232791 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.951C>A p.Ser317Arg p.S317R ENST00000425468 5/5 318 297 21 476 475 1 strelka-varscan-mutect ZSCAN9,missense_variant,p.Ser317Arg,ENST00000425468,NM_001199479.1;ZSCAN9,missense_variant,p.Ser266Arg,ENST00000252207,NM_006299.4;ZSCAN9,missense_variant,p.Ser266Arg,ENST00000531979,NM_001199480.1;ZSCAN9,missense_variant,p.Ser295Arg,ENST00000527844,;ZSCAN9,downstream_gene_variant,,ENST00000527436,;ZSCAN9,downstream_gene_variant,,ENST00000531981,;ZSCAN9,downstream_gene_variant,,ENST00000526391,; A ENST00000425468 Transcript missense_variant 1116/1791 951/1338 317/445 S/R agC/agA 1 1 ZSCAN9 HGNC HGNC:12984 protein_coding YES CCDS56407.1 ENSP00000404074 O15535 UPI0000E09E19 NM_001199479.1 tolerated(0.15) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR23226:SF15,hmmpanther:PTHR23226,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 28232791 28232791 C A 1 0 0 0 0 1 0 0 0 18840 796 28 2 2 ZSCAN9 6 28232791 Missense_Mutation SNP C C3L-00009_T 28232791 142573188 118 1910 MCCD1 0 . GRCh38 6 31529163 31529163 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.149G>A p.Gly50Glu p.G50E ENST00000376191 1/2 122 99 23 155 155 0 strelka-varscan-mutect MCCD1,missense_variant,p.Gly50Glu,ENST00000376191,NM_001011700.2;DDX39B,downstream_gene_variant,,ENST00000396172,NM_004640.6;DDX39B,downstream_gene_variant,,ENST00000458640,NM_080598.5;DDX39B,downstream_gene_variant,,ENST00000376177,;DDX39B,downstream_gene_variant,,ENST00000427214,;DDX39B,downstream_gene_variant,,ENST00000431908,;DDX39B,downstream_gene_variant,,ENST00000417023,;DDX39B,downstream_gene_variant,,ENST00000462421,;DDX39B,downstream_gene_variant,,ENST00000481456,;DDX39B,downstream_gene_variant,,ENST00000462256,;ATP6V1G2-DDX39B,downstream_gene_variant,,ENST00000376185,;DDX39B,downstream_gene_variant,,ENST00000482195,;DDX39B,downstream_gene_variant,,ENST00000474961,;DDX39B,downstream_gene_variant,,ENST00000484566,;DDX39B,downstream_gene_variant,,ENST00000478365,;RPL15P4,downstream_gene_variant,,ENST00000416625,; A ENST00000376191 Transcript missense_variant 447/955 149/360 50/119 G/E gGg/gAg 1 1 MCCD1 HGNC HGNC:20668 protein_coding YES CCDS34396.1 ENSP00000365362 P59942 UPI00004192D0 NM_001011700.2 tolerated(0.27) 1/2 Pfam_domain:PF15707,hmmpanther:PTHR37877,hmmpanther:PTHR37877:SF1 MODERATE 1 SNV 1 1 PASS rs756340259 . 0 206 2 2 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 6 31529163 31529163 G A 1 0 0 0 0 1 0 0 0 9306 1232 43 3 3 MCCD1 6 31529163 Missense_Mutation SNP G C3L-00009_T 3296372 31529163 139276816 119 1911 DNAH8 0 . GRCh38 6 38872932 38872932 + Missense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.7264G>T p.Gly2422Cys p.G2422C ENST00000327475 51/93 260 239 21 377 377 0 strelka-varscan-mutect DNAH8,missense_variant,p.Gly2422Cys,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Gly2205Cys,ENST00000359357,;DNAH8,missense_variant,p.Gly2422Cys,ENST00000449981,;DNAH8,downstream_gene_variant,,ENST00000394393,; T ENST00000327475 Transcript missense_variant 7373/14360 7264/14124 2422/4707 G/C Ggt/Tgt COSM5272172,COSM596418,COSM596419 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 51/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF07728,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 38872932 38872932 G T 1 0 0 0 0 1 0 0 0 4422 1348 47 2 2 DNAH8 6 38872932 Missense_Mutation SNP G C3L-00009_T 7343769 38872932 131933047 120 1912 DAAM2 0 . GRCh38 6 39856430 39856430 + Missense_Mutation SNP C C A rs772573007 C3L-00009_T C3L-00009_N C C c.128C>A p.Pro43Gln p.P43Q ENST00000398904 2/25 42 36 6 53 53 0 strelka-mutect DAAM2,missense_variant,p.Pro43Gln,ENST00000538976,NM_015345.3;DAAM2,missense_variant,p.Pro43Gln,ENST00000398904,;DAAM2,missense_variant,p.Pro43Gln,ENST00000274867,NM_001201427.1;DAAM2,missense_variant,p.Pro43Gln,ENST00000633794,;DAAM2,missense_variant,p.Pro43Gln,ENST00000405961,;DAAM2,missense_variant,p.Pro43Gln,ENST00000494405,;DAAM2,non_coding_transcript_exon_variant,,ENST00000491083,;DAAM2,non_coding_transcript_exon_variant,,ENST00000475489,; A ENST00000398904 Transcript missense_variant 310/6224 128/3207 43/1068 P/Q cCg/cAg rs772573007,COSM1079041 1 1 DAAM2 HGNC HGNC:18143 protein_coding YES CCDS56426.1 ENSP00000381876 Q86T65 UPI000020DC88 deleterious(0) 2/25 PROSITE_profiles:PS51232,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF171,Pfam_domain:PF06371,SMART_domains:SM01140 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs772573007 . 0 205 5 0 0 0 0 0 -15.12875 1 1 1 1 0 A 3 1 6 39856430 39856430 C A 1 0 0 0 0 1 0 0 0 4017 652 23 1 1 DAAM2 6 39856430 Missense_Mutation SNP C C3L-00009_T 983498 39856430 130949549 121 1913 UBR2 0 . GRCh38 6 42632827 42632827 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.1468A>T p.Thr490Ser p.T490S ENST00000372899 13/47 136 125 11 126 126 0 strelka-varscan-mutect UBR2,missense_variant,p.Thr490Ser,ENST00000372899,NM_015255.2;UBR2,missense_variant,p.Thr490Ser,ENST00000372901,; T ENST00000372899 Transcript missense_variant 1726/7857 1468/5268 490/1755 T/S Act/Tct 1 1 UBR2 HGNC HGNC:21289 protein_coding YES CCDS4870.1 ENSP00000361990 Q8IWV8 UPI0000074466 NM_015255.2 tolerated(0.48) 13/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF28 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 42632827 42632827 A T 1 0 0 0 0 1 0 0 0 17426 43 2 4 4 UBR2 6 42632827 Missense_Mutation SNP A C3L-00009_T 2776397 42632827 128173152 122 1914 NFKBIE 0 . GRCh38 6 44265635 44265635 + Frame_Shift_Del DEL G G - rs189481001 C3L-00009_T C3L-00009_N G G c.129delC p.Ala45ProfsTer4 p.A45Pfs*4 ENST00000275015 1/6 187 177 10 228 228 0 varindel-pindel NFKBIE,frameshift_variant,p.Ala45ProfsTer4,ENST00000275015,NM_004556.2;TMEM151B,upstream_gene_variant,,ENST00000451188,NM_001137560.1;NFKBIE,upstream_gene_variant,,ENST00000619360,;NFKBIE,upstream_gene_variant,,ENST00000477930,; - ENST00000275015 Transcript frameshift_variant 154/2581 129/1503 43/500 G/X ggC/gg rs189481001 1 -1 NFKBIE HGNC HGNC:7799 protein_coding YES CCDS34463.1 ENSP00000275015 O00221 A0A024RD24 UPI000013DA3C NM_004556.2 1/6 Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 206 0 4 0 0 0 0 -12.39805 0.999346 1 1 1 0 - 7 5 6 44265635 44265635 G - 1 0 1 0 1 0 0 0 0 10417 1074 38 0 0 NFKBIE 6 44265635 Frame_Shift_Del DEL G C3L-00009_T 1632808 44265635 126540344 123 1915 TMEM151B 0 . GRCh38 6 44273241 44273241 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.311A>G p.His104Arg p.H104R ENST00000451188 2/3 101 87 14 162 162 0 strelka-varscan-mutect TMEM151B,missense_variant,p.His104Arg,ENST00000451188,NM_001137560.1;TMEM151B,missense_variant,p.His104Arg,ENST00000438774,;RP11-444E17.6,missense_variant,p.His17Arg,ENST00000505802,; G ENST00000451188 Transcript missense_variant 588/4895 311/1701 104/566 H/R cAt/cGt 1 1 TMEM151B HGNC HGNC:21315 protein_coding YES CCDS47437.1 ENSP00000393161 Q8IW70 UPI00006C0A4E NM_001137560.1 tolerated(0.14) 2/3 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF4 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 44273241 44273241 A G 1 0 0 0 0 1 0 0 0 16513 217 8 5 5 TMEM151B 6 44273241 Missense_Mutation SNP A C3L-00009_T 7606 44273241 126532738 124 1916 CDC5L 0 . GRCh38 6 44424464 44424464 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.1450C>T p.Pro484Ser p.P484S ENST00000371477 11/16 167 157 10 199 199 0 strelka-varscan CDC5L,missense_variant,p.Pro484Ser,ENST00000371477,NM_001253.3; T ENST00000371477 Transcript missense_variant 1749/6423 1450/2409 484/802 P/S Cct/Tct 1 1 CDC5L HGNC HGNC:1743 protein_coding YES CCDS4912.1 ENSP00000360532 Q99459 UPI000006EE42 NM_001253.3 deleterious(0) 11/16 Pfam_domain:PF11831 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 44424464 44424464 C T 1 0 0 0 0 1 0 0 0 2785 855 30 3 3 CDC5L 6 44424464 Missense_Mutation SNP C C3L-00009_T 151223 44424464 126381515 125 1917 COL9A1 0 . GRCh38 6 70294510 70294510 + Missense_Mutation SNP C C G rs143848379 C3L-00009_T C3L-00009_N C C c.353G>C p.Arg118Pro p.R118P ENST00000357250 5/38 323 297 26 421 421 0 strelka-varscan-mutect COL9A1,missense_variant,p.Arg118Pro,ENST00000357250,NM_001851.4;COL9A1,missense_variant,p.Arg118Pro,ENST00000370496,; G ENST00000357250 Transcript missense_variant 512/4761 353/2766 118/921 R/P cGa/cCa rs143848379,COSM274631 1 -1 COL9A1 HGNC HGNC:2217 protein_coding YES CCDS4971.1 ENSP00000349790 P20849 UPI000020D14B NM_001851.4 5/38 Gene3D:2.60.120.200,SMART_domains:SM00210,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs143848379 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 70294510 70294510 C G 1 0 0 0 0 1 0 0 0 3496 884 31 4 4 COL9A1 6 70294510 Missense_Mutation SNP C C3L-00009_T 25870046 70294510 100511469 126 1918 RIMS1 0 . GRCh38 6 72179863 72179863 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.760C>T p.Pro254Ser p.P254S ENST00000521978 5/34 40 33 7 60 60 0 strelka-varscan-mutect RIMS1,missense_variant,p.Pro254Ser,ENST00000264839,;RIMS1,missense_variant,p.Pro254Ser,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Pro254Ser,ENST00000491071,;RIMS1,missense_variant,p.Pro254Ser,ENST00000520567,;RIMS1,missense_variant,p.Pro254Ser,ENST00000517960,;RIMS1,missense_variant,p.Pro254Ser,ENST00000518273,;RIMS1,missense_variant,p.Pro254Ser,ENST00000522291,;RIMS1,upstream_gene_variant,,ENST00000517433,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,; T ENST00000521978 Transcript missense_variant 760/5079 760/5079 254/1692 P/S Cct/Tct 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 tolerated(0.67) 5/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.04882 1 1 1 1 0 T 3 4 6 72179863 72179863 C T 1 0 0 0 0 1 0 0 0 13542 739 26 3 3 RIMS1 6 72179863 Missense_Mutation SNP C C3L-00009_T 1885353 72179863 98626116 127 1919 RIMS1 0 . GRCh38 6 72182989 72182989 + Silent SNP C C G novel C3L-00009_T C3L-00009_N C C c.1518C>G p.= p.S506S ENST00000521978 6/34 653 591 62 967 967 0 strelka-varscan-mutect RIMS1,synonymous_variant,p.=,ENST00000264839,;RIMS1,synonymous_variant,p.=,ENST00000521978,NM_014989.5;RIMS1,synonymous_variant,p.=,ENST00000491071,;RIMS1,synonymous_variant,p.=,ENST00000520567,;RIMS1,synonymous_variant,p.=,ENST00000517960,;RIMS1,synonymous_variant,p.=,ENST00000518273,;RIMS1,synonymous_variant,p.=,ENST00000522291,;RIMS1,synonymous_variant,p.=,ENST00000517433,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,; G ENST00000521978 Transcript synonymous_variant 1518/5079 1518/5079 506/1692 S tcC/tcG 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 6/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 LOW 1 SNV 1 1 PASS rs1465177083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 72182989 72182989 C G 1 0 0 0 0 0 0 0 1 13542 639 23 4 4 RIMS1 6 72182989 Silent SNP C C3L-00009_T 3126 72182989 98622990 128 1920 SNX14 0 . GRCh38 6 85517774 85517774 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.2250T>C p.= p.T750T ENST00000314673 23/29 113 95 18 148 148 0 strelka-varscan-mutect SNX14,synonymous_variant,p.=,ENST00000314673,NM_153816.5;SNX14,synonymous_variant,p.=,ENST00000346348,NM_020468.5;SNX14,synonymous_variant,p.=,ENST00000515216,;SNX14,synonymous_variant,p.=,ENST00000505648,NM_001304479.1;SNX14,synonymous_variant,p.=,ENST00000369627,NM_001297614.2;SNX14,synonymous_variant,p.=,ENST00000513865,;SNX14,synonymous_variant,p.=,ENST00000418862,;SNX14,upstream_gene_variant,,ENST00000508658,;SNX14,non_coding_transcript_exon_variant,,ENST00000508980,;SNX14,3_prime_UTR_variant,,ENST00000369635,;SNX14,non_coding_transcript_exon_variant,,ENST00000503491,;SNX14,non_coding_transcript_exon_variant,,ENST00000503608,; G ENST00000314673 Transcript synonymous_variant 2427/3486 2250/2841 750/946 T acT/acC 1 -1 SNX14 HGNC HGNC:14977 protein_coding YES CCDS5004.1 ENSP00000313121 Q9Y5W7 UPI000013F8C8 NM_153816.5 23/29 hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF3 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 85517774 85517774 A G 1 0 0 0 0 0 0 0 1 15206 59 3 5 5 SNX14 6 85517774 Silent SNP A C3L-00009_T 13334785 85517774 85288205 129 1921 POU3F2 0 . GRCh38 6 98835511 98835511 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.638A>T p.His213Leu p.H213L ENST00000328345 1/1 270 229 41 300 300 0 strelka-varscan-mutect POU3F2,missense_variant,p.His213Leu,ENST00000328345,NM_005604.3;RP1-273N12.4,upstream_gene_variant,,ENST00000635423,; T ENST00000328345 Transcript missense_variant 920/4879 638/1332 213/443 H/L cAc/cTc 1 1 POU3F2 HGNC HGNC:9215 protein_coding YES CCDS5040.1 ENSP00000329170 P20265 UPI000016A1E7 NM_005604.3 tolerated(0.21) 1/1 hmmpanther:PTHR11636:SF88,hmmpanther:PTHR11636,PIRSF_domain:PIRSF002629 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 98835511 98835511 A T 1 0 0 0 0 1 0 0 0 12391 159 6 4 4 POU3F2 6 98835511 Missense_Mutation SNP A C3L-00009_T 13317737 98835511 71970468 130 1922 GRIK2 0 . GRCh38 6 101621951 101621951 + Missense_Mutation SNP G G T rs770760798 C3L-00009_T C3L-00009_N G G c.118G>T p.Gly40Cys p.G40C ENST00000421544 2/16 248 231 17 353 353 0 strelka-varscan-mutect GRIK2,missense_variant,p.Gly40Cys,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Gly40Cys,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Gly40Cys,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Gly2Cys,ENST00000318991,;GRIK2,missense_variant,p.Gly2Cys,ENST00000369137,;GRIK2,missense_variant,p.Gly2Cys,ENST00000369134,;GRIK2,missense_variant,p.Gly40Cys,ENST00000358361,; T ENST00000421544 Transcript missense_variant,splice_region_variant 608/4789 118/2727 40/908 G/C Ggt/Tgt rs770760798 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 deleterious(0) 2/16 Gene3D:3.40.50.2300,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs770760798 . 0 204 0 3 3 0 0 0 -5.063316 0.6675155 1 1 1 0 T 3 4 6 101621951 101621951 G T 1 0 0 0 0 1 0 0 0 6656 1362 47 2 2 GRIK2 6 101621951 Missense_Mutation SNP G C3L-00009_T 2786440 101621951 69184028 131 1923 GRIK2 0 . GRCh38 6 101686274 101686274 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.872C>T p.Ser291Phe p.S291F ENST00000421544 6/16 139 132 7 167 167 0 strelka-varscan-mutect GRIK2,missense_variant,p.Ser291Phe,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Ser291Phe,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Ser291Phe,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Ser253Phe,ENST00000318991,;GRIK2,missense_variant,p.Ser253Phe,ENST00000369137,;GRIK2,missense_variant,p.Ser253Phe,ENST00000369134,;GRIK2,missense_variant,p.Ser291Phe,ENST00000358361,;GRIK2,intron_variant,,ENST00000455610,; T ENST00000421544 Transcript missense_variant 1362/4789 872/2727 291/908 S/F tCc/tTc 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 deleterious(0.01) 6/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 101686274 101686274 C T 1 0 0 0 0 1 0 0 0 6656 855 30 3 3 GRIK2 6 101686274 Missense_Mutation SNP C C3L-00009_T 64323 101686274 69119705 132 1924 FIG4 0 . GRCh38 6 109743749 109743749 + Missense_Mutation SNP A A C novel C3L-00009_T C3L-00009_N A A c.1114A>C p.Ile372Leu p.I372L ENST00000230124 10/23 492 463 29 693 693 0 strelka-varscan-mutect FIG4,missense_variant,p.Ile372Leu,ENST00000230124,NM_014845.5;FIG4,downstream_gene_variant,,ENST00000368941,; C ENST00000230124 Transcript missense_variant 1238/3011 1114/2724 372/907 I/L Atc/Ctc 1 1 FIG4 HGNC HGNC:16873 protein_coding YES CCDS5078.1 ENSP00000230124 Q92562 UPI000000D9A3 NM_014845.5 tolerated(0.18) 10/23 PROSITE_profiles:PS50275,hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF9,Pfam_domain:PF02383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 109743749 109743749 A C 1 0 0 0 0 1 0 0 0 5753 217 8 5 5 FIG4 6 109743749 Missense_Mutation SNP A C3L-00009_T 8057475 109743749 61062230 133 1925 SLC35F1 0 . GRCh38 6 118154482 118154482 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.211T>A p.Ser71Thr p.S71T ENST00000360388 2/8 117 111 6 165 165 0 strelka-mutect SLC35F1,missense_variant,p.Ser71Thr,ENST00000360388,NM_001029858.3;SLC35F1,missense_variant,p.Ser12Thr,ENST00000621341,; A ENST00000360388 Transcript missense_variant 412/4852 211/1227 71/408 S/T Tcc/Acc 1 1 SLC35F1 HGNC HGNC:21483 protein_coding YES CCDS34524.1 ENSP00000353557 Q5T1Q4 UPI00001609C1 NM_001029858.3 deleterious(0) 2/8 Pfam_domain:PF06027,hmmpanther:PTHR14233,hmmpanther:PTHR14233:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -8.909909 0.999937 1 1 1 0 A 3 1 6 118154482 118154482 T A 1 0 0 0 0 1 0 0 0 14859 1435 50 4 4 SLC35F1 6 118154482 Missense_Mutation SNP T C3L-00009_T 8410733 118154482 52651497 134 1926 EPB41L2 0 . GRCh38 6 130955240 130955240 + Silent SNP T T A novel C3L-00009_T C3L-00009_N T T c.570A>T p.= p.A190A ENST00000337057 3/20 394 357 37 552 552 0 strelka-varscan-mutect EPB41L2,synonymous_variant,p.=,ENST00000337057,NM_001431.3;EPB41L2,synonymous_variant,p.=,ENST00000368128,;EPB41L2,synonymous_variant,p.=,ENST00000628542,;EPB41L2,synonymous_variant,p.=,ENST00000527411,;EPB41L2,synonymous_variant,p.=,ENST00000530481,NM_001199388.2;EPB41L2,synonymous_variant,p.=,ENST00000445890,;EPB41L2,synonymous_variant,p.=,ENST00000528282,NM_001252660.1;EPB41L2,synonymous_variant,p.=,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,synonymous_variant,p.=,ENST00000529208,;EPB41L2,synonymous_variant,p.=,ENST00000525271,;EPB41L2,synonymous_variant,p.=,ENST00000527659,;EPB41L2,synonymous_variant,p.=,ENST00000525193,;EPB41L2,downstream_gene_variant,,ENST00000532499,;EPB41L2,downstream_gene_variant,,ENST00000531356,;EPB41L2,downstream_gene_variant,,ENST00000529709,;EPB41L2,downstream_gene_variant,,ENST00000530707,;EPB41L2,downstream_gene_variant,,ENST00000526983,;EPB41L2,intron_variant,,ENST00000530148,;EPB41L2,intron_variant,,ENST00000528179,;EPB41L2,intron_variant,,ENST00000526333,; A ENST00000337057 Transcript synonymous_variant 752/4457 570/3018 190/1005 A gcA/gcT 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 3/20 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF002304,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 130955240 130955240 T A 1 0 0 0 0 0 0 0 1 5000 1799 63 4 4 EPB41L2 6 130955240 Silent SNP T C3L-00009_T 12800758 130955240 39850739 135 1927 PPP1R14C 0 . GRCh38 6 150143477 150143477 + Silent SNP G G C novel C3L-00009_T C3L-00009_N G G c.285G>C p.= p.L95L ENST00000361131 1/4 289 269 20 437 436 1 strelka-varscan-mutect PPP1R14C,synonymous_variant,p.=,ENST00000361131,NM_030949.2; C ENST00000361131 Transcript synonymous_variant 402/2152 285/498 95/165 L ctG/ctC 1 1 PPP1R14C HGNC HGNC:14952 protein_coding YES CCDS5226.1 ENSP00000355260 Q8TAE6 UPI0000071936 NM_030949.2 1/4 hmmpanther:PTHR16188,hmmpanther:PTHR16188:SF6,Gene3D:1j2mA00,Pfam_domain:PF05361,Superfamily_domains:0039331 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 150143477 150143477 G C 1 0 0 0 0 0 0 0 1 12471 1335 47 4 4 PPP1R14C 6 150143477 Silent SNP G C3L-00009_T 19188237 150143477 20662502 136 1928 IPCEF1 0 . GRCh38 6 154246602 154246602 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.235A>G p.Ser79Gly p.S79G ENST00000422970 6/13 54 50 4 67 67 0 strelka-varscan-mutect IPCEF1,missense_variant,p.Ser78Gly,ENST00000265198,NM_015553.2;IPCEF1,missense_variant,p.Ser79Gly,ENST00000422970,NM_001130699.1;IPCEF1,missense_variant,p.Ser79Gly,ENST00000367220,NM_001130700.1;IPCEF1,missense_variant,p.Ser50Gly,ENST00000519344,;IPCEF1,missense_variant,p.Ser50Gly,ENST00000517438,;IPCEF1,missense_variant,p.Ser50Gly,ENST00000519190,;IPCEF1,missense_variant,p.Ser50Gly,ENST00000519405,;IPCEF1,missense_variant,p.Ser78Gly,ENST00000520261,;OPRM1,intron_variant,,ENST00000337049,NM_001008503.2;IPCEF1,non_coding_transcript_exon_variant,,ENST00000518162,;OPRM1,intron_variant,,ENST00000524150,; C ENST00000422970 Transcript missense_variant 431/3267 235/1317 79/438 S/G Agc/Ggc 1 -1 IPCEF1 HGNC HGNC:21204 protein_coding YES CCDS47509.1 ENSP00000394751 Q8WWN9 UPI000022CD0D NM_001130699.1 tolerated(0.06) 6/13 PROSITE_profiles:PS50003,hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF24,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.49786 1 1 1 1 0 C 3 2 6 154246602 154246602 T C 1 0 0 0 0 1 0 0 0 7694 1522 53 5 5 IPCEF1 6 154246602 Missense_Mutation SNP T C3L-00009_T 4103125 154246602 16559377 137 1929 THBS2 0 . GRCh38 6 169248738 169248738 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.288C>T p.= p.S96S ENST00000366787 4/23 159 133 26 248 247 1 strelka-varscan-mutect THBS2,synonymous_variant,p.=,ENST00000366787,NM_003247.3;THBS2,synonymous_variant,p.=,ENST00000617924,;THBS2,downstream_gene_variant,,ENST00000435791,;THBS2,upstream_gene_variant,,ENST00000472733,; A ENST00000366787 Transcript synonymous_variant 538/5811 288/3519 96/1172 S tcC/tcT 1 -1 THBS2 HGNC HGNC:11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 UPI0000231C7F NM_003247.3 4/23 hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF10,SMART_domains:SM00210,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 169248738 169248738 G A 1 0 0 0 0 0 0 0 1 16287 1335 47 3 3 THBS2 6 169248738 Silent SNP G C3L-00009_T 15002136 169248738 1557241 138 1930 NEUROD6 0 . GRCh38 7 31338840 31338840 + Silent SNP G G T rs12666896 C3L-00009_T C3L-00009_N G G c.429C>A p.= p.I143I ENST00000297142 2/2 319 253 66 358 358 0 strelka-varscan-mutect NEUROD6,synonymous_variant,p.=,ENST00000297142,NM_022728.3; T ENST00000297142 Transcript synonymous_variant 752/2131 429/1014 143/337 I atC/atA rs12666896 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 2/2 PROSITE_profiles:PS50888,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS rs12666896 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 31338840 31338840 G T 1 0 0 0 0 0 0 0 1 10388 932 33 2 2 NEUROD6 7 31338840 Silent SNP G C3L-00009_T 31338840 128007133 139 1931 INHBA 0 . GRCh38 7 41690392 41690392 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.539A>G p.Lys180Arg p.K180R ENST00000242208 3/3 319 300 19 353 353 0 strelka-varscan-mutect INHBA,missense_variant,p.Lys180Arg,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Lys180Arg,ENST00000638023,;INHBA,missense_variant,p.Lys180Arg,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; C ENST00000242208 Transcript missense_variant 786/6064 539/1281 180/426 K/R aAg/aGg 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 tolerated(0.69) 3/3 hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00688 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 41690392 41690392 T C 1 0 0 0 0 1 0 0 0 7643 1609 56 5 5 INHBA 7 41690392 Missense_Mutation SNP T C3L-00009_T 10351552 41690392 117655581 140 1932 POM121L12 0 . GRCh38 7 53036319 53036319 + Silent SNP C C T rs746891586 C3L-00009_T C3L-00009_N C C c.648C>T p.= p.A216A ENST00000408890 1/1 165 129 36 271 271 0 strelka-varscan-mutect POM121L12,synonymous_variant,p.=,ENST00000408890,NM_182595.3; T ENST00000408890 Transcript synonymous_variant 678/1283 648/891 216/296 A gcC/gcT rs746891586 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30,Pfam_domain:PF15229 LOW 1 SNV 1 PASS rs746891586 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 53036319 53036319 C T 1 0 0 0 0 0 0 0 1 12352 668 24 3 3 POM121L12 7 53036319 Silent SNP C C3L-00009_T 11345927 53036319 106309654 141 1933 WBSCR17 0 . GRCh38 7 71571361 71571361 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.1039A>T p.Met347Leu p.M347L ENST00000333538 6/11 223 176 47 304 303 1 strelka-varscan-mutect WBSCR17,missense_variant,p.Met347Leu,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Met268Leu,ENST00000618959,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; T ENST00000333538 Transcript missense_variant 1673/3884 1039/1797 347/598 M/L Atg/Ttg 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 deleterious(0) 6/11 Gene3D:3.90.550.10,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 71571361 71571361 A T 1 0 0 0 0 1 0 0 0 17823 217 8 4 4 WBSCR17 7 71571361 Missense_Mutation SNP A C3L-00009_T 18535042 71571361 87774612 142 1934 ABCB1 0 . GRCh38 7 87516615 87516615 + Nonsense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.2978C>G p.Ser993Ter p.S993* ENST00000622132 24/28 587 447 140 711 711 0 strelka-varscan-mutect ABCB1,stop_gained,p.Ser993Ter,ENST00000622132,;ABCB1,stop_gained,p.Ser993Ter,ENST00000265724,NM_000927.4;ABCB1,stop_gained,p.Ser929Ter,ENST00000543898,;ABCB1,non_coding_transcript_exon_variant,,ENST00000488737,;ABCB1,non_coding_transcript_exon_variant,,ENST00000496821,;ABCB1,non_coding_transcript_exon_variant,,ENST00000475929,;ABCB1,non_coding_transcript_exon_variant,,ENST00000483831,;HNRNPA1P9,upstream_gene_variant,,ENST00000450624,; C ENST00000622132 Transcript stop_gained 3303/4778 2978/3843 993/1280 S/* tCa/tGa 1 -1 ABCB1 HGNC HGNC:40 protein_coding YES CCDS5608.1 ENSP00000478255 P08183 A4D1D2 UPI000013D66C 24/28 Gene3D:2hydA01,PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 6 87516615 87516615 G C 1 0 0 0 0 0 1 0 0 44 1294 45 4 4 ABCB1 7 87516615 Nonsense_Mutation SNP G C3L-00009_T 15945254 87516615 71829358 143 1935 CALCR 0 . GRCh38 7 93426557 93426557 + Missense_Mutation SNP T T A rs781657977 C3L-00009_T C3L-00009_N T T c.1326A>T p.Gln442His p.Q442H ENST00000359558 16/16 69 64 5 89 89 0 strelka-varscan-mutect CALCR,missense_variant,p.Gln442His,ENST00000359558,NM_001164737.1;CALCR,missense_variant,p.Gln424His,ENST00000421592,;CALCR,missense_variant,p.Gln408His,ENST00000394441,NM_001164738.1;CALCR,missense_variant,p.Gln408His,ENST00000426151,NM_001742.3;CALCR,3_prime_UTR_variant,,ENST00000360249,;CALCR,3_prime_UTR_variant,,ENST00000423724,;CALCR,3_prime_UTR_variant,,ENST00000415529,; A ENST00000359558 Transcript missense_variant 1626/3696 1326/1527 442/508 Q/H caA/caT rs781657977 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 deleterious(0) 16/16 hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Superfamily_domains:SSF81321,Prints_domain:PR01350 MODERATE 1 SNV 5 1 PASS rs781657977 . 0 197 12 0 0 0 0 0 -11.1492 0.9996366 1 1 1 0 A 3 1 6 93426557 93426557 T A 1 0 0 0 0 1 0 0 0 2269 1490 52 4 4 CALCR 7 93426557 Missense_Mutation SNP T C3L-00009_T 5909942 93426557 65919416 144 1936 CALCR 0 . GRCh38 7 93468803 93468803 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.487G>T p.Ala163Ser p.A163S ENST00000359558 8/16 134 102 32 171 170 1 strelka-varscan-mutect CALCR,missense_variant,p.Ala163Ser,ENST00000359558,NM_001164737.1;CALCR,missense_variant,p.Ala145Ser,ENST00000421592,;CALCR,missense_variant,p.Ala145Ser,ENST00000394441,NM_001164738.1;CALCR,missense_variant,p.Ala145Ser,ENST00000426151,NM_001742.3;CALCR,missense_variant,p.Ala145Ser,ENST00000360249,;CALCR,missense_variant,p.Ala145Ser,ENST00000423724,;CALCR,missense_variant,p.Ala145Ser,ENST00000415529,; A ENST00000359558 Transcript missense_variant 787/3696 487/1527 163/508 A/S Gca/Tca 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 deleterious(0) 8/16 hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Superfamily_domains:SSF111418,Prints_domain:PR01350,Prints_domain:PR00361 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 93468803 93468803 C A 1 0 0 0 0 1 0 0 0 2269 724 25 2 2 CALCR 7 93468803 Missense_Mutation SNP C C3L-00009_T 42246 93468803 65877170 145 1937 PPP1R9A 0 . GRCh38 7 94910367 94910367 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.254C>T p.Ala85Val p.A85V ENST00000433360 2/20 155 116 39 240 240 0 strelka-varscan-mutect PPP1R9A,missense_variant,p.Ala85Val,ENST00000456331,NM_001166162.1;PPP1R9A,missense_variant,p.Ala85Val,ENST00000433881,;PPP1R9A,missense_variant,p.Ala85Val,ENST00000340694,NM_017650.2,NM_001166163.1;PPP1R9A,missense_variant,p.Ala85Val,ENST00000433360,NM_001166160.1;PPP1R9A,missense_variant,p.Ala85Val,ENST00000424654,;PPP1R9A,missense_variant,p.Ala85Val,ENST00000289495,NM_001166161.1;PPP1R9A,downstream_gene_variant,,ENST00000413325,;PPP1R9A,downstream_gene_variant,,ENST00000422324,; T ENST00000433360 Transcript missense_variant 536/5369 254/4125 85/1374 A/V gCc/gTc COSM4587635,COSM4587636 1 1 PPP1R9A HGNC HGNC:14946 protein_coding YES CCDS55127.1 ENSP00000405514 Q9ULJ8 UPI000198CF27 NM_001166160.1 deleterious(0.02) 2/20 hmmpanther:PTHR16154,hmmpanther:PTHR16154:SF22 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999978 1 1 1 0 T 3 4 6 94910367 94910367 C T 1 0 0 0 0 1 0 0 0 12501 739 26 3 3 PPP1R9A 7 94910367 Missense_Mutation SNP C C3L-00009_T 1441564 94910367 64435606 146 1938 CYP3A7 0 . GRCh38 7 99709253 99709253 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.1035C>T p.= p.P345P ENST00000336374 11/13 362 341 21 386 386 0 strelka-varscan-mutect CYP3A7,synonymous_variant,p.=,ENST00000336374,NM_000765.4;CYP3A7-CYP3A51P,synonymous_variant,p.=,ENST00000620220,;CYP3A7-CYP3A51P,synonymous_variant,p.=,ENST00000611620,NM_001256497.2;CYP3A7,non_coding_transcript_exon_variant,,ENST00000477357,; A ENST00000336374 Transcript synonymous_variant 1038/1971 1035/1512 345/503 P ccC/ccT 1 -1 CYP3A7 HGNC HGNC:2640 protein_coding YES CCDS5673.1 ENSP00000337450 P24462 UPI00001281C6 NM_000765.4 11/13 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24302,hmmpanther:PTHR24302:SF14,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 99709253 99709253 G A 1 0 0 0 0 0 0 0 1 3984 1335 47 3 3 CYP3A7 7 99709253 Silent SNP G C3L-00009_T 4798886 99709253 59636720 147 1939 CUX1 0 . GRCh38 7 102227496 102227496 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.3293G>T p.Ser1098Ile p.S1098I ENST00000360264 21/24 303 286 17 379 378 1 strelka-varscan-mutect CUX1,missense_variant,p.Ser1098Ile,ENST00000360264,NM_001202543.1;CUX1,missense_variant,p.Ser1087Ile,ENST00000292535,NM_181552.3;CUX1,missense_variant,p.Ser1065Ile,ENST00000549414,;CUX1,missense_variant,p.Ser1031Ile,ENST00000550008,;CUX1,missense_variant,p.Ser985Ile,ENST00000546411,;CUX1,missense_variant,p.Ser929Ile,ENST00000556210,;CUX1,intron_variant,,ENST00000437600,NM_001913.4;CUX1,intron_variant,,ENST00000622516,NM_181500.3;CUX1,intron_variant,,ENST00000292538,;CUX1,intron_variant,,ENST00000547394,NM_001202544.2;CUX1,intron_variant,,ENST00000425244,NM_001202545.2;CUX1,intron_variant,,ENST00000393824,NM_001202546.2;CUX1,intron_variant,,ENST00000560541,;CUX1,intron_variant,,ENST00000558836,; T ENST00000360264 Transcript missense_variant 3313/13762 3293/4551 1098/1516 S/I aGc/aTc 1 1 CUX1 HGNC HGNC:2557 protein_coding YES CCDS56498.1 ENSP00000353401 P39880 UPI00001AEB98 NM_001202543.1 deleterious(0.01) 21/24 Low_complexity_(Seg):seg,hmmpanther:PTHR14043:SF4,hmmpanther:PTHR14043 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 102227496 102227496 G T 1 0 0 0 0 1 0 0 0 3874 971 34 2 2 CUX1 7 102227496 Missense_Mutation SNP G C3L-00009_T 2518243 102227496 57118477 148 1940 NRCAM 0 . GRCh38 7 108207566 108207566 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1169C>A p.Pro390His p.P390H ENST00000379028 13/33 160 145 15 193 193 0 strelka-varscan-mutect NRCAM,missense_variant,p.Pro390His,ENST00000379028,;NRCAM,missense_variant,p.Pro390His,ENST00000413765,NM_001193582.1;NRCAM,missense_variant,p.Pro384His,ENST00000351718,NM_005010.4;NRCAM,missense_variant,p.Pro371His,ENST00000379024,NM_001193583.1,NM_001193584.1;NRCAM,missense_variant,p.Pro390His,ENST00000425651,NM_001037132.2;NRCAM,missense_variant,p.Pro385His,ENST00000379022,;NRCAM,missense_variant,p.Pro384His,ENST00000613830,;NRCAM,missense_variant,p.Pro384His,ENST00000417701,;NRCAM,non_coding_transcript_exon_variant,,ENST00000489800,; T ENST00000379028 Transcript missense_variant 1655/6685 1169/3915 390/1304 P/H cCc/cAc 1 -1 NRCAM HGNC HGNC:7994 protein_coding YES CCDS47686.1 ENSP00000368314 Q92823 UPI00005E2661 deleterious(0) 13/33 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 108207566 108207566 G T 1 0 0 0 0 1 0 0 0 10700 1232 43 2 2 NRCAM 7 108207566 Missense_Mutation SNP G C3L-00009_T 5980070 108207566 51138407 149 1941 RP11-286H14.4 0 . GRCh38 7 129127143 129127143 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.626T>A p.Leu209Gln p.L209Q ENST00000467614 1/2 424 334 90 617 616 1 strelka-varscan-mutect RP11-286H14.4,missense_variant,p.Leu209Gln,ENST00000467614,; A ENST00000467614 Transcript missense_variant 626/1263 626/1218 209/405 L/Q cTg/cAg 1 1 RP11-286H14.4 Clone_based_vega_gene protein_coding YES ENSP00000490163 deleterious(0) 1/2 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF314,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 129127143 129127143 T A 1 0 0 0 0 1 0 0 0 13725 1580 55 4 4 RP11-286H14.4 7 129127143 Missense_Mutation SNP T C3L-00009_T 20919577 129127143 30218830 150 1942 OR2A5 0 . GRCh38 7 144050933 144050933 + Missense_Mutation SNP T T G C3L-00009_T C3L-00009_N T T c.532T>G p.Phe178Val p.F178V ENST00000408906 1/1 443 377 66 627 627 0 strelka-varscan-mutect OR2A5,missense_variant,p.Phe178Val,ENST00000408906,NM_012365.1; G ENST00000408906 Transcript missense_variant 566/1013 532/936 178/311 F/V Ttc/Gtc COSM1568560 1 1 OR2A5 HGNC HGNC:8232 protein_coding YES CCDS43668.1 ENSP00000386208 Q96R48 A0A126GW49 UPI0000061F52 NM_012365.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF232,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 144050933 144050933 T G 1 0 0 0 0 1 0 0 0 11058 1609 56 5 5 OR2A5 7 144050933 Missense_Mutation SNP T C3L-00009_T 14923790 144050933 15295040 151 1943 KMT2C 0 . GRCh38 7 152222673 152222673 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.3333T>C p.= p.H1111H ENST00000262189 21/59 148 109 39 174 174 0 strelka-varscan-mutect KMT2C,synonymous_variant,p.=,ENST00000262189,NM_170606.2;KMT2C,synonymous_variant,p.=,ENST00000355193,;KMT2C,downstream_gene_variant,,ENST00000418673,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;KMT2C,upstream_gene_variant,,ENST00000489110,; G ENST00000262189 Transcript synonymous_variant 3552/16862 3333/14736 1111/4911 H caT/caC 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 21/59 PROSITE_profiles:PS50016,hmmpanther:PTHR22884:SF373,hmmpanther:PTHR22884,Gene3D:3.30.40.10,SMART_domains:SM00249,Superfamily_domains:SSF57903 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 152222673 152222673 A G 1 0 0 0 0 0 0 0 1 8297 214 8 5 5 KMT2C 7 152222673 Silent SNP A C3L-00009_T 8171740 152222673 7123300 152 1944 CSMD1 0 . GRCh38 8 2955655 2955655 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.9931G>T p.Gly3311Trp p.G3311W ENST00000520002 65/71 189 168 21 261 261 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly3172Trp,ENST00000537824,;CSMD1,missense_variant,p.Gly2728Trp,ENST00000335551,;CSMD1,missense_variant,p.Gly3311Trp,ENST00000520002,;CSMD1,missense_variant,p.Gly3311Trp,ENST00000602557,;CSMD1,missense_variant,p.Gly3310Trp,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly3134Trp,ENST00000400186,;CSMD1,missense_variant,p.Gly3134Trp,ENST00000602723,; A ENST00000520002 Transcript missense_variant 10487/11740 9931/10698 3311/3565 G/W Ggg/Tgg 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 65/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs1450764141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 2955655 2955655 C A 1 0 0 0 0 1 0 0 0 3745 681 24 2 2 CSMD1 8 2955655 Missense_Mutation SNP C C3L-00009_T 2955655 142182981 153 1945 C8orf4 0 . GRCh38 8 40153793 40153793 + Missense_Mutation SNP G G T rs766270756 C3L-00009_T C3L-00009_N G G c.261G>T p.Arg87Ser p.R87S ENST00000315792 1/1 128 111 17 185 184 1 strelka-varscan-mutect C8orf4,missense_variant,p.Arg87Ser,ENST00000315792,NM_020130.4; T ENST00000315792 Transcript missense_variant 339/1854 261/321 87/106 R/S agG/agT rs766270756,COSM1635793 1 1 C8orf4 HGNC HGNC:1357 protein_coding YES CCDS6115.1 ENSP00000319914 Q9NR00 UPI000013FBD4 NM_020130.4 deleterious(0.01) 1/1 hmmpanther:PTHR32358,hmmpanther:PTHR32358:SF1,PD287216 0,1 MODERATE 1 SNV 0,1 1 PASS rs766270756 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 40153793 40153793 G T 1 0 0 0 0 1 0 0 0 2157 1165 41 2 2 C8orf4 8 40153793 Missense_Mutation SNP G C3L-00009_T 37198138 40153793 104984843 154 1946 PXDNL 0 . GRCh38 8 51409432 51409432 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.2192A>G p.Asp731Gly p.D731G ENST00000356297 17/23 195 169 26 239 239 0 strelka-varscan-mutect PXDNL,missense_variant,p.Asp731Gly,ENST00000356297,NM_144651.4;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,upstream_gene_variant,,ENST00000522628,; C ENST00000356297 Transcript missense_variant 2293/4805 2192/4392 731/1463 D/G gAc/gGc 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 51409432 51409432 T C 1 0 0 0 0 1 0 0 0 13002 1667 58 5 5 PXDNL 8 51409432 Missense_Mutation SNP T C3L-00009_T 11255639 51409432 93729204 155 1947 RP1 0 . GRCh38 8 54629350 54629350 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.5468A>T p.His1823Leu p.H1823L ENST00000220676 4/4 373 349 24 516 516 0 strelka-varscan-mutect RP1,missense_variant,p.His1823Leu,ENST00000220676,NM_006269.1;RP1,intron_variant,,ENST00000637698,;RP1,intron_variant,,ENST00000636932,; T ENST00000220676 Transcript missense_variant 5616/7100 5468/6471 1823/2156 H/L cAt/cTt 1 1 RP1 HGNC HGNC:10263 protein_coding YES CCDS6160.1 ENSP00000220676 P56715 UPI000013455B NM_006269.1 deleterious(0) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF4 MODERATE 1 SNV 1 1 PASS rs1477893507 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 54629350 54629350 A T 1 0 0 0 0 1 0 0 0 13709 217 8 4 4 RP1 8 54629350 Missense_Mutation SNP A C3L-00009_T 3219918 54629350 90509286 156 1948 CA8 0 . GRCh38 8 60222660 60222660 + Missense_Mutation SNP A A C novel C3L-00009_T C3L-00009_N A A c.727T>G p.Ser243Ala p.S243A ENST00000317995 7/9 453 419 34 558 557 1 strelka-varscan-mutect CA8,missense_variant,p.Ser243Ala,ENST00000317995,NM_004056.4;CA8,non_coding_transcript_exon_variant,,ENST00000528666,;CA8,non_coding_transcript_exon_variant,,ENST00000524872,; C ENST00000317995 Transcript missense_variant 992/3812 727/873 243/290 S/A Tcc/Gcc 1 -1 CA8 HGNC HGNC:1382 protein_coding YES CCDS6174.1 ENSP00000314407 P35219 UPI000000D816 NM_004056.4 deleterious(0.01) 7/9 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF104,Gene3D:3.10.200.10,Pfam_domain:PF00194,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 60222660 60222660 A C 1 0 0 0 0 1 0 0 0 2209 333 12 5 5 CA8 8 60222660 Missense_Mutation SNP A C3L-00009_T 5593310 60222660 84915976 157 1949 SLCO5A1 0 . GRCh38 8 69673108 69673108 + Missense_Mutation SNP G G A rs544002796 C3L-00009_T C3L-00009_N G G c.2308C>T p.Arg770Trp p.R770W ENST00000260126 10/10 454 406 48 600 600 0 strelka-varscan-mutect SLCO5A1,missense_variant,p.Arg770Trp,ENST00000260126,NM_030958.2;SLCO5A1,missense_variant,p.Arg715Trp,ENST00000530307,NM_001146009.1;SLCO5A1,3_prime_UTR_variant,,ENST00000524945,NM_001146008.1;SLCO5A1,3_prime_UTR_variant,,ENST00000526750,; A ENST00000260126 Transcript missense_variant 3015/9076 2308/2547 770/848 R/W Cgg/Tgg rs544002796,COSM1101369 1 -1 SLCO5A1 HGNC HGNC:19046 protein_coding YES CCDS6205.1 ENSP00000260126 Q9H2Y9 UPI0000140F53 NM_030958.2 tolerated(0.19) 10/10 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF91 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs544002796 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 69673108 69673108 G A 1 0 0 0 0 1 0 0 0 15018 1086 38 1 1 SLCO5A1 8 69673108 Missense_Mutation SNP G C3L-00009_T 9450448 69673108 75465528 158 1950 ZFHX4 0 . GRCh38 8 76855959 76855959 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.9038G>T p.Gly3013Val p.G3013V ENST00000521891 10/11 239 218 21 288 288 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Gly3013Val,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Gly2987Val,ENST00000518282,; T ENST00000521891 Transcript missense_variant 9486/14019 9038/10851 3013/3616 G/V gGg/gTg 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 PROSITE_patterns:PS00028,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,SMART_domains:SM00451,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 6 76855959 76855959 G T 1 0 0 0 0 1 0 0 0 18213 1232 43 2 2 ZFHX4 8 76855959 Missense_Mutation SNP G C3L-00009_T 7182851 76855959 68282677 159 1951 PKHD1L1 0 . GRCh38 8 109425140 109425140 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.2753G>T p.Gly918Val p.G918V ENST00000378402 24/78 149 119 30 168 168 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Gly918Val,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript missense_variant 2857/13076 2753/12732 918/4243 G/V gGc/gTc 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 24/78 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 109425140 109425140 G T 1 0 0 0 0 1 0 0 0 12068 1203 42 2 2 PKHD1L1 8 109425140 Missense_Mutation SNP G C3L-00009_T 32569181 109425140 35713496 160 1952 ZNF572 0 . GRCh38 8 124977284 124977284 + Missense_Mutation SNP G G A rs201968418 C3L-00009_T C3L-00009_N G G c.1016G>A p.Arg339His p.R339H ENST00000319286 3/3 153 140 13 220 220 0 strelka-varscan-mutect ZNF572,missense_variant,p.Arg339His,ENST00000319286,NM_152412.2; A ENST00000319286 Transcript missense_variant 1170/3275 1016/1590 339/529 R/H cGt/cAt rs201968418,COSM5441792 1 1 ZNF572 HGNC HGNC:26758 protein_coding YES CCDS6354.1 ENSP00000319305 Q7Z3I7 UPI0000140576 NM_152412.2 tolerated(0.13) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201968418 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 124977284 124977284 G A 1 0 0 0 0 1 0 0 0 18578 1145 40 1 1 ZNF572 8 124977284 Missense_Mutation SNP G C3L-00009_T 15552144 124977284 20161352 161 1953 FAM135B 0 . GRCh38 8 138137219 138137219 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.3943C>A p.Gln1315Lys p.Q1315K ENST00000395297 19/20 344 274 70 352 352 0 strelka-varscan-mutect FAM135B,missense_variant,p.Gln1315Lys,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,; T ENST00000395297 Transcript missense_variant 4114/6962 3943/4221 1315/1406 Q/K Caa/Aaa 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0.01) 19/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482,Gene3D:3.40.50.1820,Pfam_domain:PF05057,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 138137219 138137219 G T 1 0 0 0 0 1 0 0 0 5299 1357 47 2 2 FAM135B 8 138137219 Missense_Mutation SNP G C3L-00009_T 13159935 138137219 7001417 162 1954 COL22A1 0 . GRCh38 8 138623761 138623761 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.3742G>T p.Asp1248Tyr p.D1248Y ENST00000303045 52/65 128 118 10 169 169 0 strelka-varscan-mutect COL22A1,missense_variant,p.Asp1248Tyr,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Asp941Tyr,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,;COL22A1,upstream_gene_variant,,ENST00000487854,; A ENST00000303045 Transcript missense_variant 4189/6346 3742/4881 1248/1626 D/Y Gat/Tat 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 deleterious(0) 52/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 138623761 138623761 C A 1 0 0 0 0 1 0 0 0 3469 913 32 2 2 COL22A1 8 138623761 Missense_Mutation SNP C C3L-00009_T 486542 138623761 6514875 163 1955 COMMD5 0 . GRCh38 8 144850778 144850778 + Silent SNP T T C novel C3L-00009_T C3L-00009_N T T c.561A>G p.= p.A187A ENST00000450361 2/2 410 388 22 469 469 0 strelka-varscan COMMD5,synonymous_variant,p.=,ENST00000450361,NM_001081003.2;COMMD5,synonymous_variant,p.=,ENST00000543949,NM_001287237.1;COMMD5,synonymous_variant,p.=,ENST00000305103,NM_014066.3;COMMD5,synonymous_variant,p.=,ENST00000402718,NM_001081004.2;ZNF7,downstream_gene_variant,,ENST00000525266,NM_001282796.1;COMMD5,downstream_gene_variant,,ENST00000529143,;COMMD5,downstream_gene_variant,,ENST00000533270,;ZNF7,downstream_gene_variant,,ENST00000325217,;COMMD5,synonymous_variant,p.=,ENST00000530332,; C ENST00000450361 Transcript synonymous_variant 983/1573 561/675 187/224 A gcA/gcG 1 -1 COMMD5 HGNC HGNC:17902 protein_coding YES CCDS6436.1 ENSP00000394331 Q9GZQ3 UPI000004A08E NM_001081003.2 2/2 PROSITE_profiles:PS51269,hmmpanther:PTHR15666,hmmpanther:PTHR15666:SF1,Pfam_domain:PF07258 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 144850778 144850778 T C 1 0 0 0 0 0 0 0 1 3511 1451 51 5 5 COMMD5 8 144850778 Silent SNP T C3L-00009_T 6227017 144850778 287858 164 1956 IZUMO3 0 . GRCh38 9 24545496 24545496 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.154G>C p.Glu52Gln p.E52Q ENST00000604921 1/6 304 284 20 539 539 0 strelka-mutect IZUMO3,missense_variant,p.Glu52Gln,ENST00000543880,;IZUMO3,missense_variant,p.Glu52Gln,ENST00000604921,NM_001271706.1;IZUMO3,intron_variant,,ENST00000418122,;RP11-20A20.2,upstream_gene_variant,,ENST00000602851,;RP11-20A20.2,upstream_gene_variant,,ENST00000602614,; G ENST00000604921 Transcript missense_variant 181/743 154/702 52/233 E/Q Gaa/Caa 1 -1 IZUMO3 HGNC HGNC:31421 protein_coding YES CCDS65020.1 ENSP00000474246 S4R3E6 UPI0002742D6C NM_001271706.1 tolerated(0.29) 1/6 hmmpanther:PTHR36470,Pfam_domain:PF15005 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 24545496 24545496 C G 1 0 0 0 0 1 0 0 0 7842 835 29 4 4 IZUMO3 9 24545496 Missense_Mutation SNP C C3L-00009_T 24545496 113849221 165 1957 DAPK1 0 . GRCh38 9 87686602 87686602 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.2276G>T p.Arg759Met p.R759M ENST00000408954 21/26 183 146 37 219 219 0 strelka-mutect DAPK1,missense_variant,p.Arg759Met,ENST00000469640,;DAPK1,missense_variant,p.Arg759Met,ENST00000408954,NM_004938.3;DAPK1,missense_variant,p.Arg759Met,ENST00000622514,NM_001288729.1;DAPK1,missense_variant,p.Arg759Met,ENST00000472284,NM_001288730.1;DAPK1,missense_variant,p.Arg759Met,ENST00000358077,NM_001288731.1;DAPK1,missense_variant,p.Arg759Met,ENST00000491893,;DAPK1,3_prime_UTR_variant,,ENST00000489291,; T ENST00000408954 Transcript missense_variant 2611/5892 2276/4293 759/1430 R/M aGg/aTg 1 1 DAPK1 HGNC HGNC:2674 protein_coding YES CCDS43842.1 ENSP00000386135 P53355 UPI0000210C2F NM_004938.3 tolerated(0.14) 21/26 PROSITE_profiles:PS51424 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 87686602 87686602 G T 1 0 0 0 0 1 0 0 0 4036 1000 35 2 2 DAPK1 9 87686602 Missense_Mutation SNP G C3L-00009_T 63141106 87686602 50708115 166 1958 COL15A1 0 . GRCh38 9 99061970 99061970 + Splice_Site SNP G G T novel C3L-00009_T C3L-00009_N G G c.3403-1G>T p.X1135_splice ENST00000375001 87 71 16 103 103 0 strelka-varscan-mutect COL15A1,splice_acceptor_variant,,ENST00000375001,NM_001855.4;COL15A1,splice_acceptor_variant,,ENST00000610452,; T ENST00000375001 Transcript splice_acceptor_variant -/5496 3403/4167 1135/1388 1 1 COL15A1 HGNC HGNC:2192 protein_coding YES CCDS35081.1 ENSP00000364140 P39059 UPI0000211506 NM_001855.4 36/41 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 6 99061970 99061970 G T 1 0 0 0 0 0 0 1 0 3460 1014 35 2 2 COL15A1 9 99061970 Splice_Site SNP G C3L-00009_T 11375368 99061970 39332747 167 1959 OR13C9 0 . GRCh38 9 104617449 104617449 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.756T>C p.= p.Y252Y ENST00000259362 1/1 81 67 14 117 117 0 strelka-varscan-mutect OR13C9,synonymous_variant,p.=,ENST00000259362,NM_001001956.1; G ENST00000259362 Transcript synonymous_variant 756/957 756/957 252/318 Y taT/taC 1 -1 OR13C9 HGNC HGNC:15104 protein_coding YES CCDS35093.1 ENSP00000259362 Q8NGT0 UPI0000041D56 NM_001001956.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF23,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 104617449 104617449 A G 1 0 0 0 0 0 0 0 1 11015 224 8 5 5 OR13C9 9 104617449 Silent SNP A C3L-00009_T 5555479 104617449 33777268 168 1960 EPB41L4B 0 . GRCh38 9 109192336 109192336 + Missense_Mutation SNP C C T rs199718023 C3L-00009_T C3L-00009_N C C c.2243G>A p.Gly748Asp p.G748D ENST00000374566 22/26 92 72 20 132 132 0 strelka-varscan-mutect EPB41L4B,missense_variant,p.Gly748Asp,ENST00000374566,NM_019114.4;RNU6-984P,downstream_gene_variant,,ENST00000363236,; T ENST00000374566 Transcript missense_variant 2761/5800 2243/2703 748/900 G/D gGt/gAt rs199718023 1 -1 EPB41L4B HGNC HGNC:19818 protein_coding YES CCDS43859.1 ENSP00000363694 Q9H329 UPI0000458994 NM_019114.4 tolerated_low_confidence(0.07) 22/26 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF18 26872740 MODERATE 1 SNV 1 1 PASS rs199718023 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 109192336 109192336 C T 1 0 0 0 0 1 0 0 0 5003 507 18 3 3 EPB41L4B 9 109192336 Missense_Mutation SNP C C3L-00009_T 4574887 109192336 29202381 169 1961 LPAR1 0 . GRCh38 9 110941541 110941541 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.673T>C p.Tyr225His p.Y225H ENST00000374431 4/5 250 200 50 368 368 0 strelka-varscan-mutect LPAR1,missense_variant,p.Tyr225His,ENST00000374431,NM_057159.2;LPAR1,missense_variant,p.Tyr225His,ENST00000374430,;LPAR1,missense_variant,p.Tyr225His,ENST00000358883,NM_001401.3;LPAR1,missense_variant,p.Tyr207His,ENST00000541779,;LPAR1,downstream_gene_variant,,ENST00000441240,; G ENST00000374431 Transcript missense_variant 1057/3637 673/1095 225/364 Y/H Tat/Cat 1 -1 LPAR1 HGNC HGNC:3166 protein_coding YES CCDS6777.1 ENSP00000363553 Q92633 Q5VZX0 UPI000011DBF9 NM_057159.2 deleterious(0) 4/5 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF22,hmmpanther:PTHR22750,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 110941541 110941541 A G 1 0 0 0 0 1 0 0 0 8807 420 15 5 5 LPAR1 9 110941541 Missense_Mutation SNP A C3L-00009_T 1749205 110941541 27453176 170 1962 SNAPC4 0 . GRCh38 9 136379110 136379110 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.2717G>A p.Arg906His p.R906H ENST00000298532 21/23 59 50 9 118 118 0 strelka-varscan-mutect SNAPC4,missense_variant,p.Arg906His,ENST00000298532,NM_003086.2; T ENST00000298532 Transcript missense_variant 3086/5010 2717/4410 906/1469 R/H cGt/cAt COSM5441447 1 -1 SNAPC4 HGNC HGNC:11137 protein_coding YES CCDS6998.1 ENSP00000298532 Q5SXM2 A0A024R8F4 UPI000013E4EC NM_003086.2 tolerated(0.06) 21/23 1 MODERATE 1 SNV 1 1 1 PASS rs1023537386 . 0 203 7 0 0 0 0 0 -19.90653 0.9999996 1 1 1 0 T 3 4 6 136379110 136379110 C T 1 0 0 0 0 1 0 0 0 15158 536 19 1 1 SNAPC4 9 136379110 Missense_Mutation SNP C C3L-00009_T 25437569 136379110 2015607 171 1963 SFMBT2 0 . GRCh38 10 7283906 7283906 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.770C>T p.Ser257Leu p.S257L ENST00000397167 6/21 136 128 8 169 169 0 strelka-varscan-mutect SFMBT2,missense_variant,p.Ser257Leu,ENST00000397167,NM_001029880.2;SFMBT2,missense_variant,p.Ser257Leu,ENST00000361972,NM_001018039.1;SFMBT2,downstream_gene_variant,,ENST00000379713,; A ENST00000397167 Transcript missense_variant,splice_region_variant 963/8024 770/2685 257/894 S/L tCa/tTa 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 tolerated(0.43) 6/21 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF02820,Gene3D:2.30.30.160,Superfamily_domains:SSF63748 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 7283906 7283906 G A 1 0 0 0 0 1 0 0 0 14436 1304 45 3 3 SFMBT2 10 7283906 Missense_Mutation SNP G C3L-00009_T 7283906 126513516 172 1964 ITIH5 0 . GRCh38 10 7563160 7563160 + Frame_Shift_Del DEL C C - novel C3L-00009_T C3L-00009_N C C c.2752delG p.Glu918SerfsTer15 p.E918Sfs*15 ENST00000397146 14/14 344 301 43 448 447 1 sindel-varindel-pindel ITIH5,frameshift_variant,p.Glu918SerfsTer15,ENST00000397146,NM_030569.6;ITIH5,frameshift_variant,p.Glu704SerfsTer15,ENST00000613909,NM_032817.5;ITIH5,downstream_gene_variant,,ENST00000473591,; - ENST00000397146 Transcript frameshift_variant 2831/6721 2752/2829 918/942 E/X Gag/ag 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 14/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 6 7563160 7563160 C - 1 0 1 0 1 0 0 0 0 7813 864 30 0 0 ITIH5 10 7563160 Frame_Shift_Del DEL C C3L-00009_T 279254 7563160 126234262 173 1965 NMT2 0 . GRCh38 10 15141535 15141546 + In_Frame_Del DEL CTCCCAAATACC CTCCCAAATACC - novel C3L-00009_T C3L-00009_N CTCCCAAATACC CTCCCAAATACC c.122_133delGGTATTTGGGAG p.Gly41_Gly44del p.G41_G44del ENST00000378165 2/12 139 112 27 166 166 0 sindel-varindel-pindel NMT2,inframe_deletion,p.Gly41_Gly44del,ENST00000378165,NM_004808.2;NMT2,inframe_deletion,p.Gly14_Glu17del,ENST00000378150,NM_001308295.1;NMT2,upstream_gene_variant,,ENST00000478580,;RPP38,downstream_gene_variant,,ENST00000451677,; - ENST00000378165 Transcript inframe_deletion 203-214/2907 122-133/1497 41-45/498 GYLGA/A gGGTATTTGGGAGcc/gcc 1 -1 NMT2 HGNC HGNC:7858 protein_coding YES CCDS7109.1 ENSP00000367407 O60551 UPI0000130278 NM_004808.2 2/12 hmmpanther:PTHR11377,hmmpanther:PTHR11377:SF6 MODERATE 1 deletion 1 1 PASS . . 0 204 0 5 0 0 0 0 -20 0.9997146 1 1 1 0 - 7 5 6 15141535 15141535 CTCCCAAATACC - 1 0 1 0 1 0 0 0 0 10545 797 28 0 0 NMT2 10 15141535 In_Frame_Del DEL CTCCCAAATACC C3L-00009_T 7578375 15141535 118655887 174 1966 HACD1 0 . GRCh38 10 17617288 17617288 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.52G>T p.Gly18Cys p.G18C ENST00000361271 1/7 99 81 18 119 119 0 strelka-varscan-mutect HACD1,missense_variant,p.Gly18Cys,ENST00000361271,NM_014241.3;HACD1,missense_variant,p.Gly18Cys,ENST00000326961,;HACD1,upstream_gene_variant,,ENST00000466335,;HACD1,non_coding_transcript_exon_variant,,ENST00000632169,; A ENST00000361271 Transcript missense_variant 90/2237 52/867 18/288 G/C Ggc/Tgc 1 -1 HACD1 HGNC HGNC:9639 protein_coding YES CCDS7121.1 ENSP00000355308 B0YJ81 UPI000036666A NM_014241.3 tolerated_low_confidence(0.09) 1/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 17617288 17617288 C A 1 0 0 0 0 1 0 0 0 6822 681 24 2 2 HACD1 10 17617288 Missense_Mutation SNP C C3L-00009_T 2475753 17617288 116180134 175 1967 TMEM236 0 . GRCh38 10 17795958 17795958 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.510A>T p.Gln170His p.Q170H ENST00000377495 4/4 642 556 86 856 856 0 strelka-varscan-mutect TMEM236,missense_variant,p.Gln170His,ENST00000377495,NM_001098844.2; T ENST00000377495 Transcript missense_variant 554/5464 510/1056 170/351 Q/H caA/caT 1 1 TMEM236 HGNC HGNC:23473 protein_coding YES CCDS41492.1 ENSP00000366715 Q5W0B7 UPI000041A684 NM_001098844.2 tolerated(0.13) 4/4 hmmpanther:PTHR31453,hmmpanther:PTHR31453:SF2,PD098445 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 17795958 17795958 A T 1 0 0 0 0 1 0 0 0 16597 40 2 4 4 TMEM236 10 17795958 Missense_Mutation SNP A C3L-00009_T 178670 17795958 116001464 176 1968 MLLT10 0 . GRCh38 10 21732902 21732902 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.2222T>C p.Leu741Ser p.L741S ENST00000307729 18/23 93 82 11 119 119 0 strelka-varscan-mutect MLLT10,missense_variant,p.Leu757Ser,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Leu741Ser,ENST00000307729,;MLLT10,missense_variant,p.Leu741Ser,ENST00000631589,;MLLT10,missense_variant,p.Leu741Ser,ENST00000377059,NM_001195626.1;MLLT10,downstream_gene_variant,,ENST00000438473,; C ENST00000307729 Transcript missense_variant 2400/5032 2222/3207 741/1068 L/S tTa/tCa 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 deleterious(0) 18/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99973 1 1 1 1 0 C 3 2 6 21732902 21732902 T C 1 0 0 0 0 1 0 0 0 9589 1768 61 5 5 MLLT10 10 21732902 Missense_Mutation SNP T C3L-00009_T 3936944 21732902 112064520 177 1969 ANKRD30A 0 . GRCh38 10 37217747 37217747 + Nonsense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.2968G>T p.Glu990Ter p.E990* ENST00000361713 33/36 102 95 7 152 152 0 varscan-mutect ANKRD30A,stop_gained,p.Glu1109Ter,ENST00000374660,;ANKRD30A,stop_gained,p.Glu1046Ter,ENST00000611781,;ANKRD30A,stop_gained,p.Glu990Ter,ENST00000602533,;ANKRD30A,stop_gained,p.Glu990Ter,ENST00000361713,NM_052997.2; T ENST00000361713 Transcript stop_gained 3067/4405 2968/4026 990/1341 E/* Gaa/Taa COSM1956535,COSM1956536 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 33/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 1,1 HIGH 1 SNV 5 1,1 1 PASS rs1308226053 . 0 208 0 2 0 0 0 0 -10.93815 0.9999996 1 1 1 0 T 4 4 6 37217747 37217747 G T 1 0 0 0 0 0 1 0 0 761 1291 45 2 2 ANKRD30A 10 37217747 Nonsense_Mutation SNP G C3L-00009_T 15484845 37217747 96579675 178 1970 WDFY4 0 . GRCh38 10 48807916 48807916 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.4796T>A p.Leu1599Gln p.L1599Q ENST00000325239 27/61 133 123 10 143 143 0 strelka-varscan-mutect WDFY4,missense_variant,p.Leu1599Gln,ENST00000325239,NM_020945.1;WDFY4,missense_variant,p.Leu146Gln,ENST00000374161,; A ENST00000325239 Transcript missense_variant 4796/9555 4796/9555 1599/3184 L/Q cTg/cAg 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 deleterious(0) 27/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 48807916 48807916 T A 1 0 0 0 0 1 0 0 0 17831 1580 55 4 4 WDFY4 10 48807916 Missense_Mutation SNP T C3L-00009_T 11590169 48807916 84989506 179 1971 OGDHL 0 . GRCh38 10 49752176 49752176 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.551C>A p.Ser184Tyr p.S184Y ENST00000374103 5/23 336 288 48 435 434 1 strelka-varscan-mutect OGDHL,missense_variant,p.Ser184Tyr,ENST00000374103,NM_018245.2;OGDHL,missense_variant,p.Ser127Tyr,ENST00000419399,NM_001143996.1;OGDHL,5_prime_UTR_variant,,ENST00000432695,NM_001143997.1;OGDHL,downstream_gene_variant,,ENST00000471460,; T ENST00000374103 Transcript missense_variant 637/3704 551/3033 184/1010 S/Y tCt/tAt 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 deleterious(0.01) 5/23 PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 49752176 49752176 G T 1 0 0 0 0 1 0 0 0 10914 942 33 2 2 OGDHL 10 49752176 Missense_Mutation SNP G C3L-00009_T 944260 49752176 84045246 180 1972 PCDH15 0 . GRCh38 10 54317280 54317280 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.882G>C p.Leu294Phe p.L294F ENST00000373957 9/35 372 347 25 516 516 0 strelka-varscan-mutect PCDH15,missense_variant,p.Leu294Phe,ENST00000614895,;PCDH15,missense_variant,p.Leu289Phe,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000414778,;PCDH15,missense_variant,p.Leu294Phe,ENST00000617051,;PCDH15,missense_variant,p.Leu294Phe,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Leu267Phe,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Leu252Phe,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Leu289Phe,ENST00000622048,;PCDH15,missense_variant,p.Leu289Phe,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Leu294Phe,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000395445,;PCDH15,missense_variant,p.Leu289Phe,ENST00000616114,;PCDH15,missense_variant,p.Leu289Phe,ENST00000395438,;PCDH15,missense_variant,p.Leu294Phe,ENST00000612394,;PCDH15,missense_variant,p.Leu294Phe,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Leu289Phe,ENST00000373955,;PCDH15,missense_variant,p.Leu289Phe,ENST00000395446,;PCDH15,missense_variant,p.Leu289Phe,ENST00000395440,;PCDH15,missense_variant,p.Leu289Phe,ENST00000395442,;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Leu289Phe,ENST00000448885,;PCDH15,missense_variant,p.Leu289Phe,ENST00000373956,;PCDH15,missense_variant,p.Leu289Phe,ENST00000414367,; G ENST00000373957 Transcript missense_variant 1277/7032 882/5889 294/1962 L/F ttG/ttC 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.47) 9/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 54317280 54317280 C G 1 0 0 0 0 1 0 0 0 11598 825 29 4 4 PCDH15 10 54317280 Missense_Mutation SNP C C3L-00009_T 4565104 54317280 79480142 181 1973 ANK3 0 . GRCh38 10 60279636 60279636 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.118G>T p.Asp40Tyr p.D40Y ENST00000280772 2/44 172 149 23 230 230 0 strelka-varscan-mutect ANK3,missense_variant,p.Asp40Tyr,ENST00000280772,NM_020987.3;ANK3,missense_variant,p.Asp34Tyr,ENST00000373827,NM_001204403.1;ANK3,missense_variant,p.Asp23Tyr,ENST00000503366,NM_001204404.1;ANK3,missense_variant,p.Asp14Tyr,ENST00000503925,;ANK3,missense_variant,p.Asp23Tyr,ENST00000622427,; A ENST00000280772 Transcript missense_variant 310/16874 118/13134 40/4377 D/Y Gat/Tat 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 deleterious(0) 2/44 Low_complexity_(Seg):seg,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22 MODERATE 1 SNV 1 1 PASS rs1430387975 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 60279636 60279636 C A 1 0 0 0 0 1 0 0 0 722 840 29 2 2 ANK3 10 60279636 Missense_Mutation SNP C C3L-00009_T 5962356 60279636 73517786 182 1974 MYPN 0 . GRCh38 10 68210431 68210431 + Missense_Mutation SNP T T A rs750175617 C3L-00009_T C3L-00009_N T T c.3939T>A p.Ser1313Arg p.S1313R ENST00000358913 20/20 607 521 86 899 896 3 strelka-varscan-mutect MYPN,missense_variant,p.Ser1019Arg,ENST00000613327,NM_001256268.1;MYPN,missense_variant,p.Ser1313Arg,ENST00000358913,NM_032578.3;MYPN,missense_variant,p.Ser1313Arg,ENST00000540630,NM_001256267.1;MYPN,missense_variant,p.Ser1038Arg,ENST00000354393,; A ENST00000358913 Transcript missense_variant 4427/6013 3939/3963 1313/1320 S/R agT/agA rs750175617 1 1 MYPN HGNC HGNC:23246 protein_coding YES CCDS7275.1 ENSP00000351790 Q86TC9 UPI00002288CF NM_032578.3 tolerated(0.13) 20/20 MODERATE 1 SNV 1 1 PASS rs750175617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 68210431 68210431 T A 1 0 0 0 0 1 0 0 0 10099 1693 59 4 4 MYPN 10 68210431 Missense_Mutation SNP T C3L-00009_T 7930795 68210431 65586991 183 1975 OPN4 0 . GRCh38 10 86658669 86658669 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.643C>G p.Pro215Ala p.P215A ENST00000372071 5/11 269 223 46 352 352 0 strelka-varscan-mutect OPN4,missense_variant,p.Pro215Ala,ENST00000372071,NM_001030015.2;OPN4,missense_variant,p.Pro204Ala,ENST00000241891,NM_033282.3;OPN4,missense_variant,p.Pro215Ala,ENST00000443292,; G ENST00000372071 Transcript missense_variant 870/2401 643/1470 215/489 P/A Cca/Gca 1 1 OPN4 HGNC HGNC:14449 protein_coding YES CCDS31237.1 ENSP00000361141 Q9UHM6 UPI00001544ED NM_001030015.2 tolerated(0.3) 5/11 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24240,hmmpanther:PTHR24240:SF72,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 86658669 86658669 C G 1 0 0 0 0 1 0 0 0 10958 739 26 4 4 OPN4 10 86658669 Missense_Mutation SNP C C3L-00009_T 18448238 86658669 47138753 184 1976 PLCE1 0 . GRCh38 10 94031394 94031394 + Silent SNP C C G rs374493261 C3L-00009_T C3L-00009_N C C c.348C>G p.= p.G116G ENST00000371380 1/32 563 478 85 688 688 0 strelka-varscan-mutect PLCE1,synonymous_variant,p.=,ENST00000371380,NM_016341.3,NM_001288989.1; G ENST00000371380 Transcript synonymous_variant 583/12024 348/6909 116/2302 G ggC/ggG rs374493261 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 1/32 LOW 1 SNV 1 1 PASS rs374493261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 94031394 94031394 C G 1 0 0 0 0 0 0 0 1 12128 726 26 4 4 PLCE1 10 94031394 Silent SNP C C3L-00009_T 7372725 94031394 39766028 185 1977 SLIT1 0 . GRCh38 10 97057251 97057251 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.1116C>T p.= p.L372L ENST00000266058 12/37 175 160 15 171 171 0 strelka-varscan-mutect SLIT1,synonymous_variant,p.=,ENST00000266058,NM_003061.2;SLIT1,synonymous_variant,p.=,ENST00000371070,;SLIT1,synonymous_variant,p.=,ENST00000314867,;SLIT1,downstream_gene_variant,,ENST00000371041,; A ENST00000266058 Transcript synonymous_variant 1362/7925 1116/4605 372/1534 L ctC/ctT 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 12/37 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 97057251 97057251 G A 1 0 0 0 0 0 0 0 1 15030 1161 41 3 3 SLIT1 10 97057251 Silent SNP G C3L-00009_T 3025857 97057251 36740171 186 1978 HOGA1 0 . GRCh38 10 97584743 97584743 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.40C>T p.= p.L14L ENST00000370646 1/7 78 73 5 98 98 0 strelka-mutect HOGA1,synonymous_variant,p.=,ENST00000370646,NM_138413.3;HOGA1,synonymous_variant,p.=,ENST00000370647,NM_001134670.1;RP11-548K23.11,synonymous_variant,p.=,ENST00000370649,;ANKRD2,downstream_gene_variant,,ENST00000370655,;ANKRD2,downstream_gene_variant,,ENST00000307518,NM_001291218.1,NM_020349.3;ANKRD2,downstream_gene_variant,,ENST00000298808,NM_001291219.1,NM_001129981.2;C10orf62,upstream_gene_variant,,ENST00000370640,NM_001009997.2;ANKRD2,downstream_gene_variant,,ENST00000455090,;HOGA1,non_coding_transcript_exon_variant,,ENST00000465608,; T ENST00000370646 Transcript synonymous_variant 401/2488 40/984 14/327 L Cta/Tta 1 1 HOGA1 HGNC HGNC:25155 protein_coding YES CCDS7467.1 ENSP00000359680 Q86XE5 UPI000000DAE5 NM_138413.3 1/7 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -11.0603 0.9999973 1 1 1 0 T 2 4 6 97584743 97584743 C T 1 0 0 0 0 0 0 0 1 7171 796 28 3 3 HOGA1 10 97584743 Silent SNP C C3L-00009_T 527492 97584743 36212679 187 1979 CALHM1 0 . GRCh38 10 103458590 103458590 + Silent SNP C C T rs377477951 C3L-00009_T C3L-00009_N C C c.162G>A p.= p.A54A ENST00000329905 1/2 316 268 48 418 417 1 strelka-varscan-mutect CALHM1,synonymous_variant,p.=,ENST00000329905,NM_001001412.3;RP11-225H22.4,intron_variant,,ENST00000411906,; T ENST00000329905 Transcript synonymous_variant 299/3053 162/1041 54/346 A gcG/gcA rs377477951,COSM4011394 1 -1 CALHM1 HGNC HGNC:23494 protein_coding YES CCDS7550.1 ENSP00000329926 Q8IU99 UPI000016144D NM_001001412.3 1/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR32261,hmmpanther:PTHR32261:SF2,Pfam_domain:PF14798 0,1 LOW 1 SNV 1 0,1 1 PASS rs377477951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 103458590 103458590 C T 1 0 0 0 0 0 0 0 1 2272 639 23 1 1 CALHM1 10 103458590 Silent SNP C C3L-00009_T 5873847 103458590 30338832 188 1980 ADD3 0 . GRCh38 10 110124107 110124107 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.1234G>A p.Ala412Thr p.A412T ENST00000356080 10/15 293 276 17 404 404 0 strelka-varscan-mutect ADD3,missense_variant,p.Ala412Thr,ENST00000277900,NM_001121.2;ADD3,missense_variant,p.Ala412Thr,ENST00000360162,NM_019903.3;ADD3,missense_variant,p.Ala412Thr,ENST00000356080,NM_016824.3;ADD3,non_coding_transcript_exon_variant,,ENST00000472568,;ADD3,non_coding_transcript_exon_variant,,ENST00000488837,;ADD3,non_coding_transcript_exon_variant,,ENST00000486014,;ADD3,upstream_gene_variant,,ENST00000479805,;ADD3,upstream_gene_variant,,ENST00000488799,;ADD3,downstream_gene_variant,,ENST00000488104,;ADD3,upstream_gene_variant,,ENST00000492162,; A ENST00000356080 Transcript missense_variant 1601/3081 1234/2121 412/706 A/T Gct/Act 1 1 ADD3 HGNC HGNC:245 protein_coding YES CCDS7561.1 ENSP00000348381 Q9UEY8 Q5VU08 UPI0000125505 NM_016824.3 tolerated(0.06) 10/15 hmmpanther:PTHR10672:SF5,hmmpanther:PTHR10672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 110124107 110124107 G A 1 0 0 0 0 1 0 0 0 350 1319 46 3 3 ADD3 10 110124107 Missense_Mutation SNP G C3L-00009_T 6665517 110124107 23673315 189 1981 MXI1 0 . GRCh38 10 110208025 110208025 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.217G>T p.Val73Leu p.V73L ENST00000332674 1/6 434 400 34 570 570 0 strelka-varscan-mutect MXI1,missense_variant,p.Val73Leu,ENST00000332674,NM_130439.3;MXI1,missense_variant,p.Val73Leu,ENST00000453116,;MXI1,upstream_gene_variant,,ENST00000361248,NM_001008541.1;RP11-549L6.3,non_coding_transcript_exon_variant,,ENST00000451656,; T ENST00000332674 Transcript missense_variant 421/3470 217/888 73/295 V/L Gtg/Ttg 1 1 MXI1 HGNC HGNC:7534 protein_coding YES CCDS7563.1 ENSP00000331152 P50539 UPI0000376B16 NM_130439.3 tolerated(0.26) 1/6 hmmpanther:PTHR11969:SF13,hmmpanther:PTHR11969 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 110208025 110208025 G T 1 0 0 0 0 1 0 0 0 10001 1145 40 1 1 MXI1 10 110208025 Missense_Mutation SNP G C3L-00009_T 83918 110208025 23589397 190 1982 SMNDC1 0 . GRCh38 10 110297644 110297644 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.348G>T p.= p.V116V ENST00000369603 4/6 221 201 20 248 248 0 strelka-varscan-mutect SMNDC1,synonymous_variant,p.=,ENST00000369603,NM_005871.3;SMNDC1,synonymous_variant,p.=,ENST00000369592,;SMNDC1,non_coding_transcript_exon_variant,,ENST00000471297,;SMNDC1,non_coding_transcript_exon_variant,,ENST00000460483,;SMNDC1,downstream_gene_variant,,ENST00000477763,; A ENST00000369603 Transcript synonymous_variant 552/4341 348/717 116/238 V gtG/gtT 1 -1 SMNDC1 HGNC HGNC:16900 protein_coding YES CCDS7565.1 ENSP00000358616 O75940 UPI000006D4F3 NM_005871.3 4/6 PROSITE_profiles:PS50304,hmmpanther:PTHR13681:SF24,hmmpanther:PTHR13681,Gene3D:2.30.30.140,Pfam_domain:PF06003,SMART_domains:SM00333,Superfamily_domains:SSF63748 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 110297644 110297644 C A 1 0 0 0 0 0 0 0 1 15120 813 29 2 2 SMNDC1 10 110297644 Silent SNP C C3L-00009_T 89619 110297644 23499778 191 1983 C10orf82 0 . GRCh38 10 116664948 116664948 + Splice_Site SNP C C T novel C3L-00009_T C3L-00009_N C C c.275-1G>A p.X92_splice ENST00000369210 80 75 5 112 112 0 strelka-varscan-mutect C10orf82,splice_acceptor_variant,,ENST00000369210,NM_144661.2;C10orf82,splice_acceptor_variant,,ENST00000588184,;C10orf82,non_coding_transcript_exon_variant,,ENST00000588224,;C10orf82,non_coding_transcript_exon_variant,,ENST00000467153,; T ENST00000369210 Transcript splice_acceptor_variant -/994 275/465 92/154 1 -1 C10orf82 HGNC HGNC:28500 protein_coding YES CCDS7596.1 ENSP00000358212 Q8WW14 UPI000006DC12 NM_144661.2 3/4 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -11.2368 1 1 1 1 0 T 5 4 6 116664948 116664948 C T 1 0 0 0 0 0 0 1 0 1771 927 32 3 3 C10orf82 10 116664948 Splice_Site SNP C C3L-00009_T 6367304 116664948 17132474 192 1984 SLC18A2 0 . GRCh38 10 117255342 117255342 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.766G>T p.Ala256Ser p.A256S ENST00000298472 7/16 298 262 36 427 427 0 strelka-varscan-mutect SLC18A2,missense_variant,p.Ala256Ser,ENST00000298472,NM_003054.4;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,; T ENST00000298472 Transcript missense_variant 909/3852 766/1545 256/514 A/S Gcc/Tcc 1 1 SLC18A2 HGNC HGNC:10935 protein_coding YES CCDS7599.1 ENSP00000298472 Q05940 UPI00001389DE NM_003054.4 tolerated(0.12) 7/16 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF8,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 117255342 117255342 G T 1 0 0 0 0 1 0 0 0 14691 1203 42 2 2 SLC18A2 10 117255342 Missense_Mutation SNP G C3L-00009_T 590394 117255342 16542080 193 1985 BAG3 0 . GRCh38 10 119677050 119677050 + Missense_Mutation SNP T T G novel C3L-00009_T C3L-00009_N T T c.1496T>G p.Ile499Ser p.I499S ENST00000369085 4/4 550 494 56 715 714 1 strelka-varscan-mutect BAG3,missense_variant,p.Ile499Ser,ENST00000369085,NM_004281.3;BAG3,downstream_gene_variant,,ENST00000450186,; G ENST00000369085 Transcript missense_variant 1802/2571 1496/1728 499/575 I/S aTt/aGt 1 1 BAG3 HGNC HGNC:939 protein_coding YES CCDS7615.1 ENSP00000358081 O95817 UPI0000000C7A NM_004281.3 tolerated(0.65) 4/4 hmmpanther:PTHR12329,hmmpanther:PTHR12329:SF12,Superfamily_domains:SSF63491 MODERATE 1 SNV 1 1 PASS rs1405717595 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 119677050 119677050 T G 1 0 0 0 0 1 0 0 0 1446 1493 52 5 5 BAG3 10 119677050 Missense_Mutation SNP T C3L-00009_T 2421708 119677050 14120372 194 1986 BTBD16 0 . GRCh38 10 122334917 122334917 + Nonsense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.1201G>T p.Gly401Ter p.G401* ENST00000260723 14/16 154 133 21 167 167 0 strelka-varscan-mutect BTBD16,stop_gained,p.Gly401Ter,ENST00000260723,NM_001318189.1,NM_144587.2;BTBD16,non_coding_transcript_exon_variant,,ENST00000495370,; T ENST00000260723 Transcript stop_gained 1452/1849 1201/1521 401/506 G/* Gga/Tga COSM4396444 1 1 BTBD16 HGNC HGNC:26340 protein_coding YES CCDS31301.1 ENSP00000260723 Q32M84 UPI00003CEFB9 NM_001318189.1,NM_144587.2 14/16 hmmpanther:PTHR23231,hmmpanther:PTHR23231:SF4 1 HIGH 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 6 122334917 122334917 G T 1 0 0 0 0 0 1 0 0 1715 1349 47 2 2 BTBD16 10 122334917 Nonsense_Mutation SNP G C3L-00009_T 2657867 122334917 11462505 195 1987 OR2AG1 0 . GRCh38 11 6785517 6785517 + Silent SNP C C G C3L-00009_T C3L-00009_N C C c.480C>G p.= p.T160T ENST00000307401 1/1 250 227 23 381 381 0 strelka-varscan-mutect OR2AG1,synonymous_variant,p.=,ENST00000307401,NM_001004489.2; G ENST00000307401 Transcript synonymous_variant 501/998 480/951 160/316 T acC/acG COSM237888 1 1 OR2AG1 HGNC HGNC:15142 protein_coding YES CCDS31414.1 ENSP00000307447 Q9H205 A0A126GVD0 UPI00000015AF NM_001004489.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF267,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS rs930003422 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 6785517 6785517 C G 1 0 0 0 0 0 0 0 1 11061 639 23 4 4 OR2AG1 11 6785517 Silent SNP C C3L-00009_T 6785517 128301105 196 1988 TUB 0 . GRCh38 11 8097351 8097351 + Missense_Mutation SNP C C T rs766908413 C3L-00009_T C3L-00009_N C C c.976C>T p.Arg326Trp p.R326W ENST00000305253 8/13 495 452 43 674 674 0 strelka-varscan-mutect TUB,missense_variant,p.Arg326Trp,ENST00000305253,NM_003320.4;TUB,missense_variant,p.Arg271Trp,ENST00000299506,NM_177972.2;TUB,missense_variant,p.Arg277Trp,ENST00000534099,; T ENST00000305253 Transcript missense_variant 1217/6420 976/1686 326/561 R/W Cgg/Tgg rs766908413 1 1 TUB HGNC HGNC:12406 protein_coding YES CCDS7786.1 ENSP00000305426 P50607 UPI000013EA27 NM_003320.4 deleterious(0) 8/13 Gene3D:3c5nA00,Pfam_domain:PF01167,hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF20,Superfamily_domains:SSF54518 MODERATE 1 SNV 1 1 PASS rs766908413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 8097351 8097351 C T 1 0 0 0 0 1 0 0 0 17252 875 31 1 1 TUB 11 8097351 Missense_Mutation SNP C C3L-00009_T 1311834 8097351 126989271 197 1989 DENND5A 0 . GRCh38 11 9203776 9203776 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.833A>T p.Glu278Val p.E278V ENST00000328194 4/23 332 293 39 474 473 1 strelka-varscan-mutect DENND5A,missense_variant,p.Glu278Val,ENST00000328194,NM_015213.3;DENND5A,missense_variant,p.Glu278Val,ENST00000530044,NM_001243254.1;DENND5A,missense_variant,p.Glu254Val,ENST00000526707,;DENND5A,non_coding_transcript_exon_variant,,ENST00000532696,;DENND5A,downstream_gene_variant,,ENST00000530780,; A ENST00000328194 Transcript missense_variant 1154/5031 833/3864 278/1287 E/V gAg/gTg 1 -1 DENND5A HGNC HGNC:19344 protein_coding YES CCDS31423.1 ENSP00000328524 Q6IQ26 UPI00001C1F29 NM_015213.3 deleterious(0) 4/23 PROSITE_profiles:PS50211,hmmpanther:PTHR10877:SF109,hmmpanther:PTHR10877,Pfam_domain:PF02141,SMART_domains:SM00799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 9203776 9203776 T A 1 0 0 0 0 1 0 0 0 4240 1551 54 4 4 DENND5A 11 9203776 Missense_Mutation SNP T C3L-00009_T 1106425 9203776 125882846 198 1990 SLC17A6 0 . GRCh38 11 22359453 22359453 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.499A>G p.Met167Val p.M167V ENST00000263160 4/12 136 120 16 196 196 0 strelka-varscan-mutect SLC17A6,missense_variant,p.Met167Val,ENST00000263160,NM_020346.2;CTD-2140G10.4,downstream_gene_variant,,ENST00000534543,;SLC17A6,non_coding_transcript_exon_variant,,ENST00000534115,; G ENST00000263160 Transcript missense_variant 936/3949 499/1749 167/582 M/V Atg/Gtg 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 deleterious(0.05) 4/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 22359453 22359453 A G 1 0 0 0 0 1 0 0 0 14686 449 16 5 5 SLC17A6 11 22359453 Missense_Mutation SNP A C3L-00009_T 13155677 22359453 112727169 199 1991 CHST1 0 . GRCh38 11 45649952 45649952 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.972G>T p.= p.L324L ENST00000308064 4/4 241 213 28 336 336 0 strelka-varscan-mutect CHST1,synonymous_variant,p.=,ENST00000308064,NM_003654.5;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,upstream_gene_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,; A ENST00000308064 Transcript synonymous_variant 1643/2718 972/1236 324/411 L ctG/ctT 1 -1 CHST1 HGNC HGNC:1969 protein_coding YES CCDS7913.1 ENSP00000309270 O43916 UPI0000073EA0 NM_003654.5 4/4 hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF36,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs1290815465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 45649952 45649952 C A 1 0 0 0 0 0 0 0 1 3157 581 21 2 2 CHST1 11 45649952 Silent SNP C C3L-00009_T 23290499 45649952 89436670 200 1992 FOLH1 0 . GRCh38 11 49156760 49156760 + Missense_Mutation SNP C C G C3L-00009_T C3L-00009_N C C c.1580G>C p.Arg527Pro p.R527P ENST00000256999 15/19 170 159 11 229 229 0 varscan-mutect FOLH1,missense_variant,p.Arg512Pro,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Arg527Pro,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Arg527Pro,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Arg219Pro,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Arg512Pro,ENST00000533034,NM_001193472.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,;FOLH1,upstream_gene_variant,,ENST00000532018,; G ENST00000256999 Transcript missense_variant 1841/2635 1580/2253 527/750 R/P cGa/cCa COSM1321653 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0.01) 15/19 Gene3D:3.40.630.10,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF53187 1 MODERATE 1 SNV 1 1 1 PASS rs1262353651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 49156760 49156760 C G 1 0 0 0 0 1 0 0 0 5840 884 31 4 4 FOLH1 11 49156760 Missense_Mutation SNP C C3L-00009_T 3506808 49156760 85929862 201 1993 OR5T3 0 . GRCh38 11 56252958 56252958 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.759G>T p.Leu253Phe p.L253F ENST00000303059 1/1 200 176 24 313 313 0 strelka-varscan-mutect OR5T3,missense_variant,p.Leu253Phe,ENST00000303059,NM_001004747.1; T ENST00000303059 Transcript missense_variant 759/1023 759/1023 253/340 L/F ttG/ttT 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 56252958 56252958 G T 1 0 0 0 0 1 0 0 0 11251 1368 48 2 2 OR5T3 11 56252958 Missense_Mutation SNP G C3L-00009_T 7096198 56252958 78833664 202 1994 OR5M11 0 . GRCh38 11 56543149 56543149 + Missense_Mutation SNP C C A rs772024624 C3L-00009_T C3L-00009_N C C c.109G>T p.Val37Phe p.V37F ENST00000528616 1/1 209 190 19 310 309 1 strelka-varscan-mutect OR5M11,missense_variant,p.Val37Phe,ENST00000528616,NM_001005245.1; A ENST00000528616 Transcript missense_variant 109/918 109/918 37/305 V/F Gtc/Ttc rs772024624,COSM1354670 1 -1 OR5M11 HGNC HGNC:15291 protein_coding YES CCDS53629.1 ENSP00000432417 Q96RB7 A0A126GVL9 UPI00000405CF NM_001005245.1 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF97,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs772024624 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 56543149 56543149 C A 1 0 0 0 0 1 0 0 0 11243 536 19 1 1 OR5M11 11 56543149 Missense_Mutation SNP C C3L-00009_T 290191 56543149 78543473 203 1995 OR5B2 0 . GRCh38 11 58422480 58422480 + Missense_Mutation SNP C C A rs140988128 C3L-00009_T C3L-00009_N C C c.782G>T p.Ser261Ile p.S261I ENST00000302581 1/1 273 233 40 341 341 0 strelka-varscan-mutect OR5B2,missense_variant,p.Ser261Ile,ENST00000302581,NM_001005566.2; A ENST00000302581 Transcript missense_variant 834/1049 782/930 261/309 S/I aGc/aTc rs140988128 1 -1 OR5B2 HGNC HGNC:8323 protein_coding YES CCDS31550.1 ENSP00000303076 Q96R09 UPI000004B227 NM_001005566.2 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF3,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs140988128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 58422480 58422480 C A 1 0 0 0 0 1 0 0 0 11221 797 28 2 2 OR5B2 11 58422480 Missense_Mutation SNP C C3L-00009_T 1879331 58422480 76664142 204 1996 LPXN 0 . GRCh38 11 58570571 58570571 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.171C>T p.= p.N57N ENST00000528954 2/9 110 104 6 104 104 0 strelka-varscan-mutect LPXN,missense_variant,p.Thr48Ile,ENST00000528489,NM_001307951.1;LPXN,synonymous_variant,p.=,ENST00000528954,NM_001143995.1;LPXN,synonymous_variant,p.=,ENST00000395074,NM_004811.2;LPXN,synonymous_variant,p.=,ENST00000530561,;LPXN,non_coding_transcript_exon_variant,,ENST00000529915,; A ENST00000528954 Transcript synonymous_variant 291/1879 171/1176 57/391 N aaC/aaT 1 -1 LPXN HGNC HGNC:14061 protein_coding YES CCDS53635.1 ENSP00000431284 O60711 UPI00001FA7B3 NM_001143995.1 2/9 PIRSF_domain:PIRSF037881,hmmpanther:PTHR24216,hmmpanther:PTHR24216:SF23 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 58570571 58570571 G A 1 0 0 0 0 0 0 0 1 8823 1368 48 3 3 LPXN 11 58570571 Silent SNP G C3L-00009_T 148091 58570571 76516051 205 1997 FAT3 0 . GRCh38 11 92801324 92801324 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.7861C>A p.Leu2621Ile p.L2621I ENST00000525166 9/27 129 111 18 182 182 0 strelka-varscan-mutect FAT3,missense_variant,p.Leu2771Ile,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Leu2621Ile,ENST00000525166,; A ENST00000525166 Transcript missense_variant 7883/18699 7861/13320 2621/4439 L/I Ctt/Att 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.03) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 6 92801324 92801324 C A 1 0 0 0 0 1 0 0 0 5551 681 24 2 2 FAT3 11 92801324 Missense_Mutation SNP C C3L-00009_T 34230753 92801324 42285298 206 1998 TRPC6 0 . GRCh38 11 101473593 101473593 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.1925T>C p.Ile642Thr p.I642T ENST00000344327 7/13 237 210 27 310 310 0 strelka-varscan-mutect TRPC6,missense_variant,p.Ile642Thr,ENST00000344327,NM_004621.5;TRPC6,missense_variant,p.Ile564Thr,ENST00000532133,;TRPC6,missense_variant,p.Ile587Thr,ENST00000360497,;TRPC6,missense_variant,p.Ile526Thr,ENST00000348423,; G ENST00000344327 Transcript missense_variant 2350/4612 1925/2796 642/931 I/T aTt/aCt 1 -1 TRPC6 HGNC HGNC:12338 protein_coding YES CCDS8311.1 ENSP00000340913 Q9Y210 UPI00001374BA NM_004621.5 tolerated(0.11) 7/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 101473593 101473593 A G 1 0 0 0 0 1 0 0 0 17089 101 4 5 5 TRPC6 11 101473593 Missense_Mutation SNP A C3L-00009_T 8672269 101473593 33613029 207 1999 OAF 0 . GRCh38 11 120211375 120211375 + Silent SNP G G T novel C3L-00009_T C3L-00009_N G G c.96G>T p.= p.L32L ENST00000328965 1/4 126 100 26 108 108 0 strelka-varscan-mutect OAF,synonymous_variant,p.=,ENST00000328965,NM_178507.2;OAF,5_prime_UTR_variant,,ENST00000531220,;OAF,upstream_gene_variant,,ENST00000534735,; T ENST00000328965 Transcript synonymous_variant 609/2525 96/822 32/273 L ctG/ctT 1 1 OAF HGNC HGNC:28752 protein_coding YES CCDS8430.1 ENSP00000332613 Q86UD1 UPI000000DC44 NM_178507.2 1/4 Pfam_domain:PF14941,hmmpanther:PTHR13423,hmmpanther:PTHR13423:SF2,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999789 1 1 1 0 T 2 4 6 120211375 120211375 G T 1 0 0 0 0 0 0 0 1 10876 1306 46 2 2 OAF 11 120211375 Silent SNP G C3L-00009_T 18737782 120211375 14875247 208 2000 UBASH3B 0 . GRCh38 11 122796276 122796276 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.1234G>C p.Gly412Arg p.G412R ENST00000284273 8/14 77 65 12 92 92 0 strelka-varscan-mutect UBASH3B,missense_variant,p.Gly412Arg,ENST00000284273,NM_032873.4;UBASH3B,splice_region_variant,,ENST00000530578,;UBASH3B,downstream_gene_variant,,ENST00000526493,; C ENST00000284273 Transcript missense_variant,splice_region_variant 1609/6912 1234/1950 412/649 G/R Ggc/Cgc 1 1 UBASH3B HGNC HGNC:29884 protein_coding YES CCDS31694.1 ENSP00000284273 Q8TF42 UPI0000047471 NM_032873.4 deleterious(0.02) 8/14 hmmpanther:PTHR16469,hmmpanther:PTHR16469:SF29,Gene3D:3.40.50.1240 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999941 1 1 1 0 C 3 2 6 122796276 122796276 G C 1 0 0 0 0 1 0 0 0 17362 1014 35 4 4 UBASH3B 11 122796276 Missense_Mutation SNP G C3L-00009_T 2584901 122796276 12290346 209 2001 ARHGAP32 0 . GRCh38 11 128972707 128972707 + Nonsense_Mutation SNP C C A rs768865360 C3L-00009_T C3L-00009_N C C c.3757G>T p.Glu1253Ter p.E1253* ENST00000310343 21/22 140 101 39 197 196 1 strelka-varscan-mutect ARHGAP32,stop_gained,p.Glu1253Ter,ENST00000310343,NM_001142685.1;ARHGAP32,stop_gained,p.Glu904Ter,ENST00000392657,NM_014715.3;ARHGAP32,stop_gained,p.Glu904Ter,ENST00000527272,;ARHGAP32,3_prime_UTR_variant,,ENST00000524655,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000526162,; A ENST00000310343 Transcript stop_gained 3757/10111 3757/6264 1253/2087 E/* Gaa/Taa rs768865360,COSM173337,COSM173338 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 21/22 hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs768865360 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 128972707 128972707 C A 1 0 0 0 0 0 1 0 0 1006 893 31 1 1 ARHGAP32 11 128972707 Nonsense_Mutation SNP C C3L-00009_T 6176431 128972707 6113915 210 2002 ATN1 0 . GRCh38 12 6935832 6935832 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.565G>T p.Val189Leu p.V189L ENST00000356654 5/10 121 108 13 134 134 0 strelka-varscan-mutect ATN1,missense_variant,p.Val189Leu,ENST00000356654,NM_001007026.1;ATN1,missense_variant,p.Val189Leu,ENST00000396684,NM_001940.3;ATN1,upstream_gene_variant,,ENST00000537488,;ATN1,upstream_gene_variant,,ENST00000541029,; T ENST00000356654 Transcript missense_variant 802/4351 565/3573 189/1190 V/L Gtg/Ttg 1 1 ATN1 HGNC HGNC:3033 protein_coding YES CCDS31734.1 ENSP00000349076 P54259 UPI000006F554 NM_001007026.1 tolerated_low_confidence(0.11) 5/10 Pfam_domain:PF03154 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 6935832 6935832 G T 1 0 0 0 0 1 0 0 0 1263 1377 48 2 2 ATN1 12 6935832 Missense_Mutation SNP G C3L-00009_T 6935832 126339477 211 2003 YBX3 0 . GRCh38 12 10715731 10715731 + Missense_Mutation SNP C C A C3L-00009_T C3L-00009_N C C c.413G>T p.Gly138Val p.G138V ENST00000228251 4/10 405 368 37 494 494 0 strelka-varscan-mutect YBX3,missense_variant,p.Gly138Val,ENST00000228251,NM_003651.4;YBX3,missense_variant,p.Gly138Val,ENST00000279550,NM_001145426.1;YBX3,missense_variant,p.Gly30Val,ENST00000544622,;YBX3,non_coding_transcript_exon_variant,,ENST00000539204,;YBX3,non_coding_transcript_exon_variant,,ENST00000546298,;YBX3,non_coding_transcript_exon_variant,,ENST00000544501,;YBX3,downstream_gene_variant,,ENST00000540747,;YBX3,non_coding_transcript_exon_variant,,ENST00000540447,;YBX3,non_coding_transcript_exon_variant,,ENST00000542002,;YBX3,non_coding_transcript_exon_variant,,ENST00000542641,;YBX3,downstream_gene_variant,,ENST00000536107,; A ENST00000228251 Transcript missense_variant 614/1796 413/1119 138/372 G/V gGa/gTa COSM94104 1 -1 YBX3 HGNC HGNC:2428 protein_coding YES CCDS8630.1 ENSP00000228251 P16989 A0A024RAQ1 UPI000013DBD6 NM_003651.4 deleterious(0) 4/10 Gene3D:2.40.50.140,Pfam_domain:PF00313,Prints_domain:PR00050,hmmpanther:PTHR11544,SMART_domains:SM00357,Superfamily_domains:SSF50249 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 10715731 10715731 C A 1 0 0 0 0 1 0 0 0 18032 855 30 2 2 YBX3 12 10715731 Missense_Mutation SNP C C3L-00009_T 3779899 10715731 122559578 212 2004 GYS2 0 . GRCh38 12 21580512 21580512 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.133T>C p.Tyr45His p.Y45H ENST00000261195 2/16 401 326 75 476 476 0 strelka-varscan-mutect GYS2,missense_variant,p.Tyr45His,ENST00000261195,NM_021957.3; G ENST00000261195 Transcript missense_variant 388/3132 133/2112 45/703 Y/H Tat/Cat 1 -1 GYS2 HGNC HGNC:4707 protein_coding YES CCDS8690.1 ENSP00000261195 P54840 UPI000013D13D NM_021957.3 tolerated(0.06) 2/16 hmmpanther:PTHR10176:SF1,hmmpanther:PTHR10176,Pfam_domain:PF05693 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 21580512 21580512 A G 1 0 0 0 0 1 0 0 0 6795 420 15 5 5 GYS2 12 21580512 Missense_Mutation SNP A C3L-00009_T 10864781 21580512 111694797 213 2005 SOX5 0 . GRCh38 12 23604488 23604488 + Missense_Mutation SNP C C A C3L-00009_T C3L-00009_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000451604 9/15 233 187 46 291 291 0 strelka-varscan-mutect SOX5,missense_variant,p.Gly342Trp,ENST00000546136,NM_152989.3;SOX5,missense_variant,p.Gly355Trp,ENST00000451604,NM_006940.4;SOX5,missense_variant,p.Gly342Trp,ENST00000381381,;SOX5,missense_variant,p.Gly320Trp,ENST00000537393,;SOX5,missense_variant,p.Gly345Trp,ENST00000545921,NM_001261415.1;SOX5,missense_variant,p.Gly342Trp,ENST00000541536,NM_001261414.1;SOX5,non_coding_transcript_exon_variant,,ENST00000535530,;SOX5,non_coding_transcript_exon_variant,,ENST00000536629,;SOX5,non_coding_transcript_exon_variant,,ENST00000542241,;SOX5,missense_variant,p.Gly345Trp,ENST00000367206,;SOX5,non_coding_transcript_exon_variant,,ENST00000536911,; A ENST00000451604 Transcript missense_variant 1165/4261 1063/2292 355/763 G/W Ggg/Tgg COSM547555 1 -1 SOX5 HGNC HGNC:11201 protein_coding YES CCDS8699.1 ENSP00000398273 P35711 A0A024RB06 UPI000007405E NM_006940.4 deleterious(0) 9/15 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF30 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 23604488 23604488 C A 1 0 0 0 0 1 0 0 0 15280 681 24 2 2 SOX5 12 23604488 Missense_Mutation SNP C C3L-00009_T 2023976 23604488 109670821 214 2006 TMTC1 0 . GRCh38 12 29755792 29755792 + Missense_Mutation SNP C C A rs201140526 C3L-00009_T C3L-00009_N C C c.648G>T p.Met216Ile p.M216I ENST00000539277 4/18 284 235 49 309 309 0 strelka-varscan-mutect TMTC1,missense_variant,p.Met108Ile,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Met216Ile,ENST00000551659,;TMTC1,missense_variant,p.Met216Ile,ENST00000552618,;TMTC1,missense_variant,p.Met216Ile,ENST00000539277,NM_001193451.1;TMTC1,non_coding_transcript_exon_variant,,ENST00000553189,; A ENST00000539277 Transcript missense_variant 707/2758 648/2649 216/882 M/I atG/atT rs201140526 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 deleterious(0.04) 4/18 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs201140526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 29755792 29755792 C A 1 0 0 0 0 1 0 0 0 16734 710 25 2 2 TMTC1 12 29755792 Missense_Mutation SNP C C3L-00009_T 6151304 29755792 103519517 215 2007 OVOS2 0 . GRCh38 12 31200503 31200503 + Missense_Mutation SNP C C G rs748445015 C3L-00009_T C3L-00009_N C C c.293G>C p.Arg98Thr p.R98T ENST00000632817 3/34 121 104 17 120 120 0 strelka-varscan-mutect OVOS2,missense_variant,p.Arg98Thr,ENST00000398963,;OVOS2,missense_variant,p.Arg98Thr,ENST00000632817,; G ENST00000632817 Transcript missense_variant 293/4299 293/4299 98/1432 R/T aGg/aCg rs748445015 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 deleterious(0.04) 3/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 MODERATE 1 SNV 5 1 PASS rs748445015 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 31200503 31200503 C G 1 0 0 0 0 1 0 0 0 11399 681 24 4 4 OVOS2 12 31200503 Missense_Mutation SNP C C3L-00009_T 1444711 31200503 102074806 216 2008 PKP2 0 . GRCh38 12 32841139 32841139 + Missense_Mutation SNP G G A rs146882581 C3L-00009_T C3L-00009_N G G c.1577C>T p.Thr526Met p.T526M ENST00000070846 7/14 346 326 20 312 312 0 strelka-varscan-mutect PKP2,missense_variant,p.Thr482Met,ENST00000340811,NM_001005242.2;PKP2,missense_variant,p.Thr526Met,ENST00000070846,NM_004572.3; A ENST00000070846 Transcript missense_variant 1602/4241 1577/2646 526/881 T/M aCg/aTg rs146882581,CM113820 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 tolerated(0.1) 7/14 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Superfamily_domains:SSF48371 benign,likely_benign MODERATE 1 SNV 1 1,1 1 PASS rs146882581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 32841139 32841139 G A 1 0 0 0 0 1 0 0 0 12081 1145 40 1 1 PKP2 12 32841139 Missense_Mutation SNP G C3L-00009_T 1640636 32841139 100434170 217 2009 SYT10 0 . GRCh38 12 33379957 33379957 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.1375G>C p.Gly459Arg p.G459R ENST00000228567 6/7 199 170 29 231 231 0 strelka-varscan-mutect SYT10,missense_variant,p.Gly459Arg,ENST00000228567,NM_198992.3;SYT10,3_prime_UTR_variant,,ENST00000539102,; G ENST00000228567 Transcript missense_variant 1672/4461 1375/1572 459/523 G/R Gga/Cga 1 -1 SYT10 HGNC HGNC:19266 protein_coding YES CCDS8732.1 ENSP00000228567 Q6XYQ8 UPI0000052B30 NM_198992.3 deleterious(0.01) 6/7 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 6 33379957 33379957 C G 1 0 0 0 0 1 0 0 0 15860 695 24 4 4 SYT10 12 33379957 Missense_Mutation SNP C C3L-00009_T 538818 33379957 99895352 218 2010 LRRK2 0 . GRCh38 12 40367729 40367729 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.7548A>T p.Glu2516Asp p.E2516D ENST00000298910 51/51 187 143 44 202 202 0 strelka-varscan-mutect LRRK2,missense_variant,p.Glu2516Asp,ENST00000298910,NM_198578.3;LRRK2,missense_variant,p.Glu443Asp,ENST00000636518,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; T ENST00000298910 Transcript missense_variant 7606/9158 7548/7584 2516/2527 E/D gaA/gaT 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 deleterious(0) 51/51 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 40367729 40367729 A T 1 0 0 0 0 1 0 0 0 8939 98 4 4 4 LRRK2 12 40367729 Missense_Mutation SNP A C3L-00009_T 6987772 40367729 92907580 219 2011 ADAMTS20 0 . GRCh38 12 43376600 43376600 + Frame_Shift_Del DEL G G - novel C3L-00009_T C3L-00009_N G G c.5049delC p.Lys1684AsnfsTer10 p.K1684Nfs*10 ENST00000389420 33/39 119 101 18 148 148 0 sindel-varindel-pindel ADAMTS20,frameshift_variant,p.Lys1684AsnfsTer10,ENST00000389420,NM_025003.3; - ENST00000389420 Transcript frameshift_variant 5049/6076 5049/5733 1683/1910 T/X acC/ac 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 33/39 PROSITE_profiles:PS50092,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 HIGH 1 deletion 1 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999197 1 1 1 0 - 7 5 6 43376600 43376600 G - 1 0 1 0 1 0 0 0 0 310 1335 47 0 0 ADAMTS20 12 43376600 Frame_Shift_Del DEL G C3L-00009_T 3008871 43376600 89898709 220 2012 ADAMTS20 0 . GRCh38 12 43399187 43399187 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.4331G>C p.Cys1444Ser p.C1444S ENST00000389420 29/39 128 110 18 154 154 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Cys1444Ser,ENST00000389420,NM_025003.3; G ENST00000389420 Transcript missense_variant 4331/6076 4331/5733 1444/1910 C/S tGc/tCc 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0) 29/39 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 6 43399187 43399187 C G 1 0 0 0 0 1 0 0 0 310 710 25 4 4 ADAMTS20 12 43399187 Missense_Mutation SNP C C3L-00009_T 22587 43399187 89876122 221 2013 KRT6B 0 . GRCh38 12 52449523 52449523 + Nonsense_Mutation SNP A A C rs367709654 C3L-00009_T C3L-00009_N A A c.1023T>G p.Tyr341Ter p.Y341* ENST00000252252 5/9 889 777 112 1024 1023 1 strelka-varscan-mutect KRT6B,stop_gained,p.Tyr341Ter,ENST00000252252,NM_005555.3; C ENST00000252252 Transcript stop_gained 1071/2282 1023/1695 341/564 Y/* taT/taG rs367709654 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 5/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Pfam_domain:PF00038,SMART_domains:SM01391 HIGH 1 SNV 1 1 PASS rs4079521 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 6 52449523 52449523 A C 1 0 0 0 0 0 1 0 0 8363 224 8 5 5 KRT6B 12 52449523 Nonsense_Mutation SNP A C3L-00009_T 9050336 52449523 80825786 222 2014 EIF4B 0 . GRCh38 12 53039278 53039278 + Missense_Mutation SNP A A T rs576098700 C3L-00009_T C3L-00009_N A A c.1632A>T p.Gln544His p.Q544H ENST00000420463 13/15 185 161 24 193 193 0 strelka-varscan-mutect EIF4B,missense_variant,p.Gln539His,ENST00000262056,NM_001417.5;EIF4B,missense_variant,p.Gln500His,ENST00000416762,;EIF4B,missense_variant,p.Gln544His,ENST00000420463,NM_001300821.1;EIF4B,downstream_gene_variant,,ENST00000549481,;RP11-983P16.4,non_coding_transcript_exon_variant,,ENST00000546566,;RP11-983P16.4,intron_variant,,ENST00000552905,;RP11-983P16.4,downstream_gene_variant,,ENST00000546793,;RP11-983P16.4,downstream_gene_variant,,ENST00000550601,;RP11-983P16.4,downstream_gene_variant,,ENST00000607643,;RP11-983P16.4,downstream_gene_variant,,ENST00000546767,;EIF4B,non_coding_transcript_exon_variant,,ENST00000549592,;EIF4B,downstream_gene_variant,,ENST00000550704,;EIF4B,downstream_gene_variant,,ENST00000553209,; T ENST00000420463 Transcript missense_variant 1660/1936 1632/1851 544/616 Q/H caA/caT rs576098700,COSM4575532 1 1 EIF4B HGNC HGNC:3285 protein_coding YES CCDS73474.1 ENSP00000388806 E7EX17 UPI0001AE6B15 NM_001300821.1 tolerated_low_confidence(0.06) 13/15 hmmpanther:PTHR23236:SF2,hmmpanther:PTHR23236 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs576098700 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 53039278 53039278 A T 1 0 0 0 0 1 0 0 0 4861 11 1 4 4 EIF4B 12 53039278 Missense_Mutation SNP A C3L-00009_T 589755 53039278 80236031 223 2015 MDM1 0 . GRCh38 12 68321619 68321619 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.811A>T p.Ile271Leu p.I271L ENST00000303145 6/14 123 99 24 133 133 0 strelka-varscan-mutect MDM1,missense_variant,p.Ile271Leu,ENST00000303145,NM_017440.4;MDM1,missense_variant,p.Ile226Leu,ENST00000411698,NM_001205028.1;MDM1,missense_variant,p.Ile266Leu,ENST00000541686,;MDM1,downstream_gene_variant,,ENST00000393543,NM_001205029.1;MDM1,downstream_gene_variant,,ENST00000430606,NM_020128.2;MDM1,non_coding_transcript_exon_variant,,ENST00000540476,;MDM1,downstream_gene_variant,,ENST00000545724,;MDM1,3_prime_UTR_variant,,ENST00000540418,;MDM1,non_coding_transcript_exon_variant,,ENST00000538454,;MDM1,non_coding_transcript_exon_variant,,ENST00000536997,; A ENST00000303145 Transcript missense_variant 898/2918 811/2145 271/714 I/L Ata/Tta 1 -1 MDM1 HGNC HGNC:29917 protein_coding YES CCDS8983.1 ENSP00000302537 Q8TC05 UPI00001FC70C NM_017440.4 tolerated(0.3) 6/14 hmmpanther:PTHR32078:SF1,hmmpanther:PTHR32078,Pfam_domain:PF15501 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 68321619 68321619 T A 1 0 0 0 0 1 0 0 0 9350 1493 52 4 4 MDM1 12 68321619 Missense_Mutation SNP T C3L-00009_T 15282341 68321619 64953690 224 2016 TPH2 0 . GRCh38 12 72031557 72031557 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.1335A>G p.= p.V445V ENST00000333850 11/11 297 268 29 396 396 0 strelka-varscan-mutect TPH2,synonymous_variant,p.=,ENST00000333850,NM_173353.3;TPH2,intron_variant,,ENST00000550403,;TPH2,intron_variant,,ENST00000547348,;TPH2,intron_variant,,ENST00000547278,;TPH2,intron_variant,,ENST00000551074,; G ENST00000333850 Transcript synonymous_variant 1476/2360 1335/1473 445/490 V gtA/gtG 1 1 TPH2 HGNC HGNC:20692 protein_coding YES CCDS31859.1 ENSP00000329093 Q8IWU9 UPI000007446F NM_173353.3 11/11 Gene3D:1.10.800.10,Pfam_domain:PF00351,PIRSF_domain:PIRSF000336,Prints_domain:PR00372,PROSITE_profiles:PS51410,hmmpanther:PTHR11473,hmmpanther:PTHR11473:SF16,Superfamily_domains:SSF56534,TIGRFAM_domain:TIGR01270 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 72031557 72031557 A G 1 0 0 0 0 0 0 0 1 16883 436 16 5 5 TPH2 12 72031557 Silent SNP A C3L-00009_T 3709938 72031557 61243752 225 2017 ANKS1B 0 . GRCh38 12 98832045 98832045 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.2870G>T p.Arg957Leu p.R957L ENST00000547776 18/26 339 273 66 358 358 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Arg957Leu,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Arg183Leu,ENST00000550693,NM_001204069.1;ANKS1B,missense_variant,p.Arg183Leu,ENST00000549493,NM_181670.3;ANKS1B,missense_variant,p.Arg533Leu,ENST00000547010,;ANKS1B,missense_variant,p.Arg183Leu,ENST00000549558,NM_020140.3;ANKS1B,missense_variant,p.Arg229Leu,ENST00000550778,;ANKS1B,missense_variant,p.Arg152Leu,ENST00000547446,NM_001204067.1;ANKS1B,missense_variant,p.Arg183Leu,ENST00000546960,NM_001204068.1;ANKS1B,missense_variant,p.Arg183Leu,ENST00000546568,NM_001204070.1;ANKS1B,5_prime_UTR_variant,,ENST00000341752,NM_001204081.1;ANKS1B,5_prime_UTR_variant,,ENST00000333732,NM_001204079.1,NM_001204080.1,NM_001204065.1;ANKS1B,5_prime_UTR_variant,,ENST00000546364,;ANKS1B,5_prime_UTR_variant,,ENST00000549797,;ANKS1B,5_prime_UTR_variant,,ENST00000551560,;ANKS1B,5_prime_UTR_variant,,ENST00000552407,;ANKS1B,5_prime_UTR_variant,,ENST00000552748,;ANKS1B,5_prime_UTR_variant,,ENST00000551613,;ANKS1B,5_prime_UTR_variant,,ENST00000548447,;ANKS1B,intron_variant,,ENST00000549025,NM_001204066.1;ANKS1B,non_coding_transcript_exon_variant,,ENST00000551830,;ANKS1B,5_prime_UTR_variant,,ENST00000547362,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000552245,; A ENST00000547776 Transcript missense_variant 2870/3885 2870/3747 957/1248 R/L cGg/cTg 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 deleterious(0.05) 18/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 98832045 98832045 C A 1 0 0 0 0 1 0 0 0 795 652 23 1 1 ANKS1B 12 98832045 Missense_Mutation SNP C C3L-00009_T 26800488 98832045 34443264 226 2018 MPHOSPH9 0 . GRCh38 12 123218410 123218410 + Frame_Shift_Del DEL C C - novel C3L-00009_T C3L-00009_N C C c.962delG p.Gly321GlufsTer44 p.G321Efs*44 ENST00000606320 6/24 190 163 27 195 195 0 sindel-varindel-pindel MPHOSPH9,frameshift_variant,p.Gly321GlufsTer44,ENST00000606320,NM_022782.3;MPHOSPH9,frameshift_variant,p.Gly291GlufsTer44,ENST00000541076,;MPHOSPH9,frameshift_variant,p.Gly178GlufsTer44,ENST00000539336,;MPHOSPH9,downstream_gene_variant,,ENST00000541437,;MPHOSPH9,downstream_gene_variant,,ENST00000537854,;MPHOSPH9,downstream_gene_variant,,ENST00000539639,;MPHOSPH9,downstream_gene_variant,,ENST00000538169,;MPHOSPH9,frameshift_variant,p.Gly24GlufsTer44,ENST00000539024,;MPHOSPH9,frameshift_variant,p.Gly189GlufsTer44,ENST00000302373,;MPHOSPH9,3_prime_UTR_variant,,ENST00000545556,;MPHOSPH9,downstream_gene_variant,,ENST00000535049,; - ENST00000606320 Transcript frameshift_variant 1169/6351 962/3552 321/1183 G/X gGa/ga 1 -1 MPHOSPH9 HGNC HGNC:7215 protein_coding YES CCDS9243.2 ENSP00000475489 Q99550 UPI00001FB90F NM_022782.3 6/24 hmmpanther:PTHR14926,hmmpanther:PTHR14926:SF1 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 6 123218410 123218410 C - 1 0 1 0 1 0 0 0 0 9693 855 30 0 0 MPHOSPH9 12 123218410 Frame_Shift_Del DEL C C3L-00009_T 24386365 123218410 10056899 227 2019 TMED2 0 . GRCh38 12 123584692 123584692 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.56C>T p.Ser19Leu p.S19L ENST00000262225 1/4 194 170 24 271 271 0 strelka-varscan-mutect TMED2,missense_variant,p.Ser19Leu,ENST00000262225,NM_006815.3;TMED2,missense_variant,p.Ser19Leu,ENST00000438031,;TMED2,upstream_gene_variant,,ENST00000509052,;RP11-486O12.2,non_coding_transcript_exon_variant,,ENST00000498967,;TMED2,non_coding_transcript_exon_variant,,ENST00000543425,;TMED2,non_coding_transcript_exon_variant,,ENST00000544188,; T ENST00000262225 Transcript missense_variant 162/2560 56/606 19/201 S/L tCg/tTg 1 1 TMED2 HGNC HGNC:16996 protein_coding YES CCDS9250.1 ENSP00000262225 Q15363 Q6FHT8 UPI0000001296 NM_006815.3 tolerated(0.53) 1/4 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22811,hmmpanther:PTHR22811:SF53 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 123584692 123584692 C T 1 0 0 0 0 1 0 0 0 16449 893 31 1 1 TMED2 12 123584692 Missense_Mutation SNP C C3L-00009_T 366282 123584692 9690617 228 2020 TCTN2 0 . GRCh38 12 123707002 123707002 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.1913C>T p.Thr638Ile p.T638I ENST00000303372 17/18 361 320 41 465 465 0 strelka-varscan-mutect TCTN2,missense_variant,p.Thr638Ile,ENST00000303372,NM_024809.4;TCTN2,missense_variant,p.Thr637Ile,ENST00000426174,NM_001143850.2;RP11-338K17.8,downstream_gene_variant,,ENST00000538837,;TCTN2,non_coding_transcript_exon_variant,,ENST00000543998,; T ENST00000303372 Transcript missense_variant 2041/2912 1913/2094 638/697 T/I aCa/aTa 1 1 TCTN2 HGNC HGNC:25774 protein_coding YES CCDS9253.1 ENSP00000304941 Q96GX1 UPI0000038A56 NM_024809.4 deleterious(0) 17/18 hmmpanther:PTHR14611,hmmpanther:PTHR14611:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 123707002 123707002 C T 1 0 0 0 0 1 0 0 0 16131 478 17 3 3 TCTN2 12 123707002 Missense_Mutation SNP C C3L-00009_T 122310 123707002 9568307 229 2021 TMEM132D 0 . GRCh38 12 129074239 129074239 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.2936A>T p.Asn979Ile p.N979I ENST00000422113 9/9 215 193 22 324 324 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Asn979Ile,ENST00000422113,NM_133448.2;TMEM132D,missense_variant,p.Asn517Ile,ENST00000389441,; A ENST00000422113 Transcript missense_variant 3263/5776 2936/3300 979/1099 N/I aAc/aTc 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 deleterious(0.01) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS rs771741034 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 129074239 129074239 T A 1 0 0 0 0 1 0 0 0 16492 1725 60 4 4 TMEM132D 12 129074239 Missense_Mutation SNP T C3L-00009_T 5367237 129074239 4201070 230 2022 ANHX 0 . GRCh38 12 133234111 133234111 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.246G>T p.= p.L82L ENST00000545940 1/8 179 166 13 230 229 1 strelka-varscan-mutect ANHX,synonymous_variant,p.=,ENST00000545940,;ANHX,synonymous_variant,p.=,ENST00000419717,NM_001191054.1;RNU6-717P,downstream_gene_variant,,ENST00000459076,;Y_RNA,upstream_gene_variant,,ENST00000459107,; A ENST00000545940 Transcript synonymous_variant 1985/3452 246/1140 82/379 L ctG/ctT 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 1/8 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34,Pfam_domain:PF16878 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 133234111 133234111 C A 1 0 0 0 0 0 0 0 1 719 608 21 2 2 ANHX 12 133234111 Silent SNP C C3L-00009_T 4159872 133234111 41198 231 2023 FRY 0 . GRCh38 13 32210987 32210987 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.4544C>A p.Pro1515His p.P1515H ENST00000542859 34/61 184 173 11 299 299 0 strelka-varscan-mutect FRY,missense_variant,p.Pro1515His,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Pro1514His,ENST00000380250,; A ENST00000542859 Transcript missense_variant 5040/13200 4544/9042 1515/3013 P/H cCc/cAc 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0) 34/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 32210987 32210987 C A 1 0 0 0 0 1 0 0 0 5935 623 22 2 2 FRY 13 32210987 Missense_Mutation SNP C C3L-00009_T 32210987 82153341 232 2024 KLHL1 0 . GRCh38 13 69740427 69740427 + Missense_Mutation SNP C C G rs748882149 C3L-00009_T C3L-00009_N C C c.1769G>C p.Arg590Pro p.R590P ENST00000377844 8/11 110 96 14 173 173 0 strelka-varscan-mutect KLHL1,missense_variant,p.Arg590Pro,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Arg529Pro,ENST00000545028,NM_001286725.1; G ENST00000377844 Transcript missense_variant 2529/4115 1769/2247 590/748 R/P cGg/cCg rs748882149,COSM3469504,COSM393237 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 deleterious(0) 8/11 hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412,Pfam_domain:PF01344,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748882149 . 0 205 3 2 0 0 0 0 -19.99389 0.9999911 1 1 1 0 G 3 3 6 69740427 69740427 C G 1 0 0 0 0 1 0 0 0 8229 652 23 4 4 KLHL1 13 69740427 Missense_Mutation SNP C C3L-00009_T 37529440 69740427 44623901 233 2025 KLF12 0 . GRCh38 13 73846003 73846003 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.494A>G p.His165Arg p.H165R ENST00000377669 3/7 158 137 21 257 257 0 strelka-varscan-mutect KLF12,missense_variant,p.His165Arg,ENST00000377669,NM_007249.4;RP11-157H4.1,upstream_gene_variant,,ENST00000625150,;KLF12,non_coding_transcript_exon_variant,,ENST00000472022,; C ENST00000377669 Transcript missense_variant 521/10637 494/1209 165/402 H/R cAt/cGt 1 -1 KLF12 HGNC HGNC:6346 protein_coding YES CCDS9449.1 ENSP00000366897 Q9Y4X4 UPI000013D144 NM_007249.4 deleterious(0) 3/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 73846003 73846003 T C 1 0 0 0 0 1 0 0 0 8205 1464 51 5 5 KLF12 13 73846003 Missense_Mutation SNP T C3L-00009_T 4105576 73846003 40518325 234 2026 NALCN 0 . GRCh38 13 101191963 101191963 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1718C>A p.Pro573His p.P573H ENST00000251127 14/44 132 117 15 169 169 0 strelka-varscan-mutect NALCN,missense_variant,p.Pro573His,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; T ENST00000251127 Transcript missense_variant 1800/6818 1718/5217 573/1738 P/H cCc/cAc 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 deleterious(0) 14/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 101191963 101191963 G T 1 0 0 0 0 1 0 0 0 10155 1232 43 2 2 NALCN 13 101191963 Missense_Mutation SNP G C3L-00009_T 27345960 101191963 13172365 235 2027 TMEM255B 0 . GRCh38 13 113801713 113801713 + Silent SNP G G A C3L-00009_T C3L-00009_N G G c.570G>A p.= p.L190L ENST00000375353 7/9 151 136 15 179 179 0 strelka-mutect TMEM255B,synonymous_variant,p.=,ENST00000375353,NM_182614.2;TMEM255B,downstream_gene_variant,,ENST00000488362,;TMEM255B,non_coding_transcript_exon_variant,,ENST00000498692,;TMEM255B,upstream_gene_variant,,ENST00000467169,;TMEM255B,downstream_gene_variant,,ENST00000375348,; A ENST00000375353 Transcript synonymous_variant 597/6100 570/981 190/326 L ctG/ctA COSM1721220 1 1 TMEM255B HGNC HGNC:28297 protein_coding YES CCDS45071.1 ENSP00000364502 Q8WV15 UPI0000071C2C NM_182614.2 7/9 hmmpanther:PTHR33721:SF3,hmmpanther:PTHR33721,Pfam_domain:PF14967 1 LOW 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.97971 0.9999998 1 1 1 0 A 2 1 6 113801713 113801713 G A 1 0 0 0 0 0 0 0 1 16615 1306 46 3 3 TMEM255B 13 113801713 Silent SNP G C3L-00009_T 12609750 113801713 562615 236 2028 TMEM255B 0 . GRCh38 13 113801800 113801800 + Silent SNP C C A novel C3L-00009_T C3L-00009_N C C c.657C>A p.= p.A219A ENST00000375353 7/9 84 72 12 108 108 0 strelka-varscan-mutect TMEM255B,synonymous_variant,p.=,ENST00000375353,NM_182614.2;TMEM255B,downstream_gene_variant,,ENST00000488362,;TMEM255B,non_coding_transcript_exon_variant,,ENST00000498692,;TMEM255B,upstream_gene_variant,,ENST00000467169,;TMEM255B,downstream_gene_variant,,ENST00000375348,; A ENST00000375353 Transcript synonymous_variant 684/6100 657/981 219/326 A gcC/gcA 1 1 TMEM255B HGNC HGNC:28297 protein_coding YES CCDS45071.1 ENSP00000364502 Q8WV15 UPI0000071C2C NM_182614.2 7/9 hmmpanther:PTHR33721:SF3,hmmpanther:PTHR33721,Pfam_domain:PF14967 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 113801800 113801800 C A 1 0 0 0 0 0 0 0 1 16615 668 24 2 2 TMEM255B 13 113801800 Silent SNP C C3L-00009_T 87 113801800 562528 237 2029 TEP1 0 . GRCh38 14 20382333 20382333 + Silent SNP C C A rs778960243 C3L-00009_T C3L-00009_N C C c.4164G>T p.= p.L1388L ENST00000262715 29/55 110 76 34 129 129 0 strelka-varscan-mutect TEP1,synonymous_variant,p.=,ENST00000262715,NM_007110.4;TEP1,synonymous_variant,p.=,ENST00000556935,;TEP1,synonymous_variant,p.=,ENST00000555727,;TEP1,synonymous_variant,p.=,ENST00000555008,;TEP1,upstream_gene_variant,,ENST00000557314,;TEP1,upstream_gene_variant,,ENST00000556488,;TEP1,upstream_gene_variant,,ENST00000471684,; A ENST00000262715 Transcript synonymous_variant 4205/10695 4164/7884 1388/2627 L ctG/ctT rs778960243 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 29/55 PROSITE_profiles:PS50837,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF448 LOW 1 SNV 1 1 PASS rs778960243 . 0 200 9 0 0 0 0 0 -20 0.9999984 1 1 1 0 A 2 1 6 20382333 20382333 C A 1 0 0 0 0 0 0 0 1 16175 697 25 2 2 TEP1 14 20382333 Silent SNP C C3L-00009_T 20382333 86661385 238 2030 MYH7 0 . GRCh38 14 23429292 23429292 + Silent SNP C C A C3L-00009_T C3L-00009_N C C c.1194G>T p.= p.G398G ENST00000355349 13/40 399 289 110 598 598 0 strelka-varscan-mutect MYH7,synonymous_variant,p.=,ENST00000355349,NM_000257.3; A ENST00000355349 Transcript synonymous_variant 1357/6087 1194/5808 398/1935 G ggG/ggT COSM4704657 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 13/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 23429292 23429292 C A 1 0 0 0 0 0 0 0 1 10039 726 26 2 2 MYH7 14 23429292 Silent SNP C C3L-00009_T 3046959 23429292 83614426 239 2031 MDGA2 0 . GRCh38 14 47061337 47061337 + Silent SNP C C T rs776675809 C3L-00009_T C3L-00009_N C C c.1230G>A p.= p.T410T ENST00000399232 7/17 226 170 56 277 277 0 strelka-varscan-mutect MDGA2,synonymous_variant,p.=,ENST00000426342,;MDGA2,synonymous_variant,p.=,ENST00000399232,NM_001113498.2;MDGA2,synonymous_variant,p.=,ENST00000357362,NM_182830.4;MDGA2,synonymous_variant,p.=,ENST00000554762,;MDGA2,synonymous_variant,p.=,ENST00000557238,;MDGA2,synonymous_variant,p.=,ENST00000482848,; T ENST00000399232 Transcript synonymous_variant 1595/5075 1230/2871 410/956 T acG/acA rs776675809,COSM5143926,COSM5143927,COSM5143928 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 7/17 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs776675809 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 47061337 47061337 C T 1 0 0 0 0 0 0 0 1 9345 639 23 1 1 MDGA2 14 47061337 Silent SNP C C3L-00009_T 23632045 47061337 59982381 240 2032 SYNE2 0 . GRCh38 14 64051579 64051579 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.7666T>C p.Tyr2556His p.Y2556H ENST00000358025 48/116 205 158 47 278 278 0 strelka-varscan-mutect SYNE2,missense_variant,p.Tyr2556His,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Tyr2556His,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Tyr2589His,ENST00000357395,;SYNE2,missense_variant,p.Tyr2589His,ENST00000554584,;SYNE2,downstream_gene_variant,,ENST00000557005,; C ENST00000358025 Transcript missense_variant 7878/21842 7666/20724 2556/6907 Y/H Tat/Cat 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(0.56) 48/116 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 64051579 64051579 T C 1 0 0 0 0 1 0 0 0 15838 1638 57 5 5 SYNE2 14 64051579 Missense_Mutation SNP T C3L-00009_T 16990242 64051579 42992139 241 2033 C14orf177 0 . GRCh38 14 98717259 98717259 + Silent SNP G G A rs762783972 C3L-00009_T C3L-00009_N G G c.363G>A p.= p.Q121Q ENST00000325812 4/4 114 99 15 139 139 0 strelka-varscan-mutect C14orf177,synonymous_variant,p.=,ENST00000325812,NM_182560.2;C14orf177,downstream_gene_variant,,ENST00000541516,;C14orf177,downstream_gene_variant,,ENST00000546029,; A ENST00000325812 Transcript synonymous_variant 782/1284 363/378 121/125 Q caG/caA rs762783972 1 1 C14orf177 HGNC HGNC:26375 protein_coding YES CCDS9948.1 ENSP00000321360 Q52M58 UPI0000141766 NM_182560.2 4/4 LOW 1 SNV 2 1 PASS rs762783972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 98717259 98717259 G A 1 0 0 0 0 0 0 0 1 1833 933 33 3 3 C14orf177 14 98717259 Silent SNP G C3L-00009_T 34665680 98717259 8326459 242 2034 HDC 0 . GRCh38 15 50253634 50253634 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.753T>C p.= p.C251C ENST00000267845 7/12 403 326 77 556 556 0 strelka-varscan-mutect HDC,synonymous_variant,p.=,ENST00000267845,NM_002112.3;HDC,synonymous_variant,p.=,ENST00000543581,NM_001306146.1;HDC,downstream_gene_variant,,ENST00000559683,;HDC,non_coding_transcript_exon_variant,,ENST00000558761,;HDC,non_coding_transcript_exon_variant,,ENST00000559190,;HDC,upstream_gene_variant,,ENST00000559816,;HDC,downstream_gene_variant,,ENST00000558679,; G ENST00000267845 Transcript synonymous_variant 1156/2705 753/1989 251/662 C tgT/tgC 1 -1 HDC HGNC HGNC:4855 protein_coding YES CCDS10134.1 ENSP00000267845 P19113 UPI0000128FB4 NM_002112.3 7/12 Gene3D:3.40.640.10,Pfam_domain:PF00282,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF68,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 50253634 50253634 A G 1 0 0 0 0 0 0 0 1 6902 157 6 5 5 HDC 15 50253634 Silent SNP A C3L-00009_T 50253634 51737555 243 2035 DYX1C1 0 . GRCh38 15 55434920 55434920 + Silent SNP A A G novel C3L-00009_T C3L-00009_N A A c.1032T>C p.= p.I344I ENST00000321149 8/10 76 57 19 122 122 0 strelka-varscan-mutect DYX1C1,synonymous_variant,p.=,ENST00000321149,NM_130810.3;DYX1C1,synonymous_variant,p.=,ENST00000348518,;DYX1C1,synonymous_variant,p.=,ENST00000457155,NM_001033559.2;DYX1C1,synonymous_variant,p.=,ENST00000448430,NM_001033560.1;DYX1C1-CCPG1,non_coding_transcript_exon_variant,,ENST00000565113,;DYX1C1-CCPG1,intron_variant,,ENST00000568310,;DYX1C1,3_prime_UTR_variant,,ENST00000524160,; G ENST00000321149 Transcript synonymous_variant 1400/1993 1032/1263 344/420 I atT/atC 1 -1 DYX1C1 HGNC HGNC:21493 protein_coding YES CCDS10154.1 ENSP00000323275 Q8WXU2 UPI000013E5B8 NM_130810.3 8/10 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF281,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 55434920 55434920 A G 1 0 0 0 0 0 0 0 1 4685 126 5 5 5 DYX1C1 15 55434920 Silent SNP A C3L-00009_T 5181286 55434920 46556269 244 2036 ACSBG1 0 . GRCh38 15 78173754 78173754 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1928C>A p.Ala643Asp p.A643D ENST00000258873 13/14 315 288 27 398 398 0 strelka-varscan-mutect ACSBG1,missense_variant,p.Ala643Asp,ENST00000258873,NM_001199377.1,NM_015162.4;ACSBG1,missense_variant,p.Ala401Asp,ENST00000560817,;IDH3A,downstream_gene_variant,,ENST00000299518,NM_005530.2;IDH3A,downstream_gene_variant,,ENST00000558554,;IDH3A,downstream_gene_variant,,ENST00000559205,;IDH3A,downstream_gene_variant,,ENST00000558535,;ACSBG1,3_prime_UTR_variant,,ENST00000560124,;ACSBG1,non_coding_transcript_exon_variant,,ENST00000560183,;IDH3A,downstream_gene_variant,,ENST00000559889,;IDH3A,downstream_gene_variant,,ENST00000558602,;IDH3A,downstream_gene_variant,,ENST00000560667,;IDH3A,downstream_gene_variant,,ENST00000559803,;IDH3A,downstream_gene_variant,,ENST00000558016,;IDH3A,downstream_gene_variant,,ENST00000557960,; T ENST00000258873 Transcript missense_variant 2134/6357 1928/2175 643/724 A/D gCc/gAc 1 -1 ACSBG1 HGNC HGNC:29567 protein_coding YES CCDS10298.1 ENSP00000258873 Q96GR2 UPI000006E955 NM_001199377.1,NM_015162.4 deleterious(0) 13/14 hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 78173754 78173754 G T 1 0 0 0 0 1 0 0 0 215 1203 42 2 2 ACSBG1 15 78173754 Missense_Mutation SNP G C3L-00009_T 22738834 78173754 23817435 245 2037 BNC1 0 . GRCh38 15 83263443 83263443 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1808C>A p.Pro603His p.P603H ENST00000345382 4/5 314 253 61 442 442 0 strelka-varscan-mutect BNC1,missense_variant,p.Pro603His,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Pro596His,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; T ENST00000345382 Transcript missense_variant 1894/4610 1808/2985 603/994 P/H cCt/cAt 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0.02) 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 83263443 83263443 G T 1 0 0 0 0 1 0 0 0 1630 1000 35 2 2 BNC1 15 83263443 Missense_Mutation SNP G C3L-00009_T 5089689 83263443 18727746 246 2038 NTRK3 0 . GRCh38 15 87940689 87940689 + Silent SNP T T C novel C3L-00009_T C3L-00009_N T T c.1650A>G p.= p.G550G ENST00000360948 15/20 579 531 48 738 738 0 strelka-varscan-mutect NTRK3,synonymous_variant,p.=,ENST00000394480,NM_002530.3;NTRK3,synonymous_variant,p.=,ENST00000558676,;NTRK3,synonymous_variant,p.=,ENST00000360948,NM_001012338.2;NTRK3,synonymous_variant,p.=,ENST00000357724,;NTRK3,synonymous_variant,p.=,ENST00000355254,NM_001243101.1;NTRK3,synonymous_variant,p.=,ENST00000626019,;NTRK3,synonymous_variant,p.=,ENST00000629765,;NTRK3,synonymous_variant,p.=,ENST00000557856,;NTRK3,synonymous_variant,p.=,ENST00000542733,NM_001320135.1;NTRK3,non_coding_transcript_exon_variant,,ENST00000559680,; C ENST00000360948 Transcript synonymous_variant 1956/3004 1650/2520 550/839 G ggA/ggG 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 15/20 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 6 87940689 87940689 T C 1 0 0 0 0 0 0 0 1 10774 1770 62 5 5 NTRK3 15 87940689 Silent SNP T C3L-00009_T 4677246 87940689 14050500 247 2039 SYNM 0 . GRCh38 15 99105636 99105636 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.437C>A p.Ala146Glu p.A146E ENST00000336292 1/4 111 90 21 118 117 1 strelka-varscan-mutect SYNM,missense_variant,p.Ala146Glu,ENST00000336292,NM_145728.2;SYNM,missense_variant,p.Ala146Glu,ENST00000594047,NM_015286.5;SYNM,missense_variant,p.Ala146Glu,ENST00000328642,;SYNM,intron_variant,,ENST00000560674,;RP11-654A16.3,intron_variant,,ENST00000559468,; A ENST00000336292 Transcript missense_variant 602/7394 437/4698 146/1565 A/E gCg/gAg 1 1 SYNM HGNC HGNC:24466 protein_coding YES CCDS73787.1 ENSP00000336775 O15061 UPI0000DC3AA9 NM_145728.2 tolerated(0.85) 1/4 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF194,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 99105636 99105636 C A 1 0 0 0 0 1 0 0 0 15849 768 27 1 1 SYNM 15 99105636 Missense_Mutation SNP C C3L-00009_T 11164947 99105636 2885553 248 2040 CERS3 0 . GRCh38 15 100501767 100501767 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.83A>T p.His28Leu p.H28L ENST00000284382 4/13 265 219 46 283 283 0 strelka-varscan-mutect CERS3,missense_variant,p.His28Leu,ENST00000284382,NM_178842.3,NM_001290343.1;CERS3,missense_variant,p.His28Leu,ENST00000394113,NM_001290341.1;CERS3,missense_variant,p.His28Leu,ENST00000538112,NM_001290342.1;CERS3,missense_variant,p.His28Leu,ENST00000558884,;CERS3,downstream_gene_variant,,ENST00000559639,;CERS3,intron_variant,,ENST00000560944,;CERS3,non_coding_transcript_exon_variant,,ENST00000559023,; A ENST00000284382 Transcript missense_variant 507/3894 83/1152 28/383 H/L cAc/cTc 1 -1 CERS3 HGNC HGNC:23752 protein_coding YES CCDS10384.1 ENSP00000284382 Q8IU89 UPI00001975AB NM_178842.3,NM_001290343.1 tolerated(0.19) 4/13 PIRSF_domain:PIRSF005225,hmmpanther:PTHR12560,hmmpanther:PTHR12560:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 100501767 100501767 T A 1 0 0 0 0 1 0 0 0 2997 1696 59 4 4 CERS3 15 100501767 Missense_Mutation SNP T C3L-00009_T 1396131 100501767 1489422 249 2041 XYLT1 0 . GRCh38 16 17200548 17200548 + Silent SNP C C G novel C3L-00009_T C3L-00009_N C C c.1020G>C p.= p.R340R ENST00000261381 4/12 240 222 18 278 278 0 strelka-varscan-mutect XYLT1,synonymous_variant,p.=,ENST00000261381,NM_022166.3;XYLT1,non_coding_transcript_exon_variant,,ENST00000575674,; G ENST00000261381 Transcript synonymous_variant 1105/9891 1020/2880 340/959 R cgG/cgC 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 4/12 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF91,Pfam_domain:PF02485 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 17200548 17200548 C G 1 0 0 0 0 0 0 0 1 18022 726 26 4 4 XYLT1 16 17200548 Silent SNP C C3L-00009_T 17200548 73137797 250 2042 C16orf78 0 . GRCh38 16 49396465 49396465 + Missense_Mutation SNP G G T rs546860439 C3L-00009_T C3L-00009_N G G c.437G>T p.Arg146Leu p.R146L ENST00000299191 4/5 187 172 15 241 241 0 strelka-varscan-mutect C16orf78,missense_variant,p.Arg146Leu,ENST00000299191,NM_144602.3; T ENST00000299191 Transcript missense_variant 554/1068 437/798 146/265 R/L cGg/cTg rs546860439,COSM1378073 1 1 C16orf78 HGNC HGNC:28479 protein_coding YES CCDS10738.1 ENSP00000299191 Q8WTQ4 UPI0000071013 NM_144602.3 deleterious(0.02) 4/5 Pfam_domain:PF15472,hmmpanther:PTHR35679 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs546860439 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 49396465 49396465 G T 1 0 0 0 0 1 0 0 0 1866 1116 39 1 1 C16orf78 16 49396465 Missense_Mutation SNP G C3L-00009_T 32195917 49396465 40941880 251 2043 PLA2G15 0 . GRCh38 16 68245437 68245437 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.11A>T p.His4Leu p.H4L ENST00000219345 1/6 174 154 20 206 206 0 strelka-varscan-mutect PLA2G15,missense_variant,p.His4Leu,ENST00000219345,NM_012320.3;PLA2G15,missense_variant,p.His4Leu,ENST00000413021,;PLA2G15,missense_variant,p.His4Leu,ENST00000566188,;PLA2G15,missense_variant,p.His4Leu,ENST00000444212,;PLA2G15,missense_variant,p.His4Leu,ENST00000568082,;PLA2G15,missense_variant,p.His4Leu,ENST00000564827,;PLA2G15,missense_variant,p.His4Leu,ENST00000565744,;PLA2G15,upstream_gene_variant,,ENST00000568599,;PLA2G15,missense_variant,p.His4Leu,ENST00000566978,;PLA2G15,non_coding_transcript_exon_variant,,ENST00000562966,; T ENST00000219345 Transcript missense_variant 94/2727 11/1239 4/412 H/L cAc/cTc 1 1 PLA2G15 HGNC HGNC:17163 protein_coding YES CCDS10864.1 ENSP00000219345 Q8NCC3 UPI00000359EF NM_012320.3 tolerated_low_confidence(0.34) 1/6 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11440:SF47,hmmpanther:PTHR11440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 68245437 68245437 A T 1 0 0 0 0 1 0 0 0 12088 159 6 4 4 PLA2G15 16 68245437 Missense_Mutation SNP A C3L-00009_T 18848972 68245437 22092908 252 2044 PHLPP2 0 . GRCh38 16 71658661 71658661 + Nonsense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.2140C>T p.Gln714Ter p.Q714* ENST00000568954 14/19 128 109 19 160 160 0 strelka-varscan-mutect PHLPP2,stop_gained,p.Gln647Ter,ENST00000393524,NM_001289003.1;PHLPP2,stop_gained,p.Gln714Ter,ENST00000568954,NM_015020.3;PHLPP2,stop_gained,p.Gln749Ter,ENST00000567016,;RP11-432I5.6,intron_variant,,ENST00000567077,;PHLPP2,stop_gained,p.Gln452Ter,ENST00000568004,;PHLPP2,stop_gained,p.Gln77Ter,ENST00000564884,; A ENST00000568954 Transcript stop_gained 2519/8317 2140/3972 714/1323 Q/* Cag/Tag 1 -1 PHLPP2 HGNC HGNC:29149 protein_coding YES CCDS32479.1 ENSP00000457991 Q6ZVD8 UPI0000229F5A NM_015020.3 14/19 PROSITE_profiles:PS51450,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 6 71658661 71658661 G A 1 0 0 0 0 0 1 0 0 11943 1299 45 3 3 PHLPP2 16 71658661 Nonsense_Mutation SNP G C3L-00009_T 3413224 71658661 18679684 253 2045 ZFHX3 0 . GRCh38 16 72794657 72794657 + Silent SNP T T G novel C3L-00009_T C3L-00009_N T T c.8025A>C p.= p.A2675A ENST00000268489 9/10 225 190 35 341 340 1 strelka-varscan-mutect ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,synonymous_variant,p.=,ENST00000397992,NM_001164766.1;RP5-991G20.1,downstream_gene_variant,,ENST00000563328,; G ENST00000268489 Transcript synonymous_variant 8698/16064 8025/11112 2675/3703 A gcA/gcC 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 9/10 PROSITE_profiles:PS50071,hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 72794657 72794657 T G 1 0 0 0 0 0 0 0 1 18212 1683 59 5 5 ZFHX3 16 72794657 Silent SNP T C3L-00009_T 1135996 72794657 17543688 254 2046 CNTNAP4 0 . GRCh38 16 76476030 76476030 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1747G>T p.Ala583Ser p.A583S ENST00000611870 11/24 181 166 15 278 278 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Ala583Ser,ENST00000307431,;CNTNAP4,missense_variant,p.Ala583Ser,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Ala535Ser,ENST00000377504,;CNTNAP4,missense_variant,p.Ala586Ser,ENST00000476707,;CNTNAP4,missense_variant,p.Ala535Ser,ENST00000622250,;CNTNAP4,missense_variant,p.Ala510Ser,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; T ENST00000611870 Transcript missense_variant 2132/4867 1747/3927 583/1308 A/S Gct/Tct 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0.02) 11/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00181,Superfamily_domains:SSF56496,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 76476030 76476030 G T 1 0 0 0 0 1 0 0 0 3431 971 34 2 2 CNTNAP4 16 76476030 Missense_Mutation SNP G C3L-00009_T 3681373 76476030 13862315 255 2047 WWOX 0 . GRCh38 16 79211636 79211636 + Missense_Mutation SNP G G C rs778218106 C3L-00009_T C3L-00009_N G G c.1085G>C p.Cys362Ser p.C362S ENST00000566780 9/9 463 395 68 600 599 1 strelka-varscan-mutect WWOX,missense_variant,p.Cys362Ser,ENST00000566780,NM_001291997.1,NM_016373.3;WWOX,missense_variant,p.Cys182Ser,ENST00000406884,;WWOX,missense_variant,p.Val172Leu,ENST00000539474,;WWOX,synonymous_variant,p.=,ENST00000402655,;RP11-679B19.2,downstream_gene_variant,,ENST00000569677,;RP11-679B19.1,upstream_gene_variant,,ENST00000622621,;WWOX,non_coding_transcript_exon_variant,,ENST00000566103,;WWOX,3_prime_UTR_variant,,ENST00000569332,; C ENST00000566780 Transcript missense_variant 1451/2482 1085/1245 362/414 C/S tGt/tCt rs778218106 1 1 WWOX HGNC HGNC:12799 protein_coding YES CCDS42196.1 ENSP00000457230 Q9NZC7 UPI000004C797 NM_001291997.1,NM_016373.3 deleterious(0.02) 9/9 Gene3D:3.40.50.720,hmmpanther:PTHR24320,hmmpanther:PTHR24320:SF72,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs778218106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 79211636 79211636 G C 1 0 0 0 0 1 0 0 0 17972 1377 48 4 4 WWOX 16 79211636 Missense_Mutation SNP G C3L-00009_T 2735606 79211636 11126709 256 2048 ZNF594 0 . GRCh38 17 5183491 5183491 + Missense_Mutation SNP T T A rs757201606 C3L-00009_T C3L-00009_N T T c.766A>T p.Ile256Leu p.I256L ENST00000399604 1/1 177 144 33 293 293 0 strelka-varscan-mutect ZNF594,missense_variant,p.Ile256Leu,ENST00000399604,;ZNF594,missense_variant,p.Ile256Leu,ENST00000575779,NM_032530.1;ZNF594,downstream_gene_variant,,ENST00000576772,; A ENST00000399604 Transcript missense_variant 907/4862 766/2424 256/807 I/L Ata/Tta rs757201606 1 -1 ZNF594 HGNC HGNC:29392 protein_coding YES CCDS42241.1 ENSP00000382513 Q96JF6 UPI00001C1FDF tolerated(0.37) 1/1 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF155,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS rs757201606 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 5183491 5183491 T A 1 0 0 0 0 1 0 0 0 18599 1406 49 4 4 ZNF594 17 5183491 Missense_Mutation SNP T C3L-00009_T 5183491 78073950 257 2049 TP53 0 . GRCh38 17 7674227 7674227 + Missense_Mutation SNP T T C rs483352695 C3L-00009_T C3L-00009_N T T c.736A>G p.Met246Val p.M246V ENST00000269305 7/11 279 225 54 380 380 0 strelka-varscan-mutect TP53,missense_variant,p.Met246Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Met246Val,ENST00000420246,;TP53,missense_variant,p.Met207Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Met207Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Met246Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Met207Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Met246Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Met207Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Met246Val,ENST00000445888,;TP53,missense_variant,p.Met207Val,ENST00000619485,;TP53,missense_variant,p.Met114Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Met87Val,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Met114Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Met87Val,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Met114Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Met87Val,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Met246Val,ENST00000359597,;TP53,missense_variant,p.Met235Val,ENST00000615910,;TP53,missense_variant,p.Met246Val,ENST00000413465,;TP53,missense_variant,p.Met114Val,ENST00000509690,;TP53,missense_variant,p.Met153Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Met207Val,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 926/2579 736/1182 246/393 M/V Atg/Gtg rs483352695,CM942294,TP53_g.13373A>T,TP53_g.13373A>G,TP53_g.13373A>C,TP53_g.13373del,COSM1726382,COSM251429,COSM251430,COSM251431,COSM3958808,COSM4166414,COSM4166415,COSM4166416,COSM4166417,COSM4166418,COSM43555,COSM44903,COSM45992 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs483352695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 7674227 7674227 T C 1 0 0 0 0 1 0 0 0 16859 1464 51 5 5 TP53 17 7674227 Missense_Mutation SNP T C3L-00009_T 2490736 7674227 75583214 258 2050 DNAH2 0 . GRCh38 17 7805286 7805286 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.9335A>G p.Glu3112Gly p.E3112G ENST00000572933 61/86 174 139 35 290 290 0 strelka-varscan-mutect DNAH2,missense_variant,p.Glu3112Gly,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Glu3112Gly,ENST00000389173,;DNAH2,missense_variant,p.Glu61Gly,ENST00000575105,; G ENST00000572933 Transcript missense_variant 10795/14955 9335/13284 3112/4427 E/G gAg/gGg 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious(0) 61/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183,Pfam_domain:PF12777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 7805286 7805286 A G 1 0 0 0 0 1 0 0 0 4417 304 11 5 5 DNAH2 17 7805286 Missense_Mutation SNP A C3L-00009_T 131059 7805286 75452155 259 2051 MYH1 0 . GRCh38 17 10497893 10497893 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.4206G>A p.= p.Q1402Q ENST00000226207 31/40 97 91 6 152 152 0 strelka-varscan-mutect MYH1,synonymous_variant,p.=,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript synonymous_variant 4301/6024 4206/5820 1402/1939 Q caG/caA 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 31/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -12.73871 1 1 1 1 0 T 2 4 6 10497893 10497893 C T 1 0 0 0 0 0 0 0 1 10029 680 24 3 3 MYH1 17 10497893 Silent SNP C C3L-00009_T 2692607 10497893 72759548 260 2052 TMEM220 0 . GRCh38 17 10726227 10726227 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.140T>A p.Val47Asp p.V47D ENST00000341871 3/6 231 190 41 272 272 0 strelka-varscan-mutect TMEM220,missense_variant,p.Val47Asp,ENST00000341871,NM_001004313.1;TMEM220,missense_variant,p.Val37Asp,ENST00000455996,;TMEM220,missense_variant,p.Val37Asp,ENST00000578345,;TMEM220,upstream_gene_variant,,ENST00000580787,;TMEM220,upstream_gene_variant,,ENST00000581949,;TMEM220-AS1,upstream_gene_variant,,ENST00000583343,;TMEM220-AS1,upstream_gene_variant,,ENST00000583012,;TMEM220-AS1,upstream_gene_variant,,ENST00000579114,;TMEM220-AS1,upstream_gene_variant,,ENST00000581366,;TMEM220-AS1,upstream_gene_variant,,ENST00000580899,;TMEM220-AS1,upstream_gene_variant,,ENST00000584714,;TMEM220-AS1,upstream_gene_variant,,ENST00000583115,;TMEM220,non_coding_transcript_exon_variant,,ENST00000580186,; T ENST00000341871 Transcript missense_variant 605/3106 140/483 47/160 V/D gTt/gAt 1 -1 TMEM220 HGNC HGNC:33757 protein_coding YES CCDS32567.1 ENSP00000339830 Q6QAJ8 UPI00001D79BC NM_001004313.1 deleterious(0) 3/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR34262:SF1,hmmpanther:PTHR34262,Pfam_domain:PF15071 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 10726227 10726227 A T 1 0 0 0 0 1 0 0 0 16584 43 2 4 4 TMEM220 17 10726227 Missense_Mutation SNP A C3L-00009_T 228334 10726227 72531214 261 2053 RNF135 0 . GRCh38 17 30988074 30988074 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.647C>T p.Thr216Ile p.T216I ENST00000328381 3/5 576 484 92 563 563 0 strelka-varscan-mutect RNF135,missense_variant,p.Thr216Ile,ENST00000328381,NM_032322.3;RNF135,missense_variant,p.Thr216Ile,ENST00000535306,NM_001184992.1;RNF135,missense_variant,p.Thr146Ile,ENST00000580444,;RNF135,intron_variant,,ENST00000324689,NM_197939.1;RNF135,intron_variant,,ENST00000443677,;RNF135,upstream_gene_variant,,ENST00000434242,; T ENST00000328381 Transcript missense_variant 1520/2892 647/1299 216/432 T/I aCc/aTc 1 1 RNF135 HGNC HGNC:21158 protein_coding YES CCDS11262.1 ENSP00000328340 Q8IUD6 UPI00001AF795 NM_032322.3 tolerated(0.33) 3/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF386 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 30988074 30988074 C T 1 0 0 0 0 1 0 0 0 13618 507 18 3 3 RNF135 17 30988074 Missense_Mutation SNP C C3L-00009_T 20261847 30988074 52269367 262 2054 CCL3L3 0 . GRCh38 17 36195367 36195367 + Silent SNP G G A novel C3L-00009_T C3L-00009_N G G c.201C>T p.= p.T67T ENST00000619989 3/3 620 536 84 824 824 0 strelka-varscan-mutect CCL3L3,synonymous_variant,p.=,ENST00000619989,NM_001001437.3;AC131056.3,intron_variant,,ENST00000618848,;AC131056.3,intron_variant,,ENST00000614777,;CCL3L3,non_coding_transcript_exon_variant,,ENST00000616702,;CCL3L3,non_coding_transcript_exon_variant,,ENST00000612839,; A ENST00000619989 Transcript synonymous_variant 286/784 201/282 67/93 T acC/acT 1 -1 CCL3L3 HGNC HGNC:30554 protein_coding YES CCDS32626.1 ENSP00000480558 P16619 UPI000004457D NM_001001437.3 3/3 Gene3D:2.40.50.40,Pfam_domain:PF00048,PROSITE_patterns:PS00472,hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF91,SMART_domains:SM00199,Superfamily_domains:SSF54117 LOW 1 SNV 1 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 6 36195367 36195367 G A 1 0 0 0 0 0 0 0 1 2600 1335 47 3 3 CCL3L3 17 36195367 Silent SNP G C3L-00009_T 5207293 36195367 47062074 263 2055 KRT31 0 . GRCh38 17 41397532 41397532 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.8A>G p.Tyr3Cys p.Y3C ENST00000251645 1/7 96 78 18 205 205 0 strelka-varscan-mutect KRT31,missense_variant,p.Tyr3Cys,ENST00000251645,NM_002277.2;AC003958.2,upstream_gene_variant,,ENST00000432258,;AC003958.2,upstream_gene_variant,,ENST00000430006,; C ENST00000251645 Transcript missense_variant 61/1596 8/1251 3/416 Y/C tAc/tGc 1 -1 KRT31 HGNC HGNC:6448 protein_coding YES CCDS11391.1 ENSP00000251645 Q15323 UPI000006F564 NM_002277.2 deleterious_low_confidence(0.01) 1/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF99 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 C 3 2 6 41397532 41397532 T C 1 0 0 0 0 1 0 0 0 8349 1638 57 5 5 KRT31 17 41397532 Missense_Mutation SNP T C3L-00009_T 5202165 41397532 41859909 264 2056 PLCD3 0 . GRCh38 17 45118853 45118853 + Missense_Mutation SNP G G A novel C3L-00009_T C3L-00009_N G G c.875C>T p.Ala292Val p.A292V ENST00000619929 5/15 187 158 29 197 197 0 strelka-varscan-mutect PLCD3,missense_variant,p.Ala292Val,ENST00000619929,NM_133373.4;PLCD3,downstream_gene_variant,,ENST00000590644,;PLCD3,downstream_gene_variant,,ENST00000538093,;MIR6784,upstream_gene_variant,,ENST00000611997,;PLCD3,non_coding_transcript_exon_variant,,ENST00000538988,;PLCD3,upstream_gene_variant,,ENST00000543623,;PLCD3,upstream_gene_variant,,ENST00000611986,;PLCD3,downstream_gene_variant,,ENST00000544446,;PLCD3,upstream_gene_variant,,ENST00000615898,;PLCD3,non_coding_transcript_exon_variant,,ENST00000546350,;PLCD3,non_coding_transcript_exon_variant,,ENST00000542173,;PLCD3,upstream_gene_variant,,ENST00000618022,; A ENST00000619929 Transcript missense_variant 963/6107 875/2370 292/789 A/V gCc/gTc 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 deleterious(0) 5/15 Gene3D:1.10.238.10,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 45118853 45118853 G A 1 0 0 0 0 1 0 0 0 12126 1203 42 3 3 PLCD3 17 45118853 Missense_Mutation SNP G C3L-00009_T 3721321 45118853 38138588 265 2057 ITGB4 0 . GRCh38 17 75755732 75755732 + Silent SNP G G T rs144407069 C3L-00009_T C3L-00009_N G G c.4590G>T p.= p.T1530T ENST00000200181 35/40 599 530 69 626 626 0 strelka-varscan-mutect ITGB4,synonymous_variant,p.=,ENST00000200181,NM_000213.3;ITGB4,synonymous_variant,p.=,ENST00000449880,NM_001005619.1;ITGB4,synonymous_variant,p.=,ENST00000450894,NM_001005731.1;ITGB4,synonymous_variant,p.=,ENST00000579662,NM_001321123.1;GALK1,intron_variant,,ENST00000225614,;ITGB4,intron_variant,,ENST00000584939,;ITGB4,intron_variant,,ENST00000582629,;GALK1,downstream_gene_variant,,ENST00000588479,NM_000154.1;GALK1,downstream_gene_variant,,ENST00000592997,;ITGB4,upstream_gene_variant,,ENST00000578318,;ITGB4,non_coding_transcript_exon_variant,,ENST00000583327,;ITGB4,non_coding_transcript_exon_variant,,ENST00000579211,;GALK1,intron_variant,,ENST00000589643,;GALK1,downstream_gene_variant,,ENST00000592494,;GALK1,downstream_gene_variant,,ENST00000587707,;GALK1,downstream_gene_variant,,ENST00000586733,; T ENST00000200181 Transcript synonymous_variant 4777/5919 4590/5469 1530/1822 T acG/acT rs144407069 1 1 ITGB4 HGNC HGNC:6158 protein_coding YES CCDS11727.1 ENSP00000200181 P16144 A0A024R8T0 UPI00001AE5C0 NM_000213.3 35/40 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF002513,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs144407069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 75755732 75755732 G T 1 0 0 0 0 0 0 0 1 7803 1074 38 1 1 ITGB4 17 75755732 Silent SNP G C3L-00009_T 30636879 75755732 7501709 266 2058 MGAT5B 0 . GRCh38 17 76906053 76906053 + Silent SNP C C A rs112338799 C3L-00009_T C3L-00009_N C C c.924C>A p.= p.S308S ENST00000428789 7/16 163 141 22 188 188 0 strelka-mutect MGAT5B,synonymous_variant,p.=,ENST00000569840,NM_001199172.1;MGAT5B,synonymous_variant,p.=,ENST00000301618,NM_144677.2;MGAT5B,synonymous_variant,p.=,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,synonymous_variant,p.=,ENST00000565043,; A ENST00000428789 Transcript synonymous_variant 1027/4053 924/2406 308/801 S tcC/tcA rs112338799 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 7/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 LOW 1 SNV 1 1 PASS rs112338799 . 0 203 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 A 2 1 6 76906053 76906053 C A 1 0 0 0 0 0 0 0 1 9510 639 23 1 1 MGAT5B 17 76906053 Silent SNP C C3L-00009_T 1150321 76906053 6351388 267 2059 CCDC40 0 . GRCh38 17 80089814 80089814 + Missense_Mutation SNP G G T rs745319642 C3L-00009_T C3L-00009_N G G c.2762G>T p.Arg921Leu p.R921L ENST00000397545 17/20 593 439 154 584 584 0 strelka-varscan-mutect CCDC40,missense_variant,p.Arg921Leu,ENST00000397545,NM_017950.3;CCDC40,missense_variant,p.Arg921Leu,ENST00000374877,NM_001243342.1;CCDC40,non_coding_transcript_exon_variant,,ENST00000573903,;CCDC40,non_coding_transcript_exon_variant,,ENST00000572253,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;CCDC40,non_coding_transcript_exon_variant,,ENST00000575431,;CCDC40,downstream_gene_variant,,ENST00000574933,; T ENST00000397545 Transcript missense_variant 2789/4294 2762/3429 921/1142 R/L cGt/cTt rs745319642,COSM4669947,COSM4669948 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 deleterious(0) 17/20 hmmpanther:PTHR16275 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs745319642 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 80089814 80089814 G T 1 0 0 0 0 1 0 0 0 2521 1145 40 1 1 CCDC40 17 80089814 Missense_Mutation SNP G C3L-00009_T 3183761 80089814 3167627 268 2060 MPPE1 0 . GRCh38 18 11884518 11884518 + Missense_Mutation SNP A A T novel C3L-00009_T C3L-00009_N A A c.1118T>A p.Leu373His p.L373H ENST00000588072 11/11 235 220 15 262 262 0 strelka-varscan-mutect MPPE1,missense_variant,p.Leu373His,ENST00000588072,NM_023075.5;MPPE1,missense_variant,p.Leu310His,ENST00000317235,;MPPE1,missense_variant,p.Leu351His,ENST00000344987,;MPPE1,missense_variant,p.Leu310His,ENST00000309976,NM_001242904.1;GNAL,3_prime_UTR_variant,,ENST00000334049,NM_182978.3;GNAL,downstream_gene_variant,,ENST00000423027,;GNAL,downstream_gene_variant,,ENST00000269162,NM_001142339.2;GNAL,downstream_gene_variant,,ENST00000535121,NM_001261443.1;MPPE1,downstream_gene_variant,,ENST00000588191,;MPPE1,downstream_gene_variant,,ENST00000588186,;MPPE1,downstream_gene_variant,,ENST00000592977,;GNAL,downstream_gene_variant,,ENST00000602628,NM_001261444.1;MPPE1,downstream_gene_variant,,ENST00000589267,;MPPE1,downstream_gene_variant,,ENST00000587724,;MPPE1,downstream_gene_variant,,ENST00000592331,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592755,;MPPE1,3_prime_UTR_variant,,ENST00000496196,;MPPE1,3_prime_UTR_variant,,ENST00000317251,;MPPE1,3_prime_UTR_variant,,ENST00000592306,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592447,;MPPE1,downstream_gene_variant,,ENST00000589731,;MPPE1,downstream_gene_variant,,ENST00000592894,; T ENST00000588072 Transcript missense_variant 2340/4236 1118/1191 373/396 L/H cTc/cAc 1 -1 MPPE1 HGNC HGNC:15988 protein_coding YES CCDS11853.1 ENSP00000465894 Q53F39 UPI000013DDD8 NM_023075.5 deleterious(0) 11/11 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR13315:SF0,hmmpanther:PTHR13315 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 11884518 11884518 A T 1 0 0 0 0 1 0 0 0 9706 304 11 4 4 MPPE1 18 11884518 Missense_Mutation SNP A C3L-00009_T 11884518 68488767 269 2061 NOL4 0 . GRCh38 18 34104142 34104142 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.544A>G p.Thr182Ala p.T182A ENST00000261592 4/11 194 169 25 247 247 0 strelka-mutect NOL4,missense_variant,p.Thr182Ala,ENST00000261592,NM_003787.4;NOL4,missense_variant,p.Thr182Ala,ENST00000589544,NM_001198548.1;NOL4,missense_variant,p.Thr108Ala,ENST00000538587,NM_001198547.1;NOL4,missense_variant,p.Thr166Ala,ENST00000590712,NM_001198546.1;NOL4,non_coding_transcript_exon_variant,,ENST00000588280,;NOL4,non_coding_transcript_exon_variant,,ENST00000587971,;NOL4,non_coding_transcript_exon_variant,,ENST00000587953,;NOL4,3_prime_UTR_variant,,ENST00000586314,;NOL4,3_prime_UTR_variant,,ENST00000591917,;NOL4,downstream_gene_variant,,ENST00000586309,; C ENST00000261592 Transcript missense_variant 842/3957 544/1917 182/638 T/A Act/Gct 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 tolerated(0.15) 4/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 34104142 34104142 T C 1 0 0 0 0 1 0 0 0 10567 1696 59 5 5 NOL4 18 34104142 Missense_Mutation SNP T C3L-00009_T 22219624 34104142 46269143 270 2062 CELF4 0 . GRCh38 18 37273143 37273143 + Silent SNP G G T novel C3L-00009_T C3L-00009_N G G c.822C>A p.= p.A274A ENST00000420428 7/13 109 97 12 131 131 0 strelka-varscan-mutect CELF4,synonymous_variant,p.=,ENST00000420428,NM_020180.3;CELF4,synonymous_variant,p.=,ENST00000591287,;CELF4,synonymous_variant,p.=,ENST00000334919,NM_001025089.1;CELF4,synonymous_variant,p.=,ENST00000603232,NM_001025087.1;CELF4,synonymous_variant,p.=,ENST00000361795,NM_001025088.1;CELF4,synonymous_variant,p.=,ENST00000601019,;CELF4,synonymous_variant,p.=,ENST00000591282,;CELF4,synonymous_variant,p.=,ENST00000588597,;CELF4,synonymous_variant,p.=,ENST00000601392,;CELF4,synonymous_variant,p.=,ENST00000587819,;CELF4,synonymous_variant,p.=,ENST00000589229,;CELF4,upstream_gene_variant,,ENST00000588591,;CELF4,upstream_gene_variant,,ENST00000586009,;CELF4,upstream_gene_variant,,ENST00000589386,;CELF4,upstream_gene_variant,,ENST00000593271,;CELF4,upstream_gene_variant,,ENST00000587657,;CELF4,downstream_gene_variant,,ENST00000587924,;RP11-797E24.3,upstream_gene_variant,,ENST00000586610,;RP11-797E24.3,upstream_gene_variant,,ENST00000588766,;CELF4,non_coding_transcript_exon_variant,,ENST00000587074,;CELF4,3_prime_UTR_variant,,ENST00000590112,;CELF4,non_coding_transcript_exon_variant,,ENST00000591421,; T ENST00000420428 Transcript synonymous_variant 1218/4052 822/1461 274/486 A gcC/gcA 1 -1 CELF4 HGNC HGNC:14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 UPI00000726FC NM_020180.3 7/13 Low_complexity_(Seg):seg LOW SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 2 4 6 37273143 37273143 G T 1 0 0 0 0 0 0 0 1 2925 1219 43 2 2 CELF4 18 37273143 Silent SNP G C3L-00009_T 3169001 37273143 43100142 271 2063 DCC 0 . GRCh38 18 53530634 53530634 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.4325T>A p.Ile1442Asn p.I1442N ENST00000442544 29/29 483 414 69 634 633 1 strelka-varscan-mutect DCC,missense_variant,p.Ile1442Asn,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Ile1419Asn,ENST00000412726,;DCC,downstream_gene_variant,,ENST00000581580,;RP11-671P2.1,intron_variant,,ENST00000582064,;DCC,downstream_gene_variant,,ENST00000577224,;DCC,downstream_gene_variant,,ENST00000579702,; A ENST00000442544 Transcript missense_variant 4941/10206 4325/4344 1442/1447 I/N aTc/aAc 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 deleterious(0) 29/29 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06583,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 53530634 53530634 T A 1 0 0 0 0 1 0 0 0 4084 1435 50 4 4 DCC 18 53530634 Missense_Mutation SNP T C3L-00009_T 16257491 53530634 26842651 272 2064 ZNF407 0 . GRCh38 18 74877302 74877302 + Silent SNP C C G novel C3L-00009_T C3L-00009_N C C c.4983C>G p.= p.P1661P ENST00000299687 4/8 158 150 8 227 227 0 strelka-varscan-mutect ZNF407,synonymous_variant,p.=,ENST00000299687,NM_017757.2;ZNF407,synonymous_variant,p.=,ENST00000577538,NM_001146189.1;ZNF407,synonymous_variant,p.=,ENST00000584235,;ZNF407,synonymous_variant,p.=,ENST00000581829,; G ENST00000299687 Transcript synonymous_variant 4983/7948 4983/6747 1661/2248 P ccC/ccG 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 4/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF5,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 6 74877302 74877302 C G 1 0 0 0 0 0 0 0 1 18459 581 21 4 4 ZNF407 18 74877302 Silent SNP C C3L-00009_T 21346668 74877302 5495983 273 2065 ZNF236 0 . GRCh38 18 76899190 76899190 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.1862C>T p.Pro621Leu p.P621L ENST00000320610 11/31 160 138 22 259 259 0 strelka-varscan-mutect ZNF236,missense_variant,p.Pro619Leu,ENST00000253159,NM_007345.3;ZNF236,missense_variant,p.Pro621Leu,ENST00000320610,NM_001306089.1;ZNF236,downstream_gene_variant,,ENST00000584565,;ZNF236,missense_variant,p.Pro619Leu,ENST00000543926,;ZNF236,downstream_gene_variant,,ENST00000583488,; T ENST00000320610 Transcript missense_variant 1863/7124 1862/5544 621/1847 P/L cCt/cTt 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 deleterious(0.01) 11/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 76899190 76899190 C T 1 0 0 0 0 1 0 0 0 18366 681 24 3 3 ZNF236 18 76899190 Missense_Mutation SNP C C3L-00009_T 2021888 76899190 3474095 274 2066 KEAP1 0 . GRCh38 19 10486719 10486719 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.1808G>T p.Gly603Val p.G603V ENST00000171111 6/6 244 203 41 315 315 0 strelka-varscan-mutect KEAP1,missense_variant,p.Gly603Val,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Gly603Val,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Gly151Val,ENST00000592478,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,3_prime_UTR_variant,,ENST00000590593,;KEAP1,non_coding_transcript_exon_variant,,ENST00000590237,; A ENST00000171111 Transcript missense_variant 2356/2955 1808/1875 603/624 G/V gGg/gTg 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 6/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 10486719 10486719 C A 1 0 0 0 0 1 0 0 0 8061 623 22 2 2 KEAP1 19 10486719 Missense_Mutation SNP C C3L-00009_T 10486719 48130897 275 2067 SLC7A9 0 . GRCh38 19 32859911 32859911 + Missense_Mutation SNP A A T rs751210035 C3L-00009_T C3L-00009_N A A c.803T>A p.Ile268Asn p.I268N ENST00000023064 8/13 613 578 35 542 542 0 strelka-varscan-mutect SLC7A9,missense_variant,p.Ile268Asn,ENST00000023064,NM_001243036.1,NM_001126335.1,NM_014270.4;SLC7A9,missense_variant,p.Ile268Asn,ENST00000590341,;SLC7A9,missense_variant,p.Ile268Asn,ENST00000587772,;RN7SKP22,downstream_gene_variant,,ENST00000365097,;SLC7A9,3_prime_UTR_variant,,ENST00000590465,;SLC7A9,3_prime_UTR_variant,,ENST00000592232,;SLC7A9,non_coding_transcript_exon_variant,,ENST00000589659,; T ENST00000023064 Transcript missense_variant 995/1761 803/1464 268/487 I/N aTc/aAc rs751210035 1 -1 SLC7A9 HGNC HGNC:11067 protein_coding YES CCDS12425.1 ENSP00000023064 P82251 UPI0000037773 NM_001243036.1,NM_001126335.1,NM_014270.4 deleterious(0) 8/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785:SF354,hmmpanther:PTHR11785,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS rs751210035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 32859911 32859911 A T 1 0 0 0 0 1 0 0 0 14988 333 12 4 4 SLC7A9 19 32859911 Missense_Mutation SNP A C3L-00009_T 22373192 32859911 25757705 276 2068 KMT2B 0 . GRCh38 19 35738304 35738304 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.7895G>T p.Arg2632Leu p.R2632L ENST00000420124 37/37 249 209 40 283 282 1 strelka-varscan-mutect KMT2B,missense_variant,p.Arg2632Leu,ENST00000420124,NM_014727.2;IGFLR1,downstream_gene_variant,,ENST00000246532,;IGFLR1,downstream_gene_variant,,ENST00000592537,NM_024660.2;U2AF1L4,downstream_gene_variant,,ENST00000412391,;IGFLR1,downstream_gene_variant,,ENST00000592889,;U2AF1L4,downstream_gene_variant,,ENST00000378975,NM_001040425.2;IGFLR1,downstream_gene_variant,,ENST00000588992,;U2AF1L4,downstream_gene_variant,,ENST00000292879,NM_144987.3;IGFLR1,downstream_gene_variant,,ENST00000591277,;IGFLR1,downstream_gene_variant,,ENST00000591748,;IGFLR1,downstream_gene_variant,,ENST00000586140,;IGFLR1,downstream_gene_variant,,ENST00000587101,;KMT2B,non_coding_transcript_exon_variant,,ENST00000585476,;KMT2B,non_coding_transcript_exon_variant,,ENST00000586308,;U2AF1L4,downstream_gene_variant,,ENST00000588892,;U2AF1L4,downstream_gene_variant,,ENST00000588980,;U2AF1L4,downstream_gene_variant,,ENST00000586476,;AD000671.6,downstream_gene_variant,,ENST00000589807,;U2AF1L4,downstream_gene_variant,,ENST00000590135,;U2AF1L4,downstream_gene_variant,,ENST00000585554,;IGFLR1,downstream_gene_variant,,ENST00000588018,;U2AF1L4,downstream_gene_variant,,ENST00000587987,;U2AF1L4,downstream_gene_variant,,ENST00000592913,;KMT2B,downstream_gene_variant,,ENST00000592092,;U2AF1L4,downstream_gene_variant,,ENST00000591855,;U2AF1L4,downstream_gene_variant,,ENST00000591084,;U2AF1L4,downstream_gene_variant,,ENST00000594792,;IGFLR1,downstream_gene_variant,,ENST00000592693,;U2AF1L4,downstream_gene_variant,,ENST00000591057,;IGFLR1,downstream_gene_variant,,ENST00000589175,;U2AF1L4,downstream_gene_variant,,ENST00000589429,;U2AF1L4,downstream_gene_variant,,ENST00000600296,; T ENST00000420124 Transcript missense_variant 7895/8469 7895/8148 2632/2715 R/L cGc/cTc 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 deleterious(0) 37/37 Gene3D:2.170.270.10,Pfam_domain:PF00856,PROSITE_profiles:PS50280,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF341,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 35738304 35738304 G T 1 0 0 0 0 1 0 0 0 8296 1087 38 1 1 KMT2B 19 35738304 Missense_Mutation SNP G C3L-00009_T 2878393 35738304 22879312 277 2069 ZNF850 0 . GRCh38 19 36748020 36748021 + Frame_Shift_Ins INS - - A novel C3L-00009_T C3L-00009_N - - c.3019_3020insT p.Lys1007IlefsTer4 p.K1007Ifs*4 ENST00000591344 5/5 202 185 17 187 187 0 sindel-varindel-pindel ZNF850,frameshift_variant,p.Lys1007IlefsTer4,ENST00000591344,NM_001193552.1;ZNF850,frameshift_variant,p.Lys975IlefsTer4,ENST00000614887,NM_001267779.1;ZNF850,intron_variant,,ENST00000589390,; A ENST00000591344 Transcript frameshift_variant 3178-3179/7714 3019-3020/3273 1007/1090 K/IX aaa/aTaa 1 -1 ZNF850 HGNC HGNC:27994 protein_coding YES CCDS59379.1 ENSP00000464976 A8MQ14 UPI00001D815D NM_001193552.1 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF167,Superfamily_domains:SSF57667 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 6 36748020 36748020 - A 1 0 1 1 0 0 0 0 0 18782 1841 64 0 0 ZNF850 19 36748020 Frame_Shift_Ins INS - C3L-00009_T 1009716 36748020 21869596 278 2070 ZNF229 0 . GRCh38 19 44429439 44429439 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1342C>A p.Leu448Met p.L448M ENST00000614049 6/6 172 139 33 257 256 1 strelka-varscan-mutect ZNF229,missense_variant,p.Leu442Met,ENST00000613197,NM_001278510.2;ZNF229,missense_variant,p.Leu448Met,ENST00000614049,NM_014518.3;ZNF229,downstream_gene_variant,,ENST00000592308,;CTC-512J12.4,intron_variant,,ENST00000588655,;ZNF229,intron_variant,,ENST00000591289,;ZNF229,3_prime_UTR_variant,,ENST00000620012,; T ENST00000614049 Transcript missense_variant 1776/4507 1342/2478 448/825 L/M Ctg/Atg 1 -1 ZNF229 HGNC HGNC:13022 protein_coding YES CCDS42574.1 ENSP00000479884 Q9UJW7 UPI0001747B51 NM_014518.3 deleterious(0.01) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF348,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 44429439 44429439 G T 1 0 0 0 0 1 0 0 0 18359 1020 36 2 2 ZNF229 19 44429439 Missense_Mutation SNP G C3L-00009_T 7681419 44429439 14188177 279 2071 ACPT 0 . GRCh38 19 50794843 50794843 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.1044C>T p.= p.L348L ENST00000270593 10/11 99 92 7 111 111 0 strelka-varscan-mutect ACPT,synonymous_variant,p.=,ENST00000270593,NM_033068.2;C19orf48,downstream_gene_variant,,ENST00000598463,NM_001290149.1;C19orf48,downstream_gene_variant,,ENST00000345523,NM_001290152.1,NM_001290155.1,NM_199250.2,NM_001290151.1,NM_001290150.1;C19orf48,downstream_gene_variant,,ENST00000391812,NM_199249.2,NM_001290154.1,NM_001290153.1;C19orf48,downstream_gene_variant,,ENST00000596655,NM_032712.2;C19orf48,downstream_gene_variant,,ENST00000597493,;C19orf48,downstream_gene_variant,,ENST00000597705,;C19orf48,downstream_gene_variant,,ENST00000596287,;C19orf48,downstream_gene_variant,,ENST00000601267,;C19orf48,downstream_gene_variant,,ENST00000600373,;C19orf48,downstream_gene_variant,,ENST00000593287,;CTD-2568A17.1,upstream_gene_variant,,ENST00000636757,;SNORD88A,downstream_gene_variant,,ENST00000408314,;SNORD88B,downstream_gene_variant,,ENST00000408454,;CTD-2568A17.8,upstream_gene_variant,,ENST00000594114,;C19orf48,downstream_gene_variant,,ENST00000595794,;C19orf48,downstream_gene_variant,,ENST00000599004,;C19orf48,downstream_gene_variant,,ENST00000596554,; T ENST00000270593 Transcript synonymous_variant 1044/1347 1044/1281 348/426 L ctC/ctT 1 1 ACPT HGNC HGNC:14376 protein_coding YES CCDS12802.1 ENSP00000270593 Q9BZG2 UPI0000048D54 NM_033068.2 10/11 hmmpanther:PTHR11567,hmmpanther:PTHR11567:SF110,Gene3D:3.40.50.1240,Superfamily_domains:SSF53254 LOW SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -14.78698 1 1 1 1 0 T 2 4 6 50794843 50794843 C T 1 0 0 0 0 0 0 0 1 210 813 29 3 3 ACPT 19 50794843 Silent SNP C C3L-00009_T 6365404 50794843 7822773 280 2072 FPR1 0 . GRCh38 19 51746646 51746646 + Missense_Mutation SNP C C A rs547228145 C3L-00009_T C3L-00009_N C C c.349G>T p.Ala117Ser p.A117S ENST00000595042 3/3 348 328 20 373 372 1 strelka-varscan-mutect FPR1,missense_variant,p.Ala117Ser,ENST00000595042,NM_001193306.1;FPR1,missense_variant,p.Ala117Ser,ENST00000304748,NM_002029.3;FPR1,missense_variant,p.Ala117Ser,ENST00000600815,;FPR1,downstream_gene_variant,,ENST00000594900,; A ENST00000595042 Transcript missense_variant 491/1965 349/1053 117/350 A/S Gcc/Tcc rs547228145,COSM475129 1 -1 FPR1 HGNC HGNC:3826 protein_coding YES CCDS12839.1 ENSP00000471493 P21462 UPI0000050484 NM_001193306.1 tolerated(0.12) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF15,hmmpanther:PTHR24225,PROSITE_patterns:PS00237,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs547228145 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 51746646 51746646 C A 1 0 0 0 0 1 0 0 0 5904 768 27 1 1 FPR1 19 51746646 Missense_Mutation SNP C C3L-00009_T 951803 51746646 6870970 281 2073 ZNF836 0 . GRCh38 19 52156800 52156800 + Missense_Mutation SNP T T A novel C3L-00009_T C3L-00009_N T T c.883A>T p.Ser295Cys p.S295C ENST00000597252 5/5 237 143 94 254 254 0 strelka-varscan-mutect ZNF836,missense_variant,p.Ser295Cys,ENST00000597252,NM_001102657.1;ZNF836,missense_variant,p.Ser295Cys,ENST00000322146,;ZNF836,downstream_gene_variant,,ENST00000597065,;ZNF836,downstream_gene_variant,,ENST00000596428,;CTC-471J1.8,intron_variant,,ENST00000594362,;CTC-471J1.8,intron_variant,,ENST00000598982,;ZNF836,upstream_gene_variant,,ENST00000599618,; A ENST00000597252 Transcript missense_variant 1257/3209 883/2811 295/936 S/C Agt/Tgt 1 -1 ZNF836 HGNC HGNC:34333 protein_coding YES CCDS46162.1 ENSP00000470239 Q6ZNA1 UPI00001D818C NM_001102657.1 tolerated(0.12) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF330,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 52156800 52156800 T A 1 0 0 0 0 1 0 0 0 18772 1609 56 4 4 ZNF836 19 52156800 Missense_Mutation SNP T C3L-00009_T 410154 52156800 6460816 282 2074 ZNF415 0 . GRCh38 19 53108738 53108738 + Missense_Mutation SNP C C T C3L-00009_T C3L-00009_N C C c.1307G>A p.Gly436Glu p.G436E ENST00000500065 4/4 355 328 27 322 322 0 strelka-varscan-mutect ZNF415,missense_variant,p.Gly436Glu,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Gly436Glu,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Gly436Glu,ENST00000243643,NM_018355.3;ZNF415,missense_variant,p.Gly206Glu,ENST00000601493,;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; T ENST00000500065 Transcript missense_variant 1641/2496 1307/1668 436/555 G/E gGa/gAa COSM4862813,COSM712945 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,Gene3D:3.30.160.60,SMART_domains:SM00614,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 4 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 53108738 53108738 C T 1 0 0 0 0 1 0 0 0 18464 855 30 3 3 ZNF415 19 53108738 Missense_Mutation SNP C C3L-00009_T 951938 53108738 5508878 283 2075 LILRB5 0 . GRCh38 19 54250834 54250834 + Silent SNP C C T novel C3L-00009_T C3L-00009_N C C c.1728G>A p.= p.R576R ENST00000449561 13/13 346 151 195 344 344 0 strelka-varscan-mutect LILRB5,synonymous_variant,p.=,ENST00000316219,NM_006840.4;LILRB5,synonymous_variant,p.=,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,synonymous_variant,p.=,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000621581,;LILRB5,non_coding_transcript_exon_variant,,ENST00000615654,;RPS9,downstream_gene_variant,,ENST00000448962,;AC010492.4,upstream_gene_variant,,ENST00000506567,; T ENST00000449561 Transcript synonymous_variant 1799/2137 1728/1776 576/591 R agG/agA 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 13/13 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 54250834 54250834 C T 1 0 0 0 0 0 0 0 1 8702 622 22 3 3 LILRB5 19 54250834 Silent SNP C C3L-00009_T 1142096 54250834 4366782 284 2076 LILRB2 0 . GRCh38 19 54277595 54277595 + Missense_Mutation SNP G G C novel C3L-00009_T C3L-00009_N G G c.1315C>G p.Pro439Ala p.P439A ENST00000391749 9/14 170 146 24 169 169 0 varscan-mutect LILRB2,missense_variant,p.Pro438Ala,ENST00000391748,NM_001278403.2;LILRB2,missense_variant,p.Pro323Ala,ENST00000434421,NM_001278404.2;LILRB2,missense_variant,p.Pro438Ala,ENST00000314446,NM_001080978.3;LILRB2,missense_variant,p.Pro439Ala,ENST00000391749,NM_005874.4;LILRB2,missense_variant,p.Pro439Ala,ENST00000391746,NM_001278405.2;MIR4752,upstream_gene_variant,,ENST00000579672,;LILRB2,downstream_gene_variant,,ENST00000471216,;LILRB2,missense_variant,p.Pro115Ala,ENST00000455108,;LILRB2,non_coding_transcript_exon_variant,,ENST00000493242,; C ENST00000391749 Transcript missense_variant 1587/2286 1315/1797 439/598 P/A Cct/Gct 1 -1 LILRB2 HGNC HGNC:6606 protein_coding YES CCDS12886.1 ENSP00000375629 Q8N423 UPI00034F23A2 NM_005874.4 tolerated(0.08) 9/14 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 54277595 54277595 G C 1 0 0 0 0 1 0 0 0 8699 1246 43 4 4 LILRB2 19 54277595 Missense_Mutation SNP G C3L-00009_T 26761 54277595 4340021 285 2077 ZNF835 0 . GRCh38 19 56664873 56664873 + Missense_Mutation SNP G G A rs576625581 C3L-00009_T C3L-00009_N G G c.326C>T p.Pro109Leu p.P109L ENST00000537055 2/2 413 326 87 617 617 0 strelka-varscan-mutect ZNF835,missense_variant,p.Pro109Leu,ENST00000537055,NM_001005850.2;ZNF835,downstream_gene_variant,,ENST00000601659,; A ENST00000537055 Transcript missense_variant 558/3450 326/1614 109/537 P/L cCg/cTg rs576625581 1 -1 ZNF835 HGNC HGNC:34332 protein_coding YES CCDS56105.1 ENSP00000444747 Q9Y2P0 UPI0000EE7244 NM_001005850.2 tolerated(0.24) 2/2 Gene3D:3.30.160.60,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF368,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs576625581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 56664873 56664873 G A 1 0 0 0 0 1 0 0 0 18771 1116 39 1 1 ZNF835 19 56664873 Missense_Mutation SNP G C3L-00009_T 2387278 56664873 1952743 286 2078 ZSCAN4 0 . GRCh38 19 57678749 57678749 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.1146C>A p.Asn382Lys p.N382K ENST00000318203 5/5 182 128 54 256 256 0 strelka-varscan-mutect ZSCAN4,missense_variant,p.Asn382Lys,ENST00000318203,NM_152677.2;ZSCAN4,missense_variant,p.Asn382Lys,ENST00000612521,;ZNF551,upstream_gene_variant,,ENST00000282296,NM_138347.4;ZNF551,upstream_gene_variant,,ENST00000601064,NM_001270938.1;AC003006.7,upstream_gene_variant,,ENST00000594684,;ZNF551,upstream_gene_variant,,ENST00000596085,;ZNF551,upstream_gene_variant,,ENST00000599402,;AC003006.7,upstream_gene_variant,,ENST00000599221,; A ENST00000318203 Transcript missense_variant 1843/2246 1146/1302 382/433 N/K aaC/aaA 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS rs1171193212 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 57678749 57678749 C A 1 0 0 0 0 1 0 0 0 18836 506 18 2 2 ZSCAN4 19 57678749 Missense_Mutation SNP C C3L-00009_T 1013876 57678749 938867 287 2079 ADRA1D 0 . GRCh38 20 4248624 4248624 + Frame_Shift_Del DEL C C - novel C3L-00009_T C3L-00009_N C C c.334delG p.Ala112GlnfsTer25 p.A112Qfs*25 ENST00000379453 1/2 237 187 50 417 417 0 sindel-varindel-pindel ADRA1D,frameshift_variant,p.Ala112GlnfsTer25,ENST00000379453,NM_000678.3; - ENST00000379453 Transcript frameshift_variant 451/2728 334/1719 112/572 A/X Gca/ca 1 -1 ADRA1D HGNC HGNC:280 protein_coding YES CCDS13079.1 ENSP00000368766 P25100 B0ZBE0 UPI000003B078 NM_000678.3 1/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF14,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 6 4248624 4248624 C - 1 0 1 0 1 0 0 0 0 412 739 26 0 0 ADRA1D 20 4248624 Frame_Shift_Del DEL C C3L-00009_T 4248624 60195543 288 2080 PAX1 0 . GRCh38 20 21709376 21709376 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1214G>T p.Gly405Val p.G405V ENST00000398485 4/5 130 104 26 181 181 0 strelka-varscan-mutect PAX1,missense_variant,p.Gly405Val,ENST00000613128,NM_001257096.1;PAX1,missense_variant,p.Gly405Val,ENST00000398485,NM_006192.4;PAX1,missense_variant,p.Gly381Val,ENST00000444366,;PAX1,non_coding_transcript_exon_variant,,ENST00000460221,;PAX1,downstream_gene_variant,,ENST00000485038,; T ENST00000398485 Transcript missense_variant 1268/2838 1214/1605 405/534 G/V gGg/gTg 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious_low_confidence(0) 4/5 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 21709376 21709376 G T 1 0 0 0 0 1 0 0 0 11563 1232 43 2 2 PAX1 20 21709376 Missense_Mutation SNP G C3L-00009_T 17460752 21709376 42734791 289 2081 PTPRT 0 . GRCh38 20 42248737 42248737 + Silent SNP G G T novel C3L-00009_T C3L-00009_N G G c.2319C>A p.= p.L773L ENST00000373198 15/32 143 121 22 185 184 1 strelka-varscan-mutect PTPRT,synonymous_variant,p.=,ENST00000373198,NM_133170.3;PTPRT,synonymous_variant,p.=,ENST00000373193,;PTPRT,synonymous_variant,p.=,ENST00000373201,;PTPRT,synonymous_variant,p.=,ENST00000373190,;PTPRT,synonymous_variant,p.=,ENST00000373184,;PTPRT,synonymous_variant,p.=,ENST00000356100,;PTPRT,synonymous_variant,p.=,ENST00000373187,NM_007050.5;PTPRT,synonymous_variant,p.=,ENST00000612229,;PTPRT,synonymous_variant,p.=,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript synonymous_variant 2555/12746 2319/4383 773/1460 L ctC/ctA 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 15/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 6 42248737 42248737 G T 1 0 0 0 0 0 0 0 1 12967 1161 41 2 2 PTPRT 20 42248737 Silent SNP G C3L-00009_T 20539361 42248737 22195430 290 2082 EDN3 0 . GRCh38 20 59300822 59300822 + Missense_Mutation SNP G G T rs567434377 C3L-00009_T C3L-00009_N G G c.10G>T p.Gly4Trp p.G4W ENST00000337938 1/5 277 222 55 353 353 0 strelka-varscan-mutect EDN3,missense_variant,p.Gly4Trp,ENST00000311585,NM_207032.2;EDN3,missense_variant,p.Gly4Trp,ENST00000337938,NM_001302455.1,NM_207034.2;EDN3,missense_variant,p.Gly4Trp,ENST00000371028,;EDN3,missense_variant,p.Gly4Trp,ENST00000395654,NM_207033.2;EDN3,missense_variant,p.Gly4Trp,ENST00000371025,NM_001302456.1; T ENST00000337938 Transcript missense_variant 396/2636 10/717 4/238 G/W Ggg/Tgg rs567434377 1 1 EDN3 HGNC HGNC:3178 protein_coding YES CCDS13477.1 ENSP00000337128 P14138 UPI000012A221 NM_001302455.1,NM_207034.2 deleterious(0) 1/5 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13874,hmmpanther:PTHR13874:SF11 MODERATE 1 SNV 1 1 PASS rs567434377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 59300822 59300822 G T 1 0 0 0 0 1 0 0 0 4746 1232 43 2 2 EDN3 20 59300822 Missense_Mutation SNP G C3L-00009_T 17052085 59300822 5143345 291 2083 BACH1 0 . GRCh38 21 29326059 29326059 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.235G>T p.Val79Leu p.V79L ENST00000399921 3/5 50 41 9 55 55 0 strelka-varscan-mutect BACH1,missense_variant,p.Val79Leu,ENST00000399921,NM_206866.2;BACH1,missense_variant,p.Val79Leu,ENST00000286800,NM_001186.3;BACH1,missense_variant,p.Val79Leu,ENST00000451655,;BACH1,missense_variant,p.Val79Leu,ENST00000447177,;BACH1,missense_variant,p.Val79Leu,ENST00000435072,;BACH1,upstream_gene_variant,,ENST00000422809,;BACH1,upstream_gene_variant,,ENST00000468059,;BACH1,downstream_gene_variant,,ENST00000546469,;BACH1,downstream_gene_variant,,ENST00000550131,;BACH1,downstream_gene_variant,,ENST00000548219,;BACH1,downstream_gene_variant,,ENST00000547141,;BACH1,downstream_gene_variant,,ENST00000548467,; T ENST00000399921 Transcript missense_variant,splice_region_variant 478/5769 235/2211 79/736 V/L Gtg/Ttg 1 1 BACH1 HGNC HGNC:935 protein_coding YES CCDS13585.1 ENSP00000382805 O14867 UPI000012673F NM_206866.2 deleterious(0) 3/5 PROSITE_profiles:PS50097,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF176,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.98254 0.9999997 1 1 1 0 T 3 4 6 29326059 29326059 G T 1 0 0 0 0 1 0 0 0 1441 1275 44 2 2 BACH1 21 29326059 Missense_Mutation SNP G C3L-00009_T 29326059 17383924 292 2084 KRTAP8-1 0 . GRCh38 21 30813078 30813078 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.143G>T p.Gly48Val p.G48V ENST00000329621 1/1 215 194 21 274 273 1 strelka-varscan-mutect KRTAP8-1,missense_variant,p.Gly48Val,ENST00000329621,NM_175857.3; A ENST00000329621 Transcript missense_variant 175/556 143/192 48/63 G/V gGc/gTc 1 -1 KRTAP8-1 HGNC HGNC:18935 protein_coding YES CCDS13607.1 ENSP00000332805 Q8IUC2 UPI00000747A5 NM_175857.3 deleterious_low_confidence(0.02) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR36131,Pfam_domain:PF11759,PD027172 MODERATE 1 SNV 1 PASS rs925971216 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 6 30813078 30813078 C A 1 0 0 0 0 1 0 0 0 8468 739 26 2 2 KRTAP8-1 21 30813078 Missense_Mutation SNP C C3L-00009_T 1487019 30813078 15896905 293 2085 UBASH3A 0 . GRCh38 21 42404034 42404034 + Frame_Shift_Del DEL C C - novel C3L-00009_T C3L-00009_N C C c.90delC p.Met31TrpfsTer9 p.M31Wfs*9 ENST00000319294 1/15 83 70 13 100 100 0 sindel-varindel-pindel UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000319294,NM_018961.3;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000291535,NM_001001895.2;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000398367,NM_001243467.1;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000635189,;UBASH3A,non_coding_transcript_exon_variant,,ENST00000634453,;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000473381,;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000635325,;UBASH3A,frameshift_variant,p.Met31TrpfsTer20,ENST00000634718,;UBASH3A,frameshift_variant,p.Met31TrpfsTer9,ENST00000635108,; - ENST00000319294 Transcript frameshift_variant 120/2504 89/1986 30/661 A/X gCc/gc 1 1 UBASH3A HGNC HGNC:12462 protein_coding YES CCDS13687.1 ENSP00000317327 P57075 UPI0000137941 NM_018961.3 1/15 PROSITE_profiles:PS50030,hmmpanther:PTHR16469:SF7,hmmpanther:PTHR16469,Gene3D:1.10.8.10,Superfamily_domains:SSF46934 HIGH 1 deletion 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 6 42404034 42404034 C - 1 0 1 0 1 0 0 0 0 17361 739 26 0 0 UBASH3A 21 42404034 Frame_Shift_Del DEL C C3L-00009_T 11590956 42404034 4305949 294 2086 CCT8L2 0 . GRCh38 22 16590923 16590923 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.1628A>G p.His543Arg p.H543R ENST00000359963 1/1 172 159 13 263 263 0 varscan-mutect CCT8L2,missense_variant,p.His543Arg,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; C ENST00000359963 Transcript missense_variant 1888/2060 1628/1674 543/557 H/R cAc/cGc 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 tolerated_low_confidence(0.71) 1/1 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100 MODERATE 1 SNV 1 PASS rs1413206111 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 16590923 16590923 T C 1 0 0 0 0 1 0 0 0 2662 1696 59 5 5 CCT8L2 22 16590923 Missense_Mutation SNP T C3L-00009_T 16590923 34227545 295 2087 SLC7A4 0 . GRCh38 22 21031801 21031801 + Frame_Shift_Del DEL C C - novel C3L-00009_T C3L-00009_N C C c.12delG p.Leu5CysfsTer14 p.L5Cfs*14 ENST00000382932 2/5 19 10 9 23 23 0 sindel-varindel-pindel SLC7A4,frameshift_variant,p.Leu5CysfsTer14,ENST00000382932,NM_004173.2;SLC7A4,frameshift_variant,p.Leu5CysfsTer14,ENST00000403586,;SLC7A4,frameshift_variant,p.Leu5CysfsTer14,ENST00000426145,;P2RX6,downstream_gene_variant,,ENST00000413302,NM_005446.3;P2RX6,downstream_gene_variant,,ENST00000401443,NM_001159554.1;MIR649,downstream_gene_variant,,ENST00000384843,;AC002472.11,intron_variant,,ENST00000450652,;P2RX6P,downstream_gene_variant,,ENST00000439119,;P2RX6,downstream_gene_variant,,ENST00000442475,;P2RX6,downstream_gene_variant,,ENST00000432930,;P2RX6,downstream_gene_variant,,ENST00000422210,; - ENST00000382932 Transcript frameshift_variant 80/2313 12/1908 4/635 G/X ggG/gg 1 -1 SLC7A4 HGNC HGNC:11062 protein_coding YES CCDS33608.1 ENSP00000372390 O43246 UPI0000169EC7 NM_004173.2 2/5 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF410 HIGH 1 deletion 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999982 1 1 1 0 - 7 5 6 21031801 21031801 C - 1 0 1 0 1 0 0 0 0 14982 726 26 0 0 SLC7A4 22 21031801 Frame_Shift_Del DEL C C3L-00009_T 4440878 21031801 29786667 296 2088 PIM3 0 . GRCh38 22 49961175 49961175 + Missense_Mutation SNP C C G novel C3L-00009_T C3L-00009_N C C c.136C>G p.Leu46Val p.L46V ENST00000360612 2/6 168 133 35 209 209 0 strelka-varscan-mutect PIM3,missense_variant,p.Leu46Val,ENST00000360612,NM_001001852.3;MIR6821,upstream_gene_variant,,ENST00000617625,;PIM3,non_coding_transcript_exon_variant,,ENST00000467480,; G ENST00000360612 Transcript missense_variant 571/2369 136/981 46/326 L/V Ctg/Gtg 1 1 PIM3 HGNC HGNC:19310 protein_coding YES CCDS33678.1 ENSP00000353824 Q86V86 UPI00001582C4 NM_001001852.3 deleterious(0.01) 2/6 Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF037993,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR22984,hmmpanther:PTHR22984:SF8,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs956855982 . 0 207 0 3 0 0 0 0 -20 0.9999967 1 1 1 0 G 3 3 6 49961175 49961175 C G 1 0 0 0 0 1 0 0 0 12024 796 28 4 4 PIM3 22 49961175 Missense_Mutation SNP C C3L-00009_T 28929374 49961175 857293 297 2089 MAGEB6 0 . GRCh38 X 26194530 26194530 + Missense_Mutation SNP G G T C3L-00009_T C3L-00009_N G G c.684G>T p.Glu228Asp p.E228D ENST00000379034 2/2 50 32 18 64 64 0 strelka-varscan-mutect MAGEB6,missense_variant,p.Glu228Asp,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript missense_variant 833/1949 684/1224 228/407 E/D gaG/gaT COSM1119598 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 deleterious(0.01) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 26194530 26194530 G T 1 0 0 0 0 1 0 0 0 9096 1020 36 2 2 MAGEB6 23 26194530 Missense_Mutation SNP G C3L-00009_T 26194530 129846365 298 2090 GPR173 0 . GRCh38 X 53077132 53077132 + Nonsense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.511G>T p.Glu171Ter p.E171* ENST00000332582 2/2 127 103 24 187 187 0 strelka-varscan-mutect GPR173,stop_gained,p.Glu171Ter,ENST00000332582,NM_018969.5;GPR173,downstream_gene_variant,,ENST00000375466,; T ENST00000332582 Transcript stop_gained 1002/4485 511/1122 171/373 E/* Gag/Tag 1 1 GPR173 HGNC HGNC:18186 protein_coding YES CCDS14349.1 ENSP00000331600 Q9NS66 UPI0000050480 NM_018969.5 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF4,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 6 53077132 53077132 G T 1 0 0 0 0 0 1 0 0 6555 1175 41 2 2 GPR173 23 53077132 Nonsense_Mutation SNP G C3L-00009_T 26882602 53077132 102963763 299 2091 PAGE5 0 . GRCh38 X 55222728 55222728 + Missense_Mutation SNP A A G novel C3L-00009_T C3L-00009_N A A c.358A>G p.Thr120Ala p.T120A ENST00000289619 4/5 146 106 40 166 166 0 strelka-varscan-mutect PAGE5,missense_variant,p.Thr120Ala,ENST00000289619,NM_130467.4;PAGE5,missense_variant,p.Thr100Ala,ENST00000374955,NM_001013435.2;PAGE5,missense_variant,p.Thr83Ala,ENST00000374952,; G ENST00000289619 Transcript missense_variant 603/741 358/393 120/130 T/A Act/Gct 1 1 PAGE5 HGNC HGNC:29992 protein_coding YES CCDS14368.1 ENSP00000289619 Q96GU1 UPI0000071A52 NM_130467.4 tolerated(0.59) 4/5 Pfam_domain:PF05831,hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF14,SMART_domains:SM01379 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 6 55222728 55222728 A G 1 0 0 0 0 1 0 0 0 11472 159 6 5 5 PAGE5 23 55222728 Missense_Mutation SNP A C3L-00009_T 2145596 55222728 100818167 300 2092 NHSL2 0 . GRCh38 X 72134662 72134662 + Missense_Mutation SNP C C T novel C3L-00009_T C3L-00009_N C C c.718C>T p.Leu240Phe p.L240F ENST00000633930 4/8 91 70 21 71 71 0 strelka-varscan-mutect NHSL2,missense_variant,p.Leu240Phe,ENST00000633930,NM_001013627.2;NHSL2,5_prime_UTR_variant,,ENST00000510661,;NHSL2,intron_variant,,ENST00000631375,;NHSL2,intron_variant,,ENST00000632230,;RGAG4,upstream_gene_variant,,ENST00000609883,NM_001024455.3;NHSL2,downstream_gene_variant,,ENST00000631833,;NHSL2,non_coding_transcript_exon_variant,,ENST00000373677,;RGAG4,upstream_gene_variant,,ENST00000479991,; T ENST00000633930 Transcript missense_variant 988/13660 718/3678 240/1225 L/F Ctt/Ttt 1 1 NHSL2 HGNC HGNC:33737 protein_coding YES ENSP00000488668 A0A0J9YY34 UPI0001B09231 NM_001013627.2 deleterious(0.02) 4/8 hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF2 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 72134662 72134662 C T 1 0 0 0 0 1 0 0 0 10445 797 28 3 3 NHSL2 23 72134662 Missense_Mutation SNP C C3L-00009_T 16911934 72134662 83906233 301 2093 TENM1 0 . GRCh38 X 124422576 124422576 + Missense_Mutation SNP C C A C3L-00009_T C3L-00009_N C C c.4167G>T p.Leu1389Phe p.L1389F ENST00000422452 24/32 117 84 33 167 167 0 strelka-varscan-mutect TENM1,missense_variant,p.Leu1389Phe,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Leu1382Phe,ENST00000371130,NM_014253.3;STAG2,non_coding_transcript_exon_variant,,ENST00000469481,; A ENST00000422452 Transcript missense_variant 4231/12891 4167/8199 1389/2732 L/F ttG/ttT COSM5411930,COSM5411931 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 24/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,Gene3D:2.120.10.30,Superfamily_domains:SSF101898 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 124422576 124422576 C A 1 0 0 0 0 1 0 0 0 16171 593 21 2 2 TENM1 23 124422576 Missense_Mutation SNP C C3L-00009_T 52287914 124422576 31618319 302 2094 TENM1 0 . GRCh38 X 124651982 124651982 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.1511C>A p.Pro504His p.P504H ENST00000422452 8/32 142 101 41 218 218 0 strelka-varscan-mutect TENM1,missense_variant,p.Pro504His,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Pro504His,ENST00000371130,NM_014253.3; T ENST00000422452 Transcript missense_variant 1575/12891 1511/8199 504/2732 P/H cCt/cAt 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 tolerated(0.34) 8/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 124651982 124651982 G T 1 0 0 0 0 1 0 0 0 16171 1000 35 2 2 TENM1 23 124651982 Missense_Mutation SNP G C3L-00009_T 229406 124651982 31388913 303 2095 TEX13C 0 . GRCh38 X 125321968 125321968 + Missense_Mutation SNP C C A novel C3L-00009_T C3L-00009_N C C c.1849C>A p.Pro617Thr p.P617T ENST00000632600 1/1 305 269 36 375 374 1 strelka-varscan-mutect TEX13C,missense_variant,p.Pro617Thr,ENST00000632600,NM_001195272.1;RP13-147D17.1,downstream_gene_variant,,ENST00000394467,; A ENST00000632600 Transcript missense_variant 1849/5095 1849/2982 617/993 P/T Ccc/Acc 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 tolerated(0.06) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 6 125321968 125321968 C A 1 0 0 0 0 1 0 0 0 16199 739 26 2 2 TEX13C 23 125321968 Missense_Mutation SNP C C3L-00009_T 669986 125321968 30718927 304 2096 SMARCA1 0 . GRCh38 X 129481130 129481130 + Missense_Mutation SNP G G T novel C3L-00009_T C3L-00009_N G G c.2273C>A p.Ala758Glu p.A758E ENST00000371121 18/25 163 122 41 149 149 0 strelka-varscan-mutect SMARCA1,missense_variant,p.Ala758Glu,ENST00000371122,NM_003069.4;SMARCA1,missense_variant,p.Ala746Glu,ENST00000371123,NM_001282875.1;SMARCA1,missense_variant,p.Ala758Glu,ENST00000371121,NM_001282874.1;SMARCA1,non_coding_transcript_exon_variant,,ENST00000617310,; T ENST00000371121 Transcript missense_variant 2308/3564 2273/3213 758/1070 A/E gCa/gAa 1 -1 SMARCA1 HGNC HGNC:11097 protein_coding YES CCDS76019.1 ENSP00000360162 B7ZLQ5 UPI00004258DE NM_001282874.1 deleterious(0) 18/25 Pfam_domain:PF09110 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 6 129481130 129481130 G T 1 0 0 0 0 1 0 0 0 15061 1319 46 2 2 SMARCA1 23 129481130 Missense_Mutation SNP G C3L-00009_T 4159162 129481130 26559765 305 2097 GPC3 0 . GRCh38 X 133536284 133536284 + Missense_Mutation SNP T T C novel C3L-00009_T C3L-00009_N T T c.1652A>G p.Tyr551Cys p.Y551C ENST00000394299 9/9 197 135 62 243 243 0 strelka-varscan-mutect GPC3,missense_variant,p.Tyr528Cys,ENST00000370818,NM_004484.3,NM_001164618.1;GPC3,missense_variant,p.Tyr551Cys,ENST00000394299,NM_001164617.1;GPC3,missense_variant,p.Tyr474Cys,ENST00000631057,NM_001164619.1;RNU6-203P,upstream_gene_variant,,ENST00000384038,; C ENST00000394299 Transcript missense_variant 1849/2379 1652/1812 551/603 Y/C tAt/tGt 1 -1 GPC3 HGNC HGNC:4451 protein_coding YES CCDS55496.1 ENSP00000377836 P51654 UPI00015E044A NM_001164617.1 tolerated(0.06) 9/9 Pfam_domain:PF01153,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 6 133536284 133536284 T C 1 0 0 0 0 1 0 0 0 6501 1406 49 5 5 GPC3 23 133536284 Missense_Mutation SNP T C3L-00009_T 4055154 133536284 22504611 306 2098 SKI 0 . GRCh38 1 2306196 2306196 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1944G>T p.= p.R648R ENST00000378536 6/7 219 135 84 177 176 1 strelka-varscan-mutect SKI,synonymous_variant,p.=,ENST00000378536,NM_003036.3;SKI,downstream_gene_variant,,ENST00000478223,;SKI,downstream_gene_variant,,ENST00000508416,;SKI,downstream_gene_variant,,ENST00000507179,; T ENST00000378536 Transcript synonymous_variant 2016/5613 1944/2187 648/728 R cgG/cgT 1 1 SKI HGNC HGNC:10896 protein_coding YES CCDS39.1 ENSP00000367797 P12755 UPI00001359DE NM_003036.3 6/7 hmmpanther:PTHR10005:SF15,hmmpanther:PTHR10005 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 2306196 2306196 G T 1 0 0 0 0 0 0 0 1 14619 1219 43 2 2 SKI 1 2306196 Silent SNP G C3L-00080_T 2306196 246650226 1 2099 CEP104 0 . GRCh38 1 3829949 3829949 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1885G>T p.Ala629Ser p.A629S ENST00000378230 14/22 303 251 52 278 278 0 strelka-varscan-mutect CEP104,missense_variant,p.Ala629Ser,ENST00000378230,NM_014704.3;CEP104,upstream_gene_variant,,ENST00000461667,;CEP104,upstream_gene_variant,,ENST00000438539,;CEP104,downstream_gene_variant,,ENST00000460038,;CEP104,non_coding_transcript_exon_variant,,ENST00000495701,;CEP104,downstream_gene_variant,,ENST00000494653,; A ENST00000378230 Transcript missense_variant 2210/6424 1885/2778 629/925 A/S Gcg/Tcg 1 -1 CEP104 HGNC HGNC:24866 protein_coding YES CCDS30571.1 ENSP00000367476 O60308 UPI0000139AA8 NM_014704.3 tolerated(0.05) 14/22 hmmpanther:PTHR13371:SF0,hmmpanther:PTHR13371,Gene3D:1.25.10.10,SMART_domains:SM01349,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 3829949 3829949 C A 1 0 0 0 0 1 0 0 0 2954 739 26 2 2 CEP104 1 3829949 Missense_Mutation SNP C C3L-00080_T 1523753 3829949 245126473 2 2100 PRAMEF6 0 . GRCh38 1 12941314 12941314 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.539T>A p.Leu180Gln p.L180Q ENST00000376189 3/4 137 110 27 143 143 0 strelka-varscan-mutect PRAMEF6,missense_variant,p.Leu180Gln,ENST00000376189,NM_001010889.2;PRAMEF6,missense_variant,p.Leu180Gln,ENST00000415464,; T ENST00000376189 Transcript missense_variant 625/1720 539/1431 180/476 L/Q cTg/cAg 1 -1 PRAMEF6 HGNC HGNC:30583 protein_coding YES CCDS30594.1 ENSP00000365360 Q5VXH4 UPI0000418E57 NM_001010889.2 deleterious(0) 3/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,Low_complexity_(Seg):seg,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 9 198 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 12941314 12941314 A T 1 0 0 0 0 1 0 0 0 12568 188 7 4 4 PRAMEF6 1 12941314 Missense_Mutation SNP A C3L-00080_T 9111365 12941314 236015108 3 2101 PRAMEF8 0 . GRCh38 1 13283862 13283862 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.230C>A p.Ser77Ter p.S77* ENST00000357367 2/4 174 148 26 161 161 0 strelka-varscan-mutect PRAMEF8,stop_gained,p.Ser77Ter,ENST00000357367,NM_001012276.3;PRAMEF8,stop_gained,p.Ser77Ter,ENST00000621519,;PRAMEF8,stop_gained,p.Ser77Ter,ENST00000614831,;RNU6-443P,upstream_gene_variant,,ENST00000384780,; T ENST00000357367 Transcript stop_gained 313/1844 230/1425 77/474 S/* tCa/tAa 1 -1 PRAMEF8 HGNC HGNC:24074 protein_coding YES CCDS72709.1 ENSP00000349931 Q5VWM4 UPI000191706C NM_001012276.3 2/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,PIRSF_domain:PIRSF038286 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 13283862 13283862 G T 1 0 0 0 0 0 1 0 0 12570 1294 45 2 2 PRAMEF8 1 13283862 Nonsense_Mutation SNP G C3L-00080_T 342548 13283862 235672560 4 2102 PRAMEF14 0 . GRCh38 1 13344440 13344440 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.464T>G p.Leu155Arg p.L155R ENST00000334600 3/4 400 328 72 373 373 0 strelka-varscan-mutect PRAMEF14,missense_variant,p.Leu155Arg,ENST00000334600,NM_001024661.2;PRAMEF14,upstream_gene_variant,,ENST00000602491,; C ENST00000334600 Transcript missense_variant 567/1690 464/1425 155/474 L/R cTc/cGc 1 -1 PRAMEF14 HGNC HGNC:13576 protein_coding YES CCDS76109.1 ENSP00000334410 A6NFR9 UPI000013DEF2 NM_001024661.2 deleterious(0) 3/4 hmmpanther:PTHR14224:SF2,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 13344440 13344440 A C 1 0 0 0 0 1 0 0 0 12558 304 11 5 5 PRAMEF14 1 13344440 Missense_Mutation SNP A C3L-00080_T 60578 13344440 235611982 5 2103 CLCNKA 0 . GRCh38 1 16033218 16033218 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1978T>A p.Ser660Thr p.S660T ENST00000331433 19/20 201 134 67 154 154 0 strelka-varscan-mutect CLCNKA,missense_variant,p.Ser659Thr,ENST00000375692,NM_001042704.1;CLCNKA,missense_variant,p.Ser660Thr,ENST00000331433,NM_004070.3;CLCNKA,missense_variant,p.Ser617Thr,ENST00000439316,NM_001257139.1;CLCNKA,non_coding_transcript_exon_variant,,ENST00000464764,;CLCNKA,downstream_gene_variant,,ENST00000491433,;RP11-5P18.10,downstream_gene_variant,,ENST00000447882,; A ENST00000331433 Transcript missense_variant 1997/2475 1978/2064 660/687 S/T Tcg/Acg 1 1 CLCNKA HGNC HGNC:2026 protein_coding YES CCDS167.1 ENSP00000332771 P51800 UPI0000127993 NM_004070.3 deleterious(0.02) 19/20 Gene3D:3.10.580.10,PROSITE_profiles:PS51371,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF95,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS rs753873720 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 16033218 16033218 T A 1 0 0 0 0 1 0 0 0 3233 1435 50 4 4 CLCNKA 1 16033218 Missense_Mutation SNP T C3L-00080_T 2688778 16033218 232923204 6 2104 PADI2 0 . GRCh38 1 17069164 17069164 + Silent SNP G G T C3L-00080_T C3L-00080_N G G c.1878C>A p.= p.G626G ENST00000375486 16/16 570 495 75 431 430 1 strelka-varscan-mutect PADI2,synonymous_variant,p.=,ENST00000375486,NM_007365.2;PADI2,non_coding_transcript_exon_variant,,ENST00000466151,;PADI2,non_coding_transcript_exon_variant,,ENST00000479534,; T ENST00000375486 Transcript synonymous_variant 1942/4345 1878/1998 626/665 G ggC/ggA COSM1473015,COSM4813635 1 -1 PADI2 HGNC HGNC:18341 protein_coding YES CCDS177.1 ENSP00000364635 Q9Y2J8 A0A024RA98 UPI00001314AF NM_007365.2 16/16 Pfam_domain:PF03068,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF12,Superfamily_domains:SSF55909 1,1 LOW 1 SNV 1 1,1 1 PASS rs762865566 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 17069164 17069164 G T 1 0 0 0 0 0 0 0 1 11456 1190 42 2 2 PADI2 1 17069164 Silent SNP G C3L-00080_T 1035946 17069164 231887258 7 2105 PADI6 0 . GRCh38 1 17382002 17382002 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.589C>G p.Gln197Glu p.Q197E ENST00000619609 6/16 428 361 67 379 379 0 strelka-varscan-mutect PADI6,missense_variant,p.Gln197Glu,ENST00000619609,NM_207421.4; G ENST00000619609 Transcript missense_variant 639/2396 589/2085 197/694 Q/E Caa/Gaa 1 1 PADI6 HGNC HGNC:20449 protein_coding YES CCDS72715.1 ENSP00000483125 Q6TGC4 UPI0000253BE7 NM_207421.4 tolerated(0.33) 6/16 hmmpanther:PTHR10837:SF4,hmmpanther:PTHR10837,PIRSF_domain:PIRSF001247,Pfam_domain:PF08527,Superfamily_domains:0044952,PD936484 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 17382002 17382002 C G 1 0 0 0 0 1 0 0 0 11459 595 21 4 4 PADI6 1 17382002 Missense_Mutation SNP C C3L-00080_T 312838 17382002 231574420 8 2106 EMC1 0 . GRCh38 1 19220793 19220793 + Silent SNP G G C novel C3L-00080_T C3L-00080_N G G c.2643C>G p.= p.R881R ENST00000477853 21/23 140 121 19 125 125 0 strelka-varscan-mutect EMC1,missense_variant,p.Pro114Ala,ENST00000486405,;EMC1,synonymous_variant,p.=,ENST00000477853,NM_001271428.1,NM_015047.2;EMC1,synonymous_variant,p.=,ENST00000375199,NM_001271427.1;EMC1,synonymous_variant,p.=,ENST00000375208,NM_001271429.1;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,non_coding_transcript_exon_variant,,ENST00000480380,;EMC1,non_coding_transcript_exon_variant,,ENST00000461353,;EMC1,non_coding_transcript_exon_variant,,ENST00000494770,;EMC1,non_coding_transcript_exon_variant,,ENST00000496654,;EMC1,synonymous_variant,p.=,ENST00000486238,;EMC1,non_coding_transcript_exon_variant,,ENST00000462505,; C ENST00000477853 Transcript synonymous_variant 2686/6664 2643/2982 881/993 R cgC/cgG 1 -1 EMC1 HGNC HGNC:28957 protein_coding YES CCDS190.1 ENSP00000420608 Q8N766 UPI0000070A23 NM_001271428.1,NM_015047.2 21/23 hmmpanther:PTHR21573:SF0,hmmpanther:PTHR21573,Pfam_domain:PF07774 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 19220793 19220793 G C 1 0 0 0 0 0 0 0 1 4921 1190 42 4 4 EMC1 1 19220793 Silent SNP G C3L-00080_T 1838791 19220793 229735629 9 2107 HSPG2 0 . GRCh38 1 21846243 21846243 + Silent SNP G G T rs759622393 C3L-00080_T C3L-00080_N G G c.8329C>A p.= p.R2777R ENST00000374695 64/97 417 259 158 346 346 0 strelka-varscan-mutect HSPG2,synonymous_variant,p.=,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,non_coding_transcript_exon_variant,,ENST00000453796,; T ENST00000374695 Transcript synonymous_variant 8409/14327 8329/13176 2777/4391 R Cgg/Agg rs759622393 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 64/97 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs759622393 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 21846243 21846243 G T 1 0 0 0 0 0 0 0 1 7326 1144 40 1 1 HSPG2 1 21846243 Silent SNP G C3L-00080_T 2625450 21846243 227110179 10 2108 C1QB 0 . GRCh38 1 22661195 22661195 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.571G>A p.Ala191Thr p.A191T ENST00000314933 3/3 155 86 69 159 159 0 strelka-varscan-mutect C1QB,missense_variant,p.Ala189Thr,ENST00000509305,;C1QB,missense_variant,p.Ala191Thr,ENST00000314933,NM_000491.3;C1QB,missense_variant,p.Ala189Thr,ENST00000432749,;C1QB,downstream_gene_variant,,ENST00000510260,; A ENST00000314933 Transcript missense_variant 703/1044 571/762 191/253 A/T Gca/Aca 1 1 C1QB HGNC HGNC:1242 protein_coding YES CCDS228.1 ENSP00000313967 P02746 A0A024RAB9 UPI000013F024 NM_000491.3 tolerated(0.36) 3/3 Gene3D:2.60.120.40,Pfam_domain:PF00386,PROSITE_profiles:PS50871,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF558,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 22661195 22661195 G A 1 0 0 0 0 1 0 0 0 1933 1319 46 3 3 C1QB 1 22661195 Missense_Mutation SNP G C3L-00080_T 814952 22661195 226295227 11 2109 ZNF362 0 . GRCh38 1 33280330 33280330 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.556G>T p.Gly186Cys p.G186C ENST00000539719 5/9 238 197 41 212 212 0 strelka-varscan-mutect ZNF362,missense_variant,p.Gly186Cys,ENST00000539719,NM_152493.2;ZNF362,missense_variant,p.Gly186Cys,ENST00000373428,;ZNF362,missense_variant,p.Gly173Cys,ENST00000483388,;ZNF362,upstream_gene_variant,,ENST00000477934,; T ENST00000539719 Transcript missense_variant 726/3106 556/1263 186/420 G/C Ggc/Tgc COSM681072 1 1 ZNF362 HGNC HGNC:18079 protein_coding YES CCDS377.1 ENSP00000446335 Q5T0B9 UPI000013E046 NM_152493.2 tolerated(0.13) 5/9 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 33280330 33280330 G T 1 0 0 0 0 1 0 0 0 18440 1348 47 2 2 ZNF362 1 33280330 Missense_Mutation SNP G C3L-00080_T 10619135 33280330 215676092 12 2110 PHC2 0 . GRCh38 1 33371074 33371074 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.354A>G p.= p.R118R ENST00000257118 3/14 212 119 93 179 179 0 strelka-varscan-mutect PHC2,synonymous_variant,p.=,ENST00000257118,NM_198040.2;PHC2,synonymous_variant,p.=,ENST00000431992,;PHC2,non_coding_transcript_exon_variant,,ENST00000468406,;PHC2,downstream_gene_variant,,ENST00000484692,; C ENST00000257118 Transcript synonymous_variant 408/3870 354/2577 118/858 R agA/agG 1 -1 PHC2 HGNC HGNC:3183 protein_coding YES CCDS378.1 ENSP00000257118 Q8IXK0 UPI0000074391 NM_198040.2 3/14 hmmpanther:PTHR12247:SF86,hmmpanther:PTHR12247 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 33371074 33371074 T C 1 0 0 0 0 0 0 0 1 11906 1664 58 5 5 PHC2 1 33371074 Silent SNP T C3L-00080_T 90744 33371074 215585348 13 2111 C1orf94 0 . GRCh38 1 34197628 34197628 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.724C>T p.Gln242Ter p.Q242* ENST00000488417 2/7 180 143 37 149 149 0 strelka-varscan-mutect C1orf94,stop_gained,p.Gln242Ter,ENST00000488417,NM_001134734.1;C1orf94,stop_gained,p.Gln52Ter,ENST00000373374,NM_032884.4; T ENST00000488417 Transcript stop_gained 844/2287 724/1797 242/598 Q/* Cag/Tag 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 2/7 hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1,Pfam_domain:PF15752 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 34197628 34197628 C T 1 0 0 0 0 0 1 0 0 2000 595 21 3 3 C1orf94 1 34197628 Nonsense_Mutation SNP C C3L-00080_T 826554 34197628 214758794 14 2112 SZT2 0 . GRCh38 1 43441271 43441271 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.7231G>T p.Asp2411Tyr p.D2411Y ENST00000562955 52/71 219 186 33 196 196 0 strelka-varscan-mutect SZT2,missense_variant,p.Asp2411Tyr,ENST00000562955,NM_015284.3;SZT2,missense_variant,p.Asp2468Tyr,ENST00000634258,;SZT2,downstream_gene_variant,,ENST00000471177,;SZT2,upstream_gene_variant,,ENST00000460536,;SZT2,downstream_gene_variant,,ENST00000470897,; T ENST00000562955 Transcript missense_variant 7231/12281 7231/10128 2411/3375 D/Y Gat/Tat 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 deleterious(0) 52/71 hmmpanther:PTHR14918 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 43441271 43441271 G T 1 0 0 0 0 1 0 0 0 15883 1174 41 2 2 SZT2 1 43441271 Missense_Mutation SNP G C3L-00080_T 9243643 43441271 205515151 15 2113 MUTYH 0 . GRCh38 1 45332227 45332227 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.863C>A p.Thr288Asn p.T288N ENST00000372098 10/16 716 595 121 634 634 0 strelka-varscan-mutect MUTYH,missense_variant,p.Thr291Asn,ENST00000450313,NM_001128425.1;MUTYH,missense_variant,p.Thr277Asn,ENST00000372115,NM_001048171.1;MUTYH,missense_variant,p.Thr288Asn,ENST00000372098,NM_012222.2;MUTYH,missense_variant,p.Thr263Asn,ENST00000372104,NM_001293195.1;MUTYH,missense_variant,p.Thr278Asn,ENST00000372110,NM_001293190.1;MUTYH,missense_variant,p.Thr263Asn,ENST00000355498,NM_001293196.1,NM_001293192.1,NM_001048173.1;MUTYH,missense_variant,p.Thr264Asn,ENST00000354383,NM_001048172.1;MUTYH,missense_variant,p.Thr274Asn,ENST00000448481,NM_001293191.1;MUTYH,missense_variant,p.Thr263Asn,ENST00000456914,NM_001048174.1;MUTYH,missense_variant,p.Thr277Asn,ENST00000528013,;MUTYH,missense_variant,p.Thr274Asn,ENST00000435155,;MUTYH,missense_variant,p.Thr135Asn,ENST00000412971,;MUTYH,missense_variant,p.Thr18Asn,ENST00000529892,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;HPDL,downstream_gene_variant,,ENST00000334815,NM_032756.2;MUTYH,downstream_gene_variant,,ENST00000483127,;MUTYH,missense_variant,p.Thr61Asn,ENST00000467459,;MUTYH,3_prime_UTR_variant,,ENST00000481571,;MUTYH,3_prime_UTR_variant,,ENST00000475516,;MUTYH,3_prime_UTR_variant,,ENST00000533178,;MUTYH,3_prime_UTR_variant,,ENST00000467940,;MUTYH,3_prime_UTR_variant,,ENST00000461495,;MUTYH,3_prime_UTR_variant,,ENST00000470256,;MUTYH,non_coding_transcript_exon_variant,,ENST00000462388,;MUTYH,non_coding_transcript_exon_variant,,ENST00000478796,;MUTYH,non_coding_transcript_exon_variant,,ENST00000466231,;MUTYH,downstream_gene_variant,,ENST00000483642,;MUTYH,downstream_gene_variant,,ENST00000481139,;MUTYH,downstream_gene_variant,,ENST00000492494,;MUTYH,downstream_gene_variant,,ENST00000479746,;MUTYH,downstream_gene_variant,,ENST00000476789,;MUTYH,upstream_gene_variant,,ENST00000482094,;MUTYH,downstream_gene_variant,,ENST00000462387,;MUTYH,downstream_gene_variant,,ENST00000485484,;MUTYH,downstream_gene_variant,,ENST00000534453,;MUTYH,downstream_gene_variant,,ENST00000525160,;MUTYH,downstream_gene_variant,,ENST00000474703,;MUTYH,upstream_gene_variant,,ENST00000485271,; T ENST00000372098 Transcript missense_variant 997/1839 863/1641 288/546 T/N aCc/aAc 1 -1 MUTYH HGNC HGNC:7527 protein_coding YES CCDS520.1 ENSP00000361170 Q9UIF7 E5KP26 UPI000006EB4F NM_012222.2 deleterious(0) 10/16 hmmpanther:PTHR10359,PROSITE_patterns:PS00764,Gene3D:1.10.1670.10,SMART_domains:SM00525,Superfamily_domains:SSF48150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 45332227 45332227 G T 1 0 0 0 0 1 0 0 0 9990 1261 44 2 2 MUTYH 1 45332227 Missense_Mutation SNP G C3L-00080_T 1890956 45332227 203624195 16 2114 SGIP1 0 . GRCh38 1 66739349 66739349 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.2046C>A p.= p.G682G ENST00000371037 22/25 260 153 107 211 211 0 strelka-varscan-mutect SGIP1,synonymous_variant,p.=,ENST00000371037,NM_032291.2;SGIP1,synonymous_variant,p.=,ENST00000371039,NM_001308203.1;SGIP1,synonymous_variant,p.=,ENST00000237247,;SGIP1,synonymous_variant,p.=,ENST00000435165,; A ENST00000371037 Transcript synonymous_variant 2123/7768 2046/2487 682/828 G ggC/ggA 1 1 SGIP1 HGNC HGNC:25412 protein_coding YES CCDS30744.1 ENSP00000360076 Q9BQI5 UPI000045891B NM_032291.2 22/25 Superfamily_domains:0038852,Pfam_domain:PF10291,PROSITE_profiles:PS51072,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF8 LOW 1 SNV 1 1 PASS rs1181717196 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 66739349 66739349 C A 1 0 0 0 0 0 0 0 1 14466 697 25 2 2 SGIP1 1 66739349 Silent SNP C C3L-00080_T 21407122 66739349 182217073 17 2115 IL12RB2 0 . GRCh38 1 67395591 67395591 + Silent SNP C C A rs140587981 C3L-00080_T C3L-00080_N C C c.2091C>A p.= p.P697P ENST00000262345 16/16 323 209 114 273 273 0 strelka-varscan-mutect IL12RB2,missense_variant,p.His634Asn,ENST00000541374,NM_001258216.1;IL12RB2,synonymous_variant,p.=,ENST00000262345,NM_001559.2;IL12RB2,synonymous_variant,p.=,ENST00000544434,NM_001258215.1;IL12RB2,3_prime_UTR_variant,,ENST00000371000,NM_001258214.1;IL12RB2,non_coding_transcript_exon_variant,,ENST00000465396,; A ENST00000262345 Transcript synonymous_variant 2731/4040 2091/2589 697/862 P ccC/ccA rs140587981 1 1 IL12RB2 HGNC HGNC:5972 protein_coding YES CCDS638.1 ENSP00000262345 Q99665 UPI0000046B13 NM_001559.2 16/16 hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF79 LOW 1 SNV 1 1 PASS rs140587981 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 67395591 67395591 C A 1 0 0 0 0 0 0 0 1 7535 594 21 2 2 IL12RB2 1 67395591 Silent SNP C C3L-00080_T 656242 67395591 181560831 18 2116 PKN2 0 . GRCh38 1 88741224 88741224 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.285A>G p.= p.E95E ENST00000370521 2/22 37 30 7 53 53 0 strelka-varscan-mutect PKN2,synonymous_variant,p.=,ENST00000370521,NM_006256.2;PKN2,synonymous_variant,p.=,ENST00000370513,;PKN2,synonymous_variant,p.=,ENST00000316005,; G ENST00000370521 Transcript synonymous_variant 644/6121 285/2955 95/984 E gaA/gaG 1 1 PKN2 HGNC HGNC:9406 protein_coding YES CCDS714.1 ENSP00000359552 Q16513 UPI000004D291 NM_006256.2 2/22 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Gene3D:1.10.287.160,Pfam_domain:PF02185,SMART_domains:SM00742,Superfamily_domains:SSF46585 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.03764 1 1 1 1 0 G 2 3 7 88741224 88741224 A G 1 0 0 0 0 0 0 0 1 12076 40 2 5 5 PKN2 1 88741224 Silent SNP A C3L-00080_T 21345633 88741224 160215198 19 2117 LRRC8C 0 . GRCh38 1 89713281 89713281 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.711G>T p.Gln237His p.Q237H ENST00000370454 3/3 207 170 37 203 203 0 strelka-varscan-mutect LRRC8C,missense_variant,p.Gln237His,ENST00000370454,NM_032270.4;LRRC8C,intron_variant,,ENST00000479252,;RP11-302M6.4,intron_variant,,ENST00000370453,;LRRC8C,downstream_gene_variant,,ENST00000482063,; T ENST00000370454 Transcript missense_variant 966/7218 711/2412 237/803 Q/H caG/caT 1 1 LRRC8C HGNC HGNC:25075 protein_coding YES CCDS725.1 ENSP00000359483 Q8TDW0 UPI000013E814 NM_032270.4 deleterious(0) 3/3 Pfam_domain:PF12534 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 89713281 89713281 G T 1 0 0 0 0 1 0 0 0 8927 991 35 2 2 LRRC8C 1 89713281 Missense_Mutation SNP G C3L-00080_T 972057 89713281 159243141 20 2118 BARHL2 0 . GRCh38 1 90714598 90714598 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.784C>A p.Arg262Ser p.R262S ENST00000370445 2/3 416 286 130 339 339 0 strelka-varscan-mutect BARHL2,missense_variant,p.Arg262Ser,ENST00000370445,NM_020063.1; T ENST00000370445 Transcript missense_variant 826/1979 784/1164 262/387 R/S Cgc/Agc COSM226451 1 -1 BARHL2 HGNC HGNC:954 protein_coding YES CCDS730.1 ENSP00000359474 Q9NY43 UPI00001B50ED NM_020063.1 deleterious(0) 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24330:SF4,hmmpanther:PTHR24330,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 1 MODERATE 1 SNV 1 1 1 PASS rs1178542684 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 90714598 90714598 G T 1 0 0 0 0 1 0 0 0 1466 1058 37 1 1 BARHL2 1 90714598 Missense_Mutation SNP G C3L-00080_T 1001317 90714598 158241824 21 2119 EPHX4 0 . GRCh38 1 92042879 92042879 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.374T>C p.Leu125Pro p.L125P ENST00000370383 3/7 127 106 21 167 167 0 strelka-varscan-mutect EPHX4,missense_variant,p.Leu125Pro,ENST00000370383,NM_173567.4;EPHX4,non_coding_transcript_exon_variant,,ENST00000480758,; C ENST00000370383 Transcript missense_variant 472/1437 374/1089 125/362 L/P cTg/cCg 1 1 EPHX4 HGNC HGNC:23758 protein_coding YES CCDS736.1 ENSP00000359410 Q8IUS5 UPI000013E9F5 NM_173567.4 tolerated(0.08) 3/7 Gene3D:3.40.50.1820,Pfam_domain:PF00561,Prints_domain:PR00111,hmmpanther:PTHR10992,hmmpanther:PTHR10992:SF278,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 92042879 92042879 T C 1 0 0 0 0 1 0 0 0 5029 1580 55 5 5 EPHX4 1 92042879 Missense_Mutation SNP T C3L-00080_T 1328281 92042879 156913543 22 2120 PLPPR4 0 . GRCh38 1 99306891 99306891 + Missense_Mutation SNP G G C rs777387972 C3L-00080_T C3L-00080_N G G c.2173G>C p.Asp725His p.D725H ENST00000370185 7/7 265 169 96 318 318 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Asp725His,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Asp667His,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Asp567His,ENST00000370184,; C ENST00000370185 Transcript missense_variant 2670/5369 2173/2292 725/763 D/H Gac/Cac rs777387972 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0) 7/7 MODERATE 1 SNV 1 1 PASS rs777387972 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 99306891 99306891 G C 1 0 0 0 0 1 0 0 0 12212 1058 37 4 4 PLPPR4 1 99306891 Missense_Mutation SNP G C3L-00080_T 7264012 99306891 149649531 23 2121 VCAM1 0 . GRCh38 1 100738199 100738199 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.2136C>A p.= p.A712A ENST00000294728 9/9 118 103 15 167 167 0 strelka-varscan-mutect VCAM1,synonymous_variant,p.=,ENST00000294728,NM_001078.3;VCAM1,synonymous_variant,p.=,ENST00000347652,NM_080682.2;VCAM1,synonymous_variant,p.=,ENST00000370119,NM_001199834.1;VCAM1,synonymous_variant,p.=,ENST00000370115,;VCAM1,non_coding_transcript_exon_variant,,ENST00000603679,; A ENST00000294728 Transcript synonymous_variant 2237/3083 2136/2220 712/739 A gcC/gcA 1 1 VCAM1 HGNC HGNC:12663 protein_coding YES CCDS773.1 ENSP00000294728 P19320 UPI0000000E06 NM_001078.3 9/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 100738199 100738199 C A 1 0 0 0 0 0 0 0 1 17682 581 21 2 2 VCAM1 1 100738199 Silent SNP C C3L-00080_T 1431308 100738199 148218223 24 2122 COL11A1 0 . GRCh38 1 102978912 102978912 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2657G>T p.Gly886Val p.G886V ENST00000370096 34/67 358 202 156 497 497 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly898Val,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly886Val,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly847Val,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly770Val,ENST00000512756,NM_080630.3;COL11A1,splice_region_variant,p.=,ENST00000635193,; A ENST00000370096 Transcript missense_variant,splice_region_variant 2970/7286 2657/5421 886/1806 G/V gGt/gTt 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 34/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 102978912 102978912 C A 1 0 0 0 0 1 0 0 0 3455 521 18 2 2 COL11A1 1 102978912 Missense_Mutation SNP C C3L-00080_T 2240713 102978912 145977510 25 2123 COL11A1 0 . GRCh38 1 103006074 103006074 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1785G>T p.= p.G595G ENST00000370096 17/67 226 171 55 293 293 0 strelka-varscan-mutect COL11A1,synonymous_variant,p.=,ENST00000358392,NM_080629.2;COL11A1,synonymous_variant,p.=,ENST00000370096,NM_001854.3;COL11A1,synonymous_variant,p.=,ENST00000353414,NM_001190709.1;COL11A1,synonymous_variant,p.=,ENST00000512756,NM_080630.3;COL11A1,downstream_gene_variant,,ENST00000427239,;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,upstream_gene_variant,,ENST00000475980,;COL11A1,synonymous_variant,p.=,ENST00000635193,; A ENST00000370096 Transcript synonymous_variant 2098/7286 1785/5421 595/1806 G ggG/ggT 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 17/67 Pfam_domain:PF01391,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 103006074 103006074 C A 1 0 0 0 0 0 0 0 1 3455 610 22 2 2 COL11A1 1 103006074 Silent SNP C C3L-00080_T 27162 103006074 145950348 26 2124 SPAG17 0 . GRCh38 1 118008145 118008145 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.4486T>C p.Ser1496Pro p.S1496P ENST00000336338 31/49 237 194 43 293 293 0 strelka-varscan-mutect SPAG17,missense_variant,p.Ser1496Pro,ENST00000336338,NM_206996.2;SPAG17,upstream_gene_variant,,ENST00000437255,; G ENST00000336338 Transcript missense_variant 4552/6924 4486/6672 1496/2223 S/P Tca/Cca 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 tolerated(1) 31/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 118008145 118008145 A G 1 0 0 0 0 1 0 0 0 15310 304 11 5 5 SPAG17 1 118008145 Missense_Mutation SNP A C3L-00080_T 15002071 118008145 130948277 27 2125 NOTCH2 0 . GRCh38 1 119919427 119919427 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.5666G>T p.Arg1889Leu p.R1889L ENST00000256646 31/34 192 108 84 215 215 0 strelka-varscan-mutect NOTCH2,missense_variant,p.Arg1889Leu,ENST00000256646,NM_024408.3;NOTCH2,downstream_gene_variant,,ENST00000493703,; A ENST00000256646 Transcript missense_variant 5886/11389 5666/7416 1889/2471 R/L cGg/cTg 1 -1 NOTCH2 HGNC HGNC:7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 UPI000013CF1D NM_024408.3 deleterious(0.01) 31/34 Gene3D:1.25.40.20,Pfam_domain:PF12796,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF66,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 119919427 119919427 C A 1 0 0 0 0 1 0 0 0 10593 652 23 1 1 NOTCH2 1 119919427 Missense_Mutation SNP C C3L-00080_T 1911282 119919427 129036995 28 2126 NBPF14 0 . GRCh38 1 148533927 148533927 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.8657G>C p.Arg2886Thr p.R2886T ENST00000619423 70/71 249 179 70 184 184 0 strelka-varscan-mutect NBPF14,missense_variant,p.Arg2886Thr,ENST00000619423,NM_015383.2;NBPF14,missense_variant,p.Arg2717Thr,ENST00000614999,;NBPF14,intron_variant,,ENST00000621066,;NBPF14,intron_variant,,ENST00000581201,;NBPF14,intron_variant,,ENST00000621070,;NBPF14,intron_variant,,ENST00000620240,;NBPF14,intron_variant,,ENST00000614329,;NBPF14,intron_variant,,ENST00000616120,;NBPF14,intron_variant,,ENST00000611826,; G ENST00000619423 Transcript missense_variant 8849/10779 8657/8967 2886/2988 R/T aGa/aCa 1 -1 NBPF14 HGNC HGNC:25232 protein_coding YES ENSP00000479693 A0A087WVU4 UPI000387D10E NM_015383.2 tolerated_low_confidence(0.24) 70/71 Low_complexity_(Seg):seg,PROSITE_profiles:PS51316 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 148533927 148533927 C G 1 0 0 0 0 1 0 0 0 10207 913 32 4 4 NBPF14 1 148533927 Missense_Mutation SNP C C3L-00080_T 28614500 148533927 100422495 29 2127 SEMA6C 0 . GRCh38 1 151136896 151136896 + Missense_Mutation SNP C C T rs754066193 C3L-00080_T C3L-00080_N C C c.935G>A p.Arg312His p.R312H ENST00000368913 11/20 402 352 50 196 196 0 strelka-varscan-mutect SEMA6C,missense_variant,p.Arg312His,ENST00000341697,;SEMA6C,missense_variant,p.Arg312His,ENST00000368914,NM_030913.4;SEMA6C,missense_variant,p.Arg312His,ENST00000368913,NM_001178061.1;SEMA6C,missense_variant,p.Arg272His,ENST00000368912,NM_001178062.1;SEMA6C,missense_variant,p.Arg312His,ENST00000613223,;SEMA6C,missense_variant,p.Arg312His,ENST00000621728,;SEMA6C,upstream_gene_variant,,ENST00000479820,;SEMA6C,upstream_gene_variant,,ENST00000464018,;SEMA6C,upstream_gene_variant,,ENST00000489944,;SEMA6C,downstream_gene_variant,,ENST00000485745,; T ENST00000368913 Transcript missense_variant 1064/3817 935/2889 312/962 R/H cGc/cAc rs754066193,COSM361407 1 -1 SEMA6C HGNC HGNC:10740 protein_coding YES CCDS53364.1 ENSP00000357909 Q9H3T2 UPI00001414D0 NM_001178061.1 tolerated(0.06) 11/20 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF11,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754066193 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 7 151136896 151136896 C T 1 0 0 0 0 1 0 0 0 14317 768 27 1 1 SEMA6C 1 151136896 Missense_Mutation SNP C C3L-00080_T 2602969 151136896 97819526 30 2128 FLG 0 . GRCh38 1 152303953 152303953 + Missense_Mutation SNP C C T rs750903733 C3L-00080_T C3L-00080_N C C c.10933G>A p.Gly3645Arg p.G3645R ENST00000368799 3/3 899 802 97 460 460 0 varscan-mutect FLG,missense_variant,p.Gly3645Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 10969/12747 10933/12186 3645/4061 G/R Gga/Aga rs750903733 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.05) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 PASS rs750903733 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 152303953 152303953 C T 1 0 0 0 0 1 0 0 0 5784 661 23 1 1 FLG 1 152303953 Missense_Mutation SNP C C3L-00080_T 1167057 152303953 96652469 31 2129 PGLYRP3 0 . GRCh38 1 153298103 153298103 + Silent SNP C C A rs750203950 C3L-00080_T C3L-00080_N C C c.879G>T p.= p.A293A ENST00000290722 7/7 371 160 211 197 197 0 strelka-varscan-mutect PGLYRP3,synonymous_variant,p.=,ENST00000290722,NM_052891.2; A ENST00000290722 Transcript synonymous_variant 932/1173 879/1026 293/341 A gcG/gcT rs750203950 1 -1 PGLYRP3 HGNC HGNC:30014 protein_coding YES CCDS1035.1 ENSP00000290722 Q96LB9 UPI000006F12B NM_052891.2 7/7 hmmpanther:PTHR11022,hmmpanther:PTHR11022:SF12,Gene3D:3.40.80.10,Pfam_domain:PF01510,SMART_domains:SM00701,SMART_domains:SM00644,Superfamily_domains:SSF55846 LOW 1 SNV 1 1 PASS rs750203950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 153298103 153298103 C A 1 0 0 0 0 0 0 0 1 11884 639 23 1 1 PGLYRP3 1 153298103 Silent SNP C C3L-00080_T 994150 153298103 95658319 32 2130 INSRR 0 . GRCh38 1 156840971 156840971 + Frame_Shift_Del DEL G G - rs35627952 C3L-00080_T C3L-00080_N G G c.3796delC p.Arg1266GlyfsTer112 p.R1266Gfs*112 ENST00000368195 22/22 670 455 215 558 556 2 sindel-varindel-pindel INSRR,frameshift_variant,p.Arg1266GlyfsTer112,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; - ENST00000368195 Transcript frameshift_variant 4193/5101 3796/3894 1266/1297 R/X Cgg/gg rs35627952 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 22/22 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF338,PIRSF_domain:PIRSF000620 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 156840971 156840971 G - 1 0 1 0 1 0 0 0 0 7676 1115 39 0 0 INSRR 1 156840971 Frame_Shift_Del DEL G C3L-00080_T 3542868 156840971 92115451 33 2131 LRRC71 0 . GRCh38 1 156929400 156929400 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1117G>T p.Gly373Cys p.G373C ENST00000337428 10/15 309 219 90 164 164 0 strelka-varscan-mutect LRRC71,missense_variant,p.Gly373Cys,ENST00000337428,NM_144702.2;LRRC71,non_coding_transcript_exon_variant,,ENST00000490146,;LRRC71,intron_variant,,ENST00000476550,;LRRC71,upstream_gene_variant,,ENST00000472465,; T ENST00000337428 Transcript missense_variant 1271/1959 1117/1680 373/559 G/C Ggc/Tgc 1 1 LRRC71 HGNC HGNC:26556 protein_coding YES CCDS44249.1 ENSP00000336661 Q8N4P6 UPI00000719B9 NM_144702.2 deleterious(0) 10/15 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 156929400 156929400 G T 1 0 0 0 0 1 0 0 0 8918 1232 43 2 2 LRRC71 1 156929400 Missense_Mutation SNP G C3L-00080_T 88429 156929400 92027022 34 2132 CD1A 0 . GRCh38 1 158255169 158255169 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.144G>T p.Trp48Cys p.W48C ENST00000289429 2/6 365 260 105 294 293 1 strelka-varscan-mutect CD1A,missense_variant,p.Trp48Cys,ENST00000289429,NM_001763.2; T ENST00000289429 Transcript missense_variant 677/2096 144/984 48/327 W/C tgG/tgT COSM5645942 1 1 CD1A HGNC HGNC:1634 protein_coding YES CCDS1174.1 ENSP00000289429 P06126 UPI0000161A54 NM_001763.2 deleterious(0) 2/6 Gene3D:3.30.500.10,Pfam_domain:PF16497,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF160,Superfamily_domains:SSF54452 1 MODERATE 1 SNV 1 1 1 PASS rs1336412613 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 158255169 158255169 G T 1 0 0 0 0 1 0 0 0 2677 1212 42 2 2 CD1A 1 158255169 Missense_Mutation SNP G C3L-00080_T 1325769 158255169 90701253 35 2133 CD1C 0 . GRCh38 1 158292847 158292847 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.862G>T p.Gly288Ter p.G288* ENST00000368170 4/6 204 148 56 143 143 0 strelka-varscan-mutect CD1C,stop_gained,p.Gly288Ter,ENST00000368170,NM_001765.2;CD1C,stop_gained,p.Gly223Ter,ENST00000443761,; T ENST00000368170 Transcript stop_gained 1141/1435 862/1002 288/333 G/* Gga/Tga 1 1 CD1C HGNC HGNC:1636 protein_coding YES CCDS1175.1 ENSP00000357152 P29017 UPI000013DF78 NM_001765.2 4/6 hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS rs1426916552 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 158292847 158292847 G T 1 0 0 0 0 0 1 0 0 2679 1001 35 2 2 CD1C 1 158292847 Nonsense_Mutation SNP G C3L-00080_T 37678 158292847 90663575 36 2134 OR10K2 0 . GRCh38 1 158420545 158420545 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.322G>T p.Gly108Cys p.G108C ENST00000314902 1/1 458 314 144 338 338 0 strelka-varscan-mutect OR10K2,missense_variant,p.Gly108Cys,ENST00000314902,NM_001004476.1; A ENST00000314902 Transcript missense_variant 322/939 322/939 108/312 G/C Ggc/Tgc COSM1986129 1 -1 OR10K2 HGNC HGNC:14826 protein_coding YES CCDS30896.1 ENSP00000324251 Q6IF99 A0A126GV65 UPI0000041BC2 NM_001004476.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF400,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 158420545 158420545 C A 1 0 0 0 0 1 0 0 0 10991 594 21 2 2 OR10K2 1 158420545 Missense_Mutation SNP C C3L-00080_T 127698 158420545 90535877 37 2135 ATP1A2 0 . GRCh38 1 160130265 160130266 + Frame_Shift_Ins INS - - G novel C3L-00080_T C3L-00080_N - - c.1631dupG p.Leu545ThrfsTer28 p.L545Tfs*28 ENST00000361216 12/23 282 177 105 207 206 1 sindel-varindel-pindel ATP1A2,frameshift_variant,p.Leu545ThrfsTer28,ENST00000361216,NM_000702.3;ATP1A2,frameshift_variant,p.Leu256ThrfsTer28,ENST00000447527,;ATP1A2,frameshift_variant,p.Leu545ThrfsTer28,ENST00000392233,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,downstream_gene_variant,,ENST00000468587,; G ENST00000361216 Transcript frameshift_variant 1714-1715/5421 1625-1626/3063 542/1020 L/LX ctg/ctGg 1 1 ATP1A2 HGNC HGNC:800 protein_coding YES CCDS1196.1 ENSP00000354490 P50993 A0A0S2Z3W6 UPI0000124FC1 NM_000702.3 12/23 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01106,Gene3D:3.40.1110.10,Superfamily_domains:SSF81660 HIGH 1 insertion 1 6 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 7 160130265 160130265 - G 1 0 1 1 0 0 0 0 0 1281 1580 55 0 0 ATP1A2 1 160130265 Frame_Shift_Ins INS - C3L-00080_T 1709720 160130265 88826157 38 2136 RGS5 0 . GRCh38 1 163161937 163161937 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.195G>T p.= p.L65L ENST00000530507 3/5 417 202 215 284 281 3 strelka-varscan-mutect RGS5,synonymous_variant,p.=,ENST00000313961,NM_003617.3;RGS5,synonymous_variant,p.=,ENST00000367903,;RGS5,synonymous_variant,p.=,ENST00000530507,NM_001254749.1;RGS5,synonymous_variant,p.=,ENST00000531476,;RGS5,5_prime_UTR_variant,,ENST00000618415,NM_001254748.1;RGS5,intron_variant,,ENST00000527988,NM_001195303.2;RP11-267N12.1,intron_variant,,ENST00000415437,;RGS5,non_coding_transcript_exon_variant,,ENST00000534288,;RGS5,non_coding_transcript_exon_variant,,ENST00000531954,;RGS5,non_coding_transcript_exon_variant,,ENST00000530241,;RGS5,downstream_gene_variant,,ENST00000428971,;RGS5,non_coding_transcript_exon_variant,,ENST00000525894,; A ENST00000530507 Transcript synonymous_variant 263/851 195/558 65/185 L ctG/ctT 1 -1 RGS5 HGNC HGNC:10001 protein_coding YES CCDS58041.1 ENSP00000433001 O15539 UPI0001F78466 NM_001254749.1 3/5 Gene3D:1.10.196.10,Pfam_domain:PF00615,Prints_domain:PR01301,PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF42,SMART_domains:SM00315,Superfamily_domains:SSF48097 LOW SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 163161937 163161937 C A 1 0 0 0 0 0 0 0 1 13479 581 21 2 2 RGS5 1 163161937 Silent SNP C C3L-00080_T 3031672 163161937 85794485 39 2137 DCAF6 0 . GRCh38 1 167993422 167993422 + Silent SNP G G T rs781580588 C3L-00080_T C3L-00080_N G G c.885G>T p.= p.A295A ENST00000367840 7/22 119 106 13 116 116 0 varscan-mutect DCAF6,synonymous_variant,p.=,ENST00000432587,NM_001198957.1;DCAF6,synonymous_variant,p.=,ENST00000367840,NM_001198956.1;DCAF6,synonymous_variant,p.=,ENST00000367843,NM_018442.3;DCAF6,synonymous_variant,p.=,ENST00000312263,NM_001017977.2;DCAF6,downstream_gene_variant,,ENST00000470919,;DCAF6,downstream_gene_variant,,ENST00000455334,;DCAF6,downstream_gene_variant,,ENST00000491067,;DCAF6,synonymous_variant,p.=,ENST00000470721,; T ENST00000367840 Transcript synonymous_variant 979/3349 885/2856 295/951 A gcG/gcT rs781580588 1 1 DCAF6 HGNC HGNC:30002 protein_coding YES CCDS55657.1 ENSP00000356814 Q58WW2 UPI00000743AB NM_001198956.1 7/22 hmmpanther:PTHR15574:SF39,hmmpanther:PTHR15574 LOW 1 SNV 1 1 PASS rs781580588 . 0 205 0 4 0 0 0 0 -19.25716 0.9998411 1 1 1 0 T 2 4 7 167993422 167993422 G T 1 0 0 0 0 0 0 0 1 4075 1103 39 1 1 DCAF6 1 167993422 Silent SNP G C3L-00080_T 4831485 167993422 80963000 40 2138 SELL 0 . GRCh38 1 169704573 169704573 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.800G>A p.Cys267Tyr p.C267Y ENST00000236147 5/9 78 55 23 69 69 0 strelka-varscan-mutect SELL,missense_variant,p.Cys267Tyr,ENST00000236147,NM_000655.4;SELL,non_coding_transcript_exon_variant,,ENST00000463108,;SELL,non_coding_transcript_exon_variant,,ENST00000479657,;SELL,non_coding_transcript_exon_variant,,ENST00000460650,;C1orf112,intron_variant,,ENST00000498289,;SELL,downstream_gene_variant,,ENST00000466340,;SELL,upstream_gene_variant,,ENST00000497295,; T ENST00000236147 Transcript missense_variant 961/2436 800/1158 267/385 C/Y tGt/tAt 1 -1 SELL HGNC HGNC:10720 protein_coding YES CCDS53427.1 ENSP00000236147 P14151 A0A024R8Z0 UPI000007083D NM_000655.4 deleterious(0) 5/9 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF352,hmmpanther:PTHR19325,Gene3D:2.10.70.10,PIRSF_domain:PIRSF002421,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535,Prints_domain:PR00343 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 169704573 169704573 C T 1 0 0 0 0 1 0 0 0 14293 492 17 3 3 SELL 1 169704573 Missense_Mutation SNP C C3L-00080_T 1711151 169704573 79251849 41 2139 FMO3 0 . GRCh38 1 171117185 171117185 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1342C>G p.Pro448Ala p.P448A ENST00000367755 9/9 323 217 106 265 265 0 strelka-varscan-mutect FMO3,missense_variant,p.Pro448Ala,ENST00000367755,NM_001002294.2,NM_006894.5; G ENST00000367755 Transcript missense_variant 1453/2087 1342/1599 448/532 P/A Cca/Gca 1 1 FMO3 HGNC HGNC:3771 protein_coding YES CCDS1292.1 ENSP00000356729 P31513 A0A024R8Z4 UPI000016A103 NM_001002294.2,NM_006894.5 tolerated(0.2) 9/9 Gene3D:3.50.50.60,Pfam_domain:PF00743,PIRSF_domain:PIRSF000332,hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF44,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 171117185 171117185 C G 1 0 0 0 0 1 0 0 0 5812 623 22 4 4 FMO3 1 171117185 Missense_Mutation SNP C C3L-00080_T 1412612 171117185 77839237 42 2140 ASTN1 0 . GRCh38 1 177030847 177030847 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.971C>A p.Thr324Asn p.T324N ENST00000361833 4/23 319 218 101 264 264 0 strelka-varscan-mutect ASTN1,missense_variant,p.Thr324Asn,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Thr324Asn,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Thr324Asn,ENST00000424564,NM_207108.2;MIR488,upstream_gene_variant,,ENST00000365739,;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;ASTN1,non_coding_transcript_exon_variant,,ENST00000473640,; T ENST00000361833 Transcript missense_variant 985/7116 971/3885 324/1294 T/N aCc/aAc 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious_low_confidence(0.03) 4/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 MODERATE 1 SNV 1 1 PASS rs1384795767 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 177030847 177030847 G T 1 0 0 0 0 1 0 0 0 1211 1261 44 2 2 ASTN1 1 177030847 Missense_Mutation SNP G C3L-00080_T 5913662 177030847 71925575 43 2141 KIAA1614 0 . GRCh38 1 180938667 180938667 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2874C>A p.Ser958Arg p.S958R ENST00000367588 6/9 211 153 58 202 201 1 strelka-varscan-mutect KIAA1614,missense_variant,p.Ser958Arg,ENST00000367588,NM_020950.1;KIAA1614,missense_variant,p.Ser579Arg,ENST00000367587,;KIAA1614,non_coding_transcript_exon_variant,,ENST00000483705,;KIAA1614,upstream_gene_variant,,ENST00000461346,; A ENST00000367588 Transcript missense_variant 2929/9654 2874/3573 958/1190 S/R agC/agA 1 1 KIAA1614 HGNC HGNC:29327 protein_coding YES CCDS41442.1 ENSP00000356560 Q5VZ46 UPI00001C1D75 NM_020950.1 tolerated(0.07) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR17130,hmmpanther:PTHR17130:SF21 MODERATE 1 SNV 1 1 PASS rs1426453800 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 180938667 180938667 C A 1 0 0 0 0 1 0 0 0 8124 738 26 2 2 KIAA1614 1 180938667 Missense_Mutation SNP C C3L-00080_T 3907820 180938667 68017755 44 2142 CACNA1E 0 . GRCh38 1 181580696 181580696 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.871C>A p.Gln291Lys p.Q291K ENST00000367573 6/48 377 296 81 318 317 1 strelka-varscan-mutect CACNA1E,missense_variant,p.Gln291Lys,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Gln291Lys,ENST00000621551,;CACNA1E,missense_variant,p.Gln291Lys,ENST00000367567,;CACNA1E,missense_variant,p.Gln291Lys,ENST00000358338,;CACNA1E,missense_variant,p.Gln291Lys,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Gln291Lys,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Gln291Lys,ENST00000357570,;CACNA1E,missense_variant,p.Gln291Lys,ENST00000360108,;CACNA1E,missense_variant,p.Gln291Lys,ENST00000524607,;CACNA1E,non_coding_transcript_exon_variant,,ENST00000533229,; A ENST00000367573 Transcript missense_variant 871/7067 871/6942 291/2313 Q/K Cag/Aag 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 tolerated(0.06) 6/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 181580696 181580696 C A 1 0 0 0 0 1 0 0 0 2230 595 21 2 2 CACNA1E 1 181580696 Missense_Mutation SNP C C3L-00080_T 642029 181580696 67375726 45 2143 CACNA1E 0 . GRCh38 1 181798489 181798489 + Silent SNP T T A novel C3L-00080_T C3L-00080_N T T c.6597T>A p.= p.A2199A ENST00000367573 48/48 343 218 125 246 246 0 strelka-varscan-mutect CACNA1E,synonymous_variant,p.=,ENST00000621791,NM_001205294.1;CACNA1E,synonymous_variant,p.=,ENST00000621551,;CACNA1E,synonymous_variant,p.=,ENST00000367567,;CACNA1E,synonymous_variant,p.=,ENST00000358338,;CACNA1E,synonymous_variant,p.=,ENST00000367570,NM_000721.3;CACNA1E,synonymous_variant,p.=,ENST00000367573,NM_001205293.1;CACNA1E,synonymous_variant,p.=,ENST00000357570,;CACNA1E,synonymous_variant,p.=,ENST00000360108,; A ENST00000367573 Transcript synonymous_variant 6597/7067 6597/6942 2199/2313 A gcT/gcA 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 48/48 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 181798489 181798489 T A 1 0 0 0 0 0 0 0 1 2230 1538 54 4 4 CACNA1E 1 181798489 Silent SNP T C3L-00080_T 217793 181798489 67157933 46 2144 DHX9 0 . GRCh38 1 182883202 182883202 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.2978C>G p.Ser993Cys p.S993C ENST00000367549 25/28 300 252 48 306 306 0 strelka-varscan-mutect DHX9,missense_variant,p.Ser993Cys,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000473076,;DHX9,downstream_gene_variant,,ENST00000474446,; G ENST00000367549 Transcript missense_variant 3088/4240 2978/3813 993/1270 S/C tCc/tGc 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 deleterious(0.01) 25/28 Pfam_domain:PF07717,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 182883202 182883202 C G 1 0 0 0 0 1 0 0 0 4320 855 30 4 4 DHX9 1 182883202 Missense_Mutation SNP C C3L-00080_T 1084713 182883202 66073220 47 2145 SHCBP1L 0 . GRCh38 1 182904275 182904275 + Missense_Mutation SNP G G T rs751325803 C3L-00080_T C3L-00080_N G G c.1492C>A p.Leu498Ile p.L498I ENST00000367547 8/10 391 301 90 361 360 1 strelka-varscan-mutect SHCBP1L,missense_variant,p.Leu498Ile,ENST00000367547,NM_030933.2;SHCBP1L,non_coding_transcript_exon_variant,,ENST00000488956,;SHCBP1L,non_coding_transcript_exon_variant,,ENST00000483655,; T ENST00000367547 Transcript missense_variant 1729/2317 1492/1962 498/653 L/I Cta/Ata rs751325803 1 -1 SHCBP1L HGNC HGNC:16788 protein_coding YES CCDS30955.1 ENSP00000356518 Q9BZQ2 UPI000006F7B9 NM_030933.2 deleterious(0.02) 8/10 Gene3D:2.160.20.10,Pfam_domain:PF13229,hmmpanther:PTHR14695,hmmpanther:PTHR14695:SF7,SMART_domains:SM00710,SMART_domains:SM00722,Superfamily_domains:SSF51126 MODERATE 1 SNV 1 1 PASS rs751325803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 182904275 182904275 G T 1 0 0 0 0 1 0 0 0 14534 933 33 2 2 SHCBP1L 1 182904275 Missense_Mutation SNP G C3L-00080_T 21073 182904275 66052147 48 2146 COLGALT2 0 . GRCh38 1 183944281 183944281 + Missense_Mutation SNP C C A rs777342761 C3L-00080_T C3L-00080_N C C c.1312G>T p.Asp438Tyr p.D438Y ENST00000361927 10/12 66 46 20 101 101 0 strelka-varscan-mutect COLGALT2,missense_variant,p.Asp438Tyr,ENST00000361927,NM_001303420.1,NM_015101.3,NM_001303421.1;COLGALT2,missense_variant,p.Asp46Tyr,ENST00000367521,;COLGALT2,missense_variant,p.Asp175Tyr,ENST00000367520,;COLGALT2,upstream_gene_variant,,ENST00000486375,; A ENST00000361927 Transcript missense_variant 1684/5177 1312/1881 438/626 D/Y Gat/Tat rs777342761,COSM275306,COSM5477855 1 -1 COLGALT2 HGNC HGNC:16790 protein_coding YES CCDS1360.1 ENSP00000354960 Q8IYK4 UPI000007423A NM_001303420.1,NM_015101.3,NM_001303421.1 deleterious(0) 10/12 hmmpanther:PTHR10730,Pfam_domain:PF01755 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs777342761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 183944281 183944281 C A 1 0 0 0 0 1 0 0 0 3504 884 31 1 1 COLGALT2 1 183944281 Missense_Mutation SNP C C3L-00080_T 1040006 183944281 65012141 49 2147 KCNT2 0 . GRCh38 1 196285721 196285721 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.2633T>C p.Phe878Ser p.F878S ENST00000294725 23/28 173 125 48 200 200 0 strelka-varscan-mutect KCNT2,missense_variant,p.Phe854Ser,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Phe878Ser,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Phe804Ser,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; G ENST00000294725 Transcript missense_variant 3549/4409 2633/3408 878/1135 F/S tTt/tCt 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious(0) 23/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 196285721 196285721 A G 1 0 0 0 0 1 0 0 0 8008 14 1 5 5 KCNT2 1 196285721 Missense_Mutation SNP A C3L-00080_T 12341440 196285721 52670701 50 2148 ASPM 0 . GRCh38 1 197146332 197146332 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.106C>T p.Pro36Ser p.P36S ENST00000367409 1/28 363 241 122 264 264 0 strelka-varscan-mutect ASPM,missense_variant,p.Pro36Ser,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Pro36Ser,ENST00000294732,NM_001206846.1;ASPM,missense_variant,p.Pro36Ser,ENST00000612785,; A ENST00000367409 Transcript missense_variant 363/10887 106/10434 36/3477 P/S Ccg/Tcg 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 deleterious(0.02) 1/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 197146332 197146332 G A 1 0 0 0 0 1 0 0 0 1203 1232 43 3 3 ASPM 1 197146332 Missense_Mutation SNP G C3L-00080_T 860611 197146332 51810090 51 2149 LRRN2 0 . GRCh38 1 204618569 204618569 + Missense_Mutation SNP C C T rs558201537 C3L-00080_T C3L-00080_N C C c.1424G>A p.Arg475Gln p.R475Q ENST00000367175 1/1 264 182 82 175 175 0 strelka-varscan-mutect LRRN2,missense_variant,p.Arg475Gln,ENST00000367175,;LRRN2,missense_variant,p.Arg475Gln,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Arg475Gln,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; T ENST00000367175 Transcript missense_variant 3637/5036 1424/2142 475/713 R/Q cGg/cAg rs558201537 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC tolerated(0.24) 1/1 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF162,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 1 PASS rs558201537 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 204618569 204618569 C T 1 0 0 0 0 1 0 0 0 8941 652 23 1 1 LRRN2 1 204618569 Missense_Mutation SNP C C3L-00080_T 7472237 204618569 44337853 52 2150 CNTN2 0 . GRCh38 1 205059117 205059117 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.521C>A p.Pro174His p.P174H ENST00000331830 6/23 336 213 123 277 276 1 strelka-varscan-mutect CNTN2,missense_variant,p.Pro174His,ENST00000331830,NM_005076.3;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,;CNTN2,non_coding_transcript_exon_variant,,ENST00000530117,;CNTN2,downstream_gene_variant,,ENST00000532366,;CNTN2,upstream_gene_variant,,ENST00000527340,; A ENST00000331830 Transcript missense_variant 878/8214 521/3123 174/1040 P/H cCc/cAc COSM3803598 1 1 CNTN2 HGNC HGNC:2172 protein_coding YES CCDS1449.1 ENSP00000330633 Q02246 A0A024R9B4 UPI00001266A5 NM_005076.3 deleterious(0) 6/23 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS rs1455768620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 205059117 205059117 C A 1 0 0 0 0 1 0 0 0 3422 623 22 2 2 CNTN2 1 205059117 Missense_Mutation SNP C C3L-00080_T 440548 205059117 43897305 53 2151 SRGAP2 0 . GRCh38 1 206453206 206453206 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.2186A>C p.Glu729Ala p.E729A ENST00000573034 19/22 52 31 21 31 31 0 strelka-varscan-mutect SRGAP2,missense_variant,p.Glu729Ala,ENST00000573034,NM_015326.4;SRGAP2,missense_variant,p.Glu728Ala,ENST00000624873,NM_001170637.3;SRGAP2,missense_variant,p.Glu728Ala,ENST00000605610,NM_001300952.1;SRGAP2,missense_variant,p.Glu343Ala,ENST00000605476,;SRGAP2,missense_variant,p.Glu112Ala,ENST00000604925,;SRGAP2,missense_variant,p.Glu3Ala,ENST00000604010,;SRGAP2,upstream_gene_variant,,ENST00000604247,; C ENST00000573034 Transcript missense_variant 2248/6301 2186/3216 729/1071 E/A gAg/gCg 1 1 SRGAP2 HGNC HGNC:19751 protein_coding YES CCDS73017.1 ENSP00000459615 A2RUF3 UPI0000DC3AA7 NM_015326.4 deleterious(0.04) 19/22 Gene3D:2.30.30.40,PROSITE_profiles:PS50002,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF6 MODERATE 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 206453206 206453206 A C 1 0 0 0 0 1 0 0 0 15505 304 11 5 5 SRGAP2 1 206453206 Missense_Mutation SNP A C3L-00080_T 1394089 206453206 42503216 54 2152 USH2A 0 . GRCh38 1 215648638 215648638 + Silent SNP G G T C3L-00080_T C3L-00080_N G G c.14472C>A p.= p.T4824T ENST00000307340 66/72 571 411 160 464 462 2 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript synonymous_variant 14859/18883 14472/15609 4824/5202 T acC/acA COSM4865624,COSM903828 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 66/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 215648638 215648638 G T 1 0 0 0 0 0 0 0 1 17570 1219 43 2 2 USH2A 1 215648638 Silent SNP G C3L-00080_T 9195432 215648638 33307784 55 2153 USH2A 0 . GRCh38 1 215674325 215674325 + Missense_Mutation SNP G G T rs754560573 C3L-00080_T C3L-00080_N G G c.13586C>A p.Pro4529His p.P4529H ENST00000307340 63/72 155 109 46 121 121 0 strelka-varscan-mutect USH2A,missense_variant,p.Pro4529His,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 13973/18883 13586/15609 4529/5202 P/H cCc/cAc rs754560573,COSM5668917,COSM5668918 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 63/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF49265 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs754560573 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 215674325 215674325 G T 1 0 0 0 0 1 0 0 0 17570 1232 43 2 2 USH2A 1 215674325 Missense_Mutation SNP G C3L-00080_T 25687 215674325 33282097 56 2154 USH2A 0 . GRCh38 1 215743272 215743272 + Missense_Mutation SNP G G T rs774188386 C3L-00080_T C3L-00080_N G G c.11453C>A p.Pro3818His p.P3818H ENST00000307340 59/72 281 241 40 245 244 1 strelka-varscan-mutect USH2A,missense_variant,p.Pro3818His,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 11840/18883 11453/15609 3818/5202 P/H cCt/cAt rs774188386,COSM4873226,COSM903863 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.23) 59/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs774188386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 215743272 215743272 G T 1 0 0 0 0 1 0 0 0 17570 1000 35 2 2 USH2A 1 215743272 Missense_Mutation SNP G C3L-00080_T 68947 215743272 33213150 57 2155 USH2A 0 . GRCh38 1 216199670 216199670 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.3768T>A p.= p.S1256S ENST00000307340 17/72 296 212 84 253 253 0 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;USH2A,synonymous_variant,p.=,ENST00000366942,NM_007123.5;RP5-1099E6.3,intron_variant,,ENST00000420867,;MRPS18BP1,downstream_gene_variant,,ENST00000414228,; T ENST00000307340 Transcript synonymous_variant 4155/18883 3768/15609 1256/5202 S tcT/tcA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 17/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 216199670 216199670 A T 1 0 0 0 0 0 0 0 1 17570 407 15 4 4 USH2A 1 216199670 Silent SNP A C3L-00080_T 456398 216199670 32756752 58 2156 USH2A 0 . GRCh38 1 216200035 216200035 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.3403A>T p.Arg1135Trp p.R1135W ENST00000307340 17/72 160 113 47 160 159 1 strelka-varscan-mutect USH2A,missense_variant,p.Arg1135Trp,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Arg1135Trp,ENST00000366942,NM_007123.5;RP5-1099E6.3,intron_variant,,ENST00000420867,;MRPS18BP1,downstream_gene_variant,,ENST00000414228,; A ENST00000307340 Transcript missense_variant 3790/18883 3403/15609 1135/5202 R/W Agg/Tgg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.03) 17/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 216200035 216200035 T A 1 0 0 0 0 1 0 0 0 17570 1608 56 4 4 USH2A 1 216200035 Missense_Mutation SNP T C3L-00080_T 365 216200035 32756387 59 2157 ZC3H11B 0 . GRCh38 1 219611330 219611330 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.733C>A p.His245Asn p.H245N ENST00000636126 2/2 89 55 34 60 60 0 varscan-mutect ZC3H11B,missense_variant,p.His245Asn,ENST00000636126,;ZC3H11B,missense_variant,p.His245Asn,ENST00000367211,; T ENST00000636126 Transcript missense_variant 1449/4432 733/2418 245/805 H/N Cac/Aac 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C deleterious(0) 2/2 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 MODERATE 1 SNV 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 7 219611330 219611330 G T 1 0 0 0 0 1 0 0 0 18135 1348 47 2 2 ZC3H11B 1 219611330 Missense_Mutation SNP G C3L-00080_T 3411295 219611330 29345092 60 2158 LEFTY2 0 . GRCh38 1 225940920 225940921 + Frame_Shift_Ins INS - - T novel C3L-00080_T C3L-00080_N - - c.220_221insA p.Arg74GlnfsTer179 p.R74Qfs*179 ENST00000366820 1/4 306 214 92 272 272 0 sindel-varindel-pindel LEFTY2,frameshift_variant,p.Arg74GlnfsTer179,ENST00000366820,NM_003240.3;LEFTY2,frameshift_variant,p.Arg74GlnfsTer145,ENST00000420304,NM_001172425.1;RP4-559A3.6,upstream_gene_variant,,ENST00000513672,;LEFTY2,upstream_gene_variant,,ENST00000474493,; T ENST00000366820 Transcript frameshift_variant 569-570/2287 220-221/1101 74/366 R/QX cgc/cAgc 1 -1 LEFTY2 HGNC HGNC:3122 protein_coding YES CCDS1549.1 ENSP00000355785 O00292 A0A024R3P5 UPI0000136CBB NM_003240.3 1/4 PIRSF_domain:PIRSF037402,Prints_domain:PR01427,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF167 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 7 225940920 225940920 - T 1 0 1 1 0 0 0 0 0 8624 768 27 0 0 LEFTY2 1 225940920 Frame_Shift_Ins INS - C3L-00080_T 6329590 225940920 23015502 61 2159 CAPN9 0 . GRCh38 1 230767652 230767652 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.648C>T p.= p.F216F ENST00000271971 5/20 273 207 66 195 195 0 strelka-varscan-mutect CAPN9,synonymous_variant,p.=,ENST00000354537,NM_016452.1;CAPN9,synonymous_variant,p.=,ENST00000271971,NM_006615.2;CAPN9,synonymous_variant,p.=,ENST00000366666,NM_001319676.1;RP11-99J16__A.2,intron_variant,,ENST00000412344,; T ENST00000271971 Transcript synonymous_variant 761/2362 648/2073 216/690 F ttC/ttT 1 1 CAPN9 HGNC HGNC:1486 protein_coding YES CCDS1586.1 ENSP00000271971 O14815 UPI000006E882 NM_006615.2 5/20 PROSITE_profiles:PS50203,hmmpanther:PTHR10183:SF311,hmmpanther:PTHR10183,Gene3D:3.90.70.10,Pfam_domain:PF00648,SMART_domains:SM00230,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 230767652 230767652 C T 1 0 0 0 0 0 0 0 1 2327 912 32 3 3 CAPN9 1 230767652 Silent SNP C C3L-00080_T 4826732 230767652 18188770 62 2160 TRIM67 0 . GRCh38 1 231204000 231204000 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1668G>T p.= p.G556G ENST00000366653 6/10 174 125 49 144 144 0 strelka-varscan-mutect TRIM67,synonymous_variant,p.=,ENST00000444294,;TRIM67,synonymous_variant,p.=,ENST00000366653,NM_001004342.3;TRIM67,synonymous_variant,p.=,ENST00000449018,NM_001300889.1; T ENST00000366653 Transcript synonymous_variant 1668/3936 1668/2352 556/783 G ggG/ggT 1 1 TRIM67 HGNC HGNC:31859 protein_coding YES CCDS44333.1 ENSP00000355613 Q6ZTA4 UPI0000418F23 NM_001004342.3 6/10 PROSITE_profiles:PS50853,hmmpanther:PTHR24103:SF292,hmmpanther:PTHR24103,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 231204000 231204000 G T 1 0 0 0 0 0 0 0 1 17036 1219 43 2 2 TRIM67 1 231204000 Silent SNP G C3L-00080_T 436348 231204000 17752422 63 2161 DISC1 0 . GRCh38 1 231694435 231694435 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.677C>T p.Ala226Val p.A226V ENST00000366633 2/10 587 444 143 476 476 0 strelka-varscan-mutect DISC1,missense_variant,p.Ala226Val,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,missense_variant,p.Ala226Val,ENST00000622252,;DISC1,missense_variant,p.Ala226Val,ENST00000366637,NM_001012957.1;DISC1,missense_variant,p.Ala226Val,ENST00000620189,NM_001164540.1;DISC1,missense_variant,p.Ala226Val,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,missense_variant,p.Ala226Val,ENST00000366633,NM_001164539.1;DISC1,missense_variant,p.Ala226Val,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,missense_variant,p.Ala226Val,ENST00000317586,NM_001012958.1;DISC1,missense_variant,p.Ala226Val,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,missense_variant,p.Ala226Val,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,missense_variant,p.Ala226Val,ENST00000537876,;DISC1,missense_variant,p.Ala226Val,ENST00000366636,NM_001012959.1;DISC1,intron_variant,,ENST00000602873,NM_001164556.1;DISC1,downstream_gene_variant,,ENST00000602600,;DISC1,missense_variant,p.Ala226Val,ENST00000535944,;DISC1,missense_variant,p.Ala226Val,ENST00000295051,;DISC1,missense_variant,p.Ala226Val,ENST00000602822,;DISC1,missense_variant,p.Ala226Val,ENST00000602713,;DISC1,missense_variant,p.Ala226Val,ENST00000602700,;DISC1,missense_variant,p.Ala226Val,ENST00000366632,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,non_coding_transcript_exon_variant,,ENST00000468399,; T ENST00000366633 Transcript missense_variant 730/2676 677/2268 226/755 A/V gCa/gTa 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 tolerated(0.08) 2/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 231694435 231694435 C T 1 0 0 0 0 1 0 0 0 4344 710 25 3 3 DISC1 1 231694435 Missense_Mutation SNP C C3L-00080_T 490435 231694435 17261987 64 2162 PCNX2 0 . GRCh38 1 233054326 233054326 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.4293C>A p.His1431Gln p.H1431Q ENST00000258229 25/34 440 301 139 377 377 0 strelka-varscan-mutect PCNX2,missense_variant,p.His1431Gln,ENST00000258229,NM_014801.3;PCNX2,missense_variant,p.His83Gln,ENST00000344698,;PCNX2,missense_variant,p.His453Gln,ENST00000462233,;PCNX2,non_coding_transcript_exon_variant,,ENST00000429988,; T ENST00000258229 Transcript missense_variant 4528/7518 4293/6414 1431/2137 H/Q caC/caA 1 -1 PCNX2 HGNC HGNC:8736 protein_coding YES CCDS44335.1 ENSP00000258229 A6NKB5 UPI0000F58F23 NM_014801.3 deleterious(0.01) 25/34 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5 MODERATE 1 SNV 5 1 PASS rs1007084323 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 233054326 233054326 G T 1 0 0 0 0 1 0 0 0 11680 1252 44 2 2 PCNX2 1 233054326 Missense_Mutation SNP G C3L-00080_T 1359891 233054326 15902096 65 2163 RYR2 0 . GRCh38 1 237633656 237633656 + Nonsense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.6634A>T p.Lys2212Ter p.K2212* ENST00000366574 43/105 159 119 40 147 147 0 strelka-varscan-mutect RYR2,stop_gained,p.Lys2212Ter,ENST00000366574,NM_001035.2;RYR2,stop_gained,p.Lys2196Ter,ENST00000360064,; T ENST00000366574 Transcript stop_gained 6951/16562 6634/14904 2212/4967 K/* Aaa/Taa 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 43/105 Superfamily_domains:0048280,Gene3D:1n4kA02,Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 237633656 237633656 A T 1 0 0 0 0 0 1 0 0 14029 15 1 4 4 RYR2 1 237633656 Nonsense_Mutation SNP A C3L-00080_T 4579330 237633656 11322766 66 2164 RYR2 0 . GRCh38 1 237788033 237788033 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.13374C>T p.= p.G4458G ENST00000366574 92/105 294 224 70 207 207 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,downstream_gene_variant,,ENST00000609119,;RYR2,upstream_gene_variant,,ENST00000608590,; T ENST00000366574 Transcript synonymous_variant 13691/16562 13374/14904 4458/4967 G ggC/ggT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 92/105 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 237788033 237788033 C T 1 0 0 0 0 0 0 0 1 14029 697 25 3 3 RYR2 1 237788033 Silent SNP C C3L-00080_T 154377 237788033 11168389 67 2165 RYR2 0 . GRCh38 1 237792141 237792141 + Missense_Mutation SNP C C A rs199624074 C3L-00080_T C3L-00080_N C C c.13600C>A p.Pro4534Thr p.P4534T ENST00000366574 94/105 282 188 94 241 240 1 strelka-varscan-mutect RYR2,missense_variant,p.Pro4534Thr,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Pro4517Thr,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,; A ENST00000366574 Transcript missense_variant 13917/16562 13600/14904 4534/4967 P/T Ccc/Acc rs199624074,COSM4234675,COSM679829 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.49) 94/105 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs199624074 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 237792141 237792141 C A 1 0 0 0 0 1 0 0 0 14029 623 22 2 2 RYR2 1 237792141 Missense_Mutation SNP C C3L-00080_T 4108 237792141 11164281 68 2166 RGS7 0 . GRCh38 1 240868594 240868594 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.602G>T p.Arg201Met p.R201M ENST00000366565 9/18 542 385 157 455 454 1 strelka-varscan-mutect RGS7,missense_variant,p.Arg201Met,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Arg201Met,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Arg201Met,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Arg148Met,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Arg32Met,ENST00000440928,; A ENST00000366565 Transcript missense_variant 984/2494 602/1464 201/487 R/M aGg/aTg COSM3486063,COSM3486064,COSM3486065 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 deleterious(0) 9/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 240868594 240868594 C A 1 0 0 0 0 1 0 0 0 13481 681 24 2 2 RGS7 1 240868594 Missense_Mutation SNP C C3L-00080_T 3076453 240868594 8087828 69 2167 SDCCAG8 0 . GRCh38 1 243286367 243286367 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.516A>T p.= p.T172T ENST00000366541 5/18 518 436 82 366 366 0 strelka-varscan-mutect SDCCAG8,synonymous_variant,p.=,ENST00000366541,NM_006642.3;SDCCAG8,synonymous_variant,p.=,ENST00000476722,;SDCCAG8,upstream_gene_variant,,ENST00000435549,;SDCCAG8,non_coding_transcript_exon_variant,,ENST00000490065,;SDCCAG8,non_coding_transcript_exon_variant,,ENST00000482234,; T ENST00000366541 Transcript synonymous_variant 634/2567 516/2142 172/713 T acA/acT 1 1 SDCCAG8 HGNC HGNC:10671 protein_coding YES CCDS31075.1 ENSP00000355499 Q86SQ7 UPI000000D77E NM_006642.3 5/18 hmmpanther:PTHR34343,Pfam_domain:PF15964 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 243286367 243286367 A T 1 0 0 0 0 0 0 0 1 14230 146 6 4 4 SDCCAG8 1 243286367 Silent SNP A C3L-00080_T 2417773 243286367 5670055 70 2168 OR2G3 0 . GRCh38 1 247605688 247605688 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.103T>A p.Tyr35Asn p.Y35N ENST00000320002 1/1 161 136 25 117 117 0 strelka-varscan-mutect OR2G3,missense_variant,p.Tyr35Asn,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000320002 Transcript missense_variant 103/930 103/930 35/309 Y/N Tac/Aac 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 deleterious(0) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 247605688 247605688 T A 1 0 0 0 0 1 0 0 0 11077 1522 53 4 4 OR2G3 1 247605688 Missense_Mutation SNP T C3L-00080_T 4319321 247605688 1350734 71 2169 OR14K1 0 . GRCh38 1 247739352 247739352 + Silent SNP C C T C3L-00080_T C3L-00080_N C C c.738C>T p.= p.V246V ENST00000283225 1/1 152 124 28 200 199 1 strelka-varscan-mutect OR14K1,synonymous_variant,p.=,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; T ENST00000283225 Transcript synonymous_variant 738/945 738/945 246/314 V gtC/gtT COSM3386016 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 247739352 247739352 C T 1 0 0 0 0 0 0 0 1 11026 813 29 3 3 OR14K1 1 247739352 Silent SNP C C3L-00080_T 133664 247739352 1217070 72 2170 OR14A16 0 . GRCh38 1 247815436 247815437 + Frame_Shift_Ins INS - - T novel C3L-00080_T C3L-00080_N - - c.293dupA p.Val99GlyfsTer21 p.V99Gfs*21 ENST00000357627 1/1 199 131 68 249 249 0 sindel-varindel-pindel OR14A16,frameshift_variant,p.Val99GlyfsTer21,ENST00000357627,NM_001001966.1; T ENST00000357627 Transcript frameshift_variant 293-294/930 293-294/930 98/309 Q/QX cag/caAg 1 -1 OR14A16 HGNC HGNC:15022 protein_coding YES CCDS31097.1 ENSP00000350248 Q8NHC5 UPI0000041CE2 NM_001001966.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF352,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 insertion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 7 247815436 247815436 - T 1 0 1 1 0 0 0 0 0 11021 680 24 0 0 OR14A16 1 247815436 Frame_Shift_Ins INS - C3L-00080_T 76084 247815436 1140986 73 2171 TRIM58 0 . GRCh38 1 247864726 247864726 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.538C>A p.Gln180Lys p.Q180K ENST00000366481 3/6 243 142 101 240 240 0 strelka-varscan-mutect TRIM58,missense_variant,p.Gln180Lys,ENST00000366481,NM_015431.3; A ENST00000366481 Transcript missense_variant 586/3225 538/1461 180/486 Q/K Cag/Aag COSM3977434 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0.03) 3/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393 1 MODERATE 1 SNV 1 1 1 PASS rs1460168750 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 247864726 247864726 C A 1 0 0 0 0 1 0 0 0 17024 711 25 2 2 TRIM58 1 247864726 Missense_Mutation SNP C C3L-00080_T 49290 247864726 1091696 74 2172 OR2AK2 0 . GRCh38 1 247965717 247965717 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.386T>C p.Leu129Pro p.L129P ENST00000366480 1/1 27 23 4 17 17 0 strelka-mutect OR2AK2,missense_variant,p.Leu129Pro,ENST00000366480,NM_001004491.1; C ENST00000366480 Transcript missense_variant 485/1107 386/1008 129/335 L/P cTc/cCc 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 deleterious(0) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -12.03705 1 1 1 1 0 C 3 2 7 247965717 247965717 T C 1 0 0 0 0 1 0 0 0 11064 1551 54 5 5 OR2AK2 1 247965717 Missense_Mutation SNP T C3L-00080_T 100991 247965717 990705 75 2173 OR2M7 0 . GRCh38 1 248323831 248323831 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.738G>T p.Met246Ile p.M246I ENST00000317965 1/1 235 191 44 197 196 1 strelka-varscan-mutect OR2M7,missense_variant,p.Met246Ile,ENST00000317965,NM_001004691.1; A ENST00000317965 Transcript missense_variant 738/939 738/939 246/312 M/I atG/atT 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 tolerated(0.38) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1395227553 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 248323831 248323831 C A 1 0 0 0 0 1 0 0 0 11092 594 21 2 2 OR2M7 1 248323831 Missense_Mutation SNP C C3L-00080_T 358114 248323831 632591 76 2174 OR14C36 0 . GRCh38 1 248348939 248348939 + Missense_Mutation SNP G G T rs766976784 C3L-00080_T C3L-00080_N G G c.165G>T p.Met55Ile p.M55I ENST00000317861 1/1 148 97 51 151 149 2 strelka-varscan-mutect OR14C36,missense_variant,p.Met55Ile,ENST00000317861,NM_001001918.1; T ENST00000317861 Transcript missense_variant 165/939 165/939 55/312 M/I atG/atT rs766976784 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs766976784 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 248348939 248348939 G T 1 0 0 0 0 1 0 0 0 11023 1319 46 2 2 OR14C36 1 248348939 Missense_Mutation SNP G C3L-00080_T 25108 248348939 607483 77 2175 OR2T5 0 . GRCh38 1 248488832 248488832 + Missense_Mutation SNP G G T rs758791792 C3L-00080_T C3L-00080_N G G c.244G>T p.Val82Leu p.V82L ENST00000366473 1/1 110 97 13 98 98 0 varscan-mutect OR2T5,missense_variant,p.Val82Leu,ENST00000366473,NM_001004697.1;RP11-407H12.8,upstream_gene_variant,,ENST00000450847,; T ENST00000366473 Transcript missense_variant 244/948 244/948 82/315 V/L Gtg/Ttg rs758791792 1 1 OR2T5 HGNC HGNC:15017 protein_coding YES CCDS31118.1 ENSP00000355429 Q6IEZ7 UPI0000041C43 NM_001004697.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF161,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs758791792 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 248488832 248488832 G T 1 0 0 0 0 1 0 0 0 11105 1377 48 2 2 OR2T5 1 248488832 Missense_Mutation SNP G C3L-00080_T 139893 248488832 467590 78 2176 TRAPPC12 0 . GRCh38 2 3388011 3388011 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.388G>T p.Ala130Ser p.A130S ENST00000324266 2/12 75 39 36 58 58 0 strelka-varscan-mutect TRAPPC12,missense_variant,p.Ala130Ser,ENST00000324266,NM_016030.5;TRAPPC12,missense_variant,p.Ala130Ser,ENST00000382110,NM_001321102.1;TRAPPC12,upstream_gene_variant,,ENST00000441983,;TRAPPC12,upstream_gene_variant,,ENST00000457845,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000482645,;TRAPPC12,upstream_gene_variant,,ENST00000411973,; T ENST00000324266 Transcript missense_variant 583/2508 388/2208 130/735 A/S Gcc/Tcc 1 1 TRAPPC12 HGNC HGNC:24284 protein_coding YES CCDS1652.1 ENSP00000324318 Q8WVT3 UPI000014132D NM_016030.5 tolerated_low_confidence(1) 2/12 hmmpanther:PTHR21581,hmmpanther:PTHR21581:SF6 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 3388011 3388011 G T 1 0 0 0 0 1 0 0 0 16942 1203 42 2 2 TRAPPC12 2 3388011 Missense_Mutation SNP G C3L-00080_T 3388011 238805518 79 2177 APOB 0 . GRCh38 2 21041074 21041074 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.247G>T p.Glu83Ter p.E83* ENST00000233242 4/29 232 125 107 255 255 0 strelka-varscan-mutect APOB,stop_gained,p.Glu83Ter,ENST00000233242,NM_000384.2;APOB,stop_gained,p.Glu83Ter,ENST00000399256,; A ENST00000233242 Transcript stop_gained 375/14121 247/13692 83/4563 E/* Gag/Tag 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 4/29 PROSITE_profiles:PS51211,hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF01347,Gene3D:1lshA01,SMART_domains:SM00638,Superfamily_domains:SSF56968 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 21041074 21041074 C A 1 0 0 0 0 0 1 0 0 907 864 30 2 2 APOB 2 21041074 Nonsense_Mutation SNP C C3L-00080_T 17653063 21041074 221152455 80 2178 OTOF 0 . GRCh38 2 26460910 26460910 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.5654G>C p.Arg1885Pro p.R1885P ENST00000272371 44/47 454 355 99 263 263 0 strelka-varscan-mutect OTOF,missense_variant,p.Arg1885Pro,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Arg1885Pro,ENST00000403946,NM_001287489.1;OTOF,missense_variant,p.Arg1195Pro,ENST00000402415,NM_194322.2;OTOF,missense_variant,p.Arg1118Pro,ENST00000338581,NM_004802.3;OTOF,missense_variant,p.Arg1118Pro,ENST00000339598,NM_194323.2;DRC1,downstream_gene_variant,,ENST00000288710,NM_145038.3;OTOF,downstream_gene_variant,,ENST00000464574,; G ENST00000272371 Transcript missense_variant 5781/7156 5654/5994 1885/1997 R/P cGc/cCc 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 deleterious(0) 44/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs1470759825 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 26460910 26460910 C G 1 0 0 0 0 1 0 0 0 11369 768 27 4 4 OTOF 2 26460910 Missense_Mutation SNP C C3L-00080_T 5419836 26460910 215732619 81 2179 C2orf16 0 . GRCh38 2 27579223 27579223 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.2651T>A p.Leu884Gln p.L884Q ENST00000408964 1/1 490 446 44 274 274 0 strelka-varscan-mutect C2orf16,missense_variant,p.Leu884Gln,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; A ENST00000408964 Transcript missense_variant 2702/6199 2651/5955 884/1984 L/Q cTa/cAa 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 deleterious(0) 1/1 hmmpanther:PTHR33888 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 27579223 27579223 T A 1 0 0 0 0 1 0 0 0 2032 1522 53 4 4 C2orf16 2 27579223 Missense_Mutation SNP T C3L-00080_T 1118313 27579223 214614306 82 2180 C2orf71 0 . GRCh38 2 29071399 29071399 + Silent SNP G G T rs750992193 C3L-00080_T C3L-00080_N G G c.2863C>A p.= p.R955R ENST00000331664 1/2 481 426 55 250 250 0 strelka-varscan-mutect C2orf71,synonymous_variant,p.=,ENST00000331664,NM_001029883.2; T ENST00000331664 Transcript synonymous_variant 2863/7044 2863/3867 955/1288 R Cgg/Agg rs750992193 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 LOW 1 SNV 2 1 PASS rs750992193 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 29071399 29071399 G T 1 0 0 0 0 0 0 0 1 2045 1115 39 1 1 C2orf71 2 29071399 Silent SNP G C3L-00080_T 1492176 29071399 213122130 83 2181 VIT 0 . GRCh38 2 36808731 36808731 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.1649G>T p.Gly550Val p.G550V ENST00000379242 15/16 266 239 27 173 173 0 strelka-varscan-mutect VIT,missense_variant,p.Gly550Val,ENST00000379242,NM_053276.3;VIT,missense_variant,p.Gly535Val,ENST00000389975,NM_001177969.1;VIT,missense_variant,p.Gly204Val,ENST00000497382,;VIT,missense_variant,p.Gly513Val,ENST00000379241,NM_001177971.1;VIT,missense_variant,p.Gly487Val,ENST00000404084,;VIT,missense_variant,p.Gly514Val,ENST00000401530,NM_001177970.1; T ENST00000379242 Transcript missense_variant 1951/2810 1649/2082 550/693 G/V gGg/gTg COSM1196421 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 deleterious(0) 15/16 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF107,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300,Prints_domain:PR00453 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 36808731 36808731 G T 1 0 0 0 0 1 0 0 0 17718 1232 43 2 2 VIT 2 36808731 Missense_Mutation SNP G C3L-00080_T 7737332 36808731 205384798 84 2182 GALM 0 . GRCh38 2 38675954 38675954 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.233G>T p.Arg78Met p.R78M ENST00000272252 2/7 334 171 163 186 186 0 strelka-varscan-mutect GALM,missense_variant,p.Arg78Met,ENST00000272252,NM_138801.2;GALM,intron_variant,,ENST00000410063,;AC074366.3,upstream_gene_variant,,ENST00000446277,;GALM,non_coding_transcript_exon_variant,,ENST00000427858,;GALM,missense_variant,p.Arg51Met,ENST00000444351,; T ENST00000272252 Transcript missense_variant 485/2484 233/1029 78/342 R/M aGg/aTg 1 1 GALM HGNC HGNC:24063 protein_coding YES CCDS1797.1 ENSP00000272252 Q96C23 UPI00000702E1 NM_138801.2 deleterious(0) 2/7 Gene3D:2.70.98.10,Pfam_domain:PF01263,PIRSF_domain:PIRSF005096,hmmpanther:PTHR10091,hmmpanther:PTHR10091:SF0,Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 38675954 38675954 G T 1 0 0 0 0 1 0 0 0 6073 1000 35 2 2 GALM 2 38675954 Missense_Mutation SNP G C3L-00080_T 1867223 38675954 203517575 85 2183 TMEM178A 0 . GRCh38 2 39666024 39666024 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.50G>C p.Cys17Ser p.C17S ENST00000281961 1/4 190 147 43 133 133 0 strelka-varscan-mutect TMEM178A,missense_variant,p.Cys17Ser,ENST00000281961,NM_152390.2;TMEM178A,missense_variant,p.Cys17Ser,ENST00000618232,;AC007246.3,downstream_gene_variant,,ENST00000415640,;TMEM178A,intron_variant,,ENST00000482239,;TMEM178A,intron_variant,,ENST00000437068,; C ENST00000281961 Transcript missense_variant 106/1662 50/894 17/297 C/S tGc/tCc 1 1 TMEM178A HGNC HGNC:28517 protein_coding YES CCDS1804.1 ENSP00000281961 Q8NBL3 UPI000003B0C0 NM_152390.2 deleterious(0.04) 1/4 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR32005:SF4,hmmpanther:PTHR32005,Pfam_domain:PF13903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 39666024 39666024 G C 1 0 0 0 0 1 0 0 0 16539 1319 46 4 4 TMEM178A 2 39666024 Missense_Mutation SNP G C3L-00080_T 990070 39666024 202527505 86 2184 FSHR 0 . GRCh38 2 48963484 48963484 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1337G>T p.Gly446Val p.G446V ENST00000406846 10/10 316 181 135 202 202 0 strelka-varscan-mutect FSHR,missense_variant,p.Gly446Val,ENST00000406846,NM_000145.3;FSHR,missense_variant,p.Gly420Val,ENST00000304421,NM_181446.2;FSHR,downstream_gene_variant,,ENST00000454032,;RP11-460M2.1,intron_variant,,ENST00000634588,; A ENST00000406846 Transcript missense_variant 1457/2784 1337/2088 446/695 G/V gGc/gTc 1 -1 FSHR HGNC HGNC:3969 protein_coding YES CCDS1843.1 ENSP00000384708 UPI000013E97A NM_000145.3 deleterious(0) 10/10 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00373,PROSITE_profiles:PS50262,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF5,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 48963484 48963484 C A 1 0 0 0 0 1 0 0 0 5947 739 26 2 2 FSHR 2 48963484 Missense_Mutation SNP C C3L-00080_T 9297460 48963484 193230045 87 2185 NRXN1 0 . GRCh38 2 50538600 50538600 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1916C>A p.Thr639Asn p.T639N ENST00000404971 11/24 22 12 10 15 15 0 strelka-varscan-mutect NRXN1,missense_variant,p.Thr599Asn,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Thr591Asn,ENST00000625672,;NRXN1,missense_variant,p.Thr639Asn,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Thr599Asn,ENST00000401669,;NRXN1,missense_variant,p.Thr587Asn,ENST00000405472,;NRXN1,missense_variant,p.Thr591Asn,ENST00000630543,;NRXN1,missense_variant,p.Thr329Asn,ENST00000406859,;NRXN1,missense_variant,p.Thr314Asn,ENST00000402717,;NRXN1,intron_variant,,ENST00000495871,;NRXN1,downstream_gene_variant,,ENST00000638037,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637207,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637653,;NRXN1,missense_variant,p.Thr326Asn,ENST00000331040,; T ENST00000404971 Transcript missense_variant 3256/7578 1916/4644 639/1547 T/N aCt/aAt 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 tolerated(0.37) 11/24 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 4 204 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 50538600 50538600 G T 1 0 0 0 0 1 0 0 0 10724 1029 36 2 2 NRXN1 2 50538600 Missense_Mutation SNP G C3L-00080_T 1575116 50538600 191654929 88 2186 PSME4 0 . GRCh38 2 53970740 53970740 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.45G>T p.= p.P15P ENST00000404125 1/47 220 117 103 113 113 0 strelka-varscan-mutect PSME4,synonymous_variant,p.=,ENST00000404125,NM_014614.2;ACYP2,upstream_gene_variant,,ENST00000422521,;ACYP2,upstream_gene_variant,,ENST00000607452,;ACYP2,upstream_gene_variant,,ENST00000606082,;PSME4,non_coding_transcript_exon_variant,,ENST00000481518,;ACYP2,upstream_gene_variant,,ENST00000458030,;PSME4,synonymous_variant,p.=,ENST00000389993,; A ENST00000404125 Transcript synonymous_variant 101/7099 45/5532 15/1843 P ccG/ccT 1 -1 PSME4 HGNC HGNC:20635 protein_coding YES CCDS33197.2 ENSP00000384211 Q14997 UPI0000F3BE4A NM_014614.2 1/47 hmmpanther:PTHR32170,hmmpanther:PTHR32170:SF3,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 53970740 53970740 C A 1 0 0 0 0 0 0 0 1 12860 639 23 1 1 PSME4 2 53970740 Silent SNP C C3L-00080_T 3432140 53970740 188222789 89 2187 DYSF 0 . GRCh38 2 71669200 71669200 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.5635G>T p.Val1879Leu p.V1879L ENST00000410020 50/56 571 360 211 376 375 1 strelka-varscan-mutect DYSF,missense_variant,p.Val1840Leu,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Val1878Leu,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Val1871Leu,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Val1861Leu,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Val1857Leu,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Val1879Leu,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Val1872Leu,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Val1862Leu,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Val1858Leu,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Val1848Leu,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Val1841Leu,ENST00000394120,NM_001130455.1;DYSF,non_coding_transcript_exon_variant,,ENST00000479049,; T ENST00000410020 Transcript missense_variant 5776/6657 5635/6360 1879/2119 V/L Gtg/Ttg 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0.01) 50/56 Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs886042880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 71669200 71669200 G T 1 0 0 0 0 1 0 0 0 4683 1377 48 2 2 DYSF 2 71669200 Missense_Mutation SNP G C3L-00080_T 17698460 71669200 170524329 90 2188 C2orf78 0 . GRCh38 2 73816169 73816169 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1946G>T p.Gly649Val p.G649V ENST00000409561 3/3 357 264 93 231 231 0 strelka-varscan-mutect C2orf78,missense_variant,p.Gly649Val,ENST00000409561,NM_001080474.1; T ENST00000409561 Transcript missense_variant 2067/3045 1946/2769 649/922 G/V gGa/gTa 1 1 C2orf78 HGNC HGNC:34349 protein_coding YES CCDS46338.1 ENSP00000387124 A6NCI8 UPI000015FD87 NM_001080474.1 deleterious(0) 3/3 hmmpanther:PTHR31466,hmmpanther:PTHR31466:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 73816169 73816169 G T 1 0 0 0 0 1 0 0 0 2050 1174 41 2 2 C2orf78 2 73816169 Missense_Mutation SNP G C3L-00080_T 2146969 73816169 168377360 91 2189 TET3 0 . GRCh38 2 74046517 74046517 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.601delG p.Val201TrpfsTer28 p.V201Wfs*28 ENST00000409262 3/11 217 146 71 173 173 0 sindel-varindel-pindel TET3,frameshift_variant,p.Val201TrpfsTer28,ENST00000409262,NM_001287491.1;TET3,frameshift_variant,p.Val108TrpfsTer28,ENST00000305799,;TET3,upstream_gene_variant,,ENST00000475405,; - ENST00000409262 Transcript frameshift_variant 600/11388 600/5388 200/1795 L/X ctG/ct 1 1 TET3 HGNC HGNC:28313 protein_coding YES CCDS46339.2 ENSP00000386869 O43151 K9JJH7 UPI0002A87FCB NM_001287491.1 3/11 hmmpanther:PTHR23358:SF4,hmmpanther:PTHR23358 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 - 7 5 7 74046517 74046517 G - 1 0 1 0 1 0 0 0 0 16192 1335 47 0 0 TET3 2 74046517 Frame_Shift_Del DEL G C3L-00080_T 230348 74046517 168147012 92 2190 REG3A 0 . GRCh38 2 79158350 79158350 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.309G>T p.Trp103Cys p.W103C ENST00000393878 3/5 206 155 51 132 131 1 strelka-varscan-mutect REG3A,missense_variant,p.Trp103Cys,ENST00000393878,NM_138938.2;REG3A,missense_variant,p.Trp103Cys,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,missense_variant,p.Trp103Cys,ENST00000305165,;AC011754.1,upstream_gene_variant,,ENST00000415201,;REG3A,downstream_gene_variant,,ENST00000464746,;REG3A,downstream_gene_variant,,ENST00000490901,; A ENST00000393878 Transcript missense_variant 657/1095 309/528 103/175 W/C tgG/tgT 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 deleterious(0.02) 3/5 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 79158350 79158350 C A 1 0 0 0 0 1 0 0 0 13382 856 30 2 2 REG3A 2 79158350 Missense_Mutation SNP C C3L-00080_T 5111833 79158350 163035179 93 2191 REG3A 0 . GRCh38 2 79159336 79159336 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.70G>T p.Val24Phe p.V24F ENST00000393878 1/5 291 180 111 145 145 0 strelka-varscan-mutect REG3A,missense_variant,p.Val24Phe,ENST00000393878,NM_138938.2;REG3A,missense_variant,p.Val24Phe,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,missense_variant,p.Val24Phe,ENST00000305165,;AC011754.1,intron_variant,,ENST00000415201,;REG3A,non_coding_transcript_exon_variant,,ENST00000464746,;REG3A,non_coding_transcript_exon_variant,,ENST00000490901,; A ENST00000393878 Transcript missense_variant 418/1095 70/528 24/175 V/F Gtt/Ttt COSM4095898 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 tolerated(0.07) 1/5 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 79159336 79159336 C A 1 0 0 0 0 1 0 0 0 13382 507 18 2 2 REG3A 2 79159336 Missense_Mutation SNP C C3L-00080_T 986 79159336 163034193 94 2192 SMYD1 0 . GRCh38 2 88087986 88087986 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.439C>T p.= p.L147L ENST00000419482 3/10 332 287 45 194 194 0 strelka-varscan-mutect SMYD1,synonymous_variant,p.=,ENST00000419482,NM_198274.3;SMYD1,synonymous_variant,p.=,ENST00000444564,;SMYD1,intron_variant,,ENST00000438570,;SMYD1,non_coding_transcript_exon_variant,,ENST00000468008,; T ENST00000419482 Transcript synonymous_variant 524/4433 439/1473 147/490 L Ctg/Ttg 1 1 SMYD1 HGNC HGNC:20986 protein_coding YES CCDS33240.1 ENSP00000393453 Q8NB12 A0A0A6YYB2 UPI000006EB68 NM_198274.3 3/10 PROSITE_profiles:PS50280,hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF184,Pfam_domain:PF00856,SMART_domains:SM00317,Superfamily_domains:SSF82199 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 88087986 88087986 C T 1 0 0 0 0 0 0 0 1 15142 680 24 3 3 SMYD1 2 88087986 Silent SNP C C3L-00080_T 8928650 88087986 154105543 95 2193 RGPD4 0 . GRCh38 2 107880082 107880082 + Missense_Mutation SNP G G T rs149740184 C3L-00080_T C3L-00080_N G G c.5039G>T p.Ser1680Ile p.S1680I ENST00000408999 21/23 563 494 69 399 399 0 strelka-varscan-mutect RGPD4,missense_variant,p.Ser1680Ile,ENST00000408999,NM_182588.2; T ENST00000408999 Transcript missense_variant 5116/5464 5039/5277 1680/1758 S/I aGt/aTt rs149740184 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 deleterious_low_confidence(0.02) 21/23 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF16704 MODERATE 1 SNV 1 1 PASS rs149740184 . 0 190 0 0 18 0 0 2 -8.157184 0 0 1 0 0 T 3 4 7 107880082 107880082 G T 1 0 0 0 0 1 0 0 0 13460 1029 36 2 2 RGPD4 2 107880082 Missense_Mutation SNP G C3L-00080_T 19792096 107880082 134313447 96 2194 ANAPC1 0 . GRCh38 2 111769405 111769405 + Frame_Shift_Del DEL C C - rs774751273 C3L-00080_T C3L-00080_N C C c.5721delG p.Ser1908AlafsTer14 p.S1908Afs*14 ENST00000341068 48/48 109 74 35 79 79 0 sindel-varindel ANAPC1,frameshift_variant,p.Ser1908AlafsTer14,ENST00000341068,NM_022662.3;ANAPC1,intron_variant,,ENST00000427997,;MIR4771-2,downstream_gene_variant,,ENST00000577758,;ANAPC1,splice_region_variant,,ENST00000462785,; - ENST00000341068 Transcript frameshift_variant,splice_region_variant 6494/8262 5721/5835 1907/1944 G/X ggG/gg rs774751273 1 -1 ANAPC1 HGNC HGNC:19988 protein_coding YES CCDS2093.1 ENSP00000339109 Q9H1A4 UPI000006EC6E NM_022662.3 48/48 hmmpanther:PTHR12827 HIGH 1 deletion 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 111769405 111769405 C - 1 0 1 0 1 0 0 0 0 695 869 30 0 0 ANAPC1 2 111769405 Frame_Shift_Del DEL C C3L-00080_T 3889323 111769405 130424124 97 2195 GLI2 0 . GRCh38 2 120984695 120984695 + Silent SNP C C A rs200619416 C3L-00080_T C3L-00080_N C C c.1908C>A p.= p.A636A ENST00000452319 12/14 346 243 103 234 234 0 strelka-varscan-mutect GLI2,synonymous_variant,p.=,ENST00000452319,;GLI2,synonymous_variant,p.=,ENST00000361492,NM_005270.4;GLI2,non_coding_transcript_exon_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,3_prime_UTR_variant,,ENST00000437950,; A ENST00000452319 Transcript synonymous_variant 1968/6799 1908/4761 636/1586 A gcC/gcA rs200619416 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 12/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 LOW 1 SNV 5 1 PASS rs200619416 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 120984695 120984695 C A 1 0 0 0 0 0 0 0 1 6316 639 23 1 1 GLI2 2 120984695 Silent SNP C C3L-00080_T 9215290 120984695 121208834 98 2196 NCKAP5 0 . GRCh38 2 132784987 132784987 + Silent SNP G G T rs373377710 C3L-00080_T C3L-00080_N G G c.1824C>A p.= p.A608A ENST00000409261 14/20 113 76 37 88 88 0 strelka-varscan-mutect NCKAP5,synonymous_variant,p.=,ENST00000409261,NM_207363.2;NCKAP5,synonymous_variant,p.=,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; T ENST00000409261 Transcript synonymous_variant 2198/7594 1824/5730 608/1909 A gcC/gcA rs373377710 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 LOW 1 SNV 5 1 PASS rs373377710 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 132784987 132784987 G T 1 0 0 0 0 0 0 0 1 10241 1103 39 1 1 NCKAP5 2 132784987 Silent SNP G C3L-00080_T 11800292 132784987 109408542 99 2197 DARS 0 . GRCh38 2 135933983 135933986 + Frame_Shift_Del DEL ACAT ACAT - novel C3L-00080_T C3L-00080_N ACAT ACAT c.428_431delATGT p.Tyr143Ter p.Y143* ENST00000264161 6/16 152 106 46 177 177 0 sindel-varindel-pindel DARS,frameshift_variant,p.Tyr143Ter,ENST00000264161,NM_001293312.1,NM_001349.3;DARS,frameshift_variant,p.Tyr110Ter,ENST00000456565,;DARS,frameshift_variant,p.Tyr110Ter,ENST00000441323,;DARS,frameshift_variant,p.Tyr110Ter,ENST00000449218,; - ENST00000264161 Transcript frameshift_variant 644-647/2361 428-431/1506 143-144/501 YV/X tATGTg/tg 1 -1 DARS HGNC HGNC:2678 protein_coding YES CCDS2180.1 ENSP00000264161 P14868 A0A140VJW5 UPI000013639B NM_001293312.1,NM_001349.3 6/16 Gene3D:2.40.50.140,Pfam_domain:PF01336,hmmpanther:PTHR22594,hmmpanther:PTHR22594:SF33,Superfamily_domains:SSF50249,TIGRFAM_domain:TIGR00458 HIGH 1 deletion 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.999979 1 1 1 0 - 7 5 7 135933983 135933983 ACAT - 1 0 1 0 1 0 0 0 0 4041 159 6 0 0 DARS 2 135933983 Frame_Shift_Del DEL ACAT C3L-00080_T 3148996 135933983 106259546 100 2198 LRP1B 0 . GRCh38 2 140351015 140351015 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.11674A>T p.Ile3892Phe p.I3892F ENST00000389484 77/91 141 101 40 198 198 0 strelka-varscan-mutect LRP1B,missense_variant,p.Ile3892Phe,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Ile124Phe,ENST00000437977,; A ENST00000389484 Transcript missense_variant 12646/16535 11674/13800 3892/4599 I/F Att/Ttt 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.06) 77/91 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 140351015 140351015 T A 1 0 0 0 0 1 0 0 0 8850 1464 51 4 4 LRP1B 2 140351015 Missense_Mutation SNP T C3L-00080_T 4417032 140351015 101842514 101 2199 ZEB2 0 . GRCh38 2 144424818 144424818 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.381G>T p.Gln127His p.Q127H ENST00000637267 5/11 464 402 62 364 363 1 strelka-varscan-mutect ZEB2,missense_variant,p.Gln127His,ENST00000637267,;ZEB2,missense_variant,p.Gln127His,ENST00000636471,;ZEB2,missense_variant,p.Gln127His,ENST00000627532,NM_014795.3;ZEB2,missense_variant,p.Gln127His,ENST00000636026,;ZEB2,missense_variant,p.Gln15His,ENST00000638087,;ZEB2,missense_variant,p.Gln15His,ENST00000637304,;ZEB2,missense_variant,p.Gln15His,ENST00000638007,;ZEB2,missense_variant,p.Gln15His,ENST00000637045,;ZEB2,missense_variant,p.Gln15His,ENST00000636413,;ZEB2,missense_variant,p.Gln127His,ENST00000409487,;ZEB2,missense_variant,p.Gln127His,ENST00000558170,;ZEB2,missense_variant,p.Gln126His,ENST00000303660,;ZEB2,missense_variant,p.Gln156His,ENST00000427902,;ZEB2,missense_variant,p.Gln122His,ENST00000440875,;ZEB2,missense_variant,p.Gln155His,ENST00000392861,;ZEB2,missense_variant,p.Gln127His,ENST00000465308,;ZEB2,intron_variant,,ENST00000638128,;ZEB2,intron_variant,,ENST00000539609,NM_001171653.1;ZEB2,intron_variant,,ENST00000419938,;ZEB2,intron_variant,,ENST00000431672,;ZEB2,intron_variant,,ENST00000409211,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,downstream_gene_variant,,ENST00000479735,;ZEB2,3_prime_UTR_variant,,ENST00000636732,;ZEB2,downstream_gene_variant,,ENST00000472146,;ZEB2,downstream_gene_variant,,ENST00000461784,;ZEB2,downstream_gene_variant,,ENST00000476394,;ZEB2,downstream_gene_variant,,ENST00000434448,; A ENST00000637267 Transcript missense_variant 1222/9856 381/3645 127/1214 Q/H caG/caT 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 tolerated(0.45) 5/11 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11 MODERATE 1 SNV 1 PASS rs1194832899 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 144424818 144424818 C A 1 0 0 0 0 1 0 0 0 18200 912 32 2 2 ZEB2 2 144424818 Missense_Mutation SNP C C3L-00080_T 4073803 144424818 97768711 102 2200 KCNH7 0 . GRCh38 2 162517811 162517811 + Silent SNP G G T rs372420734 C3L-00080_T C3L-00080_N G G c.811C>A p.= p.R271R ENST00000332142 4/16 193 144 49 174 174 0 strelka-varscan-mutect KCNH7,synonymous_variant,p.=,ENST00000332142,NM_033272.3;KCNH7,synonymous_variant,p.=,ENST00000618399,;KCNH7,synonymous_variant,p.=,ENST00000328032,NM_173162.2;KCNH7,synonymous_variant,p.=,ENST00000621889,;KCNH7,non_coding_transcript_exon_variant,,ENST00000477019,; T ENST00000332142 Transcript synonymous_variant 911/4113 811/3591 271/1196 R Cgg/Agg rs372420734,COSM3391050,COSM3391051 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 4/16 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs372420734 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 7 162517811 162517811 G T 1 0 0 0 0 0 0 0 1 7953 1144 40 1 1 KCNH7 2 162517811 Silent SNP G C3L-00080_T 18092993 162517811 79675718 103 2201 ABCB11 0 . GRCh38 2 168944916 168944916 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2389G>T p.Gly797Cys p.G797C ENST00000263817 20/28 125 91 34 125 124 1 strelka-varscan-mutect ABCB11,missense_variant,p.Gly797Cys,ENST00000263817,NM_003742.2;ABCB11,3_prime_UTR_variant,,ENST00000439188,; A ENST00000263817 Transcript missense_variant 2514/4775 2389/3966 797/1321 G/C Ggt/Tgt 1 -1 ABCB11 HGNC HGNC:42 protein_coding YES CCDS46444.1 ENSP00000263817 O95342 UPI0000163BFA NM_003742.2 tolerated(0.18) 20/28 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF165,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 168944916 168944916 C A 1 0 0 0 0 1 0 0 0 46 594 21 2 2 ABCB11 2 168944916 Missense_Mutation SNP C C3L-00080_T 6427105 168944916 73248613 104 2202 LRP2 0 . GRCh38 2 169177869 169177869 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.10327A>T p.Thr3443Ser p.T3443S ENST00000263816 53/79 572 411 161 462 462 0 strelka-varscan-mutect LRP2,missense_variant,p.Thr3443Ser,ENST00000263816,NM_004525.2;LRP2,non_coding_transcript_exon_variant,,ENST00000461418,; A ENST00000263816 Transcript missense_variant 10613/15808 10327/13968 3443/4655 T/S Aca/Tca 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 tolerated(0.1) 53/79 Gene3D:2.120.10.30,PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF232,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 169177869 169177869 T A 1 0 0 0 0 1 0 0 0 8851 1667 58 4 4 LRP2 2 169177869 Missense_Mutation SNP T C3L-00080_T 232953 169177869 73015660 105 2203 LRP2 0 . GRCh38 2 169188094 169188094 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.9204C>A p.Cys3068Ter p.C3068* ENST00000263816 49/79 517 372 145 446 445 1 strelka-varscan-mutect LRP2,stop_gained,p.Cys3068Ter,ENST00000263816,NM_004525.2; T ENST00000263816 Transcript stop_gained 9490/15808 9204/13968 3068/4655 C/* tgC/tgA 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 49/79 PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF232,SMART_domains:SM00181,SMART_domains:SM00192 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 169188094 169188094 G T 1 0 0 0 0 0 1 0 0 8851 1195 42 2 2 LRP2 2 169188094 Nonsense_Mutation SNP G C3L-00080_T 10225 169188094 73005435 106 2204 GORASP2 0 . GRCh38 2 170965987 170965987 + Missense_Mutation SNP G G A rs773046298 C3L-00080_T C3L-00080_N G G c.1216G>A p.Ala406Thr p.A406T ENST00000234160 10/10 403 276 127 329 329 0 strelka-varscan-mutect GORASP2,missense_variant,p.Ala406Thr,ENST00000234160,NM_001201428.1,NM_015530.4;GORASP2,downstream_gene_variant,,ENST00000493692,;GORASP2,3_prime_UTR_variant,,ENST00000442798,;GORASP2,non_coding_transcript_exon_variant,,ENST00000486498,; A ENST00000234160 Transcript missense_variant 2031/3173 1216/1359 406/452 A/T Gct/Act rs773046298,COSM1401234 1 1 GORASP2 HGNC HGNC:17500 protein_coding YES CCDS33325.1 ENSP00000234160 Q9H8Y8 UPI000007373B NM_001201428.1,NM_015530.4 tolerated_low_confidence(0.34) 10/10 hmmpanther:PTHR12893,hmmpanther:PTHR12893:SF1,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773046298 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 170965987 170965987 G A 1 0 0 0 0 1 0 0 0 6470 1087 38 1 1 GORASP2 2 170965987 Missense_Mutation SNP G C3L-00080_T 1777893 170965987 71227542 107 2205 CHN1 0 . GRCh38 2 174812322 174812322 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.873G>A p.= p.E291E ENST00000409900 9/13 118 96 22 62 62 0 strelka-varscan-mutect CHN1,synonymous_variant,p.=,ENST00000409900,NM_001822.5;CHN1,synonymous_variant,p.=,ENST00000295497,NM_001206602.1;CHN1,synonymous_variant,p.=,ENST00000409156,NM_001025201.3;CHN1,synonymous_variant,p.=,ENST00000409597,;CHN1,synonymous_variant,p.=,ENST00000444394,;CHN1,synonymous_variant,p.=,ENST00000409089,;CHN1,synonymous_variant,p.=,ENST00000413882,;CHN1,synonymous_variant,p.=,ENST00000443238,;CHN1,downstream_gene_variant,,ENST00000444573,;CHN1,non_coding_transcript_exon_variant,,ENST00000488080,;CHN1,3_prime_UTR_variant,,ENST00000425395,;CHN1,non_coding_transcript_exon_variant,,ENST00000491801,;CHN1,non_coding_transcript_exon_variant,,ENST00000485882,; T ENST00000409900 Transcript synonymous_variant 1187/2447 873/1380 291/459 E gaG/gaA 1 -1 CHN1 HGNC HGNC:1943 protein_coding YES CCDS46455.1 ENSP00000386741 P15882 UPI000012781D NM_001822.5 9/13 Gene3D:1.10.555.10,Pfam_domain:PF00620,PIRSF_domain:PIRSF038015,PROSITE_profiles:PS50238,hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF34,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 2 4 7 174812322 174812322 C T 1 0 0 0 0 0 0 0 1 3122 912 32 3 3 CHN1 2 174812322 Silent SNP C C3L-00080_T 3846335 174812322 67381207 108 2206 TTN 0 . GRCh38 2 178585108 178585108 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.64636G>A p.Gly21546Arg p.G21546R ENST00000589042 309/363 82 56 26 75 75 0 strelka-varscan-mutect TTN,missense_variant,p.Gly21546Arg,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gly19905Arg,ENST00000591111,;TTN,missense_variant,p.Gly19905Arg,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gly18978Arg,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Gly12481Arg,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Gly12673Arg,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Gly12606Arg,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000590743,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000629117,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000626517,;RP11-171I2.2,downstream_gene_variant,,ENST00000603521,;TTN-AS1,downstream_gene_variant,,ENST00000586707,;TTN-AS1,downstream_gene_variant,,ENST00000592600,;TTN-AS1,downstream_gene_variant,,ENST00000586831,;TTN-AS1,downstream_gene_variant,,ENST00000438095,; T ENST00000589042 Transcript missense_variant 64861/109224 64636/107976 21546/35991 G/R Ggg/Agg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 309/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 178585108 178585108 C T 1 0 0 0 0 1 0 0 0 17245 594 21 3 3 TTN 2 178585108 Missense_Mutation SNP C C3L-00080_T 3772786 178585108 63608421 109 2207 TTN 0 . GRCh38 2 178605542 178605542 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.53753delC p.Pro17918GlnfsTer37 p.P17918Qfs*37 ENST00000589042 279/363 168 143 25 159 159 0 sindel-varindel-pindel TTN,frameshift_variant,p.Pro17918GlnfsTer37,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Pro16277GlnfsTer37,ENST00000591111,;TTN,frameshift_variant,p.Pro16277GlnfsTer37,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Pro15350GlnfsTer37,ENST00000342992,NM_133378.4;TTN,frameshift_variant,p.Pro8853GlnfsTer37,ENST00000460472,NM_003319.4;TTN,frameshift_variant,p.Pro9045GlnfsTer37,ENST00000342175,NM_133437.4;TTN,frameshift_variant,p.Pro8978GlnfsTer37,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000419746,;TTN-AS1,downstream_gene_variant,,ENST00000586452,;TTN-AS1,upstream_gene_variant,,ENST00000627527,;TTN-AS1,downstream_gene_variant,,ENST00000626517,; - ENST00000589042 Transcript frameshift_variant 53978/109224 53753/107976 17918/35991 P/X cCa/ca 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 279/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH deletion 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 7 178605542 178605542 G - 1 0 1 0 1 0 0 0 0 17245 1348 47 0 0 TTN 2 178605542 Frame_Shift_Del DEL G C3L-00080_T 20434 178605542 63587987 110 2208 ITGA4 0 . GRCh38 2 181482517 181482517 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.907G>A p.Gly303Arg p.G303R ENST00000397033 9/28 203 175 28 157 157 0 strelka-varscan-mutect ITGA4,missense_variant,p.Gly303Arg,ENST00000397033,NM_000885.4;ITGA4,missense_variant,p.Gly303Arg,ENST00000233573,;ITGA4,downstream_gene_variant,,ENST00000478440,;ITGA4,non_coding_transcript_exon_variant,,ENST00000465522,; A ENST00000397033 Transcript missense_variant 1337/4189 907/3099 303/1032 G/R Gga/Aga 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 deleterious(0) 9/28 PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318,Prints_domain:PR01185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 181482517 181482517 G A 1 0 0 0 0 1 0 0 0 7785 1362 47 3 3 ITGA4 2 181482517 Missense_Mutation SNP G C3L-00080_T 2876975 181482517 60711012 111 2209 PDE1A 0 . GRCh38 2 182201456 182201456 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1156G>T p.Glu386Ter p.E386* ENST00000435564 10/15 170 120 50 135 135 0 strelka-varscan-mutect PDE1A,stop_gained,p.Glu386Ter,ENST00000435564,NM_005019.4,NM_001258312.1;PDE1A,stop_gained,p.Glu370Ter,ENST00000351439,NM_001258313.1;PDE1A,stop_gained,p.Glu370Ter,ENST00000409365,;PDE1A,stop_gained,p.Glu352Ter,ENST00000358139,NM_001258314.1;PDE1A,stop_gained,p.Glu386Ter,ENST00000410103,NM_001003683.2; A ENST00000435564 Transcript stop_gained 1357/4885 1156/1638 386/545 E/* Gag/Tag 1 -1 PDE1A HGNC HGNC:8774 protein_coding YES CCDS2285.1 ENSP00000410309 P54750 UPI0000001072 NM_005019.4,NM_001258312.1 10/15 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604,Prints_domain:PR00387 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 182201456 182201456 C A 1 0 0 0 0 0 1 0 0 11721 864 30 2 2 PDE1A 2 182201456 Nonsense_Mutation SNP C C3L-00080_T 718939 182201456 59992073 112 2210 PDE1A 0 . GRCh38 2 182240161 182240161 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.347C>A p.Pro116Gln p.P116Q ENST00000435564 3/15 155 114 41 140 140 0 strelka-varscan-mutect PDE1A,missense_variant,p.Pro116Gln,ENST00000435564,NM_005019.4,NM_001258312.1;PDE1A,missense_variant,p.Pro100Gln,ENST00000351439,NM_001258313.1;PDE1A,missense_variant,p.Pro100Gln,ENST00000409365,;PDE1A,missense_variant,p.Pro82Gln,ENST00000358139,NM_001258314.1;PDE1A,missense_variant,p.Pro116Gln,ENST00000410103,NM_001003683.2;PDE1A,non_coding_transcript_exon_variant,,ENST00000482538,;PDE1A,non_coding_transcript_exon_variant,,ENST00000495511,;PDE1A,non_coding_transcript_exon_variant,,ENST00000482782,;PDE1A,non_coding_transcript_exon_variant,,ENST00000462938,; T ENST00000435564 Transcript missense_variant 548/4885 347/1638 116/545 P/Q cCa/cAa 1 -1 PDE1A HGNC HGNC:8774 protein_coding YES CCDS2285.1 ENSP00000410309 P54750 UPI0000001072 NM_005019.4,NM_001258312.1 deleterious(0) 3/15 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Pfam_domain:PF08499 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 182240161 182240161 G T 1 0 0 0 0 1 0 0 0 11721 1348 47 2 2 PDE1A 2 182240161 Missense_Mutation SNP G C3L-00080_T 38705 182240161 59953368 113 2211 PDE1A 0 . GRCh38 2 182240200 182240200 + Missense_Mutation SNP C C T rs761155078 C3L-00080_T C3L-00080_N C C c.308G>A p.Arg103Gln p.R103Q ENST00000435564 3/15 231 162 69 190 190 0 strelka-varscan-mutect PDE1A,missense_variant,p.Arg103Gln,ENST00000435564,NM_005019.4,NM_001258312.1;PDE1A,missense_variant,p.Arg87Gln,ENST00000351439,NM_001258313.1;PDE1A,missense_variant,p.Arg87Gln,ENST00000409365,;PDE1A,missense_variant,p.Arg69Gln,ENST00000358139,NM_001258314.1;PDE1A,missense_variant,p.Arg103Gln,ENST00000410103,NM_001003683.2;PDE1A,non_coding_transcript_exon_variant,,ENST00000482538,;PDE1A,non_coding_transcript_exon_variant,,ENST00000495511,;PDE1A,non_coding_transcript_exon_variant,,ENST00000482782,;PDE1A,non_coding_transcript_exon_variant,,ENST00000462938,; T ENST00000435564 Transcript missense_variant 509/4885 308/1638 103/545 R/Q cGg/cAg rs761155078,COSM3574967,COSM3574968,COSM3574969,COSM3574970,COSM3574971 1 -1 PDE1A HGNC HGNC:8774 protein_coding YES CCDS2285.1 ENSP00000410309 P54750 UPI0000001072 NM_005019.4,NM_001258312.1 tolerated(0.17) 3/15 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Pfam_domain:PF08499 0,1,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1,1 1 PASS rs761155078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 182240200 182240200 C T 1 0 0 0 0 1 0 0 0 11721 652 23 1 1 PDE1A 2 182240200 Missense_Mutation SNP C C3L-00080_T 39 182240200 59953329 114 2212 ZNF804A 0 . GRCh38 2 184938587 184938587 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.3191A>T p.Lys1064Met p.K1064M ENST00000302277 4/4 319 224 95 237 237 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Lys1064Met,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Lys979Met,ENST00000613975,; T ENST00000302277 Transcript missense_variant 3785/4690 3191/3630 1064/1209 K/M aAg/aTg 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 deleterious(0.04) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 184938587 184938587 A T 1 0 0 0 0 1 0 0 0 18755 72 3 4 4 ZNF804A 2 184938587 Missense_Mutation SNP A C3L-00080_T 2698387 184938587 57254942 115 2213 FSIP2 0 . GRCh38 2 185796791 185796791 + Nonsense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.9922A>T p.Lys3308Ter p.K3308* ENST00000343098 16/23 96 79 17 109 109 0 strelka-varscan-mutect FSIP2,stop_gained,p.Lys3308Ter,ENST00000343098,NM_173651.2;FSIP2,stop_gained,p.Lys3219Ter,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,stop_gained,p.Lys726Ter,ENST00000415915,; T ENST00000343098 Transcript stop_gained 9922/21054 9922/20991 3308/6996 K/* Aaa/Taa 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 185796791 185796791 A T 1 0 0 0 0 0 1 0 0 5949 363 13 4 4 FSIP2 2 185796791 Nonsense_Mutation SNP A C3L-00080_T 858204 185796791 56396738 116 2214 SATB2 0 . GRCh38 2 199349084 199349084 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.790C>A p.Leu264Met p.L264M ENST00000417098 7/11 197 169 28 186 186 0 strelka-varscan-mutect SATB2,missense_variant,p.Leu205Met,ENST00000443023,;SATB2,missense_variant,p.Leu264Met,ENST00000417098,NM_001172509.1;SATB2,missense_variant,p.Leu264Met,ENST00000260926,NM_001172517.1;SATB2,missense_variant,p.Leu146Met,ENST00000614512,;SATB2,missense_variant,p.Leu264Met,ENST00000457245,NM_015265.3;SATB2,missense_variant,p.Leu146Met,ENST00000428695,;SATB2,non_coding_transcript_exon_variant,,ENST00000483346,; T ENST00000417098 Transcript missense_variant 1607/5730 790/2202 264/733 L/M Ctg/Atg 1 -1 SATB2 HGNC HGNC:21637 protein_coding YES CCDS2327.1 ENSP00000401112 Q9UPW6 A0A024R3U6 UPI00000336B1 NM_001172509.1 tolerated(0.26) 7/11 hmmpanther:PTHR15116:SF15,hmmpanther:PTHR15116 MODERATE 1 SNV 2 1 PASS rs1316738790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 199349084 199349084 G T 1 0 0 0 0 1 0 0 0 14115 991 35 2 2 SATB2 2 199349084 Missense_Mutation SNP G C3L-00080_T 13552293 199349084 42844445 117 2215 UNC80 0 . GRCh38 2 209816965 209816965 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.1392A>T p.= p.T464T ENST00000439458 10/64 345 318 27 287 287 0 strelka-varscan UNC80,synonymous_variant,p.=,ENST00000439458,NM_032504.1;UNC80,synonymous_variant,p.=,ENST00000272845,NM_182587.3; T ENST00000439458 Transcript synonymous_variant 1472/13562 1392/9777 464/3258 T acA/acT 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 10/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 209816965 209816965 A T 1 0 0 0 0 0 0 0 1 17521 175 7 4 4 UNC80 2 209816965 Silent SNP A C3L-00080_T 10467881 209816965 32376564 118 2216 ERBB4 0 . GRCh38 2 211665407 211665407 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1787G>T p.Gly596Val p.G596V ENST00000342788 15/28 600 430 170 513 512 1 strelka-varscan-mutect ERBB4,missense_variant,p.Gly596Val,ENST00000342788,NM_005235.2;ERBB4,missense_variant,p.Gly596Val,ENST00000436443,NM_001042599.1;ERBB4,missense_variant,p.Gly570Val,ENST00000402597,;ERBB4,missense_variant,p.Gly596Val,ENST00000260943,;ERBB4,upstream_gene_variant,,ENST00000463121,;ERBB4,non_coding_transcript_exon_variant,,ENST00000484594,; A ENST00000342788 Transcript missense_variant 2098/12136 1787/3927 596/1308 G/V gGc/gTc 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 deleterious(0) 15/28 hmmpanther:PTHR24416:SF90,hmmpanther:PTHR24416,Pfam_domain:PF14843,PIRSF_domain:PIRSF000619,Gene3D:2.10.220.10,SMART_domains:SM00261,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 211665407 211665407 C A 1 0 0 0 0 1 0 0 0 5057 739 26 2 2 ERBB4 2 211665407 Missense_Mutation SNP C C3L-00080_T 1848442 211665407 30528122 119 2217 FN1 0 . GRCh38 2 215372258 215372258 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6365G>T p.Gly2122Val p.G2122V ENST00000354785 40/46 476 353 123 421 421 0 strelka-varscan-mutect FN1,missense_variant,p.Gly2122Val,ENST00000354785,NM_212482.1;FN1,missense_variant,p.Gly2122Val,ENST00000323926,NM_001306129.1;FN1,missense_variant,p.Gly2031Val,ENST00000359671,;FN1,missense_variant,p.Gly2031Val,ENST00000336916,NM_002026.2;FN1,missense_variant,p.Gly1916Val,ENST00000421182,NM_001306132.1;FN1,missense_variant,p.Gly2006Val,ENST00000446046,NM_212478.1;FN1,missense_variant,p.Gly1941Val,ENST00000356005,NM_212476.1;FN1,missense_variant,p.Gly1941Val,ENST00000443816,NM_001306131.1;FN1,missense_variant,p.Gly748Val,ENST00000456923,;FN1,missense_variant,p.Gly125Val,ENST00000438981,;FN1,intron_variant,,ENST00000357867,NM_212474.1;FN1,intron_variant,,ENST00000432072,NM_001306130.1;FN1,non_coding_transcript_exon_variant,,ENST00000492816,;FN1,non_coding_transcript_exon_variant,,ENST00000460217,;FN1,non_coding_transcript_exon_variant,,ENST00000485567,;FN1,non_coding_transcript_exon_variant,,ENST00000461974,;FN1,downstream_gene_variant,,ENST00000474036,;FN1,upstream_gene_variant,,ENST00000480024,; A ENST00000354785 Transcript missense_variant 6735/8905 6365/7434 2122/2477 G/V gGa/gTa 1 -1 FN1 HGNC HGNC:3778 protein_coding YES CCDS42814.1 ENSP00000346839 P02751 UPI0000E5A2B5 NM_212482.1 tolerated(0.09) 40/46 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 215372258 215372258 C A 1 0 0 0 0 1 0 0 0 5818 855 30 2 2 FN1 2 215372258 Missense_Mutation SNP C C3L-00080_T 3706851 215372258 26821271 120 2218 ATG9A 0 . GRCh38 2 219223998 219223998 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1290G>T p.Met430Ile p.M430I ENST00000409618 9/16 126 83 43 102 102 0 strelka-mutect ATG9A,missense_variant,p.Met430Ile,ENST00000409618,;ATG9A,missense_variant,p.Met430Ile,ENST00000396761,NM_024085.4;ATG9A,missense_variant,p.Met430Ile,ENST00000361242,NM_001077198.2;ATG9A,missense_variant,p.Met369Ile,ENST00000409422,;ATG9A,downstream_gene_variant,,ENST00000436856,;ATG9A,downstream_gene_variant,,ENST00000432520,;ATG9A,upstream_gene_variant,,ENST00000429920,;ATG9A,downstream_gene_variant,,ENST00000428226,;ATG9A,downstream_gene_variant,,ENST00000457841,;ATG9A,downstream_gene_variant,,ENST00000443140,;ATG9A,downstream_gene_variant,,ENST00000439812,;ATG9A,downstream_gene_variant,,ENST00000431715,;ATG9A,downstream_gene_variant,,ENST00000434939,;ATG9A,downstream_gene_variant,,ENST00000455079,;ATG9A,downstream_gene_variant,,ENST00000488833,;ATG9A,missense_variant,p.Met430Ile,ENST00000409033,;ATG9A,upstream_gene_variant,,ENST00000446716,;ATG9A,upstream_gene_variant,,ENST00000475339,;ATG9A,downstream_gene_variant,,ENST00000466217,;ATG9A,downstream_gene_variant,,ENST00000486766,;ATG9A,downstream_gene_variant,,ENST00000456708,;ATG9A,downstream_gene_variant,,ENST00000412355,; A ENST00000409618 Transcript missense_variant 1730/4025 1290/2520 430/839 M/I atG/atT 1 -1 ATG9A HGNC HGNC:22408 protein_coding YES CCDS42820.1 ENSP00000386710 Q7Z3C6 A0A024R438 UPI0000209615 tolerated(0.06) 9/16 hmmpanther:PTHR13038,hmmpanther:PTHR13038:SF13,Pfam_domain:PF04109 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 219223998 219223998 C A 1 0 0 0 0 1 0 0 0 1254 594 21 2 2 ATG9A 2 219223998 Missense_Mutation SNP C C3L-00080_T 3851740 219223998 22969531 121 2219 SPEG 0 . GRCh38 2 219488245 219488245 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.7793G>A p.Gly2598Glu p.G2598E ENST00000312358 32/41 186 136 50 147 146 1 strelka-varscan-mutect SPEG,missense_variant,p.Gly2598Glu,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000412982,;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; A ENST00000312358 Transcript missense_variant 7925/10782 7793/9804 2598/3267 G/E gGg/gAg 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 32/41 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 219488245 219488245 G A 1 0 0 0 0 1 0 0 0 15387 1232 43 3 3 SPEG 2 219488245 Missense_Mutation SNP G C3L-00080_T 264247 219488245 22705284 122 2220 OBSL1 0 . GRCh38 2 219566889 219566889 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2075G>T p.Gly692Val p.G692V ENST00000404537 5/21 110 72 38 93 93 0 strelka-varscan-mutect OBSL1,missense_variant,p.Gly692Val,ENST00000404537,NM_015311.2;OBSL1,missense_variant,p.Gly692Val,ENST00000603926,NM_001173431.1;OBSL1,missense_variant,p.Gly692Val,ENST00000373876,;OBSL1,missense_variant,p.Gly692Val,ENST00000373873,NM_001173408.1;OBSL1,missense_variant,p.Gly279Val,ENST00000289656,;OBSL1,upstream_gene_variant,,ENST00000604031,;INHA,upstream_gene_variant,,ENST00000489456,;OBSL1,downstream_gene_variant,,ENST00000491370,;OBSL1,downstream_gene_variant,,ENST00000465589,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,;OBSL1,upstream_gene_variant,,ENST00000462385,; A ENST00000404537 Transcript missense_variant 2132/5841 2075/5691 692/1896 G/V gGt/gTt 1 -1 OBSL1 HGNC HGNC:29092 protein_coding YES CCDS46520.1 ENSP00000385636 O75147 UPI0000E07EA0 NM_015311.2 deleterious(0) 5/21 hmmpanther:PTHR13817,Gene3D:2.60.40.10,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 219566889 219566889 C A 1 0 0 0 0 1 0 0 0 10890 507 18 2 2 OBSL1 2 219566889 Missense_Mutation SNP C C3L-00080_T 78644 219566889 22626640 123 2221 EPHA4 0 . GRCh38 2 221434142 221434142 + Missense_Mutation SNP A A T rs749973188 C3L-00080_T C3L-00080_N A A c.2496T>A p.Asp832Glu p.D832E ENST00000281821 14/18 86 71 15 74 74 0 strelka-varscan-mutect EPHA4,missense_variant,p.Asp832Glu,ENST00000281821,NM_001304536.1,NM_001304537.1,NM_004438.4;EPHA4,missense_variant,p.Asp832Glu,ENST00000409854,;EPHA4,missense_variant,p.Asp832Glu,ENST00000409938,;EPHA4,missense_variant,p.Asp36Glu,ENST00000424339,;EPHA4,downstream_gene_variant,,ENST00000495693,; T ENST00000281821 Transcript missense_variant,splice_region_variant 2538/6346 2496/2961 832/986 D/E gaT/gaA rs749973188 1 -1 EPHA4 HGNC HGNC:3388 protein_coding YES CCDS2447.1 ENSP00000281821 P54764 A0A024R452 UPI000012A077 NM_001304536.1,NM_001304537.1,NM_004438.4 tolerated(0.12) 14/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF337,hmmpanther:PTHR24416,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Gene3D:1.10.510.10,SMART_domains:SM00220,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs749973188 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 221434142 221434142 A T 1 0 0 0 0 1 0 0 0 5016 231 8 4 4 EPHA4 2 221434142 Missense_Mutation SNP A C3L-00080_T 1867253 221434142 20759387 124 2222 EPHA4 0 . GRCh38 2 221564236 221564236 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.318G>T p.Arg106Ser p.R106S ENST00000281821 3/18 251 210 41 195 195 0 strelka-varscan-mutect EPHA4,missense_variant,p.Arg106Ser,ENST00000281821,NM_001304536.1,NM_001304537.1,NM_004438.4;EPHA4,missense_variant,p.Arg106Ser,ENST00000409854,;EPHA4,missense_variant,p.Arg106Ser,ENST00000409938,;EPHA4,missense_variant,p.Arg106Ser,ENST00000541600,;EPHA4,missense_variant,p.Arg47Ser,ENST00000419964,;EPHA4,intron_variant,,ENST00000443796,;EPHA4,downstream_gene_variant,,ENST00000434266,;EPHA4,3_prime_UTR_variant,,ENST00000415749,; A ENST00000281821 Transcript missense_variant 360/6346 318/2961 106/986 R/S agG/agT COSM4799084,COSM4799085 1 -1 EPHA4 HGNC HGNC:3388 protein_coding YES CCDS2447.1 ENSP00000281821 P54764 A0A024R452 UPI000012A077 NM_001304536.1,NM_001304537.1,NM_004438.4 deleterious(0) 3/18 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF337,hmmpanther:PTHR24416,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 221564236 221564236 C A 1 0 0 0 0 1 0 0 0 5016 622 22 2 2 EPHA4 2 221564236 Missense_Mutation SNP C C3L-00080_T 130094 221564236 20629293 125 2223 SPHKAP 0 . GRCh38 2 228018204 228018204 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2650C>A p.Gln884Lys p.Q884K ENST00000392056 7/12 179 111 68 152 152 0 strelka-varscan-mutect SPHKAP,missense_variant,p.Gln884Lys,ENST00000392056,NM_001142644.1;SPHKAP,missense_variant,p.Gln884Lys,ENST00000344657,NM_030623.3; T ENST00000392056 Transcript missense_variant 2697/6917 2650/5103 884/1700 Q/K Caa/Aaa 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 deleterious(0.04) 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 228018204 228018204 G T 1 0 0 0 0 1 0 0 0 15399 1357 47 2 2 SPHKAP 2 228018204 Missense_Mutation SNP G C3L-00080_T 6453968 228018204 14175325 126 2224 PTMA 0 . GRCh38 2 231711923 231711923 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.154G>A p.Glu52Lys p.E52K ENST00000341369 3/5 245 161 84 177 177 0 strelka-varscan-mutect PTMA,missense_variant,p.Glu51Lys,ENST00000409115,NM_002823.4;PTMA,missense_variant,p.Glu52Lys,ENST00000341369,NM_001099285.1;PTMA,missense_variant,p.Glu51Lys,ENST00000409683,;PTMA,missense_variant,p.Glu89Lys,ENST00000412128,;PTMA,missense_variant,p.Glu77Lys,ENST00000410064,;PTMA,missense_variant,p.Glu72Lys,ENST00000409321,;PTMA,downstream_gene_variant,,ENST00000440384,;U4,downstream_gene_variant,,ENST00000617137,;PTMA,upstream_gene_variant,,ENST00000612829,;PTMA,non_coding_transcript_exon_variant,,ENST00000466801,;PTMA,3_prime_UTR_variant,,ENST00000448874,;PTMA,non_coding_transcript_exon_variant,,ENST00000481928,;PTMA,non_coding_transcript_exon_variant,,ENST00000468027,;PTMA,non_coding_transcript_exon_variant,,ENST00000467816,; A ENST00000341369 Transcript missense_variant 345/1212 154/336 52/111 E/K Gag/Aag 1 1 PTMA HGNC HGNC:9623 protein_coding YES CCDS42833.1 ENSP00000344547 P06454 UPI0000047512 NM_001099285.1 tolerated(0.14) 3/5 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22745,Pfam_domain:PF03247 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 231711923 231711923 G A 1 0 0 0 0 1 0 0 0 12922 1291 45 3 3 PTMA 2 231711923 Missense_Mutation SNP G C3L-00080_T 3693719 231711923 10481606 127 2225 UGT1A7 0 . GRCh38 2 233682564 233682564 + Missense_Mutation SNP C C G rs780627101 C3L-00080_T C3L-00080_N C C c.627C>G p.Asn209Lys p.N209K ENST00000373426 1/5 538 418 120 505 505 0 strelka-varscan-mutect UGT1A7,missense_variant,p.Asn209Lys,ENST00000373426,NM_019077.2;UGT1A7,missense_variant,p.Asn66Lys,ENST00000485022,;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A10,intron_variant,,ENST00000373445,; G ENST00000373426 Transcript missense_variant 627/2333 627/1593 209/530 N/K aaC/aaG rs780627101 1 1 UGT1A7 HGNC HGNC:12539 protein_coding YES CCDS2506.1 ENSP00000362525 Q9HAW7 Q5DSZ7 UPI000013EA12 NM_019077.2 deleterious(0.01) 1/5 hmmpanther:PTHR11926:SF405,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs780627101 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 233682564 233682564 C G 1 0 0 0 0 1 0 0 0 17475 506 18 4 4 UGT1A7 2 233682564 Missense_Mutation SNP C C3L-00080_T 1970641 233682564 8510965 128 2226 OR6B2 0 . GRCh38 2 240030259 240030259 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.171G>T p.Arg57Ser p.R57S ENST00000402971 1/1 409 359 50 294 294 0 varscan-mutect OR6B2,missense_variant,p.Arg57Ser,ENST00000402971,NM_001005853.1;NDUFA10,upstream_gene_variant,,ENST00000252711,NM_004544.3;NDUFA10,upstream_gene_variant,,ENST00000404554,;NDUFA10,upstream_gene_variant,,ENST00000620965,;NDUFA10,upstream_gene_variant,,ENST00000307300,;NDUFA10,upstream_gene_variant,,ENST00000443626,;NDUFA10,upstream_gene_variant,,ENST00000407129,;NDUFA10,upstream_gene_variant,,ENST00000485344,;NDUFA10,upstream_gene_variant,,ENST00000497536,;NDUFA10,upstream_gene_variant,,ENST00000414580,; A ENST00000402971 Transcript missense_variant 198/1492 171/939 57/312 R/S agG/agT 1 -1 OR6B2 HGNC HGNC:15041 protein_coding YES CCDS46559.1 ENSP00000384563 Q6IFH4 UPI0000061EBF NM_001005853.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF313,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 240030259 240030259 C A 1 0 0 0 0 1 0 0 0 11256 738 26 2 2 OR6B2 2 240030259 Missense_Mutation SNP C C3L-00080_T 6347695 240030259 2163270 129 2227 OR6B3 0 . GRCh38 2 240045902 240045902 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.171G>T p.Arg57Ser p.R57S ENST00000319423 1/1 261 221 40 209 207 2 strelka-varscan-mutect OR6B3,missense_variant,p.Arg57Ser,ENST00000319423,NM_173351.1;PRR21,upstream_gene_variant,,ENST00000408934,NM_001080835.1; A ENST00000319423 Transcript missense_variant 171/996 171/996 57/331 R/S agG/agT 1 -1 OR6B3 HGNC HGNC:15042 protein_coding YES CCDS42837.1 ENSP00000322435 Q8NGW1 UPI0000061EBE NM_173351.1 deleterious(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF313,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 240045902 240045902 C A 1 0 0 0 0 1 0 0 0 11257 738 26 2 2 OR6B3 2 240045902 Missense_Mutation SNP C C3L-00080_T 15643 240045902 2147627 130 2228 SNED1 0 . GRCh38 2 241030525 241030525 + Missense_Mutation SNP C C T rs749953659 C3L-00080_T C3L-00080_N C C c.455C>T p.Ala152Val p.A152V ENST00000310397 2/32 217 155 62 183 183 0 strelka-varscan-mutect SNED1,missense_variant,p.Ala152Val,ENST00000310397,NM_001080437.1;SNED1,missense_variant,p.Ala152Val,ENST00000405547,;SNED1,missense_variant,p.Ala152Val,ENST00000401884,;AC005237.4,intron_variant,,ENST00000458377,; T ENST00000310397 Transcript missense_variant 455/8174 455/4242 152/1413 A/V gCc/gTc rs749953659 1 1 SNED1 HGNC HGNC:24696 protein_coding YES CCDS46562.1 ENSP00000308893 Q8TER0 UPI0000DD7AB0 NM_001080437.1 deleterious(0.05) 2/32 PROSITE_profiles:PS51220,SMART_domains:SM00539 MODERATE SNV 5 1 PASS rs749953659 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 241030525 241030525 C T 1 0 0 0 0 1 0 0 0 15166 739 26 3 3 SNED1 2 241030525 Missense_Mutation SNP C C3L-00080_T 984623 241030525 1163004 131 2229 ANO7 0 . GRCh38 2 241199393 241199393 + Silent SNP C C A rs752923367 C3L-00080_T C3L-00080_N C C c.549C>A p.= p.A183A ENST00000274979 5/25 328 232 96 257 257 0 strelka-varscan-mutect ANO7,synonymous_variant,p.=,ENST00000274979,NM_001001891.3;ANO7,synonymous_variant,p.=,ENST00000402430,;ANO7,downstream_gene_variant,,ENST00000402530,NM_001001666.3;ANO7,non_coding_transcript_exon_variant,,ENST00000475532,; A ENST00000274979 Transcript synonymous_variant 652/4128 549/2802 183/933 A gcC/gcA rs752923367 1 1 ANO7 HGNC HGNC:31677 protein_coding YES CCDS33423.1 ENSP00000274979 Q6IWH7 UPI0000D612DB NM_001001891.3 5/25 hmmpanther:PTHR12308:SF22,hmmpanther:PTHR12308,Pfam_domain:PF16178 LOW 1 SNV 1 1 PASS rs752923367 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 241199393 241199393 C A 1 0 0 0 0 0 0 0 1 809 639 23 1 1 ANO7 2 241199393 Silent SNP C C3L-00080_T 168868 241199393 994136 132 2230 CNTN6 0 . GRCh38 3 1382968 1382968 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.2193G>T p.= p.G731G ENST00000446702 18/23 147 92 55 164 164 0 strelka-varscan-mutect CNTN6,synonymous_variant,p.=,ENST00000446702,;CNTN6,synonymous_variant,p.=,ENST00000350110,NM_014461.3,NM_001289080.1,NM_001289081.1;CNTN6,3_prime_UTR_variant,,ENST00000397479,; T ENST00000446702 Transcript synonymous_variant 2820/4513 2193/3087 731/1028 G ggG/ggT 1 1 CNTN6 HGNC HGNC:2176 protein_coding YES CCDS2557.1 ENSP00000407822 Q9UQ52 A0A024R2C7 UPI0000072430 18/23 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF52,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 1382968 1382968 G T 1 0 0 0 0 0 0 0 1 3426 1219 43 2 2 CNTN6 3 1382968 Silent SNP G C3L-00080_T 1382968 196912591 133 2231 SSUH2 0 . GRCh38 3 8619923 8619923 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1073A>T p.Gln358Leu p.Q358L ENST00000544814 12/12 132 80 52 123 123 0 strelka-varscan-mutect SSUH2,missense_variant,p.Gln336Leu,ENST00000317371,;SSUH2,missense_variant,p.Gln336Leu,ENST00000341795,NM_015931.2,NM_001256749.1;SSUH2,missense_variant,p.Gln358Leu,ENST00000544814,NM_001256748.1;SSUH2,3_prime_UTR_variant,,ENST00000455157,;SSUH2,3_prime_UTR_variant,,ENST00000435138,;SSUH2,3_prime_UTR_variant,,ENST00000413305,;SSUH2,3_prime_UTR_variant,,ENST00000415132,;SSUH2,3_prime_UTR_variant,,ENST00000420394,;SSUH2,non_coding_transcript_exon_variant,,ENST00000495366,; A ENST00000544814 Transcript missense_variant 1113/1636 1073/1128 358/375 Q/L cAg/cTg 1 -1 SSUH2 HGNC HGNC:24809 protein_coding YES CCDS58815.1 ENSP00000439378 Q9Y2M2 UPI000206527B NM_001256748.1 deleterious(0.01) 12/12 hmmpanther:PTHR15852,hmmpanther:PTHR15852:SF7 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 8619923 8619923 T A 1 0 0 0 0 1 0 0 0 15580 1580 55 4 4 SSUH2 3 8619923 Missense_Mutation SNP T C3L-00080_T 7236955 8619923 189675636 134 2232 MTMR14 0 . GRCh38 3 9672709 9672709 + Missense_Mutation SNP C C G rs767978492 C3L-00080_T C3L-00080_N C C c.702C>G p.Asp234Glu p.D234E ENST00000296003 7/19 325 262 63 366 366 0 strelka-varscan-mutect MTMR14,missense_variant,p.Asp234Glu,ENST00000296003,NM_001077525.2;MTMR14,missense_variant,p.Asp234Glu,ENST00000353332,NM_001077526.2;MTMR14,missense_variant,p.Asp234Glu,ENST00000351233,NM_022485.4;MTMR14,intron_variant,,ENST00000420925,;MTMR14,upstream_gene_variant,,ENST00000431250,;MTMR14,missense_variant,p.Asp152Glu,ENST00000447144,;MTMR14,3_prime_UTR_variant,,ENST00000414996,;MTMR14,3_prime_UTR_variant,,ENST00000430020,;MTMR14,3_prime_UTR_variant,,ENST00000416864,;MTMR14,3_prime_UTR_variant,,ENST00000449543,;MTMR14,downstream_gene_variant,,ENST00000437997,; G ENST00000296003 Transcript missense_variant 824/2494 702/1953 234/650 D/E gaC/gaG rs767978492 1 1 MTMR14 HGNC HGNC:26190 protein_coding YES CCDS43043.1 ENSP00000296003 Q8NCE2 UPI000007423D NM_001077525.2 deleterious(0) 7/19 Gene3D:3.90.190.10,hmmpanther:PTHR13524,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS rs767978492 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 9672709 9672709 C G 1 0 0 0 0 1 0 0 0 9930 477 17 4 4 MTMR14 3 9672709 Missense_Mutation SNP C C3L-00080_T 1052786 9672709 188622850 135 2233 ZNF385D 0 . GRCh38 3 21437121 21437121 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.522C>A p.= p.T174T ENST00000281523 5/8 222 121 101 269 268 1 strelka-varscan-mutect ZNF385D,synonymous_variant,p.=,ENST00000281523,NM_024697.2;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494118,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000495739,;ZNF385D,3_prime_UTR_variant,,ENST00000446749,; T ENST00000281523 Transcript synonymous_variant 1041/10699 522/1188 174/395 T acC/acA 1 -1 ZNF385D HGNC HGNC:26191 protein_coding YES CCDS2636.1 ENSP00000281523 Q9H6B1 UPI00000724AC NM_024697.2 5/8 hmmpanther:PTHR23067:SF12,hmmpanther:PTHR23067 LOW 1 SNV 1 1 PASS rs1453615634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 21437121 21437121 G T 1 0 0 0 0 0 0 0 1 18451 987 35 2 2 ZNF385D 3 21437121 Silent SNP G C3L-00080_T 11764412 21437121 176858438 136 2234 ZNF385D 0 . GRCh38 3 21564630 21564630 + Frame_Shift_Del DEL G G - C3L-00080_T C3L-00080_N G G c.220delC p.His74ThrfsTer14 p.H74Tfs*14 ENST00000281523 3/8 83 40 43 109 108 1 sindel-varindel-pindel ZNF385D,frameshift_variant,p.His74ThrfsTer14,ENST00000281523,NM_024697.2;ZNF385D-AS1,intron_variant,,ENST00000412369,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494118,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494108,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000478967,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000469927,;ZNF385D,frameshift_variant,p.His74ThrfsTer14,ENST00000446749,; - ENST00000281523 Transcript frameshift_variant 739/10699 220/1188 74/395 H/X Cac/ac COSM5672847 1 -1 ZNF385D HGNC HGNC:26191 protein_coding YES CCDS2636.1 ENSP00000281523 Q9H6B1 UPI00000724AC NM_024697.2 3/8 hmmpanther:PTHR23067:SF12,hmmpanther:PTHR23067,Superfamily_domains:SSF57667 1 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 21564630 21564630 G - 1 0 1 0 1 0 0 0 0 18451 1348 47 0 0 ZNF385D 3 21564630 Frame_Shift_Del DEL G C3L-00080_T 127509 21564630 176730929 137 2235 TRANK1 0 . GRCh38 3 36833904 36833904 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.5547A>G p.= p.L1849L ENST00000429976 21/23 49 33 16 60 60 0 strelka-varscan-mutect TRANK1,synonymous_variant,p.=,ENST00000429976,NM_014831.2; C ENST00000429976 Transcript synonymous_variant 5795/10481 5547/8778 1849/2925 L ctA/ctG 1 -1 TRANK1 HGNC HGNC:29011 protein_coding YES CCDS46789.2 ENSP00000416168 O15050 UPI00017BE82B NM_014831.2 21/23 hmmpanther:PTHR21529,hmmpanther:PTHR21529:SF4 LOW 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 C 2 2 7 36833904 36833904 T C 1 0 0 0 0 0 0 0 1 16937 1741 61 5 5 TRANK1 3 36833904 Silent SNP T C3L-00080_T 15269274 36833904 161461655 138 2236 ITGA9 0 . GRCh38 3 37481523 37481523 + Missense_Mutation SNP G G T rs760915010 C3L-00080_T C3L-00080_N G G c.460G>T p.Asp154Tyr p.D154Y ENST00000264741 4/28 593 318 275 659 659 0 strelka-varscan-mutect ITGA9,missense_variant,p.Asp154Tyr,ENST00000264741,NM_002207.2;ITGA9,missense_variant,p.Asp154Tyr,ENST00000422441,; T ENST00000264741 Transcript missense_variant 716/7889 460/3108 154/1035 D/Y Gac/Tac rs760915010,COSM1211005 1 1 ITGA9 HGNC HGNC:6145 protein_coding YES CCDS2669.1 ENSP00000264741 Q13797 UPI00001AE8BB NM_002207.2 deleterious(0) 4/28 PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF69,Gene3D:3nigC00,Superfamily_domains:SSF69318 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760915010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 37481523 37481523 G T 1 0 0 0 0 1 0 0 0 7790 1058 37 1 1 ITGA9 3 37481523 Missense_Mutation SNP G C3L-00080_T 647619 37481523 160814036 139 2237 SCN5A 0 . GRCh38 3 38633125 38633125 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.183C>T p.= p.S61S ENST00000413689 2/28 76 42 34 114 114 0 strelka-varscan-mutect SCN5A,synonymous_variant,p.=,ENST00000413689,NM_001099404.1;SCN5A,synonymous_variant,p.=,ENST00000333535,NM_198056.2;SCN5A,synonymous_variant,p.=,ENST00000425664,NM_001099405.1;SCN5A,synonymous_variant,p.=,ENST00000423572,NM_000335.4;SCN5A,synonymous_variant,p.=,ENST00000451551,NM_001160161.1;SCN5A,synonymous_variant,p.=,ENST00000414099,;SCN5A,synonymous_variant,p.=,ENST00000455624,NM_001160160.1;SCN5A,synonymous_variant,p.=,ENST00000450102,;SCN5A,synonymous_variant,p.=,ENST00000449557,;SCN5A,synonymous_variant,p.=,ENST00000612060,;SCN5A,synonymous_variant,p.=,ENST00000327956,;SCN5A,non_coding_transcript_exon_variant,,ENST00000491944,;SCN5A,non_coding_transcript_exon_variant,,ENST00000476683,; A ENST00000413689 Transcript synonymous_variant 377/8504 183/6051 61/2016 S tcC/tcT 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 2/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 LOW 1 SNV 5 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999899 1 1 1 0 A 2 1 7 38633125 38633125 G A 1 0 0 0 0 0 0 0 1 14191 1335 47 3 3 SCN5A 3 38633125 Silent SNP G C3L-00080_T 1151602 38633125 159662434 140 2238 ULK4 0 . GRCh38 3 41663698 41663698 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2980T>A p.Tyr994Asn p.Y994N ENST00000301831 30/37 164 118 46 240 240 0 strelka-varscan-mutect ULK4,missense_variant,p.Tyr994Asn,ENST00000301831,NM_017886.2; T ENST00000301831 Transcript missense_variant,splice_region_variant 3443/4613 2980/3828 994/1275 Y/N Tat/Aat 1 -1 ULK4 HGNC HGNC:15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 UPI0000E8267C NM_017886.2 deleterious(0) 30/37 Gene3D:1.25.10.10,hmmpanther:PTHR22983,hmmpanther:PTHR22983:SF15,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 41663698 41663698 A T 1 0 0 0 0 1 0 0 0 17501 405 14 4 4 ULK4 3 41663698 Missense_Mutation SNP A C3L-00080_T 3030573 41663698 156631861 141 2239 ZNF502 0 . GRCh38 3 44721978 44721978 + Silent SNP G G A rs149761315 C3L-00080_T C3L-00080_N G G c.1161G>A p.= p.A387A ENST00000296091 4/4 179 151 28 232 232 0 strelka-varscan-mutect ZNF502,synonymous_variant,p.=,ENST00000296091,NM_001134440.1,NM_001282880.1,NM_033210.4;ZNF502,synonymous_variant,p.=,ENST00000449836,NM_001134441.1,NM_001134442.1;ZNF502,synonymous_variant,p.=,ENST00000436624,;ZNF502,downstream_gene_variant,,ENST00000411443,; A ENST00000296091 Transcript synonymous_variant 1417/3270 1161/1635 387/544 A gcG/gcA rs149761315,COSM5171160 1 1 ZNF502 HGNC HGNC:23718 protein_coding YES CCDS2719.1 ENSP00000296091 Q8TBZ5 A0A024R2Z2 UPI0000072CFB NM_001134440.1,NM_001282880.1,NM_033210.4 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF133,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 LOW 1 SNV 1 0,1 1 PASS rs149761315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 44721978 44721978 G A 1 0 0 0 0 0 0 0 1 18522 1132 40 1 1 ZNF502 3 44721978 Silent SNP G C3L-00080_T 3058280 44721978 153573581 142 2240 ALS2CL 0 . GRCh38 3 46671520 46671520 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.2749G>A p.Gly917Ser p.G917S ENST00000318962 25/26 147 103 44 208 208 0 strelka-varscan-mutect ALS2CL,missense_variant,p.Gly917Ser,ENST00000318962,NM_147129.3;ALS2CL,missense_variant,p.Gly917Ser,ENST00000415953,NM_001190707.1;ALS2CL,missense_variant,p.Gly264Ser,ENST00000383742,NM_182775.2;ALS2CL,non_coding_transcript_exon_variant,,ENST00000473484,;ALS2CL,3_prime_UTR_variant,,ENST00000423707,;ALS2CL,3_prime_UTR_variant,,ENST00000434140,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000450172,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000431015,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000486301,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000498817,; T ENST00000318962 Transcript missense_variant 2833/4741 2749/2862 917/953 G/S Ggc/Agc 1 -1 ALS2CL HGNC HGNC:20605 protein_coding YES CCDS2743.1 ENSP00000313670 Q60I27 A0A024R2U1 UPI00001B5641 NM_147129.3 deleterious(0) 25/26 Superfamily_domains:0044157,Pfam_domain:PF02204,PROSITE_profiles:PS51205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 46671520 46671520 C T 1 0 0 0 0 1 0 0 0 651 681 24 3 3 ALS2CL 3 46671520 Missense_Mutation SNP C C3L-00080_T 1949542 46671520 151624039 143 2241 GRM2 0 . GRCh38 3 51712714 51712714 + Missense_Mutation SNP G G T rs147501226 C3L-00080_T C3L-00080_N G G c.692G>T p.Arg231Leu p.R231L ENST00000395052 3/6 318 189 129 323 322 1 strelka-varscan-mutect GRM2,missense_variant,p.Arg231Leu,ENST00000395052,NM_000839.3;GRM2,missense_variant,p.Arg231Leu,ENST00000442933,;GRM2,downstream_gene_variant,,ENST00000419928,;GRM2,non_coding_transcript_exon_variant,,ENST00000496661,;GRM2,intron_variant,,ENST00000475478,;GRM2,downstream_gene_variant,,ENST00000477330,;GRM2,missense_variant,p.Arg231Leu,ENST00000296479,;GRM2,non_coding_transcript_exon_variant,,ENST00000464585,; T ENST00000395052 Transcript missense_variant 926/3151 692/2619 231/872 R/L cGc/cTc rs147501226,COSM1566707 1 1 GRM2 HGNC HGNC:4594 protein_coding YES CCDS2834.1 ENSP00000378492 Q14416 UPI000013E346 NM_000839.3 tolerated(0.42) 3/6 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF111,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs147501226 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 51712714 51712714 G T 1 0 0 0 0 1 0 0 0 6679 1087 38 1 1 GRM2 3 51712714 Missense_Mutation SNP G C3L-00080_T 5041194 51712714 146582845 144 2242 ITIH3 0 . GRCh38 3 52806365 52806365 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.2015C>T p.Ala672Val p.A672V ENST00000449956 18/22 134 69 65 126 125 1 strelka-varscan-mutect ITIH3,missense_variant,p.Ala672Val,ENST00000449956,NM_002217.3;ITIH3,3_prime_UTR_variant,,ENST00000621946,;ITIH3,intron_variant,,ENST00000416872,;ITIH3,non_coding_transcript_exon_variant,,ENST00000493136,;ITIH3,non_coding_transcript_exon_variant,,ENST00000495622,;ITIH3,downstream_gene_variant,,ENST00000475931,;ITIH3,downstream_gene_variant,,ENST00000464804,;ITIH3,downstream_gene_variant,,ENST00000465314,; T ENST00000449956 Transcript missense_variant 2021/3007 2015/2673 672/890 A/V gCc/gTc 1 1 ITIH3 HGNC HGNC:6168 protein_coding YES CCDS46845.1 ENSP00000415769 Q06033 UPI00005CE290 NM_002217.3 tolerated(0.1) 18/22 hmmpanther:PTHR10338:SF115,hmmpanther:PTHR10338 MODERATE 1 SNV 1 1 PASS . . 0 204 0 5 0 0 0 0 -20 0.9999474 1 1 1 0 T 3 4 7 52806365 52806365 C T 1 0 0 0 0 1 0 0 0 7811 739 26 3 3 ITIH3 3 52806365 Missense_Mutation SNP C C3L-00080_T 1093651 52806365 145489194 145 2243 FAM19A4 0 . GRCh38 3 68752886 68752886 + Missense_Mutation SNP C C A rs148065010 C3L-00080_T C3L-00080_N C C c.263G>T p.Arg88Leu p.R88L ENST00000295569 4/6 329 188 141 435 434 1 strelka-varscan-mutect FAM19A4,missense_variant,p.Arg88Leu,ENST00000295569,NM_001005527.2,NM_182522.4;FAM19A4,downstream_gene_variant,,ENST00000634242,;FAM19A4,downstream_gene_variant,,ENST00000495737,; A ENST00000295569 Transcript missense_variant 756/2292 263/423 88/140 R/L cGg/cTg rs148065010,COSM166557 1 -1 FAM19A4 HGNC HGNC:21591 protein_coding YES CCDS2907.1 ENSP00000295569 Q96LR4 A0A024R369 UPI0000071129 NM_001005527.2,NM_182522.4 deleterious(0) 4/6 PD298472,Pfam_domain:PF12020,hmmpanther:PTHR31770,hmmpanther:PTHR31770:SF7 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs148065010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 68752886 68752886 C A 1 0 0 0 0 1 0 0 0 5381 652 23 1 1 FAM19A4 3 68752886 Missense_Mutation SNP C C3L-00080_T 15946521 68752886 129542673 146 2244 POU1F1 0 . GRCh38 3 87276405 87276405 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.58T>A p.Ser20Thr p.S20T ENST00000344265 1/6 304 166 138 384 384 0 strelka-varscan-mutect POU1F1,missense_variant,p.Ser20Thr,ENST00000350375,NM_000306.3;POU1F1,missense_variant,p.Ser20Thr,ENST00000344265,NM_001122757.2;POU1F1,missense_variant,p.Ser20Thr,ENST00000561167,;POU1F1,missense_variant,p.Ser20Thr,ENST00000560656,; T ENST00000344265 Transcript missense_variant 100/1149 58/954 20/317 S/T Tct/Act 1 -1 POU1F1 HGNC HGNC:9210 protein_coding YES CCDS46873.1 ENSP00000342931 P28069 UPI000002B11B NM_001122757.2 deleterious_low_confidence(0.01) 1/6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 87276405 87276405 A T 1 0 0 0 0 1 0 0 0 12385 304 11 4 4 POU1F1 3 87276405 Missense_Mutation SNP A C3L-00080_T 18523519 87276405 111019154 147 2245 HTR1F 0 . GRCh38 3 87991477 87991477 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.728C>T p.Thr243Ile p.T243I ENST00000319595 1/1 80 50 30 123 123 0 strelka-varscan-mutect HTR1F,missense_variant,p.Thr243Ile,ENST00000319595,NM_001322210.1,NM_001322209.1,NM_000866.3; T ENST00000319595 Transcript missense_variant 782/3140 728/1101 243/366 T/I aCa/aTa 1 1 HTR1F HGNC HGNC:5292 protein_coding YES CCDS2920.1 ENSP00000322924 P30939 UPI00000503DF NM_001322210.1,NM_001322209.1,NM_000866.3 tolerated(0.31) 1/1 Pfam_domain:PF00001,Prints_domain:PR00515,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF34,SMART_domains:SM01381 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 87991477 87991477 C T 1 0 0 0 0 1 0 0 0 7336 478 17 3 3 HTR1F 3 87991477 Missense_Mutation SNP C C3L-00080_T 715072 87991477 110304082 148 2246 EPHA6 0 . GRCh38 3 96987738 96987738 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.859G>T p.Ala287Ser p.A287S ENST00000389672 3/18 77 52 25 51 51 0 strelka-varscan-mutect EPHA6,missense_variant,p.Ala287Ser,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Ala287Ser,ENST00000470610,;EPHA6,missense_variant,p.Ala232Ser,ENST00000506569,NM_001278301.1; T ENST00000389672 Transcript missense_variant 897/3971 859/3393 287/1130 A/S Gcg/Tcg 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0.01) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_patterns:PS00790,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 7 96987738 96987738 G T 1 0 0 0 0 1 0 0 0 5018 1203 42 2 2 EPHA6 3 96987738 Missense_Mutation SNP G C3L-00080_T 8996261 96987738 101307821 149 2247 EPHA6 0 . GRCh38 3 97244144 97244144 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1463G>T p.Gly488Val p.G488V ENST00000389672 5/18 295 194 101 192 192 0 strelka-varscan-mutect EPHA6,missense_variant,p.Gly488Val,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Gly488Val,ENST00000470610,; T ENST00000389672 Transcript missense_variant 1501/3971 1463/3393 488/1130 G/V gGc/gTc 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 5/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 97244144 97244144 G T 1 0 0 0 0 1 0 0 0 5018 1203 42 2 2 EPHA6 3 97244144 Missense_Mutation SNP G C3L-00080_T 256406 97244144 101051415 150 2248 EPHA6 0 . GRCh38 3 97720284 97720284 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2808G>T p.Trp936Cys p.W936C ENST00000389672 15/18 105 64 41 48 48 0 strelka-varscan-mutect EPHA6,missense_variant,p.Trp936Cys,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Trp260Cys,ENST00000477384,; T ENST00000389672 Transcript missense_variant 2846/3971 2808/3393 936/1130 W/C tgG/tgT 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS rs1215321701 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 97720284 97720284 G T 1 0 0 0 0 1 0 0 0 5018 1183 41 2 2 EPHA6 3 97720284 Missense_Mutation SNP G C3L-00080_T 476140 97720284 100575275 151 2249 OR5H1 0 . GRCh38 3 98133027 98133027 + Silent SNP G G C rs113686881 C3L-00080_T C3L-00080_N G G c.330G>C p.= p.T110T ENST00000354565 1/1 381 248 133 310 309 1 strelka-varscan-mutect OR5H1,synonymous_variant,p.=,ENST00000354565,NM_001005338.1;RP11-343D2.11,intron_variant,,ENST00000508964,; C ENST00000354565 Transcript synonymous_variant 330/942 330/942 110/313 T acG/acC rs113686881,COSM3598244 1 1 OR5H1 HGNC HGNC:8346 protein_coding YES CCDS33797.1 ENSP00000346575 A6NKK0 A0A126GW79 UPI0000197652 NM_001005338.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW SNV 0,1 1 PASS rs113686881 . 0 159 0 0 50 0 0 0 -20 0 0 1 0 0 C 2 2 7 98133027 98133027 G C 1 0 0 0 0 0 0 0 1 11229 1103 39 4 4 OR5H1 3 98133027 Silent SNP G C3L-00080_T 412743 98133027 100162532 152 2250 CEP97 0 . GRCh38 3 101765130 101765130 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2177A>T p.Glu726Val p.E726V ENST00000341893 11/11 183 159 24 133 133 0 strelka-varscan-mutect CEP97,missense_variant,p.Glu726Val,ENST00000341893,NM_024548.3;CEP97,missense_variant,p.Glu667Val,ENST00000494050,NM_001303401.1;CEP97,downstream_gene_variant,,ENST00000467655,; T ENST00000341893 Transcript missense_variant 2929/8361 2177/2598 726/865 E/V gAa/gTa 1 1 CEP97 HGNC HGNC:26244 protein_coding YES CCDS2944.1 ENSP00000342510 Q8IW35 UPI0000074569 NM_024548.3 deleterious(0.03) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 101765130 101765130 A T 1 0 0 0 0 1 0 0 0 2989 246 9 4 4 CEP97 3 101765130 Missense_Mutation SNP A C3L-00080_T 3632103 101765130 96530429 153 2251 ZPLD1 0 . GRCh38 3 102469039 102469039 + Frame_Shift_Del DEL C C - rs746914724 C3L-00080_T C3L-00080_N C C c.886delC p.Arg296AspfsTer3 p.R296Dfs*3 ENST00000306176 8/11 175 116 59 110 110 0 sindel-varindel-pindel ZPLD1,frameshift_variant,p.Arg296AspfsTer3,ENST00000306176,NM_175056.1;ZPLD1,frameshift_variant,p.Arg280AspfsTer3,ENST00000491959,;ZPLD1,frameshift_variant,p.Arg280AspfsTer3,ENST00000466937,; - ENST00000306176 Transcript frameshift_variant 985/3619 885/1296 295/431 F/X ttC/tt rs746914724,COSM3584724 1 1 ZPLD1 HGNC HGNC:27022 protein_coding YES CCDS2947.1 ENSP00000307801 Q8TCW7 UPI000006EC89 NM_175056.1 8/11 PROSITE_profiles:PS51034,hmmpanther:PTHR24044:SF333,hmmpanther:PTHR24044,Pfam_domain:PF00100,SMART_domains:SM00241 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 102469039 102469039 C - 1 0 1 0 1 0 0 0 0 18813 854 30 0 0 ZPLD1 3 102469039 Frame_Shift_Del DEL C C3L-00080_T 703909 102469039 95826520 154 2252 CBLB 0 . GRCh38 3 105740601 105740601 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.876G>T p.Leu292Phe p.L292F ENST00000264122 7/19 597 515 82 387 387 0 strelka-varscan-mutect CBLB,missense_variant,p.Leu292Phe,ENST00000264122,NM_001321786.1,NM_001321788.1,NM_170662.3;CBLB,missense_variant,p.Leu292Phe,ENST00000403724,;CBLB,missense_variant,p.Leu292Phe,ENST00000405772,; A ENST00000264122 Transcript missense_variant 1198/6780 876/2949 292/982 L/F ttG/ttT 1 -1 CBLB HGNC HGNC:1542 protein_coding YES CCDS2948.1 ENSP00000264122 Q13191 UPI00001AE89F NM_001321786.1,NM_001321788.1,NM_170662.3 deleterious(0) 7/19 PROSITE_profiles:PS51506,hmmpanther:PTHR23007:SF3,hmmpanther:PTHR23007,Gene3D:3.30.505.10,Pfam_domain:PF02762,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 105740601 105740601 C A 1 0 0 0 0 1 0 0 0 2402 593 21 2 2 CBLB 3 105740601 Missense_Mutation SNP C C3L-00080_T 3271562 105740601 92554958 155 2253 MORC1 0 . GRCh38 3 109054862 109054862 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1196G>C p.Gly399Ala p.G399A ENST00000232603 14/28 304 267 37 268 268 0 strelka-varscan-mutect MORC1,missense_variant,p.Gly399Ala,ENST00000232603,NM_014429.3;MORC1,missense_variant,p.Gly399Ala,ENST00000483760,; G ENST00000232603 Transcript missense_variant 1279/3764 1196/2955 399/984 G/A gGa/gCa 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 deleterious(0.03) 14/28 hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 109054862 109054862 C G 1 0 0 0 0 1 0 0 0 9665 855 30 4 4 MORC1 3 109054862 Missense_Mutation SNP C C3L-00080_T 3314261 109054862 89240697 156 2254 MORC1 0 . GRCh38 3 109069736 109069736 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.711C>A p.Phe237Leu p.F237L ENST00000232603 9/28 153 106 47 146 146 0 strelka-varscan-mutect MORC1,missense_variant,p.Phe237Leu,ENST00000232603,NM_014429.3;MORC1,missense_variant,p.Phe237Leu,ENST00000483760,; T ENST00000232603 Transcript missense_variant 794/3764 711/2955 237/984 F/L ttC/ttA 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 tolerated(0.24) 9/28 hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337,Superfamily_domains:SSF55874 MODERATE 1 SNV 1 1 PASS rs1411876590 . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 7 109069736 109069736 G T 1 0 0 0 0 1 0 0 0 9665 1281 45 2 2 MORC1 3 109069736 Missense_Mutation SNP G C3L-00080_T 14874 109069736 89225823 157 2255 PHLDB2 0 . GRCh38 3 111884960 111884960 + Missense_Mutation SNP G G T rs548907756 C3L-00080_T C3L-00080_N G G c.883G>T p.Val295Leu p.V295L ENST00000431670 2/18 263 181 82 202 202 0 strelka-varscan-mutect PHLDB2,missense_variant,p.Val295Leu,ENST00000431670,NM_001134438.1;PHLDB2,missense_variant,p.Val295Leu,ENST00000412622,NM_145753.2;PHLDB2,missense_variant,p.Val295Leu,ENST00000477695,;PHLDB2,missense_variant,p.Val322Leu,ENST00000393923,NM_001134437.1;PHLDB2,missense_variant,p.Val295Leu,ENST00000393925,NM_001134439.1;PHLDB2,missense_variant,p.Val295Leu,ENST00000481953,;PHLDB2,missense_variant,p.Val295Leu,ENST00000498699,;PHLDB2,missense_variant,p.Val295Leu,ENST00000478922,; T ENST00000431670 Transcript missense_variant 1294/6127 883/3762 295/1253 V/L Gta/Tta rs548907756,COSM5005064,COSM5005065,COSM5005066,COSM5571150,COSM5571151,COSM5571152 1 1 PHLDB2 HGNC HGNC:29573 protein_coding YES CCDS46886.1 ENSP00000405405 Q86SQ0 UPI0000457152 NM_001134438.1 tolerated(0.61) 2/18 0,1,1,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1,1,1 1 PASS rs548907756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 111884960 111884960 G T 1 0 0 0 0 1 0 0 0 11940 1145 40 1 1 PHLDB2 3 111884960 Missense_Mutation SNP G C3L-00080_T 2815224 111884960 86410599 158 2256 DRD3 0 . GRCh38 3 114131214 114131214 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.910G>T p.Gly304Cys p.G304C ENST00000383673 6/7 465 319 146 292 291 1 strelka-varscan-mutect DRD3,missense_variant,p.Gly304Cys,ENST00000383673,NM_000796.5;DRD3,missense_variant,p.Gly304Cys,ENST00000460779,NM_001282563.2;DRD3,missense_variant,p.Gly304Cys,ENST00000467632,NM_001290809.1;DRD3,intron_variant,,ENST00000295881,NM_033663.5; A ENST00000383673 Transcript missense_variant 1341/1640 910/1203 304/400 G/C Ggc/Tgc 1 -1 DRD3 HGNC HGNC:3024 protein_coding YES CCDS2978.1 ENSP00000373169 P35462 X5D2G4 UPI000013E2C2 NM_000796.5 deleterious(0) 6/7 PROSITE_profiles:PS50262,Pfam_domain:PF00001,SMART_domains:SM01381,Prints_domain:PR00568 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 114131214 114131214 C A 1 0 0 0 0 1 0 0 0 4577 594 21 2 2 DRD3 3 114131214 Missense_Mutation SNP C C3L-00080_T 2246254 114131214 84164345 159 2257 TMEM39A 0 . GRCh38 3 119436848 119436848 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.1055A>C p.His352Pro p.H352P ENST00000319172 7/9 129 110 19 83 83 0 strelka-varscan-mutect TMEM39A,missense_variant,p.His352Pro,ENST00000319172,NM_018266.2;TMEM39A,downstream_gene_variant,,ENST00000491685,;TMEM39A,downstream_gene_variant,,ENST00000486159,;TMEM39A,3_prime_UTR_variant,,ENST00000438581,;TMEM39A,non_coding_transcript_exon_variant,,ENST00000468545,;TMEM39A,upstream_gene_variant,,ENST00000473684,; G ENST00000319172 Transcript missense_variant 1476/4369 1055/1467 352/488 H/P cAc/cCc 1 -1 TMEM39A HGNC HGNC:25600 protein_coding YES CCDS2987.1 ENSP00000326063 Q9NV64 UPI00000715E5 NM_018266.2 deleterious(0) 7/9 hmmpanther:PTHR12995,hmmpanther:PTHR12995:SF3,Pfam_domain:PF10271 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 119436848 119436848 T G 1 0 0 0 0 1 0 0 0 16638 1696 59 5 5 TMEM39A 3 119436848 Missense_Mutation SNP T C3L-00080_T 5305634 119436848 78858711 160 2258 CCDC58 0 . GRCh38 3 122371781 122371781 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.71G>A p.Arg24Lys p.R24K ENST00000291458 2/5 238 134 104 184 183 1 strelka-varscan-mutect CCDC58,missense_variant,p.Arg24Lys,ENST00000291458,NM_001017928.2;CCDC58,missense_variant,p.Arg10Lys,ENST00000479899,NM_001308326.1;CCDC58,missense_variant,p.Arg21Lys,ENST00000479414,;CCDC58,intron_variant,,ENST00000497726,;CCDC58,non_coding_transcript_exon_variant,,ENST00000498466,; T ENST00000291458 Transcript missense_variant 78/720 71/435 24/144 R/K aGg/aAg 1 -1 CCDC58 HGNC HGNC:31136 protein_coding YES CCDS33838.1 ENSP00000291458 Q4VC31 UPI000020A069 NM_001017928.2 deleterious(0) 2/5 Pfam_domain:PF09774,hmmpanther:PTHR31905 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 122371781 122371781 C T 1 0 0 0 0 1 0 0 0 2530 681 24 3 3 CCDC58 3 122371781 Missense_Mutation SNP C C3L-00080_T 2934933 122371781 75923778 161 2259 COL6A6 0 . GRCh38 3 130571208 130571208 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.2792C>T p.Ala931Val p.A931V ENST00000358511 6/36 181 142 39 137 137 0 strelka-varscan-mutect COL6A6,missense_variant,p.Ala931Val,ENST00000358511,NM_001102608.1; T ENST00000358511 Transcript missense_variant 2823/9581 2792/6792 931/2263 A/V gCc/gTc 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 tolerated(0.28) 6/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999991 1 1 1 0 T 3 4 7 130571208 130571208 C T 1 0 0 0 0 1 0 0 0 3492 739 26 3 3 COL6A6 3 130571208 Missense_Mutation SNP C C3L-00080_T 8199427 130571208 67724351 162 2260 RYK 0 . GRCh38 3 134175957 134175957 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1397A>T p.His466Leu p.H466L ENST00000620660 12/15 565 413 152 367 367 0 strelka-varscan-mutect RYK,missense_variant,p.His466Leu,ENST00000620660,NM_001005861.2;RYK,missense_variant,p.His463Leu,ENST00000623711,NM_002958.3;RYK,missense_variant,p.His404Leu,ENST00000460933,;RYK,missense_variant,p.His83Leu,ENST00000484106,;RYK,3_prime_UTR_variant,,ENST00000486725,;RYK,non_coding_transcript_exon_variant,,ENST00000473208,;RYK,non_coding_transcript_exon_variant,,ENST00000481382,;HMGB3P14,downstream_gene_variant,,ENST00000494195,; A ENST00000620660 Transcript missense_variant 1487/2942 1397/1833 466/610 H/L cAc/cTc 1 -1 RYK HGNC HGNC:10481 protein_coding YES CCDS75016.1 ENSP00000478721 A0A087WUK1 UPI0000451C9D NM_001005861.2 deleterious(0) 12/15 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF349,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 134175957 134175957 T A 1 0 0 0 0 1 0 0 0 14027 1696 59 4 4 RYK 3 134175957 Missense_Mutation SNP T C3L-00080_T 3604749 134175957 64119602 163 2261 EPHB1 0 . GRCh38 3 134951633 134951633 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.386G>C p.Trp129Ser p.W129S ENST00000398015 3/16 321 194 127 198 198 0 strelka-varscan-mutect EPHB1,missense_variant,p.Trp129Ser,ENST00000398015,NM_004441.4;EPHB1,missense_variant,p.Trp107Ser,ENST00000460895,;EPHB1,missense_variant,p.Trp107Ser,ENST00000474732,;EPHB1,downstream_gene_variant,,ENST00000473867,;EPHB1,downstream_gene_variant,,ENST00000497173,;EPHB1,non_coding_transcript_exon_variant,,ENST00000488154,;EPHB1,missense_variant,p.Trp129Ser,ENST00000482618,; C ENST00000398015 Transcript missense_variant 756/4672 386/2955 129/984 W/S tGg/tCg 1 1 EPHB1 HGNC HGNC:3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 UPI000012A07E NM_004441.4 deleterious(0.01) 3/16 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 134951633 134951633 G C 1 0 0 0 0 1 0 0 0 5021 1357 47 4 4 EPHB1 3 134951633 Missense_Mutation SNP G C3L-00080_T 775676 134951633 63343926 164 2262 STAG1 0 . GRCh38 3 136464981 136464981 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1213G>T p.Glu405Ter p.E405* ENST00000383202 13/34 160 104 56 129 129 0 strelka-varscan-mutect STAG1,stop_gained,p.Glu405Ter,ENST00000383202,NM_005862.2;STAG1,stop_gained,p.Glu405Ter,ENST00000236698,;STAG1,stop_gained,p.Glu179Ter,ENST00000434713,;STAG1,3_prime_UTR_variant,,ENST00000629124,;STAG1,intron_variant,,ENST00000492318,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,; A ENST00000383202 Transcript stop_gained 1470/6055 1213/3777 405/1258 E/* Gaa/Taa 1 -1 STAG1 HGNC HGNC:11354 protein_coding YES CCDS3090.1 ENSP00000372689 Q8WVM7 UPI000020A2DE NM_005862.2 13/34 hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 136464981 136464981 C A 1 0 0 0 0 0 1 0 0 15620 835 29 2 2 STAG1 3 136464981 Nonsense_Mutation SNP C C3L-00080_T 1513348 136464981 61830578 165 2263 ESYT3 0 . GRCh38 3 138464500 138464500 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.1071G>C p.Trp357Cys p.W357C ENST00000389567 9/23 206 150 56 121 121 0 strelka-varscan-mutect ESYT3,missense_variant,p.Trp357Cys,ENST00000389567,NM_031913.3;ESYT3,downstream_gene_variant,,ENST00000289135,;ESYT3,missense_variant,p.Trp357Cys,ENST00000490835,;ESYT3,non_coding_transcript_exon_variant,,ENST00000486831,;ESYT3,upstream_gene_variant,,ENST00000468103,; C ENST00000389567 Transcript missense_variant 1257/4407 1071/2661 357/886 W/C tgG/tgC 1 1 ESYT3 HGNC HGNC:24295 protein_coding YES CCDS3101.2 ENSP00000374218 A0FGR9 UPI0000251E45 NM_031913.3 deleterious(0) 9/23 Gene3D:2.60.40.150,Pfam_domain:PF00168,Prints_domain:PR00360,PROSITE_profiles:PS50004,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF74,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 138464500 138464500 G C 1 0 0 0 0 1 0 0 0 5128 1183 41 4 4 ESYT3 3 138464500 Missense_Mutation SNP G C3L-00080_T 1999519 138464500 59831059 166 2264 CPB1 0 . GRCh38 3 148845476 148845476 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.831A>T p.= p.A277A ENST00000491148 10/12 354 249 105 225 225 0 strelka-varscan-mutect CPB1,synonymous_variant,p.=,ENST00000491148,;CPB1,synonymous_variant,p.=,ENST00000282957,NM_001871.2;CPB1,downstream_gene_variant,,ENST00000468341,;CPB1,downstream_gene_variant,,ENST00000462345,;CPB1,downstream_gene_variant,,ENST00000484877,;CPB1,downstream_gene_variant,,ENST00000465718,; T ENST00000491148 Transcript synonymous_variant 1165/1773 831/1254 277/417 A gcA/gcT 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD 10/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 148845476 148845476 A T 1 0 0 0 0 0 0 0 1 3590 175 7 4 4 CPB1 3 148845476 Silent SNP A C3L-00080_T 10380976 148845476 49450083 167 2265 PLCH1 0 . GRCh38 3 155481659 155481659 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.4391G>T p.Ser1464Ile p.S1464I ENST00000340059 23/23 296 176 120 186 186 0 strelka-varscan-mutect PLCH1,missense_variant,p.Ser1426Ile,ENST00000460012,;PLCH1,missense_variant,p.Ser1464Ile,ENST00000340059,NM_001130960.1;PLCH1,missense_variant,p.Ser1426Ile,ENST00000334686,NM_014996.2;PLCH1,3_prime_UTR_variant,,ENST00000447496,NM_001130961.1;PLCH1,intron_variant,,ENST00000494598,;PLCH1-AS2,upstream_gene_variant,,ENST00000472913,; A ENST00000340059 Transcript missense_variant 4391/6168 4391/5082 1464/1693 S/I aGt/aTt 1 -1 PLCH1 HGNC HGNC:29185 protein_coding YES CCDS46939.1 ENSP00000345988 Q4KWH8 UPI00001D800E NM_001130960.1 deleterious_low_confidence(0.04) 23/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 155481659 155481659 C A 1 0 0 0 0 1 0 0 0 12131 565 20 2 2 PLCH1 3 155481659 Missense_Mutation SNP C C3L-00080_T 6636183 155481659 42813900 168 2266 MFSD1 0 . GRCh38 3 158814000 158814000 + Silent SNP G G C novel C3L-00080_T C3L-00080_N G G c.732G>C p.= p.L244L ENST00000415822 7/16 229 202 27 180 180 0 strelka-varscan-mutect MFSD1,synonymous_variant,p.=,ENST00000415822,;MFSD1,synonymous_variant,p.=,ENST00000622669,NM_001289407.1,NM_022736.2;MFSD1,synonymous_variant,p.=,ENST00000392813,NM_001167903.1,NM_001289406.1;MFSD1,synonymous_variant,p.=,ENST00000264266,;MFSD1,synonymous_variant,p.=,ENST00000477743,;MFSD1,downstream_gene_variant,,ENST00000474670,;MFSD1,3_prime_UTR_variant,,ENST00000480292,;MFSD1,3_prime_UTR_variant,,ENST00000484166,;MFSD1,3_prime_UTR_variant,,ENST00000471500,;MFSD1,non_coding_transcript_exon_variant,,ENST00000489639,;MFSD1,downstream_gene_variant,,ENST00000471266,;MFSD1,downstream_gene_variant,,ENST00000476860,; C ENST00000415822 Transcript synonymous_variant 873/2423 732/1545 244/514 L ctG/ctC 1 1 MFSD1 HGNC HGNC:25874 protein_coding YES CCDS3185.2 ENSP00000403117 Q9H3U5 UPI0001AE7604 7/16 PROSITE_profiles:PS50850,hmmpanther:PTHR23512:SF3,hmmpanther:PTHR23512,Gene3D:1.20.1250.20,Pfam_domain:PF07690,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS rs1347104192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 158814000 158814000 G C 1 0 0 0 0 0 0 0 1 9479 1364 48 4 4 MFSD1 3 158814000 Silent SNP G C3L-00080_T 3332341 158814000 39481559 169 2267 SMC4 0 . GRCh38 3 160417864 160417864 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1579C>G p.Leu527Val p.L527V ENST00000357388 11/24 282 206 76 208 208 0 strelka-varscan-mutect SMC4,missense_variant,p.Leu527Val,ENST00000357388,NM_001002800.2;SMC4,missense_variant,p.Leu527Val,ENST00000344722,NM_005496.3;SMC4,missense_variant,p.Leu527Val,ENST00000462787,;SMC4,missense_variant,p.Leu502Val,ENST00000469762,NM_001288753.1;SMC4,downstream_gene_variant,,ENST00000489573,;SMC4,downstream_gene_variant,,ENST00000487747,;SMC4,downstream_gene_variant,,ENST00000494612,;SMC4,downstream_gene_variant,,ENST00000497984,;SMC4,3_prime_UTR_variant,,ENST00000469858,;SMC4,non_coding_transcript_exon_variant,,ENST00000462668,;SMC4,non_coding_transcript_exon_variant,,ENST00000484799,;RP11-432B6.3,intron_variant,,ENST00000483754,;SMC4,downstream_gene_variant,,ENST00000468653,;SMC4,downstream_gene_variant,,ENST00000465563,;SMC4,upstream_gene_variant,,ENST00000497203,;SMC4,downstream_gene_variant,,ENST00000493695,;SMC4,downstream_gene_variant,,ENST00000467263,; G ENST00000357388 Transcript missense_variant 2030/5471 1579/3867 527/1288 L/V Cta/Gta 1 1 SMC4 HGNC HGNC:14013 protein_coding YES CCDS3189.1 ENSP00000349961 Q9NTJ3 UPI000006DA0A NM_001002800.2 tolerated(0.08) 11/24 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF277,Superfamily_domains:SSF57997 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 160417864 160417864 C G 1 0 0 0 0 1 0 0 0 15078 912 32 4 4 SMC4 3 160417864 Missense_Mutation SNP C C3L-00080_T 1603864 160417864 37877695 170 2268 BCHE 0 . GRCh38 3 165830743 165830743 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.291A>G p.Ile97Met p.I97M ENST00000264381 2/4 177 148 29 166 166 0 strelka-varscan-mutect BCHE,missense_variant,p.Ile97Met,ENST00000264381,NM_000055.2;BCHE,intron_variant,,ENST00000488954,;BCHE,intron_variant,,ENST00000479451,;BCHE,missense_variant,p.Ile97Met,ENST00000482958,;BCHE,missense_variant,p.Ile97Met,ENST00000497011,; C ENST00000264381 Transcript missense_variant 458/2454 291/1809 97/602 I/M atA/atG 1 -1 BCHE HGNC HGNC:983 protein_coding YES CCDS3198.1 ENSP00000264381 P06276 UPI0000127866 NM_000055.2 tolerated(0.1) 2/4 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF215,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 165830743 165830743 T C 1 0 0 0 0 1 0 0 0 1505 1512 53 5 5 BCHE 3 165830743 Missense_Mutation SNP T C3L-00080_T 5412879 165830743 32464816 171 2269 WDR49 0 . GRCh38 3 167604460 167604460 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.138A>T p.Asn47Tyr p.N47Y ENST00000472600 2/14 115 79 36 88 87 1 varscan-mutect WDR49,missense_variant,p.Asn47Tyr,ENST00000472600,;WDR49,missense_variant,p.Asn323Tyr,ENST00000479765,;WDR49,5_prime_UTR_variant,,ENST00000308378,NM_178824.3;WDR49,intron_variant,,ENST00000466760,;WDR49,synonymous_variant,p.=,ENST00000460448,; A ENST00000472600 Transcript missense_variant 138/2215 139/2025 47/674 N/Y Aat/Tat 1 -1 WDR49 HGNC HGNC:26587 protein_coding ENSP00000419130 H0Y8A5 UPI0001B7975B tolerated(0.14) 2/14 Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF219,SMART_domains:SM00320 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 167604460 167604460 T A 1 0 0 0 0 1 0 0 0 17862 1812 63 4 4 WDR49 3 167604460 Missense_Mutation SNP T C3L-00080_T 1773717 167604460 30691099 172 2270 GOLIM4 0 . GRCh38 3 168029964 168029964 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1249G>T p.Ala417Ser p.A417S ENST00000470487 10/16 406 308 98 277 277 0 strelka-varscan-mutect GOLIM4,missense_variant,p.Ala417Ser,ENST00000470487,NM_014498.3;GOLIM4,missense_variant,p.Ala389Ser,ENST00000309027,NM_001308155.1; A ENST00000470487 Transcript missense_variant 1939/4373 1249/2091 417/696 A/S Gca/Tca 1 -1 GOLIM4 HGNC HGNC:15448 protein_coding YES CCDS3204.1 ENSP00000417354 O00461 UPI0000073BF8 NM_014498.3 deleterious(0.01) 10/16 hmmpanther:PTHR22909:SF22,hmmpanther:PTHR22909 MODERATE 1 SNV 1 1 PASS rs1490698044 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 168029964 168029964 C A 1 0 0 0 0 1 0 0 0 6460 739 26 2 2 GOLIM4 3 168029964 Missense_Mutation SNP C C3L-00080_T 425504 168029964 30265595 173 2271 SLC7A14 0 . GRCh38 3 170483349 170483349 + Silent SNP G G T C3L-00080_T C3L-00080_N G G c.1080C>A p.= p.V360V ENST00000231706 6/8 350 215 135 312 312 0 strelka-varscan-mutect SLC7A14,synonymous_variant,p.=,ENST00000231706,NM_020949.2;CLDN11,intron_variant,,ENST00000486975,;CLDN11,intron_variant,,ENST00000480067,;CLDN11,intron_variant,,ENST00000471373,; T ENST00000231706 Transcript synonymous_variant 1396/10103 1080/2316 360/771 V gtC/gtA COSM3590056 1 -1 SLC7A14 HGNC HGNC:29326 protein_coding YES CCDS33892.1 ENSP00000231706 Q8TBB6 UPI0000051F6B NM_020949.2 6/8 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF361,Pfam_domain:PF13520 1 LOW 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 170483349 170483349 G T 1 0 0 0 0 0 0 0 1 14979 1277 45 2 2 SLC7A14 3 170483349 Silent SNP G C3L-00080_T 2453385 170483349 27812210 174 2272 NLGN1 0 . GRCh38 3 174280914 174280914 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.2083G>A p.Ala695Thr p.A695T ENST00000457714 7/7 319 277 42 196 196 0 strelka-varscan-mutect NLGN1,missense_variant,p.Ala695Thr,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Ala695Thr,ENST00000361589,;NLGN1,missense_variant,p.Ala480Thr,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,; A ENST00000457714 Transcript missense_variant 2512/8242 2083/2472 695/823 A/T Gca/Aca 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 deleterious(0) 7/7 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Prints_domain:PR01090 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 7 174280914 174280914 G A 1 0 0 0 0 1 0 0 0 10498 1319 46 3 3 NLGN1 3 174280914 Missense_Mutation SNP G C3L-00080_T 3797565 174280914 24014645 175 2273 RTP1 0 . GRCh38 3 187199946 187199946 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.668C>A p.Pro223His p.P223H ENST00000312295 2/2 46 42 4 32 32 0 strelka-mutect RTP1,missense_variant,p.Pro223His,ENST00000312295,NM_153708.2;RP11-208N14.4,non_coding_transcript_exon_variant,,ENST00000356133,; A ENST00000312295 Transcript missense_variant 698/2217 668/792 223/263 P/H cCc/cAc 1 1 RTP1 HGNC HGNC:28580 protein_coding YES CCDS3287.2 ENSP00000311712 P59025 UPI00004E18F3 NM_153708.2 tolerated(0.14) 2/2 hmmpanther:PTHR14402,hmmpanther:PTHR14402:SF19 MODERATE 1 SNV 1 1 PASS rs1385844276 . 0 205 5 0 0 0 0 0 -10.45264 1 1 1 1 0 A 3 1 7 187199946 187199946 C A 1 0 0 0 0 1 0 0 0 13993 623 22 2 2 RTP1 3 187199946 Missense_Mutation SNP C C3L-00080_T 12919032 187199946 11095613 176 2274 MELTF 0 . GRCh38 3 197006608 197006608 + Missense_Mutation SNP C C A rs371828705 C3L-00080_T C3L-00080_N C C c.1879G>T p.Val627Leu p.V627L ENST00000296350 14/16 216 143 73 143 143 0 strelka-varscan-mutect MELTF,missense_variant,p.Val627Leu,ENST00000296350,NM_005929.5;MFI2-AS1,downstream_gene_variant,,ENST00000415244,;MFI2-AS1,downstream_gene_variant,,ENST00000414354,;MFI2-AS1,downstream_gene_variant,,ENST00000424769,;MFI2-AS1,downstream_gene_variant,,ENST00000437064,;MFI2-AS1,downstream_gene_variant,,ENST00000446695,;MELTF,upstream_gene_variant,,ENST00000469783,; A ENST00000296350 Transcript missense_variant 1993/3963 1879/2217 627/738 V/L Gtg/Ttg rs371828705,COSM2947662 1 -1 MELTF HGNC HGNC:7037 protein_coding YES CCDS3325.1 ENSP00000296350 P08582 UPI000013E329 NM_005929.5 deleterious(0) 14/16 Gene3D:3.40.190.10,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,PROSITE_patterns:PS00207,PROSITE_profiles:PS51408,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF21,SMART_domains:SM00094,Superfamily_domains:SSF53850 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371828705 . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 7 197006608 197006608 C A 1 0 0 0 0 1 0 0 0 9415 536 19 1 1 MELTF 3 197006608 Missense_Mutation SNP C C3L-00080_T 9806662 197006608 1288951 177 2275 RUBCN 0 . GRCh38 3 197700985 197700985 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.889A>T p.Ser297Cys p.S297C ENST00000296343 7/20 307 261 46 188 188 0 strelka-varscan-mutect RUBCN,missense_variant,p.Ser237Cys,ENST00000273582,NM_001145642.3;RUBCN,missense_variant,p.Ser276Cys,ENST00000413360,;RUBCN,missense_variant,p.Ser297Cys,ENST00000296343,NM_014687.2;RUBCN,missense_variant,p.Ser56Cys,ENST00000415452,;RUBCN,missense_variant,p.Ser297Cys,ENST00000449205,;RUBCN,downstream_gene_variant,,ENST00000474214,;RUBCN,upstream_gene_variant,,ENST00000447048,;RUBCN,downstream_gene_variant,,ENST00000467303,; A ENST00000296343 Transcript missense_variant 889/2919 889/2919 297/972 S/C Agt/Tgt 1 -1 RUBCN HGNC HGNC:28991 protein_coding YES CCDS43195.1 ENSP00000296343 Q92622 UPI00001C1DE4 NM_014687.2 tolerated(0.07) 7/20 hmmpanther:PTHR12326:SF11,hmmpanther:PTHR12326 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 197700985 197700985 T A 1 0 0 0 0 1 0 0 0 13999 1580 55 4 4 RUBCN 3 197700985 Missense_Mutation SNP T C3L-00080_T 694377 197700985 594574 178 2276 SLC26A1 0 . GRCh38 4 991558 991558 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.146T>A p.Leu49Gln p.L49Q ENST00000361661 3/4 82 57 25 61 61 0 strelka-varscan-mutect SLC26A1,missense_variant,p.Leu49Gln,ENST00000361661,NM_213613.3;SLC26A1,missense_variant,p.Leu49Gln,ENST00000398516,NM_022042.3;SLC26A1,missense_variant,p.Leu49Gln,ENST00000398520,NM_134425.2;SLC26A1,missense_variant,p.Leu49Gln,ENST00000622731,;IDUA,intron_variant,,ENST00000247933,NM_000203.4;IDUA,intron_variant,,ENST00000502910,;IDUA,intron_variant,,ENST00000504568,;IDUA,upstream_gene_variant,,ENST00000509948,;IDUA,upstream_gene_variant,,ENST00000514192,;DGKQ,upstream_gene_variant,,ENST00000510286,;IDUA,downstream_gene_variant,,ENST00000509744,;SLC26A1,upstream_gene_variant,,ENST00000513138,;IDUA,intron_variant,,ENST00000514698,;IDUA,intron_variant,,ENST00000506561,;IDUA,intron_variant,,ENST00000508168,; T ENST00000361661 Transcript missense_variant 524/3660 146/2106 49/701 L/Q cTg/cAg 1 -1 SLC26A1 HGNC HGNC:10993 protein_coding YES CCDS33934.1 ENSP00000354721 Q9H2B4 UPI000013D9D4 NM_213613.3 tolerated(0.29) 3/4 hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF31 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 991558 991558 A T 1 0 0 0 0 1 0 0 0 14784 188 7 4 4 SLC26A1 4 991558 Missense_Mutation SNP A C3L-00080_T 991558 189222997 179 2277 ZFYVE28 0 . GRCh38 4 2320222 2320222 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.751G>A p.Glu251Lys p.E251K ENST00000290974 7/13 267 226 41 267 267 0 strelka-varscan-mutect ZFYVE28,missense_variant,p.Glu251Lys,ENST00000290974,NM_020972.2;ZFYVE28,missense_variant,p.Glu221Lys,ENST00000511071,NM_001172656.1;ZFYVE28,missense_variant,p.Glu181Lys,ENST00000515312,NM_001172659.1;RP11-478C1.7,downstream_gene_variant,,ENST00000510632,;RN7SL589P,upstream_gene_variant,,ENST00000481268,;RP11-478C1.8,upstream_gene_variant,,ENST00000506116,; T ENST00000290974 Transcript missense_variant 1091/4131 751/2664 251/887 E/K Gaa/Aaa 1 -1 ZFYVE28 HGNC HGNC:29334 protein_coding YES CCDS33942.1 ENSP00000290974 Q9HCC9 UPI00001C1E08 NM_020972.2 deleterious(0) 7/13 hmmpanther:PTHR22835:SF41,hmmpanther:PTHR22835 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 2320222 2320222 C T 1 0 0 0 0 1 0 0 0 18247 864 30 3 3 ZFYVE28 4 2320222 Missense_Mutation SNP C C3L-00080_T 1328664 2320222 187894333 180 2278 C4orf50 0 . GRCh38 4 5980264 5980264 + Silent SNP C C G novel C3L-00080_T C3L-00080_N C C c.3774G>C p.= p.L1258L ENST00000531445 7/12 149 85 64 143 143 0 strelka-varscan-mutect C4orf50,synonymous_variant,p.=,ENST00000531445,;C4orf50,synonymous_variant,p.=,ENST00000324058,; G ENST00000531445 Transcript synonymous_variant 3850/6860 3774/4527 1258/1508 L ctG/ctC 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 7/12 hmmpanther:PTHR36866,Pfam_domain:PF15030 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 5980264 5980264 C G 1 0 0 0 0 0 0 0 1 2089 813 29 4 4 C4orf50 4 5980264 Silent SNP C C3L-00080_T 3660042 5980264 184234291 181 2279 AFAP1 0 . GRCh38 4 7800485 7800485 + Missense_Mutation SNP G G A rs774337434 C3L-00080_T C3L-00080_N G G c.1223C>T p.Thr408Met p.T408M ENST00000420658 10/18 405 335 70 406 406 0 strelka-varscan-mutect AFAP1,missense_variant,p.Thr408Met,ENST00000420658,NM_001134647.1;AFAP1,missense_variant,p.Thr408Met,ENST00000358461,NM_198595.2;AFAP1,missense_variant,p.Thr408Met,ENST00000360265,;AFAP1,missense_variant,p.Thr408Met,ENST00000382543,;AFAP1,upstream_gene_variant,,ENST00000513842,; A ENST00000420658 Transcript missense_variant 1496/7768 1223/2445 408/814 T/M aCg/aTg rs774337434,COSM4168027,COSM4168028 1 -1 AFAP1 HGNC HGNC:24017 protein_coding YES CCDS47010.1 ENSP00000410689 Q8N556 UPI000048041E NM_001134647.1 deleterious(0) 10/18 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF8,SMART_domains:SM00233,Superfamily_domains:SSF50729 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs774337434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 7800485 7800485 G A 1 0 0 0 0 1 0 0 0 430 1145 40 1 1 AFAP1 4 7800485 Missense_Mutation SNP G C3L-00080_T 1820221 7800485 182414070 182 2280 DRD5 0 . GRCh38 4 9782248 9782248 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.219C>A p.= p.A73A ENST00000304374 1/1 115 95 20 98 98 0 varscan-mutect DRD5,synonymous_variant,p.=,ENST00000304374,NM_000798.4;SLC2A9,intron_variant,,ENST00000503803,;SLC2A9,intron_variant,,ENST00000508585,; A ENST00000304374 Transcript synonymous_variant 569/2330 219/1434 73/477 A gcC/gcA 1 1 DRD5 HGNC HGNC:3026 protein_coding YES CCDS3405.1 ENSP00000306129 P21918 UPI000004E905 NM_000798.4 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF295,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 9782248 9782248 C A 1 0 0 0 0 0 0 0 1 4579 581 21 2 2 DRD5 4 9782248 Silent SNP C C3L-00080_T 1981763 9782248 180432307 183 2281 RBPJ 0 . GRCh38 4 26430427 26430427 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.1092C>T p.= p.G364G ENST00000342295 11/12 193 164 29 180 180 0 strelka-varscan-mutect RBPJ,synonymous_variant,p.=,ENST00000355476,NM_203284.2;RBPJ,synonymous_variant,p.=,ENST00000342295,NM_005349.3;RBPJ,synonymous_variant,p.=,ENST00000342320,;RBPJ,synonymous_variant,p.=,ENST00000348160,NM_015874.4;RBPJ,synonymous_variant,p.=,ENST00000361572,;RBPJ,synonymous_variant,p.=,ENST00000507561,;RBPJ,synonymous_variant,p.=,ENST00000345843,NM_203283.2;RBPJ,synonymous_variant,p.=,ENST00000504423,;RBPJ,intron_variant,,ENST00000504907,;RBPJ,non_coding_transcript_exon_variant,,ENST00000514380,;RBPJ,non_coding_transcript_exon_variant,,ENST00000505727,;RBPJ,downstream_gene_variant,,ENST00000510725,; T ENST00000342295 Transcript synonymous_variant 1328/5860 1092/1503 364/500 G ggC/ggT 1 1 RBPJ HGNC HGNC:5724 protein_coding YES CCDS3437.1 ENSP00000345206 Q06330 UPI000020BDF1 NM_005349.3 11/12 hmmpanther:PTHR10665:SF3,hmmpanther:PTHR10665,Gene3D:2.60.40.10,Superfamily_domains:SSF81296 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 7 26430427 26430427 C T 1 0 0 0 0 0 0 0 1 13329 755 27 1 1 RBPJ 4 26430427 Silent SNP C C3L-00080_T 16648179 26430427 163784128 184 2282 CENPC 0 . GRCh38 4 67514173 67514173 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1345A>T p.Ile449Phe p.I449F ENST00000273853 8/19 93 70 23 199 199 0 strelka-varscan-mutect CENPC,missense_variant,p.Ile449Phe,ENST00000273853,NM_001812.2;CENPC,missense_variant,p.Ile449Phe,ENST00000506882,;CENPC,missense_variant,p.Ile356Phe,ENST00000513216,;CENPC,non_coding_transcript_exon_variant,,ENST00000510189,;CENPC,non_coding_transcript_exon_variant,,ENST00000506410,; A ENST00000273853 Transcript missense_variant 1596/6940 1345/2832 449/943 I/F Att/Ttt 1 -1 CENPC HGNC HGNC:1854 protein_coding YES CCDS47063.1 ENSP00000273853 Q03188 UPI00004135A3 NM_001812.2 deleterious(0.02) 8/19 Pfam_domain:PF15620,hmmpanther:PTHR16684 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 67514173 67514173 T A 1 0 0 0 0 1 0 0 0 2937 1406 49 4 4 CENPC 4 67514173 Missense_Mutation SNP T C3L-00080_T 41083746 67514173 122700382 185 2283 CSN3 0 . GRCh38 4 70249305 70249305 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.395C>A p.Pro132His p.P132H ENST00000304954 4/5 387 305 82 457 454 3 strelka-varscan-mutect CSN3,missense_variant,p.Pro132His,ENST00000304954,NM_005212.2; A ENST00000304954 Transcript missense_variant 481/836 395/549 132/182 P/H cCt/cAt 1 1 CSN3 HGNC HGNC:2446 protein_coding YES CCDS3538.1 ENSP00000304822 P07498 UPI000004F262 NM_005212.2 deleterious(0) 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11470:SF2,hmmpanther:PTHR11470,Pfam_domain:PF00997,PIRSF_domain:PIRSF002374 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 70249305 70249305 C A 1 0 0 0 0 1 0 0 0 3749 681 24 2 2 CSN3 4 70249305 Missense_Mutation SNP C C3L-00080_T 2735132 70249305 119965250 186 2284 GRID2 0 . GRCh38 4 93085065 93085065 + Silent SNP C C A rs746205784 C3L-00080_T C3L-00080_N C C c.315C>A p.= p.L105L ENST00000282020 3/16 226 122 104 266 266 0 strelka-varscan-mutect GRID2,synonymous_variant,p.=,ENST00000282020,NM_001510.3;GRID2,synonymous_variant,p.=,ENST00000611049,;GRID2,intron_variant,,ENST00000510992,NM_001286838.1;GRID2,non_coding_transcript_exon_variant,,ENST00000505687,;GRID2,non_coding_transcript_exon_variant,,ENST00000515744,;GRID2,synonymous_variant,p.=,ENST00000502699,; A ENST00000282020 Transcript synonymous_variant 1350/6117 315/3024 105/1007 L ctC/ctA rs746205784,COSM5258127 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 3/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 0,1 LOW 1 SNV 1 0,1 1 PASS rs746205784 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 93085065 93085065 C A 1 0 0 0 0 0 0 0 1 6652 842 30 2 2 GRID2 4 93085065 Silent SNP C C3L-00080_T 22835760 93085065 97129490 187 2285 MTTP 0 . GRCh38 4 99608856 99608856 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1729A>T p.Asn577Tyr p.N577Y ENST00000511045 12/18 294 154 140 342 342 0 strelka-varscan-mutect MTTP,missense_variant,p.Asn550Tyr,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Asn550Tyr,ENST00000265517,;MTTP,missense_variant,p.Asn577Tyr,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; T ENST00000511045 Transcript missense_variant 1742/3154 1729/2766 577/921 N/Y Aac/Tac 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 deleterious(0) 12/18 Superfamily_domains:0040642,Gene3D:1lshA02,Pfam_domain:PF01347,PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1,SMART_domains:SM00638 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 99608856 99608856 A T 1 0 0 0 0 1 0 0 0 9961 362 13 4 4 MTTP 4 99608856 Missense_Mutation SNP A C3L-00080_T 6523791 99608856 90605699 188 2286 NDST3 0 . GRCh38 4 118255661 118255661 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.2571G>A p.= p.L857L ENST00000296499 14/14 79 47 32 95 95 0 strelka-varscan-mutect NDST3,synonymous_variant,p.=,ENST00000296499,NM_004784.2; A ENST00000296499 Transcript synonymous_variant 2974/5961 2571/2622 857/873 L ctG/ctA 1 1 NDST3 HGNC HGNC:7682 protein_coding YES CCDS3708.1 ENSP00000296499 O95803 UPI0000071C44 NM_004784.2 14/14 Gene3D:3.40.50.300,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF29,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 118255661 118255661 G A 1 0 0 0 0 0 0 0 1 10278 1335 47 3 3 NDST3 4 118255661 Silent SNP G C3L-00080_T 18646805 118255661 71958894 189 2287 FREM3 0 . GRCh38 4 143577842 143577842 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.6189T>C p.= p.D2063D ENST00000329798 8/8 111 62 49 173 173 0 strelka-varscan-mutect FREM3,synonymous_variant,p.=,ENST00000329798,NM_001168235.1;GUSBP5,intron_variant,,ENST00000511042,;GUSBP5,downstream_gene_variant,,ENST00000396724,; G ENST00000329798 Transcript synonymous_variant 6189/6729 6189/6420 2063/2139 D gaT/gaC 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 8/8 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31,SMART_domains:SM00237,Superfamily_domains:SSF141072 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 143577842 143577842 A G 1 0 0 0 0 0 0 0 1 5913 98 4 5 5 FREM3 4 143577842 Silent SNP A C3L-00080_T 25322181 143577842 46636713 190 2288 FAM160A1 0 . GRCh38 4 151577741 151577741 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.397C>T p.= p.L133L ENST00000435205 5/14 330 266 64 444 444 0 strelka-varscan-mutect FAM160A1,synonymous_variant,p.=,ENST00000435205,NM_001109977.1;FAM160A1,synonymous_variant,p.=,ENST00000505231,;FAM160A1,downstream_gene_variant,,ENST00000503146,;FAM160A1,downstream_gene_variant,,ENST00000513962,;FAM160A1,downstream_gene_variant,,ENST00000512597,;RN7SKP35,downstream_gene_variant,,ENST00000517210,; T ENST00000435205 Transcript synonymous_variant 972/4576 397/3123 133/1040 L Ctg/Ttg 1 1 FAM160A1 HGNC HGNC:34237 protein_coding YES CCDS47146.1 ENSP00000413196 Q05DH4 UPI00015DE720 NM_001109977.1 5/14 Low_complexity_(Seg):seg,hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF6,Pfam_domain:PF10257 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 151577741 151577741 C T 1 0 0 0 0 0 0 0 1 5317 912 32 3 3 FAM160A1 4 151577741 Silent SNP C C3L-00080_T 7999899 151577741 38636814 191 2289 KIAA0922 0 . GRCh38 4 153598602 153598602 + Silent SNP T T A novel C3L-00080_T C3L-00080_N T T c.2136T>A p.= p.T712T ENST00000409959 21/35 122 60 62 151 150 1 strelka-varscan-mutect KIAA0922,synonymous_variant,p.=,ENST00000409663,NM_015196.3;KIAA0922,synonymous_variant,p.=,ENST00000409959,NM_001131007.1;KIAA0922,synonymous_variant,p.=,ENST00000240487,;KIAA0922,upstream_gene_variant,,ENST00000497247,; A ENST00000409959 Transcript synonymous_variant 2185/5017 2136/4833 712/1610 T acT/acA 1 1 KIAA0922 HGNC HGNC:29146 protein_coding YES CCDS47148.1 ENSP00000386787 A2VDJ0 UPI00017BE9AB NM_001131007.1 21/35 hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF2 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 153598602 153598602 T A 1 0 0 0 0 0 0 0 1 8095 1567 55 4 4 KIAA0922 4 153598602 Silent SNP T C3L-00080_T 2020861 153598602 36615953 192 2290 CLCN3 0 . GRCh38 4 169689080 169689080 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.456G>T p.Trp152Cys p.W152C ENST00000347613 5/14 271 156 115 372 372 0 strelka-varscan-mutect CLCN3,missense_variant,p.Trp152Cys,ENST00000513761,NM_001829.3;CLCN3,missense_variant,p.Trp125Cys,ENST00000613795,NM_001243374.1;CLCN3,missense_variant,p.Trp135Cys,ENST00000504131,;CLCN3,missense_variant,p.Trp152Cys,ENST00000347613,NM_173872.3;CLCN3,missense_variant,p.Trp152Cys,ENST00000360642,NM_001243372.1;CLCN3,missense_variant,p.Trp125Cys,ENST00000507875,;CLCN3,missense_variant,p.Trp152Cys,ENST00000511092,;CLCN3,downstream_gene_variant,,ENST00000512813,; T ENST00000347613 Transcript missense_variant 1010/3635 456/2601 152/866 W/C tgG/tgT 1 1 CLCN3 HGNC HGNC:2021 protein_coding YES CCDS34100.1 ENSP00000261514 P51790 UPI000015F952 NM_173872.3 deleterious(0) 5/14 Gene3D:1otsB00,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF85,Superfamily_domains:SSF81340 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 169689080 169689080 G T 1 0 0 0 0 1 0 0 0 3228 1183 41 2 2 CLCN3 4 169689080 Missense_Mutation SNP G C3L-00080_T 16090478 169689080 20525475 193 2291 LRRC14B 0 . GRCh38 5 194957 194957 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1149C>A p.= p.G383G ENST00000328278 2/2 283 108 175 121 121 0 strelka-varscan-mutect LRRC14B,synonymous_variant,p.=,ENST00000328278,NM_001080478.1;PLEKHG4B,downstream_gene_variant,,ENST00000637938,;PLEKHG4B,downstream_gene_variant,,ENST00000283426,NM_052909.3;CCDC127,downstream_gene_variant,,ENST00000296824,NM_145265.2;CTD-2083E4.7,upstream_gene_variant,,ENST00000563761,; A ENST00000328278 Transcript synonymous_variant 1177/1573 1149/1545 383/514 G ggC/ggA 1 1 LRRC14B HGNC HGNC:37268 protein_coding YES CCDS47184.1 ENSP00000327675 A6NHZ5 UPI0000237324 NM_001080478.1 2/2 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF27,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 A 2 1 7 194957 194957 C A 1 0 0 0 0 0 0 0 1 8865 726 26 2 2 LRRC14B 5 194957 Silent SNP C C3L-00080_T 194957 181343302 194 2292 ADAMTS16 0 . GRCh38 5 5239152 5239152 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.2156G>C p.Arg719Thr p.R719T ENST00000274181 15/23 62 51 11 36 36 0 strelka-mutect ADAMTS16,missense_variant,p.Arg719Thr,ENST00000274181,NM_139056.2;ADAMTS16,splice_region_variant,,ENST00000513709,;ADAMTS16,splice_region_variant,,ENST00000433402,; C ENST00000274181 Transcript missense_variant,splice_region_variant 2294/4979 2156/3675 719/1224 R/T aGa/aCa 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 tolerated(0.43) 15/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Prints_domain:PR01857 MODERATE 1 SNV 2 1 PASS rs1360875546 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 5239152 5239152 G C 1 0 0 0 0 1 0 0 0 305 956 33 4 4 ADAMTS16 5 5239152 Missense_Mutation SNP G C3L-00080_T 5044195 5239152 176299107 195 2293 ANKRD33B 0 . GRCh38 5 10649561 10649561 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.933G>T p.Met311Ile p.M311I ENST00000296657 4/4 243 103 140 82 82 0 strelka-varscan-mutect ANKRD33B,missense_variant,p.Met311Ile,ENST00000296657,NM_001164440.1;ANKRD33B,3_prime_UTR_variant,,ENST00000504806,;RP11-54F2.1,downstream_gene_variant,,ENST00000508690,; T ENST00000296657 Transcript missense_variant 933/9188 933/1485 311/494 M/I atG/atT 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 tolerated(0.27) 4/4 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 10649561 10649561 G T 1 0 0 0 0 1 0 0 0 766 1290 45 2 2 ANKRD33B 5 10649561 Missense_Mutation SNP G C3L-00080_T 5410409 10649561 170888698 196 2294 CTNND2 0 . GRCh38 5 11159683 11159683 + Missense_Mutation SNP G G T rs777161615 C3L-00080_T C3L-00080_N G G c.2052C>A p.Asn684Lys p.N684K ENST00000304623 12/22 269 221 48 127 127 0 strelka-varscan-mutect CTNND2,missense_variant,p.Asn684Lys,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Asn593Lys,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Asn347Lys,ENST00000503622,NM_001288716.1;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,missense_variant,p.Asn438Lys,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 2242/5481 2052/3678 684/1225 N/K aaC/aaA rs777161615 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0.01) 12/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs777161615 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 11159683 11159683 G T 1 0 0 0 0 1 0 0 0 3829 1136 40 1 1 CTNND2 5 11159683 Missense_Mutation SNP G C3L-00080_T 510122 11159683 170378576 197 2295 CDH6 0 . GRCh38 5 31305260 31305260 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1086G>T p.= p.G362G ENST00000265071 7/12 395 284 111 335 334 1 strelka-varscan-mutect CDH6,synonymous_variant,p.=,ENST00000265071,NM_004932.3;CDH6,synonymous_variant,p.=,ENST00000514738,;CDH6,downstream_gene_variant,,ENST00000508132,; T ENST00000265071 Transcript synonymous_variant 1351/8476 1086/2373 362/790 G ggG/ggT 1 1 CDH6 HGNC HGNC:1765 protein_coding YES CCDS3894.1 ENSP00000265071 P55285 UPI0000126D9B NM_004932.3 7/12 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF322,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 31305260 31305260 G T 1 0 0 0 0 0 0 0 1 2817 1190 42 2 2 CDH6 5 31305260 Silent SNP G C3L-00080_T 20145577 31305260 150232999 198 2296 DROSHA 0 . GRCh38 5 31422825 31422825 + Silent SNP T T A novel C3L-00080_T C3L-00080_N T T c.3381A>T p.= p.A1127A ENST00000511367 28/35 298 203 95 253 252 1 strelka-varscan-mutect DROSHA,synonymous_variant,p.=,ENST00000511367,NM_013235.4;DROSHA,synonymous_variant,p.=,ENST00000344624,;DROSHA,synonymous_variant,p.=,ENST00000442743,;DROSHA,synonymous_variant,p.=,ENST00000513349,NM_001100412.1;DROSHA,non_coding_transcript_exon_variant,,ENST00000510178,;DROSHA,non_coding_transcript_exon_variant,,ENST00000511778,;DROSHA,non_coding_transcript_exon_variant,,ENST00000504133,; A ENST00000511367 Transcript synonymous_variant 3626/5305 3381/4125 1127/1374 A gcA/gcT 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 28/35 Gene3D:1.10.1520.10,HAMAP:MF_00104,PROSITE_profiles:PS50142,hmmpanther:PTHR11207,SMART_domains:SM00535,Superfamily_domains:SSF69065 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 31422825 31422825 T A 1 0 0 0 0 0 0 0 1 4584 1451 51 4 4 DROSHA 5 31422825 Silent SNP T C3L-00080_T 117565 31422825 150115434 199 2297 NPR3 0 . GRCh38 5 32782937 32782937 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1335G>T p.= p.R445R ENST00000265074 6/8 170 123 47 142 142 0 strelka-varscan-mutect NPR3,synonymous_variant,p.=,ENST00000265074,NM_001204375.1;NPR3,synonymous_variant,p.=,ENST00000326958,NM_001204376.1;NPR3,synonymous_variant,p.=,ENST00000434067,;NPR3,synonymous_variant,p.=,ENST00000415167,NM_000908.3;NPR3,synonymous_variant,p.=,ENST00000509104,;NPR3,non_coding_transcript_exon_variant,,ENST00000506712,; T ENST00000265074 Transcript synonymous_variant 1678/7344 1335/1626 445/541 R cgG/cgT 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 6/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 32782937 32782937 G T 1 0 0 0 0 0 0 0 1 10652 1190 42 2 2 NPR3 5 32782937 Silent SNP G C3L-00080_T 1360112 32782937 148755322 200 2298 SPEF2 0 . GRCh38 5 35641546 35641546 + Missense_Mutation SNP G G T rs149043842 C3L-00080_T C3L-00080_N G G c.277G>T p.Ala93Ser p.A93S ENST00000356031 3/37 418 300 118 371 370 1 strelka-varscan-mutect SPEF2,missense_variant,p.Ala93Ser,ENST00000637569,;SPEF2,missense_variant,p.Ala93Ser,ENST00000440995,;SPEF2,missense_variant,p.Ala93Ser,ENST00000356031,NM_024867.3;SPEF2,missense_variant,p.Ala93Ser,ENST00000509059,;SPEF2,missense_variant,p.Ala93Ser,ENST00000282469,NM_144722.3;SPEF2,missense_variant,p.Ala93Ser,ENST00000510777,;SPEF2,non_coding_transcript_exon_variant,,ENST00000505847,;SPEF2,non_coding_transcript_exon_variant,,ENST00000505088,;SPEF2,upstream_gene_variant,,ENST00000502454,; T ENST00000356031 Transcript missense_variant 431/5681 277/5469 93/1822 A/S Gca/Tca rs149043842 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 deleterious(0) 3/37 Pfam_domain:PF06294,PROSITE_profiles:PS50021,hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0 MODERATE 1 SNV 2 1 PASS rs149043842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 35641546 35641546 G T 1 0 0 0 0 1 0 0 0 15386 1203 42 2 2 SPEF2 5 35641546 Missense_Mutation SNP G C3L-00080_T 2858609 35641546 145896713 201 2299 SLC1A3 0 . GRCh38 5 36677000 36677000 + Silent SNP C C A rs201069745 C3L-00080_T C3L-00080_N C C c.676C>A p.= p.R226R ENST00000265113 6/10 395 277 118 324 324 0 strelka-varscan-mutect SLC1A3,synonymous_variant,p.=,ENST00000265113,NM_004172.4;SLC1A3,synonymous_variant,p.=,ENST00000613445,NM_001289939.1;SLC1A3,synonymous_variant,p.=,ENST00000381918,NM_001166695.2;SLC1A3,intron_variant,,ENST00000612708,NM_001289940.1;CTD-2353F22.1,intron_variant,,ENST00000510740,;SLC1A3,non_coding_transcript_exon_variant,,ENST00000505376,;SLC1A3,upstream_gene_variant,,ENST00000506178,; A ENST00000265113 Transcript synonymous_variant 1152/4170 676/1629 226/542 R Cga/Aga rs201069745 1 1 SLC1A3 HGNC HGNC:10941 protein_coding YES CCDS3919.1 ENSP00000265113 P43003 A0A024R050 UPI0000129B0F NM_004172.4 6/10 hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF24,Pfam_domain:PF00375 LOW 1 SNV 1 1 PASS rs201069745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 36677000 36677000 C A 1 0 0 0 0 0 0 0 1 14699 644 23 1 1 SLC1A3 5 36677000 Silent SNP C C3L-00080_T 1035454 36677000 144861259 202 2300 NIPBL 0 . GRCh38 5 37064729 37064729 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.8252C>G p.Ala2751Gly p.A2751G ENST00000282516 47/47 263 216 47 189 189 0 strelka-varscan-mutect NIPBL,missense_variant,p.Ala2751Gly,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Ala51Gly,ENST00000621733,;NIPBL,downstream_gene_variant,,ENST00000448238,NM_015384.4;NIPBL,downstream_gene_variant,,ENST00000513819,;NIPBL,non_coding_transcript_exon_variant,,ENST00000514335,; G ENST00000282516 Transcript missense_variant 8751/10435 8252/8415 2751/2804 A/G gCt/gGt 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 deleterious_low_confidence(0.01) 47/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 37064729 37064729 C G 1 0 0 0 0 1 0 0 0 10463 797 28 4 4 NIPBL 5 37064729 Missense_Mutation SNP C C3L-00080_T 387729 37064729 144473530 203 2301 PTGER4 0 . GRCh38 5 40692058 40692058 + Missense_Mutation SNP C C T rs199975495 C3L-00080_T C3L-00080_N C C c.1147C>T p.Arg383Trp p.R383W ENST00000302472 3/3 312 220 92 231 231 0 strelka-varscan-mutect PTGER4,missense_variant,p.Arg383Trp,ENST00000302472,NM_000958.2;TTC33,intron_variant,,ENST00000636106,;TTC33,intron_variant,,ENST00000637375,;TTC33,intron_variant,,ENST00000636863,;PTGER4,downstream_gene_variant,,ENST00000512578,;PTGER4,downstream_gene_variant,,ENST00000513635,; T ENST00000302472 Transcript missense_variant 2171/3848 1147/1467 383/488 R/W Cgg/Tgg rs199975495,COSM5339464 1 1 PTGER4 HGNC HGNC:9596 protein_coding YES CCDS3930.1 ENSP00000302846 P35408 UPI000005042F NM_000958.2 deleterious(0.04) 3/3 hmmpanther:PTHR11866:SF6,hmmpanther:PTHR11866 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199975495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 40692058 40692058 C T 1 0 0 0 0 1 0 0 0 12900 643 23 1 1 PTGER4 5 40692058 Missense_Mutation SNP C C3L-00080_T 3627329 40692058 140846201 204 2302 GHR 0 . GRCh38 5 42718854 42718854 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1368C>A p.= p.I456I ENST00000620156 10/10 293 201 92 272 271 1 strelka-varscan-mutect GHR,synonymous_variant,p.=,ENST00000615111,NM_001242400.2;GHR,synonymous_variant,p.=,ENST00000612382,NM_001242403.2;GHR,synonymous_variant,p.=,ENST00000230882,NM_000163.4;GHR,synonymous_variant,p.=,ENST00000620156,NM_001242399.2;GHR,synonymous_variant,p.=,ENST00000612626,NM_001242404.2;GHR,synonymous_variant,p.=,ENST00000618088,NM_001242401.3,NM_001242402.2,NM_001242406.2;GHR,synonymous_variant,p.=,ENST00000537449,NM_001242405.2;GHR,synonymous_variant,p.=,ENST00000357703,NM_001242460.1;GHR,3_prime_UTR_variant,,ENST00000622294,NM_001242462.1;GHR,downstream_gene_variant,,ENST00000513625,;GHR,3_prime_UTR_variant,,ENST00000511135,; A ENST00000620156 Transcript synonymous_variant 1505/4529 1368/1938 456/645 I atC/atA 1 1 GHR HGNC HGNC:4263 protein_coding YES CCDS75239.1 ENSP00000483403 A0A087X0H5 UPI0002104C22 NM_001242399.2 10/10 hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF108,Pfam_domain:PF12772 LOW 1 SNV 5 1 PASS rs1049383599 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 42718854 42718854 C A 1 0 0 0 0 0 0 0 1 6249 845 30 2 2 GHR 5 42718854 Silent SNP C C3L-00080_T 2026796 42718854 138819405 205 2303 OTP 0 . GRCh38 5 77636998 77636998 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.270G>A p.= p.P90P ENST00000306422 2/3 130 100 30 133 133 0 strelka-varscan-mutect OTP,synonymous_variant,p.=,ENST00000306422,NM_032109.2;OTP,upstream_gene_variant,,ENST00000515716,; T ENST00000306422 Transcript synonymous_variant 1409/3669 270/978 90/325 P ccG/ccA 1 -1 OTP HGNC HGNC:8518 protein_coding YES CCDS4039.1 ENSP00000302814 Q5XKR4 UPI0000021CAA NM_032109.2 2/3 Gene3D:1.10.10.60,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF316,Low_complexity_(Seg):seg,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS rs1417485043 . 0 208 0 0 2 0 0 0 -19.87235 0.9985839 1 1 1 0 T 2 4 7 77636998 77636998 C T 1 0 0 0 0 0 0 0 1 11378 871 31 1 1 OTP 5 77636998 Silent SNP C C3L-00080_T 34918144 77636998 103901261 206 2304 VCAN 0 . GRCh38 5 83539499 83539499 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.6496G>A p.Asp2166Asn p.D2166N ENST00000265077 8/15 64 40 24 121 121 0 strelka-varscan-mutect VCAN,missense_variant,p.Asp2166Asn,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Asp1179Asn,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Asp1179Asn,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 7061/12625 6496/10191 2166/3396 D/N Gat/Aat 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.36) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 83539499 83539499 G A 1 0 0 0 0 1 0 0 0 17683 1290 45 3 3 VCAN 5 83539499 Missense_Mutation SNP G C3L-00080_T 5902501 83539499 97998760 207 2305 RASA1 0 . GRCh38 5 87389500 87389508 + In_Frame_Del DEL GCTCAGTAA GCTCAGTAA - novel C3L-00080_T C3L-00080_N GCTCAGTAA GCTCAGTAA c.3033_3041delGCTCAGTAA p.Leu1012_Asn1014del p.L1012_N1014del ENST00000274376 24/25 253 155 98 359 358 1 sindel-varindel-pindel RASA1,inframe_deletion,p.Leu835_Asn837del,ENST00000456692,NM_022650.2;RASA1,inframe_deletion,p.Leu1012_Asn1014del,ENST00000274376,NM_002890.2;RASA1,inframe_deletion,p.Leu845_Asn847del,ENST00000512763,;RASA1,inframe_deletion,p.Leu846_Asn848del,ENST00000506290,;CCNH,downstream_gene_variant,,ENST00000508855,;CCNH,downstream_gene_variant,,ENST00000504878,NM_001199189.1;CCNH,downstream_gene_variant,,ENST00000256897,NM_001239.3;CCNH,downstream_gene_variant,,ENST00000510921,;RASA1,3_prime_UTR_variant,,ENST00000515800,;CCNH,downstream_gene_variant,,ENST00000505587,;CCNH,downstream_gene_variant,,ENST00000504115,;CCNH,downstream_gene_variant,,ENST00000511207,; - ENST00000274376 Transcript inframe_deletion 3597-3605/3752 3033-3041/3144 1011-1014/1047 TLSN/T acGCTCAGTAAt/act 1 1 RASA1 HGNC HGNC:9871 protein_coding YES CCDS34200.1 ENSP00000274376 P20936 UPI00001351F3 NM_002890.2 24/25 hmmpanther:PTHR10194:SF19,hmmpanther:PTHR10194,SMART_domains:SM00323,Superfamily_domains:SSF48350 MODERATE 1 deletion 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9994398 1 1 1 0 - 7 5 7 87389500 87389500 GCTCAGTAA - 1 0 1 0 1 0 0 0 0 13219 1074 38 0 0 RASA1 5 87389500 In_Frame_Del DEL GCTCAGTAA C3L-00080_T 3850001 87389500 94148759 208 2306 FBN2 0 . GRCh38 5 128290782 128290782 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.6395C>T p.Pro2132Leu p.P2132L ENST00000508053 56/71 241 181 60 261 261 0 strelka-varscan-mutect FBN2,missense_variant,p.Pro2132Leu,ENST00000508053,;FBN2,missense_variant,p.Pro2132Leu,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Pro2131Leu,ENST00000619499,; A ENST00000508053 Transcript missense_variant 7370/11132 6395/8739 2132/2912 P/L cCa/cTa 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 56/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 128290782 128290782 G A 1 0 0 0 0 1 0 0 0 5566 1348 47 3 3 FBN2 5 128290782 Missense_Mutation SNP G C3L-00080_T 40901282 128290782 53247477 209 2307 ADAMTS19 0 . GRCh38 5 129654318 129654318 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.2171C>G p.Ala724Gly p.A724G ENST00000274487 14/23 109 55 54 156 156 0 strelka-varscan-mutect ADAMTS19,missense_variant,p.Ala724Gly,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,; G ENST00000274487 Transcript missense_variant 2316/5234 2171/3624 724/1207 A/G gCc/gGc 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 tolerated(0.07) 14/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 129654318 129654318 C G 1 0 0 0 0 1 0 0 0 308 739 26 4 4 ADAMTS19 5 129654318 Missense_Mutation SNP C C3L-00080_T 1363536 129654318 51883941 210 2308 GFRA3 0 . GRCh38 5 138257699 138257699 + Missense_Mutation SNP G G C rs573286530 C3L-00080_T C3L-00080_N G G c.725C>G p.Pro242Arg p.P242R ENST00000274721 4/8 190 163 27 136 135 1 strelka-varscan-mutect GFRA3,missense_variant,p.Pro242Arg,ENST00000274721,NM_001496.3;GFRA3,missense_variant,p.Pro211Arg,ENST00000378362,; C ENST00000274721 Transcript missense_variant 972/2039 725/1203 242/400 P/R cCg/cGg rs573286530 1 -1 GFRA3 HGNC HGNC:4245 protein_coding YES CCDS4201.1 ENSP00000274721 O60609 UPI0000030833 NM_001496.3 deleterious(0.03) 4/8 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF15 MODERATE 1 SNV 1 1 PASS rs573286530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 138257699 138257699 G C 1 0 0 0 0 1 0 0 0 6223 1116 39 4 4 GFRA3 5 138257699 Missense_Mutation SNP G C3L-00080_T 8603381 138257699 43280560 211 2309 HARS2 0 . GRCh38 5 140695568 140695568 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.460G>T p.Gly154Ter p.G154* ENST00000230771 5/13 666 467 199 527 527 0 strelka-varscan-mutect HARS2,stop_gained,p.Gly154Ter,ENST00000230771,NM_012208.3;HARS2,stop_gained,p.Gly129Ter,ENST00000508522,NM_001278731.1;HARS2,stop_gained,p.Gly160Ter,ENST00000509299,;HARS2,intron_variant,,ENST00000448069,;HARS,upstream_gene_variant,,ENST00000504156,NM_001289094.1,NM_002109.5;HARS,upstream_gene_variant,,ENST00000457527,NM_001258041.2;HARS,upstream_gene_variant,,ENST00000438307,NM_001258040.2;HARS,upstream_gene_variant,,ENST00000307633,NM_001258042.2;HARS,upstream_gene_variant,,ENST00000431330,NM_001289093.1;ZMAT2,upstream_gene_variant,,ENST00000274712,NM_144723.1;HARS,upstream_gene_variant,,ENST00000415192,NM_001289092.1;HARS,upstream_gene_variant,,ENST00000507746,;HARS2,downstream_gene_variant,,ENST00000503873,;ZMAT2,upstream_gene_variant,,ENST00000519913,;HARS2,non_coding_transcript_exon_variant,,ENST00000502303,;HARS2,3_prime_UTR_variant,,ENST00000510104,;HARS2,non_coding_transcript_exon_variant,,ENST00000513688,;HARS2,intron_variant,,ENST00000520095,;HARS,upstream_gene_variant,,ENST00000506579,;HARS,upstream_gene_variant,,ENST00000518126,;ZMAT2,upstream_gene_variant,,ENST00000506644,;HARS,upstream_gene_variant,,ENST00000502888,;HARS2,downstream_gene_variant,,ENST00000511913,;HARS2,downstream_gene_variant,,ENST00000506318,;HARS,upstream_gene_variant,,ENST00000512396,;HARS2,downstream_gene_variant,,ENST00000513912,; T ENST00000230771 Transcript stop_gained 683/2483 460/1521 154/506 G/* Gga/Tga 1 1 HARS2 HGNC HGNC:4817 protein_coding YES CCDS4238.1 ENSP00000230771 P49590 UPI00001364C4 NM_012208.3 5/13 Gene3D:3.30.930.10,Pfam_domain:PF13393,PIRSF_domain:PIRSF001549,PROSITE_profiles:PS50862,hmmpanther:PTHR11476,hmmpanther:PTHR11476:SF6,Superfamily_domains:SSF55681,TIGRFAM_domain:TIGR00442 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 140695568 140695568 G T 1 0 0 0 0 0 1 0 0 6846 1349 47 2 2 HARS2 5 140695568 Nonsense_Mutation SNP G C3L-00080_T 2437869 140695568 40842691 212 2310 PCDHA1 0 . GRCh38 5 140787902 140787902 + Silent SNP C C A C3L-00080_T C3L-00080_N C C c.1612C>A p.= p.R538R ENST00000504120 1/4 894 630 264 711 711 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript synonymous_variant 1612/5263 1612/2853 538/950 R Cgg/Agg COSM5113494,COSM5113495 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 140787902 140787902 C A 1 0 0 0 0 0 0 0 1 11606 759 27 1 1 PCDHA1 5 140787902 Silent SNP C C3L-00080_T 92334 140787902 40750357 213 2311 PCDHA3 0 . GRCh38 5 140802199 140802199 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1002C>A p.Cys334Ter p.C334* ENST00000522353 1/4 487 342 145 414 414 0 strelka-varscan-mutect PCDHA3,stop_gained,p.Cys334Ter,ENST00000522353,NM_018906.2;PCDHA3,stop_gained,p.Cys334Ter,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000530339,NM_018907.3;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; A ENST00000522353 Transcript stop_gained 1002/5260 1002/2853 334/950 C/* tgC/tgA 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 140802199 140802199 C A 1 0 0 0 0 0 1 0 0 11612 718 25 2 2 PCDHA3 5 140802199 Nonsense_Mutation SNP C C3L-00080_T 14297 140802199 40736060 214 2312 PCDHA3 0 . GRCh38 5 140803449 140803449 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2252C>A p.Ser751Ter p.S751* ENST00000522353 1/4 355 254 101 241 241 0 strelka-varscan-mutect PCDHA3,stop_gained,p.Ser751Ter,ENST00000522353,NM_018906.2;PCDHA3,stop_gained,p.Ser751Ter,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000530339,NM_018907.3;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; A ENST00000522353 Transcript stop_gained 2252/5260 2252/2853 751/950 S/* tCg/tAg 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93 HIGH 1 SNV 1 1 PASS rs1214042918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 140803449 140803449 C A 1 0 0 0 0 0 1 0 0 11612 893 31 1 1 PCDHA3 5 140803449 Nonsense_Mutation SNP C C3L-00080_T 1250 140803449 40734810 215 2313 PCDHA8 0 . GRCh38 5 140843066 140843066 + Missense_Mutation SNP C C T rs782077054 C3L-00080_T C3L-00080_N C C c.1745C>T p.Pro582Leu p.P582L ENST00000531613 1/4 636 544 92 471 471 0 strelka-varscan-mutect PCDHA8,missense_variant,p.Pro582Leu,ENST00000531613,NM_018911.2;PCDHA8,missense_variant,p.Pro582Leu,ENST00000378123,NM_031856.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,upstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA9,upstream_gene_variant,,ENST00000532602,NM_031857.1; T ENST00000531613 Transcript missense_variant 1745/5260 1745/2853 582/950 P/L cCg/cTg rs782077054,COSM590069,COSM590070 1 1 PCDHA8 HGNC HGNC:8674 protein_coding YES CCDS54919.1 ENSP00000434655 Q9Y5H6 UPI00001273D0 NM_018911.2 tolerated_low_confidence(0.06) 1/4 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF125,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782077054 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 140843066 140843066 C T 1 0 0 0 0 1 0 0 0 11617 652 23 1 1 PCDHA8 5 140843066 Missense_Mutation SNP C C3L-00080_T 39617 140843066 40695193 216 2314 PCDHA9 0 . GRCh38 5 140850481 140850481 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1986G>T p.= p.T662T ENST00000532602 1/4 564 387 177 361 359 2 strelka-varscan-mutect PCDHA9,synonymous_variant,p.=,ENST00000378122,NM_014005.4;PCDHA9,synonymous_variant,p.=,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; T ENST00000532602 Transcript synonymous_variant 3019/6293 1986/2853 662/950 T acG/acT 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 140850481 140850481 G T 1 0 0 0 0 0 0 0 1 11618 1103 39 1 1 PCDHA9 5 140850481 Silent SNP G C3L-00080_T 7415 140850481 40687778 217 2315 PCDHA10 0 . GRCh38 5 140857864 140857864 + Missense_Mutation SNP C C A rs782625866 C3L-00080_T C3L-00080_N C C c.1816C>A p.Leu606Met p.L606M ENST00000307360 1/4 235 171 64 182 182 0 strelka-varscan-mutect PCDHA10,missense_variant,p.Leu606Met,ENST00000562220,NM_031859.2;PCDHA10,missense_variant,p.Leu606Met,ENST00000307360,NM_018901.3;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; A ENST00000307360 Transcript missense_variant 1816/5254 1816/2847 606/948 L/M Ctg/Atg rs782625866 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 deleterious_low_confidence(0.01) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs782625866 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 140857864 140857864 C A 1 0 0 0 0 1 0 0 0 11607 796 28 2 2 PCDHA10 5 140857864 Missense_Mutation SNP C C3L-00080_T 7383 140857864 40680395 218 2316 PCDHA10 0 . GRCh38 5 140858078 140858078 + Missense_Mutation SNP C C A rs782110139 C3L-00080_T C3L-00080_N C C c.2030C>A p.Ala677Asp p.A677D ENST00000307360 1/4 262 174 88 194 194 0 strelka-varscan-mutect PCDHA10,missense_variant,p.Ala677Asp,ENST00000562220,NM_031859.2;PCDHA10,missense_variant,p.Ala677Asp,ENST00000307360,NM_018901.3;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; A ENST00000307360 Transcript missense_variant 2030/5254 2030/2847 677/948 A/D gCc/gAc rs782110139 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124 MODERATE 1 SNV 1 1 PASS rs782110139 . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 140858078 140858078 C A 1 0 0 0 0 1 0 0 0 11607 739 26 2 2 PCDHA10 5 140858078 Missense_Mutation SNP C C3L-00080_T 214 140858078 40680181 219 2317 PCDHA11 0 . GRCh38 5 140869981 140869981 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.878C>T p.Thr293Ile p.T293I ENST00000398640 1/4 193 163 30 151 151 0 strelka-varscan-mutect PCDHA11,missense_variant,p.Thr293Ile,ENST00000398640,NM_018902.4;PCDHA11,missense_variant,p.Thr293Ile,ENST00000616325,NM_031861.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA10,downstream_gene_variant,,ENST00000562220,NM_031859.2;PCDHA11,upstream_gene_variant,,ENST00000617408,;AC005609.20,upstream_gene_variant,,ENST00000625071,; T ENST00000398640 Transcript missense_variant 1736/6115 878/2850 293/949 T/I aCa/aTa 1 1 PCDHA11 HGNC HGNC:8665 protein_coding YES CCDS47284.1 ENSP00000381636 Q9Y5I1 UPI00001273D4 NM_018902.4 tolerated_low_confidence(0.42) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF68,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 140869981 140869981 C T 1 0 0 0 0 1 0 0 0 11608 478 17 3 3 PCDHA11 5 140869981 Missense_Mutation SNP C C3L-00080_T 11903 140869981 40668278 220 2318 PCDHB3 0 . GRCh38 5 141101330 141101330 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.681G>T p.Gln227His p.Q227H ENST00000231130 1/1 194 139 55 190 190 0 strelka-varscan-mutect PCDHB3,missense_variant,p.Gln227His,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000194155,NM_018936.3;PCDHB2,downstream_gene_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000624513,;PCDHB2,downstream_gene_variant,,ENST00000624994,;AC005754.7,intron_variant,,ENST00000607216,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;CTC-270D5.1,upstream_gene_variant,,ENST00000623615,;CTC-270D5.1,upstream_gene_variant,,ENST00000623741,; T ENST00000231130 Transcript missense_variant 858/3355 681/2391 227/796 Q/H caG/caT 1 1 PCDHB3 HGNC HGNC:8688 protein_coding YES CCDS4245.1 ENSP00000231130 Q9Y5E6 UPI0003CC25DF NM_018937.4 tolerated_low_confidence(0.14) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 141101330 141101330 G T 1 0 0 0 0 1 0 0 0 11630 933 33 2 2 PCDHB3 5 141101330 Missense_Mutation SNP G C3L-00080_T 231349 141101330 40436929 221 2319 PCDHB9 0 . GRCh38 5 141189495 141189495 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2177C>A p.Ser726Ter p.S726* ENST00000316105 1/1 322 217 105 234 234 0 strelka-varscan-mutect PCDHB9,stop_gained,p.Ser726Ter,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; A ENST00000316105 Transcript stop_gained 2369/4415 2177/2394 726/797 S/* tCg/tAg 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Pfam_domain:PF16492 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 141189495 141189495 C A 1 0 0 0 0 0 1 0 0 11636 893 31 1 1 PCDHB9 5 141189495 Nonsense_Mutation SNP C C3L-00080_T 88165 141189495 40348764 222 2320 PCDHB14 0 . GRCh38 5 141225278 141225278 + Silent SNP G G A rs782044670 C3L-00080_T C3L-00080_N G G c.1773G>A p.= p.A591A ENST00000239449 1/1 253 154 99 167 167 0 strelka-varscan-mutect PCDHB14,synonymous_variant,p.=,ENST00000239449,NM_018934.3;PCDHB14,synonymous_variant,p.=,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239449 Transcript synonymous_variant 2347/4828 1773/2397 591/798 A gcG/gcA rs782044670 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW SNV 1 PASS rs782044670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 141225278 141225278 G A 1 0 0 0 0 0 0 0 1 11626 1103 39 1 1 PCDHB14 5 141225278 Silent SNP G C3L-00080_T 35783 141225278 40312981 223 2321 PCDHB15 0 . GRCh38 5 141245746 141245746 + Silent SNP G G A rs376867312 C3L-00080_T C3L-00080_N G G c.168G>A p.= p.V56V ENST00000231173 1/1 335 235 100 268 268 0 strelka-varscan-mutect PCDHB15,synonymous_variant,p.=,ENST00000231173,NM_018935.3;CH17-140K24.8,3_prime_UTR_variant,,ENST00000624396,;PCDHB15,intron_variant,,ENST00000623671,;CH17-140K24.2,upstream_gene_variant,,ENST00000624424,;CH17-140K24.2,upstream_gene_variant,,ENST00000624192,;CH17-140K24.2,upstream_gene_variant,,ENST00000624560,;CH17-140K24.2,upstream_gene_variant,,ENST00000623336,;CH17-140K24.2,upstream_gene_variant,,ENST00000624991,;PCDHB19P,downstream_gene_variant,,ENST00000625133,;PCDHB19P,downstream_gene_variant,,ENST00000570871,; A ENST00000231173 Transcript synonymous_variant 398/4017 168/2364 56/787 V gtG/gtA rs376867312 1 1 PCDHB15 HGNC HGNC:8686 protein_coding YES CCDS4257.1 ENSP00000231173 Q9Y5E8 UPI00001273E8 NM_018935.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF97,Pfam_domain:PF08266,Superfamily_domains:SSF49313 LOW SNV 1 PASS rs376867312 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 141245746 141245746 G A 1 0 0 0 0 0 0 0 1 11627 1335 47 3 3 PCDHB15 5 141245746 Silent SNP G C3L-00080_T 20468 141245746 40292513 224 2322 PCDHGA6 0 . GRCh38 5 141376342 141376342 + Frame_Shift_Del DEL T T - novel C3L-00080_T C3L-00080_N T T c.2260delT p.Ser754ProfsTer15 p.S754Pfs*15 ENST00000517434 1/4 470 332 138 379 379 0 sindel-varindel-pindel PCDHGA6,frameshift_variant,p.Ser754ProfsTer15,ENST00000610583,NM_032086.1;PCDHGA6,frameshift_variant,p.Ser754ProfsTer15,ENST00000517434,NM_018919.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; - ENST00000517434 Transcript frameshift_variant 2429/4775 2259/2799 753/932 Y/X taT/ta 1 1 PCDHGA6 HGNC HGNC:8704 protein_coding YES CCDS54926.1 ENSP00000429601 Q9Y5G7 UPI00000715C8 NM_018919.2 1/4 hmmpanther:PTHR24028:SF107,hmmpanther:PTHR24028,Pfam_domain:PF16492 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 141376342 141376342 T - 1 0 1 0 1 0 0 0 0 11645 1500 52 0 0 PCDHGA6 5 141376342 Frame_Shift_Del DEL T C3L-00080_T 130596 141376342 40161917 225 2323 PCDHGB5 0 . GRCh38 5 141399661 141399661 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1534G>A p.Ala512Thr p.A512T ENST00000617380 1/4 572 500 72 422 421 1 strelka-varscan-mutect PCDHGB5,missense_variant,p.Ala512Thr,ENST00000617380,NM_018925.2;PCDHGB5,missense_variant,p.Ala512Thr,ENST00000621169,NM_032099.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGA8,downstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA9,upstream_gene_variant,,ENST00000573521,NM_018921.2;PCDHGA9,upstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000617380 Transcript missense_variant 1534/4578 1534/2772 512/923 A/T Gcg/Acg 1 1 PCDHGB5 HGNC HGNC:8712 protein_coding YES CCDS75339.1 ENSP00000478258 Q9Y5G0 UPI000007279C NM_018925.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF126,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS rs1021211609 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 141399661 141399661 G A 1 0 0 0 0 1 0 0 0 11653 1087 38 1 1 PCDHGB5 5 141399661 Missense_Mutation SNP G C3L-00080_T 23319 141399661 40138598 226 2324 PCDHGA12 0 . GRCh38 5 141432931 141432931 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.2172G>T p.= p.L724L ENST00000252085 1/4 601 432 169 426 426 0 strelka-varscan-mutect PCDHGA12,synonymous_variant,p.=,ENST00000252085,NM_003735.2;PCDHGA12,synonymous_variant,p.=,ENST00000613314,NM_032094.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB7,intron_variant,,ENST00000398594,NM_018927.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA11,intron_variant,,ENST00000398587,NM_018914.2;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,intron_variant,,ENST00000518882,NM_032092.1;PCDHGB8P,downstream_gene_variant,,ENST00000502926,;PCDHGA3,intron_variant,,ENST00000612467,;PCDHGB8P,downstream_gene_variant,,ENST00000507007,; T ENST00000252085 Transcript synonymous_variant 2314/4747 2172/2799 724/932 L ctG/ctT 1 1 PCDHGA12 HGNC HGNC:8699 protein_coding YES CCDS4260.1 ENSP00000252085 O60330 UPI0000073EA1 NM_003735.2 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF109,Pfam_domain:PF16492 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 141432931 141432931 G T 1 0 0 0 0 0 0 0 1 11640 1306 46 2 2 PCDHGA12 5 141432931 Silent SNP G C3L-00080_T 33270 141432931 40105328 227 2325 SPRY4 0 . GRCh38 5 142314904 142314904 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.274G>T p.Gly92Cys p.G92C ENST00000344120 3/3 85 56 29 67 67 0 strelka-varscan-mutect SPRY4,missense_variant,p.Gly92Cys,ENST00000344120,NM_030964.3;SPRY4,missense_variant,p.Gly69Cys,ENST00000434127,NM_001293290.1,NM_001127496.1,NM_001293289.1;SPRY4,downstream_gene_variant,,ENST00000511815,;SPRY4-IT1,downstream_gene_variant,,ENST00000630558,;SPRY4-IT1_2,upstream_gene_variant,,ENST00000612613,;SPRY4-IT1_1,upstream_gene_variant,,ENST00000611334,;SPRY4,downstream_gene_variant,,ENST00000503582,; A ENST00000344120 Transcript missense_variant 461/4938 274/969 92/322 G/C Ggc/Tgc 1 -1 SPRY4 HGNC HGNC:15533 protein_coding YES CCDS4274.1 ENSP00000344967 A0A0C4DFS6 UPI0000167871 NM_030964.3 tolerated(0.05) 3/3 hmmpanther:PTHR12365,hmmpanther:PTHR12365:SF6 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 7 142314904 142314904 C A 1 0 0 0 0 1 0 0 0 15464 623 22 2 2 SPRY4 5 142314904 Missense_Mutation SNP C C3L-00080_T 881973 142314904 39223355 228 2326 ARSI 0 . GRCh38 5 150298447 150298447 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.477delC p.Thr160ProfsTer108 p.T160Pfs*108 ENST00000328668 2/2 430 193 237 403 403 0 sindel-varindel-pindel ARSI,frameshift_variant,p.Thr160ProfsTer108,ENST00000328668,NM_001012301.2;ARSI,frameshift_variant,p.Thr17ProfsTer108,ENST00000515301,;ARSI,frameshift_variant,p.Thr17ProfsTer?,ENST00000509146,; - ENST00000328668 Transcript frameshift_variant 1057/3161 477/1710 159/569 P/X ccC/cc 1 -1 ARSI HGNC HGNC:32521 protein_coding YES CCDS34275.1 ENSP00000333395 Q5FYB1 UPI000003FD83 NM_001012301.2 2/2 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF68,Superfamily_domains:SSF53649 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 150298447 150298447 G - 1 0 1 0 1 0 0 0 0 1137 1335 47 0 0 ARSI 5 150298447 Frame_Shift_Del DEL G C3L-00080_T 7983543 150298447 31239812 229 2327 KIF4B 0 . GRCh38 5 155014428 155014428 + Missense_Mutation SNP G G T rs778427433 C3L-00080_T C3L-00080_N G G c.569G>T p.Cys190Phe p.C190F ENST00000435029 1/1 683 389 294 401 401 0 strelka-varscan-mutect KIF4B,missense_variant,p.Cys190Phe,ENST00000435029,NM_001099293.1; T ENST00000435029 Transcript missense_variant 674/4378 569/3705 190/1234 C/F tGt/tTt rs778427433 1 1 KIF4B HGNC HGNC:6322 protein_coding YES CCDS47324.1 ENSP00000387875 Q2VIQ3 UPI000013D5DB NM_001099293.1 deleterious(0.01) 1/1 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF392,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS rs778427433 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 155014428 155014428 G T 1 0 0 0 0 1 0 0 0 8169 1377 48 2 2 KIF4B 5 155014428 Missense_Mutation SNP G C3L-00080_T 4715981 155014428 26523831 230 2328 GABRA1 0 . GRCh38 5 161897370 161897370 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1319C>A p.Ala440Asp p.A440D ENST00000393943 10/10 230 136 94 158 158 0 strelka-varscan-mutect GABRA1,missense_variant,p.Ala440Asp,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Ala440Asp,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Ala455Asp,ENST00000638159,;GABRA1,missense_variant,p.Ala440Asp,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Ala440Asp,ENST00000638112,;GABRA1,missense_variant,p.Ala440Asp,ENST00000636573,;GABRA1,missense_variant,p.Ala440Asp,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Ala440Asp,ENST00000637827,;GABRA1,missense_variant,p.Ala440Asp,ENST00000635880,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,; A ENST00000393943 Transcript missense_variant 2102/4686 1319/1371 440/456 A/D gCt/gAt 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 tolerated(0.08) 10/10 Gene3D:1.20.58.390,Prints_domain:PR00253,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,Superfamily_domains:SSF90112,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 161897370 161897370 C A 1 0 0 0 0 1 0 0 0 6031 797 28 2 2 GABRA1 5 161897370 Missense_Mutation SNP C C3L-00080_T 6882942 161897370 19640889 231 2329 TENM2 0 . GRCh38 5 168218314 168218314 + Nonsense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.4423G>T p.Glu1475Ter p.E1475* ENST00000518659 23/29 277 162 115 193 193 0 strelka-varscan-mutect TENM2,stop_gained,p.Glu1354Ter,ENST00000519204,;TENM2,stop_gained,p.Glu1475Ter,ENST00000518659,NM_001122679.1;TENM2,stop_gained,p.Glu1236Ter,ENST00000520394,; T ENST00000518659 Transcript stop_gained 4462/8550 4423/8325 1475/2774 E/* Gag/Tag COSM4548094,COSM4548095,COSM4548096,COSM4548097 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 23/29 Low_complexity_(Seg):seg,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2.120.10.30,Superfamily_domains:SSF101898,Superfamily_domains:SSF50969 1,1,1,1 HIGH 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 168218314 168218314 G T 1 0 0 0 0 0 1 0 0 16172 1175 41 2 2 TENM2 5 168218314 Nonsense_Mutation SNP G C3L-00080_T 6320944 168218314 13319945 232 2330 FAM153B 0 . GRCh38 5 176103249 176103249 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.456G>A p.= p.Q152Q ENST00000515817 12/20 670 588 82 394 394 0 varscan-mutect FAM153B,synonymous_variant,p.=,ENST00000515817,NM_001265615.1;FAM153B,synonymous_variant,p.=,ENST00000253490,;FAM153B,synonymous_variant,p.=,ENST00000510151,;FAM153B,intron_variant,,ENST00000512862,;FAM153B,intron_variant,,ENST00000611539,;FAM153B,downstream_gene_variant,,ENST00000503724,;FAM153B,non_coding_transcript_exon_variant,,ENST00000393522,;FAM153B,synonymous_variant,p.=,ENST00000508296,; A ENST00000515817 Transcript synonymous_variant 740/1966 456/933 152/310 Q caG/caA 1 1 FAM153B HGNC HGNC:27323 protein_coding YES CCDS43401.2 ENSP00000427684 D6RF84 UPI00001D7EF3 NM_001265615.1 12/20 Pfam_domain:PF15722,hmmpanther:PTHR40712,hmmpanther:PTHR40712:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 176103249 176103249 G A 1 0 0 0 0 0 0 0 1 5311 991 35 3 3 FAM153B 5 176103249 Silent SNP G C3L-00080_T 7884935 176103249 5435010 233 2331 UNC5A 0 . GRCh38 5 176878551 176878551 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2096C>A p.Pro699His p.P699H ENST00000329542 13/15 301 227 74 171 170 1 strelka-varscan-mutect UNC5A,missense_variant,p.Pro699His,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000292432,NM_002115.2;UNC5A,downstream_gene_variant,,ENST00000509580,;HK3,downstream_gene_variant,,ENST00000514058,;HK3,downstream_gene_variant,,ENST00000506834,;UNC5A,downstream_gene_variant,,ENST00000513890,;HK3,downstream_gene_variant,,ENST00000514666,; A ENST00000329542 Transcript missense_variant 2370/3812 2096/2529 699/842 P/H cCc/cAc 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 tolerated(0.09) 13/15 hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 176878551 176878551 C A 1 0 0 0 0 1 0 0 0 17515 623 22 2 2 UNC5A 5 176878551 Missense_Mutation SNP C C3L-00080_T 775302 176878551 4659708 234 2332 FGFR4 0 . GRCh38 5 177096287 177096287 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1945G>T p.Gly649Cys p.G649C ENST00000292408 15/18 158 124 34 86 85 1 strelka-varscan-mutect FGFR4,missense_variant,p.Gly649Cys,ENST00000292408,NM_213647.2,NM_002011.4;FGFR4,missense_variant,p.Gly581Cys,ENST00000393648,NM_001291980.1;FGFR4,missense_variant,p.Gly649Cys,ENST00000502906,;FGFR4,missense_variant,p.Gly609Cys,ENST00000393637,NM_022963.3;FGFR4,downstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000509511,;FGFR4,downstream_gene_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000483872,;FGFR4,upstream_gene_variant,,ENST00000513423,; T ENST00000292408 Transcript missense_variant,splice_region_variant 2190/3122 1945/2409 649/802 G/C Ggc/Tgc 1 1 FGFR4 HGNC HGNC:3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 UPI000012A72D NM_213647.2,NM_002011.4 deleterious(0) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF343,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 177096287 177096287 G T 1 0 0 0 0 1 0 0 0 5732 1246 43 2 2 FGFR4 5 177096287 Missense_Mutation SNP G C3L-00080_T 217736 177096287 4441972 235 2333 DDX41 0 . GRCh38 5 177515714 177515714 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.542A>T p.Lys181Met p.K181M ENST00000507955 6/17 173 95 78 93 93 0 strelka-varscan-mutect DDX41,missense_variant,p.Lys181Met,ENST00000507955,NM_016222.2;DDX41,missense_variant,p.Lys199Met,ENST00000330503,;DDX41,missense_variant,p.Lys181Met,ENST00000629036,;FAM193B,downstream_gene_variant,,ENST00000514747,NM_001190946.1;FAM193B,downstream_gene_variant,,ENST00000524677,;DOK3,upstream_gene_variant,,ENST00000509310,;DOK3,upstream_gene_variant,,ENST00000510389,;DDX41,downstream_gene_variant,,ENST00000625286,;DDX41,intron_variant,,ENST00000506965,;FAM193B,downstream_gene_variant,,ENST00000504130,;DDX41,missense_variant,p.Lys181Met,ENST00000509576,;DDX41,missense_variant,p.Lys7Met,ENST00000508279,;DDX41,missense_variant,p.Lys94Met,ENST00000504781,;DDX41,non_coding_transcript_exon_variant,,ENST00000505081,;DDX41,non_coding_transcript_exon_variant,,ENST00000503078,;DDX41,non_coding_transcript_exon_variant,,ENST00000515562,;DDX41,non_coding_transcript_exon_variant,,ENST00000512431,;FAM193B,downstream_gene_variant,,ENST00000506955,;FAM193B,downstream_gene_variant,,ENST00000510479,;FAM193B,downstream_gene_variant,,ENST00000510163,;FAM193B,downstream_gene_variant,,ENST00000505569,;DDX41,upstream_gene_variant,,ENST00000507900,;DDX41,upstream_gene_variant,,ENST00000504807,;DDX41,upstream_gene_variant,,ENST00000511040,;FAM193B,downstream_gene_variant,,ENST00000507212,;DDX41,upstream_gene_variant,,ENST00000512334,;FAM193B,downstream_gene_variant,,ENST00000513282,;DDX41,upstream_gene_variant,,ENST00000512027,;FAM193B,downstream_gene_variant,,ENST00000506879,;DDX41,downstream_gene_variant,,ENST00000510171,;DDX41,upstream_gene_variant,,ENST00000513562,; A ENST00000507955 Transcript missense_variant 1066/2607 542/1869 181/622 K/M aAg/aTg 1 -1 DDX41 HGNC HGNC:18674 protein_coding YES CCDS4427.1 ENSP00000422753 Q9UJV9 UPI0000125164 NM_016222.2 deleterious(0.03) 6/17 PROSITE_profiles:PS51195,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF20,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 177515714 177515714 T A 1 0 0 0 0 1 0 0 0 4164 1609 56 4 4 DDX41 5 177515714 Missense_Mutation SNP T C3L-00080_T 419427 177515714 4022545 236 2334 GRM6 0 . GRCh38 5 178989069 178989069 + Missense_Mutation SNP G G A rs778444272 C3L-00080_T C3L-00080_N G G c.1220C>T p.Ala407Val p.A407V ENST00000231188 6/10 489 353 136 367 367 0 strelka-varscan-mutect GRM6,missense_variant,p.Ala407Val,ENST00000231188,NM_000843.3;GRM6,missense_variant,p.Ala407Val,ENST00000517717,;RP11-281O15.4,intron_variant,,ENST00000519491,;GRM6,upstream_gene_variant,,ENST00000518082,;GRM6,upstream_gene_variant,,ENST00000519003,; A ENST00000231188 Transcript missense_variant 1399/6143 1220/2634 407/877 A/V gCg/gTg rs778444272,COSM1209068 1 -1 GRM6 HGNC HGNC:4598 protein_coding YES CCDS4442.1 ENSP00000231188 O15303 UPI000013C947 NM_000843.3 deleterious(0) 6/10 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF24,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00593 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs778444272 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 178989069 178989069 G A 1 0 0 0 0 1 0 0 0 6683 1087 38 1 1 GRM6 5 178989069 Missense_Mutation SNP G C3L-00080_T 1473355 178989069 2549190 237 2335 ZNF354C 0 . GRCh38 5 179079425 179079425 + Silent SNP C C T C3L-00080_T C3L-00080_N C C c.993C>T p.= p.G331G ENST00000315475 5/5 482 428 54 375 375 0 strelka-varscan-mutect ZNF354C,synonymous_variant,p.=,ENST00000315475,NM_014594.1;RP11-281O15.7,downstream_gene_variant,,ENST00000523735,; T ENST00000315475 Transcript synonymous_variant 1299/5411 993/1665 331/554 G ggC/ggT COSM4653952 1 1 ZNF354C HGNC HGNC:16736 protein_coding YES CCDS4443.1 ENSP00000324064 Q86Y25 UPI0000161A6A NM_014594.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF140,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 LOW 1 SNV 1 1 1 PASS rs1022352715 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 179079425 179079425 C T 1 0 0 0 0 0 0 0 1 18438 755 27 1 1 ZNF354C 5 179079425 Silent SNP C C3L-00080_T 90356 179079425 2458834 238 2336 ADAMTS2 0 . GRCh38 5 179113896 179113896 + Missense_Mutation SNP G G A rs144078893 C3L-00080_T C3L-00080_N G G c.3607C>T p.Arg1203Trp p.R1203W ENST00000251582 22/22 404 301 103 336 333 3 strelka-varscan-mutect ADAMTS2,missense_variant,p.Arg1203Trp,ENST00000251582,NM_014244.4;ADAMTS2,downstream_gene_variant,,ENST00000522937,;ADAMTS2,downstream_gene_variant,,ENST00000523450,; A ENST00000251582 Transcript missense_variant 3709/6754 3607/3636 1203/1211 R/W Cgg/Tgg rs144078893 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 tolerated_low_confidence(0.05) 22/22 MODERATE 1 SNV 1 1 PASS rs144078893 . 0 208 0 0 2 0 0 0 -20 0.9988172 1 1 1 0 A 3 1 7 179113896 179113896 G A 1 0 0 0 0 1 0 0 0 309 1086 38 1 1 ADAMTS2 5 179113896 Missense_Mutation SNP G C3L-00080_T 34471 179113896 2424363 239 2337 TBC1D9B 0 . GRCh38 5 179891561 179891561 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.862G>T p.Glu288Ter p.E288* ENST00000356834 6/22 363 272 91 267 267 0 strelka-varscan-mutect TBC1D9B,stop_gained,p.Glu288Ter,ENST00000356834,NM_198868.2;TBC1D9B,stop_gained,p.Glu288Ter,ENST00000355235,NM_015043.3;TBC1D9B,stop_gained,p.Glu18Ter,ENST00000524222,;TBC1D9B,downstream_gene_variant,,ENST00000630103,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000522029,;TBC1D9B,intron_variant,,ENST00000517782,;TBC1D9B,upstream_gene_variant,,ENST00000518120,;TBC1D9B,downstream_gene_variant,,ENST00000522224,; A ENST00000356834 Transcript stop_gained 900/5173 862/3753 288/1250 E/* Gag/Tag 1 -1 TBC1D9B HGNC HGNC:29097 protein_coding YES CCDS43408.1 ENSP00000349291 Q66K14 UPI000034ECFF NM_198868.2 6/22 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF225,SMART_domains:SM00568 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 179891561 179891561 C A 1 0 0 0 0 0 1 0 0 16033 835 29 2 2 TBC1D9B 5 179891561 Nonsense_Mutation SNP C C3L-00080_T 777665 179891561 1646698 240 2338 IRF4 0 . GRCh38 6 401556 401556 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.878C>A p.Pro293His p.P293H ENST00000380956 7/9 334 241 93 365 365 0 strelka-varscan-mutect IRF4,missense_variant,p.Pro293His,ENST00000380956,NM_002460.3,NM_001195286.1;IRF4,downstream_gene_variant,,ENST00000495137,;IRF4,missense_variant,p.Pro293His,ENST00000493114,; A ENST00000380956 Transcript missense_variant 1004/5331 878/1356 293/451 P/H cCc/cAc 1 1 IRF4 HGNC HGNC:6119 protein_coding YES CCDS4469.1 ENSP00000370343 Q15306 UPI000012D88B NM_002460.3,NM_001195286.1 deleterious(0) 7/9 Gene3D:2.60.200.10,Pfam_domain:PF10401,hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF6,SMART_domains:SM01243,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 401556 401556 C A 1 0 0 0 0 1 0 0 0 7739 623 22 2 2 IRF4 6 401556 Missense_Mutation SNP C C3L-00080_T 401556 170404423 241 2339 SYCP2L 0 . GRCh38 6 10907579 10907579 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.714T>C p.= p.C238C ENST00000283141 10/30 121 90 31 131 131 0 strelka-varscan-mutect SYCP2L,synonymous_variant,p.=,ENST00000283141,NM_001040274.2;SYCP2L,synonymous_variant,p.=,ENST00000543878,;SYCP2L,synonymous_variant,p.=,ENST00000341041,;RP11-637O19.3,3_prime_UTR_variant,,ENST00000480294,;SYCP2L,intron_variant,,ENST00000487561,; C ENST00000283141 Transcript synonymous_variant 1010/3130 714/2439 238/812 C tgT/tgC 1 1 SYCP2L HGNC HGNC:21537 protein_coding YES CCDS43423.1 ENSP00000283141 Q5T4T6 UPI000022CA18 NM_001040274.2 10/30 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF14 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 10907579 10907579 T C 1 0 0 0 0 0 0 0 1 15823 1644 57 5 5 SYCP2L 6 10907579 Silent SNP T C3L-00080_T 10506023 10907579 159898400 242 2340 ELOVL2 0 . GRCh38 6 11005530 11005530 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.97G>T p.Asp33Tyr p.D33Y ENST00000354666 3/8 92 73 19 103 103 0 strelka-varscan-mutect ELOVL2,missense_variant,p.Asp33Tyr,ENST00000354666,NM_017770.3; A ENST00000354666 Transcript missense_variant 181/3997 97/891 33/296 D/Y Gac/Tac 1 -1 ELOVL2 HGNC HGNC:14416 protein_coding YES CCDS4518.1 ENSP00000346693 Q9NXB9 A0A024QZV3 UPI0000051C66 NM_017770.3 deleterious(0) 3/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11157:SF16,hmmpanther:PTHR11157,Pfam_domain:PF01151 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 11005530 11005530 C A 1 0 0 0 0 1 0 0 0 4909 855 30 2 2 ELOVL2 6 11005530 Missense_Mutation SNP C C3L-00080_T 97951 11005530 159800449 243 2341 KIF13A 0 . GRCh38 6 17764548 17764548 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.4980A>G p.= p.V1660V ENST00000259711 39/39 183 144 39 145 145 0 strelka-varscan-mutect KIF13A,synonymous_variant,p.=,ENST00000378814,NM_001105568.2;KIF13A,synonymous_variant,p.=,ENST00000259711,NM_022113.5;KIF13A,synonymous_variant,p.=,ENST00000378826,NM_001105566.2;KIF13A,synonymous_variant,p.=,ENST00000378843,NM_001105567.2;KIF13A,synonymous_variant,p.=,ENST00000636847,;KIF13A,synonymous_variant,p.=,ENST00000502297,; C ENST00000259711 Transcript synonymous_variant 5086/5941 4980/5418 1660/1805 V gtA/gtG 1 -1 KIF13A HGNC HGNC:14566 protein_coding YES CCDS47381.1 ENSP00000259711 Q9H1H9 UPI0000E20DA3 NM_022113.5 39/39 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 17764548 17764548 T C 1 0 0 0 0 0 0 0 1 8138 1741 61 5 5 KIF13A 6 17764548 Silent SNP T C3L-00080_T 6759018 17764548 153041431 244 2342 GPX5 0 . GRCh38 6 28534098 28534098 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.597C>A p.= p.S199S ENST00000412168 5/5 129 88 41 92 92 0 strelka-varscan-mutect GPX5,synonymous_variant,p.=,ENST00000412168,NM_001509.2;GPX5,downstream_gene_variant,,ENST00000469384,NM_003996.3;GPX5,non_coding_transcript_exon_variant,,ENST00000442674,;GPX5,downstream_gene_variant,,ENST00000483784,; A ENST00000412168 Transcript synonymous_variant 686/1540 597/666 199/221 S tcC/tcA 1 1 GPX5 HGNC HGNC:4557 protein_coding YES CCDS4652.1 ENSP00000392398 O75715 V9HWN8 UPI0000031FD7 NM_001509.2 5/5 Gene3D:3.40.30.10,PIRSF_domain:PIRSF000303,PROSITE_profiles:PS51355,hmmpanther:PTHR11592,hmmpanther:PTHR11592:SF29,Superfamily_domains:SSF52833 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999986 1 1 1 0 A 2 1 7 28534098 28534098 C A 1 0 0 0 0 0 0 0 1 6622 610 22 2 2 GPX5 6 28534098 Silent SNP C C3L-00080_T 10769550 28534098 142271881 245 2343 OR2W1 0 . GRCh38 6 29044949 29044949 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.227G>T p.Ser76Ile p.S76I ENST00000377175 1/1 216 170 46 212 212 0 strelka-varscan-mutect OR2W1,missense_variant,p.Ser76Ile,ENST00000377175,NM_030903.3;XXbac-BPG258E24.10,intron_variant,,ENST00000623334,;XXbac-BPG258E24.10,intron_variant,,ENST00000623946,; A ENST00000377175 Transcript missense_variant 292/1028 227/963 76/320 S/I aGc/aTc COSM313614 1 -1 OR2W1 HGNC HGNC:8281 protein_coding YES CCDS4656.1 ENSP00000366380 Q9Y3N9 A0A126GVA1 UPI000003FF8A NM_030903.3 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF169,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 29044949 29044949 C A 1 0 0 0 0 1 0 0 0 11110 797 28 2 2 OR2W1 6 29044949 Missense_Mutation SNP C C3L-00080_T 510851 29044949 141761030 246 2344 OR10C1 0 . GRCh38 6 29440120 29440120 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.105G>T p.= p.L35L ENST00000444197 1/1 295 246 49 263 263 0 strelka-varscan-mutect OR10C1,synonymous_variant,p.=,ENST00000444197,NM_013941.3;OR10C1,synonymous_variant,p.=,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript synonymous_variant 815/1649 105/939 35/312 L ctG/ctT 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 29440120 29440120 G T 1 0 0 0 0 0 0 0 1 10973 1306 46 2 2 OR10C1 6 29440120 Silent SNP G C3L-00080_T 395171 29440120 141365859 247 2345 HLA-G 0 . GRCh38 6 29827901 29827901 + Silent SNP G G T rs755278031 C3L-00080_T C3L-00080_N G G c.57G>T p.= p.L19L ENST00000428701 2/8 153 124 29 91 91 0 strelka-varscan-mutect HLA-G,synonymous_variant,p.=,ENST00000428701,NM_002127.5;HLA-G,synonymous_variant,p.=,ENST00000376828,;HLA-G,synonymous_variant,p.=,ENST00000360323,;HLA-G,synonymous_variant,p.=,ENST00000376818,;HLA-G,synonymous_variant,p.=,ENST00000376815,;HLA-G,synonymous_variant,p.=,ENST00000478519,;HLA-G,non_coding_transcript_exon_variant,,ENST00000478355,;HCG4P8,non_coding_transcript_exon_variant,,ENST00000443049,; T ENST00000428701 Transcript synonymous_variant 235/1578 57/1017 19/338 L ctG/ctT rs755278031 1 1 HLA-G HGNC HGNC:4964 protein_coding YES CCDS4668.1 ENSP00000412927 P17693 Q6DU14 UPI000000166E NM_002127.5 2/8 Low_complexity_(Seg):seg,hmmpanther:PTHR16675:SF169,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 PASS rs755278031 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 29827901 29827901 G T 1 0 0 0 0 0 0 0 1 7102 1277 45 2 2 HLA-G 6 29827901 Silent SNP G C3L-00080_T 387781 29827901 140978078 248 2346 DDX39B 0 . GRCh38 6 31531317 31531317 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.956G>A p.Arg319His p.R319H ENST00000396172 8/11 227 173 54 228 228 0 strelka-varscan-mutect DDX39B,missense_variant,p.Arg319His,ENST00000396172,NM_004640.6;DDX39B,missense_variant,p.Arg319His,ENST00000458640,NM_080598.5;DDX39B,missense_variant,p.Arg319His,ENST00000376177,;DDX39B,missense_variant,p.Arg241His,ENST00000431908,;DDX39B,missense_variant,p.Arg83His,ENST00000417023,;DDX39B,downstream_gene_variant,,ENST00000427214,;MCCD1,downstream_gene_variant,,ENST00000376191,NM_001011700.2;DDX39B,downstream_gene_variant,,ENST00000456662,;DDX39B,downstream_gene_variant,,ENST00000419338,;DDX39B,downstream_gene_variant,,ENST00000428098,;DDX39B,upstream_gene_variant,,ENST00000462421,;DDX39B,missense_variant,p.Arg111His,ENST00000484566,;ATP6V1G2-DDX39B,3_prime_UTR_variant,,ENST00000376185,;DDX39B,non_coding_transcript_exon_variant,,ENST00000462256,;DDX39B,non_coding_transcript_exon_variant,,ENST00000482195,;DDX39B,non_coding_transcript_exon_variant,,ENST00000474961,;DDX39B,non_coding_transcript_exon_variant,,ENST00000478365,;DDX39B,downstream_gene_variant,,ENST00000481456,;RPL15P4,downstream_gene_variant,,ENST00000416625,; T ENST00000396172 Transcript missense_variant 1587/2133 956/1287 319/428 R/H cGt/cAt 1 -1 DDX39B HGNC HGNC:13917 protein_coding YES CCDS4697.1 ENSP00000379475 Q13838 A0A024RCM3 UPI0000001D0B NM_004640.6 tolerated(0.1) 8/11 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF204,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 31531317 31531317 C T 1 0 0 0 0 1 0 0 0 4160 536 19 1 1 DDX39B 6 31531317 Missense_Mutation SNP C C3L-00080_T 1703416 31531317 139274662 249 2347 TAP2 0 . GRCh38 6 32832730 32832730 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1040C>A p.Ala347Asp p.A347D ENST00000374897 6/12 557 441 116 511 511 0 strelka-varscan-mutect TAP2,missense_variant,p.Ala347Asp,ENST00000374897,NM_001290043.1;TAP2,missense_variant,p.Ala347Asp,ENST00000620123,NM_000544.3;XXbac-BPG246D15.9,missense_variant,p.Ala347Asp,ENST00000452392,;TAP2,missense_variant,p.Ala347Asp,ENST00000374899,NM_018833.2;TAP2,non_coding_transcript_exon_variant,,ENST00000485701,;TAP2,upstream_gene_variant,,ENST00000464100,; T ENST00000374897 Transcript missense_variant 1172/5684 1040/2061 347/686 A/D gCc/gAc 1 -1 TAP2 HGNC HGNC:44 protein_coding YES CCDS78129.1 ENSP00000364032 Q03519 Q5JNW1 UPI000011D578 NM_001290043.1 deleterious(0) 6/12 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF237,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,PIRSF_domain:PIRSF002773,TIGRFAM_domain:TIGR00958,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 32832730 32832730 G T 1 0 0 0 0 1 0 0 0 15950 1203 42 2 2 TAP2 6 32832730 Missense_Mutation SNP G C3L-00080_T 1301413 32832730 137973249 250 2348 HLA-DMA 0 . GRCh38 6 32949800 32949800 + Missense_Mutation SNP G G C rs112631644 C3L-00080_T C3L-00080_N G G c.463C>G p.Pro155Ala p.P155A ENST00000374843 3/5 399 332 67 355 355 0 strelka-varscan-mutect HLA-DMA,missense_variant,p.Pro155Ala,ENST00000374843,NM_006120.3;HLA-DMA,missense_variant,p.Pro185Ala,ENST00000456800,;HLA-DMA,missense_variant,p.Pro60Ala,ENST00000395305,;HLA-DMA,missense_variant,p.Pro122Ala,ENST00000422832,;HLA-DMA,intron_variant,,ENST00000395303,;XXbac-BPG181M17.5,intron_variant,,ENST00000429234,;HLA-DMA,non_coding_transcript_exon_variant,,ENST00000464392,;HLA-DMA,non_coding_transcript_exon_variant,,ENST00000477541,;HLA-DMA,downstream_gene_variant,,ENST00000475627,;HLA-DMA,upstream_gene_variant,,ENST00000480785,; C ENST00000374843 Transcript missense_variant 549/1123 463/786 155/261 P/A Ccc/Gcc rs112631644 1 -1 HLA-DMA HGNC HGNC:4934 protein_coding YES CCDS4761.1 ENSP00000363976 P28067 Q31604,Q6ICR9 UPI000006F879 NM_006120.3 tolerated(0.09) 3/5 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR19944,hmmpanther:PTHR19944:SF50,SMART_domains:SM00407,Superfamily_domains:SSF48726 MODERATE SNV 1 PASS rs112631644 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 32949800 32949800 G C 1 0 0 0 0 1 0 0 0 7087 1261 44 4 4 HLA-DMA 6 32949800 Missense_Mutation SNP G C3L-00080_T 117070 32949800 137856179 251 2349 RING1 0 . GRCh38 6 33211413 33211413 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.711G>T p.= p.G237G ENST00000374656 5/7 112 65 47 114 114 0 strelka-varscan-mutect RING1,synonymous_variant,p.=,ENST00000374656,NM_002931.3;HSD17B8,downstream_gene_variant,,ENST00000374662,NM_014234.4;MIR219A1,downstream_gene_variant,,ENST00000362166,;RING1,non_coding_transcript_exon_variant,,ENST00000478431,;HSD17B8,downstream_gene_variant,,ENST00000469186,;ZNF70P1,upstream_gene_variant,,ENST00000417480,; T ENST00000374656 Transcript synonymous_variant 919/1752 711/1221 237/406 G ggG/ggT 1 1 RING1 HGNC HGNC:10018 protein_coding YES CCDS34424.1 ENSP00000363787 Q06587 UPI000019273E NM_002931.3 5/7 hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF6,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 33211413 33211413 G T 1 0 0 0 0 0 0 0 1 13548 1161 41 2 2 RING1 6 33211413 Silent SNP G C3L-00080_T 261613 33211413 137594566 252 2350 MDGA1 0 . GRCh38 6 37652132 37652132 + Silent SNP G G A rs768355120 C3L-00080_T C3L-00080_N G G c.1191C>T p.= p.T397T ENST00000434837 7/17 281 214 67 232 232 0 strelka-varscan-mutect MDGA1,synonymous_variant,p.=,ENST00000434837,NM_153487.3;MDGA1,synonymous_variant,p.=,ENST00000505425,;MDGA1,downstream_gene_variant,,ENST00000515437,;MDGA1,downstream_gene_variant,,ENST00000508399,;MDGA1,upstream_gene_variant,,ENST00000510077,;MDGA1,non_coding_transcript_exon_variant,,ENST00000478143,;MDGA1,upstream_gene_variant,,ENST00000502298,; A ENST00000434837 Transcript synonymous_variant 2370/10736 1191/2868 397/955 T acC/acT rs768355120 1 -1 MDGA1 HGNC HGNC:19267 protein_coding YES CCDS47417.1 ENSP00000402584 Q8NFP4 UPI0000071D28 NM_153487.3 7/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF66,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs768355120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 37652132 37652132 G A 1 0 0 0 0 0 0 0 1 9344 1335 47 3 3 MDGA1 6 37652132 Silent SNP G C3L-00080_T 4440719 37652132 133153847 253 2351 TREML1 0 . GRCh38 6 41153947 41153947 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.187G>T p.Val63Leu p.V63L ENST00000426005 2/6 386 306 80 372 371 1 strelka-varscan-mutect TREML1,missense_variant,p.Val63Leu,ENST00000373127,NM_001271807.1;TREML1,missense_variant,p.Val63Leu,ENST00000426005,NM_178174.3;TREML1,intron_variant,,ENST00000437044,NM_001271808.1;TREM2,downstream_gene_variant,,ENST00000373113,NM_018965.3;TREM2,downstream_gene_variant,,ENST00000373122,;TREM2,downstream_gene_variant,,ENST00000338469,NM_001271821.1;TREML1,upstream_gene_variant,,ENST00000590581,; A ENST00000426005 Transcript missense_variant 231/981 187/936 63/311 V/L Gtg/Ttg 1 -1 TREML1 HGNC HGNC:20434 protein_coding YES CCDS4851.1 ENSP00000402855 Q86YW5 UPI0000074451 NM_178174.3 deleterious(0.04) 2/6 hmmpanther:PTHR11860,hmmpanther:PTHR11860:SF37,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 41153947 41153947 C A 1 0 0 0 0 1 0 0 0 16961 507 18 2 2 TREML1 6 41153947 Missense_Mutation SNP C C3L-00080_T 3501815 41153947 129652032 254 2352 ZNF318 0 . GRCh38 6 43340189 43340189 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.3809C>A p.Ser1270Ter p.S1270* ENST00000361428 10/10 234 195 39 288 288 0 strelka-varscan-mutect ZNF318,stop_gained,p.Ser1270Ter,ENST00000361428,NM_014345.2;ZNF318,intron_variant,,ENST00000606599,;ZNF318,intron_variant,,ENST00000605935,; T ENST00000361428 Transcript stop_gained 3887/8006 3809/6840 1270/2279 S/* tCa/tAa 1 -1 ZNF318 HGNC HGNC:13578 protein_coding YES CCDS4895.2 ENSP00000354964 Q5VUA4 UPI000049E044 NM_014345.2 10/10 hmmpanther:PTHR15577:SF2,hmmpanther:PTHR15577 HIGH 1 SNV 1 1 PASS rs1292342861 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 43340189 43340189 G T 1 0 0 0 0 0 1 0 0 18411 1294 45 2 2 ZNF318 6 43340189 Nonsense_Mutation SNP G C3L-00080_T 2186242 43340189 127465790 255 2353 TMEM63B 0 . GRCh38 6 44154399 44154399 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.2261G>A p.Arg754Lys p.R754K ENST00000259746 23/24 229 143 86 167 167 0 strelka-varscan-mutect TMEM63B,missense_variant,p.Arg754Lys,ENST00000259746,NM_001318792.1;TMEM63B,missense_variant,p.Arg754Lys,ENST00000323267,NM_018426.1;TMEM63B,missense_variant,p.Arg683Lys,ENST00000371893,;CAPN11,upstream_gene_variant,,ENST00000398776,NM_007058.3;CAPN11,upstream_gene_variant,,ENST00000532171,;TMEM63B,3_prime_UTR_variant,,ENST00000533121,;CAPN11,upstream_gene_variant,,ENST00000526118,; A ENST00000259746 Transcript missense_variant 2444/3318 2261/2499 754/832 R/K aGa/aAa 1 1 TMEM63B HGNC HGNC:17735 protein_coding YES CCDS34461.1 ENSP00000259746 Q5T3F8 UPI000020DDEE NM_001318792.1 tolerated(0.9) 23/24 hmmpanther:PTHR13018:SF38,hmmpanther:PTHR13018 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 44154399 44154399 G A 1 0 0 0 0 1 0 0 0 16667 942 33 3 3 TMEM63B 6 44154399 Missense_Mutation SNP G C3L-00080_T 814210 44154399 126651580 256 2354 CENPQ 0 . GRCh38 6 49488420 49488424 + Frame_Shift_Del DEL AATTC AATTC - novel C3L-00080_T C3L-00080_N AATTC AATTC c.547_551delATTCA p.Ile183AspfsTer5 p.I183Dfs*5 ENST00000335783 7/9 64 48 16 126 126 0 sindel-varindel-pindel CENPQ,frameshift_variant,p.Ile183AspfsTer5,ENST00000335783,NM_018132.3; - ENST00000335783 Transcript frameshift_variant 640-644/1733 546-550/807 182-184/268 KIQ/KX aaAATTCag/aaag 1 1 CENPQ HGNC HGNC:21347 protein_coding YES CCDS4925.1 ENSP00000337289 Q7L2Z9 UPI000020DE7B NM_018132.3 7/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF13094,hmmpanther:PTHR31345,hmmpanther:PTHR31345:SF3 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 49488420 49488420 AATTC - 1 0 1 0 1 0 0 0 0 2949 11 1 0 0 CENPQ 6 49488420 Frame_Shift_Del DEL AATTC C3L-00080_T 5334021 49488420 121317559 257 2355 TFAP2D 0 . GRCh38 6 50715549 50715549 + Missense_Mutation SNP C C A rs770678203 C3L-00080_T C3L-00080_N C C c.473C>A p.Pro158Gln p.P158Q ENST00000008391 2/8 130 109 21 142 142 0 strelka-varscan-mutect TFAP2D,missense_variant,p.Pro158Gln,ENST00000008391,NM_172238.3;TFAP2D,upstream_gene_variant,,ENST00000492804,; A ENST00000008391 Transcript missense_variant 701/1711 473/1359 158/452 P/Q cCa/cAa rs770678203 1 1 TFAP2D HGNC HGNC:15581 protein_coding YES CCDS4933.1 ENSP00000008391 Q7Z6R9 UPI00001A3A89 NM_172238.3 deleterious(0.01) 2/8 hmmpanther:PTHR10812:SF5,hmmpanther:PTHR10812 MODERATE 1 SNV 1 1 PASS rs770678203 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 50715549 50715549 C A 1 0 0 0 0 1 0 0 0 16223 594 21 2 2 TFAP2D 6 50715549 Missense_Mutation SNP C C3L-00080_T 1227129 50715549 120090430 258 2356 TFAP2B 0 . GRCh38 6 50840169 50840169 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.954C>A p.His318Gln p.H318Q ENST00000393655 6/7 526 438 88 463 462 1 strelka-varscan-mutect TFAP2B,missense_variant,p.His318Gln,ENST00000393655,NM_003221.3; A ENST00000393655 Transcript missense_variant 1123/5773 954/1383 318/460 H/Q caC/caA 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 deleterious(0) 6/7 Pfam_domain:PF03299,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 50840169 50840169 C A 1 0 0 0 0 1 0 0 0 16221 564 20 2 2 TFAP2B 6 50840169 Missense_Mutation SNP C C3L-00080_T 124620 50840169 119965810 259 2357 KLHL31 0 . GRCh38 6 53651880 53651880 + Silent SNP C C A rs772350477 C3L-00080_T C3L-00080_N C C c.1623G>T p.= p.A541A ENST00000370905 3/3 211 155 56 210 210 0 strelka-varscan-mutect KLHL31,synonymous_variant,p.=,ENST00000370905,NM_001003760.4;KLHL31,synonymous_variant,p.=,ENST00000407079,; A ENST00000370905 Transcript synonymous_variant 1764/5743 1623/1905 541/634 A gcG/gcT rs772350477 1 -1 KLHL31 HGNC HGNC:21353 protein_coding YES CCDS34478.1 ENSP00000359942 Q9H511 UPI000006D624 NM_001003760.4 3/3 hmmpanther:PTHR24412:SF247,hmmpanther:PTHR24412,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 LOW 1 SNV 1 1 PASS rs772350477 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 53651880 53651880 C A 1 0 0 0 0 0 0 0 1 8250 871 31 1 1 KLHL31 6 53651880 Silent SNP C C3L-00080_T 2811711 53651880 117154099 260 2358 DST 0 . GRCh38 6 56572100 56572100 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.6950A>C p.Lys2317Thr p.K2317T ENST00000312431 45/95 86 53 33 146 146 0 strelka-varscan-mutect DST,missense_variant,p.Lys4363Thr,ENST00000361203,;DST,missense_variant,p.Lys2277Thr,ENST00000421834,NM_183380.3;DST,missense_variant,p.Lys2317Thr,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Lys2277Thr,ENST00000370788,;DST,missense_variant,p.Lys1951Thr,ENST00000244364,NM_015548.4;DST,3_prime_UTR_variant,,ENST00000518398,; G ENST00000312431 Transcript missense_variant,splice_region_variant 7076/17756 6950/16614 2317/5537 K/T aAa/aCa 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 deleterious(0) 45/95 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 56572100 56572100 T G 1 0 0 0 0 1 0 0 0 4604 1623 56 5 5 DST 6 56572100 Missense_Mutation SNP T C3L-00080_T 2920220 56572100 114233879 261 2359 CD109 0 . GRCh38 6 73788533 73788533 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.2622G>C p.Gln874His p.Q874H ENST00000287097 22/33 99 66 33 218 218 0 strelka-varscan-mutect CD109,missense_variant,p.Gln874His,ENST00000437994,NM_001159587.2;CD109,missense_variant,p.Gln797His,ENST00000422508,NM_001159588.2;CD109,missense_variant,p.Gln874His,ENST00000287097,NM_133493.4;CD109,upstream_gene_variant,,ENST00000474094,; C ENST00000287097 Transcript missense_variant 2734/9130 2622/4338 874/1445 Q/H caG/caC 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 deleterious(0.01) 22/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 73788533 73788533 G C 1 0 0 0 0 1 0 0 0 2666 933 33 4 4 CD109 6 73788533 Missense_Mutation SNP G C3L-00080_T 17216433 73788533 97017446 262 2360 ZNF292 0 . GRCh38 6 87260570 87260570 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.6941A>T p.Lys2314Ile p.K2314I ENST00000369577 8/8 156 95 61 169 169 0 strelka-varscan-mutect ZNF292,missense_variant,p.Lys2314Ile,ENST00000369577,NM_015021.1;ZNF292,missense_variant,p.Lys2309Ile,ENST00000339907,;ZNF292,missense_variant,p.Lys232Ile,ENST00000496806,; T ENST00000369577 Transcript missense_variant 6984/10610 6941/8172 2314/2723 K/I aAa/aTa 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 deleterious(0.01) 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 87260570 87260570 A T 1 0 0 0 0 1 0 0 0 18402 14 1 4 4 ZNF292 6 87260570 Missense_Mutation SNP A C3L-00080_T 13472037 87260570 83545409 263 2361 FAM229B 0 . GRCh38 6 112099299 112099299 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.16G>T p.Gly6Ter p.G6* ENST00000368656 3/4 131 65 66 163 162 1 strelka-varscan-mutect FAM229B,stop_gained,p.Gly6Ter,ENST00000368656,NM_001033564.2;FAM229B,stop_gained,p.Gly6Ter,ENST00000604268,; T ENST00000368656 Transcript stop_gained 313/2543 16/243 6/80 G/* Gga/Tga 1 1 FAM229B HGNC HGNC:33858 protein_coding YES CCDS34513.1 ENSP00000357645 Q4G0N7 UPI000000DAC0 NM_001033564.2 3/4 Pfam_domain:PF14982,hmmpanther:PTHR35355,hmmpanther:PTHR35355:SF2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 112099299 112099299 G T 1 0 0 0 0 0 1 0 0 5422 1349 47 2 2 FAM229B 6 112099299 Nonsense_Mutation SNP G C3L-00080_T 24838729 112099299 58706680 264 2362 LAMA4 0 . GRCh38 6 112216385 112216385 + Missense_Mutation SNP C C A rs35349917 C3L-00080_T C3L-00080_N C C c.280G>T p.Gly94Cys p.G94C ENST00000230538 3/39 381 243 138 476 474 2 strelka-varscan-mutect LAMA4,missense_variant,p.Gly94Cys,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Gly94Cys,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Gly94Cys,ENST00000389463,;LAMA4,missense_variant,p.Gly94Cys,ENST00000424408,;LAMA4,missense_variant,p.Gly94Cys,ENST00000521398,;LAMA4,missense_variant,p.Gly94Cys,ENST00000431543,;LAMA4,missense_variant,p.Gly94Cys,ENST00000519932,;LAMA4,downstream_gene_variant,,ENST00000243219,;LAMA4,downstream_gene_variant,,ENST00000521690,;RP1-142L7.9,downstream_gene_variant,,ENST00000603682,;LAMA4,non_coding_transcript_exon_variant,,ENST00000524032,;LAMA4,non_coding_transcript_exon_variant,,ENST00000423735,; A ENST00000230538 Transcript missense_variant 678/6547 280/5472 94/1823 G/C Ggc/Tgc rs35349917 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0.02) 3/39 PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 benign MODERATE 1 SNV 1 1 1 PASS rs35349917 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 112216385 112216385 C A 1 0 0 0 0 1 0 0 0 8512 652 23 1 1 LAMA4 6 112216385 Missense_Mutation SNP C C3L-00080_T 117086 112216385 58589594 265 2363 GPRC6A 0 . GRCh38 6 116806425 116806425 + Missense_Mutation SNP C C A rs563483944 C3L-00080_T C3L-00080_N C C c.1280G>T p.Arg427Leu p.R427L ENST00000310357 3/6 106 100 6 94 94 0 strelka-mutect GPRC6A,missense_variant,p.Arg427Leu,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Arg427Leu,ENST00000368549,NM_001286355.1;GPRC6A,intron_variant,,ENST00000530250,NM_001286354.1; A ENST00000310357 Transcript missense_variant 1302/2860 1280/2781 427/926 R/L cGg/cTg rs563483944,COSM1072464 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated(0.09) 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs563483944 . 0 199 11 0 0 0 0 0 -11.90258 0.9997125 1 1 1 0 A 3 1 7 116806425 116806425 C A 1 0 0 0 0 1 0 0 0 6607 652 23 1 1 GPRC6A 6 116806425 Missense_Mutation SNP C C3L-00080_T 4590040 116806425 53999554 266 2364 C6orf58 0 . GRCh38 6 127578768 127578768 + Missense_Mutation SNP G G T rs773914066 C3L-00080_T C3L-00080_N G G c.384G>T p.Trp128Cys p.W128C ENST00000329722 2/6 61 33 28 89 89 0 strelka-varscan-mutect C6orf58,missense_variant,p.Trp128Cys,ENST00000329722,NM_001010905.2;C6orf58,downstream_gene_variant,,ENST00000498112,; T ENST00000329722 Transcript missense_variant 396/1200 384/993 128/330 W/C tgG/tgT rs773914066 1 1 C6orf58 HGNC HGNC:20960 protein_coding YES CCDS34533.1 ENSP00000328069 Q6P5S2 UPI00001D80C9 NM_001010905.2 deleterious(0) 2/6 Pfam_domain:PF05612,hmmpanther:PTHR18820,hmmpanther:PTHR18820:SF4 MODERATE 1 SNV 1 1 PASS rs773914066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 127578768 127578768 G T 1 0 0 0 0 1 0 0 0 2131 1246 43 2 2 C6orf58 6 127578768 Missense_Mutation SNP G C3L-00080_T 10772343 127578768 43227211 267 2365 LAMA2 0 . GRCh38 6 129287876 129287876 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.2567C>G p.Ser856Cys p.S856C ENST00000421865 19/65 361 303 58 349 349 0 strelka-varscan-mutect LAMA2,missense_variant,p.Ser856Cys,ENST00000618192,;LAMA2,missense_variant,p.Ser856Cys,ENST00000617695,;LAMA2,missense_variant,p.Ser856Cys,ENST00000421865,NM_001079823.1,NM_000426.3; G ENST00000421865 Transcript missense_variant 2616/9640 2567/9369 856/3122 S/C tCt/tGt 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 deleterious(0.01) 19/65 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 129287876 129287876 C G 1 0 0 0 0 1 0 0 0 8510 913 32 4 4 LAMA2 6 129287876 Missense_Mutation SNP C C3L-00080_T 1709108 129287876 41518103 268 2366 LAMA2 0 . GRCh38 6 129393096 129393096 + Silent SNP G G T rs747795505 C3L-00080_T C3L-00080_N G G c.5286G>T p.= p.R1762R ENST00000421865 37/65 222 195 27 197 197 0 strelka-varscan-mutect LAMA2,synonymous_variant,p.=,ENST00000618192,;LAMA2,synonymous_variant,p.=,ENST00000617695,;LAMA2,synonymous_variant,p.=,ENST00000421865,NM_001079823.1,NM_000426.3; T ENST00000421865 Transcript synonymous_variant 5335/9640 5286/9369 1762/3122 R cgG/cgT rs747795505 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 37/65 Coiled-coils_(Ncoils):Coil,PD936484,Pfam_domain:PF06008 LOW 1 SNV 5 1 PASS rs747795505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 129393096 129393096 G T 1 0 0 0 0 0 0 0 1 8510 1219 43 2 2 LAMA2 6 129393096 Silent SNP G C3L-00080_T 105220 129393096 41412883 269 2367 LAMA2 0 . GRCh38 6 129464308 129464308 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.7011T>C p.= p.S2337S ENST00000421865 50/65 242 122 120 240 240 0 strelka-varscan-mutect LAMA2,synonymous_variant,p.=,ENST00000618192,;LAMA2,synonymous_variant,p.=,ENST00000617695,;LAMA2,synonymous_variant,p.=,ENST00000421865,NM_001079823.1,NM_000426.3; C ENST00000421865 Transcript synonymous_variant 7060/9640 7011/9369 2337/3122 S agT/agC 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 50/65 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,Superfamily_domains:SSF49899 LOW 1 SNV 5 1 PASS rs1283730544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 129464308 129464308 T C 1 0 0 0 0 0 0 0 1 8510 1693 59 5 5 LAMA2 6 129464308 Silent SNP T C3L-00080_T 71212 129464308 41341671 270 2368 VNN1 0 . GRCh38 6 132692259 132692259 + Silent SNP G G A rs767890224 C3L-00080_T C3L-00080_N G G c.1152C>T p.= p.D384D ENST00000367928 5/7 81 75 6 61 61 0 strelka-mutect VNN1,synonymous_variant,p.=,ENST00000367928,NM_004666.2; A ENST00000367928 Transcript synonymous_variant 1166/3106 1152/1542 384/513 D gaC/gaT rs767890224 1 -1 VNN1 HGNC HGNC:12705 protein_coding YES CCDS5159.1 ENSP00000356905 O95497 UPI000013C91E NM_004666.2 5/7 hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF16,PIRSF_domain:PIRSF011861 LOW 1 SNV 1 1 PASS rs767890224 . 0 203 7 0 0 0 0 0 -12.92564 0.999998 1 1 1 0 A 2 1 7 132692259 132692259 G A 1 0 0 0 0 0 0 0 1 17729 1136 40 1 1 VNN1 6 132692259 Silent SNP G C3L-00080_T 3227951 132692259 38113720 271 2369 VNN2 0 . GRCh38 6 132757434 132757434 + Missense_Mutation SNP G G T rs149351884 C3L-00080_T C3L-00080_N G G c.326C>A p.Pro109Gln p.P109Q ENST00000326499 2/7 62 25 37 51 51 0 strelka-varscan-mutect VNN2,missense_variant,p.Pro109Gln,ENST00000326499,NM_004665.4;VNN2,missense_variant,p.Pro56Gln,ENST00000525270,NM_078488.2;VNN2,missense_variant,p.Pro109Gln,ENST00000525289,NM_001242350.2;VNN2,missense_variant,p.Pro109Gln,ENST00000524919,;VNN2,missense_variant,p.Pro56Gln,ENST00000530536,;VNN2,downstream_gene_variant,,ENST00000532012,;RP1-55C23.7,downstream_gene_variant,,ENST00000430895,;VNN2,non_coding_transcript_exon_variant,,ENST00000526192,;VNN2,non_coding_transcript_exon_variant,,ENST00000526157,;VNN2,missense_variant,p.Pro109Gln,ENST00000392389,;VNN2,missense_variant,p.Pro109Gln,ENST00000422400,;VNN2,missense_variant,p.Pro109Gln,ENST00000418593,;VNN2,missense_variant,p.Pro109Gln,ENST00000525674,;VNN2,missense_variant,p.Pro109Gln,ENST00000533835,;VNN2,missense_variant,p.Pro109Gln,ENST00000532053,;VNN2,missense_variant,p.Pro109Gln,ENST00000528801,;VNN2,missense_variant,p.Pro56Gln,ENST00000531279,; T ENST00000326499 Transcript missense_variant 451/2118 326/1563 109/520 P/Q cCg/cAg rs149351884,COSM3410595 1 -1 VNN2 HGNC HGNC:12706 protein_coding YES CCDS5161.1 ENSP00000322276 O95498 UPI000014194E NM_004665.4 deleterious(0) 2/7 PROSITE_profiles:PS50263,hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF15,PIRSF_domain:PIRSF011861,Gene3D:3.60.110.10,Pfam_domain:PF00795,Superfamily_domains:SSF56317 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs149351884 . 0 201 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 7 132757434 132757434 G T 1 0 0 0 0 1 0 0 0 17730 1116 39 1 1 VNN2 6 132757434 Missense_Mutation SNP G C3L-00080_T 65175 132757434 38048545 272 2370 BCLAF1 0 . GRCh38 6 136269574 136269574 + Silent SNP C C A rs62431288 C3L-00080_T C3L-00080_N C C c.2082G>T p.= p.R694R ENST00000531224 9/13 184 133 51 144 144 0 strelka-varscan-mutect BCLAF1,synonymous_variant,p.=,ENST00000531224,NM_014739.2;BCLAF1,synonymous_variant,p.=,ENST00000353331,NM_001077440.1;BCLAF1,synonymous_variant,p.=,ENST00000527536,;BCLAF1,synonymous_variant,p.=,ENST00000527759,NM_001301038.1;BCLAF1,synonymous_variant,p.=,ENST00000530767,NM_001077441.1;BCLAF1,synonymous_variant,p.=,ENST00000392348,;BCLAF1,synonymous_variant,p.=,ENST00000628517,;BCLAF1,synonymous_variant,p.=,ENST00000529826,;BCLAF1,upstream_gene_variant,,ENST00000534762,;BCLAF1,non_coding_transcript_exon_variant,,ENST00000529917,;BCLAF1,synonymous_variant,p.=,ENST00000527613,;BCLAF1,synonymous_variant,p.=,ENST00000532384,;BCLAF1,synonymous_variant,p.=,ENST00000530429,;BCLAF1,3_prime_UTR_variant,,ENST00000534269,;BCLAF1,non_coding_transcript_exon_variant,,ENST00000532076,;BCLAF1,non_coding_transcript_exon_variant,,ENST00000534792,;BCLAF1,non_coding_transcript_exon_variant,,ENST00000534321,;BCLAF1,upstream_gene_variant,,ENST00000529522,;BCLAF1,upstream_gene_variant,,ENST00000533422,;BCLAF1,downstream_gene_variant,,ENST00000476194,;BCLAF1,upstream_gene_variant,,ENST00000526228,; A ENST00000531224 Transcript synonymous_variant 2335/7263 2082/2763 694/920 R cgG/cgT rs62431288 1 -1 BCLAF1 HGNC HGNC:16863 protein_coding YES CCDS5177.1 ENSP00000435210 Q9NYF8 UPI000006FCE7 NM_014739.2 9/13 Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4 LOW 1 SNV 1 1 PASS rs62431288 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 136269574 136269574 C A 1 0 0 0 0 0 0 0 1 1530 726 26 2 2 BCLAF1 6 136269574 Silent SNP C C3L-00080_T 3512140 136269574 34536405 273 2371 OLIG3 0 . GRCh38 6 137493983 137493983 + Missense_Mutation SNP G G T rs62434134 C3L-00080_T C3L-00080_N G G c.188C>A p.Ala63Asp p.A63D ENST00000367734 1/1 579 368 211 422 422 0 strelka-varscan-mutect OLIG3,missense_variant,p.Ala63Asp,ENST00000367734,NM_175747.2; T ENST00000367734 Transcript missense_variant 268/2049 188/819 63/272 A/D gCc/gAc rs62434134 1 -1 OLIG3 HGNC HGNC:18003 protein_coding YES CCDS5186.1 ENSP00000356708 Q7RTU3 UPI000006F9D6 NM_175747.2 tolerated(0.07) 1/1 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF96 MODERATE 1 SNV 1 PASS rs62434134 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 137493983 137493983 G T 1 0 0 0 0 1 0 0 0 10937 1203 42 2 2 OLIG3 6 137493983 Missense_Mutation SNP G C3L-00080_T 1224409 137493983 33311996 274 2372 ARFGEF3 0 . GRCh38 6 138334951 138334951 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.6105G>T p.Gln2035His p.Q2035H ENST00000251691 33/34 362 261 101 221 221 0 strelka-varscan-mutect ARFGEF3,missense_variant,p.Gln2035His,ENST00000251691,NM_020340.4; T ENST00000251691 Transcript missense_variant 6271/14877 6105/6534 2035/2177 Q/H caG/caT 1 1 ARFGEF3 HGNC HGNC:21213 protein_coding YES CCDS5189.2 ENSP00000251691 Q5TH69 UPI000150AF4A NM_020340.4 tolerated(0.2) 33/34 MODERATE 1 SNV 1 1 PASS rs1477146541 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 138334951 138334951 G T 1 0 0 0 0 1 0 0 0 977 962 34 2 2 ARFGEF3 6 138334951 Missense_Mutation SNP G C3L-00080_T 840968 138334951 32471028 275 2373 GRM1 0 . GRCh38 6 146434704 146434704 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.3493C>A p.Pro1165Thr p.P1165T ENST00000361719 9/9 455 390 65 360 359 1 strelka-varscan-mutect GRM1,missense_variant,p.Pro1165Thr,ENST00000361719,;GRM1,missense_variant,p.Pro1165Thr,ENST00000282753,NM_001278064.1;GRM1,3_prime_UTR_variant,,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,3_prime_UTR_variant,,ENST00000355289,NM_001278067.1;GRM1,3_prime_UTR_variant,,ENST00000507907,; A ENST00000361719 Transcript missense_variant 3860/6754 3493/3585 1165/1194 P/T Ccc/Acc 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD deleterious_low_confidence(0) 9/9 Low_complexity_(Seg):seg,Pfam_domain:PF10606,SMART_domains:SM01229 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 146434704 146434704 C A 1 0 0 0 0 1 0 0 0 6678 623 22 2 2 GRM1 6 146434704 Missense_Mutation SNP C C3L-00080_T 8099753 146434704 24371275 276 2374 ADGB 0 . GRCh38 6 146685820 146685820 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1303G>T p.Glu435Ter p.E435* ENST00000397944 10/36 69 60 9 108 107 1 strelka-varscan-mutect ADGB,stop_gained,p.Glu435Ter,ENST00000397944,NM_024694.3;ADGB,3_prime_UTR_variant,,ENST00000493950,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,; T ENST00000397944 Transcript stop_gained 1379/5325 1303/5004 435/1667 E/* Gag/Tag 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 10/36 SMART_domains:SM00230 HIGH 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -19.72253 1 1 1 1 0 T 4 4 7 146685820 146685820 G T 1 0 0 0 0 0 1 0 0 351 943 33 2 2 ADGB 6 146685820 Nonsense_Mutation SNP G C3L-00080_T 251116 146685820 24120159 277 2375 ULBP1 0 . GRCh38 6 149968818 149968818 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.297T>C p.= p.D99D ENST00000229708 2/5 205 172 33 164 164 0 strelka-varscan-mutect ULBP1,synonymous_variant,p.=,ENST00000229708,NM_025218.2; C ENST00000229708 Transcript synonymous_variant 340/3142 297/735 99/244 D gaT/gaC 1 1 ULBP1 HGNC HGNC:14893 protein_coding YES CCDS5223.1 ENSP00000229708 Q9BZM6 UPI000006D47B NM_025218.2 2/5 Gene3D:3.30.500.10,Pfam_domain:PF00129,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF170,Superfamily_domains:SSF54452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 149968818 149968818 T C 1 0 0 0 0 0 0 0 1 17496 1490 52 5 5 ULBP1 6 149968818 Silent SNP T C3L-00080_T 3282998 149968818 20837161 278 2376 MTHFD1L 0 . GRCh38 6 151009887 151009887 + Missense_Mutation SNP G G T rs539434475 C3L-00080_T C3L-00080_N G G c.2197G>T p.Gly733Cys p.G733C ENST00000611279 21/28 267 211 56 231 231 0 strelka-mutect MTHFD1L,missense_variant,p.Gly732Cys,ENST00000367321,NM_015440.4;MTHFD1L,missense_variant,p.Gly733Cys,ENST00000611279,NM_001242767.1;MTHFD1L,missense_variant,p.Gly667Cys,ENST00000618312,NM_001242768.1;MTHFD1L,upstream_gene_variant,,ENST00000420192,;MTHFD1L,non_coding_transcript_exon_variant,,ENST00000478643,; T ENST00000611279 Transcript missense_variant 2341/3475 2197/2940 733/979 G/C Ggc/Tgc rs539434475 1 1 MTHFD1L HGNC HGNC:21055 protein_coding YES CCDS75535.1 ENSP00000478253 B7ZM99 UPI000166C73D NM_001242767.1 deleterious(0) 21/28 Low_complexity_(Seg):seg,HAMAP:MF_01543,hmmpanther:PTHR10025,hmmpanther:PTHR10025:SF14,Gene3D:3.40.50.300,Pfam_domain:PF01268,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs539434475 . 0 207 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 T 3 4 7 151009887 151009887 G T 1 0 0 0 0 1 0 0 0 9917 1116 39 1 1 MTHFD1L 6 151009887 Missense_Mutation SNP G C3L-00080_T 1041069 151009887 19796092 279 2377 SYNE1 0 . GRCh38 6 152447511 152447511 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.3616G>C p.Glu1206Gln p.E1206Q ENST00000367255 29/146 296 249 47 248 248 0 strelka-varscan-mutect SYNE1,missense_variant,p.Glu1206Gln,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Glu1213Gln,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Glu1255Gln,ENST00000341594,;SYNE1,missense_variant,p.Glu1196Gln,ENST00000367248,;SYNE1,missense_variant,p.Glu1206Gln,ENST00000367253,;SYNE1,missense_variant,p.Glu1206Gln,ENST00000413186,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; G ENST00000367255 Transcript missense_variant 4218/27748 3616/26394 1206/8797 E/Q Gag/Cag 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 29/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 152447511 152447511 C G 1 0 0 0 0 1 0 0 0 15837 835 29 4 4 SYNE1 6 152447511 Missense_Mutation SNP C C3L-00080_T 1437624 152447511 18358468 280 2378 SYNE1 0 . GRCh38 6 152511575 152511575 + Nonsense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.326C>G p.Ser109Ter p.S109* ENST00000423061 6/146 145 131 14 190 190 0 strelka-varscan-mutect SYNE1,stop_gained,p.Ser109Ter,ENST00000423061,NM_033071.3;SYNE1,stop_gained,p.Ser109Ter,ENST00000367248,;SYNE1,stop_gained,p.Ser92Ter,ENST00000610489,;SYNE1,intron_variant,,ENST00000367255,NM_182961.3;SYNE1,intron_variant,,ENST00000341594,;SYNE1,intron_variant,,ENST00000367253,;SYNE1,intron_variant,,ENST00000413186,;SYNE1,intron_variant,,ENST00000537750,;SYNE1,intron_variant,,ENST00000466159,;SYNE1,intron_variant,,ENST00000461872,; C ENST00000423061 Transcript stop_gained 763/27436 326/26250 109/8749 S/* tCa/tGa 1 -1 SYNE1 HGNC HGNC:17089 protein_coding CCDS5235.1 ENSP00000396024 A0A0C4DG40 UPI0000110103 NM_033071.3 6/146 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 7 152511575 152511575 G C 1 0 0 0 0 0 1 0 0 15837 1304 45 4 4 SYNE1 6 152511575 Nonsense_Mutation SNP G C3L-00080_T 64064 152511575 18294404 281 2379 LPA 0 . GRCh38 6 160531795 160531795 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6057G>T p.Lys2019Asn p.K2019N ENST00000316300 39/39 378 305 73 335 335 0 strelka-varscan-mutect LPA,missense_variant,p.Lys2019Asn,ENST00000316300,NM_005577.2; A ENST00000316300 Transcript missense_variant 6102/6414 6057/6123 2019/2040 K/N aaG/aaT 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 deleterious(0.01) 39/39 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 160531795 160531795 C A 1 0 0 0 0 1 0 0 0 8806 796 28 2 2 LPA 6 160531795 Missense_Mutation SNP C C3L-00080_T 8020220 160531795 10274184 282 2380 C6orf118 0 . GRCh38 6 165298053 165298053 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.985G>C p.Ala329Pro p.A329P ENST00000230301 5/9 112 61 51 90 90 0 strelka-varscan-mutect C6orf118,missense_variant,p.Ala329Pro,ENST00000230301,NM_144980.3;C6orf118,upstream_gene_variant,,ENST00000494696,; G ENST00000230301 Transcript missense_variant 1006/1812 985/1410 329/469 A/P Gcg/Ccg 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 tolerated(0.06) 5/9 hmmpanther:PTHR34916,Pfam_domain:PF15739 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 165298053 165298053 C G 1 0 0 0 0 1 0 0 0 2115 739 26 4 4 C6orf118 6 165298053 Missense_Mutation SNP C C3L-00080_T 4766258 165298053 5507926 283 2381 KIF25 0 . GRCh38 6 168030803 168030803 + Silent SNP G G T rs775332458 C3L-00080_T C3L-00080_N G G c.123G>T p.= p.A41A ENST00000443060 4/10 93 60 33 83 83 0 strelka-varscan-mutect KIF25,synonymous_variant,p.=,ENST00000443060,;KIF25,synonymous_variant,p.=,ENST00000354419,NM_030615.2;KIF25,synonymous_variant,p.=,ENST00000351261,NM_005355.3;KIF25,upstream_gene_variant,,ENST00000496008,;KIF25,downstream_gene_variant,,ENST00000515361,;KIF25,non_coding_transcript_exon_variant,,ENST00000504593,; T ENST00000443060 Transcript synonymous_variant 514/1613 123/1155 41/384 A gcG/gcT rs775332458 1 1 KIF25 HGNC HGNC:6390 protein_coding YES CCDS5305.1 ENSP00000388878 Q9UIL4 UPI000012DDAB 4/10 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF421,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs775332458 . 0 207 0 3 0 0 0 0 -20 0.9999989 1 1 1 0 T 2 4 7 168030803 168030803 G T 1 0 0 0 0 0 0 0 1 8158 1103 39 1 1 KIF25 6 168030803 Silent SNP G C3L-00080_T 2732750 168030803 2775176 284 2382 UNCX 0 . GRCh38 7 1236585 1236585 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.1204C>T p.= p.L402L ENST00000316333 3/3 79 64 15 44 44 0 strelka-varscan-mutect UNCX,synonymous_variant,p.=,ENST00000316333,NM_001080461.1; T ENST00000316333 Transcript synonymous_variant 1315/2048 1204/1596 402/531 L Ctg/Ttg 1 1 UNCX HGNC HGNC:33194 protein_coding YES CCDS34583.1 ENSP00000314480 A6NJT0 UPI0000D61BE6 NM_001080461.1 3/3 LOW 1 SNV 1 1 PASS rs1391348357 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 1236585 1236585 C T 1 0 0 0 0 0 0 0 1 17524 680 24 3 3 UNCX 7 1236585 Silent SNP C C3L-00080_T 1236585 158109388 285 2383 FOXK1 0 . GRCh38 7 4682585 4682585 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.277G>T p.Ala93Ser p.A93S ENST00000328914 1/9 40 26 14 14 14 0 strelka-varscan-mutect FOXK1,missense_variant,p.Ala93Ser,ENST00000328914,NM_001037165.1; T ENST00000328914 Transcript missense_variant 277/11181 277/2202 93/733 A/S Gcg/Tcg 1 1 FOXK1 HGNC HGNC:23480 protein_coding YES CCDS34591.1 ENSP00000328720 P85037 UPI00004158EB NM_001037165.1 tolerated_low_confidence(1) 1/9 Low_complexity_(Seg):seg,Superfamily_domains:SSF49879 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 4682585 4682585 G T 1 0 0 0 0 1 0 0 0 5877 1087 38 1 1 FOXK1 7 4682585 Missense_Mutation SNP G C3L-00080_T 3446000 4682585 154663388 286 2384 FAM220A 0 . GRCh38 7 6331086 6331086 + Silent SNP C C G rs200129623 C3L-00080_T C3L-00080_N C C c.69G>C p.= p.S23S ENST00000313324 2/2 248 202 46 236 236 0 strelka-varscan-mutect FAM220A,synonymous_variant,p.=,ENST00000313324,NM_001037163.1;FAM220A,synonymous_variant,p.=,ENST00000616824,;FAM220A,synonymous_variant,p.=,ENST00000530143,;FAM220A,synonymous_variant,p.=,ENST00000524898,;FAM220A,downstream_gene_variant,,ENST00000578372,;FAM220A,downstream_gene_variant,,ENST00000533877,; G ENST00000313324 Transcript synonymous_variant 537/2214 69/780 23/259 S tcG/tcC rs200129623,COSM4682946 1 -1 FAM220A HGNC HGNC:22422 protein_coding YES CCDS34599.1 ENSP00000317289 Q7Z4H9 UPI000013F4F0 NM_001037163.1 2/2 Pfam_domain:PF15487,hmmpanther:PTHR31980,hmmpanther:PTHR31980:SF2 0,1 LOW 1 SNV 1 0,1 1 PASS rs200129623 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 6331086 6331086 C G 1 0 0 0 0 0 0 0 1 5413 639 23 4 4 FAM220A 7 6331086 Silent SNP C C3L-00080_T 1648501 6331086 153014887 287 2385 ABCB5 0 . GRCh38 7 20643191 20643191 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.322C>T p.= p.L108L ENST00000404938 6/28 85 59 26 98 98 0 strelka-varscan-mutect ABCB5,synonymous_variant,p.=,ENST00000404938,NM_001163941.1;ABCB5,upstream_gene_variant,,ENST00000258738,NM_178559.5;ABCB5,upstream_gene_variant,,ENST00000443026,NM_001163942.1;ABCB5,upstream_gene_variant,,ENST00000406935,NM_001163993.2;ABCB5,upstream_gene_variant,,ENST00000477094,;AC002486.3,upstream_gene_variant,,ENST00000435098,; T ENST00000404938 Transcript synonymous_variant 974/5811 322/3774 108/1257 L Ctg/Ttg 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 6/28 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999958 1 1 1 0 T 2 4 7 20643191 20643191 C T 1 0 0 0 0 0 0 0 1 48 680 24 3 3 ABCB5 7 20643191 Silent SNP C C3L-00080_T 14312105 20643191 138702782 288 2386 DNAH11 0 . GRCh38 7 21773934 21773934 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.9271G>T p.Glu3091Ter p.E3091* ENST00000409508 56/82 113 81 32 96 96 0 strelka-varscan-mutect DNAH11,stop_gained,p.Glu3091Ter,ENST00000409508,NM_001277115.1;DNAH11,stop_gained,p.Glu3098Ter,ENST00000328843,;DNAH11,stop_gained,p.Glu3098Ter,ENST00000620169,; T ENST00000409508 Transcript stop_gained 9302/14167 9271/13551 3091/4516 E/* Gag/Tag 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 56/82 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Superfamily_domains:SSF52540 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 21773934 21773934 G T 1 0 0 0 0 0 1 0 0 4413 1291 45 2 2 DNAH11 7 21773934 Nonsense_Mutation SNP G C3L-00080_T 1130743 21773934 137572039 289 2387 MPP6 0 . GRCh38 7 24665613 24665613 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.809G>T p.Ser270Ile p.S270I ENST00000222644 7/12 198 155 43 163 163 0 strelka-varscan-mutect MPP6,missense_variant,p.Ser270Ile,ENST00000222644,NM_001303037.1,NM_016447.3;MPP6,missense_variant,p.Ser270Ile,ENST00000396475,;MPP6,missense_variant,p.Ser158Ile,ENST00000409761,;MPP6,missense_variant,p.Ser270Ile,ENST00000430180,;MPP6,non_coding_transcript_exon_variant,,ENST00000472674,;MPP6,upstream_gene_variant,,ENST00000464384,; T ENST00000222644 Transcript missense_variant 1059/8452 809/1623 270/540 S/I aGc/aTc 1 1 MPP6 HGNC HGNC:18167 protein_coding YES CCDS5388.1 ENSP00000222644 Q9NZW5 A0A024RA25 UPI0000001C1B NM_001303037.1,NM_016447.3 tolerated(0.08) 7/12 Gene3D:2.30.30.40,Pfam_domain:PF07653,PROSITE_profiles:PS50002,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF44,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 24665613 24665613 G T 1 0 0 0 0 1 0 0 0 9704 971 34 2 2 MPP6 7 24665613 Missense_Mutation SNP G C3L-00080_T 2891679 24665613 134680360 290 2388 OSBPL3 0 . GRCh38 7 24849121 24849121 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1214C>T p.Ser405Phe p.S405F ENST00000313367 12/23 211 152 59 174 174 0 strelka-varscan-mutect OSBPL3,missense_variant,p.Ser405Phe,ENST00000313367,NM_015550.3;OSBPL3,missense_variant,p.Ser374Phe,ENST00000396431,NM_145320.2;OSBPL3,intron_variant,,ENST00000396429,NM_145321.2;OSBPL3,intron_variant,,ENST00000409069,NM_145322.2;OSBPL3,missense_variant,p.Ser374Phe,ENST00000409863,;OSBPL3,missense_variant,p.Ser405Phe,ENST00000409452,;OSBPL3,non_coding_transcript_exon_variant,,ENST00000461835,;OSBPL3,intron_variant,,ENST00000409759,;OSBPL3,intron_variant,,ENST00000409555,; A ENST00000313367 Transcript missense_variant 1666/6760 1214/2664 405/887 S/F tCt/tTt 1 -1 OSBPL3 HGNC HGNC:16370 protein_coding YES CCDS5390.1 ENSP00000315410 Q9H4L5 UPI0000001244 NM_015550.3 deleterious(0) 12/23 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 24849121 24849121 G A 1 0 0 0 0 1 0 0 0 11345 942 33 3 3 OSBPL3 7 24849121 Missense_Mutation SNP G C3L-00080_T 183508 24849121 134496852 291 2389 HOXA3 0 . GRCh38 7 27110213 27110213 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.428G>A p.Ser143Asn p.S143N ENST00000612286 3/4 335 276 59 204 204 0 strelka-varscan-mutect HOXA3,missense_variant,p.Ser143Asn,ENST00000612286,NM_153631.2;HOXA3,missense_variant,p.Ser143Asn,ENST00000396352,NM_030661.4;HOXA3,missense_variant,p.Ser143Asn,ENST00000317201,;HOXA3,downstream_gene_variant,,ENST00000522788,;HOXA3,downstream_gene_variant,,ENST00000522456,;HOXA-AS2,intron_variant,,ENST00000518088,;HOXA-AS2,upstream_gene_variant,,ENST00000522193,;HOXA3,downstream_gene_variant,,ENST00000521401,; T ENST00000612286 Transcript missense_variant 767/3396 428/1332 143/443 S/N aGc/aAc 1 -1 HOXA3 HGNC HGNC:5104 protein_coding YES CCDS5404.1 ENSP00000484411 O43365 A0A024RA33 UPI000012CF22 NM_153631.2 tolerated(0.21) 3/4 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF137 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 27110213 27110213 C T 1 0 0 0 0 1 0 0 0 7187 797 28 3 3 HOXA3 7 27110213 Missense_Mutation SNP C C3L-00080_T 2261092 27110213 132235760 292 2390 ADCYAP1R1 0 . GRCh38 7 31086486 31086486 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.772A>T p.Thr258Ser p.T258S ENST00000614107 10/17 226 198 28 157 157 0 strelka-varscan-mutect ADCYAP1R1,missense_variant,p.Thr258Ser,ENST00000614107,NM_001199635.1,NM_001199636.1;ADCYAP1R1,missense_variant,p.Thr258Ser,ENST00000304166,NM_001118.4;ADCYAP1R1,missense_variant,p.Thr237Ser,ENST00000409363,NM_001199637.1;ADCYAP1R1,missense_variant,p.Thr258Ser,ENST00000409489,;ADCYAP1R1,missense_variant,p.Thr258Ser,ENST00000396211,;ADCYAP1R1,upstream_gene_variant,,ENST00000436116,; T ENST00000614107 Transcript missense_variant 1061/6575 772/1491 258/496 T/S Acc/Tcc 1 1 ADCYAP1R1 HGNC HGNC:242 protein_coding YES CCDS56480.1 ENSP00000483721 P41586 UPI0000DA58BA NM_001199635.1,NM_001199636.1 tolerated(1) 10/17 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF228,Superfamily_domains:SSF81321 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 31086486 31086486 A T 1 0 0 0 0 1 0 0 0 347 275 10 4 4 ADCYAP1R1 7 31086486 Missense_Mutation SNP A C3L-00080_T 3976273 31086486 128259487 293 2391 GPR141 0 . GRCh38 7 37740483 37740483 + Silent SNP C C T rs368456046 C3L-00080_T C3L-00080_N C C c.90C>T p.= p.G30G ENST00000447769 4/4 146 109 37 81 81 0 strelka-varscan-mutect GPR141,synonymous_variant,p.=,ENST00000447769,;GPR141,synonymous_variant,p.=,ENST00000334425,NM_181791.1;GPR141,synonymous_variant,p.=,ENST00000450180,;EPDR1,intron_variant,,ENST00000476620,;GPR141,intron_variant,,ENST00000461610,; T ENST00000447769 Transcript synonymous_variant 379/1270 90/918 30/305 G ggC/ggT rs368456046,COSM161345 1 1 GPR141 HGNC HGNC:19997 protein_coding YES CCDS5451.1 ENSP00000390410 Q7Z602 UPI000004B92B 4/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF0,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW 1 SNV 3 0,1 1 PASS rs368456046 . 0 202 0 6 2 0 0 0 -20 0.9576441 1 1 1 0 T 2 4 7 37740483 37740483 C T 1 0 0 0 0 0 0 0 1 6535 755 27 1 1 GPR141 7 37740483 Silent SNP C C3L-00080_T 6653997 37740483 121605490 294 2392 ABCA13 0 . GRCh38 7 48229915 48229915 + Silent SNP G G A rs754765359 C3L-00080_T C3L-00080_N G G c.723G>A p.= p.S241S ENST00000435803 7/62 175 131 44 149 149 0 strelka-varscan-mutect ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000417403,; A ENST00000435803 Transcript synonymous_variant 747/17184 723/15177 241/5058 S tcG/tcA rs754765359,COSM3881460,COSM3881461 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 7/62 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs754765359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 48229915 48229915 G A 1 0 0 0 0 0 0 0 1 35 1045 37 1 1 ABCA13 7 48229915 Silent SNP G C3L-00080_T 10489432 48229915 111116058 295 2393 ZNF479 0 . GRCh38 7 57119852 57119852 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1563C>A p.Tyr521Ter p.Y521* ENST00000331162 5/5 167 122 45 161 161 0 strelka-varscan-mutect ZNF479,stop_gained,p.Tyr521Ter,ENST00000331162,NM_033273.2;ZNF479,stop_gained,p.Tyr521Ter,ENST00000319636,;ZNF479,stop_gained,p.Tyr409Ter,ENST00000620639,; T ENST00000331162 Transcript stop_gained 1834/2072 1563/1575 521/524 Y/* taC/taA 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 5/5 Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 57119852 57119852 G T 1 0 0 0 0 0 1 0 0 18505 1372 48 2 2 ZNF479 7 57119852 Nonsense_Mutation SNP G C3L-00080_T 8889937 57119852 102226121 296 2394 ZNF727 0 . GRCh38 7 64077540 64077552 + Frame_Shift_Del DEL AGAAAATTTTTAG AGAAAATTTTTAG - novel C3L-00080_T C3L-00080_N AGAAAATTTTTAG AGAAAATTTTTAG c.491_503delAGAAAATTTTTAG p.Lys164ThrfsTer198 p.K164Tfs*198 ENST00000456806 4/4 99 85 14 166 166 0 sindel-varindel-pindel ZNF727,frameshift_variant,p.Lys164ThrfsTer198,ENST00000456806,NM_001159522.1; - ENST00000456806 Transcript frameshift_variant 670-682/1679 491-503/1500 164-168/499 KKIFS/X aAGAAAATTTTTAGc/ac 1 1 ZNF727 HGNC HGNC:22785 protein_coding YES CCDS55113.1 ENSP00000485448 A8MUV8 UPI0001A23134 NM_001159522.1 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF98,hmmpanther:PTHR24384,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 deletion 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 64077540 64077540 AGAAAATTTTTAG - 1 0 1 0 1 0 0 0 0 18701 72 3 0 0 ZNF727 7 64077540 Frame_Shift_Del DEL AGAAAATTTTTAG C3L-00080_T 6957688 64077540 95268433 297 2395 FZD9 0 . GRCh38 7 73435106 73435106 + Missense_Mutation SNP G G A rs542138331 C3L-00080_T C3L-00080_N G G c.1099G>A p.Ala367Thr p.A367T ENST00000344575 1/1 72 54 18 109 109 0 strelka-varscan-mutect FZD9,missense_variant,p.Ala367Thr,ENST00000344575,NM_003508.2; A ENST00000344575 Transcript missense_variant 1324/2338 1099/1776 367/591 A/T Gcg/Acg rs542138331 1 1 FZD9 HGNC HGNC:4047 protein_coding YES CCDS5548.1 ENSP00000345785 O00144 UPI000004EC98 NM_003508.2 deleterious(0) 1/1 Pfam_domain:PF01534,Prints_domain:PR00489,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF79,SMART_domains:SM01330,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs542138331 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 73435106 73435106 G A 1 0 0 0 0 1 0 0 0 6008 1087 38 1 1 FZD9 7 73435106 Missense_Mutation SNP G C3L-00080_T 9357566 73435106 85910867 298 2396 SSC4D 0 . GRCh38 7 76395269 76395269 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.930G>A p.Trp310Ter p.W310* ENST00000275560 7/11 144 97 47 230 230 0 strelka-varscan-mutect SSC4D,stop_gained,p.Trp310Ter,ENST00000275560,NM_080744.1;ZP3,upstream_gene_variant,,ENST00000336517,NM_007155.5;SSC4D,upstream_gene_variant,,ENST00000492979,; T ENST00000275560 Transcript stop_gained 1278/2801 930/1728 310/575 W/* tgG/tgA 1 -1 SSC4D HGNC HGNC:14461 protein_coding YES CCDS5585.1 ENSP00000275560 Q8WTU2 UPI000006D197 NM_080744.1 7/11 hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF276 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 76395269 76395269 C T 1 0 0 0 0 0 1 0 0 15557 740 26 3 3 SSC4D 7 76395269 Nonsense_Mutation SNP C C3L-00080_T 2960163 76395269 82950704 299 2397 HGF 0 . GRCh38 7 81729604 81729604 + Splice_Site SNP C C A novel C3L-00080_T C3L-00080_N C C c.1040+1G>T p.X347_splice ENST00000222390 291 259 32 293 293 0 strelka-varscan-mutect HGF,splice_donor_variant,,ENST00000222390,NM_000601.4;HGF,splice_donor_variant,,ENST00000457544,NM_001010932.1; A ENST00000222390 Transcript splice_donor_variant -/5989 1040/2187 347/728 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 8/17 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 7 81729604 81729604 C A 1 0 0 0 0 0 0 1 0 6969 579 20 2 2 HGF 7 81729604 Splice_Site SNP C C3L-00080_T 5334335 81729604 77616369 300 2398 7 2 HGF 0 . GRCh38 7 81729606 81729606 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.1039A>C p.Lys347Gln p.K347Q ENST00000222390 8/18 292 259 33 288 287 1 strelka-varscan-mutect HGF,missense_variant,p.Lys347Gln,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Lys342Gln,ENST00000457544,NM_001010932.1; G ENST00000222390 Transcript missense_variant,splice_region_variant 1266/5989 1039/2187 347/728 K/Q Aag/Cag 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 deleterious(0.02) 8/18 PROSITE_profiles:PS50070,hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 81729606 81729606 T G 1 0 0 0 0 1 0 0 0 6969 1826 63 5 5 HGF 7 81729606 Missense_Mutation SNP T C3L-00080_T 2 81729606 77616367 301 2399 7 2 RUNDC3B 0 . GRCh38 7 87829979 87829979 + Nonsense_Mutation SNP C C G rs780246287 C3L-00080_T C3L-00080_N C C c.1371C>G p.Tyr457Ter p.Y457* ENST00000338056 12/12 67 50 17 71 71 0 strelka-varscan-mutect RUNDC3B,stop_gained,p.Tyr457Ter,ENST00000338056,NM_138290.2;RUNDC3B,stop_gained,p.Tyr440Ter,ENST00000394654,NM_001134405.1;RUNDC3B,stop_gained,p.Tyr391Ter,ENST00000493037,NM_001134406.1;SLC25A40,downstream_gene_variant,,ENST00000341119,NM_018843.3;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000312373,; G ENST00000338056 Transcript stop_gained 1782/4099 1371/1422 457/473 Y/* taC/taG rs780246287 1 1 RUNDC3B HGNC HGNC:30286 protein_coding YES CCDS5609.1 ENSP00000337732 Q96NL0 UPI0000071425 NM_138290.2 12/12 hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835 HIGH SNV 2 1 PASS rs780246287 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 7 87829979 87829979 C G 1 0 0 0 0 0 1 0 0 14006 518 18 4 4 RUNDC3B 7 87829979 Nonsense_Mutation SNP C C3L-00080_T 6100373 87829979 71515994 302 2400 CDK6 0 . GRCh38 7 92774788 92774788 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.277A>C p.Lys93Gln p.K93Q ENST00000265734 3/8 250 221 29 214 214 0 strelka-varscan-mutect CDK6,missense_variant,p.Lys93Gln,ENST00000265734,NM_001259.6;CDK6,missense_variant,p.Lys93Gln,ENST00000424848,NM_001145306.1; G ENST00000265734 Transcript missense_variant 689/11612 277/981 93/326 K/Q Aaa/Caa 1 -1 CDK6 HGNC HGNC:1777 protein_coding YES CCDS5628.1 ENSP00000265734 Q00534 UPI00001108FA NM_001259.6 tolerated(0.41) 3/8 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF130,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 92774788 92774788 T G 1 0 0 0 0 1 0 0 0 2852 1821 63 5 5 CDK6 7 92774788 Missense_Mutation SNP T C3L-00080_T 4944809 92774788 66571185 303 2401 GNG11 0 . GRCh38 7 93926205 93926205 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.211G>T p.Val71Phe p.V71F ENST00000248564 2/2 40 20 20 49 49 0 strelka-varscan-mutect GNG11,missense_variant,p.Val71Phe,ENST00000248564,NM_004126.3; T ENST00000248564 Transcript missense_variant 650/3055 211/222 71/73 V/F Gtt/Ttt 1 1 GNG11 HGNC HGNC:4403 protein_coding YES CCDS5634.1 ENSP00000248564 P61952 Q53Y01 UPI0000001AD4 NM_004126.3 deleterious(0.03) 2/2 PROSITE_profiles:PS50058,hmmpanther:PTHR13809:SF1,hmmpanther:PTHR13809,Gene3D:4.10.260.10,Pfam_domain:PF00631,SMART_domains:SM01224,SMART_domains:SM00224 MODERATE 1 SNV 1 1 PASS . . 1 201 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 7 93926205 93926205 G T 1 0 0 0 0 1 0 0 0 6403 1377 48 2 2 GNG11 7 93926205 Missense_Mutation SNP G C3L-00080_T 1151417 93926205 65419768 304 2402 TRRAP 0 . GRCh38 7 98984134 98984134 + Missense_Mutation SNP A A T C3L-00080_T C3L-00080_N A A c.9076A>T p.Ser3026Cys p.S3026C ENST00000359863 60/72 73 61 12 40 40 0 strelka-varscan-mutect TRRAP,missense_variant,p.Ser3026Cys,ENST00000359863,NM_001244580.1;TRRAP,missense_variant,p.Ser2997Cys,ENST00000628380,;TRRAP,missense_variant,p.Ser2997Cys,ENST00000355540,NM_003496.3;TRRAP,missense_variant,p.Ser2997Cys,ENST00000446306,;TRRAP,missense_variant,p.Ser2737Cys,ENST00000456197,; T ENST00000359863 Transcript missense_variant 9285/12677 9076/11580 3026/3859 S/C Agt/Tgt COSM1187374,COSM1187375 1 1 TRRAP HGNC HGNC:12347 protein_coding YES CCDS59066.1 ENSP00000352925 Q9Y4A5 UPI00004575B4 NM_001244580.1 deleterious(0.02) 60/72 Pfam_domain:PF02259,PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF1 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 98984134 98984134 A T 1 0 0 0 0 1 0 0 0 17107 188 7 4 4 TRRAP 7 98984134 Missense_Mutation SNP A C3L-00080_T 5057929 98984134 60361839 305 2403 ZAN 0 . GRCh38 7 100750784 100750784 + Missense_Mutation SNP G G C rs758826727 C3L-00080_T C3L-00080_N G G c.1409G>C p.Gly470Ala p.G470A ENST00000613979 12/48 131 72 59 106 106 0 varscan-mutect ZAN,missense_variant,p.Gly470Ala,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Gly470Ala,ENST00000618565,;ZAN,missense_variant,p.Gly470Ala,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Gly470Ala,ENST00000546292,;ZAN,missense_variant,p.Gly470Ala,ENST00000542585,;ZAN,missense_variant,p.Gly470Ala,ENST00000538115,;ZAN,missense_variant,p.Gly470Ala,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; C ENST00000613979 Transcript missense_variant 1574/8669 1409/8439 470/2812 G/A gGa/gCa rs758826727,COSM3630912 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 tolerated(0.45) 12/48 Pfam_domain:PF00629,PROSITE_profiles:PS50060,Low_complexity_(Seg):seg,SMART_domains:SM00137,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758826727 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 100750784 100750784 G C 1 0 0 0 0 1 0 0 0 18074 1174 41 4 4 ZAN 7 100750784 Missense_Mutation SNP G C3L-00080_T 1766650 100750784 58595189 306 2404 ZAN 0 . GRCh38 7 100764127 100764127 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.4198T>A p.Ser1400Thr p.S1400T ENST00000613979 22/48 142 120 22 119 119 0 strelka-varscan-mutect ZAN,missense_variant,p.Ser1400Thr,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Ser1400Thr,ENST00000618565,;ZAN,missense_variant,p.Ser1400Thr,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Ser1400Thr,ENST00000546292,;ZAN,missense_variant,p.Ser1400Thr,ENST00000542585,;ZAN,missense_variant,p.Ser1400Thr,ENST00000538115,;ZAN,missense_variant,p.Ser1400Thr,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; A ENST00000613979 Transcript missense_variant 4363/8669 4198/8439 1400/2812 S/T Tcc/Acc 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 deleterious(0.02) 22/48 Pfam_domain:PF08742,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221,SMART_domains:SM00832 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 100764127 100764127 T A 1 0 0 0 0 1 0 0 0 18074 1667 58 4 4 ZAN 7 100764127 Missense_Mutation SNP T C3L-00080_T 13343 100764127 58581846 307 2405 SLC12A9 0 . GRCh38 7 100859969 100859969 + Silent SNP G G A rs140502011 C3L-00080_T C3L-00080_N G G c.1062G>A p.= p.A354A ENST00000354161 8/14 254 143 111 191 191 0 strelka-varscan-mutect SLC12A9,synonymous_variant,p.=,ENST00000354161,NM_020246.3;SLC12A9,synonymous_variant,p.=,ENST00000540482,NM_001267812.1;SLC12A9,synonymous_variant,p.=,ENST00000415287,NM_001267814.1;SLC12A9,synonymous_variant,p.=,ENST00000418037,;SLC12A9,synonymous_variant,p.=,ENST00000416675,;SLC12A9,downstream_gene_variant,,ENST00000434158,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475623,;SLC12A9,upstream_gene_variant,,ENST00000482184,;SLC12A9,downstream_gene_variant,,ENST00000461016,;SLC12A9,3_prime_UTR_variant,,ENST00000448342,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000487651,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000497958,;SLC12A9,downstream_gene_variant,,ENST00000462106,; A ENST00000354161 Transcript synonymous_variant 1187/3273 1062/2745 354/914 A gcG/gcA rs140502011,COSM3698053,COSM3698054 1 1 SLC12A9 HGNC HGNC:17435 protein_coding YES CCDS5707.1 ENSP00000275730 Q9BXP2 UPI000006CD28 NM_020246.3 8/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF52,Pfam_domain:PF00324 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs140502011 . 0 206 2 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 7 100859969 100859969 G A 1 0 0 0 0 0 0 0 1 14655 1074 38 1 1 SLC12A9 7 100859969 Silent SNP G C3L-00080_T 95842 100859969 58486004 308 2406 MUC3A 0 . GRCh38 7 100957502 100957502 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.5723C>T p.Thr1908Ile p.T1908I ENST00000379458 2/12 76 66 10 36 36 0 varscan-mutect MUC3A,missense_variant,p.Thr1908Ile,ENST00000379458,NM_005960.1;MUC3A,missense_variant,p.Thr1908Ile,ENST00000483366,;MUC3A,upstream_gene_variant,,ENST00000414964,; T ENST00000379458 Transcript missense_variant 5793/11226 5723/9972 1908/3323 T/I aCt/aTt 1 1 MUC3A HGNC HGNC:7513 protein_coding YES CCDS78262.1 ENSP00000368771 Q02505 UPI000455B941 NM_005960.1 deleterious_low_confidence(0) 2/12 MODERATE 1 SNV 5 1 PASS . . 0 162 41 7 0 0 0 0 -16.48264 0.4457805 0 1 0 0 T 3 4 7 100957502 100957502 C T 1 0 0 0 0 1 0 0 0 9976 565 20 3 3 MUC3A 7 100957502 Missense_Mutation SNP C C3L-00080_T 97533 100957502 58388471 309 2407 MUC17 0 . GRCh38 7 101053406 101053406 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.13333T>A p.Phe4445Ile p.F4445I ENST00000306151 11/13 290 249 41 223 223 0 strelka-varscan-mutect MUC17,missense_variant,p.Phe4445Ile,ENST00000306151,NM_001040105.1;RN7SKP54,upstream_gene_variant,,ENST00000410704,;MUC17,3_prime_UTR_variant,,ENST00000379439,;MUC17,non_coding_transcript_exon_variant,,ENST00000497859,; A ENST00000306151 Transcript missense_variant 13397/14247 13333/13482 4445/4493 F/I Ttc/Atc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 11/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 101053406 101053406 T A 1 0 0 0 0 1 0 0 0 9973 1609 56 4 4 MUC17 7 101053406 Missense_Mutation SNP T C3L-00080_T 95904 101053406 58292567 310 2408 LRWD1 0 . GRCh38 7 102466254 102466254 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.416G>C p.Arg139Pro p.R139P ENST00000292616 3/15 121 69 52 94 94 0 strelka-varscan-mutect LRWD1,missense_variant,p.Arg139Pro,ENST00000292616,NM_001317721.1,NM_152892.1;LRWD1,5_prime_UTR_variant,,ENST00000463739,;ALKBH4,upstream_gene_variant,,ENST00000292566,NM_017621.3;LRWD1,upstream_gene_variant,,ENST00000468175,;LRWD1,downstream_gene_variant,,ENST00000626402,;LRWD1,downstream_gene_variant,,ENST00000582533,;LRWD1,missense_variant,p.Arg116Pro,ENST00000485808,;LRWD1,3_prime_UTR_variant,,ENST00000476270,;LRWD1,3_prime_UTR_variant,,ENST00000464107,;LRWD1,non_coding_transcript_exon_variant,,ENST00000473880,;ALKBH4,upstream_gene_variant,,ENST00000490528,;LRWD1,upstream_gene_variant,,ENST00000485417,;ALKBH4,upstream_gene_variant,,ENST00000498283,; C ENST00000292616 Transcript missense_variant 568/2215 416/1944 139/647 R/P cGg/cCg 1 1 LRWD1 HGNC HGNC:21769 protein_coding YES CCDS34715.1 ENSP00000292616 Q9UFC0 A0A140VJD0 UPI0000071D2E NM_001317721.1,NM_152892.1 deleterious(0.03) 3/15 hmmpanther:PTHR24370:SF10,hmmpanther:PTHR24370 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999992 1 1 1 0 C 3 2 7 102466254 102466254 G C 1 0 0 0 0 1 0 0 0 8953 1116 39 4 4 LRWD1 7 102466254 Missense_Mutation SNP G C3L-00080_T 1412848 102466254 56879719 311 2409 RELN 0 . GRCh38 7 103566722 103566722 + Silent SNP G G C novel C3L-00080_T C3L-00080_N G G c.4626C>G p.= p.L1542L ENST00000428762 32/65 292 194 98 276 276 0 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; C ENST00000428762 Transcript synonymous_variant 4786/11571 4626/10383 1542/3460 L ctC/ctG 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 32/65 hmmpanther:PTHR11841 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 103566722 103566722 G C 1 0 0 0 0 0 0 0 1 13390 929 33 4 4 RELN 7 103566722 Silent SNP G C3L-00080_T 1100468 103566722 55779251 312 2410 LAMB4 0 . GRCh38 7 108055671 108055671 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.3716G>A p.Gly1239Glu p.G1239E ENST00000388781 25/34 118 93 25 130 130 0 strelka-varscan-mutect LAMB4,missense_variant,p.Gly1239Glu,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Gly1239Glu,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Gly265Glu,ENST00000422975,; T ENST00000388781 Transcript missense_variant 3800/5858 3716/5286 1239/1761 G/E gGg/gAg 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 tolerated(1) 25/34 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 108055671 108055671 C T 1 0 0 0 0 1 0 0 0 8517 623 22 3 3 LAMB4 7 108055671 Missense_Mutation SNP C C3L-00080_T 4488949 108055671 51290302 313 2411 ASZ1 0 . GRCh38 7 117427366 117427366 + Missense_Mutation SNP C C A rs145791114 C3L-00080_T C3L-00080_N C C c.95G>T p.Arg32Leu p.R32L ENST00000284629 1/13 199 161 38 180 180 0 strelka-varscan-mutect ASZ1,missense_variant,p.Arg32Leu,ENST00000284629,NM_001301822.1,NM_001301821.1,NM_130768.2;ASZ1,intron_variant,,ENST00000428663,;ASZ1,missense_variant,p.Arg32Leu,ENST00000450714,;ASZ1,non_coding_transcript_exon_variant,,ENST00000463182,;ASZ1,non_coding_transcript_exon_variant,,ENST00000465832,;ASZ1,non_coding_transcript_exon_variant,,ENST00000479454,; A ENST00000284629 Transcript missense_variant 158/1865 95/1428 32/475 R/L cGg/cTg rs145791114 1 -1 ASZ1 HGNC HGNC:1350 protein_coding YES CCDS5772.1 ENSP00000284629 Q8WWH4 UPI0000070EE2 NM_001301822.1,NM_001301821.1,NM_130768.2 tolerated(0.06) 1/13 hmmpanther:PTHR24157 MODERATE 1 SNV 1 1 PASS rs145791114 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 117427366 117427366 C A 1 0 0 0 0 1 0 0 0 1217 652 23 1 1 ASZ1 7 117427366 Missense_Mutation SNP C C3L-00080_T 9371695 117427366 41918607 314 2412 KCND2 0 . GRCh38 7 120741600 120741600 + Missense_Mutation SNP C C T rs561063026 C3L-00080_T C3L-00080_N C C c.1345C>T p.Arg449Trp p.R449W ENST00000331113 3/6 439 370 69 386 386 0 strelka-varscan-mutect KCND2,missense_variant,p.Arg449Trp,ENST00000331113,NM_012281.2;KCND2,missense_variant,p.Arg35Trp,ENST00000425288,;KCND2,upstream_gene_variant,,ENST00000473190,; T ENST00000331113 Transcript missense_variant 2310/5331 1345/1893 449/630 R/W Cgg/Tgg rs561063026,COSM1737355 1 1 KCND2 HGNC HGNC:6238 protein_coding YES CCDS5776.1 ENSP00000333496 Q9NZV8 A4D0V9 UPI0000073D37 NM_012281.2 deleterious(0) 3/6 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF159,Pfam_domain:PF11879 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs561063026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 120741600 120741600 C T 1 0 0 0 0 1 0 0 0 7935 527 19 1 1 KCND2 7 120741600 Missense_Mutation SNP C C3L-00080_T 3314234 120741600 38604373 315 2413 HYAL4 0 . GRCh38 7 123868729 123868729 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.456G>A p.= p.Q152Q ENST00000223026 3/5 173 142 31 133 133 0 strelka-varscan-mutect HYAL4,synonymous_variant,p.=,ENST00000223026,NM_012269.2;HYAL4,synonymous_variant,p.=,ENST00000476325,;HYAL4,downstream_gene_variant,,ENST00000489978,;HYAL4,downstream_gene_variant,,ENST00000488323,;HYAL4,synonymous_variant,p.=,ENST00000483878,; A ENST00000223026 Transcript synonymous_variant 1094/2407 456/1446 152/481 Q caG/caA 1 1 HYAL4 HGNC HGNC:5323 protein_coding YES CCDS5789.1 ENSP00000223026 Q2M3T9 UPI000006F62B NM_012269.2 3/5 Gene3D:3.20.20.70,Pfam_domain:PF01630,PIRSF_domain:PIRSF038193,Prints_domain:PR00846,hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF7,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 123868729 123868729 G A 1 0 0 0 0 0 0 0 1 7362 1020 36 3 3 HYAL4 7 123868729 Silent SNP G C3L-00080_T 3127129 123868729 35477244 316 2414 SPAM1 0 . GRCh38 7 123953729 123953729 + Missense_Mutation SNP G G T rs554458086 C3L-00080_T C3L-00080_N G G c.159G>T p.Trp53Cys p.W53C ENST00000340011 3/7 100 69 31 85 85 0 strelka-varscan-mutect SPAM1,missense_variant,p.Trp53Cys,ENST00000340011,NM_003117.4;SPAM1,missense_variant,p.Trp53Cys,ENST00000439500,NM_001174046.1,NM_001174045.1;SPAM1,missense_variant,p.Trp53Cys,ENST00000460182,NM_001174044.1,NM_153189.2;SPAM1,missense_variant,p.Trp53Cys,ENST00000223028,;SPAM1,missense_variant,p.Trp53Cys,ENST00000402183,;SPAM1,missense_variant,p.Trp53Cys,ENST00000413927,; T ENST00000340011 Transcript missense_variant 516/2349 159/1536 53/511 W/C tgG/tgT rs554458086,COSM4529270,COSM4529271 1 1 SPAM1 HGNC HGNC:11217 protein_coding YES CCDS5790.1 ENSP00000345849 P38567 UPI0000072166 NM_003117.4 deleterious(0) 3/7 hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF20,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Gene3D:3.20.20.70,Pfam_domain:PF01630,Superfamily_domains:SSF51445,Prints_domain:PR00846 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs554458086 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 123953729 123953729 G T 1 0 0 0 0 1 0 0 0 15317 1183 41 2 2 SPAM1 7 123953729 Missense_Mutation SNP G C3L-00080_T 85000 123953729 35392244 317 2415 FLNC 0 . GRCh38 7 128856782 128856782 + Silent SNP C C T rs755019331 C3L-00080_T C3L-00080_N C C c.7422C>T p.= p.G2474G ENST00000325888 45/48 530 419 111 475 475 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; T ENST00000325888 Transcript synonymous_variant 7683/9188 7422/8178 2474/2725 G ggC/ggT rs755019331,COSM3878002 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 45/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 0,1 LOW 1 SNV 1 0,1 1 PASS rs755019331 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 128856782 128856782 C T 1 0 0 0 0 0 0 0 1 5791 755 27 1 1 FLNC 7 128856782 Silent SNP C C3L-00080_T 4903053 128856782 30489191 318 2416 AHCYL2 0 . GRCh38 7 129405152 129405152 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1081G>A p.Asp361Asn p.D361N ENST00000325006 8/17 92 81 11 102 102 0 strelka-varscan-mutect AHCYL2,missense_variant,p.Asp361Asn,ENST00000325006,NM_015328.3;AHCYL2,missense_variant,p.Asp360Asn,ENST00000446544,NM_001130720.2;AHCYL2,missense_variant,p.Asp258Asn,ENST00000474594,NM_001130723.2;AHCYL2,missense_variant,p.Asp258Asn,ENST00000490911,NM_001130722.2;AHCYL2,missense_variant,p.Asp268Asn,ENST00000466924,;AHCYL2,downstream_gene_variant,,ENST00000466993,;AHCYL2,non_coding_transcript_exon_variant,,ENST00000492628,;AHCYL2,downstream_gene_variant,,ENST00000491079,;RP11-305M3.2,downstream_gene_variant,,ENST00000450566,; A ENST00000325006 Transcript missense_variant 1135/5056 1081/1836 361/611 D/N Gac/Aac 1 1 AHCYL2 HGNC HGNC:22204 protein_coding YES CCDS5812.1 ENSP00000315931 Q96HN2 UPI00001354E4 NM_015328.3 deleterious(0.02) 8/17 hmmpanther:PTHR23420:SF2,hmmpanther:PTHR23420,TIGRFAM_domain:TIGR00936,Gene3D:3.40.50.1480,SMART_domains:SM00996,Superfamily_domains:SSF52283 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 129405152 129405152 G A 1 0 0 0 0 1 0 0 0 488 1290 45 3 3 AHCYL2 7 129405152 Missense_Mutation SNP G C3L-00080_T 548370 129405152 29940821 319 2417 STRA8 0 . GRCh38 7 135246703 135246703 + Splice_Site SNP G G T novel C3L-00080_T C3L-00080_N G G c.732+1G>T p.X244_splice ENST00000275764 95 79 16 74 74 0 strelka-varscan-mutect STRA8,splice_donor_variant,,ENST00000275764,NM_182489.1;RP11-260N14.1,non_coding_transcript_exon_variant,,ENST00000637483,; T ENST00000275764 Transcript splice_donor_variant -/993 732/993 244/330 1 1 STRA8 HGNC HGNC:30653 protein_coding YES CCDS5839.1 ENSP00000275764 Q7Z7C7 UPI00001A36D9 NM_182489.1 6/8 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 7 135246703 135246703 G T 1 0 0 0 0 0 0 1 0 15704 1275 44 2 2 STRA8 7 135246703 Splice_Site SNP G C3L-00080_T 5841551 135246703 24099270 320 2418 SVOPL 0 . GRCh38 7 138678975 138678975 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.71C>A p.Pro24Gln p.P24Q ENST00000419765 1/15 198 165 33 168 168 0 strelka-varscan-mutect SVOPL,missense_variant,p.Pro24Gln,ENST00000421622,;SVOPL,missense_variant,p.Pro24Gln,ENST00000419765,NM_001139456.1; T ENST00000419765 Transcript missense_variant 105/1523 71/1479 24/492 P/Q cCa/cAa 1 -1 SVOPL HGNC HGNC:27034 protein_coding YES CCDS47721.1 ENSP00000405482 Q8N434 UPI0001565476 NM_001139456.1 deleterious(0.04) 1/15 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF168 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 138678975 138678975 G T 1 0 0 0 0 1 0 0 0 15809 1348 47 2 2 SVOPL 7 138678975 Missense_Mutation SNP G C3L-00080_T 3432272 138678975 20666998 321 2419 KIAA1549 0 . GRCh38 7 138903591 138903593 + In_Frame_Del DEL CAC CAC - novel C3L-00080_T C3L-00080_N CAC CAC c.3664_3666delGTG p.Val1222del p.V1222del ENST00000422774 8/20 86 75 11 89 89 0 sindel-varindel-pindel KIAA1549,inframe_deletion,p.Val1222del,ENST00000440172,NM_020910.2;KIAA1549,inframe_deletion,p.Val1222del,ENST00000422774,NM_001164665.1; - ENST00000422774 Transcript inframe_deletion 3713-3715/6283 3664-3666/5853 1222/1950 V/- GTG/- 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 8/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590,Pfam_domain:PF12877 MODERATE 1 deletion 1 1 PASS . . 0 206 2 2 0 0 0 0 -18.13122 0.9999973 1 1 1 0 - 7 5 7 138903591 138903591 CAC - 1 0 1 0 1 0 0 0 0 8120 724 25 0 0 KIAA1549 7 138903591 In_Frame_Del DEL CAC C3L-00080_T 224616 138903591 20442382 322 2420 HIPK2 0 . GRCh38 7 139716114 139716114 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.921G>A p.= p.Q307Q ENST00000406875 2/15 242 196 46 235 235 0 strelka-varscan-mutect HIPK2,synonymous_variant,p.=,ENST00000406875,NM_022740.4;HIPK2,synonymous_variant,p.=,ENST00000428878,NM_001113239.2;HIPK2,synonymous_variant,p.=,ENST00000342645,; T ENST00000406875 Transcript synonymous_variant 1016/15049 921/3597 307/1198 Q caG/caA 1 -1 HIPK2 HGNC HGNC:14402 protein_coding YES CCDS75667.1 ENSP00000385571 Q9H2X6 UPI000012C71E NM_022740.4 2/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF53,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 139716114 139716114 C T 1 0 0 0 0 0 0 0 1 7005 680 24 3 3 HIPK2 7 139716114 Silent SNP C C3L-00080_T 812523 139716114 19629859 323 2421 SSBP1 0 . GRCh38 7 141743702 141743702 + Splice_Site SNP G G T novel C3L-00080_T C3L-00080_N G G c.226+1G>T p.X76_splice ENST00000481508 68 52 16 95 95 0 varscan-mutect SSBP1,splice_donor_variant,,ENST00000481508,NM_001256510.1;SSBP1,splice_donor_variant,,ENST00000612337,NM_001256513.1,NM_001256512.1,NM_001256511.1;SSBP1,splice_donor_variant,,ENST00000465582,;SSBP1,splice_donor_variant,,ENST00000265304,NM_003143.2;SSBP1,splice_donor_variant,,ENST00000484178,;SSBP1,splice_donor_variant,,ENST00000498107,;SSBP1,splice_donor_variant,,ENST00000467681,;SSBP1,splice_donor_variant,,ENST00000463093,;SSBP1,downstream_gene_variant,,ENST00000473783,;SSBP1,splice_donor_variant,,ENST00000469123,;SSBP1,splice_donor_variant,,ENST00000465167,;SSBP1,splice_donor_variant,,ENST00000489378,;SSBP1,downstream_gene_variant,,ENST00000496622,;SSBP1,downstream_gene_variant,,ENST00000461433,;SSBP1,downstream_gene_variant,,ENST00000468267,; T ENST00000481508 Transcript splice_donor_variant -/989 226/447 76/148 1 1 SSBP1 HGNC HGNC:11317 protein_coding YES CCDS5866.1 ENSP00000419665 Q04837 A4D1U3 UPI0000135FAA NM_001256510.1 4/6 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 5 4 7 141743702 141743702 G T 1 0 0 0 0 0 0 1 0 15553 1275 44 2 2 SSBP1 7 141743702 Splice_Site SNP G C3L-00080_T 2027588 141743702 17602271 324 2422 TCAF2 0 . GRCh38 7 143703136 143703136 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.142G>T p.Val48Leu p.V48L ENST00000444908 2/7 176 158 18 187 187 0 varscan-mutect TCAF2,missense_variant,p.Val48Leu,ENST00000441159,;TCAF2,missense_variant,p.Val48Leu,ENST00000444908,NM_001130025.1;TCAF2,missense_variant,p.Val48Leu,ENST00000357344,NM_173678.2;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,;TCAF2,intron_variant,,ENST00000518791,; T ENST00000444908 Transcript missense_variant 227/2976 142/2538 48/845 V/L Gtg/Ttg 1 1 TCAF2 HGNC HGNC:26878 protein_coding YES CCDS34769.1 ENSP00000412724 A6NFQ2 UPI00001AF3A8 NM_001130025.1 deleterious(0) 2/7 hmmpanther:PTHR15730,hmmpanther:PTHR15730:SF4 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 143703136 143703136 G T 1 0 0 0 0 1 0 0 0 16071 1261 44 2 2 TCAF2 7 143703136 Missense_Mutation SNP G C3L-00080_T 1959434 143703136 15642837 325 2423 OR2A12 0 . GRCh38 7 144095732 144095732 + Missense_Mutation SNP C C T rs769270259 C3L-00080_T C3L-00080_N C C c.625C>T p.Pro209Ser p.P209S ENST00000408949 1/1 456 388 68 467 467 0 strelka-varscan-mutect OR2A12,missense_variant,p.Pro209Ser,ENST00000408949,NM_001004135.1; T ENST00000408949 Transcript missense_variant 685/1046 625/933 209/310 P/S Ccg/Tcg rs769270259 1 1 OR2A12 HGNC HGNC:15082 protein_coding YES CCDS43670.1 ENSP00000386174 Q8NGT7 A4D2G4 UPI0000061E6F NM_001004135.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF50,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs769270259 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 144095732 144095732 C T 1 0 0 0 0 1 0 0 0 11052 739 26 3 3 OR2A12 7 144095732 Missense_Mutation SNP C C3L-00080_T 392596 144095732 15250241 326 2424 CNTNAP2 0 . GRCh38 7 148217410 148217410 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.3133G>T p.Asp1045Tyr p.D1045Y ENST00000361727 19/24 362 217 145 308 307 1 strelka-varscan-mutect CNTNAP2,missense_variant,p.Asp1045Tyr,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Asp104Tyr,ENST00000628930,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,; T ENST00000361727 Transcript missense_variant 3651/9896 3133/3996 1045/1331 D/Y Gac/Tac COSM1248652 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0.01) 19/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 148217410 148217410 G T 1 0 0 0 0 1 0 0 0 3428 1174 41 2 2 CNTNAP2 7 148217410 Missense_Mutation SNP G C3L-00080_T 4121678 148217410 11128563 327 2425 C7orf33 0 . GRCh38 7 148615361 148615361 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.494C>G p.Ser165Cys p.S165C ENST00000307003 3/3 202 113 89 201 201 0 strelka-varscan-mutect C7orf33,missense_variant,p.Ser165Cys,ENST00000307003,NM_145304.3; G ENST00000307003 Transcript missense_variant 855/1354 494/534 165/177 S/C tCt/tGt 1 1 C7orf33 HGNC HGNC:21724 protein_coding YES CCDS5890.1 ENSP00000304071 Q8WU49 A0A090N8Y1 UPI00000707BF NM_145304.3 deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 148615361 148615361 C G 1 0 0 0 0 1 0 0 0 2138 913 32 4 4 C7orf33 7 148615361 Missense_Mutation SNP C C3L-00080_T 397951 148615361 10730612 328 2426 GALNT11 0 . GRCh38 7 152100818 152100818 + Missense_Mutation SNP G G T rs149600575 C3L-00080_T C3L-00080_N G G c.316G>T p.Asp106Tyr p.D106Y ENST00000434507 5/14 133 75 58 137 136 1 strelka-varscan-mutect GALNT11,missense_variant,p.Asp106Tyr,ENST00000434507,;GALNT11,missense_variant,p.Asp106Tyr,ENST00000430044,NM_001304514.1,NM_022087.3;GALNT11,missense_variant,p.Asp106Tyr,ENST00000415421,;GALNT11,missense_variant,p.Asp106Tyr,ENST00000422997,;GALNT11,missense_variant,p.Asp106Tyr,ENST00000447796,;GALNT11,missense_variant,p.Asp106Tyr,ENST00000419245,;GALNT11,splice_region_variant,,ENST00000423337,;GALNT11,intron_variant,,ENST00000446096,;GALNT11,intron_variant,,ENST00000482812,;GALNT11,intron_variant,,ENST00000447778,; T ENST00000434507 Transcript missense_variant 753/2747 316/1827 106/608 D/Y Gat/Tat rs149600575 1 1 GALNT11 HGNC HGNC:19875 protein_coding YES CCDS5930.1 ENSP00000416787 Q8NCW6 A0A090N7X6 UPI000004C2AA deleterious(0) 5/14 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF10 MODERATE 1 SNV 2 1 PASS rs149600575 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 152100818 152100818 G T 1 0 0 0 0 1 0 0 0 6077 1058 37 1 1 GALNT11 7 152100818 Missense_Mutation SNP G C3L-00080_T 3485457 152100818 7245155 329 2427 KMT2C 0 . GRCh38 7 152273716 152273716 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1001C>A p.Ala334Asp p.A334D ENST00000262189 7/59 322 302 20 369 369 0 varscan-mutect KMT2C,missense_variant,p.Ala334Asp,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Ala334Asp,ENST00000355193,;KMT2C,missense_variant,p.Ala334Asp,ENST00000558084,; T ENST00000262189 Transcript missense_variant 1220/16862 1001/14736 334/4911 A/D gCt/gAt 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 deleterious(0) 7/59 Gene3D:3.30.40.10 MODERATE 1 SNV 1 1 PASS rs1189358773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 152273716 152273716 G T 1 0 0 0 0 1 0 0 0 8297 971 34 2 2 KMT2C 7 152273716 Missense_Mutation SNP G C3L-00080_T 172898 152273716 7072257 330 2428 DPP6 0 . GRCh38 7 154889505 154889505 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.2426G>T p.Arg809Met p.R809M ENST00000377770 25/26 89 57 32 111 111 0 strelka-varscan-mutect DPP6,missense_variant,p.Arg745Met,ENST00000404039,NM_001039350.2;DPP6,missense_variant,p.Arg747Met,ENST00000332007,NM_001936.4;DPP6,missense_variant,p.Arg809Met,ENST00000377770,NM_130797.3;DPP6,missense_variant,p.Arg702Met,ENST00000427557,NM_001290252.1;DPP6,non_coding_transcript_exon_variant,,ENST00000480367,; T ENST00000377770 Transcript missense_variant 2567/3710 2426/2598 809/865 R/M aGg/aTg COSM3950250,COSM3950251,COSM3950252 1 1 DPP6 HGNC HGNC:3010 protein_coding YES CCDS75683.1 ENSP00000367001 P42658 UPI00001AE746 NM_130797.3 deleterious(0.04) 25/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20,Gene3D:3.40.50.1820,Pfam_domain:PF00326,Superfamily_domains:SSF53474 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 154889505 154889505 G T 1 0 0 0 0 1 0 0 0 4545 1000 35 2 2 DPP6 7 154889505 Missense_Mutation SNP G C3L-00080_T 2615789 154889505 4456468 331 2429 FBXO25 0 . GRCh38 8 449994 449994 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.386T>C p.Leu129Ser p.L129S ENST00000382824 6/11 70 41 29 70 70 0 strelka-varscan-mutect FBXO25,missense_variant,p.Leu129Ser,ENST00000382824,NM_183421.1;FBXO25,missense_variant,p.Leu62Ser,ENST00000352684,NM_012173.3;FBXO25,missense_variant,p.Leu129Ser,ENST00000350302,NM_183420.1;FBXO25,missense_variant,p.Leu62Ser,ENST00000276326,;RP11-91J19.3,downstream_gene_variant,,ENST00000607549,;FBXO25,non_coding_transcript_exon_variant,,ENST00000524125,;FBXO25,non_coding_transcript_exon_variant,,ENST00000524015,; C ENST00000382824 Transcript missense_variant 505/10386 386/1104 129/367 L/S tTg/tCg 1 1 FBXO25 HGNC HGNC:13596 protein_coding YES CCDS5953.1 ENSP00000372274 Q8TCJ0 UPI00001CE3B4 NM_183421.1 deleterious(0) 6/11 hmmpanther:PTHR13123,hmmpanther:PTHR13123:SF8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 449994 449994 T C 1 0 0 0 0 1 0 0 0 5599 1826 63 5 5 FBXO25 8 449994 Missense_Mutation SNP T C3L-00080_T 449994 144688642 332 2430 CSMD1 0 . GRCh38 8 2966712 2966712 + Missense_Mutation SNP G G T rs373386526 C3L-00080_T C3L-00080_N G G c.8961C>A p.Asn2987Lys p.N2987K ENST00000520002 59/71 143 78 65 146 146 0 strelka-varscan-mutect CSMD1,missense_variant,p.Asn2848Lys,ENST00000537824,;CSMD1,missense_variant,p.Asn2404Lys,ENST00000335551,;CSMD1,missense_variant,p.Asn2987Lys,ENST00000520002,;CSMD1,missense_variant,p.Asn2987Lys,ENST00000602557,;CSMD1,missense_variant,p.Asn2986Lys,ENST00000635120,NM_033225.5;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,; T ENST00000520002 Transcript missense_variant 9517/11740 8961/10698 2987/3565 N/K aaC/aaA rs373386526 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.05) 59/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs373386526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 2966712 2966712 G T 1 0 0 0 0 1 0 0 0 3745 1136 40 1 1 CSMD1 8 2966712 Missense_Mutation SNP G C3L-00080_T 2516718 2966712 142171924 333 2431 CSMD1 0 . GRCh38 8 3998014 3998014 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.707G>C p.Trp236Ser p.W236S ENST00000520002 5/71 180 105 75 215 215 0 strelka-varscan-mutect CSMD1,missense_variant,p.Trp98Ser,ENST00000537824,;CSMD1,missense_variant,p.Trp236Ser,ENST00000520002,;CSMD1,missense_variant,p.Trp236Ser,ENST00000602557,;CSMD1,missense_variant,p.Trp236Ser,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Trp236Ser,ENST00000400186,;CSMD1,missense_variant,p.Trp236Ser,ENST00000602723,; G ENST00000520002 Transcript missense_variant 1263/11740 707/10698 236/3565 W/S tGg/tCg 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 5/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 3998014 3998014 C G 1 0 0 0 0 1 0 0 0 3745 595 21 4 4 CSMD1 8 3998014 Missense_Mutation SNP C C3L-00080_T 1031302 3998014 141140622 334 2432 USP17L4 0 . GRCh38 8 7338247 7338247 + Nonsense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1133G>A p.Trp378Ter p.W378* ENST00000526929 1/1 255 242 13 317 317 0 varscan-mutect USP17L4,stop_gained,p.Trp378Ter,ENST00000526929,NM_001256874.1;USP17L1,downstream_gene_variant,,ENST00000529559,NM_001256873.1;FAM66B,intron_variant,,ENST00000606573,;FAM66B,intron_variant,,ENST00000529456,;AC130360.8,upstream_gene_variant,,ENST00000425489,; A ENST00000526929 Transcript stop_gained 1133/1593 1133/1593 378/530 W/* tGg/tAg 1 1 USP17L4 HGNC HGNC:37176 protein_coding YES CCDS78299.1 ENSP00000485243 A6NCW7 UPI0000251F84 NM_001256874.1 1/1 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 HIGH SNV 1 PASS . . 6 203 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 7338247 7338247 G A 1 0 0 0 0 0 1 0 0 17588 1357 47 3 3 USP17L4 8 7338247 Nonsense_Mutation SNP G C3L-00080_T 3340233 7338247 137800389 335 2433 SGK223 0 . GRCh38 8 8319035 8319035 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.3340G>T p.Glu1114Ter p.E1114* ENST00000615670 6/6 194 179 15 235 235 0 strelka-varscan-mutect SGK223,stop_gained,p.Glu1114Ter,ENST00000615670,;SGK223,stop_gained,p.Glu1114Ter,ENST00000622241,NM_001080826.2; A ENST00000615670 Transcript stop_gained 3605/4903 3340/4221 1114/1406 E/* Gag/Tag 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F 6/6 PROSITE_profiles:PS50011,hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972,Gene3D:3.30.200.20,SMART_domains:SM00220 HIGH 1 SNV 5 1 PASS rs1188055557 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 8319035 8319035 C A 1 0 0 0 0 0 1 0 0 14469 864 30 2 2 SGK223 8 8319035 Nonsense_Mutation SNP C C3L-00080_T 980788 8319035 136819601 336 2434 GATA4 0 . GRCh38 8 11708357 11708358 + Frame_Shift_Ins INS - - G novel C3L-00080_T C3L-00080_N - - c.47dupG p.Ala17CysfsTer194 p.A17Cfs*194 ENST00000532059 1/6 273 156 117 277 277 0 sindel-varindel-pindel GATA4,frameshift_variant,p.Ala17CysfsTer193,ENST00000335135,NM_002052.3;GATA4,frameshift_variant,p.Val16GlyfsTer193,ENST00000622443,;GATA4,frameshift_variant,p.Ala17CysfsTer194,ENST00000532059,NM_001308093.1;GATA4,frameshift_variant,p.Ala17CysfsTer?,ENST00000528027,;GATA4,frameshift_variant,p.Gly17GlyfsTer?,ENST00000532977,;GATA4,frameshift_variant,p.Ala17CysfsTer?,ENST00000526974,;GATA4,intron_variant,,ENST00000528712,NM_001308094.1;GATA4,intron_variant,,ENST00000526716,; G ENST00000532059 Transcript frameshift_variant 125-126/1459 45-46/1332 15-16/443 -/X -/G 1 1 GATA4 HGNC HGNC:4173 protein_coding YES CCDS78303.1 ENSP00000435712 P43694 UPI0000210221 NM_001308093.1 1/6 Pfam_domain:PF05349,PIRSF_domain:PIRSF003028,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF154,Low_complexity_(Seg):seg HIGH 1 insertion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 7 11708357 11708357 - G 1 0 1 1 0 0 0 0 0 6126 652 23 0 0 GATA4 8 11708357 Frame_Shift_Ins INS - C3L-00080_T 3389322 11708357 133430279 337 2435 LZTS1 0 . GRCh38 8 20252891 20252891 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1040A>T p.Gln347Leu p.Q347L ENST00000381569 3/4 64 35 29 70 70 0 strelka-varscan-mutect LZTS1,missense_variant,p.Gln347Leu,ENST00000381569,;LZTS1,missense_variant,p.Gln347Leu,ENST00000265801,NM_021020.3;LZTS1,missense_variant,p.Gln347Leu,ENST00000522290,;LZTS1,intron_variant,,ENST00000616228,; A ENST00000381569 Transcript missense_variant 1398/5706 1040/1791 347/596 Q/L cAg/cTg 1 -1 LZTS1 HGNC HGNC:13861 protein_coding YES CCDS6015.1 ENSP00000370981 Q9Y250 UPI000006DEE8 deleterious(0) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR19354:SF5,hmmpanther:PTHR19354,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS rs1393232019 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 20252891 20252891 T A 1 0 0 0 0 1 0 0 0 9051 1580 55 4 4 LZTS1 8 20252891 Missense_Mutation SNP T C3L-00080_T 8544534 20252891 124885745 338 2436 DPYSL2 0 . GRCh38 8 26581978 26581978 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.49C>G p.Leu17Val p.L17V ENST00000311151 2/14 95 61 34 118 118 0 strelka-varscan-mutect DPYSL2,missense_variant,p.Leu122Val,ENST00000521913,NM_001197293.2;DPYSL2,missense_variant,p.Leu17Val,ENST00000311151,NM_001386.5;DPYSL2,missense_variant,p.Leu89Val,ENST00000493789,;DPYSL2,5_prime_UTR_variant,,ENST00000523027,NM_001244604.1; G ENST00000311151 Transcript missense_variant 461/4603 49/1719 17/572 L/V Ctt/Gtt 1 1 DPYSL2 HGNC HGNC:3014 protein_coding YES CCDS6051.1 ENSP00000309539 Q16555 UPI0000129864 NM_001386.5 tolerated(0.14) 2/14 Gene3D:2.30.40.10,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF56,Superfamily_domains:SSF51338,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 26581978 26581978 C G 1 0 0 0 0 1 0 0 0 4562 913 32 4 4 DPYSL2 8 26581978 Missense_Mutation SNP C C3L-00080_T 6329087 26581978 118556658 339 2437 FGFR1 0 . GRCh38 8 38423025 38423026 + Frame_Shift_Ins INS - - T novel C3L-00080_T C3L-00080_N - - c.1089dupA p.Asp364ArgfsTer17 p.D364Rfs*17 ENST00000341462 8/19 121 82 39 106 106 0 sindel-varindel-pindel FGFR1,frameshift_variant,p.Asp364ArgfsTer17,ENST00000341462,;FGFR1,frameshift_variant,p.Ala272SerfsTer47,ENST00000397103,;FGFR1,intron_variant,,ENST00000447712,NM_023110.2;FGFR1,intron_variant,,ENST00000397091,NM_015850.3;FGFR1,intron_variant,,ENST00000532791,NM_001174063.1;FGFR1,intron_variant,,ENST00000619564,;FGFR1,intron_variant,,ENST00000425967,NM_001174067.1;FGFR1,intron_variant,,ENST00000335922,NM_001174064.1;FGFR1,intron_variant,,ENST00000356207,NM_023105.2,NM_001174066.1;FGFR1,intron_variant,,ENST00000326324,NM_023106.2;FGFR1,intron_variant,,ENST00000397113,NM_001174065.1;FGFR1,intron_variant,,ENST00000397108,;FGFR1,downstream_gene_variant,,ENST00000525001,;FGFR1,downstream_gene_variant,,ENST00000529552,;FGFR1,downstream_gene_variant,,ENST00000526742,;FGFR1,downstream_gene_variant,,ENST00000533668,;FGFR1,downstream_gene_variant,,ENST00000530568,;RP11-350N15.4,intron_variant,,ENST00000528407,;FGFR1,intron_variant,,ENST00000530701,;FGFR1,downstream_gene_variant,,ENST00000527203,;FGFR1,non_coding_transcript_exon_variant,,ENST00000464163,;FGFR1,intron_variant,,ENST00000526570,;FGFR1,intron_variant,,ENST00000487647,;FGFR1,intron_variant,,ENST00000475621,;FGFR1,downstream_gene_variant,,ENST00000470826,;FGFR1,downstream_gene_variant,,ENST00000496296,;FGFR1,upstream_gene_variant,,ENST00000527114,;FGFR1,downstream_gene_variant,,ENST00000484370,;FGFR1,upstream_gene_variant,,ENST00000466021,;FGFR1,upstream_gene_variant,,ENST00000527745,;FGFR1,downstream_gene_variant,,ENST00000474970,;FGFR1,downstream_gene_variant,,ENST00000532386,;FGFR1,upstream_gene_variant,,ENST00000524528,; T ENST00000341462 Transcript frameshift_variant,splice_region_variant 2031-2032/6054 1089-1090/1104 363-364/367 -/X -/A 1 -1 FGFR1 HGNC HGNC:3688 protein_coding ENSP00000340636 C1KBH7 UPI0001998D01 8/19 HIGH insertion 5 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999911 1 1 1 0 T 7 5 7 38423025 38423025 - T 1 0 1 1 0 0 0 0 0 5727 695 24 0 0 FGFR1 8 38423025 Frame_Shift_Ins INS - C3L-00080_T 11841047 38423025 106715611 340 2438 IKBKB 0 . GRCh38 8 42322449 42322449 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1941G>T p.Gln647His p.Q647H ENST00000520810 19/22 194 132 62 155 155 0 strelka-varscan-mutect IKBKB,missense_variant,p.Gln588His,ENST00000416505,NM_001242778.1;IKBKB,missense_variant,p.Gln647His,ENST00000520810,NM_001556.2;IKBKB,missense_variant,p.Gln645His,ENST00000520835,NM_001190720.2;IKBKB,3_prime_UTR_variant,,ENST00000629753,;IKBKB,intron_variant,,ENST00000522147,;IKBKB,downstream_gene_variant,,ENST00000522785,;IKBKB,downstream_gene_variant,,ENST00000517502,;IKBKB,upstream_gene_variant,,ENST00000521225,;IKBKB,3_prime_UTR_variant,,ENST00000342222,;IKBKB,3_prime_UTR_variant,,ENST00000520655,;IKBKB,3_prime_UTR_variant,,ENST00000518679,;IKBKB,3_prime_UTR_variant,,ENST00000517890,;IKBKB,3_prime_UTR_variant,,ENST00000523517,;IKBKB,3_prime_UTR_variant,,ENST00000521661,;IKBKB,3_prime_UTR_variant,,ENST00000523105,;IKBKB,non_coding_transcript_exon_variant,,ENST00000520201,;IKBKB,non_coding_transcript_exon_variant,,ENST00000519938,;IKBKB,non_coding_transcript_exon_variant,,ENST00000522133,;IKBKB,non_coding_transcript_exon_variant,,ENST00000523018,;IKBKB,downstream_gene_variant,,ENST00000517917,;IKBKB,upstream_gene_variant,,ENST00000523599,;IKBKB,upstream_gene_variant,,ENST00000522103,; T ENST00000520810 Transcript missense_variant 2127/3086 1941/2271 647/756 Q/H caG/caT 1 1 IKBKB HGNC HGNC:5960 protein_coding YES CCDS6128.1 ENSP00000430684 O14920 UPI0000033729 NM_001556.2 tolerated(0.06) 19/22 hmmpanther:PTHR22969:SF7,hmmpanther:PTHR22969 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 42322449 42322449 G T 1 0 0 0 0 1 0 0 0 7519 991 35 2 2 IKBKB 8 42322449 Missense_Mutation SNP G C3L-00080_T 3899424 42322449 102816187 341 2439 SNTG1 0 . GRCh38 8 50536694 50536694 + Missense_Mutation SNP C C G rs746823892 C3L-00080_T C3L-00080_N C C c.566C>G p.Ser189Trp p.S189W ENST00000522124 11/19 195 133 62 185 185 0 strelka-varscan-mutect SNTG1,missense_variant,p.Ser189Trp,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Ser189Trp,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Ser189Trp,ENST00000517473,NM_001287814.1;SNTG1,missense_variant,p.Ser189Trp,ENST00000520825,; G ENST00000522124 Transcript missense_variant 1227/3504 566/1554 189/517 S/W tCg/tGg rs746823892,COSM4728771,COSM4728772 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 11/19 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs746823892 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 50536694 50536694 C G 1 0 0 0 0 1 0 0 0 15194 893 31 4 4 SNTG1 8 50536694 Missense_Mutation SNP C C3L-00080_T 8214245 50536694 94601942 342 2440 UBXN2B 0 . GRCh38 8 58434393 58434393 + Splice_Site SNP A A G novel C3L-00080_T C3L-00080_N A A c.424-2A>G p.X142_splice ENST00000399598 57 50 7 48 48 0 strelka-varscan-mutect UBXN2B,splice_acceptor_variant,,ENST00000399598,NM_001077619.1;UBXN2B,splice_acceptor_variant,,ENST00000521796,;UBXN2B,splice_acceptor_variant,,ENST00000522978,;UBXN2B,splice_acceptor_variant,,ENST00000523409,;UBXN2B,splice_acceptor_variant,,ENST00000520732,; G ENST00000399598 Transcript splice_acceptor_variant -/5068 424/996 142/331 1 1 UBXN2B HGNC HGNC:27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 4/7 HIGH 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -16.58166 1 1 1 1 0 G 5 3 7 58434393 58434393 A G 1 0 0 0 0 0 0 1 0 17439 86 3 5 5 UBXN2B 8 58434393 Splice_Site SNP A C3L-00080_T 7897699 58434393 86704243 343 2441 CHD7 0 . GRCh38 8 60850621 60850621 + Missense_Mutation SNP G G T rs753347128 C3L-00080_T C3L-00080_N G G c.5533G>T p.Gly1845Trp p.G1845W ENST00000423902 26/38 152 101 51 119 119 0 strelka-varscan-mutect CHD7,missense_variant,p.Gly1845Trp,ENST00000423902,NM_017780.3;CHD7,intron_variant,,ENST00000524602,;CHD7,upstream_gene_variant,,ENST00000529472,;CHD7,upstream_gene_variant,,ENST00000527921,; T ENST00000423902 Transcript missense_variant,splice_region_variant 6012/11568 5533/8994 1845/2997 G/W Ggg/Tgg rs753347128,COSM3650079 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 deleterious(0) 26/38 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs753347128 . 0 206 0 4 0 0 0 0 -20 0.9999827 1 1 1 0 T 3 4 7 60850621 60850621 G T 1 0 0 0 0 1 0 0 0 3089 1130 39 1 1 CHD7 8 60850621 Missense_Mutation SNP G C3L-00080_T 2416228 60850621 84288015 344 2442 CSPP1 0 . GRCh38 8 67193590 67193590 + Missense_Mutation SNP C C A rs181079660 C3L-00080_T C3L-00080_N C C c.3442C>A p.Pro1148Thr p.P1148T ENST00000262210 28/29 101 58 43 102 102 0 strelka-varscan-mutect CSPP1,missense_variant,p.Pro1148Thr,ENST00000262210,NM_024790.6;CSPP1,missense_variant,p.Pro803Thr,ENST00000519668,NM_001291339.1;ARFGEF1,intron_variant,,ENST00000520381,;ARFGEF1,intron_variant,,ENST00000518789,;ARFGEF1,downstream_gene_variant,,ENST00000262215,NM_006421.4;CSPP1,intron_variant,,ENST00000521168,;CSPP1,downstream_gene_variant,,ENST00000521324,;ARFGEF1,downstream_gene_variant,,ENST00000518290,;ARFGEF1,downstream_gene_variant,,ENST00000517955,; A ENST00000262210 Transcript missense_variant 3473/4367 3442/3666 1148/1221 P/T Cct/Act rs181079660 1 1 CSPP1 HGNC HGNC:26193 protein_coding YES CCDS43744.1 ENSP00000262210 Q1MSJ5 UPI00005A95D7 NM_024790.6 deleterious(0.04) 28/29 hmmpanther:PTHR21616 MODERATE 1 SNV 1 1 PASS rs181079660 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 67193590 67193590 C A 1 0 0 0 0 1 0 0 0 3763 507 18 2 2 CSPP1 8 67193590 Missense_Mutation SNP C C3L-00080_T 6342969 67193590 77945046 345 2443 TRPA1 0 . GRCh38 8 72033786 72033786 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2726T>A p.Phe909Tyr p.F909Y ENST00000262209 23/27 326 248 78 293 292 1 strelka-varscan-mutect TRPA1,missense_variant,p.Phe909Tyr,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Phe761Tyr,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000512290,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;TRPA1,downstream_gene_variant,,ENST00000519720,;TRPA1,downstream_gene_variant,,ENST00000522271,; T ENST00000262209 Transcript missense_variant 2934/5223 2726/3360 909/1119 F/Y tTc/tAc 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 23/27 Pfam_domain:PF00520,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 72033786 72033786 A T 1 0 0 0 0 1 0 0 0 17082 246 9 4 4 TRPA1 8 72033786 Missense_Mutation SNP A C3L-00080_T 4840196 72033786 73104850 346 2444 ZFHX4 0 . GRCh38 8 76853772 76853772 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.6851G>A p.Ser2284Asn p.S2284N ENST00000521891 10/11 210 141 69 183 183 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Ser2284Asn,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Ser2258Asn,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; A ENST00000521891 Transcript missense_variant 7299/14019 6851/10851 2284/3616 S/N aGt/aAt 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(1) 10/11 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50071,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 76853772 76853772 G A 1 0 0 0 0 1 0 0 0 18213 1029 36 3 3 ZFHX4 8 76853772 Missense_Mutation SNP G C3L-00080_T 4819986 76853772 68284864 347 2445 LRRCC1 0 . GRCh38 8 85141469 85141469 + Silent SNP A A T rs751088822 C3L-00080_T C3L-00080_N A A c.2928A>T p.= p.A976A ENST00000360375 18/19 104 79 25 131 131 0 strelka-varscan-mutect LRRCC1,synonymous_variant,p.=,ENST00000414626,;LRRCC1,synonymous_variant,p.=,ENST00000360375,NM_033402.4;LRRCC1,downstream_gene_variant,,ENST00000522770,;LRRCC1,downstream_gene_variant,,ENST00000517875,;LRRCC1,downstream_gene_variant,,ENST00000522567,; T ENST00000360375 Transcript synonymous_variant 3077/3813 2928/3099 976/1032 A gcA/gcT rs751088822 1 1 LRRCC1 HGNC HGNC:29373 protein_coding YES CCDS43750.1 ENSP00000353538 Q9C099 UPI000021002F NM_033402.4 18/19 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs751088822 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 85141469 85141469 A T 1 0 0 0 0 0 0 0 1 8931 146 6 4 4 LRRCC1 8 85141469 Silent SNP A C3L-00080_T 8287697 85141469 59997167 348 2446 CPNE3 0 . GRCh38 8 86544738 86544738 + Splice_Site SNP A A G novel C3L-00080_T C3L-00080_N A A c.634-2A>G p.X212_splice ENST00000517490 65 46 19 82 82 0 strelka-varscan-mutect CPNE3,splice_acceptor_variant,,ENST00000517490,NM_003909.4;CPNE3,splice_acceptor_variant,,ENST00000621783,;CPNE3,splice_acceptor_variant,,ENST00000517391,;CPNE3,splice_acceptor_variant,,ENST00000517862,;CPNE3,upstream_gene_variant,,ENST00000614678,;CPNE3,upstream_gene_variant,,ENST00000517354,; G ENST00000517490 Transcript splice_acceptor_variant -/4865 634/1614 212/537 1 1 CPNE3 HGNC HGNC:2316 protein_coding YES CCDS6243.1 ENSP00000477590 O75131 A0A024R994 UPI0000127C13 NM_003909.4 8/16 HIGH 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999952 1 1 1 0 G 5 3 7 86544738 86544738 A G 1 0 0 0 0 0 0 1 0 3608 202 7 5 5 CPNE3 8 86544738 Splice_Site SNP A C3L-00080_T 1403269 86544738 58593898 349 2447 GDF6 0 . GRCh38 8 96144583 96144583 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1348G>C p.Glu450Gln p.E450Q ENST00000287020 2/2 271 178 93 218 218 0 strelka-varscan-mutect GDF6,missense_variant,p.Glu450Gln,ENST00000287020,NM_001001557.2;GDF6,3_prime_UTR_variant,,ENST00000621429,;GDF6,3_prime_UTR_variant,,ENST00000620978,;KB-1043D8.8,upstream_gene_variant,,ENST00000602571,; G ENST00000287020 Transcript missense_variant 1448/3701 1348/1368 450/455 E/Q Gag/Cag 1 -1 GDF6 HGNC HGNC:4221 protein_coding YES CCDS34926.1 ENSP00000287020 Q6KF10 A0A0S2A5D6 UPI0000047253 NM_001001557.2 deleterious(0) 2/2 Gene3D:2.10.90.10,Pfam_domain:PF00019,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF43,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 96144583 96144583 C G 1 0 0 0 0 1 0 0 0 6190 864 30 4 4 GDF6 8 96144583 Missense_Mutation SNP C C3L-00080_T 9599845 96144583 48994053 350 2448 STK3 0 . GRCh38 8 98596106 98596106 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.832G>T p.Asp278Tyr p.D278Y ENST00000523601 9/13 221 175 46 197 197 0 strelka-varscan-mutect STK3,missense_variant,p.Asp278Tyr,ENST00000523601,NM_001256312.1;STK3,missense_variant,p.Asp250Tyr,ENST00000419617,NM_006281.3;STK3,missense_variant,p.Asp139Tyr,ENST00000617590,NM_001256313.1;STK3,missense_variant,p.Asp139Tyr,ENST00000518165,;STK3,non_coding_transcript_exon_variant,,ENST00000521768,;STK3,non_coding_transcript_exon_variant,,ENST00000518582,;STK3,non_coding_transcript_exon_variant,,ENST00000523159,;STK3,non_coding_transcript_exon_variant,,ENST00000520653,;STK3,non_coding_transcript_exon_variant,,ENST00000518627,;STK3,upstream_gene_variant,,ENST00000522924,;STK3,3_prime_UTR_variant,,ENST00000424861,;STK3,3_prime_UTR_variant,,ENST00000521649,;STK3,non_coding_transcript_exon_variant,,ENST00000520053,; A ENST00000523601 Transcript missense_variant 1232/3107 832/1560 278/519 D/Y Gat/Tat 1 -1 STK3 HGNC HGNC:11406 protein_coding YES CCDS59108.1 ENSP00000429744 Q13188 UPI00004FB517 NM_001256312.1 deleterious(0) 9/13 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF425,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS rs1393163172 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 98596106 98596106 C A 1 0 0 0 0 1 0 0 0 15672 826 29 2 2 STK3 8 98596106 Missense_Mutation SNP C C3L-00080_T 2451523 98596106 46542530 351 2449 ANKRD46 0 . GRCh38 8 100510603 100510603 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.673G>T p.Asp225Tyr p.D225Y ENST00000520552 6/6 208 141 67 120 120 0 strelka-varscan-mutect ANKRD46,missense_variant,p.Asp225Tyr,ENST00000520552,NM_001270379.1; A ENST00000520552 Transcript missense_variant 835/1686 673/699 225/232 D/Y Gac/Tac 1 -1 ANKRD46 HGNC HGNC:27229 protein_coding YES CCDS59109.1 ENSP00000429015 Q86W74 A0A024R9G2 UPI000018CE82 NM_001270379.1 6/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 100510603 100510603 C A 1 0 0 0 0 1 0 0 0 779 913 32 2 2 ANKRD46 8 100510603 Missense_Mutation SNP C C3L-00080_T 1914497 100510603 44628033 352 2450 RIMS2 0 . GRCh38 8 103766273 103766273 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.434C>A p.Thr145Asn p.T145N ENST00000504942 3/24 192 123 69 136 134 2 strelka-varscan RIMS2,missense_variant,p.Thr145Asn,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Thr87Asn,ENST00000626043,;RIMS2,missense_variant,p.Thr149Asn,ENST00000632716,;RIMS2,non_coding_transcript_exon_variant,,ENST00000395361,;RP11-771F20.1,upstream_gene_variant,,ENST00000481577,; A ENST00000504942 Transcript missense_variant 573/4228 434/4050 145/1349 T/N aCt/aAt 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 3/24 Gene3D:3.30.40.10,Pfam_domain:PF02318,PROSITE_profiles:PS50916,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Superfamily_domains:SSF57903 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 103766273 103766273 C A 1 0 0 0 0 1 0 0 0 13543 565 20 2 2 RIMS2 8 103766273 Missense_Mutation SNP C C3L-00080_T 3255670 103766273 41372363 353 2451 RIMS2 0 . GRCh38 8 103942836 103942836 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.2611C>A p.His871Asn p.H871N ENST00000504942 14/24 227 161 66 194 193 1 strelka-varscan-mutect RIMS2,missense_variant,p.His663Asn,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.His649Asn,ENST00000436393,;RIMS2,missense_variant,p.His871Asn,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.His813Asn,ENST00000626043,;RIMS2,missense_variant,p.His663Asn,ENST00000408894,;RIMS2,missense_variant,p.His710Asn,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.His859Asn,ENST00000632716,;RIMS2,missense_variant,p.His265Asn,ENST00000507677,;RIMS2,missense_variant,p.His663Asn,ENST00000515551,; A ENST00000504942 Transcript missense_variant 2750/4228 2611/4050 871/1349 H/N Cat/Aat COSM1094580,COSM1094581,COSM1094582,COSM1597291,COSM1597292 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 14/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 1,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS rs1295663978 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 103942836 103942836 C A 1 0 0 0 0 1 0 0 0 13543 710 25 2 2 RIMS2 8 103942836 Missense_Mutation SNP C C3L-00080_T 176563 103942836 41195800 354 2452 RIMS2 0 . GRCh38 8 104013486 104013486 + Nonsense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.3089C>G p.Ser1030Ter p.S1030* ENST00000504942 18/24 209 162 47 170 170 0 strelka-varscan-mutect RIMS2,stop_gained,p.Ser844Ter,ENST00000507740,NM_014677.4;RIMS2,stop_gained,p.Ser1030Ter,ENST00000504942,NM_001100117.2;RIMS2,stop_gained,p.Ser972Ter,ENST00000626043,;RIMS2,stop_gained,p.Ser844Ter,ENST00000408894,;RIMS2,stop_gained,p.Ser869Ter,ENST00000262231,NM_001282881.1;RIMS2,stop_gained,p.Ser1040Ter,ENST00000632716,;RIMS2,intron_variant,,ENST00000436393,; G ENST00000504942 Transcript stop_gained 3228/4228 3089/4050 1030/1349 S/* tCa/tGa 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 18/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 HIGH 1 SNV 2 1 PASS rs1187238197 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 7 104013486 104013486 C G 1 0 0 0 0 0 1 0 0 13543 838 29 4 4 RIMS2 8 104013486 Nonsense_Mutation SNP C C3L-00080_T 70650 104013486 41125150 355 2453 DCSTAMP 0 . GRCh38 8 104348922 104348922 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.370G>T p.Gly124Cys p.G124C ENST00000297581 2/4 225 167 58 174 174 0 strelka-varscan-mutect DCSTAMP,missense_variant,p.Gly124Cys,ENST00000297581,NM_030788.3;DCSTAMP,missense_variant,p.Gly124Cys,ENST00000622554,NM_001257317.1;DCSTAMP,missense_variant,p.Gly124Cys,ENST00000517991,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000518023,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,upstream_gene_variant,,ENST00000518051,;DCSTAMP,downstream_gene_variant,,ENST00000517364,;DCSTAMP,downstream_gene_variant,,ENST00000519562,; T ENST00000297581 Transcript missense_variant 419/1953 370/1413 124/470 G/C Ggt/Tgt 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 deleterious(0) 2/4 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 104348922 104348922 G T 1 0 0 0 0 1 0 0 0 4106 1348 47 2 2 DCSTAMP 8 104348922 Missense_Mutation SNP G C3L-00080_T 335436 104348922 40789714 356 2454 TRPS1 0 . GRCh38 8 115587587 115587587 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.2114A>T p.Tyr705Phe p.Y705F ENST00000395715 5/7 301 203 98 239 239 0 strelka-varscan-mutect TRPS1,missense_variant,p.Tyr705Phe,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Tyr692Phe,ENST00000220888,;TRPS1,missense_variant,p.Tyr696Phe,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Tyr446Phe,ENST00000519076,;TRPS1,missense_variant,p.Tyr692Phe,ENST00000519674,;TRPS1,missense_variant,p.Tyr496Phe,ENST00000517323,; A ENST00000395715 Transcript missense_variant 2692/9990 2114/3885 705/1294 Y/F tAc/tTc 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 tolerated_low_confidence(0.1) 5/7 PROSITE_profiles:PS50157,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 115587587 115587587 T A 1 0 0 0 0 1 0 0 0 17099 1638 57 4 4 TRPS1 8 115587587 Missense_Mutation SNP T C3L-00080_T 11238665 115587587 29551049 357 2455 EIF3H 0 . GRCh38 8 116657288 116657288 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.484C>G p.Leu162Val p.L162V ENST00000521861 4/8 412 266 146 325 325 0 strelka-varscan-mutect EIF3H,missense_variant,p.Leu162Val,ENST00000521861,NM_003756.2;EIF3H,missense_variant,p.Leu176Val,ENST00000276682,;EIF3H,missense_variant,p.Leu159Val,ENST00000611080,;EIF3H,missense_variant,p.Leu130Val,ENST00000518949,;EIF3H,missense_variant,p.Leu178Val,ENST00000518995,;EIF3H,downstream_gene_variant,,ENST00000522453,;EIF3H,3_prime_UTR_variant,,ENST00000522800,;EIF3H,non_coding_transcript_exon_variant,,ENST00000520289,;EIF3H,downstream_gene_variant,,ENST00000518034,;EIF3H,downstream_gene_variant,,ENST00000517974,;EIF3H,downstream_gene_variant,,ENST00000519046,; C ENST00000521861 Transcript missense_variant 508/3959 484/1059 162/352 L/V Ctc/Gtc 1 -1 EIF3H HGNC HGNC:3273 protein_coding YES CCDS6319.1 ENSP00000429931 O15372 Q6IB98 UPI00000477E8 NM_003756.2 deleterious(0) 4/8 HAMAP:MF_03007,hmmpanther:PTHR10410:SF3,hmmpanther:PTHR10410,SMART_domains:SM00232 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 116657288 116657288 G C 1 0 0 0 0 1 0 0 0 4852 942 33 4 4 EIF3H 8 116657288 Missense_Mutation SNP G C3L-00080_T 1069701 116657288 28481348 358 2456 FER1L6 0 . GRCh38 8 124013444 124013444 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1835A>T p.Glu612Val p.E612V ENST00000522917 15/41 116 99 17 89 89 0 strelka-varscan-mutect FER1L6,missense_variant,p.Glu612Val,ENST00000522917,NM_001039112.2;FER1L6-AS1,intron_variant,,ENST00000518567,; T ENST00000522917 Transcript missense_variant 2041/6051 1835/5574 612/1857 E/V gAa/gTa 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 tolerated(0.13) 15/41 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 124013444 124013444 A T 1 0 0 0 0 1 0 0 0 5678 246 9 4 4 FER1L6 8 124013444 Missense_Mutation SNP A C3L-00080_T 7356156 124013444 21125192 359 2457 AGO2 0 . GRCh38 8 140532148 140532148 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2476G>T p.Glu826Ter p.E826* ENST00000220592 19/19 195 109 86 120 120 0 strelka-varscan-mutect AGO2,stop_gained,p.Glu826Ter,ENST00000220592,NM_012154.3;AGO2,stop_gained,p.Glu792Ter,ENST00000519980,NM_001164623.1;AGO2,non_coding_transcript_exon_variant,,ENST00000520628,;AGO2,3_prime_UTR_variant,,ENST00000523609,;AGO2,downstream_gene_variant,,ENST00000520412,;AGO2,downstream_gene_variant,,ENST00000519347,; A ENST00000220592 Transcript stop_gained 2589/14581 2476/2580 826/859 E/* Gaa/Taa 1 -1 AGO2 HGNC HGNC:3263 protein_coding YES CCDS6380.1 ENSP00000220592 Q9UKV8 UPI0000168652 NM_012154.3 19/19 HAMAP:MF_03031,hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891 HIGH 1 SNV 2 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999897 1 1 1 0 A 4 1 7 140532148 140532148 C A 1 0 0 0 0 0 1 0 0 465 840 29 2 2 AGO2 8 140532148 Nonsense_Mutation SNP C C3L-00080_T 16518704 140532148 4606488 360 2458 CYP11B1 0 . GRCh38 8 142879678 142879678 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.136G>T p.Gly46Cys p.G46C ENST00000292427 1/9 818 507 311 532 531 1 strelka-varscan-mutect CYP11B1,missense_variant,p.Gly46Cys,ENST00000292427,NM_000497.3;CYP11B1,missense_variant,p.Gly46Cys,ENST00000377675,;CYP11B1,missense_variant,p.Gly46Cys,ENST00000517471,NM_001026213.1;GML,intron_variant,,ENST00000522728,;CYP11B1,upstream_gene_variant,,ENST00000519285,;CYP11B1,non_coding_transcript_exon_variant,,ENST00000314111,; A ENST00000292427 Transcript missense_variant 169/2664 136/1512 46/503 G/C Ggc/Tgc COSM749811 1 -1 CYP11B1 HGNC HGNC:2591 protein_coding YES CCDS6392.1 ENSP00000292427 P15538 UPI000013E0BA NM_000497.3 deleterious(0.04) 1/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00408 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 142879678 142879678 C A 1 0 0 0 0 1 0 0 0 3948 681 24 2 2 CYP11B1 8 142879678 Missense_Mutation SNP C C3L-00080_T 2347530 142879678 2258958 361 2459 LY6H 0 . GRCh38 8 143158260 143158260 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.476C>G p.Ala159Gly p.A159G ENST00000414417 5/5 195 118 77 120 120 0 varscan-mutect LY6H,missense_variant,p.Ala159Gly,ENST00000414417,NM_001130478.1;LY6H,missense_variant,p.Ala138Gly,ENST00000615409,;LY6H,missense_variant,p.Ala159Gly,ENST00000342752,NM_001135655.1;LY6H,missense_variant,p.Ala138Gly,ENST00000430474,NM_002347.4;LY6H,non_coding_transcript_exon_variant,,ENST00000479685,; C ENST00000414417 Transcript missense_variant 710/1056 476/486 159/161 A/G gCt/gGt 1 -1 LY6H HGNC HGNC:6728 protein_coding YES CCDS47926.1 ENSP00000399485 O94772 UPI00005A7901 NM_001130478.1 tolerated(0.09) 5/5 hmmpanther:PTHR32217,hmmpanther:PTHR32217:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 143158260 143158260 G C 1 0 0 0 0 1 0 0 0 9008 971 34 4 4 LY6H 8 143158260 Missense_Mutation SNP G C3L-00080_T 278582 143158260 1980376 362 2460 EPPK1 0 . GRCh38 8 143867394 143867394 + Missense_Mutation SNP C C A rs782767924 C3L-00080_T C3L-00080_N C C c.5860G>T p.Ala1954Ser p.A1954S ENST00000615648 2/2 449 280 169 271 271 0 strelka-varscan-mutect EPPK1,missense_variant,p.Ala1954Ser,ENST00000615648,NM_031308.3;EPPK1,missense_variant,p.Ala1929Ser,ENST00000568225,; A ENST00000615648 Transcript missense_variant 5932/16002 5860/15267 1954/5088 A/S Gct/Tct rs782767924 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 deleterious(0) 2/2 Gene3D:3.90.1290.10,Pfam_domain:PF00681,SMART_domains:SM00250,Superfamily_domains:SSF75399 MODERATE 1 SNV 5 1 PASS rs782767924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 143867394 143867394 C A 1 0 0 0 0 1 0 0 0 5038 739 26 2 2 EPPK1 8 143867394 Missense_Mutation SNP C C3L-00080_T 709134 143867394 1271242 363 2461 MPDZ 0 . GRCh38 9 13168467 13168467 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.3153G>A p.= p.G1051G ENST00000541718 22/46 315 249 66 378 378 0 strelka-varscan-mutect MPDZ,synonymous_variant,p.=,ENST00000319217,;MPDZ,synonymous_variant,p.=,ENST00000541718,NM_003829.4;MPDZ,synonymous_variant,p.=,ENST00000381022,NM_001261406.1;MPDZ,synonymous_variant,p.=,ENST00000546205,;MPDZ,synonymous_variant,p.=,ENST00000447879,;MPDZ,synonymous_variant,p.=,ENST00000536827,NM_001261407.1;MPDZ,synonymous_variant,p.=,ENST00000545857,;MPDZ,upstream_gene_variant,,ENST00000538841,;MPDZ,upstream_gene_variant,,ENST00000433359,;MPDZ,upstream_gene_variant,,ENST00000542239,;MPDZ,non_coding_transcript_exon_variant,,ENST00000539508,;MPDZ,non_coding_transcript_exon_variant,,ENST00000319198,; T ENST00000541718 Transcript synonymous_variant 3375/7603 3153/6126 1051/2041 G ggG/ggA 1 -1 MPDZ HGNC HGNC:7208 protein_coding YES CCDS47951.1 ENSP00000439807 O75970 UPI00015367D3 NM_003829.4 22/46 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF10,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 13168467 13168467 C T 1 0 0 0 0 0 0 0 1 9687 610 22 3 3 MPDZ 9 13168467 Silent SNP C C3L-00080_T 13168467 125226250 364 2462 MPDZ 0 . GRCh38 9 13193216 13193216 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1754G>T p.Gly585Val p.G585V ENST00000541718 14/46 76 64 12 85 85 0 strelka-varscan-mutect MPDZ,missense_variant,p.Gly585Val,ENST00000319217,;MPDZ,missense_variant,p.Gly585Val,ENST00000541718,NM_003829.4;MPDZ,missense_variant,p.Gly585Val,ENST00000381022,NM_001261406.1;MPDZ,missense_variant,p.Gly585Val,ENST00000546205,;MPDZ,missense_variant,p.Gly585Val,ENST00000447879,;MPDZ,missense_variant,p.Gly585Val,ENST00000536827,NM_001261407.1;MPDZ,upstream_gene_variant,,ENST00000539508,; A ENST00000541718 Transcript missense_variant 1976/7603 1754/6126 585/2041 G/V gGt/gTt 1 -1 MPDZ HGNC HGNC:7208 protein_coding YES CCDS47951.1 ENSP00000439807 O75970 UPI00015367D3 NM_003829.4 deleterious(0) 14/46 Gene3D:2.30.42.10,PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 7 13193216 13193216 C A 1 0 0 0 0 1 0 0 0 9687 507 18 2 2 MPDZ 9 13193216 Missense_Mutation SNP C C3L-00080_T 24749 13193216 125201501 365 2463 FREM1 0 . GRCh38 9 14789057 14789057 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.4039G>T p.Asp1347Tyr p.D1347Y ENST00000422223 24/38 120 96 24 122 122 0 strelka-varscan-mutect FREM1,missense_variant,p.Asp1347Tyr,ENST00000422223,NM_144966.5;FREM1,missense_variant,p.Asp1347Tyr,ENST00000380880,;RP11-265B7.1,upstream_gene_variant,,ENST00000635735,;FREM1,non_coding_transcript_exon_variant,,ENST00000466679,;FREM1,upstream_gene_variant,,ENST00000485068,;FREM1,non_coding_transcript_exon_variant,,ENST00000497634,;FREM1,intron_variant,,ENST00000380875,; A ENST00000422223 Transcript missense_variant 4855/10086 4039/6540 1347/2179 D/Y Gat/Tat 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 deleterious(0) 24/38 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 MODERATE 1 SNV 5 1 PASS rs1249220367 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 14789057 14789057 C A 1 0 0 0 0 1 0 0 0 5911 855 30 2 2 FREM1 9 14789057 Missense_Mutation SNP C C3L-00080_T 1595841 14789057 123605660 366 2464 CCDC171 0 . GRCh38 9 15724868 15724868 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.1584A>G p.= p.K528K ENST00000380701 14/26 210 155 55 283 283 0 strelka-varscan-mutect CCDC171,synonymous_variant,p.=,ENST00000380701,NM_173550.2; G ENST00000380701 Transcript synonymous_variant 1912/6512 1584/3981 528/1326 K aaA/aaG 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 14/26 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 15724868 15724868 A G 1 0 0 0 0 0 0 0 1 2488 69 3 5 5 CCDC171 9 15724868 Silent SNP A C3L-00080_T 935811 15724868 122669849 367 2465 ADAMTSL1 0 . GRCh38 9 18504862 18504862 + Missense_Mutation SNP G G A C3L-00080_T C3L-00080_N G G c.97G>A p.Asp33Asn p.D33N ENST00000380548 2/29 147 119 28 173 173 0 strelka-varscan-mutect ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000380548,NM_001040272.5;ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000276935,;ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000380566,;ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000327883,NM_052866.4;ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000380570,;ADAMTSL1,missense_variant,p.Asp33Asn,ENST00000431052,;ADAMTSL1,missense_variant,p.Asp81Asn,ENST00000636209,; A ENST00000380548 Transcript missense_variant 436/8030 97/5289 33/1762 D/N Gac/Aac COSM3906413,COSM3906414,COSM3906415 1 1 ADAMTSL1 HGNC HGNC:14632 protein_coding YES CCDS47954.1 ENSP00000369921 Q8N6G6 UPI000004FD83 NM_001040272.5 deleterious(0) 2/29 PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF157,hmmpanther:PTHR13723,Gene3D:2.20.100.10,Superfamily_domains:SSF82895 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 18504862 18504862 G A 1 0 0 0 0 1 0 0 0 318 1174 41 3 3 ADAMTSL1 9 18504862 Missense_Mutation SNP G C3L-00080_T 2779994 18504862 119889855 368 2466 DENND4C 0 . GRCh38 9 19305363 19305363 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.1323A>T p.= p.P441P ENST00000602925 10/32 80 55 25 98 98 0 strelka-varscan-mutect DENND4C,synonymous_variant,p.=,ENST00000602925,NM_017925.6;DENND4C,synonymous_variant,p.=,ENST00000434457,;DENND4C,synonymous_variant,p.=,ENST00000494124,;DENND4C,non_coding_transcript_exon_variant,,ENST00000380437,; T ENST00000602925 Transcript synonymous_variant 1739/6831 1323/5730 441/1909 P ccA/ccT 1 1 DENND4C HGNC HGNC:26079 protein_coding YES CCDS6491.3 ENSP00000473565 R4GNB2 UPI0000EE421F NM_017925.6 10/32 PROSITE_profiles:PS50211,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF17,Pfam_domain:PF02141,SMART_domains:SM00799 LOW 1 SNV 5 1 PASS rs897024840 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 19305363 19305363 A T 1 0 0 0 0 0 0 0 1 4239 204 8 4 4 DENND4C 9 19305363 Silent SNP A C3L-00080_T 800501 19305363 119089354 369 2467 TOPORS 0 . GRCh38 9 32541934 32541934 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.2591G>T p.Ser864Ile p.S864I ENST00000360538 3/3 107 81 26 190 190 0 strelka-varscan-mutect TOPORS,missense_variant,p.Ser864Ile,ENST00000360538,NM_005802.4;TOPORS,missense_variant,p.Ser799Ile,ENST00000379858,NM_001195622.1; A ENST00000360538 Transcript missense_variant 2708/4098 2591/3138 864/1045 S/I aGc/aTc COSM3996510 1 -1 TOPORS HGNC HGNC:21653 protein_coding YES CCDS6527.1 ENSP00000353735 Q9NS56 UPI000006F223 NM_005802.4 deleterious(0) 3/3 hmmpanther:PTHR22937:SF61,hmmpanther:PTHR22937 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 32541934 32541934 C A 1 0 0 0 0 1 0 0 0 16847 797 28 2 2 TOPORS 9 32541934 Missense_Mutation SNP C C3L-00080_T 13236571 32541934 105852783 370 2468 TAF1L 0 . GRCh38 9 32631534 32631534 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.4046T>G p.Ile1349Ser p.I1349S ENST00000242310 1/1 431 337 94 479 479 0 strelka-varscan-mutect TAF1L,missense_variant,p.Ile1349Ser,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; C ENST00000242310 Transcript missense_variant 4136/6216 4046/5481 1349/1826 I/S aTt/aGt 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 32631534 32631534 A C 1 0 0 0 0 1 0 0 0 15919 101 4 5 5 TAF1L 9 32631534 Missense_Mutation SNP A C3L-00080_T 89600 32631534 105763183 371 2469 TAF1L 0 . GRCh38 9 32634008 32634008 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1572T>A p.Asn524Lys p.N524K ENST00000242310 1/1 235 180 55 262 262 0 strelka-varscan-mutect TAF1L,missense_variant,p.Asn524Lys,ENST00000242310,NM_153809.2;RP11-555J4.4,non_coding_transcript_exon_variant,,ENST00000430787,; T ENST00000242310 Transcript missense_variant 1662/6216 1572/5481 524/1826 N/K aaT/aaA 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 32634008 32634008 A T 1 0 0 0 0 1 0 0 0 15919 214 8 4 4 TAF1L 9 32634008 Missense_Mutation SNP A C3L-00080_T 2474 32634008 105760709 372 2470 GLIPR2 0 . GRCh38 9 36162431 36162431 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.374G>T p.Gly125Val p.G125V ENST00000377960 5/5 181 139 42 193 193 0 strelka-varscan-mutect GLIPR2,missense_variant,p.Gly125Val,ENST00000377960,NM_001287013.1,NM_022343.3,NM_001287011.1;GLIPR2,missense_variant,p.Gly43Val,ENST00000619700,NM_001287014.1;GLIPR2,missense_variant,p.Gly99Val,ENST00000377959,NM_001287010.1;GLIPR2,3_prime_UTR_variant,,ENST00000396613,NM_001287012.1;GLIPR2,non_coding_transcript_exon_variant,,ENST00000474050,; T ENST00000377960 Transcript missense_variant 408/1890 374/465 125/154 G/V gGg/gTg 1 1 GLIPR2 HGNC HGNC:18007 protein_coding YES CCDS6598.1 ENSP00000367196 Q9H4G4 UPI000006DF50 NM_001287013.1,NM_022343.3,NM_001287011.1 deleterious(0) 5/5 Gene3D:3.40.33.10,Pfam_domain:PF00188,hmmpanther:PTHR10334,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 36162431 36162431 G T 1 0 0 0 0 1 0 0 0 6322 1232 43 2 2 GLIPR2 9 36162431 Missense_Mutation SNP G C3L-00080_T 3528423 36162431 102232286 373 2471 FBXO10 0 . GRCh38 9 37518330 37518330 + Missense_Mutation SNP C C A rs778381633 C3L-00080_T C3L-00080_N C C c.2309G>T p.Arg770Leu p.R770L ENST00000432825 9/11 228 180 48 260 260 0 strelka-varscan-mutect FBXO10,missense_variant,p.Arg770Leu,ENST00000432825,NM_012166.2;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000544475,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000541804,;FBXO10,downstream_gene_variant,,ENST00000543968,;FBXO10,downstream_gene_variant,,ENST00000544208,;FBXO10,3_prime_UTR_variant,,ENST00000276960,; A ENST00000432825 Transcript missense_variant 2358/4575 2309/2871 770/956 R/L cGa/cTa rs778381633,COSM5075040 1 -1 FBXO10 HGNC HGNC:13589 protein_coding YES CCDS47966.1 ENSP00000403802 Q9UK96 UPI00001C1EC6 NM_012166.2 tolerated(0.16) 9/11 hmmpanther:PTHR22990:SF19,hmmpanther:PTHR22990,Pfam_domain:PF05048,Gene3D:2.160.20.10,SMART_domains:SM00722,SMART_domains:SM00710,Superfamily_domains:SSF51126 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778381633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 37518330 37518330 C A 1 0 0 0 0 1 0 0 0 5589 884 31 1 1 FBXO10 9 37518330 Missense_Mutation SNP C C3L-00080_T 1355899 37518330 100876387 374 2472 SPATA31A1 0 . GRCh38 9 39359172 39359172 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1449C>A p.= p.A483A ENST00000377647 4/4 659 509 150 878 876 2 strelka-varscan-mutect SPATA31A1,synonymous_variant,p.=,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript synonymous_variant 1469/4256 1449/4086 483/1361 A gcC/gcA 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF14650 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 39359172 39359172 C A 1 0 0 0 0 0 0 0 1 15343 610 22 2 2 SPATA31A1 9 39359172 Silent SNP C C3L-00080_T 1840842 39359172 99035545 375 2473 TRPM3 0 . GRCh38 9 71121214 71121214 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.141C>T p.= p.C47C ENST00000377110 1/25 130 92 38 113 113 0 strelka-varscan-mutect TRPM3,synonymous_variant,p.=,ENST00000377110,NM_001007471.2;TRPM3,synonymous_variant,p.=,ENST00000377111,;TRPM3,intron_variant,,ENST00000357533,;TRPM3,intron_variant,,ENST00000354500,; A ENST00000377110 Transcript synonymous_variant 385/12258 141/5124 47/1707 C tgC/tgT 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 1/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 71121214 71121214 G A 1 0 0 0 0 0 0 0 1 17093 1195 42 3 3 TRPM3 9 71121214 Silent SNP G C3L-00080_T 31762042 71121214 67273503 376 2474 PRUNE2 0 . GRCh38 9 76705573 76705573 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6701G>T p.Ser2234Ile p.S2234I ENST00000376718 8/19 162 118 44 195 195 0 strelka-varscan-mutect PRUNE2,missense_variant,p.Ser2234Ile,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Ser1875Ile,ENST00000428286,;PRUNE2,missense_variant,p.Ser2234Ile,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,missense_variant,p.Ser1556Ile,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; A ENST00000376718 Transcript missense_variant 6825/12584 6701/9267 2234/3088 S/I aGc/aTc 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 deleterious(0.05) 8/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112 MODERATE 1 SNV 5 1 PASS rs887129397 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 76705573 76705573 C A 1 0 0 0 0 1 0 0 0 12791 797 28 2 2 PRUNE2 9 76705573 Missense_Mutation SNP C C3L-00080_T 5584359 76705573 61689144 377 2475 SPATA31D1 0 . GRCh38 9 81993013 81993013 + Missense_Mutation SNP G G T rs759725073 C3L-00080_T C3L-00080_N G G c.2543G>T p.Gly848Val p.G848V ENST00000344803 4/4 426 343 83 415 413 2 strelka-varscan-mutect SPATA31D1,missense_variant,p.Gly848Val,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; T ENST00000344803 Transcript missense_variant 2590/4833 2543/4731 848/1576 G/V gGg/gTg rs759725073 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.54) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12,Pfam_domain:PF14650 MODERATE 1 SNV 2 1 PASS rs759725073 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 81993013 81993013 G T 1 0 0 0 0 1 0 0 0 15347 1232 43 2 2 SPATA31D1 9 81993013 Missense_Mutation SNP G C3L-00080_T 5287440 81993013 56401704 378 2476 SPATA31D1 0 . GRCh38 9 81993774 81993774 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.3304C>T p.Gln1102Ter p.Q1102* ENST00000344803 4/4 107 86 21 140 140 0 strelka-varscan-mutect SPATA31D1,stop_gained,p.Gln1102Ter,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; T ENST00000344803 Transcript stop_gained 3351/4833 3304/4731 1102/1576 Q/* Cag/Tag 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 4/4 hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 81993774 81993774 C T 1 0 0 0 0 0 1 0 0 15347 827 29 3 3 SPATA31D1 9 81993774 Nonsense_Mutation SNP C C3L-00080_T 761 81993774 56400943 379 2477 PTCH1 0 . GRCh38 9 95459694 95459694 + Silent SNP G G A C3L-00080_T C3L-00080_N G G c.2793C>T p.= p.P931P ENST00000331920 17/24 294 225 69 350 350 0 strelka-varscan-mutect PTCH1,synonymous_variant,p.=,ENST00000430669,;PTCH1,synonymous_variant,p.=,ENST00000331920,NM_000264.3;PTCH1,synonymous_variant,p.=,ENST00000437951,NM_001083602.1;PTCH1,synonymous_variant,p.=,ENST00000418258,NM_001083607.1;PTCH1,synonymous_variant,p.=,ENST00000421141,NM_001083604.1,NM_001083605.1;PTCH1,synonymous_variant,p.=,ENST00000429896,NM_001083606.1;PTCH1,synonymous_variant,p.=,ENST00000375274,NM_001083603.1;PTCH1,non_coding_transcript_exon_variant,,ENST00000547615,;PTCH1,3_prime_UTR_variant,,ENST00000375290,; A ENST00000331920 Transcript synonymous_variant 3093/8057 2793/4344 931/1447 P ccC/ccT COSM327215,COSM327216,COSM327217,COSM327218 1 -1 PTCH1 HGNC HGNC:9585 protein_coding YES CCDS6714.1 ENSP00000332353 Q13635 UPI00001AFF9C NM_000264.3 17/24 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF61,TIGRFAM_domain:TIGR00918 1,1,1,1 LOW 1 SNV 5 1,1,1,1 1 PASS rs1162747889 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 95459694 95459694 G A 1 0 0 0 0 0 0 0 1 12883 1103 39 1 1 PTCH1 9 95459694 Silent SNP G C3L-00080_T 13465920 95459694 42935023 380 2478 OR13C4 0 . GRCh38 9 104526772 104526772 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.438T>C p.= p.S146S ENST00000277216 1/1 155 119 36 139 139 0 strelka-varscan-mutect OR13C4,synonymous_variant,p.=,ENST00000277216,NM_001001919.1;RP11-317C20.9,intron_variant,,ENST00000635678,; G ENST00000277216 Transcript synonymous_variant 438/957 438/957 146/318 S tcT/tcC 1 -1 OR13C4 HGNC HGNC:14722 protein_coding YES CCDS35088.1 ENSP00000277216 Q8NGS5 A0A126GVC9 UPI0000041B46 NM_001001919.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF14,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 104526772 104526772 A G 1 0 0 0 0 0 0 0 1 11012 175 7 5 5 OR13C4 9 104526772 Silent SNP A C3L-00080_T 9067078 104526772 33867945 381 2479 KIAA1958 0 . GRCh38 9 112659493 112659493 + Silent SNP G G T rs752839862 C3L-00080_T C3L-00080_N G G c.1659G>T p.= p.A553A ENST00000536272 5/5 216 168 48 301 301 0 strelka-varscan-mutect KIAA1958,synonymous_variant,p.=,ENST00000337530,NM_133465.3;KIAA1958,synonymous_variant,p.=,ENST00000536272,NM_001287036.1; T ENST00000536272 Transcript synonymous_variant 1834/7650 1659/2235 553/744 A gcG/gcT rs752839862 1 1 KIAA1958 HGNC HGNC:23427 protein_coding YES CCDS69642.1 ENSP00000440504 Q8N8K9 UPI000189A74D NM_001287036.1 5/5 hmmpanther:PTHR11697:SF95,hmmpanther:PTHR11697 LOW 1 SNV 1 1 PASS rs752839862 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 112659493 112659493 G T 1 0 0 0 0 0 0 0 1 8130 1074 38 1 1 KIAA1958 9 112659493 Silent SNP G C3L-00080_T 8132721 112659493 25735224 382 2480 RGS3 0 . GRCh38 9 113506453 113506453 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1045G>T p.Val349Leu p.V349L ENST00000374140 13/26 188 149 39 203 202 1 strelka-varscan-mutect RGS3,missense_variant,p.Val349Leu,ENST00000374140,NM_144488.5;RGS3,missense_variant,p.Val349Leu,ENST00000350696,NM_001282923.1;RGS3,missense_variant,p.Val68Leu,ENST00000343817,NM_130795.3;RGS3,missense_variant,p.Val68Leu,ENST00000394646,NM_001276261.1;RGS3,missense_variant,p.Val237Leu,ENST00000317613,NM_017790.4;RGS3,5_prime_UTR_variant,,ENST00000374136,NM_001322214.1;RGS3,non_coding_transcript_exon_variant,,ENST00000464306,;RGS3,non_coding_transcript_exon_variant,,ENST00000466314,;RGS3,non_coding_transcript_exon_variant,,ENST00000478599,; T ENST00000374140 Transcript missense_variant 1254/4591 1045/3597 349/1198 V/L Gtg/Ttg 1 1 RGS3 HGNC HGNC:9999 protein_coding YES CCDS43869.1 ENSP00000363255 P49796 UPI00001C0F58 NM_144488.5 deleterious(0) 13/26 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 113506453 113506453 G T 1 0 0 0 0 1 0 0 0 13477 1377 48 2 2 RGS3 9 113506453 Missense_Mutation SNP G C3L-00080_T 846960 113506453 24888264 383 2481 ASTN2 0 . GRCh38 9 117096090 117096090 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1077G>C p.Gln359His p.Q359H ENST00000361209 4/22 174 132 42 206 206 0 strelka-varscan-mutect ASTN2,missense_variant,p.Gln410His,ENST00000313400,;ASTN2,missense_variant,p.Gln359His,ENST00000361209,NM_014010.4;ASTN2,missense_variant,p.Gln137His,ENST00000373986,;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; G ENST00000361209 Transcript missense_variant 1209/4622 1077/3867 359/1288 Q/H caG/caC 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 tolerated_low_confidence(0.05) 4/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 117096090 117096090 C G 1 0 0 0 0 1 0 0 0 1212 796 28 4 4 ASTN2 9 117096090 Missense_Mutation SNP C C3L-00080_T 3589637 117096090 21298627 384 2482 ASTN2 0 . GRCh38 9 117214566 117214566 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.807T>A p.= p.R269R ENST00000361209 3/22 88 61 27 76 76 0 strelka-varscan-mutect ASTN2,synonymous_variant,p.=,ENST00000313400,;ASTN2,synonymous_variant,p.=,ENST00000361209,NM_014010.4;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3;ASTN2,upstream_gene_variant,,ENST00000373986,; T ENST00000361209 Transcript synonymous_variant 939/4622 807/3867 269/1288 R cgT/cgA 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 3/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 117214566 117214566 A T 1 0 0 0 0 0 0 0 1 1212 30 2 4 4 ASTN2 9 117214566 Silent SNP A C3L-00080_T 118476 117214566 21180151 385 2483 ASTN2 0 . GRCh38 9 117414673 117414673 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.266G>T p.Gly89Val p.G89V ENST00000361209 1/22 34 26 8 16 16 0 strelka-varscan-mutect ASTN2,missense_variant,p.Gly89Val,ENST00000313400,;ASTN2,missense_variant,p.Gly89Val,ENST00000361209,NM_014010.4;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; A ENST00000361209 Transcript missense_variant 398/4622 266/3867 89/1288 G/V gGg/gTg 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 deleterious_low_confidence(0) 1/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs917011968 . 0 206 4 0 0 0 0 0 -19.94639 1 1 1 1 0 A 3 1 7 117414673 117414673 C A 1 0 0 0 0 1 0 0 0 1212 623 22 2 2 ASTN2 9 117414673 Missense_Mutation SNP C C3L-00080_T 200107 117414673 20980044 386 2484 TLR4 0 . GRCh38 9 117712966 117712966 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.838C>A p.Leu280Met p.L280M ENST00000355622 3/3 201 167 34 271 270 1 strelka-varscan-mutect TLR4,missense_variant,p.Leu280Met,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Leu240Met,ENST00000394487,NM_003266.3;RNU6-1082P,upstream_gene_variant,,ENST00000364574,;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; A ENST00000355622 Transcript missense_variant 939/4844 838/2520 280/839 L/M Ctg/Atg 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 deleterious(0) 3/3 hmmpanther:PTHR24365:SF230,hmmpanther:PTHR24365,Gene3D:3.80.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 117712966 117712966 C A 1 0 0 0 0 1 0 0 0 16399 680 24 2 2 TLR4 9 117712966 Missense_Mutation SNP C C3L-00080_T 298293 117712966 20681751 387 2485 DENND1A 0 . GRCh38 9 123630432 123630432 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.663G>T p.Met221Ile p.M221I ENST00000373624 10/22 129 104 25 194 194 0 strelka-varscan-mutect DENND1A,missense_variant,p.Met221Ile,ENST00000373624,NM_020946.1;DENND1A,missense_variant,p.Met221Ile,ENST00000373620,NM_024820.2;DENND1A,missense_variant,p.Met189Ile,ENST00000373618,;DENND1A,missense_variant,p.Met121Ile,ENST00000394215,;DENND1A,non_coding_transcript_exon_variant,,ENST00000473039,;DENND1A,non_coding_transcript_exon_variant,,ENST00000474676,;DENND1A,non_coding_transcript_exon_variant,,ENST00000475615,; A ENST00000373624 Transcript missense_variant 865/5010 663/3030 221/1009 M/I atG/atT 1 -1 DENND1A HGNC HGNC:29324 protein_coding YES CCDS35133.1 ENSP00000362727 Q8TEH3 UPI00004589D2 NM_020946.1 deleterious(0) 10/22 Pfam_domain:PF02141,PROSITE_profiles:PS50211,hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF22,SMART_domains:SM00799 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 123630432 123630432 C A 1 0 0 0 0 1 0 0 0 4230 478 17 2 2 DENND1A 9 123630432 Missense_Mutation SNP C C3L-00080_T 5917466 123630432 14764285 388 2486 LMX1B 0 . GRCh38 9 126695959 126695959 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1040G>T p.Gly347Val p.G347V ENST00000355497 7/8 67 50 17 72 72 0 strelka-varscan-mutect LMX1B,missense_variant,p.Gly347Val,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Gly336Val,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Gly324Val,ENST00000561065,;LMX1B,missense_variant,p.Gly336Val,ENST00000526117,NM_002316.3; T ENST00000355497 Transcript missense_variant 1047/5809 1040/1221 347/406 G/V gGc/gTc 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 deleterious(0) 7/8 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96 MODERATE 1 SNV 1 1 PASS rs1015245215 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 126695959 126695959 G T 1 0 0 0 0 1 0 0 0 8789 1203 42 2 2 LMX1B 9 126695959 Missense_Mutation SNP G C3L-00080_T 3065527 126695959 11698758 389 2487 ADAMTS13 0 . GRCh38 9 133424472 133424472 + Silent SNP C C A C3L-00080_T C3L-00080_N C C c.324C>A p.= p.L108L ENST00000371929 3/29 329 257 72 345 345 0 strelka-varscan-mutect ADAMTS13,synonymous_variant,p.=,ENST00000371929,NM_139025.4;ADAMTS13,synonymous_variant,p.=,ENST00000355699,NM_139027.4;ADAMTS13,synonymous_variant,p.=,ENST00000356589,NM_139026.4;ADAMTS13,synonymous_variant,p.=,ENST00000371911,;ADAMTS13,5_prime_UTR_variant,,ENST00000371916,;ADAMTS13,non_coding_transcript_exon_variant,,ENST00000485925,;ADAMTS13,synonymous_variant,p.=,ENST00000495234,;ADAMTS13,synonymous_variant,p.=,ENST00000474918,; A ENST00000371929 Transcript synonymous_variant 768/4934 324/4284 108/1427 L ctC/ctA COSM384862,COSM5217763,COSM5217764 1 1 ADAMTS13 HGNC HGNC:1366 protein_coding YES CCDS6970.1 ENSP00000360997 Q76LX8 UPI0000000DAD NM_139025.4 3/29 PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF20,hmmpanther:PTHR13723,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 133424472 133424472 C A 1 0 0 0 0 0 0 0 1 302 813 29 2 2 ADAMTS13 9 133424472 Silent SNP C C3L-00080_T 6728513 133424472 4970245 390 2488 PMPCA 0 . GRCh38 9 136412864 136412864 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.413delG p.Gly138ValfsTer39 p.G138Vfs*39 ENST00000371717 4/13 151 125 26 210 210 0 sindel-varindel-pindel PMPCA,frameshift_variant,p.Gly138ValfsTer39,ENST00000371717,NM_015160.2;PMPCA,frameshift_variant,p.Val39TyrfsTer3,ENST00000399219,NM_001282946.1,NM_001282944.1;PMPCA,upstream_gene_variant,,ENST00000444897,;SDCCAG3,upstream_gene_variant,,ENST00000298537,NM_006643.3;SDCCAG3,upstream_gene_variant,,ENST00000357365,NM_001039707.1;SDCCAG3,upstream_gene_variant,,ENST00000371725,NM_001039708.1;SDCCAG3,upstream_gene_variant,,ENST00000371723,;SDCCAG3,upstream_gene_variant,,ENST00000446833,;PMPCA,non_coding_transcript_exon_variant,,ENST00000610649,;SDCCAG3,upstream_gene_variant,,ENST00000468963,;PMPCA,non_coding_transcript_exon_variant,,ENST00000612553,;PMPCA,non_coding_transcript_exon_variant,,ENST00000371720,;PMPCA,non_coding_transcript_exon_variant,,ENST00000620895,;PMPCA,non_coding_transcript_exon_variant,,ENST00000614402,;PMPCA,intron_variant,,ENST00000622209,;PMPCA,upstream_gene_variant,,ENST00000462616,;PMPCA,downstream_gene_variant,,ENST00000620412,;PMPCA,downstream_gene_variant,,ENST00000619192,; - ENST00000371717 Transcript frameshift_variant 508/2174 409/1578 137/525 G/X Ggg/gg 1 1 PMPCA HGNC HGNC:18667 protein_coding YES CCDS35180.1 ENSP00000360782 Q10713 UPI00000703D3 NM_015160.2 4/13 Gene3D:3.30.830.10,Pfam_domain:PF00675,hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF49,Superfamily_domains:SSF63411 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 136412864 136412864 G - 1 0 1 0 1 0 0 0 0 12247 1348 47 0 0 PMPCA 9 136412864 Frame_Shift_Del DEL G C3L-00080_T 2988392 136412864 1981853 391 2489 CLIC3 0 . GRCh38 9 136995272 136995272 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.290G>T p.Arg97Leu p.R97L ENST00000494426 4/6 209 172 37 245 244 1 strelka-varscan-mutect CLIC3,missense_variant,p.Arg97Leu,ENST00000494426,NM_004669.2;C9orf142,downstream_gene_variant,,ENST00000371620,NM_183241.1;CLIC3,non_coding_transcript_exon_variant,,ENST00000480181,;CLIC3,non_coding_transcript_exon_variant,,ENST00000473911,;C9orf142,downstream_gene_variant,,ENST00000498095,;C9orf142,downstream_gene_variant,,ENST00000493968,;C9orf142,downstream_gene_variant,,ENST00000481187,;C9orf142,downstream_gene_variant,,ENST00000467845,;C9orf142,downstream_gene_variant,,ENST00000483807,;C9orf142,downstream_gene_variant,,ENST00000492564,;C9orf142,downstream_gene_variant,,ENST00000463765,; A ENST00000494426 Transcript missense_variant 550/1017 290/711 97/236 R/L cGt/cTt 1 -1 CLIC3 HGNC HGNC:2064 protein_coding YES CCDS7021.1 ENSP00000419378 O95833 UPI00001AE551 NM_004669.2 tolerated(0.34) 4/6 PROSITE_profiles:PS50405,hmmpanther:PTHR11260:SF266,hmmpanther:PTHR11260,Superfamily_domains:SSF47616 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 136995272 136995272 C A 1 0 0 0 0 1 0 0 0 3296 536 19 1 1 CLIC3 9 136995272 Missense_Mutation SNP C C3L-00080_T 582408 136995272 1399445 392 2490 PRR26 0 . GRCh38 10 650396 650396 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.174C>A p.= p.P58P ENST00000441152 2/3 316 211 105 304 303 1 strelka-varscan-mutect PRR26,missense_variant,p.Pro96Thr,ENST00000381489,;PRR26,synonymous_variant,p.=,ENST00000441152,;DIP2C,intron_variant,,ENST00000280886,NM_014974.2;DIP2C,intron_variant,,ENST00000634311,; A ENST00000441152 Transcript synonymous_variant 337/2251 174/666 58/221 P ccC/ccA 1 1 PRR26 HGNC HGNC:30724 protein_coding YES ENSP00000414034 Q8N8Z3 UPI000006F105 2/3 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 650396 650396 C A 1 0 0 0 0 0 0 0 1 12733 623 22 2 2 PRR26 10 650396 Silent SNP C C3L-00080_T 650396 133147026 393 2491 UPF2 0 . GRCh38 10 11956523 11956523 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.2371G>A p.Val791Ile p.V791I ENST00000356352 12/21 217 146 71 226 224 2 strelka-varscan-mutect UPF2,missense_variant,p.Val791Ile,ENST00000356352,;UPF2,missense_variant,p.Val791Ile,ENST00000397053,NM_080599.2;UPF2,missense_variant,p.Val791Ile,ENST00000357604,NM_015542.3; T ENST00000356352 Transcript missense_variant,splice_region_variant 2845/5569 2371/3819 791/1272 V/I Gtt/Att 1 -1 UPF2 HGNC HGNC:17854 protein_coding YES CCDS7086.1 ENSP00000348708 Q9HAU5 UPI0000070D5E tolerated(0.4) 12/21 Gene3D:1.25.40.180,Pfam_domain:PF02854,hmmpanther:PTHR12839,SMART_domains:SM00543,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 189 0 9 12 0 0 0 -20 0.1176187 1 1 0 0 T 3 4 7 11956523 11956523 C T 1 0 0 0 0 1 0 0 0 17530 521 18 3 3 UPF2 10 11956523 Missense_Mutation SNP C C3L-00080_T 11306127 11956523 121840899 394 2492 MCM10 0 . GRCh38 10 13183098 13183098 + Nonsense_Mutation SNP G G T rs376624218 C3L-00080_T C3L-00080_N G G c.1099G>T p.Glu367Ter p.E367* ENST00000484800 8/20 138 107 31 111 111 0 strelka-varscan-mutect MCM10,stop_gained,p.Glu366Ter,ENST00000378694,;MCM10,stop_gained,p.Glu366Ter,ENST00000378714,NM_018518.4;MCM10,stop_gained,p.Glu367Ter,ENST00000484800,NM_182751.2; T ENST00000484800 Transcript stop_gained,splice_region_variant 1202/3157 1099/2628 367/875 E/* Gag/Tag rs376624218 1 1 MCM10 HGNC HGNC:18043 protein_coding YES CCDS7096.1 ENSP00000418268 Q7L590 UPI000013C5E2 NM_182751.2 8/20 hmmpanther:PTHR13454 HIGH 1 SNV 1 1 PASS rs376624218 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 13183098 13183098 G T 1 0 0 0 0 0 1 0 0 9317 1188 41 2 2 MCM10 10 13183098 Nonsense_Mutation SNP G C3L-00080_T 1226575 13183098 120614324 395 2493 RSU1 0 . GRCh38 10 16593474 16593474 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.754G>T p.Ala252Ser p.A252S ENST00000377921 8/8 315 227 88 251 251 0 strelka-varscan-mutect RSU1,missense_variant,p.Ala252Ser,ENST00000377921,;RSU1,missense_variant,p.Ala252Ser,ENST00000345264,NM_012425.3;RSU1,missense_variant,p.Ala199Ser,ENST00000602389,NM_152724.2;RSU1,non_coding_transcript_exon_variant,,ENST00000464074,;RSU1,non_coding_transcript_exon_variant,,ENST00000377911,; A ENST00000377921 Transcript missense_variant 1056/3919 754/834 252/277 A/S Gcc/Tcc 1 -1 RSU1 HGNC HGNC:10464 protein_coding YES CCDS7112.1 ENSP00000367154 Q15404 UPI0000000C72 tolerated(0.16) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9989967 1 1 1 0 A 3 1 7 16593474 16593474 C A 1 0 0 0 0 1 0 0 0 13975 739 26 2 2 RSU1 10 16593474 Missense_Mutation SNP C C3L-00080_T 3410376 16593474 117203948 396 2494 SPAG6 0 . GRCh38 10 22368548 22368548 + Silent SNP T T A novel C3L-00080_T C3L-00080_N T T c.342T>A p.= p.S114S ENST00000376624 4/11 287 206 81 209 209 0 strelka-varscan-mutect SPAG6,synonymous_variant,p.=,ENST00000376603,NM_001253855.1;SPAG6,synonymous_variant,p.=,ENST00000376624,NM_012443.3;SPAG6,synonymous_variant,p.=,ENST00000313311,NM_172242.2;SPAG6,synonymous_variant,p.=,ENST00000538630,NM_001253854.1;SPAG6,synonymous_variant,p.=,ENST00000435326,;SPAG6,intron_variant,,ENST00000456231,;RP11-301N24.3,intron_variant,,ENST00000422675,;SPAG6,intron_variant,,ENST00000488555,; A ENST00000376624 Transcript synonymous_variant 484/2605 342/1530 114/509 S tcT/tcA 1 1 SPAG6 HGNC HGNC:11215 protein_coding YES CCDS7139.1 ENSP00000365811 O75602 A0A140VJU9 UPI0000073ED7 NM_012443.3 4/11 hmmpanther:PTHR23314:SF1,hmmpanther:PTHR23314,Pfam_domain:PF00514,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 22368548 22368548 T A 1 0 0 0 0 0 0 0 1 15313 1538 54 4 4 SPAG6 10 22368548 Silent SNP T C3L-00080_T 5775074 22368548 111428874 397 2495 ARMC3 0 . GRCh38 10 23037402 23037402 + Missense_Mutation SNP G G T rs773656092 C3L-00080_T C3L-00080_N G G c.2542G>T p.Val848Leu p.V848L ENST00000298032 19/19 167 119 48 130 130 0 strelka-varscan-mutect ARMC3,missense_variant,p.Val585Leu,ENST00000376528,NM_001282747.1;ARMC3,missense_variant,p.Val848Leu,ENST00000298032,NM_173081.4;ARMC3,missense_variant,p.Val841Leu,ENST00000409983,NM_001282745.1; T ENST00000298032 Transcript missense_variant 2626/2811 2542/2619 848/872 V/L Gtg/Ttg rs773656092,COSM1245485 1 1 ARMC3 HGNC HGNC:30964 protein_coding YES CCDS7142.1 ENSP00000298032 Q5W041 UPI0000161785 NM_173081.4 deleterious(0.01) 19/19 hmmpanther:PTHR23315:SF78,hmmpanther:PTHR23315,Pfam_domain:PF14381 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773656092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23037402 23037402 G T 1 0 0 0 0 1 0 0 0 1093 1145 40 1 1 ARMC3 10 23037402 Missense_Mutation SNP G C3L-00080_T 668854 23037402 110760020 398 2496 PTF1A 0 . GRCh38 10 23192749 23192749 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.219G>T p.= p.A73A ENST00000376504 1/2 77 39 38 52 52 0 strelka-mutect PTF1A,synonymous_variant,p.=,ENST00000376504,NM_178161.2; T ENST00000376504 Transcript synonymous_variant 423/1537 219/987 73/328 A gcG/gcT 1 1 PTF1A HGNC HGNC:23734 protein_coding YES CCDS7143.1 ENSP00000365687 Q7RTS3 UPI000018F612 NM_178161.2 1/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF59,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs1038858636 . 0 196 13 0 0 0 0 0 -20 0.9999832 1 1 1 0 T 2 4 7 23192749 23192749 G T 1 0 0 0 0 0 0 0 1 12893 1074 38 1 1 PTF1A 10 23192749 Silent SNP G C3L-00080_T 155347 23192749 110604673 399 2497 THNSL1 0 . GRCh38 10 25024898 25024898 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1675A>T p.Thr559Ser p.T559S ENST00000524413 3/3 113 84 29 140 140 0 strelka-varscan-mutect THNSL1,missense_variant,p.Thr559Ser,ENST00000524413,;THNSL1,missense_variant,p.Thr559Ser,ENST00000376356,NM_024838.4;ENKUR,intron_variant,,ENST00000615958,NM_001270383.1; T ENST00000524413 Transcript missense_variant 2022/3788 1675/2232 559/743 T/S Acc/Tcc 1 1 THNSL1 HGNC HGNC:26160 protein_coding YES CCDS7147.1 ENSP00000434887 Q8IYQ7 UPI00001F9045 tolerated(0.52) 3/3 hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF118,TIGRFAM_domain:TIGR00260,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 25024898 25024898 A T 1 0 0 0 0 1 0 0 0 16297 43 2 4 4 THNSL1 10 25024898 Missense_Mutation SNP A C3L-00080_T 1832149 25024898 108772524 400 2498 ARMC4 0 . GRCh38 10 27936732 27936732 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.2246T>C p.Val749Ala p.V749A ENST00000305242 15/20 370 311 59 329 329 0 strelka-varscan-mutect ARMC4,missense_variant,p.Val749Ala,ENST00000305242,NM_018076.3,NM_001290020.1; G ENST00000305242 Transcript missense_variant 2339/3572 2246/3135 749/1044 V/A gTt/gCt 1 -1 ARMC4 HGNC HGNC:25583 protein_coding YES CCDS7157.1 ENSP00000306410 Q5T2S8 A0A140VKF7 UPI00001A95E1 NM_018076.3,NM_001290020.1 tolerated(0.06) 15/20 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF44,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 27936732 27936732 A G 1 0 0 0 0 1 0 0 0 1094 43 2 5 5 ARMC4 10 27936732 Missense_Mutation SNP A C3L-00080_T 2911834 27936732 105860690 401 2499 ARHGAP12 0 . GRCh38 10 31807659 31807659 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.2540G>A p.= p.*847* ENST00000344936 20/20 130 109 21 138 138 0 strelka-varscan-mutect ARHGAP12,stop_retained_variant,p.=,ENST00000396144,NM_001270695.1;ARHGAP12,stop_retained_variant,p.=,ENST00000375245,NM_001270697.1;ARHGAP12,stop_retained_variant,p.=,ENST00000375250,NM_001270696.1,NM_001270698.1;ARHGAP12,stop_retained_variant,p.=,ENST00000311380,NM_001270699.1;ARHGAP12,stop_retained_variant,p.=,ENST00000344936,NM_018287.6;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000492028,;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000493008,;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000497085,;ARHGAP12,downstream_gene_variant,,ENST00000497103,; T ENST00000344936 Transcript stop_retained_variant 2775/4128 2540/2541 847/846 * tGa/tAa 1 -1 ARHGAP12 HGNC HGNC:16348 protein_coding YES CCDS7170.1 ENSP00000345808 Q8IWW6 UPI000007445E NM_018287.6 20/20 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 31807659 31807659 C T 1 0 0 0 0 0 0 0 1 989 837 29 3 3 ARHGAP12 10 31807659 Silent SNP C C3L-00080_T 3870927 31807659 101989763 402 2500 FZD8 0 . GRCh38 10 35640727 35640727 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.703C>T p.Arg235Cys p.R235C ENST00000374694 1/1 90 58 32 57 57 0 strelka-varscan-mutect FZD8,missense_variant,p.Arg235Cys,ENST00000374694,NM_031866.2;FZD8,downstream_gene_variant,,ENST00000579659,; A ENST00000374694 Transcript missense_variant 1552/4030 703/2085 235/694 R/C Cgc/Tgc 1 -1 FZD8 HGNC HGNC:4046 protein_coding YES CCDS7192.1 ENSP00000363826 Q9H461 UPI0000047F3B NM_031866.2 deleterious(0) 1/1 hmmpanther:PTHR11309:SF89,hmmpanther:PTHR11309 MODERATE 1 SNV 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 35640727 35640727 G A 1 0 0 0 0 1 0 0 0 6007 1116 39 1 1 FZD8 10 35640727 Missense_Mutation SNP G C3L-00080_T 3833068 35640727 98156695 403 2501 ANTXRL 0 . GRCh38 10 46330012 46330012 + Silent SNP G G C novel C3L-00080_T C3L-00080_N G G c.1824G>C p.= p.P608P ENST00000620264 17/17 168 130 38 100 100 0 strelka-varscan-mutect ANTXRL,missense_variant,p.Arg535Pro,ENST00000622632,;ANTXRL,synonymous_variant,p.=,ENST00000620264,NM_001278688.2;ANTXRL,3_prime_UTR_variant,,ENST00000617088,; C ENST00000620264 Transcript synonymous_variant 2089/2206 1824/1896 608/631 P ccG/ccC 1 1 ANTXRL HGNC HGNC:27277 protein_coding YES CCDS60524.1 ENSP00000480615 A6NF34 UPI00015B6A6A NM_001278688.2 17/17 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1214044949 . 0 202 3 5 0 0 0 0 -20 0.9992609 1 1 1 0 C 2 2 7 46330012 46330012 G C 1 0 0 0 0 0 0 0 1 820 1074 38 4 4 ANTXRL 10 46330012 Silent SNP G C3L-00080_T 10689285 46330012 87467410 404 2502 RBP3 0 . GRCh38 10 47350925 47350925 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2441A>T p.Asp814Val p.D814V ENST00000584701 1/4 680 463 217 495 495 0 strelka-varscan-mutect RBP3,missense_variant,p.Asp814Val,ENST00000584701,NM_002900.2; T ENST00000584701 Transcript missense_variant 2555/4276 2441/3744 814/1247 D/V gAc/gTc 1 1 RBP3 HGNC HGNC:9921 protein_coding YES CCDS73119.1 ENSP00000463151 P10745 UPI000012D87A NM_002900.2 deleterious(0) 1/4 Gene3D:3.90.226.10,Pfam_domain:PF03572,hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF3,SMART_domains:SM00245,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 47350925 47350925 A T 1 0 0 0 0 1 0 0 0 13325 275 10 4 4 RBP3 10 47350925 Missense_Mutation SNP A C3L-00080_T 1020913 47350925 86446497 405 2503 WDFY4 0 . GRCh38 10 48735933 48735933 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1741G>T p.Glu581Ter p.E581* ENST00000325239 10/61 262 179 83 238 238 0 strelka-varscan-mutect WDFY4,stop_gained,p.Glu581Ter,ENST00000325239,NM_020945.1;WDFY4,stop_gained,p.Glu581Ter,ENST00000360890,; T ENST00000325239 Transcript stop_gained 1741/9555 1741/9555 581/3184 E/* Gag/Tag 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 10/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 HIGH SNV 5 1 PASS rs961602324 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 48735933 48735933 G T 1 0 0 0 0 0 1 0 0 17831 1059 37 1 1 WDFY4 10 48735933 Nonsense_Mutation SNP G C3L-00080_T 1385008 48735933 85061489 406 2504 FAM21A 0 . GRCh38 10 50129629 50129629 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.3298G>C p.Ala1100Pro p.A1100P ENST00000282633 29/31 813 431 382 893 893 0 strelka-varscan-mutect FAM21A,missense_variant,p.Ala1079Pro,ENST00000351071,NM_001291398.1;FAM21A,missense_variant,p.Ala1038Pro,ENST00000314664,;FAM21A,missense_variant,p.Ala1004Pro,ENST00000611324,;FAM21A,missense_variant,p.Ala1012Pro,ENST00000399339,;FAM21A,missense_variant,p.Ala1100Pro,ENST00000282633,NM_001005751.2;FAM21A,downstream_gene_variant,,ENST00000454806,;FAM21A,3_prime_UTR_variant,,ENST00000434114,; C ENST00000282633 Transcript missense_variant 3343/4272 3298/4026 1100/1341 A/P Gct/Cct 1 1 FAM21A HGNC HGNC:23416 protein_coding YES CCDS41527.1 ENSP00000282633 Q641Q2 UPI000044FEAB NM_001005751.2 tolerated(0.27) 29/31 hmmpanther:PTHR21669,hmmpanther:PTHR21669:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1358423847 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 50129629 50129629 G C 1 0 0 0 0 1 0 0 0 5411 1087 38 4 4 FAM21A 10 50129629 Missense_Mutation SNP G C3L-00080_T 1393696 50129629 83667793 407 2505 TET1 0 . GRCh38 10 68573977 68573977 + Nonsense_Mutation SNP C C T rs754378171 C3L-00080_T C3L-00080_N C C c.1639C>T p.Gln547Ter p.Q547* ENST00000373644 2/12 309 230 79 334 332 2 strelka-varscan-mutect TET1,stop_gained,p.Gln547Ter,ENST00000373644,NM_030625.2; T ENST00000373644 Transcript stop_gained 1848/9288 1639/6411 547/2136 Q/* Cag/Tag rs754378171 1 1 TET1 HGNC HGNC:29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 2/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 HIGH 1 SNV 1 1 PASS rs754378171 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 68573977 68573977 C T 1 0 0 0 0 0 1 0 0 16190 595 21 3 3 TET1 10 68573977 Nonsense_Mutation SNP C C3L-00080_T 18444348 68573977 65223445 408 2506 UNC5B 0 . GRCh38 10 71288712 71288712 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.1046C>T p.Thr349Ile p.T349I ENST00000335350 7/17 83 61 22 99 99 0 strelka-varscan-mutect UNC5B,missense_variant,p.Thr349Ile,ENST00000335350,NM_170744.4;UNC5B,missense_variant,p.Thr349Ile,ENST00000373192,NM_001244889.1; T ENST00000335350 Transcript missense_variant 1462/6841 1046/2838 349/945 T/I aCa/aTa 1 1 UNC5B HGNC HGNC:12568 protein_coding YES CCDS7309.1 ENSP00000334329 Q8IZJ1 UPI000000D753 NM_170744.4 deleterious(0) 7/17 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF6,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 71288712 71288712 C T 1 0 0 0 0 1 0 0 0 17516 478 17 3 3 UNC5B 10 71288712 Missense_Mutation SNP C C3L-00080_T 2714735 71288712 62508710 409 2507 KCNMA1 0 . GRCh38 10 76944868 76944868 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.2807C>T p.Thr936Ile p.T936I ENST00000286628 23/28 324 267 57 412 411 1 strelka-varscan-mutect KCNMA1,missense_variant,p.Thr743Ile,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,missense_variant,p.Thr878Ile,ENST00000286627,NM_002247.3;KCNMA1,missense_variant,p.Thr936Ile,ENST00000286628,NM_001161352.1;KCNMA1,missense_variant,p.Thr771Ile,ENST00000354353,;KCNMA1,missense_variant,p.Thr713Ile,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,missense_variant,p.Thr878Ile,ENST00000372443,;KCNMA1,missense_variant,p.Thr878Ile,ENST00000372440,NM_001014797.2;KCNMA1,missense_variant,p.Thr936Ile,ENST00000404771,;KCNMA1,missense_variant,p.Thr910Ile,ENST00000457953,;KCNMA1,missense_variant,p.Thr919Ile,ENST00000626620,NM_001161353.1;KCNMA1,missense_variant,p.Thr871Ile,ENST00000372437,;KCNMA1,missense_variant,p.Thr852Ile,ENST00000372421,;KCNMA1,missense_variant,p.Thr815Ile,ENST00000372408,;KCNMA1,missense_variant,p.Thr829Ile,ENST00000372403,;KCNMA1,missense_variant,p.Thr714Ile,ENST00000404857,NM_001271518.1;KCNMA1,missense_variant,p.Thr586Ile,ENST00000434208,;KCNMA1-AS1,intron_variant,,ENST00000600782,;KCNMA1-AS1,intron_variant,,ENST00000598613,;KCNMA1-AS1,intron_variant,,ENST00000617241,;KCNMA1-AS1,intron_variant,,ENST00000426234,;KCNMA1-AS1,intron_variant,,ENST00000458661,;KCNMA1-AS1,intron_variant,,ENST00000608791,;KCNMA1-AS1,intron_variant,,ENST00000611475,; A ENST00000286628 Transcript missense_variant 2807/6100 2807/3711 936/1236 T/I aCt/aTt 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 deleterious(0.01) 23/28 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 76944868 76944868 G A 1 0 0 0 0 1 0 0 0 7990 1029 36 3 3 KCNMA1 10 76944868 Missense_Mutation SNP G C3L-00080_T 5656156 76944868 56852554 410 2508 DLG5 0 . GRCh38 10 77821114 77821114 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.3370G>T p.Ala1124Ser p.A1124S ENST00000372391 15/32 92 74 18 81 81 0 strelka-varscan-mutect DLG5,missense_variant,p.Ala1124Ser,ENST00000372391,NM_004747.3;DLG5,intron_variant,,ENST00000424842,;DLG5,non_coding_transcript_exon_variant,,ENST00000459739,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;DLG5,upstream_gene_variant,,ENST00000463362,;DLG5,upstream_gene_variant,,ENST00000476354,;DLG5,downstream_gene_variant,,ENST00000466198,; A ENST00000372391 Transcript missense_variant 3376/7415 3370/5760 1124/1919 A/S Gct/Tct 1 -1 DLG5 HGNC HGNC:2904 protein_coding YES CCDS7353.2 ENSP00000361467 Q8TDM6 UPI0000470041 NM_004747.3 tolerated(0.11) 15/32 hmmpanther:PTHR13865:SF31,hmmpanther:PTHR13865 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 77821114 77821114 C A 1 0 0 0 0 1 0 0 0 4365 710 25 2 2 DLG5 10 77821114 Missense_Mutation SNP C C3L-00080_T 876246 77821114 55976308 411 2509 LRIT2 0 . GRCh38 10 84224679 84224679 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.546G>C p.Gln182His p.Q182H ENST00000538192 2/4 122 80 42 134 134 0 strelka-varscan-mutect LRIT2,missense_variant,p.Gln182His,ENST00000538192,NM_001284223.1;LRIT2,missense_variant,p.Gln182His,ENST00000372113,NM_001017924.3; G ENST00000538192 Transcript missense_variant 615/3177 546/1683 182/560 Q/H caG/caC 1 -1 LRIT2 HGNC HGNC:23443 protein_coding YES CCDS60581.1 ENSP00000438264 A6NDA9 UPI000189A8DA NM_001284223.1 tolerated(0.1) 2/4 Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 84224679 84224679 C G 1 0 0 0 0 1 0 0 0 8843 796 28 4 4 LRIT2 10 84224679 Missense_Mutation SNP C C3L-00080_T 6403565 84224679 49572743 412 2510 EXOC6 0 . GRCh38 10 92899613 92899613 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.427A>G p.Ser143Gly p.S143G ENST00000260762 5/22 69 55 14 132 132 0 strelka-varscan-mutect EXOC6,missense_variant,p.Ser143Gly,ENST00000260762,NM_001319195.1,NM_019053.4;EXOC6,missense_variant,p.Ser138Gly,ENST00000371552,NM_001319194.1,NM_001013848.2;EXOC6,missense_variant,p.Ser143Gly,ENST00000443748,NM_001319200.1;EXOC6,missense_variant,p.Ser143Gly,ENST00000371543,; G ENST00000260762 Transcript missense_variant 441/3564 427/2415 143/804 S/G Agt/Ggt 1 1 EXOC6 HGNC HGNC:23196 protein_coding YES CCDS7424.2 ENSP00000260762 Q8TAG9 UPI0000141914 NM_001319195.1,NM_019053.4 tolerated(0.27) 5/22 hmmpanther:PTHR12702,hmmpanther:PTHR12702:SF2,PIRSF_domain:PIRSF025007 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 92899613 92899613 A G 1 0 0 0 0 1 0 0 0 5176 188 7 5 5 EXOC6 10 92899613 Missense_Mutation SNP A C3L-00080_T 8674934 92899613 40897809 413 2511 SLC18A2 0 . GRCh38 10 117255290 117255290 + Silent SNP C C T rs549412168 C3L-00080_T C3L-00080_N C C c.714C>T p.= p.F238F ENST00000298472 7/16 169 97 72 113 113 0 strelka-varscan-mutect SLC18A2,synonymous_variant,p.=,ENST00000298472,NM_003054.4;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,; T ENST00000298472 Transcript synonymous_variant 857/3852 714/1545 238/514 F ttC/ttT rs549412168,COSM2055062 1 1 SLC18A2 HGNC HGNC:10935 protein_coding YES CCDS7599.1 ENSP00000298472 Q05940 UPI00001389DE NM_003054.4 7/16 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF8,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs549412168 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 117255290 117255290 C T 1 0 0 0 0 0 0 0 1 14691 883 31 1 1 SLC18A2 10 117255290 Silent SNP C C3L-00080_T 24355677 117255290 16542132 414 2512 TACC2 0 . GRCh38 10 122210981 122210981 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.6556G>T p.Ala2186Ser p.A2186S ENST00000369005 9/23 168 136 32 150 150 0 strelka-varscan-mutect TACC2,missense_variant,p.Ala2186Ser,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Ala2186Ser,ENST00000334433,;TACC2,missense_variant,p.Ala2190Ser,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Ala2190Ser,ENST00000453444,;TACC2,missense_variant,p.Ala2141Ser,ENST00000515603,NM_001291876.1;TACC2,missense_variant,p.Ala332Ser,ENST00000513429,NM_206861.2;TACC2,missense_variant,p.Ala264Ser,ENST00000360561,NM_206860.2;TACC2,missense_variant,p.Ala264Ser,ENST00000368999,;TACC2,missense_variant,p.Ala332Ser,ENST00000358010,;TACC2,missense_variant,p.Ala264Ser,ENST00000369004,NM_001291878.1;TACC2,missense_variant,p.Ala264Ser,ENST00000260733,NM_006997.3;TACC2,missense_variant,p.Ala281Ser,ENST00000514539,;TACC2,missense_variant,p.Ala27Ser,ENST00000505639,;TACC2,5_prime_UTR_variant,,ENST00000369000,;TACC2,5_prime_UTR_variant,,ENST00000369001,NM_001291879.1;TACC2,upstream_gene_variant,,ENST00000496913,;TACC2,upstream_gene_variant,,ENST00000508411,;TACC2,downstream_gene_variant,,ENST00000493951,;TACC2,downstream_gene_variant,,ENST00000492237,;TACC2,missense_variant,p.Ala33Ser,ENST00000440764,;TACC2,non_coding_transcript_exon_variant,,ENST00000368997,; T ENST00000369005 Transcript missense_variant 6896/9673 6556/8847 2186/2948 A/S Gcc/Tcc 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 tolerated(0.26) 9/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS rs914335011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 122210981 122210981 G T 1 0 0 0 0 1 0 0 0 15898 971 34 2 2 TACC2 10 122210981 Missense_Mutation SNP G C3L-00080_T 4955691 122210981 11586441 415 2513 TEX36 0 . GRCh38 10 125655908 125655908 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.553G>T p.Glu185Ter p.E185* ENST00000368821 4/4 53 41 12 69 69 0 strelka-varscan-mutect TEX36,stop_gained,p.Glu185Ter,ENST00000368821,NM_001128202.1;TEX36,intron_variant,,ENST00000532135,NM_001318133.1;TEX36,intron_variant,,ENST00000526819,; A ENST00000368821 Transcript stop_gained 708/922 553/561 185/186 E/* Gag/Tag 1 -1 TEX36 HGNC HGNC:31653 protein_coding YES CCDS44493.1 ENSP00000357811 Q5VZQ5 UPI00001D808E NM_001128202.1 4/4 hmmpanther:PTHR35440,hmmpanther:PTHR35440:SF1 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 125655908 125655908 C A 1 0 0 0 0 0 1 0 0 16212 864 30 2 2 TEX36 10 125655908 Nonsense_Mutation SNP C C3L-00080_T 3444927 125655908 8141514 416 2514 AP2A2 0 . GRCh38 11 1008034 1008034 + Silent SNP C C T rs369597745 C3L-00080_T C3L-00080_N C C c.2322C>T p.= p.P774P ENST00000332231 18/22 363 269 94 337 337 0 strelka-varscan-mutect AP2A2,synonymous_variant,p.=,ENST00000332231,NM_001242837.1;AP2A2,synonymous_variant,p.=,ENST00000448903,NM_012305.3;AP2A2,intron_variant,,ENST00000534328,;MUC6,downstream_gene_variant,,ENST00000421673,NM_005961.2;AP2A2,non_coding_transcript_exon_variant,,ENST00000525891,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529438,;AP2A2,3_prime_UTR_variant,,ENST00000528815,;AP2A2,non_coding_transcript_exon_variant,,ENST00000531497,;AP2A2,non_coding_transcript_exon_variant,,ENST00000526401,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529427,;AP2A2,upstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526376,; T ENST00000332231 Transcript synonymous_variant 2535/4656 2322/2823 774/940 P ccC/ccT rs369597745,COSM5037487 1 1 AP2A2 HGNC HGNC:562 protein_coding YES CCDS73234.1 ENSP00000327694 O94973 UPI000050AA18 NM_001242837.1 18/22 Gene3D:1kyfA01,PIRSF_domain:PIRSF037091,Pfam_domain:PF02883,SMART_domains:SM00809,Superfamily_domains:SSF49348 0,1 LOW 1 SNV 1 0,1 1 PASS rs369597745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 1008034 1008034 C T 1 0 0 0 0 0 0 0 1 856 639 23 1 1 AP2A2 11 1008034 Silent SNP C C3L-00080_T 1008034 134078588 417 2515 MUC5AC 0 . GRCh38 11 1194539 1194539 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.15059T>A p.Val5020Glu p.V5020E ENST00000621226 35/49 151 81 70 172 171 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Val5020Glu,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 15106/17448 15059/16965 5020/5654 V/E gTg/gAg 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated(0.33) 35/49 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS rs1397134509 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 1194539 1194539 T A 1 0 0 0 0 1 0 0 0 9978 1696 59 4 4 MUC5AC 11 1194539 Missense_Mutation SNP T C3L-00080_T 186505 1194539 133892083 418 2516 TRPM5 0 . GRCh38 11 2420360 2420360 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.511G>T p.Gly171Cys p.G171C ENST00000155858 4/24 128 77 51 143 143 0 strelka-varscan-mutect TRPM5,missense_variant,p.Gly171Cys,ENST00000155858,NM_014555.3;TRPM5,missense_variant,p.Gly165Cys,ENST00000533881,;TRPM5,missense_variant,p.Gly171Cys,ENST00000533060,;TRPM5,missense_variant,p.Gly171Cys,ENST00000528453,; A ENST00000155858 Transcript missense_variant 520/3929 511/3498 171/1165 G/C Ggc/Tgc 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 deleterious(0.03) 4/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 2420360 2420360 C A 1 0 0 0 0 1 0 0 0 17095 623 22 2 2 TRPM5 11 2420360 Missense_Mutation SNP C C3L-00080_T 1225821 2420360 132666262 419 2517 CHRNA10 0 . GRCh38 11 3667268 3667268 + Nonsense_Mutation SNP C C A rs769677015 C3L-00080_T C3L-00080_N C C c.859G>T p.Glu287Ter p.E287* ENST00000250699 4/5 201 157 44 206 206 0 strelka-varscan-mutect CHRNA10,stop_gained,p.Glu287Ter,ENST00000250699,NM_020402.3;CHRNA10,synonymous_variant,p.=,ENST00000534359,NM_001303034.1,NM_001303035.1;ART1,downstream_gene_variant,,ENST00000250693,NM_004314.2;NUP98,downstream_gene_variant,,ENST00000533346,;Y_RNA,upstream_gene_variant,,ENST00000364409,;Y_RNA,upstream_gene_variant,,ENST00000363331,;CHRNA10,downstream_gene_variant,,ENST00000493827,;CHRNA10,3_prime_UTR_variant,,ENST00000526599,; A ENST00000250699 Transcript stop_gained 931/1945 859/1353 287/450 E/* Gag/Tag rs769677015 1 -1 CHRNA10 HGNC HGNC:13800 protein_coding YES CCDS7745.1 ENSP00000250699 Q9GZZ6 UPI0000038CF1 NM_020402.3 4/5 hmmpanther:PTHR18945:SF566,hmmpanther:PTHR18945,Gene3D:1.20.120.370,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112 HIGH 1 SNV 1 1 PASS rs769677015 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 3667268 3667268 C A 1 0 0 0 0 0 1 0 0 3142 893 31 1 1 CHRNA10 11 3667268 Nonsense_Mutation SNP C C3L-00080_T 1246908 3667268 131419354 420 2518 OR51F2 0 . GRCh38 11 4821760 4821760 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.375G>T p.Glu125Asp p.E125D ENST00000322110 1/1 47 29 18 68 68 0 strelka-varscan-mutect OR51F2,missense_variant,p.Glu125Asp,ENST00000322110,NM_001004753.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322110 Transcript missense_variant 375/1029 375/1029 125/342 E/D gaG/gaT 1 1 OR51F2 HGNC HGNC:15197 protein_coding YES CCDS31361.1 ENSP00000323952 Q8NH61 UPI000004B219 NM_001004753.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF87,hmmpanther:PTHR26450,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS rs1033058177 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 4821760 4821760 G T 1 0 0 0 0 1 0 0 0 11170 1020 36 2 2 OR51F2 11 4821760 Missense_Mutation SNP G C3L-00080_T 1154492 4821760 130264862 421 2519 DCHS1 0 . GRCh38 11 6630054 6630054 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.4740G>T p.= p.V1580V ENST00000299441 10/21 33 12 21 23 23 0 strelka-varscan-mutect DCHS1,synonymous_variant,p.=,ENST00000299441,NM_003737.3;RP11-732A19.6,upstream_gene_variant,,ENST00000526633,; A ENST00000299441 Transcript synonymous_variant 5152/10765 4740/9897 1580/3298 V gtG/gtT 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 10/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 6630054 6630054 C A 1 0 0 0 0 0 0 0 1 4090 465 17 2 2 DCHS1 11 6630054 Silent SNP C C3L-00080_T 1808294 6630054 128456568 422 2520 ASCL3 0 . GRCh38 11 8937932 8937932 + Missense_Mutation SNP G G C rs147479456 C3L-00080_T C3L-00080_N G G c.230C>G p.Pro77Arg p.P77R ENST00000531618 1/1 200 131 69 216 216 0 strelka-varscan-mutect ASCL3,missense_variant,p.Pro77Arg,ENST00000531618,NM_020646.2;C11orf16,upstream_gene_variant,,ENST00000326053,NM_020643.2;C11orf16,upstream_gene_variant,,ENST00000525780,;C11orf16,upstream_gene_variant,,ENST00000528998,;C11orf16,upstream_gene_variant,,ENST00000526227,;C11orf16,upstream_gene_variant,,ENST00000527607,;C11orf16,upstream_gene_variant,,ENST00000528830,; C ENST00000531618 Transcript missense_variant 280/633 230/546 77/181 P/R cCg/cGg rs147479456 1 -1 ASCL3 HGNC HGNC:740 protein_coding YES CCDS7795.1 ENSP00000435770 Q9NQ33 UPI0000141305 NM_020646.2 tolerated(0.1) 1/1 hmmpanther:PTHR13935 MODERATE SNV 1 PASS rs147479456 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 8937932 8937932 G C 1 0 0 0 0 1 0 0 0 1177 1116 39 4 4 ASCL3 11 8937932 Missense_Mutation SNP G C3L-00080_T 2307878 8937932 126148690 423 2521 OTOG 0 . GRCh38 11 17642190 17642190 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.8395G>T p.Val2799Leu p.V2799L ENST00000399391 52/55 114 52 62 100 100 0 strelka-varscan-mutect OTOG,missense_variant,p.Val2787Leu,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Val2799Leu,ENST00000399391,NM_001277269.1;OTOG,downstream_gene_variant,,ENST00000342528,; T ENST00000399391 Transcript missense_variant 8395/8778 8395/8778 2799/2925 V/L Gtg/Ttg 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0.01) 52/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 MODERATE 1 SNV 5 1 PASS rs1210145910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 17642190 17642190 G T 1 0 0 0 0 1 0 0 0 11370 1145 40 1 1 OTOG 11 17642190 Missense_Mutation SNP G C3L-00080_T 8704258 17642190 117444432 424 2522 KCNA4 0 . GRCh38 11 30011517 30011517 + Missense_Mutation SNP C C A rs375741098 C3L-00080_T C3L-00080_N C C c.1162G>T p.Val388Phe p.V388F ENST00000328224 2/2 87 56 31 128 128 0 strelka-varscan-mutect KCNA4,missense_variant,p.Val388Phe,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript missense_variant 2396/4172 1162/1962 388/653 V/F Gtt/Ttt rs375741098 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 deleterious(0) 2/2 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs375741098 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 30011517 30011517 C A 1 0 0 0 0 1 0 0 0 7921 507 18 2 2 KCNA4 11 30011517 Missense_Mutation SNP C C3L-00080_T 12369327 30011517 105075105 425 2523 ARL14EP 0 . GRCh38 11 30332941 30332941 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.502G>T p.Gly168Cys p.G168C ENST00000282032 3/4 200 116 84 275 275 0 strelka-varscan-mutect ARL14EP,missense_variant,p.Gly168Cys,ENST00000530909,;ARL14EP,missense_variant,p.Gly168Cys,ENST00000282032,NM_152316.2;ARL14EP,non_coding_transcript_exon_variant,,ENST00000533457,;ARL14EP,downstream_gene_variant,,ENST00000532047,; T ENST00000282032 Transcript missense_variant 717/2430 502/783 168/260 G/C Ggt/Tgt 1 1 ARL14EP HGNC HGNC:26798 protein_coding YES CCDS7869.1 ENSP00000282032 Q8N8R7 UPI000000DC5B NM_152316.2 deleterious(0.03) 3/4 hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF72,Pfam_domain:PF14949 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 30332941 30332941 G T 1 0 0 0 0 1 0 0 0 1068 1348 47 2 2 ARL14EP 11 30332941 Missense_Mutation SNP G C3L-00080_T 321424 30332941 104753681 426 2524 DCDC1 0 . GRCh38 11 30920871 30920871 + Silent SNP T T A novel C3L-00080_T C3L-00080_N T T c.519A>T p.= p.V173V ENST00000406071 6/20 137 78 59 176 176 0 strelka-varscan-mutect DCDC1,synonymous_variant,p.=,ENST00000597505,;DCDC1,synonymous_variant,p.=,ENST00000406071,NM_020869.3;DCDC1,synonymous_variant,p.=,ENST00000444572,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,; A ENST00000406071 Transcript synonymous_variant 835/4758 519/2673 173/890 V gtA/gtT 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 6/20 hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 30920871 30920871 T A 1 0 0 0 0 0 0 0 1 4086 1509 53 4 4 DCDC1 11 30920871 Silent SNP T C3L-00080_T 587930 30920871 104165751 427 2525 HIPK3 0 . GRCh38 11 33347396 33347396 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.2001A>T p.= p.R667R ENST00000303296 9/17 154 77 77 173 173 0 strelka-varscan-mutect HIPK3,synonymous_variant,p.=,ENST00000303296,NM_005734.4;HIPK3,synonymous_variant,p.=,ENST00000456517,NM_001278162.1;HIPK3,synonymous_variant,p.=,ENST00000379016,NM_001048200.2;HIPK3,synonymous_variant,p.=,ENST00000525975,NM_001278163.1; T ENST00000303296 Transcript synonymous_variant 2306/7408 2001/3648 667/1215 R cgA/cgT 1 1 HIPK3 HGNC HGNC:4915 protein_coding YES CCDS7884.1 ENSP00000304226 Q9H422 UPI000006D7F8 NM_005734.4 9/17 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 33347396 33347396 A T 1 0 0 0 0 0 0 0 1 7006 262 10 4 4 HIPK3 11 33347396 Silent SNP A C3L-00080_T 2426525 33347396 101739226 428 2526 KIAA1549L 0 . GRCh38 11 33545378 33545378 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2494G>T p.Val832Phe p.V832F ENST00000321505 2/20 64 35 29 73 73 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Val832Phe,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Val838Phe,ENST00000265654,;KIAA1549L,missense_variant,p.Val230Phe,ENST00000526400,; T ENST00000321505 Transcript missense_variant,splice_region_variant 2674/11678 2494/5550 832/1849 V/F Gtt/Ttt 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 deleterious(0) 2/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999954 1 1 1 0 T 3 4 7 33545378 33545378 G T 1 0 0 0 0 1 0 0 0 8121 1014 35 2 2 KIAA1549L 11 33545378 Missense_Mutation SNP G C3L-00080_T 197982 33545378 101541244 429 2527 LMO2 0 . GRCh38 11 33859388 33859388 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.652T>A p.Tyr218Asn p.Y218N ENST00000257818 6/6 198 109 89 255 255 0 strelka-varscan-mutect LMO2,missense_variant,p.Tyr218Asn,ENST00000257818,NM_005574.3;LMO2,missense_variant,p.Tyr149Asn,ENST00000395833,NM_001142315.1,NM_001142316.1;LMO2,3_prime_UTR_variant,,ENST00000411482,;LMO2,non_coding_transcript_exon_variant,,ENST00000464025,; T ENST00000257818 Transcript missense_variant 1482/2294 652/684 218/227 Y/N Tac/Aac 1 -1 LMO2 HGNC HGNC:6642 protein_coding YES CCDS7888.2 ENSP00000257818 P25791 UPI00001F9F84 NM_005574.3 tolerated(0.28) 6/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF109,Pfam_domain:PF00412,Gene3D:2.10.110.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 33859388 33859388 A T 1 0 0 0 0 1 0 0 0 8778 420 15 4 4 LMO2 11 33859388 Missense_Mutation SNP A C3L-00080_T 314010 33859388 101227234 430 2528 OR4A47 0 . GRCh38 11 48489408 48489408 + Missense_Mutation SNP A A T rs770678138 C3L-00080_T C3L-00080_N A A c.616A>T p.Thr206Ser p.T206S ENST00000446524 1/1 160 132 28 131 131 0 strelka-varscan-mutect OR4A47,missense_variant,p.Thr206Ser,ENST00000446524,NM_001005512.2;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,; T ENST00000446524 Transcript missense_variant 692/1064 616/930 206/309 T/S Act/Tct rs770678138 1 1 OR4A47 HGNC HGNC:31266 protein_coding YES CCDS31490.1 ENSP00000412752 Q6IF82 UPI00001971E5 NM_001005512.2 tolerated_low_confidence(0.22) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF87,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs770678138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 48489408 48489408 A T 1 0 0 0 0 1 0 0 0 11119 159 6 4 4 OR4A47 11 48489408 Missense_Mutation SNP A C3L-00080_T 14630020 48489408 86597214 431 2529 OR4A16 0 . GRCh38 11 55343732 55343732 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.532G>T p.Asp178Tyr p.D178Y ENST00000314721 1/1 261 186 75 226 225 1 strelka-varscan-mutect OR4A16,missense_variant,p.Asp178Tyr,ENST00000314721,NM_001005274.1; T ENST00000314721 Transcript missense_variant 532/987 532/987 178/328 D/Y Gac/Tac COSM543558 1 1 OR4A16 HGNC HGNC:15153 protein_coding YES CCDS31499.1 ENSP00000325128 Q8NH70 A0A126GW87 UPI0000061EB2 NM_001005274.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF355,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 55343732 55343732 G T 1 0 0 0 0 1 0 0 0 11118 1290 45 2 2 OR4A16 11 55343732 Missense_Mutation SNP G C3L-00080_T 6854324 55343732 79742890 432 2530 OR4C15 0 . GRCh38 11 55554533 55554533 + Missense_Mutation SNP A A T rs761756464 C3L-00080_T C3L-00080_N A A c.227A>T p.Gln76Leu p.Q76L ENST00000314644 1/1 245 166 79 220 220 0 strelka-varscan-mutect OR4C15,missense_variant,p.Gln76Leu,ENST00000314644,NM_001001920.1; T ENST00000314644 Transcript missense_variant 227/1113 227/1113 76/370 Q/L cAg/cTg rs761756464 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF14,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs761756464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 55554533 55554533 A T 1 0 0 0 0 1 0 0 0 11125 188 7 4 4 OR4C15 11 55554533 Missense_Mutation SNP A C3L-00080_T 210801 55554533 79532089 433 2531 OR5D18 0 . GRCh38 11 55820364 55820364 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.735C>T p.= p.H245H ENST00000333976 1/1 205 142 63 160 160 0 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; T ENST00000333976 Transcript synonymous_variant 735/942 735/942 245/313 H caC/caT 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 55820364 55820364 C T 1 0 0 0 0 0 0 0 1 11227 506 18 3 3 OR5D18 11 55820364 Silent SNP C C3L-00080_T 265831 55820364 79266258 434 2532 OR8K1 0 . GRCh38 11 56346896 56346896 + Silent SNP G G T rs757527323 C3L-00080_T C3L-00080_N G G c.858G>T p.= p.L286L ENST00000279783 1/1 133 92 41 160 160 0 strelka-varscan-mutect OR8K1,synonymous_variant,p.=,ENST00000279783,NM_001002907.1; T ENST00000279783 Transcript synonymous_variant 858/960 858/960 286/319 L ctG/ctT rs757527323 1 1 OR8K1 HGNC HGNC:14831 protein_coding YES CCDS31528.1 ENSP00000279783 Q8NGG5 A0A126GVZ6 UPI0000041BC6 NM_001002907.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF298,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs757527323 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 56346896 56346896 G T 1 0 0 0 0 0 0 0 1 11311 1364 48 2 2 OR8K1 11 56346896 Silent SNP G C3L-00080_T 526532 56346896 78739726 435 2533 OR6Q1 0 . GRCh38 11 58031088 58031088 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.136G>T p.Ala46Ser p.A46S ENST00000302622 1/1 317 251 66 273 271 2 strelka-varscan-mutect OR6Q1,missense_variant,p.Ala46Ser,ENST00000302622,NM_001005186.2;OR9Q1,intron_variant,,ENST00000335397,NM_001005212.3;RNU6-899P,upstream_gene_variant,,ENST00000363947,; T ENST00000302622 Transcript missense_variant 159/1002 136/954 46/317 A/S Gcc/Tcc 1 1 OR6Q1 HGNC HGNC:15302 protein_coding YES CCDS31541.1 ENSP00000307734 Q8NGQ2 A0A126GVP6 UPI000013E7FD NM_001005186.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF140,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1217528290 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 58031088 58031088 G T 1 0 0 0 0 1 0 0 0 11278 1203 42 2 2 OR6Q1 11 58031088 Missense_Mutation SNP G C3L-00080_T 1684192 58031088 77055534 436 2534 OR10Q1 0 . GRCh38 11 58228534 58228534 + Silent SNP C C A rs747598804 C3L-00080_T C3L-00080_N C C c.342G>T p.= p.T114T ENST00000316770 1/1 219 145 74 138 138 0 strelka-varscan-mutect OR10Q1,synonymous_variant,p.=,ENST00000316770,NM_001004471.2; A ENST00000316770 Transcript synonymous_variant 385/1037 342/960 114/319 T acG/acT rs747598804,COSM4543726 1 -1 OR10Q1 HGNC HGNC:15134 protein_coding YES CCDS31547.1 ENSP00000314324 Q8NGQ4 UPI0000041C4C NM_001004471.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF253,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 0,1 1 PASS rs747598804 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 58228534 58228534 C A 1 0 0 0 0 0 0 0 1 10993 639 23 1 1 OR10Q1 11 58228534 Silent SNP C C3L-00080_T 197446 58228534 76858088 437 2535 OR5B12 0 . GRCh38 11 58439985 58439985 + Missense_Mutation SNP G G T rs763580476 C3L-00080_T C3L-00080_N G G c.167C>A p.Pro56His p.P56H ENST00000302572 1/1 282 232 50 197 197 0 strelka-varscan-mutect OR5B12,missense_variant,p.Pro56His,ENST00000302572,NM_001004733.2; T ENST00000302572 Transcript missense_variant 189/1054 167/945 56/314 P/H cCc/cAc rs763580476 1 -1 OR5B12 HGNC HGNC:15432 protein_coding YES CCDS31551.1 ENSP00000306657 Q96R08 UPI00000015B2 NM_001004733.2 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs763580476 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 58439985 58439985 G T 1 0 0 0 0 1 0 0 0 11219 1232 43 2 2 OR5B12 11 58439985 Missense_Mutation SNP G C3L-00080_T 211451 58439985 76646637 438 2536 MPEG1 0 . GRCh38 11 59211523 59211523 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.1343T>C p.Val448Ala p.V448A ENST00000361050 1/1 424 380 44 315 315 0 strelka-varscan-mutect MPEG1,missense_variant,p.Val448Ala,ENST00000361050,NM_001039396.1;DTX4,downstream_gene_variant,,ENST00000227451,NM_015177.1;RN7SL42P,downstream_gene_variant,,ENST00000579786,; G ENST00000361050 Transcript missense_variant 1429/4442 1343/2151 448/716 V/A gTg/gCg 1 -1 MPEG1 HGNC HGNC:29619 protein_coding YES CCDS41650.1 ENSP00000354335 Q2M385 UPI0000049D9F NM_001039396.1 tolerated(0.3) 1/1 hmmpanther:PTHR31463,hmmpanther:PTHR31463:SF4 MODERATE SNV 1 PASS rs748476155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 59211523 59211523 A G 1 0 0 0 0 1 0 0 0 9688 159 6 5 5 MPEG1 11 59211523 Missense_Mutation SNP A C3L-00080_T 771538 59211523 75875099 439 2537 PATL1 0 . GRCh38 11 59639137 59639137 + Silent SNP G G C novel C3L-00080_T C3L-00080_N G G c.2202C>G p.= p.A734A ENST00000300146 18/19 284 215 69 244 244 0 strelka-varscan-mutect PATL1,synonymous_variant,p.=,ENST00000300146,NM_152716.2;AP000442.1,intron_variant,,ENST00000531311,;AP000442.1,intron_variant,,ENST00000531108,;PATL1,downstream_gene_variant,,ENST00000531919,; C ENST00000300146 Transcript synonymous_variant 2287/4072 2202/2313 734/770 A gcC/gcG 1 -1 PATL1 HGNC HGNC:26721 protein_coding YES CCDS44613.1 ENSP00000300146 Q86TB9 UPI00001FA7D8 NM_152716.2 18/19 hmmpanther:PTHR21551:SF2,hmmpanther:PTHR21551 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 59639137 59639137 G C 1 0 0 0 0 0 0 0 1 11559 1335 47 4 4 PATL1 11 59639137 Silent SNP G C3L-00080_T 427614 59639137 75447485 440 2538 MS4A12 0 . GRCh38 11 60501162 60501162 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.394C>A p.Pro132Thr p.P132T ENST00000016913 3/7 74 67 7 65 65 0 strelka-varscan-mutect MS4A12,missense_variant,p.Pro132Thr,ENST00000016913,NM_017716.2;MS4A12,intron_variant,,ENST00000537076,NM_001164470.1;MS4A12,intron_variant,,ENST00000526784,;MS4A12,downstream_gene_variant,,ENST00000530007,;MS4A12,downstream_gene_variant,,ENST00000525951,; A ENST00000016913 Transcript missense_variant 451/1167 394/804 132/267 P/T Cca/Aca COSM3450502 1 1 MS4A12 HGNC HGNC:13370 protein_coding YES CCDS7988.1 ENSP00000016913 Q9NXJ0 UPI000006D9F8 NM_017716.2 tolerated(0.12) 3/7 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF72,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 60501162 60501162 C A 1 0 0 0 0 1 0 0 0 9833 623 22 2 2 MS4A12 11 60501162 Missense_Mutation SNP C C3L-00080_T 862025 60501162 74585460 441 2539 INCENP 0 . GRCh38 11 62150171 62150171 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2506G>T p.Ala836Ser p.A836S ENST00000394818 18/19 193 126 67 151 151 0 strelka-varscan-mutect INCENP,missense_variant,p.Ala836Ser,ENST00000394818,NM_001040694.1;INCENP,missense_variant,p.Ala832Ser,ENST00000278849,NM_020238.2;INCENP,upstream_gene_variant,,ENST00000531099,; T ENST00000394818 Transcript missense_variant 2708/3964 2506/2757 836/918 A/S Gcc/Tcc 1 1 INCENP HGNC HGNC:6058 protein_coding YES CCDS44624.1 ENSP00000378295 Q9NQS7 UPI0000D7D6F3 NM_001040694.1 tolerated(1) 18/19 hmmpanther:PTHR13142:SF1,hmmpanther:PTHR13142,Pfam_domain:PF03941 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 62150171 62150171 G T 1 0 0 0 0 1 0 0 0 7635 1203 42 2 2 INCENP 11 62150171 Missense_Mutation SNP G C3L-00080_T 1649009 62150171 72936451 442 2540 SLC22A6 0 . GRCh38 11 62984580 62984580 + Silent SNP C C A rs759569649 C3L-00080_T C3L-00080_N C C c.111G>T p.= p.L37L ENST00000377871 1/10 465 349 116 405 404 1 strelka-varscan-mutect SLC22A6,synonymous_variant,p.=,ENST00000377871,NM_004790.4;SLC22A6,synonymous_variant,p.=,ENST00000360421,NM_153276.2;SLC22A6,synonymous_variant,p.=,ENST00000421062,NM_153278.2;SLC22A6,synonymous_variant,p.=,ENST00000458333,NM_153277.2;SLC22A6,upstream_gene_variant,,ENST00000537349,;SLC22A6,synonymous_variant,p.=,ENST00000540654,;SLC22A8,downstream_gene_variant,,ENST00000539841,; A ENST00000377871 Transcript synonymous_variant 378/2151 111/1692 37/563 L ctG/ctT rs759569649 1 -1 SLC22A6 HGNC HGNC:10970 protein_coding YES CCDS31591.1 ENSP00000367102 Q4U2R8 UPI00000747EC NM_004790.4 1/10 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF231,TIGRFAM_domain:TIGR00898 LOW 1 SNV 1 1 PASS rs759569649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 62984580 62984580 C A 1 0 0 0 0 0 0 0 1 14724 697 25 2 2 SLC22A6 11 62984580 Silent SNP C C3L-00080_T 834409 62984580 72102042 443 2541 GPR137 0 . GRCh38 11 64286731 64286731 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.381G>T p.Trp127Cys p.W127C ENST00000411458 3/9 143 108 35 74 74 0 strelka-varscan-mutect GPR137,missense_variant,p.Trp69Cys,ENST00000539851,NM_001177358.1;GPR137,missense_variant,p.Trp69Cys,ENST00000438980,NM_001170880.1;GPR137,missense_variant,p.Trp127Cys,ENST00000411458,NM_001170726.1;GPR137,missense_variant,p.Trp69Cys,ENST00000313074,NM_020155.3;GPR137,missense_variant,p.Trp69Cys,ENST00000377702,NM_001170881.1;GPR137,missense_variant,p.Trp75Cys,ENST00000546139,;GPR137,missense_variant,p.Trp69Cys,ENST00000539833,;GPR137,missense_variant,p.Trp69Cys,ENST00000543383,;GPR137,missense_variant,p.Trp69Cys,ENST00000538032,;GPR137,missense_variant,p.Trp69Cys,ENST00000535675,;GPR137,missense_variant,p.Trp69Cys,ENST00000540370,;GPR137,missense_variant,p.Trp69Cys,ENST00000541952,;GPR137,missense_variant,p.Trp69Cys,ENST00000542190,;GPR137,5_prime_UTR_variant,,ENST00000536667,;KCNK4,upstream_gene_variant,,ENST00000422670,NM_033310.2;KCNK4,upstream_gene_variant,,ENST00000538767,;BAD,upstream_gene_variant,,ENST00000394532,NM_004322.3;BAD,upstream_gene_variant,,ENST00000309032,NM_032989.2;BAD,upstream_gene_variant,,ENST00000394531,;BAD,upstream_gene_variant,,ENST00000544785,;GPR137,upstream_gene_variant,,ENST00000536282,;GPR137,downstream_gene_variant,,ENST00000538244,;KCNK4-TEX40,upstream_gene_variant,,ENST00000539086,;KCNK4,upstream_gene_variant,,ENST00000539651,;GPR137,missense_variant,p.Trp69Cys,ENST00000546201,;GPR137,non_coding_transcript_exon_variant,,ENST00000536017,;KCNK4,upstream_gene_variant,,ENST00000453423,;KCNK4,upstream_gene_variant,,ENST00000538846,;BAD,upstream_gene_variant,,ENST00000544271,;GPR137,upstream_gene_variant,,ENST00000545366,; T ENST00000411458 Transcript missense_variant 409/1495 381/1428 127/475 W/C tgG/tgT 1 1 GPR137 HGNC HGNC:24300 protein_coding YES CCDS53655.1 ENSP00000411827 Q96N19 UPI00017A7FAD NM_001170726.1 deleterious(0) 3/9 hmmpanther:PTHR15146,hmmpanther:PTHR15146:SF5,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 64286731 64286731 G T 1 0 0 0 0 1 0 0 0 6531 1241 43 2 2 GPR137 11 64286731 Missense_Mutation SNP G C3L-00080_T 1302151 64286731 70799891 444 2542 ATG2A 0 . GRCh38 11 64913917 64913917 + Missense_Mutation SNP C C A rs370194802 C3L-00080_T C3L-00080_N C C c.494G>T p.Arg165Leu p.R165L ENST00000377264 4/41 267 159 108 132 132 0 strelka-varscan-mutect ATG2A,missense_variant,p.Arg165Leu,ENST00000377264,NM_015104.2;ATG2A,intron_variant,,ENST00000421419,;ATG2A,upstream_gene_variant,,ENST00000418259,;PPP2R5B,upstream_gene_variant,,ENST00000526559,;PPP2R5B,upstream_gene_variant,,ENST00000413292,;ATG2A,non_coding_transcript_exon_variant,,ENST00000461701,;ATG2A,downstream_gene_variant,,ENST00000461955,; A ENST00000377264 Transcript missense_variant 607/6357 494/5817 165/1938 R/L cGg/cTg rs370194802 1 -1 ATG2A HGNC HGNC:29028 protein_coding YES CCDS31602.1 ENSP00000366475 Q2TAZ0 UPI00001C1F21 NM_015104.2 deleterious(0.01) 4/41 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF21 MODERATE 1 SNV 1 1 PASS rs370194802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 64913917 64913917 C A 1 0 0 0 0 1 0 0 0 1245 652 23 1 1 ATG2A 11 64913917 Missense_Mutation SNP C C3L-00080_T 627186 64913917 70172705 445 2543 CATSPER1 0 . GRCh38 11 66025314 66025314 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1066C>A p.Pro356Thr p.P356T ENST00000312106 1/12 678 422 256 453 451 2 strelka-varscan-mutect CATSPER1,missense_variant,p.Pro356Thr,ENST00000312106,NM_053054.3;CATSPER1,upstream_gene_variant,,ENST00000529244,; T ENST00000312106 Transcript missense_variant 1204/2619 1066/2343 356/780 P/T Cca/Aca 1 -1 CATSPER1 HGNC HGNC:17116 protein_coding YES CCDS8127.1 ENSP00000309052 Q8NEC5 UPI000045651C NM_053054.3 tolerated(0.64) 1/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 66025314 66025314 G T 1 0 0 0 0 1 0 0 0 2387 1232 43 2 2 CATSPER1 11 66025314 Missense_Mutation SNP G C3L-00080_T 1111397 66025314 69061308 446 2544 TMEM151A 0 . GRCh38 11 66294752 66294752 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.506G>T p.Arg169Leu p.R169L ENST00000327259 2/2 399 252 147 261 261 0 strelka-varscan-mutect TMEM151A,missense_variant,p.Arg169Leu,ENST00000327259,NM_153266.3; T ENST00000327259 Transcript missense_variant 650/2562 506/1407 169/468 R/L cGc/cTc COSM4963661 1 1 TMEM151A HGNC HGNC:28497 protein_coding YES CCDS8133.1 ENSP00000326244 Q8N4L1 UPI0000070F9B NM_153266.3 deleterious(0) 2/2 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 66294752 66294752 G T 1 0 0 0 0 1 0 0 0 16512 1087 38 1 1 TMEM151A 11 66294752 Missense_Mutation SNP G C3L-00080_T 269438 66294752 68791870 447 2545 NPAS4 0 . GRCh38 11 66422856 66422856 + Missense_Mutation SNP C C A rs752901221 C3L-00080_T C3L-00080_N C C c.613C>A p.Pro205Thr p.P205T ENST00000311034 4/8 515 316 199 352 352 0 strelka-varscan-mutect NPAS4,missense_variant,p.Pro205Thr,ENST00000311034,NM_178864.3;NPAS4,missense_variant,p.Pro205Thr,ENST00000525148,;NPAS4,upstream_gene_variant,,ENST00000524617,; A ENST00000311034 Transcript missense_variant 789/3303 613/2409 205/802 P/T Cct/Act rs752901221 1 1 NPAS4 HGNC HGNC:18983 protein_coding YES CCDS8138.1 ENSP00000311196 Q8IUM7 UPI0000074744 NM_178864.3 tolerated(0.32) 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF24,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS rs752901221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 66422856 66422856 C A 1 0 0 0 0 1 0 0 0 10613 623 22 2 2 NPAS4 11 66422856 Missense_Mutation SNP C C3L-00080_T 128104 66422856 68663766 448 2546 TESMIN 0 . GRCh38 11 68750577 68750577 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.84C>G p.Phe28Leu p.F28L ENST00000255087 2/10 115 65 50 56 56 0 strelka-varscan-mutect TESMIN,missense_variant,p.Phe28Leu,ENST00000443940,;TESMIN,missense_variant,p.Phe28Leu,ENST00000255087,NM_004923.3;TESMIN,missense_variant,p.Phe28Leu,ENST00000544963,NM_001039656.1;CPT1A,downstream_gene_variant,,ENST00000265641,NM_001876.3;CPT1A,downstream_gene_variant,,ENST00000376618,NM_001031847.2;CPT1A,downstream_gene_variant,,ENST00000540367,;TESMIN,non_coding_transcript_exon_variant,,ENST00000432435,;TESMIN,upstream_gene_variant,,ENST00000540869,;TESMIN,upstream_gene_variant,,ENST00000538944,; C ENST00000255087 Transcript missense_variant 268/2579 84/1527 28/508 F/L ttC/ttG 1 -1 TESMIN HGNC HGNC:7446 protein_coding YES CCDS8184.1 ENSP00000255087 Q9Y4I5 UPI00001FAE07 NM_004923.3 deleterious_low_confidence(0.03) 2/10 hmmpanther:PTHR12446:SF22,hmmpanther:PTHR12446 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999992 1 1 1 0 C 3 2 7 68750577 68750577 G C 1 0 0 0 0 1 0 0 0 16188 1049 37 4 4 TESMIN 11 68750577 Missense_Mutation SNP G C3L-00080_T 2327721 68750577 66336045 449 2547 IGHMBP2 0 . GRCh38 11 68936363 68936363 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.1883A>C p.Glu628Ala p.E628A ENST00000255078 13/15 640 328 312 365 365 0 strelka-varscan-mutect IGHMBP2,missense_variant,p.Glu628Ala,ENST00000255078,NM_002180.2;IGHMBP2,downstream_gene_variant,,ENST00000541229,;IGHMBP2,downstream_gene_variant,,ENST00000568742,;IGHMBP2,downstream_gene_variant,,ENST00000536803,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000543739,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000539064,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000545475,;IGHMBP2,upstream_gene_variant,,ENST00000544521,;IGHMBP2,downstream_gene_variant,,ENST00000537458,; C ENST00000255078 Transcript missense_variant 1994/3961 1883/2982 628/993 E/A gAg/gCg 1 1 IGHMBP2 HGNC HGNC:5542 protein_coding YES CCDS8187.1 ENSP00000255078 P38935 UPI000013CE82 NM_002180.2 tolerated(0.05) 13/15 Gene3D:3.40.50.300,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF375,TIGRFAM_domain:TIGR00376 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 68936363 68936363 A C 1 0 0 0 0 1 0 0 0 7498 304 11 5 5 IGHMBP2 11 68936363 Missense_Mutation SNP A C3L-00080_T 185786 68936363 66150259 450 2548 CHRDL2 0 . GRCh38 11 74697284 74697284 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1189G>C p.Asp397His p.D397H ENST00000263671 11/12 157 109 48 140 140 0 strelka-varscan-mutect CHRDL2,missense_variant,p.Leu378Phe,ENST00000376332,NM_001278473.2;CHRDL2,missense_variant,p.Asp397His,ENST00000263671,NM_015424.5,NM_001304391.1,NM_001304390.1;CHRDL2,missense_variant,p.Asp37His,ENST00000529912,;CHRDL2,intron_variant,,ENST00000622063,;CHRDL2,intron_variant,,ENST00000525413,;CHRDL2,downstream_gene_variant,,ENST00000534159,;RP11-864N7.4,downstream_gene_variant,,ENST00000624759,;CHRDL2,3_prime_UTR_variant,,ENST00000376324,NM_001304416.1; G ENST00000263671 Transcript missense_variant 1476/1712 1189/1356 397/451 D/H Gac/Cac 1 -1 CHRDL2 HGNC HGNC:24168 protein_coding YES CCDS8234.1 ENSP00000263671 Q6WN34 UPI0000034E41 NM_015424.5,NM_001304391.1,NM_001304390.1 tolerated_low_confidence(0.11) 11/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 74697284 74697284 C G 1 0 0 0 0 1 0 0 0 3134 826 29 4 4 CHRDL2 11 74697284 Missense_Mutation SNP C C3L-00080_T 5760921 74697284 60389338 451 2549 OMP 0 . GRCh38 11 77103276 77103276 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.437G>C p.Gly146Ala p.G146A ENST00000529803 1/1 160 134 26 128 128 0 strelka-varscan-mutect OMP,missense_variant,p.Gly146Ala,ENST00000529803,NM_006189.1;CAPN5,intron_variant,,ENST00000278559,NM_004055.4;CAPN5,intron_variant,,ENST00000456580,;CAPN5,intron_variant,,ENST00000529629,;CAPN5,intron_variant,,ENST00000531028,;CAPN5,intron_variant,,ENST00000533889,; C ENST00000529803 Transcript missense_variant 437/492 437/492 146/163 G/A gGc/gCc 1 1 OMP HGNC HGNC:8136 protein_coding YES CCDS53682.1 ENSP00000436376 P47874 UPI00001637C1 NM_006189.1 tolerated_low_confidence(0.83) 1/1 Superfamily_domains:0037362,Gene3D:1f35A00,PD022055,Pfam_domain:PF06554,hmmpanther:PTHR15357 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 77103276 77103276 G C 1 0 0 0 0 1 0 0 0 10942 1203 42 4 4 OMP 11 77103276 Missense_Mutation SNP G C3L-00080_T 2405992 77103276 57983346 452 2550 TRIM77 0 . GRCh38 11 89710509 89710509 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.211G>C p.Glu71Gln p.E71Q ENST00000398290 1/6 122 98 24 137 137 0 strelka-varscan-mutect TRIM77,missense_variant,p.Glu71Gln,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,upstream_gene_variant,,ENST00000534392,; C ENST00000398290 Transcript missense_variant 211/1353 211/1353 71/450 E/Q Gag/Cag 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 deleterious(0.02) 1/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353 MODERATE 1 SNV 5 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999769 1 1 1 0 C 3 2 7 89710509 89710509 G C 1 0 0 0 0 1 0 0 0 17044 1291 45 4 4 TRIM77 11 89710509 Missense_Mutation SNP G C3L-00080_T 12607233 89710509 45376113 453 2551 TRIM77 0 . GRCh38 11 89715911 89715911 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.783C>A p.= p.A261A ENST00000398290 5/6 123 76 47 121 121 0 strelka-varscan-mutect TRIM77,synonymous_variant,p.=,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,synonymous_variant,p.=,ENST00000534392,; A ENST00000398290 Transcript synonymous_variant 783/1353 783/1353 261/450 A gcC/gcA 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 5/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353 LOW 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 2 1 7 89715911 89715911 C A 1 0 0 0 0 0 0 0 1 17044 581 21 2 2 TRIM77 11 89715911 Silent SNP C C3L-00080_T 5402 89715911 45370711 454 2552 TRIM49 0 . GRCh38 11 89798397 89798397 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1092G>T p.Glu364Asp p.E364D ENST00000329758 8/8 323 302 21 298 298 0 varscan-mutect TRIM49,missense_variant,p.Glu364Asp,ENST00000329758,NM_020358.2;TRIM49,missense_variant,p.Glu287Asp,ENST00000532501,; A ENST00000329758 Transcript missense_variant 1421/2163 1092/1359 364/452 E/D gaG/gaT 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 tolerated(0.27) 8/8 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 89798397 89798397 C A 1 0 0 0 0 1 0 0 0 17014 912 32 2 2 TRIM49 11 89798397 Missense_Mutation SNP C C3L-00080_T 82486 89798397 45288225 455 2553 TRIM49C 0 . GRCh38 11 90035298 90035298 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.87C>A p.Asp29Glu p.D29E ENST00000448984 3/8 212 174 38 197 196 1 strelka-varscan-mutect TRIM49C,missense_variant,p.Asp29Glu,ENST00000448984,NM_001195234.1; A ENST00000448984 Transcript missense_variant 416/2163 87/1359 29/452 D/E gaC/gaA 1 1 TRIM49C HGNC HGNC:38877 protein_coding YES CCDS53694.1 ENSP00000388299 P0CI26 UPI000013EA2B NM_001195234.1 tolerated(0.16) 3/8 Gene3D:3.30.40.10,Pfam_domain:PF15227,PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 90035298 90035298 C A 1 0 0 0 0 1 0 0 0 17016 564 20 2 2 TRIM49C 11 90035298 Missense_Mutation SNP C C3L-00080_T 236901 90035298 45051324 456 2554 CARD16 0 . GRCh38 11 105041591 105041591 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.403A>G p.Asn135Asp p.N135D ENST00000375706 3/3 415 333 82 495 495 0 strelka-varscan-mutect CARD16,missense_variant,p.Asn135Asp,ENST00000375706,NM_001017534.1;CARD16,3_prime_UTR_variant,,ENST00000375704,NM_052889.2;CARD16,3_prime_UTR_variant,,ENST00000525374,;CARD16,downstream_gene_variant,,ENST00000528513,;CARD16,downstream_gene_variant,,ENST00000527065,; C ENST00000375706 Transcript missense_variant 421/686 403/594 135/197 N/D Aat/Gat 1 -1 CARD16 HGNC HGNC:33701 protein_coding YES CCDS31661.1 ENSP00000364858 Q5EG05 UPI00004C9CE7 NM_001017534.1 deleterious_low_confidence(0.01) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 105041591 105041591 T C 1 0 0 0 0 1 0 0 0 2342 1783 62 5 5 CARD16 11 105041591 Missense_Mutation SNP T C3L-00080_T 15006293 105041591 30045031 457 2555 DRD2 0 . GRCh38 11 113410801 113410801 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1258G>T p.Ala420Ser p.A420S ENST00000362072 8/8 312 220 92 270 270 0 strelka-varscan-mutect DRD2,missense_variant,p.Ala420Ser,ENST00000362072,NM_000795.3;DRD2,missense_variant,p.Ala419Ser,ENST00000544518,;DRD2,missense_variant,p.Ala420Ser,ENST00000542968,;DRD2,missense_variant,p.Ala391Ser,ENST00000346454,NM_016574.3;DRD2,missense_variant,p.Ala422Ser,ENST00000538967,;RP11-159N11.3,intron_variant,,ENST00000546284,;DRD2,downstream_gene_variant,,ENST00000535984,;DRD2,downstream_gene_variant,,ENST00000540600,;DRD2,downstream_gene_variant,,ENST00000539420,; A ENST00000362072 Transcript missense_variant 1603/2789 1258/1332 420/443 A/S Gcc/Tcc 1 -1 DRD2 HGNC HGNC:3023 protein_coding YES CCDS8361.1 ENSP00000354859 P14416 A0A024R3C5 UPI0000001315 NM_000795.3 deleterious(0.01) 8/8 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF68,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 113410801 113410801 C A 1 0 0 0 0 1 0 0 0 4576 768 27 1 1 DRD2 11 113410801 Missense_Mutation SNP C C3L-00080_T 8369210 113410801 21675821 458 2556 APOA4 0 . GRCh38 11 116821056 116821056 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1002G>T p.= p.G334G ENST00000357780 3/3 538 334 204 508 506 2 strelka-varscan-mutect APOA4,synonymous_variant,p.=,ENST00000357780,NM_000482.3; A ENST00000357780 Transcript synonymous_variant 1117/1473 1002/1191 334/396 G ggG/ggT 1 -1 APOA4 HGNC HGNC:602 protein_coding YES CCDS31681.1 ENSP00000350425 P06727 UPI00001AE660 NM_000482.3 3/3 hmmpanther:PTHR18976:SF1,hmmpanther:PTHR18976,Gene3D:1.20.120.20,Pfam_domain:PF01442,Superfamily_domains:0053393 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 116821056 116821056 C A 1 0 0 0 0 0 0 0 1 905 610 22 2 2 APOA4 11 116821056 Silent SNP C C3L-00080_T 3410255 116821056 18265566 459 2557 TECTA 0 . GRCh38 11 121118670 121118670 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1155G>T p.= p.V385V ENST00000392793 7/24 319 216 103 274 274 0 strelka-varscan-mutect TECTA,synonymous_variant,p.=,ENST00000392793,;TECTA,synonymous_variant,p.=,ENST00000264037,NM_005422.2; T ENST00000392793 Transcript synonymous_variant 1426/7426 1155/6468 385/2155 V gtG/gtT 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D 7/24 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF235,hmmpanther:PTHR11339,Pfam_domain:PF00094,SMART_domains:SM00216 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 121118670 121118670 G T 1 0 0 0 0 0 0 0 1 16158 1277 45 2 2 TECTA 11 121118670 Silent SNP G C3L-00080_T 4297614 121118670 13967952 460 2558 GRAMD1B 0 . GRCh38 11 123430898 123430898 + Missense_Mutation SNP C C A rs768783016 C3L-00080_T C3L-00080_N C C c.106C>A p.Pro36Thr p.P36T ENST00000635736 1/20 323 254 69 291 291 0 strelka-varscan-mutect GRAMD1B,missense_variant,p.Pro36Thr,ENST00000635736,;GRAMD1B,missense_variant,p.Pro36Thr,ENST00000533341,;GRAMD1B,intron_variant,,ENST00000638157,; A ENST00000635736 Transcript missense_variant 205/2814 106/2634 36/877 P/T Ccc/Acc rs768783016 1 1 GRAMD1B HGNC HGNC:29214 protein_coding ENSP00000490062 UPI0003EAFB61 1/20 Low_complexity_(Seg):seg,hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF3 MODERATE SNV 1 PASS rs768783016 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 123430898 123430898 C A 1 0 0 0 0 1 0 0 0 6627 623 22 2 2 GRAMD1B 11 123430898 Missense_Mutation SNP C C3L-00080_T 2312228 123430898 11655724 461 2559 ACRV1 0 . GRCh38 11 125677874 125677874 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.476C>A p.Ala159Asp p.A159D ENST00000533904 2/4 381 257 124 330 330 0 strelka-varscan-mutect ACRV1,missense_variant,p.Ala159Asp,ENST00000533904,NM_001612.5;ACRV1,missense_variant,p.Ala159Asp,ENST00000315608,NM_020069.4;ACRV1,missense_variant,p.Ala104Asp,ENST00000530048,NM_020107.4;ACRV1,missense_variant,p.Ala89Asp,ENST00000527795,NM_020108.4;CHEK1,downstream_gene_variant,,ENST00000428830,NM_001114121.2;CHEK1,downstream_gene_variant,,ENST00000498122,; T ENST00000533904 Transcript missense_variant 819/2212 476/798 159/265 A/D gCc/gAc 1 -1 ACRV1 HGNC HGNC:127 protein_coding YES CCDS8460.1 ENSP00000432816 P26436 UPI000012615C NM_001612.5 tolerated(0.1) 2/4 hmmpanther:PTHR17571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 125677874 125677874 G T 1 0 0 0 0 1 0 0 0 214 1203 42 2 2 ACRV1 11 125677874 Missense_Mutation SNP G C3L-00080_T 2246976 125677874 9408748 462 2560 PRDM10 0 . GRCh38 11 129947205 129947205 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.460G>T p.Asp154Tyr p.D154Y ENST00000358825 5/22 263 165 98 248 247 1 strelka-varscan-mutect PRDM10,missense_variant,p.Asp154Tyr,ENST00000358825,NM_020228.2;PRDM10,missense_variant,p.Asp154Tyr,ENST00000360871,NM_199437.1;PRDM10,missense_variant,p.Asp128Tyr,ENST00000528746,;PRDM10,missense_variant,p.Asp68Tyr,ENST00000423662,NM_199438.1;PRDM10,missense_variant,p.Asp68Tyr,ENST00000304538,NM_199439.1;PRDM10,missense_variant,p.Asp68Tyr,ENST00000526082,;PRDM10,missense_variant,p.Asp134Tyr,ENST00000527581,;PRDM10,upstream_gene_variant,,ENST00000533431,;PRDM10,downstream_gene_variant,,ENST00000531431,; A ENST00000358825 Transcript missense_variant 692/6322 460/3483 154/1160 D/Y Gac/Tac 1 -1 PRDM10 HGNC HGNC:13995 protein_coding YES CCDS44771.1 ENSP00000351686 Q9NQV6 UPI00002371B3 NM_020228.2 deleterious_low_confidence(0.01) 5/22 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 129947205 129947205 C A 1 0 0 0 0 1 0 0 0 12582 855 30 2 2 PRDM10 11 129947205 Missense_Mutation SNP C C3L-00080_T 4269331 129947205 5139417 463 2561 P3H3 0 . GRCh38 12 6837479 6837479 + Missense_Mutation SNP C C A rs782015917 C3L-00080_T C3L-00080_N C C c.1617C>A p.Ser539Arg p.S539R ENST00000290510 11/15 241 115 126 219 219 0 strelka-varscan-mutect P3H3,missense_variant,p.Ser539Arg,ENST00000290510,NM_014262.4;GNB3,upstream_gene_variant,,ENST00000229264,NM_002075.3;GNB3,upstream_gene_variant,,ENST00000435982,NM_001297571.1;GNB3,upstream_gene_variant,,ENST00000541978,;GNB3,upstream_gene_variant,,ENST00000537035,;GNB3,upstream_gene_variant,,ENST00000541257,;P3H3,downstream_gene_variant,,ENST00000538102,;P3H3,non_coding_transcript_exon_variant,,ENST00000536140,;P3H3,non_coding_transcript_exon_variant,,ENST00000612048,;P3H3,non_coding_transcript_exon_variant,,ENST00000541956,;P3H3,non_coding_transcript_exon_variant,,ENST00000544200,;P3H3,non_coding_transcript_exon_variant,,ENST00000544949,;P3H3,non_coding_transcript_exon_variant,,ENST00000540406,;P3H3,non_coding_transcript_exon_variant,,ENST00000542976,;GNB3,upstream_gene_variant,,ENST00000540458,;GNB3,upstream_gene_variant,,ENST00000542868,;GNB3,upstream_gene_variant,,ENST00000539127,;P3H3,downstream_gene_variant,,ENST00000545596,; A ENST00000290510 Transcript missense_variant 1648/2632 1617/2211 539/736 S/R agC/agA rs782015917 1 1 P3H3 HGNC HGNC:19318 protein_coding YES CCDS61027.1 ENSP00000478600 Q8IVL6 UPI000007460A NM_014262.4 deleterious(0) 11/15 hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF14,SMART_domains:SM00702 MODERATE 1 SNV 1 1 PASS rs782015917 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 6837479 6837479 C A 1 0 0 0 0 1 0 0 0 11431 767 27 1 1 P3H3 12 6837479 Missense_Mutation SNP C C3L-00080_T 6837479 126437830 464 2562 GRIN2B 0 . GRCh38 12 13564446 13564446 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2792T>A p.Val931Asp p.V931D ENST00000609686 13/13 378 206 172 418 416 2 strelka-varscan-mutect GRIN2B,missense_variant,p.Val931Asp,ENST00000609686,NM_000834.3;GRIN2B,intron_variant,,ENST00000637214,;GRIN2B,non_coding_transcript_exon_variant,,ENST00000628166,;GRIN2B,upstream_gene_variant,,ENST00000636207,; T ENST00000609686 Transcript missense_variant 3246/30355 2792/4455 931/1484 V/D gTc/gAc 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 deleterious(0) 13/13 Pfam_domain:PF10565 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 13564446 13564446 A T 1 0 0 0 0 1 0 0 0 6662 275 10 4 4 GRIN2B 12 13564446 Missense_Mutation SNP A C3L-00080_T 6726967 13564446 119710863 465 2563 WBP11 0 . GRCh38 12 14787080 14787080 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1911G>T p.Met637Ile p.M637I ENST00000261167 12/12 80 71 9 69 69 0 varscan-mutect WBP11,missense_variant,p.Met637Ile,ENST00000261167,NM_016312.2;WBP11,downstream_gene_variant,,ENST00000535638,; A ENST00000261167 Transcript missense_variant 2145/4646 1911/1926 637/641 M/I atG/atT 1 -1 WBP11 HGNC HGNC:16461 protein_coding YES CCDS8666.1 ENSP00000261167 Q9Y2W2 A0A024RAW9 UPI0000035FC2 NM_016312.2 deleterious(0.04) 12/12 hmmpanther:PTHR13361:SF1,hmmpanther:PTHR13361 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -19.06819 0.999988 1 1 1 0 A 3 1 7 14787080 14787080 C A 1 0 0 0 0 1 0 0 0 17818 594 21 2 2 WBP11 12 14787080 Missense_Mutation SNP C C3L-00080_T 1222634 14787080 118488229 466 2564 RP11-545J16.1 0 . GRCh38 12 20862472 20862472 + Missense_Mutation SNP G G C rs180875376 C3L-00080_T C3L-00080_N G G c.542G>C p.Arg181Pro p.R181P ENST00000261196 5/14 224 109 115 260 260 0 strelka-varscan-mutect SLCO1B3,missense_variant,p.Arg181Pro,ENST00000261196,;SLCO1B3,missense_variant,p.Arg181Pro,ENST00000381545,NM_019844.3;RP11-545J16.1,missense_variant,p.Arg181Pro,ENST00000540229,;SLCO1B3,missense_variant,p.Arg5Pro,ENST00000544370,;SLCO1B3,missense_variant,p.Arg181Pro,ENST00000540853,;RP11-545J16.1,intron_variant,,ENST00000381541,;SLCO1B3,downstream_gene_variant,,ENST00000545880,; C ENST00000261196 Transcript missense_variant 609/2840 542/2109 181/702 R/P cGt/cCt rs180875376 1 1 SLCO1B3 HGNC HGNC:10961 protein_coding YES CCDS8684.1 ENSP00000261196 Q9NPD5 UPI000013544A deleterious(0) 5/14 PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Pfam_domain:PF03137,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs180875376 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 20862472 20862472 G C 1 0 0 0 0 1 0 0 0 13751 1145 40 4 4 RP11-545J16.1 12 20862472 Missense_Mutation SNP G C3L-00080_T 6075392 20862472 112412837 467 2565 TMTC1 0 . GRCh38 12 29518494 29518494 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.2002A>G p.Met668Val p.M668V ENST00000539277 13/18 156 139 17 142 142 0 strelka-varscan-mutect TMTC1,missense_variant,p.Met560Val,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Met730Val,ENST00000551659,;TMTC1,missense_variant,p.Met692Val,ENST00000552618,;TMTC1,missense_variant,p.Met668Val,ENST00000539277,NM_001193451.1;RP11-310I24.1,upstream_gene_variant,,ENST00000549070,;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,non_coding_transcript_exon_variant,,ENST00000552925,; C ENST00000539277 Transcript missense_variant 2061/2758 2002/2649 668/882 M/V Atg/Gtg 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 tolerated(0.09) 13/18 Gene3D:1.25.40.10,Pfam_domain:PF13424,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 29518494 29518494 T C 1 0 0 0 0 1 0 0 0 16734 1464 51 5 5 TMTC1 12 29518494 Missense_Mutation SNP T C3L-00080_T 8656022 29518494 103756815 468 2566 ABCD2 0 . GRCh38 12 39607603 39607603 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.1232A>G p.Lys411Arg p.K411R ENST00000308666 3/10 180 146 34 170 170 0 varscan-mutect ABCD2,missense_variant,p.Lys411Arg,ENST00000308666,NM_005164.3; C ENST00000308666 Transcript missense_variant 1368/6238 1232/2223 411/740 K/R aAa/aGa 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 deleterious(0.02) 3/10 hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 39607603 39607603 T C 1 0 0 0 0 1 0 0 0 65 1855 64 5 5 ABCD2 12 39607603 Missense_Mutation SNP T C3L-00080_T 10089109 39607603 93667706 469 2567 LRRK2 0 . GRCh38 12 40365014 40365014 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.7354T>C p.Cys2452Arg p.C2452R ENST00000298910 49/51 203 166 37 190 190 0 strelka-varscan-mutect LRRK2,missense_variant,p.Cys2452Arg,ENST00000298910,NM_198578.3;LRRK2,missense_variant,p.Cys385Arg,ENST00000636518,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; C ENST00000298910 Transcript missense_variant 7412/9158 7354/7584 2452/2527 C/R Tgt/Cgt 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 deleterious(0) 49/51 Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 40365014 40365014 T C 1 0 0 0 0 1 0 0 0 8939 1812 63 5 5 LRRK2 12 40365014 Missense_Mutation SNP T C3L-00080_T 757411 40365014 92910295 470 2568 ANO6 0 . GRCh38 12 45390464 45390464 + Missense_Mutation SNP G G C rs759903940 C3L-00080_T C3L-00080_N G G c.1415G>C p.Arg472Pro p.R472P ENST00000423947 13/21 450 290 160 352 352 0 strelka-varscan-mutect ANO6,missense_variant,p.Arg451Pro,ENST00000320560,NM_001025356.2;ANO6,missense_variant,p.Arg433Pro,ENST00000441606,NM_001142678.1;ANO6,missense_variant,p.Arg472Pro,ENST00000423947,NM_001204803.1;ANO6,missense_variant,p.Arg451Pro,ENST00000425752,NM_001142679.1;ANO6,non_coding_transcript_exon_variant,,ENST00000426898,; C ENST00000423947 Transcript missense_variant 1652/5504 1415/2796 472/931 R/P cGg/cCg rs759903940 1 1 ANO6 HGNC HGNC:25240 protein_coding YES CCDS55819.1 ENSP00000409126 Q4KMQ2 UPI000022935A NM_001204803.1 deleterious(0.03) 13/21 hmmpanther:PTHR12308:SF21,hmmpanther:PTHR12308,Pfam_domain:PF04547 MODERATE 1 SNV 1 1 PASS rs759903940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 45390464 45390464 G C 1 0 0 0 0 1 0 0 0 808 1116 39 4 4 ANO6 12 45390464 Missense_Mutation SNP G C3L-00080_T 5025450 45390464 87884845 471 2569 NCKAP5L 0 . GRCh38 12 49802976 49802976 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.213G>T p.Gln71His p.Q71H ENST00000335999 5/13 287 193 94 227 226 1 strelka-varscan-mutect NCKAP5L,missense_variant,p.Gln71His,ENST00000335999,NM_001037806.3;NCKAP5L,downstream_gene_variant,,ENST00000480927,;NCKAP5L,non_coding_transcript_exon_variant,,ENST00000477361,;NCKAP5L,non_coding_transcript_exon_variant,,ENST00000491441,; A ENST00000335999 Transcript missense_variant 415/4900 213/4005 71/1334 Q/H caG/caT 1 -1 NCKAP5L HGNC HGNC:29321 protein_coding YES CCDS41781.2 ENSP00000337998 Q9HCH0 UPI00006C1298 NM_001037806.3 deleterious(0) 5/13 hmmpanther:PTHR21740 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 49802976 49802976 C A 1 0 0 0 0 1 0 0 0 10242 680 24 2 2 NCKAP5L 12 49802976 Missense_Mutation SNP C C3L-00080_T 4412512 49802976 83472333 472 2570 KRT1 0 . GRCh38 12 52677330 52677330 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.1114T>G p.Leu372Val p.L372V ENST00000252244 5/9 459 411 48 336 335 1 strelka-varscan-mutect KRT1,missense_variant,p.Leu372Val,ENST00000252244,NM_006121.3;KRT1,non_coding_transcript_exon_variant,,ENST00000548765,; C ENST00000252244 Transcript missense_variant 1173/2451 1114/1935 372/644 L/V Ttg/Gtg 1 -1 KRT1 HGNC HGNC:6412 protein_coding YES CCDS8836.1 ENSP00000252244 P04264 UPI000013CD4D NM_006121.3 tolerated(0.08) 5/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF95,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 52677330 52677330 A C 1 0 0 0 0 1 0 0 0 8329 69 3 5 5 KRT1 12 52677330 Missense_Mutation SNP A C3L-00080_T 2874354 52677330 80597979 473 2571 HOXC13 0 . GRCh38 12 53939579 53939579 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.673A>T p.Ser225Cys p.S225C ENST00000243056 1/2 141 98 43 143 143 0 strelka-varscan-mutect HOXC13,missense_variant,p.Ser225Cys,ENST00000243056,NM_017410.2;HOXC13-AS,non_coding_transcript_exon_variant,,ENST00000512916,; T ENST00000243056 Transcript missense_variant 815/2423 673/993 225/330 S/C Agt/Tgt 1 1 HOXC13 HGNC HGNC:5125 protein_coding YES CCDS8865.1 ENSP00000243056 P31276 UPI000012CF7F NM_017410.2 deleterious(0) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF39 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 53939579 53939579 A T 1 0 0 0 0 1 0 0 0 7206 188 7 4 4 HOXC13 12 53939579 Missense_Mutation SNP A C3L-00080_T 1262249 53939579 79335730 474 2572 GTSF1 0 . GRCh38 12 54460419 54460419 + Nonsense_Mutation SNP G G A C3L-00080_T C3L-00080_N G G c.445C>T p.Arg149Ter p.R149* ENST00000552397 7/9 245 169 76 184 182 2 strelka-varscan-mutect GTSF1,stop_gained,p.Arg149Ter,ENST00000552397,;GTSF1,stop_gained,p.Arg149Ter,ENST00000305879,NM_144594.2;RP11-753H16.3,intron_variant,,ENST00000550474,;RP11-753H16.5,intron_variant,,ENST00000552785,;GTSF1,non_coding_transcript_exon_variant,,ENST00000552395,;GTSF1,downstream_gene_variant,,ENST00000548538,;GTSF1,upstream_gene_variant,,ENST00000552336,;GTSF1,stop_gained,p.Arg149Ter,ENST00000546931,;GTSF1,non_coding_transcript_exon_variant,,ENST00000546575,;GTSF1,downstream_gene_variant,,ENST00000546739,; A ENST00000552397 Transcript stop_gained 1342/1621 445/504 149/167 R/* Cga/Tga COSM941146 1 -1 GTSF1 HGNC HGNC:26565 protein_coding YES CCDS8881.1 ENSP00000446485 Q8WW33 A0A024RB57 UPI0000169CBC 7/9 hmmpanther:PTHR21402,hmmpanther:PTHR21402:SF9 1 HIGH 1 SNV 2 1 1 PASS rs1228656789 . 0 206 0 2 2 0 0 0 -20 0.9959112 1 1 1 0 A 4 1 7 54460419 54460419 G A 1 0 0 0 0 0 1 0 0 6767 1095 38 1 1 GTSF1 12 54460419 Nonsense_Mutation SNP G C3L-00080_T 520840 54460419 78814890 475 2573 RP11-644F5.10 0 . GRCh38 12 55719173 55719173 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.301C>T p.Gln101Ter p.Q101* ENST00000550412 3/4 603 424 179 381 381 0 strelka-varscan-mutect RP11-644F5.10,stop_gained,p.Gln101Ter,ENST00000550412,;BLOC1S1,stop_gained,p.Gln101Ter,ENST00000549147,;BLOC1S1,stop_gained,p.Gln23Ter,ENST00000547076,;BLOC1S1,stop_gained,p.Gln101Ter,ENST00000548925,NM_001487.3;BLOC1S1,stop_gained,p.Gln23Ter,ENST00000551926,;BLOC1S1,stop_gained,p.Gln23Ter,ENST00000548556,;RP11-644F5.10,stop_gained,p.Gln23Ter,ENST00000549424,;RDH5,upstream_gene_variant,,ENST00000257895,NM_002905.3,NM_001199771.1;RDH5,upstream_gene_variant,,ENST00000548082,;RDH5,upstream_gene_variant,,ENST00000547072,;RDH5,upstream_gene_variant,,ENST00000552930,;RDH5,upstream_gene_variant,,ENST00000553160,;RP11-644F5.10,stop_gained,p.Gln93Ter,ENST00000257899,;RP11-644F5.10,3_prime_UTR_variant,,ENST00000551946,;BLOC1S1,3_prime_UTR_variant,,ENST00000553100,;RDH5,upstream_gene_variant,,ENST00000550608,;RDH5,upstream_gene_variant,,ENST00000551444,;RDH5,upstream_gene_variant,,ENST00000548486,;RDH5,upstream_gene_variant,,ENST00000553187,;RDH5,upstream_gene_variant,,ENST00000548123,;ITGA7,upstream_gene_variant,,ENST00000553737,;RDH5,upstream_gene_variant,,ENST00000547301,;ITGA7,upstream_gene_variant,,ENST00000553893,;ITGA7,upstream_gene_variant,,ENST00000556273,; T ENST00000550412 Transcript stop_gained 317/3382 301/369 101/122 Q/* Cag/Tag 1 1 RP11-644F5.10 Clone_based_vega_gene protein_coding YES ENSP00000447650 F8W036 UPI0000D46D68 3/4 Pfam_domain:PF06320,hmmpanther:PTHR13073,hmmpanther:PTHR13073:SF1 HIGH SNV 2 1 PASS rs1254700722 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 55719173 55719173 C T 1 0 0 0 0 0 1 0 0 13755 711 25 3 3 RP11-644F5.10 12 55719173 Nonsense_Mutation SNP C C3L-00080_T 1258754 55719173 77556136 476 2574 GDF11 0 . GRCh38 12 55748923 55748923 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.783C>A p.= p.A261A ENST00000257868 2/3 131 81 50 68 68 0 strelka-varscan-mutect GDF11,synonymous_variant,p.=,ENST00000257868,NM_005811.3;GDF11,synonymous_variant,p.=,ENST00000546799,;SARNP,downstream_gene_variant,,ENST00000546604,;SARNP,downstream_gene_variant,,ENST00000552884,; A ENST00000257868 Transcript synonymous_variant 820/8657 783/1224 261/407 A gcC/gcA 1 1 GDF11 HGNC HGNC:4216 protein_coding YES CCDS8891.1 ENSP00000257868 O95390 A0A024RB20 UPI000004C158 NM_005811.3 2/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF166,Pfam_domain:PF00688 LOW 1 SNV 1 1 PASS rs922930513 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 55748923 55748923 C A 1 0 0 0 0 0 0 0 1 6185 668 24 2 2 GDF11 12 55748923 Silent SNP C C3L-00080_T 29750 55748923 77526386 477 2575 SMARCC2 0 . GRCh38 12 56169912 56169912 + Splice_Site SNP C C T novel C3L-00080_T C3L-00080_N C C c.2320-1G>A p.X774_splice ENST00000267064 233 207 26 145 145 0 strelka-varscan-mutect SMARCC2,splice_acceptor_variant,,ENST00000394023,NM_001130420.1;SMARCC2,splice_acceptor_variant,,ENST00000550164,;SMARCC2,splice_acceptor_variant,,ENST00000267064,NM_003075.3;SMARCC2,splice_acceptor_variant,,ENST00000347471,NM_139067.2;RP11-977G19.5,intron_variant,,ENST00000553176,;SMARCC2,downstream_gene_variant,,ENST00000549209,;SMARCC2,splice_acceptor_variant,,ENST00000552674,;SMARCC2,downstream_gene_variant,,ENST00000548130,;SMARCC2,downstream_gene_variant,,ENST00000552931,;SMARCC2,downstream_gene_variant,,ENST00000552566,; T ENST00000267064 Transcript splice_acceptor_variant -/4076 2320/3645 774/1214 1 -1 SMARCC2 HGNC HGNC:11105 protein_coding YES CCDS8907.1 ENSP00000267064 Q8TAQ2 A0A024RB22 UPI0000071C4E NM_003075.3 22/27 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 7 56169912 56169912 C T 1 0 0 0 0 0 0 1 0 15069 695 24 3 3 SMARCC2 12 56169912 Splice_Site SNP C C3L-00080_T 420989 56169912 77105397 478 2576 LRP1 0 . GRCh38 12 57185808 57185808 + Silent SNP C C G novel C3L-00080_T C3L-00080_N C C c.6741C>G p.= p.T2247T ENST00000243077 41/89 472 327 145 320 320 0 strelka-varscan-mutect LRP1,synonymous_variant,p.=,ENST00000243077,NM_002332.2;LRP1,upstream_gene_variant,,ENST00000554118,; G ENST00000243077 Transcript synonymous_variant 7207/14897 6741/13635 2247/4544 T acC/acG 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 41/89 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 57185808 57185808 C G 1 0 0 0 0 0 0 0 1 8846 668 24 4 4 LRP1 12 57185808 Silent SNP C C3L-00080_T 1015896 57185808 76089501 479 2577 GLI1 0 . GRCh38 12 57469680 57469680 + Frame_Shift_Del DEL C C - novel C3L-00080_T C3L-00080_N C C c.1560delC p.Ser521AlafsTer92 p.S521Afs*92 ENST00000228682 11/12 195 136 59 175 175 0 sindel-varindel-pindel GLI1,frameshift_variant,p.Ser521AlafsTer92,ENST00000228682,NM_005269.2;GLI1,frameshift_variant,p.Ser480AlafsTer92,ENST00000546141,NM_001167609.1;GLI1,frameshift_variant,p.Ser393AlafsTer92,ENST00000543426,NM_001160045.1;GLI1,frameshift_variant,p.Ser480AlafsTer92,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;GLI1,downstream_gene_variant,,ENST00000528432,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;GLI1,downstream_gene_variant,,ENST00000527742,;ARHGAP9,downstream_gene_variant,,ENST00000546704,;GLI1,downstream_gene_variant,,ENST00000530789,; - ENST00000228682 Transcript frameshift_variant 1649/3613 1558/3321 520/1106 P/X Ccc/cc 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 11/12 hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818 HIGH 1 deletion 1 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 57469680 57469680 C - 1 0 1 0 1 0 0 0 0 6315 739 26 0 0 GLI1 12 57469680 Frame_Shift_Del DEL C C3L-00080_T 283872 57469680 75805629 480 2578 ARHGAP9 0 . GRCh38 12 57477482 57477482 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.733C>A p.Pro245Thr p.P245T ENST00000393791 4/18 280 192 88 218 218 0 strelka-varscan-mutect ARHGAP9,missense_variant,p.Pro316Thr,ENST00000393797,NM_001319850.1;ARHGAP9,missense_variant,p.Pro324Thr,ENST00000550288,;ARHGAP9,missense_variant,p.Pro245Thr,ENST00000393791,NM_032496.2;ARHGAP9,missense_variant,p.Pro245Thr,ENST00000424809,NM_001080157.1;ARHGAP9,missense_variant,p.Pro61Thr,ENST00000430041,NM_001080156.1;ARHGAP9,missense_variant,p.Pro61Thr,ENST00000548139,;ARHGAP9,missense_variant,p.Pro61Thr,ENST00000552066,;ARHGAP9,missense_variant,p.Pro61Thr,ENST00000552604,;ARHGAP9,missense_variant,p.Pro61Thr,ENST00000549602,;ARHGAP9,missense_variant,p.Pro98Thr,ENST00000551452,;ARHGAP9,upstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552249,;ARHGAP9,upstream_gene_variant,,ENST00000550130,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000550454,;MARS,intron_variant,,ENST00000549133,;ARHGAP9,upstream_gene_variant,,ENST00000547200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000546200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000552420,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000548148,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000547216,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000551000,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000551574,;ARHGAP9,upstream_gene_variant,,ENST00000552953,;ARHGAP9,upstream_gene_variant,,ENST00000550440,;ARHGAP9,upstream_gene_variant,,ENST00000546704,; T ENST00000393791 Transcript missense_variant 872/2597 733/2196 245/731 P/T Ccg/Acg 1 -1 ARHGAP9 HGNC HGNC:14130 protein_coding YES CCDS8941.2 ENSP00000377380 Q9BRR9 UPI000007131B NM_032496.2 deleterious(0) 4/18 PROSITE_profiles:PS50020,hmmpanther:PTHR23181:SF4,hmmpanther:PTHR23181,Gene3D:2.20.70.10,Superfamily_domains:SSF51045 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 57477482 57477482 G T 1 0 0 0 0 1 0 0 0 1019 1232 43 2 2 ARHGAP9 12 57477482 Missense_Mutation SNP G C3L-00080_T 7802 57477482 75797827 481 2579 ARHGAP9 0 . GRCh38 12 57479136 57479136 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.271C>A p.Gln91Lys p.Q91K ENST00000393791 2/18 291 183 108 210 210 0 strelka-varscan-mutect ARHGAP9,missense_variant,p.Gln162Lys,ENST00000393797,NM_001319850.1;ARHGAP9,missense_variant,p.Gln170Lys,ENST00000550288,;ARHGAP9,missense_variant,p.Gln91Lys,ENST00000393791,NM_032496.2;ARHGAP9,missense_variant,p.Gln91Lys,ENST00000424809,NM_001080157.1;ARHGAP9,missense_variant,p.Gln9Lys,ENST00000552249,;ARHGAP9,upstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,upstream_gene_variant,,ENST00000548139,;ARHGAP9,upstream_gene_variant,,ENST00000550399,;ARHGAP9,upstream_gene_variant,,ENST00000552066,;ARHGAP9,upstream_gene_variant,,ENST00000552604,;ARHGAP9,upstream_gene_variant,,ENST00000549602,;ARHGAP9,upstream_gene_variant,,ENST00000551452,;ARHGAP9,upstream_gene_variant,,ENST00000550130,;MARS,intron_variant,,ENST00000549133,;ARHGAP9,upstream_gene_variant,,ENST00000550454,;ARHGAP9,upstream_gene_variant,,ENST00000547200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000552420,;ARHGAP9,upstream_gene_variant,,ENST00000546200,;ARHGAP9,upstream_gene_variant,,ENST00000552953,;ARHGAP9,upstream_gene_variant,,ENST00000548148,;ARHGAP9,upstream_gene_variant,,ENST00000550440,;ARHGAP9,upstream_gene_variant,,ENST00000547216,;ARHGAP9,upstream_gene_variant,,ENST00000546704,;ARHGAP9,upstream_gene_variant,,ENST00000551000,;ARHGAP9,upstream_gene_variant,,ENST00000551574,; T ENST00000393791 Transcript missense_variant 410/2597 271/2196 91/731 Q/K Cag/Aag 1 -1 ARHGAP9 HGNC HGNC:14130 protein_coding YES CCDS8941.2 ENSP00000377380 Q9BRR9 UPI000007131B NM_032496.2 tolerated(1) 2/18 hmmpanther:PTHR23181:SF4,hmmpanther:PTHR23181,Gene3D:2.30.30.40,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 57479136 57479136 G T 1 0 0 0 0 1 0 0 0 1019 1357 47 2 2 ARHGAP9 12 57479136 Missense_Mutation SNP G C3L-00080_T 1654 57479136 75796173 482 2580 LRIG3 0 . GRCh38 12 58880628 58880628 + Missense_Mutation SNP T T A rs200549484 C3L-00080_T C3L-00080_N T T c.1754A>T p.Asn585Ile p.N585I ENST00000320743 13/19 265 215 50 156 156 0 strelka-varscan-mutect LRIG3,missense_variant,p.Asn585Ile,ENST00000320743,NM_153377.4;LRIG3,missense_variant,p.Asn525Ile,ENST00000379141,NM_001136051.2;LRIG3,missense_variant,p.Asn585Ile,ENST00000433272,;LRIG3,non_coding_transcript_exon_variant,,ENST00000547329,;LRIG3,upstream_gene_variant,,ENST00000552646,; A ENST00000320743 Transcript missense_variant 2041/4070 1754/3360 585/1119 N/I aAt/aTt rs200549484 1 -1 LRIG3 HGNC HGNC:30991 protein_coding YES CCDS8960.1 ENSP00000326759 Q6UXM1 UPI0000035BB5 NM_153377.4 deleterious(0.01) 13/19 PROSITE_profiles:PS50835,hmmpanther:PTHR24367:SF242,hmmpanther:PTHR24367,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs200549484 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 58880628 58880628 T A 1 0 0 0 0 1 0 0 0 8841 1493 52 4 4 LRIG3 12 58880628 Missense_Mutation SNP T C3L-00080_T 1401492 58880628 74394681 483 2581 XPOT 0 . GRCh38 12 64430121 64430121 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1810G>T p.Val604Phe p.V604F ENST00000332707 17/25 171 98 73 125 125 0 strelka-varscan-mutect XPOT,missense_variant,p.Val604Phe,ENST00000332707,NM_007235.4;XPOT,3_prime_UTR_variant,,ENST00000538086,;XPOT,non_coding_transcript_exon_variant,,ENST00000542958,;XPOT,non_coding_transcript_exon_variant,,ENST00000541842,; T ENST00000332707 Transcript missense_variant 2339/6414 1810/2889 604/962 V/F Gtt/Ttt 1 1 XPOT HGNC HGNC:12826 protein_coding YES CCDS31852.1 ENSP00000327821 O43592 UPI0000161BA5 NM_007235.4 deleterious(0) 17/25 Gene3D:1.25.10.10,hmmpanther:PTHR15952,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS rs957698124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 64430121 64430121 G T 1 0 0 0 0 1 0 0 0 18009 1377 48 2 2 XPOT 12 64430121 Missense_Mutation SNP G C3L-00080_T 5549493 64430121 68845188 484 2582 CPM 0 . GRCh38 12 68856461 68856481 + In_Frame_Del DEL ACTCACTAAAAATAAGAACAA ACTCACTAAAAATAAGAACAA - novel C3L-00080_T C3L-00080_N ACTCACTAAAAATAAGAACAA ACTCACTAAAAATAAGAACAA c.1288_1308delTTGTTCTTATTTTTAGTGAGT p.Phe431_Leu437del p.F431_L437del ENST00000551568 9/9 267 220 47 153 153 0 sindel-varindel-pindel CPM,inframe_deletion,p.Phe431_Leu437del,ENST00000551568,NM_001005502.2,NM_198320.3;CPM,inframe_deletion,p.Phe431_Leu437del,ENST00000338356,;CPM,inframe_deletion,p.Phe431_Leu437del,ENST00000546373,NM_001874.4;CPM,intron_variant,,ENST00000551897,;CPM,inframe_deletion,p.Phe23_Leu29del,ENST00000546556,; - ENST00000551568 Transcript inframe_deletion 1349-1369/6655 1288-1308/1332 430-436/443 LFLFLVS/- TTGTTCTTATTTTTAGTGAGT/- 1 -1 CPM HGNC HGNC:2311 protein_coding YES CCDS8987.1 ENSP00000448517 P14384 UPI00001271D4 NM_001005502.2,NM_198320.3 9/9 MODERATE 1 deletion 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999876 1 1 1 0 - 7 5 7 68856461 68856461 ACTCACTAAAAATAAGAACAA - 1 0 1 0 1 0 0 0 0 3603 272 10 0 0 CPM 12 68856461 In_Frame_Del DEL ACTCACTAAAAATAAGAACAA C3L-00080_T 4426340 68856461 64418848 485 2583 PTPRB 0 . GRCh38 12 70536092 70536092 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6014G>T p.Trp2005Leu p.W2005L ENST00000334414 29/34 364 290 74 187 187 0 strelka-varscan-mutect PTPRB,missense_variant,p.Trp2005Leu,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Trp1917Leu,ENST00000550358,;PTPRB,missense_variant,p.Trp1787Leu,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Trp1697Leu,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Trp1697Leu,ENST00000550857,NM_001206971.1;RP11-588H23.3,intron_variant,,ENST00000548687,;RP11-588H23.3,intron_variant,,ENST00000546836,;RP11-588H23.3,intron_variant,,ENST00000551438,;RP11-588H23.3,intron_variant,,ENST00000549460,;RP11-588H23.3,intron_variant,,ENST00000547656,;PTPRB,downstream_gene_variant,,ENST00000549400,; A ENST00000334414 Transcript missense_variant 6059/12316 6014/6648 2005/2215 W/L tGg/tTg 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious(0) 29/34 PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 70536092 70536092 C A 1 0 0 0 0 1 0 0 0 12950 595 21 2 2 PTPRB 12 70536092 Missense_Mutation SNP C C3L-00080_T 1679631 70536092 62739217 486 2584 PTPRB 0 . GRCh38 12 70556146 70556146 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.4717C>A p.Pro1573Thr p.P1573T ENST00000334414 19/34 171 76 95 113 113 0 strelka-varscan-mutect PTPRB,missense_variant,p.Pro1573Thr,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Pro1485Thr,ENST00000550358,;PTPRB,missense_variant,p.Pro1355Thr,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Pro1265Thr,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Pro1265Thr,ENST00000550857,NM_001206971.1;PTPRB,downstream_gene_variant,,ENST00000551525,;PTPRB,downstream_gene_variant,,ENST00000548122,; T ENST00000334414 Transcript missense_variant,splice_region_variant 4762/12316 4717/6648 1573/2215 P/T Cct/Act 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious(0) 19/34 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 70556146 70556146 G T 1 0 0 0 0 1 0 0 0 12950 1217 42 2 2 PTPRB 12 70556146 Missense_Mutation SNP G C3L-00080_T 20054 70556146 62719163 487 2585 ZFC3H1 0 . GRCh38 12 71620300 71620300 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.4760G>T p.Cys1587Phe p.C1587F ENST00000378743 25/35 380 304 76 202 202 0 strelka-varscan-mutect ZFC3H1,missense_variant,p.Cys1587Phe,ENST00000378743,NM_144982.4;ZFC3H1,missense_variant,p.Cys1587Phe,ENST00000552994,;ZFC3H1,upstream_gene_variant,,ENST00000546771,; A ENST00000378743 Transcript missense_variant 5119/7285 4760/5970 1587/1989 C/F tGc/tTc COSM5280117 1 -1 ZFC3H1 HGNC HGNC:28328 protein_coding YES CCDS41813.1 ENSP00000368017 O60293 UPI00003668E9 NM_144982.4 deleterious(0) 25/35 hmmpanther:PTHR21563,Superfamily_domains:SSF48452 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 71620300 71620300 C A 1 0 0 0 0 1 0 0 0 18210 710 25 2 2 ZFC3H1 12 71620300 Missense_Mutation SNP C C3L-00080_T 1064154 71620300 61655009 488 2586 TBC1D15 0 . GRCh38 12 71920748 71920748 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.1668A>T p.= p.L556L ENST00000550746 16/18 320 296 24 302 302 0 strelka-varscan-mutect TBC1D15,synonymous_variant,p.=,ENST00000550746,NM_022771.4;TBC1D15,synonymous_variant,p.=,ENST00000485960,NM_001146213.1;TBC1D15,synonymous_variant,p.=,ENST00000319106,NM_001146214.1;TBC1D15,downstream_gene_variant,,ENST00000548679,;TBC1D15,3_prime_UTR_variant,,ENST00000462788,;TBC1D15,non_coding_transcript_exon_variant,,ENST00000546450,;TBC1D15,downstream_gene_variant,,ENST00000483828,; T ENST00000550746 Transcript synonymous_variant 1732/6184 1668/2076 556/691 L ctA/ctT 1 1 TBC1D15 HGNC HGNC:25694 protein_coding YES CCDS31858.1 ENSP00000448182 Q8TC07 UPI000049DD7C NM_022771.4 16/18 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF300,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 71920748 71920748 A T 1 0 0 0 0 0 0 0 1 16004 378 14 4 4 TBC1D15 12 71920748 Silent SNP A C3L-00080_T 300448 71920748 61354561 489 2587 NAV3 0 . GRCh38 12 77831672 77831672 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.211C>A p.Gln71Lys p.Q71K ENST00000397909 1/40 157 75 82 95 95 0 strelka-varscan-mutect NAV3,missense_variant,p.Gln71Lys,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Gln71Lys,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Gln71Lys,ENST00000549464,;NAV3,intron_variant,,ENST00000550042,; A ENST00000397909 Transcript missense_variant 384/9821 211/7158 71/2385 Q/K Caa/Aaa 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 tolerated_low_confidence(0.31) 1/40 Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 77831672 77831672 C A 1 0 0 0 0 1 0 0 0 10194 595 21 2 2 NAV3 12 77831672 Missense_Mutation SNP C C3L-00080_T 5910924 77831672 55443637 490 2588 NAV3 0 . GRCh38 12 78159276 78159276 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.4859C>T p.Ala1620Val p.A1620V ENST00000397909 23/40 163 151 12 113 113 0 strelka-varscan-mutect NAV3,missense_variant,p.Ala1620Val,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Ala1620Val,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Ala515Val,ENST00000552895,;NAV3,missense_variant,p.Ala249Val,ENST00000550788,; T ENST00000397909 Transcript missense_variant 5032/9821 4859/7158 1620/2385 A/V gCg/gTg 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 23/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS rs1184879413 . 0 203 0 5 0 0 0 0 -15.8167 0.9980769 1 1 1 0 T 3 4 7 78159276 78159276 C T 1 0 0 0 0 1 0 0 0 10194 768 27 1 1 NAV3 12 78159276 Missense_Mutation SNP C C3L-00080_T 327604 78159276 55116033 491 2589 PTPRQ 0 . GRCh38 12 80669450 80669450 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.6439C>T p.= p.L2147L ENST00000614701 41/45 158 141 17 123 123 0 strelka-varscan-mutect PTPRQ,synonymous_variant,p.=,ENST00000614701,NM_001145026.1;PTPRQ,synonymous_variant,p.=,ENST00000616559,; T ENST00000614701 Transcript synonymous_variant 6617/8289 6439/6900 2147/2299 L Ctg/Ttg 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 41/45 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 80669450 80669450 C T 1 0 0 0 0 0 0 0 1 12964 912 32 3 3 PTPRQ 12 80669450 Silent SNP C C3L-00080_T 2510174 80669450 52605859 492 2590 PPFIA2 0 . GRCh38 12 81353313 81353313 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1800G>C p.Trp600Cys p.W600C ENST00000549396 17/33 314 279 35 223 223 0 strelka-varscan-mutect PPFIA2,missense_variant,p.Trp501Cys,ENST00000333447,NM_001220478.2;PPFIA2,missense_variant,p.Trp600Cys,ENST00000550584,NM_001220473.2;PPFIA2,missense_variant,p.Trp600Cys,ENST00000549396,NM_003625.4;PPFIA2,missense_variant,p.Trp582Cys,ENST00000549325,NM_001220474.2;PPFIA2,missense_variant,p.Trp600Cys,ENST00000548586,NM_001220476.2;PPFIA2,missense_variant,p.Trp600Cys,ENST00000552948,NM_001220475.2;PPFIA2,missense_variant,p.Trp526Cys,ENST00000407050,NM_001220477.2;PPFIA2,missense_variant,p.Trp447Cys,ENST00000550359,NM_001282536.1;PPFIA2,missense_variant,p.Trp501Cys,ENST00000443686,;PPFIA2,missense_variant,p.Trp167Cys,ENST00000541570,NM_001220479.2;PPFIA2,missense_variant,p.Trp181Cys,ENST00000553058,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,NM_001220480.2;PPFIA2,downstream_gene_variant,,ENST00000548670,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,upstream_gene_variant,,ENST00000549917,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,; G ENST00000549396 Transcript missense_variant 1961/5363 1800/3774 600/1257 W/C tgG/tgC 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 deleterious(0.01) 17/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 81353313 81353313 C G 1 0 0 0 0 1 0 0 0 12419 856 30 4 4 PPFIA2 12 81353313 Missense_Mutation SNP C C3L-00080_T 683863 81353313 51921996 493 2591 PPFIA2 0 . GRCh38 12 81445641 81445641 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.485A>C p.Gln162Pro p.Q162P ENST00000549396 6/33 321 298 23 175 175 0 strelka-varscan-mutect PPFIA2,missense_variant,p.Gln88Pro,ENST00000333447,NM_001220478.2;PPFIA2,missense_variant,p.Gln162Pro,ENST00000550584,NM_001220473.2;PPFIA2,missense_variant,p.Gln162Pro,ENST00000549396,NM_003625.4;PPFIA2,missense_variant,p.Gln144Pro,ENST00000549325,NM_001220474.2;PPFIA2,missense_variant,p.Gln162Pro,ENST00000548586,NM_001220476.2;PPFIA2,missense_variant,p.Gln162Pro,ENST00000552948,NM_001220475.2;PPFIA2,missense_variant,p.Gln88Pro,ENST00000407050,NM_001220477.2;PPFIA2,missense_variant,p.Gln9Pro,ENST00000550359,NM_001282536.1;PPFIA2,missense_variant,p.Gln88Pro,ENST00000443686,;PPFIA2,missense_variant,p.Gln144Pro,ENST00000551442,;PPFIA2,upstream_gene_variant,,ENST00000548790,;RP11-315E17.1,intron_variant,,ENST00000550272,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000545296,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000548453,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000552020,; G ENST00000549396 Transcript missense_variant 646/5363 485/3774 162/1257 Q/P cAg/cCg 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 tolerated(0.08) 6/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 MODERATE 1 SNV 1 1 PASS rs1322961143 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 81445641 81445641 T G 1 0 0 0 0 1 0 0 0 12419 1580 55 5 5 PPFIA2 12 81445641 Missense_Mutation SNP T C3L-00080_T 92328 81445641 51829668 494 2592 C12orf50 0 . GRCh38 12 87998182 87998182 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.142C>T p.= p.L48L ENST00000298699 4/13 136 81 55 118 118 0 strelka-varscan-mutect C12orf50,synonymous_variant,p.=,ENST00000298699,NM_152589.1;C12orf50,synonymous_variant,p.=,ENST00000550553,;C12orf50,synonymous_variant,p.=,ENST00000551163,;C12orf50,non_coding_transcript_exon_variant,,ENST00000551944,; A ENST00000298699 Transcript synonymous_variant 323/1722 142/1245 48/414 L Cta/Tta 1 -1 C12orf50 HGNC HGNC:26665 protein_coding YES CCDS9031.1 ENSP00000298699 Q8NA57 UPI0000071382 NM_152589.1 4/13 hmmpanther:PTHR15725:SF1,hmmpanther:PTHR15725,Pfam_domain:PF15663 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 87998182 87998182 G A 1 0 0 0 0 0 0 0 1 1814 1020 36 3 3 C12orf50 12 87998182 Silent SNP G C3L-00080_T 6552541 87998182 45277127 495 2593 IKBIP 0 . GRCh38 12 98644636 98644636 + Missense_Mutation SNP C C A rs763887899 C3L-00080_T C3L-00080_N C C c.66G>T p.Lys22Asn p.K22N ENST00000299157 1/3 297 195 102 177 177 0 strelka-varscan-mutect IKBIP,missense_variant,p.Lys22Asn,ENST00000299157,NM_153687.3;IKBIP,missense_variant,p.Lys22Asn,ENST00000342502,NM_201612.2;IKBIP,missense_variant,p.Lys22Asn,ENST00000393042,NM_201613.2;APAF1,upstream_gene_variant,,ENST00000357310,NM_181868.1;APAF1,upstream_gene_variant,,ENST00000359972,NM_001160.2;APAF1,upstream_gene_variant,,ENST00000550527,NM_013229.2;APAF1,upstream_gene_variant,,ENST00000551964,NM_181861.1;APAF1,upstream_gene_variant,,ENST00000333991,NM_181869.1;APAF1,upstream_gene_variant,,ENST00000547045,;APAF1,upstream_gene_variant,,ENST00000549007,;APAF1,upstream_gene_variant,,ENST00000552268,;APAF1,upstream_gene_variant,,ENST00000547743,; A ENST00000299157 Transcript missense_variant 440/3189 66/1134 22/377 K/N aaG/aaT rs763887899 1 -1 IKBIP HGNC HGNC:26430 protein_coding YES CCDS9068.1 ENSP00000299157 Q70UQ0 UPI0000070C12 NM_153687.3 deleterious(0.01) 1/3 hmmpanther:PTHR21734:SF11,hmmpanther:PTHR21734 MODERATE 1 SNV 1 1 PASS rs763887899 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 98644636 98644636 C A 1 0 0 0 0 1 0 0 0 7517 796 28 2 2 IKBIP 12 98644636 Missense_Mutation SNP C C3L-00080_T 10646454 98644636 34630673 496 2594 ANO4 0 . GRCh38 12 101020140 101020140 + Missense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.841G>T p.Gly281Cys p.G281C ENST00000392977 9/28 113 99 14 104 104 0 strelka-varscan-mutect ANO4,missense_variant,p.Gly246Cys,ENST00000392979,NM_178826.3;ANO4,missense_variant,p.Gly281Cys,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,splice_region_variant,,ENST00000549234,;ANO4,downstream_gene_variant,,ENST00000549155,; T ENST00000392977 Transcript missense_variant,splice_region_variant 1051/3509 841/2868 281/955 G/C Ggt/Tgt COSM1582986 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 deleterious(0) 9/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF16178 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 101020140 101020140 G T 1 0 0 0 0 1 0 0 0 806 1362 47 2 2 ANO4 12 101020140 Missense_Mutation SNP G C3L-00080_T 2375504 101020140 32255169 497 2595 ANO4 0 . GRCh38 12 101116776 101116776 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.2548G>C p.Gly850Arg p.G850R ENST00000392977 25/28 407 245 162 220 220 0 strelka-varscan-mutect ANO4,missense_variant,p.Gly815Arg,ENST00000392979,NM_178826.3;ANO4,missense_variant,p.Gly850Arg,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,missense_variant,p.Gly370Arg,ENST00000550015,; C ENST00000392977 Transcript missense_variant 2758/3509 2548/2868 850/955 G/R Ggg/Cgg 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 tolerated(0.14) 25/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 101116776 101116776 G C 1 0 0 0 0 1 0 0 0 806 1232 43 4 4 ANO4 12 101116776 Missense_Mutation SNP G C3L-00080_T 96636 101116776 32158533 498 2596 CMKLR1 0 . GRCh38 12 108291964 108291965 + Frame_Shift_Del DEL GC GC - novel C3L-00080_T C3L-00080_N GC GC c.998_999delGC p.Arg333ProfsTer7 p.R333Pfs*7 ENST00000312143 3/3 256 230 26 181 181 0 sindel-varindel-pindel CMKLR1,frameshift_variant,p.Arg333ProfsTer7,ENST00000312143,NM_001142344.1;CMKLR1,frameshift_variant,p.Arg333ProfsTer7,ENST00000412676,NM_001142345.1;CMKLR1,frameshift_variant,p.Arg333ProfsTer7,ENST00000550402,NM_001142343.1;CMKLR1,frameshift_variant,p.Arg331ProfsTer7,ENST00000552995,NM_004072.2;CMKLR1,downstream_gene_variant,,ENST00000550573,;CMKLR1,downstream_gene_variant,,ENST00000549466,; - ENST00000312143 Transcript frameshift_variant 1362-1363/5283 998-999/1122 333/373 R/X cGC/c 1 -1 CMKLR1 HGNC HGNC:2121 protein_coding YES CCDS44965.1 ENSP00000311733 Q99788 UPI0000127BD4 NM_001142344.1 3/3 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF696,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01126 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 108291964 108291964 GC - 1 0 1 0 1 0 0 0 0 3354 1190 42 0 0 CMKLR1 12 108291964 Frame_Shift_Del DEL GC C3L-00080_T 7175188 108291964 24983345 499 2597 SELPLG 0 . GRCh38 12 108623317 108623317 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1039G>T p.Ala347Ser p.A347S ENST00000228463 2/2 272 160 112 198 198 0 strelka-varscan-mutect SELPLG,missense_variant,p.Ala331Ser,ENST00000550948,NM_003006.4;SELPLG,missense_variant,p.Ala347Ser,ENST00000228463,NM_001206609.1;SELPLG,missense_variant,p.Ala321Ser,ENST00000388962,; A ENST00000228463 Transcript missense_variant 1216/1704 1039/1287 347/428 A/S Gcc/Tcc 1 -1 SELPLG HGNC HGNC:10722 protein_coding YES CCDS55881.1 ENSP00000228463 Q14242 UPI0002065776 NM_001206609.1 deleterious(0.01) 2/2 hmmpanther:PTHR17384,hmmpanther:PTHR17384:SF0,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 108623317 108623317 C A 1 0 0 0 0 1 0 0 0 14297 739 26 2 2 SELPLG 12 108623317 Missense_Mutation SNP C C3L-00080_T 331353 108623317 24651992 500 2598 CUX2 0 . GRCh38 12 111293449 111293449 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.440A>G p.Gln147Arg p.Q147R ENST00000261726 6/22 147 88 59 109 109 0 strelka-varscan-mutect CUX2,missense_variant,p.Gln147Arg,ENST00000261726,NM_015267.3;CUX2,missense_variant,p.Gln207Arg,ENST00000397643,; G ENST00000261726 Transcript missense_variant 594/6844 440/4461 147/1486 Q/R cAg/cGg 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 tolerated(0.14) 6/22 hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 111293449 111293449 A G 1 0 0 0 0 1 0 0 0 3875 202 7 5 5 CUX2 12 111293449 Missense_Mutation SNP A C3L-00080_T 2670132 111293449 21981860 501 2599 CUX2 0 . GRCh38 12 111320094 111320094 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2085C>A p.Ser695Arg p.S695R ENST00000261726 17/22 181 148 33 111 111 0 strelka-varscan-mutect CUX2,missense_variant,p.Ser695Arg,ENST00000261726,NM_015267.3; A ENST00000261726 Transcript missense_variant 2239/6844 2085/4461 695/1486 S/R agC/agA 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 deleterious(0.01) 17/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 111320094 111320094 C A 1 0 0 0 0 1 0 0 0 3875 709 25 2 2 CUX2 12 111320094 Missense_Mutation SNP C C3L-00080_T 26645 111320094 21955215 502 2600 HECTD4 0 . GRCh38 12 112251096 112251096 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.3585G>T p.= p.L1195L ENST00000377560 24/76 273 164 109 152 152 0 strelka-varscan-mutect HECTD4,synonymous_variant,p.=,ENST00000377560,;HECTD4,synonymous_variant,p.=,ENST00000550722,NM_001109662.3;HECTD4,non_coding_transcript_exon_variant,,ENST00000311694,; A ENST00000377560 Transcript synonymous_variant 3896/15759 3585/13251 1195/4416 L ctG/ctT 1 -1 HECTD4 HGNC HGNC:26611 protein_coding YES ENSP00000366783 J3KPF0 UPI000387D324 24/76 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 112251096 112251096 C A 1 0 0 0 0 0 0 0 1 6923 581 21 2 2 HECTD4 12 112251096 Silent SNP C C3L-00080_T 931002 112251096 21024213 503 2601 TBX3 0 . GRCh38 12 114680963 114680963 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.573C>T p.= p.P191P ENST00000257566 2/8 855 762 93 545 545 0 strelka-varscan-mutect TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,non_coding_transcript_exon_variant,,ENST00000552054,;TBX3,upstream_gene_variant,,ENST00000548503,; A ENST00000257566 Transcript synonymous_variant 963/4208 573/2232 191/743 P ccC/ccT 1 -1 TBX3 HGNC HGNC:11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 A0A024RBL6 UPI0000136AA0 NM_016569.3 2/8 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,PROSITE_patterns:PS01264,Gene3D:1h6fA00,Pfam_domain:PF00907,SMART_domains:SM00425,Superfamily_domains:SSF49417 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 114680963 114680963 G A 1 0 0 0 0 0 0 0 1 16064 1103 39 1 1 TBX3 12 114680963 Silent SNP G C3L-00080_T 2429867 114680963 18594346 504 2602 CCDC60 0 . GRCh38 12 119488764 119488764 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.455C>G p.Pro152Arg p.P152R ENST00000327554 5/14 102 88 14 135 135 0 strelka-varscan-mutect CCDC60,missense_variant,p.Pro152Arg,ENST00000327554,NM_178499.4;RP11-768F21.1,intron_variant,,ENST00000509470,;RP11-768F21.1,intron_variant,,ENST00000537366,;RP11-768F21.1,intron_variant,,ENST00000535511,; G ENST00000327554 Transcript missense_variant 920/2450 455/1653 152/550 P/R cCc/cGc 1 1 CCDC60 HGNC HGNC:28610 protein_coding YES CCDS9190.1 ENSP00000333374 Q8IWA6 UPI000019906E NM_178499.4 tolerated(0.15) 5/14 Pfam_domain:PF15769,hmmpanther:PTHR34754 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -19.9953 0.9994663 1 1 1 0 G 3 3 7 119488764 119488764 C G 1 0 0 0 0 1 0 0 0 2533 637 22 4 4 CCDC60 12 119488764 Missense_Mutation SNP C C3L-00080_T 4807801 119488764 13786545 505 2603 ZCCHC8 0 . GRCh38 12 122480204 122480204 + Nonsense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1126A>T p.Arg376Ter p.R376* ENST00000633063 11/14 49 32 17 80 80 0 strelka-varscan-mutect ZCCHC8,stop_gained,p.Arg138Ter,ENST00000543897,;ZCCHC8,stop_gained,p.Arg376Ter,ENST00000633063,NM_017612.4;ZCCHC8,stop_gained,p.Arg138Ter,ENST00000536306,;ZCCHC8,stop_gained,p.Arg138Ter,ENST00000544054,;ZCCHC8,stop_gained,p.Arg138Ter,ENST00000536663,;ZCCHC8,downstream_gene_variant,,ENST00000540586,;ZCCHC8,non_coding_transcript_exon_variant,,ENST00000542892,;ZCCHC8,upstream_gene_variant,,ENST00000538116,;ZCCHC8,downstream_gene_variant,,ENST00000538493,;ZCCHC8,downstream_gene_variant,,ENST00000546149,; A ENST00000633063 Transcript stop_gained 1359/2955 1126/2124 376/707 R/* Aga/Tga 1 -1 ZCCHC8 HGNC HGNC:25265 protein_coding YES ENSP00000488055 Q6NZY4 UPI00001E0582 NM_017612.4 11/14 hmmpanther:PTHR13316,hmmpanther:PTHR13316:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 122480204 122480204 T A 1 0 0 0 0 0 1 0 0 18169 1588 55 4 4 ZCCHC8 12 122480204 Nonsense_Mutation SNP T C3L-00080_T 2991440 122480204 10795105 506 2604 FBRSL1 0 . GRCh38 12 132583070 132583070 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.2430G>T p.= p.L810L ENST00000434748 17/17 55 29 26 37 37 0 strelka-varscan-mutect FBRSL1,synonymous_variant,p.=,ENST00000434748,NM_001142641.1;MIR6763,downstream_gene_variant,,ENST00000612332,;FBRSL1,downstream_gene_variant,,ENST00000542306,; T ENST00000434748 Transcript synonymous_variant 3450/5568 2430/3138 810/1045 L ctG/ctT 1 1 FBRSL1 HGNC HGNC:29308 protein_coding YES CCDS45010.1 ENSP00000396160 Q9HCM7 UPI00018830C3 NM_001142641.1 17/17 hmmpanther:PTHR14429,hmmpanther:PTHR14429:SF20 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999957 1 1 1 0 T 2 4 7 132583070 132583070 G T 1 0 0 0 0 0 0 0 1 5571 1335 47 2 2 FBRSL1 12 132583070 Silent SNP G C3L-00080_T 10102866 132583070 692239 507 2605 VWA8 0 . GRCh38 13 41891491 41891491 + Nonsense_Mutation SNP C C A rs768100252 C3L-00080_T C3L-00080_N C C c.580G>T p.Glu194Ter p.E194* ENST00000379310 5/45 159 101 58 221 221 0 strelka-varscan-mutect VWA8,stop_gained,p.Glu194Ter,ENST00000379310,NM_015058.1;VWA8,stop_gained,p.Glu194Ter,ENST00000281496,NM_001009814.1; A ENST00000379310 Transcript stop_gained 649/7147 580/5718 194/1905 E/* Gaa/Taa rs768100252 1 -1 VWA8 HGNC HGNC:29071 protein_coding YES CCDS41881.1 ENSP00000368612 A3KMH1 UPI00001606AC NM_015058.1 5/45 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR21610,Low_complexity_(Seg):seg,Superfamily_domains:SSF52540 HIGH 1 SNV 2 1 PASS rs768100252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 41891491 41891491 C A 1 0 0 0 0 0 1 0 0 17800 864 30 2 2 VWA8 13 41891491 Nonsense_Mutation SNP C C3L-00080_T 41891491 72472837 508 2606 SPERT 0 . GRCh38 13 45713451 45713451 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.426delG p.Gln143SerfsTer87 p.Q143Sfs*87 ENST00000310521 3/3 285 155 130 338 338 0 sindel-varindel-pindel SPERT,frameshift_variant,p.Gln107SerfsTer87,ENST00000378966,;SPERT,frameshift_variant,p.Gln143SerfsTer87,ENST00000310521,NM_152719.2;SPERT,frameshift_variant,p.Gln107SerfsTer87,ENST00000610924,NM_001286342.1;SPERT,frameshift_variant,p.Gln116SerfsTer?,ENST00000533564,; - ENST00000310521 Transcript frameshift_variant 506/1613 426/1347 142/448 L/X ctG/ct 1 1 SPERT HGNC HGNC:30720 protein_coding YES CCDS9399.1 ENSP00000309189 Q8NA61 A0A140VJV5 UPI0000070F5F NM_152719.2 3/3 Pfam_domain:PF14645,hmmpanther:PTHR21533,hmmpanther:PTHR21533:SF13 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 45713451 45713451 G - 1 0 1 0 1 0 0 0 0 15390 1306 46 0 0 SPERT 13 45713451 Frame_Shift_Del DEL G C3L-00080_T 3821960 45713451 68650877 509 2607 KPNA3 0 . GRCh38 13 49706142 49706142 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1165G>T p.Ala389Ser p.A389S ENST00000261667 14/17 67 39 28 86 85 1 strelka-varscan-mutect KPNA3,missense_variant,p.Ala389Ser,ENST00000261667,NM_002267.3;KPNA3,upstream_gene_variant,,ENST00000436760,; A ENST00000261667 Transcript missense_variant 1580/4474 1165/1566 389/521 A/S Gct/Tct 1 -1 KPNA3 HGNC HGNC:6396 protein_coding YES CCDS9421.1 ENSP00000261667 O00505 A0A024RDV7 UPI000012D5F9 NM_002267.3 deleterious(0.01) 14/17 hmmpanther:PTHR23316,hmmpanther:PTHR23316:SF6,PIRSF_domain:PIRSF005673,Gene3D:1.25.10.10,Pfam_domain:PF00514,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 49706142 49706142 C A 1 0 0 0 0 1 0 0 0 8311 710 25 2 2 KPNA3 13 49706142 Missense_Mutation SNP C C3L-00080_T 3992691 49706142 64658186 510 2608 KCNRG 0 . GRCh38 13 50016044 50016044 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.551G>C p.Ser184Thr p.S184T ENST00000312942 1/2 89 67 22 124 124 0 strelka-varscan-mutect KCNRG,missense_variant,p.Ser184Thr,ENST00000360473,NM_199464.2;KCNRG,missense_variant,p.Ser184Thr,ENST00000312942,NM_173605.1;TRIM13,3_prime_UTR_variant,,ENST00000378182,NM_213590.2,NM_052811.3;TRIM13,downstream_gene_variant,,ENST00000420995,NM_005798.4;TRIM13,downstream_gene_variant,,ENST00000356017,NM_001007278.2;TRIM13,downstream_gene_variant,,ENST00000457662,;TRIM13,downstream_gene_variant,,ENST00000378183,;TRIM13,downstream_gene_variant,,ENST00000442421,;DLEU2,intron_variant,,ENST00000621282,;TRIM13,intron_variant,,ENST00000478111,;TRIM13,intron_variant,,ENST00000474805,; C ENST00000312942 Transcript missense_variant 791/1527 551/819 184/272 S/T aGc/aCc 1 1 KCNRG HGNC HGNC:18893 protein_coding YES CCDS9424.1 ENSP00000324191 Q8N5I3 UPI000000D8AF NM_173605.1 tolerated(0.38) 1/2 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF5 MODERATE 1 SNV 1 1 PASS rs1440604784 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 50016044 50016044 G C 1 0 0 0 0 1 0 0 0 8003 971 34 4 4 KCNRG 13 50016044 Missense_Mutation SNP G C3L-00080_T 309902 50016044 64348284 511 2609 NALCN 0 . GRCh38 13 101283952 101283952 + Missense_Mutation SNP C C T rs75772824 C3L-00080_T C3L-00080_N C C c.1115G>A p.Arg372His p.R372H ENST00000251127 10/44 146 112 34 183 183 0 strelka-varscan-mutect NALCN,missense_variant,p.Arg372His,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; T ENST00000251127 Transcript missense_variant 1197/6818 1115/5217 372/1738 R/H cGc/cAc rs75772824,COSM259190 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 tolerated(0.55) 10/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs75772824 . 0 206 0 4 0 0 0 0 -20 0.9999653 1 1 1 0 T 3 4 7 101283952 101283952 C T 1 0 0 0 0 1 0 0 0 10155 768 27 1 1 NALCN 13 101283952 Missense_Mutation SNP C C3L-00080_T 51267908 101283952 13080376 512 2610 MYO16 0 . GRCh38 13 109125117 109125117 + Silent SNP A A C rs867188147 C3L-00080_T C3L-00080_N A A c.3541A>C p.= p.R1181R ENST00000457511 30/35 155 123 32 173 172 1 strelka-varscan-mutect MYO16,synonymous_variant,p.=,ENST00000457511,NM_001198950.1;MYO16,synonymous_variant,p.=,ENST00000356711,NM_015011.1;MYO16,synonymous_variant,p.=,ENST00000357550,; C ENST00000457511 Transcript synonymous_variant 4163/7436 3541/5643 1181/1880 R Aga/Cga rs867188147 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 30/35 PROSITE_profiles:PS50096,hmmpanther:PTHR13140,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs867188147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 109125117 109125117 A C 1 0 0 0 0 0 0 0 1 10065 202 7 5 5 MYO16 13 109125117 Silent SNP A C3L-00080_T 7841165 109125117 5239211 513 2611 COL4A1 0 . GRCh38 13 110187297 110187297 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1569G>T p.Gln523His p.Q523H ENST00000375820 25/52 220 114 106 258 258 0 strelka-varscan-mutect COL4A1,missense_variant,p.Gln523His,ENST00000375820,NM_001845.5;COL4A1,downstream_gene_variant,,ENST00000543140,NM_001303110.1; A ENST00000375820 Transcript missense_variant 1691/6532 1569/5010 523/1669 Q/H caG/caT 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 tolerated(0.48) 25/52 Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 110187297 110187297 C A 1 0 0 0 0 1 0 0 0 3478 796 28 2 2 COL4A1 13 110187297 Missense_Mutation SNP C C3L-00080_T 1062180 110187297 4177031 514 2612 MCF2L 0 . GRCh38 13 112909255 112909255 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.172G>T p.Val58Phe p.V58F ENST00000397036 2/2 143 80 63 130 130 0 strelka-varscan-mutect MCF2L,missense_variant,p.Val58Phe,ENST00000397036,;MCF2L,intron_variant,,ENST00000375608,;MCF2L,intron_variant,,ENST00000442625,; T ENST00000397036 Transcript missense_variant,splice_region_variant 180/1544 172/195 58/64 V/F Gtc/Ttc 1 1 MCF2L HGNC HGNC:14576 protein_coding ENSP00000380230 A2A3H1 UPI0000E59B13 tolerated_low_confidence(0.17) 2/2 MODERATE SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999993 1 1 1 0 T 3 4 7 112909255 112909255 G T 1 0 0 0 0 1 0 0 0 9310 1275 44 2 2 MCF2L 13 112909255 Missense_Mutation SNP G C3L-00080_T 2721958 112909255 1455073 515 2613 POTEG 0 . GRCh38 14 19433771 19433771 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.519G>T p.Lys173Asn p.K173N ENST00000547848 1/11 202 177 25 204 204 0 varscan-mutect POTEG,missense_variant,p.Lys173Asn,ENST00000547848,NM_001005356.2;POTEG,missense_variant,p.Lys173Asn,ENST00000547722,;POTEG,missense_variant,p.Lys173Asn,ENST00000622767,; A ENST00000547848 Transcript missense_variant,splice_region_variant 571/2204 519/1527 173/508 K/N aaG/aaT 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 tolerated(0.44) 1/11 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415 MODERATE 1 SNV 1 1 PASS rs1173296642 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 19433771 19433771 C A 1 0 0 0 0 1 0 0 0 12380 927 32 2 2 POTEG 14 19433771 Missense_Mutation SNP C C3L-00080_T 19433771 87609947 516 2614 OR4K13 0 . GRCh38 14 20034481 20034481 + Nonsense_Mutation SNP G G T rs760036674 C3L-00080_T C3L-00080_N G G c.278C>A p.Ser93Ter p.S93* ENST00000315693 1/1 377 210 167 226 225 1 strelka-varscan-mutect OR4K13,stop_gained,p.Ser93Ter,ENST00000315693,NM_001004714.1; T ENST00000315693 Transcript stop_gained 280/917 278/915 93/304 S/* tCa/tAa rs760036674 1 -1 OR4K13 HGNC HGNC:15351 protein_coding YES CCDS32028.1 ENSP00000319322 Q8NH42 A0A126GVS2 UPI0000041CEB NM_001004714.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF123,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH 1 SNV 1 PASS rs760036674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 20034481 20034481 G T 1 0 0 0 0 0 1 0 0 11145 1294 45 2 2 OR4K13 14 20034481 Nonsense_Mutation SNP G C3L-00080_T 600710 20034481 87009237 517 2615 OR4L1 0 . GRCh38 14 20060273 20060273 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.229A>T p.Thr77Ser p.T77S ENST00000315683 1/1 298 175 123 134 134 0 strelka-varscan-mutect OR4L1,missense_variant,p.Thr77Ser,ENST00000315683,NM_001004717.1; T ENST00000315683 Transcript missense_variant 229/939 229/939 77/312 T/S Aca/Tca 1 1 OR4L1 HGNC HGNC:15356 protein_coding YES CCDS32029.1 ENSP00000319217 Q8NH43 UPI0000041CE3 NM_001004717.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF221,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 20060273 20060273 A T 1 0 0 0 0 1 0 0 0 11151 159 6 4 4 OR4L1 14 20060273 Missense_Mutation SNP A C3L-00080_T 25792 20060273 86983445 518 2616 RNASE7 0 . GRCh38 14 21043404 21043404 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.412C>T p.Gln138Ter p.Q138* ENST00000298690 2/2 219 116 103 109 109 0 strelka-varscan-mutect RNASE7,stop_gained,p.Gln138Ter,ENST00000298690,NM_032572.3;NDRG2,intron_variant,,ENST00000403829,NM_001282211.1;NDRG2,intron_variant,,ENST00000555026,;RNASE7,stop_gained,p.Gln138Ter,ENST00000481538,; T ENST00000298690 Transcript stop_gained 669/1498 412/471 138/156 Q/* Cag/Tag 1 1 RNASE7 HGNC HGNC:19278 protein_coding YES CCDS41914.1 ENSP00000298690 Q9H1E1 UPI000013E505 NM_032572.3 2/2 hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF31,Gene3D:3.10.130.10,Pfam_domain:PF00074,SMART_domains:SM00092,Superfamily_domains:SSF54076,Prints_domain:PR00794,PD000535 HIGH 1 SNV 1 1 PASS rs1236573064 . 0 197 3 6 4 0 0 0 -20 0.8734033 1 1 1 0 T 4 4 7 21043404 21043404 C T 1 0 0 0 0 0 1 0 0 13587 595 21 3 3 RNASE7 14 21043404 Nonsense_Mutation SNP C C3L-00080_T 983131 21043404 86000314 519 2617 EFS 0 . GRCh38 14 23358933 23358933 + Silent SNP C C A rs754723164 C3L-00080_T C3L-00080_N C C c.1194G>T p.= p.P398P ENST00000216733 5/6 157 90 67 86 86 0 strelka-varscan-mutect EFS,synonymous_variant,p.=,ENST00000216733,NM_005864.3;EFS,synonymous_variant,p.=,ENST00000351354,NM_032459.2;EFS,synonymous_variant,p.=,ENST00000429593,NM_001277174.1;RP11-124D2.3,downstream_gene_variant,,ENST00000554010,; A ENST00000216733 Transcript synonymous_variant 1802/3118 1194/1686 398/561 P ccG/ccT rs754723164,COSM5037128 1 -1 EFS HGNC HGNC:16898 protein_coding YES CCDS9595.1 ENSP00000216733 O43281 UPI0000129D21 NM_005864.3 5/6 hmmpanther:PTHR10654,hmmpanther:PTHR10654:SF14,Pfam_domain:PF12026 0,1 LOW 1 SNV 1 0,1 1 PASS rs748164198 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 23358933 23358933 C A 1 0 0 0 0 0 0 0 1 4796 639 23 1 1 EFS 14 23358933 Silent SNP C C3L-00080_T 2315529 23358933 83684785 520 2618 MYH7 0 . GRCh38 14 23432750 23432750 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.391C>A p.Leu131Met p.L131M ENST00000355349 5/40 738 437 301 420 420 0 strelka-varscan-mutect MYH7,missense_variant,p.Leu131Met,ENST00000355349,NM_000257.3; T ENST00000355349 Transcript missense_variant 554/6087 391/5808 131/1935 L/M Ctg/Atg 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 deleterious(0.01) 5/40 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23432750 23432750 G T 1 0 0 0 0 1 0 0 0 10039 962 34 2 2 MYH7 14 23432750 Missense_Mutation SNP G C3L-00080_T 73817 23432750 83610968 521 2619 ZFHX2 0 . GRCh38 14 23532862 23532862 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2264G>T p.Gly755Val p.G755V ENST00000419474 3/10 324 236 88 202 202 0 strelka-varscan-mutect ZFHX2,missense_variant,p.Gly755Val,ENST00000419474,NM_033400.2;ZFHX2,intron_variant,,ENST00000615307,;ZFHX2,downstream_gene_variant,,ENST00000412565,;ZFHX2,downstream_gene_variant,,ENST00000555334,;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;RP11-66N24.7,downstream_gene_variant,,ENST00000622438,;RP11-66N24.4,intron_variant,,ENST00000554403,; A ENST00000419474 Transcript missense_variant 2620/9182 2264/7719 755/2572 G/V gGt/gTt 1 -1 ZFHX2 HGNC HGNC:20152 protein_coding YES CCDS55907.1 ENSP00000413418 Q9C0A1 UPI000198D01B NM_033400.2 deleterious(0) 3/10 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF119 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 23532862 23532862 C A 1 0 0 0 0 1 0 0 0 18211 507 18 2 2 ZFHX2 14 23532862 Missense_Mutation SNP C C3L-00080_T 100112 23532862 83510856 522 2620 GPR33 0 . GRCh38 14 31483001 31483001 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.965T>G p.Phe322Cys p.F322C ENST00000399285 2/2 56 28 28 40 40 0 strelka-varscan-mutect GPR33,missense_variant,p.Phe322Cys,ENST00000399285,NM_001197184.2; C ENST00000399285 Transcript missense_variant 1020/1057 965/1002 322/333 F/C tTt/tGt 1 -1 GPR33 HGNC HGNC:4489 protein_coding YES CCDS73628.1 ENSP00000421557 Q49SQ1 UPI0000585CCE NM_001197184.2 deleterious(0) 2/2 hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF5,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 31483001 31483001 A C 1 0 0 0 0 1 0 0 0 6573 14 1 5 5 GPR33 14 31483001 Missense_Mutation SNP A C3L-00080_T 7950139 31483001 75560717 523 2621 NPAS3 0 . GRCh38 14 33800833 33800833 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2526C>A p.Ser842Arg p.S842R ENST00000356141 12/12 783 444 339 482 482 0 strelka-varscan-mutect NPAS3,missense_variant,p.Ser810Arg,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Ser812Arg,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Ser847Arg,ENST00000551492,;NPAS3,missense_variant,p.Ser842Arg,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Ser829Arg,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Ser816Arg,ENST00000551634,; A ENST00000356141 Transcript missense_variant 2526/2802 2526/2802 842/933 S/R agC/agA 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious_low_confidence(0) 12/12 hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS rs1444367913 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 33800833 33800833 C A 1 0 0 0 0 1 0 0 0 10612 709 25 2 2 NPAS3 14 33800833 Missense_Mutation SNP C C3L-00080_T 2317832 33800833 73242885 524 2622 SNX6 0 . GRCh38 14 34608106 34608106 + Missense_Mutation SNP G G A C3L-00080_T C3L-00080_N G G c.230C>T p.Ser77Leu p.S77L ENST00000362031 4/14 145 82 63 101 101 0 strelka-varscan-mutect SNX6,missense_variant,p.Ser77Leu,ENST00000362031,NM_152233.2;SNX6,missense_variant,p.Ser95Leu,ENST00000555648,;SNX6,5_prime_UTR_variant,,ENST00000396526,NM_021249.3;SNX6,intron_variant,,ENST00000557265,;SNX6,missense_variant,p.Ser77Leu,ENST00000555416,;SNX6,missense_variant,p.Ser71Leu,ENST00000556712,;SNX6,3_prime_UTR_variant,,ENST00000556162,;SNX6,non_coding_transcript_exon_variant,,ENST00000556303,;SNX6,intron_variant,,ENST00000557341,; A ENST00000362031 Transcript missense_variant 261/2001 230/1257 77/418 S/L tCa/tTa COSM433030,COSM4814580 1 -1 SNX6 HGNC HGNC:14970 protein_coding YES CCDS41942.1 ENSP00000355217 A0A0A0MRI2 UPI00006AB832 NM_152233.2 tolerated(0.1) 4/14 PROSITE_profiles:PS50195,hmmpanther:PTHR10555:SF120,hmmpanther:PTHR10555,PIRSF_domain:PIRSF036924,Gene3D:3.30.1520.10,Pfam_domain:PF00787,Superfamily_domains:SSF64268 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 34608106 34608106 G A 1 0 0 0 0 1 0 0 0 15227 1294 45 3 3 SNX6 14 34608106 Missense_Mutation SNP G C3L-00080_T 807273 34608106 72435612 525 2623 FAM179B 0 . GRCh38 14 45008920 45008920 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2912G>T p.Ser971Ile p.S971I ENST00000361462 6/20 198 152 46 134 133 1 strelka-varscan-mutect FAM179B,missense_variant,p.Ser971Ile,ENST00000361462,NM_001308120.1;FAM179B,missense_variant,p.Ser971Ile,ENST00000361577,NM_015091.2;KLHL28,intron_variant,,ENST00000556239,;FAM179B,downstream_gene_variant,,ENST00000555874,;FAM179B,downstream_gene_variant,,ENST00000557250,;KLHL28,intron_variant,,ENST00000553817,;FAM179B,intron_variant,,ENST00000557423,;FAM179B,downstream_gene_variant,,ENST00000555607,;FAM179B,upstream_gene_variant,,ENST00000556105,; T ENST00000361462 Transcript missense_variant 3095/6375 2912/5322 971/1773 S/I aGc/aTc 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 tolerated(0.08) 6/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 45008920 45008920 G T 1 0 0 0 0 1 0 0 0 5351 971 34 2 2 FAM179B 14 45008920 Missense_Mutation SNP G C3L-00080_T 10400814 45008920 62034798 526 2624 L2HGDH 0 . GRCh38 14 50283946 50283946 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.628G>T p.Gly210Cys p.G210C ENST00000267436 5/10 375 226 149 282 282 0 strelka-varscan-mutect L2HGDH,missense_variant,p.Gly210Cys,ENST00000267436,NM_024884.2;L2HGDH,missense_variant,p.Gly210Cys,ENST00000421284,;L2HGDH,missense_variant,p.Gly210Cys,ENST00000261699,;L2HGDH,missense_variant,p.Gly210Cys,ENST00000555423,;L2HGDH,3_prime_UTR_variant,,ENST00000555610,; A ENST00000267436 Transcript missense_variant 1026/6414 628/1392 210/463 G/C Ggt/Tgt 1 -1 L2HGDH HGNC HGNC:20499 protein_coding YES CCDS9698.1 ENSP00000267436 Q9H9P8 UPI0000048F63 NM_024884.2 deleterious(0) 5/10 Gene3D:3.50.50.60,Pfam_domain:PF01266,hmmpanther:PTHR13847,hmmpanther:PTHR13847:SF191,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS rs1286021737 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 50283946 50283946 C A 1 0 0 0 0 1 0 0 0 8491 681 24 2 2 L2HGDH 14 50283946 Missense_Mutation SNP C C3L-00080_T 5275026 50283946 56759772 527 2625 DAAM1 0 . GRCh38 14 59324402 59324402 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.937A>G p.Ile313Val p.I313V ENST00000395125 7/25 120 81 39 109 109 0 strelka-varscan-mutect DAAM1,missense_variant,p.Ile313Val,ENST00000395125,NM_014992.2;DAAM1,missense_variant,p.Ile313Val,ENST00000360909,NM_001270520.1;DAAM1,downstream_gene_variant,,ENST00000557327,;DAAM1,non_coding_transcript_exon_variant,,ENST00000556894,; G ENST00000395125 Transcript missense_variant 960/5806 937/3237 313/1078 I/V Att/Gtt 1 1 DAAM1 HGNC HGNC:18142 protein_coding YES CCDS9737.1 ENSP00000378557 Q9Y4D1 UPI0000161FAA NM_014992.2 deleterious(0) 7/25 PROSITE_profiles:PS51232,hmmpanther:PTHR23213:SF181,hmmpanther:PTHR23213,Pfam_domain:PF06367,SMART_domains:SM01139,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 59324402 59324402 A G 1 0 0 0 0 1 0 0 0 4016 101 4 5 5 DAAM1 14 59324402 Missense_Mutation SNP A C3L-00080_T 9040456 59324402 47719316 528 2626 RTN1 0 . GRCh38 14 59727408 59727408 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1276G>C p.Ala426Pro p.A426P ENST00000267484 3/9 115 57 58 56 56 0 strelka-varscan-mutect RTN1,missense_variant,p.Ala426Pro,ENST00000267484,NM_021136.2;RTN1,missense_variant,p.Ala352Pro,ENST00000611068,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,; G ENST00000267484 Transcript missense_variant 1612/3435 1276/2331 426/776 A/P Gcg/Ccg 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 tolerated(0.14) 3/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 MODERATE 1 SNV 1 1 PASS rs1276026033 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 59727408 59727408 C G 1 0 0 0 0 1 0 0 0 13985 768 27 4 4 RTN1 14 59727408 Missense_Mutation SNP C C3L-00080_T 403006 59727408 47316310 529 2627 SYT16 0 . GRCh38 14 62080848 62080848 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.1008C>A p.= p.T336T ENST00000568344 4/6 212 185 27 145 145 0 strelka-varscan-mutect SYT16,synonymous_variant,p.=,ENST00000568344,NM_031914.2;SYT16,5_prime_UTR_variant,,ENST00000430451,;RP11-355I22.5,intron_variant,,ENST00000553990,;SYT16,missense_variant,p.Pro366Gln,ENST00000555409,; A ENST00000568344 Transcript synonymous_variant 1205/13978 1008/1938 336/645 T acC/acA 1 1 SYT16 HGNC HGNC:23142 protein_coding YES CCDS45121.1 ENSP00000478637 Q17RD7 UPI0000EE1AC0 NM_031914.2 4/6 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF113 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 7 62080848 62080848 C A 1 0 0 0 0 0 0 0 1 15866 581 21 2 2 SYT16 14 62080848 Silent SNP C C3L-00080_T 2353440 62080848 44962870 530 2628 PLEKHH1 0 . GRCh38 14 67583849 67583849 + Missense_Mutation SNP C C A rs200119528 C3L-00080_T C3L-00080_N C C c.3535C>A p.Arg1179Ser p.R1179S ENST00000329153 25/29 255 194 61 129 129 0 strelka-varscan-mutect PLEKHH1,missense_variant,p.Arg1179Ser,ENST00000329153,NM_020715.2;PIGH,intron_variant,,ENST00000561272,;PLEKHH1,upstream_gene_variant,,ENST00000559832,;PLEKHH1,3_prime_UTR_variant,,ENST00000561370,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000557971,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000559981,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558386,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558366,;PLEKHH1,upstream_gene_variant,,ENST00000558214,;PLEKHH1,upstream_gene_variant,,ENST00000559168,;PLEKHH1,downstream_gene_variant,,ENST00000560100,;PLEKHH1,downstream_gene_variant,,ENST00000558296,;PLEKHH1,upstream_gene_variant,,ENST00000559766,;PLEKHH1,upstream_gene_variant,,ENST00000561057,; A ENST00000329153 Transcript missense_variant 3667/6604 3535/4095 1179/1364 R/S Cgc/Agc rs200119528 1 1 PLEKHH1 HGNC HGNC:17733 protein_coding YES CCDS45128.1 ENSP00000330278 Q9ULM0 UPI00001C1F64 NM_020715.2 deleterious(0.03) 25/29 PROSITE_profiles:PS50057,hmmpanther:PTHR22903:SF4,hmmpanther:PTHR22903,Pfam_domain:PF00373,Gene3D:1.20.80.10,SMART_domains:SM00295,Superfamily_domains:SSF47031 MODERATE 1 SNV 1 1 PASS rs200119528 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 67583849 67583849 C A 1 0 0 0 0 1 0 0 0 12169 768 27 1 1 PLEKHH1 14 67583849 Missense_Mutation SNP C C3L-00080_T 5503001 67583849 39459869 531 2629 ZFYVE26 0 . GRCh38 14 67785262 67785262 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.3320C>T p.Pro1107Leu p.P1107L ENST00000347230 19/42 645 372 273 365 364 1 strelka-varscan-mutect ZFYVE26,missense_variant,p.Pro1107Leu,ENST00000347230,NM_015346.3;ZFYVE26,missense_variant,p.Pro1107Leu,ENST00000555452,;ZFYVE26,3_prime_UTR_variant,,ENST00000554557,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000554523,; A ENST00000347230 Transcript missense_variant 3459/9675 3320/7620 1107/2539 P/L cCa/cTa 1 -1 ZFYVE26 HGNC HGNC:20761 protein_coding YES CCDS9788.1 ENSP00000251119 Q68DK2 UPI00001FD735 NM_015346.3 tolerated(0.3) 19/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 67785262 67785262 G A 1 0 0 0 0 1 0 0 0 18245 1348 47 3 3 ZFYVE26 14 67785262 Missense_Mutation SNP G C3L-00080_T 201413 67785262 39258456 532 2630 ZFYVE26 0 . GRCh38 14 67794201 67794201 + Missense_Mutation SNP T T C C3L-00080_T C3L-00080_N T T c.2371A>G p.Thr791Ala p.T791A ENST00000347230 13/42 659 585 74 391 391 0 strelka-varscan-mutect ZFYVE26,missense_variant,p.Thr791Ala,ENST00000347230,NM_015346.3;ZFYVE26,missense_variant,p.Thr791Ala,ENST00000555452,;ZFYVE26,3_prime_UTR_variant,,ENST00000554557,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000554523,;ZFYVE26,downstream_gene_variant,,ENST00000557366,;ZFYVE26,downstream_gene_variant,,ENST00000557407,;RP11-1012A1.7,upstream_gene_variant,,ENST00000557141,; C ENST00000347230 Transcript missense_variant 2510/9675 2371/7620 791/2539 T/A Aca/Gca COSM1370733 1 -1 ZFYVE26 HGNC HGNC:20761 protein_coding YES CCDS9788.1 ENSP00000251119 Q68DK2 UPI00001FD735 NM_015346.3 tolerated(0.19) 13/42 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 67794201 67794201 T C 1 0 0 0 0 1 0 0 0 18245 1638 57 5 5 ZFYVE26 14 67794201 Missense_Mutation SNP T C3L-00080_T 8939 67794201 39249517 533 2631 ADAM20 0 . GRCh38 14 70524144 70524144 + Missense_Mutation SNP T T A rs761166677 C3L-00080_T C3L-00080_N T T c.764A>T p.His255Leu p.H255L ENST00000256389 2/2 389 308 81 292 292 0 strelka-varscan-mutect ADAM20,missense_variant,p.His255Leu,ENST00000256389,NM_003814.4;RP11-486O13.4,intron_variant,,ENST00000556646,; A ENST00000256389 Transcript missense_variant 1009/2795 764/2331 255/776 H/L cAt/cTt rs761166677 1 -1 ADAM20 HGNC HGNC:199 protein_coding YES CCDS32111.1 ENSP00000256389 O43506 UPI0000183495 NM_003814.4 deleterious(0) 2/2 Gene3D:3.40.390.10,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF135,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs761166677 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 70524144 70524144 T A 1 0 0 0 0 1 0 0 0 286 1464 51 4 4 ADAM20 14 70524144 Missense_Mutation SNP T C3L-00080_T 2729943 70524144 36519574 534 2632 TTLL5 0 . GRCh38 14 75669511 75669511 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.170G>T p.Arg57Ile p.R57I ENST00000298832 3/32 229 193 36 143 141 2 strelka-varscan-mutect TTLL5,missense_variant,p.Arg57Ile,ENST00000298832,NM_015072.4;TTLL5,missense_variant,p.Arg57Ile,ENST00000557636,;TTLL5,missense_variant,p.Arg57Ile,ENST00000556977,;TTLL5,missense_variant,p.Arg57Ile,ENST00000286650,;TTLL5,non_coding_transcript_exon_variant,,ENST00000556685,;TTLL5,non_coding_transcript_exon_variant,,ENST00000555290,;TTLL5,non_coding_transcript_exon_variant,,ENST00000556173,; T ENST00000298832 Transcript missense_variant 375/4683 170/3846 57/1281 R/I aGa/aTa 1 1 TTLL5 HGNC HGNC:19963 protein_coding YES CCDS32124.1 ENSP00000298832 Q6EMB2 UPI00003FF22B NM_015072.4 deleterious(0.04) 3/32 hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF16 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 7 75669511 75669511 G T 1 0 0 0 0 1 0 0 0 17241 942 33 2 2 TTLL5 14 75669511 Missense_Mutation SNP G C3L-00080_T 5145367 75669511 31374207 535 2633 CIPC 0 . GRCh38 14 77113816 77113816 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.698C>T p.Ser233Phe p.S233F ENST00000361786 4/4 225 176 49 108 108 0 strelka-varscan-mutect CIPC,missense_variant,p.Ser233Phe,ENST00000361786,NM_033426.2;CIPC,downstream_gene_variant,,ENST00000557115,;CIPC,downstream_gene_variant,,ENST00000555611,;CIPC,downstream_gene_variant,,ENST00000554447,;CIPC,downstream_gene_variant,,ENST00000554658,;TMEM63C,upstream_gene_variant,,ENST00000557408,;CIPC,downstream_gene_variant,,ENST00000555200,;CIPC,downstream_gene_variant,,ENST00000555437,;RP11-463C8.4,intron_variant,,ENST00000557752,; T ENST00000361786 Transcript missense_variant 1015/4486 698/1200 233/399 S/F tCt/tTt 1 1 CIPC HGNC HGNC:20365 protein_coding YES CCDS9855.1 ENSP00000355319 Q9C0C6 UPI0000073FD0 NM_033426.2 tolerated(0.17) 4/4 hmmpanther:PTHR34648,hmmpanther:PTHR34648:SF1,Pfam_domain:PF15800 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 77113816 77113816 C T 1 0 0 0 0 1 0 0 0 3194 913 32 3 3 CIPC 14 77113816 Missense_Mutation SNP C C3L-00080_T 1444305 77113816 29929902 536 2634 NRXN3 0 . GRCh38 14 79861542 79861542 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.4573C>A p.Arg1525Ser p.R1525S ENST00000634499 20/20 365 280 85 209 209 0 strelka-varscan-mutect NRXN3,missense_variant,p.Arg1525Ser,ENST00000634499,;NRXN3,missense_variant,p.Arg1432Ser,ENST00000635466,;NRXN3,missense_variant,p.Arg498Ser,ENST00000557594,NM_001272020.1;NRXN3,intron_variant,,ENST00000281127,NM_138970.4;NRXN3,intron_variant,,ENST00000428277,NM_001105250.2;NRXN3,intron_variant,,ENST00000554719,NM_004796.5;NRXN3,intron_variant,,ENST00000556003,;NRXN3,3_prime_UTR_variant,,ENST00000554738,;NRXN3,3_prime_UTR_variant,,ENST00000555387,; A ENST00000634499 Transcript missense_variant 5578/6069 4573/4995 1525/1664 R/S Cgt/Agt 1 1 NRXN3 HGNC HGNC:8010 protein_coding ENSP00000488920 A0A0U1RQC5 UPI000719A152 20/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 79861542 79861542 C A 1 0 0 0 0 1 0 0 0 10726 652 23 1 1 NRXN3 14 79861542 Missense_Mutation SNP C C3L-00080_T 2747726 79861542 27182176 537 2635 CATSPERB 0 . GRCh38 14 91729452 91729452 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.28G>T p.Val10Phe p.V10F ENST00000256343 2/27 61 53 8 67 67 0 strelka-varscan-mutect CATSPERB,missense_variant,p.Val10Phe,ENST00000256343,NM_024764.3;CATSPERB,missense_variant,p.Val10Phe,ENST00000553329,;CATSPERB,missense_variant,p.Val10Phe,ENST00000556661,;CATSPERB,missense_variant,p.Val10Phe,ENST00000554560,;CATSPERB,missense_variant,p.Val10Phe,ENST00000553676,; A ENST00000256343 Transcript missense_variant 185/3623 28/3351 10/1116 V/F Gtt/Ttt 1 -1 CATSPERB HGNC HGNC:20500 protein_coding YES CCDS32142.1 ENSP00000256343 Q9H7T0 UPI0000418DA1 NM_024764.3 tolerated(0.1) 2/27 hmmpanther:PTHR14705,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1390282230 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 91729452 91729452 C A 1 0 0 0 0 1 0 0 0 2391 565 20 2 2 CATSPERB 14 91729452 Missense_Mutation SNP C C3L-00080_T 11867910 91729452 15314266 538 2636 BTBD7 0 . GRCh38 14 93293967 93293967 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.1053C>T p.= p.L351L ENST00000334746 3/11 302 237 65 173 173 0 strelka-varscan-mutect BTBD7,synonymous_variant,p.=,ENST00000334746,NM_001002860.3;BTBD7,synonymous_variant,p.=,ENST00000298896,NM_018167.4;BTBD7,synonymous_variant,p.=,ENST00000553975,;BTBD7,synonymous_variant,p.=,ENST00000555525,;BTBD7,intron_variant,,ENST00000554565,NM_001289133.1;BTBD7,downstream_gene_variant,,ENST00000554968,;BTBD7,non_coding_transcript_exon_variant,,ENST00000554644,;BTBD7,upstream_gene_variant,,ENST00000355125,; A ENST00000334746 Transcript synonymous_variant 1361/8430 1053/3399 351/1132 L ctC/ctT 1 -1 BTBD7 HGNC HGNC:18269 protein_coding YES CCDS32146.1 ENSP00000335615 Q9P203 UPI00001FDA78 NM_001002860.3 3/11 Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR16064,SMART_domains:SM00225 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 93293967 93293967 G A 1 0 0 0 0 0 0 0 1 1722 1277 45 3 3 BTBD7 14 93293967 Silent SNP G C3L-00080_T 1564515 93293967 13749751 539 2637 FAM181A 0 . GRCh38 14 93928801 93928801 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.702G>T p.Lys234Asn p.K234N ENST00000267594 3/3 523 387 136 291 291 0 strelka-varscan-mutect FAM181A,missense_variant,p.Lys234Asn,ENST00000267594,NM_138344.4;FAM181A,missense_variant,p.Lys172Asn,ENST00000557000,NM_001207072.1;FAM181A,missense_variant,p.Lys172Asn,ENST00000556222,NM_001207074.1,NM_001207073.1;FAM181A,missense_variant,p.Lys172Asn,ENST00000557719,NM_001207071.1;FAM181A,missense_variant,p.Lys172Asn,ENST00000554404,;FAM181A-AS1,upstream_gene_variant,,ENST00000554742,;FAM181A-AS1,upstream_gene_variant,,ENST00000554538,;FAM181A-AS1,upstream_gene_variant,,ENST00000556290,;FAM181A-AS1,upstream_gene_variant,,ENST00000555732,; T ENST00000267594 Transcript missense_variant 1009/1816 702/1065 234/354 K/N aaG/aaT 1 1 FAM181A HGNC HGNC:20491 protein_coding YES CCDS9914.1 ENSP00000267594 Q8N9Y4 UPI00004567C0 NM_138344.4 deleterious(0.01) 3/3 Pfam_domain:PF15238,hmmpanther:PTHR33766,hmmpanther:PTHR33766:SF1 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 93928801 93928801 G T 1 0 0 0 0 1 0 0 0 5354 991 35 2 2 FAM181A 14 93928801 Missense_Mutation SNP G C3L-00080_T 634834 93928801 13114917 540 2638 SERPINA11 0 . GRCh38 14 94443107 94443107 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1036A>T p.Thr346Ser p.T346S ENST00000334708 4/5 114 60 54 56 56 0 strelka-varscan-mutect SERPINA11,missense_variant,p.Thr346Ser,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; A ENST00000334708 Transcript missense_variant 1101/1476 1036/1269 346/422 T/S Act/Tct 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 tolerated(0.2) 4/5 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 94443107 94443107 T A 1 0 0 0 0 1 0 0 0 14364 1696 59 4 4 SERPINA11 14 94443107 Missense_Mutation SNP T C3L-00080_T 514306 94443107 12600611 541 2639 BDKRB1 0 . GRCh38 14 96264401 96264418 + In_Frame_Del DEL GCGGGGGCCGCAAGGATA GCGGGGGCCGCAAGGATA - novel C3L-00080_T C3L-00080_N GCGGGGGCCGCAAGGATA GCGGGGGCCGCAAGGATA c.721_738delGGGGGCCGCAAGGATAGC p.Gly241_Ser246del p.G241_S246del ENST00000216629 3/3 315 271 44 179 179 0 sindel-varindel-pindel BDKRB1,inframe_deletion,p.Gly241_Ser246del,ENST00000216629,NM_000710.3;BDKRB1,inframe_deletion,p.Gly241_Ser246del,ENST00000611804,;BDKRB1,splice_region_variant,,ENST00000553356,;RP11-404P21.8,downstream_gene_variant,,ENST00000553811,;RP11-404P21.3,intron_variant,,ENST00000553638,;BDKRB1,upstream_gene_variant,,ENST00000557122,;RP11-404P21.8,downstream_gene_variant,,ENST00000555847,; - ENST00000216629 Transcript inframe_deletion 1325-1342/1687 719-736/1062 240-246/353 CGGRKDS/C tGCGGGGGCCGCAAGGATAgc/tgc 1 1 BDKRB1 HGNC HGNC:1029 protein_coding YES CCDS9943.1 ENSP00000216629 P46663 UPI0000000348 NM_000710.3 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF28,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00993 MODERATE 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 96264401 96264401 GCGGGGGCCGCAAGGATA - 1 0 1 0 1 0 0 0 0 1539 1333 46 0 0 BDKRB1 14 96264401 In_Frame_Del DEL GCGGGGGCCGCAAGGATA C3L-00080_T 1821294 96264401 10779317 542 2640 EML1 0 . GRCh38 14 99917788 99917788 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1816G>T p.Ala606Ser p.A606S ENST00000334192 17/23 253 194 59 147 146 1 strelka-varscan-mutect EML1,missense_variant,p.Ala587Ser,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Ala606Ser,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Ala575Ser,ENST00000327921,;EML1,intron_variant,,ENST00000557313,;EML1,downstream_gene_variant,,ENST00000554111,; T ENST00000334192 Transcript missense_variant 1950/4064 1816/2505 606/834 A/S Gct/Tct 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 tolerated(0.08) 17/23 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 99917788 99917788 G T 1 0 0 0 0 1 0 0 0 4939 971 34 2 2 EML1 14 99917788 Missense_Mutation SNP G C3L-00080_T 3653387 99917788 7125930 543 2641 RTL1 0 . GRCh38 14 100884024 100884024 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.765T>C p.= p.A255A ENST00000534062 1/1 307 223 84 172 172 0 strelka-varscan-mutect RTL1,synonymous_variant,p.=,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,downstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; G ENST00000534062 Transcript synonymous_variant 824/4193 765/4077 255/1358 A gcT/gcC 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 1/1 Pfam_domain:PF16297,hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF9 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 100884024 100884024 A G 1 0 0 0 0 0 0 0 1 13984 291 11 5 5 RTL1 14 100884024 Silent SNP A C3L-00080_T 966236 100884024 6159694 544 2642 PPP2R5C 0 . GRCh38 14 101856885 101856885 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.387G>A p.Met129Ile p.M129I ENST00000422945 4/16 141 124 17 103 103 0 strelka-varscan-mutect PPP2R5C,missense_variant,p.Met129Ile,ENST00000422945,NM_001161725.1;PPP2R5C,missense_variant,p.Met98Ile,ENST00000334743,NM_002719.3;PPP2R5C,missense_variant,p.Met153Ile,ENST00000328724,NM_001161726.1;PPP2R5C,missense_variant,p.Met98Ile,ENST00000350249,NM_178586.2;PPP2R5C,missense_variant,p.Met127Ile,ENST00000557268,;PPP2R5C,missense_variant,p.Met98Ile,ENST00000445439,NM_178587.2;PPP2R5C,missense_variant,p.Met98Ile,ENST00000557095,;PPP2R5C,missense_variant,p.Met98Ile,ENST00000557621,;PPP2R5C,non_coding_transcript_exon_variant,,ENST00000556373,;PPP2R5C,downstream_gene_variant,,ENST00000556493,;PPP2R5C,splice_region_variant,,ENST00000553730,;PPP2R5C,splice_region_variant,,ENST00000556307,; A ENST00000422945 Transcript missense_variant,splice_region_variant 483/4481 387/1668 129/555 M/I atG/atA 1 1 PPP2R5C HGNC HGNC:9311 protein_coding YES CCDS53912.1 ENSP00000412324 Q13362 UPI0001A7AE62 NM_001161725.1 deleterious(0) 4/16 hmmpanther:PTHR10257,hmmpanther:PTHR10257:SF22,PIRSF_domain:PIRSF028043,Pfam_domain:PF01603,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 101856885 101856885 G A 1 0 0 0 0 1 0 0 0 12516 1362 47 3 3 PPP2R5C 14 101856885 Missense_Mutation SNP G C3L-00080_T 972861 101856885 5186833 545 2643 AHNAK2 0 . GRCh38 14 104942262 104942262 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.13189A>C p.Lys4397Gln p.K4397Q ENST00000333244 7/7 719 641 78 332 332 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Lys4397Gln,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;PLD4,downstream_gene_variant,,ENST00000392593,NM_138790.2;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; G ENST00000333244 Transcript missense_variant 13309/18254 13189/17388 4397/5795 K/Q Aag/Cag 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0.01) 7/7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 104942262 104942262 T G 1 0 0 0 0 1 0 0 0 492 1821 63 5 5 AHNAK2 14 104942262 Missense_Mutation SNP T C3L-00080_T 3085377 104942262 2101456 546 2644 GOLGA6L22 0 . GRCh38 15 22466105 22466105 + Silent SNP G G C rs770558395 C3L-00080_T C3L-00080_N G G c.1713G>C p.= p.R571R ENST00000622895 8/9 183 131 52 169 169 0 strelka-varscan-mutect GOLGA6L22,synonymous_variant,p.=,ENST00000622895,;GOLGA6L22,synonymous_variant,p.=,ENST00000620691,; C ENST00000622895 Transcript synonymous_variant 1713/4178 1713/2433 571/810 R cgG/cgC rs770558395 1 1 GOLGA6L22 HGNC HGNC:50289 protein_coding YES ENSP00000483673 A0A087X0V3 UPI0004620C46 8/9 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs770558395 . 0 193 0 8 9 0 0 0 -20 0.2080057 1 1 0 0 C 2 2 7 22466105 22466105 G C 1 0 0 0 0 0 0 0 1 6441 1219 43 4 4 GOLGA6L22 15 22466105 Silent SNP G C3L-00080_T 22466105 79525084 547 2645 MAGEL2 0 . GRCh38 15 23646486 23646486 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1257C>A p.= p.G419G ENST00000532292 1/1 20 14 6 19 19 0 strelka-varscan-mutect MAGEL2,synonymous_variant,p.=,ENST00000532292,NM_019066.4; T ENST00000532292 Transcript synonymous_variant 1356/4298 1257/3750 419/1249 G ggC/ggA 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 1/1 Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 1 206 3 0 0 0 0 0 -17.78228 1 1 1 1 0 T 2 4 7 23646486 23646486 G T 1 0 0 0 0 0 0 0 1 9107 1190 42 2 2 MAGEL2 15 23646486 Silent SNP G C3L-00080_T 1180381 23646486 78344703 548 2646 AC124312.1 0 . GRCh38 15 25092172 25092172 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.206A>C p.Asn69Thr p.N69T ENST00000623624 1/1 222 198 24 222 222 0 strelka-varscan-mutect AC124312.1,missense_variant,p.Asn69Thr,ENST00000623624,;RP11-701H24.4,downstream_gene_variant,,ENST00000567527,;SNORD116-22,downstream_gene_variant,,ENST00000384430,;SNORD116-21,downstream_gene_variant,,ENST00000384507,;SNORD116-20,downstream_gene_variant,,ENST00000384529,;SNORD116-24,upstream_gene_variant,,ENST00000384549,;SNORD116-23,downstream_gene_variant,,ENST00000384645,;SNHG14,intron_variant,,ENST00000546682,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,intron_variant,,ENST00000553108,; G ENST00000623624 Transcript missense_variant 206/418 206/417 69/138 N/T aAc/aCc 1 -1 AC124312.1 Clone_based_ensembl_gene protein_coding YES ENSP00000485422 A0A0B4J2H5 UPI000006F2CD 1/1 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 25092172 25092172 T G 1 0 0 0 0 1 0 0 0 141 1725 60 5 5 AC124312.1 15 25092172 Missense_Mutation SNP T C3L-00080_T 1445686 25092172 76899017 549 2647 GABRB3 0 . GRCh38 15 26580415 26580415 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.586G>T p.Gly196Trp p.G196W ENST00000311550 6/9 648 550 98 619 617 2 strelka-varscan-mutect GABRB3,missense_variant,p.Gly252Trp,ENST00000541819,;GABRB3,missense_variant,p.Gly111Trp,ENST00000622697,NM_001278631.1;GABRB3,missense_variant,p.Gly196Trp,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Gly111Trp,ENST00000628124,NM_001191320.1;GABRB3,missense_variant,p.Gly111Trp,ENST00000636466,;GABRB3,missense_variant,p.Gly196Trp,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Gly163Trp,ENST00000638099,;GABRB3,missense_variant,p.Gly125Trp,ENST00000400188,NM_001191321.2;GABRB3,missense_variant,p.Gly111Trp,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,downstream_gene_variant,,ENST00000636512,;GABRB3,missense_variant,p.Gly91Trp,ENST00000635994,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;GABRB3,3_prime_UTR_variant,,ENST00000554556,;GABRB3,non_coding_transcript_exon_variant,,ENST00000557765,; A ENST00000311550 Transcript missense_variant 698/5781 586/1422 196/473 G/W Ggg/Tgg COSM5362998,COSM5362999,COSM5363000 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 deleterious(0) 6/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 26580415 26580415 C A 1 0 0 0 0 1 0 0 0 6039 652 23 1 1 GABRB3 15 26580415 Missense_Mutation SNP C C3L-00080_T 1488243 26580415 75410774 550 2648 OCA2 0 . GRCh38 15 28014813 28014813 + Missense_Mutation SNP G G C rs34010619 C3L-00080_T C3L-00080_N G G c.1007C>G p.Ala336Gly p.A336G ENST00000354638 9/24 258 160 98 288 288 0 strelka-varscan-mutect OCA2,missense_variant,p.Ala336Gly,ENST00000354638,NM_000275.2;OCA2,missense_variant,p.Ala336Gly,ENST00000353809,NM_001300984.1;OCA2,downstream_gene_variant,,ENST00000431101,;OCA2,downstream_gene_variant,,ENST00000445578,; C ENST00000354638 Transcript missense_variant 1163/3186 1007/2517 336/838 A/G gCc/gGc rs34010619 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 deleterious(0) 9/24 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283 MODERATE 1 SNV 1 1 PASS rs34010619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 28014813 28014813 G C 1 0 0 0 0 1 0 0 0 10892 1203 42 4 4 OCA2 15 28014813 Missense_Mutation SNP G C3L-00080_T 1434398 28014813 73976376 551 2649 GOLGA8M 0 . GRCh38 15 28705648 28705648 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.966C>A p.= p.L322L ENST00000563027 12/19 438 322 116 531 531 0 strelka-varscan-mutect GOLGA8M,synonymous_variant,p.=,ENST00000563027,NM_001282468.1;RN7SL719P,upstream_gene_variant,,ENST00000620196,;GOLGA8M,downstream_gene_variant,,ENST00000563213,; T ENST00000563027 Transcript synonymous_variant 966/1899 966/1899 322/632 L ctC/ctA 1 -1 GOLGA8M HGNC HGNC:44404 protein_coding YES CCDS61572.1 ENSP00000456927 H3BSY2 UPI0001A5E7A0 NM_001282468.1 12/19 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 28705648 28705648 G T 1 0 0 0 0 0 0 0 1 6454 1161 41 2 2 GOLGA8M 15 28705648 Silent SNP G C3L-00080_T 690835 28705648 73285541 552 2650 GOLGA8T 0 . GRCh38 15 30144863 30144863 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1453G>A p.Asp485Asn p.D485N ENST00000569052 16/19 198 159 39 181 181 0 strelka-varscan-mutect GOLGA8T,missense_variant,p.Asp485Asn,ENST00000569052,;RN7SL469P,downstream_gene_variant,,ENST00000621501,; A ENST00000569052 Transcript missense_variant 1453/1896 1453/1896 485/631 D/N Gac/Aac 1 1 GOLGA8T HGNC HGNC:44410 protein_coding YES ENSP00000455826 H3BQL2 UPI000246730F tolerated(0.15) 16/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 MODERATE 1 SNV 5 1 PASS rs1168516275 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 30144863 30144863 G A 1 0 0 0 0 1 0 0 0 6458 942 33 3 3 GOLGA8T 15 30144863 Missense_Mutation SNP G C3L-00080_T 1439215 30144863 71846326 553 2651 GOLGA8H 0 . GRCh38 15 30613134 30613134 + Missense_Mutation SNP G G T rs752641133 C3L-00080_T C3L-00080_N G G c.1307G>T p.Gly436Val p.G436V ENST00000566740 15/19 178 162 16 186 186 0 varscan-mutect GOLGA8H,missense_variant,p.Gly436Val,ENST00000566740,NM_001282490.1;RP11-932O9.9,upstream_gene_variant,,ENST00000602594,;RP11-932O9.7,downstream_gene_variant,,ENST00000501830,;RP11-932O9.8,upstream_gene_variant,,ENST00000602595,;RN7SL628P,downstream_gene_variant,,ENST00000619139,; T ENST00000566740 Transcript missense_variant 1307/1899 1307/1899 436/632 G/V gGg/gTg rs752641133,COSM5292880 1 1 GOLGA8H HGNC HGNC:37443 protein_coding YES CCDS61576.1 ENSP00000456894 P0CJ92 UPI0001A5E7A5 NM_001282490.1 deleterious(0.03) 15/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 0,1 MODERATE SNV 5 0,1 1 PASS rs752641133 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 30613134 30613134 G T 1 0 0 0 0 1 0 0 0 6451 1232 43 2 2 GOLGA8H 15 30613134 Missense_Mutation SNP G C3L-00080_T 468271 30613134 71378055 554 2652 ARHGAP11A 0 . GRCh38 15 32624349 32624349 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.474G>C p.Leu158Phe p.L158F ENST00000361627 4/12 441 329 112 561 561 0 strelka-varscan-mutect ARHGAP11A,missense_variant,p.Leu158Phe,ENST00000361627,NM_014783.4;ARHGAP11A,missense_variant,p.Leu158Phe,ENST00000567348,NM_199357.1;ARHGAP11A,missense_variant,p.Leu158Phe,ENST00000563864,;ARHGAP11A,5_prime_UTR_variant,,ENST00000565905,NM_001286479.1;ARHGAP11A,5_prime_UTR_variant,,ENST00000543522,NM_001286480.1;ARHGAP11A,upstream_gene_variant,,ENST00000562481,; C ENST00000361627 Transcript missense_variant 1196/5898 474/3072 158/1023 L/F ttG/ttC 1 1 ARHGAP11A HGNC HGNC:15783 protein_coding YES CCDS10028.1 ENSP00000355090 Q6P4F7 UPI0000071553 NM_014783.4 deleterious(0.03) 4/12 PROSITE_profiles:PS50238,hmmpanther:PTHR15670:SF5,hmmpanther:PTHR15670,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 32624349 32624349 G C 1 0 0 0 0 1 0 0 0 987 1310 46 4 4 ARHGAP11A 15 32624349 Missense_Mutation SNP G C3L-00080_T 2011215 32624349 69366840 555 2653 RYR3 0 . GRCh38 15 33662359 33662359 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.4829T>A p.Leu1610His p.L1610H ENST00000634891 35/104 101 82 19 94 94 0 strelka-varscan-mutect RYR3,missense_variant,p.Leu1610His,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Leu1610His,ENST00000622037,;RYR3,missense_variant,p.Leu1610His,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Leu1610His,ENST00000389232,;RYR3,missense_variant,p.Leu1610His,ENST00000634418,; A ENST00000634891 Transcript missense_variant 4930/15591 4829/14613 1610/4870 L/H cTc/cAc 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 35/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 33662359 33662359 T A 1 0 0 0 0 1 0 0 0 14030 1551 54 4 4 RYR3 15 33662359 Missense_Mutation SNP T C3L-00080_T 1038010 33662359 68328830 556 2654 RYR3 0 . GRCh38 15 33845027 33845027 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.13462T>G p.Ser4488Ala p.S4488A ENST00000634891 93/104 270 222 48 311 311 0 strelka-varscan-mutect RYR3,missense_variant,p.Ser4488Ala,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Ser4491Ala,ENST00000622037,;RYR3,missense_variant,p.Ser4483Ala,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Ser4487Ala,ENST00000389232,;RYR3,missense_variant,p.Ser4477Ala,ENST00000634418,;RYR3,missense_variant,p.Ser233Ala,ENST00000634730,;RYR3,missense_variant,p.Ser86Ala,ENST00000636568,;RYR3,non_coding_transcript_exon_variant,,ENST00000635749,;RYR3,non_coding_transcript_exon_variant,,ENST00000638052,;RYR3,non_coding_transcript_exon_variant,,ENST00000637522,;RYR3,upstream_gene_variant,,ENST00000559917,;RYR3,upstream_gene_variant,,ENST00000559333,;RYR3,downstream_gene_variant,,ENST00000636656,;RYR3,downstream_gene_variant,,ENST00000637615,;RYR3,missense_variant,p.Ser269Ala,ENST00000636845,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,3_prime_UTR_variant,,ENST00000637948,; G ENST00000634891 Transcript missense_variant 13563/15591 13462/14613 4488/4870 S/A Tct/Gct 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.24) 93/104 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 33845027 33845027 T G 1 0 0 0 0 1 0 0 0 14030 1551 54 5 5 RYR3 15 33845027 Missense_Mutation SNP T C3L-00080_T 182668 33845027 68146162 557 2655 GJD2 0 . GRCh38 15 34753199 34753199 + Missense_Mutation SNP T T C novel C3L-00080_T C3L-00080_N T T c.245A>G p.Gln82Arg p.Q82R ENST00000290374 2/2 339 275 64 335 334 1 strelka-varscan-mutect GJD2,missense_variant,p.Gln82Arg,ENST00000290374,NM_020660.2;RP11-814P5.1,upstream_gene_variant,,ENST00000503496,;RP11-814P5.1,upstream_gene_variant,,ENST00000558707,; C ENST00000290374 Transcript missense_variant 722/2889 245/966 82/321 Q/R cAg/cGg 1 -1 GJD2 HGNC HGNC:19154 protein_coding YES CCDS10040.1 ENSP00000290374 Q9UKL4 UPI00001287E3 NM_020660.2 deleterious(0) 2/2 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF47,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 34753199 34753199 T C 1 0 0 0 0 1 0 0 0 6294 1580 55 5 5 GJD2 15 34753199 Missense_Mutation SNP T C3L-00080_T 908172 34753199 67237990 558 2656 EIF2AK4 0 . GRCh38 15 40017122 40017122 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.3945G>C p.Leu1315Phe p.L1315F ENST00000263791 29/39 133 99 34 157 157 0 strelka-varscan-mutect EIF2AK4,missense_variant,p.Leu1315Phe,ENST00000263791,NM_001013703.3;EIF2AK4,missense_variant,p.Leu1093Phe,ENST00000560855,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000558629,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000558557,;EIF2AK4,upstream_gene_variant,,ENST00000559032,;EIF2AK4,upstream_gene_variant,,ENST00000558743,; C ENST00000263791 Transcript missense_variant 3988/5499 3945/4950 1315/1649 L/F ttG/ttC 1 1 EIF2AK4 HGNC HGNC:19687 protein_coding YES CCDS42016.1 ENSP00000263791 Q9P2K8 UPI0000160791 NM_001013703.3 tolerated(0.16) 29/39 Gene3D:3.30.930.10,Pfam_domain:PF13393,Superfamily_domains:SSF55681 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 40017122 40017122 G C 1 0 0 0 0 1 0 0 0 4835 1339 47 4 4 EIF2AK4 15 40017122 Missense_Mutation SNP G C3L-00080_T 5263923 40017122 61974067 559 2657 MAPKBP1 0 . GRCh38 15 41812931 41812931 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.649G>T p.Val217Leu p.V217L ENST00000456763 8/32 64 54 10 45 45 0 strelka-varscan-mutect MAPKBP1,missense_variant,p.Val217Leu,ENST00000457542,NM_014994.2;MAPKBP1,missense_variant,p.Val217Leu,ENST00000456763,NM_001128608.1;MAPKBP1,missense_variant,p.Val217Leu,ENST00000514566,NM_001265611.1;MAPKBP1,downstream_gene_variant,,ENST00000510535,;MAPKBP1,downstream_gene_variant,,ENST00000627631,;MAPKBP1,downstream_gene_variant,,ENST00000507762,;MAPKBP1,missense_variant,p.Val217Leu,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000502292,;MAPKBP1,downstream_gene_variant,,ENST00000515164,;MAPKBP1,upstream_gene_variant,,ENST00000503526,;MAPKBP1,downstream_gene_variant,,ENST00000507147,; T ENST00000456763 Transcript missense_variant 845/7158 649/4545 217/1514 V/L Gtg/Ttg 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 deleterious(0) 8/32 hmmpanther:PTHR22847:SF432,hmmpanther:PTHR22847 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.99965 1 1 1 1 0 T 3 4 7 41812931 41812931 G T 1 0 0 0 0 1 0 0 0 9216 1377 48 2 2 MAPKBP1 15 41812931 Missense_Mutation SNP G C3L-00080_T 1795809 41812931 60178258 560 2658 FBN1 0 . GRCh38 15 48432953 48432953 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6652G>T p.Ala2218Ser p.A2218S ENST00000316623 55/66 441 276 165 389 389 0 strelka-varscan-mutect FBN1,missense_variant,p.Ala2218Ser,ENST00000316623,NM_000138.4;FBN1,missense_variant,p.Ala654Ser,ENST00000559133,;FBN1,3_prime_UTR_variant,,ENST00000537463,;FBN1,upstream_gene_variant,,ENST00000560720,;FBN1,downstream_gene_variant,,ENST00000560820,; A ENST00000316623 Transcript missense_variant 7108/11756 6652/8616 2218/2871 A/S Gcc/Tcc 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 deleterious(0.01) 55/66 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs1347008355 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 48432953 48432953 C A 1 0 0 0 0 1 0 0 0 5565 710 25 2 2 FBN1 15 48432953 Missense_Mutation SNP C C3L-00080_T 6620022 48432953 53558236 561 2659 MYO5C 0 . GRCh38 15 52242112 52242112 + Missense_Mutation SNP C C A rs764763786 C3L-00080_T C3L-00080_N C C c.2492G>T p.Arg831Leu p.R831L ENST00000261839 20/41 146 130 16 146 146 0 strelka-varscan-mutect MYO5C,missense_variant,p.Arg831Leu,ENST00000261839,NM_018728.3;MYO5C,non_coding_transcript_exon_variant,,ENST00000559434,;MYO5C,intron_variant,,ENST00000560809,;MYO5C,intron_variant,,ENST00000558902,; A ENST00000261839 Transcript missense_variant 2654/6971 2492/5229 831/1742 R/L cGc/cTc rs764763786 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 tolerated(0.11) 20/41 PROSITE_profiles:PS50096,PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF313,Pfam_domain:PF00612,Gene3D:1wdcA00,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs764763786 . 0 205 0 5 0 0 0 0 -19.99931 0.999176 1 1 1 0 A 3 1 7 52242112 52242112 C A 1 0 0 0 0 1 0 0 0 10081 768 27 1 1 MYO5C 15 52242112 Missense_Mutation SNP C C3L-00080_T 3809159 52242112 49749077 562 2660 SLTM 0 . GRCh38 15 58889430 58889430 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2204G>T p.Arg735Met p.R735M ENST00000380516 16/21 180 133 47 176 176 0 strelka-varscan-mutect SLTM,missense_variant,p.Arg735Met,ENST00000380516,NM_024755.2,NM_001013843.1;SLTM,missense_variant,p.Arg301Met,ENST00000432750,;SLTM,missense_variant,p.Ser21Ile,ENST00000557791,;RNF111,intron_variant,,ENST00000559757,;SLTM,downstream_gene_variant,,ENST00000249736,;SLTM,upstream_gene_variant,,ENST00000560494,;AC025918.2,upstream_gene_variant,,ENST00000452467,;SLTM,splice_region_variant,,ENST00000492526,;SLTM,splice_region_variant,,ENST00000557924,;SLTM,non_coding_transcript_exon_variant,,ENST00000558734,;SLTM,upstream_gene_variant,,ENST00000493062,;SLTM,downstream_gene_variant,,ENST00000558756,;SLTM,upstream_gene_variant,,ENST00000558052,;SLTM,downstream_gene_variant,,ENST00000497088,;SLTM,downstream_gene_variant,,ENST00000473359,;SLTM,upstream_gene_variant,,ENST00000560695,; A ENST00000380516 Transcript missense_variant,splice_region_variant 2292/4147 2204/3105 735/1034 R/M aGg/aTg 1 -1 SLTM HGNC HGNC:20709 protein_coding YES CCDS10168.2 ENSP00000369887 Q9NWH9 UPI0000039EA4 NM_024755.2,NM_001013843.1 deleterious(0) 16/21 Low_complexity_(Seg):seg,hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 58889430 58889430 C A 1 0 0 0 0 1 0 0 0 15043 695 24 2 2 SLTM 15 58889430 Missense_Mutation SNP C C3L-00080_T 6647318 58889430 43101759 563 2661 SLTM 0 . GRCh38 15 58889453 58889453 + Missense_Mutation SNP T T G C3L-00080_T C3L-00080_N T T c.2181A>C p.Lys727Asn p.K727N ENST00000380516 16/21 249 190 59 257 257 0 strelka-varscan-mutect SLTM,missense_variant,p.Lys727Asn,ENST00000380516,NM_024755.2,NM_001013843.1;SLTM,missense_variant,p.Lys293Asn,ENST00000432750,;SLTM,missense_variant,p.Lys13Asn,ENST00000557791,;RNF111,intron_variant,,ENST00000559757,;SLTM,downstream_gene_variant,,ENST00000249736,;SLTM,upstream_gene_variant,,ENST00000560494,;AC025918.2,upstream_gene_variant,,ENST00000452467,;SLTM,3_prime_UTR_variant,,ENST00000492526,;SLTM,3_prime_UTR_variant,,ENST00000557924,;SLTM,non_coding_transcript_exon_variant,,ENST00000558734,;SLTM,upstream_gene_variant,,ENST00000493062,;SLTM,downstream_gene_variant,,ENST00000558756,;SLTM,upstream_gene_variant,,ENST00000558052,;SLTM,downstream_gene_variant,,ENST00000497088,;SLTM,downstream_gene_variant,,ENST00000473359,;SLTM,upstream_gene_variant,,ENST00000560695,; G ENST00000380516 Transcript missense_variant 2269/4147 2181/3105 727/1034 K/N aaA/aaC COSM339626 1 -1 SLTM HGNC HGNC:20709 protein_coding YES CCDS10168.2 ENSP00000369887 Q9NWH9 UPI0000039EA4 NM_024755.2,NM_001013843.1 deleterious(0) 16/21 hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 58889453 58889453 T G 1 0 0 0 0 1 0 0 0 15043 1722 60 5 5 SLTM 15 58889453 Missense_Mutation SNP T C3L-00080_T 23 58889453 43101736 564 2662 HERC1 0 . GRCh38 15 63732984 63732984 + Silent SNP T T A rs755656959 C3L-00080_T C3L-00080_N T T c.2808A>T p.= p.P936P ENST00000443617 14/78 399 319 80 381 381 0 strelka-varscan-mutect HERC1,synonymous_variant,p.=,ENST00000443617,NM_003922.3;HERC1,intron_variant,,ENST00000561400,;HERC1,downstream_gene_variant,,ENST00000560519,; A ENST00000443617 Transcript synonymous_variant 2896/15137 2808/14586 936/4861 P ccA/ccT rs755656959 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 14/78 LOW 1 SNV 1 1 PASS rs755656959 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 63732984 63732984 T A 1 0 0 0 0 0 0 0 1 6941 1567 55 4 4 HERC1 15 63732984 Silent SNP T C3L-00080_T 4843531 63732984 38258205 565 2663 PDCD7 0 . GRCh38 15 65129090 65129090 + Silent SNP G G A C3L-00080_T C3L-00080_N G G c.951C>T p.= p.D317D ENST00000204549 2/5 230 197 33 214 214 0 strelka-varscan-mutect PDCD7,synonymous_variant,p.=,ENST00000204549,NM_005707.1;PDCD7,synonymous_variant,p.=,ENST00000560313,; A ENST00000204549 Transcript synonymous_variant 1006/2851 951/1458 317/485 D gaC/gaT COSM964002 1 -1 PDCD7 HGNC HGNC:8767 protein_coding YES CCDS10201.1 ENSP00000204549 Q8N8D1 Q6IEG3 UPI00000731D7 NM_005707.1 2/5 Pfam_domain:PF16021 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 65129090 65129090 G A 1 0 0 0 0 0 0 0 1 11713 1368 48 3 3 PDCD7 15 65129090 Silent SNP G C3L-00080_T 1396106 65129090 36862099 566 2664 IGDCC4 0 . GRCh38 15 65388470 65388470 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.2824A>T p.Thr942Ser p.T942S ENST00000352385 16/20 244 200 44 214 214 0 strelka-varscan-mutect IGDCC4,missense_variant,p.Thr942Ser,ENST00000352385,NM_020962.2;IGDCC4,upstream_gene_variant,,ENST00000558048,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,;IGDCC4,upstream_gene_variant,,ENST00000560319,;IGDCC4,upstream_gene_variant,,ENST00000561309,; A ENST00000352385 Transcript missense_variant 3034/6508 2824/3753 942/1250 T/S Acg/Tcg 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 deleterious(0.03) 16/20 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 65388470 65388470 T A 1 0 0 0 0 1 0 0 0 7475 1696 59 4 4 IGDCC4 15 65388470 Missense_Mutation SNP T C3L-00080_T 259380 65388470 36602719 567 2665 ZWILCH 0 . GRCh38 15 66519011 66519011 + Silent SNP A A G novel C3L-00080_T C3L-00080_N A A c.453A>G p.= p.L151L ENST00000307897 5/19 226 150 76 242 242 0 strelka-varscan-mutect ZWILCH,synonymous_variant,p.=,ENST00000307897,NM_017975.4;ZWILCH,synonymous_variant,p.=,ENST00000446801,NM_001287823.1,NM_001287821.1;ZWILCH,synonymous_variant,p.=,ENST00000613446,NM_001287822.1;ZWILCH,synonymous_variant,p.=,ENST00000535141,;ZWILCH,synonymous_variant,p.=,ENST00000565627,;ZWILCH,synonymous_variant,p.=,ENST00000564179,;RPL4,intron_variant,,ENST00000568588,;ZWILCH,intron_variant,,ENST00000565960,;RPL4,intron_variant,,ENST00000564517,;ZWILCH,downstream_gene_variant,,ENST00000564309,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000567926,;ZWILCH,non_coding_transcript_exon_variant,,ENST00000563698,;ZWILCH,upstream_gene_variant,,ENST00000561583,;ZWILCH,upstream_gene_variant,,ENST00000562645,; G ENST00000307897 Transcript synonymous_variant 833/3960 453/1776 151/591 L ctA/ctG 1 1 ZWILCH HGNC HGNC:25468 protein_coding YES CCDS10219.1 ENSP00000311429 Q9H900 UPI000013EC73 NM_017975.4 5/19 Pfam_domain:PF09817,hmmpanther:PTHR15995 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 66519011 66519011 A G 1 0 0 0 0 0 0 0 1 18851 407 15 5 5 ZWILCH 15 66519011 Silent SNP A C3L-00080_T 1130541 66519011 35472178 568 2666 SCAPER 0 . GRCh38 15 76764991 76764991 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1695A>T p.Lys565Asn p.K565N ENST00000563290 14/32 77 62 15 105 105 0 strelka-mutect SCAPER,missense_variant,p.Lys565Asn,ENST00000563290,;SCAPER,missense_variant,p.Lys319Asn,ENST00000538941,NM_001145923.1;SCAPER,missense_variant,p.Lys565Asn,ENST00000324767,NM_020843.2;SCAPER,missense_variant,p.Lys571Asn,ENST00000564590,;SCAPER,missense_variant,p.Lys571Asn,ENST00000565970,;SCAPER,downstream_gene_variant,,ENST00000564022,;SCAPER,3_prime_UTR_variant,,ENST00000565507,;SCAPER,non_coding_transcript_exon_variant,,ENST00000303521,; A ENST00000563290 Transcript missense_variant 1791/5028 1695/4203 565/1400 K/N aaA/aaT 1 -1 SCAPER HGNC HGNC:13081 protein_coding YES CCDS53962.1 ENSP00000454973 Q9BY12 UPI0000E59CC3 deleterious(0) 14/32 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31434:SF2,hmmpanther:PTHR31434 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 76764991 76764991 T A 1 0 0 0 0 1 0 0 0 14144 1838 64 4 4 SCAPER 15 76764991 Missense_Mutation SNP T C3L-00080_T 10245980 76764991 25226198 569 2667 TMC3 0 . GRCh38 15 81333177 81333177 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.2545G>A p.Asp849Asn p.D849N ENST00000359440 22/22 201 172 29 158 158 0 strelka-mutect TMC3,missense_variant,p.Asp850Asn,ENST00000558726,;TMC3,missense_variant,p.Asp849Asn,ENST00000359440,NM_001080532.1;TMC3-AS1,intron_variant,,ENST00000559781,;TMC3-AS1,intron_variant,,ENST00000560851,;TMC3-AS1,intron_variant,,ENST00000560973,;RP11-761I4.5,upstream_gene_variant,,ENST00000621471,;TMC3,downstream_gene_variant,,ENST00000559982,; T ENST00000359440 Transcript missense_variant 2681/4641 2545/3303 849/1100 D/N Gat/Aat 1 -1 TMC3 HGNC HGNC:22995 protein_coding YES CCDS45324.1 ENSP00000352413 Q7Z5M5 UPI00006C154A NM_001080532.1 tolerated_low_confidence(0.19) 22/22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 81333177 81333177 C T 1 0 0 0 0 1 0 0 0 16432 913 32 3 3 TMC3 15 81333177 Missense_Mutation SNP C C3L-00080_T 4568186 81333177 20658012 570 2668 ANPEP 0 . GRCh38 15 89803502 89803502 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.1443C>T p.= p.A481A ENST00000300060 9/21 189 168 21 156 155 1 strelka-varscan-mutect ANPEP,synonymous_variant,p.=,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,missense_variant,p.Pro89Leu,ENST00000560030,;ANPEP,downstream_gene_variant,,ENST00000560028,;ANPEP,downstream_gene_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000559761,; A ENST00000300060 Transcript synonymous_variant 1757/3678 1443/2904 481/967 A gcC/gcT 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 9/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 89803502 89803502 G A 1 0 0 0 0 0 0 0 1 817 1014 35 3 3 ANPEP 15 89803502 Silent SNP G C3L-00080_T 8470325 89803502 12187687 571 2669 ADAMTS17 0 . GRCh38 15 99997464 99997464 + Missense_Mutation SNP G G T rs778303777 C3L-00080_T C3L-00080_N G G c.2717C>A p.Pro906Gln p.P906Q ENST00000268070 19/22 316 243 73 271 271 0 strelka-varscan-mutect ADAMTS17,missense_variant,p.Pro906Gln,ENST00000268070,NM_139057.2; T ENST00000268070 Transcript missense_variant 2823/6207 2717/3288 906/1095 P/Q cCg/cAg rs778303777 1 -1 ADAMTS17 HGNC HGNC:17109 protein_coding YES CCDS10383.1 ENSP00000268070 Q8TE56 UPI00001AE929 NM_139057.2 tolerated(0.66) 19/22 PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF151,hmmpanther:PTHR13723,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS rs778303777 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 99997464 99997464 G T 1 0 0 0 0 1 0 0 0 306 1116 39 1 1 ADAMTS17 15 99997464 Missense_Mutation SNP G C3L-00080_T 10193962 99997464 1993725 572 2670 ASB7 0 . GRCh38 15 100629608 100629608 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.383G>A p.Gly128Asp p.G128D ENST00000332783 5/6 299 175 124 300 300 0 strelka-varscan-mutect ASB7,missense_variant,p.Gly128Asp,ENST00000332783,NM_198243.2;ASB7,missense_variant,p.Gly128Asp,ENST00000343276,NM_024708.3;ASB7,intron_variant,,ENST00000558747,; A ENST00000332783 Transcript missense_variant 1168/4985 383/957 128/318 G/D gGc/gAc 1 1 ASB7 HGNC HGNC:17182 protein_coding YES CCDS10387.1 ENSP00000328327 Q9H672 A0A024RC94 UPI00001B3F4D NM_198243.2 deleterious(0) 5/6 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 100629608 100629608 G A 1 0 0 0 0 1 0 0 0 1170 1203 42 3 3 ASB7 15 100629608 Missense_Mutation SNP G C3L-00080_T 632144 100629608 1361581 573 2671 WDR90 0 . GRCh38 16 661628 661628 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.3705G>T p.Trp1235Cys p.W1235C ENST00000293879 31/41 76 55 21 40 40 0 strelka-varscan-mutect WDR90,missense_variant,p.Trp1235Cys,ENST00000549091,;WDR90,missense_variant,p.Trp1235Cys,ENST00000293879,NM_145294.4;WDR90,upstream_gene_variant,,ENST00000547944,;WDR90,upstream_gene_variant,,ENST00000315764,;WDR90,upstream_gene_variant,,ENST00000551100,;WDR90,downstream_gene_variant,,ENST00000550739,;WDR90,upstream_gene_variant,,ENST00000547543,;WDR90,downstream_gene_variant,,ENST00000552648,;WDR90,upstream_gene_variant,,ENST00000548603,;WDR90,downstream_gene_variant,,ENST00000548844,;WDR90,3_prime_UTR_variant,,ENST00000552728,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;WDR90,non_coding_transcript_exon_variant,,ENST00000546516,;WDR90,non_coding_transcript_exon_variant,,ENST00000552683,;WDR90,non_coding_transcript_exon_variant,,ENST00000549024,;WDR90,non_coding_transcript_exon_variant,,ENST00000550902,;WDR90,downstream_gene_variant,,ENST00000552943,;WDR90,upstream_gene_variant,,ENST00000553080,;WDR90,upstream_gene_variant,,ENST00000546923,;WDR90,downstream_gene_variant,,ENST00000548859,;WDR90,upstream_gene_variant,,ENST00000548448,; T ENST00000293879 Transcript missense_variant 3705/5488 3705/5247 1235/1748 W/C tgG/tgT 1 1 WDR90 HGNC HGNC:26960 protein_coding YES CCDS42092.1 ENSP00000293879 Q96KV7 UPI0000D67C48 NM_145294.4 deleterious(0) 31/41 PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF24,hmmpanther:PTHR13720,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS rs1437679810 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 661628 661628 G T 1 0 0 0 0 1 0 0 0 17893 1241 43 2 2 WDR90 16 661628 Missense_Mutation SNP G C3L-00080_T 661628 89676717 574 2672 HAGHL 0 . GRCh38 16 728449 728449 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.422A>T p.His141Leu p.H141L ENST00000549114 5/6 250 163 87 193 191 2 strelka-varscan-mutect HAGHL,missense_variant,p.His141Leu,ENST00000549114,;HAGHL,missense_variant,p.His141Leu,ENST00000564537,;HAGHL,missense_variant,p.His141Leu,ENST00000568141,;HAGHL,intron_variant,,ENST00000341413,;HAGHL,intron_variant,,ENST00000389703,NM_001290137.1,NM_001290139.1,NM_032304.3;HAGHL,intron_variant,,ENST00000561546,;HAGHL,intron_variant,,ENST00000567414,;HAGHL,intron_variant,,ENST00000564545,;HAGHL,intron_variant,,ENST00000562141,;NARFL,downstream_gene_variant,,ENST00000540986,NM_001304799.1;NARFL,downstream_gene_variant,,ENST00000568545,;NARFL,downstream_gene_variant,,ENST00000251588,NM_022493.2;CCDC78,upstream_gene_variant,,ENST00000293889,NM_001031737.2;CCDC78,upstream_gene_variant,,ENST00000345165,;NARFL,downstream_gene_variant,,ENST00000562421,;CCDC78,upstream_gene_variant,,ENST00000423653,;HAGHL,downstream_gene_variant,,ENST00000563792,;HAGHL,downstream_gene_variant,,ENST00000562187,;HAGHL,upstream_gene_variant,,ENST00000569604,;NARFL,downstream_gene_variant,,ENST00000562862,;HAGHL,upstream_gene_variant,,ENST00000563156,;HAGHL,missense_variant,p.His33Leu,ENST00000561561,;HAGHL,non_coding_transcript_exon_variant,,ENST00000567696,;HAGHL,non_coding_transcript_exon_variant,,ENST00000561750,;HAGHL,intron_variant,,ENST00000389701,;CCDC78,upstream_gene_variant,,ENST00000482878,;CCDC78,upstream_gene_variant,,ENST00000481804,;CCDC78,upstream_gene_variant,,ENST00000478979,;NARFL,downstream_gene_variant,,ENST00000563051,;NARFL,downstream_gene_variant,,ENST00000566650,;NARFL,downstream_gene_variant,,ENST00000565425,;CCDC78,upstream_gene_variant,,ENST00000466708,;CCDC78,upstream_gene_variant,,ENST00000463539,;CCDC78,upstream_gene_variant,,ENST00000485091,;NARFL,downstream_gene_variant,,ENST00000564285,;CCDC78,upstream_gene_variant,,ENST00000538176,;CCDC78,upstream_gene_variant,,ENST00000439619,;CCDC78,upstream_gene_variant,,ENST00000482152,;CCDC78,upstream_gene_variant,,ENST00000460023,;CCDC78,upstream_gene_variant,,ENST00000471861,;HAGHL,downstream_gene_variant,,ENST00000569143,;CCDC78,upstream_gene_variant,,ENST00000544996,;CCDC78,upstream_gene_variant,,ENST00000474647,;HAGHL,upstream_gene_variant,,ENST00000569385,; T ENST00000549114 Transcript missense_variant 725/1820 422/609 141/202 H/L cAc/cTc 1 1 HAGHL HGNC HGNC:14177 protein_coding ENSP00000447170 Q6PII5 UPI000006EE13 tolerated_low_confidence(0.08) 5/6 SMART_domains:SM00849 MODERATE SNV 5 1 PASS rs1355919837 . 0 140 0 7 63 0 0 0 -20 0 0 1 0 0 T 3 4 7 728449 728449 A T 1 0 0 0 0 1 0 0 0 6832 159 6 4 4 HAGHL 16 728449 Missense_Mutation SNP A C3L-00080_T 66821 728449 89609896 575 2673 MEFV 0 . GRCh38 16 3243279 3243279 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.2208C>A p.= p.A736A ENST00000219596 10/10 428 294 134 361 361 0 strelka-varscan-mutect MEFV,synonymous_variant,p.=,ENST00000219596,NM_000243.2;MEFV,synonymous_variant,p.=,ENST00000339854,;MEFV,synonymous_variant,p.=,ENST00000536379,;MEFV,3_prime_UTR_variant,,ENST00000541159,NM_001198536.1;MEFV,3_prime_UTR_variant,,ENST00000542898,;MEFV,3_prime_UTR_variant,,ENST00000537682,;MEFV,3_prime_UTR_variant,,ENST00000538326,;MEFV,3_prime_UTR_variant,,ENST00000536980,;MEFV,3_prime_UTR_variant,,ENST00000570511,;MEFV,3_prime_UTR_variant,,ENST00000539145,;MEFV,3_prime_UTR_variant,,ENST00000576315,;MEFV,3_prime_UTR_variant,,ENST00000574583,;MEFV,3_prime_UTR_variant,,ENST00000572244,;MEFV,downstream_gene_variant,,ENST00000539154,; T ENST00000219596 Transcript synonymous_variant 2248/3499 2208/2346 736/781 A gcC/gcA 1 -1 MEFV HGNC HGNC:6998 protein_coding YES CCDS10498.1 ENSP00000219596 O15553 UPI000004C0CA NM_000243.2 10/10 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 3243279 3243279 G T 1 0 0 0 0 0 0 0 1 9399 1335 47 2 2 MEFV 16 3243279 Silent SNP G C3L-00080_T 2514830 3243279 87095066 576 2674 RP11-166B2.1 0 . GRCh38 16 11937593 11937593 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.139G>A p.Ala47Thr p.A47T ENST00000399147 2/8 283 243 40 234 233 1 strelka-varscan-mutect RP11-166B2.1,missense_variant,p.Ala51Thr,ENST00000620285,;RP11-166B2.1,missense_variant,p.Ala47Thr,ENST00000399147,;RP11-166B2.1,missense_variant,p.Ala47Thr,ENST00000547494,;RP11-166B2.1,5_prime_UTR_variant,,ENST00000538896,;RP11-166B2.1,non_coding_transcript_exon_variant,,ENST00000532936,; T ENST00000399147 Transcript missense_variant 139/1194 139/1194 47/397 A/T Gca/Aca 1 -1 RP11-166B2.1 Clone_based_vega_gene protein_coding YES ENSP00000382101 A6NJ64 A0A0A6YYH2 UPI000204A8FF tolerated_low_confidence(0.06) 2/8 hmmpanther:PTHR15438,Pfam_domain:PF06409 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 11937593 11937593 C T 1 0 0 0 0 1 0 0 0 13716 710 25 3 3 RP11-166B2.1 16 11937593 Missense_Mutation SNP C C3L-00080_T 8694314 11937593 78400752 577 2675 TNFRSF17 0 . GRCh38 16 11965452 11965452 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.128C>A p.Ala43Glu p.A43E ENST00000053243 1/3 105 91 14 107 107 0 strelka-varscan-mutect TNFRSF17,missense_variant,p.Ala43Glu,ENST00000053243,NM_001192.2;TNFRSF17,missense_variant,p.Ala43Glu,ENST00000396495,;TNFRSF17,missense_variant,p.Ala35Glu,ENST00000562385,;RP11-166B2.1,intron_variant,,ENST00000538896,;RP11-166B2.1,intron_variant,,ENST00000532936,;UBL5P4,downstream_gene_variant,,ENST00000562584,; A ENST00000053243 Transcript missense_variant,splice_region_variant 346/994 128/555 43/184 A/E gCa/gAa 1 1 TNFRSF17 HGNC HGNC:11913 protein_coding YES CCDS10552.1 ENSP00000053243 Q02223 UPI000013C562 NM_001192.2 tolerated(0.39) 1/3 hmmpanther:PTHR20437,hmmpanther:PTHR20437:SF0,Pfam_domain:PF09257,PIRSF_domain:PIRSF011859,Superfamily_domains:SSF57586 MODERATE 1 SNV 1 1 PASS rs771330300 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 11965452 11965452 C A 1 0 0 0 0 1 0 0 0 16764 724 25 2 2 TNFRSF17 16 11965452 Missense_Mutation SNP C C3L-00080_T 27859 11965452 78372893 578 2676 PARN 0 . GRCh38 16 14482759 14482759 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.1549C>G p.Gln517Glu p.Q517E ENST00000437198 22/24 86 61 25 94 94 0 strelka-varscan-mutect PARN,missense_variant,p.Gln517Glu,ENST00000437198,NM_002582.3;PARN,missense_variant,p.Gln471Glu,ENST00000420015,NM_001242992.1;PARN,missense_variant,p.Gln456Glu,ENST00000341484,NM_001134477.2;PARN,missense_variant,p.Gln342Glu,ENST00000539279,;PARN,non_coding_transcript_exon_variant,,ENST00000564904,;PARN,non_coding_transcript_exon_variant,,ENST00000564882,; C ENST00000437198 Transcript missense_variant 1691/3078 1549/1920 517/639 Q/E Cag/Gag 1 -1 PARN HGNC HGNC:8609 protein_coding YES CCDS45419.1 ENSP00000387911 O95453 UPI0000031F7A NM_002582.3 tolerated(0.18) 22/24 Gene3D:3.30.70.330,hmmpanther:PTHR15092,hmmpanther:PTHR15092:SF26,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 14482759 14482759 G C 1 0 0 0 0 1 0 0 0 11533 1386 48 4 4 PARN 16 14482759 Missense_Mutation SNP G C3L-00080_T 2517307 14482759 75855586 579 2677 GP2 0 . GRCh38 16 20317336 20317336 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1302G>C p.Glu434Asp p.E434D ENST00000381362 9/12 215 179 36 152 152 0 strelka-varscan-mutect GP2,missense_variant,p.Glu431Asp,ENST00000302555,NM_001502.3;GP2,missense_variant,p.Glu434Asp,ENST00000381362,NM_001007240.2;GP2,missense_variant,p.Glu287Asp,ENST00000381360,NM_001007241.2;GP2,missense_variant,p.Glu284Asp,ENST00000341642,NM_001007242.2;GP2,downstream_gene_variant,,ENST00000572347,;GP2,downstream_gene_variant,,ENST00000575582,;GP2,downstream_gene_variant,,ENST00000572478,;GP2,downstream_gene_variant,,ENST00000573897,;GP2,downstream_gene_variant,,ENST00000574982,; G ENST00000381362 Transcript missense_variant 1379/2425 1302/1614 434/537 E/D gaG/gaC 1 -1 GP2 HGNC HGNC:4441 protein_coding YES CCDS42128.1 ENSP00000370767 P55259 UPI000059D333 NM_001007240.2 deleterious(0.01) 9/12 PROSITE_profiles:PS51034,hmmpanther:PTHR24044:SF284,hmmpanther:PTHR24044,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 20317336 20317336 C G 1 0 0 0 0 1 0 0 0 6477 912 32 4 4 GP2 16 20317336 Missense_Mutation SNP C C3L-00080_T 5834577 20317336 70021009 580 2678 ACSM1 0 . GRCh38 16 20691125 20691125 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.64C>T p.Pro22Ser p.P22S ENST00000307493 1/13 152 95 57 149 149 0 strelka-varscan-mutect ACSM1,missense_variant,p.Pro22Ser,ENST00000307493,NM_001318890.1,NM_052956.2;ACSM1,missense_variant,p.Pro22Ser,ENST00000520010,;ACSM1,missense_variant,p.Pro22Ser,ENST00000523065,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;ACSM1,missense_variant,p.Pro22Ser,ENST00000519745,; A ENST00000307493 Transcript missense_variant 132/2051 64/1734 22/577 P/S Cct/Tct 1 -1 ACSM1 HGNC HGNC:18049 protein_coding YES CCDS10587.1 ENSP00000301956 Q08AH1 UPI00000558D0 NM_001318890.1,NM_052956.2 tolerated(0.55) 1/13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 20691125 20691125 G A 1 0 0 0 0 1 0 0 0 224 1232 43 3 3 ACSM1 16 20691125 Missense_Mutation SNP G C3L-00080_T 373789 20691125 69647220 581 2679 DNAH3 0 . GRCh38 16 21111746 21111746 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1979C>A p.Pro660His p.P660H ENST00000261383 14/62 191 136 55 209 208 1 strelka-varscan-mutect DNAH3,missense_variant,p.Pro660His,ENST00000261383,NM_017539.2;DNAH3,non_coding_transcript_exon_variant,,ENST00000396036,; T ENST00000261383 Transcript missense_variant 1979/12394 1979/12351 660/4116 P/H cCt/cAt 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 tolerated(0.65) 14/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 21111746 21111746 G T 1 0 0 0 0 1 0 0 0 4418 1000 35 2 2 DNAH3 16 21111746 Missense_Mutation SNP G C3L-00080_T 420621 21111746 69226599 582 2680 OTOA 0 . GRCh38 16 21687584 21687584 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.571T>G p.Phe191Val p.F191V ENST00000388958 7/28 277 216 61 257 257 0 strelka-varscan-mutect OTOA,missense_variant,p.Phe191Val,ENST00000388958,NM_144672.3;OTOA,missense_variant,p.Phe191Val,ENST00000286149,;OTOA,missense_variant,p.Phe112Val,ENST00000388956,NM_001161683.1; G ENST00000388958 Transcript missense_variant 572/3610 571/3420 191/1139 F/V Ttt/Gtt 1 1 OTOA HGNC HGNC:16378 protein_coding YES CCDS10600.2 ENSP00000373610 Q7RTW8 UPI00005C8607 NM_144672.3 deleterious(0.01) 7/28 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 21687584 21687584 T G 1 0 0 0 0 1 0 0 0 11368 1609 56 5 5 OTOA 16 21687584 Missense_Mutation SNP T C3L-00080_T 575838 21687584 68650761 583 2681 NPIPB5 0 . GRCh38 16 22534014 22534014 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1031A>T p.Glu344Val p.E344V ENST00000424340 7/7 438 333 105 330 330 0 strelka-varscan-mutect NPIPB5,missense_variant,p.Glu344Val,ENST00000424340,NM_001135865.1;NPIPB5,missense_variant,p.Glu344Val,ENST00000451409,;NPIPB5,missense_variant,p.Glu344Val,ENST00000517539,;NPIPB5,missense_variant,p.Glu344Val,ENST00000415833,;NPIPB5,missense_variant,p.Glu344Val,ENST00000528249,;NPIPB5,missense_variant,p.Glu128Val,ENST00000357370,;NPIPB5,downstream_gene_variant,,ENST00000621622,;NPIPB5,non_coding_transcript_exon_variant,,ENST00000415654,;NPIPB5,3_prime_UTR_variant,,ENST00000521555,;NPIPB5,downstream_gene_variant,,ENST00000541664,;NPIPB5,downstream_gene_variant,,ENST00000442450,;NPIPB5,downstream_gene_variant,,ENST00000539604,;NPIPB5,downstream_gene_variant,,ENST00000543997,;RP11-368J21.4,downstream_gene_variant,,ENST00000610646,; T ENST00000424340 Transcript missense_variant 1310/3801 1031/3402 344/1133 E/V gAg/gTg 1 1 NPIPB5 HGNC HGNC:37233 protein_coding YES CCDS45443.1 ENSP00000440703 A8MRT5 UPI000181EF82 NM_001135865.1 deleterious_low_confidence(0) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 22534014 22534014 A T 1 0 0 0 0 1 0 0 0 10639 304 11 4 4 NPIPB5 16 22534014 Missense_Mutation SNP A C3L-00080_T 846430 22534014 67804331 584 2682 NPIPB5 0 . GRCh38 16 22534096 22534096 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1113G>T p.Glu371Asp p.E371D ENST00000424340 7/7 95 72 23 75 75 0 strelka-varscan-mutect NPIPB5,missense_variant,p.Glu371Asp,ENST00000424340,NM_001135865.1;NPIPB5,missense_variant,p.Glu371Asp,ENST00000451409,;NPIPB5,missense_variant,p.Glu371Asp,ENST00000517539,;NPIPB5,missense_variant,p.Glu371Asp,ENST00000415833,;NPIPB5,missense_variant,p.Glu371Asp,ENST00000528249,;NPIPB5,missense_variant,p.Glu155Asp,ENST00000357370,;NPIPB5,downstream_gene_variant,,ENST00000621622,;NPIPB5,non_coding_transcript_exon_variant,,ENST00000415654,;NPIPB5,3_prime_UTR_variant,,ENST00000521555,;NPIPB5,downstream_gene_variant,,ENST00000541664,;NPIPB5,downstream_gene_variant,,ENST00000442450,;NPIPB5,downstream_gene_variant,,ENST00000539604,;NPIPB5,downstream_gene_variant,,ENST00000543997,;RP11-368J21.4,downstream_gene_variant,,ENST00000610646,; T ENST00000424340 Transcript missense_variant 1392/3801 1113/3402 371/1133 E/D gaG/gaT 1 1 NPIPB5 HGNC HGNC:37233 protein_coding YES CCDS45443.1 ENSP00000440703 A8MRT5 UPI000181EF82 NM_001135865.1 deleterious_low_confidence(0.04) 7/7 hmmpanther:PTHR15438,hmmpanther:PTHR15438:SF0 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 22534096 22534096 G T 1 0 0 0 0 1 0 0 0 10639 1020 36 2 2 NPIPB5 16 22534096 Missense_Mutation SNP G C3L-00080_T 82 22534096 67804249 585 2683 ERN2 0 . GRCh38 16 23702697 23702697 + Missense_Mutation SNP G G T rs148979151 C3L-00080_T C3L-00080_N G G c.1004C>A p.Thr335Lys p.T335K ENST00000634482 9/22 207 163 44 188 188 0 strelka-varscan-mutect ERN2,missense_variant,p.Thr335Lys,ENST00000634482,NM_033266.3;ERN2,missense_variant,p.Thr287Lys,ENST00000256797,;ERN2,missense_variant,p.Thr287Lys,ENST00000457008,NM_001308220.1;ERN2,3_prime_UTR_variant,,ENST00000562562,;ERN2,downstream_gene_variant,,ENST00000561478,;ERN2,downstream_gene_variant,,ENST00000566565,; T ENST00000634482 Transcript missense_variant 1173/3616 1004/2925 335/974 T/K aCg/aAg rs148979151 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 deleterious(0) 9/22 hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15 MODERATE 1 SNV 1 1 PASS rs148979151 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23702697 23702697 G T 1 0 0 0 0 1 0 0 0 5096 1159 40 1 1 ERN2 16 23702697 Missense_Mutation SNP G C3L-00080_T 1168601 23702697 66635648 586 2684 SEPHS2 0 . GRCh38 16 30445458 30445458 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.270G>T p.= p.V90V ENST00000478753 1/1 268 180 88 193 193 0 strelka-varscan-mutect SEPHS2,synonymous_variant,p.=,ENST00000478753,NM_012248.3; A ENST00000478753 Transcript synonymous_variant 724/2551 270/1347 90/448 V gtG/gtT 1 -1 SEPHS2 HGNC HGNC:19686 protein_coding YES ENSP00000418669 Q99611 J3KR58 UPI00001678A0 NM_012248.3 1/1 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 30445458 30445458 C A 1 0 0 0 0 0 0 0 1 14331 581 21 2 2 SEPHS2 16 30445458 Silent SNP C C3L-00080_T 6742761 30445458 59892887 587 2685 ITGAM 0 . GRCh38 16 31329906 31329906 + Splice_Site SNP G G A novel C3L-00080_T C3L-00080_N G G c.2979+1G>A p.X993_splice ENST00000544665 177 143 34 125 125 0 strelka-varscan-mutect ITGAM,splice_donor_variant,,ENST00000544665,NM_001145808.1;ITGAM,splice_donor_variant,,ENST00000287497,NM_000632.3;ITGAM,upstream_gene_variant,,ENST00000565142,;ITGAM,non_coding_transcript_exon_variant,,ENST00000569746,;ITGAM,downstream_gene_variant,,ENST00000561838,;ITGAM,downstream_gene_variant,,ENST00000567178,; A ENST00000544665 Transcript splice_donor_variant -/4718 2979/3462 993/1153 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 25/29 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 7 31329906 31329906 G A 1 0 0 0 0 0 0 1 0 7794 1275 44 3 3 ITGAM 16 31329906 Splice_Site SNP G C3L-00080_T 884448 31329906 59008439 588 2686 ITGAX 0 . GRCh38 16 31371728 31371728 + Missense_Mutation SNP C C G rs775006242 C3L-00080_T C3L-00080_N C C c.2104C>G p.Arg702Gly p.R702G ENST00000562522 17/31 287 235 52 235 235 0 strelka-varscan-mutect ITGAX,missense_variant,p.Arg702Gly,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Arg702Gly,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,non_coding_transcript_exon_variant,,ENST00000562138,; G ENST00000562522 Transcript missense_variant 2137/3990 2104/3510 702/1169 R/G Cga/Gga rs775006242 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.05) 17/31 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs775006242 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 31371728 31371728 C G 1 0 0 0 0 1 0 0 0 7796 644 23 4 4 ITGAX 16 31371728 Missense_Mutation SNP C C3L-00080_T 41822 31371728 58966617 589 2687 ITGAD 0 . GRCh38 16 31411096 31411096 + Silent SNP C C A rs780689628 C3L-00080_T C3L-00080_N C C c.1377C>A p.= p.A459A ENST00000389202 13/30 226 204 22 136 136 0 strelka-varscan-mutect ITGAD,synonymous_variant,p.=,ENST00000389202,NM_001318185.1,NM_005353.2;ITGAD,downstream_gene_variant,,ENST00000444228,; A ENST00000389202 Transcript synonymous_variant 1426/3912 1377/3486 459/1161 A gcC/gcA rs780689628 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 13/30 Gene3D:3nigC00,Pfam_domain:PF01839,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,SMART_domains:SM00191,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS rs780689628 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 31411096 31411096 C A 1 0 0 0 0 0 0 0 1 7791 668 24 2 2 ITGAD 16 31411096 Silent SNP C C3L-00080_T 39368 31411096 58927249 590 2688 SHCBP1 0 . GRCh38 16 46604126 46604126 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.941A>C p.Gln314Pro p.Q314P ENST00000303383 7/13 147 100 47 123 123 0 strelka-mutect SHCBP1,missense_variant,p.Gln314Pro,ENST00000303383,NM_024745.4;SHCBP1,missense_variant,p.Gln54Pro,ENST00000569702,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000566016,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000565887,;SHCBP1,upstream_gene_variant,,ENST00000563219,; G ENST00000303383 Transcript missense_variant 1208/3461 941/2019 314/672 Q/P cAg/cCg 1 -1 SHCBP1 HGNC HGNC:29547 protein_coding YES CCDS10720.1 ENSP00000306473 Q8NEM2 UPI000013E898 NM_024745.4 tolerated(0.12) 7/13 hmmpanther:PTHR14695:SF8,hmmpanther:PTHR14695 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 46604126 46604126 T G 1 0 0 0 0 1 0 0 0 14533 1580 55 5 5 SHCBP1 16 46604126 Missense_Mutation SNP T C3L-00080_T 15193030 46604126 43734219 591 2689 MYLK3 0 . GRCh38 16 46747966 46747966 + Silent SNP G G T rs368349751 C3L-00080_T C3L-00080_N G G c.228C>A p.= p.G76G ENST00000394809 1/13 320 229 91 242 240 2 strelka-varscan-mutect MYLK3,synonymous_variant,p.=,ENST00000394809,NM_182493.2;MYLK3,intron_variant,,ENST00000536476,NM_001308301.1;MYLK3,intron_variant,,ENST00000569810,; T ENST00000394809 Transcript synonymous_variant 344/6911 228/2460 76/819 G ggC/ggA rs368349751 1 -1 MYLK3 HGNC HGNC:29826 protein_coding YES CCDS10723.2 ENSP00000378288 Q32MK0 UPI000059D380 NM_182493.2 1/13 LOW 1 SNV 1 1 PASS rs368349751 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 46747966 46747966 G T 1 0 0 0 0 0 0 0 1 10058 1074 38 1 1 MYLK3 16 46747966 Silent SNP G C3L-00080_T 143840 46747966 43590379 592 2690 ABCC11 0 . GRCh38 16 48198179 48198179 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2179G>T p.Ala727Ser p.A727S ENST00000394747 15/29 243 179 64 247 247 0 strelka-varscan-mutect ABCC11,missense_variant,p.Ala727Ser,ENST00000394747,NM_033151.3;ABCC11,missense_variant,p.Ala727Ser,ENST00000356608,;ABCC11,missense_variant,p.Ala727Ser,ENST00000394748,NM_032583.3;ABCC11,missense_variant,p.Ala727Ser,ENST00000353782,NM_145186.2;ABCC11,non_coding_transcript_exon_variant,,ENST00000569172,; A ENST00000394747 Transcript missense_variant 2529/4862 2179/4149 727/1382 A/S Gcc/Tcc 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 deleterious(0.03) 15/29 PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 48198179 48198179 C A 1 0 0 0 0 1 0 0 0 55 710 25 2 2 ABCC11 16 48198179 Missense_Mutation SNP C C3L-00080_T 1450213 48198179 42140166 593 2691 NKD1 0 . GRCh38 16 50633385 50633385 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1017G>T p.Gln339His p.Q339H ENST00000268459 10/10 186 134 52 120 120 0 strelka-varscan-mutect NKD1,missense_variant,p.Gln339His,ENST00000268459,NM_033119.4;NKD1,downstream_gene_variant,,ENST00000566396,; T ENST00000268459 Transcript missense_variant 1241/17105 1017/1413 339/470 Q/H caG/caT 1 1 NKD1 HGNC HGNC:17045 protein_coding YES CCDS10743.1 ENSP00000268459 Q969G9 UPI0000073F02 NM_033119.4 deleterious(0) 10/10 hmmpanther:PTHR22611:SF2,hmmpanther:PTHR22611 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 50633385 50633385 G T 1 0 0 0 0 1 0 0 0 10476 991 35 2 2 NKD1 16 50633385 Missense_Mutation SNP G C3L-00080_T 2435206 50633385 39704960 594 2692 MMP2 0 . GRCh38 16 55488558 55488558 + Missense_Mutation SNP G G T rs760811855 C3L-00080_T C3L-00080_N G G c.848G>T p.Gly283Val p.G283V ENST00000219070 6/13 256 189 67 268 268 0 strelka-varscan-mutect MMP2,missense_variant,p.Gly283Val,ENST00000219070,NM_004530.5;MMP2,missense_variant,p.Gly207Val,ENST00000570308,;MMP2,missense_variant,p.Gly233Val,ENST00000437642,NM_001127891.2;MMP2,missense_variant,p.Gly207Val,ENST00000543485,NM_001302508.1,NM_001302510.1,NM_001302509.1;MMP2,upstream_gene_variant,,ENST00000570283,;MMP2,downstream_gene_variant,,ENST00000564864,;MMP2,downstream_gene_variant,,ENST00000568715,;RP11-212I21.3,non_coding_transcript_exon_variant,,ENST00000623886,; T ENST00000219070 Transcript missense_variant 1357/3741 848/1983 283/660 G/V gGc/gTc rs760811855 1 1 MMP2 HGNC HGNC:7166 protein_coding YES CCDS10752.1 ENSP00000219070 P08253 A0A024R6R4 UPI00000422C4 NM_004530.5 deleterious(0) 6/13 Gene3D:2.10.10.10,Pfam_domain:PF00413,SMART_domains:SM00235,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS rs760811855 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 55488558 55488558 G T 1 0 0 0 0 1 0 0 0 9621 1203 42 2 2 MMP2 16 55488558 Missense_Mutation SNP G C3L-00080_T 4855173 55488558 34849787 595 2693 SF3B3 0 . GRCh38 16 70530846 70530846 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.499G>A p.Val167Met p.V167M ENST00000302516 4/26 177 131 46 220 220 0 strelka-varscan-mutect SF3B3,missense_variant,p.Val167Met,ENST00000302516,NM_012426.4;SF3B3,downstream_gene_variant,,ENST00000564899,;SF3B3,downstream_gene_variant,,ENST00000577085,;SF3B3,downstream_gene_variant,,ENST00000566095,;SF3B3,downstream_gene_variant,,ENST00000567654,;SF3B3,downstream_gene_variant,,ENST00000569687,;SNORD111B,downstream_gene_variant,,ENST00000408587,; A ENST00000302516 Transcript missense_variant 710/9720 499/3654 167/1217 V/M Gtg/Atg 1 1 SF3B3 HGNC HGNC:10770 protein_coding YES CCDS10894.1 ENSP00000305790 Q15393 UPI0000167878 NM_012426.4 deleterious(0.01) 4/26 hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF1,Pfam_domain:PF10433 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 70530846 70530846 G A 1 0 0 0 0 1 0 0 0 14430 1029 36 3 3 SF3B3 16 70530846 Missense_Mutation SNP G C3L-00080_T 15042288 70530846 19807499 596 2694 GLG1 0 . GRCh38 16 74480394 74480394 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1674G>T p.Lys558Asn p.K558N ENST00000205061 11/27 91 65 26 123 123 0 strelka-varscan-mutect GLG1,missense_variant,p.Lys558Asn,ENST00000205061,NM_012201.5;GLG1,missense_variant,p.Lys558Asn,ENST00000422840,NM_001145667.1;GLG1,missense_variant,p.Lys547Asn,ENST00000447066,NM_001145666.1;GLG1,missense_variant,p.Lys558Asn,ENST00000627032,;GLG1,missense_variant,p.Lys558Asn,ENST00000562090,;GLG1,intron_variant,,ENST00000567951,;GLG1,upstream_gene_variant,,ENST00000567911,; A ENST00000205061 Transcript missense_variant,splice_region_variant 1694/8261 1674/3612 558/1203 K/N aaG/aaT 1 -1 GLG1 HGNC HGNC:4316 protein_coding YES CCDS32485.1 ENSP00000205061 Q92896 UPI00001FFBD9 NM_012201.5 deleterious(0.01) 11/27 PROSITE_profiles:PS51289,hmmpanther:PTHR11884:SF1,hmmpanther:PTHR11884,Pfam_domain:PF00839 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 74480394 74480394 C A 1 0 0 0 0 1 0 0 0 6314 753 26 2 2 GLG1 16 74480394 Missense_Mutation SNP C C3L-00080_T 3949548 74480394 15857951 597 2695 FOXC2 0 . GRCh38 16 86567826 86567826 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.491G>T p.Arg164Leu p.R164L ENST00000320354 1/1 195 152 43 219 219 0 strelka-varscan-mutect FOXC2,missense_variant,p.Arg164Leu,ENST00000320354,NM_005251.2;FOXC2-AS1,upstream_gene_variant,,ENST00000563280,; T ENST00000320354 Transcript missense_variant 576/2478 491/1506 164/501 R/L cGc/cTc 1 1 FOXC2 HGNC HGNC:3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 UPI000012ADC6 NM_005251.2 deleterious(0) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF189,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 86567826 86567826 G T 1 0 0 0 0 1 0 0 0 5855 1087 38 1 1 FOXC2 16 86567826 Missense_Mutation SNP G C3L-00080_T 12087432 86567826 3770519 598 2696 ZNF469 0 . GRCh38 16 88433709 88433709 + Frame_Shift_Del DEL A A - novel C3L-00080_T C3L-00080_N A A c.6155delA p.Glu2052GlyfsTer13 p.E2052Gfs*13 ENST00000437464 2/2 106 79 27 112 112 0 sindel-varindel ZNF469,frameshift_variant,p.Glu2080GlyfsTer13,ENST00000565624,;ZNF469,frameshift_variant,p.Glu2052GlyfsTer13,ENST00000437464,NM_001127464.2; - ENST00000437464 Transcript frameshift_variant 6155/13203 6155/11778 2052/3925 E/X gAg/gg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 88433709 88433709 A - 1 0 1 0 1 0 0 0 0 18500 304 11 0 0 ZNF469 16 88433709 Frame_Shift_Del DEL A C3L-00080_T 1865883 88433709 1904636 599 2697 DPEP1 0 . GRCh38 16 89636557 89636557 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.395G>T p.Gly132Val p.G132V ENST00000393092 5/11 93 69 24 88 88 0 strelka-varscan-mutect DPEP1,missense_variant,p.Gly132Val,ENST00000393092,NM_004413.3;DPEP1,missense_variant,p.Gly132Val,ENST00000421184,NM_001128141.2;DPEP1,missense_variant,p.Gly132Val,ENST00000261615,;DPEP1,downstream_gene_variant,,ENST00000570029,;DPEP1,downstream_gene_variant,,ENST00000568281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000564281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000565249,;DPEP1,downstream_gene_variant,,ENST00000561484,;DPEP1,upstream_gene_variant,,ENST00000564645,; T ENST00000393092 Transcript missense_variant 686/1734 395/1236 132/411 G/V gGg/gTg 1 1 DPEP1 HGNC HGNC:3002 protein_coding YES CCDS10982.1 ENSP00000376807 P16444 A0A140VJI3 UPI000006DF95 NM_004413.3 deleterious(0.03) 5/11 PROSITE_profiles:PS51365,hmmpanther:PTHR10443,hmmpanther:PTHR10443:SF17,Gene3D:3.20.20.140,Pfam_domain:PF01244,Superfamily_domains:SSF51556 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 89636557 89636557 G T 1 0 0 0 0 1 0 0 0 4527 1232 43 2 2 DPEP1 16 89636557 Missense_Mutation SNP G C3L-00080_T 1202848 89636557 701788 600 2698 TCF25 0 . GRCh38 16 89893748 89893748 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.718G>T p.Glu240Ter p.E240* ENST00000263346 7/18 238 180 58 217 217 0 strelka-varscan-mutect TCF25,stop_gained,p.Glu5Ter,ENST00000263347,;TCF25,stop_gained,p.Glu240Ter,ENST00000263346,NM_014972.2;TCF25,stop_gained,p.Glu102Ter,ENST00000562256,;TCF25,stop_gained,p.Glu59Ter,ENST00000568409,;TCF25,stop_gained,p.Glu228Ter,ENST00000561958,;TCF25,intron_variant,,ENST00000568412,;TCF25,downstream_gene_variant,,ENST00000614813,;TCF25,downstream_gene_variant,,ENST00000565196,;TCF25,upstream_gene_variant,,ENST00000562193,;TCF25,intron_variant,,ENST00000566751,;TCF25,non_coding_transcript_exon_variant,,ENST00000568870,;TCF25,upstream_gene_variant,,ENST00000570116,;TCF25,downstream_gene_variant,,ENST00000564652,;TCF25,upstream_gene_variant,,ENST00000563636,;TCF25,upstream_gene_variant,,ENST00000562184,;TCF25,upstream_gene_variant,,ENST00000566158,; T ENST00000263346 Transcript stop_gained 774/2233 718/2031 240/676 E/* Gaa/Taa 1 1 TCF25 HGNC HGNC:29181 protein_coding YES CCDS10987.1 ENSP00000263346 Q9BQ70 UPI000012A80B NM_014972.2 7/18 hmmpanther:PTHR22684,hmmpanther:PTHR22684:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 89893748 89893748 G T 1 0 0 0 0 0 1 0 0 16100 1175 41 2 2 TCF25 16 89893748 Nonsense_Mutation SNP G C3L-00080_T 257191 89893748 444597 601 2699 YWHAE 0 . GRCh38 17 1361926 1361934 + In_Frame_Del DEL TCGCCAGTG TCGCCAGTG - novel C3L-00080_T C3L-00080_N TCGCCAGTG TCGCCAGTG c.339_347delCACTGGCGA p.Asn113_Glu116delinsLys p.N113_E116delinsK ENST00000264335 3/6 114 105 9 153 153 0 varindel-pindel YWHAE,inframe_deletion,p.Asn113_Glu116delinsLys,ENST00000264335,NM_006761.4;YWHAE,inframe_deletion,p.Asn91_Glu94delinsLys,ENST00000571732,;YWHAE,intron_variant,,ENST00000573026,;YWHAE,intron_variant,,ENST00000575977,;YWHAE,upstream_gene_variant,,ENST00000496706,;YWHAE,splice_donor_variant,,ENST00000466227,;YWHAE,non_coding_transcript_exon_variant,,ENST00000486241,;YWHAE,non_coding_transcript_exon_variant,,ENST00000469398,;YWHAE,intron_variant,,ENST00000573196,;YWHAE,downstream_gene_variant,,ENST00000489287,; - ENST00000264335 Transcript inframe_deletion 607-615/2211 339-347/768 113-116/255 NTGE/K aaCACTGGCGAg/aag 1 -1 YWHAE HGNC HGNC:12851 protein_coding YES CCDS11001.1 ENSP00000264335 P62258 V9HW98 UPI0000021A46 NM_006761.4 3/6 hmmpanther:PTHR18860,PIRSF_domain:PIRSF000868,Pfam_domain:PF00244,Gene3D:3iquA00,SMART_domains:SM00101,Superfamily_domains:SSF48445,Prints_domain:PR00305 MODERATE 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -18.18358 1 1 1 1 0 - 7 5 7 1361926 1361926 TCGCCAGTG - 1 0 1 0 1 0 0 0 0 18063 1551 54 0 0 YWHAE 17 1361926 In_Frame_Del DEL TCGCCAGTG C3L-00080_T 1361926 81895515 602 2700 SGSM2 0 . GRCh38 17 2377953 2377953 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.2899G>C p.Glu967Gln p.E967Q ENST00000268989 22/24 172 119 53 121 121 0 strelka-varscan-mutect SGSM2,missense_variant,p.Glu967Gln,ENST00000268989,NM_014853.2;SGSM2,missense_variant,p.Glu922Gln,ENST00000426855,NM_001098509.1;SGSM2,missense_variant,p.Glu922Gln,ENST00000574563,;SGSM2,missense_variant,p.Glu15Gln,ENST00000573851,;SGSM2,upstream_gene_variant,,ENST00000572925,;RP1-59D14.5,intron_variant,,ENST00000574290,;RP1-59D14.5,upstream_gene_variant,,ENST00000573007,;SGSM2,splice_region_variant,,ENST00000572841,;SGSM2,downstream_gene_variant,,ENST00000574857,;SGSM2,downstream_gene_variant,,ENST00000573717,;SGSM2,downstream_gene_variant,,ENST00000574250,; C ENST00000268989 Transcript missense_variant,splice_region_variant 3076/4863 2899/3156 967/1051 E/Q Gaa/Caa 1 1 SGSM2 HGNC HGNC:29026 protein_coding YES CCDS32526.1 ENSP00000268989 O43147 UPI0000160300 NM_014853.2 deleterious(0) 22/24 Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF194,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 2377953 2377953 G C 1 0 0 0 0 1 0 0 0 14481 1014 35 4 4 SGSM2 17 2377953 Missense_Mutation SNP G C3L-00080_T 1016027 2377953 80879488 603 2701 OR3A2 0 . GRCh38 17 3278731 3278731 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.205T>C p.Tyr69His p.Y69H ENST00000408891 1/1 24 18 6 30 30 0 varscan-mutect OR3A2,missense_variant,p.Tyr69His,ENST00000408891,NM_002551.3;RP11-64J4.2,downstream_gene_variant,,ENST00000573491,;RP11-64J4.2,downstream_gene_variant,,ENST00000576166,; G ENST00000408891 Transcript missense_variant 244/1076 205/966 69/321 Y/H Tac/Cac 1 -1 OR3A2 HGNC HGNC:8283 protein_coding YES CCDS42233.1 ENSP00000386180 P47893 A0A126GVQ3 UPI0000050B3C NM_002551.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF449,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 205 5 0 0 0 0 0 -16.94783 1 1 1 1 0 G 3 3 7 3278731 3278731 A G 1 0 0 0 0 1 0 0 0 11115 391 14 5 5 OR3A2 17 3278731 Missense_Mutation SNP A C3L-00080_T 900778 3278731 79978710 604 2702 OR3A3 0 . GRCh38 17 3421203 3421203 + Silent SNP A A C novel C3L-00080_T C3L-00080_N A A c.636A>C p.= p.A212A ENST00000291231 1/1 724 651 73 360 360 0 strelka-varscan-mutect OR3A3,synonymous_variant,p.=,ENST00000291231,NM_012373.2; C ENST00000291231 Transcript synonymous_variant 636/966 636/966 212/321 A gcA/gcC 1 1 OR3A3 HGNC HGNC:8284 protein_coding YES CCDS11025.1 ENSP00000291231 P47888 UPI000013E033 NM_012373.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF7,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 3421203 3421203 A C 1 0 0 0 0 0 0 0 1 11116 175 7 5 5 OR3A3 17 3421203 Silent SNP A C3L-00080_T 142472 3421203 79836238 605 2703 WSCD1 0 . GRCh38 17 6120425 6120425 + Missense_Mutation SNP G G C rs748708422 C3L-00080_T C3L-00080_N G G c.1492G>C p.Val498Leu p.V498L ENST00000574946 9/9 502 428 74 353 353 0 strelka-varscan-mutect WSCD1,missense_variant,p.Val498Leu,ENST00000574946,;WSCD1,missense_variant,p.Val498Leu,ENST00000317744,NM_015253.1;WSCD1,missense_variant,p.Val498Leu,ENST00000539421,;WSCD1,missense_variant,p.Val498Leu,ENST00000574232,;WSCD1,missense_variant,p.Val382Leu,ENST00000573634,;WSCD1,3_prime_UTR_variant,,ENST00000571494,; C ENST00000574946 Transcript missense_variant 1882/5884 1492/1728 498/575 V/L Gtg/Ctg rs748708422 1 1 WSCD1 HGNC HGNC:29060 protein_coding YES CCDS32538.1 ENSP00000460825 Q658N2 UPI0000197208 tolerated(0.31) 9/9 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF90,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS rs748708422 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 6120425 6120425 G C 1 0 0 0 0 1 0 0 0 17963 1261 44 4 4 WSCD1 17 6120425 Missense_Mutation SNP G C3L-00080_T 2699222 6120425 77137016 606 2704 ACAP1 0 . GRCh38 17 7343880 7343880 + Frame_Shift_Del DEL C C - novel C3L-00080_T C3L-00080_N C C c.595delC p.Gln199ArgfsTer12 p.Q199Rfs*12 ENST00000158762 8/22 213 149 64 163 163 0 sindel-varindel-pindel ACAP1,frameshift_variant,p.Gln199ArgfsTer12,ENST00000158762,NM_014716.3;ACAP1,frameshift_variant,p.Gln125ArgfsTer12,ENST00000570457,;ACAP1,downstream_gene_variant,,ENST00000575425,;ACAP1,non_coding_transcript_exon_variant,,ENST00000573893,;ACAP1,non_coding_transcript_exon_variant,,ENST00000571220,;ACAP1,upstream_gene_variant,,ENST00000570439,;ACAP1,downstream_gene_variant,,ENST00000576628,;ACAP1,upstream_gene_variant,,ENST00000576594,; - ENST00000158762 Transcript frameshift_variant 799/2512 593/2223 198/740 A/X gCc/gc 1 1 ACAP1 HGNC HGNC:16467 protein_coding YES CCDS11101.1 ENSP00000158762 Q15027 UPI000012749A NM_014716.3 8/22 hmmpanther:PTHR23180:SF197,hmmpanther:PTHR23180,Pfam_domain:PF16746,Gene3D:1.20.1270.60,Superfamily_domains:SSF103657 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 7343880 7343880 C - 1 0 1 0 1 0 0 0 0 161 739 26 0 0 ACAP1 17 7343880 Frame_Shift_Del DEL C C3L-00080_T 1223455 7343880 75913561 607 2705 ZBTB4 0 . GRCh38 17 7466063 7466063 + Nonsense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.739A>T p.Lys247Ter p.K247* ENST00000311403 3/4 86 67 19 65 65 0 strelka-varscan-mutect ZBTB4,stop_gained,p.Lys247Ter,ENST00000311403,NM_020899.3;ZBTB4,stop_gained,p.Lys247Ter,ENST00000380599,NM_001128833.1; A ENST00000311403 Transcript stop_gained 1079/5956 739/3042 247/1013 K/* Aaa/Taa 1 -1 ZBTB4 HGNC HGNC:23847 protein_coding YES CCDS11107.1 ENSP00000307858 Q9P1Z0 UPI00001A9C9A NM_020899.3 3/4 PROSITE_profiles:PS50157,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF302,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 7466063 7466063 T A 1 0 0 0 0 0 1 0 0 18110 1821 63 4 4 ZBTB4 17 7466063 Nonsense_Mutation SNP T C3L-00080_T 122183 7466063 75791378 608 2706 TP53 0 . GRCh38 17 7674229 7674229 + Missense_Mutation SNP C C A rs121912656 C3L-00080_T C3L-00080_N C C c.734G>T p.Gly245Val p.G245V ENST00000269305 7/11 409 168 241 302 302 0 strelka-varscan-mutect TP53,missense_variant,p.Gly245Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly245Val,ENST00000420246,;TP53,missense_variant,p.Gly206Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly206Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly245Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly206Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly245Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly206Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly245Val,ENST00000445888,;TP53,missense_variant,p.Gly206Val,ENST00000619485,;TP53,missense_variant,p.Gly113Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly86Val,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly113Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly86Val,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly113Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly86Val,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly245Val,ENST00000359597,;TP53,missense_variant,p.Gly234Val,ENST00000615910,;TP53,missense_variant,p.Gly245Val,ENST00000413465,;TP53,missense_variant,p.Gly113Val,ENST00000509690,;TP53,missense_variant,p.Gly152Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly206Val,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 924/2579 734/1182 245/393 G/V gGc/gTc rs121912656,CM010464,CM900209,TP53_g.13371G>C,TP53_g.13371del,TP53_g.13371G>A,TP53_g.13371G>T,COSM11196,COSM131475,COSM131476,COSM131477,COSM1640832,COSM1646856,COSM179805,COSM179806,COSM179807,COSM3388184,COSM3388185,COSM3388186,COSM3388187,COSM3388188,COSM3388189,COSM3717638,COSM43606,COSM43965,COSM45770 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912656 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 7674229 7674229 C A 1 0 0 0 0 1 0 0 0 16859 739 26 2 2 TP53 17 7674229 Missense_Mutation SNP C C3L-00080_T 208166 7674229 75583212 609 2707 MYH8 0 . GRCh38 17 10409279 10409279 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.1897G>A p.Asp633Asn p.D633N ENST00000403437 16/40 382 337 45 318 318 0 strelka-varscan-mutect MYH8,missense_variant,p.Asp633Asn,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript missense_variant,splice_region_variant 1992/6041 1897/5814 633/1937 D/N Gat/Aat 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 tolerated(0.26) 16/40 Low_complexity_(Seg):seg,PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 10409279 10409279 C T 1 0 0 0 0 1 0 0 0 10041 695 24 3 3 MYH8 17 10409279 Missense_Mutation SNP C C3L-00080_T 2735050 10409279 72848162 610 2708 MYH4 0 . GRCh38 17 10453330 10453330 + Splice_Site SNP T T G novel C3L-00080_T C3L-00080_N T T c.2935-2A>C p.X979_splice ENST00000255381 266 172 94 220 218 2 strelka-varscan-mutect MYH4,splice_acceptor_variant,,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; G ENST00000255381 Transcript splice_acceptor_variant -/6016 2935/5820 979/1939 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 23/39 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 7 10453330 10453330 T G 1 0 0 0 0 0 0 1 0 10037 1623 56 5 5 MYH4 17 10453330 Splice_Site SNP T C3L-00080_T 44051 10453330 72804111 611 2709 MYH2 0 . GRCh38 17 10537461 10537461 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1669G>C p.Asp557His p.D557H ENST00000245503 16/40 249 170 79 144 144 0 strelka-varscan-mutect MYH2,missense_variant,p.Asp557His,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.Asp557His,ENST00000397183,NM_001100112.1;MYH2,missense_variant,p.Asp557His,ENST00000532183,;MYH2,missense_variant,p.Asp557His,ENST00000622564,;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,downstream_gene_variant,,ENST00000581304,; G ENST00000245503 Transcript missense_variant 2054/6339 1669/5826 557/1941 D/H Gac/Cac 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 deleterious(0) 16/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1025369497 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 10537461 10537461 C G 1 0 0 0 0 1 0 0 0 10035 826 29 4 4 MYH2 17 10537461 Missense_Mutation SNP C C3L-00080_T 84131 10537461 72719980 612 2710 MYH3 0 . GRCh38 17 10654945 10654945 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.120G>T p.= p.V40V ENST00000583535 3/41 738 304 434 621 620 1 strelka-varscan-mutect MYH3,synonymous_variant,p.=,ENST00000583535,NM_002470.3;CTC-297N7.1,downstream_gene_variant,,ENST00000569543,;MYH3,non_coding_transcript_exon_variant,,ENST00000582580,;MYH3,upstream_gene_variant,,ENST00000579489,; A ENST00000583535 Transcript synonymous_variant 208/6037 120/5823 40/1940 V gtG/gtT 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 3/41 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF427,Pfam_domain:PF02736 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 10654945 10654945 C A 1 0 0 0 0 0 0 0 1 10036 581 21 2 2 MYH3 17 10654945 Silent SNP C C3L-00080_T 117484 10654945 72602496 613 2711 MYOCD 0 . GRCh38 17 12763640 12763640 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2957G>T p.Trp986Leu p.W986L ENST00000425538 14/14 41 15 26 36 36 0 strelka-varscan-mutect MYOCD,missense_variant,p.Trp986Leu,ENST00000425538,NM_001146312.2;MYOCD,missense_variant,p.Trp648Leu,ENST00000443061,;MYOCD,missense_variant,p.Trp938Leu,ENST00000343344,NM_153604.3;RP11-1090M7.1,non_coding_transcript_exon_variant,,ENST00000584772,; T ENST00000425538 Transcript missense_variant 3157/8466 2957/2961 986/986 W/L tGg/tTg 1 1 MYOCD HGNC HGNC:16067 protein_coding YES CCDS54091.1 ENSP00000401678 Q8IZQ8 UPI000022A2E2 NM_001146312.2 deleterious(0) 14/14 hmmpanther:PTHR22793:SF11,hmmpanther:PTHR22793 MODERATE 1 SNV 1 1 PASS . . 0 196 14 0 0 0 0 0 -20 0.9999816 1 1 1 0 T 3 4 7 12763640 12763640 G T 1 0 0 0 0 1 0 0 0 10088 1362 47 2 2 MYOCD 17 12763640 Missense_Mutation SNP G C3L-00080_T 2108695 12763640 70493801 614 2712 CDRT15 0 . GRCh38 17 14236307 14236307 + Missense_Mutation SNP G G T rs760712390 C3L-00080_T C3L-00080_N G G c.386C>A p.Thr129Asn p.T129N ENST00000420162 2/3 183 95 88 114 114 0 strelka-varscan-mutect CDRT15,missense_variant,p.Thr129Asn,ENST00000420162,NM_001007530.1;CDRT15,missense_variant,p.Thr63Asn,ENST00000431716,; T ENST00000420162 Transcript missense_variant 402/766 386/567 129/188 T/N aCc/aAc rs760712390 1 -1 CDRT15 HGNC HGNC:14395 protein_coding YES CCDS32569.1 ENSP00000402355 Q96T59 UPI00000702CA NM_001007530.1 tolerated_low_confidence(0.07) 2/3 hmmpanther:PTHR16471,hmmpanther:PTHR16471:SF3 MODERATE 1 SNV 1 1 PASS rs760712390 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 14236307 14236307 G T 1 0 0 0 0 1 0 0 0 2880 1261 44 2 2 CDRT15 17 14236307 Missense_Mutation SNP G C3L-00080_T 1472667 14236307 69021134 615 2713 NCOR1 0 . GRCh38 17 16032297 16032297 + Nonstop_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.7322G>C p.Ter2441SerextTer15 p.*2441Sext*15 ENST00000268712 46/46 284 194 90 228 228 0 strelka-varscan-mutect NCOR1,stop_lost,p.Ter2441SerextTer15,ENST00000268712,NM_006311.3;NCOR1,stop_lost,p.Ter2344SerextTer15,ENST00000395857,;NCOR1,stop_lost,p.Ter2338SerextTer15,ENST00000395851,NM_001190440.1;NCOR1,stop_lost,p.Ter1072SerextTer15,ENST00000395849,;TTC19,intron_variant,,ENST00000470649,;TTC19,downstream_gene_variant,,ENST00000261647,NM_017775.3,NM_001271420.1;NCOR1,downstream_gene_variant,,ENST00000579573,;TTC19,downstream_gene_variant,,ENST00000497842,;NCOR1,non_coding_transcript_exon_variant,,ENST00000470782,;NCOR1,non_coding_transcript_exon_variant,,ENST00000464381,;NCOR1,non_coding_transcript_exon_variant,,ENST00000580617,;TTC19,downstream_gene_variant,,ENST00000481107,;TTC19,downstream_gene_variant,,ENST00000465567,;TTC19,downstream_gene_variant,,ENST00000475723,;NCOR1,downstream_gene_variant,,ENST00000582565,; G ENST00000268712 Transcript stop_lost 7580/10720 7322/7323 2441/2440 */S tGa/tCa 1 -1 NCOR1 HGNC HGNC:7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 A0A024RD47 UPI000013D7D5 NM_006311.3 46/46 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 7 16032297 16032297 C G 1 0 0 0 0 0 0 0 0 10254 837 29 4 4 NCOR1 17 16032297 Nonstop_Mutation SNP C C3L-00080_T 1795990 16032297 67225144 616 2714 SLC5A10 0 . GRCh38 17 18959636 18959636 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.321G>T p.= p.V107V ENST00000395647 4/15 343 152 191 311 311 0 strelka-varscan-mutect SLC5A10,synonymous_variant,p.=,ENST00000317977,NM_001282417.1;SLC5A10,synonymous_variant,p.=,ENST00000395647,NM_152351.4;SLC5A10,synonymous_variant,p.=,ENST00000395645,NM_001042450.2;SLC5A10,synonymous_variant,p.=,ENST00000417251,NM_001270649.1;SLC5A10,synonymous_variant,p.=,ENST00000395643,NM_001270648.1; T ENST00000395647 Transcript synonymous_variant 362/2140 321/1839 107/612 V gtG/gtT 1 1 SLC5A10 HGNC HGNC:23155 protein_coding YES CCDS11201.2 ENSP00000379008 A0PJK1 UPI00001401D2 NM_152351.4 4/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF128,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 18959636 18959636 G T 1 0 0 0 0 0 0 0 1 14945 1364 48 2 2 SLC5A10 17 18959636 Silent SNP G C3L-00080_T 2927339 18959636 64297805 617 2715 KRTAP4-2 0 . GRCh38 17 41177978 41177978 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.187C>A p.Pro63Thr p.P63T ENST00000377726 1/1 537 465 72 299 299 0 strelka-varscan-mutect KRTAP4-2,missense_variant,p.Pro63Thr,ENST00000377726,NM_033062.3; T ENST00000377726 Transcript missense_variant 231/763 187/411 63/136 P/T Ccc/Acc 1 -1 KRTAP4-2 HGNC HGNC:18900 protein_coding YES CCDS11384.1 ENSP00000366955 Q9BYR5 UPI0000246F2E NM_033062.3 deleterious(0.03) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF14,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS rs1183341790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 41177978 41177978 G T 1 0 0 0 0 1 0 0 0 8445 1232 43 2 2 KRTAP4-2 17 41177978 Missense_Mutation SNP G C3L-00080_T 22218342 41177978 42079463 618 2716 WNK4 0 . GRCh38 17 42784552 42784552 + Silent SNP C C G novel C3L-00080_T C3L-00080_N C C c.1143C>G p.= p.A381A ENST00000246914 4/19 647 515 132 448 448 0 strelka-varscan-mutect WNK4,synonymous_variant,p.=,ENST00000246914,NM_032387.4;VPS25,downstream_gene_variant,,ENST00000253794,NM_032353.3;WNK4,upstream_gene_variant,,ENST00000587705,;WNK4,synonymous_variant,p.=,ENST00000591448,NM_001321299.1;WNK4,upstream_gene_variant,,ENST00000592072,;WNK4,downstream_gene_variant,,ENST00000592669,; G ENST00000246914 Transcript synonymous_variant 1164/4001 1143/3732 381/1243 A gcC/gcG 1 1 WNK4 HGNC HGNC:14544 protein_coding YES CCDS11439.1 ENSP00000246914 Q96J92 UPI000006FC0F NM_032387.4 4/19 PROSITE_profiles:PS50011,hmmpanther:PTHR13902:SF52,hmmpanther:PTHR13902,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs1212608085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 7 42784552 42784552 C G 1 0 0 0 0 0 0 0 1 17936 639 23 4 4 WNK4 17 42784552 Silent SNP C C3L-00080_T 1606574 42784552 40472889 619 2717 SPPL2C 0 . GRCh38 17 45845129 45845130 + Frame_Shift_Ins INS - - C novel C3L-00080_T C3L-00080_N - - c.229dupC p.His77ProfsTer24 p.H77Pfs*24 ENST00000329196 1/1 144 122 22 108 108 0 sindel-varindel-pindel SPPL2C,frameshift_variant,p.His77ProfsTer24,ENST00000329196,NM_175882.2;MAPT-AS1,intron_variant,,ENST00000634876,;MAPT-AS1,intron_variant,,ENST00000579599,;MAPT-AS1,intron_variant,,ENST00000579244,;MAPT-AS1,upstream_gene_variant,,ENST00000581125,; C ENST00000329196 Transcript frameshift_variant 295-296/2238 223-224/2055 75/684 S/SX tcc/tCcc 1 1 SPPL2C HGNC HGNC:28902 protein_coding YES CCDS32673.1 ENSP00000332488 Q8IUH8 UPI0000EE80B4 NM_175882.2 1/1 hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF38 HIGH insertion 6 1 PASS . . 0 193 16 0 0 0 0 0 -20 0.9992895 1 1 1 0 C 7 5 7 45845129 45845129 - C 1 0 1 1 0 0 0 0 0 15443 1783 62 0 0 SPPL2C 17 45845129 Frame_Shift_Ins INS - C3L-00080_T 3060577 45845129 37412312 620 2718 NPEPPS 0 . GRCh38 17 47587345 47587345 + Splice_Site SNP G G T novel C3L-00080_T C3L-00080_N G G c.1095+1G>T p.X365_splice ENST00000322157 128 99 29 105 105 0 strelka-mutect NPEPPS,splice_donor_variant,,ENST00000322157,NM_006310.3;NPEPPS,splice_donor_variant,,ENST00000530173,;NPEPPS,splice_donor_variant,,ENST00000527964,;NPEPPS,splice_donor_variant,,ENST00000527360,;NPEPPS,downstream_gene_variant,,ENST00000525007,;NPEPPS,splice_donor_variant,,ENST00000525037,;NPEPPS,splice_donor_variant,,ENST00000534814,;NPEPPS,splice_donor_variant,,ENST00000602788,;NPEPPS,splice_donor_variant,,ENST00000530514,;NPEPPS,splice_donor_variant,,ENST00000527298,;NPEPPS,splice_donor_variant,,ENST00000533538,;NPEPPS,splice_donor_variant,,ENST00000525021,;NPEPPS,downstream_gene_variant,,ENST00000532729,;NPEPPS,downstream_gene_variant,,ENST00000527824,;NPEPPS,downstream_gene_variant,,ENST00000526247,;NPEPPS,downstream_gene_variant,,ENST00000534691,;NPEPPS,downstream_gene_variant,,ENST00000534727,;NPEPPS,upstream_gene_variant,,ENST00000529602,;NPEPPS,downstream_gene_variant,,ENST00000525401,; T ENST00000322157 Transcript splice_donor_variant -/4353 1095/2760 365/919 1 1 NPEPPS HGNC HGNC:7900 protein_coding YES CCDS45721.1 ENSP00000320324 P55786 UPI0000140D51 NM_006310.3 9/22 HIGH 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999817 1 1 1 0 T 5 4 7 47587345 47587345 G T 1 0 0 0 0 0 0 1 0 10623 1275 44 2 2 NPEPPS 17 47587345 Splice_Site SNP G C3L-00080_T 1742216 47587345 35670096 621 2719 SCRN2 0 . GRCh38 17 47839445 47839445 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.555G>T p.Gln185His p.Q185H ENST00000290216 4/8 274 233 41 186 184 2 strelka-varscan-mutect SCRN2,missense_variant,p.Gln185His,ENST00000407215,NM_001145023.1;SCRN2,missense_variant,p.Gln193His,ENST00000584123,;SCRN2,missense_variant,p.Gln185His,ENST00000290216,NM_138355.3;SCRN2,missense_variant,p.Gln51His,ENST00000584567,;LRRC46,downstream_gene_variant,,ENST00000269025,NM_033413.3;SCRN2,downstream_gene_variant,,ENST00000578323,;SCRN2,missense_variant,p.Gln185His,ENST00000581645,;SCRN2,splice_region_variant,,ENST00000582459,;SCRN2,splice_region_variant,,ENST00000579856,;SCRN2,splice_region_variant,,ENST00000583090,;SCRN2,splice_region_variant,,ENST00000582656,;LRRC46,downstream_gene_variant,,ENST00000584580,;SCRN2,downstream_gene_variant,,ENST00000581546,;SCRN2,downstream_gene_variant,,ENST00000578840,;LRRC46,downstream_gene_variant,,ENST00000579971,;LRRC46,downstream_gene_variant,,ENST00000584809,;LRRC46,downstream_gene_variant,,ENST00000579742,;SCRN2,downstream_gene_variant,,ENST00000580428,; A ENST00000290216 Transcript missense_variant,splice_region_variant 681/1548 555/1278 185/425 Q/H caG/caT 1 -1 SCRN2 HGNC HGNC:30381 protein_coding YES CCDS11519.1 ENSP00000290216 Q96FV2 UPI000013DFCB NM_138355.3 deleterious(0.04) 4/8 Pfam_domain:PF03577,hmmpanther:PTHR12994,hmmpanther:PTHR12994:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 47839445 47839445 C A 1 0 0 0 0 1 0 0 0 14209 695 24 2 2 SCRN2 17 47839445 Missense_Mutation SNP C C3L-00080_T 252100 47839445 35417996 622 2720 CACNA1G 0 . GRCh38 17 50617450 50617450 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.5034G>A p.= p.L1678L ENST00000359106 29/38 147 96 51 58 58 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CACNA1G,synonymous_variant,p.=,ENST00000506406,;CACNA1G,synonymous_variant,p.=,ENST00000504076,;CACNA1G,synonymous_variant,p.=,ENST00000511765,;CACNA1G,synonymous_variant,p.=,ENST00000503436,;CACNA1G,synonymous_variant,p.=,ENST00000511768,;CACNA1G,synonymous_variant,p.=,ENST00000503607,; A ENST00000359106 Transcript synonymous_variant 5034/7648 5034/7134 1678/2377 L ctG/ctA 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 29/38 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999988 1 1 1 0 A 2 1 7 50617450 50617450 G A 1 0 0 0 0 0 0 0 1 2232 1335 47 3 3 CACNA1G 17 50617450 Silent SNP G C3L-00080_T 2778005 50617450 32639991 623 2721 NOG 0 . GRCh38 17 56594829 56594829 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.606G>T p.= p.V202V ENST00000332822 1/1 124 65 59 84 84 0 strelka-varscan-mutect NOG,synonymous_variant,p.=,ENST00000332822,NM_005450.4; T ENST00000332822 Transcript synonymous_variant 1131/1892 606/699 202/232 V gtG/gtT 1 1 NOG HGNC HGNC:7866 protein_coding YES CCDS11589.1 ENSP00000328181 Q13253 UPI0000130342 NM_005450.4 1/1 Gene3D:2.10.90.10,Pfam_domain:PF05806,PIRSF_domain:PIRSF008129,hmmpanther:PTHR10494,hmmpanther:PTHR10494:SF5,Superfamily_domains:SSF57501 LOW 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 56594829 56594829 G T 1 0 0 0 0 0 0 0 1 10562 1306 46 2 2 NOG 17 56594829 Silent SNP G C3L-00080_T 5977379 56594829 26662612 624 2722 BRIP1 0 . GRCh38 17 61780288 61780288 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1908G>T p.Glu636Asp p.E636D ENST00000259008 13/20 178 88 90 229 229 0 strelka-varscan-mutect BRIP1,missense_variant,p.Glu636Asp,ENST00000259008,NM_032043.2;BRIP1,missense_variant,p.Glu636Asp,ENST00000577598,;BRIP1,upstream_gene_variant,,ENST00000584322,;BRIP1,upstream_gene_variant,,ENST00000583837,;BRIP1,3_prime_UTR_variant,,ENST00000579028,; A ENST00000259008 Transcript missense_variant 2176/6048 1908/3750 636/1249 E/D gaG/gaT 1 -1 BRIP1 HGNC HGNC:20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 A0A024QZ45 UPI000013D01F NM_032043.2 deleterious(0) 13/20 hmmpanther:PTHR11472:SF6,hmmpanther:PTHR11472,TIGRFAM_domain:TIGR00604 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 61780288 61780288 C A 1 0 0 0 0 1 0 0 0 1688 680 24 2 2 BRIP1 17 61780288 Missense_Mutation SNP C C3L-00080_T 5185459 61780288 21477153 625 2723 ACE 0 . GRCh38 17 63482610 63482610 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1263G>T p.= p.G421G ENST00000290866 8/25 291 166 125 205 204 1 strelka-varscan-mutect ACE,synonymous_variant,p.=,ENST00000428043,;ACE,synonymous_variant,p.=,ENST00000290866,NM_000789.3;ACE,upstream_gene_variant,,ENST00000290863,NM_152830.2;ACE,upstream_gene_variant,,ENST00000413513,NM_001178057.1;ACE,downstream_gene_variant,,ENST00000582627,;ACE,upstream_gene_variant,,ENST00000582761,;ACE,non_coding_transcript_exon_variant,,ENST00000584529,;ACE,downstream_gene_variant,,ENST00000583336,;ACE,3_prime_UTR_variant,,ENST00000582678,;CTD-2501B8.1,upstream_gene_variant,,ENST00000577647,;ACE,upstream_gene_variant,,ENST00000579314,;ACE,upstream_gene_variant,,ENST00000578839,;ACE,upstream_gene_variant,,ENST00000584865,;ACE,upstream_gene_variant,,ENST00000582005,;ACE,downstream_gene_variant,,ENST00000580318,;ACE,upstream_gene_variant,,ENST00000579726,;ACE,downstream_gene_variant,,ENST00000579462,;ACE,upstream_gene_variant,,ENST00000579204,; T ENST00000290866 Transcript synonymous_variant 1287/4959 1263/3921 421/1306 G ggG/ggT 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 8/25 Pfam_domain:PF01401,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999992 1 1 1 0 T 2 4 7 63482610 63482610 G T 1 0 0 0 0 0 0 0 1 174 1219 43 2 2 ACE 17 63482610 Silent SNP G C3L-00080_T 1702322 63482610 19774831 626 2724 KCNH6 0 . GRCh38 17 63543629 63543629 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2202C>A p.His734Gln p.H734Q ENST00000583023 10/14 211 184 27 184 184 0 strelka-varscan-mutect KCNH6,missense_variant,p.His734Gln,ENST00000583023,NM_030779.3;KCNH6,missense_variant,p.His734Gln,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,missense_variant,p.His681Gln,ENST00000581784,NM_173092.2;KCNH6,missense_variant,p.His681Gln,ENST00000456941,;KCNH6,3_prime_UTR_variant,,ENST00000583465,; A ENST00000583023 Transcript missense_variant 2213/3821 2202/2985 734/994 H/Q caC/caA 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 tolerated(0.61) 10/14 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 63543629 63543629 C A 1 0 0 0 0 1 0 0 0 7952 506 18 2 2 KCNH6 17 63543629 Missense_Mutation SNP C C3L-00080_T 61019 63543629 19713812 627 2725 CCDC47 0 . GRCh38 17 63766080 63766080 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.96A>G p.= p.V32V ENST00000225726 2/13 354 298 56 289 289 0 strelka-varscan-mutect CCDC47,synonymous_variant,p.=,ENST00000225726,NM_020198.2;CCDC47,synonymous_variant,p.=,ENST00000403162,;CCDC47,synonymous_variant,p.=,ENST00000582252,;CCDC47,upstream_gene_variant,,ENST00000612558,;CCDC47,downstream_gene_variant,,ENST00000580986,;CCDC47,non_coding_transcript_exon_variant,,ENST00000584112,;CCDC47,upstream_gene_variant,,ENST00000582331,; C ENST00000225726 Transcript synonymous_variant 479/3466 96/1452 32/483 V gtA/gtG 1 -1 CCDC47 HGNC HGNC:24856 protein_coding YES CCDS11643.1 ENSP00000225726 Q96A33 UPI000003B0A2 NM_020198.2 2/13 hmmpanther:PTHR12883,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 63766080 63766080 T C 1 0 0 0 0 0 0 0 1 2524 1509 53 5 5 CCDC47 17 63766080 Silent SNP T C3L-00080_T 222451 63766080 19491361 628 2726 SMURF2 0 . GRCh38 17 64580915 64580915 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.646A>T p.Asn216Tyr p.N216Y ENST00000262435 8/19 400 330 70 331 331 0 strelka-varscan-mutect SMURF2,missense_variant,p.Asn216Tyr,ENST00000262435,NM_022739.3;SMURF2,missense_variant,p.Asn203Tyr,ENST00000585301,;SMURF2,intron_variant,,ENST00000578200,;SMURF2,3_prime_UTR_variant,,ENST00000582081,;SMURF2,3_prime_UTR_variant,,ENST00000578386,; A ENST00000262435 Transcript missense_variant 834/2918 646/2247 216/748 N/Y Aat/Tat 1 -1 SMURF2 HGNC HGNC:16809 protein_coding YES CCDS32707.1 ENSP00000262435 Q9HAU4 UPI00001361C5 NM_022739.3 deleterious(0.01) 8/19 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 64580915 64580915 T A 1 0 0 0 0 1 0 0 0 15141 1841 64 4 4 SMURF2 17 64580915 Missense_Mutation SNP T C3L-00080_T 814835 64580915 18676526 629 2727 SDK2 0 . GRCh38 17 73435501 73435501 + Missense_Mutation SNP C C A rs148243066 C3L-00080_T C3L-00080_N C C c.1144G>T p.Ala382Ser p.A382S ENST00000392650 9/45 125 66 59 68 68 0 strelka-varscan-mutect SDK2,missense_variant,p.Ala382Ser,ENST00000392650,NM_001144952.1;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; A ENST00000392650 Transcript missense_variant 1145/10723 1144/6519 382/2172 A/S Gcc/Tcc rs148243066,COSM4883693,COSM4883694 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 deleterious(0.02) 9/45 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs148243066 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 73435501 73435501 C A 1 0 0 0 0 1 0 0 0 14244 768 27 1 1 SDK2 17 73435501 Missense_Mutation SNP C C3L-00080_T 8854586 73435501 9821940 630 2728 RNF157 0 . GRCh38 17 76158479 76158479 + Missense_Mutation SNP C C T rs201495655 C3L-00080_T C3L-00080_N C C c.1327G>A p.Val443Met p.V443M ENST00000269391 13/19 292 258 34 231 231 0 strelka-varscan-mutect RNF157,missense_variant,p.Val443Met,ENST00000269391,NM_052916.2;RNF157,missense_variant,p.Val443Met,ENST00000319945,;RNF157,downstream_gene_variant,,ENST00000591615,;RNF157,upstream_gene_variant,,ENST00000591355,;RP11-449J21.5,downstream_gene_variant,,ENST00000590137,;RP11-449J21.5,downstream_gene_variant,,ENST00000586661,;RP11-449J21.5,downstream_gene_variant,,ENST00000585542,;RP11-449J21.5,downstream_gene_variant,,ENST00000592748,;RNF157,non_coding_transcript_exon_variant,,ENST00000592869,;RNF157,downstream_gene_variant,,ENST00000593155,; T ENST00000269391 Transcript missense_variant 1460/4955 1327/2040 443/679 V/M Gtg/Atg rs201495655,COSM5656104,COSM5656105 1 -1 RNF157 HGNC HGNC:29402 protein_coding YES CCDS32740.1 ENSP00000269391 Q96PX1 UPI00001C1FDD NM_052916.2 tolerated_low_confidence(0.09) 13/19 hmmpanther:PTHR22996:SF1,hmmpanther:PTHR22996 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs201495655 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 76158479 76158479 C T 1 0 0 0 0 1 0 0 0 13632 536 19 1 1 RNF157 17 76158479 Missense_Mutation SNP C C3L-00080_T 2722978 76158479 7098962 631 2729 GAA 0 . GRCh38 17 80118298 80118298 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.2587G>T p.Glu863Ter p.E863* ENST00000302262 18/20 48 42 6 33 33 0 strelka-varscan-mutect GAA,stop_gained,p.Glu863Ter,ENST00000302262,NM_000152.3;GAA,stop_gained,p.Glu863Ter,ENST00000390015,NM_001079803.1,NM_001079804.1;GAA,non_coding_transcript_exon_variant,,ENST00000573556,;GAA,downstream_gene_variant,,ENST00000572080,; T ENST00000302262 Transcript stop_gained 2806/3626 2587/2859 863/952 E/* Gag/Tag 1 1 GAA HGNC HGNC:4065 protein_coding YES CCDS32760.1 ENSP00000305692 P10253 UPI00000744FF NM_000152.3 18/20 hmmpanther:PTHR22762:SF92,hmmpanther:PTHR22762 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -14.70521 1 1 1 1 0 T 4 4 7 80118298 80118298 G T 1 0 0 0 0 0 1 0 0 6018 943 33 2 2 GAA 17 80118298 Nonsense_Mutation SNP G C3L-00080_T 3959819 80118298 3139143 632 2730 AKAIN1 0 . GRCh38 18 5145621 5145621 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.151A>T p.Asn51Tyr p.N51Y ENST00000434239 2/2 177 102 75 178 178 0 strelka-varscan-mutect AKAIN1,missense_variant,p.Asn51Tyr,ENST00000434239,NM_001145194.1;AKAIN1,missense_variant,p.Asn58Tyr,ENST00000580650,; A ENST00000434239 Transcript missense_variant 323/575 151/210 51/69 N/Y Aac/Tac 1 -1 AKAIN1 HGNC HGNC:28285 protein_coding YES CCDS54179.1 ENSP00000399075 P0CW23 UPI0000201977 NM_001145194.1 deleterious_low_confidence(0.02) 2/2 hmmpanther:PTHR15934 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 5145621 5145621 T A 1 0 0 0 0 1 0 0 0 527 1812 63 4 4 AKAIN1 18 5145621 Missense_Mutation SNP T C3L-00080_T 5145621 75227664 633 2731 ARHGAP28 0 . GRCh38 18 6890540 6890540 + Silent SNP G G T rs371935284 C3L-00080_T C3L-00080_N G G c.1368G>T p.= p.R456R ENST00000419673 13/17 58 49 9 59 58 1 strelka-varscan-mutect ARHGAP28,synonymous_variant,p.=,ENST00000419673,NM_001010000.2;ARHGAP28,synonymous_variant,p.=,ENST00000314319,;ARHGAP28,synonymous_variant,p.=,ENST00000262227,;ARHGAP28,synonymous_variant,p.=,ENST00000383472,;ARHGAP28,synonymous_variant,p.=,ENST00000531294,;ARHGAP28,synonymous_variant,p.=,ENST00000532996,;ARHGAP28,downstream_gene_variant,,ENST00000579689,; T ENST00000419673 Transcript synonymous_variant 1585/5492 1368/1713 456/570 R cgG/cgT rs371935284 1 1 ARHGAP28 HGNC HGNC:25509 protein_coding YES CCDS32785.1 ENSP00000392660 Q9P2N2 UPI00004CEC5C NM_001010000.2 13/17 hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF5,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs371935284 . 0 200 10 0 0 0 0 0 -19.89071 0.9999841 1 1 1 0 T 2 4 7 6890540 6890540 G T 1 0 0 0 0 0 0 0 1 1002 1246 43 2 2 ARHGAP28 18 6890540 Silent SNP G C3L-00080_T 1744919 6890540 73482745 634 2732 LAMA1 0 . GRCh38 18 6948448 6948448 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.8665G>A p.Ala2889Thr p.A2889T ENST00000389658 60/63 529 432 97 487 487 0 strelka-varscan-mutect LAMA1,missense_variant,p.Ala2889Thr,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488064,;LAMA1,non_coding_transcript_exon_variant,,ENST00000492048,; T ENST00000389658 Transcript missense_variant 8759/9657 8665/9228 2889/3075 A/T Gcc/Acc 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 tolerated(0.34) 60/63 Gene3D:2.60.120.200,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 6948448 6948448 C T 1 0 0 0 0 1 0 0 0 8509 739 26 3 3 LAMA1 18 6948448 Missense_Mutation SNP C C3L-00080_T 57908 6948448 73424837 635 2733 PIEZO2 0 . GRCh38 18 10807211 10807211 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.981C>T p.= p.N327N ENST00000503781 8/52 242 219 23 160 160 0 strelka-varscan-mutect PIEZO2,synonymous_variant,p.=,ENST00000383408,;PIEZO2,synonymous_variant,p.=,ENST00000302079,;PIEZO2,synonymous_variant,p.=,ENST00000580640,;PIEZO2,synonymous_variant,p.=,ENST00000503781,NM_022068.3;PIEZO2,synonymous_variant,p.=,ENST00000579112,;PIEZO2,synonymous_variant,p.=,ENST00000582913,; A ENST00000503781 Transcript synonymous_variant 981/8259 981/8259 327/2752 N aaC/aaT 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 8/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 10807211 10807211 G A 1 0 0 0 0 0 0 0 1 11975 1252 44 3 3 PIEZO2 18 10807211 Silent SNP G C3L-00080_T 3858763 10807211 69566074 636 2734 PIEZO2 0 . GRCh38 18 10857001 10857001 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.703G>T p.Gly235Cys p.G235C ENST00000503781 6/52 283 244 39 219 219 0 varscan-mutect PIEZO2,missense_variant,p.Gly184Cys,ENST00000383408,;PIEZO2,missense_variant,p.Gly235Cys,ENST00000302079,;PIEZO2,missense_variant,p.Gly235Cys,ENST00000580640,;PIEZO2,missense_variant,p.Gly235Cys,ENST00000503781,NM_022068.3;PIEZO2,upstream_gene_variant,,ENST00000579112,;PIEZO2,downstream_gene_variant,,ENST00000579899,;PIEZO2,missense_variant,p.Gly235Cys,ENST00000582913,; A ENST00000503781 Transcript missense_variant,splice_region_variant 703/8259 703/8259 235/2752 G/C Ggc/Tgc 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 6/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 10857001 10857001 C A 1 0 0 0 0 1 0 0 0 11975 637 22 2 2 PIEZO2 18 10857001 Missense_Mutation SNP C C3L-00080_T 49790 10857001 69516284 637 2735 ANKRD30B 0 . GRCh38 18 14851569 14851569 + Nonsense_Mutation SNP G G T C3L-00080_T C3L-00080_N G G c.3268G>T p.Glu1090Ter p.E1090* ENST00000358984 36/36 79 34 45 89 89 0 strelka-varscan-mutect ANKRD30B,stop_gained,p.Glu1090Ter,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; T ENST00000358984 Transcript stop_gained 3448/4359 3268/4179 1090/1392 E/* Gaa/Taa COSM4542857 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 36/36 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 1 HIGH 1 SNV 1 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 14851569 14851569 G T 1 0 0 0 0 0 1 0 0 762 1175 41 2 2 ANKRD30B 18 14851569 Nonsense_Mutation SNP G C3L-00080_T 3994568 14851569 65521716 638 2736 1 2 3 3 250 N G_C_A 1.828257e-05 ANKRD30B 0 . GRCh38 18 14851708 14851708 + Missense_Mutation SNP C C A rs762515915 C3L-00080_T C3L-00080_N C C c.3407C>A p.Thr1136Lys p.T1136K ENST00000358984 36/36 204 157 47 154 153 1 strelka-varscan-mutect ANKRD30B,missense_variant,p.Thr1136Lys,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; A ENST00000358984 Transcript missense_variant 3587/4359 3407/4179 1136/1392 T/K aCa/aAa rs762515915 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 deleterious(0.03) 36/36 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS rs762515915 . 0 197 10 3 0 0 0 0 -20 0.9989792 1 1 1 0 A 3 1 7 14851708 14851708 C A 1 0 0 0 0 1 0 0 0 762 478 17 2 2 ANKRD30B 18 14851708 Missense_Mutation SNP C C3L-00080_T 139 14851708 65521577 639 2737 1 2 3 3 250 N G_C_A 1.828257e-05 ANKRD30B 0 . GRCh38 18 14851818 14851818 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.3517A>C p.Thr1173Pro p.T1173P ENST00000358984 36/36 184 92 92 129 129 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Thr1173Pro,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; C ENST00000358984 Transcript missense_variant 3697/4359 3517/4179 1173/1392 T/P Aca/Cca 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 deleterious(0) 36/36 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 14851818 14851818 A C 1 0 0 0 0 1 0 0 0 762 275 10 5 5 ANKRD30B 18 14851818 Missense_Mutation SNP A C3L-00080_T 110 14851818 65521467 640 2738 1 2 3 3 250 N G_C_A 1.828257e-05 DSG3 0 . GRCh38 18 31475662 31475662 + Missense_Mutation SNP C C T rs745351504 C3L-00080_T C3L-00080_N C C c.2402C>T p.Ala801Val p.A801V ENST00000257189 16/16 241 228 13 107 106 1 strelka-varscan-mutect DSG3,missense_variant,p.Ala801Val,ENST00000257189,NM_001944.2; T ENST00000257189 Transcript missense_variant 2485/5525 2402/3000 801/999 A/V gCg/gTg rs745351504 1 1 DSG3 HGNC HGNC:3050 protein_coding YES CCDS11898.1 ENSP00000257189 P32926 UPI000013CF4B NM_001944.2 deleterious(0) 16/16 Gene3D:4.10.900.10,Prints_domain:PR01819,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF3 MODERATE 1 SNV 1 1 PASS rs745351504 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 31475662 31475662 C T 1 0 0 0 0 1 0 0 0 4599 768 27 1 1 DSG3 18 31475662 Missense_Mutation SNP C C3L-00080_T 16623844 31475662 48897623 641 2739 SETBP1 0 . GRCh38 18 45063555 45063555 + Frame_Shift_Del DEL G G - novel C3L-00080_T C3L-00080_N G G c.4649delG p.Gly1550AlafsTer30 p.G1550Afs*30 ENST00000282030 6/6 394 36 358 33 33 0 sindel-varindel-pindel SETBP1,frameshift_variant,p.Gly1550AlafsTer30,ENST00000282030,NM_015559.2; - ENST00000282030 Transcript frameshift_variant 4944/9899 4648/4791 1550/1596 G/X Ggc/gc 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 6/6 HIGH 1 deletion 1 1 1 PASS . . 0 193 16 0 0 0 0 0 -20 0.9999724 1 1 1 0 - 7 5 7 45063555 45063555 G - 1 0 1 0 1 0 0 0 0 14406 1000 35 0 0 SETBP1 18 45063555 Frame_Shift_Del DEL G C3L-00080_T 13587893 45063555 35309730 642 2740 LOXHD1 0 . GRCh38 18 46533236 46533236 + Frame_Shift_Del DEL T T - novel C3L-00080_T C3L-00080_N T T c.968delA p.Asp323AlafsTer8 p.D323Afs*8 ENST00000300591 10/24 235 187 48 256 256 0 sindel-varindel-pindel LOXHD1,frameshift_variant,p.Asp1434AlafsTer8,ENST00000536736,NM_144612.6;LOXHD1,frameshift_variant,p.Asp1228AlafsTer8,ENST00000441551,;LOXHD1,frameshift_variant,p.Asp323AlafsTer8,ENST00000300591,NM_001145472.2;LOXHD1,frameshift_variant,p.Asp323AlafsTer8,ENST00000582408,;LOXHD1,frameshift_variant,p.Asp227AlafsTer8,ENST00000579038,NM_001308013.1;LOXHD1,3_prime_UTR_variant,,ENST00000536111,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; - ENST00000300591 Transcript frameshift_variant 1382/3970 968/3345 323/1114 D/X gAc/gc 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 10/24 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 46533236 46533236 T - 1 0 1 0 1 0 0 0 0 8801 1667 58 0 0 LOXHD1 18 46533236 Frame_Shift_Del DEL T C3L-00080_T 1469681 46533236 33840049 643 2741 LOXHD1 0 . GRCh38 18 46656913 46656913 + Nonsense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.121A>T p.Lys41Ter p.K41* ENST00000536736 1/40 88 69 19 110 110 0 strelka-varscan-mutect LOXHD1,stop_gained,p.Lys41Ter,ENST00000536736,NM_144612.6;LOXHD1,stop_gained,p.Lys41Ter,ENST00000441551,; A ENST00000536736 Transcript stop_gained 121/6848 121/6636 41/2211 K/* Aag/Tag 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 1/40 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137,Superfamily_domains:SSF49723 HIGH 1 SNV 5 1 PASS rs1309898946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 46656913 46656913 T A 1 0 0 0 0 0 1 0 0 8801 1821 63 4 4 LOXHD1 18 46656913 Nonsense_Mutation SNP T C3L-00080_T 123677 46656913 33716372 644 2742 ZBTB7C 0 . GRCh38 18 48040990 48040990 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.118G>T p.Val40Leu p.V40L ENST00000588982 3/4 163 140 23 188 187 1 strelka-varscan-mutect ZBTB7C,missense_variant,p.Val40Leu,ENST00000588982,;ZBTB7C,missense_variant,p.Val40Leu,ENST00000590800,;ZBTB7C,missense_variant,p.Val40Leu,ENST00000586438,;ZBTB7C,missense_variant,p.Val40Leu,ENST00000535628,NM_001039360.2;ZBTB7C,missense_variant,p.Val40Leu,ENST00000590437,;ZBTB7C,downstream_gene_variant,,ENST00000589170,;ZBTB7C,downstream_gene_variant,,ENST00000589194,;ZBTB7C,downstream_gene_variant,,ENST00000587107,;ZBTB7C,downstream_gene_variant,,ENST00000592656,;ZBTB7C,downstream_gene_variant,,ENST00000590374,;ZBTB7C,downstream_gene_variant,,ENST00000585404,;ZBTB7C,downstream_gene_variant,,ENST00000588970,;ZBTB7C,downstream_gene_variant,,ENST00000588053,;ZBTB7C,downstream_gene_variant,,ENST00000590178,;ZBTB7C,downstream_gene_variant,,ENST00000590855,;ZBTB7C,downstream_gene_variant,,ENST00000589619,;ZBTB7C,downstream_gene_variant,,ENST00000586743,;ZBTB7C,downstream_gene_variant,,ENST00000593159,;ZBTB7C,downstream_gene_variant,,ENST00000588028,;ZBTB7C,downstream_gene_variant,,ENST00000588149,;ZBTB7C,downstream_gene_variant,,ENST00000591526,;ZBTB7C,downstream_gene_variant,,ENST00000591279,;ZBTB7C,downstream_gene_variant,,ENST00000588566,;ZBTB7C,downstream_gene_variant,,ENST00000589077,;ZBTB7C,downstream_gene_variant,,ENST00000591405,;ZBTB7C,downstream_gene_variant,,ENST00000592387,;ZBTB7C,downstream_gene_variant,,ENST00000586525,;ZBTB7C,downstream_gene_variant,,ENST00000586047,; A ENST00000588982 Transcript missense_variant 620/4949 118/1860 40/619 V/L Gtg/Ttg 1 -1 ZBTB7C HGNC HGNC:31700 protein_coding YES CCDS32830.1 ENSP00000468782 A1YPR0 B2RG49 UPI0000073FE3 deleterious(0) 3/4 PROSITE_profiles:PS50097,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF250,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 48040990 48040990 C A 1 0 0 0 0 1 0 0 0 18125 507 18 2 2 ZBTB7C 18 48040990 Missense_Mutation SNP C C3L-00080_T 1384077 48040990 32332295 645 2743 ALPK2 0 . GRCh38 18 58535575 58535575 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.4612A>T p.Thr1538Ser p.T1538S ENST00000361673 5/13 176 127 49 167 167 0 strelka-varscan-mutect ALPK2,missense_variant,p.Thr1538Ser,ENST00000361673,NM_052947.3;RP11-1151B14.4,splice_region_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; A ENST00000361673 Transcript missense_variant 4826/7303 4612/6513 1538/2170 T/S Act/Tct 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(0.24) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 58535575 58535575 T A 1 0 0 0 0 1 0 0 0 645 1696 59 4 4 ALPK2 18 58535575 Missense_Mutation SNP T C3L-00080_T 10494585 58535575 21837710 646 2744 CDH7 0 . GRCh38 18 65822235 65822235 + Silent SNP T T C novel C3L-00080_T C3L-00080_N T T c.780T>C p.= p.P260P ENST00000397968 5/12 155 96 59 172 172 0 strelka-varscan-mutect CDH7,synonymous_variant,p.=,ENST00000397968,NM_004361.2;CDH7,synonymous_variant,p.=,ENST00000536984,NM_001317214.1;CDH7,synonymous_variant,p.=,ENST00000323011,NM_033646.1; C ENST00000397968 Transcript synonymous_variant 1206/12231 780/2358 260/785 P ccT/ccC 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 5/12 Gene3D:2.60.40.60,Prints_domain:PR00205,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 7 65822235 65822235 T C 1 0 0 0 0 0 0 0 1 2818 1538 54 5 5 CDH7 18 65822235 Silent SNP T C3L-00080_T 7286660 65822235 14551050 647 2745 DSEL 0 . GRCh38 18 67514052 67514052 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.587A>T p.Asn196Ile p.N196I ENST00000310045 2/2 126 83 43 148 148 0 strelka-varscan-mutect DSEL,missense_variant,p.Asn196Ile,ENST00000310045,NM_032160.2;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,downstream_gene_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,; A ENST00000310045 Transcript missense_variant 2061/9531 587/3669 196/1222 N/I aAc/aTc 1 -1 DSEL HGNC HGNC:18144 protein_coding YES CCDS11995.1 ENSP00000310565 Q8IZU8 UPI00000740A1 NM_032160.2 tolerated(0.08) 2/2 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 67514052 67514052 T A 1 0 0 0 0 1 0 0 0 4596 1725 60 4 4 DSEL 18 67514052 Missense_Mutation SNP T C3L-00080_T 1691817 67514052 12859233 648 2746 RTTN 0 . GRCh38 18 70150650 70150650 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.2013G>T p.= p.L671L ENST00000255674 15/49 159 138 21 200 199 1 strelka-varscan-mutect RTTN,synonymous_variant,p.=,ENST00000255674,NM_173630.3;RTTN,non_coding_transcript_exon_variant,,ENST00000584659,;RTTN,synonymous_variant,p.=,ENST00000583043,;RTTN,3_prime_UTR_variant,,ENST00000581161,NM_001318520.1; A ENST00000255674 Transcript synonymous_variant 2300/7326 2013/6681 671/2226 L ctG/ctT 1 -1 RTTN HGNC HGNC:18654 protein_coding YES CCDS42443.1 ENSP00000255674 Q86VV8 UPI0000201E92 NM_173630.3 15/49 hmmpanther:PTHR31691,hmmpanther:PTHR31691:SF1,Superfamily_domains:SSF48371 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 70150650 70150650 C A 1 0 0 0 0 0 0 0 1 13998 465 17 2 2 RTTN 18 70150650 Silent SNP C C3L-00080_T 2636598 70150650 10222635 649 2747 NETO1 0 . GRCh38 18 72783743 72783743 + Missense_Mutation SNP C C T rs370635787 C3L-00080_T C3L-00080_N C C c.803G>A p.Arg268His p.R268H ENST00000327305 7/11 386 330 56 426 426 0 strelka-varscan-mutect NETO1,missense_variant,p.Arg268His,ENST00000327305,NM_138966.3;NETO1,missense_variant,p.Arg268His,ENST00000583169,NM_001201465.1;NETO1,downstream_gene_variant,,ENST00000579730,; T ENST00000327305 Transcript missense_variant 1461/3058 803/1602 268/533 R/H cGc/cAc rs370635787,COSM283212 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 deleterious(0) 7/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs370635787 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 72783743 72783743 C T 1 0 0 0 0 1 0 0 0 10374 768 27 1 1 NETO1 18 72783743 Missense_Mutation SNP C C3L-00080_T 2633093 72783743 7589542 650 2748 CNDP1 0 . GRCh38 18 74559336 74559336 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.167G>T p.Trp56Leu p.W56L ENST00000358821 3/12 456 390 66 455 455 0 strelka-varscan-mutect CNDP1,missense_variant,p.Trp13Leu,ENST00000582365,;CNDP1,missense_variant,p.Trp56Leu,ENST00000358821,NM_032649.5;RP11-231E4.3,downstream_gene_variant,,ENST00000583702,;CNDP1,non_coding_transcript_exon_variant,,ENST00000585136,;CNDP1,upstream_gene_variant,,ENST00000584316,; T ENST00000358821 Transcript missense_variant 395/2215 167/1524 56/507 W/L tGg/tTg 1 1 CNDP1 HGNC HGNC:20675 protein_coding YES CCDS12007.1 ENSP00000351682 Q96KN2 UPI00000463FC NM_032649.5 tolerated(0.07) 3/12 Gene3D:3.40.630.10,PIRSF_domain:PIRSF037242,hmmpanther:PTHR11014,hmmpanther:PTHR11014:SF58,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 74559336 74559336 G T 1 0 0 0 0 1 0 0 0 3372 1357 47 2 2 CNDP1 18 74559336 Missense_Mutation SNP G C3L-00080_T 1775593 74559336 5813949 651 2749 ATP9B 0 . GRCh38 18 79345573 79345573 + Splice_Site SNP G G T novel C3L-00080_T C3L-00080_N G G c.2617+1G>T p.X873_splice ENST00000426216 91 77 14 77 77 0 strelka-varscan-mutect ATP9B,splice_donor_variant,,ENST00000426216,NM_198531.3;ATP9B,splice_donor_variant,,ENST00000307671,NM_001306085.1;ATP9B,intron_variant,,ENST00000458297,;RP11-800A18.4,upstream_gene_variant,,ENST00000592906,;ATP9B,splice_donor_variant,,ENST00000490210,;ATP9B,splice_donor_variant,,ENST00000590477,;ATP9B,splice_donor_variant,,ENST00000586774,;ATP9B,upstream_gene_variant,,ENST00000588921,;ATP9B,upstream_gene_variant,,ENST00000589951,;ATP9B,downstream_gene_variant,,ENST00000588895,; T ENST00000426216 Transcript splice_donor_variant -/4361 2617/3444 873/1147 1 1 ATP9B HGNC HGNC:13541 protein_coding YES CCDS12014.1 ENSP00000398076 O43861 UPI00002371AF NM_198531.3 22/29 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 7 79345573 79345573 G T 1 0 0 0 0 0 0 1 0 1352 1275 44 2 2 ATP9B 18 79345573 Splice_Site SNP G C3L-00080_T 4786237 79345573 1027712 652 2750 NFATC1 0 . GRCh38 18 79448875 79448875 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1480G>T p.Val494Leu p.V494L ENST00000427363 4/10 461 379 82 375 374 1 strelka-varscan-mutect NFATC1,missense_variant,p.Val494Leu,ENST00000591814,NM_172390.2;NFATC1,missense_variant,p.Val494Leu,ENST00000253506,NM_006162.4;NFATC1,missense_variant,p.Val481Leu,ENST00000329101,NM_172387.2;NFATC1,missense_variant,p.Val481Leu,ENST00000318065,NM_172389.2;NFATC1,missense_variant,p.Val22Leu,ENST00000545796,NM_001278673.1;NFATC1,missense_variant,p.Val22Leu,ENST00000397790,NM_172388.2;NFATC1,missense_variant,p.Val494Leu,ENST00000427363,NM_001278669.1;NFATC1,missense_variant,p.Val481Leu,ENST00000592223,NM_001278675.1;NFATC1,missense_variant,p.Val494Leu,ENST00000587635,;NFATC1,missense_variant,p.Val494Leu,ENST00000542384,NM_001278670.1;NFATC1,missense_variant,p.Val481Leu,ENST00000586434,NM_001278672.1;NFATC1,non_coding_transcript_exon_variant,,ENST00000590224,;NFATC1,3_prime_UTR_variant,,ENST00000590313,;NFATC1,non_coding_transcript_exon_variant,,ENST00000591065,;NFATC1,upstream_gene_variant,,ENST00000591089,; T ENST00000427363 Transcript missense_variant 1480/2832 1480/2832 494/943 V/L Gtg/Ttg 1 1 NFATC1 HGNC HGNC:7775 protein_coding YES CCDS62467.1 ENSP00000389377 O95644 UPI000012FFB5 NM_001278669.1 deleterious(0.03) 4/10 PROSITE_profiles:PS50254,hmmpanther:PTHR12533:SF5,hmmpanther:PTHR12533,Gene3D:2.60.40.340,Pfam_domain:PF00554,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 79448875 79448875 G T 1 0 0 0 0 1 0 0 0 10398 1261 44 2 2 NFATC1 18 79448875 Missense_Mutation SNP G C3L-00080_T 103302 79448875 924410 653 2751 C2CD4C 0 . GRCh38 19 407274 407274 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.1088T>A p.Val363Glu p.V363E ENST00000332235 2/2 134 69 65 167 167 0 strelka-varscan-mutect C2CD4C,missense_variant,p.Val363Glu,ENST00000332235,NM_001136263.1; T ENST00000332235 Transcript missense_variant 1293/3129 1088/1266 363/421 V/E gTg/gAg 1 -1 C2CD4C HGNC HGNC:29417 protein_coding YES CCDS45890.1 ENSP00000328677 Q8TF44 UPI00001C2016 NM_001136263.1 deleterious(0) 2/2 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF116,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 407274 407274 A T 1 0 0 0 0 1 0 0 0 2028 159 6 4 4 C2CD4C 19 407274 Missense_Mutation SNP A C3L-00080_T 407274 58210342 654 2752 ODF3L2 0 . GRCh38 19 467742 467742 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.256C>A p.Pro86Thr p.P86T ENST00000315489 3/4 82 38 44 91 91 0 strelka-varscan-mutect ODF3L2,missense_variant,p.Pro86Thr,ENST00000315489,NM_182577.2;ODF3L2,missense_variant,p.Pro50Thr,ENST00000382696,;ODF3L2,non_coding_transcript_exon_variant,,ENST00000591681,; T ENST00000315489 Transcript missense_variant 492/1604 256/870 86/289 P/T Ccg/Acg 1 -1 ODF3L2 HGNC HGNC:26841 protein_coding YES CCDS12027.1 ENSP00000318029 Q3SX64 UPI0000072898 NM_182577.2 deleterious(0) 3/4 Prints_domain:PR01217,hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF0 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 7 467742 467742 G T 1 0 0 0 0 1 0 0 0 10910 1232 43 2 2 ODF3L2 19 467742 Missense_Mutation SNP G C3L-00080_T 60468 467742 58149874 655 2753 ABCA7 0 . GRCh38 19 1047597 1047597 + Silent SNP C C T C3L-00080_T C3L-00080_N C C c.2212C>T p.= p.L738L ENST00000263094 16/47 195 114 81 164 164 0 strelka-varscan-mutect ABCA7,synonymous_variant,p.=,ENST00000263094,NM_019112.3;ABCA7,synonymous_variant,p.=,ENST00000433129,;ABCA7,synonymous_variant,p.=,ENST00000435683,;ABCA7,downstream_gene_variant,,ENST00000533574,;ABCA7,downstream_gene_variant,,ENST00000526885,; T ENST00000263094 Transcript synonymous_variant 2443/6816 2212/6441 738/2146 L Ctg/Ttg COSM1398373 1 1 ABCA7 HGNC HGNC:37 protein_coding YES CCDS12055.1 ENSP00000263094 Q8IZY2 UPI000013D3A4 NM_019112.3 16/47 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF49,Low_complexity_(Seg):seg 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 1047597 1047597 C T 1 0 0 0 0 0 0 0 1 41 796 28 3 3 ABCA7 19 1047597 Silent SNP C C3L-00080_T 579855 1047597 57570019 656 2754 DIRAS1 0 . GRCh38 19 2717231 2717248 + In_Frame_Del DEL CTTGACGCGGTCTGTCCT CTTGACGCGGTCTGTCCT - novel C3L-00080_T C3L-00080_N CTTGACGCGGTCTGTCCT CTTGACGCGGTCTGTCCT c.559_576delAGGACAGACCGCGTCAAG p.Arg187_Lys192del p.R187_K192del ENST00000323469 2/2 52 35 17 66 66 0 sindel-varindel-pindel DIRAS1,inframe_deletion,p.Arg187_Lys192del,ENST00000323469,NM_145173.3;DIRAS1,inframe_deletion,p.Arg187_Lys192del,ENST00000585334,;DIRAS1,downstream_gene_variant,,ENST00000588128,;AC006538.4,downstream_gene_variant,,ENST00000586572,; - ENST00000323469 Transcript inframe_deletion 743-760/3424 559-576/597 187-192/198 RTDRVK/- AGGACAGACCGCGTCAAG/- 1 -1 DIRAS1 HGNC HGNC:19127 protein_coding YES CCDS12092.1 ENSP00000325836 O95057 UPI000000D876 NM_145173.3 2/2 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF213 MODERATE 1 deletion 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 7 2717231 2717231 CTTGACGCGGTCTGTCCT - 1 0 1 0 1 0 0 0 0 4335 680 24 0 0 DIRAS1 19 2717231 In_Frame_Del DEL CTTGACGCGGTCTGTCCT C3L-00080_T 1669634 2717231 55900385 657 2755 DOHH 0 . GRCh38 19 3491581 3491581 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.820G>T p.Glu274Ter p.E274* ENST00000427575 5/5 420 236 184 423 420 3 strelka-varscan-mutect DOHH,stop_gained,p.Glu274Ter,ENST00000427575,NM_001145165.1;DOHH,stop_gained,p.Glu274Ter,ENST00000250937,NM_031304.4;DOHH,downstream_gene_variant,,ENST00000592858,;DOHH,downstream_gene_variant,,ENST00000587122,;DOHH,non_coding_transcript_exon_variant,,ENST00000586906,; A ENST00000427575 Transcript stop_gained 1272/2031 820/909 274/302 E/* Gag/Tag 1 -1 DOHH HGNC HGNC:28662 protein_coding YES CCDS12108.1 ENSP00000398882 Q9BU89 UPI0000071C59 NM_001145165.1 5/5 HAMAP:MF_03101,hmmpanther:PTHR12697,Pfam_domain:PF13646,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 3 1 PASS rs1241296124 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 7 3491581 3491581 C A 1 0 0 0 0 0 1 0 0 4510 893 31 1 1 DOHH 19 3491581 Nonsense_Mutation SNP C C3L-00080_T 774350 3491581 55126035 658 2756 SAFB 0 . GRCh38 19 5641909 5641909 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.509A>G p.Glu170Gly p.E170G ENST00000588852 4/21 245 184 61 270 270 0 strelka-varscan-mutect SAFB,missense_variant,p.Glu170Gly,ENST00000292123,NM_001320572.1,NM_002967.3;SAFB,missense_variant,p.Glu170Gly,ENST00000592224,NM_001201339.1;SAFB,missense_variant,p.Glu170Gly,ENST00000588852,NM_001201338.1;SAFB,intron_variant,,ENST00000454510,NM_001201340.1;SAFB,non_coding_transcript_exon_variant,,ENST00000586934,;SAFB,non_coding_transcript_exon_variant,,ENST00000590485,;SAFB,intron_variant,,ENST00000589863,NM_001320571.1;SAFB,intron_variant,,ENST00000591666,; G ENST00000588852 Transcript missense_variant 562/2842 509/2754 170/917 E/G gAa/gGa 1 1 SAFB HGNC HGNC:10520 protein_coding YES CCDS59339.1 ENSP00000467423 Q15424 UPI0000E5BE82 NM_001201338.1 deleterious(0.01) 4/21 hmmpanther:PTHR15683:SF6,hmmpanther:PTHR15683 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 5641909 5641909 A G 1 0 0 0 0 1 0 0 0 14065 246 9 5 5 SAFB 19 5641909 Missense_Mutation SNP A C3L-00080_T 2150328 5641909 52975707 659 2757 CATSPERD 0 . GRCh38 19 5751785 5751785 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1126C>A p.Leu376Ile p.L376I ENST00000381624 12/22 121 58 63 112 112 0 strelka-varscan-mutect CATSPERD,missense_variant,p.Leu376Ile,ENST00000381624,NM_152784.3;CATSPERD,upstream_gene_variant,,ENST00000309164,; A ENST00000381624 Transcript missense_variant 1187/2516 1126/2397 376/798 L/I Ctt/Att 1 1 CATSPERD HGNC HGNC:28598 protein_coding YES CCDS12149.2 ENSP00000371037 Q86XM0 UPI000059D641 NM_152784.3 tolerated(0.9) 12/22 Pfam_domain:PF15020,hmmpanther:PTHR33722,hmmpanther:PTHR33722:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 5751785 5751785 C A 1 0 0 0 0 1 0 0 0 2392 797 28 2 2 CATSPERD 19 5751785 Missense_Mutation SNP C C3L-00080_T 109876 5751785 52865831 660 2758 ZNF557 0 . GRCh38 19 7083047 7083047 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.596A>G p.Lys199Arg p.K199R ENST00000252840 8/8 131 63 68 146 145 1 strelka-varscan-mutect ZNF557,missense_variant,p.Lys192Arg,ENST00000414706,NM_001044388.1;ZNF557,missense_variant,p.Lys199Arg,ENST00000252840,NM_024341.2,NM_001044387.1; G ENST00000252840 Transcript missense_variant 1097/2268 596/1293 199/430 K/R aAg/aGg 1 1 ZNF557 HGNC HGNC:28632 protein_coding YES CCDS42485.1 ENSP00000252840 Q8N988 UPI000020324B NM_024341.2,NM_001044387.1 tolerated(0.06) 8/8 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF145,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 7083047 7083047 A G 1 0 0 0 0 1 0 0 0 18562 72 3 5 5 ZNF557 19 7083047 Missense_Mutation SNP A C3L-00080_T 1331262 7083047 51534569 661 2759 ZNF699 0 . GRCh38 19 9297425 9297425 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.341G>C p.Gly114Ala p.G114A ENST00000591998 5/6 84 64 20 143 143 0 strelka-varscan-mutect ZNF699,missense_variant,p.Gly114Ala,ENST00000591998,;ZNF699,missense_variant,p.Gly114Ala,ENST00000308650,NM_198535.1;CTC-325H20.4,downstream_gene_variant,,ENST00000591336,; G ENST00000591998 Transcript missense_variant 570/3358 341/1929 114/642 G/A gGa/gCa 1 -1 ZNF699 HGNC HGNC:24750 protein_coding YES CCDS42495.1 ENSP00000467723 Q32M78 UPI00001D825F tolerated(0.11) 5/6 hmmpanther:PTHR24377:SF132,hmmpanther:PTHR24377 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 9297425 9297425 C G 1 0 0 0 0 1 0 0 0 18674 855 30 4 4 ZNF699 19 9297425 Missense_Mutation SNP C C3L-00080_T 2214378 9297425 49320191 662 2760 OLFM2 0 . GRCh38 19 9857342 9857342 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.501G>A p.Met167Ile p.M167I ENST00000264833 4/6 328 186 142 343 342 1 strelka-varscan-mutect OLFM2,missense_variant,p.Met167Ile,ENST00000264833,NM_058164.3;OLFM2,missense_variant,p.Met89Ile,ENST00000590841,NM_001304348.1;OLFM2,missense_variant,p.Met191Ile,ENST00000593091,NM_001304347.1;OLFM2,non_coding_transcript_exon_variant,,ENST00000590410,;OLFM2,intron_variant,,ENST00000592448,; T ENST00000264833 Transcript missense_variant 687/2019 501/1365 167/454 M/I atG/atA 1 -1 OLFM2 HGNC HGNC:17189 protein_coding YES CCDS12221.1 ENSP00000264833 O95897 UPI000013D57B NM_058164.3 tolerated(1) 4/6 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 9857342 9857342 C T 1 0 0 0 0 1 0 0 0 10928 594 21 3 3 OLFM2 19 9857342 Missense_Mutation SNP C C3L-00080_T 559917 9857342 48760274 663 2761 COL5A3 0 . GRCh38 19 9977282 9977282 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.3235G>A p.Gly1079Arg p.G1079R ENST00000264828 44/67 179 96 83 172 172 0 strelka-varscan-mutect COL5A3,missense_variant,p.Gly1079Arg,ENST00000264828,NM_015719.3; T ENST00000264828 Transcript missense_variant,splice_region_variant 3321/6174 3235/5238 1079/1745 G/R Ggg/Agg 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 deleterious(0) 44/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 9977282 9977282 C T 1 0 0 0 0 1 0 0 0 3487 637 22 3 3 COL5A3 19 9977282 Missense_Mutation SNP C C3L-00080_T 119940 9977282 48640334 664 2762 RDH8 0 . GRCh38 19 10021591 10021591 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.838C>T p.Arg280Cys p.R280C ENST00000591589 6/6 266 224 42 306 306 0 strelka-mutect RDH8,missense_variant,p.Arg280Cys,ENST00000591589,NM_015725.2;RDH8,synonymous_variant,p.=,ENST00000587782,;RDH8,downstream_gene_variant,,ENST00000589570,; T ENST00000591589 Transcript missense_variant 1027/1715 838/996 280/331 R/C Cgc/Tgc 1 1 RDH8 HGNC HGNC:14423 protein_coding YES CCDS12223.2 ENSP00000466058 K7ELF7 UPI000059D661 NM_015725.2 tolerated(0.18) 6/6 PIRSF_domain:PIRSF000095 MODERATE 1 SNV 1 1 PASS rs1330743396 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 10021591 10021591 C T 1 0 0 0 0 1 0 0 0 13365 652 23 1 1 RDH8 19 10021591 Missense_Mutation SNP C C3L-00080_T 44309 10021591 48596025 665 2763 KANK2 0 . GRCh38 19 11176641 11176641 + Missense_Mutation SNP C C A rs111233026 C3L-00080_T C3L-00080_N C C c.1721G>T p.Arg574Leu p.R574L ENST00000589359 7/13 126 102 24 109 108 1 strelka-varscan-mutect KANK2,missense_variant,p.Arg566Leu,ENST00000586659,NM_001136191.2;KANK2,missense_variant,p.Arg574Leu,ENST00000589359,NM_015493.6;KANK2,missense_variant,p.Arg566Leu,ENST00000589894,;KANK2,upstream_gene_variant,,ENST00000588787,; A ENST00000589359 Transcript missense_variant 2189/3048 1721/2580 574/859 R/L cGa/cTa rs111233026 1 -1 KANK2 HGNC HGNC:29300 protein_coding YES CCDS54219.1 ENSP00000468002 Q63ZY3 UPI00003B5C5D NM_015493.6 tolerated(0.33) 7/13 hmmpanther:PTHR24168:SF0,hmmpanther:PTHR24168 MODERATE 1 SNV 5 1 PASS rs111233026 . 0 203 5 2 0 0 0 0 -20 0.9999753 1 1 1 0 A 3 1 7 11176641 11176641 C A 1 0 0 0 0 1 0 0 0 7886 884 31 1 1 KANK2 19 11176641 Missense_Mutation SNP C C3L-00080_T 1155050 11176641 47440975 666 2764 OR1I1 0 . GRCh38 19 15087500 15087500 + Silent SNP G G T rs774024174 C3L-00080_T C3L-00080_N G G c.435G>T p.= p.L145L ENST00000209540 1/1 203 103 100 253 253 0 strelka-varscan-mutect OR1I1,synonymous_variant,p.=,ENST00000209540,NM_001004713.1; T ENST00000209540 Transcript synonymous_variant 521/1242 435/1068 145/355 L ctG/ctT rs774024174 1 1 OR1I1 HGNC HGNC:8207 protein_coding YES CCDS32937.1 ENSP00000209540 O60431 UPI0000130B3E NM_001004713.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF304,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs774024174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 15087500 15087500 G T 1 0 0 0 0 0 0 0 1 11036 1335 47 2 2 OR1I1 19 15087500 Silent SNP G C3L-00080_T 3910859 15087500 43530116 667 2765 WIZ 0 . GRCh38 19 15425563 15425563 + Silent SNP C C A rs779118906 C3L-00080_T C3L-00080_N C C c.1287G>T p.= p.P429P ENST00000263381 5/8 134 77 57 132 132 0 strelka-varscan-mutect WIZ,synonymous_variant,p.=,ENST00000263381,NM_021241.2;WIZ,synonymous_variant,p.=,ENST00000599910,;WIZ,synonymous_variant,p.=,ENST00000545156,;WIZ,synonymous_variant,p.=,ENST00000389282,;WIZ,synonymous_variant,p.=,ENST00000599686,;WIZ,upstream_gene_variant,,ENST00000600632,; A ENST00000263381 Transcript synonymous_variant 1501/5695 1287/2385 429/794 P ccG/ccT rs779118906 1 -1 WIZ HGNC HGNC:30917 protein_coding YES CCDS42516.1 ENSP00000263381 O95785 UPI000041F888 NM_021241.2 5/8 hmmpanther:PTHR24396:SF20,hmmpanther:PTHR24396 LOW 1 SNV 2 1 PASS rs779118906 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 15425563 15425563 C A 1 0 0 0 0 0 0 0 1 17931 639 23 1 1 WIZ 19 15425563 Silent SNP C C3L-00080_T 338063 15425563 43192053 668 2766 KCNN1 0 . GRCh38 19 17981726 17981726 + Missense_Mutation SNP C C A rs376771442 C3L-00080_T C3L-00080_N C C c.516C>A p.Asn172Lys p.N172K ENST00000222249 5/11 32 20 12 17 17 0 varscan-mutect KCNN1,missense_variant,p.Asn172Lys,ENST00000222249,NM_002248.4;KCNN1,missense_variant,p.Asn172Lys,ENST00000615435,; A ENST00000222249 Transcript missense_variant 835/3625 516/1632 172/543 N/K aaC/aaA rs376771442 1 1 KCNN1 HGNC HGNC:6290 protein_coding YES CCDS67611.1 ENSP00000476519 Q92952 UPI00001649F9 NM_002248.4 deleterious(0.01) 5/11 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF38,Pfam_domain:PF03530,Gene3D:1.10.287.70 MODERATE 1 SNV 1 1 PASS rs376771442 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 7 17981726 17981726 C A 1 0 0 0 0 1 0 0 0 7994 535 19 1 1 KCNN1 19 17981726 Missense_Mutation SNP C C3L-00080_T 2556163 17981726 40635890 669 2767 ZNF100 0 . GRCh38 19 21727168 21727168 + Missense_Mutation SNP A A C novel C3L-00080_T C3L-00080_N A A c.1144T>G p.Phe382Val p.F382V ENST00000358296 5/5 222 177 45 247 246 1 strelka-varscan-mutect ZNF100,missense_variant,p.Phe382Val,ENST00000358296,NM_173531.3;ZNF100,missense_variant,p.Phe318Val,ENST00000305570,;ZNF100,missense_variant,p.Phe381Val,ENST00000608416,;ZNF100,downstream_gene_variant,,ENST00000594401,; C ENST00000358296 Transcript missense_variant 1343/5745 1144/1629 382/542 F/V Ttt/Gtt 1 -1 ZNF100 HGNC HGNC:12880 protein_coding YES CCDS42538.1 ENSP00000351042 Q8IYN0 UPI00001614AC NM_173531.3 deleterious(0) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF131,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 21727168 21727168 A C 1 0 0 0 0 1 0 0 0 18292 14 1 5 5 ZNF100 19 21727168 Missense_Mutation SNP A C3L-00080_T 3745442 21727168 36890448 670 2768 ZNF208 0 . GRCh38 19 21974779 21974779 + Silent SNP A A T novel C3L-00080_T C3L-00080_N A A c.255T>A p.= p.L85L ENST00000397126 4/4 24 16 8 41 41 0 strelka-varscan-mutect ZNF208,synonymous_variant,p.=,ENST00000397126,NM_007153.3;ZNF208,synonymous_variant,p.=,ENST00000609966,;ZNF208,synonymous_variant,p.=,ENST00000599916,;ZNF208,intron_variant,,ENST00000601773,; T ENST00000397126 Transcript synonymous_variant 404/3992 255/3843 85/1280 L ctT/ctA 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 4/4 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103 LOW 1 SNV 3 1 PASS . . 3 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 21974779 21974779 A T 1 0 0 0 0 0 0 0 1 18343 1 1 4 4 ZNF208 19 21974779 Silent SNP A C3L-00080_T 247611 21974779 36642837 671 2769 ZNF728 0 . GRCh38 19 22975539 22975539 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.1798G>C p.Asp600His p.D600H ENST00000594710 4/4 32 24 8 48 48 0 strelka-varscan-mutect ZNF728,missense_variant,p.Asp600His,ENST00000594710,NM_001267716.1;ZNF728,downstream_gene_variant,,ENST00000599851,; G ENST00000594710 Transcript missense_variant 1944/2015 1798/1869 600/622 D/H Gac/Cac 1 -1 ZNF728 HGNC HGNC:32463 protein_coding YES CCDS59370.1 ENSP00000471593 P0DKX0 UPI0002656E4B NM_001267716.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF239,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 1 203 6 0 0 0 0 0 -19.95552 1 1 1 1 0 G 3 3 7 22975539 22975539 C G 1 0 0 0 0 1 0 0 0 18702 913 32 4 4 ZNF728 19 22975539 Missense_Mutation SNP C C3L-00080_T 1000760 22975539 35642077 672 2770 ZNF536 0 . GRCh38 19 30549271 30549271 + Missense_Mutation SNP G G A rs138308449 C3L-00080_T C3L-00080_N G G c.3652G>A p.Val1218Ile p.V1218I ENST00000355537 4/5 188 77 111 166 166 0 strelka-varscan-mutect ZNF536,missense_variant,p.Val1218Ile,ENST00000355537,NM_014717.1;ZNF536,downstream_gene_variant,,ENST00000585628,;ZNF536,upstream_gene_variant,,ENST00000592773,;CTD-2001J20.1,upstream_gene_variant,,ENST00000623331,; A ENST00000355537 Transcript missense_variant 3799/4945 3652/3903 1218/1300 V/I Gtc/Atc rs138308449 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated_low_confidence(0.39) 4/5 MODERATE 1 SNV 1 1 PASS rs138308449 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 30549271 30549271 G A 1 0 0 0 0 1 0 0 0 18547 1145 40 1 1 ZNF536 19 30549271 Missense_Mutation SNP G C3L-00080_T 7573732 30549271 28068345 673 2771 TSHZ3 0 . GRCh38 19 31277953 31277953 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1840G>T p.Val614Leu p.V614L ENST00000240587 2/2 90 47 43 102 102 0 strelka-varscan-mutect TSHZ3,missense_variant,p.Val614Leu,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; A ENST00000240587 Transcript missense_variant 2168/5176 1840/3246 614/1081 V/L Gtg/Ttg 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0.02) 2/2 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 31277953 31277953 C A 1 0 0 0 0 1 0 0 0 17130 507 18 2 2 TSHZ3 19 31277953 Missense_Mutation SNP C C3L-00080_T 728682 31277953 27339663 674 2772 FFAR1 0 . GRCh38 19 35351798 35351798 + Missense_Mutation SNP G G A rs768158175 C3L-00080_T C3L-00080_N G G c.247G>A p.Ala83Thr p.A83T ENST00000246553 1/1 212 165 47 185 185 0 strelka-varscan-mutect FFAR1,missense_variant,p.Ala83Thr,ENST00000246553,NM_005303.2;CD22,downstream_gene_variant,,ENST00000085219,NM_001771.3;CD22,downstream_gene_variant,,ENST00000536635,NM_001185099.1;CD22,downstream_gene_variant,,ENST00000341773,NM_001185101.1;CD22,downstream_gene_variant,,ENST00000544992,NM_001185100.1;CD22,downstream_gene_variant,,ENST00000419549,NM_001278417.1;CD22,downstream_gene_variant,,ENST00000601769,; A ENST00000246553 Transcript missense_variant 247/2311 247/903 83/300 A/T Gcg/Acg rs768158175 1 1 FFAR1 HGNC HGNC:4498 protein_coding YES CCDS12458.1 ENSP00000246553 O14842 UPI000005045B NM_005303.2 tolerated(0.46) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01905,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF33,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs768158175 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 35351798 35351798 G A 1 0 0 0 0 1 0 0 0 5690 1087 38 1 1 FFAR1 19 35351798 Missense_Mutation SNP G C3L-00080_T 4073845 35351798 23265818 675 2773 ZFP82 0 . GRCh38 19 36393549 36393549 + Missense_Mutation SNP C C G rs763398603 C3L-00080_T C3L-00080_N C C c.791G>C p.Arg264Thr p.R264T ENST00000392161 5/5 236 110 126 253 253 0 strelka-varscan-mutect ZFP82,missense_variant,p.Arg264Thr,ENST00000392161,NM_133466.2;ZFP82,intron_variant,,ENST00000445543,;ZFP82,non_coding_transcript_exon_variant,,ENST00000590993,; G ENST00000392161 Transcript missense_variant 1034/2623 791/1599 264/532 R/T aGg/aCg rs763398603 1 -1 ZFP82 HGNC HGNC:28682 protein_coding YES CCDS12493.1 ENSP00000431265 Q8N141 D3Y299 UPI0000071159 NM_133466.2 tolerated(0.3) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF252,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs763398603 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 36393549 36393549 C G 1 0 0 0 0 1 0 0 0 18230 681 24 4 4 ZFP82 19 36393549 Missense_Mutation SNP C C3L-00080_T 1041751 36393549 22224067 676 2774 ZNF850 0 . GRCh38 19 36749766 36749766 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1274A>T p.Glu425Val p.E425V ENST00000591344 5/5 269 177 92 246 246 0 strelka-varscan-mutect ZNF850,missense_variant,p.Glu425Val,ENST00000591344,NM_001193552.1;ZNF850,missense_variant,p.Glu393Val,ENST00000614887,NM_001267779.1;ZNF850,intron_variant,,ENST00000589390,; A ENST00000591344 Transcript missense_variant 1433/7714 1274/3273 425/1090 E/V gAa/gTa 1 -1 ZNF850 HGNC HGNC:27994 protein_coding YES CCDS59379.1 ENSP00000464976 A8MQ14 UPI00001D815D NM_001193552.1 tolerated(0.06) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF167,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 36749766 36749766 T A 1 0 0 0 0 1 0 0 0 18782 1783 62 4 4 ZNF850 19 36749766 Missense_Mutation SNP T C3L-00080_T 356217 36749766 21867850 677 2775 LGALS16 0 . GRCh38 19 39658583 39658583 + Missense_Mutation SNP G G T rs762301779 C3L-00080_T C3L-00080_N G G c.216G>T p.Trp72Cys p.W72C ENST00000392051 3/4 464 217 247 437 437 0 strelka-varscan-mutect LGALS16,missense_variant,p.Trp72Cys,ENST00000392051,NM_001190441.2;LGALS16,3_prime_UTR_variant,,ENST00000594480,; T ENST00000392051 Transcript missense_variant 284/624 216/429 72/142 W/C tgG/tgT rs762301779 1 1 LGALS16 HGNC HGNC:40039 protein_coding YES CCDS54267.1 ENSP00000375904 A8MUM7 UPI00006C1A40 NM_001190441.2 deleterious(0.03) 3/4 PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF77,Pfam_domain:PF00337,Gene3D:2.60.120.200,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs762301779 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 39658583 39658583 G T 1 0 0 0 0 1 0 0 0 8649 1183 41 2 2 LGALS16 19 39658583 Missense_Mutation SNP G C3L-00080_T 2908817 39658583 18959033 678 2776 CEACAM8 0 . GRCh38 19 42589019 42589019 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.723C>A p.= p.T241T ENST00000244336 4/6 120 57 63 95 95 0 strelka-varscan-mutect CEACAM8,synonymous_variant,p.=,ENST00000244336,NM_001816.3;CEACAM8,intron_variant,,ENST00000599005,;LIPE-AS1,intron_variant,,ENST00000594688,;LIPE-AS1,intron_variant,,ENST00000594624,; T ENST00000244336 Transcript synonymous_variant 825/2305 723/1050 241/349 T acC/acA 1 -1 CEACAM8 HGNC HGNC:1820 protein_coding YES CCDS12610.1 ENSP00000244336 P31997 Q0Z7S6 UPI00000012A3 NM_001816.3 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF615,hmmpanther:PTHR10489,Pfam_domain:PF13895,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 42589019 42589019 G T 1 0 0 0 0 0 0 0 1 2904 1335 47 2 2 CEACAM8 19 42589019 Silent SNP G C3L-00080_T 2930436 42589019 16028597 679 2777 ZNF404 0 . GRCh38 19 43873572 43873572 + Silent SNP G G T rs775057171 C3L-00080_T C3L-00080_N G G c.642C>A p.= p.P214P ENST00000587539 3/3 97 61 36 108 108 0 strelka-varscan-mutect ZNF404,synonymous_variant,p.=,ENST00000587539,NM_001033719.2;ZNF404,synonymous_variant,p.=,ENST00000324394,; T ENST00000587539 Transcript synonymous_variant 642/1851 642/1659 214/552 P ccC/ccA rs775057171 1 -1 ZNF404 HGNC HGNC:19417 protein_coding YES CCDS59394.1 ENSP00000466051 Q494X3 UPI00001D8172 NM_001033719.2 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF53,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS rs775057171 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 43873572 43873572 G T 1 0 0 0 0 0 0 0 1 18458 987 35 2 2 ZNF404 19 43873572 Silent SNP G C3L-00080_T 1284553 43873572 14744044 680 2778 ZNF229 0 . GRCh38 19 44429377 44429377 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.1404G>T p.Lys468Asn p.K468N ENST00000614049 6/6 370 339 31 274 273 1 strelka-varscan-mutect ZNF229,missense_variant,p.Lys462Asn,ENST00000613197,NM_001278510.2;ZNF229,missense_variant,p.Lys468Asn,ENST00000614049,NM_014518.3;ZNF229,downstream_gene_variant,,ENST00000592308,;CTC-512J12.4,intron_variant,,ENST00000588655,;ZNF229,intron_variant,,ENST00000591289,;ZNF229,3_prime_UTR_variant,,ENST00000620012,; A ENST00000614049 Transcript missense_variant 1838/4507 1404/2478 468/825 K/N aaG/aaT COSM3535579 1 -1 ZNF229 HGNC HGNC:13022 protein_coding YES CCDS42574.1 ENSP00000479884 Q9UJW7 UPI0001747B51 NM_014518.3 tolerated(0.17) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF348,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 44429377 44429377 C A 1 0 0 0 0 1 0 0 0 18359 680 24 2 2 ZNF229 19 44429377 Missense_Mutation SNP C C3L-00080_T 555805 44429377 14188239 681 2779 DACT3 0 . GRCh38 19 46652710 46652710 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.449G>C p.Gly150Ala p.G150A ENST00000391916 3/4 331 285 46 216 216 0 strelka-varscan-mutect DACT3,missense_variant,p.Gly150Ala,ENST00000410105,;DACT3,missense_variant,p.Gly150Ala,ENST00000391916,NM_145056.2;DACT3,5_prime_UTR_variant,,ENST00000300875,NM_001301046.1; G ENST00000391916 Transcript missense_variant 523/2834 449/1890 150/629 G/A gGt/gCt 1 -1 DACT3 HGNC HGNC:30745 protein_coding YES CCDS12688.2 ENSP00000375783 Q96B18 UPI0000202707 NM_145056.2 deleterious(0.02) 3/4 hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 7 46652710 46652710 C G 1 0 0 0 0 1 0 0 0 4025 507 18 4 4 DACT3 19 46652710 Missense_Mutation SNP C C3L-00080_T 2223333 46652710 11964906 682 2780 DHX34 0 . GRCh38 19 47353648 47353648 + Missense_Mutation SNP T T G novel C3L-00080_T C3L-00080_N T T c.618T>G p.His206Gln p.H206Q ENST00000328771 2/17 187 113 74 132 132 0 strelka-varscan-mutect DHX34,missense_variant,p.His206Gln,ENST00000328771,NM_014681.5;DHX34,upstream_gene_variant,,ENST00000471451,; G ENST00000328771 Transcript missense_variant 967/4372 618/3432 206/1143 H/Q caT/caG 1 1 DHX34 HGNC HGNC:16719 protein_coding YES CCDS12700.1 ENSP00000331907 Q14147 UPI0000202759 NM_014681.5 tolerated(0.15) 2/17 PROSITE_profiles:PS51192,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF148,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs1448704373 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 47353648 47353648 T G 1 0 0 0 0 1 0 0 0 4311 1461 51 5 5 DHX34 19 47353648 Missense_Mutation SNP T C3L-00080_T 700938 47353648 11263968 683 2781 ZNF541 0 . GRCh38 19 47521880 47521880 + Missense_Mutation SNP C C G novel C3L-00080_T C3L-00080_N C C c.3685G>C p.Glu1229Gln p.E1229Q ENST00000391901 13/15 172 94 78 120 120 0 strelka-varscan-mutect ZNF541,missense_variant,p.Glu1248Gln,ENST00000314121,;ZNF541,missense_variant,p.Glu1229Gln,ENST00000391901,NM_001277075.1;ZNF541,missense_variant,p.Glu749Gln,ENST00000595558,;ZNF541,missense_variant,p.Glu562Gln,ENST00000263351,; G ENST00000391901 Transcript missense_variant 3685/4580 3685/4041 1229/1346 E/Q Gag/Cag 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 tolerated(0.06) 13/15 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 47521880 47521880 C G 1 0 0 0 0 1 0 0 0 18549 864 30 4 4 ZNF541 19 47521880 Missense_Mutation SNP C C3L-00080_T 168232 47521880 11095736 684 2782 GRIN2D 0 . GRCh38 19 48442250 48442250 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.2541C>T p.= p.G847G ENST00000263269 12/13 450 401 49 297 297 0 strelka-varscan-mutect GRIN2D,synonymous_variant,p.=,ENST00000263269,NM_000836.2;GRWD1,upstream_gene_variant,,ENST00000253237,NM_031485.3;GRWD1,upstream_gene_variant,,ENST00000598711,;GRWD1,upstream_gene_variant,,ENST00000599949,; T ENST00000263269 Transcript synonymous_variant 2629/5093 2541/4011 847/1336 G ggC/ggT 1 1 GRIN2D HGNC HGNC:4588 protein_coding YES CCDS12719.1 ENSP00000263269 O15399 UPI000013D3DA NM_000836.2 12/13 Pfam_domain:PF00060,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF105,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1239668404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 48442250 48442250 C T 1 0 0 0 0 0 0 0 1 6664 755 27 1 1 GRIN2D 19 48442250 Silent SNP C C3L-00080_T 920370 48442250 10175366 685 2783 SHANK1 0 . GRCh38 19 50702567 50702567 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1647G>T p.Lys549Asn p.K549N ENST00000293441 11/23 270 189 81 251 251 0 strelka-varscan-mutect SHANK1,missense_variant,p.Lys549Asn,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Lys549Asn,ENST00000391814,;SHANK1,missense_variant,p.Lys549Asn,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000461154,; A ENST00000293441 Transcript missense_variant 1666/6643 1647/6486 549/2161 K/N aaG/aaT 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 deleterious(0) 11/23 hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 50702567 50702567 C A 1 0 0 0 0 1 0 0 0 14523 796 28 2 2 SHANK1 19 50702567 Missense_Mutation SNP C C3L-00080_T 2260317 50702567 7915049 686 2784 SIGLEC7 0 . GRCh38 19 51142527 51142527 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.158A>G p.Asp53Gly p.D53G ENST00000317643 1/7 560 268 292 493 493 0 strelka-varscan-mutect SIGLEC7,missense_variant,p.Asp53Gly,ENST00000317643,NM_014385.3;SIGLEC7,missense_variant,p.Asp53Gly,ENST00000305628,NM_016543.3;SIGLEC7,missense_variant,p.Asp53Gly,ENST00000601682,;SIGLEC7,missense_variant,p.Asp53Gly,ENST00000600577,NM_001277201.1;SIGLEC7,missense_variant,p.Asp53Gly,ENST00000536156,;SIGLEC7,upstream_gene_variant,,ENST00000599250,;CTD-3187F8.15,downstream_gene_variant,,ENST00000601996,;SIGLEC19P,upstream_gene_variant,,ENST00000600623,; G ENST00000317643 Transcript missense_variant 227/1754 158/1404 53/467 D/G gAc/gGc 1 1 SIGLEC7 HGNC HGNC:10876 protein_coding YES CCDS12826.1 ENSP00000323328 Q9Y286 UPI000011B40B NM_014385.3 tolerated(0.34) 1/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF43,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 51142527 51142527 A G 1 0 0 0 0 1 0 0 0 14577 275 10 5 5 SIGLEC7 19 51142527 Missense_Mutation SNP A C3L-00080_T 439960 51142527 7475089 687 2785 ZNF841 0 . GRCh38 19 52066327 52066327 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1555G>T p.Gly519Cys p.G519C ENST00000594295 6/6 119 66 53 101 101 0 strelka-varscan-mutect ZNF841,missense_variant,p.Gly519Cys,ENST00000594295,NM_001136499.1;ZNF841,missense_variant,p.Gly403Cys,ENST00000426391,NM_001321349.1;ZNF841,missense_variant,p.Gly519Cys,ENST00000389534,;ZNF841,intron_variant,,ENST00000601738,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,; A ENST00000594295 Transcript missense_variant 1958/3819 1555/2775 519/924 G/C Ggc/Tgc 1 -1 ZNF841 HGNC HGNC:27611 protein_coding YES CCDS46161.1 ENSP00000470746 Q6ZN19 UPI00001D818B NM_001136499.1 deleterious(0) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF75,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 52066327 52066327 C A 1 0 0 0 0 1 0 0 0 18776 594 21 2 2 ZNF841 19 52066327 Missense_Mutation SNP C C3L-00080_T 923800 52066327 6551289 688 2786 ERVV-1 0 . GRCh38 19 53014969 53014969 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.879G>T p.= p.T293T ENST00000602168 1/1 306 157 149 211 211 0 strelka-varscan-mutect ERVV-1,synonymous_variant,p.=,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; T ENST00000602168 Transcript synonymous_variant 1049/2202 879/1434 293/477 T acG/acT 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 1/1 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424 LOW SNV 1 PASS rs1389825285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 53014969 53014969 G T 1 0 0 0 0 0 0 0 1 5106 1103 39 1 1 ERVV-1 19 53014969 Silent SNP G C3L-00080_T 948642 53014969 5602647 689 2787 LILRB5 0 . GRCh38 19 54256212 54256212 + Silent SNP G G T rs750903433 C3L-00080_T C3L-00080_N G G c.486C>A p.= p.L162L ENST00000449561 4/13 202 181 21 146 146 0 strelka-varscan-mutect LILRB5,synonymous_variant,p.=,ENST00000316219,NM_006840.4;LILRB5,synonymous_variant,p.=,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,intron_variant,,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000615654,;LILRB5,intron_variant,,ENST00000621581,; T ENST00000449561 Transcript synonymous_variant 557/2137 486/1776 162/591 L ctC/ctA rs750903433,COSM1001070,COSM375029 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 4/13 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs750903433 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 54256212 54256212 G T 1 0 0 0 0 0 0 0 1 8702 1161 41 2 2 LILRB5 19 54256212 Silent SNP G C3L-00080_T 1241243 54256212 4361404 690 2788 KIR3DX1 0 . GRCh38 19 54535640 54535640 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.404G>A p.Gly135Glu p.G135E ENST00000221567 4/9 123 61 62 116 115 1 strelka-varscan-mutect KIR3DX1,missense_variant,p.Gly135Glu,ENST00000610811,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000611588,;KIR3DX1,missense_variant,p.Gly135Glu,ENST00000221567,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000613375,;KIR3DX1,intron_variant,,ENST00000612759,;KIR3DX1,intron_variant,,ENST00000446586,;KIR3DX1,intron_variant,,ENST00000447145,;KIR3DX1,intron_variant,,ENST00000434659,; A ENST00000221567 Transcript missense_variant,NMD_transcript_variant 411/1378 404/1059 135/352 G/E gGa/gAa 1 1 KIR3DX1 HGNC HGNC:25043 nonsense_mediated_decay YES ENSP00000221567 Q9H7L2 UPI0000DE238B tolerated(0.09) 4/9 hmmpanther:PTHR11738:SF113,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 54535640 54535640 G A 1 0 0 0 0 1 0 0 0 8187 1174 41 3 3 KIR3DX1 19 54535640 Missense_Mutation SNP G C3L-00080_T 279428 54535640 4081976 691 2789 FAM71E2 0 . GRCh38 19 55358743 55358743 + Nonsense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2125G>T p.Glu709Ter p.E709* ENST00000424985 9/11 58 52 6 49 49 0 strelka-varscan-mutect FAM71E2,stop_gained,p.Glu709Ter,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;CTD-2105E13.6,stop_gained,p.Glu259Ter,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; A ENST00000424985 Transcript stop_gained 2319/3191 2125/2769 709/922 E/* Gag/Tag 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 HIGH SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -14.03088 0.9999999 1 1 1 0 A 4 1 7 55358743 55358743 C A 1 0 0 0 0 0 1 0 0 5476 922 32 2 2 FAM71E2 19 55358743 Nonsense_Mutation SNP C C3L-00080_T 823103 55358743 3258873 692 2790 NLRP11 0 . GRCh38 19 55810165 55810165 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.445G>T p.Val149Leu p.V149L ENST00000589093 3/10 212 102 110 168 168 0 strelka-varscan-mutect NLRP11,missense_variant,p.Val149Leu,ENST00000589093,NM_145007.3;NLRP11,missense_variant,p.Val149Leu,ENST00000589824,;NLRP11,missense_variant,p.Val50Leu,ENST00000592953,NM_001297743.1;NLRP11,downstream_gene_variant,,ENST00000593208,;NLRP11,missense_variant,p.Val50Leu,ENST00000590409,;NLRP11,missense_variant,p.Val149Leu,ENST00000593244,; A ENST00000589093 Transcript missense_variant 539/3417 445/3102 149/1033 V/L Gtg/Ttg COSM1681387 1 -1 NLRP11 HGNC HGNC:22945 protein_coding YES CCDS12935.1 ENSP00000466285 P59045 UPI000013ED9D NM_145007.3 tolerated(0.1) 3/10 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF62,hmmpanther:PTHR24106,Pfam_domain:PF05729 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 55810165 55810165 C A 1 0 0 0 0 1 0 0 0 10510 478 17 2 2 NLRP11 19 55810165 Missense_Mutation SNP C C3L-00080_T 451422 55810165 2807451 693 2791 NLRP5 0 . GRCh38 19 56053748 56053748 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.3239G>T p.Gly1080Val p.G1080V ENST00000390649 13/15 226 121 105 170 170 0 strelka-varscan-mutect NLRP5,missense_variant,p.Gly1080Val,ENST00000390649,NM_153447.4;NLRP5,missense_variant,p.Gly1080Val,ENST00000621651,; T ENST00000390649 Transcript missense_variant 3239/3888 3239/3603 1080/1200 G/V gGt/gTt 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 tolerated(0.32) 13/15 hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Pfam_domain:PF13516,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 56053748 56053748 G T 1 0 0 0 0 1 0 0 0 10518 1261 44 2 2 NLRP5 19 56053748 Missense_Mutation SNP G C3L-00080_T 243583 56053748 2563868 694 2792 ZNF667 0 . GRCh38 19 56441669 56441669 + Silent SNP A A T rs748296008 C3L-00080_T C3L-00080_N A A c.1326T>A p.= p.P442P ENST00000504904 7/7 165 145 20 141 141 0 strelka-varscan-mutect ZNF667,synonymous_variant,p.=,ENST00000504904,NM_001321356.1;ZNF667,synonymous_variant,p.=,ENST00000292069,NM_022103.3;ZNF667,synonymous_variant,p.=,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; T ENST00000504904 Transcript synonymous_variant 2046/4390 1326/1833 442/610 P ccT/ccA rs748296008 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS rs748296008 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 56441669 56441669 A T 1 0 0 0 0 0 0 0 1 18648 59 3 4 4 ZNF667 19 56441669 Silent SNP A C3L-00080_T 387921 56441669 2175947 695 2793 PEG3 0 . GRCh38 19 56814323 56814323 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.4119A>T p.Glu1373Asp p.E1373D ENST00000326441 10/10 357 223 134 216 216 0 strelka-varscan-mutect PEG3,missense_variant,p.Glu1373Asp,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Glu1249Asp,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Glu1373Asp,ENST00000599534,;PEG3,missense_variant,p.Glu1373Asp,ENST00000599577,;PEG3,missense_variant,p.Glu1247Asp,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 4483/8723 4119/4767 1373/1588 E/D gaA/gaT 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 tolerated(0.12) 10/10 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 56814323 56814323 T A 1 0 0 0 0 1 0 0 0 11808 1606 56 4 4 PEG3 19 56814323 Missense_Mutation SNP T C3L-00080_T 372654 56814323 1803293 696 2794 PEG3 0 . GRCh38 19 56816701 56816701 + Missense_Mutation SNP G G C C3L-00080_T C3L-00080_N G G c.1741C>G p.His581Asp p.H581D ENST00000326441 10/10 224 138 86 122 122 0 strelka-varscan-mutect PEG3,missense_variant,p.His581Asp,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.His457Asp,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.His581Asp,ENST00000599534,;PEG3,missense_variant,p.His581Asp,ENST00000599577,;PEG3,missense_variant,p.His455Asp,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; C ENST00000326441 Transcript missense_variant 2105/8723 1741/4767 581/1588 H/D Cac/Gac COSM5300196,COSM5300197 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0) 10/10 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 56816701 56816701 G C 1 0 0 0 0 1 0 0 0 11808 1319 46 4 4 PEG3 19 56816701 Missense_Mutation SNP G C3L-00080_T 2378 56816701 1800915 697 2795 ZNF549 0 . GRCh38 19 57537264 57537264 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.260G>T p.Gly87Val p.G87V ENST00000376233 4/4 229 146 83 122 122 0 strelka-varscan-mutect ZNF549,missense_variant,p.Gly87Val,ENST00000376233,NM_001199295.1;ZNF549,missense_variant,p.Gly74Val,ENST00000240719,NM_153263.2;ZNF549,intron_variant,,ENST00000602149,;ZNF549,intron_variant,,ENST00000594943,;ZNF550,intron_variant,,ENST00000601415,;ZNF550,downstream_gene_variant,,ENST00000325134,NM_001277090.1,NM_001277091.1;ZNF550,downstream_gene_variant,,ENST00000457177,NM_001277092.1,NM_001277093.1;ZNF550,downstream_gene_variant,,ENST00000447310,;ZNF550,downstream_gene_variant,,ENST00000376230,; T ENST00000376233 Transcript missense_variant 441/4053 260/1923 87/640 G/V gGa/gTa 1 1 ZNF549 HGNC HGNC:26632 protein_coding YES CCDS56106.1 ENSP00000365407 Q6P9A3 UPI0000202D31 NM_001199295.1 tolerated(0.18) 4/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24387:SF30,hmmpanther:PTHR24387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 57537264 57537264 G T 1 0 0 0 0 1 0 0 0 18555 1174 41 2 2 ZNF549 19 57537264 Missense_Mutation SNP G C3L-00080_T 720563 57537264 1080352 698 2796 SSTR4 0 . GRCh38 20 23036155 23036155 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.672G>T p.= p.V224V ENST00000255008 1/1 112 68 44 92 92 0 strelka-varscan-mutect SSTR4,synonymous_variant,p.=,ENST00000255008,NM_001052.2;RP4-753D10.3,intron_variant,,ENST00000440921,;RP4-753D10.3,upstream_gene_variant,,ENST00000419734,; T ENST00000255008 Transcript synonymous_variant 770/1427 672/1167 224/388 V gtG/gtT 1 1 SSTR4 HGNC HGNC:11333 protein_coding YES CCDS42856.1 ENSP00000255008 P31391 UPI000013CE7A NM_001052.2 1/1 Transmembrane_helices:TMhelix,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF0,Prints_domain:PR00237 LOW SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 23036155 23036155 G T 1 0 0 0 0 0 0 0 1 15577 1306 46 2 2 SSTR4 20 23036155 Silent SNP G C3L-00080_T 23036155 41408012 699 2797 CST9 0 . GRCh38 20 23605732 23605732 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.133C>A p.Pro45Thr p.P45T ENST00000376971 1/2 204 129 75 214 214 0 strelka-varscan-mutect CST9,missense_variant,p.Pro45Thr,ENST00000376971,NM_001008693.2; T ENST00000376971 Transcript missense_variant 145/1592 133/480 45/159 P/T Cct/Act 1 -1 CST9 HGNC HGNC:13261 protein_coding YES CCDS33450.1 ENSP00000366170 Q5W186 UPI000013ED7B NM_001008693.2 tolerated(0.62) 1/2 hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF47,Gene3D:3.10.450.10,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23605732 23605732 G T 1 0 0 0 0 1 0 0 0 3779 1174 41 2 2 CST9 20 23605732 Missense_Mutation SNP G C3L-00080_T 569577 23605732 40838435 700 2798 DEFB118 0 . GRCh38 20 31372869 31372869 + Frame_Shift_Del DEL A A - rs756355406 C3L-00080_T C3L-00080_N A A c.78delA p.Lys26AsnfsTer19 p.K26Nfs*19 ENST00000253381 2/2 107 81 26 93 92 1 sindel-varindel DEFB118,frameshift_variant,p.Lys26AsnfsTer19,ENST00000253381,NM_054112.2;DEFB119,downstream_gene_variant,,ENST00000339144,;DEFB119,downstream_gene_variant,,ENST00000376321,NM_153289.3;SNORA40,upstream_gene_variant,,ENST00000390832,;DEFB119,downstream_gene_variant,,ENST00000492344,; - ENST00000253381 Transcript frameshift_variant 104/1158 71/372 24/123 E/X gAa/ga rs756355406,TMP_ESP_20_29960672_29960672,COSM1163730 1 1 DEFB118 HGNC HGNC:16196 protein_coding YES CCDS13177.1 ENSP00000253381 Q96PH6 UPI0000128D91 NM_054112.2 2/2 PD866254,hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF24 0,0,1 HIGH 1 deletion 1 7 0,0,1 1 PASS . . 0 135 18 36 17 4 0 0 -2.638292 0 0 1 0 0 - 7 5 7 31372869 31372869 A - 1 0 1 0 1 0 0 0 0 4209 246 9 0 0 DEFB118 20 31372869 Frame_Shift_Del DEL A C3L-00080_T 7767137 31372869 33071298 701 2799 KIF3B 0 . GRCh38 20 32316786 32316786 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1660G>T p.Glu554Ter p.E554* ENST00000375712 5/9 295 197 98 243 243 0 strelka-varscan-mutect KIF3B,stop_gained,p.Glu554Ter,ENST00000375712,NM_004798.3; T ENST00000375712 Transcript stop_gained 1827/6103 1660/2244 554/747 E/* Gag/Tag 1 1 KIF3B HGNC HGNC:6320 protein_coding YES CCDS13200.1 ENSP00000364864 O15066 UPI000012DDB1 NM_004798.3 5/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF476 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 32316786 32316786 G T 1 0 0 0 0 0 1 0 0 8166 1291 45 2 2 KIF3B 20 32316786 Nonsense_Mutation SNP G C3L-00080_T 943917 32316786 32127381 702 2800 C20orf173 0 . GRCh38 20 35528275 35528276 + Frame_Shift_Ins INS - - T novel C3L-00080_T C3L-00080_N - - c.591dupA p.Asp198ArgfsTer61 p.D198Rfs*61 ENST00000444723 5/6 273 221 52 256 256 0 sindel-varindel C20orf173,frameshift_variant,p.Asp198ArgfsTer61,ENST00000444723,NM_001145350.1;C20orf173,frameshift_variant,p.Asp145ArgfsTer61,ENST00000246199,;C20orf173,frameshift_variant,p.Asp198ArgfsTer74,ENST00000374345,;C20orf173,downstream_gene_variant,,ENST00000424444,;RP3-477O4.5,upstream_gene_variant,,ENST00000422009,; T ENST00000444723 Transcript frameshift_variant 736-737/1059 591-592/609 197-198/202 -/X -/A 1 -1 C20orf173 HGNC HGNC:16166 protein_coding YES CCDS46594.1 ENSP00000403566 Q96LM9 UPI0001948489 NM_001145350.1 5/6 HIGH 1 insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 7 35528275 35528275 - T 1 0 1 1 0 0 0 0 0 2004 913 32 0 0 C20orf173 20 35528275 Frame_Shift_Ins INS - C3L-00080_T 3211489 35528275 28915892 703 2801 SLC13A3 0 . GRCh38 20 46596169 46596169 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.782G>A p.Gly261Asp p.G261D ENST00000279027 5/13 136 101 35 82 82 0 strelka-varscan-mutect SLC13A3,missense_variant,p.Gly261Asp,ENST00000279027,NM_022829.5;SLC13A3,missense_variant,p.Gly214Asp,ENST00000290317,NM_001193342.1,NM_001011554.2;SLC13A3,missense_variant,p.Gly214Asp,ENST00000472148,NM_001193340.1;SLC13A3,missense_variant,p.Ala239Thr,ENST00000413164,NM_001193339.1;SLC13A3,missense_variant,p.Gly214Asp,ENST00000495082,;SLC13A3,missense_variant,p.Gly214Asp,ENST00000468915,;SLC13A3,missense_variant,p.Ala202Thr,ENST00000420568,;SLC13A3,missense_variant,p.Ala192Thr,ENST00000372121,;SLC13A3,missense_variant,p.Gly91Asp,ENST00000450298,; T ENST00000279027 Transcript missense_variant 801/4017 782/1809 261/602 G/D gGc/gAc 1 -1 SLC13A3 HGNC HGNC:14430 protein_coding YES CCDS13400.1 ENSP00000279027 Q8WWT9 UPI000013542F NM_022829.5 deleterious(0) 5/13 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF62 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 46596169 46596169 C T 1 0 0 0 0 1 0 0 0 14658 739 26 3 3 SLC13A3 20 46596169 Missense_Mutation SNP C C3L-00080_T 11067894 46596169 17847998 704 2802 CDH4 0 . GRCh38 20 61852870 61852870 + Missense_Mutation SNP C C G rs139703524 C3L-00080_T C3L-00080_N C C c.849C>G p.Asn283Lys p.N283K ENST00000614565 6/16 250 168 82 203 203 0 strelka-varscan-mutect CDH4,missense_variant,p.Asn283Lys,ENST00000614565,NM_001794.4;CDH4,missense_variant,p.Asn189Lys,ENST00000611855,;CDH4,missense_variant,p.Asn209Lys,ENST00000543233,NM_001252338.2,NM_001252339.2; G ENST00000614565 Transcript missense_variant 937/6513 849/2751 283/916 N/K aaC/aaG rs139703524,COSM1028753 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 tolerated(0.15) 6/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs139703524 . 0 207 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 G 3 3 7 61852870 61852870 C G 1 0 0 0 0 1 0 0 0 2815 535 19 4 4 CDH4 20 61852870 Missense_Mutation SNP C C3L-00080_T 15256701 61852870 2591297 705 2803 CDH4 0 . GRCh38 20 61928213 61928213 + Missense_Mutation SNP G G A rs777402708 C3L-00080_T C3L-00080_N G G c.1795G>A p.Gly599Arg p.G599R ENST00000614565 12/16 341 288 53 225 225 0 strelka-varscan-mutect CDH4,missense_variant,p.Gly599Arg,ENST00000614565,NM_001794.4;CDH4,missense_variant,p.Gly505Arg,ENST00000611855,;CDH4,missense_variant,p.Gly525Arg,ENST00000543233,NM_001252338.2,NM_001252339.2; A ENST00000614565 Transcript missense_variant 1883/6513 1795/2751 599/916 G/R Ggg/Agg rs777402708,COSM193106 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 deleterious(0) 12/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777402708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 61928213 61928213 G A 1 0 0 0 0 1 0 0 0 2815 1116 39 1 1 CDH4 20 61928213 Missense_Mutation SNP G C3L-00080_T 75343 61928213 2515954 706 2804 LAMA5 0 . GRCh38 20 62312487 62312487 + Frame_Shift_Del DEL G G - rs375474277 C3L-00080_T C3L-00080_N G G c.9273delC p.Gly3093AlafsTer14 p.G3093Afs*14 ENST00000252999 68/80 314 238 76 226 226 0 sindel-varindel-pindel LAMA5,frameshift_variant,p.Gly3093AlafsTer14,ENST00000252999,NM_005560.4;ADRM1,downstream_gene_variant,,ENST00000491935,;ADRM1,downstream_gene_variant,,ENST00000253003,NM_007002.3,NM_175573.2;ADRM1,downstream_gene_variant,,ENST00000620230,NM_001281437.1,NM_001281438.1;LAMA5,upstream_gene_variant,,ENST00000492698,;LAMA5,non_coding_transcript_exon_variant,,ENST00000370691,;LAMA5,non_coding_transcript_exon_variant,,ENST00000491036,;LAMA5,upstream_gene_variant,,ENST00000495695,;LAMA5,upstream_gene_variant,,ENST00000462415,;LAMA5,downstream_gene_variant,,ENST00000471042,;LAMA5,downstream_gene_variant,,ENST00000468786,; - ENST00000252999 Transcript frameshift_variant 9340/11426 9273/11088 3091/3695 V/X gtC/gt rs375474277 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 68/80 PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF261,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 7 62312487 62312487 G - 1 0 1 0 1 0 0 0 0 8513 1277 45 0 0 LAMA5 20 62312487 Frame_Shift_Del DEL G C3L-00080_T 384274 62312487 2131680 707 2805 LAMA5 0 . GRCh38 20 62323485 62323485 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.6035G>T p.Gly2012Val p.G2012V ENST00000252999 45/80 130 96 34 87 87 0 strelka-varscan-mutect LAMA5,missense_variant,p.Gly2012Val,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000497363,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000481120,; A ENST00000252999 Transcript missense_variant 6102/11426 6035/11088 2012/3695 G/V gGc/gTc 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 deleterious(0) 45/80 PROSITE_profiles:PS50027,PROSITE_patterns:PS01248,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1404433333 . 0 199 10 0 0 0 0 0 -20 0.9999941 1 1 1 0 A 3 1 7 62323485 62323485 C A 1 0 0 0 0 1 0 0 0 8513 739 26 2 2 LAMA5 20 62323485 Missense_Mutation SNP C C3L-00080_T 10998 62323485 2120682 708 2806 ADAMTS5 0 . GRCh38 21 26932139 26932139 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.1914C>A p.= p.G638G ENST00000284987 6/8 153 107 46 134 134 0 strelka-varscan-mutect ADAMTS5,synonymous_variant,p.=,ENST00000284987,NM_007038.3;AP001601.2,intron_variant,,ENST00000426771,; T ENST00000284987 Transcript synonymous_variant 2036/9056 1914/2793 638/930 G ggC/ggA 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 6/8 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 26932139 26932139 G T 1 0 0 0 0 0 0 0 1 313 958 34 2 2 ADAMTS5 21 26932139 Silent SNP G C3L-00080_T 26932139 19777844 709 2807 KRTAP20-3 0 . GRCh38 21 30642959 30642959 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.71G>T p.Gly24Val p.G24V ENST00000382826 1/1 209 174 35 161 161 0 strelka-varscan-mutect KRTAP20-3,missense_variant,p.Gly24Val,ENST00000382826,NM_001128077.1; T ENST00000382826 Transcript missense_variant 96/273 71/135 24/44 G/V gGc/gTc 1 1 KRTAP20-3 HGNC HGNC:34001 protein_coding YES CCDS46642.1 ENSP00000372276 Q3LI60 UPI00003D4D74 NM_001128077.1 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 30642959 30642959 G T 1 0 0 0 0 1 0 0 0 8425 1203 42 2 2 KRTAP20-3 21 30642959 Missense_Mutation SNP G C3L-00080_T 3710820 30642959 16067024 710 2808 KRTAP21-2 0 . GRCh38 21 30746998 30746998 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.205G>T p.Gly69Cys p.G69C ENST00000333892 1/1 260 203 57 195 195 0 strelka-varscan-mutect KRTAP21-2,missense_variant,p.Gly69Cys,ENST00000333892,NM_181617.1;KRTAP21-4P,upstream_gene_variant,,ENST00000454921,; A ENST00000333892 Transcript missense_variant 236/440 205/252 69/83 G/C Ggc/Tgc COSM5234627 1 -1 KRTAP21-2 HGNC HGNC:18946 protein_coding YES CCDS13605.1 ENSP00000334287 Q3LI59 UPI00001A9E4D NM_181617.1 deleterious_low_confidence(0.03) 1/1 Pfam_domain:PF11759,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 PASS rs1203154675 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 30746998 30746998 C A 1 0 0 0 0 1 0 0 0 8428 594 21 2 2 KRTAP21-2 21 30746998 Missense_Mutation SNP C C3L-00080_T 104039 30746998 15962985 711 2809 HUNK 0 . GRCh38 21 31974601 31974601 + Nonsense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1057G>T p.Glu353Ter p.E353* ENST00000270112 7/11 189 153 36 136 136 0 strelka-varscan-mutect HUNK,stop_gained,p.Glu353Ter,ENST00000270112,NM_014586.1;HUNK,upstream_gene_variant,,ENST00000439107,;HUNK,non_coding_transcript_exon_variant,,ENST00000465574,; T ENST00000270112 Transcript stop_gained 1417/7385 1057/2145 353/714 E/* Gag/Tag 1 1 HUNK HGNC HGNC:13326 protein_coding YES CCDS13610.1 ENSP00000270112 P57058 UPI0000035B66 NM_014586.1 7/11 hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF188 HIGH 1 SNV 1 1 PASS rs1419673405 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 31974601 31974601 G T 1 0 0 0 0 0 1 0 0 7354 1059 37 1 1 HUNK 21 31974601 Nonsense_Mutation SNP G C3L-00080_T 1227603 31974601 14735382 712 2810 BRWD1 0 . GRCh38 21 39312874 39312874 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.165G>T p.Glu55Asp p.E55D ENST00000333229 4/42 275 234 41 196 195 1 strelka-varscan-mutect BRWD1,missense_variant,p.Glu55Asp,ENST00000342449,NM_033656.3;BRWD1,missense_variant,p.Glu55Asp,ENST00000333229,NM_018963.4;BRWD1,missense_variant,p.Glu55Asp,ENST00000380800,;BRWD1,missense_variant,p.Glu55Asp,ENST00000341322,NM_001007246.2;BRWD1-AS2,upstream_gene_variant,,ENST00000603064,;BRWD1-AS1,upstream_gene_variant,,ENST00000423274,;BRWD1,non_coding_transcript_exon_variant,,ENST00000470108,;BRWD1,non_coding_transcript_exon_variant,,ENST00000484090,; A ENST00000333229 Transcript missense_variant 493/10141 165/6963 55/2320 E/D gaG/gaT 1 -1 BRWD1 HGNC HGNC:12760 protein_coding YES CCDS13662.1 ENSP00000330753 Q9NSI6 UPI0000163C12 NM_018963.4 tolerated(0.15) 4/42 hmmpanther:PTHR16266:SF26,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 39312874 39312874 C A 1 0 0 0 0 1 0 0 0 1699 680 24 2 2 BRWD1 21 39312874 Missense_Mutation SNP C C3L-00080_T 7338273 39312874 7397109 713 2811 DSCAM 0 . GRCh38 21 40080256 40080256 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.4316A>T p.Glu1439Val p.E1439V ENST00000400454 25/33 146 102 44 111 111 0 strelka-varscan-mutect DSCAM,missense_variant,p.Glu1439Val,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Glu1274Val,ENST00000617870,;DSCAM,missense_variant,p.Glu1191Val,ENST00000404019,; A ENST00000400454 Transcript missense_variant 4794/8552 4316/6039 1439/2012 E/V gAa/gTa 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 deleterious(0.05) 25/33 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 40080256 40080256 T A 1 0 0 0 0 1 0 0 0 4589 1783 62 4 4 DSCAM 21 40080256 Missense_Mutation SNP T C3L-00080_T 767382 40080256 6629727 714 2812 SLC37A1 0 . GRCh38 21 42543599 42543599 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.727G>A p.Glu243Lys p.E243K ENST00000352133 8/20 61 37 24 53 53 0 strelka-varscan-mutect SLC37A1,missense_variant,p.Glu243Lys,ENST00000352133,NM_001320537.1;SLC37A1,missense_variant,p.Glu243Lys,ENST00000398341,NM_018964.3;SLC37A1,non_coding_transcript_exon_variant,,ENST00000487951,; A ENST00000352133 Transcript missense_variant 1709/3664 727/1602 243/533 E/K Gaa/Aaa 1 1 SLC37A1 HGNC HGNC:11024 protein_coding YES CCDS13689.1 ENSP00000344648 P57057 UPI00001AEB81 NM_001320537.1 tolerated(0.06) 8/20 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PIRSF_domain:PIRSF002808,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF225,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 42543599 42543599 G A 1 0 0 0 0 1 0 0 0 14875 1304 45 3 3 SLC37A1 21 42543599 Missense_Mutation SNP G C3L-00080_T 2463343 42543599 4166384 715 2813 AIRE 0 . GRCh38 21 44293837 44293837 + Missense_Mutation SNP G G C rs557522986 C3L-00080_T C3L-00080_N G G c.1327G>C p.Val443Leu p.V443L ENST00000291582 11/14 493 324 169 452 452 0 strelka-varscan-mutect AIRE,missense_variant,p.Val443Leu,ENST00000291582,NM_000383.3;AIRE,non_coding_transcript_exon_variant,,ENST00000530812,;AIRE,non_coding_transcript_exon_variant,,ENST00000527919,;AIRE,non_coding_transcript_exon_variant,,ENST00000337909,;AIRE,non_coding_transcript_exon_variant,,ENST00000397994,; C ENST00000291582 Transcript missense_variant 1454/2257 1327/1638 443/545 V/L Gtg/Ctg rs557522986 1 1 AIRE HGNC HGNC:360 protein_coding YES CCDS13706.1 ENSP00000291582 O43918 UPI0000030FA6 NM_000383.3 tolerated(0.79) 11/14 Gene3D:3.30.40.10,PROSITE_patterns:PS01359,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF15,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS rs557522986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 44293837 44293837 G C 1 0 0 0 0 1 0 0 0 514 1145 40 4 4 AIRE 21 44293837 Missense_Mutation SNP G C3L-00080_T 1750238 44293837 2416146 716 2814 CLTCL1 0 . GRCh38 22 19196382 19196382 + Missense_Mutation SNP C C A rs111922411 C3L-00080_T C3L-00080_N C C c.4075G>T p.Ala1359Ser p.A1359S ENST00000427926 26/33 107 86 21 100 100 0 strelka-varscan-mutect CLTCL1,missense_variant,p.Ala1359Ser,ENST00000427926,NM_007098.3;CLTCL1,missense_variant,p.Ala1359Ser,ENST00000621271,NM_001835.3;CLTCL1,missense_variant,p.Ala182Ser,ENST00000622493,;CLTCL1,missense_variant,p.Ala182Ser,ENST00000617926,;CLTCL1,3_prime_UTR_variant,,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000611723,; A ENST00000427926 Transcript missense_variant 4148/5513 4075/4923 1359/1640 A/S Gct/Tct rs111922411 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 tolerated(0.51) 26/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:1.25.40.10,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs111922411 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 19196382 19196382 C A 1 0 0 0 0 1 0 0 0 3339 739 26 2 2 CLTCL1 22 19196382 Missense_Mutation SNP C C3L-00080_T 19196382 31622086 717 2815 SEPT5 0 . GRCh38 22 19720870 19720870 + Splice_Site SNP G G A novel C3L-00080_T C3L-00080_N G G c.717+1G>A p.X239_splice ENST00000455784 212 161 51 201 201 0 strelka-varscan-mutect SEPT5,splice_donor_variant,,ENST00000438754,NM_001009939.2;SEPT5,splice_donor_variant,,ENST00000455784,NM_002688.5;SEPT5,splice_donor_variant,,ENST00000406395,;SEPT5,splice_donor_variant,,ENST00000383045,;SEPT5,splice_donor_variant,,ENST00000412544,;SEPT5,splice_donor_variant,,ENST00000431124,;SEPT5,missense_variant,p.Val106Met,ENST00000413258,;GP1BB,upstream_gene_variant,,ENST00000366425,NM_000407.4;SEPT5,downstream_gene_variant,,ENST00000395109,;SEPT5,downstream_gene_variant,,ENST00000622227,;SEPT5,downstream_gene_variant,,ENST00000490204,;SEPT5,splice_donor_variant,,ENST00000455843,;SEPT5,splice_donor_variant,,ENST00000431044,;SEPT5,splice_donor_variant,,ENST00000470814,;SEPT5,splice_donor_variant,,ENST00000406172,;SEPT5,splice_donor_variant,,ENST00000480423,;SEPT5,downstream_gene_variant,,ENST00000477238,; A ENST00000455784 Transcript splice_donor_variant -/2070 717/1110 239/369 1 1 SEPT5 HGNC HGNC:9164 protein_coding YES CCDS13764.1 ENSP00000391311 Q99719 X5DNA9 UPI000000127F NM_002688.5 8/11 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 7 19720870 19720870 G A 1 0 0 0 0 0 0 1 0 14343 1275 44 3 3 SEPT5 22 19720870 Splice_Site SNP G C3L-00080_T 524488 19720870 31097598 718 2816 TOP3B 0 . GRCh38 22 21962571 21962571 + Silent SNP C C A rs767429764 C3L-00080_T C3L-00080_N C C c.1383G>T p.= p.V461V ENST00000398793 13/18 139 123 16 161 161 0 strelka-varscan-mutect TOP3B,synonymous_variant,p.=,ENST00000398793,NM_003935.4;TOP3B,synonymous_variant,p.=,ENST00000457270,;TOP3B,synonymous_variant,p.=,ENST00000357179,NM_001282112.1,NM_001282113.1;LL22NC03-86G7.1,non_coding_transcript_exon_variant,,ENST00000458178,;TOP3B,3_prime_UTR_variant,,ENST00000444502,;TOP3B,3_prime_UTR_variant,,ENST00000457179,;TOP3B,3_prime_UTR_variant,,ENST00000436282,;TOP3B,non_coding_transcript_exon_variant,,ENST00000470338,; A ENST00000398793 Transcript synonymous_variant 1818/3107 1383/2589 461/862 V gtG/gtT rs767429764 1 -1 TOP3B HGNC HGNC:11993 protein_coding YES CCDS13797.1 ENSP00000381773 O95985 A0A024R1C2 UPI00001371A1 NM_003935.4 13/18 Gene3D:2.70.20.10,Pfam_domain:PF01131,hmmpanther:PTHR11390,hmmpanther:PTHR11390:SF20,SMART_domains:SM00437,Superfamily_domains:SSF56712 LOW 1 SNV 1 1 PASS rs767429764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 21962571 21962571 C A 1 0 0 0 0 0 0 0 1 16844 697 25 2 2 TOP3B 22 21962571 Silent SNP C C3L-00080_T 2241701 21962571 28855897 719 2817 RSPH14 0 . GRCh38 22 23134073 23134073 + Missense_Mutation SNP C C T rs369415088 C3L-00080_T C3L-00080_N C C c.374G>A p.Arg125Gln p.R125Q ENST00000216036 4/7 171 132 39 193 193 0 strelka-varscan-mutect RSPH14,missense_variant,p.Arg125Gln,ENST00000216036,NM_014433.2;RSPH14,missense_variant,p.Arg50Gln,ENST00000439064,;RSPH14,missense_variant,p.Arg1Gln,ENST00000421213,;RSPH14,downstream_gene_variant,,ENST00000406876,;RSPH14,downstream_gene_variant,,ENST00000452757,;U7,downstream_gene_variant,,ENST00000459276,;Metazoa_SRP,upstream_gene_variant,,ENST00000635920,; T ENST00000216036 Transcript missense_variant 571/1291 374/1047 125/348 R/Q cGg/cAg rs369415088,COSM3309399 1 -1 RSPH14 HGNC HGNC:13437 protein_coding YES CCDS13803.1 ENSP00000216036 Q9UHP6 UPI000004A0CE NM_014433.2 deleterious(0.01) 4/7 Gene3D:1.25.10.10,hmmpanther:PTHR15599,Superfamily_domains:SSF48371 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369415088 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23134073 23134073 C T 1 0 0 0 0 1 0 0 0 13962 652 23 1 1 RSPH14 22 23134073 Missense_Mutation SNP C C3L-00080_T 1171502 23134073 27684395 720 2818 BCR 0 . GRCh38 22 23181772 23181772 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.812G>T p.Trp271Leu p.W271L ENST00000305877 1/23 201 156 45 233 232 1 strelka-varscan-mutect BCR,missense_variant,p.Trp271Leu,ENST00000305877,NM_004327.3;BCR,missense_variant,p.Trp271Leu,ENST00000398512,;BCR,missense_variant,p.Trp271Leu,ENST00000359540,NM_021574.2;BCR,intron_variant,,ENST00000479188,;BCRP8,upstream_gene_variant,,ENST00000412037,; T ENST00000305877 Transcript missense_variant 1563/7082 812/3816 271/1271 W/L tGg/tTg 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 deleterious_low_confidence(0.01) 1/23 hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 23181772 23181772 G T 1 0 0 0 0 1 0 0 0 1535 1357 47 2 2 BCR 22 23181772 Missense_Mutation SNP G C3L-00080_T 47699 23181772 27636696 721 2819 MYO18B 0 . GRCh38 22 26026943 26026943 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.6969C>A p.= p.S2323S ENST00000335473 43/44 99 81 18 105 105 0 strelka-varscan-mutect MYO18B,synonymous_variant,p.=,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,synonymous_variant,p.=,ENST00000407587,;MYO18B,synonymous_variant,p.=,ENST00000536101,;MYO18B,synonymous_variant,p.=,ENST00000543971,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,;MYO18B,upstream_gene_variant,,ENST00000540454,; A ENST00000335473 Transcript synonymous_variant 7219/8565 6969/7704 2323/2567 S tcC/tcA 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 43/44 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 26026943 26026943 C A 1 0 0 0 0 0 0 0 1 10067 581 21 2 2 MYO18B 22 26026943 Silent SNP C C3L-00080_T 2845171 26026943 24791525 722 2820 SEZ6L 0 . GRCh38 22 26169675 26169675 + Silent SNP C C A novel C3L-00080_T C3L-00080_N C C c.6C>A p.= p.P2P ENST00000248933 1/17 87 47 40 40 40 0 strelka-varscan-mutect SEZ6L,synonymous_variant,p.=,ENST00000529632,NM_001184775.1;SEZ6L,synonymous_variant,p.=,ENST00000360929,NM_001184776.1;SEZ6L,synonymous_variant,p.=,ENST00000404234,NM_001184773.1;SEZ6L,synonymous_variant,p.=,ENST00000248933,NM_021115.4;SEZ6L,synonymous_variant,p.=,ENST00000629590,NM_001184774.1;SEZ6L,synonymous_variant,p.=,ENST00000343706,NM_001184777.1; A ENST00000248933 Transcript synonymous_variant 101/3248 6/3075 2/1024 P ccC/ccA 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 1/17 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs915540078 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 26169675 26169675 C A 1 0 0 0 0 0 0 0 1 14422 639 23 1 1 SEZ6L 22 26169675 Silent SNP C C3L-00080_T 142732 26169675 24648793 723 2821 GATSL3 0 . GRCh38 22 30287203 30287203 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.1024C>G p.Pro342Ala p.P342A ENST00000434291 9/13 45 37 8 53 53 0 strelka-varscan-mutect RP1-130H16.18,missense_variant,p.Pro342Ala,ENST00000434291,;GATSL3,missense_variant,p.Pro153Ala,ENST00000407689,NM_001037666.2;GATSL3,missense_variant,p.Pro153Ala,ENST00000404953,;TBC1D10A,downstream_gene_variant,,ENST00000215790,NM_031937.2;TBC1D10A,downstream_gene_variant,,ENST00000403477,NM_001204240.1;TBC1D10A,downstream_gene_variant,,ENST00000403362,;GATSL3,non_coding_transcript_exon_variant,,ENST00000464854,;GATSL3,intron_variant,,ENST00000459785,;GATSL3,downstream_gene_variant,,ENST00000498572,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000330168,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000447976,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000434987,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000418047,;GATSL3,3_prime_UTR_variant,,ENST00000421236,;GATSL3,3_prime_UTR_variant,,ENST00000425691,;GATSL3,3_prime_UTR_variant,,ENST00000440839,;GATSL3,3_prime_UTR_variant,,ENST00000415484,;GATSL3,3_prime_UTR_variant,,ENST00000440704,;GATSL3,non_coding_transcript_exon_variant,,ENST00000497605,;GATSL3,non_coding_transcript_exon_variant,,ENST00000471480,;GATSL3,non_coding_transcript_exon_variant,,ENST00000463795,;GATSL3,non_coding_transcript_exon_variant,,ENST00000492159,;TBC1D10A,downstream_gene_variant,,ENST00000462073,;TBC1D10A,downstream_gene_variant,,ENST00000467596,;TBC1D10A,downstream_gene_variant,,ENST00000433426,; C ENST00000434291 Transcript missense_variant 1024/1818 1024/1443 342/480 P/A Cct/Gct 1 -1 RP1-130H16.18 Clone_based_vega_gene protein_coding YES ENSP00000401535 H7C1Q1 UPI0001610F54 tolerated_low_confidence(0.88) 9/13 MODERATE SNV 2 1 PASS . . 0 202 7 0 0 0 0 0 -19.34179 0.9999997 1 1 1 0 C 3 2 7 30287203 30287203 G C 1 0 0 0 0 1 0 0 0 6137 1203 42 4 4 GATSL3 22 30287203 Missense_Mutation SNP G C3L-00080_T 4117528 30287203 20531265 724 2822 INPP5J 0 . GRCh38 22 31128060 31128060 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.1897C>T p.Gln633Ter p.Q633* ENST00000331075 7/13 141 111 30 133 132 1 strelka-varscan-mutect INPP5J,stop_gained,p.Gln566Ter,ENST00000412277,NM_001284286.1;INPP5J,stop_gained,p.Gln633Ter,ENST00000331075,NM_001284285.1;INPP5J,stop_gained,p.Gln266Ter,ENST00000405300,NM_001284289.1;INPP5J,stop_gained,p.Gln266Ter,ENST00000400294,NM_001284288.1;INPP5J,stop_gained,p.Gln198Ter,ENST00000620191,NM_001284287.1;INPP5J,stop_gained,p.Gln265Ter,ENST00000404390,NM_001002837.2;INPP5J,splice_region_variant,,ENST00000404453,;INPP5J,splice_region_variant,,ENST00000402238,;INPP5J,5_prime_UTR_variant,,ENST00000401755,;INPP5J,downstream_gene_variant,,ENST00000412985,;INPP5J,downstream_gene_variant,,ENST00000420017,;INPP5J,downstream_gene_variant,,ENST00000463528,;INPP5J,splice_region_variant,,ENST00000461241,; T ENST00000331075 Transcript stop_gained,splice_region_variant 1946/3347 1897/3021 633/1006 Q/* Cag/Tag 1 1 INPP5J HGNC HGNC:8956 protein_coding YES CCDS63453.1 ENSP00000333262 Q15735 UPI000004CB11 NM_001284285.1 7/13 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF127,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 31128060 31128060 C T 1 0 0 0 0 0 1 0 0 7662 608 21 3 3 INPP5J 22 31128060 Nonsense_Mutation SNP C C3L-00080_T 840857 31128060 19690408 725 2823 BPIFC 0 . GRCh38 22 32435793 32435793 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.835T>A p.Tyr279Asn p.Y279N ENST00000397452 9/16 305 267 38 308 308 0 strelka-varscan-mutect BPIFC,missense_variant,p.Tyr279Asn,ENST00000397452,;BPIFC,missense_variant,p.Tyr279Asn,ENST00000300399,NM_174932.2;BPIFC,missense_variant,p.Tyr93Asn,ENST00000534972,; T ENST00000397452 Transcript missense_variant 946/2091 835/1524 279/507 Y/N Tac/Aac 1 -1 BPIFC HGNC HGNC:16503 protein_coding YES CCDS13906.1 ENSP00000380594 Q8NFQ6 UPI0000071B53 deleterious(0.02) 9/16 hmmpanther:PTHR10504:SF17,hmmpanther:PTHR10504,Pfam_domain:PF02886,PIRSF_domain:PIRSF002417,Gene3D:1ewfA02,SMART_domains:SM00329,Superfamily_domains:SSF55394 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 32435793 32435793 A T 1 0 0 0 0 1 0 0 0 1662 420 15 4 4 BPIFC 22 32435793 Missense_Mutation SNP A C3L-00080_T 1307733 32435793 18382675 726 2824 CSF2RB 0 . GRCh38 22 36935390 36935390 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.1355T>A p.Leu452His p.L452H ENST00000403662 11/14 451 357 94 398 398 0 strelka-varscan-mutect CSF2RB,missense_variant,p.Leu452His,ENST00000403662,NM_000395.2;CSF2RB,missense_variant,p.Leu452His,ENST00000262825,;CSF2RB,missense_variant,p.Leu458His,ENST00000406230,;CSF2RB,downstream_gene_variant,,ENST00000421539,; A ENST00000403662 Transcript missense_variant 1577/4863 1355/2694 452/897 L/H cTc/cAc 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 deleterious(0.01) 11/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR23037:SF22,hmmpanther:PTHR23037,PIRSF_domain:PIRSF001956 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 36935390 36935390 T A 1 0 0 0 0 1 0 0 0 3736 1551 54 4 4 CSF2RB 22 36935390 Missense_Mutation SNP T C3L-00080_T 4499597 36935390 13883078 727 2825 RIBC2 0 . GRCh38 22 45422343 45422343 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.610C>T p.Gln204Ter p.Q204* ENST00000614167 4/7 132 113 19 149 148 1 strelka-varscan-mutect RIBC2,stop_gained,p.Gln204Ter,ENST00000614167,NM_015653.4;RIBC2,non_coding_transcript_exon_variant,,ENST00000466226,;RIBC2,non_coding_transcript_exon_variant,,ENST00000621287,; T ENST00000614167 Transcript stop_gained 806/1479 610/1149 204/382 Q/* Cag/Tag 1 1 RIBC2 HGNC HGNC:13241 protein_coding YES ENSP00000483356 A0A087X0F7 UPI00003735F7 NM_015653.4 4/7 Pfam_domain:PF05914,hmmpanther:PTHR14517,hmmpanther:PTHR14517:SF10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 7 45422343 45422343 C T 1 0 0 0 0 0 1 0 0 13526 595 21 3 3 RIBC2 22 45422343 Nonsense_Mutation SNP C C3L-00080_T 8486953 45422343 5396125 728 2826 FBLN1 0 . GRCh38 22 45563090 45563090 + Missense_Mutation SNP G G A novel C3L-00080_T C3L-00080_N G G c.1990G>A p.Glu664Lys p.E664K ENST00000402984 16/16 195 155 40 214 214 0 strelka-varscan-mutect FBLN1,missense_variant,p.Glu664Lys,ENST00000402984,;FBLN1,missense_variant,p.Glu626Lys,ENST00000262722,NM_001996.3;FBLN1,intron_variant,,ENST00000327858,NM_006486.2;FBLN1,intron_variant,,ENST00000442170,NM_006485.3;FBLN1,downstream_gene_variant,,ENST00000340923,NM_006487.2; A ENST00000402984 Transcript missense_variant 2093/2355 1990/2166 664/721 E/K Gag/Aag 1 1 FBLN1 HGNC HGNC:3600 protein_coding ENSP00000385521 B1AHL2 UPI000165DBD3 tolerated(0.35) 16/16 PIRSF_domain:PIRSF036313,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF303 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 45563090 45563090 G A 1 0 0 0 0 1 0 0 0 5561 1291 45 3 3 FBLN1 22 45563090 Missense_Mutation SNP G C3L-00080_T 140747 45563090 5255378 729 2827 GTSE1 0 . GRCh38 22 46316323 46316323 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1343G>T p.Ser448Ile p.S448I ENST00000454366 7/12 104 81 23 117 117 0 strelka-mutect GTSE1,missense_variant,p.Ser448Ile,ENST00000454366,NM_016426.6;GTSE1,non_coding_transcript_exon_variant,,ENST00000466510,;GTSE1,non_coding_transcript_exon_variant,,ENST00000479645,; T ENST00000454366 Transcript missense_variant 1555/3112 1343/2220 448/739 S/I aGt/aTt 1 1 GTSE1 HGNC HGNC:13698 protein_coding YES CCDS14074.2 ENSP00000415430 Q9NYZ3 UPI000021D19B NM_016426.6 deleterious(0) 7/12 hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 46316323 46316323 G T 1 0 0 0 0 1 0 0 0 6766 1029 36 2 2 GTSE1 22 46316323 Missense_Mutation SNP G C3L-00080_T 753233 46316323 4502145 730 2828 VCX3A 0 . GRCh38 X 6533751 6533751 + Missense_Mutation SNP A A T rs755627458 C3L-00080_T C3L-00080_N A A c.555T>A p.Ser185Arg p.S185R ENST00000381089 3/3 331 159 172 370 369 1 strelka-varscan-mutect VCX3A,missense_variant,p.Ser185Arg,ENST00000381089,NM_016379.3;VCX3A,missense_variant,p.Ser125Arg,ENST00000612369,;VCX3A,missense_variant,p.Ser165Arg,ENST00000398729,; T ENST00000381089 Transcript missense_variant 862/995 555/561 185/186 S/R agT/agA rs755627458 1 -1 VCX3A HGNC HGNC:18159 protein_coding YES CCDS35199.1 ENSP00000370479 Q9NNX9 UPI0000138292 NM_016379.3 tolerated_low_confidence(0.27) 3/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs755627458 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 6533751 6533751 A T 1 0 0 0 0 1 0 0 0 17689 156 6 4 4 VCX3A 23 6533751 Missense_Mutation SNP A C3L-00080_T 6533751 149507144 731 2829 ANOS1 0 . GRCh38 X 8570636 8570636 + Missense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.925G>A p.Val309Met p.V309M ENST00000262648 7/14 217 113 104 232 232 0 strelka-varscan-mutect ANOS1,missense_variant,p.Val309Met,ENST00000262648,NM_000216.2;ANOS1,non_coding_transcript_exon_variant,,ENST00000488294,; T ENST00000262648 Transcript missense_variant 1075/6314 925/2043 309/680 V/M Gtg/Atg 1 -1 ANOS1 HGNC HGNC:6211 protein_coding YES CCDS14130.1 ENSP00000262648 P23352 UPI00001AE843 NM_000216.2 deleterious(0.02) 7/14 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR14131,hmmpanther:PTHR14131:SF3,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 8570636 8570636 C T 1 0 0 0 0 1 0 0 0 812 478 17 3 3 ANOS1 23 8570636 Missense_Mutation SNP C C3L-00080_T 2036885 8570636 147470259 732 2830 PHKA2 0 . GRCh38 X 18926483 18926483 + Missense_Mutation SNP G G C rs376233279 C3L-00080_T C3L-00080_N G G c.1429C>G p.Arg477Gly p.R477G ENST00000379942 14/33 260 123 137 231 231 0 strelka-varscan-mutect PHKA2,missense_variant,p.Arg477Gly,ENST00000379942,NM_000292.2;PHKA2,upstream_gene_variant,,ENST00000464455,; C ENST00000379942 Transcript missense_variant 2095/5559 1429/3708 477/1235 R/G Cgg/Ggg rs376233279 1 -1 PHKA2 HGNC HGNC:8926 protein_coding YES CCDS14190.1 ENSP00000369274 P46019 UPI000012DF4B NM_000292.2 deleterious(0) 14/33 Pfam_domain:PF00723,hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF5 MODERATE 1 SNV 1 1 PASS rs376233279 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 18926483 18926483 G C 1 0 0 0 0 1 0 0 0 11932 1115 39 4 4 PHKA2 23 18926483 Missense_Mutation SNP G C3L-00080_T 10355847 18926483 137114412 733 2831 MBTPS2 0 . GRCh38 X 21845312 21845312 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.366C>T p.= p.S122S ENST00000379484 3/11 130 56 74 174 174 0 strelka-varscan-mutect MBTPS2,synonymous_variant,p.=,ENST00000365779,;MBTPS2,synonymous_variant,p.=,ENST00000379484,NM_015884.3;MBTPS2,non_coding_transcript_exon_variant,,ENST00000465888,;LL0XNC01-138C3.2,upstream_gene_variant,,ENST00000618062,; T ENST00000379484 Transcript synonymous_variant 465/4428 366/1560 122/519 S tcC/tcT 1 1 MBTPS2 HGNC HGNC:15455 protein_coding YES CCDS14201.1 ENSP00000368798 O43462 UPI000012F5A0 NM_015884.3 3/11 Low_complexity_(Seg):seg,hmmpanther:PTHR13325:SF3,hmmpanther:PTHR13325 LOW 1 SNV 1 1 PASS rs773969619 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 21845312 21845312 C T 1 0 0 0 0 0 0 0 1 9295 668 24 3 3 MBTPS2 23 21845312 Silent SNP C C3L-00080_T 2918829 21845312 134195583 734 2832 ZNF645 0 . GRCh38 X 22273451 22273451 + Missense_Mutation SNP C C A C3L-00080_T C3L-00080_N C C c.460C>A p.Arg154Ser p.R154S ENST00000323684 1/1 98 48 50 78 78 0 strelka-varscan-mutect ZNF645,missense_variant,p.Arg154Ser,ENST00000323684,NM_152577.3;PTCHD1-AS,intron_variant,,ENST00000608254,; A ENST00000323684 Transcript missense_variant 509/1519 460/1278 154/425 R/S Cgt/Agt COSM1119284 1 1 ZNF645 HGNC HGNC:26371 protein_coding YES CCDS14205.1 ENSP00000323348 Q8N7E2 UPI0000073BD5 NM_152577.3 tolerated(0.42) 1/1 hmmpanther:PTHR13480,hmmpanther:PTHR13480:SF1 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 22273451 22273451 C A 1 0 0 0 0 1 0 0 0 18634 884 31 1 1 ZNF645 23 22273451 Missense_Mutation SNP C C3L-00080_T 428139 22273451 133767444 735 2833 POLA1 0 . GRCh38 X 24699489 24699489 + Silent SNP G G A novel C3L-00080_T C3L-00080_N G G c.90G>A p.= p.G30G ENST00000379059 2/37 68 28 40 101 101 0 strelka-varscan-mutect POLA1,synonymous_variant,p.=,ENST00000379068,;POLA1,synonymous_variant,p.=,ENST00000379059,NM_016937.3;POLA1,synonymous_variant,p.=,ENST00000611764,; A ENST00000379059 Transcript synonymous_variant 105/5440 90/4389 30/1462 G ggG/ggA 1 1 POLA1 HGNC HGNC:9173 protein_coding YES CCDS14214.1 ENSP00000368349 P09884 UPI000014D383 NM_016937.3 2/37 Low_complexity_(Seg):seg,hmmpanther:PTHR10322:SF21,hmmpanther:PTHR10322 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 7 24699489 24699489 G A 1 0 0 0 0 0 0 0 1 12297 1190 42 3 3 POLA1 23 24699489 Silent SNP G C3L-00080_T 2426038 24699489 131341406 736 2834 TAB3 0 . GRCh38 X 30854913 30854913 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.752A>T p.Gln251Leu p.Q251L ENST00000378933 7/12 116 62 54 107 106 1 strelka-varscan-mutect TAB3,missense_variant,p.Gln251Leu,ENST00000378933,NM_152787.4;TAB3,missense_variant,p.Gln251Leu,ENST00000378930,;TAB3,missense_variant,p.Gln251Leu,ENST00000378932,;TAB3,downstream_gene_variant,,ENST00000288422,;TAB3-AS2,downstream_gene_variant,,ENST00000445240,;TAB3,upstream_gene_variant,,ENST00000378928,;TAB3,missense_variant,p.Gln251Leu,ENST00000467136,; A ENST00000378933 Transcript missense_variant 1299/6671 752/2139 251/712 Q/L cAg/cTg 1 -1 TAB3 HGNC HGNC:30681 protein_coding YES CCDS14226.1 ENSP00000368215 Q8N5C8 UPI0000071648 NM_152787.4 tolerated(0.67) 7/12 hmmpanther:PTHR10351:SF45,hmmpanther:PTHR10351 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 30854913 30854913 T A 1 0 0 0 0 1 0 0 0 15893 1580 55 4 4 TAB3 23 30854913 Missense_Mutation SNP T C3L-00080_T 6155424 30854913 125185982 737 2835 MAGEB16 0 . GRCh38 X 35802406 35802406 + Silent SNP C C T novel C3L-00080_T C3L-00080_N C C c.210C>T p.= p.S70S ENST00000399989 2/2 109 31 78 81 81 0 strelka-varscan-mutect MAGEB16,synonymous_variant,p.=,ENST00000399989,NM_001099921.1;MAGEB16,synonymous_variant,p.=,ENST00000399987,;MAGEB16,synonymous_variant,p.=,ENST00000399992,;MAGEB16,synonymous_variant,p.=,ENST00000399988,;MAGEB16,synonymous_variant,p.=,ENST00000399985,; T ENST00000399989 Transcript synonymous_variant 489/1818 210/975 70/324 S tcC/tcT 1 1 MAGEB16 HGNC HGNC:21188 protein_coding YES CCDS43927.1 ENSP00000382871 A2A368 UPI00006C1BC1 NM_001099921.1 2/2 Pfam_domain:PF12440,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF24,Low_complexity_(Seg):seg,SMART_domains:SM01392 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 35802406 35802406 C T 1 0 0 0 0 0 0 0 1 9089 668 24 3 3 MAGEB16 23 35802406 Silent SNP C C3L-00080_T 4947493 35802406 120238489 738 2836 FAM47C 0 . GRCh38 X 37010521 37010521 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.2111C>A p.Pro704Gln p.P704Q ENST00000358047 1/1 353 155 198 284 284 0 strelka-varscan-mutect FAM47C,missense_variant,p.Pro704Gln,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript missense_variant 2125/3270 2111/3108 704/1035 P/Q cCa/cAa 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 tolerated(0.16) 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 37010521 37010521 C A 1 0 0 0 0 1 0 0 0 5449 594 21 2 2 FAM47C 23 37010521 Missense_Mutation SNP C C3L-00080_T 1208115 37010521 119030374 739 2837 DGKK 0 . GRCh38 X 50386574 50386574 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.2131T>A p.Tyr711Asn p.Y711N ENST00000611977 15/28 63 25 38 56 56 0 strelka-varscan-mutect DGKK,missense_variant,p.Tyr711Asn,ENST00000611977,NM_001013742.3; T ENST00000611977 Transcript missense_variant 2191/7407 2131/3816 711/1271 Y/N Tat/Aat 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 tolerated(0.41) 15/28 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 50386574 50386574 A T 1 0 0 0 0 1 0 0 0 4278 391 14 4 4 DGKK 23 50386574 Missense_Mutation SNP A C3L-00080_T 13376053 50386574 105654321 740 2838 P2RY10 0 . GRCh38 X 78960630 78960630 + Missense_Mutation SNP A A G novel C3L-00080_T C3L-00080_N A A c.110A>G p.Tyr37Cys p.Y37C ENST00000171757 4/4 180 74 106 153 153 0 strelka-varscan-mutect P2RY10,missense_variant,p.Tyr37Cys,ENST00000171757,NM_014499.2;P2RY10,missense_variant,p.Tyr37Cys,ENST00000544091,NM_198333.1;P2RY10,non_coding_transcript_exon_variant,,ENST00000475374,;P2RY10,non_coding_transcript_exon_variant,,ENST00000461541,; G ENST00000171757 Transcript missense_variant 390/1714 110/1020 37/339 Y/C tAt/tGt 1 1 P2RY10 HGNC HGNC:19906 protein_coding YES CCDS14442.1 ENSP00000171757 O00398 UPI0000050471 NM_014499.2 deleterious(0) 4/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR24232:SF47,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 7 78960630 78960630 A G 1 0 0 0 0 1 0 0 0 11420 449 16 5 5 P2RY10 23 78960630 Missense_Mutation SNP A C3L-00080_T 28574056 78960630 77080265 741 2839 PCDH11X 0 . GRCh38 X 91878534 91878534 + Missense_Mutation SNP T T A novel C3L-00080_T C3L-00080_N T T c.2294T>A p.Val765Asp p.V765D ENST00000373094 2/7 220 92 128 174 174 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Val765Asp,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Val765Asp,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Val765Asp,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Val765Asp,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Val765Asp,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Val765Asp,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Val765Asp,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; A ENST00000373094 Transcript missense_variant 3139/9179 2294/4044 765/1347 V/D gTt/gAt 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0) 2/7 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 91878534 91878534 T A 1 0 0 0 0 1 0 0 0 11595 1725 60 4 4 PCDH11X 23 91878534 Missense_Mutation SNP T C3L-00080_T 12917904 91878534 64162361 742 2840 MORF4L2 0 . GRCh38 X 103676195 103676195 + Missense_Mutation SNP A A T novel C3L-00080_T C3L-00080_N A A c.833T>A p.Val278Glu p.V278E ENST00000422154 4/4 31 22 9 21 21 0 strelka-varscan-mutect MORF4L2,missense_variant,p.Val278Glu,ENST00000422154,NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1;MORF4L2,missense_variant,p.Val278Glu,ENST00000433176,NM_001142421.1,NM_001142428.1,NM_001142419.1,NM_001142431.1,NM_001142422.1,NM_001142420.1,NM_001142427.1,NM_001142432.1;MORF4L2,missense_variant,p.Val278Glu,ENST00000451301,NM_001142430.1,NM_001142426.1;MORF4L2,missense_variant,p.Val278Glu,ENST00000441076,;MORF4L2,missense_variant,p.Val278Glu,ENST00000360458,;MORF4L2,missense_variant,p.Val227Glu,ENST00000423833,;MORF4L2,downstream_gene_variant,,ENST00000434230,;MORF4L2,downstream_gene_variant,,ENST00000442614,;MORF4L2,downstream_gene_variant,,ENST00000418819,;MORF4L2,downstream_gene_variant,,ENST00000422355,;MORF4L2,downstream_gene_variant,,ENST00000492116,;MORF4L2,downstream_gene_variant,,ENST00000474653,;MORF4L2,downstream_gene_variant,,ENST00000498064,;MORF4L2,downstream_gene_variant,,ENST00000467755,; T ENST00000422154 Transcript missense_variant 1288/1983 833/867 278/288 V/E gTg/gAg 1 -1 MORF4L2 HGNC HGNC:16849 protein_coding YES CCDS14512.1 ENSP00000394417 Q15014 UPI000012F567 NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1 deleterious(0.02) 4/4 PROSITE_profiles:PS51640,hmmpanther:PTHR10880,hmmpanther:PTHR10880:SF25 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99997 1 1 1 1 0 T 3 4 7 103676195 103676195 A T 1 0 0 0 0 1 0 0 0 9670 159 6 4 4 MORF4L2 23 103676195 Missense_Mutation SNP A C3L-00080_T 11797661 103676195 52364700 743 2841 H2BFM 0 . GRCh38 X 104040068 104040068 + Missense_Mutation SNP C C A rs373863467 C3L-00080_T C3L-00080_N C C c.92C>A p.Thr31Lys p.T31K ENST00000355016 1/3 79 33 46 50 50 0 strelka-varscan-mutect H2BFM,missense_variant,p.Thr31Lys,ENST00000355016,NM_001164416.1;H2BFM,missense_variant,p.Thr31Lys,ENST00000598335,;H2BFM,upstream_gene_variant,,ENST00000417637,; A ENST00000355016 Transcript missense_variant 120/1882 92/465 31/154 T/K aCg/aAg rs373863467 1 1 H2BFM HGNC HGNC:27867 protein_coding YES CCDS55468.1 ENSP00000347119 P0C1H6 W0TYI6 UPI0000161AB5 NM_001164416.1 tolerated(0.46) 1/3 Gene3D:1.10.20.10,Pfam_domain:PF00125,hmmpanther:PTHR23428,hmmpanther:PTHR23428:SF34 MODERATE 1 SNV 2 1 PASS rs373863467 . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 7 104040068 104040068 C A 1 0 0 0 0 1 0 0 0 6813 536 19 1 1 H2BFM 23 104040068 Missense_Mutation SNP C C3L-00080_T 363873 104040068 52000827 744 2842 ATG4A 0 . GRCh38 X 108126094 108126094 + Missense_Mutation SNP G G C novel C3L-00080_T C3L-00080_N G G c.28G>C p.Asp10His p.D10H ENST00000372232 2/13 116 43 73 102 102 0 strelka-varscan-mutect ATG4A,missense_variant,p.Asp10His,ENST00000372232,NM_001321288.1,NM_052936.3;ATG4A,missense_variant,p.Asp10His,ENST00000345734,NM_178270.2;ATG4A,missense_variant,p.Asp7His,ENST00000394892,;ATG4A,5_prime_UTR_variant,,ENST00000457035,;ATG4A,missense_variant,p.Asp10His,ENST00000372246,NM_178271.2,NM_001321290.1;ATG4A,missense_variant,p.Asp10His,ENST00000343524,; C ENST00000372232 Transcript missense_variant 187/2315 28/1197 10/398 D/H Gat/Cat 1 1 ATG4A HGNC HGNC:16489 protein_coding YES CCDS14538.1 ENSP00000361306 Q8WYN0 UPI000000DCAF NM_001321288.1,NM_052936.3 deleterious(0.02) 2/13 hmmpanther:PTHR22624,hmmpanther:PTHR22624:SF35 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 108126094 108126094 G C 1 0 0 0 0 1 0 0 0 1248 942 33 4 4 ATG4A 23 108126094 Missense_Mutation SNP G C3L-00080_T 4086026 108126094 47914801 745 2843 SAGE1 0 . GRCh38 X 135910446 135910446 + Missense_Mutation SNP G G C C3L-00080_T C3L-00080_N G G c.1896G>C p.Glu632Asp p.E632D ENST00000324447 16/20 75 39 36 82 82 0 strelka-varscan-mutect SAGE1,missense_variant,p.Glu632Asp,ENST00000324447,;SAGE1,missense_variant,p.Glu632Asp,ENST00000370709,NM_018666.2;SAGE1,missense_variant,p.Glu256Asp,ENST00000537770,; C ENST00000324447 Transcript missense_variant 1970/2952 1896/2715 632/904 E/D gaG/gaC COSM3363826,COSM3363827 1 1 SAGE1 HGNC HGNC:30369 protein_coding YES CCDS14652.1 ENSP00000323191 Q9NXZ1 UPI00001413AB deleterious(0.01) 16/20 hmmpanther:PTHR12957:SF25,hmmpanther:PTHR12957 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 7 135910446 135910446 G C 1 0 0 0 0 1 0 0 0 14068 933 33 4 4 SAGE1 23 135910446 Missense_Mutation SNP G C3L-00080_T 27784352 135910446 20130449 746 2844 ARHGEF6 0 . GRCh38 X 136681907 136681907 + Missense_Mutation SNP C C A novel C3L-00080_T C3L-00080_N C C c.1541G>T p.Cys514Phe p.C514F ENST00000250617 14/22 77 46 31 167 166 1 strelka-varscan-mutect ARHGEF6,missense_variant,p.Cys514Phe,ENST00000250617,NM_004840.2;ARHGEF6,missense_variant,p.Cys360Phe,ENST00000370622,;ARHGEF6,missense_variant,p.Cys360Phe,ENST00000370620,NM_001306177.1; A ENST00000250617 Transcript missense_variant 2747/6019 1541/2331 514/776 C/F tGc/tTc 1 -1 ARHGEF6 HGNC HGNC:685 protein_coding YES CCDS14660.1 ENSP00000250617 Q15052 UPI0000001C8E NM_004840.2 tolerated(0.08) 14/22 PROSITE_profiles:PS50003,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF123,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1170028473 . 0 207 0 0 2 0 0 0 -20 0.9994604 1 1 1 0 A 3 1 7 136681907 136681907 C A 1 0 0 0 0 1 0 0 0 1046 710 25 2 2 ARHGEF6 23 136681907 Missense_Mutation SNP C C3L-00080_T 771461 136681907 19358988 747 2845 ZIC3 0 . GRCh38 X 137568998 137568998 + Missense_Mutation SNP A A T C3L-00080_T C3L-00080_N A A c.1157A>T p.Lys386Met p.K386M ENST00000287538 2/3 121 68 53 134 134 0 strelka-varscan-mutect ZIC3,missense_variant,p.Lys386Met,ENST00000287538,NM_003413.3;ZIC3,missense_variant,p.Lys386Met,ENST00000370606,;RP11-158M9.1,upstream_gene_variant,,ENST00000636095,;RP11-158M9.1,upstream_gene_variant,,ENST00000637564,;RP1-137H15.2,upstream_gene_variant,,ENST00000442841,;ZIC3,non_coding_transcript_exon_variant,,ENST00000478471,; T ENST00000287538 Transcript missense_variant 1707/3469 1157/1404 386/467 K/M aAg/aTg COSM1270939 1 1 ZIC3 HGNC HGNC:12874 protein_coding YES CCDS14663.1 ENSP00000287538 O60481 UPI000013C3DD NM_003413.3 deleterious(0) 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF25,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 137568998 137568998 A T 1 0 0 0 0 1 0 0 0 18259 72 3 4 4 ZIC3 23 137568998 Missense_Mutation SNP A C3L-00080_T 887091 137568998 18471897 748 2846 MAMLD1 0 . GRCh38 X 150470772 150470772 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1124G>T p.Gly375Val p.G375V ENST00000432680 3/5 178 101 77 235 235 0 strelka-varscan-mutect MAMLD1,missense_variant,p.Gly400Val,ENST00000370401,;MAMLD1,missense_variant,p.Gly400Val,ENST00000262858,NM_005491.4;MAMLD1,missense_variant,p.Gly375Val,ENST00000426613,NM_001177466.2;MAMLD1,missense_variant,p.Gly375Val,ENST00000432680,NM_001177465.2;MAMLD1,downstream_gene_variant,,ENST00000358892,;MAMLD1,downstream_gene_variant,,ENST00000468306,; T ENST00000432680 Transcript missense_variant 1299/3224 1124/2997 375/998 G/V gGg/gTg 1 1 MAMLD1 HGNC HGNC:2568 protein_coding YES CCDS55526.1 ENSP00000414517 Q13495 UPI00017A6EBC NM_001177465.2 deleterious(0.02) 3/5 hmmpanther:PTHR15275,hmmpanther:PTHR15275:SF0 MODERATE 1 SNV 2 1 PASS rs1161206329 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 150470772 150470772 G T 1 0 0 0 0 1 0 0 0 9129 1232 43 2 2 MAMLD1 23 150470772 Missense_Mutation SNP G C3L-00080_T 12901774 150470772 5570123 749 2847 GPR50 0 . GRCh38 X 151180698 151180698 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1115G>T p.Gly372Val p.G372V ENST00000218316 2/2 136 70 66 141 141 0 strelka-varscan-mutect GPR50,missense_variant,p.Gly372Val,ENST00000218316,NM_004224.3;AF003625.3,upstream_gene_variant,,ENST00000602313,;GPR50-AS1,upstream_gene_variant,,ENST00000454196,; T ENST00000218316 Transcript missense_variant 1184/1951 1115/1854 372/617 G/V gGt/gTt 1 1 GPR50 HGNC HGNC:4506 protein_coding YES CCDS44012.1 ENSP00000218316 Q13585 UPI000013C755 NM_004224.3 deleterious(0.03) 2/2 Prints_domain:PR01151 MODERATE 1 SNV 1 1 PASS rs1419443084 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 151180698 151180698 G T 1 0 0 0 0 1 0 0 0 6582 1261 44 2 2 GPR50 23 151180698 Missense_Mutation SNP G C3L-00080_T 709926 151180698 4860197 750 2848 PASD1 0 . GRCh38 X 151672221 151672221 + Missense_Mutation SNP G G T novel C3L-00080_T C3L-00080_N G G c.1476G>T p.Gln492His p.Q492H ENST00000370357 14/16 50 23 27 57 57 0 strelka-varscan-mutect PASD1,missense_variant,p.Gln492His,ENST00000370357,NM_173493.2;PASD1,non_coding_transcript_exon_variant,,ENST00000464219,;RP11-45D17.1,downstream_gene_variant,,ENST00000413236,; T ENST00000370357 Transcript missense_variant 1721/3163 1476/2322 492/773 Q/H caG/caT 1 1 PASD1 HGNC HGNC:20686 protein_coding YES CCDS35431.1 ENSP00000359382 Q8IV76 UPI0000074686 NM_173493.2 tolerated(0.24) 14/16 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 7 151672221 151672221 G T 1 0 0 0 0 1 0 0 0 11552 962 34 2 2 PASD1 23 151672221 Missense_Mutation SNP G C3L-00080_T 491523 151672221 4368674 751 2849 GABRA3 0 . GRCh38 X 152189767 152189767 + Nonsense_Mutation SNP C C T novel C3L-00080_T C3L-00080_N C C c.1106G>A p.Trp369Ter p.W369* ENST00000370314 9/10 46 24 22 28 28 0 strelka-varscan-mutect GABRA3,stop_gained,p.Trp369Ter,ENST00000370314,NM_000808.3;GABRA3,stop_gained,p.Trp369Ter,ENST00000535043,;RP11-329E24.6,downstream_gene_variant,,ENST00000453915,;GABRA3,non_coding_transcript_exon_variant,,ENST00000497894,; T ENST00000370314 Transcript stop_gained 1345/3712 1106/1479 369/492 W/* tGg/tAg 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 9/10 hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 HIGH 1 SNV 1 1 PASS . . 0 202 5 3 0 0 0 0 -20 0.9999692 1 1 1 0 T 4 4 7 152189767 152189767 C T 1 0 0 0 0 0 1 0 0 6033 595 21 3 3 GABRA3 23 152189767 Nonsense_Mutation SNP C C3L-00080_T 517546 152189767 3851128 752 2850 PNCK 0 . GRCh38 X 153671674 153671674 + Splice_Site SNP T T A novel C3L-00080_T C3L-00080_N T T c.664-2A>T p.X222_splice ENST00000447676 15 10 5 18 18 0 strelka-varscan-mutect PNCK,splice_acceptor_variant,,ENST00000370150,;PNCK,splice_acceptor_variant,,ENST00000447676,NM_001039582.3;PNCK,splice_acceptor_variant,,ENST00000370142,;PNCK,splice_acceptor_variant,,ENST00000340888,;PNCK,splice_acceptor_variant,,ENST00000370145,NM_001135740.1;PNCK,splice_acceptor_variant,,ENST00000422811,;PNCK,splice_acceptor_variant,,ENST00000439087,;PNCK,downstream_gene_variant,,ENST00000425526,;PNCK,downstream_gene_variant,,ENST00000418241,;PNCK,downstream_gene_variant,,ENST00000419804,;PNCK,downstream_gene_variant,,ENST00000458354,;PNCK,downstream_gene_variant,,ENST00000423545,;PNCK,upstream_gene_variant,,ENST00000438984,;PNCK,downstream_gene_variant,,ENST00000434652,;PNCK,splice_acceptor_variant,,ENST00000475172,;PNCK,downstream_gene_variant,,ENST00000462280,;PNCK,downstream_gene_variant,,ENST00000460106,;PNCK,splice_acceptor_variant,,ENST00000466074,;PNCK,splice_acceptor_variant,,ENST00000488994,;PNCK,splice_acceptor_variant,,ENST00000466638,;PNCK,splice_acceptor_variant,,ENST00000489536,;PNCK,splice_acceptor_variant,,ENST00000433470,;PNCK,splice_acceptor_variant,,ENST00000411968,;PNCK,non_coding_transcript_exon_variant,,ENST00000472324,;PNCK,non_coding_transcript_exon_variant,,ENST00000473680,;PNCK,non_coding_transcript_exon_variant,,ENST00000488168,;PNCK,non_coding_transcript_exon_variant,,ENST00000465303,;PNCK,downstream_gene_variant,,ENST00000463548,;PNCK,downstream_gene_variant,,ENST00000466662,; A ENST00000447676 Transcript splice_acceptor_variant -/1585 664/1281 222/426 1 -1 PNCK HGNC HGNC:13415 protein_coding YES CCDS35503.2 ENSP00000405950 Q6P2M8 UPI0000237966 NM_001039582.3 5/11 HIGH 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -15.94526 1 1 1 1 0 A 5 1 7 153671674 153671674 T A 1 0 0 0 0 0 0 1 0 12252 1594 55 4 4 PNCK 23 153671674 Splice_Site SNP T C3L-00080_T 1481907 153671674 2369221 753 2851 VAMP7 0 . GRCh38 X 155889544 155889544 + Silent SNP G G T novel C3L-00080_T C3L-00080_N G G c.78G>T p.= p.L26L ENST00000262640 2/7 346 271 75 218 218 0 strelka-varscan-mutect VAMP7,synonymous_variant,p.=,ENST00000286448,NM_005638.5;VAMP7,synonymous_variant,p.=,ENST00000262640,NM_001185183.1;VAMP7,synonymous_variant,p.=,ENST00000460621,NM_001145149.2;VAMP7,non_coding_transcript_exon_variant,,ENST00000479687,;VAMP7,non_coding_transcript_exon_variant,,ENST00000463317,;VAMP7,synonymous_variant,p.=,ENST00000488344,; T ENST00000262640 Transcript synonymous_variant 161/2496 78/783 26/260 L ctG/ctT 1 1 VAMP7 HGNC HGNC:11486 protein_coding YES CCDS55548.1 ENSP00000262640 P51809 A0A024R074 UPI000006F699 NM_001185183.1 2/7 Gene3D:3.30.450.50,PROSITE_profiles:PS50859,hmmpanther:PTHR21136,hmmpanther:PTHR21136:SF86,Superfamily_domains:SSF64356 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 7 155889544 155889544 G T 1 0 0 0 0 0 0 0 1 17662 1362 47 2 2 VAMP7 23 155889544 Silent SNP G C3L-00080_T 2217870 155889544 151351 754 2852 PRAMEF12 0 . GRCh38 1 12775102 12775102 + Silent SNP C C A rs746102731 C3L-00093_T C3L-00093_N C C c.235C>A p.= p.R79R ENST00000357726 1/3 121 110 11 93 93 0 strelka-varscan-mutect PRAMEF12,synonymous_variant,p.=,ENST00000357726,NM_001080830.4; A ENST00000357726 Transcript synonymous_variant 262/1786 235/1452 79/483 R Cga/Aga rs746102731 1 1 PRAMEF12 HGNC HGNC:22125 protein_coding YES CCDS41254.1 ENSP00000350358 O95522 UPI0000EE6E0A NM_001080830.4 1/3 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF31,PIRSF_domain:PIRSF038286 LOW 1 SNV 2 1 PASS rs746102731 . 0 208 2 0 0 0 0 0 -19.99518 1 1 1 1 0 A 2 1 8 12775102 12775102 C A 1 0 0 0 0 0 0 0 1 12557 876 31 1 1 PRAMEF12 1 12775102 Silent SNP C C3L-00093_T 12775102 236181320 1 2853 KAZN 0 . GRCh38 1 15101607 15101607 + Missense_Mutation SNP C C A novel C3L-00093_T C3L-00093_N C C c.1612C>A p.Leu538Met p.L538M ENST00000376030 11/15 349 327 22 244 244 0 strelka-varscan-mutect KAZN,missense_variant,p.Leu626Met,ENST00000636203,;KAZN,missense_variant,p.Leu538Met,ENST00000376030,NM_201628.2; A ENST00000376030 Transcript missense_variant 1906/6030 1612/2328 538/775 L/M Ctg/Atg 1 1 KAZN HGNC HGNC:29173 protein_coding YES CCDS152.2 ENSP00000365198 Q674X7 UPI0000E1E68A NM_201628.2 deleterious(0) 11/15 Gene3D:1.10.150.50,Pfam_domain:PF00536,PROSITE_profiles:PS50105,hmmpanther:PTHR12776,hmmpanther:PTHR12776:SF1,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 15101607 15101607 C A 1 0 0 0 0 1 0 0 0 7907 680 24 2 2 KAZN 1 15101607 Missense_Mutation SNP C C3L-00093_T 2326505 15101607 233854815 2 2854 CLCNKA 0 . GRCh38 1 16031815 16031815 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.1728G>A p.= p.V576V ENST00000331433 16/20 370 350 20 267 267 0 varscan-mutect CLCNKA,synonymous_variant,p.=,ENST00000375692,NM_001042704.1;CLCNKA,synonymous_variant,p.=,ENST00000331433,NM_004070.3;CLCNKA,synonymous_variant,p.=,ENST00000439316,NM_001257139.1;CLCNKA,non_coding_transcript_exon_variant,,ENST00000464764,;CLCNKA,downstream_gene_variant,,ENST00000491433,;RP11-5P18.10,downstream_gene_variant,,ENST00000447882,; A ENST00000331433 Transcript synonymous_variant 1747/2475 1728/2064 576/687 V gtG/gtA 1 1 CLCNKA HGNC HGNC:2026 protein_coding YES CCDS167.1 ENSP00000332771 P51800 UPI0000127993 NM_004070.3 16/20 Gene3D:3.10.580.10,Pfam_domain:PF00571,PROSITE_profiles:PS51371,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF95,SMART_domains:SM00116,Superfamily_domains:SSF54631 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 16031815 16031815 G A 1 0 0 0 0 0 0 0 1 3233 1277 45 3 3 CLCNKA 1 16031815 Silent SNP G C3L-00093_T 930208 16031815 232924607 3 2855 ADGRL2 0 . GRCh38 1 81990608 81990608 + Silent SNP C C G rs549347800 C3L-00093_T C3L-00093_N C C c.3675C>G p.= p.L1225L ENST00000319517 20/20 305 268 37 214 214 0 strelka-varscan-mutect ADGRL2,synonymous_variant,p.=,ENST00000370728,;ADGRL2,synonymous_variant,p.=,ENST00000370730,;ADGRL2,synonymous_variant,p.=,ENST00000370717,;ADGRL2,synonymous_variant,p.=,ENST00000627151,;ADGRL2,synonymous_variant,p.=,ENST00000319517,NM_012302.3;ADGRL2,synonymous_variant,p.=,ENST00000370725,;ADGRL2,synonymous_variant,p.=,ENST00000370723,;ADGRL2,synonymous_variant,p.=,ENST00000370727,;ADGRL2,synonymous_variant,p.=,ENST00000370721,;ADGRL2,synonymous_variant,p.=,ENST00000359929,NM_001297704.1;ADGRL2,synonymous_variant,p.=,ENST00000449420,;ADGRL2,synonymous_variant,p.=,ENST00000402328,;ADGRL2,3_prime_UTR_variant,,ENST00000370715,NM_001297705.1;ADGRL2,3_prime_UTR_variant,,ENST00000370713,NM_001297706.1;ADGRL2,non_coding_transcript_exon_variant,,ENST00000469377,;ADGRL2,non_coding_transcript_exon_variant,,ENST00000472424,;ADGRL2,non_coding_transcript_exon_variant,,ENST00000464775,;ADGRL2,non_coding_transcript_exon_variant,,ENST00000464551,; G ENST00000319517 Transcript synonymous_variant 3891/5479 3675/4212 1225/1403 L ctC/ctG rs549347800 1 1 ADGRL2 HGNC HGNC:18582 protein_coding YES CCDS689.1 ENSP00000322270 O95490 UPI000005046B NM_012302.3 20/20 Pfam_domain:PF02354 LOW 1 SNV 1 1 PASS rs549347800 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 8 81990608 81990608 C G 1 0 0 0 0 0 0 0 1 376 871 31 4 4 ADGRL2 1 81990608 Silent SNP C C3L-00093_T 65958793 81990608 166965814 4 2856 ARNT 0 . GRCh38 1 150836353 150836353 + Silent SNP G G A rs368471232 C3L-00093_T C3L-00093_N G G c.627C>T p.= p.L209L ENST00000358595 7/22 288 262 26 222 222 0 strelka-varscan-mutect ARNT,synonymous_variant,p.=,ENST00000358595,NM_001668.3;ARNT,synonymous_variant,p.=,ENST00000354396,NM_001286036.1;ARNT,synonymous_variant,p.=,ENST00000515192,NM_001286035.1;ARNT,synonymous_variant,p.=,ENST00000505755,NM_178427.2,NM_001197325.1;ARNT,non_coding_transcript_exon_variant,,ENST00000468970,;ARNT,downstream_gene_variant,,ENST00000497108,;ARNT,synonymous_variant,p.=,ENST00000471844,;ARNT,downstream_gene_variant,,ENST00000504358,;ARNT,downstream_gene_variant,,ENST00000505979,;ARNT,upstream_gene_variant,,ENST00000512296,; A ENST00000358595 Transcript synonymous_variant 828/4887 627/2370 209/789 L ctC/ctT rs368471232 1 -1 ARNT HGNC HGNC:700 protein_coding YES CCDS970.1 ENSP00000351407 P27540 UPI0000030984 NM_001668.3 7/22 PROSITE_profiles:PS50112,hmmpanther:PTHR23042,hmmpanther:PTHR23042:SF50,Gene3D:3.30.450.20,Pfam_domain:PF00989,SMART_domains:SM00091,Superfamily_domains:SSF55785 LOW 1 SNV 1 1 PASS rs368471232 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 150836353 150836353 G A 1 0 0 0 0 0 0 0 1 1107 929 33 3 3 ARNT 1 150836353 Silent SNP G C3L-00093_T 68845745 150836353 98120069 5 2857 FLAD1 0 . GRCh38 1 154988192 154988192 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.460G>A p.Asp154Asn p.D154N ENST00000292180 2/7 436 392 44 231 231 0 strelka-varscan-mutect FLAD1,missense_variant,p.Asp154Asn,ENST00000368433,;FLAD1,missense_variant,p.Asp154Asn,ENST00000292180,NM_025207.4;FLAD1,missense_variant,p.Asp57Asn,ENST00000368432,NM_001184891.1;FLAD1,missense_variant,p.Asp55Asn,ENST00000368431,NM_001184892.1;FLAD1,missense_variant,p.Asp57Asn,ENST00000315144,NM_201398.2;FLAD1,5_prime_UTR_variant,,ENST00000295530,;FLAD1,upstream_gene_variant,,ENST00000368428,;FLAD1,non_coding_transcript_exon_variant,,ENST00000487371,;FLAD1,downstream_gene_variant,,ENST00000492620,;FLAD1,upstream_gene_variant,,ENST00000489992,;FLAD1,upstream_gene_variant,,ENST00000477609,;FLAD1,upstream_gene_variant,,ENST00000481758,; A ENST00000292180 Transcript missense_variant 782/2160 460/1764 154/587 D/N Gat/Aat 1 1 FLAD1 HGNC HGNC:24671 protein_coding YES CCDS1078.1 ENSP00000292180 Q8NFF5 UPI00000735B2 NM_025207.4 deleterious(0) 2/7 hmmpanther:PTHR23293,hmmpanther:PTHR23293:SF9,Gene3D:3.40.980.10,PIRSF_domain:PIRSF036620,Pfam_domain:PF00994,SMART_domains:SM00852,Superfamily_domains:SSF53218 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 154988192 154988192 G A 1 0 0 0 0 1 0 0 0 5782 1290 45 3 3 FLAD1 1 154988192 Missense_Mutation SNP G C3L-00093_T 4151839 154988192 93968230 6 2858 SUCO 0 . GRCh38 1 172553263 172553263 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.181G>A p.Glu61Lys p.E61K ENST00000263688 3/24 84 79 5 70 70 0 strelka-varscan SUCO,missense_variant,p.Glu61Lys,ENST00000263688,NM_014283.4;SUCO,5_prime_UTR_variant,,ENST00000616058,NM_001282751.1;SUCO,intron_variant,,ENST00000367723,NM_016227.3;SUCO,intron_variant,,ENST00000608151,;SUCO,intron_variant,,ENST00000610051,NM_001282750.1;SUCO,upstream_gene_variant,,ENST00000608804,;SUCO,downstream_gene_variant,,ENST00000608566,; A ENST00000263688 Transcript missense_variant 400/5556 181/3765 61/1254 E/K Gaa/Aaa 1 1 SUCO HGNC HGNC:1240 protein_coding CCDS1303.1 ENSP00000263688 Q9UBS9 UPI0000070BAC NM_014283.4 tolerated_low_confidence(0.1) 3/24 hmmpanther:PTHR12953,hmmpanther:PTHR12953:SF0 MODERATE SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.10873 1 1 1 1 0 A 3 1 8 172553263 172553263 G A 1 0 0 0 0 1 0 0 0 15751 1304 45 3 3 SUCO 1 172553263 Missense_Mutation SNP G C3L-00093_T 17565071 172553263 76403159 7 2859 KIF14 0 . GRCh38 1 200581236 200581236 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.3300C>T p.= p.I1100I ENST00000367350 20/30 181 167 14 108 108 0 strelka-varscan KIF14,synonymous_variant,p.=,ENST00000367350,NM_014875.2;KIF14,synonymous_variant,p.=,ENST00000614960,; A ENST00000367350 Transcript synonymous_variant 3739/7274 3300/4947 1100/1648 I atC/atT 1 -1 KIF14 HGNC HGNC:19181 protein_coding YES CCDS30963.1 ENSP00000356319 Q15058 UPI000012DDA3 NM_014875.2 20/30 hmmpanther:PTHR24115:SF546,hmmpanther:PTHR24115 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 200581236 200581236 G A 1 0 0 0 0 0 0 0 1 8140 1280 45 3 3 KIF14 1 200581236 Silent SNP G C3L-00093_T 28027973 200581236 48375186 8 2860 NAV1 0 . GRCh38 1 201812631 201812631 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.5191G>C p.Glu1731Gln p.E1731Q ENST00000367296 27/30 190 167 23 107 107 0 strelka-varscan NAV1,missense_variant,p.Glu1731Gln,ENST00000367296,NM_020443.4;NAV1,missense_variant,p.Glu1337Gln,ENST00000367295,NM_001167738.1;NAV1,missense_variant,p.Glu1684Gln,ENST00000367302,;NAV1,downstream_gene_variant,,ENST00000438083,;MIR1231,downstream_gene_variant,,ENST00000408101,;IPO9-AS1,intron_variant,,ENST00000413035,;IPO9-AS1,downstream_gene_variant,,ENST00000421449,; C ENST00000367296 Transcript missense_variant 5611/13091 5191/5634 1731/1877 E/Q Gag/Cag 1 1 NAV1 HGNC HGNC:15989 protein_coding YES CCDS1414.2 ENSP00000356265 Q8NEY1 UPI00004562D4 NM_020443.4 deleterious(0) 27/30 hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 201812631 201812631 G C 1 0 0 0 0 1 0 0 0 10192 1291 45 4 4 NAV1 1 201812631 Missense_Mutation SNP G C3L-00093_T 1231395 201812631 47143791 9 2861 RASSF5 0 . GRCh38 1 206507686 206507686 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.84G>A p.= p.L28L ENST00000579436 1/6 273 257 16 178 178 0 strelka-varscan RASSF5,synonymous_variant,p.=,ENST00000581503,;RASSF5,synonymous_variant,p.=,ENST00000579436,NM_182663.3;RASSF5,synonymous_variant,p.=,ENST00000580449,NM_182664.3;RP11-534L20.5,downstream_gene_variant,,ENST00000562504,; A ENST00000579436 Transcript synonymous_variant 157/2064 84/1257 28/418 L ctG/ctA 1 1 RASSF5 HGNC HGNC:17609 protein_coding YES CCDS30998.1 ENSP00000462099 Q8WWW0 UPI0000072CF5 NM_182663.3 1/6 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 206507686 206507686 G A 1 0 0 0 0 0 0 0 1 13250 1277 45 3 3 RASSF5 1 206507686 Silent SNP G C3L-00093_T 4695055 206507686 42448736 10 2862 PLXNA2 0 . GRCh38 1 208217814 208217814 + Missense_Mutation SNP G G T novel C3L-00093_T C3L-00093_N G G c.109C>A p.Gln37Lys p.Q37K ENST00000367033 2/32 335 317 18 227 227 0 strelka-varscan PLXNA2,missense_variant,p.Gln37Lys,ENST00000367033,NM_025179.3;PLXNA2,upstream_gene_variant,,ENST00000460870,; T ENST00000367033 Transcript missense_variant 867/11444 109/5685 37/1894 Q/K Cag/Aag 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 tolerated(0.85) 2/32 PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 208217814 208217814 G T 1 0 0 0 0 1 0 0 0 12226 1299 45 2 2 PLXNA2 1 208217814 Missense_Mutation SNP G C3L-00093_T 1710128 208217814 40738608 11 2863 INTS7 0 . GRCh38 1 211975331 211975331 + Silent SNP C C A novel C3L-00093_T C3L-00093_N C C c.1650G>T p.= p.L550L ENST00000366994 13/20 374 330 44 270 269 1 strelka-varscan INTS7,synonymous_variant,p.=,ENST00000366994,NM_015434.3;INTS7,synonymous_variant,p.=,ENST00000366993,NM_001199811.1;INTS7,synonymous_variant,p.=,ENST00000366992,NM_001199812.1;INTS7,synonymous_variant,p.=,ENST00000440600,NM_001199809.1;INTS7,synonymous_variant,p.=,ENST00000475798,;INTS7,3_prime_UTR_variant,,ENST00000469606,;INTS7,non_coding_transcript_exon_variant,,ENST00000461212,; A ENST00000366994 Transcript synonymous_variant 1755/4417 1650/2889 550/962 L ctG/ctT 1 -1 INTS7 HGNC HGNC:24484 protein_coding YES CCDS1501.1 ENSP00000355961 Q9NVH2 UPI000006FE2E NM_015434.3 13/20 hmmpanther:PTHR13322,hmmpanther:PTHR13322:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 211975331 211975331 C A 1 0 0 0 0 0 0 0 1 7686 813 29 2 2 INTS7 1 211975331 Silent SNP C C3L-00093_T 3757517 211975331 36981091 12 2864 ANGEL2 0 . GRCh38 1 213008345 213008345 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.507G>A p.= p.V169V ENST00000366962 3/9 316 290 26 228 228 0 strelka-varscan ANGEL2,synonymous_variant,p.=,ENST00000366962,NM_144567.4;ANGEL2,5_prime_UTR_variant,,ENST00000360506,NM_001300758.1,NM_001300755.1,NM_001300753.1,NM_001300757.1;ANGEL2,5_prime_UTR_variant,,ENST00000535388,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000460337,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000476904,;ANGEL2,non_coding_transcript_exon_variant,,ENST00000481918,; T ENST00000366962 Transcript synonymous_variant 662/4649 507/1635 169/544 V gtG/gtA 1 -1 ANGEL2 HGNC HGNC:30534 protein_coding YES CCDS1512.1 ENSP00000355929 Q5VTE6 UPI00001D3EF4 NM_144567.4 3/9 hmmpanther:PTHR12121,hmmpanther:PTHR12121:SF27,Gene3D:3.60.10.10,Superfamily_domains:SSF56219 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 213008345 213008345 C T 1 0 0 0 0 0 0 0 1 707 813 29 3 3 ANGEL2 1 213008345 Silent SNP C C3L-00093_T 1033014 213008345 35948077 13 2865 NLRP3 0 . GRCh38 1 247424250 247424250 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.807G>A p.= p.Q269Q ENST00000336119 3/9 208 189 19 145 145 0 strelka-varscan NLRP3,synonymous_variant,p.=,ENST00000366497,NM_001127461.2;NLRP3,synonymous_variant,p.=,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,synonymous_variant,p.=,ENST00000366496,;NLRP3,synonymous_variant,p.=,ENST00000391828,NM_001079821.2;NLRP3,synonymous_variant,p.=,ENST00000348069,NM_183395.2;NLRP3,synonymous_variant,p.=,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript synonymous_variant 1553/4170 807/3111 269/1036 Q caG/caA 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Pfam_domain:PF05729,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 247424250 247424250 G A 1 0 0 0 0 0 0 0 1 10516 933 33 3 3 NLRP3 1 247424250 Silent SNP G C3L-00093_T 34415905 247424250 1532172 14 2866 ABCG5 0 . GRCh38 2 43824400 43824400 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.937G>A p.Glu313Lys p.E313K ENST00000260645 8/13 620 568 52 437 437 0 strelka-varscan ABCG5,missense_variant,p.Glu142Lys,ENST00000405322,;ABCG5,missense_variant,p.Glu313Lys,ENST00000260645,NM_022436.2;ABCG5,intron_variant,,ENST00000486512,;ABCG5,intron_variant,,ENST00000409962,; T ENST00000260645 Transcript missense_variant 1077/2740 937/1956 313/651 E/K Gaa/Aaa 1 -1 ABCG5 HGNC HGNC:13886 protein_coding YES CCDS1814.1 ENSP00000260645 Q9H222 UPI0000046560 NM_022436.2 tolerated(0.11) 8/13 hmmpanther:PTHR19241:SF193,hmmpanther:PTHR19241 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 43824400 43824400 C T 1 0 0 0 0 1 0 0 0 75 864 30 3 3 ABCG5 2 43824400 Missense_Mutation SNP C C3L-00093_T 43824400 198369129 15 2867 PPP3R1 0 . GRCh38 2 68188683 68188683 + Silent SNP C C T rs140640493 C3L-00093_T C3L-00093_N C C c.51G>A p.= p.A17A ENST00000234310 3/6 103 89 14 76 76 0 strelka-varscan-mutect PPP3R1,synonymous_variant,p.=,ENST00000234310,NM_000945.3;PPP3R1,synonymous_variant,p.=,ENST00000409752,;PPP3R1,synonymous_variant,p.=,ENST00000409377,;RP11-474G23.1,synonymous_variant,p.=,ENST00000406334,; T ENST00000234310 Transcript synonymous_variant 455/3023 51/513 17/170 A gcG/gcA rs140640493 1 -1 PPP3R1 HGNC HGNC:9317 protein_coding YES CCDS46310.1 ENSP00000234310 P63098 UPI00000012AE NM_000945.3 3/6 Gene3D:1.10.238.10,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF43,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS rs140640493 . 0 202 8 0 0 0 0 0 -20 0.9999977 1 1 1 0 T 2 4 8 68188683 68188683 C T 1 0 0 0 0 0 0 0 1 12522 639 23 1 1 PPP3R1 2 68188683 Silent SNP C C3L-00093_T 24364283 68188683 174004846 16 2868 DPP10 0 . GRCh38 2 115727906 115727906 + Missense_Mutation SNP T T G novel C3L-00093_T C3L-00093_N T T c.679T>G p.Phe227Val p.F227V ENST00000393147 8/26 170 153 17 161 161 0 strelka-varscan-mutect DPP10,missense_variant,p.Phe223Val,ENST00000410059,NM_001321910.1,NM_001321911.1,NM_001321914.1,NM_001321905.1,NM_001321906.1,NM_020868.3;DPP10,missense_variant,p.Phe173Val,ENST00000409163,NM_001178036.1,NM_001178037.1;DPP10,missense_variant,p.Phe216Val,ENST00000310323,NM_001004360.3;DPP10,missense_variant,p.Phe227Val,ENST00000393147,NM_001178034.1;DPP10,missense_variant,p.Phe219Val,ENST00000393146,;DPP10,non_coding_transcript_exon_variant,,ENST00000488208,; G ENST00000393147 Transcript missense_variant 1034/2758 679/2403 227/800 F/V Ttt/Gtt 1 1 DPP10 HGNC HGNC:20823 protein_coding YES CCDS54388.1 ENSP00000376855 Q8N608 UPI00015E0A22 NM_001178034.1 tolerated(0.21) 8/26 hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 115727906 115727906 T G 1 0 0 0 0 1 0 0 0 4542 1841 64 5 5 DPP10 2 115727906 Missense_Mutation SNP T C3L-00093_T 47539223 115727906 126465623 17 2869 SCN2A 0 . GRCh38 2 165323224 165323224 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.1740C>G p.Phe580Leu p.F580L ENST00000636071 13/28 287 256 31 189 189 0 strelka-varscan-mutect SCN2A,missense_variant,p.Phe580Leu,ENST00000636071,;SCN2A,missense_variant,p.Phe448Leu,ENST00000636985,;SCN2A,missense_variant,p.Phe580Leu,ENST00000637266,;SCN2A,missense_variant,p.Phe580Leu,ENST00000375437,NM_001040142.1;SCN2A,missense_variant,p.Phe580Leu,ENST00000283256,NM_021007.2;SCN2A,missense_variant,p.Phe580Leu,ENST00000375427,NM_001040143.1;SCN2A,missense_variant,p.Phe580Leu,ENST00000631182,;SCN2A,non_coding_transcript_exon_variant,,ENST00000635945,;SCN2A,non_coding_transcript_exon_variant,,ENST00000638151,;SCN2A,missense_variant,p.Phe580Leu,ENST00000636384,;SCN2A,missense_variant,p.Phe580Leu,ENST00000636769,;SCN2A,3_prime_UTR_variant,,ENST00000636662,;SCN2A,3_prime_UTR_variant,,ENST00000636135,;SCN2A,3_prime_UTR_variant,,ENST00000637367,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,; G ENST00000636071 Transcript missense_variant 2117/9303 1740/6018 580/2005 F/L ttC/ttG 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 deleterious(0.05) 13/28 Pfam_domain:PF11933 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 8 165323224 165323224 C G 1 0 0 0 0 1 0 0 0 14185 825 29 4 4 SCN2A 2 165323224 Missense_Mutation SNP C C3L-00093_T 49595318 165323224 76870305 18 2870 PDK1 0 . GRCh38 2 172566915 172566915 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.811G>C p.Glu271Gln p.E271Q ENST00000392571 7/12 216 186 30 191 191 0 strelka-varscan-mutect PDK1,missense_variant,p.Glu251Gln,ENST00000282077,;PDK1,missense_variant,p.Glu251Gln,ENST00000410055,NM_002610.4;PDK1,missense_variant,p.Glu271Gln,ENST00000392571,NM_001278549.1;PDK1,missense_variant,p.Glu169Gln,ENST00000416991,;PDK1,downstream_gene_variant,,ENST00000443353,;PDK1,downstream_gene_variant,,ENST00000439519,;PDK1,3_prime_UTR_variant,,ENST00000431718,;PDK1,upstream_gene_variant,,ENST00000466437,;PDK1,downstream_gene_variant,,ENST00000436490,; C ENST00000392571 Transcript missense_variant 955/1515 811/1371 271/456 E/Q Gaa/Caa 1 1 PDK1 HGNC HGNC:8809 protein_coding YES CCDS63059.1 ENSP00000376352 Q15118 UPI0000D6BFDD NM_001278549.1 tolerated(0.17) 7/12 Gene3D:3.30.565.10,hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF14 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 172566915 172566915 G C 1 0 0 0 0 1 0 0 0 11763 943 33 4 4 PDK1 2 172566915 Missense_Mutation SNP G C3L-00093_T 7243691 172566915 69626614 19 2871 IMPDH2 0 . GRCh38 3 49026375 49026375 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.955G>C p.Asp319His p.D319H ENST00000326739 9/14 204 181 23 134 134 0 strelka-varscan IMPDH2,missense_variant,p.Asp319His,ENST00000326739,NM_000884.2;IMPDH2,missense_variant,p.Asp251His,ENST00000429182,;QRICH1,downstream_gene_variant,,ENST00000395443,NM_198880.1;QRICH1,downstream_gene_variant,,ENST00000357496,NM_017730.2;QRICH1,downstream_gene_variant,,ENST00000424300,;NDUFAF3,downstream_gene_variant,,ENST00000326925,NM_199069.1;IMPDH2,downstream_gene_variant,,ENST00000442157,;DALRD3,upstream_gene_variant,,ENST00000496568,;NDUFAF3,downstream_gene_variant,,ENST00000395458,NM_199073.1;NDUFAF3,downstream_gene_variant,,ENST00000451378,NM_199070.1;NDUFAF3,downstream_gene_variant,,ENST00000326912,NM_199074.1;RP13-131K19.6,upstream_gene_variant,,ENST00000607245,;DALRD3,upstream_gene_variant,,ENST00000492585,;IMPDH2,non_coding_transcript_exon_variant,,ENST00000462980,;QRICH1,downstream_gene_variant,,ENST00000498392,;QRICH1,downstream_gene_variant,,ENST00000489642,;IMPDH2,downstream_gene_variant,,ENST00000485500,;IMPDH2,downstream_gene_variant,,ENST00000491610,;IMPDH2,upstream_gene_variant,,ENST00000481274,;NDUFAF3,downstream_gene_variant,,ENST00000496152,;NDUFAF3,downstream_gene_variant,,ENST00000480392,;IMPDH2,downstream_gene_variant,,ENST00000496837,;IMPDH2,upstream_gene_variant,,ENST00000466147,;IMPDH2,upstream_gene_variant,,ENST00000484872,;IMPDH2,upstream_gene_variant,,ENST00000472328,;IMPDH2,upstream_gene_variant,,ENST00000463903,; G ENST00000326739 Transcript missense_variant 995/1643 955/1545 319/514 D/H Gat/Cat 1 -1 IMPDH2 HGNC HGNC:6053 protein_coding YES CCDS2786.1 ENSP00000321584 P12268 UPI000004A47A NM_000884.2 deleterious(0.01) 9/14 HAMAP:MF_01964,PIRSF_domain:PIRSF000130,Pfam_domain:PF00478,TIGRFAM_domain:TIGR01302,Gene3D:3.20.20.70,SMART_domains:SM01240,Superfamily_domains:SSF51412 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 8 49026375 49026375 C G 1 0 0 0 0 1 0 0 0 7629 855 30 4 4 IMPDH2 3 49026375 Missense_Mutation SNP C C3L-00093_T 49026375 149269184 20 2872 IL17RD 0 . GRCh38 3 57104395 57104395 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.760G>A p.Glu254Lys p.E254K ENST00000296318 8/13 191 179 12 152 152 0 strelka-varscan IL17RD,missense_variant,p.Glu254Lys,ENST00000296318,NM_001318864.1,NM_017563.3;IL17RD,missense_variant,p.Glu110Lys,ENST00000320057,;IL17RD,missense_variant,p.Glu110Lys,ENST00000463523,;IL17RD,downstream_gene_variant,,ENST00000467210,;IL17RD,non_coding_transcript_exon_variant,,ENST00000469841,; T ENST00000296318 Transcript missense_variant 849/8720 760/2220 254/739 E/K Gag/Aag 1 -1 IL17RD HGNC HGNC:17616 protein_coding YES CCDS2880.2 ENSP00000296318 Q8NFM7 UPI0000047CC3 NM_001318864.1,NM_017563.3 tolerated(0.53) 8/13 Low_complexity_(Seg):seg,hmmpanther:PTHR15583:SF14,hmmpanther:PTHR15583 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 57104395 57104395 C T 1 0 0 0 0 1 0 0 0 7550 922 32 3 3 IL17RD 3 57104395 Missense_Mutation SNP C C3L-00093_T 8078020 57104395 141191164 21 2873 KALRN 0 . GRCh38 3 124268854 124268854 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.562C>T p.Leu188Phe p.L188F ENST00000240874 5/34 479 420 59 299 299 0 strelka-varscan KALRN,missense_variant,p.Leu188Phe,ENST00000360013,NM_001024660.3;KALRN,missense_variant,p.Leu166Phe,ENST00000354186,;KALRN,missense_variant,p.Leu188Phe,ENST00000240874,NM_003947.4;KALRN,missense_variant,p.Leu188Phe,ENST00000460856,NM_001322989.1;KALRN,missense_variant,p.Leu216Phe,ENST00000448253,;KALRN,non_coding_transcript_exon_variant,,ENST00000498499,; T ENST00000240874 Transcript missense_variant 719/6537 562/4992 188/1663 L/F Ctc/Ttc 1 1 KALRN HGNC HGNC:4814 protein_coding YES CCDS3027.1 ENSP00000240874 O60229 UPI000012C095 NM_003947.4 deleterious(0.01) 5/34 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 124268854 124268854 C T 1 0 0 0 0 1 0 0 0 7884 797 28 3 3 KALRN 3 124268854 Missense_Mutation SNP C C3L-00093_T 67164459 124268854 74026705 22 2874 TNIK 0 . GRCh38 3 171085154 171085154 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.2962G>A p.Asp988Asn p.D988N ENST00000436636 25/33 145 131 14 104 104 0 strelka-varscan TNIK,missense_variant,p.Asp988Asn,ENST00000436636,NM_015028.2;TNIK,missense_variant,p.Asp904Asn,ENST00000341852,NM_001161565.1;TNIK,missense_variant,p.Asp980Asn,ENST00000284483,NM_001161560.1;TNIK,missense_variant,p.Asp959Asn,ENST00000357327,NM_001161561.1;TNIK,missense_variant,p.Asp951Asn,ENST00000470834,NM_001161562.1;TNIK,missense_variant,p.Asp933Asn,ENST00000488470,NM_001161563.1;TNIK,missense_variant,p.Asp925Asn,ENST00000460047,NM_001161564.1;TNIK,missense_variant,p.Asp896Asn,ENST00000475336,NM_001161566.1;TNIK,non_coding_transcript_exon_variant,,ENST00000496492,;TNIK,upstream_gene_variant,,ENST00000484051,; T ENST00000436636 Transcript missense_variant 3307/6970 2962/4083 988/1360 D/N Gat/Aat 1 -1 TNIK HGNC HGNC:30765 protein_coding YES CCDS46956.1 ENSP00000399511 Q9UKE5 UPI000003ABDF NM_015028.2 tolerated(0.35) 25/33 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 171085154 171085154 C T 1 0 0 0 0 1 0 0 0 16786 826 29 3 3 TNIK 3 171085154 Missense_Mutation SNP C C3L-00093_T 46816300 171085154 27210405 23 2875 ACAP2 0 . GRCh38 3 195320750 195320750 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.808G>A p.Glu270Lys p.E270K ENST00000326793 10/23 168 155 13 143 143 0 strelka-varscan ACAP2,missense_variant,p.Glu270Lys,ENST00000326793,NM_012287.5;ACAP2,missense_variant,p.Glu269Lys,ENST00000618471,;ACAP2,missense_variant,p.Glu270Lys,ENST00000635383,;ACAP2,missense_variant,p.Glu145Lys,ENST00000439758,; T ENST00000326793 Transcript missense_variant 1039/7160 808/2337 270/778 E/K Gaa/Aaa 1 -1 ACAP2 HGNC HGNC:16469 protein_coding YES CCDS33924.1 ENSP00000324287 Q15057 UPI0000141A1A NM_012287.5 deleterious(0) 10/23 PROSITE_profiles:PS50003,hmmpanther:PTHR23180:SF241,hmmpanther:PTHR23180,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.51895 0.9999997 1 1 1 0 T 3 4 8 195320750 195320750 C T 1 0 0 0 0 1 0 0 0 162 864 30 3 3 ACAP2 3 195320750 Missense_Mutation SNP C C3L-00093_T 24235596 195320750 2974809 24 2876 LRRC66 0 . GRCh38 4 51995604 51995604 + Missense_Mutation SNP C C G C3L-00093_T C3L-00093_N C C c.1418G>C p.Arg473Thr p.R473T ENST00000343457 4/4 273 237 36 178 178 0 strelka-varscan LRRC66,missense_variant,p.Arg473Thr,ENST00000343457,NM_001024611.1; G ENST00000343457 Transcript missense_variant 1425/3327 1418/2643 473/880 R/T aGa/aCa COSM4699160 1 -1 LRRC66 HGNC HGNC:34299 protein_coding YES CCDS43229.1 ENSP00000341944 Q68CR7 UPI0000425C5B NM_001024611.1 tolerated(0.11) 4/4 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 51995604 51995604 C G 1 0 0 0 0 1 0 0 0 8914 913 32 4 4 LRRC66 4 51995604 Missense_Mutation SNP C C3L-00093_T 51995604 138218951 25 2877 PDGFRA 0 . GRCh38 4 54285470 54285470 + Missense_Mutation SNP T T A novel C3L-00093_T C3L-00093_N T T c.2423T>A p.Phe808Tyr p.F808Y ENST00000257290 17/23 494 423 71 362 362 0 strelka-varscan PDGFRA,missense_variant,p.Phe808Tyr,ENST00000257290,NM_006206.4;RP11-231C18.3,missense_variant,p.Phe568Tyr,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000509490,;PDGFRA,downstream_gene_variant,,ENST00000509092,;PDGFRA,downstream_gene_variant,,ENST00000507536,; A ENST00000257290 Transcript missense_variant 2754/6576 2423/3270 808/1089 F/Y tTt/tAt 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 deleterious(0) 17/23 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00220,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 54285470 54285470 T A 1 0 0 0 0 1 0 0 0 11749 1841 64 4 4 PDGFRA 4 54285470 Missense_Mutation SNP T C3L-00093_T 2289866 54285470 135929085 26 2878 FAT4 0 . GRCh38 4 125316769 125316769 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.358G>A p.Glu120Lys p.E120K ENST00000394329 1/17 286 265 21 170 170 0 strelka-varscan-mutect FAT4,missense_variant,p.Glu120Lys,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; A ENST00000394329 Transcript missense_variant 371/16123 358/14946 120/4981 E/K Gaa/Aaa 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.01) 1/17 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs1165902550 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 125316769 125316769 G A 1 0 0 0 0 1 0 0 0 5552 1059 37 1 1 FAT4 4 125316769 Missense_Mutation SNP G C3L-00093_T 71031299 125316769 64897786 27 2879 FAM160A1 0 . GRCh38 4 151586691 151586691 + Silent SNP A A T novel C3L-00093_T C3L-00093_N A A c.783A>T p.= p.L261L ENST00000435205 6/14 113 104 9 76 76 0 strelka-varscan-mutect FAM160A1,synonymous_variant,p.=,ENST00000435205,NM_001109977.1;FAM160A1,synonymous_variant,p.=,ENST00000505231,; T ENST00000435205 Transcript synonymous_variant 1358/4576 783/3123 261/1040 L ctA/ctT 1 1 FAM160A1 HGNC HGNC:34237 protein_coding YES CCDS47146.1 ENSP00000413196 Q05DH4 UPI00015DE720 NM_001109977.1 6/14 hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF6,Pfam_domain:PF10257 LOW 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -18.0484 1 1 1 1 0 T 2 4 8 151586691 151586691 A T 1 0 0 0 0 0 0 0 1 5317 407 15 4 4 FAM160A1 4 151586691 Silent SNP A C3L-00093_T 26269922 151586691 38627864 28 2880 SLC45A2 0 . GRCh38 5 33963919 33963919 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.660C>G p.Phe220Leu p.F220L ENST00000296589 3/7 444 408 36 273 273 0 strelka-varscan-mutect SLC45A2,missense_variant,p.Phe220Leu,ENST00000382102,NM_001012509.3;SLC45A2,missense_variant,p.Phe220Leu,ENST00000296589,NM_016180.4;SLC45A2,missense_variant,p.Phe45Leu,ENST00000510600,;SLC45A2,intron_variant,,ENST00000509381,NM_001297417.2;SLC45A2,non_coding_transcript_exon_variant,,ENST00000505056,; C ENST00000296589 Transcript missense_variant 807/1772 660/1593 220/530 F/L ttC/ttG 1 -1 SLC45A2 HGNC HGNC:16472 protein_coding YES CCDS3901.1 ENSP00000296589 Q9UMX9 A0A076YIB8 UPI00001AEC19 NM_016180.4 tolerated(0.29) 3/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF34,Gene3D:1.20.1250.20,Pfam_domain:PF13347,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 33963919 33963919 G C 1 0 0 0 0 1 0 0 0 14918 933 33 4 4 SLC45A2 5 33963919 Missense_Mutation SNP G C3L-00093_T 33963919 147574340 29 2881 MCIDAS 0 . GRCh38 5 55220555 55220555 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.969C>T p.= p.F323F ENST00000513312 7/7 334 308 26 165 165 0 strelka-varscan MCIDAS,synonymous_variant,p.=,ENST00000513312,NM_001190787.1;MCIDAS,downstream_gene_variant,,ENST00000515336,;MCIDAS,3_prime_UTR_variant,,ENST00000513468,; A ENST00000513312 Transcript synonymous_variant 1146/1736 969/1158 323/385 F ttC/ttT 1 -1 MCIDAS HGNC HGNC:40050 protein_coding YES CCDS54853.1 ENSP00000426359 D6RGH6 UPI000020C760 NM_001190787.1 7/7 hmmpanther:PTHR13372,hmmpanther:PTHR13372:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 55220555 55220555 G A 1 0 0 0 0 0 0 0 1 9315 1165 41 3 3 MCIDAS 5 55220555 Silent SNP G C3L-00093_T 21256636 55220555 126317704 30 2882 RAD50 0 . GRCh38 5 132579432 132579432 + Missense_Mutation SNP G G C rs770695705 C3L-00093_T C3L-00093_N G G c.481G>C p.Asp161His p.D161H ENST00000378823 4/25 282 260 22 172 172 0 strelka-varscan-mutect RAD50,missense_variant,p.Asp161His,ENST00000378823,NM_005732.3;RAD50,missense_variant,p.Asp161His,ENST00000453394,;RAD50,missense_variant,p.Asp62His,ENST00000416135,;RAD50,missense_variant,p.Asp161His,ENST00000423956,;RAD50,3_prime_UTR_variant,,ENST00000533482,;RAD50,upstream_gene_variant,,ENST00000487596,; C ENST00000378823 Transcript missense_variant 868/8306 481/3939 161/1312 D/H Gat/Cat rs770695705 1 1 RAD50 HGNC HGNC:9816 protein_coding YES CCDS34233.1 ENSP00000368100 Q92878 UPI000006E9ED NM_005732.3 deleterious(0) 4/25 Gene3D:3.40.50.300,Pfam_domain:PF13476,hmmpanther:PTHR18867,hmmpanther:PTHR18867:SF12,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00606 MODERATE 1 SNV 1 1 PASS rs770695705 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 132579432 132579432 G C 1 0 0 0 0 1 0 0 0 13145 942 33 4 4 RAD50 5 132579432 Missense_Mutation SNP G C3L-00093_T 77358877 132579432 48958827 31 2883 SIL1 0 . GRCh38 5 139050992 139050992 + Missense_Mutation SNP C C T C3L-00093_T C3L-00093_N C C c.299G>A p.Arg100Lys p.R100K ENST00000394817 4/10 643 589 54 405 405 0 strelka-varscan-mutect SIL1,missense_variant,p.Arg100Lys,ENST00000394817,NM_022464.4;SIL1,missense_variant,p.Arg100Lys,ENST00000265195,NM_001037633.1;SIL1,missense_variant,p.Arg107Lys,ENST00000509534,;SIL1,missense_variant,p.Arg100Lys,ENST00000508639,;SIL1,missense_variant,p.Arg110Lys,ENST00000507002,;SIL1,missense_variant,p.Arg100Lys,ENST00000513453,;SIL1,missense_variant,p.Arg110Lys,ENST00000505830,;SIL1,downstream_gene_variant,,ENST00000505353,;CTB-46B19.2,intron_variant,,ENST00000512875,;SIL1,non_coding_transcript_exon_variant,,ENST00000503732,; T ENST00000394817 Transcript missense_variant 439/1923 299/1386 100/461 R/K aGa/aAa COSM5232714 1 -1 SIL1 HGNC HGNC:24624 protein_coding YES CCDS4209.1 ENSP00000378294 Q9H173 A0A0S2Z6B4 UPI000003ED21 NM_022464.4 tolerated(0.16) 4/10 hmmpanther:PTHR19316:SF6,hmmpanther:PTHR19316 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 139050992 139050992 C T 1 0 0 0 0 1 0 0 0 14585 913 32 3 3 SIL1 5 139050992 Missense_Mutation SNP C C3L-00093_T 6471560 139050992 42487267 32 2884 SLC23A1 0 . GRCh38 5 139372233 139372233 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.1582C>T p.= p.L528L ENST00000353963 14/15 201 184 17 100 100 0 strelka-varscan-mutect SLC23A1,synonymous_variant,p.=,ENST00000353963,NM_152685.3;SLC23A1,synonymous_variant,p.=,ENST00000348729,NM_005847.4;PAIP2,downstream_gene_variant,,ENST00000394795,;PAIP2,downstream_gene_variant,,ENST00000265192,NM_016480.4;PAIP2,downstream_gene_variant,,ENST00000510080,NM_001033112.2;PAIP2,downstream_gene_variant,,ENST00000511706,;CTB-43P18.1,upstream_gene_variant,,ENST00000503553,;PAIP2,downstream_gene_variant,,ENST00000511381,; A ENST00000353963 Transcript synonymous_variant 1621/2303 1582/1809 528/602 L Ctg/Ttg 1 -1 SLC23A1 HGNC HGNC:10974 protein_coding YES CCDS4213.1 ENSP00000302851 Q9UHI7 UPI000002B46B NM_152685.3 14/15 hmmpanther:PTHR11119,hmmpanther:PTHR11119:SF21 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 139372233 139372233 G A 1 0 0 0 0 0 0 0 1 14728 933 33 3 3 SLC23A1 5 139372233 Silent SNP G C3L-00093_T 321241 139372233 42166026 33 2885 PCDHA9 0 . GRCh38 5 140850124 140850124 + Silent SNP G G A C3L-00093_T C3L-00093_N G G c.1629G>A p.= p.P543P ENST00000532602 1/4 824 752 72 509 509 0 varscan-mutect PCDHA9,synonymous_variant,p.=,ENST00000378122,NM_014005.4;PCDHA9,synonymous_variant,p.=,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; A ENST00000532602 Transcript synonymous_variant 2662/6293 1629/2853 543/950 P ccG/ccA COSM262781,COSM262782 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 LOW 1 SNV 1 1,1 1 PASS rs1321633502 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 140850124 140850124 G A 1 0 0 0 0 0 0 0 1 11618 1074 38 1 1 PCDHA9 5 140850124 Silent SNP G C3L-00093_T 1477891 140850124 40688135 34 2886 PCDHB14 0 . GRCh38 5 141224472 141224472 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.967G>C p.Asp323His p.D323H ENST00000239449 1/1 143 131 12 108 108 0 strelka-varscan-mutect PCDHB14,missense_variant,p.Asp323His,ENST00000239449,NM_018934.3;PCDHB14,missense_variant,p.Asp170His,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; C ENST00000239449 Transcript missense_variant 1541/4828 967/2397 323/798 D/H Gat/Cat 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 141224472 141224472 G C 1 0 0 0 0 1 0 0 0 11626 942 33 4 4 PCDHB14 5 141224472 Missense_Mutation SNP G C3L-00093_T 374348 141224472 40313787 35 2887 PCDHGA5 0 . GRCh38 5 141365200 141365200 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.870G>A p.= p.E290E ENST00000518069 1/4 259 235 24 149 149 0 strelka-varscan-mutect PCDHGA5,synonymous_variant,p.=,ENST00000518069,NM_018918.2;PCDHGA5,synonymous_variant,p.=,ENST00000611914,NM_032054.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,downstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000518069 Transcript synonymous_variant 870/4602 870/2796 290/931 E gaG/gaA 1 1 PCDHGA5 HGNC HGNC:8703 protein_coding YES CCDS54925.1 ENSP00000429834 Q9Y5G8 UPI000006CD9F NM_018918.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF105,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 141365200 141365200 G A 1 0 0 0 0 0 0 0 1 11644 933 33 3 3 PCDHGA5 5 141365200 Silent SNP G C3L-00093_T 140728 141365200 40173059 36 2888 GRPEL2 0 . GRCh38 5 149349707 149349707 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.285G>C p.Gln95His p.Q95H ENST00000329271 3/4 253 234 19 195 195 0 strelka-varscan-mutect GRPEL2,missense_variant,p.Gln95His,ENST00000329271,NM_152407.3;GRPEL2,missense_variant,p.Gln95His,ENST00000513661,;GRPEL2,intron_variant,,ENST00000416916,;GRPEL2-AS1,intron_variant,,ENST00000521295,;GRPEL2,non_coding_transcript_exon_variant,,ENST00000507562,; C ENST00000329271 Transcript missense_variant 395/4089 285/678 95/225 Q/H caG/caC 1 1 GRPEL2 HGNC HGNC:21060 protein_coding YES CCDS4295.1 ENSP00000329558 Q8TAA5 UPI000004A0F1 NM_152407.3 deleterious(0.02) 3/4 HAMAP:MF_01151,hmmpanther:PTHR21237,hmmpanther:PTHR21237:SF10,Pfam_domain:PF01025,Gene3D:1dkgA01,Superfamily_domains:0053405,Prints_domain:PR00773 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 149349707 149349707 G C 1 0 0 0 0 1 0 0 0 6689 933 33 4 4 GRPEL2 5 149349707 Missense_Mutation SNP G C3L-00093_T 7984507 149349707 32188552 37 2889 FAM196B 0 . GRCh38 5 169882744 169882744 + Silent SNP C C T C3L-00093_T C3L-00093_N C C c.1155G>A p.= p.R385R ENST00000377365 2/4 315 296 19 187 187 0 strelka-varscan-mutect FAM196B,synonymous_variant,p.=,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; T ENST00000377365 Transcript synonymous_variant 2537/2999 1155/1608 385/535 R agG/agA COSM1435934 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 1 LOW SNV 2 1 1 PASS rs1218956347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 169882744 169882744 C T 1 0 0 0 0 0 0 0 1 5374 854 30 3 3 FAM196B 5 169882744 Silent SNP C C3L-00093_T 20533037 169882744 11655515 38 2890 MOG 0 . GRCh38 6 29659462 29659462 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.232C>T p.His78Tyr p.H78Y ENST00000376898 2/8 308 282 26 186 186 0 strelka-varscan-mutect MOG,missense_variant,p.His78Tyr,ENST00000376894,;MOG,missense_variant,p.His78Tyr,ENST00000376917,NM_206809.3;MOG,missense_variant,p.His78Tyr,ENST00000431798,NM_206812.3;MOG,missense_variant,p.His78Tyr,ENST00000376898,NM_002433.4;MOG,missense_variant,p.His78Tyr,ENST00000494692,NM_206811.3;MOG,missense_variant,p.His78Tyr,ENST00000396701,NM_206810.3;MOG,missense_variant,p.His78Tyr,ENST00000376891,NM_001008229.2;MOG,missense_variant,p.His78Tyr,ENST00000396704,NM_001008228.2;MOG,missense_variant,p.His78Tyr,ENST00000416766,;MOG,intron_variant,,ENST00000376888,NM_206814.5;MOG,intron_variant,,ENST00000490427,NM_001170418.1;MOG,intron_variant,,ENST00000483013,;MOG,non_coding_transcript_exon_variant,,ENST00000469603,;MOG,non_coding_transcript_exon_variant,,ENST00000476244,;MOG,missense_variant,p.His49Tyr,ENST00000376889,;MOG,missense_variant,p.His49Tyr,ENST00000485211,;MOG,3_prime_UTR_variant,,ENST00000376903,;MOG,non_coding_transcript_exon_variant,,ENST00000469353,; T ENST00000376898 Transcript missense_variant 232/1027 232/759 78/252 H/Y Cat/Tat 1 1 MOG HGNC HGNC:7197 protein_coding YES CCDS4667.1 ENSP00000366095 Q16653 UPI00004573E8 NM_002433.4 tolerated(0.05) 2/8 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,Gene3D:2.60.40.10,PIRSF_domain:PIRSF016522,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 29659462 29659462 C T 1 0 0 0 0 1 0 0 0 9656 826 29 3 3 MOG 6 29659462 Missense_Mutation SNP C C3L-00093_T 29659462 141146517 39 2891 USP49 0 . GRCh38 6 41806332 41806332 + Missense_Mutation SNP C C T rs548556992 C3L-00093_T C3L-00093_N C C c.652G>A p.Asp218Asn p.D218N ENST00000394253 3/7 87 81 6 59 59 0 strelka-mutect USP49,missense_variant,p.Asp218Asn,ENST00000394253,NM_001286554.1;USP49,missense_variant,p.Asp218Asn,ENST00000373006,NM_018561.4;USP49,missense_variant,p.Asp218Asn,ENST00000373010,;USP49,downstream_gene_variant,,ENST00000423567,;USP49,upstream_gene_variant,,ENST00000448078,; T ENST00000394253 Transcript missense_variant 982/9034 652/2067 218/688 D/N Gac/Aac rs548556992,COSM4811987,COSM596684 1 -1 USP49 HGNC HGNC:20078 protein_coding YES CCDS69111.1 ENSP00000377797 Q70CQ1 UPI000020DCE0 NM_001286554.1 tolerated(0.49) 3/7 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs548556992 . 0 208 2 0 0 0 0 0 -13.24931 1 1 1 1 0 T 3 4 8 41806332 41806332 C T 1 0 0 0 0 1 0 0 0 17623 884 31 1 1 USP49 6 41806332 Missense_Mutation SNP C C3L-00093_T 12146870 41806332 128999647 40 2892 CUL7 0 . GRCh38 6 43048397 43048398 + Frame_Shift_Ins INS - - A novel C3L-00093_T C3L-00093_N - - c.2249dupT p.Leu751ProfsTer13 p.L751Pfs*13 ENST00000535468 8/26 354 299 55 273 273 0 sindel-varindel-pindel CUL7,frameshift_variant,p.Leu751ProfsTer13,ENST00000535468,NM_001168370.1;CUL7,frameshift_variant,p.Leu667ProfsTer13,ENST00000265348,NM_014780.4;CUL7,upstream_gene_variant,,ENST00000478630,;KLC4,intron_variant,,ENST00000467906,; A ENST00000535468 Transcript frameshift_variant 2336-2337/5504 2249-2250/5349 750/1782 F/FX ttc/ttTc 1 -1 CUL7 HGNC HGNC:21024 protein_coding YES CCDS55003.1 ENSP00000438788 Q14999 UPI0001BE8116 NM_001168370.1 8/26 Low_complexity_(Seg):seg,hmmpanther:PTHR22771,hmmpanther:PTHR22771:SF3,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 insertion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 8 43048397 43048397 - A 1 0 1 1 0 0 0 0 0 3870 1165 41 0 0 CUL7 6 43048397 Frame_Shift_Ins INS - C3L-00093_T 1242065 43048397 127757582 41 2893 ICK 0 . GRCh38 6 53013683 53013683 + Silent SNP G G C novel C3L-00093_T C3L-00093_N G G c.1131C>G p.= p.L377L ENST00000356971 10/15 213 195 18 131 131 0 strelka-varscan-mutect ICK,synonymous_variant,p.=,ENST00000356971,NM_016513.4;ICK,synonymous_variant,p.=,ENST00000350082,NM_014920.3; C ENST00000356971 Transcript synonymous_variant 1621/6227 1131/1899 377/632 L ctC/ctG 1 -1 ICK HGNC HGNC:21219 protein_coding YES CCDS4949.1 ENSP00000349458 Q9UPZ9 A0A024RD59 UPI0000073DE8 NM_016513.4 10/15 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 8 53013683 53013683 G C 1 0 0 0 0 0 0 0 1 7386 1161 41 4 4 ICK 6 53013683 Silent SNP G C3L-00093_T 9965286 53013683 117792296 42 2894 BMP5 0 . GRCh38 6 55874616 55874616 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.250C>T p.Leu84Phe p.L84F ENST00000370830 1/7 524 479 45 359 359 0 strelka-varscan-mutect BMP5,missense_variant,p.Leu84Phe,ENST00000370830,NM_021073.2; A ENST00000370830 Transcript missense_variant 949/3952 250/1365 84/454 L/F Ctc/Ttc 1 -1 BMP5 HGNC HGNC:1072 protein_coding YES CCDS4958.1 ENSP00000359866 P22003 M9VUD0 UPI0000126A2C NM_021073.2 deleterious(0) 1/7 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF139 MODERATE 1 SNV 1 1 PASS rs1220935838 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 55874616 55874616 G A 1 0 0 0 0 1 0 0 0 1618 942 33 3 3 BMP5 6 55874616 Missense_Mutation SNP G C3L-00093_T 2860933 55874616 114931363 43 2895 MDN1 0 . GRCh38 6 89790200 89790200 + Nonsense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.1057C>T p.Gln353Ter p.Q353* ENST00000369393 6/102 320 301 19 197 197 0 strelka-varscan-mutect MDN1,stop_gained,p.Gln353Ter,ENST00000369393,NM_014611.2;MDN1,stop_gained,p.Gln353Ter,ENST00000629399,;MDN1,stop_gained,p.Gln353Ter,ENST00000439638,; A ENST00000369393 Transcript stop_gained 1173/18413 1057/16791 353/5596 Q/* Cag/Tag 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 6/102 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64,SMART_domains:SM00382,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 8 89790200 89790200 G A 1 0 0 0 0 0 1 0 0 9353 1299 45 3 3 MDN1 6 89790200 Nonsense_Mutation SNP G C3L-00093_T 33915584 89790200 81015779 44 2896 C6orf203 0 . GRCh38 6 107039980 107039980 + Missense_Mutation SNP C C G C3L-00093_T C3L-00093_N C C c.235C>G p.Pro79Ala p.P79A ENST00000625458 3/5 373 341 32 241 241 0 strelka-varscan-mutect C6orf203,missense_variant,p.Pro74Ala,ENST00000405204,NM_001142468.2;C6orf203,missense_variant,p.Pro79Ala,ENST00000625458,NM_001142470.2;C6orf203,missense_variant,p.Pro74Ala,ENST00000311381,NM_016487.4;C6orf203,upstream_gene_variant,,ENST00000489790,; G ENST00000625458 Transcript missense_variant 544/1146 235/738 79/245 P/A Cca/Gca COSM5697989 1 1 C6orf203 HGNC HGNC:17971 protein_coding YES CCDS78167.1 ENSP00000485698 A0A0D9SEI0 UPI0000D4EA45 NM_001142470.2 deleterious(0.03) 3/5 hmmpanther:PTHR13633,hmmpanther:PTHR13633:SF3 1 MODERATE 1 SNV 3 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 107039980 107039980 C G 1 0 0 0 0 1 0 0 0 2123 855 30 4 4 C6orf203 6 107039980 Missense_Mutation SNP C C3L-00093_T 17249780 107039980 63765999 45 2897 TRDN 0 . GRCh38 6 123377899 123377899 + Splice_Site SNP C C G novel C3L-00093_T C3L-00093_N C C c.1187-1G>C p.X396_splice ENST00000334268 96 88 8 71 71 0 strelka-varscan-mutect TRDN,splice_acceptor_variant,,ENST00000334268,NM_006073.3; G ENST00000334268 Transcript splice_acceptor_variant -/4770 1187/2190 396/729 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 16/40 HIGH 1 SNV 1 1 PASS rs1478639470 . 0 207 3 0 0 0 0 0 -16.72419 1 1 1 1 0 G 5 3 8 123377899 123377899 C G 1 0 0 0 0 0 0 1 0 16957 927 32 4 4 TRDN 6 123377899 Splice_Site SNP C C3L-00093_T 16337919 123377899 47428080 46 2898 EPB41L2 0 . GRCh38 6 130904533 130904533 + Silent SNP T T C novel C3L-00093_T C3L-00093_N T T c.861A>G p.= p.P287P ENST00000337057 6/20 109 103 6 79 79 0 strelka-varscan-mutect EPB41L2,synonymous_variant,p.=,ENST00000337057,NM_001431.3;EPB41L2,synonymous_variant,p.=,ENST00000368128,;EPB41L2,synonymous_variant,p.=,ENST00000628542,;EPB41L2,synonymous_variant,p.=,ENST00000527411,;EPB41L2,synonymous_variant,p.=,ENST00000530481,NM_001199388.2;EPB41L2,synonymous_variant,p.=,ENST00000445890,;EPB41L2,synonymous_variant,p.=,ENST00000528282,NM_001252660.1;EPB41L2,synonymous_variant,p.=,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,synonymous_variant,p.=,ENST00000529208,;EPB41L2,synonymous_variant,p.=,ENST00000525271,;EPB41L2,synonymous_variant,p.=,ENST00000527659,;EPB41L2,synonymous_variant,p.=,ENST00000525193,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000530148,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000528179,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000526333,; C ENST00000337057 Transcript synonymous_variant 1043/4457 861/3018 287/1005 P ccA/ccG 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 6/20 Gene3D:3.10.20.90,PIRSF_domain:PIRSF002304,Prints_domain:PR00661,PROSITE_patterns:PS00660,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF17,SMART_domains:SM00295,Superfamily_domains:SSF54236 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 8 130904533 130904533 T C 1 0 0 0 0 0 0 0 1 5000 1451 51 5 5 EPB41L2 6 130904533 Silent SNP T C3L-00093_T 7526634 130904533 39901446 47 2899 SDK1 0 . GRCh38 7 4017336 4017336 + Missense_Mutation SNP G G C rs774036784 C3L-00093_T C3L-00093_N G G c.2586G>C p.Glu862Asp p.E862D ENST00000404826 17/45 114 108 6 63 63 0 strelka-mutect SDK1,missense_variant,p.Glu862Asp,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Glu862Asp,ENST00000615806,;SDK1,missense_variant,p.Glu862Asp,ENST00000389531,; C ENST00000404826 Transcript missense_variant 2725/10397 2586/6642 862/2213 E/D gaG/gaC rs774036784 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0.05) 17/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs774036784 . 0 207 3 0 0 0 0 0 -12.24452 1 1 1 1 0 C 3 2 8 4017336 4017336 G C 1 0 0 0 0 1 0 0 0 14243 1020 36 4 4 SDK1 7 4017336 Missense_Mutation SNP G C3L-00093_T 4017336 155328637 48 2900 SDK1 0 . GRCh38 7 4114254 4114254 + Missense_Mutation SNP G G A rs750500679 C3L-00093_T C3L-00093_N G G c.3803G>A p.Arg1268Gln p.R1268Q ENST00000404826 25/45 299 273 26 156 156 0 strelka-varscan-mutect SDK1,missense_variant,p.Arg1268Gln,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Arg1268Gln,ENST00000615806,;SDK1,missense_variant,p.Arg1268Gln,ENST00000389531,; A ENST00000404826 Transcript missense_variant 3942/10397 3803/6642 1268/2213 R/Q cGg/cAg rs750500679,COSM1450686 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 tolerated(0.45) 25/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs750500679 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 4114254 4114254 G A 1 0 0 0 0 1 0 0 0 14243 1116 39 1 1 SDK1 7 4114254 Missense_Mutation SNP G C3L-00093_T 96918 4114254 155231719 49 2901 NXPH1 0 . GRCh38 7 8751580 8751580 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.627C>T p.= p.L209L ENST00000405863 3/3 234 214 20 116 116 0 strelka-varscan-mutect NXPH1,synonymous_variant,p.=,ENST00000405863,NM_152745.2;NXPH1,synonymous_variant,p.=,ENST00000602349,;NXPH1,downstream_gene_variant,,ENST00000429542,;NXPH1,downstream_gene_variant,,ENST00000438764,;NXPH1,non_coding_transcript_exon_variant,,ENST00000497400,; T ENST00000405863 Transcript synonymous_variant 1538/2921 627/816 209/271 L ctC/ctT 1 1 NXPH1 HGNC HGNC:20693 protein_coding YES CCDS47540.1 ENSP00000384551 P58417 Q3LID8 UPI000000DC02 NM_152745.2 3/3 hmmpanther:PTHR17103:SF13,hmmpanther:PTHR17103,PIRSF_domain:PIRSF038019,Pfam_domain:PF06312 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 8751580 8751580 C T 1 0 0 0 0 0 0 0 1 10866 900 32 3 3 NXPH1 7 8751580 Silent SNP C C3L-00093_T 4637326 8751580 150594393 50 2902 CDK13 0 . GRCh38 7 39988196 39988196 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.1809C>T p.= p.V603V ENST00000181839 2/14 328 288 40 165 165 0 strelka-varscan-mutect CDK13,synonymous_variant,p.=,ENST00000181839,NM_003718.4;CDK13,synonymous_variant,p.=,ENST00000340829,NM_031267.3;CDK13,5_prime_UTR_variant,,ENST00000613626,;CDK13,5_prime_UTR_variant,,ENST00000611390,;CDK13,non_coding_transcript_exon_variant,,ENST00000484589,; T ENST00000181839 Transcript synonymous_variant 2414/7298 1809/4539 603/1512 V gtC/gtT 1 1 CDK13 HGNC HGNC:1733 protein_coding YES CCDS5461.1 ENSP00000181839 Q14004 A0A024RA85 UPI000013C5E3 NM_003718.4 2/14 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 39988196 39988196 C T 1 0 0 0 0 0 0 0 1 2833 813 29 3 3 CDK13 7 39988196 Silent SNP C C3L-00093_T 31236616 39988196 119357777 51 2903 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3L-00093_T C3L-00093_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 652 495 157 362 362 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3L-00093_T 15203626 55191822 104154151 52 2904 EGFR 0 . GRCh38 7 55191861 55191861 + Missense_Mutation SNP C C G rs397517134 C3L-00093_T C3L-00093_N C C c.2612C>G p.Ala871Gly p.A871G ENST00000275493 21/28 577 430 147 376 376 0 strelka-varscan-mutect EGFR,missense_variant,p.Ala871Gly,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Ala826Gly,ENST00000454757,;EGFR,missense_variant,p.Ala826Gly,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2789/9821 2612/3633 871/1210 A/G gCa/gGa rs397517134,COSM13008,COSM710350 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0.04) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs397517134 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 55191861 55191861 C G 1 0 0 0 0 1 0 0 0 4803 710 25 4 4 EGFR 7 55191861 Missense_Mutation SNP C C3L-00093_T 39 55191861 104154112 53 2905 ASL 0 . GRCh38 7 66089680 66089680 + Silent SNP C C T rs187877947 C3L-00093_T C3L-00093_N C C c.1047C>T p.= p.V349V ENST00000304874 14/17 736 694 42 403 403 0 strelka-varscan-mutect ASL,synonymous_variant,p.=,ENST00000304874,NM_000048.3;ASL,synonymous_variant,p.=,ENST00000380839,NM_001024946.1;ASL,synonymous_variant,p.=,ENST00000395332,NM_001024943.1;ASL,synonymous_variant,p.=,ENST00000395331,NM_001024944.1;AC068533.7,synonymous_variant,p.=,ENST00000450043,;ASL,downstream_gene_variant,,ENST00000362000,;ASL,non_coding_transcript_exon_variant,,ENST00000464970,;ASL,intron_variant,,ENST00000488343,;ASL,non_coding_transcript_exon_variant,,ENST00000493708,;ASL,downstream_gene_variant,,ENST00000487982,; T ENST00000304874 Transcript synonymous_variant 1149/2143 1047/1395 349/464 V gtC/gtT rs187877947 1 1 ASL HGNC HGNC:746 protein_coding YES CCDS5531.1 ENSP00000307188 P04424 A0A024RDL8 UPI0000001634 NM_000048.3 14/17 HAMAP:MF_00006,hmmpanther:PTHR11444:SF3,hmmpanther:PTHR11444,Gene3D:1.20.200.10,TIGRFAM_domain:TIGR00838,Superfamily_domains:SSF48557 LOW 1 SNV 1 1 PASS rs187877947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 66089680 66089680 C T 1 0 0 0 0 0 0 0 1 1191 813 29 3 3 ASL 7 66089680 Silent SNP C C3L-00093_T 10897819 66089680 93256293 54 2906 ADAM22 0 . GRCh38 7 88179037 88179037 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.2403G>A p.= p.K801K ENST00000265727 27/31 294 262 32 212 212 0 strelka-varscan-mutect ADAM22,synonymous_variant,p.=,ENST00000265727,NM_021723.3;ADAM22,synonymous_variant,p.=,ENST00000398201,NM_004194.3,NM_021721.3;ADAM22,synonymous_variant,p.=,ENST00000398203,;ADAM22,synonymous_variant,p.=,ENST00000426930,;ADAM22,synonymous_variant,p.=,ENST00000413139,;ADAM22,intron_variant,,ENST00000398204,NM_001324417.1,NM_016351.4;ADAM22,intron_variant,,ENST00000398209,NM_021722.4;ADAM22,upstream_gene_variant,,ENST00000476330,; A ENST00000265727 Transcript synonymous_variant 2482/2891 2403/2721 801/906 K aaG/aaA 1 1 ADAM22 HGNC HGNC:201 protein_coding YES CCDS47637.1 ENSP00000265727 Q9P0K1 UPI00001254DC NM_021723.3 27/31 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF14,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 88179037 88179037 G A 1 0 0 0 0 0 0 0 1 288 956 33 3 3 ADAM22 7 88179037 Silent SNP G C3L-00093_T 22089357 88179037 71166936 55 2907 AKAP9 0 . GRCh38 7 91995658 91995659 + Frame_Shift_Ins INS - - A novel C3L-00093_T C3L-00093_N - - c.789dupA p.Leu264ThrfsTer15 p.L264Tfs*15 ENST00000356239 7/50 381 289 92 245 245 0 sindel-varindel-pindel AKAP9,frameshift_variant,p.Leu264ThrfsTer15,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,frameshift_variant,p.Leu275ThrfsTer15,ENST00000359028,;AKAP9,frameshift_variant,p.Leu264ThrfsTer15,ENST00000358100,;AKAP9,frameshift_variant,p.Leu272ThrfsTer15,ENST00000619023,;AKAP9,frameshift_variant,p.Leu264ThrfsTer15,ENST00000394564,;AKAP9,frameshift_variant,p.Leu215ThrfsTer15,ENST00000438114,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; A ENST00000356239 Transcript frameshift_variant 1021-1022/12471 788-789/11724 263/3907 L/LX tta/ttAa 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 7/50 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 8 91995658 91995658 - A 1 0 1 1 0 0 0 0 0 543 1764 61 0 0 AKAP9 7 91995658 Frame_Shift_Ins INS - C3L-00093_T 3816621 91995658 67350315 56 2908 AKAP9 0 . GRCh38 7 92102758 92102758 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.11262G>A p.= p.V3754V ENST00000356239 46/50 375 350 25 200 200 0 strelka-varscan-mutect AKAP9,synonymous_variant,p.=,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,synonymous_variant,p.=,ENST00000359028,;AKAP9,synonymous_variant,p.=,ENST00000394534,;AKAP9,non_coding_transcript_exon_variant,,ENST00000486313,;AKAP9,non_coding_transcript_exon_variant,,ENST00000487258,;AKAP9,non_coding_transcript_exon_variant,,ENST00000463118,;AKAP9,downstream_gene_variant,,ENST00000487692,;AKAP9,upstream_gene_variant,,ENST00000493976,; A ENST00000356239 Transcript synonymous_variant 11495/12471 11262/11724 3754/3907 V gtG/gtA 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 46/50 hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF252,Pfam_domain:PF10495 LOW 1 SNV 1 1 PASS rs1346274347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 92102758 92102758 G A 1 0 0 0 0 0 0 0 1 543 1277 45 3 3 AKAP9 7 92102758 Silent SNP G C3L-00093_T 107100 92102758 67243215 57 2909 MGAM2 0 . GRCh38 7 142220427 142220427 + Missense_Mutation SNP C C A novel C3L-00093_T C3L-00093_N C C c.5916C>A p.Ser1972Arg p.S1972R ENST00000477922 48/48 412 367 45 246 246 0 strelka-varscan-mutect MGAM2,missense_variant,p.Ser1972Arg,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript missense_variant 5970/7867 5916/7548 1972/2515 S/R agC/agA 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated_low_confidence(0.22) 48/48 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 142220427 142220427 C A 1 0 0 0 0 1 0 0 0 9500 709 25 2 2 MGAM2 7 142220427 Missense_Mutation SNP C C3L-00093_T 50117669 142220427 17125546 58 2910 PRSS58 0 . GRCh38 7 142255270 142255270 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.221C>T p.Ser74Phe p.S74F ENST00000552471 3/5 238 215 23 135 135 0 strelka-mutect PRSS58,missense_variant,p.Ser74Phe,ENST00000552471,;PRSS58,missense_variant,p.Ser74Phe,ENST00000547058,NM_001001317.4; A ENST00000552471 Transcript missense_variant 541/1123 221/726 74/241 S/F tCt/tTt 1 -1 PRSS58 HGNC HGNC:39125 protein_coding YES CCDS5871.1 ENSP00000446916 Q8IYP2 UPI000004C649 tolerated(0.71) 3/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF185,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 142255270 142255270 G A 1 0 0 0 0 1 0 0 0 12785 942 33 3 3 PRSS58 7 142255270 Missense_Mutation SNP G C3L-00093_T 34843 142255270 17090703 59 2911 SGK223 0 . GRCh38 8 8318930 8318930 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.3445G>C p.Glu1149Gln p.E1149Q ENST00000615670 6/6 95 85 10 63 63 0 strelka-varscan-mutect SGK223,missense_variant,p.Glu1149Gln,ENST00000615670,;SGK223,missense_variant,p.Glu1149Gln,ENST00000622241,NM_001080826.2; G ENST00000615670 Transcript missense_variant 3710/4903 3445/4221 1149/1406 E/Q Gag/Cag 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F deleterious(0) 6/6 PROSITE_profiles:PS50011,hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972,PROSITE_patterns:PS00109,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -19.90901 0.9999999 1 1 1 0 G 3 3 8 8318930 8318930 C G 1 0 0 0 0 1 0 0 0 14469 864 30 4 4 SGK223 8 8318930 Missense_Mutation SNP C C3L-00093_T 8318930 136819706 60 2912 PLEKHA2 0 . GRCh38 8 38918040 38918040 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.111C>T p.= p.N37N ENST00000617275 2/12 203 187 16 126 126 0 strelka-varscan-mutect PLEKHA2,synonymous_variant,p.=,ENST00000617275,NM_021623.1;PLEKHA2,synonymous_variant,p.=,ENST00000616834,;PLEKHA2,synonymous_variant,p.=,ENST00000521746,;PLEKHA2,synonymous_variant,p.=,ENST00000519640,;PLEKHA2,intron_variant,,ENST00000616927,; T ENST00000617275 Transcript synonymous_variant 289/5582 111/1278 37/425 N aaC/aaT 1 1 PLEKHA2 HGNC HGNC:14336 protein_coding YES CCDS75732.1 ENSP00000482228 A8K727 UPI0001596C50 NM_021623.1 2/12 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR14336,hmmpanther:PTHR14336:SF5,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 38918040 38918040 C T 1 0 0 0 0 0 0 0 1 12149 564 20 3 3 PLEKHA2 8 38918040 Silent SNP C C3L-00093_T 30599110 38918040 106220596 61 2913 CHRNB3 0 . GRCh38 8 42736592 42736592 + Nonsense_Mutation SNP A A T rs35327613 C3L-00093_T C3L-00093_N A A c.1351A>T p.Lys451Ter p.K451* ENST00000289957 6/6 343 299 44 219 219 0 strelka-varscan-mutect CHRNB3,stop_gained,p.Lys451Ter,ENST00000289957,NM_000749.3; T ENST00000289957 Transcript stop_gained 1479/2294 1351/1377 451/458 K/* Aag/Tag rs35327613 1 1 CHRNB3 HGNC HGNC:1963 protein_coding YES CCDS6134.1 ENSP00000289957 Q05901 UPI0000125272 NM_000749.3 6/6 hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945,Gene3D:1.20.120.370,Superfamily_domains:SSF90112 22042774 HIGH 1 SNV 1 1 PASS rs35327613 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 8 42736592 42736592 A T 1 0 0 0 0 0 1 0 0 3152 247 9 4 4 CHRNB3 8 42736592 Nonsense_Mutation SNP A C3L-00093_T 3818552 42736592 102402044 62 2914 IMPAD1 0 . GRCh38 8 56993225 56993225 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.361C>T p.Leu121Phe p.L121F ENST00000262644 1/5 298 267 31 189 189 0 strelka-varscan-mutect IMPAD1,missense_variant,p.Leu121Phe,ENST00000262644,NM_017813.4;IMPAD1,missense_variant,p.Leu46Phe,ENST00000517461,; A ENST00000262644 Transcript missense_variant 620/7199 361/1080 121/359 L/F Ctc/Ttc 1 -1 IMPAD1 HGNC HGNC:26019 protein_coding YES CCDS6169.1 ENSP00000262644 Q9NX62 A0A024R7W0 UPI000006DE7A NM_017813.4 tolerated(0.2) 1/5 hmmpanther:PTHR20854,hmmpanther:PTHR20854:SF23,Pfam_domain:PF00459,Gene3D:3.30.540.10,Superfamily_domains:SSF56655 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 56993225 56993225 G A 1 0 0 0 0 1 0 0 0 7627 971 34 3 3 IMPAD1 8 56993225 Missense_Mutation SNP G C3L-00093_T 14256633 56993225 88145411 63 2915 TRPS1 0 . GRCh38 8 115604525 115604525 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.1444C>G p.Pro482Ala p.P482A ENST00000395715 4/7 494 458 36 371 371 0 strelka-varscan-mutect TRPS1,missense_variant,p.Pro482Ala,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Pro469Ala,ENST00000220888,;TRPS1,missense_variant,p.Pro473Ala,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Pro469Ala,ENST00000519674,;TRPS1,intron_variant,,ENST00000519076,;TRPS1,intron_variant,,ENST00000517323,; C ENST00000395715 Transcript missense_variant 2022/9990 1444/3885 482/1294 P/A Cca/Gca 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 tolerated_low_confidence(0.11) 4/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 115604525 115604525 G C 1 0 0 0 0 1 0 0 0 17099 1174 41 4 4 TRPS1 8 115604525 Missense_Mutation SNP G C3L-00093_T 58611300 115604525 29534111 64 2916 IFNE 0 . GRCh38 9 21481155 21481155 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.540C>T p.= p.F180F ENST00000448696 1/1 353 331 22 166 166 0 strelka-varscan-mutect IFNE,synonymous_variant,p.=,ENST00000448696,NM_176891.4;MIR31HG,intron_variant,,ENST00000304425,; A ENST00000448696 Transcript synonymous_variant 1159/1475 540/627 180/208 F ttC/ttT 1 -1 IFNE HGNC HGNC:18163 protein_coding YES CCDS34997.1 ENSP00000418018 Q86WN2 UPI000000D8A7 NM_176891.4 1/1 Gene3D:1.20.1250.10,Pfam_domain:PF00143,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF8,Superfamily_domains:SSF47266 LOW SNV 1 PASS rs1375015874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 21481155 21481155 G A 1 0 0 0 0 0 0 0 1 7447 1281 45 3 3 IFNE 9 21481155 Silent SNP G C3L-00093_T 21481155 116913562 65 2917 TUSC1 0 . GRCh38 9 25677757 25677757 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.565G>C p.Glu189Gln p.E189Q ENST00000358022 1/1 230 209 21 176 176 0 strelka-varscan-mutect TUSC1,missense_variant,p.Glu189Gln,ENST00000358022,NM_001004125.2; G ENST00000358022 Transcript missense_variant 684/2052 565/639 189/212 E/Q Gag/Cag 1 -1 TUSC1 HGNC HGNC:31010 protein_coding YES CCDS34999.1 ENSP00000350716 Q2TAM9 UPI0000161A7E NM_001004125.2 tolerated_low_confidence(0.07) 1/1 hmmpanther:PTHR22952:SF134,hmmpanther:PTHR22952 MODERATE 1 SNV 1 PASS rs1269712240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 25677757 25677757 C G 1 0 0 0 0 1 0 0 0 17288 864 30 4 4 TUSC1 9 25677757 Missense_Mutation SNP C C3L-00093_T 4196602 25677757 112716960 66 2918 UNC13B 0 . GRCh38 9 35396875 35396875 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.3223G>A p.Glu1075Lys p.E1075K ENST00000378495 27/39 317 295 22 257 257 0 strelka-varscan-mutect UNC13B,missense_variant,p.Glu3824Lys,ENST00000635942,;UNC13B,missense_variant,p.Glu1455Lys,ENST00000636694,;UNC13B,missense_variant,p.Glu662Lys,ENST00000617908,;UNC13B,missense_variant,p.Glu1075Lys,ENST00000619578,;UNC13B,missense_variant,p.Glu1075Lys,ENST00000378495,NM_006377.3;UNC13B,missense_variant,p.Glu1087Lys,ENST00000396787,;UNC13B,missense_variant,p.Glu662Lys,ENST00000378496,;UNC13B,missense_variant,p.Glu34Lys,ENST00000481299,;UNC13B,non_coding_transcript_exon_variant,,ENST00000637271,;UNC13B,3_prime_UTR_variant,,ENST00000634487,; A ENST00000378495 Transcript missense_variant 3445/6303 3223/4776 1075/1591 E/K Gag/Aag 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 deleterious(0.01) 27/39 PROSITE_profiles:PS51258,hmmpanther:PTHR10480 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 35396875 35396875 G A 1 0 0 0 0 1 0 0 0 17509 1291 45 3 3 UNC13B 9 35396875 Missense_Mutation SNP G C3L-00093_T 9719118 35396875 102997842 67 2919 CA9 0 . GRCh38 9 35679886 35679886 + Silent SNP T T C novel C3L-00093_T C3L-00093_N T T c.1098T>C p.= p.P366P ENST00000378357 8/11 94 73 21 66 66 0 strelka-varscan-mutect CA9,synonymous_variant,p.=,ENST00000378357,NM_001216.2;CA9,intron_variant,,ENST00000617161,;TPM2,downstream_gene_variant,,ENST00000378292,NM_213674.1;TPM2,downstream_gene_variant,,ENST00000378300,;TPM2,downstream_gene_variant,,ENST00000360958,NM_003289.3;TPM2,downstream_gene_variant,,ENST00000329305,NM_001301226.1;TPM2,downstream_gene_variant,,ENST00000607559,;CA9,non_coding_transcript_exon_variant,,ENST00000493245,;CA9,upstream_gene_variant,,ENST00000485665,;ARHGEF39,upstream_gene_variant,,ENST00000490638,;TPM2,downstream_gene_variant,,ENST00000471212,;TPM2,downstream_gene_variant,,ENST00000486018,; C ENST00000378357 Transcript synonymous_variant 1202/1618 1098/1380 366/459 P ccT/ccC 1 1 CA9 HGNC HGNC:1383 protein_coding YES CCDS6585.1 ENSP00000367608 Q16790 A0A0S2Z3D0 UPI000013E02C NM_001216.2 8/11 Gene3D:3.10.200.10,Pfam_domain:PF00194,PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF18,SMART_domains:SM01057,Superfamily_domains:SSF51069 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 8 35679886 35679886 T C 1 0 0 0 0 0 0 0 1 2210 1567 55 5 5 CA9 9 35679886 Silent SNP T C3L-00093_T 283011 35679886 102714831 68 2920 LAMC3 0 . GRCh38 9 131052585 131052585 + Silent SNP G G A C3L-00093_T C3L-00093_N G G c.1725G>A p.= p.L575L ENST00000361069 10/28 210 185 25 127 127 0 strelka-varscan-mutect LAMC3,synonymous_variant,p.=,ENST00000361069,NM_006059.3;LAMC3,intron_variant,,ENST00000480883,; A ENST00000361069 Transcript synonymous_variant 1858/6133 1725/4728 575/1575 L ctG/ctA COSM421926 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 10/28 Pfam_domain:PF00052,PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240,SMART_domains:SM00281 1 LOW 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 131052585 131052585 G A 1 0 0 0 0 0 0 0 1 8520 1277 45 3 3 LAMC3 9 131052585 Silent SNP G C3L-00093_T 95372699 131052585 7342132 69 2921 DBH 0 . GRCh38 9 133643469 133643469 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.801C>T p.= p.F267F ENST00000393056 4/12 336 299 37 237 236 1 strelka-varscan-mutect DBH,synonymous_variant,p.=,ENST00000393056,NM_000787.3;DBH,synonymous_variant,p.=,ENST00000263611,; T ENST00000393056 Transcript synonymous_variant 813/2763 801/1854 267/617 F ttC/ttT 1 1 DBH HGNC HGNC:2689 protein_coding YES CCDS6977.2 ENSP00000376776 P09172 UPI0000E5D219 NM_000787.3 4/12 Gene3D:1yi9A01,Pfam_domain:PF01082,Prints_domain:PR00767,PROSITE_patterns:PS00084,hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF29,Superfamily_domains:SSF49742 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 133643469 133643469 C T 1 0 0 0 0 0 0 0 1 4050 854 30 3 3 DBH 9 133643469 Silent SNP C C3L-00093_T 2590884 133643469 4751248 70 2922 NSMF 0 . GRCh38 9 137459070 137459070 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.33G>A p.= p.L11L ENST00000371475 1/16 30 25 5 30 30 0 strelka-mutect NSMF,synonymous_variant,p.=,ENST00000371475,NM_001130969.1;NSMF,synonymous_variant,p.=,ENST00000265663,NM_015537.4;NSMF,synonymous_variant,p.=,ENST00000437259,NM_001130970.1;NSMF,synonymous_variant,p.=,ENST00000371474,NM_001130971.1;NSMF,synonymous_variant,p.=,ENST00000371473,NM_001178064.1;NSMF,synonymous_variant,p.=,ENST00000371472,;PNPLA7,downstream_gene_variant,,ENST00000406427,NM_001098537.2;PNPLA7,downstream_gene_variant,,ENST00000277531,NM_152286.4;NSMF,upstream_gene_variant,,ENST00000339554,;PNPLA7,downstream_gene_variant,,ENST00000492278,;PNPLA7,downstream_gene_variant,,ENST00000469998,;PNPLA7,downstream_gene_variant,,ENST00000487228,;NSMF,upstream_gene_variant,,ENST00000371482,;NSMF,upstream_gene_variant,,ENST00000484316,;NSMF,upstream_gene_variant,,ENST00000371468,; T ENST00000371475 Transcript synonymous_variant 265/3646 33/1593 11/530 L ctG/ctA 1 -1 NSMF HGNC HGNC:29843 protein_coding YES CCDS48069.1 ENSP00000360530 Q6X4W1 UPI000035198D NM_001130969.1 1/16 Low_complexity_(Seg):seg,hmmpanther:PTHR32061 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.86242 1 1 1 1 0 T 2 4 8 137459070 137459070 C T 1 0 0 0 0 0 0 0 1 10739 813 29 3 3 NSMF 9 137459070 Silent SNP C C3L-00093_T 3815601 137459070 935647 71 2923 ZFAND4 0 . GRCh38 10 45626122 45626122 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.1701C>G p.Ile567Met p.I567M ENST00000344646 7/10 379 352 27 277 277 0 strelka-varscan-mutect ZFAND4,missense_variant,p.Ile493Met,ENST00000374366,NM_001282906.1,NM_001282905.1;ZFAND4,missense_variant,p.Ile567Met,ENST00000344646,NM_001128324.2,NM_174890.3;ZFAND4,intron_variant,,ENST00000374371,;ZFAND4,non_coding_transcript_exon_variant,,ENST00000374370,; C ENST00000344646 Transcript missense_variant 1917/3241 1701/2184 567/727 I/M atC/atG 1 -1 ZFAND4 HGNC HGNC:23504 protein_coding YES CCDS7214.1 ENSP00000339484 Q86XD8 A0A024R7V9 UPI0000161363 NM_001128324.2,NM_174890.3 tolerated(0.13) 7/10 hmmpanther:PTHR10666,hmmpanther:PTHR10666:SF109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 45626122 45626122 G C 1 0 0 0 0 1 0 0 0 18206 1280 45 4 4 ZFAND4 10 45626122 Missense_Mutation SNP G C3L-00093_T 45626122 88171300 72 2924 SGMS1 0 . GRCh38 10 50307154 50307154 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.1230G>A p.= p.V410V ENST00000361781 11/11 99 92 7 74 74 0 strelka-varscan-mutect SGMS1,synonymous_variant,p.=,ENST00000361781,NM_147156.3;SGMS1,3_prime_UTR_variant,,ENST00000429490,;SGMS1,downstream_gene_variant,,ENST00000602619,; T ENST00000361781 Transcript synonymous_variant 2190/3744 1230/1242 410/413 V gtG/gtA 1 -1 SGMS1 HGNC HGNC:29799 protein_coding YES CCDS7240.1 ENSP00000354829 D3DWC4 UPI000000D9FC NM_147156.3 11/11 hmmpanther:PTHR21290,hmmpanther:PTHR21290:SF28 LOW 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -14.08801 0.9999203 1 1 1 0 T 2 4 8 50307154 50307154 C T 1 0 0 0 0 0 0 0 1 14472 813 29 3 3 SGMS1 10 50307154 Silent SNP C C3L-00093_T 4681032 50307154 83490268 73 2925 RNLS 0 . GRCh38 10 88362633 88362633 + Missense_Mutation SNP C C T C3L-00093_T C3L-00093_N C C c.619G>A p.Asp207Asn p.D207N ENST00000331772 5/7 327 301 26 226 226 0 strelka-varscan-mutect RNLS,missense_variant,p.Asp207Asn,ENST00000371947,NM_018363.3;RNLS,missense_variant,p.Asp207Asn,ENST00000331772,NM_001031709.2;RNLS,non_coding_transcript_exon_variant,,ENST00000466945,;RNLS,non_coding_transcript_exon_variant,,ENST00000481793,; T ENST00000331772 Transcript missense_variant 642/1447 619/1029 207/342 D/N Gat/Aat COSM4411585,COSM4411586 1 -1 RNLS HGNC HGNC:25641 protein_coding YES CCDS31239.1 ENSP00000332530 Q5VYX0 UPI00001AFF46 NM_001031709.2 tolerated(0.3) 5/7 hmmpanther:PTHR23357,Gene3D:3.90.660.10,Pfam_domain:PF01593 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 88362633 88362633 C T 1 0 0 0 0 1 0 0 0 13685 826 29 3 3 RNLS 10 88362633 Missense_Mutation SNP C C3L-00093_T 38055479 88362633 45434789 74 2926 PDCD11 0 . GRCh38 10 103434301 103434301 + Silent SNP C C T rs200479386 C3L-00093_T C3L-00093_N C C c.3618C>T p.= p.T1206T ENST00000369797 24/36 232 217 15 180 180 0 strelka-varscan-mutect PDCD11,synonymous_variant,p.=,ENST00000369797,NM_014976.1;PDCD11,non_coding_transcript_exon_variant,,ENST00000466959,; T ENST00000369797 Transcript synonymous_variant 3712/6453 3618/5616 1206/1871 T acC/acT rs200479386 1 1 PDCD11 HGNC HGNC:13408 protein_coding YES CCDS31276.1 ENSP00000358812 Q14690 UPI00001C1ED1 NM_014976.1 24/36 PROSITE_profiles:PS50126,hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF10,Gene3D:2.40.50.140,SMART_domains:SM00316,Superfamily_domains:SSF50249 LOW 1 SNV 1 1 PASS rs200479386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 103434301 103434301 C T 1 0 0 0 0 0 0 0 1 11705 639 23 1 1 PDCD11 10 103434301 Silent SNP C C3L-00093_T 15071668 103434301 30363121 75 2927 VAX1 0 . GRCh38 10 117134578 117134578 + Missense_Mutation SNP C C A novel C3L-00093_T C3L-00093_N C C c.435G>T p.Lys145Asn p.K145N ENST00000369206 3/3 95 82 13 75 75 0 strelka-mutect VAX1,missense_variant,p.Lys145Asn,ENST00000369206,NM_001112704.1;VAX1,intron_variant,,ENST00000277905,NM_199131.2; A ENST00000369206 Transcript missense_variant 435/1723 435/1005 145/334 K/N aaG/aaT 1 -1 VAX1 HGNC HGNC:12660 protein_coding YES CCDS44483.1 ENSP00000358207 Q5SQQ9 UPI000013DB43 NM_001112704.1 deleterious(0.01) 3/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,Prints_domain:PR00031,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF32,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 8 117134578 117134578 C A 1 0 0 0 0 1 0 0 0 17679 695 24 2 2 VAX1 10 117134578 Missense_Mutation SNP C C3L-00093_T 13700277 117134578 16662844 76 2928 MKI67 0 . GRCh38 10 128104394 128104394 + Silent SNP G G C novel C3L-00093_T C3L-00093_N G G c.7446C>G p.= p.L2482L ENST00000368654 13/15 244 222 22 198 198 0 strelka-varscan-mutect MKI67,synonymous_variant,p.=,ENST00000368654,NM_002417.4;MKI67,synonymous_variant,p.=,ENST00000368653,NM_001145966.1;MKI67,upstream_gene_variant,,ENST00000464771,; C ENST00000368654 Transcript synonymous_variant 7822/12678 7446/9771 2482/3256 L ctC/ctG 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 13/15 Pfam_domain:PF08065,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM01295 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 8 128104394 128104394 G C 1 0 0 0 0 0 0 0 1 9566 1277 45 4 4 MKI67 10 128104394 Silent SNP G C3L-00093_T 10969816 128104394 5693028 77 2929 TRIM21 0 . GRCh38 11 4390121 4390121 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.289G>A p.Glu97Lys p.E97K ENST00000254436 2/7 385 358 27 273 273 0 strelka-varscan-mutect TRIM21,missense_variant,p.Glu97Lys,ENST00000254436,NM_003141.3;TRIM21,upstream_gene_variant,,ENST00000533692,; T ENST00000254436 Transcript missense_variant 402/1924 289/1428 97/475 E/K Gag/Aag 1 -1 TRIM21 HGNC HGNC:11312 protein_coding YES CCDS44525.1 ENSP00000254436 P19474 UPI000013450B NM_003141.3 tolerated(0.07) 2/7 PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF46,Gene3D:1freA00,Pfam_domain:PF00643,SMART_domains:SM00336,Superfamily_domains:SSF57845 MODERATE 1 SNV 1 1 PASS rs1216089333 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 4390121 4390121 C T 1 0 0 0 0 1 0 0 0 16984 922 32 3 3 TRIM21 11 4390121 Missense_Mutation SNP C C3L-00093_T 4390121 130696501 78 2930 FAM160A2 0 . GRCh38 11 6222478 6222478 + Silent SNP G G A rs766402546 C3L-00093_T C3L-00093_N G G c.1155C>T p.= p.L385L ENST00000265978 6/12 229 213 16 141 141 0 strelka-varscan-mutect FAM160A2,synonymous_variant,p.=,ENST00000265978,NM_032127.3;FAM160A2,synonymous_variant,p.=,ENST00000449352,NM_001098794.1;FAM160A2,synonymous_variant,p.=,ENST00000524416,;FAM160A2,upstream_gene_variant,,ENST00000532797,; A ENST00000265978 Transcript synonymous_variant 1514/3481 1155/2961 385/986 L ctC/ctT rs766402546,COSM362855 1 -1 FAM160A2 HGNC HGNC:25378 protein_coding YES CCDS7760.1 ENSP00000265978 Q8N612 UPI000013D6B5 NM_032127.3 6/12 hmmpanther:PTHR21705:SF4,hmmpanther:PTHR21705,Pfam_domain:PF10257 0,1 LOW 1 SNV 1 0,1 1 PASS rs766402546 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 6222478 6222478 G A 1 0 0 0 0 0 0 0 1 5318 1045 37 1 1 FAM160A2 11 6222478 Silent SNP G C3L-00093_T 1832357 6222478 128864144 79 2931 SYT9 0 . GRCh38 11 7303109 7303109 + Silent SNP C C T rs772136021 C3L-00093_T C3L-00093_N C C c.216C>T p.= p.F72F ENST00000318881 2/7 346 315 31 181 180 1 strelka-varscan-mutect SYT9,synonymous_variant,p.=,ENST00000318881,NM_175733.3;SYT9,synonymous_variant,p.=,ENST00000532592,;SYT9,synonymous_variant,p.=,ENST00000524820,; T ENST00000318881 Transcript synonymous_variant 453/3955 216/1476 72/491 F ttC/ttT rs772136021,COSM2017011 1 1 SYT9 HGNC HGNC:19265 protein_coding YES CCDS7778.1 ENSP00000324419 Q86SS6 UPI000000DB7B NM_175733.3 2/7 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF180,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs772136021 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 7303109 7303109 C T 1 0 0 0 0 0 0 0 1 15875 883 31 1 1 SYT9 11 7303109 Silent SNP C C3L-00093_T 1080631 7303109 127783513 80 2932 STIP1 0 . GRCh38 11 64197276 64197276 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.819G>A p.= p.L273L ENST00000358794 6/14 171 160 11 139 139 0 varscan-mutect STIP1,synonymous_variant,p.=,ENST00000358794,NM_001282652.1;STIP1,synonymous_variant,p.=,ENST00000305218,NM_006819.2;STIP1,synonymous_variant,p.=,ENST00000538945,NM_001282653.1;STIP1,upstream_gene_variant,,ENST00000540887,;STIP1,downstream_gene_variant,,ENST00000543847,;STIP1,non_coding_transcript_exon_variant,,ENST00000537479,;STIP1,non_coding_transcript_exon_variant,,ENST00000544739,;STIP1,downstream_gene_variant,,ENST00000540501,;STIP1,non_coding_transcript_exon_variant,,ENST00000538497,;STIP1,intron_variant,,ENST00000536973,;STIP1,downstream_gene_variant,,ENST00000540736,; A ENST00000358794 Transcript synonymous_variant 1372/2743 819/1773 273/590 L ctG/ctA 1 1 STIP1 HGNC HGNC:11387 protein_coding YES CCDS60827.1 ENSP00000351646 P31948 UPI00001FAA4C NM_001282652.1 6/14 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,SMART_domains:SM00028,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 64197276 64197276 G A 1 0 0 0 0 0 0 0 1 15662 1304 45 3 3 STIP1 11 64197276 Silent SNP G C3L-00093_T 56894167 64197276 70889346 81 2933 RCE1 0 . GRCh38 11 66843507 66843507 + Missense_Mutation SNP G G C rs111716594 C3L-00093_T C3L-00093_N G G c.52G>C p.Glu18Gln p.E18Q ENST00000309657 1/8 208 194 14 142 142 0 strelka-varscan-mutect RCE1,missense_variant,p.Glu18Gln,ENST00000309657,NM_005133.2;RCE1,missense_variant,p.Glu18Gln,ENST00000524506,;C11orf80,downstream_gene_variant,,ENST00000525908,NM_024650.3;C11orf80,downstream_gene_variant,,ENST00000532565,;C11orf80,downstream_gene_variant,,ENST00000525449,;C11orf80,downstream_gene_variant,,ENST00000360962,;C11orf80,downstream_gene_variant,,ENST00000540737,NM_001302084.1;C11orf80,downstream_gene_variant,,ENST00000527634,;PC,downstream_gene_variant,,ENST00000529047,;RCE1,upstream_gene_variant,,ENST00000525356,NM_001032279.1;C11orf80,downstream_gene_variant,,ENST00000531415,;RCE1,upstream_gene_variant,,ENST00000534645,;RCE1,missense_variant,p.Glu18Gln,ENST00000524849,;RCE1,non_coding_transcript_exon_variant,,ENST00000533277,;C11orf80,downstream_gene_variant,,ENST00000532727,;RCE1,upstream_gene_variant,,ENST00000532775,;RCE1,upstream_gene_variant,,ENST00000530610,;RCE1,upstream_gene_variant,,ENST00000534822,; C ENST00000309657 Transcript missense_variant 96/1485 52/990 18/329 E/Q Gag/Cag rs111716594 1 1 RCE1 HGNC HGNC:13721 protein_coding YES CCDS8151.1 ENSP00000309163 Q9Y256 UPI000012A4C6 NM_005133.2 tolerated(0.18) 1/8 hmmpanther:PTHR13046,hmmpanther:PTHR13046:SF1 MODERATE 1 SNV 1 1 PASS rs111716594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 66843507 66843507 G C 1 0 0 0 0 1 0 0 0 13346 1175 41 4 4 RCE1 11 66843507 Missense_Mutation SNP G C3L-00093_T 2646231 66843507 68243115 82 2934 TENM4 0 . GRCh38 11 78670466 78670466 + Missense_Mutation SNP T T A rs113698645 C3L-00093_T C3L-00093_N T T c.5879A>T p.Asn1960Ile p.N1960I ENST00000278550 32/34 232 208 24 147 147 0 strelka-varscan-mutect TENM4,missense_variant,p.Asn1960Ile,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Asn424Ile,ENST00000530738,; A ENST00000278550 Transcript missense_variant 6342/14000 5879/8310 1960/2769 N/I aAc/aTc rs113698645 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 deleterious(0) 32/34 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9 MODERATE 1 SNV 5 1 PASS rs113698645 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 78670466 78670466 T A 1 0 0 0 0 1 0 0 0 16174 1725 60 4 4 TENM4 11 78670466 Missense_Mutation SNP T C3L-00093_T 11826959 78670466 56416156 83 2935 APOA5 0 . GRCh38 11 116790518 116790518 + Silent SNP G G C novel C3L-00093_T C3L-00093_N G G c.711C>G p.= p.L237L ENST00000542499 4/4 160 149 11 100 100 0 strelka-varscan-mutect APOA5,synonymous_variant,p.=,ENST00000542499,NM_052968.4,NM_001166598.1;APOA5,synonymous_variant,p.=,ENST00000227665,;ZPR1,upstream_gene_variant,,ENST00000227322,NM_003904.3;ZPR1,upstream_gene_variant,,ENST00000444935,;ZPR1,upstream_gene_variant,,ENST00000429220,;APOA5,downstream_gene_variant,,ENST00000433069,;ZPR1,upstream_gene_variant,,ENST00000449430,;ZPR1,upstream_gene_variant,,ENST00000425791,;ZPR1,upstream_gene_variant,,ENST00000487030,;ZPR1,upstream_gene_variant,,ENST00000431973,;ZPR1,upstream_gene_variant,,ENST00000498065,; C ENST00000542499 Transcript synonymous_variant 784/1929 711/1101 237/366 L ctC/ctG 1 -1 APOA5 HGNC HGNC:17288 protein_coding YES CCDS8376.2 ENSP00000445002 Q6Q788 A0A0B4RUS7 UPI00000361EF NM_052968.4,NM_001166598.1 4/4 hmmpanther:PTHR18976:SF13,hmmpanther:PTHR18976,Pfam_domain:PF01442,Gene3D:1.20.120.20,Superfamily_domains:0053393,Coiled-coils_(Ncoils):Coil LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 8 116790518 116790518 G C 1 0 0 0 0 0 0 0 1 906 1277 45 4 4 APOA5 11 116790518 Silent SNP G C3L-00093_T 38120052 116790518 18296104 84 2936 OPCML 0 . GRCh38 11 132420230 132420230 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.1001C>T p.Ser334Leu p.S334L ENST00000331898 7/7 268 249 19 192 192 0 strelka-varscan-mutect OPCML,missense_variant,p.Ser334Leu,ENST00000331898,NM_001319106.1,NM_001319105.1,NM_002545.3;OPCML,missense_variant,p.Ser327Leu,ENST00000524381,NM_001012393.1;OPCML,missense_variant,p.Ser343Leu,ENST00000541867,;OPCML,missense_variant,p.Ser334Leu,ENST00000612177,;OPCML,missense_variant,p.Ser293Leu,ENST00000374778,;OPCML,non_coding_transcript_exon_variant,,ENST00000529038,; A ENST00000331898 Transcript missense_variant 1580/6833 1001/1038 334/345 S/L tCa/tTa 1 -1 OPCML HGNC HGNC:8143 protein_coding YES CCDS8492.1 ENSP00000330862 Q14982 A8K0Y0 UPI0000055AE0 NM_001319106.1,NM_001319105.1,NM_002545.3 tolerated(1) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 132420230 132420230 G A 1 0 0 0 0 1 0 0 0 10951 1294 45 3 3 OPCML 11 132420230 Missense_Mutation SNP G C3L-00093_T 15629712 132420230 2666392 85 2937 HAL 0 . GRCh38 12 95995790 95995790 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.121G>A p.Asp41Asn p.D41N ENST00000261208 2/21 453 425 28 285 285 0 strelka-varscan-mutect HAL,missense_variant,p.Asp41Asn,ENST00000261208,NM_002108.3;HAL,missense_variant,p.Asp41Asn,ENST00000538703,NM_001258334.1;HAL,missense_variant,p.Asp41Asn,ENST00000552509,;HAL,5_prime_UTR_variant,,ENST00000541929,NM_001258333.1;HAL,upstream_gene_variant,,ENST00000546579,;RP11-256L6.3,upstream_gene_variant,,ENST00000551849,;HAL,missense_variant,p.Asp41Asn,ENST00000544080,;HAL,missense_variant,p.Asp41Asn,ENST00000546999,;HAL,upstream_gene_variant,,ENST00000549376,; T ENST00000261208 Transcript missense_variant 490/3913 121/1974 41/657 D/N Gac/Aac 1 -1 HAL HGNC HGNC:4806 protein_coding YES CCDS9058.1 ENSP00000261208 P42357 UPI000012CE8E NM_002108.3 tolerated_low_confidence(0.11) 2/21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 95995790 95995790 C T 1 0 0 0 0 1 0 0 0 6833 884 31 1 1 HAL 12 95995790 Missense_Mutation SNP C C3L-00093_T 95995790 37279519 86 2938 MYO1H 0 . GRCh38 12 109401210 109401210 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.640G>C p.Glu214Gln p.E214Q ENST00000431443 5/31 238 226 12 118 118 0 strelka-varscan-mutect MYO1H,missense_variant,p.Glu230Gln,ENST00000310903,;MYO1H,missense_variant,p.Glu214Gln,ENST00000431443,NM_001101421.3;MYO1H,upstream_gene_variant,,ENST00000542883,; C ENST00000431443 Transcript missense_variant 640/4258 640/3069 214/1022 E/Q Gag/Cag 1 1 MYO1H HGNC HGNC:13879 protein_coding YES CCDS53826.1 ENSP00000444076 Q8N1T3 UPI0001AFF951 NM_001101421.3 tolerated(0.1) 5/31 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF353,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 109401210 109401210 G C 1 0 0 0 0 1 0 0 0 10076 943 33 4 4 MYO1H 12 109401210 Missense_Mutation SNP G C3L-00093_T 13405420 109401210 23874099 87 2939 WDR66 0 . GRCh38 12 121960664 121960664 + Missense_Mutation SNP G G A rs200928405 C3L-00093_T C3L-00093_N G G c.2213G>A p.Arg738His p.R738H ENST00000288912 14/22 322 295 27 233 233 0 strelka-varscan-mutect WDR66,missense_variant,p.Arg738His,ENST00000288912,NM_144668.5;WDR66,missense_variant,p.Arg738His,ENST00000397454,NM_001178003.1;WDR66,upstream_gene_variant,,ENST00000545752,;WDR66,downstream_gene_variant,,ENST00000543211,;WDR66,downstream_gene_variant,,ENST00000535257,; A ENST00000288912 Transcript missense_variant 3067/4467 2213/3450 738/1149 R/H cGc/cAc rs200928405,COSM264693 1 1 WDR66 HGNC HGNC:28506 protein_coding YES CCDS41853.1 ENSP00000288912 Q8TBY9 UPI00001AEB2C NM_144668.5 tolerated(0.47) 14/22 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF13,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978,Superfamily_domains:SSF50998 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200928405 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 121960664 121960664 G A 1 0 0 0 0 1 0 0 0 17875 1087 38 1 1 WDR66 12 121960664 Missense_Mutation SNP G C3L-00093_T 12559454 121960664 11314645 88 2940 SHISA2 0 . GRCh38 13 26050738 26050738 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.238G>C p.Glu80Gln p.E80Q ENST00000319420 1/2 166 157 9 95 95 0 strelka-varscan-mutect SHISA2,missense_variant,p.Glu80Gln,ENST00000319420,NM_001007538.1;LINC00415,downstream_gene_variant,,ENST00000439079,; G ENST00000319420 Transcript missense_variant 294/2860 238/888 80/295 E/Q Gag/Cag 1 -1 SHISA2 HGNC HGNC:20366 protein_coding YES CCDS31951.1 ENSP00000313079 Q6UWI4 UPI000004BA7B NM_001007538.1 deleterious(0.02) 1/2 hmmpanther:PTHR31395:SF0,hmmpanther:PTHR31395,Pfam_domain:PF13908 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 26050738 26050738 C G 1 0 0 0 0 1 0 0 0 14540 893 31 4 4 SHISA2 13 26050738 Missense_Mutation SNP C C3L-00093_T 26050738 88313590 89 2941 FRY 0 . GRCh38 13 32261728 32261728 + Missense_Mutation SNP G G T rs769465756 C3L-00093_T C3L-00093_N G G c.7529G>T p.Ser2510Ile p.S2510I ENST00000542859 52/61 419 367 52 302 302 0 strelka-varscan-mutect FRY,missense_variant,p.Ser2510Ile,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Ser2509Ile,ENST00000380250,;FRY,non_coding_transcript_exon_variant,,ENST00000602645,;FRY,upstream_gene_variant,,ENST00000477712,; T ENST00000542859 Transcript missense_variant 8025/13200 7529/9042 2510/3013 S/I aGc/aTc rs769465756,COSM239921 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 tolerated(0.07) 52/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs769465756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 32261728 32261728 G T 1 0 0 0 0 1 0 0 0 5935 971 34 2 2 FRY 13 32261728 Missense_Mutation SNP G C3L-00093_T 6210990 32261728 82102600 90 2942 CCDC168 0 . GRCh38 13 102739204 102739204 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.11493G>A p.= p.R3831R ENST00000322527 4/4 168 150 18 146 146 0 strelka-varscan-mutect CCDC168,synonymous_variant,p.=,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; T ENST00000322527 Transcript synonymous_variant 11631/21466 11493/21246 3831/7081 R cgG/cgA 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 Pfam_domain:PF15804 LOW 1 SNV 3 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 102739204 102739204 C T 1 0 0 0 0 0 0 0 1 2484 842 30 3 3 CCDC168 13 102739204 Silent SNP C C3L-00093_T 70477476 102739204 11625124 91 2943 AP1G2 0 . GRCh38 14 23565145 23565145 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.796G>A p.Glu266Lys p.E266K ENST00000308724 7/21 238 212 26 182 182 0 strelka-varscan-mutect AP1G2,missense_variant,p.Glu266Lys,ENST00000308724,NM_001282475.1;AP1G2,missense_variant,p.Glu266Lys,ENST00000397120,NM_001282474.1,NM_003917.4;JPH4,downstream_gene_variant,,ENST00000397118,NM_032452.2;JPH4,downstream_gene_variant,,ENST00000356300,NM_001146028.1;JPH4,downstream_gene_variant,,ENST00000622501,;THTPA,downstream_gene_variant,,ENST00000288014,;JPH4,downstream_gene_variant,,ENST00000544177,;AP1G2,downstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000554477,;AP1G2,downstream_gene_variant,,ENST00000556843,;RP11-66N24.3,intron_variant,,ENST00000555968,;RP11-66N24.4,downstream_gene_variant,,ENST00000553985,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000555510,;AP1G2,upstream_gene_variant,,ENST00000555118,;AP1G2,3_prime_UTR_variant,,ENST00000556943,;AP1G2,non_coding_transcript_exon_variant,,ENST00000460049,;AP1G2,non_coding_transcript_exon_variant,,ENST00000465445,;AP1G2,non_coding_transcript_exon_variant,,ENST00000535852,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556743,;AP1G2,non_coding_transcript_exon_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000554554,;AP1G2,upstream_gene_variant,,ENST00000556966,;AP1G2,downstream_gene_variant,,ENST00000557619,;AP1G2,downstream_gene_variant,,ENST00000555896,;AP1G2,downstream_gene_variant,,ENST00000554069,;AP1G2,downstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000554982,;AP1G2,upstream_gene_variant,,ENST00000556152,;AP1G2,upstream_gene_variant,,ENST00000554892,;AP1G2,downstream_gene_variant,,ENST00000553756,;AP1G2,downstream_gene_variant,,ENST00000554312,;AP1G2,upstream_gene_variant,,ENST00000554977,;AP1G2,downstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000557132,;AP1G2,upstream_gene_variant,,ENST00000557391,;AP1G2,upstream_gene_variant,,ENST00000556741,;AP1G2,upstream_gene_variant,,ENST00000555974,;AP1G2,upstream_gene_variant,,ENST00000555789,;AP1G2,downstream_gene_variant,,ENST00000554816,; T ENST00000308724 Transcript missense_variant 1552/3298 796/2358 266/785 E/K Gag/Aag 1 -1 AP1G2 HGNC HGNC:556 protein_coding YES CCDS9602.1 ENSP00000312442 O75843 UPI0000124FE8 NM_001282475.1 deleterious(0) 7/21 Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF037094,hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF28,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 23565145 23565145 C T 1 0 0 0 0 1 0 0 0 849 835 29 3 3 AP1G2 14 23565145 Missense_Mutation SNP C C3L-00093_T 23565145 83478573 92 2944 SYNE2 0 . GRCh38 14 64052575 64052575 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.8662G>C p.Asp2888His p.D2888H ENST00000358025 48/116 336 316 20 244 244 0 strelka-varscan-mutect SYNE2,missense_variant,p.Asp2888His,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Asp2888His,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Asp2921His,ENST00000357395,;SYNE2,missense_variant,p.Asp2921His,ENST00000554584,;SYNE2,downstream_gene_variant,,ENST00000557005,; C ENST00000358025 Transcript missense_variant 8874/21842 8662/20724 2888/6907 D/H Gac/Cac 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0) 48/116 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 64052575 64052575 G C 1 0 0 0 0 1 0 0 0 15838 1290 45 4 4 SYNE2 14 64052575 Missense_Mutation SNP G C3L-00093_T 40487430 64052575 42991143 93 2945 C2CD4A 0 . GRCh38 15 62068447 62068447 + Missense_Mutation SNP G G C rs530494685 C3L-00093_T C3L-00093_N G G c.834G>C p.Glu278Asp p.E278D ENST00000355522 2/2 125 115 10 92 92 0 strelka-varscan-mutect C2CD4A,missense_variant,p.Glu278Asp,ENST00000355522,NM_207322.2; C ENST00000355522 Transcript missense_variant 975/3445 834/1110 278/369 E/D gaG/gaC rs530494685 1 1 C2CD4A HGNC HGNC:33627 protein_coding YES CCDS32258.1 ENSP00000347712 Q8NCU7 UPI0000140CF2 NM_207322.2 deleterious(0.01) 2/2 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF224,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs530494685 . 0 208 2 0 0 0 0 0 -19.56204 1 1 1 1 0 C 3 2 8 62068447 62068447 G C 1 0 0 0 0 1 0 0 0 2027 933 33 4 4 C2CD4A 15 62068447 Missense_Mutation SNP G C3L-00093_T 62068447 39922742 94 2946 CILP 0 . GRCh38 15 65205378 65205378 + Missense_Mutation SNP C C A novel C3L-00093_T C3L-00093_N C C c.513G>T p.Gln171His p.Q171H ENST00000261883 5/9 183 169 14 110 110 0 strelka-varscan-mutect CILP,missense_variant,p.Gln171His,ENST00000261883,NM_003613.3; A ENST00000261883 Transcript missense_variant 680/5695 513/3555 171/1184 Q/H caG/caT 1 -1 CILP HGNC HGNC:1980 protein_coding YES CCDS10203.1 ENSP00000261883 O75339 UPI000013D21B NM_003613.3 deleterious(0.02) 5/9 PROSITE_profiles:PS50092,hmmpanther:PTHR15031,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 65205378 65205378 C A 1 0 0 0 0 1 0 0 0 3191 912 32 2 2 CILP 15 65205378 Missense_Mutation SNP C C3L-00093_T 3136931 65205378 36785811 95 2947 TMEM8A 0 . GRCh38 16 374321 374321 + Missense_Mutation SNP G G A rs374093452 C3L-00093_T C3L-00093_N G G c.1655C>T p.Thr552Met p.T552M ENST00000431232 10/13 121 104 17 72 71 1 strelka-varscan-mutect TMEM8A,missense_variant,p.Thr552Met,ENST00000431232,NM_021259.2;TMEM8A,missense_variant,p.Thr359Met,ENST00000250930,;TMEM8A,missense_variant,p.Thr100Met,ENST00000448854,;TMEM8A,missense_variant,p.Thr59Met,ENST00000424078,;MRPL28,upstream_gene_variant,,ENST00000199706,NM_006428.4;MRPL28,upstream_gene_variant,,ENST00000389675,;MRPL28,upstream_gene_variant,,ENST00000441883,;MRPL28,upstream_gene_variant,,ENST00000447696,;MRPL28,upstream_gene_variant,,ENST00000450882,;TMEM8A,downstream_gene_variant,,ENST00000427313,;MRPL28,upstream_gene_variant,,ENST00000429738,;TMEM8A,downstream_gene_variant,,ENST00000476735,;TMEM8A,non_coding_transcript_exon_variant,,ENST00000467452,;MRPL28,upstream_gene_variant,,ENST00000481453,;MRPL28,upstream_gene_variant,,ENST00000483764,;MRPL28,upstream_gene_variant,,ENST00000461550,;MRPL28,upstream_gene_variant,,ENST00000469744,;TMEM8A,downstream_gene_variant,,ENST00000475348,; A ENST00000431232 Transcript missense_variant 1816/3691 1655/2316 552/771 T/M aCg/aTg rs374093452 1 -1 TMEM8A HGNC HGNC:17205 protein_coding YES CCDS10407.1 ENSP00000401338 Q9HCN3 UPI000013CCD4 NM_021259.2 deleterious(0) 10/13 Pfam_domain:PF12036,hmmpanther:PTHR14319,hmmpanther:PTHR14319:SF7,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs374093452 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 374321 374321 G A 1 0 0 0 0 1 0 0 0 16691 1145 40 1 1 TMEM8A 16 374321 Missense_Mutation SNP G C3L-00093_T 374321 89964024 96 2948 PRRT2 0 . GRCh38 16 29813082 29813082 + Missense_Mutation SNP G G C rs529418384 C3L-00093_T C3L-00093_N G G c.28G>C p.Glu10Gln p.E10Q ENST00000567659 2/3 98 88 10 70 70 0 strelka-varscan-mutect PRRT2,missense_variant,p.Glu10Gln,ENST00000300797,NM_001256443.1;PRRT2,missense_variant,p.Glu10Gln,ENST00000358758,NM_145239.2;PRRT2,missense_variant,p.Glu10Gln,ENST00000572820,;PRRT2,missense_variant,p.Glu10Gln,ENST00000637064,;PRRT2,missense_variant,p.Glu10Gln,ENST00000636619,;PRRT2,missense_variant,p.Glu10Gln,ENST00000637403,;PRRT2,missense_variant,p.Glu10Gln,ENST00000637565,;PRRT2,missense_variant,p.Glu10Gln,ENST00000567659,NM_001256442.1;PRRT2,missense_variant,p.Glu10Gln,ENST00000567551,;PRRT2,missense_variant,p.Glu10Gln,ENST00000562148,;PRRT2,missense_variant,p.Glu10Gln,ENST00000637596,;PRRT2,missense_variant,p.Glu10Gln,ENST00000636246,;MAZ,downstream_gene_variant,,ENST00000219782,NM_001042539.2;MAZ,downstream_gene_variant,,ENST00000322945,NM_002383.3;MAZ,downstream_gene_variant,,ENST00000545521,NM_001276275.1;PAGR1,upstream_gene_variant,,ENST00000320330,NM_024516.3;MAZ,downstream_gene_variant,,ENST00000568282,;MAZ,downstream_gene_variant,,ENST00000562337,NM_001276276.1;MAZ,downstream_gene_variant,,ENST00000568544,;MAZ,downstream_gene_variant,,ENST00000563402,;MAZ,downstream_gene_variant,,ENST00000566906,;MAZ,downstream_gene_variant,,ENST00000616501,;MAZ,downstream_gene_variant,,ENST00000563012,;MAZ,downstream_gene_variant,,ENST00000567444,;MAZ,downstream_gene_variant,,ENST00000568411,;MAZ,downstream_gene_variant,,ENST00000569978,;MAZ,downstream_gene_variant,,ENST00000562557,;PRRT2,upstream_gene_variant,,ENST00000636902,;AC009133.12,intron_variant,,ENST00000569039,;AC009133.12,upstream_gene_variant,,ENST00000569981,;AC009133.12,downstream_gene_variant,,ENST00000569809,;AC009133.12,upstream_gene_variant,,ENST00000563806,;PRRT2,intron_variant,,ENST00000636019,;PRRT2,downstream_gene_variant,,ENST00000568516,;AC009133.24,downstream_gene_variant,,ENST00000562594,;PRRT2,downstream_gene_variant,,ENST00000636001,;PRRT2,upstream_gene_variant,,ENST00000637425,;PRRT2,downstream_gene_variant,,ENST00000637542,;PRRT2,missense_variant,p.Glu10Gln,ENST00000636131,;AC009133.23,missense_variant,p.Glu10Gln,ENST00000609618,;PRRT2,missense_variant,p.Glu10Gln,ENST00000637290,;MAZ,downstream_gene_variant,,ENST00000565777,;MAZ,downstream_gene_variant,,ENST00000561855,;CTD-2574D22.6,upstream_gene_variant,,ENST00000562285,; C ENST00000567659 Transcript missense_variant 226/1470 28/1185 10/394 E/Q Gag/Cag rs529418384,COSM1301837 1 1 PRRT2 HGNC HGNC:30500 protein_coding YES CCDS58445.1 ENSP00000456226 Q7Z6L0 UPI00000712B6 NM_001256442.1 deleterious_low_confidence(0) 2/3 hmmpanther:PTHR14948,hmmpanther:PTHR14948:SF20 0,1 MODERATE SNV 2 0,1 1 PASS rs529418384 . 0 206 4 0 0 0 0 0 -19.91311 1 1 1 1 0 C 3 2 8 29813082 29813082 G C 1 0 0 0 0 1 0 0 0 12756 1291 45 4 4 PRRT2 16 29813082 Missense_Mutation SNP G C3L-00093_T 29438761 29813082 60525263 97 2949 ZNF629 0 . GRCh38 16 30782592 30782592 + Missense_Mutation SNP T T C novel C3L-00093_T C3L-00093_N T T c.1736A>G p.Asn579Ser p.N579S ENST00000262525 3/3 435 391 44 236 236 0 strelka-varscan-mutect ZNF629,missense_variant,p.Asn579Ser,ENST00000262525,NM_001080417.1; C ENST00000262525 Transcript missense_variant 1944/6087 1736/2610 579/869 N/S aAc/aGc 1 -1 ZNF629 HGNC HGNC:29008 protein_coding YES CCDS45463.1 ENSP00000262525 Q9UEG4 UPI00001C1FA5 NM_001080417.1 tolerated(0.66) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF299,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 30782592 30782592 T C 1 0 0 0 0 1 0 0 0 18628 1725 60 5 5 ZNF629 16 30782592 Missense_Mutation SNP T C3L-00093_T 969510 30782592 59555753 98 2950 SLC38A8 0 . GRCh38 16 84016571 84016571 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.1110G>C p.Glu370Asp p.E370D ENST00000299709 8/10 313 295 18 149 149 0 strelka-mutect SLC38A8,missense_variant,p.Glu370Asp,ENST00000299709,NM_001080442.2;SLC38A8,non_coding_transcript_exon_variant,,ENST00000568003,; G ENST00000299709 Transcript missense_variant 1110/1308 1110/1308 370/435 E/D gaG/gaC 1 -1 SLC38A8 HGNC HGNC:32434 protein_coding YES CCDS32495.1 ENSP00000299709 A6NNN8 UPI0000D61A1F NM_001080442.2 tolerated(0.23) 8/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF226 MODERATE 1 SNV 5 1 PASS rs1400195404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 84016571 84016571 C G 1 0 0 0 0 1 0 0 0 14888 912 32 4 4 SLC38A8 16 84016571 Missense_Mutation SNP C C3L-00093_T 53233979 84016571 6321774 99 2951 1 3 2 2 12 C 4.416624e-05 SLC38A8 0 . GRCh38 16 84016582 84016582 + Missense_Mutation SNP C C G novel C3L-00093_T C3L-00093_N C C c.1099G>C p.Asp367His p.D367H ENST00000299709 8/10 341 319 22 159 159 0 strelka-mutect SLC38A8,missense_variant,p.Asp367His,ENST00000299709,NM_001080442.2;SLC38A8,non_coding_transcript_exon_variant,,ENST00000568003,; G ENST00000299709 Transcript missense_variant 1099/1308 1099/1308 367/435 D/H Gac/Cac 1 -1 SLC38A8 HGNC HGNC:32434 protein_coding YES CCDS32495.1 ENSP00000299709 A6NNN8 UPI0000D61A1F NM_001080442.2 deleterious(0) 8/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF226 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 84016582 84016582 C G 1 0 0 0 0 1 0 0 0 14888 826 29 4 4 SLC38A8 16 84016582 Missense_Mutation SNP C C3L-00093_T 11 84016582 6321763 100 2952 1 3 2 2 12 C 4.416624e-05 ANKRD11 0 . GRCh38 16 89285036 89285036 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.1506C>T p.= p.L502L ENST00000301030 9/13 387 344 43 260 259 1 strelka-varscan-mutect ANKRD11,synonymous_variant,p.=,ENST00000301030,NM_013275.5,NM_001256183.1;ANKRD11,synonymous_variant,p.=,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,downstream_gene_variant,,ENST00000613312,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,;ANKRD11,downstream_gene_variant,,ENST00000562275,;ANKRD11,downstream_gene_variant,,ENST00000378332,;ANKRD11,downstream_gene_variant,,ENST00000568100,; A ENST00000301030 Transcript synonymous_variant 1967/9301 1506/7992 502/2663 L ctC/ctT 1 -1 ANKRD11 HGNC HGNC:21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_013275.5,NM_001256183.1 9/13 hmmpanther:PTHR24145:SF3,hmmpanther:PTHR24145 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 89285036 89285036 G A 1 0 0 0 0 0 0 0 1 740 1277 45 3 3 ANKRD11 16 89285036 Silent SNP G C3L-00093_T 5268454 89285036 1053309 101 2953 TP53 0 . GRCh38 17 7673537 7673537 + Nonsense_Mutation SNP G G A C3L-00093_T C3L-00093_N G G c.991C>T p.Gln331Ter p.Q331* ENST00000269305 9/11 382 351 31 290 289 1 strelka-varscan-mutect TP53,stop_gained,p.Gln331Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Gln331Ter,ENST00000420246,;TP53,stop_gained,p.Gln292Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Gln292Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Gln331Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Gln292Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Gln331Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Gln292Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Gln331Ter,ENST00000445888,;TP53,stop_gained,p.Gln292Ter,ENST00000619485,;TP53,stop_gained,p.Gln199Ter,ENST00000510385,NM_001126116.1;TP53,stop_gained,p.Gln172Ter,ENST00000618944,NM_001276698.1;TP53,stop_gained,p.Gln199Ter,ENST00000504290,NM_001126117.1;TP53,stop_gained,p.Gln172Ter,ENST00000610623,NM_001276699.1;TP53,stop_gained,p.Gln199Ter,ENST00000504937,NM_001126115.1;TP53,stop_gained,p.Gln172Ter,ENST00000619186,NM_001276697.1;TP53,stop_gained,p.Gln331Ter,ENST00000359597,;TP53,stop_gained,p.Gln320Ter,ENST00000615910,;TP53,stop_gained,p.Gln199Ter,ENST00000509690,;TP53,stop_gained,p.Gln18Ter,ENST00000576024,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Gln292Ter,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained,splice_region_variant 1181/2579 991/1182 331/393 Q/* Cag/Tag TP53_g.14063C>G,TP53_g.14063C>T,TP53_g.14063del,COSM11354,COSM1649348,COSM289612,COSM3522688 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 9/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:1olgA00,Pfam_domain:PF07710,Superfamily_domains:SSF47719,Prints_domain:PR00386 0,0,0,1,1,1,1 HIGH 1 SNV 1 0,0,0,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 8 7673537 7673537 G A 1 0 0 0 0 0 1 0 0 16859 1304 45 3 3 TP53 17 7673537 Nonsense_Mutation SNP G C3L-00093_T 7673537 75583904 102 2954 KRT13 0 . GRCh38 17 41503421 41503421 + Missense_Mutation SNP G G A rs746117318 C3L-00093_T C3L-00093_N G G c.601C>T p.Arg201Cys p.R201C ENST00000246635 3/8 349 311 38 240 240 0 strelka-varscan-mutect KRT13,missense_variant,p.Arg201Cys,ENST00000246635,NM_153490.2;KRT13,missense_variant,p.Arg201Cys,ENST00000336861,NM_002274.3;KRT13,missense_variant,p.Arg201Cys,ENST00000587544,;KRT13,missense_variant,p.Arg94Cys,ENST00000590425,;KRT13,intron_variant,,ENST00000587435,;AC019349.5,downstream_gene_variant,,ENST00000411759,;KRT13,downstream_gene_variant,,ENST00000587118,;KRT13,upstream_gene_variant,,ENST00000475217,;KRT13,3_prime_UTR_variant,,ENST00000464634,;KRT13,non_coding_transcript_exon_variant,,ENST00000468313,; A ENST00000246635 Transcript missense_variant 648/1699 601/1377 201/458 R/C Cgc/Tgc rs746117318,COSM3402887 1 -1 KRT13 HGNC HGNC:6415 protein_coding YES CCDS11396.1 ENSP00000246635 P13646 UPI000013CBF6 NM_153490.2 deleterious(0.02) 3/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF121,SMART_domains:SM01391 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746117318 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 41503421 41503421 G A 1 0 0 0 0 1 0 0 0 8332 1087 38 1 1 KRT13 17 41503421 Missense_Mutation SNP G C3L-00093_T 33829884 41503421 41754020 103 2955 KLHL11 0 . GRCh38 17 41864961 41864961 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.410G>A p.Arg137Gln p.R137Q ENST00000319121 1/2 131 122 9 82 82 0 strelka-varscan-mutect KLHL11,missense_variant,p.Arg137Gln,ENST00000319121,NM_018143.2;ACLY,downstream_gene_variant,,ENST00000352035,NM_001303274.1,NM_001096.2;ACLY,downstream_gene_variant,,ENST00000353196,NM_001303275.1,NM_198830.1;ACLY,downstream_gene_variant,,ENST00000590151,;ACLY,downstream_gene_variant,,ENST00000393896,;ACLY,downstream_gene_variant,,ENST00000537919,;RP11-229E13.4,upstream_gene_variant,,ENST00000619176,;ACLY,downstream_gene_variant,,ENST00000588779,; T ENST00000319121 Transcript missense_variant 471/2383 410/2127 137/708 R/Q cGg/cAg 1 -1 KLHL11 HGNC HGNC:19008 protein_coding YES CCDS11411.1 ENSP00000314608 Q9NVR0 A0A024R1T8 UPI00000719F8 NM_018143.2 tolerated(0.18) 1/2 PROSITE_profiles:PS50097,hmmpanther:PTHR24413:SF115,hmmpanther:PTHR24413,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS rs1299648807 . 0 208 2 0 0 0 0 0 -17.57349 1 1 1 1 0 T 3 4 8 41864961 41864961 C T 1 0 0 0 0 1 0 0 0 8231 652 23 1 1 KLHL11 17 41864961 Missense_Mutation SNP C C3L-00093_T 361540 41864961 41392480 104 2956 KCNH6 0 . GRCh38 17 63524210 63524210 + Nonsense_Mutation SNP G G T C3L-00093_T C3L-00093_N G G c.148G>T p.Glu50Ter p.E50* ENST00000583023 2/14 427 405 22 244 244 0 strelka-varscan-mutect KCNH6,stop_gained,p.Glu50Ter,ENST00000583023,NM_030779.3;KCNH6,stop_gained,p.Glu50Ter,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,stop_gained,p.Glu50Ter,ENST00000581784,NM_173092.2;KCNH6,stop_gained,p.Glu50Ter,ENST00000456941,;KCNH6,stop_gained,p.Glu50Ter,ENST00000580652,;KCNH6,stop_gained,p.Glu50Ter,ENST00000583465,;CTD-2501B8.1,downstream_gene_variant,,ENST00000577647,;ACE3P,downstream_gene_variant,,ENST00000423435,; T ENST00000583023 Transcript stop_gained 159/3821 148/2985 50/994 E/* Gaa/Taa COSM4694353 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 2/14 Gene3D:3.30.450.20,Pfam_domain:PF13426,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468,Superfamily_domains:SSF55785 1 HIGH 1 SNV 1 1 1 PASS rs1398129760 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 8 63524210 63524210 G T 1 0 0 0 0 0 1 0 0 7952 1059 37 1 1 KCNH6 17 63524210 Nonsense_Mutation SNP G C3L-00093_T 21659249 63524210 19733231 105 2957 STRADA 0 . GRCh38 17 63706724 63706724 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.769G>A p.Asp257Asn p.D257N ENST00000336174 10/13 197 175 22 98 98 0 strelka-varscan-mutect STRADA,missense_variant,p.Asp196Asn,ENST00000245865,;STRADA,missense_variant,p.Asp220Asn,ENST00000392950,NM_153335.5;STRADA,missense_variant,p.Asp257Asn,ENST00000336174,NM_001003787.2;STRADA,missense_variant,p.Asp199Asn,ENST00000375840,NM_001003786.2,NM_001003788.2;STRADA,missense_variant,p.Asp213Asn,ENST00000447001,NM_001165970.1;STRADA,missense_variant,p.Met141Ile,ENST00000579340,;STRADA,missense_variant,p.Asp228Asn,ENST00000582137,NM_001165969.1;STRADA,missense_variant,p.Asp129Asn,ENST00000578008,;STRADA,missense_variant,p.Asp196Asn,ENST00000617949,;STRADA,missense_variant,p.Met96Ile,ENST00000578801,;STRADA,upstream_gene_variant,,ENST00000582026,;STRADA,downstream_gene_variant,,ENST00000580338,;STRADA,non_coding_transcript_exon_variant,,ENST00000580039,;RP11-51F16.1,downstream_gene_variant,,ENST00000623228,;STRADA,downstream_gene_variant,,ENST00000581505,;RP11-51F16.8,3_prime_UTR_variant,,ENST00000580553,;STRADA,upstream_gene_variant,,ENST00000583085,;STRADA,downstream_gene_variant,,ENST00000581243,;STRADA,downstream_gene_variant,,ENST00000577375,; T ENST00000336174 Transcript missense_variant 882/2143 769/1296 257/431 D/N Gat/Aat 1 -1 STRADA HGNC HGNC:30172 protein_coding YES CCDS32703.1 ENSP00000336655 Q7RTN6 UPI000013CBBE NM_001003787.2 tolerated(0.71) 10/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF382,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 63706724 63706724 C T 1 0 0 0 0 1 0 0 0 15705 826 29 3 3 STRADA 17 63706724 Missense_Mutation SNP C C3L-00093_T 182514 63706724 19550717 106 2958 CD300C 0 . GRCh38 17 74544936 74544936 + Silent SNP G G A novel C3L-00093_T C3L-00093_N G G c.73C>T p.= p.L25L ENST00000330793 2/4 128 114 14 65 65 0 strelka-varscan-mutect CD300C,synonymous_variant,p.=,ENST00000330793,NM_006678.4;AC079325.5,downstream_gene_variant,,ENST00000430386,; A ENST00000330793 Transcript synonymous_variant 434/1517 73/675 25/224 L Ctg/Ttg 1 -1 CD300C HGNC HGNC:19320 protein_coding YES CCDS11701.1 ENSP00000329507 Q08708 UPI0000127BB8 NM_006678.4 2/4 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS50835,hmmpanther:PTHR11860:SF56,hmmpanther:PTHR11860 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 8 74544936 74544936 G A 1 0 0 0 0 0 0 0 1 2701 933 33 3 3 CD300C 17 74544936 Silent SNP G C3L-00093_T 10838212 74544936 8712505 107 2959 C19orf71 0 . GRCh38 19 3543401 3543401 + Missense_Mutation SNP G G T novel C3L-00093_T C3L-00093_N G G c.250G>T p.Ala84Ser p.A84S ENST00000329493 2/4 221 199 22 173 173 0 strelka-varscan-mutect C19orf71,missense_variant,p.Ala84Ser,ENST00000329493,NM_001135580.1;MFSD12,intron_variant,,ENST00000398558,;MFSD12,intron_variant,,ENST00000615073,;MFSD12,downstream_gene_variant,,ENST00000355415,NM_174983.4;MFSD12,downstream_gene_variant,,ENST00000389395,NM_001287529.1;MFSD12,downstream_gene_variant,,ENST00000589995,;MFSD12,upstream_gene_variant,,ENST00000615613,;MFSD12,downstream_gene_variant,,ENST00000589063,;MFSD12,downstream_gene_variant,,ENST00000592652,;AC005786.7,upstream_gene_variant,,ENST00000589360,;MFSD12,downstream_gene_variant,,ENST00000591878,;MFSD12,downstream_gene_variant,,ENST00000588918,;MFSD12,upstream_gene_variant,,ENST00000585788,;MFSD12,downstream_gene_variant,,ENST00000585814,;MFSD12,upstream_gene_variant,,ENST00000589157,; T ENST00000329493 Transcript missense_variant 274/674 250/630 84/209 A/S Gcc/Tcc 1 1 C19orf71 HGNC HGNC:34496 protein_coding YES CCDS45918.1 ENSP00000327950 A6NCJ1 UPI000041AAB7 NM_001135580.1 tolerated(0.23) 2/4 hmmpanther:PTHR31254,Pfam_domain:PF15041 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 3543401 3543401 G T 1 0 0 0 0 1 0 0 0 1924 1203 42 2 2 C19orf71 19 3543401 Missense_Mutation SNP G C3L-00093_T 3543401 55074215 108 2960 TJP3 0 . GRCh38 19 3746506 3746506 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.2059G>A p.Val687Met p.V687M ENST00000589378 17/21 230 200 30 156 156 0 strelka-varscan-mutect TJP3,missense_variant,p.Val678Met,ENST00000541714,NM_001267560.1;TJP3,missense_variant,p.Val687Met,ENST00000589378,NM_001267561.1;TJP3,missense_variant,p.Val697Met,ENST00000587686,;TJP3,missense_variant,p.Val642Met,ENST00000539908,;APBA3,downstream_gene_variant,,ENST00000316757,NM_004886.3;TJP3,upstream_gene_variant,,ENST00000587641,;TJP3,non_coding_transcript_exon_variant,,ENST00000591493,;APBA3,downstream_gene_variant,,ENST00000590064,;APBA3,downstream_gene_variant,,ENST00000588984,;TJP3,upstream_gene_variant,,ENST00000586032,;APBA3,downstream_gene_variant,,ENST00000591678,;APBA3,downstream_gene_variant,,ENST00000586991,; A ENST00000589378 Transcript missense_variant 2215/3068 2059/2787 687/928 V/M Gtg/Atg 1 1 TJP3 HGNC HGNC:11829 protein_coding YES CCDS59332.1 ENSP00000465419 O95049 UPI00003E3015 NM_001267561.1 deleterious(0) 17/21 Gene3D:3.40.50.300,Pfam_domain:PF00625,PROSITE_profiles:PS50052,hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF11,SMART_domains:SM00072,Superfamily_domains:SSF52540 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 3746506 3746506 G A 1 0 0 0 0 1 0 0 0 16373 1377 48 3 3 TJP3 19 3746506 Missense_Mutation SNP G C3L-00093_T 203105 3746506 54871110 109 2961 KEAP1 0 . GRCh38 19 10491944 10491944 + Missense_Mutation SNP G G A C3L-00093_T C3L-00093_N G G c.958C>T p.Arg320Trp p.R320W ENST00000171111 3/6 199 182 17 156 155 1 strelka-mutect KEAP1,missense_variant,p.Arg320Trp,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Arg320Trp,ENST00000393623,NM_012289.3;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590593,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENST00000171111 Transcript missense_variant 1506/2955 958/1875 320/624 R/W Cgg/Tgg COSM1524062 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 10491944 10491944 G A 1 0 0 0 0 1 0 0 0 8061 1115 39 1 1 KEAP1 19 10491944 Missense_Mutation SNP G C3L-00093_T 6745438 10491944 48125672 110 2962 FXYD1 0 . GRCh38 19 35141181 35141181 + Silent SNP C C T rs762504988 C3L-00093_T C3L-00093_N C C c.144C>T p.= p.F48F ENST00000612146 4/8 339 205 134 118 118 0 strelka-varscan-mutect FXYD1,synonymous_variant,p.=,ENST00000612146,NM_001278717.1;FXYD1,synonymous_variant,p.=,ENST00000588081,;FXYD1,synonymous_variant,p.=,ENST00000588607,;FXYD1,synonymous_variant,p.=,ENST00000455515,NM_005031.4;FXYD1,synonymous_variant,p.=,ENST00000351325,NM_021902.3;FXYD1,synonymous_variant,p.=,ENST00000589121,;FXYD1,synonymous_variant,p.=,ENST00000588715,NM_001278718.1;FXYD1,synonymous_variant,p.=,ENST00000589209,;FXYD7,upstream_gene_variant,,ENST00000270310,NM_022006.1;FXYD7,upstream_gene_variant,,ENST00000588265,;FXYD7,upstream_gene_variant,,ENST00000586063,;CTD-2527I21.4,non_coding_transcript_exon_variant,,ENST00000592174,;CTD-2527I21.4,non_coding_transcript_exon_variant,,ENST00000586871,;LGI4,intron_variant,,ENST00000493050,;CTD-2527I21.5,upstream_gene_variant,,ENST00000624372,;FXYD1,non_coding_transcript_exon_variant,,ENST00000592818,;FXYD1,non_coding_transcript_exon_variant,,ENST00000590462,;FXYD1,non_coding_transcript_exon_variant,,ENST00000587056,;FXYD7,upstream_gene_variant,,ENST00000439441,; T ENST00000612146 Transcript synonymous_variant 388/690 144/279 48/92 F ttC/ttT rs762504988 1 1 FXYD1 HGNC HGNC:4025 protein_coding YES CCDS12445.1 ENSP00000481244 O00168 UPI0000032CBA NM_001278717.1 4/8 Gene3D:1.20.5.780,PD005989,Pfam_domain:PF02038,hmmpanther:PTHR14132,hmmpanther:PTHR14132:SF12,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 3 1 PASS rs762504988 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 8 35141181 35141181 C T 1 0 0 0 0 0 0 0 1 5988 825 29 3 3 FXYD1 19 35141181 Silent SNP C C3L-00093_T 24649237 35141181 23476435 111 2963 GPR42 0 . GRCh38 19 35372313 35372313 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.954G>C p.Gln318His p.Q318H ENST00000597214 1/1 297 192 105 99 99 0 strelka-varscan-mutect GPR42,missense_variant,p.Gln318His,ENST00000454971,;GPR42,missense_variant,p.Gln318His,ENST00000597214,; C ENST00000597214 Transcript missense_variant 1024/1182 954/1041 318/346 Q/H caG/caC 1 1 GPR42 HGNC HGNC:4500 protein_coding YES ENSP00000473212 O15529 A0A0K0PUY3 UPI0000040740 tolerated(0.16) 1/1 hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40 MODERATE 1 SNV 1 PASS . . 8 201 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 8 35372313 35372313 G C 1 0 0 0 0 1 0 0 0 6580 933 33 4 4 GPR42 19 35372313 Missense_Mutation SNP G C3L-00093_T 231132 35372313 23245303 112 2964 SLC8A2 0 . GRCh38 19 47465941 47465941 + Missense_Mutation SNP A A G novel C3L-00093_T C3L-00093_N A A c.463T>C p.Phe155Leu p.F155L ENST00000236877 2/10 284 249 35 200 199 1 strelka-varscan-mutect SLC8A2,missense_variant,p.Phe155Leu,ENST00000236877,NM_015063.2;SLC8A2,missense_variant,p.Phe62Leu,ENST00000594353,;SLC8A2,missense_variant,p.Phe77Leu,ENST00000597014,;SLC8A2,intron_variant,,ENST00000542837,;SLC8A2,intron_variant,,ENST00000539381,; G ENST00000236877 Transcript missense_variant 859/5234 463/2766 155/921 F/L Ttc/Ctc 1 -1 SLC8A2 HGNC HGNC:11069 protein_coding YES CCDS33065.1 ENSP00000236877 Q9UPR5 UPI000012FC49 NM_015063.2 deleterious(0) 2/10 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF8,TIGRFAM_domain:TIGR00845,Pfam_domain:PF01699 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 47465941 47465941 A G 1 0 0 0 0 1 0 0 0 14990 72 3 5 5 SLC8A2 19 47465941 Missense_Mutation SNP A C3L-00093_T 12093628 47465941 11151675 113 2965 ZNF8 0 . GRCh38 19 58279097 58279097 + Missense_Mutation SNP G G A C3L-00093_T C3L-00093_N G G c.16G>A p.Glu6Lys p.E6K ENST00000621650 1/4 29 25 4 24 24 0 strelka-mutect ZNF8,missense_variant,p.Glu6Lys,ENST00000621650,NM_021089.2;ZNF544,downstream_gene_variant,,ENST00000595981,;ZNF544,downstream_gene_variant,,ENST00000596929,;CTD-3138B18.5,upstream_gene_variant,,ENST00000597230,;AC010642.1,missense_variant,p.Glu6Lys,ENST00000591325,;CTD-3138B18.4,intron_variant,,ENST00000637233,;CTD-3138B18.4,intron_variant,,ENST00000637310,; A ENST00000621650 Transcript missense_variant 147/9128 16/1728 6/575 E/K Gaa/Aaa COSM5441315 1 1 ZNF8 HGNC HGNC:13154 protein_coding YES CCDS12974.1 ENSP00000477716 P17098 UPI0000185FEA NM_021089.2 tolerated(0.11) 1/4 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF186 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 58279097 58279097 G A 1 0 0 0 0 1 0 0 0 18752 1059 37 1 1 ZNF8 19 58279097 Missense_Mutation SNP G C3L-00093_T 10813156 58279097 338519 114 2966 C20orf196 0 . GRCh38 20 5863369 5863369 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.524G>A p.Gly175Glu p.G175E ENST00000303142 3/3 258 245 13 143 143 0 strelka-varscan-mutect C20orf196,missense_variant,p.Gly175Glu,ENST00000303142,NM_001303477.1,NM_152504.3;C20orf196,downstream_gene_variant,,ENST00000442185,;C20orf196,downstream_gene_variant,,ENST00000445603,; A ENST00000303142 Transcript missense_variant 611/1154 524/618 175/205 G/E gGa/gAa 1 1 C20orf196 HGNC HGNC:26318 protein_coding YES CCDS13091.1 ENSP00000305875 Q8IYI0 UPI0000074251 NM_001303477.1,NM_152504.3 tolerated(0.11) 3/3 Pfam_domain:PF15021,hmmpanther:PTHR36863,hmmpanther:PTHR36863:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 5863369 5863369 G A 1 0 0 0 0 1 0 0 0 2006 1174 41 3 3 C20orf196 20 5863369 Missense_Mutation SNP G C3L-00093_T 5863369 58580798 115 2967 MKKS 0 . GRCh38 20 10405300 10405300 + Missense_Mutation SNP C C G C3L-00093_T C3L-00093_N C C c.1660G>C p.Glu554Gln p.E554Q ENST00000347364 6/6 144 131 13 100 100 0 strelka-mutect MKKS,missense_variant,p.Glu554Gln,ENST00000347364,NM_170784.2;MKKS,missense_variant,p.Glu554Gln,ENST00000399054,NM_018848.3; G ENST00000347364 Transcript missense_variant 2423/6714 1660/1713 554/570 E/Q Gag/Cag COSM5208246 1 -1 MKKS HGNC HGNC:7108 protein_coding YES CCDS13111.1 ENSP00000246062 Q9NPJ1 UPI000012F199 NM_170784.2 deleterious(0) 6/6 Gene3D:1.10.560.10,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF77,Superfamily_domains:SSF48592 1 MODERATE 1 SNV 1 1 1 PASS . . 0 199 10 0 0 0 0 0 -19.99998 0.99995 1 1 1 0 G 3 3 8 10405300 10405300 C G 1 0 0 0 0 1 0 0 0 9567 922 32 4 4 MKKS 20 10405300 Missense_Mutation SNP C C3L-00093_T 4541931 10405300 54038867 116 2968 MKKS 0 . GRCh38 20 10412944 10412944 + Missense_Mutation SNP C C T novel C3L-00093_T C3L-00093_N C C c.571G>A p.Glu191Lys p.E191K ENST00000347364 3/6 262 236 26 143 143 0 strelka-varscan-mutect MKKS,missense_variant,p.Glu191Lys,ENST00000347364,NM_170784.2;MKKS,missense_variant,p.Glu191Lys,ENST00000399054,NM_018848.3;MKKS,downstream_gene_variant,,ENST00000609375,; T ENST00000347364 Transcript missense_variant 1334/6714 571/1713 191/570 E/K Gaa/Aaa 1 -1 MKKS HGNC HGNC:7108 protein_coding YES CCDS13111.1 ENSP00000246062 Q9NPJ1 UPI000012F199 NM_170784.2 tolerated(0.47) 3/6 Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF77 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 8 10412944 10412944 C T 1 0 0 0 0 1 0 0 0 9567 835 29 3 3 MKKS 20 10412944 Missense_Mutation SNP C C3L-00093_T 7644 10412944 54031223 117 2969 KIF16B 0 . GRCh38 20 16526129 16526129 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.194C>T p.Ala65Val p.A65V ENST00000408042 3/23 182 154 28 142 142 0 strelka-varscan-mutect KIF16B,missense_variant,p.Ala65Val,ENST00000354981,NM_024704.4;KIF16B,missense_variant,p.Ala65Val,ENST00000636835,NM_001199865.1;KIF16B,missense_variant,p.Ala65Val,ENST00000408042,NM_001199866.1; A ENST00000408042 Transcript missense_variant 352/4640 194/4179 65/1392 A/V gCt/gTt 1 -1 KIF16B HGNC HGNC:15869 protein_coding YES CCDS56178.1 ENSP00000384164 Q96L93 UPI00003BF77C NM_001199866.1 tolerated(0.71) 3/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF400,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 205 0 3 2 0 0 0 -14.50061 0.9746969 1 1 1 0 A 3 1 8 16526129 16526129 G A 1 0 0 0 0 1 0 0 0 8142 971 34 3 3 KIF16B 20 16526129 Missense_Mutation SNP G C3L-00093_T 6113185 16526129 47918038 118 2970 PCMTD2 0 . GRCh38 20 64264502 64264502 + Silent SNP C C T novel C3L-00093_T C3L-00093_N C C c.381C>T p.= p.F127F ENST00000308824 3/6 246 231 15 187 187 0 strelka-varscan-mutect PCMTD2,synonymous_variant,p.=,ENST00000308824,NM_018257.2;PCMTD2,synonymous_variant,p.=,ENST00000369758,NM_001104925.1;PCMTD2,synonymous_variant,p.=,ENST00000299468,;PCMTD2,synonymous_variant,p.=,ENST00000609764,;PCMTD2,synonymous_variant,p.=,ENST00000610074,;PCMTD2,intron_variant,,ENST00000609372,;PCMTD2,upstream_gene_variant,,ENST00000609818,;PCMTD2,downstream_gene_variant,,ENST00000610196,;PCMTD2,downstream_gene_variant,,ENST00000609297,;PCMTD2,downstream_gene_variant,,ENST00000608844,; T ENST00000308824 Transcript synonymous_variant 508/3843 381/1086 127/361 F ttC/ttT 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 3/6 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2,Superfamily_domains:SSF53335 LOW 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -17.91998 0.9999995 1 1 1 0 T 2 4 8 64264502 64264502 C T 1 0 0 0 0 0 0 0 1 11675 912 32 3 3 PCMTD2 20 64264502 Silent SNP C C3L-00093_T 47738373 64264502 179665 119 2971 SH3BGR 0 . GRCh38 21 39452125 39452125 + Missense_Mutation SNP C C G C3L-00093_T C3L-00093_N C C c.218C>G p.Ser73Cys p.S73C ENST00000333634 1/7 445 403 42 271 271 0 strelka-varscan-mutect SH3BGR,missense_variant,p.Ser73Cys,ENST00000333634,NM_007341.2;SH3BGR,missense_variant,p.Ser2Cys,ENST00000452550,;SH3BGR,intron_variant,,ENST00000380637,NM_001317742.1,NM_001001713.1;SH3BGR,intron_variant,,ENST00000380634,;SH3BGR,intron_variant,,ENST00000458295,;SH3BGR,intron_variant,,ENST00000380631,;SH3BGR,intron_variant,,ENST00000440288,; G ENST00000333634 Transcript missense_variant 296/1251 218/720 73/239 S/C tCt/tGt COSM1713998 1 1 SH3BGR HGNC HGNC:10822 protein_coding YES CCDS13666.1 ENSP00000332513 P55822 UPI00001B03C6 NM_007341.2 deleterious(0.02) 1/7 Gene3D:3.40.30.10,Pfam_domain:PF04908,hmmpanther:PTHR12232,hmmpanther:PTHR12232:SF1,Superfamily_domains:SSF52833 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 8 39452125 39452125 C G 1 0 0 0 0 1 0 0 0 14498 913 32 4 4 SH3BGR 21 39452125 Missense_Mutation SNP C C3L-00093_T 39452125 7257858 120 2972 OTC 0 . GRCh38 X 38403712 38403712 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.635G>A p.Gly212Glu p.G212E ENST00000039007 6/10 565 521 44 415 415 0 strelka-varscan-mutect OTC,missense_variant,p.Gly212Glu,ENST00000039007,NM_000531.5;RP5-972B16.2,intron_variant,,ENST00000465127,;OTC,downstream_gene_variant,,ENST00000488812,; A ENST00000039007 Transcript missense_variant 787/1585 635/1065 212/354 G/E gGa/gAa 1 1 OTC HGNC HGNC:8512 protein_coding YES CCDS14247.1 ENSP00000039007 P00480 UPI000013C550 NM_000531.5 deleterious(0) 6/10 Gene3D:3.40.50.1370,Pfam_domain:PF00185,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF1,Superfamily_domains:SSF53671,TIGRFAM_domain:TIGR00658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 38403712 38403712 G A 1 0 0 0 0 1 0 0 0 11367 1174 41 3 3 OTC 23 38403712 Missense_Mutation SNP G C3L-00093_T 38403712 117637183 121 2973 FRMPD3 0 . GRCh38 X 107602138 107602138 + Missense_Mutation SNP G G A novel C3L-00093_T C3L-00093_N G G c.4198G>A p.Glu1400Lys p.E1400K ENST00000276185 16/16 133 126 7 102 102 0 strelka-varscan-mutect FRMPD3,missense_variant,p.Glu1400Lys,ENST00000276185,NM_032428.1;FRMPD3,missense_variant,p.Glu1348Lys,ENST00000439554,; A ENST00000276185 Transcript missense_variant 4198/7304 4198/5433 1400/1810 E/K Gag/Aag 1 1 FRMPD3 HGNC HGNC:29382 protein_coding YES CCDS76006.1 ENSP00000276185 Q5JV73 UPI00006C1C33 NM_032428.1 deleterious_low_confidence(0) 16/16 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 8 107602138 107602138 G A 1 0 0 0 0 1 0 0 0 5929 1291 45 3 3 FRMPD3 23 107602138 Missense_Mutation SNP G C3L-00093_T 69198426 107602138 48438757 122 2974 MAGEA4 0 . GRCh38 X 151924554 151924554 + Missense_Mutation SNP G G C novel C3L-00093_T C3L-00093_N G G c.890G>C p.Arg297Thr p.R297T ENST00000360243 3/3 135 126 9 80 80 0 varscan-mutect MAGEA4,missense_variant,p.Arg297Thr,ENST00000360243,NM_001011550.1;MAGEA4,missense_variant,p.Arg297Thr,ENST00000370335,;MAGEA4,missense_variant,p.Arg297Thr,ENST00000370340,;MAGEA4,missense_variant,p.Arg297Thr,ENST00000393921,;MAGEA4,missense_variant,p.Arg297Thr,ENST00000276344,NM_001011548.1;MAGEA4,missense_variant,p.Arg297Thr,ENST00000393920,NM_002362.4,NM_001011549.1;MAGEA4,downstream_gene_variant,,ENST00000416020,;MAGEA4,downstream_gene_variant,,ENST00000431971,;MAGEA4,downstream_gene_variant,,ENST00000441865,;MAGEA4,downstream_gene_variant,,ENST00000457310,;MAGEA4,downstream_gene_variant,,ENST00000430273,;MAGEA4,downstream_gene_variant,,ENST00000425182,;MAGEA4,downstream_gene_variant,,ENST00000448295,;MAGEA4,downstream_gene_variant,,ENST00000431963,; C ENST00000360243 Transcript missense_variant 1157/1773 890/954 297/317 R/T aGa/aCa 1 1 MAGEA4 HGNC HGNC:6802 protein_coding YES CCDS14702.1 ENSP00000353379 P43358 A0A024RC12 UPI000013EA1F NM_001011550.1 tolerated(1) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF48,hmmpanther:PTHR11736 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.04406 1 1 1 1 0 C 3 2 8 151924554 151924554 G C 1 0 0 0 0 1 0 0 0 9084 942 33 4 4 MAGEA4 23 151924554 Missense_Mutation SNP G C3L-00093_T 44322416 151924554 4116341 123 2975 TREX2 0 . GRCh38 X 153445128 153445128 + Silent SNP C C A novel C3L-00093_T C3L-00093_N C C c.303G>T p.= p.L101L ENST00000330912 13/13 144 125 19 119 119 0 strelka-mutect TREX2,synonymous_variant,p.=,ENST00000330912,;TREX2,synonymous_variant,p.=,ENST00000338525,;TREX2,synonymous_variant,p.=,ENST00000334497,;TREX2,synonymous_variant,p.=,ENST00000370232,;TREX2,synonymous_variant,p.=,ENST00000370231,NM_080701.3;TREX2,synonymous_variant,p.=,ENST00000393862,;TREX2,synonymous_variant,p.=,ENST00000370212,;HAUS7,downstream_gene_variant,,ENST00000370211,NM_017518.7;HAUS7,downstream_gene_variant,,ENST00000435662,;HAUS7,downstream_gene_variant,,ENST00000484394,;HAUS7,downstream_gene_variant,,ENST00000491286,;HAUS7,downstream_gene_variant,,ENST00000437046,;HAUS7,downstream_gene_variant,,ENST00000460898,; A ENST00000330912 Transcript synonymous_variant 1854/2262 303/711 101/236 L ctG/ctT 1 -1 TREX2 HGNC HGNC:12270 protein_coding YES CCDS35437.1 ENSP00000333441 Q9BQ50 UPI000006F0D9 13/13 Gene3D:3.30.420.10,hmmpanther:PTHR13058,hmmpanther:PTHR13058:SF20,SMART_domains:SM00479,Superfamily_domains:SSF53098 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999975 1 1 1 0 A 2 1 8 153445128 153445128 C A 1 0 0 0 0 0 0 0 1 16966 697 25 2 2 TREX2 23 153445128 Silent SNP C C3L-00093_T 1520574 153445128 2595767 124 2976 C1orf94 0 . GRCh38 1 34200854 34200854 + Silent SNP C C A novel C3L-00094_T C3L-00094_N C C c.1092C>A p.= p.A364A ENST00000488417 3/7 331 251 80 342 342 0 strelka-varscan-mutect C1orf94,synonymous_variant,p.=,ENST00000488417,NM_001134734.1;C1orf94,synonymous_variant,p.=,ENST00000373374,NM_032884.4; A ENST00000488417 Transcript synonymous_variant 1212/2287 1092/1797 364/598 A gcC/gcA 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 3/7 hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1,Pfam_domain:PF15752 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 34200854 34200854 C A 1 0 0 0 0 0 0 0 1 2000 668 24 2 2 C1orf94 1 34200854 Silent SNP C C3L-00094_T 34200854 214755568 1 2977 ADPRHL2 0 . GRCh38 1 36091260 36091260 + Silent SNP A A T novel C3L-00094_T C3L-00094_N A A c.228A>T p.= p.T76T ENST00000373178 2/6 198 156 42 187 187 0 strelka-varscan-mutect ADPRHL2,synonymous_variant,p.=,ENST00000373178,NM_017825.2;COL8A2,downstream_gene_variant,,ENST00000397799,NM_005202.3;COL8A2,downstream_gene_variant,,ENST00000303143,;TEKT2,downstream_gene_variant,,ENST00000207457,NM_014466.2;TEKT2,downstream_gene_variant,,ENST00000473120,;TEKT2,downstream_gene_variant,,ENST00000469024,; T ENST00000373178 Transcript synonymous_variant 258/1668 228/1092 76/363 T acA/acT 1 1 ADPRHL2 HGNC HGNC:21304 protein_coding YES CCDS402.1 ENSP00000362273 Q9NX46 UPI0000039EBB NM_017825.2 2/6 hmmpanther:PTHR16222:SF19,hmmpanther:PTHR16222,Pfam_domain:PF03747,Superfamily_domains:0043888 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 36091260 36091260 A T 1 0 0 0 0 0 0 0 1 408 175 7 4 4 ADPRHL2 1 36091260 Silent SNP A C3L-00094_T 1890406 36091260 212865162 2 2978 VCAM1 0 . GRCh38 1 100734534 100734534 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1825C>A p.Pro609Thr p.P609T ENST00000294728 8/9 127 120 7 182 179 3 strelka-varscan-mutect VCAM1,missense_variant,p.Pro609Thr,ENST00000294728,NM_001078.3;VCAM1,missense_variant,p.Pro517Thr,ENST00000347652,NM_080682.2;VCAM1,missense_variant,p.Pro547Thr,ENST00000370119,NM_001199834.1;VCAM1,missense_variant,p.Pro410Thr,ENST00000370115,;VCAM1,upstream_gene_variant,,ENST00000603679,; A ENST00000294728 Transcript missense_variant 1926/3083 1825/2220 609/739 P/T Cct/Act 1 1 VCAM1 HGNC HGNC:12663 protein_coding YES CCDS773.1 ENSP00000294728 P19320 UPI0000000E06 NM_001078.3 deleterious(0) 8/9 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF729,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.18793 0.9999994 1 1 1 0 A 3 1 9 100734534 100734534 C A 1 0 0 0 0 1 0 0 0 17682 855 30 2 2 VCAM1 1 100734534 Missense_Mutation SNP C C3L-00094_T 64643274 100734534 148221888 3 2979 TCHH 0 . GRCh38 1 152108635 152108635 + Missense_Mutation SNP G G C rs200833723 C3L-00094_T C3L-00094_N G G c.4582C>G p.Gln1528Glu p.Q1528E ENST00000614923 3/3 163 154 9 203 201 2 varscan-mutect TCHH,missense_variant,p.Gln1528Glu,ENST00000614923,NM_007113.3;TCHH,missense_variant,p.Gln1528Glu,ENST00000368804,; C ENST00000614923 Transcript missense_variant 4677/6995 4582/5832 1528/1943 Q/E Caa/Gaa rs200833723,COSM2184176 1 -1 TCHH HGNC HGNC:11791 protein_coding YES CCDS41396.1 ENSP00000480484 Q07283 UPI0000458A5E NM_007113.3 tolerated_low_confidence(1) 3/3 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR34855:SF1,hmmpanther:PTHR34855 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs200833723 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 152108635 152108635 G C 1 0 0 0 0 1 0 0 0 16107 1328 46 4 4 TCHH 1 152108635 Missense_Mutation SNP G C3L-00094_T 51374101 152108635 96847787 4 2980 VSIG8 0 . GRCh38 1 159856014 159856014 + Silent SNP G G T novel C3L-00094_T C3L-00094_N G G c.840C>A p.= p.A280A ENST00000368100 6/7 344 261 83 219 219 0 strelka-varscan-mutect VSIG8,synonymous_variant,p.=,ENST00000368100,NM_001013661.1;C1orf204,upstream_gene_variant,,ENST00000368102,NM_001134233.1;C1orf204,upstream_gene_variant,,ENST00000621242,;SNORD64,upstream_gene_variant,,ENST00000390859,;C1orf204,upstream_gene_variant,,ENST00000491974,;RP11-190A12.7,downstream_gene_variant,,ENST00000537167,;RP11-190A12.7,downstream_gene_variant,,ENST00000536764,;RP11-190A12.7,downstream_gene_variant,,ENST00000543372,;RP11-190A12.7,downstream_gene_variant,,ENST00000544342,;RP11-190A12.7,downstream_gene_variant,,ENST00000536779,; T ENST00000368100 Transcript synonymous_variant 976/1818 840/1245 280/414 A gcC/gcA 1 -1 VSIG8 HGNC HGNC:32063 protein_coding YES CCDS30913.1 ENSP00000357080 Q5VU13 UPI0000458A8F NM_001013661.1 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR12231:SF142,hmmpanther:PTHR12231 LOW 1 SNV 1 1 PASS rs1310780074 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 159856014 159856014 G T 1 0 0 0 0 0 0 0 1 17777 1103 39 1 1 VSIG8 1 159856014 Silent SNP G C3L-00094_T 7747379 159856014 89100408 5 2981 FCGR2B 0 . GRCh38 1 161677545 161677545 + Missense_Mutation SNP C C T C3L-00094_T C3L-00094_N C C c.925C>T p.Arg309Cys p.R309C ENST00000358671 8/8 186 146 40 137 137 0 strelka-varscan-mutect FCGR2B,missense_variant,p.Arg309Cys,ENST00000358671,NM_004001.4,NM_001002275.2;FCGR2B,missense_variant,p.Arg302Cys,ENST00000367961,NM_001190828.1;FCGR2B,missense_variant,p.Arg290Cys,ENST00000236937,NM_001002274.2,NM_001002273.2;RP11-25K21.1,upstream_gene_variant,,ENST00000626340,;RP11-25K21.1,upstream_gene_variant,,ENST00000453111,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000480308,;FCGR2B,downstream_gene_variant,,ENST00000485778,; T ENST00000358671 Transcript missense_variant 1006/2115 925/933 309/310 R/C Cgt/Tgt COSM5052744 1 1 FCGR2B HGNC HGNC:3618 protein_coding YES CCDS30924.1 ENSP00000351497 P31994 UPI0000001600 NM_004001.4,NM_001002275.2 deleterious(0) 8/8 1 MODERATE 1 SNV 1 1 1 PASS rs1429964368 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 161677545 161677545 C T 1 0 0 0 0 1 0 0 0 5645 652 23 1 1 FCGR2B 1 161677545 Missense_Mutation SNP C C3L-00094_T 1821531 161677545 87278877 6 2982 MYOC 0 . GRCh38 1 171652475 171652475 + Missense_Mutation SNP C C A rs769391104 C3L-00094_T C3L-00094_N C C c.137G>T p.Arg46Leu p.R46L ENST00000037502 1/3 386 345 41 257 256 1 strelka-varscan-mutect MYOC,missense_variant,p.Arg46Leu,ENST00000037502,NM_000261.1; A ENST00000037502 Transcript missense_variant 209/2095 137/1515 46/504 R/L cGa/cTa rs769391104 1 -1 MYOC HGNC HGNC:7610 protein_coding YES CCDS1297.1 ENSP00000037502 Q99972 A0A0S2Z421 UPI00000012D6 NM_000261.1 tolerated(0.06) 1/3 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF33 MODERATE 1 SNV 1 1 PASS rs769391104 . 0 202 8 0 0 0 0 0 -20 0.9999961 1 1 1 0 A 3 1 9 171652475 171652475 C A 1 0 0 0 0 1 0 0 0 10087 884 31 1 1 MYOC 1 171652475 Missense_Mutation SNP C C3L-00094_T 9974930 171652475 77303947 7 2983 LAD1 0 . GRCh38 1 201386778 201386778 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.583C>T p.= p.L195L ENST00000391967 3/10 317 282 35 208 208 0 strelka-varscan-mutect LAD1,synonymous_variant,p.=,ENST00000391967,NM_005558.3;LAD1,synonymous_variant,p.=,ENST00000367313,;LAD1,downstream_gene_variant,,ENST00000633953,;LAD1,upstream_gene_variant,,ENST00000503578,;LAD1,downstream_gene_variant,,ENST00000632743,;LAD1,downstream_gene_variant,,ENST00000631576,;LAD1,upstream_gene_variant,,ENST00000488842,;LAD1,upstream_gene_variant,,ENST00000475136,; A ENST00000391967 Transcript synonymous_variant 885/2906 583/1554 195/517 L Ctg/Ttg 1 -1 LAD1 HGNC HGNC:6472 protein_coding YES CCDS1410.1 ENSP00000375829 O00515 UPI000006CD59 NM_005558.3 3/10 hmmpanther:PTHR12392,PIRSF_domain:PIRSF038144 LOW 1 SNV 1 1 PASS rs1200525264 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 201386778 201386778 G A 1 0 0 0 0 0 0 0 1 8503 991 35 3 3 LAD1 1 201386778 Silent SNP G C3L-00094_T 29734303 201386778 47569644 8 2984 PPP1R15B 0 . GRCh38 1 204411350 204411350 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.62G>T p.Trp21Leu p.W21L ENST00000367188 1/2 239 119 120 202 202 0 strelka-varscan-mutect PPP1R15B,missense_variant,p.Trp21Leu,ENST00000367188,NM_032833.4;RP11-739N20.2,intron_variant,,ENST00000443515,; A ENST00000367188 Transcript missense_variant 442/5227 62/2142 21/713 W/L tGg/tTg 1 -1 PPP1R15B HGNC HGNC:14951 protein_coding YES CCDS1445.1 ENSP00000356156 Q5SWA1 UPI0000EE3EB3 NM_032833.4 tolerated_low_confidence(0.18) 1/2 Low_complexity_(Seg):seg,Pfam_domain:PF10472 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 204411350 204411350 C A 1 0 0 0 0 1 0 0 0 12474 595 21 2 2 PPP1R15B 1 204411350 Missense_Mutation SNP C C3L-00094_T 3024572 204411350 44545072 9 2985 USH2A 0 . GRCh38 1 215786744 215786744 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.10313C>A p.Ala3438Glu p.A3438E ENST00000307340 52/72 556 520 36 450 449 1 strelka-varscan-mutect USH2A,missense_variant,p.Ala3438Glu,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 10700/18883 10313/15609 3438/5202 A/E gCa/gAa 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(1) 52/72 PROSITE_profiles:PS50853,SMART_domains:SM00060 MODERATE 1 SNV 1 1 PASS rs1319722709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 215786744 215786744 G T 1 0 0 0 0 1 0 0 0 17570 1319 46 2 2 USH2A 1 215786744 Missense_Mutation SNP G C3L-00094_T 11375394 215786744 33169678 10 2986 MARK1 0 . GRCh38 1 220653137 220653137 + Silent SNP T T A novel C3L-00094_T C3L-00094_N T T c.1776T>A p.= p.A592A ENST00000611084 16/18 396 349 47 258 257 1 strelka-varscan-mutect MARK1,synonymous_variant,p.=,ENST00000611084,NM_001286124.1;MARK1,synonymous_variant,p.=,ENST00000402574,NM_001286126.1;MARK1,synonymous_variant,p.=,ENST00000366918,NM_001286128.1;MARK1,synonymous_variant,p.=,ENST00000366917,NM_018650.4; A ENST00000611084 Transcript synonymous_variant 2416/5321 1776/2391 592/796 A gcT/gcA 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 16/18 hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 220653137 220653137 T A 1 0 0 0 0 0 0 0 1 9237 1538 54 4 4 MARK1 1 220653137 Silent SNP T C3L-00094_T 4866393 220653137 28303285 11 2987 CCDC185 0 . GRCh38 1 223394802 223394802 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1327G>A p.Ala443Thr p.A443T ENST00000366875 1/1 73 51 22 59 59 0 strelka-varscan-mutect CCDC185,missense_variant,p.Ala443Thr,ENST00000366875,NM_152610.2; A ENST00000366875 Transcript missense_variant 1386/2054 1327/1872 443/623 A/T Gct/Act 1 1 CCDC185 HGNC HGNC:26654 protein_coding YES CCDS1537.1 ENSP00000355840 Q8N715 UPI000006F948 NM_152610.2 deleterious(0) 1/1 hmmpanther:PTHR33663,hmmpanther:PTHR33663:SF3,Pfam_domain:PF15558 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 223394802 223394802 G A 1 0 0 0 0 1 0 0 0 2501 1203 42 3 3 CCDC185 1 223394802 Missense_Mutation SNP G C3L-00094_T 2741665 223394802 25561620 12 2988 DNAH14 0 . GRCh38 1 225324242 225324242 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.9237A>T p.Lys3079Asn p.K3079N ENST00000430092 61/84 271 252 19 204 204 0 strelka-mutect DNAH14,missense_variant,p.Lys3079Asn,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Lys3079Asn,ENST00000439375,;DNAH14,missense_variant,p.Lys2426Asn,ENST00000445597,;DNAH14,missense_variant,p.Lys877Asn,ENST00000327794,; T ENST00000430092 Transcript missense_variant 9452/13763 9237/13548 3079/4515 K/N aaA/aaT 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 deleterious(0.04) 61/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676,Pfam_domain:PF12777 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 225324242 225324242 A T 1 0 0 0 0 1 0 0 0 4415 11 1 4 4 DNAH14 1 225324242 Missense_Mutation SNP A C3L-00094_T 1929440 225324242 23632180 13 2989 RYR2 0 . GRCh38 1 237808904 237808904 + Missense_Mutation SNP G G T rs775534249 C3L-00094_T C3L-00094_N G G c.14302G>T p.Val4768Leu p.V4768L ENST00000366574 100/105 283 249 34 239 239 0 strelka-varscan-mutect RYR2,missense_variant,p.Val4768Leu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Val4751Leu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,; T ENST00000366574 Transcript missense_variant 14619/16562 14302/14904 4768/4967 V/L Gta/Tta rs775534249 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.02) 100/105 Pfam_domain:PF00520,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs775534249 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 237808904 237808904 G T 1 0 0 0 0 1 0 0 0 14029 1159 40 1 1 RYR2 1 237808904 Missense_Mutation SNP G C3L-00094_T 12484662 237808904 11147518 14 2990 TRIM58 0 . GRCh38 1 247864907 247864907 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.719G>A p.Cys240Tyr p.C240Y ENST00000366481 3/6 300 277 23 204 204 0 strelka-varscan-mutect TRIM58,missense_variant,p.Cys240Tyr,ENST00000366481,NM_015431.3; A ENST00000366481 Transcript missense_variant 767/3225 719/1461 240/486 C/Y tGc/tAc 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0) 3/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 9 247864907 247864907 G A 1 0 0 0 0 1 0 0 0 17024 1319 46 3 3 TRIM58 1 247864907 Missense_Mutation SNP G C3L-00094_T 10056003 247864907 1091515 15 2991 OR14C36 0 . GRCh38 1 248349313 248349313 + Missense_Mutation SNP C C A rs753138282 C3L-00094_T C3L-00094_N C C c.539C>A p.Pro180His p.P180H ENST00000317861 1/1 206 154 52 185 185 0 strelka-varscan-mutect OR14C36,missense_variant,p.Pro180His,ENST00000317861,NM_001001918.1; A ENST00000317861 Transcript missense_variant 539/939 539/939 180/312 P/H cCc/cAc rs753138282 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs753138282 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 248349313 248349313 C A 1 0 0 0 0 1 0 0 0 11023 623 22 2 2 OR14C36 1 248349313 Missense_Mutation SNP C C3L-00094_T 484406 248349313 607109 16 2992 OR2T6 0 . GRCh38 1 248388153 248388153 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.545C>A p.Pro182His p.P182H ENST00000355728 1/1 231 169 62 177 177 0 strelka-varscan-mutect OR2T6,missense_variant,p.Pro182His,ENST00000355728,NM_001005471.1; A ENST00000355728 Transcript missense_variant 545/927 545/927 182/308 P/H cCc/cAc COSM5536117 1 1 OR2T6 HGNC HGNC:15018 protein_coding YES CCDS31114.1 ENSP00000347965 Q8NHC8 UPI0000199147 NM_001005471.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF57,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 248388153 248388153 C A 1 0 0 0 0 1 0 0 0 11106 623 22 2 2 OR2T6 1 248388153 Missense_Mutation SNP C C3L-00094_T 38840 248388153 568269 17 2993 NT5C1B 0 . GRCh38 2 18576868 18576868 + Missense_Mutation SNP G G T C3L-00094_T C3L-00094_N G G c.1229C>A p.Thr410Asn p.T410N ENST00000359846 8/10 457 291 166 413 413 0 strelka-varscan-mutect NT5C1B,missense_variant,p.Thr350Asn,ENST00000304081,NM_033253.3;NT5C1B,missense_variant,p.Thr410Asn,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Thr410Asn,ENST00000532967,NM_001199104.1;NT5C1B-RDH14,missense_variant,p.Thr352Asn,ENST00000444297,NM_001199103.1;NT5C1B,missense_variant,p.Thr65Asn,ENST00000418427,;NT5C1B,3_prime_UTR_variant,,ENST00000406971,; T ENST00000359846 Transcript missense_variant 1307/2475 1229/1833 410/610 T/N aCc/aAc COSM5136956 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 deleterious(0) 8/10 Pfam_domain:PF06189,hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0 1 MODERATE 1 SNV 1 1 1 PASS rs1316399227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 18576868 18576868 G T 1 0 0 0 0 1 0 0 0 10749 1261 44 2 2 NT5C1B 2 18576868 Missense_Mutation SNP G C3L-00094_T 18576868 223616661 18 2994 AAK1 0 . GRCh38 2 69479048 69479048 + Silent SNP C C A novel C3L-00094_T C3L-00094_N C C c.2583G>T p.= p.G861G ENST00000409085 20/22 159 130 29 147 147 0 strelka-varscan-mutect AAK1,synonymous_variant,p.=,ENST00000409085,NM_014911.3;AAK1,intron_variant,,ENST00000606389,;AAK1,intron_variant,,ENST00000409068,;AAK1,intron_variant,,ENST00000623317,;AAK1,downstream_gene_variant,,ENST00000406297,;AAK1,non_coding_transcript_exon_variant,,ENST00000489327,; A ENST00000409085 Transcript synonymous_variant 2960/11345 2583/2886 861/961 G ggG/ggT 1 -1 AAK1 HGNC HGNC:19679 protein_coding YES CCDS1893.2 ENSP00000386456 Q2M2I8 UPI0001881663 NM_014911.3 20/22 hmmpanther:PTHR22967:SF57,hmmpanther:PTHR22967 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 69479048 69479048 C A 1 0 0 0 0 0 0 0 1 17 610 22 2 2 AAK1 2 69479048 Silent SNP C C3L-00094_T 50902180 69479048 172714481 19 2995 DYSF 0 . GRCh38 2 71549361 71549361 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.1492G>T p.Gly498Cys p.G498C ENST00000258104 17/55 355 296 59 264 263 1 strelka-varscan-mutect DYSF,missense_variant,p.Gly498Cys,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Gly529Cys,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Gly498Cys,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Gly530Cys,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Gly499Cys,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Gly499Cys,ENST00000394120,NM_001130455.1;DYSF,intron_variant,,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,intron_variant,,ENST00000409762,NM_001130980.1;DYSF,intron_variant,,ENST00000410020,NM_001130987.1;DYSF,intron_variant,,ENST00000410041,NM_001130985.1;DYSF,intron_variant,,ENST00000409744,NM_001130984.1,NM_001130986.1; T ENST00000258104 Transcript missense_variant 1769/6796 1492/6243 498/2080 G/C Ggt/Tgt 1 1 DYSF HGNC HGNC:3097 protein_coding CCDS1918.1 ENSP00000258104 O75923 UPI0000129A56 NM_003494.3,NM_001130976.1 deleterious(0.03) 17/55 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 71549361 71549361 G T 1 0 0 0 0 1 0 0 0 4683 1000 35 2 2 DYSF 2 71549361 Missense_Mutation SNP G C3L-00094_T 2070313 71549361 170644168 20 2996 CTNNA2 0 . GRCh38 2 80604074 80604074 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.2190A>T p.Arg730Ser p.R730S ENST00000402739 15/18 154 126 28 133 133 0 strelka-varscan-mutect CTNNA2,missense_variant,p.Arg730Ser,ENST00000466387,;CTNNA2,missense_variant,p.Arg730Ser,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Arg730Ser,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Arg730Ser,ENST00000629316,NM_001164883.1;CTNNA2,missense_variant,p.Arg346Ser,ENST00000361291,NM_001320810.1;CTNNA2,missense_variant,p.Arg409Ser,ENST00000343114,NM_001282599.1;CTNNA2,missense_variant,p.Arg362Ser,ENST00000541047,NM_001282600.1;CTNNA2,missense_variant,p.Arg346Ser,ENST00000540488,;AC008067.2,non_coding_transcript_exon_variant,,ENST00000596783,;AC008067.2,non_coding_transcript_exon_variant,,ENST00000599412,;AC008067.2,non_coding_transcript_exon_variant,,ENST00000595478,;AC008067.2,intron_variant,,ENST00000630660,;AC008067.2,intron_variant,,ENST00000626463,;AC008067.2,intron_variant,,ENST00000596887,;AC008067.2,intron_variant,,ENST00000626199,;AC008067.2,intron_variant,,ENST00000627235,;AC008067.2,intron_variant,,ENST00000430876,;AC008067.2,intron_variant,,ENST00000609950,;AC008067.2,intron_variant,,ENST00000627307,;CTNNA2,splice_region_variant,,ENST00000467892,; T ENST00000402739 Transcript missense_variant,splice_region_variant 2195/3684 2190/2862 730/953 R/S agA/agT 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0) 15/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,Prints_domain:PR00805,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 80604074 80604074 A T 1 0 0 0 0 1 0 0 0 3822 318 11 4 4 CTNNA2 2 80604074 Missense_Mutation SNP A C3L-00094_T 9054713 80604074 161589455 21 2997 CNGA3 0 . GRCh38 2 98396785 98396785 + Missense_Mutation SNP G G T rs374275399 C3L-00094_T C3L-00094_N G G c.1615G>T p.Val539Leu p.V539L ENST00000393504 8/8 509 295 214 435 435 0 strelka-varscan-mutect CNGA3,missense_variant,p.Val539Leu,ENST00000393504,NM_001298.2;CNGA3,missense_variant,p.Val539Leu,ENST00000272602,;CNGA3,missense_variant,p.Val543Leu,ENST00000409937,;CNGA3,missense_variant,p.Val521Leu,ENST00000436404,NM_001079878.1; T ENST00000393504 Transcript missense_variant 2032/3841 1615/2085 539/694 V/L Gtg/Ttg rs374275399 1 1 CNGA3 HGNC HGNC:2150 protein_coding YES CCDS2034.1 ENSP00000377140 Q16281 UPI000004717B NM_001298.2 deleterious(0.02) 8/8 PROSITE_profiles:PS50042,hmmpanther:PTHR10217:SF390,hmmpanther:PTHR10217,Gene3D:2.60.120.10,Pfam_domain:PF00027,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 5 1 PASS rs374275399 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 98396785 98396785 G T 1 0 0 0 0 1 0 0 0 3378 1145 40 1 1 CNGA3 2 98396785 Missense_Mutation SNP G C3L-00094_T 17792711 98396785 143796744 22 2998 LRP1B 0 . GRCh38 2 140516892 140516892 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.8146T>C p.Cys2716Arg p.C2716R ENST00000389484 50/91 255 213 42 321 321 0 strelka-varscan-mutect LRP1B,missense_variant,p.Cys2716Arg,ENST00000389484,NM_018557.2; G ENST00000389484 Transcript missense_variant 9118/16535 8146/13800 2716/4599 C/R Tgt/Cgt 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 50/91 PROSITE_profiles:PS50068,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 140516892 140516892 A G 1 0 0 0 0 1 0 0 0 8850 202 7 5 5 LRP1B 2 140516892 Missense_Mutation SNP A C3L-00094_T 42120107 140516892 101676637 23 2999 ZEB2 0 . GRCh38 2 144396465 144396465 + Frame_Shift_Del DEL T T - novel C3L-00094_T C3L-00094_N T T c.3014delA p.Asp1005AlafsTer70 p.D1005Afs*70 ENST00000637267 10/11 461 299 162 440 440 0 sindel-varindel-pindel ZEB2,frameshift_variant,p.Asp1005AlafsTer70,ENST00000637267,;ZEB2,frameshift_variant,p.Asp1030AlafsTer70,ENST00000636471,;ZEB2,frameshift_variant,p.Asp1005AlafsTer70,ENST00000627532,NM_014795.3;ZEB2,frameshift_variant,p.Asp1005AlafsTer70,ENST00000636026,;ZEB2,frameshift_variant,p.Asp893AlafsTer70,ENST00000638087,;ZEB2,frameshift_variant,p.Asp893AlafsTer70,ENST00000637304,;ZEB2,frameshift_variant,p.Asp893AlafsTer70,ENST00000638007,;ZEB2,frameshift_variant,p.Asp893AlafsTer70,ENST00000637045,;ZEB2,frameshift_variant,p.Asp893AlafsTer70,ENST00000636413,;ZEB2,frameshift_variant,p.Asp746AlafsTer70,ENST00000638128,;ZEB2,frameshift_variant,p.Asp1005AlafsTer70,ENST00000409487,;ZEB2,frameshift_variant,p.Asp981AlafsTer70,ENST00000539609,NM_001171653.1;ZEB2,frameshift_variant,p.Asp1005AlafsTer70,ENST00000558170,;ZEB2,frameshift_variant,p.Asp1004AlafsTer70,ENST00000303660,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000440875,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,upstream_gene_variant,,ENST00000637873,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,3_prime_UTR_variant,,ENST00000636732,; - ENST00000637267 Transcript frameshift_variant 3855/9856 3014/3645 1005/1214 D/X gAc/gc 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 10/11 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 144396465 144396465 T - 1 0 1 0 1 0 0 0 0 18200 1667 58 0 0 ZEB2 2 144396465 Frame_Shift_Del DEL T C3L-00094_T 3879573 144396465 97797064 24 3000 ARL6IP6 0 . GRCh38 2 152718642 152718642 + Missense_Mutation SNP C C A rs751435605 C3L-00094_T C3L-00094_N C C c.18C>A p.Ser6Arg p.S6R ENST00000326446 1/4 37 19 18 35 35 0 strelka-mutect ARL6IP6,missense_variant,p.Ser6Arg,ENST00000326446,NM_152522.5;PRPF40A,upstream_gene_variant,,ENST00000410080,NM_017892.3;PRPF40A,upstream_gene_variant,,ENST00000545856,;PRPF40A,upstream_gene_variant,,ENST00000493468,;PRPF40A,upstream_gene_variant,,ENST00000448428,;ARL6IP6,intron_variant,,ENST00000495469,;ARL6IP6,upstream_gene_variant,,ENST00000463690,;PRPF40A,upstream_gene_variant,,ENST00000486100,;PRPF40A,upstream_gene_variant,,ENST00000354363,;PRPF40A,upstream_gene_variant,,ENST00000489741,;PRPF40A,upstream_gene_variant,,ENST00000450303,;ARL6IP6,upstream_gene_variant,,ENST00000455875,;ARL6IP6,upstream_gene_variant,,ENST00000425034,; A ENST00000326446 Transcript missense_variant 729/2805 18/681 6/226 S/R agC/agA rs751435605 1 1 ARL6IP6 HGNC HGNC:24048 protein_coding YES CCDS2197.1 ENSP00000315357 Q8N6S5 UPI000006EA01 NM_152522.5 deleterious_low_confidence(0.04) 1/4 hmmpanther:PTHR28640,hmmpanther:PTHR28640:SF1 MODERATE 1 SNV 1 1 PASS rs751435605 . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 9 152718642 152718642 C A 1 0 0 0 0 1 0 0 0 1085 767 27 1 1 ARL6IP6 2 152718642 Missense_Mutation SNP C C3L-00094_T 8322177 152718642 89474887 25 3001 GCA 0 . GRCh38 2 162359049 162359049 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.460A>T p.Arg154Trp p.R154W ENST00000437150 6/8 138 116 22 125 125 0 strelka-varscan-mutect GCA,missense_variant,p.Arg154Trp,ENST00000437150,NM_012198.3;GCA,missense_variant,p.Arg135Trp,ENST00000233612,;GCA,missense_variant,p.Arg67Trp,ENST00000414723,;GCA,intron_variant,,ENST00000429691,;GCA,downstream_gene_variant,,ENST00000446271,;GCA,downstream_gene_variant,,ENST00000453113,;GCA,downstream_gene_variant,,ENST00000473240,;GCA,non_coding_transcript_exon_variant,,ENST00000487445,;GCA,downstream_gene_variant,,ENST00000481161,;GCA,downstream_gene_variant,,ENST00000479199,; T ENST00000437150 Transcript missense_variant 621/1992 460/654 154/217 R/W Agg/Tgg 1 1 GCA HGNC HGNC:15990 protein_coding YES CCDS2218.1 ENSP00000394842 P28676 UPI000012BA7D NM_012198.3 deleterious(0) 6/8 PROSITE_profiles:PS50222,hmmpanther:PTHR10183:SF139,hmmpanther:PTHR10183,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 162359049 162359049 A T 1 0 0 0 0 1 0 0 0 6153 434 15 4 4 GCA 2 162359049 Missense_Mutation SNP A C3L-00094_T 9640407 162359049 79834480 26 3002 PLCL1 0 . GRCh38 2 198085539 198085539 + Silent SNP G G T rs558973603 C3L-00094_T C3L-00094_N G G c.2022G>T p.= p.P674P ENST00000428675 2/6 252 167 85 205 205 0 strelka-varscan-mutect PLCL1,synonymous_variant,p.=,ENST00000437704,;PLCL1,synonymous_variant,p.=,ENST00000428675,NM_006226.3;PLCL1,synonymous_variant,p.=,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript synonymous_variant 2420/5125 2022/3288 674/1095 P ccG/ccT rs558973603,COSM1530062,COSM1530063 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 2/6 PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF00387,Gene3D:3.20.20.190,SMART_domains:SM00149,Superfamily_domains:SSF51695,Prints_domain:PR00390 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs558973603 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 198085539 198085539 G T 1 0 0 0 0 0 0 0 1 12133 1103 39 1 1 PLCL1 2 198085539 Silent SNP G C3L-00094_T 35726490 198085539 44107990 27 3003 MPP4 0 . GRCh38 2 201675245 201675245 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.956A>T p.Gln319Leu p.Q319L ENST00000409474 11/22 240 166 74 152 152 0 strelka-varscan-mutect MPP4,missense_variant,p.Gln319Leu,ENST00000409474,NM_033066.2;MPP4,missense_variant,p.Gln319Leu,ENST00000359962,;MPP4,missense_variant,p.Gln319Leu,ENST00000620095,;MPP4,missense_variant,p.Gln306Leu,ENST00000315506,;MPP4,missense_variant,p.Gln319Leu,ENST00000428900,;MPP4,missense_variant,p.Gln275Leu,ENST00000396886,;MPP4,missense_variant,p.Gln292Leu,ENST00000409143,;MPP4,missense_variant,p.Gln319Leu,ENST00000447335,;MPP4,missense_variant,p.Gln332Leu,ENST00000409818,;MPP4,intron_variant,,ENST00000486212,;MPP4,downstream_gene_variant,,ENST00000483841,; A ENST00000409474 Transcript missense_variant 1164/2462 956/1914 319/637 Q/L cAg/cTg 1 -1 MPP4 HGNC HGNC:13680 protein_coding YES CCDS46491.1 ENSP00000387278 Q96JB8 UPI000050A341 NM_033066.2 deleterious(0.04) 11/22 hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF34,Gene3D:2.30.30.40,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 201675245 201675245 T A 1 0 0 0 0 1 0 0 0 9702 1580 55 4 4 MPP4 2 201675245 Missense_Mutation SNP T C3L-00094_T 3589706 201675245 40518284 28 3004 KIAA2012 0 . GRCh38 2 202102967 202102967 + Missense_Mutation SNP C C G novel C3L-00094_T C3L-00094_N C C c.1177C>G p.Pro393Ala p.P393A ENST00000498697 8/24 138 101 37 95 95 0 strelka-varscan-mutect KIAA2012,missense_variant,p.Pro393Ala,ENST00000498697,;KIAA2012,missense_variant,p.Pro393Ala,ENST00000541917,NM_001277372.1;KIAA2012,missense_variant,p.Pro449Ala,ENST00000459709,;KIAA2012,non_coding_transcript_exon_variant,,ENST00000409515,; G ENST00000498697 Transcript missense_variant 1177/3772 1177/3546 393/1181 P/A Cct/Gct 1 1 KIAA2012 HGNC HGNC:51250 protein_coding YES ENSP00000419834 H7C5G6 UPI0005D0279F 8/24 hmmpanther:PTHR21937,hmmpanther:PTHR21937:SF3,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 202102967 202102967 C G 1 0 0 0 0 1 0 0 0 8131 507 18 4 4 KIAA2012 2 202102967 Missense_Mutation SNP C C3L-00094_T 427722 202102967 40090562 29 3005 CHRND 0 . GRCh38 2 232534037 232534037 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1154C>A p.Ser385Tyr p.S385Y ENST00000258385 10/12 533 432 101 391 391 0 strelka-varscan-mutect CHRND,missense_variant,p.Ser370Tyr,ENST00000543200,NM_001256657.1;CHRND,missense_variant,p.Ser385Tyr,ENST00000258385,NM_000751.2;CHRND,3_prime_UTR_variant,,ENST00000441621,;CHRND,3_prime_UTR_variant,,ENST00000446616,;CHRND,downstream_gene_variant,,ENST00000412233,; A ENST00000258385 Transcript missense_variant 1186/2112 1154/1554 385/517 S/Y tCc/tAc 1 1 CHRND HGNC HGNC:1965 protein_coding YES CCDS2494.1 ENSP00000258385 Q07001 UPI000012525E NM_000751.2 tolerated(0.43) 10/12 Pfam_domain:PF02932,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs1397329609 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 232534037 232534037 C A 1 0 0 0 0 1 0 0 0 3154 855 30 2 2 CHRND 2 232534037 Missense_Mutation SNP C C3L-00094_T 30431070 232534037 9659492 30 3006 CHL1 0 . GRCh38 3 405512 405512 + Missense_Mutation SNP C C A rs138591815 C3L-00094_T C3L-00094_N C C c.3476C>A p.Pro1159His p.P1159H ENST00000256509 28/28 108 85 23 105 105 0 strelka-varscan-mutect CHL1,missense_variant,p.Pro1159His,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Pro1106His,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Pro1143His,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Pro293His,ENST00000445697,; A ENST00000256509 Transcript missense_variant 4118/8023 3476/3675 1159/1224 P/H cCt/cAt rs138591815 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 deleterious(0) 28/28 Pfam_domain:PF13882,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653 MODERATE 1 SNV 1 1 PASS rs138591815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 405512 405512 C A 1 0 0 0 0 1 0 0 0 3108 681 24 2 2 CHL1 3 405512 Missense_Mutation SNP C C3L-00094_T 405512 197890047 31 3007 KCNH8 0 . GRCh38 3 19148744 19148744 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.25G>T p.Ala9Ser p.A9S ENST00000328405 1/16 230 216 14 225 225 0 strelka-varscan-mutect KCNH8,missense_variant,p.Ala9Ser,ENST00000328405,NM_144633.2;KCNH8,missense_variant,p.Ala9Ser,ENST00000452398,; T ENST00000328405 Transcript missense_variant 291/5137 25/3324 9/1107 A/S Gcg/Tcg 1 1 KCNH8 HGNC HGNC:18864 protein_coding YES CCDS2632.1 ENSP00000328813 Q96L42 UPI0000167D12 NM_144633.2 deleterious(0) 1/16 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 19148744 19148744 G T 1 0 0 0 0 1 0 0 0 7954 1203 42 2 2 KCNH8 3 19148744 Missense_Mutation SNP G C3L-00094_T 18743232 19148744 179146815 32 3008 RBMS3 0 . GRCh38 3 29739732 29739732 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.412G>T p.Asp138Tyr p.D138Y ENST00000383767 5/15 89 70 19 94 94 0 strelka-varscan-mutect RBMS3,missense_variant,p.Asp137Tyr,ENST00000434693,;RBMS3,missense_variant,p.Asp137Tyr,ENST00000383766,NM_001003792.2;RBMS3,missense_variant,p.Asp138Tyr,ENST00000383767,NM_001003793.2;RBMS3,missense_variant,p.Asp204Tyr,ENST00000636680,;RBMS3,missense_variant,p.Asp138Tyr,ENST00000273139,NM_014483.3;RBMS3,missense_variant,p.Asp138Tyr,ENST00000452462,NM_001177711.1;RBMS3,missense_variant,p.Asp138Tyr,ENST00000456853,NM_001177712.1;RBMS3,missense_variant,p.Asp138Tyr,ENST00000445033,;RBMS3,non_coding_transcript_exon_variant,,ENST00000478716,;RP11-9J18.1,3_prime_UTR_variant,,ENST00000635992,;RBMS3,3_prime_UTR_variant,,ENST00000637842,;RBMS3,non_coding_transcript_exon_variant,,ENST00000497205,; T ENST00000383767 Transcript missense_variant 748/1864 412/1314 138/437 D/Y Gac/Tac 1 1 RBMS3 HGNC HGNC:13427 protein_coding YES CCDS33724.1 ENSP00000373277 Q6XE24 UPI000023FE75 NM_001003793.2 deleterious(0) 5/15 hmmpanther:PTHR24012:SF473,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 29739732 29739732 G T 1 0 0 0 0 1 0 0 0 13316 942 33 2 2 RBMS3 3 29739732 Missense_Mutation SNP G C3L-00094_T 10590988 29739732 168555827 33 3009 WDR48 0 . GRCh38 3 39066772 39066772 + Silent SNP C C G novel C3L-00094_T C3L-00094_N C C c.378C>G p.= p.A126A ENST00000302313 5/19 177 149 28 214 214 0 strelka-varscan-mutect WDR48,synonymous_variant,p.=,ENST00000302313,NM_020839.3,NM_001303403.1,NM_001303402.1;WDR48,synonymous_variant,p.=,ENST00000441361,;WDR48,missense_variant,p.Gln133Glu,ENST00000423296,;WDR48,3_prime_UTR_variant,,ENST00000413099,;WDR48,3_prime_UTR_variant,,ENST00000433841,;WDR48,intron_variant,,ENST00000420940,; G ENST00000302313 Transcript synonymous_variant 406/3707 378/2034 126/677 A gcC/gcG 1 1 WDR48 HGNC HGNC:30914 protein_coding YES CCDS33738.1 ENSP00000307491 Q8TAF3 A0A024R2L1 UPI000006FF8C NM_020839.3,NM_001303403.1,NM_001303402.1 5/19 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19862,hmmpanther:PTHR19862:SF14,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 9 39066772 39066772 C G 1 0 0 0 0 0 0 0 1 17861 581 21 4 4 WDR48 3 39066772 Silent SNP C C3L-00094_T 9327040 39066772 159228787 34 3010 ITIH4 0 . GRCh38 3 52818157 52818157 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.2191G>T p.Ala731Ser p.A731S ENST00000266041 20/24 102 80 22 93 93 0 strelka-varscan-mutect ITIH4,missense_variant,p.Ala731Ser,ENST00000266041,NM_002218.4;ITIH4,missense_variant,p.Ala736Ser,ENST00000485816,;ITIH4,missense_variant,p.Ala701Ser,ENST00000406595,NM_001166449.1;ITIH4,intron_variant,,ENST00000441637,;ITIH4,downstream_gene_variant,,ENST00000467462,;ITIH4,downstream_gene_variant,,ENST00000471505,;ITIH4,downstream_gene_variant,,ENST00000484632,;RP5-966M1.6,3_prime_UTR_variant,,ENST00000468472,;ITIH4,non_coding_transcript_exon_variant,,ENST00000491663,;ITIH4,non_coding_transcript_exon_variant,,ENST00000461966,;ITIH4,non_coding_transcript_exon_variant,,ENST00000481977,;ITIH4,downstream_gene_variant,,ENST00000537897,;ITIH4,upstream_gene_variant,,ENST00000464000,;ITIH4,downstream_gene_variant,,ENST00000485894,; A ENST00000266041 Transcript missense_variant 2288/3336 2191/2793 731/930 A/S Gct/Tct 1 -1 ITIH4 HGNC HGNC:6169 protein_coding YES CCDS2865.1 ENSP00000266041 Q14624 UPI000013D6C3 NM_002218.4 tolerated(0.4) 20/24 hmmpanther:PTHR10338:SF119,hmmpanther:PTHR10338 MODERATE 1 SNV 1 1 PASS rs954413947 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 52818157 52818157 C A 1 0 0 0 0 1 0 0 0 7812 739 26 2 2 ITIH4 3 52818157 Missense_Mutation SNP C C3L-00094_T 13751385 52818157 145477402 35 3011 AC026348.1 0 . GRCh38 3 113373556 113373556 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.2299G>A p.Gly767Ser p.G767S ENST00000393845 17/34 46 36 10 53 53 0 strelka-varscan-mutect AC026348.1,missense_variant,p.Gly767Ser,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Gly767Ser,ENST00000295868,NM_018338.3;CFAP44,intron_variant,,ENST00000488854,; T ENST00000393845 Transcript missense_variant,splice_region_variant 2299/5565 2299/5565 767/1854 G/S Ggt/Agt 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 deleterious(0.01) 17/34 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 9 113373556 113373556 C T 1 0 0 0 0 1 0 0 0 128 637 22 3 3 AC026348.1 3 113373556 Missense_Mutation SNP C C3L-00094_T 60555399 113373556 84922003 36 3012 TRPC1 0 . GRCh38 3 142792854 142792854 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1468G>A p.Asp490Asn p.D490N ENST00000476941 9/13 97 82 15 136 136 0 strelka-varscan-mutect TRPC1,missense_variant,p.Asp456Asn,ENST00000273482,;TRPC1,missense_variant,p.Asp456Asn,ENST00000612385,NM_003304.4;TRPC1,missense_variant,p.Asp490Asn,ENST00000476941,NM_001251845.1; A ENST00000476941 Transcript missense_variant 1954/3061 1468/2382 490/793 D/N Gat/Aat 1 1 TRPC1 HGNC HGNC:12333 protein_coding YES CCDS58856.1 ENSP00000419313 P48995 UPI00001374A4 NM_001251845.1 tolerated(0.15) 9/13 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF56,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 142792854 142792854 G A 1 0 0 0 0 1 0 0 0 17083 1174 41 3 3 TRPC1 3 142792854 Missense_Mutation SNP G C3L-00094_T 29419298 142792854 55502705 37 3013 NCEH1 0 . GRCh38 3 172710857 172710857 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.224C>T p.Ala75Val p.A75V ENST00000538775 1/5 122 94 28 134 134 0 strelka-varscan-mutect NCEH1,missense_variant,p.Ala75Val,ENST00000475381,NM_020792.4;NCEH1,missense_variant,p.Ala75Val,ENST00000538775,NM_001146276.1;NCEH1,missense_variant,p.Ala66Val,ENST00000424772,;NCEH1,5_prime_UTR_variant,,ENST00000543711,NM_001146277.1,NM_001146278.1;NCEH1,missense_variant,p.Ala75Val,ENST00000421723,; A ENST00000538775 Transcript missense_variant 362/4315 224/1347 75/448 A/V gCa/gTa 1 -1 NCEH1 HGNC HGNC:29260 protein_coding YES CCDS54682.1 ENSP00000442464 A0A0A0MTJ9 UPI000199A4B7 NM_001146276.1 tolerated(0.9) 1/5 PIRSF_domain:PIRSF037251 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 172710857 172710857 G A 1 0 0 0 0 1 0 0 0 10233 1319 46 3 3 NCEH1 3 172710857 Missense_Mutation SNP G C3L-00094_T 29918003 172710857 25584702 38 3014 PIGX 0 . GRCh38 3 196727922 196727922 + Splice_Site SNP G G T rs763608495 C3L-00094_T C3L-00094_N G G c.319-1G>T p.X107_splice ENST00000296333 64 53 11 78 78 0 strelka-varscan-mutect PIGX,splice_acceptor_variant,,ENST00000392391,NM_017861.3;PIGX,splice_acceptor_variant,,ENST00000296333,NM_001166304.1;PIGX,splice_acceptor_variant,,ENST00000451319,;PIGX,splice_acceptor_variant,,ENST00000426755,;PIGX,splice_acceptor_variant,,ENST00000421265,;PIGX,splice_acceptor_variant,,ENST00000415832,;PIGX,splice_acceptor_variant,,ENST00000453218,;PIGX,splice_acceptor_variant,,ENST00000457284,; T ENST00000296333 Transcript splice_acceptor_variant -/953 319/831 107/276 rs763608495 1 1 PIGX HGNC HGNC:26046 protein_coding YES CCDS54701.1 ENSP00000296333 H0Y2P9 UPI00015E0960 NM_001166304.1 3/6 HIGH 1 SNV 2 1 PASS rs763608495 . 0 194 13 3 0 0 0 0 -19.43888 0.99564 1 1 1 0 T 5 4 9 196727922 196727922 G T 1 0 0 0 0 0 0 1 0 11997 1014 35 2 2 PIGX 3 196727922 Splice_Site SNP G C3L-00094_T 24017065 196727922 1567637 39 3015 JAKMIP1 0 . GRCh38 4 6085604 6085604 + Missense_Mutation SNP C C G rs748298581 C3L-00094_T C3L-00094_N C C c.650G>C p.Arg217Pro p.R217P ENST00000409021 4/21 219 149 70 172 172 0 strelka-varscan-mutect JAKMIP1,missense_variant,p.Arg217Pro,ENST00000409021,NM_001099433.1;JAKMIP1,missense_variant,p.Arg217Pro,ENST00000282924,NM_144720.3;JAKMIP1,missense_variant,p.Arg52Pro,ENST00000409371,;JAKMIP1,missense_variant,p.Arg217Pro,ENST00000409831,NM_001306133.1;JAKMIP1,missense_variant,p.Arg52Pro,ENST00000410077,NM_001306134.1;JAKMIP1,non_coding_transcript_exon_variant,,ENST00000457227,;JAKMIP1,missense_variant,p.Arg217Pro,ENST00000473053,; G ENST00000409021 Transcript missense_variant 1100/2975 650/2496 217/831 R/P cGt/cCt rs748298581 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 deleterious(0) 4/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 MODERATE 1 SNV 1 1 PASS rs748298581 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 6085604 6085604 C G 1 0 0 0 0 1 0 0 0 7853 536 19 4 4 JAKMIP1 4 6085604 Missense_Mutation SNP C C3L-00094_T 6085604 184128951 40 3016 AFAP1 0 . GRCh38 4 7768939 7768939 + Missense_Mutation SNP C C A rs757167105 C3L-00094_T C3L-00094_N C C c.2323G>T p.Gly775Cys p.G775C ENST00000420658 17/18 121 107 14 114 114 0 strelka-varscan-mutect AFAP1,missense_variant,p.Gly775Cys,ENST00000420658,NM_001134647.1;AFAP1,missense_variant,p.Gly691Cys,ENST00000358461,NM_198595.2;AFAP1,missense_variant,p.Gly691Cys,ENST00000360265,;AFAP1,missense_variant,p.Gly775Cys,ENST00000382543,;AFAP1-AS1,intron_variant,,ENST00000608442,;AFAP1,non_coding_transcript_exon_variant,,ENST00000513842,;AFAP1,non_coding_transcript_exon_variant,,ENST00000505447,; A ENST00000420658 Transcript missense_variant 2596/7768 2323/2445 775/814 G/C Ggc/Tgc rs757167105 1 -1 AFAP1 HGNC HGNC:24017 protein_coding YES CCDS47010.1 ENSP00000410689 Q8N556 UPI000048041E NM_001134647.1 tolerated(0.14) 17/18 hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF8 MODERATE SNV 2 1 PASS rs757167105 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 7768939 7768939 C A 1 0 0 0 0 1 0 0 0 430 623 22 2 2 AFAP1 4 7768939 Missense_Mutation SNP C C3L-00094_T 1683335 7768939 182445616 41 3017 DHX15 0 . GRCh38 4 24570761 24570761 + Silent SNP T T G novel C3L-00094_T C3L-00094_N T T c.594A>C p.= p.A198A ENST00000336812 3/14 268 247 21 259 259 0 strelka-varscan-mutect DHX15,synonymous_variant,p.=,ENST00000336812,NM_001358.2; G ENST00000336812 Transcript synonymous_variant 751/2994 594/2388 198/795 A gcA/gcC 1 -1 DHX15 HGNC HGNC:2738 protein_coding YES CCDS33966.1 ENSP00000336741 O43143 UPI000012907A NM_001358.2 3/14 PROSITE_profiles:PS51192,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF95,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 9 24570761 24570761 T G 1 0 0 0 0 0 0 0 1 4305 1799 63 5 5 DHX15 4 24570761 Silent SNP T C3L-00094_T 16801822 24570761 165643794 42 3018 GUF1 0 . GRCh38 4 44686570 44686570 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.795G>A p.= p.Q265Q ENST00000281543 8/17 273 256 17 355 355 0 strelka-varscan-mutect GUF1,synonymous_variant,p.=,ENST00000281543,NM_021927.2;GNPDA2,intron_variant,,ENST00000608855,;GNPDA2,intron_variant,,ENST00000609092,;GUF1,non_coding_transcript_exon_variant,,ENST00000506793,;GUF1,3_prime_UTR_variant,,ENST00000513775,; A ENST00000281543 Transcript synonymous_variant 989/4449 795/2010 265/669 Q caG/caA 1 1 GUF1 HGNC HGNC:25799 protein_coding YES CCDS3468.1 ENSP00000281543 Q8N442 A0A024R9T3 UPI000006FFEC NM_021927.2 8/17 Gene3D:2.40.30.10,HAMAP:MF_00071,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF97,Superfamily_domains:SSF50447,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR01393 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 44686570 44686570 G A 1 0 0 0 0 0 0 0 1 6781 1020 36 3 3 GUF1 4 44686570 Silent SNP G C3L-00094_T 20115809 44686570 145527985 43 3019 ODAM 0 . GRCh38 4 70202839 70202839 + Silent SNP T T A rs190328480 C3L-00094_T C3L-00094_N T T c.732T>A p.= p.T244T ENST00000396094 9/11 149 141 8 230 230 0 strelka-varscan-mutect ODAM,synonymous_variant,p.=,ENST00000396094,NM_017855.3;ODAM,synonymous_variant,p.=,ENST00000510709,;ODAM,synonymous_variant,p.=,ENST00000514097,;ODAM,3_prime_UTR_variant,,ENST00000510847,;ODAM,downstream_gene_variant,,ENST00000506248,; A ENST00000396094 Transcript synonymous_variant 780/1319 732/840 244/279 T acT/acA rs190328480 1 1 ODAM HGNC HGNC:26043 protein_coding YES CCDS3536.2 ENSP00000379401 A1E959 UPI0000413A02 NM_017855.3 9/11 hmmpanther:PTHR16237:SF3,hmmpanther:PTHR16237,Pfam_domain:PF15424 LOW 1 SNV 5 1 PASS rs190328480 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 70202839 70202839 T A 1 0 0 0 0 0 0 0 1 10902 1596 56 4 4 ODAM 4 70202839 Silent SNP T C3L-00094_T 25516269 70202839 120011716 44 3020 ENAM 0 . GRCh38 4 70644336 70644336 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.2910G>T p.Met970Ile p.M970I ENST00000396073 9/9 588 528 60 660 658 2 strelka-varscan-mutect ENAM,missense_variant,p.Met970Ile,ENST00000396073,NM_031889.2;ENAM,intron_variant,,ENST00000472903,;ENAM,downstream_gene_variant,,ENST00000472597,; T ENST00000396073 Transcript missense_variant 3191/5679 2910/3429 970/1142 M/I atG/atT 1 1 ENAM HGNC HGNC:3344 protein_coding YES CCDS3544.2 ENSP00000379383 Q9NRM1 UPI000013CE60 NM_031889.2 tolerated(0.14) 9/9 hmmpanther:PTHR16784:SF2,hmmpanther:PTHR16784,Pfam_domain:PF15362 MODERATE 1 SNV 1 1 PASS rs1156773891 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 70644336 70644336 G T 1 0 0 0 0 1 0 0 0 4954 1319 46 2 2 ENAM 4 70644336 Missense_Mutation SNP G C3L-00094_T 441497 70644336 119570219 45 3021 RP11-766F14.2 0 . GRCh38 4 99650400 99650400 + Nonsense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.4249C>T p.Gln1417Ter p.Q1417* ENST00000511828 1/2 208 195 13 248 248 0 strelka-varscan-mutect RP11-766F14.2,stop_gained,p.Gln1417Ter,ENST00000511828,; A ENST00000511828 Transcript stop_gained 4249/10086 4249/5382 1417/1793 Q/* Caa/Taa 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE 1/2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 99650400 99650400 G A 1 0 0 0 0 0 1 0 0 13762 1386 48 3 3 RP11-766F14.2 4 99650400 Nonsense_Mutation SNP G C3L-00094_T 29006064 99650400 90564155 46 3022 BBS7 0 . GRCh38 4 121861657 121861657 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.188G>T p.Gly63Val p.G63V ENST00000264499 4/19 253 223 30 295 294 1 strelka-varscan-mutect BBS7,missense_variant,p.Gly63Val,ENST00000264499,NM_176824.2;BBS7,missense_variant,p.Gly63Val,ENST00000506636,NM_018190.3;BBS7,non_coding_transcript_exon_variant,,ENST00000505692,;BBS7,non_coding_transcript_exon_variant,,ENST00000502444,;BBS7,upstream_gene_variant,,ENST00000508536,; A ENST00000264499 Transcript missense_variant 372/3752 188/2148 63/715 G/V gGg/gTg 1 -1 BBS7 HGNC HGNC:18758 protein_coding YES CCDS3724.1 ENSP00000264499 Q8IWZ6 UPI00001684D7 NM_176824.2 deleterious(0) 4/19 hmmpanther:PTHR16074,hmmpanther:PTHR16074:SF4,PIRSF_domain:PIRSF011091,Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 121861657 121861657 C A 1 0 0 0 0 1 0 0 0 1488 623 22 2 2 BBS7 4 121861657 Missense_Mutation SNP C C3L-00094_T 22211257 121861657 68352898 47 3023 ADAD1 0 . GRCh38 4 122380188 122380188 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.119C>A p.Ser40Tyr p.S40Y ENST00000296513 3/13 172 128 44 193 193 0 strelka-varscan-mutect ADAD1,missense_variant,p.Ser40Tyr,ENST00000296513,NM_139243.3;ADAD1,missense_variant,p.Ser22Tyr,ENST00000388725,NM_001159295.1;ADAD1,missense_variant,p.Ser40Tyr,ENST00000388724,NM_001159285.1;ADAD1,missense_variant,p.Ser40Tyr,ENST00000439307,;ADAD1,missense_variant,p.Ser40Tyr,ENST00000446706,;ADAD1,upstream_gene_variant,,ENST00000492454,;ADAD1,downstream_gene_variant,,ENST00000464160,; A ENST00000296513 Transcript missense_variant 304/1961 119/1731 40/576 S/Y tCc/tAc 1 1 ADAD1 HGNC HGNC:30713 protein_coding YES CCDS34058.1 ENSP00000296513 Q96M93 UPI000006DF76 NM_139243.3 tolerated(0.07) 3/13 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 122380188 122380188 C A 1 0 0 0 0 1 0 0 0 275 855 30 2 2 ADAD1 4 122380188 Missense_Mutation SNP C C3L-00094_T 518531 122380188 67834367 48 3024 ADAD1 0 . GRCh38 4 122381078 122381078 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.259A>T p.Ile87Leu p.I87L ENST00000296513 4/13 175 163 12 221 221 0 strelka-varscan-mutect ADAD1,missense_variant,p.Ile87Leu,ENST00000296513,NM_139243.3;ADAD1,missense_variant,p.Ile69Leu,ENST00000388725,NM_001159295.1;ADAD1,missense_variant,p.Ile87Leu,ENST00000388724,NM_001159285.1;ADAD1,missense_variant,p.Ile87Leu,ENST00000439307,;ADAD1,missense_variant,p.Ile87Leu,ENST00000446706,;ADAD1,non_coding_transcript_exon_variant,,ENST00000492454,;ADAD1,downstream_gene_variant,,ENST00000464160,; T ENST00000296513 Transcript missense_variant 444/1961 259/1731 87/576 I/L Ata/Tta 1 1 ADAD1 HGNC HGNC:30713 protein_coding YES CCDS34058.1 ENSP00000296513 Q96M93 UPI000006DF76 NM_139243.3 tolerated(0.08) 4/13 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF103 MODERATE 1 SNV 2 1 PASS rs1289716320 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 122381078 122381078 A T 1 0 0 0 0 1 0 0 0 275 449 16 4 4 ADAD1 4 122381078 Missense_Mutation SNP A C3L-00094_T 890 122381078 67833477 49 3025 PABPC4L 0 . GRCh38 4 134200056 134200056 + Missense_Mutation SNP C C A rs756917832 C3L-00094_T C3L-00094_N C C c.964G>T p.Val322Phe p.V322F ENST00000421491 2/2 385 365 20 406 405 1 strelka-varscan-mutect PABPC4L,missense_variant,p.Val322Phe,ENST00000421491,NM_001114734.1; A ENST00000421491 Transcript missense_variant 1221/4944 964/1113 322/370 V/F Gtt/Ttt rs756917832,COSM4939554,COSM4939555 1 -1 PABPC4L HGNC HGNC:31955 protein_coding YES ENSP00000463233 P0CB38 UPI00004DF2EA NM_001114734.1 deleterious(0) 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01628 0,1,1 MODERATE 1 SNV 3 0,1,1 1 PASS rs756917832 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 134200056 134200056 C A 1 0 0 0 0 1 0 0 0 11444 565 20 2 2 PABPC4L 4 134200056 Missense_Mutation SNP C C3L-00094_T 11818978 134200056 56014499 50 3026 TBC1D9 0 . GRCh38 4 140679660 140679660 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.544A>T p.Ser182Cys p.S182C ENST00000442267 4/21 206 142 64 237 236 1 strelka-varscan-mutect TBC1D9,missense_variant,p.Ser182Cys,ENST00000442267,NM_015130.2;TBC1D9,upstream_gene_variant,,ENST00000514787,; A ENST00000442267 Transcript missense_variant 619/5306 544/3801 182/1266 S/C Agc/Tgc 1 -1 TBC1D9 HGNC HGNC:21710 protein_coding YES CCDS47136.1 ENSP00000411197 Q6ZT07 UPI00001C1E18 NM_015130.2 deleterious(0) 4/21 hmmpanther:PTHR22957:SF190,hmmpanther:PTHR22957,Pfam_domain:PF02893,SMART_domains:SM00568 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 140679660 140679660 T A 1 0 0 0 0 1 0 0 0 16032 1580 55 4 4 TBC1D9 4 140679660 Missense_Mutation SNP T C3L-00094_T 6479604 140679660 49534895 51 3027 CTNND2 0 . GRCh38 5 11397041 11397041 + Missense_Mutation SNP C C A rs146014959 C3L-00094_T C3L-00094_N C C c.602G>T p.Ser201Ile p.S201I ENST00000304623 6/22 137 125 12 80 80 0 strelka-varscan-mutect CTNND2,missense_variant,p.Ser201Ile,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Ser110Ile,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Ser110Ile,ENST00000513598,;CTNND2,intron_variant,,ENST00000503622,NM_001288716.1;CTNND2,intron_variant,,ENST00000502551,;CTNND2,downstream_gene_variant,,ENST00000508761,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,intron_variant,,ENST00000511278,;CTNND2,missense_variant,p.Ser201Ile,ENST00000504499,;CTNND2,intron_variant,,ENST00000513588,; A ENST00000304623 Transcript missense_variant 792/5481 602/3678 201/1225 S/I aGc/aTc rs146014959 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.08) 6/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS rs146014959 . 0 202 7 0 0 0 0 0 -19.99924 0.9999986 1 1 1 0 A 3 1 9 11397041 11397041 C A 1 0 0 0 0 1 0 0 0 3829 797 28 2 2 CTNND2 5 11397041 Missense_Mutation SNP C C3L-00094_T 11397041 170141218 52 3028 NPR3 0 . GRCh38 5 32710721 32710721 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.59A>G p.Gln20Arg p.Q20R ENST00000326958 1/8 112 86 26 95 95 0 strelka-varscan-mutect NPR3,missense_variant,p.Gln20Arg,ENST00000326958,NM_001204376.1;NPR3,missense_variant,p.Gln20Arg,ENST00000434067,;NPR3,intron_variant,,ENST00000509104,;NPR3,upstream_gene_variant,,ENST00000265074,NM_001204375.1;NPR3,upstream_gene_variant,,ENST00000415167,NM_000908.3;NPR3,upstream_gene_variant,,ENST00000507141,;NPR3,non_coding_transcript_exon_variant,,ENST00000506712,; G ENST00000326958 Transcript missense_variant 85/6380 59/975 20/324 Q/R cAg/cGg 1 1 NPR3 HGNC HGNC:7945 protein_coding CCDS56356.1 ENSP00000318340 P17342 UPI0000E094A2 NM_001204376.1 tolerated_low_confidence(0.43) 1/8 MODERATE SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999974 1 1 1 0 G 3 3 9 32710721 32710721 A G 1 0 0 0 0 1 0 0 0 10652 188 7 5 5 NPR3 5 32710721 Missense_Mutation SNP A C3L-00094_T 21313680 32710721 148827538 53 3029 C7 0 . GRCh38 5 40976789 40976789 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.2114G>T p.Trp705Leu p.W705L ENST00000313164 16/18 118 88 30 103 103 0 strelka-varscan-mutect C7,missense_variant,p.Trp705Leu,ENST00000313164,NM_000587.2;C7,non_coding_transcript_exon_variant,,ENST00000494960,;C7,non_coding_transcript_exon_variant,,ENST00000464864,;C7,non_coding_transcript_exon_variant,,ENST00000513922,;C7,downstream_gene_variant,,ENST00000486779,; T ENST00000313164 Transcript missense_variant 2473/4257 2114/2532 705/843 W/L tGg/tTg 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 16/18 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00057 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 40976789 40976789 G T 1 0 0 0 0 1 0 0 0 2134 1357 47 2 2 C7 5 40976789 Missense_Mutation SNP G C3L-00094_T 8266068 40976789 140561470 54 3030 PARP8 0 . GRCh38 5 50760360 50760360 + Nonsense_Mutation SNP G G T C3L-00094_T C3L-00094_N G G c.343G>T p.Glu115Ter p.E115* ENST00000281631 5/26 30 14 16 61 61 0 strelka-varscan-mutect PARP8,stop_gained,p.Glu115Ter,ENST00000281631,NM_024615.3;PARP8,stop_gained,p.Glu94Ter,ENST00000505554,;PARP8,stop_gained,p.Glu115Ter,ENST00000514067,NM_001178056.1;PARP8,stop_gained,p.Glu115Ter,ENST00000505697,NM_001178055.1;PARP8,stop_gained,p.Glu115Ter,ENST00000503046,;PARP8,splice_region_variant,,ENST00000514342,;PARP8,intron_variant,,ENST00000515175,;PARP8,downstream_gene_variant,,ENST00000502524,;PARP8,splice_region_variant,,ENST00000505180,;PARP8,intron_variant,,ENST00000511363,;PARP8,intron_variant,,ENST00000503561,;PARP8,intron_variant,,ENST00000503790,;PARP8,stop_gained,p.Glu115Ter,ENST00000515166,;PARP8,splice_region_variant,,ENST00000510303,;PARP8,splice_region_variant,,ENST00000503888,;PARP8,splice_region_variant,,ENST00000503193,;PARP8,splice_region_variant,,ENST00000507812,;PARP8,intron_variant,,ENST00000503707,; T ENST00000281631 Transcript stop_gained,splice_region_variant 501/7177 343/2565 115/854 E/* Gag/Tag COSM5536488 1 1 PARP8 HGNC HGNC:26124 protein_coding YES CCDS3954.1 ENSP00000281631 Q8N3A8 UPI0000073D19 NM_024615.3 5/26 hmmpanther:PTHR21328,hmmpanther:PTHR21328:SF3 1 HIGH 1 SNV 1 1 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 9 50760360 50760360 G T 1 0 0 0 0 0 1 0 0 11545 1188 41 2 2 PARP8 5 50760360 Nonsense_Mutation SNP G C3L-00094_T 9783571 50760360 130777899 55 3031 ITGA1 0 . GRCh38 5 52910263 52910263 + Nonsense_Mutation SNP C C A rs565973897 C3L-00094_T C3L-00094_N C C c.1701C>A p.Cys567Ter p.C567* ENST00000282588 14/29 266 239 27 297 297 0 strelka-varscan-mutect ITGA1,stop_gained,p.Cys567Ter,ENST00000282588,NM_181501.1;ITGA1,non_coding_transcript_exon_variant,,ENST00000504669,; A ENST00000282588 Transcript stop_gained 2159/10757 1701/3540 567/1179 C/* tgC/tgA rs565973897,COSM1068602 1 1 ITGA1 HGNC HGNC:6134 protein_coding YES CCDS3955.1 ENSP00000282588 P56199 UPI00001A95E8 NM_181501.1 14/29 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF22,SMART_domains:SM00191,Superfamily_domains:SSF69318 0,1 HIGH 1 SNV 1 0,1 1 PASS rs565973897 . 0 207 0 3 0 0 0 0 -20 0.9999858 1 1 1 0 A 4 1 9 52910263 52910263 C A 1 0 0 0 0 0 1 0 0 7779 776 27 1 1 ITGA1 5 52910263 Nonsense_Mutation SNP C C3L-00094_T 2149903 52910263 128627996 56 3032 CAST 0 . GRCh38 5 96742691 96742691 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.1012G>T p.Ala338Ser p.A338S ENST00000395812 14/30 172 129 43 192 192 0 strelka-varscan-mutect CAST,missense_variant,p.Ala338Ser,ENST00000395812,NM_001042440.3;CAST,missense_variant,p.Ala296Ser,ENST00000395813,;CAST,missense_variant,p.Ala274Ser,ENST00000309190,NM_173060.3,NM_001284212.1;CAST,missense_variant,p.Ala48Ser,ENST00000437034,;CAST,missense_variant,p.Ala282Ser,ENST00000511049,;CAST,missense_variant,p.Ala283Ser,ENST00000338252,NM_001190442.1;CAST,missense_variant,p.Ala379Ser,ENST00000508830,;CAST,missense_variant,p.Ala296Ser,ENST00000341926,;CAST,missense_variant,p.Ala282Ser,ENST00000511782,;CAST,missense_variant,p.Ala342Ser,ENST00000508608,;CAST,missense_variant,p.Ala224Ser,ENST00000504465,NM_001284213.1;CAST,missense_variant,p.Ala357Ser,ENST00000510756,;CAST,missense_variant,p.Ala261Ser,ENST00000509903,;CAST,missense_variant,p.Ala296Ser,ENST00000510156,;CAST,missense_variant,p.Ala54Ser,ENST00000510500,;CAST,missense_variant,p.Ala11Ser,ENST00000508579,;CAST,missense_variant,p.Ala344Ser,ENST00000511097,;CAST,missense_variant,p.Ala11Ser,ENST00000509259,;CAST,missense_variant,p.Ala11Ser,ENST00000503828,;CAST,upstream_gene_variant,,ENST00000325674,;CAST,upstream_gene_variant,,ENST00000515663,;CAST,downstream_gene_variant,,ENST00000421689,;CAST,downstream_gene_variant,,ENST00000512620,;CAST,downstream_gene_variant,,ENST00000505143,;CAST,downstream_gene_variant,,ENST00000508197,;CTC-506B8.1,non_coding_transcript_exon_variant,,ENST00000502568,;CAST,non_coding_transcript_exon_variant,,ENST00000348386,;CAST,non_coding_transcript_exon_variant,,ENST00000513666,;CAST,upstream_gene_variant,,ENST00000484552,;CAST,downstream_gene_variant,,ENST00000515063,;CAST,upstream_gene_variant,,ENST00000512191,; T ENST00000395812 Transcript missense_variant 1198/4506 1012/2253 338/750 A/S Gct/Tct 1 1 CAST HGNC HGNC:1515 protein_coding YES CCDS54882.1 ENSP00000379157 P20810 UPI0000DA4C59 NM_001042440.3 tolerated(0.2) 14/30 hmmpanther:PTHR10077,hmmpanther:PTHR10077:SF0,Pfam_domain:PF00748 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 96742691 96742691 G T 1 0 0 0 0 1 0 0 0 2383 1203 42 2 2 CAST 5 96742691 Missense_Mutation SNP G C3L-00094_T 43832428 96742691 84795568 57 3033 TSSK1B 0 . GRCh38 5 113434014 113434014 + Missense_Mutation SNP C C G novel C3L-00094_T C3L-00094_N C C c.826G>C p.Ala276Pro p.A276P ENST00000390666 1/1 246 212 34 294 294 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Ala276Pro,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; G ENST00000390666 Transcript missense_variant 1018/2478 826/1104 276/367 A/P Gca/Cca 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 tolerated(0.63) 1/1 hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Gene3D:1.10.510.10 MODERATE SNV 1 PASS rs1404433291 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 113434014 113434014 C G 1 0 0 0 0 1 0 0 0 17176 739 26 4 4 TSSK1B 5 113434014 Missense_Mutation SNP C C3L-00094_T 16691323 113434014 68104245 58 3034 FBN2 0 . GRCh38 5 128328737 128328737 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.4430A>T p.Glu1477Val p.E1477V ENST00000508053 40/71 409 284 125 413 413 0 strelka-varscan-mutect FBN2,missense_variant,p.Glu1477Val,ENST00000508053,;FBN2,missense_variant,p.Glu1477Val,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Glu1476Val,ENST00000619499,;FBN2,missense_variant,p.Glu1444Val,ENST00000508989,;FBN2,missense_variant,p.Glu327Val,ENST00000507835,; A ENST00000508053 Transcript missense_variant 5405/11132 4430/8739 1477/2912 E/V gAg/gTg 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 40/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 128328737 128328737 T A 1 0 0 0 0 1 0 0 0 5566 1551 54 4 4 FBN2 5 128328737 Missense_Mutation SNP T C3L-00094_T 14894723 128328737 53209522 59 3035 PCDHB16 0 . GRCh38 5 141183468 141183468 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.909G>A p.= p.L303L ENST00000609684 1/1 249 182 67 289 288 1 strelka-varscan-mutect PCDHB16,synonymous_variant,p.=,ENST00000609684,NM_020957.3;PCDHB16,intron_variant,,ENST00000625044,;CH17-140K24.5,intron_variant,,ENST00000623884,;PCDHB9,upstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB8,downstream_gene_variant,,ENST00000239444,NM_019120.4;PCDHB9,upstream_gene_variant,,ENST00000624909,;CH17-140K24.7,non_coding_transcript_exon_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;PCDHB9,upstream_gene_variant,,ENST00000623266,;CH17-140K24.4,downstream_gene_variant,,ENST00000623995,;CH17-140K24.5,intron_variant,,ENST00000623407,; A ENST00000609684 Transcript synonymous_variant 2070/5001 909/2331 303/776 L ctG/ctA 1 1 PCDHB16 HGNC HGNC:14546 protein_coding YES CCDS4251.1 ENSP00000477314 Q9NRJ7 UPI00001273E9 NM_020957.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF71,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 141183468 141183468 G A 1 0 0 0 0 0 0 0 1 11628 1277 45 3 3 PCDHB16 5 141183468 Silent SNP G C3L-00094_T 12854731 141183468 40354791 60 3036 IL17B 0 . GRCh38 5 149374572 149374572 + Missense_Mutation SNP C C A rs757888351 C3L-00094_T C3L-00094_N C C c.340G>T p.Val114Leu p.V114L ENST00000261796 3/3 70 56 14 104 104 0 varscan-mutect IL17B,missense_variant,p.Val114Leu,ENST00000261796,NM_014443.2;PCYOX1L,downstream_gene_variant,,ENST00000514349,;PCYOX1L,downstream_gene_variant,,ENST00000274569,NM_001301055.1,NM_024028.3,NM_001301054.1,NM_001301057.1;RP11-394O4.3,intron_variant,,ENST00000521756,;IL17B,non_coding_transcript_exon_variant,,ENST00000505432,;IL17B,upstream_gene_variant,,ENST00000518814,;PCYOX1L,downstream_gene_variant,,ENST00000507621,;PCYOX1L,downstream_gene_variant,,ENST00000503240,;PCYOX1L,downstream_gene_variant,,ENST00000511945,;PCYOX1L,downstream_gene_variant,,ENST00000505669,; A ENST00000261796 Transcript missense_variant 391/696 340/543 114/180 V/L Gtg/Ttg rs757888351,COSM4692182 1 -1 IL17B HGNC HGNC:5982 protein_coding YES CCDS4297.1 ENSP00000261796 Q9UHF5 UPI0000034D64 NM_014443.2 tolerated(0.17) 3/3 hmmpanther:PTHR21295:SF3,hmmpanther:PTHR21295,Gene3D:2.10.90.10,Pfam_domain:PF06083,Superfamily_domains:SSF57501 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757888351 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 149374572 149374572 C A 1 0 0 0 0 1 0 0 0 7543 536 19 1 1 IL17B 5 149374572 Missense_Mutation SNP C C3L-00094_T 8191104 149374572 32163687 61 3037 MRPL22 0 . GRCh38 5 154957186 154957186 + Nonsense_Mutation SNP A A T rs200195885 C3L-00094_T C3L-00094_N A A c.313A>T p.Lys105Ter p.K105* ENST00000523037 5/7 138 126 12 175 175 0 strelka-varscan-mutect MRPL22,stop_gained,p.Lys105Ter,ENST00000523037,NM_014180.3;MRPL22,stop_gained,p.Lys111Ter,ENST00000522038,;MRPL22,stop_gained,p.Lys25Ter,ENST00000265229,NM_001014990.2;MRPL22,stop_gained,p.Lys131Ter,ENST00000439747,;MRPL22,upstream_gene_variant,,ENST00000518364,;MRPL22,3_prime_UTR_variant,,ENST00000519059,;MRPL22,non_coding_transcript_exon_variant,,ENST00000520040,; T ENST00000523037 Transcript stop_gained 354/3176 313/621 105/206 K/* Aaa/Taa rs200195885 1 1 MRPL22 HGNC HGNC:14480 protein_coding YES CCDS4331.1 ENSP00000431040 Q9NWU5 UPI0000046801 NM_014180.3 5/7 hmmpanther:PTHR13501:SF2,hmmpanther:PTHR13501,Gene3D:3.90.470.10,Pfam_domain:PF00237,Superfamily_domains:SSF54843 HIGH 1 SNV 1 1 PASS rs200195885 . 0 202 0 4 3 0 0 0 -5.358331 0.6804676 1 1 1 0 T 4 4 9 154957186 154957186 A T 1 0 0 0 0 0 1 0 0 9763 131 5 4 4 MRPL22 5 154957186 Nonsense_Mutation SNP A C3L-00094_T 5582614 154957186 26581073 62 3038 FAM196B 0 . GRCh38 5 169883659 169883659 + Silent SNP C C T C3L-00094_T C3L-00094_N C C c.240G>A p.= p.S80S ENST00000377365 2/4 72 59 13 77 77 0 strelka-varscan-mutect FAM196B,synonymous_variant,p.=,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; T ENST00000377365 Transcript synonymous_variant 1622/2999 240/1608 80/535 S tcG/tcA COSM5486475 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 1 LOW SNV 2 1 1 PASS rs1033924671 . 0 197 13 0 0 0 0 0 -20 0.9998922 1 1 1 0 T 2 4 9 169883659 169883659 C T 1 0 0 0 0 0 0 0 1 5374 755 27 1 1 FAM196B 5 169883659 Silent SNP C C3L-00094_T 14926473 169883659 11654600 63 3039 NKX2-5 0 . GRCh38 5 173234819 173234819 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.265G>T p.Ala89Ser p.A89S ENST00000329198 1/2 33 27 6 35 35 0 strelka-varscan-mutect NKX2-5,missense_variant,p.Ala89Ser,ENST00000329198,NM_004387.3;NKX2-5,missense_variant,p.Ala89Ser,ENST00000424406,NM_001166175.1;NKX2-5,missense_variant,p.Ala89Ser,ENST00000521848,NM_001166176.1;NKX2-5,missense_variant,p.Ala89Ser,ENST00000517440,; A ENST00000329198 Transcript missense_variant 539/1709 265/975 89/324 A/S Gcc/Tcc 1 -1 NKX2-5 HGNC HGNC:2488 protein_coding YES CCDS4387.1 ENSP00000327758 P52952 A0A0S2Z383 UPI0000062197 NM_004387.3 tolerated(0.6) 1/2 hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF28,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 197 12 0 0 0 0 0 -15.52254 0.9999417 1 1 1 0 A 3 1 9 173234819 173234819 C A 1 0 0 0 0 1 0 0 0 10489 768 27 1 1 NKX2-5 5 173234819 Missense_Mutation SNP C C3L-00094_T 3351160 173234819 8303440 64 3040 CDHR2 0 . GRCh38 5 176568747 176568747 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.194C>A p.Pro65His p.P65H ENST00000510636 4/32 237 211 26 220 218 2 strelka-varscan-mutect CDHR2,missense_variant,p.Pro65His,ENST00000510636,NM_001171976.1;CDHR2,missense_variant,p.Pro65His,ENST00000261944,NM_017675.4;CDHR2,missense_variant,p.Pro65His,ENST00000506348,;CDHR2,3_prime_UTR_variant,,ENST00000510124,; A ENST00000510636 Transcript missense_variant 468/4509 194/3933 65/1310 P/H cCc/cAc 1 1 CDHR2 HGNC HGNC:18231 protein_coding YES CCDS34297.1 ENSP00000424565 Q9BYE9 UPI0000DBEE8C NM_001171976.1 tolerated(0.08) 4/32 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF312,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 176568747 176568747 C A 1 0 0 0 0 1 0 0 0 2822 623 22 2 2 CDHR2 5 176568747 Missense_Mutation SNP C C3L-00094_T 3333928 176568747 4969512 65 3041 HIST1H2AA 0 . GRCh38 6 25726188 25726188 + Missense_Mutation SNP C C A rs780173095 C3L-00094_T C3L-00094_N C C c.340G>T p.Ala114Ser p.A114S ENST00000297012 1/1 41 23 18 47 47 0 strelka-varscan-mutect HIST1H2AA,missense_variant,p.Ala114Ser,ENST00000297012,NM_170745.3;HIST1H2BA,upstream_gene_variant,,ENST00000274764,NM_170610.2; A ENST00000297012 Transcript missense_variant 340/396 340/396 114/131 A/S Gca/Tca rs780173095 1 -1 HIST1H2AA HGNC HGNC:18729 protein_coding YES CCDS4562.1 ENSP00000297012 Q96QV6 UPI0000073CDD NM_170745.3 tolerated_low_confidence(0.24) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF16211,Prints_domain:PR00620,hmmpanther:PTHR23430,SMART_domains:SM00414,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS rs780173095 . 0 201 9 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 9 25726188 25726188 C A 1 0 0 0 0 1 0 0 0 7016 739 26 2 2 HIST1H2AA 6 25726188 Missense_Mutation SNP C C3L-00094_T 25726188 145079791 66 3042 MOG 0 . GRCh38 6 29667916 29667916 + Missense_Mutation SNP G G T rs530778894 C3L-00094_T C3L-00094_N G G c.584G>T p.Arg195Leu p.R195L ENST00000376898 5/8 354 305 49 328 327 1 strelka-varscan-mutect MOG,missense_variant,p.Arg195Leu,ENST00000376894,;MOG,missense_variant,p.Arg195Leu,ENST00000376917,NM_206809.3;MOG,missense_variant,p.Arg195Leu,ENST00000431798,NM_206812.3;MOG,missense_variant,p.Arg79Leu,ENST00000376888,NM_206814.5;MOG,missense_variant,p.Arg195Leu,ENST00000376898,NM_002433.4;MOG,missense_variant,p.Arg195Leu,ENST00000494692,NM_206811.3;MOG,missense_variant,p.Arg195Leu,ENST00000396701,NM_206810.3;MOG,missense_variant,p.Arg195Leu,ENST00000376891,NM_001008229.2;MOG,missense_variant,p.Arg195Leu,ENST00000396704,NM_001008228.2;MOG,missense_variant,p.Arg157Leu,ENST00000416766,;MOG,missense_variant,p.Arg79Leu,ENST00000490427,NM_001170418.1;MOG,missense_variant,p.Arg79Leu,ENST00000483013,;ZFP57,downstream_gene_variant,,ENST00000376883,;ZFP57,downstream_gene_variant,,ENST00000488757,NM_001109809.2;ZFP57,downstream_gene_variant,,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000469603,;MOG,downstream_gene_variant,,ENST00000476244,;MOG,3_prime_UTR_variant,,ENST00000376889,;MOG,3_prime_UTR_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000376903,;MOG,upstream_gene_variant,,ENST00000485885,; T ENST00000376898 Transcript missense_variant 584/1027 584/759 195/252 R/L cGg/cTg rs530778894,COSM4553243,COSM4553244 1 1 MOG HGNC HGNC:7197 protein_coding YES CCDS4667.1 ENSP00000366095 Q16653 UPI00004573E8 NM_002433.4 tolerated(0.19) 5/8 hmmpanther:PTHR24100,PIRSF_domain:PIRSF016522 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs530778894 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 29667916 29667916 G T 1 0 0 0 0 1 0 0 0 9656 1116 39 1 1 MOG 6 29667916 Missense_Mutation SNP G C3L-00094_T 3941728 29667916 141138063 67 3043 DNAH8 0 . GRCh38 6 38923146 38923146 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.10751G>C p.Trp3584Ser p.W3584S ENST00000327475 72/93 210 179 31 185 185 0 strelka-varscan-mutect DNAH8,missense_variant,p.Trp3584Ser,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Trp3367Ser,ENST00000359357,;DNAH8,missense_variant,p.Trp3584Ser,ENST00000449981,;RP1-207H1.3,non_coding_transcript_exon_variant,,ENST00000416948,;RP1-207H1.3,non_coding_transcript_exon_variant,,ENST00000418399,;RP1-207H1.2,upstream_gene_variant,,ENST00000407768,; C ENST00000327475 Transcript missense_variant 10860/14360 10751/14124 3584/4707 W/S tGg/tCg 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 72/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF12777 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 38923146 38923146 G C 1 0 0 0 0 1 0 0 0 4422 1357 47 4 4 DNAH8 6 38923146 Missense_Mutation SNP G C3L-00094_T 9255230 38923146 131882833 68 3044 HSP90AB1 0 . GRCh38 6 44248673 44248673 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.44T>C p.Phe15Ser p.F15S ENST00000371554 2/12 191 158 33 148 148 0 strelka-varscan-mutect HSP90AB1,missense_variant,p.Phe15Ser,ENST00000371554,;HSP90AB1,missense_variant,p.Phe15Ser,ENST00000620073,NM_001271970.1;HSP90AB1,missense_variant,p.Phe15Ser,ENST00000353801,NM_001271969.1;HSP90AB1,missense_variant,p.Phe15Ser,ENST00000371646,NM_001271971.1,NM_007355.3,NM_001271972.1; C ENST00000371554 Transcript missense_variant 258/2674 44/2175 15/724 F/S tTt/tCt 1 1 HSP90AB1 HGNC HGNC:5258 protein_coding YES CCDS4909.1 ENSP00000360609 P08238 A0A024RD80 UPI00001411EF deleterious(0) 2/12 Gene3D:3.30.565.10,HAMAP:MF_00505,PIRSF_domain:PIRSF002583,Prints_domain:PR00775,hmmpanther:PTHR11528,Superfamily_domains:SSF55874 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 44248673 44248673 T C 1 0 0 0 0 1 0 0 0 7298 1841 64 5 5 HSP90AB1 6 44248673 Missense_Mutation SNP T C3L-00094_T 5325527 44248673 126557306 69 3045 PGK2 0 . GRCh38 6 49786674 49786674 + Missense_Mutation SNP C C T rs546049695 C3L-00094_T C3L-00094_N C C c.514G>A p.Ala172Thr p.A172T ENST00000304801 1/1 225 147 78 205 205 0 strelka-varscan-mutect PGK2,missense_variant,p.Ala172Thr,ENST00000304801,NM_138733.4; T ENST00000304801 Transcript missense_variant 634/1657 514/1254 172/417 A/T Gct/Act rs546049695 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 deleterious(0) 1/1 Gene3D:3.40.50.1260,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,Prints_domain:PR00477,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 MODERATE 1 SNV 1 PASS rs546049695 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 49786674 49786674 C T 1 0 0 0 0 1 0 0 0 11880 768 27 1 1 PGK2 6 49786674 Missense_Mutation SNP C C3L-00094_T 5538001 49786674 121019305 70 3046 PKHD1 0 . GRCh38 6 51748666 51748666 + Splice_Site SNP C C T novel C3L-00094_T C3L-00094_N C C c.8951-1G>A p.X2984_splice ENST00000371117 182 133 49 206 206 0 strelka-varscan-mutect PKHD1,splice_acceptor_variant,,ENST00000371117,NM_138694.3;PKHD1,splice_acceptor_variant,,ENST00000340994,NM_170724.2; T ENST00000371117 Transcript splice_acceptor_variant -/16282 8951/12225 2984/4074 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 57/66 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 9 51748666 51748666 C T 1 0 0 0 0 0 0 1 0 12067 695 24 3 3 PKHD1 6 51748666 Splice_Site SNP C C3L-00094_T 1961992 51748666 119057313 71 3047 EYS 0 . GRCh38 6 64945869 64945869 + Nonsense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.2305G>T p.Glu769Ter p.E769* ENST00000370621 15/44 111 79 32 108 107 1 strelka-varscan-mutect EYS,stop_gained,p.Glu769Ter,ENST00000503581,NM_001142800.1;EYS,stop_gained,p.Glu769Ter,ENST00000370621,NM_001292009.1; A ENST00000370621 Transcript stop_gained 2832/10485 2305/9498 769/3165 E/* Gaa/Taa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 15/44 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 HIGH 1 SNV 1 1 PASS rs1441459124 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 64945869 64945869 C A 1 0 0 0 0 0 1 0 0 5200 835 29 2 2 EYS 6 64945869 Nonsense_Mutation SNP C C3L-00094_T 13197203 64945869 105860110 72 3048 HTR1E 0 . GRCh38 6 87016062 87016062 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.728G>C p.Cys243Ser p.C243S ENST00000305344 2/2 231 198 33 228 228 0 strelka-varscan-mutect HTR1E,missense_variant,p.Cys243Ser,ENST00000305344,NM_000865.2; C ENST00000305344 Transcript missense_variant 1431/2052 728/1098 243/365 C/S tGt/tCt 1 1 HTR1E HGNC HGNC:5291 protein_coding YES CCDS5006.1 ENSP00000307766 P28566 UPI000000126D NM_000865.2 tolerated(0.69) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF33,Pfam_domain:PF00001,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 87016062 87016062 G C 1 0 0 0 0 1 0 0 0 7335 1377 48 4 4 HTR1E 6 87016062 Missense_Mutation SNP G C3L-00094_T 22070193 87016062 83789917 73 3049 MANEA 0 . GRCh38 6 95605833 95605833 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.817A>T p.Thr273Ser p.T273S ENST00000358812 5/5 210 182 28 227 227 0 strelka-varscan-mutect MANEA,missense_variant,p.Thr273Ser,ENST00000358812,NM_024641.3;MANEA,non_coding_transcript_exon_variant,,ENST00000474553,; T ENST00000358812 Transcript missense_variant 951/4575 817/1389 273/462 T/S Acc/Tcc 1 1 MANEA HGNC HGNC:21072 protein_coding YES CCDS5032.1 ENSP00000351669 Q5SRI9 UPI000020DF99 NM_024641.3 deleterious(0.01) 5/5 Pfam_domain:PF16317,hmmpanther:PTHR13572,hmmpanther:PTHR13572:SF1 MODERATE 1 SNV 1 1 PASS rs912621200 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 95605833 95605833 A T 1 0 0 0 0 1 0 0 0 9142 391 14 4 4 MANEA 6 95605833 Missense_Mutation SNP A C3L-00094_T 8589771 95605833 75200146 74 3050 FYN 0 . GRCh38 6 111707941 111707941 + Missense_Mutation SNP C C G novel C3L-00094_T C3L-00094_N C C c.424G>C p.Asp142His p.D142H ENST00000354650 6/14 188 165 23 176 176 0 strelka-varscan-mutect FYN,missense_variant,p.Asp142His,ENST00000354650,NM_002037.5;FYN,missense_variant,p.Asp142His,ENST00000368682,;FYN,missense_variant,p.Asp142His,ENST00000538466,NM_153047.3;FYN,missense_variant,p.Asp142His,ENST00000368678,;FYN,missense_variant,p.Asp142His,ENST00000368667,;FYN,missense_variant,p.Asp142His,ENST00000229471,NM_153048.3;FYN,missense_variant,p.Asp142His,ENST00000518295,;FYN,missense_variant,p.Asp142His,ENST00000523238,;FYN,missense_variant,p.Asp142His,ENST00000462856,;FYN,missense_variant,p.Asp142His,ENST00000520518,;FYN,missense_variant,p.Asp142His,ENST00000517419,;FYN,missense_variant,p.Asp142His,ENST00000524310,;FYN,downstream_gene_variant,,ENST00000523570,;FYN,downstream_gene_variant,,ENST00000518630,;FYN,downstream_gene_variant,,ENST00000523574,;FYN,non_coding_transcript_exon_variant,,ENST00000476769,;FYN,non_coding_transcript_exon_variant,,ENST00000523322,;FYN,non_coding_transcript_exon_variant,,ENST00000496864,;FYN,non_coding_transcript_exon_variant,,ENST00000495927,;FYN,non_coding_transcript_exon_variant,,ENST00000467899,;FYN,upstream_gene_variant,,ENST00000495935,; G ENST00000354650 Transcript missense_variant 1031/3628 424/1614 142/537 D/H Gac/Cac 1 -1 FYN HGNC HGNC:4037 protein_coding YES CCDS5094.1 ENSP00000346671 P06241 UPI0000141141 NM_002037.5 deleterious(0.03) 6/14 Gene3D:2.30.30.40,PROSITE_profiles:PS50002,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF44,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 111707941 111707941 C G 1 0 0 0 0 1 0 0 0 5997 826 29 4 4 FYN 6 111707941 Missense_Mutation SNP C C3L-00094_T 16102108 111707941 59098038 75 3051 NHSL1 0 . GRCh38 6 138431420 138431420 + Silent SNP C C A novel C3L-00094_T C3L-00094_N C C c.2937G>T p.= p.P979P ENST00000427025 5/7 114 95 19 109 109 0 strelka-varscan-mutect NHSL1,synonymous_variant,p.=,ENST00000427025,NM_020464.1;NHSL1,synonymous_variant,p.=,ENST00000343505,NM_001144060.1;NHSL1,downstream_gene_variant,,ENST00000342260,;MIR3145,downstream_gene_variant,,ENST00000580727,; A ENST00000427025 Transcript synonymous_variant 3566/7500 2937/4833 979/1610 P ccG/ccT 1 -1 NHSL1 HGNC HGNC:21021 protein_coding YES CCDS55063.1 ENSP00000394546 Q5SYE7 UPI0001750345 NM_020464.1 5/7 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs983992489 . 0 196 10 4 0 0 0 0 -20 0.9953897 1 1 1 0 A 2 1 9 138431420 138431420 C A 1 0 0 0 0 0 0 0 1 10444 755 27 1 1 NHSL1 6 138431420 Silent SNP C C3L-00094_T 26723479 138431420 32374559 76 3052 CCDC28A 0 . GRCh38 6 138779890 138779890 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.497A>G p.His166Arg p.H166R ENST00000611852 3/6 171 150 21 158 158 0 strelka-varscan-mutect CCDC28A,missense_variant,p.His166Arg,ENST00000611852,;CCDC28A,missense_variant,p.His166Arg,ENST00000332797,NM_015439.2;CCDC28A,missense_variant,p.His76Arg,ENST00000617445,; G ENST00000611852 Transcript missense_variant 663/1505 497/825 166/274 H/R cAc/cGc 1 1 CCDC28A HGNC HGNC:21098 protein_coding YES CCDS5192.1 ENSP00000479060 Q8IWP9 UPI0000049DA5 deleterious(0.03) 3/6 hmmpanther:PTHR13400,hmmpanther:PTHR13400:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 138779890 138779890 A G 1 0 0 0 0 1 0 0 0 2512 159 6 5 5 CCDC28A 6 138779890 Missense_Mutation SNP A C3L-00094_T 348470 138779890 32026089 77 3053 GRID2IP 0 . GRCh38 7 6503643 6503643 + Nonsense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.2755C>T p.Gln919Ter p.Q919* ENST00000457091 16/22 117 85 32 91 91 0 strelka-varscan-mutect GRID2IP,stop_gained,p.Gln919Ter,ENST00000457091,NM_001145118.1;GRID2IP,stop_gained,p.Gln728Ter,ENST00000452113,;GRID2IP,stop_gained,p.Gln735Ter,ENST00000435185,; A ENST00000457091 Transcript stop_gained 2755/3636 2755/3636 919/1211 Q/* Cag/Tag 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 16/22 Pfam_domain:PF02181,PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,SMART_domains:SM00498,Superfamily_domains:SSF101447 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 6503643 6503643 G A 1 0 0 0 0 0 1 0 0 6653 1357 47 3 3 GRID2IP 7 6503643 Nonsense_Mutation SNP G C3L-00094_T 6503643 152842330 78 3054 SP4 0 . GRCh38 7 21477272 21477272 + Silent SNP C C A novel C3L-00094_T C3L-00094_N C C c.1872C>A p.= p.A624A ENST00000222584 4/6 214 157 57 216 216 0 strelka-varscan-mutect SP4,synonymous_variant,p.=,ENST00000222584,NM_001326542.1,NM_001326543.1,NM_003112.3;SP4,downstream_gene_variant,,ENST00000432066,;SP4,3_prime_UTR_variant,,ENST00000448246,; A ENST00000222584 Transcript synonymous_variant 2090/6126 1872/2355 624/784 A gcC/gcA 1 1 SP4 HGNC HGNC:11209 protein_coding YES CCDS5373.1 ENSP00000222584 Q02446 UPI000013C807 NM_001326542.1,NM_001326543.1,NM_003112.3 4/6 hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 21477272 21477272 C A 1 0 0 0 0 0 0 0 1 15292 668 24 2 2 SP4 7 21477272 Silent SNP C C3L-00094_T 14973629 21477272 137868701 79 3055 JAZF1 0 . GRCh38 7 27895336 27895336 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.269G>T p.Ser90Ile p.S90I ENST00000283928 3/5 118 100 18 86 86 0 strelka-varscan-mutect JAZF1,missense_variant,p.Ser90Ile,ENST00000283928,NM_175061.3;JAZF1,missense_variant,p.Ser77Ile,ENST00000427814,;JAZF1,missense_variant,p.Ser66Ile,ENST00000447620,;JAZF1,missense_variant,p.Ser57Ile,ENST00000430432,;JAZF1,non_coding_transcript_exon_variant,,ENST00000420835,;JAZF1,3_prime_UTR_variant,,ENST00000452993,;JAZF1,3_prime_UTR_variant,,ENST00000454041,; A ENST00000283928 Transcript missense_variant 435/3125 269/732 90/243 S/I aGc/aTc 1 -1 JAZF1 HGNC HGNC:28917 protein_coding YES CCDS5416.1 ENSP00000283928 Q86VZ6 UPI00001B2E49 NM_175061.3 deleterious(0.04) 3/5 hmmpanther:PTHR23057 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 27895336 27895336 C A 1 0 0 0 0 1 0 0 0 7860 797 28 2 2 JAZF1 7 27895336 Missense_Mutation SNP C C3L-00094_T 6418064 27895336 131450637 80 3056 ZNF479 0 . GRCh38 7 57120463 57120484 + Frame_Shift_Del DEL TTCTCTTGTGGTCAGTGAGGGT TTCTCTTGTGGTCAGTGAGGGT - novel C3L-00094_T C3L-00094_N TTCTCTTGTGGTCAGTGAGGGT TTCTCTTGTGGTCAGTGAGGGT c.931_952delACCCTCACTGACCACAAGAGAA p.Thr311PhefsTer52 p.T311Ffs*52 ENST00000331162 5/5 194 164 30 223 223 0 sindel-varindel-pindel ZNF479,splice_acceptor_variant,,ENST00000620639,;ZNF479,frameshift_variant,p.Thr311PhefsTer52,ENST00000331162,NM_033273.2;ZNF479,frameshift_variant,p.Thr311PhefsTer52,ENST00000319636,; - ENST00000331162 Transcript frameshift_variant 1202-1223/2072 931-952/1575 311-318/524 TLTDHKRI/X ACCCTCACTGACCACAAGAGAAtt/tt 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 57120463 57120463 TTCTCTTGTGGTCAGTGAGGGT - 1 0 1 0 1 0 0 0 0 18505 1507 52 0 0 ZNF479 7 57120463 Frame_Shift_Del DEL TTCTCTTGTGGTCAGTGAGGGT C3L-00094_T 29225127 57120463 102225510 81 3057 NCF1 0 . GRCh38 7 74779389 74779389 + Missense_Mutation SNP G G T rs782205505 C3L-00094_T C3L-00094_N G G c.362G>T p.Arg121Leu p.R121L ENST00000289473 4/11 233 178 55 181 180 1 strelka-varscan-mutect NCF1,missense_variant,p.Arg121Leu,ENST00000289473,NM_000265.5;NCF1,missense_variant,p.Arg97Leu,ENST00000433458,;NCF1,missense_variant,p.Arg128Leu,ENST00000442021,;NCF1,non_coding_transcript_exon_variant,,ENST00000443956,;NCF1,non_coding_transcript_exon_variant,,ENST00000438106,;NCF1,3_prime_UTR_variant,,ENST00000464878,;NCF1,non_coding_transcript_exon_variant,,ENST00000398421,;NCF1,non_coding_transcript_exon_variant,,ENST00000449343,;NCF1,intron_variant,,ENST00000455062,;NCF1,upstream_gene_variant,,ENST00000488197,;NCF1,upstream_gene_variant,,ENST00000486097,; T ENST00000289473 Transcript missense_variant 432/1396 362/1173 121/390 R/L cGc/cTc rs782205505 1 1 NCF1 HGNC HGNC:7660 protein_coding YES CCDS34657.1 ENSP00000289473 P14598 UPI000013E46E NM_000265.5 deleterious(0.04) 4/11 PROSITE_profiles:PS50195,hmmpanther:PTHR15706,Gene3D:3.30.1520.10,SMART_domains:SM00312,Superfamily_domains:SSF64268,Prints_domain:PR00498 MODERATE 1 SNV 1 1 PASS rs782205505 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 74779389 74779389 G T 1 0 0 0 0 1 0 0 0 10234 1087 38 1 1 NCF1 7 74779389 Missense_Mutation SNP G C3L-00094_T 17658926 74779389 84566584 82 3058 ANKIB1 0 . GRCh38 7 92391338 92391338 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.2225G>C p.Arg742Thr p.R742T ENST00000265742 16/20 70 40 30 62 62 0 strelka-varscan-mutect ANKIB1,missense_variant,p.Arg742Thr,ENST00000265742,NM_019004.1;ANKIB1,3_prime_UTR_variant,,ENST00000422095,;ANKIB1,upstream_gene_variant,,ENST00000465883,; C ENST00000265742 Transcript missense_variant 2601/6081 2225/3270 742/1089 R/T aGg/aCg 1 1 ANKIB1 HGNC HGNC:22215 protein_coding YES CCDS47639.1 ENSP00000265742 Q9P2G1 UPI00001C1E7C NM_019004.1 deleterious(0) 16/20 hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF95 MODERATE 1 SNV 1 1 PASS rs1241150364 . 0 198 12 0 0 0 0 0 -20 0.9999891 1 1 1 0 C 3 2 9 92391338 92391338 G C 1 0 0 0 0 1 0 0 0 731 1000 35 4 4 ANKIB1 7 92391338 Missense_Mutation SNP G C3L-00094_T 17611949 92391338 66954635 83 3059 SLC12A9 0 . GRCh38 7 100859969 100859969 + Silent SNP G G T rs140502011 C3L-00094_T C3L-00094_N G G c.1062G>T p.= p.A354A ENST00000354161 8/14 192 145 47 169 169 0 strelka-varscan-mutect SLC12A9,synonymous_variant,p.=,ENST00000354161,NM_020246.3;SLC12A9,synonymous_variant,p.=,ENST00000540482,NM_001267812.1;SLC12A9,synonymous_variant,p.=,ENST00000415287,NM_001267814.1;SLC12A9,synonymous_variant,p.=,ENST00000418037,;SLC12A9,synonymous_variant,p.=,ENST00000416675,;SLC12A9,downstream_gene_variant,,ENST00000434158,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475623,;SLC12A9,upstream_gene_variant,,ENST00000482184,;SLC12A9,downstream_gene_variant,,ENST00000461016,;SLC12A9,3_prime_UTR_variant,,ENST00000448342,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000487651,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000497958,;SLC12A9,downstream_gene_variant,,ENST00000462106,; T ENST00000354161 Transcript synonymous_variant 1187/3273 1062/2745 354/914 A gcG/gcT rs140502011,COSM3698053,COSM3698054 1 1 SLC12A9 HGNC HGNC:17435 protein_coding YES CCDS5707.1 ENSP00000275730 Q9BXP2 UPI000006CD28 NM_020246.3 8/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF52,Pfam_domain:PF00324 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs140502011 . 0 206 2 2 0 0 0 0 -20 0.9999993 1 1 1 0 T 2 4 9 100859969 100859969 G T 1 0 0 0 0 0 0 0 1 14655 1074 38 1 1 SLC12A9 7 100859969 Silent SNP G C3L-00094_T 8468631 100859969 58486004 84 3060 SLC13A1 0 . GRCh38 7 123134519 123134519 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.823G>T p.Asp275Tyr p.D275Y ENST00000194130 8/15 111 96 15 141 141 0 strelka-mutect SLC13A1,missense_variant,p.Asp275Tyr,ENST00000194130,NM_022444.3;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; A ENST00000194130 Transcript missense_variant 863/3815 823/1788 275/595 D/Y Gac/Tac COSM744776 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 deleterious(0) 8/15 hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283,Pfam_domain:PF00939 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 123134519 123134519 C A 1 0 0 0 0 1 0 0 0 14656 826 29 2 2 SLC13A1 7 123134519 Missense_Mutation SNP C C3L-00094_T 22274550 123134519 36211454 85 3061 SPAM1 0 . GRCh38 7 123959837 123959837 + Missense_Mutation SNP T T A rs753779870 C3L-00094_T C3L-00094_N T T c.1398T>A p.Asp466Glu p.D466E ENST00000340011 5/7 243 205 38 237 237 0 strelka-varscan-mutect SPAM1,missense_variant,p.Asp466Glu,ENST00000340011,NM_003117.4;SPAM1,missense_variant,p.Asp466Glu,ENST00000439500,NM_001174046.1,NM_001174045.1;SPAM1,missense_variant,p.Asp466Glu,ENST00000460182,NM_001174044.1,NM_153189.2;SPAM1,missense_variant,p.Asp466Glu,ENST00000223028,;SPAM1,missense_variant,p.Asp466Glu,ENST00000402183,; A ENST00000340011 Transcript missense_variant 1755/2349 1398/1536 466/511 D/E gaT/gaA rs753779870 1 1 SPAM1 HGNC HGNC:11217 protein_coding YES CCDS5790.1 ENSP00000345849 P38567 UPI0000072166 NM_003117.4 tolerated(0.32) 5/7 hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF20,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Prints_domain:PR00848 MODERATE 1 SNV 1 1 PASS rs753779870 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 123959837 123959837 T A 1 0 0 0 0 1 0 0 0 15317 1461 51 4 4 SPAM1 7 123959837 Missense_Mutation SNP T C3L-00094_T 825318 123959837 35386136 86 3062 ZNF800 0 . GRCh38 7 127374693 127374693 + Nonsense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.643C>T p.Gln215Ter p.Q215* ENST00000393313 5/6 127 107 20 127 127 0 strelka-varscan-mutect ZNF800,stop_gained,p.Gln215Ter,ENST00000393313,;ZNF800,stop_gained,p.Gln215Ter,ENST00000265827,NM_176814.4;ZNF800,stop_gained,p.Gln215Ter,ENST00000393312,;ZNF800,stop_gained,p.Gln215Ter,ENST00000619291,;ZNF800,stop_gained,p.Gln215Ter,ENST00000434602,;ZNF800,downstream_gene_variant,,ENST00000436992,;ZNF800,downstream_gene_variant,,ENST00000439506,;ZNF800,upstream_gene_variant,,ENST00000485577,; A ENST00000393313 Transcript stop_gained 1235/4358 643/1995 215/664 Q/* Cag/Tag 1 -1 ZNF800 HGNC HGNC:27267 protein_coding YES CCDS5795.1 ENSP00000376989 Q2TB10 UPI000020FA03 5/6 hmmpanther:PTHR21020 HIGH 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 127374693 127374693 G A 1 0 0 0 0 0 1 0 0 18754 1328 46 3 3 ZNF800 7 127374693 Nonsense_Mutation SNP G C3L-00094_T 3414856 127374693 31971280 87 3063 PTN 0 . GRCh38 7 137251286 137251286 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.395A>T p.Gln132Leu p.Q132L ENST00000348225 4/5 364 232 132 267 267 0 strelka-varscan-mutect PTN,missense_variant,p.Gln132Leu,ENST00000348225,NM_001321387.1,NM_002825.5;PTN,missense_variant,p.Gln132Leu,ENST00000393083,; A ENST00000348225 Transcript missense_variant 823/1614 395/507 132/168 Q/L cAg/cTg 1 -1 PTN HGNC HGNC:9630 protein_coding YES CCDS5844.1 ENSP00000341170 P21246 A0A024R778 UPI000013297B NM_001321387.1,NM_002825.5 deleterious(0.02) 4/5 Gene3D:1mkcA00,Pfam_domain:PF01091,Prints_domain:PR00269,hmmpanther:PTHR13850,Superfamily_domains:SSF57288 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 137251286 137251286 T A 1 0 0 0 0 1 0 0 0 12924 1580 55 4 4 PTN 7 137251286 Missense_Mutation SNP T C3L-00094_T 9876593 137251286 22094687 88 3064 SSPO 0 . GRCh38 7 149780115 149780115 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.1383G>A p.= p.R461R ENST00000378016 10/107 43 39 4 47 47 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,intron_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000493502,; A ENST00000378016 Transcript synonymous_variant 1383/15589 1383/15453 461/5150 R agG/agA 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 10/107 Pfam_domain:PF08742,SMART_domains:SM00832,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 149780115 149780115 G A 1 0 0 0 0 0 0 0 1 15566 1165 41 3 3 SSPO 7 149780115 Silent SNP G C3L-00094_T 12528829 149780115 9565858 89 3065 USP17L7 0 . GRCh38 8 12133134 12133134 + Silent SNP G G C novel C3L-00094_T C3L-00094_N G G c.876C>G p.= p.A292A ENST00000530447 1/1 509 291 218 569 568 1 strelka-varscan-mutect USP17L7,synonymous_variant,p.=,ENST00000530447,NM_001256869.1;USP17L2,downstream_gene_variant,,ENST00000333796,NM_201402.2;FAM66D,intron_variant,,ENST00000434078,;RP11-1236K1.8,upstream_gene_variant,,ENST00000526505,; C ENST00000530447 Transcript synonymous_variant 1311/2028 876/1593 292/530 A gcC/gcG 1 -1 USP17L7 HGNC HGNC:37180 protein_coding YES CCDS78305.1 ENSP00000485337 P0C7H9 UPI00001972BD NM_001256869.1 1/1 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 LOW SNV 1 PASS rs992727440 . 22 188 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 9 12133134 12133134 G C 1 0 0 0 0 0 0 0 1 17589 1335 47 4 4 USP17L7 8 12133134 Silent SNP G C3L-00094_T 12133134 133005502 90 3066 USP17L2 0 . GRCh38 8 12137885 12137885 + Silent SNP G G C rs771568275 C3L-00094_T C3L-00094_N G G c.876C>G p.= p.A292A ENST00000333796 1/1 800 756 44 743 743 0 varscan-mutect USP17L2,synonymous_variant,p.=,ENST00000333796,NM_201402.2;USP17L7,upstream_gene_variant,,ENST00000530447,NM_001256869.1;FAM66D,intron_variant,,ENST00000434078,; C ENST00000333796 Transcript synonymous_variant 1193/1910 876/1593 292/530 A gcC/gcG rs771568275 1 -1 USP17L2 HGNC HGNC:34434 protein_coding YES CCDS43713.1 ENSP00000333329 Q6R6M4 UPI0000198137 NM_201402.2 1/1 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 LOW SNV 1 PASS rs771568275 . 23 187 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 9 12137885 12137885 G C 1 0 0 0 0 0 0 0 1 17586 1335 47 4 4 USP17L2 8 12137885 Silent SNP G C3L-00094_T 4751 12137885 133000751 91 3067 NRG1 0 . GRCh38 8 32756408 32756408 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.824A>T p.Gln275Leu p.Q275L ENST00000287842 10/13 66 37 29 98 98 0 strelka-varscan-mutect NRG1,missense_variant,p.Gln267Leu,ENST00000356819,NM_013957.3;NRG1,missense_variant,p.Gln343Leu,ENST00000523534,;NRG1,missense_variant,p.Gln116Leu,ENST00000539990,NM_001159996.1;NRG1,missense_variant,p.Gln267Leu,ENST00000523079,NM_001160008.1,NM_001160004.1;NRG1,missense_variant,p.Gln275Leu,ENST00000287842,NM_013956.3;NRG1,missense_variant,p.Gln270Leu,ENST00000405005,NM_013964.3;NRG1,missense_variant,p.Gln220Leu,ENST00000519301,NM_001160001.1;NRG1,missense_variant,p.Gln270Leu,ENST00000521670,NM_013960.3;NRG1,missense_variant,p.Gln237Leu,ENST00000518104,NM_001159995.1,NM_001159999.1;NRG1,missense_variant,p.Gln116Leu,ENST00000522402,;NRG1,missense_variant,p.Gln113Leu,ENST00000519240,;NRG1,downstream_gene_variant,,ENST00000518084,;NRG1,non_coding_transcript_exon_variant,,ENST00000522569,; T ENST00000287842 Transcript missense_variant 916/2035 824/1938 275/645 Q/L cAg/cTg 1 1 NRG1 HGNC HGNC:7997 protein_coding YES CCDS6083.1 ENSP00000287842 Q02297 UPI000013DED7 NM_013956.3 deleterious(0) 10/13 hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF7,Pfam_domain:PF02158 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 32756408 32756408 A T 1 0 0 0 0 1 0 0 0 10705 202 7 4 4 NRG1 8 32756408 Missense_Mutation SNP A C3L-00094_T 20618523 32756408 112382228 92 3068 ADAM2 0 . GRCh38 8 39821171 39821171 + Splice_Site SNP C C A novel C3L-00094_T C3L-00094_N C C c.345-1G>T p.X115_splice ENST00000265708 34 20 14 50 49 1 strelka-varscan-mutect ADAM2,splice_acceptor_variant,,ENST00000265708,NM_001464.4;ADAM2,splice_acceptor_variant,,ENST00000347580,NM_001278113.1;ADAM2,splice_acceptor_variant,,ENST00000622267,;ADAM2,splice_acceptor_variant,,ENST00000379853,;ADAM2,splice_acceptor_variant,,ENST00000521880,NM_001278114.1;ADAM2,splice_acceptor_variant,,ENST00000523181,; A ENST00000265708 Transcript splice_acceptor_variant -/2672 345/2208 115/735 1 -1 ADAM2 HGNC HGNC:198 protein_coding YES CCDS34884.1 ENSP00000265708 Q99965 UPI00001254C2 NM_001464.4 5/20 HIGH 1 SNV 1 1 PASS rs1333713505 . 1 195 12 2 0 0 0 0 -20 0.999742 1 1 1 0 A 5 1 9 39821171 39821171 C A 1 0 0 0 0 0 0 1 0 285 695 24 2 2 ADAM2 8 39821171 Splice_Site SNP C C3L-00094_T 7064763 39821171 105317465 93 3069 C8orf34 0 . GRCh38 8 68533134 68533134 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1090G>A p.Ala364Thr p.A364T ENST00000518698 7/14 71 66 5 72 72 0 varscan-mutect C8orf34,missense_variant,p.Ala253Thr,ENST00000337103,;C8orf34,missense_variant,p.Ala278Thr,ENST00000348340,NM_001195639.1;C8orf34,missense_variant,p.Ala364Thr,ENST00000518698,NM_052958.2;C8orf34,non_coding_transcript_exon_variant,,ENST00000518515,;C8orf34,3_prime_UTR_variant,,ENST00000521406,; A ENST00000518698 Transcript missense_variant 1381/2223 1090/1617 364/538 A/T Gca/Aca 1 1 C8orf34 HGNC HGNC:30905 protein_coding YES CCDS6203.2 ENSP00000427820 Q49A92 UPI000021D12D NM_052958.2 deleterious(0) 7/14 hmmpanther:PTHR32000,hmmpanther:PTHR32000:SF3 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 68533134 68533134 G A 1 0 0 0 0 1 0 0 0 2155 1319 46 3 3 C8orf34 8 68533134 Missense_Mutation SNP G C3L-00094_T 28711963 68533134 76605502 94 3070 TRPA1 0 . GRCh38 8 72050868 72050868 + Missense_Mutation SNP C C A rs777465678 C3L-00094_T C3L-00094_N C C c.1815G>T p.Trp605Cys p.W605C ENST00000262209 15/27 123 76 47 174 174 0 strelka-varscan-mutect TRPA1,missense_variant,p.Trp605Cys,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Trp457Cys,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000512290,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;TRPA1,downstream_gene_variant,,ENST00000520788,;TRPA1,upstream_gene_variant,,ENST00000522271,; A ENST00000262209 Transcript missense_variant 2023/5223 1815/3360 605/1119 W/C tgG/tgT rs777465678 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 tolerated(0.27) 15/27 hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248 MODERATE 1 SNV 1 1 PASS rs777465678 . 0 207 0 3 0 0 0 0 -20 0.999999 1 1 1 0 A 3 1 9 72050868 72050868 C A 1 0 0 0 0 1 0 0 0 17082 637 22 2 2 TRPA1 8 72050868 Missense_Mutation SNP C C3L-00094_T 3517734 72050868 73087768 95 3071 NBN 0 . GRCh38 8 89943258 89943258 + Frame_Shift_Del DEL T T - novel C3L-00094_T C3L-00094_N T T c.2179delA p.Met727TrpfsTer24 p.M727Wfs*24 ENST00000265433 14/16 352 207 145 402 402 0 sindel-varindel-pindel NBN,frameshift_variant,p.Met727TrpfsTer24,ENST00000265433,NM_002485.4;NBN,frameshift_variant,p.Met645TrpfsTer24,ENST00000409330,;NBN,frameshift_variant,p.Met97TrpfsTer24,ENST00000613033,;NBN,3_prime_UTR_variant,,ENST00000396252,NM_001024688.2;NBN,downstream_gene_variant,,ENST00000520325,; - ENST00000265433 Transcript frameshift_variant 2334/4666 2179/2265 727/754 M/X Atg/tg 1 -1 NBN HGNC HGNC:7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 UPI0000073BF4 NM_002485.4 14/16 hmmpanther:PTHR12162,hmmpanther:PTHR12162:SF0,PIRSF_domain:PIRSF011869,Pfam_domain:PF08599,SMART_domains:SM01348 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 89943258 89943258 T - 1 0 1 0 1 0 0 0 0 10202 1507 52 0 0 NBN 8 89943258 Frame_Shift_Del DEL T C3L-00094_T 17892390 89943258 55195378 96 3072 HAS2 0 . GRCh38 8 121614953 121614953 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.815C>G p.Ser272Cys p.S272C ENST00000303924 4/4 187 90 97 177 177 0 strelka-varscan-mutect HAS2,missense_variant,p.Ser272Cys,ENST00000303924,NM_005328.2; C ENST00000303924 Transcript missense_variant 1353/4190 815/1659 272/552 S/C tCt/tGt 1 -1 HAS2 HGNC HGNC:4819 protein_coding YES CCDS6335.1 ENSP00000306991 Q92819 UPI000012C0A9 NM_005328.2 deleterious(0) 4/4 Gene3D:3.90.550.10,Pfam_domain:PF13641,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF7,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 121614953 121614953 G C 1 0 0 0 0 1 0 0 0 6848 942 33 4 4 HAS2 8 121614953 Missense_Mutation SNP G C3L-00094_T 31671695 121614953 23523683 97 3073 FAM135B 0 . GRCh38 8 138132680 138132680 + Missense_Mutation SNP G G C rs371041013 C3L-00094_T C3L-00094_N G G c.4134C>G p.Ile1378Met p.I1378M ENST00000395297 20/20 441 229 212 455 455 0 strelka-varscan-mutect FAM135B,missense_variant,p.Ile1378Met,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,; C ENST00000395297 Transcript missense_variant 4305/6962 4134/4221 1378/1406 I/M atC/atG rs371041013,COSM1551721,COSM1551722 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 20/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs371041013 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 138132680 138132680 G C 1 0 0 0 0 1 0 0 0 5299 1048 37 4 4 FAM135B 8 138132680 Missense_Mutation SNP G C3L-00094_T 16517727 138132680 7005956 98 3074 ARHGAP39 0 . GRCh38 8 144530492 144530492 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.3275G>T p.Arg1092Leu p.R1092L ENST00000377307 11/11 197 79 118 141 141 0 strelka-varscan-mutect ARHGAP39,missense_variant,p.Arg1061Leu,ENST00000276826,NM_001308208.1,NM_001308207.1;ARHGAP39,missense_variant,p.Arg1092Leu,ENST00000377307,NM_025251.1;C8orf82,upstream_gene_variant,,ENST00000524821,NM_001001795.1;C8orf82,upstream_gene_variant,,ENST00000313465,;LRRC24,upstream_gene_variant,,ENST00000529415,NM_001024678.3;LRRC24,upstream_gene_variant,,ENST00000533758,;C8orf82,upstream_gene_variant,,ENST00000532827,;C8orf82,upstream_gene_variant,,ENST00000527462,;C8orf82,upstream_gene_variant,,ENST00000534680,; A ENST00000377307 Transcript missense_variant 3360/4673 3275/3345 1092/1114 R/L cGc/cTc 1 -1 ARHGAP39 HGNC HGNC:29351 protein_coding YES CCDS34971.1 ENSP00000366522 Q9C0H5 UPI000021015B NM_025251.1 deleterious(0) 11/11 PROSITE_profiles:PS50238,hmmpanther:PTHR23177,hmmpanther:PTHR23177:SF9,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 144530492 144530492 C A 1 0 0 0 0 1 0 0 0 1010 768 27 1 1 ARHGAP39 8 144530492 Missense_Mutation SNP C C3L-00094_T 6397812 144530492 608144 99 3075 PTPRD 0 . GRCh38 9 8518372 8518372 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1019C>T p.Thr340Ile p.T340I ENST00000381196 18/43 109 81 28 90 90 0 strelka-varscan-mutect PTPRD,missense_variant,p.Thr340Ile,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Thr340Ile,ENST00000356435,;PTPRD,missense_variant,p.Thr340Ile,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Thr330Ile,ENST00000397617,;PTPRD,missense_variant,p.Thr337Ile,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Thr334Ile,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Thr340Ile,ENST00000540109,;PTPRD,missense_variant,p.Thr340Ile,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Thr330Ile,ENST00000397606,NM_001171025.1; A ENST00000381196 Transcript missense_variant 1563/9911 1019/5739 340/1912 T/I aCa/aTa 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0) 18/43 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 8518372 8518372 G A 1 0 0 0 0 1 0 0 0 12953 1377 48 3 3 PTPRD 9 8518372 Missense_Mutation SNP G C3L-00094_T 8518372 129876345 100 3076 BNC2 0 . GRCh38 9 16436593 16436593 + Frame_Shift_Del DEL G G - novel C3L-00094_T C3L-00094_N G G c.1601delC p.Pro534LeufsTer13 p.P534Lfs*13 ENST00000380672 6/7 252 217 35 301 301 0 sindel-varindel-pindel BNC2,frameshift_variant,p.Pro534LeufsTer13,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,frameshift_variant,p.Pro360LeufsTer13,ENST00000545497,;BNC2,frameshift_variant,p.Pro491LeufsTer13,ENST00000418777,;BNC2,frameshift_variant,p.Pro467LeufsTer13,ENST00000380667,;BNC2,upstream_gene_variant,,ENST00000411752,;BNC2,downstream_gene_variant,,ENST00000380666,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,frameshift_variant,p.Pro534LeufsTer13,ENST00000484726,; - ENST00000380672 Transcript frameshift_variant 1659/12844 1601/3300 534/1099 P/X cCt/ct 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 16436593 16436593 G - 1 0 1 0 1 0 0 0 0 1631 1000 35 0 0 BNC2 9 16436593 Frame_Shift_Del DEL G C3L-00094_T 7918221 16436593 121958124 101 3077 UNC13B 0 . GRCh38 9 35310754 35310754 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.1049A>G p.Lys350Arg p.K350R ENST00000378495 9/39 114 87 27 106 105 1 strelka-varscan-mutect UNC13B,missense_variant,p.Lys3099Arg,ENST00000635942,;UNC13B,missense_variant,p.Lys350Arg,ENST00000619578,;UNC13B,missense_variant,p.Lys350Arg,ENST00000378495,NM_006377.3;UNC13B,missense_variant,p.Lys362Arg,ENST00000396787,;UNC13B,5_prime_UTR_variant,,ENST00000617908,;UNC13B,5_prime_UTR_variant,,ENST00000378496,;UNC13B,missense_variant,p.Lys350Arg,ENST00000634487,; G ENST00000378495 Transcript missense_variant 1271/6303 1049/4776 350/1591 K/R aAa/aGa 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 tolerated_low_confidence(0.33) 9/39 hmmpanther:PTHR10480 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 35310754 35310754 A G 1 0 0 0 0 1 0 0 0 17509 14 1 5 5 UNC13B 9 35310754 Missense_Mutation SNP A C3L-00094_T 18874161 35310754 103083963 102 3078 ANKRD20A4 0 . GRCh38 9 64409437 64409437 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.1319G>T p.Cys440Phe p.C440F ENST00000357336 14/15 34 26 8 81 81 0 strelka-varscan-mutect ANKRD20A4,missense_variant,p.Cys440Phe,ENST00000357336,NM_001098805.1; T ENST00000357336 Transcript missense_variant,splice_region_variant 1600/4137 1319/2472 440/823 C/F tGc/tTc 1 1 ANKRD20A4 HGNC HGNC:31982 protein_coding YES CCDS43828.1 ENSP00000349891 Q4UJ75 UPI000051917A NM_001098805.1 tolerated(0.94) 14/15 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF1 MODERATE 1 SNV 1 1 PASS . . 5 199 4 2 0 0 0 0 -16.90839 0.9999913 1 1 1 0 T 3 4 9 64409437 64409437 G T 1 0 0 0 0 1 0 0 0 753 1333 46 2 2 ANKRD20A4 9 64409437 Missense_Mutation SNP G C3L-00094_T 29098683 64409437 73985280 103 3079 ABHD17B 0 . GRCh38 9 71874678 71874678 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.403G>T p.Gly135Trp p.G135W ENST00000377041 2/5 67 49 18 78 78 0 strelka-varscan-mutect ABHD17B,missense_variant,p.Gly135Trp,ENST00000333421,NM_001025780.1;ABHD17B,missense_variant,p.Gly135Trp,ENST00000377041,NM_016014.2; A ENST00000377041 Transcript missense_variant 704/1312 403/882 135/293 G/W Ggg/Tgg COSM5338721,COSM5338722 1 -1 ABHD17B HGNC HGNC:24278 protein_coding YES CCDS35042.1 ENSP00000366240 Q5VST6 UPI0000210B1F NM_016014.2 deleterious(0) 2/5 Gene3D:3.40.50.1820,Pfam_domain:PF12146,hmmpanther:PTHR12277,hmmpanther:PTHR12277:SF48,Low_complexity_(Seg):seg,Superfamily_domains:SSF53474 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs768914021 . 0 199 10 0 0 0 0 0 -20 0.9999944 1 1 1 0 A 3 1 9 71874678 71874678 C A 1 0 0 0 0 1 0 0 0 89 652 23 1 1 ABHD17B 9 71874678 Missense_Mutation SNP C C3L-00094_T 7465241 71874678 66520039 104 3080 GCNT1 0 . GRCh38 9 76502952 76502952 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.571A>T p.Ser191Cys p.S191C ENST00000442371 3/3 198 162 36 206 206 0 strelka-varscan-mutect GCNT1,missense_variant,p.Ser191Cys,ENST00000442371,NM_001097634.1;GCNT1,missense_variant,p.Ser191Cys,ENST00000376730,NM_001490.4;GCNT1,missense_variant,p.Ser191Cys,ENST00000444201,NM_001097633.1,NM_001097635.1,NM_001097636.1;GCNT1,downstream_gene_variant,,ENST00000488136,;GCNT1,downstream_gene_variant,,ENST00000480311,; T ENST00000442371 Transcript missense_variant 1510/5972 571/1287 191/428 S/C Agc/Tgc 1 1 GCNT1 HGNC HGNC:4203 protein_coding YES CCDS6653.1 ENSP00000415454 Q02742 UPI000013CF63 NM_001097634.1 deleterious(0) 3/3 Pfam_domain:PF02485,hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF81 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 76502952 76502952 A T 1 0 0 0 0 1 0 0 0 6170 304 11 4 4 GCNT1 9 76502952 Missense_Mutation SNP A C3L-00094_T 4628274 76502952 61891765 105 3081 WNK2 0 . GRCh38 9 93234879 93234879 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1147G>A p.Gly383Arg p.G383R ENST00000297954 4/30 187 127 60 170 170 0 strelka-varscan-mutect WNK2,missense_variant,p.Gly379Arg,ENST00000432730,;WNK2,missense_variant,p.Gly383Arg,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Gly383Arg,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Gly383Arg,ENST00000448039,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000411624,; A ENST00000297954 Transcript missense_variant 1147/7138 1147/6894 383/2297 G/R Ggg/Agg 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0) 4/30 PROSITE_profiles:PS50011,hmmpanther:PTHR13902:SF10,hmmpanther:PTHR13902,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 93234879 93234879 G A 1 0 0 0 0 1 0 0 0 17934 1348 47 3 3 WNK2 9 93234879 Missense_Mutation SNP G C3L-00094_T 16731927 93234879 45159838 106 3082 HABP4 0 . GRCh38 9 96488119 96488119 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.1030C>T p.His344Tyr p.H344Y ENST00000375249 7/8 134 91 43 100 99 1 strelka-varscan-mutect HABP4,missense_variant,p.His344Tyr,ENST00000375249,NM_014282.3;HABP4,missense_variant,p.His239Tyr,ENST00000375251,;HABP4,non_coding_transcript_exon_variant,,ENST00000466976,;CDC14B,downstream_gene_variant,,ENST00000474602,; T ENST00000375249 Transcript missense_variant 1105/2615 1030/1242 344/413 H/Y Cat/Tat 1 1 HABP4 HGNC HGNC:17062 protein_coding YES CCDS6719.1 ENSP00000364398 Q5JVS0 UPI000013E8DB NM_014282.3 tolerated(0.11) 7/8 hmmpanther:PTHR12299,hmmpanther:PTHR12299:SF30 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 96488119 96488119 C T 1 0 0 0 0 1 0 0 0 6821 594 21 3 3 HABP4 9 96488119 Missense_Mutation SNP C C3L-00094_T 3253240 96488119 41906598 107 3083 MRRF 0 . GRCh38 9 122280513 122280513 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.255G>T p.Leu85Phe p.L85F ENST00000344641 3/7 295 274 21 292 291 1 strelka-varscan-mutect MRRF,missense_variant,p.Leu85Phe,ENST00000344641,NM_138777.3;MRRF,missense_variant,p.Leu85Phe,ENST00000394315,NM_199177.2;MRRF,missense_variant,p.Leu85Phe,ENST00000373723,;MRRF,missense_variant,p.Leu41Phe,ENST00000373729,;MRRF,missense_variant,p.Leu85Phe,ENST00000441707,;MRRF,intron_variant,,ENST00000297908,NM_001173512.1;MRRF,non_coding_transcript_exon_variant,,ENST00000373724,;MRRF,missense_variant,p.Leu85Phe,ENST00000489572,;MRRF,missense_variant,p.Leu85Phe,ENST00000470366,;MRRF,missense_variant,p.Leu85Phe,ENST00000467864,;MRRF,non_coding_transcript_exon_variant,,ENST00000373728,;MRRF,non_coding_transcript_exon_variant,,ENST00000373727,; T ENST00000344641 Transcript missense_variant 566/9826 255/789 85/262 L/F ttG/ttT 1 1 MRRF HGNC HGNC:7234 protein_coding YES CCDS6840.1 ENSP00000343867 Q96E11 UPI000007291D NM_138777.3 tolerated(0.06) 3/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR20982,Superfamily_domains:SSF55194 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 122280513 122280513 G T 1 0 0 0 0 1 0 0 0 9827 1339 47 2 2 MRRF 9 122280513 Missense_Mutation SNP G C3L-00094_T 25792394 122280513 16114204 108 3084 PDCL 0 . GRCh38 9 122826649 122826649 + Nonsense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.139G>T p.Glu47Ter p.E47* ENST00000259467 2/4 187 157 30 140 140 0 strelka-varscan-mutect PDCL,stop_gained,p.Glu47Ter,ENST00000259467,NM_005388.4;PDCL,stop_gained,p.Glu36Ter,ENST00000394285,;PDCL,stop_gained,p.Glu14Ter,ENST00000436632,; A ENST00000259467 Transcript stop_gained 305/2813 139/906 47/301 E/* Gag/Tag 1 -1 PDCL HGNC HGNC:8770 protein_coding YES CCDS6845.1 ENSP00000259467 Q13371 UPI0000131988 NM_005388.4 2/4 Pfam_domain:PF02114,Prints_domain:PR00677,hmmpanther:PTHR21148,hmmpanther:PTHR21148:SF21,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 122826649 122826649 C A 1 0 0 0 0 0 1 0 0 11714 835 29 2 2 PDCL 9 122826649 Nonsense_Mutation SNP C C3L-00094_T 546136 122826649 15568068 109 3085 SURF1 0 . GRCh38 9 133353770 133353770 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.494C>T p.Pro165Leu p.P165L ENST00000371974 5/9 301 211 90 291 291 0 strelka-varscan-mutect SURF1,missense_variant,p.Pro165Leu,ENST00000371974,NM_003172.3;SURF1,missense_variant,p.Pro56Leu,ENST00000615505,NM_001280787.1;RPL7A,downstream_gene_variant,,ENST00000426651,;RPL7A,downstream_gene_variant,,ENST00000323345,NM_000972.2;SURF2,upstream_gene_variant,,ENST00000371964,NM_001278928.1,NM_017503.4;RPL7A,downstream_gene_variant,,ENST00000315731,;SNORD24,downstream_gene_variant,,ENST00000383884,;SNORD36B,downstream_gene_variant,,ENST00000363961,;SNORD36A,downstream_gene_variant,,ENST00000362874,;SNORD36C,downstream_gene_variant,,ENST00000516733,;SURF1,non_coding_transcript_exon_variant,,ENST00000495952,;RPL7A,downstream_gene_variant,,ENST00000463740,;RPL7A,downstream_gene_variant,,ENST00000489392,;RPL7A,downstream_gene_variant,,ENST00000496554,;RPL7A,downstream_gene_variant,,ENST00000468019,;RPL7A,downstream_gene_variant,,ENST00000485706,;SURF2,upstream_gene_variant,,ENST00000495524,;SURF1,downstream_gene_variant,,ENST00000463965,;RPL7A,downstream_gene_variant,,ENST00000492798,;SURF2,upstream_gene_variant,,ENST00000486887,;SURF1,non_coding_transcript_exon_variant,,ENST00000437995,; A ENST00000371974 Transcript missense_variant 526/1093 494/903 165/300 P/L cCc/cTc 1 -1 SURF1 HGNC HGNC:11474 protein_coding YES CCDS6966.1 ENSP00000361042 Q15526 E5KRX5 UPI000013622E NM_003172.3 deleterious(0) 5/9 Pfam_domain:PF02104,PROSITE_profiles:PS50895,hmmpanther:PTHR23427,hmmpanther:PTHR23427:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 133353770 133353770 G A 1 0 0 0 0 1 0 0 0 15789 1232 43 3 3 SURF1 9 133353770 Missense_Mutation SNP G C3L-00094_T 10527121 133353770 5040947 110 3086 IL2RA 0 . GRCh38 10 6018115 6018115 + Silent SNP G G T rs779403244 C3L-00094_T C3L-00094_N G G c.732C>A p.= p.A244A ENST00000379959 7/8 306 185 121 282 281 1 strelka-varscan-mutect IL2RA,synonymous_variant,p.=,ENST00000379959,NM_000417.2;IL2RA,synonymous_variant,p.=,ENST00000379954,NM_001308242.1;IL2RA,synonymous_variant,p.=,ENST00000256876,;IL2RA,downstream_gene_variant,,ENST00000447847,;SNORA14,upstream_gene_variant,,ENST00000516113,; T ENST00000379959 Transcript synonymous_variant 906/3176 732/819 244/272 A gcC/gcA rs779403244 1 -1 IL2RA HGNC HGNC:6008 protein_coding YES CCDS7076.1 ENSP00000369293 P01589 UPI000012D4A3 NM_000417.2 7/8 hmmpanther:PTHR10573,hmmpanther:PTHR10573:SF0,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs779403244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 6018115 6018115 G T 1 0 0 0 0 0 0 0 1 7585 1130 39 1 1 IL2RA 10 6018115 Silent SNP G C3L-00094_T 6018115 127779307 111 3087 EBLN1 0 . GRCh38 10 22209347 22209347 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.637G>A p.Glu213Lys p.E213K ENST00000422359 1/1 223 200 23 258 258 0 strelka-mutect EBLN1,missense_variant,p.Glu213Lys,ENST00000422359,NM_001199938.1; T ENST00000422359 Transcript missense_variant 675/1208 637/1101 213/366 E/K Gaa/Aaa 1 -1 EBLN1 HGNC HGNC:39430 protein_coding YES CCDS60498.1 ENSP00000473842 P0CF75 UPI0000199CEF NM_001199938.1 tolerated(0.24) 1/1 Pfam_domain:PF06407,Gene3D:1n93X01,Superfamily_domains:0041272 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 22209347 22209347 C T 1 0 0 0 0 1 0 0 0 4709 922 32 3 3 EBLN1 10 22209347 Missense_Mutation SNP C C3L-00094_T 16191232 22209347 111588075 112 3088 ARMC3 0 . GRCh38 10 23003277 23003277 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.1594T>C p.Ser532Pro p.S532P ENST00000298032 13/19 119 79 40 121 121 0 strelka-varscan-mutect ARMC3,missense_variant,p.Ser269Pro,ENST00000376528,NM_001282747.1;ARMC3,missense_variant,p.Ser532Pro,ENST00000298032,NM_173081.4;ARMC3,missense_variant,p.Ser532Pro,ENST00000409983,NM_001282745.1;ARMC3,missense_variant,p.Ser532Pro,ENST00000409049,NM_001282746.1;ARMC3,upstream_gene_variant,,ENST00000491803,; C ENST00000298032 Transcript missense_variant 1678/2811 1594/2619 532/872 S/P Tca/Cca 1 1 ARMC3 HGNC HGNC:30964 protein_coding YES CCDS7142.1 ENSP00000298032 Q5W041 UPI0000161785 NM_173081.4 deleterious(0.04) 13/19 hmmpanther:PTHR23315:SF78,hmmpanther:PTHR23315 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 23003277 23003277 T C 1 0 0 0 0 1 0 0 0 1093 1435 50 5 5 ARMC3 10 23003277 Missense_Mutation SNP T C3L-00094_T 793930 23003277 110794145 113 3089 ACBD5 0 . GRCh38 10 27218124 27218124 + Missense_Mutation SNP C C A rs201245034 C3L-00094_T C3L-00094_N C C c.685G>T p.Gly229Cys p.G229C ENST00000396271 7/13 332 228 104 315 315 0 strelka-varscan-mutect ACBD5,missense_variant,p.Gly227Cys,ENST00000375897,NM_001271512.3;ACBD5,missense_variant,p.Gly229Cys,ENST00000396271,NM_145698.4;ACBD5,missense_variant,p.Gly194Cys,ENST00000375905,NM_001042473.3;ACBD5,missense_variant,p.Gly120Cys,ENST00000375901,NM_001301252.1,NM_001301253.1,NM_001301251.1,NM_001301254.1;ACBD5,missense_variant,p.Gly238Cys,ENST00000375888,;ACBD5,missense_variant,p.Gly205Cys,ENST00000426079,;ACBD5,missense_variant,p.Gly205Cys,ENST00000412279,;ACBD5,3_prime_UTR_variant,,ENST00000476758,; A ENST00000396271 Transcript missense_variant 812/3921 685/1578 229/525 G/C Ggc/Tgc rs201245034 1 -1 ACBD5 HGNC HGNC:23338 protein_coding YES CCDS44368.1 ENSP00000379568 Q5T8D3 UPI000046FE2B NM_145698.4 deleterious(0) 7/13 hmmpanther:PTHR23310:SF6,hmmpanther:PTHR23310,PIRSF_domain:PIRSF002412 MODERATE 1 SNV 1 1 PASS rs201245034 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 27218124 27218124 C A 1 0 0 0 0 1 0 0 0 168 594 21 2 2 ACBD5 10 27218124 Missense_Mutation SNP C C3L-00094_T 4214847 27218124 106579298 114 3090 ZEB1 0 . GRCh38 10 31520604 31520604 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.1272T>A p.Asn424Lys p.N424K ENST00000361642 7/9 182 119 63 189 189 0 strelka-varscan-mutect ZEB1,missense_variant,p.Asn407Lys,ENST00000446923,NM_001323656.1,NM_001323664.1,NM_001323657.1,NM_001323650.1,NM_001128128.2,NM_001174094.1;ZEB1,missense_variant,p.Asn424Lys,ENST00000361642,NM_001174096.1;ZEB1,missense_variant,p.Asn423Lys,ENST00000320985,NM_030751.5;ZEB1,missense_variant,p.Asn403Lys,ENST00000560721,NM_001174093.1;ZEB1,missense_variant,p.Asn356Lys,ENST00000542815,NM_001174095.1;ZEB1,missense_variant,p.Asn205Lys,ENST00000561212,;ZEB1,downstream_gene_variant,,ENST00000559476,;ZEB1,downstream_gene_variant,,ENST00000424869,;ZEB1,downstream_gene_variant,,ENST00000558440,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,NM_001323663.1,NM_001323661.1,NM_001323644.1,NM_001323649.1,NM_001323659.1,NM_001323652.1,NM_001323673.1,NM_001323662.1,NM_001323676.1,NM_001323653.1,NM_001323655.1,NM_001323645.1,NM_001323647.1,NM_001323660.1,NM_001323671.1,NM_001323638.1,NM_001323665.1,NM_001323643.1,NM_001323677.1,NM_001323641.1,NM_001323642.1,NM_001323658.1,NM_001323651.1,NM_001323672.1,NM_001323654.1;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558863,; A ENST00000361642 Transcript missense_variant 1335/5990 1272/3378 424/1125 N/K aaT/aaA 1 1 ZEB1 HGNC HGNC:11642 protein_coding YES CCDS53505.1 ENSP00000354487 P37275 UPI000068F51D NM_001174096.1 deleterious(0.01) 7/9 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 31520604 31520604 T A 1 0 0 0 0 1 0 0 0 18199 1461 51 4 4 ZEB1 10 31520604 Missense_Mutation SNP T C3L-00094_T 4302480 31520604 102276818 115 3091 C10orf71 0 . GRCh38 10 49325843 49325843 + Missense_Mutation SNP G G T rs761308417 C3L-00094_T C3L-00094_N G G c.3298G>T p.Ala1100Ser p.A1100S ENST00000374144 3/3 108 100 8 116 116 0 strelka-varscan-mutect C10orf71,missense_variant,p.Ala1100Ser,ENST00000374144,NM_001135196.1; T ENST00000374144 Transcript missense_variant 3586/5230 3298/4308 1100/1435 A/S Gcc/Tcc rs761308417 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 tolerated(0.1) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS rs761308417 . 0 205 5 0 0 0 0 0 -16.03253 1 1 1 1 0 T 3 4 9 49325843 49325843 G T 1 0 0 0 0 1 0 0 0 1769 1203 42 2 2 C10orf71 10 49325843 Missense_Mutation SNP G C3L-00094_T 17805239 49325843 84471579 116 3092 CTNNA3 0 . GRCh38 10 66520745 66520745 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.1403C>A p.Ala468Glu p.A468E ENST00000433211 11/18 275 175 100 338 338 0 strelka-varscan-mutect CTNNA3,missense_variant,p.Ala468Glu,ENST00000433211,NM_001127384.2,NM_013266.3; T ENST00000433211 Transcript missense_variant 1578/10675 1403/2688 468/895 A/E gCa/gAa 1 -1 CTNNA3 HGNC HGNC:2511 protein_coding YES CCDS7269.1 ENSP00000389714 Q9UI47 UPI000004A0E6 NM_001127384.2,NM_013266.3 deleterious(0.04) 11/18 hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF21,Gene3D:1.20.120.230,Pfam_domain:PF01044,Superfamily_domains:SSF47220 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 66520745 66520745 G T 1 0 0 0 0 1 0 0 0 3823 1319 46 2 2 CTNNA3 10 66520745 Missense_Mutation SNP G C3L-00094_T 17194902 66520745 67276677 117 3093 PBLD 0 . GRCh38 10 68288630 68288630 + Nonsense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.544G>T p.Glu182Ter p.E182* ENST00000358769 8/10 180 110 70 148 148 0 strelka-varscan-mutect PBLD,stop_gained,p.Glu182Ter,ENST00000358769,NM_022129.3;PBLD,stop_gained,p.Glu149Ter,ENST00000336578,;PBLD,stop_gained,p.Glu182Ter,ENST00000309049,;PBLD,stop_gained,p.Glu182Ter,ENST00000495025,NM_001033083.1;PBLD,stop_gained,p.Glu23Ter,ENST00000468798,;PBLD,non_coding_transcript_exon_variant,,ENST00000277795,; A ENST00000358769 Transcript stop_gained 747/2587 544/867 182/288 E/* Gag/Tag 1 -1 PBLD HGNC HGNC:23301 protein_coding YES CCDS7277.2 ENSP00000351619 P30039 A0A024QZK5 UPI0000000DCA NM_022129.3 8/10 hmmpanther:PTHR13774:SF17,hmmpanther:PTHR13774,PIRSF_domain:PIRSF016184,Pfam_domain:PF02567,Gene3D:3.10.310.10,TIGRFAM_domain:TIGR00654,Superfamily_domains:SSF54506 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 68288630 68288630 C A 1 0 0 0 0 0 1 0 0 11576 864 30 2 2 PBLD 10 68288630 Nonsense_Mutation SNP C C3L-00094_T 1767885 68288630 65508792 118 3094 C10orf62 0 . GRCh38 10 97590427 97590427 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.530A>T p.Lys177Met p.K177M ENST00000370640 1/1 315 202 113 318 318 0 strelka-varscan-mutect C10orf62,missense_variant,p.Lys177Met,ENST00000370640,NM_001009997.2;HOGA1,intron_variant,,ENST00000370646,NM_138413.3;HOGA1,intron_variant,,ENST00000370647,NM_001134670.1;RP11-548K23.11,intron_variant,,ENST00000370649,;HOGA1,intron_variant,,ENST00000465608,; T ENST00000370640 Transcript missense_variant 701/1208 530/672 177/223 K/M aAg/aTg 1 1 C10orf62 HGNC HGNC:23294 protein_coding YES CCDS31261.1 ENSP00000359674 Q5T681 UPI000046FEE3 NM_001009997.2 deleterious(0) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23008:SF0,hmmpanther:PTHR23008 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 97590427 97590427 A T 1 0 0 0 0 1 0 0 0 1767 72 3 4 4 C10orf62 10 97590427 Missense_Mutation SNP A C3L-00094_T 29301797 97590427 36206995 119 3095 C10orf90 0 . GRCh38 10 126504842 126504842 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.358G>T p.Ala120Ser p.A120S ENST00000284694 3/9 44 40 4 52 52 0 strelka-mutect C10orf90,missense_variant,p.Ala120Ser,ENST00000284694,NM_001004298.2;C10orf90,missense_variant,p.Ala73Ser,ENST00000356858,;C10orf90,missense_variant,p.Ala120Ser,ENST00000432642,;C10orf90,missense_variant,p.Ala73Ser,ENST00000488181,;C10orf90,upstream_gene_variant,,ENST00000424927,;C10orf90,non_coding_transcript_exon_variant,,ENST00000368674,;C10orf90,downstream_gene_variant,,ENST00000463082,; A ENST00000284694 Transcript missense_variant 479/3076 358/2100 120/699 A/S Gca/Tca 1 -1 C10orf90 HGNC HGNC:26563 protein_coding YES CCDS31310.1 ENSP00000284694 Q96M02 UPI00001D808F NM_001004298.2 tolerated(0.46) 3/9 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF24 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.94868 1 1 1 1 0 A 3 1 9 126504842 126504842 C A 1 0 0 0 0 1 0 0 0 1773 739 26 2 2 C10orf90 10 126504842 Missense_Mutation SNP C C3L-00094_T 28914415 126504842 7292580 120 3096 FRG2B 0 . GRCh38 10 133626598 133626598 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.145T>A p.Ser49Thr p.S49T ENST00000425520 1/4 267 252 15 287 287 0 varscan-mutect FRG2B,missense_variant,p.Ser49Thr,ENST00000443774,;FRG2B,missense_variant,p.Ser49Thr,ENST00000425520,NM_001080998.1; T ENST00000425520 Transcript missense_variant 198/890 145/837 49/278 S/T Tcc/Acc 1 -1 FRG2B HGNC HGNC:33518 protein_coding YES CCDS44502.1 ENSP00000401310 Q96QU4 UPI00000727C6 NM_001080998.1 deleterious(0.02) 1/4 hmmpanther:PTHR31883,hmmpanther:PTHR31883:SF3,Prints_domain:PR02074 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 133626598 133626598 A T 1 0 0 0 0 1 0 0 0 5916 304 11 4 4 FRG2B 10 133626598 Missense_Mutation SNP A C3L-00094_T 7121756 133626598 170824 121 3097 CDHR5 0 . GRCh38 11 624841 624841 + Missense_Mutation SNP G G T rs200807618 C3L-00094_T C3L-00094_N G G c.62C>A p.Pro21Gln p.P21Q ENST00000358353 2/16 119 82 37 95 95 0 strelka-varscan-mutect CDHR5,missense_variant,p.Pro21Gln,ENST00000358353,;CDHR5,missense_variant,p.Pro21Gln,ENST00000397542,NM_001171968.1,NM_021924.4;CDHR5,missense_variant,p.Pro21Gln,ENST00000349570,NM_031264.3;CDHR5,missense_variant,p.Pro21Gln,ENST00000526077,;CDHR5,missense_variant,p.Pro21Gln,ENST00000534311,;CDHR5,intron_variant,,ENST00000531088,;SCT,downstream_gene_variant,,ENST00000176195,NM_021920.2;CDHR5,intron_variant,,ENST00000529337,;CDHR5,upstream_gene_variant,,ENST00000532949,;CDHR5,missense_variant,p.Pro21Gln,ENST00000531177,;CDHR5,non_coding_transcript_exon_variant,,ENST00000531899,; T ENST00000358353 Transcript missense_variant 385/3635 62/2538 21/845 P/Q cCg/cAg rs200807618 1 -1 CDHR5 HGNC HGNC:7521 protein_coding YES CCDS7707.1 ENSP00000351118 Q9HBB8 UPI0000456444 tolerated(0.06) 2/16 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24027:SF313,hmmpanther:PTHR24027 MODERATE SNV 5 1 PASS rs200807618 . 0 201 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 9 624841 624841 G T 1 0 0 0 0 1 0 0 0 2825 1116 39 1 1 CDHR5 11 624841 Missense_Mutation SNP G C3L-00094_T 624841 134461781 122 3098 NUP98 0 . GRCh38 11 3776016 3776016 + Nonsense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.361G>T p.Gly121Ter p.G121* ENST00000324932 5/33 111 75 36 97 97 0 strelka-varscan-mutect NUP98,stop_gained,p.Gly121Ter,ENST00000359171,;NUP98,stop_gained,p.Gly121Ter,ENST00000324932,NM_016320.4;NUP98,stop_gained,p.Gly121Ter,ENST00000355260,NM_139132.3;NUP98,stop_gained,p.Gly121Ter,ENST00000397004,NM_139131.3;NUP98,stop_gained,p.Gly121Ter,ENST00000397007,NM_005387.5;NUP98,stop_gained,p.Gly84Ter,ENST00000532475,; A ENST00000324932 Transcript stop_gained 782/6973 361/5403 121/1800 G/* Gga/Tga 1 -1 NUP98 HGNC HGNC:8068 protein_coding YES CCDS7746.1 ENSP00000316032 P52948 UPI000013CD36 NM_016320.4 5/33 Low_complexity_(Seg):seg,hmmpanther:PTHR23198,hmmpanther:PTHR23198:SF6 HIGH 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999808 1 1 1 0 A 4 1 9 3776016 3776016 C A 1 0 0 0 0 0 1 0 0 10839 608 21 2 2 NUP98 11 3776016 Nonsense_Mutation SNP C C3L-00094_T 3151175 3776016 131310606 123 3099 MMP26 0 . GRCh38 11 4992012 4992012 + Missense_Mutation SNP G G T rs758222762 C3L-00094_T C3L-00094_N G G c.644G>T p.Gly215Val p.G215V ENST00000380390 6/7 130 102 28 129 129 0 strelka-varscan-mutect MMP26,missense_variant,p.Gly215Val,ENST00000380390,;MMP26,missense_variant,p.Gly215Val,ENST00000300762,NM_021801.3;MMP26,downstream_gene_variant,,ENST00000477339,; T ENST00000380390 Transcript missense_variant 860/1189 644/786 215/261 G/V gGc/gTc rs758222762 1 1 MMP26 HGNC HGNC:14249 protein_coding YES CCDS7752.1 ENSP00000369753 Q9NRE1 UPI0000047AFC deleterious(0) 6/7 hmmpanther:PTHR10201:SF76,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 MODERATE 1 SNV 5 1 PASS rs758222762 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 4992012 4992012 G T 1 0 0 0 0 1 0 0 0 9626 1203 42 2 2 MMP26 11 4992012 Missense_Mutation SNP G C3L-00094_T 1215996 4992012 130094610 124 3100 OR52E2 0 . GRCh38 11 5059405 5059405 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.223C>A p.Leu75Ile p.L75I ENST00000321522 1/1 103 77 26 79 79 0 strelka-varscan-mutect OR52E2,missense_variant,p.Leu75Ile,ENST00000321522,NM_001005164.2; T ENST00000321522 Transcript missense_variant 223/978 223/978 75/325 L/I Ctc/Atc 1 -1 OR52E2 HGNC HGNC:14769 protein_coding YES CCDS31371.1 ENSP00000322088 Q8NGJ4 UPI0000046AE3 NM_001005164.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF169,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 5059405 5059405 G T 1 0 0 0 0 1 0 0 0 11187 942 33 2 2 OR52E2 11 5059405 Missense_Mutation SNP G C3L-00094_T 67393 5059405 130027217 125 3101 OR51J1 0 . GRCh38 11 5402930 5402930 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.334C>A p.His112Asn p.H112N ENST00000332043 1/1 285 234 51 294 293 1 strelka-varscan-mutect OR51J1,missense_variant,p.His112Asn,ENST00000332043,;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000332043 Transcript missense_variant 334/951 334/951 112/316 H/N Cat/Aat 1 1 OR51J1 HGNC HGNC:14856 protein_coding YES ENSP00000332473 Q9H342 UPI00001AFFE3 deleterious(0.01) 1/1 Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF81 MODERATE SNV 1 PASS rs1198338973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 5402930 5402930 C A 1 0 0 0 0 1 0 0 0 11175 594 21 2 2 OR51J1 11 5402930 Missense_Mutation SNP C C3L-00094_T 343525 5402930 129683692 126 3102 UBQLN3 0 . GRCh38 11 5507676 5507676 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.1883T>C p.Phe628Ser p.F628S ENST00000311659 2/2 147 138 9 133 133 0 strelka-varscan-mutect UBQLN3,missense_variant,p.Phe628Ser,ENST00000311659,NM_017481.2;HBG2,intron_variant,,ENST00000380259,;HBE1,upstream_gene_variant,,ENST00000380237,;UBQLN3,downstream_gene_variant,,ENST00000445998,;HBG2,upstream_gene_variant,,ENST00000380252,;HBE1,upstream_gene_variant,,ENST00000396895,;AC104389.28,upstream_gene_variant,,ENST00000415970,;AC104389.28,upstream_gene_variant,,ENST00000418729,;AC104389.28,upstream_gene_variant,,ENST00000420465,;AC104389.28,upstream_gene_variant,,ENST00000420726,; G ENST00000311659 Transcript missense_variant 2031/2407 1883/1968 628/655 F/S tTt/tCt 1 -1 UBQLN3 HGNC HGNC:12510 protein_coding YES CCDS7758.1 ENSP00000347997 Q9H347 A0A140VJZ3 UPI000006E3A0 NM_017481.2 deleterious(0) 2/2 PROSITE_profiles:PS50030,hmmpanther:PTHR10677:SF4,hmmpanther:PTHR10677,Gene3D:1.10.8.10,Pfam_domain:PF00627,SMART_domains:SM00165,Superfamily_domains:SSF46934 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 5507676 5507676 A G 1 0 0 0 0 1 0 0 0 17422 14 1 5 5 UBQLN3 11 5507676 Missense_Mutation SNP A C3L-00094_T 104746 5507676 129578946 127 3103 CNGA4 0 . GRCh38 11 6240443 6240443 + Missense_Mutation SNP C C G novel C3L-00094_T C3L-00094_N C C c.649C>G p.Gln217Glu p.Q217E ENST00000379936 4/6 277 206 71 282 282 0 strelka-varscan-mutect CNGA4,missense_variant,p.Gln217Glu,ENST00000379936,NM_001037329.3;CNGA4,intron_variant,,ENST00000533426,; G ENST00000379936 Transcript missense_variant 764/1863 649/1728 217/575 Q/E Cag/Gag 1 1 CNGA4 HGNC HGNC:2152 protein_coding YES CCDS31408.1 ENSP00000369268 Q8IV77 UPI000004C7EC NM_001037329.3 tolerated(0.2) 4/6 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF388,Superfamily_domains:SSF81324 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 6240443 6240443 C G 1 0 0 0 0 1 0 0 0 3379 595 21 4 4 CNGA4 11 6240443 Missense_Mutation SNP C C3L-00094_T 732767 6240443 128846179 128 3104 TSG101 0 . GRCh38 11 18481656 18481656 + Missense_Mutation SNP C C A rs770747339 C3L-00094_T C3L-00094_N C C c.1057G>T p.Val353Leu p.V353L ENST00000251968 9/10 199 164 35 179 179 0 strelka-varscan-mutect TSG101,missense_variant,p.Val353Leu,ENST00000536719,;TSG101,missense_variant,p.Val353Leu,ENST00000251968,NM_006292.3;LDHAL6A,downstream_gene_variant,,ENST00000280706,NM_144972.4;LDHAL6A,downstream_gene_variant,,ENST00000396213,NM_001144071.1;LDHAL6A,downstream_gene_variant,,ENST00000615355,;TSG101,missense_variant,p.Val40Leu,ENST00000584526,;TSG101,missense_variant,p.Val26Leu,ENST00000580814,;TSG101,non_coding_transcript_exon_variant,,ENST00000540555,;TSG101,downstream_gene_variant,,ENST00000545247,;TSG101,downstream_gene_variant,,ENST00000543054,; A ENST00000251968 Transcript missense_variant 1473/1824 1057/1173 353/390 V/L Gtg/Ttg rs770747339,COSM147157 1 -1 TSG101 HGNC HGNC:15971 protein_coding YES CCDS7842.1 ENSP00000251968 Q99816 UPI000004750C NM_006292.3 deleterious(0.01) 9/10 Pfam_domain:PF09454,PROSITE_profiles:PS51312,hmmpanther:PTHR23306,hmmpanther:PTHR23306:SF17,Superfamily_domains:SSF140111 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770747339 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 18481656 18481656 C A 1 0 0 0 0 1 0 0 0 17122 536 19 1 1 TSG101 11 18481656 Missense_Mutation SNP C C3L-00094_T 12241213 18481656 116604966 129 3105 DGKZ 0 . GRCh38 11 46372659 46372659 + Silent SNP G G T rs115107241 C3L-00094_T C3L-00094_N G G c.1617G>T p.= p.A539A ENST00000454345 13/32 147 120 27 158 158 0 strelka-varscan-mutect DGKZ,synonymous_variant,p.=,ENST00000454345,NM_001105540.1;DGKZ,synonymous_variant,p.=,ENST00000343674,NM_201532.2;DGKZ,synonymous_variant,p.=,ENST00000456247,NM_001199267.1;DGKZ,synonymous_variant,p.=,ENST00000527911,NM_001199266.1;DGKZ,synonymous_variant,p.=,ENST00000318201,NM_001199268.1;DGKZ,synonymous_variant,p.=,ENST00000532868,NM_201533.3;DGKZ,synonymous_variant,p.=,ENST00000421244,NM_003646.3;DGKZ,synonymous_variant,p.=,ENST00000528615,;DGKZ,upstream_gene_variant,,ENST00000524869,;DGKZ,downstream_gene_variant,,ENST00000525242,;DGKZ,downstream_gene_variant,,ENST00000524448,;MIR4688,upstream_gene_variant,,ENST00000577966,;DGKZ,downstream_gene_variant,,ENST00000534215,;DGKZ,upstream_gene_variant,,ENST00000529660,;DGKZ,3_prime_UTR_variant,,ENST00000524984,;DGKZ,non_coding_transcript_exon_variant,,ENST00000528173,;DGKZ,non_coding_transcript_exon_variant,,ENST00000531879,;DGKZ,non_coding_transcript_exon_variant,,ENST00000527903,;DGKZ,upstream_gene_variant,,ENST00000527211,;DGKZ,downstream_gene_variant,,ENST00000527674,;DGKZ,upstream_gene_variant,,ENST00000529698,;DGKZ,downstream_gene_variant,,ENST00000533376,; T ENST00000454345 Transcript synonymous_variant 1742/4086 1617/3354 539/1117 A gcG/gcT rs115107241 1 1 DGKZ HGNC HGNC:2857 protein_coding YES CCDS41640.1 ENSP00000412178 Q13574 UPI000013DB71 NM_001105540.1 13/32 Pfam_domain:PF00781,PROSITE_profiles:PS50146,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF43,SMART_domains:SM00046,Superfamily_domains:SSF111331 LOW 1 SNV 1 1 PASS rs115107241 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 46372659 46372659 G T 1 0 0 0 0 0 0 0 1 4280 1132 40 1 1 DGKZ 11 46372659 Silent SNP G C3L-00094_T 27891003 46372659 88713963 130 3106 TPCN2 0 . GRCh38 11 69054090 69054090 + Missense_Mutation SNP C C T rs144833208 C3L-00094_T C3L-00094_N C C c.167C>T p.Ala56Val p.A56V ENST00000294309 2/25 206 186 20 165 165 0 strelka-varscan-mutect TPCN2,missense_variant,p.Ala56Val,ENST00000294309,NM_139075.3;TPCN2,missense_variant,p.Ala56Val,ENST00000637342,;TPCN2,missense_variant,p.Ala56Val,ENST00000637504,;TPCN2,missense_variant,p.Ala56Val,ENST00000542467,;TPCN2,non_coding_transcript_exon_variant,,ENST00000534832,;TPCN2,upstream_gene_variant,,ENST00000442692,;TPCN2,missense_variant,p.Ala56Val,ENST00000635811,;TPCN2,non_coding_transcript_exon_variant,,ENST00000535009,; T ENST00000294309 Transcript missense_variant 268/2931 167/2259 56/752 A/V gCt/gTt rs144833208 1 1 TPCN2 HGNC HGNC:20820 protein_coding YES CCDS8189.1 ENSP00000294309 Q8NHX9 UPI000013E149 NM_139075.3 deleterious(0) 2/25 hmmpanther:PTHR10037 MODERATE 1 SNV 1 1 PASS rs144833208 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 69054090 69054090 C T 1 0 0 0 0 1 0 0 0 16875 797 28 3 3 TPCN2 11 69054090 Missense_Mutation SNP C C3L-00094_T 22681431 69054090 66032532 131 3107 FAT3 0 . GRCh38 11 92353320 92353320 + Missense_Mutation SNP A A C novel C3L-00094_T C3L-00094_N A A c.758A>C p.Glu253Ala p.E253A ENST00000525166 1/27 228 168 60 237 237 0 strelka-varscan-mutect FAT3,missense_variant,p.Glu403Ala,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Glu253Ala,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; C ENST00000525166 Transcript missense_variant 780/18699 758/13320 253/4439 E/A gAa/gCa 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.8) 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 92353320 92353320 A C 1 0 0 0 0 1 0 0 0 5551 246 9 5 5 FAT3 11 92353320 Missense_Mutation SNP A C3L-00094_T 23299230 92353320 42733302 132 3108 AMOTL1 0 . GRCh38 11 94768531 94768531 + Missense_Mutation SNP G G C rs373449240 C3L-00094_T C3L-00094_N G G c.20G>C p.Arg7Pro p.R7P ENST00000433060 1/13 264 225 39 250 250 0 strelka-varscan-mutect AMOTL1,missense_variant,p.Arg7Pro,ENST00000433060,NM_130847.2;AMOTL1,missense_variant,p.Arg7Pro,ENST00000317829,NM_001301007.1;AMOTL1,intron_variant,,ENST00000299004,; C ENST00000433060 Transcript missense_variant 161/8970 20/2871 7/956 R/P cGc/cCc rs373449240 1 1 AMOTL1 HGNC HGNC:17811 protein_coding YES CCDS44712.1 ENSP00000387739 Q8IY63 A0A024R3A6 UPI00000742C2 NM_130847.2 tolerated_low_confidence(0.15) 1/13 MODERATE 1 SNV 1 1 PASS rs373449240 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 94768531 94768531 G C 1 0 0 0 0 1 0 0 0 681 1087 38 4 4 AMOTL1 11 94768531 Missense_Mutation SNP G C3L-00094_T 2415211 94768531 40318091 133 3109 PZP 0 . GRCh38 12 9182060 9182060 + Missense_Mutation SNP C C T rs183830886 C3L-00094_T C3L-00094_N C C c.1604G>A p.Arg535Gln p.R535Q ENST00000261336 14/36 158 149 9 162 162 0 strelka-varscan-mutect PZP,missense_variant,p.Arg535Gln,ENST00000261336,NM_002864.2;PZP,3_prime_UTR_variant,,ENST00000535230,; T ENST00000261336 Transcript missense_variant 1633/4610 1604/4449 535/1482 R/Q cGa/cAa rs183830886,COSM4529352,COSM4529353 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 tolerated(0.72) 14/36 Pfam_domain:PF07703,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92,SMART_domains:SM01359 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs183830886 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 9182060 9182060 C T 1 0 0 0 0 1 0 0 0 13025 884 31 1 1 PZP 12 9182060 Missense_Mutation SNP C C3L-00094_T 9182060 124093249 134 3110 GRIN2B 0 . GRCh38 12 13866188 13866188 + Nonsense_Mutation SNP G G T rs751673148 C3L-00094_T C3L-00094_N G G c.21C>A p.Cys7Ter p.C7* ENST00000609686 2/13 231 211 20 216 215 1 strelka-varscan-mutect GRIN2B,stop_gained,p.Cys7Ter,ENST00000609686,NM_000834.3;GRIN2B,stop_gained,p.Cys7Ter,ENST00000630791,;GRIN2B,stop_gained,p.Cys7Ter,ENST00000627535,; T ENST00000609686 Transcript stop_gained 475/30355 21/4455 7/1484 C/* tgC/tgA rs751673148 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 2/13 Cleavage_site_(Signalp):SignalP-noTM HIGH 1 SNV 1 1 PASS rs751673148 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 9 13866188 13866188 G T 1 0 0 0 0 0 1 0 0 6662 963 34 2 2 GRIN2B 12 13866188 Nonsense_Mutation SNP G C3L-00094_T 4684128 13866188 119409121 135 3111 RP11-545J16.1 0 . GRCh38 12 20880919 20880919 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1396G>A p.Asp466Asn p.D466N ENST00000261196 10/14 135 108 27 144 143 1 strelka-mutect SLCO1B3,missense_variant,p.Asp466Asn,ENST00000261196,;SLCO1B3,missense_variant,p.Asp466Asn,ENST00000381545,NM_019844.3;RP11-545J16.1,missense_variant,p.Asp466Asn,ENST00000540229,;SLCO1B3,missense_variant,p.Asp290Asn,ENST00000544370,;RP11-545J16.1,intron_variant,,ENST00000381541,; A ENST00000261196 Transcript missense_variant 1463/2840 1396/2109 466/702 D/N Gat/Aat 1 1 SLCO1B3 HGNC HGNC:10961 protein_coding YES CCDS8684.1 ENSP00000261196 Q9NPD5 UPI000013544A tolerated(0.1) 10/14 PROSITE_profiles:PS50850,PROSITE_profiles:PS51465,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Pfam_domain:PF07648,Pfam_domain:PF03137,Gene3D:3.30.60.30,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 20880919 20880919 G A 1 0 0 0 0 1 0 0 0 13751 1290 45 3 3 RP11-545J16.1 12 20880919 Missense_Mutation SNP G C3L-00094_T 7014731 20880919 112394390 136 3112 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3L-00094_T C3L-00094_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 327 219 108 350 347 3 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3L-00094_T 4364431 25245350 108029959 137 3113 SLC4A8 0 . GRCh38 12 51425014 51425014 + Silent SNP G G T novel C3L-00094_T C3L-00094_N G G c.27G>T p.= p.P9P ENST00000453097 1/25 137 88 49 115 115 0 strelka-varscan-mutect SLC4A8,synonymous_variant,p.=,ENST00000453097,NM_001039960.2;SLC4A8,intron_variant,,ENST00000358657,NM_001258401.2;SLC4A8,intron_variant,,ENST00000535225,NM_001267615.1,NM_001258402.1;SLC4A8,upstream_gene_variant,,ENST00000514353,NM_001258403.1;RP11-607P23.1,upstream_gene_variant,,ENST00000604939,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000548811,;SLC4A8,intron_variant,,ENST00000548352,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000319957,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000546497,;SLC4A8,intron_variant,,ENST00000604314,;SLC4A8,intron_variant,,ENST00000547697,; T ENST00000453097 Transcript synonymous_variant 244/11824 27/3282 9/1093 P ccG/ccT 1 1 SLC4A8 HGNC HGNC:11034 protein_coding YES CCDS44890.1 ENSP00000405812 Q2Y0W8 UPI00005E6FB4 NM_001039960.2 1/25 LOW 1 SNV 1 1 PASS rs1433110698 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 51425014 51425014 G T 1 0 0 0 0 0 0 0 1 14936 1103 39 1 1 SLC4A8 12 51425014 Silent SNP G C3L-00094_T 26179664 51425014 81850295 138 3114 AVPR1A 0 . GRCh38 12 63150484 63150484 + Missense_Mutation SNP C C G C3L-00094_T C3L-00094_N C C c.353G>C p.Arg118Pro p.R118P ENST00000299178 1/2 213 140 73 212 212 0 strelka-varscan-mutect AVPR1A,missense_variant,p.Arg118Pro,ENST00000299178,NM_000706.4;AVPR1A,upstream_gene_variant,,ENST00000550940,;RP11-715H19.2,upstream_gene_variant,,ENST00000624438,; G ENST00000299178 Transcript missense_variant 459/5963 353/1257 118/418 R/P cGc/cCc COSM4832222 1 -1 AVPR1A HGNC HGNC:895 protein_coding YES CCDS8965.1 ENSP00000299178 P37288 X5D2B0 UPI0000050439 NM_000706.4 tolerated(0.07) 1/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF17,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00896 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 63150484 63150484 C G 1 0 0 0 0 1 0 0 0 1387 768 27 4 4 AVPR1A 12 63150484 Missense_Mutation SNP C C3L-00094_T 11725470 63150484 70124825 139 3115 PPFIA2 0 . GRCh38 12 81263311 81263311 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.3635T>A p.Met1212Lys p.M1212K ENST00000549396 31/33 212 181 31 186 186 0 strelka-varscan-mutect PPFIA2,missense_variant,p.Met1107Lys,ENST00000333447,NM_001220478.2;PPFIA2,missense_variant,p.Met1212Lys,ENST00000550584,NM_001220473.2;PPFIA2,missense_variant,p.Met1212Lys,ENST00000549396,NM_003625.4;PPFIA2,missense_variant,p.Met1197Lys,ENST00000549325,NM_001220474.2;PPFIA2,missense_variant,p.Met398Lys,ENST00000541017,NM_001220480.2;PPFIA2,missense_variant,p.Met1206Lys,ENST00000548586,NM_001220476.2;PPFIA2,missense_variant,p.Met1191Lys,ENST00000552948,NM_001220475.2;PPFIA2,missense_variant,p.Met1111Lys,ENST00000407050,NM_001220477.2;PPFIA2,missense_variant,p.Met1059Lys,ENST00000550359,NM_001282536.1;PPFIA2,missense_variant,p.Met1107Lys,ENST00000443686,;PPFIA2,missense_variant,p.Met748Lys,ENST00000541570,NM_001220479.2;ACSS3,downstream_gene_variant,,ENST00000548058,NM_024560.2;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,; T ENST00000549396 Transcript missense_variant 3796/5363 3635/3774 1212/1257 M/K aTg/aAg 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 deleterious_low_confidence(0) 31/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 81263311 81263311 A T 1 0 0 0 0 1 0 0 0 12419 217 8 4 4 PPFIA2 12 81263311 Missense_Mutation SNP A C3L-00094_T 18112827 81263311 52011998 140 3116 SCYL2 0 . GRCh38 12 100282995 100282995 + Nonsense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.25A>T p.Lys9Ter p.K9* ENST00000360820 2/18 79 56 23 58 58 0 strelka-varscan-mutect SCYL2,stop_gained,p.Lys9Ter,ENST00000360820,NM_001317784.1,NM_017988.4;SCYL2,stop_gained,p.Lys9Ter,ENST00000635101,;SCYL2,stop_gained,p.Lys9Ter,ENST00000549687,;SCYL2,intron_variant,,ENST00000548392,;SCYL2,non_coding_transcript_exon_variant,,ENST00000550067,;SCYL2,upstream_gene_variant,,ENST00000549486,; T ENST00000360820 Transcript stop_gained 462/5779 25/2790 9/929 K/* Aag/Tag 1 1 SCYL2 HGNC HGNC:19286 protein_coding YES CCDS9076.1 ENSP00000354061 Q6P3W7 UPI000004FD59 NM_001317784.1,NM_017988.4 2/18 hmmpanther:PTHR12984:SF6,hmmpanther:PTHR12984 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 9 100282995 100282995 A T 1 0 0 0 0 0 1 0 0 14220 247 9 4 4 SCYL2 12 100282995 Nonsense_Mutation SNP A C3L-00094_T 19019684 100282995 32992314 141 3117 ANAPC7 0 . GRCh38 12 110386437 110386437 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.809A>T p.Asn270Ile p.N270I ENST00000455511 6/11 230 153 77 245 245 0 strelka-varscan-mutect ANAPC7,missense_variant,p.Asn270Ile,ENST00000455511,NM_016238.2;ANAPC7,missense_variant,p.Asn270Ile,ENST00000450008,NM_001137664.1;ANAPC7,upstream_gene_variant,,ENST00000552087,;ANAPC7,non_coding_transcript_exon_variant,,ENST00000546720,;ANAPC7,3_prime_UTR_variant,,ENST00000552170,;ANAPC7,non_coding_transcript_exon_variant,,ENST00000548234,;RP11-478C19.2,downstream_gene_variant,,ENST00000550231,;ANAPC7,upstream_gene_variant,,ENST00000471602,;ANAPC7,downstream_gene_variant,,ENST00000464697,; A ENST00000455511 Transcript missense_variant 810/3045 809/1800 270/599 N/I aAc/aTc 1 -1 ANAPC7 HGNC HGNC:17380 protein_coding YES CCDS9145.2 ENSP00000394394 Q9UJX3 A0A024RBJ3 UPI0000EE28AF NM_016238.2 deleterious(0) 6/11 hmmpanther:PTHR12558,hmmpanther:PTHR12558:SF8,Gene3D:1.25.40.10 MODERATE 1 SNV 1 1 PASS rs1237018261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 110386437 110386437 T A 1 0 0 0 0 1 0 0 0 704 1725 60 4 4 ANAPC7 12 110386437 Missense_Mutation SNP T C3L-00094_T 10103442 110386437 22888872 142 3118 PXN 0 . GRCh38 12 120212390 120212390 + Missense_Mutation SNP T T G novel C3L-00094_T C3L-00094_N T T c.1742A>C p.Gln581Pro p.Q581P ENST00000267257 11/11 244 167 77 184 184 0 strelka-varscan-mutect PXN,missense_variant,p.Gln565Pro,ENST00000536957,;PXN,missense_variant,p.Gln581Pro,ENST00000267257,NM_001243756.1;PXN,missense_variant,p.Gln400Pro,ENST00000458477,NM_025157.4;PXN,missense_variant,p.Gln567Pro,ENST00000228307,NM_001080855.2;PXN,missense_variant,p.Gln533Pro,ENST00000424649,NM_002859.3;PXN,missense_variant,p.Gln1057Pro,ENST00000637617,;PXN,downstream_gene_variant,,ENST00000637386,;PXN-AS1,non_coding_transcript_exon_variant,,ENST00000535200,;PXN-AS1,non_coding_transcript_exon_variant,,ENST00000542265,;PXN-AS1,non_coding_transcript_exon_variant,,ENST00000620336,;PXN-AS1,downstream_gene_variant,,ENST00000539446,;PXN-AS1,downstream_gene_variant,,ENST00000542314,;PXN-AS1,downstream_gene_variant,,ENST00000538804,;PXN,non_coding_transcript_exon_variant,,ENST00000538144,;PXN,downstream_gene_variant,,ENST00000550795,;PXN,3_prime_UTR_variant,,ENST00000323871,;PXN,3_prime_UTR_variant,,ENST00000637624,; G ENST00000267257 Transcript missense_variant 1884/3835 1742/1818 581/605 Q/P cAg/cCg 1 -1 PXN HGNC HGNC:9718 protein_coding YES CCDS58281.1 ENSP00000267257 P49023 UPI000013C8CD NM_001243756.1 tolerated(0.17) 11/11 PROSITE_profiles:PS50023,hmmpanther:PTHR24216,hmmpanther:PTHR24216:SF11,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 120212390 120212390 T G 1 0 0 0 0 1 0 0 0 13006 1580 55 5 5 PXN 12 120212390 Missense_Mutation SNP T C3L-00094_T 9825953 120212390 13062919 143 3119 FZD10 0 . GRCh38 12 130163616 130163616 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.674G>T p.Arg225Leu p.R225L ENST00000229030 1/1 130 90 40 91 91 0 strelka-varscan-mutect FZD10,missense_variant,p.Arg225Leu,ENST00000229030,NM_007197.3;FZD10,synonymous_variant,p.=,ENST00000539839,;FZD10-AS1,upstream_gene_variant,,ENST00000505807,;FZD10-AS1,upstream_gene_variant,,ENST00000509760,;FZD10-AS1,upstream_gene_variant,,ENST00000537095,;FZD10-AS1,upstream_gene_variant,,ENST00000542000,; T ENST00000229030 Transcript missense_variant 1158/3281 674/1746 225/581 R/L cGc/cTc 1 1 FZD10 HGNC HGNC:4039 protein_coding YES CCDS9267.1 ENSP00000229030 Q9ULW2 UPI000004EC92 NM_007197.3 tolerated(0.26) 1/1 hmmpanther:PTHR11309:SF86,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 130163616 130163616 G T 1 0 0 0 0 1 0 0 0 6000 1087 38 1 1 FZD10 12 130163616 Missense_Mutation SNP G C3L-00094_T 9951226 130163616 3111693 144 3120 ANHX 0 . GRCh38 12 133227029 133227029 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.625G>T p.Asp209Tyr p.D209Y ENST00000545940 4/8 190 118 72 110 110 0 strelka-varscan-mutect ANHX,missense_variant,p.Asp209Tyr,ENST00000545940,;ANHX,missense_variant,p.Asp209Tyr,ENST00000419717,NM_001191054.1; A ENST00000545940 Transcript missense_variant 2364/3452 625/1140 209/379 D/Y Gac/Tac 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 deleterious(0.05) 4/8 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 133227029 133227029 C A 1 0 0 0 0 1 0 0 0 719 913 32 2 2 ANHX 12 133227029 Missense_Mutation SNP C C3L-00094_T 3063413 133227029 48280 145 3121 TUBA3C 0 . GRCh38 13 19177542 19177542 + Silent SNP A A T novel C3L-00094_T C3L-00094_N A A c.441T>A p.= p.S147S ENST00000400113 4/5 52 40 12 66 66 0 strelka-varscan-mutect TUBA3C,synonymous_variant,p.=,ENST00000400113,NM_006001.2;TUBA3C,synonymous_variant,p.=,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; T ENST00000400113 Transcript synonymous_variant 546/1551 441/1353 147/450 S tcT/tcA 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,PROSITE_patterns:PS00227,Gene3D:3.40.50.1440,Pfam_domain:PF00091,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161 LOW 1 SNV 5 1 PASS . . 0 203 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 19177542 19177542 A T 1 0 0 0 0 0 0 0 1 17256 175 7 4 4 TUBA3C 13 19177542 Silent SNP A C3L-00094_T 19177542 95186786 146 3122 FLT1 0 . GRCh38 13 28433920 28433920 + Missense_Mutation SNP G G T rs139202898 C3L-00094_T C3L-00094_N G G c.712C>A p.Arg238Ser p.R238S ENST00000282397 6/30 409 288 121 406 405 1 strelka-varscan-mutect FLT1,missense_variant,p.Arg238Ser,ENST00000282397,NM_002019.4;FLT1,missense_variant,p.Arg238Ser,ENST00000615840,NM_001159920.1;FLT1,missense_variant,p.Arg238Ser,ENST00000541932,NM_001160030.1;FLT1,missense_variant,p.Arg238Ser,ENST00000539099,NM_001160031.1; T ENST00000282397 Transcript missense_variant 964/7092 712/4017 238/1338 R/S Cgc/Agc rs139202898,COSM1140373,COSM1152639,COSM1649038,COSM550880 1 -1 FLT1 HGNC HGNC:3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 L7RSL3 UPI000013DCDD NM_002019.4 tolerated(0.71) 6/30 Gene3D:2.60.40.10,Pfam_domain:PF00047,Prints_domain:PR01833,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF259,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs139202898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 28433920 28433920 G T 1 0 0 0 0 1 0 0 0 5797 1145 40 1 1 FLT1 13 28433920 Missense_Mutation SNP G C3L-00094_T 9256378 28433920 85930408 147 3123 NBEA 0 . GRCh38 13 35232556 35232556 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.5713G>T p.Asp1905Tyr p.D1905Y ENST00000400445 34/58 162 124 38 208 208 0 strelka-varscan-mutect NBEA,missense_variant,p.Asp1905Tyr,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Asp1906Tyr,ENST00000310336,;NBEA,missense_variant,p.Asp1905Tyr,ENST00000629018,;NBEA,missense_variant,p.Asp1902Tyr,ENST00000379939,; T ENST00000400445 Transcript missense_variant 6247/11119 5713/8841 1905/2946 D/Y Gac/Tac 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 deleterious(0) 34/58 PD329443,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF62 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 35232556 35232556 G T 1 0 0 0 0 1 0 0 0 10198 942 33 2 2 NBEA 13 35232556 Missense_Mutation SNP G C3L-00094_T 6798636 35232556 79131772 148 3124 TBC1D4 0 . GRCh38 13 75306363 75306363 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.2702G>T p.Arg901Ile p.R901I ENST00000377636 15/21 154 123 31 193 191 2 strelka-varscan-mutect TBC1D4,missense_variant,p.Arg901Ile,ENST00000377636,NM_014832.3;TBC1D4,missense_variant,p.Arg893Ile,ENST00000431480,NM_001286658.1;TBC1D4,missense_variant,p.Arg838Ile,ENST00000377625,NM_001286659.1;TBC1D4,downstream_gene_variant,,ENST00000413735,;TBC1D4,upstream_gene_variant,,ENST00000478591,;TBC1D4,downstream_gene_variant,,ENST00000493487,; A ENST00000377636 Transcript missense_variant 3049/6364 2702/3897 901/1298 R/I aGa/aTa 1 -1 TBC1D4 HGNC HGNC:19165 protein_coding YES CCDS41901.1 ENSP00000366863 O60343 UPI00001AE7B3 NM_014832.3 deleterious(0) 15/21 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF195,Superfamily_domains:SSF47923 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 75306363 75306363 C A 1 0 0 0 0 1 0 0 0 16027 913 32 2 2 TBC1D4 13 75306363 Missense_Mutation SNP C C3L-00094_T 40073807 75306363 39057965 149 3125 DCT 0 . GRCh38 13 94462105 94462105 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.948C>G p.Ser316Arg p.S316R ENST00000446125 5/10 305 236 69 304 304 0 strelka-varscan-mutect DCT,missense_variant,p.Ser316Arg,ENST00000377028,NM_001922.3;DCT,missense_variant,p.Ser316Arg,ENST00000446125,NM_001129889.1;DCT,downstream_gene_variant,,ENST00000490854,;DCT,missense_variant,p.Ser126Arg,ENST00000483392,;DCT,downstream_gene_variant,,ENST00000472871,; C ENST00000446125 Transcript missense_variant 1375/2395 948/1659 316/552 S/R agC/agG 1 -1 DCT HGNC HGNC:2709 protein_coding YES CCDS45060.1 ENSP00000392762 P40126 UPI0000E13F02 NM_001129889.1 tolerated(0.56) 5/10 Gene3D:1.10.1280.10,Pfam_domain:PF00264,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF4,Superfamily_domains:SSF48056 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 94462105 94462105 G C 1 0 0 0 0 1 0 0 0 4107 1310 46 4 4 DCT 13 94462105 Missense_Mutation SNP G C3L-00094_T 19155742 94462105 19902223 150 3126 MYO16 0 . GRCh38 13 109140699 109140699 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.4487A>T p.Asp1496Val p.D1496V ENST00000457511 32/35 72 53 19 78 78 0 strelka-varscan-mutect MYO16,missense_variant,p.Asp1496Val,ENST00000457511,NM_001198950.1;MYO16,missense_variant,p.Asp1474Val,ENST00000356711,NM_015011.1;MYO16,missense_variant,p.Asp1474Val,ENST00000357550,; T ENST00000457511 Transcript missense_variant 5109/7436 4487/5643 1496/1880 D/V gAc/gTc 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 deleterious_low_confidence(0.02) 32/35 Pfam_domain:PF15439 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 109140699 109140699 A T 1 0 0 0 0 1 0 0 0 10065 275 10 4 4 MYO16 13 109140699 Missense_Mutation SNP A C3L-00094_T 14678594 109140699 5223629 151 3127 OR4M1 0 . GRCh38 14 19780557 19780557 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.235C>A p.Pro79Thr p.P79T ENST00000315957 1/1 307 289 18 263 262 1 varscan-mutect OR4M1,missense_variant,p.Pro79Thr,ENST00000315957,NM_001005500.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000315957 Transcript missense_variant 316/1116 235/942 79/313 P/T Cct/Act COSM1649083 1 1 OR4M1 HGNC HGNC:14735 protein_coding YES CCDS32021.1 ENSP00000319654 Q8NGD0 A0A126GWC3 UPI0000061F0F NM_001005500.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF53,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS rs1280030056 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 19780557 19780557 C A 1 0 0 0 0 1 0 0 0 11152 623 22 2 2 OR4M1 14 19780557 Missense_Mutation SNP C C3L-00094_T 19780557 87263161 152 3128 OR4K15 0 . GRCh38 14 19975598 19975598 + Missense_Mutation SNP A A T rs146301798 C3L-00094_T C3L-00094_N A A c.80A>T p.Glu27Val p.E27V ENST00000305051 1/1 180 120 60 178 178 0 strelka-varscan-mutect OR4K15,missense_variant,p.Glu27Val,ENST00000305051,NM_001005486.1; T ENST00000305051 Transcript missense_variant 155/1216 80/1047 27/348 E/V gAg/gTg rs146301798 1 1 OR4K15 HGNC HGNC:15353 protein_coding YES CCDS32026.1 ENSP00000304077 Q8NH41 UPI000015F249 NM_001005486.1 tolerated(0.29) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF287,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs146301798 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 19975598 19975598 A T 1 0 0 0 0 1 0 0 0 11147 304 11 4 4 OR4K15 14 19975598 Missense_Mutation SNP A C3L-00094_T 195041 19975598 87068120 153 3129 NYNRIN 0 . GRCh38 14 24414659 24414659 + Silent SNP T T C novel C3L-00094_T C3L-00094_N T T c.2910T>C p.= p.S970S ENST00000382554 9/9 328 107 221 118 118 0 strelka-varscan-mutect NYNRIN,synonymous_variant,p.=,ENST00000382554,NM_025081.2;NYNRIN,non_coding_transcript_exon_variant,,ENST00000554505,; C ENST00000382554 Transcript synonymous_variant 3228/7857 2910/5697 970/1898 S agT/agC 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 9/9 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 9 24414659 24414659 T C 1 0 0 0 0 0 0 0 1 10874 1693 59 5 5 NYNRIN 14 24414659 Silent SNP T C3L-00094_T 4439061 24414659 82629059 154 3130 STXBP6 0 . GRCh38 14 24857089 24857089 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.223G>T p.Val75Phe p.V75F ENST00000323944 3/6 325 115 210 174 174 0 strelka-varscan-mutect STXBP6,missense_variant,p.Val75Phe,ENST00000323944,;STXBP6,missense_variant,p.Val75Phe,ENST00000396700,NM_001304476.1;STXBP6,missense_variant,p.Val75Phe,ENST00000419632,NM_014178.7;STXBP6,missense_variant,p.Val75Phe,ENST00000550887,;STXBP6,missense_variant,p.Val75Phe,ENST00000546511,NM_001304477.1;STXBP6,3_prime_UTR_variant,,ENST00000548182,; A ENST00000323944 Transcript missense_variant 675/4132 223/633 75/210 V/F Gtt/Ttt 1 -1 STXBP6 HGNC HGNC:19666 protein_coding YES CCDS9634.1 ENSP00000324302 Q8NFX7 UPI000006DD7D deleterious(0.04) 3/6 Pfam_domain:PF15277,hmmpanther:PTHR16092,SMART_domains:SM01313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 24857089 24857089 C A 1 0 0 0 0 1 0 0 0 15742 478 17 2 2 STXBP6 14 24857089 Missense_Mutation SNP C C3L-00094_T 442430 24857089 82186629 155 3131 AKAP6 0 . GRCh38 14 32545611 32545611 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.958G>T p.Gly320Cys p.G320C ENST00000280979 4/14 561 131 430 203 202 1 strelka-varscan-mutect AKAP6,missense_variant,p.Gly320Cys,ENST00000280979,NM_004274.4;AKAP6,missense_variant,p.Gly320Cys,ENST00000557354,;AKAP6,missense_variant,p.Gly320Cys,ENST00000557272,;AKAP6,missense_variant,p.Gly78Cys,ENST00000553547,;AKAP6,downstream_gene_variant,,ENST00000556638,;AKAP6,downstream_gene_variant,,ENST00000554410,; T ENST00000280979 Transcript missense_variant 1128/15006 958/6960 320/2319 G/C Ggc/Tgc 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 tolerated(0.18) 4/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 32545611 32545611 G T 1 0 0 0 0 1 0 0 0 539 1000 35 2 2 AKAP6 14 32545611 Missense_Mutation SNP G C3L-00094_T 7688522 32545611 74498107 156 3132 PYGL 0 . GRCh38 14 50905404 50905404 + Silent SNP G G T novel C3L-00094_T C3L-00094_N G G c.2532C>A p.= p.V844V ENST00000216392 20/20 208 184 24 283 282 1 strelka-varscan-mutect PYGL,synonymous_variant,p.=,ENST00000216392,NM_002863.4;PYGL,synonymous_variant,p.=,ENST00000544180,NM_001163940.1;PYGL,intron_variant,,ENST00000532462,;ABHD12B,downstream_gene_variant,,ENST00000337334,NM_001206673.1;ABHD12B,downstream_gene_variant,,ENST00000353130,NM_181814.1;ABHD12B,downstream_gene_variant,,ENST00000554566,;ABHD12B,downstream_gene_variant,,ENST00000556857,;ABHD12B,downstream_gene_variant,,ENST00000553715,;ABHD12B,downstream_gene_variant,,ENST00000382029,NM_181533.3;ABHD12B,downstream_gene_variant,,ENST00000557345,;PYGL,downstream_gene_variant,,ENST00000532107,; T ENST00000216392 Transcript synonymous_variant 2865/3048 2532/2544 844/847 V gtC/gtA 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 20/20 PIRSF_domain:PIRSF000460 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 50905404 50905404 G T 1 0 0 0 0 0 0 0 1 13015 1277 45 2 2 PYGL 14 50905404 Silent SNP G C3L-00094_T 18359793 50905404 56138314 157 3133 PCNX4 0 . GRCh38 14 60118482 60118482 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.1030G>A p.Val344Ile p.V344I ENST00000317623 6/10 175 156 19 243 243 0 strelka-varscan-mutect PCNX4,missense_variant,p.Val344Ile,ENST00000317623,NM_022495.5;PCNX4,missense_variant,p.Val578Ile,ENST00000406854,;PCNX4,missense_variant,p.Val344Ile,ENST00000406949,;PCNX4,intron_variant,,ENST00000554534,;PCNX4,downstream_gene_variant,,ENST00000556907,;PCNX4,missense_variant,p.Val14Ile,ENST00000555740,;PCNX4,non_coding_transcript_exon_variant,,ENST00000483571,;PCNX4,non_coding_transcript_exon_variant,,ENST00000553513,;PCNX4,upstream_gene_variant,,ENST00000555929,;PCNX4,downstream_gene_variant,,ENST00000555569,; A ENST00000317623 Transcript missense_variant 1552/17339 1030/2817 344/938 V/I Gtc/Atc 1 1 PCNX4 HGNC HGNC:20349 protein_coding YES ENSP00000317396 B6ZDM2 UPI00014F7B83 NM_022495.5 tolerated(0.31) 6/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR12372 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 60118482 60118482 G A 1 0 0 0 0 1 0 0 0 11682 1261 44 3 3 PCNX4 14 60118482 Missense_Mutation SNP G C3L-00094_T 9213078 60118482 46925236 158 3134 STON2 0 . GRCh38 14 81371027 81371027 + Nonsense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.532G>T p.Glu178Ter p.E178* ENST00000555447 5/8 249 175 74 234 234 0 strelka-varscan-mutect STON2,stop_gained,p.Glu178Ter,ENST00000555447,NM_001256430.1;STON2,stop_gained,p.Glu178Ter,ENST00000267540,NM_033104.3;STON2,stop_gained,p.Glu178Ter,ENST00000614646,; A ENST00000555447 Transcript stop_gained 945/4302 532/2763 178/920 E/* Gag/Tag 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 5/8 PIRSF_domain:PIRSF037099,Pfam_domain:PF12016 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 81371027 81371027 C A 1 0 0 0 0 0 1 0 0 15696 864 30 2 2 STON2 14 81371027 Nonsense_Mutation SNP C C3L-00094_T 21252545 81371027 25672691 159 3135 UNC79 0 . GRCh38 14 93621978 93621978 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.4214G>C p.Arg1405Thr p.R1405T ENST00000256339 30/50 253 214 39 276 276 0 strelka-varscan-mutect UNC79,missense_variant,p.Arg1604Thr,ENST00000553484,;UNC79,missense_variant,p.Arg1582Thr,ENST00000555664,;UNC79,missense_variant,p.Arg1405Thr,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Arg1582Thr,ENST00000393151,;UNC79,missense_variant,p.Arg1405Thr,ENST00000621021,; C ENST00000256339 Transcript missense_variant 4869/8400 4214/7377 1405/2458 R/T aGg/aCg 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious_low_confidence(0) 30/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 93621978 93621978 G C 1 0 0 0 0 1 0 0 0 17520 1000 35 4 4 UNC79 14 93621978 Missense_Mutation SNP G C3L-00094_T 12250951 93621978 13421740 160 3136 AHNAK2 0 . GRCh38 14 104944092 104944092 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.11359G>T p.Gly3787Trp p.G3787W ENST00000333244 7/7 470 314 156 532 531 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Gly3787Trp,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript missense_variant 11479/18254 11359/17388 3787/5795 G/W Ggg/Tgg 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS rs1224025041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 104944092 104944092 C A 1 0 0 0 0 1 0 0 0 492 623 22 2 2 AHNAK2 14 104944092 Missense_Mutation SNP C C3L-00094_T 11322114 104944092 2099626 161 3137 NPAP1 0 . GRCh38 15 24676527 24676527 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.660C>A p.Ser220Arg p.S220R ENST00000329468 1/1 107 89 18 116 116 0 strelka-varscan-mutect NPAP1,missense_variant,p.Ser220Arg,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 660/7526 660/3471 220/1156 S/R agC/agA 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 deleterious(0.02) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 24676527 24676527 C A 1 0 0 0 0 1 0 0 0 10609 709 25 2 2 NPAP1 15 24676527 Missense_Mutation SNP C C3L-00094_T 24676527 77314662 162 3138 GABRA5 0 . GRCh38 15 26948122 26948122 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.1278C>A p.Asp426Glu p.D426E ENST00000335625 11/11 343 301 42 446 446 0 strelka-varscan-mutect GABRA5,missense_variant,p.Asp426Glu,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Asp426Glu,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Asp426Glu,ENST00000355395,; A ENST00000335625 Transcript missense_variant 2166/3251 1278/1389 426/462 D/E gaC/gaA COSM3500240 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0) 11/11 Gene3D:1.20.58.390,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 26948122 26948122 C A 1 0 0 0 0 1 0 0 0 6035 477 17 2 2 GABRA5 15 26948122 Missense_Mutation SNP C C3L-00094_T 2271595 26948122 75043067 163 3139 8 2 GABRA5 0 . GRCh38 15 26948127 26948127 + Missense_Mutation SNP T T G novel C3L-00094_T C3L-00094_N T T c.1283T>G p.Met428Arg p.M428R ENST00000335625 11/11 338 298 40 445 444 1 strelka-varscan-mutect GABRA5,missense_variant,p.Met428Arg,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Met428Arg,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Met428Arg,ENST00000355395,; G ENST00000335625 Transcript missense_variant 2171/3251 1283/1389 428/462 M/R aTg/aGg 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0.01) 11/11 Gene3D:1.20.58.390,Prints_domain:PR00253,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 26948127 26948127 T G 1 0 0 0 0 1 0 0 0 6035 1464 51 5 5 GABRA5 15 26948127 Missense_Mutation SNP T C3L-00094_T 5 26948127 75043062 164 3140 8 2 SPINT1 0 . GRCh38 15 40845018 40845018 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.464A>T p.Gln155Leu p.Q155L ENST00000344051 2/11 45 34 11 44 44 0 strelka-varscan-mutect SPINT1,missense_variant,p.Gln155Leu,ENST00000344051,NM_181642.2;SPINT1,missense_variant,p.Gln155Leu,ENST00000562057,NM_003710.3,NM_001032367.1;SPINT1,missense_variant,p.Gln115Leu,ENST00000568580,;SPINT1,missense_variant,p.Gln155Leu,ENST00000563656,;SPINT1,missense_variant,p.Gln217Leu,ENST00000568823,;RP11-532F12.5,upstream_gene_variant,,ENST00000564302,;RP11-532F12.5,upstream_gene_variant,,ENST00000565315,;RP11-532F12.5,upstream_gene_variant,,ENST00000568419,;RP11-532F12.5,upstream_gene_variant,,ENST00000568525,;RP11-532F12.5,upstream_gene_variant,,ENST00000563217,; T ENST00000344051 Transcript missense_variant 698/3056 464/1590 155/529 Q/L cAg/cTg 1 1 SPINT1 HGNC HGNC:11246 protein_coding YES CCDS10067.1 ENSP00000342098 O43278 UPI00001AE46F NM_181642.2 tolerated(0.13) 2/11 hmmpanther:PTHR10083:SF231,hmmpanther:PTHR10083 MODERATE 1 SNV 1 1 PASS rs1277654309 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 40845018 40845018 A T 1 0 0 0 0 1 0 0 0 15420 188 7 4 4 SPINT1 15 40845018 Missense_Mutation SNP A C3L-00094_T 13896891 40845018 61146171 165 3141 VPS39 0 . GRCh38 15 42166608 42166608 + Missense_Mutation SNP G G T rs749429530 C3L-00094_T C3L-00094_N G G c.1594C>A p.Pro532Thr p.P532T ENST00000348544 16/26 211 166 45 253 252 1 strelka-varscan-mutect VPS39,missense_variant,p.Pro521Thr,ENST00000318006,NM_015289.3;VPS39,missense_variant,p.Pro532Thr,ENST00000348544,NM_001301138.1;VPS39,non_coding_transcript_exon_variant,,ENST00000563692,;VPS39,upstream_gene_variant,,ENST00000562258,;VPS39,downstream_gene_variant,,ENST00000568029,;VPS39,upstream_gene_variant,,ENST00000564994,;VPS39,upstream_gene_variant,,ENST00000568755,;VPS39,upstream_gene_variant,,ENST00000561797,;VPS39,upstream_gene_variant,,ENST00000561818,;VPS39,upstream_gene_variant,,ENST00000562662,; T ENST00000348544 Transcript missense_variant 1594/2661 1594/2661 532/886 P/T Cct/Act rs749429530,COSM4468775,COSM4468776 1 -1 VPS39 HGNC HGNC:20593 protein_coding YES CCDS73710.1 ENSP00000335193 Q96JC1 UPI000013E629 NM_001301138.1 tolerated(0.07) 16/26 Pfam_domain:PF10366,hmmpanther:PTHR12894,hmmpanther:PTHR12894:SF10 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs749429530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 42166608 42166608 G T 1 0 0 0 0 1 0 0 0 17755 1232 43 2 2 VPS39 15 42166608 Missense_Mutation SNP G C3L-00094_T 1321590 42166608 59824581 166 3142 HDC 0 . GRCh38 15 50254193 50254193 + Silent SNP G G T C3L-00094_T C3L-00094_N G G c.657C>A p.= p.L219L ENST00000267845 6/12 349 262 87 363 363 0 strelka-varscan-mutect HDC,synonymous_variant,p.=,ENST00000267845,NM_002112.3;HDC,synonymous_variant,p.=,ENST00000543581,NM_001306146.1;HDC,downstream_gene_variant,,ENST00000559683,;HDC,non_coding_transcript_exon_variant,,ENST00000558679,;HDC,non_coding_transcript_exon_variant,,ENST00000558761,;HDC,non_coding_transcript_exon_variant,,ENST00000559190,;HDC,upstream_gene_variant,,ENST00000559816,; T ENST00000267845 Transcript synonymous_variant 1060/2705 657/1989 219/662 L ctC/ctA COSM4251926 1 -1 HDC HGNC HGNC:4855 protein_coding YES CCDS10134.1 ENSP00000267845 P19113 UPI0000128FB4 NM_002112.3 6/12 Gene3D:3.40.640.10,Pfam_domain:PF00282,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF68,Superfamily_domains:SSF53383 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 50254193 50254193 G T 1 0 0 0 0 0 0 0 1 6902 1161 41 2 2 HDC 15 50254193 Silent SNP G C3L-00094_T 8087585 50254193 51736996 167 3143 TRPM7 0 . GRCh38 15 50614264 50614264 + Splice_Site SNP C C T novel C3L-00094_T C3L-00094_N C C c.1495-1G>A p.X499_splice ENST00000313478 53 43 10 53 53 0 strelka-varscan-mutect TRPM7,splice_acceptor_variant,,ENST00000313478,NM_017672.5;TRPM7,splice_acceptor_variant,,ENST00000560955,NM_001301212.1;TRPM7,splice_acceptor_variant,,ENST00000560638,; T ENST00000313478 Transcript splice_acceptor_variant -/10400 1495/5598 499/1865 1 -1 TRPM7 HGNC HGNC:17994 protein_coding YES CCDS42035.1 ENSP00000320239 Q96QT4 A0A024R5V1 UPI0000071CBA NM_017672.5 13/38 HIGH 1 SNV 1 1 PASS . . 1 204 5 0 0 0 0 0 -19.9999 1 1 1 1 0 T 5 4 9 50614264 50614264 C T 1 0 0 0 0 0 0 1 0 17097 695 24 3 3 TRPM7 15 50614264 Splice_Site SNP C C3L-00094_T 360071 50614264 51376925 168 3144 SPPL2A 0 . GRCh38 15 50748113 50748113 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.450G>T p.Gln150His p.Q150H ENST00000261854 4/15 54 41 13 113 112 1 strelka-varscan-mutect SPPL2A,missense_variant,p.Gln150His,ENST00000261854,NM_032802.3;SPPL2A,missense_variant,p.Gln108His,ENST00000558414,;SPPL2A,upstream_gene_variant,,ENST00000558934,;RP11-507J18.2,intron_variant,,ENST00000558317,;RP11-507J18.5,upstream_gene_variant,,ENST00000624738,;SPPL2A,non_coding_transcript_exon_variant,,ENST00000560288,;SPPL2A,upstream_gene_variant,,ENST00000559527,; A ENST00000261854 Transcript missense_variant,splice_region_variant 725/7372 450/1563 150/520 Q/H caG/caT 1 -1 SPPL2A HGNC HGNC:30227 protein_coding YES CCDS10138.1 ENSP00000261854 Q8TCT8 UPI0000013591 NM_032802.3 tolerated(0.25) 4/15 Gene3D:3.50.30.30,hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF34,Superfamily_domains:SSF52025 MODERATE 1 SNV 1 1 PASS . . 2 198 8 2 0 0 0 0 -19.99999 0.9998815 1 1 1 0 A 3 1 9 50748113 50748113 C A 1 0 0 0 0 1 0 0 0 15441 695 24 2 2 SPPL2A 15 50748113 Missense_Mutation SNP C C3L-00094_T 133849 50748113 51243076 169 3145 DMXL2 0 . GRCh38 15 51536436 51536436 + Nonsense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.2044C>T p.Gln682Ter p.Q682* ENST00000543779 12/43 124 106 18 166 166 0 strelka-varscan-mutect DMXL2,stop_gained,p.Gln682Ter,ENST00000251076,NM_015263.3;DMXL2,stop_gained,p.Gln682Ter,ENST00000543779,NM_001174116.1;DMXL2,stop_gained,p.Gln682Ter,ENST00000449909,NM_001174117.1; A ENST00000543779 Transcript stop_gained 2134/10400 2044/9114 682/3037 Q/* Cag/Tag 1 -1 DMXL2 HGNC HGNC:2938 protein_coding YES CCDS53946.1 ENSP00000441858 Q8TDJ6 UPI00001FE4C2 NM_001174116.1 12/43 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF11 HIGH 1 SNV 1 1 PASS rs1410214912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 9 51536436 51536436 G A 1 0 0 0 0 0 1 0 0 4404 1299 45 3 3 DMXL2 15 51536436 Nonsense_Mutation SNP G C3L-00094_T 788323 51536436 50454753 170 3146 KIAA1024 0 . GRCh38 15 79456699 79456699 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.552G>C p.Glu184Asp p.E184D ENST00000305428 2/4 169 126 43 232 232 0 strelka-varscan-mutect KIAA1024,missense_variant,p.Glu184Asp,ENST00000305428,NM_015206.2;KIAA1024,missense_variant,p.Glu184Asp,ENST00000559272,; C ENST00000305428 Transcript missense_variant 627/6732 552/2751 184/916 E/D gaG/gaC 1 1 KIAA1024 HGNC HGNC:29172 protein_coding YES CCDS32306.1 ENSP00000307461 Q9UPX6 UPI00001B2F56 NM_015206.2 tolerated(0.53) 2/4 hmmpanther:PTHR31530,hmmpanther:PTHR31530:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 79456699 79456699 G C 1 0 0 0 0 1 0 0 0 8097 991 35 4 4 KIAA1024 15 79456699 Missense_Mutation SNP G C3L-00094_T 27920263 79456699 22534490 171 3147 TRAF7 0 . GRCh38 16 2175845 2175845 + Silent SNP C C T novel C3L-00094_T C3L-00094_N C C c.1638C>T p.= p.I546I ENST00000326181 18/21 74 55 19 56 56 0 strelka-varscan-mutect TRAF7,synonymous_variant,p.=,ENST00000326181,NM_032271.2;CASKIN1,downstream_gene_variant,,ENST00000343516,NM_020764.3;TRAF7,downstream_gene_variant,,ENST00000567645,;TRAF7,downstream_gene_variant,,ENST00000564067,;TRAF7,downstream_gene_variant,,ENST00000569686,;TRAF7,downstream_gene_variant,,ENST00000570169,; T ENST00000326181 Transcript synonymous_variant 1770/3700 1638/2013 546/670 I atC/atT 1 1 TRAF7 HGNC HGNC:20456 protein_coding YES CCDS10461.1 ENSP00000318944 Q6Q0C0 UPI000014186F NM_032271.2 18/21 PROSITE_profiles:PS50294,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF165,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 2175845 2175845 C T 1 0 0 0 0 0 0 0 1 16929 845 30 3 3 TRAF7 16 2175845 Silent SNP C C3L-00094_T 2175845 88162500 172 3148 SRCAP 0 . GRCh38 16 30738129 30738129 + Nonsense_Mutation SNP G G T rs144963691 C3L-00094_T C3L-00094_N G G c.8089G>T p.Glu2697Ter p.E2697* ENST00000262518 34/34 162 112 50 121 121 0 strelka-varscan-mutect SRCAP,stop_gained,p.Glu2697Ter,ENST00000262518,NM_006662.2;SRCAP,stop_gained,p.Glu2438Ter,ENST00000395059,;TMEM265,upstream_gene_variant,,ENST00000615541,NM_001256829.1;RP11-2C24.4,upstream_gene_variant,,ENST00000483578,;RP11-2C24.9,stop_gained,p.Glu2520Ter,ENST00000380361,;SRCAP,downstream_gene_variant,,ENST00000474008,; T ENST00000262518 Transcript stop_gained 8474/11754 8089/9693 2697/3230 E/* Gag/Tag rs144963691 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 34/34 Low_complexity_(Seg):seg HIGH SNV 2 1 PASS rs144963691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 9 30738129 30738129 G T 1 0 0 0 0 0 1 0 0 15493 1291 45 2 2 SRCAP 16 30738129 Nonsense_Mutation SNP G C3L-00094_T 28562284 30738129 59600216 173 3149 IRX6 0 . GRCh38 16 55327610 55327610 + Silent SNP C C A rs202243145 C3L-00094_T C3L-00094_N C C c.438C>A p.= p.G146G ENST00000290552 4/6 56 41 15 63 63 0 strelka-varscan-mutect IRX6,synonymous_variant,p.=,ENST00000290552,NM_024335.2;RP11-26L20.4,upstream_gene_variant,,ENST00000573934,;RP11-26L20.5,upstream_gene_variant,,ENST00000637882,;RP11-26L20.3,intron_variant,,ENST00000558730,;IRX6,non_coding_transcript_exon_variant,,ENST00000558315,; A ENST00000290552 Transcript synonymous_variant 1770/3128 438/1341 146/446 G ggC/ggA rs202243145,COSM1163124 1 1 IRX6 HGNC HGNC:14675 protein_coding YES CCDS32449.1 ENSP00000290552 P78412 UPI00001C0A88 NM_024335.2 4/6 PROSITE_profiles:PS50071,hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF11,SMART_domains:SM00389 0,1 LOW 1 SNV 1 0,1 1 PASS rs202243145 . 0 199 11 0 0 0 0 0 -20 0.9999873 1 1 1 0 A 2 1 9 55327610 55327610 C A 1 0 0 0 0 0 0 0 1 7756 755 27 1 1 IRX6 16 55327610 Silent SNP C C3L-00094_T 24589481 55327610 35010735 174 3150 GNAO1 0 . GRCh38 16 56343851 56343851 + Missense_Mutation SNP C C A C3L-00094_T C3L-00094_N C C c.966C>A p.His322Gln p.H322Q ENST00000262494 8/8 300 244 56 221 221 0 strelka-varscan-mutect GNAO1,missense_variant,p.His322Gln,ENST00000262494,NM_138736.2;GNAO1,intron_variant,,ENST00000262493,NM_020988.2;GNAO1,intron_variant,,ENST00000568375,;GNAO1,non_coding_transcript_exon_variant,,ENST00000564798,; A ENST00000262494 Transcript missense_variant 1226/5574 966/1065 322/354 H/Q caC/caA COSM5450865 1 1 GNAO1 HGNC HGNC:4389 protein_coding YES CCDS10757.1 ENSP00000262494 P09471 UPI000007349C NM_138736.2 deleterious(0.01) 8/8 Gene3D:3.40.50.300,Pfam_domain:PF00503,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF203,SMART_domains:SM00275,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs1225155824 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 56343851 56343851 C A 1 0 0 0 0 1 0 0 0 6388 535 19 1 1 GNAO1 16 56343851 Missense_Mutation SNP C C3L-00094_T 1016241 56343851 33994494 175 3151 CLEC18B 0 . GRCh38 16 74413129 74413129 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.584T>A p.Ile195Asn p.I195N ENST00000339953 5/13 1384 1225 159 1248 1247 1 strelka-varscan-mutect CLEC18B,missense_variant,p.Ile195Asn,ENST00000617101,;CLEC18B,missense_variant,p.Ile195Asn,ENST00000619275,;CLEC18B,missense_variant,p.Ile195Asn,ENST00000339953,NM_001011880.2;CLEC18B,missense_variant,p.Ile195Asn,ENST00000620745,;CLEC18B,non_coding_transcript_exon_variant,,ENST00000425714,;CLEC18B,upstream_gene_variant,,ENST00000564842,; T ENST00000339953 Transcript missense_variant 706/1865 584/1368 195/455 I/N aTc/aAc 1 -1 CLEC18B HGNC HGNC:33849 protein_coding YES CCDS32484.1 ENSP00000341051 Q6UXF7 UPI000025210E NM_001011880.2 deleterious(0.02) 5/13 Gene3D:3.40.33.10,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF245,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS rs1358827890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 74413129 74413129 A T 1 0 0 0 0 1 0 0 0 3269 333 12 4 4 CLEC18B 16 74413129 Missense_Mutation SNP A C3L-00094_T 18069278 74413129 15925216 176 3152 NEURL4 0 . GRCh38 17 7320826 7320826 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.3458G>T p.Arg1153Leu p.R1153L ENST00000399464 21/29 153 113 40 122 122 0 strelka-varscan-mutect NEURL4,missense_variant,p.Arg1153Leu,ENST00000399464,NM_032442.2;NEURL4,missense_variant,p.Arg1151Leu,ENST00000315614,NM_001005408.1;NEURL4,missense_variant,p.Arg1129Leu,ENST00000570460,;NEURL4,missense_variant,p.Arg1116Leu,ENST00000571887,;NEURL4,upstream_gene_variant,,ENST00000574120,;NEURL4,missense_variant,p.Arg898Leu,ENST00000573186,;RP11-542C16.2,upstream_gene_variant,,ENST00000575474,;RP11-542C16.2,upstream_gene_variant,,ENST00000315601,;NEURL4,downstream_gene_variant,,ENST00000573651,;NEURL4,upstream_gene_variant,,ENST00000576794,;NEURL4,upstream_gene_variant,,ENST00000572680,;NEURL4,downstream_gene_variant,,ENST00000576966,;NEURL4,downstream_gene_variant,,ENST00000576485,;NEURL4,downstream_gene_variant,,ENST00000571508,;NEURL4,upstream_gene_variant,,ENST00000572029,;NEURL4,downstream_gene_variant,,ENST00000571243,; A ENST00000399464 Transcript missense_variant 3474/5200 3458/4689 1153/1562 R/L cGg/cTg 1 -1 NEURL4 HGNC HGNC:34410 protein_coding YES CCDS42251.1 ENSP00000382390 Q96JN8 UPI000020081C NM_032442.2 deleterious(0) 21/29 PROSITE_profiles:PS51065,hmmpanther:PTHR12429:SF14,hmmpanther:PTHR12429,Pfam_domain:PF07177,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 7320826 7320826 C A 1 0 0 0 0 1 0 0 0 10384 652 23 1 1 NEURL4 17 7320826 Missense_Mutation SNP C C3L-00094_T 7320826 75936615 177 3153 KCTD11 0 . GRCh38 17 7352947 7352947 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.5T>C p.Leu2Pro p.L2P ENST00000333751 1/1 41 36 5 49 49 0 strelka-varscan-mutect KCTD11,missense_variant,p.Leu2Pro,ENST00000333751,NM_001002914.2;ACAP1,downstream_gene_variant,,ENST00000158762,NM_014716.3;TMEM95,upstream_gene_variant,,ENST00000389982,NM_001320435.1,NM_001320436.1;TMEM95,upstream_gene_variant,,ENST00000330767,NM_198154.1;TMEM95,upstream_gene_variant,,ENST00000576060,;ACAP1,downstream_gene_variant,,ENST00000574499,;ACAP1,downstream_gene_variant,,ENST00000571471,;ACAP1,downstream_gene_variant,,ENST00000575415,;ACAP1,downstream_gene_variant,,ENST00000570504,;RP11-542C16.1,intron_variant,,ENST00000572417,;KCTD11,downstream_gene_variant,,ENST00000576980,;ACAP1,downstream_gene_variant,,ENST00000570439,;ACAP1,downstream_gene_variant,,ENST00000576594,; C ENST00000333751 Transcript missense_variant 786/2783 5/699 2/232 L/P cTg/cCg 1 1 KCTD11 HGNC HGNC:21302 protein_coding YES CCDS32545.1 ENSP00000328352 Q693B1 A0A158RFT7 UPI00001A82F7 NM_001002914.2 deleterious(0) 1/1 hmmpanther:PTHR14499:SF7,hmmpanther:PTHR14499,Gene3D:3.30.710.10 MODERATE SNV 1 PASS rs1444697069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 7352947 7352947 T C 1 0 0 0 0 1 0 0 0 8015 1580 55 5 5 KCTD11 17 7352947 Missense_Mutation SNP T C3L-00094_T 32121 7352947 75904494 178 3154 CHD3 0 . GRCh38 17 7910586 7910586 + Missense_Mutation SNP A A G novel C3L-00094_T C3L-00094_N A A c.5926A>G p.Thr1976Ala p.T1976A ENST00000380358 38/40 120 97 23 119 119 0 strelka-varscan-mutect CHD3,missense_variant,p.Thr1976Ala,ENST00000380358,NM_001005271.2;CHD3,missense_variant,p.Thr1917Ala,ENST00000330494,NM_001005273.2;CHD3,missense_variant,p.Thr1883Ala,ENST00000358181,NM_005852.3;CHD3,missense_variant,p.His260Arg,ENST00000439235,;CHD3,missense_variant,p.His232Arg,ENST00000573936,;CHD3,intron_variant,,ENST00000449744,;AC025335.1,downstream_gene_variant,,ENST00000324348,;AC025335.1,downstream_gene_variant,,ENST00000635932,;SCARNA21,downstream_gene_variant,,ENST00000517026,;CHD3,3_prime_UTR_variant,,ENST00000470531,;CHD3,non_coding_transcript_exon_variant,,ENST00000481999,;CHD3,downstream_gene_variant,,ENST00000572750,;CHD3,downstream_gene_variant,,ENST00000466233,; G ENST00000380358 Transcript missense_variant 5927/7356 5926/6180 1976/2059 T/A Aca/Gca 1 1 CHD3 HGNC HGNC:1918 protein_coding YES CCDS32553.2 ENSP00000369716 Q12873 UPI00004DDA7C NM_001005271.2 tolerated(0.48) 38/40 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 7910586 7910586 A G 1 0 0 0 0 1 0 0 0 3085 173 6 5 5 CHD3 17 7910586 Missense_Mutation SNP A C3L-00094_T 557639 7910586 75346855 179 3155 MYH1 0 . GRCh38 17 10501225 10501225 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.3623G>T p.Gly1208Val p.G1208V ENST00000226207 27/40 388 284 104 380 378 2 strelka-varscan-mutect MYH1,missense_variant,p.Gly1208Val,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 3718/6024 3623/5820 1208/1939 G/V gGg/gTg 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0.02) 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 10501225 10501225 C A 1 0 0 0 0 1 0 0 0 10029 623 22 2 2 MYH1 17 10501225 Missense_Mutation SNP C C3L-00094_T 2590639 10501225 72756216 180 3156 CORO6 0 . GRCh38 17 29615786 29615786 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1365G>T p.Gln455His p.Q455H ENST00000345068 11/11 159 129 30 126 126 0 strelka-varscan-mutect CORO6,missense_variant,p.Gln455His,ENST00000345068,;CORO6,missense_variant,p.Gln455His,ENST00000388767,NM_032854.3;CORO6,missense_variant,p.Gln415His,ENST00000580212,;CORO6,missense_variant,p.Gln454His,ENST00000584969,;ANKRD13B,downstream_gene_variant,,ENST00000394859,NM_152345.4;ANKRD13B,downstream_gene_variant,,ENST00000614878,;CORO6,downstream_gene_variant,,ENST00000492276,;CORO6,downstream_gene_variant,,ENST00000584602,;ANKRD13B,downstream_gene_variant,,ENST00000579719,;ABHD15-AS1,intron_variant,,ENST00000581474,;CORO6,downstream_gene_variant,,ENST00000577909,;CORO6,3_prime_UTR_variant,,ENST00000480954,;CORO6,non_coding_transcript_exon_variant,,ENST00000459686,;CORO6,non_coding_transcript_exon_variant,,ENST00000467534,;CORO6,non_coding_transcript_exon_variant,,ENST00000469090,;CORO6,non_coding_transcript_exon_variant,,ENST00000579388,;ANKRD13B,downstream_gene_variant,,ENST00000487527,;ANKRD13B,downstream_gene_variant,,ENST00000488766,;ANKRD13B,downstream_gene_variant,,ENST00000493506,; A ENST00000345068 Transcript missense_variant 1579/2603 1365/1419 455/472 Q/H caG/caT 1 -1 CORO6 HGNC HGNC:21356 protein_coding YES CCDS11252.2 ENSP00000344562 Q6QEF8 UPI0000DA4C55 tolerated(0.07) 11/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF23 MODERATE SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 29615786 29615786 C A 1 0 0 0 0 1 0 0 0 3552 796 28 2 2 CORO6 17 29615786 Missense_Mutation SNP C C3L-00094_T 19114561 29615786 53641655 181 3157 PEX12 0 . GRCh38 17 35577939 35577943 + Frame_Shift_Del DEL CTGTC CTGTC - novel C3L-00094_T C3L-00094_N CTGTC CTGTC c.79_83delGACAG p.Asp27PhefsTer32 p.D27Ffs*32 ENST00000613219 1/3 607 445 162 532 532 0 sindel-varindel-pindel PEX12,frameshift_variant,p.Asp27PhefsTer32,ENST00000613219,NM_000286.2;PEX12,frameshift_variant,p.Asp27PhefsTer32,ENST00000225873,;PEX12,frameshift_variant,p.Asp27PhefsTer32,ENST00000585380,;AP2B1,upstream_gene_variant,,ENST00000589774,;RP11-1094M14.11,downstream_gene_variant,,ENST00000592381,;SNORD7,downstream_gene_variant,,ENST00000384567,;PEX12,frameshift_variant,p.Asp27PhefsTer32,ENST00000586663,; - ENST00000613219 Transcript frameshift_variant 695-699/2682 79-83/1080 27-28/359 DS/X GACAGt/t 1 -1 PEX12 HGNC HGNC:8854 protein_coding YES CCDS11296.1 ENSP00000482609 O00623 UPI0000131703 NM_000286.2 1/3 hmmpanther:PTHR12888:SF0,hmmpanther:PTHR12888,Pfam_domain:PF04757,PIRSF_domain:PIRSF038074 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 35577939 35577939 CTGTC - 1 0 1 0 1 0 0 0 0 11830 565 20 0 0 PEX12 17 35577939 Frame_Shift_Del DEL CTGTC C3L-00094_T 5962153 35577939 47679502 182 3158 LRRC3C 0 . GRCh38 17 39944280 39944280 + Missense_Mutation SNP G G C novel C3L-00094_T C3L-00094_N G G c.374G>C p.Gly125Ala p.G125A ENST00000377924 2/2 133 94 39 103 103 0 strelka-varscan-mutect LRRC3C,missense_variant,p.Gly125Ala,ENST00000377924,NM_001195545.1;RP11-387H17.4,downstream_gene_variant,,ENST00000582263,; C ENST00000377924 Transcript missense_variant 424/891 374/828 125/275 G/A gGc/gCc 1 1 LRRC3C HGNC HGNC:40034 protein_coding YES CCDS54121.1 ENSP00000367157 A6NJW4 UPI0000198ACC NM_001195545.1 deleterious(0) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 3 1 PASS rs1469635409 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 9 39944280 39944280 G C 1 0 0 0 0 1 0 0 0 8892 1203 42 4 4 LRRC3C 17 39944280 Missense_Mutation SNP G C3L-00094_T 4366341 39944280 43313161 183 3159 MPP2 0 . GRCh38 17 43880697 43880697 + Frame_Shift_Del DEL C C - novel C3L-00094_T C3L-00094_N C C c.1279delG p.Val427CysfsTer72 p.V427Cfs*72 ENST00000518766 10/13 52 35 17 39 39 0 sindel-varindel MPP2,frameshift_variant,p.Val382CysfsTer72,ENST00000612133,NM_001278381.1;MPP2,frameshift_variant,p.Val403CysfsTer72,ENST00000625880,;MPP2,frameshift_variant,p.Val382CysfsTer72,ENST00000269095,NM_005374.4;MPP2,frameshift_variant,p.Val371CysfsTer72,ENST00000536246,NM_001278375.1;MPP2,frameshift_variant,p.Val371CysfsTer72,ENST00000622681,NM_001278371.1;MPP2,frameshift_variant,p.Val399CysfsTer72,ENST00000377184,NM_001278376.2;MPP2,frameshift_variant,p.Val406CysfsTer72,ENST00000461854,NM_001278372.1;MPP2,frameshift_variant,p.Val371CysfsTer72,ENST00000523501,NM_001278373.1;MPP2,frameshift_variant,p.Val243CysfsTer72,ENST00000520305,NM_001278374.1;MPP2,frameshift_variant,p.Val427CysfsTer72,ENST00000518766,NM_001278370.1;MPP2,downstream_gene_variant,,ENST00000523220,;MPP2,downstream_gene_variant,,ENST00000473246,;MPP2,downstream_gene_variant,,ENST00000520406,;MPP2,downstream_gene_variant,,ENST00000524294,;MPP2,downstream_gene_variant,,ENST00000522172,;MPP2,downstream_gene_variant,,ENST00000523934,;MPP2,downstream_gene_variant,,ENST00000523762,;MPP2,downstream_gene_variant,,ENST00000521178,;MPP2,downstream_gene_variant,,ENST00000520241,;MPP2,downstream_gene_variant,,ENST00000520319,; - ENST00000518766 Transcript frameshift_variant 1336/1896 1279/1794 427/597 V/X Gtg/tg 1 -1 MPP2 HGNC HGNC:7220 protein_coding YES CCDS62210.1 ENSP00000428182 A0A0C4DH75 UPI0001914C39 NM_001278370.1 10/13 PROSITE_profiles:PS50052,hmmpanther:PTHR23122:SF35,hmmpanther:PTHR23122,Pfam_domain:PF00625,Gene3D:3.30.63.10,SMART_domains:SM00072,Superfamily_domains:SSF52540 HIGH 1 deletion 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 9 43880697 43880697 C - 1 0 1 0 1 0 0 0 0 9700 507 18 0 0 MPP2 17 43880697 Frame_Shift_Del DEL C C3L-00094_T 3936417 43880697 39376744 184 3160 RNF213 0 . GRCh38 17 80393464 80393464 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.15590C>T p.Ala5197Val p.A5197V ENST00000582970 68/68 374 296 78 236 236 0 strelka-varscan-mutect RNF213,missense_variant,p.Ala5197Val,ENST00000582970,NM_001256071.2;RNF213,missense_variant,p.Ala5246Val,ENST00000508628,;CTD-2047H16.4,intron_variant,,ENST00000575034,;CTD-2047H16.4,intron_variant,,ENST00000572151,;CTD-2047H16.4,intron_variant,,ENST00000573394,;RNF213,non_coding_transcript_exon_variant,,ENST00000427003,;RNF213,non_coding_transcript_exon_variant,,ENST00000411702,;RNF213,non_coding_transcript_exon_variant,,ENST00000560083,;RNF213,downstream_gene_variant,,ENST00000573919,; T ENST00000582970 Transcript missense_variant 15733/21055 15590/15624 5197/5207 A/V gCt/gTt 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 tolerated(0.09) 68/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 80393464 80393464 C T 1 0 0 0 0 1 0 0 0 13656 797 28 3 3 RNF213 17 80393464 Missense_Mutation SNP C C3L-00094_T 36512767 80393464 2863977 185 3161 FHOD3 0 . GRCh38 18 36718399 36718400 + Frame_Shift_Ins INS - - G novel C3L-00094_T C3L-00094_N - - c.3101_3102insG p.Pro1036ThrfsTer17 p.P1036Tfs*17 ENST00000590592 19/29 99 74 25 116 115 1 varindel-pindel FHOD3,frameshift_variant,p.Pro861ThrfsTer17,ENST00000257209,NM_025135.3;FHOD3,frameshift_variant,p.Pro1036ThrfsTer17,ENST00000590592,NM_001281740.1;FHOD3,frameshift_variant,p.Pro844ThrfsTer17,ENST00000359247,NM_001281739.1;FHOD3,frameshift_variant,p.Pro622ThrfsTer17,ENST00000592930,;FHOD3,intron_variant,,ENST00000591635,;FHOD3,upstream_gene_variant,,ENST00000592128,;FHOD3,downstream_gene_variant,,ENST00000587493,; G ENST00000590592 Transcript frameshift_variant 3101-3102/4869 3101-3102/4869 1034/1622 P/PX ccc/ccGc 1 1 FHOD3 HGNC HGNC:26178 protein_coding YES CCDS62418.1 ENSP00000466937 Q2V2M9 UPI0002840E0A NM_001281740.1 19/29 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF213,Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 200 8 2 0 0 0 0 -20 0.9998992 1 1 1 0 G 7 5 9 36718399 36718399 - G 1 0 1 1 0 0 0 0 0 5748 623 22 0 0 FHOD3 18 36718399 Frame_Shift_Ins INS - C3L-00094_T 36718399 43654886 186 3162 SETBP1 0 . GRCh38 18 45038596 45038596 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.4112C>T p.Thr1371Ile p.T1371I ENST00000282030 5/6 382 343 39 400 400 0 strelka-varscan-mutect SETBP1,missense_variant,p.Thr1371Ile,ENST00000282030,NM_015559.2; T ENST00000282030 Transcript missense_variant 4408/9899 4112/4791 1371/1596 T/I aCa/aTa 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 tolerated(0.2) 5/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 45038596 45038596 C T 1 0 0 0 0 1 0 0 0 14406 478 17 3 3 SETBP1 18 45038596 Missense_Mutation SNP C C3L-00094_T 8320197 45038596 35334689 187 3163 LOXHD1 0 . GRCh38 18 46534344 46534344 + Silent SNP C C A rs758206438 C3L-00094_T C3L-00094_N C C c.870G>T p.= p.P290P ENST00000300591 9/24 129 84 45 103 103 0 strelka-varscan-mutect LOXHD1,synonymous_variant,p.=,ENST00000536736,NM_144612.6;LOXHD1,synonymous_variant,p.=,ENST00000441551,;LOXHD1,synonymous_variant,p.=,ENST00000300591,NM_001145472.2;LOXHD1,synonymous_variant,p.=,ENST00000582408,;LOXHD1,synonymous_variant,p.=,ENST00000579038,NM_001308013.1;LOXHD1,synonymous_variant,p.=,ENST00000536111,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; A ENST00000300591 Transcript synonymous_variant 1284/3970 870/3345 290/1114 P ccG/ccT rs758206438 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 9/24 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137,Superfamily_domains:SSF49723 LOW 1 SNV 1 1 PASS rs758206438 . 0 204 3 3 0 0 0 0 -20 0.9999839 1 1 1 0 A 2 1 9 46534344 46534344 C A 1 0 0 0 0 0 0 0 1 8801 639 23 1 1 LOXHD1 18 46534344 Silent SNP C C3L-00094_T 1495748 46534344 33838941 188 3164 CDH7 0 . GRCh38 18 65809726 65809726 + Missense_Mutation SNP G G A rs867768827 C3L-00094_T C3L-00094_N G G c.233G>A p.Gly78Glu p.G78E ENST00000397968 3/12 99 85 14 120 119 1 strelka-varscan-mutect CDH7,missense_variant,p.Gly78Glu,ENST00000397968,NM_004361.2;CDH7,missense_variant,p.Gly78Glu,ENST00000536984,NM_001317214.1;CDH7,missense_variant,p.Gly78Glu,ENST00000323011,NM_033646.1; A ENST00000397968 Transcript missense_variant 659/12231 233/2358 78/785 G/E gGa/gAa rs867768827,COSM1480427,COSM1480428,COSM3527192,COSM3527193 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 deleterious(0.03) 3/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs867768827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 65809726 65809726 G A 1 0 0 0 0 1 0 0 0 2818 1174 41 3 3 CDH7 18 65809726 Missense_Mutation SNP G C3L-00094_T 19275382 65809726 14563559 189 3165 STK11 0 . GRCh38 19 1207064 1207065 + Frame_Shift_Ins INS - - TG novel C3L-00094_T C3L-00094_N - - c.152_153dupTG p.Gly52TrpfsTer13 p.G52Wfs*13 ENST00000326873 1/10 295 168 127 343 343 0 sindel-varindel-pindel STK11,frameshift_variant,p.Gly52TrpfsTer13,ENST00000586243,;STK11,frameshift_variant,p.Gly52TrpfsTer13,ENST00000326873,NM_000455.4;STK11,frameshift_variant,p.Gly52TrpfsTer13,ENST00000585851,;STK11,intron_variant,,ENST00000585748,;STK11,frameshift_variant,p.Gly52TrpfsTer13,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,upstream_gene_variant,,ENST00000586358,;HMGB2P1,downstream_gene_variant,,ENST00000591146,; TG ENST00000326873 Transcript frameshift_variant 601-602/2611 151-152/1302 51/433 M/MX atg/aTGtg 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 1/10 Gene3D:3.30.200.20,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 TG 7 5 9 1207064 1207064 - TG 1 0 1 1 0 0 0 0 0 15664 333 12 0 0 STK11 19 1207064 Frame_Shift_Ins INS - C3L-00094_T 1207064 57410552 190 3166 ONECUT3 0 . GRCh38 19 1775300 1775300 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.1340T>C p.Ile447Thr p.I447T ENST00000382349 2/2 170 130 40 193 193 0 strelka-varscan-mutect ONECUT3,missense_variant,p.Ile447Thr,ENST00000382349,NM_001080488.1; C ENST00000382349 Transcript missense_variant 2630/8318 1340/1485 447/494 I/T aTc/aCc 1 1 ONECUT3 HGNC HGNC:13399 protein_coding YES CCDS45900.1 ENSP00000371786 O60422 UPI000059D61D NM_001080488.1 deleterious(0.01) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR14057,hmmpanther:PTHR14057:SF34,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 1775300 1775300 T C 1 0 0 0 0 1 0 0 0 10945 1435 50 5 5 ONECUT3 19 1775300 Missense_Mutation SNP T C3L-00094_T 568236 1775300 56842316 191 3167 GMIP 0 . GRCh38 19 19637403 19637403 + Frame_Shift_Del DEL G G - C3L-00094_T C3L-00094_N G G c.1086delC p.Ala363ProfsTer11 p.A363Pfs*11 ENST00000203556 11/21 40 23 17 38 38 0 sindel-varindel-pindel GMIP,frameshift_variant,p.Ala363ProfsTer11,ENST00000203556,NM_016573.3;GMIP,frameshift_variant,p.Ala363ProfsTer11,ENST00000587238,NM_001288998.1,NM_001288999.1;GMIP,frameshift_variant,p.Ala110ProfsTer11,ENST00000593186,;GMIP,downstream_gene_variant,,ENST00000587205,;GMIP,upstream_gene_variant,,ENST00000586269,;GMIP,non_coding_transcript_exon_variant,,ENST00000587713,;GMIP,downstream_gene_variant,,ENST00000588171,;GMIP,downstream_gene_variant,,ENST00000591047,; - ENST00000203556 Transcript frameshift_variant 1224/3538 1086/2913 362/970 P/X ccC/cc COSM4648235 1 -1 GMIP HGNC HGNC:24852 protein_coding YES CCDS12408.1 ENSP00000203556 Q9P107 A0A024R7N1 UPI0000203862 NM_016573.3 11/21 hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF16,Low_complexity_(Seg):seg,Superfamily_domains:SSF103657 1 HIGH 1 deletion 1 1 1 PASS . . 0 192 18 0 0 0 0 0 -20 0.9997639 1 1 1 0 - 7 5 9 19637403 19637403 G - 1 0 1 0 1 0 0 0 0 6370 1103 39 0 0 GMIP 19 19637403 Frame_Shift_Del DEL G C3L-00094_T 17862103 19637403 38980213 192 3168 ZNF676 0 . GRCh38 19 22180587 22180587 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.1130T>A p.Val377Asp p.V377D ENST00000397121 3/3 297 271 26 373 373 0 varscan-mutect ZNF676,missense_variant,p.Val377Asp,ENST00000397121,NM_001001411.2; T ENST00000397121 Transcript missense_variant 1448/2944 1130/1767 377/588 V/D gTc/gAc 1 -1 ZNF676 HGNC HGNC:20429 protein_coding YES CCDS42539.1 ENSP00000380310 Q8N7Q3 UPI00002376EC NM_001001411.2 tolerated(0.17) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 22180587 22180587 A T 1 0 0 0 0 1 0 0 0 18656 275 10 4 4 ZNF676 19 22180587 Missense_Mutation SNP A C3L-00094_T 2543184 22180587 36437029 193 3169 TSHZ3 0 . GRCh38 19 31278249 31278249 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1544G>T p.Ser515Ile p.S515I ENST00000240587 2/2 324 206 118 237 236 1 strelka-varscan-mutect TSHZ3,missense_variant,p.Ser515Ile,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; A ENST00000240587 Transcript missense_variant 1872/5176 1544/3246 515/1081 S/I aGt/aTt 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 31278249 31278249 C A 1 0 0 0 0 1 0 0 0 17130 565 20 2 2 TSHZ3 19 31278249 Missense_Mutation SNP C C3L-00094_T 9097662 31278249 27339367 194 3170 HSPB6 0 . GRCh38 19 35755602 35755602 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.403G>A p.Ala135Thr p.A135T ENST00000592984 4/4 152 110 42 101 101 0 strelka-varscan-mutect HSPB6,missense_variant,p.Ala135Thr,ENST00000592984,;HSPB6,missense_variant,p.Ala135Thr,ENST00000004982,NM_144617.2;HSPB6,3_prime_UTR_variant,,ENST00000587965,;PROSER3,upstream_gene_variant,,ENST00000396908,NM_001039887.2;PROSER3,upstream_gene_variant,,ENST00000536950,;LIN37,downstream_gene_variant,,ENST00000301159,NM_019104.2;PROSER3,upstream_gene_variant,,ENST00000301165,;PROSER3,upstream_gene_variant,,ENST00000537459,;PROSER3,upstream_gene_variant,,ENST00000421853,;PROSER3,upstream_gene_variant,,ENST00000545674,;PROSER3,upstream_gene_variant,,ENST00000444637,;LIN37,downstream_gene_variant,,ENST00000591163,;PROSER3,upstream_gene_variant,,ENST00000542134,;LIN37,downstream_gene_variant,,ENST00000587751,;AC002398.11,upstream_gene_variant,,ENST00000591091,;AC002398.12,downstream_gene_variant,,ENST00000587767,;PROSER3,upstream_gene_variant,,ENST00000544876,;LIN37,downstream_gene_variant,,ENST00000591076,;PROSER3,upstream_gene_variant,,ENST00000620918,;PROSER3,upstream_gene_variant,,ENST00000600988,;LIN37,downstream_gene_variant,,ENST00000595455,;LIN37,downstream_gene_variant,,ENST00000587108,;LIN37,downstream_gene_variant,,ENST00000590706,;AC002398.9,downstream_gene_variant,,ENST00000591613,;PROSER3,upstream_gene_variant,,ENST00000601095,;LIN37,downstream_gene_variant,,ENST00000590890,;LIN37,downstream_gene_variant,,ENST00000592871,;PROSER3,upstream_gene_variant,,ENST00000539771,; T ENST00000592984 Transcript missense_variant 600/1634 403/483 135/160 A/T Gcg/Acg 1 -1 HSPB6 HGNC HGNC:26511 protein_coding YES CCDS12475.1 ENSP00000468057 O14558 V9HWB6 UPI000012CCD5 tolerated(0.1) 4/4 Gene3D:2.60.40.790,Pfam_domain:PF00011,Prints_domain:PR00299,PROSITE_profiles:PS01031,hmmpanther:PTHR11527,hmmpanther:PTHR11527:SF109,Superfamily_domains:SSF49764 MODERATE SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 35755602 35755602 C T 1 0 0 0 0 1 0 0 0 7318 768 27 1 1 HSPB6 19 35755602 Missense_Mutation SNP C C3L-00094_T 4477353 35755602 22862014 195 3171 ARHGAP33 0 . GRCh38 19 35784220 35784220 + Silent SNP G G T rs745495013 C3L-00094_T C3L-00094_N G G c.1470G>T p.= p.R490R ENST00000314737 16/21 146 106 40 97 97 0 strelka-varscan-mutect ARHGAP33,synonymous_variant,p.=,ENST00000378944,NM_001172630.1;ARHGAP33,synonymous_variant,p.=,ENST00000314737,NM_052948.3;ARHGAP33,synonymous_variant,p.=,ENST00000587447,;ARHGAP33,synonymous_variant,p.=,ENST00000007510,;ARHGAP33,synonymous_variant,p.=,ENST00000588248,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000591438,;LINC01529,downstream_gene_variant,,ENST00000637421,;LINC01529,downstream_gene_variant,,ENST00000433059,;LINC01529,downstream_gene_variant,,ENST00000637365,;ARHGAP33,downstream_gene_variant,,ENST00000221905,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000601474,;ARHGAP33,upstream_gene_variant,,ENST00000593034,;ARHGAP33,upstream_gene_variant,,ENST00000587984,;ARHGAP33,downstream_gene_variant,,ENST00000590893,;ARHGAP33,downstream_gene_variant,,ENST00000586918,;LINC01529,downstream_gene_variant,,ENST00000636474,; T ENST00000314737 Transcript synonymous_variant 1554/3858 1470/3381 490/1126 R cgG/cgT rs745495013 1 1 ARHGAP33 HGNC HGNC:23085 protein_coding YES CCDS12477.1 ENSP00000320038 O14559 UPI000013F8F9 NM_052948.3 16/21 PROSITE_profiles:PS50238,hmmpanther:PTHR15729,hmmpanther:PTHR15729:SF11,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 2 1 PASS rs745495013 . 0 203 4 3 0 0 0 0 -20 0.9999514 1 1 1 0 T 2 4 9 35784220 35784220 G T 1 0 0 0 0 0 0 0 1 1007 1219 43 2 2 ARHGAP33 19 35784220 Silent SNP G C3L-00094_T 28618 35784220 22833396 196 3172 RYR1 0 . GRCh38 19 38516212 38516212 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.9680G>T p.Arg3227Leu p.R3227L ENST00000359596 65/106 251 178 73 152 152 0 strelka-varscan-mutect RYR1,missense_variant,p.Arg3227Leu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Arg3227Leu,ENST00000359596,NM_000540.2;RYR1,missense_variant,p.Arg163Leu,ENST00000599547,;RYR1,3_prime_UTR_variant,,ENST00000594335,; T ENST00000359596 Transcript missense_variant 9680/15117 9680/15117 3227/5038 R/L cGg/cTg 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.04) 65/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS rs878984852 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 38516212 38516212 G T 1 0 0 0 0 1 0 0 0 14028 1130 39 1 1 RYR1 19 38516212 Missense_Mutation SNP G C3L-00094_T 2731992 38516212 20101404 197 3173 SPTBN4 0 . GRCh38 19 40534323 40534323 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.4339A>T p.Ser1447Cys p.S1447C ENST00000352632 20/36 179 123 56 132 132 0 strelka-varscan-mutect SPTBN4,missense_variant,p.Ser1447Cys,ENST00000338932,;SPTBN4,missense_variant,p.Ser1447Cys,ENST00000352632,;SPTBN4,missense_variant,p.Ser1447Cys,ENST00000392025,;SPTBN4,missense_variant,p.Ser1447Cys,ENST00000598249,NM_020971.2;SPTBN4,missense_variant,p.Ser1447Cys,ENST00000595535,;SPTBN4,missense_variant,p.Ser123Cys,ENST00000392023,NM_025213.2;SPTBN4,3_prime_UTR_variant,,ENST00000597389,;SPTBN4,non_coding_transcript_exon_variant,,ENST00000596900,;SPTBN4,non_coding_transcript_exon_variant,,ENST00000593932,; T ENST00000352632 Transcript missense_variant 4425/8676 4339/7695 1447/2564 S/C Agt/Tgt 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB tolerated(0.13) 20/36 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 40534323 40534323 A T 1 0 0 0 0 1 0 0 0 15477 188 7 4 4 SPTBN4 19 40534323 Missense_Mutation SNP A C3L-00094_T 2018111 40534323 18083293 198 3174 PSG6 0 . GRCh38 19 42916165 42916165 + Silent SNP C C A rs565072082 C3L-00094_T C3L-00094_N C C c.387G>T p.= p.G129G ENST00000292125 2/6 192 132 60 135 135 0 strelka-varscan-mutect PSG6,synonymous_variant,p.=,ENST00000601833,;PSG6,synonymous_variant,p.=,ENST00000187910,NM_001031850.3;PSG6,synonymous_variant,p.=,ENST00000402603,;PSG6,synonymous_variant,p.=,ENST00000292125,NM_002782.4;PSG7,intron_variant,,ENST00000617049,;PSG6,intron_variant,,ENST00000594375,;PSG6,non_coding_transcript_exon_variant,,ENST00000402456,;PSG6,non_coding_transcript_exon_variant,,ENST00000595062,;PSG6,intron_variant,,ENST00000484292,; A ENST00000292125 Transcript synonymous_variant 432/1391 387/1308 129/435 G ggG/ggT rs565072082 1 -1 PSG6 HGNC HGNC:9523 protein_coding YES CCDS12613.1 ENSP00000292125 Q00889 UPI00001327A1 NM_002782.4 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs565072082 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 42916165 42916165 C A 1 0 0 0 0 0 0 0 1 12810 842 30 2 2 PSG6 19 42916165 Silent SNP C C3L-00094_T 2381842 42916165 15701451 199 3175 SLC8A2 0 . GRCh38 19 47465744 47465744 + Silent SNP G G A rs769251136 C3L-00094_T C3L-00094_N G G c.660C>T p.= p.S220S ENST00000236877 2/10 106 65 41 84 83 1 strelka-varscan-mutect SLC8A2,synonymous_variant,p.=,ENST00000236877,NM_015063.2;SLC8A2,synonymous_variant,p.=,ENST00000594353,;SLC8A2,synonymous_variant,p.=,ENST00000597014,;SLC8A2,intron_variant,,ENST00000542837,;SLC8A2,intron_variant,,ENST00000539381,; A ENST00000236877 Transcript synonymous_variant 1056/5234 660/2766 220/921 S tcC/tcT rs769251136,COSM4504288 1 -1 SLC8A2 HGNC HGNC:11069 protein_coding YES CCDS33065.1 ENSP00000236877 Q9UPR5 UPI000012FC49 NM_015063.2 2/10 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF8,TIGRFAM_domain:TIGR00845,Pfam_domain:PF01699 0,1 LOW 1 SNV 1 0,1 1 PASS rs769251136 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 47465744 47465744 G A 1 0 0 0 0 0 0 0 1 14990 1219 43 3 3 SLC8A2 19 47465744 Silent SNP G C3L-00094_T 4549579 47465744 11151872 200 3176 ZNF541 0 . GRCh38 19 47544278 47544278 + Missense_Mutation SNP C C T novel C3L-00094_T C3L-00094_N C C c.2251G>A p.Ala751Thr p.A751T ENST00000391901 3/15 523 354 169 319 319 0 strelka-varscan-mutect ZNF541,missense_variant,p.Ala751Thr,ENST00000314121,;ZNF541,missense_variant,p.Ala751Thr,ENST00000391901,NM_001277075.1;ZNF541,missense_variant,p.Ala329Thr,ENST00000595558,;ZNF541,missense_variant,p.Ala342Thr,ENST00000263351,;ZNF541,upstream_gene_variant,,ENST00000487275,; T ENST00000391901 Transcript missense_variant 2251/4580 2251/4041 751/1346 A/T Gcc/Acc 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 deleterious(0.03) 3/15 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 47544278 47544278 C T 1 0 0 0 0 1 0 0 0 18549 739 26 3 3 ZNF541 19 47544278 Missense_Mutation SNP C C3L-00094_T 78534 47544278 11073338 201 3177 C19orf68 0 . GRCh38 19 48195016 48195017 + Frame_Shift_Del DEL CG CG - novel C3L-00094_T C3L-00094_N CG CG c.957_958delGC p.Gln320GlyfsTer137 p.Q320Gfs*137 ENST00000614654 4/4 76 71 5 61 61 0 varindel-pindel C19orf68,frameshift_variant,p.Gln320GlyfsTer137,ENST00000614654,NM_199341.3;C19orf68,frameshift_variant,p.Gln320GlyfsTer137,ENST00000328759,;ZNF114,intron_variant,,ENST00000597695,NM_001301062.1;CARD8,intron_variant,,ENST00000600800,;CTC-453G23.7,downstream_gene_variant,,ENST00000623064,; - ENST00000614654 Transcript frameshift_variant 984-985/3588 952-953/2763 318/920 R/X CGc/c 1 1 C19orf68 HGNC HGNC:34495 protein_coding YES CCDS74411.1 ENSP00000480314 A0A087WWL5 UPI000387AD70 NM_199341.3 4/4 HIGH 1 deletion 5 5 1 PASS . . 0 203 6 0 0 0 0 0 -11.19557 0.9999996 1 1 1 0 - 7 5 9 48195016 48195016 CG - 1 0 1 0 1 0 0 0 0 1922 652 23 0 0 C19orf68 19 48195016 Frame_Shift_Del DEL CG C3L-00094_T 650738 48195016 10422600 202 3178 IZUMO1 0 . GRCh38 19 48742269 48742269 + Silent SNP C C T novel C3L-00094_T C3L-00094_N C C c.540G>A p.= p.L180L ENST00000332955 7/10 240 190 50 196 196 0 strelka-varscan-mutect IZUMO1,synonymous_variant,p.=,ENST00000332955,NM_182575.2;RASIP1,upstream_gene_variant,,ENST00000222145,NM_017805.2;RASIP1,upstream_gene_variant,,ENST00000599291,;IZUMO1,downstream_gene_variant,,ENST00000602105,;RASIP1,upstream_gene_variant,,ENST00000594232,;IZUMO1,missense_variant,p.Gly193Arg,ENST00000595937,NM_001321865.1;IZUMO1,3_prime_UTR_variant,,ENST00000595517,;IZUMO1,downstream_gene_variant,,ENST00000597553,;IZUMO1,upstream_gene_variant,,ENST00000599871,; T ENST00000332955 Transcript synonymous_variant 1088/1621 540/1053 180/350 L ctG/ctA 1 -1 IZUMO1 HGNC HGNC:28539 protein_coding YES CCDS12732.1 ENSP00000327786 Q8IYV9 UPI00001609C7 NM_182575.2 7/10 hmmpanther:PTHR35540,hmmpanther:PTHR35540:SF1,Gene3D:2.60.40.10,Pfam_domain:PF16706,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 48742269 48742269 C T 1 0 0 0 0 0 0 0 1 7839 581 21 3 3 IZUMO1 19 48742269 Silent SNP C C3L-00094_T 547253 48742269 9875347 203 3179 IGLON5 0 . GRCh38 19 51326874 51326874 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.622C>A p.Arg208Ser p.R208S ENST00000270642 5/8 395 278 117 255 255 0 strelka-varscan-mutect IGLON5,missense_variant,p.Arg208Ser,ENST00000270642,NM_001101372.1;VSIG10L,downstream_gene_variant,,ENST00000335624,NM_001163922.1;VSIG10L,downstream_gene_variant,,ENST00000600663,; A ENST00000270642 Transcript missense_variant 622/2606 622/1011 208/336 R/S Cgc/Agc 1 1 IGLON5 HGNC HGNC:34550 protein_coding YES CCDS46158.1 ENSP00000270642 A6NGN9 UPI000058F1A8 NM_001101372.1 deleterious(0) 5/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF148,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1361591491 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 51326874 51326874 C A 1 0 0 0 0 1 0 0 0 7502 652 23 1 1 IGLON5 19 51326874 Missense_Mutation SNP C C3L-00094_T 2584605 51326874 7290742 204 3180 CEACAM18 0 . GRCh38 19 51480504 51480504 + Missense_Mutation SNP G G T C3L-00094_T C3L-00094_N G G c.224G>T p.Ser75Ile p.S75I ENST00000396477 2/6 528 367 161 335 333 2 strelka-varscan-mutect CEACAM18,missense_variant,p.Ser75Ile,ENST00000396477,NM_001278392.1; T ENST00000396477 Transcript missense_variant 245/1476 224/1155 75/384 S/I aGc/aTc COSM1000038,COSM1000039 1 1 CEACAM18 HGNC HGNC:31949 protein_coding YES ENSP00000379738 A8MTB9 UPI0002C5E52C NM_001278392.1 deleterious(0) 2/6 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 51480504 51480504 G T 1 0 0 0 0 1 0 0 0 2895 971 34 2 2 CEACAM18 19 51480504 Missense_Mutation SNP G C3L-00094_T 153630 51480504 7137112 205 3181 ERVV-1 0 . GRCh38 19 53015439 53015439 + Missense_Mutation SNP T T A novel C3L-00094_T C3L-00094_N T T c.1349T>A p.Leu450His p.L450H ENST00000602168 1/1 65 46 19 51 51 0 strelka-varscan-mutect ERVV-1,missense_variant,p.Leu450His,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; A ENST00000602168 Transcript missense_variant 1519/2202 1349/1434 450/477 L/H cTc/cAc 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 deleterious(0) 1/1 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424 MODERATE SNV 1 PASS . . 0 200 6 4 0 0 0 0 -20 0.999537 1 1 1 0 A 3 1 9 53015439 53015439 T A 1 0 0 0 0 1 0 0 0 5106 1551 54 4 4 ERVV-1 19 53015439 Missense_Mutation SNP T C3L-00094_T 1534935 53015439 5602177 206 3182 ZNF677 0 . GRCh38 19 53237967 53237967 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.760G>T p.Gly254Trp p.G254W ENST00000598513 5/5 174 127 47 164 164 0 strelka-varscan-mutect ZNF677,missense_variant,p.Gly254Trp,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,missense_variant,p.Gly254Trp,ENST00000333952,;ZNF677,downstream_gene_variant,,ENST00000594681,;ZNF677,downstream_gene_variant,,ENST00000599012,;ZNF677,downstream_gene_variant,,ENST00000598806,;ZNF677,downstream_gene_variant,,ENST00000594517,;CTD-2245F17.6,upstream_gene_variant,,ENST00000596041,;ZNF677,downstream_gene_variant,,ENST00000599328,;ZNF677,downstream_gene_variant,,ENST00000593539,; A ENST00000598513 Transcript missense_variant 911/3497 760/1755 254/584 G/W Ggg/Tgg 1 -1 ZNF677 HGNC HGNC:28730 protein_coding YES CCDS12861.1 ENSP00000469391 Q86XU0 UPI000017DF85 NM_001317998.1,NM_182609.2 deleterious(0.02) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF38 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 53237967 53237967 C A 1 0 0 0 0 1 0 0 0 18657 594 21 2 2 ZNF677 19 53237967 Missense_Mutation SNP C C3L-00094_T 222528 53237967 5379649 207 3183 CACNG8 0 . GRCh38 19 53982342 53982342 + Silent SNP C C A rs762479578 C3L-00094_T C3L-00094_N C C c.771C>A p.= p.P257P ENST00000270458 4/4 524 485 39 428 428 0 strelka-varscan-mutect CACNG8,synonymous_variant,p.=,ENST00000270458,NM_031895.5;CACNG8,non_coding_transcript_exon_variant,,ENST00000401179,; A ENST00000270458 Transcript synonymous_variant 874/8747 771/1278 257/425 P ccC/ccA rs762479578 1 1 CACNG8 HGNC HGNC:13628 protein_coding YES CCDS33104.1 ENSP00000270458 Q8WXS5 UPI000013D88B NM_031895.5 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR12107:SF2,hmmpanther:PTHR12107 LOW 1 SNV 1 1 PASS rs762479578 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 53982342 53982342 C A 1 0 0 0 0 0 0 0 1 2251 668 24 2 2 CACNG8 19 53982342 Silent SNP C C3L-00094_T 744375 53982342 4635274 208 3184 NCR1 0 . GRCh38 19 54909455 54909455 + Missense_Mutation SNP G G A rs772041783 C3L-00094_T C3L-00094_N G G c.566G>A p.Arg189Gln p.R189Q ENST00000291890 4/7 239 209 30 191 191 0 strelka-varscan-mutect NCR1,missense_variant,p.Arg189Gln,ENST00000594765,NM_001145457.2;NCR1,missense_variant,p.Arg189Gln,ENST00000291890,NM_004829.6;NCR1,missense_variant,p.Arg177Gln,ENST00000598576,;NCR1,missense_variant,p.Arg189Gln,ENST00000338835,NM_001145458.2,NM_001242357.2;NCR1,missense_variant,p.Arg94Gln,ENST00000350790,NM_001242356.2;NCR1,missense_variant,p.Arg82Gln,ENST00000357397,;NCR1,downstream_gene_variant,,ENST00000601137,;NCR1,downstream_gene_variant,,ENST00000601903,; A ENST00000291890 Transcript missense_variant 604/1155 566/915 189/304 R/Q cGa/cAa rs772041783 1 1 NCR1 HGNC HGNC:6731 protein_coding YES CCDS12911.1 ENSP00000291890 A0A0A0MQZ0 UPI00034F23C0 NM_004829.6 deleterious(0) 4/7 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF14,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs772041783 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 54909455 54909455 G A 1 0 0 0 0 1 0 0 0 10256 1058 37 1 1 NCR1 19 54909455 Missense_Mutation SNP G C3L-00094_T 927113 54909455 3708161 209 3185 ZIM3 0 . GRCh38 19 57138517 57138517 + Missense_Mutation SNP A A T C3L-00094_T C3L-00094_N A A c.97T>A p.Tyr33Asn p.Y33N ENST00000269834 3/5 355 243 112 247 247 0 strelka-varscan-mutect ZIM3,missense_variant,p.Tyr33Asn,ENST00000269834,NM_052882.1; T ENST00000269834 Transcript missense_variant 483/2627 97/1419 33/472 Y/N Tac/Aac COSM341169 1 -1 ZIM3 HGNC HGNC:16366 protein_coding YES CCDS33125.1 ENSP00000269834 Q96PE6 UPI000013C3E0 NM_052882.1 deleterious(0) 3/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF30,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 1 MODERATE 1 SNV 1 1 1 PASS rs1277834317 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 57138517 57138517 A T 1 0 0 0 0 1 0 0 0 18263 391 14 4 4 ZIM3 19 57138517 Missense_Mutation SNP A C3L-00094_T 2229062 57138517 1479099 210 3186 XKR7 0 . GRCh38 20 31968537 31968537 + Missense_Mutation SNP G G A novel C3L-00094_T C3L-00094_N G G c.362G>A p.Gly121Glu p.G121E ENST00000562532 1/3 164 108 56 95 95 0 strelka-varscan-mutect XKR7,missense_variant,p.Gly121Glu,ENST00000562532,NM_001011718.1;RP1-310O13.13,upstream_gene_variant,,ENST00000616850,; A ENST00000562532 Transcript missense_variant 536/7844 362/1740 121/579 G/E gGg/gAg 1 1 XKR7 HGNC HGNC:23062 protein_coding YES CCDS33459.1 ENSP00000477059 Q5GH72 UPI00004C7A9E NM_001011718.1 tolerated(0.39) 1/3 Pfam_domain:PF09815 MODERATE 1 SNV 1 1 PASS rs920686009 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 31968537 31968537 G A 1 0 0 0 0 1 0 0 0 17995 1232 43 3 3 XKR7 20 31968537 Missense_Mutation SNP G C3L-00094_T 31968537 32475630 211 3187 NCOA6 0 . GRCh38 20 34727406 34727406 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.6001A>G p.Ser2001Gly p.S2001G ENST00000374796 15/16 157 98 59 117 117 0 strelka-varscan-mutect NCOA6,missense_variant,p.Ser2001Gly,ENST00000374796,NM_001318240.1;NCOA6,missense_variant,p.Ser2001Gly,ENST00000359003,NM_014071.3;NCOA6,missense_variant,p.Ser1008Gly,ENST00000612493,NM_001242539.1;NCOA6,missense_variant,p.Ser138Gly,ENST00000628752,;NCOA6,splice_region_variant,,ENST00000471897,; C ENST00000374796 Transcript missense_variant,splice_region_variant 8572/9311 6001/6192 2001/2063 S/G Agt/Ggt 1 -1 NCOA6 HGNC HGNC:15936 protein_coding YES CCDS13241.1 ENSP00000363929 Q14686 UPI000013C634 NM_001318240.1 tolerated_low_confidence(0.22) 15/16 hmmpanther:PTHR15690,hmmpanther:PTHR15690:SF0 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 34727406 34727406 T C 1 0 0 0 0 1 0 0 0 10252 1594 55 5 5 NCOA6 20 34727406 Missense_Mutation SNP T C3L-00094_T 2758869 34727406 29716761 212 3188 SEMG2 0 . GRCh38 20 45222741 45222741 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1109C>A p.Ser370Tyr p.S370Y ENST00000372769 2/3 329 278 51 302 301 1 strelka-varscan-mutect SEMG2,missense_variant,p.Ser370Tyr,ENST00000372769,NM_003008.2; A ENST00000372769 Transcript missense_variant 1199/2051 1109/1749 370/582 S/Y tCc/tAc 1 1 SEMG2 HGNC HGNC:10743 protein_coding YES CCDS13346.1 ENSP00000361855 Q02383 UPI0000135845 NM_003008.2 tolerated(0.27) 2/3 Pfam_domain:PF05474,hmmpanther:PTHR10547,hmmpanther:PTHR10547:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 45222741 45222741 C A 1 0 0 0 0 1 0 0 0 14321 855 30 2 2 SEMG2 20 45222741 Missense_Mutation SNP C C3L-00094_T 10495335 45222741 19221426 213 3189 PREX1 0 . GRCh38 20 48690980 48690980 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1153G>T p.Asp385Tyr p.D385Y ENST00000371941 9/40 262 247 15 179 179 0 strelka-varscan-mutect PREX1,missense_variant,p.Asp385Tyr,ENST00000371941,NM_020820.3;PREX1,downstream_gene_variant,,ENST00000620554,; A ENST00000371941 Transcript missense_variant 1176/6636 1153/4980 385/1659 D/Y Gat/Tat 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 deleterious(0) 9/40 PROSITE_profiles:PS50003,hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 48690980 48690980 C A 1 0 0 0 0 1 0 0 0 12610 855 30 2 2 PREX1 20 48690980 Missense_Mutation SNP C C3L-00094_T 3468239 48690980 15753187 214 3190 BCAS1 0 . GRCh38 20 53953555 53953555 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.1557C>T p.= p.A519A ENST00000395961 11/12 666 494 172 512 512 0 strelka-varscan-mutect BCAS1,synonymous_variant,p.=,ENST00000448484,;BCAS1,synonymous_variant,p.=,ENST00000395961,NM_003657.2;BCAS1,synonymous_variant,p.=,ENST00000371435,NM_001316361.2,NM_001323347.1;BCAS1,synonymous_variant,p.=,ENST00000422805,; A ENST00000395961 Transcript synonymous_variant 1724/3303 1557/1755 519/584 A gcC/gcT 1 -1 BCAS1 HGNC HGNC:974 protein_coding YES CCDS13444.1 ENSP00000379290 O75363 UPI000013D2E2 NM_003657.2 11/12 hmmpanther:PTHR15016 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 53953555 53953555 G A 1 0 0 0 0 0 0 0 1 1497 1335 47 3 3 BCAS1 20 53953555 Silent SNP G C3L-00094_T 5262575 53953555 10490612 215 3191 TFAP2C 0 . GRCh38 20 56634149 56634149 + Splice_Site SNP G G T novel C3L-00094_T C3L-00094_N G G c.804-1G>T p.X268_splice ENST00000201031 197 186 11 149 147 2 varscan-mutect TFAP2C,splice_acceptor_variant,,ENST00000201031,NM_003222.3;TFAP2C,downstream_gene_variant,,ENST00000416606,; T ENST00000201031 Transcript splice_acceptor_variant -/2866 804/1353 268/450 1 1 TFAP2C HGNC HGNC:11744 protein_coding YES CCDS13454.1 ENSP00000201031 Q92754 UPI0000125BC8 NM_003222.3 4/6 HIGH 1 SNV 1 1 PASS . . 0 181 0 15 14 0 0 0 -2.941613 0 0 1 0 0 T 5 4 9 56634149 56634149 G T 1 0 0 0 0 0 0 1 0 16222 956 33 2 2 TFAP2C 20 56634149 Splice_Site SNP G C3L-00094_T 2680594 56634149 7810018 216 3192 ZNF831 0 . GRCh38 20 59194281 59194281 + Missense_Mutation SNP A A T novel C3L-00094_T C3L-00094_N A A c.3262A>T p.Arg1088Trp p.R1088W ENST00000637017 4/8 273 191 82 201 201 0 strelka-varscan-mutect ZNF831,missense_variant,p.Arg1088Trp,ENST00000637017,;ZNF831,missense_variant,p.Arg1088Trp,ENST00000371030,NM_178457.2; T ENST00000637017 Transcript missense_variant 4811/10953 3262/5034 1088/1677 R/W Agg/Tgg 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 deleterious(0.01) 4/8 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 59194281 59194281 A T 1 0 0 0 0 1 0 0 0 18770 179 7 4 4 ZNF831 20 59194281 Missense_Mutation SNP A C3L-00094_T 2560132 59194281 5249886 217 3193 COL9A3 0 . GRCh38 20 62821507 62821507 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.346G>T p.Gly116Cys p.G116C ENST00000343916 7/32 488 359 129 341 341 0 strelka-varscan-mutect COL9A3,missense_variant,p.Gly116Cys,ENST00000343916,NM_001853.3;COL9A3,missense_variant,p.Gly79Cys,ENST00000452372,;COL9A3,splice_region_variant,,ENST00000489045,;COL9A3,splice_region_variant,,ENST00000477612,;COL9A3,upstream_gene_variant,,ENST00000463487,; T ENST00000343916 Transcript missense_variant,splice_region_variant 349/2485 346/2055 116/684 G/C Ggc/Tgc 1 1 COL9A3 HGNC HGNC:2219 protein_coding YES CCDS13505.1 ENSP00000341640 Q14050 UPI0000126D51 NM_001853.3 deleterious(0.01) 7/32 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF529,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1362214057 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 62821507 62821507 G T 1 0 0 0 0 1 0 0 0 3498 1246 43 2 2 COL9A3 20 62821507 Missense_Mutation SNP G C3L-00094_T 3627226 62821507 1622660 218 3194 DIDO1 0 . GRCh38 20 62894153 62894154 + Frame_Shift_Ins INS - - T novel C3L-00094_T C3L-00094_N - - c.2613dupA p.Gln872ThrfsTer8 p.Q872Tfs*8 ENST00000266070 12/16 137 117 20 114 114 0 sindel-varindel-pindel DIDO1,frameshift_variant,p.Gln872ThrfsTer8,ENST00000266070,NM_033081.2;DIDO1,frameshift_variant,p.Gln872ThrfsTer8,ENST00000395343,NM_001193369.1;DIDO1,frameshift_variant,p.Gln872ThrfsTer8,ENST00000395340,NM_080797.3,NM_001193370.1; T ENST00000266070 Transcript frameshift_variant 2969-2970/8574 2613-2614/6723 871-872/2240 -/X -/A 1 -1 DIDO1 HGNC HGNC:2680 protein_coding YES CCDS33506.1 ENSP00000266070 Q9BTC0 UPI0000206380 NM_033081.2 12/16 hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF13 HIGH 1 insertion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 9 62894153 62894153 - T 1 0 1 1 0 0 0 0 0 4326 1386 48 0 0 DIDO1 20 62894153 Frame_Shift_Ins INS - C3L-00094_T 72646 62894153 1550014 219 3195 POTED 0 . GRCh38 21 13639623 13639623 + Silent SNP G G A novel C3L-00094_T C3L-00094_N G G c.1518G>A p.= p.Q506Q ENST00000299443 10/11 22 11 11 24 24 0 strelka-varscan-mutect POTED,synonymous_variant,p.=,ENST00000299443,NM_174981.3; A ENST00000299443 Transcript synonymous_variant 1570/1826 1518/1755 506/584 Q caG/caA 1 1 POTED HGNC HGNC:23822 protein_coding YES CCDS13562.1 ENSP00000299443 Q86YR6 UPI00001AECB3 NM_174981.3 10/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38 LOW 1 SNV 1 1 PASS . . 93 116 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 13639623 13639623 G A 1 0 0 0 0 0 0 0 1 12377 933 33 3 3 POTED 21 13639623 Silent SNP G C3L-00094_T 13639623 33070360 220 3196 ABCG1 0 . GRCh38 21 42294594 42294594 + Missense_Mutation SNP G G T novel C3L-00094_T C3L-00094_N G G c.1742G>T p.Gly581Val p.G581V ENST00000361802 14/15 252 227 25 252 251 1 strelka-mutect ABCG1,missense_variant,p.Gly727Val,ENST00000398437,;ABCG1,missense_variant,p.Gly571Val,ENST00000398457,NM_207627.1,NM_207628.1;ABCG1,missense_variant,p.Gly580Val,ENST00000343687,NM_207174.1;ABCG1,missense_variant,p.Gly581Val,ENST00000361802,NM_004915.3;ABCG1,missense_variant,p.Gly569Val,ENST00000398449,NM_016818.2;ABCG1,missense_variant,p.Gly566Val,ENST00000347800,NM_207629.1;ABCG1,non_coding_transcript_exon_variant,,ENST00000462050,;ABCG1,non_coding_transcript_exon_variant,,ENST00000472587,;ABCG1,non_coding_transcript_exon_variant,,ENST00000496783,; T ENST00000361802 Transcript missense_variant 1887/3034 1742/2037 581/678 G/V gGg/gTg 1 1 ABCG1 HGNC HGNC:73 protein_coding YES CCDS13682.1 ENSP00000354995 P45844 UPI0000125130 NM_004915.3 deleterious(0) 14/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF177,TIGRFAM_domain:TIGR00955,Pfam_domain:PF01061 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 42294594 42294594 G T 1 0 0 0 0 1 0 0 0 72 1232 43 2 2 ABCG1 21 42294594 Missense_Mutation SNP G C3L-00094_T 28654971 42294594 4415389 221 3197 HSF2BP 0 . GRCh38 21 43592323 43592323 + Missense_Mutation SNP A A T rs760990550 C3L-00094_T C3L-00094_N A A c.698T>A p.Met233Lys p.M233K ENST00000291560 8/9 101 89 12 118 118 0 strelka-varscan-mutect HSF2BP,missense_variant,p.Met233Lys,ENST00000291560,NM_007031.1; T ENST00000291560 Transcript missense_variant 1030/1899 698/1005 233/334 M/K aTg/aAg rs760990550 1 -1 HSF2BP HGNC HGNC:5226 protein_coding YES CCDS13697.1 ENSP00000291560 O75031 Q6IAT7 UPI000012C321 NM_007031.1 deleterious(0) 8/9 Gene3D:1.25.10.10,hmmpanther:PTHR15434,hmmpanther:PTHR15434:SF2,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs760990550 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 43592323 43592323 A T 1 0 0 0 0 1 0 0 0 7291 231 8 4 4 HSF2BP 21 43592323 Missense_Mutation SNP A C3L-00094_T 1297729 43592323 3117660 222 3198 CLTCL1 0 . GRCh38 22 19242796 19242796 + Silent SNP T T A novel C3L-00094_T C3L-00094_N T T c.660A>T p.= p.V220V ENST00000427926 4/33 188 146 42 145 145 0 strelka-varscan-mutect CLTCL1,synonymous_variant,p.=,ENST00000427926,NM_007098.3;CLTCL1,synonymous_variant,p.=,ENST00000621271,NM_001835.3;CLTCL1,synonymous_variant,p.=,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;AC000081.2,upstream_gene_variant,,ENST00000433141,; A ENST00000427926 Transcript synonymous_variant 733/5513 660/4923 220/1640 V gtA/gtT 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 4/33 hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Pfam_domain:PF01394,PIRSF_domain:PIRSF002290,Gene3D:3gc3B00,Superfamily_domains:0046096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 19242796 19242796 T A 1 0 0 0 0 0 0 0 1 3339 1625 57 4 4 CLTCL1 22 19242796 Silent SNP T C3L-00094_T 19242796 31575672 223 3199 MYO18B 0 . GRCh38 22 25777646 25777646 + Missense_Mutation SNP T T C novel C3L-00094_T C3L-00094_N T T c.1933T>C p.Trp645Arg p.W645R ENST00000335473 8/44 78 69 9 51 51 0 strelka-varscan-mutect MYO18B,missense_variant,p.Trp645Arg,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Trp645Arg,ENST00000407587,;MYO18B,missense_variant,p.Trp645Arg,ENST00000536101,;MYO18B,missense_variant,p.Trp645Arg,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; C ENST00000335473 Transcript missense_variant 2183/8565 1933/7704 645/2567 W/R Tgg/Cgg 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated(1) 8/44 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs752540028 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 25777646 25777646 T C 1 0 0 0 0 1 0 0 0 10067 1580 55 5 5 MYO18B 22 25777646 Missense_Mutation SNP T C3L-00094_T 6534850 25777646 25040822 224 3200 CRYBA4 0 . GRCh38 22 26622603 26622603 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.7C>A p.Leu3Met p.L3M ENST00000354760 2/6 345 203 142 244 243 1 strelka-varscan-mutect CRYBA4,missense_variant,p.Leu3Met,ENST00000354760,NM_001886.2;CRYBB1,upstream_gene_variant,,ENST00000215939,NM_001887.3;CRYBA4,non_coding_transcript_exon_variant,,ENST00000466315,; A ENST00000354760 Transcript missense_variant 42/811 7/591 3/196 L/M Ctg/Atg 1 1 CRYBA4 HGNC HGNC:2396 protein_coding YES CCDS13841.1 ENSP00000346805 P53673 A0A097PIJ6 UPI0000167B21 NM_001886.2 tolerated(0.22) 2/6 hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 26622603 26622603 C A 1 0 0 0 0 1 0 0 0 3711 680 24 2 2 CRYBA4 22 26622603 Missense_Mutation SNP C C3L-00094_T 844957 26622603 24195865 225 3201 SSTR3 0 . GRCh38 22 37206638 37206638 + Missense_Mutation SNP G G C rs753297506 C3L-00094_T C3L-00094_N G G c.1166C>G p.Pro389Arg p.P389R ENST00000610913 2/2 182 168 14 173 173 0 strelka-varscan-mutect SSTR3,missense_variant,p.Pro389Arg,ENST00000610913,NM_001051.4;SSTR3,missense_variant,p.Pro389Arg,ENST00000617123,NM_001278687.2; C ENST00000610913 Transcript missense_variant 1700/4100 1166/1257 389/418 P/R cCc/cGc rs753297506 1 -1 SSTR3 HGNC HGNC:11332 protein_coding YES CCDS13944.1 ENSP00000480971 P32745 UPI0000050435 NM_001051.4 tolerated_low_confidence(0.2) 2/2 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF42 MODERATE 1 SNV 1 1 PASS rs753297506 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 9 37206638 37206638 G C 1 0 0 0 0 1 0 0 0 15576 1232 43 4 4 SSTR3 22 37206638 Missense_Mutation SNP G C3L-00094_T 10584035 37206638 13611830 226 3202 P2RY8 0 . GRCh38 X 1466258 1466258 + Missense_Mutation SNP C C A rs750116034 C3L-00094_T C3L-00094_N C C c.301G>T p.Val101Leu p.V101L ENST00000381297 2/2 430 268 162 426 426 0 strelka-varscan-mutect P2RY8,missense_variant,p.Val101Leu,ENST00000381297,NM_178129.4;P2RY8,downstream_gene_variant,,ENST00000460672,; A ENST00000381297 Transcript missense_variant 512/4198 301/1080 101/359 V/L Gtg/Ttg rs750116034 1 -1 P2RY8 HGNC HGNC:15524 protein_coding YES CCDS14115.1 ENSP00000370697 Q86VZ1 UPI000000DA6D NM_178129.4 tolerated(0.47) 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF25,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01157 MODERATE 1 SNV 1 1 PASS rs750116034 . 0 208 0 0 2 0 0 0 -20 0.9994116 1 1 1 0 A 3 1 9 1466258 1466258 C A 1 0 0 0 0 1 0 0 0 11428 536 19 1 1 P2RY8 23 1466258 Missense_Mutation SNP C C3L-00094_T 1466258 154574637 227 3203 DMD 0 . GRCh38 X 32573625 32573625 + Missense_Mutation SNP C C A novel C3L-00094_T C3L-00094_N C C c.1717G>T p.Ala573Ser p.A573S ENST00000357033 15/79 227 118 109 229 228 1 strelka-varscan-mutect DMD,missense_variant,p.Ala573Ser,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Ala569Ser,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Ala573Ser,ENST00000620040,;DMD,missense_variant,p.Ala569Ser,ENST00000619831,;DMD,missense_variant,p.Ala565Ser,ENST00000288447,;DMD,missense_variant,p.Ala121Ser,ENST00000447523,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,non_coding_transcript_exon_variant,,ENST00000480751,;DMD,intron_variant,,ENST00000488902,; A ENST00000357033 Transcript missense_variant 1924/13956 1717/11058 573/3685 A/S Gca/Tca 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 tolerated(0.43) 15/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs1388666944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 9 32573625 32573625 C A 1 0 0 0 0 1 0 0 0 4387 710 25 2 2 DMD 23 32573625 Missense_Mutation SNP C C3L-00094_T 31107367 32573625 123467270 228 3204 FAM47B 0 . GRCh38 X 34943912 34943912 + Silent SNP C C A C3L-00094_T C3L-00094_N C C c.1081C>A p.= p.R361R ENST00000329357 1/1 133 51 82 108 108 0 strelka-varscan-mutect FAM47B,synonymous_variant,p.=,ENST00000329357,NM_152631.2; A ENST00000329357 Transcript synonymous_variant 1117/2120 1081/1938 361/645 R Cgg/Agg COSM1120794 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 1/1 Pfam_domain:PF14642 1 LOW 1 SNV 1 1 PASS rs1209259469 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 9 34943912 34943912 C A 1 0 0 0 0 0 0 0 1 5448 527 19 1 1 FAM47B 23 34943912 Silent SNP C C3L-00094_T 2370287 34943912 121096983 229 3205 UBA1 0 . GRCh38 X 47214335 47214335 + Missense_Mutation SNP C C G novel C3L-00094_T C3L-00094_N C C c.2847C>G p.Asn949Lys p.N949K ENST00000335972 24/26 243 212 31 189 189 0 strelka-varscan-mutect UBA1,missense_variant,p.Asn949Lys,ENST00000335972,NM_003334.3;UBA1,missense_variant,p.Asn949Lys,ENST00000377351,NM_153280.2;UBA1,missense_variant,p.Asn397Lys,ENST00000377269,;CDK16,upstream_gene_variant,,ENST00000457458,NM_033018.3;CDK16,upstream_gene_variant,,ENST00000357227,NM_006201.4;CDK16,upstream_gene_variant,,ENST00000622098,;CDK16,upstream_gene_variant,,ENST00000517426,;CDK16,upstream_gene_variant,,ENST00000519758,;CDK16,upstream_gene_variant,,ENST00000520893,;CDK16,upstream_gene_variant,,ENST00000522883,;CDK16,upstream_gene_variant,,ENST00000517997,;CDK16,upstream_gene_variant,,ENST00000517479,;CDK16,upstream_gene_variant,,ENST00000522234,;CDK16,upstream_gene_variant,,ENST00000520295,; G ENST00000335972 Transcript missense_variant 3030/3559 2847/3177 949/1058 N/K aaC/aaG 1 1 UBA1 HGNC HGNC:12469 protein_coding YES CCDS14275.1 ENSP00000338413 P22314 A0A024R1A3 UPI0000137946 NM_003334.3 tolerated(0.08) 24/26 hmmpanther:PTHR10953:SF144,hmmpanther:PTHR10953,TIGRFAM_domain:TIGR01408,SMART_domains:SM00985 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 9 47214335 47214335 C G 1 0 0 0 0 1 0 0 0 17346 506 18 4 4 UBA1 23 47214335 Missense_Mutation SNP C C3L-00094_T 12270423 47214335 108826560 230 3206 GDPD2 0 . GRCh38 X 70429496 70429496 + Nonsense_Mutation SNP C C T C3L-00094_T C3L-00094_N C C c.940C>T p.Arg314Ter p.R314* ENST00000453994 11/17 61 52 9 33 33 0 strelka-varscan-mutect GDPD2,stop_gained,p.Arg314Ter,ENST00000453994,NM_001171192.1;GDPD2,stop_gained,p.Arg235Ter,ENST00000536730,NM_001171193.1;GDPD2,stop_gained,p.Arg314Ter,ENST00000374382,NM_017711.3;GDPD2,stop_gained,p.Arg235Ter,ENST00000538649,NM_001171191.1;GDPD2,non_coding_transcript_exon_variant,,ENST00000472623,; T ENST00000453994 Transcript stop_gained 1301/2438 940/1773 314/590 R/* Cga/Tga COSM1124476,COSM1599671 1 1 GDPD2 HGNC HGNC:25974 protein_coding YES CCDS55437.1 ENSP00000414019 Q9HCC8 UPI00017A7EF7 NM_001171192.1 11/17 PROSITE_profiles:PS51704,hmmpanther:PTHR23344:SF1,hmmpanther:PTHR23344,Pfam_domain:PF03009,Gene3D:3.20.20.190,Superfamily_domains:SSF51695 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 203 7 0 0 0 0 0 -19.8723 0.9999996 1 1 1 0 T 4 4 9 70429496 70429496 C T 1 0 0 0 0 0 1 0 0 6197 782 27 1 1 GDPD2 23 70429496 Nonsense_Mutation SNP C C3L-00094_T 23215161 70429496 85611399 231 3207 MAGEE1 0 . GRCh38 X 76430755 76430755 + Missense_Mutation SNP A A T rs781799258 C3L-00094_T C3L-00094_N A A c.2825A>T p.Asn942Ile p.N942I ENST00000361470 1/1 61 26 35 52 52 0 strelka-varscan-mutect MAGEE1,missense_variant,p.Asn942Ile,ENST00000361470,NM_020932.2; T ENST00000361470 Transcript missense_variant 3032/3630 2825/2874 942/957 N/I aAt/aTt rs781799258 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 deleterious(0) 1/1 MODERATE 1 SNV 1 PASS rs781799258 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 9 76430755 76430755 A T 1 0 0 0 0 1 0 0 0 9103 101 4 4 4 MAGEE1 23 76430755 Missense_Mutation SNP A C3L-00094_T 6001259 76430755 79610140 232 3208 TRPC5 0 . GRCh38 X 111912678 111912678 + Silent SNP G G T novel C3L-00094_T C3L-00094_N G G c.513C>A p.= p.P171P ENST00000262839 3/11 162 73 89 116 116 0 strelka-varscan-mutect TRPC5,synonymous_variant,p.=,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript synonymous_variant 1432/5839 513/2922 171/973 P ccC/ccA 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 3/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,TIGRFAM_domain:TIGR00870 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 9 111912678 111912678 G T 1 0 0 0 0 0 0 0 1 17087 1219 43 2 2 TRPC5 23 111912678 Silent SNP G C3L-00094_T 35481923 111912678 44128217 233 3209 TTLL10 0 . GRCh38 1 1179242 1179242 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.27C>T p.= p.I9I ENST00000379290 4/16 85 75 10 122 122 0 strelka-varscan-mutect TTLL10,synonymous_variant,p.=,ENST00000379290,;TTLL10,synonymous_variant,p.=,ENST00000379289,NM_001130045.1;TTLL10,upstream_gene_variant,,ENST00000379288,NM_153254.2;TTLL10-AS1,intron_variant,,ENST00000379317,;TTLL10,downstream_gene_variant,,ENST00000506177,;TTLL10,upstream_gene_variant,,ENST00000460998,;TTLL10,upstream_gene_variant,,ENST00000514695,; T ENST00000379290 Transcript synonymous_variant 200/2283 27/2022 9/673 I atC/atT 1 1 TTLL10 HGNC HGNC:26693 protein_coding YES CCDS44036.1 ENSP00000368592 Q6ZVT0 UPI0000205ADB 4/16 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.98606 1 1 1 1 0 T 2 4 10 1179242 1179242 C T 1 0 0 0 0 0 0 0 1 17235 845 30 3 3 TTLL10 1 1179242 Silent SNP C C3L-00095_T 1179242 247777180 1 3210 FAM132A 0 . GRCh38 1 1244406 1244406 + Missense_Mutation SNP C C A rs576319696 C3L-00095_T C3L-00095_N C C c.269G>T p.Arg90Leu p.R90L ENST00000330388 2/8 151 142 9 220 220 0 strelka-varscan-mutect FAM132A,missense_variant,p.Arg90Leu,ENST00000330388,NM_001014980.2;FAM132A,non_coding_transcript_exon_variant,,ENST00000468365,;FAM132A,non_coding_transcript_exon_variant,,ENST00000486627,;FAM132A,upstream_gene_variant,,ENST00000462849,;FAM132A,upstream_gene_variant,,ENST00000478606,; A ENST00000330388 Transcript missense_variant 301/1036 269/909 90/302 R/L cGg/cTg rs576319696 1 -1 FAM132A HGNC HGNC:32308 protein_coding YES CCDS30554.1 ENSP00000329137 Q5T7M4 UPI00001D7E7A NM_001014980.2 deleterious(0) 2/8 hmmpanther:PTHR24019:SF12,hmmpanther:PTHR24019 MODERATE 1 SNV 1 1 PASS rs576319696 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 1244406 1244406 C A 1 0 0 0 0 1 0 0 0 5292 652 23 1 1 FAM132A 1 1244406 Missense_Mutation SNP C C3L-00095_T 65164 1244406 247712016 2 3211 ACOT7 0 . GRCh38 1 6264683 6264683 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1057G>T p.Asp353Tyr p.D353Y ENST00000377855 9/9 96 91 5 117 117 0 varscan-mutect ACOT7,missense_variant,p.Asp343Tyr,ENST00000361521,;ACOT7,missense_variant,p.Asp302Tyr,ENST00000377842,NM_181866.2;ACOT7,missense_variant,p.Asp343Tyr,ENST00000545482,NM_007274.3;ACOT7,missense_variant,p.Asp353Tyr,ENST00000377855,NM_181864.2;ACOT7,missense_variant,p.Asp323Tyr,ENST00000377845,NM_181865.2;ACOT7,missense_variant,p.Asp311Tyr,ENST00000608083,;GPR153,upstream_gene_variant,,ENST00000377893,NM_207370.2;ACOT7,3_prime_UTR_variant,,ENST00000418124,;ACOT7,3_prime_UTR_variant,,ENST00000377860,; A ENST00000377855 Transcript missense_variant 1204/1614 1057/1143 353/380 D/Y Gac/Tac 1 -1 ACOT7 HGNC HGNC:24157 protein_coding YES CCDS65.1 ENSP00000367086 O00154 UPI000012674F NM_181864.2 tolerated(0.08) 9/9 Gene3D:3.10.129.10,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF14,Superfamily_domains:SSF54637 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 6264683 6264683 C A 1 0 0 0 0 1 0 0 0 197 855 30 2 2 ACOT7 1 6264683 Missense_Mutation SNP C C3L-00095_T 5020277 6264683 242691739 3 3212 RERE 0 . GRCh38 1 8358427 8358427 + Missense_Mutation SNP C C A rs756183537 C3L-00095_T C3L-00095_N C C c.4108G>T p.Gly1370Cys p.G1370C ENST00000337907 21/24 95 88 7 133 133 0 strelka-mutect RERE,missense_variant,p.Gly1370Cys,ENST00000337907,NM_012102.3;RERE,missense_variant,p.Gly1102Cys,ENST00000377464,;RERE,missense_variant,p.Gly1370Cys,ENST00000400908,NM_001042681.1;RERE,missense_variant,p.Gly816Cys,ENST00000476556,NM_001042682.1;RERE,intron_variant,,ENST00000400907,;RERE,intron_variant,,ENST00000505225,;RERE,upstream_gene_variant,,ENST00000467350,; A ENST00000337907 Transcript missense_variant 4743/8026 4108/4701 1370/1566 G/C Ggc/Tgc rs756183537 1 -1 RERE HGNC HGNC:9965 protein_coding YES CCDS95.1 ENSP00000338629 Q9P2R6 A0A024R4E9 UPI00001419CC NM_012102.3 deleterious_low_confidence(0) 21/24 hmmpanther:PTHR13859,hmmpanther:PTHR13859:SF12,Pfam_domain:PF03154 MODERATE 1 SNV 1 1 PASS rs756183537 . 0 208 2 0 0 0 0 0 -14.93261 1 1 1 1 0 A 3 1 10 8358427 8358427 C A 1 0 0 0 0 1 0 0 0 13401 623 22 2 2 RERE 1 8358427 Missense_Mutation SNP C C3L-00095_T 2093744 8358427 240597995 4 3213 DISP3 0 . GRCh38 1 11501900 11501900 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.908G>T p.Arg303Leu p.R303L ENST00000294484 2/21 130 121 9 189 188 1 strelka-varscan-mutect DISP3,missense_variant,p.Arg303Leu,ENST00000294484,NM_020780.1; T ENST00000294484 Transcript missense_variant 1046/5215 908/4179 303/1392 R/L cGc/cTc 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 deleterious(0.01) 2/21 hmmpanther:PTHR10796:SF125,hmmpanther:PTHR10796 MODERATE 1 SNV 1 1 PASS rs1015515395 . 0 206 4 0 0 0 0 0 -17.30703 1 1 1 1 0 T 3 4 10 11501900 11501900 G T 1 0 0 0 0 1 0 0 0 4347 1087 38 1 1 DISP3 1 11501900 Missense_Mutation SNP G C3L-00095_T 3143473 11501900 237454522 5 3214 FBXO2 0 . GRCh38 1 11648729 11648729 + Missense_Mutation SNP G G A rs763877988 C3L-00095_T C3L-00095_N G G c.856C>T p.Arg286Trp p.R286W ENST00000354287 6/6 263 246 17 291 291 0 strelka-varscan-mutect FBXO2,missense_variant,p.Arg286Trp,ENST00000354287,NM_012168.5;FBXO2,downstream_gene_variant,,ENST00000465901,;FBXO2,downstream_gene_variant,,ENST00000475961,;FBXO2,downstream_gene_variant,,ENST00000466919,;FBXO2,downstream_gene_variant,,ENST00000471501,; A ENST00000354287 Transcript missense_variant 1198/1560 856/891 286/296 R/W Cgg/Tgg rs763877988 1 -1 FBXO2 HGNC HGNC:13581 protein_coding YES CCDS130.1 ENSP00000346240 Q9UK22 UPI00000711D1 NM_012168.5 deleterious(0) 6/6 PROSITE_profiles:PS51114,hmmpanther:PTHR12125:SF11,hmmpanther:PTHR12125,Gene3D:2.60.120.260,Pfam_domain:PF04300,SMART_domains:SM01198,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS rs763877988 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 11648729 11648729 G A 1 0 0 0 0 1 0 0 0 5595 1115 39 1 1 FBXO2 1 11648729 Missense_Mutation SNP G C3L-00095_T 146829 11648729 237307693 6 3215 UBR4 0 . GRCh38 1 19197748 19197748 + Missense_Mutation SNP C C A rs771173222 C3L-00095_T C3L-00095_N C C c.815G>T p.Arg272Leu p.R272L ENST00000375254 7/106 233 220 13 284 284 0 strelka-varscan-mutect UBR4,missense_variant,p.Arg272Leu,ENST00000375254,NM_020765.2; A ENST00000375254 Transcript missense_variant 843/15906 815/15552 272/5183 R/L cGg/cTg rs771173222 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 deleterious(0.01) 7/106 hmmpanther:PTHR21725 MODERATE 1 SNV 1 1 PASS rs771173222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 19197748 19197748 C A 1 0 0 0 0 1 0 0 0 17428 652 23 1 1 UBR4 1 19197748 Missense_Mutation SNP C C3L-00095_T 7549019 19197748 229758674 7 3216 ALPL 0 . GRCh38 1 21563171 21563171 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.359G>T p.Gly120Val p.G120V ENST00000374840 5/12 288 273 15 363 363 0 strelka-varscan-mutect ALPL,missense_variant,p.Gly120Val,ENST00000374840,NM_000478.4;ALPL,missense_variant,p.Gly43Val,ENST00000539907,NM_001177520.1;ALPL,missense_variant,p.Gly120Val,ENST00000374832,;ALPL,missense_variant,p.Gly65Val,ENST00000540617,NM_001127501.2;ALPL,non_coding_transcript_exon_variant,,ENST00000468526,; T ENST00000374840 Transcript missense_variant 609/2589 359/1575 120/524 G/V gGg/gTg 1 1 ALPL HGNC HGNC:438 protein_coding YES CCDS217.1 ENSP00000363973 P05186 A0A024RAG0 UPI000013E17C NM_000478.4 deleterious(0) 5/12 hmmpanther:PTHR11596:SF49,hmmpanther:PTHR11596,Pfam_domain:PF00245,Gene3D:3.40.720.10,SMART_domains:SM00098,Superfamily_domains:SSF53649,Prints_domain:PR00113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 21563171 21563171 G T 1 0 0 0 0 1 0 0 0 647 1232 43 2 2 ALPL 1 21563171 Missense_Mutation SNP G C3L-00095_T 2365423 21563171 227393251 8 3217 C1orf234 0 . GRCh38 1 23010981 23010981 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.286C>T p.Pro96Ser p.P96S ENST00000566855 3/3 169 159 10 199 199 0 strelka-varscan-mutect C1orf234,missense_variant,p.Pro96Ser,ENST00000566855,NM_001242521.1;C1orf234,missense_variant,p.Pro122Ser,ENST00000440767,;C1orf234,missense_variant,p.Pro96Ser,ENST00000622840,; A ENST00000566855 Transcript missense_variant 363/510 286/366 96/121 P/S Ccc/Tcc 1 -1 C1orf234 HGNC HGNC:44651 protein_coding YES CCDS57978.1 ENSP00000457161 H3BTG2 UPI0000204668 NM_001242521.1 tolerated_low_confidence(0.63) 3/3 hmmpanther:PTHR39412,hmmpanther:PTHR39412:SF1 MODERATE 1 SNV 2 1 PASS . . 0 195 6 9 0 0 0 0 -12.51922 0.7752746 1 1 1 0 A 3 1 10 23010981 23010981 G A 1 0 0 0 0 1 0 0 0 1986 1174 41 3 3 C1orf234 1 23010981 Missense_Mutation SNP G C3L-00095_T 1447810 23010981 225945441 9 3218 HNRNPR 0 . GRCh38 1 23310573 23310573 + Missense_Mutation SNP C C A rs752978432 C3L-00095_T C3L-00095_N C C c.1792G>T p.Gly598Cys p.G598C ENST00000374616 11/11 220 203 17 305 303 2 strelka-varscan-mutect HNRNPR,missense_variant,p.Gly497Cys,ENST00000478691,NM_001102399.2,NM_001297621.1,NM_001102397.2;HNRNPR,missense_variant,p.Gly595Cys,ENST00000374612,NM_005826.4;HNRNPR,missense_variant,p.Gly598Cys,ENST00000374616,NM_001102398.2;HNRNPR,missense_variant,p.Gly595Cys,ENST00000302271,;HNRNPR,missense_variant,p.Gly456Cys,ENST00000606561,NM_001297622.1;HNRNPR,missense_variant,p.Gly557Cys,ENST00000427764,NM_001297620.1;HNRNPR,non_coding_transcript_exon_variant,,ENST00000476660,;HNRNPR,downstream_gene_variant,,ENST00000463552,;HNRNPR,downstream_gene_variant,,ENST00000470941,;HNRNPR,upstream_gene_variant,,ENST00000464516,; A ENST00000374616 Transcript missense_variant 1901/2691 1792/1911 598/636 G/C Ggt/Tgt rs752978432 1 -1 HNRNPR HGNC HGNC:5047 protein_coding YES CCDS44085.1 ENSP00000363745 O43390 UPI000006F30B NM_001102398.2 deleterious_low_confidence(0) 11/11 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF482,TIGRFAM_domain:TIGR01648 MODERATE 1 SNV 1 1 PASS rs752978432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 23310573 23310573 C A 1 0 0 0 0 1 0 0 0 7167 623 22 2 2 HNRNPR 1 23310573 Missense_Mutation SNP C C3L-00095_T 299592 23310573 225645849 10 3219 IL22RA1 0 . GRCh38 1 24121390 24121390 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1140G>T p.Gln380His p.Q380H ENST00000270800 7/7 31 23 8 36 36 0 strelka-varscan-mutect IL22RA1,missense_variant,p.Gln380His,ENST00000270800,NM_021258.3; A ENST00000270800 Transcript missense_variant 1179/2798 1140/1725 380/574 Q/H caG/caT 1 -1 IL22RA1 HGNC HGNC:13700 protein_coding YES CCDS247.1 ENSP00000270800 Q8N6P7 UPI0000071143 NM_021258.3 deleterious(0) 7/7 hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF20 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.97785 1 1 1 1 0 A 3 1 10 24121390 24121390 C A 1 0 0 0 0 1 0 0 0 7576 680 24 2 2 IL22RA1 1 24121390 Missense_Mutation SNP C C3L-00095_T 810817 24121390 224835032 11 3220 EXTL1 0 . GRCh38 1 26029240 26029240 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.827C>A p.Ser276Tyr p.S276Y ENST00000374280 2/11 118 112 6 153 153 0 strelka-varscan-mutect EXTL1,missense_variant,p.Ser276Tyr,ENST00000374280,NM_004455.2;EXTL1,non_coding_transcript_exon_variant,,ENST00000484339,;EXTL1,non_coding_transcript_exon_variant,,ENST00000481377,;EXTL1,upstream_gene_variant,,ENST00000470037,; A ENST00000374280 Transcript missense_variant 1694/4015 827/2031 276/676 S/Y tCt/tAt COSM1748305 1 1 EXTL1 HGNC HGNC:3515 protein_coding YES CCDS271.1 ENSP00000363398 Q92935 UPI000013DF48 NM_004455.2 deleterious(0) 2/11 hmmpanther:PTHR11062:SF8,hmmpanther:PTHR11062,Pfam_domain:PF03016 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 26029240 26029240 C A 1 0 0 0 0 1 0 0 0 5193 913 32 2 2 EXTL1 1 26029240 Missense_Mutation SNP C C3L-00095_T 1907850 26029240 222927182 12 3221 AIM1L 0 . GRCh38 1 26344557 26344557 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2101G>T p.Asp701Tyr p.D701Y ENST00000308182 2/20 109 91 18 188 188 0 strelka-varscan-mutect AIM1L,missense_variant,p.Asp701Tyr,ENST00000308182,NM_001039775.3;AIM1L,upstream_gene_variant,,ENST00000527815,;AIM1L,downstream_gene_variant,,ENST00000475866,;AIM1L,intron_variant,,ENST00000374207,; A ENST00000308182 Transcript missense_variant 2251/5245 2101/4986 701/1661 D/Y Gac/Tac 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 deleterious_low_confidence(0.01) 2/20 hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF50 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 26344557 26344557 C A 1 0 0 0 0 1 0 0 0 508 855 30 2 2 AIM1L 1 26344557 Missense_Mutation SNP C C3L-00095_T 315317 26344557 222611865 13 3222 COL16A1 0 . GRCh38 1 31655397 31655397 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.4207C>T p.Pro1403Ser p.P1403S ENST00000373672 67/71 250 228 22 304 304 0 strelka-varscan-mutect COL16A1,missense_variant,p.Pro1403Ser,ENST00000373672,NM_001856.3;COL16A1,downstream_gene_variant,,ENST00000440437,;RP11-73M7.6,intron_variant,,ENST00000610043,;RP11-73M7.6,intron_variant,,ENST00000591929,;RP11-73M7.6,intron_variant,,ENST00000585413,;RP11-73M7.6,intron_variant,,ENST00000609549,;RP11-73M7.6,intron_variant,,ENST00000609033,;RP11-73M7.6,intron_variant,,ENST00000589462,;RP11-73M7.6,intron_variant,,ENST00000609625,;RP11-73M7.6,intron_variant,,ENST00000607926,;RP11-73M7.6,intron_variant,,ENST00000587445,;RP11-73M7.6,intron_variant,,ENST00000585660,;RP11-73M7.6,intron_variant,,ENST00000610216,;RP11-73M7.6,intron_variant,,ENST00000623791,;RP11-73M7.6,intron_variant,,ENST00000609373,;RP11-73M7.6,intron_variant,,ENST00000608246,;RP11-73M7.6,intron_variant,,ENST00000593188,;RP11-73M7.6,intron_variant,,ENST00000623425,;RP11-73M7.6,intron_variant,,ENST00000608888,;RP11-73M7.6,intron_variant,,ENST00000624388,;RP11-73M7.6,intron_variant,,ENST00000608332,;RP11-73M7.6,intron_variant,,ENST00000591592,;RP11-73M7.6,intron_variant,,ENST00000609338,;RP11-73M7.6,upstream_gene_variant,,ENST00000623786,;RP11-73M7.6,upstream_gene_variant,,ENST00000588288,;RP11-73M7.6,upstream_gene_variant,,ENST00000445166,;COL16A1,non_coding_transcript_exon_variant,,ENST00000461217,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488128,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488897,; A ENST00000373672 Transcript missense_variant 4724/5736 4207/4815 1403/1604 P/S Ccg/Tcg 1 -1 COL16A1 HGNC HGNC:2193 protein_coding YES CCDS41297.1 ENSP00000362776 Q07092 UPI0000203DD1 NM_001856.3 tolerated(0.57) 67/71 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 31655397 31655397 G A 1 0 0 0 0 1 0 0 0 3461 1261 44 3 3 COL16A1 1 31655397 Missense_Mutation SNP G C3L-00095_T 5310840 31655397 217301025 14 3223 KHDRBS1 0 . GRCh38 1 32037929 32037929 + Frame_Shift_Del DEL C C - novel C3L-00095_T C3L-00095_N C C c.1001delC p.Pro334HisfsTer6 p.P334Hfs*6 ENST00000327300 6/9 320 304 16 348 348 0 varindel-pindel KHDRBS1,frameshift_variant,p.Pro334HisfsTer6,ENST00000327300,NM_006559.2;KHDRBS1,frameshift_variant,p.Pro295HisfsTer6,ENST00000492989,NM_001271878.1;KHDRBS1,non_coding_transcript_exon_variant,,ENST00000307714,;KHDRBS1,non_coding_transcript_exon_variant,,ENST00000484270,; - ENST00000327300 Transcript frameshift_variant 1167/2757 1000/1332 334/443 P/X Cca/ca 1 1 KHDRBS1 HGNC HGNC:18116 protein_coding YES CCDS350.1 ENSP00000313829 Q07666 UPI0000073DA7 NM_006559.2 6/9 hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF30,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 32037929 32037929 C - 1 0 1 0 1 0 0 0 0 8067 739 26 0 0 KHDRBS1 1 32037929 Frame_Shift_Del DEL C C3L-00095_T 382532 32037929 216918493 15 3224 TMEM39B 0 . GRCh38 1 32076818 32076818 + Missense_Mutation SNP G G T rs756802102 C3L-00095_T C3L-00095_N G G c.407G>T p.Arg136Leu p.R136L ENST00000336294 4/9 336 312 24 382 381 1 strelka-varscan-mutect TMEM39B,missense_variant,p.Arg136Leu,ENST00000336294,NM_018056.2;TMEM39B,intron_variant,,ENST00000438825,;RP11-277A4.4,upstream_gene_variant,,ENST00000366152,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000487305,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000476968,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000468135,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000472503,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000498613,;TMEM39B,non_coding_transcript_exon_variant,,ENST00000466321,;TMEM39B,intron_variant,,ENST00000441402,NM_001319678.1,NM_001319679.1; T ENST00000336294 Transcript missense_variant 553/1813 407/1479 136/492 R/L cGc/cTc rs756802102 1 1 TMEM39B HGNC HGNC:25510 protein_coding YES CCDS351.2 ENSP00000338165 Q9GZU3 UPI0000037B9F NM_018056.2 deleterious(0) 4/9 Pfam_domain:PF10271,hmmpanther:PTHR12995,hmmpanther:PTHR12995:SF2,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs756802102 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32076818 32076818 G T 1 0 0 0 0 1 0 0 0 16639 1087 38 1 1 TMEM39B 1 32076818 Missense_Mutation SNP G C3L-00095_T 38889 32076818 216879604 16 3225 KPNA6 0 . GRCh38 1 32157365 32157365 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.251A>T p.Glu84Val p.E84V ENST00000373625 4/14 125 112 13 129 129 0 strelka-mutect KPNA6,missense_variant,p.Glu84Val,ENST00000373625,NM_012316.4;KPNA6,missense_variant,p.Glu35Val,ENST00000446515,;KPNA6,non_coding_transcript_exon_variant,,ENST00000469790,;KPNA6,missense_variant,p.Glu78Val,ENST00000471599,; T ENST00000373625 Transcript missense_variant 344/7378 251/1611 84/536 E/V gAg/gTg 1 1 KPNA6 HGNC HGNC:6399 protein_coding YES CCDS352.1 ENSP00000362728 O60684 UPI000006D3B6 NM_012316.4 deleterious(0.02) 4/14 hmmpanther:PTHR23316:SF8,hmmpanther:PTHR23316,PIRSF_domain:PIRSF005673,Gene3D:1.25.10.10,Pfam_domain:PF01749,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32157365 32157365 A T 1 0 0 0 0 1 0 0 0 8314 304 11 4 4 KPNA6 1 32157365 Missense_Mutation SNP A C3L-00095_T 80547 32157365 216799057 17 3226 CSMD2 0 . GRCh38 1 33541206 33541206 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.9381G>T p.Met3127Ile p.M3127I ENST00000373381 59/71 254 235 19 301 300 1 strelka-varscan-mutect CSMD2,missense_variant,p.Met3127Ile,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Met3087Ile,ENST00000619121,;CSMD2,missense_variant,p.Met2983Ile,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Met2983Ile,ENST00000241312,; A ENST00000373381 Transcript missense_variant 9558/13698 9381/10896 3127/3631 M/I atG/atT 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 tolerated(0.3) 59/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF371,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 33541206 33541206 C A 1 0 0 0 0 1 0 0 0 3746 826 29 2 2 CSMD2 1 33541206 Missense_Mutation SNP C C3L-00095_T 1383841 33541206 215415216 18 3227 C1orf94 0 . GRCh38 1 34202195 34202195 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1382G>T p.Trp461Leu p.W461L ENST00000488417 4/7 152 140 12 238 238 0 strelka-varscan-mutect C1orf94,missense_variant,p.Trp461Leu,ENST00000488417,NM_001134734.1;C1orf94,missense_variant,p.Trp271Leu,ENST00000373374,NM_032884.4; T ENST00000488417 Transcript missense_variant 1502/2287 1382/1797 461/598 W/L tGg/tTg 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 tolerated(0.09) 4/7 Low_complexity_(Seg):seg,hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1,Pfam_domain:PF15752 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 34202195 34202195 G T 1 0 0 0 0 1 0 0 0 2000 1357 47 2 2 C1orf94 1 34202195 Missense_Mutation SNP G C3L-00095_T 660989 34202195 214754227 19 3228 CLSPN 0 . GRCh38 1 35749779 35749779 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.2061A>G p.Ile687Met p.I687M ENST00000318121 11/25 88 79 9 97 97 0 varscan-mutect CLSPN,missense_variant,p.Ile687Met,ENST00000251195,;CLSPN,missense_variant,p.Ile687Met,ENST00000318121,NM_022111.3;CLSPN,missense_variant,p.Ile623Met,ENST00000373220,NM_001190481.1;CLSPN,intron_variant,,ENST00000520551,;CLSPN,upstream_gene_variant,,ENST00000517467,; C ENST00000318121 Transcript missense_variant 2119/4169 2061/4020 687/1339 I/M atA/atG 1 -1 CLSPN HGNC HGNC:19715 protein_coding YES CCDS396.1 ENSP00000312995 Q9HAW4 UPI0000161087 NM_022111.3 tolerated(0.08) 11/25 hmmpanther:PTHR14396:SF10,hmmpanther:PTHR14396 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 35749779 35749779 T C 1 0 0 0 0 1 0 0 0 3332 1512 53 5 5 CLSPN 1 35749779 Missense_Mutation SNP T C3L-00095_T 1547584 35749779 213206643 20 3229 GRIK3 0 . GRCh38 1 36825804 36825804 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1553C>A p.Pro518His p.P518H ENST00000373091 11/16 60 50 10 54 53 1 strelka-varscan-mutect GRIK3,missense_variant,p.Pro518His,ENST00000373091,NM_000831.3;GRIK3,missense_variant,p.Pro518His,ENST00000373093,; T ENST00000373091 Transcript missense_variant 1570/9101 1553/2760 518/919 P/H cCc/cAc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 deleterious(0) 11/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.9995 1 1 1 1 0 T 3 4 10 36825804 36825804 G T 1 0 0 0 0 1 0 0 0 6657 1232 43 2 2 GRIK3 1 36825804 Missense_Mutation SNP G C3L-00095_T 1076025 36825804 212130618 21 3230 KCNQ4 0 . GRCh38 1 40831299 40831299 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1508C>T p.Ala503Val p.A503V ENST00000347132 10/14 137 129 8 157 157 0 strelka-mutect KCNQ4,missense_variant,p.Ala503Val,ENST00000347132,NM_004700.3;KCNQ4,missense_variant,p.Ala364Val,ENST00000443478,;KCNQ4,missense_variant,p.Ala449Val,ENST00000509682,NM_172163.2;KCNQ4,non_coding_transcript_exon_variant,,ENST00000506017,; T ENST00000347132 Transcript missense_variant 1590/4099 1508/2088 503/695 A/V gCt/gTt 1 1 KCNQ4 HGNC HGNC:6298 protein_coding YES CCDS456.1 ENSP00000262916 P56696 UPI000013D35B NM_004700.3 tolerated(0.32) 10/14 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF4,Pfam_domain:PF03520 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 40831299 40831299 C T 1 0 0 0 0 1 0 0 0 8001 811 28 3 3 KCNQ4 1 40831299 Missense_Mutation SNP C C3L-00095_T 4005495 40831299 208125123 22 3231 SCMH1 0 . GRCh38 1 41143024 41143024 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.236C>A p.Thr79Lys p.T79K ENST00000326197 5/15 241 222 19 332 332 0 strelka-varscan-mutect SCMH1,missense_variant,p.Thr18Lys,ENST00000372596,NM_001172220.1,NM_001172218.1;SCMH1,missense_variant,p.Thr79Lys,ENST00000326197,NM_001031694.2;SCMH1,missense_variant,p.Thr32Lys,ENST00000372597,NM_012236.3;SCMH1,missense_variant,p.Thr18Lys,ENST00000372595,NM_001172221.1;SCMH1,missense_variant,p.Thr18Lys,ENST00000402904,;SCMH1,missense_variant,p.Thr18Lys,ENST00000397171,;SCMH1,missense_variant,p.Thr32Lys,ENST00000361705,;SCMH1,missense_variant,p.Thr89Lys,ENST00000337495,NM_001172219.1;SCMH1,missense_variant,p.Thr79Lys,ENST00000397174,;SCMH1,missense_variant,p.Thr18Lys,ENST00000361191,;SCMH1,missense_variant,p.Thr32Lys,ENST00000456518,NM_001172222.1; T ENST00000326197 Transcript missense_variant 536/3275 236/1983 79/660 T/K aCa/aAa 1 -1 SCMH1 HGNC HGNC:19003 protein_coding YES CCDS30688.1 ENSP00000318094 Q96GD3 UPI000006FD9B NM_001031694.2 deleterious(0) 5/15 PROSITE_profiles:PS51079,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF68,Gene3D:2.30.30.160,Pfam_domain:PF02820,SMART_domains:SM00561,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 41143024 41143024 G T 1 0 0 0 0 1 0 0 0 14177 1377 48 2 2 SCMH1 1 41143024 Missense_Mutation SNP G C3L-00095_T 311725 41143024 207813398 23 3232 P3H1 0 . GRCh38 1 42766636 42766636 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.336C>T p.= p.G112G ENST00000236040 1/14 169 150 19 207 207 0 strelka-varscan-mutect P3H1,synonymous_variant,p.=,ENST00000236040,NM_001243246.1;P3H1,synonymous_variant,p.=,ENST00000397054,NM_001146289.1;P3H1,synonymous_variant,p.=,ENST00000296388,NM_022356.3;P3H1,synonymous_variant,p.=,ENST00000372526,;C1orf50,upstream_gene_variant,,ENST00000372525,NM_024097.3;C1orf50,upstream_gene_variant,,ENST00000468913,;P3H1,non_coding_transcript_exon_variant,,ENST00000492956,;P3H1,non_coding_transcript_exon_variant,,ENST00000495874,;P3H1,non_coding_transcript_exon_variant,,ENST00000460031,;RP5-994D16.12,upstream_gene_variant,,ENST00000603943,;P3H1,upstream_gene_variant,,ENST00000463465,;RP5-994D16.12,upstream_gene_variant,,ENST00000464081,; A ENST00000236040 Transcript synonymous_variant 377/2993 336/2415 112/804 G ggC/ggT 1 -1 P3H1 HGNC HGNC:19316 protein_coding YES CCDS57986.1 ENSP00000236040 Q32P28 UPI000013E32E NM_001243246.1 1/14 hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF5,Low_complexity_(Seg):seg LOW SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 42766636 42766636 G A 1 0 0 0 0 0 0 0 1 11429 1190 42 3 3 P3H1 1 42766636 Silent SNP G C3L-00095_T 1623612 42766636 206189786 24 3233 IPO13 0 . GRCh38 1 43967619 43967619 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2829G>T p.Met943Ile p.M943I ENST00000372343 20/20 268 252 16 364 364 0 strelka-varscan-mutect IPO13,missense_variant,p.Met943Ile,ENST00000372343,NM_014652.3;IPO13,missense_variant,p.Met161Ile,ENST00000372339,;DPH2,upstream_gene_variant,,ENST00000255108,NM_001319165.1,NM_001384.4;DPH2,upstream_gene_variant,,ENST00000396758,NM_001039589.1;DPH2,upstream_gene_variant,,ENST00000459879,;IPO13,non_coding_transcript_exon_variant,,ENST00000486876,;DPH2,upstream_gene_variant,,ENST00000529729,;DPH2,upstream_gene_variant,,ENST00000477294,;DPH2,upstream_gene_variant,,ENST00000471934,;DPH2,upstream_gene_variant,,ENST00000495421,NM_001319168.1;DPH2,upstream_gene_variant,,ENST00000524776,;DPH2,upstream_gene_variant,,ENST00000490861,;DPH2,upstream_gene_variant,,ENST00000476260,;DPH2,upstream_gene_variant,,ENST00000492306,;DPH2,upstream_gene_variant,,ENST00000527567,;DPH2,upstream_gene_variant,,ENST00000534786,;DPH2,upstream_gene_variant,,ENST00000527319,;DPH2,upstream_gene_variant,,ENST00000530988,;DPH2,upstream_gene_variant,,ENST00000534655,;DPH2,upstream_gene_variant,,ENST00000532140,; T ENST00000372343 Transcript missense_variant 3491/3894 2829/2892 943/963 M/I atG/atT 1 1 IPO13 HGNC HGNC:16853 protein_coding YES CCDS503.1 ENSP00000361418 O94829 UPI0000073F11 NM_014652.3 tolerated(0.78) 20/20 hmmpanther:PTHR12363:SF29,hmmpanther:PTHR12363 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 43967619 43967619 G T 1 0 0 0 0 1 0 0 0 7697 1348 47 2 2 IPO13 1 43967619 Missense_Mutation SNP G C3L-00095_T 1200983 43967619 204988803 25 3234 STIL 0 . GRCh38 1 47301589 47301589 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.425G>A p.Ser142Asn p.S142N ENST00000371877 5/17 355 332 23 282 282 0 strelka-varscan-mutect STIL,missense_variant,p.Ser142Asn,ENST00000360380,NM_001282936.1,NM_003035.2;STIL,missense_variant,p.Ser142Asn,ENST00000337817,NM_001282939.1,NM_001282938.1;STIL,missense_variant,p.Ser142Asn,ENST00000371877,NM_001048166.1;STIL,missense_variant,p.Ser142Asn,ENST00000396221,NM_001282937.1;STIL,missense_variant,p.Ser142Asn,ENST00000447475,;STIL,downstream_gene_variant,,ENST00000413565,;STIL,non_coding_transcript_exon_variant,,ENST00000433827,; T ENST00000371877 Transcript missense_variant 573/5009 425/3867 142/1288 S/N aGt/aAt 1 -1 STIL HGNC HGNC:10879 protein_coding YES CCDS41329.1 ENSP00000360944 Q15468 UPI00002042D5 NM_001048166.1 tolerated(0.72) 5/17 Pfam_domain:PF15253,hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 47301589 47301589 C T 1 0 0 0 0 1 0 0 0 15659 565 20 3 3 STIL 1 47301589 Missense_Mutation SNP C C3L-00095_T 3333970 47301589 201654833 26 3235 TRABD2B 0 . GRCh38 1 47765961 47765961 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1495C>A p.Pro499Thr p.P499T ENST00000606738 7/7 122 110 12 185 185 0 strelka-varscan-mutect TRABD2B,missense_variant,p.Pro499Thr,ENST00000606738,NM_001194986.1;RP11-543D5.2,upstream_gene_variant,,ENST00000438589,; T ENST00000606738 Transcript missense_variant 1601/7034 1495/1554 499/517 P/T Ccc/Acc 1 -1 TRABD2B HGNC HGNC:44200 protein_coding YES CCDS58000.1 ENSP00000476820 A6NFA1 UPI00017BE8EF NM_001194986.1 tolerated_low_confidence(0.25) 7/7 hmmpanther:PTHR31120:SF8,hmmpanther:PTHR31120 MODERATE 1 SNV 1 1 PASS rs1191453504 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 47765961 47765961 G T 1 0 0 0 0 1 0 0 0 16918 1232 43 2 2 TRABD2B 1 47765961 Missense_Mutation SNP G C3L-00095_T 464372 47765961 201190461 27 3236 CDCP2 0 . GRCh38 1 54139788 54139788 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1082C>A p.Thr361Asn p.T361N ENST00000371330 4/4 242 213 29 376 375 1 strelka-varscan-mutect CDCP2,missense_variant,p.Thr361Asn,ENST00000371330,NM_201546.3;CDCP2,missense_variant,p.Thr361Asn,ENST00000530059,;RP11-446E24.3,non_coding_transcript_exon_variant,,ENST00000623663,;RP11-446E24.4,downstream_gene_variant,,ENST00000525949,;RP11-446E24.4,3_prime_UTR_variant,,ENST00000637610,;RP11-446E24.4,downstream_gene_variant,,ENST00000311841,; T ENST00000371330 Transcript missense_variant 1930/2723 1082/1350 361/449 T/N aCc/aAc 1 -1 CDCP2 HGNC HGNC:27297 protein_coding YES CCDS588.2 ENSP00000360381 Q5VXM1 UPI0000458963 NM_201546.3 deleterious(0.02) 4/4 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF41,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 2 1 PASS rs1170920516 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 54139788 54139788 G T 1 0 0 0 0 1 0 0 0 2797 1261 44 2 2 CDCP2 1 54139788 Missense_Mutation SNP G C3L-00095_T 6373827 54139788 194816634 28 3237 ANGPTL3 0 . GRCh38 1 62597654 62597654 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.88T>G p.Ser30Ala p.S30A ENST00000371129 1/7 192 174 18 169 169 0 strelka-varscan-mutect ANGPTL3,missense_variant,p.Ser30Ala,ENST00000371129,NM_014495.3;DOCK7,intron_variant,,ENST00000251157,;DOCK7,intron_variant,,ENST00000454575,NM_001271999.1;DOCK7,intron_variant,,ENST00000340370,NM_033407.3;DOCK7,intron_variant,,ENST00000635253,;DOCK7,intron_variant,,ENST00000634264,NM_001272000.1;DOCK7,intron_variant,,ENST00000635123,NM_001272001.1;DOCK7,intron_variant,,ENST00000404627,NM_001272002.1;DOCK7,intron_variant,,ENST00000637227,;ANGPTL3,upstream_gene_variant,,ENST00000493994,;ANGPTL3,upstream_gene_variant,,ENST00000482591,;DOCK7,intron_variant,,ENST00000637208,;DOCK7,intron_variant,,ENST00000614472,;DOCK7,intron_variant,,ENST00000634223,; G ENST00000371129 Transcript missense_variant 168/2805 88/1383 30/460 S/A Tct/Gct 1 1 ANGPTL3 HGNC HGNC:491 protein_coding YES CCDS622.1 ENSP00000360170 Q9Y5C1 UPI000003722C NM_014495.3 tolerated(0.31) 1/7 hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF222 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 62597654 62597654 T G 1 0 0 0 0 1 0 0 0 713 1435 50 5 5 ANGPTL3 1 62597654 Missense_Mutation SNP T C3L-00095_T 8457866 62597654 186358768 29 3238 LEPR 0 . GRCh38 1 65636552 65636552 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.3035G>A p.Cys1012Tyr p.C1012Y ENST00000349533 20/20 223 205 18 216 216 0 strelka-varscan-mutect LEPR,missense_variant,p.Cys1012Tyr,ENST00000349533,NM_002303.5;LEPR,missense_variant,p.Cys79Tyr,ENST00000406510,;LEPR,downstream_gene_variant,,ENST00000371060,NM_001003679.3;LEPR,downstream_gene_variant,,ENST00000616738,NM_001198689.1; A ENST00000349533 Transcript missense_variant 3220/8227 3035/3498 1012/1165 C/Y tGc/tAc 1 1 LEPR HGNC HGNC:6554 protein_coding YES CCDS631.1 ENSP00000330393 P48357 UPI000014C37B NM_002303.5 deleterious(0.05) 20/20 hmmpanther:PTHR23036:SF109,hmmpanther:PTHR23036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 65636552 65636552 G A 1 0 0 0 0 1 0 0 0 8636 1319 46 3 3 LEPR 1 65636552 Missense_Mutation SNP G C3L-00095_T 3038898 65636552 183319870 30 3239 PDE4B 0 . GRCh38 1 66257830 66257830 + Missense_Mutation SNP C C A rs773736586 C3L-00095_T C3L-00095_N C C c.551C>A p.Thr184Asn p.T184N ENST00000329654 6/17 263 244 19 227 227 0 strelka-varscan-mutect PDE4B,missense_variant,p.Thr169Asn,ENST00000423207,NM_001037340.2;PDE4B,missense_variant,p.Thr184Asn,ENST00000329654,NM_001297440.1,NM_001037341.1,NM_001297441.1;PDE4B,missense_variant,p.Thr184Asn,ENST00000341517,NM_002600.3;PDE4B,missense_variant,p.Thr92Asn,ENST00000412480,;PDE4B,missense_variant,p.Thr26Asn,ENST00000491340,;PDE4B,non_coding_transcript_exon_variant,,ENST00000371048,;PDE4B,non_coding_transcript_exon_variant,,ENST00000490695,; A ENST00000329654 Transcript missense_variant 738/3998 551/2211 184/736 T/N aCt/aAt rs773736586 1 1 PDE4B HGNC HGNC:8781 protein_coding YES CCDS632.1 ENSP00000332116 Q07343 X5DNX5 UPI0000127BF6 NM_001297440.1,NM_001037341.1,NM_001297441.1 deleterious(0.04) 6/17 hmmpanther:PTHR11347:SF108,hmmpanther:PTHR11347 MODERATE 1 SNV 1 1 PASS rs773736586 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 66257830 66257830 C A 1 0 0 0 0 1 0 0 0 11728 565 20 2 2 PDE4B 1 66257830 Missense_Mutation SNP C C3L-00095_T 621278 66257830 182698592 31 3240 LRRC7 0 . GRCh38 1 70038976 70038976 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.3038G>T p.Ser1013Ile p.S1013I ENST00000035383 19/25 276 255 21 277 276 1 strelka-varscan-mutect LRRC7,missense_variant,p.Ser1018Ile,ENST00000310961,;LRRC7,missense_variant,p.Ser1013Ile,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Ser297Ile,ENST00000415775,; T ENST00000035383 Transcript missense_variant 3068/5000 3038/4614 1013/1537 S/I aGt/aTt COSM426651 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious(0.04) 19/25 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 70038976 70038976 G T 1 0 0 0 0 1 0 0 0 8916 1029 36 2 2 LRRC7 1 70038976 Missense_Mutation SNP G C3L-00095_T 3781146 70038976 178917446 32 3241 NEGR1 0 . GRCh38 1 71407479 71407479 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1032C>A p.Ser344Arg p.S344R ENST00000357731 7/7 214 199 15 202 202 0 strelka-varscan-mutect NEGR1,missense_variant,p.Ser344Arg,ENST00000357731,NM_173808.2;NEGR1,missense_variant,p.Ser216Arg,ENST00000306821,;ZRANB2-AS2,intron_variant,,ENST00000628450,;ZRANB2-AS2,intron_variant,,ENST00000628635,;ZRANB2-AS2,intron_variant,,ENST00000627548,;ZRANB2-AS2,intron_variant,,ENST00000630350,;ZRANB2-AS2,intron_variant,,ENST00000628797,;ZRANB2-AS2,intron_variant,,ENST00000630994,;ZRANB2-AS2,intron_variant,,ENST00000599146,;ZRANB2-AS2,intron_variant,,ENST00000600103,;ZRANB2-AS2,intron_variant,,ENST00000630926,;ZRANB2-AS2,intron_variant,,ENST00000627902,;ZRANB2-AS2,intron_variant,,ENST00000627516,;ZRANB2-AS2,intron_variant,,ENST00000628670,;ZRANB2-AS2,intron_variant,,ENST00000594152,;ZRANB2-AS2,intron_variant,,ENST00000630885,;ZRANB2-AS2,intron_variant,,ENST00000583678,;ZRANB2-AS2,intron_variant,,ENST00000626510,;ZRANB2-AS2,intron_variant,,ENST00000625896,;ZRANB2-AS2,intron_variant,,ENST00000628683,;ZRANB2-AS2,intron_variant,,ENST00000608579,;ZRANB2-AS2,intron_variant,,ENST00000430605,;ZRANB2-AS2,upstream_gene_variant,,ENST00000623721,;ZRANB2-AS2,upstream_gene_variant,,ENST00000586006,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585499,;ZRANB2-AS2,upstream_gene_variant,,ENST00000585415,;ZRANB2-AS2,upstream_gene_variant,,ENST00000590186,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587306,;ZRANB2-AS2,upstream_gene_variant,,ENST00000587066,;NEGR1,downstream_gene_variant,,ENST00000474357,; T ENST00000357731 Transcript missense_variant 1272/12811 1032/1065 344/354 S/R agC/agA 1 -1 NEGR1 HGNC HGNC:17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 UPI00000477EE NM_173808.2 tolerated(0.18) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.84956 0.9999997 1 1 1 0 T 3 4 10 71407479 71407479 G T 1 0 0 0 0 1 0 0 0 10345 1310 46 2 2 NEGR1 1 71407479 Missense_Mutation SNP G C3L-00095_T 1368503 71407479 177548943 33 3242 LRRIQ3 0 . GRCh38 1 74041401 74041401 + Missense_Mutation SNP T T A rs756749538 C3L-00095_T C3L-00095_N T T c.1530A>T p.Gln510His p.Q510H ENST00000354431 7/8 226 210 16 215 215 0 strelka-varscan-mutect LRRIQ3,missense_variant,p.Gln510His,ENST00000354431,NM_001105659.1;LRRIQ3,missense_variant,p.Gln510His,ENST00000395089,;LRRIQ3,intron_variant,,ENST00000417067,;LRRIQ3,intron_variant,,ENST00000415760,; A ENST00000354431 Transcript missense_variant 1722/2849 1530/1875 510/624 Q/H caA/caT rs756749538 1 -1 LRRIQ3 HGNC HGNC:28318 protein_coding YES CCDS41350.1 ENSP00000346414 A6PVS8 UPI000155D493 NM_001105659.1 deleterious(0.04) 7/8 MODERATE 1 SNV 5 1 PASS rs756749538 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 74041401 74041401 T A 1 0 0 0 0 1 0 0 0 8936 1838 64 4 4 LRRIQ3 1 74041401 Missense_Mutation SNP T C3L-00095_T 2633922 74041401 174915021 34 3243 FPGT 0 . GRCh38 1 74205724 74205724 + Nonsense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.1716T>A p.Tyr572Ter p.Y572* ENST00000370898 4/4 180 165 15 146 146 0 strelka-varscan-mutect FPGT,stop_gained,p.Tyr572Ter,ENST00000370898,NM_003838.4;FPGT,stop_gained,p.Tyr305Ter,ENST00000534056,NM_001199328.2;FPGT,3_prime_UTR_variant,,ENST00000370894,NM_001199329.2;FPGT-TNNI3K,intron_variant,,ENST00000370895,;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,intron_variant,,ENST00000370899,NM_001199327.1;FPGT-TNNI3K,intron_variant,,ENST00000370893,;FPGT-TNNI3K,intron_variant,,ENST00000534632,;FPGT,downstream_gene_variant,,ENST00000467578,;FPGT,downstream_gene_variant,,ENST00000482102,;FPGT,downstream_gene_variant,,ENST00000472069,;FPGT,intron_variant,,ENST00000524915,;FPGT-TNNI3K,intron_variant,,ENST00000533006,;FPGT,downstream_gene_variant,,ENST00000529485,; A ENST00000370898 Transcript stop_gained 1744/3254 1716/1824 572/607 Y/* taT/taA 1 1 FPGT HGNC HGNC:3825 protein_coding YES CCDS663.2 ENSP00000359935 A0A0A0MRP2 UPI0003348FC3 NM_003838.4 4/4 PIRSF_domain:PIRSF036640,hmmpanther:PTHR15045 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 74205724 74205724 T A 1 0 0 0 0 0 1 0 0 5903 1413 49 4 4 FPGT 1 74205724 Nonsense_Mutation SNP T C3L-00095_T 164323 74205724 174750698 35 3244 ERICH3 0 . GRCh38 1 74589787 74589787 + Nonsense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.2020G>T p.Glu674Ter p.E674* ENST00000326665 12/15 286 266 20 357 357 0 strelka-varscan-mutect ERICH3,stop_gained,p.Glu674Ter,ENST00000326665,NM_001002912.4;ERICH3,stop_gained,p.Glu477Ter,ENST00000420661,;ERICH3-AS1,non_coding_transcript_exon_variant,,ENST00000416017,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,upstream_gene_variant,,ENST00000620678,; A ENST00000326665 Transcript stop_gained 2239/7159 2020/4593 674/1530 E/* Gag/Tag COSM5694949,COSM5694950 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 12/15 hmmpanther:PTHR23034 1,1 HIGH SNV 5 1,1 1 PASS rs1274251958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 74589787 74589787 C A 1 0 0 0 0 0 1 0 0 5083 864 30 2 2 ERICH3 1 74589787 Nonsense_Mutation SNP C C3L-00095_T 384063 74589787 174366635 36 3245 ERICH3 0 . GRCh38 1 74612628 74612628 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1182C>G p.Cys394Trp p.C394W ENST00000326665 9/15 86 75 11 139 139 0 strelka-varscan-mutect ERICH3,missense_variant,p.Cys394Trp,ENST00000326665,NM_001002912.4;ERICH3,missense_variant,p.Cys197Trp,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,;ERICH3,downstream_gene_variant,,ENST00000479666,; C ENST00000326665 Transcript missense_variant 1401/7159 1182/4593 394/1530 C/W tgC/tgG 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0) 9/15 hmmpanther:PTHR23034,Pfam_domain:PF15257 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.9999 1 1 1 1 0 C 3 2 10 74612628 74612628 G C 1 0 0 0 0 1 0 0 0 5083 985 34 4 4 ERICH3 1 74612628 Missense_Mutation SNP G C3L-00095_T 22841 74612628 174343794 37 3246 ERICH3 0 . GRCh38 1 74620750 74620750 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.984C>A p.= p.G328G ENST00000326665 8/15 100 87 13 89 89 0 strelka-varscan ERICH3,synonymous_variant,p.=,ENST00000326665,NM_001002912.4;ERICH3,synonymous_variant,p.=,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,;ERICH3,3_prime_UTR_variant,,ENST00000479666,; T ENST00000326665 Transcript synonymous_variant 1203/7159 984/4593 328/1530 G ggC/ggA 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 8/15 hmmpanther:PTHR23034,Pfam_domain:PF15257 LOW SNV 5 1 PASS . . 0 197 10 3 0 0 0 0 -19.8946 0.9970656 1 1 1 0 T 2 4 10 74620750 74620750 G T 1 0 0 0 0 0 0 0 1 5083 1306 46 2 2 ERICH3 1 74620750 Silent SNP G C3L-00095_T 8122 74620750 174335672 38 3247 ADGRL2 0 . GRCh38 1 81969283 81969283 + Missense_Mutation SNP C C A rs777702018 C3L-00095_T C3L-00095_N C C c.2578C>A p.Arg860Ser p.R860S ENST00000319517 13/20 341 312 29 388 388 0 strelka-varscan-mutect ADGRL2,missense_variant,p.Arg873Ser,ENST00000370728,;ADGRL2,missense_variant,p.Arg873Ser,ENST00000370730,;ADGRL2,missense_variant,p.Arg873Ser,ENST00000370717,;ADGRL2,missense_variant,p.Arg873Ser,ENST00000627151,;ADGRL2,missense_variant,p.Arg860Ser,ENST00000370715,NM_001297705.1;ADGRL2,missense_variant,p.Arg860Ser,ENST00000319517,NM_012302.3;ADGRL2,missense_variant,p.Arg860Ser,ENST00000370713,NM_001297706.1;ADGRL2,missense_variant,p.Arg873Ser,ENST00000370725,;ADGRL2,missense_variant,p.Arg860Ser,ENST00000370723,;ADGRL2,missense_variant,p.Arg873Ser,ENST00000370727,;ADGRL2,missense_variant,p.Arg798Ser,ENST00000370721,;ADGRL2,missense_variant,p.Arg860Ser,ENST00000359929,NM_001297704.1;ADGRL2,missense_variant,p.Arg741Ser,ENST00000449420,;ADGRL2,intron_variant,,ENST00000469377,;ADGRL2,downstream_gene_variant,,ENST00000468283,; A ENST00000319517 Transcript missense_variant 2794/5479 2578/4212 860/1403 R/S Cgt/Agt rs777702018 1 1 ADGRL2 HGNC HGNC:18582 protein_coding YES CCDS689.1 ENSP00000322270 O95490 UPI000005046B NM_012302.3 deleterious(0.01) 13/20 PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249 MODERATE 1 SNV 1 1 PASS rs777702018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 81969283 81969283 C A 1 0 0 0 0 1 0 0 0 376 652 23 1 1 ADGRL2 1 81969283 Missense_Mutation SNP C C3L-00095_T 7348533 81969283 166987139 39 3248 SYDE2 0 . GRCh38 1 85159075 85159075 + Missense_Mutation SNP C C A rs753938811 C3L-00095_T C3L-00095_N C C c.3260G>T p.Arg1087Leu p.R1087L ENST00000341460 7/7 498 458 40 498 496 2 strelka-varscan-mutect SYDE2,missense_variant,p.Arg1087Leu,ENST00000341460,NM_032184.1;RP11-33E12.2,upstream_gene_variant,,ENST00000624216,; A ENST00000341460 Transcript missense_variant 3310/5512 3260/3585 1087/1194 R/L cGt/cTt rs753938811 1 -1 SYDE2 HGNC HGNC:25841 protein_coding YES CCDS44169.1 ENSP00000340594 Q5VT97 UPI0001553B04 NM_032184.1 deleterious(0) 7/7 hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF47 MODERATE 1 SNV 5 1 PASS rs753938811 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 85159075 85159075 C A 1 0 0 0 0 1 0 0 0 15826 536 19 1 1 SYDE2 1 85159075 Missense_Mutation SNP C C3L-00095_T 3189792 85159075 163797347 40 3249 COL24A1 0 . GRCh38 1 85744784 85744784 + Missense_Mutation SNP G G C C3L-00095_T C3L-00095_N G G c.4554C>G p.Phe1518Leu p.F1518L ENST00000370571 57/60 138 122 16 122 122 0 strelka-varscan-mutect COL24A1,missense_variant,p.Phe1518Leu,ENST00000370571,NM_152890.5;COL24A1,3_prime_UTR_variant,,ENST00000426639,;COL24A1,upstream_gene_variant,,ENST00000473734,; C ENST00000370571 Transcript missense_variant 4921/6825 4554/5145 1518/1714 F/L ttC/ttG COSM4495504 1 -1 COL24A1 HGNC HGNC:20821 protein_coding YES CCDS41353.1 ENSP00000359603 Q17RW2 UPI000013E81F NM_152890.5 tolerated(0.12) 57/60 Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF590,SMART_domains:SM00038 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.9999 0.9999999 1 1 1 0 C 3 2 10 85744784 85744784 G C 1 0 0 0 0 1 0 0 0 3471 1281 45 4 4 COL24A1 1 85744784 Missense_Mutation SNP G C3L-00095_T 585709 85744784 163211638 41 3250 LRRC8D 0 . GRCh38 1 89933669 89933669 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.601G>T p.Gly201Ter p.G201* ENST00000337338 3/3 263 231 32 328 327 1 strelka-varscan-mutect LRRC8D,stop_gained,p.Gly201Ter,ENST00000337338,NM_001134479.1;LRRC8D,stop_gained,p.Gly201Ter,ENST00000394593,NM_018103.4;LRRC8D,stop_gained,p.Gly201Ter,ENST00000441269,;LRRC8D,downstream_gene_variant,,ENST00000527156,;LRRC8D,downstream_gene_variant,,ENST00000414841,;LRRC8D,downstream_gene_variant,,ENST00000532201,;LRRC8D,downstream_gene_variant,,ENST00000525774,;RP11-302M6.4,downstream_gene_variant,,ENST00000370453,; T ENST00000337338 Transcript stop_gained 1008/3950 601/2577 201/858 G/* Gga/Tga 1 1 LRRC8D HGNC HGNC:16992 protein_coding YES CCDS726.1 ENSP00000338887 Q7L1W4 UPI00001BBFBA NM_001134479.1 3/3 Pfam_domain:PF12534 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 89933669 89933669 G T 1 0 0 0 0 0 1 0 0 8928 1001 35 2 2 LRRC8D 1 89933669 Nonsense_Mutation SNP G C3L-00095_T 4188885 89933669 159022753 42 3251 DPYD 0 . GRCh38 1 97679118 97679118 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.827A>T p.Tyr276Phe p.Y276F ENST00000370192 8/23 262 244 18 163 163 0 strelka-varscan-mutect DPYD,missense_variant,p.Tyr276Phe,ENST00000370192,NM_000110.3; A ENST00000370192 Transcript missense_variant 928/4412 827/3078 276/1025 Y/F tAc/tTc 1 -1 DPYD HGNC HGNC:3012 protein_coding YES CCDS30777.1 ENSP00000359211 Q12882 UPI00000727C7 NM_000110.3 tolerated(0.32) 8/23 hmmpanther:PTHR11938,hmmpanther:PTHR11938:SF5,Gene3D:3.50.50.60,Pfam_domain:PF07992,Superfamily_domains:SSF51971 MODERATE 1 SNV 1 1 PASS rs1313976976 . 0 206 0 3 0 0 0 0 -19.98576 0.9999663 1 1 1 0 A 3 1 10 97679118 97679118 T A 1 0 0 0 0 1 0 0 0 4560 1638 57 4 4 DPYD 1 97679118 Missense_Mutation SNP T C3L-00095_T 7745449 97679118 151277304 43 3252 PLPPR4 0 . GRCh38 1 99305978 99305978 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.1260C>T p.= p.A420A ENST00000370185 7/7 184 168 16 203 203 0 strelka-varscan-mutect PLPPR4,synonymous_variant,p.=,ENST00000370185,NM_014839.4;PLPPR4,synonymous_variant,p.=,ENST00000457765,NM_001166252.1;PLPPR4,synonymous_variant,p.=,ENST00000370184,; T ENST00000370185 Transcript synonymous_variant 1757/5369 1260/2292 420/763 A gcC/gcT 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 7/7 hmmpanther:PTHR10165:SF13,hmmpanther:PTHR10165 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 99305978 99305978 C T 1 0 0 0 0 0 0 0 1 12212 581 21 3 3 PLPPR4 1 99305978 Silent SNP C C3L-00095_T 1626860 99305978 149650444 44 3253 COL11A1 0 . GRCh38 1 102984176 102984176 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.2518C>G p.Pro840Ala p.P840A ENST00000370096 31/67 215 200 15 132 132 0 strelka-varscan-mutect COL11A1,missense_variant,p.Pro852Ala,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro840Ala,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro801Ala,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro724Ala,ENST00000512756,NM_080630.3;COL11A1,missense_variant,p.Pro613Ala,ENST00000635193,; C ENST00000370096 Transcript missense_variant 2831/7286 2518/5421 840/1806 P/A Cca/Gca 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.02) 31/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 102984176 102984176 G C 1 0 0 0 0 1 0 0 0 3455 1174 41 4 4 COL11A1 1 102984176 Missense_Mutation SNP G C3L-00095_T 3678198 102984176 145972246 45 3254 COL11A1 0 . GRCh38 1 103008506 103008506 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.1640G>T p.Gly547Val p.G547V ENST00000370096 15/67 281 243 38 321 320 1 strelka-varscan-mutect COL11A1,missense_variant,p.Gly559Val,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly547Val,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly508Val,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly431Val,ENST00000512756,NM_080630.3;COL11A1,missense_variant,p.Gly559Val,ENST00000427239,;COL11A1,upstream_gene_variant,,ENST00000461720,;COL11A1,upstream_gene_variant,,ENST00000475980,;COL11A1,missense_variant,p.Gly320Val,ENST00000635193,; A ENST00000370096 Transcript missense_variant 1953/7286 1640/5421 547/1806 G/V gGt/gTt COSM674588,COSM674589 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 15/67 Pfam_domain:PF01391,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 103008506 103008506 C A 1 0 0 0 0 1 0 0 0 3455 507 18 2 2 COL11A1 1 103008506 Missense_Mutation SNP C C3L-00095_T 24330 103008506 145947916 46 3255 NTNG1 0 . GRCh38 1 107430772 107430772 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1110C>A p.= p.S370S ENST00000370068 6/8 163 148 15 179 179 0 strelka-varscan-mutect NTNG1,synonymous_variant,p.=,ENST00000370068,;NTNG1,synonymous_variant,p.=,ENST00000370073,NM_001113226.1;NTNG1,synonymous_variant,p.=,ENST00000370065,;NTNG1,intron_variant,,ENST00000370067,;NTNG1,intron_variant,,ENST00000370071,NM_001113228.1;NTNG1,intron_variant,,ENST00000370074,NM_014917.2;NTNG1,intron_variant,,ENST00000370066,; A ENST00000370068 Transcript synonymous_variant 1956/4034 1110/1620 370/539 S tcC/tcA 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E 6/8 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 LOW 1 SNV 5 1 PASS rs1319398180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 107430772 107430772 C A 1 0 0 0 0 0 0 0 1 10769 581 21 2 2 NTNG1 1 107430772 Silent SNP C C3L-00095_T 4422266 107430772 141525650 47 3256 CHI3L2 0 . GRCh38 1 111230908 111230908 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.237G>C p.= p.V79V ENST00000445067 5/13 206 192 14 243 243 0 strelka-mutect CHI3L2,synonymous_variant,p.=,ENST00000445067,;CHI3L2,synonymous_variant,p.=,ENST00000369744,NM_001025197.1;CHI3L2,synonymous_variant,p.=,ENST00000369748,NM_004000.2;CHI3L2,synonymous_variant,p.=,ENST00000528451,;CHI3L2,synonymous_variant,p.=,ENST00000486561,;CHI3L2,synonymous_variant,p.=,ENST00000474304,;CHI3L2,synonymous_variant,p.=,ENST00000533831,;CHI3L2,5_prime_UTR_variant,,ENST00000466741,NM_001025199.1;CHI3L2,5_prime_UTR_variant,,ENST00000524472,;CHI3L2,5_prime_UTR_variant,,ENST00000477185,;CHI3L2,5_prime_UTR_variant,,ENST00000467038,;CHI3L2,5_prime_UTR_variant,,ENST00000497587,;CHI3L2,upstream_gene_variant,,ENST00000497220,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000526684,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000530597,; C ENST00000445067 Transcript synonymous_variant 1008/2169 237/1173 79/390 V gtG/gtC 1 1 CHI3L2 HGNC HGNC:1933 protein_coding YES CCDS30802.1 ENSP00000437082 Q15782 UPI0000126C1A 5/13 hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF82,Pfam_domain:PF00704,Gene3D:3.20.20.80,SMART_domains:SM00636,Superfamily_domains:SSF51445 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 111230908 111230908 G C 1 0 0 0 0 0 0 0 1 3100 1277 45 4 4 CHI3L2 1 111230908 Silent SNP G C3L-00095_T 3800136 111230908 137725514 48 3257 HMGCS2 0 . GRCh38 1 119755583 119755583 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.1031A>C p.Glu344Ala p.E344A ENST00000369406 6/10 406 385 21 499 499 0 strelka-varscan-mutect HMGCS2,missense_variant,p.Glu344Ala,ENST00000369406,NM_005518.3;HMGCS2,missense_variant,p.Glu302Ala,ENST00000544913,NM_001166107.1;HMGCS2,non_coding_transcript_exon_variant,,ENST00000476640,;HMGCS2,non_coding_transcript_exon_variant,,ENST00000472375,; G ENST00000369406 Transcript missense_variant 1081/2428 1031/1527 344/508 E/A gAa/gCa 1 -1 HMGCS2 HGNC HGNC:5008 protein_coding YES CCDS905.1 ENSP00000358414 P54868 A0A140VJL2 UPI000000DA7A NM_005518.3 tolerated(0.08) 6/10 hmmpanther:PTHR11877,hmmpanther:PTHR11877:SF16,Pfam_domain:PF08540,TIGRFAM_domain:TIGR01833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 119755583 119755583 T G 1 0 0 0 0 1 0 0 0 7125 1783 62 5 5 HMGCS2 1 119755583 Missense_Mutation SNP T C3L-00095_T 8524675 119755583 129200839 49 3258 ACP6 0 . GRCh38 1 147659527 147659527 + Splice_Site SNP C C T C3L-00095_T C3L-00095_N C C c.349-1G>A p.X117_splice ENST00000583509 188 176 12 172 172 0 strelka-mutect ACP6,splice_acceptor_variant,,ENST00000583509,NM_016361.4;ACP6,splice_acceptor_variant,,ENST00000392988,;ACP6,splice_acceptor_variant,,ENST00000487562,;ACP6,splice_acceptor_variant,,ENST00000611629,;ACP6,splice_acceptor_variant,,ENST00000493129,;ACP6,upstream_gene_variant,,ENST00000609196,;ACP6,splice_acceptor_variant,,ENST00000613673,;ACP6,intron_variant,,ENST00000620634,;ACP6,upstream_gene_variant,,ENST00000614551,; T ENST00000583509 Transcript splice_acceptor_variant -/6923 349/1287 117/428 COSM4862336,COSM674759 1 -1 ACP6 HGNC HGNC:29609 protein_coding YES CCDS928.1 ENSP00000463574 X5D289 UPI000003F07E NM_016361.4 2/9 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 10 147659527 147659527 C T 1 0 0 0 0 0 0 1 0 207 695 24 3 3 ACP6 1 147659527 Splice_Site SNP C C3L-00095_T 27903944 147659527 101296895 50 3259 OTUD7B 0 . GRCh38 1 149944533 149944533 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.1856A>G p.His619Arg p.H619R ENST00000581312 12/12 374 350 24 441 441 0 strelka-varscan-mutect OTUD7B,missense_variant,p.His619Arg,ENST00000581312,NM_020205.3;OTUD7B,downstream_gene_variant,,ENST00000417191,; C ENST00000581312 Transcript missense_variant 2151/8872 1856/2532 619/843 H/R cAc/cGc 1 -1 OTUD7B HGNC HGNC:16683 protein_coding YES CCDS72903.1 ENSP00000462729 Q6GQQ9 UPI000020415D NM_020205.3 tolerated(0.07) 12/12 hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 149944533 149944533 T C 1 0 0 0 0 1 0 0 0 11388 1696 59 5 5 OTUD7B 1 149944533 Missense_Mutation SNP T C3L-00095_T 2285006 149944533 99011889 51 3260 FLG2 0 . GRCh38 1 152351280 152351280 + Missense_Mutation SNP C C A rs748312063 C3L-00095_T C3L-00095_N C C c.6506G>T p.Gly2169Val p.G2169V ENST00000388718 3/3 378 348 30 404 403 1 strelka-varscan-mutect FLG2,missense_variant,p.Gly2169Val,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; A ENST00000388718 Transcript missense_variant 6579/9124 6506/7176 2169/2391 G/V gGt/gTt rs748312063 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious(0.02) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS rs748312063 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 152351280 152351280 C A 1 0 0 0 0 1 0 0 0 5785 507 18 2 2 FLG2 1 152351280 Missense_Mutation SNP C C3L-00095_T 2406747 152351280 96605142 52 3261 DENND4B 0 . GRCh38 1 153933606 153933606 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.3207C>T p.= p.R1069R ENST00000361217 20/28 51 45 6 81 81 0 strelka-mutect DENND4B,synonymous_variant,p.=,ENST00000361217,NM_014856.2;DENND4B,synonymous_variant,p.=,ENST00000368646,;DENND4B,upstream_gene_variant,,ENST00000474386,;DENND4B,upstream_gene_variant,,ENST00000480340,;DENND4B,upstream_gene_variant,,ENST00000492898,;DENND4B,upstream_gene_variant,,ENST00000462423,;DENND4B,upstream_gene_variant,,ENST00000531748,;DENND4B,downstream_gene_variant,,ENST00000477746,; A ENST00000361217 Transcript synonymous_variant 3626/5706 3207/4491 1069/1496 R cgC/cgT 1 -1 DENND4B HGNC HGNC:29044 protein_coding YES CCDS44228.1 ENSP00000354597 O75064 UPI000047EA3E NM_014856.2 20/28 hmmpanther:PTHR12296:SF18,hmmpanther:PTHR12296 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -14.51394 1 1 1 1 0 A 2 1 10 153933606 153933606 G A 1 0 0 0 0 0 0 0 1 4238 1190 42 3 3 DENND4B 1 153933606 Silent SNP G C3L-00095_T 1582326 153933606 95022816 53 3262 ATP8B2 0 . GRCh38 1 154331064 154331064 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.320C>A p.Ser107Tyr p.S107Y ENST00000368489 5/28 230 213 17 244 243 1 strelka-mutect ATP8B2,missense_variant,p.Ser107Tyr,ENST00000368489,NM_020452.3;ATP8B2,missense_variant,p.Ser74Tyr,ENST00000368487,NM_001005855.1;ATP8B2,non_coding_transcript_exon_variant,,ENST00000426445,;ATP8B2,downstream_gene_variant,,ENST00000368490,;ATP8B2,upstream_gene_variant,,ENST00000514107,; A ENST00000368489 Transcript missense_variant 320/5861 320/3672 107/1223 S/Y tCt/tAt COSM253246 1 1 ATP8B2 HGNC HGNC:13534 protein_coding YES CCDS1066.1 ENSP00000357475 P98198 UPI00001B92AB NM_020452.3 deleterious(0) 5/28 Superfamily_domains:0049473,Gene3D:2.70.150.10,Pfam_domain:PF16209,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF46,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR01652,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 154331064 154331064 C A 1 0 0 0 0 1 0 0 0 1348 913 32 2 2 ATP8B2 1 154331064 Missense_Mutation SNP C C3L-00095_T 397458 154331064 94625358 54 3263 OR10T2 0 . GRCh38 1 158399211 158399211 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.256C>A p.Leu86Met p.L86M ENST00000334438 1/1 210 193 17 286 286 0 strelka-varscan-mutect OR10T2,missense_variant,p.Leu86Met,ENST00000334438,NM_001004475.1; T ENST00000334438 Transcript missense_variant 256/945 256/945 86/314 L/M Ctg/Atg 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1319148747 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 158399211 158399211 G T 1 0 0 0 0 1 0 0 0 10996 991 35 2 2 OR10T2 1 158399211 Missense_Mutation SNP G C3L-00095_T 4068147 158399211 90557211 55 3264 OR6P1 0 . GRCh38 1 158562819 158562819 + Silent SNP G G T rs758406845 C3L-00095_T C3L-00095_N G G c.786C>A p.= p.P262P ENST00000334632 1/1 444 415 29 564 564 0 strelka-varscan-mutect OR6P1,synonymous_variant,p.=,ENST00000334632,NM_001160325.1; T ENST00000334632 Transcript synonymous_variant 786/954 786/954 262/317 P ccC/ccA rs758406845 1 -1 OR6P1 HGNC HGNC:15036 protein_coding YES CCDS53391.1 ENSP00000334721 Q8NGX9 A0A126GV72 UPI000004B1FF NM_001160325.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs758406845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 158562819 158562819 G T 1 0 0 0 0 0 0 0 1 11277 1219 43 2 2 OR6P1 1 158562819 Silent SNP G C3L-00095_T 163608 158562819 90393603 56 3265 SPTA1 0 . GRCh38 1 158611328 158611328 + Missense_Mutation SNP C C A rs745616202 C3L-00095_T C3L-00095_N C C c.7196G>T p.Arg2399Leu p.R2399L ENST00000368147 52/52 297 282 15 357 357 0 strelka-varscan-mutect SPTA1,missense_variant,p.Arg2399Leu,ENST00000368147,NM_003126.2;OR10Z1,downstream_gene_variant,,ENST00000361284,NM_001004478.1;SPTA1,non_coding_transcript_exon_variant,,ENST00000485680,;SPTA1,downstream_gene_variant,,ENST00000492934,;SPTA1,downstream_gene_variant,,ENST00000481212,;SPTA1,downstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript missense_variant 7377/7999 7196/7260 2399/2419 R/L cGg/cTg rs745616202,COSM5251198,COSM5256445 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.02) 52/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF08726,Gene3D:1.10.238.10,SMART_domains:SM01184,Superfamily_domains:SSF47473 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs745616202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 158611328 158611328 C A 1 0 0 0 0 1 0 0 0 15472 652 23 1 1 SPTA1 1 158611328 Missense_Mutation SNP C C3L-00095_T 48509 158611328 90345094 57 3266 CADM3 0 . GRCh38 1 159191998 159191999 + Frame_Shift_Ins INS - - A novel C3L-00095_T C3L-00095_N - - c.255dupA p.Val86SerfsTer13 p.V86Sfs*13 ENST00000368124 3/10 339 307 32 343 343 0 sindel-varindel-pindel CADM3,frameshift_variant,p.Val52SerfsTer13,ENST00000368125,NM_001127173.1;CADM3,frameshift_variant,p.Val86SerfsTer13,ENST00000368124,NM_021189.3;CADM3,frameshift_variant,p.Val52SerfsTer13,ENST00000416746,;CADM3-AS1,downstream_gene_variant,,ENST00000415675,; A ENST00000368124 Transcript frameshift_variant 410-411/2546 253-254/1299 85/432 Q/QX caa/cAaa 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 3/10 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 10 159191998 159191998 - A 1 0 1 1 0 0 0 0 0 2258 595 21 0 0 CADM3 1 159191998 Frame_Shift_Ins INS - C3L-00095_T 580670 159191998 89764424 58 3267 FCER1A 0 . GRCh38 1 159306038 159306038 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.382C>A p.Leu128Ile p.L128I ENST00000368115 5/6 310 287 23 343 343 0 strelka-varscan-mutect FCER1A,missense_variant,p.Leu128Ile,ENST00000368115,NM_002001.3;FCER1A,missense_variant,p.Leu95Ile,ENST00000368114,; A ENST00000368115 Transcript missense_variant 481/1165 382/774 128/257 L/I Ctc/Atc 1 1 FCER1A HGNC HGNC:3609 protein_coding YES CCDS1184.1 ENSP00000357097 P12319 UPI000002CFDB NM_002001.3 tolerated(0.07) 5/6 Gene3D:2.60.40.10,Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF12,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1387764560 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 159306038 159306038 C A 1 0 0 0 0 1 0 0 0 5637 681 24 2 2 FCER1A 1 159306038 Missense_Mutation SNP C C3L-00095_T 114040 159306038 89650384 59 3268 OR10J1 0 . GRCh38 1 159440306 159440306 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.548A>T p.Lys183Met p.K183M ENST00000423932 1/1 347 326 21 407 407 0 strelka-varscan-mutect OR10J1,missense_variant,p.Lys183Met,ENST00000423932,NM_012351.2;RP11-550P17.5,intron_variant,,ENST00000431862,; T ENST00000423932 Transcript missense_variant 585/1090 548/963 183/320 K/M aAg/aTg 1 1 OR10J1 HGNC HGNC:8175 protein_coding YES CCDS1185.1 ENSP00000399078 P30954 UPI000013E7DA NM_012351.2 tolerated(0.1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF417,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 159440306 159440306 A T 1 0 0 0 0 1 0 0 0 10987 72 3 4 4 OR10J1 1 159440306 Missense_Mutation SNP A C3L-00095_T 134268 159440306 89516116 60 3269 ATP1A2 0 . GRCh38 1 160125179 160125179 + Missense_Mutation SNP G G T rs778741638 C3L-00095_T C3L-00095_N G G c.674G>T p.Arg225Leu p.R225L ENST00000361216 7/23 324 297 27 315 315 0 strelka-varscan-mutect ATP1A2,missense_variant,p.Arg225Leu,ENST00000361216,NM_000702.3;ATP1A2,missense_variant,p.Arg225Leu,ENST00000392233,;ATP1A2,upstream_gene_variant,,ENST00000447527,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000468587,;ATP1A2,downstream_gene_variant,,ENST00000478587,; T ENST00000361216 Transcript missense_variant 763/5421 674/3063 225/1020 R/L cGc/cTc rs778741638,COSM5462040 1 1 ATP1A2 HGNC HGNC:800 protein_coding YES CCDS1196.1 ENSP00000354490 P50993 A0A0S2Z3W6 UPI0000124FC1 NM_000702.3 deleterious(0) 7/23 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01106,Gene3D:2.70.150.10,Pfam_domain:PF00122,Superfamily_domains:0049471,Prints_domain:PR00119 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778741638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 160125179 160125179 G T 1 0 0 0 0 1 0 0 0 1281 1087 38 1 1 ATP1A2 1 160125179 Missense_Mutation SNP G C3L-00095_T 684873 160125179 88831243 61 3270 CASQ1 0 . GRCh38 1 160190880 160190880 + Nonsense_Mutation SNP C C A rs543422219 C3L-00095_T C3L-00095_N C C c.129C>A p.Tyr43Ter p.Y43* ENST00000368078 1/11 423 381 42 456 454 2 strelka-varscan-mutect CASQ1,stop_gained,p.Tyr43Ter,ENST00000368078,NM_001231.4;ATP1A4,downstream_gene_variant,,ENST00000368081,NM_144699.3;ATP1A4,downstream_gene_variant,,ENST00000470705,NM_001001734.1;ATP1A4,downstream_gene_variant,,ENST00000469023,;ATP1A4,downstream_gene_variant,,ENST00000477338,;CASQ1,upstream_gene_variant,,ENST00000481081,; A ENST00000368078 Transcript stop_gained 325/1897 129/1191 43/396 Y/* taC/taA rs543422219,COSM4669401 1 1 CASQ1 HGNC HGNC:1512 protein_coding YES CCDS1198.2 ENSP00000357057 P31415 UPI0000204B81 NM_001231.4 1/11 Gene3D:3.40.30.10,Pfam_domain:PF01216,Prints_domain:PR00312,PROSITE_patterns:PS00863,hmmpanther:PTHR10033,hmmpanther:PTHR10033:SF14,Superfamily_domains:SSF52833 0,1 HIGH 1 SNV 1 0,1 1 PASS rs543422219 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 160190880 160190880 C A 1 0 0 0 0 0 1 0 0 2379 547 19 1 1 CASQ1 1 160190880 Nonsense_Mutation SNP C C3L-00095_T 65701 160190880 88765542 62 3271 SLAMF6 0 . GRCh38 1 160496155 160496155 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.288C>G p.= p.L96L ENST00000368057 2/8 336 317 19 418 418 0 strelka-varscan-mutect SLAMF6,synonymous_variant,p.=,ENST00000368059,NM_052931.4,NM_001184715.1;SLAMF6,synonymous_variant,p.=,ENST00000368057,NM_001184714.1;SLAMF6,intron_variant,,ENST00000368055,NM_001184716.1; C ENST00000368057 Transcript synonymous_variant 349/2712 288/999 96/332 L ctC/ctG 1 -1 SLAMF6 HGNC HGNC:21392 protein_coding YES CCDS53394.1 ENSP00000357036 Q96DU3 UPI0000051E34 NM_001184714.1 2/8 hmmpanther:PTHR12080:SF16,hmmpanther:PTHR12080,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 160496155 160496155 G C 1 0 0 0 0 0 0 0 1 14633 1277 45 4 4 SLAMF6 1 160496155 Silent SNP G C3L-00095_T 305275 160496155 88460267 63 3272 FCGR2B 0 . GRCh38 1 161673219 161673219 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.636C>G p.Ile212Met p.I212M ENST00000358671 4/8 142 134 8 158 158 0 varscan-mutect FCGR2B,missense_variant,p.Ile212Met,ENST00000358671,NM_004001.4,NM_001002275.2;FCGR2B,missense_variant,p.Ile205Met,ENST00000367961,NM_001190828.1;FCGR2B,missense_variant,p.Ile212Met,ENST00000236937,NM_001002274.2,NM_001002273.2;RP11-25K21.1,intron_variant,,ENST00000453111,;RP11-25K21.1,downstream_gene_variant,,ENST00000626340,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000480308,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000485778,; G ENST00000358671 Transcript missense_variant 717/2115 636/933 212/310 I/M atC/atG 1 1 FCGR2B HGNC HGNC:3618 protein_coding YES CCDS30924.1 ENSP00000351497 P31994 UPI0000001600 NM_004001.4,NM_001002275.2 deleterious(0) 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF51,hmmpanther:PTHR11481,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 161673219 161673219 C G 1 0 0 0 0 1 0 0 0 5645 816 29 4 4 FCGR2B 1 161673219 Missense_Mutation SNP C C3L-00095_T 1177064 161673219 87283203 64 3273 METTL11B 0 . GRCh38 1 170166595 170166595 + Missense_Mutation SNP G G T rs749589550 C3L-00095_T C3L-00095_N G G c.424G>T p.Val142Leu p.V142L ENST00000439373 3/4 458 382 76 575 575 0 strelka-varscan-mutect METTL11B,missense_variant,p.Val142Leu,ENST00000439373,NM_001136107.1;METTL11B,non_coding_transcript_exon_variant,,ENST00000367764,; T ENST00000439373 Transcript missense_variant 531/992 424/852 142/283 V/L Gtg/Ttg rs749589550 1 1 METTL11B HGNC HGNC:31932 protein_coding YES CCDS44275.1 ENSP00000408058 Q5VVY1 UPI0000418EF1 NM_001136107.1 deleterious(0.03) 3/4 hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS rs749589550 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 170166595 170166595 G T 1 0 0 0 0 1 0 0 0 9437 1377 48 2 2 METTL11B 1 170166595 Missense_Mutation SNP G C3L-00095_T 8493376 170166595 78789827 65 3274 TNR 0 . GRCh38 1 175379618 175379618 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1897G>T p.Gly633Cys p.G633C ENST00000367674 9/23 171 152 19 229 228 1 strelka-varscan-mutect TNR,missense_variant,p.Gly633Cys,ENST00000367674,;TNR,missense_variant,p.Gly633Cys,ENST00000263525,NM_003285.2; A ENST00000367674 Transcript missense_variant 2606/12949 1897/4077 633/1358 G/C Ggt/Tgt 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0) 9/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 175379618 175379618 C A 1 0 0 0 0 1 0 0 0 16811 623 22 2 2 TNR 1 175379618 Missense_Mutation SNP C C3L-00095_T 5213023 175379618 73576804 66 3275 TNR 0 . GRCh38 1 175391342 175391342 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1453G>T p.Val485Leu p.V485L ENST00000367674 7/23 286 269 17 317 317 0 strelka-varscan-mutect TNR,missense_variant,p.Val485Leu,ENST00000367674,;TNR,missense_variant,p.Val485Leu,ENST00000263525,NM_003285.2;TNR,downstream_gene_variant,,ENST00000422274,; A ENST00000367674 Transcript missense_variant 2162/12949 1453/4077 485/1358 V/L Gtg/Ttg 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C tolerated(0.63) 7/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 175391342 175391342 C A 1 0 0 0 0 1 0 0 0 16811 507 18 2 2 TNR 1 175391342 Missense_Mutation SNP C C3L-00095_T 11724 175391342 73565080 67 3276 PAPPA2 0 . GRCh38 1 176556935 176556935 + Silent SNP C C A C3L-00095_T C3L-00095_N C C c.613C>A p.= p.R205R ENST00000367662 2/23 166 151 15 218 217 1 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2;PAPPA2,synonymous_variant,p.=,ENST00000367661,NM_021936.2;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,; A ENST00000367662 Transcript synonymous_variant 1777/9691 613/5376 205/1791 R Cgg/Agg COSM1158421,COSM216893 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 2/23 1,1 LOW 1 SNV 1 1,1 1 PASS rs1467869802 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 176556935 176556935 C A 1 0 0 0 0 0 0 0 1 11513 759 27 1 1 PAPPA2 1 176556935 Silent SNP C C3L-00095_T 1165593 176556935 72399487 68 3277 ASTN1 0 . GRCh38 1 176934218 176934218 + Missense_Mutation SNP A A G C3L-00095_T C3L-00095_N A A c.2605T>C p.Ser869Pro p.S869P ENST00000361833 16/23 237 220 17 238 238 0 strelka-varscan-mutect ASTN1,missense_variant,p.Ser869Pro,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Ser869Pro,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Ser869Pro,ENST00000424564,NM_207108.2;ASTN1,downstream_gene_variant,,ENST00000281881,; G ENST00000361833 Transcript missense_variant 2619/7116 2605/3885 869/1294 S/P Tct/Cct COSM4875456,COSM900048 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious(0.01) 16/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592,SMART_domains:SM00457 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 176934218 176934218 A G 1 0 0 0 0 1 0 0 0 1211 246 9 5 5 ASTN1 1 176934218 Missense_Mutation SNP A C3L-00095_T 377283 176934218 72022204 69 3278 TDRD5 0 . GRCh38 1 179650912 179650912 + Missense_Mutation SNP G G A rs199784694 C3L-00095_T C3L-00095_N G G c.1846G>A p.Gly616Ser p.G616S ENST00000444136 12/18 335 289 46 397 397 0 strelka-varscan-mutect TDRD5,missense_variant,p.Gly616Ser,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,missense_variant,p.Gly616Ser,ENST00000367614,NM_001199091.1;TDRD5,missense_variant,p.Gly616Ser,ENST00000294848,NM_173533.3;TDRD5,missense_variant,p.Gly72Ser,ENST00000417329,; A ENST00000444136 Transcript missense_variant 2364/3946 1846/3108 616/1035 G/S Ggt/Agt rs199784694,COSM4025615,COSM4025616 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 tolerated(0.28) 12/18 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF19 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs199784694 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 179650912 179650912 G A 1 0 0 0 0 1 0 0 0 16143 1116 39 1 1 TDRD5 1 179650912 Missense_Mutation SNP G C3L-00095_T 2716694 179650912 69305510 70 3279 RGS16 0 . GRCh38 1 182603277 182603277 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.107C>T p.Thr36Ile p.T36I ENST00000367558 2/5 315 292 23 372 372 0 strelka-varscan-mutect RGS16,missense_variant,p.Thr36Ile,ENST00000367558,NM_002928.3; A ENST00000367558 Transcript missense_variant 256/2427 107/609 36/202 T/I aCt/aTt 1 -1 RGS16 HGNC HGNC:9997 protein_coding YES CCDS1348.1 ENSP00000356529 O15492 UPI000013D8E9 NM_002928.3 tolerated(0.45) 2/5 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 182603277 182603277 G A 1 0 0 0 0 1 0 0 0 13469 1029 36 3 3 RGS16 1 182603277 Missense_Mutation SNP G C3L-00095_T 2952365 182603277 66353145 71 3280 RNF2 0 . GRCh38 1 185087560 185087560 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.7C>T p.Gln3Ter p.Q3* ENST00000367510 2/7 235 214 21 201 201 0 strelka-varscan-mutect RNF2,stop_gained,p.Gln3Ter,ENST00000367510,NM_007212.3;RNF2,stop_gained,p.Gln3Ter,ENST00000367509,;RNF2,stop_gained,p.Gln3Ter,ENST00000453650,;RNF2,non_coding_transcript_exon_variant,,ENST00000498201,; T ENST00000367510 Transcript stop_gained 295/3606 7/1011 3/336 Q/* Cag/Tag 1 1 RNF2 HGNC HGNC:10061 protein_coding YES CCDS1365.1 ENSP00000356480 Q99496 UPI000007131D NM_007212.3 2/7 hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF41 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 185087560 185087560 C T 1 0 0 0 0 0 1 0 0 13650 827 29 3 3 RNF2 1 185087560 Nonsense_Mutation SNP C C3L-00095_T 2484283 185087560 63868862 72 3281 PRG4 0 . GRCh38 1 186307063 186307063 + Silent SNP C C A rs767246572 C3L-00095_T C3L-00095_N C C c.1344C>A p.= p.P448P ENST00000445192 7/13 518 485 33 720 720 0 varscan-mutect PRG4,synonymous_variant,p.=,ENST00000445192,NM_005807.4;PRG4,synonymous_variant,p.=,ENST00000367483,NM_001127708.2;PRG4,synonymous_variant,p.=,ENST00000635041,NM_001303232.1;PRG4,synonymous_variant,p.=,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,synonymous_variant,p.=,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; A ENST00000445192 Transcript synonymous_variant 1389/5044 1344/4215 448/1404 P ccC/ccA rs767246572 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 LOW SNV 5 1 PASS rs767246572 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 186307063 186307063 C A 1 0 0 0 0 0 0 0 1 12615 581 21 2 2 PRG4 1 186307063 Silent SNP C C3L-00095_T 1219503 186307063 62649359 73 3282 BRINP3 0 . GRCh38 1 190226191 190226191 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.852C>G p.= p.P284P ENST00000367462 6/8 148 138 10 160 160 0 strelka-varscan-mutect BRINP3,synonymous_variant,p.=,ENST00000367462,NM_199051.1;BRINP3,non_coding_transcript_exon_variant,,ENST00000463404,; C ENST00000367462 Transcript synonymous_variant 1337/3142 852/2301 284/766 P ccC/ccG 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 6/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 190226191 190226191 G C 1 0 0 0 0 0 0 0 1 1687 1335 47 4 4 BRINP3 1 190226191 Silent SNP G C3L-00095_T 3919128 190226191 58730231 74 3283 LHX9 0 . GRCh38 1 197918325 197918325 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.127C>A p.= p.R43R ENST00000367388 3/3 264 236 28 279 279 0 strelka-varscan LHX9,synonymous_variant,p.=,ENST00000367388,;LHX9,intron_variant,,ENST00000367387,NM_020204.2;LHX9,intron_variant,,ENST00000367390,NM_001014434.1;LHX9,intron_variant,,ENST00000561173,;LHX9,intron_variant,,ENST00000367391,;LHX9,downstream_gene_variant,,ENST00000606127,;LHX9,downstream_gene_variant,,ENST00000475727,; A ENST00000367388 Transcript synonymous_variant 317/758 127/165 43/54 R Cgg/Agg 1 1 LHX9 HGNC HGNC:14222 protein_coding ENSP00000356358 H0Y330 UPI0000EE3EC7 3/3 Low_complexity_(Seg):seg LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 197918325 197918325 C A 1 0 0 0 0 0 0 0 1 8686 643 23 1 1 LHX9 1 197918325 Silent SNP C C3L-00095_T 7692134 197918325 51038097 75 3284 GPR25 0 . GRCh38 1 200873154 200873154 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.117C>A p.Tyr39Ter p.Y39* ENST00000304244 1/1 237 216 21 281 280 1 strelka-varscan GPR25,stop_gained,p.Tyr39Ter,ENST00000304244,NM_005298.3; A ENST00000304244 Transcript stop_gained 200/1224 117/1086 39/361 Y/* taC/taA 1 1 GPR25 HGNC HGNC:4480 protein_coding YES CCDS1405.1 ENSP00000301917 O00155 UPI000013E957 NM_005298.3 1/1 hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF9,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 200873154 200873154 C A 1 0 0 0 0 0 1 0 0 6567 547 19 1 1 GPR25 1 200873154 Nonsense_Mutation SNP C C3L-00095_T 2954829 200873154 48083268 76 3285 KIF21B 0 . GRCh38 1 200974812 200974812 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.4716G>T p.Trp1572Cys p.W1572C ENST00000422435 34/35 562 480 82 608 607 1 strelka-varscan KIF21B,missense_variant,p.Trp1559Cys,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Trp1572Cys,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Trp1572Cys,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Trp1559Cys,ENST00000360529,NM_001252103.1; A ENST00000422435 Transcript missense_variant 5033/5519 4716/4914 1572/1637 W/C tgG/tgT 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0) 34/35 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 200974812 200974812 C A 1 0 0 0 0 1 0 0 0 8154 856 30 2 2 KIF21B 1 200974812 Missense_Mutation SNP C C3L-00095_T 101658 200974812 47981610 77 3286 IGFN1 0 . GRCh38 1 201206993 201206993 + Silent SNP T T C novel C3L-00095_T C3L-00095_N T T c.2100T>C p.= p.G700G ENST00000335211 12/24 112 104 8 123 123 0 strelka-varscan IGFN1,synonymous_variant,p.=,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,downstream_gene_variant,,ENST00000444705,; C ENST00000335211 Transcript synonymous_variant 2230/11810 2100/11127 700/3708 G ggT/ggC 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 12/24 LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -15.80871 0.9999997 1 1 1 0 C 2 2 10 201206993 201206993 T C 1 0 0 0 0 0 0 0 1 7497 1625 57 5 5 IGFN1 1 201206993 Silent SNP T C3L-00095_T 232181 201206993 47749429 78 3287 IGFN1 0 . GRCh38 1 201224821 201224821 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.10433T>A p.Leu3478Gln p.L3478Q ENST00000335211 21/24 148 125 23 181 181 0 strelka-varscan IGFN1,missense_variant,p.Leu3478Gln,ENST00000335211,NM_001164586.1;IGFN1,missense_variant,p.Leu1021Gln,ENST00000295591,;IGFN1,missense_variant,p.Leu896Gln,ENST00000412892,;RP11-567E21.3,upstream_gene_variant,,ENST00000453155,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,intron_variant,,ENST00000473483,; A ENST00000335211 Transcript missense_variant 10563/11810 10433/11127 3478/3708 L/Q cTg/cAg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0) 21/24 PROSITE_profiles:PS50835,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 201224821 201224821 T A 1 0 0 0 0 1 0 0 0 7497 1580 55 4 4 IGFN1 1 201224821 Missense_Mutation SNP T C3L-00095_T 17828 201224821 47731601 79 3288 IPO9 0 . GRCh38 1 201872944 201872944 + Missense_Mutation SNP G G T rs778640930 C3L-00095_T C3L-00095_N G G c.2693G>T p.Arg898Leu p.R898L ENST00000361565 20/24 67 61 6 74 74 0 strelka-varscan IPO9,missense_variant,p.Arg898Leu,ENST00000361565,NM_018085.4;IPO9,upstream_gene_variant,,ENST00000456707,; T ENST00000361565 Transcript missense_variant 2762/11435 2693/3126 898/1041 R/L cGc/cTc rs778640930,COSM2212620 1 1 IPO9 HGNC HGNC:19425 protein_coding YES CCDS1415.1 ENSP00000354742 Q96P70 UPI000007304B NM_018085.4 deleterious(0.02) 20/24 hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF9 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 197 12 0 0 0 0 0 -13.2797 0.9997634 1 1 1 0 T 3 4 10 201872944 201872944 G T 1 0 0 0 0 1 0 0 0 7702 1087 38 1 1 IPO9 1 201872944 Missense_Mutation SNP G C3L-00095_T 648123 201872944 47083478 80 3289 BTG2 0 . GRCh38 1 203305700 203305700 + Missense_Mutation SNP G G A rs772251147 C3L-00095_T C3L-00095_N G G c.94G>A p.Glu32Lys p.E32K ENST00000290551 1/2 300 284 16 317 316 1 strelka-varscan BTG2,missense_variant,p.Glu32Lys,ENST00000290551,NM_006763.2;LINC01136,upstream_gene_variant,,ENST00000457348,;LINC01136,upstream_gene_variant,,ENST00000432511,;LINC01136,upstream_gene_variant,,ENST00000425698,;BTG2,missense_variant,p.Glu32Lys,ENST00000475157,; A ENST00000290551 Transcript missense_variant 165/2712 94/477 32/158 E/K Gag/Aag rs772251147 1 1 BTG2 HGNC HGNC:1131 protein_coding YES CCDS1437.1 ENSP00000290551 P78543 UPI000011DD3B NM_006763.2 tolerated(0.09) 1/2 hmmpanther:PTHR22978,hmmpanther:PTHR22978:SF29,Pfam_domain:PF07742,SMART_domains:SM00099,Superfamily_domains:SSF160696,Prints_domain:PR00310 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 203305700 203305700 G A 1 0 0 0 0 1 0 0 0 1730 1059 37 1 1 BTG2 1 203305700 Missense_Mutation SNP G C3L-00095_T 1432756 203305700 45650722 81 3290 9 2 BTG2 0 . GRCh38 1 203305705 203305705 + Silent SNP G G A C3L-00095_T C3L-00095_N G G c.99G>A p.= p.Q33Q ENST00000290551 1/2 293 278 15 315 315 0 strelka-varscan BTG2,synonymous_variant,p.=,ENST00000290551,NM_006763.2;LINC01136,upstream_gene_variant,,ENST00000457348,;LINC01136,upstream_gene_variant,,ENST00000432511,;LINC01136,upstream_gene_variant,,ENST00000425698,;BTG2,synonymous_variant,p.=,ENST00000475157,; A ENST00000290551 Transcript synonymous_variant 170/2712 99/477 33/158 Q caG/caA COSM5649087 1 1 BTG2 HGNC HGNC:1131 protein_coding YES CCDS1437.1 ENSP00000290551 P78543 UPI000011DD3B NM_006763.2 1/2 hmmpanther:PTHR22978,hmmpanther:PTHR22978:SF29,Pfam_domain:PF07742,SMART_domains:SM00099,Superfamily_domains:SSF160696,Prints_domain:PR00310 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 203305705 203305705 G A 1 0 0 0 0 0 0 0 1 1730 933 33 3 3 BTG2 1 203305705 Silent SNP G C3L-00095_T 5 203305705 45650717 82 3291 9 2 CNTN2 0 . GRCh38 1 205059602 205059602 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.717C>A p.= p.P239P ENST00000331830 7/23 349 314 35 344 343 1 strelka-varscan CNTN2,synonymous_variant,p.=,ENST00000331830,NM_005076.3;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,;CNTN2,non_coding_transcript_exon_variant,,ENST00000530117,;CNTN2,downstream_gene_variant,,ENST00000532366,;CNTN2,upstream_gene_variant,,ENST00000527340,; A ENST00000331830 Transcript synonymous_variant 1074/8214 717/3123 239/1040 P ccC/ccA 1 1 CNTN2 HGNC HGNC:2172 protein_coding YES CCDS1449.1 ENSP00000330633 Q02246 A0A024R9B4 UPI00001266A5 NM_005076.3 7/23 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,Pfam_domain:PF13927,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 205059602 205059602 C A 1 0 0 0 0 0 0 0 1 3422 581 21 2 2 CNTN2 1 205059602 Silent SNP C C3L-00095_T 1753897 205059602 43896820 83 3292 TMEM81 0 . GRCh38 1 205084161 205084161 + Missense_Mutation SNP C C A rs748791365 C3L-00095_T C3L-00095_N C C c.160G>T p.Gly54Cys p.G54C ENST00000367167 1/1 269 231 38 297 297 0 strelka-varscan TMEM81,missense_variant,p.Gly54Cys,ENST00000367167,NM_203376.1;RBBP5,downstream_gene_variant,,ENST00000264515,NM_001193273.1,NM_005057.3;RBBP5,downstream_gene_variant,,ENST00000367164,NM_001193272.1; A ENST00000367167 Transcript missense_variant 300/1332 160/768 54/255 G/C Ggc/Tgc rs748791365 1 -1 TMEM81 HGNC HGNC:32349 protein_coding YES CCDS1450.1 ENSP00000356135 Q6P7N7 UPI0000199A1E NM_203376.1 deleterious(0) 1/1 hmmpanther:PTHR35670,hmmpanther:PTHR35670:SF1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 205084161 205084161 C A 1 0 0 0 0 1 0 0 0 16682 594 21 2 2 TMEM81 1 205084161 Missense_Mutation SNP C C3L-00095_T 24559 205084161 43872261 84 3293 PTPN14 0 . GRCh38 1 214394939 214394939 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.806T>C p.Val269Ala p.V269A ENST00000366956 9/19 354 333 21 301 301 0 strelka-varscan-mutect PTPN14,missense_variant,p.Val269Ala,ENST00000366956,NM_005401.4;PTPN14,3_prime_UTR_variant,,ENST00000543945,; G ENST00000366956 Transcript missense_variant 1001/12985 806/3564 269/1187 V/A gTg/gCg 1 -1 PTPN14 HGNC HGNC:9647 protein_coding YES CCDS1514.1 ENSP00000355923 Q15678 UPI000013DCA6 NM_005401.4 tolerated(0.08) 9/19 PROSITE_profiles:PS50057,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,Pfam_domain:PF09380,PIRSF_domain:PIRSF000934,Gene3D:2.30.29.30,SMART_domains:SM01196,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 214394939 214394939 A G 1 0 0 0 0 1 0 0 0 12936 159 6 5 5 PTPN14 1 214394939 Missense_Mutation SNP A C3L-00095_T 9310778 214394939 34561483 85 3294 USH2A 0 . GRCh38 1 215970777 215970777 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.6806-1G>T p.X2269_splice ENST00000307340 347 326 21 292 292 0 strelka-varscan-mutect USH2A,splice_acceptor_variant,,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript splice_acceptor_variant -/18883 6806/15609 2269/5202 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 35/71 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 215970777 215970777 C A 1 0 0 0 0 0 0 1 0 17570 695 24 2 2 USH2A 1 215970777 Splice_Site SNP C C3L-00095_T 1575838 215970777 32985645 86 3295 USH2A 0 . GRCh38 1 216199934 216199934 + Silent SNP G G C C3L-00095_T C3L-00095_N G G c.3504C>G p.= p.T1168T ENST00000307340 17/72 577 513 64 550 550 0 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;USH2A,synonymous_variant,p.=,ENST00000366942,NM_007123.5;RP5-1099E6.3,intron_variant,,ENST00000420867,;MRPS18BP1,downstream_gene_variant,,ENST00000414228,; C ENST00000307340 Transcript synonymous_variant 3891/18883 3504/15609 1168/5202 T acC/acG COSM4983542,COSM4983543,COSM4983544 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 17/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 216199934 216199934 G C 1 0 0 0 0 0 0 0 1 17570 987 35 4 4 USH2A 1 216199934 Silent SNP G C3L-00095_T 229157 216199934 32756488 87 3296 LYPLAL1 0 . GRCh38 1 219211490 219211490 + Splice_Site SNP A A T rs200260515 C3L-00095_T C3L-00095_N A A c.478-2A>T p.X160_splice ENST00000366928 104 86 18 99 99 0 strelka-varscan-mutect LYPLAL1,splice_acceptor_variant,,ENST00000366928,NM_001300772.1,NM_001300771.1,NM_138794.4;LYPLAL1,splice_acceptor_variant,,ENST00000366927,NM_001300770.1;LYPLAL1,splice_acceptor_variant,,ENST00000483635,;LYPLAL1,splice_acceptor_variant,,ENST00000463964,;LYPLAL1,splice_acceptor_variant,,ENST00000475724,;LYPLAL1,splice_acceptor_variant,,ENST00000477938,;LYPLAL1,splice_acceptor_variant,,ENST00000460522,;LYPLAL1,splice_acceptor_variant,,ENST00000469590,;LYPLAL1,splice_acceptor_variant,,ENST00000474379,;LYPLAL1,splice_acceptor_variant,,ENST00000481007,;LYPLAL1,splice_acceptor_variant,,ENST00000478794,; T ENST00000366928 Transcript splice_acceptor_variant -/1898 478/714 160/237 rs200260515 1 1 LYPLAL1 HGNC HGNC:20440 protein_coding YES CCDS1522.1 ENSP00000355895 Q5VWZ2 UPI000013D8ED NM_001300772.1,NM_001300771.1,NM_138794.4 4/4 HIGH 1 SNV 1 1 PASS rs200260515 . 0 202 8 0 0 0 0 0 -20 0.9999986 1 1 1 0 T 5 4 10 219211490 219211490 A T 1 0 0 0 0 0 0 1 0 9030 434 15 4 4 LYPLAL1 1 219211490 Splice_Site SNP A C3L-00095_T 3011556 219211490 29744932 88 3297 MAP10 0 . GRCh38 1 232805336 232805336 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.313C>G p.Gln105Glu p.Q105E ENST00000418460 1/1 395 371 24 513 513 0 strelka-varscan MAP10,missense_variant,p.Gln105Glu,ENST00000418460,NM_019090.2; G ENST00000418460 Transcript missense_variant 445/3516 313/3144 105/1047 Q/E Caa/Gaa 1 1 MAP10 HGNC HGNC:29265 protein_coding YES CCDS44334.1 ENSP00000403208 Q9P2G4 UPI0000418F25 NM_019090.2 tolerated_low_confidence(0.48) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 232805336 232805336 C G 1 0 0 0 0 1 0 0 0 9149 711 25 4 4 MAP10 1 232805336 Missense_Mutation SNP C C3L-00095_T 13593846 232805336 16151086 89 3298 GPR137B 0 . GRCh38 1 236142662 236142662 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.40G>T p.Gly14Cys p.G14C ENST00000366592 1/7 126 114 12 141 141 0 strelka-varscan GPR137B,missense_variant,p.Gly14Cys,ENST00000366592,NM_003272.3;GPR137B,missense_variant,p.Gly14Cys,ENST00000419162,;GPR137B,non_coding_transcript_exon_variant,,ENST00000366591,; T ENST00000366592 Transcript missense_variant 131/2042 40/1200 14/399 G/C Ggc/Tgc 1 1 GPR137B HGNC HGNC:11862 protein_coding YES CCDS1609.1 ENSP00000355551 O60478 UPI0000050441 NM_003272.3 deleterious(0.02) 1/7 hmmpanther:PTHR15146:SF0,hmmpanther:PTHR15146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 236142662 236142662 G T 1 0 0 0 0 1 0 0 0 6532 1116 39 1 1 GPR137B 1 236142662 Missense_Mutation SNP G C3L-00095_T 3337326 236142662 12813760 90 3299 RYR2 0 . GRCh38 1 237330980 237330980 + Missense_Mutation SNP G G T rs559267608 C3L-00095_T C3L-00095_N G G c.271G>T p.Gly91Trp p.G91W ENST00000366574 3/105 369 336 33 421 420 1 strelka-varscan RYR2,missense_variant,p.Gly91Trp,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly75Trp,ENST00000360064,; T ENST00000366574 Transcript missense_variant,splice_region_variant 588/16562 271/14904 91/4967 G/W Ggg/Tgg rs559267608 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 3/105 Gene3D:2.80.10.50,Pfam_domain:PF08709,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 237330980 237330980 G T 1 0 0 0 0 1 0 0 0 14029 1014 35 2 2 RYR2 1 237330980 Missense_Mutation SNP G C3L-00095_T 1188318 237330980 11625442 91 3300 RYR2 0 . GRCh38 1 237566596 237566596 + Missense_Mutation SNP G G T rs774797663 C3L-00095_T C3L-00095_N G G c.3244G>T p.Gly1082Trp p.G1082W ENST00000366574 28/105 186 171 15 195 195 0 strelka-varscan RYR2,missense_variant,p.Gly1082Trp,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly1066Trp,ENST00000360064,; T ENST00000366574 Transcript missense_variant 3561/16562 3244/14904 1082/4967 G/W Ggg/Tgg rs774797663 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.08) 28/105 PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -19.34761 0.9984985 1 1 1 0 T 3 4 10 237566596 237566596 G T 1 0 0 0 0 1 0 0 0 14029 1116 39 1 1 RYR2 1 237566596 Missense_Mutation SNP G C3L-00095_T 235616 237566596 11389826 92 3301 RYR2 0 . GRCh38 1 237756316 237756316 + Missense_Mutation SNP T T A rs727505346 C3L-00095_T C3L-00095_N T T c.11174T>A p.Leu3725Gln p.L3725Q ENST00000366574 81/105 166 146 20 166 166 0 strelka-varscan RYR2,missense_variant,p.Leu3725Gln,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu3709Gln,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript missense_variant 11491/16562 11174/14904 3725/4967 L/Q cTa/cAa rs727505346 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 81/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 uncertain_significance MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 10 237756316 237756316 T A 1 0 0 0 0 1 0 0 0 14029 1522 53 4 4 RYR2 1 237756316 Missense_Mutation SNP T C3L-00095_T 189720 237756316 11200106 93 3302 ZP4 0 . GRCh38 1 237884786 237884786 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1373C>A p.Thr458Asn p.T458N ENST00000611898 10/13 182 159 23 194 194 0 strelka-varscan ZP4,missense_variant,p.Thr458Asn,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Thr458Asn,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; T ENST00000611898 Transcript missense_variant 1660/2474 1373/1623 458/540 T/N aCc/aAc 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0.04) 10/13 Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 237884786 237884786 G T 1 0 0 0 0 1 0 0 0 18810 1261 44 2 2 ZP4 1 237884786 Missense_Mutation SNP G C3L-00095_T 128470 237884786 11071636 94 3303 ZP4 0 . GRCh38 1 237886789 237886789 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.821C>A p.Thr274Asn p.T274N ENST00000611898 6/13 118 112 6 115 114 1 strelka-varscan ZP4,missense_variant,p.Thr274Asn,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Thr274Asn,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; T ENST00000611898 Transcript missense_variant 1108/2474 821/1623 274/540 T/N aCt/aAt 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0) 6/13 Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 237886789 237886789 G T 1 0 0 0 0 1 0 0 0 18810 1029 36 2 2 ZP4 1 237886789 Missense_Mutation SNP G C3L-00095_T 2003 237886789 11069633 95 3304 NLRP3 0 . GRCh38 1 247423949 247423949 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.506C>A p.Thr169Lys p.T169K ENST00000336119 3/9 549 503 46 626 626 0 strelka-varscan NLRP3,missense_variant,p.Thr169Lys,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Thr169Lys,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Thr169Lys,ENST00000366496,;NLRP3,missense_variant,p.Thr169Lys,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Thr169Lys,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Thr169Lys,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript missense_variant 1252/4170 506/3111 169/1036 T/K aCa/aAa 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 deleterious(0) 3/9 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Pfam_domain:PF14484,SMART_domains:SM01288 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 247423949 247423949 C A 1 0 0 0 0 1 0 0 0 10516 478 17 2 2 NLRP3 1 247423949 Missense_Mutation SNP C C3L-00095_T 9537160 247423949 1532473 96 3305 OR2G3 0 . GRCh38 1 247606393 247606394 + Frame_Shift_Ins INS - - A novel C3L-00095_T C3L-00095_N - - c.810dupA p.Gly271ArgfsTer? p.G271Rfs*? ENST00000320002 1/1 171 162 9 167 167 0 varindel-pindel OR2G3,frameshift_variant,p.Gly271ArgfsTer?,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000320002 Transcript frameshift_variant 808-809/930 808-809/930 270/309 Q/QX caa/cAaa 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH insertion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 10 247606393 247606393 - A 1 0 1 1 0 0 0 0 0 11077 595 21 0 0 OR2G3 1 247606393 Frame_Shift_Ins INS - C3L-00095_T 182444 247606393 1350029 97 3306 OR2L5 0 . GRCh38 1 248022705 248022705 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.758C>A p.Pro253His p.P253H ENST00000355281 1/1 239 220 19 251 248 3 strelka-varscan OR2L5,missense_variant,p.Pro253His,ENST00000355281,NM_001258284.1; A ENST00000355281 Transcript missense_variant 758/939 758/939 253/312 P/H cCc/cAc 1 1 OR2L5 HGNC HGNC:15011 protein_coding YES CCDS58068.1 ENSP00000347428 Q8NG80 A0A126GWR8 UPI0000061EEE NM_001258284.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF287,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 248022705 248022705 C A 1 0 0 0 0 1 0 0 0 11087 623 22 2 2 OR2L5 1 248022705 Missense_Mutation SNP C C3L-00095_T 416312 248022705 933717 98 3307 OR2M3 0 . GRCh38 1 248203453 248203453 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.386C>A p.Pro129His p.P129H ENST00000456743 1/1 196 156 40 231 231 0 strelka-varscan OR2M3,missense_variant,p.Pro129His,ENST00000456743,NM_001004689.1; A ENST00000456743 Transcript missense_variant 386/939 386/939 129/312 P/H cCt/cAt 1 1 OR2M3 HGNC HGNC:8269 protein_coding YES CCDS31107.1 ENSP00000389625 Q8NG83 A0A126GV67 UPI000004B234 NM_001004689.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 248203453 248203453 C A 1 0 0 0 0 1 0 0 0 11089 681 24 2 2 OR2M3 1 248203453 Missense_Mutation SNP C C3L-00095_T 180748 248203453 752969 99 3308 10 2 OR2M3 0 . GRCh38 1 248203463 248203463 + Nonsense_Mutation SNP C C G rs61736249 C3L-00095_T C3L-00095_N C C c.396C>G p.Tyr132Ter p.Y132* ENST00000456743 1/1 196 177 19 237 237 0 strelka-varscan OR2M3,stop_gained,p.Tyr132Ter,ENST00000456743,NM_001004689.1; G ENST00000456743 Transcript stop_gained 396/939 396/939 132/312 Y/* taC/taG rs61736249 1 1 OR2M3 HGNC HGNC:8269 protein_coding YES CCDS31107.1 ENSP00000389625 Q8NG83 A0A126GV67 UPI000004B234 NM_001004689.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 10 248203463 248203463 C G 1 0 0 0 0 0 1 0 0 11089 489 17 4 4 OR2M3 1 248203463 Nonsense_Mutation SNP C C3L-00095_T 10 248203463 752959 100 3309 10 2 GREB1 0 . GRCh38 2 11615278 11615278 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.3310C>G p.Leu1104Val p.L1104V ENST00000381486 20/33 141 130 11 201 201 0 strelka-varscan-mutect GREB1,missense_variant,p.Leu1104Val,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Leu1104Val,ENST00000234142,;GREB1,missense_variant,p.Leu102Val,ENST00000396123,;GREB1,downstream_gene_variant,,ENST00000432985,;GREB1,non_coding_transcript_exon_variant,,ENST00000472040,; G ENST00000381486 Transcript missense_variant 3610/8484 3310/5850 1104/1949 L/V Ctg/Gtg 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 deleterious(0.05) 20/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -15.33644 0.9999754 1 1 1 0 G 3 3 10 11615278 11615278 C G 1 0 0 0 0 1 0 0 0 6639 796 28 4 4 GREB1 2 11615278 Missense_Mutation SNP C C3L-00095_T 11615278 230578251 101 3310 NT5C1B 0 . GRCh38 2 18564064 18564064 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1565C>A p.Ala522Asp p.A522D ENST00000359846 10/10 94 85 9 92 92 0 strelka-varscan-mutect NT5C1B,missense_variant,p.Ala462Asp,ENST00000304081,NM_033253.3;NT5C1B,missense_variant,p.Ala522Asp,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Ala522Asp,ENST00000532967,NM_001199104.1;NT5C1B,missense_variant,p.Ala177Asp,ENST00000418427,;NT5C1B-RDH14,intron_variant,,ENST00000444297,NM_001199103.1;RDH14,upstream_gene_variant,,ENST00000381249,NM_020905.3;RDH14,upstream_gene_variant,,ENST00000468071,;NT5C1B,3_prime_UTR_variant,,ENST00000406971,; T ENST00000359846 Transcript missense_variant 1643/2475 1565/1833 522/610 A/D gCc/gAc 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 tolerated(0.1) 10/10 Pfam_domain:PF06189,hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.55714 0.9999998 1 1 1 0 T 3 4 10 18564064 18564064 G T 1 0 0 0 0 1 0 0 0 10749 1203 42 2 2 NT5C1B 2 18564064 Missense_Mutation SNP G C3L-00095_T 6948786 18564064 223629465 102 3311 TDRD15 0 . GRCh38 2 21138073 21138073 + Silent SNP A A G novel C3L-00095_T C3L-00095_N A A c.606A>G p.= p.Q202Q ENST00000405799 4/4 121 112 9 119 119 0 strelka-varscan-mutect TDRD15,synonymous_variant,p.=,ENST00000405799,;TDRD15,synonymous_variant,p.=,ENST00000622654,; G ENST00000405799 Transcript synonymous_variant 936/6135 606/5805 202/1934 Q caA/caG 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 21138073 21138073 A G 1 0 0 0 0 0 0 0 1 16141 40 2 5 5 TDRD15 2 21138073 Silent SNP A C3L-00095_T 2574009 21138073 221055456 103 3312 ASXL2 0 . GRCh38 2 25742568 25742568 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.2218G>C p.Asp740His p.D740H ENST00000404843 10/10 215 199 16 229 229 0 strelka-varscan ASXL2,missense_variant,p.Asp1257His,ENST00000435504,NM_018263.4;ASXL2,missense_variant,p.Asp1229His,ENST00000336112,;ASXL2,missense_variant,p.Asp740His,ENST00000404843,; G ENST00000404843 Transcript missense_variant 2656/3299 2218/2757 740/918 D/H Gat/Cat 1 -1 ASXL2 HGNC HGNC:23805 protein_coding YES ENSP00000383920 Q76L83 UPI0000246C78 deleterious(0) 10/10 hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 25742568 25742568 C G 1 0 0 0 0 1 0 0 0 1215 826 29 4 4 ASXL2 2 25742568 Missense_Mutation SNP C C3L-00095_T 4604495 25742568 216450961 104 3313 C2orf70 0 . GRCh38 2 26576065 26576065 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.238C>A p.Leu80Ile p.L80I ENST00000329615 2/4 417 378 39 588 588 0 strelka-varscan C2orf70,missense_variant,p.Pro67His,ENST00000409392,NM_001322426.1;C2orf70,missense_variant,p.Leu80Ile,ENST00000329615,NM_001105519.1;C2orf70,upstream_gene_variant,,ENST00000453368,;C2orf70,non_coding_transcript_exon_variant,,ENST00000479453,; A ENST00000329615 Transcript missense_variant 269/731 238/606 80/201 L/I Ctc/Atc 1 1 C2orf70 HGNC HGNC:27938 protein_coding YES CCDS42661.1 ENSP00000332875 A6NJV1 UPI00001AFA74 NM_001105519.1 deleterious(0.02) 2/4 hmmpanther:PTHR34924:SF1,hmmpanther:PTHR34924,Pfam_domain:PF10629 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 26576065 26576065 C A 1 0 0 0 0 1 0 0 0 2044 681 24 2 2 C2orf70 2 26576065 Missense_Mutation SNP C C3L-00095_T 833497 26576065 215617464 105 3314 CAD 0 . GRCh38 2 27223927 27223927 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1006C>T p.His336Tyr p.H336Y ENST00000264705 8/44 161 147 14 203 203 0 strelka-varscan CAD,missense_variant,p.His336Tyr,ENST00000264705,NM_004341.3;CAD,missense_variant,p.His336Tyr,ENST00000403525,NM_001306079.1;CAD,upstream_gene_variant,,ENST00000464159,;CAD,upstream_gene_variant,,ENST00000491891,; T ENST00000264705 Transcript missense_variant 1168/7265 1006/6678 336/2225 H/Y Cac/Tac 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 deleterious(0.02) 8/44 Gene3D:3.40.50.880,HAMAP:MF_01209,Pfam_domain:PF00117,PROSITE_profiles:PS51273,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF5,Superfamily_domains:SSF52317,TIGRFAM_domain:TIGR01368 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 27223927 27223927 C T 1 0 0 0 0 1 0 0 0 2255 826 29 3 3 CAD 2 27223927 Missense_Mutation SNP C C3L-00095_T 647862 27223927 214969602 106 3315 GPN1 0 . GRCh38 2 27629390 27629390 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.23G>T p.Ser8Ile p.S8I ENST00000407583 2/15 187 174 13 156 155 1 strelka-varscan GPN1,missense_variant,p.Ser8Ile,ENST00000407583,NM_001145047.1;GPN1,intron_variant,,ENST00000264718,;GPN1,intron_variant,,ENST00000616939,NM_007266.3;GPN1,intron_variant,,ENST00000610189,;GPN1,intron_variant,,ENST00000424214,NM_001145048.1;GPN1,intron_variant,,ENST00000515877,;GPN1,intron_variant,,ENST00000458167,NM_001145049.1;GPN1,intron_variant,,ENST00000503738,;CCDC121,upstream_gene_variant,,ENST00000324364,NM_024584.4;CCDC121,upstream_gene_variant,,ENST00000394775,NM_001142683.2;CCDC121,upstream_gene_variant,,ENST00000522876,;GPN1,non_coding_transcript_exon_variant,,ENST00000461249,;RP11-158I13.2,intron_variant,,ENST00000505973,;GPN1,intron_variant,,ENST00000481754,;GPN1,intron_variant,,ENST00000478484,;GPN1,intron_variant,,ENST00000436280,; T ENST00000407583 Transcript missense_variant 73/1395 23/1089 8/362 S/I aGc/aTc 1 1 GPN1 HGNC HGNC:17030 protein_coding CCDS46248.1 ENSP00000384255 Q9HCN4 UPI000173A56D NM_001145047.1 tolerated(0.09) 2/15 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 27629390 27629390 G T 1 0 0 0 0 1 0 0 0 6519 971 34 2 2 GPN1 2 27629390 Missense_Mutation SNP G C3L-00095_T 405463 27629390 214564139 107 3316 C2orf71 0 . GRCh38 2 29072023 29072023 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.2239C>A p.Leu747Met p.L747M ENST00000331664 1/2 128 120 8 227 227 0 strelka-varscan C2orf71,missense_variant,p.Leu747Met,ENST00000331664,NM_001029883.2; T ENST00000331664 Transcript missense_variant 2239/7044 2239/3867 747/1288 L/M Ctg/Atg COSM1019982 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.16) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 29072023 29072023 G T 1 0 0 0 0 1 0 0 0 2045 962 34 2 2 C2orf71 2 29072023 Missense_Mutation SNP G C3L-00095_T 1442633 29072023 213121506 108 3317 ALK 0 . GRCh38 2 29532061 29532061 + Silent SNP C C A rs757878984 C3L-00095_T C3L-00095_N C C c.1008G>T p.= p.P336P ENST00000389048 4/29 641 608 33 793 793 0 strelka-varscan ALK,synonymous_variant,p.=,ENST00000389048,NM_004304.4;ALK,5_prime_UTR_variant,,ENST00000618119,; A ENST00000389048 Transcript synonymous_variant 1915/6220 1008/4863 336/1620 P ccG/ccT rs757878984 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 4/29 PROSITE_profiles:PS50060,Pfam_domain:PF00629,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 29532061 29532061 C A 1 0 0 0 0 0 0 0 1 625 523 19 1 1 ALK 2 29532061 Silent SNP C C3L-00095_T 460038 29532061 212661468 109 3318 CAPN13 0 . GRCh38 2 30758118 30758118 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.794G>T p.Trp265Leu p.W265L ENST00000295055 8/23 87 78 9 92 92 0 strelka-varscan CAPN13,missense_variant,p.Trp265Leu,ENST00000295055,NM_144575.2;CAPN13,non_coding_transcript_exon_variant,,ENST00000465960,;CAPN13,missense_variant,p.Trp265Leu,ENST00000458085,; A ENST00000295055 Transcript missense_variant 971/2683 794/2010 265/669 W/L tGg/tTg 1 -1 CAPN13 HGNC HGNC:16663 protein_coding YES CCDS46252.1 ENSP00000295055 Q6MZZ7 UPI00000463E5 NM_144575.2 deleterious(0.03) 8/23 Gene3D:3.90.70.10,Pfam_domain:PF00648,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF282,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 30758118 30758118 C A 1 0 0 0 0 1 0 0 0 2318 595 21 2 2 CAPN13 2 30758118 Missense_Mutation SNP C C3L-00095_T 1226057 30758118 211435411 110 3319 SPAST 0 . GRCh38 2 32114737 32114737 + Missense_Mutation SNP C C T rs768241184 C3L-00095_T C3L-00095_N C C c.782C>T p.Ser261Leu p.S261L ENST00000615843 5/17 374 343 31 446 446 0 strelka-varscan SPAST,missense_variant,p.Ser261Leu,ENST00000615843,NM_014946.3;SPAST,missense_variant,p.Ser261Leu,ENST00000315285,;SPAST,missense_variant,p.Ser229Leu,ENST00000345662,NM_199436.1;SPAST,missense_variant,p.Ser175Leu,ENST00000621856,; T ENST00000615843 Transcript missense_variant 1003/5212 782/1851 261/616 S/L tCa/tTa rs768241184,CM000430,CM107565,COSM4508630 1 1 SPAST HGNC HGNC:11233 protein_coding YES CCDS1778.1 ENSP00000480893 Q9UBP0 E5KRP5 UPI0000038A6B NM_014946.3 tolerated(0.05) 5/17 HAMAP:MF_03021,PIRSF_domain:PIRSF037338,hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF86 0,0,0,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32114737 32114737 C T 1 0 0 0 0 1 0 0 0 15328 838 29 3 3 SPAST 2 32114737 Missense_Mutation SNP C C3L-00095_T 1356619 32114737 210078792 111 3320 LTBP1 0 . GRCh38 2 33187010 33187010 + Silent SNP G G T rs1065324 C3L-00095_T C3L-00095_N G G c.1356G>T p.= p.A452A ENST00000404816 6/34 278 255 23 305 305 0 strelka-varscan LTBP1,synonymous_variant,p.=,ENST00000404816,NM_206943.2;LTBP1,synonymous_variant,p.=,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,synonymous_variant,p.=,ENST00000404525,NM_001166265.1;LTBP1,synonymous_variant,p.=,ENST00000407925,NM_000627.3;LTBP1,synonymous_variant,p.=,ENST00000402934,;LTBP1,synonymous_variant,p.=,ENST00000432635,; T ENST00000404816 Transcript synonymous_variant 1709/6333 1356/5166 452/1721 A gcG/gcT rs1065324 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 6/34 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 LOW 1 SNV 5 1 PASS . . 0 80 0 0 0 0 0 130 -7.475411 0 0 1 0 0 T 2 4 10 33187010 33187010 G T 1 0 0 0 0 0 0 0 1 8979 1132 40 1 1 LTBP1 2 33187010 Silent SNP G C3L-00095_T 1072273 33187010 209006519 112 3321 NRXN1 0 . GRCh38 2 50620119 50620119 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.1343T>C p.Leu448Pro p.L448P ENST00000404971 9/24 167 155 12 231 231 0 strelka-varscan NRXN1,missense_variant,p.Leu408Pro,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Leu400Pro,ENST00000625672,;NRXN1,missense_variant,p.Leu448Pro,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Leu408Pro,ENST00000401669,;NRXN1,missense_variant,p.Leu396Pro,ENST00000405472,;NRXN1,missense_variant,p.Leu400Pro,ENST00000630543,;NRXN1,missense_variant,p.Leu380Pro,ENST00000628515,;NRXN1,missense_variant,p.Leu138Pro,ENST00000406859,;NRXN1,missense_variant,p.Leu123Pro,ENST00000402717,;NRXN1,missense_variant,p.Leu135Pro,ENST00000625891,;NRXN1,upstream_gene_variant,,ENST00000495871,;RP11-358H12.1,upstream_gene_variant,,ENST00000634985,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000628761,;NRXN1,downstream_gene_variant,,ENST00000630431,;NRXN1,upstream_gene_variant,,ENST00000637605,;NRXN1,missense_variant,p.Leu135Pro,ENST00000331040,;NRXN1,3_prime_UTR_variant,,ENST00000626249,; G ENST00000404971 Transcript missense_variant 2683/7578 1343/4644 448/1547 L/P cTg/cCg 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 50620119 50620119 A G 1 0 0 0 0 1 0 0 0 10724 188 7 5 5 NRXN1 2 50620119 Missense_Mutation SNP A C3L-00095_T 17433109 50620119 191573410 113 3322 SPTBN1 0 . GRCh38 2 54668375 54668375 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.6901G>A p.Ala2301Thr p.A2301T ENST00000356805 36/36 284 254 30 381 381 0 strelka-varscan SPTBN1,missense_variant,p.Ala2303Thr,ENST00000615901,;SPTBN1,missense_variant,p.Ala2301Thr,ENST00000356805,NM_003128.2;AC093110.3,intron_variant,,ENST00000626206,;SPTBN1,non_coding_transcript_exon_variant,,ENST00000467371,; A ENST00000356805 Transcript missense_variant 7182/8482 6901/7095 2301/2364 A/T Gct/Act 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 tolerated(0.19) 36/36 PROSITE_profiles:PS50003,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,PIRSF_domain:PIRSF002297,Gene3D:2.30.29.30,Pfam_domain:PF15410,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 54668375 54668375 G A 1 0 0 0 0 1 0 0 0 15475 1203 42 3 3 SPTBN1 2 54668375 Missense_Mutation SNP G C3L-00095_T 4048256 54668375 187525154 114 3323 USP34 0 . GRCh38 2 61347963 61347963 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2192G>T p.Gly731Val p.G731V ENST00000398571 15/80 255 240 15 366 365 1 strelka-varscan USP34,missense_variant,p.Gly731Val,ENST00000398571,NM_014709.3;USP34,non_coding_transcript_exon_variant,,ENST00000460004,;USP34,downstream_gene_variant,,ENST00000453133,; A ENST00000398571 Transcript missense_variant 2269/11357 2192/10641 731/3546 G/V gGg/gTg 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 deleterious_low_confidence(0.02) 15/80 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 61347963 61347963 C A 1 0 0 0 0 1 0 0 0 17607 623 22 2 2 USP34 2 61347963 Missense_Mutation SNP C C3L-00095_T 6679588 61347963 180845566 115 3324 OTX1 0 . GRCh38 2 63055997 63055997 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.746G>T p.Ser249Ile p.S249I ENST00000282549 5/5 447 401 46 572 572 0 strelka-varscan OTX1,missense_variant,p.Ser249Ile,ENST00000282549,NM_014562.3;OTX1,missense_variant,p.Ser249Ile,ENST00000366671,NM_001199770.1;OTX1,3_prime_UTR_variant,,ENST00000405984,;OTX1,downstream_gene_variant,,ENST00000484066,;OTX1,downstream_gene_variant,,ENST00000477348,;OTX1,downstream_gene_variant,,ENST00000476383,; T ENST00000282549 Transcript missense_variant 1022/2861 746/1065 249/354 S/I aGc/aTc 1 1 OTX1 HGNC HGNC:8521 protein_coding YES CCDS1873.1 ENSP00000282549 P32242 UPI0000130F36 NM_014562.3 deleterious(0) 5/5 hmmpanther:PTHR24329:SF310,hmmpanther:PTHR24329,Pfam_domain:PF03529,Prints_domain:PR01255 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 63055997 63055997 G T 1 0 0 0 0 1 0 0 0 11390 971 34 2 2 OTX1 2 63055997 Missense_Mutation SNP G C3L-00095_T 1708034 63055997 179137532 116 3325 MEIS1 0 . GRCh38 2 66571280 66571280 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.1143G>T p.= p.R381R ENST00000398506 11/11 279 254 25 354 354 0 strelka-varscan MEIS1,synonymous_variant,p.=,ENST00000398506,;MEIS1,3_prime_UTR_variant,,ENST00000488550,;MEIS1,3_prime_UTR_variant,,ENST00000272369,NM_002398.2;MEIS1,3_prime_UTR_variant,,ENST00000495021,;MEIS1,downstream_gene_variant,,ENST00000560281,;AC007392.3,upstream_gene_variant,,ENST00000433396,;MEIS1,non_coding_transcript_exon_variant,,ENST00000409517,;MEIS1,downstream_gene_variant,,ENST00000475239,;MEIS1,downstream_gene_variant,,ENST00000606455,;MEIS1,downstream_gene_variant,,ENST00000450027,;MEIS1,downstream_gene_variant,,ENST00000542964,; T ENST00000398506 Transcript synonymous_variant 1481/3530 1143/1392 381/463 R cgG/cgT 1 1 MEIS1 HGNC HGNC:7000 protein_coding ENSP00000381518 O00470 UPI00005BDA98 11/11 hmmpanther:PTHR11850:SF126,hmmpanther:PTHR11850 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 66571280 66571280 G T 1 0 0 0 0 0 0 0 1 9411 1219 43 2 2 MEIS1 2 66571280 Silent SNP G C3L-00095_T 3515283 66571280 175622249 117 3326 GFPT1 0 . GRCh38 2 69358361 69358361 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.511A>T p.Thr171Ser p.T171S ENST00000357308 6/20 415 384 31 372 372 0 strelka-varscan GFPT1,missense_variant,p.Thr171Ser,ENST00000357308,NM_001244710.1;GFPT1,missense_variant,p.Thr171Ser,ENST00000361060,NM_002056.3;GFPT1,non_coding_transcript_exon_variant,,ENST00000493759,; A ENST00000357308 Transcript missense_variant 694/8703 511/2100 171/699 T/S Act/Tct 1 -1 GFPT1 HGNC HGNC:4241 protein_coding YES CCDS58713.1 ENSP00000349860 Q06210 UPI000015C8AD NM_001244710.1 tolerated(1) 6/20 PROSITE_profiles:PS51278,hmmpanther:PTHR10937,hmmpanther:PTHR10937:SF2,Gene3D:3.60.20.10,Pfam_domain:PF13522,Superfamily_domains:SSF56235 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 69358361 69358361 T A 1 0 0 0 0 1 0 0 0 6219 1638 57 4 4 GFPT1 2 69358361 Missense_Mutation SNP T C3L-00095_T 2787081 69358361 172835168 118 3327 EMX1 0 . GRCh38 2 72918167 72918167 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.315G>T p.= p.A105A ENST00000258106 1/3 102 94 8 148 148 0 strelka-varscan EMX1,synonymous_variant,p.=,ENST00000258106,NM_004097.2;EMX1,intron_variant,,ENST00000394111,;EMX1,upstream_gene_variant,,ENST00000473732,; T ENST00000258106 Transcript synonymous_variant 693/2188 315/873 105/290 A gcG/gcT 1 1 EMX1 HGNC HGNC:3340 protein_coding YES CCDS1921.2 ENSP00000258106 Q04741 UPI0000D47CF7 NM_004097.2 1/3 hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF26,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 72918167 72918167 G T 1 0 0 0 0 0 0 0 1 4949 1103 39 1 1 EMX1 2 72918167 Silent SNP G C3L-00095_T 3559806 72918167 169275362 119 3328 LRRTM1 0 . GRCh38 2 80302937 80302937 + Missense_Mutation SNP T T A rs76300062 C3L-00095_T C3L-00095_N T T c.883A>T p.Ile295Phe p.I295F ENST00000295057 2/2 149 131 18 245 245 0 strelka-varscan LRRTM1,missense_variant,p.Ile295Phe,ENST00000295057,;LRRTM1,missense_variant,p.Ile295Phe,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Ile295Phe,ENST00000433224,;LRRTM1,missense_variant,p.Ile295Phe,ENST00000417012,; A ENST00000295057 Transcript missense_variant 1540/2599 883/1569 295/522 I/F Atc/Ttc rs76300062 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE deleterious(0) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 198 0 0 0 0 0 12 -3.404874 0 0 1 0 0 A 3 1 10 80302937 80302937 T A 1 0 0 0 0 1 0 0 0 8945 1464 51 4 4 LRRTM1 2 80302937 Missense_Mutation SNP T C3L-00095_T 7384770 80302937 161890592 120 3329 DNAH6 0 . GRCh38 2 84685387 84685387 + Silent SNP C C T rs761172209 C3L-00095_T C3L-00095_N C C c.6978C>T p.= p.C2326C ENST00000389394 43/77 187 177 10 146 146 0 strelka-varscan DNAH6,synonymous_variant,p.=,ENST00000389394,NM_001370.1;DNAH6,synonymous_variant,p.=,ENST00000237449,;DNAH6,intron_variant,,ENST00000602588,; T ENST00000389394 Transcript synonymous_variant 7115/12795 6978/12477 2326/4158 C tgC/tgT rs761172209,COSM4141267 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 43/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF12775,Superfamily_domains:SSF52540 0,1 LOW 1 SNV 5 0,1 1 PASS . . 0 208 0 2 0 0 0 0 -12.69908 0.9999994 1 1 1 0 T 2 4 10 84685387 84685387 C T 1 0 0 0 0 0 0 0 1 4420 747 26 3 3 DNAH6 2 84685387 Silent SNP C C3L-00095_T 4382450 84685387 157508142 121 3330 ZNF514 0 . GRCh38 2 95149708 95149708 + Silent SNP G G C rs140564139 C3L-00095_T C3L-00095_N G G c.777C>G p.= p.P259P ENST00000295208 5/5 237 217 20 284 284 0 strelka-varscan ZNF514,synonymous_variant,p.=,ENST00000295208,NM_032788.1;ZNF514,synonymous_variant,p.=,ENST00000411425,;ZNF514,downstream_gene_variant,,ENST00000447814,;MRPS5,upstream_gene_variant,,ENST00000475040,;ZNF514,non_coding_transcript_exon_variant,,ENST00000496060,; C ENST00000295208 Transcript synonymous_variant 1240/3011 777/1203 259/400 P ccC/ccG rs140564139,COSM3583972 1 -1 ZNF514 HGNC HGNC:25894 protein_coding YES CCDS2011.1 ENSP00000295208 Q96K75 UPI0000070647 NM_032788.1 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF2,Superfamily_domains:SSF57667 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 95149708 95149708 G C 1 0 0 0 0 0 0 0 1 18531 987 35 4 4 ZNF514 2 95149708 Silent SNP G C3L-00095_T 10464321 95149708 147043821 122 3331 NCAPH 0 . GRCh38 2 96360710 96360710 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1587G>T p.Arg529Ser p.R529S ENST00000240423 12/18 121 110 11 164 163 1 strelka-varscan NCAPH,missense_variant,p.Arg518Ser,ENST00000455200,;NCAPH,missense_variant,p.Arg529Ser,ENST00000240423,NM_015341.4,NM_001281710.1,NM_001281711.1;NCAPH,missense_variant,p.Arg393Ser,ENST00000427946,NM_001281712.1;NCAPH,missense_variant,p.Arg518Ser,ENST00000435975,;NCAPH,upstream_gene_variant,,ENST00000435349,;NCAPH,downstream_gene_variant,,ENST00000477409,; T ENST00000240423 Transcript missense_variant,splice_region_variant 1630/2763 1587/2226 529/741 R/S agG/agT 1 1 NCAPH HGNC HGNC:1112 protein_coding YES CCDS2021.1 ENSP00000240423 Q15003 UPI0000163F72 NM_015341.4,NM_001281710.1,NM_001281711.1 tolerated(0.27) 12/18 hmmpanther:PTHR13108,Pfam_domain:PF05786,PIRSF_domain:PIRSF017126 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 96360710 96360710 G T 1 0 0 0 0 1 0 0 0 10225 1246 43 2 2 NCAPH 2 96360710 Missense_Mutation SNP G C3L-00095_T 1211002 96360710 145832819 123 3332 MFSD9 0 . GRCh38 2 102719105 102719105 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.740C>T p.Thr247Ile p.T247I ENST00000258436 6/6 249 214 35 282 281 1 strelka-varscan MFSD9,missense_variant,p.Thr247Ile,ENST00000258436,NM_032718.3;MFSD9,upstream_gene_variant,,ENST00000496253,;MFSD9,3_prime_UTR_variant,,ENST00000438943,;MFSD9,3_prime_UTR_variant,,ENST00000437075,;MFSD9,3_prime_UTR_variant,,ENST00000411991,;MFSD9,3_prime_UTR_variant,,ENST00000428085,; A ENST00000258436 Transcript missense_variant 784/4049 740/1425 247/474 T/I aCa/aTa 1 -1 MFSD9 HGNC HGNC:28158 protein_coding YES CCDS2063.1 ENSP00000258436 Q8NBP5 UPI0000070215 NM_032718.3 tolerated(0.18) 6/6 PROSITE_profiles:PS50850,hmmpanther:PTHR23504,hmmpanther:PTHR23504:SF14,Pfam_domain:PF07690 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 102719105 102719105 G A 1 0 0 0 0 1 0 0 0 9497 1377 48 3 3 MFSD9 2 102719105 Missense_Mutation SNP G C3L-00095_T 6358395 102719105 139474424 124 3333 GCC2 0 . GRCh38 2 108481725 108481725 + Nonsense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.3089C>G p.Ser1030Ter p.S1030* ENST00000309863 10/23 134 120 14 118 118 0 strelka-varscan GCC2,stop_gained,p.Ser1030Ter,ENST00000309863,NM_181453.3;GCC2,stop_gained,p.Ser10Ter,ENST00000393321,;GCC2,missense_variant,p.Gln64Glu,ENST00000447558,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,upstream_gene_variant,,ENST00000481729,; G ENST00000309863 Transcript stop_gained 3803/7537 3089/5055 1030/1684 S/* tCa/tGa 1 1 GCC2 HGNC HGNC:23218 protein_coding YES CCDS33268.1 ENSP00000307939 Q8IWJ2 UPI000049DF0C NM_181453.3 10/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF25 HIGH 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -19.88611 0.9999999 1 1 1 0 G 4 3 10 108481725 108481725 C G 1 0 0 0 0 0 1 0 0 6156 838 29 4 4 GCC2 2 108481725 Nonsense_Mutation SNP C C3L-00095_T 5762620 108481725 133711804 125 3334 SH3RF3 0 . GRCh38 2 109490820 109490820 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2364G>T p.Met788Ile p.M788I ENST00000309415 9/10 122 115 7 181 181 0 strelka-varscan SH3RF3,missense_variant,p.Met788Ile,ENST00000309415,NM_001099289.2; T ENST00000309415 Transcript missense_variant 2557/5803 2364/2649 788/882 M/I atG/atT 1 1 SH3RF3 HGNC HGNC:24699 protein_coding YES CCDS74557.1 ENSP00000309186 Q8TEJ3 UPI0000DD7AEA NM_001099289.2 tolerated(0.08) 9/10 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -10.32454 0.9999852 1 1 1 0 T 3 4 10 109490820 109490820 G T 1 0 0 0 0 1 0 0 0 14519 1348 47 2 2 SH3RF3 2 109490820 Missense_Mutation SNP G C3L-00095_T 1009095 109490820 132702709 126 3335 POLR1B 0 . GRCh38 2 112549295 112549295 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.635G>T p.Gly212Val p.G212V ENST00000541869 5/16 228 215 13 189 189 0 strelka-varscan POLR1B,missense_variant,p.Gly212Val,ENST00000541869,NM_001282772.1;POLR1B,missense_variant,p.Gly174Val,ENST00000263331,NM_019014.5;POLR1B,missense_variant,p.Gly174Val,ENST00000409894,NM_001282774.1;POLR1B,missense_variant,p.Gly118Val,ENST00000417433,NM_001137604.2,NM_001282779.1,NM_001282777.1;POLR1B,intron_variant,,ENST00000537335,NM_001282776.1;POLR1B,downstream_gene_variant,,ENST00000430769,;POLR1B,downstream_gene_variant,,ENST00000438748,;POLR1B,non_coding_transcript_exon_variant,,ENST00000496238,;POLR1B,upstream_gene_variant,,ENST00000498054,;POLR1B,3_prime_UTR_variant,,ENST00000333990,;POLR1B,3_prime_UTR_variant,,ENST00000424062,;POLR1B,non_coding_transcript_exon_variant,,ENST00000468475,;POLR1B,intron_variant,,ENST00000448770,;POLR1B,intron_variant,,ENST00000430293,;POLR1B,upstream_gene_variant,,ENST00000475318,; T ENST00000541869 Transcript missense_variant 751/5059 635/3522 212/1173 G/V gGc/gTc 1 1 POLR1B HGNC HGNC:20454 protein_coding YES CCDS62988.1 ENSP00000444136 Q9H9Y6 UPI0002065A70 NM_001282772.1 deleterious(0.01) 5/16 Gene3D:2a6hC02,Pfam_domain:PF04563,hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF5,Superfamily_domains:SSF64484 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 112549295 112549295 G T 1 0 0 0 0 1 0 0 0 12320 1203 42 2 2 POLR1B 2 112549295 Missense_Mutation SNP G C3L-00095_T 3058475 112549295 129644234 127 3336 DPP10 0 . GRCh38 2 115746135 115746135 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.914G>C p.Gly305Ala p.G305A ENST00000393147 10/26 249 228 21 257 257 0 strelka-varscan DPP10,missense_variant,p.Gly301Ala,ENST00000410059,NM_001321910.1,NM_001321911.1,NM_001321914.1,NM_001321905.1,NM_001321906.1,NM_020868.3;DPP10,missense_variant,p.Gly251Ala,ENST00000409163,NM_001178036.1,NM_001178037.1;DPP10,missense_variant,p.Gly294Ala,ENST00000310323,NM_001004360.3;DPP10,missense_variant,p.Gly305Ala,ENST00000393147,NM_001178034.1; C ENST00000393147 Transcript missense_variant 1269/2758 914/2403 305/800 G/A gGa/gCa 1 1 DPP10 HGNC HGNC:20823 protein_coding YES CCDS54388.1 ENSP00000376855 Q8N608 UPI00015E0A22 NM_001178034.1 deleterious(0.02) 10/26 hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 115746135 115746135 G C 1 0 0 0 0 1 0 0 0 4542 1174 41 4 4 DPP10 2 115746135 Missense_Mutation SNP G C3L-00095_T 3196840 115746135 126447394 128 3337 GLI2 0 . GRCh38 2 120988976 120988976 + Missense_Mutation SNP G G T rs749819734 C3L-00095_T C3L-00095_N G G c.3062G>T p.Arg1021Leu p.R1021L ENST00000452319 14/14 180 158 22 199 198 1 strelka-varscan GLI2,missense_variant,p.Arg1021Leu,ENST00000452319,;GLI2,missense_variant,p.Arg1021Leu,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,downstream_gene_variant,,ENST00000437950,; T ENST00000452319 Transcript missense_variant 3122/6799 3062/4761 1021/1586 R/L cGc/cTc rs749819734,COSM4168845 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 deleterious(0.02) 14/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 0,1 MODERATE 1 SNV 5 0,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999904 1 1 1 0 T 3 4 10 120988976 120988976 G T 1 0 0 0 0 1 0 0 0 6316 1087 38 1 1 GLI2 2 120988976 Missense_Mutation SNP G C3L-00095_T 5242841 120988976 121204553 129 3338 GLI2 0 . GRCh38 2 120989047 120989047 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.3133G>T p.Asp1045Tyr p.D1045Y ENST00000452319 14/14 190 178 12 235 234 1 strelka-varscan GLI2,missense_variant,p.Asp1045Tyr,ENST00000452319,;GLI2,missense_variant,p.Asp1045Tyr,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,downstream_gene_variant,,ENST00000437950,; T ENST00000452319 Transcript missense_variant 3193/6799 3133/4761 1045/1586 D/Y Gac/Tac 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 deleterious(0) 14/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 120989047 120989047 G T 1 0 0 0 0 1 0 0 0 6316 1174 41 2 2 GLI2 2 120989047 Missense_Mutation SNP G C3L-00095_T 71 120989047 121204482 130 3339 CYP27C1 0 . GRCh38 2 127199539 127199539 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.389G>T p.Ser130Ile p.S130I ENST00000335247 4/8 112 104 8 138 138 0 strelka-varscan CYP27C1,missense_variant,p.Ser130Ile,ENST00000335247,NM_001001665.3;CYP27C1,missense_variant,p.Ser130Ile,ENST00000409327,; A ENST00000335247 Transcript missense_variant,splice_region_variant 520/4401 389/1119 130/372 S/I aGc/aTc COSM1202844 1 -1 CYP27C1 HGNC HGNC:33480 protein_coding YES CCDS33285.1 ENSP00000334128 Q4G0S4 A0A024RAI7 UPI00001995F8 NM_001001665.3 deleterious(0) 4/8 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF9,Superfamily_domains:SSF48264 1 MODERATE 1 SNV 1 1 1 PASS . . 0 197 11 2 0 0 0 0 -12.07294 0.9955223 1 1 1 0 A 3 1 10 127199539 127199539 C A 1 0 0 0 0 1 0 0 0 3963 753 26 2 2 CYP27C1 2 127199539 Missense_Mutation SNP C C3L-00095_T 6210492 127199539 114993990 131 3340 IWS1 0 . GRCh38 2 127505570 127505570 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.333G>C p.Glu111Asp p.E111D ENST00000295321 3/14 180 163 17 258 258 0 strelka-varscan IWS1,missense_variant,p.Glu111Asp,ENST00000295321,NM_017969.2;IWS1,missense_variant,p.Glu116Asp,ENST00000409725,;AC010976.2,intron_variant,,ENST00000630740,;AC010976.2,intron_variant,,ENST00000628607,;AC010976.2,intron_variant,,ENST00000629356,;AC010976.2,intron_variant,,ENST00000629464,;AC010976.2,intron_variant,,ENST00000599001,;AC010976.2,intron_variant,,ENST00000625623,;AC010976.2,intron_variant,,ENST00000626901,;AC010976.2,downstream_gene_variant,,ENST00000627205,;IWS1,non_coding_transcript_exon_variant,,ENST00000486662,;IWS1,non_coding_transcript_exon_variant,,ENST00000495369,;IWS1,non_coding_transcript_exon_variant,,ENST00000436740,;IWS1,non_coding_transcript_exon_variant,,ENST00000460511,;IWS1,non_coding_transcript_exon_variant,,ENST00000483889,;IWS1,non_coding_transcript_exon_variant,,ENST00000479083,;IWS1,non_coding_transcript_exon_variant,,ENST00000478949,;IWS1,upstream_gene_variant,,ENST00000497888,; G ENST00000295321 Transcript missense_variant 593/2958 333/2460 111/819 E/D gaG/gaC 1 -1 IWS1 HGNC HGNC:25467 protein_coding YES CCDS2146.1 ENSP00000295321 Q96ST2 UPI000006EA82 NM_017969.2 tolerated_low_confidence(0.22) 3/14 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF56 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 127505570 127505570 C G 1 0 0 0 0 1 0 0 0 7837 680 24 4 4 IWS1 2 127505570 Missense_Mutation SNP C C3L-00095_T 306031 127505570 114687959 132 3341 MAP3K19 0 . GRCh38 2 134986143 134986143 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2729C>A p.Ala910Glu p.A910E ENST00000392915 10/13 168 156 12 110 110 0 strelka-varscan MAP3K19,missense_variant,p.Ala910Glu,ENST00000392915,;MAP3K19,missense_variant,p.Ala910Glu,ENST00000375845,NM_025052.4;MAP3K19,missense_variant,p.Ala797Glu,ENST00000358371,NM_001018044.2;MAP3K19,missense_variant,p.Ala815Glu,ENST00000637841,;MAP3K19,missense_variant,p.Ala300Glu,ENST00000437365,;MAP3K19,intron_variant,,ENST00000392917,NM_001282883.1;MAP3K19,intron_variant,,ENST00000375844,NM_001018046.2;MAP3K19,intron_variant,,ENST00000392918,NM_001018047.2;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,;MAP3K19,upstream_gene_variant,,ENST00000478805,; T ENST00000392915 Transcript missense_variant 3413/5030 2729/3987 910/1328 A/E gCa/gAa 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 tolerated(1) 10/13 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 134986143 134986143 G T 1 0 0 0 0 1 0 0 0 9172 1319 46 2 2 MAP3K19 2 134986143 Missense_Mutation SNP G C3L-00095_T 7480573 134986143 107207386 133 3342 THSD7B 0 . GRCh38 2 137242550 137242550 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2244C>A p.= p.P748P ENST00000272643 9/27 208 194 14 239 238 1 strelka-varscan THSD7B,synonymous_variant,p.=,ENST00000409968,NM_001316349.1;THSD7B,synonymous_variant,p.=,ENST00000272643,;THSD7B,synonymous_variant,p.=,ENST00000413152,NM_001080427.1; A ENST00000272643 Transcript synonymous_variant 2244/5939 2244/4827 748/1608 P ccC/ccA 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A 9/27 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 137242550 137242550 C A 1 0 0 0 0 0 0 0 1 16314 668 24 2 2 THSD7B 2 137242550 Silent SNP C C3L-00095_T 2256407 137242550 104950979 134 3343 GALNT13 0 . GRCh38 2 153944598 153944598 + Missense_Mutation SNP G G T rs145025659 C3L-00095_T C3L-00095_N G G c.101G>T p.Cys34Phe p.C34F ENST00000409237 1/12 163 145 18 188 187 1 strelka-varscan GALNT13,missense_variant,p.Cys34Phe,ENST00000392825,NM_052917.3;GALNT13,missense_variant,p.Cys34Phe,ENST00000409237,NM_001301627.1;GALNT13,downstream_gene_variant,,ENST00000434213,; T ENST00000409237 Transcript missense_variant 101/2591 101/1686 34/561 C/F tGt/tTt rs145025659 1 1 GALNT13 HGNC HGNC:23242 protein_coding YES CCDS77472.1 ENSP00000387239 Q8IUC8 UPI0000E4465D NM_001301627.1 tolerated(0.16) 1/12 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF47 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 153944598 153944598 G T 1 0 0 0 0 1 0 0 0 6079 1377 48 2 2 GALNT13 2 153944598 Missense_Mutation SNP G C3L-00095_T 16702048 153944598 88248931 135 3344 PSMD14 0 . GRCh38 2 161370139 161370139 + Silent SNP C C T rs201192422 C3L-00095_T C3L-00095_N C C c.273C>T p.= p.F91F ENST00000409682 6/12 213 192 21 209 209 0 strelka-varscan PSMD14,synonymous_variant,p.=,ENST00000409682,NM_005805.5;PSMD14,downstream_gene_variant,,ENST00000437630,; T ENST00000409682 Transcript synonymous_variant 977/1954 273/933 91/310 F ttC/ttT rs201192422 1 1 PSMD14 HGNC HGNC:16889 protein_coding YES CCDS46437.1 ENSP00000386541 O00487 A0A140VKF2 UPI0000027819 NM_005805.5 6/12 Superfamily_domains:0048572,Gene3D:3.40.140.10,Pfam_domain:PF01398,hmmpanther:PTHR10410,hmmpanther:PTHR10410:SF5,SMART_domains:SM00232 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 161370139 161370139 C T 1 0 0 0 0 0 0 0 1 12848 854 30 3 3 PSMD14 2 161370139 Silent SNP C C3L-00095_T 7425541 161370139 80823390 136 3345 TBR1 0 . GRCh38 2 161424123 161424123 + Missense_Mutation SNP G G A rs753825497 C3L-00095_T C3L-00095_N G G c.1945G>A p.Glu649Lys p.E649K ENST00000389554 6/6 265 243 22 336 336 0 strelka-varscan TBR1,missense_variant,p.Glu649Lys,ENST00000389554,NM_006593.2;TBR1,missense_variant,p.Glu362Lys,ENST00000410035,;TBR1,downstream_gene_variant,,ENST00000411412,;AC009487.5,non_coding_transcript_exon_variant,,ENST00000505579,;AC009487.4,upstream_gene_variant,,ENST00000444164,;AC009487.4,upstream_gene_variant,,ENST00000437683,;SLC4A10,upstream_gene_variant,,ENST00000605990,;SLC4A10,upstream_gene_variant,,ENST00000482861,;TBR1,downstream_gene_variant,,ENST00000489530,;SLC4A10,upstream_gene_variant,,ENST00000606386,;TBR1,downstream_gene_variant,,ENST00000477804,;TBR1,downstream_gene_variant,,ENST00000463544,; A ENST00000389554 Transcript missense_variant 2262/4009 1945/2049 649/682 E/K Gag/Aag rs753825497,COSM5291869 1 1 TBR1 HGNC HGNC:11590 protein_coding YES CCDS33310.1 ENSP00000374205 Q16650 UPI0000136A99 NM_006593.2 deleterious(0.01) 6/6 hmmpanther:PTHR11267:SF88,hmmpanther:PTHR11267,Pfam_domain:PF16176 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 161424123 161424123 G A 1 0 0 0 0 1 0 0 0 16052 1059 37 1 1 TBR1 2 161424123 Missense_Mutation SNP G C3L-00095_T 53984 161424123 80769406 137 3346 SCN3A 0 . GRCh38 2 165090980 165090980 + Missense_Mutation SNP C C A rs746475565 C3L-00095_T C3L-00095_N C C c.5173G>T p.Asp1725Tyr p.D1725Y ENST00000283254 28/28 523 476 47 673 671 2 strelka-varscan SCN3A,missense_variant,p.Asp1725Tyr,ENST00000360093,;SCN3A,missense_variant,p.Asp1725Tyr,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Asp1676Tyr,ENST00000409101,NM_001081677.1;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000431341,;AC013463.2,upstream_gene_variant,,ENST00000625505,;SCN3A,downstream_gene_variant,,ENST00000465043,;SCN3A,downstream_gene_variant,,ENST00000471697,; A ENST00000283254 Transcript missense_variant 5641/9091 5173/6003 1725/2000 D/Y Gac/Tac rs746475565 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 tolerated(0.42) 28/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 165090980 165090980 C A 1 0 0 0 0 1 0 0 0 14187 884 31 1 1 SCN3A 2 165090980 Missense_Mutation SNP C C3L-00095_T 3666857 165090980 77102549 138 3347 SCN3A 0 . GRCh38 2 165095536 165095536 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.4406A>G p.Asp1469Gly p.D1469G ENST00000283254 25/28 309 286 23 134 134 0 strelka-varscan SCN3A,missense_variant,p.Asp1469Gly,ENST00000360093,;SCN3A,missense_variant,p.Asp1469Gly,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Asp1420Gly,ENST00000409101,NM_001081677.1;SCN3A,downstream_gene_variant,,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000431341,;SCN3A,upstream_gene_variant,,ENST00000465043,;SCN3A,non_coding_transcript_exon_variant,,ENST00000471697,; C ENST00000283254 Transcript missense_variant 4874/9091 4406/6003 1469/2000 D/G gAt/gGt 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 25/28 Gene3D:1byyA00,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 165095536 165095536 T C 1 0 0 0 0 1 0 0 0 14187 1435 50 5 5 SCN3A 2 165095536 Missense_Mutation SNP T C3L-00095_T 4556 165095536 77097993 139 3348 SCN1A 0 . GRCh38 2 165998175 165998175 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.4339G>C p.Val1447Leu p.V1447L ENST00000303395 25/28 183 173 10 136 136 0 strelka-varscan SCN1A,missense_variant,p.Val1436Leu,ENST00000635776,;SCN1A,missense_variant,p.Val1436Leu,ENST00000637988,;SCN1A,missense_variant,p.Val1447Leu,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Val1436Leu,ENST00000635750,;SCN1A,missense_variant,p.Val1447Leu,ENST00000423058,;SCN1A,missense_variant,p.Val1436Leu,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Val1419Leu,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000597623,;AC010127.3,intron_variant,,ENST00000630226,;SCN1A,splice_region_variant,,ENST00000636194,;SCN1A,splice_region_variant,,ENST00000637038,;SCN1A,splice_region_variant,,ENST00000473295,;SCN1A,splice_region_variant,,ENST00000491429,;SCN1A,splice_region_variant,,ENST00000635893,;SCN1A,upstream_gene_variant,,ENST00000625916,; G ENST00000303395 Transcript missense_variant,splice_region_variant 4757/8533 4339/6030 1447/2009 V/L Gtg/Ctg 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 tolerated(0.11) 25/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 165998175 165998175 C G 1 0 0 0 0 1 0 0 0 14183 521 18 4 4 SCN1A 2 165998175 Missense_Mutation SNP C C3L-00095_T 902639 165998175 76195354 140 3349 XIRP2 0 . GRCh38 2 167244372 167244372 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2980C>A p.Pro994Thr p.P994T ENST00000409195 9/11 92 82 10 96 95 1 strelka-varscan XIRP2,missense_variant,p.Pro994Thr,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Pro772Thr,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Pro819Thr,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 3069/12675 2980/10650 994/3549 P/T Ccc/Acc 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.34) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.97722 1 1 1 1 0 A 3 1 10 167244372 167244372 C A 1 0 0 0 0 1 0 0 0 17989 855 30 2 2 XIRP2 2 167244372 Missense_Mutation SNP C C3L-00095_T 1246197 167244372 74949157 141 3350 XIRP2 0 . GRCh38 2 167251464 167251464 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.10072G>A p.Gly3358Arg p.G3358R ENST00000409195 9/11 199 189 10 193 193 0 strelka-varscan XIRP2,missense_variant,p.Gly3358Arg,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Gly3136Arg,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Gly3183Arg,ENST00000628543,;XIRP2,missense_variant,p.Gly772Arg,ENST00000295237,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; A ENST00000409195 Transcript missense_variant 10161/12675 10072/10650 3358/3549 G/R Gga/Aga COSM3569547 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 167251464 167251464 G A 1 0 0 0 0 1 0 0 0 17989 1233 43 3 3 XIRP2 2 167251464 Missense_Mutation SNP G C3L-00095_T 7092 167251464 74942065 142 3351 LRP2 0 . GRCh38 2 169273017 169273017 + Missense_Mutation SNP G G A rs764130643 C3L-00095_T C3L-00095_N G G c.2026C>T p.Leu676Phe p.L676F ENST00000263816 15/79 468 441 27 568 567 1 strelka-varscan LRP2,missense_variant,p.Leu676Phe,ENST00000263816,NM_004525.2;LRP2,missense_variant,p.Leu607Phe,ENST00000443831,;LRP2,non_coding_transcript_exon_variant,,ENST00000493501,; A ENST00000263816 Transcript missense_variant 2312/15808 2026/13968 676/4655 L/F Ctc/Ttc rs764130643 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 deleterious(0) 15/79 Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 169273017 169273017 G A 1 0 0 0 0 1 0 0 0 8851 1000 35 3 3 LRP2 2 169273017 Missense_Mutation SNP G C3L-00095_T 2021553 169273017 72920512 143 3352 HOXD11 0 . GRCh38 2 176109055 176109055 + Silent SNP C C G novel C3L-00095_T C3L-00095_N C C c.930C>G p.= p.V310V ENST00000249504 2/2 394 363 31 483 483 0 strelka-varscan-mutect HOXD11,synonymous_variant,p.=,ENST00000249504,NM_021192.2;HOXD11,synonymous_variant,p.=,ENST00000619244,;HOXD11,non_coding_transcript_exon_variant,,ENST00000498438,;HOXD10,non_coding_transcript_exon_variant,,ENST00000490088,;HOXD10,non_coding_transcript_exon_variant,,ENST00000549469,; G ENST00000249504 Transcript synonymous_variant 1000/1533 930/1017 310/338 V gtC/gtG 1 1 HOXD11 HGNC HGNC:5134 protein_coding YES CCDS2265.1 ENSP00000249504 P31277 UPI000013CC88 NM_021192.2 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF125,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 176109055 176109055 C G 1 0 0 0 0 0 0 0 1 7214 813 29 4 4 HOXD11 2 176109055 Silent SNP C C3L-00095_T 6836038 176109055 66084474 144 3353 TTN 0 . GRCh38 2 178595551 178595551 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.57803C>T p.Pro19268Leu p.P19268L ENST00000589042 295/363 526 484 42 593 592 1 strelka-varscan-mutect TTN,missense_variant,p.Pro19268Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro17627Leu,ENST00000591111,;TTN,missense_variant,p.Pro17627Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro16700Leu,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Pro10203Leu,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Pro10395Leu,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Pro10328Leu,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000629117,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000626517,;TTN-AS1,downstream_gene_variant,,ENST00000590743,;TTN-AS1,upstream_gene_variant,,ENST00000589830,; A ENST00000589042 Transcript missense_variant 58028/109224 57803/107976 19268/35991 P/L cCa/cTa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 295/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 178595551 178595551 G A 1 0 0 0 0 1 0 0 0 17245 1348 47 3 3 TTN 2 178595551 Missense_Mutation SNP G C3L-00095_T 2486496 178595551 63597978 145 3354 TTN 0 . GRCh38 2 178723059 178723059 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.21948G>T p.= p.L7316L ENST00000589042 75/363 98 93 5 134 134 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,; A ENST00000589042 Transcript synonymous_variant 22173/109224 21948/107976 7316/35991 L ctG/ctT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 75/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -11.00637 1 1 1 1 0 A 2 1 10 178723059 178723059 C A 1 0 0 0 0 0 0 0 1 17245 581 21 2 2 TTN 2 178723059 Silent SNP C C3L-00095_T 127508 178723059 63470470 146 3355 ITGA4 0 . GRCh38 2 181498638 181498638 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.1556T>A p.Met519Lys p.M519K ENST00000397033 15/28 90 82 8 78 78 0 strelka-varscan-mutect ITGA4,missense_variant,p.Met519Lys,ENST00000397033,NM_000885.4;ITGA4,missense_variant,p.Met519Lys,ENST00000233573,;ITGA4,non_coding_transcript_exon_variant,,ENST00000476824,;ITGA4,non_coding_transcript_exon_variant,,ENST00000490435,;ITGA4,downstream_gene_variant,,ENST00000473002,; A ENST00000397033 Transcript missense_variant 1986/4189 1556/3099 519/1032 M/K aTg/aAg 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 deleterious(0) 15/28 hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,Pfam_domain:PF08441,Gene3D:1jv2A02,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 181498638 181498638 T A 1 0 0 0 0 1 0 0 0 7785 1464 51 4 4 ITGA4 2 181498638 Missense_Mutation SNP T C3L-00095_T 2775579 181498638 60694891 147 3356 FSIP2 0 . GRCh38 2 185790769 185790769 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.3900C>A p.= p.V1300V ENST00000343098 16/23 80 69 11 51 51 0 strelka-varscan-mutect FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,; A ENST00000343098 Transcript synonymous_variant 3900/21054 3900/20991 1300/6996 V gtC/gtA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS rs1301225195 . 0 205 4 0 0 0 0 0 -19.99995 1 1 1 1 0 A 2 1 10 185790769 185790769 C A 1 0 0 0 0 0 0 0 1 5949 813 29 2 2 FSIP2 2 185790769 Silent SNP C C3L-00095_T 4292131 185790769 56402760 148 3357 FSIP2 0 . GRCh38 2 185795570 185795570 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.8701C>A p.Pro2901Thr p.P2901T ENST00000343098 16/23 143 133 10 126 126 0 strelka-varscan-mutect FSIP2,missense_variant,p.Pro2901Thr,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Pro2812Thr,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,missense_variant,p.Pro319Thr,ENST00000415915,; A ENST00000343098 Transcript missense_variant 8701/21054 8701/20991 2901/6996 P/T Cct/Act 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 tolerated(0.19) 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 185795570 185795570 C A 1 0 0 0 0 1 0 0 0 5949 855 30 2 2 FSIP2 2 185795570 Missense_Mutation SNP C C3L-00095_T 4801 185795570 56397959 149 3358 COL3A1 0 . GRCh38 2 189010690 189010690 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.4054G>A p.Val1352Met p.V1352M ENST00000304636 50/51 282 264 18 326 326 0 strelka-varscan-mutect COL3A1,missense_variant,p.Val1352Met,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Val1049Met,ENST00000317840,;COL3A1,non_coding_transcript_exon_variant,,ENST00000487010,; A ENST00000304636 Transcript missense_variant 4224/5543 4054/4401 1352/1466 V/M Gtg/Atg 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0.01) 50/51 PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604,Pfam_domain:PF01410,SMART_domains:SM00038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 189010690 189010690 G A 1 0 0 0 0 1 0 0 0 3477 1377 48 3 3 COL3A1 2 189010690 Missense_Mutation SNP G C3L-00095_T 3215120 189010690 53182839 150 3359 RFTN2 0 . GRCh38 2 197646585 197646585 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.221A>G p.Tyr74Cys p.Y74C ENST00000295049 2/9 226 214 12 246 246 0 strelka-varscan-mutect RFTN2,missense_variant,p.Tyr74Cys,ENST00000295049,NM_144629.2;RFTN2,missense_variant,p.Tyr74Cys,ENST00000429081,; C ENST00000295049 Transcript missense_variant 758/5827 221/1506 74/501 Y/C tAt/tGt 1 -1 RFTN2 HGNC HGNC:26402 protein_coding YES CCDS2323.1 ENSP00000295049 Q52LD8 UPI000013E1F9 NM_144629.2 deleterious(0) 2/9 hmmpanther:PTHR17601,hmmpanther:PTHR17601:SF1,Pfam_domain:PF15250 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 197646585 197646585 T C 1 0 0 0 0 1 0 0 0 13433 1406 49 5 5 RFTN2 2 197646585 Missense_Mutation SNP T C3L-00095_T 8635895 197646585 44546944 151 3360 PLCL1 0 . GRCh38 2 198085364 198085364 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1847G>T p.Ser616Ile p.S616I ENST00000428675 2/6 170 142 28 149 149 0 strelka-varscan-mutect PLCL1,missense_variant,p.Ser539Ile,ENST00000437704,;PLCL1,missense_variant,p.Ser616Ile,ENST00000428675,NM_006226.3;PLCL1,missense_variant,p.Ser542Ile,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript missense_variant 2245/5125 1847/3288 616/1095 S/I aGt/aTt 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 deleterious(0.01) 2/6 PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF00387,Gene3D:3.20.20.190,SMART_domains:SM00149,Superfamily_domains:SSF51695 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 198085364 198085364 G T 1 0 0 0 0 1 0 0 0 12133 1029 36 2 2 PLCL1 2 198085364 Missense_Mutation SNP G C3L-00095_T 438779 198085364 44108165 152 3361 TMEM237 0 . GRCh38 2 201632134 201632134 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.470A>T p.Gln157Leu p.Q157L ENST00000409883 7/13 261 239 22 245 245 0 strelka-varscan-mutect TMEM237,missense_variant,p.Gln149Leu,ENST00000409444,NM_152388.3;TMEM237,missense_variant,p.Gln157Leu,ENST00000409883,NM_001044385.2;TMEM237,missense_variant,p.Gln149Leu,ENST00000621467,;TMEM237,non_coding_transcript_exon_variant,,ENST00000466641,;TMEM237,upstream_gene_variant,,ENST00000466839,;TMEM237,upstream_gene_variant,,ENST00000471318,;TMEM237,downstream_gene_variant,,ENST00000489550,;TMEM237,3_prime_UTR_variant,,ENST00000286196,;TMEM237,3_prime_UTR_variant,,ENST00000432684,;TMEM237,3_prime_UTR_variant,,ENST00000444047,;TMEM237,downstream_gene_variant,,ENST00000480124,; A ENST00000409883 Transcript missense_variant 587/5415 470/1227 157/408 Q/L cAa/cTa 1 -1 TMEM237 HGNC HGNC:14432 protein_coding YES CCDS46489.1 ENSP00000386264 Q96Q45 UPI0000DD5A47 NM_001044385.2 tolerated(0.15) 7/13 hmmpanther:PTHR28388,hmmpanther:PTHR28388:SF1,Pfam_domain:PF15383 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 201632134 201632134 T A 1 0 0 0 0 1 0 0 0 16598 1812 63 4 4 TMEM237 2 201632134 Missense_Mutation SNP T C3L-00095_T 3546770 201632134 40561395 153 3362 ZDBF2 0 . GRCh38 2 206306386 206306386 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.1858A>T p.Ser620Cys p.S620C ENST00000374423 5/5 211 199 12 235 234 1 strelka-varscan-mutect ZDBF2,missense_variant,p.Ser620Cys,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Ser618Cys,ENST00000611847,NM_001285549.1; T ENST00000374423 Transcript missense_variant 2244/10286 1858/7065 620/2354 S/C Agt/Tgt 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 deleterious(0.02) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS rs1261857986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 206306386 206306386 A T 1 0 0 0 0 1 0 0 0 18174 188 7 4 4 ZDBF2 2 206306386 Missense_Mutation SNP A C3L-00095_T 4674252 206306386 35887143 154 3363 1 4 5 5 3774 N T_G_A_- 3.686678e-06 ZDBF2 0 . GRCh38 2 206306478 206306478 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.1950G>A p.= p.K650K ENST00000374423 5/5 258 233 25 311 311 0 strelka-varscan-mutect ZDBF2,synonymous_variant,p.=,ENST00000374423,NM_020923.2;ZDBF2,synonymous_variant,p.=,ENST00000611847,NM_001285549.1; A ENST00000374423 Transcript synonymous_variant 2336/10286 1950/7065 650/2354 K aaG/aaA 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 206306478 206306478 G A 1 0 0 0 0 0 0 0 1 18174 991 35 3 3 ZDBF2 2 206306478 Silent SNP G C3L-00095_T 92 206306478 35887051 155 3364 1 4 5 5 3774 N T_G_A_- 3.686678e-06 ZDBF2 0 . GRCh38 2 206306688 206306688 + Silent SNP T T C novel C3L-00095_T C3L-00095_N T T c.2160T>C p.= p.D720D ENST00000374423 5/5 266 249 17 326 326 0 strelka-varscan-mutect ZDBF2,synonymous_variant,p.=,ENST00000374423,NM_020923.2;ZDBF2,synonymous_variant,p.=,ENST00000611847,NM_001285549.1; C ENST00000374423 Transcript synonymous_variant 2546/10286 2160/7065 720/2354 D gaT/gaC 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 206306688 206306688 T C 1 0 0 0 0 0 0 0 1 18174 1461 51 5 5 ZDBF2 2 206306688 Silent SNP T C3L-00095_T 210 206306688 35886841 156 3365 1 4 5 5 3774 N T_G_A_- 3.686678e-06 ZDBF2 0 . GRCh38 2 206309143 206309143 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.4615G>C p.Val1539Leu p.V1539L ENST00000374423 5/5 281 260 21 255 255 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Val1539Leu,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Val1537Leu,ENST00000611847,NM_001285549.1; C ENST00000374423 Transcript missense_variant 5001/10286 4615/7065 1539/2354 V/L Gta/Cta 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.05) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 206309143 206309143 G C 1 0 0 0 0 1 0 0 0 18174 1029 36 4 4 ZDBF2 2 206309143 Missense_Mutation SNP G C3L-00095_T 2455 206309143 35884386 157 3366 1 4 5 5 3774 N T_G_A_- 3.686678e-06 ZDBF2 0 . GRCh38 2 206310159 206310160 + Frame_Shift_Ins INS - - T novel C3L-00095_T C3L-00095_N - - c.5632dupT p.Trp1878LeufsTer3 p.W1878Lfs*3 ENST00000374423 5/5 125 104 21 181 181 0 sindel-varindel-pindel ZDBF2,frameshift_variant,p.Trp1878LeufsTer3,ENST00000374423,NM_020923.2;ZDBF2,frameshift_variant,p.Trp1876LeufsTer3,ENST00000611847,NM_001285549.1; T ENST00000374423 Transcript frameshift_variant 6017-6018/10286 5631-5632/7065 1877-1878/2354 -/X -/T 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 HIGH 1 insertion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 10 206310159 206310159 - T 1 0 1 1 0 0 0 0 0 18174 668 24 0 0 ZDBF2 2 206310159 Frame_Shift_Ins INS - C3L-00095_T 1016 206310159 35883370 158 3367 1 4 5 5 3774 N T_G_A_- 3.686678e-06 PTH2R 0 . GRCh38 2 208489103 208489103 + Missense_Mutation SNP G G T rs776936901 C3L-00095_T C3L-00095_N G G c.1168G>T p.Gly390Trp p.G390W ENST00000272847 11/13 220 202 18 265 265 0 strelka-varscan-mutect PTH2R,missense_variant,p.Gly390Trp,ENST00000272847,NM_005048.3;PTH2R,missense_variant,p.Gly279Trp,ENST00000617735,;AC019185.4,intron_variant,,ENST00000424628,;PTH2R,missense_variant,p.Gly7Trp,ENST00000419079,; T ENST00000272847 Transcript missense_variant 1381/2713 1168/1653 390/550 G/W Ggg/Tgg rs776936901 1 1 PTH2R HGNC HGNC:9609 protein_coding YES CCDS2383.1 ENSP00000272847 P49190 UPI000005041E NM_005048.3 deleterious(0.04) 11/13 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF69,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs776936901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 208489103 208489103 G T 1 0 0 0 0 1 0 0 0 12916 1116 39 1 1 PTH2R 2 208489103 Missense_Mutation SNP G C3L-00095_T 2178944 208489103 33704426 159 3368 MAP2 0 . GRCh38 2 209694194 209694194 + Missense_Mutation SNP G G T rs766835859 C3L-00095_T C3L-00095_N G G c.2024G>T p.Ser675Ile p.S675I ENST00000360351 7/15 114 104 10 128 127 1 strelka-varscan-mutect MAP2,missense_variant,p.Ser675Ile,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Ser671Ile,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; T ENST00000360351 Transcript missense_variant 2530/9711 2024/5484 675/1827 S/I aGt/aTt rs766835859,COSM573062 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs766835859 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 209694194 209694194 G T 1 0 0 0 0 1 0 0 0 9157 1029 36 2 2 MAP2 2 209694194 Missense_Mutation SNP G C3L-00095_T 1205091 209694194 32499335 160 3369 UNC80 0 . GRCh38 2 209921566 209921566 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.5212C>T p.Gln1738Ter p.Q1738* ENST00000439458 33/64 208 188 20 249 249 0 strelka-varscan-mutect UNC80,stop_gained,p.Gln1738Ter,ENST00000439458,NM_032504.1;UNC80,stop_gained,p.Gln1733Ter,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; T ENST00000439458 Transcript stop_gained 5292/13562 5212/9777 1738/3258 Q/* Cag/Tag 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 33/64 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 HIGH 1 SNV 5 1 PASS . . 0 207 0 0 3 0 0 0 -7.618358 0.9323209 1 1 1 0 T 4 4 10 209921566 209921566 C T 1 0 0 0 0 0 1 0 0 17521 711 25 3 3 UNC80 2 209921566 Nonsense_Mutation SNP C C3L-00095_T 227372 209921566 32271963 161 3370 CATIP 0 . GRCh38 2 218360640 218360640 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.443G>C p.Arg148Thr p.R148T ENST00000289388 5/10 173 146 27 177 177 0 strelka-varscan-mutect CATIP,missense_variant,p.Arg148Thr,ENST00000289388,NM_198559.1;CATIP-AS2,upstream_gene_variant,,ENST00000411433,;CATIP,non_coding_transcript_exon_variant,,ENST00000481940,;CATIP,upstream_gene_variant,,ENST00000494447,;CATIP,downstream_gene_variant,,ENST00000480532,;CATIP,downstream_gene_variant,,ENST00000495773,; C ENST00000289388 Transcript missense_variant 472/1323 443/1164 148/387 R/T aGa/aCa 1 1 CATIP HGNC HGNC:25062 protein_coding YES CCDS2414.1 ENSP00000289388 Q7Z7H3 UPI000019B2D3 NM_198559.1 deleterious(0.02) 5/10 hmmpanther:PTHR15505,hmmpanther:PTHR15505:SF3 MODERATE 1 SNV 1 1 PASS rs1277844073 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 218360640 218360640 G C 1 0 0 0 0 1 0 0 0 2386 942 33 4 4 CATIP 2 218360640 Missense_Mutation SNP G C3L-00095_T 8439074 218360640 23832889 162 3371 STK36 0 . GRCh38 2 218680663 218680663 + Silent SNP G G T rs752332276 C3L-00095_T C3L-00095_N G G c.1197G>T p.= p.L399L ENST00000295709 10/27 257 243 14 270 270 0 strelka-varscan-mutect STK36,synonymous_variant,p.=,ENST00000295709,NM_015690.4;STK36,synonymous_variant,p.=,ENST00000392105,NM_001243313.1;STK36,synonymous_variant,p.=,ENST00000440309,;STK36,downstream_gene_variant,,ENST00000424080,;STK36,synonymous_variant,p.=,ENST00000414413,;STK36,upstream_gene_variant,,ENST00000422778,;STK36,upstream_gene_variant,,ENST00000470568,; T ENST00000295709 Transcript synonymous_variant 1476/4933 1197/3948 399/1315 L ctG/ctT rs752332276 1 1 STK36 HGNC HGNC:17209 protein_coding YES CCDS2421.1 ENSP00000295709 Q9NRP7 A0A140VJW1 UPI00000342FC NM_015690.4 10/27 hmmpanther:PTHR22983,hmmpanther:PTHR22983:SF17,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs752332276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 218680663 218680663 G T 1 0 0 0 0 0 0 0 1 15679 1335 47 2 2 STK36 2 218680663 Silent SNP G C3L-00095_T 320023 218680663 23512866 163 3372 SPHKAP 0 . GRCh38 2 228019512 228019512 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1342C>A p.Pro448Thr p.P448T ENST00000392056 7/12 281 247 34 343 342 1 strelka-varscan-mutect SPHKAP,missense_variant,p.Pro448Thr,ENST00000392056,NM_001142644.1;SPHKAP,missense_variant,p.Pro448Thr,ENST00000344657,NM_030623.3; T ENST00000392056 Transcript missense_variant 1389/6917 1342/5103 448/1700 P/T Ccc/Acc 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 deleterious(0) 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 MODERATE 1 SNV 1 1 PASS rs1351682940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 228019512 228019512 G T 1 0 0 0 0 1 0 0 0 15399 1232 43 2 2 SPHKAP 2 228019512 Missense_Mutation SNP G C3L-00095_T 9338849 228019512 14174017 164 3373 TRPM8 0 . GRCh38 2 233955193 233955193 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.1305G>A p.= p.E435E ENST00000324695 11/26 192 182 10 173 173 0 strelka-varscan-mutect TRPM8,synonymous_variant,p.=,ENST00000324695,NM_024080.4;TRPM8,synonymous_variant,p.=,ENST00000433712,;AC005538.5,non_coding_transcript_exon_variant,,ENST00000455991,;TRPM8,3_prime_UTR_variant,,ENST00000444298,;TRPM8,non_coding_transcript_exon_variant,,ENST00000487033,; A ENST00000324695 Transcript synonymous_variant 1345/5621 1305/3315 435/1104 E gaG/gaA 1 1 TRPM8 HGNC HGNC:17961 protein_coding YES CCDS33407.1 ENSP00000323926 Q7Z2W7 W8DTH1 UPI0000456F32 NM_024080.4 11/26 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 233955193 233955193 G A 1 0 0 0 0 0 0 0 1 17098 1020 36 3 3 TRPM8 2 233955193 Silent SNP G C3L-00095_T 5935681 233955193 8238336 165 3374 COL6A3 0 . GRCh38 2 237333507 237333507 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.9271T>C p.Ser3091Pro p.S3091P ENST00000295550 42/44 466 437 29 535 535 0 strelka-varscan-mutect COL6A3,missense_variant,p.Ser3091Pro,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Ser2885Pro,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Ser2885Pro,ENST00000409809,;COL6A3,missense_variant,p.Ser2484Pro,ENST00000472056,NM_057166.4;COL6A3,missense_variant,p.Ser2483Pro,ENST00000347401,;COL6A3,non_coding_transcript_exon_variant,,ENST00000493608,;COL6A3,upstream_gene_variant,,ENST00000473258,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,; G ENST00000295550 Transcript missense_variant 9724/10749 9271/9534 3091/3177 S/P Tct/Cct 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 tolerated(0.06) 42/44 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 237333507 237333507 A G 1 0 0 0 0 1 0 0 0 3490 246 9 5 5 COL6A3 2 237333507 Missense_Mutation SNP A C3L-00095_T 3378314 237333507 4860022 166 3375 NDUFA10 0 . GRCh38 2 240021361 240021361 + Missense_Mutation SNP C C A rs771444488 C3L-00095_T C3L-00095_N C C c.296G>T p.Gly99Val p.G99V ENST00000252711 3/10 343 318 25 498 497 1 strelka-varscan-mutect NDUFA10,missense_variant,p.Gly99Val,ENST00000252711,NM_004544.3;NDUFA10,missense_variant,p.Gly99Val,ENST00000404554,;NDUFA10,missense_variant,p.Gly99Val,ENST00000620965,;NDUFA10,missense_variant,p.Gly99Val,ENST00000307300,;NDUFA10,missense_variant,p.Gly99Val,ENST00000443626,;NDUFA10,missense_variant,p.Gly99Val,ENST00000407129,;NDUFA10,stop_gained,p.Glu43Ter,ENST00000414580,;NDUFA10,non_coding_transcript_exon_variant,,ENST00000485344,;NDUFA10,non_coding_transcript_exon_variant,,ENST00000497536,; A ENST00000252711 Transcript missense_variant 397/4915 296/1068 99/355 G/V gGa/gTa rs771444488,CM120094 1 -1 NDUFA10 HGNC HGNC:7684 protein_coding YES CCDS2531.1 ENSP00000252711 O95299 A0A024R4B3 UPI000013090A NM_004544.3 deleterious(0) 3/10 hmmpanther:PTHR10513:SF15,hmmpanther:PTHR10513,Gene3D:3.40.50.300,PIRSF_domain:PIRSF000543,Pfam_domain:PF01712,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 0,1 1 PASS rs771444488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 240021361 240021361 C A 1 0 0 0 0 1 0 0 0 10281 855 30 2 2 NDUFA10 2 240021361 Missense_Mutation SNP C C3L-00095_T 2687854 240021361 2172168 167 3376 ANKMY1 0 . GRCh38 2 240529482 240529482 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.508G>T p.Gly170Trp p.G170W ENST00000401804 5/18 96 90 6 130 130 0 strelka-varscan-mutect ANKMY1,missense_variant,p.Gly170Trp,ENST00000401804,NM_001282771.1;ANKMY1,missense_variant,p.Gly81Trp,ENST00000272972,NM_016552.3;ANKMY1,missense_variant,p.Gly81Trp,ENST00000391987,;ANKMY1,missense_variant,p.Gly81Trp,ENST00000418708,;ANKMY1,missense_variant,p.Gly26Trp,ENST00000443318,;ANKMY1,intron_variant,,ENST00000405002,;ANKMY1,intron_variant,,ENST00000403283,NM_001308375.1;ANKMY1,intron_variant,,ENST00000361678,NM_017844.3;ANKMY1,intron_variant,,ENST00000373318,NM_001282780.1;ANKMY1,intron_variant,,ENST00000406958,NM_001282781.1;ANKMY1,intron_variant,,ENST00000405523,;ANKMY1,intron_variant,,ENST00000441168,;ANKMY1,intron_variant,,ENST00000462004,;ANKMY1,downstream_gene_variant,,ENST00000418505,;ANKMY1,non_coding_transcript_exon_variant,,ENST00000496300,;ANKMY1,intron_variant,,ENST00000459901,;ANKMY1,intron_variant,,ENST00000484526,;ANKMY1,upstream_gene_variant,,ENST00000480230,; A ENST00000401804 Transcript missense_variant 647/3232 508/3093 170/1030 G/W Ggg/Tgg 1 -1 ANKMY1 HGNC HGNC:20987 protein_coding YES CCDS63185.1 ENSP00000385887 J3KQ21 UPI0000209839 NM_001282771.1 deleterious(0) 5/18 hmmpanther:PTHR15897,Pfam_domain:PF02493,Gene3D:1h3iA01,SMART_domains:SM00698,Superfamily_domains:0038399 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.77052 1 1 1 1 0 A 3 1 10 240529482 240529482 C A 1 0 0 0 0 1 0 0 0 735 594 21 2 2 ANKMY1 2 240529482 Missense_Mutation SNP C C3L-00095_T 508121 240529482 1664047 168 3377 KIF1A 0 . GRCh38 2 240760800 240760800 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2309C>T p.Pro770Leu p.P770L ENST00000498729 25/49 128 116 12 162 162 0 strelka-varscan-mutect KIF1A,missense_variant,p.Pro770Leu,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Pro761Leu,ENST00000320389,NM_004321.6;KIF1A,missense_variant,p.Pro770Leu,ENST00000404283,; A ENST00000498729 Transcript missense_variant 2556/9223 2309/5376 770/1791 P/L cCt/cTt 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 deleterious(0) 25/49 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99987 1 1 1 1 0 A 3 1 10 240760800 240760800 G A 1 0 0 0 0 1 0 0 0 8147 1000 35 3 3 KIF1A 2 240760800 Missense_Mutation SNP G C3L-00095_T 231318 240760800 1432729 169 3378 KIF1A 0 . GRCh38 2 240788141 240788141 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.273G>T p.= p.V91V ENST00000498729 4/49 341 323 18 464 462 2 strelka-varscan-mutect KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,synonymous_variant,p.=,ENST00000404283,;KIF1A,upstream_gene_variant,,ENST00000428768,;KIF1A,downstream_gene_variant,,ENST00000448728,; A ENST00000498729 Transcript synonymous_variant 520/9223 273/5376 91/1791 V gtG/gtT 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 4/49 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs1409707032 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 240788141 240788141 C A 1 0 0 0 0 0 0 0 1 8147 465 17 2 2 KIF1A 2 240788141 Silent SNP C C3L-00095_T 27341 240788141 1405388 170 3379 PPP1R7 0 . GRCh38 2 241153605 241153605 + Splice_Site SNP G G T novel C3L-00095_T C3L-00095_N G G c.181+1G>T p.X61_splice ENST00000234038 116 107 9 155 154 1 strelka-varscan-mutect PPP1R7,splice_donor_variant,,ENST00000234038,NM_002712.2;PPP1R7,splice_donor_variant,,ENST00000407025,;PPP1R7,splice_donor_variant,,ENST00000450367,;PPP1R7,splice_donor_variant,,ENST00000404405,;PPP1R7,splice_donor_variant,,ENST00000438799,NM_001282412.1;PPP1R7,splice_donor_variant,,ENST00000406106,NM_001282410.1;PPP1R7,splice_donor_variant,,ENST00000439916,;PPP1R7,splice_donor_variant,,ENST00000427172,;PPP1R7,intron_variant,,ENST00000272983,NM_001282409.1;PPP1R7,intron_variant,,ENST00000423280,NM_001282413.1;PPP1R7,intron_variant,,ENST00000402734,NM_001282414.1;PPP1R7,intron_variant,,ENST00000401987,NM_001282411.1;PASK,upstream_gene_variant,,ENST00000403638,NM_001252124.1;PASK,upstream_gene_variant,,ENST00000405260,;PASK,upstream_gene_variant,,ENST00000544142,NM_001252120.1;PASK,upstream_gene_variant,,ENST00000234040,NM_015148.3,NM_001252122.1;PASK,upstream_gene_variant,,ENST00000358649,NM_001252119.1;PASK,upstream_gene_variant,,ENST00000452907,;PASK,upstream_gene_variant,,ENST00000415234,;PPP1R7,upstream_gene_variant,,ENST00000485630,;PPP1R7,upstream_gene_variant,,ENST00000467159,;PPP1R7,splice_donor_variant,,ENST00000473017,;PPP1R7,splice_donor_variant,,ENST00000498170,;PPP1R7,intron_variant,,ENST00000493374,;PASK,upstream_gene_variant,,ENST00000437780,; T ENST00000234038 Transcript splice_donor_variant -/2386 181/1083 61/360 1 1 PPP1R7 HGNC HGNC:9295 protein_coding YES CCDS2546.1 ENSP00000234038 Q15435 A0A140VK83 UPI000006E65A NM_002712.2 2/9 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -17.50962 0.9999923 1 1 1 0 T 5 4 10 241153605 241153605 G T 1 0 0 0 0 0 0 1 0 12499 1275 44 2 2 PPP1R7 2 241153605 Splice_Site SNP G C3L-00095_T 365464 241153605 1039924 171 3380 FBLN2 0 . GRCh38 3 13609517 13609517 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1423G>T p.Ala475Ser p.A475S ENST00000404922 4/18 110 100 10 112 112 0 strelka-varscan-mutect FBLN2,missense_variant,p.Ala475Ser,ENST00000404922,NM_001004019.1;FBLN2,missense_variant,p.Ala475Ser,ENST00000492059,NM_001165035.1;FBLN2,missense_variant,p.Ala475Ser,ENST00000295760,NM_001998.2;FBLN2,upstream_gene_variant,,ENST00000477845,; T ENST00000404922 Transcript missense_variant 1542/4318 1423/3696 475/1231 A/S Gcc/Tcc 1 1 FBLN2 HGNC HGNC:3601 protein_coding YES CCDS46761.1 ENSP00000384169 P98095 UPI000042B0C1 NM_001004019.1 deleterious(0.04) 4/18 PROSITE_profiles:PS01178,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF303,PROSITE_patterns:PS01177,Pfam_domain:PF01821,SMART_domains:SM00104,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 13609517 13609517 G T 1 0 0 0 0 1 0 0 0 5562 985 34 2 2 FBLN2 3 13609517 Missense_Mutation SNP G C3L-00095_T 13609517 184686042 172 3381 DAZL 0 . GRCh38 3 16598563 16598563 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.99C>T p.= p.I33I ENST00000250863 2/11 341 308 33 443 443 0 strelka-varscan-mutect DAZL,synonymous_variant,p.=,ENST00000250863,NM_001190811.1;DAZL,synonymous_variant,p.=,ENST00000399444,NM_001351.3;DAZL,synonymous_variant,p.=,ENST00000454457,; A ENST00000250863 Transcript synonymous_variant 387/3104 99/948 33/315 I atC/atT 1 -1 DAZL HGNC HGNC:2685 protein_coding YES CCDS54556.1 ENSP00000250863 Q92904 UPI0000412129 NM_001190811.1 2/11 Low_complexity_(Seg):seg,hmmpanther:PTHR11176,hmmpanther:PTHR11176:SF4,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 16598563 16598563 G A 1 0 0 0 0 0 0 0 1 4047 932 33 3 3 DAZL 3 16598563 Silent SNP G C3L-00095_T 2989046 16598563 181696996 173 3382 ZNF385D 0 . GRCh38 3 21421357 21421357 + Missense_Mutation SNP C C A rs532679293 C3L-00095_T C3L-00095_N C C c.1045G>T p.Val349Leu p.V349L ENST00000281523 8/8 342 319 23 458 458 0 strelka-varscan-mutect ZNF385D,missense_variant,p.Val349Leu,ENST00000281523,NM_024697.2;ZNF385D,downstream_gene_variant,,ENST00000467140,; A ENST00000281523 Transcript missense_variant 1564/10699 1045/1188 349/395 V/L Gtg/Ttg rs532679293 1 -1 ZNF385D HGNC HGNC:26191 protein_coding YES CCDS2636.1 ENSP00000281523 Q9H6B1 UPI00000724AC NM_024697.2 tolerated(0.21) 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23067:SF12,hmmpanther:PTHR23067 MODERATE 1 SNV 1 1 PASS rs532679293 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 21421357 21421357 C A 1 0 0 0 0 1 0 0 0 18451 565 20 2 2 ZNF385D 3 21421357 Missense_Mutation SNP C C3L-00095_T 4822794 21421357 176874202 174 3383 CCR8 0 . GRCh38 3 39333378 39333378 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1047C>A p.= p.S349S ENST00000326306 2/2 79 72 7 95 95 0 strelka-varscan-mutect CCR8,synonymous_variant,p.=,ENST00000326306,NM_005201.3;CCR8,3_prime_UTR_variant,,ENST00000414803,;HNRNPA1P21,upstream_gene_variant,,ENST00000424115,;RP11-241K18.2,downstream_gene_variant,,ENST00000435940,; A ENST00000326306 Transcript synonymous_variant 1185/1253 1047/1068 349/355 S tcC/tcA 1 1 CCR8 HGNC HGNC:1609 protein_coding YES CCDS2684.1 ENSP00000326432 P51685 UPI0000043587 NM_005201.3 2/2 Prints_domain:PR01530,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF627,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -15.41067 1 1 1 1 0 A 2 1 10 39333378 39333378 C A 1 0 0 0 0 0 0 0 1 2647 581 21 2 2 CCR8 3 39333378 Silent SNP C C3L-00095_T 17912021 39333378 158962181 175 3384 TOPAZ1 0 . GRCh38 3 44242234 44242234 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.181G>T p.Gly61Cys p.G61C ENST00000309765 1/20 130 123 7 142 141 1 strelka-mutect TOPAZ1,missense_variant,p.Gly61Cys,ENST00000309765,NM_001145030.1; T ENST00000309765 Transcript missense_variant 349/5334 181/5079 61/1692 G/C Ggc/Tgc 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 deleterious_low_confidence(0.04) 1/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1 MODERATE 1 SNV 5 1 PASS rs998537680 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 44242234 44242234 G T 1 0 0 0 0 1 0 0 0 16845 1000 35 2 2 TOPAZ1 3 44242234 Missense_Mutation SNP G C3L-00095_T 4908856 44242234 154053325 176 3385 USP4 0 . GRCh38 3 49327817 49327817 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.230-1G>T p.X77_splice ENST00000265560 127 116 11 140 140 0 strelka-varscan USP4,splice_acceptor_variant,,ENST00000351842,NM_199443.2;USP4,splice_acceptor_variant,,ENST00000265560,NM_003363.3;USP4,splice_acceptor_variant,,ENST00000416417,NM_001251877.1;USP4,splice_acceptor_variant,,ENST00000415188,;USP4,splice_acceptor_variant,,ENST00000491791,;USP4,splice_acceptor_variant,,ENST00000486549,;USP4,splice_acceptor_variant,,ENST00000464168,; A ENST00000265560 Transcript splice_acceptor_variant -/3126 230/2892 77/963 1 -1 USP4 HGNC HGNC:12627 protein_coding YES CCDS2793.1 ENSP00000265560 Q13107 A0A024R2T0 UPI000013D63C NM_003363.3 2/21 HIGH 1 SNV 1 1 PASS . . 0 196 10 3 0 0 0 0 -15.88395 0.993491 1 1 1 0 A 5 1 10 49327817 49327817 C A 1 0 0 0 0 0 0 1 0 17613 927 32 2 2 USP4 3 49327817 Splice_Site SNP C C3L-00095_T 5085583 49327817 148967742 177 3386 CACNA2D3 0 . GRCh38 3 54562854 54562854 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.599T>C p.Val200Ala p.V200A ENST00000474759 6/38 215 202 13 244 244 0 strelka-varscan-mutect CACNA2D3,missense_variant,p.Val200Ala,ENST00000474759,NM_018398.2;CACNA2D3,missense_variant,p.Val200Ala,ENST00000288197,;CACNA2D3,missense_variant,p.Val200Ala,ENST00000415676,;CACNA2D3,missense_variant,p.Val106Ala,ENST00000490478,;CACNA2D3,missense_variant,p.Val106Ala,ENST00000620722,;CACNA2D3,missense_variant,p.Val106Ala,ENST00000492460,;CACNA2D3,missense_variant,p.Val106Ala,ENST00000471363,;CACNA2D3,missense_variant,p.Val106Ala,ENST00000477024,;CACNA2D3,3_prime_UTR_variant,,ENST00000468658,; C ENST00000474759 Transcript missense_variant 647/3675 599/3276 200/1091 V/A gTa/gCa 1 1 CACNA2D3 HGNC HGNC:15460 protein_coding YES CCDS54598.1 ENSP00000419101 Q8IZS8 UPI000004A7BF NM_018398.2 deleterious(0.03) 6/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF25,Gene3D:3.30.450.20,Pfam_domain:PF08399 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 54562854 54562854 T C 1 0 0 0 0 1 0 0 0 2238 1638 57 5 5 CACNA2D3 3 54562854 Missense_Mutation SNP T C3L-00095_T 5235037 54562854 143732705 178 3387 DNASE1L3 0 . GRCh38 3 58193420 58193420 + Frame_Shift_Del DEL C C - C3L-00095_T C3L-00095_N C C c.724delG p.Glu242LysfsTer22 p.E242Kfs*22 ENST00000394549 7/8 84 75 9 142 142 0 sindel-varindel-pindel DNASE1L3,frameshift_variant,p.Glu242LysfsTer22,ENST00000483681,;DNASE1L3,frameshift_variant,p.Glu212LysfsTer22,ENST00000486455,NM_001256560.1;DNASE1L3,frameshift_variant,p.Glu242LysfsTer22,ENST00000394549,NM_004944.3;DNASE1L3,intron_variant,,ENST00000477209,; - ENST00000394549 Transcript frameshift_variant 1041/1294 724/918 242/305 E/X Gaa/aa COSM1204233 1 -1 DNASE1L3 HGNC HGNC:2959 protein_coding YES CCDS2886.1 ENSP00000378053 Q13609 A0A024R365 UPI0000129890 NM_004944.3 7/8 hmmpanther:PTHR11371,hmmpanther:PTHR11371:SF32,Gene3D:3.60.10.10,Pfam_domain:PF03372,PIRSF_domain:PIRSF000988,SMART_domains:SM00476,Superfamily_domains:SSF56219 1 HIGH 1 deletion 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.18261 1 1 1 1 0 - 7 5 10 58193420 58193420 C - 1 0 1 0 1 0 0 0 0 4476 922 32 0 0 DNASE1L3 3 58193420 Frame_Shift_Del DEL C C3L-00095_T 3630566 58193420 140102139 179 3388 TMEM45A 0 . GRCh38 3 100558547 100558547 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.546G>A p.= p.L182L ENST00000323523 4/6 178 165 13 228 228 0 strelka-varscan-mutect TMEM45A,synonymous_variant,p.=,ENST00000403410,;TMEM45A,synonymous_variant,p.=,ENST00000323523,NM_018004.1;TMEM45A,downstream_gene_variant,,ENST00000449609,;TMEM45A,downstream_gene_variant,,ENST00000462884,; A ENST00000323523 Transcript synonymous_variant 859/1567 546/828 182/275 L ttG/ttA 1 1 TMEM45A HGNC HGNC:25480 protein_coding YES CCDS2937.1 ENSP00000319009 Q9NWC5 UPI0000039E49 NM_018004.1 4/6 Pfam_domain:PF04819,hmmpanther:PTHR16007,hmmpanther:PTHR16007:SF21,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 100558547 100558547 G A 1 0 0 0 0 0 0 0 1 16646 1310 46 3 3 TMEM45A 3 100558547 Silent SNP G C3L-00095_T 42365127 100558547 97737012 180 3389 DZIP3 0 . GRCh38 3 108672596 108672596 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.2529C>T p.= p.S843S ENST00000361582 23/33 210 194 16 183 183 0 strelka-varscan-mutect DZIP3,synonymous_variant,p.=,ENST00000361582,NM_014648.3;DZIP3,synonymous_variant,p.=,ENST00000463306,;DZIP3,3_prime_UTR_variant,,ENST00000495008,; T ENST00000361582 Transcript synonymous_variant 2759/5350 2529/3627 843/1208 S agC/agT 1 1 DZIP3 HGNC HGNC:30938 protein_coding YES CCDS2952.1 ENSP00000355028 Q86Y13 UPI000006E7D4 NM_014648.3 23/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF55 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 108672596 108672596 C T 1 0 0 0 0 0 0 0 1 4689 709 25 3 3 DZIP3 3 108672596 Silent SNP C C3L-00095_T 8114049 108672596 89622963 181 3390 TIGIT 0 . GRCh38 3 114295549 114295549 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.66G>T p.Met22Ile p.M22I ENST00000486257 3/5 96 86 10 123 123 0 strelka-varscan-mutect TIGIT,start_lost,p.Met1?,ENST00000461158,;TIGIT,start_lost,p.Met1?,ENST00000484319,;TIGIT,missense_variant,p.Met89Ile,ENST00000481065,;TIGIT,missense_variant,p.Met22Ile,ENST00000486257,;TIGIT,missense_variant,p.Met22Ile,ENST00000383671,NM_173799.3;TIGIT,non_coding_transcript_exon_variant,,ENST00000485814,; T ENST00000486257 Transcript missense_variant 323/3149 66/735 22/244 M/I atG/atT 1 1 TIGIT HGNC HGNC:26838 protein_coding YES CCDS2980.1 ENSP00000419085 Q495A1 UPI000013F7B8 tolerated(0.15) 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF49 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 114295549 114295549 G T 1 0 0 0 0 1 0 0 0 16340 1304 45 2 2 TIGIT 3 114295549 Missense_Mutation SNP G C3L-00095_T 5622953 114295549 84000010 182 3391 POLQ 0 . GRCh38 3 121512025 121512025 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1473G>T p.Glu491Asp p.E491D ENST00000264233 10/30 79 70 9 89 89 0 strelka-varscan-mutect POLQ,missense_variant,p.Glu626Asp,ENST00000621776,;POLQ,missense_variant,p.Glu491Asp,ENST00000264233,NM_199420.3; A ENST00000264233 Transcript missense_variant 1602/8775 1473/7773 491/2590 E/D gaG/gaT 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious(0) 10/30 PROSITE_profiles:PS51194,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 121512025 121512025 C A 1 0 0 0 0 1 0 0 0 12318 927 32 2 2 POLQ 3 121512025 Missense_Mutation SNP C C3L-00095_T 7216476 121512025 76783534 183 3392 CASR 0 . GRCh38 3 122276043 122276043 + Splice_Site SNP G G T novel C3L-00095_T C3L-00095_N G G c.1608+1G>T p.X536_splice ENST00000498619 361 337 24 468 467 1 strelka-varscan-mutect CASR,splice_donor_variant,,ENST00000498619,NM_001178065.1;CASR,splice_donor_variant,,ENST00000490131,NM_000388.3; T ENST00000498619 Transcript splice_donor_variant -/5011 1608/3267 536/1088 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 5/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 10 122276043 122276043 G T 1 0 0 0 0 0 0 1 0 2381 1275 44 2 2 CASR 3 122276043 Splice_Site SNP G C3L-00095_T 764018 122276043 76019516 184 3393 SEMA5B 0 . GRCh38 3 122915510 122915510 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.2080G>C p.Asp694His p.D694H ENST00000451055 14/23 140 130 10 187 187 0 strelka-varscan-mutect SEMA5B,missense_variant,p.Asp640His,ENST00000616742,NM_001256346.1;SEMA5B,missense_variant,p.Asp640His,ENST00000357599,NM_001031702.3;SEMA5B,missense_variant,p.Asp694His,ENST00000451055,NM_001256347.1;SEMA5B,missense_variant,p.Asp582His,ENST00000195173,NM_001256348.1;SEMA5B,missense_variant,p.Asp640His,ENST00000393583,;SEMA5B,upstream_gene_variant,,ENST00000451541,;SEMA5B,missense_variant,p.Asp640His,ENST00000475244,; G ENST00000451055 Transcript missense_variant 2091/4579 2080/3618 694/1205 D/H Gat/Cat 1 -1 SEMA5B HGNC HGNC:10737 protein_coding YES CCDS58848.1 ENSP00000389588 Q9P283 UPI0002065011 NM_001256347.1 deleterious(0) 14/23 Gene3D:2.20.100.10 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 122915510 122915510 C G 1 0 0 0 0 1 0 0 0 14314 826 29 4 4 SEMA5B 3 122915510 Missense_Mutation SNP C C3L-00095_T 639467 122915510 75380049 185 3394 MYLK 0 . GRCh38 3 123738925 123738925 + Missense_Mutation SNP C C A rs762477499 C3L-00095_T C3L-00095_N C C c.560G>T p.Arg187Leu p.R187L ENST00000360304 6/33 450 413 37 489 488 1 strelka-varscan-mutect MYLK,missense_variant,p.Arg187Leu,ENST00000360772,;MYLK,missense_variant,p.Arg187Leu,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,missense_variant,p.Arg187Leu,ENST00000359169,NM_053027.3;MYLK,missense_variant,p.Arg187Leu,ENST00000354792,;MYLK,missense_variant,p.Arg187Leu,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,missense_variant,p.Arg187Leu,ENST00000475616,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000506361,;MYLK,upstream_gene_variant,,ENST00000514623,;MYLK,downstream_gene_variant,,ENST00000510571,; A ENST00000360304 Transcript missense_variant 746/7738 560/5745 187/1914 R/L cGg/cTg rs762477499 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 tolerated(0.18) 6/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs762477499 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 123738925 123738925 C A 1 0 0 0 0 1 0 0 0 10056 652 23 1 1 MYLK 3 123738925 Missense_Mutation SNP C C3L-00095_T 823415 123738925 74556634 186 3395 UROC1 0 . GRCh38 3 126505986 126505986 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.628T>C p.Tyr210His p.Y210H ENST00000383579 7/21 344 312 32 381 381 0 strelka-varscan-mutect UROC1,missense_variant,p.Tyr210His,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.Tyr210His,ENST00000383579,NM_001165974.1; G ENST00000383579 Transcript missense_variant 662/2735 628/2211 210/736 Y/H Tac/Cac 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 deleterious(0.03) 7/21 Gene3D:1x87B01,HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 126505986 126505986 A G 1 0 0 0 0 1 0 0 0 17560 420 15 5 5 UROC1 3 126505986 Missense_Mutation SNP A C3L-00095_T 2767061 126505986 71789573 187 3396 COL6A6 0 . GRCh38 3 130582035 130582035 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3937C>A p.Leu1313Ile p.L1313I ENST00000358511 9/36 135 125 10 100 100 0 strelka-varscan-mutect COL6A6,missense_variant,p.Leu1313Ile,ENST00000358511,NM_001102608.1;COL6A6,missense_variant,p.Leu71Ile,ENST00000511332,;COL6A6,missense_variant,p.Leu91Ile,ENST00000506143,; A ENST00000358511 Transcript missense_variant 3968/9581 3937/6792 1313/2263 L/I Ctt/Att 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 deleterious(0) 9/36 Gene3D:3.40.50.410,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 130582035 130582035 C A 1 0 0 0 0 1 0 0 0 3492 565 20 2 2 COL6A6 3 130582035 Missense_Mutation SNP C C3L-00095_T 4076049 130582035 67713524 188 3397 PIK3R4 0 . GRCh38 3 130728475 130728475 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.1795G>C p.Asp599His p.D599H ENST00000356763 6/20 62 58 4 65 65 0 strelka-varscan-mutect PIK3R4,missense_variant,p.Asp599His,ENST00000356763,NM_014602.2;PIK3R4,upstream_gene_variant,,ENST00000508273,;PIK3R4,upstream_gene_variant,,ENST00000512430,;PIK3R4,upstream_gene_variant,,ENST00000507330,;PIK3R4,intron_variant,,ENST00000504834,; G ENST00000356763 Transcript missense_variant 2353/5015 1795/4077 599/1358 D/H Gat/Cat 1 -1 PIK3R4 HGNC HGNC:8982 protein_coding YES CCDS3067.1 ENSP00000349205 Q99570 UPI0000071EF3 NM_014602.2 deleterious(0) 6/20 Gene3D:1.25.10.10,hmmpanther:PTHR17583,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -9.894261 1 1 1 1 0 G 3 3 10 130728475 130728475 C G 1 0 0 0 0 1 0 0 0 12016 826 29 4 4 PIK3R4 3 130728475 Missense_Mutation SNP C C3L-00095_T 146440 130728475 67567084 189 3398 PRR23C 0 . GRCh38 3 139043900 139043900 + Missense_Mutation SNP G G C rs749283724 C3L-00095_T C3L-00095_N G G c.721C>G p.Pro241Ala p.P241A ENST00000413199 1/1 166 154 12 198 198 0 strelka-varscan-mutect PRR23C,missense_variant,p.Pro241Ala,ENST00000413199,NM_001134657.1;MRPS22,intron_variant,,ENST00000495075,; C ENST00000413199 Transcript missense_variant 993/2791 721/789 241/262 P/A Ccc/Gcc rs749283724 1 -1 PRR23C HGNC HGNC:37173 protein_coding YES CCDS46924.1 ENSP00000396648 Q6ZRP0 UPI00001C0F48 NM_001134657.1 deleterious(0.04) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF6,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE SNV 1 PASS rs749283724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 139043900 139043900 G C 1 0 0 0 0 1 0 0 0 12731 1174 41 4 4 PRR23C 3 139043900 Missense_Mutation SNP G C3L-00095_T 8315425 139043900 59251659 190 3399 XRN1 0 . GRCh38 3 142405044 142405044 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1746C>G p.Asn582Lys p.N582K ENST00000264951 16/42 243 220 23 296 296 0 strelka-varscan-mutect XRN1,missense_variant,p.Asn582Lys,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Asn48Lys,ENST00000498077,;XRN1,missense_variant,p.Asn582Lys,ENST00000392981,NM_001282857.1;RNU6-1294P,downstream_gene_variant,,ENST00000515995,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,; C ENST00000264951 Transcript missense_variant 1864/10143 1746/5121 582/1706 N/K aaC/aaG 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 tolerated(0.07) 16/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 142405044 142405044 G C 1 0 0 0 0 1 0 0 0 18017 1252 44 4 4 XRN1 3 142405044 Missense_Mutation SNP G C3L-00095_T 3361144 142405044 55890515 191 3400 ATR 0 . GRCh38 3 142505261 142505261 + Missense_Mutation SNP C C T C3L-00095_T C3L-00095_N C C c.5074G>A p.Val1692Ile p.V1692I ENST00000350721 29/47 342 321 21 425 425 0 strelka-varscan-mutect ATR,missense_variant,p.Val1692Ile,ENST00000350721,NM_001184.3; T ENST00000350721 Transcript missense_variant 5196/8249 5074/7935 1692/2644 V/I Gtc/Atc COSM5575473 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 tolerated(0.13) 29/47 Gene3D:1.25.40.10,PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69 1 MODERATE 1 SNV 1 1 1 PASS rs1448553710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 142505261 142505261 C T 1 0 0 0 0 1 0 0 0 1356 565 20 3 3 ATR 3 142505261 Missense_Mutation SNP C C3L-00095_T 100217 142505261 55790298 192 3401 PCOLCE2 0 . GRCh38 3 142848448 142848448 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.217C>A p.Leu73Ile p.L73I ENST00000295992 3/9 96 90 6 129 129 0 strelka-varscan-mutect PCOLCE2,missense_variant,p.Leu73Ile,ENST00000295992,NM_013363.3;PCOLCE2,missense_variant,p.Leu73Ile,ENST00000485766,;PCOLCE2,non_coding_transcript_exon_variant,,ENST00000495732,;PCOLCE2,upstream_gene_variant,,ENST00000480473,;PCOLCE2,upstream_gene_variant,,ENST00000483986,; T ENST00000295992 Transcript missense_variant 524/2021 217/1248 73/415 L/I Ctc/Atc COSM3588323 1 -1 PCOLCE2 HGNC HGNC:8739 protein_coding YES CCDS3127.1 ENSP00000295992 Q9UKZ9 UPI0000073F93 NM_013363.3 deleterious(0.02) 3/9 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF40,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.94661 1 1 1 1 0 T 3 4 10 142848448 142848448 G T 1 0 0 0 0 1 0 0 0 11684 942 33 2 2 PCOLCE2 3 142848448 Missense_Mutation SNP G C3L-00095_T 343187 142848448 55447111 193 3402 PLSCR5 0 . GRCh38 3 146600378 146600378 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.99A>T p.= p.P33P ENST00000443512 2/8 261 245 16 328 328 0 strelka-varscan-mutect PLSCR5,synonymous_variant,p.=,ENST00000443512,NM_001085420.1;PLSCR5,synonymous_variant,p.=,ENST00000492200,;PLSCR5,synonymous_variant,p.=,ENST00000482567,; A ENST00000443512 Transcript synonymous_variant 1103/1969 99/816 33/271 P ccA/ccT 1 -1 PLSCR5 HGNC HGNC:19952 protein_coding YES CCDS46931.1 ENSP00000390111 A0PG75 UPI0000425F34 NM_001085420.1 2/8 hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF25 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 146600378 146600378 T A 1 0 0 0 0 0 0 0 1 12220 1567 55 4 4 PLSCR5 3 146600378 Silent SNP T C3L-00095_T 3751930 146600378 51695181 194 3403 MED12L 0 . GRCh38 3 151388108 151388108 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.5282C>G p.Thr1761Arg p.T1761R ENST00000474524 35/43 158 149 9 174 174 0 strelka-varscan-mutect MED12L,missense_variant,p.Thr1761Arg,ENST00000474524,NM_053002.5;MED12L,missense_variant,p.Thr1621Arg,ENST00000273432,;P2RY12,upstream_gene_variant,,ENST00000302632,NM_176876.2,NM_022788.4; G ENST00000474524 Transcript missense_variant 5320/10744 5282/6438 1761/2145 T/R aCa/aGa 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 tolerated(0.29) 35/43 Low_complexity_(Seg):seg,hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 151388108 151388108 C G 1 0 0 0 0 1 0 0 0 9368 478 17 4 4 MED12L 3 151388108 Missense_Mutation SNP C C3L-00095_T 4787730 151388108 46907451 195 3404 PQLC2L 0 . GRCh38 3 157571966 157571966 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.225C>T p.= p.A75A ENST00000449199 4/5 123 112 11 119 119 0 strelka-mutect PQLC2L,synonymous_variant,p.=,ENST00000449199,NM_001130002.2;PQLC2L,synonymous_variant,p.=,ENST00000312275,NM_001099777.3;PQLC2L,intron_variant,,ENST00000426338,NM_001130001.2;PQLC2L,intron_variant,,ENST00000459838,NM_001243729.1;PQLC2L,intron_variant,,ENST00000461040,;PQLC2L,downstream_gene_variant,,ENST00000468043,;PQLC2L,downstream_gene_variant,,ENST00000498159,; T ENST00000449199 Transcript synonymous_variant 366/1484 225/408 75/135 A gcC/gcT 1 1 PQLC2L HGNC HGNC:25146 protein_coding YES CCDS46943.1 ENSP00000413228 A1A4F0 UPI0000161AB6 NM_001130002.2 4/5 hmmpanther:PTHR16201,hmmpanther:PTHR16201:SF42 LOW 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -16.22835 0.9999511 1 1 1 0 T 2 4 10 157571966 157571966 C T 1 0 0 0 0 0 0 0 1 12546 581 21 3 3 PQLC2L 3 157571966 Silent SNP C C3L-00095_T 6183858 157571966 40723593 196 3405 PQLC2L 0 . GRCh38 3 157600242 157600242 + Nonsense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.352A>T p.Arg118Ter p.R118* ENST00000449199 5/5 379 357 22 330 329 1 strelka-varscan-mutect PQLC2L,stop_gained,p.Arg118Ter,ENST00000449199,NM_001130002.2;PQLC2L,missense_variant,p.Gln88Leu,ENST00000426338,NM_001130001.2;PQLC2L,intron_variant,,ENST00000461040,; T ENST00000449199 Transcript stop_gained 493/1484 352/408 118/135 R/* Aga/Tga 1 1 PQLC2L HGNC HGNC:25146 protein_coding YES CCDS46943.1 ENSP00000413228 A1A4F0 UPI0000161AB6 NM_001130002.2 5/5 hmmpanther:PTHR16201,hmmpanther:PTHR16201:SF42 HIGH 1 SNV 1 1 PASS rs1423900619 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 157600242 157600242 A T 1 0 0 0 0 0 1 0 0 12546 180 7 4 4 PQLC2L 3 157600242 Nonsense_Mutation SNP A C3L-00095_T 28276 157600242 40695317 197 3406 SLITRK3 0 . GRCh38 3 165188477 165188477 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.2354C>A p.Pro785Gln p.P785Q ENST00000475390 2/2 101 95 6 144 144 0 strelka-varscan-mutect SLITRK3,missense_variant,p.Pro785Gln,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Pro785Gln,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; T ENST00000475390 Transcript missense_variant 2798/4555 2354/2934 785/977 P/Q cCg/cAg COSM76519 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 tolerated(0.15) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 1 MODERATE 1 SNV 1 1 1 PASS rs1490316717 . 0 207 3 0 0 0 0 0 -12.6148 1 1 1 1 0 T 3 4 10 165188477 165188477 G T 1 0 0 0 0 1 0 0 0 15035 1116 39 1 1 SLITRK3 3 165188477 Missense_Mutation SNP G C3L-00095_T 7588235 165188477 33107082 198 3407 ZBBX 0 . GRCh38 3 167317065 167317065 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.1134A>T p.= p.P378P ENST00000455345 13/21 183 162 21 116 116 0 strelka-varscan-mutect ZBBX,synonymous_variant,p.=,ENST00000392766,NM_024687.3;ZBBX,synonymous_variant,p.=,ENST00000455345,NM_001199201.1;ZBBX,synonymous_variant,p.=,ENST00000307529,;ZBBX,synonymous_variant,p.=,ENST00000392767,;ZBBX,synonymous_variant,p.=,ENST00000392764,NM_001199202.1;ZBBX,non_coding_transcript_exon_variant,,ENST00000469220,; A ENST00000455345 Transcript synonymous_variant 1418/3185 1134/2520 378/839 P ccA/ccT 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 13/21 hmmpanther:PTHR28634 LOW 1 SNV 1 1 PASS rs1270173418 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 167317065 167317065 T A 1 0 0 0 0 0 0 0 1 18078 1567 55 4 4 ZBBX 3 167317065 Silent SNP T C3L-00095_T 2128588 167317065 30978494 199 3408 SERPINI1 0 . GRCh38 3 167792614 167792614 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.506C>T p.Pro169Leu p.P169L ENST00000295777 4/9 177 165 12 205 202 3 varscan-mutect SERPINI1,missense_variant,p.Pro169Leu,ENST00000295777,NM_005025.4;SERPINI1,missense_variant,p.Pro169Leu,ENST00000446050,NM_001122752.1;SERPINI1,missense_variant,p.Pro169Leu,ENST00000472747,;SERPINI1,downstream_gene_variant,,ENST00000472941,; T ENST00000295777 Transcript missense_variant 937/1907 506/1233 169/410 P/L cCa/cTa 1 1 SERPINI1 HGNC HGNC:8943 protein_coding YES CCDS3203.1 ENSP00000295777 Q99574 A0A0S2Z455 UPI000002FBA4 NM_005025.4 tolerated(0.25) 4/9 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF50,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -15.45098 0.9995991 1 1 1 0 T 3 4 10 167792614 167792614 C T 1 0 0 0 0 1 0 0 0 14394 594 21 3 3 SERPINI1 3 167792614 Missense_Mutation SNP C C3L-00095_T 475549 167792614 30502945 200 3409 SPATA16 0 . GRCh38 3 173117395 173117395 + Missense_Mutation SNP G G T rs778611950 C3L-00095_T C3L-00095_N G G c.337C>A p.Pro113Thr p.P113T ENST00000351008 2/11 676 639 37 747 746 1 strelka-varscan-mutect SPATA16,missense_variant,p.Pro113Thr,ENST00000351008,NM_031955.5; T ENST00000351008 Transcript missense_variant 521/2106 337/1710 113/569 P/T Cct/Act rs778611950 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 tolerated(0.09) 2/11 Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336 MODERATE 1 SNV 1 1 PASS rs778611950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 173117395 173117395 G T 1 0 0 0 0 1 0 0 0 15331 1203 42 2 2 SPATA16 3 173117395 Missense_Mutation SNP G C3L-00095_T 5324781 173117395 25178164 201 3410 NLGN1 0 . GRCh38 3 173604861 173604861 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.263C>A p.Pro88Gln p.P88Q ENST00000457714 3/7 204 189 15 227 227 0 strelka-varscan-mutect NLGN1,missense_variant,p.Pro88Gln,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Pro88Gln,ENST00000361589,;NLGN1,missense_variant,p.Pro88Gln,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000423427,;NLGN1,downstream_gene_variant,,ENST00000413821,; A ENST00000457714 Transcript missense_variant 692/8242 263/2472 88/823 P/Q cCa/cAa 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 deleterious(0) 3/7 hmmpanther:PTHR11559:SF52,hmmpanther:PTHR11559,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs966805126 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 173604861 173604861 C A 1 0 0 0 0 1 0 0 0 10498 594 21 2 2 NLGN1 3 173604861 Missense_Mutation SNP C C3L-00095_T 487466 173604861 24690698 202 3411 ABCC5 0 . GRCh38 3 183987724 183987724 + Silent SNP G G T rs781462439 C3L-00095_T C3L-00095_N G G c.637C>A p.= p.R213R ENST00000427120 5/5 243 228 15 282 282 0 strelka-varscan-mutect ABCC5,synonymous_variant,p.=,ENST00000427120,;ABCC5,intron_variant,,ENST00000334444,NM_005688.2;ABCC5,intron_variant,,ENST00000265586,;ABCC5,intron_variant,,ENST00000382494,NM_001023587.1;ABCC5,intron_variant,,ENST00000392579,;ABCC5,downstream_gene_variant,,ENST00000437341,;ABCC5,upstream_gene_variant,,ENST00000492216,;ABCC5,intron_variant,,ENST00000437205,NM_001320032.1;ABCC5,intron_variant,,ENST00000443376,;ABCC5,downstream_gene_variant,,ENST00000438979,; T ENST00000427120 Transcript synonymous_variant 726/4697 637/696 213/231 R Cgg/Agg rs781462439 1 -1 ABCC5 HGNC HGNC:56 protein_coding ENSP00000404809 A5PKY6 UPI000020A881 5/5 LOW SNV 1 1 PASS rs781462439 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 183987724 183987724 G T 1 0 0 0 0 0 0 0 1 60 1144 40 1 1 ABCC5 3 183987724 Silent SNP G C3L-00095_T 10382863 183987724 14307835 203 3412 DVL3 0 . GRCh38 3 184164830 184164830 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.498G>T p.= p.R166R ENST00000313143 5/15 205 194 11 265 265 0 strelka-varscan-mutect DVL3,synonymous_variant,p.=,ENST00000313143,NM_004423.3;DVL3,synonymous_variant,p.=,ENST00000431765,;DVL3,synonymous_variant,p.=,ENST00000423300,;DVL3,non_coding_transcript_exon_variant,,ENST00000462665,;DVL3,non_coding_transcript_exon_variant,,ENST00000478247,;DVL3,non_coding_transcript_exon_variant,,ENST00000467873,;DVL3,downstream_gene_variant,,ENST00000435708,;DVL3,upstream_gene_variant,,ENST00000478639,; T ENST00000313143 Transcript synonymous_variant 746/5254 498/2151 166/716 R cgG/cgT 1 1 DVL3 HGNC HGNC:3087 protein_coding YES CCDS3253.1 ENSP00000316054 Q92997 UPI00001299A9 NM_004423.3 5/15 Pfam_domain:PF02377,hmmpanther:PTHR10878,hmmpanther:PTHR10878:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 184164830 184164830 G T 1 0 0 0 0 0 0 0 1 4659 1190 42 2 2 DVL3 3 184164830 Silent SNP G C3L-00095_T 177106 184164830 14130729 204 3413 DGKG 0 . GRCh38 3 186288782 186288782 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.472G>T p.Val158Leu p.V158L ENST00000265022 6/25 194 178 16 265 265 0 strelka-varscan-mutect DGKG,missense_variant,p.Val158Leu,ENST00000265022,NM_001346.2;DGKG,missense_variant,p.Val158Leu,ENST00000344484,NM_001080744.1;DGKG,missense_variant,p.Val158Leu,ENST00000382164,NM_001080745.1;DGKG,non_coding_transcript_exon_variant,,ENST00000480809,; A ENST00000265022 Transcript missense_variant 1012/5805 472/2376 158/791 V/L Gtg/Ttg 1 -1 DGKG HGNC HGNC:2853 protein_coding YES CCDS3274.1 ENSP00000265022 P49619 UPI000013D5AB NM_001346.2 tolerated(0.27) 6/25 Low_complexity_(Seg):seg,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF36,Gene3D:1tuzA00,Pfam_domain:PF14513,Superfamily_domains:SSF47473,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 186288782 186288782 C A 1 0 0 0 0 1 0 0 0 4275 565 20 2 2 DGKG 3 186288782 Missense_Mutation SNP C C3L-00095_T 2123952 186288782 12006777 205 3414 KNG1 0 . GRCh38 3 186739413 186739413 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.1124T>C p.Met375Thr p.M375T ENST00000265023 9/10 535 497 38 516 516 0 strelka-varscan-mutect KNG1,missense_variant,p.Met375Thr,ENST00000265023,NM_001102416.2;KNG1,missense_variant,p.Met375Thr,ENST00000287611,NM_000893.3;KNG1,missense_variant,p.Met339Thr,ENST00000447445,NM_001166451.1;RP11-573D15.8,intron_variant,,ENST00000627551,;RP11-573D15.8,intron_variant,,ENST00000630864,;RP11-573D15.8,intron_variant,,ENST00000625303,;RP11-573D15.8,intron_variant,,ENST00000629126,;RP11-573D15.8,intron_variant,,ENST00000629106,;RP11-573D15.8,intron_variant,,ENST00000627830,;RP11-573D15.8,intron_variant,,ENST00000625710,;RP11-573D15.8,intron_variant,,ENST00000628253,;RP11-573D15.8,intron_variant,,ENST00000354642,;RP11-573D15.8,intron_variant,,ENST00000599314,;RP11-573D15.8,intron_variant,,ENST00000628601,;RP11-573D15.8,intron_variant,,ENST00000630178,;RP11-573D15.8,intron_variant,,ENST00000628858,;RP11-573D15.8,intron_variant,,ENST00000628505,;RP11-573D15.8,intron_variant,,ENST00000627015,;RP11-573D15.8,intron_variant,,ENST00000625741,;RP11-573D15.8,intron_variant,,ENST00000627268,;RP11-573D15.8,intron_variant,,ENST00000626845,;RP11-573D15.8,intron_variant,,ENST00000629451,;RP11-573D15.8,intron_variant,,ENST00000627469,;RP11-573D15.8,intron_variant,,ENST00000631299,;RP11-573D15.8,intron_variant,,ENST00000627919,;RP11-573D15.8,intron_variant,,ENST00000628020,;RP11-573D15.8,intron_variant,,ENST00000626151,;RP11-573D15.8,intron_variant,,ENST00000628190,;RP11-573D15.8,intron_variant,,ENST00000625386,;RP11-573D15.8,intron_variant,,ENST00000628831,;RP11-573D15.8,intron_variant,,ENST00000630331,;RP11-573D15.8,intron_variant,,ENST00000628728,;RP11-573D15.8,intron_variant,,ENST00000629734,;RP11-573D15.8,intron_variant,,ENST00000626633,;RP11-573D15.8,intron_variant,,ENST00000626306,;RP11-573D15.8,intron_variant,,ENST00000625839,;RP11-573D15.8,downstream_gene_variant,,ENST00000626586,;RP11-573D15.8,downstream_gene_variant,,ENST00000596329,;RP11-573D15.8,downstream_gene_variant,,ENST00000625690,;RP11-573D15.8,downstream_gene_variant,,ENST00000596632,;RP11-573D15.8,downstream_gene_variant,,ENST00000626978,;RP11-573D15.8,downstream_gene_variant,,ENST00000629201,;RP11-573D15.8,downstream_gene_variant,,ENST00000628928,;RP11-573D15.8,downstream_gene_variant,,ENST00000625869,;RP11-573D15.8,downstream_gene_variant,,ENST00000609726,;RP11-573D15.8,downstream_gene_variant,,ENST00000629954,;RP11-573D15.8,downstream_gene_variant,,ENST00000628291,;RP11-573D15.8,downstream_gene_variant,,ENST00000609652,;RP11-573D15.8,downstream_gene_variant,,ENST00000626520,; C ENST00000265023 Transcript missense_variant,splice_region_variant 1336/3435 1124/1935 375/644 M/T aTg/aCg 1 1 KNG1 HGNC HGNC:6383 protein_coding YES CCDS43183.1 ENSP00000265023 P01042 UPI000013D5AC NM_001102416.2 tolerated(0.44) 9/10 PROSITE_profiles:PS51647,hmmpanther:PTHR13814:SF12,hmmpanther:PTHR13814 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 186739413 186739413 T C 1 0 0 0 0 1 0 0 0 8305 1478 51 5 5 KNG1 3 186739413 Missense_Mutation SNP T C3L-00095_T 450631 186739413 11556146 206 3415 OPA1 0 . GRCh38 3 193615690 193615690 + Missense_Mutation SNP A A C novel C3L-00095_T C3L-00095_N A A c.368A>C p.Lys123Thr p.K123T ENST00000361908 3/30 357 329 28 257 257 0 strelka-varscan-mutect OPA1,missense_variant,p.Lys123Thr,ENST00000361510,NM_130837.2;OPA1,missense_variant,p.Lys123Thr,ENST00000361908,NM_130836.2;OPA1,missense_variant,p.Lys123Thr,ENST00000361715,NM_130835.2;OPA1,missense_variant,p.Lys123Thr,ENST00000361828,NM_130832.2,NM_130834.2;OPA1,missense_variant,p.Lys123Thr,ENST00000392438,NM_015560.2;OPA1,missense_variant,p.Lys123Thr,ENST00000361150,NM_130833.2,NM_130831.2;OPA1,missense_variant,p.Lys123Thr,ENST00000392436,;OPA1,missense_variant,p.Lys123Thr,ENST00000392437,;OPA1,missense_variant,p.Lys23Thr,ENST00000434811,;OPA1,5_prime_UTR_variant,,ENST00000419435,;OPA1-AS1,downstream_gene_variant,,ENST00000433105,;OPA1-AS1,downstream_gene_variant,,ENST00000444085,;OPA1,non_coding_transcript_exon_variant,,ENST00000487986,;OPA1,upstream_gene_variant,,ENST00000497189,; C ENST00000361908 Transcript missense_variant 602/6439 368/2994 123/997 K/T aAa/aCa 1 1 OPA1 HGNC HGNC:8140 protein_coding YES CCDS33917.1 ENSP00000354681 O60313 E5KLJ7 UPI0000422960 NM_130836.2 deleterious(0) 3/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 193615690 193615690 A C 1 0 0 0 0 1 0 0 0 10948 14 1 5 5 OPA1 3 193615690 Missense_Mutation SNP A C3L-00095_T 6876277 193615690 4679869 207 3416 TNK2 0 . GRCh38 3 195885006 195885006 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.451G>C p.Glu151Gln p.E151Q ENST00000381916 4/15 61 56 5 85 85 0 strelka-varscan-mutect TNK2,missense_variant,p.Glu88Gln,ENST00000333602,NM_005781.4;TNK2,missense_variant,p.Glu120Gln,ENST00000428187,NM_001308046.1;TNK2,missense_variant,p.Glu151Gln,ENST00000381916,NM_001010938.1;TNK2,missense_variant,p.Glu88Gln,ENST00000433111,;TNK2,intron_variant,,ENST00000438207,;TNK2,downstream_gene_variant,,ENST00000427576,;MIR6829,upstream_gene_variant,,ENST00000620375,;TNK2,non_coding_transcript_exon_variant,,ENST00000468819,;TNK2,intron_variant,,ENST00000486523,;TNK2,missense_variant,p.Glu88Gln,ENST00000439230,;TNK2,missense_variant,p.Glu10Gln,ENST00000430929,;TNK2,3_prime_UTR_variant,,ENST00000447060,;TNK2,non_coding_transcript_exon_variant,,ENST00000481865,;TNK2,non_coding_transcript_exon_variant,,ENST00000464041,; G ENST00000381916 Transcript missense_variant 596/4223 451/3261 151/1086 E/Q Gag/Cag 1 -1 TNK2 HGNC HGNC:19297 protein_coding YES CCDS33927.1 ENSP00000371341 Q07912 UPI00004C9B08 NM_001010938.1 tolerated(0.12) 4/15 hmmpanther:PTHR24418 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -11.8554 1 1 1 1 0 G 3 3 10 195885006 195885006 C G 1 0 0 0 0 1 0 0 0 16791 835 29 4 4 TNK2 3 195885006 Missense_Mutation SNP C C3L-00095_T 2269316 195885006 2410553 208 3417 SENP5 0 . GRCh38 3 196885434 196885434 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.253G>T p.Ala85Ser p.A85S ENST00000323460 2/10 195 182 13 239 239 0 strelka-varscan-mutect SENP5,missense_variant,p.Ala85Ser,ENST00000323460,NM_152699.4;SENP5,missense_variant,p.Ala85Ser,ENST00000445299,NM_001308045.1;SENP5,intron_variant,,ENST00000419026,; T ENST00000323460 Transcript missense_variant 502/6308 253/2268 85/755 A/S Gct/Tct 1 1 SENP5 HGNC HGNC:28407 protein_coding YES CCDS3322.1 ENSP00000327197 Q96HI0 UPI00001AF3BE NM_152699.4 tolerated_low_confidence(0.1) 2/10 hmmpanther:PTHR12606:SF10,hmmpanther:PTHR12606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 196885434 196885434 G T 1 0 0 0 0 1 0 0 0 14325 1203 42 2 2 SENP5 3 196885434 Missense_Mutation SNP G C3L-00095_T 1000428 196885434 1410125 209 3418 CRMP1 0 . GRCh38 4 5841330 5841330 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.1131C>A p.= p.I377I ENST00000324989 8/14 358 339 19 433 432 1 strelka-varscan-mutect CRMP1,synonymous_variant,p.=,ENST00000324989,NM_001288662.1,NM_001014809.2;CRMP1,synonymous_variant,p.=,ENST00000397890,NM_001313.4;CRMP1,synonymous_variant,p.=,ENST00000512574,NM_001288661.1;CRMP1,non_coding_transcript_exon_variant,,ENST00000511535,;CRMP1,non_coding_transcript_exon_variant,,ENST00000506216,; T ENST00000324989 Transcript synonymous_variant 1220/3146 1131/2061 377/686 I atC/atA 1 -1 CRMP1 HGNC HGNC:2365 protein_coding YES CCDS33950.1 ENSP00000321606 Q14194 X5DNI1 UPI000020BA92 NM_001288662.1,NM_001014809.2 8/14 hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF54,Pfam_domain:PF01979,TIGRFAM_domain:TIGR02033,Gene3D:3.20.20.140,Superfamily_domains:SSF51556 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 5841330 5841330 G T 1 0 0 0 0 0 0 0 1 3691 1280 45 2 2 CRMP1 4 5841330 Silent SNP G C3L-00095_T 5841330 184373225 210 3419 LGI2 0 . GRCh38 4 25003949 25003949 + Silent SNP A A G novel C3L-00095_T C3L-00095_N A A c.1140T>C p.= p.D380D ENST00000382114 8/8 141 133 8 200 200 0 strelka-varscan-mutect LGI2,synonymous_variant,p.=,ENST00000382114,NM_018176.3;LGI2,intron_variant,,ENST00000512108,; G ENST00000382114 Transcript synonymous_variant 1326/6428 1140/1638 380/545 D gaT/gaC 1 -1 LGI2 HGNC HGNC:18710 protein_coding YES CCDS3431.1 ENSP00000371548 Q8N0V4 UPI0000047256 NM_018176.3 8/8 PROSITE_profiles:PS50912,hmmpanther:PTHR24367:SF21,hmmpanther:PTHR24367,Pfam_domain:PF03736,Superfamily_domains:0049172 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 25003949 25003949 A G 1 0 0 0 0 0 0 0 1 8662 446 16 5 5 LGI2 4 25003949 Silent SNP A C3L-00095_T 19162619 25003949 165210606 211 3420 FAM114A1 0 . GRCh38 4 38932267 38932267 + Silent SNP G G C rs145069128 C3L-00095_T C3L-00095_N G G c.1356G>C p.= p.A452A ENST00000358869 12/15 164 153 11 184 184 0 strelka-varscan-mutect FAM114A1,synonymous_variant,p.=,ENST00000358869,NM_138389.2;FAM114A1,synonymous_variant,p.=,ENST00000515037,;FAM114A1,upstream_gene_variant,,ENST00000513966,;FAM114A1,non_coding_transcript_exon_variant,,ENST00000508737,;FAM114A1,downstream_gene_variant,,ENST00000512889,; C ENST00000358869 Transcript synonymous_variant 1532/4050 1356/1692 452/563 A gcG/gcC rs145069128 1 1 FAM114A1 HGNC HGNC:25087 protein_coding YES CCDS3447.1 ENSP00000351740 Q8IWE2 A0A024R9V7 UPI00001DFE17 NM_138389.2 12/15 hmmpanther:PTHR12842,hmmpanther:PTHR12842:SF4 LOW 1 SNV 1 1 PASS rs145069128 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 38932267 38932267 G C 1 0 0 0 0 0 0 0 1 5266 1103 39 4 4 FAM114A1 4 38932267 Silent SNP G C3L-00095_T 13928318 38932267 151282288 212 3421 GABRA4 0 . GRCh38 4 46965107 46965107 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.997G>T p.Ala333Ser p.A333S ENST00000264318 8/9 168 158 10 208 208 0 strelka-varscan-mutect GABRA4,missense_variant,p.Ala333Ser,ENST00000264318,NM_000809.3,NM_001204266.1;GABRA4,3_prime_UTR_variant,,ENST00000508560,;GABRA4,3_prime_UTR_variant,,ENST00000511523,; A ENST00000264318 Transcript missense_variant 1980/11973 997/1665 333/554 A/S Gcc/Tcc 1 -1 GABRA4 HGNC HGNC:4078 protein_coding YES CCDS3473.1 ENSP00000264318 P48169 X5D7F5 UPI0000074200 NM_000809.3,NM_001204266.1 deleterious(0.01) 8/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF393,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Gene3D:1.20.58.390,Superfamily_domains:SSF90112,Prints_domain:PR00253 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 46965107 46965107 C A 1 0 0 0 0 1 0 0 0 6034 739 26 2 2 GABRA4 4 46965107 Missense_Mutation SNP C C3L-00095_T 8032840 46965107 143249448 213 3422 KIAA1211 0 . GRCh38 4 56315188 56315188 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1686G>C p.Lys562Asn p.K562N ENST00000504228 6/9 159 140 19 206 206 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Lys562Asn,ENST00000504228,;KIAA1211,missense_variant,p.Lys555Asn,ENST00000541073,;KIAA1211,missense_variant,p.Lys562Asn,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; C ENST00000504228 Transcript missense_variant 1791/4628 1686/3702 562/1233 K/N aaG/aaC 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 deleterious(0) 6/9 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 56315188 56315188 G C 1 0 0 0 0 1 0 0 0 8107 991 35 4 4 KIAA1211 4 56315188 Missense_Mutation SNP G C3L-00095_T 9350081 56315188 133899367 214 3423 SRP72 0 . GRCh38 4 56501837 56501837 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1992G>T p.Lys664Asn p.K664N ENST00000342756 19/19 259 230 29 324 324 0 strelka-varscan-mutect SRP72,missense_variant,p.Lys664Asn,ENST00000342756,NM_006947.3;SRP72,missense_variant,p.Lys603Asn,ENST00000510663,NM_001267722.1;ARL9,upstream_gene_variant,,ENST00000360096,NM_206919.1;SRP72,non_coding_transcript_exon_variant,,ENST00000507126,; T ENST00000342756 Transcript missense_variant 2713/3983 1992/2016 664/671 K/N aaG/aaT 1 1 SRP72 HGNC HGNC:11303 protein_coding YES CCDS3506.1 ENSP00000342181 O76094 V9HWK0 UPI000013EEB0 NM_006947.3 tolerated_low_confidence(0.1) 19/19 Low_complexity_(Seg):seg,hmmpanther:PTHR14094:SF9,hmmpanther:PTHR14094,PIRSF_domain:PIRSF038922 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 56501837 56501837 G T 1 0 0 0 0 1 0 0 0 15518 933 33 2 2 SRP72 4 56501837 Missense_Mutation SNP G C3L-00095_T 186649 56501837 133712718 215 3424 ADGRL3 0 . GRCh38 4 61892937 61892937 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1558C>A p.Pro520Thr p.P520T ENST00000514591 9/25 14 11 3 31 31 0 strelka-mutect ADGRL3,missense_variant,p.Pro520Thr,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.Pro520Thr,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Pro588Thr,ENST00000509896,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000511324,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000508693,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000507164,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000506720,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000506746,;ADGRL3,missense_variant,p.Pro588Thr,ENST00000507625,;ADGRL3,missense_variant,p.Pro520Thr,ENST00000506700,;ADGRL3,missense_variant,p.Pro520Thr,ENST00000504896,;ADGRL3,missense_variant,p.Pro520Thr,ENST00000514157,;ADGRL3,missense_variant,p.Pro520Thr,ENST00000508946,;ADGRL3,missense_variant,p.Pro520Thr,ENST00000514996,;ADGRL3,upstream_gene_variant,,ENST00000502815,; A ENST00000514591 Transcript missense_variant 1887/6297 1558/4410 520/1469 P/T Cca/Aca 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0) 9/25 PROSITE_profiles:PS50227,Pfam_domain:PF02793,SMART_domains:SM00008 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -10.71379 1 1 1 1 0 A 3 1 10 61892937 61892937 C A 1 0 0 0 0 1 0 0 0 377 739 26 2 2 ADGRL3 4 61892937 Missense_Mutation SNP C C3L-00095_T 5391100 61892937 128321618 216 3425 TECRL 0 . GRCh38 4 64280148 64280148 + Frame_Shift_Del DEL T T - novel C3L-00095_T C3L-00095_N T T c.1016delA p.Lys339ArgfsTer7 p.K339Rfs*7 ENST00000381210 12/12 175 157 18 92 92 0 sindel-varindel-pindel TECRL,frameshift_variant,p.Lys339ArgfsTer7,ENST00000381210,NM_001010874.4;TECRL,3_prime_UTR_variant,,ENST00000511997,;TECRL,intron_variant,,ENST00000507440,; - ENST00000381210 Transcript frameshift_variant 1127/3573 1016/1092 339/363 K/X aAg/ag 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 12/12 Pfam_domain:PF02544,hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27 HIGH 1 deletion 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999158 1 1 1 0 - 7 5 10 64280148 64280148 T - 1 0 1 0 1 0 0 0 0 16157 1609 56 0 0 TECRL 4 64280148 Frame_Shift_Del DEL T C3L-00095_T 2387211 64280148 125934407 217 3426 STAP1 0 . GRCh38 4 67581334 67581334 + Silent SNP A A C novel C3L-00095_T C3L-00095_N A A c.393A>C p.= p.L131L ENST00000265404 5/9 91 84 7 121 121 0 strelka-varscan-mutect STAP1,synonymous_variant,p.=,ENST00000265404,NM_012108.2;STAP1,synonymous_variant,p.=,ENST00000396225,NM_001317769.1; C ENST00000265404 Transcript synonymous_variant 475/1511 393/888 131/295 L ctA/ctC 1 1 STAP1 HGNC HGNC:24133 protein_coding YES CCDS3515.1 ENSP00000265404 Q9ULZ2 A0A024RD91 UPI0000073E6C NM_012108.2 5/9 hmmpanther:PTHR16186,hmmpanther:PTHR16186:SF10,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 67581334 67581334 A C 1 0 0 0 0 0 0 0 1 15627 378 14 5 5 STAP1 4 67581334 Silent SNP A C3L-00095_T 3301186 67581334 122633221 218 3427 UGT2B7 0 . GRCh38 4 69107240 69107240 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1068G>T p.Trp356Cys p.W356C ENST00000305231 4/6 235 223 12 235 235 0 varscan-mutect UGT2B7,missense_variant,p.Trp356Cys,ENST00000305231,NM_001074.2;UGT2B7,missense_variant,p.Trp356Cys,ENST00000508661,;UGT2B7,missense_variant,p.Trp107Cys,ENST00000502942,;UGT2B7,intron_variant,,ENST00000622664,;UGT2B7,non_coding_transcript_exon_variant,,ENST00000509763,; T ENST00000305231 Transcript missense_variant 1114/1887 1068/1590 356/529 W/C tgG/tgT 1 1 UGT2B7 HGNC HGNC:12554 protein_coding YES CCDS3526.1 ENSP00000304811 P16662 UPI00000015EC NM_001074.2 deleterious(0) 4/6 hmmpanther:PTHR11926:SF382,hmmpanther:PTHR11926,PROSITE_patterns:PS00375,Gene3D:3.40.50.2000,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 69107240 69107240 G T 1 0 0 0 0 1 0 0 0 17486 1183 41 2 2 UGT2B7 4 69107240 Missense_Mutation SNP G C3L-00095_T 1525906 69107240 121107315 219 3428 CABS1 0 . GRCh38 4 70335740 70335740 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.701T>A p.Leu234His p.L234H ENST00000273936 1/2 235 221 14 290 290 0 strelka-varscan-mutect CABS1,missense_variant,p.Leu234His,ENST00000273936,NM_033122.3; A ENST00000273936 Transcript missense_variant 775/1532 701/1188 234/395 L/H cTt/cAt 1 1 CABS1 HGNC HGNC:30710 protein_coding YES CCDS3539.1 ENSP00000273936 Q96KC9 UPI0000071735 NM_033122.3 deleterious(0.04) 1/2 Pfam_domain:PF15367,hmmpanther:PTHR22810 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 70335740 70335740 T A 1 0 0 0 0 1 0 0 0 2222 1609 56 4 4 CABS1 4 70335740 Missense_Mutation SNP T C3L-00095_T 1228500 70335740 119878815 220 3429 GRID2 0 . GRCh38 4 93515316 93515316 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2098G>T p.Glu700Ter p.E700* ENST00000282020 13/16 211 188 23 271 271 0 strelka-varscan-mutect GRID2,stop_gained,p.Glu700Ter,ENST00000282020,NM_001510.3;GRID2,stop_gained,p.Glu619Ter,ENST00000611049,;GRID2,stop_gained,p.Glu605Ter,ENST00000510992,NM_001286838.1; T ENST00000282020 Transcript stop_gained 3133/6117 2098/3024 700/1007 E/* Gag/Tag 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 13/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 93515316 93515316 G T 1 0 0 0 0 0 1 0 0 6652 1291 45 2 2 GRID2 4 93515316 Nonsense_Mutation SNP G C3L-00095_T 23179576 93515316 96699239 221 3430 ANK2 0 . GRCh38 4 113354073 113354073 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.5455G>T p.Ala1819Ser p.A1819S ENST00000357077 38/46 164 150 14 184 184 0 strelka-varscan-mutect ANK2,missense_variant,p.Ala1819Ser,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala1786Ser,ENST00000264366,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; T ENST00000357077 Transcript missense_variant 5508/14196 5455/11874 1819/3957 A/S Gcg/Tcg 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(0.9) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 113354073 113354073 G T 1 0 0 0 0 1 0 0 0 721 1319 46 2 2 ANK2 4 113354073 Missense_Mutation SNP G C3L-00095_T 19838757 113354073 76860482 222 3431 ANK2 0 . GRCh38 4 113355276 113355276 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.6658G>C p.Glu2220Gln p.E2220Q ENST00000357077 38/46 131 121 10 210 210 0 strelka-varscan-mutect ANK2,missense_variant,p.Glu2220Gln,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Glu2187Gln,ENST00000264366,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; C ENST00000357077 Transcript missense_variant 6711/14196 6658/11874 2220/3957 E/Q Gag/Cag 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0.01) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 113355276 113355276 G C 1 0 0 0 0 1 0 0 0 721 1175 41 4 4 ANK2 4 113355276 Missense_Mutation SNP G C3L-00095_T 1203 113355276 76859279 223 3432 UGT8 0 . GRCh38 4 114623292 114623292 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.412G>T p.Asp138Tyr p.D138Y ENST00000310836 2/6 278 249 29 371 371 0 strelka-varscan-mutect UGT8,missense_variant,p.Asp138Tyr,ENST00000310836,NM_001128174.1;UGT8,missense_variant,p.Asp138Tyr,ENST00000394511,NM_003360.3;UGT8,missense_variant,p.Asp138Tyr,ENST00000507710,; T ENST00000310836 Transcript missense_variant 934/4084 412/1626 138/541 D/Y Gac/Tac 1 1 UGT8 HGNC HGNC:12555 protein_coding YES CCDS3705.1 ENSP00000311648 Q16880 UPI000013F094 NM_001128174.1 deleterious(0) 2/6 Gene3D:3.40.50.2000,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF313,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 114623292 114623292 G T 1 0 0 0 0 1 0 0 0 17489 1174 41 2 2 UGT8 4 114623292 Missense_Mutation SNP G C3L-00095_T 1268016 114623292 75591263 224 3433 SYNPO2 0 . GRCh38 4 119057769 119057769 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.3621G>T p.Met1207Ile p.M1207I ENST00000307142 5/5 420 379 41 436 436 0 strelka-varscan-mutect SYNPO2,missense_variant,p.Met1207Ile,ENST00000307142,NM_133477.2;SYNPO2,missense_variant,p.Met1101Ile,ENST00000504178,;SYNPO2,missense_variant,p.Met1176Ile,ENST00000610556,NM_001286754.1;SYNPO2,3_prime_UTR_variant,,ENST00000448416,NM_001286755.1; T ENST00000307142 Transcript missense_variant 3817/7295 3621/3786 1207/1261 M/I atG/atT 1 1 SYNPO2 HGNC HGNC:17732 protein_coding YES CCDS34054.1 ENSP00000306015 Q9UMS6 UPI00001D75EB NM_133477.2 tolerated(0.61) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 119057769 119057769 G T 1 0 0 0 0 1 0 0 0 15851 1377 48 2 2 SYNPO2 4 119057769 Missense_Mutation SNP G C3L-00095_T 4434477 119057769 71156786 225 3434 PRDM5 0 . GRCh38 4 120799663 120799663 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1028C>T p.Ser343Leu p.S343L ENST00000264808 9/16 179 168 11 94 94 0 strelka-varscan-mutect PRDM5,missense_variant,p.Ser343Leu,ENST00000264808,NM_018699.3;PRDM5,missense_variant,p.Ser312Leu,ENST00000428209,NM_001300823.1;PRDM5,missense_variant,p.Ser312Leu,ENST00000515109,NM_001300824.1;PRDM5,splice_region_variant,,ENST00000505484,;PRDM5,splice_region_variant,,ENST00000502409,;PRDM5,splice_region_variant,,ENST00000503661,; A ENST00000264808 Transcript missense_variant,splice_region_variant 1269/5330 1028/1893 343/630 S/L tCa/tTa 1 -1 PRDM5 HGNC HGNC:9349 protein_coding YES CCDS3716.1 ENSP00000264808 Q9NQX1 UPI000013D572 NM_018699.3 deleterious(0) 9/16 Gene3D:3.30.160.60,PIRSF_domain:PIRSF037162,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 120799663 120799663 G A 1 0 0 0 0 1 0 0 0 12591 1304 45 3 3 PRDM5 4 120799663 Missense_Mutation SNP G C3L-00095_T 1741894 120799663 69414892 226 3435 PCDH10 0 . GRCh38 4 133151031 133151031 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.891G>T p.= p.A297A ENST00000264360 1/5 297 269 28 338 336 2 strelka-varscan-mutect PCDH10,synonymous_variant,p.=,ENST00000264360,NM_032961.2;PCDH10,synonymous_variant,p.=,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; T ENST00000264360 Transcript synonymous_variant 1717/8489 891/3123 297/1040 A gcG/gcT 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 1/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs1245308353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 133151031 133151031 G T 1 0 0 0 0 0 0 0 1 11594 1074 38 1 1 PCDH10 4 133151031 Silent SNP G C3L-00095_T 12351368 133151031 57063524 227 3436 SLC7A11 0 . GRCh38 4 138179280 138179280 + Missense_Mutation SNP C C T rs775459597 C3L-00095_T C3L-00095_N C C c.1381G>A p.Val461Ile p.V461I ENST00000280612 11/12 238 214 24 268 268 0 strelka-varscan-mutect SLC7A11,missense_variant,p.Val461Ile,ENST00000280612,NM_014331.3;SLC7A11-AS1,downstream_gene_variant,,ENST00000510767,;SLC7A11-AS1,downstream_gene_variant,,ENST00000512786,;SLC7A11-AS1,downstream_gene_variant,,ENST00000512538,;SLC7A11,3_prime_UTR_variant,,ENST00000509248,; T ENST00000280612 Transcript missense_variant 1661/9645 1381/1506 461/501 V/I Gtc/Atc rs775459597 1 -1 SLC7A11 HGNC HGNC:11059 protein_coding YES CCDS3742.1 ENSP00000280612 Q9UPY5 UPI0000138FD5 NM_014331.3 tolerated(0.7) 11/12 PIRSF_domain:PIRSF006060,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF323,TIGRFAM_domain:TIGR00911,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs775459597 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 138179280 138179280 C T 1 0 0 0 0 1 0 0 0 14977 565 20 3 3 SLC7A11 4 138179280 Missense_Mutation SNP C C3L-00095_T 5028249 138179280 52035275 228 3437 NPY5R 0 . GRCh38 4 163351030 163351030 + Nonsense_Mutation SNP G G T rs749896146 C3L-00095_T C3L-00095_N G G c.757G>T p.Glu253Ter p.E253* ENST00000515560 4/4 245 214 31 247 247 0 strelka-varscan-mutect NPY5R,stop_gained,p.Glu253Ter,ENST00000515560,NM_001317091.1;NPY5R,stop_gained,p.Glu253Ter,ENST00000338566,NM_006174.2;NPY5R,stop_gained,p.Glu253Ter,ENST00000506953,; T ENST00000515560 Transcript stop_gained 2279/3183 757/1338 253/445 E/* Gag/Tag rs749896146 1 1 NPY5R HGNC HGNC:7958 protein_coding YES CCDS3804.1 ENSP00000423917 Q15761 UPI000000D9D7 NM_001317091.1 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF217,hmmpanther:PTHR24242,Pfam_domain:PF00001,SMART_domains:SM01381,Prints_domain:PR01016 HIGH 1 SNV 2 1 PASS rs749896146 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 163351030 163351030 G T 1 0 0 0 0 0 1 0 0 10666 1291 45 2 2 NPY5R 4 163351030 Nonsense_Mutation SNP G C3L-00095_T 25171750 163351030 26863525 229 3438 KLHL2 0 . GRCh38 4 165310603 165310603 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.1102T>C p.Ser368Pro p.S368P ENST00000514860 10/15 421 386 35 489 489 0 strelka-varscan-mutect KLHL2,missense_variant,p.Ser364Pro,ENST00000226725,NM_007246.3;KLHL2,missense_variant,p.Ser276Pro,ENST00000538127,NM_001161522.1;KLHL2,missense_variant,p.Ser267Pro,ENST00000421009,;KLHL2,missense_variant,p.Ser368Pro,ENST00000514860,NM_001161521.1;KLHL2,missense_variant,p.Ser198Pro,ENST00000506761,;KLHL2,non_coding_transcript_exon_variant,,ENST00000509028,;KLHL2,non_coding_transcript_exon_variant,,ENST00000506541,;KLHL2,3_prime_UTR_variant,,ENST00000506824,; C ENST00000514860 Transcript missense_variant 1352/2442 1102/1794 368/597 S/P Tca/Cca 1 1 KLHL2 HGNC HGNC:6353 protein_coding YES CCDS54815.1 ENSP00000424198 O95198 UPI0000E20649 NM_001161521.1 deleterious(0.03) 10/15 hmmpanther:PTHR24412:SF155,hmmpanther:PTHR24412,Pfam_domain:PF01344,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 165310603 165310603 T C 1 0 0 0 0 1 0 0 0 8238 1551 54 5 5 KLHL2 4 165310603 Missense_Mutation SNP T C3L-00095_T 1959573 165310603 24903952 230 3439 TENM3 0 . GRCh38 4 182346759 182346759 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.341C>A p.Ala114Glu p.A114E ENST00000511685 3/28 266 245 21 301 299 2 strelka-varscan-mutect TENM3,missense_variant,p.Ala114Glu,ENST00000511685,NM_001080477.2;TENM3,missense_variant,p.Ala114Glu,ENST00000512480,;TENM3,non_coding_transcript_exon_variant,,ENST00000513201,; A ENST00000511685 Transcript missense_variant 464/10896 341/8100 114/2699 A/E gCa/gAa 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 tolerated_low_confidence(0.22) 3/28 Pfam_domain:PF06484,PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 182346759 182346759 C A 1 0 0 0 0 1 0 0 0 16173 710 25 2 2 TENM3 4 182346759 Missense_Mutation SNP C C3L-00095_T 17036156 182346759 7867796 231 3440 TENM3 0 . GRCh38 4 182799850 182799850 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.7599C>T p.= p.Y2533Y ENST00000511685 28/28 322 297 25 539 538 1 strelka-varscan-mutect TENM3,synonymous_variant,p.=,ENST00000511685,NM_001080477.2; T ENST00000511685 Transcript synonymous_variant 7722/10896 7599/8100 2533/2699 Y taC/taT 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 28/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 182799850 182799850 C T 1 0 0 0 0 0 0 0 1 16173 518 18 3 3 TENM3 4 182799850 Silent SNP C C3L-00095_T 453091 182799850 7414705 232 3441 FAT1 0 . GRCh38 4 186706747 186706747 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.3081G>A p.= p.E1027E ENST00000441802 2/27 184 167 17 234 234 0 strelka-varscan-mutect FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,;FAT1,downstream_gene_variant,,ENST00000509647,; T ENST00000441802 Transcript synonymous_variant 3291/14786 3081/13767 1027/4588 E gaG/gaA 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 2/27 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,Low_complexity_(Seg):seg,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 186706747 186706747 C T 1 0 0 0 0 0 0 0 1 5549 912 32 3 3 FAT1 4 186706747 Silent SNP C C3L-00095_T 3906897 186706747 3507808 233 3442 SLC6A18 0 . GRCh38 5 1244242 1244242 + Silent SNP C C G rs144703302 C3L-00095_T C3L-00095_N C C c.1365C>G p.= p.S455S ENST00000324642 10/12 115 107 8 163 163 0 strelka-varscan-mutect SLC6A18,synonymous_variant,p.=,ENST00000324642,NM_182632.2; G ENST00000324642 Transcript synonymous_variant 1488/2121 1365/1887 455/628 S tcC/tcG rs144703302 1 1 SLC6A18 HGNC HGNC:26441 protein_coding YES CCDS3860.1 ENSP00000323549 Q96N87 UPI0000197EA2 NM_182632.2 10/12 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF109,Pfam_domain:PF00209,Superfamily_domains:0053687 LOW 1 SNV 1 1 PASS rs144703302 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 1244242 1244242 C G 1 0 0 0 0 0 0 0 1 14964 639 23 4 4 SLC6A18 5 1244242 Silent SNP C C3L-00095_T 1244242 180294017 234 3443 TERT 0 . GRCh38 5 1279418 1279418 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.2003A>T p.Glu668Val p.E668V ENST00000310581 5/16 190 170 20 245 245 0 strelka-varscan-mutect TERT,missense_variant,p.Glu668Val,ENST00000310581,NM_198253.2;TERT,missense_variant,p.Glu668Val,ENST00000334602,NM_001193376.1;TERT,missense_variant,p.Glu668Val,ENST00000508104,;TERT,missense_variant,p.Glu668Val,ENST00000460137,;TERT,non_coding_transcript_exon_variant,,ENST00000484238,; A ENST00000310581 Transcript missense_variant 2061/4018 2003/3399 668/1132 E/V gAg/gTg 1 -1 TERT HGNC HGNC:11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 UPI0000031309 NM_198253.2 deleterious(0) 5/16 PROSITE_profiles:PS50878,hmmpanther:PTHR12066,hmmpanther:PTHR12066:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 1279418 1279418 T A 1 0 0 0 0 1 0 0 0 16183 1551 54 4 4 TERT 5 1279418 Missense_Mutation SNP T C3L-00095_T 35176 1279418 180258841 235 3444 LPCAT1 0 . GRCh38 5 1466876 1466876 + Silent SNP T T C novel C3L-00095_T C3L-00095_N T T c.1293A>G p.= p.Q431Q ENST00000283415 13/14 106 94 12 116 116 0 strelka-varscan-mutect LPCAT1,synonymous_variant,p.=,ENST00000283415,NM_024830.3;LPCAT1,non_coding_transcript_exon_variant,,ENST00000503252,;LPCAT1,synonymous_variant,p.=,ENST00000475622,; C ENST00000283415 Transcript synonymous_variant 1426/3966 1293/1605 431/534 Q caA/caG 1 -1 LPCAT1 HGNC HGNC:25718 protein_coding YES CCDS3864.1 ENSP00000283415 Q8NF37 UPI000004771C NM_024830.3 13/14 hmmpanther:PTHR23063:SF11,hmmpanther:PTHR23063,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99999 1 1 1 1 0 C 2 2 10 1466876 1466876 T C 1 0 0 0 0 0 0 0 1 8813 1606 56 5 5 LPCAT1 5 1466876 Silent SNP T C3L-00095_T 187458 1466876 180071383 236 3445 SRD5A1 0 . GRCh38 5 6662871 6662871 + Missense_Mutation SNP G G C rs757174529 C3L-00095_T C3L-00095_N G G c.618G>C p.Trp206Cys p.W206C ENST00000274192 4/5 308 288 20 350 350 0 strelka-varscan-mutect SRD5A1,missense_variant,p.Trp206Cys,ENST00000274192,NM_001047.2;SRD5A1,3_prime_UTR_variant,,ENST00000510531,;SRD5A1,3_prime_UTR_variant,,ENST00000513117,; C ENST00000274192 Transcript missense_variant 852/7132 618/780 206/259 W/C tgG/tgC rs757174529,COSM3947678 1 1 SRD5A1 HGNC HGNC:11284 protein_coding YES CCDS3870.1 ENSP00000274192 P18405 UPI00000534C8 NM_001047.2 deleterious(0) 4/5 PROSITE_profiles:PS50244,hmmpanther:PTHR10556:SF41,hmmpanther:PTHR10556,Pfam_domain:PF02544,PIRSF_domain:PIRSF015596 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757174529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 6662871 6662871 G C 1 0 0 0 0 1 0 0 0 15495 1270 44 4 4 SRD5A1 5 6662871 Missense_Mutation SNP G C3L-00095_T 5195995 6662871 174875388 237 3446 SEMA5A 0 . GRCh38 5 9044497 9044497 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.2981A>T p.Gln994Leu p.Q994L ENST00000382496 22/23 453 382 71 466 466 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Gln994Leu,ENST00000382496,NM_003966.2;CTD-2215L10.1,intron_variant,,ENST00000506519,; A ENST00000382496 Transcript missense_variant 3647/11762 2981/3225 994/1074 Q/L cAg/cTg 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0.05) 22/23 hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 9044497 9044497 T A 1 0 0 0 0 1 0 0 0 14313 1580 55 4 4 SEMA5A 5 9044497 Missense_Mutation SNP T C3L-00095_T 2381626 9044497 172493762 238 3447 ANKRD33B 0 . GRCh38 5 10649799 10649799 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.1171C>T p.= p.L391L ENST00000296657 4/4 34 28 6 31 31 0 strelka-varscan-mutect ANKRD33B,synonymous_variant,p.=,ENST00000296657,NM_001164440.1;ANKRD33B,downstream_gene_variant,,ENST00000504806,;RP11-54F2.1,downstream_gene_variant,,ENST00000508690,; T ENST00000296657 Transcript synonymous_variant 1171/9188 1171/1485 391/494 L Ctg/Ttg 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 4/4 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -16.2041 1 1 1 1 0 T 2 4 10 10649799 10649799 C T 1 0 0 0 0 0 0 0 1 766 680 24 3 3 ANKRD33B 5 10649799 Silent SNP C C3L-00095_T 1605302 10649799 170888460 239 3448 CTNND2 0 . GRCh38 5 11098750 11098750 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.2464-2A>T p.X822_splice ENST00000304623 124 114 10 165 165 0 strelka-varscan-mutect CTNND2,splice_acceptor_variant,,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,splice_acceptor_variant,,ENST00000511377,NM_001288715.1;CTNND2,splice_acceptor_variant,,ENST00000503622,NM_001288716.1;CTNND2,splice_acceptor_variant,,ENST00000458100,;CTNND2,splice_acceptor_variant,,ENST00000495388,;CTNND2,splice_acceptor_variant,,ENST00000513588,;CTNND2,splice_acceptor_variant,,ENST00000504499,; A ENST00000304623 Transcript splice_acceptor_variant -/5481 2464/3678 822/1225 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 14/21 HIGH 1 SNV 1 1 PASS . . 0 203 4 3 0 0 0 0 -14.46477 0.9994745 1 1 1 0 A 5 1 10 11098750 11098750 T A 1 0 0 0 0 0 0 1 0 3829 1594 55 4 4 CTNND2 5 11098750 Splice_Site SNP T C3L-00095_T 448951 11098750 170439509 240 3449 CTNND2 0 . GRCh38 5 11159666 11159666 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.2069A>T p.His690Leu p.H690L ENST00000304623 12/22 167 149 18 186 185 1 strelka-varscan-mutect CTNND2,missense_variant,p.His690Leu,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.His599Leu,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.His353Leu,ENST00000503622,NM_001288716.1;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,missense_variant,p.His444Leu,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; A ENST00000304623 Transcript missense_variant 2259/5481 2069/3678 690/1225 H/L cAc/cTc 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0.02) 12/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 11159666 11159666 T A 1 0 0 0 0 1 0 0 0 3829 1696 59 4 4 CTNND2 5 11159666 Missense_Mutation SNP T C3L-00095_T 60916 11159666 170378593 241 3450 CDH12 0 . GRCh38 5 21751857 21751857 + Silent SNP G G A rs761207356 C3L-00095_T C3L-00095_N G G c.2265C>T p.= p.D755D ENST00000382254 15/15 394 360 34 496 496 0 strelka-varscan-mutect CDH12,synonymous_variant,p.=,ENST00000382254,NM_004061.3;CDH12,synonymous_variant,p.=,ENST00000504376,;CDH12,synonymous_variant,p.=,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; A ENST00000382254 Transcript synonymous_variant 3352/4164 2265/2385 755/794 D gaC/gaT rs761207356 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 15/15 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96 LOW 1 SNV 1 1 PASS rs761207356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 21751857 21751857 G A 1 0 0 0 0 0 0 0 1 2801 1020 36 3 3 CDH12 5 21751857 Silent SNP G C3L-00095_T 10592191 21751857 159786402 242 3451 CDH9 0 . GRCh38 5 26886041 26886041 + Missense_Mutation SNP G G C C3L-00095_T C3L-00095_N G G c.1555C>G p.Arg519Gly p.R519G ENST00000231021 10/12 99 89 10 103 103 0 strelka-varscan-mutect CDH9,missense_variant,p.Arg519Gly,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505020,; C ENST00000231021 Transcript missense_variant 1728/3079 1555/2370 519/789 R/G Cga/Gga COSM5633368 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 tolerated(0.55) 10/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS rs1257661796 . 0 208 0 2 0 0 0 0 -15.72803 0.9999999 1 1 1 0 C 3 2 10 26886041 26886041 G C 1 0 0 0 0 1 0 0 0 2820 1124 39 4 4 CDH9 5 26886041 Missense_Mutation SNP G C3L-00095_T 5134184 26886041 154652218 243 3452 DROSHA 0 . GRCh38 5 31511108 31511108 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1359G>T p.= p.G453G ENST00000511367 8/35 206 194 12 213 213 0 strelka-varscan-mutect DROSHA,synonymous_variant,p.=,ENST00000511367,NM_013235.4;DROSHA,synonymous_variant,p.=,ENST00000344624,;DROSHA,synonymous_variant,p.=,ENST00000442743,;DROSHA,synonymous_variant,p.=,ENST00000513349,NM_001100412.1;DROSHA,synonymous_variant,p.=,ENST00000512076,;DROSHA,downstream_gene_variant,,ENST00000512302,; A ENST00000511367 Transcript synonymous_variant 1604/5305 1359/4125 453/1374 G ggG/ggT 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 8/35 hmmpanther:PTHR11207 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 31511108 31511108 C A 1 0 0 0 0 0 0 0 1 4584 842 30 2 2 DROSHA 5 31511108 Silent SNP C C3L-00095_T 4625067 31511108 150027151 244 3453 ADAMTS12 0 . GRCh38 5 33624314 33624314 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2060C>T p.Thr687Ile p.T687I ENST00000504830 14/24 143 134 9 162 162 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Thr687Ile,ENST00000504830,NM_030955.2;ADAMTS12,intron_variant,,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000506952,; A ENST00000504830 Transcript missense_variant 2396/8774 2060/4785 687/1594 T/I aCc/aTc 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.11) 14/24 Prints_domain:PR01857,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 33624314 33624314 G A 1 0 0 0 0 1 0 0 0 301 1261 44 3 3 ADAMTS12 5 33624314 Missense_Mutation SNP G C3L-00095_T 2113206 33624314 147913945 245 3454 SPEF2 0 . GRCh38 5 35793209 35793209 + Missense_Mutation SNP G G T rs755698487 C3L-00095_T C3L-00095_N G G c.4605G>T p.Trp1535Cys p.W1535C ENST00000356031 32/37 127 113 14 169 169 0 strelka-varscan-mutect SPEF2,missense_variant,p.Trp1530Cys,ENST00000440995,;SPEF2,missense_variant,p.Trp1535Cys,ENST00000356031,NM_024867.3;SPEF2,downstream_gene_variant,,ENST00000637569,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,downstream_gene_variant,,ENST00000635995,;SPEF2,3_prime_UTR_variant,,ENST00000506526,;SPEF2,3_prime_UTR_variant,,ENST00000513078,;SPEF2,3_prime_UTR_variant,,ENST00000637061,; T ENST00000356031 Transcript missense_variant 4759/5681 4605/5469 1535/1822 W/C tgG/tgT rs755698487,COSM5061065,COSM5061066 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 deleterious(0.04) 32/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0,Superfamily_domains:SSF47473 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs755698487 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 35793209 35793209 G T 1 0 0 0 0 1 0 0 0 15386 1212 42 2 2 SPEF2 5 35793209 Missense_Mutation SNP G C3L-00095_T 2168895 35793209 145745050 246 3455 IL7R 0 . GRCh38 5 35876154 35876154 + Missense_Mutation SNP C C A rs111803690 C3L-00095_T C3L-00095_N C C c.1048C>A p.Pro350Thr p.P350T ENST00000303115 8/8 295 264 31 376 375 1 strelka-varscan-mutect IL7R,missense_variant,p.Pro350Thr,ENST00000303115,NM_002185.3;IL7R,3_prime_UTR_variant,,ENST00000505093,;IL7R,downstream_gene_variant,,ENST00000506850,;IL7R,3_prime_UTR_variant,,ENST00000514217,;IL7R,non_coding_transcript_exon_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000509668,; A ENST00000303115 Transcript missense_variant 1177/4626 1048/1380 350/459 P/T Cca/Aca rs111803690 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 tolerated(0.27) 8/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS rs111803690 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 35876154 35876154 C A 1 0 0 0 0 1 0 0 0 7609 623 22 2 2 IL7R 5 35876154 Missense_Mutation SNP C C3L-00095_T 82945 35876154 145662105 247 3456 UGT3A1 0 . GRCh38 5 35988481 35988481 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.165G>T p.Met55Ile p.M55I ENST00000274278 2/7 184 164 20 194 194 0 strelka-varscan-mutect UGT3A1,start_lost,p.Met1?,ENST00000625798,NM_001171873.1;UGT3A1,start_lost,p.Met1?,ENST00000333811,;UGT3A1,missense_variant,p.Met55Ile,ENST00000274278,NM_152404.3;UGT3A1,missense_variant,p.Met55Ile,ENST00000503189,;UGT3A1,intron_variant,,ENST00000507113,;UGT3A1,intron_variant,,ENST00000513233,;UGT3A1,3_prime_UTR_variant,,ENST00000515801,; A ENST00000274278 Transcript missense_variant 523/5122 165/1572 55/523 M/I atG/atT 1 -1 UGT3A1 HGNC HGNC:26625 protein_coding YES CCDS3913.1 ENSP00000274278 Q6NUS8 A8K444 UPI000003C38B NM_152404.3 deleterious(0.03) 2/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF208,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 35988481 35988481 C A 1 0 0 0 0 1 0 0 0 17487 710 25 2 2 UGT3A1 5 35988481 Missense_Mutation SNP C C3L-00095_T 112327 35988481 145549778 248 3457 RANBP3L 0 . GRCh38 5 36260823 36260823 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.701G>A p.Ser234Asn p.S234N ENST00000502994 9/15 199 184 15 90 90 0 strelka-varscan-mutect RANBP3L,missense_variant,p.Ser209Asn,ENST00000296604,NM_145000.3;RANBP3L,missense_variant,p.Ser234Asn,ENST00000502994,NM_001161429.1;RANBP3L,missense_variant,p.Ser209Asn,ENST00000515759,;RANBP3L,downstream_gene_variant,,ENST00000505865,; T ENST00000502994 Transcript missense_variant 1185/2278 701/1473 234/490 S/N aGt/aAt 1 -1 RANBP3L HGNC HGNC:26353 protein_coding YES CCDS54843.1 ENSP00000421853 Q86VV4 UPI0001A5C4B2 NM_001161429.1 tolerated(0.5) 9/15 hmmpanther:PTHR23138:SF88,hmmpanther:PTHR23138 MODERATE 1 SNV 2 1 PASS rs1210754022 . 0 207 0 2 0 0 0 0 -19.29042 0.9999997 1 1 1 0 T 3 4 10 36260823 36260823 C T 1 0 0 0 0 1 0 0 0 13189 565 20 3 3 RANBP3L 5 36260823 Missense_Mutation SNP C C3L-00095_T 272342 36260823 145277436 249 3458 FBXO4 0 . GRCh38 5 41939497 41939497 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.955G>C p.Gly319Arg p.G319R ENST00000281623 6/7 195 178 17 174 174 0 strelka-varscan-mutect FBXO4,missense_variant,p.Gly319Arg,ENST00000281623,NM_012176.2;FBXO4,intron_variant,,ENST00000509134,NM_001297437.1;FBXO4,downstream_gene_variant,,ENST00000296812,NM_033484.2;FBXO4,non_coding_transcript_exon_variant,,ENST00000505566,; C ENST00000281623 Transcript missense_variant 1011/1682 955/1164 319/387 G/R Ggg/Cgg 1 1 FBXO4 HGNC HGNC:13583 protein_coding YES CCDS3938.1 ENSP00000281623 Q9UKT5 UPI0000062307 NM_012176.2 deleterious(0) 6/7 hmmpanther:PTHR16008,hmmpanther:PTHR16008:SF4 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99877 0.9999998 1 1 1 0 C 3 2 10 41939497 41939497 G C 1 0 0 0 0 1 0 0 0 5611 1348 47 4 4 FBXO4 5 41939497 Missense_Mutation SNP G C3L-00095_T 5678674 41939497 139598762 250 3459 HCN1 0 . GRCh38 5 45262491 45262491 + Silent SNP G G C rs762033519 C3L-00095_T C3L-00095_N G G c.2103C>G p.= p.T701T ENST00000303230 8/8 150 132 18 211 211 0 strelka-varscan-mutect HCN1,synonymous_variant,p.=,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; C ENST00000303230 Transcript synonymous_variant 2344/9885 2103/2673 701/890 T acC/acG rs762033519,COSM395308,COSM4969051 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs762033519 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 45262491 45262491 G C 1 0 0 0 0 0 0 0 1 6883 1103 39 4 4 HCN1 5 45262491 Silent SNP G C3L-00095_T 3322994 45262491 136275768 251 3460 ADAMTS6 0 . GRCh38 5 65172889 65172889 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.3030C>A p.= p.I1010I ENST00000381055 23/25 251 226 25 315 315 0 strelka-varscan-mutect ADAMTS6,synonymous_variant,p.=,ENST00000381055,NM_197941.2;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000314351,;ADAMTS6,downstream_gene_variant,,ENST00000417396,;ADAMTS6,3_prime_UTR_variant,,ENST00000381052,; T ENST00000381055 Transcript synonymous_variant 3887/7311 3030/3354 1010/1117 I atC/atA 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 23/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 65172889 65172889 G T 1 0 0 0 0 0 0 0 1 314 1164 41 2 2 ADAMTS6 5 65172889 Silent SNP G C3L-00095_T 19910398 65172889 116365370 252 3461 ADAMTS6 0 . GRCh38 5 65215363 65215363 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2397G>T p.Leu799Phe p.L799F ENST00000381055 19/25 103 95 8 126 126 0 strelka-varscan-mutect ADAMTS6,missense_variant,p.Leu799Phe,ENST00000381055,NM_197941.2;ADAMTS6,upstream_gene_variant,,ENST00000417396,;ADAMTS6,3_prime_UTR_variant,,ENST00000381052,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000470597,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000464680,;CTD-2194F4.2,downstream_gene_variant,,ENST00000509786,; A ENST00000381055 Transcript missense_variant 3254/7311 2397/3354 799/1117 L/F ttG/ttT 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 deleterious(0) 19/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 65215363 65215363 C A 1 0 0 0 0 1 0 0 0 314 593 21 2 2 ADAMTS6 5 65215363 Missense_Mutation SNP C C3L-00095_T 42474 65215363 116322896 253 3462 ARHGEF28 0 . GRCh38 5 73885902 73885902 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.3108C>T p.= p.D1036D ENST00000545377 25/37 193 175 18 165 165 0 strelka-varscan-mutect ARHGEF28,synonymous_variant,p.=,ENST00000545377,NM_001080479.2;ARHGEF28,synonymous_variant,p.=,ENST00000513042,NM_001177693.1;ARHGEF28,synonymous_variant,p.=,ENST00000426542,;ARHGEF28,synonymous_variant,p.=,ENST00000437974,;ARHGEF28,synonymous_variant,p.=,ENST00000296794,;ARHGEF28,synonymous_variant,p.=,ENST00000296799,NM_001244364.1;ARHGEF28,upstream_gene_variant,,ENST00000512883,;ARHGEF28,non_coding_transcript_exon_variant,,ENST00000510312,;ARHGEF28,upstream_gene_variant,,ENST00000504003,; T ENST00000545377 Transcript synonymous_variant 3284/6351 3108/5196 1036/1731 D gaC/gaT 1 1 ARHGEF28 HGNC HGNC:30322 protein_coding YES CCDS47231.2 ENSP00000441913 Q8N1W1 UPI00004DF58E NM_001080479.2 25/37 Gene3D:1.20.900.10,Pfam_domain:PF00621,PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF133,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 73885902 73885902 C T 1 0 0 0 0 0 0 0 1 1036 477 17 3 3 ARHGEF28 5 73885902 Silent SNP C C3L-00095_T 8670539 73885902 107652357 254 3463 DMGDH 0 . GRCh38 5 79042470 79042470 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.1006G>C p.Glu336Gln p.E336Q ENST00000255189 7/16 379 347 32 438 438 0 strelka-varscan-mutect DMGDH,missense_variant,p.Glu336Gln,ENST00000255189,NM_013391.3;DMGDH,missense_variant,p.Glu175Gln,ENST00000523732,;DMGDH,3_prime_UTR_variant,,ENST00000518477,;DMGDH,3_prime_UTR_variant,,ENST00000521052,;DMGDH,intron_variant,,ENST00000517853,; G ENST00000255189 Transcript missense_variant 1035/3106 1006/2601 336/866 E/Q Gaa/Caa 1 -1 DMGDH HGNC HGNC:24475 protein_coding YES CCDS4044.1 ENSP00000255189 Q9UI17 UPI000013CE96 NM_013391.3 deleterious(0.01) 7/16 Gene3D:3.30.9.10,Pfam_domain:PF01266,hmmpanther:PTHR13847,hmmpanther:PTHR13847:SF187,Superfamily_domains:SSF54373 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 79042470 79042470 C G 1 0 0 0 0 1 0 0 0 4388 864 30 4 4 DMGDH 5 79042470 Missense_Mutation SNP C C3L-00095_T 5156568 79042470 102495789 255 3464 YTHDC2 0 . GRCh38 5 113567116 113567116 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2867G>T p.Gly956Val p.G956V ENST00000161863 22/30 194 178 16 224 222 2 strelka-varscan-mutect YTHDC2,missense_variant,p.Gly956Val,ENST00000161863,NM_022828.3;YTHDC2,non_coding_transcript_exon_variant,,ENST00000506333,; T ENST00000161863 Transcript missense_variant 3080/6316 2867/4293 956/1430 G/V gGt/gTt 1 1 YTHDC2 HGNC HGNC:24721 protein_coding YES CCDS4113.1 ENSP00000161863 Q9H6S0 UPI0000367311 NM_022828.3 deleterious(0.05) 22/30 hmmpanther:PTHR18934:SF125,hmmpanther:PTHR18934,Pfam_domain:PF07717 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 113567116 113567116 G T 1 0 0 0 0 1 0 0 0 18058 1261 44 2 2 YTHDC2 5 113567116 Missense_Mutation SNP G C3L-00095_T 34524646 113567116 67971143 256 3465 DMXL1 0 . GRCh38 5 119193853 119193853 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.7340G>T p.Arg2447Ile p.R2447I ENST00000539542 30/44 349 301 48 256 255 1 strelka-varscan-mutect DMXL1,missense_variant,p.Arg2447Ile,ENST00000539542,NM_001290321.2;DMXL1,missense_variant,p.Arg2447Ile,ENST00000311085,NM_001290322.2,NM_005509.5;DMXL1,upstream_gene_variant,,ENST00000511622,;DMXL1,upstream_gene_variant,,ENST00000502516,; T ENST00000539542 Transcript missense_variant 7521/11236 7340/9147 2447/3048 R/I aGa/aTa 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 tolerated(0.22) 30/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 119193853 119193853 G T 1 0 0 0 0 1 0 0 0 4403 942 33 2 2 DMXL1 5 119193853 Missense_Mutation SNP G C3L-00095_T 5626737 119193853 62344406 257 3466 GDF9 0 . GRCh38 5 132864487 132864487 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.47G>A p.Trp16Ter p.W16* ENST00000378673 2/3 173 158 15 202 202 0 strelka-varscan-mutect GDF9,stop_gained,p.Trp16Ter,ENST00000378673,NM_005260.4;GDF9,intron_variant,,ENST00000621295,NM_001288825.2;GDF9,intron_variant,,ENST00000624492,NM_001288824.2;GDF9,intron_variant,,ENST00000624495,NM_001288828.2,NM_001288826.2;GDF9,intron_variant,,ENST00000296875,NM_001288827.2;UQCRQ,upstream_gene_variant,,ENST00000378670,;UQCRQ,upstream_gene_variant,,ENST00000378665,;UQCRQ,upstream_gene_variant,,ENST00000378667,NM_014402.4;GDF9,intron_variant,,ENST00000464378,;GDF9,intron_variant,,ENST00000472320,;UQCRQ,upstream_gene_variant,,ENST00000496429,;UQCRQ,upstream_gene_variant,,ENST00000498309,;UQCRQ,upstream_gene_variant,,ENST00000480372,; T ENST00000378673 Transcript stop_gained 914/2640 47/1365 16/454 W/* tGg/tAg 1 -1 GDF9 HGNC HGNC:4224 protein_coding YES CCDS4162.1 ENSP00000367942 O60383 UPI000012B396 NM_005260.4 2/3 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF19 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 132864487 132864487 C T 1 0 0 0 0 0 1 0 0 6192 595 21 3 3 GDF9 5 132864487 Nonsense_Mutation SNP C C3L-00095_T 13670634 132864487 48673772 258 3467 PCDHB3 0 . GRCh38 5 141100844 141100844 + Missense_Mutation SNP A A C C3L-00095_T C3L-00095_N A A c.195A>C p.Gln65His p.Q65H ENST00000231130 1/1 108 101 7 152 152 0 strelka-varscan-mutect PCDHB3,missense_variant,p.Gln65His,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000194155,NM_018936.3;PCDHB2,downstream_gene_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000624513,;PCDHB2,downstream_gene_variant,,ENST00000624994,;AC005754.7,intron_variant,,ENST00000607216,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;CTC-270D5.1,upstream_gene_variant,,ENST00000623615,;CTC-270D5.1,upstream_gene_variant,,ENST00000623741,; C ENST00000231130 Transcript missense_variant 372/3355 195/2391 65/796 Q/H caA/caC COSM1173092 1 1 PCDHB3 HGNC HGNC:8688 protein_coding YES CCDS4245.1 ENSP00000231130 Q9Y5E6 UPI0003CC25DF NM_018937.4 deleterious_low_confidence(0.01) 1/1 Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.48049 1 1 1 1 0 C 3 2 10 141100844 141100844 A C 1 0 0 0 0 1 0 0 0 11630 69 3 5 5 PCDHB3 5 141100844 Missense_Mutation SNP A C3L-00095_T 8236357 141100844 40437415 259 3468 PCDHB9 0 . GRCh38 5 141188012 141188012 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.694G>T p.Val232Phe p.V232F ENST00000316105 1/1 150 141 9 205 204 1 varscan-mutect PCDHB9,missense_variant,p.Val232Phe,ENST00000316105,NM_019119.4;PCDHB9,intron_variant,,ENST00000624909,;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,intron_variant,,ENST00000623266,;CH17-140K24.5,intron_variant,,ENST00000623407,; T ENST00000316105 Transcript missense_variant 886/4415 694/2394 232/797 V/F Gtc/Ttc 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,PROSITE_patterns:PS00232,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 141188012 141188012 G T 1 0 0 0 0 1 0 0 0 11636 1261 44 2 2 PCDHB9 5 141188012 Missense_Mutation SNP G C3L-00095_T 87168 141188012 40350247 260 3469 PCDHB14 0 . GRCh38 5 141224465 141224465 + Missense_Mutation SNP G G T rs372009610 C3L-00095_T C3L-00095_N G G c.960G>T p.Gln320His p.Q320H ENST00000239449 1/1 81 75 6 127 127 0 strelka-mutect PCDHB14,missense_variant,p.Gln320His,ENST00000239449,NM_018934.3;PCDHB14,missense_variant,p.Gln167His,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239449 Transcript missense_variant 1534/4828 960/2397 320/798 Q/H caG/caT rs372009610 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS rs372009610 . 0 206 4 0 0 0 0 0 -13.16867 1 1 1 1 0 T 3 4 10 141224465 141224465 G T 1 0 0 0 0 1 0 0 0 11626 991 35 2 2 PCDHB14 5 141224465 Missense_Mutation SNP G C3L-00095_T 36453 141224465 40313794 261 3470 PCDHGB5 0 . GRCh38 5 141398853 141398853 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.726C>A p.Phe242Leu p.F242L ENST00000617380 1/4 187 167 20 267 267 0 strelka-varscan-mutect PCDHGB5,missense_variant,p.Phe242Leu,ENST00000617380,NM_018925.2;PCDHGB5,missense_variant,p.Phe242Leu,ENST00000621169,NM_032099.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGA8,downstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA9,upstream_gene_variant,,ENST00000573521,NM_018921.2;PCDHGA9,upstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000617380 Transcript missense_variant 726/4578 726/2772 242/923 F/L ttC/ttA 1 1 PCDHGB5 HGNC HGNC:8712 protein_coding YES CCDS75339.1 ENSP00000478258 Q9Y5G0 UPI000007279C NM_018925.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF126,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 141398853 141398853 C A 1 0 0 0 0 1 0 0 0 11653 825 29 2 2 PCDHGB5 5 141398853 Missense_Mutation SNP C C3L-00095_T 174388 141398853 40139406 262 3471 PCDHGB5 0 . GRCh38 5 141399044 141399044 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.917A>T p.Glu306Val p.E306V ENST00000617380 1/4 187 172 15 227 226 1 strelka-varscan-mutect PCDHGB5,missense_variant,p.Glu306Val,ENST00000617380,NM_018925.2;PCDHGB5,missense_variant,p.Glu306Val,ENST00000621169,NM_032099.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGA8,downstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA9,upstream_gene_variant,,ENST00000573521,NM_018921.2;PCDHGA9,upstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000617380 Transcript missense_variant 917/4578 917/2772 306/923 E/V gAa/gTa 1 1 PCDHGB5 HGNC HGNC:8712 protein_coding YES CCDS75339.1 ENSP00000478258 Q9Y5G0 UPI000007279C NM_018925.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF126,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 141399044 141399044 A T 1 0 0 0 0 1 0 0 0 11653 246 9 4 4 PCDHGB5 5 141399044 Missense_Mutation SNP A C3L-00095_T 191 141399044 40139215 263 3472 PCDHGA10 0 . GRCh38 5 141413590 141413590 + Missense_Mutation SNP G G T rs759901330 C3L-00095_T C3L-00095_N G G c.415G>T p.Ala139Ser p.A139S ENST00000398610 1/4 169 159 10 250 250 0 strelka-varscan-mutect PCDHGA10,missense_variant,p.Ala139Ser,ENST00000398610,NM_018913.2;PCDHGA10,missense_variant,p.Ala139Ser,ENST00000612503,NM_032090.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGB7,upstream_gene_variant,,ENST00000398594,NM_018927.3;PCDHGB6,downstream_gene_variant,,ENST00000616430,NM_032100.1;PCDHGB7,upstream_gene_variant,,ENST00000612073,NM_032101.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398610 Transcript missense_variant 415/4617 415/2811 139/936 A/S Gca/Tca rs759901330 1 1 PCDHGA10 HGNC HGNC:8697 protein_coding YES CCDS47292.1 ENSP00000381611 Q9Y5H3 UPI00000726C3 NM_018913.2 tolerated_low_confidence(0.52) 1/4 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF110,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs759901330 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 141413590 141413590 G T 1 0 0 0 0 1 0 0 0 11638 971 34 2 2 PCDHGA10 5 141413590 Missense_Mutation SNP G C3L-00095_T 14546 141413590 40124669 264 3473 PCDHGA12 0 . GRCh38 5 141430944 141430944 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.185G>T p.Arg62Leu p.R62L ENST00000252085 1/4 68 59 9 94 94 0 strelka-varscan-mutect PCDHGA12,missense_variant,p.Arg62Leu,ENST00000252085,NM_003735.2;PCDHGA12,missense_variant,p.Arg62Leu,ENST00000613314,NM_032094.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB7,intron_variant,,ENST00000398594,NM_018927.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA11,intron_variant,,ENST00000398587,NM_018914.2;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,intron_variant,,ENST00000518882,NM_032092.1;AC005618.9,upstream_gene_variant,,ENST00000624928,;PCDHGB8P,downstream_gene_variant,,ENST00000502926,;PCDHGA3,intron_variant,,ENST00000612467,;PCDHGB8P,downstream_gene_variant,,ENST00000507007,; T ENST00000252085 Transcript missense_variant 327/4747 185/2799 62/932 R/L cGc/cTc COSM5344868,COSM5344869 1 1 PCDHGA12 HGNC HGNC:8699 protein_coding YES CCDS4260.1 ENSP00000252085 O60330 UPI0000073EA1 NM_003735.2 deleterious_low_confidence(0.01) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF109,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1417018095 . 0 207 3 0 0 0 0 0 -19.83553 1 1 1 1 0 T 3 4 10 141430944 141430944 G T 1 0 0 0 0 1 0 0 0 11640 1087 38 1 1 PCDHGA12 5 141430944 Missense_Mutation SNP G C3L-00095_T 17354 141430944 40107315 265 3474 PDE6A 0 . GRCh38 5 149931127 149931127 + Silent SNP C C G novel C3L-00095_T C3L-00095_N C C c.759G>C p.= p.T253T ENST00000255266 4/22 381 347 34 510 509 1 strelka-varscan-mutect PDE6A,synonymous_variant,p.=,ENST00000255266,NM_000440.2;PDE6A,synonymous_variant,p.=,ENST00000613228,;PDE6A,synonymous_variant,p.=,ENST00000617647,;PDE6A,non_coding_transcript_exon_variant,,ENST00000508173,;AC008427.2,downstream_gene_variant,,ENST00000503102,; G ENST00000255266 Transcript synonymous_variant 879/5642 759/2583 253/860 T acG/acC 1 -1 PDE6A HGNC HGNC:8785 protein_coding YES CCDS4299.1 ENSP00000255266 P16499 UPI000013CE9F NM_000440.2 4/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF115,Gene3D:3.30.450.40,Superfamily_domains:SSF55781 LOW 1 SNV 1 1 PASS rs879171832 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 149931127 149931127 C G 1 0 0 0 0 0 0 0 1 11733 639 23 4 4 PDE6A 5 149931127 Silent SNP C C3L-00095_T 8500183 149931127 31607132 266 3475 NMUR2 0 . GRCh38 5 152398146 152398146 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.727-2A>T p.X243_splice ENST00000255262 124 110 14 115 114 1 strelka-varscan-mutect NMUR2,splice_acceptor_variant,,ENST00000255262,NM_020167.4;NMUR2,splice_acceptor_variant,,ENST00000518933,; A ENST00000255262 Transcript splice_acceptor_variant -/2073 727/1248 243/415 1 -1 NMUR2 HGNC HGNC:16454 protein_coding YES CCDS4321.1 ENSP00000255262 Q9GZQ4 UPI000013CE9D NM_020167.4 1/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 152398146 152398146 T A 1 0 0 0 0 0 0 1 0 10548 1594 55 4 4 NMUR2 5 152398146 Splice_Site SNP T C3L-00095_T 2467019 152398146 29140113 267 3476 KIF4B 0 . GRCh38 5 155017164 155017164 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.3305G>A p.Arg1102Lys p.R1102K ENST00000435029 1/1 424 389 35 529 528 1 varscan-mutect KIF4B,missense_variant,p.Arg1102Lys,ENST00000435029,NM_001099293.1; A ENST00000435029 Transcript missense_variant 3410/4378 3305/3705 1102/1234 R/K aGg/aAg 1 1 KIF4B HGNC HGNC:6322 protein_coding YES CCDS47324.1 ENSP00000387875 Q2VIQ3 UPI000013D5DB NM_001099293.1 tolerated(0.17) 1/1 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF392,SMART_domains:SM01114 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 155017164 155017164 G A 1 0 0 0 0 1 0 0 0 8169 1000 35 3 3 KIF4B 5 155017164 Missense_Mutation SNP G C3L-00095_T 2619018 155017164 26521095 268 3477 HAVCR2 0 . GRCh38 5 157095347 157095347 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.635G>T p.Gly212Val p.G212V ENST00000307851 5/7 257 230 27 296 295 1 strelka-varscan-mutect HAVCR2,missense_variant,p.Gly212Val,ENST00000307851,NM_032782.4;HAVCR2,missense_variant,p.Gly184Val,ENST00000522593,;HAVCR2,downstream_gene_variant,,ENST00000524219,;HAVCR2,downstream_gene_variant,,ENST00000521665,; A ENST00000307851 Transcript missense_variant 1366/2907 635/906 212/301 G/V gGg/gTg 1 -1 HAVCR2 HGNC HGNC:18437 protein_coding YES CCDS4333.1 ENSP00000312002 Q8TDQ0 UPI000011AAFA NM_032782.4 tolerated(0.16) 5/7 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 157095347 157095347 C A 1 0 0 0 0 1 0 0 0 6860 623 22 2 2 HAVCR2 5 157095347 Missense_Mutation SNP C C3L-00095_T 2078183 157095347 24442912 269 3478 GABRA6 0 . GRCh38 5 161686008 161686008 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.19T>A p.Trp7Arg p.W7R ENST00000274545 1/9 301 279 22 412 412 0 strelka-varscan-mutect GABRA6,missense_variant,p.Trp7Arg,ENST00000523217,;GABRA6,missense_variant,p.Trp7Arg,ENST00000274545,NM_000811.2;GABRA6,upstream_gene_variant,,ENST00000520000,;GABRA6,upstream_gene_variant,,ENST00000523691,;GABRA6,upstream_gene_variant,,ENST00000517823,;RP11-348M17.2,downstream_gene_variant,,ENST00000521984,;GABRA6,intron_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,upstream_gene_variant,,ENST00000521520,;GABRA6,upstream_gene_variant,,ENST00000524220,; A ENST00000274545 Transcript missense_variant 452/2128 19/1362 7/453 W/R Tgg/Agg 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 deleterious_low_confidence(0.03) 1/9 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,Prints_domain:PR01619 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 161686008 161686008 T A 1 0 0 0 0 1 0 0 0 6036 1580 55 4 4 GABRA6 5 161686008 Missense_Mutation SNP T C3L-00095_T 4590661 161686008 19852251 270 3479 TENM2 0 . GRCh38 5 168124947 168124947 + Silent SNP G G A rs752804454 C3L-00095_T C3L-00095_N G G c.2106G>A p.= p.A702A ENST00000518659 11/29 194 178 16 295 294 1 strelka-varscan-mutect TENM2,synonymous_variant,p.=,ENST00000519204,;TENM2,synonymous_variant,p.=,ENST00000518659,NM_001122679.1;TENM2,synonymous_variant,p.=,ENST00000520394,;CTB-178M22.1,intron_variant,,ENST00000517408,;CTB-105N12.2,upstream_gene_variant,,ENST00000624423,; A ENST00000518659 Transcript synonymous_variant 2145/8550 2106/8325 702/2774 A gcG/gcA rs752804454,COSM1065510,COSM1065511,COSM1154427 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 11/29 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 0,1,1,1 LOW SNV 5 0,1,1,1 1 PASS rs752804454 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 168124947 168124947 G A 1 0 0 0 0 0 0 0 1 16172 1045 37 1 1 TENM2 5 168124947 Silent SNP G C3L-00095_T 6438939 168124947 13413312 271 3480 DOCK2 0 . GRCh38 5 169708233 169708233 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.1448A>G p.Gln483Arg p.Q483R ENST00000256935 15/52 223 209 14 273 273 0 strelka-varscan-mutect DOCK2,missense_variant,p.Gln483Arg,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Lys10Glu,ENST00000520908,;DOCK2,intron_variant,,ENST00000540750,;DOCK2,missense_variant,p.Gln483Arg,ENST00000524185,; G ENST00000256935 Transcript missense_variant 1528/6097 1448/5493 483/1830 Q/R cAa/cGa 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0.01) 15/52 PROSITE_profiles:PS51650,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF14429 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 169708233 169708233 A G 1 0 0 0 0 1 0 0 0 4502 131 5 5 5 DOCK2 5 169708233 Missense_Mutation SNP A C3L-00095_T 1583286 169708233 11830026 272 3481 LMAN2 0 . GRCh38 5 177337376 177337376 + Missense_Mutation SNP C C A rs761995183 C3L-00095_T C3L-00095_N C C c.662G>T p.Arg221Leu p.R221L ENST00000303127 5/8 184 161 23 264 263 1 strelka-varscan-mutect LMAN2,missense_variant,p.Arg221Leu,ENST00000303127,NM_006816.2;LMAN2,missense_variant,p.Arg221Leu,ENST00000515209,;LMAN2,missense_variant,p.Arg214Leu,ENST00000502560,;LMAN2,missense_variant,p.Arg150Leu,ENST00000513877,;LMAN2,intron_variant,,ENST00000514458,;LMAN2,downstream_gene_variant,,ENST00000506310,;LMAN2,non_coding_transcript_exon_variant,,ENST00000502721,;LMAN2,upstream_gene_variant,,ENST00000504071,; A ENST00000303127 Transcript missense_variant 867/1800 662/1071 221/356 R/L cGg/cTg rs761995183,COSM302563 1 -1 LMAN2 HGNC HGNC:16986 protein_coding YES CCDS4417.1 ENSP00000303366 Q12907 UPI0000037B35 NM_006816.2 tolerated(0.05) 5/8 Gene3D:2.60.120.200,Pfam_domain:PF03388,PROSITE_profiles:PS51328,hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF22,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761995183 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 177337376 177337376 C A 1 0 0 0 0 1 0 0 0 8762 652 23 1 1 LMAN2 5 177337376 Missense_Mutation SNP C C3L-00095_T 7629143 177337376 4200883 273 3482 GRK6 0 . GRCh38 5 177432780 177432780 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.414C>A p.Cys138Ter p.C138* ENST00000528793 5/16 121 113 8 144 144 0 strelka-varscan-mutect GRK6,stop_gained,p.Cys138Ter,ENST00000355472,NM_001004106.2;GRK6,stop_gained,p.Cys138Ter,ENST00000393576,;GRK6,stop_gained,p.Cys138Ter,ENST00000528793,NM_002082.3;GRK6,stop_gained,p.Cys138Ter,ENST00000355958,NM_001004105.2;GRK6,stop_gained,p.Cys138Ter,ENST00000507633,;GRK6,stop_gained,p.Cys106Ter,ENST00000506296,;GRK6,stop_gained,p.Cys106Ter,ENST00000511244,;GRK6,downstream_gene_variant,,ENST00000502598,;GRK6,downstream_gene_variant,,ENST00000512684,;GRK6,non_coding_transcript_exon_variant,,ENST00000515666,;GRK6,intron_variant,,ENST00000508705,; A ENST00000528793 Transcript stop_gained 417/2571 414/1770 138/589 C/* tgC/tgA 1 1 GRK6 HGNC HGNC:4545 protein_coding YES CCDS47348.1 ENSP00000433511 P43250 UPI000002AAC9 NM_002082.3 5/16 Pfam_domain:PF00615,PROSITE_profiles:PS50132,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF15,SMART_domains:SM00315,Superfamily_domains:SSF48097 HIGH 1 SNV 1 1 PASS rs1464617742 . 0 203 6 0 0 0 0 0 -15.50198 0.9999996 1 1 1 0 A 4 1 10 177432780 177432780 C A 1 0 0 0 0 0 1 0 0 6676 718 25 2 2 GRK6 5 177432780 Nonsense_Mutation SNP C C3L-00095_T 95404 177432780 4105479 274 3483 11 2 GRK6 0 . GRCh38 5 177432784 177432784 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.418G>T p.Asp140Tyr p.D140Y ENST00000528793 5/16 119 111 8 140 140 0 strelka-varscan-mutect GRK6,missense_variant,p.Asp140Tyr,ENST00000355472,NM_001004106.2;GRK6,missense_variant,p.Asp140Tyr,ENST00000393576,;GRK6,missense_variant,p.Asp140Tyr,ENST00000528793,NM_002082.3;GRK6,missense_variant,p.Asp140Tyr,ENST00000355958,NM_001004105.2;GRK6,missense_variant,p.Asp140Tyr,ENST00000507633,;GRK6,missense_variant,p.Asp108Tyr,ENST00000506296,;GRK6,missense_variant,p.Asp108Tyr,ENST00000511244,;GRK6,downstream_gene_variant,,ENST00000502598,;GRK6,downstream_gene_variant,,ENST00000512684,;GRK6,non_coding_transcript_exon_variant,,ENST00000515666,;GRK6,intron_variant,,ENST00000508705,; T ENST00000528793 Transcript missense_variant 421/2571 418/1770 140/589 D/Y Gac/Tac 1 1 GRK6 HGNC HGNC:4545 protein_coding YES CCDS47348.1 ENSP00000433511 P43250 UPI000002AAC9 NM_002082.3 deleterious(0.02) 5/16 Pfam_domain:PF00615,PROSITE_profiles:PS50132,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF15,SMART_domains:SM00315,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -15.86906 1 1 1 1 0 T 3 4 10 177432784 177432784 G T 1 0 0 0 0 1 0 0 0 6676 942 33 2 2 GRK6 5 177432784 Missense_Mutation SNP G C3L-00095_T 4 177432784 4105475 275 3484 11 2 TBC1D9B 0 . GRCh38 5 179899283 179899283 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.254A>T p.Lys85Ile p.K85I ENST00000356834 3/22 215 195 20 265 265 0 strelka-varscan-mutect TBC1D9B,missense_variant,p.Lys85Ile,ENST00000356834,NM_198868.2;TBC1D9B,missense_variant,p.Lys85Ile,ENST00000355235,NM_015043.3;TBC1D9B,intron_variant,,ENST00000630103,;TBC1D9B,upstream_gene_variant,,ENST00000517782,;TBC1D9B,intron_variant,,ENST00000522224,; A ENST00000356834 Transcript missense_variant 292/5173 254/3753 85/1250 K/I aAa/aTa 1 -1 TBC1D9B HGNC HGNC:29097 protein_coding YES CCDS43408.1 ENSP00000349291 Q66K14 UPI000034ECFF NM_198868.2 deleterious(0.03) 3/22 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF225 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 179899283 179899283 T A 1 0 0 0 0 1 0 0 0 16033 1841 64 4 4 TBC1D9B 5 179899283 Missense_Mutation SNP T C3L-00095_T 2466499 179899283 1638976 276 3485 DEK 0 . GRCh38 6 18255772 18255772 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.532A>G p.Arg178Gly p.R178G ENST00000397239 6/11 99 93 6 82 82 0 strelka-mutect DEK,missense_variant,p.Arg178Gly,ENST00000397239,NM_003472.3;DEK,missense_variant,p.Arg144Gly,ENST00000244776,NM_001134709.1;DEK,missense_variant,p.Arg111Gly,ENST00000503715,;DEK,downstream_gene_variant,,ENST00000515742,;DEK,missense_variant,p.Arg150Gly,ENST00000505224,;DEK,missense_variant,p.Arg54Gly,ENST00000515770,;DEK,non_coding_transcript_exon_variant,,ENST00000512145,; C ENST00000397239 Transcript missense_variant 980/3427 532/1128 178/375 R/G Agg/Ggg 1 -1 DEK HGNC HGNC:2768 protein_coding YES CCDS34344.1 ENSP00000380414 P35659 UPI0000001C2C NM_003472.3 deleterious(0) 6/11 hmmpanther:PTHR13468,SMART_domains:SM00513 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 18255772 18255772 T C 1 0 0 0 0 1 0 0 0 4229 1550 54 5 5 DEK 6 18255772 Missense_Mutation SNP T C3L-00095_T 18255772 152550207 277 3486 LRRC16A 0 . GRCh38 6 25604881 25604881 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.3622G>T p.Gly1208Ter p.G1208* ENST00000329474 34/37 215 202 13 249 248 1 strelka-varscan LRRC16A,stop_gained,p.Gly1208Ter,ENST00000329474,NM_001173977.1,NM_017640.5;LRRC16A,stop_gained,p.Gly808Ter,ENST00000635618,; T ENST00000329474 Transcript stop_gained 3990/5431 3622/4116 1208/1371 G/* Gga/Tga 1 1 LRRC16A HGNC HGNC:21581 protein_coding YES CCDS54973.1 ENSP00000331983 Q5VZK9 UPI00004588AB NM_001173977.1,NM_017640.5 34/37 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 25604881 25604881 G T 1 0 0 0 0 0 1 0 0 8867 1349 47 2 2 LRRC16A 6 25604881 Nonsense_Mutation SNP G C3L-00095_T 7349109 25604881 145201098 278 3487 POM121L2 0 . GRCh38 6 27311928 27311928 + Missense_Mutation SNP C C A rs558295499 C3L-00095_T C3L-00095_N C C c.243G>T p.Met81Ile p.M81I ENST00000444565 1/1 115 109 6 152 152 0 strelka-varscan POM121L2,missense_variant,p.Met81Ile,ENST00000444565,NM_033482.3;POM121L2,upstream_gene_variant,,ENST00000429945,; A ENST00000444565 Transcript missense_variant 243/3108 243/3108 81/1035 M/I atG/atT rs558295499 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 tolerated(0.52) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 27311928 27311928 C A 1 0 0 0 0 1 0 0 0 12353 826 29 2 2 POM121L2 6 27311928 Missense_Mutation SNP C C3L-00095_T 1707047 27311928 143494051 279 3488 OR2B2 0 . GRCh38 6 27912104 27912104 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.216C>A p.Cys72Ter p.C72* ENST00000303324 1/1 94 87 7 100 98 2 strelka-varscan OR2B2,stop_gained,p.Cys72Ter,ENST00000303324,NM_033057.2; T ENST00000303324 Transcript stop_gained 293/1212 216/1074 72/357 C/* tgC/tgA 1 -1 OR2B2 HGNC HGNC:13966 protein_coding YES CCDS4641.1 ENSP00000304419 Q9GZK3 A0A126GWD0 UPI000004187A NM_033057.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF254,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 27912104 27912104 G T 1 0 0 0 0 0 1 0 0 11068 963 34 2 2 OR2B2 6 27912104 Nonsense_Mutation SNP G C3L-00095_T 600176 27912104 142893875 280 3489 OR2J3 0 . GRCh38 6 29112403 29112403 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.513G>T p.= p.L171L ENST00000377169 1/1 256 224 32 314 313 1 strelka-varscan OR2J3,synonymous_variant,p.=,ENST00000377169,NM_001005216.3; T ENST00000377169 Transcript synonymous_variant 513/936 513/936 171/311 L ctG/ctT 1 1 OR2J3 HGNC HGNC:8261 protein_coding YES CCDS43433.1 ENSP00000366374 O76001 A0A126GWT2 UPI000014073A NM_001005216.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF209,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 29112403 29112403 G T 1 0 0 0 0 0 0 0 1 11082 1364 48 2 2 OR2J3 6 29112403 Silent SNP G C3L-00095_T 1200299 29112403 141693576 281 3490 OR2J2 0 . GRCh38 6 29174443 29174443 + Missense_Mutation SNP G G T rs761974714 C3L-00095_T C3L-00095_N G G c.808G>T p.Asp270Tyr p.D270Y ENST00000377167 1/1 214 189 25 204 203 1 strelka-varscan OR2J2,missense_variant,p.Asp270Tyr,ENST00000377167,NM_030905.2; T ENST00000377167 Transcript missense_variant 1141/1272 808/939 270/312 D/Y Gat/Tat rs761974714 1 1 OR2J2 HGNC HGNC:8260 protein_coding YES CCDS43434.1 ENSP00000366372 O76002 A0A126GWS4 UPI000004B9D1 NM_030905.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF184,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 29174443 29174443 G T 1 0 0 0 0 1 0 0 0 11081 1290 45 2 2 OR2J2 6 29174443 Missense_Mutation SNP G C3L-00095_T 62040 29174443 141631536 282 3491 MDC1 0 . GRCh38 6 30705436 30705436 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3747G>T p.Glu1249Asp p.E1249D ENST00000376406 10/15 74 70 4 137 137 0 varscan-mutect MDC1,missense_variant,p.Glu1249Asp,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; A ENST00000376406 Transcript missense_variant 4395/7576 3747/6270 1249/2089 E/D gaG/gaT 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 deleterious(0.04) 10/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 30705436 30705436 C A 1 0 0 0 0 1 0 0 0 9341 796 28 2 2 MDC1 6 30705436 Missense_Mutation SNP C C3L-00095_T 1530993 30705436 140100543 283 3492 C2 0 . GRCh38 6 31943657 31943657 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1122C>A p.= p.S374S ENST00000456570 10/30 350 320 30 437 437 0 strelka-varscan-mutect XXbac-BPG116M5.17,synonymous_variant,p.=,ENST00000456570,;XXbac-BPG116M5.17,synonymous_variant,p.=,ENST00000477310,;C2,synonymous_variant,p.=,ENST00000299367,NM_001282458.1,NM_000063.5;C2,synonymous_variant,p.=,ENST00000442278,NM_001145903.2;C2,synonymous_variant,p.=,ENST00000452323,NM_001178063.2;C2,synonymous_variant,p.=,ENST00000469372,NM_001282457.1;C2,synonymous_variant,p.=,ENST00000383177,;C2,synonymous_variant,p.=,ENST00000497706,;CFB,upstream_gene_variant,,ENST00000425368,NM_001710.5;CFB,upstream_gene_variant,,ENST00000475617,;C2-AS1,upstream_gene_variant,,ENST00000630806,;CFB,upstream_gene_variant,,ENST00000497841,;C2,upstream_gene_variant,,ENST00000468407,;C2,3_prime_UTR_variant,,ENST00000482060,;C2,3_prime_UTR_variant,,ENST00000485690,;C2,non_coding_transcript_exon_variant,,ENST00000486124,;CFB,upstream_gene_variant,,ENST00000452035,;CFB,upstream_gene_variant,,ENST00000461483,;CFB,upstream_gene_variant,,ENST00000472581,;CFB,upstream_gene_variant,,ENST00000460718,;CFB,upstream_gene_variant,,ENST00000465750,;CFB,upstream_gene_variant,,ENST00000482886,; A ENST00000456570 Transcript synonymous_variant 1177/3874 1122/3801 374/1266 S tcC/tcA 1 1 XXbac-BPG116M5.17 Clone_based_vega_gene protein_coding YES ENSP00000410815 B4E1Z4 UPI00017A8869 10/30 PROSITE_profiles:PS50240,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 31943657 31943657 C A 1 0 0 0 0 0 0 0 1 2001 610 22 2 2 C2 6 31943657 Silent SNP C C3L-00095_T 1238221 31943657 138862322 284 3493 EGFL8 0 . GRCh38 6 32167355 32167355 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.607G>A p.Glu203Lys p.E203K ENST00000395512 7/9 228 210 18 281 281 0 strelka-varscan-mutect EGFL8,missense_variant,p.Glu203Lys,ENST00000395512,;EGFL8,missense_variant,p.Glu203Lys,ENST00000333845,NM_030652.3;EGFL8,missense_variant,p.Glu183Lys,ENST00000432129,;AGPAT1,downstream_gene_variant,,ENST00000395499,;AGPAT1,downstream_gene_variant,,ENST00000375107,NM_006411.3;AGPAT1,downstream_gene_variant,,ENST00000395497,;PPT2,downstream_gene_variant,,ENST00000395523,;AGPAT1,downstream_gene_variant,,ENST00000395496,;PPT2,downstream_gene_variant,,ENST00000324816,NM_001204103.1,NM_005155.6;AGPAT1,downstream_gene_variant,,ENST00000336984,NM_032741.4;AGPAT1,downstream_gene_variant,,ENST00000375104,;PPT2,downstream_gene_variant,,ENST00000375137,;PPT2,downstream_gene_variant,,ENST00000361568,NM_138717.2;PPT2,downstream_gene_variant,,ENST00000375143,;AGPAT1,downstream_gene_variant,,ENST00000617181,;AGPAT1,downstream_gene_variant,,ENST00000490711,;PPT2-EGFL8,downstream_gene_variant,,ENST00000453656,;PPT2,downstream_gene_variant,,ENST00000493548,;AGPAT1,downstream_gene_variant,,ENST00000476663,;EGFL8,upstream_gene_variant,,ENST00000489721,;PPT2-EGFL8,3_prime_UTR_variant,,ENST00000422437,;PPT2-EGFL8,3_prime_UTR_variant,,ENST00000428388,;EGFL8,non_coding_transcript_exon_variant,,ENST00000466239,;PPT2-EGFL8,downstream_gene_variant,,ENST00000583227,;PPT2-EGFL8,downstream_gene_variant,,ENST00000585246,;PPT2-EGFL8,downstream_gene_variant,,ENST00000421600,;PPT2-EGFL8,downstream_gene_variant,,ENST00000479001,;EGFL8,downstream_gene_variant,,ENST00000482938,; A ENST00000395512 Transcript missense_variant 712/1312 607/882 203/293 E/K Gag/Aag 1 1 EGFL8 HGNC HGNC:13944 protein_coding YES CCDS4743.1 ENSP00000378888 Q99944 UPI000006FB40 tolerated(0.11) 7/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14949:SF27,hmmpanther:PTHR14949 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 32167355 32167355 G A 1 0 0 0 0 1 0 0 0 4801 1188 41 3 3 EGFL8 6 32167355 Missense_Mutation SNP G C3L-00095_T 223698 32167355 138638624 285 3494 DAXX 0 . GRCh38 6 33321916 33321916 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.10G>T p.Ala4Ser p.A4S ENST00000374542 2/8 107 98 9 162 162 0 strelka-varscan-mutect DAXX,missense_variant,p.Ala4Ser,ENST00000374542,NM_001141969.1,NM_001141970.1,NM_001350.4;DAXX,missense_variant,p.Ala4Ser,ENST00000266000,;DAXX,missense_variant,p.Ala4Ser,ENST00000620164,;DAXX,missense_variant,p.Ala4Ser,ENST00000453407,;DAXX,missense_variant,p.Ala4Ser,ENST00000446403,;DAXX,missense_variant,p.Ala4Ser,ENST00000446511,;DAXX,intron_variant,,ENST00000414083,NM_001254717.1;ZBTB22,upstream_gene_variant,,ENST00000431845,NM_005453.4;ZBTB22,upstream_gene_variant,,ENST00000418724,NM_001145338.1;ZBTB22,upstream_gene_variant,,ENST00000441117,;DAXX,intron_variant,,ENST00000468536,;DAXX,intron_variant,,ENST00000477370,;DAXX,upstream_gene_variant,,ENST00000477162,;DAXX,downstream_gene_variant,,ENST00000494082,;DAXX,non_coding_transcript_exon_variant,,ENST00000498030,;DAXX,upstream_gene_variant,,ENST00000490173,; A ENST00000374542 Transcript missense_variant 215/2613 10/2223 4/740 A/S Gct/Tct COSM3349831 1 -1 DAXX HGNC HGNC:2681 protein_coding YES CCDS4776.1 ENSP00000363668 Q9UER7 A0A024RCS3 UPI0000128ED8 NM_001141969.1,NM_001141970.1,NM_001350.4 tolerated(0.11) 2/8 hmmpanther:PTHR12766 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 33321916 33321916 C A 1 0 0 0 0 1 0 0 0 4044 768 27 1 1 DAXX 6 33321916 Missense_Mutation SNP C C3L-00095_T 1154561 33321916 137484063 286 3495 CMTR1 0 . GRCh38 6 37458668 37458668 + Silent SNP A A T rs771664404 C3L-00095_T C3L-00095_N A A c.834A>T p.= p.A278A ENST00000373451 9/24 374 351 23 458 458 0 strelka-varscan-mutect CMTR1,synonymous_variant,p.=,ENST00000373451,NM_015050.2;CMTR1,synonymous_variant,p.=,ENST00000455891,;CMTR1,upstream_gene_variant,,ENST00000493656,; T ENST00000373451 Transcript synonymous_variant 998/4033 834/2508 278/835 A gcA/gcT rs771664404 1 1 CMTR1 HGNC HGNC:21077 protein_coding YES CCDS4835.1 ENSP00000362550 Q8N1G2 UPI00000700C2 NM_015050.2 9/24 PROSITE_profiles:PS51613,hmmpanther:PTHR16121:SF0,hmmpanther:PTHR16121,Gene3D:3.40.50.150,Pfam_domain:PF01728,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS rs771664404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 37458668 37458668 A T 1 0 0 0 0 0 0 0 1 3366 175 7 4 4 CMTR1 6 37458668 Silent SNP A C3L-00095_T 4136752 37458668 133347311 287 3496 UBR2 0 . GRCh38 6 42658115 42658115 + Missense_Mutation SNP G G C rs765852315 C3L-00095_T C3L-00095_N G G c.2964G>C p.Met988Ile p.M988I ENST00000372899 27/47 162 152 10 153 153 0 strelka-varscan-mutect UBR2,missense_variant,p.Met988Ile,ENST00000372899,NM_015255.2;UBR2,missense_variant,p.Met988Ile,ENST00000372901,; C ENST00000372899 Transcript missense_variant 3222/7857 2964/5268 988/1755 M/I atG/atC rs765852315 1 1 UBR2 HGNC HGNC:21289 protein_coding YES CCDS4870.1 ENSP00000361990 Q8IWV8 UPI0000074466 NM_015255.2 deleterious(0.02) 27/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF28 MODERATE 1 SNV 1 1 PASS rs765852315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 42658115 42658115 G C 1 0 0 0 0 1 0 0 0 17426 1290 45 4 4 UBR2 6 42658115 Missense_Mutation SNP G C3L-00095_T 5199447 42658115 128147864 288 3497 PTK7 0 . GRCh38 6 43158827 43158827 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2756G>T p.Cys919Phe p.C919F ENST00000481273 18/20 136 127 9 170 170 0 varscan-mutect PTK7,missense_variant,p.Cys911Phe,ENST00000230419,NM_002821.4;PTK7,missense_variant,p.Cys871Phe,ENST00000345201,NM_152880.3;PTK7,missense_variant,p.Cys855Phe,ENST00000352931,NM_152882.3;PTK7,missense_variant,p.Cys781Phe,ENST00000349241,NM_152881.3;PTK7,missense_variant,p.Cys919Phe,ENST00000481273,NM_001270398.1;PTK7,missense_variant,p.Cys206Phe,ENST00000489707,;PTK7,missense_variant,p.Cys179Phe,ENST00000473339,;PTK7,3_prime_UTR_variant,,ENST00000470019,;PTK7,3_prime_UTR_variant,,ENST00000230418,;PTK7,3_prime_UTR_variant,,ENST00000461389,;PTK7,non_coding_transcript_exon_variant,,ENST00000487673,; T ENST00000481273 Transcript missense_variant 2826/3436 2756/3237 919/1078 C/F tGc/tTc 1 1 PTK7 HGNC HGNC:9618 protein_coding YES CCDS59021.1 ENSP00000418754 Q13308 UPI0001B79423 NM_001270398.1 deleterious(0) 18/20 PROSITE_profiles:PS50011,hmmpanther:PTHR26391,hmmpanther:PTHR26391:SF15,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 43158827 43158827 G T 1 0 0 0 0 1 0 0 0 12921 1319 46 2 2 PTK7 6 43158827 Missense_Mutation SNP G C3L-00095_T 500712 43158827 127647152 289 3498 CRISP1 0 . GRCh38 6 49838464 49838464 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.595C>A p.Pro199Thr p.P199T ENST00000335847 7/8 167 142 25 156 156 0 strelka-varscan CRISP1,missense_variant,p.Pro199Thr,ENST00000335847,NM_001131.2;CRISP1,missense_variant,p.Pro199Thr,ENST00000505118,NM_001205220.1;CRISP1,intron_variant,,ENST00000507853,NM_170609.1;CRISP1,intron_variant,,ENST00000329411,; T ENST00000335847 Transcript missense_variant 697/1911 595/750 199/249 P/T Cca/Aca 1 -1 CRISP1 HGNC HGNC:304 protein_coding YES CCDS4931.1 ENSP00000338276 P54107 A0A0K0K1I1 UPI0000128482 NM_001131.2 deleterious(0) 7/8 hmmpanther:PTHR10334:SF213,hmmpanther:PTHR10334,Gene3D:3.40.33.10,Pfam_domain:PF08562,Superfamily_domains:SSF57546 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 49838464 49838464 G T 1 0 0 0 0 1 0 0 0 3680 1232 43 2 2 CRISP1 6 49838464 Missense_Mutation SNP G C3L-00095_T 6679637 49838464 120967515 290 3499 TFAP2B 0 . GRCh38 6 50823829 50823829 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.504delG p.His169ThrfsTer22 p.H169Tfs*22 ENST00000393655 2/7 219 192 27 323 323 0 sindel-varindel TFAP2B,frameshift_variant,p.His169ThrfsTer22,ENST00000393655,NM_003221.3;TFAP2B,frameshift_variant,p.His167ThrfsTer22,ENST00000344788,;TFAP2B,non_coding_transcript_exon_variant,,ENST00000489228,; - ENST00000393655 Transcript frameshift_variant 673/5773 504/1383 168/460 L/X ctG/ct 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 2/7 Prints_domain:PR01750,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 2 0 0 0 -11.77887 0.9955232 1 1 1 0 - 7 5 10 50823829 50823829 G - 1 0 1 0 1 0 0 0 0 16221 1306 46 0 0 TFAP2B 6 50823829 Frame_Shift_Del DEL G C3L-00095_T 985365 50823829 119982150 291 3500 ADGRB3 0 . GRCh38 6 68639386 68639386 + Silent SNP C C A rs267601101 C3L-00095_T C3L-00095_N C C c.711C>A p.= p.T237T ENST00000370598 3/32 85 77 8 88 88 0 strelka-varscan ADGRB3,synonymous_variant,p.=,ENST00000370598,NM_001704.2;ADGRB3,synonymous_variant,p.=,ENST00000546190,;RP3-525N10.2,upstream_gene_variant,,ENST00000604392,;RP3-525N10.2,upstream_gene_variant,,ENST00000603261,; A ENST00000370598 Transcript synonymous_variant 1532/6010 711/4569 237/1522 T acC/acA rs267601101,COSM22122 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 3/32 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 201 9 0 0 0 0 0 -16.73522 0.9999834 1 1 1 0 A 2 1 10 68639386 68639386 C A 1 0 0 0 0 0 0 0 1 357 610 22 2 2 ADGRB3 6 68639386 Silent SNP C C3L-00095_T 17815557 68639386 102166593 292 3501 COL12A1 0 . GRCh38 6 75121443 75121443 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.6947-2A>T p.X2316_splice ENST00000322507 71 67 4 84 84 0 strelka-varscan COL12A1,splice_acceptor_variant,,ENST00000322507,NM_004370.5;COL12A1,splice_acceptor_variant,,ENST00000615798,;COL12A1,splice_acceptor_variant,,ENST00000483888,;COL12A1,splice_acceptor_variant,,ENST00000416123,;COL12A1,splice_acceptor_variant,,ENST00000345356,NM_080645.2;COL12A1,upstream_gene_variant,,ENST00000425443,;COL12A1,upstream_gene_variant,,ENST00000493109,; A ENST00000322507 Transcript splice_acceptor_variant -/11723 6947/9192 2316/3063 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 43/65 HIGH 1 SNV 1 1 PASS . . 0 177 28 5 0 0 0 0 -7.155344 0.4712604 0 1 0 0 A 5 1 10 75121443 75121443 T A 1 0 0 0 0 0 0 1 0 3457 1594 55 4 4 COL12A1 6 75121443 Splice_Site SNP T C3L-00095_T 6482057 75121443 95684536 293 3502 ME1 0 . GRCh38 6 83239608 83239608 + Silent SNP G G T C3L-00095_T C3L-00095_N G G c.843C>A p.= p.L281L ENST00000369705 8/14 164 145 19 201 201 0 strelka-varscan ME1,synonymous_variant,p.=,ENST00000369705,NM_002395.5; T ENST00000369705 Transcript synonymous_variant 960/3371 843/1719 281/572 L ctC/ctA COSM4510638 1 -1 ME1 HGNC HGNC:6983 protein_coding YES CCDS34492.1 ENSP00000358719 P48163 UPI000000127E NM_002395.5 8/14 Gene3D:3.40.50.720,Pfam_domain:PF03949,PIRSF_domain:PIRSF000106,Prints_domain:PR00072,PROSITE_patterns:PS00331,hmmpanther:PTHR23406,hmmpanther:PTHR23406:SF17,Low_complexity_(Seg):seg,SMART_domains:SM00919,Superfamily_domains:SSF51735 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 83239608 83239608 G T 1 0 0 0 0 0 0 0 1 9356 1161 41 2 2 ME1 6 83239608 Silent SNP G C3L-00095_T 8118165 83239608 87566371 294 3503 TBX18 0 . GRCh38 6 84760279 84760279 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.575T>A p.Val192Glu p.V192E ENST00000369663 3/8 155 138 17 155 155 0 strelka-varscan TBX18,missense_variant,p.Val192Glu,ENST00000369663,NM_001080508.2;TBX18,missense_variant,p.Val34Glu,ENST00000606784,;TBX18,missense_variant,p.Val34Glu,ENST00000606325,;TBX18,downstream_gene_variant,,ENST00000606621,;TBX18,non_coding_transcript_exon_variant,,ENST00000606521,; T ENST00000369663 Transcript missense_variant 913/6245 575/1824 192/607 V/E gTa/gAa 1 -1 TBX18 HGNC HGNC:11595 protein_coding YES CCDS34495.1 ENSP00000358677 O95935 UPI00001A3A8A NM_001080508.2 deleterious(0.02) 3/8 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF20,Pfam_domain:PF00907,Gene3D:1h6fA00,SMART_domains:SM00425,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999963 1 1 1 0 T 3 4 10 84760279 84760279 A T 1 0 0 0 0 1 0 0 0 16058 391 14 4 4 TBX18 6 84760279 Missense_Mutation SNP A C3L-00095_T 1520671 84760279 86045700 295 3504 SOBP 0 . GRCh38 6 107635400 107635400 + Silent SNP C C A rs768485665 C3L-00095_T C3L-00095_N C C c.2556C>A p.= p.A852A ENST00000317357 6/7 317 297 20 412 411 1 strelka-varscan-mutect SOBP,synonymous_variant,p.=,ENST00000317357,NM_018013.3;SOBP,non_coding_transcript_exon_variant,,ENST00000494935,; A ENST00000317357 Transcript synonymous_variant 3215/5245 2556/2622 852/873 A gcC/gcA rs768485665 1 1 SOBP HGNC HGNC:29256 protein_coding YES CCDS43488.1 ENSP00000318900 A7XYQ1 UPI0000E6A8ED NM_018013.3 6/7 hmmpanther:PTHR23186:SF2,hmmpanther:PTHR23186 LOW 1 SNV 5 1 PASS rs768485665 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 107635400 107635400 C A 1 0 0 0 0 0 0 0 1 15233 639 23 1 1 SOBP 6 107635400 Silent SNP C C3L-00095_T 22875121 107635400 63170579 296 3505 FOXO3 0 . GRCh38 6 108663969 108663969 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.1136A>G p.Asn379Ser p.N379S ENST00000406360 2/3 132 124 8 224 223 1 varscan-mutect FOXO3,missense_variant,p.Asn379Ser,ENST00000406360,NM_001455.3;FOXO3,missense_variant,p.Asn379Ser,ENST00000343882,NM_201559.2;FOXO3,missense_variant,p.Asn159Ser,ENST00000540898,; G ENST00000406360 Transcript missense_variant 1479/7341 1136/2022 379/673 N/S aAt/aGt 1 1 FOXO3 HGNC HGNC:3821 protein_coding YES CCDS5068.1 ENSP00000385824 O43524 UPI000012ADEA NM_001455.3 deleterious(0.04) 2/3 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF97 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 108663969 108663969 A G 1 0 0 0 0 1 0 0 0 5888 101 4 5 5 FOXO3 6 108663969 Missense_Mutation SNP A C3L-00095_T 1028569 108663969 62142010 297 3506 FIG4 0 . GRCh38 6 109825212 109825212 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2671G>T p.Gly891Ter p.G891* ENST00000230124 23/23 260 239 21 270 269 1 strelka-varscan-mutect FIG4,stop_gained,p.Gly891Ter,ENST00000230124,NM_014845.5;RP1-249I4.2,upstream_gene_variant,,ENST00000458693,; T ENST00000230124 Transcript stop_gained 2795/3011 2671/2724 891/907 G/* Gga/Tga 1 1 FIG4 HGNC HGNC:16873 protein_coding YES CCDS5078.1 ENSP00000230124 Q92562 UPI000000D9A3 NM_014845.5 23/23 hmmpanther:PTHR11200:SF9,hmmpanther:PTHR11200 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 109825212 109825212 G T 1 0 0 0 0 0 1 0 0 5753 1001 35 2 2 FIG4 6 109825212 Nonsense_Mutation SNP G C3L-00095_T 1161243 109825212 60980767 298 3507 SLC22A16 0 . GRCh38 6 110442701 110442701 + Silent SNP C C A rs544491266 C3L-00095_T C3L-00095_N C C c.726G>T p.= p.A242A ENST00000368919 4/8 227 214 13 268 268 0 strelka-varscan SLC22A16,synonymous_variant,p.=,ENST00000330550,;SLC22A16,synonymous_variant,p.=,ENST00000368919,NM_033125.3;SLC22A16,synonymous_variant,p.=,ENST00000451557,;SLC22A16,synonymous_variant,p.=,ENST00000437378,;SLC22A16,synonymous_variant,p.=,ENST00000434949,;SLC22A16,downstream_gene_variant,,ENST00000424139,;RN7SL617P,upstream_gene_variant,,ENST00000485298,; A ENST00000368919 Transcript synonymous_variant 793/1987 726/1734 242/577 A gcG/gcT rs544491266 1 -1 SLC22A16 HGNC HGNC:20302 protein_coding YES CCDS5084.1 ENSP00000357915 Q86VW1 A0A0K0K1K9 UPI000000DC13 NM_033125.3 4/8 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF186,Gene3D:1.20.1250.20,Pfam_domain:PF00083,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 110442701 110442701 C A 1 0 0 0 0 0 0 0 1 14713 523 19 1 1 SLC22A16 6 110442701 Silent SNP C C3L-00095_T 617489 110442701 60363278 299 3508 DSE 0 . GRCh38 6 116433436 116433436 + Missense_Mutation SNP G G A rs371480627 C3L-00095_T C3L-00095_N G G c.1004G>A p.Arg335His p.R335H ENST00000452085 5/6 317 296 21 332 332 0 strelka-varscan-mutect DSE,missense_variant,p.Arg335His,ENST00000452085,NM_001080976.1;DSE,missense_variant,p.Arg335His,ENST00000331677,;DSE,missense_variant,p.Arg335His,ENST00000359564,NM_013352.2;DSE,non_coding_transcript_exon_variant,,ENST00000606712,; A ENST00000452085 Transcript missense_variant 1198/10586 1004/2877 335/958 R/H cGt/cAt rs371480627 1 1 DSE HGNC HGNC:21144 protein_coding YES CCDS5107.1 ENSP00000404049 Q9UL01 UPI0000073CB8 NM_001080976.1 deleterious(0.01) 5/6 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF3 MODERATE 1 SNV 1 1 PASS rs371480627 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 116433436 116433436 G A 1 0 0 0 0 1 0 0 0 4595 1145 40 1 1 DSE 6 116433436 Missense_Mutation SNP G C3L-00095_T 5990735 116433436 54372543 300 3509 GPRC6A 0 . GRCh38 6 116807187 116807187 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.518C>A p.Ala173Glu p.A173E ENST00000310357 3/6 73 67 6 90 90 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Ala173Glu,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Ala173Glu,ENST00000368549,NM_001286355.1;GPRC6A,missense_variant,p.Ala173Glu,ENST00000530250,NM_001286354.1; T ENST00000310357 Transcript missense_variant 540/2860 518/2781 173/926 A/E gCa/gAa 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 deleterious(0.01) 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -13.05112 0.9998672 1 1 1 0 T 3 4 10 116807187 116807187 G T 1 0 0 0 0 1 0 0 0 6607 1319 46 2 2 GPRC6A 6 116807187 Missense_Mutation SNP G C3L-00095_T 373751 116807187 53998792 301 3510 TAAR8 0 . GRCh38 6 132553309 132553309 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.617T>C p.Phe206Ser p.F206S ENST00000275200 1/1 192 175 17 224 224 0 strelka-varscan-mutect TAAR8,missense_variant,p.Phe206Ser,ENST00000275200,NM_053278.1; C ENST00000275200 Transcript missense_variant 617/1029 617/1029 206/342 F/S tTc/tCc 1 1 TAAR8 HGNC HGNC:14964 protein_coding YES CCDS5154.1 ENSP00000275200 Q969N4 UPI000000D87F NM_053278.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF272,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs764847735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 132553309 132553309 T C 1 0 0 0 0 1 0 0 0 15889 1783 62 5 5 TAAR8 6 132553309 Missense_Mutation SNP T C3L-00095_T 15746122 132553309 38252670 302 3511 VNN1 0 . GRCh38 6 132693189 132693189 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.661G>T p.Val221Phe p.V221F ENST00000367928 4/7 183 171 12 202 202 0 strelka-varscan VNN1,missense_variant,p.Val221Phe,ENST00000367928,NM_004666.2; A ENST00000367928 Transcript missense_variant 675/3106 661/1542 221/513 V/F Gtt/Ttt 1 -1 VNN1 HGNC HGNC:12705 protein_coding YES CCDS5159.1 ENSP00000356905 O95497 UPI000013C91E NM_004666.2 deleterious(0) 4/7 PROSITE_profiles:PS50263,hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF16,PIRSF_domain:PIRSF011861,Pfam_domain:PF00795,Gene3D:3.60.110.10,Superfamily_domains:SSF56317 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 132693189 132693189 C A 1 0 0 0 0 1 0 0 0 17729 478 17 2 2 VNN1 6 132693189 Missense_Mutation SNP C C3L-00095_T 139880 132693189 38112790 303 3512 IFNGR1 0 . GRCh38 6 137198371 137198371 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.1130A>C p.Glu377Ala p.E377A ENST00000367739 7/7 135 127 8 154 154 0 strelka-varscan IFNGR1,missense_variant,p.Glu377Ala,ENST00000367739,NM_000416.2; G ENST00000367739 Transcript missense_variant 1252/2139 1130/1470 377/489 E/A gAg/gCg 1 -1 IFNGR1 HGNC HGNC:5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 A0A0S2Z3Y2 UPI000002CE40 NM_000416.2 tolerated(0.12) 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR20859:SF5,hmmpanther:PTHR20859 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 137198371 137198371 T G 1 0 0 0 0 1 0 0 0 7449 1551 54 5 5 IFNGR1 6 137198371 Missense_Mutation SNP T C3L-00095_T 4505182 137198371 33607608 304 3513 ARFGEF3 0 . GRCh38 6 138291970 138291970 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.3285G>T p.= p.R1095R ENST00000251691 19/34 47 42 5 80 80 0 strelka-varscan ARFGEF3,synonymous_variant,p.=,ENST00000251691,NM_020340.4; T ENST00000251691 Transcript synonymous_variant 3451/14877 3285/6534 1095/2177 R cgG/cgT 1 1 ARFGEF3 HGNC HGNC:21213 protein_coding YES CCDS5189.2 ENSP00000251691 Q5TH69 UPI000150AF4A NM_020340.4 19/34 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.94793 1 1 1 1 0 T 2 4 10 138291970 138291970 G T 1 0 0 0 0 0 0 0 1 977 1219 43 2 2 ARFGEF3 6 138291970 Silent SNP G C3L-00095_T 1093599 138291970 32514009 305 3514 ADGRG6 0 . GRCh38 6 142415919 142415919 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.2793T>A p.= p.I931I ENST00000367609 20/25 402 370 32 484 484 0 strelka-varscan ADGRG6,synonymous_variant,p.=,ENST00000230173,NM_020455.5;ADGRG6,synonymous_variant,p.=,ENST00000367609,NM_198569.2;ADGRG6,synonymous_variant,p.=,ENST00000367608,NM_001032395.2;ADGRG6,synonymous_variant,p.=,ENST00000296932,NM_001032394.2;ADGRG6,upstream_gene_variant,,ENST00000472054,;ADGRG6,downstream_gene_variant,,ENST00000540208,; A ENST00000367609 Transcript synonymous_variant 3194/6887 2793/3753 931/1250 I atT/atA 1 1 ADGRG6 HGNC HGNC:13841 protein_coding YES CCDS47489.1 ENSP00000356581 Q86SQ4 UPI000022CCE4 NM_198569.2 20/25 Gene3D:1.20.1070.10,Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF290,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 142415919 142415919 T A 1 0 0 0 0 0 0 0 1 373 1800 63 4 4 ADGRG6 6 142415919 Silent SNP T C3L-00095_T 4123949 142415919 28390060 306 3515 AKAP12 0 . GRCh38 6 151352525 151352525 + Silent SNP G G T C3L-00095_T C3L-00095_N G G c.4134G>T p.= p.V1378V ENST00000402676 4/5 279 265 14 355 355 0 strelka-varscan AKAP12,synonymous_variant,p.=,ENST00000402676,NM_005100.3;AKAP12,synonymous_variant,p.=,ENST00000253332,;AKAP12,synonymous_variant,p.=,ENST00000354675,NM_144497.2;AKAP12,synonymous_variant,p.=,ENST00000359755,;AKAP12,downstream_gene_variant,,ENST00000490177,; T ENST00000402676 Transcript synonymous_variant 4374/8432 4134/5349 1378/1782 V gtG/gtT COSM3621474 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 4/5 hmmpanther:PTHR23209 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 151352525 151352525 G T 1 0 0 0 0 0 0 0 1 531 1277 45 2 2 AKAP12 6 151352525 Silent SNP G C3L-00095_T 8936606 151352525 19453454 307 3516 CCDC170 0 . GRCh38 6 151593260 151593260 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1447G>A p.Ala483Thr p.A483T ENST00000239374 8/11 183 171 12 238 238 0 strelka-varscan CCDC170,missense_variant,p.Ala483Thr,ENST00000239374,NM_025059.3;CCDC170,non_coding_transcript_exon_variant,,ENST00000537358,; A ENST00000239374 Transcript missense_variant 1546/5293 1447/2148 483/715 A/T Gcc/Acc 1 1 CCDC170 HGNC HGNC:21177 protein_coding YES CCDS43515.1 ENSP00000239374 Q8IYT3 UPI000020D0BA NM_025059.3 tolerated(0.11) 8/11 hmmpanther:PTHR18863:SF4,hmmpanther:PTHR18863,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 151593260 151593260 G A 1 0 0 0 0 1 0 0 0 2487 1319 46 3 3 CCDC170 6 151593260 Missense_Mutation SNP G C3L-00095_T 240735 151593260 19212719 308 3517 ARID1B 0 . GRCh38 6 157196179 157196179 + Nonsense_Mutation SNP G G T rs752398721 C3L-00095_T C3L-00095_N G G c.3877G>T p.Glu1293Ter p.E1293* ENST00000346085 16/20 359 332 27 394 393 1 strelka-varscan ARID1B,stop_gained,p.Glu1293Ter,ENST00000346085,NM_020732.3;ARID1B,stop_gained,p.Glu1333Ter,ENST00000636930,;ARID1B,stop_gained,p.Glu1280Ter,ENST00000350026,NM_017519.2;ARID1B,stop_gained,p.Glu802Ter,ENST00000414678,;ARID1B,stop_gained,p.Glu583Ter,ENST00000637904,;ARID1B,stop_gained,p.Glu523Ter,ENST00000635849,;ARID1B,stop_gained,p.Glu539Ter,ENST00000637015,;ARID1B,stop_gained,p.Glu530Ter,ENST00000637810,;ARID1B,stop_gained,p.Glu400Ter,ENST00000635957,;ARID1B,non_coding_transcript_exon_variant,,ENST00000637741,;ARID1B,3_prime_UTR_variant,,ENST00000637568,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636227,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636940,;ARID1B,upstream_gene_variant,,ENST00000636254,; T ENST00000346085 Transcript stop_gained 4433/10194 3877/6750 1293/2249 E/* Gag/Tag rs752398721 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 16/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 157196179 157196179 G T 1 0 0 0 0 0 1 0 0 1050 1059 37 1 1 ARID1B 6 157196179 Nonsense_Mutation SNP G C3L-00095_T 5602919 157196179 13609800 309 3518 SYNJ2 0 . GRCh38 6 158033665 158033665 + Silent SNP C C T rs778933903 C3L-00095_T C3L-00095_N C C c.696C>T p.= p.F232F ENST00000355585 4/27 76 70 6 125 125 0 strelka-varscan SYNJ2,synonymous_variant,p.=,ENST00000355585,NM_003898.3,NM_001178088.1;SYNJ2,downstream_gene_variant,,ENST00000449320,;SYNJ2,downstream_gene_variant,,ENST00000367113,;SYNJ2,synonymous_variant,p.=,ENST00000485863,; T ENST00000355585 Transcript synonymous_variant 771/7378 696/4491 232/1496 F ttC/ttT rs778933903,COSM1075392,COSM4399666 1 1 SYNJ2 HGNC HGNC:11504 protein_coding YES CCDS5254.1 ENSP00000347792 O15056 UPI000006E2F8 NM_003898.3,NM_001178088.1 4/27 PROSITE_profiles:PS50275,hmmpanther:PTHR11200:SF148,hmmpanther:PTHR11200,Pfam_domain:PF02383 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -13.26877 1 1 1 1 0 T 2 4 10 158033665 158033665 C T 1 0 0 0 0 0 0 0 1 15847 883 31 1 1 SYNJ2 6 158033665 Silent SNP C C3L-00095_T 837486 158033665 12772314 310 3519 MAP3K4 0 . GRCh38 6 161048712 161048712 + Missense_Mutation SNP G G C rs200950731 C3L-00095_T C3L-00095_N G G c.440G>C p.Arg147Pro p.R147P ENST00000392142 3/27 222 203 19 204 204 0 strelka-varscan-mutect MAP3K4,missense_variant,p.Arg147Pro,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,missense_variant,p.Arg147Pro,ENST00000366920,NM_001301072.1;MAP3K4,missense_variant,p.Arg147Pro,ENST00000366919,NM_006724.3;MAP3K4,missense_variant,p.Arg147Pro,ENST00000348824,;MAP3K4,non_coding_transcript_exon_variant,,ENST00000446500,;MAP3K4,missense_variant,p.Arg147Pro,ENST00000490904,;MAP3K4,missense_variant,p.Arg147Pro,ENST00000544041,;MAP3K4,intron_variant,,ENST00000542952,; C ENST00000392142 Transcript missense_variant 588/5490 440/4827 147/1608 R/P cGa/cCa rs200950731 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 deleterious(0.01) 3/27 MODERATE 1 SNV 1 1 PASS rs200950731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 161048712 161048712 G C 1 0 0 0 0 1 0 0 0 9175 1058 37 4 4 MAP3K4 6 161048712 Missense_Mutation SNP G C3L-00095_T 3015047 161048712 9757267 311 3520 AGPAT4 0 . GRCh38 6 161232188 161232188 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.26C>G p.Ser9Cys p.S9C ENST00000320285 2/9 143 133 10 181 181 0 strelka-varscan-mutect AGPAT4,missense_variant,p.Ser9Cys,ENST00000320285,NM_020133.2;AGPAT4,missense_variant,p.Ser9Cys,ENST00000366911,;AGPAT4,missense_variant,p.Ser9Cys,ENST00000366905,;AGPAT4,missense_variant,p.Ser9Cys,ENST00000436279,; C ENST00000320285 Transcript missense_variant 239/7865 26/1137 9/378 S/C tCt/tGt 1 -1 AGPAT4 HGNC HGNC:20885 protein_coding YES CCDS5280.1 ENSP00000314036 Q9NRZ5 UPI0000035BB6 NM_020133.2 deleterious(0) 2/9 hmmpanther:PTHR10983,hmmpanther:PTHR10983:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 161232188 161232188 G C 1 0 0 0 0 1 0 0 0 471 942 33 4 4 AGPAT4 6 161232188 Missense_Mutation SNP G C3L-00095_T 183476 161232188 9573791 312 3521 KIF25 0 . GRCh38 6 168042085 168042085 + Missense_Mutation SNP G G T rs2073634 C3L-00095_T C3L-00095_N G G c.763G>T p.Ala255Ser p.A255S ENST00000443060 8/10 231 219 12 301 299 2 strelka-varscan-mutect KIF25,missense_variant,p.Ala255Ser,ENST00000443060,;KIF25,missense_variant,p.Ala255Ser,ENST00000354419,NM_030615.2;KIF25,missense_variant,p.Ala255Ser,ENST00000351261,NM_005355.3; T ENST00000443060 Transcript missense_variant 1154/1613 763/1155 255/384 A/S Gca/Tca rs2073634 1 1 KIF25 HGNC HGNC:6390 protein_coding YES CCDS5305.1 ENSP00000388878 Q9UIL4 UPI000012DDAB tolerated(0.49) 8/10 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF421,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs2073634 . 0 156 0 0 0 0 0 53 -10.62231 0 0 1 0 0 T 3 4 10 168042085 168042085 G T 1 0 0 0 0 1 0 0 0 8158 1087 38 1 1 KIF25 6 168042085 Missense_Mutation SNP G C3L-00095_T 6809897 168042085 2763894 313 3522 SMOC2 0 . GRCh38 6 168653165 168653165 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.1255G>A p.Glu419Lys p.E419K ENST00000354536 11/13 220 198 22 291 291 0 strelka-varscan-mutect SMOC2,missense_variant,p.Glu419Lys,ENST00000354536,NM_022138.2;SMOC2,missense_variant,p.Glu408Lys,ENST00000356284,NM_001166412.1;SMOC2,missense_variant,p.Glu28Lys,ENST00000417208,;SMOC2,5_prime_UTR_variant,,ENST00000535039,;SMOC2,upstream_gene_variant,,ENST00000477998,;SMOC2,missense_variant,p.Glu41Lys,ENST00000392100,; A ENST00000354536 Transcript missense_variant 1475/3150 1255/1374 419/457 E/K Gaa/Aaa COSM1266298,COSM3622950 1 1 SMOC2 HGNC HGNC:20323 protein_coding YES CCDS5307.1 ENSP00000346537 Q9H3U7 UPI0000072A56 NM_022138.2 deleterious(0) 11/13 PROSITE_profiles:PS50222,hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF14,PROSITE_patterns:PS00018,Pfam_domain:PF10591,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1041903275 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 168653165 168653165 G A 1 0 0 0 0 1 0 0 0 15123 943 33 3 3 SMOC2 6 168653165 Missense_Mutation SNP G C3L-00095_T 611080 168653165 2152814 314 3523 SDK1 0 . GRCh38 7 4010999 4010999 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2165G>T p.Gly722Val p.G722V ENST00000404826 15/45 229 216 13 212 212 0 strelka-varscan-mutect SDK1,missense_variant,p.Gly722Val,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Gly722Val,ENST00000615806,;SDK1,missense_variant,p.Gly722Val,ENST00000389531,; T ENST00000404826 Transcript missense_variant 2304/10397 2165/6642 722/2213 G/V gGc/gTc 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0) 15/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 4010999 4010999 G T 1 0 0 0 0 1 0 0 0 14243 1203 42 2 2 SDK1 7 4010999 Missense_Mutation SNP G C3L-00095_T 4010999 155334974 315 3524 FBXL18 0 . GRCh38 7 5501708 5501708 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.561G>T p.= p.V187V ENST00000382368 3/5 82 74 8 69 68 1 strelka-varscan-mutect FBXL18,synonymous_variant,p.=,ENST00000382368,NM_024963.4;FBXL18,synonymous_variant,p.=,ENST00000458142,;FBXL18,synonymous_variant,p.=,ENST00000453700,;FBXL18,upstream_gene_variant,,ENST00000620087,;FBXL18,synonymous_variant,p.=,ENST00000415009,; A ENST00000382368 Transcript synonymous_variant 685/3498 561/2157 187/718 V gtG/gtT 1 -1 FBXL18 HGNC HGNC:21874 protein_coding YES CCDS43546.1 ENSP00000371805 Q96ME1 A0A024R857 UPI000020EA59 NM_024963.4 3/5 Superfamily_domains:SSF52047 LOW 1 SNV 5 1 PASS . . 0 201 8 0 0 0 0 0 -16.93089 0.999995 1 1 1 0 A 2 1 10 5501708 5501708 C A 1 0 0 0 0 0 0 0 1 5578 581 21 2 2 FBXL18 7 5501708 Silent SNP C C3L-00095_T 1490709 5501708 153844265 316 3525 GRID2IP 0 . GRCh38 7 6498064 6498064 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3564G>T p.Glu1188Asp p.E1188D ENST00000457091 21/22 51 44 7 49 49 0 strelka-varscan-mutect GRID2IP,missense_variant,p.Glu1188Asp,ENST00000457091,NM_001145118.1;GRID2IP,missense_variant,p.Glu997Asp,ENST00000452113,;GRID2IP,missense_variant,p.Glu1004Asp,ENST00000435185,; A ENST00000457091 Transcript missense_variant,splice_region_variant 3564/3636 3564/3636 1188/1211 E/D gaG/gaT 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 deleterious(0.04) 21/22 PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,SMART_domains:SM00498,Superfamily_domains:SSF101447 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -16.55943 0.9999977 1 1 1 0 A 3 1 10 6498064 6498064 C A 1 0 0 0 0 1 0 0 0 6653 695 24 2 2 GRID2IP 7 6498064 Missense_Mutation SNP C C3L-00095_T 996356 6498064 152847909 317 3526 MEOX2 0 . GRCh38 7 15686341 15686341 + Missense_Mutation SNP G G T rs377671894 C3L-00095_T C3L-00095_N G G c.62C>A p.Pro21Gln p.P21Q ENST00000262041 1/3 173 114 59 155 154 1 strelka-varscan MEOX2,missense_variant,p.Pro21Gln,ENST00000262041,NM_005924.4;MEOX2-AS1,upstream_gene_variant,,ENST00000442176,;AC005550.5,downstream_gene_variant,,ENST00000438923,;AC005550.3,downstream_gene_variant,,ENST00000451240,; T ENST00000262041 Transcript missense_variant 472/2500 62/915 21/304 P/Q cCg/cAg rs377671894 1 -1 MEOX2 HGNC HGNC:7014 protein_coding YES CCDS34605.1 ENSP00000262041 P50222 UPI000013D247 NM_005924.4 tolerated(0.11) 1/3 hmmpanther:PTHR24328,hmmpanther:PTHR24328:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 15686341 15686341 G T 1 0 0 0 0 1 0 0 0 9419 1116 39 1 1 MEOX2 7 15686341 Missense_Mutation SNP G C3L-00095_T 9188277 15686341 143659632 318 3527 HDAC9 0 . GRCh38 7 18585369 18585369 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.111G>T p.= p.V37V ENST00000441542 2/25 347 324 23 401 401 0 strelka-varscan HDAC9,synonymous_variant,p.=,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,synonymous_variant,p.=,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,synonymous_variant,p.=,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,synonymous_variant,p.=,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,synonymous_variant,p.=,ENST00000401921,;HDAC9,synonymous_variant,p.=,ENST00000441542,NM_178425.2;HDAC9,synonymous_variant,p.=,ENST00000432645,NM_058176.2;HDAC9,synonymous_variant,p.=,ENST00000417496,NM_001204144.1;HDAC9,synonymous_variant,p.=,ENST00000428307,NM_001204145.1;HDAC9,synonymous_variant,p.=,ENST00000456174,NM_001204148.1;HDAC9,synonymous_variant,p.=,ENST00000524023,NM_001204147.1;HDAC9,synonymous_variant,p.=,ENST00000413380,;HDAC9,synonymous_variant,p.=,ENST00000441986,;HDAC9,synonymous_variant,p.=,ENST00000413509,;HDAC9,synonymous_variant,p.=,ENST00000430454,;HDAC9,downstream_gene_variant,,ENST00000433709,;HDAC9,non_coding_transcript_exon_variant,,ENST00000476135,;HDAC9,stop_gained,p.Gly34Ter,ENST00000446646,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; T ENST00000441542 Transcript synonymous_variant 111/3210 111/3210 37/1069 V gtG/gtT 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 2/25 Low_complexity_(Seg):seg,Pfam_domain:PF12203,PIRSF_domain:PIRSF037911 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 18585369 18585369 G T 1 0 0 0 0 0 0 0 1 6901 1335 47 2 2 HDAC9 7 18585369 Silent SNP G C3L-00095_T 2899028 18585369 140760604 319 3528 HDAC9 0 . GRCh38 7 18629424 18629424 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.739A>T p.Arg247Trp p.R247W ENST00000441542 6/25 245 230 15 298 298 0 strelka-varscan HDAC9,missense_variant,p.Arg244Trp,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Arg244Trp,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Arg247Trp,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Arg244Trp,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Arg216Trp,ENST00000456174,NM_001204148.1;HDAC9,intron_variant,,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,intron_variant,,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,intron_variant,,ENST00000401921,;HDAC9,intron_variant,,ENST00000417496,NM_001204144.1;HDAC9,intron_variant,,ENST00000428307,NM_001204145.1;HDAC9,intron_variant,,ENST00000524023,NM_001204147.1;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,intron_variant,,ENST00000461159,; T ENST00000441542 Transcript missense_variant 739/3210 739/3210 247/1069 R/W Agg/Tgg 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0) 6/25 PIRSF_domain:PIRSF037911 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 18629424 18629424 A T 1 0 0 0 0 1 0 0 0 6901 179 7 4 4 HDAC9 7 18629424 Missense_Mutation SNP A C3L-00095_T 44055 18629424 140716549 320 3529 CREB5 0 . GRCh38 7 28804350 28804350 + Missense_Mutation SNP C C A rs746199510 C3L-00095_T C3L-00095_N C C c.854C>A p.Pro285Gln p.P285Q ENST00000357727 8/11 542 498 44 663 662 1 strelka-varscan CREB5,missense_variant,p.Pro285Gln,ENST00000357727,NM_182898.3;CREB5,missense_variant,p.Pro278Gln,ENST00000396300,NM_004904.3;CREB5,missense_variant,p.Pro252Gln,ENST00000396299,NM_182899.4;CREB5,missense_variant,p.Pro146Gln,ENST00000396298,NM_001011666.2;CREB5,missense_variant,p.Pro252Gln,ENST00000409603,;CREB5,missense_variant,p.Pro111Gln,ENST00000426500,; A ENST00000357727 Transcript missense_variant 1244/8532 854/1527 285/508 P/Q cCa/cAa rs746199510 1 1 CREB5 HGNC HGNC:16844 protein_coding YES CCDS5417.1 ENSP00000350359 Q02930 UPI0000457534 NM_182898.3 tolerated(0.29) 8/11 PIRSF_domain:PIRSF003153,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 28804350 28804350 C A 1 0 0 0 0 1 0 0 0 3660 594 21 2 2 CREB5 7 28804350 Missense_Mutation SNP C C3L-00095_T 10174926 28804350 130541623 321 3530 WIPF3 0 . GRCh38 7 29884085 29884085 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.591A>T p.Lys197Asn p.K197N ENST00000242140 5/9 59 54 5 108 108 0 strelka-varscan WIPF3,missense_variant,p.Lys197Asn,ENST00000242140,NM_001080529.2;WIPF3,missense_variant,p.Lys197Asn,ENST00000409290,;WIPF3,missense_variant,p.Lys197Asn,ENST00000409123,; T ENST00000242140 Transcript missense_variant 773/4184 591/1452 197/483 K/N aaA/aaT 1 1 WIPF3 HGNC HGNC:22004 protein_coding YES CCDS56472.1 ENSP00000242140 A6NGB9 UPI00006C0B79 NM_001080529.2 tolerated_low_confidence(0.09) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23202:SF31,hmmpanther:PTHR23202 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -11.73971 0.9999936 1 1 1 0 T 3 4 10 29884085 29884085 A T 1 0 0 0 0 1 0 0 0 17925 11 1 4 4 WIPF3 7 29884085 Missense_Mutation SNP A C3L-00095_T 1079735 29884085 129461888 322 3531 CRHR2 0 . GRCh38 7 30655072 30655072 + Missense_Mutation SNP G G T rs552742156 C3L-00095_T C3L-00095_N G G c.1143C>A p.Phe381Leu p.F381L ENST00000348438 12/13 112 105 7 201 200 1 strelka-varscan CRHR2,missense_variant,p.Phe340Leu,ENST00000341843,NM_001202481.1;CRHR2,missense_variant,p.Phe354Leu,ENST00000506074,NM_001202483.1;CRHR2,missense_variant,p.Phe354Leu,ENST00000471646,NM_001883.4,NM_001202482.1;CRHR2,missense_variant,p.Phe381Leu,ENST00000348438,NM_001202475.1;CRHR2,3_prime_UTR_variant,,ENST00000452278,; T ENST00000348438 Transcript missense_variant 1213/1600 1143/1317 381/438 F/L ttC/ttA rs552742156,COSM1450345,COSM167089,COSM4949205 1 -1 CRHR2 HGNC HGNC:2358 protein_coding YES CCDS56478.1 ENSP00000340943 Q13324 UPI000002A720 NM_001202475.1 tolerated(0.1) 12/13 Pfam_domain:PF00002,Prints_domain:PR00249,PROSITE_patterns:PS00650,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF274,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 30655072 30655072 G T 1 0 0 0 0 1 0 0 0 3673 1049 37 1 1 CRHR2 7 30655072 Missense_Mutation SNP G C3L-00095_T 770987 30655072 128690901 323 3532 INHBA 0 . GRCh38 7 41700207 41700207 + Missense_Mutation SNP C C A rs755524019 C3L-00095_T C3L-00095_N C C c.168G>T p.Glu56Asp p.E56D ENST00000242208 2/3 102 90 12 122 122 0 strelka-varscan INHBA,missense_variant,p.Glu56Asp,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Glu56Asp,ENST00000638023,;INHBA,missense_variant,p.Glu56Asp,ENST00000442711,;INHBA-AS1,intron_variant,,ENST00000415848,;INHBA-AS1,intron_variant,,ENST00000422822,;INHBA-AS1,intron_variant,,ENST00000420821,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript missense_variant 415/6064 168/1281 56/426 E/D gaG/gaT rs755524019 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0.02) 2/3 hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00688 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 41700207 41700207 C A 1 0 0 0 0 1 0 0 0 7643 680 24 2 2 INHBA 7 41700207 Missense_Mutation SNP C C3L-00095_T 11045135 41700207 117645766 324 3533 HECW1 0 . GRCh38 7 43320743 43320743 + Splice_Site SNP G G T C3L-00095_T C3L-00095_N G G c.460+1G>T p.X154_splice ENST00000395891 194 177 17 205 205 0 strelka-varscan HECW1,splice_donor_variant,,ENST00000395891,NM_015052.4;HECW1,splice_donor_variant,,ENST00000453890,NM_001287059.1;HECW1,splice_donor_variant,,ENST00000492310,; T ENST00000395891 Transcript splice_donor_variant -/9501 460/4821 154/1606 COSM1450773,COSM1450774 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 5/29 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 10 43320743 43320743 G T 1 0 0 0 0 0 0 1 0 6924 1159 40 1 1 HECW1 7 43320743 Splice_Site SNP G C3L-00095_T 1620536 43320743 116025230 325 3534 HECW1 0 . GRCh38 7 43445561 43445561 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2389C>A p.= p.R797R ENST00000395891 11/30 46 40 6 67 67 0 strelka-varscan HECW1,synonymous_variant,p.=,ENST00000395891,NM_015052.4;HECW1,synonymous_variant,p.=,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript synonymous_variant 2994/9501 2389/4821 797/1606 R Cgg/Agg 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 11/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 LOW 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -14.42489 0.9997974 1 1 1 0 A 2 1 10 43445561 43445561 C A 1 0 0 0 0 0 0 0 1 6924 875 31 1 1 HECW1 7 43445561 Silent SNP C C3L-00095_T 124818 43445561 115900412 326 3535 AEBP1 0 . GRCh38 7 44110962 44110962 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1535C>A p.Pro512Gln p.P512Q ENST00000223357 13/21 206 190 16 256 255 1 strelka-varscan AEBP1,missense_variant,p.Pro512Gln,ENST00000223357,NM_001129.4;AEBP1,missense_variant,p.Pro55Gln,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,NM_001256879.1;POLD2,downstream_gene_variant,,ENST00000452185,NM_001127218.2;POLD2,downstream_gene_variant,,ENST00000610533,NM_006230.3;POLD2,downstream_gene_variant,,ENST00000223361,;AEBP1,downstream_gene_variant,,ENST00000455443,;AEBP1,downstream_gene_variant,,ENST00000449162,;POLD2,downstream_gene_variant,,ENST00000436400,;AEBP1,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,3_prime_UTR_variant,,ENST00000434445,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,downstream_gene_variant,,ENST00000453052,;POLD2,downstream_gene_variant,,ENST00000489883,; A ENST00000223357 Transcript missense_variant 1840/4081 1535/3477 512/1158 P/Q cCa/cAa 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 deleterious(0) 13/21 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF48,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 44110962 44110962 C A 1 0 0 0 0 1 0 0 0 424 594 21 2 2 AEBP1 7 44110962 Missense_Mutation SNP C C3L-00095_T 665401 44110962 115235011 327 3536 NPC1L1 0 . GRCh38 7 44517231 44517231 + Missense_Mutation SNP G G T rs374386282 C3L-00095_T C3L-00095_N G G c.3344C>A p.Pro1115Gln p.P1115Q ENST00000289547 16/20 433 408 25 528 527 1 strelka-varscan NPC1L1,missense_variant,p.Pro1115Gln,ENST00000289547,NM_013389.2;NPC1L1,missense_variant,p.Pro1042Gln,ENST00000546276,;NPC1L1,missense_variant,p.Pro1088Gln,ENST00000381160,NM_001101648.1; T ENST00000289547 Transcript missense_variant 3400/5048 3344/4080 1115/1359 P/Q cCg/cAg rs374386282,COSM5244032 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 deleterious(0.02) 16/20 hmmpanther:PTHR10796:SF89,hmmpanther:PTHR10796,Pfam_domain:PF02460,Gene3D:2j8sB01,Superfamily_domains:SSF82866 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 44517231 44517231 G T 1 0 0 0 0 1 0 0 0 10619 1116 39 1 1 NPC1L1 7 44517231 Missense_Mutation SNP G C3L-00095_T 406269 44517231 114828742 328 3537 ABCA13 0 . GRCh38 7 48273861 48273861 + Missense_Mutation SNP G G T rs756550750 C3L-00095_T C3L-00095_N G G c.4195G>T p.Asp1399Tyr p.D1399Y ENST00000435803 17/62 333 306 27 213 212 1 strelka-varscan ABCA13,missense_variant,p.Asp1399Tyr,ENST00000435803,NM_152701.4;ABCA13,downstream_gene_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant 4219/17184 4195/15177 1399/5058 D/Y Gat/Tat rs756550750 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.08) 17/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 48273861 48273861 G T 1 0 0 0 0 1 0 0 0 35 942 33 2 2 ABCA13 7 48273861 Missense_Mutation SNP G C3L-00095_T 3756630 48273861 111072112 329 3538 ABCA13 0 . GRCh38 7 48274556 48274556 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.4890T>A p.= p.L1630L ENST00000435803 17/62 361 329 32 359 358 1 strelka-varscan ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,upstream_gene_variant,,ENST00000544596,;ABCA13,upstream_gene_variant,,ENST00000611776,;ABCA13,downstream_gene_variant,,ENST00000417403,; A ENST00000435803 Transcript synonymous_variant 4914/17184 4890/15177 1630/5058 L ctT/ctA 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 17/62 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 48274556 48274556 T A 1 0 0 0 0 0 0 0 1 35 1799 63 4 4 ABCA13 7 48274556 Silent SNP T C3L-00095_T 695 48274556 111071417 330 3539 DDC 0 . GRCh38 7 50543886 50543886 + Missense_Mutation SNP C C A rs147802058 C3L-00095_T C3L-00095_N C C c.200G>T p.Gly67Val p.G67V ENST00000444124 2/15 492 452 40 595 595 0 strelka-varscan DDC,missense_variant,p.Gly67Val,ENST00000444124,NM_001082971.1;DDC,missense_variant,p.Gly67Val,ENST00000357936,NM_000790.3;DDC,missense_variant,p.Gly67Val,ENST00000622873,NM_001242886.1;DDC,missense_variant,p.Gly67Val,ENST00000617822,NM_001242887.1;DDC,missense_variant,p.Gly67Val,ENST00000426377,NM_001242888.1;DDC,missense_variant,p.Gly67Val,ENST00000615193,NM_001242889.1;DDC,missense_variant,p.Gly67Val,ENST00000431062,;DDC,missense_variant,p.Gly33Val,ENST00000430300,;DDC,missense_variant,p.Gly67Val,ENST00000380984,NM_001242890.1;FIGNL1,upstream_gene_variant,,ENST00000613602,;DDC,downstream_gene_variant,,ENST00000420203,;DDC-AS1,downstream_gene_variant,,ENST00000454521,;DDC,upstream_gene_variant,,ENST00000489162,;DDC,missense_variant,p.Gly67Val,ENST00000444733,; A ENST00000444124 Transcript missense_variant,splice_region_variant 401/2041 200/1443 67/480 G/V gGg/gTg rs147802058 1 -1 DDC HGNC HGNC:2719 protein_coding YES CCDS5511.1 ENSP00000403644 P20711 A0A0S2Z3N4 UPI000013F150 NM_001082971.1 deleterious(0) 2/15 Gene3D:3k40A01,Pfam_domain:PF00282,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF70,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 50543886 50543886 C A 1 0 0 0 0 1 0 0 0 4128 637 22 2 2 DDC 7 50543886 Missense_Mutation SNP C C3L-00095_T 2269330 50543886 108802087 331 3540 POM121L12 0 . GRCh38 7 53036252 53036252 + Missense_Mutation SNP G G C rs200587634 C3L-00095_T C3L-00095_N G G c.581G>C p.Gly194Ala p.G194A ENST00000408890 1/1 270 244 26 380 380 0 strelka-varscan POM121L12,missense_variant,p.Gly194Ala,ENST00000408890,NM_182595.3; C ENST00000408890 Transcript missense_variant 611/1283 581/891 194/296 G/A gGg/gCg rs200587634 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.11) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 53036252 53036252 G C 1 0 0 0 0 1 0 0 0 12352 1232 43 4 4 POM121L12 7 53036252 Missense_Mutation SNP G C3L-00095_T 2492366 53036252 106309721 332 3541 LANCL2 0 . GRCh38 7 55428374 55428374 + Splice_Site SNP G G A novel C3L-00095_T C3L-00095_N G G c.1186-1G>A p.X396_splice ENST00000254770 199 186 13 199 199 0 strelka-varscan LANCL2,splice_acceptor_variant,,ENST00000254770,NM_018697.3;LANCL2,splice_acceptor_variant,,ENST00000476479,;LANCL2,splice_acceptor_variant,,ENST00000452107,;LANCL2,non_coding_transcript_exon_variant,,ENST00000466041,; A ENST00000254770 Transcript splice_acceptor_variant -/4353 1186/1353 396/450 1 1 LANCL2 HGNC HGNC:6509 protein_coding YES CCDS5517.1 ENSP00000254770 Q9NS86 UPI000006F7D0 NM_018697.3 7/8 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 55428374 55428374 G A 1 0 0 0 0 0 0 1 0 8531 1043 36 3 3 LANCL2 7 55428374 Splice_Site SNP G C3L-00095_T 2392122 55428374 103917599 333 3542 SEPT14 0 . GRCh38 7 55846592 55846592 + Missense_Mutation SNP C C A rs750565046 C3L-00095_T C3L-00095_N C C c.100G>T p.Gly34Cys p.G34C ENST00000388975 3/10 136 124 12 111 111 0 strelka-varscan SEPT14,missense_variant,p.Gly34Cys,ENST00000388975,NM_207366.2;SEPT14,non_coding_transcript_exon_variant,,ENST00000477628,; A ENST00000388975 Transcript missense_variant 217/3785 100/1299 34/432 G/C Ggt/Tgt rs750565046 1 -1 SEPT14 HGNC HGNC:33280 protein_coding YES CCDS5519.2 ENSP00000373627 Q6ZU15 UPI0000E0AB69 NM_207366.2 deleterious(0) 3/10 hmmpanther:PTHR18884:SF51,hmmpanther:PTHR18884,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 55846592 55846592 C A 1 0 0 0 0 1 0 0 0 14339 594 21 2 2 SEPT14 7 55846592 Missense_Mutation SNP C C3L-00095_T 418218 55846592 103499381 334 3543 ZNF713 0 . GRCh38 7 55939601 55939601 + Silent SNP A A T rs373984730 C3L-00095_T C3L-00095_N A A c.927A>T p.= p.T309T ENST00000429591 7/7 132 121 11 103 103 0 strelka-varscan ZNF713,synonymous_variant,p.=,ENST00000429591,NM_182633.2;ZNF713,synonymous_variant,p.=,ENST00000633730,;RP11-15K19.2,intron_variant,,ENST00000426595,; T ENST00000429591 Transcript synonymous_variant 1715/4339 927/1332 309/443 T acA/acT rs373984730 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 7/7 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 55939601 55939601 A T 1 0 0 0 0 0 0 0 1 18692 175 7 4 4 ZNF713 7 55939601 Silent SNP A C3L-00095_T 93009 55939601 103406372 335 3544 RSBN1L 0 . GRCh38 7 77778606 77778606 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.1979A>G p.Tyr660Cys p.Y660C ENST00000334955 8/8 99 93 6 90 90 0 strelka-varscan-mutect RSBN1L,missense_variant,p.Tyr660Cys,ENST00000334955,NM_198467.2;RSBN1L,missense_variant,p.Tyr390Cys,ENST00000445288,;RSBN1L,missense_variant,p.Tyr198Cys,ENST00000445512,;RSBN1L,intron_variant,,ENST00000441514,; G ENST00000334955 Transcript missense_variant 2006/6422 1979/2541 660/846 Y/C tAt/tGt 1 1 RSBN1L HGNC HGNC:24765 protein_coding YES CCDS43607.1 ENSP00000334040 Q6PCB5 UPI000020F469 NM_198467.2 tolerated(0.33) 8/8 hmmpanther:PTHR13354:SF9,hmmpanther:PTHR13354 MODERATE 1 SNV 1 1 PASS rs1322580432 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 77778606 77778606 A G 1 0 0 0 0 1 0 0 0 13953 449 16 5 5 RSBN1L 7 77778606 Missense_Mutation SNP A C3L-00095_T 21839005 77778606 81567367 336 3545 CD36 0 . GRCh38 7 80661078 80661078 + Silent SNP C C A C3L-00095_T C3L-00095_N C C c.297C>A p.= p.A99A ENST00000435819 8/17 283 260 23 368 366 2 strelka-varscan-mutect CD36,synonymous_variant,p.=,ENST00000435819,;CD36,synonymous_variant,p.=,ENST00000447544,NM_001001548.2;CD36,synonymous_variant,p.=,ENST00000309881,NM_001001547.2;CD36,synonymous_variant,p.=,ENST00000433696,NM_001289908.1;CD36,synonymous_variant,p.=,ENST00000394788,NM_000072.3;CD36,synonymous_variant,p.=,ENST00000538969,NM_001289909.1;CD36,synonymous_variant,p.=,ENST00000544133,;CD36,synonymous_variant,p.=,ENST00000432207,NM_001127443.1,NM_001127444.1;CD36,synonymous_variant,p.=,ENST00000534394,NM_001289911.1;CD36,synonymous_variant,p.=,ENST00000419819,;CD36,synonymous_variant,p.=,ENST00000413265,;CD36,synonymous_variant,p.=,ENST00000438020,;CD36,synonymous_variant,p.=,ENST00000426978,;CD36,downstream_gene_variant,,ENST00000482059,;CD36,downstream_gene_variant,,ENST00000428497,;CD36,downstream_gene_variant,,ENST00000436384,;CD36,downstream_gene_variant,,ENST00000441109,;CD36,intron_variant,,ENST00000441034,;CD36,upstream_gene_variant,,ENST00000464213,;AC073850.6,downstream_gene_variant,,ENST00000449243,; A ENST00000435819 Transcript synonymous_variant 981/2365 297/1419 99/472 A gcC/gcA COSM1150750,COSM748023,COSM748024,COSM748025 1 1 CD36 HGNC HGNC:1663 protein_coding YES CCDS34673.1 ENSP00000399421 P16671 A4D1B1 UPI0000000C91 8/17 hmmpanther:PTHR11923:SF12,hmmpanther:PTHR11923,Pfam_domain:PF01130,Prints_domain:PR01610 1,1,1,1 LOW 1 SNV 2 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 80661078 80661078 C A 1 0 0 0 0 0 0 0 1 2711 581 21 2 2 CD36 7 80661078 Silent SNP C C3L-00095_T 2882472 80661078 78684895 337 3546 SEMA3D 0 . GRCh38 7 84999710 84999710 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.2064G>A p.= p.Q688Q ENST00000284136 17/17 460 426 34 616 616 0 strelka-varscan-mutect SEMA3D,synonymous_variant,p.=,ENST00000284136,NM_152754.2;SEMA3D,non_coding_transcript_exon_variant,,ENST00000484038,; T ENST00000284136 Transcript synonymous_variant 2108/6265 2064/2334 688/777 Q caG/caA 1 -1 SEMA3D HGNC HGNC:10726 protein_coding YES CCDS34676.1 ENSP00000284136 O95025 UPI0000135A66 NM_152754.2 17/17 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF36 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 84999710 84999710 C T 1 0 0 0 0 0 0 0 1 14303 912 32 3 3 SEMA3D 7 84999710 Silent SNP C C3L-00095_T 4338632 84999710 74346263 338 3547 CALCR 0 . GRCh38 7 93468802 93468802 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.488C>T p.Ala163Val p.A163V ENST00000359558 8/16 148 133 15 147 147 0 strelka-varscan-mutect CALCR,missense_variant,p.Ala163Val,ENST00000359558,NM_001164737.1;CALCR,missense_variant,p.Ala145Val,ENST00000421592,;CALCR,missense_variant,p.Ala145Val,ENST00000394441,NM_001164738.1;CALCR,missense_variant,p.Ala145Val,ENST00000426151,NM_001742.3;CALCR,missense_variant,p.Ala145Val,ENST00000360249,;CALCR,missense_variant,p.Ala145Val,ENST00000423724,;CALCR,missense_variant,p.Ala145Val,ENST00000415529,; A ENST00000359558 Transcript missense_variant 788/3696 488/1527 163/508 A/V gCa/gTa 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 tolerated(0.08) 8/16 hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Superfamily_domains:SSF111418,Prints_domain:PR01350,Prints_domain:PR00361 MODERATE 1 SNV 5 1 PASS . . 0 205 0 3 0 0 0 0 -19.97811 0.9999844 1 1 1 0 A 3 1 10 93468802 93468802 G A 1 0 0 0 0 1 0 0 0 2269 1333 46 3 3 CALCR 7 93468802 Missense_Mutation SNP G C3L-00095_T 8469092 93468802 65877171 339 3548 DYNC1I1 0 . GRCh38 7 95810471 95810471 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.188T>A p.Leu63Gln p.L63Q ENST00000324972 3/17 99 93 6 97 97 0 strelka-varscan-mutect DYNC1I1,missense_variant,p.Leu63Gln,ENST00000324972,NM_004411.4;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000447467,NM_001135556.1;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000437599,NM_001278421.1;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000359388,NM_001135557.1;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000457059,;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000630942,NM_001278422.1;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000413338,;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000524053,;DYNC1I1,missense_variant,p.Leu63Gln,ENST00000518089,;DYNC1I1,5_prime_UTR_variant,,ENST00000537881,; A ENST00000324972 Transcript missense_variant 381/2950 188/1938 63/645 L/Q cTg/cAg 1 1 DYNC1I1 HGNC HGNC:2963 protein_coding YES CCDS5644.1 ENSP00000320130 O14576 A4D1I7 UPI0000129A01 NM_004411.4 deleterious(0) 3/17 hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 95810471 95810471 T A 1 0 0 0 0 1 0 0 0 4666 1580 55 4 4 DYNC1I1 7 95810471 Missense_Mutation SNP T C3L-00095_T 2341669 95810471 63535502 340 3549 SLC25A13 0 . GRCh38 7 96121931 96121932 + Frame_Shift_Ins INS - - G novel C3L-00095_T C3L-00095_N - - c.1660dupC p.Arg554ProfsTer15 p.R554Pfs*15 ENST00000416240 16/18 363 327 36 451 451 0 sindel-varindel SLC25A13,frameshift_variant,p.Arg554ProfsTer15,ENST00000416240,NM_001160210.1;SLC25A13,frameshift_variant,p.Arg553ProfsTer15,ENST00000265631,NM_014251.2;SLC25A13,non_coding_transcript_exon_variant,,ENST00000494085,;GS1-25M2.1,downstream_gene_variant,,ENST00000625023,; G ENST00000416240 Transcript frameshift_variant 1851-1852/3192 1660-1661/2031 554/676 R/PX cgg/cCgg 1 -1 SLC25A13 HGNC HGNC:10983 protein_coding YES CCDS55130.1 ENSP00000400101 Q9UJS0 UPI0000001663 NM_001160210.1 16/18 PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF265,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 10 96121931 96121931 - G 1 0 1 1 0 0 0 0 0 14740 652 23 0 0 SLC25A13 7 96121931 Frame_Shift_Ins INS - C3L-00095_T 311460 96121931 63224042 341 3550 GPC2 0 . GRCh38 7 100171539 100171539 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1310G>T p.Arg437Leu p.R437L ENST00000292377 8/10 70 63 7 87 87 0 strelka-varscan-mutect GPC2,missense_variant,p.Arg437Leu,ENST00000292377,NM_152742.2;GAL3ST4,upstream_gene_variant,,ENST00000360039,NM_024637.4;GAL3ST4,upstream_gene_variant,,ENST00000413800,;GAL3ST4,upstream_gene_variant,,ENST00000423751,;GAL3ST4,upstream_gene_variant,,ENST00000411994,;GAL3ST4,upstream_gene_variant,,ENST00000482469,;GAL3ST4,upstream_gene_variant,,ENST00000498000,;GAL3ST4,upstream_gene_variant,,ENST00000460995,;GPC2,downstream_gene_variant,,ENST00000490629,;GPC2,splice_region_variant,,ENST00000486702,;GAL3ST4,upstream_gene_variant,,ENST00000495882,;GPC2,downstream_gene_variant,,ENST00000471717,;GPC2,downstream_gene_variant,,ENST00000480087,; A ENST00000292377 Transcript missense_variant,splice_region_variant 1478/2532 1310/1740 437/579 R/L cGg/cTg 1 -1 GPC2 HGNC HGNC:4450 protein_coding YES CCDS5689.1 ENSP00000292377 Q8N158 UPI000005340D NM_152742.2 deleterious(0.02) 8/10 hmmpanther:PTHR10822:SF24,hmmpanther:PTHR10822,Pfam_domain:PF01153 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -15.47453 0.999999 1 1 1 0 A 3 1 10 100171539 100171539 C A 1 0 0 0 0 1 0 0 0 6500 666 23 1 1 GPC2 7 100171539 Missense_Mutation SNP C C3L-00095_T 4049608 100171539 59174434 342 3551 MOSPD3 0 . GRCh38 7 100614871 100614871 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.516C>A p.= p.P172P ENST00000393950 4/5 88 83 5 115 115 0 strelka-varscan-mutect MOSPD3,synonymous_variant,p.=,ENST00000393950,NM_023948.4;MOSPD3,synonymous_variant,p.=,ENST00000424091,NM_001040099.1;MOSPD3,synonymous_variant,p.=,ENST00000223054,NM_001040097.1;MOSPD3,synonymous_variant,p.=,ENST00000379527,NM_001040098.1;MOSPD3,synonymous_variant,p.=,ENST00000493970,;MOSPD3,3_prime_UTR_variant,,ENST00000462372,;MOSPD3,downstream_gene_variant,,ENST00000490309,;MOSPD3,downstream_gene_variant,,ENST00000497456,; A ENST00000393950 Transcript synonymous_variant 798/1191 516/708 172/235 P ccC/ccA 1 1 MOSPD3 HGNC HGNC:25078 protein_coding YES CCDS5701.1 ENSP00000377522 O75425 UPI000004A079 NM_023948.4 4/5 hmmpanther:PTHR10809:SF55,hmmpanther:PTHR10809 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.98679 1 1 1 1 0 A 2 1 10 100614871 100614871 C A 1 0 0 0 0 0 0 0 1 9679 637 22 2 2 MOSPD3 7 100614871 Silent SNP C C3L-00095_T 443332 100614871 58731102 343 3552 ZAN 0 . GRCh38 7 100793898 100793898 + Silent SNP C C A rs763131843 C3L-00095_T C3L-00095_N C C c.7866C>A p.= p.P2622P ENST00000613979 43/48 108 95 13 122 122 0 strelka-varscan-mutect ZAN,synonymous_variant,p.=,ENST00000613979,NM_003386.2;ZAN,synonymous_variant,p.=,ENST00000618565,;ZAN,intron_variant,,ENST00000620596,NM_173059.2;ZAN,intron_variant,,ENST00000546292,;ZAN,missense_variant,p.Pro2644His,ENST00000542585,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,;ZAN,intron_variant,,ENST00000538115,;ZAN,intron_variant,,ENST00000546213,; A ENST00000613979 Transcript synonymous_variant 8031/8669 7866/8439 2622/2812 P ccC/ccA rs763131843 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 43/48 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs763131843 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 100793898 100793898 C A 1 0 0 0 0 0 0 0 1 18074 610 22 2 2 ZAN 7 100793898 Silent SNP C C3L-00095_T 179027 100793898 58552075 344 3553 COL26A1 0 . GRCh38 7 101420022 101420022 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.204G>T p.= p.V68V ENST00000313669 2/13 266 250 16 324 324 0 strelka-varscan-mutect COL26A1,synonymous_variant,p.=,ENST00000313669,NM_001278563.2;COL26A1,synonymous_variant,p.=,ENST00000613501,NM_133457.4; T ENST00000313669 Transcript synonymous_variant 417/3033 204/1326 68/441 V gtG/gtT 1 1 COL26A1 HGNC HGNC:18038 protein_coding YES CCDS64739.1 ENSP00000318234 Q96A83 UPI000006F04C NM_001278563.2 2/13 PROSITE_profiles:PS51041,Pfam_domain:PF07546 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 101420022 101420022 G T 1 0 0 0 0 0 0 0 1 3473 1306 46 2 2 COL26A1 7 101420022 Silent SNP G C3L-00095_T 626124 101420022 57925951 345 3554 SRPK2 0 . GRCh38 7 105142254 105142254 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1297G>A p.Glu433Lys p.E433K ENST00000393651 11/16 328 301 27 400 400 0 strelka-mutect SRPK2,missense_variant,p.Glu422Lys,ENST00000357311,NM_182691.2;SRPK2,missense_variant,p.Glu433Lys,ENST00000393651,NM_182692.2;SRPK2,missense_variant,p.Glu422Lys,ENST00000489828,NM_001278273.1;SRPK2,missense_variant,p.Glu29Lys,ENST00000477925,;SRPK2,intron_variant,,ENST00000485455,;SRPK2,non_coding_transcript_exon_variant,,ENST00000466917,; T ENST00000393651 Transcript missense_variant 1385/3650 1297/2100 433/699 E/K Gaa/Aaa 1 -1 SRPK2 HGNC HGNC:11306 protein_coding YES CCDS34724.1 ENSP00000377262 P78362 UPI00001A4785 NM_182692.2 tolerated(0.34) 11/16 PROSITE_profiles:PS50011,SMART_domains:SM00220 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 105142254 105142254 C T 1 0 0 0 0 1 0 0 0 15521 922 32 3 3 SRPK2 7 105142254 Missense_Mutation SNP C C3L-00095_T 3722232 105142254 54203719 346 3555 ATXN7L1 0 . GRCh38 7 105665077 105665077 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.567G>T p.Arg189Ser p.R189S ENST00000419735 4/12 185 171 14 237 237 0 varscan-mutect ATXN7L1,missense_variant,p.Arg189Ser,ENST00000419735,NM_020725.1;ATXN7L1,missense_variant,p.Arg65Ser,ENST00000477775,NM_138495.1;ATXN7L1,missense_variant,p.Arg65Ser,ENST00000472195,;ATXN7L1,non_coding_transcript_exon_variant,,ENST00000472910,;ATXN7L1,non_coding_transcript_exon_variant,,ENST00000485652,;ATXN7L1,missense_variant,p.Arg65Ser,ENST00000474433,NM_001318229.1; A ENST00000419735 Transcript missense_variant 613/5417 567/2586 189/861 R/S agG/agT 1 -1 ATXN7L1 HGNC HGNC:22210 protein_coding YES CCDS47682.1 ENSP00000410759 Q9ULK2 UPI000162C85E NM_020725.1 tolerated(0.06) 4/12 hmmpanther:PTHR15117,hmmpanther:PTHR15117:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 105665077 105665077 C A 1 0 0 0 0 1 0 0 0 1370 622 22 2 2 ATXN7L1 7 105665077 Missense_Mutation SNP C C3L-00095_T 522823 105665077 53680896 347 3556 NRCAM 0 . GRCh38 7 108232368 108232368 + Missense_Mutation SNP G G T rs763460173 C3L-00095_T C3L-00095_N G G c.385C>A p.Arg129Ser p.R129S ENST00000379028 7/33 74 67 7 86 86 0 strelka-varscan-mutect NRCAM,missense_variant,p.Arg129Ser,ENST00000379028,;NRCAM,missense_variant,p.Arg129Ser,ENST00000413765,NM_001193582.1;NRCAM,missense_variant,p.Arg123Ser,ENST00000351718,NM_005010.4;NRCAM,missense_variant,p.Arg129Ser,ENST00000379024,NM_001193583.1,NM_001193584.1;NRCAM,missense_variant,p.Arg129Ser,ENST00000425651,NM_001037132.2;NRCAM,missense_variant,p.Arg124Ser,ENST00000379022,;NRCAM,missense_variant,p.Arg123Ser,ENST00000613830,;NRCAM,missense_variant,p.Arg123Ser,ENST00000417701,;NRCAM,downstream_gene_variant,,ENST00000456431,;NRCAM,downstream_gene_variant,,ENST00000442580,;NRCAM,downstream_gene_variant,,ENST00000419936,;NRCAM,downstream_gene_variant,,ENST00000418239,; T ENST00000379028 Transcript missense_variant 871/6685 385/3915 129/1304 R/S Cgc/Agc rs763460173,COSM5062102,COSM5062103,COSM5062104 1 -1 NRCAM HGNC HGNC:7994 protein_coding YES CCDS47686.1 ENSP00000368314 Q92823 UPI00005E2661 tolerated(0.16) 7/33 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs763460173 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 108232368 108232368 G T 1 0 0 0 0 1 0 0 0 10700 1145 40 1 1 NRCAM 7 108232368 Missense_Mutation SNP G C3L-00095_T 2567291 108232368 51113605 348 3557 PPP1R3A 0 . GRCh38 7 113880029 113880029 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000284601 4/4 96 85 11 95 95 0 strelka-varscan-mutect PPP1R3A,missense_variant,p.Gly355Trp,ENST00000284601,NM_002711.3;PPP1R3A,missense_variant,p.Gly34Trp,ENST00000449795,;PPP1R3A,3_prime_UTR_variant,,ENST00000284602,; A ENST00000284601 Transcript missense_variant 1132/4384 1063/3369 355/1122 G/W Ggg/Tgg COSM1635064,COSM4780671 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 deleterious(0.01) 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99946 1 1 1 1 0 A 3 1 10 113880029 113880029 C A 1 0 0 0 0 1 0 0 0 12492 623 22 2 2 PPP1R3A 7 113880029 Missense_Mutation SNP C C3L-00095_T 5647661 113880029 45465944 349 3558 LMOD2 0 . GRCh38 7 123662910 123662910 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1324C>A p.Pro442Thr p.P442T ENST00000458573 2/3 78 71 7 105 105 0 strelka-varscan-mutect LMOD2,missense_variant,p.Pro442Thr,ENST00000458573,NM_207163.1;LMOD2,intron_variant,,ENST00000456238,; A ENST00000458573 Transcript missense_variant 1481/2346 1324/1644 442/547 P/T Cct/Act 1 1 LMOD2 HGNC HGNC:6648 protein_coding YES CCDS47693.1 ENSP00000411932 Q6P5Q4 UPI0001572CCA NM_207163.1 deleterious(0.01) 2/3 hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF12,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 123662910 123662910 C A 1 0 0 0 0 1 0 0 0 8784 855 30 2 2 LMOD2 7 123662910 Missense_Mutation SNP C C3L-00095_T 9782881 123662910 35683063 350 3559 GPR37 0 . GRCh38 7 124764105 124764105 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.872A>G p.Tyr291Cys p.Y291C ENST00000303921 1/2 96 82 14 138 138 0 strelka-varscan-mutect GPR37,missense_variant,p.Tyr291Cys,ENST00000303921,NM_005302.3; C ENST00000303921 Transcript missense_variant 1523/3021 872/1842 291/613 Y/C tAc/tGc 1 -1 GPR37 HGNC HGNC:4494 protein_coding YES CCDS5792.1 ENSP00000306449 O15354 UPI0000001C92 NM_005302.3 tolerated(0.22) 1/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF32,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 124764105 124764105 T C 1 0 0 0 0 1 0 0 0 6576 1638 57 5 5 GPR37 7 124764105 Missense_Mutation SNP T C3L-00095_T 1101195 124764105 34581868 351 3560 KCP 0 . GRCh38 7 128907368 128907368 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.305C>A p.Ala102Asp p.A102D ENST00000610776 3/40 73 69 4 90 90 0 varscan-mutect KCP,missense_variant,p.Ala102Asp,ENST00000610776,;KCP,missense_variant,p.Ala102Asp,ENST00000613019,;KCP,missense_variant,p.Ala102Asp,ENST00000620378,NM_001135914.1;KCP,non_coding_transcript_exon_variant,,ENST00000612224,;KCP,missense_variant,p.Ala102Asp,ENST00000611280,;KCP,upstream_gene_variant,,ENST00000616669,; T ENST00000610776 Transcript missense_variant 348/5108 305/4887 102/1628 A/D gCc/gAc 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 tolerated(0.19) 3/40 Gene3D:2.10.70.10,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -9.295021 0.9999961 1 1 1 0 T 3 4 10 128907368 128907368 G T 1 0 0 0 0 1 0 0 0 8012 1203 42 2 2 KCP 7 128907368 Missense_Mutation SNP G C3L-00095_T 4143263 128907368 30438605 352 3561 NUP205 0 . GRCh38 7 135593006 135593006 + Silent SNP A A C rs775354528 C3L-00095_T C3L-00095_N A A c.1644A>C p.= p.A548A ENST00000285968 12/43 133 120 13 191 191 0 strelka-varscan-mutect NUP205,synonymous_variant,p.=,ENST00000285968,NM_015135.2;NUP205,upstream_gene_variant,,ENST00000607647,;NUP205,upstream_gene_variant,,ENST00000462316,; C ENST00000285968 Transcript synonymous_variant 1670/6266 1644/6039 548/2012 A gcA/gcC rs775354528 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 12/43 Pfam_domain:PF11894,hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 LOW 1 SNV 1 1 PASS rs775354528 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 135593006 135593006 A C 1 0 0 0 0 0 0 0 1 10824 175 7 5 5 NUP205 7 135593006 Silent SNP A C3L-00095_T 6685638 135593006 23752967 353 3562 CHRM2 0 . GRCh38 7 137015024 137015024 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.159C>A p.His53Gln p.H53Q ENST00000445907 3/3 315 290 25 452 450 2 strelka-varscan-mutect CHRM2,missense_variant,p.His53Gln,ENST00000445907,NM_001006630.1,NM_001006627.1;CHRM2,missense_variant,p.His53Gln,ENST00000401861,NM_000739.2,NM_001006626.1,NM_001006628.1;CHRM2,missense_variant,p.His53Gln,ENST00000453373,NM_001006631.1,NM_001006629.1;CHRM2,missense_variant,p.His53Gln,ENST00000320658,NM_001006632.1;AC009264.1,intron_variant,,ENST00000439694,;AC009264.1,intron_variant,,ENST00000425981,;AC009264.1,intron_variant,,ENST00000586239,;AC009264.1,intron_variant,,ENST00000597642,;AC009264.1,intron_variant,,ENST00000598184,;AC009264.1,intron_variant,,ENST00000593789,;AC009264.1,intron_variant,,ENST00000592183,; A ENST00000445907 Transcript missense_variant 687/5918 159/1401 53/466 H/Q caC/caA 1 1 CHRM2 HGNC HGNC:1951 protein_coding YES CCDS5843.1 ENSP00000399745 P08172 A4D1Q0 UPI0000050410 NM_001006630.1,NM_001006627.1 tolerated(1) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00243,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 137015024 137015024 C A 1 0 0 0 0 1 0 0 0 3137 506 18 2 2 CHRM2 7 137015024 Missense_Mutation SNP C C3L-00095_T 1422018 137015024 22330949 354 3563 KIAA1549 0 . GRCh38 7 138917699 138917699 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1927G>T p.Glu643Ter p.E643* ENST00000422774 2/20 142 130 12 220 219 1 strelka-varscan-mutect KIAA1549,stop_gained,p.Glu643Ter,ENST00000440172,NM_020910.2;KIAA1549,stop_gained,p.Glu643Ter,ENST00000422774,NM_001164665.1; A ENST00000422774 Transcript stop_gained 1976/6283 1927/5853 643/1950 E/* Gaa/Taa 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 2/20 Low_complexity_(Seg):seg,hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590 HIGH 1 SNV 1 1 PASS rs992612288 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 138917699 138917699 C A 1 0 0 0 0 0 1 0 0 8120 864 30 2 2 KIAA1549 7 138917699 Nonsense_Mutation SNP C C3L-00095_T 1902675 138917699 20428274 355 3564 LUC7L2 0 . GRCh38 7 139417717 139417717 + Missense_Mutation SNP G G T rs772791148 C3L-00095_T C3L-00095_N G G c.989G>T p.Arg330Leu p.R330L ENST00000354926 9/10 123 115 8 126 126 0 strelka-varscan-mutect LUC7L2,missense_variant,p.Arg329Leu,ENST00000619796,NM_001270643.1;LUC7L2,missense_variant,p.Arg330Leu,ENST00000354926,NM_016019.4;LUC7L2,missense_variant,p.Arg327Leu,ENST00000263545,;C7orf55-LUC7L2,missense_variant,p.Arg396Leu,ENST00000541515,NM_001244584.2;LUC7L2,missense_variant,p.Arg327Leu,ENST00000541170,NM_001244585.1;LUC7L2,non_coding_transcript_exon_variant,,ENST00000482860,;LUC7L2,3_prime_UTR_variant,,ENST00000456182,;LUC7L2,non_coding_transcript_exon_variant,,ENST00000498518,;LUC7L2,downstream_gene_variant,,ENST00000463912,; T ENST00000354926 Transcript missense_variant 1343/2645 989/1179 330/392 R/L cGa/cTa rs772791148 1 1 LUC7L2 HGNC HGNC:21608 protein_coding YES CCDS43656.1 ENSP00000347005 Q9Y383 UPI000003F000 NM_016019.4 deleterious_low_confidence(0.01) 9/10 hmmpanther:PTHR12375,hmmpanther:PTHR12375:SF28,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs772791148 . 0 207 3 0 0 0 0 0 -15.73806 1 1 1 1 0 T 3 4 10 139417717 139417717 G T 1 0 0 0 0 1 0 0 0 8990 1058 37 1 1 LUC7L2 7 139417717 Missense_Mutation SNP G C3L-00095_T 500018 139417717 19928256 356 3565 DENND2A 0 . GRCh38 7 140522101 140522101 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.2666-1G>T p.X889_splice ENST00000275884 124 116 8 158 158 0 strelka-varscan-mutect DENND2A,splice_acceptor_variant,,ENST00000275884,NM_001318052.1;DENND2A,splice_acceptor_variant,,ENST00000496613,;DENND2A,splice_acceptor_variant,,ENST00000537639,NM_015689.3;DENND2A,splice_acceptor_variant,,ENST00000461883,; A ENST00000275884 Transcript splice_acceptor_variant -/3735 2666/3030 889/1009 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 16/18 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 140522101 140522101 C A 1 0 0 0 0 0 0 1 0 4233 695 24 2 2 DENND2A 7 140522101 Splice_Site SNP C C3L-00095_T 1104384 140522101 18823872 357 3566 MGAM 0 . GRCh38 7 142055615 142055615 + Silent SNP C C A C3L-00095_T C3L-00095_N C C c.3372C>A p.= p.T1124T ENST00000549489 28/48 467 430 37 526 525 1 strelka-varscan-mutect MGAM,synonymous_variant,p.=,ENST00000475668,;MGAM,synonymous_variant,p.=,ENST00000549489,NM_004668.2;MGAM,synonymous_variant,p.=,ENST00000620571,; A ENST00000549489 Transcript synonymous_variant 3467/6525 3372/5574 1124/1857 T acC/acA COSM4919046,COSM4919047,COSM4919048 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 28/48 Pfam_domain:PF16863,Superfamily_domains:SSF74650 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 142055615 142055615 C A 1 0 0 0 0 0 0 0 1 9499 610 22 2 2 MGAM 7 142055615 Silent SNP C C3L-00095_T 1533514 142055615 17290358 358 3567 MGAM2 0 . GRCh38 7 142197464 142197464 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.4697G>T p.Arg1566Ile p.R1566I ENST00000477922 41/48 260 244 16 286 286 0 strelka-varscan-mutect MGAM2,missense_variant,p.Arg1566Ile,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; T ENST00000477922 Transcript missense_variant 4751/7867 4697/7548 1566/2515 R/I aGa/aTa 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 41/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Low_complexity_(Seg):seg,Superfamily_domains:SSF51445 MODERATE 1 SNV 5 1 PASS rs1408540085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 142197464 142197464 G T 1 0 0 0 0 1 0 0 0 9500 942 33 2 2 MGAM2 7 142197464 Missense_Mutation SNP G C3L-00095_T 141849 142197464 17148509 359 3568 TRPV5 0 . GRCh38 7 142928190 142928190 + Silent SNP C C A rs768142599 C3L-00095_T C3L-00095_N C C c.807G>T p.= p.T269T ENST00000265310 7/15 255 225 30 306 306 0 strelka-varscan-mutect TRPV5,synonymous_variant,p.=,ENST00000265310,NM_019841.6;TRPV5,synonymous_variant,p.=,ENST00000442623,;TRPV5,intron_variant,,ENST00000439304,; A ENST00000265310 Transcript synonymous_variant 1156/2952 807/2190 269/729 T acG/acT rs768142599 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 7/15 hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870 LOW 1 SNV 1 1 PASS rs768142599 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 142928190 142928190 C A 1 0 0 0 0 0 0 0 1 17105 523 19 1 1 TRPV5 7 142928190 Silent SNP C C3L-00095_T 730726 142928190 16417783 360 3569 TRPV5 0 . GRCh38 7 142928773 142928773 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.680A>T p.Asp227Val p.D227V ENST00000265310 6/15 344 295 49 365 365 0 strelka-varscan-mutect TRPV5,missense_variant,p.Asp227Val,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Asp227Val,ENST00000442623,;TRPV5,missense_variant,p.Asp221Val,ENST00000439304,; A ENST00000265310 Transcript missense_variant 1029/2952 680/2190 227/729 D/V gAc/gTc 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 deleterious(0.04) 6/15 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,Superfamily_domains:SSF48403,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS rs1159620418 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 142928773 142928773 T A 1 0 0 0 0 1 0 0 0 17105 1667 58 4 4 TRPV5 7 142928773 Missense_Mutation SNP T C3L-00095_T 583 142928773 16417200 361 3570 OR2A25 0 . GRCh38 7 144074363 144074363 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.144C>T p.= p.I48I ENST00000408898 1/1 480 408 72 550 550 0 strelka-varscan-mutect OR2A25,synonymous_variant,p.=,ENST00000408898,NM_001004488.1;OR2A41P,upstream_gene_variant,,ENST00000473586,; T ENST00000408898 Transcript synonymous_variant 182/1014 144/933 48/310 I atC/atT 1 1 OR2A25 HGNC HGNC:19562 protein_coding YES CCDS43669.1 ENSP00000386167 A4D2G3 A0A126GVV5 UPI00002373C5 NM_001004488.1 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF146,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 144074363 144074363 C T 1 0 0 0 0 0 0 0 1 11055 903 32 3 3 OR2A25 7 144074363 Silent SNP C C3L-00095_T 1145590 144074363 15271610 362 3571 ARHGEF5 0 . GRCh38 7 144365252 144365252 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.2583G>T p.Arg861Ser p.R861S ENST00000056217 2/15 341 322 19 407 407 0 varscan-mutect ARHGEF5,missense_variant,p.Arg861Ser,ENST00000056217,NM_005435.3;ARHGEF5,missense_variant,p.Arg115Ser,ENST00000474817,;ARHGEF5,intron_variant,,ENST00000498580,;ARHGEF5,upstream_gene_variant,,ENST00000471847,; T ENST00000056217 Transcript missense_variant 2757/5544 2583/4794 861/1597 R/S agG/agT COSM3259027 1 1 ARHGEF5 HGNC HGNC:13209 protein_coding YES CCDS34771.1 ENSP00000056217 Q12774 UPI00004028DC NM_005435.3 deleterious(0) 2/15 hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF2,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 144365252 144365252 G T 1 0 0 0 0 1 0 0 0 1045 1165 41 2 2 ARHGEF5 7 144365252 Missense_Mutation SNP G C3L-00095_T 290889 144365252 14980721 363 3572 SSPO 0 . GRCh38 7 149827902 149827902 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.14908C>T p.Gln4970Ter p.Q4970* ENST00000378016 102/107 180 169 11 247 247 0 strelka-varscan-mutect SSPO,stop_gained,p.Gln4970Ter,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000492965,;SSPO,downstream_gene_variant,,ENST00000488835,;SSPO,downstream_gene_variant,,ENST00000461331,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,; T ENST00000378016 Transcript stop_gained 14908/15589 14908/15453 4970/5150 Q/* Cag/Tag 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 102/107 Gene3D:2.10.25.10,Superfamily_domains:SSF57567,hmmpanther:PTHR11339:SF294,hmmpanther:PTHR11339 HIGH 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -14.07291 0.9999587 1 1 1 0 T 4 4 10 149827902 149827902 C T 1 0 0 0 0 0 1 0 0 15566 595 21 3 3 SSPO 7 149827902 Nonsense_Mutation SNP C C3L-00095_T 5462650 149827902 9518071 364 3573 ASB10 0 . GRCh38 7 151181331 151181331 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.712G>C p.Gly238Arg p.G238R ENST00000420175 3/6 170 161 9 221 221 0 strelka-mutect ASB10,missense_variant,p.Gly238Arg,ENST00000275838,NM_001142460.1;ASB10,missense_variant,p.Gly223Arg,ENST00000377867,NM_080871.3;ASB10,missense_variant,p.Gly238Arg,ENST00000420175,NM_001142459.1; G ENST00000420175 Transcript missense_variant 737/1694 712/1404 238/467 G/R Ggg/Cgg 1 -1 ASB10 HGNC HGNC:17185 protein_coding YES CCDS47750.2 ENSP00000391137 Q8WXI3 UPI000020F32F NM_001142459.1 deleterious(0) 3/6 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF33,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1448233333 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 151181331 151181331 C G 1 0 0 0 0 1 0 0 0 1156 623 22 4 4 ASB10 7 151181331 Missense_Mutation SNP C C3L-00095_T 1353429 151181331 8164642 365 3574 EN2 0 . GRCh38 7 155459033 155459033 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.656G>C p.Cys219Ser p.C219S ENST00000297375 1/2 233 217 16 293 293 0 strelka-varscan-mutect EN2,missense_variant,p.Cys219Ser,ENST00000297375,NM_001427.3;AC008060.8,upstream_gene_variant,,ENST00000419225,; C ENST00000297375 Transcript missense_variant 905/3395 656/1002 219/333 C/S tGt/tCt 1 1 EN2 HGNC HGNC:3343 protein_coding YES CCDS5940.1 ENSP00000297375 P19622 UPI000012CA05 NM_001427.3 deleterious(0) 1/2 hmmpanther:PTHR24341:SF5,hmmpanther:PTHR24341 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 155459033 155459033 G C 1 0 0 0 0 1 0 0 0 4952 1377 48 4 4 EN2 7 155459033 Missense_Mutation SNP G C3L-00095_T 4277702 155459033 3886940 366 3575 DLGAP2 0 . GRCh38 8 1632910 1632910 + Silent SNP C C A rs755779128 C3L-00095_T C3L-00095_N C C c.1434C>A p.= p.A478A ENST00000612087 5/11 168 152 16 207 207 0 strelka-varscan-mutect DLGAP2,synonymous_variant,p.=,ENST00000612087,NM_001277161.1;DLGAP2,synonymous_variant,p.=,ENST00000520901,;DLGAP2,synonymous_variant,p.=,ENST00000637795,;DLGAP2,synonymous_variant,p.=,ENST00000421627,;DLGAP2,synonymous_variant,p.=,ENST00000637152,NM_004745.4; A ENST00000612087 Transcript synonymous_variant 1568/10088 1434/2886 478/961 A gcC/gcA rs755779128 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 5/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3 LOW 1 SNV 5 1 PASS rs755779128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 1632910 1632910 C A 1 0 0 0 0 0 0 0 1 4367 610 22 2 2 DLGAP2 8 1632910 Silent SNP C C3L-00095_T 1632910 143505726 367 3576 PRSS55 0 . GRCh38 8 10525725 10525725 + Missense_Mutation SNP C C A rs780054130 C3L-00095_T C3L-00095_N C C c.140C>A p.Pro47His p.P47H ENST00000328655 1/5 108 97 11 138 138 0 varscan-mutect PRSS55,missense_variant,p.Pro47His,ENST00000328655,NM_198464.3;PRSS55,missense_variant,p.Pro47His,ENST00000522210,NM_001197020.1;PRSS51,intron_variant,,ENST00000637190,;PRSS51,intron_variant,,ENST00000523024,;PRSS55,upstream_gene_variant,,ENST00000518641,; A ENST00000328655 Transcript missense_variant 180/1124 140/1059 47/352 P/H cCc/cAc rs780054130 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 deleterious(0.04) 1/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF191,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs780054130 . 0 207 3 0 0 0 0 0 -19.99823 1 1 1 1 0 A 3 1 10 10525725 10525725 C A 1 0 0 0 0 1 0 0 0 12783 623 22 2 2 PRSS55 8 10525725 Missense_Mutation SNP C C3L-00095_T 8892815 10525725 134612911 368 3577 XKR6 0 . GRCh38 8 11201280 11201280 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.60G>T p.= p.L20L ENST00000416569 1/3 212 199 13 300 300 0 strelka-varscan-mutect XKR6,synonymous_variant,p.=,ENST00000416569,NM_173683.3;XKR6,synonymous_variant,p.=,ENST00000297303,;AF131215.8,upstream_gene_variant,,ENST00000602443,;XKR6,upstream_gene_variant,,ENST00000529336,; A ENST00000416569 Transcript synonymous_variant 87/3382 60/1926 20/641 L ctG/ctT 1 -1 XKR6 HGNC HGNC:27806 protein_coding YES CCDS5978.2 ENSP00000416707 Q5GH73 UPI00004C7A9D NM_173683.3 1/3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 11201280 11201280 C A 1 0 0 0 0 0 0 0 1 17994 581 21 2 2 XKR6 8 11201280 Silent SNP C C3L-00095_T 675555 11201280 133937356 369 3578 MTUS1 0 . GRCh38 8 17754642 17754642 + Missense_Mutation SNP T T G rs200555209 C3L-00095_T C3L-00095_N T T c.1166A>C p.Gln389Pro p.Q389P ENST00000262102 2/15 228 213 15 355 355 0 strelka-varscan-mutect MTUS1,missense_variant,p.Gln389Pro,ENST00000381869,NM_001001925.2;MTUS1,missense_variant,p.Gln389Pro,ENST00000262102,NM_001001924.2;MTUS1,missense_variant,p.Gln389Pro,ENST00000519263,;MTUS1,downstream_gene_variant,,ENST00000518755,;MTUS1,downstream_gene_variant,,ENST00000518891,;MTUS1,missense_variant,p.Gln124Pro,ENST00000520196,;MTUS1,non_coding_transcript_exon_variant,,ENST00000523718,; G ENST00000262102 Transcript missense_variant 1391/6160 1166/3813 389/1270 Q/P cAa/cCa rs200555209 1 -1 MTUS1 HGNC HGNC:29789 protein_coding YES CCDS43717.1 ENSP00000262102 Q9ULD2 UPI000003FF3C NM_001001924.2 tolerated(0.17) 2/15 hmmpanther:PTHR24200,hmmpanther:PTHR24200:SF7 MODERATE 1 SNV 1 1 PASS rs200555209 . 0 207 0 0 0 0 0 2 -10.02909 0 0 1 0 0 G 3 3 10 17754642 17754642 T G 1 0 0 0 0 1 0 0 0 9963 1812 63 5 5 MTUS1 8 17754642 Missense_Mutation SNP T C3L-00095_T 6553362 17754642 127383994 370 3579 WRN 0 . GRCh38 8 31157382 31157382 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.3834G>C p.Glu1278Asp p.E1278D ENST00000298139 33/35 249 232 17 342 342 0 strelka-mutect WRN,missense_variant,p.Glu1278Asp,ENST00000298139,NM_000553.4;WRN,non_coding_transcript_exon_variant,,ENST00000521620,; C ENST00000298139 Transcript missense_variant 4083/5215 3834/4299 1278/1432 E/D gaG/gaC 1 1 WRN HGNC HGNC:12791 protein_coding YES CCDS6082.1 ENSP00000298139 Q14191 UPI000013E49D NM_000553.4 tolerated(0.15) 33/35 hmmpanther:PTHR13710:SF87,hmmpanther:PTHR13710,Pfam_domain:PF14493 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 31157382 31157382 G C 1 0 0 0 0 1 0 0 0 17959 933 33 4 4 WRN 8 31157382 Missense_Mutation SNP G C3L-00095_T 13402740 31157382 113981254 371 3580 NRG1 0 . GRCh38 8 32764190 32764190 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.1726A>T p.Ser576Cys p.S576C ENST00000287842 13/13 346 325 21 467 467 0 strelka-varscan-mutect NRG1,missense_variant,p.Ser568Cys,ENST00000356819,NM_013957.3;NRG1,missense_variant,p.Ser644Cys,ENST00000523534,;NRG1,missense_variant,p.Ser576Cys,ENST00000287842,NM_013956.3;NRG1,missense_variant,p.Ser571Cys,ENST00000405005,NM_013964.3;NRG1,missense_variant,p.Ser521Cys,ENST00000519301,NM_001160001.1;NRG1,3_prime_UTR_variant,,ENST00000539990,NM_001159996.1;NRG1,downstream_gene_variant,,ENST00000523079,NM_001160008.1,NM_001160004.1;NRG1,downstream_gene_variant,,ENST00000521670,NM_013960.3;NRG1,downstream_gene_variant,,ENST00000518104,NM_001159995.1,NM_001159999.1; T ENST00000287842 Transcript missense_variant 1818/2035 1726/1938 576/645 S/C Agt/Tgt 1 1 NRG1 HGNC HGNC:7997 protein_coding YES CCDS6083.1 ENSP00000287842 Q02297 UPI000013DED7 NM_013956.3 tolerated(0.25) 13/13 Low_complexity_(Seg):seg,hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF7,Pfam_domain:PF02158 MODERATE 1 SNV 1 1 PASS rs1395641427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32764190 32764190 A T 1 0 0 0 0 1 0 0 0 10705 188 7 4 4 NRG1 8 32764190 Missense_Mutation SNP A C3L-00095_T 1606808 32764190 112374446 372 3581 PRKDC 0 . GRCh38 8 47800987 47800987 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.9923-1G>T p.X3308_splice ENST00000314191 179 169 10 206 206 0 strelka-varscan-mutect PRKDC,splice_acceptor_variant,,ENST00000314191,NM_006904.6;PRKDC,splice_acceptor_variant,,ENST00000338368,NM_001081640.1;Y_RNA,downstream_gene_variant,,ENST00000384719,; A ENST00000314191 Transcript splice_acceptor_variant -/13509 9923/12387 3308/4128 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 70/85 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 47800987 47800987 C A 1 0 0 0 0 0 0 1 0 12654 927 32 2 2 PRKDC 8 47800987 Splice_Site SNP C C3L-00095_T 15036797 47800987 97337649 373 3582 SNTG1 0 . GRCh38 8 50704631 50704631 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1070G>T p.Cys357Phe p.C357F ENST00000522124 16/19 284 264 20 446 443 3 strelka-varscan-mutect SNTG1,missense_variant,p.Cys357Phe,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Cys357Phe,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Cys357Phe,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,;SNTG1,3_prime_UTR_variant,,ENST00000524004,; T ENST00000522124 Transcript missense_variant 1731/3504 1070/1554 357/517 C/F tGc/tTc 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 16/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 50704631 50704631 G T 1 0 0 0 0 1 0 0 0 15194 1319 46 2 2 SNTG1 8 50704631 Missense_Mutation SNP G C3L-00095_T 2903644 50704631 94434005 374 3583 OPRK1 0 . GRCh38 8 53250900 53250900 + Missense_Mutation SNP G G C rs758030791 C3L-00095_T C3L-00095_N G G c.138C>G p.Asp46Glu p.D46E ENST00000265572 2/4 234 204 30 319 319 0 strelka-varscan-mutect OPRK1,missense_variant,p.Asp46Glu,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,missense_variant,p.Asp32Glu,ENST00000613482,;OPRK1,missense_variant,p.Asp46Glu,ENST00000520287,;OPRK1,5_prime_UTR_variant,,ENST00000612786,NM_001282904.1;OPRK1,missense_variant,p.Asp46Glu,ENST00000522508,; C ENST00000265572 Transcript missense_variant 436/5014 138/1143 46/380 D/E gaC/gaG rs758030791,COSM4333181,COSM5078347 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 tolerated(0.38) 2/4 Gene3D:1.20.1070.10,Prints_domain:PR00532,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF1,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs758030791 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 10 53250900 53250900 G C 1 0 0 0 0 1 0 0 0 10961 1136 40 4 4 OPRK1 8 53250900 Missense_Mutation SNP G C3L-00095_T 2546269 53250900 91887736 375 3584 TRPA1 0 . GRCh38 8 72055781 72055781 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1269G>T p.Gln423His p.Q423H ENST00000262209 11/27 303 283 20 365 365 0 varscan-mutect TRPA1,missense_variant,p.Gln423His,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Gln275His,ENST00000523582,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;MSC-AS1,downstream_gene_variant,,ENST00000519751,;MSC-AS1,downstream_gene_variant,,ENST00000524152,;TRPA1,upstream_gene_variant,,ENST00000520788,; A ENST00000262209 Transcript missense_variant 1477/5223 1269/3360 423/1119 Q/H caG/caT 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 tolerated(0.24) 11/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs764890261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 72055781 72055781 C A 1 0 0 0 0 1 0 0 0 17082 680 24 2 2 TRPA1 8 72055781 Missense_Mutation SNP C C3L-00095_T 18804881 72055781 73082855 376 3585 POP1 0 . GRCh38 8 98156344 98156344 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2352G>T p.Glu784Asp p.E784D ENST00000401707 15/16 85 66 19 112 111 1 strelka-varscan-mutect POP1,missense_variant,p.Glu784Asp,ENST00000401707,NM_001145860.1,NM_001145861.1;POP1,missense_variant,p.Glu784Asp,ENST00000349693,NM_015029.2;POP1,non_coding_transcript_exon_variant,,ENST00000517435,; T ENST00000401707 Transcript missense_variant 2433/4719 2352/3075 784/1024 E/D gaG/gaT 1 1 POP1 HGNC HGNC:30129 protein_coding YES CCDS6277.1 ENSP00000385787 Q99575 UPI0000131F33 NM_001145860.1,NM_001145861.1 tolerated(0.21) 15/16 hmmpanther:PTHR22731,hmmpanther:PTHR22731:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 98156344 98156344 G T 1 0 0 0 0 1 0 0 0 12365 933 33 2 2 POP1 8 98156344 Missense_Mutation SNP G C3L-00095_T 26100563 98156344 46982292 377 3586 STK3 0 . GRCh38 8 98774804 98774804 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.126G>T p.= p.L42L ENST00000523601 4/13 209 183 26 114 114 0 strelka-mutect STK3,synonymous_variant,p.=,ENST00000523601,NM_001256312.1;STK3,synonymous_variant,p.=,ENST00000419617,NM_006281.3;STK3,synonymous_variant,p.=,ENST00000617590,NM_001256313.1;STK3,synonymous_variant,p.=,ENST00000518165,;STK3,synonymous_variant,p.=,ENST00000424861,;STK3,synonymous_variant,p.=,ENST00000521649,; A ENST00000523601 Transcript synonymous_variant 526/3107 126/1560 42/519 L ctG/ctT 1 -1 STK3 HGNC HGNC:11406 protein_coding YES CCDS59108.1 ENSP00000429744 Q13188 UPI00004FB517 NM_001256312.1 4/13 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF425 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 98774804 98774804 C A 1 0 0 0 0 0 0 0 1 15672 813 29 2 2 STK3 8 98774804 Silent SNP C C3L-00095_T 618460 98774804 46363832 378 3587 CSMD3 0 . GRCh38 8 112352514 112352514 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.6157C>A p.Pro2053Thr p.P2053T ENST00000297405 39/71 331 278 53 244 244 0 strelka-varscan-mutect CSMD3,missense_variant,p.Pro2053Thr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro2013Thr,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro1949Thr,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Pro1323Thr,ENST00000339701,; T ENST00000297405 Transcript missense_variant 6402/13212 6157/11124 2053/3707 P/T Cct/Act 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.01) 39/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 112352514 112352514 G T 1 0 0 0 0 1 0 0 0 3747 1174 41 2 2 CSMD3 8 112352514 Missense_Mutation SNP G C3L-00095_T 13577710 112352514 32786122 379 3588 CSMD3 0 . GRCh38 8 112975930 112975930 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1249C>A p.Pro417Thr p.P417T ENST00000297405 7/71 158 146 12 219 218 1 strelka-varscan-mutect CSMD3,missense_variant,p.Pro417Thr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro377Thr,ENST00000343508,NM_198124.1;CSMD3,intron_variant,,ENST00000455883,NM_052900.2; T ENST00000297405 Transcript missense_variant 1494/13212 1249/11124 417/3707 P/T Cct/Act 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(1) 7/71 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 112975930 112975930 G T 1 0 0 0 0 1 0 0 0 3747 1174 41 2 2 CSMD3 8 112975930 Missense_Mutation SNP G C3L-00095_T 623416 112975930 32162706 380 3589 FER1L6 0 . GRCh38 8 124035333 124035333 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.2343G>C p.= p.L781L ENST00000522917 19/41 255 235 20 286 286 0 strelka-varscan-mutect FER1L6,synonymous_variant,p.=,ENST00000522917,NM_001039112.2;FER1L6-AS1,intron_variant,,ENST00000518567,;RP11-959I15.4,downstream_gene_variant,,ENST00000522005,; C ENST00000522917 Transcript synonymous_variant 2549/6051 2343/5574 781/1857 L ctG/ctC 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 19/41 hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546,Pfam_domain:PF08150,SMART_domains:SM01201 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 124035333 124035333 G C 1 0 0 0 0 0 0 0 1 5678 1364 48 4 4 FER1L6 8 124035333 Silent SNP G C3L-00095_T 11059403 124035333 21103303 381 3590 FER1L6 0 . GRCh38 8 124082372 124082372 + Missense_Mutation SNP C C A rs558150924 C3L-00095_T C3L-00095_N C C c.4305C>A p.Asp1435Glu p.D1435E ENST00000522917 33/41 236 207 29 247 246 1 strelka-varscan-mutect FER1L6,missense_variant,p.Asp1435Glu,ENST00000522917,NM_001039112.2;FER1L6-AS2,intron_variant,,ENST00000520031,; A ENST00000522917 Transcript missense_variant 4511/6051 4305/5574 1435/1857 D/E gaC/gaA rs558150924 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 deleterious(0.01) 33/41 PROSITE_profiles:PS50004,hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs558150924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 124082372 124082372 C A 1 0 0 0 0 1 0 0 0 5678 506 18 2 2 FER1L6 8 124082372 Missense_Mutation SNP C C3L-00095_T 47039 124082372 21056264 382 3591 COL22A1 0 . GRCh38 8 138760281 138760281 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1864C>A p.Pro622Thr p.P622T ENST00000303045 18/65 116 110 6 105 105 0 strelka-varscan-mutect COL22A1,missense_variant,p.Pro622Thr,ENST00000303045,NM_152888.2;COL22A1,intron_variant,,ENST00000435777,; T ENST00000303045 Transcript missense_variant 2311/6346 1864/4881 622/1626 P/T Ccc/Acc 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.14) 18/65 hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 138760281 138760281 G T 1 0 0 0 0 1 0 0 0 3469 1203 42 2 2 COL22A1 8 138760281 Missense_Mutation SNP G C3L-00095_T 14677909 138760281 6378355 383 3592 KCNK9 0 . GRCh38 8 139618540 139618540 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.843C>A p.= p.P281P ENST00000520439 2/2 239 225 14 219 219 0 strelka-mutect KCNK9,synonymous_variant,p.=,ENST00000520439,NM_001282534.1;KCNK9,synonymous_variant,p.=,ENST00000303015,;KCNK9,upstream_gene_variant,,ENST00000523477,;KCNK9,upstream_gene_variant,,ENST00000519923,;KCNK9,synonymous_variant,p.=,ENST00000522317,; T ENST00000520439 Transcript synonymous_variant 907/1441 843/1125 281/374 P ccC/ccA 1 -1 KCNK9 HGNC HGNC:6283 protein_coding YES CCDS6377.1 ENSP00000430676 Q9NPC2 A0A024R9H3 UPI000000D8AC NM_001282534.1 2/2 hmmpanther:PTHR11003:SF75,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 139618540 139618540 G T 1 0 0 0 0 0 0 0 1 7989 1335 47 2 2 KCNK9 8 139618540 Silent SNP G C3L-00095_T 858259 139618540 5520096 384 3593 JRK 0 . GRCh38 8 142665414 142665414 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.645G>T p.= p.R215R ENST00000612905 2/2 228 194 34 255 255 0 strelka-varscan-mutect JRK,synonymous_variant,p.=,ENST00000612905,NM_003724.3;JRK,synonymous_variant,p.=,ENST00000614134,;JRK,synonymous_variant,p.=,ENST00000615982,NM_001279352.1;JRK,synonymous_variant,p.=,ENST00000571961,NM_001077527.2;JRK,downstream_gene_variant,,ENST00000503272,;PSCA,upstream_gene_variant,,ENST00000505305,;PSCA,upstream_gene_variant,,ENST00000510969,;JRK,downstream_gene_variant,,ENST00000591357,;JRK,upstream_gene_variant,,ENST00000506774,; A ENST00000612905 Transcript synonymous_variant 1170/9124 645/1707 215/568 R cgG/cgT 1 -1 JRK HGNC HGNC:6199 protein_coding YES CCDS75796.1 ENSP00000482410 Q86XJ5 UPI000000DA37 NM_003724.3 2/2 hmmpanther:PTHR19303:SF191,hmmpanther:PTHR19303,Pfam_domain:PF03184 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 142665414 142665414 C A 1 0 0 0 0 0 0 0 1 7876 726 26 2 2 JRK 8 142665414 Silent SNP C C3L-00095_T 3046874 142665414 2473222 385 3594 CYP11B2 0 . GRCh38 8 142913366 142913366 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1040C>T p.Ala347Val p.A347V ENST00000323110 6/9 416 391 25 406 406 0 varscan-mutect CYP11B2,missense_variant,p.Ala347Val,ENST00000323110,NM_000498.3;GML,intron_variant,,ENST00000522728,; A ENST00000323110 Transcript missense_variant 1043/2936 1040/1512 347/503 A/V gCc/gTc 1 -1 CYP11B2 HGNC HGNC:2592 protein_coding YES CCDS6393.1 ENSP00000325822 P19099 UPI00001282CF NM_000498.3 deleterious(0.04) 6/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 142913366 142913366 G A 1 0 0 0 0 1 0 0 0 3949 1203 42 3 3 CYP11B2 8 142913366 Missense_Mutation SNP G C3L-00095_T 247952 142913366 2225270 386 3595 NAPRT 0 . GRCh38 8 143576431 143576431 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.1022+1G>T p.X341_splice ENST00000449291 62 52 10 59 59 0 strelka-varscan-mutect NAPRT,splice_donor_variant,,ENST00000449291,NM_145201.5;NAPRT,splice_donor_variant,,ENST00000435154,;NAPRT,splice_donor_variant,,ENST00000426292,NM_001286829.1;MROH6,upstream_gene_variant,,ENST00000398882,NM_001100878.1;EEF1D,downstream_gene_variant,,ENST00000532741,;EEF1D,downstream_gene_variant,,ENST00000423316,NM_001130053.2;EEF1D,downstream_gene_variant,,ENST00000618139,;EEF1D,downstream_gene_variant,,ENST00000442189,NM_032378.4;MROH6,upstream_gene_variant,,ENST00000529971,;EEF1D,downstream_gene_variant,,ENST00000317198,NM_001130057.2;EEF1D,downstream_gene_variant,,ENST00000419152,NM_001130055.2;EEF1D,downstream_gene_variant,,ENST00000529272,;EEF1D,downstream_gene_variant,,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,downstream_gene_variant,,ENST00000530445,;EEF1D,downstream_gene_variant,,ENST00000524624,;EEF1D,downstream_gene_variant,,ENST00000534380,;EEF1D,downstream_gene_variant,,ENST00000526838,NM_001195203.1;EEF1D,downstream_gene_variant,,ENST00000528610,NM_001130056.2;EEF1D,downstream_gene_variant,,ENST00000530191,;EEF1D,downstream_gene_variant,,ENST00000533204,;EEF1D,downstream_gene_variant,,ENST00000531621,;EEF1D,downstream_gene_variant,,ENST00000531218,;EEF1D,downstream_gene_variant,,ENST00000533494,;EEF1D,downstream_gene_variant,,ENST00000530616,;EEF1D,downstream_gene_variant,,ENST00000533749,;EEF1D,downstream_gene_variant,,ENST00000534377,;EEF1D,downstream_gene_variant,,ENST00000530109,;EEF1D,downstream_gene_variant,,ENST00000529516,;EEF1D,downstream_gene_variant,,ENST00000529576,;EEF1D,downstream_gene_variant,,ENST00000532400,;EEF1D,downstream_gene_variant,,ENST00000528382,;RP11-661A12.9,intron_variant,,ENST00000531730,;RP11-661A12.7,upstream_gene_variant,,ENST00000529247,;RP11-661A12.8,upstream_gene_variant,,ENST00000623257,;NAPRT,splice_donor_variant,,ENST00000340490,;NAPRT,splice_donor_variant,,ENST00000525583,;NAPRT,splice_donor_variant,,ENST00000488096,;NAPRT,splice_donor_variant,,ENST00000532645,;NAPRT,non_coding_transcript_exon_variant,,ENST00000464332,;EEF1D,downstream_gene_variant,,ENST00000527741,;EEF1D,downstream_gene_variant,,ENST00000526786,;NAPRT,downstream_gene_variant,,ENST00000480946,;EEF1D,downstream_gene_variant,,ENST00000524397,;EEF1D,downstream_gene_variant,,ENST00000529007,;EEF1D,downstream_gene_variant,,ENST00000533833,;EEF1D,downstream_gene_variant,,ENST00000534232,;NAPRT,downstream_gene_variant,,ENST00000462059,;NAPRT,upstream_gene_variant,,ENST00000460623,;EEF1D,downstream_gene_variant,,ENST00000530848,;NAPRT,downstream_gene_variant,,ENST00000491904,;NAPRT,upstream_gene_variant,,ENST00000529179,;NAPRT,upstream_gene_variant,,ENST00000498076,; A ENST00000449291 Transcript splice_donor_variant -/1965 1022/1617 341/538 1 -1 NAPRT HGNC HGNC:30450 protein_coding YES CCDS6403.2 ENSP00000401508 Q6XQN6 UPI000058EC33 NM_145201.5 7/12 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99964 1 1 1 1 0 A 5 1 10 143576431 143576431 C A 1 0 0 0 0 0 0 1 0 10175 579 20 2 2 NAPRT 8 143576431 Splice_Site SNP C C3L-00095_T 663065 143576431 1562205 387 3596 ZNF250 0 . GRCh38 8 144882720 144882720 + Missense_Mutation SNP C C T C3L-00095_T C3L-00095_N C C c.478G>A p.Glu160Lys p.E160K ENST00000292579 6/6 309 282 27 325 325 0 strelka-varscan-mutect ZNF250,missense_variant,p.Glu160Lys,ENST00000292579,NM_021061.4;ZNF250,missense_variant,p.Glu155Lys,ENST00000417550,NM_001109689.3;ZNF250,missense_variant,p.Glu155Lys,ENST00000533622,;ZNF250,missense_variant,p.Glu134Lys,ENST00000533221,;ZNF250,downstream_gene_variant,,ENST00000525694,;ZNF250,intron_variant,,ENST00000533543,;ZNF250,intron_variant,,ENST00000529780,;ZNF250,intron_variant,,ENST00000528258,; T ENST00000292579 Transcript missense_variant 595/6364 478/1683 160/560 E/K Gaa/Aaa COSM750260 1 -1 ZNF250 HGNC HGNC:13044 protein_coding YES CCDS34972.1 ENSP00000292579 P15622 UPI0000197F51 NM_021061.4 tolerated(0.37) 6/6 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF112 1 MODERATE 1 SNV 1 1 1 PASS rs763607592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 144882720 144882720 C T 1 0 0 0 0 1 0 0 0 18371 835 29 3 3 ZNF250 8 144882720 Missense_Mutation SNP C C3L-00095_T 1306289 144882720 255916 388 3597 GLIS3 0 . GRCh38 9 4117924 4117924 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1554G>T p.= p.V518V ENST00000381971 4/11 237 219 18 354 354 0 strelka-varscan-mutect GLIS3,synonymous_variant,p.=,ENST00000324333,NM_152629.3;GLIS3,synonymous_variant,p.=,ENST00000381971,NM_001042413.1;GLIS3,downstream_gene_variant,,ENST00000477901,;GLIS3,downstream_gene_variant,,ENST00000481827,;GLIS3,downstream_gene_variant,,ENST00000462164,;GLIS3,downstream_gene_variant,,ENST00000478315,;GLIS3,downstream_gene_variant,,ENST00000478844,;GLIS3,downstream_gene_variant,,ENST00000490709,;GLIS3,downstream_gene_variant,,ENST00000473846,;GLIS3,non_coding_transcript_exon_variant,,ENST00000467497,;GLIS3,downstream_gene_variant,,ENST00000491889,; A ENST00000381971 Transcript synonymous_variant 2148/3961 1554/2793 518/930 V gtG/gtT 1 -1 GLIS3 HGNC HGNC:28510 protein_coding YES CCDS43784.1 ENSP00000371398 Q8NEA6 UPI0000DA4C5E NM_001042413.1 4/11 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF83,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 4117924 4117924 C A 1 0 0 0 0 0 0 0 1 6325 697 25 2 2 GLIS3 9 4117924 Silent SNP C C3L-00095_T 4117924 134276793 389 3598 DCTN3 0 . GRCh38 9 34617919 34617919 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.234A>G p.Ile78Met p.I78M ENST00000259632 3/7 146 130 16 202 202 0 strelka-varscan-mutect DCTN3,missense_variant,p.Ile78Met,ENST00000378913,;DCTN3,missense_variant,p.Ile78Met,ENST00000341694,NM_024348.3,NM_001281426.1;DCTN3,missense_variant,p.Ile78Met,ENST00000259632,NM_007234.4;DCTN3,missense_variant,p.Ile78Met,ENST00000378916,NM_001281425.1;DCTN3,missense_variant,p.Ile78Met,ENST00000477738,NM_001281427.1;DCTN3,missense_variant,p.Ile71Met,ENST00000421919,;DCTN3,missense_variant,p.Ile78Met,ENST00000378911,;ARID3C,downstream_gene_variant,,ENST00000378909,NM_001017363.1;DCTN3,upstream_gene_variant,,ENST00000479399,;DCTN3,upstream_gene_variant,,ENST00000472418,;DCTN3,upstream_gene_variant,,ENST00000472074,;DCTN3,upstream_gene_variant,,ENST00000481438,; C ENST00000259632 Transcript missense_variant 250/808 234/561 78/186 I/M atA/atG 1 -1 DCTN3 HGNC HGNC:2713 protein_coding YES CCDS6560.1 ENSP00000259632 O75935 UPI0000072AE5 NM_007234.4 tolerated(0.16) 3/7 Pfam_domain:PF07426,hmmpanther:PTHR28360 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 34617919 34617919 T C 1 0 0 0 0 1 0 0 0 4111 1628 57 5 5 DCTN3 9 34617919 Missense_Mutation SNP T C3L-00095_T 30499995 34617919 103776798 390 3599 FRMPD1 0 . GRCh38 9 37745077 37745077 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.3045C>T p.= p.L1015L ENST00000539465 16/16 255 232 23 372 371 1 strelka-varscan-mutect FRMPD1,synonymous_variant,p.=,ENST00000539465,;FRMPD1,synonymous_variant,p.=,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; T ENST00000539465 Transcript synonymous_variant 3638/5465 3045/4737 1015/1578 L ctC/ctT 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC 16/16 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 37745077 37745077 C T 1 0 0 0 0 0 0 0 1 5927 900 32 3 3 FRMPD1 9 37745077 Silent SNP C C3L-00095_T 3127158 37745077 100649640 391 3600 SPATA31A6 0 . GRCh38 9 42183847 42183847 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.160C>G p.Pro54Ala p.P54A ENST00000332857 1/4 268 230 38 345 345 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Pro54Ala,ENST00000332857,NM_001145196.1;SPATA31A6,upstream_gene_variant,,ENST00000496386,; G ENST00000332857 Transcript missense_variant 189/4209 160/4032 54/1343 P/A Cca/Gca 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 deleterious(0.02) 1/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 MODERATE 1 SNV 5 1 PASS rs1404098663 . 10 200 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 42183847 42183847 C G 1 0 0 0 0 1 0 0 0 15345 623 22 4 4 SPATA31A6 9 42183847 Missense_Mutation SNP C C3L-00095_T 4438770 42183847 96210870 392 3601 RORB 0 . GRCh38 9 74660702 74660702 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.723C>A p.= p.T241T ENST00000376896 5/10 147 127 20 186 186 0 strelka-varscan-mutect RORB,synonymous_variant,p.=,ENST00000376896,NM_006914.3;RORB,synonymous_variant,p.=,ENST00000396204,; A ENST00000376896 Transcript synonymous_variant 1335/9551 723/1380 241/459 T acC/acA 1 1 RORB HGNC HGNC:10259 protein_coding YES CCDS6646.1 ENSP00000366093 Q92753 Q58EY0 UPI000015FD94 NM_006914.3 5/10 Superfamily_domains:SSF48508 LOW 1 SNV 1 1 PASS rs957849516 . 0 207 0 3 0 0 0 0 -20 0.9999923 1 1 1 0 A 2 1 10 74660702 74660702 C A 1 0 0 0 0 0 0 0 1 13706 610 22 2 2 RORB 9 74660702 Silent SNP C C3L-00095_T 32476855 74660702 63734015 393 3602 TRPM6 0 . GRCh38 9 74786107 74786107 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2686G>T p.Gly896Trp p.G896W ENST00000360774 21/39 264 240 24 258 258 0 strelka-varscan-mutect TRPM6,missense_variant,p.Gly896Trp,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Gly891Trp,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Gly891Trp,ENST00000449912,NM_001177310.1; A ENST00000360774 Transcript missense_variant 2924/8425 2686/6069 896/2022 G/W Ggg/Tgg 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 deleterious(0) 21/39 Pfam_domain:PF00520,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 74786107 74786107 C A 1 0 0 0 0 1 0 0 0 17096 594 21 2 2 TRPM6 9 74786107 Missense_Mutation SNP C C3L-00095_T 125405 74786107 63608610 394 3603 TRPM6 0 . GRCh38 9 74840035 74840035 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.533G>T p.Gly178Val p.G178V ENST00000360774 5/39 247 231 16 338 336 2 strelka-varscan-mutect TRPM6,missense_variant,p.Gly178Val,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Gly173Val,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Gly173Val,ENST00000449912,NM_001177310.1;TRPM6,missense_variant,p.Gly178Val,ENST00000359047,; A ENST00000360774 Transcript missense_variant 771/8425 533/6069 178/2022 G/V gGc/gTc COSM3908005,COSM3908006,COSM3908007,COSM3908008 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 deleterious(0) 5/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 74840035 74840035 C A 1 0 0 0 0 1 0 0 0 17096 739 26 2 2 TRPM6 9 74840035 Missense_Mutation SNP C C3L-00095_T 53928 74840035 63554682 395 3604 SPATA31E1 0 . GRCh38 9 87885151 87885151 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.664T>A p.Ser222Thr p.S222T ENST00000325643 4/4 145 124 21 208 207 1 strelka-varscan-mutect SPATA31E1,missense_variant,p.Ser222Thr,ENST00000325643,NM_178828.4; A ENST00000325643 Transcript missense_variant 730/4478 664/4338 222/1445 S/T Tcc/Acc 1 1 SPATA31E1 HGNC HGNC:26672 protein_coding YES CCDS6676.1 ENSP00000322640 Q6ZUB1 UPI000036764A NM_178828.4 tolerated(0.3) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 87885151 87885151 T A 1 0 0 0 0 1 0 0 0 15350 1551 54 4 4 SPATA31E1 9 87885151 Missense_Mutation SNP T C3L-00095_T 13045116 87885151 50509566 396 3605 PTPN3 0 . GRCh38 9 109379591 109379591 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.2707G>A p.Glu903Lys p.E903K ENST00000374541 26/26 139 126 13 194 194 0 strelka-mutect PTPN3,missense_variant,p.Glu772Lys,ENST00000412145,NM_001145369.1;PTPN3,missense_variant,p.Glu727Lys,ENST00000446349,NM_001145370.1;PTPN3,missense_variant,p.Glu903Lys,ENST00000374541,NM_001145368.1,NM_002829.3;PTPN3,3_prime_UTR_variant,,ENST00000262539,;PTPN3,upstream_gene_variant,,ENST00000447271,; T ENST00000374541 Transcript missense_variant 2812/6703 2707/2742 903/913 E/K Gaa/Aaa 1 -1 PTPN3 HGNC HGNC:9655 protein_coding YES CCDS6776.1 ENSP00000363667 P26045 UPI000013D2D2 NM_001145368.1,NM_002829.3 tolerated(0.74) 26/26 Gene3D:3.90.190.10,PIRSF_domain:PIRSF000927,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF309,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 109379591 109379591 C T 1 0 0 0 0 1 0 0 0 12943 835 29 3 3 PTPN3 9 109379591 Missense_Mutation SNP C C3L-00095_T 21494440 109379591 29015126 397 3606 KIAA0368 0 . GRCh38 9 111374039 111374039 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.4645-1G>T p.X1549_splice ENST00000259335 139 129 10 167 167 0 strelka-varscan-mutect KIAA0368,splice_acceptor_variant,,ENST00000259335,NM_001080398.1;KIAA0368,splice_acceptor_variant,,ENST00000338205,;KIAA0368,upstream_gene_variant,,ENST00000374383,;KIAA0368,upstream_gene_variant,,ENST00000465499,; A ENST00000259335 Transcript splice_acceptor_variant -/7391 4645/6054 1549/2017 1 -1 KIAA0368 HGNC HGNC:29020 protein_coding YES CCDS48006.1 ENSP00000259335 J3KN16 UPI0000DD7F7A NM_001080398.1 39/50 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 111374039 111374039 C A 1 0 0 0 0 0 0 1 0 8083 695 24 2 2 KIAA0368 9 111374039 Splice_Site SNP C C3L-00095_T 1994448 111374039 27020678 398 3607 CNTRL 0 . GRCh38 9 121096527 121096527 + Missense_Mutation SNP G G T rs767370614 C3L-00095_T C3L-00095_N G G c.585G>T p.Leu195Phe p.L195F ENST00000373855 6/44 93 84 9 69 69 0 strelka-varscan-mutect CNTRL,missense_variant,p.Leu195Phe,ENST00000373855,;CNTRL,missense_variant,p.Leu195Phe,ENST00000238341,NM_007018.4;CNTRL,missense_variant,p.Leu195Phe,ENST00000373865,; T ENST00000373855 Transcript missense_variant 845/7660 585/6978 195/2325 L/F ttG/ttT rs767370614 1 1 CNTRL HGNC HGNC:1858 protein_coding YES CCDS35118.1 ENSP00000362962 Q7Z7A1 UPI0000211718 deleterious(0) 6/44 Gene3D:3.80.10.10,Pfam_domain:PF14580,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF273,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 5 1 PASS rs767370614 . 0 202 8 0 0 0 0 0 -18.48267 0.9999952 1 1 1 0 T 3 4 10 121096527 121096527 G T 1 0 0 0 0 1 0 0 0 3433 1310 46 2 2 CNTRL 9 121096527 Missense_Mutation SNP G C3L-00095_T 9722488 121096527 17298190 399 3608 WDR38 0 . GRCh38 9 124856737 124856737 + Silent SNP C C A rs375509008 C3L-00095_T C3L-00095_N C C c.624C>A p.= p.S208S ENST00000613760 7/9 146 126 20 177 177 0 strelka-varscan-mutect WDR38,synonymous_variant,p.=,ENST00000613760,NM_001276375.1,NM_001276374.1;WDR38,synonymous_variant,p.=,ENST00000618744,NM_001276376.1;WDR38,synonymous_variant,p.=,ENST00000373574,NM_001045476.2;RPL35,downstream_gene_variant,,ENST00000373570,;RPL35,downstream_gene_variant,,ENST00000348462,NM_007209.3;RPL35,downstream_gene_variant,,ENST00000629845,;RPL35,downstream_gene_variant,,ENST00000487431,;RPL35,downstream_gene_variant,,ENST00000493018,;RPL35,downstream_gene_variant,,ENST00000495728,; A ENST00000613760 Transcript synonymous_variant 739/1323 624/948 208/315 S tcC/tcA rs375509008,COSM1105101 1 1 WDR38 HGNC HGNC:23745 protein_coding YES CCDS75898.1 ENSP00000483312 A0A087X0D8 UPI00006C0F22 NM_001276375.1,NM_001276374.1 7/9 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 0,1 LOW 1 SNV 1 0,1 1 PASS rs375509008 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 10 124856737 124856737 C A 1 0 0 0 0 0 0 0 1 17852 666 23 1 1 WDR38 9 124856737 Silent SNP C C3L-00095_T 3760210 124856737 13537980 400 3609 SET 0 . GRCh38 9 128692670 128692670 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.322C>T p.= p.L108L ENST00000372692 4/8 174 151 23 219 219 0 strelka-varscan-mutect SET,synonymous_variant,p.=,ENST00000322030,NM_003011.3;SET,synonymous_variant,p.=,ENST00000372692,NM_001122821.1;SET,synonymous_variant,p.=,ENST00000372686,;SET,synonymous_variant,p.=,ENST00000409104,NM_001248000.1;SET,synonymous_variant,p.=,ENST00000372688,NM_001248001.1;SET,non_coding_transcript_exon_variant,,ENST00000477806,;SET,non_coding_transcript_exon_variant,,ENST00000480217,;SET,downstream_gene_variant,,ENST00000466009,;SET,non_coding_transcript_exon_variant,,ENST00000485056,;SET,non_coding_transcript_exon_variant,,ENST00000480536,; T ENST00000372692 Transcript synonymous_variant 563/2850 322/873 108/290 L Ctg/Ttg 1 1 SET HGNC HGNC:10760 protein_coding YES CCDS48037.1 ENSP00000361777 Q01105 Q5VXV3 UPI000006D7FF NM_001122821.1 4/8 hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF74,Pfam_domain:PF00956,Superfamily_domains:SSF143113 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 128692670 128692670 C T 1 0 0 0 0 0 0 0 1 14405 564 20 3 3 SET 9 128692670 Silent SNP C C3L-00095_T 3835933 128692670 9702047 401 3610 LAMC3 0 . GRCh38 9 131036287 131036287 + Missense_Mutation SNP C C G rs761933914 C3L-00095_T C3L-00095_N C C c.931C>G p.Arg311Gly p.R311G ENST00000361069 4/28 346 308 38 413 413 0 strelka-varscan-mutect LAMC3,missense_variant,p.Arg311Gly,ENST00000361069,NM_006059.3;LAMC3,non_coding_transcript_exon_variant,,ENST00000480883,; G ENST00000361069 Transcript missense_variant 1064/6133 931/4728 311/1575 R/G Cgc/Ggc rs761933914,COSM1330686 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 deleterious(0) 4/28 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240,SMART_domains:SM00180,Superfamily_domains:SSF57196 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs761933914 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 131036287 131036287 C G 1 0 0 0 0 1 0 0 0 8520 652 23 4 4 LAMC3 9 131036287 Missense_Mutation SNP C C3L-00095_T 2343617 131036287 7358430 402 3611 NTNG2 0 . GRCh38 9 132239248 132239248 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.1199T>A p.Leu400Gln p.L400Q ENST00000393229 6/8 359 318 41 432 431 1 strelka-varscan-mutect NTNG2,missense_variant,p.Leu400Gln,ENST00000393229,NM_032536.2;NTNG2,upstream_gene_variant,,ENST00000490694,;NTNG2,upstream_gene_variant,,ENST00000483055,; A ENST00000393229 Transcript missense_variant 1975/4792 1199/1593 400/530 L/Q cTg/cAg 1 1 NTNG2 HGNC HGNC:14288 protein_coding YES CCDS6946.1 ENSP00000376921 Q96CW9 UPI0000367698 NM_032536.2 deleterious(0.01) 6/8 Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 132239248 132239248 T A 1 0 0 0 0 1 0 0 0 10770 1580 55 4 4 NTNG2 9 132239248 Missense_Mutation SNP T C3L-00095_T 1202961 132239248 6155469 403 3612 SETX 0 . GRCh38 9 132334618 132334618 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.828G>T p.Arg276Ser p.R276S ENST00000224140 7/26 390 360 30 361 359 2 strelka-varscan-mutect SETX,missense_variant,p.Arg276Ser,ENST00000224140,NM_015046.5; A ENST00000224140 Transcript missense_variant 1011/11100 828/8034 276/2677 R/S agG/agT 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 deleterious(0) 7/26 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF377 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 132334618 132334618 C A 1 0 0 0 0 1 0 0 0 14420 622 22 2 2 SETX 9 132334618 Missense_Mutation SNP C C3L-00095_T 95370 132334618 6060099 404 3613 VAV2 0 . GRCh38 9 133768570 133768570 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.2461G>T p.Ala821Ser p.A821S ENST00000371850 29/30 112 103 9 131 131 0 strelka-varscan-mutect VAV2,missense_variant,p.Ala811Ser,ENST00000371851,;VAV2,missense_variant,p.Ala821Ser,ENST00000371850,NM_001134398.1;VAV2,missense_variant,p.Ala782Ser,ENST00000406606,NM_003371.3; A ENST00000371850 Transcript missense_variant 2493/4837 2461/2637 821/878 A/S Gct/Tct COSM204605,COSM5123577 1 -1 VAV2 HGNC HGNC:12658 protein_coding YES CCDS48053.1 ENSP00000360916 P52735 UPI000013E06E NM_001134398.1 deleterious(0) 29/30 Gene3D:2.30.30.40,Prints_domain:PR00452,PROSITE_profiles:PS50002,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF95,SMART_domains:SM00326,Superfamily_domains:SSF50044 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 133768570 133768570 C A 1 0 0 0 0 1 0 0 0 17677 797 28 2 2 VAV2 9 133768570 Missense_Mutation SNP C C3L-00095_T 1433952 133768570 4626147 405 3614 OLFM1 0 . GRCh38 9 135077046 135077046 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.331G>T p.Glu111Ter p.E111* ENST00000371799 2/2 118 103 15 143 143 0 strelka-varscan-mutect OLFM1,stop_gained,p.Glu111Ter,ENST00000371799,;OLFM1,intron_variant,,ENST00000252854,NM_014279.4;OLFM1,intron_variant,,ENST00000277415,NM_006334.3;OLFM1,downstream_gene_variant,,ENST00000371801,; T ENST00000371799 Transcript stop_gained 616/961 331/504 111/167 E/* Gag/Tag 1 1 OLFM1 HGNC HGNC:17187 protein_coding ENSP00000360864 Q6IMJ6 UPI00003B288C 2/2 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 135077046 135077046 G T 1 0 0 0 0 0 1 0 0 10927 1175 41 2 2 OLFM1 9 135077046 Nonsense_Mutation SNP G C3L-00095_T 1308476 135077046 3317671 406 3615 MCM10 0 . GRCh38 10 13172468 13172468 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.442C>G p.Gln148Glu p.Q148E ENST00000484800 4/20 186 173 13 225 225 0 strelka-varscan-mutect MCM10,missense_variant,p.Gln148Glu,ENST00000378694,;MCM10,missense_variant,p.Gln148Glu,ENST00000378714,NM_018518.4;MCM10,missense_variant,p.Gln148Glu,ENST00000484800,NM_182751.2;MCM10,missense_variant,p.Gln68Glu,ENST00000479669,; G ENST00000484800 Transcript missense_variant 545/3157 442/2628 148/875 Q/E Caa/Gaa 1 1 MCM10 HGNC HGNC:18043 protein_coding YES CCDS7096.1 ENSP00000418268 Q7L590 UPI000013C5E2 NM_182751.2 tolerated(0.75) 4/20 hmmpanther:PTHR13454 MODERATE 1 SNV 1 1 PASS . . 0 204 0 4 2 0 0 0 -4.797402 0.8459278 1 1 1 0 G 3 3 10 13172468 13172468 C G 1 0 0 0 0 1 0 0 0 9317 711 25 4 4 MCM10 10 13172468 Missense_Mutation SNP C C3L-00095_T 13172468 120624954 407 3616 SEPHS1 0 . GRCh38 10 13333914 13333914 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.463G>T p.Ala155Ser p.A155S ENST00000327347 5/9 215 201 14 261 261 0 strelka-varscan-mutect SEPHS1,missense_variant,p.Ala155Ser,ENST00000327347,NM_012247.4;SEPHS1,missense_variant,p.Ala88Ser,ENST00000545675,NM_001195602.1;SEPHS1,missense_variant,p.Ala155Ser,ENST00000378614,NM_001195604.1;SEPHS1,missense_variant,p.Ala155Ser,ENST00000413411,;SEPHS1,missense_variant,p.Ala88Ser,ENST00000425947,;SEPHS1,downstream_gene_variant,,ENST00000494329,; A ENST00000327347 Transcript missense_variant 839/3273 463/1179 155/392 A/S Gca/Tca 1 -1 SEPHS1 HGNC HGNC:19685 protein_coding YES CCDS7098.1 ENSP00000367893 P49903 UPI0000135E82 NM_012247.4 deleterious(0.03) 5/9 Gene3D:3.30.1330.10,Pfam_domain:PF00586,PIRSF_domain:PIRSF036407,hmmpanther:PTHR10256,hmmpanther:PTHR10256:SF2,Superfamily_domains:SSF55326,TIGRFAM_domain:TIGR00476 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 13333914 13333914 C A 1 0 0 0 0 1 0 0 0 14330 797 28 2 2 SEPHS1 10 13333914 Missense_Mutation SNP C C3L-00095_T 161446 13333914 120463508 408 3617 VIM 0 . GRCh38 10 17233858 17233858 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.809G>T p.Arg270Leu p.R270L ENST00000544301 5/10 324 292 32 449 448 1 strelka-varscan-mutect VIM,missense_variant,p.Arg270Leu,ENST00000544301,NM_003380.3;VIM,missense_variant,p.Arg270Leu,ENST00000224237,;VIM,missense_variant,p.Arg96Leu,ENST00000421459,;VIM,downstream_gene_variant,,ENST00000478317,;VIM,downstream_gene_variant,,ENST00000478746,;VIM,downstream_gene_variant,,ENST00000497849,;RP11-124N14.3,non_coding_transcript_exon_variant,,ENST00000456355,;VIM-AS1,upstream_gene_variant,,ENST00000605833,;VIM,non_coding_transcript_exon_variant,,ENST00000495528,;VIM,non_coding_transcript_exon_variant,,ENST00000637053,;VIM,downstream_gene_variant,,ENST00000485947,;VIM,missense_variant,p.Arg88Leu,ENST00000469543,;VIM,missense_variant,p.Arg270Leu,ENST00000487938,; T ENST00000544301 Transcript missense_variant 1222/2128 809/1401 270/466 R/L cGt/cTt COSM4013120,COSM4013121 1 1 VIM HGNC HGNC:12692 protein_coding YES CCDS7120.1 ENSP00000446007 P08670 V9HWE1 UPI00000012EB NM_003380.3 deleterious(0) 5/10 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF27,Pfam_domain:PF00038,SMART_domains:SM01391 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1452626097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 17233858 17233858 G T 1 0 0 0 0 1 0 0 0 17712 1145 40 1 1 VIM 10 17233858 Missense_Mutation SNP G C3L-00095_T 3899944 17233858 116563564 409 3618 NEBL 0 . GRCh38 10 20850413 20850413 + Silent SNP A A G novel C3L-00095_T C3L-00095_N A A c.1098T>C p.= p.A366A ENST00000377122 11/28 263 242 21 239 239 0 strelka-varscan-mutect NEBL,synonymous_variant,p.=,ENST00000377122,NM_006393.2;NEBL,intron_variant,,ENST00000417816,NM_213569.2,NM_001173484.1;NEBL,upstream_gene_variant,,ENST00000482754,; G ENST00000377122 Transcript synonymous_variant 1495/9216 1098/3045 366/1014 A gcT/gcC 1 -1 NEBL HGNC HGNC:16932 protein_coding YES CCDS7134.1 ENSP00000366326 O76041 UPI000012FEE8 NM_006393.2 11/28 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,Pfam_domain:PF00880,SMART_domains:SM00227 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 20850413 20850413 A G 1 0 0 0 0 0 0 0 1 10327 291 11 5 5 NEBL 10 20850413 Silent SNP A C3L-00095_T 3616555 20850413 112947009 410 3619 NEBL 0 . GRCh38 10 20858258 20858258 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.885C>T p.= p.A295A ENST00000377122 9/28 370 335 35 447 447 0 strelka-varscan-mutect NEBL,synonymous_variant,p.=,ENST00000377122,NM_006393.2;NEBL,intron_variant,,ENST00000417816,NM_213569.2,NM_001173484.1; A ENST00000377122 Transcript synonymous_variant 1282/9216 885/3045 295/1014 A gcC/gcT 1 -1 NEBL HGNC HGNC:16932 protein_coding YES CCDS7134.1 ENSP00000366326 O76041 UPI000012FEE8 NM_006393.2 9/28 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,Pfam_domain:PF00880,SMART_domains:SM00227 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 20858258 20858258 G A 1 0 0 0 0 0 0 0 1 10327 1335 47 3 3 NEBL 10 20858258 Silent SNP G C3L-00095_T 7845 20858258 112939164 411 3620 ARMC3 0 . GRCh38 10 23032861 23032861 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2247G>T p.Lys749Asn p.K749N ENST00000298032 18/19 119 112 7 109 109 0 strelka-varscan-mutect ARMC3,missense_variant,p.Lys486Asn,ENST00000376528,NM_001282747.1;ARMC3,missense_variant,p.Lys749Asn,ENST00000298032,NM_173081.4;ARMC3,missense_variant,p.Lys742Asn,ENST00000409983,NM_001282745.1;ARMC3,downstream_gene_variant,,ENST00000473919,; T ENST00000298032 Transcript missense_variant,splice_region_variant 2331/2811 2247/2619 749/872 K/N aaG/aaT 1 1 ARMC3 HGNC HGNC:30964 protein_coding YES CCDS7142.1 ENSP00000298032 Q5W041 UPI0000161785 NM_173081.4 deleterious(0.04) 18/19 hmmpanther:PTHR23315:SF78,hmmpanther:PTHR23315,Pfam_domain:PF14381 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -14.14 1 1 1 1 0 T 3 4 10 23032861 23032861 G T 1 0 0 0 0 1 0 0 0 1093 1275 44 2 2 ARMC3 10 23032861 Missense_Mutation SNP G C3L-00095_T 2174603 23032861 110764561 412 3621 GPR158 0 . GRCh38 10 25598218 25598218 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.2592C>T p.= p.D864D ENST00000376351 11/11 251 236 15 337 337 0 strelka-varscan-mutect GPR158,synonymous_variant,p.=,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; T ENST00000376351 Transcript synonymous_variant 2951/6959 2592/3648 864/1215 D gaC/gaT 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 11/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 25598218 25598218 C T 1 0 0 0 0 0 0 0 1 6549 477 17 3 3 GPR158 10 25598218 Silent SNP C C3L-00095_T 2565357 25598218 108199204 413 3622 ARMC4 0 . GRCh38 10 27907701 27907701 + Missense_Mutation SNP C C G rs200363248 C3L-00095_T C3L-00095_N C C c.2572G>C p.Ala858Pro p.A858P ENST00000305242 17/20 276 259 17 282 282 0 strelka-varscan-mutect ARMC4,missense_variant,p.Ala858Pro,ENST00000305242,NM_018076.3,NM_001290020.1;RPL36AP55,downstream_gene_variant,,ENST00000454114,; G ENST00000305242 Transcript missense_variant 2665/3572 2572/3135 858/1044 A/P Gca/Cca rs200363248 1 -1 ARMC4 HGNC HGNC:25583 protein_coding YES CCDS7157.1 ENSP00000306410 Q5T2S8 A0A140VKF7 UPI00001A95E1 NM_018076.3,NM_001290020.1 deleterious(0) 17/20 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF44,Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS rs200363248 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 27907701 27907701 C G 1 0 0 0 0 1 0 0 0 1094 768 27 4 4 ARMC4 10 27907701 Missense_Mutation SNP C C3L-00095_T 2309483 27907701 105889721 414 3623 SVIL 0 . GRCh38 10 29524505 29524505 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.2553A>T p.Gln851His p.Q851H ENST00000355867 14/38 259 231 28 275 275 0 strelka-varscan-mutect SVIL,missense_variant,p.Gln819His,ENST00000375398,;SVIL,missense_variant,p.Gln851His,ENST00000355867,NM_021738.2;SVIL,missense_variant,p.Gln425His,ENST00000375400,NM_003174.3;SVIL,upstream_gene_variant,,ENST00000632315,;SVIL,upstream_gene_variant,,ENST00000464984,; A ENST00000355867 Transcript missense_variant 3306/7586 2553/6645 851/2214 Q/H caA/caT 1 -1 SVIL HGNC HGNC:11480 protein_coding YES CCDS7164.1 ENSP00000348128 O95425 UPI0000366678 NM_021738.2 deleterious(0) 14/38 hmmpanther:PTHR11977:SF45,hmmpanther:PTHR11977 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 29524505 29524505 T A 1 0 0 0 0 1 0 0 0 15806 1838 64 4 4 SVIL 10 29524505 Missense_Mutation SNP T C3L-00095_T 1616804 29524505 104272917 415 3624 ZEB1 0 . GRCh38 10 31526783 31526783 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2897G>A p.Cys966Tyr p.C966Y ENST00000361642 9/9 490 460 30 508 508 0 strelka-varscan-mutect ZEB1,missense_variant,p.Cys949Tyr,ENST00000446923,NM_001323656.1,NM_001323664.1,NM_001323657.1,NM_001323650.1,NM_001128128.2,NM_001174094.1;ZEB1,missense_variant,p.Cys966Tyr,ENST00000361642,NM_001174096.1;ZEB1,missense_variant,p.Cys965Tyr,ENST00000320985,NM_030751.5;ZEB1,missense_variant,p.Cys945Tyr,ENST00000560721,NM_001174093.1;ZEB1,missense_variant,p.Cys898Tyr,ENST00000542815,NM_001174095.1;ZEB1,downstream_gene_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,NM_001323663.1,NM_001323661.1,NM_001323644.1,NM_001323649.1,NM_001323659.1,NM_001323652.1,NM_001323673.1,NM_001323662.1,NM_001323676.1,NM_001323653.1,NM_001323655.1,NM_001323645.1,NM_001323647.1,NM_001323660.1,NM_001323671.1,NM_001323638.1,NM_001323665.1,NM_001323643.1,NM_001323677.1,NM_001323641.1,NM_001323642.1,NM_001323658.1,NM_001323651.1,NM_001323672.1,NM_001323654.1;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,downstream_gene_variant,,ENST00000558655,; A ENST00000361642 Transcript missense_variant 2960/5990 2897/3378 966/1125 C/Y tGt/tAt 1 1 ZEB1 HGNC HGNC:11642 protein_coding YES CCDS53505.1 ENSP00000354487 P37275 UPI000068F51D NM_001174096.1 deleterious(0) 9/9 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF17,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 31526783 31526783 G A 1 0 0 0 0 1 0 0 0 18199 1377 48 3 3 ZEB1 10 31526783 Missense_Mutation SNP G C3L-00095_T 2002278 31526783 102270639 416 3625 ALOX5 0 . GRCh38 10 45382494 45382494 + Nonsense_Mutation SNP C C A rs764154625 C3L-00095_T C3L-00095_N C C c.162C>A p.Tyr54Ter p.Y54* ENST00000374391 2/14 282 262 20 353 352 1 strelka-varscan-mutect ALOX5,stop_gained,p.Tyr54Ter,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,stop_gained,p.Tyr54Ter,ENST00000542434,NM_001256154.1;ALOX5,stop_gained,p.Tyr54Ter,ENST00000612635,; A ENST00000374391 Transcript stop_gained 215/2506 162/2025 54/674 Y/* taC/taA rs764154625,COSM189215 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 2/14 PROSITE_profiles:PS50095,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Pfam_domain:PF01477,Gene3D:2.60.60.20,SMART_domains:SM00308,Superfamily_domains:SSF49723 0,1 HIGH 1 SNV 1 0,1 1 PASS rs764154625 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 45382494 45382494 C A 1 0 0 0 0 0 1 0 0 640 547 19 1 1 ALOX5 10 45382494 Nonsense_Mutation SNP C C3L-00095_T 13855711 45382494 88414928 417 3626 ANXA8L1 0 . GRCh38 10 46384816 46384816 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.535G>T p.Ala179Ser p.A179S ENST00000619162 7/12 440 414 26 562 562 0 varscan-mutect ANXA8L1,missense_variant,p.Ala217Ser,ENST00000584982,;ANXA8L1,missense_variant,p.Ala117Ser,ENST00000613703,;ANXA8L1,missense_variant,p.Ala160Ser,ENST00000622769,NM_001278924.1;ANXA8L1,missense_variant,p.Ala122Ser,ENST00000611655,NM_001278923.1;ANXA8L1,missense_variant,p.Ala179Ser,ENST00000619162,NM_001098845.2;ANXA8L1,intron_variant,,ENST00000616785,;CH17-335B8.4,downstream_gene_variant,,ENST00000623463,;ANXA8L1,downstream_gene_variant,,ENST00000620353,; T ENST00000619162 Transcript missense_variant 660/1109 535/984 179/327 A/S Gcc/Tcc 1 1 ANXA8L1 HGNC HGNC:23334 protein_coding YES CCDS73098.1 ENSP00000480221 Q5VT79 UPI000002BA02 NM_001098845.2 deleterious(0) 7/12 Low_complexity_(Seg):seg,hmmpanther:PTHR10502,Gene3D:1.10.220.10,Superfamily_domains:SSF47874,Prints_domain:PR01808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 46384816 46384816 G T 1 0 0 0 0 1 0 0 0 833 1203 42 2 2 ANXA8L1 10 46384816 Missense_Mutation SNP G C3L-00095_T 1002322 46384816 87412606 418 3627 ARHGAP22 0 . GRCh38 10 48479642 48479642 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.445G>T p.Gly149Cys p.G149C ENST00000417912 4/10 186 176 10 240 240 0 strelka-varscan-mutect ARHGAP22,missense_variant,p.Gly149Cys,ENST00000249601,NM_021226.3;ARHGAP22,missense_variant,p.Gly155Cys,ENST00000435790,NM_001256025.2;ARHGAP22,missense_variant,p.Gly24Cys,ENST00000374172,;ARHGAP22,missense_variant,p.Gly149Cys,ENST00000417912,NM_001256024.1;ARHGAP22,missense_variant,p.Gly59Cys,ENST00000417247,NM_001256026.1;ARHGAP22,missense_variant,p.Gly59Cys,ENST00000374170,;ARHGAP22,intron_variant,,ENST00000471013,;ARHGAP22,upstream_gene_variant,,ENST00000515523,;ARHGAP22,missense_variant,p.Gly155Cys,ENST00000460425,; A ENST00000417912 Transcript missense_variant 601/2352 445/2145 149/714 G/C Ggc/Tgc 1 -1 ARHGAP22 HGNC HGNC:30320 protein_coding YES CCDS58080.1 ENSP00000412461 Q7Z5H3 UPI0000E5BE9D NM_001256024.1 deleterious(0) 4/10 Gene3D:2.30.29.30,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 48479642 48479642 C A 1 0 0 0 0 1 0 0 0 996 623 22 2 2 ARHGAP22 10 48479642 Missense_Mutation SNP C C3L-00095_T 2094826 48479642 85317780 419 3628 PCDH15 0 . GRCh38 10 53822215 53822215 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.5532C>A p.= p.S1844S ENST00000373957 35/35 347 316 31 468 466 2 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000617271,NM_001142770.1;PCDH15,intron_variant,,ENST00000613657,NM_001142769.1;PCDH15,intron_variant,,ENST00000395445,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000395438,;PCDH15,intron_variant,,ENST00000612394,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,;PCDH15,upstream_gene_variant,,ENST00000476074,; T ENST00000373957 Transcript synonymous_variant 5927/7032 5532/5889 1844/1962 S tcC/tcA 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 35/35 Low_complexity_(Seg):seg,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 53822215 53822215 G T 1 0 0 0 0 0 0 0 1 11598 1335 47 2 2 PCDH15 10 53822215 Silent SNP G C3L-00095_T 5342573 53822215 79975207 420 3629 PCDH15 0 . GRCh38 10 53961828 53961828 + Missense_Mutation SNP A A T C3L-00095_T C3L-00095_N A A c.2948T>A p.Ile983Asn p.I983N ENST00000373957 23/35 233 217 16 161 161 0 strelka-varscan-mutect PCDH15,missense_variant,p.Ile983Asn,ENST00000614895,;PCDH15,missense_variant,p.Ile978Asn,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Ile978Asn,ENST00000414778,;PCDH15,missense_variant,p.Ile983Asn,ENST00000617051,;PCDH15,missense_variant,p.Ile983Asn,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Ile978Asn,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Ile978Asn,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Ile956Asn,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Ile941Asn,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Ile978Asn,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Ile907Asn,ENST00000622048,;PCDH15,missense_variant,p.Ile907Asn,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Ile978Asn,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Ile990Asn,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Ile985Asn,ENST00000395445,;PCDH15,missense_variant,p.Ile978Asn,ENST00000616114,;PCDH15,missense_variant,p.Ile978Asn,ENST00000395438,;PCDH15,missense_variant,p.Ile990Asn,ENST00000612394,;PCDH15,missense_variant,p.Ile983Asn,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Ile589Asn,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; T ENST00000373957 Transcript missense_variant 3343/7032 2948/5889 983/1962 I/N aTt/aAt COSM1585002,COSM918991,COSM918992,COSM918993 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 deleterious(0) 23/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 53961828 53961828 A T 1 0 0 0 0 1 0 0 0 11598 101 4 4 4 PCDH15 10 53961828 Missense_Mutation SNP A C3L-00095_T 139613 53961828 79835594 421 3630 BICC1 0 . GRCh38 10 58786950 58786950 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.415G>A p.Val139Ile p.V139I ENST00000373886 5/21 70 64 6 69 69 0 strelka-varscan-mutect BICC1,missense_variant,p.Val139Ile,ENST00000373886,NM_001080512.2; A ENST00000373886 Transcript missense_variant 419/5475 415/2925 139/974 V/I Gtt/Att 1 1 BICC1 HGNC HGNC:19351 protein_coding YES CCDS31206.1 ENSP00000362993 Q9H694 UPI000059D156 NM_001080512.2 deleterious(0) 5/21 Gene3D:3.30.1370.10,Pfam_domain:PF00013,PROSITE_profiles:PS50084,hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF38,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 2 1 PASS . . 0 201 6 3 0 0 0 0 -10.45417 0.9986684 1 1 1 0 A 3 1 10 58786950 58786950 G A 1 0 0 0 0 1 0 0 0 1576 1377 48 3 3 BICC1 10 58786950 Missense_Mutation SNP G C3L-00095_T 4825122 58786950 75010472 422 3631 LRRTM3 0 . GRCh38 10 66927032 66927032 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.116G>T p.Arg39Met p.R39M ENST00000361320 2/3 227 213 14 239 239 0 strelka-varscan-mutect LRRTM3,missense_variant,p.Arg39Met,ENST00000361320,NM_178011.4;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2,NM_013266.3;CTNNA3,intron_variant,,ENST00000494580,; T ENST00000361320 Transcript missense_variant 694/4358 116/1746 39/581 R/M aGg/aTg COSM4935865,COSM4935866,COSM539355,COSM539356 1 1 LRRTM3 HGNC HGNC:19410 protein_coding YES CCDS7270.1 ENSP00000355187 Q86VH5 UPI0000088C0F NM_178011.4 deleterious(0) 2/3 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54,SMART_domains:SM00013,Superfamily_domains:SSF52058 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 66927032 66927032 G T 1 0 0 0 0 1 0 0 0 8947 1000 35 2 2 LRRTM3 10 66927032 Missense_Mutation SNP G C3L-00095_T 8140082 66927032 66870390 423 3632 CFAP70 0 . GRCh38 10 73299613 73299613 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1519G>A p.Ala507Thr p.A507T ENST00000310715 14/28 222 204 18 239 239 0 strelka-varscan-mutect CFAP70,missense_variant,p.Ala507Thr,ENST00000310715,NM_145170.3;CFAP70,5_prime_UTR_variant,,ENST00000355577,;CFAP70,intron_variant,,ENST00000340329,;CFAP70,upstream_gene_variant,,ENST00000433268,;CFAP70,non_coding_transcript_exon_variant,,ENST00000493787,; T ENST00000310715 Transcript missense_variant 1640/3703 1519/3366 507/1121 A/T Gct/Act 1 -1 CFAP70 HGNC HGNC:30726 protein_coding YES CCDS7324.3 ENSP00000310829 Q5T0N1 UPI00001AEF7A NM_145170.3 deleterious(0) 14/28 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF394 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 73299613 73299613 C T 1 0 0 0 0 1 0 0 0 3031 797 28 3 3 CFAP70 10 73299613 Missense_Mutation SNP C C3L-00095_T 6372581 73299613 60497809 424 3633 ANXA7 0 . GRCh38 10 73387778 73387778 + Missense_Mutation SNP C C G rs771660159 C3L-00095_T C3L-00095_N C C c.610G>C p.Asp204His p.D204H ENST00000372919 8/14 247 221 26 278 278 0 strelka-varscan-mutect ANXA7,missense_variant,p.Asp182His,ENST00000372921,NM_001320879.1,NM_001156.3;ANXA7,missense_variant,p.Asp204His,ENST00000372919,NM_004034.2;RP11-537A6.9,downstream_gene_variant,,ENST00000427492,;ANXA7,non_coding_transcript_exon_variant,,ENST00000492380,; G ENST00000372919 Transcript missense_variant 667/2174 610/1467 204/488 D/H Gat/Cat rs771660159 1 -1 ANXA7 HGNC HGNC:545 protein_coding YES CCDS7326.1 ENSP00000362010 P20073 UPI000013DB45 NM_004034.2 deleterious(0) 8/14 hmmpanther:PTHR10502:SF110,hmmpanther:PTHR10502,PROSITE_patterns:PS00223,Pfam_domain:PF00191,Gene3D:1.10.220.10,SMART_domains:SM00335,Superfamily_domains:SSF47874,Prints_domain:PR00196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 73387778 73387778 C G 1 0 0 0 0 1 0 0 0 831 927 32 4 4 ANXA7 10 73387778 Missense_Mutation SNP C C3L-00095_T 88165 73387778 60409644 425 3634 CDHR1 0 . GRCh38 10 84202987 84202987 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.647G>T p.Gly216Val p.G216V ENST00000623527 8/17 379 346 33 462 462 0 strelka-varscan-mutect CDHR1,missense_variant,p.Gly216Val,ENST00000623527,NM_033100.3;CDHR1,missense_variant,p.Gly10Val,ENST00000372117,;CDHR1,missense_variant,p.Gly216Val,ENST00000332904,NM_001171971.2;CDHR1,upstream_gene_variant,,ENST00000624091,; T ENST00000623527 Transcript missense_variant 773/6781 647/2580 216/859 G/V gGt/gTt 1 1 CDHR1 HGNC HGNC:14550 protein_coding YES CCDS7372.1 ENSP00000485478 Q96JP9 F1T0L2 UPI0000161C2F NM_033100.3 deleterious(0) 8/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF340,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 84202987 84202987 G T 1 0 0 0 0 1 0 0 0 2821 1261 44 2 2 CDHR1 10 84202987 Missense_Mutation SNP G C3L-00095_T 10815209 84202987 49594435 426 3635 LRIT2 0 . GRCh38 10 84222129 84222129 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.1474T>A p.Tyr492Asn p.Y492N ENST00000538192 4/4 66 59 7 128 127 1 strelka-varscan-mutect LRIT2,missense_variant,p.Tyr492Asn,ENST00000538192,NM_001284223.1;LRIT2,missense_variant,p.Tyr482Asn,ENST00000372113,NM_001017924.3;CDHR1,downstream_gene_variant,,ENST00000623527,NM_033100.3;CDHR1,downstream_gene_variant,,ENST00000372117,;CDHR1,downstream_gene_variant,,ENST00000332904,NM_001171971.2;CDHR1,downstream_gene_variant,,ENST00000623399,;CDHR1,downstream_gene_variant,,ENST00000459673,; T ENST00000538192 Transcript missense_variant 1543/3177 1474/1683 492/560 Y/N Tat/Aat 1 -1 LRIT2 HGNC HGNC:23443 protein_coding YES CCDS60581.1 ENSP00000438264 A6NDA9 UPI000189A8DA NM_001284223.1 deleterious(0) 4/4 Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 199 9 2 0 0 0 0 -12.45791 0.9991219 1 1 1 0 T 3 4 10 84222129 84222129 A T 1 0 0 0 0 1 0 0 0 8843 420 15 4 4 LRIT2 10 84222129 Missense_Mutation SNP A C3L-00095_T 19142 84222129 49575293 427 3636 LRIT1 0 . GRCh38 10 84241388 84241388 + Nonsense_Mutation SNP G G A rs759958964,rs779621124 C3L-00095_T C3L-00095_N G G c.52C>T p.Gln18Ter p.Q18* ENST00000372105 1/4 124 116 8 160 160 0 strelka-varscan-mutect LRIT1,stop_gained,p.Gln18Ter,ENST00000372105,NM_015613.2;RGR,upstream_gene_variant,,ENST00000359452,NM_002921.3,NM_001012720.1;RGR,upstream_gene_variant,,ENST00000358110,NM_001012722.1;RGR,upstream_gene_variant,,ENST00000372092,;RGR,upstream_gene_variant,,ENST00000478727,;RGR,upstream_gene_variant,,ENST00000483660,;RGR,upstream_gene_variant,,ENST00000469446,;RGR,upstream_gene_variant,,ENST00000483771,; A ENST00000372105 Transcript stop_gained 74/2228 52/1872 18/623 Q/* Cag/Tag rs759958964,rs779621124,COSM1967218 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 1/4 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,Cleavage_site_(Signalp):SignalP-noTM 0,0,1 HIGH 1 SNV 1 0,0,1 1 PASS rs779621124 . 0 199 0 8 0 0 0 0 -11.07664 0.9532288 1 1 1 0 A 4 1 10 84241388 84241388 G A 1 0 0 0 0 0 1 0 0 8842 1357 47 3 3 LRIT1 10 84241388 Nonsense_Mutation SNP G C3L-00095_T 19259 84241388 49556034 428 3637 WAPL 0 . GRCh38 10 86453286 86453286 + Silent SNP C C A rs143872928 C3L-00095_T C3L-00095_N C C c.2883G>T p.= p.A961A ENST00000298767 14/19 310 291 19 363 362 1 strelka-varscan-mutect WAPL,synonymous_variant,p.=,ENST00000298767,NM_001318328.1,NM_015045.2;WAPL,synonymous_variant,p.=,ENST00000618527,;WAPL,synonymous_variant,p.=,ENST00000263070,;WAPL,synonymous_variant,p.=,ENST00000372075,;WAPL,non_coding_transcript_exon_variant,,ENST00000495124,; A ENST00000298767 Transcript synonymous_variant 3356/6333 2883/3573 961/1190 A gcG/gcT rs143872928 1 -1 WAPL HGNC HGNC:23293 protein_coding YES CCDS7375.1 ENSP00000298767 Q7Z5K2 UPI00001AE41A NM_001318328.1,NM_015045.2 14/19 PROSITE_profiles:PS51271,hmmpanther:PTHR22100:SF13,hmmpanther:PTHR22100,Pfam_domain:PF07814,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs143872928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 86453286 86453286 C A 1 0 0 0 0 0 0 0 1 17808 755 27 1 1 WAPL 10 86453286 Silent SNP C C3L-00095_T 2211898 86453286 47344136 429 3638 RBP4 0 . GRCh38 10 93593978 93593978 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.413G>T p.Cys138Phe p.C138F ENST00000371467 5/6 528 480 48 678 676 2 strelka-varscan-mutect RBP4,missense_variant,p.Cys138Phe,ENST00000371467,;RBP4,missense_variant,p.Cys138Phe,ENST00000371464,NM_006744.3;RBP4,missense_variant,p.Cys136Phe,ENST00000629763,NM_001323518.1;RBP4,missense_variant,p.Cys136Phe,ENST00000371469,;FFAR4,intron_variant,,ENST00000604414,;FFAR4,downstream_gene_variant,,ENST00000371483,NM_181745.3;FFAR4,downstream_gene_variant,,ENST00000371481,NM_001195755.1; A ENST00000371467 Transcript missense_variant 733/1314 413/606 138/201 C/F tGc/tTc 1 -1 RBP4 HGNC HGNC:9922 protein_coding YES CCDS31249.1 ENSP00000360522 P02753 UPI0000044958 deleterious(0) 5/6 hmmpanther:PTHR11873,hmmpanther:PTHR11873:SF2,Gene3D:2.40.128.20,PIRSF_domain:PIRSF500204,PIRSF_domain:PIRSF036893,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR01174 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 93593978 93593978 C A 1 0 0 0 0 1 0 0 0 13326 710 25 2 2 RBP4 10 93593978 Missense_Mutation SNP C C3L-00095_T 7140692 93593978 40203444 430 3639 CYP2C18 0 . GRCh38 10 94735295 94735295 + Missense_Mutation SNP C C A rs79500998 C3L-00095_T C3L-00095_N C C c.1324C>A p.Arg442Ser p.R442S ENST00000285979 9/9 243 227 16 256 253 3 strelka-varscan-mutect CYP2C18,missense_variant,p.Arg442Ser,ENST00000285979,NM_000772.2;CYP2C18,missense_variant,p.Arg383Ser,ENST00000339022,NM_001128925.1;RP11-400G3.5,intron_variant,,ENST00000464755,; A ENST00000285979 Transcript missense_variant 1523/2418 1324/1473 442/490 R/S Cgc/Agc rs79500998 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 deleterious(0.01) 9/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463,Prints_domain:PR00385 MODERATE 1 SNV 1 1 PASS rs79500998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 94735295 94735295 C A 1 0 0 0 0 1 0 0 0 3968 652 23 1 1 CYP2C18 10 94735295 Missense_Mutation SNP C C3L-00095_T 1141317 94735295 39062127 431 3640 ZNF518A 0 . GRCh38 10 96157050 96157050 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.728G>T p.Cys243Phe p.C243F ENST00000624776 6/6 87 80 7 80 80 0 strelka-varscan-mutect ZNF518A,missense_variant,p.Cys243Phe,ENST00000624776,NM_001278525.1;ZNF518A,missense_variant,p.Cys243Phe,ENST00000614149,;ZNF518A,missense_variant,p.Cys243Phe,ENST00000316045,NM_001278524.1,NM_014803.3;ZNF518A,missense_variant,p.Cys243Phe,ENST00000478086,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000488700,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,; T ENST00000624776 Transcript missense_variant 1292/7994 728/4452 243/1483 C/F tGt/tTt 1 1 ZNF518A HGNC HGNC:29009 protein_coding YES CCDS73170.1 ENSP00000485614 Q6AHZ1 UPI00003FEC7C NM_001278525.1 deleterious(0.03) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF198,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 96157050 96157050 G T 1 0 0 0 0 1 0 0 0 18534 1377 48 2 2 ZNF518A 10 96157050 Missense_Mutation SNP G C3L-00095_T 1421755 96157050 37640372 432 3641 DNTT 0 . GRCh38 10 96324298 96324298 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.783G>T p.Lys261Asn p.K261N ENST00000371174 6/11 140 131 9 175 175 0 strelka-varscan-mutect DNTT,missense_variant,p.Lys261Asn,ENST00000371174,NM_004088.3;DNTT,missense_variant,p.Lys261Asn,ENST00000630152,NM_001017520.1; T ENST00000371174 Transcript missense_variant 885/1972 783/1530 261/509 K/N aaG/aaT 1 1 DNTT HGNC HGNC:2983 protein_coding YES CCDS7447.1 ENSP00000360216 P04053 UPI000013C84B NM_004088.3 deleterious(0) 6/11 Gene3D:1.10.150.20,Pfam_domain:PF10391,PIRSF_domain:PIRSF000817,PIRSF_domain:PIRSF501175,Prints_domain:PR00869,hmmpanther:PTHR11276,hmmpanther:PTHR11276:SF21,SMART_domains:SM00483,Superfamily_domains:SSF81585 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 96324298 96324298 G T 1 0 0 0 0 1 0 0 0 4494 933 33 2 2 DNTT 10 96324298 Missense_Mutation SNP G C3L-00095_T 167248 96324298 37473124 433 3642 SLIT1 0 . GRCh38 10 97030826 97030826 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.2513C>G p.Ser838Cys p.S838C ENST00000266058 25/37 244 222 22 316 316 0 strelka-varscan-mutect SLIT1,missense_variant,p.Ser838Cys,ENST00000266058,NM_003061.2;SLIT1,missense_variant,p.Ser838Cys,ENST00000371070,; C ENST00000266058 Transcript missense_variant,splice_region_variant 2759/7925 2513/4605 838/1534 S/C tCt/tGt 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 deleterious(0) 25/37 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,Low_complexity_(Seg):seg,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 97030826 97030826 G C 1 0 0 0 0 1 0 0 0 15030 956 33 4 4 SLIT1 10 97030826 Missense_Mutation SNP G C3L-00095_T 706528 97030826 36766596 434 3643 SLF2 0 . GRCh38 10 100924796 100924796 + Missense_Mutation SNP G G T rs574250929 C3L-00095_T C3L-00095_N G G c.1795G>T p.Gly599Cys p.G599C ENST00000370269 5/19 330 301 29 395 395 0 strelka-varscan-mutect SLF2,missense_variant,p.Gly599Cys,ENST00000238961,NM_018121.3;SLF2,missense_variant,p.Gly599Cys,ENST00000370269,NM_001136123.1;SLF2,missense_variant,p.Gly599Cys,ENST00000370271,; T ENST00000370269 Transcript missense_variant 1927/3712 1795/3561 599/1186 G/C Ggt/Tgt rs574250929 1 1 SLF2 HGNC HGNC:17814 protein_coding YES CCDS44470.1 ENSP00000359292 Q8IX21 UPI0000458847 NM_001136123.1 deleterious(0.01) 5/19 hmmpanther:PTHR16046,hmmpanther:PTHR16046:SF10 MODERATE 1 SNV 1 1 PASS rs574250929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 100924796 100924796 G T 1 0 0 0 0 1 0 0 0 15021 1232 43 2 2 SLF2 10 100924796 Missense_Mutation SNP G C3L-00095_T 3893970 100924796 32872626 435 3644 PSD 0 . GRCh38 10 102416483 102416483 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.556G>T p.Asp186Tyr p.D186Y ENST00000020673 2/17 154 141 13 194 194 0 strelka-varscan-mutect PSD,missense_variant,p.Asp186Tyr,ENST00000020673,NM_002779.4;PSD,missense_variant,p.Asp186Tyr,ENST00000406432,NM_001270965.1;PSD,5_prime_UTR_variant,,ENST00000611678,NM_001270966.1;FBXL15,upstream_gene_variant,,ENST00000224862,NM_024326.3;FBXL15,upstream_gene_variant,,ENST00000369956,;FBXL15,upstream_gene_variant,,ENST00000432590,;FBXL15,upstream_gene_variant,,ENST00000440407,;FBXL15,upstream_gene_variant,,ENST00000425536,;FBXL15,upstream_gene_variant,,ENST00000457067,;PSD,downstream_gene_variant,,ENST00000492902,;FBXL15,upstream_gene_variant,,ENST00000481808,;PSD,downstream_gene_variant,,ENST00000472685,;PSD,upstream_gene_variant,,ENST00000488194,; A ENST00000020673 Transcript missense_variant 1083/4183 556/3075 186/1024 D/Y Gat/Tat 1 -1 PSD HGNC HGNC:9507 protein_coding YES CCDS31272.1 ENSP00000020673 A5PKW4 UPI0000404928 NM_002779.4 deleterious_low_confidence(0) 2/17 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115 MODERATE 1 SNV 1 1 PASS rs1371062329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 102416483 102416483 C A 1 0 0 0 0 1 0 0 0 12797 913 32 2 2 PSD 10 102416483 Missense_Mutation SNP C C3L-00095_T 1491687 102416483 31380939 436 3645 NT5C2 0 . GRCh38 10 103089782 103089782 + Missense_Mutation SNP G G C rs745326714 C3L-00095_T C3L-00095_N G G c.1576C>G p.Arg526Gly p.R526G ENST00000343289 18/18 146 137 9 140 140 0 strelka-varscan-mutect NT5C2,missense_variant,p.Arg526Gly,ENST00000343289,NM_001134373.2,NM_012229.4;NT5C2,missense_variant,p.Arg526Gly,ENST00000404739,;CNNM2,3_prime_UTR_variant,,ENST00000369878,NM_017649.4;NT5C2,downstream_gene_variant,,ENST00000421281,;NT5C2,non_coding_transcript_exon_variant,,ENST00000369857,;NT5C2,downstream_gene_variant,,ENST00000469228,; C ENST00000343289 Transcript missense_variant 1671/3435 1576/1686 526/561 R/G Cgg/Ggg rs745326714 1 -1 NT5C2 HGNC HGNC:8022 protein_coding YES CCDS7544.1 ENSP00000339479 P49902 UPI0000124F44 NM_001134373.2,NM_012229.4 tolerated(0.16) 18/18 MODERATE 1 SNV 1 1 PASS rs745326714 . 0 206 3 0 0 0 0 0 -16.92132 1 1 1 1 0 C 3 2 10 103089782 103089782 G C 1 0 0 0 0 1 0 0 0 10750 1144 40 4 4 NT5C2 10 103089782 Missense_Mutation SNP G C3L-00095_T 673299 103089782 30707640 437 3646 PCGF6 0 . GRCh38 10 103326570 103326570 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.873C>T p.= p.F291F ENST00000369847 8/10 159 146 13 101 101 0 strelka-varscan-mutect PCGF6,synonymous_variant,p.=,ENST00000369847,NM_001011663.1;PCGF6,synonymous_variant,p.=,ENST00000337211,NM_032154.3;PCGF6,non_coding_transcript_exon_variant,,ENST00000490296,; A ENST00000369847 Transcript synonymous_variant 941/2230 873/1053 291/350 F ttC/ttT 1 -1 PCGF6 HGNC HGNC:21156 protein_coding YES CCDS31275.1 ENSP00000358862 Q9BYE7 UPI00001F9669 NM_001011663.1 8/10 hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF15,Superfamily_domains:SSF54236 LOW 1 SNV 1 1 PASS . . 0 202 2 3 3 0 0 0 -5.283101 0.6857512 1 1 1 0 A 2 1 10 103326570 103326570 G A 1 0 0 0 0 0 0 0 1 11666 1165 41 3 3 PCGF6 10 103326570 Silent SNP G C3L-00095_T 236788 103326570 30470852 438 3647 PCGF6 0 . GRCh38 10 103348799 103348799 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.474C>T p.= p.C158C ENST00000369847 3/10 120 112 8 88 88 0 strelka-varscan-mutect PCGF6,synonymous_variant,p.=,ENST00000369847,NM_001011663.1;PCGF6,synonymous_variant,p.=,ENST00000337211,NM_032154.3;PCGF6,non_coding_transcript_exon_variant,,ENST00000490296,;PCGF6,non_coding_transcript_exon_variant,,ENST00000492755,; A ENST00000369847 Transcript synonymous_variant 542/2230 474/1053 158/350 C tgC/tgT 1 -1 PCGF6 HGNC HGNC:21156 protein_coding YES CCDS31275.1 ENSP00000358862 Q9BYE7 UPI00001F9669 NM_001011663.1 3/10 PROSITE_profiles:PS50089,hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF15,PROSITE_patterns:PS00518,Pfam_domain:PF13923,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -11.80545 0.9999893 1 1 1 0 A 2 1 10 103348799 103348799 G A 1 0 0 0 0 0 0 0 1 11666 1311 46 3 3 PCGF6 10 103348799 Silent SNP G C3L-00095_T 22229 103348799 30448623 439 3648 SORCS3 0 . GRCh38 10 105214550 105214550 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.2484G>T p.= p.T828T ENST00000369701 18/27 93 85 8 133 133 0 strelka-varscan-mutect SORCS3,synonymous_variant,p.=,ENST00000369701,NM_014978.2;SORCS3,synonymous_variant,p.=,ENST00000369699,;SORCS3,downstream_gene_variant,,ENST00000393176,; T ENST00000369701 Transcript synonymous_variant 2711/5757 2484/3669 828/1222 T acG/acT 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 18/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Superfamily_domains:SSF49299 LOW 1 SNV 1 1 PASS rs904560113 . 0 208 0 2 0 0 0 0 -12.8 0.9999998 1 1 1 0 T 2 4 10 105214550 105214550 G T 1 0 0 0 0 0 0 0 1 15254 1045 37 1 1 SORCS3 10 105214550 Silent SNP G C3L-00095_T 1865751 105214550 28582872 440 3649 HABP2 0 . GRCh38 10 113584157 113584157 + Missense_Mutation SNP A A T rs149811202 C3L-00095_T C3L-00095_N A A c.1247A>T p.Lys416Met p.K416M ENST00000351270 11/13 87 81 6 136 136 0 strelka-varscan-mutect HABP2,missense_variant,p.Lys416Met,ENST00000351270,NM_004132.3;HABP2,missense_variant,p.Lys390Met,ENST00000542051,NM_001177660.1;NRAP,downstream_gene_variant,,ENST00000359988,NM_198060.3;NRAP,downstream_gene_variant,,ENST00000369360,;NRAP,downstream_gene_variant,,ENST00000369358,NM_001261463.1;NRAP,downstream_gene_variant,,ENST00000360478,NM_006175.4; T ENST00000351270 Transcript missense_variant 1343/3009 1247/1683 416/560 K/M aAg/aTg rs149811202 1 1 HABP2 HGNC HGNC:4798 protein_coding YES CCDS7577.1 ENSP00000277903 Q14520 UPI0000049411 NM_004132.3 deleterious(0) 11/13 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF265,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 MODERATE 1 SNV 1 1 PASS rs149811202 . 0 208 2 0 0 0 0 0 -13.24931 1 1 1 1 0 T 3 4 10 113584157 113584157 A T 1 0 0 0 0 1 0 0 0 6820 72 3 4 4 HABP2 10 113584157 Missense_Mutation SNP A C3L-00095_T 8369607 113584157 20213265 441 3650 PLEKHS1 0 . GRCh38 10 113774292 113774292 + Silent SNP C C A rs753681547 C3L-00095_T C3L-00095_N C C c.720C>A p.= p.V240V ENST00000369310 8/12 145 137 8 121 121 0 strelka-varscan-mutect PLEKHS1,synonymous_variant,p.=,ENST00000369312,NM_001193434.1;PLEKHS1,synonymous_variant,p.=,ENST00000361048,NM_024889.4;PLEKHS1,synonymous_variant,p.=,ENST00000619563,NM_001193435.1;PLEKHS1,synonymous_variant,p.=,ENST00000369309,;PLEKHS1,synonymous_variant,p.=,ENST00000369310,NM_182601.1;PLEKHS1,5_prime_UTR_variant,,ENST00000354462,;PLEKHS1,upstream_gene_variant,,ENST00000448805,;MIR4483,downstream_gene_variant,,ENST00000636551,; A ENST00000369310 Transcript synonymous_variant 1282/2046 720/1398 240/465 V gtC/gtA rs753681547 1 1 PLEKHS1 HGNC HGNC:26285 protein_coding YES CCDS53580.1 ENSP00000358316 Q5SXH7 UPI000047020C NM_182601.1 8/12 hmmpanther:PTHR12156:SF19,hmmpanther:PTHR12156 LOW 1 SNV 1 1 PASS rs753681547 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 113774292 113774292 C A 1 0 0 0 0 0 0 0 1 12179 900 32 2 2 PLEKHS1 10 113774292 Silent SNP C C3L-00095_T 190135 113774292 20023130 442 3651 ATRNL1 0 . GRCh38 10 115847915 115847915 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.3942G>T p.= p.G1314G ENST00000355044 28/29 243 230 13 301 299 2 strelka-varscan ATRNL1,synonymous_variant,p.=,ENST00000355044,NM_207303.4; T ENST00000355044 Transcript synonymous_variant 4068/8479 3942/4140 1314/1379 G ggG/ggT 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 28/29 hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 115847915 115847915 G T 1 0 0 0 0 0 0 0 1 1360 1161 41 2 2 ATRNL1 10 115847915 Silent SNP G C3L-00095_T 2073623 115847915 17949507 443 3652 PNLIPRP3 0 . GRCh38 10 116461228 116461228 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.746T>G p.Met249Arg p.M249R ENST00000369230 7/12 318 302 16 319 318 1 strelka-varscan-mutect PNLIPRP3,missense_variant,p.Met249Arg,ENST00000369230,NM_001011709.2; G ENST00000369230 Transcript missense_variant 892/2354 746/1404 249/467 M/R aTg/aGg 1 1 PNLIPRP3 HGNC HGNC:23492 protein_coding YES CCDS31292.1 ENSP00000358232 Q17RR3 UPI000013DB40 NM_001011709.2 deleterious(0) 7/12 hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF100,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs903518394 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 116461228 116461228 T G 1 0 0 0 0 1 0 0 0 12259 1464 51 5 5 PNLIPRP3 10 116461228 Missense_Mutation SNP T C3L-00095_T 613313 116461228 17336194 444 3653 KCNK18 0 . GRCh38 10 117209905 117209905 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.761C>A p.Pro254His p.P254H ENST00000334549 3/3 330 308 22 399 397 2 strelka-varscan-mutect KCNK18,missense_variant,p.Pro254His,ENST00000334549,NM_181840.1; A ENST00000334549 Transcript missense_variant 761/1155 761/1155 254/384 P/H cCc/cAc 1 1 KCNK18 HGNC HGNC:19439 protein_coding YES CCDS7598.1 ENSP00000334650 Q7Z418 UPI0000046427 NM_181840.1 deleterious(0) 3/3 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF124 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 117209905 117209905 C A 1 0 0 0 0 1 0 0 0 7982 623 22 2 2 KCNK18 10 117209905 Missense_Mutation SNP C C3L-00095_T 748677 117209905 16587517 445 3654 PRLHR 0 . GRCh38 10 118595058 118595058 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.187A>T p.Ile63Phe p.I63F ENST00000239032 2/2 48 44 4 77 77 0 varscan-mutect PRLHR,missense_variant,p.Ile63Phe,ENST00000239032,NM_004248.2;PRLHR,missense_variant,p.Ile63Phe,ENST00000636925,; A ENST00000239032 Transcript missense_variant 377/5446 187/1113 63/370 I/F Atc/Ttc 1 -1 PRLHR HGNC HGNC:4464 protein_coding YES CCDS7606.1 ENSP00000239032 P49683 UPI000013CA6F NM_004248.2 tolerated(0.68) 2/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.45576 1 1 1 1 0 A 3 1 10 118595058 118595058 T A 1 0 0 0 0 1 0 0 0 12662 1435 50 4 4 PRLHR 10 118595058 Missense_Mutation SNP T C3L-00095_T 1385153 118595058 15202364 446 3655 ADAM12 0 . GRCh38 10 126043119 126043119 + Nonsense_Mutation SNP G G T rs764008989 C3L-00095_T C3L-00095_N G G c.2034C>A p.Cys678Ter p.C678* ENST00000368679 18/23 236 224 12 287 287 0 strelka-mutect ADAM12,stop_gained,p.Cys678Ter,ENST00000368679,NM_003474.5,NM_001288973.1;ADAM12,stop_gained,p.Cys678Ter,ENST00000368676,NM_021641.4,NM_001288974.1,NM_001288975.1; T ENST00000368679 Transcript stop_gained 2344/7938 2034/2730 678/909 C/* tgC/tgA rs764008989,COSM915893,COSM915894,COSM915895 1 -1 ADAM12 HGNC HGNC:190 protein_coding YES CCDS7653.1 ENSP00000357668 O43184 UPI000036672C NM_003474.5,NM_001288973.1 18/23 PROSITE_profiles:PS50026,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF112 0,1,1,1 HIGH 1 SNV 1 0,1,1,1 1 PASS rs764008989 . 0 206 0 3 0 0 0 0 -13.98152 0.9999359 1 1 1 0 T 4 4 10 126043119 126043119 G T 1 0 0 0 0 0 1 0 0 280 1079 38 1 1 ADAM12 10 126043119 Nonsense_Mutation SNP G C3L-00095_T 7448061 126043119 7754303 447 3656 DOCK1 0 . GRCh38 10 126987607 126987607 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.314A>T p.Gln105Leu p.Q105L ENST00000623213 5/52 207 191 16 258 258 0 strelka-varscan-mutect DOCK1,missense_variant,p.Gln105Leu,ENST00000280333,NM_001380.4;DOCK1,missense_variant,p.Gln105Leu,ENST00000623213,NM_001290223.1;RP11-223P11.3,downstream_gene_variant,,ENST00000627944,; T ENST00000623213 Transcript missense_variant 376/5761 314/5661 105/1886 Q/L cAg/cTg 1 1 DOCK1 HGNC HGNC:2987 protein_coding YES CCDS76359.1 ENSP00000485033 A0A096LNH6 UPI0003EAEE97 NM_001290223.1 deleterious(0.01) 5/52 hmmpanther:PTHR23317:SF79,hmmpanther:PTHR23317,Pfam_domain:PF16172 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 126987607 126987607 A T 1 0 0 0 0 1 0 0 0 4499 188 7 4 4 DOCK1 10 126987607 Missense_Mutation SNP A C3L-00095_T 944488 126987607 6809815 448 3657 MUC5AC 0 . GRCh38 11 1164487 1164487 + Silent SNP C C A rs758986452 C3L-00095_T C3L-00095_N C C c.1084C>A p.= p.R362R ENST00000621226 9/49 137 125 12 228 228 0 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript synonymous_variant 1131/17448 1084/16965 362/5654 R Cgg/Agg rs758986452 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 9/49 Gene3D:2.10.25.10,Pfam_domain:PF01826,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,Superfamily_domains:SSF57567 LOW 1 SNV 5 1 PASS rs758986452 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 1164487 1164487 C A 1 0 0 0 0 0 0 0 1 9978 643 23 1 1 MUC5AC 11 1164487 Silent SNP C C3L-00095_T 1164487 133922135 449 3658 C11orf21 0 . GRCh38 11 2301826 2301826 + Silent SNP C C G rs767855802 C3L-00095_T C3L-00095_N C C c.36G>C p.= p.A12A ENST00000456145 1/5 163 147 16 276 276 0 strelka-varscan-mutect C11orf21,synonymous_variant,p.=,ENST00000456145,NM_001142946.1;C11orf21,5_prime_UTR_variant,,ENST00000381153,;TSPAN32,upstream_gene_variant,,ENST00000182290,NM_139022.2;TSPAN32,upstream_gene_variant,,ENST00000612299,;TSPAN32,upstream_gene_variant,,ENST00000451520,;TSPAN32,upstream_gene_variant,,ENST00000381121,;TSPAN32,upstream_gene_variant,,ENST00000381117,;C11orf21,non_coding_transcript_exon_variant,,ENST00000470369,;C11orf21,intron_variant,,ENST00000495467,;TSPAN32,upstream_gene_variant,,ENST00000483227,;TSPAN32,upstream_gene_variant,,ENST00000479508,;TSPAN32,upstream_gene_variant,,ENST00000461200,;TSPAN32,upstream_gene_variant,,ENST00000493924,;TSPAN32,upstream_gene_variant,,ENST00000446063,;TSPAN32,upstream_gene_variant,,ENST00000339046,;TSPAN32,upstream_gene_variant,,ENST00000498313,;TSPAN32,upstream_gene_variant,,ENST00000437313,;TSPAN32,upstream_gene_variant,,ENST00000484104,;TSPAN32,upstream_gene_variant,,ENST00000493948,; G ENST00000456145 Transcript synonymous_variant 88/1366 36/537 12/178 A gcG/gcC rs767855802 1 -1 C11orf21 HGNC HGNC:13231 protein_coding YES CCDS44518.1 ENSP00000406541 E9PAM5 UPI0000DD806C NM_001142946.1 1/5 LOW 1 SNV 1 1 PASS rs767855802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 2301826 2301826 C G 1 0 0 0 0 0 0 0 1 1778 755 27 4 4 C11orf21 11 2301826 Silent SNP C C3L-00095_T 1137339 2301826 132784796 450 3659 OR51G2 0 . GRCh38 11 4915204 4915204 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.460C>A p.Leu154Met p.L154M ENST00000322013 1/1 107 97 10 177 177 0 strelka-varscan-mutect OR51G2,missense_variant,p.Leu154Met,ENST00000322013,NM_001005238.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322013 Transcript missense_variant 460/945 460/945 154/314 L/M Ctg/Atg 1 -1 OR51G2 HGNC HGNC:15198 protein_coding YES CCDS31365.1 ENSP00000322593 Q8NGK0 UPI0000041C2F NM_001005238.1 tolerated(0.07) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF133,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 4915204 4915204 G T 1 0 0 0 0 1 0 0 0 11171 933 33 2 2 OR51G2 11 4915204 Missense_Mutation SNP G C3L-00095_T 2613378 4915204 130171418 451 3660 OR56B1 0 . GRCh38 11 5736827 5736827 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.311C>G p.Pro104Arg p.P104R ENST00000317121 1/1 229 206 23 379 379 0 strelka-varscan-mutect OR56B1,missense_variant,p.Pro104Arg,ENST00000317121,NM_001005180.2;TRIM22,3_prime_UTR_variant,,ENST00000444844,;TRIM22,3_prime_UTR_variant,,ENST00000429063,;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; G ENST00000317121 Transcript missense_variant 311/975 311/975 104/324 P/R cCt/cGt 1 1 OR56B1 HGNC HGNC:15245 protein_coding YES CCDS31395.1 ENSP00000322939 Q8NGI3 UPI0000046199 NM_001005180.2 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF69,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 5736827 5736827 C G 1 0 0 0 0 1 0 0 0 11209 681 24 4 4 OR56B1 11 5736827 Missense_Mutation SNP C C3L-00095_T 821623 5736827 129349795 452 3661 OR52N4 0 . GRCh38 11 5754811 5754812 + Frame_Shift_Del DEL AC AC - novel C3L-00095_T C3L-00095_N AC AC c.76_77delCA p.Gln26ThrfsTer28 p.Q26Tfs*28 ENST00000317254 1/1 110 95 15 138 138 0 sindel-varindel-pindel OR52N4,frameshift_variant,p.Gln26ThrfsTer28,ENST00000317254,NM_001005175.3;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; - ENST00000317254 Transcript frameshift_variant 119-120/1037 71-72/966 24/321 D/X gAC/g 1 1 OR52N4 HGNC HGNC:15230 protein_coding YES CCDS44528.1 ENSP00000323224 Q8NGI2 UPI00001AF18B NM_001005175.3 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF74,Superfamily_domains:SSF81321 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 5754811 5754811 AC - 1 0 1 0 1 0 0 0 0 11202 275 10 0 0 OR52N4 11 5754811 Frame_Shift_Del DEL AC C3L-00095_T 17984 5754811 129331811 453 3662 CNGA4 0 . GRCh38 11 6244351 6244351 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1670G>C p.Gly557Ala p.G557A ENST00000379936 6/6 221 204 17 294 294 0 strelka-varscan-mutect CNGA4,missense_variant,p.Gly557Ala,ENST00000379936,NM_001037329.3;CNGA4,downstream_gene_variant,,ENST00000533426,; C ENST00000379936 Transcript missense_variant 1785/1863 1670/1728 557/575 G/A gGa/gCa 1 1 CNGA4 HGNC HGNC:2152 protein_coding YES CCDS31408.1 ENSP00000369268 Q8IV77 UPI000004C7EC NM_001037329.3 tolerated(0.33) 6/6 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF388,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 6244351 6244351 G C 1 0 0 0 0 1 0 0 0 3379 1174 41 4 4 CNGA4 11 6244351 Missense_Mutation SNP G C3L-00095_T 489540 6244351 128842271 454 3663 RRP8 0 . GRCh38 11 6601190 6601190 + Silent SNP T T G rs777644387 C3L-00095_T C3L-00095_N T T c.876A>C p.= p.P292P ENST00000254605 3/7 112 101 11 145 145 0 strelka-varscan-mutect RRP8,synonymous_variant,p.=,ENST00000254605,NM_015324.3;RRP8,intron_variant,,ENST00000534343,;ILK,upstream_gene_variant,,ENST00000396751,NM_001014795.2;ILK,upstream_gene_variant,,ENST00000299421,NM_001014794.2,NM_004517.3;ILK,upstream_gene_variant,,ENST00000537806,;ILK,upstream_gene_variant,,ENST00000420936,;ILK,upstream_gene_variant,,ENST00000532063,NM_001278442.1;ILK,upstream_gene_variant,,ENST00000528995,NM_001278441.1;ILK,upstream_gene_variant,,ENST00000526318,;ILK,upstream_gene_variant,,ENST00000627400,;RP11-732A19.8,downstream_gene_variant,,ENST00000527191,;ILK,upstream_gene_variant,,ENST00000534565,;RRP8,synonymous_variant,p.=,ENST00000533907,;RRP8,non_coding_transcript_exon_variant,,ENST00000526352,;ILK,upstream_gene_variant,,ENST00000530016,;ILK,upstream_gene_variant,,ENST00000526711,;RRP8,downstream_gene_variant,,ENST00000530762,;ILK,upstream_gene_variant,,ENST00000527121,;ILK,upstream_gene_variant,,ENST00000526114,; G ENST00000254605 Transcript synonymous_variant 994/6560 876/1371 292/456 P ccA/ccC rs777644387 1 -1 RRP8 HGNC HGNC:29030 protein_coding YES CCDS31411.1 ENSP00000254605 O43159 UPI00001580F8 NM_015324.3 3/7 Gene3D:3.40.50.150,Pfam_domain:PF05148,hmmpanther:PTHR12787,hmmpanther:PTHR12787:SF0,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS rs777644387 . 0 208 0 2 0 0 0 0 -16.72317 0.9999998 1 1 1 0 G 2 3 10 6601190 6601190 T G 1 0 0 0 0 0 0 0 1 13946 1683 59 5 5 RRP8 11 6601190 Silent SNP T C3L-00095_T 356839 6601190 128485432 455 3664 SYT9 0 . GRCh38 11 7303325 7303325 + Silent SNP C C A rs368849587 C3L-00095_T C3L-00095_N C C c.432C>A p.= p.I144I ENST00000318881 2/7 190 164 26 276 275 1 strelka-varscan-mutect SYT9,synonymous_variant,p.=,ENST00000318881,NM_175733.3;SYT9,synonymous_variant,p.=,ENST00000532592,;SYT9,synonymous_variant,p.=,ENST00000524820,; A ENST00000318881 Transcript synonymous_variant 669/3955 432/1476 144/491 I atC/atA rs368849587 1 1 SYT9 HGNC HGNC:19265 protein_coding YES CCDS7778.1 ENSP00000324419 Q86SS6 UPI000000DB7B NM_175733.3 2/7 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF180 LOW 1 SNV 1 1 PASS rs368849587 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 7303325 7303325 C A 1 0 0 0 0 0 0 0 1 15875 845 30 2 2 SYT9 11 7303325 Silent SNP C C3L-00095_T 702135 7303325 127783297 456 3665 AMPD3 0 . GRCh38 11 10500110 10500110 + Missense_Mutation SNP G G C rs763590271 C3L-00095_T C3L-00095_N G G c.1609G>C p.Asp537His p.D537H ENST00000396554 11/15 228 215 13 332 332 0 strelka-varscan-mutect AMPD3,missense_variant,p.Asp369His,ENST00000444303,NM_001172431.1;AMPD3,missense_variant,p.Asp537His,ENST00000396554,NM_000480.2;AMPD3,missense_variant,p.Asp528His,ENST00000396553,NM_001025389.1;AMPD3,missense_variant,p.Asp528His,ENST00000529507,NM_001172430.1;AMPD3,missense_variant,p.Asp535His,ENST00000528723,NM_001025390.1;AMPD3,non_coding_transcript_exon_variant,,ENST00000530864,;AMPD3,missense_variant,p.Asp528His,ENST00000529834,;AMPD3,3_prime_UTR_variant,,ENST00000534047,;AMPD3,upstream_gene_variant,,ENST00000529744,;AMPD3,downstream_gene_variant,,ENST00000533116,; C ENST00000396554 Transcript missense_variant 1950/3806 1609/2331 537/776 D/H Gat/Cat rs763590271 1 1 AMPD3 HGNC HGNC:470 protein_coding YES CCDS7802.1 ENSP00000379802 Q01432 UPI0000161AFD NM_000480.2 deleterious(0) 11/15 hmmpanther:PTHR11359,hmmpanther:PTHR11359:SF2,PIRSF_domain:PIRSF001251,Pfam_domain:PF00962,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR01429,Superfamily_domains:SSF51556 MODERATE 1 SNV 1 1 PASS rs763590271 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 10500110 10500110 G C 1 0 0 0 0 1 0 0 0 685 1290 45 4 4 AMPD3 11 10500110 Missense_Mutation SNP G C3L-00095_T 3196785 10500110 124586512 457 3666 CYP2R1 0 . GRCh38 11 14879411 14879411 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1033G>T p.Gly345Cys p.G345C ENST00000334636 4/5 183 167 16 208 208 0 strelka-varscan-mutect CYP2R1,missense_variant,p.Gly345Cys,ENST00000334636,NM_024514.4;CYP2R1,missense_variant,p.Gly112Cys,ENST00000532378,;CYP2R1,downstream_gene_variant,,ENST00000526489,;CYP2R1,downstream_gene_variant,,ENST00000526276,;CYP2R1,downstream_gene_variant,,ENST00000532641,;CYP2R1,downstream_gene_variant,,ENST00000529043,;CYP2R1,3_prime_UTR_variant,,ENST00000530609,;CYP2R1,intron_variant,,ENST00000532805,;CYP2R1,intron_variant,,ENST00000534686,;CYP2R1,intron_variant,,ENST00000525015,; A ENST00000334636 Transcript missense_variant 1080/2235 1033/1506 345/501 G/C Ggc/Tgc 1 -1 CYP2R1 HGNC HGNC:20580 protein_coding YES CCDS7818.1 ENSP00000334592 Q6VVX0 UPI000003F04B NM_024514.4 deleterious(0) 4/5 hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF48,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 14879411 14879411 C A 1 0 0 0 0 1 0 0 0 3976 623 22 2 2 CYP2R1 11 14879411 Missense_Mutation SNP C C3L-00095_T 4379301 14879411 120207211 458 3667 MRGPRX4 0 . GRCh38 11 18173944 18173944 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.688C>A p.Leu230Met p.L230M ENST00000314254 1/1 206 195 11 296 294 2 strelka-mutect MRGPRX4,missense_variant,p.Leu230Met,ENST00000314254,NM_054032.3;MRGPRX4,missense_variant,p.Leu230Met,ENST00000618161,;RP11-113D6.6,intron_variant,,ENST00000527671,; A ENST00000314254 Transcript missense_variant 1108/1444 688/969 230/322 L/M Ctg/Atg COSM5325889 1 1 MRGPRX4 HGNC HGNC:17617 protein_coding YES CCDS7831.1 ENSP00000314042 Q96LA9 UPI0000061F60 NM_054032.3 deleterious(0.01) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF23,hmmpanther:PTHR11334,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 18173944 18173944 C A 1 0 0 0 0 1 0 0 0 9736 680 24 2 2 MRGPRX4 11 18173944 Missense_Mutation SNP C C3L-00095_T 3294533 18173944 116912678 459 3668 BBOX1 0 . GRCh38 11 27093198 27093198 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.365T>A p.Leu122Gln p.L122Q ENST00000263182 5/9 208 190 18 258 257 1 strelka-varscan-mutect BBOX1,missense_variant,p.Leu122Gln,ENST00000263182,NM_003986.2;BBOX1,missense_variant,p.Leu122Gln,ENST00000529202,;BBOX1,missense_variant,p.Leu122Gln,ENST00000528583,;BBOX1,missense_variant,p.Leu122Gln,ENST00000525090,;BBOX1-AS1,intron_variant,,ENST00000530430,;BBOX1-AS1,intron_variant,,ENST00000525302,;BBOX1-AS1,intron_variant,,ENST00000526061,;BBOX1,intron_variant,,ENST00000527505,; A ENST00000263182 Transcript missense_variant 733/1886 365/1164 122/387 L/Q cTa/cAa 1 1 BBOX1 HGNC HGNC:964 protein_coding YES CCDS7862.1 ENSP00000263182 O75936 UPI0000126A4C NM_003986.2 deleterious(0) 5/9 hmmpanther:PTHR10696:SF33,hmmpanther:PTHR10696,TIGRFAM_domain:TIGR02409,Gene3D:3.60.130.10,Pfam_domain:PF02668,Superfamily_domains:SSF51197 MODERATE SNV 5 1 PASS rs944670504 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 27093198 27093198 T A 1 0 0 0 0 1 0 0 0 1481 1522 53 4 4 BBOX1 11 27093198 Missense_Mutation SNP T C3L-00095_T 8919254 27093198 107993424 460 3669 KCNA4 0 . GRCh38 11 30012597 30012597 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.82delC p.Arg28GlyfsTer81 p.R28Gfs*81 ENST00000328224 2/2 50 45 5 84 84 0 sindel-pindel KCNA4,frameshift_variant,p.Arg28GlyfsTer81,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; - ENST00000328224 Transcript frameshift_variant 1316/4172 82/1962 28/653 R/X Cgg/gg 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 2/2 Gene3D:1kn7A00,Pfam_domain:PF07941,Prints_domain:PR01511,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 200 10 0 0 0 0 0 -12.08347 0.9999611 1 1 1 0 - 7 5 10 30012597 30012597 G - 1 0 1 0 1 0 0 0 0 7921 1115 39 0 0 KCNA4 11 30012597 Frame_Shift_Del DEL G C3L-00095_T 2919399 30012597 105074025 461 3670 DCDC1 0 . GRCh38 11 30881263 30881263 + Nonsense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.2440A>T p.Arg814Ter p.R814* ENST00000406071 18/20 245 229 16 236 236 0 strelka-varscan-mutect DCDC1,stop_gained,p.Arg1707Ter,ENST00000597505,;DCDC1,stop_gained,p.Arg814Ter,ENST00000406071,NM_020869.3;DCDC1,stop_gained,p.Arg742Ter,ENST00000444572,;DCDC1,3_prime_UTR_variant,,ENST00000303697,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,; A ENST00000406071 Transcript stop_gained 2756/4758 2440/2673 814/890 R/* Aga/Tga 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 18/20 hmmpanther:PTHR14958,hmmpanther:PTHR14958:SF27,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 30881263 30881263 T A 1 0 0 0 0 0 1 0 0 4086 1530 53 4 4 DCDC1 11 30881263 Nonsense_Mutation SNP T C3L-00095_T 868666 30881263 104205359 462 3671 ABTB2 0 . GRCh38 11 34170944 34170944 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1525G>T p.Ala509Ser p.A509S ENST00000435224 5/17 111 102 9 124 124 0 strelka-varscan-mutect ABTB2,missense_variant,p.Ala509Ser,ENST00000435224,NM_145804.2;ABTB2,downstream_gene_variant,,ENST00000530814,; A ENST00000435224 Transcript missense_variant 1950/4902 1525/3078 509/1025 A/S Gcc/Tcc 1 -1 ABTB2 HGNC HGNC:23842 protein_coding YES CCDS7890.2 ENSP00000410157 Q8N961 UPI0001DD21BB NM_145804.2 deleterious(0) 5/17 Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 34170944 34170944 C A 1 0 0 0 0 1 0 0 0 113 739 26 2 2 ABTB2 11 34170944 Missense_Mutation SNP C C3L-00095_T 3289681 34170944 100915678 463 3672 RAG2 0 . GRCh38 11 36592935 36592935 + Missense_Mutation SNP C C T rs773624427 C3L-00095_T C3L-00095_N C C c.1234G>A p.Glu412Lys p.E412K ENST00000618712 3/3 374 337 37 485 484 1 strelka-varscan-mutect RAG2,missense_variant,p.Glu412Lys,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,missense_variant,p.Glu412Lys,ENST00000311485,NM_000536.3;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000529083,;RAG2,downstream_gene_variant,,ENST00000527033,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,intron_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; T ENST00000618712 Transcript missense_variant 1828/2818 1234/1584 412/527 E/K Gag/Aag rs773624427 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 tolerated(0.06) 3/3 hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0 MODERATE 1 SNV 4 1 PASS rs773624427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 36592935 36592935 C T 1 0 0 0 0 1 0 0 0 13165 835 29 3 3 RAG2 11 36592935 Missense_Mutation SNP C C3L-00095_T 2421991 36592935 98493687 464 3673 OR4A47 0 . GRCh38 11 48489173 48489173 + Silent SNP C C A rs776153456 C3L-00095_T C3L-00095_N C C c.381C>A p.= p.P127P ENST00000446524 1/1 125 116 9 156 156 0 varscan-mutect OR4A47,synonymous_variant,p.=,ENST00000446524,NM_001005512.2;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,; A ENST00000446524 Transcript synonymous_variant 457/1064 381/930 127/309 P ccC/ccA rs776153456 1 1 OR4A47 HGNC HGNC:31266 protein_coding YES CCDS31490.1 ENSP00000412752 Q6IF82 UPI00001971E5 NM_001005512.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF87,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs776153456 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 48489173 48489173 C A 1 0 0 0 0 0 0 0 1 11119 668 24 2 2 OR4A47 11 48489173 Silent SNP C C3L-00095_T 11896238 48489173 86597449 465 3674 TRIM49B 0 . GRCh38 11 49031847 49031847 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.248G>T p.Trp83Leu p.W83L ENST00000622138 3/8 360 323 37 549 547 2 strelka-varscan-mutect TRIM49B,missense_variant,p.Trp83Leu,ENST00000622138,;TRIM49B,missense_variant,p.Trp83Leu,ENST00000332682,NM_001206626.1; T ENST00000622138 Transcript missense_variant 577/2162 248/1359 83/452 W/L tGg/tTg 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 tolerated(0.61) 3/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 49031847 49031847 G T 1 0 0 0 0 1 0 0 0 17015 1357 47 2 2 TRIM49B 11 49031847 Missense_Mutation SNP G C3L-00095_T 542674 49031847 86054775 466 3675 OR4C15 0 . GRCh38 11 55554871 55554871 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.565A>T p.Met189Leu p.M189L ENST00000314644 1/1 163 146 17 193 193 0 strelka-varscan-mutect OR4C15,missense_variant,p.Met189Leu,ENST00000314644,NM_001001920.1; T ENST00000314644 Transcript missense_variant 565/1113 565/1113 189/370 M/L Atg/Ttg 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 deleterious_low_confidence(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF14,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 55554871 55554871 A T 1 0 0 0 0 1 0 0 0 11125 217 8 4 4 OR4C15 11 55554871 Missense_Mutation SNP A C3L-00095_T 6523024 55554871 79531751 467 3676 OR5I1 0 . GRCh38 11 55935820 55935820 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.581C>A p.Thr194Lys p.T194K ENST00000301532 1/1 154 144 10 212 212 0 strelka-varscan-mutect OR5I1,missense_variant,p.Thr194Lys,ENST00000301532,NM_006637.1; T ENST00000301532 Transcript missense_variant 581/945 581/945 194/314 T/K aCa/aAa 1 -1 OR5I1 HGNC HGNC:8347 protein_coding YES CCDS7949.1 ENSP00000301532 Q13606 A0A126GVE5 UPI00000405D5 NM_006637.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF69,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 55935820 55935820 G T 1 0 0 0 0 1 0 0 0 11234 1377 48 2 2 OR5I1 11 55935820 Missense_Mutation SNP G C3L-00095_T 380949 55935820 79150802 468 3677 OR8K5 0 . GRCh38 11 56160074 56160074 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.244C>G p.Leu82Val p.L82V ENST00000313447 1/1 179 168 11 180 180 0 strelka-varscan-mutect OR8K5,missense_variant,p.Leu82Val,ENST00000313447,NM_001004058.2; C ENST00000313447 Transcript missense_variant 244/924 244/924 82/307 L/V Ctg/Gtg 1 -1 OR8K5 HGNC HGNC:15315 protein_coding YES CCDS31521.1 ENSP00000323853 Q8NH50 UPI000004B231 NM_001004058.2 deleterious_low_confidence(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1051067133 . 0 208 0 2 0 0 0 0 -14.27759 0.9999995 1 1 1 0 C 3 2 10 56160074 56160074 G C 1 0 0 0 0 1 0 0 0 11312 962 34 4 4 OR8K5 11 56160074 Missense_Mutation SNP G C3L-00095_T 224254 56160074 78926548 469 3678 SLC43A3 0 . GRCh38 11 57410087 57410087 + Silent SNP C C A rs566601116 C3L-00095_T C3L-00095_N C C c.1134G>T p.= p.T378T ENST00000533524 12/14 79 67 12 103 103 0 strelka-varscan-mutect SLC43A3,synonymous_variant,p.=,ENST00000395123,NM_014096.3;SLC43A3,synonymous_variant,p.=,ENST00000395124,NM_001278201.1,NM_199329.2;SLC43A3,synonymous_variant,p.=,ENST00000352187,NM_017611.2;SLC43A3,synonymous_variant,p.=,ENST00000529554,;SLC43A3,synonymous_variant,p.=,ENST00000533524,NM_001278206.1;RP11-872D17.8,synonymous_variant,p.=,ENST00000529411,;SLC43A3,downstream_gene_variant,,ENST00000530005,;SLC43A3,upstream_gene_variant,,ENST00000625097,;RP11-872D17.8,intron_variant,,ENST00000534081,;SLC43A3,intron_variant,,ENST00000525205,;RP11-872D17.8,upstream_gene_variant,,ENST00000528835,; A ENST00000533524 Transcript synonymous_variant 1476/1879 1134/1515 378/504 T acG/acT rs566601116 1 -1 SLC43A3 HGNC HGNC:17466 protein_coding YES CCDS60784.1 ENSP00000434515 Q8NBI5 UPI0001AE6BEC NM_001278206.1 12/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR20765:SF1,hmmpanther:PTHR20765,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW 1 SNV 2 1 PASS rs566601116 . 0 199 10 0 0 0 0 0 -20 0.9999826 1 1 1 0 A 2 1 10 57410087 57410087 C A 1 0 0 0 0 0 0 0 1 14912 639 23 1 1 SLC43A3 11 57410087 Silent SNP C C3L-00095_T 1250013 57410087 77676535 470 3679 OR4D9 0 . GRCh38 11 59515100 59515100 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.188T>A p.Leu63His p.L63H ENST00000329328 1/1 155 138 17 230 230 0 strelka-varscan-mutect OR4D9,missense_variant,p.Leu63His,ENST00000329328,NM_001004711.1; A ENST00000329328 Transcript missense_variant 188/945 188/945 63/314 L/H cTc/cAc 1 1 OR4D9 HGNC HGNC:15178 protein_coding YES CCDS31564.1 ENSP00000328563 Q8NGE8 A0A126GVP8 UPI0000061EE8 NM_001004711.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF272,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 59515100 59515100 T A 1 0 0 0 0 1 0 0 0 11136 1551 54 4 4 OR4D9 11 59515100 Missense_Mutation SNP T C3L-00095_T 2105013 59515100 75571522 471 3680 MS4A3 0 . GRCh38 11 60061263 60061263 + Missense_Mutation SNP C C G C3L-00095_T C3L-00095_N C C c.103C>G p.Gln35Glu p.Q35E ENST00000278865 2/7 98 92 6 118 118 0 strelka-varscan-mutect MS4A3,missense_variant,p.Gln35Glu,ENST00000278865,NM_006138.4;MS4A3,missense_variant,p.Gln35Glu,ENST00000358152,NM_001031809.1;MS4A3,missense_variant,p.Gln35Glu,ENST00000534744,;MS4A3,intron_variant,,ENST00000395032,NM_001031666.1;MS4A3,non_coding_transcript_exon_variant,,ENST00000526199,;MS4A3,missense_variant,p.Gln35Glu,ENST00000525686,;MS4A3,non_coding_transcript_exon_variant,,ENST00000528298,; G ENST00000278865 Transcript missense_variant 176/1613 103/645 35/214 Q/E Cag/Gag COSM2153930 1 1 MS4A3 HGNC HGNC:7317 protein_coding YES CCDS31567.1 ENSP00000278865 Q96HJ5 UPI000006E45E NM_006138.4 tolerated(0.14) 2/7 hmmpanther:PTHR23320:SF74,hmmpanther:PTHR23320 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 60061263 60061263 C G 1 0 0 0 0 1 0 0 0 9839 595 21 4 4 MS4A3 11 60061263 Missense_Mutation SNP C C3L-00095_T 546163 60061263 75025359 472 3681 SLC22A24 0 . GRCh38 11 63104231 63104231 + Nonsense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.898A>T p.Arg300Ter p.R300* ENST00000612278 5/10 189 172 17 206 206 0 strelka-varscan-mutect SLC22A24,stop_gained,p.Arg300Ter,ENST00000612278,NM_001136506.2;SLC22A24,stop_gained,p.Arg300Ter,ENST00000417740,; A ENST00000612278 Transcript stop_gained 1340/2101 898/1659 300/552 R/* Aga/Tga 1 -1 SLC22A24 HGNC HGNC:28542 protein_coding YES CCDS73308.1 ENSP00000480336 A0A087WWM3 UPI000004DAF7 NM_001136506.2 5/10 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF208,Pfam_domain:PF00083,Superfamily_domains:SSF103473 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 63104231 63104231 T A 1 0 0 0 0 0 1 0 0 14718 1530 53 4 4 SLC22A24 11 63104231 Nonsense_Mutation SNP T C3L-00095_T 3042968 63104231 71982391 473 3682 PCNX3 0 . GRCh38 11 65618071 65618071 + Missense_Mutation SNP A A T rs773268285 C3L-00095_T C3L-00095_N A A c.709A>T p.Met237Leu p.M237L ENST00000355703 6/35 195 181 14 196 195 1 strelka-varscan-mutect PCNX3,missense_variant,p.Met237Leu,ENST00000355703,NM_032223.3;MAP3K11,upstream_gene_variant,,ENST00000309100,NM_002419.3;MAP3K11,upstream_gene_variant,,ENST00000526293,;MAP3K11,upstream_gene_variant,,ENST00000529839,;PCNX3,upstream_gene_variant,,ENST00000531045,;MAP3K11,upstream_gene_variant,,ENST00000527304,;MAP3K11,upstream_gene_variant,,ENST00000524856,; T ENST00000355703 Transcript missense_variant 1248/7105 709/6105 237/2034 M/L Atg/Ttg rs773268285 1 1 PCNX3 HGNC HGNC:18760 protein_coding YES CCDS44650.1 ENSP00000347931 Q9H6A9 UPI0000405B22 NM_032223.3 tolerated(0.92) 6/35 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF4 MODERATE SNV 5 1 PASS rs773268285 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 65618071 65618071 A T 1 0 0 0 0 1 0 0 0 11681 217 8 4 4 PCNX3 11 65618071 Missense_Mutation SNP A C3L-00095_T 2513840 65618071 69468551 474 3683 PCNX3 0 . GRCh38 11 65624344 65624344 + Silent SNP C C T C3L-00095_T C3L-00095_N C C c.2694C>T p.= p.F898F ENST00000355703 14/35 196 184 12 198 198 0 strelka-varscan-mutect PCNX3,synonymous_variant,p.=,ENST00000355703,NM_032223.3;PCNX3,downstream_gene_variant,,ENST00000531045,;PCNX3,upstream_gene_variant,,ENST00000439247,;PCNX3,upstream_gene_variant,,ENST00000530174,; T ENST00000355703 Transcript synonymous_variant 3233/7105 2694/6105 898/2034 F ttC/ttT COSM4636569,COSM4636570,COSM4636571 1 1 PCNX3 HGNC HGNC:18760 protein_coding YES CCDS44650.1 ENSP00000347931 Q9H6A9 UPI0000405B22 NM_032223.3 14/35 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF4,Transmembrane_helices:TMhelix 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS rs1156324903 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 65624344 65624344 C T 1 0 0 0 0 0 0 0 1 11681 912 32 3 3 PCNX3 11 65624344 Silent SNP C C3L-00095_T 6273 65624344 69462278 475 3684 NPAS4 0 . GRCh38 11 66424589 66424589 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.1699T>A p.Cys567Ser p.C567S ENST00000311034 7/8 128 120 8 201 201 0 strelka-varscan-mutect NPAS4,missense_variant,p.Cys567Ser,ENST00000311034,NM_178864.3;NPAS4,3_prime_UTR_variant,,ENST00000525148,;NPAS4,downstream_gene_variant,,ENST00000524617,; A ENST00000311034 Transcript missense_variant 1875/3303 1699/2409 567/802 C/S Tgc/Agc 1 1 NPAS4 HGNC HGNC:18983 protein_coding YES CCDS8138.1 ENSP00000311196 Q8IUM7 UPI0000074744 NM_178864.3 tolerated(0.1) 7/8 hmmpanther:PTHR23043:SF24,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 66424589 66424589 T A 1 0 0 0 0 1 0 0 0 10613 1464 51 4 4 NPAS4 11 66424589 Missense_Mutation SNP T C3L-00095_T 800245 66424589 68662033 476 3685 MRGPRD 0 . GRCh38 11 68980717 68980717 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.270G>A p.= p.L90L ENST00000309106 1/1 114 106 8 127 127 0 strelka-mutect MRGPRD,synonymous_variant,p.=,ENST00000309106,NM_198923.2; T ENST00000309106 Transcript synonymous_variant 270/966 270/966 90/321 L ctG/ctA 1 -1 MRGPRD HGNC HGNC:29626 protein_coding YES CCDS31625.1 ENSP00000310631 Q8TDS7 UPI000003BCCA NM_198923.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF29,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 68980717 68980717 C T 1 0 0 0 0 0 0 0 1 9729 581 21 3 3 MRGPRD 11 68980717 Silent SNP C C3L-00095_T 2556128 68980717 66105905 477 3686 SLCO2B1 0 . GRCh38 11 75169222 75169222 + Frame_Shift_Del DEL G G - rs147147496 C3L-00095_T C3L-00095_N G G c.499delG p.Ala167ProfsTer20 p.A167Pfs*20 ENST00000289575 5/14 109 100 9 194 194 0 sindel-varindel-pindel SLCO2B1,frameshift_variant,p.Ala167ProfsTer20,ENST00000289575,NM_007256.4;SLCO2B1,frameshift_variant,p.Ala51ProfsTer20,ENST00000532236,;SLCO2B1,frameshift_variant,p.Ala145ProfsTer20,ENST00000428359,NM_001145211.2;SLCO2B1,frameshift_variant,p.Ala23ProfsTer20,ENST00000525650,NM_001145212.2;SLCO2B1,frameshift_variant,p.Ala43ProfsTer20,ENST00000526839,;SLCO2B1,frameshift_variant,p.Ala145ProfsTer?,ENST00000527180,;SLCO2B1,intron_variant,,ENST00000454962,;SLCO2B1,downstream_gene_variant,,ENST00000531713,;SLCO2B1,downstream_gene_variant,,ENST00000534186,;SLCO2B1,intron_variant,,ENST00000526660,;SLCO2B1,intron_variant,,ENST00000531756,; - ENST00000289575 Transcript frameshift_variant 893/4494 498/2130 166/709 S/X tcG/tc rs147147496 1 1 SLCO2B1 HGNC HGNC:10962 protein_coding YES CCDS8235.1 ENSP00000289575 A0A024R5I4 UPI000000D99A NM_007256.4 5/14 Pfam_domain:PF03137,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF87,TIGRFAM_domain:TIGR00805 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 75169222 75169222 G - 1 0 1 0 1 0 0 0 0 15014 1103 39 0 0 SLCO2B1 11 75169222 Frame_Shift_Del DEL G C3L-00095_T 6188505 75169222 59917400 478 3687 EMSY 0 . GRCh38 11 76545865 76545865 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.3387C>T p.= p.P1129P ENST00000524767 20/21 102 90 12 116 116 0 strelka-varscan-mutect EMSY,synonymous_variant,p.=,ENST00000529032,;EMSY,synonymous_variant,p.=,ENST00000334736,NM_020193.4;EMSY,synonymous_variant,p.=,ENST00000525038,NM_001300944.1;EMSY,synonymous_variant,p.=,ENST00000524767,NM_001300942.1;EMSY,synonymous_variant,p.=,ENST00000525919,NM_001300943.1;EMSY,synonymous_variant,p.=,ENST00000524490,;EMSY,synonymous_variant,p.=,ENST00000533248,;EMSY,intron_variant,,ENST00000532719,;EMSY,downstream_gene_variant,,ENST00000524451,;EMSY,upstream_gene_variant,,ENST00000531793,;EMSY,downstream_gene_variant,,ENST00000531641,;EMSY,downstream_gene_variant,,ENST00000534573,; T ENST00000524767 Transcript synonymous_variant 3426/4116 3387/4014 1129/1337 P ccC/ccT 1 1 EMSY HGNC HGNC:18071 protein_coding YES CCDS73349.1 ENSP00000433205 Q7Z589 UPI000191704B NM_001300942.1 20/21 hmmpanther:PTHR16500,hmmpanther:PTHR16500:SF3 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 76545865 76545865 C T 1 0 0 0 0 0 0 0 1 4948 581 21 3 3 EMSY 11 76545865 Silent SNP C C3L-00095_T 1376643 76545865 58540757 479 3688 MYO7A 0 . GRCh38 11 77156904 77156904 + Missense_Mutation SNP G G A rs28934610 C3L-00095_T C3L-00095_N G G c.635G>A p.Arg212His p.R212H ENST00000409709 7/49 222 206 16 248 248 0 strelka-varscan-mutect MYO7A,missense_variant,p.Arg212His,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Arg212His,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Arg201His,ENST00000409619,;MYO7A,missense_variant,p.Arg212His,ENST00000409893,NM_001127179.2;MYO7A,missense_variant,p.Arg212His,ENST00000620575,; A ENST00000409709 Transcript missense_variant 907/7462 635/6648 212/2215 R/H cGt/cAt rs28934610,CM950827,COSM2018675 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 deleterious(0) 7/49 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF369,hmmpanther:PTHR13140,Pfam_domain:PF00063,Gene3D:3.40.50.300,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193 pathogenic 0,0,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs28934610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 77156904 77156904 G A 1 0 0 0 0 1 0 0 0 10083 1145 40 1 1 MYO7A 11 77156904 Missense_Mutation SNP G C3L-00095_T 611039 77156904 57929718 480 3689 KCTD14 0 . GRCh38 11 78016870 78016870 + Missense_Mutation SNP C C G rs372373172 C3L-00095_T C3L-00095_N C C c.491G>C p.Arg164Pro p.R164P ENST00000353172 2/2 242 216 26 293 293 0 strelka-varscan-mutect KCTD14,missense_variant,p.Arg164Pro,ENST00000353172,NM_023930.3;KCTD14,missense_variant,p.Arg134Pro,ENST00000533144,NM_001282406.1;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000530054,NM_001203261.1;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000528251,;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000612612,NM_001203260.1;NDUFC2-KCTD14,downstream_gene_variant,,ENST00000614236,NM_001203262.1;RP11-7I15.3,downstream_gene_variant,,ENST00000533697,; G ENST00000353172 Transcript missense_variant 536/1691 491/768 164/255 R/P cGg/cCg rs372373172,COSM2019198 1 -1 KCTD14 HGNC HGNC:23295 protein_coding YES CCDS8255.2 ENSP00000316482 Q9BQ13 UPI000003E7AB NM_023930.3 deleterious(0) 2/2 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372373172 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 78016870 78016870 C G 1 0 0 0 0 1 0 0 0 8018 652 23 4 4 KCTD14 11 78016870 Missense_Mutation SNP C C3L-00095_T 859966 78016870 57069752 481 3690 TENM4 0 . GRCh38 11 78670509 78670509 + Missense_Mutation SNP C C G C3L-00095_T C3L-00095_N C C c.5836G>C p.Glu1946Gln p.E1946Q ENST00000278550 32/34 94 89 5 109 109 0 strelka-varscan-mutect TENM4,missense_variant,p.Glu1946Gln,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Glu410Gln,ENST00000530738,; G ENST00000278550 Transcript missense_variant 6299/14000 5836/8310 1946/2769 E/Q Gag/Cag COSM690523,COSM690524 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 tolerated(0.14) 32/34 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 202 8 0 0 0 0 0 -10.51317 0.9999825 1 1 1 0 G 3 3 10 78670509 78670509 C G 1 0 0 0 0 1 0 0 0 16174 835 29 4 4 TENM4 11 78670509 Missense_Mutation SNP C C3L-00095_T 653639 78670509 56416113 482 3691 CCDC89 0 . GRCh38 11 85685173 85685173 + Missense_Mutation SNP C C A rs747276710 C3L-00095_T C3L-00095_N C C c.958G>T p.Ala320Ser p.A320S ENST00000316398 1/1 297 267 30 355 354 1 strelka-varscan-mutect CCDC89,missense_variant,p.Ala320Ser,ENST00000316398,NM_152723.2;CREBZF,upstream_gene_variant,,ENST00000534224,;CREBZF,upstream_gene_variant,,ENST00000531515,; A ENST00000316398 Transcript missense_variant 1105/1412 958/1125 320/374 A/S Gct/Tct rs747276710 1 -1 CCDC89 HGNC HGNC:26762 protein_coding YES CCDS8270.1 ENSP00000320649 Q8N998 UPI000000DAB1 NM_152723.2 deleterious(0.03) 1/1 hmmpanther:PTHR34768,hmmpanther:PTHR34768:SF1 MODERATE 1 SNV 1 PASS rs747276710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 85685173 85685173 C A 1 0 0 0 0 1 0 0 0 2565 739 26 2 2 CCDC89 11 85685173 Missense_Mutation SNP C C3L-00095_T 7014664 85685173 49401449 483 3692 TRIM49 0 . GRCh38 11 89804157 89804157 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.313G>C p.Glu105Gln p.E105Q ENST00000329758 3/8 135 127 8 179 179 0 varscan-mutect TRIM49,missense_variant,p.Glu105Gln,ENST00000329758,NM_020358.2;TRIM49,missense_variant,p.Glu105Gln,ENST00000532501,; G ENST00000329758 Transcript missense_variant 642/2163 313/1359 105/452 E/Q Gaa/Caa 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 deleterious(0.04) 3/8 Gene3D:1freA00,Pfam_domain:PF00643,PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00336,Superfamily_domains:SSF57845 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 89804157 89804157 C G 1 0 0 0 0 1 0 0 0 17014 835 29 4 4 TRIM49 11 89804157 Missense_Mutation SNP C C3L-00095_T 4118984 89804157 45282465 484 3693 TRIM49C 0 . GRCh38 11 90041120 90041120 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.929G>T p.Cys310Phe p.C310F ENST00000448984 8/8 377 355 22 412 412 0 varscan-mutect TRIM49C,missense_variant,p.Cys310Phe,ENST00000448984,NM_001195234.1; T ENST00000448984 Transcript missense_variant 1258/2163 929/1359 310/452 C/F tGt/tTt 1 1 TRIM49C HGNC HGNC:38877 protein_coding YES CCDS53694.1 ENSP00000388299 P0CI26 UPI000013EA2B NM_001195234.1 tolerated(0.37) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 90041120 90041120 G T 1 0 0 0 0 1 0 0 0 17016 1377 48 2 2 TRIM49C 11 90041120 Missense_Mutation SNP G C3L-00095_T 236963 90041120 45045502 485 3694 TRPC6 0 . GRCh38 11 101488964 101488964 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.1266C>A p.= p.L422L ENST00000344327 4/13 260 244 16 324 324 0 strelka-varscan-mutect TRPC6,synonymous_variant,p.=,ENST00000344327,NM_004621.5;TRPC6,synonymous_variant,p.=,ENST00000532133,;TRPC6,intron_variant,,ENST00000360497,;TRPC6,intron_variant,,ENST00000348423,;TRPC6,downstream_gene_variant,,ENST00000527240,; T ENST00000344327 Transcript synonymous_variant 1691/4612 1266/2796 422/931 L ctC/ctA 1 -1 TRPC6 HGNC HGNC:12338 protein_coding YES CCDS8311.1 ENSP00000340913 Q9Y210 UPI00001374BA NM_004621.5 4/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7,TIGRFAM_domain:TIGR00870 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 101488964 101488964 G T 1 0 0 0 0 0 0 0 1 17089 1277 45 2 2 TRPC6 11 101488964 Silent SNP G C3L-00095_T 11447844 101488964 33597658 486 3695 DYNC2H1 0 . GRCh38 11 103456347 103456347 + Silent SNP A A T rs756987000 C3L-00095_T C3L-00095_N A A c.12660A>T p.= p.L4220L ENST00000398093 88/90 149 141 8 142 142 0 strelka-varscan-mutect DYNC2H1,synonymous_variant,p.=,ENST00000375735,NM_001377.2;DYNC2H1,synonymous_variant,p.=,ENST00000398093,NM_001080463.1;DYNC2H1,synonymous_variant,p.=,ENST00000334267,;DYNC2H1,synonymous_variant,p.=,ENST00000533197,;DYNC2H1,3_prime_UTR_variant,,ENST00000528670,;DYNC2H1,non_coding_transcript_exon_variant,,ENST00000530547,; T ENST00000398093 Transcript synonymous_variant 12660/12945 12660/12945 4220/4314 L ctA/ctT rs756987000 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 88/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF03028 LOW 1 SNV 5 1 PASS rs756987000 . 0 208 2 0 0 0 0 0 -15.15748 1 1 1 1 0 T 2 4 10 103456347 103456347 A T 1 0 0 0 0 0 0 0 1 4670 378 14 4 4 DYNC2H1 11 103456347 Silent SNP A C3L-00095_T 1967383 103456347 31630275 487 3696 EXPH5 0 . GRCh38 11 108528146 108528146 + Missense_Mutation SNP C C A rs780915750 C3L-00095_T C3L-00095_N C C c.482G>T p.Gly161Val p.G161V ENST00000265843 4/6 188 174 14 254 254 0 strelka-varscan-mutect EXPH5,missense_variant,p.Gly161Val,ENST00000265843,NM_001144764.1,NM_001144765.1,NM_001144763.1,NM_015065.2;EXPH5,missense_variant,p.Gly154Val,ENST00000525344,NM_001308019.1;EXPH5,missense_variant,p.Gly85Val,ENST00000526312,;EXPH5,missense_variant,p.Gly5Val,ENST00000524840,;EXPH5,intron_variant,,ENST00000533052,;EXPH5,downstream_gene_variant,,ENST00000531386,; A ENST00000265843 Transcript missense_variant 593/10187 482/5970 161/1989 G/V gGa/gTa rs780915750 1 -1 EXPH5 HGNC HGNC:30578 protein_coding YES CCDS8341.1 ENSP00000265843 Q8NEV8 UPI00018E24EB NM_001144764.1,NM_001144765.1,NM_001144763.1,NM_015065.2 tolerated(0.12) 4/6 hmmpanther:PTHR21469 MODERATE 1 SNV 1 1 PASS rs780915750 . 0 208 0 2 0 0 0 0 -18.28579 0.9999997 1 1 1 0 A 3 1 10 108528146 108528146 C A 1 0 0 0 0 1 0 0 0 5190 855 30 2 2 EXPH5 11 108528146 Missense_Mutation SNP C C3L-00095_T 5071799 108528146 26558476 488 3697 DDX10 0 . GRCh38 11 108723069 108723069 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1572G>T p.Leu524Phe p.L524F ENST00000322536 13/18 176 155 21 196 196 0 varscan-mutect DDX10,missense_variant,p.Leu524Phe,ENST00000526794,;DDX10,missense_variant,p.Leu524Phe,ENST00000322536,NM_004398.3;RP11-801G16.2,downstream_gene_variant,,ENST00000533503,; T ENST00000322536 Transcript missense_variant 1701/3264 1572/2628 524/875 L/F ttG/ttT 1 1 DDX10 HGNC HGNC:2735 protein_coding YES CCDS8342.1 ENSP00000314348 Q13206 UPI0000140E62 NM_004398.3 deleterious(0.05) 13/18 hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF281 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 10 108723069 108723069 G T 1 0 0 0 0 1 0 0 0 4146 1339 47 2 2 DDX10 11 108723069 Missense_Mutation SNP G C3L-00095_T 194923 108723069 26363553 489 3698 ANKK1 0 . GRCh38 11 113397337 113397337 + Missense_Mutation SNP G G A rs11604671 C3L-00095_T C3L-00095_N G G c.952G>A p.Gly318Arg p.G318R ENST00000303941 6/8 134 127 7 182 182 0 strelka-varscan-mutect ANKK1,missense_variant,p.Gly318Arg,ENST00000303941,NM_178510.1;ANKK1,downstream_gene_variant,,ENST00000542948,; A ENST00000303941 Transcript missense_variant 1046/2543 952/2298 318/765 G/R Ggg/Agg rs11604671 1 1 ANKK1 HGNC HGNC:21027 protein_coding YES CCDS44734.1 ENSP00000306678 Q8NFD2 UPI000000DCCF NM_178510.1 tolerated(0.61) 6/8 2.36910921979666e+79 MODERATE 1 SNV 1 1 PASS rs11604671 . 0 129 0 3 0 0 0 77 -6.489797 0 0 1 0 0 A 3 1 10 113397337 113397337 G A 1 0 0 0 0 1 0 0 0 732 1130 39 1 1 ANKK1 11 113397337 Missense_Mutation SNP G C3L-00095_T 4674268 113397337 21689285 490 3699 SIK3 0 . GRCh38 11 116875453 116875453 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.1240-2A>T p.X414_splice ENST00000375300 206 189 17 240 240 0 strelka-varscan-mutect SIK3,splice_acceptor_variant,,ENST00000445177,;SIK3,splice_acceptor_variant,,ENST00000375300,NM_025164.4,NM_001281748.1;SIK3,splice_acceptor_variant,,ENST00000446921,NM_001281749.1;SIK3,splice_acceptor_variant,,ENST00000413553,;SIK3,splice_acceptor_variant,,ENST00000415541,;SIK3,non_coding_transcript_exon_variant,,ENST00000472648,;SIK3,upstream_gene_variant,,ENST00000480222,; A ENST00000375300 Transcript splice_acceptor_variant -/6213 1240/3966 414/1321 1 -1 SIK3 HGNC HGNC:29165 protein_coding YES CCDS8379.2 ENSP00000364449 J3KPC8 UPI000066D90F NM_025164.4,NM_001281748.1 9/23 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 116875453 116875453 T A 1 0 0 0 0 0 0 1 0 14583 1594 55 4 4 SIK3 11 116875453 Splice_Site SNP T C3L-00095_T 3478116 116875453 18211169 491 3700 KMT2A 0 . GRCh38 11 118502639 118502639 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.6747C>T p.= p.V2249V ENST00000534358 27/36 122 108 14 144 142 2 varscan-mutect KMT2A,synonymous_variant,p.=,ENST00000534358,NM_001197104.1;KMT2A,synonymous_variant,p.=,ENST00000389506,NM_005933.3;KMT2A,non_coding_transcript_exon_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534085,; T ENST00000534358 Transcript synonymous_variant 6770/16602 6747/11919 2249/3972 V gtC/gtT 1 1 KMT2A HGNC HGNC:7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 UPI0001E5E732 NM_001197104.1 27/36 PIRSF_domain:PIRSF010354 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 118502639 118502639 C T 1 0 0 0 0 0 0 0 1 8295 900 32 3 3 KMT2A 11 118502639 Silent SNP C C3L-00095_T 1627186 118502639 16583983 492 3701 BCL9L 0 . GRCh38 11 118898692 118898692 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.4223A>C p.Gln1408Pro p.Q1408P ENST00000334801 8/8 100 92 8 129 128 1 strelka-varscan-mutect BCL9L,missense_variant,p.Gln1408Pro,ENST00000334801,NM_182557.2;BCL9L,missense_variant,p.Gln1371Pro,ENST00000526143,;CXCR5,downstream_gene_variant,,ENST00000292174,NM_001716.4;BCL9L,downstream_gene_variant,,ENST00000527266,;BCL9L,downstream_gene_variant,,ENST00000530293,; G ENST00000334801 Transcript missense_variant 5188/10005 4223/4500 1408/1499 Q/P cAg/cCg 1 -1 BCL9L HGNC HGNC:23688 protein_coding YES CCDS8403.1 ENSP00000335320 Q86UU0 UPI0000192102 NM_182557.2 deleterious(0.05) 8/8 hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF3 MODERATE 1 SNV 1 1 PASS rs1209837729 . 0 207 2 0 0 0 0 0 -16.73712 1 1 1 1 0 G 3 3 10 118898692 118898692 T G 1 0 0 0 0 1 0 0 0 1529 1580 55 5 5 BCL9L 11 118898692 Missense_Mutation SNP T C3L-00095_T 396053 118898692 16187930 493 3702 FOXR1 0 . GRCh38 11 118980526 118980526 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.648C>A p.= p.G216G ENST00000317011 5/6 252 233 19 300 296 4 strelka-varscan-mutect FOXR1,missense_variant,p.Leu122Met,ENST00000533282,;FOXR1,synonymous_variant,p.=,ENST00000317011,NM_181721.2;FOXR1,intron_variant,,ENST00000531539,; A ENST00000317011 Transcript synonymous_variant 873/1159 648/879 216/292 G ggC/ggA 1 1 FOXR1 HGNC HGNC:29980 protein_coding YES CCDS31688.1 ENSP00000314806 Q6PIV2 UPI0000192103 NM_181721.2 5/6 Gene3D:1.10.10.10,Pfam_domain:PF00250,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF152,SMART_domains:SM00339,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 118980526 118980526 C A 1 0 0 0 0 0 0 0 1 5896 784 28 2 2 FOXR1 11 118980526 Silent SNP C C3L-00095_T 81834 118980526 16106096 494 3703 C2CD2L 0 . GRCh38 11 119114210 119114210 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1757C>T p.Pro586Leu p.P586L ENST00000336702 13/14 431 395 36 608 607 1 strelka-varscan-mutect C2CD2L,missense_variant,p.Pro586Leu,ENST00000336702,NM_014807.4,NM_001290474.1;C2CD2L,missense_variant,p.Pro333Leu,ENST00000528586,;C2CD2L,non_coding_transcript_exon_variant,,ENST00000525598,;C2CD2L,downstream_gene_variant,,ENST00000533458,;C2CD2L,downstream_gene_variant,,ENST00000529874,; T ENST00000336702 Transcript missense_variant 2116/4771 1757/2124 586/707 P/L cCa/cTa 1 1 C2CD2L HGNC HGNC:29000 protein_coding YES CCDS8413.1 ENSP00000338885 O14523 UPI0000192105 NM_014807.4,NM_001290474.1 tolerated(0.1) 13/14 hmmpanther:PTHR21119,hmmpanther:PTHR21119:SF8,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 119114210 119114210 C T 1 0 0 0 0 1 0 0 0 2025 594 21 3 3 C2CD2L 11 119114210 Missense_Mutation SNP C C3L-00095_T 133684 119114210 15972412 495 3704 HINFP 0 . GRCh38 11 119127087 119127087 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.143G>T p.Gly48Val p.G48V ENST00000350777 2/10 186 165 21 185 185 0 strelka-varscan-mutect HINFP,missense_variant,p.Gly48Val,ENST00000350777,NM_198971.2,NM_015517.4;HINFP,missense_variant,p.Gly48Val,ENST00000527410,NM_001243259.1;HINFP,missense_variant,p.Gly48Val,ENST00000530678,;HINFP,missense_variant,p.Gly48Val,ENST00000529988,;HINFP,non_coding_transcript_exon_variant,,ENST00000532312,;HINFP,intron_variant,,ENST00000527354,;HINFP,non_coding_transcript_exon_variant,,ENST00000529354,;HINFP,non_coding_transcript_exon_variant,,ENST00000527206,;HINFP,intron_variant,,ENST00000531360,;HINFP,upstream_gene_variant,,ENST00000527755,;HINFP,upstream_gene_variant,,ENST00000531022,;HINFP,upstream_gene_variant,,ENST00000529808,;HINFP,upstream_gene_variant,,ENST00000529610,; T ENST00000350777 Transcript missense_variant 206/3163 143/1554 48/517 G/V gGg/gTg 1 1 HINFP HGNC HGNC:17850 protein_coding YES CCDS8414.1 ENSP00000318085 Q9BQA5 A0A024R3F5 UPI000013EB5D NM_198971.2,NM_015517.4 tolerated(0.1) 2/10 hmmpanther:PTHR24391 MODERATE 1 SNV 1 1 PASS rs1416138554 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 119127087 119127087 G T 1 0 0 0 0 1 0 0 0 6998 1232 43 2 2 HINFP 11 119127087 Missense_Mutation SNP G C3L-00095_T 12877 119127087 15959535 496 3705 USP2 0 . GRCh38 11 119356922 119356922 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1731C>G p.Ser577Arg p.S577R ENST00000260187 13/13 256 238 18 320 320 0 strelka-varscan-mutect USP2,missense_variant,p.Ser577Arg,ENST00000260187,NM_004205.4;USP2,missense_variant,p.Ser334Arg,ENST00000455332,NM_001243759.1;USP2,missense_variant,p.Ser368Arg,ENST00000525735,NM_171997.2;USP2,downstream_gene_variant,,ENST00000525189,;USP2,downstream_gene_variant,,ENST00000532613,; C ENST00000260187 Transcript missense_variant,splice_region_variant 2026/3732 1731/1818 577/605 S/R agC/agG 1 -1 USP2 HGNC HGNC:12618 protein_coding YES CCDS8422.1 ENSP00000260187 O75604 UPI00001379D8 NM_004205.4 tolerated(1) 13/13 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF454,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs1168146217 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 119356922 119356922 G C 1 0 0 0 0 1 0 0 0 17592 1101 38 4 4 USP2 11 119356922 Missense_Mutation SNP G C3L-00095_T 229835 119356922 15729700 497 3706 GRIK4 0 . GRCh38 11 120819850 120819850 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.441C>A p.Ser147Arg p.S147R ENST00000527524 6/21 262 243 19 342 341 1 strelka-varscan-mutect GRIK4,missense_variant,p.Ser147Arg,ENST00000527524,NM_014619.4;GRIK4,missense_variant,p.Ser147Arg,ENST00000438375,NM_001282473.2,NM_001282470.2;GRIK4,downstream_gene_variant,,ENST00000526536,;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,; A ENST00000527524 Transcript missense_variant 728/5802 441/2871 147/956 S/R agC/agA COSM923970 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 deleterious(0) 6/21 hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 1 MODERATE 1 SNV 2 1 1 PASS rs1458696523 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 120819850 120819850 C A 1 0 0 0 0 1 0 0 0 6658 767 27 1 1 GRIK4 11 120819850 Missense_Mutation SNP C C3L-00095_T 1462928 120819850 14266772 498 3707 GRIK4 0 . GRCh38 11 120905428 120905428 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.1411G>T p.Gly471Cys p.G471C ENST00000527524 13/21 398 365 33 520 520 0 strelka-varscan-mutect GRIK4,missense_variant,p.Gly471Cys,ENST00000527524,NM_014619.4;GRIK4,missense_variant,p.Gly471Cys,ENST00000438375,NM_001282473.2,NM_001282470.2;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,; T ENST00000527524 Transcript missense_variant 1698/5802 1411/2871 471/956 G/C Ggc/Tgc COSM3444282 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 deleterious(0) 13/21 hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:3.40.190.10,Pfam_domain:PF10613,SMART_domains:SM00918,SMART_domains:SM00079,Superfamily_domains:SSF53850,Prints_domain:PR00177 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 120905428 120905428 G T 1 0 0 0 0 1 0 0 0 6658 1348 47 2 2 GRIK4 11 120905428 Missense_Mutation SNP G C3L-00095_T 85578 120905428 14181194 499 3708 GRAMD1B 0 . GRCh38 11 123613615 123613615 + Silent SNP G G T C3L-00095_T C3L-00095_N G G c.1776G>T p.= p.T592T ENST00000456860 16/21 173 153 20 233 233 0 strelka-varscan-mutect GRAMD1B,synonymous_variant,p.=,ENST00000529750,NM_020716.2;GRAMD1B,synonymous_variant,p.=,ENST00000529432,NM_001286564.1;GRAMD1B,synonymous_variant,p.=,ENST00000638157,;GRAMD1B,synonymous_variant,p.=,ENST00000635736,;GRAMD1B,synonymous_variant,p.=,ENST00000456860,NM_001286563.1;GRAMD1B,synonymous_variant,p.=,ENST00000638086,;GRAMD1B,synonymous_variant,p.=,ENST00000322282,;GRAMD1B,synonymous_variant,p.=,ENST00000450171,;GRAMD1B,downstream_gene_variant,,ENST00000534764,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000525945,; T ENST00000456860 Transcript synonymous_variant 2289/2805 1776/2238 592/745 T acG/acT COSM4018822,COSM4018823 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 16/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319 1,1 LOW 1 SNV 2 1,1 1 PASS rs1351653711 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 123613615 123613615 G T 1 0 0 0 0 0 0 0 1 6627 1074 38 1 1 GRAMD1B 11 123613615 Silent SNP G C3L-00095_T 2708187 123613615 11473007 500 3709 OR6X1 0 . GRCh38 11 123753960 123753960 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.559T>C p.Cys187Arg p.C187R ENST00000327930 1/1 191 178 13 254 254 0 strelka-varscan-mutect OR6X1,missense_variant,p.Cys187Arg,ENST00000327930,NM_001005188.1; G ENST00000327930 Transcript missense_variant 586/1058 559/939 187/312 C/R Tgc/Cgc 1 -1 OR6X1 HGNC HGNC:14737 protein_coding YES CCDS31695.1 ENSP00000333724 Q8NH79 A0A126GVM0 UPI000004B1D5 NM_001005188.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF30,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 123753960 123753960 A G 1 0 0 0 0 1 0 0 0 11282 188 7 5 5 OR6X1 11 123753960 Missense_Mutation SNP A C3L-00095_T 140345 123753960 11332662 501 3710 ROBO3 0 . GRCh38 11 124865595 124865595 + Silent SNP G G T C3L-00095_T C3L-00095_N G G c.18G>T p.= p.L6L ENST00000397801 1/28 171 149 22 193 193 0 strelka-varscan-mutect ROBO3,synonymous_variant,p.=,ENST00000397801,NM_022370.3;ROBO3,upstream_gene_variant,,ENST00000538940,; T ENST00000397801 Transcript synonymous_variant 210/4569 18/4161 6/1386 L ctG/ctT COSM4722359,COSM4722360 1 1 ROBO3 HGNC HGNC:13433 protein_coding YES CCDS44755.1 ENSP00000380903 Q96MS0 UPI000035AA82 NM_022370.3 1/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF724,Cleavage_site_(Signalp):SignalP-noTM 1,1 LOW 1 SNV 1 1,1 1 PASS rs945854353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 124865595 124865595 G T 1 0 0 0 0 0 0 0 1 13693 1277 45 2 2 ROBO3 11 124865595 Silent SNP G C3L-00095_T 1111635 124865595 10221027 502 3711 HEPN1 0 . GRCh38 11 124919907 124919907 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.157T>C p.Ser53Pro p.S53P ENST00000408930 1/1 319 298 21 398 398 0 strelka-varscan-mutect HEPN1,missense_variant,p.Ser53Pro,ENST00000408930,NM_001037558.2;HEPACAM,3_prime_UTR_variant,,ENST00000298251,NM_152722.4;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; C ENST00000408930 Transcript missense_variant 664/1434 157/267 53/88 S/P Tct/Cct 1 1 HEPN1 HGNC HGNC:34400 protein_coding YES CCDS41729.1 ENSP00000386143 Q6WQI6 UPI0000D6269C NM_001037558.2 deleterious_low_confidence(0.01) 1/1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 124919907 124919907 T C 1 0 0 0 0 1 0 0 0 6940 1551 54 5 5 HEPN1 11 124919907 Missense_Mutation SNP T C3L-00095_T 54312 124919907 10166715 503 3712 STT3A 0 . GRCh38 11 125602927 125602927 + Frame_Shift_Del DEL C C - novel C3L-00095_T C3L-00095_N C C c.397delC p.His133ThrfsTer18 p.H133Tfs*18 ENST00000392708 5/18 238 218 20 279 278 1 sindel-varindel-pindel STT3A,frameshift_variant,p.His133ThrfsTer18,ENST00000392708,NM_152713.4,NM_001278503.1;STT3A,frameshift_variant,p.His133ThrfsTer18,ENST00000529196,;STT3A,frameshift_variant,p.His41ThrfsTer18,ENST00000531491,NM_001278504.1;STT3A,downstream_gene_variant,,ENST00000525652,;STT3A,upstream_gene_variant,,ENST00000526726,;STT3A,downstream_gene_variant,,ENST00000527606,;STT3A,downstream_gene_variant,,ENST00000529886,;STT3A,upstream_gene_variant,,ENST00000527456,;STT3A,non_coding_transcript_exon_variant,,ENST00000534472,;STT3A,non_coding_transcript_exon_variant,,ENST00000526213,;STT3A,upstream_gene_variant,,ENST00000525431,; - ENST00000392708 Transcript frameshift_variant 555/4558 396/2118 132/705 Y/X taC/ta 1 1 STT3A HGNC HGNC:6172 protein_coding YES CCDS8458.1 ENSP00000376472 P46977 UPI0000071627 NM_152713.4,NM_001278503.1 5/18 Pfam_domain:PF02516,hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF26 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 125602927 125602927 C - 1 0 1 0 1 0 0 0 0 15716 518 18 0 0 STT3A 11 125602927 Frame_Shift_Del DEL C C3L-00095_T 683020 125602927 9483695 504 3713 KIRREL3 0 . GRCh38 11 126463233 126463233 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.666C>A p.= p.G222G ENST00000525144 6/17 98 93 5 134 134 0 strelka-varscan-mutect KIRREL3,synonymous_variant,p.=,ENST00000525144,NM_032531.3;KIRREL3,synonymous_variant,p.=,ENST00000529097,NM_001301097.1;KIRREL3,synonymous_variant,p.=,ENST00000525704,NM_001161707.1; T ENST00000525144 Transcript synonymous_variant 916/3808 666/2337 222/778 G ggC/ggA 1 -1 KIRREL3 HGNC HGNC:23204 protein_coding YES CCDS53723.1 ENSP00000435466 Q8IZU9 UPI00000740A0 NM_032531.3 6/17 Gene3D:2.60.40.10,Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF49,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 126463233 126463233 G T 1 0 0 0 0 0 0 0 1 8190 1190 42 2 2 KIRREL3 11 126463233 Silent SNP G C3L-00095_T 860306 126463233 8623389 505 3714 IGSF9B 0 . GRCh38 11 133944295 133944295 + Nonsense_Mutation SNP C C A rs756264444 C3L-00095_T C3L-00095_N C C c.334G>T p.Glu112Ter p.E112* ENST00000533871 3/20 193 183 10 227 226 1 strelka-varscan-mutect IGSF9B,stop_gained,p.Glu112Ter,ENST00000533871,NM_001277285.1;IGSF9B,stop_gained,p.Glu112Ter,ENST00000321016,;IGSF9B,stop_gained,p.Glu102Ter,ENST00000533160,;IGSF9B,stop_gained,p.Glu159Ter,ENST00000526663,; A ENST00000533871 Transcript stop_gained 565/5050 334/4314 112/1437 E/* Gag/Tag rs756264444 1 -1 IGSF9B HGNC HGNC:32326 protein_coding YES CCDS61010.1 ENSP00000436552 Q9UPX0 UPI0002C439DB NM_001277285.1 3/20 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF681,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS rs756264444 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 133944295 133944295 C A 1 0 0 0 0 0 1 0 0 7514 835 29 2 2 IGSF9B 11 133944295 Nonsense_Mutation SNP C C3L-00095_T 7481062 133944295 1142327 506 3715 KDM5A 0 . GRCh38 12 295655 295655 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.4373C>T p.Ser1458Phe p.S1458F ENST00000399788 26/28 376 349 27 530 530 0 strelka-varscan-mutect KDM5A,missense_variant,p.Ser1458Phe,ENST00000399788,NM_001042603.2;KDM5A,upstream_gene_variant,,ENST00000540838,; A ENST00000399788 Transcript missense_variant 4736/10763 4373/5073 1458/1690 S/F tCt/tTt 1 -1 KDM5A HGNC HGNC:9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.2 deleterious(0.01) 26/28 hmmpanther:PTHR10694:SF17,hmmpanther:PTHR10694 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 295655 295655 G A 1 0 0 0 0 1 0 0 0 8051 942 33 3 3 KDM5A 12 295655 Missense_Mutation SNP G C3L-00095_T 295655 132979654 507 3716 CACNA1C 0 . GRCh38 12 2449069 2449069 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.571C>A p.Leu191Ile p.L191I ENST00000347598 4/49 102 95 7 148 147 1 strelka-varscan-mutect CACNA1C,missense_variant,p.Leu191Ile,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000406454,;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000335762,;CACNA1C,missense_variant,p.Leu191Ile,ENST00000480911,;CACNA1C,missense_variant,p.Leu191Ile,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Leu191Ile,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Leu191Ile,ENST00000399644,NM_001129841.1; A ENST00000347598 Transcript missense_variant 571/6655 571/6561 191/2186 L/I Ctc/Atc 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 tolerated(0.29) 4/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 2449069 2449069 C A 1 0 0 0 0 1 0 0 0 2228 681 24 2 2 CACNA1C 12 2449069 Missense_Mutation SNP C C3L-00095_T 2153414 2449069 130826240 508 3717 CACNA1C 0 . GRCh38 12 2651702 2651702 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.4152G>T p.= p.L1384L ENST00000347598 34/49 93 86 7 91 91 0 strelka-mutect CACNA1C,synonymous_variant,p.=,ENST00000399655,NM_000719.6;CACNA1C,synonymous_variant,p.=,ENST00000399634,NM_001167625.1;CACNA1C,synonymous_variant,p.=,ENST00000406454,;CACNA1C,synonymous_variant,p.=,ENST00000399617,NM_001167624.2;CACNA1C,synonymous_variant,p.=,ENST00000399603,NM_001167623.1;CACNA1C,synonymous_variant,p.=,ENST00000335762,;CACNA1C,synonymous_variant,p.=,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,synonymous_variant,p.=,ENST00000344100,NM_001129829.1;CACNA1C,synonymous_variant,p.=,ENST00000327702,NM_001129830.2;CACNA1C,synonymous_variant,p.=,ENST00000399638,NM_001129831.1;CACNA1C,synonymous_variant,p.=,ENST00000399606,NM_001129832.1;CACNA1C,synonymous_variant,p.=,ENST00000399621,NM_001129834.1;CACNA1C,synonymous_variant,p.=,ENST00000399637,NM_001129835.1;CACNA1C,synonymous_variant,p.=,ENST00000402845,NM_001129833.1;CACNA1C,synonymous_variant,p.=,ENST00000399629,NM_001129836.1;CACNA1C,synonymous_variant,p.=,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,synonymous_variant,p.=,ENST00000399595,NM_001129837.1;CACNA1C,synonymous_variant,p.=,ENST00000399649,NM_001129839.1;CACNA1C,synonymous_variant,p.=,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,synonymous_variant,p.=,ENST00000399601,NM_001129843.1;CACNA1C,synonymous_variant,p.=,ENST00000399641,NM_001129840.1;CACNA1C,synonymous_variant,p.=,ENST00000399644,NM_001129841.1;CACNA1C,synonymous_variant,p.=,ENST00000616390,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000483136,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000492150,; T ENST00000347598 Transcript synonymous_variant 4152/6655 4152/6561 1384/2186 L ctG/ctT 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 34/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS rs1396500469 . 0 206 3 0 0 0 0 0 -14.83174 1 1 1 1 0 T 2 4 10 2651702 2651702 G T 1 0 0 0 0 0 0 0 1 2228 1335 47 2 2 CACNA1C 12 2651702 Silent SNP G C3L-00095_T 202633 2651702 130623607 509 3718 NTF3 0 . GRCh38 12 5494245 5494245 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.70G>A p.Ala24Thr p.A24T ENST00000423158 2/2 194 162 32 195 195 0 strelka-varscan-mutect NTF3,missense_variant,p.Ala24Thr,ENST00000423158,NM_001102654.1;NTF3,missense_variant,p.Ala11Thr,ENST00000331010,NM_002527.4;NTF3,non_coding_transcript_exon_variant,,ENST00000543548,;NTF3,intron_variant,,ENST00000535299,; A ENST00000423158 Transcript missense_variant 282/1336 70/813 24/270 A/T Gct/Act COSM941346 1 1 NTF3 HGNC HGNC:8023 protein_coding YES CCDS44806.1 ENSP00000397297 P20783 UPI0000D4F126 NM_001102654.1 tolerated(0.09) 2/2 PIRSF_domain:PIRSF001789,Prints_domain:PR01914,hmmpanther:PTHR11589,hmmpanther:PTHR11589:SF4,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS rs954273394 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 5494245 5494245 G A 1 0 0 0 0 1 0 0 0 10760 1087 38 1 1 NTF3 12 5494245 Missense_Mutation SNP G C3L-00095_T 2842543 5494245 127781064 510 3719 TMEM52B 0 . GRCh38 12 10186468 10186468 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.186C>T p.= p.S62S ENST00000381923 5/6 107 95 12 139 139 0 strelka-mutect TMEM52B,synonymous_variant,p.=,ENST00000298530,NM_153022.3;TMEM52B,synonymous_variant,p.=,ENST00000381923,NM_001079815.1;TMEM52B,synonymous_variant,p.=,ENST00000543484,;TMEM52B,non_coding_transcript_exon_variant,,ENST00000546153,; T ENST00000381923 Transcript synonymous_variant 590/2601 186/552 62/183 S tcC/tcT 1 1 TMEM52B HGNC HGNC:26438 protein_coding YES CCDS66314.1 ENSP00000371348 Q4KMG9 UPI000003777F NM_001079815.1 5/6 Pfam_domain:PF14979,hmmpanther:PTHR33955,hmmpanther:PTHR33955:SF1,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -19.99998 0.9999999 1 1 1 0 T 2 4 10 10186468 10186468 C T 1 0 0 0 0 0 0 0 1 16654 610 22 3 3 TMEM52B 12 10186468 Silent SNP C C3L-00095_T 4692223 10186468 123088841 511 3720 FAM234B 0 . GRCh38 12 13061612 13061612 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.570G>T p.= p.S190S ENST00000197268 4/13 93 84 9 112 112 0 strelka-varscan-mutect FAM234B,synonymous_variant,p.=,ENST00000197268,NM_020853.1;FAM234B,upstream_gene_variant,,ENST00000537625,;FAM234B,upstream_gene_variant,,ENST00000535974,;FAM234B,synonymous_variant,p.=,ENST00000416494,;FAM234B,upstream_gene_variant,,ENST00000541950,; T ENST00000197268 Transcript synonymous_variant 690/4808 570/1869 190/622 S tcG/tcT 1 1 FAM234B HGNC HGNC:29288 protein_coding YES CCDS31750.1 ENSP00000197268 A2RU67 UPI00001FB6A1 NM_020853.1 4/13 hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF25,Gene3D:2.140.10.10,Superfamily_domains:SSF50998 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -14.39328 0.9999952 1 1 1 0 T 2 4 10 13061612 13061612 G T 1 0 0 0 0 0 0 0 1 5425 1103 39 1 1 FAM234B 12 13061612 Silent SNP G C3L-00095_T 2875144 13061612 120213697 512 3721 REP15 0 . GRCh38 12 27697145 27697145 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.583G>T p.Gly195Trp p.G195W ENST00000310791 1/1 257 235 22 285 284 1 strelka-varscan-mutect REP15,missense_variant,p.Gly195Trp,ENST00000310791,NM_001029874.1;PPFIBP1,downstream_gene_variant,,ENST00000318304,NM_177444.2;PPFIBP1,downstream_gene_variant,,ENST00000228425,NM_003622.3;PPFIBP1,downstream_gene_variant,,ENST00000537927,NM_001198915.1;PPFIBP1,downstream_gene_variant,,ENST00000542629,NM_001198916.1;PPFIBP1,downstream_gene_variant,,ENST00000539326,;RP11-1060J15.4,non_coding_transcript_exon_variant,,ENST00000542660,;RP11-1060J15.4,intron_variant,,ENST00000536317,;RP11-1060J15.4,intron_variant,,ENST00000536922,;RP11-1060J15.9,upstream_gene_variant,,ENST00000619202,; T ENST00000310791 Transcript missense_variant 627/1078 583/711 195/236 G/W Ggg/Tgg 1 1 REP15 HGNC HGNC:33748 protein_coding YES CCDS31762.1 ENSP00000310335 Q6BDI9 UPI000013F083 NM_001029874.1 deleterious(0.02) 1/1 hmmpanther:PTHR36682:SF1,hmmpanther:PTHR36682,Pfam_domain:PF15208 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 27697145 27697145 G T 1 0 0 0 0 1 0 0 0 13396 1000 35 2 2 REP15 12 27697145 Missense_Mutation SNP G C3L-00095_T 14635533 27697145 105578164 513 3722 H3F3C 0 . GRCh38 12 31791881 31791881 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.286A>G p.Ser96Gly p.S96G ENST00000340398 1/1 267 239 28 372 372 0 strelka-varscan-mutect H3F3C,missense_variant,p.Ser96Gly,ENST00000340398,NM_001013699.2; C ENST00000340398 Transcript missense_variant 361/1057 286/408 96/135 S/G Agc/Ggc 1 -1 H3F3C HGNC HGNC:33164 protein_coding YES CCDS31769.1 ENSP00000339835 Q6NXT2 UPI0000185FBF NM_001013699.2 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 31791881 31791881 T C 1 0 0 0 0 1 0 0 0 6817 1522 53 5 5 H3F3C 12 31791881 Missense_Mutation SNP T C3L-00095_T 4094736 31791881 101483428 514 3723 12 2 H3F3C 0 . GRCh38 12 31791883 31791883 + Missense_Mutation SNP G G A rs754924469 C3L-00095_T C3L-00095_N G G c.284C>T p.Ala95Val p.A95V ENST00000340398 1/1 264 237 27 374 374 0 strelka-varscan-mutect H3F3C,missense_variant,p.Ala95Val,ENST00000340398,NM_001013699.2; A ENST00000340398 Transcript missense_variant 359/1057 284/408 95/135 A/V gCt/gTt rs754924469 1 -1 H3F3C HGNC HGNC:33164 protein_coding YES CCDS31769.1 ENSP00000339835 Q6NXT2 UPI0000185FBF NM_001013699.2 deleterious_low_confidence(0.01) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS rs754924469 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 31791883 31791883 G A 1 0 0 0 0 1 0 0 0 6817 971 34 3 3 H3F3C 12 31791883 Missense_Mutation SNP G C3L-00095_T 2 31791883 101483426 515 3724 12 2 BICD1 0 . GRCh38 12 32327610 32327610 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1155G>T p.Lys385Asn p.K385N ENST00000281474 5/10 156 148 8 218 218 0 strelka-varscan-mutect BICD1,missense_variant,p.Lys385Asn,ENST00000548411,NM_001003398.1;BICD1,missense_variant,p.Lys385Asn,ENST00000281474,NM_001714.2;BICD1,upstream_gene_variant,,ENST00000547680,;BICD1,missense_variant,p.Lys385Asn,ENST00000395758,; T ENST00000281474 Transcript missense_variant 1258/3281 1155/2928 385/975 K/N aaG/aaT 1 1 BICD1 HGNC HGNC:1049 protein_coding YES CCDS8726.1 ENSP00000281474 Q96G01 UPI00001AEA67 NM_001714.2 tolerated(0.09) 5/10 hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF3,Pfam_domain:PF09730 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.79865 0.9999993 1 1 1 0 T 3 4 10 32327610 32327610 G T 1 0 0 0 0 1 0 0 0 1577 991 35 2 2 BICD1 12 32327610 Missense_Mutation SNP G C3L-00095_T 535727 32327610 100947699 516 3725 PDZRN4 0 . GRCh38 12 41194095 41194095 + Silent SNP A A T novel C3L-00095_T C3L-00095_N A A c.750A>T p.= p.G250G ENST00000402685 3/10 190 173 17 186 186 0 strelka-varscan-mutect PDZRN4,synonymous_variant,p.=,ENST00000402685,NM_001164595.1; T ENST00000402685 Transcript synonymous_variant 758/3347 750/3111 250/1036 G ggA/ggT 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 3/10 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 41194095 41194095 A T 1 0 0 0 0 0 0 0 1 11798 233 9 4 4 PDZRN4 12 41194095 Silent SNP A C3L-00095_T 8866485 41194095 92081214 517 3726 ADAMTS20 0 . GRCh38 12 43551029 43551029 + Silent SNP G G A rs779415291 C3L-00095_T C3L-00095_N G G c.333C>T p.= p.T111T ENST00000389420 2/39 194 180 14 266 266 0 strelka-mutect ADAMTS20,synonymous_variant,p.=,ENST00000389420,NM_025003.3;ADAMTS20,synonymous_variant,p.=,ENST00000395541,;ADAMTS20,synonymous_variant,p.=,ENST00000553158,; A ENST00000389420 Transcript synonymous_variant 333/6076 333/5733 111/1910 T acC/acT rs779415291 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 2/39 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01562 LOW 1 SNV 1 1 PASS rs779415291 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 43551029 43551029 G A 1 0 0 0 0 0 0 0 1 310 1219 43 3 3 ADAMTS20 12 43551029 Silent SNP G C3L-00095_T 2356934 43551029 89724280 518 3727 KRT71 0 . GRCh38 12 52550094 52550094 + Silent SNP C C G novel C3L-00095_T C3L-00095_N C C c.591G>C p.= p.G197G ENST00000267119 2/9 339 313 26 493 492 1 varscan-mutect KRT71,synonymous_variant,p.=,ENST00000267119,NM_033448.2; G ENST00000267119 Transcript synonymous_variant 661/2265 591/1572 197/523 G ggG/ggC 1 -1 KRT71 HGNC HGNC:28927 protein_coding YES CCDS8831.1 ENSP00000267119 Q3SY84 UPI0000052B57 NM_033448.2 2/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF116,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 52550094 52550094 C G 1 0 0 0 0 0 0 0 1 8366 610 22 4 4 KRT71 12 52550094 Silent SNP C C3L-00095_T 8999065 52550094 80725215 519 3728 KRT3 0 . GRCh38 12 52791312 52791312 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1429G>A p.Asp477Asn p.D477N ENST00000417996 7/9 281 254 27 375 374 1 strelka-varscan-mutect KRT3,missense_variant,p.Asp477Asn,ENST00000417996,NM_057088.2; T ENST00000417996 Transcript missense_variant 1504/2319 1429/1887 477/628 D/N Gac/Aac 1 -1 KRT3 HGNC HGNC:6440 protein_coding YES CCDS44895.1 ENSP00000413479 P12035 UPI000013EEC8 NM_057088.2 deleterious(0.02) 7/9 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF140,Low_complexity_(Seg):seg,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 52791312 52791312 C T 1 0 0 0 0 1 0 0 0 8348 826 29 3 3 KRT3 12 52791312 Missense_Mutation SNP C C3L-00095_T 241218 52791312 80483997 520 3729 MMP19 0 . GRCh38 12 55838516 55838516 + Nonsense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.739C>T p.Gln247Ter p.Q247* ENST00000409200 5/7 387 357 30 512 512 0 strelka-varscan-mutect MMP19,stop_gained,p.Gln247Ter,ENST00000409200,NM_001272101.1;MMP19,intron_variant,,ENST00000322569,NM_002429.5;MMP19,intron_variant,,ENST00000548629,;TMEM198B,downstream_gene_variant,,ENST00000478241,;TMEM198B,downstream_gene_variant,,ENST00000508246,;TMEM198B,downstream_gene_variant,,ENST00000482378,;TMEM198B,downstream_gene_variant,,ENST00000471276,;TMEM198B,downstream_gene_variant,,ENST00000487582,;TMEM198B,downstream_gene_variant,,ENST00000636428,;TMEM198B,downstream_gene_variant,,ENST00000636659,;TMEM198B,downstream_gene_variant,,ENST00000635938,;TMEM198B,downstream_gene_variant,,ENST00000637783,;TMEM198B,downstream_gene_variant,,ENST00000637951,;MMP19,downstream_gene_variant,,ENST00000547487,;TMEM198B,downstream_gene_variant,,ENST00000637092,;TMEM198B,downstream_gene_variant,,ENST00000637087,;MMP19,downstream_gene_variant,,ENST00000547299,;MMP19,3_prime_UTR_variant,,ENST00000548882,;MMP19,3_prime_UTR_variant,,ENST00000552872,;MMP19,3_prime_UTR_variant,,ENST00000552763,;MMP19,non_coding_transcript_exon_variant,,ENST00000547685,;TMEM198B,downstream_gene_variant,,ENST00000484016,; A ENST00000409200 Transcript stop_gained 845/1431 739/918 247/305 Q/* Cag/Tag 1 -1 MMP19 HGNC HGNC:7165 protein_coding CCDS61146.1 ENSP00000386625 Q99542 UPI00017A8387 NM_001272101.1 5/7 SMART_domains:SM00235 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 55838516 55838516 G A 1 0 0 0 0 0 1 0 0 9620 1299 45 3 3 MMP19 12 55838516 Nonsense_Mutation SNP G C3L-00095_T 3047204 55838516 77436793 521 3730 MMP19 0 . GRCh38 12 55840821 55840821 + Silent SNP G G T rs772008075 C3L-00095_T C3L-00095_N G G c.366C>A p.= p.P122P ENST00000322569 4/9 102 91 11 151 150 1 strelka-varscan-mutect MMP19,splice_region_variant,,ENST00000548629,;MMP19,synonymous_variant,p.=,ENST00000322569,NM_002429.5;MMP19,synonymous_variant,p.=,ENST00000409200,NM_001272101.1;TMEM198B,downstream_gene_variant,,ENST00000478241,;TMEM198B,downstream_gene_variant,,ENST00000508246,;TMEM198B,downstream_gene_variant,,ENST00000482378,;TMEM198B,downstream_gene_variant,,ENST00000471276,;TMEM198B,downstream_gene_variant,,ENST00000487582,;MMP19,downstream_gene_variant,,ENST00000547487,;MMP19,downstream_gene_variant,,ENST00000547299,;MMP19,missense_variant,p.Pro79Thr,ENST00000552763,;MMP19,3_prime_UTR_variant,,ENST00000552872,;MMP19,intron_variant,,ENST00000548882,;MMP19,upstream_gene_variant,,ENST00000547685,; T ENST00000322569 Transcript synonymous_variant 458/2229 366/1527 122/508 P ccC/ccA rs772008075 1 -1 MMP19 HGNC HGNC:7165 protein_coding YES CCDS8895.1 ENSP00000313437 Q99542 UPI0000030AE6 NM_002429.5 4/9 hmmpanther:PTHR10201:SF158,hmmpanther:PTHR10201,PIRSF_domain:PIRSF001191,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS rs772008075 . 0 204 6 0 0 0 0 0 -19.99826 0.9999999 1 1 1 0 T 2 4 10 55840821 55840821 G T 1 0 0 0 0 0 0 0 1 9620 1219 43 2 2 MMP19 12 55840821 Silent SNP G C3L-00095_T 2305 55840821 77434488 522 3731 DPY19L2 0 . GRCh38 12 63626475 63626475 + Silent SNP A A G novel C3L-00095_T C3L-00095_N A A c.855T>C p.= p.H285H ENST00000324472 7/22 150 142 8 87 87 0 varscan-mutect DPY19L2,synonymous_variant,p.=,ENST00000324472,NM_173812.4;RP11-415I12.3,intron_variant,,ENST00000509615,;DPY19L2,3_prime_UTR_variant,,ENST00000306389,; G ENST00000324472 Transcript synonymous_variant 1039/4060 855/2277 285/758 H caT/caC 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 7/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 63626475 63626475 A G 1 0 0 0 0 0 0 0 1 4556 214 8 5 5 DPY19L2 12 63626475 Silent SNP A C3L-00095_T 7785654 63626475 69648834 523 3732 PTPRB 0 . GRCh38 12 70569783 70569783 + Missense_Mutation SNP C C T rs527418611 C3L-00095_T C3L-00095_N C C c.3526G>A p.Val1176Ile p.V1176I ENST00000334414 14/34 597 559 38 690 690 0 strelka-varscan-mutect PTPRB,missense_variant,p.Val1176Ile,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Val1088Ile,ENST00000550358,;PTPRB,missense_variant,p.Val958Ile,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Val958Ile,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Val868Ile,ENST00000550857,NM_001206971.1;PTPRB,missense_variant,p.Val1175Ile,ENST00000551525,;PTPRB,missense_variant,p.Val1055Ile,ENST00000548122,;RP11-785D18.3,upstream_gene_variant,,ENST00000615051,; T ENST00000334414 Transcript missense_variant 3571/12316 3526/6648 1176/2215 V/I Gtc/Atc rs527418611 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 tolerated(0.49) 14/34 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs527418611 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 70569783 70569783 C T 1 0 0 0 0 1 0 0 0 12950 536 19 1 1 PTPRB 12 70569783 Missense_Mutation SNP C C3L-00095_T 6943308 70569783 62705526 524 3733 PTPRR 0 . GRCh38 12 70745864 70745864 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.961G>T p.Val321Phe p.V321F ENST00000283228 6/14 254 235 19 361 361 0 strelka-varscan-mutect PTPRR,missense_variant,p.Val321Phe,ENST00000283228,NM_002849.3;PTPRR,missense_variant,p.Val76Phe,ENST00000440835,NM_130846.2;PTPRR,missense_variant,p.Val115Phe,ENST00000378778,NM_001207016.1;PTPRR,missense_variant,p.Val209Phe,ENST00000342084,NM_001207015.1;PTPRR,missense_variant,p.Val76Phe,ENST00000549308,;PTPRR,missense_variant,p.Val76Phe,ENST00000550661,;PTPRR,non_coding_transcript_exon_variant,,ENST00000548220,;PTPRR,5_prime_UTR_variant,,ENST00000551219,; A ENST00000283228 Transcript missense_variant 1414/3529 961/1974 321/657 V/F Gtt/Ttt 1 -1 PTPRR HGNC HGNC:9680 protein_coding YES CCDS8998.1 ENSP00000283228 Q15256 UPI000013DD2F NM_002849.3 tolerated(0.08) 6/14 hmmpanther:PTHR19134:SF264,hmmpanther:PTHR19134,PIRSF_domain:PIRSF001997 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 70745864 70745864 C A 1 0 0 0 0 1 0 0 0 12965 478 17 2 2 PTPRR 12 70745864 Missense_Mutation SNP C C3L-00095_T 176081 70745864 62529445 525 3734 NAV3 0 . GRCh38 12 77968652 77968652 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.621C>A p.= p.S207S ENST00000397909 5/40 192 170 22 279 279 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,synonymous_variant,p.=,ENST00000550042,;NAV3,synonymous_variant,p.=,ENST00000550503,;NAV3,non_coding_transcript_exon_variant,,ENST00000547725,; A ENST00000397909 Transcript synonymous_variant 794/9821 621/7158 207/2385 S tcC/tcA 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 5/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS rs1362077082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 77968652 77968652 C A 1 0 0 0 0 0 0 0 1 10194 610 22 2 2 NAV3 12 77968652 Silent SNP C C3L-00095_T 7222788 77968652 55306657 526 3735 PTPRQ 0 . GRCh38 12 80634952 80634952 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.5794C>A p.Gln1932Lys p.Q1932K ENST00000614701 35/45 187 171 16 222 222 0 strelka-varscan-mutect PTPRQ,missense_variant,p.Gln1932Lys,ENST00000614701,NM_001145026.1;PTPRQ,missense_variant,p.Gln1974Lys,ENST00000616559,;PTPRQ,missense_variant,p.Gln27Lys,ENST00000547881,;PTPRQ,non_coding_transcript_exon_variant,,ENST00000549355,; A ENST00000614701 Transcript missense_variant 5972/8289 5794/6900 1932/2299 Q/K Cag/Aag 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 deleterious(0.02) 35/45 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 80634952 80634952 C A 1 0 0 0 0 1 0 0 0 12964 479 17 2 2 PTPRQ 12 80634952 Missense_Mutation SNP C C3L-00095_T 2666300 80634952 52640357 527 3736 ACSS3 0 . GRCh38 12 81134895 81134895 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.536C>G p.Pro179Arg p.P179R ENST00000548058 3/16 144 130 14 196 196 0 strelka-varscan-mutect ACSS3,missense_variant,p.Pro179Arg,ENST00000548058,NM_024560.2;ACSS3,missense_variant,p.Pro178Arg,ENST00000261206,;ACSS3,missense_variant,p.Pro71Arg,ENST00000549175,;ACSS3,non_coding_transcript_exon_variant,,ENST00000548387,; G ENST00000548058 Transcript missense_variant 1446/9254 536/2061 179/686 P/R cCa/cGa 1 1 ACSS3 HGNC HGNC:24723 protein_coding YES CCDS9022.1 ENSP00000449535 Q9H6R3 UPI000007060A NM_024560.2 deleterious(0) 3/16 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF199,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 81134895 81134895 C G 1 0 0 0 0 1 0 0 0 233 594 21 4 4 ACSS3 12 81134895 Missense_Mutation SNP C C3L-00095_T 499943 81134895 52140414 528 3737 NTS 0 . GRCh38 12 85876697 85876697 + Nonsense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.131C>G p.Ser44Ter p.S44* ENST00000256010 2/4 144 136 8 76 76 0 strelka-mutect NTS,stop_gained,p.Ser44Ter,ENST00000256010,NM_006183.4;NTS,stop_gained,p.Ser44Ter,ENST00000551529,;NTS,upstream_gene_variant,,ENST00000550879,; G ENST00000256010 Transcript stop_gained 238/1237 131/513 44/170 S/* tCa/tGa 1 1 NTS HGNC HGNC:8038 protein_coding YES CCDS9029.1 ENSP00000256010 P30990 Q6FH20 UPI0000000CAD NM_006183.4 2/4 PD016590,Pfam_domain:PF07421,Prints_domain:PR01668,hmmpanther:PTHR15356,hmmpanther:PTHR15356:SF0 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 10 85876697 85876697 C G 1 0 0 0 0 0 1 0 0 10775 840 29 4 4 NTS 12 85876697 Nonsense_Mutation SNP C C3L-00095_T 4741802 85876697 47398612 529 3738 C12orf42 0 . GRCh38 12 103306314 103306314 + Silent SNP C C A rs762265739 C3L-00095_T C3L-00095_N C C c.291G>T p.= p.A97A ENST00000378113 5/6 108 98 10 158 158 0 strelka-varscan-mutect C12orf42,synonymous_variant,p.=,ENST00000548048,;C12orf42,synonymous_variant,p.=,ENST00000378113,NM_001099336.2,NM_001278419.1;C12orf42,synonymous_variant,p.=,ENST00000548883,NM_198521.3;C12orf42,synonymous_variant,p.=,ENST00000552578,;C12orf42,non_coding_transcript_exon_variant,,ENST00000548789,;C12orf42,intron_variant,,ENST00000546526,;C12orf42,intron_variant,,ENST00000552977,;C12orf42,intron_variant,,ENST00000550650,;C12orf42,3_prime_UTR_variant,,ENST00000551134,;C12orf42,intron_variant,,ENST00000547347,; A ENST00000378113 Transcript synonymous_variant 556/1513 291/1083 97/360 A gcG/gcT rs762265739,COSM934132 1 -1 C12orf42 HGNC HGNC:24729 protein_coding YES CCDS44963.1 ENSP00000367353 Q96LP6 UPI00001D7906 NM_001099336.2,NM_001278419.1 5/6 Pfam_domain:PF15380,hmmpanther:PTHR40708,hmmpanther:PTHR40708:SF1 0,1 LOW 1 SNV 5 0,1 1 PASS rs762265739 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 103306314 103306314 C A 1 0 0 0 0 0 0 0 1 1810 523 19 1 1 C12orf42 12 103306314 Silent SNP C C3L-00095_T 17429617 103306314 29968995 530 3739 STAB2 0 . GRCh38 12 103594429 103594429 + Missense_Mutation SNP C C A rs767043794 C3L-00095_T C3L-00095_N C C c.250C>A p.Leu84Ile p.L84I ENST00000388887 3/69 249 218 31 314 314 0 strelka-mutect STAB2,missense_variant,p.Leu84Ile,ENST00000388887,NM_017564.9;U8,downstream_gene_variant,,ENST00000391292,; A ENST00000388887 Transcript missense_variant 454/8251 250/7656 84/2551 L/I Ctc/Atc rs767043794 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 tolerated(0.18) 3/69 hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038 MODERATE 1 SNV 1 1 PASS rs767043794 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 103594429 103594429 C A 1 0 0 0 0 1 0 0 0 15616 913 32 2 2 STAB2 12 103594429 Missense_Mutation SNP C C3L-00095_T 288115 103594429 29680880 531 3740 STAB2 0 . GRCh38 12 103683277 103683277 + Frame_Shift_Del DEL C C - novel C3L-00095_T C3L-00095_N C C c.2878delC p.Gln960LysfsTer55 p.Q960Kfs*55 ENST00000388887 26/69 159 142 17 150 150 0 sindel-varindel-pindel STAB2,frameshift_variant,p.Gln960LysfsTer55,ENST00000388887,NM_017564.9; - ENST00000388887 Transcript frameshift_variant 3082/8251 2878/7656 960/2551 Q/X Caa/aa 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 26/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2.40.155.10,Pfam_domain:PF12947,SMART_domains:SM00181 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 103683277 103683277 C - 1 0 1 0 1 0 0 0 0 15616 479 17 0 0 STAB2 12 103683277 Frame_Shift_Del DEL C C3L-00095_T 88848 103683277 29592032 532 3741 TBX5 0 . GRCh38 12 114403776 114403776 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.123C>G p.= p.S41S ENST00000310346 2/9 153 141 12 223 223 0 strelka-varscan-mutect TBX5,synonymous_variant,p.=,ENST00000310346,NM_000192.3;TBX5,synonymous_variant,p.=,ENST00000405440,NM_181486.2;TBX5,synonymous_variant,p.=,ENST00000526441,;TBX5,intron_variant,,ENST00000349716,NM_080717.2;TBX5-AS1,upstream_gene_variant,,ENST00000528549,;TBX5-AS1,upstream_gene_variant,,ENST00000532697,;TBX5-AS1,upstream_gene_variant,,ENST00000531202,;TBX5-AS1,upstream_gene_variant,,ENST00000531024,;TBX5,non_coding_transcript_exon_variant,,ENST00000552726,; C ENST00000310346 Transcript synonymous_variant 790/3825 123/1557 41/518 S tcC/tcG 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 2/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 114403776 114403776 G C 1 0 0 0 0 0 0 0 1 16065 1219 43 4 4 TBX5 12 114403776 Silent SNP G C3L-00095_T 10720499 114403776 18871533 533 3742 FBXO21 0 . GRCh38 12 117146165 117146165 + Silent SNP C C A rs762203194 C3L-00095_T C3L-00095_N C C c.1809G>T p.= p.R603R ENST00000330622 12/12 185 169 16 218 218 0 strelka-varscan-mutect FBXO21,synonymous_variant,p.=,ENST00000622495,NM_015002.2;FBXO21,synonymous_variant,p.=,ENST00000427718,;FBXO21,synonymous_variant,p.=,ENST00000330622,NM_033624.2;FBXO21,synonymous_variant,p.=,ENST00000550180,;TESC-AS1,downstream_gene_variant,,ENST00000547006,; A ENST00000330622 Transcript synonymous_variant 1809/2906 1809/1887 603/628 R cgG/cgT rs762203194 1 -1 FBXO21 HGNC HGNC:13592 protein_coding YES CCDS9184.1 ENSP00000328187 O94952 A0A024RBR2 UPI000013CF6D NM_033624.2 12/12 hmmpanther:PTHR31350,hmmpanther:PTHR31350:SF7 LOW 1 SNV 1 1 PASS rs762203194 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 117146165 117146165 C A 1 0 0 0 0 0 0 0 1 5596 494 18 2 2 FBXO21 12 117146165 Silent SNP C C3L-00095_T 2742389 117146165 16129144 534 3743 TAOK3 0 . GRCh38 12 118238112 118238112 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.398A>C p.His133Pro p.H133P ENST00000392533 7/21 175 162 13 225 225 0 strelka-varscan-mutect TAOK3,missense_variant,p.His133Pro,ENST00000392533,NM_016281.3;TAOK3,missense_variant,p.His133Pro,ENST00000419821,;TAOK3,missense_variant,p.His133Pro,ENST00000535570,;TAOK3,missense_variant,p.His31Pro,ENST00000538601,;TAOK3,non_coding_transcript_exon_variant,,ENST00000537305,; G ENST00000392533 Transcript missense_variant 889/4384 398/2697 133/898 H/P cAt/cCt 1 -1 TAOK3 HGNC HGNC:18133 protein_coding YES CCDS9188.1 ENSP00000376317 Q9H2K8 UPI000007231B NM_016281.3 tolerated(0.07) 7/21 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF372,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 118238112 118238112 T G 1 0 0 0 0 1 0 0 0 15948 1464 51 5 5 TAOK3 12 118238112 Missense_Mutation SNP T C3L-00095_T 1091947 118238112 15037197 535 3744 SETD1B 0 . GRCh38 12 121817621 121817621 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.3151G>C p.Glu1051Gln p.E1051Q ENST00000542440 10/18 162 152 10 203 203 0 strelka-varscan-mutect SETD1B,missense_variant,p.Glu1051Gln,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Glu1077Gln,ENST00000604567,;SETD1B,missense_variant,p.Glu1077Gln,ENST00000619791,;SETD1B,missense_variant,p.Glu1051Gln,ENST00000267197,; C ENST00000542440 Transcript missense_variant 3219/8185 3151/5772 1051/1923 E/Q Gaa/Caa 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 tolerated_low_confidence(0.32) 10/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -18.48511 1 1 1 1 0 C 3 2 10 121817621 121817621 G C 1 0 0 0 0 1 0 0 0 14408 1175 41 4 4 SETD1B 12 121817621 Missense_Mutation SNP G C3L-00095_T 3579509 121817621 11457688 536 3745 TUBA3C 0 . GRCh38 13 19177143 19177143 + Missense_Mutation SNP C C A rs773729698 C3L-00095_T C3L-00095_N C C c.840G>T p.Lys280Asn p.K280N ENST00000400113 4/5 177 155 22 221 221 0 strelka-varscan-mutect TUBA3C,missense_variant,p.Lys280Asn,ENST00000400113,NM_006001.2;TUBA3C,missense_variant,p.Lys280Asn,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; A ENST00000400113 Transcript missense_variant 945/1551 840/1353 280/450 K/N aaG/aaT rs773729698,COSM3467500 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 deleterious_low_confidence(0.02) 4/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.30.1330.20,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01162 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs773729698 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 19177143 19177143 C A 1 0 0 0 0 1 0 0 0 17256 680 24 2 2 TUBA3C 13 19177143 Missense_Mutation SNP C C3L-00095_T 19177143 95187185 537 3746 GJB6 0 . GRCh38 13 20223313 20223313 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.168G>A p.= p.L56L ENST00000356192 5/5 152 144 8 206 206 0 varscan-mutect GJB6,synonymous_variant,p.=,ENST00000356192,NM_001110219.2;GJB6,synonymous_variant,p.=,ENST00000400066,NM_001110220.2;GJB6,synonymous_variant,p.=,ENST00000636852,;GJB6,synonymous_variant,p.=,ENST00000241124,NM_006783.4;GJB6,synonymous_variant,p.=,ENST00000400065,NM_001110221.2; T ENST00000356192 Transcript synonymous_variant 789/2131 168/786 56/261 L ctG/ctA 1 -1 GJB6 HGNC HGNC:4288 protein_coding YES CCDS9291.1 ENSP00000348521 O95452 A0A024RDS4 UPI0000074737 NM_001110219.2 5/5 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,PROSITE_patterns:PS00407,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF23,SMART_domains:SM00037 LOW 1 SNV 2 1 PASS . . 0 201 8 0 0 0 0 0 -14.47707 0.9999812 1 1 1 0 T 2 4 10 20223313 20223313 C T 1 0 0 0 0 0 0 0 1 6289 697 25 3 3 GJB6 13 20223313 Silent SNP C C3L-00095_T 1046170 20223313 94141015 538 3747 LATS2 0 . GRCh38 13 20988403 20988403 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1377G>T p.= p.G459G ENST00000382592 4/8 29 24 5 35 35 0 strelka-varscan-mutect LATS2,synonymous_variant,p.=,ENST00000382592,NM_014572.2;LATS2,downstream_gene_variant,,ENST00000472754,; A ENST00000382592 Transcript synonymous_variant 1783/5511 1377/3267 459/1088 G ggG/ggT 1 -1 LATS2 HGNC HGNC:6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 A0A024RDM3 UPI000013DBF5 NM_014572.2 4/8 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -13.65444 0.9999986 1 1 1 0 A 2 1 10 20988403 20988403 C A 1 0 0 0 0 0 0 0 1 8552 726 26 2 2 LATS2 13 20988403 Silent SNP C C3L-00095_T 765090 20988403 93375925 539 3748 SHISA2 0 . GRCh38 13 26046769 26046769 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.632G>T p.Gly211Val p.G211V ENST00000319420 2/2 329 300 29 378 378 0 strelka-varscan-mutect SHISA2,missense_variant,p.Gly211Val,ENST00000319420,NM_001007538.1; A ENST00000319420 Transcript missense_variant 688/2860 632/888 211/295 G/V gGg/gTg 1 -1 SHISA2 HGNC HGNC:20366 protein_coding YES CCDS31951.1 ENSP00000313079 Q6UWI4 UPI000004BA7B NM_001007538.1 deleterious(0.02) 2/2 hmmpanther:PTHR31395:SF0,hmmpanther:PTHR31395 MODERATE 1 SNV 1 1 PASS rs1441402223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 26046769 26046769 C A 1 0 0 0 0 1 0 0 0 14540 623 22 2 2 SHISA2 13 26046769 Missense_Mutation SNP C C3L-00095_T 5058366 26046769 88317559 540 3749 CDK8 0 . GRCh38 13 26401538 26401538 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.1183C>G p.His395Asp p.H395D ENST00000381527 12/13 307 284 23 382 382 0 strelka-varscan-mutect CDK8,missense_variant,p.His395Asp,ENST00000381527,NM_001318368.1,NM_001260.1;CDK8,missense_variant,p.His176Asp,ENST00000465820,;CDK8,intron_variant,,ENST00000625988,;CDK8,3_prime_UTR_variant,,ENST00000536792,;CDK8,non_coding_transcript_exon_variant,,ENST00000480323,;CDK8,non_coding_transcript_exon_variant,,ENST00000477277,; G ENST00000381527 Transcript missense_variant 1686/3055 1183/1395 395/464 H/D Cac/Gac 1 1 CDK8 HGNC HGNC:1779 protein_coding YES CCDS9317.1 ENSP00000370938 P49336 UPI000002E531 NM_001318368.1,NM_001260.1 tolerated(0.65) 12/13 hmmpanther:PTHR24056:SF131,hmmpanther:PTHR24056 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 26401538 26401538 C G 1 0 0 0 0 1 0 0 0 2854 826 29 4 4 CDK8 13 26401538 Missense_Mutation SNP C C3L-00095_T 354769 26401538 87962790 541 3750 RXFP2 0 . GRCh38 13 31791990 31791990 + Frame_Shift_Del DEL A A - novel C3L-00095_T C3L-00095_N A A c.1332delA p.Ala445LeufsTer19 p.A445Lfs*19 ENST00000298386 15/18 141 125 16 178 178 0 sindel-varindel-pindel RXFP2,frameshift_variant,p.Ala445LeufsTer19,ENST00000298386,NM_130806.3;RXFP2,frameshift_variant,p.Ala421LeufsTer19,ENST00000380314,NM_001166058.1; - ENST00000298386 Transcript frameshift_variant 1401/3319 1330/2265 444/754 K/X Aaa/aa 1 1 RXFP2 HGNC HGNC:17318 protein_coding YES CCDS9342.1 ENSP00000298386 Q8WXD0 UPI0000049589 NM_130806.3 15/18 PROSITE_profiles:PS50262,hmmpanther:PTHR24365:SF226,hmmpanther:PTHR24365,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 31791990 31791990 A - 1 0 1 0 1 0 0 0 0 14021 363 13 0 0 RXFP2 13 31791990 Frame_Shift_Del DEL A C3L-00095_T 5390452 31791990 82572338 542 3751 ZAR1L 0 . GRCh38 13 32311751 32311751 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.175T>A p.Cys59Ser p.C59S ENST00000533490 3/6 415 370 45 483 483 0 strelka-varscan-mutect ZAR1L,missense_variant,p.Cys59Ser,ENST00000533490,;ZAR1L,missense_variant,p.Cys59Ser,ENST00000345108,NM_001136571.1;BRCA2,upstream_gene_variant,,ENST00000380152,;BRCA2,upstream_gene_variant,,ENST00000544455,NM_000059.3;BRCA2,upstream_gene_variant,,ENST00000614259,;BRCA2,upstream_gene_variant,,ENST00000530893,; T ENST00000533490 Transcript missense_variant 594/1564 175/966 59/321 C/S Tgc/Agc 1 -1 ZAR1L HGNC HGNC:37116 protein_coding YES CCDS45023.1 ENSP00000437289 A6NP61 UPI00006C1387 tolerated(0.17) 3/6 hmmpanther:PTHR31054:SF5,hmmpanther:PTHR31054 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32311751 32311751 A T 1 0 0 0 0 1 0 0 0 18077 188 7 4 4 ZAR1L 13 32311751 Missense_Mutation SNP A C3L-00095_T 519761 32311751 82052577 543 3752 N4BP2L2 0 . GRCh38 13 32443474 32443474 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1063G>A p.Val355Met p.V355M ENST00000399396 7/10 221 208 13 181 180 1 strelka-varscan-mutect N4BP2L2,missense_variant,p.Val340Met,ENST00000357505,NM_001278432.1;N4BP2L2,missense_variant,p.Val355Met,ENST00000399396,NM_033111.4;N4BP2L2,missense_variant,p.Val340Met,ENST00000504114,;N4BP2L2,intron_variant,,ENST00000446957,;N4BP2L2,downstream_gene_variant,,ENST00000505213,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000380121,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000503296,;N4BP2L2,downstream_gene_variant,,ENST00000473025,;N4BP2L2,non_coding_transcript_exon_variant,,ENST00000509076,; T ENST00000399396 Transcript missense_variant 1171/2872 1063/2259 355/752 V/M Gtg/Atg 1 -1 N4BP2L2 HGNC HGNC:26916 protein_coding YES CCDS45024.1 ENSP00000382328 Q92802 UPI00015C73C2 NM_033111.4 tolerated(0.08) 7/10 hmmpanther:PTHR13308,hmmpanther:PTHR13308:SF23 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 32443474 32443474 C T 1 0 0 0 0 1 0 0 0 10116 565 20 3 3 N4BP2L2 13 32443474 Missense_Mutation SNP C C3L-00095_T 131723 32443474 81920854 544 3753 STARD13 0 . GRCh38 13 33127390 33127390 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.1905C>T p.= p.N635N ENST00000336934 6/14 123 116 7 181 181 0 strelka-varscan-mutect STARD13,synonymous_variant,p.=,ENST00000336934,NM_178006.3;STARD13,synonymous_variant,p.=,ENST00000255486,NM_178007.2;STARD13,synonymous_variant,p.=,ENST00000399365,NM_052851.2;STARD13,downstream_gene_variant,,ENST00000567873,; A ENST00000336934 Transcript synonymous_variant 2022/5917 1905/3342 635/1113 N aaC/aaT 1 -1 STARD13 HGNC HGNC:19164 protein_coding YES CCDS9348.1 ENSP00000338785 Q9Y3M8 A0A024RDV4 UPI000006226E NM_178006.3 6/14 hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF6 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.62627 1 1 1 1 0 A 2 1 10 33127390 33127390 G A 1 0 0 0 0 0 0 0 1 15631 1368 48 3 3 STARD13 13 33127390 Silent SNP G C3L-00095_T 683916 33127390 81236938 545 3754 NBEA 0 . GRCh38 13 35593382 35593382 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.7231G>T p.Asp2411Tyr p.D2411Y ENST00000400445 47/58 153 141 12 173 173 0 strelka-varscan-mutect NBEA,missense_variant,p.Asp2411Tyr,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Asp2412Tyr,ENST00000310336,;NBEA,missense_variant,p.Asp2411Tyr,ENST00000629018,;NBEA,missense_variant,p.Asp2408Tyr,ENST00000379939,;NBEA,missense_variant,p.Asp204Tyr,ENST00000537702,NM_001204197.1;NBEA,5_prime_UTR_variant,,ENST00000379922,; T ENST00000400445 Transcript missense_variant 7765/11119 7231/8841 2411/2946 D/Y Gat/Tat 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 deleterious(0) 47/58 Gene3D:1t77A02,Pfam_domain:PF02138,PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF62,SMART_domains:SM01026,Superfamily_domains:SSF81837 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 35593382 35593382 G T 1 0 0 0 0 1 0 0 0 10198 942 33 2 2 NBEA 13 35593382 Missense_Mutation SNP G C3L-00095_T 2465992 35593382 78770946 546 3755 FREM2 0 . GRCh38 13 38687424 38687424 + Missense_Mutation SNP C C A rs745648044 C3L-00095_T C3L-00095_N C C c.80C>A p.Pro27Gln p.P27Q ENST00000280481 1/24 129 119 10 146 146 0 strelka-varscan-mutect FREM2,missense_variant,p.Pro27Gln,ENST00000280481,NM_207361.5; A ENST00000280481 Transcript missense_variant 296/16070 80/9510 27/3169 P/Q cCg/cAg rs745648044 1 1 FREM2 HGNC HGNC:25396 protein_coding YES CCDS31960.1 ENSP00000280481 Q5SZK8 UPI000443805C NM_207361.5 tolerated_low_confidence(0.06) 1/24 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11878:SF32,hmmpanther:PTHR11878 MODERATE 1 SNV 2 1 PASS rs745648044 . 0 207 2 0 0 0 0 0 -19.4582 1 1 1 1 0 A 3 1 10 38687424 38687424 C A 1 0 0 0 0 1 0 0 0 5912 652 23 1 1 FREM2 13 38687424 Missense_Mutation SNP C C3L-00095_T 3094042 38687424 75676904 547 3756 RGCC 0 . GRCh38 13 41470482 41470482 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.411G>T p.Met137Ile p.M137I ENST00000379359 5/5 227 208 19 215 215 0 strelka-varscan-mutect RGCC,missense_variant,p.Met137Ile,ENST00000379359,NM_014059.2;RGCC,downstream_gene_variant,,ENST00000487837,; T ENST00000379359 Transcript missense_variant 560/960 411/414 137/137 M/I atG/atT 1 1 RGCC HGNC HGNC:20369 protein_coding YES CCDS41880.1 ENSP00000368664 Q9H4X1 UPI000006D63E NM_014059.2 deleterious(0.01) 5/5 Pfam_domain:PF15151,hmmpanther:PTHR32193,hmmpanther:PTHR32193:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 41470482 41470482 G T 1 0 0 0 0 1 0 0 0 13448 1391 48 2 2 RGCC 13 41470482 Missense_Mutation SNP G C3L-00095_T 2783058 41470482 72893846 548 3757 PCDH8 0 . GRCh38 13 52844827 52844827 + Silent SNP G G C novel C3L-00095_T C3L-00095_N G G c.2946C>G p.= p.A982A ENST00000377942 3/3 77 71 6 114 114 0 strelka-varscan-mutect PCDH8,synonymous_variant,p.=,ENST00000377942,NM_002590.3;PCDH8,synonymous_variant,p.=,ENST00000338862,NM_032949.2;PCDH8,non_coding_transcript_exon_variant,,ENST00000613548,; C ENST00000377942 Transcript synonymous_variant 3150/5088 2946/3213 982/1070 A gcC/gcG 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 3/3 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.22831 1 1 1 1 0 C 2 2 10 52844827 52844827 G C 1 0 0 0 0 0 0 0 1 11604 1219 43 4 4 PCDH8 13 52844827 Silent SNP G C3L-00095_T 11374345 52844827 61519501 549 3758 KLF5 0 . GRCh38 13 73075762 73075762 + Missense_Mutation SNP C C T C3L-00095_T C3L-00095_N C C c.1250C>T p.Ser417Leu p.S417L ENST00000377687 4/4 172 160 12 204 204 0 strelka-varscan-mutect KLF5,missense_variant,p.Ser417Leu,ENST00000377687,NM_001730.4;KLF5,missense_variant,p.Ser326Leu,ENST00000539231,NM_001286818.1;KLF5,non_coding_transcript_exon_variant,,ENST00000464404,; T ENST00000377687 Transcript missense_variant 1786/3566 1250/1374 417/457 S/L tCg/tTg COSM358797 1 1 KLF5 HGNC HGNC:6349 protein_coding YES CCDS9448.1 ENSP00000366915 Q13887 Q5T6X2 UPI0000000C89 NM_001730.4 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF60,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.98675 0.9999997 1 1 1 0 T 3 4 10 73075762 73075762 C T 1 0 0 0 0 1 0 0 0 8214 893 31 1 1 KLF5 13 73075762 Missense_Mutation SNP C C3L-00095_T 20230935 73075762 41288566 550 3759 13 2 KLF5 0 . GRCh38 13 73075764 73075764 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.1252G>A p.Asp418Asn p.D418N ENST00000377687 4/4 176 164 12 208 208 0 strelka-varscan-mutect KLF5,missense_variant,p.Asp418Asn,ENST00000377687,NM_001730.4;KLF5,missense_variant,p.Asp327Asn,ENST00000539231,NM_001286818.1;KLF5,non_coding_transcript_exon_variant,,ENST00000464404,; A ENST00000377687 Transcript missense_variant 1788/3566 1252/1374 418/457 D/N Gat/Aat COSM353847 1 1 KLF5 HGNC HGNC:6349 protein_coding YES CCDS9448.1 ENSP00000366915 Q13887 Q5T6X2 UPI0000000C89 NM_001730.4 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF60,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.98506 1 1 1 1 0 A 3 1 10 73075764 73075764 G A 1 0 0 0 0 1 0 0 0 8214 1174 41 3 3 KLF5 13 73075764 Missense_Mutation SNP G C3L-00095_T 2 73075764 41288564 551 3760 13 2 POU4F1 0 . GRCh38 13 78602492 78602492 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.183G>T p.= p.L61L ENST00000377208 2/2 37 31 6 50 50 0 strelka-varscan-mutect POU4F1,synonymous_variant,p.=,ENST00000377208,NM_006237.3;RNF219-AS1,intron_variant,,ENST00000606429,;RNF219-AS1,intron_variant,,ENST00000560584,;RNF219-AS1,intron_variant,,ENST00000444769,;RNF219-AS1,intron_variant,,ENST00000560209,;RNF219-AS1,intron_variant,,ENST00000607860,;RNF219-AS1,intron_variant,,ENST00000607205,;RNF219-AS1,intron_variant,,ENST00000606124,;RNF219-AS1,intron_variant,,ENST00000606376,;RNF219-AS1,intron_variant,,ENST00000607220,;RNF219-AS1,intron_variant,,ENST00000430549,;RP11-52L5.6,downstream_gene_variant,,ENST00000607269,; A ENST00000377208 Transcript synonymous_variant 417/4547 183/1260 61/419 L ctG/ctT 1 -1 POU4F1 HGNC HGNC:9218 protein_coding YES CCDS31996.1 ENSP00000366413 Q01851 UPI000013DCAA NM_006237.3 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11636:SF42,hmmpanther:PTHR11636 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.53395 1 1 1 1 0 A 2 1 10 78602492 78602492 C A 1 0 0 0 0 0 0 0 1 12394 581 21 2 2 POU4F1 13 78602492 Silent SNP C C3L-00095_T 5526728 78602492 35761836 552 3761 SLITRK6 0 . GRCh38 13 85794229 85794229 + Missense_Mutation SNP T T A rs766553493 C3L-00095_T C3L-00095_N T T c.2280A>T p.Leu760Phe p.L760F ENST00000400286 2/2 200 180 20 218 218 0 strelka-varscan-mutect SLITRK6,missense_variant,p.Leu760Phe,ENST00000400286,NM_032229.2; A ENST00000400286 Transcript missense_variant 2879/4318 2280/2526 760/841 L/F ttA/ttT rs766553493 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 deleterious(0) 2/2 MODERATE 1 SNV 1 1 PASS rs766553493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 85794229 85794229 T A 1 0 0 0 0 1 0 0 0 15038 1519 53 4 4 SLITRK6 13 85794229 Missense_Mutation SNP T C3L-00095_T 7191737 85794229 28570099 553 3762 SLITRK6 0 . GRCh38 13 85795623 85795623 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.886A>T p.Met296Leu p.M296L ENST00000400286 2/2 200 189 11 222 222 0 strelka-varscan-mutect SLITRK6,missense_variant,p.Met296Leu,ENST00000400286,NM_032229.2; A ENST00000400286 Transcript missense_variant 1485/4318 886/2526 296/841 M/L Atg/Ttg 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 tolerated(0.74) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 85795623 85795623 T A 1 0 0 0 0 1 0 0 0 15038 1464 51 4 4 SLITRK6 13 85795623 Missense_Mutation SNP T C3L-00095_T 1394 85795623 28568705 554 3763 SLITRK6 0 . GRCh38 13 85796300 85796300 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.209G>T p.Ser70Ile p.S70I ENST00000400286 2/2 91 81 10 117 116 1 strelka-varscan-mutect SLITRK6,missense_variant,p.Ser70Ile,ENST00000400286,NM_032229.2; A ENST00000400286 Transcript missense_variant 808/4318 209/2526 70/841 S/I aGc/aTc 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 tolerated(0.46) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF5,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.97009 1 1 1 1 0 A 3 1 10 85796300 85796300 C A 1 0 0 0 0 1 0 0 0 15038 797 28 2 2 SLITRK6 13 85796300 Missense_Mutation SNP C C3L-00095_T 677 85796300 28568028 555 3764 SLITRK5 0 . GRCh38 13 87676448 87676448 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1060G>T p.Gly354Cys p.G354C ENST00000325089 2/2 206 189 17 271 271 0 strelka-varscan-mutect SLITRK5,missense_variant,p.Gly354Cys,ENST00000325089,NM_015567.1; T ENST00000325089 Transcript missense_variant 1279/21103 1060/2877 354/958 G/C Ggc/Tgc 1 1 SLITRK5 HGNC HGNC:20295 protein_coding YES CCDS9465.1 ENSP00000366283 O94991 UPI000015F6F7 NM_015567.1 deleterious(0.04) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 87676448 87676448 G T 1 0 0 0 0 1 0 0 0 15037 1232 43 2 2 SLITRK5 13 87676448 Missense_Mutation SNP G C3L-00095_T 1880148 87676448 26687880 556 3765 NALCN 0 . GRCh38 13 101073637 101073637 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.4144C>A p.Leu1382Met p.L1382M ENST00000251127 37/44 221 204 17 229 227 2 strelka-varscan-mutect NALCN,missense_variant,p.Leu1382Met,ENST00000251127,NM_052867.2; T ENST00000251127 Transcript missense_variant 4226/6818 4144/5217 1382/1738 L/M Ctg/Atg 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 deleterious(0) 37/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs1394846721 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 101073637 101073637 G T 1 0 0 0 0 1 0 0 0 10155 1020 36 2 2 NALCN 13 101073637 Missense_Mutation SNP G C3L-00095_T 13397189 101073637 13290691 557 3766 NALCN 0 . GRCh38 13 101110661 101110661 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2322G>T p.Gln774His p.Q774H ENST00000251127 20/44 311 287 24 276 276 0 strelka-varscan-mutect NALCN,missense_variant,p.Gln774His,ENST00000251127,NM_052867.2; A ENST00000251127 Transcript missense_variant 2404/6818 2322/5217 774/1738 Q/H caG/caT 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 tolerated(0.14) 20/44 MODERATE 1 SNV 1 1 PASS rs1385381268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 101110661 101110661 C A 1 0 0 0 0 1 0 0 0 10155 912 32 2 2 NALCN 13 101110661 Missense_Mutation SNP C C3L-00095_T 37024 101110661 13253667 558 3767 NALCN 0 . GRCh38 13 101395299 101395299 + Missense_Mutation SNP T T A rs77203309 C3L-00095_T C3L-00095_N T T c.175A>T p.Met59Leu p.M59L ENST00000251127 3/44 93 87 6 119 119 0 strelka-varscan-mutect NALCN,missense_variant,p.Met59Leu,ENST00000251127,NM_052867.2;NALCN,missense_variant,p.Met59Leu,ENST00000376200,;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; A ENST00000251127 Transcript missense_variant 257/6818 175/5217 59/1738 M/L Atg/Ttg rs77203309 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 tolerated(0.11) 3/44 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 24227479 MODERATE 1 SNV 1 1 PASS rs77203309 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 101395299 101395299 T A 1 0 0 0 0 1 0 0 0 10155 1493 52 4 4 NALCN 13 101395299 Missense_Mutation SNP T C3L-00095_T 284638 101395299 12969029 559 3768 CCDC168 0 . GRCh38 13 102736551 102736551 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.14146C>A p.Pro4716Thr p.P4716T ENST00000322527 4/4 267 253 14 306 305 1 strelka-varscan-mutect CCDC168,missense_variant,p.Pro4716Thr,ENST00000322527,NM_001146197.1; T ENST00000322527 Transcript missense_variant 14284/21466 14146/21246 4716/7081 P/T Cca/Aca 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.29) 4/4 Pfam_domain:PF15804,hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 102736551 102736551 G T 1 0 0 0 0 1 0 0 0 2484 1261 44 2 2 CCDC168 13 102736551 Missense_Mutation SNP G C3L-00095_T 1341252 102736551 11627777 560 3769 CCDC168 0 . GRCh38 13 102745485 102745485 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.5212A>G p.Asn1738Asp p.N1738D ENST00000322527 4/4 158 143 15 184 184 0 strelka-varscan-mutect CCDC168,missense_variant,p.Asn1738Asp,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; C ENST00000322527 Transcript missense_variant 5350/21466 5212/21246 1738/7081 N/D Aac/Gac 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.22) 4/4 Pfam_domain:PF15804 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 102745485 102745485 T C 1 0 0 0 0 1 0 0 0 2484 1754 61 5 5 CCDC168 13 102745485 Missense_Mutation SNP T C3L-00095_T 8934 102745485 11618843 561 3770 SLC10A2 0 . GRCh38 13 103058304 103058304 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.456G>T p.Trp152Cys p.W152C ENST00000245312 2/6 450 421 29 454 451 3 strelka-varscan-mutect SLC10A2,missense_variant,p.Trp152Cys,ENST00000245312,NM_000452.2; A ENST00000245312 Transcript missense_variant 1053/3779 456/1047 152/348 W/C tgG/tgT COSM1730416 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 deleterious(0) 2/6 hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841,Pfam_domain:PF01758 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 103058304 103058304 C A 1 0 0 0 0 1 0 0 0 14639 624 22 2 2 SLC10A2 13 103058304 Missense_Mutation SNP C C3L-00095_T 312819 103058304 11306024 562 3771 COL4A1 0 . GRCh38 13 110176625 110176625 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.2968+1G>T p.X990_splice ENST00000375820 334 309 25 456 456 0 strelka-varscan-mutect COL4A1,splice_donor_variant,,ENST00000375820,NM_001845.5; A ENST00000375820 Transcript splice_donor_variant -/6532 2968/5010 990/1669 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 35/51 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 110176625 110176625 C A 1 0 0 0 0 0 0 1 0 3478 521 18 2 2 COL4A1 13 110176625 Splice_Site SNP C C3L-00095_T 7118321 110176625 4187703 563 3772 F10 0 . GRCh38 13 113143966 113143966 + Silent SNP C C A rs764063729 C3L-00095_T C3L-00095_N C C c.618C>A p.= p.A206A ENST00000375559 6/8 268 248 20 360 360 0 strelka-varscan-mutect F10,synonymous_variant,p.=,ENST00000375559,NM_000504.3;F10,synonymous_variant,p.=,ENST00000375551,NM_001312675.1;F10,synonymous_variant,p.=,ENST00000409306,;F10,3_prime_UTR_variant,,ENST00000410083,;F10,non_coding_transcript_exon_variant,,ENST00000477269,;F10,non_coding_transcript_exon_variant,,ENST00000498455,; A ENST00000375559 Transcript synonymous_variant 656/1517 618/1467 206/488 A gcC/gcA rs764063729 1 1 F10 HGNC HGNC:3528 protein_coding YES CCDS9530.1 ENSP00000364709 P00742 Q5JVE7 UPI000000DB39 NM_000504.3 6/8 hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF192,PIRSF_domain:PIRSF001143 LOW 1 SNV 1 1 PASS rs764063729 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 113143966 113143966 C A 1 0 0 0 0 0 0 0 1 5204 639 23 1 1 F10 13 113143966 Silent SNP C C3L-00095_T 2967341 113143966 1220362 564 3773 POTEM 0 . GRCh38 14 18967654 18967654 + Missense_Mutation SNP C C A rs763554455 C3L-00095_T C3L-00095_N C C c.169C>A p.Leu57Ile p.L57I ENST00000547889 1/11 293 278 15 330 330 0 varscan-mutect POTEM,missense_variant,p.Leu57Ile,ENST00000547889,NM_001145442.1;POTEM,missense_variant,p.Leu57Ile,ENST00000552966,;POTEM,missense_variant,p.Leu57Ile,ENST00000616847,; A ENST00000547889 Transcript missense_variant 221/1817 169/1527 57/508 L/I Ctc/Atc rs763554455 1 1 POTEM HGNC HGNC:37096 protein_coding YES CCDS73609.1 ENSP00000448062 A6NI47 UPI00006C1407 NM_001145442.1 tolerated_low_confidence(0.09) 1/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43 MODERATE 1 SNV 1 1 PASS rs763554455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 18967654 18967654 C A 1 0 0 0 0 1 0 0 0 12384 565 20 2 2 POTEM 14 18967654 Missense_Mutation SNP C C3L-00095_T 18967654 88076064 565 3774 RNASE12 0 . GRCh38 14 20590358 20590358 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.366C>A p.His122Gln p.H122Q ENST00000556526 1/1 311 290 21 385 384 1 strelka-varscan-mutect RNASE12,missense_variant,p.His122Gln,ENST00000556526,NM_001024822.2;RNASE11,intron_variant,,ENST00000413502,;RP11-14J7.7,intron_variant,,ENST00000555283,;RNASE11,upstream_gene_variant,,ENST00000553849,NM_145250.3;RNASE11,upstream_gene_variant,,ENST00000398009,;RNASE11,upstream_gene_variant,,ENST00000432835,;RNASE11,upstream_gene_variant,,ENST00000555841,;RNASE11,upstream_gene_variant,,ENST00000620912,;RNASE11,upstream_gene_variant,,ENST00000398008,;RNASE11,upstream_gene_variant,,ENST00000443456,;RNASE11,upstream_gene_variant,,ENST00000557105,;RNASE11,upstream_gene_variant,,ENST00000557503,;RNASE11,upstream_gene_variant,,ENST00000554842,;RP11-14J7.6,intron_variant,,ENST00000553604,;RP11-14J7.6,intron_variant,,ENST00000554529,;RP11-14J7.6,intron_variant,,ENST00000556487,;RP11-14J7.6,upstream_gene_variant,,ENST00000554993,;RP11-14J7.6,downstream_gene_variant,,ENST00000554006,;RP11-14J7.7,missense_variant,p.His60Gln,ENST00000335950,; T ENST00000556526 Transcript missense_variant 466/631 366/444 122/147 H/Q caC/caA 1 -1 RNASE12 HGNC HGNC:24211 protein_coding YES CCDS32037.1 ENSP00000450580 Q5GAN4 W0UV30 UPI00004C6F5C NM_001024822.2 tolerated(0.41) 1/1 Gene3D:3.10.130.10,Pfam_domain:PF00074,Prints_domain:PR00794,hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF20,SMART_domains:SM00092,Superfamily_domains:SSF54076 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 20590358 20590358 G T 1 0 0 0 0 1 0 0 0 13581 1020 36 2 2 RNASE12 14 20590358 Missense_Mutation SNP G C3L-00095_T 1622704 20590358 86453360 566 3775 ARHGEF40 0 . GRCh38 14 21074340 21074340 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.610G>C p.Glu204Gln p.E204Q ENST00000298694 3/24 245 231 14 333 333 0 strelka-varscan-mutect ARHGEF40,missense_variant,p.Glu204Gln,ENST00000298694,NM_001278530.1,NM_001278529.1,NM_018071.4;ARHGEF40,missense_variant,p.Glu204Gln,ENST00000555038,;NDRG2,upstream_gene_variant,,ENST00000403829,NM_001282211.1;ARHGEF40,missense_variant,p.Glu204Gln,ENST00000553709,;ARHGEF40,missense_variant,p.Glu204Gln,ENST00000556399,;ARHGEF40,intron_variant,,ENST00000555232,;ARHGEF40,upstream_gene_variant,,ENST00000555052,; C ENST00000298694 Transcript missense_variant 737/5919 610/4560 204/1519 E/Q Gaa/Caa 1 1 ARHGEF40 HGNC HGNC:25516 protein_coding YES CCDS32041.1 ENSP00000298694 Q8TER5 UPI00001FCFB7 NM_001278530.1,NM_001278529.1,NM_018071.4 tolerated(0.12) 3/24 Low_complexity_(Seg):seg,hmmpanther:PTHR22826:SF143,hmmpanther:PTHR22826 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 21074340 21074340 G C 1 0 0 0 0 1 0 0 0 1044 943 33 4 4 ARHGEF40 14 21074340 Missense_Mutation SNP G C3L-00095_T 483982 21074340 85969378 567 3776 REM2 0 . GRCh38 14 22886777 22886777 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.893delG p.Gly298AlafsTer152 p.G298Afs*152 ENST00000267396 5/5 100 90 10 151 151 0 sindel-varindel-pindel REM2,frameshift_variant,p.Gly298AlafsTer152,ENST00000267396,NM_173527.2;REM2,3_prime_UTR_variant,,ENST00000536884,; - ENST00000267396 Transcript frameshift_variant 1014/1923 891/1023 297/340 E/X gaG/ga 1 1 REM2 HGNC HGNC:20248 protein_coding YES CCDS45082.1 ENSP00000267396 Q8IYK8 UPI00000716C5 NM_173527.2 5/5 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF270,hmmpanther:PTHR24070 HIGH 1 deletion 1 2 1 PASS . . 0 206 3 0 0 0 0 0 -19.91755 1 1 1 1 0 - 7 5 10 22886777 22886777 G - 1 0 1 0 1 0 0 0 0 13393 991 35 0 0 REM2 14 22886777 Frame_Shift_Del DEL G C3L-00095_T 1812437 22886777 84156941 568 3777 CEBPE 0 . GRCh38 14 23117556 23117556 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.777C>A p.= p.T259T ENST00000206513 2/2 192 177 15 240 238 2 strelka-varscan-mutect CEBPE,synonymous_variant,p.=,ENST00000206513,NM_001805.3; T ENST00000206513 Transcript synonymous_variant 1302/1554 777/846 259/281 T acC/acA 1 -1 CEBPE HGNC HGNC:1836 protein_coding YES CCDS9589.1 ENSP00000206513 Q15744 UPI000013C660 NM_001805.3 2/2 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF005879,PROSITE_profiles:PS50217,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF27,SMART_domains:SM00338,Superfamily_domains:SSF57959 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 23117556 23117556 G T 1 0 0 0 0 0 0 0 1 2908 1219 43 2 2 CEBPE 14 23117556 Silent SNP G C3L-00095_T 230779 23117556 83926162 569 3778 EFS 0 . GRCh38 14 23360718 23360718 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.134G>T p.Gly45Val p.G45V ENST00000216733 2/6 236 224 12 287 285 2 strelka-varscan-mutect EFS,missense_variant,p.Gly45Val,ENST00000216733,NM_005864.3;EFS,intron_variant,,ENST00000351354,NM_032459.2;EFS,intron_variant,,ENST00000429593,NM_001277174.1;RP11-124D2.3,downstream_gene_variant,,ENST00000554010,; A ENST00000216733 Transcript missense_variant 742/3118 134/1686 45/561 G/V gGc/gTc COSM1191837 1 -1 EFS HGNC HGNC:16898 protein_coding YES CCDS9595.1 ENSP00000216733 O43281 UPI0000129D21 NM_005864.3 deleterious(0) 2/6 PROSITE_profiles:PS50002,hmmpanther:PTHR10654,hmmpanther:PTHR10654:SF14,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 23360718 23360718 C A 1 0 0 0 0 1 0 0 0 4796 739 26 2 2 EFS 14 23360718 Missense_Mutation SNP C C3L-00095_T 243162 23360718 83683000 570 3779 RPL10L 0 . GRCh38 14 46651280 46651280 + Missense_Mutation SNP G G C rs199562673 C3L-00095_T C3L-00095_N G G c.457C>G p.Arg153Gly p.R153G ENST00000298283 1/1 277 240 37 300 300 0 strelka-varscan-mutect RPL10L,missense_variant,p.Arg153Gly,ENST00000298283,NM_080746.2; C ENST00000298283 Transcript missense_variant 542/812 457/645 153/214 R/G Cgc/Ggc rs199562673,COSM2197635 1 -1 RPL10L HGNC HGNC:17976 protein_coding YES CCDS32071.1 ENSP00000298283 Q96L21 UPI0000073CA8 NM_080746.2 deleterious(0) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11726:SF11,hmmpanther:PTHR11726,Pfam_domain:PF00252,TIGRFAM_domain:TIGR00279,Gene3D:3.90.1170.10,PIRSF_domain:PIRSF005590,Superfamily_domains:SSF54686 0,1 MODERATE 1 SNV 0,1 1 PASS rs199562673 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 46651280 46651280 G C 1 0 0 0 0 1 0 0 0 13808 1087 38 4 4 RPL10L 14 46651280 Missense_Mutation SNP G C3L-00095_T 23290562 46651280 60392438 571 3780 NID2 0 . GRCh38 14 52053884 52053884 + Missense_Mutation SNP C C T C3L-00095_T C3L-00095_N C C c.1124G>A p.Gly375Glu p.G375E ENST00000216286 5/22 172 159 13 199 198 1 strelka-varscan-mutect NID2,missense_variant,p.Gly375Glu,ENST00000216286,NM_007361.3;NID2,intron_variant,,ENST00000617139,; T ENST00000216286 Transcript missense_variant 1124/4811 1124/4128 375/1375 G/E gGg/gAg COSM553099 1 -1 NID2 HGNC HGNC:13389 protein_coding YES CCDS9706.1 ENSP00000216286 Q14112 UPI000013C6E1 NM_007361.3 tolerated(1) 5/22 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 52053884 52053884 C T 1 0 0 0 0 1 0 0 0 10448 623 22 3 3 NID2 14 52053884 Missense_Mutation SNP C C3L-00095_T 5402604 52053884 54989834 572 3781 TXNDC16 0 . GRCh38 14 52439378 52439378 + Missense_Mutation SNP C C A rs779633860 C3L-00095_T C3L-00095_N C C c.2020G>T p.Gly674Trp p.G674W ENST00000281741 20/21 187 174 13 197 197 0 strelka-varscan-mutect TXNDC16,missense_variant,p.Gly674Trp,ENST00000281741,NM_001160047.1,NM_020784.2;TXNDC16,non_coding_transcript_exon_variant,,ENST00000554399,; A ENST00000281741 Transcript missense_variant 2392/4564 2020/2478 674/825 G/W Ggg/Tgg rs779633860 1 -1 TXNDC16 HGNC HGNC:19965 protein_coding YES CCDS32083.1 ENSP00000281741 Q9P2K2 UPI000059D245 NM_001160047.1,NM_020784.2 deleterious(0) 20/21 hmmpanther:PTHR22699,hmmpanther:PTHR22699:SF1,Pfam_domain:PF13848 MODERATE 1 SNV 1 1 PASS rs779633860 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 52439378 52439378 C A 1 0 0 0 0 1 0 0 0 17311 623 22 2 2 TXNDC16 14 52439378 Missense_Mutation SNP C C3L-00095_T 385494 52439378 54604340 573 3782 SIX4 0 . GRCh38 14 60719883 60719883 + Missense_Mutation SNP C C A rs530684279 C3L-00095_T C3L-00095_N C C c.1426G>T p.Val476Leu p.V476L ENST00000216513 2/3 287 270 17 322 321 1 strelka-varscan-mutect SIX4,missense_variant,p.Val476Leu,ENST00000216513,NM_017420.4;SIX4,missense_variant,p.Val468Leu,ENST00000556952,;SIX4,non_coding_transcript_exon_variant,,ENST00000554079,; A ENST00000216513 Transcript missense_variant 1486/6285 1426/2346 476/781 V/L Gtg/Ttg rs530684279 1 -1 SIX4 HGNC HGNC:10890 protein_coding YES CCDS9749.2 ENSP00000216513 Q9UIU6 UPI000066D924 NM_017420.4 tolerated(0.56) 2/3 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF36 MODERATE 1 SNV 1 1 PASS rs530684279 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 60719883 60719883 C A 1 0 0 0 0 1 0 0 0 14612 565 20 2 2 SIX4 14 60719883 Missense_Mutation SNP C C3L-00095_T 8280505 60719883 46323835 574 3783 SYNE2 0 . GRCh38 14 64186472 64186472 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.17605C>T p.Gln5869Ter p.Q5869* ENST00000358025 97/116 528 471 57 545 545 0 strelka-varscan-mutect SYNE2,stop_gained,p.Gln5869Ter,ENST00000358025,NM_182914.2;SYNE2,stop_gained,p.Gln5869Ter,ENST00000344113,NM_015180.4;SYNE2,stop_gained,p.Gln2503Ter,ENST00000555002,;SYNE2,stop_gained,p.Gln2254Ter,ENST00000394768,;SYNE2,intron_variant,,ENST00000357395,;SYNE2,intron_variant,,ENST00000554584,;ESR2,intron_variant,,ENST00000556275,;SYNE2,stop_gained,p.Gln831Ter,ENST00000555612,;SYNE2,stop_gained,p.Gln454Ter,ENST00000553289,; T ENST00000358025 Transcript stop_gained 17817/21842 17605/20724 5869/6907 Q/* Caa/Taa 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 97/116 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 64186472 64186472 C T 1 0 0 0 0 0 1 0 0 15838 827 29 3 3 SYNE2 14 64186472 Nonsense_Mutation SNP C C3L-00095_T 3466589 64186472 42857246 575 3784 SYNE2 0 . GRCh38 14 64216370 64216370 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.19525C>T p.Pro6509Ser p.P6509S ENST00000358025 108/116 437 377 60 489 487 2 strelka-varscan-mutect SYNE2,missense_variant,p.Pro6509Ser,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Pro6486Ser,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Pro6434Ser,ENST00000357395,;SYNE2,missense_variant,p.Pro6428Ser,ENST00000554584,;SYNE2,missense_variant,p.Pro3143Ser,ENST00000555002,;SYNE2,missense_variant,p.Pro2871Ser,ENST00000394768,;SYNE2,missense_variant,p.Pro364Ser,ENST00000555022,;SYNE2,missense_variant,p.Pro269Ser,ENST00000554805,;SYNE2,missense_variant,p.Pro17Ser,ENST00000441438,NM_182910.2;SYNE2,missense_variant,p.Pro143Ser,ENST00000458046,NM_182913.2;ESR2,intron_variant,,ENST00000556275,;SYNE2,3_prime_UTR_variant,,ENST00000555612,;SYNE2,3_prime_UTR_variant,,ENST00000553289,;SYNE2,3_prime_UTR_variant,,ENST00000557084,;SYNE2,upstream_gene_variant,,ENST00000554928,;SYNE2,downstream_gene_variant,,ENST00000553806,;SYNE2,downstream_gene_variant,,ENST00000554997,;SYNE2,downstream_gene_variant,,ENST00000557307,; T ENST00000358025 Transcript missense_variant 19737/21842 19525/20724 6509/6907 P/S Cct/Tct 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(0.09) 108/116 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 64216370 64216370 C T 1 0 0 0 0 1 0 0 0 15838 623 22 3 3 SYNE2 14 64216370 Missense_Mutation SNP C C3L-00095_T 29898 64216370 42827348 576 3785 ZNF410 0 . GRCh38 14 73898224 73898224 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.593G>T p.Arg198Leu p.R198L ENST00000442160 6/14 394 347 47 547 546 1 strelka-varscan-mutect ZNF410,missense_variant,p.Arg181Leu,ENST00000555044,NM_021188.2,NM_001242928.1;ZNF410,missense_variant,p.Arg181Leu,ENST00000324593,NM_001242926.1;ZNF410,missense_variant,p.Arg128Leu,ENST00000334521,;ZNF410,missense_variant,p.Arg198Leu,ENST00000442160,NM_001242924.1;ZNF410,missense_variant,p.Arg108Leu,ENST00000540593,NM_001242927.1;ZNF410,missense_variant,p.Arg198Leu,ENST00000615736,;ZNF410,missense_variant,p.Arg128Leu,ENST00000556797,;ZNF410,missense_variant,p.Arg128Leu,ENST00000557363,;ZNF410,downstream_gene_variant,,ENST00000556160,;ZNF410,downstream_gene_variant,,ENST00000556659,;ZNF410,downstream_gene_variant,,ENST00000557495,;ZNF410,downstream_gene_variant,,ENST00000555730,;ZNF410,downstream_gene_variant,,ENST00000554797,;RP5-1021I20.5,intron_variant,,ENST00000554009,;ZNF410,non_coding_transcript_exon_variant,,ENST00000412490,;ZNF410,non_coding_transcript_exon_variant,,ENST00000541357,;ZNF410,non_coding_transcript_exon_variant,,ENST00000555602,;ZNF410,missense_variant,p.Arg181Leu,ENST00000398139,;RP5-1021I20.4,3_prime_UTR_variant,,ENST00000556551,;ZNF410,3_prime_UTR_variant,,ENST00000556396,;ZNF410,3_prime_UTR_variant,,ENST00000554582,; T ENST00000442160 Transcript missense_variant 787/2076 593/1551 198/516 R/L cGt/cTt 1 1 ZNF410 HGNC HGNC:20144 protein_coding YES CCDS55929.1 ENSP00000407130 Q86VK4 UPI00017A6BE1 NM_001242924.1 deleterious(0) 6/14 MODERATE 1 SNV 1 1 PASS rs1465082702 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 73898224 73898224 G T 1 0 0 0 0 1 0 0 0 18462 1145 40 1 1 ZNF410 14 73898224 Missense_Mutation SNP G C3L-00095_T 9681854 73898224 33145494 577 3786 TGFB3 0 . GRCh38 14 75971584 75971584 + Silent SNP G G T rs142601521 C3L-00095_T C3L-00095_N G G c.487C>A p.= p.R163R ENST00000238682 2/7 341 320 21 454 453 1 strelka-varscan-mutect TGFB3,synonymous_variant,p.=,ENST00000238682,NM_003239.3;TGFB3,synonymous_variant,p.=,ENST00000556285,;RP11-270M14.5,non_coding_transcript_exon_variant,,ENST00000553732,;TGFB3,upstream_gene_variant,,ENST00000557493,;IFT43,intron_variant,,ENST00000555677,;TGFB3,upstream_gene_variant,,ENST00000554980,; T ENST00000238682 Transcript synonymous_variant 785/2522 487/1239 163/412 R Cgg/Agg rs142601521 1 -1 TGFB3 HGNC HGNC:11769 protein_coding YES CCDS9846.1 ENSP00000238682 P10600 A5YM40 UPI000000D8EC NM_003239.3 2/7 hmmpanther:PTHR11848:SF34,hmmpanther:PTHR11848,Pfam_domain:PF00688,PIRSF_domain:PIRSF001787,Prints_domain:PR01423,Prints_domain:PR01426 uncertain_significance LOW 1 SNV 1 1 1 PASS rs142601521 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 75971584 75971584 G T 1 0 0 0 0 0 0 0 1 16252 1086 38 1 1 TGFB3 14 75971584 Silent SNP G C3L-00095_T 2073360 75971584 31072134 578 3787 KCNK13 0 . GRCh38 14 90184901 90184901 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.1125C>A p.= p.P375P ENST00000282146 2/2 131 123 8 174 173 1 strelka-varscan-mutect KCNK13,synonymous_variant,p.=,ENST00000282146,NM_022054.3; A ENST00000282146 Transcript synonymous_variant 1566/2522 1125/1227 375/408 P ccC/ccA 1 1 KCNK13 HGNC HGNC:6275 protein_coding YES CCDS9889.1 ENSP00000282146 Q9HB14 UPI0000127A55 NM_022054.3 2/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF57 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -11.46697 0.9999995 1 1 1 0 A 2 1 10 90184901 90184901 C A 1 0 0 0 0 0 0 0 1 7978 610 22 2 2 KCNK13 14 90184901 Silent SNP C C3L-00095_T 14213317 90184901 16858817 579 3788 DDX24 0 . GRCh38 14 94060481 94060481 + Silent SNP G G T C3L-00095_T C3L-00095_N G G c.1530C>A p.= p.L510L ENST00000621632 5/9 321 294 27 452 449 3 strelka-varscan-mutect DDX24,synonymous_variant,p.=,ENST00000621632,NM_020414.3;DDX24,synonymous_variant,p.=,ENST00000555054,;DDX24,synonymous_variant,p.=,ENST00000330836,;DDX24,synonymous_variant,p.=,ENST00000544005,;DDX24,synonymous_variant,p.=,ENST00000622786,;DDX24,upstream_gene_variant,,ENST00000553451,;DDX24,non_coding_transcript_exon_variant,,ENST00000555762,; T ENST00000621632 Transcript synonymous_variant 1662/5612 1530/2580 510/859 L ctC/ctA COSM3815587 1 -1 DDX24 HGNC HGNC:13266 protein_coding YES CCDS9918.1 ENSP00000481495 Q9GZR7 UPI0000129082 NM_020414.3 5/9 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF91,hmmpanther:PTHR24031,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS rs1311558427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 94060481 94060481 G T 1 0 0 0 0 0 0 0 1 4154 1277 45 2 2 DDX24 14 94060481 Silent SNP G C3L-00095_T 3875580 94060481 12983237 580 3789 SERPINA10 0 . GRCh38 14 94289941 94289941 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.653C>A p.Pro218His p.P218H ENST00000261994 2/5 237 209 28 370 369 1 strelka-varscan-mutect SERPINA10,missense_variant,p.Pro218His,ENST00000261994,NM_001100607.2;SERPINA10,missense_variant,p.Pro258His,ENST00000554723,;SERPINA10,missense_variant,p.Pro218His,ENST00000393096,NM_016186.2;SERPINA10,missense_variant,p.Pro218His,ENST00000554173,; T ENST00000261994 Transcript missense_variant 786/4978 653/1335 218/444 P/H cCc/cAc 1 -1 SERPINA10 HGNC HGNC:15996 protein_coding YES CCDS9923.1 ENSP00000261994 Q9UK55 A0A024R6I6 UPI000013C46E NM_001100607.2 tolerated(0.06) 2/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF191,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs1348115369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 94289941 94289941 G T 1 0 0 0 0 1 0 0 0 14363 1232 43 2 2 SERPINA10 14 94289941 Missense_Mutation SNP G C3L-00095_T 229460 94289941 12753777 581 3790 AK7 0 . GRCh38 14 96458148 96458148 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1293G>T p.Glu431Asp p.E431D ENST00000267584 12/18 153 139 14 203 201 2 strelka-varscan-mutect AK7,missense_variant,p.Glu431Asp,ENST00000267584,NM_152327.3;RPL23AP10,upstream_gene_variant,,ENST00000489946,; T ENST00000267584 Transcript missense_variant 1337/3300 1293/2172 431/723 E/D gaG/gaT 1 1 AK7 HGNC HGNC:20091 protein_coding YES CCDS9945.1 ENSP00000267584 Q96M32 UPI00001FDB1D NM_152327.3 tolerated(0.52) 12/18 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs954819283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 96458148 96458148 G T 1 0 0 0 0 1 0 0 0 524 991 35 2 2 AK7 14 96458148 Missense_Mutation SNP G C3L-00095_T 2168207 96458148 10585570 582 3791 HSP90AA1 0 . GRCh38 14 102084515 102084515 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1397C>T p.Pro466Leu p.P466L ENST00000334701 7/12 384 331 53 420 420 0 strelka-varscan-mutect HSP90AA1,missense_variant,p.Pro466Leu,ENST00000334701,NM_001017963.2;HSP90AA1,missense_variant,p.Pro344Leu,ENST00000216281,NM_005348.3;HSP90AA1,downstream_gene_variant,,ENST00000553585,;HSP90AA1,3_prime_UTR_variant,,ENST00000554401,;HSP90AA1,non_coding_transcript_exon_variant,,ENST00000560130,;HSP90AA1,upstream_gene_variant,,ENST00000557089,;HSP90AA1,downstream_gene_variant,,ENST00000557234,;HSP90AA1,downstream_gene_variant,,ENST00000556554,;HSP90AA1,downstream_gene_variant,,ENST00000555662,; A ENST00000334701 Transcript missense_variant 1679/3510 1397/2565 466/854 P/L cCa/cTa 1 -1 HSP90AA1 HGNC HGNC:5253 protein_coding YES CCDS32160.1 ENSP00000335153 P07900 UPI0000408144 NM_001017963.2 deleterious_low_confidence(0.01) 7/12 HAMAP:MF_00505,hmmpanther:PTHR11528,hmmpanther:PTHR11528:SF58,Pfam_domain:PF00183,PIRSF_domain:PIRSF002583,Superfamily_domains:SSF54211 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 102084515 102084515 G A 1 0 0 0 0 1 0 0 0 7297 1348 47 3 3 HSP90AA1 14 102084515 Missense_Mutation SNP G C3L-00095_T 5626367 102084515 4959203 583 3792 APOPT1 0 . GRCh38 14 103590241 103590241 + Missense_Mutation SNP G G T rs549160910 C3L-00095_T C3L-00095_N G G c.576G>T p.Arg192Ser p.R192S ENST00000409074 5/5 284 246 38 271 271 0 strelka-varscan-mutect APOPT1,missense_variant,p.Arg192Ser,ENST00000409074,NM_032374.4,NM_001302652.1;APOPT1,missense_variant,p.Arg41Ser,ENST00000477116,;APOPT1,missense_variant,p.Gly58Val,ENST00000476323,;APOPT1,missense_variant,p.Arg41Ser,ENST00000473127,;APOPT1,missense_variant,p.Arg104Ser,ENST00000440963,;APOPT1,missense_variant,p.Arg41Ser,ENST00000492189,;APOPT1,3_prime_UTR_variant,,ENST00000556253,NM_001302653.1;RP11-73M18.2,intron_variant,,ENST00000472726,;KLC1,intron_variant,,ENST00000557172,;APOPT1,downstream_gene_variant,,ENST00000554876,;APOPT1,intron_variant,,ENST00000474271,;APOPT1,3_prime_UTR_variant,,ENST00000458117,;APOPT1,3_prime_UTR_variant,,ENST00000489117,;APOPT1,non_coding_transcript_exon_variant,,ENST00000557079,;APOPT1,downstream_gene_variant,,ENST00000555660,; T ENST00000409074 Transcript missense_variant 577/2523 576/621 192/206 R/S agG/agT rs549160910 1 1 APOPT1 HGNC HGNC:20492 protein_coding YES CCDS9983.2 ENSP00000386485 Q96IL0 UPI0000EE34A7 NM_032374.4,NM_001302652.1 tolerated(0.11) 5/5 hmmpanther:PTHR31107,hmmpanther:PTHR31107:SF2,Pfam_domain:PF10231 MODERATE 1 SNV 1 1 PASS rs549160910 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 103590241 103590241 G T 1 0 0 0 0 1 0 0 0 937 1174 41 2 2 APOPT1 14 103590241 Missense_Mutation SNP G C3L-00095_T 1505726 103590241 3453477 584 3793 APBA2 0 . GRCh38 15 29098508 29098508 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1270C>A p.Gln424Lys p.Q424K ENST00000558402 10/16 344 303 41 401 401 0 strelka-varscan-mutect APBA2,missense_variant,p.Gln424Lys,ENST00000558402,;APBA2,missense_variant,p.Gln424Lys,ENST00000558259,NM_005503.3;APBA2,missense_variant,p.Gln412Lys,ENST00000411764,NM_001130414.1;APBA2,missense_variant,p.Gln412Lys,ENST00000558330,;APBA2,missense_variant,p.Gln424Lys,ENST00000561069,;APBA2,non_coding_transcript_exon_variant,,ENST00000559814,;APBA2,non_coding_transcript_exon_variant,,ENST00000382938,; A ENST00000558402 Transcript missense_variant 1869/4031 1270/2250 424/749 Q/K Cag/Aag 1 1 APBA2 HGNC HGNC:579 protein_coding YES CCDS10022.1 ENSP00000453293 Q99767 UPI0000046798 deleterious(0) 10/16 PROSITE_profiles:PS01179,hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF12,Gene3D:2.30.29.30,Pfam_domain:PF00640,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 29098508 29098508 C A 1 0 0 0 0 1 0 0 0 877 595 21 2 2 APBA2 15 29098508 Missense_Mutation SNP C C3L-00095_T 29098508 72892681 585 3794 GOLGA8T 0 . GRCh38 15 30144778 30144778 + Splice_Site SNP G G T novel C3L-00095_T C3L-00095_N G G c.1369-1G>T p.X457_splice ENST00000569052 208 185 23 246 246 0 varscan-mutect GOLGA8T,splice_acceptor_variant,,ENST00000569052,;RN7SL469P,downstream_gene_variant,,ENST00000621501,; T ENST00000569052 Transcript splice_acceptor_variant -/1896 1369/1896 457/631 1 1 GOLGA8T HGNC HGNC:44410 protein_coding YES ENSP00000455826 H3BQL2 UPI000246730F 15/18 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 10 30144778 30144778 G T 1 0 0 0 0 0 0 1 0 6458 956 33 2 2 GOLGA8T 15 30144778 Splice_Site SNP G C3L-00095_T 1046270 30144778 71846411 586 3795 ARHGAP11B 0 . GRCh38 15 30634382 30634382 + Silent SNP A A G novel C3L-00095_T C3L-00095_N A A c.510A>G p.= p.V170V ENST00000622744 4/11 296 275 21 323 323 0 varscan-mutect ARHGAP11B,synonymous_variant,p.=,ENST00000622744,;ARHGAP11B,synonymous_variant,p.=,ENST00000428041,NM_001039841.1;ARHGAP11B,non_coding_transcript_exon_variant,,ENST00000564902,;ARHGAP11B,non_coding_transcript_exon_variant,,ENST00000566362,;ARHGAP11B,synonymous_variant,p.=,ENST00000563110,;ARHGAP11B,non_coding_transcript_exon_variant,,ENST00000568574,; G ENST00000622744 Transcript synonymous_variant 1131/2042 510/804 170/267 V gtA/gtG 1 1 ARHGAP11B HGNC HGNC:15782 protein_coding YES CCDS32185.1 ENSP00000481934 Q3KRB8 UPI000041D252 4/11 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR15670,hmmpanther:PTHR15670:SF5,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 30634382 30634382 A G 1 0 0 0 0 0 0 0 1 988 436 16 5 5 ARHGAP11B 15 30634382 Silent SNP A C3L-00095_T 489604 30634382 71356807 587 3796 RYR3 0 . GRCh38 15 33635662 33635662 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.3224G>T p.Arg1075Leu p.R1075L ENST00000634891 26/104 336 316 20 510 509 1 strelka-varscan-mutect RYR3,missense_variant,p.Arg1075Leu,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Arg1075Leu,ENST00000622037,;RYR3,missense_variant,p.Arg1075Leu,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Arg1075Leu,ENST00000389232,;RYR3,missense_variant,p.Arg1075Leu,ENST00000634418,; T ENST00000634891 Transcript missense_variant 3325/15591 3224/14613 1075/4870 R/L cGg/cTg COSM1372397 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 26/104 PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 1 MODERATE 1 SNV 1 1 1 PASS rs944419972 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 33635662 33635662 G T 1 0 0 0 0 1 0 0 0 14030 1116 39 1 1 RYR3 15 33635662 Missense_Mutation SNP G C3L-00095_T 3001280 33635662 68355527 588 3797 UBR1 0 . GRCh38 15 43048433 43048433 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.1498G>C p.Glu500Gln p.E500Q ENST00000290650 13/47 273 256 17 175 175 0 strelka-varscan-mutect UBR1,missense_variant,p.Glu500Gln,ENST00000290650,NM_174916.2;UBR1,missense_variant,p.Glu500Gln,ENST00000546274,;UBR1,3_prime_UTR_variant,,ENST00000569971,;UBR1,intron_variant,,ENST00000563239,; G ENST00000290650 Transcript missense_variant 1577/7761 1498/5250 500/1749 E/Q Gaa/Caa 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 tolerated(0.06) 13/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.65919 0.9999996 1 1 1 0 G 3 3 10 43048433 43048433 C G 1 0 0 0 0 1 0 0 0 17425 835 29 4 4 UBR1 15 43048433 Missense_Mutation SNP C C3L-00095_T 9412771 43048433 58942756 589 3798 UBR1 0 . GRCh38 15 43048453 43048453 + Missense_Mutation SNP C C T rs765893686 C3L-00095_T C3L-00095_N C C c.1478G>A p.Arg493Lys p.R493K ENST00000290650 13/47 283 265 18 189 189 0 strelka-varscan-mutect UBR1,missense_variant,p.Arg493Lys,ENST00000290650,NM_174916.2;UBR1,missense_variant,p.Arg493Lys,ENST00000546274,;UBR1,3_prime_UTR_variant,,ENST00000569971,;UBR1,intron_variant,,ENST00000563239,; T ENST00000290650 Transcript missense_variant 1557/7761 1478/5250 493/1749 R/K aGa/aAa rs765893686 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 tolerated(0.77) 13/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27 MODERATE 1 SNV 1 1 PASS rs765893686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 43048453 43048453 C T 1 0 0 0 0 1 0 0 0 17425 913 32 3 3 UBR1 15 43048453 Missense_Mutation SNP C C3L-00095_T 20 43048453 58942736 590 3799 TGM5 0 . GRCh38 15 43233346 43233346 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.2010-2A>T p.X670_splice ENST00000220420 413 380 33 555 555 0 strelka-varscan-mutect TGM5,splice_acceptor_variant,,ENST00000220420,NM_201631.3;TGM5,splice_acceptor_variant,,ENST00000610827,;TGM5,splice_acceptor_variant,,ENST00000611276,;TGM5,splice_acceptor_variant,,ENST00000622115,;TGM5,splice_acceptor_variant,,ENST00000349114,NM_004245.3;TGM5,splice_acceptor_variant,,ENST00000396996,; A ENST00000220420 Transcript splice_acceptor_variant -/2767 2010/2163 670/720 1 -1 TGM5 HGNC HGNC:11781 protein_coding YES CCDS32212.1 ENSP00000220420 O43548 UPI0000136CCF NM_201631.3 12/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 43233346 43233346 T A 1 0 0 0 0 0 0 1 0 16266 1594 55 4 4 TGM5 15 43233346 Splice_Site SNP T C3L-00095_T 184893 43233346 58757843 591 3800 STRC 0 . GRCh38 15 43604054 43604054 + Silent SNP A A T novel C3L-00095_T C3L-00095_N A A c.4317T>A p.= p.A1439A ENST00000450892 22/29 252 224 28 376 376 0 varscan-mutect STRC,synonymous_variant,p.=,ENST00000450892,NM_153700.2;STRC,synonymous_variant,p.=,ENST00000541030,;CKMT1B,downstream_gene_variant,,ENST00000300283,NM_020990.3;CKMT1B,downstream_gene_variant,,ENST00000441322,;RNU6-554P,downstream_gene_variant,,ENST00000410466,;CKMT1B,intron_variant,,ENST00000411560,;STRC,3_prime_UTR_variant,,ENST00000428650,;STRC,3_prime_UTR_variant,,ENST00000440125,;STRC,non_coding_transcript_exon_variant,,ENST00000485556,;STRC,non_coding_transcript_exon_variant,,ENST00000471703,;STRC,intron_variant,,ENST00000448437,;CKMT1B,downstream_gene_variant,,ENST00000437534,;STRC,downstream_gene_variant,,ENST00000455136,;STRC,upstream_gene_variant,,ENST00000460952,;STRC,upstream_gene_variant,,ENST00000493750,; T ENST00000450892 Transcript synonymous_variant 4395/5680 4317/5328 1439/1775 A gcT/gcA 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 22/29 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF14,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 43604054 43604054 A T 1 0 0 0 0 0 0 0 1 15709 175 7 4 4 STRC 15 43604054 Silent SNP A C3L-00095_T 370708 43604054 58387135 592 3801 FBN1 0 . GRCh38 15 48415650 48415650 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.7937G>T p.Cys2646Phe p.C2646F ENST00000316623 64/66 451 413 38 539 535 4 strelka-varscan-mutect FBN1,missense_variant,p.Cys2646Phe,ENST00000316623,NM_000138.4;FBN1,non_coding_transcript_exon_variant,,ENST00000561429,;FBN1,3_prime_UTR_variant,,ENST00000559133,; A ENST00000316623 Transcript missense_variant 8393/11756 7937/8616 2646/2871 C/F tGc/tTc 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 deleterious(0) 64/66 Gene3D:2.10.25.10,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 48415650 48415650 C A 1 0 0 0 0 1 0 0 0 5565 710 25 2 2 FBN1 15 48415650 Missense_Mutation SNP C C3L-00095_T 4811596 48415650 53575539 593 3802 UNC13C 0 . GRCh38 15 54014226 54014226 + Silent SNP C C T C3L-00095_T C3L-00095_N C C c.1323C>T p.= p.I441I ENST00000260323 1/32 192 173 19 214 214 0 strelka-varscan-mutect UNC13C,synonymous_variant,p.=,ENST00000260323,NM_001080534.1; T ENST00000260323 Transcript synonymous_variant 1323/12946 1323/6645 441/2214 I atC/atT COSM4804175,COSM4804176,COSM4804177 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS rs746069739 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 10 54014226 54014226 C T 1 0 0 0 0 0 0 0 1 17510 816 29 3 3 UNC13C 15 54014226 Silent SNP C C3L-00095_T 5598576 54014226 47976963 594 3803 PIF1 0 . GRCh38 15 64821417 64821417 + Missense_Mutation SNP C C G C3L-00095_T C3L-00095_N C C c.921G>C p.Glu307Asp p.E307D ENST00000333425 5/13 73 67 6 100 100 0 strelka-varscan-mutect PIF1,missense_variant,p.Glu307Asp,ENST00000268043,NM_001286499.1,NM_025049.3,NM_001286496.1;PIF1,missense_variant,p.Glu307Asp,ENST00000559239,;PIF1,missense_variant,p.Glu307Asp,ENST00000333425,NM_001286497.1;PIF1,non_coding_transcript_exon_variant,,ENST00000558380,;PIF1,non_coding_transcript_exon_variant,,ENST00000558547,;PIF1,downstream_gene_variant,,ENST00000560444,;PIF1,downstream_gene_variant,,ENST00000560504,;PIF1,upstream_gene_variant,,ENST00000559522,;PIF1,upstream_gene_variant,,ENST00000559872,; G ENST00000333425 Transcript missense_variant 1016/2278 921/2124 307/707 E/D gaG/gaC COSM1608592,COSM3706681 1 -1 PIF1 HGNC HGNC:26220 protein_coding YES CCDS66797.1 ENSP00000328174 Q9H611 UPI00005DB2E0 NM_001286497.1 deleterious(0) 5/13 Gene3D:3.40.50.300,HAMAP:MF_03176,Pfam_domain:PF05970,hmmpanther:PTHR23274,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 64821417 64821417 C G 1 0 0 0 0 1 0 0 0 11976 912 32 4 4 PIF1 15 64821417 Missense_Mutation SNP C C3L-00095_T 10807191 64821417 37169772 595 3804 IGDCC3 0 . GRCh38 15 65334763 65334763 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.788G>T p.Gly263Val p.G263V ENST00000327987 5/14 80 74 6 88 88 0 strelka-mutect IGDCC3,missense_variant,p.Gly263Val,ENST00000327987,NM_004884.3;IGDCC3,missense_variant,p.Gly126Val,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559058,;IGDCC3,upstream_gene_variant,,ENST00000559231,; A ENST00000327987 Transcript missense_variant 1040/4479 788/2445 263/814 G/V gGc/gTc 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 deleterious(0) 5/14 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs918855313 . 0 205 3 2 0 0 0 0 -10.22434 0.9999733 1 1 1 0 A 3 1 10 65334763 65334763 C A 1 0 0 0 0 1 0 0 0 7474 739 26 2 2 IGDCC3 15 65334763 Missense_Mutation SNP C C3L-00095_T 513346 65334763 36656426 596 3805 THSD4 0 . GRCh38 15 71243026 71243026 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.842C>A p.Ser281Tyr p.S281Y ENST00000355327 5/18 113 103 10 159 159 0 strelka-varscan-mutect THSD4,missense_variant,p.Ser281Tyr,ENST00000355327,NM_024817.2; A ENST00000355327 Transcript missense_variant 976/9200 842/3057 281/1018 S/Y tCt/tAt 1 1 THSD4 HGNC HGNC:25835 protein_coding YES CCDS10238.2 ENSP00000347484 Q6ZMP0 UPI00001A797D NM_024817.2 tolerated(1) 5/18 PROSITE_profiles:PS50092 MODERATE 1 SNV 5 1 PASS rs1490838746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 71243026 71243026 C A 1 0 0 0 0 1 0 0 0 16312 913 32 2 2 THSD4 15 71243026 Missense_Mutation SNP C C3L-00095_T 5908263 71243026 30748163 597 3806 ISLR2 0 . GRCh38 15 74133057 74133057 + Silent SNP C C A C3L-00095_T C3L-00095_N C C c.303C>A p.= p.L101L ENST00000361742 4/4 252 231 21 281 280 1 strelka-varscan-mutect ISLR2,synonymous_variant,p.=,ENST00000361742,NM_001130136.1;ISLR2,synonymous_variant,p.=,ENST00000435464,NM_001130138.1;ISLR2,synonymous_variant,p.=,ENST00000565159,NM_001130137.1;ISLR2,synonymous_variant,p.=,ENST00000453268,NM_020851.2;ISLR2,synonymous_variant,p.=,ENST00000565540,;ISLR2,synonymous_variant,p.=,ENST00000419208,;ISLR2,synonymous_variant,p.=,ENST00000561740,;ISLR2,synonymous_variant,p.=,ENST00000565332,;ISLR2,downstream_gene_variant,,ENST00000569886,;ISLR2,downstream_gene_variant,,ENST00000567206,;RP11-247C2.2,upstream_gene_variant,,ENST00000563727,;RP11-247C2.2,upstream_gene_variant,,ENST00000514871,;ISLR2,intron_variant,,ENST00000561975,;ISLR2,downstream_gene_variant,,ENST00000565068,; A ENST00000361742 Transcript synonymous_variant 1072/4817 303/2238 101/745 L ctC/ctA COSM4855582 1 1 ISLR2 HGNC HGNC:29286 protein_coding YES CCDS10259.1 ENSP00000355402 Q6UXK2 UPI000004C60F NM_001130136.1 4/4 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF15,SMART_domains:SM00369,Superfamily_domains:SSF52058 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 74133057 74133057 C A 1 0 0 0 0 0 0 0 1 7766 813 29 2 2 ISLR2 15 74133057 Silent SNP C C3L-00095_T 2890031 74133057 27858132 598 3807 CSPG4 0 . GRCh38 15 75688344 75688344 + Silent SNP G G T rs146393812 C3L-00095_T C3L-00095_N G G c.2721C>A p.= p.L907L ENST00000308508 3/10 174 164 10 237 236 1 strelka-varscan-mutect CSPG4,synonymous_variant,p.=,ENST00000308508,NM_001897.4; T ENST00000308508 Transcript synonymous_variant 2814/8290 2721/6969 907/2322 L ctC/ctA rs146393812 1 -1 CSPG4 HGNC HGNC:2466 protein_coding YES CCDS10284.1 ENSP00000312506 Q6UVK1 UPI00001AEEB6 NM_001897.4 3/10 hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF16,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs146393812 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 75688344 75688344 G T 1 0 0 0 0 0 0 0 1 3761 1045 37 1 1 CSPG4 15 75688344 Silent SNP G C3L-00095_T 1555287 75688344 26302845 599 3808 ACAN 0 . GRCh38 15 88854985 88854985 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2400C>A p.= p.S800S ENST00000439576 12/18 69 58 11 86 86 0 strelka-varscan-mutect ACAN,synonymous_variant,p.=,ENST00000439576,NM_013227.3;ACAN,synonymous_variant,p.=,ENST00000617301,;ACAN,synonymous_variant,p.=,ENST00000559004,;ACAN,synonymous_variant,p.=,ENST00000561243,;ACAN,synonymous_variant,p.=,ENST00000352105,NM_001135.3;ACAN,downstream_gene_variant,,ENST00000558207,;ACAN,upstream_gene_variant,,ENST00000560601,; A ENST00000439576 Transcript synonymous_variant 2774/8840 2400/7593 800/2530 S tcC/tcA 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 12/18 Low_complexity_(Seg):seg,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 LOW 1 SNV 5 1 PASS . . 0 196 12 2 0 0 0 0 -19.25297 0.9985888 1 1 1 0 A 2 1 10 88854985 88854985 C A 1 0 0 0 0 0 0 0 1 160 610 22 2 2 ACAN 15 88854985 Silent SNP C C3L-00095_T 13166641 88854985 13136204 600 3809 ARPIN 0 . GRCh38 15 89908370 89908370 + Missense_Mutation SNP G G A rs374275505 C3L-00095_T C3L-00095_N G G c.211C>T p.Arg71Cys p.R71C ENST00000357484 3/6 234 206 28 299 299 0 strelka-varscan-mutect ARPIN,missense_variant,p.Arg71Cys,ENST00000357484,NM_182616.3;C15orf38-AP3S2,missense_variant,p.Arg71Cys,ENST00000398333,NM_001199058.1;ARPIN,5_prime_UTR_variant,,ENST00000460685,NM_001282380.1;C15orf38-AP3S2,5_prime_UTR_variant,,ENST00000559629,;C15orf38-AP3S2,5_prime_UTR_variant,,ENST00000558648,;ARPIN,upstream_gene_variant,,ENST00000560096,; A ENST00000357484 Transcript missense_variant 332/7591 211/681 71/226 R/C Cgc/Tgc rs374275505,COSM3402007 1 -1 ARPIN HGNC HGNC:28782 protein_coding YES CCDS42080.1 ENSP00000350075 Q7Z6K5 UPI0000161A90 NM_182616.3 tolerated(0.07) 3/6 Pfam_domain:PF10574,hmmpanther:PTHR31199,hmmpanther:PTHR31199:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374275505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 89908370 89908370 G A 1 0 0 0 0 1 0 0 0 1119 1058 37 1 1 ARPIN 15 89908370 Missense_Mutation SNP G C3L-00095_T 1053385 89908370 12082819 601 3810 ZNF774 0 . GRCh38 15 90360410 90360410 + Silent SNP C C T rs779514301 C3L-00095_T C3L-00095_N C C c.579C>T p.= p.D193D ENST00000354377 4/4 149 134 15 154 154 0 strelka-varscan-mutect ZNF774,synonymous_variant,p.=,ENST00000354377,NM_001004309.2;ZNF774,intron_variant,,ENST00000379090,;ZNF774,downstream_gene_variant,,ENST00000558586,;ZNF774,non_coding_transcript_exon_variant,,ENST00000558115,;ZNF774,downstream_gene_variant,,ENST00000560038,; T ENST00000354377 Transcript synonymous_variant 765/3202 579/1452 193/483 D gaC/gaT rs779514301 1 1 ZNF774 HGNC HGNC:33108 protein_coding YES CCDS32330.1 ENSP00000346348 Q6NX45 UPI00001A73D8 NM_001004309.2 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF66,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs779514301 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 90360410 90360410 C T 1 0 0 0 0 0 0 0 1 18730 506 18 3 3 ZNF774 15 90360410 Silent SNP C C3L-00095_T 452040 90360410 11630779 602 3811 CHSY1 0 . GRCh38 15 101177938 101177938 + Missense_Mutation SNP T T A rs372012197 C3L-00095_T C3L-00095_N T T c.1859A>T p.Gln620Leu p.Q620L ENST00000254190 3/3 279 252 27 371 371 0 strelka-varscan-mutect CHSY1,missense_variant,p.Gln620Leu,ENST00000254190,NM_014918.4;CHSY1,non_coding_transcript_exon_variant,,ENST00000543813,;CHSY1,downstream_gene_variant,,ENST00000561414,;CHSY1,downstream_gene_variant,,ENST00000560766,; A ENST00000254190 Transcript missense_variant 2335/4550 1859/2409 620/802 Q/L cAg/cTg rs372012197 1 -1 CHSY1 HGNC HGNC:17198 protein_coding YES CCDS10390.1 ENSP00000254190 Q86X52 UPI000000DB6C NM_014918.4 tolerated(0.15) 3/3 hmmpanther:PTHR12369:SF16,hmmpanther:PTHR12369,Gene3D:3.90.550.10,Pfam_domain:PF05679,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs372012197 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 101177938 101177938 T A 1 0 0 0 0 1 0 0 0 3172 1580 55 4 4 CHSY1 15 101177938 Missense_Mutation SNP T C3L-00095_T 10817528 101177938 813251 603 3812 RHBDF1 0 . GRCh38 16 61395 61395 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1385G>T p.Gly462Val p.G462V ENST00000262316 10/18 257 242 15 310 309 1 strelka-varscan-mutect RHBDF1,missense_variant,p.Gly462Val,ENST00000262316,NM_022450.3;SNRNP25,downstream_gene_variant,,ENST00000293861,;SNRNP25,downstream_gene_variant,,ENST00000383018,NM_024571.3;RHBDF1,upstream_gene_variant,,ENST00000448893,;RHBDF1,downstream_gene_variant,,ENST00000450643,;RHBDF1,downstream_gene_variant,,ENST00000419764,;SNRNP25,downstream_gene_variant,,ENST00000417493,;RHBDF1,3_prime_UTR_variant,,ENST00000428730,;RHBDF1,downstream_gene_variant,,ENST00000487201,;SNRNP25,downstream_gene_variant,,ENST00000481947,;SNRNP25,downstream_gene_variant,,ENST00000466183,;RHBDF1,upstream_gene_variant,,ENST00000493647,;RHBDF1,upstream_gene_variant,,ENST00000486045,;SNRNP25,downstream_gene_variant,,ENST00000397876,;RHBDF1,downstream_gene_variant,,ENST00000417043,;RHBDF1,downstream_gene_variant,,ENST00000472390,;RHBDF1,downstream_gene_variant,,ENST00000482904,; A ENST00000262316 Transcript missense_variant 1528/2992 1385/2568 462/855 G/V gGg/gTg 1 -1 RHBDF1 HGNC HGNC:20561 protein_coding YES CCDS32344.1 ENSP00000262316 Q96CC6 UPI00001A5206 NM_022450.3 deleterious(0) 10/18 hmmpanther:PTHR22936,hmmpanther:PTHR22936:SF26 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 61395 61395 C A 1 0 0 0 0 1 0 0 0 13491 623 22 2 2 RHBDF1 16 61395 Missense_Mutation SNP C C3L-00095_T 61395 90276950 604 3813 CAPN15 0 . GRCh38 16 552492 552492 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.2699A>T p.His900Leu p.H900L ENST00000219611 11/14 306 281 25 380 379 1 strelka-varscan-mutect CAPN15,missense_variant,p.His900Leu,ENST00000219611,NM_005632.2;CAPN15,downstream_gene_variant,,ENST00000637507,;CAPN15,downstream_gene_variant,,ENST00000568988,;CAPN15,upstream_gene_variant,,ENST00000566977,;LA16c-366D1.3,intron_variant,,ENST00000565879,;CAPN15,non_coding_transcript_exon_variant,,ENST00000565010,; T ENST00000219611 Transcript missense_variant 3062/4744 2699/3261 900/1086 H/L cAc/cTc 1 1 CAPN15 HGNC HGNC:11182 protein_coding YES CCDS10410.1 ENSP00000219611 O75808 UPI0000071B68 NM_005632.2 deleterious(0) 11/14 hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF294 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 552492 552492 A T 1 0 0 0 0 1 0 0 0 2320 159 6 4 4 CAPN15 16 552492 Missense_Mutation SNP A C3L-00095_T 491097 552492 89785853 605 3814 ZG16B 0 . GRCh38 16 2830472 2830472 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.139G>T p.Gly47Trp p.G47W ENST00000382280 2/4 109 100 9 155 154 1 strelka-varscan-mutect ZG16B,missense_variant,p.Gly46Trp,ENST00000570670,;ZG16B,missense_variant,p.Gly47Trp,ENST00000382280,NM_145252.2;ZG16B,missense_variant,p.Gly17Trp,ENST00000572863,;ZG16B,missense_variant,p.Gly28Trp,ENST00000571723,;PRSS21,downstream_gene_variant,,ENST00000575739,;ZG16B,non_coding_transcript_exon_variant,,ENST00000576423,;ZG16B,non_coding_transcript_exon_variant,,ENST00000573019,; T ENST00000382280 Transcript missense_variant 218/831 139/627 47/208 G/W Ggg/Tgg 1 1 ZG16B HGNC HGNC:30456 protein_coding YES CCDS10479.2 ENSP00000371715 Q96DA0 G8H6I3 UPI000059D2F8 NM_145252.2 deleterious(0.05) 2/4 hmmpanther:PTHR33589,hmmpanther:PTHR33589:SF1 MODERATE 1 SNV 1 1 PASS rs1455625210 . 0 208 2 0 0 0 0 0 -18.379 1 1 1 1 0 T 3 4 10 2830472 2830472 G T 1 0 0 0 0 1 0 0 0 18250 1232 43 2 2 ZG16B 16 2830472 Missense_Mutation SNP G C3L-00095_T 2277980 2830472 87507873 606 3815 OR2C1 0 . GRCh38 16 3356382 3356382 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.442G>T p.Ala148Ser p.A148S ENST00000304936 1/1 257 237 20 308 307 1 strelka-varscan-mutect OR2C1,missense_variant,p.Ala148Ser,ENST00000304936,NM_012368.2; T ENST00000304936 Transcript missense_variant 494/1406 442/939 148/312 A/S Gcc/Tcc 1 1 OR2C1 HGNC HGNC:8242 protein_coding YES CCDS10502.1 ENSP00000307726 O95371 UPI000013E9E9 NM_012368.2 tolerated(0.52) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 3356382 3356382 G T 1 0 0 0 0 1 0 0 0 11071 1319 46 2 2 OR2C1 16 3356382 Missense_Mutation SNP G C3L-00095_T 525910 3356382 86981963 607 3816 ANKS3 0 . GRCh38 16 4729993 4729993 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.157G>T p.Glu53Ter p.E53* ENST00000304283 3/18 32 25 7 49 49 0 strelka-varscan-mutect ANKS3,stop_gained,p.Glu53Ter,ENST00000304283,NM_133450.3;ANKS3,stop_gained,p.Glu53Ter,ENST00000614075,;ANKS3,stop_gained,p.Glu53Ter,ENST00000450067,NM_001242929.1;ANKS3,stop_gained,p.Glu53Ter,ENST00000592421,;ANKS3,stop_gained,p.Glu53Ter,ENST00000590147,;ANKS3,stop_gained,p.Glu53Ter,ENST00000592711,;ANKS3,stop_gained,p.Glu53Ter,ENST00000592190,;ANKS3,stop_gained,p.Glu53Ter,ENST00000589065,;ANKS3,5_prime_UTR_variant,,ENST00000446014,NM_001308089.1;ANKS3,5_prime_UTR_variant,,ENST00000592698,;ANKS3,intron_variant,,ENST00000585773,;ANKS3,intron_variant,,ENST00000586605,;ANKS3,intron_variant,,ENST00000586166,;C16orf71,upstream_gene_variant,,ENST00000299320,NM_139170.2;C16orf71,upstream_gene_variant,,ENST00000590191,;C16orf71,upstream_gene_variant,,ENST00000586724,;RP11-127I20.7,downstream_gene_variant,,ENST00000588099,;ANKS3,stop_gained,p.Glu53Ter,ENST00000592077,;ANKS3,stop_gained,p.Glu53Ter,ENST00000590193,;ANKS3,stop_gained,p.Glu53Ter,ENST00000590730,;ANKS3,stop_gained,p.Glu53Ter,ENST00000592068,;ANKS3,stop_gained,p.Glu53Ter,ENST00000586159,;ANKS3,stop_gained,p.Glu53Ter,ENST00000587005,;ANKS3,stop_gained,p.Glu53Ter,ENST00000591281,;ANKS3,non_coding_transcript_exon_variant,,ENST00000590689,;ANKS3,non_coding_transcript_exon_variant,,ENST00000593120,;C16orf71,upstream_gene_variant,,ENST00000586256,;ANKS3,upstream_gene_variant,,ENST00000591653,;ANKS3,upstream_gene_variant,,ENST00000590803,;ANKS3,upstream_gene_variant,,ENST00000586632,; A ENST00000304283 Transcript stop_gained 452/2662 157/1971 53/656 E/* Gag/Tag 1 -1 ANKS3 HGNC HGNC:29422 protein_coding YES CCDS10520.1 ENSP00000304586 Q6ZW76 UPI00001C08FE NM_133450.3 3/18 PROSITE_profiles:PS50297,hmmpanther:PTHR24184:SF6,hmmpanther:PTHR24184,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 4729993 4729993 C A 1 0 0 0 0 0 1 0 0 796 864 30 2 2 ANKS3 16 4729993 Nonsense_Mutation SNP C C3L-00095_T 1373611 4729993 85608352 608 3817 SHISA9 0 . GRCh38 16 13235113 13235113 + Missense_Mutation SNP G G T rs774111296 C3L-00095_T C3L-00095_N G G c.979G>T p.Val327Leu p.V327L ENST00000558583 5/5 189 177 12 250 250 0 strelka-mutect SHISA9,missense_variant,p.Val327Leu,ENST00000558583,NM_001145204.2;SHISA9,non_coding_transcript_exon_variant,,ENST00000566106,; T ENST00000558583 Transcript missense_variant 1424/6724 979/1275 327/424 V/L Gta/Tta rs774111296,COSM1166403 1 1 SHISA9 HGNC HGNC:37231 protein_coding YES CCDS45417.2 ENSP00000454014 B4DS77 UPI0001CE6F1C NM_001145204.2 tolerated(0.29) 5/5 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF1 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs774111296 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 13235113 13235113 G T 1 0 0 0 0 1 0 0 0 14546 1145 40 1 1 SHISA9 16 13235113 Missense_Mutation SNP G C3L-00095_T 8505120 13235113 77103232 609 3818 SMG1 0 . GRCh38 16 18850123 18850123 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.5287C>T p.Pro1763Ser p.P1763S ENST00000446231 35/63 140 130 10 167 167 0 strelka-varscan-mutect SMG1,missense_variant,p.Pro1763Ser,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Pro1653Ser,ENST00000565324,;SMG1,non_coding_transcript_exon_variant,,ENST00000563448,;SMG1,upstream_gene_variant,,ENST00000562668,; A ENST00000446231 Transcript missense_variant 5700/16115 5287/10986 1763/3661 P/S Cct/Tct COSM48772 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 tolerated_low_confidence(0.89) 35/63 PROSITE_profiles:PS51189,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 18850123 18850123 G A 1 0 0 0 0 1 0 0 0 15089 1188 41 3 3 SMG1 16 18850123 Missense_Mutation SNP G C3L-00095_T 5615010 18850123 71488222 610 3819 UMOD 0 . GRCh38 16 20349105 20349105 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.295C>A p.Leu99Met p.L99M ENST00000396134 4/12 485 452 33 596 594 2 strelka-varscan-mutect UMOD,missense_variant,p.Leu66Met,ENST00000302509,NM_001008389.2,NM_003361.3;UMOD,missense_variant,p.Leu99Met,ENST00000396134,NM_001278614.1;UMOD,missense_variant,p.Leu115Met,ENST00000396138,;UMOD,missense_variant,p.Leu66Met,ENST00000570689,;UMOD,missense_variant,p.Leu120Met,ENST00000574195,;UMOD,missense_variant,p.Leu66Met,ENST00000571174,;UMOD,missense_variant,p.Leu94Met,ENST00000577168,;UMOD,missense_variant,p.Leu89Met,ENST00000573567,;UMOD,missense_variant,p.Leu66Met,ENST00000576546,;UMOD,missense_variant,p.Leu66Met,ENST00000570757,;UMOD,missense_variant,p.Leu66Met,ENST00000576688,;UMOD,downstream_gene_variant,,ENST00000570972,; T ENST00000396134 Transcript missense_variant 419/2408 295/2022 99/673 L/M Ctg/Atg 1 -1 UMOD HGNC HGNC:12559 protein_coding YES CCDS61876.1 ENSP00000379438 P07911 UPI000059D336 NM_001278614.1 tolerated(0.08) 4/12 PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF263,hmmpanther:PTHR24044,PROSITE_patterns:PS01187,Gene3D:2.40.155.10,Pfam_domain:PF07645,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 20349105 20349105 G T 1 0 0 0 0 1 0 0 0 17503 991 35 2 2 UMOD 16 20349105 Missense_Mutation SNP G C3L-00095_T 1498982 20349105 69989240 611 3820 ACSM2A 0 . GRCh38 16 20471144 20471144 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.668G>C p.Gly223Ala p.G223A ENST00000573854 5/14 130 122 8 174 174 0 varscan-mutect ACSM2A,missense_variant,p.Gly223Ala,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,missense_variant,p.Gly223Ala,ENST00000396104,;ACSM2A,missense_variant,p.Gly223Ala,ENST00000575690,;ACSM2A,missense_variant,p.Gly223Ala,ENST00000219054,;ACSM2A,missense_variant,p.Gly144Ala,ENST00000417235,NM_001308169.1;ACSM2A,downstream_gene_variant,,ENST00000574251,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,upstream_gene_variant,,ENST00000572921,;ACSM2A,3_prime_UTR_variant,,ENST00000574692,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,;ACSM2A,upstream_gene_variant,,ENST00000572843,; C ENST00000573854 Transcript missense_variant 782/2837 668/1734 223/577 G/A gGg/gCg 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 deleterious(0.01) 5/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,PROSITE_patterns:PS00455,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS rs1440376614 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 20471144 20471144 G C 1 0 0 0 0 1 0 0 0 225 1232 43 4 4 ACSM2A 16 20471144 Missense_Mutation SNP G C3L-00095_T 122039 20471144 69867201 612 3821 TMEM265 0 . GRCh38 16 30741818 30741818 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.75C>T p.= p.C25C ENST00000615541 2/3 214 192 22 259 259 0 strelka-varscan-mutect TMEM265,synonymous_variant,p.=,ENST00000615541,NM_001256829.1;SRCAP,downstream_gene_variant,,ENST00000262518,NM_006662.2;SRCAP,downstream_gene_variant,,ENST00000395059,;RP11-2C24.4,non_coding_transcript_exon_variant,,ENST00000483578,;RP11-2C24.9,3_prime_UTR_variant,,ENST00000380361,; T ENST00000615541 Transcript synonymous_variant 405/995 75/327 25/108 C tgC/tgT 1 1 TMEM265 HGNC HGNC:51241 protein_coding YES CCDS73870.1 ENSP00000477871 A0A087WTH1 UPI0000D4C221 NM_001256829.1 2/3 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 30741818 30741818 C T 1 0 0 0 0 0 0 0 1 16625 805 28 3 3 TMEM265 16 30741818 Silent SNP C C3L-00095_T 10270674 30741818 59596527 613 3822 ITGAM 0 . GRCh38 16 31321615 31321615 + Silent SNP C C A rs372150584 C3L-00095_T C3L-00095_N C C c.1993C>A p.= p.R665R ENST00000544665 16/30 108 100 8 139 139 0 strelka-varscan-mutect ITGAM,synonymous_variant,p.=,ENST00000544665,NM_001145808.1;ITGAM,synonymous_variant,p.=,ENST00000287497,NM_000632.3;ITGAM,intron_variant,,ENST00000567031,;ITGAM,upstream_gene_variant,,ENST00000561838,; A ENST00000544665 Transcript synonymous_variant 2064/4718 1993/3462 665/1153 R Cgg/Agg rs372150584 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 16/30 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179 LOW 1 SNV 1 1 PASS rs372150584 . 0 207 3 0 0 0 0 0 -16.25435 1 1 1 1 0 A 2 1 10 31321615 31321615 C A 1 0 0 0 0 0 0 0 1 7794 875 31 1 1 ITGAM 16 31321615 Silent SNP C C3L-00095_T 579797 31321615 59016730 614 3823 SLC5A2 0 . GRCh38 16 31488704 31488704 + Silent SNP C C G novel C3L-00095_T C3L-00095_N C C c.1212C>G p.= p.L404L ENST00000330498 10/14 147 132 15 203 202 1 strelka-varscan-mutect SLC5A2,synonymous_variant,p.=,ENST00000330498,NM_003041.3;C16orf58,downstream_gene_variant,,ENST00000327237,NM_022744.3;C16orf58,downstream_gene_variant,,ENST00000570164,;C16orf58,downstream_gene_variant,,ENST00000430477,;C16orf58,downstream_gene_variant,,ENST00000567994,;SLC5A2,downstream_gene_variant,,ENST00000569576,;AC026471.6,upstream_gene_variant,,ENST00000565137,;SLC5A2,upstream_gene_variant,,ENST00000564197,;SLC5A2,upstream_gene_variant,,ENST00000567051,;SLC5A2,non_coding_transcript_exon_variant,,ENST00000568188,;SLC5A2,intron_variant,,ENST00000419665,;SLC5A2,intron_variant,,ENST00000568891,;C16orf58,downstream_gene_variant,,ENST00000568491,;C16orf58,downstream_gene_variant,,ENST00000541442,;SLC5A2,downstream_gene_variant,,ENST00000562006,;C16orf58,downstream_gene_variant,,ENST00000567673,;SLC5A2,downstream_gene_variant,,ENST00000565446,; G ENST00000330498 Transcript synonymous_variant 1231/2271 1212/2019 404/672 L ctC/ctG 1 1 SLC5A2 HGNC HGNC:11037 protein_coding YES CCDS10714.1 ENSP00000327943 P31639 UPI000004D0A0 NM_003041.3 10/14 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF145,TIGRFAM_domain:TIGR00813 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 31488704 31488704 C G 1 0 0 0 0 0 0 0 1 14948 900 32 4 4 SLC5A2 16 31488704 Silent SNP C C3L-00095_T 167089 31488704 58849641 615 3824 ABCC12 0 . GRCh38 16 48104231 48104231 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2811G>T p.= p.V937V ENST00000311303 20/29 506 479 27 555 553 2 strelka-varscan-mutect ABCC12,synonymous_variant,p.=,ENST00000311303,NM_033226.2;ABCC12,synonymous_variant,p.=,ENST00000534418,;ABCC12,synonymous_variant,p.=,ENST00000497206,;ABCC12,synonymous_variant,p.=,ENST00000532494,;ABCC12,3_prime_UTR_variant,,ENST00000529084,;ABCC12,intron_variant,,ENST00000529504,; A ENST00000311303 Transcript synonymous_variant 3157/5168 2811/4080 937/1359 V gtG/gtT 1 -1 ABCC12 HGNC HGNC:14640 protein_coding YES CCDS10730.1 ENSP00000311030 Q96J65 UPI0000456987 NM_033226.2 20/29 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF10,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS rs904993671 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 48104231 48104231 C A 1 0 0 0 0 0 0 0 1 56 581 21 2 2 ABCC12 16 48104231 Silent SNP C C3L-00095_T 16615527 48104231 42234114 616 3825 ADCY7 0 . GRCh38 16 50294705 50294705 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.902T>G p.Val301Gly p.V301G ENST00000394697 7/26 128 118 10 153 153 0 strelka-varscan-mutect ADCY7,missense_variant,p.Val301Gly,ENST00000394697,;ADCY7,missense_variant,p.Val301Gly,ENST00000254235,NM_001114.4;ADCY7,missense_variant,p.Val301Gly,ENST00000566433,NM_001286057.1;ADCY7,missense_variant,p.Val301Gly,ENST00000537579,;ADCY7,downstream_gene_variant,,ENST00000566761,;ADCY7,downstream_gene_variant,,ENST00000564965,;MIR6771,downstream_gene_variant,,ENST00000619793,;ADCY7,non_coding_transcript_exon_variant,,ENST00000564044,;ADCY7,non_coding_transcript_exon_variant,,ENST00000563677,;ADCY7,missense_variant,p.Val301Gly,ENST00000567277,; G ENST00000394697 Transcript missense_variant 1242/6213 902/3243 301/1080 V/G gTg/gGg 1 1 ADCY7 HGNC HGNC:238 protein_coding YES CCDS10741.1 ENSP00000378187 P51828 UPI000004C5DB deleterious(0) 7/26 PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF273,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 50294705 50294705 T G 1 0 0 0 0 1 0 0 0 343 1696 59 5 5 ADCY7 16 50294705 Missense_Mutation SNP T C3L-00095_T 2190474 50294705 40043640 617 3826 SALL1 0 . GRCh38 16 51137456 51137456 + Missense_Mutation SNP C C A rs377652797 C3L-00095_T C3L-00095_N C C c.3631G>T p.Val1211Phe p.V1211F ENST00000251020 3/3 246 231 15 322 322 0 strelka-varscan-mutect SALL1,missense_variant,p.Val1114Phe,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Val1211Phe,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Val1114Phe,ENST00000570206,;SALL1,3_prime_UTR_variant,,ENST00000566102,; A ENST00000251020 Transcript missense_variant 3665/5146 3631/3975 1211/1324 V/F Gtc/Ttc rs377652797 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.06) 3/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS rs377652797 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 51137456 51137456 C A 1 0 0 0 0 1 0 0 0 14069 536 19 1 1 SALL1 16 51137456 Missense_Mutation SNP C C3L-00095_T 842751 51137456 39200889 618 3827 SALL1 0 . GRCh38 16 51140846 51140846 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1376G>T p.Gly459Val p.G459V ENST00000251020 2/3 210 188 22 250 248 2 strelka-varscan-mutect SALL1,missense_variant,p.Gly362Val,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Gly459Val,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Gly362Val,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 1410/5146 1376/3975 459/1324 G/V gGg/gTg 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0) 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 51140846 51140846 C A 1 0 0 0 0 1 0 0 0 14069 623 22 2 2 SALL1 16 51140846 Missense_Mutation SNP C C3L-00095_T 3390 51140846 39197499 619 3828 CHD9 0 . GRCh38 16 53235185 53235185 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2512G>T p.Asp838Tyr p.D838Y ENST00000447540 11/39 62 57 5 53 53 0 strelka-varscan-mutect CHD9,missense_variant,p.Asp838Tyr,ENST00000566029,NM_025134.4;CHD9,missense_variant,p.Asp838Tyr,ENST00000447540,NM_001308319.1;CHD9,missense_variant,p.Asp838Tyr,ENST00000564845,;CHD9,missense_variant,p.Asp838Tyr,ENST00000398510,;CHD9,missense_variant,p.Asp364Tyr,ENST00000565803,;CHD9,splice_region_variant,,ENST00000615216,;CHD9,intron_variant,,ENST00000622617,;CHD9,splice_region_variant,,ENST00000564255,;CHD9,non_coding_transcript_exon_variant,,ENST00000219084,;CHD9,non_coding_transcript_exon_variant,,ENST00000569225,; T ENST00000447540 Transcript missense_variant,splice_region_variant 2721/11509 2512/8694 838/2897 D/Y Gac/Tac 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 deleterious(0) 11/39 PROSITE_profiles:PS50013,hmmpanther:PTHR10799:SF48,hmmpanther:PTHR10799,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 203 4 3 0 0 0 0 -9.213631 0.9994745 1 1 1 0 T 3 4 10 53235185 53235185 G T 1 0 0 0 0 1 0 0 0 3091 1188 41 2 2 CHD9 16 53235185 Missense_Mutation SNP G C3L-00095_T 2094339 53235185 37103160 620 3829 MMP2 0 . GRCh38 16 55484156 55484156 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.521G>T p.Gly174Val p.G174V ENST00000219070 3/13 278 259 19 356 355 1 strelka-mutect MMP2,missense_variant,p.Gly174Val,ENST00000219070,NM_004530.5;MMP2,missense_variant,p.Gly98Val,ENST00000570308,;MMP2,missense_variant,p.Gly124Val,ENST00000437642,NM_001127891.2;MMP2,missense_variant,p.Gly98Val,ENST00000543485,NM_001302508.1,NM_001302510.1,NM_001302509.1;MMP2,missense_variant,p.Gly98Val,ENST00000564864,;MMP2,missense_variant,p.Gly98Val,ENST00000568715,;MMP2,upstream_gene_variant,,ENST00000570283,;RP11-212I21.3,upstream_gene_variant,,ENST00000623886,; T ENST00000219070 Transcript missense_variant 1030/3741 521/1983 174/660 G/V gGc/gTc 1 1 MMP2 HGNC HGNC:7166 protein_coding YES CCDS10752.1 ENSP00000219070 P08253 A0A024R6R4 UPI00000422C4 NM_004530.5 deleterious(0.01) 3/13 Gene3D:3.40.390.10,Pfam_domain:PF00413,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF29,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 55484156 55484156 G T 1 0 0 0 0 1 0 0 0 9621 1203 42 2 2 MMP2 16 55484156 Missense_Mutation SNP G C3L-00095_T 2248971 55484156 34854189 621 3830 SLC6A2 0 . GRCh38 16 55696318 55696318 + Missense_Mutation SNP C C G rs201586185 C3L-00095_T C3L-00095_N C C c.1241C>G p.Ala414Gly p.A414G ENST00000219833 8/14 386 352 34 420 420 0 strelka-varscan-mutect SLC6A2,missense_variant,p.Ala414Gly,ENST00000379906,NM_001043.3;SLC6A2,missense_variant,p.Ala414Gly,ENST00000414754,;SLC6A2,missense_variant,p.Ala309Gly,ENST00000567238,NM_001172502.1;SLC6A2,missense_variant,p.Ala414Gly,ENST00000219833,NM_001172504.1;SLC6A2,missense_variant,p.Ala414Gly,ENST00000568943,NM_001172501.1;SLC6A2,missense_variant,p.Ala414Gly,ENST00000561820,;SLC6A2,missense_variant,p.Ala369Gly,ENST00000566163,;SLC6A2,downstream_gene_variant,,ENST00000568529,;SLC6A2,upstream_gene_variant,,ENST00000574918,; G ENST00000219833 Transcript missense_variant 1292/2858 1241/1887 414/628 A/G gCg/gGg rs201586185,COSM4970876,COSM4970877 1 1 SLC6A2 HGNC HGNC:11048 protein_coding YES CCDS54011.1 ENSP00000219833 P23975 UPI00000734FD NM_001172504.1 deleterious(0) 8/14 Superfamily_domains:0053687,Pfam_domain:PF00209,Prints_domain:PR00176,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF37,Transmembrane_helices:TMhelix 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs201586185 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 55696318 55696318 C G 1 0 0 0 0 1 0 0 0 14966 768 27 4 4 SLC6A2 16 55696318 Missense_Mutation SNP C C3L-00095_T 212162 55696318 34642027 622 3831 CETP 0 . GRCh38 16 56969919 56969919 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.445G>A p.Asp149Asn p.D149N ENST00000200676 5/16 424 396 28 541 541 0 strelka-varscan-mutect CETP,missense_variant,p.Asp149Asn,ENST00000200676,NM_000078.2;CETP,missense_variant,p.Asp84Asn,ENST00000566128,;CETP,missense_variant,p.Asp149Asn,ENST00000379780,NM_001286085.1;CETP,non_coding_transcript_exon_variant,,ENST00000569082,; A ENST00000200676 Transcript missense_variant 575/1791 445/1482 149/493 D/N Gac/Aac 1 1 CETP HGNC HGNC:1869 protein_coding YES CCDS10772.1 ENSP00000200676 P11597 A0A0S2Z3F6 UPI000013C62C NM_000078.2 tolerated(0.37) 5/16 hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF12,Gene3D:1ewfA01,Pfam_domain:PF01273,PIRSF_domain:PIRSF037185,SMART_domains:SM00328,Superfamily_domains:SSF55394 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 56969919 56969919 G A 1 0 0 0 0 1 0 0 0 3009 1304 45 3 3 CETP 16 56969919 Missense_Mutation SNP G C3L-00095_T 1273601 56969919 33368426 623 3832 AGRP 0 . GRCh38 16 67482642 67482642 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.393C>A p.= p.R131R ENST00000290953 4/4 168 147 21 196 196 0 strelka-varscan-mutect AGRP,synonymous_variant,p.=,ENST00000290953,NM_001138.1;ATP6V0D1,upstream_gene_variant,,ENST00000290949,NM_004691.4;ATP6V0D1,upstream_gene_variant,,ENST00000602876,;ATP6V0D1,upstream_gene_variant,,ENST00000540149,;ATP6V0D1,upstream_gene_variant,,ENST00000565835,;RP11-297D21.4,intron_variant,,ENST00000635000,;RP11-297D21.4,intron_variant,,ENST00000602596,;RP11-297D21.4,downstream_gene_variant,,ENST00000602592,;RP11-297D21.4,upstream_gene_variant,,ENST00000602476,;ATP6V0D1,upstream_gene_variant,,ENST00000561658,;ATP6V0D1,upstream_gene_variant,,ENST00000568298,;ATP6V0D1,upstream_gene_variant,,ENST00000563064,;ATP6V0D1,upstream_gene_variant,,ENST00000564191,;ATP6V0D1,upstream_gene_variant,,ENST00000561852,;ATP6V0D1,upstream_gene_variant,,ENST00000564788,; T ENST00000290953 Transcript synonymous_variant 693/764 393/399 131/132 R cgC/cgA 1 -1 AGRP HGNC HGNC:330 protein_coding YES CCDS10839.1 ENSP00000290953 O00253 C6SUN5 UPI0000046BA7 NM_001138.1 4/4 hmmpanther:PTHR16551:SF4,hmmpanther:PTHR16551 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 67482642 67482642 G T 1 0 0 0 0 0 0 0 1 477 1306 46 2 2 AGRP 16 67482642 Silent SNP G C3L-00095_T 10512723 67482642 22855703 624 3833 DPEP3 0 . GRCh38 16 67975914 67975914 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1393C>A p.Pro465Thr p.P465T ENST00000268793 10/10 296 279 17 315 314 1 strelka-varscan-mutect DPEP3,missense_variant,p.Pro465Thr,ENST00000268793,NM_022357.3,NM_001129758.1;DPEP3,downstream_gene_variant,,ENST00000574342,; T ENST00000268793 Transcript missense_variant 1767/2018 1393/1542 465/513 P/T Cct/Act 1 -1 DPEP3 HGNC HGNC:23029 protein_coding YES CCDS10856.1 ENSP00000268793 Q9H4B8 UPI000006F093 NM_022357.3,NM_001129758.1 tolerated(0.12) 10/10 PROSITE_profiles:PS51365,hmmpanther:PTHR10443,hmmpanther:PTHR10443:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 67975914 67975914 G T 1 0 0 0 0 1 0 0 0 4529 1203 42 2 2 DPEP3 16 67975914 Missense_Mutation SNP G C3L-00095_T 493272 67975914 22362431 625 3834 CDH1 0 . GRCh38 16 68815698 68815698 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1504G>T p.Gly502Cys p.G502C ENST00000261769 10/16 349 323 26 423 422 1 strelka-varscan-mutect CDH1,missense_variant,p.Gly502Cys,ENST00000261769,NM_004360.3;CDH1,missense_variant,p.Gly523Cys,ENST00000611625,NM_001317185.1;CDH1,missense_variant,p.Gly502Cys,ENST00000621016,;CDH1,missense_variant,p.Gly441Cys,ENST00000422392,;CDH1,missense_variant,p.Gly502Cys,ENST00000612417,;RP11-354M1.2,intron_variant,,ENST00000563916,;CDH1,non_coding_transcript_exon_variant,,ENST00000562836,;CDH1,missense_variant,p.Gly502Cys,ENST00000566612,;CDH1,3_prime_UTR_variant,,ENST00000566510,;CDH1,downstream_gene_variant,,ENST00000561751,;CDH1,downstream_gene_variant,,ENST00000565810,; T ENST00000261769 Transcript missense_variant 1695/4889 1504/2649 502/882 G/C Ggc/Tgc 1 1 CDH1 HGNC HGNC:1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 A0A0U2ZQU7 UPI00000341EF NM_004360.3 deleterious(0) 10/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF267,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 68815698 68815698 G T 1 0 0 0 0 1 0 0 0 2798 1232 43 2 2 CDH1 16 68815698 Missense_Mutation SNP G C3L-00095_T 839784 68815698 21522647 626 3835 HYDIN 0 . GRCh38 16 71069431 71069431 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1810C>A p.Pro604Thr p.P604T ENST00000393567 14/86 238 221 17 263 263 0 varscan-mutect HYDIN,missense_variant,p.Pro604Thr,ENST00000393567,NM_001270974.1;HYDIN,missense_variant,p.Pro604Thr,ENST00000321489,NM_017558.4;HYDIN,missense_variant,p.Pro631Thr,ENST00000538248,NM_001198542.1;HYDIN,missense_variant,p.Pro621Thr,ENST00000541601,NM_001198543.1;HYDIN,missense_variant,p.Pro621Thr,ENST00000288168,;HYDIN,missense_variant,p.Pro6Thr,ENST00000542890,;HYDIN,non_coding_transcript_exon_variant,,ENST00000543639,;HYDIN,missense_variant,p.Pro222Thr,ENST00000393552,;HYDIN,missense_variant,p.Pro407Thr,ENST00000545230,;HYDIN,3_prime_UTR_variant,,ENST00000539447,; T ENST00000393567 Transcript missense_variant 1961/15719 1810/15366 604/5121 P/T Cct/Act 1 -1 HYDIN HGNC HGNC:19368 protein_coding YES CCDS59269.1 ENSP00000377197 Q4G0P3 UPI0001FEF4F9 NM_001270974.1 deleterious(0.02) 14/86 Pfam_domain:PF15780,hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF16 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 71069431 71069431 G T 1 0 0 0 0 1 0 0 0 7363 1232 43 2 2 HYDIN 16 71069431 Missense_Mutation SNP G C3L-00095_T 2253733 71069431 19268914 627 3836 PKD1L3 0 . GRCh38 16 71930133 71930133 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.4977C>A p.= p.V1659V ENST00000620267 29/30 185 175 10 170 170 0 strelka-varscan-mutect PKD1L3,synonymous_variant,p.=,ENST00000620267,NM_181536.1;IST1,3_prime_UTR_variant,,ENST00000378799,NM_001270975.1;IST1,3_prime_UTR_variant,,ENST00000535424,NM_001270976.1;IST1,3_prime_UTR_variant,,ENST00000606369,NM_001270978.1,NM_001270979.1;IST1,downstream_gene_variant,,ENST00000329908,NM_014761.3;IST1,downstream_gene_variant,,ENST00000378798,NM_001270977.1;IST1,downstream_gene_variant,,ENST00000456820,;IST1,downstream_gene_variant,,ENST00000541571,;IST1,downstream_gene_variant,,ENST00000544564,;IST1,downstream_gene_variant,,ENST00000538850,;IST1,downstream_gene_variant,,ENST00000538565,;IST1,downstream_gene_variant,,ENST00000439924,;IST1,downstream_gene_variant,,ENST00000536027,;IST1,downstream_gene_variant,,ENST00000541180,; T ENST00000620267 Transcript synonymous_variant 4977/5199 4977/5199 1659/1732 V gtC/gtA 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 29/30 Transmembrane_helices:TMhelix,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136,Pfam_domain:PF08016 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 71930133 71930133 G T 1 0 0 0 0 0 0 0 1 12061 1277 45 2 2 PKD1L3 16 71930133 Silent SNP G C3L-00095_T 860702 71930133 18408212 628 3837 CNTNAP4 0 . GRCh38 16 76522257 76522257 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2755G>T p.Gly919Cys p.G919C ENST00000611870 17/24 160 149 11 178 177 1 strelka-varscan-mutect CNTNAP4,missense_variant,p.Gly919Cys,ENST00000307431,;CNTNAP4,missense_variant,p.Gly919Cys,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Gly871Cys,ENST00000377504,;CNTNAP4,missense_variant,p.Gly922Cys,ENST00000476707,;CNTNAP4,missense_variant,p.Gly871Cys,ENST00000622250,;CNTNAP4,missense_variant,p.Gly846Cys,ENST00000478060,NM_138994.3; T ENST00000611870 Transcript missense_variant,splice_region_variant 3140/4867 2755/3927 919/1308 G/C Ggt/Tgt 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0) 17/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -14.67972 0.9999679 1 1 1 0 T 3 4 10 76522257 76522257 G T 1 0 0 0 0 1 0 0 0 3431 1246 43 2 2 CNTNAP4 16 76522257 Missense_Mutation SNP G C3L-00095_T 4592124 76522257 13816088 629 3838 CNTNAP4 0 . GRCh38 16 76535766 76535766 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2977G>T p.Gly993Trp p.G993W ENST00000611870 18/24 148 139 9 192 189 3 strelka-varscan-mutect CNTNAP4,missense_variant,p.Gly993Trp,ENST00000307431,;CNTNAP4,missense_variant,p.Gly993Trp,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Gly945Trp,ENST00000377504,;CNTNAP4,missense_variant,p.Gly996Trp,ENST00000476707,;CNTNAP4,missense_variant,p.Gly945Trp,ENST00000622250,;CNTNAP4,missense_variant,p.Gly920Trp,ENST00000478060,NM_138994.3; T ENST00000611870 Transcript missense_variant 3362/4867 2977/3927 993/1308 G/W Ggg/Tgg 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0) 18/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 76535766 76535766 G T 1 0 0 0 0 1 0 0 0 3431 1000 35 2 2 CNTNAP4 16 76535766 Missense_Mutation SNP G C3L-00095_T 13509 76535766 13802579 630 3839 CNTNAP4 0 . GRCh38 16 76538195 76538195 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3075C>A p.Ser1025Arg p.S1025R ENST00000611870 19/24 218 199 19 256 255 1 strelka-varscan-mutect CNTNAP4,missense_variant,p.Ser1025Arg,ENST00000307431,;CNTNAP4,missense_variant,p.Ser1025Arg,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Ser977Arg,ENST00000377504,;CNTNAP4,missense_variant,p.Ser1028Arg,ENST00000476707,;CNTNAP4,missense_variant,p.Ser977Arg,ENST00000622250,;CNTNAP4,missense_variant,p.Ser952Arg,ENST00000478060,NM_138994.3; A ENST00000611870 Transcript missense_variant 3460/4867 3075/3927 1025/1308 S/R agC/agA 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0.04) 19/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1306716252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 76538195 76538195 C A 1 0 0 0 0 1 0 0 0 3431 796 28 2 2 CNTNAP4 16 76538195 Missense_Mutation SNP C C3L-00095_T 2429 76538195 13800150 631 3840 CDYL2 0 . GRCh38 16 80684673 80684673 + Missense_Mutation SNP C C A rs144219171 C3L-00095_T C3L-00095_N C C c.481G>T p.Ala161Ser p.A161S ENST00000570137 2/7 264 250 14 331 330 1 strelka-varscan-mutect CDYL2,missense_variant,p.Ala161Ser,ENST00000570137,NM_152342.2;CDYL2,missense_variant,p.Ala161Ser,ENST00000562812,;CDYL2,missense_variant,p.Ala161Ser,ENST00000563890,;CDYL2,missense_variant,p.Ala161Ser,ENST00000566173,;CDYL2,non_coding_transcript_exon_variant,,ENST00000562753,; A ENST00000570137 Transcript missense_variant 637/8159 481/1521 161/506 A/S Gcc/Tcc rs144219171 1 -1 CDYL2 HGNC HGNC:23030 protein_coding YES CCDS32493.1 ENSP00000476295 Q8N8U2 UPI00001B2954 NM_152342.2 tolerated(0.5) 2/7 MODERATE 1 SNV 1 1 PASS rs144219171 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 80684673 80684673 C A 1 0 0 0 0 1 0 0 0 2892 768 27 1 1 CDYL2 16 80684673 Missense_Mutation SNP C C3L-00095_T 4146478 80684673 9653672 632 3841 FOXL1 0 . GRCh38 16 86579585 86579585 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.862G>C p.Gly288Arg p.G288R ENST00000320241 1/1 205 187 18 260 260 0 strelka-varscan-mutect FOXL1,missense_variant,p.Gly288Arg,ENST00000320241,NM_005250.2;FOXL1,downstream_gene_variant,,ENST00000593625,; C ENST00000320241 Transcript missense_variant 1080/3655 862/1038 288/345 G/R Ggg/Cgg 1 1 FOXL1 HGNC HGNC:3817 protein_coding YES CCDS10959.1 ENSP00000326272 Q12952 UPI000012ADE2 NM_005250.2 tolerated(0.19) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 86579585 86579585 G C 1 0 0 0 0 1 0 0 0 5879 1348 47 4 4 FOXL1 16 86579585 Missense_Mutation SNP G C3L-00095_T 5894912 86579585 3758760 633 3842 ZNF469 0 . GRCh38 16 88428017 88428017 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.547T>A p.Cys183Ser p.C183S ENST00000437464 1/2 568 528 40 774 773 1 strelka-varscan-mutect ZNF469,missense_variant,p.Cys183Ser,ENST00000565624,;ZNF469,missense_variant,p.Cys183Ser,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 547/13203 547/11778 183/3925 C/S Tgc/Agc 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 deleterious(0.03) 1/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 88428017 88428017 T A 1 0 0 0 0 1 0 0 0 18500 1696 59 4 4 ZNF469 16 88428017 Missense_Mutation SNP T C3L-00095_T 1848432 88428017 1910328 634 3843 RP11-566K11.2 0 . GRCh38 16 89919723 89919723 + Silent SNP C C T rs374878766 C3L-00095_T C3L-00095_N C C c.465C>T p.= p.I155I ENST00000555147 1/1 159 140 19 182 182 0 strelka-varscan-mutect MC1R,synonymous_variant,p.=,ENST00000555427,;MC1R,synonymous_variant,p.=,ENST00000555147,NM_002386.3;RP11-566K11.2,synonymous_variant,p.=,ENST00000556922,;TUBB3,upstream_gene_variant,,ENST00000554444,NM_001197181.1;TUBB3,upstream_gene_variant,,ENST00000315491,NM_006086.3;TUBB3,upstream_gene_variant,,ENST00000554336,;TUBB3,upstream_gene_variant,,ENST00000555810,;TUBB3,upstream_gene_variant,,ENST00000553967,;TUBB3,upstream_gene_variant,,ENST00000555576,;TUBB3,upstream_gene_variant,,ENST00000625617,;TUBB3,upstream_gene_variant,,ENST00000556565,;RP11-566K11.4,downstream_gene_variant,,ENST00000554623,;TUBB3,upstream_gene_variant,,ENST00000554116,;MC1R,downstream_gene_variant,,ENST00000539976,;TUBB3,upstream_gene_variant,,ENST00000555609,;TUBB3,upstream_gene_variant,,ENST00000556536,;TUBB3,upstream_gene_variant,,ENST00000557262,;TUBB3,upstream_gene_variant,,ENST00000557490,;TUBB3,upstream_gene_variant,,ENST00000554927,;RP11-566K11.7,downstream_gene_variant,,ENST00000570217,;TUBB3,upstream_gene_variant,,ENST00000553656,; T ENST00000555147 Transcript synonymous_variant 1845/3099 465/954 155/317 I atC/atT rs374878766 1 1 MC1R HGNC HGNC:6929 protein_coding YES CCDS56011.1 ENSP00000451605 Q01726 Q1JUL4 UPI00000622C3 NM_002386.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF2,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00534 LOW SNV 1 PASS rs374878766 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 89919723 89919723 C T 1 0 0 0 0 0 0 0 1 13753 874 31 1 1 RP11-566K11.2 16 89919723 Silent SNP C C3L-00095_T 1491706 89919723 418622 635 3844 TLCD2 0 . GRCh38 17 1709558 1709558 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.283G>T p.Asp95Tyr p.D95Y ENST00000330676 3/4 206 188 18 236 235 1 strelka-varscan-mutect TLCD2,missense_variant,p.Asp95Tyr,ENST00000330676,NM_001164407.1;MIR22HG,downstream_gene_variant,,ENST00000574306,;MIR22HG,downstream_gene_variant,,ENST00000334146,;MIR22HG,downstream_gene_variant,,ENST00000577164,;MIR22HG,downstream_gene_variant,,ENST00000573127,;MIR22HG,downstream_gene_variant,,ENST00000571595,;MIR22HG,downstream_gene_variant,,ENST00000576749,;MIR22HG,downstream_gene_variant,,ENST00000576489,;MIR22HG,downstream_gene_variant,,ENST00000575626,;MIR22HG,downstream_gene_variant,,ENST00000609990,;MIR22HG,downstream_gene_variant,,ENST00000609398,;MIR22HG,downstream_gene_variant,,ENST00000608198,;MIR22HG,downstream_gene_variant,,ENST00000608913,;MIR22HG,downstream_gene_variant,,ENST00000574016,;MIR22HG,downstream_gene_variant,,ENST00000573075,;MIR22HG,downstream_gene_variant,,ENST00000609442,;MIR22HG,downstream_gene_variant,,ENST00000570416,;MIR22HG,downstream_gene_variant,,ENST00000571091,;MIR22HG,downstream_gene_variant,,ENST00000608245,;MIR22HG,downstream_gene_variant,,ENST00000610106,;MIR22HG,downstream_gene_variant,,ENST00000362190,; A ENST00000330676 Transcript missense_variant 479/5971 283/795 95/264 D/Y Gac/Tac 1 -1 TLCD2 HGNC HGNC:33522 protein_coding YES CCDS45567.1 ENSP00000331965 A6NGC4 UPI00001D79C7 NM_001164407.1 deleterious(0.04) 3/4 Pfam_domain:PF03798,PROSITE_profiles:PS50922,hmmpanther:PTHR13439,hmmpanther:PTHR13439:SF2,SMART_domains:SM00724,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS rs1305222873 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 1709558 1709558 C A 1 0 0 0 0 1 0 0 0 16381 826 29 2 2 TLCD2 17 1709558 Missense_Mutation SNP C C3L-00095_T 1709558 81547883 636 3845 SHPK 0 . GRCh38 17 3610875 3610875 + Silent SNP C C A rs148679980 C3L-00095_T C3L-00095_N C C c.1122G>T p.= p.G374G ENST00000225519 7/7 180 171 9 241 241 0 strelka-varscan-mutect SHPK,synonymous_variant,p.=,ENST00000225519,NM_013276.2;TRPV1,upstream_gene_variant,,ENST00000572705,NM_080704.3;RP11-235E17.2,synonymous_variant,p.=,ENST00000572919,; A ENST00000225519 Transcript synonymous_variant 1225/3838 1122/1437 374/478 G ggG/ggT rs148679980 1 -1 SHPK HGNC HGNC:1492 protein_coding YES CCDS11030.1 ENSP00000225519 Q9UHJ6 UPI0000070BB8 NM_013276.2 7/7 hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF67,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS rs148679980 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 3610875 3610875 C A 1 0 0 0 0 0 0 0 1 14553 610 22 2 2 SHPK 17 3610875 Silent SNP C C3L-00095_T 1901317 3610875 79646566 637 3846 ALOX15 0 . GRCh38 17 4638931 4638931 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.461G>T p.Gly154Val p.G154V ENST00000570836 5/15 200 184 16 301 300 1 strelka-varscan-mutect ALOX15,missense_variant,p.Gly154Val,ENST00000570836,;ALOX15,missense_variant,p.Gly154Val,ENST00000293761,NM_001140.3;ALOX15,missense_variant,p.Gly115Val,ENST00000574640,;ALOX15,missense_variant,p.Gly3Val,ENST00000572265,;ALOX15,downstream_gene_variant,,ENST00000576394,;ALOX15,non_coding_transcript_exon_variant,,ENST00000573740,;ALOX15,non_coding_transcript_exon_variant,,ENST00000576572,; A ENST00000570836 Transcript missense_variant 558/2784 461/1989 154/662 G/V gGg/gTg 1 -1 ALOX15 HGNC HGNC:433 protein_coding YES CCDS11049.1 ENSP00000458832 P16050 UPI000013E118 tolerated(0.06) 5/15 PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF33,Superfamily_domains:SSF48484 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 4638931 4638931 C A 1 0 0 0 0 1 0 0 0 638 623 22 2 2 ALOX15 17 4638931 Missense_Mutation SNP C C3L-00095_T 1028056 4638931 78618510 638 3847 TP53 0 . GRCh38 17 7675145 7675145 + Missense_Mutation SNP C C G rs371524413 C3L-00095_T C3L-00095_N C C c.467G>C p.Arg156Pro p.R156P ENST00000269305 5/11 239 220 19 348 348 0 strelka-varscan-mutect TP53,missense_variant,p.Arg156Pro,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg156Pro,ENST00000420246,;TP53,missense_variant,p.Arg117Pro,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg117Pro,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg156Pro,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg117Pro,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg156Pro,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg117Pro,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg156Pro,ENST00000445888,;TP53,missense_variant,p.Arg117Pro,ENST00000619485,;TP53,missense_variant,p.Arg24Pro,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg24Pro,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg24Pro,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg156Pro,ENST00000359597,;TP53,missense_variant,p.Arg145Pro,ENST00000615910,;TP53,missense_variant,p.Arg156Pro,ENST00000413465,;TP53,missense_variant,p.Arg24Pro,ENST00000509690,;TP53,missense_variant,p.Arg156Pro,ENST00000508793,;TP53,missense_variant,p.Arg63Pro,ENST00000514944,;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg117Pro,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 657/2579 467/1182 156/393 R/P cGc/cCc rs371524413,CM984589,TP53_g.12455G>A,TP53_g.12455del,TP53_g.12455G>C,TP53_g.12455G>T,COSM10760,COSM1522489,COSM1522490,COSM1522491,COSM1522492,COSM2744905,COSM3712457,COSM3970367,COSM3970368,COSM3970369,COSM3970370,COSM3970371,COSM3970372,COSM43548,COSM43739,COSM45530 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 tolerated(0.22) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs371524413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 7675145 7675145 C G 1 0 0 0 0 1 0 0 0 16859 768 27 4 4 TP53 17 7675145 Missense_Mutation SNP C C3L-00095_T 3036214 7675145 75582296 639 3848 PIK3R6 0 . GRCh38 17 8836893 8836893 + Nonsense_Mutation SNP T T A rs756493237 C3L-00095_T C3L-00095_N T T c.289A>T p.Arg97Ter p.R97* ENST00000619866 6/20 185 172 13 239 239 0 strelka-varscan-mutect PIK3R6,stop_gained,p.Arg97Ter,ENST00000619866,NM_001010855.3,NM_001290211.1;PIK3R6,stop_gained,p.Arg97Ter,ENST00000614407,;PIK3R6,3_prime_UTR_variant,,ENST00000611951,;PIK3R6,3_prime_UTR_variant,,ENST00000613555,; A ENST00000619866 Transcript stop_gained 529/3041 289/2265 97/754 R/* Aga/Tga rs756493237 1 -1 PIK3R6 HGNC HGNC:27101 protein_coding YES CCDS73985.1 ENSP00000480157 Q5UE93 UPI0000043463 NM_001010855.3,NM_001290211.1 6/20 hmmpanther:PTHR15593:SF1,hmmpanther:PTHR15593,Pfam_domain:PF10486 HIGH 1 SNV 5 1 PASS rs756493237 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 8836893 8836893 T A 1 0 0 0 0 0 1 0 0 12018 1559 54 4 4 PIK3R6 17 8836893 Nonsense_Mutation SNP T C3L-00095_T 1161748 8836893 74420548 640 3849 MYH8 0 . GRCh38 17 10398592 10398592 + Missense_Mutation SNP C C A rs775346508 C3L-00095_T C3L-00095_N C C c.4030G>T p.Asp1344Tyr p.D1344Y ENST00000403437 30/40 418 378 40 629 627 2 strelka-varscan-mutect MYH8,missense_variant,p.Asp1344Tyr,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript missense_variant 4125/6041 4030/5814 1344/1937 D/Y Gac/Tac rs775346508 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0) 30/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS rs775346508 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 10398592 10398592 C A 1 0 0 0 0 1 0 0 0 10041 884 31 1 1 MYH8 17 10398592 Missense_Mutation SNP C C3L-00095_T 1561699 10398592 72858849 641 3850 MYH8 0 . GRCh38 17 10418802 10418802 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.355-1G>T p.X119_splice ENST00000403437 249 226 23 373 373 0 varscan-mutect MYH8,splice_acceptor_variant,,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript splice_acceptor_variant -/6041 355/5814 119/1937 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 4/39 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 10418802 10418802 C A 1 0 0 0 0 0 0 1 0 10041 927 32 2 2 MYH8 17 10418802 Splice_Site SNP C C3L-00095_T 20210 10418802 72838639 642 3851 MYH8 0 . GRCh38 17 10420130 10420130 + Missense_Mutation SNP G G T rs753981095 C3L-00095_T C3L-00095_N G G c.98C>A p.Pro33Gln p.P33Q ENST00000403437 3/40 487 444 43 602 599 3 strelka-varscan-mutect MYH8,missense_variant,p.Pro33Gln,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript missense_variant 193/6041 98/5814 33/1937 P/Q cCg/cAg rs753981095,COSM4514864 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0) 3/40 0,1 MODERATE SNV 5 0,1 1 PASS rs753981095 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 10420130 10420130 G T 1 0 0 0 0 1 0 0 0 10041 1116 39 1 1 MYH8 17 10420130 Missense_Mutation SNP G C3L-00095_T 1328 10420130 72837311 643 3852 RHOT1 0 . GRCh38 17 32209374 32209374 + Frame_Shift_Del DEL C C - C3L-00095_T C3L-00095_N C C c.1764delC p.Ser589ProfsTer10 p.S589Pfs*10 ENST00000358365 19/21 132 121 11 111 111 0 sindel-varindel-pindel RHOT1,frameshift_variant,p.Ser589ProfsTer10,ENST00000358365,NM_001033568.2;RHOT1,frameshift_variant,p.Ser589ProfsTer10,ENST00000394692,NM_001288758.1,NM_001288754.1;RHOT1,3_prime_UTR_variant,,ENST00000581094,;RHOT1,intron_variant,,ENST00000333942,NM_018307.4;RHOT1,intron_variant,,ENST00000354266,NM_001288755.1,NM_001033567.2;RHOT1,intron_variant,,ENST00000545287,NM_001033566.2;RHOT1,intron_variant,,ENST00000580392,;RHOT1,intron_variant,,ENST00000581148,;RHOT1,intron_variant,,ENST00000582602,;RHOT1,intron_variant,,ENST00000584852,;RHOT1,upstream_gene_variant,,ENST00000582586,;RHOT1,3_prime_UTR_variant,,ENST00000583994,;RHOT1,intron_variant,,ENST00000581031,;RHOT1,intron_variant,,ENST00000578205,;RHOT1,intron_variant,,ENST00000584692,;RHOT1,downstream_gene_variant,,ENST00000581567,; - ENST00000358365 Transcript frameshift_variant 1991/3297 1764/2076 588/691 L/X ctC/ct COSM4472161 1 1 RHOT1 HGNC HGNC:21168 protein_coding YES CCDS32610.1 ENSP00000351132 Q8IXI2 UPI0000074394 NM_001033568.2 19/21 PIRSF_domain:PIRSF037488 1 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -15.68133 0.9999786 1 1 1 0 - 7 5 10 32209374 32209374 C - 1 0 1 0 1 0 0 0 0 13516 900 32 0 0 RHOT1 17 32209374 Frame_Shift_Del DEL C C3L-00095_T 21789244 32209374 51048067 644 3853 LYZL6 0 . GRCh38 17 35939296 35939296 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.61C>A p.Leu21Ile p.L21I ENST00000615905 2/5 173 157 16 217 217 0 strelka-varscan-mutect LYZL6,missense_variant,p.Leu21Ile,ENST00000615905,NM_020426.2;LYZL6,missense_variant,p.Leu21Ile,ENST00000618542,NM_001199951.2;LYZL6,upstream_gene_variant,,ENST00000617692,; T ENST00000615905 Transcript missense_variant 396/1047 61/447 21/148 L/I Ctc/Atc 1 -1 LYZL6 HGNC HGNC:29614 protein_coding YES CCDS11302.1 ENSP00000483897 O75951 UPI000006E183 NM_020426.2 tolerated(1) 2/5 PROSITE_profiles:PS51348,hmmpanther:PTHR11407,hmmpanther:PTHR11407:SF9,SMART_domains:SM00263,Prints_domain:PR00137 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 35939296 35939296 G T 1 0 0 0 0 1 0 0 0 9047 1000 35 2 2 LYZL6 17 35939296 Missense_Mutation SNP G C3L-00095_T 3729922 35939296 47318145 645 3854 PLXDC1 0 . GRCh38 17 39109352 39109352 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.295C>G p.Pro99Ala p.P99A ENST00000315392 3/14 238 224 14 278 278 0 strelka-varscan-mutect PLXDC1,missense_variant,p.Pro99Ala,ENST00000315392,NM_020405.4;PLXDC1,missense_variant,p.Pro59Ala,ENST00000444911,;PLXDC1,missense_variant,p.Pro26Ala,ENST00000441877,;PLXDC1,missense_variant,p.Pro26Ala,ENST00000415163,;PLXDC1,missense_variant,p.Pro26Ala,ENST00000579190,;PLXDC1,upstream_gene_variant,,ENST00000579279,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000493200,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000580667,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000577941,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000577838,;CTD-2206N4.4,intron_variant,,ENST00000578423,;CTD-2206N4.4,upstream_gene_variant,,ENST00000577328,;PLXDC1,upstream_gene_variant,,ENST00000444435,;PLXDC1,missense_variant,p.Pro99Ala,ENST00000578390,;PLXDC1,missense_variant,p.Pro59Arg,ENST00000578808,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000461225,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000394318,;PLXDC1,non_coding_transcript_exon_variant,,ENST00000578517,; C ENST00000315392 Transcript missense_variant 507/6252 295/1503 99/500 P/A Ccc/Gcc 1 -1 PLXDC1 HGNC HGNC:20945 protein_coding YES CCDS11333.1 ENSP00000323927 Q8IUK5 UPI0000049814 NM_020405.4 deleterious(0.02) 3/14 hmmpanther:PTHR13055:SF10,hmmpanther:PTHR13055 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 39109352 39109352 G C 1 0 0 0 0 1 0 0 0 12223 1232 43 4 4 PLXDC1 17 39109352 Missense_Mutation SNP G C3L-00095_T 3170056 39109352 44148089 646 3855 ZNF385C 0 . GRCh38 17 42037813 42037813 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.86C>A p.Pro29Gln p.P29Q ENST00000618554 2/8 43 39 4 66 66 0 strelka-varscan-mutect ZNF385C,missense_variant,p.Pro29Gln,ENST00000618554,NM_001242704.1;ZNF385C,missense_variant,p.Pro108Gln,ENST00000436535,;ZNF385C,downstream_gene_variant,,ENST00000587304,; T ENST00000618554 Transcript missense_variant 86/2596 86/1275 29/424 P/Q cCg/cAg 1 -1 ZNF385C HGNC HGNC:33722 protein_coding YES CCDS74065.1 ENSP00000480744 A0A087WX54 UPI0001E6F8A9 NM_001242704.1 tolerated(0.47) 2/8 hmmpanther:PTHR23067,hmmpanther:PTHR23067:SF6,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS rs1387006920 . 0 203 6 0 0 0 0 0 -10.52235 0.9999998 1 1 1 0 T 3 4 10 42037813 42037813 G T 1 0 0 0 0 1 0 0 0 18450 1116 39 1 1 ZNF385C 17 42037813 Missense_Mutation SNP G C3L-00095_T 2928461 42037813 41219628 647 3856 EZH1 0 . GRCh38 17 42719109 42719109 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.763G>T p.Glu255Ter p.E255* ENST00000428826 8/21 148 128 20 169 168 1 strelka-varscan-mutect EZH1,stop_gained,p.Glu255Ter,ENST00000428826,NM_001321079.1,NM_001991.3;EZH1,stop_gained,p.Glu246Ter,ENST00000415827,NM_001321081.1;EZH1,stop_gained,p.Glu255Ter,ENST00000592743,;EZH1,stop_gained,p.Glu215Ter,ENST00000585893,;EZH1,stop_gained,p.Glu185Ter,ENST00000590078,;EZH1,stop_gained,p.Glu206Ter,ENST00000586382,;EZH1,downstream_gene_variant,,ENST00000593214,;EZH1,downstream_gene_variant,,ENST00000586089,;EZH1,stop_gained,p.Glu45Ter,ENST00000588239,;EZH1,3_prime_UTR_variant,,ENST00000588897,;EZH1,3_prime_UTR_variant,,ENST00000586867,;EZH1,non_coding_transcript_exon_variant,,ENST00000586103,;EZH1,non_coding_transcript_exon_variant,,ENST00000591330,;EZH1,non_coding_transcript_exon_variant,,ENST00000585912,;EZH1,non_coding_transcript_exon_variant,,ENST00000593148,;EZH1,intron_variant,,ENST00000585550,;EZH1,intron_variant,,ENST00000587179,;EZH1,intron_variant,,ENST00000586935,;CTD-3193K9.1,downstream_gene_variant,,ENST00000479088,; A ENST00000428826 Transcript stop_gained 885/4623 763/2244 255/747 E/* Gag/Tag 1 -1 EZH1 HGNC HGNC:3526 protein_coding YES CCDS32659.1 ENSP00000404658 Q92800 UPI000012A3BA NM_001321079.1,NM_001991.3 8/21 hmmpanther:PTHR22884:SF333,hmmpanther:PTHR22884,SMART_domains:SM00717 HIGH 1 SNV 1 1 PASS rs1366545814 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 42719109 42719109 C A 1 0 0 0 0 0 1 0 0 5201 869 30 2 2 EZH1 17 42719109 Nonsense_Mutation SNP C C3L-00095_T 681296 42719109 40538332 648 3857 WNK4 0 . GRCh38 17 42787865 42787865 + Missense_Mutation SNP C C A rs377697081 C3L-00095_T C3L-00095_N C C c.1829C>A p.Ser610Tyr p.S610Y ENST00000246914 8/19 255 238 17 333 332 1 strelka-varscan-mutect WNK4,missense_variant,p.Ser610Tyr,ENST00000246914,NM_032387.4;WNK4,intron_variant,,ENST00000587705,;WNK4,3_prime_UTR_variant,,ENST00000591448,NM_001321299.1;WNK4,intron_variant,,ENST00000592072,;WNK4,downstream_gene_variant,,ENST00000592669,; A ENST00000246914 Transcript missense_variant 1850/4001 1829/3732 610/1243 S/Y tCc/tAc rs377697081 1 1 WNK4 HGNC HGNC:14544 protein_coding YES CCDS11439.1 ENSP00000246914 Q96J92 UPI000006FC0F NM_032387.4 tolerated(0.05) 8/19 hmmpanther:PTHR13902:SF52,hmmpanther:PTHR13902 MODERATE 1 SNV 1 1 PASS rs377697081 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 42787865 42787865 C A 1 0 0 0 0 1 0 0 0 17936 855 30 2 2 WNK4 17 42787865 Missense_Mutation SNP C C3L-00095_T 68756 42787865 40469576 649 3858 SLC4A1 0 . GRCh38 17 44259905 44259905 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.513G>T p.= p.G171G ENST00000262418 7/20 536 485 51 644 644 0 strelka-varscan-mutect SLC4A1,synonymous_variant,p.=,ENST00000262418,NM_000342.3;SLC4A1,synonymous_variant,p.=,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; A ENST00000262418 Transcript synonymous_variant 669/4965 513/2736 171/911 G ggG/ggT 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 7/20 Gene3D:1hynR00,Pfam_domain:PF07565,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 44259905 44259905 C A 1 0 0 0 0 0 0 0 1 14927 610 22 2 2 SLC4A1 17 44259905 Silent SNP C C3L-00095_T 1472040 44259905 38997536 650 3859 PLCD3 0 . GRCh38 17 45112627 45112627 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.2359C>A p.Gln787Lys p.Q787K ENST00000619929 15/15 267 244 23 349 349 0 strelka-varscan-mutect PLCD3,missense_variant,p.Gln787Lys,ENST00000619929,NM_133373.4;PLCD3,missense_variant,p.Gln109Lys,ENST00000539433,;NMT1,downstream_gene_variant,,ENST00000592782,;NMT1,downstream_gene_variant,,ENST00000258960,NM_021079.4;MIR6784,downstream_gene_variant,,ENST00000611997,;PLCD3,non_coding_transcript_exon_variant,,ENST00000543623,;PLCD3,downstream_gene_variant,,ENST00000611986,;NMT1,downstream_gene_variant,,ENST00000587120,;NMT1,downstream_gene_variant,,ENST00000587670,;PLCD3,downstream_gene_variant,,ENST00000615898,;PLCD3,downstream_gene_variant,,ENST00000618022,; T ENST00000619929 Transcript missense_variant 2447/6107 2359/2370 787/789 Q/K Cag/Aag 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 tolerated(0.6) 15/15 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 45112627 45112627 G T 1 0 0 0 0 1 0 0 0 12126 1357 47 2 2 PLCD3 17 45112627 Missense_Mutation SNP G C3L-00095_T 852722 45112627 38144814 651 3860 PLCD3 0 . GRCh38 17 45112657 45112657 + Missense_Mutation SNP G G C rs375970055 C3L-00095_T C3L-00095_N G G c.2329C>G p.Pro777Ala p.P777A ENST00000619929 15/15 324 300 24 412 412 0 strelka-varscan-mutect PLCD3,missense_variant,p.Pro777Ala,ENST00000619929,NM_133373.4;PLCD3,missense_variant,p.Pro99Ala,ENST00000539433,;NMT1,downstream_gene_variant,,ENST00000592782,;NMT1,downstream_gene_variant,,ENST00000258960,NM_021079.4;MIR6784,downstream_gene_variant,,ENST00000611997,;PLCD3,non_coding_transcript_exon_variant,,ENST00000543623,;PLCD3,downstream_gene_variant,,ENST00000611986,;NMT1,downstream_gene_variant,,ENST00000587120,;NMT1,downstream_gene_variant,,ENST00000587670,;PLCD3,downstream_gene_variant,,ENST00000615898,;PLCD3,downstream_gene_variant,,ENST00000618022,; C ENST00000619929 Transcript missense_variant 2417/6107 2329/2370 777/789 P/A Cca/Gca rs375970055 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 deleterious(0.01) 15/15 Gene3D:2.60.40.150,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs375970055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 45112657 45112657 G C 1 0 0 0 0 1 0 0 0 12126 1261 44 4 4 PLCD3 17 45112657 Missense_Mutation SNP G C3L-00095_T 30 45112657 38144784 652 3861 14 2 PLCD3 0 . GRCh38 17 45112665 45112665 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2321C>T p.Ser774Leu p.S774L ENST00000619929 15/15 322 298 24 406 406 0 strelka-varscan-mutect PLCD3,missense_variant,p.Ser774Leu,ENST00000619929,NM_133373.4;PLCD3,missense_variant,p.Ser96Leu,ENST00000539433,;NMT1,downstream_gene_variant,,ENST00000592782,;NMT1,downstream_gene_variant,,ENST00000258960,NM_021079.4;MIR6784,downstream_gene_variant,,ENST00000611997,;PLCD3,non_coding_transcript_exon_variant,,ENST00000543623,;PLCD3,downstream_gene_variant,,ENST00000611986,;NMT1,downstream_gene_variant,,ENST00000587120,;NMT1,downstream_gene_variant,,ENST00000587670,;PLCD3,downstream_gene_variant,,ENST00000615898,;PLCD3,downstream_gene_variant,,ENST00000618022,; A ENST00000619929 Transcript missense_variant 2409/6107 2321/2370 774/789 S/L tCa/tTa 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 deleterious(0.02) 15/15 Gene3D:2.60.40.150,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 45112665 45112665 G A 1 0 0 0 0 1 0 0 0 12126 1294 45 3 3 PLCD3 17 45112665 Missense_Mutation SNP G C3L-00095_T 8 45112665 38144776 653 3862 14 2 FMNL1 0 . GRCh38 17 45245344 45245344 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2820G>A p.Met940Ile p.M940I ENST00000331495 22/27 313 293 20 379 379 0 strelka-varscan-mutect FMNL1,missense_variant,p.Met940Ile,ENST00000331495,NM_005892.3;FMNL1,missense_variant,p.Met518Ile,ENST00000587489,;FMNL1,missense_variant,p.Met595Ile,ENST00000328118,;FMNL1,missense_variant,p.Met270Ile,ENST00000586643,;FMNL1,missense_variant,p.Met7Ile,ENST00000589911,;FMNL1,missense_variant,p.Met7Ile,ENST00000586092,;CTD-2020K17.4,intron_variant,,ENST00000420431,;CTD-2020K17.3,upstream_gene_variant,,ENST00000587534,;MAP3K14-AS1,upstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,upstream_gene_variant,,ENST00000592422,;CTD-2020K17.4,downstream_gene_variant,,ENST00000591361,;MAP3K14-AS1,upstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,upstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,upstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,upstream_gene_variant,,ENST00000591263,;CTD-2020K17.4,downstream_gene_variant,,ENST00000589518,;CTD-2020K17.3,upstream_gene_variant,,ENST00000393507,;FMNL1,non_coding_transcript_exon_variant,,ENST00000587856,; A ENST00000331495 Transcript missense_variant 3156/4101 2820/3303 940/1100 M/I atG/atA 1 1 FMNL1 HGNC HGNC:1212 protein_coding YES CCDS11497.1 ENSP00000329219 O95466 UPI0000246EE9 NM_005892.3 tolerated(0.48) 22/27 Pfam_domain:PF02181,PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF188,SMART_domains:SM00498,Superfamily_domains:SSF101447 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 45245344 45245344 G A 1 0 0 0 0 1 0 0 0 5807 1348 47 3 3 FMNL1 17 45245344 Missense_Mutation SNP G C3L-00095_T 132679 45245344 38012097 654 3863 PLEKHM1 0 . GRCh38 17 45475112 45475112 + Missense_Mutation SNP C C A rs2684710 C3L-00095_T C3L-00095_N C C c.911G>T p.Arg304Leu p.R304L ENST00000430334 4/12 374 349 25 469 468 1 varscan-mutect PLEKHM1,missense_variant,p.Arg304Leu,ENST00000430334,NM_014798.2;PLEKHM1,downstream_gene_variant,,ENST00000584420,;PLEKHM1,downstream_gene_variant,,ENST00000589780,;PLEKHM1,downstream_gene_variant,,ENST00000636800,;PLEKHM1,intron_variant,,ENST00000582119,;PLEKHM1,downstream_gene_variant,,ENST00000586562,;PLEKHM1,missense_variant,p.Arg304Leu,ENST00000581448,;PLEKHM1,3_prime_UTR_variant,,ENST00000579197,;PLEKHM1,3_prime_UTR_variant,,ENST00000446609,;PLEKHM1,downstream_gene_variant,,ENST00000581932,;PLEKHM1,downstream_gene_variant,,ENST00000586084,; A ENST00000430334 Transcript missense_variant 1045/5263 911/3171 304/1056 R/L cGg/cTg rs2684710 1 -1 PLEKHM1 HGNC HGNC:29017 protein_coding YES CCDS32671.1 ENSP00000389913 Q9Y4G2 UPI00001C1FC4 NM_014798.2 tolerated(0.1) 4/12 hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF5 MODERATE 1 SNV 1 1 PASS rs2684710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 45475112 45475112 C A 1 0 0 0 0 1 0 0 0 12173 652 23 1 1 PLEKHM1 17 45475112 Missense_Mutation SNP C C3L-00095_T 229768 45475112 37782329 655 3864 MAPT 0 . GRCh38 17 45983754 45983754 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.950A>T p.His317Leu p.H317L ENST00000344290 6/15 411 381 30 502 500 2 strelka-varscan-mutect MAPT,missense_variant,p.His317Leu,ENST00000344290,NM_001123066.3;MAPT,missense_variant,p.His317Leu,ENST00000262410,NM_016835.4;MAPT,missense_variant,p.His317Leu,ENST00000415613,;MAPT,missense_variant,p.His317Leu,ENST00000571987,;MAPT,intron_variant,,ENST00000351559,NM_005910.5;MAPT,intron_variant,,ENST00000340799,NM_001123067.3;MAPT,intron_variant,,ENST00000535772,NM_001203251.1,NM_001203252.1;MAPT,intron_variant,,ENST00000446361,NM_016834.4;MAPT,intron_variant,,ENST00000574436,;MAPT,intron_variant,,ENST00000420682,;MAPT,intron_variant,,ENST00000431008,;MAPT,intron_variant,,ENST00000334239,NM_016841.4;MAPT,intron_variant,,ENST00000570299,;MAPT,upstream_gene_variant,,ENST00000577017,;MAPT,non_coding_transcript_exon_variant,,ENST00000576238,;MAPT,intron_variant,,ENST00000576518,;MAPT,downstream_gene_variant,,ENST00000572440,; T ENST00000344290 Transcript missense_variant 1272/6816 950/2331 317/776 H/L cAc/cTc 1 1 MAPT HGNC HGNC:6893 protein_coding YES CCDS45715.1 ENSP00000340820 P10636 UPI0001AE66E9 NM_001123066.3 tolerated(0.69) 6/15 hmmpanther:PTHR11501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 45983754 45983754 A T 1 0 0 0 0 1 0 0 0 9220 159 6 4 4 MAPT 17 45983754 Missense_Mutation SNP A C3L-00095_T 508642 45983754 37273687 656 3865 IGF2BP1 0 . GRCh38 17 49044006 49044006 + Missense_Mutation SNP G G A rs761776197 C3L-00095_T C3L-00095_N G G c.1240G>A p.Ala414Thr p.A414T ENST00000290341 11/15 250 237 13 321 321 0 strelka-varscan-mutect IGF2BP1,missense_variant,p.Ala414Thr,ENST00000290341,NM_006546.3;IGF2BP1,missense_variant,p.Ala275Thr,ENST00000431824,NM_001160423.1; A ENST00000290341 Transcript missense_variant 1574/8274 1240/1734 414/577 A/T Gcc/Acc rs761776197,COSM5039503 1 1 IGF2BP1 HGNC HGNC:28866 protein_coding YES CCDS11543.1 ENSP00000290341 Q9NZI8 UPI0000117170 NM_006546.3 tolerated(0.76) 11/15 PROSITE_profiles:PS50084,hmmpanther:PTHR10288:SF92,hmmpanther:PTHR10288,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761776197 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 49044006 49044006 G A 1 0 0 0 0 1 0 0 0 7479 1087 38 1 1 IGF2BP1 17 49044006 Missense_Mutation SNP G C3L-00095_T 3060252 49044006 34213435 657 3866 B4GALNT2 0 . GRCh38 17 49133182 49133182 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.157G>T p.Gly53Cys p.G53C ENST00000300404 1/11 163 149 14 247 247 0 strelka-varscan-mutect B4GALNT2,missense_variant,p.Gly53Cys,ENST00000300404,NM_153446.2;B4GALNT2,intron_variant,,ENST00000393354,NM_001159387.1;B4GALNT2,intron_variant,,ENST00000504681,NM_001159388.1; T ENST00000300404 Transcript missense_variant 216/1906 157/1701 53/566 G/C Ggc/Tgc 1 1 B4GALNT2 HGNC HGNC:24136 protein_coding YES CCDS11544.1 ENSP00000300404 Q8NHY0 UPI000013E655 NM_153446.2 deleterious_low_confidence(0.01) 1/11 MODERATE 1 SNV 1 1 PASS rs1466581928 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 49133182 49133182 G T 1 0 0 0 0 1 0 0 0 1423 1232 43 2 2 B4GALNT2 17 49133182 Missense_Mutation SNP G C3L-00095_T 89176 49133182 34124259 658 3867 COL1A1 0 . GRCh38 17 50189378 50189378 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2828C>T p.Ala943Val p.A943V ENST00000225964 39/51 610 563 47 693 692 1 strelka-varscan-mutect COL1A1,missense_variant,p.Ala943Val,ENST00000225964,NM_000088.3;COL1A1,downstream_gene_variant,,ENST00000471344,;COL1A1,upstream_gene_variant,,ENST00000510710,;COL1A1,upstream_gene_variant,,ENST00000486572,;COL1A1,upstream_gene_variant,,ENST00000511732,;COL1A1,downstream_gene_variant,,ENST00000463440,;COL1A1,downstream_gene_variant,,ENST00000476387,;COL1A1,downstream_gene_variant,,ENST00000504289,;COL1A1,downstream_gene_variant,,ENST00000494334,; A ENST00000225964 Transcript missense_variant,splice_region_variant 2947/6727 2828/4395 943/1464 A/V gCt/gTt 1 -1 COL1A1 HGNC HGNC:2197 protein_coding YES CCDS11561.1 ENSP00000225964 P02452 UPI0000DACAC3 NM_000088.3 tolerated(0.12) 39/51 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF569,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 50189378 50189378 G A 1 0 0 0 0 1 0 0 0 3465 985 34 3 3 COL1A1 17 50189378 Missense_Mutation SNP G C3L-00095_T 1056196 50189378 33068063 659 3868 CACNA1G 0 . GRCh38 17 50576280 50576280 + Silent SNP C C G rs369327128 C3L-00095_T C3L-00095_N C C c.1878C>G p.= p.P626P ENST00000359106 8/38 369 340 29 402 402 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CACNA1G,synonymous_variant,p.=,ENST00000416767,;CACNA1G,downstream_gene_variant,,ENST00000570567,;CACNA1G,synonymous_variant,p.=,ENST00000506406,;CACNA1G,synonymous_variant,p.=,ENST00000504076,;CACNA1G,synonymous_variant,p.=,ENST00000511765,;CACNA1G,synonymous_variant,p.=,ENST00000503436,;CACNA1G,synonymous_variant,p.=,ENST00000511768,;CACNA1G,synonymous_variant,p.=,ENST00000503607,; G ENST00000359106 Transcript synonymous_variant 1878/7648 1878/7134 626/2377 P ccC/ccG rs369327128 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 8/38 LOW 1 SNV 1 1 PASS rs369327128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 10 50576280 50576280 C G 1 0 0 0 0 0 0 0 1 2232 639 23 4 4 CACNA1G 17 50576280 Silent SNP C C3L-00095_T 386902 50576280 32681161 660 3869 KIF2B 0 . GRCh38 17 53824837 53824837 + Missense_Mutation SNP C C T C3L-00095_T C3L-00095_N C C c.1804C>T p.Pro602Ser p.P602S ENST00000268919 1/1 78 73 5 84 84 0 varscan-mutect KIF2B,missense_variant,p.Pro602Ser,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 1937/2313 1804/2022 602/673 P/S Ccc/Tcc COSM706804 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 tolerated(0.77) 1/1 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 53824837 53824837 C T 1 0 0 0 0 1 0 0 0 8163 507 18 3 3 KIF2B 17 53824837 Missense_Mutation SNP C C3L-00095_T 3248557 53824837 29432604 661 3870 MSI2 0 . GRCh38 17 57616075 57616075 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.643G>T p.Gly215Trp p.G215W ENST00000284073 9/14 124 108 16 113 113 0 strelka-varscan-mutect MSI2,missense_variant,p.Gly215Trp,ENST00000284073,NM_138962.2;MSI2,missense_variant,p.Gly211Trp,ENST00000322684,NM_170721.1;MSI2,missense_variant,p.Gly193Trp,ENST00000416426,;MSI2,missense_variant,p.Gly111Trp,ENST00000579180,;MSI2,missense_variant,p.Gly154Trp,ENST00000442934,;RN7SL449P,upstream_gene_variant,,ENST00000464937,;MSI2,non_coding_transcript_exon_variant,,ENST00000579505,;MSI2,non_coding_transcript_exon_variant,,ENST00000579205,;MSI2,non_coding_transcript_exon_variant,,ENST00000577241,; T ENST00000284073 Transcript missense_variant 852/6364 643/987 215/328 G/W Ggg/Tgg 1 1 MSI2 HGNC HGNC:18585 protein_coding YES CCDS11596.1 ENSP00000284073 Q96DH6 UPI0000070D73 NM_138962.2 deleterious(0) 9/14 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF476 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -19.99997 0.9998901 1 1 1 0 T 3 4 10 57616075 57616075 G T 1 0 0 0 0 1 0 0 0 9859 1232 43 2 2 MSI2 17 57616075 Missense_Mutation SNP G C3L-00095_T 3791238 57616075 25641366 662 3871 INTS2 0 . GRCh38 17 61897492 61897492 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1495G>T p.Val499Phe p.V499F ENST00000444766 11/25 163 149 14 199 196 3 strelka-varscan-mutect INTS2,missense_variant,p.Val499Phe,ENST00000444766,NM_020748.2;INTS2,missense_variant,p.Val499Phe,ENST00000617492,;INTS2,missense_variant,p.Val491Phe,ENST00000251334,;INTS2,upstream_gene_variant,,ENST00000578805,; A ENST00000444766 Transcript missense_variant 1571/5878 1495/3615 499/1204 V/F Gtc/Ttc 1 -1 INTS2 HGNC HGNC:29241 protein_coding YES CCDS45750.1 ENSP00000414237 Q9H0H0 UPI0000E5A03A NM_020748.2 deleterious(0) 11/25 Pfam_domain:PF14750,Prints_domain:PR02105,hmmpanther:PTHR28608 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 61897492 61897492 C A 1 0 0 0 0 1 0 0 0 7680 507 18 2 2 INTS2 17 61897492 Missense_Mutation SNP C C3L-00095_T 4281417 61897492 21359949 663 3872 ACE 0 . GRCh38 17 63496855 63496855 + Silent SNP G G A rs141429845 C3L-00095_T C3L-00095_N G G c.3561G>A p.= p.T1187T ENST00000290866 24/25 428 387 41 556 555 1 strelka-varscan-mutect ACE,synonymous_variant,p.=,ENST00000428043,;ACE,synonymous_variant,p.=,ENST00000290866,NM_000789.3;ACE,synonymous_variant,p.=,ENST00000290863,NM_152830.2;ACE,synonymous_variant,p.=,ENST00000413513,NM_001178057.1;ACE,synonymous_variant,p.=,ENST00000579409,;ACE,downstream_gene_variant,,ENST00000582761,;ACE,non_coding_transcript_exon_variant,,ENST00000577418,;CTD-2501B8.1,synonymous_variant,p.=,ENST00000577647,;ACE,3_prime_UTR_variant,,ENST00000579314,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,non_coding_transcript_exon_variant,,ENST00000582244,;ACE,downstream_gene_variant,,ENST00000584865,;ACE,downstream_gene_variant,,ENST00000583645,;ACE,downstream_gene_variant,,ENST00000578679,; A ENST00000290866 Transcript synonymous_variant 3585/4959 3561/3921 1187/1306 T acG/acA rs141429845,COSM4068566,COSM4068567,COSM4068568 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 24/25 hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs141429845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 63496855 63496855 G A 1 0 0 0 0 0 0 0 1 174 1103 39 1 1 ACE 17 63496855 Silent SNP G C3L-00095_T 1599363 63496855 19760586 664 3873 CD79B 0 . GRCh38 17 63929842 63929842 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.480T>A p.Asp160Glu p.D160E ENST00000392795 4/6 632 587 45 773 773 0 strelka-varscan-mutect CD79B,missense_variant,p.Asp159Glu,ENST00000006750,NM_000626.2;CD79B,missense_variant,p.Asp160Glu,ENST00000392795,NM_001039933.1;CD79B,missense_variant,p.Asp55Glu,ENST00000349817,NM_021602.2;CD79B,non_coding_transcript_exon_variant,,ENST00000559358,;CD79B,downstream_gene_variant,,ENST00000558969,;CD79B,downstream_gene_variant,,ENST00000583260,; T ENST00000392795 Transcript missense_variant 555/1254 480/693 160/230 D/E gaT/gaA 1 -1 CD79B HGNC HGNC:1699 protein_coding YES CCDS42372.1 ENSP00000376544 P40259 UPI00001B2490 NM_001039933.1 deleterious(0.03) 4/6 hmmpanther:PTHR14334:SF2,hmmpanther:PTHR14334 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 63929842 63929842 A T 1 0 0 0 0 1 0 0 0 2741 214 8 4 4 CD79B 17 63929842 Missense_Mutation SNP A C3L-00095_T 432987 63929842 19327599 665 3874 PRKAR1A 0 . GRCh38 17 68524067 68524067 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.492G>T p.= p.V164V ENST00000392711 5/11 457 423 34 523 522 1 strelka-varscan-mutect PRKAR1A,synonymous_variant,p.=,ENST00000392711,NM_212472.2,NM_002734.4;PRKAR1A,synonymous_variant,p.=,ENST00000589228,NM_001278433.1;PRKAR1A,synonymous_variant,p.=,ENST00000536854,NM_001276289.1;PRKAR1A,synonymous_variant,p.=,ENST00000358598,NM_212471.2;PRKAR1A,synonymous_variant,p.=,ENST00000586397,;PRKAR1A,synonymous_variant,p.=,ENST00000588188,NM_001276290.1;PRKAR1A,synonymous_variant,p.=,ENST00000589017,;PRKAR1A,synonymous_variant,p.=,ENST00000585981,;PRKAR1A,synonymous_variant,p.=,ENST00000588702,;PRKAR1A,synonymous_variant,p.=,ENST00000588178,;PRKAR1A,upstream_gene_variant,,ENST00000592800,;PRKAR1A,downstream_gene_variant,,ENST00000585427,;PRKAR1A,downstream_gene_variant,,ENST00000585815,;PRKAR1A,downstream_gene_variant,,ENST00000589480,;RP11-120M18.2,non_coding_transcript_exon_variant,,ENST00000590353,;PRKAR1A,3_prime_UTR_variant,,ENST00000392710,;PRKAR1A,3_prime_UTR_variant,,ENST00000585608,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000585460,;PRKAR1A,upstream_gene_variant,,ENST00000586541,;PRKAR1A,upstream_gene_variant,,ENST00000585907,; T ENST00000392711 Transcript synonymous_variant 699/4327 492/1146 164/381 V gtG/gtT 1 1 PRKAR1A HGNC HGNC:9388 protein_coding YES CCDS11678.1 ENSP00000376475 P10644 B2R5T5 UPI0000001C57 NM_212472.2,NM_002734.4 5/11 PROSITE_profiles:PS50042,hmmpanther:PTHR11635:SF129,hmmpanther:PTHR11635,PROSITE_patterns:PS00888,Gene3D:2.60.120.10,PIRSF_domain:PIRSF000548,Pfam_domain:PF00027,SMART_domains:SM00100,Superfamily_domains:SSF51206,Prints_domain:PR00103 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 68524067 68524067 G T 1 0 0 0 0 0 0 0 1 12636 1277 45 2 2 PRKAR1A 17 68524067 Silent SNP G C3L-00095_T 4594225 68524067 14733374 666 3875 MYO15B 0 . GRCh38 17 75610170 75610170 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.4246C>A p.= p.R1416R ENST00000610510 22/63 60 54 6 80 80 0 strelka-mutect MYO15B,synonymous_variant,p.=,ENST00000610510,;MYO15B,synonymous_variant,p.=,ENST00000633867,;MYO15B,synonymous_variant,p.=,ENST00000583560,;MYO15B,upstream_gene_variant,,ENST00000578462,;MYO15B,synonymous_variant,p.=,ENST00000621743,;MYO15B,3_prime_UTR_variant,,ENST00000619501,;MYO15B,3_prime_UTR_variant,,ENST00000584516,;MYO15B,3_prime_UTR_variant,,ENST00000582012,;MYO15B,upstream_gene_variant,,ENST00000612587,;MYO15B,downstream_gene_variant,,ENST00000580724,; A ENST00000610510 Transcript synonymous_variant 4246/9195 4246/9195 1416/3064 R Cgg/Agg 1 1 MYO15B HGNC HGNC:14083 protein_coding YES ENSP00000488624 A0A0J9YY01 UPI00064546F0 22/63 LOW 1 SNV 5 1 PASS rs1269927689 . 0 191 15 4 0 0 0 0 -10.80153 0.9630438 1 1 1 0 A 2 1 10 75610170 75610170 C A 1 0 0 0 0 0 0 0 1 10064 782 27 1 1 MYO15B 17 75610170 Silent SNP C C3L-00095_T 7086103 75610170 7647271 667 3876 MYO15B 0 . GRCh38 17 75611929 75611929 + Silent SNP G G T rs138855884 C3L-00095_T C3L-00095_N G G c.4497G>T p.= p.P1499P ENST00000610510 25/63 195 183 12 221 221 0 strelka-varscan-mutect MYO15B,synonymous_variant,p.=,ENST00000610510,;MYO15B,synonymous_variant,p.=,ENST00000633867,;MYO15B,downstream_gene_variant,,ENST00000583560,;MYO15B,non_coding_transcript_exon_variant,,ENST00000578462,;MYO15B,synonymous_variant,p.=,ENST00000621743,;MYO15B,3_prime_UTR_variant,,ENST00000619501,;MYO15B,3_prime_UTR_variant,,ENST00000584516,;MYO15B,upstream_gene_variant,,ENST00000612587,;MYO15B,upstream_gene_variant,,ENST00000577342,;MYO15B,upstream_gene_variant,,ENST00000578005,;MYO15B,upstream_gene_variant,,ENST00000584723,;MYO15B,upstream_gene_variant,,ENST00000610429,;MYO15B,downstream_gene_variant,,ENST00000582012,;MYO15B,downstream_gene_variant,,ENST00000580724,; T ENST00000610510 Transcript synonymous_variant 4497/9195 4497/9195 1499/3064 P ccG/ccT rs138855884 1 1 MYO15B HGNC HGNC:14083 protein_coding YES ENSP00000488624 A0A0J9YY01 UPI00064546F0 25/63 hmmpanther:PTHR22692,hmmpanther:PTHR22692:SF8 LOW 1 SNV 5 1 PASS rs138855884 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 75611929 75611929 G T 1 0 0 0 0 0 0 0 1 10064 1074 38 1 1 MYO15B 17 75611929 Silent SNP G C3L-00095_T 1759 75611929 7645512 668 3877 FOXJ1 0 . GRCh38 17 76137789 76137789 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.830C>A p.Pro277Gln p.P277Q ENST00000322957 3/3 91 86 5 154 154 0 strelka-varscan-mutect FOXJ1,missense_variant,p.Pro277Gln,ENST00000322957,NM_001454.3;RNF157,downstream_gene_variant,,ENST00000269391,NM_052916.2;RP11-449J21.5,upstream_gene_variant,,ENST00000590137,;RP11-449J21.5,upstream_gene_variant,,ENST00000586627,;RP11-449J21.5,upstream_gene_variant,,ENST00000585542,;RNF157,downstream_gene_variant,,ENST00000589912,; T ENST00000322957 Transcript missense_variant 1185/2641 830/1266 277/421 P/Q cCg/cAg 1 -1 FOXJ1 HGNC HGNC:3816 protein_coding YES CCDS32739.1 ENSP00000323880 Q92949 A0A024R8P1 UPI000000DB81 NM_001454.3 tolerated(0.05) 3/3 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF119 MODERATE 1 SNV 1 1 PASS rs1351956108 . 0 207 3 0 0 0 0 0 -11.02397 1 1 1 1 0 T 3 4 10 76137789 76137789 G T 1 0 0 0 0 1 0 0 0 5874 1116 39 1 1 FOXJ1 17 76137789 Missense_Mutation SNP G C3L-00095_T 525860 76137789 7119652 669 3878 ENPP7 0 . GRCh38 17 79735301 79735301 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.658G>A p.Asp220Asn p.D220N ENST00000328313 3/6 363 332 31 472 472 0 strelka-varscan-mutect ENPP7,missense_variant,p.Asp220Asn,ENST00000328313,NM_178543.4;ENPP7,upstream_gene_variant,,ENST00000576512,; A ENST00000328313 Transcript missense_variant 879/2043 658/1377 220/458 D/N Gac/Aac 1 1 ENPP7 HGNC HGNC:23764 protein_coding YES CCDS11763.1 ENSP00000332656 Q6UWV6 UPI000019219F NM_178543.4 deleterious(0.04) 3/6 Gene3D:3.40.720.10,Pfam_domain:PF01663,hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF63,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 79735301 79735301 G A 1 0 0 0 0 1 0 0 0 4980 1174 41 3 3 ENPP7 17 79735301 Missense_Mutation SNP G C3L-00095_T 3597512 79735301 3522140 670 3879 BAHCC1 0 . GRCh38 17 81445642 81445642 + Missense_Mutation SNP G G T rs782031139 C3L-00095_T C3L-00095_N G G c.3124G>T p.Gly1042Cys p.G1042C ENST00000584436 10/29 240 225 15 302 300 2 strelka-varscan-mutect BAHCC1,missense_variant,p.Gly1042Cys,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Gly1042Cys,ENST00000307745,;BAHCC1,downstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 3491/10801 3124/7920 1042/2639 G/C Ggt/Tgt rs782031139 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0.05) 10/29 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22 MODERATE 1 SNV 5 1 PASS rs782031139 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 81445642 81445642 G T 1 0 0 0 0 1 0 0 0 1451 1232 43 2 2 BAHCC1 17 81445642 Missense_Mutation SNP G C3L-00095_T 1710341 81445642 1811799 671 3880 MRPL12 0 . GRCh38 17 81704427 81704427 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.258G>A p.= p.L86L ENST00000571730 2/15 84 74 10 100 100 0 strelka-varscan-mutect RP13-1032I1.10,synonymous_variant,p.=,ENST00000571730,;MRPL12,synonymous_variant,p.=,ENST00000333676,NM_002949.3;HGS,downstream_gene_variant,,ENST00000329138,NM_004712.4;HGS,downstream_gene_variant,,ENST00000573320,;HGS,downstream_gene_variant,,ENST00000575078,;RP13-1032I1.7,upstream_gene_variant,,ENST00000575312,;HGS,downstream_gene_variant,,ENST00000570355,;HGS,downstream_gene_variant,,ENST00000570652,;HGS,downstream_gene_variant,,ENST00000573949,; A ENST00000571730 Transcript synonymous_variant 389/1922 258/1329 86/442 L ctG/ctA 1 1 RP13-1032I1.10 Clone_based_vega_gene protein_coding YES ENSP00000461324 B4DLN1 UPI00017A75DC 2/15 Pfam_domain:PF16320,Superfamily_domains:SSF48300 LOW SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.99183 1 1 1 1 0 A 2 1 10 81704427 81704427 G A 1 0 0 0 0 0 0 0 1 9752 1304 45 3 3 MRPL12 17 81704427 Silent SNP G C3L-00095_T 258785 81704427 1553014 672 3881 FASN 0 . GRCh38 17 82084020 82084020 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.5053A>T p.Ile1685Phe p.I1685F ENST00000306749 29/43 279 256 23 323 323 0 strelka-varscan-mutect FASN,missense_variant,p.Ile1685Phe,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Ile1683Phe,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000636628,;FASN,upstream_gene_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,upstream_gene_variant,,ENST00000580382,;FASN,downstream_gene_variant,,ENST00000579410,; A ENST00000306749 Transcript missense_variant 5272/8565 5053/7536 1685/2511 I/F Atc/Ttc 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 deleterious(0) 29/43 Gene3D:3.40.50.720,Pfam_domain:PF00107,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,SMART_domains:SM00829,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs899592172 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 82084020 82084020 T A 1 0 0 0 0 1 0 0 0 5543 1464 51 4 4 FASN 17 82084020 Missense_Mutation SNP T C3L-00095_T 379593 82084020 1173421 673 3882 NARF 0 . GRCh38 17 82464307 82464307 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.129G>T p.Leu43Phe p.L43F ENST00000309794 3/11 121 109 12 190 190 0 strelka-mutect NARF,missense_variant,p.Leu43Phe,ENST00000309794,NM_031968.2,NM_012336.3;NARF,missense_variant,p.Leu43Phe,ENST00000412079,;NARF,missense_variant,p.Leu43Phe,ENST00000457415,;NARF,missense_variant,p.Leu43Phe,ENST00000577432,;NARF,5_prime_UTR_variant,,ENST00000390006,NM_001038618.2;NARF,5_prime_UTR_variant,,ENST00000577410,;NARF,5_prime_UTR_variant,,ENST00000580296,;NARF,5_prime_UTR_variant,,ENST00000579198,;NARF,5_prime_UTR_variant,,ENST00000584411,;NARF,intron_variant,,ENST00000345415,NM_001083608.1;NARF,non_coding_transcript_exon_variant,,ENST00000581743,;NARF,intron_variant,,ENST00000583181,;NARF,intron_variant,,ENST00000584192,;RP13-20L14.10,downstream_gene_variant,,ENST00000623828,;NARF,missense_variant,p.Leu43Phe,ENST00000374611,;NARF,missense_variant,p.Leu43Phe,ENST00000582907,;NARF,missense_variant,p.Leu43Phe,ENST00000581795,;NARF,missense_variant,p.Leu43Phe,ENST00000581202,;NARF,3_prime_UTR_variant,,ENST00000580748,;NARF,non_coding_transcript_exon_variant,,ENST00000577812,;NARF,intron_variant,,ENST00000578082,;NARF,downstream_gene_variant,,ENST00000582585,;NARF,upstream_gene_variant,,ENST00000579083,; T ENST00000309794 Transcript missense_variant 327/3949 129/1371 43/456 L/F ttG/ttT 1 1 NARF HGNC HGNC:29916 protein_coding YES CCDS32777.1 ENSP00000309899 Q9UHQ1 UPI0000073D0C NM_031968.2,NM_012336.3 deleterious(0) 3/11 Gene3D:1hfeL01,hmmpanther:PTHR11615,hmmpanther:PTHR11615:SF124 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 10 82464307 82464307 G T 1 0 0 0 0 1 0 0 0 10177 1339 47 2 2 NARF 17 82464307 Missense_Mutation SNP G C3L-00095_T 380287 82464307 793134 674 3883 CLUL1 0 . GRCh38 18 633328 633328 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.1043T>C p.Met348Thr p.M348T ENST00000540035 8/11 205 185 20 232 232 0 strelka-varscan-mutect CLUL1,missense_variant,p.Met321Thr,ENST00000581619,;CLUL1,missense_variant,p.Met348Thr,ENST00000540035,NM_001289036.1;CLUL1,missense_variant,p.Met348Thr,ENST00000620089,;CLUL1,missense_variant,p.Met296Thr,ENST00000400606,NM_014410.4;CLUL1,missense_variant,p.Met296Thr,ENST00000338387,NM_001318522.1,NM_199167.1;CLUL1,missense_variant,p.Met296Thr,ENST00000579494,; C ENST00000540035 Transcript missense_variant 1252/2199 1043/1557 348/518 M/T aTg/aCg 1 1 CLUL1 HGNC HGNC:2096 protein_coding YES CCDS74187.1 ENSP00000441726 F5GWQ8 UPI000206520E NM_001289036.1 tolerated(0.51) 8/11 hmmpanther:PTHR10970:SF2,hmmpanther:PTHR10970,Pfam_domain:PF01093,SMART_domains:SM00035 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 633328 633328 T C 1 0 0 0 0 1 0 0 0 3343 1464 51 5 5 CLUL1 18 633328 Missense_Mutation SNP T C3L-00095_T 633328 79739957 675 3884 PTPRM 0 . GRCh38 18 8378264 8378264 + Splice_Site SNP G G T novel C3L-00095_T C3L-00095_N G G c.3463-1G>T p.X1155_splice ENST00000580170 63 58 5 78 78 0 strelka-varscan-mutect PTPRM,splice_acceptor_variant,,ENST00000332175,NM_002845.3;PTPRM,splice_acceptor_variant,,ENST00000580170,NM_001105244.1;PTPRM,splice_acceptor_variant,,ENST00000400053,;PTPRM,splice_acceptor_variant,,ENST00000400060,;PTPRM,splice_acceptor_variant,,ENST00000583153,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,; T ENST00000580170 Transcript splice_acceptor_variant -/5941 3463/4398 1155/1465 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 26/32 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.16787 1 1 1 1 0 T 5 4 10 8378264 8378264 G T 1 0 0 0 0 0 0 1 0 12960 1014 35 2 2 PTPRM 18 8378264 Splice_Site SNP G C3L-00095_T 7744936 8378264 71995021 676 3885 APCDD1 0 . GRCh38 18 10487760 10487760 + Missense_Mutation SNP G G C rs763105125 C3L-00095_T C3L-00095_N G G c.1267G>C p.Glu423Gln p.E423Q ENST00000355285 5/5 340 311 29 438 438 0 strelka-varscan-mutect APCDD1,missense_variant,p.Glu423Gln,ENST00000355285,NM_153000.4;APCDD1,downstream_gene_variant,,ENST00000578882,;APCDD1,3_prime_UTR_variant,,ENST00000423585,;APCDD1,3_prime_UTR_variant,,ENST00000579685,;APCDD1,downstream_gene_variant,,ENST00000582723,; C ENST00000355285 Transcript missense_variant 1621/3809 1267/1545 423/514 E/Q Gag/Cag rs763105125 1 1 APCDD1 HGNC HGNC:15718 protein_coding YES CCDS11849.1 ENSP00000347433 Q8J025 UPI000000D766 NM_153000.4 tolerated(0.08) 5/5 Pfam_domain:PF14921,hmmpanther:PTHR31021,hmmpanther:PTHR31021:SF2,SMART_domains:SM01352 MODERATE 1 SNV 1 1 PASS rs763105125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 10487760 10487760 G C 1 0 0 0 0 1 0 0 0 885 1059 37 4 4 APCDD1 18 10487760 Missense_Mutation SNP G C3L-00095_T 2109496 10487760 69885525 677 3886 PIEZO2 0 . GRCh38 18 10691261 10691261 + Frame_Shift_Del DEL T T - novel C3L-00095_T C3L-00095_N T T c.6974delA p.Lys2325ArgfsTer20 p.K2325Rfs*20 ENST00000503781 44/52 87 81 6 111 110 1 varindel-pindel PIEZO2,frameshift_variant,p.Lys2276ArgfsTer20,ENST00000383408,;PIEZO2,frameshift_variant,p.Lys2325ArgfsTer20,ENST00000302079,;PIEZO2,frameshift_variant,p.Lys2350ArgfsTer20,ENST00000580640,;PIEZO2,frameshift_variant,p.Lys2325ArgfsTer20,ENST00000503781,NM_022068.3;PIEZO2,frameshift_variant,p.Lys282ArgfsTer20,ENST00000538948,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; - ENST00000503781 Transcript frameshift_variant 6974/8259 6974/8259 2325/2752 K/X aAg/ag 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 44/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 10691261 10691261 T - 1 0 1 0 1 0 0 0 0 11975 1609 56 0 0 PIEZO2 18 10691261 Frame_Shift_Del DEL T C3L-00095_T 203501 10691261 69682024 678 3887 ZNF521 0 . GRCh38 18 25227061 25227061 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.857G>T p.Cys286Phe p.C286F ENST00000361524 4/8 292 270 22 361 360 1 strelka-varscan-mutect ZNF521,missense_variant,p.Cys286Phe,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Cys66Phe,ENST00000584787,NM_001308225.1;ZNF521,missense_variant,p.Cys286Phe,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,missense_variant,p.Cys286Phe,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; A ENST00000361524 Transcript missense_variant 1006/4871 857/3936 286/1311 C/F tGc/tTc COSM3724302 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 tolerated(0.1) 4/8 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 25227061 25227061 C A 1 0 0 0 0 1 0 0 0 18537 710 25 2 2 ZNF521 18 25227061 Missense_Mutation SNP C C3L-00095_T 14535800 25227061 55146224 679 3888 CDH2 0 . GRCh38 18 27952196 27952196 + Missense_Mutation SNP C C A rs201294768 C3L-00095_T C3L-00095_N C C c.2678G>T p.Arg893Leu p.R893L ENST00000269141 16/16 290 271 19 344 342 2 strelka-mutect CDH2,missense_variant,p.Arg893Leu,ENST00000269141,NM_001792.3;CDH2,missense_variant,p.Arg862Leu,ENST00000399380,NM_001308176.1;AC015933.2,upstream_gene_variant,,ENST00000423367,; A ENST00000269141 Transcript missense_variant 3102/4332 2678/2721 893/906 R/L cGg/cTg rs201294768,COSM385442 1 -1 CDH2 HGNC HGNC:1759 protein_coding YES CCDS11891.1 ENSP00000269141 P19022 A0A024RC42 UPI000013D7FD NM_001792.3 deleterious(0) 16/16 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF79 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201294768 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 27952196 27952196 C A 1 0 0 0 0 1 0 0 0 2808 652 23 1 1 CDH2 18 27952196 Missense_Mutation SNP C C3L-00095_T 2725135 27952196 52421089 680 3889 DSG2 0 . GRCh38 18 31538759 31538759 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1660G>T p.Val554Leu p.V554L ENST00000261590 12/15 499 466 33 541 540 1 strelka-varscan-mutect DSG2,missense_variant,p.Val554Leu,ENST00000261590,NM_001943.3;DSG2-AS1,downstream_gene_variant,,ENST00000583706,; T ENST00000261590 Transcript missense_variant 1869/5831 1660/3357 554/1118 V/L Gtg/Ttg 1 1 DSG2 HGNC HGNC:3049 protein_coding YES CCDS42423.1 ENSP00000261590 Q14126 UPI0000048E38 NM_001943.3 deleterious(0.03) 12/15 Gene3D:2.60.40.60,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF1,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 31538759 31538759 G T 1 0 0 0 0 1 0 0 0 4598 1377 48 2 2 DSG2 18 31538759 Missense_Mutation SNP G C3L-00095_T 3586563 31538759 48834526 681 3890 ATP5A1 0 . GRCh38 18 46088115 46088115 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.793G>A p.Asp265Asn p.D265N ENST00000398752 6/12 199 185 14 147 147 0 strelka-varscan-mutect ATP5A1,missense_variant,p.Asp265Asn,ENST00000398752,NM_004046.5;ATP5A1,missense_variant,p.Asp215Asn,ENST00000593152,NM_001001935.2,NM_001257335.1;ATP5A1,missense_variant,p.Asp265Asn,ENST00000282050,NM_001001937.1;ATP5A1,missense_variant,p.Asp243Asn,ENST00000590665,NM_001257334.1;ATP5A1,missense_variant,p.Asp176Asn,ENST00000589252,;ATP5A1,downstream_gene_variant,,ENST00000589869,;ATP5A1,downstream_gene_variant,,ENST00000590324,;ATP5A1,downstream_gene_variant,,ENST00000590406,;ATP5A1,downstream_gene_variant,,ENST00000592989,;ATP5A1,3_prime_UTR_variant,,ENST00000586592,;ATP5A1,3_prime_UTR_variant,,ENST00000590156,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000586523,;ATP5A1,intron_variant,,ENST00000592364,;ATP5A1,downstream_gene_variant,,ENST00000589611,;ATP5A1,downstream_gene_variant,,ENST00000590448,;ATP5A1,upstream_gene_variant,,ENST00000587902,;ATP5A1,downstream_gene_variant,,ENST00000591981,;ATP5A1,downstream_gene_variant,,ENST00000585650,; T ENST00000398752 Transcript missense_variant 915/5818 793/1662 265/553 D/N Gat/Aat 1 -1 ATP5A1 HGNC HGNC:823 protein_coding YES CCDS11927.1 ENSP00000381736 P25705 V9HW26 UPI000006221A NM_004046.5 deleterious_low_confidence(0.02) 6/12 HAMAP:MF_01346,hmmpanther:PTHR15184:SF3,hmmpanther:PTHR15184,TIGRFAM_domain:TIGR00962,PIRSF_domain:PIRSF039088,Pfam_domain:PF00006,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 46088115 46088115 C T 1 0 0 0 0 1 0 0 0 1300 913 32 3 3 ATP5A1 18 46088115 Missense_Mutation SNP C C3L-00095_T 14549356 46088115 34285170 682 3891 PIAS2 0 . GRCh38 18 46812613 46812613 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.1687-1G>T p.X563_splice ENST00000585916 120 110 10 162 162 0 strelka-varscan-mutect PIAS2,splice_acceptor_variant,,ENST00000585916,NM_001324049.1,NM_001324048.1,NM_001324047.1,NM_004671.3;PIAS2,downstream_gene_variant,,ENST00000324794,NM_001324051.1,NM_001324054.1,NM_173206.3;PIAS2,splice_acceptor_variant,,ENST00000398654,; A ENST00000585916 Transcript splice_acceptor_variant -/11075 1687/1866 563/621 1 -1 PIAS2 HGNC HGNC:17311 protein_coding YES CCDS32824.1 ENSP00000465676 O75928 UPI0000201CB9 NM_001324049.1,NM_001324048.1,NM_001324047.1,NM_004671.3 13/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 46812613 46812613 C A 1 0 0 0 0 0 0 1 0 11966 579 20 2 2 PIAS2 18 46812613 Splice_Site SNP C C3L-00095_T 724498 46812613 33560672 683 3892 TCEB3B 0 . GRCh38 18 47034104 47034104 + Silent SNP G G T rs748442026 C3L-00095_T C3L-00095_N G G c.1161C>A p.= p.L387L ENST00000332567 1/1 273 253 20 347 346 1 strelka-varscan-mutect TCEB3B,synonymous_variant,p.=,ENST00000332567,NM_016427.2;KATNAL2,intron_variant,,ENST00000245121,NM_031303.2;TCEB3B,intron_variant,,ENST00000620522,;KATNAL2,intron_variant,,ENST00000356157,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,intron_variant,,ENST00000585469,;TCEB3C,upstream_gene_variant,,ENST00000330682,NM_145653.3; T ENST00000332567 Transcript synonymous_variant 1518/3050 1161/2262 387/753 L ctC/ctA rs748442026 1 -1 TCEB3B HGNC HGNC:30771 protein_coding YES CCDS11932.1 ENSP00000331302 Q8IYF1 UPI0000140A82 NM_016427.2 1/1 hmmpanther:PTHR15141:SF7,hmmpanther:PTHR15141 LOW SNV 1 PASS rs748442026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 47034104 47034104 G T 1 0 0 0 0 0 0 0 1 16089 1277 45 2 2 TCEB3B 18 47034104 Silent SNP G C3L-00095_T 221491 47034104 33339181 684 3893 LIPG 0 . GRCh38 18 49569535 49569535 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.558G>A p.= p.V186V ENST00000261292 4/10 426 401 25 523 522 1 strelka-varscan-mutect LIPG,synonymous_variant,p.=,ENST00000261292,NM_006033.2;LIPG,synonymous_variant,p.=,ENST00000577628,;LIPG,synonymous_variant,p.=,ENST00000427224,NM_001308006.1;LIPG,synonymous_variant,p.=,ENST00000580036,;LIPG,downstream_gene_variant,,ENST00000583083,;LIPG,downstream_gene_variant,,ENST00000579750,; A ENST00000261292 Transcript synonymous_variant 836/10441 558/1503 186/500 V gtG/gtA 1 1 LIPG HGNC HGNC:6623 protein_coding YES CCDS11938.1 ENSP00000261292 Q9Y5X9 A0A024R2B5 UPI000012E706 NM_006033.2 4/10 hmmpanther:PTHR11610:SF13,hmmpanther:PTHR11610,Pfam_domain:PF00151,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474,Prints_domain:PR00822 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 49569535 49569535 G A 1 0 0 0 0 0 0 0 1 8744 1335 47 3 3 LIPG 18 49569535 Silent SNP G C3L-00095_T 2535431 49569535 30803750 685 3894 ACAA2 0 . GRCh38 18 49787293 49787293 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.952G>C p.Glu318Gln p.E318Q ENST00000285093 8/10 96 89 7 115 115 0 varscan-mutect ACAA2,missense_variant,p.Glu318Gln,ENST00000285093,NM_006111.2;ACAA2,missense_variant,p.Glu263Gln,ENST00000589432,;ACAA2,missense_variant,p.Glu315Gln,ENST00000587994,;ACAA2,upstream_gene_variant,,ENST00000591171,; G ENST00000285093 Transcript missense_variant,splice_region_variant 1428/3350 952/1194 318/397 E/Q Gag/Cag 1 -1 ACAA2 HGNC HGNC:83 protein_coding YES CCDS11939.1 ENSP00000285093 P42765 UPI000006FECE NM_006111.2 deleterious(0) 8/10 hmmpanther:PTHR18919,hmmpanther:PTHR18919:SF107,TIGRFAM_domain:TIGR01930,Gene3D:3.40.47.10,Pfam_domain:PF02803,PIRSF_domain:PIRSF000429,Superfamily_domains:SSF53901 MODERATE 1 SNV 1 1 PASS rs1358976747 . 0 203 7 0 0 0 0 0 -14.35155 0.999998 1 1 1 0 G 3 3 10 49787293 49787293 C G 1 0 0 0 0 1 0 0 0 148 927 32 4 4 ACAA2 18 49787293 Missense_Mutation SNP C C3L-00095_T 217758 49787293 30585992 686 3895 MYO5B 0 . GRCh38 18 49953328 49953328 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.1684G>T p.Asp562Tyr p.D562Y ENST00000285039 14/40 452 416 36 581 580 1 strelka-varscan-mutect MYO5B,missense_variant,p.Asp562Tyr,ENST00000285039,NM_001080467.2; A ENST00000285039 Transcript missense_variant 1984/9505 1684/5547 562/1848 D/Y Gat/Tat COSM5430355 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 deleterious(0) 14/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 49953328 49953328 C A 1 0 0 0 0 1 0 0 0 10080 826 29 2 2 MYO5B 18 49953328 Missense_Mutation SNP C C3L-00095_T 166035 49953328 30419957 687 3896 MBD1 0 . GRCh38 18 50279920 50279920 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.73G>T p.Gly25Trp p.G25W ENST00000590208 2/16 273 248 25 388 388 0 strelka-varscan-mutect MBD1,missense_variant,p.Gly25Trp,ENST00000591416,;MBD1,missense_variant,p.Gly25Trp,ENST00000269468,NM_015846.3;MBD1,missense_variant,p.Gly25Trp,ENST00000347968,NM_015844.2;MBD1,missense_variant,p.Gly25Trp,ENST00000269471,NM_015845.3;MBD1,missense_variant,p.Gly25Trp,ENST00000339998,NM_001204142.1;MBD1,missense_variant,p.Gly25Trp,ENST00000590208,NM_001204136.1;MBD1,missense_variant,p.Gly25Trp,ENST00000353909,NM_015847.3;MBD1,missense_variant,p.Gly25Trp,ENST00000585672,NM_001204141.1;MBD1,missense_variant,p.Gly25Trp,ENST00000457839,NM_001204137.1,NM_001204138.1;MBD1,missense_variant,p.Gly25Trp,ENST00000382948,NM_001204139.1;MBD1,missense_variant,p.Gly25Trp,ENST00000585595,;MBD1,missense_variant,p.Gly25Trp,ENST00000398495,NM_001204140.1;MBD1,missense_variant,p.Gly25Trp,ENST00000587605,NM_001204143.1;MBD1,missense_variant,p.Gly25Trp,ENST00000398493,;MBD1,missense_variant,p.Gly25Trp,ENST00000588937,;MBD1,missense_variant,p.Gly25Trp,ENST00000591535,NM_001204151.1;MBD1,missense_variant,p.Gly25Trp,ENST00000398488,NM_002384.2;CXXC1,downstream_gene_variant,,ENST00000285106,NM_014593.3;CXXC1,downstream_gene_variant,,ENST00000412036,NM_001101654.1;CXXC1,downstream_gene_variant,,ENST00000589940,;MBD1,upstream_gene_variant,,ENST00000592060,;CXXC1,downstream_gene_variant,,ENST00000591474,;MBD1,upstream_gene_variant,,ENST00000589541,;MBD1,upstream_gene_variant,,ENST00000589733,;MBD1,missense_variant,p.Gly25Trp,ENST00000590215,;MBD1,non_coding_transcript_exon_variant,,ENST00000586118,;MBD1,non_coding_transcript_exon_variant,,ENST00000589867,;MBD1,non_coding_transcript_exon_variant,,ENST00000589758,;CXXC1,downstream_gene_variant,,ENST00000590901,;CXXC1,downstream_gene_variant,,ENST00000591190,;CXXC1,downstream_gene_variant,,ENST00000586568,;CXXC1,downstream_gene_variant,,ENST00000587342,;CXXC1,downstream_gene_variant,,ENST00000590234,;CXXC1,downstream_gene_variant,,ENST00000592078,;CXXC1,downstream_gene_variant,,ENST00000586502,;MBD1,upstream_gene_variant,,ENST00000586679,;MBD1,upstream_gene_variant,,ENST00000591661,;CXXC1,downstream_gene_variant,,ENST00000587170,;CXXC1,downstream_gene_variant,,ENST00000586144,; A ENST00000590208 Transcript missense_variant 420/2913 73/1968 25/655 G/W Ggg/Tgg 1 -1 MBD1 HGNC HGNC:6916 protein_coding YES CCDS59320.1 ENSP00000468785 Q9UIS9 UPI0001F995B6 NM_001204136.1 deleterious(0) 2/16 Gene3D:3.30.890.10,Pfam_domain:PF01429,PROSITE_profiles:PS50982,hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF8,SMART_domains:SM00391,Superfamily_domains:SSF54171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 50279920 50279920 C A 1 0 0 0 0 1 0 0 0 9271 681 24 2 2 MBD1 18 50279920 Missense_Mutation SNP C C3L-00095_T 326592 50279920 30093365 688 3897 CCDC68 0 . GRCh38 18 54942787 54942787 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.5C>T p.Thr2Ile p.T2I ENST00000591504 3/12 253 236 17 211 211 0 strelka-varscan-mutect CCDC68,missense_variant,p.Thr2Ile,ENST00000591504,NM_025214.2;CCDC68,missense_variant,p.Thr2Ile,ENST00000432185,;CCDC68,missense_variant,p.Thr2Ile,ENST00000337363,NM_001143829.1;CCDC68,non_coding_transcript_exon_variant,,ENST00000587148,; A ENST00000591504 Transcript missense_variant 280/4132 5/1008 2/335 T/I aCa/aTa 1 -1 CCDC68 HGNC HGNC:24350 protein_coding YES CCDS11959.1 ENSP00000466690 Q9H2F9 A0A024R2B9 UPI00000435F1 NM_025214.2 deleterious(0) 3/12 hmmpanther:PTHR23171,hmmpanther:PTHR23171:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 54942787 54942787 G A 1 0 0 0 0 1 0 0 0 2540 1377 48 3 3 CCDC68 18 54942787 Missense_Mutation SNP G C3L-00095_T 4662867 54942787 25430498 689 3898 ZNF532 0 . GRCh38 18 58920224 58920224 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1937G>T p.Cys646Phe p.C646F ENST00000336078 4/11 113 105 8 156 156 0 strelka-varscan-mutect ZNF532,missense_variant,p.Cys646Phe,ENST00000336078,NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4;ZNF532,missense_variant,p.Cys646Phe,ENST00000589288,;ZNF532,missense_variant,p.Cys646Phe,ENST00000591083,;ZNF532,missense_variant,p.Cys646Phe,ENST00000591808,;ZNF532,missense_variant,p.Cys646Phe,ENST00000591230,;ZNF532,downstream_gene_variant,,ENST00000588601,;ZNF532,downstream_gene_variant,,ENST00000589481,;ZNF532,downstream_gene_variant,,ENST00000592452,;ZNF532,downstream_gene_variant,,ENST00000591049,;ZNF532,downstream_gene_variant,,ENST00000588456,;ZNF532,downstream_gene_variant,,ENST00000590285,;ZNF532,downstream_gene_variant,,ENST00000590287,;ZNF532,downstream_gene_variant,,ENST00000587755,;ZNF532,downstream_gene_variant,,ENST00000586085,;ZNF532,downstream_gene_variant,,ENST00000588543,;ZNF532,upstream_gene_variant,,ENST00000586997,;ZNF532,upstream_gene_variant,,ENST00000590157,;ZNF532,upstream_gene_variant,,ENST00000589156,; T ENST00000336078 Transcript missense_variant 2713/6696 1937/3906 646/1301 C/F tGc/tTc 1 1 ZNF532 HGNC HGNC:30940 protein_coding YES CCDS11969.1 ENSP00000338217 Q9HCE3 A0A024R283 UPI000013D30C NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4 deleterious(0) 4/11 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF204,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 58920224 58920224 G T 1 0 0 0 0 1 0 0 0 18545 1319 46 2 2 ZNF532 18 58920224 Missense_Mutation SNP G C3L-00095_T 3977437 58920224 21453061 690 3899 CDH20 0 . GRCh38 18 61490690 61490690 + Missense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.137T>A p.Leu46His p.L46H ENST00000262717 2/12 432 387 45 548 548 0 strelka-varscan-mutect CDH20,missense_variant,p.Leu46His,ENST00000262717,;CDH20,missense_variant,p.Leu46His,ENST00000536675,NM_031891.2;CDH20,missense_variant,p.Leu46His,ENST00000538374,; A ENST00000262717 Transcript missense_variant 535/3882 137/2406 46/801 L/H cTc/cAc 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D tolerated(0.45) 2/12 hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 61490690 61490690 T A 1 0 0 0 0 1 0 0 0 2809 1551 54 4 4 CDH20 18 61490690 Missense_Mutation SNP T C3L-00095_T 2570466 61490690 18882595 691 3900 CDH20 0 . GRCh38 18 61554583 61554583 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.2294C>A p.Ser765Ter p.S765* ENST00000262717 12/12 223 209 14 300 300 0 strelka-varscan-mutect CDH20,stop_gained,p.Ser765Ter,ENST00000262717,;CDH20,stop_gained,p.Ser765Ter,ENST00000536675,NM_031891.2;CDH20,stop_gained,p.Ser765Ter,ENST00000538374,;CDH20,downstream_gene_variant,,ENST00000587582,; A ENST00000262717 Transcript stop_gained 2692/3882 2294/2406 765/801 S/* tCg/tAg 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 HIGH 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -17.18994 0.9999996 1 1 1 0 A 4 1 10 61554583 61554583 C A 1 0 0 0 0 0 1 0 0 2809 893 31 1 1 CDH20 18 61554583 Nonsense_Mutation SNP C C3L-00095_T 63893 61554583 18818702 692 3901 CDH7 0 . GRCh38 18 65880701 65880701 + Missense_Mutation SNP C C A rs773946370 C3L-00095_T C3L-00095_N C C c.2165C>A p.Pro722His p.P722H ENST00000397968 12/12 426 388 38 496 493 3 strelka-varscan-mutect CDH7,missense_variant,p.Pro722His,ENST00000397968,NM_004361.2;CDH7,missense_variant,p.Pro722His,ENST00000323011,NM_033646.1; A ENST00000397968 Transcript missense_variant 2591/12231 2165/2358 722/785 P/H cCt/cAt rs773946370 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 deleterious(0.03) 12/12 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91 MODERATE 1 SNV 1 1 PASS rs773946370 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 65880701 65880701 C A 1 0 0 0 0 1 0 0 0 2818 681 24 2 2 CDH7 18 65880701 Missense_Mutation SNP C C3L-00095_T 4326118 65880701 14492584 693 3902 CCDC102B 0 . GRCh38 18 68836805 68836805 + Missense_Mutation SNP G G T rs745397622 C3L-00095_T C3L-00095_N G G c.42G>T p.Gln14His p.Q14H ENST00000360242 2/8 157 148 9 240 239 1 strelka-varscan-mutect CCDC102B,missense_variant,p.Gln14His,ENST00000360242,NM_001093729.1,NM_024781.2;CCDC102B,missense_variant,p.Gln14His,ENST00000584156,;CCDC102B,missense_variant,p.Gln14His,ENST00000584775,;CCDC102B,missense_variant,p.Gln14His,ENST00000582371,;CCDC102B,missense_variant,p.Gln14His,ENST00000578970,;CCDC102B,missense_variant,p.Gln14His,ENST00000581520,;CCDC102B,upstream_gene_variant,,ENST00000358653,;CCDC102B,non_coding_transcript_exon_variant,,ENST00000577772,; T ENST00000360242 Transcript missense_variant 159/2711 42/1542 14/513 Q/H caG/caT rs745397622 1 1 CCDC102B HGNC HGNC:26295 protein_coding YES CCDS11996.2 ENSP00000353377 Q68D86 UPI0000201E87 NM_001093729.1,NM_024781.2 tolerated(0.1) 2/8 MODERATE 1 SNV 1 1 PASS rs745397622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 68836805 68836805 G T 1 0 0 0 0 1 0 0 0 2435 933 33 2 2 CCDC102B 18 68836805 Missense_Mutation SNP G C3L-00095_T 2956104 68836805 11536480 694 3903 ODF3L2 0 . GRCh38 19 472416 472416 + Silent SNP C C A rs563807265 C3L-00095_T C3L-00095_N C C c.213G>T p.= p.S71S ENST00000315489 2/4 83 74 9 121 121 0 strelka-varscan-mutect ODF3L2,synonymous_variant,p.=,ENST00000315489,NM_182577.2;ODF3L2,intron_variant,,ENST00000382696,;ODF3L2,non_coding_transcript_exon_variant,,ENST00000591681,; A ENST00000315489 Transcript synonymous_variant 449/1604 213/870 71/289 S tcG/tcT rs563807265 1 -1 ODF3L2 HGNC HGNC:26841 protein_coding YES CCDS12027.1 ENSP00000318029 Q3SX64 UPI0000072898 NM_182577.2 2/4 hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF0 LOW 1 SNV 1 1 PASS rs563807265 . 0 196 11 3 0 0 0 0 -14.72048 0.99431 1 1 1 0 A 2 1 10 472416 472416 C A 1 0 0 0 0 0 0 0 1 10910 755 27 1 1 ODF3L2 19 472416 Silent SNP C C3L-00095_T 472416 58145200 695 3904 ELANE 0 . GRCh38 19 852899 852899 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.91delG p.Val31TrpfsTer29 p.V31Wfs*29 ENST00000590230 3/6 121 110 11 197 197 0 sindel-varindel ELANE,frameshift_variant,p.Val31TrpfsTer29,ENST00000590230,;ELANE,frameshift_variant,p.Val31TrpfsTer29,ENST00000263621,NM_001972.2;PRTN3,downstream_gene_variant,,ENST00000544537,;PRTN3,downstream_gene_variant,,ENST00000234347,NM_002777.3; - ENST00000590230 Transcript frameshift_variant 232/1028 91/804 31/267 V/X Gtg/tg 1 1 ELANE HGNC HGNC:3309 protein_coding YES CCDS12045.1 ENSP00000466090 P08246 UPI0000129E6B 3/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24257,hmmpanther:PTHR24257:SF16,SMART_domains:SM00020,Superfamily_domains:SSF50494 HIGH deletion 5 1 PASS . . 0 201 6 2 0 0 0 0 -16.31471 0.9997704 1 1 1 0 - 7 5 10 852899 852899 G - 1 0 1 0 1 0 0 0 0 4881 1377 48 0 0 ELANE 19 852899 Frame_Shift_Del DEL G C3L-00095_T 380483 852899 57764717 696 3905 STK11 0 . GRCh38 19 1222987 1222987 + Missense_Mutation SNP G G T rs864622488 C3L-00095_T C3L-00095_N G G c.923G>T p.Trp308Leu p.W308L ENST00000326873 8/10 51 46 5 64 64 0 strelka-varscan-mutect STK11,missense_variant,p.Trp308Leu,ENST00000586243,;STK11,missense_variant,p.Trp308Leu,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,splice_region_variant,,ENST00000589152,;STK11,splice_region_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript missense_variant,splice_region_variant 1373/2611 923/1302 308/433 W/L tGg/tTg rs864622488,CM991159,KinMutBase_STK11_DNA:g.17074G>A,COSM26041 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 8/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 likely_pathogenic 0,0,0,1 MODERATE 1 SNV 1 1,1,0,1 1 PASS rs864622488 . 0 206 4 0 0 0 0 0 -12.42854 1 1 1 1 0 T 3 4 10 1222987 1222987 G T 1 0 0 0 0 1 0 0 0 15664 1362 47 2 2 STK11 19 1222987 Missense_Mutation SNP G C3L-00095_T 370088 1222987 57394629 697 3906 SF3A2 0 . GRCh38 19 2247870 2247870 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.719G>T p.Gly240Val p.G240V ENST00000221494 9/9 143 125 18 242 242 0 strelka-varscan-mutect SF3A2,missense_variant,p.Gly240Val,ENST00000221494,NM_007165.4;AMH,upstream_gene_variant,,ENST00000221496,NM_000479.3;JSRP1,downstream_gene_variant,,ENST00000300961,NM_144616.3;SF3A2,downstream_gene_variant,,ENST00000586396,;AMH,upstream_gene_variant,,ENST00000592276,;AMH,upstream_gene_variant,,ENST00000592877,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592314,;AMH,upstream_gene_variant,,ENST00000589313,;SF3A2,downstream_gene_variant,,ENST00000589118,;SF3A2,downstream_gene_variant,,ENST00000592839,;SF3A2,downstream_gene_variant,,ENST00000590034,;SF3A2,downstream_gene_variant,,ENST00000587637,; T ENST00000221494 Transcript missense_variant 1154/1963 719/1395 240/464 G/V gGt/gTt 1 1 SF3A2 HGNC HGNC:10766 protein_coding YES CCDS12084.1 ENSP00000221494 Q15428 UPI0000135468 NM_007165.4 deleterious_low_confidence(0.01) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23205,hmmpanther:PTHR23205:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 2247870 2247870 G T 1 0 0 0 0 1 0 0 0 14426 1261 44 2 2 SF3A2 19 2247870 Missense_Mutation SNP G C3L-00095_T 1024883 2247870 56369746 698 3907 AMH 0 . GRCh38 19 2250345 2250345 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.421G>T p.Glu141Ter p.E141* ENST00000221496 2/5 418 389 29 559 558 1 strelka-varscan-mutect AMH,stop_gained,p.Glu141Ter,ENST00000221496,NM_000479.3;SF3A2,downstream_gene_variant,,ENST00000221494,NM_007165.4;JSRP1,downstream_gene_variant,,ENST00000300961,NM_144616.3;JSRP1,downstream_gene_variant,,ENST00000593238,;SF3A2,downstream_gene_variant,,ENST00000586396,;AMH,upstream_gene_variant,,ENST00000592276,;AMH,intron_variant,,ENST00000592877,;AMH,non_coding_transcript_exon_variant,,ENST00000589313,;SF3A2,downstream_gene_variant,,ENST00000592314,;SF3A2,downstream_gene_variant,,ENST00000592839,;SF3A2,downstream_gene_variant,,ENST00000587637,; T ENST00000221496 Transcript stop_gained 443/1821 421/1683 141/560 E/* Gag/Tag 1 1 AMH HGNC HGNC:464 protein_coding YES CCDS12085.1 ENSP00000221496 P03971 UPI000013C7D0 NM_000479.3 2/5 hmmpanther:PTHR15009,Pfam_domain:PF04709,PIRSF_domain:PIRSF037270 HIGH 1 SNV 1 1 PASS rs1276693838 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 2250345 2250345 G T 1 0 0 0 0 0 1 0 0 671 1175 41 2 2 AMH 19 2250345 Nonsense_Mutation SNP G C3L-00095_T 2475 2250345 56367271 699 3908 TMPRSS9 0 . GRCh38 19 2425975 2425975 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.3067G>T p.Val1023Leu p.V1023L ENST00000332578 17/17 105 93 12 174 174 0 strelka-varscan-mutect TMPRSS9,missense_variant,p.Val1023Leu,ENST00000332578,NM_182973.1;TIMM13,3_prime_UTR_variant,,ENST00000215570,NM_012458.3;LMNB2,downstream_gene_variant,,ENST00000325327,NM_032737.3;TMPRSS9,downstream_gene_variant,,ENST00000613480,;TIMM13,downstream_gene_variant,,ENST00000591871,;LMNB2,downstream_gene_variant,,ENST00000475819,;LMNB2,downstream_gene_variant,,ENST00000532465,; T ENST00000332578 Transcript missense_variant 3067/3331 3067/3180 1023/1059 V/L Gtg/Ttg 1 1 TMPRSS9 HGNC HGNC:30079 protein_coding YES CCDS12088.1 ENSP00000330264 Q7Z410 UPI00001B4EC6 NM_182973.1 deleterious(0.04) 17/17 PROSITE_profiles:PS50240,PIRSF_domain:PIRSF037931,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs1005208420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 2425975 2425975 G T 1 0 0 0 0 1 0 0 0 16729 1261 44 2 2 TMPRSS9 19 2425975 Missense_Mutation SNP G C3L-00095_T 175630 2425975 56191641 700 3909 THOP1 0 . GRCh38 19 2806971 2806971 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.805C>T p.= p.L269L ENST00000307741 7/13 148 139 9 266 265 1 strelka-varscan-mutect THOP1,synonymous_variant,p.=,ENST00000307741,NM_003249.3;THOP1,synonymous_variant,p.=,ENST00000586677,;THOP1,upstream_gene_variant,,ENST00000395212,;THOP1,upstream_gene_variant,,ENST00000590970,;THOP1,upstream_gene_variant,,ENST00000587401,;THOP1,upstream_gene_variant,,ENST00000587468,;THOP1,upstream_gene_variant,,ENST00000591363,;THOP1,upstream_gene_variant,,ENST00000591149,;THOP1,downstream_gene_variant,,ENST00000585673,;THOP1,upstream_gene_variant,,ENST00000592639,;THOP1,non_coding_transcript_exon_variant,,ENST00000589087,;THOP1,upstream_gene_variant,,ENST00000590533,; T ENST00000307741 Transcript synonymous_variant 1008/4804 805/2070 269/689 L Ctg/Ttg 1 1 THOP1 HGNC HGNC:11793 protein_coding YES CCDS12095.1 ENSP00000304467 P52888 UPI0000000C3E NM_003249.3 7/13 Gene3D:2o36A02,Pfam_domain:PF01432,hmmpanther:PTHR11804,hmmpanther:PTHR11804:SF50,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 2806971 2806971 C T 1 0 0 0 0 0 0 0 1 16305 680 24 3 3 THOP1 19 2806971 Silent SNP C C3L-00095_T 380996 2806971 55810645 701 3910 CELF5 0 . GRCh38 19 3224895 3224895 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.156C>A p.= p.I52I ENST00000292672 1/13 264 243 21 327 325 2 strelka-varscan-mutect CELF5,synonymous_variant,p.=,ENST00000541430,NM_001172673.1;CELF5,synonymous_variant,p.=,ENST00000292672,NM_021938.3;CELF5,upstream_gene_variant,,ENST00000334293,; A ENST00000292672 Transcript synonymous_variant 193/1854 156/1458 52/485 I atC/atA 1 1 CELF5 HGNC HGNC:14058 protein_coding YES CCDS12106.1 ENSP00000292672 Q8N6W0 UPI00000705EC NM_021938.3 1/13 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF444,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 3224895 3224895 C A 1 0 0 0 0 0 0 0 1 2926 845 30 2 2 CELF5 19 3224895 Silent SNP C C3L-00095_T 417924 3224895 55392721 702 3911 SEMA6B 0 . GRCh38 19 4556040 4556040 + Missense_Mutation SNP G G T rs770360894 C3L-00095_T C3L-00095_N G G c.419C>A p.Thr140Lys p.T140K ENST00000586582 6/17 172 159 13 243 243 0 strelka-varscan-mutect SEMA6B,missense_variant,p.Thr140Lys,ENST00000586582,NM_032108.3;SEMA6B,missense_variant,p.Thr140Lys,ENST00000586965,; T ENST00000586582 Transcript missense_variant 730/3986 419/2667 140/888 T/K aCg/aAg rs770360894,COSM5446732 1 -1 SEMA6B HGNC HGNC:10739 protein_coding YES CCDS12131.1 ENSP00000467290 Q9H3T3 UPI000004BA6B NM_032108.3 deleterious(0.04) 6/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF10,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770360894 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 4556040 4556040 G T 1 0 0 0 0 1 0 0 0 14316 1145 40 1 1 SEMA6B 19 4556040 Missense_Mutation SNP G C3L-00095_T 1331145 4556040 54061576 703 3912 ACSBG2 0 . GRCh38 19 6147515 6147515 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.137G>A p.Gly46Asp p.G46D ENST00000586696 3/15 489 445 44 568 568 0 strelka-varscan-mutect ACSBG2,missense_variant,p.Gly46Asp,ENST00000586696,NM_001289177.1,NM_001289179.1,NM_030924.4;ACSBG2,missense_variant,p.Gly46Asp,ENST00000591403,NM_001289178.1;ACSBG2,missense_variant,p.Gly46Asp,ENST00000591738,;ACSBG2,missense_variant,p.Gly46Asp,ENST00000589401,;ACSBG2,missense_variant,p.Gly46Asp,ENST00000588722,;ACSBG2,5_prime_UTR_variant,,ENST00000588304,NM_001321384.1;ACSBG2,5_prime_UTR_variant,,ENST00000588485,NM_001289180.1;RFX2,intron_variant,,ENST00000592883,;ACSBG2,missense_variant,p.Gly46Asp,ENST00000592677,;ACSBG2,missense_variant,p.Gly46Asp,ENST00000587617,; A ENST00000586696 Transcript missense_variant 413/2739 137/2001 46/666 G/D gGc/gAc 1 1 ACSBG2 HGNC HGNC:24174 protein_coding YES CCDS12159.1 ENSP00000465589 Q5FVE4 A0A140VJD4 UPI00001414E6 NM_001289177.1,NM_001289179.1,NM_030924.4 deleterious(0.02) 3/15 hmmpanther:PTHR24096:SF38,hmmpanther:PTHR24096 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 6147515 6147515 G A 1 0 0 0 0 1 0 0 0 216 1203 42 3 3 ACSBG2 19 6147515 Missense_Mutation SNP G C3L-00095_T 1591475 6147515 52470101 704 3913 ADGRE1 0 . GRCh38 19 6904064 6904064 + Silent SNP A A C novel C3L-00095_T C3L-00095_N A A c.831A>C p.= p.S277S ENST00000312053 8/21 216 192 24 303 303 0 strelka-varscan-mutect ADGRE1,synonymous_variant,p.=,ENST00000312053,NM_001974.4;ADGRE1,synonymous_variant,p.=,ENST00000381404,NM_001256252.1;ADGRE1,synonymous_variant,p.=,ENST00000250572,NM_001256253.1;ADGRE1,synonymous_variant,p.=,ENST00000381407,NM_001256254.1;ADGRE1,intron_variant,,ENST00000450315,NM_001256255.1;ADGRE1,intron_variant,,ENST00000595026,;ADGRE1,downstream_gene_variant,,ENST00000601198,; C ENST00000312053 Transcript synonymous_variant 868/3128 831/2661 277/886 S tcA/tcC 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 8/21 PROSITE_profiles:PS50026,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 10 6904064 6904064 A C 1 0 0 0 0 0 0 0 1 359 117 5 5 5 ADGRE1 19 6904064 Silent SNP A C3L-00095_T 756549 6904064 51713552 705 3914 KANK3 0 . GRCh38 19 8333858 8333858 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.221G>T p.Gly74Val p.G74V ENST00000610351 1/4 114 107 7 120 120 0 strelka-mutect KANK3,missense_variant,p.Gly74Val,ENST00000610351,;KANK3,intron_variant,,ENST00000330915,NM_198471.2;KANK3,intron_variant,,ENST00000593649,;KANK3,intron_variant,,ENST00000595639,;KANK3,downstream_gene_variant,,ENST00000593331,; A ENST00000610351 Transcript missense_variant 573/1191 221/639 74/212 G/V gGt/gTt 1 -1 KANK3 HGNC HGNC:24796 protein_coding ENSP00000484877 A0A087X2C6 UPI0004E4CC7C deleterious_low_confidence(0) 1/4 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -13.81342 0.9999995 1 1 1 0 A 3 1 10 8333858 8333858 C A 1 0 0 0 0 1 0 0 0 7887 507 18 2 2 KANK3 19 8333858 Missense_Mutation SNP C C3L-00095_T 1429794 8333858 50283758 706 3915 MUC16 0 . GRCh38 19 8861050 8861050 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.42866C>A p.Ser14289Ter p.S14289* ENST00000397910 78/84 181 169 12 226 226 0 strelka-varscan-mutect MUC16,stop_gained,p.Ser14289Ter,ENST00000397910,NM_024690.2;MUC16,stop_gained,p.Ser1112Ter,ENST00000599436,;MUC16,downstream_gene_variant,,ENST00000596956,;MUC16,stop_gained,p.Ser1107Ter,ENST00000601404,;MUC16,3_prime_UTR_variant,,ENST00000596768,; T ENST00000397910 Transcript stop_gained 43070/43816 42866/43524 14289/14507 S/* tCa/tAa 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 78/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Superfamily_domains:0047452 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 8861050 8861050 G T 1 0 0 0 0 0 1 0 0 9972 1294 45 2 2 MUC16 19 8861050 Nonsense_Mutation SNP G C3L-00095_T 527192 8861050 49756566 707 3916 COL5A3 0 . GRCh38 19 9960792 9960792 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.4950C>T p.= p.S1650S ENST00000264828 66/67 262 231 31 361 361 0 strelka-varscan-mutect COL5A3,synonymous_variant,p.=,ENST00000264828,NM_015719.3; A ENST00000264828 Transcript synonymous_variant 5036/6174 4950/5238 1650/1745 S tcC/tcT 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 66/67 PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516,Pfam_domain:PF01410,SMART_domains:SM00038,PD002078 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 9960792 9960792 G A 1 0 0 0 0 0 0 0 1 3487 987 35 3 3 COL5A3 19 9960792 Silent SNP G C3L-00095_T 1099742 9960792 48656824 708 3917 RDH8 0 . GRCh38 19 10013485 10013485 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.48G>T p.Arg16Ser p.R16S ENST00000591589 1/6 109 97 12 172 171 1 strelka-varscan-mutect RDH8,missense_variant,p.Arg16Ser,ENST00000591589,NM_015725.2;COL5A3,upstream_gene_variant,,ENST00000264828,NM_015719.3;RDH8,upstream_gene_variant,,ENST00000589570,; T ENST00000591589 Transcript missense_variant 237/1715 48/996 16/331 R/S agG/agT 1 1 RDH8 HGNC HGNC:14423 protein_coding YES CCDS12223.2 ENSP00000466058 K7ELF7 UPI000059D661 NM_015725.2 deleterious_low_confidence(0.03) 1/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 10013485 10013485 G T 1 0 0 0 0 1 0 0 0 13365 1223 43 2 2 RDH8 19 10013485 Missense_Mutation SNP G C3L-00095_T 52693 10013485 48604131 709 3918 TYK2 0 . GRCh38 19 10362364 10362364 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.1569C>T p.= p.F523F ENST00000525621 11/25 185 169 16 248 248 0 strelka-varscan-mutect TYK2,synonymous_variant,p.=,ENST00000525621,NM_003331.4;TYK2,synonymous_variant,p.=,ENST00000264818,;TYK2,synonymous_variant,p.=,ENST00000524462,;TYK2,synonymous_variant,p.=,ENST00000529370,;TYK2,downstream_gene_variant,,ENST00000525220,;TYK2,upstream_gene_variant,,ENST00000533334,;TYK2,upstream_gene_variant,,ENST00000529412,;TYK2,upstream_gene_variant,,ENST00000531620,; A ENST00000525621 Transcript synonymous_variant 2051/4347 1569/3564 523/1187 F ttC/ttT 1 -1 TYK2 HGNC HGNC:12440 protein_coding YES CCDS12236.1 ENSP00000431885 P29597 A0A024R7E4 UPI000013D573 NM_003331.4 11/25 Gene3D:3.30.505.10,PIRSF_domain:PIRSF000636,Prints_domain:PR01827,SMART_domains:SM00252,Superfamily_domains:SSF55550 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 10362364 10362364 G A 1 0 0 0 0 0 0 0 1 17325 1165 41 3 3 TYK2 19 10362364 Silent SNP G C3L-00095_T 348879 10362364 48255252 710 3919 CARM1 0 . GRCh38 19 10909209 10909209 + Splice_Site SNP T T A novel C3L-00095_T C3L-00095_N T T c.558+2T>A p.X186_splice ENST00000327064 115 108 7 167 167 0 strelka-varscan-mutect CARM1,splice_donor_variant,,ENST00000327064,NM_199141.1;CARM1,splice_donor_variant,,ENST00000344150,;CARM1,downstream_gene_variant,,ENST00000588947,;CARM1,splice_donor_variant,,ENST00000586221,;CARM1,splice_donor_variant,,ENST00000590699,;CARM1,splice_donor_variant,,ENST00000589693,;CARM1,splice_donor_variant,,ENST00000590039,; A ENST00000327064 Transcript splice_donor_variant -/3330 558/1827 186/608 1 1 CARM1 HGNC HGNC:23393 protein_coding YES CCDS12250.1 ENSP00000325690 Q86X55 UPI000004B825 NM_199141.1 4/15 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 10909209 10909209 T A 1 0 0 0 0 0 0 1 0 2351 1710 59 4 4 CARM1 19 10909209 Splice_Site SNP T C3L-00095_T 546845 10909209 47708407 711 3920 DOCK6 0 . GRCh38 19 11215800 11215800 + Splice_Site SNP C C A novel C3L-00095_T C3L-00095_N C C c.4021+1G>T p.X1341_splice ENST00000294618 126 116 10 171 171 0 strelka-varscan-mutect DOCK6,splice_donor_variant,,ENST00000294618,NM_020812.3;DOCK6,splice_donor_variant,,ENST00000587656,;CTC-510F12.2,intron_variant,,ENST00000588634,;DOCK6,non_coding_transcript_exon_variant,,ENST00000588429,;DOCK6,downstream_gene_variant,,ENST00000592403,; A ENST00000294618 Transcript splice_donor_variant -/6358 4021/6144 1341/2047 1 -1 DOCK6 HGNC HGNC:19189 protein_coding YES CCDS45975.1 ENSP00000294618 Q96HP0 UPI000059D66F NM_020812.3 31/47 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 10 11215800 11215800 C A 1 0 0 0 0 0 0 1 0 4506 521 18 2 2 DOCK6 19 11215800 Splice_Site SNP C C3L-00095_T 306591 11215800 47401816 712 3921 ADGRE3 0 . GRCh38 19 14641613 14641613 + Nonsense_Mutation SNP C C A rs747402538 C3L-00095_T C3L-00095_N C C c.1054G>T p.Glu352Ter p.E352* ENST00000253673 10/16 217 187 30 322 322 0 strelka-varscan-mutect ADGRE3,stop_gained,p.Glu300Ter,ENST00000344373,NM_001289158.1;ADGRE3,stop_gained,p.Glu352Ter,ENST00000253673,NM_032571.4;ADGRE3,stop_gained,p.Glu137Ter,ENST00000599900,;ADGRE3,stop_gained,p.Glu226Ter,ENST00000443157,NM_001289159.1; A ENST00000253673 Transcript stop_gained 1155/2254 1054/1959 352/652 E/* Gag/Tag rs747402538 1 -1 ADGRE3 HGNC HGNC:23647 protein_coding YES CCDS12315.1 ENSP00000253673 Q9BY15 UPI0000456C29 NM_032571.4 10/16 hmmpanther:PTHR12011:SF328,hmmpanther:PTHR12011,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS rs747402538 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 14641613 14641613 C A 1 0 0 0 0 0 1 0 0 361 869 30 2 2 ADGRE3 19 14641613 Nonsense_Mutation SNP C C3L-00095_T 3425813 14641613 43976003 713 3922 SLC1A6 0 . GRCh38 19 14956709 14956709 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.936G>A p.Trp312Ter p.W312* ENST00000221742 6/9 67 59 8 84 84 0 strelka-varscan-mutect SLC1A6,stop_gained,p.Trp248Ter,ENST00000430939,;SLC1A6,stop_gained,p.Trp312Ter,ENST00000221742,NM_005071.2;SLC1A6,intron_variant,,ENST00000600144,;SLC1A6,downstream_gene_variant,,ENST00000598504,NM_001272087.1;SLC1A6,downstream_gene_variant,,ENST00000544886,NM_001272088.1; T ENST00000221742 Transcript stop_gained,splice_region_variant 944/1719 936/1695 312/564 W/* tgG/tgA 1 -1 SLC1A6 HGNC HGNC:10944 protein_coding YES CCDS12321.1 ENSP00000221742 P48664 UPI0000129B1A NM_005071.2 6/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR11958:SF67,hmmpanther:PTHR11958,Pfam_domain:PF00375,Gene3D:2nwlC00,Superfamily_domains:0053221,Prints_domain:PR00173 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.16903 1 1 1 1 0 T 4 4 10 14956709 14956709 C T 1 0 0 0 0 0 1 0 0 14702 521 18 3 3 SLC1A6 19 14956709 Nonsense_Mutation SNP C C3L-00095_T 315096 14956709 43660907 714 3923 CYP4F3 0 . GRCh38 19 15649210 15649210 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.576T>G p.Phe192Leu p.F192L ENST00000221307 6/13 263 246 17 374 374 0 strelka-varscan-mutect CYP4F3,missense_variant,p.Phe192Leu,ENST00000221307,NM_000896.2;CYP4F3,missense_variant,p.Phe192Leu,ENST00000591058,NM_001199208.1;CYP4F3,missense_variant,p.Phe192Leu,ENST00000586182,NM_001199209.1;CYP4F3,missense_variant,p.Phe192Leu,ENST00000585846,;CYP4F3,missense_variant,p.Phe192Leu,ENST00000620621,;CYP4F3,3_prime_UTR_variant,,ENST00000587360,;CYP4F3,non_coding_transcript_exon_variant,,ENST00000592279,;CYP4F3,upstream_gene_variant,,ENST00000592424,;CYP4F3,downstream_gene_variant,,ENST00000609670,; G ENST00000221307 Transcript missense_variant 623/5050 576/1563 192/520 F/L ttT/ttG 1 1 CYP4F3 HGNC HGNC:2646 protein_coding YES CCDS12332.1 ENSP00000221307 Q08477 A0A024R7J8 UPI0000052BE3 NM_000896.2 deleterious(0.04) 6/13 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF25,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 15649210 15649210 T G 1 0 0 0 0 1 0 0 0 3993 1809 63 5 5 CYP4F3 19 15649210 Missense_Mutation SNP T C3L-00095_T 692501 15649210 42968406 715 3924 OR10H5 0 . GRCh38 19 15794286 15794286 + Missense_Mutation SNP C C A rs142693914 C3L-00095_T C3L-00095_N C C c.238C>A p.Arg80Ser p.R80S ENST00000308940 1/1 81 73 8 153 153 0 varscan-mutect OR10H5,missense_variant,p.Arg80Ser,ENST00000308940,NM_001004466.1; A ENST00000308940 Transcript missense_variant 336/1132 238/948 80/315 R/S Cgc/Agc rs142693914 1 1 OR10H5 HGNC HGNC:15389 protein_coding YES CCDS32940.1 ENSP00000310704 Q8NGA6 A0A126GWE9 UPI0000041C8F NM_001004466.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF122,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs142693914 . 0 207 0 2 0 0 0 0 -13.34581 0.9999998 1 1 1 0 A 3 1 10 15794286 15794286 C A 1 0 0 0 0 1 0 0 0 10986 768 27 1 1 OR10H5 19 15794286 Missense_Mutation SNP C C3L-00095_T 145076 15794286 42823330 716 3925 AP1M1 0 . GRCh38 19 16234430 16234430 + Nonsense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1303C>T p.Gln435Ter p.Q435* ENST00000444449 13/13 199 182 17 256 256 0 strelka-varscan-mutect AP1M1,stop_gained,p.Gln423Ter,ENST00000291439,NM_032493.3;AP1M1,stop_gained,p.Gln435Ter,ENST00000444449,NM_001130524.1;AP1M1,stop_gained,p.Gln351Ter,ENST00000590756,;AP1M1,stop_gained,p.Gln370Ter,ENST00000429941,;AP1M1,intron_variant,,ENST00000586543,;AP1M1,non_coding_transcript_exon_variant,,ENST00000592703,; T ENST00000444449 Transcript stop_gained 1396/2311 1303/1308 435/435 Q/* Cag/Tag 1 1 AP1M1 HGNC HGNC:13667 protein_coding YES CCDS46008.1 ENSP00000388996 Q9BXS5 UPI000051DDEE NM_001130524.1 13/13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 16234430 16234430 C T 1 0 0 0 0 0 1 0 0 850 595 21 3 3 AP1M1 19 16234430 Nonsense_Mutation SNP C C3L-00095_T 440144 16234430 42383186 717 3926 UNC13A 0 . GRCh38 19 17630147 17630147 + Nonsense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.3667A>T p.Lys1223Ter p.K1223* ENST00000519716 30/44 112 103 9 142 142 0 strelka-varscan-mutect UNC13A,stop_gained,p.Lys1223Ter,ENST00000519716,NM_001080421.2;UNC13A,stop_gained,p.Lys1223Ter,ENST00000551649,;UNC13A,stop_gained,p.Lys1223Ter,ENST00000552293,;UNC13A,stop_gained,p.Lys1221Ter,ENST00000550896,;UNC13A,upstream_gene_variant,,ENST00000601528,; A ENST00000519716 Transcript stop_gained,splice_region_variant 3667/9838 3667/5112 1223/1703 K/* Aag/Tag 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 30/44 PROSITE_profiles:PS51258,hmmpanther:PTHR10480 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 17630147 17630147 T A 1 0 0 0 0 0 1 0 0 17508 1826 63 4 4 UNC13A 19 17630147 Nonsense_Mutation SNP T C3L-00095_T 1395717 17630147 40987469 718 3927 ZNF486 0 . GRCh38 19 20197998 20197998 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1288G>A p.Gly430Arg p.G430R ENST00000335117 4/4 348 319 29 320 320 0 strelka-varscan-mutect ZNF486,missense_variant,p.Gly430Arg,ENST00000335117,NM_052852.3;CTC-260E6.6,intron_variant,,ENST00000585498,;CTC-260E6.6,intron_variant,,ENST00000593655,;CTC-260E6.6,intron_variant,,ENST00000586657,; A ENST00000335117 Transcript missense_variant 1345/3837 1288/1392 430/463 G/R Gga/Aga 1 1 ZNF486 HGNC HGNC:20807 protein_coding YES CCDS46029.1 ENSP00000335042 Q96H40 UPI00002376E8 NM_052852.3 deleterious(0.05) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF95,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 20197998 20197998 G A 1 0 0 0 0 1 0 0 0 18511 1349 47 3 3 ZNF486 19 20197998 Missense_Mutation SNP G C3L-00095_T 2567851 20197998 38419618 719 3928 ZNF43 0 . GRCh38 19 21809109 21809109 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.955G>T p.Gly319Ter p.G319* ENST00000357491 4/4 312 285 27 258 258 0 strelka-varscan-mutect ZNF43,stop_gained,p.Gly304Ter,ENST00000594012,NM_001256649.1;ZNF43,stop_gained,p.Gly319Ter,ENST00000357491,NM_001256653.1;ZNF43,stop_gained,p.Gly304Ter,ENST00000595461,NM_001256648.1;ZNF43,stop_gained,p.Gly304Ter,ENST00000598381,NM_001256650.1;ZNF43,stop_gained,p.Gly310Ter,ENST00000354959,NM_003423.3;ZNF43,downstream_gene_variant,,ENST00000599906,;ZNF43,downstream_gene_variant,,ENST00000598288,;ZNF43,downstream_gene_variant,,ENST00000596899,; A ENST00000357491 Transcript stop_gained 1089/5249 955/2457 319/818 G/* Gga/Tga 1 -1 ZNF43 HGNC HGNC:13109 protein_coding YES CCDS74321.1 ENSP00000350085 A0A087WSW2 UPI00002038CF NM_001256653.1 4/4 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF344,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 4 1 10 21809109 21809109 C A 1 0 0 0 0 0 1 0 0 18475 603 21 2 2 ZNF43 19 21809109 Nonsense_Mutation SNP C C3L-00095_T 1611111 21809109 36808507 720 3929 ZNF208 0 . GRCh38 19 21973910 21973910 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1124G>T p.Gly375Val p.G375V ENST00000397126 4/4 315 285 30 286 286 0 varscan-mutect ZNF208,missense_variant,p.Gly375Val,ENST00000397126,NM_007153.3;ZNF208,missense_variant,p.Gly375Val,ENST00000609966,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,; A ENST00000397126 Transcript missense_variant 1273/3992 1124/3843 375/1280 G/V gGc/gTc 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF103,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS rs1160600789 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 21973910 21973910 C A 1 0 0 0 0 1 0 0 0 18343 739 26 2 2 ZNF208 19 21973910 Missense_Mutation SNP C C3L-00095_T 164801 21973910 36643706 721 3930 ZNF492 0 . GRCh38 19 22665123 22665123 + Missense_Mutation SNP C C A rs776673156 C3L-00095_T C3L-00095_N C C c.1454C>A p.Ala485Asp p.A485D ENST00000456783 4/4 252 233 19 231 231 0 varscan-mutect ZNF492,missense_variant,p.Ala485Asp,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; A ENST00000456783 Transcript missense_variant 1698/4245 1454/1596 485/531 A/D gCc/gAc rs776673156 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs776673156 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 22665123 22665123 C A 1 0 0 0 0 1 0 0 0 18516 739 26 2 2 ZNF492 19 22665123 Missense_Mutation SNP C C3L-00095_T 691213 22665123 35952493 722 3931 VSTM2B 0 . GRCh38 19 29529947 29529947 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.426C>A p.= p.A142A ENST00000335523 4/5 373 349 24 525 525 0 strelka-varscan-mutect VSTM2B,synonymous_variant,p.=,ENST00000335523,NM_001146339.1;CTC-525D6.1,upstream_gene_variant,,ENST00000582581,;CTC-525D6.2,upstream_gene_variant,,ENST00000579268,;CTC-525D6.1,upstream_gene_variant,,ENST00000577849,; A ENST00000335523 Transcript synonymous_variant 511/1488 426/858 142/285 A gcC/gcA 1 1 VSTM2B HGNC HGNC:33595 protein_coding YES CCDS46034.1 ENSP00000335038 A6NLU5 UPI00001D8158 NM_001146339.1 4/5 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF23,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 29529947 29529947 C A 1 0 0 0 0 0 0 0 1 17781 610 22 2 2 VSTM2B 19 29529947 Silent SNP C C3L-00095_T 6864824 29529947 29087669 723 3932 C19orf12 0 . GRCh38 19 29708327 29708327 + Frame_Shift_Del DEL C C - novel C3L-00095_T C3L-00095_N C C c.120delG p.Lys41ArgfsTer32 p.K41Rfs*32 ENST00000392278 2/3 292 267 25 446 446 0 sindel-varindel-pindel C19orf12,frameshift_variant,p.Lys30ArgfsTer32,ENST00000614091,NM_001256047.1;C19orf12,frameshift_variant,p.Lys30ArgfsTer32,ENST00000323670,NM_031448.4;C19orf12,frameshift_variant,p.Lys30ArgfsTer32,ENST00000592153,NM_001256046.1;C19orf12,frameshift_variant,p.Lys41ArgfsTer32,ENST00000392278,NM_001031726.3;C19orf12,frameshift_variant,p.Lys30ArgfsTer32,ENST00000591243,;C19orf12,intron_variant,,ENST00000623113,NM_001282929.1;C19orf12,intron_variant,,ENST00000392276,NM_001282930.1,NM_001282931.1;C19orf12,intron_variant,,ENST00000392275,;C19orf12,frameshift_variant,p.Lys30ArgfsTer28,ENST00000342680,; - ENST00000392278 Transcript frameshift_variant 247/895 120/459 40/152 G/X ggG/gg 1 -1 C19orf12 HGNC HGNC:25443 protein_coding YES CCDS42542.1 ENSP00000376103 Q9NSK7 UPI0000DB2738 NM_001031726.3 2/3 hmmpanther:PTHR31493 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 29708327 29708327 C - 1 0 1 0 1 0 0 0 0 1903 842 30 0 0 C19orf12 19 29708327 Frame_Shift_Del DEL C C3L-00095_T 178380 29708327 28909289 724 3933 ZNF536 0 . GRCh38 19 30443959 30443959 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.397C>A p.Pro133Thr p.P133T ENST00000355537 2/5 547 517 30 765 764 1 strelka-varscan-mutect ZNF536,missense_variant,p.Pro133Thr,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Pro133Thr,ENST00000585628,;ZNF536,missense_variant,p.Pro133Thr,ENST00000591488,; A ENST00000355537 Transcript missense_variant 544/4945 397/3903 133/1300 P/T Cca/Aca 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated(0.23) 2/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1465546066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 30443959 30443959 C A 1 0 0 0 0 1 0 0 0 18547 623 22 2 2 ZNF536 19 30443959 Missense_Mutation SNP C C3L-00095_T 735632 30443959 28173657 725 3934 USF2 0 . GRCh38 19 35270529 35270529 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.512C>A p.Pro171Gln p.P171Q ENST00000222305 5/10 95 88 7 144 143 1 strelka-varscan-mutect USF2,missense_variant,p.Pro171Gln,ENST00000222305,NM_003367.2;USF2,missense_variant,p.Pro171Gln,ENST00000595068,;USF2,missense_variant,p.Pro104Gln,ENST00000343550,NM_207291.1;USF2,missense_variant,p.Pro169Gln,ENST00000594064,;USF2,missense_variant,p.Pro27Gln,ENST00000599471,;USF2,missense_variant,p.Pro49Gln,ENST00000596380,;USF2,intron_variant,,ENST00000379134,;LSR,downstream_gene_variant,,ENST00000602122,NM_001260489.1;LSR,downstream_gene_variant,,ENST00000621372,NM_205834.3;LSR,downstream_gene_variant,,ENST00000361790,;LSR,downstream_gene_variant,,ENST00000354900,NM_015925.6;LSR,downstream_gene_variant,,ENST00000360798,NM_205835.3;LSR,downstream_gene_variant,,ENST00000605618,;LSR,downstream_gene_variant,,ENST00000347609,;LSR,downstream_gene_variant,,ENST00000427250,NM_001260490.1;USF2,downstream_gene_variant,,ENST00000598058,;USF2,upstream_gene_variant,,ENST00000599625,;LSR,downstream_gene_variant,,ENST00000599658,;USF2,upstream_gene_variant,,ENST00000600341,;USF2,missense_variant,p.Pro13Gln,ENST00000597671,;USF2,non_coding_transcript_exon_variant,,ENST00000607959,;USF2,downstream_gene_variant,,ENST00000602164,;LSR,downstream_gene_variant,,ENST00000597446,;USF2,downstream_gene_variant,,ENST00000593708,; A ENST00000222305 Transcript missense_variant 549/1634 512/1041 171/346 P/Q cCa/cAa 1 1 USF2 HGNC HGNC:12594 protein_coding YES CCDS12452.1 ENSP00000222305 Q15853 UPI0000137E4A NM_003367.2 deleterious(0.01) 5/10 hmmpanther:PTHR12565:SF11,hmmpanther:PTHR12565 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -11.18365 0.9999997 1 1 1 0 A 3 1 10 35270529 35270529 C A 1 0 0 0 0 1 0 0 0 17566 594 21 2 2 USF2 19 35270529 Missense_Mutation SNP C C3L-00095_T 4826570 35270529 23347087 726 3935 SPRED3 0 . GRCh38 19 38395786 38395786 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.874G>C p.Glu292Gln p.E292Q ENST00000338502 5/5 72 63 9 100 99 1 strelka-varscan-mutect SPRED3,missense_variant,p.Glu292Gln,ENST00000338502,NM_001042522.2;SPRED3,missense_variant,p.Glu336Gln,ENST00000587013,;SPRED3,missense_variant,p.Glu292Gln,ENST00000586301,;SPRED3,downstream_gene_variant,,ENST00000587947,;SPRED3,downstream_gene_variant,,ENST00000587564,;SPRED3,downstream_gene_variant,,ENST00000590962,;SPRED3,downstream_gene_variant,,ENST00000586958,; C ENST00000338502 Transcript missense_variant 977/4778 874/1233 292/410 E/Q Gag/Cag 1 1 SPRED3 HGNC HGNC:31041 protein_coding YES CCDS42560.1 ENSP00000345405 Q2MJR0 UPI000040BCE3 NM_001042522.2 tolerated(0.53) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11202:SF19,hmmpanther:PTHR11202 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.67416 1 1 1 1 0 C 3 2 10 38395786 38395786 G C 1 0 0 0 0 1 0 0 0 15448 1175 41 4 4 SPRED3 19 38395786 Missense_Mutation SNP G C3L-00095_T 3125257 38395786 20221830 727 3936 CYP2S1 0 . GRCh38 19 41205963 41205963 + Silent SNP G G T rs754290434 C3L-00095_T C3L-00095_N G G c.1170G>T p.= p.T390T ENST00000310054 8/9 80 69 11 82 82 0 strelka-varscan-mutect CYP2S1,missense_variant,p.Arg29Leu,ENST00000593890,;CYP2S1,synonymous_variant,p.=,ENST00000310054,NM_030622.7;CYP2S1,synonymous_variant,p.=,ENST00000597754,;CYP2S1,downstream_gene_variant,,ENST00000600561,;CYP2S1,3_prime_UTR_variant,,ENST00000593545,;CYP2S1,3_prime_UTR_variant,,ENST00000595590,; T ENST00000310054 Transcript synonymous_variant 1386/2782 1170/1515 390/504 T acG/acT rs754290434 1 1 CYP2S1 HGNC HGNC:15654 protein_coding YES CCDS12573.1 ENSP00000308032 Q96SQ9 UPI00000467C9 NM_030622.7 8/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF23,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs754290434 . 0 207 3 0 0 0 0 0 -19.99996 1 1 1 1 0 T 2 4 10 41205963 41205963 G T 1 0 0 0 0 0 0 0 1 3977 1130 39 1 1 CYP2S1 19 41205963 Silent SNP G C3L-00095_T 2810177 41205963 17411653 728 3937 AXL 0 . GRCh38 19 41230966 41230966 + Splice_Site DEL G G - novel C3L-00095_T C3L-00095_N G G c.588delG p.Leu197Ter p.X196_splice ENST00000301178 152 130 22 245 245 0 sindel-varindel-pindel AXL,splice_acceptor_variant,p.Leu197Ter,ENST00000301178,NM_021913.4;AXL,splice_acceptor_variant,p.Leu197Ter,ENST00000359092,NM_001699.5;AXL,splice_acceptor_variant,,ENST00000593513,NM_001278599.1;AXL,splice_acceptor_variant,,ENST00000599659,; - ENST00000301178 Transcript splice_acceptor_variant -/4737 588/2685 196/894 1 1 AXL HGNC HGNC:905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 UPI000014319B NM_021913.4 4/19 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 10 41230966 41230966 G - 1 0 1 0 1 0 0 1 0 1395 1014 35 0 0 AXL 19 41230966 Splice_Site DEL G C3L-00095_T 25003 41230966 17386650 729 3938 ETHE1 0 . GRCh38 19 43527114 43527114 + Missense_Mutation SNP G G T rs778916161 C3L-00095_T C3L-00095_N G G c.64C>A p.Pro22Thr p.P22T ENST00000292147 1/7 279 241 38 380 380 0 strelka-varscan-mutect ETHE1,missense_variant,p.Pro22Thr,ENST00000600651,;ETHE1,missense_variant,p.Pro22Thr,ENST00000292147,NM_014297.3;ZNF575,intron_variant,,ENST00000458714,;ETHE1,missense_variant,p.Pro22Thr,ENST00000598330,;ETHE1,missense_variant,p.Pro22Thr,ENST00000594342,;ETHE1,missense_variant,p.Pro22Thr,ENST00000602138,;ETHE1,non_coding_transcript_exon_variant,,ENST00000595115,; T ENST00000292147 Transcript missense_variant 131/963 64/765 22/254 P/T Ccc/Acc rs778916161 1 -1 ETHE1 HGNC HGNC:23287 protein_coding YES CCDS12622.1 ENSP00000292147 O95571 A0A0S2Z5B3 UPI0000073C7C NM_014297.3 tolerated(0.2) 1/7 hmmpanther:PTHR11935:SF102,hmmpanther:PTHR11935 MODERATE 1 SNV 1 1 PASS rs778916161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 43527114 43527114 G T 1 0 0 0 0 1 0 0 0 5135 1232 43 2 2 ETHE1 19 43527114 Missense_Mutation SNP G C3L-00095_T 2296148 43527114 15090502 730 3939 IRGC 0 . GRCh38 19 43719271 43719271 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.713C>G p.Ser238Cys p.S238C ENST00000244314 2/2 38 33 5 37 37 0 strelka-varscan-mutect IRGC,missense_variant,p.Ser238Cys,ENST00000244314,NM_019612.3;IRGC,missense_variant,p.Ser275Cys,ENST00000596627,; G ENST00000244314 Transcript missense_variant 912/1662 713/1392 238/463 S/C tCc/tGc 1 1 IRGC HGNC HGNC:28835 protein_coding YES CCDS12629.1 ENSP00000244314 Q6NXR0 J7NNX4 UPI000011DFC0 NM_019612.3 deleterious(0.01) 2/2 Pfam_domain:PF05049,hmmpanther:PTHR32341,hmmpanther:PTHR32341:SF7,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -13.04279 0.9999999 1 1 1 0 G 3 3 10 43719271 43719271 C G 1 0 0 0 0 1 0 0 0 7745 855 30 4 4 IRGC 19 43719271 Missense_Mutation SNP C C3L-00095_T 192157 43719271 14898345 731 3940 ZNF112 0 . GRCh38 19 44329564 44329564 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.611A>G p.Lys204Arg p.K204R ENST00000337401 5/5 131 108 23 142 142 0 strelka-varscan-mutect ZNF112,missense_variant,p.Lys198Arg,ENST00000354340,NM_013380.3;ZNF112,missense_variant,p.Lys204Arg,ENST00000337401,NM_001083335.1;ZNF112,missense_variant,p.Lys137Arg,ENST00000587909,;ZNF112,downstream_gene_variant,,ENST00000590687,;CTC-512J12.6,downstream_gene_variant,,ENST00000588212,;ZNF112,downstream_gene_variant,,ENST00000588057,;ZNF112,downstream_gene_variant,,ENST00000592151,; C ENST00000337401 Transcript missense_variant 700/3321 611/2742 204/913 K/R aAa/aGa 1 -1 ZNF112 HGNC HGNC:12892 protein_coding YES CCDS54276.1 ENSP00000337081 Q9UJU3 UPI000006EC70 NM_001083335.1 tolerated(0.27) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 44329564 44329564 T C 1 0 0 0 0 1 0 0 0 18296 1841 64 5 5 ZNF112 19 44329564 Missense_Mutation SNP T C3L-00095_T 610293 44329564 14288052 732 3941 IRF2BP1 0 . GRCh38 19 45885076 45885076 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.699A>T p.= p.L233L ENST00000302165 1/1 267 209 58 278 278 0 strelka-varscan-mutect IRF2BP1,synonymous_variant,p.=,ENST00000302165,NM_015649.2;MYPOP,downstream_gene_variant,,ENST00000322217,NM_001012643.3; A ENST00000302165 Transcript synonymous_variant 1095/2564 699/1755 233/584 L ctA/ctT 1 -1 IRF2BP1 HGNC HGNC:21728 protein_coding YES CCDS12678.1 ENSP00000307265 Q8IU81 UPI00000747C7 NM_015649.2 1/1 hmmpanther:PTHR10816 LOW SNV 1 PASS rs1370881778 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 45885076 45885076 T A 1 0 0 0 0 0 0 0 1 7735 1625 57 4 4 IRF2BP1 19 45885076 Silent SNP T C3L-00095_T 1555512 45885076 12732540 733 3942 SLC8A2 0 . GRCh38 19 47430228 47430228 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.2627G>A p.Arg876Gln p.R876Q ENST00000236877 10/10 233 206 27 324 324 0 strelka-varscan-mutect SLC8A2,missense_variant,p.Arg876Gln,ENST00000236877,NM_015063.2;SLC8A2,missense_variant,p.Arg632Gln,ENST00000542837,;SLC8A2,non_coding_transcript_exon_variant,,ENST00000539381,;SLC8A2,downstream_gene_variant,,ENST00000601757,;SLC8A2,downstream_gene_variant,,ENST00000600576,; T ENST00000236877 Transcript missense_variant 3023/5234 2627/2766 876/921 R/Q cGg/cAg 1 -1 SLC8A2 HGNC HGNC:11069 protein_coding YES CCDS33065.1 ENSP00000236877 Q9UPR5 UPI000012FC49 NM_015063.2 deleterious(0) 10/10 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF8,TIGRFAM_domain:TIGR00845,Pfam_domain:PF01699 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 47430228 47430228 C T 1 0 0 0 0 1 0 0 0 14990 652 23 1 1 SLC8A2 19 47430228 Missense_Mutation SNP C C3L-00095_T 1545152 47430228 11187388 734 3943 CCDC155 0 . GRCh38 19 49417190 49417190 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1471G>T p.Val491Leu p.V491L ENST00000447857 19/20 138 116 22 202 202 0 strelka-varscan-mutect CCDC155,missense_variant,p.Val491Leu,ENST00000447857,NM_144688.4;CCDC155,missense_variant,p.Val453Leu,ENST00000600570,;CCDC155,downstream_gene_variant,,ENST00000593362,; T ENST00000447857 Transcript missense_variant 1676/2378 1471/1689 491/562 V/L Gtg/Ttg 1 1 CCDC155 HGNC HGNC:26520 protein_coding YES CCDS46140.1 ENSP00000404220 Q8N6L0 UPI000006F690 NM_144688.4 deleterious_low_confidence(0.02) 19/20 hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF341 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 49417190 49417190 G T 1 0 0 0 0 1 0 0 0 2476 1261 44 2 2 CCDC155 19 49417190 Missense_Mutation SNP G C3L-00095_T 1986962 49417190 9200426 735 3944 CPT1C 0 . GRCh38 19 49713543 49713543 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.2350T>G p.Cys784Gly p.C784G ENST00000392518 20/20 176 150 26 195 195 0 strelka-varscan-mutect CPT1C,splice_donor_variant,,ENST00000597099,;CPT1C,missense_variant,p.Cys784Gly,ENST00000392518,NM_001199752.2;CPT1C,missense_variant,p.Cys773Gly,ENST00000405931,NM_001136052.2;CPT1C,missense_variant,p.Cys784Gly,ENST00000323446,NM_152359.2;CPT1C,missense_variant,p.Cys784Gly,ENST00000598293,NM_001199753.1;CPT1C,missense_variant,p.Cys317Gly,ENST00000595031,;CPT1C,non_coding_transcript_exon_variant,,ENST00000595901,;CPT1C,non_coding_transcript_exon_variant,,ENST00000599937,;CPT1C,non_coding_transcript_exon_variant,,ENST00000598647,;CPT1C,non_coding_transcript_exon_variant,,ENST00000598072,;CPT1C,downstream_gene_variant,,ENST00000596701,;CPT1C,downstream_gene_variant,,ENST00000598259,;CPT1C,downstream_gene_variant,,ENST00000599023,;CPT1C,downstream_gene_variant,,ENST00000295404,; G ENST00000392518 Transcript missense_variant 2722/2910 2350/2412 784/803 C/G Tgt/Ggt 1 1 CPT1C HGNC HGNC:18540 protein_coding YES CCDS12779.1 ENSP00000376303 Q8TCG5 A0A024QZE3 UPI0000071C78 NM_001199752.2 tolerated_low_confidence(0.51) 20/20 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 49713543 49713543 T G 1 0 0 0 0 1 0 0 0 3630 1696 59 5 5 CPT1C 19 49713543 Missense_Mutation SNP T C3L-00095_T 296353 49713543 8904073 736 3945 KIR3DL2 0 . GRCh38 19 54865803 54865803 + Splice_Site SNP A A C rs113681719 C3L-00095_T C3L-00095_N A A c.1001-2A>C p.X334_splice ENST00000326321 192 175 17 265 265 0 strelka-varscan-mutect KIR3DL2,splice_acceptor_variant,,ENST00000326321,NM_006737.3;KIR3DL1,splice_acceptor_variant,,ENST00000402254,;KIR3DL2,splice_acceptor_variant,,ENST00000270442,NM_001242867.1;RNU6-222P,downstream_gene_variant,,ENST00000362438,; C ENST00000326321 Transcript splice_acceptor_variant -/1877 1001/1368 334/455 rs113681719 1 1 KIR3DL2 HGNC HGNC:6339 protein_coding YES CCDS12906.1 ENSP00000325525 P43630 A0A0U1WNF3 UPI000012DB25 NM_006737.3 6/8 HIGH 1 SNV 1 1 PASS rs113681719 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 10 54865803 54865803 A C 1 0 0 0 0 0 0 1 0 8185 202 7 5 5 KIR3DL2 19 54865803 Splice_Site SNP A C3L-00095_T 5152260 54865803 3751813 737 3946 NLRP8 0 . GRCh38 19 55966335 55966335 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.2336T>C p.Leu779Pro p.L779P ENST00000291971 5/10 143 130 13 173 173 0 strelka-varscan-mutect NLRP8,missense_variant,p.Leu779Pro,ENST00000291971,NM_176811.2;NLRP8,missense_variant,p.Leu779Pro,ENST00000590542,; C ENST00000291971 Transcript missense_variant 2407/3934 2336/3147 779/1048 L/P cTa/cCa 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 deleterious(0) 5/10 hmmpanther:PTHR24106:SF54,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 55966335 55966335 T C 1 0 0 0 0 1 0 0 0 10521 1522 53 5 5 NLRP8 19 55966335 Missense_Mutation SNP T C3L-00095_T 1100532 55966335 2651281 738 3947 ZNF835 0 . GRCh38 19 56664223 56664223 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.976C>A p.Arg326Ser p.R326S ENST00000537055 2/2 199 188 11 301 301 0 strelka-varscan-mutect ZNF835,missense_variant,p.Arg326Ser,ENST00000537055,NM_001005850.2;ZNF835,downstream_gene_variant,,ENST00000601659,; T ENST00000537055 Transcript missense_variant 1208/3450 976/1614 326/537 R/S Cgc/Agc COSM4848175 1 -1 ZNF835 HGNC HGNC:34332 protein_coding YES CCDS56105.1 ENSP00000444747 Q9Y2P0 UPI0000EE7244 NM_001005850.2 deleterious(0.03) 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF368,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS rs922601671 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 56664223 56664223 G T 1 0 0 0 0 1 0 0 0 18771 1087 38 1 1 ZNF835 19 56664223 Missense_Mutation SNP G C3L-00095_T 697888 56664223 1953393 739 3948 PEG3 0 . GRCh38 19 56815448 56815448 + Silent SNP T T A novel C3L-00095_T C3L-00095_N T T c.2994A>T p.= p.G998G ENST00000326441 10/10 103 95 8 114 114 0 strelka-varscan-mutect PEG3,synonymous_variant,p.=,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,synonymous_variant,p.=,ENST00000598410,NM_001146187.1;PEG3,synonymous_variant,p.=,ENST00000599534,;PEG3,synonymous_variant,p.=,ENST00000599577,;PEG3,synonymous_variant,p.=,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript synonymous_variant 3358/8723 2994/4767 998/1588 G ggA/ggT 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 10/10 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.44318 1 1 1 1 0 A 2 1 10 56815448 56815448 T A 1 0 0 0 0 0 0 0 1 11808 1770 62 4 4 PEG3 19 56815448 Silent SNP T C3L-00095_T 151225 56815448 1802168 740 3949 ZSCAN1 0 . GRCh38 19 58053974 58053974 + Missense_Mutation SNP G G T rs764113791 C3L-00095_T C3L-00095_N G G c.1150G>T p.Val384Phe p.V384F ENST00000282326 6/6 43 39 4 64 64 0 strelka-mutect ZSCAN1,missense_variant,p.Val384Phe,ENST00000282326,NM_182572.3;HNRNPDLP4,upstream_gene_variant,,ENST00000605144,; T ENST00000282326 Transcript missense_variant 1397/2054 1150/1227 384/408 V/F Gtc/Ttc rs764113791,COSM88711 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 tolerated(0.12) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs764113791 . 0 202 8 0 0 0 0 0 -10.39741 0.9999948 1 1 1 0 T 3 4 10 58053974 58053974 G T 1 0 0 0 0 1 0 0 0 18820 1145 40 1 1 ZSCAN1 19 58053974 Missense_Mutation SNP G C3L-00095_T 1238526 58053974 563642 741 3950 SIRPB1 0 . GRCh38 20 1571104 1571104 + Missense_Mutation SNP A A T rs780249101 C3L-00095_T C3L-00095_N A A c.785T>A p.Met262Lys p.M262K ENST00000381605 4/6 126 119 7 172 172 0 varscan-mutect SIRPB1,missense_variant,p.Met262Lys,ENST00000381605,NM_006065.3;SIRPB1,missense_variant,p.Met76Lys,ENST00000565076,;SIRPB1,intron_variant,,ENST00000381603,NM_001083910.2;SIRPB1,intron_variant,,ENST00000262929,;RP4-576H24.4,intron_variant,,ENST00000564763,;SIRPB1,intron_variant,,ENST00000563840,;RP4-576H24.4,intron_variant,,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPB1,intron_variant,,ENST00000569629,; T ENST00000381605 Transcript missense_variant 850/3241 785/1197 262/398 M/K aTg/aAg rs780249101 1 -1 SIRPB1 HGNC HGNC:15928 protein_coding YES CCDS13019.1 ENSP00000371018 O00241 UPI000036700F NM_006065.3 tolerated(0.1) 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs780249101 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 1571104 1571104 A T 1 0 0 0 0 1 0 0 0 14596 217 8 4 4 SIRPB1 20 1571104 Missense_Mutation SNP A C3L-00095_T 1571104 62873063 742 3951 15 2 SIRPB1 0 . GRCh38 20 1571106 1571106 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.783C>A p.= p.P261P ENST00000381605 4/6 122 115 7 171 171 0 varscan-mutect SIRPB1,synonymous_variant,p.=,ENST00000381605,NM_006065.3;SIRPB1,synonymous_variant,p.=,ENST00000565076,;SIRPB1,intron_variant,,ENST00000381603,NM_001083910.2;SIRPB1,intron_variant,,ENST00000262929,;RP4-576H24.4,intron_variant,,ENST00000564763,;SIRPB1,intron_variant,,ENST00000563840,;RP4-576H24.4,intron_variant,,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPB1,intron_variant,,ENST00000569629,; T ENST00000381605 Transcript synonymous_variant 848/3241 783/1197 261/398 P ccC/ccA 1 -1 SIRPB1 HGNC HGNC:15928 protein_coding YES CCDS13019.1 ENSP00000371018 O00241 UPI000036700F NM_006065.3 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 1571106 1571106 G T 1 0 0 0 0 0 0 0 1 14596 1335 47 2 2 SIRPB1 20 1571106 Silent SNP G C3L-00095_T 2 1571106 62873061 743 3952 15 2 TGM3 0 . GRCh38 20 2317142 2317142 + Silent SNP G G A novel C3L-00095_T C3L-00095_N G G c.744G>A p.= p.R248R ENST00000381458 6/13 291 269 22 296 296 0 strelka-varscan-mutect TGM3,synonymous_variant,p.=,ENST00000381458,NM_003245.3;TGM3,non_coding_transcript_exon_variant,,ENST00000463090,; A ENST00000381458 Transcript synonymous_variant 807/2642 744/2082 248/693 R agG/agA 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 6/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 2317142 2317142 G A 1 0 0 0 0 0 0 0 1 16264 1165 41 3 3 TGM3 20 2317142 Silent SNP G C3L-00095_T 746036 2317142 62127025 744 3953 CFAP61 0 . GRCh38 20 20277341 20277341 + Silent SNP C C A rs772522238 C3L-00095_T C3L-00095_N C C c.2679C>A p.= p.A893A ENST00000245957 22/27 156 147 9 211 211 0 strelka-varscan-mutect CFAP61,synonymous_variant,p.=,ENST00000245957,NM_015585.3;CFAP61,intron_variant,,ENST00000488640,;CFAP61,synonymous_variant,p.=,ENST00000377308,; A ENST00000245957 Transcript synonymous_variant 2755/4082 2679/3714 893/1237 A gcC/gcA rs772522238,COSM5486119 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 22/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 0,1 LOW 1 SNV 1 0,1 1 PASS rs772522238 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 20277341 20277341 C A 1 0 0 0 0 0 0 0 1 3028 639 23 1 1 CFAP61 20 20277341 Silent SNP C C3L-00095_T 17960199 20277341 44166826 745 3954 KIZ 0 . GRCh38 20 21132118 21132118 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.111G>T p.= p.L37L ENST00000619189 2/13 165 148 17 142 142 0 strelka-varscan-mutect KIZ,synonymous_variant,p.=,ENST00000619189,NM_018474.4;KIZ,5_prime_UTR_variant,,ENST00000620891,NM_001163022.1;KIZ,5_prime_UTR_variant,,ENST00000616848,NM_001163023.1;KIZ,intron_variant,,ENST00000619574,NM_001276389.1;KIZ,intron_variant,,ENST00000611685,;KIZ,non_coding_transcript_exon_variant,,ENST00000620553,;KIZ,non_coding_transcript_exon_variant,,ENST00000622184,;KIZ,3_prime_UTR_variant,,ENST00000612654,; T ENST00000619189 Transcript synonymous_variant 173/2130 111/2022 37/673 L ctG/ctT 1 1 KIZ HGNC HGNC:15865 protein_coding YES CCDS74706.1 ENSP00000479542 Q2M2Z5 UPI0000E826A7 NM_018474.4 2/13 hmmpanther:PTHR16299,hmmpanther:PTHR16299:SF2 LOW 1 SNV 1 1 PASS rs1258765560 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 21132118 21132118 G T 1 0 0 0 0 0 0 0 1 8195 1335 47 2 2 KIZ 20 21132118 Silent SNP G C3L-00095_T 854777 21132118 43312049 746 3955 CST4 0 . GRCh38 20 23688773 23688773 + Missense_Mutation SNP C C G rs571931083 C3L-00095_T C3L-00095_N C C c.197G>C p.Arg66Pro p.R66P ENST00000217423 1/3 183 167 16 249 249 0 strelka-varscan-mutect CST4,missense_variant,p.Arg66Pro,ENST00000217423,NM_001899.2; G ENST00000217423 Transcript missense_variant 268/751 197/426 66/141 R/P cGc/cCc rs571931083 1 -1 CST4 HGNC HGNC:2476 protein_coding YES CCDS13159.1 ENSP00000217423 P01036 UPI0000049812 NM_001899.2 deleterious(0) 1/3 Gene3D:3.10.450.10,Pfam_domain:PF00031,hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF54,SMART_domains:SM00043,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS rs571931083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 23688773 23688773 C G 1 0 0 0 0 1 0 0 0 3774 768 27 4 4 CST4 20 23688773 Missense_Mutation SNP C C3L-00095_T 2556655 23688773 40755394 747 3956 GGTLC1 0 . GRCh38 20 23985240 23985240 + Missense_Mutation SNP T T G novel C3L-00095_T C3L-00095_N T T c.654A>C p.Lys218Asn p.K218N ENST00000335694 6/6 484 457 27 624 624 0 varscan-mutect GGTLC1,missense_variant,p.Lys218Asn,ENST00000335694,NM_178311.2;GGTLC1,missense_variant,p.Lys218Asn,ENST00000286890,;GGTLC1,missense_variant,p.Lys218Asn,ENST00000278765,NM_178312.2;POM121L3P,upstream_gene_variant,,ENST00000419331,;RP5-831C21.1,upstream_gene_variant,,ENST00000447582,; G ENST00000335694 Transcript missense_variant 859/1046 654/678 218/225 K/N aaA/aaC 1 -1 GGTLC1 HGNC HGNC:16437 protein_coding YES CCDS13163.1 ENSP00000337587 Q9BX51 UPI0000073C4D NM_178311.2 deleterious(0) 6/6 hmmpanther:PTHR11686:SF28,hmmpanther:PTHR11686,Pfam_domain:PF01019,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 23985240 23985240 T G 1 0 0 0 0 1 0 0 0 6242 1606 56 5 5 GGTLC1 20 23985240 Missense_Mutation SNP T C3L-00095_T 296467 23985240 40458927 748 3957 BPIFB4 0 . GRCh38 20 33086028 33086028 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.790G>T p.Gly264Cys p.G264C ENST00000375483 5/16 129 121 8 147 147 0 strelka-varscan-mutect BPIFB4,missense_variant,p.Gly264Cys,ENST00000375483,NM_182519.2;BPIFB4,intron_variant,,ENST00000445356,; T ENST00000375483 Transcript missense_variant 790/2159 790/1845 264/614 G/C Ggc/Tgc 1 1 BPIFB4 HGNC HGNC:16179 protein_coding YES CCDS13213.2 ENSP00000364632 P59827 UPI0000206190 NM_182519.2 deleterious(0) 5/16 Gene3D:1ewfA01,Pfam_domain:PF01273,hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF78,SMART_domains:SM00328,Superfamily_domains:SSF55394 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -15.54962 1 1 1 1 0 T 3 4 10 33086028 33086028 G T 1 0 0 0 0 1 0 0 0 1660 1348 47 2 2 BPIFB4 20 33086028 Missense_Mutation SNP G C3L-00095_T 9100788 33086028 31358139 749 3958 DLGAP4 0 . GRCh38 20 36497013 36497013 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.1957G>A p.Glu653Lys p.E653K ENST00000373913 8/13 127 113 14 160 160 0 strelka-varscan-mutect DLGAP4,missense_variant,p.Glu653Lys,ENST00000373913,NM_014902.5;DLGAP4,missense_variant,p.Glu653Lys,ENST00000339266,;DLGAP4,missense_variant,p.Glu653Lys,ENST00000401952,;DLGAP4,missense_variant,p.Glu653Lys,ENST00000373907,;DLGAP4,missense_variant,p.Glu114Lys,ENST00000340491,NM_183006.3;DLGAP4,5_prime_UTR_variant,,ENST00000475894,NM_001042486.3;DLGAP4,5_prime_UTR_variant,,ENST00000489701,;DLGAP4,5_prime_UTR_variant,,ENST00000482872,;DLGAP4,5_prime_UTR_variant,,ENST00000495241,;DLGAP4,non_coding_transcript_exon_variant,,ENST00000479951,;DLGAP4,non_coding_transcript_exon_variant,,ENST00000482037,;DLGAP4,non_coding_transcript_exon_variant,,ENST00000479220,;DLGAP4,non_coding_transcript_exon_variant,,ENST00000491207,;DLGAP4,upstream_gene_variant,,ENST00000497862,;DLGAP4,upstream_gene_variant,,ENST00000478910,; A ENST00000373913 Transcript missense_variant 2437/5056 1957/2970 653/989 E/K Gag/Aag 1 1 DLGAP4 HGNC HGNC:24476 protein_coding YES CCDS13274.1 ENSP00000363023 Q9Y2H0 UPI000013D34B NM_014902.5 tolerated(0.08) 8/13 Pfam_domain:PF03359,hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 36497013 36497013 G A 1 0 0 0 0 1 0 0 0 4369 1291 45 3 3 DLGAP4 20 36497013 Missense_Mutation SNP G C3L-00095_T 3410985 36497013 27947154 750 3959 SLC32A1 0 . GRCh38 20 38728000 38728000 + Silent SNP C C A rs758524437 C3L-00095_T C3L-00095_N C C c.939C>A p.= p.I313I ENST00000217420 2/2 376 348 28 482 481 1 strelka-varscan-mutect SLC32A1,synonymous_variant,p.=,ENST00000217420,NM_080552.2; A ENST00000217420 Transcript synonymous_variant 1202/2574 939/1578 313/525 I atC/atA rs758524437 1 1 SLC32A1 HGNC HGNC:11018 protein_coding YES CCDS13307.1 ENSP00000217420 Q9H598 UPI0000043423 NM_080552.2 2/2 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF221,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs758524437 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 38728000 38728000 C A 1 0 0 0 0 0 0 0 1 14835 874 31 1 1 SLC32A1 20 38728000 Silent SNP C C3L-00095_T 2230987 38728000 25716167 751 3960 SLC2A10 0 . GRCh38 20 46725248 46725248 + Missense_Mutation SNP G G T rs377305511 C3L-00095_T C3L-00095_N G G c.212G>T p.Cys71Phe p.C71F ENST00000359271 2/5 226 196 30 323 322 1 strelka-varscan-mutect SLC2A10,missense_variant,p.Cys71Phe,ENST00000359271,NM_030777.3;SLC2A10,non_coding_transcript_exon_variant,,ENST00000611837,; T ENST00000359271 Transcript missense_variant 462/4389 212/1626 71/541 C/F tGc/tTc rs377305511,COSM1196376 1 1 SLC2A10 HGNC HGNC:13444 protein_coding YES CCDS13402.1 ENSP00000352216 O95528 UPI000012BC8D NM_030777.3 deleterious(0) 2/5 PROSITE_profiles:PS50850,hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF81,PROSITE_patterns:PS00216,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs377305511 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 46725248 46725248 G T 1 0 0 0 0 1 0 0 0 14809 1319 46 2 2 SLC2A10 20 46725248 Missense_Mutation SNP G C3L-00095_T 7997248 46725248 17718919 752 3961 ZNF831 0 . GRCh38 20 59191517 59191517 + Missense_Mutation SNP C C A rs759605825 C3L-00095_T C3L-00095_N C C c.498C>A p.His166Gln p.H166Q ENST00000637017 4/8 200 188 12 265 265 0 strelka-varscan-mutect ZNF831,missense_variant,p.His166Gln,ENST00000637017,;ZNF831,missense_variant,p.His166Gln,ENST00000371030,NM_178457.2; A ENST00000637017 Transcript missense_variant 2047/10953 498/5034 166/1677 H/Q caC/caA rs759605825 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 deleterious(0) 4/8 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS rs759605825 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 59191517 59191517 C A 1 0 0 0 0 1 0 0 0 18770 477 17 2 2 ZNF831 20 59191517 Missense_Mutation SNP C C3L-00095_T 12466269 59191517 5252650 753 3962 ZNF831 0 . GRCh38 20 59193891 59193891 + Missense_Mutation SNP T T A C3L-00095_T C3L-00095_N T T c.2872T>A p.Trp958Arg p.W958R ENST00000637017 4/8 105 96 9 120 120 0 strelka-varscan-mutect ZNF831,missense_variant,p.Trp958Arg,ENST00000637017,;ZNF831,missense_variant,p.Trp958Arg,ENST00000371030,NM_178457.2; A ENST00000637017 Transcript missense_variant 4421/10953 2872/5034 958/1677 W/R Tgg/Agg COSM5312422 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 tolerated(0.7) 4/8 1 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -18.15179 1 1 1 1 0 A 3 1 10 59193891 59193891 T A 1 0 0 0 0 1 0 0 0 18770 1580 55 4 4 ZNF831 20 59193891 Missense_Mutation SNP T C3L-00095_T 2374 59193891 5250276 754 3963 CDH4 0 . GRCh38 20 61743648 61743648 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.255C>A p.= p.V85V ENST00000614565 3/16 383 352 31 475 475 0 strelka-varscan-mutect CDH4,synonymous_variant,p.=,ENST00000614565,NM_001794.4;CDH4,synonymous_variant,p.=,ENST00000543233,NM_001252338.2,NM_001252339.2;CDH4,intron_variant,,ENST00000611855,;RP11-429E11.2,intron_variant,,ENST00000447909,;RP11-429E11.2,intron_variant,,ENST00000442888,; A ENST00000614565 Transcript synonymous_variant 343/6513 255/2751 85/916 V gtC/gtA 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 3/16 hmmpanther:PTHR24027:SF81,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF08758,SMART_domains:SM01055,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 61743648 61743648 C A 1 0 0 0 0 0 0 0 1 2815 900 32 2 2 CDH4 20 61743648 Silent SNP C C3L-00095_T 2549757 61743648 2700519 755 3964 OGFR 0 . GRCh38 20 62812266 62812266 + Silent SNP C C G novel C3L-00095_T C3L-00095_N C C c.651C>G p.= p.L217L ENST00000290291 7/7 40 36 4 67 67 0 strelka-mutect OGFR,synonymous_variant,p.=,ENST00000370461,;OGFR,synonymous_variant,p.=,ENST00000290291,NM_007346.2;OGFR,synonymous_variant,p.=,ENST00000621591,;COL9A3,upstream_gene_variant,,ENST00000343916,NM_001853.3;OGFR,downstream_gene_variant,,ENST00000450048,;COL9A3,upstream_gene_variant,,ENST00000477612,; G ENST00000290291 Transcript synonymous_variant 676/2410 651/2034 217/677 L ctC/ctG 1 1 OGFR HGNC HGNC:15768 protein_coding YES CCDS13504.1 ENSP00000290291 Q9NZT2 UPI000013F107 NM_007346.2 7/7 Pfam_domain:PF04664,hmmpanther:PTHR14015,hmmpanther:PTHR14015:SF1 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.76157 1 1 1 1 0 G 2 3 10 62812266 62812266 C G 1 0 0 0 0 0 0 0 1 10918 813 29 4 4 OGFR 20 62812266 Silent SNP C C3L-00095_T 1068618 62812266 1631901 756 3965 CHRNA4 0 . GRCh38 20 63350240 63350240 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1171G>T p.Glu391Ter p.E391* ENST00000370263 5/6 174 162 12 214 214 0 varscan-mutect CHRNA4,stop_gained,p.Glu320Ter,ENST00000615287,;CHRNA4,stop_gained,p.Glu391Ter,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,non_coding_transcript_exon_variant,,ENST00000463705,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,downstream_gene_variant,,ENST00000628665,;CHRNA4,downstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000637243,;CHRNA4,3_prime_UTR_variant,,ENST00000627000,;CHRNA4,3_prime_UTR_variant,,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000630240,;CHRNA4,upstream_gene_variant,,ENST00000631289,; A ENST00000370263 Transcript stop_gained 1349/5577 1171/1884 391/627 E/* Gag/Tag 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 5/6 Pfam_domain:PF02932,Superfamily_domains:SSF90112 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -15.84775 0.9999997 1 1 1 0 A 4 1 10 63350240 63350240 C A 1 0 0 0 0 0 1 0 0 3145 864 30 2 2 CHRNA4 20 63350240 Nonsense_Mutation SNP C C3L-00095_T 537974 63350240 1093927 757 3966 HELZ2 0 . GRCh38 20 63572158 63572158 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.228G>T p.Trp76Cys p.W76C ENST00000467148 1/19 174 164 10 231 230 1 strelka-varscan-mutect HELZ2,missense_variant,p.Trp76Cys,ENST00000467148,NM_001037335.2;HELZ2,upstream_gene_variant,,ENST00000427522,NM_033405.3;HELZ2,non_coding_transcript_exon_variant,,ENST00000479540,;HELZ2,upstream_gene_variant,,ENST00000454223,;HELZ2,non_coding_transcript_exon_variant,,ENST00000370082,; A ENST00000467148 Transcript missense_variant 298/8064 228/7950 76/2649 W/C tgG/tgT 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 tolerated(0.07) 1/19 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF376 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.03572 0.9999995 1 1 1 0 A 3 1 10 63572158 63572158 C A 1 0 0 0 0 1 0 0 0 6932 624 22 2 2 HELZ2 20 63572158 Missense_Mutation SNP C C3L-00095_T 221918 63572158 872009 758 3967 LTN1 0 . GRCh38 21 28931183 28931183 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.5348G>T p.Cys1783Phe p.C1783F ENST00000614971 29/30 103 97 6 99 98 1 strelka-mutect LTN1,missense_variant,p.Cys1783Phe,ENST00000614971,NM_015565.2;LTN1,missense_variant,p.Cys1783Phe,ENST00000389194,;LTN1,missense_variant,p.Cys1737Phe,ENST00000361371,; A ENST00000614971 Transcript missense_variant 5361/7756 5348/5439 1783/1812 C/F tGc/tTc 1 -1 LTN1 HGNC HGNC:13082 protein_coding YES CCDS33527.2 ENSP00000478783 O94822 UPI000049DF6C NM_015565.2 deleterious(0) 29/30 Gene3D:3.30.40.10,Pfam_domain:PF13639,PROSITE_profiles:PS50089,hmmpanther:PTHR12389,SMART_domains:SM00744,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs1317028095 . 0 194 4 9 3 0 0 0 -3.27151 0.1733089 1 1 0 0 A 3 1 10 28931183 28931183 C A 1 0 0 0 0 1 0 0 0 8987 710 25 2 2 LTN1 21 28931183 Missense_Mutation SNP C C3L-00095_T 28931183 17778800 759 3968 KRTAP6-2 0 . GRCh38 21 30598759 30598759 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.116G>T p.Gly39Val p.G39V ENST00000334897 1/1 223 205 18 244 244 0 strelka-mutect KRTAP6-2,missense_variant,p.Gly39Val,ENST00000334897,NM_181604.1;KRTAP22-1,upstream_gene_variant,,ENST00000334680,NM_181620.1; A ENST00000334897 Transcript missense_variant 144/313 116/189 39/62 G/V gGc/gTc 1 -1 KRTAP6-2 HGNC HGNC:18932 protein_coding YES CCDS13600.1 ENSP00000334560 Q3LI66 UPI00001A9E59 NM_181604.1 1/1 Pfam_domain:PF11759,hmmpanther:PTHR31678,hmmpanther:PTHR31678:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 30598759 30598759 C A 1 0 0 0 0 1 0 0 0 8465 739 26 2 2 KRTAP6-2 21 30598759 Missense_Mutation SNP C C3L-00095_T 1667576 30598759 16111224 760 3969 TIAM1 0 . GRCh38 21 31245542 31245542 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1530G>T p.Lys510Asn p.K510N ENST00000286827 7/29 70 64 6 85 84 1 strelka-mutect TIAM1,missense_variant,p.Lys510Asn,ENST00000286827,NM_003253.2;TIAM1,missense_variant,p.Lys510Asn,ENST00000541036,;TIAM1,non_coding_transcript_exon_variant,,ENST00000469412,; A ENST00000286827 Transcript missense_variant 2002/7200 1530/4776 510/1591 K/N aaG/aaT 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 deleterious(0.01) 7/29 PROSITE_profiles:PS50003,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -13.92169 1 1 1 1 0 A 3 1 10 31245542 31245542 C A 1 0 0 0 0 1 0 0 0 16324 912 32 2 2 TIAM1 21 31245542 Missense_Mutation SNP C C3L-00095_T 646783 31245542 15464441 761 3970 URB1 0 . GRCh38 21 32350800 32350800 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2736G>T p.= p.L912L ENST00000382751 20/39 366 341 25 446 446 0 strelka-varscan-mutect URB1,synonymous_variant,p.=,ENST00000382751,NM_014825.2; A ENST00000382751 Transcript synonymous_variant 2852/10832 2736/6816 912/2271 L ctG/ctT 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 20/39 hmmpanther:PTHR13500 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 32350800 32350800 C A 1 0 0 0 0 0 0 0 1 17554 697 25 2 2 URB1 21 32350800 Silent SNP C C3L-00095_T 1105258 32350800 14359183 762 3971 PAXBP1 0 . GRCh38 21 32759199 32759199 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1264G>T p.Asp422Tyr p.D422Y ENST00000331923 7/18 252 221 31 308 308 0 strelka-varscan-mutect PAXBP1,missense_variant,p.Asp422Tyr,ENST00000331923,NM_016631.3;PAXBP1,missense_variant,p.Asp422Tyr,ENST00000290178,NM_013329.3;PAXBP1,non_coding_transcript_exon_variant,,ENST00000472588,;PAXBP1,missense_variant,p.Asp422Tyr,ENST00000443785,;PAXBP1,upstream_gene_variant,,ENST00000466846,;PAXBP1,downstream_gene_variant,,ENST00000464256,;PAXBP1,upstream_gene_variant,,ENST00000421049,; A ENST00000331923 Transcript missense_variant 1454/3995 1264/2754 422/917 D/Y Gac/Tac 1 -1 PAXBP1 HGNC HGNC:13579 protein_coding YES CCDS13619.1 ENSP00000328992 Q9Y5B6 UPI000012B294 NM_016631.3 deleterious(0.03) 7/18 hmmpanther:PTHR12214:SF2,hmmpanther:PTHR12214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 32759199 32759199 C A 1 0 0 0 0 1 0 0 0 11572 855 30 2 2 PAXBP1 21 32759199 Missense_Mutation SNP C C3L-00095_T 408399 32759199 13950784 763 3972 RCAN1 0 . GRCh38 21 34614902 34614902 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.110C>T p.Ser37Leu p.S37L ENST00000313806 1/4 221 204 17 279 279 0 strelka-varscan-mutect RCAN1,missense_variant,p.Ser37Leu,ENST00000313806,NM_004414.6;RCAN1,upstream_gene_variant,,ENST00000443408,NM_203417.2;RCAN1,upstream_gene_variant,,ENST00000399272,NM_001285389.2;RCAN1,non_coding_transcript_exon_variant,,ENST00000463276,;RCAN1,upstream_gene_variant,,ENST00000489903,; A ENST00000313806 Transcript missense_variant 241/2490 110/759 37/252 S/L tCg/tTg 1 -1 RCAN1 HGNC HGNC:3040 protein_coding CCDS13637.1 ENSP00000320768 P53805 UPI00001B4EA7 NM_004414.6 deleterious(0.04) 1/4 hmmpanther:PTHR10300:SF4,hmmpanther:PTHR10300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 34614902 34614902 G A 1 0 0 0 0 1 0 0 0 13337 1059 37 1 1 RCAN1 21 34614902 Missense_Mutation SNP G C3L-00095_T 1855703 34614902 12095081 764 3973 CLDN14 0 . GRCh38 21 36461487 36461487 + Missense_Mutation SNP A A T rs767565332 C3L-00095_T C3L-00095_N A A c.209T>A p.Leu70Gln p.L70Q ENST00000399137 3/3 515 466 49 610 610 0 strelka-varscan-mutect CLDN14,missense_variant,p.Leu70Gln,ENST00000399137,NM_144492.2;CLDN14,missense_variant,p.Leu70Gln,ENST00000399135,NM_001146079.1;CLDN14,missense_variant,p.Leu70Gln,ENST00000342108,NM_001146077.1;CLDN14,missense_variant,p.Leu70Gln,ENST00000399136,NM_001146078.2;CLDN14,missense_variant,p.Leu70Gln,ENST00000399139,NM_012130.3;AP000695.6,intron_variant,,ENST00000429588,;AP000695.4,intron_variant,,ENST00000428667,;AP000695.4,downstream_gene_variant,,ENST00000454980,; T ENST00000399137 Transcript missense_variant 1076/1942 209/720 70/239 L/Q cTg/cAg rs767565332 1 -1 CLDN14 HGNC HGNC:2035 protein_coding YES CCDS13645.1 ENSP00000382090 O95500 UPI0000048F0B NM_144492.2 tolerated(0.21) 3/3 hmmpanther:PTHR12002:SF99,hmmpanther:PTHR12002,Pfam_domain:PF00822,Prints_domain:PR01385 MODERATE 1 SNV 1 1 PASS rs767565332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 36461487 36461487 A T 1 0 0 0 0 1 0 0 0 3239 188 7 4 4 CLDN14 21 36461487 Missense_Mutation SNP A C3L-00095_T 1846585 36461487 10248496 765 3974 B3GALT5 0 . GRCh38 21 39661102 39661102 + Silent SNP T T A rs768724281 C3L-00095_T C3L-00095_N T T c.555T>A p.= p.T185T ENST00000398714 2/2 198 179 19 202 202 0 strelka-varscan-mutect B3GALT5,synonymous_variant,p.=,ENST00000380620,;B3GALT5,synonymous_variant,p.=,ENST00000380618,NM_006057.2,NM_033170.2,NM_033171.2;B3GALT5,synonymous_variant,p.=,ENST00000615480,NM_001278650.1;B3GALT5,synonymous_variant,p.=,ENST00000343118,;B3GALT5,synonymous_variant,p.=,ENST00000398714,NM_033172.2;AF064860.5,intron_variant,,ENST00000416555,; A ENST00000398714 Transcript synonymous_variant 555/2341 555/945 185/314 T acT/acA rs768724281 1 1 B3GALT5 HGNC HGNC:920 protein_coding YES CCDS74795.1 ENSP00000381699 A0A0A0MS93 UPI000354A018 NM_033172.2 2/2 hmmpanther:PTHR11214:SF18,hmmpanther:PTHR11214,Pfam_domain:PF01762 LOW SNV 5 1 PASS rs768724281 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 39661102 39661102 T A 1 0 0 0 0 0 0 0 1 1407 1567 55 4 4 B3GALT5 21 39661102 Silent SNP T C3L-00095_T 3199615 39661102 7048881 766 3975 DSCAM 0 . GRCh38 21 40080297 40080297 + Silent SNP C C A C3L-00095_T C3L-00095_N C C c.4275G>T p.= p.G1425G ENST00000400454 25/33 71 66 5 73 73 0 strelka-varscan-mutect DSCAM,synonymous_variant,p.=,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,synonymous_variant,p.=,ENST00000617870,;DSCAM,synonymous_variant,p.=,ENST00000404019,; A ENST00000400454 Transcript synonymous_variant 4753/8552 4275/6039 1425/2012 G ggG/ggT COSM5392906 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 25/33 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.45402 1 1 1 1 0 A 2 1 10 40080297 40080297 C A 1 0 0 0 0 0 0 0 1 4589 842 30 2 2 DSCAM 21 40080297 Silent SNP C C3L-00095_T 419195 40080297 6629686 767 3976 MCM3AP 0 . GRCh38 21 46260857 46260857 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3517G>T p.Ala1173Ser p.A1173S ENST00000397708 16/29 292 270 22 366 366 0 strelka-varscan-mutect MCM3AP,missense_variant,p.Ala1173Ser,ENST00000397708,;MCM3AP,missense_variant,p.Ala1173Ser,ENST00000291688,NM_003906.4;MCM3AP-AS1,downstream_gene_variant,,ENST00000590829,;MCM3AP,upstream_gene_variant,,ENST00000467026,;MCM3AP,upstream_gene_variant,,ENST00000481113,;MCM3AP,non_coding_transcript_exon_variant,,ENST00000486937,;MCM3AP,non_coding_transcript_exon_variant,,ENST00000496607,;MCM3AP,upstream_gene_variant,,ENST00000494755,; A ENST00000397708 Transcript missense_variant 3772/6333 3517/5943 1173/1980 A/S Gcc/Tcc 1 -1 MCM3AP HGNC HGNC:6946 protein_coding YES CCDS13734.1 ENSP00000380820 O60318 UPI000012ED4A tolerated(0.18) 16/29 hmmpanther:PTHR12436:SF3,hmmpanther:PTHR12436,Pfam_domain:PF16766 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 46260857 46260857 C A 1 0 0 0 0 1 0 0 0 9320 739 26 2 2 MCM3AP 21 46260857 Missense_Mutation SNP C C3L-00095_T 6180560 46260857 449126 768 3977 CABIN1 0 . GRCh38 22 24171869 24171869 + Missense_Mutation SNP G G T rs751498073 C3L-00095_T C3L-00095_N G G c.5914G>T p.Ala1972Ser p.A1972S ENST00000398319 34/37 342 320 22 473 472 1 strelka-varscan-mutect CABIN1,missense_variant,p.Ala1972Ser,ENST00000398319,NM_001199281.1;CABIN1,missense_variant,p.Ala1972Ser,ENST00000263119,NM_012295.3;CABIN1,missense_variant,p.Ala1922Ser,ENST00000617531,NM_001201429.1;CABIN1,missense_variant,p.Ala1893Ser,ENST00000405822,;CABIN1,missense_variant,p.Ala397Ser,ENST00000337989,;CABIN1,non_coding_transcript_exon_variant,,ENST00000485008,;CABIN1,upstream_gene_variant,,ENST00000459824,; T ENST00000398319 Transcript missense_variant 6299/7480 5914/6663 1972/2220 A/S Gcc/Tcc rs751498073 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 tolerated_low_confidence(0.83) 34/37 hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7 MODERATE 1 SNV 1 1 PASS rs751498073 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 24171869 24171869 G T 1 0 0 0 0 1 0 0 0 2214 1319 46 2 2 CABIN1 22 24171869 Missense_Mutation SNP G C3L-00095_T 24171869 26646599 769 3978 MTMR3 0 . GRCh38 22 29978455 29978455 + Missense_Mutation SNP G G T rs765053016 C3L-00095_T C3L-00095_N G G c.17G>T p.Arg6Leu p.R6L ENST00000401950 4/20 220 208 12 241 241 0 strelka-varscan-mutect MTMR3,missense_variant,p.Arg6Leu,ENST00000333027,NM_153050.2;MTMR3,missense_variant,p.Arg6Leu,ENST00000401950,NM_021090.3;MTMR3,missense_variant,p.Arg6Leu,ENST00000351488,NM_153051.2;MTMR3,missense_variant,p.Arg6Leu,ENST00000406629,;MTMR3,missense_variant,p.Arg6Leu,ENST00000445401,;MTMR3,5_prime_UTR_variant,,ENST00000323630,;RP3-394A18.1,downstream_gene_variant,,ENST00000624945,;MTMR3,non_coding_transcript_exon_variant,,ENST00000415511,;MTMR3,non_coding_transcript_exon_variant,,ENST00000495098,;MTMR3,non_coding_transcript_exon_variant,,ENST00000480776,; T ENST00000401950 Transcript missense_variant 359/6018 17/3597 6/1198 R/L cGg/cTg rs765053016 1 1 MTMR3 HGNC HGNC:7451 protein_coding YES CCDS13870.1 ENSP00000384651 Q13615 UPI0000073EF2 NM_021090.3 tolerated(0.12) 4/20 hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF66 MODERATE 1 SNV 1 1 PASS rs765053016 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 29978455 29978455 G T 1 0 0 0 0 1 0 0 0 9932 1116 39 1 1 MTMR3 22 29978455 Missense_Mutation SNP G C3L-00095_T 5806586 29978455 20840013 770 3979 DEPDC5 0 . GRCh38 22 31810526 31810526 + Missense_Mutation SNP G G T rs201394709 C3L-00095_T C3L-00095_N G G c.1330G>T p.Gly444Trp p.G444W ENST00000400246 20/43 194 184 10 245 245 0 strelka-varscan-mutect DEPDC5,missense_variant,p.Gly444Trp,ENST00000400246,NM_001242896.1;DEPDC5,missense_variant,p.Gly444Trp,ENST00000400249,;DEPDC5,missense_variant,p.Gly444Trp,ENST00000382112,NM_001136029.2;DEPDC5,missense_variant,p.Gly444Trp,ENST00000400248,NM_014662.4;DEPDC5,missense_variant,p.Gly444Trp,ENST00000382111,;DEPDC5,missense_variant,p.Gly444Trp,ENST00000535622,NM_001242897.1;DEPDC5,missense_variant,p.Gly444Trp,ENST00000400242,NM_001007188.2; T ENST00000400246 Transcript missense_variant 1532/5551 1330/4812 444/1603 G/W Ggg/Tgg rs201394709 1 1 DEPDC5 HGNC HGNC:18423 protein_coding YES CCDS74849.1 ENSP00000383105 O75140 UPI000192C426 NM_001242896.1 deleterious(0.02) 20/43 hmmpanther:PTHR13179 MODERATE 1 SNV 1 1 PASS rs201394709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 31810526 31810526 G T 1 0 0 0 0 1 0 0 0 4248 1130 39 1 1 DEPDC5 22 31810526 Missense_Mutation SNP G C3L-00095_T 1832071 31810526 19007942 771 3980 CSF2RB 0 . GRCh38 22 36932854 36932854 + Missense_Mutation SNP A A G novel C3L-00095_T C3L-00095_N A A c.1102A>G p.Ile368Val p.I368V ENST00000403662 9/14 273 254 19 357 357 0 strelka-varscan-mutect CSF2RB,missense_variant,p.Ile368Val,ENST00000403662,NM_000395.2;CSF2RB,missense_variant,p.Ile368Val,ENST00000262825,;CSF2RB,missense_variant,p.Ile374Val,ENST00000406230,;CSF2RB,downstream_gene_variant,,ENST00000421539,; G ENST00000403662 Transcript missense_variant 1324/4863 1102/2694 368/897 I/V Ata/Gta 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 deleterious(0.05) 9/14 PROSITE_profiles:PS50853,hmmpanther:PTHR23037:SF22,hmmpanther:PTHR23037,Gene3D:2.60.40.10,PIRSF_domain:PIRSF001956,Pfam_domain:PF09294,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 36932854 36932854 A G 1 0 0 0 0 1 0 0 0 3736 217 8 5 5 CSF2RB 22 36932854 Missense_Mutation SNP A C3L-00095_T 5122328 36932854 13885614 772 3981 SEPT3 0 . GRCh38 22 41991638 41991638 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.736delG p.Glu246ArgfsTer27 p.E246Rfs*27 ENST00000396426 7/11 257 239 18 340 340 0 sindel-varindel-pindel SEPT3,frameshift_variant,p.Glu246ArgfsTer27,ENST00000396425,NM_019106.5;SEPT3,frameshift_variant,p.Glu246ArgfsTer27,ENST00000396426,NM_145733.2;SEPT3,frameshift_variant,p.Glu182ArgfsTer27,ENST00000406029,;SEPT3,downstream_gene_variant,,ENST00000449288,;SEPT3,3_prime_UTR_variant,,ENST00000396417,;SEPT3,downstream_gene_variant,,ENST00000460267,; - ENST00000396426 Transcript frameshift_variant 990/2586 735/1077 245/358 L/X ttG/tt 1 1 SEPT3 HGNC HGNC:10750 protein_coding YES CCDS14026.2 ENSP00000379704 Q9UH03 UPI000067DA91 NM_145733.2 7/11 Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Prints_domain:PR01741,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF62,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 10 41991638 41991638 G - 1 0 1 0 1 0 0 0 0 14341 1339 47 0 0 SEPT3 22 41991638 Frame_Shift_Del DEL G C3L-00095_T 5058784 41991638 8826830 773 3982 TCF20 0 . GRCh38 22 42211155 42211155 + Missense_Mutation SNP T T C novel C3L-00095_T C3L-00095_N T T c.4151A>G p.Asp1384Gly p.D1384G ENST00000359486 1/5 229 216 13 280 280 0 strelka-varscan-mutect TCF20,missense_variant,p.Asp1384Gly,ENST00000359486,NM_005650.2;TCF20,missense_variant,p.Asp1384Gly,ENST00000335626,NM_181492.2;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,; C ENST00000359486 Transcript missense_variant 4288/7410 4151/5883 1384/1960 D/G gAt/gGt 1 -1 TCF20 HGNC HGNC:11631 protein_coding YES CCDS14033.1 ENSP00000352463 Q9UGU0 W5ZR30 UPI00001A95D9 NM_005650.2 tolerated(0.07) 1/5 hmmpanther:PTHR14955,hmmpanther:PTHR14955:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 42211155 42211155 T C 1 0 0 0 0 1 0 0 0 16097 1435 50 5 5 TCF20 22 42211155 Missense_Mutation SNP T C3L-00095_T 219517 42211155 8607313 774 3983 PARVB 0 . GRCh38 22 44132958 44132958 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.681G>T p.Arg227Ser p.R227S ENST00000406477 7/14 178 163 15 187 186 1 strelka-varscan-mutect PARVB,missense_variant,p.Arg194Ser,ENST00000338758,NM_013327.4;PARVB,missense_variant,p.Arg157Ser,ENST00000404989,NM_001243385.1;PARVB,missense_variant,p.Arg227Ser,ENST00000406477,NM_001003828.2;PARVB,missense_variant,p.Arg142Ser,ENST00000619710,NM_001243386.1;PARVB,missense_variant,p.Arg192Ser,ENST00000444029,;PARVB,upstream_gene_variant,,ENST00000495824,; T ENST00000406477 Transcript missense_variant 811/1569 681/1194 227/397 R/S agG/agT 1 1 PARVB HGNC HGNC:14653 protein_coding YES CCDS46724.1 ENSP00000384515 Q9HBI1 UPI000041A256 NM_001003828.2 tolerated(0.05) 7/14 Gene3D:1.10.418.10,Pfam_domain:PF00307,PIRSF_domain:PIRSF039131,PROSITE_profiles:PS50021,hmmpanther:PTHR12114,hmmpanther:PTHR12114:SF7,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 44132958 44132958 G T 1 0 0 0 0 1 0 0 0 11550 1223 43 2 2 PARVB 22 44132958 Missense_Mutation SNP G C3L-00095_T 1921803 44132958 6685510 775 3984 PHF21B 0 . GRCh38 22 44893480 44893480 + Missense_Mutation SNP A A T C3L-00095_T C3L-00095_N A A c.937T>A p.Tyr313Asn p.Y313N ENST00000313237 7/13 191 174 17 228 228 0 strelka-varscan-mutect PHF21B,missense_variant,p.Tyr313Asn,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Tyr109Asn,ENST00000403565,NM_001284296.1;PHF21B,missense_variant,p.Tyr259Asn,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Tyr271Asn,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Tyr109Asn,ENST00000414269,; T ENST00000313237 Transcript missense_variant 1088/3671 937/1596 313/531 Y/N Tac/Aac COSM4628042 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious(0) 7/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 44893480 44893480 A T 1 0 0 0 0 1 0 0 0 11920 420 15 4 4 PHF21B 22 44893480 Missense_Mutation SNP A C3L-00095_T 760522 44893480 5924988 776 3985 16 2 PHF21B 0 . GRCh38 22 44893482 44893482 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.935C>A p.Ala312Asp p.A312D ENST00000313237 7/13 187 168 19 230 230 0 strelka-varscan-mutect PHF21B,missense_variant,p.Ala312Asp,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Ala108Asp,ENST00000403565,NM_001284296.1;PHF21B,missense_variant,p.Ala258Asp,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Ala270Asp,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Ala108Asp,ENST00000414269,; T ENST00000313237 Transcript missense_variant 1086/3671 935/1596 312/531 A/D gCc/gAc 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious(0.01) 7/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 44893482 44893482 G T 1 0 0 0 0 1 0 0 0 11920 1203 42 2 2 PHF21B 22 44893482 Missense_Mutation SNP G C3L-00095_T 2 44893482 5924986 777 3986 16 2 PLXNB2 0 . GRCh38 22 50281102 50281102 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.3750G>T p.Lys1250Asn p.K1250N ENST00000449103 23/37 195 176 19 243 243 0 strelka-mutect PLXNB2,missense_variant,p.Lys1250Asn,ENST00000449103,;PLXNB2,missense_variant,p.Lys1250Asn,ENST00000359337,NM_012401.3;PLXNB2,5_prime_UTR_variant,,ENST00000610984,;PLXNB2,intron_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000614805,;PLXNB2,downstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000434732,;PLXNB2,downstream_gene_variant,,ENST00000496720,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,;PLXNB2,upstream_gene_variant,,ENST00000479818,;PLXNB2,downstream_gene_variant,,ENST00000492578,; A ENST00000449103 Transcript missense_variant 3891/6383 3750/5517 1250/1838 K/N aaG/aaT 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D deleterious(0) 23/37 hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 50281102 50281102 C A 1 0 0 0 0 1 0 0 0 12230 912 32 2 2 PLXNB2 22 50281102 Missense_Mutation SNP C C3L-00095_T 5387620 50281102 537366 778 3987 PPP2R3B 0 . GRCh38 X 386544 386544 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.148G>T p.Gly50Trp p.G50W ENST00000390665 1/13 99 92 7 122 121 1 strelka-varscan-mutect PPP2R3B,missense_variant,p.Gly50Trp,ENST00000390665,NM_013239.4;RP13-465B17.4,upstream_gene_variant,,ENST00000627721,;Metazoa_SRP,downstream_gene_variant,,ENST00000610676,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000445792,; A ENST00000390665 Transcript missense_variant 167/2151 148/1728 50/575 G/W Ggg/Tgg 1 -1 PPP2R3B HGNC HGNC:13417 protein_coding YES CCDS14104.1 ENSP00000375080 Q9Y5P8 UPI00001BB8B8 NM_013239.4 deleterious(0) 1/13 hmmpanther:PTHR14095:SF1,hmmpanther:PTHR14095 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 386544 386544 C A 1 0 0 0 0 1 0 0 0 12512 623 22 2 2 PPP2R3B 23 386544 Missense_Mutation SNP C C3L-00095_T 386544 155654351 779 3988 ARSF 0 . GRCh38 X 3103889 3103889 + Silent SNP C C A rs201866054 C3L-00095_T C3L-00095_N C C c.1230C>A p.= p.V410V ENST00000381127 9/11 75 67 8 102 102 0 strelka-varscan-mutect ARSF,synonymous_variant,p.=,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,synonymous_variant,p.=,ENST00000359361,NM_004042.4; A ENST00000381127 Transcript synonymous_variant 1451/2164 1230/1773 410/590 V gtC/gtA rs201866054 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 9/11 hmmpanther:PTHR10342:SF220,hmmpanther:PTHR10342,Gene3D:3.40.720.10,Pfam_domain:PF00884,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS rs201866054 . 0 206 3 0 0 0 0 0 -17.71532 1 1 1 1 0 A 2 1 10 3103889 3103889 C A 1 0 0 0 0 0 0 0 1 1134 871 31 1 1 ARSF 23 3103889 Silent SNP C C3L-00095_T 2717345 3103889 152937006 780 3989 MXRA5 0 . GRCh38 X 3322272 3322272 + Missense_Mutation SNP G G T rs140078324 C3L-00095_T C3L-00095_N G G c.3413C>A p.Pro1138Gln p.P1138Q ENST00000217939 5/7 34 30 4 40 40 0 strelka-varscan-mutect MXRA5,missense_variant,p.Pro1138Gln,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 3568/9793 3413/8487 1138/2828 P/Q cCg/cAg rs140078324 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.06) 5/7 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF680 MODERATE 1 SNV 5 1 PASS rs140078324 . 0 204 6 0 0 0 0 0 -11.04353 0.9999999 1 1 1 0 T 3 4 10 3322272 3322272 G T 1 0 0 0 0 1 0 0 0 10002 1116 39 1 1 MXRA5 23 3322272 Missense_Mutation SNP G C3L-00095_T 218383 3322272 152718623 781 3990 ARHGAP6 0 . GRCh38 X 11179332 11179332 + Nonsense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1450G>T p.Glu484Ter p.E484* ENST00000337414 7/13 64 51 13 76 76 0 strelka-varscan-mutect ARHGAP6,stop_gained,p.Glu484Ter,ENST00000337414,NM_013427.2;ARHGAP6,stop_gained,p.Glu281Ter,ENST00000303025,NM_013423.2;ARHGAP6,stop_gained,p.Glu281Ter,ENST00000380736,NM_001287242.1;ARHGAP6,stop_gained,p.Glu484Ter,ENST00000380718,NM_006125.2;ARHGAP6,stop_gained,p.Glu320Ter,ENST00000380717,;ARHGAP6,non_coding_transcript_exon_variant,,ENST00000491514,;ARHGAP6,stop_gained,p.Glu516Ter,ENST00000495242,;ARHGAP6,non_coding_transcript_exon_variant,,ENST00000489330,; A ENST00000337414 Transcript stop_gained 2323/5117 1450/2925 484/974 E/* Gag/Tag 1 -1 ARHGAP6 HGNC HGNC:676 protein_coding YES CCDS14140.1 ENSP00000338967 O43182 UPI00001AED54 NM_013427.2 7/13 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR12635,hmmpanther:PTHR12635:SF6,SMART_domains:SM00324,Superfamily_domains:SSF48350 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 11179332 11179332 C A 1 0 0 0 0 0 1 0 0 1017 864 30 2 2 ARHGAP6 23 11179332 Nonsense_Mutation SNP C C3L-00095_T 7857060 11179332 144861563 782 3991 BEND2 0 . GRCh38 X 18177677 18177677 + Missense_Mutation SNP A A T novel C3L-00095_T C3L-00095_N A A c.1522T>A p.Tyr508Asn p.Y508N ENST00000380033 10/14 211 194 17 263 263 0 strelka-varscan-mutect BEND2,missense_variant,p.Tyr508Asn,ENST00000380033,NM_153346.4;BEND2,missense_variant,p.Tyr417Asn,ENST00000380030,NM_001184767.1; T ENST00000380033 Transcript missense_variant 1655/4611 1522/2400 508/799 Y/N Tac/Aac 1 -1 BEND2 HGNC HGNC:28509 protein_coding YES CCDS14184.1 ENSP00000369372 Q8NDZ0 UPI000013FE0F NM_153346.4 deleterious(0) 10/14 PROSITE_profiles:PS51457,Pfam_domain:PF10523,SMART_domains:SM01025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 18177677 18177677 A T 1 0 0 0 0 1 0 0 0 1546 420 15 4 4 BEND2 23 18177677 Missense_Mutation SNP A C3L-00095_T 6998345 18177677 137863218 783 3992 KLHL34 0 . GRCh38 X 21656255 21656255 + Missense_Mutation SNP T T A rs767421393 C3L-00095_T C3L-00095_N T T c.1534A>T p.Met512Leu p.M512L ENST00000379499 1/1 75 67 8 85 85 0 strelka-varscan-mutect KLHL34,missense_variant,p.Met512Leu,ENST00000379499,NM_153270.2;CNKSR2,downstream_gene_variant,,ENST00000425654,NM_001168647.1;CNKSR2,downstream_gene_variant,,ENST00000379510,NM_014927.3; A ENST00000379499 Transcript missense_variant 2076/3641 1534/1935 512/644 M/L Atg/Ttg rs767421393 1 -1 KLHL34 HGNC HGNC:26634 protein_coding YES CCDS14199.1 ENSP00000368813 Q8N239 UPI0000072CC4 NM_153270.2 tolerated(0.1) 1/1 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF199,SMART_domains:SM00612 MODERATE SNV 1 PASS rs767421393 . 0 208 2 0 0 0 0 0 -17.89028 1 1 1 1 0 A 3 1 10 21656255 21656255 T A 1 0 0 0 0 1 0 0 0 8253 1464 51 4 4 KLHL34 23 21656255 Missense_Mutation SNP T C3L-00095_T 3478578 21656255 134384640 784 3993 PTCHD1 0 . GRCh38 X 23392973 23392973 + Nonsense_Mutation SNP T T A novel C3L-00095_T C3L-00095_N T T c.1455T>A p.Cys485Ter p.C485* ENST00000379361 3/3 203 185 18 247 246 1 strelka-varscan-mutect PTCHD1,stop_gained,p.Cys485Ter,ENST00000379361,NM_173495.2;PTCHD1,3_prime_UTR_variant,,ENST00000456522,; A ENST00000379361 Transcript stop_gained 2315/13714 1455/2667 485/888 C/* tgT/tgA 1 1 PTCHD1 HGNC HGNC:26392 protein_coding YES CCDS35215.2 ENSP00000368666 Q96NR3 X5DNX9 UPI000059DAD8 NM_173495.2 3/3 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF36 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 10 23392973 23392973 T A 1 0 0 0 0 0 1 0 0 12885 1731 60 4 4 PTCHD1 23 23392973 Nonsense_Mutation SNP T C3L-00095_T 1736718 23392973 132647922 785 3994 MAGEB18 0 . GRCh38 X 26139097 26139097 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.112C>A p.Pro38Thr p.P38T ENST00000325250 2/3 149 140 9 165 165 0 strelka-varscan-mutect MAGEB18,missense_variant,p.Pro38Thr,ENST00000325250,NM_173699.3; A ENST00000325250 Transcript missense_variant 299/1811 112/1032 38/343 P/T Ccc/Acc 1 1 MAGEB18 HGNC HGNC:28515 protein_coding YES CCDS14216.1 ENSP00000314543 Q96M61 UPI00001415E3 NM_173699.3 tolerated(0.23) 2/3 hmmpanther:PTHR11736:SF23,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 MODERATE 1 SNV 1 1 PASS rs1381649903 . 0 206 0 3 0 0 0 0 -12.17165 0.9999557 1 1 1 0 A 3 1 10 26139097 26139097 C A 1 0 0 0 0 1 0 0 0 9091 507 18 2 2 MAGEB18 23 26139097 Missense_Mutation SNP C C3L-00095_T 2746124 26139097 129901798 786 3995 DMD 0 . GRCh38 X 32573575 32573575 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.1767C>A p.= p.G589G ENST00000357033 15/79 196 176 20 155 155 0 strelka-varscan-mutect DMD,synonymous_variant,p.=,ENST00000357033,NM_000109.3,NM_004006.2;DMD,synonymous_variant,p.=,ENST00000378677,NM_004010.3,NM_004009.3;DMD,synonymous_variant,p.=,ENST00000620040,;DMD,synonymous_variant,p.=,ENST00000619831,;DMD,synonymous_variant,p.=,ENST00000288447,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,downstream_gene_variant,,ENST00000447523,;DMD,intron_variant,,ENST00000488902,;DMD,downstream_gene_variant,,ENST00000480751,; T ENST00000357033 Transcript synonymous_variant 1974/13956 1767/11058 589/3685 G ggC/ggA 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 15/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 32573575 32573575 G T 1 0 0 0 0 0 0 0 1 4387 958 34 2 2 DMD 23 32573575 Silent SNP G C3L-00095_T 6434478 32573575 123467320 787 3996 FAM47A 0 . GRCh38 X 34131623 34131623 + Frame_Shift_Del DEL G G - rs750698635 C3L-00095_T C3L-00095_N G G c.656delC p.Pro219ArgfsTer47 p.P219Rfs*47 ENST00000346193 1/1 81 72 9 167 167 0 sindel-varindel-pindel FAM47A,frameshift_variant,p.Pro219ArgfsTer47,ENST00000346193,NM_203408.3;FAM47A,frameshift_variant,p.Pro219ArgfsTer47,ENST00000613251,; - ENST00000346193 Transcript frameshift_variant 689/2556 656/2376 219/791 P/X cCg/cg rs750698635,COSM123010 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 0,1 HIGH 1 deletion 0,1 1 PASS . . 0 204 4 2 0 0 0 0 -15.00502 0.9999687 1 1 1 0 - 7 5 10 34131623 34131623 G - 1 0 1 0 1 0 0 0 0 5447 1116 39 0 0 FAM47A 23 34131623 Frame_Shift_Del DEL G C3L-00095_T 1558048 34131623 121909272 788 3997 FAM47A 0 . GRCh38 X 34131679 34131679 + Silent SNP G G T novel C3L-00095_T C3L-00095_N G G c.600C>A p.= p.L200L ENST00000346193 1/1 72 64 8 119 119 0 strelka-varscan-mutect FAM47A,synonymous_variant,p.=,ENST00000346193,NM_203408.3;FAM47A,synonymous_variant,p.=,ENST00000613251,; T ENST00000346193 Transcript synonymous_variant 633/2556 600/2376 200/791 L ctC/ctA 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -17.75556 1 1 1 1 0 T 2 4 10 34131679 34131679 G T 1 0 0 0 0 0 0 0 1 5447 1161 41 2 2 FAM47A 23 34131679 Silent SNP G C3L-00095_T 56 34131679 121909216 789 3998 SRPX 0 . GRCh38 X 38164854 38164854 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.568C>A p.Arg190Ser p.R190S ENST00000378533 5/10 108 102 6 134 134 0 strelka-varscan-mutect SRPX,missense_variant,p.Arg190Ser,ENST00000378533,NM_006307.4;SRPX,missense_variant,p.Arg170Ser,ENST00000544439,NM_001170750.1;SRPX,missense_variant,p.Arg190Ser,ENST00000538295,NM_001170752.1;SRPX,missense_variant,p.Arg131Ser,ENST00000432886,NM_001170751.1;RP5-972B16.2,intron_variant,,ENST00000465127,;SRPX,upstream_gene_variant,,ENST00000479015,; T ENST00000378533 Transcript missense_variant 675/1874 568/1395 190/464 R/S Cgc/Agc 1 -1 SRPX HGNC HGNC:11309 protein_coding YES CCDS14245.1 ENSP00000367794 P78539 UPI0000135F5C NM_006307.4 deleterious(0.03) 5/10 PROSITE_profiles:PS50825,hmmpanther:PTHR19325:SF375,hmmpanther:PTHR19325,Pfam_domain:PF02494 MODERATE 1 SNV 1 1 PASS rs1245921366 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 38164854 38164854 G T 1 0 0 0 0 1 0 0 0 15525 1145 40 1 1 SRPX 23 38164854 Missense_Mutation SNP G C3L-00095_T 4033175 38164854 117876041 790 3999 RBM10 0 . GRCh38 X 47171134 47171134 + Missense_Mutation SNP G G T rs782467531 C3L-00095_T C3L-00095_N G G c.503G>T p.Arg168Leu p.R168L ENST00000329236 4/24 238 210 28 307 307 0 strelka-varscan-mutect RBM10,missense_variant,p.Arg103Leu,ENST00000377604,NM_005676.4,NM_001204467.1;RBM10,missense_variant,p.Arg168Leu,ENST00000329236,NM_001204468.1;RBM10,intron_variant,,ENST00000345781,NM_001204466.1;RBM10,intron_variant,,ENST00000628161,NM_152856.2;RBM10,upstream_gene_variant,,ENST00000496012,; T ENST00000329236 Transcript missense_variant 503/3201 503/2988 168/995 R/L cGg/cTg rs782467531 1 1 RBM10 HGNC HGNC:9896 protein_coding YES CCDS75969.1 ENSP00000328848 A0A0A0MR66 UPI0000211F0E NM_001204468.1 tolerated(0.06) 4/24 Gene3D:3.30.70.330,hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF4 MODERATE 1 SNV 1 1 PASS rs782467531 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 47171134 47171134 G T 1 0 0 0 0 1 0 0 0 13277 1116 39 1 1 RBM10 23 47171134 Missense_Mutation SNP G C3L-00095_T 9006280 47171134 108869761 791 4000 KDM5C 0 . GRCh38 X 53211531 53211531 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1367G>T p.Ser456Ile p.S456I ENST00000375401 10/26 158 140 18 191 191 0 strelka-varscan-mutect KDM5C,missense_variant,p.Ser389Ile,ENST00000452825,NM_001146702.1;KDM5C,missense_variant,p.Ser456Ile,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Ser455Ile,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Ser456Ile,ENST00000375379,;KDM5C,missense_variant,p.Ser415Ile,ENST00000375383,;KDM5C-IT1,downstream_gene_variant,,ENST00000412242,;KDM5C,upstream_gene_variant,,ENST00000465402,;KDM5C,non_coding_transcript_exon_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000497995,; A ENST00000375401 Transcript missense_variant 1900/6031 1367/4683 456/1560 S/I aGt/aTt 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 deleterious(0.04) 10/26 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43 MODERATE 1 SNV 1 1 PASS rs1418726370 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 53211531 53211531 C A 1 0 0 0 0 1 0 0 0 8053 565 20 2 2 KDM5C 23 53211531 Missense_Mutation SNP C C3L-00095_T 6040397 53211531 102829364 792 4001 ITIH6 0 . GRCh38 X 54751344 54751344 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.3389C>G p.Pro1130Arg p.P1130R ENST00000218436 12/13 51 44 7 87 87 0 strelka-varscan-mutect ITIH6,missense_variant,p.Pro1130Arg,ENST00000218436,NM_198510.2; C ENST00000218436 Transcript missense_variant 3419/4968 3389/3942 1130/1313 P/R cCa/cGa 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 deleterious(0) 12/13 Pfam_domain:PF06668,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10 MODERATE 1 SNV 1 1 PASS rs1394050572 . 0 202 8 0 0 0 0 0 -16.55943 0.9999977 1 1 1 0 C 3 2 10 54751344 54751344 G C 1 0 0 0 0 1 0 0 0 7814 1348 47 4 4 ITIH6 23 54751344 Missense_Mutation SNP G C3L-00095_T 1539813 54751344 101289551 793 4002 ITIH6 0 . GRCh38 X 54758981 54758981 + Missense_Mutation SNP C C T novel C3L-00095_T C3L-00095_N C C c.1093G>A p.Ala365Thr p.A365T ENST00000218436 8/13 16 13 3 21 21 0 strelka-mutect ITIH6,missense_variant,p.Ala365Thr,ENST00000218436,NM_198510.2; T ENST00000218436 Transcript missense_variant 1123/4968 1093/3942 365/1313 A/T Gct/Act 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 deleterious(0) 8/13 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10,Low_complexity_(Seg):seg,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -10.64913 1 1 1 1 0 T 3 4 10 54758981 54758981 C T 1 0 0 0 0 1 0 0 0 7814 797 28 3 3 ITIH6 23 54758981 Missense_Mutation SNP C C3L-00095_T 7637 54758981 101281914 794 4003 ZC3H12B 0 . GRCh38 X 65502768 65502768 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.2070C>A p.= p.P690P ENST00000338957 5/5 59 46 13 62 62 0 strelka-varscan-mutect ZC3H12B,synonymous_variant,p.=,ENST00000338957,NM_001010888.3;ZC3H12B,downstream_gene_variant,,ENST00000617377,; A ENST00000338957 Transcript synonymous_variant 2137/7256 2070/2511 690/836 P ccC/ccA 1 1 ZC3H12B HGNC HGNC:17407 protein_coding YES CCDS48131.2 ENSP00000340839 Q5HYM0 UPI00001D7BEA NM_001010888.3 5/5 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF27 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 65502768 65502768 C A 1 0 0 0 0 0 0 0 1 18137 610 22 2 2 ZC3H12B 23 65502768 Silent SNP C C3L-00095_T 10743787 65502768 90538127 795 4004 HEPH 0 . GRCh38 X 66207265 66207265 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.2524G>A p.Glu842Lys p.E842K ENST00000519389 14/21 130 112 18 140 140 0 strelka-varscan-mutect HEPH,missense_variant,p.Glu842Lys,ENST00000519389,NM_138737.4;HEPH,missense_variant,p.Glu788Lys,ENST00000343002,;HEPH,missense_variant,p.Glu791Lys,ENST00000441993,NM_001130860.3;HEPH,missense_variant,p.Glu521Lys,ENST00000336279,NM_014799.3;HEPH,missense_variant,p.Glu599Lys,ENST00000419594,NM_001282141.1;HEPH,missense_variant,p.Glu745Lys,ENST00000425114,;HEPH,non_coding_transcript_exon_variant,,ENST00000471121,; A ENST00000519389 Transcript missense_variant 2703/6013 2524/3639 842/1212 E/K Gaa/Aaa 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 deleterious(0.01) 14/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 66207265 66207265 G A 1 0 0 0 0 1 0 0 0 6938 1175 41 3 3 HEPH 23 66207265 Missense_Mutation SNP G C3L-00095_T 704497 66207265 89833630 796 4005 EDA2R 0 . GRCh38 X 66599627 66599627 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.814C>A p.Pro272Thr p.P272T ENST00000396050 6/7 72 57 15 108 108 0 strelka-mutect EDA2R,missense_variant,p.Pro251Thr,ENST00000451436,NM_001199687.2;EDA2R,missense_variant,p.Pro272Thr,ENST00000396050,NM_001242310.1;EDA2R,missense_variant,p.Pro251Thr,ENST00000374719,NM_001324206.1,NM_021783.3;EDA2R,missense_variant,p.Pro272Thr,ENST00000253392,; T ENST00000396050 Transcript missense_variant 824/3429 814/957 272/318 P/T Ccc/Acc 1 -1 EDA2R HGNC HGNC:17756 protein_coding YES CCDS56603.1 ENSP00000379365 Q9HAV5 UPI00001B037F NM_001242310.1 deleterious(0) 6/7 hmmpanther:PTHR12120:SF8,hmmpanther:PTHR12120,Prints_domain:PR01973 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 66599627 66599627 G T 1 0 0 0 0 1 0 0 0 4732 1232 43 2 2 EDA2R 23 66599627 Missense_Mutation SNP G C3L-00095_T 392362 66599627 89441268 797 4006 DGAT2L6 0 . GRCh38 X 70204425 70204425 + Silent SNP C C A novel C3L-00095_T C3L-00095_N C C c.768C>A p.= p.I256I ENST00000333026 6/7 192 172 20 223 222 1 strelka-varscan-mutect DGAT2L6,synonymous_variant,p.=,ENST00000333026,NM_198512.2; A ENST00000333026 Transcript synonymous_variant 868/1553 768/1014 256/337 I atC/atA 1 1 DGAT2L6 HGNC HGNC:23250 protein_coding YES CCDS14397.1 ENSP00000328036 Q6ZPD8 UPI00001C10BF NM_198512.2 6/7 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF19 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 10 70204425 70204425 C A 1 0 0 0 0 0 0 0 1 4266 845 30 2 2 DGAT2L6 23 70204425 Silent SNP C C3L-00095_T 3604798 70204425 85836470 798 4007 SATL1 0 . GRCh38 X 85108179 85108179 + Missense_Mutation SNP G G C C3L-00095_T C3L-00095_N G G c.790C>G p.Pro264Ala p.P264A ENST00000509231 1/5 253 213 40 326 326 0 strelka-varscan-mutect SATL1,missense_variant,p.Pro264Ala,ENST00000509231,NM_001012980.2;SATL1,missense_variant,p.Pro77Ala,ENST00000395409,; C ENST00000509231 Transcript missense_variant 870/2224 790/1899 264/632 P/A Cca/Gca COSM4387114,COSM4387115 1 -1 SATL1 HGNC HGNC:27992 protein_coding YES CCDS35343.2 ENSP00000425421 Q86VE3 UPI000041ABBC NM_001012980.2 tolerated(0.05) 1/5 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 85108179 85108179 G C 1 0 0 0 0 1 0 0 0 14116 1203 42 4 4 SATL1 23 85108179 Missense_Mutation SNP G C3L-00095_T 14903754 85108179 70932716 799 4008 PCDH11X 0 . GRCh38 X 91835521 91835521 + Missense_Mutation SNP G G T C3L-00095_T C3L-00095_N G G c.17G>T p.Gly6Val p.G6V ENST00000373094 1/7 215 195 20 264 263 1 varscan-mutect PCDH11X,missense_variant,p.Gly6Val,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Gly6Val,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Gly6Val,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Gly6Val,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Gly6Val,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Gly6Val,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Gly6Val,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 862/9179 17/4044 6/1347 G/V gGg/gTg COSM1151737,COSM758172,COSM758173 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0.01) 1/7 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,Cleavage_site_(Signalp):SignalP-noTM 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 91835521 91835521 G T 1 0 0 0 0 1 0 0 0 11595 1232 43 2 2 PCDH11X 23 91835521 Missense_Mutation SNP G C3L-00095_T 6727342 91835521 64205374 800 4009 PCDH11X 0 . GRCh38 X 91835556 91835556 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.52G>T p.Val18Leu p.V18L ENST00000373094 1/7 242 212 30 296 296 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Val18Leu,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Val18Leu,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Val18Leu,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Val18Leu,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Val18Leu,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Val18Leu,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Val18Leu,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 897/9179 52/4044 18/1347 V/L Gtg/Ttg 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 tolerated(0.28) 1/7 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 91835556 91835556 G T 1 0 0 0 0 1 0 0 0 11595 1261 44 2 2 PCDH11X 23 91835556 Missense_Mutation SNP G C3L-00095_T 35 91835556 64205339 801 4010 DIAPH2 0 . GRCh38 X 96942043 96942043 + Nonsense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.1351G>T p.Glu451Ter p.E451* ENST00000324765 13/27 74 64 10 87 87 0 strelka-mutect DIAPH2,stop_gained,p.Glu451Ter,ENST00000324765,NM_006729.4;DIAPH2,stop_gained,p.Glu451Ter,ENST00000373061,;DIAPH2,stop_gained,p.Glu451Ter,ENST00000355827,;DIAPH2,stop_gained,p.Glu451Ter,ENST00000373049,NM_007309.3;DIAPH2,stop_gained,p.Glu458Ter,ENST00000373054,; T ENST00000324765 Transcript stop_gained 1698/9333 1351/3306 451/1101 E/* Gaa/Taa 1 1 DIAPH2 HGNC HGNC:2877 protein_coding YES CCDS14467.1 ENSP00000321348 O60879 UPI00001293C8 NM_006729.4 13/27 PROSITE_profiles:PS51232,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF174,Pfam_domain:PF06367,SMART_domains:SM01139,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 10 96942043 96942043 G T 1 0 0 0 0 0 1 0 0 4323 1175 41 2 2 DIAPH2 23 96942043 Nonsense_Mutation SNP G C3L-00095_T 5106487 96942043 59098852 802 4011 BTK 0 . GRCh38 X 101358368 101358368 + Missense_Mutation SNP C C A novel C3L-00095_T C3L-00095_N C C c.1146G>T p.Glu382Asp p.E382D ENST00000621635 12/19 305 270 35 372 372 0 strelka-varscan-mutect BTK,missense_variant,p.Glu382Asp,ENST00000621635,NM_001287344.1;BTK,missense_variant,p.Glu348Asp,ENST00000308731,NM_000061.2;BTK,missense_variant,p.Glu348Asp,ENST00000618050,;BTK,splice_region_variant,,ENST00000372880,NM_001287345.1;BTK,upstream_gene_variant,,ENST00000470069,;BTK,upstream_gene_variant,,ENST00000488970,;BTK,downstream_gene_variant,,ENST00000464006,;BTK,upstream_gene_variant,,ENST00000478995,;BTK,upstream_gene_variant,,ENST00000470329,; A ENST00000621635 Transcript missense_variant 1393/2767 1146/2082 382/693 E/D gaG/gaT 1 -1 BTK HGNC HGNC:1133 protein_coding YES CCDS76003.1 ENSP00000483570 Q06187 UPI000021216F NM_001287344.1 deleterious(0.02) 12/19 Gene3D:3.30.505.10,Pfam_domain:PF00017,PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF92,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs868950482 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 101358368 101358368 C A 1 0 0 0 0 1 0 0 0 1733 927 32 2 2 BTK 23 101358368 Missense_Mutation SNP C C3L-00095_T 4416325 101358368 54682527 803 4012 TCEAL2 0 . GRCh38 X 102127394 102127394 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.564G>T p.Leu188Phe p.L188F ENST00000372780 3/3 64 58 6 96 96 0 varscan-mutect TCEAL2,missense_variant,p.Leu188Phe,ENST00000372780,NM_080390.3;TCEAL2,missense_variant,p.Leu188Phe,ENST00000329035,;TCEAL2,downstream_gene_variant,,ENST00000476749,; T ENST00000372780 Transcript missense_variant 783/1100 564/684 188/227 L/F ttG/ttT 1 1 TCEAL2 HGNC HGNC:29818 protein_coding YES CCDS14496.1 ENSP00000361866 Q9H3H9 UPI00000709E1 NM_080390.3 deleterious(0.01) 3/3 hmmpanther:PTHR14754,hmmpanther:PTHR14754:SF15,Pfam_domain:PF04538 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.02441 1 1 1 1 0 T 3 4 10 102127394 102127394 G T 1 0 0 0 0 1 0 0 0 16078 1339 47 2 2 TCEAL2 23 102127394 Missense_Mutation SNP G C3L-00095_T 769026 102127394 53913501 804 4013 PLP1 0 . GRCh38 X 103787888 103787888 + Missense_Mutation SNP A A T rs132630282 C3L-00095_T C3L-00095_N A A c.544A>T p.Thr182Ser p.T182S ENST00000612423 5/8 267 247 20 257 257 0 strelka-varscan-mutect PLP1,missense_variant,p.Thr182Ser,ENST00000612423,NM_001128834.2;PLP1,missense_variant,p.Thr182Ser,ENST00000621218,NM_000533.4,NM_001305004.1;PLP1,missense_variant,p.Thr147Ser,ENST00000619236,NM_199478.2;PLP1,downstream_gene_variant,,ENST00000434483,;PLP1,downstream_gene_variant,,ENST00000494475,;PLP1,downstream_gene_variant,,ENST00000443502,;PLP1,downstream_gene_variant,,ENST00000422393,;PLP1,downstream_gene_variant,,ENST00000433491,;PLP1,downstream_gene_variant,,ENST00000455268,;PLP1,non_coding_transcript_exon_variant,,ENST00000466486,;PLP1,non_coding_transcript_exon_variant,,ENST00000479569,;PLP1,non_coding_transcript_exon_variant,,ENST00000478642,;PLP1,non_coding_transcript_exon_variant,,ENST00000485688,;PLP1,non_coding_transcript_exon_variant,,ENST00000494119,;PLP1,non_coding_transcript_exon_variant,,ENST00000461231,;PLP1,downstream_gene_variant,,ENST00000619257,;PLP1,downstream_gene_variant,,ENST00000495678,;PLP1,downstream_gene_variant,,ENST00000464776,;PLP1,downstream_gene_variant,,ENST00000465975,;PLP1,downstream_gene_variant,,ENST00000485931,;PLP1,upstream_gene_variant,,ENST00000496836,;PLP1,downstream_gene_variant,,ENST00000476160,;PLP1,downstream_gene_variant,,ENST00000480325,; T ENST00000612423 Transcript missense_variant 824/3132 544/834 182/277 T/S Acc/Tcc rs132630282,CM920582 1 1 PLP1 HGNC HGNC:9086 protein_coding YES CCDS14513.1 ENSP00000481006 P60201 A8K9L3 UPI000000031E NM_001128834.2 tolerated(0.89) 5/8 Pfam_domain:PF01275,hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF11,SMART_domains:SM00002 pathogenic MODERATE 1 SNV 2 1,1 1 PASS rs132630282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 103787888 103787888 A T 1 0 0 0 0 1 0 0 0 12200 275 10 4 4 PLP1 23 103787888 Missense_Mutation SNP A C3L-00095_T 1660494 103787888 52253007 805 4014 PLP1 0 . GRCh38 X 103788463 103788463 + Missense_Mutation SNP G G A C3L-00095_T C3L-00095_N G G c.649G>A p.Gly217Ser p.G217S ENST00000612423 6/8 303 254 49 331 331 0 strelka-varscan-mutect PLP1,missense_variant,p.Gly217Ser,ENST00000612423,NM_001128834.2;PLP1,missense_variant,p.Gly217Ser,ENST00000621218,NM_000533.4,NM_001305004.1;PLP1,missense_variant,p.Gly182Ser,ENST00000619236,NM_199478.2;PLP1,downstream_gene_variant,,ENST00000434483,;PLP1,downstream_gene_variant,,ENST00000494475,;PLP1,downstream_gene_variant,,ENST00000443502,;PLP1,downstream_gene_variant,,ENST00000422393,;PLP1,downstream_gene_variant,,ENST00000433491,;PLP1,downstream_gene_variant,,ENST00000455268,;PLP1,non_coding_transcript_exon_variant,,ENST00000466486,;PLP1,non_coding_transcript_exon_variant,,ENST00000485688,;PLP1,non_coding_transcript_exon_variant,,ENST00000494119,;PLP1,non_coding_transcript_exon_variant,,ENST00000461231,;PLP1,downstream_gene_variant,,ENST00000479569,;PLP1,downstream_gene_variant,,ENST00000478642,;PLP1,downstream_gene_variant,,ENST00000619257,;PLP1,downstream_gene_variant,,ENST00000495678,;PLP1,downstream_gene_variant,,ENST00000464776,;PLP1,downstream_gene_variant,,ENST00000465975,;PLP1,downstream_gene_variant,,ENST00000485931,;PLP1,upstream_gene_variant,,ENST00000496836,;PLP1,downstream_gene_variant,,ENST00000476160,;PLP1,downstream_gene_variant,,ENST00000480325,; A ENST00000612423 Transcript missense_variant 929/3132 649/834 217/277 G/S Ggc/Agc CM952022 1 1 PLP1 HGNC HGNC:9086 protein_coding YES CCDS14513.1 ENSP00000481006 P60201 A8K9L3 UPI000000031E NM_001128834.2 deleterious(0.05) 6/8 Pfam_domain:PF01275,Prints_domain:PR00214,hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF11,SMART_domains:SM00002 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 103788463 103788463 G A 1 0 0 0 0 1 0 0 0 12200 1348 47 3 3 PLP1 23 103788463 Missense_Mutation SNP G C3L-00095_T 575 103788463 52252432 806 4015 VSIG1 0 . GRCh38 X 108076113 108076113 + Missense_Mutation SNP G G A novel C3L-00095_T C3L-00095_N G G c.833G>A p.Gly278Asp p.G278D ENST00000415430 7/8 112 103 9 142 142 0 strelka-varscan-mutect VSIG1,missense_variant,p.Gly278Asp,ENST00000415430,NM_001170553.1;VSIG1,missense_variant,p.Gly242Asp,ENST00000217957,NM_182607.4;VSIG1,downstream_gene_variant,,ENST00000485533,;VSIG1,downstream_gene_variant,,ENST00000479635,; A ENST00000415430 Transcript missense_variant 994/3236 833/1272 278/423 G/D gGt/gAt 1 1 VSIG1 HGNC HGNC:28675 protein_coding YES CCDS55474.1 ENSP00000402219 Q86XK7 UPI00017A7E2F NM_001170553.1 deleterious(0) 7/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF115 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 108076113 108076113 G A 1 0 0 0 0 1 0 0 0 17772 1261 44 3 3 VSIG1 23 108076113 Missense_Mutation SNP G C3L-00095_T 4287650 108076113 47964782 807 4016 CHRDL1 0 . GRCh38 X 110700663 110700663 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.600C>A p.Asn200Lys p.N200K ENST00000372042 7/12 95 77 18 114 113 1 strelka-varscan-mutect CHRDL1,missense_variant,p.Asn193Lys,ENST00000372045,;CHRDL1,missense_variant,p.Asn199Lys,ENST00000394797,NM_145234.3;CHRDL1,missense_variant,p.Asn200Lys,ENST00000372042,NM_001143981.1;CHRDL1,missense_variant,p.Asn199Lys,ENST00000444321,NM_001143982.1;CHRDL1,missense_variant,p.Asn120Lys,ENST00000482160,NM_001143983.2; T ENST00000372042 Transcript missense_variant 702/1934 600/1377 200/458 N/K aaC/aaA 1 -1 CHRDL1 HGNC HGNC:29861 protein_coding YES CCDS48149.1 ENSP00000361112 Q9BU40 UPI0000367765 NM_001143981.1 deleterious(0.01) 7/12 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 110700663 110700663 G T 1 0 0 0 0 1 0 0 0 3133 1368 48 2 2 CHRDL1 23 110700663 Missense_Mutation SNP G C3L-00095_T 2624550 110700663 45340232 808 4017 CAPN6 0 . GRCh38 X 111249039 111249039 + Missense_Mutation SNP C C G novel C3L-00095_T C3L-00095_N C C c.1177G>C p.Glu393Gln p.E393Q ENST00000324068 9/13 100 82 18 134 134 0 strelka-varscan-mutect CAPN6,missense_variant,p.Glu393Gln,ENST00000324068,NM_014289.3; G ENST00000324068 Transcript missense_variant 1345/3568 1177/1926 393/641 E/Q Gag/Cag 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 deleterious(0.05) 9/13 hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183,Pfam_domain:PF01067,Gene3D:2.60.120.380,SMART_domains:SM00720,Superfamily_domains:SSF49758 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 10 111249039 111249039 C G 1 0 0 0 0 1 0 0 0 2324 835 29 4 4 CAPN6 23 111249039 Missense_Mutation SNP C C3L-00095_T 548376 111249039 44791856 809 4018 TRPC5 0 . GRCh38 X 111952103 111952103 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.318G>A p.= p.K106K ENST00000262839 2/11 79 64 15 104 104 0 strelka-varscan-mutect TRPC5,synonymous_variant,p.=,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript synonymous_variant 1237/5839 318/2922 106/973 K aaG/aaA 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 2/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Pfam_domain:PF12796,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 10 111952103 111952103 C T 1 0 0 0 0 0 0 0 1 17087 680 24 3 3 TRPC5 23 111952103 Silent SNP C C3L-00095_T 703064 111952103 44088792 810 4019 RP13-347D8.7 0 . GRCh38 X 119073734 119073734 + Frame_Shift_Del DEL G G - novel C3L-00095_T C3L-00095_N G G c.510delG p.Leu171CysfsTer148 p.L171Cfs*148 ENST00000620151 1/3 38 33 5 63 63 0 sindel-pindel RP13-347D8.7,frameshift_variant,p.Leu171CysfsTer148,ENST00000620151,;KIAA1210,downstream_gene_variant,,ENST00000402510,NM_020721.1; - ENST00000620151 Transcript frameshift_variant 509/1147 509/975 170/324 R/X cGg/cg 1 1 RP13-347D8.7 Clone_based_vega_gene protein_coding YES ENSP00000488984 A0A0U1RQG5 UPI000719A0D1 1/3 hmmpanther:PTHR32157,hmmpanther:PTHR32157:SF2,Pfam_domain:PF15623 HIGH 1 deletion 5 1 1 PASS . . 0 203 6 0 0 0 0 0 -13.04279 0.9999999 1 1 1 0 - 7 5 10 119073734 119073734 G - 1 0 1 0 1 0 0 0 0 13772 1116 39 0 0 RP13-347D8.7 23 119073734 Frame_Shift_Del DEL G C3L-00095_T 7121631 119073734 36967161 811 4020 DCAF12L2 0 . GRCh38 X 126165225 126165225 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.700C>A p.His234Asn p.H234N ENST00000360028 1/1 58 46 12 89 88 1 strelka-varscan-mutect DCAF12L2,missense_variant,p.His234Asn,ENST00000360028,NM_001013628.2; T ENST00000360028 Transcript missense_variant 873/2599 700/1392 234/463 H/N Cac/Aac 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 tolerated(0.25) 1/1 hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 PASS rs1375390881 . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 126165225 126165225 G T 1 0 0 0 0 1 0 0 0 4066 1319 46 2 2 DCAF12L2 23 126165225 Missense_Mutation SNP G C3L-00095_T 7091491 126165225 29875670 812 4021 PRR32 0 . GRCh38 X 126821034 126821034 + Silent SNP C C T novel C3L-00095_T C3L-00095_N C C c.396C>T p.= p.V132V ENST00000371125 2/2 53 49 4 54 54 0 strelka-mutect PRR32,synonymous_variant,p.=,ENST00000371125,NM_001122716.1; T ENST00000371125 Transcript synonymous_variant 476/1228 396/897 132/298 V gtC/gtT 1 1 PRR32 HGNC HGNC:34498 protein_coding YES CCDS48163.1 ENSP00000360166 B1ATL7 UPI00004A3B00 NM_001122716.1 2/2 Pfam_domain:PF15488,hmmpanther:PTHR37343,hmmpanther:PTHR37343:SF1 LOW 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -9.99482 0.9999981 1 1 1 0 T 2 4 10 126821034 126821034 C T 1 0 0 0 0 0 0 0 1 12738 900 32 3 3 PRR32 23 126821034 Silent SNP C C3L-00095_T 655809 126821034 29219861 813 4022 SMARCA1 0 . GRCh38 X 129515899 129515899 + Missense_Mutation SNP G G C C3L-00095_T C3L-00095_N G G c.524C>G p.Pro175Arg p.P175R ENST00000371121 4/25 77 62 15 74 74 0 strelka-varscan-mutect SMARCA1,missense_variant,p.Pro175Arg,ENST00000371122,NM_003069.4;SMARCA1,missense_variant,p.Pro175Arg,ENST00000371123,NM_001282875.1;SMARCA1,missense_variant,p.Pro175Arg,ENST00000371121,NM_001282874.1;SNORD112,upstream_gene_variant,,ENST00000516361,;SMARCA1,non_coding_transcript_exon_variant,,ENST00000478420,;SMARCA1,non_coding_transcript_exon_variant,,ENST00000617310,; C ENST00000371121 Transcript missense_variant 559/3564 524/3213 175/1070 P/R cCt/cGt COSM1114815 1 -1 SMARCA1 HGNC HGNC:11097 protein_coding YES CCDS76019.1 ENSP00000360162 B7ZLQ5 UPI00004258DE NM_001282874.1 deleterious(0) 4/25 hmmpanther:PTHR10799:SF691,hmmpanther:PTHR10799,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 10 129515899 129515899 G C 1 0 0 0 0 1 0 0 0 15061 1014 35 4 4 SMARCA1 23 129515899 Missense_Mutation SNP G C3L-00095_T 2694865 129515899 26524996 814 4023 ARHGAP36 0 . GRCh38 X 131084301 131084301 + Silent SNP A A T novel C3L-00095_T C3L-00095_N A A c.642A>T p.= p.P214P ENST00000276211 5/12 50 44 6 81 81 0 strelka-varscan-mutect ARHGAP36,synonymous_variant,p.=,ENST00000276211,NM_144967.3;ARHGAP36,synonymous_variant,p.=,ENST00000370922,NM_001282607.1;ARHGAP36,synonymous_variant,p.=,ENST00000412432,;ARHGAP36,synonymous_variant,p.=,ENST00000370921,;ARHGAP36,synonymous_variant,p.=,ENST00000423277,; T ENST00000276211 Transcript synonymous_variant 987/3083 642/1644 214/547 P ccA/ccT 1 1 ARHGAP36 HGNC HGNC:26388 protein_coding YES CCDS14628.1 ENSP00000276211 Q6ZRI8 UPI0000041347 NM_144967.3 5/12 hmmpanther:PTHR12635 LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -14.7982 1 1 1 1 0 T 2 4 10 131084301 131084301 A T 1 0 0 0 0 0 0 0 1 1009 117 5 4 4 ARHGAP36 23 131084301 Silent SNP A C3L-00095_T 1568402 131084301 24956594 815 4024 SAGE1 0 . GRCh38 X 135908554 135908554 + Missense_Mutation SNP G G C novel C3L-00095_T C3L-00095_N G G c.1378G>C p.Val460Leu p.V460L ENST00000324447 12/20 93 82 11 109 109 0 strelka-varscan-mutect SAGE1,missense_variant,p.Val460Leu,ENST00000324447,;SAGE1,missense_variant,p.Val460Leu,ENST00000370709,NM_018666.2;SAGE1,intron_variant,,ENST00000537770,; C ENST00000324447 Transcript missense_variant 1452/2952 1378/2715 460/904 V/L Gtt/Ctt 1 1 SAGE1 HGNC HGNC:30369 protein_coding YES CCDS14652.1 ENSP00000323191 Q9NXZ1 UPI00001413AB tolerated(0.1) 12/20 hmmpanther:PTHR12957:SF25,hmmpanther:PTHR12957 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99963 1 1 1 1 0 C 3 2 10 135908554 135908554 G C 1 0 0 0 0 1 0 0 0 14068 1377 48 4 4 SAGE1 23 135908554 Missense_Mutation SNP G C3L-00095_T 4824253 135908554 20132341 816 4025 SLITRK4 0 . GRCh38 X 143629271 143629271 + Missense_Mutation SNP C C A C3L-00095_T C3L-00095_N C C c.1838G>T p.Gly613Val p.G613V ENST00000596188 2/2 123 106 17 179 179 0 strelka-varscan-mutect SLITRK4,missense_variant,p.Gly613Val,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.Gly613Val,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.Gly613Val,ENST00000356928,NM_001184749.2; A ENST00000596188 Transcript missense_variant 2064/8545 1838/2514 613/837 G/V gGg/gTg COSM756078 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 tolerated(0.47) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 10 143629271 143629271 C A 1 0 0 0 0 1 0 0 0 15036 623 22 2 2 SLITRK4 23 143629271 Missense_Mutation SNP C C3L-00095_T 7720717 143629271 12411624 817 4026 MAGEA11 0 . GRCh38 X 149715868 149715868 + Missense_Mutation SNP G G T novel C3L-00095_T C3L-00095_N G G c.382G>T p.Ala128Ser p.A128S ENST00000355220 5/5 90 78 12 105 105 0 strelka-varscan-mutect MAGEA11,missense_variant,p.Ala128Ser,ENST00000355220,NM_005366.4;MAGEA11,missense_variant,p.Ala99Ser,ENST00000333104,NM_001011544.1;MAGEA11,missense_variant,p.Ala99Ser,ENST00000412632,;MAGEA11,non_coding_transcript_exon_variant,,ENST00000518694,; T ENST00000355220 Transcript missense_variant 484/1864 382/1290 128/429 A/S Gcc/Tcc 1 1 MAGEA11 HGNC HGNC:6798 protein_coding YES CCDS48180.1 ENSP00000347358 P43364 UPI0000211BB0 NM_005366.4 tolerated(0.15) 5/5 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF71,Pfam_domain:PF12440,SMART_domains:SM01392 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 10 149715868 149715868 G T 1 0 0 0 0 1 0 0 0 9081 1203 42 2 2 MAGEA11 23 149715868 Missense_Mutation SNP G C3L-00095_T 6086597 149715868 6325027 818 4027 TMEM57 0 . GRCh38 1 25458479 25458479 + Missense_Mutation SNP G G T novel C3L-00140_T C3L-00140_N G G c.741G>T p.Leu247Phe p.L247F ENST00000374343 6/11 103 89 14 139 139 0 strelka-varscan-mutect TMEM57,missense_variant,p.Leu247Phe,ENST00000374343,NM_018202.5;TMEM57,intron_variant,,ENST00000399766,NM_001282564.1;TMEM57,non_coding_transcript_exon_variant,,ENST00000470035,; T ENST00000374343 Transcript missense_variant 920/3917 741/1995 247/664 L/F ttG/ttT 1 1 TMEM57 HGNC HGNC:25572 protein_coding YES CCDS30638.1 ENSP00000363463 Q8N5G2 UPI000004A074 NM_018202.5 tolerated(0.7) 6/11 hmmpanther:PTHR13289:SF5,hmmpanther:PTHR13289,Pfam_domain:PF09726 MODERATE 1 SNV 1 1 PASS rs1186494608 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 25458479 25458479 G T 1 0 0 0 0 1 0 0 0 16660 1310 46 2 2 TMEM57 1 25458479 Missense_Mutation SNP G C3L-00140_T 25458479 223497943 1 4028 GLIS1 0 . GRCh38 1 53594454 53594454 + Missense_Mutation SNP G G T rs184554996 C3L-00140_T C3L-00140_N G G c.449C>A p.Ala150Glu p.A150E ENST00000312233 3/10 243 209 34 237 237 0 strelka-varscan-mutect GLIS1,missense_variant,p.Ala150Glu,ENST00000312233,NM_147193.2;GLIS1,missense_variant,p.Ala325Glu,ENST00000628545,; T ENST00000312233 Transcript missense_variant 1016/2812 449/1863 150/620 A/E gCg/gAg rs184554996 1 -1 GLIS1 HGNC HGNC:29525 protein_coding YES CCDS582.1 ENSP00000309653 Q8NBF1 UPI000013F293 NM_147193.2 tolerated(0.27) 3/10 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF93 MODERATE 1 SNV 2 1 PASS rs184554996 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 53594454 53594454 G T 1 0 0 0 0 1 0 0 0 6323 1087 38 1 1 GLIS1 1 53594454 Missense_Mutation SNP G C3L-00140_T 28135975 53594454 195361968 2 4029 ERICH3 0 . GRCh38 1 74572006 74572006 + Missense_Mutation SNP G G T novel C3L-00140_T C3L-00140_N G G c.3704C>A p.Pro1235Gln p.P1235Q ENST00000326665 14/15 193 152 41 236 235 1 strelka-varscan-mutect ERICH3,missense_variant,p.Pro1235Gln,ENST00000326665,NM_001002912.4;ERICH3,non_coding_transcript_exon_variant,,ENST00000433746,;ERICH3,downstream_gene_variant,,ENST00000614534,; T ENST00000326665 Transcript missense_variant 3923/7159 3704/4593 1235/1530 P/Q cCa/cAa 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 tolerated(0.08) 14/15 hmmpanther:PTHR23034 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 74572006 74572006 G T 1 0 0 0 0 1 0 0 0 5083 1348 47 2 2 ERICH3 1 74572006 Missense_Mutation SNP G C3L-00140_T 20977552 74572006 174384416 3 4030 TMCO1 0 . GRCh38 1 165759557 165759557 + Missense_Mutation SNP T T A novel C3L-00140_T C3L-00140_N T T c.329A>T p.Glu110Val p.E110V ENST00000612311 3/7 107 72 35 308 308 0 strelka-varscan-mutect TMCO1,missense_variant,p.Glu110Val,ENST00000612311,NM_019026.4,NM_001256164.1;TMCO1,missense_variant,p.Glu110Val,ENST00000367881,;TMCO1,missense_variant,p.Glu59Val,ENST00000392129,;TMCO1,missense_variant,p.Glu47Val,ENST00000481278,NM_001256165.1;TMCO1,missense_variant,p.Glu110Val,ENST00000628579,;TMCO1,5_prime_UTR_variant,,ENST00000580248,;TMCO1,5_prime_UTR_variant,,ENST00000464650,;TMCO1,missense_variant,p.Glu110Val,ENST00000465705,;TMCO1,intron_variant,,ENST00000476143,; A ENST00000612311 Transcript missense_variant 347/4468 329/720 110/239 E/V gAg/gTg 1 -1 TMCO1 HGNC HGNC:18188 protein_coding YES CCDS1251.2 ENSP00000480514 J9JIE6 UPI0000EE3C5A NM_019026.4,NM_001256164.1 tolerated(0.13) 3/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01956,hmmpanther:PTHR20917,SMART_domains:SM01415 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 165759557 165759557 T A 1 0 0 0 0 1 0 0 0 16441 1551 54 4 4 TMCO1 1 165759557 Missense_Mutation SNP T C3L-00140_T 91187551 165759557 83196865 4 4031 XPO1 0 . GRCh38 2 61482462 61482462 + Missense_Mutation SNP G G A novel C3L-00140_T C3L-00140_N G G c.2890C>T p.Pro964Ser p.P964S ENST00000401558 23/25 63 54 9 144 144 0 strelka-mutect XPO1,missense_variant,p.Pro964Ser,ENST00000401558,NM_003400.3;XPO1,missense_variant,p.Pro964Ser,ENST00000404992,;XPO1,missense_variant,p.Pro964Ser,ENST00000406957,;RP11-355B11.2,intron_variant,,ENST00000603652,;RP11-355B11.2,intron_variant,,ENST00000578974,;RP11-355B11.2,intron_variant,,ENST00000603028,;RP11-355B11.2,upstream_gene_variant,,ENST00000605437,;RP11-355B11.2,downstream_gene_variant,,ENST00000603199,;XPO1,downstream_gene_variant,,ENST00000494468,;XPO1,3_prime_UTR_variant,,ENST00000428210,;XPO1,non_coding_transcript_exon_variant,,ENST00000481073,;XPO1,downstream_gene_variant,,ENST00000461407,;XPO1,downstream_gene_variant,,ENST00000492182,; A ENST00000401558 Transcript missense_variant 3618/4915 2890/3216 964/1071 P/S Cct/Tct 1 -1 XPO1 HGNC HGNC:12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 UPI0000001C23 NM_003400.3 deleterious(0.03) 23/25 Gene3D:1.25.10.10,Pfam_domain:PF08767,SMART_domains:SM01102,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 61482462 61482462 G A 1 0 0 0 0 1 0 0 0 18004 1174 41 3 3 XPO1 2 61482462 Missense_Mutation SNP G C3L-00140_T 61482462 180711067 5 4032 CEP120 0 . GRCh38 5 123382886 123382886 + Missense_Mutation SNP C C A rs766153970 C3L-00140_T C3L-00140_N C C c.1864G>T p.Val622Leu p.V622L ENST00000306467 13/20 123 102 21 110 110 0 strelka-varscan-mutect CEP120,missense_variant,p.Val622Leu,ENST00000306467,;CEP120,missense_variant,p.Val622Leu,ENST00000328236,NM_153223.3;CEP120,missense_variant,p.Val596Leu,ENST00000306481,NM_001166226.1;CEP120,missense_variant,p.Val596Leu,ENST00000508442,;CEP120,3_prime_UTR_variant,,ENST00000508138,;CEP120,3_prime_UTR_variant,,ENST00000513565,; A ENST00000306467 Transcript missense_variant 2169/4900 1864/2961 622/986 V/L Gta/Tta rs766153970 1 -1 CEP120 HGNC HGNC:26690 protein_coding YES CCDS4134.2 ENSP00000303058 Q8N960 UPI0000D79C73 tolerated(0.96) 13/20 hmmpanther:PTHR21574 MODERATE 1 SNV 5 1 PASS rs766153970 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 123382886 123382886 C A 1 0 0 0 0 1 0 0 0 2956 492 17 2 2 CEP120 5 123382886 Missense_Mutation SNP C C3L-00140_T 123382886 58155373 6 4033 PDE6A 0 . GRCh38 5 149863219 149863219 + Silent SNP G G A novel C3L-00140_T C3L-00140_N G G c.2406C>T p.= p.I802I ENST00000255266 21/22 458 371 87 499 499 0 strelka-varscan-mutect PDE6A,synonymous_variant,p.=,ENST00000255266,NM_000440.2;PDE6A,synonymous_variant,p.=,ENST00000613228,;PDE6A,synonymous_variant,p.=,ENST00000617647,;PDE6A,non_coding_transcript_exon_variant,,ENST00000508173,;PDE6A,non_coding_transcript_exon_variant,,ENST00000512670,; A ENST00000255266 Transcript synonymous_variant 2526/5642 2406/2583 802/860 I atC/atT 1 -1 PDE6A HGNC HGNC:8785 protein_coding YES CCDS4299.1 ENSP00000255266 P16499 UPI000013CE9F NM_000440.2 21/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF115,Gene3D:1.10.1300.10,Pfam_domain:PF00233,Superfamily_domains:SSF109604 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 11 149863219 149863219 G A 1 0 0 0 0 0 0 0 1 11733 1280 45 3 3 PDE6A 5 149863219 Silent SNP G C3L-00140_T 26480333 149863219 31675040 7 4034 PRRC2A 0 . GRCh38 6 31627823 31627823 + Missense_Mutation SNP G G T C3L-00140_T C3L-00140_N G G c.1349G>T p.Arg450Leu p.R450L ENST00000376033 12/31 190 133 57 221 221 0 strelka-varscan-mutect PRRC2A,missense_variant,p.Arg450Leu,ENST00000376033,NM_004638.3;PRRC2A,missense_variant,p.Arg450Leu,ENST00000376007,NM_080686.2;SNORA38,downstream_gene_variant,,ENST00000363946,;PRRC2A,downstream_gene_variant,,ENST00000469577,;PRRC2A,upstream_gene_variant,,ENST00000483470,;PRRC2A,downstream_gene_variant,,ENST00000464890,;PRRC2A,downstream_gene_variant,,ENST00000464079,; T ENST00000376033 Transcript missense_variant 1583/6893 1349/6474 450/2157 R/L cGg/cTg COSM3861722 1 1 PRRC2A HGNC HGNC:13918 protein_coding YES CCDS4708.1 ENSP00000365201 P48634 UPI000020E56F NM_004638.3 tolerated(0.07) 12/31 hmmpanther:PTHR14038:SF5,hmmpanther:PTHR14038 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 31627823 31627823 G T 1 0 0 0 0 1 0 0 0 12748 1116 39 1 1 PRRC2A 6 31627823 Missense_Mutation SNP G C3L-00140_T 31627823 139178156 8 4035 EYA4 0 . GRCh38 6 133461141 133461141 + Missense_Mutation SNP G G A novel C3L-00140_T C3L-00140_N G G c.398G>A p.Arg133Lys p.R133K ENST00000531901 7/20 339 275 64 340 340 0 strelka-varscan-mutect EYA4,missense_variant,p.Arg133Lys,ENST00000367895,NM_004100.4;EYA4,missense_variant,p.Arg133Lys,ENST00000355167,NM_172105.3;EYA4,missense_variant,p.Arg110Lys,ENST00000355286,NM_172103.3;EYA4,missense_variant,p.Arg110Lys,ENST00000525849,;EYA4,missense_variant,p.Arg133Lys,ENST00000531901,NM_001301013.1;EYA4,missense_variant,p.Arg79Lys,ENST00000452339,NM_001301012.1;EYA4,missense_variant,p.Arg79Lys,ENST00000430974,;EYA4,missense_variant,p.Arg133Lys,ENST00000431403,;RP1-283K11.2,upstream_gene_variant,,ENST00000457081,;EYA4,non_coding_transcript_exon_variant,,ENST00000531861,;EYA4,non_coding_transcript_exon_variant,,ENST00000421413,;EYA4,upstream_gene_variant,,ENST00000532518,;EYA4,downstream_gene_variant,,ENST00000525614,;EYA4,upstream_gene_variant,,ENST00000497350,; A ENST00000531901 Transcript missense_variant 627/2892 398/1938 133/645 R/K aGa/aAa 1 1 EYA4 HGNC HGNC:3522 protein_coding YES CCDS75521.1 ENSP00000432770 F2Z2Y1 UPI0001AE72E3 NM_001301013.1 tolerated(0.11) 7/20 hmmpanther:PTHR10190:SF17,hmmpanther:PTHR10190 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 133461141 133461141 G A 1 0 0 0 0 1 0 0 0 5199 942 33 3 3 EYA4 6 133461141 Missense_Mutation SNP G C3L-00140_T 101833318 133461141 37344838 9 4036 SLC35D3 0 . GRCh38 6 136924028 136924028 + Missense_Mutation SNP G G T rs370964074 C3L-00140_T C3L-00140_N G G c.583G>T p.Val195Phe p.V195F ENST00000331858 2/2 205 169 36 245 245 0 strelka-varscan-mutect SLC35D3,missense_variant,p.Val195Phe,ENST00000331858,NM_001008783.2; T ENST00000331858 Transcript missense_variant 748/2359 583/1251 195/416 V/F Gtc/Ttc rs370964074 1 1 SLC35D3 HGNC HGNC:15621 protein_coding YES CCDS34544.1 ENSP00000333591 Q5M8T2 UPI00003673E9 NM_001008783.2 tolerated(0.1) 2/2 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF62,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs370964074 . 0 206 0 4 0 0 0 0 -20 0.99994 1 1 1 0 T 3 4 11 136924028 136924028 G T 1 0 0 0 0 1 0 0 0 14853 1145 40 1 1 SLC35D3 6 136924028 Missense_Mutation SNP G C3L-00140_T 3462887 136924028 33881951 10 4037 LATS1 0 . GRCh38 6 149676591 149676591 + Missense_Mutation SNP G G A novel C3L-00140_T C3L-00140_N G G c.2740C>T p.Pro914Ser p.P914S ENST00000543571 6/8 135 113 22 153 153 0 strelka-varscan-mutect LATS1,missense_variant,p.Pro914Ser,ENST00000543571,NM_004690.3;LATS1,missense_variant,p.Pro914Ser,ENST00000253339,;LATS1,non_coding_transcript_exon_variant,,ENST00000542747,;LATS1,3_prime_UTR_variant,,ENST00000441107,; A ENST00000543571 Transcript missense_variant 3288/7517 2740/3393 914/1130 P/S Ccc/Tcc 1 -1 LATS1 HGNC HGNC:6514 protein_coding YES CCDS34551.1 ENSP00000437550 O95835 UPI0000073DC2 NM_004690.3 deleterious(0) 6/8 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF138,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 149676591 149676591 G A 1 0 0 0 0 1 0 0 0 8551 1174 41 3 3 LATS1 6 149676591 Missense_Mutation SNP G C3L-00140_T 12752563 149676591 21129388 11 4038 TTLL2 0 . GRCh38 6 167340836 167340836 + Silent SNP C C A novel C3L-00140_T C3L-00140_N C C c.936C>A p.= p.I312I ENST00000239587 3/3 235 194 41 281 281 0 strelka-varscan-mutect TTLL2,synonymous_variant,p.=,ENST00000239587,NM_031949.4;TTLL2,synonymous_variant,p.=,ENST00000515138,;TTLL2,downstream_gene_variant,,ENST00000512917,; A ENST00000239587 Transcript synonymous_variant 1024/2075 936/1779 312/592 I atC/atA 1 1 TTLL2 HGNC HGNC:21211 protein_coding YES CCDS5301.1 ENSP00000239587 Q9BWV7 UPI00001A3A8B NM_031949.4 3/3 Pfam_domain:PF03133,PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF11 LOW 1 SNV 1 1 PASS rs1261849765 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 11 167340836 167340836 C A 1 0 0 0 0 0 0 0 1 17238 816 29 2 2 TTLL2 6 167340836 Silent SNP C C3L-00140_T 17664245 167340836 3465143 12 4039 HDAC9 0 . GRCh38 7 18648593 18648593 + Missense_Mutation SNP G G T novel C3L-00140_T C3L-00140_N G G c.1377G>T p.Gln459His p.Q459H ENST00000441542 10/25 385 334 51 454 451 3 strelka-varscan-mutect HDAC9,missense_variant,p.Gln456His,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Gln415His,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,missense_variant,p.Gln456His,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Gln443His,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,missense_variant,p.Gln415His,ENST00000401921,;HDAC9,missense_variant,p.Gln459His,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Gln456His,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Gln454His,ENST00000417496,NM_001204144.1;HDAC9,missense_variant,p.Gln412His,ENST00000428307,NM_001204145.1;HDAC9,missense_variant,p.Gln428His,ENST00000456174,NM_001204148.1;HDAC9,missense_variant,p.Gln379His,ENST00000524023,NM_001204147.1;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; T ENST00000441542 Transcript missense_variant 1377/3210 1377/3210 459/1069 Q/H caG/caT 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0.02) 10/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,PIRSF_domain:PIRSF037911 MODERATE 1 SNV 1 1 PASS rs1260202588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 18648593 18648593 G T 1 0 0 0 0 1 0 0 0 6901 933 33 2 2 HDAC9 7 18648593 Missense_Mutation SNP G C3L-00140_T 18648593 140697380 13 4040 BRAF 0 . GRCh38 7 140753354 140753354 + Missense_Mutation SNP T T C rs121913338 C3L-00140_T C3L-00140_N T T c.1781A>G p.Asp594Gly p.D594G ENST00000288602 15/18 267 221 46 371 371 0 strelka-varscan-mutect BRAF,missense_variant,p.Asp202Gly,ENST00000496384,;BRAF,missense_variant,p.Asp594Gly,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Asp22Gly,ENST00000479537,;BRAF,3_prime_UTR_variant,,ENST00000497784,; C ENST00000288602 Transcript missense_variant 1842/2480 1781/2301 594/766 D/G gAt/gGt rs121913338,COSM1583010,COSM466,COSM467 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious(0) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF43,SMART_domains:SM00220,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 11 140753354 140753354 T C 1 0 0 0 0 1 0 0 0 1665 1435 50 5 5 BRAF 7 140753354 Missense_Mutation SNP T C3L-00140_T 122104761 140753354 18592619 14 4041 INSIG1 0 . GRCh38 7 155308255 155308255 + Missense_Mutation SNP G G T novel C3L-00140_T C3L-00140_N G G c.819G>T p.Lys273Asn p.K273N ENST00000340368 6/6 108 96 12 91 91 0 strelka-varscan-mutect INSIG1,missense_variant,p.Lys273Asn,ENST00000340368,NM_005542.4;INSIG1,missense_variant,p.Ser145Ile,ENST00000344756,NM_198336.2;INSIG1,missense_variant,p.Ser206Ile,ENST00000476756,;INSIG1,3_prime_UTR_variant,,ENST00000342407,NM_198337.2; T ENST00000340368 Transcript missense_variant 1030/3010 819/834 273/277 K/N aaG/aaT 1 1 INSIG1 HGNC HGNC:6083 protein_coding YES CCDS5938.1 ENSP00000344741 O15503 A0A024RD68 UPI00000015DE NM_005542.4 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR15301:SF11,hmmpanther:PTHR15301 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -19.99995 0.999928 1 1 1 0 T 3 4 11 155308255 155308255 G T 1 0 0 0 0 1 0 0 0 7667 971 34 2 2 INSIG1 7 155308255 Missense_Mutation SNP G C3L-00140_T 14554901 155308255 4037718 15 4042 GOT1L1 0 . GRCh38 8 37937745 37937745 + Missense_Mutation SNP C C A rs374820148 C3L-00140_T C3L-00140_N C C c.302G>T p.Gly101Val p.G101V ENST00000307599 3/9 180 152 28 175 174 1 strelka-varscan-mutect GOT1L1,missense_variant,p.Gly101Val,ENST00000307599,NM_152413.2;GOT1L1,missense_variant,p.Gly133Val,ENST00000524298,;GOT1L1,upstream_gene_variant,,ENST00000518826,; A ENST00000307599 Transcript missense_variant 402/1378 302/1266 101/421 G/V gGg/gTg rs374820148 1 -1 GOT1L1 HGNC HGNC:28487 protein_coding YES CCDS47839.1 ENSP00000303077 Q8NHS2 UPI000004E052 NM_152413.2 deleterious(0.02) 3/9 Gene3D:3.90.1150.10,Pfam_domain:PF00155,hmmpanther:PTHR11879,hmmpanther:PTHR11879:SF6,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs374820148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 37937745 37937745 C A 1 0 0 0 0 1 0 0 0 6474 637 22 2 2 GOT1L1 8 37937745 Missense_Mutation SNP C C3L-00140_T 37937745 107200891 16 4043 SPATA31E1 0 . GRCh38 9 87888495 87888495 + Silent SNP A A G novel C3L-00140_T C3L-00140_N A A c.4008A>G p.= p.G1336G ENST00000325643 4/4 267 211 56 247 247 0 strelka-varscan-mutect SPATA31E1,synonymous_variant,p.=,ENST00000325643,NM_178828.4; G ENST00000325643 Transcript synonymous_variant 4074/4478 4008/4338 1336/1445 G ggA/ggG 1 1 SPATA31E1 HGNC HGNC:26672 protein_coding YES CCDS6676.1 ENSP00000322640 Q6ZUB1 UPI000036764A NM_178828.4 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF19 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 11 87888495 87888495 A G 1 0 0 0 0 0 0 0 1 15350 262 10 5 5 SPATA31E1 9 87888495 Silent SNP A C3L-00140_T 87888495 50506222 17 4044 GPR107 0 . GRCh38 9 130114576 130114576 + Splice_Site SNP G G T novel C3L-00140_T C3L-00140_N G G c.1364-1G>T p.X455_splice ENST00000372406 79 72 7 91 91 0 strelka-varscan-mutect GPR107,splice_acceptor_variant,,ENST00000372406,NM_001136557.1;GPR107,stop_gained,p.Glu455Ter,ENST00000610997,;GPR107,intron_variant,,ENST00000347136,NM_020960.4,NM_001287346.1;GPR107,intron_variant,,ENST00000372410,NM_001136558.1;GPR107,intron_variant,,ENST00000483935,;GPR107,intron_variant,,ENST00000493417,; T ENST00000372406 Transcript splice_acceptor_variant -/7353 1364/1803 455/600 1 1 GPR107 HGNC HGNC:17830 protein_coding YES CCDS48041.1 ENSP00000361483 Q5VW38 UPI00004589E0 NM_001136557.1 15/19 HIGH 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -15.0427 0.9999986 1 1 1 0 T 5 4 11 130114576 130114576 G T 1 0 0 0 0 0 0 1 0 6525 956 33 2 2 GPR107 9 130114576 Splice_Site SNP G C3L-00140_T 42226081 130114576 8280141 18 4045 ANXA8 0 . GRCh38 10 47477163 47477163 + Missense_Mutation SNP C C A novel C3L-00140_T C3L-00140_N C C c.353G>T p.Ser118Ile p.S118I ENST00000611843 4/12 730 676 54 765 765 0 varscan-mutect ANXA8,missense_variant,p.Ser118Ile,ENST00000611843,NM_001271702.1;ANXA8,missense_variant,p.Ser80Ile,ENST00000585281,NM_001040084.2;ANXA8,missense_variant,p.Ser18Ile,ENST00000583911,NM_001271703.1;ANXA8,missense_variant,p.Ser118Ile,ENST00000583874,;ANXA8,intron_variant,,ENST00000583448,;ANXA8,missense_variant,p.Ser80Ile,ENST00000577813,;ANXA8,downstream_gene_variant,,ENST00000602877,; A ENST00000611843 Transcript missense_variant 578/2174 353/1098 118/365 S/I aGt/aTt 1 -1 ANXA8 HGNC HGNC:546 protein_coding YES CCDS73123.1 ENSP00000478026 A0A087WTN9 UPI000299A05A NM_001271702.1 deleterious(0) 4/12 hmmpanther:PTHR10502,PROSITE_patterns:PS00223,Gene3D:1.10.220.10,Pfam_domain:PF00191,SMART_domains:SM00335,Superfamily_domains:SSF47874,Prints_domain:PR00196 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 47477163 47477163 C A 1 0 0 0 0 1 0 0 0 832 565 20 2 2 ANXA8 10 47477163 Missense_Mutation SNP C C3L-00140_T 47477163 86320259 19 4046 TBATA 0 . GRCh38 10 70779659 70779659 + Missense_Mutation SNP C C A rs752753016 C3L-00140_T C3L-00140_N C C c.361G>T p.Gly121Trp p.G121W ENST00000299290 5/11 58 51 7 49 49 0 strelka-mutect TBATA,missense_variant,p.Gly121Trp,ENST00000456372,NM_001318241.1;TBATA,missense_variant,p.Gly121Trp,ENST00000299290,NM_001318243.1,NM_152710.2; A ENST00000299290 Transcript missense_variant 751/1583 361/1056 121/351 G/W Ggg/Tgg rs752753016 1 -1 TBATA HGNC HGNC:23511 protein_coding YES CCDS7308.1 ENSP00000299290 Q96M53 UPI000013E57C NM_001318243.1,NM_152710.2 deleterious(0) 5/11 hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF3,Pfam_domain:PF15256 MODERATE 1 SNV 1 1 PASS rs752753016 . 0 200 10 0 0 0 0 0 -15.99601 0.9999735 1 1 1 0 A 3 1 11 70779659 70779659 C A 1 0 0 0 0 1 0 0 0 15996 623 22 2 2 TBATA 10 70779659 Missense_Mutation SNP C C3L-00140_T 23302496 70779659 63017763 20 4047 SFTPA1 0 . GRCh38 10 79613209 79613211 + In_Frame_Del DEL GAG GAG - novel C3L-00140_T C3L-00140_N GAG GAG c.361_363delGAG p.Glu121del p.E121del ENST00000419470 5/6 217 194 23 239 239 0 sindel-varindel-pindel SFTPA1,inframe_deletion,p.Glu106del,ENST00000398636,NM_001164646.1,NM_005411.4,NM_001164644.1;SFTPA1,inframe_deletion,p.Glu121del,ENST00000419470,NM_001093770.2,NM_001164645.1;SFTPA1,inframe_deletion,p.Glu106del,ENST00000428376,NM_001164647.1;SFTPA1,inframe_deletion,p.Glu106del,ENST00000439264,;SFTPA1,inframe_deletion,p.Glu106del,ENST00000429958,;SFTPA1,downstream_gene_variant,,ENST00000486922,; - ENST00000419470 Transcript inframe_deletion 434-436/2210 358-360/792 120/263 E/- GAG/- 1 1 SFTPA1 HGNC HGNC:10798 protein_coding YES CCDS44444.2 ENSP00000397082 Q8IWL2 UPI00006C104C NM_001093770.2,NM_001164645.1 5/6 hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF21,Superfamily_domains:SSF57944 MODERATE 1 deletion 1 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 11 79613209 79613209 GAG - 1 0 1 0 1 0 0 0 0 14449 1291 45 0 0 SFTPA1 10 79613209 In_Frame_Del DEL GAG C3L-00140_T 8833550 79613209 54184213 21 4048 GBF1 0 . GRCh38 10 102351312 102351312 + Missense_Mutation SNP C C G novel C3L-00140_T C3L-00140_N C C c.352C>G p.His118Asp p.H118D ENST00000369983 5/40 146 129 17 205 205 0 strelka-varscan-mutect GBF1,missense_variant,p.His118Asp,ENST00000369983,NM_001199379.1,NM_001199378.1,NM_004193.2; G ENST00000369983 Transcript missense_variant 612/6403 352/5580 118/1859 H/D Cat/Gat 1 1 GBF1 HGNC HGNC:4181 protein_coding YES CCDS7533.1 ENSP00000359000 Q92538 UPI000012B228 NM_001199379.1,NM_001199378.1,NM_004193.2 deleterious(0) 5/40 hmmpanther:PTHR10663:SF167,hmmpanther:PTHR10663 MODERATE 1 SNV 1 1 PASS rs1243761951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 102351312 102351312 C G 1 0 0 0 0 1 0 0 0 6142 594 21 4 4 GBF1 10 102351312 Missense_Mutation SNP C C3L-00140_T 22738103 102351312 31446110 22 4049 KDM2A 0 . GRCh38 11 67254353 67254353 + Missense_Mutation SNP C C A novel C3L-00140_T C3L-00140_N C C c.3242C>A p.Ser1081Tyr p.S1081Y ENST00000529006 20/21 274 232 42 295 295 0 strelka-varscan-mutect KDM2A,missense_variant,p.Ser1081Tyr,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Ser1064Tyr,ENST00000308783,;KDM2A,missense_variant,p.Ser642Tyr,ENST00000530342,NM_001256405.1;KDM2A,3_prime_UTR_variant,,ENST00000398645,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000524657,; A ENST00000529006 Transcript missense_variant 3688/6967 3242/3489 1081/1162 S/Y tCc/tAc 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 deleterious(0) 20/21 Gene3D:3.80.10.10,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,SMART_domains:SM00367,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 67254353 67254353 C A 1 0 0 0 0 1 0 0 0 8042 855 30 2 2 KDM2A 11 67254353 Missense_Mutation SNP C C3L-00140_T 67254353 67832269 23 4050 KIAA1551 0 . GRCh38 12 31983725 31983725 + Nonsense_Mutation SNP C C T novel C3L-00140_T C3L-00140_N C C c.2770C>T p.Gln924Ter p.Q924* ENST00000312561 4/6 153 133 20 185 185 0 strelka-varscan-mutect KIAA1551,stop_gained,p.Gln924Ter,ENST00000312561,NM_018169.3;KIAA1551,downstream_gene_variant,,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,;KIAA1551,upstream_gene_variant,,ENST00000543763,; T ENST00000312561 Transcript stop_gained 3184/6230 2770/5244 924/1747 Q/* Cag/Tag 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 4/6 Pfam_domain:PF15395,hmmpanther:PTHR21604 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 11 31983725 31983725 C T 1 0 0 0 0 0 1 0 0 8122 479 17 3 3 KIAA1551 12 31983725 Nonsense_Mutation SNP C C3L-00140_T 31983725 101291584 24 4051 GRASP 0 . GRCh38 12 52011048 52011048 + Missense_Mutation SNP C C G novel C3L-00140_T C3L-00140_N C C c.361C>G p.Leu121Val p.L121V ENST00000293662 4/8 332 275 57 299 299 0 strelka-varscan-mutect GRASP,missense_variant,p.Leu121Val,ENST00000293662,NM_181711.3;GRASP,5_prime_UTR_variant,,ENST00000552049,NM_001271856.1;GRASP,5_prime_UTR_variant,,ENST00000546756,;GRASP,non_coding_transcript_exon_variant,,ENST00000552963,;GRASP,upstream_gene_variant,,ENST00000547749,;GRASP,non_coding_transcript_exon_variant,,ENST00000550809,;GRASP,upstream_gene_variant,,ENST00000552508,;GRASP,upstream_gene_variant,,ENST00000548505,; G ENST00000293662 Transcript missense_variant 441/1933 361/1188 121/395 L/V Ctt/Gtt 1 1 GRASP HGNC HGNC:18707 protein_coding YES CCDS8817.1 ENSP00000293662 Q7Z6J2 UPI00001A9479 NM_181711.3 deleterious(0) 4/8 PROSITE_profiles:PS50106,hmmpanther:PTHR15963,hmmpanther:PTHR15963:SF3,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs1438354260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 52011048 52011048 C G 1 0 0 0 0 1 0 0 0 6634 681 24 4 4 GRASP 12 52011048 Missense_Mutation SNP C C3L-00140_T 20027323 52011048 81264261 25 4052 ESPL1 0 . GRCh38 12 53286680 53286680 + Missense_Mutation SNP G G T rs780384845 C3L-00140_T C3L-00140_N G G c.3944G>T p.Arg1315Leu p.R1315L ENST00000257934 18/31 173 145 28 202 202 0 strelka-varscan-mutect ESPL1,missense_variant,p.Arg1315Leu,ENST00000257934,NM_012291.4;ESPL1,missense_variant,p.Arg1315Leu,ENST00000552462,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;ESPL1,intron_variant,,ENST00000553016,;ESPL1,intron_variant,,ENST00000535123,;ESPL1,upstream_gene_variant,,ENST00000549154,;ESPL1,upstream_gene_variant,,ENST00000552600,; T ENST00000257934 Transcript missense_variant 4035/6623 3944/6363 1315/2120 R/L cGt/cTt rs780384845 1 1 ESPL1 HGNC HGNC:16856 protein_coding YES CCDS8852.1 ENSP00000257934 Q14674 UPI00003668C3 NM_012291.4 tolerated(0.31) 18/31 MODERATE 1 SNV 5 1 PASS rs780384845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 53286680 53286680 G T 1 0 0 0 0 1 0 0 0 5115 1145 40 1 1 ESPL1 12 53286680 Missense_Mutation SNP G C3L-00140_T 1275632 53286680 79988629 26 4053 TMEM19 0 . GRCh38 12 71700946 71700946 + Missense_Mutation SNP T T A rs746676238 C3L-00140_T C3L-00140_N T T c.962T>A p.Ile321Asn p.I321N ENST00000266673 6/6 179 150 29 178 178 0 strelka-varscan-mutect TMEM19,missense_variant,p.Ile321Asn,ENST00000266673,NM_018279.3;TMEM19,missense_variant,p.Ile137Asn,ENST00000550787,;TMEM19,intron_variant,,ENST00000546795,;TMEM19,downstream_gene_variant,,ENST00000549735,;TMEM19,downstream_gene_variant,,ENST00000550524,;TMEM19,downstream_gene_variant,,ENST00000546677,;RP11-293I14.2,downstream_gene_variant,,ENST00000548802,; A ENST00000266673 Transcript missense_variant 1556/5656 962/1011 321/336 I/N aTt/aAt rs746676238 1 1 TMEM19 HGNC HGNC:25605 protein_coding YES CCDS9002.1 ENSP00000266673 Q96HH6 A0A024RBA1 UPI000006EFAF NM_018279.3 deleterious(0) 6/6 Pfam_domain:PF01940,hmmpanther:PTHR13353,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs746676238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 71700946 71700946 T A 1 0 0 0 0 1 0 0 0 16555 1493 52 4 4 TMEM19 12 71700946 Missense_Mutation SNP T C3L-00140_T 18414266 71700946 61574363 27 4054 KLHL1 0 . GRCh38 13 70107547 70107547 + Silent SNP G G T novel C3L-00140_T C3L-00140_N G G c.153C>A p.= p.P51P ENST00000377844 1/11 67 53 14 82 82 0 strelka-varscan-mutect KLHL1,synonymous_variant,p.=,ENST00000377844,NM_020866.2;KLHL1,synonymous_variant,p.=,ENST00000545028,NM_001286725.1;ATXN8OS,non_coding_transcript_exon_variant,,ENST00000414504,;ATXN8OS,upstream_gene_variant,,ENST00000424524,; T ENST00000377844 Transcript synonymous_variant 913/4115 153/2247 51/748 P ccC/ccA 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 1/11 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.999999 1 1 1 0 T 2 4 11 70107547 70107547 G T 1 0 0 0 0 0 0 0 1 8229 1335 47 2 2 KLHL1 13 70107547 Silent SNP G C3L-00140_T 70107547 44256781 28 4055 PSMA6 0 . GRCh38 14 35310794 35310794 + Missense_Mutation SNP A A T novel C3L-00140_T C3L-00140_N A A c.308A>T p.Tyr103Phe p.Y103F ENST00000261479 4/7 395 342 53 404 403 1 strelka-varscan-mutect PSMA6,missense_variant,p.Tyr103Phe,ENST00000261479,NM_002791.2;PSMA6,missense_variant,p.Tyr24Phe,ENST00000555764,NM_001282232.1;PSMA6,missense_variant,p.Tyr24Phe,ENST00000622405,NM_001282233.1;PSMA6,missense_variant,p.Tyr84Phe,ENST00000540871,NM_001282234.1;PSMA6,missense_variant,p.Tyr103Phe,ENST00000553809,;PSMA6,missense_variant,p.Tyr103Phe,ENST00000556506,;PSMA6,downstream_gene_variant,,ENST00000627895,;PSMA6,upstream_gene_variant,,ENST00000556221,;PSMA6,missense_variant,p.Tyr103Phe,ENST00000554961,;RP11-561B11.2,3_prime_UTR_variant,,ENST00000557565,;PSMA6,3_prime_UTR_variant,,ENST00000554541,;PSMA6,3_prime_UTR_variant,,ENST00000554620,;PSMA6,3_prime_UTR_variant,,ENST00000553688,;PSMA6,non_coding_transcript_exon_variant,,ENST00000554843,;PSMA6,non_coding_transcript_exon_variant,,ENST00000555050,;PSMA6,upstream_gene_variant,,ENST00000554457,;PSMA6,downstream_gene_variant,,ENST00000556167,; T ENST00000261479 Transcript missense_variant 428/1029 308/741 103/246 Y/F tAc/tTc 1 1 PSMA6 HGNC HGNC:9535 protein_coding YES CCDS9655.1 ENSP00000261479 P60900 A0A140VK44 UPI0000001C1E NM_002791.2 tolerated(0.26) 4/7 PROSITE_profiles:PS51475,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF64,Gene3D:3.60.20.10,Pfam_domain:PF00227,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 35310794 35310794 A T 1 0 0 0 0 1 0 0 0 12822 391 14 4 4 PSMA6 14 35310794 Missense_Mutation SNP A C3L-00140_T 35310794 71732924 29 4056 SEL1L 0 . GRCh38 14 81477157 81477157 + Missense_Mutation SNP C C G novel C3L-00140_T C3L-00140_N C C c.2200G>C p.Asp734His p.D734H ENST00000336735 21/21 169 137 32 164 164 0 strelka-varscan-mutect SEL1L,missense_variant,p.Asp734His,ENST00000336735,NM_005065.5;SEL1L,downstream_gene_variant,,ENST00000554293,; G ENST00000336735 Transcript missense_variant 2317/7925 2200/2385 734/794 D/H Gat/Cat 1 -1 SEL1L HGNC HGNC:10717 protein_coding YES CCDS9876.1 ENSP00000337053 Q9UBV2 UPI0000135746 NM_005065.5 deleterious(0.01) 21/21 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 81477157 81477157 C G 1 0 0 0 0 1 0 0 0 14287 826 29 4 4 SEL1L 14 81477157 Missense_Mutation SNP C C3L-00140_T 46166363 81477157 25566561 30 4057 ADAMTS7 0 . GRCh38 15 78798008 78798008 + Missense_Mutation SNP C C A novel C3L-00140_T C3L-00140_N C C c.562G>T p.Ala188Ser p.A188S ENST00000388820 3/24 175 144 31 191 191 0 strelka-varscan-mutect ADAMTS7,missense_variant,p.Ala188Ser,ENST00000388820,NM_014272.3;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000566303,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000565793,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000568712,; A ENST00000388820 Transcript missense_variant 773/5490 562/5061 188/1686 A/S Gcc/Tcc 1 -1 ADAMTS7 HGNC HGNC:223 protein_coding YES CCDS32303.1 ENSP00000373472 Q9UKP4 UPI00002263B3 NM_014272.3 tolerated(0.17) 3/24 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF142 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 78798008 78798008 C A 1 0 0 0 0 1 0 0 0 315 739 26 2 2 ADAMTS7 15 78798008 Missense_Mutation SNP C C3L-00140_T 78798008 23193181 31 4058 CPEB1 0 . GRCh38 15 82553467 82553467 + Missense_Mutation SNP C C A novel C3L-00140_T C3L-00140_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000615198 7/12 198 165 33 181 181 0 strelka-varscan-mutect CPEB1,missense_variant,p.Gly382Trp,ENST00000614918,;CPEB1,missense_variant,p.Gly355Trp,ENST00000611031,;CPEB1,missense_variant,p.Gly415Cys,ENST00000617958,;CPEB1,missense_variant,p.Gly280Cys,ENST00000618449,NM_001079533.1;CPEB1,missense_variant,p.Gly280Trp,ENST00000620182,NM_001288819.1;CPEB1,missense_variant,p.Gly280Trp,ENST00000617522,;CPEB1,missense_variant,p.Gly355Trp,ENST00000615198,NM_030594.4;CPEB1,missense_variant,p.Gly280Trp,ENST00000617462,NM_001079535.1;CPEB1,missense_variant,p.Gly358Trp,ENST00000616959,;CPEB1,missense_variant,p.Gly280Trp,ENST00000611163,NM_001079534.1,NM_001288820.1;RP11-152F13.10,missense_variant,p.Gly90Trp,ENST00000562833,;CPEB1,downstream_gene_variant,,ENST00000568994,;RP11-379H8.1,intron_variant,,ENST00000621893,;CPEB1,splice_region_variant,,ENST00000618698,;CPEB1,splice_region_variant,,ENST00000614977,;CPEB1,downstream_gene_variant,,ENST00000570205,; A ENST00000615198 Transcript missense_variant,splice_region_variant 1170/2112 1063/1686 355/561 G/W Ggg/Tgg 1 -1 CPEB1 HGNC HGNC:21744 protein_coding YES CCDS45329.2 ENSP00000477715 Q9BZB8 UPI000018CEBD NM_030594.4 deleterious(0) 7/12 Gene3D:3.30.70.330,Pfam_domain:PF16367,PROSITE_profiles:PS50102,hmmpanther:PTHR12566,hmmpanther:PTHR12566:SF9,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 82553467 82553467 C A 1 0 0 0 0 1 0 0 0 3594 695 24 2 2 CPEB1 15 82553467 Missense_Mutation SNP C C3L-00140_T 3755459 82553467 19437722 32 4059 FANCA 0 . GRCh38 16 89792016 89792016 + Missense_Mutation SNP A A T novel C3L-00140_T C3L-00140_N A A c.1136T>A p.Leu379Gln p.L379Q ENST00000389301 13/43 496 420 76 512 512 0 strelka-varscan-mutect FANCA,missense_variant,p.Leu379Gln,ENST00000389301,NM_000135.2;FANCA,missense_variant,p.Leu379Gln,ENST00000568369,NM_001286167.1;FANCA,3_prime_UTR_variant,,ENST00000567621,;FANCA,non_coding_transcript_exon_variant,,ENST00000566133,;FANCA,upstream_gene_variant,,ENST00000563767,;FANCA,downstream_gene_variant,,ENST00000566409,; T ENST00000389301 Transcript missense_variant 1167/5451 1136/4368 379/1455 L/Q cTg/cAg 1 -1 FANCA HGNC HGNC:3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 UPI0000520A1A NM_000135.2 deleterious(0) 13/43 Pfam_domain:PF15865,hmmpanther:PTHR12047,hmmpanther:PTHR12047:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 89792016 89792016 A T 1 0 0 0 0 1 0 0 0 5521 188 7 4 4 FANCA 16 89792016 Missense_Mutation SNP A C3L-00140_T 89792016 546329 33 4060 ATAD5 0 . GRCh38 17 30835976 30835976 + Missense_Mutation SNP A A G novel C3L-00140_T C3L-00140_N A A c.1895A>G p.Asn632Ser p.N632S ENST00000321990 2/23 133 109 24 129 129 0 strelka-varscan-mutect ATAD5,missense_variant,p.Asn632Ser,ENST00000321990,NM_024857.4;CTD-2349P21.11,intron_variant,,ENST00000580873,;ATAD5,missense_variant,p.Asn632Ser,ENST00000578295,;ATAD5,non_coding_transcript_exon_variant,,ENST00000585133,;CTD-2349P21.1,downstream_gene_variant,,ENST00000490847,; G ENST00000321990 Transcript missense_variant 2273/6869 1895/5535 632/1844 N/S aAc/aGc 1 1 ATAD5 HGNC HGNC:25752 protein_coding YES CCDS11260.1 ENSP00000313171 Q96QE3 UPI0000071E9E NM_024857.4 tolerated(0.91) 2/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 30835976 30835976 A G 1 0 0 0 0 1 0 0 0 1224 43 2 5 5 ATAD5 17 30835976 Missense_Mutation SNP A C3L-00140_T 30835976 52421465 34 4061 KRT12 0 . GRCh38 17 40861707 40861707 + Missense_Mutation SNP C C A novel C3L-00140_T C3L-00140_N C C c.1439G>T p.Gly480Val p.G480V ENST00000251643 8/8 284 234 50 278 278 0 strelka-varscan-mutect KRT12,missense_variant,p.Gly480Val,ENST00000251643,NM_000223.3;RP5-1110E20.1,intron_variant,,ENST00000579136,; A ENST00000251643 Transcript missense_variant 1463/1867 1439/1485 480/494 G/V gGt/gTt 1 -1 KRT12 HGNC HGNC:6414 protein_coding YES CCDS11378.1 ENSP00000251643 Q99456 UPI000012DAE4 NM_000223.3 deleterious(0) 8/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF115 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 40861707 40861707 C A 1 0 0 0 0 1 0 0 0 8331 507 18 2 2 KRT12 17 40861707 Missense_Mutation SNP C C3L-00140_T 10025731 40861707 42395734 35 4062 SGCA 0 . GRCh38 17 50167983 50167983 + Missense_Mutation SNP C C T rs200075504 C3L-00140_T C3L-00140_N C C c.349C>T p.Arg117Trp p.R117W ENST00000262018 4/10 461 381 80 481 481 0 strelka-varscan-mutect SGCA,missense_variant,p.Arg117Trp,ENST00000262018,NM_000023.2;SGCA,missense_variant,p.Arg117Trp,ENST00000344627,NM_001135697.1;SGCA,missense_variant,p.Arg24Trp,ENST00000511303,;SGCA,upstream_gene_variant,,ENST00000504073,;RP11-893F2.14,upstream_gene_variant,,ENST00000572855,;SGCA,non_coding_transcript_exon_variant,,ENST00000513942,;HILS1,downstream_gene_variant,,ENST00000504307,;SGCA,upstream_gene_variant,,ENST00000508382,;SGCA,missense_variant,p.Arg117Trp,ENST00000513821,;SGCA,3_prime_UTR_variant,,ENST00000502555,;SGCA,3_prime_UTR_variant,,ENST00000512526,;SGCA,3_prime_UTR_variant,,ENST00000514934,;HILS1,downstream_gene_variant,,ENST00000545329,; T ENST00000262018 Transcript missense_variant 385/1432 349/1164 117/387 R/W Cgg/Tgg rs200075504 1 1 SGCA HGNC HGNC:10805 protein_coding YES CCDS32679.1 ENSP00000262018 Q16586 A0A0S2Z4Q1 UPI0000135907 NM_000023.2 deleterious(0.03) 4/10 Gene3D:2.60.40.10,Pfam_domain:PF05510,hmmpanther:PTHR10132,hmmpanther:PTHR10132:SF16,SMART_domains:SM00736,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs200075504 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 11 50167983 50167983 C T 1 0 0 0 0 1 0 0 0 14459 875 31 1 1 SGCA 17 50167983 Missense_Mutation SNP C C3L-00140_T 9306276 50167983 33089458 36 4063 KIF2B 0 . GRCh38 17 53824508 53824508 + Missense_Mutation SNP C C A rs374451533 C3L-00140_T C3L-00140_N C C c.1475C>A p.Thr492Asn p.T492N ENST00000268919 1/1 94 73 21 161 161 0 strelka-varscan-mutect KIF2B,missense_variant,p.Thr492Asn,ENST00000268919,NM_032559.4; A ENST00000268919 Transcript missense_variant 1608/2313 1475/2022 492/673 T/N aCc/aAc rs374451533 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 deleterious(0.01) 1/1 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380 MODERATE 1 SNV 1 PASS rs374451533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 11 53824508 53824508 C A 1 0 0 0 0 1 0 0 0 8163 507 18 2 2 KIF2B 17 53824508 Missense_Mutation SNP C C3L-00140_T 3656525 53824508 29432933 37 4064 STK11 0 . GRCh38 19 1207126 1207126 + Silent SNP G G A rs768532101 C3L-00140_T C3L-00140_N G G c.213G>A p.= p.T71T ENST00000326873 1/10 214 180 34 280 280 0 strelka-mutect STK11,synonymous_variant,p.=,ENST00000586243,;STK11,synonymous_variant,p.=,ENST00000326873,NM_000455.4;STK11,synonymous_variant,p.=,ENST00000585851,;STK11,intron_variant,,ENST00000585748,;STK11,synonymous_variant,p.=,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;HMGB2P1,downstream_gene_variant,,ENST00000591146,; A ENST00000326873 Transcript synonymous_variant 663/2611 213/1302 71/433 T acG/acA rs768532101 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 1/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs768532101 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 11 1207126 1207126 G A 1 0 0 0 0 0 0 0 1 15664 1074 38 1 1 STK11 19 1207126 Silent SNP G C3L-00140_T 1207126 57410490 38 4065 SCAMP4 0 . GRCh38 19 1918950 1918950 + Missense_Mutation SNP A A G novel C3L-00140_T C3L-00140_N A A c.355A>G p.Thr119Ala p.T119A ENST00000316097 5/7 257 224 33 330 330 0 strelka-varscan-mutect SCAMP4,missense_variant,p.Thr119Ala,ENST00000316097,NM_079834.2;SCAMP4,missense_variant,p.Thr75Ala,ENST00000414057,;SCAMP4,missense_variant,p.Thr119Ala,ENST00000621748,;SCAMP4,missense_variant,p.Thr119Ala,ENST00000411971,;SCAMP4,intron_variant,,ENST00000409472,;SCAMP4,downstream_gene_variant,,ENST00000590266,;SCAMP4,downstream_gene_variant,,ENST00000588907,;SCAMP4,non_coding_transcript_exon_variant,,ENST00000489554,;SCAMP4,intron_variant,,ENST00000585335,;SCAMP4,3_prime_UTR_variant,,ENST00000460767,;SCAMP4,non_coding_transcript_exon_variant,,ENST00000452128,;SCAMP4,upstream_gene_variant,,ENST00000472442,; G ENST00000316097 Transcript missense_variant 622/2684 355/690 119/229 T/A Acc/Gcc 1 1 SCAMP4 HGNC HGNC:30385 protein_coding YES CCDS45903.1 ENSP00000316007 Q969E2 UPI000006F786 NM_079834.2 tolerated(0.5) 5/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR10687:SF11,hmmpanther:PTHR10687,Pfam_domain:PF04144 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 1918950 1918950 A G 1 0 0 0 0 1 0 0 0 14140 275 10 5 5 SCAMP4 19 1918950 Missense_Mutation SNP A C3L-00140_T 711824 1918950 56698666 39 4066 MKNK2 0 . GRCh38 19 2039836 2039836 + Missense_Mutation SNP A A G novel C3L-00140_T C3L-00140_N A A c.1175T>C p.Leu392Pro p.L392P ENST00000250896 14/14 88 74 14 89 89 0 strelka-varscan-mutect MKNK2,missense_variant,p.Leu392Pro,ENST00000250896,NM_199054.2;MKNK2,missense_variant,p.Leu392Pro,ENST00000591601,;MKNK2,3_prime_UTR_variant,,ENST00000588014,;MKNK2,intron_variant,,ENST00000309340,NM_017572.3;MKNK2,intron_variant,,ENST00000591142,;MKNK2,downstream_gene_variant,,ENST00000591588,;BTBD2,upstream_gene_variant,,ENST00000590646,;BTBD2,upstream_gene_variant,,ENST00000587742,;BTBD2,upstream_gene_variant,,ENST00000588395,;MKNK2,3_prime_UTR_variant,,ENST00000586828,;MKNK2,3_prime_UTR_variant,,ENST00000589441,;MKNK2,non_coding_transcript_exon_variant,,ENST00000587416,;MKNK2,downstream_gene_variant,,ENST00000586620,;MKNK2,downstream_gene_variant,,ENST00000585667,; G ENST00000250896 Transcript missense_variant 1420/3774 1175/1398 392/465 L/P cTc/cCc 1 -1 MKNK2 HGNC HGNC:7111 protein_coding YES CCDS12080.1 ENSP00000250896 Q9HBH9 UPI000006E9B4 NM_199054.2 deleterious(0) 14/14 hmmpanther:PTHR24349:SF158,hmmpanther:PTHR24349,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 11 2039836 2039836 A G 1 0 0 0 0 1 0 0 0 9572 304 11 5 5 MKNK2 19 2039836 Missense_Mutation SNP A C3L-00140_T 120886 2039836 56577780 40 4067 OR7A17 0 . GRCh38 19 14880810 14880810 + Silent SNP A A G novel C3L-00140_T C3L-00140_N A A c.546T>C p.= p.N182N ENST00000327462 1/1 203 173 30 257 257 0 strelka-varscan-mutect OR7A17,synonymous_variant,p.=,ENST00000327462,NM_030901.1; G ENST00000327462 Transcript synonymous_variant 643/1027 546/930 182/309 N aaT/aaC 1 -1 OR7A17 HGNC HGNC:8363 protein_coding YES CCDS12319.1 ENSP00000328144 O14581 A0A126GVR5 UPI0000041DF9 NM_030901.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF263,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 11 14880810 14880810 A G 1 0 0 0 0 0 0 0 1 11285 330 12 5 5 OR7A17 19 14880810 Silent SNP A C3L-00140_T 12840974 14880810 43736806 41 4068 HM13 0 . GRCh38 20 31527510 31527510 + Silent SNP C C T novel C3L-00140_T C3L-00140_N C C c.210C>T p.= p.I70I ENST00000398174 2/13 127 114 13 116 116 0 strelka-mutect HM13,synonymous_variant,p.=,ENST00000498035,NM_178582.2;HM13,synonymous_variant,p.=,ENST00000398174,NM_178581.2;HM13,synonymous_variant,p.=,ENST00000335574,NM_178580.2;HM13,synonymous_variant,p.=,ENST00000340852,NM_030789.3;HM13,synonymous_variant,p.=,ENST00000344042,;HM13,non_coding_transcript_exon_variant,,ENST00000496438,;HM13,non_coding_transcript_exon_variant,,ENST00000460225,;HM13,non_coding_transcript_exon_variant,,ENST00000466766,; T ENST00000398174 Transcript synonymous_variant 334/3792 210/1281 70/426 I atC/atT 1 1 HM13 HGNC HGNC:16435 protein_coding YES CCDS42861.1 ENSP00000381237 Q8TCT9 UPI000001358F NM_178581.2 2/13 Pfam_domain:PF04258,hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF23,SMART_domains:SM00730 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 11 31527510 31527510 C T 1 0 0 0 0 0 0 0 1 7107 816 29 3 3 HM13 20 31527510 Silent SNP C C3L-00140_T 31527510 32916657 42 4069 SIM2 0 . GRCh38 21 36726165 36726165 + Missense_Mutation SNP A A C rs752152751 C3L-00140_T C3L-00140_N A A c.590A>C p.Asp197Ala p.D197A ENST00000290399 6/11 245 212 33 224 224 0 strelka-varscan-mutect SIM2,missense_variant,p.Asp197Ala,ENST00000290399,NM_005069.4,NM_009586.3;SIM2,missense_variant,p.Asp135Ala,ENST00000431229,;SIM2,non_coding_transcript_exon_variant,,ENST00000481185,; C ENST00000290399 Transcript missense_variant 1203/4442 590/2004 197/667 D/A gAc/gCc rs752152751 1 1 SIM2 HGNC HGNC:10883 protein_coding YES CCDS13646.1 ENSP00000290399 Q14190 UPI000013599A NM_005069.4,NM_009586.3 deleterious(0.01) 6/11 hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF19 MODERATE 1 SNV 1 1 PASS rs752152751 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 11 36726165 36726165 A C 1 0 0 0 0 1 0 0 0 14587 275 10 5 5 SIM2 21 36726165 Missense_Mutation SNP A C3L-00140_T 36726165 9983818 43 4070 MSN 0 . GRCh38 X 65737229 65737229 + Missense_Mutation SNP G G T rs368873074 C3L-00140_T C3L-00140_N G G c.1142G>T p.Arg381Leu p.R381L ENST00000360270 10/13 84 56 28 99 99 0 strelka-varscan-mutect MSN,missense_variant,p.Arg381Leu,ENST00000360270,NM_002444.2; T ENST00000360270 Transcript missense_variant 1314/3944 1142/1734 381/577 R/L cGt/cTt rs368873074,COSM1124087 1 1 MSN HGNC HGNC:7373 protein_coding YES CCDS14382.1 ENSP00000353408 P26038 V9HWC0 UPI000013DA94 NM_002444.2 tolerated(0.3) 10/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23281,hmmpanther:PTHR23281:SF26,Pfam_domain:PF00769,PIRSF_domain:PIRSF002305 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs368873074 . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 11 65737229 65737229 G T 1 0 0 0 0 1 0 0 0 9868 1145 40 1 1 MSN 23 65737229 Missense_Mutation SNP G C3L-00140_T 65737229 90303666 44 4071 FO538757.1 0 . GRCh38 1 187375 187375 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.880+1G>T p.X294_splice ENST00000623083 389 365 24 293 293 0 varscan-mutect FO538757.1,splice_donor_variant,,ENST00000623083,;FO538757.1,splice_donor_variant,,ENST00000623834,;FO538757.1,splice_region_variant,,ENST00000624735,;FO538757.2,downstream_gene_variant,,ENST00000624431,;MIR6859-2,downstream_gene_variant,,ENST00000612080,; A ENST00000623083 Transcript splice_donor_variant -/1687 880/1395 294/464 1 -1 FO538757.1 Clone_based_ensembl_gene protein_coding YES ENSP00000485442 A0A096LP75 UPI000514C5DF 7/10 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 187375 187375 C A 1 0 0 0 0 0 0 1 0 5837 521 18 2 2 FO538757.1 1 187375 Splice_Site SNP C C3L-00144_T 187375 248769047 1 4072 CDK11A 0 . GRCh38 1 1708180 1708180 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1069G>A p.Val357Ile p.V357I ENST00000404249 10/20 22 17 5 40 40 0 strelka-varscan-mutect CDK11A,missense_variant,p.Val323Ile,ENST00000356200,;CDK11A,missense_variant,p.Val360Ile,ENST00000378633,;CDK11A,missense_variant,p.Val357Ile,ENST00000404249,NM_024011.2;CDK11A,missense_variant,p.Val356Ile,ENST00000357760,;CDK11A,missense_variant,p.Val323Ile,ENST00000378638,;CDK11A,missense_variant,p.Val347Ile,ENST00000358779,NM_033529.2;RP1-283E3.8,splice_region_variant,,ENST00000598846,;CDK11A,upstream_gene_variant,,ENST00000495016,;CDK11A,missense_variant,p.Val357Ile,ENST00000460465,;CDK11A,missense_variant,p.Val370Ile,ENST00000509982,;CDK11A,splice_region_variant,,ENST00000356937,;CDK11A,splice_region_variant,,ENST00000492390,;CDK11A,splice_region_variant,,ENST00000474916,;CDK11A,upstream_gene_variant,,ENST00000463652,;CDK11A,upstream_gene_variant,,ENST00000478901,;CDK11A,upstream_gene_variant,,ENST00000468800,;CDK11A,upstream_gene_variant,,ENST00000468397,;CDK11A,upstream_gene_variant,,ENST00000491311,;CDK11A,upstream_gene_variant,,ENST00000489300,;CDK11A,upstream_gene_variant,,ENST00000464748,; T ENST00000404249 Transcript missense_variant,splice_region_variant 1149/2449 1069/2343 357/780 V/I Gtt/Att 1 -1 CDK11A HGNC HGNC:1730 protein_coding YES CCDS44042.1 ENSP00000384442 Q9UQ88 UPI000022B1E1 NM_024011.2 deleterious_low_confidence(0.05) 10/20 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.72239 1 1 1 1 0 T 3 4 12 1708180 1708180 C T 1 0 0 0 0 1 0 0 0 2830 608 21 3 3 CDK11A 1 1708180 Missense_Mutation SNP C C3L-00144_T 1520805 1708180 247248242 2 4073 PRKCZ 0 . GRCh38 1 2184687 2184687 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.1680C>G p.= p.T560T ENST00000378567 17/18 97 69 28 79 79 0 strelka-varscan-mutect PRKCZ,synonymous_variant,p.=,ENST00000378567,NM_002744.4;PRKCZ,synonymous_variant,p.=,ENST00000400921,NM_001033581.1,NM_001033582.1;PRKCZ,synonymous_variant,p.=,ENST00000461106,NM_001242874.1;FAAP20,3_prime_UTR_variant,,ENST00000400919,NM_001256945.1;FAAP20,downstream_gene_variant,,ENST00000400918,NM_001282673.1;FAAP20,downstream_gene_variant,,ENST00000378546,NM_182533.2;FAAP20,downstream_gene_variant,,ENST00000378543,NM_001256947.1;RP11-181G12.2,upstream_gene_variant,,ENST00000333854,;RP11-181G12.2,upstream_gene_variant,,ENST00000444529,;FAAP20,non_coding_transcript_exon_variant,,ENST00000469733,;PRKCZ,non_coding_transcript_exon_variant,,ENST00000479263,;FAAP20,downstream_gene_variant,,ENST00000487186,;FAAP20,downstream_gene_variant,,ENST00000401813,;FAAP20,downstream_gene_variant,,ENST00000476803,;FAAP20,3_prime_UTR_variant,,ENST00000428120,NM_001282671.1;FAAP20,3_prime_UTR_variant,,ENST00000414253,NM_001282672.1;PRKCZ,3_prime_UTR_variant,,ENST00000478770,;PRKCZ,non_coding_transcript_exon_variant,,ENST00000505322,;FAAP20,downstream_gene_variant,,ENST00000497675,;FAAP20,downstream_gene_variant,,ENST00000440825,; G ENST00000378567 Transcript synonymous_variant 1841/2326 1680/1779 560/592 T acC/acG 1 1 PRKCZ HGNC HGNC:9412 protein_coding YES CCDS37.1 ENSP00000367830 Q05513 UPI0000169EB7 NM_002744.4 17/18 Pfam_domain:PF00433,PIRSF_domain:PIRSF000554,PROSITE_profiles:PS51285,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF170,SMART_domains:SM00133,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 2184687 2184687 C G 1 0 0 0 0 0 0 0 1 12650 610 22 4 4 PRKCZ 1 2184687 Silent SNP C C3L-00144_T 476507 2184687 246771735 3 4074 MORN1 0 . GRCh38 1 2336759 2336759 + Silent SNP C C A rs750153953 C3L-00144_T C3L-00144_N C C c.1128G>T p.= p.P376P ENST00000378531 11/14 60 35 25 51 51 0 strelka-varscan-mutect MORN1,synonymous_variant,p.=,ENST00000378531,NM_024848.2;MORN1,non_coding_transcript_exon_variant,,ENST00000606372,; A ENST00000378531 Transcript synonymous_variant 1302/1798 1128/1494 376/497 P ccG/ccT rs750153953 1 -1 MORN1 HGNC HGNC:25852 protein_coding YES CCDS40.1 ENSP00000367792 Q5T089 UPI000007293C NM_024848.2 11/14 LOW 1 SNV 2 1 PASS rs750153953 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 12 2336759 2336759 C A 1 0 0 0 0 0 0 0 1 9671 755 27 1 1 MORN1 1 2336759 Silent SNP C C3L-00144_T 152072 2336759 246619663 4 4075 PLCH2 0 . GRCh38 1 2494922 2494922 + Missense_Mutation SNP G G T rs371640065 C3L-00144_T C3L-00144_N G G c.1726G>T p.Val576Phe p.V576F ENST00000378486 12/22 158 121 37 168 168 0 strelka-varscan-mutect PLCH2,missense_variant,p.Val549Phe,ENST00000449969,NM_001303012.1;PLCH2,missense_variant,p.Val576Phe,ENST00000378486,NM_014638.3,NM_001303013.1;PLCH2,missense_variant,p.Val576Phe,ENST00000419816,;PLCH2,missense_variant,p.Val435Phe,ENST00000278878,;RP3-395M20.3,upstream_gene_variant,,ENST00000442305,;RP3-395M20.2,upstream_gene_variant,,ENST00000424657,;PLCH2,non_coding_transcript_exon_variant,,ENST00000343889,;PLCH2,upstream_gene_variant,,ENST00000473964,;PLCH2,upstream_gene_variant,,ENST00000462379,; T ENST00000378486 Transcript missense_variant 2000/4837 1726/4251 576/1416 V/F Gtc/Ttc rs371640065 1 1 PLCH2 HGNC HGNC:29037 protein_coding YES CCDS59959.1 ENSP00000367747 O75038 UPI00005B72F8 NM_014638.3,NM_001303013.1 tolerated(0.25) 12/22 Superfamily_domains:SSF51695 MODERATE 1 SNV 1 1 PASS rs371640065 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 2494922 2494922 G T 1 0 0 0 0 1 0 0 0 12132 1145 40 1 1 PLCH2 1 2494922 Missense_Mutation SNP G C3L-00144_T 158163 2494922 246461500 5 4076 H6PD 0 . GRCh38 1 9264518 9264518 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2058G>T p.Arg686Ser p.R686S ENST00000602477 5/5 192 148 44 189 189 0 strelka-varscan-mutect H6PD,missense_variant,p.Arg675Ser,ENST00000377403,NM_004285.3;H6PD,missense_variant,p.Arg686Ser,ENST00000602477,NM_001282587.1;H6PD,upstream_gene_variant,,ENST00000495451,; T ENST00000602477 Transcript missense_variant 2210/5590 2058/2409 686/802 R/S agG/agT 1 1 H6PD HGNC HGNC:4795 protein_coding YES CCDS72697.1 ENSP00000473348 R4GMU1 UPI0000D61E40 NM_001282587.1 tolerated(0.72) 5/5 Gene3D:3.40.50.1360,Pfam_domain:PF01182,TIGRFAM_domain:TIGR01198,Superfamily_domains:SSF100950 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 9264518 9264518 G T 1 0 0 0 0 1 0 0 0 6818 1223 43 2 2 H6PD 1 9264518 Missense_Mutation SNP G C3L-00144_T 6769596 9264518 239691904 6 4077 DISP3 0 . GRCh38 1 11525277 11525277 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.2578G>A p.Val860Met p.V860M ENST00000294484 12/21 177 133 44 153 153 0 strelka-varscan-mutect DISP3,missense_variant,p.Val860Met,ENST00000294484,NM_020780.1; A ENST00000294484 Transcript missense_variant 2716/5215 2578/4179 860/1392 V/M Gtg/Atg 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 deleterious_low_confidence(0.02) 12/21 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF125 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 11525277 11525277 G A 1 0 0 0 0 1 0 0 0 4347 1377 48 3 3 DISP3 1 11525277 Missense_Mutation SNP G C3L-00144_T 2260759 11525277 237431145 7 4078 DISP3 0 . GRCh38 1 11536347 11536347 + Missense_Mutation SNP G G T rs767878802 C3L-00144_T C3L-00144_N G G c.3840G>T p.Trp1280Cys p.W1280C ENST00000294484 21/21 78 65 13 66 66 0 strelka-varscan-mutect DISP3,missense_variant,p.Trp1280Cys,ENST00000294484,NM_020780.1;DISP3,missense_variant,p.Ala167Ser,ENST00000304391,; T ENST00000294484 Transcript missense_variant 3978/5215 3840/4179 1280/1392 W/C tgG/tgT rs767878802 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 tolerated(0.09) 21/21 hmmpanther:PTHR10796:SF125,hmmpanther:PTHR10796,Gene3D:2j8sB01,Pfam_domain:PF03176,Superfamily_domains:SSF82866 MODERATE 1 SNV 1 1 PASS rs767878802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 11536347 11536347 G T 1 0 0 0 0 1 0 0 0 4347 1212 42 2 2 DISP3 1 11536347 Missense_Mutation SNP G C3L-00144_T 11070 11536347 237420075 8 4079 C1orf158 0 . GRCh38 1 12760928 12760928 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.562C>A p.Leu188Met p.L188M ENST00000614859 4/4 49 31 18 48 48 0 strelka-varscan-mutect C1orf158,missense_variant,p.Leu188Met,ENST00000614859,NM_152290.3;C1orf158,missense_variant,p.Leu150Met,ENST00000376210,; A ENST00000614859 Transcript missense_variant 778/3549 562/585 188/194 L/M Ctg/Atg 1 1 C1orf158 HGNC HGNC:28567 protein_coding YES CCDS147.1 ENSP00000477802 Q8N1D5 UPI000006E055 NM_152290.3 deleterious(0.01) 4/4 hmmpanther:PTHR31180,hmmpanther:PTHR31180:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 12760928 12760928 C A 1 0 0 0 0 1 0 0 0 1969 680 24 2 2 C1orf158 1 12760928 Missense_Mutation SNP C C3L-00144_T 1224581 12760928 236195494 9 4080 PRAMEF10 0 . GRCh38 1 12893141 12893141 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1200C>A p.His400Gln p.H400Q ENST00000235347 4/4 209 173 36 280 280 0 strelka-varscan-mutect PRAMEF10,missense_variant,p.His400Gln,ENST00000235347,NM_001039361.4; T ENST00000235347 Transcript missense_variant 1280/1525 1200/1425 400/474 H/Q caC/caA 1 -1 PRAMEF10 HGNC HGNC:27997 protein_coding YES CCDS41255.1 ENSP00000235347 O60809 UPI000442CF00 NM_001039361.4 deleterious(0.02) 4/4 hmmpanther:PTHR14224:SF28,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 12893141 12893141 G T 1 0 0 0 0 1 0 0 0 12555 1368 48 2 2 PRAMEF10 1 12893141 Missense_Mutation SNP G C3L-00144_T 132213 12893141 236063281 10 4081 PDPN 0 . GRCh38 1 13607226 13607226 + Missense_Mutation SNP G G T rs769618524 C3L-00144_T C3L-00144_N G G c.349G>T p.Val117Phe p.V117F ENST00000294489 2/6 157 122 35 136 136 0 strelka-varscan-mutect PDPN,missense_variant,p.Val117Phe,ENST00000294489,;PDPN,missense_variant,p.Val117Phe,ENST00000617617,NM_006474.4;PDPN,missense_variant,p.Val117Phe,ENST00000376057,NM_198389.2;PDPN,missense_variant,p.Val41Phe,ENST00000621990,;PDPN,missense_variant,p.Val41Phe,ENST00000510906,;PDPN,missense_variant,p.Val36Phe,ENST00000509009,;PDPN,5_prime_UTR_variant,,ENST00000376061,;PDPN,5_prime_UTR_variant,,ENST00000513143,;PDPN,5_prime_UTR_variant,,ENST00000475043,NM_001006625.1;PDPN,5_prime_UTR_variant,,ENST00000487038,NM_001006624.1;PDPN,5_prime_UTR_variant,,ENST00000488631,;PDPN,downstream_gene_variant,,ENST00000506205,; T ENST00000294489 Transcript missense_variant 690/3104 349/717 117/238 V/F Gtt/Ttt rs769618524 1 1 PDPN HGNC HGNC:29602 protein_coding YES CCDS30602.1 ENSP00000294489 Q86YL7 UPI000013E16D tolerated(0.09) 2/6 Pfam_domain:PF05808,hmmpanther:PTHR16861 MODERATE 1 SNV 1 1 PASS rs769618524 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 13607226 13607226 G T 1 0 0 0 0 1 0 0 0 11776 1145 40 1 1 PDPN 1 13607226 Missense_Mutation SNP G C3L-00144_T 714085 13607226 235349196 11 4082 DNAJC16 0 . GRCh38 1 15536650 15536650 + Nonsense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.410C>G p.Ser137Ter p.S137* ENST00000375847 4/15 252 176 76 228 228 0 strelka-varscan-mutect DNAJC16,stop_gained,p.Ser137Ter,ENST00000375847,NM_015291.3;DNAJC16,stop_gained,p.Ser137Ter,ENST00000375849,;DNAJC16,stop_gained,p.Ser137Ter,ENST00000375838,;DNAJC16,5_prime_UTR_variant,,ENST00000616884,NM_001287811.1;DNAJC16,stop_gained,p.Ser137Ter,ENST00000475133,; G ENST00000375847 Transcript stop_gained 574/6069 410/2349 137/782 S/* tCa/tGa 1 1 DNAJC16 HGNC HGNC:29157 protein_coding YES CCDS30606.1 ENSP00000365007 Q9Y2G8 UPI000000DBDB NM_015291.3 4/15 PROSITE_profiles:PS51352,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF319 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 12 15536650 15536650 C G 1 0 0 0 0 0 1 0 0 4449 838 29 4 4 DNAJC16 1 15536650 Nonsense_Mutation SNP C C3L-00144_T 1929424 15536650 233419772 12 4083 PADI1 0 . GRCh38 1 17205267 17205267 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.50C>A p.Ala17Asp p.A17D ENST00000375471 1/16 314 252 62 216 216 0 strelka-varscan-mutect PADI1,missense_variant,p.Ala17Asp,ENST00000375471,NM_013358.2;RP11-380J14.4,upstream_gene_variant,,ENST00000635428,; A ENST00000375471 Transcript missense_variant 142/3846 50/1992 17/663 A/D gCc/gAc 1 1 PADI1 HGNC HGNC:18367 protein_coding YES CCDS178.1 ENSP00000364620 Q9ULC6 UPI000013D8A2 NM_013358.2 deleterious(0) 1/16 Pfam_domain:PF08526,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF11,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17205267 17205267 C A 1 0 0 0 0 1 0 0 0 11455 739 26 2 2 PADI1 1 17205267 Missense_Mutation SNP C C3L-00144_T 1668617 17205267 231751155 13 4084 PADI1 0 . GRCh38 1 17244125 17244125 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1874T>A p.Leu625Gln p.L625Q ENST00000375471 16/16 322 283 39 275 275 0 strelka-varscan-mutect PADI1,missense_variant,p.Leu625Gln,ENST00000375471,NM_013358.2;PADI3,upstream_gene_variant,,ENST00000375460,NM_016233.2;PADI1,non_coding_transcript_exon_variant,,ENST00000460293,; A ENST00000375471 Transcript missense_variant 1966/3846 1874/1992 625/663 L/Q cTg/cAg 1 1 PADI1 HGNC HGNC:18367 protein_coding YES CCDS178.1 ENSP00000364620 Q9ULC6 UPI000013D8A2 NM_013358.2 deleterious(0) 16/16 Pfam_domain:PF03068,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF11,Superfamily_domains:SSF55909 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17244125 17244125 T A 1 0 0 0 0 1 0 0 0 11455 1580 55 4 4 PADI1 1 17244125 Missense_Mutation SNP T C3L-00144_T 38858 17244125 231712297 14 4085 PLA2G2E 0 . GRCh38 1 19923524 19923524 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.36C>A p.= p.L12L ENST00000375116 1/4 84 74 10 56 56 0 strelka-varscan-mutect PLA2G2E,synonymous_variant,p.=,ENST00000375116,NM_014589.2; T ENST00000375116 Transcript synonymous_variant 94/785 36/429 12/142 L ctC/ctA 1 -1 PLA2G2E HGNC HGNC:13414 protein_coding YES CCDS200.1 ENSP00000364257 Q9NZK7 UPI0000131139 NM_014589.2 1/4 hmmpanther:PTHR11716,hmmpanther:PTHR11716:SF56,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1443764586 . 0 207 3 0 0 0 0 0 -19.9878 1 1 1 1 0 T 2 4 12 19923524 19923524 G T 1 0 0 0 0 0 0 0 1 12094 1188 41 2 2 PLA2G2E 1 19923524 Silent SNP G C3L-00144_T 2679399 19923524 229032898 15 4086 VWA5B1 0 . GRCh38 1 20343145 20343145 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2378C>A p.Ser793Tyr p.S793Y ENST00000375079 16/22 118 87 31 107 107 0 strelka-varscan-mutect VWA5B1,missense_variant,p.Ser793Tyr,ENST00000289815,NM_001039500.2;VWA5B1,missense_variant,p.Ser793Tyr,ENST00000375079,;VWA5B1,non_coding_transcript_exon_variant,,ENST00000525343,;VWA5B1,missense_variant,p.Ser220Tyr,ENST00000467486,;VWA5B1,3_prime_UTR_variant,,ENST00000485375,;VWA5B1,downstream_gene_variant,,ENST00000473325,; A ENST00000375079 Transcript missense_variant 2574/3859 2378/3663 793/1220 S/Y tCc/tAc 1 1 VWA5B1 HGNC HGNC:26538 protein_coding YES ENSP00000364220 Q5TIE3 UPI000066D8B8 deleterious(0.04) 16/22 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF109 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 20343145 20343145 C A 1 0 0 0 0 1 0 0 0 17797 855 30 2 2 VWA5B1 1 20343145 Missense_Mutation SNP C C3L-00144_T 419621 20343145 228613277 16 4087 EIF4G3 0 . GRCh38 1 20941896 20941896 + Nonsense_Mutation SNP C C A rs35287548 C3L-00144_T C3L-00144_N C C c.1087G>T p.Glu363Ter p.E363* ENST00000400422 11/35 163 154 9 143 143 0 strelka-varscan-mutect EIF4G3,stop_gained,p.Glu370Ter,ENST00000602326,NM_001198802.1;EIF4G3,stop_gained,p.Glu364Ter,ENST00000264211,NM_003760.4;EIF4G3,stop_gained,p.Glu363Ter,ENST00000400422,NM_001198801.1;EIF4G3,stop_gained,p.Glu553Ter,ENST00000634879,;EIF4G3,stop_gained,p.Glu375Ter,ENST00000356916,NM_001198803.1;EIF4G3,intron_variant,,ENST00000374935,;EIF4G3,upstream_gene_variant,,ENST00000485722,;EIF4G3,upstream_gene_variant,,ENST00000374933,; A ENST00000400422 Transcript stop_gained 1668/5762 1087/4866 363/1621 E/* Gaa/Taa rs35287548 1 -1 EIF4G3 HGNC HGNC:3298 protein_coding YES CCDS72723.1 ENSP00000383274 A0A0A0MSA7 UPI0000D4C1EC NM_001198801.1 11/35 hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF23 HIGH 1 SNV 1 1 PASS rs35287548 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 20941896 20941896 C A 1 0 0 0 0 0 1 0 0 4871 893 31 1 1 EIF4G3 1 20941896 Nonsense_Mutation SNP C C3L-00144_T 598751 20941896 228014526 17 4088 HSPG2 0 . GRCh38 1 21854205 21854206 + Frame_Shift_Ins INS - - G novel C3L-00144_T C3L-00144_N - - c.6426dupC p.Ser2143GlnfsTer283 p.S2143Qfs*283 ENST00000374695 50/97 98 92 6 69 69 0 varindel-pindel HSPG2,frameshift_variant,p.Ser2143GlnfsTer283,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,non_coding_transcript_exon_variant,,ENST00000493940,; G ENST00000374695 Transcript frameshift_variant 6506-6507/14327 6426-6427/13176 2142-2143/4391 -/X -/C 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 50/97 PROSITE_profiles:PS50835,SMART_domains:SM00406 HIGH 1 insertion 1 1 PASS . . 0 200 10 0 0 0 0 0 -12.18436 0.9998922 1 1 1 0 G 7 5 12 21854205 21854205 - G 1 0 1 1 0 0 0 0 0 7326 1580 55 0 0 HSPG2 1 21854205 Frame_Shift_Ins INS - C3L-00144_T 912309 21854205 227102217 18 4089 C1QC 0 . GRCh38 1 22647321 22647321 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.276C>A p.= p.P92P ENST00000374639 3/3 137 94 43 117 117 0 strelka-varscan-mutect C1QC,synonymous_variant,p.=,ENST00000374639,NM_001114101.1;C1QC,synonymous_variant,p.=,ENST00000374640,NM_172369.3;C1QC,synonymous_variant,p.=,ENST00000374637,; A ENST00000374639 Transcript synonymous_variant 394/1183 276/738 92/245 P ccC/ccA 1 1 C1QC HGNC HGNC:1245 protein_coding YES CCDS227.1 ENSP00000363770 P02747 A0A024RAA7 UPI0000126BF3 NM_001114101.1 3/3 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF558,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 22647321 22647321 C A 1 0 0 0 0 0 0 0 1 1935 610 22 2 2 C1QC 1 22647321 Silent SNP C C3L-00144_T 793116 22647321 226309101 19 4090 RUNX3 0 . GRCh38 1 24907342 24907342 + Missense_Mutation SNP C C A rs746700911 C3L-00144_T C3L-00144_N C C c.662G>T p.Arg221Leu p.R221L ENST00000399916 5/6 282 222 60 286 285 1 strelka-varscan-mutect RUNX3,missense_variant,p.Arg221Leu,ENST00000399916,NM_001320672.1,NM_001031680.2;RUNX3,missense_variant,p.Arg207Leu,ENST00000308873,NM_004350.2;RUNX3,missense_variant,p.Arg221Leu,ENST00000338888,;RUNX3,non_coding_transcript_exon_variant,,ENST00000496967,; A ENST00000399916 Transcript missense_variant 1101/4340 662/1290 221/429 R/L cGg/cTg rs746700911 1 -1 RUNX3 HGNC HGNC:10473 protein_coding YES CCDS30633.1 ENSP00000382800 Q13761 A0A024RAH4 UPI000002B2FF NM_001320672.1,NM_001031680.2 deleterious(0.02) 5/6 hmmpanther:PTHR11950,hmmpanther:PTHR11950:SF26 MODERATE 1 SNV 2 1 PASS rs746700911 . 0 207 0 0 2 0 0 0 -20 0.9983088 1 1 1 0 A 3 1 12 24907342 24907342 C A 1 0 0 0 0 1 0 0 0 14010 652 23 1 1 RUNX3 1 24907342 Missense_Mutation SNP C C3L-00144_T 2260021 24907342 224049080 20 4091 RHCE 0 . GRCh38 1 25389066 25389066 + Silent SNP G G A rs778131577 C3L-00144_T C3L-00144_N G G c.849C>T p.= p.T283T ENST00000294413 6/10 445 379 66 346 346 0 strelka-varscan-mutect RHCE,synonymous_variant,p.=,ENST00000349320,;RHCE,synonymous_variant,p.=,ENST00000294413,NM_020485.4;RHCE,synonymous_variant,p.=,ENST00000349438,NM_138618.3;RHCE,synonymous_variant,p.=,ENST00000413854,;RHCE,synonymous_variant,p.=,ENST00000340849,NM_138617.3;RHCE,intron_variant,,ENST00000346452,NM_138616.3;RHCE,intron_variant,,ENST00000527747,;RHCE,3_prime_UTR_variant,,ENST00000533771,;RHCE,non_coding_transcript_exon_variant,,ENST00000527187,; A ENST00000294413 Transcript synonymous_variant 908/1591 849/1254 283/417 T acC/acT rs778131577 1 -1 RHCE HGNC HGNC:10008 protein_coding YES CCDS30635.1 ENSP00000294413 P18577 UPI00001D9627 NM_020485.4 6/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11730:SF43,hmmpanther:PTHR11730,Gene3D:1.10.3430.10,Pfam_domain:PF00909,Superfamily_domains:0044218,Prints_domain:PR00342 LOW 1 SNV 1 1 PASS rs778131577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 25389066 25389066 G A 1 0 0 0 0 0 0 0 1 13497 987 35 3 3 RHCE 1 25389066 Silent SNP G C3L-00144_T 481724 25389066 223567356 21 4092 RHCE 0 . GRCh38 1 25420746 25420746 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.41C>G p.Pro14Arg p.P14R ENST00000294413 1/10 560 494 66 497 497 0 varscan-mutect RHCE,missense_variant,p.Pro14Arg,ENST00000294413,NM_020485.4;RHCE,missense_variant,p.Pro14Arg,ENST00000349438,NM_138618.3;RHCE,missense_variant,p.Pro14Arg,ENST00000413854,;RHCE,missense_variant,p.Pro14Arg,ENST00000340849,NM_138617.3;RHCE,missense_variant,p.Pro14Arg,ENST00000346452,NM_138616.3;RHCE,intron_variant,,ENST00000349320,;RHCE,non_coding_transcript_exon_variant,,ENST00000495048,;RHCE,missense_variant,p.Pro14Arg,ENST00000533771,;RHCE,non_coding_transcript_exon_variant,,ENST00000527187,; C ENST00000294413 Transcript missense_variant 100/1591 41/1254 14/417 P/R cCc/cGc 1 -1 RHCE HGNC HGNC:10008 protein_coding YES CCDS30635.1 ENSP00000294413 P18577 UPI00001D9627 NM_020485.4 deleterious(0) 1/10 Transmembrane_helices:TMhelix,Prints_domain:PR00342 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 25420746 25420746 G C 1 0 0 0 0 1 0 0 0 13497 1232 43 4 4 RHCE 1 25420746 Missense_Mutation SNP G C3L-00144_T 31680 25420746 223535676 22 4093 ARID1A 0 . GRCh38 1 26774695 26774695 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4468G>T p.Glu1490Ter p.E1490* ENST00000324856 18/20 332 254 78 288 287 1 strelka-varscan-mutect ARID1A,stop_gained,p.Glu1490Ter,ENST00000324856,NM_006015.4;ARID1A,stop_gained,p.Glu1108Ter,ENST00000636219,;ARID1A,stop_gained,p.Glu1106Ter,ENST00000430799,;ARID1A,stop_gained,p.Glu1107Ter,ENST00000374152,;ARID1A,stop_gained,p.Glu1106Ter,ENST00000615191,;ARID1A,intron_variant,,ENST00000457599,NM_139135.2;ARID1A,non_coding_transcript_exon_variant,,ENST00000636794,;ARID1A,non_coding_transcript_exon_variant,,ENST00000636072,;ARID1A,intron_variant,,ENST00000466382,;ARID1A,downstream_gene_variant,,ENST00000636110,;ARID1A,upstream_gene_variant,,ENST00000637788,;ARID1A,upstream_gene_variant,,ENST00000532781,;ARID1A,downstream_gene_variant,,ENST00000430291,; T ENST00000324856 Transcript stop_gained 4839/8577 4468/6858 1490/2285 E/* Gag/Tag 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 18/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 26774695 26774695 G T 1 0 0 0 0 0 1 0 0 1049 1291 45 2 2 ARID1A 1 26774695 Nonsense_Mutation SNP G C3L-00144_T 1353949 26774695 222181727 23 4094 HCRTR1 0 . GRCh38 1 31623528 31623528 + Silent SNP C C G rs371204021 C3L-00144_T C3L-00144_N C C c.744C>G p.= p.P248P ENST00000403528 6/8 143 108 35 89 89 0 strelka-varscan-mutect HCRTR1,synonymous_variant,p.=,ENST00000403528,NM_001525.2;HCRTR1,synonymous_variant,p.=,ENST00000373706,;HCRTR1,synonymous_variant,p.=,ENST00000373705,;HCRTR1,non_coding_transcript_exon_variant,,ENST00000468521,;HCRTR1,non_coding_transcript_exon_variant,,ENST00000485464,; G ENST00000403528 Transcript synonymous_variant 1131/2003 744/1278 248/425 P ccC/ccG rs371204021 1 1 HCRTR1 HGNC HGNC:4848 protein_coding YES CCDS344.1 ENSP00000384387 O43613 UPI0000038135 NM_001525.2 6/8 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01064,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF30,SMART_domains:SM01381 LOW 1 SNV 5 1 PASS rs371204021 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 31623528 31623528 C G 1 0 0 0 0 0 0 0 1 6888 666 23 4 4 HCRTR1 1 31623528 Silent SNP C C3L-00144_T 4848833 31623528 217332894 24 4095 ADGRB2 0 . GRCh38 1 31740450 31740450 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1886G>T p.Arg629Leu p.R629L ENST00000373655 12/33 169 154 15 141 141 0 strelka-varscan-mutect ADGRB2,missense_variant,p.Arg629Leu,ENST00000373658,;ADGRB2,missense_variant,p.Arg629Leu,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Arg562Leu,ENST00000398542,;ADGRB2,missense_variant,p.Arg629Leu,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Arg577Leu,ENST00000398556,;ADGRB2,missense_variant,p.Arg562Leu,ENST00000398547,;ADGRB2,missense_variant,p.Arg617Leu,ENST00000398538,;ADGRB2,missense_variant,p.Arg567Leu,ENST00000420125,;ADGRB2,downstream_gene_variant,,ENST00000533175,;ADGRB2,intron_variant,,ENST00000530134,;ADGRB2,downstream_gene_variant,,ENST00000468430,;ADGRB2,upstream_gene_variant,,ENST00000465256,;ADGRB2,upstream_gene_variant,,ENST00000466109,; A ENST00000373655 Transcript missense_variant 2228/5400 1886/4755 629/1584 R/L cGc/cTc COSM908199 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 tolerated(0.07) 12/33 hmmpanther:PTHR12011:SF41,hmmpanther:PTHR12011,Pfam_domain:PF16489 1 MODERATE 1 SNV 1 1 1 PASS rs1198638899 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31740450 31740450 C A 1 0 0 0 0 1 0 0 0 356 768 27 1 1 ADGRB2 1 31740450 Missense_Mutation SNP C C3L-00144_T 116922 31740450 217215972 25 4096 SPOCD1 0 . GRCh38 1 31814027 31814027 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1307G>T p.Arg436Leu p.R436L ENST00000360482 2/16 89 71 18 73 73 0 strelka-mutect SPOCD1,missense_variant,p.Arg436Leu,ENST00000360482,NM_144569.5;SPOCD1,missense_variant,p.Arg436Leu,ENST00000533231,NM_001281987.1;SPOCD1,intron_variant,,ENST00000257100,NM_001281988.1;SPOCD1,intron_variant,,ENST00000529396,;SPOCD1,intron_variant,,ENST00000528791,;SPOCD1,intron_variant,,ENST00000525930,;SPOCD1,non_coding_transcript_exon_variant,,ENST00000485944,; A ENST00000360482 Transcript missense_variant 1437/3960 1307/3651 436/1216 R/L cGg/cTg COSM5516154 1 -1 SPOCD1 HGNC HGNC:26338 protein_coding YES CCDS347.1 ENSP00000353670 Q6ZMY3 UPI000035E7DD NM_144569.5 deleterious(0.05) 2/16 hmmpanther:PTHR11477:SF18,hmmpanther:PTHR11477 1 MODERATE 1 SNV 2 1 1 PASS rs1025569220 . 0 200 8 2 0 0 0 0 -20 0.9998467 1 1 1 0 A 3 1 12 31814027 31814027 C A 1 0 0 0 0 1 0 0 0 15431 652 23 1 1 SPOCD1 1 31814027 Missense_Mutation SNP C C3L-00144_T 73577 31814027 217142395 26 4097 CSMD2 0 . GRCh38 1 33646761 33646761 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.4661delG p.Ser1554ThrfsTer28 p.S1554Tfs*28 ENST00000373381 29/71 203 161 42 237 237 0 sindel-varindel CSMD2,frameshift_variant,p.Ser1554ThrfsTer28,ENST00000373381,NM_001281956.1;CSMD2,frameshift_variant,p.Ser1514ThrfsTer28,ENST00000619121,;CSMD2,frameshift_variant,p.Ser1514ThrfsTer28,ENST00000373388,NM_052896.4;CSMD2,frameshift_variant,p.Ser427ThrfsTer28,ENST00000373380,;CSMD2,frameshift_variant,p.Ser1514ThrfsTer28,ENST00000241312,; - ENST00000373381 Transcript frameshift_variant 4838/13698 4661/10896 1554/3631 S/X aGc/ac 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 29/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 33646761 33646761 C - 1 0 1 0 1 0 0 0 0 3746 797 28 0 0 CSMD2 1 33646761 Frame_Shift_Del DEL C C3L-00144_T 1832734 33646761 215309661 27 4098 CSMD2 0 . GRCh38 1 33726615 33726615 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2439G>T p.Lys813Asn p.K813N ENST00000373381 16/71 200 169 31 174 174 0 strelka-varscan-mutect CSMD2,missense_variant,p.Lys813Asn,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Lys773Asn,ENST00000619121,;CSMD2,missense_variant,p.Lys773Asn,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Lys773Asn,ENST00000241312,; A ENST00000373381 Transcript missense_variant 2616/13698 2439/10896 813/3631 K/N aaG/aaT 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 deleterious(0.02) 16/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 33726615 33726615 C A 1 0 0 0 0 1 0 0 0 3746 680 24 2 2 CSMD2 1 33726615 Missense_Mutation SNP C C3L-00144_T 79854 33726615 215229807 28 4099 GRIK3 0 . GRCh38 1 36802030 36802030 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2581A>T p.Thr861Ser p.T861S ENST00000373091 16/16 110 75 35 60 60 0 strelka-varscan-mutect GRIK3,missense_variant,p.Thr861Ser,ENST00000373091,NM_000831.3;GRIK3,downstream_gene_variant,,ENST00000373093,; A ENST00000373091 Transcript missense_variant 2598/9101 2581/2760 861/919 T/S Acc/Tcc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 tolerated(0.3) 16/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 36802030 36802030 T A 1 0 0 0 0 1 0 0 0 6657 1696 59 4 4 GRIK3 1 36802030 Missense_Mutation SNP T C3L-00144_T 3075415 36802030 212154392 29 4100 RSPO1 0 . GRCh38 1 37613812 37613812 + Nonsense_Mutation SNP C C A rs767855607 C3L-00144_T C3L-00144_N C C c.517G>T p.Glu173Ter p.E173* ENST00000356545 6/7 317 251 66 285 285 0 strelka-varscan-mutect RSPO1,stop_gained,p.Glu173Ter,ENST00000356545,NM_001242908.1;RSPO1,stop_gained,p.Glu146Ter,ENST00000615459,NM_001242909.1;RSPO1,stop_gained,p.Glu173Ter,ENST00000401068,NM_001038633.3;RSPO1,intron_variant,,ENST00000612451,NM_001242910.1; A ENST00000356545 Transcript stop_gained 1230/2621 517/792 173/263 E/* Gag/Tag rs767855607 1 -1 RSPO1 HGNC HGNC:21679 protein_coding YES CCDS41304.1 ENSP00000348944 Q2MKA7 UPI0000674A16 NM_001242908.1 6/7 PROSITE_profiles:PS50092,hmmpanther:PTHR23275,hmmpanther:PTHR23275:SF44,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 HIGH 1 SNV 1 1 PASS rs767855607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 37613812 37613812 C A 1 0 0 0 0 0 1 0 0 13967 893 31 1 1 RSPO1 1 37613812 Nonsense_Mutation SNP C C3L-00144_T 811782 37613812 211342610 30 4101 MACF1 0 . GRCh38 1 39434544 39434544 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.11510G>T p.Trp3837Leu p.W3837L ENST00000361689 63/93 332 261 71 275 274 1 strelka-varscan-mutect MACF1,missense_variant,p.Trp5899Leu,ENST00000564288,;MACF1,missense_variant,p.Trp5936Leu,ENST00000567887,;MACF1,missense_variant,p.Trp5795Leu,ENST00000372915,;MACF1,missense_variant,p.Trp4339Leu,ENST00000289893,;MACF1,missense_variant,p.Trp3837Leu,ENST00000361689,NM_012090.5;MACF1,missense_variant,p.Trp2841Leu,ENST00000372925,;MACF1,non_coding_transcript_exon_variant,,ENST00000473843,;MACF1,upstream_gene_variant,,ENST00000469490,; T ENST00000361689 Transcript missense_variant 11562/17538 11510/16293 3837/5430 W/L tGg/tTg 1 1 MACF1 HGNC HGNC:13664 protein_coding YES CCDS435.1 ENSP00000354573 Q9UPN3 UPI00001B3DC6 NM_012090.5 deleterious(0) 63/93 Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 39434544 39434544 G T 1 0 0 0 0 1 0 0 0 9060 1357 47 2 2 MACF1 1 39434544 Missense_Mutation SNP G C3L-00144_T 1820732 39434544 209521878 31 4102 MACF1 0 . GRCh38 1 39447864 39447864 + Missense_Mutation SNP G G C rs758478864 C3L-00144_T C3L-00144_N G G c.13757G>C p.Arg4586Pro p.R4586P ENST00000361689 77/93 375 334 41 326 326 0 strelka-varscan-mutect MACF1,missense_variant,p.Arg6645Pro,ENST00000564288,;MACF1,missense_variant,p.Arg6682Pro,ENST00000567887,;MACF1,missense_variant,p.Arg6544Pro,ENST00000372915,;MACF1,missense_variant,p.Arg5088Pro,ENST00000289893,;MACF1,missense_variant,p.Arg4586Pro,ENST00000361689,NM_012090.5;MACF1,missense_variant,p.Arg3590Pro,ENST00000372925,;MACF1,upstream_gene_variant,,ENST00000487656,; C ENST00000361689 Transcript missense_variant 13809/17538 13757/16293 4586/5430 R/P cGa/cCa rs758478864,COSM5627020,COSM5627021,COSM5627022 1 1 MACF1 HGNC HGNC:13664 protein_coding YES CCDS435.1 ENSP00000354573 Q9UPN3 UPI00001B3DC6 NM_012090.5 deleterious(0) 77/93 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF37,SMART_domains:SM00150,Superfamily_domains:SSF46966 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs758478864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 39447864 39447864 G C 1 0 0 0 0 1 0 0 0 9060 1058 37 4 4 MACF1 1 39447864 Missense_Mutation SNP G C3L-00144_T 13320 39447864 209508558 32 4103 OXCT2 0 . GRCh38 1 39770552 39770552 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.704G>T p.Cys235Phe p.C235F ENST00000327582 1/1 212 174 38 197 197 0 strelka-varscan-mutect OXCT2,missense_variant,p.Cys235Phe,ENST00000327582,NM_022120.1;BMP8B,intron_variant,,ENST00000372827,NM_001720.3; A ENST00000327582 Transcript missense_variant 797/1826 704/1554 235/517 C/F tGc/tTc 1 -1 OXCT2 HGNC HGNC:18606 protein_coding YES CCDS445.1 ENSP00000361914 Q9BYC2 UPI000006DF0A NM_022120.1 deleterious(0.01) 1/1 hmmpanther:PTHR13707:SF28,hmmpanther:PTHR13707,PIRSF_domain:PIRSF000858,Gene3D:3.40.1080.10,Pfam_domain:PF01144,SMART_domains:SM00882,Superfamily_domains:SSF100950 MODERATE SNV 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999987 1 1 1 0 A 3 1 12 39770552 39770552 C A 1 0 0 0 0 1 0 0 0 11402 710 25 2 2 OXCT2 1 39770552 Missense_Mutation SNP C C3L-00144_T 322688 39770552 209185870 33 4104 CLDN19 0 . GRCh38 1 42735113 42735113 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.648C>A p.= p.A216A ENST00000296387 5/5 259 229 30 224 224 0 strelka-varscan-mutect CLDN19,synonymous_variant,p.=,ENST00000296387,NM_148960.2;CLDN19,3_prime_UTR_variant,,ENST00000539749,NM_001185117.1;CLDN19,3_prime_UTR_variant,,ENST00000372539,NM_001123395.1; T ENST00000296387 Transcript synonymous_variant 839/2859 648/675 216/224 A gcC/gcA 1 -1 CLDN19 HGNC HGNC:2040 protein_coding YES CCDS471.1 ENSP00000296387 Q8N6F1 UPI000013E32D NM_148960.2 5/5 hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF27 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 42735113 42735113 G T 1 0 0 0 0 0 0 0 1 3244 987 35 2 2 CLDN19 1 42735113 Silent SNP G C3L-00144_T 2964561 42735113 206221309 34 4105 SZT2 0 . GRCh38 1 43441588 43441588 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.7425T>C p.= p.F2475F ENST00000562955 53/71 79 70 9 79 79 0 strelka-varscan-mutect SZT2,synonymous_variant,p.=,ENST00000562955,NM_015284.3;SZT2,synonymous_variant,p.=,ENST00000634258,;SZT2,downstream_gene_variant,,ENST00000471177,;SZT2,upstream_gene_variant,,ENST00000460536,;SZT2,downstream_gene_variant,,ENST00000470897,; C ENST00000562955 Transcript synonymous_variant 7425/12281 7425/10128 2475/3375 F ttT/ttC 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 53/71 hmmpanther:PTHR14918 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 43441588 43441588 T C 1 0 0 0 0 0 0 0 1 15883 1751 61 5 5 SZT2 1 43441588 Silent SNP T C3L-00144_T 706475 43441588 205514834 35 4106 IPO13 0 . GRCh38 1 43956590 43956590 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.993G>T p.Gln331His p.Q331H ENST00000372343 4/20 176 163 13 150 150 0 strelka-varscan-mutect IPO13,missense_variant,p.Gln331His,ENST00000372343,NM_014652.3;IPO13,non_coding_transcript_exon_variant,,ENST00000492152,;IPO13,non_coding_transcript_exon_variant,,ENST00000489773,;IPO13,upstream_gene_variant,,ENST00000480902,; T ENST00000372343 Transcript missense_variant 1655/3894 993/2892 331/963 Q/H caG/caT 1 1 IPO13 HGNC HGNC:16853 protein_coding YES CCDS503.1 ENSP00000361418 O94829 UPI0000073F11 NM_014652.3 deleterious(0.02) 4/20 hmmpanther:PTHR12363:SF29,hmmpanther:PTHR12363,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 43956590 43956590 G T 1 0 0 0 0 1 0 0 0 7697 933 33 2 2 IPO13 1 43956590 Missense_Mutation SNP G C3L-00144_T 515002 43956590 204999832 36 4107 BEST4 0 . GRCh38 1 44786171 44786171 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.539A>T p.Lys180Met p.K180M ENST00000372207 4/9 114 108 6 100 100 0 strelka-varscan-mutect BEST4,missense_variant,p.Lys180Met,ENST00000372207,NM_153274.2; A ENST00000372207 Transcript missense_variant 539/2047 539/1422 180/473 K/M aAg/aTg 1 -1 BEST4 HGNC HGNC:17106 protein_coding YES CCDS514.1 ENSP00000361281 Q8NFU0 UPI000006D85E NM_153274.2 tolerated(0.07) 4/9 Pfam_domain:PF01062,hmmpanther:PTHR10736,hmmpanther:PTHR10736:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 44786171 44786171 T A 1 0 0 0 0 1 0 0 0 1555 1609 56 4 4 BEST4 1 44786171 Missense_Mutation SNP T C3L-00144_T 829581 44786171 204170251 37 4108 PIK3R3 0 . GRCh38 1 46066077 46066077 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.598G>A p.Glu200Lys p.E200K ENST00000262741 5/10 260 226 34 307 307 0 strelka-varscan-mutect PIK3R3,missense_variant,p.Glu200Lys,ENST00000262741,NM_003629.3;PIK3R3,missense_variant,p.Glu200Lys,ENST00000420542,NM_001114172.1;PIK3R3,missense_variant,p.Glu200Lys,ENST00000372006,NM_001303428.1;PIK3R3,missense_variant,p.Glu200Lys,ENST00000423209,NM_001303429.1;PIK3R3,missense_variant,p.Glu246Lys,ENST00000540385,NM_001303427.1;PIK3R3,missense_variant,p.Glu200Lys,ENST00000425892,;PIK3R3,non_coding_transcript_exon_variant,,ENST00000493202,; T ENST00000262741 Transcript missense_variant 1288/5609 598/1386 200/461 E/K Gaa/Aaa 1 -1 PIK3R3 HGNC HGNC:8981 protein_coding YES CCDS529.1 ENSP00000262741 Q92569 UPI000013D318 NM_003629.3 tolerated(0.11) 5/10 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF16454,hmmpanther:PTHR10155 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 46066077 46066077 C T 1 0 0 0 0 1 0 0 0 12015 835 29 3 3 PIK3R3 1 46066077 Missense_Mutation SNP C C3L-00144_T 1279906 46066077 202890345 38 4109 DMBX1 0 . GRCh38 1 46510511 46510511 + Missense_Mutation SNP C C G rs762830943 C3L-00144_T C3L-00144_N C C c.190C>G p.Arg64Gly p.R64G ENST00000360032 2/4 128 117 11 108 108 0 strelka-mutect DMBX1,missense_variant,p.Arg69Gly,ENST00000371956,NM_147192.2;DMBX1,missense_variant,p.Arg64Gly,ENST00000360032,NM_172225.1; G ENST00000360032 Transcript missense_variant 204/2880 190/1134 64/377 R/G Cgc/Ggc rs762830943 1 1 DMBX1 HGNC HGNC:19026 protein_coding YES CCDS536.1 ENSP00000353132 Q8NFW5 UPI0000070B63 NM_172225.1 deleterious(0.02) 2/4 PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF383,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs762830943 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 46510511 46510511 C G 1 0 0 0 0 1 0 0 0 4385 652 23 4 4 DMBX1 1 46510511 Missense_Mutation SNP C C3L-00144_T 444434 46510511 202445911 39 4110 MKNK1 0 . GRCh38 1 46571458 46571458 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.575G>C p.Ser192Thr p.S192T ENST00000371946 8/14 41 31 10 27 27 0 strelka-varscan-mutect MKNK1,missense_variant,p.Ser192Thr,ENST00000371946,NM_003684.5;MKNK1,intron_variant,,ENST00000371945,NM_001135553.2;MKNK1,intron_variant,,ENST00000341183,;MKNK1,intron_variant,,ENST00000428112,NM_198973.3;MKNK1,intron_variant,,ENST00000496619,;MKNK1-AS1,downstream_gene_variant,,ENST00000602433,;MKNK1,intron_variant,,ENST00000342571,;MKNK1,intron_variant,,ENST00000532783,;MKNK1,upstream_gene_variant,,ENST00000470237,;MKNK1,downstream_gene_variant,,ENST00000528237,;MKNK1,upstream_gene_variant,,ENST00000460098,;MKNK1,intron_variant,,ENST00000528077,;MKNK1,intron_variant,,ENST00000531355,;MKNK1,intron_variant,,ENST00000532897,;MKNK1,downstream_gene_variant,,ENST00000484301,;MKNK1,downstream_gene_variant,,ENST00000526513,;MKNK1,downstream_gene_variant,,ENST00000480531,;MKNK1,downstream_gene_variant,,ENST00000486716,; G ENST00000371946 Transcript missense_variant 739/2719 575/1398 192/465 S/T aGt/aCt 1 -1 MKNK1 HGNC HGNC:7110 protein_coding YES CCDS538.1 ENSP00000361014 Q9BUB5 UPI0000073749 NM_003684.5 tolerated_low_confidence(0.72) 8/14 PROSITE_profiles:PS50011,SMART_domains:SM00220 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 46571458 46571458 C G 1 0 0 0 0 1 0 0 0 9571 565 20 4 4 MKNK1 1 46571458 Missense_Mutation SNP C C3L-00144_T 60947 46571458 202384964 40 4111 ZFYVE9 0 . GRCh38 1 52238202 52238202 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.785C>A p.Thr262Lys p.T262K ENST00000287727 4/19 137 117 20 190 187 3 strelka-varscan-mutect ZFYVE9,missense_variant,p.Thr262Lys,ENST00000287727,NM_004799.3;ZFYVE9,missense_variant,p.Thr262Lys,ENST00000371591,;ZFYVE9,missense_variant,p.Thr262Lys,ENST00000357206,NM_007324.3;ZFYVE9,non_coding_transcript_exon_variant,,ENST00000361625,; A ENST00000287727 Transcript missense_variant 1237/5194 785/4278 262/1425 T/K aCa/aAa 1 1 ZFYVE9 HGNC HGNC:6775 protein_coding YES CCDS563.1 ENSP00000287727 O95405 UPI0000001620 NM_004799.3 deleterious_low_confidence(0.04) 4/19 hmmpanther:PTHR22835:SF265,hmmpanther:PTHR22835 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52238202 52238202 C A 1 0 0 0 0 1 0 0 0 18248 478 17 2 2 ZFYVE9 1 52238202 Missense_Mutation SNP C C3L-00144_T 5666744 52238202 196718220 41 4112 FAM159A 0 . GRCh38 1 52656839 52656839 + Silent SNP G G T rs762346974 C3L-00144_T C3L-00144_N G G c.372G>T p.= p.A124A ENST00000517870 3/3 126 103 23 121 121 0 strelka-varscan-mutect FAM159A,synonymous_variant,p.=,ENST00000517870,NM_001042693.1;FAM159A,intron_variant,,ENST00000401050,;FAM159A,intron_variant,,ENST00000440303,;FAM159A,intron_variant,,ENST00000424164,; T ENST00000517870 Transcript synonymous_variant 522/748 372/573 124/190 A gcG/gcT rs762346974,COSM910699 1 1 FAM159A HGNC HGNC:28757 protein_coding YES CCDS41336.1 ENSP00000429726 Q6UWV7 UPI0000204364 NM_001042693.1 3/3 hmmpanther:PTHR31395,hmmpanther:PTHR31395:SF3 0,1 LOW 1 SNV 1 0,1 1 PASS rs762346974 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 52656839 52656839 G T 1 0 0 0 0 0 0 0 1 5315 1103 39 1 1 FAM159A 1 52656839 Silent SNP G C3L-00144_T 418637 52656839 196299583 42 4113 NDC1 0 . GRCh38 1 53828092 53828092 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.362A>T p.His121Leu p.H121L ENST00000371429 4/18 205 177 28 177 177 0 strelka-varscan-mutect NDC1,missense_variant,p.His121Leu,ENST00000371429,NM_001168551.1,NM_018087.4;NDC1,non_coding_transcript_exon_variant,,ENST00000480952,; A ENST00000371429 Transcript missense_variant 961/5134 362/2025 121/674 H/L cAt/cTt 1 -1 NDC1 HGNC HGNC:25525 protein_coding YES CCDS583.1 ENSP00000360483 Q9BTX1 UPI000006D8F7 NM_001168551.1,NM_018087.4 deleterious(0.01) 4/18 hmmpanther:PTHR13269:SF6,hmmpanther:PTHR13269,Pfam_domain:PF09531 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 53828092 53828092 T A 1 0 0 0 0 1 0 0 0 10262 1464 51 4 4 NDC1 1 53828092 Missense_Mutation SNP T C3L-00144_T 1171253 53828092 195128330 43 4114 DIO1 0 . GRCh38 1 53906154 53906154 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.541C>A p.Leu181Met p.L181M ENST00000361921 3/4 329 291 38 322 321 1 strelka-mutect DIO1,missense_variant,p.Leu181Met,ENST00000361921,NM_000792.5;DIO1,missense_variant,p.Leu180Met,ENST00000613679,;DIO1,missense_variant,p.Leu138Met,ENST00000529589,;DIO1,missense_variant,p.Leu52Met,ENST00000524406,;DIO1,missense_variant,p.Leu133Met,ENST00000388876,NM_001039715.1;DIO1,missense_variant,p.Leu117Met,ENST00000525202,NM_213593.3;DIO1,3_prime_UTR_variant,,ENST00000610607,;DIO1,intron_variant,,ENST00000322679,NM_001039716.1;DIO1,intron_variant,,ENST00000617230,;DIO1,intron_variant,,ENST00000532493,;DIO1,non_coding_transcript_exon_variant,,ENST00000534069,;DIO1,3_prime_UTR_variant,,ENST00000527060,;DIO1,3_prime_UTR_variant,,ENST00000530084,;DIO1,3_prime_UTR_variant,,ENST00000529329,;DIO1,intron_variant,,ENST00000528946,;DIO1,intron_variant,,ENST00000525044,;DIO1,downstream_gene_variant,,ENST00000526329,; A ENST00000361921 Transcript missense_variant 565/1861 541/750 181/249 L/M Ctg/Atg 1 1 DIO1 HGNC HGNC:2883 protein_coding YES CCDS41339.1 ENSP00000354643 P49895 UPI0000161B1A NM_000792.5 tolerated(0.12) 3/4 hmmpanther:PTHR11781:SF7,hmmpanther:PTHR11781,Gene3D:3.40.30.10,PIRSF_domain:PIRSF001330,Pfam_domain:PF00837,PIRSF_domain:PIRSF500144,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS rs1489032485 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 53906154 53906154 C A 1 0 0 0 0 1 0 0 0 4329 680 24 2 2 DIO1 1 53906154 Missense_Mutation SNP C C3L-00144_T 78062 53906154 195050268 44 4115 ACOT11 0 . GRCh38 1 54630819 54630819 + Missense_Mutation SNP G G T rs377475734 C3L-00144_T C3L-00144_N G G c.1715G>T p.Arg572Leu p.R572L ENST00000371316 16/17 68 55 13 44 44 0 strelka-varscan-mutect ACOT11,missense_variant,p.Arg572Leu,ENST00000371316,NM_015547.3;RP11-240D10.4,upstream_gene_variant,,ENST00000416119,; T ENST00000371316 Transcript missense_variant 1797/6369 1715/1824 572/607 R/L cGc/cTc rs377475734,COSM191870 1 1 ACOT11 HGNC HGNC:18156 protein_coding YES CCDS592.1 ENSP00000360366 Q8WXI4 UPI0000136D55 NM_015547.3 16/17 Pfam_domain:PF01852,SMART_domains:SM00234 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs377475734 . 0 202 5 3 0 0 0 0 -19.99961 0.9998294 1 1 1 0 T 3 4 12 54630819 54630819 G T 1 0 0 0 0 1 0 0 0 191 1087 38 1 1 ACOT11 1 54630819 Missense_Mutation SNP G C3L-00144_T 724665 54630819 194325603 45 4116 TTC22 0 . GRCh38 1 54800670 54800670 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.494G>T p.Ser165Ile p.S165I ENST00000371276 1/7 122 105 17 120 119 1 strelka-varscan-mutect TTC22,missense_variant,p.Ser165Ile,ENST00000371276,NM_001114108.1;TTC22,missense_variant,p.Ser165Ile,ENST00000371274,NM_017904.3; A ENST00000371276 Transcript missense_variant 598/3345 494/1710 165/569 S/I aGc/aTc 1 -1 TTC22 HGNC HGNC:26067 protein_coding YES CCDS44152.1 ENSP00000360323 Q5TAA0 UPI0000470B73 NM_001114108.1 deleterious(0.03) 1/7 hmmpanther:PTHR16253,hmmpanther:PTHR16253:SF4 MODERATE 1 SNV 5 1 PASS rs962846743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 54800670 54800670 C A 1 0 0 0 0 1 0 0 0 17197 797 28 2 2 TTC22 1 54800670 Missense_Mutation SNP C C3L-00144_T 169851 54800670 194155752 46 4117 BSND 0 . GRCh38 1 54999272 54999272 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.86A>G p.Asp29Gly p.D29G ENST00000371265 1/4 211 185 26 184 184 0 strelka-varscan-mutect BSND,missense_variant,p.Asp29Gly,ENST00000371265,NM_057176.2; G ENST00000371265 Transcript missense_variant 340/3472 86/963 29/320 D/G gAt/gGt 1 1 BSND HGNC HGNC:16512 protein_coding YES CCDS602.1 ENSP00000360312 Q8WZ55 Q5VU50 UPI000006DC8D NM_057176.2 deleterious(0) 1/4 PD968187,Pfam_domain:PF15462,hmmpanther:PTHR28399,hmmpanther:PTHR28399:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 54999272 54999272 A G 1 0 0 0 0 1 0 0 0 1705 333 12 5 5 BSND 1 54999272 Missense_Mutation SNP A C3L-00144_T 198602 54999272 193957150 47 4118 PCSK9 0 . GRCh38 1 55056009 55056009 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.816G>A p.= p.R272R ENST00000302118 6/12 118 99 19 108 108 0 strelka-varscan-mutect PCSK9,synonymous_variant,p.=,ENST00000302118,NM_174936.3;PCSK9,non_coding_transcript_exon_variant,,ENST00000490692,; A ENST00000302118 Transcript synonymous_variant 1106/3637 816/2079 272/692 R cgG/cgA 1 1 PCSK9 HGNC HGNC:20001 protein_coding YES CCDS603.1 ENSP00000303208 Q8NBP7 UPI00001615E1 NM_174936.3 6/12 hmmpanther:PTHR10795:SF443,hmmpanther:PTHR10795,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743 LOW 1 SNV 1 1 PASS rs746504242 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 55056009 55056009 G A 1 0 0 0 0 0 0 0 1 11694 1161 41 3 3 PCSK9 1 55056009 Silent SNP G C3L-00144_T 56737 55056009 193900413 48 4119 USP24 0 . GRCh38 1 55214939 55214939 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.175G>C p.Gly59Arg p.G59R ENST00000294383 1/68 161 150 11 143 143 0 strelka-varscan-mutect USP24,missense_variant,p.Gly59Arg,ENST00000294383,NM_015306.2;RP11-101C11.1,upstream_gene_variant,,ENST00000451250,; G ENST00000294383 Transcript missense_variant 175/10549 175/7863 59/2620 G/R Ggc/Cgc 1 -1 USP24 HGNC HGNC:12623 protein_coding YES CCDS44154.2 ENSP00000294383 Q9UPU5 UPI000059CFDE NM_015306.2 tolerated_low_confidence(0.53) 1/68 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS rs1298927281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 55214939 55214939 C G 1 0 0 0 0 1 0 0 0 17596 652 23 4 4 USP24 1 55214939 Missense_Mutation SNP C C3L-00144_T 158930 55214939 193741483 49 4120 C8B 0 . GRCh38 1 56952076 56952076 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.638C>A p.Pro213His p.P213H ENST00000371237 5/12 481 415 66 436 436 0 strelka-varscan-mutect C8B,missense_variant,p.Pro161His,ENST00000543257,NM_001278543.1;C8B,missense_variant,p.Pro151His,ENST00000535057,NM_001278544.1;C8B,missense_variant,p.Pro213His,ENST00000371237,NM_000066.3;C8B,downstream_gene_variant,,ENST00000468990,; T ENST00000371237 Transcript missense_variant 705/2037 638/1776 213/591 P/H cCc/cAc 1 -1 C8B HGNC HGNC:1353 protein_coding YES CCDS30730.1 ENSP00000360281 P07358 UPI000013C9B2 NM_000066.3 deleterious(0) 5/12 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 56952076 56952076 G T 1 0 0 0 0 1 0 0 0 2151 1232 43 2 2 C8B 1 56952076 Missense_Mutation SNP G C3L-00144_T 1737137 56952076 192004346 50 4121 C1orf87 0 . GRCh38 1 60055268 60055268 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.278A>T p.Gln93Leu p.Q93L ENST00000371201 3/12 357 321 36 354 354 0 strelka-varscan-mutect C1orf87,missense_variant,p.Gln93Leu,ENST00000371201,NM_152377.2;C1orf87,missense_variant,p.Gln93Leu,ENST00000450089,; A ENST00000371201 Transcript missense_variant 386/2028 278/1641 93/546 Q/L cAg/cTg 1 -1 C1orf87 HGNC HGNC:28547 protein_coding YES CCDS614.1 ENSP00000360244 Q8N0U7 UPI000006E066 NM_152377.2 tolerated(0.1) 3/12 hmmpanther:PTHR34830,hmmpanther:PTHR34830:SF1 MODERATE 1 SNV 1 1 PASS rs1327400882 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 60055268 60055268 T A 1 0 0 0 0 1 0 0 0 1999 1580 55 4 4 C1orf87 1 60055268 Missense_Mutation SNP T C3L-00144_T 3103192 60055268 188901154 51 4122 PATJ 0 . GRCh38 1 61864456 61864456 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2658G>T p.Met886Ile p.M886I ENST00000371158 20/43 216 178 38 173 172 1 strelka-varscan-mutect PATJ,missense_variant,p.Met886Ile,ENST00000371158,NM_176877.2;PATJ,missense_variant,p.Met886Ile,ENST00000613764,;PATJ,missense_variant,p.Met886Ile,ENST00000316485,;PATJ,non_coding_transcript_exon_variant,,ENST00000493967,;PATJ,missense_variant,p.Met345Ile,ENST00000484937,;PATJ,3_prime_UTR_variant,,ENST00000635023,;PATJ,non_coding_transcript_exon_variant,,ENST00000484562,;PATJ,non_coding_transcript_exon_variant,,ENST00000459752,;PATJ,non_coding_transcript_exon_variant,,ENST00000635214,;PATJ,non_coding_transcript_exon_variant,,ENST00000488913,; T ENST00000371158 Transcript missense_variant 2772/8505 2658/5406 886/1801 M/I atG/atT 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 tolerated(0.06) 20/43 hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF11 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 61864456 61864456 G T 1 0 0 0 0 1 0 0 0 11558 1348 47 2 2 PATJ 1 61864456 Missense_Mutation SNP G C3L-00144_T 1809188 61864456 187091966 52 4123 AK4 0 . GRCh38 1 65190749 65190749 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.185T>A p.Leu62His p.L62H ENST00000395334 3/6 189 157 32 168 168 0 strelka-varscan-mutect AK4,missense_variant,p.Leu62His,ENST00000395334,NM_001005353.2;AK4,missense_variant,p.Leu62His,ENST00000545314,NM_203464.2;AK4,missense_variant,p.Leu62His,ENST00000327299,NM_013410.3;AK4,missense_variant,p.Leu10His,ENST00000546702,;AK4,non_coding_transcript_exon_variant,,ENST00000470888,;AK4,non_coding_transcript_exon_variant,,ENST00000474968,;AK4,non_coding_transcript_exon_variant,,ENST00000479060,;AK4,non_coding_transcript_exon_variant,,ENST00000497030,; A ENST00000395334 Transcript missense_variant 543/6998 185/672 62/223 L/H cTt/cAt 1 1 AK4 HGNC HGNC:363 protein_coding YES CCDS629.1 ENSP00000378743 P27144 UPI000011E13C NM_001005353.2 tolerated(0.12) 3/6 HAMAP:MF_03169,HAMAP:MF_03170,HAMAP:MF_00235,hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF58,TIGRFAM_domain:TIGR01351,Gene3D:3.40.50.300,Pfam_domain:PF00406,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 65190749 65190749 T A 1 0 0 0 0 1 0 0 0 521 1609 56 4 4 AK4 1 65190749 Missense_Mutation SNP T C3L-00144_T 3326293 65190749 183765673 53 4124 DNAJC6 0 . GRCh38 1 65392459 65392459 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1497G>C p.Glu499Asp p.E499D ENST00000371069 12/19 31 27 4 35 35 0 strelka-varscan DNAJC6,missense_variant,p.Glu429Asp,ENST00000263441,NM_001256865.1;DNAJC6,missense_variant,p.Glu442Asp,ENST00000395325,NM_014787.3;DNAJC6,missense_variant,p.Glu499Asp,ENST00000371069,NM_001256864.1;DNAJC6,missense_variant,p.Glu473Asp,ENST00000494710,;DNAJC6,downstream_gene_variant,,ENST00000498720,; C ENST00000371069 Transcript missense_variant 1698/5365 1497/2913 499/970 E/D gaG/gaC 1 1 DNAJC6 HGNC HGNC:15469 protein_coding YES CCDS58004.1 ENSP00000360108 O75061 UPI000022AE8A NM_001256864.1 tolerated(0.37) 12/19 hmmpanther:PTHR23172:SF4,hmmpanther:PTHR23172 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -11.55086 1 1 1 1 0 C 3 2 12 65392459 65392459 G C 1 0 0 0 0 1 0 0 0 4466 991 35 4 4 DNAJC6 1 65392459 Missense_Mutation SNP G C3L-00144_T 201710 65392459 183563963 54 4125 LEPR 0 . GRCh38 1 65619955 65619955 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2423A>T p.Gln808Leu p.Q808L ENST00000349533 17/20 190 180 10 220 220 0 strelka-varscan-mutect LEPR,missense_variant,p.Gln808Leu,ENST00000349533,NM_002303.5;LEPR,missense_variant,p.Gln808Leu,ENST00000371060,NM_001003679.3;LEPR,missense_variant,p.Gln808Leu,ENST00000616738,NM_001198689.1;LEPR,missense_variant,p.Gln808Leu,ENST00000371059,NM_001003680.3,NM_001198687.1;LEPR,missense_variant,p.Gln808Leu,ENST00000344610,NM_001198688.1;LEPR,missense_variant,p.Gln808Leu,ENST00000371058,;LEPR,intron_variant,,ENST00000406510,;LEPR,non_coding_transcript_exon_variant,,ENST00000471762,; T ENST00000349533 Transcript missense_variant 2608/8227 2423/3498 808/1165 Q/L cAg/cTg 1 1 LEPR HGNC HGNC:6554 protein_coding YES CCDS631.1 ENSP00000330393 P48357 UPI000014C37B NM_002303.5 tolerated(0.05) 17/20 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF109,hmmpanther:PTHR23036,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 65619955 65619955 A T 1 0 0 0 0 1 0 0 0 8636 188 7 4 4 LEPR 1 65619955 Missense_Mutation SNP A C3L-00144_T 227496 65619955 183336467 55 4126 DEPDC1 0 . GRCh38 1 68482713 68482713 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.1095A>T p.= p.L365L ENST00000456315 8/12 103 82 21 103 103 0 strelka-varscan-mutect DEPDC1,synonymous_variant,p.=,ENST00000456315,NM_001114120.2;DEPDC1,intron_variant,,ENST00000370966,NM_017779.5;DEPDC1,downstream_gene_variant,,ENST00000525124,;RP4-694A7.2,intron_variant,,ENST00000425820,;DEPDC1,synonymous_variant,p.=,ENST00000489862,;DEPDC1,upstream_gene_variant,,ENST00000488146,; A ENST00000456315 Transcript synonymous_variant 1210/5331 1095/2436 365/811 L ctA/ctT 1 -1 DEPDC1 HGNC HGNC:22949 protein_coding YES CCDS44159.1 ENSP00000412292 Q5TB30 UPI0000204557 NM_001114120.2 8/12 LOW 1 SNV 1 1 PASS rs1434059058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 68482713 68482713 T A 1 0 0 0 0 0 0 0 1 4245 1625 57 4 4 DEPDC1 1 68482713 Silent SNP T C3L-00144_T 2862758 68482713 180473709 56 4127 LRRC7 0 . GRCh38 1 70038434 70038434 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.2496A>G p.= p.P832P ENST00000035383 19/25 203 186 17 224 224 0 strelka-varscan-mutect LRRC7,synonymous_variant,p.=,ENST00000310961,;LRRC7,synonymous_variant,p.=,ENST00000035383,NM_020794.2;LRRC7,synonymous_variant,p.=,ENST00000415775,; G ENST00000035383 Transcript synonymous_variant 2526/5000 2496/4614 832/1537 P ccA/ccG 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 19/25 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 70038434 70038434 A G 1 0 0 0 0 0 0 0 1 8916 175 7 5 5 LRRC7 1 70038434 Silent SNP A C3L-00144_T 1555721 70038434 178917988 57 4128 LRRC7 0 . GRCh38 1 70038464 70038464 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.2526G>A p.Trp842Ter p.W842* ENST00000035383 19/25 180 164 16 172 171 1 strelka-varscan-mutect LRRC7,stop_gained,p.Trp847Ter,ENST00000310961,;LRRC7,stop_gained,p.Trp842Ter,ENST00000035383,NM_020794.2;LRRC7,stop_gained,p.Trp126Ter,ENST00000415775,; A ENST00000035383 Transcript stop_gained 2556/5000 2526/4614 842/1537 W/* tgG/tgA 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 19/25 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.98969 0.9999998 1 1 1 0 A 4 1 12 70038464 70038464 G A 1 0 0 0 0 0 1 0 0 8916 1212 42 3 3 LRRC7 1 70038464 Nonsense_Mutation SNP G C3L-00144_T 30 70038464 178917958 58 4129 LRRC7 0 . GRCh38 1 70039354 70039354 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.3416C>A p.Pro1139Gln p.P1139Q ENST00000035383 19/25 286 263 23 299 297 2 strelka-varscan-mutect LRRC7,missense_variant,p.Pro1144Gln,ENST00000310961,;LRRC7,missense_variant,p.Pro1139Gln,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Pro423Gln,ENST00000415775,; A ENST00000035383 Transcript missense_variant 3446/5000 3416/4614 1139/1537 P/Q cCa/cAa COSM1687888 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated(0.23) 19/25 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 70039354 70039354 C A 1 0 0 0 0 1 0 0 0 8916 594 21 2 2 LRRC7 1 70039354 Missense_Mutation SNP C C3L-00144_T 890 70039354 178917068 59 4130 ERICH3 0 . GRCh38 1 74572337 74572337 + Missense_Mutation SNP C C A rs775619326 C3L-00144_T C3L-00144_N C C c.3373G>T p.Asp1125Tyr p.D1125Y ENST00000326665 14/15 151 128 23 182 182 0 strelka-varscan-mutect ERICH3,missense_variant,p.Asp1125Tyr,ENST00000326665,NM_001002912.4;ERICH3,non_coding_transcript_exon_variant,,ENST00000433746,;ERICH3,downstream_gene_variant,,ENST00000614534,; A ENST00000326665 Transcript missense_variant 3592/7159 3373/4593 1125/1530 D/Y Gat/Tat rs775619326 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0.01) 14/15 hmmpanther:PTHR23034 MODERATE 1 SNV 5 1 PASS rs775619326 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 74572337 74572337 C A 1 0 0 0 0 1 0 0 0 5083 826 29 2 2 ERICH3 1 74572337 Missense_Mutation SNP C C3L-00144_T 4532983 74572337 174384085 60 4131 ERICH3 0 . GRCh38 1 74572411 74572411 + Missense_Mutation SNP G G T rs564254097 C3L-00144_T C3L-00144_N G G c.3299C>A p.Ala1100Glu p.A1100E ENST00000326665 14/15 261 224 37 287 287 0 strelka-varscan-mutect ERICH3,missense_variant,p.Ala1100Glu,ENST00000326665,NM_001002912.4;ERICH3,non_coding_transcript_exon_variant,,ENST00000433746,;ERICH3,downstream_gene_variant,,ENST00000614534,; T ENST00000326665 Transcript missense_variant 3518/7159 3299/4593 1100/1530 A/E gCg/gAg rs564254097,COSM536095 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 tolerated(0.55) 14/15 Low_complexity_(Seg):seg,hmmpanther:PTHR23034 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs564254097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 74572411 74572411 G T 1 0 0 0 0 1 0 0 0 5083 1087 38 1 1 ERICH3 1 74572411 Missense_Mutation SNP G C3L-00144_T 74 74572411 174384011 61 4132 PKN2 0 . GRCh38 1 88805633 88805633 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1638G>T p.= p.V546V ENST00000370521 11/22 233 214 19 206 206 0 strelka-varscan-mutect PKN2,synonymous_variant,p.=,ENST00000370521,NM_006256.2;PKN2,synonymous_variant,p.=,ENST00000370513,;PKN2,synonymous_variant,p.=,ENST00000316005,;PKN2,downstream_gene_variant,,ENST00000436111,; T ENST00000370521 Transcript synonymous_variant 1997/6121 1638/2955 546/984 V gtG/gtT 1 1 PKN2 HGNC HGNC:9406 protein_coding YES CCDS714.1 ENSP00000359552 Q16513 UPI000004D291 NM_006256.2 11/22 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 88805633 88805633 G T 1 0 0 0 0 0 0 0 1 12076 1335 47 2 2 PKN2 1 88805633 Silent SNP G C3L-00144_T 14233222 88805633 160150789 62 4133 GBP7 0 . GRCh38 1 89150539 89150539 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.662G>A p.Arg221Lys p.R221K ENST00000294671 6/11 208 181 27 210 210 0 strelka-mutect GBP7,missense_variant,p.Arg221Lys,ENST00000294671,NM_207398.2;GBP2,upstream_gene_variant,,ENST00000464839,; T ENST00000294671 Transcript missense_variant 801/2454 662/1917 221/638 R/K aGg/aAg 1 -1 GBP7 HGNC HGNC:29606 protein_coding YES CCDS720.1 ENSP00000294671 Q8N8V2 UPI000013E1A3 NM_207398.2 deleterious(0.03) 6/11 PROSITE_profiles:PS51715,hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF17,Gene3D:3.40.50.300,Pfam_domain:PF02263,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 89150539 89150539 C T 1 0 0 0 0 1 0 0 0 6149 681 24 3 3 GBP7 1 89150539 Missense_Mutation SNP C C3L-00144_T 344906 89150539 159805883 63 4134 GBP6 0 . GRCh38 1 89381894 89381894 + Missense_Mutation SNP G G C rs781019542 C3L-00144_T C3L-00144_N G G c.1072G>C p.Ala358Pro p.A358P ENST00000370456 7/11 208 178 30 230 230 0 strelka-varscan-mutect GBP6,missense_variant,p.Ala358Pro,ENST00000370456,NM_198460.2; C ENST00000370456 Transcript missense_variant 1165/2987 1072/1902 358/633 A/P Gcc/Ccc rs781019542 1 1 GBP6 HGNC HGNC:25395 protein_coding YES CCDS723.1 ENSP00000359485 Q6ZN66 UPI00001D7DF5 NM_198460.2 deleterious(0.04) 7/11 hmmpanther:PTHR10751:SF48,hmmpanther:PTHR10751,Pfam_domain:PF02841,Gene3D:1f5nA01,Superfamily_domains:0037397 MODERATE 1 SNV 1 1 PASS rs781019542 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 89381894 89381894 G C 1 0 0 0 0 1 0 0 0 6148 1203 42 4 4 GBP6 1 89381894 Missense_Mutation SNP G C3L-00144_T 231355 89381894 159574528 64 4135 GLMN 0 . GRCh38 1 92246590 92246590 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1725G>A p.= p.V575V ENST00000370360 19/19 206 174 32 189 189 0 strelka-varscan-mutect GLMN,synonymous_variant,p.=,ENST00000370360,NM_053274.2;GLMN,downstream_gene_variant,,ENST00000495852,;C1orf146,downstream_gene_variant,,ENST00000370373,;C1orf146,downstream_gene_variant,,ENST00000370375,NM_001012425.1;GLMN,3_prime_UTR_variant,,ENST00000495106,;GLMN,non_coding_transcript_exon_variant,,ENST00000471465,; T ENST00000370360 Transcript synonymous_variant 1807/1995 1725/1785 575/594 V gtG/gtA 1 -1 GLMN HGNC HGNC:14373 protein_coding YES CCDS738.1 ENSP00000359385 Q92990 UPI0000040A53 NM_053274.2 19/19 hmmpanther:PTHR15430,hmmpanther:PTHR15430:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 92246590 92246590 C T 1 0 0 0 0 0 0 0 1 6326 581 21 3 3 GLMN 1 92246590 Silent SNP C C3L-00144_T 2864696 92246590 156709832 65 4136 ABCA4 0 . GRCh38 1 94001028 94001028 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.6360delG p.Arg2121GlyfsTer24 p.R2121Gfs*24 ENST00000370225 46/50 319 269 50 360 360 0 sindel-varindel-pindel ABCA4,frameshift_variant,p.Arg2121GlyfsTer24,ENST00000370225,NM_000350.2;ABCA4,frameshift_variant,p.Arg913GlyfsTer24,ENST00000536513,;ABCA4,downstream_gene_variant,,ENST00000465352,;ABCA4,downstream_gene_variant,,ENST00000484388,; - ENST00000370225 Transcript frameshift_variant 6447/7309 6360/6822 2120/2273 G/X ggG/gg 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 46/50 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF97,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR01257,SMART_domains:SM00382,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 94001028 94001028 C - 1 0 1 0 1 0 0 0 0 38 842 30 0 0 ABCA4 1 94001028 Frame_Shift_Del DEL C C3L-00144_T 1754438 94001028 154955394 66 4137 PLPPR4 0 . GRCh38 1 99306382 99306382 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1664C>A p.Ala555Asp p.A555D ENST00000370185 7/7 210 186 24 195 195 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Ala555Asp,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Ala497Asp,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Ala397Asp,ENST00000370184,; A ENST00000370185 Transcript missense_variant 2161/5369 1664/2292 555/763 A/D gCc/gAc 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0.02) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 99306382 99306382 C A 1 0 0 0 0 1 0 0 0 12212 739 26 2 2 PLPPR4 1 99306382 Missense_Mutation SNP C C3L-00144_T 5305354 99306382 149650040 67 4138 PLPPR4 0 . GRCh38 1 99306888 99306888 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.2170C>A p.Arg724Ser p.R724S ENST00000370185 7/7 260 244 16 269 268 1 strelka-mutect PLPPR4,missense_variant,p.Arg724Ser,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Arg666Ser,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Arg566Ser,ENST00000370184,; A ENST00000370185 Transcript missense_variant 2667/5369 2170/2292 724/763 R/S Cgc/Agc COSM1667731,COSM5533947,COSM5533948 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0) 7/7 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1181907106 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 99306888 99306888 C A 1 0 0 0 0 1 0 0 0 12212 652 23 1 1 PLPPR4 1 99306888 Missense_Mutation SNP C C3L-00144_T 506 99306888 149649534 68 4139 17 2 PLPPR4 0 . GRCh38 1 99306893 99306893 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2175C>A p.Asp725Glu p.D725E ENST00000370185 7/7 256 240 16 253 253 0 strelka-mutect PLPPR4,missense_variant,p.Asp725Glu,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Asp667Glu,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Asp567Glu,ENST00000370184,; A ENST00000370185 Transcript missense_variant 2672/5369 2175/2292 725/763 D/E gaC/gaA 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 tolerated(1) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 99306893 99306893 C A 1 0 0 0 0 1 0 0 0 12212 564 20 2 2 PLPPR4 1 99306893 Missense_Mutation SNP C C3L-00144_T 5 99306893 149649529 69 4140 17 2 AC096949.1 0 . GRCh38 1 99913625 99913625 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4048G>T p.Glu1350Ter p.E1350* ENST00000294724 30/34 295 262 33 283 283 0 strelka-varscan-mutect AGL,stop_gained,p.Glu1350Ter,ENST00000294724,NM_000028.2;AGL,stop_gained,p.Glu1350Ter,ENST00000361915,NM_000642.2;AGL,stop_gained,p.Glu1350Ter,ENST00000370163,NM_000643.2;AGL,stop_gained,p.Glu1350Ter,ENST00000370165,NM_000644.2;AGL,stop_gained,p.Glu1334Ter,ENST00000370161,NM_000646.2;AC096949.1,stop_gained,p.Glu1333Ter,ENST00000361522,NM_000645.2;AGL,3_prime_UTR_variant,,ENST00000361302,;AGL,non_coding_transcript_exon_variant,,ENST00000637337,; T ENST00000294724 Transcript stop_gained 4526/7446 4048/4599 1350/1532 E/* Gaa/Taa 1 1 AGL HGNC HGNC:321 protein_coding YES CCDS759.1 ENSP00000294724 P35573 A0A0S2A4E4 UPI00001694CB NM_000028.2 30/34 hmmpanther:PTHR10569,Pfam_domain:PF06202,TIGRFAM_domain:TIGR01531,Superfamily_domains:SSF48208 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 99913625 99913625 G T 1 0 0 0 0 0 1 0 0 135 1291 45 2 2 AC096949.1 1 99913625 Nonsense_Mutation SNP G C3L-00144_T 606732 99913625 149042797 70 4141 VCAM1 0 . GRCh38 1 100732511 100732511 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1619C>A p.Pro540His p.P540H ENST00000294728 7/9 79 64 15 57 57 0 strelka-varscan-mutect VCAM1,missense_variant,p.Pro540His,ENST00000294728,NM_001078.3;VCAM1,missense_variant,p.Pro448His,ENST00000347652,NM_080682.2;VCAM1,missense_variant,p.Pro478His,ENST00000370119,NM_001199834.1;VCAM1,missense_variant,p.Pro341His,ENST00000370115,;VCAM1,upstream_gene_variant,,ENST00000603679,; A ENST00000294728 Transcript missense_variant 1720/3083 1619/2220 540/739 P/H cCt/cAt 1 1 VCAM1 HGNC HGNC:12663 protein_coding YES CCDS773.1 ENSP00000294728 P19320 UPI0000000E06 NM_001078.3 deleterious(0) 7/9 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF729,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 100732511 100732511 C A 1 0 0 0 0 1 0 0 0 17682 681 24 2 2 VCAM1 1 100732511 Missense_Mutation SNP C C3L-00144_T 818886 100732511 148223911 71 4142 CLCC1 0 . GRCh38 1 108943980 108943980 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.417G>C p.Lys139Asn p.K139N ENST00000356970 5/12 247 209 38 220 220 0 strelka-varscan-mutect CLCC1,missense_variant,p.Lys139Asn,ENST00000356970,NM_001048210.2;CLCC1,missense_variant,p.Lys139Asn,ENST00000369976,;CLCC1,intron_variant,,ENST00000369969,NM_001278202.1;CLCC1,intron_variant,,ENST00000369968,NM_001278203.1;CLCC1,intron_variant,,ENST00000369970,NM_015127.4;CLCC1,intron_variant,,ENST00000302500,;CLCC1,intron_variant,,ENST00000348264,;RP11-475E11.9,intron_variant,,ENST00000357393,;CLCC1,upstream_gene_variant,,ENST00000482889,;CLCC1,upstream_gene_variant,,ENST00000473062,; G ENST00000356970 Transcript missense_variant 525/4803 417/1656 139/551 K/N aaG/aaC 1 -1 CLCC1 HGNC HGNC:29675 protein_coding YES CCDS41362.1 ENSP00000349456 Q96S66 A0A024R0G0 UPI0000073C42 NM_001048210.2 deleterious(0.02) 5/12 hmmpanther:PTHR34093,hmmpanther:PTHR34093:SF1,Pfam_domain:PF05934 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 108943980 108943980 C G 1 0 0 0 0 1 0 0 0 3224 564 20 4 4 CLCC1 1 108943980 Missense_Mutation SNP C C3L-00144_T 8211469 108943980 140012442 72 4143 CELSR2 0 . GRCh38 1 109264617 109264617 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5453G>T p.Ser1818Ile p.S1818I ENST00000271332 11/34 122 100 22 126 126 0 strelka-varscan-mutect CELSR2,missense_variant,p.Ser1818Ile,ENST00000271332,NM_001408.2;CELSR2,upstream_gene_variant,,ENST00000459940,; T ENST00000271332 Transcript missense_variant 5514/10534 5453/8772 1818/2923 S/I aGc/aTc 1 1 CELSR2 HGNC HGNC:3231 protein_coding YES CCDS796.1 ENSP00000271332 Q9HCU4 UPI00000015B6 NM_001408.2 tolerated(0.4) 11/34 PROSITE_profiles:PS50026,hmmpanther:PTHR24026:SF32,hmmpanther:PTHR24026,PROSITE_patterns:PS01186,PROSITE_patterns:PS00010,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 109264617 109264617 G T 1 0 0 0 0 1 0 0 0 2929 971 34 2 2 CELSR2 1 109264617 Missense_Mutation SNP G C3L-00144_T 320637 109264617 139691805 73 4144 MYBPHL 0 . GRCh38 1 109296898 109296898 + Silent SNP G G T rs771724099 C3L-00144_T C3L-00144_N G G c.615C>A p.= p.I205I ENST00000357155 5/9 261 207 54 220 220 0 strelka-varscan-mutect MYBPHL,synonymous_variant,p.=,ENST00000357155,NM_001010985.2,NM_001265613.1;MYBPHL,intron_variant,,ENST00000477962,;MYBPHL,upstream_gene_variant,,ENST00000489706,; T ENST00000357155 Transcript synonymous_variant 665/1372 615/1065 205/354 I atC/atA rs771724099,COSM2117664 1 -1 MYBPHL HGNC HGNC:30434 protein_coding YES CCDS30793.1 ENSP00000349678 A2RUH7 UPI000022B031 NM_001010985.2,NM_001265613.1 5/9 Gene3D:2.60.40.10,Pfam_domain:PF00041,Prints_domain:PR00014,PROSITE_profiles:PS50853,hmmpanther:PTHR13817,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 LOW 1 SNV 1 0,1 1 PASS rs771724099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 109296898 109296898 G T 1 0 0 0 0 0 0 0 1 10015 1048 37 1 1 MYBPHL 1 109296898 Silent SNP G C3L-00144_T 32281 109296898 139659524 74 4145 KCNC4 0 . GRCh38 1 110223348 110223348 + Silent SNP C C T rs745804664 C3L-00144_T C3L-00144_N C C c.1063C>T p.= p.L355L ENST00000369787 2/4 138 108 30 119 119 0 strelka-varscan-mutect KCNC4,synonymous_variant,p.=,ENST00000369787,NM_004978.4;KCNC4,synonymous_variant,p.=,ENST00000413138,;KCNC4,synonymous_variant,p.=,ENST00000438661,NM_001039574.2;KCNC4,upstream_gene_variant,,ENST00000636402,;KCNC4,intron_variant,,ENST00000412512,;KCNC4,synonymous_variant,p.=,ENST00000469655,;KCNC4,non_coding_transcript_exon_variant,,ENST00000459877,;KCNC4,non_coding_transcript_exon_variant,,ENST00000489935,; T ENST00000369787 Transcript synonymous_variant 1090/18750 1063/1908 355/635 L Ctg/Ttg rs745804664,COSM4827675,COSM4827676 1 1 KCNC4 HGNC HGNC:6236 protein_coding YES CCDS821.1 ENSP00000358802 Q03721 UPI000013CAC8 NM_004978.4 2/4 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF48,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs745804664 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 110223348 110223348 C T 1 0 0 0 0 0 0 0 1 7933 680 24 3 3 KCNC4 1 110223348 Silent SNP C C3L-00144_T 926450 110223348 138733074 75 4146 CHI3L2 0 . GRCh38 1 111230928 111230928 + Missense_Mutation SNP A A G C3L-00144_T C3L-00144_N A A c.257A>G p.Asn86Ser p.N86S ENST00000445067 5/13 117 108 9 140 140 0 strelka-varscan-mutect CHI3L2,missense_variant,p.Asn86Ser,ENST00000445067,;CHI3L2,missense_variant,p.Asn7Ser,ENST00000466741,NM_001025199.1;CHI3L2,missense_variant,p.Asn76Ser,ENST00000369744,NM_001025197.1;CHI3L2,missense_variant,p.Asn86Ser,ENST00000369748,NM_004000.2;CHI3L2,missense_variant,p.Asn7Ser,ENST00000524472,;CHI3L2,missense_variant,p.Asn86Ser,ENST00000528451,;CHI3L2,missense_variant,p.Asn86Ser,ENST00000486561,;CHI3L2,missense_variant,p.Asn7Ser,ENST00000477185,;CHI3L2,missense_variant,p.Asn7Ser,ENST00000467038,;CHI3L2,missense_variant,p.Asn86Ser,ENST00000474304,;CHI3L2,missense_variant,p.Asn7Ser,ENST00000497587,;CHI3L2,missense_variant,p.Asn55Ser,ENST00000533831,;CHI3L2,upstream_gene_variant,,ENST00000497220,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000526684,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000530597,; G ENST00000445067 Transcript missense_variant 1028/2169 257/1173 86/390 N/S aAc/aGc COSM4020605 1 1 CHI3L2 HGNC HGNC:1933 protein_coding YES CCDS30802.1 ENSP00000437082 Q15782 UPI0000126C1A deleterious(0.03) 5/13 hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF82,Pfam_domain:PF00704,Gene3D:3.20.20.80,SMART_domains:SM00636,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 111230928 111230928 A G 1 0 0 0 0 1 0 0 0 3100 43 2 5 5 CHI3L2 1 111230928 Missense_Mutation SNP A C3L-00144_T 1007580 111230928 137725494 76 4147 CHI3L2 0 . GRCh38 1 111230940 111230940 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.269C>T p.Thr90Ile p.T90I ENST00000445067 5/13 94 85 9 119 119 0 strelka-varscan-mutect CHI3L2,missense_variant,p.Thr90Ile,ENST00000445067,;CHI3L2,missense_variant,p.Thr11Ile,ENST00000466741,NM_001025199.1;CHI3L2,missense_variant,p.Thr80Ile,ENST00000369744,NM_001025197.1;CHI3L2,missense_variant,p.Thr90Ile,ENST00000369748,NM_004000.2;CHI3L2,missense_variant,p.Thr11Ile,ENST00000524472,;CHI3L2,missense_variant,p.Thr90Ile,ENST00000528451,;CHI3L2,missense_variant,p.Thr90Ile,ENST00000486561,;CHI3L2,missense_variant,p.Thr11Ile,ENST00000477185,;CHI3L2,missense_variant,p.Thr11Ile,ENST00000467038,;CHI3L2,missense_variant,p.Thr90Ile,ENST00000474304,;CHI3L2,missense_variant,p.Thr11Ile,ENST00000497587,;CHI3L2,missense_variant,p.Thr59Ile,ENST00000533831,;CHI3L2,upstream_gene_variant,,ENST00000497220,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000526684,;CHI3L2,non_coding_transcript_exon_variant,,ENST00000530597,; T ENST00000445067 Transcript missense_variant 1040/2169 269/1173 90/390 T/I aCc/aTc COSM5260760 1 1 CHI3L2 HGNC HGNC:1933 protein_coding YES CCDS30802.1 ENSP00000437082 Q15782 UPI0000126C1A tolerated(0.06) 5/13 hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF82,Pfam_domain:PF00704,Gene3D:3.20.20.80,SMART_domains:SM00636,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 5 1 1 PASS rs1429656804 . 0 207 3 0 0 0 0 0 -18.84278 1 1 1 1 0 T 3 4 12 111230940 111230940 C T 1 0 0 0 0 1 0 0 0 3100 521 18 3 3 CHI3L2 1 111230940 Missense_Mutation SNP C C3L-00144_T 12 111230940 137725482 77 4148 CHIA 0 . GRCh38 1 111319437 111319437 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1146C>A p.= p.T382T ENST00000369740 11/12 242 192 50 224 223 1 strelka-varscan-mutect CHIA,synonymous_variant,p.=,ENST00000369740,NM_201653.3;CHIA,synonymous_variant,p.=,ENST00000343320,;CHIA,synonymous_variant,p.=,ENST00000422815,;CHIA,synonymous_variant,p.=,ENST00000430615,NM_001258003.1,NM_021797.3,NM_001258001.1;CHIA,synonymous_variant,p.=,ENST00000451398,NM_001040623.2;CHIA,synonymous_variant,p.=,ENST00000353665,NM_001258004.1,NM_001258005.1;CHIA,synonymous_variant,p.=,ENST00000483391,NM_001258002.1;CHIA,synonymous_variant,p.=,ENST00000489524,;RP5-1125M8.2,intron_variant,,ENST00000426321,;CHIA,3_prime_UTR_variant,,ENST00000352594,;CHIA,non_coding_transcript_exon_variant,,ENST00000477918,;RP5-1125M8.3,upstream_gene_variant,,ENST00000422272,; A ENST00000369740 Transcript synonymous_variant 1249/1625 1146/1431 382/476 T acC/acA 1 1 CHIA HGNC HGNC:17432 protein_coding YES CCDS41368.1 ENSP00000358755 Q9BZP6 UPI00000727DC NM_201653.3 11/12 Gene3D:3.20.20.80,hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF188,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 111319437 111319437 C A 1 0 0 0 0 0 0 0 1 3101 610 22 2 2 CHIA 1 111319437 Silent SNP C C3L-00144_T 88497 111319437 137636985 78 4149 TSPAN2 0 . GRCh38 1 115050522 115050522 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.634T>A p.Cys212Ser p.C212S ENST00000369516 8/8 330 284 46 352 352 0 strelka-varscan-mutect TSPAN2,missense_variant,p.Cys212Ser,ENST00000369516,NM_005725.4;TSPAN2,missense_variant,p.Cys187Ser,ENST00000369515,NM_001308315.1;TSPAN2,missense_variant,p.Cys178Ser,ENST00000433172,;TSPAN2,non_coding_transcript_exon_variant,,ENST00000491992,; T ENST00000369516 Transcript missense_variant 666/3177 634/666 212/221 C/S Tgt/Agt 1 -1 TSPAN2 HGNC HGNC:20659 protein_coding YES CCDS881.1 ENSP00000358529 O60636 UPI0000137765 NM_005725.4 deleterious(0) 8/8 hmmpanther:PTHR19282:SF155,hmmpanther:PTHR19282,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Prints_domain:PR00259 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 115050522 115050522 A T 1 0 0 0 0 1 0 0 0 17149 188 7 4 4 TSPAN2 1 115050522 Missense_Mutation SNP A C3L-00144_T 3731085 115050522 133905900 79 4150 PHGDH 0 . GRCh38 1 119734682 119734682 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.559G>T p.Gly187Cys p.G187C ENST00000369409 6/12 455 395 60 394 392 2 strelka-varscan-mutect PHGDH,missense_variant,p.Gly153Cys,ENST00000369407,;PHGDH,missense_variant,p.Gly187Cys,ENST00000369409,NM_006623.3;PHGDH,non_coding_transcript_exon_variant,,ENST00000469443,;PHGDH,upstream_gene_variant,,ENST00000482968,;PHGDH,downstream_gene_variant,,ENST00000462324,;PHGDH,downstream_gene_variant,,ENST00000493622,; T ENST00000369409 Transcript missense_variant 695/1913 559/1602 187/533 G/C Ggt/Tgt 1 1 PHGDH HGNC HGNC:8923 protein_coding YES CCDS904.1 ENSP00000358417 O43175 UPI000013586A NM_006623.3 deleterious(0) 6/12 Gene3D:3.40.50.720,Pfam_domain:PF00389,Pfam_domain:PF02826,hmmpanther:PTHR10996,hmmpanther:PTHR10996:SF20,Superfamily_domains:SSF51735,TIGRFAM_domain:TIGR01327 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 119734682 119734682 G T 1 0 0 0 0 1 0 0 0 11928 1348 47 2 2 PHGDH 1 119734682 Missense_Mutation SNP G C3L-00144_T 4684160 119734682 129221740 80 4151 ANKRD34A 0 . GRCh38 1 145961494 145961494 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.266G>T p.Gly89Val p.G89V ENST00000606888 4/4 17 14 3 28 28 0 strelka-mutect ANKRD34A,missense_variant,p.Gly89Val,ENST00000606888,NM_001039888.3;ANKRD34A,missense_variant,p.Gly89Val,ENST00000619813,;ANKRD34A,missense_variant,p.Gly89Val,ENST00000619519,;CH17-270A2.2,intron_variant,,ENST00000625258,;LIX1L,upstream_gene_variant,,ENST00000604000,NM_153713.2;POLR3GL,upstream_gene_variant,,ENST00000369314,NM_032305.1;POLR3GL,upstream_gene_variant,,ENST00000369313,;CH17-270A2.1,non_coding_transcript_exon_variant,,ENST00000616257,;RP11-315I20.1,downstream_gene_variant,,ENST00000630257,;RP11-315I20.1,downstream_gene_variant,,ENST00000600340,;CH17-270A2.2,intron_variant,,ENST00000630636,;POLR3GL,upstream_gene_variant,,ENST00000622508,;POLR3GL,upstream_gene_variant,,ENST00000471706,; A ENST00000606888 Transcript missense_variant 1561/3613 266/1491 89/496 G/V gGg/gTg 1 -1 ANKRD34A HGNC HGNC:27639 protein_coding YES CCDS72874.1 ENSP00000475189 Q69YU3 UPI00001410C4 NM_001039888.3 deleterious(0.01) 4/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24156:SF4,hmmpanther:PTHR24156,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 145961494 145961494 C A 1 0 0 0 0 1 0 0 0 767 623 22 2 2 ANKRD34A 1 145961494 Missense_Mutation SNP C C3L-00144_T 26226812 145961494 102994928 81 4152 PDE4DIP 0 . GRCh38 1 148966940 148966940 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1569G>A p.= p.L523L ENST00000369356 12/44 238 210 28 176 175 1 varscan-mutect PDE4DIP,synonymous_variant,p.=,ENST00000529945,;PDE4DIP,synonymous_variant,p.=,ENST00000585156,;PDE4DIP,synonymous_variant,p.=,ENST00000369356,NM_001198834.3;PDE4DIP,synonymous_variant,p.=,ENST00000524974,;PDE4DIP,synonymous_variant,p.=,ENST00000369354,NM_014644.5;PDE4DIP,synonymous_variant,p.=,ENST00000618462,NM_001198832.2;PDE4DIP,synonymous_variant,p.=,ENST00000313431,NM_001002811.2;PDE4DIP,synonymous_variant,p.=,ENST00000369351,;PDE4DIP,synonymous_variant,p.=,ENST00000369349,NM_001002812.2;PDE4DIP,synonymous_variant,p.=,ENST00000479408,;PDE4DIP,downstream_gene_variant,,ENST00000617454,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000467859,;PDE4DIP,non_coding_transcript_exon_variant,,ENST00000496263,; A ENST00000369356 Transcript synonymous_variant 1860/8307 1569/7089 523/2362 L ctG/ctA 1 1 PDE4DIP HGNC HGNC:15580 protein_coding YES CCDS72892.1 ENSP00000358363 A0A0A0MRM1 UPI000292EFC6 NM_001198834.3 12/44 Low_complexity_(Seg):seg,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF501 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 148966940 148966940 G A 1 0 0 0 0 0 0 0 1 11731 1306 46 3 3 PDE4DIP 1 148966940 Silent SNP G C3L-00144_T 3005446 148966940 99989482 82 4153 TCHH 0 . GRCh38 1 152109107 152109107 + Missense_Mutation SNP C C A rs542702239 C3L-00144_T C3L-00144_N C C c.4110G>T p.Gln1370His p.Q1370H ENST00000614923 3/3 592 503 89 398 397 1 strelka-varscan-mutect TCHH,missense_variant,p.Gln1370His,ENST00000614923,NM_007113.3;TCHH,missense_variant,p.Gln1370His,ENST00000368804,; A ENST00000614923 Transcript missense_variant 4205/6995 4110/5832 1370/1943 Q/H caG/caT rs542702239 1 -1 TCHH HGNC HGNC:11791 protein_coding YES CCDS41396.1 ENSP00000480484 Q07283 UPI0000458A5E NM_007113.3 deleterious_low_confidence(0.01) 3/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR34855:SF1,hmmpanther:PTHR34855 MODERATE 1 SNV 5 1 PASS rs542702239 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152109107 152109107 C A 1 0 0 0 0 1 0 0 0 16107 680 24 2 2 TCHH 1 152109107 Missense_Mutation SNP C C3L-00144_T 3142167 152109107 96847315 83 4154 HRNR 0 . GRCh38 1 152219029 152219029 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2600A>G p.Tyr867Cys p.Y867C ENST00000368801 3/3 247 191 56 220 220 0 strelka-varscan-mutect HRNR,missense_variant,p.Tyr867Cys,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENST00000368801 Transcript missense_variant 2676/9623 2600/8553 867/2850 Y/C tAt/tGt 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.1) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 152219029 152219029 T C 1 0 0 0 0 1 0 0 0 7254 1406 49 5 5 HRNR 1 152219029 Missense_Mutation SNP T C3L-00144_T 109922 152219029 96737393 84 4155 HRNR 0 . GRCh38 1 152219339 152219339 + Missense_Mutation SNP C C A rs750750547 C3L-00144_T C3L-00144_N C C c.2290G>T p.Gly764Cys p.G764C ENST00000368801 3/3 345 274 71 362 360 2 strelka-varscan-mutect HRNR,missense_variant,p.Gly764Cys,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368801 Transcript missense_variant 2366/9623 2290/8553 764/2850 G/C Ggc/Tgc rs750750547,COSM3473924 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.15) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs750750547 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152219339 152219339 C A 1 0 0 0 0 1 0 0 0 7254 623 22 2 2 HRNR 1 152219339 Missense_Mutation SNP C C3L-00144_T 310 152219339 96737083 85 4156 HRNR 0 . GRCh38 1 152219657 152219657 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1972C>T p.Gln658Ter p.Q658* ENST00000368801 3/3 941 782 159 832 830 2 strelka-varscan-mutect HRNR,stop_gained,p.Gln658Ter,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368801 Transcript stop_gained 2048/9623 1972/8553 658/2850 Q/* Cag/Tag 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 152219657 152219657 G A 1 0 0 0 0 0 1 0 0 7254 1357 47 3 3 HRNR 1 152219657 Nonsense_Mutation SNP G C3L-00144_T 318 152219657 96736765 86 4157 FLG 0 . GRCh38 1 152305184 152305184 + Silent SNP A A T rs753599171 C3L-00144_T C3L-00144_N A A c.9702T>A p.= p.S3234S ENST00000368799 3/3 567 434 133 542 541 1 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript synonymous_variant 9738/12747 9702/12186 3234/4061 S tcT/tcA rs753599171 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 LOW 1 SNV 1 1 PASS rs753599171 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 152305184 152305184 A T 1 0 0 0 0 0 0 0 1 5784 175 7 4 4 FLG 1 152305184 Silent SNP A C3L-00144_T 85527 152305184 96651238 87 4158 LCE2A 0 . GRCh38 1 152699135 152699135 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.234C>A p.His78Gln p.H78Q ENST00000368779 2/2 261 207 54 255 255 0 strelka-varscan-mutect LCE2A,missense_variant,p.His78Gln,ENST00000368779,NM_178428.3; A ENST00000368779 Transcript missense_variant 285/592 234/321 78/106 H/Q caC/caA 1 1 LCE2A HGNC HGNC:29469 protein_coding YES CCDS1021.1 ENSP00000357768 Q5TA79 UPI00001927D5 NM_178428.3 tolerated_low_confidence(0.36) 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF51,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152699135 152699135 C A 1 0 0 0 0 1 0 0 0 8570 506 18 2 2 LCE2A 1 152699135 Missense_Mutation SNP C C3L-00144_T 393951 152699135 96257287 88 4159 KPRP 0 . GRCh38 1 152760486 152760486 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.898C>A p.Arg300Ser p.R300S ENST00000606109 1/1 118 100 18 107 107 0 strelka-varscan-mutect KPRP,missense_variant,p.Arg300Ser,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript missense_variant 926/2492 898/1740 300/579 R/S Cgc/Agc COSM1256056 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 deleterious(0.01) 1/1 hmmpanther:PTHR12241:SF98,hmmpanther:PTHR12241 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152760486 152760486 C A 1 0 0 0 0 1 0 0 0 8316 652 23 1 1 KPRP 1 152760486 Missense_Mutation SNP C C3L-00144_T 61351 152760486 96195936 89 4160 KPRP 0 . GRCh38 1 152760771 152760771 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1183C>T p.Pro395Ser p.P395S ENST00000606109 1/1 179 155 24 159 159 0 strelka-varscan-mutect KPRP,missense_variant,p.Pro395Ser,ENST00000606109,NM_001025231.1; T ENST00000606109 Transcript missense_variant 1211/2492 1183/1740 395/579 P/S Cca/Tca 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 tolerated(1) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 152760771 152760771 C T 1 0 0 0 0 1 0 0 0 8316 507 18 3 3 KPRP 1 152760771 Missense_Mutation SNP C C3L-00144_T 285 152760771 96195651 90 4161 LCE1C 0 . GRCh38 1 152805309 152805309 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.170G>T p.Gly57Val p.G57V ENST00000607093 1/1 542 417 125 442 441 1 strelka-varscan-mutect LCE1C,missense_variant,p.Gly57Val,ENST00000607093,NM_001276331.1,NM_178351.3;LCE1C,missense_variant,p.Gly27Val,ENST00000606576,; A ENST00000607093 Transcript missense_variant 170/644 170/357 57/118 G/V gGg/gTg 1 -1 LCE1C HGNC HGNC:29464 protein_coding YES CCDS1026.1 ENSP00000475270 Q5T751 UPI0000140B0A NM_001276331.1,NM_178351.3 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23263,Pfam_domain:PF14672 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152805309 152805309 C A 1 0 0 0 0 1 0 0 0 8566 623 22 2 2 LCE1C 1 152805309 Missense_Mutation SNP C C3L-00144_T 44538 152805309 96151113 91 4162 CHTOP 0 . GRCh38 1 153645136 153645136 + Missense_Mutation SNP C C A rs769233987 C3L-00144_T C3L-00144_N C C c.617C>A p.Ala206Asp p.A206D ENST00000368690 6/6 287 268 19 242 241 1 strelka-varscan-mutect CHTOP,missense_variant,p.Ala206Asp,ENST00000368690,NM_001206612.1;CHTOP,missense_variant,p.Ala205Asp,ENST00000368694,NM_015607.3;CHTOP,missense_variant,p.Ala159Asp,ENST00000403433,NM_001317077.1;CHTOP,missense_variant,p.Ala180Asp,ENST00000368687,;CHTOP,3_prime_UTR_variant,,ENST00000614256,NM_001244664.1;CHTOP,downstream_gene_variant,,ENST00000368686,;CHTOP,non_coding_transcript_exon_variant,,ENST00000495554,; A ENST00000368690 Transcript missense_variant 996/2165 617/750 206/249 A/D gCc/gAc rs769233987 1 1 CHTOP HGNC HGNC:24511 protein_coding YES CCDS72917.1 ENSP00000357679 Q9Y3Y2 UPI00000467E4 NM_001206612.1 tolerated(0.49) 6/6 Pfam_domain:PF13865,hmmpanther:PTHR19965,hmmpanther:PTHR19965:SF22,Low_complexity_(Seg):seg,SMART_domains:SM01218 MODERATE 1 SNV 1 1 PASS rs769233987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 153645136 153645136 C A 1 0 0 0 0 1 0 0 0 3176 739 26 2 2 CHTOP 1 153645136 Missense_Mutation SNP C C3L-00144_T 839827 153645136 95311286 92 4163 INTS3 0 . GRCh38 1 153764123 153764123 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1827C>T p.= p.D609D ENST00000318967 18/30 171 153 18 118 118 0 strelka-varscan-mutect INTS3,synonymous_variant,p.=,ENST00000318967,NM_001324475.1,NM_023015.3;INTS3,synonymous_variant,p.=,ENST00000435409,;INTS3,synonymous_variant,p.=,ENST00000512605,;INTS3,3_prime_UTR_variant,,ENST00000476843,;INTS3,3_prime_UTR_variant,,ENST00000503133,;INTS3,non_coding_transcript_exon_variant,,ENST00000481797,;INTS3,upstream_gene_variant,,ENST00000368670,;INTS3,upstream_gene_variant,,ENST00000368669,;INTS3,downstream_gene_variant,,ENST00000491790,;INTS3,downstream_gene_variant,,ENST00000480659,; T ENST00000318967 Transcript synonymous_variant 2395/5235 1827/3129 609/1042 D gaC/gaT 1 1 INTS3 HGNC HGNC:26153 protein_coding YES CCDS1052.1 ENSP00000318641 Q68E01 UPI0000231CA8 NM_001324475.1,NM_023015.3 18/30 hmmpanther:PTHR13587 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 153764123 153764123 C T 1 0 0 0 0 0 0 0 1 7681 579 20 3 3 INTS3 1 153764123 Silent SNP C C3L-00144_T 118987 153764123 95192299 93 4164 INTS3 0 . GRCh38 1 153764201 153764201 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1905G>T p.= p.L635L ENST00000318967 18/30 172 151 21 154 153 1 strelka-varscan-mutect INTS3,synonymous_variant,p.=,ENST00000318967,NM_001324475.1,NM_023015.3;INTS3,synonymous_variant,p.=,ENST00000435409,;INTS3,synonymous_variant,p.=,ENST00000512605,;INTS3,3_prime_UTR_variant,,ENST00000476843,;INTS3,3_prime_UTR_variant,,ENST00000503133,;INTS3,non_coding_transcript_exon_variant,,ENST00000481797,;INTS3,upstream_gene_variant,,ENST00000368670,;INTS3,upstream_gene_variant,,ENST00000368669,;INTS3,downstream_gene_variant,,ENST00000491790,;INTS3,downstream_gene_variant,,ENST00000480659,; T ENST00000318967 Transcript synonymous_variant 2473/5235 1905/3129 635/1042 L ctG/ctT 1 1 INTS3 HGNC HGNC:26153 protein_coding YES CCDS1052.1 ENSP00000318641 Q68E01 UPI0000231CA8 NM_001324475.1,NM_023015.3 18/30 Low_complexity_(Seg):seg,hmmpanther:PTHR13587 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 12 153764201 153764201 G T 1 0 0 0 0 0 0 0 1 7681 1306 46 2 2 INTS3 1 153764201 Silent SNP G C3L-00144_T 78 153764201 95192221 94 4165 NUP210L 0 . GRCh38 1 154089551 154089551 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2231C>A p.Pro744His p.P744H ENST00000368559 16/40 198 176 22 158 158 0 strelka-varscan-mutect NUP210L,missense_variant,p.Pro744His,ENST00000368559,NM_207308.2;NUP210L,missense_variant,p.Pro744His,ENST00000271854,NM_001159484.1; T ENST00000368559 Transcript missense_variant 2303/5889 2231/5667 744/1888 P/H cCt/cAt COSM4186461 1 -1 NUP210L HGNC HGNC:29915 protein_coding YES CCDS41399.1 ENSP00000357547 Q5VU65 UPI000023724F NM_207308.2 deleterious(0) 16/40 hmmpanther:PTHR23019,hmmpanther:PTHR23019:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 154089551 154089551 G T 1 0 0 0 0 1 0 0 0 10826 1000 35 2 2 NUP210L 1 154089551 Missense_Mutation SNP G C3L-00144_T 325350 154089551 94866871 95 4166 INSRR 0 . GRCh38 1 156841488 156841488 + Nonsense_Mutation SNP C C A rs780251872 C3L-00144_T C3L-00144_N C C c.3568G>T p.Glu1190Ter p.E1190* ENST00000368195 21/22 298 273 25 232 232 0 strelka-varscan-mutect INSRR,stop_gained,p.Glu1190Ter,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; A ENST00000368195 Transcript stop_gained 3965/5101 3568/3894 1190/1297 E/* Gaa/Taa rs780251872 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 21/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF338,PIRSF_domain:PIRSF000620,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 HIGH 1 SNV 2 1 PASS rs780251872 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 156841488 156841488 C A 1 0 0 0 0 0 1 0 0 7676 922 32 2 2 INSRR 1 156841488 Nonsense_Mutation SNP C C3L-00144_T 2751937 156841488 92114934 96 4167 ARHGEF11 0 . GRCh38 1 156948476 156948476 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1948G>T p.Gly650Cys p.G650C ENST00000368194 23/41 212 185 27 194 194 0 strelka-varscan-mutect ARHGEF11,missense_variant,p.Gly650Cys,ENST00000368194,NM_198236.2;ARHGEF11,missense_variant,p.Gly610Cys,ENST00000361409,NM_014784.3;ARHGEF11,upstream_gene_variant,,ENST00000487682,;ARHGEF11,upstream_gene_variant,,ENST00000461678,; A ENST00000368194 Transcript missense_variant 2988/6889 1948/4689 650/1562 G/C Ggc/Tgc 1 -1 ARHGEF11 HGNC HGNC:14580 protein_coding YES CCDS1163.1 ENSP00000357177 O15085 UPI00001D62A7 NM_198236.2 deleterious(0.05) 23/41 hmmpanther:PTHR12673:SF111,hmmpanther:PTHR12673 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 156948476 156948476 C A 1 0 0 0 0 1 0 0 0 1026 623 22 2 2 ARHGEF11 1 156948476 Missense_Mutation SNP C C3L-00144_T 106988 156948476 92007946 97 4168 18 2 ARHGEF11 0 . GRCh38 1 156948478 156948478 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1946T>G p.Leu649Arg p.L649R ENST00000368194 23/41 205 176 29 189 189 0 strelka-varscan-mutect ARHGEF11,missense_variant,p.Leu649Arg,ENST00000368194,NM_198236.2;ARHGEF11,missense_variant,p.Leu609Arg,ENST00000361409,NM_014784.3;ARHGEF11,upstream_gene_variant,,ENST00000487682,;ARHGEF11,upstream_gene_variant,,ENST00000461678,; C ENST00000368194 Transcript missense_variant 2986/6889 1946/4689 649/1562 L/R cTg/cGg 1 -1 ARHGEF11 HGNC HGNC:14580 protein_coding YES CCDS1163.1 ENSP00000357177 O15085 UPI00001D62A7 NM_198236.2 deleterious(0) 23/41 Low_complexity_(Seg):seg,hmmpanther:PTHR12673:SF111,hmmpanther:PTHR12673 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 12 156948478 156948478 A C 1 0 0 0 0 1 0 0 0 1026 188 7 5 5 ARHGEF11 1 156948478 Missense_Mutation SNP A C3L-00144_T 2 156948478 92007944 98 4169 18 2 CD1C 0 . GRCh38 1 158291338 158291338 + Missense_Mutation SNP G G T rs375747674 C3L-00144_T C3L-00144_N G G c.266G>T p.Arg89Leu p.R89L ENST00000368170 2/6 330 288 42 262 259 3 strelka-varscan-mutect CD1C,missense_variant,p.Arg89Leu,ENST00000368170,NM_001765.2;CD1C,missense_variant,p.Arg24Leu,ENST00000443761,; T ENST00000368170 Transcript missense_variant 545/1435 266/1002 89/333 R/L cGt/cTt rs375747674 1 1 CD1C HGNC HGNC:1636 protein_coding YES CCDS1175.1 ENSP00000357152 P29017 UPI000013DF78 NM_001765.2 tolerated(0.05) 2/6 hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Pfam_domain:PF16497,Gene3D:3.30.500.10,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS rs375747674 . 0 207 0 0 0 0 0 2 -5.522737 0 0 1 0 0 T 3 4 12 158291338 158291338 G T 1 0 0 0 0 1 0 0 0 2679 1145 40 1 1 CD1C 1 158291338 Missense_Mutation SNP G C3L-00144_T 1342860 158291338 90665084 99 4170 CD1C 0 . GRCh38 1 158292763 158292763 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.780delG p.Thr261HisfsTer6 p.T261Hfs*6 ENST00000368170 4/6 397 349 48 339 339 0 sindel-varindel-pindel CD1C,frameshift_variant,p.Thr261HisfsTer6,ENST00000368170,NM_001765.2;CD1C,frameshift_variant,p.Thr196HisfsTer6,ENST00000443761,; - ENST00000368170 Transcript frameshift_variant 1057/1435 778/1002 260/333 G/X Ggg/gg 1 1 CD1C HGNC HGNC:1636 protein_coding YES CCDS1175.1 ENSP00000357152 P29017 UPI000013DF78 NM_001765.2 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 158292763 158292763 G - 1 0 1 0 1 0 0 0 0 2679 1348 47 0 0 CD1C 1 158292763 Frame_Shift_Del DEL G C3L-00144_T 1425 158292763 90663659 100 4171 OR10T2 0 . GRCh38 1 158398669 158398669 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.798T>A p.= p.S266S ENST00000334438 1/1 191 143 48 152 152 0 strelka-varscan-mutect OR10T2,synonymous_variant,p.=,ENST00000334438,NM_001004475.1; T ENST00000334438 Transcript synonymous_variant 798/945 798/945 266/314 S tcT/tcA 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1256974808 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 158398669 158398669 A T 1 0 0 0 0 0 0 0 1 10996 175 7 4 4 OR10T2 1 158398669 Silent SNP A C3L-00144_T 105906 158398669 90557753 101 4172 OR10Z1 0 . GRCh38 1 158606763 158606763 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.325T>A p.Cys109Ser p.C109S ENST00000361284 1/1 209 187 22 169 169 0 strelka-varscan-mutect OR10Z1,missense_variant,p.Cys109Ser,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000485680,; A ENST00000361284 Transcript missense_variant 325/942 325/942 109/313 C/S Tgt/Agt 1 1 OR10Z1 HGNC HGNC:14996 protein_coding YES CCDS30901.1 ENSP00000354707 Q8NGY1 A0A126GV63 UPI000004CA23 NM_001004478.1 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs1159672050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 158606763 158606763 T A 1 0 0 0 0 1 0 0 0 10999 1580 55 4 4 OR10Z1 1 158606763 Missense_Mutation SNP T C3L-00144_T 208094 158606763 90349659 102 4173 SPTA1 0 . GRCh38 1 158620413 158620413 + Nonsense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.6174G>A p.Trp2058Ter p.W2058* ENST00000368147 44/52 201 169 32 178 178 0 strelka-varscan-mutect SPTA1,stop_gained,p.Trp2058Ter,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000498708,; T ENST00000368147 Transcript stop_gained 6355/7999 6174/7260 2058/2419 W/* tgG/tgA COSM4967424 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 44/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 158620413 158620413 C T 1 0 0 0 0 0 1 0 0 15472 508 18 3 3 SPTA1 1 158620413 Nonsense_Mutation SNP C C3L-00144_T 13650 158620413 90336009 103 4174 MNDA 0 . GRCh38 1 158844008 158844008 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.456C>A p.= p.S152S ENST00000368141 4/7 208 178 30 169 168 1 strelka-varscan-mutect MNDA,synonymous_variant,p.=,ENST00000368141,NM_002432.1;MNDA,upstream_gene_variant,,ENST00000438394,;MNDA,downstream_gene_variant,,ENST00000491210,; A ENST00000368141 Transcript synonymous_variant 717/1752 456/1224 152/407 S tcC/tcA 1 1 MNDA HGNC HGNC:7183 protein_coding YES CCDS1177.1 ENSP00000357123 P41218 Q5VUU6 UPI0000001609 NM_002432.1 4/7 hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF18 LOW 1 SNV 1 1 PASS rs1430795105 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 158844008 158844008 C A 1 0 0 0 0 0 0 0 1 9640 610 22 2 2 MNDA 1 158844008 Silent SNP C C3L-00144_T 223595 158844008 90112414 104 4175 CADM3 0 . GRCh38 1 159193511 159193511 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.573C>G p.Ser191Arg p.S191R ENST00000368124 5/10 190 147 43 147 147 0 strelka-varscan-mutect CADM3,missense_variant,p.Ser157Arg,ENST00000368125,NM_001127173.1;CADM3,missense_variant,p.Ser191Arg,ENST00000368124,NM_021189.3;CADM3,missense_variant,p.Ser157Arg,ENST00000416746,;CADM3-AS1,downstream_gene_variant,,ENST00000415675,; G ENST00000368124 Transcript missense_variant 730/2546 573/1299 191/432 S/R agC/agG 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 deleterious(0.01) 5/10 Gene3D:2.60.40.10,Pfam_domain:PF08205,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 159193511 159193511 C G 1 0 0 0 0 1 0 0 0 2258 709 25 4 4 CADM3 1 159193511 Missense_Mutation SNP C C3L-00144_T 349503 159193511 89762911 105 4176 CADM3 0 . GRCh38 1 159196433 159196433 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.863G>A p.Cys288Tyr p.C288Y ENST00000368124 7/10 163 124 39 111 111 0 strelka-varscan-mutect CADM3,missense_variant,p.Cys254Tyr,ENST00000368125,NM_001127173.1;CADM3,missense_variant,p.Cys288Tyr,ENST00000368124,NM_021189.3;CADM3,missense_variant,p.Cys208Tyr,ENST00000416746,;CADM3-AS1,non_coding_transcript_exon_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; A ENST00000368124 Transcript missense_variant 1020/2546 863/1299 288/432 C/Y tGt/tAt 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 deleterious(0) 7/10 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 159196433 159196433 G A 1 0 0 0 0 1 0 0 0 2258 1377 48 3 3 CADM3 1 159196433 Missense_Mutation SNP G C3L-00144_T 2922 159196433 89759989 106 4177 ACKR1 0 . GRCh38 1 159205749 159205749 + Missense_Mutation SNP G G T rs778208530 C3L-00144_T C3L-00144_N G G c.316G>T p.Val106Leu p.V106L ENST00000368121 1/1 183 162 21 162 162 0 strelka-varscan-mutect ACKR1,missense_variant,p.Val104Leu,ENST00000537147,;ACKR1,missense_variant,p.Val104Leu,ENST00000368122,NM_002036.3;ACKR1,missense_variant,p.Val106Leu,ENST00000368121,NM_001122951.2;ACKR1,missense_variant,p.Val106Leu,ENST00000435307,;CADM3,downstream_gene_variant,,ENST00000368125,NM_001127173.1;CADM3,downstream_gene_variant,,ENST00000368124,NM_021189.3;CADM3-AS1,intron_variant,,ENST00000609696,;CADM3-AS1,upstream_gene_variant,,ENST00000415675,; T ENST00000368121 Transcript missense_variant 491/1240 316/1017 106/338 V/L Gtg/Ttg rs778208530 1 1 ACKR1 HGNC HGNC:4035 protein_coding YES CCDS44252.1 ENSP00000357103 Q16570 Q5Y7A1 UPI000013E1B0 NM_001122951.2 tolerated(0.13) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR14181,Prints_domain:PR01559 MODERATE SNV 1 PASS rs778208530 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 159205749 159205749 G T 1 0 0 0 0 1 0 0 0 181 1377 48 2 2 ACKR1 1 159205749 Missense_Mutation SNP G C3L-00144_T 9316 159205749 89750673 107 4178 FCRL6 0 . GRCh38 1 159808438 159808438 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.313G>C p.Val105Leu p.V105L ENST00000368106 3/10 196 149 47 157 157 0 strelka-varscan-mutect FCRL6,missense_variant,p.Val112Leu,ENST00000321935,NM_001284217.1;FCRL6,missense_variant,p.Val105Leu,ENST00000339348,;FCRL6,missense_variant,p.Val105Leu,ENST00000368106,NM_001004310.2;FCRL6,missense_variant,p.Val105Leu,ENST00000392235,;FCRL6,missense_variant,p.Val100Leu,ENST00000536257,;FCRL6,non_coding_transcript_exon_variant,,ENST00000540741,;FCRL6,non_coding_transcript_exon_variant,,ENST00000541729,; C ENST00000368106 Transcript missense_variant 314/1306 313/1305 105/434 V/L Gtc/Ctc 1 1 FCRL6 HGNC HGNC:31910 protein_coding YES CCDS30912.1 ENSP00000357086 Q6DN72 UPI0000D62020 NM_001004310.2 deleterious(0.04) 3/10 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF62,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 159808438 159808438 G C 1 0 0 0 0 1 0 0 0 5661 1029 36 4 4 FCRL6 1 159808438 Missense_Mutation SNP G C3L-00144_T 602689 159808438 89147984 108 4179 ATP1A2 0 . GRCh38 1 160124355 160124355 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.555G>T p.= p.V185V ENST00000361216 6/23 257 182 75 205 204 1 strelka-varscan-mutect ATP1A2,synonymous_variant,p.=,ENST00000361216,NM_000702.3;ATP1A2,synonymous_variant,p.=,ENST00000392233,;ATP1A2,upstream_gene_variant,,ENST00000447527,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000468587,;ATP1A2,downstream_gene_variant,,ENST00000478587,; T ENST00000361216 Transcript synonymous_variant 644/5421 555/3063 185/1020 V gtG/gtT 1 1 ATP1A2 HGNC HGNC:800 protein_coding YES CCDS1196.1 ENSP00000354490 P50993 A0A0S2Z3W6 UPI0000124FC1 NM_000702.3 6/23 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01106,Gene3D:2.70.150.10,Pfam_domain:PF00122,Superfamily_domains:0049471 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 160124355 160124355 G T 1 0 0 0 0 0 0 0 1 1281 1335 47 2 2 ATP1A2 1 160124355 Silent SNP G C3L-00144_T 315917 160124355 88832067 109 4180 SLAMF1 0 . GRCh38 1 160610300 160610300 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.412G>T p.Asp138Tyr p.D138Y ENST00000235739 3/3 197 141 56 113 112 1 strelka-varscan-mutect SLAMF1,missense_variant,p.Asp138Tyr,ENST00000235739,;SLAMF1,3_prime_UTR_variant,,ENST00000302035,NM_003037.3;SLAMF1,downstream_gene_variant,,ENST00000538290,; A ENST00000235739 Transcript missense_variant 762/883 412/435 138/144 D/Y Gat/Tat 1 -1 SLAMF1 HGNC HGNC:10903 protein_coding ENSP00000235739 Q96QJ2 UPI0000070799 deleterious_low_confidence(0) 3/3 MODERATE SNV 5 1 PASS rs1274380874 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 160610300 160610300 C A 1 0 0 0 0 1 0 0 0 14632 826 29 2 2 SLAMF1 1 160610300 Missense_Mutation SNP C C3L-00144_T 485945 160610300 88346122 110 4181 ITLN1 0 . GRCh38 1 160881210 160881210 + Missense_Mutation SNP G G C rs146103631 C3L-00144_T C3L-00144_N G G c.508C>G p.Arg170Gly p.R170G ENST00000326245 5/8 115 93 22 108 108 0 strelka-varscan-mutect ITLN1,missense_variant,p.Arg170Gly,ENST00000326245,NM_017625.2;ITLN1,non_coding_transcript_exon_variant,,ENST00000487531,;ITLN1,non_coding_transcript_exon_variant,,ENST00000464077,; C ENST00000326245 Transcript missense_variant 624/1183 508/942 170/313 R/G Cgc/Ggc rs146103631 1 -1 ITLN1 HGNC HGNC:18259 protein_coding YES CCDS1211.1 ENSP00000323587 Q8WWA0 UPI0000032AA3 NM_017625.2 tolerated(0.08) 5/8 hmmpanther:PTHR16146,hmmpanther:PTHR16146:SF38,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS rs146103631 . 0 202 8 0 0 0 0 0 -20 0.9999988 1 1 1 0 C 3 2 12 160881210 160881210 G C 1 0 0 0 0 1 0 0 0 7816 1116 39 4 4 ITLN1 1 160881210 Missense_Mutation SNP G C3L-00144_T 270910 160881210 88075212 111 4182 DUSP27 0 . GRCh38 1 167128306 167128306 + Missense_Mutation SNP C C A rs147410196 C3L-00144_T C3L-00144_N C C c.3175C>A p.Arg1059Ser p.R1059S ENST00000361200 6/6 290 244 46 224 224 0 strelka-varscan-mutect DUSP27,missense_variant,p.Arg1059Ser,ENST00000361200,;DUSP27,missense_variant,p.Arg1059Ser,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Arg1059Ser,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; A ENST00000361200 Transcript missense_variant 3341/4164 3175/3477 1059/1158 R/S Cgc/Agc rs147410196,COSM899054 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 tolerated(0.1) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs147410196 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 167128306 167128306 C A 1 0 0 0 0 1 0 0 0 4646 768 27 1 1 DUSP27 1 167128306 Missense_Mutation SNP C C3L-00144_T 6247096 167128306 81828116 112 4183 F5 0 . GRCh38 1 169518547 169518547 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.6210G>A p.= p.L2070L ENST00000367797 23/25 336 249 87 286 286 0 strelka-varscan-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4;F5,upstream_gene_variant,,ENST00000495481,; T ENST00000367797 Transcript synonymous_variant 6412/7024 6210/6675 2070/2224 L ctG/ctA 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 23/25 PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.120.260,PIRSF_domain:PIRSF000354,SMART_domains:SM00231,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 169518547 169518547 C T 1 0 0 0 0 0 0 0 1 5216 581 21 3 3 F5 1 169518547 Silent SNP C C3L-00144_T 2390241 169518547 79437875 113 4184 FASLG 0 . GRCh38 1 172665716 172665716 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.546G>T p.= p.V182V ENST00000367721 4/4 205 181 24 152 152 0 strelka-varscan-mutect FASLG,synonymous_variant,p.=,ENST00000367721,NM_000639.2;FASLG,3_prime_UTR_variant,,ENST00000340030,NM_001302746.1; T ENST00000367721 Transcript synonymous_variant 730/1888 546/846 182/281 V gtG/gtT 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 4/4 Gene3D:2.60.120.40,Pfam_domain:PF00229,PROSITE_patterns:PS00251,PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF33,SMART_domains:SM00207,Superfamily_domains:SSF49842 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 172665716 172665716 G T 1 0 0 0 0 0 0 0 1 5542 1277 45 2 2 FASLG 1 172665716 Silent SNP G C3L-00144_T 3147169 172665716 76290706 114 4185 CENPL 0 . GRCh38 1 173803336 173803336 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.728G>C p.Gly243Ala p.G243A ENST00000356198 6/7 221 208 13 178 178 0 strelka-varscan-mutect CENPL,missense_variant,p.Gly243Ala,ENST00000356198,NM_001127181.2;CENPL,missense_variant,p.Gly197Ala,ENST00000345664,NM_001171182.1;CENPL,missense_variant,p.Gly197Ala,ENST00000367710,NM_033319.3;CENPL,non_coding_transcript_exon_variant,,ENST00000496683,;CENPL,non_coding_transcript_exon_variant,,ENST00000484920,;CENPL,intron_variant,,ENST00000460816,;CENPL,downstream_gene_variant,,ENST00000479159,; G ENST00000356198 Transcript missense_variant 1014/2357 728/1173 243/390 G/A gGa/gCa 1 -1 CENPL HGNC HGNC:17879 protein_coding YES CCDS44277.1 ENSP00000348527 Q8N0S6 UPI000006ED4D NM_001127181.2 tolerated(0.16) 6/7 Pfam_domain:PF13092,hmmpanther:PTHR31740,hmmpanther:PTHR31740:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 173803336 173803336 C G 1 0 0 0 0 1 0 0 0 2944 855 30 4 4 CENPL 1 173803336 Missense_Mutation SNP C C3L-00144_T 1137620 173803336 75153086 115 4186 TNR 0 . GRCh38 1 175403485 175403485 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.631C>A p.= p.R211R ENST00000367674 4/23 245 184 61 214 214 0 strelka-varscan-mutect TNR,synonymous_variant,p.=,ENST00000367674,;TNR,synonymous_variant,p.=,ENST00000263525,NM_003285.2;TNR,intron_variant,,ENST00000422274,; T ENST00000367674 Transcript synonymous_variant 1340/12949 631/4077 211/1358 R Cgg/Agg 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 4/23 Gene3D:2.10.25.10,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00181 LOW 1 SNV 5 1 PASS rs1282287119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 175403485 175403485 G T 1 0 0 0 0 0 0 0 1 16811 1115 39 1 1 TNR 1 175403485 Silent SNP G C3L-00144_T 1600149 175403485 73552937 116 4187 BRINP2 0 . GRCh38 1 177281066 177281067 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.1892dupT p.Leu631PhefsTer4 p.L631Ffs*4 ENST00000361539 8/8 174 151 23 141 141 0 sindel-varindel-pindel BRINP2,frameshift_variant,p.Leu631PhefsTer4,ENST00000361539,NM_021165.3;BRINP2,non_coding_transcript_exon_variant,,ENST00000478325,; T ENST00000361539 Transcript frameshift_variant 2202-2203/3558 1890-1891/2352 630-631/783 -/X -/T 1 1 BRINP2 HGNC HGNC:13746 protein_coding YES CCDS1320.1 ENSP00000354481 Q9C0B6 UPI000006DF55 NM_021165.3 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF8 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 12 177281066 177281066 - T 1 0 1 1 0 0 0 0 0 1686 668 24 0 0 BRINP2 1 177281066 Frame_Shift_Ins INS - C3L-00144_T 1877581 177281066 71675356 117 4188 ABL2 0 . GRCh38 1 179108581 179108581 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2686G>T p.Gly896Trp p.G896W ENST00000502732 12/12 173 148 25 165 165 0 strelka-varscan-mutect ABL2,missense_variant,p.Gly896Trp,ENST00000502732,NM_007314.3;ABL2,missense_variant,p.Gly778Trp,ENST00000344730,NM_001136000.2;ABL2,missense_variant,p.Gly881Trp,ENST00000512653,NM_005158.4;ABL2,missense_variant,p.Gly875Trp,ENST00000367623,NM_001168236.1;ABL2,missense_variant,p.Gly793Trp,ENST00000511413,NM_001168237.1;ABL2,missense_variant,p.Gly772Trp,ENST00000507173,NM_001168238.1;ABL2,missense_variant,p.Gly757Trp,ENST00000504405,NM_001168239.1;ABL2,downstream_gene_variant,,ENST00000392043,NM_001136001.1; A ENST00000502732 Transcript missense_variant 2890/12144 2686/3549 896/1182 G/W Ggg/Tgg 1 -1 ABL2 HGNC HGNC:77 protein_coding YES CCDS30947.1 ENSP00000427562 P42684 UPI0000125140 NM_007314.3 deleterious_low_confidence(0) 12/12 MODERATE 1 SNV 1 1 PASS rs1341414182 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 179108581 179108581 C A 1 0 0 0 0 1 0 0 0 103 594 21 2 2 ABL2 1 179108581 Missense_Mutation SNP C C3L-00144_T 1827515 179108581 69847841 118 4189 CACNA1E 0 . GRCh38 1 181739212 181739212 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3678C>A p.Asp1226Glu p.D1226E ENST00000367573 25/48 301 222 79 217 215 2 strelka-varscan-mutect CACNA1E,missense_variant,p.Asp1207Glu,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Asp1226Glu,ENST00000621551,;CACNA1E,missense_variant,p.Asp1226Glu,ENST00000367567,;CACNA1E,missense_variant,p.Asp1207Glu,ENST00000358338,;CACNA1E,missense_variant,p.Asp1226Glu,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Asp1226Glu,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Asp1225Glu,ENST00000357570,;CACNA1E,missense_variant,p.Asp1207Glu,ENST00000360108,; A ENST00000367573 Transcript missense_variant 3678/7067 3678/6942 1226/2313 D/E gaC/gaA 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0) 25/48 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 181739212 181739212 C A 1 0 0 0 0 1 0 0 0 2230 564 20 2 2 CACNA1E 1 181739212 Missense_Mutation SNP C C3L-00144_T 2630631 181739212 67217210 119 4190 PRG4 0 . GRCh38 1 186308130 186308130 + Missense_Mutation SNP C C G rs748737775 C3L-00144_T C3L-00144_N C C c.2411C>G p.Pro804Arg p.P804R ENST00000445192 7/13 460 386 74 469 469 0 strelka-varscan-mutect PRG4,missense_variant,p.Pro804Arg,ENST00000445192,NM_005807.4;PRG4,missense_variant,p.Pro763Arg,ENST00000367483,NM_001127708.2;PRG4,missense_variant,p.Pro761Arg,ENST00000635041,NM_001303232.1;PRG4,missense_variant,p.Pro711Arg,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,missense_variant,p.Pro670Arg,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; G ENST00000445192 Transcript missense_variant 2456/5044 2411/4215 804/1404 P/R cCc/cGc rs748737775 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 deleterious(0) 7/13 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS rs748737775 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 186308130 186308130 C G 1 0 0 0 0 1 0 0 0 12615 623 22 4 4 PRG4 1 186308130 Missense_Mutation SNP C C3L-00144_T 4568918 186308130 62648292 120 4191 BRINP3 0 . GRCh38 1 190098410 190098410 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1909G>T p.Gly637Cys p.G637C ENST00000367462 8/8 333 294 39 240 240 0 strelka-varscan-mutect BRINP3,missense_variant,p.Gly637Cys,ENST00000367462,NM_199051.1; A ENST00000367462 Transcript missense_variant 2394/3142 1909/2301 637/766 G/C Ggt/Tgt COSM3976736,COSM5323867 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 deleterious(0.02) 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 190098410 190098410 C A 1 0 0 0 0 1 0 0 0 1687 594 21 2 2 BRINP3 1 190098410 Missense_Mutation SNP C C3L-00144_T 3790280 190098410 58858012 121 4192 UCHL5 0 . GRCh38 1 193051754 193051754 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.140A>T p.Lys47Met p.K47M ENST00000367455 2/11 128 109 19 113 113 0 strelka-varscan-mutect UCHL5,missense_variant,p.Lys47Met,ENST00000367455,NM_015984.3;UCHL5,missense_variant,p.Lys47Met,ENST00000367454,NM_001199261.1;UCHL5,missense_variant,p.Lys47Met,ENST00000367448,NM_001199262.1;UCHL5,missense_variant,p.Lys47Met,ENST00000367449,NM_001199263.1;UCHL5,missense_variant,p.Lys59Met,ENST00000367450,;UCHL5,missense_variant,p.Lys47Met,ENST00000367451,;UCHL5,missense_variant,p.Lys38Met,ENST00000421683,;UCHL5,downstream_gene_variant,,ENST00000417752,;UCHL5,splice_region_variant,,ENST00000483156,; A ENST00000367455 Transcript missense_variant,splice_region_variant 376/5327 140/990 47/329 K/M aAg/aTg 1 -1 UCHL5 HGNC HGNC:19678 protein_coding YES CCDS1378.1 ENSP00000356425 Q9Y5K5 UPI000013CF2A NM_015984.3 deleterious(0.04) 2/11 Gene3D:3.40.532.10,Pfam_domain:PF01088,PIRSF_domain:PIRSF038120,Prints_domain:PR00707,hmmpanther:PTHR10589,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 193051754 193051754 T A 1 0 0 0 0 1 0 0 0 17446 1623 56 4 4 UCHL5 1 193051754 Missense_Mutation SNP T C3L-00144_T 2953344 193051754 55904668 122 4193 KCNT2 0 . GRCh38 1 196340374 196340374 + Nonsense_Mutation SNP T T A rs187537778 C3L-00144_T C3L-00144_N T T c.1750A>T p.Arg584Ter p.R584* ENST00000294725 16/28 199 137 62 205 205 0 strelka-varscan-mutect KCNT2,stop_gained,p.Arg584Ter,ENST00000367433,NM_001287819.1;KCNT2,stop_gained,p.Arg584Ter,ENST00000294725,NM_198503.3;KCNT2,stop_gained,p.Arg534Ter,ENST00000609185,NM_001287820.1;KCNT2,stop_gained,p.Arg195Ter,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,;KCNT2,downstream_gene_variant,,ENST00000466914,; A ENST00000294725 Transcript stop_gained 2666/4409 1750/3408 584/1135 R/* Aga/Tga rs187537778 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 16/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 HIGH 1 SNV 1 1 PASS rs187537778 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 196340374 196340374 T A 1 0 0 0 0 0 1 0 0 8008 1588 55 4 4 KCNT2 1 196340374 Nonsense_Mutation SNP T C3L-00144_T 3288620 196340374 52616048 123 4194 CFHR1 0 . GRCh38 1 196826987 196826987 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.412C>G p.Pro138Ala p.P138A ENST00000320493 3/6 246 189 57 228 228 0 strelka-varscan-mutect CFHR1,missense_variant,p.Pro138Ala,ENST00000320493,NM_002113.2;CFHR1,missense_variant,p.Pro138Ala,ENST00000367424,;RP4-608O15.3,intron_variant,,ENST00000367421,;CFHR1,non_coding_transcript_exon_variant,,ENST00000480960,;CFHR1,downstream_gene_variant,,ENST00000468079,; G ENST00000320493 Transcript missense_variant 500/1271 412/993 138/330 P/A Ccc/Gcc 1 1 CFHR1 HGNC HGNC:4888 protein_coding YES CCDS1386.1 ENSP00000314299 Q03591 UPI000013CCFE NM_002113.2 deleterious(0.02) 3/6 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF381,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 196826987 196826987 C G 1 0 0 0 0 1 0 0 0 3042 855 30 4 4 CFHR1 1 196826987 Missense_Mutation SNP C C3L-00144_T 486613 196826987 52129435 124 4195 CFHR2 0 . GRCh38 1 196949487 196949487 + Nonsense_Mutation SNP G G T rs775004070 C3L-00144_T C3L-00144_N G G c.91G>T p.Gly31Ter p.G31* ENST00000367415 2/5 199 176 23 146 146 0 strelka-varscan-mutect CFHR2,stop_gained,p.Gly31Ter,ENST00000367415,NM_005666.2;RP4-608O15.3,stop_gained,p.Gly31Ter,ENST00000367421,;CFHR2,stop_gained,p.Gly31Ter,ENST00000476712,;CFHR2,non_coding_transcript_exon_variant,,ENST00000489703,;CFHR2,intron_variant,,ENST00000496448,;CFHR2,intron_variant,,ENST00000473386,;CFHR2,intron_variant,,ENST00000485647,; T ENST00000367415 Transcript stop_gained 191/1059 91/813 31/270 G/* Gga/Tga rs775004070,COSM3480908 1 1 CFHR2 HGNC HGNC:4890 protein_coding YES CCDS30959.1 ENSP00000356385 P36980 UPI000012A73B NM_005666.2 2/5 Gene3D:2.10.70.10,Pfam_domain:PF00084,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF381,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1 HIGH 1 SNV 1 0,1 1 PASS rs775004070 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 196949487 196949487 G T 1 0 0 0 0 0 1 0 0 3043 1349 47 2 2 CFHR2 1 196949487 Nonsense_Mutation SNP G C3L-00144_T 122500 196949487 52006935 125 4196 ASPM 0 . GRCh38 1 197125167 197125167 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2961G>C p.Gln987His p.Q987H ENST00000367409 11/28 522 393 129 450 450 0 strelka-varscan-mutect ASPM,missense_variant,p.Gln987His,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Gln987His,ENST00000294732,NM_001206846.1;ASPM,missense_variant,p.Gln237His,ENST00000367408,;ASPM,intron_variant,,ENST00000612785,; G ENST00000367409 Transcript missense_variant 3218/10887 2961/10434 987/3477 Q/H caG/caC 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.1) 11/28 Gene3D:1.10.418.10,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF303,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 197125167 197125167 C G 1 0 0 0 0 1 0 0 0 1203 912 32 4 4 ASPM 1 197125167 Missense_Mutation SNP C C3L-00144_T 175680 197125167 51831255 126 4197 CRB1 0 . GRCh38 1 197434803 197434803 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2940C>G p.Phe980Leu p.F980L ENST00000367400 9/12 244 184 60 241 241 0 strelka-varscan-mutect CRB1,missense_variant,p.Phe361Leu,ENST00000367397,;CRB1,missense_variant,p.Phe956Leu,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Phe980Leu,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Phe868Leu,ENST00000367399,NM_001193640.1;CRB1,intron_variant,,ENST00000538660,NM_001257966.1;RP11-75C23.1,downstream_gene_variant,,ENST00000422250,;CRB1,missense_variant,p.Phe980Leu,ENST00000484075,; G ENST00000367400 Transcript missense_variant 3075/4932 2940/4221 980/1406 F/L ttC/ttG 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 tolerated(0.31) 9/12 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24049,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1290879180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 197434803 197434803 C G 1 0 0 0 0 1 0 0 0 3648 825 29 4 4 CRB1 1 197434803 Missense_Mutation SNP C C3L-00144_T 309636 197434803 51521619 127 4198 PTPRC 0 . GRCh38 1 198750552 198750552 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3133G>T p.Asp1045Tyr p.D1045Y ENST00000442510 29/33 532 462 70 388 388 0 strelka-varscan-mutect PTPRC,missense_variant,p.Asp1045Tyr,ENST00000442510,NM_002838.4;PTPRC,missense_variant,p.Asp884Tyr,ENST00000348564,NM_080921.3; T ENST00000442510 Transcript missense_variant 3274/5164 3133/3921 1045/1306 D/Y Gac/Tac 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 deleterious(0) 29/33 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF002004,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 198750552 198750552 G T 1 0 0 0 0 1 0 0 0 12951 1290 45 2 2 PTPRC 1 198750552 Missense_Mutation SNP G C3L-00144_T 1315749 198750552 50205870 128 4199 PTPRC 0 . GRCh38 1 198752659 198752659 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.3396A>G p.= p.A1132A ENST00000442510 31/33 281 196 85 213 213 0 strelka-varscan-mutect PTPRC,synonymous_variant,p.=,ENST00000442510,NM_002838.4;PTPRC,synonymous_variant,p.=,ENST00000348564,NM_080921.3; G ENST00000442510 Transcript synonymous_variant 3537/5164 3396/3921 1132/1306 A gcA/gcG 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 31/33 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF002004,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF284,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 198752659 198752659 A G 1 0 0 0 0 0 0 0 1 12951 175 7 5 5 PTPRC 1 198752659 Silent SNP A C3L-00144_T 2107 198752659 50203763 129 4200 NR5A2 0 . GRCh38 1 200048271 200048271 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.563C>A p.Ala188Asp p.A188D ENST00000367362 5/8 252 181 71 201 201 0 strelka-varscan-mutect NR5A2,missense_variant,p.Ala188Asp,ENST00000367362,NM_205860.2;NR5A2,missense_variant,p.Ala116Asp,ENST00000544748,NM_001276464.1;NR5A2,missense_variant,p.Ala142Asp,ENST00000236914,NM_003822.4;NR5A2,missense_variant,p.Ala109Asp,ENST00000367357,;NR5A2,downstream_gene_variant,,ENST00000474307,; A ENST00000367362 Transcript missense_variant 809/5086 563/1626 188/541 A/D gCc/gAc 1 1 NR5A2 HGNC HGNC:7984 protein_coding YES CCDS1401.1 ENSP00000356331 O00482 UPI0000130482 NM_205860.2 tolerated(0.06) 5/8 hmmpanther:PTHR24086,hmmpanther:PTHR24086:SF18,PIRSF_domain:PIRSF002530 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 200048271 200048271 C A 1 0 0 0 0 1 0 0 0 10692 739 26 2 2 NR5A2 1 200048271 Missense_Mutation SNP C C3L-00144_T 1295612 200048271 48908151 130 4201 ZNF281 0 . GRCh38 1 200408572 200408572 + Silent SNP T T A rs140869522 C3L-00144_T C3L-00144_N T T c.1134A>T p.= p.A378A ENST00000294740 2/2 261 220 41 187 187 0 strelka-varscan-mutect ZNF281,synonymous_variant,p.=,ENST00000294740,NM_012482.4,NM_001281293.1;ZNF281,synonymous_variant,p.=,ENST00000367353,;ZNF281,synonymous_variant,p.=,ENST00000367352,NM_001281294.1;RP11-469A15.2,intron_variant,,ENST00000637430,;RP11-469A15.2,upstream_gene_variant,,ENST00000634596,;RP11-469A15.2,upstream_gene_variant,,ENST00000635220,; A ENST00000294740 Transcript synonymous_variant 1259/4891 1134/2688 378/895 A gcA/gcT rs140869522 1 -1 ZNF281 HGNC HGNC:13075 protein_coding YES CCDS1402.1 ENSP00000294740 Q9Y2X9 UPI000013C345 NM_012482.4,NM_001281293.1 2/2 hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF65 LOW 1 SNV 1 1 PASS rs140869522 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 200408572 200408572 T A 1 0 0 0 0 0 0 0 1 18394 1567 55 4 4 ZNF281 1 200408572 Silent SNP T C3L-00144_T 360301 200408572 48547850 131 4202 CACNA1S 0 . GRCh38 1 201041542 201041542 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.5096C>T p.Thr1699Ile p.T1699I ENST00000362061 41/44 660 474 186 478 478 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Thr1699Ile,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Thr1680Ile,ENST00000367338,;RP11-168O16.2,intron_variant,,ENST00000415359,;RP11-168O16.2,downstream_gene_variant,,ENST00000610411,; A ENST00000362061 Transcript missense_variant 5323/6166 5096/5622 1699/1873 T/I aCc/aTc 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 tolerated_low_confidence(0.4) 41/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 201041542 201041542 G A 1 0 0 0 0 1 0 0 0 2235 1261 44 3 3 CACNA1S 1 201041542 Missense_Mutation SNP G C3L-00144_T 632970 201041542 47914880 132 4203 ADIPOR1 0 . GRCh38 1 202941587 202941587 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1114G>C p.Asp372His p.D372H ENST00000340990 8/8 122 101 21 87 87 0 strelka-varscan-mutect ADIPOR1,missense_variant,p.Asp372His,ENST00000340990,NM_015999.5,NM_001290553.1,NM_001290557.1,NM_001290629.1;ADIPOR1,3_prime_UTR_variant,,ENST00000367254,;ADIPOR1,downstream_gene_variant,,ENST00000417068,;ADIPOR1,downstream_gene_variant,,ENST00000426229,;ADIPOR1,non_coding_transcript_exon_variant,,ENST00000495562,; G ENST00000340990 Transcript missense_variant 1413/2177 1114/1128 372/375 D/H Gac/Cac 1 -1 ADIPOR1 HGNC HGNC:24040 protein_coding YES CCDS1430.1 ENSP00000341785 Q96A54 UPI000003779A NM_015999.5,NM_001290553.1,NM_001290557.1,NM_001290629.1 deleterious(0) 8/8 hmmpanther:PTHR20855,hmmpanther:PTHR20855:SF40 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 202941587 202941587 C G 1 0 0 0 0 1 0 0 0 391 826 29 4 4 ADIPOR1 1 202941587 Missense_Mutation SNP C C3L-00144_T 1900045 202941587 46014835 133 4204 PPFIA4 0 . GRCh38 1 203048623 203048623 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1277G>T p.Arg426Leu p.R426L ENST00000447715 15/35 354 282 72 233 233 0 strelka-varscan-mutect PPFIA4,missense_variant,p.Arg422Leu,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,missense_variant,p.Arg426Leu,ENST00000447715,;PPFIA4,missense_variant,p.Arg168Leu,ENST00000600426,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;PPFIA4,upstream_gene_variant,,ENST00000272198,;PPFIA4,upstream_gene_variant,,ENST00000599966,;PPFIA4,downstream_gene_variant,,ENST00000601609,; T ENST00000447715 Transcript missense_variant 1718/6349 1277/3558 426/1185 R/L cGg/cTg 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 deleterious(0) 15/35 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 203048623 203048623 G T 1 0 0 0 0 1 0 0 0 12421 1116 39 1 1 PPFIA4 1 203048623 Missense_Mutation SNP G C3L-00144_T 107036 203048623 45907799 134 4205 ATP2B4 0 . GRCh38 1 203698197 203698197 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.234G>T p.Gln78His p.Q78H ENST00000357681 3/21 375 282 93 308 306 2 strelka-varscan-mutect ATP2B4,missense_variant,p.Gln78His,ENST00000357681,NM_001684.4;ATP2B4,missense_variant,p.Gln78His,ENST00000367218,NM_001001396.2;ATP2B4,missense_variant,p.Gln78His,ENST00000341360,; T ENST00000357681 Transcript missense_variant 1357/8968 234/3618 78/1205 Q/H caG/caT 1 1 ATP2B4 HGNC HGNC:817 protein_coding YES CCDS1440.1 ENSP00000350310 P23634 A0A024R968 UPI000002A464 NM_001684.4 tolerated(0.08) 3/21 hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,Pfam_domain:PF00690,SMART_domains:SM00831,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 203698197 203698197 G T 1 0 0 0 0 1 0 0 0 1295 991 35 2 2 ATP2B4 1 203698197 Missense_Mutation SNP G C3L-00144_T 649574 203698197 45258225 135 4206 ATP2B4 0 . GRCh38 1 203711075 203711075 + Silent SNP G G T rs145558731 C3L-00144_T C3L-00144_N G G c.1998G>T p.= p.A666A ENST00000357681 12/21 320 268 52 238 238 0 strelka-varscan-mutect ATP2B4,synonymous_variant,p.=,ENST00000357681,NM_001684.4;ATP2B4,synonymous_variant,p.=,ENST00000367218,NM_001001396.2;ATP2B4,synonymous_variant,p.=,ENST00000341360,; T ENST00000357681 Transcript synonymous_variant 3121/8968 1998/3618 666/1205 A gcG/gcT rs145558731 1 1 ATP2B4 HGNC HGNC:817 protein_coding YES CCDS1440.1 ENSP00000350310 P23634 A0A024R968 UPI000002A464 NM_001684.4 12/21 hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00702,Gene3D:1.20.1110.10,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660,Prints_domain:PR00119 LOW 1 SNV 1 1 PASS rs145558731 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 203711075 203711075 G T 1 0 0 0 0 0 0 0 1 1295 1103 39 1 1 ATP2B4 1 203711075 Silent SNP G C3L-00144_T 12878 203711075 45245347 136 4207 GOLT1A 0 . GRCh38 1 204201683 204201683 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.246G>T p.Trp82Cys p.W82C ENST00000308302 3/5 218 157 61 164 164 0 strelka-varscan-mutect GOLT1A,missense_variant,p.Trp82Cys,ENST00000308302,NM_198447.1;GOLT1A,non_coding_transcript_exon_variant,,ENST00000475517,; A ENST00000308302 Transcript missense_variant 432/883 246/399 82/132 W/C tgG/tgT 1 -1 GOLT1A HGNC HGNC:24766 protein_coding YES CCDS1443.1 ENSP00000308535 Q6ZVE7 UPI000005287E NM_198447.1 deleterious(0) 3/5 Pfam_domain:PF04178,hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF86,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 204201683 204201683 C A 1 0 0 0 0 1 0 0 0 6464 740 26 2 2 GOLT1A 1 204201683 Missense_Mutation SNP C C3L-00144_T 490608 204201683 44754739 137 4208 LRRN2 0 . GRCh38 1 204618005 204618005 + Missense_Mutation SNP C C T rs778385692 C3L-00144_T C3L-00144_N C C c.1988G>A p.Arg663Gln p.R663Q ENST00000367175 1/1 108 94 14 90 90 0 strelka-varscan-mutect LRRN2,missense_variant,p.Arg663Gln,ENST00000367175,;LRRN2,missense_variant,p.Arg663Gln,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Arg663Gln,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; T ENST00000367175 Transcript missense_variant 4201/5036 1988/2142 663/713 R/Q cGg/cAg rs778385692 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC tolerated(0.58) 1/1 MODERATE SNV 1 PASS rs778385692 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 204618005 204618005 C T 1 0 0 0 0 1 0 0 0 8941 652 23 1 1 LRRN2 1 204618005 Missense_Mutation SNP C C3L-00144_T 416322 204618005 44338417 138 4209 AVPR1B 0 . GRCh38 1 206115962 206115962 + Missense_Mutation SNP G G C rs782300568 C3L-00144_T C3L-00144_N G G c.929C>G p.Ala310Gly p.A310G ENST00000367126 1/2 69 62 7 51 51 0 strelka-varscan-mutect AVPR1B,missense_variant,p.Ala310Gly,ENST00000367126,NM_000707.3;RP11-38J22.3,upstream_gene_variant,,ENST00000425896,;AVPR1B,intron_variant,,ENST00000612906,; C ENST00000367126 Transcript missense_variant 1394/2237 929/1275 310/424 A/G gCc/gGc rs782300568 1 -1 AVPR1B HGNC HGNC:896 protein_coding YES CCDS73015.1 ENSP00000356094 P47901 UPI000005043A NM_000707.3 tolerated(0.17) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00897,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF18,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs782300568 . 0 207 3 0 0 0 0 0 -15.89401 1 1 1 1 0 C 3 2 12 206115962 206115962 G C 1 0 0 0 0 1 0 0 0 1388 1203 42 4 4 AVPR1B 1 206115962 Missense_Mutation SNP G C3L-00144_T 1497957 206115962 42840460 139 4210 KCNH1 0 . GRCh38 1 210683366 210683366 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2885G>T p.Arg962Ile p.R962I ENST00000271751 11/11 348 293 55 259 258 1 strelka-varscan-mutect KCNH1,missense_variant,p.Arg962Ile,ENST00000271751,NM_172362.2;KCNH1,missense_variant,p.Arg935Ile,ENST00000367007,NM_002238.3;RP11-75I2.3,downstream_gene_variant,,ENST00000625140,; A ENST00000271751 Transcript missense_variant 2913/7964 2885/2970 962/989 R/I aGa/aTa 1 -1 KCNH1 HGNC HGNC:6250 protein_coding YES CCDS1496.1 ENSP00000271751 O95259 UPI000003230D NM_172362.2 deleterious_low_confidence(0.01) 11/11 hmmpanther:PTHR10217:SF533,hmmpanther:PTHR10217 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 210683366 210683366 C A 1 0 0 0 0 1 0 0 0 7947 913 32 2 2 KCNH1 1 210683366 Missense_Mutation SNP C C3L-00144_T 4567404 210683366 38273056 140 4211 FLVCR1 0 . GRCh38 1 212887989 212887989 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1295G>T p.Gly432Val p.G432V ENST00000366971 6/10 283 207 76 203 202 1 strelka-varscan-mutect FLVCR1,missense_variant,p.Gly432Val,ENST00000366971,NM_014053.3;FLVCR1,missense_variant,p.Gly231Val,ENST00000419102,;FLVCR1,intron_variant,,ENST00000483790,;FLVCR1,downstream_gene_variant,,ENST00000474693,; T ENST00000366971 Transcript missense_variant 1493/5939 1295/1668 432/555 G/V gGa/gTa 1 1 FLVCR1 HGNC HGNC:24682 protein_coding YES CCDS1510.1 ENSP00000355938 Q9Y5Y0 UPI000006D3BB NM_014053.3 deleterious(0.02) 6/10 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR10924,hmmpanther:PTHR10924:SF2,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 212887989 212887989 G T 1 0 0 0 0 1 0 0 0 5801 1174 41 2 2 FLVCR1 1 212887989 Missense_Mutation SNP G C3L-00144_T 2204623 212887989 36068433 141 4212 KCTD3 0 . GRCh38 1 215608059 215608059 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.1352G>T p.Arg451Leu p.R451L ENST00000259154 14/18 281 201 80 156 155 1 strelka-varscan-mutect KCTD3,missense_variant,p.Arg451Leu,ENST00000259154,NM_001319294.1,NM_016121.3;KCTD3,missense_variant,p.Arg83Leu,ENST00000452413,; T ENST00000259154 Transcript missense_variant 1646/3931 1352/2448 451/815 R/L cGa/cTa COSM5623753 1 1 KCTD3 HGNC HGNC:21305 protein_coding YES CCDS1515.1 ENSP00000259154 Q9Y597 UPI0000071A2E NM_001319294.1,NM_016121.3 deleterious(0) 14/18 hmmpanther:PTHR15859 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 215608059 215608059 G T 1 0 0 0 0 1 0 0 0 8027 1058 37 1 1 KCTD3 1 215608059 Missense_Mutation SNP G C3L-00144_T 2720070 215608059 33348363 142 4213 USH2A 0 . GRCh38 1 215799064 215799064 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.9801C>A p.Cys3267Ter p.C3267* ENST00000307340 50/72 435 329 106 334 333 1 strelka-varscan-mutect USH2A,stop_gained,p.Cys3267Ter,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript stop_gained 10188/18883 9801/15609 3267/5202 C/* tgC/tgA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 50/72 SMART_domains:SM00060 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 215799064 215799064 G T 1 0 0 0 0 0 1 0 0 17570 963 34 2 2 USH2A 1 215799064 Nonsense_Mutation SNP G C3L-00144_T 191005 215799064 33157358 143 4214 USH2A 0 . GRCh38 1 215846022 215846022 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.8857C>T p.= p.L2953L ENST00000307340 45/72 379 324 55 287 287 0 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript synonymous_variant 9244/18883 8857/15609 2953/5202 L Cta/Tta 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 45/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 215846022 215846022 G A 1 0 0 0 0 0 0 0 1 17570 991 35 3 3 USH2A 1 215846022 Silent SNP G C3L-00144_T 46958 215846022 33110400 144 4215 USH2A 0 . GRCh38 1 215888544 215888544 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.8105T>C p.Met2702Thr p.M2702T ENST00000307340 41/72 343 305 38 301 301 0 strelka-varscan-mutect USH2A,missense_variant,p.Met2702Thr,ENST00000307340,NM_206933.2;RP5-1111A8.3,intron_variant,,ENST00000414995,; G ENST00000307340 Transcript missense_variant 8492/18883 8105/15609 2702/5202 M/T aTg/aCg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.04) 41/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1475041474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 215888544 215888544 A G 1 0 0 0 0 1 0 0 0 17570 217 8 5 5 USH2A 1 215888544 Missense_Mutation SNP A C3L-00144_T 42522 215888544 33067878 145 4216 USH2A 0 . GRCh38 1 216246786 216246786 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.2608T>G p.Cys870Gly p.C870G ENST00000307340 13/72 593 509 84 422 422 0 strelka-varscan-mutect USH2A,missense_variant,p.Cys870Gly,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Cys870Gly,ENST00000366942,NM_007123.5; C ENST00000307340 Transcript missense_variant 2995/18883 2608/15609 870/5202 C/G Tgc/Ggc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 13/72 Gene3D:2.10.25.10,Pfam_domain:PF00053,Prints_domain:PR00011,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 216246786 216246786 A C 1 0 0 0 0 1 0 0 0 17570 130 5 5 5 USH2A 1 216246786 Missense_Mutation SNP A C3L-00144_T 358242 216246786 32709636 146 4217 SPATA17 0 . GRCh38 1 217774517 217774517 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.703A>T p.Ile235Phe p.I235F ENST00000366933 7/11 274 208 66 198 198 0 strelka-varscan-mutect SPATA17,missense_variant,p.Ile235Phe,ENST00000366933,NM_138796.3;SPATA17,non_coding_transcript_exon_variant,,ENST00000492747,;SPATA17,downstream_gene_variant,,ENST00000470448,; T ENST00000366933 Transcript missense_variant 758/5818 703/1086 235/361 I/F Att/Ttt 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 deleterious(0) 7/11 hmmpanther:PTHR22706 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 217774517 217774517 A T 1 0 0 0 0 1 0 0 0 15332 449 16 4 4 SPATA17 1 217774517 Missense_Mutation SNP A C3L-00144_T 1527731 217774517 31181905 147 4218 ZC3H11B 0 . GRCh38 1 219611441 219611441 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.622G>A p.Glu208Lys p.E208K ENST00000636126 2/2 37 28 9 33 33 0 strelka-varscan-mutect ZC3H11B,missense_variant,p.Glu208Lys,ENST00000636126,;ZC3H11B,missense_variant,p.Glu208Lys,ENST00000367211,; T ENST00000636126 Transcript missense_variant 1338/4432 622/2418 208/805 E/K Gaa/Aaa 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C tolerated(0.19) 2/2 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 MODERATE 1 SNV 1 PASS rs1297854094 . 0 206 4 0 0 0 0 0 -19.99962 1 1 1 1 0 T 3 4 12 219611441 219611441 C T 1 0 0 0 0 1 0 0 0 18135 835 29 3 3 ZC3H11B 1 219611441 Missense_Mutation SNP C C3L-00144_T 1836924 219611441 29344981 148 4219 SLC30A10 0 . GRCh38 1 219918285 219918285 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.928G>A p.Val310Ile p.V310I ENST00000366926 3/4 112 74 38 76 76 0 strelka-varscan-mutect SLC30A10,missense_variant,p.Val310Ile,ENST00000366926,NM_018713.2;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484079,;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484239,;SLC30A10,3_prime_UTR_variant,,ENST00000356609,; T ENST00000366926 Transcript missense_variant 1090/1915 928/1458 310/485 V/I Gtc/Atc 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 deleterious(0.03) 3/4 hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF14,TIGRFAM_domain:TIGR01297 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 219918285 219918285 C T 1 0 0 0 0 1 0 0 0 14824 507 18 3 3 SLC30A10 1 219918285 Missense_Mutation SNP C C3L-00144_T 306844 219918285 29038137 149 4220 MIA3 0 . GRCh38 1 222628592 222628592 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1372G>T p.Val458Leu p.V458L ENST00000344922 4/28 179 139 40 154 154 0 strelka-varscan-mutect MIA3,missense_variant,p.Val458Leu,ENST00000344922,NM_001324064.1,NM_198551.3;MIA3,missense_variant,p.Val41Leu,ENST00000354906,;MIA3,missense_variant,p.Val458Leu,ENST00000344507,;MIA3,non_coding_transcript_exon_variant,,ENST00000470521,; T ENST00000344922 Transcript missense_variant 1397/8142 1372/5724 458/1907 V/L Gta/Tta 1 1 MIA3 HGNC HGNC:24008 protein_coding YES CCDS41470.1 ENSP00000340900 Q5JRA6 UPI00001D75B3 NM_001324064.1,NM_198551.3 tolerated(0.31) 4/28 hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 222628592 222628592 G T 1 0 0 0 0 1 0 0 0 9522 1029 36 2 2 MIA3 1 222628592 Missense_Mutation SNP G C3L-00144_T 2710307 222628592 26327830 150 4221 CAPN8 0 . GRCh38 1 223619353 223619353 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1075G>A p.Val359Ile p.V359I ENST00000366872 9/21 456 403 53 272 272 0 strelka-varscan-mutect CAPN8,missense_variant,p.Val359Ile,ENST00000366873,;CAPN8,missense_variant,p.Val359Ile,ENST00000366872,;CAPN8,missense_variant,p.Val359Ile,ENST00000419193,NM_001143962.1;CAPN8,downstream_gene_variant,,ENST00000465098,;CAPN8,downstream_gene_variant,,ENST00000467384,; T ENST00000366872 Transcript missense_variant 1163/2427 1075/2112 359/703 V/I Gtc/Atc 1 -1 CAPN8 HGNC HGNC:1485 protein_coding YES CCDS73038.1 ENSP00000355837 A6NHC0 UPI0000157E1A tolerated(0.12) 9/21 Gene3D:2.60.120.380,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF52,SMART_domains:SM00720,Superfamily_domains:SSF49758 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 223619353 223619353 C T 1 0 0 0 0 1 0 0 0 2326 507 18 3 3 CAPN8 1 223619353 Missense_Mutation SNP C C3L-00144_T 990761 223619353 25337069 151 4222 DNAH14 0 . GRCh38 1 225265355 225265355 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.7378C>T p.Pro2460Ser p.P2460S ENST00000430092 48/84 215 188 27 198 196 2 strelka-varscan-mutect DNAH14,missense_variant,p.Pro2460Ser,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Pro2460Ser,ENST00000439375,;DNAH14,missense_variant,p.Pro1920Ser,ENST00000445597,;DNAH14,missense_variant,p.Pro232Ser,ENST00000450490,;DNAH14,missense_variant,p.Pro227Ser,ENST00000327794,; T ENST00000430092 Transcript missense_variant 7593/13763 7378/13548 2460/4515 P/S Cca/Tca 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 deleterious(0) 48/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12775,SMART_domains:SM00382 MODERATE SNV 5 1 PASS . . 0 205 0 2 3 0 0 0 -11.79038 0.8976574 1 1 1 0 T 3 4 12 225265355 225265355 C T 1 0 0 0 0 1 0 0 0 4415 507 18 3 3 DNAH14 1 225265355 Missense_Mutation SNP C C3L-00144_T 1646002 225265355 23691067 152 4223 DNAH14 0 . GRCh38 1 225354172 225354172 + Splice_Site SNP A A G novel C3L-00144_T C3L-00144_N A A c.8846-2A>G p.X2949_splice ENST00000445597 201 148 53 134 134 0 strelka-varscan-mutect DNAH14,splice_acceptor_variant,,ENST00000445597,;DNAH14,intron_variant,,ENST00000430092,NM_001373.1;DNAH14,intron_variant,,ENST00000439375,;DNAH14,intron_variant,,ENST00000327794,; G ENST00000445597 Transcript splice_acceptor_variant -/10524 8846/10524 2949/3507 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000409472 Q0VDD8 UPI0001642868 50/60 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 12 225354172 225354172 A G 1 0 0 0 0 0 0 1 0 4415 86 3 5 5 DNAH14 1 225354172 Splice_Site SNP A C3L-00144_T 88817 225354172 23602250 153 4224 PARP1 0 . GRCh38 1 226386374 226386374 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.786G>T p.Lys262Asn p.K262N ENST00000366794 6/23 564 499 65 425 422 3 strelka-varscan-mutect PARP1,missense_variant,p.Lys262Asn,ENST00000366794,NM_001618.3;PARP1,downstream_gene_variant,,ENST00000469663,; A ENST00000366794 Transcript missense_variant 930/3958 786/3045 262/1014 K/N aaG/aaT 1 -1 PARP1 HGNC HGNC:270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 A0A024R3T8 UPI000013D92D NM_001618.3 deleterious(0.04) 6/23 hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF62,PIRSF_domain:PIRSF000489 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 226386374 226386374 C A 1 0 0 0 0 1 0 0 0 11534 680 24 2 2 PARP1 1 226386374 Missense_Mutation SNP C C3L-00144_T 1032202 226386374 22570048 154 4225 PSEN2 0 . GRCh38 1 226891838 226891838 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1066G>T p.Glu356Ter p.E356* ENST00000366783 11/13 516 451 65 414 413 1 strelka-varscan-mutect PSEN2,stop_gained,p.Glu389Ter,ENST00000366782,;PSEN2,stop_gained,p.Glu356Ter,ENST00000366783,NM_000447.2;PSEN2,stop_gained,p.Glu389Ter,ENST00000626989,;PSEN2,stop_gained,p.Glu355Ter,ENST00000422240,NM_012486.2;PSEN2,stop_gained,p.Glu212Ter,ENST00000472139,;PSEN2,downstream_gene_variant,,ENST00000460775,;PSEN2,non_coding_transcript_exon_variant,,ENST00000471728,;PSEN2,downstream_gene_variant,,ENST00000487450,; T ENST00000366783 Transcript stop_gained 1502/2306 1066/1347 356/448 E/* Gag/Tag 1 1 PSEN2 HGNC HGNC:9509 protein_coding YES CCDS1556.1 ENSP00000355747 P49810 UPI0000049EDA NM_000447.2 11/13 Low_complexity_(Seg):seg,hmmpanther:PTHR10202:SF20,hmmpanther:PTHR10202,Pfam_domain:PF01080,SMART_domains:SM00730 HIGH 1 SNV 5 1 PASS rs1304206650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 226891838 226891838 G T 1 0 0 0 0 0 1 0 0 12802 1175 41 2 2 PSEN2 1 226891838 Nonsense_Mutation SNP G C3L-00144_T 505464 226891838 22064584 155 4226 SNAP47 0 . GRCh38 1 227780609 227780609 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1331C>T p.Ala444Val p.A444V ENST00000315781 5/5 374 339 35 274 273 1 strelka-varscan-mutect SNAP47,missense_variant,p.Ala444Val,ENST00000315781,NM_053052.3;SNAP47,missense_variant,p.Ala444Val,ENST00000366759,;SNAP47,missense_variant,p.Ala399Val,ENST00000617596,;SNAP47,missense_variant,p.Ala202Val,ENST00000366760,;SNAP47,downstream_gene_variant,,ENST00000426344,;SNAP47,downstream_gene_variant,,ENST00000418653,; T ENST00000315781 Transcript missense_variant 1745/2367 1331/1395 444/464 A/V gCa/gTa 1 1 SNAP47 HGNC HGNC:30669 protein_coding YES CCDS1562.1 ENSP00000314157 Q5SQN1 UPI000036662E NM_053052.3 tolerated(0.13) 5/5 Gene3D:1.20.5.110,PROSITE_profiles:PS50192,hmmpanther:PTHR19305,hmmpanther:PTHR19305:SF1,Superfamily_domains:SSF58038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 227780609 227780609 C T 1 0 0 0 0 1 0 0 0 15153 710 25 3 3 SNAP47 1 227780609 Missense_Mutation SNP C C3L-00144_T 888771 227780609 21175813 156 4227 WNT9A 0 . GRCh38 1 227921869 227921869 + Silent SNP C C A rs187855245 C3L-00144_T C3L-00144_N C C c.747G>T p.= p.T249T ENST00000272164 4/4 310 264 46 243 243 0 strelka-varscan-mutect WNT9A,synonymous_variant,p.=,ENST00000272164,NM_003395.2; A ENST00000272164 Transcript synonymous_variant 758/3971 747/1098 249/365 T acG/acT rs187855245 1 -1 WNT9A HGNC HGNC:12778 protein_coding YES CCDS31045.1 ENSP00000272164 O14904 D9ZGG3 UPI000005104B NM_003395.2 4/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF75,SMART_domains:SM00097 LOW 1 SNV 1 1 PASS rs187855245 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 227921869 227921869 C A 1 0 0 0 0 0 0 0 1 17954 639 23 1 1 WNT9A 1 227921869 Silent SNP C C3L-00144_T 141260 227921869 21034553 157 4228 C1orf35 0 . GRCh38 1 228102096 228102096 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.517G>T p.Asp173Tyr p.D173Y ENST00000272139 6/8 51 41 10 37 37 0 strelka-varscan-mutect C1orf35,missense_variant,p.Asp173Tyr,ENST00000272139,NM_024319.2;ARF1,downstream_gene_variant,,ENST00000541182,NM_001024227.1,NM_001024228.1;ARF1,downstream_gene_variant,,ENST00000540651,NM_001024226.1;ARF1,downstream_gene_variant,,ENST00000272102,NM_001658.3;MRPL55,downstream_gene_variant,,ENST00000366731,;MRPL55,downstream_gene_variant,,ENST00000366735,;MRPL55,downstream_gene_variant,,ENST00000366734,;MRPL55,downstream_gene_variant,,ENST00000430433,NM_181462.2;MRPL55,downstream_gene_variant,,ENST00000366733,;MRPL55,downstream_gene_variant,,ENST00000336520,NM_181463.2;MRPL55,downstream_gene_variant,,ENST00000366744,;MRPL55,downstream_gene_variant,,ENST00000336300,NM_181456.2;MRPL55,downstream_gene_variant,,ENST00000366732,;MRPL55,downstream_gene_variant,,ENST00000366738,;MRPL55,downstream_gene_variant,,ENST00000459783,;MRPL55,downstream_gene_variant,,ENST00000391867,NM_181454.2,NM_181455.2;MRPL55,downstream_gene_variant,,ENST00000348259,NM_181441.2;MRPL55,downstream_gene_variant,,ENST00000366736,;MRPL55,downstream_gene_variant,,ENST00000366740,;MRPL55,downstream_gene_variant,,ENST00000366739,;MRPL55,downstream_gene_variant,,ENST00000295008,NM_181464.2;MRPL55,downstream_gene_variant,,ENST00000366742,;MRPL55,downstream_gene_variant,,ENST00000366741,;MRPL55,downstream_gene_variant,,ENST00000366747,NM_001321284.1;MRPL55,downstream_gene_variant,,ENST00000366746,NM_181465.2;ARF1,downstream_gene_variant,,ENST00000584469,;C1orf35,non_coding_transcript_exon_variant,,ENST00000472617,;C1orf35,non_coding_transcript_exon_variant,,ENST00000469781,;C1orf35,non_coding_transcript_exon_variant,,ENST00000485896,;C1orf35,non_coding_transcript_exon_variant,,ENST00000465199,;C1orf35,non_coding_transcript_exon_variant,,ENST00000492757,;ARF1,downstream_gene_variant,,ENST00000478424,;ARF1,downstream_gene_variant,,ENST00000478336,;ARF1,downstream_gene_variant,,ENST00000490705,;C1orf35,downstream_gene_variant,,ENST00000491293,;ARF1,downstream_gene_variant,,ENST00000470558,;ARF1,downstream_gene_variant,,ENST00000477451,;ARF1,downstream_gene_variant,,ENST00000470670,;ARF1,downstream_gene_variant,,ENST00000469235,;ARF1,downstream_gene_variant,,ENST00000497165,;ARF1,downstream_gene_variant,,ENST00000482962,;ARF1,downstream_gene_variant,,ENST00000473949,;ARF1,downstream_gene_variant,,ENST00000473546,;MRPL55,downstream_gene_variant,,ENST00000465268,; A ENST00000272139 Transcript missense_variant 752/1427 517/792 173/263 D/Y Gat/Tat 1 -1 C1orf35 HGNC HGNC:19032 protein_coding YES CCDS1566.1 ENSP00000272139 Q9BU76 UPI000006F89B NM_024319.2 deleterious(0) 6/8 hmmpanther:PTHR14580,hmmpanther:PTHR14580:SF0 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99995 1 1 1 1 0 A 3 1 12 228102096 228102096 C A 1 0 0 0 0 1 0 0 0 1988 855 30 2 2 C1orf35 1 228102096 Missense_Mutation SNP C C3L-00144_T 180227 228102096 20854326 158 4229 IBA57 0 . GRCh38 1 228175297 228175297 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.855G>T p.Leu285Phe p.L285F ENST00000366711 3/3 290 249 41 186 186 0 strelka-varscan-mutect IBA57,missense_variant,p.Leu285Phe,ENST00000366711,NM_001310327.1,NM_001010867.2;IBA57,non_coding_transcript_exon_variant,,ENST00000484749,;IBA57,non_coding_transcript_exon_variant,,ENST00000546123,; T ENST00000366711 Transcript missense_variant 857/7817 855/1071 285/356 L/F ttG/ttT 1 1 IBA57 HGNC HGNC:27302 protein_coding YES CCDS31046.1 ENSP00000355672 Q5T440 UPI0000160A21 NM_001310327.1,NM_001010867.2 tolerated(0.07) 3/3 hmmpanther:PTHR22602,hmmpanther:PTHR22602:SF0,Pfam_domain:PF08669 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 228175297 228175297 G T 1 0 0 0 0 1 0 0 0 7374 1339 47 2 2 IBA57 1 228175297 Missense_Mutation SNP G C3L-00144_T 73201 228175297 20781125 159 4230 OBSCN 0 . GRCh38 1 228250109 228250109 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.4454G>T p.Ser1485Ile p.S1485I ENST00000570156 15/116 541 484 57 419 419 0 strelka-varscan-mutect OBSCN,missense_variant,p.Ser1485Ile,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Ser1485Ile,ENST00000366707,;OBSCN,missense_variant,p.Ser1393Ile,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Ser1393Ile,ENST00000636875,;OBSCN,missense_variant,p.Ser1393Ile,ENST00000284548,NM_052843.3; T ENST00000570156 Transcript missense_variant 4528/26925 4454/26772 1485/8923 S/I aGc/aTc COSM1146170,COSM1146171,COSM679272,COSM679273 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 15/116 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 228250109 228250109 G T 1 0 0 0 0 1 0 0 0 10889 971 34 2 2 OBSCN 1 228250109 Missense_Mutation SNP G C3L-00144_T 74812 228250109 20706313 160 4231 OBSCN 0 . GRCh38 1 228275990 228275990 + Missense_Mutation SNP C C A rs772291809 C3L-00144_T C3L-00144_N C C c.7309C>A p.Pro2437Thr p.P2437T ENST00000570156 25/116 147 103 44 131 131 0 strelka-varscan-mutect OBSCN,missense_variant,p.Pro2437Thr,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Pro2437Thr,ENST00000366707,;OBSCN,missense_variant,p.Pro2062Thr,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Pro2062Thr,ENST00000636875,;OBSCN,missense_variant,p.Pro2062Thr,ENST00000284548,NM_052843.3;OBSCN,upstream_gene_variant,,ENST00000483539,;OBSCN,upstream_gene_variant,,ENST00000366706,;RP5-1139B12.3,non_coding_transcript_exon_variant,,ENST00000602529,;RP5-1139B12.3,non_coding_transcript_exon_variant,,ENST00000602947,;RP5-1139B12.2,upstream_gene_variant,,ENST00000602517,;OBSCN,upstream_gene_variant,,ENST00000366704,; A ENST00000570156 Transcript missense_variant 7383/26925 7309/26772 2437/8923 P/T Ccg/Acg rs772291809 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.37) 25/116 PROSITE_profiles:PS50835,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs772291809 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 228275990 228275990 C A 1 0 0 0 0 1 0 0 0 10889 739 26 2 2 OBSCN 1 228275990 Missense_Mutation SNP C C3L-00144_T 25881 228275990 20680432 161 4232 OBSCN 0 . GRCh38 1 228294180 228294180 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.12447G>T p.= p.L4149L ENST00000570156 47/116 451 387 64 329 329 0 strelka-varscan-mutect OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000284548,NM_052843.3;OBSCN,synonymous_variant,p.=,ENST00000483539,;RP5-1139B12.4,downstream_gene_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000494839,; T ENST00000570156 Transcript synonymous_variant 12521/26925 12447/26772 4149/8923 L ctG/ctT 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 47/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 228294180 228294180 G T 1 0 0 0 0 0 0 0 1 10889 1277 45 2 2 OBSCN 1 228294180 Silent SNP G C3L-00144_T 18190 228294180 20662242 162 4233 OBSCN 0 . GRCh38 1 228294922 228294922 + Silent SNP C C T rs755214451 C3L-00144_T C3L-00144_N C C c.12825C>T p.= p.Y4275Y ENST00000570156 48/116 458 335 123 395 395 0 strelka-varscan-mutect OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000284548,NM_052843.3;OBSCN,synonymous_variant,p.=,ENST00000483539,;RP5-1139B12.4,downstream_gene_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000602685,;OBSCN,non_coding_transcript_exon_variant,,ENST00000494839,; T ENST00000570156 Transcript synonymous_variant 12899/26925 12825/26772 4275/8923 Y taC/taT rs755214451,COSM1320414,COSM1320415,COSM1320416,COSM1320417 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 48/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726 0,1,1,1,1 LOW SNV 5 0,1,1,1,1 1 PASS rs755214451 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 228294922 228294922 C T 1 0 0 0 0 0 0 0 1 10889 489 17 3 3 OBSCN 1 228294922 Silent SNP C C3L-00144_T 742 228294922 20661500 163 4234 OBSCN 0 . GRCh38 1 228368833 228368833 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.22750C>A p.Pro7584Thr p.P7584T ENST00000570156 100/116 242 220 22 174 174 0 strelka-varscan-mutect OBSCN,missense_variant,p.Pro7584Thr,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Pro7584Thr,ENST00000366707,;OBSCN,missense_variant,p.Pro6627Thr,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Pro6627Thr,ENST00000636875,;OBSCN,missense_variant,p.Pro1244Thr,ENST00000636476,; A ENST00000570156 Transcript missense_variant 22824/26925 22750/26772 7584/8923 P/T Cct/Act 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 100/116 PROSITE_profiles:PS50011,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 228368833 228368833 C A 1 0 0 0 0 1 0 0 0 10889 623 22 2 2 OBSCN 1 228368833 Missense_Mutation SNP C C3L-00144_T 73911 228368833 20587589 164 4235 HIST3H2A 0 . GRCh38 1 228457637 228457637 + Missense_Mutation SNP C C A rs369889949 C3L-00144_T C3L-00144_N C C c.181G>T p.Ala61Ser p.A61S ENST00000366695 1/1 305 223 82 296 296 0 strelka-varscan-mutect HIST3H2A,missense_variant,p.Ala61Ser,ENST00000366695,NM_033445.2;HIST3H2BB,upstream_gene_variant,,ENST00000620438,NM_175055.2;MIR4666A,upstream_gene_variant,,ENST00000580160,; A ENST00000366695 Transcript missense_variant 237/895 181/393 61/130 A/S Gcc/Tcc rs369889949 1 -1 HIST3H2A HGNC HGNC:20507 protein_coding YES CCDS1573.1 ENSP00000355656 Q7L7L0 UPI0000073CEF NM_033445.2 deleterious_low_confidence(0.03) 1/1 hmmpanther:PTHR23430,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620 MODERATE 1 SNV 1 PASS rs369889949 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 228457637 228457637 C A 1 0 0 0 0 1 0 0 0 7071 710 25 2 2 HIST3H2A 1 228457637 Missense_Mutation SNP C C3L-00144_T 88804 228457637 20498785 165 4236 ABCB10 0 . GRCh38 1 229539475 229539475 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1320G>T p.Trp440Cys p.W440C ENST00000344517 6/13 424 369 55 287 284 3 strelka-varscan-mutect ABCB10,missense_variant,p.Trp440Cys,ENST00000344517,NM_012089.2;RNU4-21P,upstream_gene_variant,,ENST00000362802,; A ENST00000344517 Transcript missense_variant 1363/3857 1320/2217 440/738 W/C tgG/tgT COSM533303 1 -1 ABCB10 HGNC HGNC:41 protein_coding YES CCDS1580.1 ENSP00000355637 Q9NRK6 UPI000013CFBF NM_012089.2 deleterious(0) 6/13 Gene3D:2hydA01,PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF121,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 229539475 229539475 C A 1 0 0 0 0 1 0 0 0 45 624 22 2 2 ABCB10 1 229539475 Missense_Mutation SNP C C3L-00144_T 1081838 229539475 19416947 166 4237 SIPA1L2 0 . GRCh38 1 232479718 232479718 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1994G>T p.Gly665Val p.G665V ENST00000366630 6/22 219 168 51 158 158 0 strelka-varscan-mutect SIPA1L2,missense_variant,p.Gly665Val,ENST00000366630,;SIPA1L2,missense_variant,p.Gly665Val,ENST00000262861,NM_020808.3; A ENST00000366630 Transcript missense_variant 2353/6690 1994/5169 665/1722 G/V gGc/gTc 1 -1 SIPA1L2 HGNC HGNC:23800 protein_coding YES CCDS41474.1 ENSP00000355589 Q9P2F8 UPI00001D7D6A deleterious(0.01) 6/22 PROSITE_profiles:PS50085,hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711,Pfam_domain:PF02145,Superfamily_domains:0043732 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 232479718 232479718 C A 1 0 0 0 0 1 0 0 0 14593 739 26 2 2 SIPA1L2 1 232479718 Missense_Mutation SNP C C3L-00144_T 2940243 232479718 16476704 167 4238 PCNX2 0 . GRCh38 1 233025188 233025188 + Missense_Mutation SNP C C A rs371347464 C3L-00144_T C3L-00144_N C C c.4563G>T p.Gln1521His p.Q1521H ENST00000258229 26/34 379 327 52 292 291 1 strelka-varscan-mutect PCNX2,missense_variant,p.Gln1521His,ENST00000258229,NM_014801.3;PCNX2,missense_variant,p.Gln173His,ENST00000344698,;PCNX2,non_coding_transcript_exon_variant,,ENST00000522067,;PCNX2,intron_variant,,ENST00000462233,;PCNX2,downstream_gene_variant,,ENST00000429988,; A ENST00000258229 Transcript missense_variant 4798/7518 4563/6414 1521/2137 Q/H caG/caT rs371347464 1 -1 PCNX2 HGNC HGNC:8736 protein_coding YES CCDS44335.1 ENSP00000258229 A6NKB5 UPI0000F58F23 NM_014801.3 deleterious(0.03) 26/34 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5 MODERATE 1 SNV 5 1 PASS rs371347464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 233025188 233025188 C A 1 0 0 0 0 1 0 0 0 11680 680 24 2 2 PCNX2 1 233025188 Missense_Mutation SNP C C3L-00144_T 545470 233025188 15931234 168 4239 ACTN2 0 . GRCh38 1 236751613 236751613 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1800C>A p.Ser600Arg p.S600R ENST00000542672 15/21 505 389 116 430 430 0 strelka-varscan-mutect ACTN2,missense_variant,p.Ser392Arg,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Ser600Arg,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Ser600Arg,ENST00000366578,NM_001103.3;ACTN2,upstream_gene_variant,,ENST00000461367,;ACTN2,downstream_gene_variant,,ENST00000492101,; A ENST00000542672 Transcript missense_variant 2020/4906 1800/2685 600/894 S/R agC/agA 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0.01) 15/21 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 236751613 236751613 C A 1 0 0 0 0 1 0 0 0 249 709 25 2 2 ACTN2 1 236751613 Missense_Mutation SNP C C3L-00144_T 3726425 236751613 12204809 169 4240 RYR2 0 . GRCh38 1 237595522 237595522 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4461G>T p.Met1487Ile p.M1487I ENST00000366574 34/105 338 291 47 272 271 1 strelka-varscan-mutect RYR2,missense_variant,p.Met1487Ile,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Met1471Ile,ENST00000360064,; T ENST00000366574 Transcript missense_variant 4778/16562 4461/14904 1487/4967 M/I atG/atT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.05) 34/105 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 237595522 237595522 G T 1 0 0 0 0 1 0 0 0 14029 1348 47 2 2 RYR2 1 237595522 Missense_Mutation SNP G C3L-00144_T 843909 237595522 11360900 170 4241 RYR2 0 . GRCh38 1 237614403 237614403 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.5275C>A p.Pro1759Thr p.P1759T ENST00000366574 37/105 325 231 94 267 266 1 strelka-varscan-mutect RYR2,missense_variant,p.Pro1759Thr,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Pro1743Thr,ENST00000360064,; A ENST00000366574 Transcript missense_variant 5592/16562 5275/14904 1759/4967 P/T Cca/Aca COSM5302147,COSM533416 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 37/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 237614403 237614403 C A 1 0 0 0 0 1 0 0 0 14029 739 26 2 2 RYR2 1 237614403 Missense_Mutation SNP C C3L-00144_T 18881 237614403 11342019 171 4242 RYR2 0 . GRCh38 1 237732125 237732125 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.11015G>T p.Ser3672Ile p.S3672I ENST00000366574 78/105 147 134 13 129 129 0 strelka-varscan-mutect RYR2,missense_variant,p.Ser3672Ile,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ser3656Ile,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;RYR2,downstream_gene_variant,,ENST00000609253,; T ENST00000366574 Transcript missense_variant 11332/16562 11015/14904 3672/4967 S/I aGt/aTt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.01) 78/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 237732125 237732125 G T 1 0 0 0 0 1 0 0 0 14029 1029 36 2 2 RYR2 1 237732125 Missense_Mutation SNP G C3L-00144_T 117722 237732125 11224297 172 4243 ZP4 0 . GRCh38 1 237885843 237885843 + Missense_Mutation SNP G G T rs34811980 C3L-00144_T C3L-00144_N G G c.883C>A p.Pro295Thr p.P295T ENST00000611898 7/13 145 129 16 126 126 0 strelka-varscan-mutect ZP4,missense_variant,p.Pro295Thr,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Pro295Thr,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; T ENST00000611898 Transcript missense_variant 1170/2474 883/1623 295/540 P/T Cca/Aca rs34811980,COSM5257682 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0) 7/13 Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 0,1 MODERATE SNV 5 0,1 1 PASS rs34811980 . 0 204 0 2 0 0 0 4 -4.293953 0 0 1 0 0 T 3 4 12 237885843 237885843 G T 1 0 0 0 0 1 0 0 0 18810 1232 43 2 2 ZP4 1 237885843 Missense_Mutation SNP G C3L-00144_T 153718 237885843 11070579 173 4244 ZP4 0 . GRCh38 1 237887539 237887539 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.576G>T p.Glu192Asp p.E192D ENST00000611898 5/13 157 105 52 114 114 0 strelka-varscan-mutect ZP4,missense_variant,p.Glu192Asp,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Glu192Asp,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; A ENST00000611898 Transcript missense_variant 863/2474 576/1623 192/540 E/D gaG/gaT 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 tolerated(1) 5/13 Gene3D:4.10.110.10,Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241,Superfamily_domains:SSF57492 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 237887539 237887539 C A 1 0 0 0 0 1 0 0 0 18810 680 24 2 2 ZP4 1 237887539 Missense_Mutation SNP C C3L-00144_T 1696 237887539 11068883 174 4245 FMN2 0 . GRCh38 1 240092733 240092733 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.624G>T p.Gln208His p.Q208H ENST00000319653 1/18 176 154 22 185 185 0 strelka-varscan-mutect FMN2,missense_variant,p.Gln208His,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,intron_variant,,ENST00000447095,; T ENST00000319653 Transcript missense_variant 854/6434 624/5169 208/1722 Q/H caG/caT 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious_low_confidence(0) 1/18 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1206006138 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 12 240092733 240092733 G T 1 0 0 0 0 1 0 0 0 5806 962 34 2 2 FMN2 1 240092733 Missense_Mutation SNP G C3L-00144_T 2205194 240092733 8863689 175 4246 FMN2 0 . GRCh38 1 240207299 240207299 + Silent SNP G G C C3L-00144_T C3L-00144_N G G c.2487G>C p.= p.P829P ENST00000319653 5/18 229 164 65 213 213 0 strelka-varscan-mutect FMN2,synonymous_variant,p.=,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; C ENST00000319653 Transcript synonymous_variant 2717/6434 2487/5169 829/1722 P ccG/ccC COSM2049379 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 5/18 SMART_domains:SM00498 1 LOW 1 SNV 5 1 1 PASS rs1372491335 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 240207299 240207299 G C 1 0 0 0 0 0 0 0 1 5806 1074 38 4 4 FMN2 1 240207299 Silent SNP G C3L-00144_T 114566 240207299 8749123 176 4247 FMN2 0 . GRCh38 1 240211090 240211090 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.3921-1G>T p.X1307_splice ENST00000319653 128 114 14 110 110 0 strelka-varscan-mutect FMN2,splice_acceptor_variant,,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; T ENST00000319653 Transcript splice_acceptor_variant -/6434 3921/5169 1307/1722 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 5/17 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 240211090 240211090 G T 1 0 0 0 0 0 0 1 0 5806 956 33 2 2 FMN2 1 240211090 Splice_Site SNP G C3L-00144_T 3791 240211090 8745332 177 4248 GREM2 0 . GRCh38 1 240493398 240493398 + Silent SNP C C A C3L-00144_T C3L-00144_N C C c.78G>T p.= p.P26P ENST00000318160 2/2 134 115 19 112 111 1 strelka-varscan-mutect GREM2,synonymous_variant,p.=,ENST00000318160,NM_022469.3; A ENST00000318160 Transcript synonymous_variant 345/4170 78/507 26/168 P ccG/ccT COSM1639766 1 -1 GREM2 HGNC HGNC:17655 protein_coding YES CCDS31070.1 ENSP00000318650 Q9H772 A0A024R3Y1 UPI000006F961 NM_022469.3 2/2 hmmpanther:PTHR15283:SF2,hmmpanther:PTHR15283,PIRSF_domain:PIRSF037254 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 240493398 240493398 C A 1 0 0 0 0 0 0 0 1 6642 639 23 1 1 GREM2 1 240493398 Silent SNP C C3L-00144_T 282308 240493398 8463024 178 4249 WDR64 0 . GRCh38 1 241801171 241801171 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3202C>A p.Gln1068Lys p.Q1068K ENST00000366552 27/27 246 192 54 171 171 0 strelka-varscan-mutect WDR64,missense_variant,p.Gln1068Lys,ENST00000366552,NM_144625.4;WDR64,missense_variant,p.Gln621Lys,ENST00000437684,;WDR64,missense_variant,p.Gln672Lys,ENST00000414635,;WDR64,missense_variant,p.Gln547Lys,ENST00000425826,;WDR64,downstream_gene_variant,,ENST00000472717,; A ENST00000366552 Transcript missense_variant 3409/4371 3202/3246 1068/1081 Q/K Caa/Aaa 1 1 WDR64 HGNC HGNC:26570 protein_coding YES ENSP00000355510 B1ANS9 UPI0000519142 NM_144625.4 tolerated_low_confidence(0.06) 27/27 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 241801171 241801171 C A 1 0 0 0 0 1 0 0 0 17874 479 17 2 2 WDR64 1 241801171 Missense_Mutation SNP C C3L-00144_T 1307773 241801171 7155251 179 4250 CEP170 0 . GRCh38 1 243186030 243186030 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1315G>T p.Gly439Trp p.G439W ENST00000366542 10/20 432 325 107 313 312 1 strelka-varscan-mutect CEP170,missense_variant,p.Gly439Trp,ENST00000366542,NM_014812.2;CEP170,missense_variant,p.Gly403Trp,ENST00000336415,;CEP170,intron_variant,,ENST00000366544,NM_001042404.1;CEP170,intron_variant,,ENST00000366543,NM_001042405.1;CEP170,intron_variant,,ENST00000522895,;CEP170,missense_variant,p.Gly23Trp,ENST00000461671,;CEP170,non_coding_transcript_exon_variant,,ENST00000521911,; A ENST00000366542 Transcript missense_variant 1367/6828 1315/4755 439/1584 G/W Ggg/Tgg 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 deleterious(0) 10/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 243186030 243186030 C A 1 0 0 0 0 1 0 0 0 2964 594 21 2 2 CEP170 1 243186030 Missense_Mutation SNP C C3L-00144_T 1384859 243186030 5770392 180 4251 KIF26B 0 . GRCh38 1 245419609 245419609 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1030G>T p.Glu344Ter p.E344* ENST00000407071 4/15 117 84 33 77 77 0 strelka-varscan-mutect KIF26B,stop_gained,p.Glu344Ter,ENST00000407071,NM_018012.3; T ENST00000407071 Transcript stop_gained 1470/7287 1030/6327 344/2108 E/* Gag/Tag 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 4/15 HIGH 1 SNV 1 1 PASS rs964844060 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 245419609 245419609 G T 1 0 0 0 0 0 1 0 0 8160 1175 41 2 2 KIF26B 1 245419609 Nonsense_Mutation SNP G C3L-00144_T 2233579 245419609 3536813 181 4252 NLRP3 0 . GRCh38 1 247424124 247424124 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.681G>T p.= p.A227A ENST00000336119 3/9 318 271 47 225 225 0 strelka-varscan-mutect NLRP3,synonymous_variant,p.=,ENST00000366497,NM_001127461.2;NLRP3,synonymous_variant,p.=,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,synonymous_variant,p.=,ENST00000366496,;NLRP3,synonymous_variant,p.=,ENST00000391828,NM_001079821.2;NLRP3,synonymous_variant,p.=,ENST00000348069,NM_183395.2;NLRP3,synonymous_variant,p.=,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; T ENST00000336119 Transcript synonymous_variant 1427/4170 681/3111 227/1036 A gcG/gcT 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Pfam_domain:PF05729,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs938034710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 247424124 247424124 G T 1 0 0 0 0 0 0 0 1 10516 1103 39 1 1 NLRP3 1 247424124 Silent SNP G C3L-00144_T 2004515 247424124 1532298 182 4253 NLRP3 0 . GRCh38 1 247436055 247436055 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2584G>T p.Val862Leu p.V862L ENST00000336119 6/9 432 310 122 389 389 0 strelka-varscan-mutect NLRP3,missense_variant,p.Val862Leu,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Val862Leu,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Val805Leu,ENST00000391827,NM_001127462.2;NLRP3,intron_variant,,ENST00000366497,NM_001127461.2;NLRP3,intron_variant,,ENST00000366496,;NLRP3,intron_variant,,ENST00000348069,NM_183395.2; T ENST00000336119 Transcript missense_variant 3330/4170 2584/3111 862/1036 V/L Gtg/Ttg 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 tolerated(1) 6/9 hmmpanther:PTHR24106:SF4,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 247436055 247436055 G T 1 0 0 0 0 1 0 0 0 10516 1377 48 2 2 NLRP3 1 247436055 Missense_Mutation SNP G C3L-00144_T 11931 247436055 1520367 183 4254 OR14K1 0 . GRCh38 1 247738752 247738752 + Silent SNP C C A rs767085763 C3L-00144_T C3L-00144_N C C c.138C>A p.= p.L46L ENST00000283225 1/1 156 120 36 169 169 0 strelka-varscan-mutect OR14K1,synonymous_variant,p.=,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; A ENST00000283225 Transcript synonymous_variant 138/945 138/945 46/314 L ctC/ctA rs767085763 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW SNV 1 PASS rs1316046289 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 247738752 247738752 C A 1 0 0 0 0 0 0 0 1 11026 813 29 2 2 OR14K1 1 247738752 Silent SNP C C3L-00144_T 302697 247738752 1217670 184 4255 OR11L1 0 . GRCh38 1 247841505 247841505 + Missense_Mutation SNP C C T rs148646914 C3L-00144_T C3L-00144_N C C c.392G>A p.Arg131His p.R131H ENST00000355784 1/1 263 185 78 246 246 0 strelka-varscan-mutect OR11L1,missense_variant,p.Arg131His,ENST00000355784,NM_001001959.1; T ENST00000355784 Transcript missense_variant 392/969 392/969 131/322 R/H cGc/cAc rs148646914 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs148646914 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 247841505 247841505 C T 1 0 0 0 0 1 0 0 0 11007 768 27 1 1 OR11L1 1 247841505 Missense_Mutation SNP C C3L-00144_T 102753 247841505 1114917 185 4256 OR2W3 0 . GRCh38 1 247896156 247896156 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.570C>G p.= p.V190V ENST00000360358 1/1 116 110 6 110 110 0 strelka-varscan-mutect OR2W3,synonymous_variant,p.=,ENST00000360358,NM_001001957.2; G ENST00000360358 Transcript synonymous_variant 570/945 570/945 190/314 V gtC/gtG 1 1 OR2W3 HGNC HGNC:15021 protein_coding YES CCDS31099.1 ENSP00000353516 Q7Z3T1 UPI0000061EA8 NM_001001957.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF223,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 247896156 247896156 C G 1 0 0 0 0 0 0 0 1 11111 813 29 4 4 OR2W3 1 247896156 Silent SNP C C3L-00144_T 54651 247896156 1060266 186 4257 OR2L3 0 . GRCh38 1 248061357 248061357 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.676C>A p.His226Asn p.H226N ENST00000359959 1/1 252 194 58 238 238 0 strelka-varscan-mutect OR2L3,missense_variant,p.His226Asn,ENST00000359959,NM_001004687.1; A ENST00000359959 Transcript missense_variant 676/939 676/939 226/312 H/N Cac/Aac 1 1 OR2L3 HGNC HGNC:15009 protein_coding YES CCDS31104.1 ENSP00000353044 Q8NG85 UPI0000061EB8 NM_001004687.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF166,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1193315031 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 248061357 248061357 C A 1 0 0 0 0 1 0 0 0 11086 594 21 2 2 OR2L3 1 248061357 Missense_Mutation SNP C C3L-00144_T 165201 248061357 895065 187 4258 OR2M7 0 . GRCh38 1 248324298 248324298 + Missense_Mutation SNP A A T C3L-00144_T C3L-00144_N A A c.271T>A p.Ser91Thr p.S91T ENST00000317965 1/1 173 156 17 203 203 0 varscan-mutect OR2M7,missense_variant,p.Ser91Thr,ENST00000317965,NM_001004691.1; T ENST00000317965 Transcript missense_variant 271/939 271/939 91/312 S/T Tcc/Acc COSM4919041 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 tolerated(0.31) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 248324298 248324298 A T 1 0 0 0 0 1 0 0 0 11092 275 10 4 4 OR2M7 1 248324298 Missense_Mutation SNP A C3L-00144_T 262941 248324298 632124 188 4259 ACP1 0 . GRCh38 2 272210 272210 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.136G>T p.Ala46Ser p.A46S ENST00000272067 3/6 454 383 71 407 407 0 strelka-varscan-mutect ACP1,missense_variant,p.Ala46Ser,ENST00000272067,NM_007099.3;ACP1,missense_variant,p.Ala46Ser,ENST00000439645,;ACP1,synonymous_variant,p.=,ENST00000405233,;ACP1,synonymous_variant,p.=,ENST00000407983,NM_001040649.2;ACP1,intron_variant,,ENST00000272065,NM_004300.3;ACP1,intron_variant,,ENST00000484464,;ACP1,synonymous_variant,p.=,ENST00000453390,;ACP1,3_prime_UTR_variant,,ENST00000405364,;ACP1,intron_variant,,ENST00000480874,;ACP1,intron_variant,,ENST00000413140,;ACP1,intron_variant,,ENST00000442386,;ACP1,upstream_gene_variant,,ENST00000463831,; T ENST00000272067 Transcript missense_variant 232/1552 136/477 46/158 A/S Gct/Tct 1 1 ACP1 HGNC HGNC:122 protein_coding YES CCDS1640.1 ENSP00000272067 P24666 UPI0000000C82 NM_007099.3 deleterious(0) 3/6 Gene3D:3.40.50.270,Pfam_domain:PF01451,hmmpanther:PTHR11717,hmmpanther:PTHR11717:SF7,SMART_domains:SM00226,Superfamily_domains:SSF52788 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 272210 272210 G T 1 0 0 0 0 1 0 0 0 204 1319 46 2 2 ACP1 2 272210 Missense_Mutation SNP G C3L-00144_T 272210 241921319 189 4260 MYT1L 0 . GRCh38 2 1917256 1917256 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1567C>A p.His523Asn p.H523N ENST00000399161 11/25 226 165 61 144 144 0 strelka-varscan-mutect MYT1L,missense_variant,p.His523Asn,ENST00000399161,NM_001303052.1;MYT1L,missense_variant,p.His521Asn,ENST00000428368,NM_015025.3;MYT1L,missense_variant,p.His177Asn,ENST00000602387,; T ENST00000399161 Transcript missense_variant 2315/7063 1567/3561 523/1186 H/N Cat/Aat 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 deleterious(0) 11/25 hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF11,Pfam_domain:PF01530,Superfamily_domains:0042508 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 1917256 1917256 G T 1 0 0 0 0 1 0 0 0 10106 1377 48 2 2 MYT1L 2 1917256 Missense_Mutation SNP G C3L-00144_T 1645046 1917256 240276273 190 4261 MYT1L 0 . GRCh38 2 1922300 1922300 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.1469C>A p.Pro490Gln p.P490Q ENST00000399161 10/25 109 73 36 103 103 0 strelka-varscan-mutect MYT1L,missense_variant,p.Pro490Gln,ENST00000399161,NM_001303052.1;MYT1L,missense_variant,p.Pro490Gln,ENST00000428368,NM_015025.3;MYT1L,missense_variant,p.Pro144Gln,ENST00000602387,; T ENST00000399161 Transcript missense_variant 2217/7063 1469/3561 490/1186 P/Q cCa/cAa COSM4918917,COSM4918918 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 deleterious(0.05) 10/25 hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF11 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 1922300 1922300 G T 1 0 0 0 0 1 0 0 0 10106 1348 47 2 2 MYT1L 2 1922300 Missense_Mutation SNP G C3L-00144_T 5044 1922300 240271229 191 4262 FAM84A 0 . GRCh38 2 14634682 14634682 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.703G>T p.Gly235Cys p.G235C ENST00000295092 2/2 36 30 6 38 38 0 strelka-varscan-mutect FAM84A,missense_variant,p.Gly235Cys,ENST00000295092,NM_145175.2;FAM84A,missense_variant,p.Gly235Cys,ENST00000331243,;AC011897.2,downstream_gene_variant,,ENST00000450715,;AC011897.2,downstream_gene_variant,,ENST00000418481,;FAM84A,upstream_gene_variant,,ENST00000497769,;FAM84A,upstream_gene_variant,,ENST00000464947,; T ENST00000295092 Transcript missense_variant 991/6355 703/879 235/292 G/C Ggc/Tgc 1 1 FAM84A HGNC HGNC:20743 protein_coding YES CCDS1684.1 ENSP00000295092 Q96KN4 UPI000013E203 NM_145175.2 deleterious(0) 2/2 hmmpanther:PTHR13943:SF38,hmmpanther:PTHR13943 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.0199 1 1 1 1 0 T 3 4 12 14634682 14634682 G T 1 0 0 0 0 1 0 0 0 5499 1000 35 2 2 FAM84A 2 14634682 Missense_Mutation SNP G C3L-00144_T 12712382 14634682 227558847 192 4263 NBAS 0 . GRCh38 2 15511282 15511282 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.815C>A p.Ser272Tyr p.S272Y ENST00000281513 10/52 527 486 41 372 371 1 strelka-varscan-mutect NBAS,missense_variant,p.Ser272Tyr,ENST00000281513,NM_015909.3;NBAS,missense_variant,p.Ser8Tyr,ENST00000427792,; T ENST00000281513 Transcript missense_variant 841/7281 815/7116 272/2371 S/Y tCt/tAt 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 deleterious(0) 10/52 Pfam_domain:PF15492,hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2,Superfamily_domains:SSF50969 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 15511282 15511282 G T 1 0 0 0 0 1 0 0 0 10197 942 33 2 2 NBAS 2 15511282 Missense_Mutation SNP G C3L-00144_T 876600 15511282 226682247 193 4264 OSR1 0 . GRCh38 2 19353496 19353496 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.310G>C p.Ala104Pro p.A104P ENST00000272223 2/3 208 169 39 175 175 0 strelka-varscan-mutect OSR1,missense_variant,p.Ala104Pro,ENST00000272223,NM_145260.2;MIR4757,downstream_gene_variant,,ENST00000584244,;OSR1,downstream_gene_variant,,ENST00000498844,;OSR1,non_coding_transcript_exon_variant,,ENST00000487581,; G ENST00000272223 Transcript missense_variant 655/1936 310/801 104/266 A/P Gct/Cct 1 -1 OSR1 HGNC HGNC:8111 protein_coding YES CCDS1694.1 ENSP00000272223 Q8TAX0 UPI000006EA6A NM_145260.2 tolerated(0.19) 2/3 hmmpanther:PTHR14196,hmmpanther:PTHR14196:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 19353496 19353496 C G 1 0 0 0 0 1 0 0 0 11360 768 27 4 4 OSR1 2 19353496 Missense_Mutation SNP C C3L-00144_T 3842214 19353496 222840033 194 4265 APOB 0 . GRCh38 2 21009499 21009499 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.7369C>A p.Leu2457Met p.L2457M ENST00000233242 26/29 580 477 103 405 404 1 strelka-varscan-mutect APOB,missense_variant,p.Leu2457Met,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 7497/14121 7369/13692 2457/4563 L/M Ctg/Atg COSM3577224 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 21009499 21009499 G T 1 0 0 0 0 1 0 0 0 907 933 33 2 2 APOB 2 21009499 Missense_Mutation SNP G C3L-00144_T 1656003 21009499 221184030 195 4266 APOB 0 . GRCh38 2 21015258 21015258 + Nonsense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.3511G>T p.Glu1171Ter p.E1171* ENST00000233242 23/29 534 437 97 369 368 1 strelka-varscan-mutect APOB,stop_gained,p.Glu1171Ter,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript stop_gained,splice_region_variant 3639/14121 3511/13692 1171/4563 E/* Gaa/Taa COSM287440 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 23/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 21015258 21015258 C A 1 0 0 0 0 0 1 0 0 907 840 29 2 2 APOB 2 21015258 Nonsense_Mutation SNP C C3L-00144_T 5759 21015258 221178271 196 4267 TDRD15 0 . GRCh38 2 21142816 21142816 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.5349C>A p.= p.P1783P ENST00000405799 4/4 220 167 53 157 157 0 strelka-varscan-mutect TDRD15,synonymous_variant,p.=,ENST00000405799,;TDRD15,synonymous_variant,p.=,ENST00000622654,; A ENST00000405799 Transcript synonymous_variant 5679/6135 5349/5805 1783/1934 P ccC/ccA 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 Gene3D:2.30.30.140,Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,SMART_domains:SM00333,Superfamily_domains:SSF63748 LOW 1 SNV 2 1 PASS rs927430740 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 21142816 21142816 C A 1 0 0 0 0 0 0 0 1 16141 639 23 1 1 TDRD15 2 21142816 Silent SNP C C3L-00144_T 127558 21142816 221050713 197 4268 OTOF 0 . GRCh38 2 26461935 26461935 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.5294G>T p.Trp1765Leu p.W1765L ENST00000272371 43/47 473 387 86 388 388 0 strelka-varscan-mutect OTOF,missense_variant,p.Trp1765Leu,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Trp1765Leu,ENST00000403946,NM_001287489.1;OTOF,missense_variant,p.Trp1075Leu,ENST00000402415,NM_194322.2;OTOF,missense_variant,p.Trp998Leu,ENST00000338581,NM_004802.3;OTOF,missense_variant,p.Trp998Leu,ENST00000339598,NM_194323.2;OTOF,downstream_gene_variant,,ENST00000464574,; A ENST00000272371 Transcript missense_variant,splice_region_variant 5421/7156 5294/5994 1765/1997 W/L tGg/tTg 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 deleterious(0) 43/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 26461935 26461935 C A 1 0 0 0 0 1 0 0 0 11369 608 21 2 2 OTOF 2 26461935 Missense_Mutation SNP C C3L-00144_T 5319119 26461935 215731594 198 4269 OTOF 0 . GRCh38 2 26479314 26479314 + Missense_Mutation SNP G G T rs746368147 C3L-00144_T C3L-00144_N G G c.2164C>A p.Arg722Ser p.R722S ENST00000272371 18/47 326 245 81 289 289 0 strelka-varscan-mutect OTOF,missense_variant,p.Arg722Ser,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Arg722Ser,ENST00000403946,NM_001287489.1;OTOF,upstream_gene_variant,,ENST00000402415,NM_194322.2;OTOF,upstream_gene_variant,,ENST00000338581,NM_004802.3;OTOF,upstream_gene_variant,,ENST00000339598,NM_194323.2; T ENST00000272371 Transcript missense_variant 2291/7156 2164/5994 722/1997 R/S Cgc/Agc rs746368147 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 tolerated(0.18) 18/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32 MODERATE 1 SNV 1 1 PASS rs746368147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 26479314 26479314 G T 1 0 0 0 0 1 0 0 0 11369 1087 38 1 1 OTOF 2 26479314 Missense_Mutation SNP G C3L-00144_T 17379 26479314 215714215 199 4270 TCF23 0 . GRCh38 2 27150143 27150143 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.243T>C p.= p.N81N ENST00000296096 2/3 116 91 25 95 94 1 varscan-mutect TCF23,synonymous_variant,p.=,ENST00000296096,NM_175769.2;TCF23,downstream_gene_variant,,ENST00000407815,; C ENST00000296096 Transcript synonymous_variant 373/4882 243/645 81/214 N aaT/aaC 1 1 TCF23 HGNC HGNC:18602 protein_coding YES CCDS33163.1 ENSP00000296096 Q7RTU1 UPI00001AEC06 NM_175769.2 2/3 Gene3D:4.10.280.10,PROSITE_profiles:PS50888,hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF58 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 27150143 27150143 T C 1 0 0 0 0 0 0 0 1 16099 1461 51 5 5 TCF23 2 27150143 Silent SNP T C3L-00144_T 670829 27150143 215043386 200 4271 SLC5A6 0 . GRCh38 2 27207327 27207327 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.324G>C p.= p.L108L ENST00000310574 3/17 276 211 65 198 198 0 strelka-varscan-mutect SLC5A6,synonymous_variant,p.=,ENST00000310574,NM_021095.2;SLC5A6,synonymous_variant,p.=,ENST00000408041,;SLC5A6,synonymous_variant,p.=,ENST00000412471,;SLC5A6,synonymous_variant,p.=,ENST00000401463,;SLC5A6,synonymous_variant,p.=,ENST00000432106,;SLC5A6,synonymous_variant,p.=,ENST00000426119,;ATRAID,upstream_gene_variant,,ENST00000611786,NM_080592.3;ATRAID,upstream_gene_variant,,ENST00000380171,;ATRAID,upstream_gene_variant,,ENST00000606999,NM_001170795.1;SLC5A6,downstream_gene_variant,,ENST00000414408,;SLC5A6,downstream_gene_variant,,ENST00000430186,;SLC5A6,downstream_gene_variant,,ENST00000428518,;SLC5A6,downstream_gene_variant,,ENST00000442731,;SLC5A6,upstream_gene_variant,,ENST00000461319,;SLC5A6,synonymous_variant,p.=,ENST00000445802,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000488743,;SLC5A6,upstream_gene_variant,,ENST00000461757,;SLC5A6,upstream_gene_variant,,ENST00000476319,;SLC5A6,upstream_gene_variant,,ENST00000492069,;SLC5A6,upstream_gene_variant,,ENST00000464538,;SLC5A6,upstream_gene_variant,,ENST00000481751,;ATRAID,upstream_gene_variant,,ENST00000484646,; G ENST00000310574 Transcript synonymous_variant 798/3231 324/1908 108/635 L ctG/ctC 1 -1 SLC5A6 HGNC HGNC:11041 protein_coding YES CCDS1740.1 ENSP00000310208 Q9Y289 UPI000006DE33 NM_021095.2 3/17 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF140,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 27207327 27207327 C G 1 0 0 0 0 0 0 0 1 14952 581 21 4 4 SLC5A6 2 27207327 Silent SNP C C3L-00144_T 57184 27207327 214986202 201 4272 C2orf16 0 . GRCh38 2 27579275 27579275 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2703C>A p.= p.T901T ENST00000408964 1/1 312 224 88 239 239 0 strelka-varscan-mutect C2orf16,synonymous_variant,p.=,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; A ENST00000408964 Transcript synonymous_variant 2754/6199 2703/5955 901/1984 T acC/acA 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 1/1 hmmpanther:PTHR33888 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 27579275 27579275 C A 1 0 0 0 0 0 0 0 1 2032 581 21 2 2 C2orf16 2 27579275 Silent SNP C C3L-00144_T 371948 27579275 214614254 202 4273 BRE 0 . GRCh38 2 27988074 27988074 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.287C>A p.Pro96His p.P96H ENST00000344773 4/13 285 232 53 240 239 1 strelka-varscan-mutect BRE,missense_variant,p.Pro96His,ENST00000344773,NM_004899.4;BRE,missense_variant,p.Pro96His,ENST00000379632,NM_199193.2;BRE,missense_variant,p.Pro96His,ENST00000361704,NM_199192.2;BRE,missense_variant,p.Pro96His,ENST00000342045,NM_199194.2;BRE,missense_variant,p.Pro96His,ENST00000379624,NM_001261840.1,NM_199191.2;BRE,missense_variant,p.Pro96His,ENST00000436924,;BRE,missense_variant,p.Pro96His,ENST00000379629,;BRE,non_coding_transcript_exon_variant,,ENST00000603461,;BRE,missense_variant,p.Pro75His,ENST00000604932,;MRPL33,3_prime_UTR_variant,,ENST00000448427,; A ENST00000344773 Transcript missense_variant 425/1852 287/1248 96/415 P/H cCc/cAc 1 1 BRE HGNC HGNC:1106 protein_coding YES CCDS1764.1 ENSP00000343412 Q9NXR7 UPI0000072A9C NM_004899.4 deleterious(0.02) 4/13 hmmpanther:PTHR15189:SF7,hmmpanther:PTHR15189,Pfam_domain:PF06113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 27988074 27988074 C A 1 0 0 0 0 1 0 0 0 1679 623 22 2 2 BRE 2 27988074 Missense_Mutation SNP C C3L-00144_T 408799 27988074 214205455 203 4274 GALNT14 0 . GRCh38 2 30911033 30911033 + Silent SNP G G T rs565883379 C3L-00144_T C3L-00144_N G G c.1542C>A p.= p.I514I ENST00000324589 16/16 146 118 28 97 97 0 strelka-varscan-mutect GALNT14,synonymous_variant,p.=,ENST00000349752,NM_024572.3;GALNT14,synonymous_variant,p.=,ENST00000406653,NM_001253827.1;GALNT14,synonymous_variant,p.=,ENST00000324589,NM_001253826.1;GALNT14,non_coding_transcript_exon_variant,,ENST00000486564,;GALNT14,non_coding_transcript_exon_variant,,ENST00000475320,; T ENST00000324589 Transcript synonymous_variant 1603/2169 1542/1674 514/557 I atC/atA rs565883379,COSM3581055 1 -1 GALNT14 HGNC HGNC:22946 protein_coding YES CCDS58706.1 ENSP00000314500 Q96FL9 UPI0000073A6F NM_001253826.1 16/16 PROSITE_profiles:PS50231,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF8,Gene3D:2.80.10.50,Pfam_domain:PF00652,SMART_domains:SM00458,Superfamily_domains:SSF50370 0,1 LOW 1 SNV 2 0,1 1 PASS rs565883379 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 30911033 30911033 G T 1 0 0 0 0 0 0 0 1 6080 1048 37 1 1 GALNT14 2 30911033 Silent SNP G C3L-00144_T 2922959 30911033 211282496 204 4275 VIT 0 . GRCh38 2 36808906 36808906 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1824G>T p.Lys608Asn p.K608N ENST00000379242 15/16 120 106 14 111 111 0 strelka-varscan-mutect VIT,missense_variant,p.Lys608Asn,ENST00000379242,NM_053276.3;VIT,missense_variant,p.Lys593Asn,ENST00000389975,NM_001177969.1;VIT,missense_variant,p.Lys262Asn,ENST00000497382,;VIT,missense_variant,p.Lys571Asn,ENST00000379241,NM_001177971.1;VIT,missense_variant,p.Lys545Asn,ENST00000404084,;VIT,missense_variant,p.Lys572Asn,ENST00000401530,NM_001177970.1; T ENST00000379242 Transcript missense_variant 2126/2810 1824/2082 608/693 K/N aaG/aaT 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 deleterious(0.04) 15/16 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF107,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 36808906 36808906 G T 1 0 0 0 0 1 0 0 0 17718 933 33 2 2 VIT 2 36808906 Missense_Mutation SNP G C3L-00144_T 5897873 36808906 205384623 205 4276 QPCT 0 . GRCh38 2 37359616 37359616 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.304T>A p.Trp102Arg p.W102R ENST00000338415 3/7 239 177 62 184 184 0 strelka-varscan-mutect QPCT,missense_variant,p.Trp102Arg,ENST00000338415,NM_012413.3;QPCT,missense_variant,p.Trp53Arg,ENST00000404976,;QPCT,non_coding_transcript_exon_variant,,ENST00000470075,;QPCT,non_coding_transcript_exon_variant,,ENST00000480050,; A ENST00000338415 Transcript missense_variant 462/1739 304/1086 102/361 W/R Tgg/Agg 1 1 QPCT HGNC HGNC:9753 protein_coding YES CCDS1790.1 ENSP00000344829 Q16769 UPI000000DC4F NM_012413.3 deleterious(0) 3/7 hmmpanther:PTHR12283,hmmpanther:PTHR12283:SF5,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 37359616 37359616 T A 1 0 0 0 0 1 0 0 0 13029 1580 55 4 4 QPCT 2 37359616 Missense_Mutation SNP T C3L-00144_T 550710 37359616 204833913 206 4277 SOS1 0 . GRCh38 2 39023119 39023119 + Missense_Mutation SNP T T A C3L-00144_T C3L-00144_N T T c.1309A>T p.Ile437Phe p.I437F ENST00000426016 11/24 162 132 30 124 124 0 strelka-varscan-mutect SOS1,missense_variant,p.Ile437Phe,ENST00000426016,;SOS1,missense_variant,p.Ile437Phe,ENST00000402219,NM_005633.3;SOS1,missense_variant,p.Ile437Phe,ENST00000395038,;SOS1,non_coding_transcript_exon_variant,,ENST00000472480,;SOS1,downstream_gene_variant,,ENST00000461545,; A ENST00000426016 Transcript missense_variant 1396/8517 1309/4002 437/1333 I/F Att/Ttt COSM3702188 1 -1 SOS1 HGNC HGNC:11187 protein_coding YES CCDS1802.1 ENSP00000387784 Q07889 UPI0000135CF0 deleterious(0) 11/24 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF168,Gene3D:2.30.29.30,Superfamily_domains:SSF50729 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 39023119 39023119 T A 1 0 0 0 0 1 0 0 0 15258 1464 51 4 4 SOS1 2 39023119 Missense_Mutation SNP T C3L-00144_T 1663503 39023119 203170410 207 4278 ABCG5 0 . GRCh38 2 43826400 43826400 + Silent SNP G G T C3L-00144_T C3L-00144_N G G c.756C>A p.= p.P252P ENST00000260645 6/13 823 674 149 583 583 0 strelka-varscan-mutect ABCG5,synonymous_variant,p.=,ENST00000260645,NM_022436.2;ABCG5,intron_variant,,ENST00000405322,;ABCG5,intron_variant,,ENST00000486512,;ABCG5,intron_variant,,ENST00000409962,; T ENST00000260645 Transcript synonymous_variant 896/2740 756/1956 252/651 P ccC/ccA COSM382701 1 -1 ABCG5 HGNC HGNC:13886 protein_coding YES CCDS1814.1 ENSP00000260645 Q9H222 UPI0000046560 NM_022436.2 6/13 PROSITE_profiles:PS50893,hmmpanther:PTHR19241:SF193,hmmpanther:PTHR19241,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 43826400 43826400 G T 1 0 0 0 0 0 0 0 1 75 1219 43 2 2 ABCG5 2 43826400 Silent SNP G C3L-00144_T 4803281 43826400 198367129 208 4279 ABCG8 0 . GRCh38 2 43872280 43872280 + Silent SNP G G T rs148836748 C3L-00144_T C3L-00144_N G G c.1185G>T p.= p.A395A ENST00000272286 8/13 627 486 141 612 610 2 strelka-varscan-mutect ABCG8,synonymous_variant,p.=,ENST00000272286,NM_022437.2; T ENST00000272286 Transcript synonymous_variant 1275/2665 1185/2022 395/673 A gcG/gcT rs148836748 1 1 ABCG8 HGNC HGNC:13887 protein_coding YES CCDS1815.1 ENSP00000272286 Q9H221 UPI000004C4CD NM_022437.2 8/13 hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF239 LOW 1 SNV 1 1 PASS rs148836748 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 43872280 43872280 G T 1 0 0 0 0 0 0 0 1 76 1103 39 1 1 ABCG8 2 43872280 Silent SNP G C3L-00144_T 45880 43872280 198321249 209 4280 SIX3 0 . GRCh38 2 44942803 44942803 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.699C>A p.= p.P233P ENST00000260653 1/2 311 263 48 189 189 0 strelka-varscan-mutect SIX3,synonymous_variant,p.=,ENST00000260653,NM_005413.3;RP11-89K21.1,upstream_gene_variant,,ENST00000437916,;SIX3-AS1,upstream_gene_variant,,ENST00000419364,;RP11-89K21.1,upstream_gene_variant,,ENST00000444871,;SIX3-AS1,upstream_gene_variant,,ENST00000456467,;Six3os1_7,downstream_gene_variant,,ENST00000621512,;Six3os1_6,downstream_gene_variant,,ENST00000620790,; A ENST00000260653 Transcript synonymous_variant 906/2523 699/999 233/332 P ccC/ccA 1 1 SIX3 HGNC HGNC:10889 protein_coding YES CCDS1821.1 ENSP00000260653 O95343 UPI00001359C4 NM_005413.3 1/2 PROSITE_profiles:PS50071,hmmpanther:PTHR10390:SF31,hmmpanther:PTHR10390,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 44942803 44942803 C A 1 0 0 0 0 0 0 0 1 14611 581 21 2 2 SIX3 2 44942803 Silent SNP C C3L-00144_T 1070523 44942803 197250726 210 4281 ATP6V1E2 0 . GRCh38 2 46512465 46512465 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.247G>T p.Val83Phe p.V83F ENST00000306448 2/2 175 130 45 130 130 0 strelka-varscan-mutect ATP6V1E2,missense_variant,p.Val83Phe,ENST00000306448,NM_080653.3;ATP6V1E2,missense_variant,p.Val83Phe,ENST00000522587,NM_001318063.1;ATP6V1E2,intron_variant,,ENST00000524249,; A ENST00000306448 Transcript missense_variant 1361/1979 247/681 83/226 V/F Gtc/Ttc 1 -1 ATP6V1E2 HGNC HGNC:18125 protein_coding YES CCDS1826.1 ENSP00000304891 Q96A05 A0A140VKA8 UPI0000073C6E NM_080653.3 deleterious(0.01) 2/2 HAMAP:MF_00311,Pfam_domain:PF01991,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF20 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 46512465 46512465 C A 1 0 0 0 0 1 0 0 0 1337 565 20 2 2 ATP6V1E2 2 46512465 Missense_Mutation SNP C C3L-00144_T 1569662 46512465 195681064 211 4282 NRXN1 0 . GRCh38 2 50531273 50531273 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.2421C>G p.= p.L807L ENST00000404971 12/24 320 263 57 266 266 0 strelka-varscan-mutect NRXN1,synonymous_variant,p.=,ENST00000406316,NM_004801.4;NRXN1,synonymous_variant,p.=,ENST00000625672,;NRXN1,synonymous_variant,p.=,ENST00000404971,NM_001135659.1;NRXN1,synonymous_variant,p.=,ENST00000401669,;NRXN1,synonymous_variant,p.=,ENST00000405472,;NRXN1,synonymous_variant,p.=,ENST00000630543,;NRXN1,synonymous_variant,p.=,ENST00000406859,;NRXN1,synonymous_variant,p.=,ENST00000402717,;NRXN1,intron_variant,,ENST00000495871,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,upstream_gene_variant,,ENST00000636342,;NRXN1,synonymous_variant,p.=,ENST00000331040,;NRXN1,upstream_gene_variant,,ENST00000474354,; C ENST00000404971 Transcript synonymous_variant 3761/7578 2421/4644 807/1547 L ctC/ctG 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 12/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 50531273 50531273 G C 1 0 0 0 0 0 0 0 1 10724 1161 41 4 4 NRXN1 2 50531273 Silent SNP G C3L-00144_T 4018808 50531273 191662256 212 4283 SPTBN1 0 . GRCh38 2 54629501 54629501 + Silent SNP G G A rs557898766 C3L-00144_T C3L-00144_N G G c.2367G>A p.= p.V789V ENST00000356805 14/36 301 276 25 240 240 0 strelka-varscan-mutect SPTBN1,synonymous_variant,p.=,ENST00000615901,;SPTBN1,synonymous_variant,p.=,ENST00000333896,NM_178313.2;SPTBN1,synonymous_variant,p.=,ENST00000356805,NM_003128.2;SPTBN1,downstream_gene_variant,,ENST00000389980,; A ENST00000356805 Transcript synonymous_variant 2648/8482 2367/7095 789/2364 V gtG/gtA rs557898766 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 14/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS rs557898766 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 54629501 54629501 G A 1 0 0 0 0 0 0 0 1 15475 1335 47 3 3 SPTBN1 2 54629501 Silent SNP G C3L-00144_T 4098228 54629501 187564028 213 4284 CCDC85A 0 . GRCh38 2 56193141 56193141 + Missense_Mutation SNP C C A rs747483421 C3L-00144_T C3L-00144_N C C c.941C>A p.Pro314Gln p.P314Q ENST00000407595 2/6 316 257 59 279 279 0 strelka-varscan-mutect CCDC85A,missense_variant,p.Pro314Gln,ENST00000407595,NM_001080433.1;RP11-482H16.1,intron_variant,,ENST00000607540,; A ENST00000407595 Transcript missense_variant 1443/3982 941/1662 314/553 P/Q cCg/cAg rs747483421 1 1 CCDC85A HGNC HGNC:29400 protein_coding YES CCDS46290.1 ENSP00000384040 Q96PX6 UPI00001C1DC1 NM_001080433.1 deleterious_low_confidence(0) 2/6 hmmpanther:PTHR13546,hmmpanther:PTHR13546:SF16 MODERATE 1 SNV 1 1 PASS rs747483421 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 56193141 56193141 C A 1 0 0 0 0 1 0 0 0 2557 652 23 1 1 CCDC85A 2 56193141 Missense_Mutation SNP C C3L-00144_T 1563640 56193141 186000388 214 4285 WDPCP 0 . GRCh38 2 63484968 63484968 + Silent SNP C C G rs370579497 C3L-00144_T C3L-00144_N C C c.273G>C p.= p.T91T ENST00000272321 5/18 624 522 102 422 422 0 strelka-varscan-mutect WDPCP,synonymous_variant,p.=,ENST00000409562,;WDPCP,synonymous_variant,p.=,ENST00000272321,NM_015910.5;WDPCP,synonymous_variant,p.=,ENST00000431065,;WDPCP,non_coding_transcript_exon_variant,,ENST00000409835,;WDPCP,non_coding_transcript_exon_variant,,ENST00000490935,;WDPCP,downstream_gene_variant,,ENST00000467687,;WDPCP,synonymous_variant,p.=,ENST00000418148,;WDPCP,3_prime_UTR_variant,,ENST00000417238,;WDPCP,upstream_gene_variant,,ENST00000493315,; G ENST00000272321 Transcript synonymous_variant 801/3392 273/2241 91/746 T acG/acC rs370579497 1 -1 WDPCP HGNC HGNC:28027 protein_coding YES CCDS42688.1 ENSP00000272321 O95876 UPI000013D946 NM_015910.5 5/18 hmmpanther:PTHR13667:SF5,hmmpanther:PTHR13667,Pfam_domain:PF11768 LOW 1 SNV 1 1 PASS rs370579497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 63484968 63484968 C G 1 0 0 0 0 0 0 0 1 17833 755 27 4 4 WDPCP 2 63484968 Silent SNP C C3L-00144_T 7291827 63484968 178708561 215 4286 MEIS1 0 . GRCh38 2 66439902 66439902 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.299C>G p.Thr100Ser p.T100S ENST00000272369 3/13 207 159 48 158 158 0 strelka-varscan-mutect MEIS1,missense_variant,p.Thr100Ser,ENST00000488550,;MEIS1,missense_variant,p.Thr100Ser,ENST00000272369,NM_002398.2;MEIS1,missense_variant,p.Thr98Ser,ENST00000398506,;MEIS1,missense_variant,p.Thr35Ser,ENST00000495021,;MEIS1,missense_variant,p.Thr100Ser,ENST00000560281,;MEIS1,upstream_gene_variant,,ENST00000437869,;MEIS1-AS2,intron_variant,,ENST00000439433,;MEIS1-AS2,intron_variant,,ENST00000454595,;MEIS1,non_coding_transcript_exon_variant,,ENST00000490726,;MEIS1,non_coding_transcript_exon_variant,,ENST00000496248,;MEIS1,upstream_gene_variant,,ENST00000606455,;MEIS1,upstream_gene_variant,,ENST00000409622,;MEIS1,upstream_gene_variant,,ENST00000466811,;MEIS1,intron_variant,,ENST00000491706,;MEIS1,upstream_gene_variant,,ENST00000498705,; G ENST00000272369 Transcript missense_variant 756/4291 299/1173 100/390 T/S aCc/aGc COSM1409013,COSM3055415 1 1 MEIS1 HGNC HGNC:7000 protein_coding YES CCDS46309.1 ENSP00000272369 O00470 UPI000000DA5A NM_002398.2 tolerated(0.54) 3/13 hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF126 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 198 0 8 3 0 0 0 -20 0.7859863 1 1 1 0 G 3 3 12 66439902 66439902 C G 1 0 0 0 0 1 0 0 0 9411 507 18 4 4 MEIS1 2 66439902 Missense_Mutation SNP C C3L-00144_T 2954934 66439902 175753627 216 4287 ATP6V1B1 0 . GRCh38 2 70961694 70961694 + Splice_Site SNP G G T rs727504746 C3L-00144_T C3L-00144_N G G c.785+1G>T p.X262_splice ENST00000234396 473 409 64 319 318 1 strelka-varscan-mutect ATP6V1B1,splice_donor_variant,,ENST00000234396,NM_001692.3;ATP6V1B1,splice_donor_variant,,ENST00000412314,;AC007040.11,intron_variant,,ENST00000606025,;ATP6V1B1,downstream_gene_variant,,ENST00000454446,;ATP6V1B1,downstream_gene_variant,,ENST00000432098,;ATP6V1B1,upstream_gene_variant,,ENST00000433895,;RN7SL160P,upstream_gene_variant,,ENST00000468558,;ATP6V1B1,splice_donor_variant,,ENST00000432367,;ATP6V1B1,non_coding_transcript_exon_variant,,ENST00000495118,;AC007040.11,intron_variant,,ENST00000453130,;ATP6V1B1,downstream_gene_variant,,ENST00000463380,; T ENST00000234396 Transcript splice_donor_variant -/1891 785/1542 262/513 rs727504746,CS991327,COSM721955 1 1 ATP6V1B1 HGNC HGNC:853 protein_coding YES CCDS1912.1 ENSP00000234396 P15313 UPI000013C9A0 NM_001692.3 8/13 pathogenic 0,0,1 HIGH 1 SNV 1 1,1,1 1 PASS rs727504746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 70961694 70961694 G T 1 0 0 0 0 0 0 1 0 1331 1159 40 1 1 ATP6V1B1 2 70961694 Splice_Site SNP G C3L-00144_T 4521792 70961694 171231835 217 4288 ZNF638 0 . GRCh38 2 71349100 71349101 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.147dupT p.Gly50TrpfsTer10 p.G50Wfs*10 ENST00000409544 2/28 161 123 38 131 131 0 sindel-varindel-pindel ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000409544,NM_001252612.1;ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000264447,NM_014497.4,NM_001014972.2,NM_001252613.1;ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000410075,;ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000437658,;ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000454278,;ZNF638,frameshift_variant,p.Gly50TrpfsTer10,ENST00000455226,;ZNF638,intron_variant,,ENST00000494621,;ZNF638,intron_variant,,ENST00000466330,;ZNF638,intron_variant,,ENST00000464375,;ZNF638,intron_variant,,ENST00000475743,;ZNF638,intron_variant,,ENST00000466975,;ZNF638,downstream_gene_variant,,ENST00000417778,;ZNF638,downstream_gene_variant,,ENST00000454122,;ZNF638,downstream_gene_variant,,ENST00000487707,; T ENST00000409544 Transcript frameshift_variant 776-777/6821 146-147/5937 49/1978 R/RX cgt/cgTt 1 1 ZNF638 HGNC HGNC:17894 protein_coding YES CCDS1917.1 ENSP00000386433 Q14966 UPI000013D51B NM_001252612.1 2/28 hmmpanther:PTHR15592,hmmpanther:PTHR15592:SF1 HIGH 1 insertion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 12 71349100 71349100 - T 1 0 1 1 0 0 0 0 0 18630 1145 40 0 0 ZNF638 2 71349100 Frame_Shift_Ins INS - C3L-00144_T 387406 71349100 170844429 218 4289 DYSF 0 . GRCh38 2 71551152 71551152 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1688G>T p.Gly563Val p.G563V ENST00000410020 18/56 590 492 98 431 431 0 strelka-varscan-mutect DYSF,missense_variant,p.Gly545Val,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Gly562Val,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Gly576Val,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Gly545Val,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Gly562Val,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Gly563Val,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Gly577Val,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Gly546Val,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Gly563Val,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Gly532Val,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Gly546Val,ENST00000394120,NM_001130455.1; T ENST00000410020 Transcript missense_variant 1829/6657 1688/6360 563/2119 G/V gGc/gTc 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0) 18/56 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 71551152 71551152 G T 1 0 0 0 0 1 0 0 0 4683 1217 42 2 2 DYSF 2 71551152 Missense_Mutation SNP G C3L-00144_T 202052 71551152 170642377 219 4290 DGUOK 0 . GRCh38 2 73926947 73926947 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.37G>T p.Ala13Ser p.A13S ENST00000264093 1/7 527 402 125 402 399 3 strelka-varscan-mutect DGUOK,missense_variant,p.Ala13Ser,ENST00000264093,NM_080916.2;DGUOK,missense_variant,p.Ala13Ser,ENST00000629438,NM_001318860.1,NM_001318863.1;DGUOK,missense_variant,p.Ala13Ser,ENST00000348222,NM_001318859.1,NM_080918.2;DGUOK,non_coding_transcript_exon_variant,,ENST00000462685,;DGUOK,non_coding_transcript_exon_variant,,ENST00000489796,;DGUOK,non_coding_transcript_exon_variant,,ENST00000493055,;DGUOK,non_coding_transcript_exon_variant,,ENST00000462551,;DGUOK,missense_variant,p.Ala13Ser,ENST00000418996,; T ENST00000264093 Transcript missense_variant 122/1144 37/834 13/277 A/S Gca/Tca 1 1 DGUOK HGNC HGNC:2858 protein_coding YES CCDS1931.1 ENSP00000264093 Q16854 E5KSL5 UPI000012921F NM_080916.2 tolerated(0.08) 1/7 hmmpanther:PTHR10513,hmmpanther:PTHR10513:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 73926947 73926947 G T 1 0 0 0 0 1 0 0 0 4281 971 34 2 2 DGUOK 2 73926947 Missense_Mutation SNP G C3L-00144_T 2375795 73926947 168266582 220 4291 TLX2 0 . GRCh38 2 74515015 74515015 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.209C>A p.Pro70His p.P70H ENST00000233638 1/3 144 118 26 110 110 0 strelka-varscan-mutect TLX2,missense_variant,p.Pro70His,ENST00000233638,NM_016170.4;TLX2,intron_variant,,ENST00000621092,;DQX1,downstream_gene_variant,,ENST00000404568,NM_133637.2;DQX1,downstream_gene_variant,,ENST00000393951,;TLX2,splice_region_variant,,ENST00000497238,;DQX1,downstream_gene_variant,,ENST00000473508,;DQX1,downstream_gene_variant,,ENST00000418139,;DQX1,downstream_gene_variant,,ENST00000483555,;TLX2,downstream_gene_variant,,ENST00000464417,; A ENST00000233638 Transcript missense_variant 532/2136 209/855 70/284 P/H cCc/cAc 1 1 TLX2 HGNC HGNC:5057 protein_coding YES CCDS1947.1 ENSP00000233638 O43763 UPI0000137060 NM_016170.4 deleterious(0.04) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF117 MODERATE 1 SNV 1 1 PASS rs1418051462 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 74515015 74515015 C A 1 0 0 0 0 1 0 0 0 16406 623 22 2 2 TLX2 2 74515015 Missense_Mutation SNP C C3L-00144_T 588068 74515015 167678514 221 4292 SEMA4F 0 . GRCh38 2 74679876 74679876 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1980G>T p.= p.G660G ENST00000357877 14/14 241 174 67 194 193 1 strelka-varscan-mutect SEMA4F,synonymous_variant,p.=,ENST00000611975,NM_001271662.1;SEMA4F,synonymous_variant,p.=,ENST00000357877,NM_004263.4;SEMA4F,synonymous_variant,p.=,ENST00000339773,NM_001271661.1;SEMA4F,non_coding_transcript_exon_variant,,ENST00000473350,;SEMA4F,3_prime_UTR_variant,,ENST00000446927,;SEMA4F,3_prime_UTR_variant,,ENST00000420077,; T ENST00000357877 Transcript synonymous_variant 2129/4312 1980/2313 660/770 G ggG/ggT 1 1 SEMA4F HGNC HGNC:10734 protein_coding YES CCDS1955.1 ENSP00000350547 O95754 UPI0000001BF5 NM_004263.4 14/14 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF72 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 74679876 74679876 G T 1 0 0 0 0 0 0 0 1 14311 1219 43 2 2 SEMA4F 2 74679876 Silent SNP G C3L-00144_T 164861 74679876 167513653 222 4293 REG3G 0 . GRCh38 2 79026806 79026806 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.170C>A p.Ser57Ter p.S57* ENST00000272324 3/6 134 100 34 125 125 0 strelka-varscan-mutect REG3G,stop_gained,p.Ser57Ter,ENST00000272324,NM_001008387.2;REG3G,stop_gained,p.Ser57Ter,ENST00000393897,NM_198448.3;REG3G,stop_gained,p.Ser57Ter,ENST00000409471,NM_001270040.1;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,non_coding_transcript_exon_variant,,ENST00000498312,; A ENST00000272324 Transcript stop_gained 354/938 170/528 57/175 S/* tCa/tAa 1 1 REG3G HGNC HGNC:29595 protein_coding YES CCDS1962.1 ENSP00000272324 Q6UW15 UPI0000048F1E NM_001008387.2 3/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF60,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 79026806 79026806 C A 1 0 0 0 0 0 1 0 0 13383 838 29 2 2 REG3G 2 79026806 Nonsense_Mutation SNP C C3L-00144_T 4346930 79026806 163166723 223 4294 REG1B 0 . GRCh38 2 79085562 79085562 + Nonsense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.363C>A p.Tyr121Ter p.Y121* ENST00000305089 5/6 217 165 52 175 175 0 strelka-varscan-mutect REG1B,stop_gained,p.Tyr121Ter,ENST00000305089,NM_006507.3;REG1B,stop_gained,p.Tyr72Ter,ENST00000454188,;REG1B,non_coding_transcript_exon_variant,,ENST00000479258,;REG1B,downstream_gene_variant,,ENST00000476554,;REG1B,downstream_gene_variant,,ENST00000469052,; T ENST00000305089 Transcript stop_gained 444/767 363/501 121/166 Y/* taC/taA COSM443252 1 -1 REG1B HGNC HGNC:9952 protein_coding YES CCDS1963.1 ENSP00000303206 P48304 Q6ICS1 UPI00000012AB NM_006507.3 5/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF55,hmmpanther:PTHR22801,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 79085562 79085562 G T 1 0 0 0 0 0 1 0 0 13381 1372 48 2 2 REG1B 2 79085562 Nonsense_Mutation SNP G C3L-00144_T 58756 79085562 163107967 224 4295 CTNNA2 0 . GRCh38 2 80545041 80545041 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.1351delG p.Ala451GlnfsTer17 p.A451Qfs*17 ENST00000402739 9/18 187 162 25 167 167 0 sindel-varindel-pindel CTNNA2,frameshift_variant,p.Ala451GlnfsTer17,ENST00000466387,;CTNNA2,frameshift_variant,p.Ala451GlnfsTer17,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,frameshift_variant,p.Ala451GlnfsTer17,ENST00000402739,NM_001282597.2;CTNNA2,frameshift_variant,p.Ala451GlnfsTer17,ENST00000629316,NM_001164883.1;CTNNA2,frameshift_variant,p.Ala67GlnfsTer17,ENST00000361291,NM_001320810.1;CTNNA2,frameshift_variant,p.Ala130GlnfsTer17,ENST00000343114,NM_001282599.1;CTNNA2,frameshift_variant,p.Ala83GlnfsTer17,ENST00000541047,NM_001282600.1;CTNNA2,frameshift_variant,p.Ala67GlnfsTer17,ENST00000540488,;CTNNA2,frameshift_variant,p.Ala116GlnfsTer17,ENST00000409550,;CTNNA2,non_coding_transcript_exon_variant,,ENST00000493024,;CTNNA2,non_coding_transcript_exon_variant,,ENST00000465616,; - ENST00000402739 Transcript frameshift_variant 1355/3684 1350/2862 450/953 M/X atG/at 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 9/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 80545041 80545041 G - 1 0 1 0 1 0 0 0 0 3822 1348 47 0 0 CTNNA2 2 80545041 Frame_Shift_Del DEL G C3L-00144_T 1459479 80545041 161648488 225 4296 CTNNA2 0 . GRCh38 2 80555847 80555847 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.1695T>A p.= p.V565V ENST00000402739 11/18 68 51 17 56 56 0 strelka-varscan-mutect CTNNA2,synonymous_variant,p.=,ENST00000466387,;CTNNA2,synonymous_variant,p.=,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,synonymous_variant,p.=,ENST00000402739,NM_001282597.2;CTNNA2,synonymous_variant,p.=,ENST00000629316,NM_001164883.1;CTNNA2,synonymous_variant,p.=,ENST00000361291,NM_001320810.1;CTNNA2,synonymous_variant,p.=,ENST00000343114,NM_001282599.1;CTNNA2,synonymous_variant,p.=,ENST00000541047,NM_001282600.1;CTNNA2,synonymous_variant,p.=,ENST00000540488,;CTNNA2,downstream_gene_variant,,ENST00000409550,; A ENST00000402739 Transcript synonymous_variant 1700/3684 1695/2862 565/953 V gtT/gtA 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 11/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 80555847 80555847 T A 1 0 0 0 0 0 0 0 1 3822 1828 64 4 4 CTNNA2 2 80555847 Silent SNP T C3L-00144_T 10806 80555847 161637682 226 4297 FOXI3 0 . GRCh38 2 88448363 88448363 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1107C>T p.= p.S369S ENST00000428390 2/2 439 330 109 354 352 2 strelka-varscan-mutect FOXI3,synonymous_variant,p.=,ENST00000428390,NM_001135649.1; A ENST00000428390 Transcript synonymous_variant 1228/2804 1107/1263 369/420 S agC/agT 1 -1 FOXI3 HGNC HGNC:35123 protein_coding YES CCDS77433.1 ENSP00000478384 A8MTJ6 UPI0001812296 NM_001135649.1 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF137 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 88448363 88448363 G A 1 0 0 0 0 0 0 0 1 5873 1310 46 3 3 FOXI3 2 88448363 Silent SNP G C3L-00144_T 7892516 88448363 153745166 227 4298 TBC1D8 0 . GRCh38 2 101050633 101050633 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.595G>T p.Val199Leu p.V199L ENST00000376840 5/20 108 73 35 94 94 0 strelka-varscan-mutect TBC1D8,missense_variant,p.Val214Leu,ENST00000409318,;TBC1D8,missense_variant,p.Val199Leu,ENST00000376840,NM_001102426.1; A ENST00000376840 Transcript missense_variant 595/3627 595/3423 199/1140 V/L Gtg/Ttg 1 -1 TBC1D8 HGNC HGNC:17791 protein_coding YES CCDS46375.1 ENSP00000366036 O95759 UPI00015ADD19 NM_001102426.1 tolerated(0.08) 5/20 Pfam_domain:PF02893,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF260,SMART_domains:SM00568 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101050633 101050633 C A 1 0 0 0 0 1 0 0 0 16030 478 17 2 2 TBC1D8 2 101050633 Missense_Mutation SNP C C3L-00144_T 12602270 101050633 141142896 228 4299 RNF149 0 . GRCh38 2 101308243 101308243 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.346G>T p.Gly116Trp p.G116W ENST00000295317 1/7 307 235 72 252 252 0 strelka-varscan-mutect RNF149,missense_variant,p.Gly116Trp,ENST00000295317,NM_173647.3;MIR5696,upstream_gene_variant,,ENST00000578474,;RNF149,missense_variant,p.Gly116Trp,ENST00000424632,; A ENST00000295317 Transcript missense_variant 454/2458 346/1203 116/400 G/W Ggg/Tgg 1 -1 RNF149 HGNC HGNC:23137 protein_coding YES CCDS2051.1 ENSP00000295317 Q8NC42 UPI0000366F4A NM_173647.3 deleterious(0) 1/7 Gene3D:3.50.30.30,Pfam_domain:PF02225,hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF39,Superfamily_domains:SSF52025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101308243 101308243 C A 1 0 0 0 0 1 0 0 0 13628 594 21 2 2 RNF149 2 101308243 Missense_Mutation SNP C C3L-00144_T 257610 101308243 140885286 229 4300 SLC9A4 0 . GRCh38 2 102479212 102479212 + Silent SNP C C A rs766734898 C3L-00144_T C3L-00144_N C C c.630C>A p.= p.A210A ENST00000295269 2/12 371 275 96 271 270 1 strelka-varscan-mutect SLC9A4,synonymous_variant,p.=,ENST00000295269,NM_001011552.3; A ENST00000295269 Transcript synonymous_variant 1087/4138 630/2397 210/798 A gcC/gcA rs766734898 1 1 SLC9A4 HGNC HGNC:11077 protein_coding YES CCDS33264.1 ENSP00000295269 Q6AI14 UPI000047F996 NM_001011552.3 2/12 Pfam_domain:PF00999,Prints_domain:PR01084,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF103,TIGRFAM_domain:TIGR00840,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs766734898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 102479212 102479212 C A 1 0 0 0 0 0 0 0 1 14998 639 23 1 1 SLC9A4 2 102479212 Silent SNP C C3L-00144_T 1170969 102479212 139714317 230 4301 POU3F3 0 . GRCh38 2 104856577 104856577 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1067C>T p.Ser356Leu p.S356L ENST00000361360 1/1 389 368 21 296 296 0 varscan-mutect POU3F3,missense_variant,p.Ser356Leu,ENST00000361360,NM_006236.1;RP11-13J10.1,intron_variant,,ENST00000598623,;LINC01158,upstream_gene_variant,,ENST00000447876,; T ENST00000361360 Transcript missense_variant 1067/3064 1067/1503 356/500 S/L tCg/tTg 1 1 POU3F3 HGNC HGNC:9216 protein_coding YES CCDS33265.1 ENSP00000355001 P20264 UPI0000131D87 NM_006236.1 deleterious(0) 1/1 Gene3D:1.10.260.40,Pfam_domain:PF00157,PIRSF_domain:PIRSF002629,Prints_domain:PR00028,PROSITE_patterns:PS00465,PROSITE_profiles:PS51179,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF73,SMART_domains:SM00352,Superfamily_domains:SSF47413 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 104856577 104856577 C T 1 0 0 0 0 1 0 0 0 12392 893 31 1 1 POU3F3 2 104856577 Missense_Mutation SNP C C3L-00144_T 2377365 104856577 137336952 231 4302 TGFBRAP1 0 . GRCh38 2 105269486 105269486 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2192A>G p.His731Arg p.H731R ENST00000393359 11/12 139 96 43 113 113 0 strelka-varscan-mutect TGFBRAP1,missense_variant,p.His731Arg,ENST00000393359,NM_001142621.2,NM_004257.5;TGFBRAP1,missense_variant,p.His731Arg,ENST00000595531,;TGFBRAP1,missense_variant,p.His731Arg,ENST00000258449,; C ENST00000393359 Transcript missense_variant 2619/5979 2192/2583 731/860 H/R cAc/cGc 1 -1 TGFBRAP1 HGNC HGNC:16836 protein_coding YES CCDS2067.1 ENSP00000377027 Q8WUH2 UPI0000072CA9 NM_001142621.2,NM_004257.5 tolerated(0.49) 11/12 hmmpanther:PTHR12894:SF17,hmmpanther:PTHR12894 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 105269486 105269486 T C 1 0 0 0 0 1 0 0 0 16257 1696 59 5 5 TGFBRAP1 2 105269486 Missense_Mutation SNP T C3L-00144_T 412909 105269486 136924043 232 4303 FHL2 0 . GRCh38 2 105373665 105373665 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.225G>T p.= p.L75L ENST00000409807 3/6 550 459 91 412 411 1 strelka-varscan-mutect FHL2,synonymous_variant,p.=,ENST00000409177,;FHL2,synonymous_variant,p.=,ENST00000344213,NM_001318895.1;FHL2,synonymous_variant,p.=,ENST00000409807,;FHL2,synonymous_variant,p.=,ENST00000393353,NM_001450.3;FHL2,synonymous_variant,p.=,ENST00000322142,NM_001039492.2,NM_201555.1;FHL2,synonymous_variant,p.=,ENST00000393352,NM_201557.3;FHL2,synonymous_variant,p.=,ENST00000408995,NM_001318896.1;FHL2,intron_variant,,ENST00000358129,NM_001318898.1;AC012360.6,intron_variant,,ENST00000457290,;AC012360.6,upstream_gene_variant,,ENST00000415627,;FHL2,3_prime_UTR_variant,,ENST00000530340,;FHL2,3_prime_UTR_variant,,ENST00000452732,; A ENST00000409807 Transcript synonymous_variant 560/1601 225/840 75/279 L ctG/ctT 1 -1 FHL2 HGNC HGNC:3703 protein_coding YES CCDS2070.1 ENSP00000386665 Q14192 Q6I9R8 UPI0000140D45 3/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24205:SF3,hmmpanther:PTHR24205,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 105373665 105373665 C A 1 0 0 0 0 0 0 0 1 5744 581 21 2 2 FHL2 2 105373665 Silent SNP C C3L-00144_T 104179 105373665 136819864 233 4304 ST6GAL2 0 . GRCh38 2 106843220 106843220 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.758G>T p.Cys253Phe p.C253F ENST00000409382 2/6 68 51 17 83 83 0 strelka-varscan-mutect ST6GAL2,missense_variant,p.Cys253Phe,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Cys253Phe,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Cys253Phe,ENST00000409087,NM_001142352.1;ST6GAL2,downstream_gene_variant,,ENST00000419159,;AC016994.2,downstream_gene_variant,,ENST00000425419,; A ENST00000409382 Transcript missense_variant 1369/7275 758/1590 253/529 C/F tGc/tTc 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 2/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713 MODERATE 1 SNV 1 1 PASS . . 0 195 15 0 0 0 0 0 -20 0.9998283 1 1 1 0 A 3 1 12 106843220 106843220 C A 1 0 0 0 0 1 0 0 0 15600 710 25 2 2 ST6GAL2 2 106843220 Missense_Mutation SNP C C3L-00144_T 1469555 106843220 135350309 234 4305 RGPD4 0 . GRCh38 2 107854570 107854570 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.993G>T p.Lys331Asn p.K331N ENST00000408999 8/23 65 53 12 59 59 0 varscan-mutect RGPD4,missense_variant,p.Lys331Asn,ENST00000408999,NM_182588.2; T ENST00000408999 Transcript missense_variant 1070/5464 993/5277 331/1758 K/N aaG/aaT 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 deleterious(0) 8/23 hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 107854570 107854570 G T 1 0 0 0 0 1 0 0 0 13460 933 33 2 2 RGPD4 2 107854570 Missense_Mutation SNP G C3L-00144_T 1011350 107854570 134338959 235 4306 SEPT10 0 . GRCh38 2 109585173 109585173 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.366C>T p.= p.T122T ENST00000397712 4/11 104 85 19 75 75 0 strelka-varscan-mutect SEPT10,synonymous_variant,p.=,ENST00000356688,NM_001321498.1;SEPT10,synonymous_variant,p.=,ENST00000397712,NM_001321509.1,NM_144710.3;SEPT10,synonymous_variant,p.=,ENST00000397714,NM_178584.2;SEPT10,synonymous_variant,p.=,ENST00000437928,;SEPT10,synonymous_variant,p.=,ENST00000415095,;SEPT10,5_prime_UTR_variant,,ENST00000461295,;SEPT10,intron_variant,,ENST00000493445,;SEPT10,intron_variant,,ENST00000423520,;SEPT10,downstream_gene_variant,,ENST00000442746,;SEPT10,downstream_gene_variant,,ENST00000411469,;SEPT10,intron_variant,,ENST00000486678,;SEPT10,intron_variant,,ENST00000425498,; A ENST00000397712 Transcript synonymous_variant 745/3071 366/1365 122/454 T acC/acT 1 -1 SEPT10 HGNC HGNC:14349 protein_coding YES CCDS46383.1 ENSP00000380824 Q9P0V9 UPI00000372DD NM_001321509.1,NM_144710.3 4/11 Gene3D:3.40.50.300,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF50,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 2 1 12 109585173 109585173 G A 1 0 0 0 0 0 0 0 1 14336 1335 47 3 3 SEPT10 2 109585173 Silent SNP G C3L-00144_T 1730603 109585173 132608356 236 4307 SEPT10 0 . GRCh38 2 109585757 109585757 + Missense_Mutation SNP T T A rs150267546 C3L-00144_T C3L-00144_N T T c.181A>T p.Ile61Phe p.I61F ENST00000397712 3/11 367 303 64 250 249 1 strelka-varscan-mutect SEPT10,missense_variant,p.Ile61Phe,ENST00000356688,NM_001321498.1;SEPT10,missense_variant,p.Ile61Phe,ENST00000397712,NM_001321509.1,NM_144710.3;SEPT10,missense_variant,p.Ile38Phe,ENST00000397714,NM_178584.2;SEPT10,missense_variant,p.Ile46Phe,ENST00000437928,;SEPT10,missense_variant,p.Ile61Phe,ENST00000415095,;SEPT10,missense_variant,p.Ile52Phe,ENST00000442746,;SEPT10,missense_variant,p.Ile46Phe,ENST00000411469,;SEPT10,intron_variant,,ENST00000493445,;SEPT10,intron_variant,,ENST00000461295,;SEPT10,intron_variant,,ENST00000423520,;SEPT10,intron_variant,,ENST00000486678,;SEPT10,intron_variant,,ENST00000425498,; A ENST00000397712 Transcript missense_variant 560/3071 181/1365 61/454 I/F Att/Ttt rs150267546 1 -1 SEPT10 HGNC HGNC:14349 protein_coding YES CCDS46383.1 ENSP00000380824 Q9P0V9 UPI00000372DD NM_001321509.1,NM_144710.3 deleterious(0.03) 3/11 PIRSF_domain:PIRSF006698,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF50,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs150267546 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 109585757 109585757 T A 1 0 0 0 0 1 0 0 0 14336 1464 51 4 4 SEPT10 2 109585757 Missense_Mutation SNP T C3L-00144_T 584 109585757 132607772 237 4308 MALL 0 . GRCh38 2 110091625 110091625 + Missense_Mutation SNP C C T rs757494098 C3L-00144_T C3L-00144_N C C c.251G>A p.Arg84Lys p.R84K ENST00000272462 2/4 226 213 13 159 159 0 varscan-mutect MALL,missense_variant,p.Arg84Lys,ENST00000272462,NM_005434.4;MALL,intron_variant,,ENST00000427178,;MALL,synonymous_variant,p.=,ENST00000424988,; T ENST00000272462 Transcript missense_variant 1025/3061 251/462 84/153 R/K aGa/aAa rs757494098 1 -1 MALL HGNC HGNC:6818 protein_coding YES CCDS2085.1 ENSP00000272462 Q13021 UPI0000126897 NM_005434.4 tolerated(0.46) 2/4 Pfam_domain:PF01284,PROSITE_profiles:PS51225,hmmpanther:PTHR22776,hmmpanther:PTHR22776:SF24 MODERATE 1 SNV 1 1 PASS rs757494098 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 110091625 110091625 C T 1 0 0 0 0 1 0 0 0 9120 913 32 3 3 MALL 2 110091625 Missense_Mutation SNP C C3L-00144_T 505868 110091625 132101904 238 4309 POLR1B 0 . GRCh38 2 112550874 112550874 + Missense_Mutation SNP A A T rs749884133 C3L-00144_T C3L-00144_N A A c.748A>T p.Met250Leu p.M250L ENST00000541869 6/16 187 134 53 120 120 0 strelka-varscan-mutect POLR1B,start_lost,p.Met1?,ENST00000537335,NM_001282776.1;POLR1B,missense_variant,p.Met250Leu,ENST00000541869,NM_001282772.1;POLR1B,missense_variant,p.Met212Leu,ENST00000263331,NM_019014.5;POLR1B,missense_variant,p.Met212Leu,ENST00000409894,NM_001282774.1;POLR1B,missense_variant,p.Met156Leu,ENST00000417433,NM_001137604.2,NM_001282779.1,NM_001282777.1;POLR1B,downstream_gene_variant,,ENST00000430769,;POLR1B,downstream_gene_variant,,ENST00000438748,;POLR1B,upstream_gene_variant,,ENST00000498054,;POLR1B,downstream_gene_variant,,ENST00000496238,;POLR1B,missense_variant,p.Gln62His,ENST00000430293,;POLR1B,3_prime_UTR_variant,,ENST00000333990,;POLR1B,non_coding_transcript_exon_variant,,ENST00000475318,;POLR1B,non_coding_transcript_exon_variant,,ENST00000468475,;POLR1B,intron_variant,,ENST00000448770,;POLR1B,downstream_gene_variant,,ENST00000424062,; T ENST00000541869 Transcript missense_variant 864/5059 748/3522 250/1173 M/L Atg/Ttg rs749884133 1 1 POLR1B HGNC HGNC:20454 protein_coding YES CCDS62988.1 ENSP00000444136 Q9H9Y6 UPI0002065A70 NM_001282772.1 tolerated(0.26) 6/16 Pfam_domain:PF04561,Pfam_domain:PF04563,hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF5,Superfamily_domains:SSF64484 MODERATE 1 SNV 2 1 PASS rs749884133 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 112550874 112550874 A T 1 0 0 0 0 1 0 0 0 12320 101 4 4 4 POLR1B 2 112550874 Missense_Mutation SNP A C3L-00144_T 2459249 112550874 129642655 239 4310 PSD4 0 . GRCh38 2 113183224 113183224 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.768C>G p.Cys256Trp p.C256W ENST00000245796 2/17 213 165 48 141 141 0 strelka-varscan-mutect PSD4,missense_variant,p.Cys256Trp,ENST00000441564,;PSD4,missense_variant,p.Cys256Trp,ENST00000245796,NM_012455.2;PSD4,intron_variant,,ENST00000485525,;PSD4,downstream_gene_variant,,ENST00000465917,;PSD4,non_coding_transcript_exon_variant,,ENST00000418251,;PSD4,upstream_gene_variant,,ENST00000409656,; G ENST00000245796 Transcript missense_variant 963/5188 768/3171 256/1056 C/W tgC/tgG 1 1 PSD4 HGNC HGNC:19096 protein_coding YES CCDS33276.1 ENSP00000245796 Q8NDX1 UPI00004A0748 NM_012455.2 deleterious_low_confidence(0.03) 2/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 113183224 113183224 C G 1 0 0 0 0 1 0 0 0 12800 805 28 4 4 PSD4 2 113183224 Missense_Mutation SNP C C3L-00144_T 632350 113183224 129010305 240 4311 DPP10 0 . GRCh38 2 115162246 115162246 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.13G>T p.Glu5Ter p.E5* ENST00000310323 1/26 210 171 39 136 136 0 strelka-varscan-mutect DPP10,stop_gained,p.Glu5Ter,ENST00000310323,NM_001004360.3;DPP10,intron_variant,,ENST00000410059,NM_001321910.1,NM_001321911.1,NM_001321914.1,NM_001321905.1,NM_001321906.1,NM_020868.3;DPP10,intron_variant,,ENST00000409163,NM_001178036.1,NM_001178037.1;DPP10,intron_variant,,ENST00000393147,NM_001178034.1;DPP10,intron_variant,,ENST00000436732,;DPP10,intron_variant,,ENST00000393146,;DPP10-AS1,upstream_gene_variant,,ENST00000432658,;DPP10-AS1,upstream_gene_variant,,ENST00000448663,;DPP10,stop_gained,p.Glu5Ter,ENST00000429914,;DPP10,non_coding_transcript_exon_variant,,ENST00000486885,;DPP10,intron_variant,,ENST00000461250,; T ENST00000310323 Transcript stop_gained 140/3052 13/2370 5/789 E/* Gag/Tag 1 1 DPP10 HGNC HGNC:20823 protein_coding CCDS33278.1 ENSP00000309066 Q8N608 UPI0000D61221 NM_001004360.3 1/26 Low_complexity_(Seg):seg HIGH SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 115162246 115162246 G T 1 0 0 0 0 0 1 0 0 4542 1175 41 2 2 DPP10 2 115162246 Nonsense_Mutation SNP G C3L-00144_T 1979022 115162246 127031283 241 4312 C1QL2 0 . GRCh38 2 119157938 119157938 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.332C>A p.Ser111Ter p.S111* ENST00000272520 1/2 191 161 30 158 158 0 strelka-varscan-mutect C1QL2,stop_gained,p.Ser111Ter,ENST00000272520,NM_182528.3; T ENST00000272520 Transcript stop_gained 952/2043 332/864 111/287 S/* tCg/tAg 1 -1 C1QL2 HGNC HGNC:24181 protein_coding YES CCDS42737.1 ENSP00000272520 Q7Z5L3 UPI000013D95E NM_182528.3 1/2 Pfam_domain:PF01391 HIGH 1 SNV 1 1 PASS rs927120716 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 119157938 119157938 G T 1 0 0 0 0 0 1 0 0 1937 1059 37 1 1 C1QL2 2 119157938 Nonsense_Mutation SNP G C3L-00144_T 3995692 119157938 123035591 242 4313 UGGT1 0 . GRCh38 2 128129059 128129059 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1257G>T p.= p.R419R ENST00000259253 13/41 138 114 24 95 94 1 strelka-mutect UGGT1,synonymous_variant,p.=,ENST00000259253,NM_020120.3;UGGT1,3_prime_UTR_variant,,ENST00000376723,;UGGT1,3_prime_UTR_variant,,ENST00000438277,; T ENST00000259253 Transcript synonymous_variant 1304/10650 1257/4668 419/1555 R cgG/cgT 1 1 UGGT1 HGNC HGNC:15663 protein_coding YES CCDS2154.1 ENSP00000259253 Q9NYU2 UPI00000707D8 NM_020120.3 13/41 Pfam_domain:PF06427,hmmpanther:PTHR11226,hmmpanther:PTHR11226:SF3 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 128129059 128129059 G T 1 0 0 0 0 0 0 0 1 17466 1219 43 2 2 UGGT1 2 128129059 Silent SNP G C3L-00144_T 8971121 128129059 114064470 243 4314 TUBA3E 0 . GRCh38 2 130192075 130192075 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1109A>T p.Lys370Met p.K370M ENST00000312988 5/5 98 87 11 65 65 0 varscan-mutect TUBA3E,missense_variant,p.Lys370Met,ENST00000312988,NM_207312.2;MZT2B,downstream_gene_variant,,ENST00000281871,NM_025029.3;MZT2B,downstream_gene_variant,,ENST00000409255,;MZT2B,downstream_gene_variant,,ENST00000425361,;MZT2B,downstream_gene_variant,,ENST00000457492,;MZT2B,downstream_gene_variant,,ENST00000455239,;MZT2B,downstream_gene_variant,,ENST00000491178,;MZT2B,downstream_gene_variant,,ENST00000480182,; A ENST00000312988 Transcript missense_variant 1210/1542 1109/1353 370/450 K/M aAg/aTg 1 -1 TUBA3E HGNC HGNC:20765 protein_coding YES CCDS2158.1 ENSP00000318197 Q6PEY2 UPI00001BE8EB NM_207312.2 deleterious_low_confidence(0) 5/5 Gene3D:3.30.1330.20,Pfam_domain:PF03953,Prints_domain:PR01162,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF94,SMART_domains:SM00865,Superfamily_domains:SSF55307 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 130192075 130192075 T A 1 0 0 0 0 1 0 0 0 17258 1609 56 4 4 TUBA3E 2 130192075 Missense_Mutation SNP T C3L-00144_T 2063016 130192075 112001454 244 4315 POTEI 0 . GRCh38 2 130463542 130463542 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2502G>T p.= p.V834V ENST00000451531 15/15 123 105 18 107 107 0 varscan-mutect POTEI,synonymous_variant,p.=,ENST00000451531,NM_001277406.1;POTEI,downstream_gene_variant,,ENST00000631234,;POTEI,downstream_gene_variant,,ENST00000615053,; A ENST00000451531 Transcript synonymous_variant 2933/7020 2502/3228 834/1075 V gtG/gtT 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 15/15 Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 5 204 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 130463542 130463542 C A 1 0 0 0 0 0 0 0 1 12382 581 21 2 2 POTEI 2 130463542 Silent SNP C C3L-00144_T 271467 130463542 111729987 245 4316 POTEI 0 . GRCh38 2 130509021 130509021 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.215G>T p.Cys72Phe p.C72F ENST00000451531 1/15 951 814 137 766 766 0 strelka-varscan-mutect POTEI,missense_variant,p.Cys72Phe,ENST00000451531,NM_001277406.1;POTEI,missense_variant,p.Cys72Phe,ENST00000631234,;POTEI,missense_variant,p.Cys72Phe,ENST00000615053,; A ENST00000451531 Transcript missense_variant 646/7020 215/3228 72/1075 C/F tGc/tTc 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0) 1/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50 MODERATE 1 SNV 1 1 PASS rs1380383492 . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 130509021 130509021 C A 1 0 0 0 0 1 0 0 0 12382 710 25 2 2 POTEI 2 130509021 Missense_Mutation SNP C C3L-00144_T 45479 130509021 111684508 246 4317 GPR148 0 . GRCh38 2 130729279 130729279 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.130delG p.Val44CysfsTer29 p.V44Cfs*29 ENST00000309926 1/1 71 55 16 62 62 0 sindel-varindel-pindel GPR148,frameshift_variant,p.Val44CysfsTer29,ENST00000309926,NM_207364.2; - ENST00000309926 Transcript frameshift_variant 210/1267 128/1044 43/347 R/X aGg/ag 1 1 GPR148 HGNC HGNC:23623 protein_coding YES CCDS2163.1 ENSP00000308908 Q8TDV2 UPI0000048E0D NM_207364.2 1/1 hmmpanther:PTHR24243:SF114,hmmpanther:PTHR24243,Superfamily_domains:SSF81321 HIGH 1 deletion 2 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999972 1 1 1 0 - 7 5 12 130729279 130729279 G - 1 0 1 0 1 0 0 0 0 6539 1000 35 0 0 GPR148 2 130729279 Frame_Shift_Del DEL G C3L-00144_T 220258 130729279 111464250 247 4318 AMER3 0 . GRCh38 2 130763194 130763194 + Missense_Mutation SNP C C A rs202240427 C3L-00144_T C3L-00144_N C C c.1122C>A p.Ser374Arg p.S374R ENST00000423981 2/2 347 282 65 281 278 3 strelka-varscan-mutect AMER3,missense_variant,p.Ser374Arg,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Ser374Arg,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; A ENST00000423981 Transcript missense_variant 1232/6172 1122/2586 374/861 S/R agC/agA rs202240427 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 deleterious(0) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2,Pfam_domain:PF09422 MODERATE 1 SNV 4 1 PASS rs202240427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 130763194 130763194 C A 1 0 0 0 0 1 0 0 0 669 767 27 1 1 AMER3 2 130763194 Missense_Mutation SNP C C3L-00144_T 33915 130763194 111430335 248 4319 THSD7B 0 . GRCh38 2 137657148 137657148 + Missense_Mutation SNP G G T rs147732921 C3L-00144_T C3L-00144_N G G c.4369G>T p.Val1457Phe p.V1457F ENST00000272643 23/27 190 152 38 142 141 1 strelka-varscan-mutect THSD7B,missense_variant,p.Val1455Phe,ENST00000409968,NM_001316349.1;THSD7B,missense_variant,p.Val1457Phe,ENST00000272643,;THSD7B,missense_variant,p.Val1426Phe,ENST00000413152,NM_001080427.1;THSD7B,downstream_gene_variant,,ENST00000480352,; T ENST00000272643 Transcript missense_variant 4369/5939 4369/4827 1457/1608 V/F Gtt/Ttt rs147732921,COSM1399646,COSM1399647 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A deleterious(0.01) 23/27 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs147732921 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 137657148 137657148 G T 1 0 0 0 0 1 0 0 0 16314 1145 40 1 1 THSD7B 2 137657148 Missense_Mutation SNP G C3L-00144_T 6893954 137657148 104536381 249 4320 LRP1B 0 . GRCh38 2 140373139 140373139 + Splice_Site SNP T T C novel C3L-00144_T C3L-00144_N T T c.10639-2A>G p.X3547_splice ENST00000389484 240 200 40 220 220 0 strelka-varscan-mutect LRP1B,splice_acceptor_variant,,ENST00000389484,NM_018557.2; C ENST00000389484 Transcript splice_acceptor_variant -/16535 10639/13800 3547/4599 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 68/90 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 12 140373139 140373139 T C 1 0 0 0 0 0 0 1 0 8850 1536 53 5 5 LRP1B 2 140373139 Splice_Site SNP T C3L-00144_T 2715991 140373139 101820390 250 4321 LRP1B 0 . GRCh38 2 140457490 140457490 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.9787G>T p.Val3263Leu p.V3263L ENST00000389484 61/91 127 108 19 105 104 1 strelka-varscan-mutect LRP1B,missense_variant,p.Val3263Leu,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 10759/16535 9787/13800 3263/4599 V/L Gtg/Ttg 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.01) 61/91 hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,Superfamily_domains:SSF57184,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 140457490 140457490 C A 1 0 0 0 0 1 0 0 0 8850 507 18 2 2 LRP1B 2 140457490 Missense_Mutation SNP C C3L-00144_T 84351 140457490 101736039 251 4322 LRP1B 0 . GRCh38 2 141015871 141015871 + Missense_Mutation SNP C C A rs150406301 C3L-00144_T C3L-00144_N C C c.2015G>T p.Ser672Ile p.S672I ENST00000389484 13/91 327 276 51 323 323 0 strelka-varscan-mutect LRP1B,missense_variant,p.Ser672Ile,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 2987/16535 2015/13800 672/4599 S/I aGc/aTc rs150406301 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.06) 13/91 PROSITE_profiles:PS51120,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS rs150406301 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 141015871 141015871 C A 1 0 0 0 0 1 0 0 0 8850 797 28 2 2 LRP1B 2 141015871 Missense_Mutation SNP C C3L-00144_T 558381 141015871 101177658 252 4323 GTDC1 0 . GRCh38 2 143957325 143957325 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1000G>T p.Ala334Ser p.A334S ENST00000392869 8/11 119 85 34 90 90 0 strelka-varscan-mutect GTDC1,missense_variant,p.Ala334Ser,ENST00000392869,;GTDC1,missense_variant,p.Ala334Ser,ENST00000409214,NM_001006636.3;GTDC1,missense_variant,p.Ala334Ser,ENST00000542155,NM_001164629.3;GTDC1,missense_variant,p.Ala334Ser,ENST00000344850,;GTDC1,missense_variant,p.Ala302Ser,ENST00000618778,NM_001284238.1;GTDC1,missense_variant,p.Ala216Ser,ENST00000409298,;GTDC1,missense_variant,p.Ala205Ser,ENST00000463875,NM_001284234.1;GTDC1,intron_variant,,ENST00000392867,NM_024659.4;GTDC1,intron_variant,,ENST00000241391,NM_001284233.1;AC016910.1,intron_variant,,ENST00000422799,;GTDC1,3_prime_UTR_variant,,ENST00000415569,;GTDC1,intron_variant,,ENST00000392871,; A ENST00000392869 Transcript missense_variant 1153/10514 1000/1377 334/458 A/S Gcc/Tcc 1 -1 GTDC1 HGNC HGNC:20887 protein_coding YES CCDS33300.1 ENSP00000376608 Q4AE62 UPI000022BC3B tolerated(0.24) 8/11 hmmpanther:PTHR13615,hmmpanther:PTHR13615:SF3,Pfam_domain:PF00534,Gene3D:3.40.50.2000,Superfamily_domains:SSF53756 MODERATE SNV 5 1 PASS . . 0 184 22 3 0 0 0 0 -20 0.987252 0 1 1 0 A 3 1 12 143957325 143957325 C A 1 0 0 0 0 1 0 0 0 6733 739 26 2 2 GTDC1 2 143957325 Missense_Mutation SNP C C3L-00144_T 2941454 143957325 98236204 253 4324 KIF5C 0 . GRCh38 2 148946914 148946914 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.605G>C p.Ser202Thr p.S202T ENST00000435030 8/26 348 279 69 275 275 0 strelka-varscan-mutect KIF5C,missense_variant,p.Ser202Thr,ENST00000435030,NM_004522.2;KIF5C,upstream_gene_variant,,ENST00000450621,;KIF5C,upstream_gene_variant,,ENST00000464066,; C ENST00000435030 Transcript missense_variant 973/6931 605/2874 202/957 S/T aGc/aCc 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 deleterious(0) 8/26 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 148946914 148946914 G C 1 0 0 0 0 1 0 0 0 8172 971 34 4 4 KIF5C 2 148946914 Missense_Mutation SNP G C3L-00144_T 4989589 148946914 93246615 254 4325 RIF1 0 . GRCh38 2 151436889 151436889 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1258G>T p.Gly420Ter p.G420* ENST00000243326 11/35 202 161 41 158 158 0 strelka-varscan-mutect RIF1,stop_gained,p.Gly420Ter,ENST00000243326,;RIF1,stop_gained,p.Gly420Ter,ENST00000453091,NM_001177663.1;RIF1,stop_gained,p.Gly420Ter,ENST00000430328,NM_001177665.1;RIF1,stop_gained,p.Gly420Ter,ENST00000444746,NM_018151.4;RIF1,stop_gained,p.Gly420Ter,ENST00000428287,NM_001177664.1;RIF1,stop_gained,p.Gly412Ter,ENST00000414861,; T ENST00000243326 Transcript stop_gained 1741/15003 1258/7419 420/2472 G/* Gga/Tga 1 1 RIF1 HGNC HGNC:23207 protein_coding YES CCDS2194.1 ENSP00000243326 Q5UIP0 UPI000023729F 11/35 hmmpanther:PTHR22928 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 151436889 151436889 G T 1 0 0 0 0 0 1 0 0 13533 1349 47 2 2 RIF1 2 151436889 Nonsense_Mutation SNP G C3L-00144_T 2489975 151436889 90756640 255 4326 PRPF40A 0 . GRCh38 2 152663935 152663935 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1912G>T p.Val638Phe p.V638F ENST00000410080 18/26 132 113 19 90 89 1 strelka-varscan-mutect PRPF40A,missense_variant,p.Val638Phe,ENST00000410080,NM_017892.3;PRPF40A,upstream_gene_variant,,ENST00000471167,;PRPF40A,upstream_gene_variant,,ENST00000471701,;PRPF40A,upstream_gene_variant,,ENST00000472760,; A ENST00000410080 Transcript missense_variant 2454/8048 1912/2793 638/930 V/F Gtt/Ttt 1 -1 PRPF40A HGNC HGNC:16463 protein_coding YES CCDS46430.1 ENSP00000386458 O75400 UPI00015743D9 NM_017892.3 deleterious(0) 18/26 Gene3D:1uzcA00,PROSITE_profiles:PS51676,hmmpanther:PTHR11864,hmmpanther:PTHR11864:SF20,SMART_domains:SM00441,Superfamily_domains:SSF81698 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 152663935 152663935 C A 1 0 0 0 0 1 0 0 0 12707 478 17 2 2 PRPF40A 2 152663935 Missense_Mutation SNP C C3L-00144_T 1227046 152663935 89529594 256 4327 ITGB6 0 . GRCh38 2 160141984 160141984 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.1105G>A p.Glu369Lys p.E369K ENST00000283249 8/15 285 264 21 203 203 0 strelka-varscan-mutect ITGB6,missense_variant,p.Glu369Lys,ENST00000283249,NM_000888.4,NM_001282389.1,NM_001282353.1;ITGB6,missense_variant,p.Glu274Lys,ENST00000620391,NM_001282354.1,NM_001282390.1;ITGB6,missense_variant,p.Glu327Lys,ENST00000428609,NM_001282388.1;ITGB6,missense_variant,p.Glu369Lys,ENST00000409872,;ITGB6,missense_variant,p.Glu369Lys,ENST00000409967,NM_001282355.1;ITGB6,non_coding_transcript_exon_variant,,ENST00000485635,;ITGB6,splice_region_variant,,ENST00000409583,; T ENST00000283249 Transcript missense_variant,splice_region_variant 1343/4675 1105/2367 369/788 E/K Gaa/Aaa COSM5601653 1 -1 ITGB6 HGNC HGNC:6161 protein_coding YES CCDS2212.1 ENSP00000283249 P18564 UPI000012DA13 NM_000888.4,NM_001282389.1,NM_001282353.1 tolerated(1) 8/15 Low_complexity_(Seg):seg,hmmpanther:PTHR10082:SF11,hmmpanther:PTHR10082,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,Gene3D:3.40.50.410,SMART_domains:SM00187,Superfamily_domains:SSF53300 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999723 1 1 1 0 T 3 4 12 160141984 160141984 C T 1 0 0 0 0 1 0 0 0 7805 840 29 3 3 ITGB6 2 160141984 Missense_Mutation SNP C C3L-00144_T 7478049 160141984 82051545 257 4328 TBR1 0 . GRCh38 2 161423653 161423653 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1475G>T p.Arg492Leu p.R492L ENST00000389554 6/6 272 220 52 179 179 0 strelka-varscan-mutect TBR1,missense_variant,p.Arg492Leu,ENST00000389554,NM_006593.2;TBR1,missense_variant,p.Arg205Leu,ENST00000410035,;TBR1,missense_variant,p.Arg192Leu,ENST00000411412,;AC009487.5,upstream_gene_variant,,ENST00000505579,;AC009487.4,upstream_gene_variant,,ENST00000444164,;AC009487.4,upstream_gene_variant,,ENST00000437683,;TBR1,non_coding_transcript_exon_variant,,ENST00000477804,;SLC4A10,upstream_gene_variant,,ENST00000605990,;SLC4A10,upstream_gene_variant,,ENST00000482861,;TBR1,downstream_gene_variant,,ENST00000489530,;SLC4A10,upstream_gene_variant,,ENST00000606386,;TBR1,non_coding_transcript_exon_variant,,ENST00000463544,; T ENST00000389554 Transcript missense_variant 1792/4009 1475/2049 492/682 R/L cGg/cTg 1 1 TBR1 HGNC HGNC:11590 protein_coding YES CCDS33310.1 ENSP00000374205 Q16650 UPI0000136A99 NM_006593.2 deleterious(0.01) 6/6 hmmpanther:PTHR11267:SF88,hmmpanther:PTHR11267,Pfam_domain:PF16176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 161423653 161423653 G T 1 0 0 0 0 1 0 0 0 16052 1116 39 1 1 TBR1 2 161423653 Missense_Mutation SNP G C3L-00144_T 1281669 161423653 80769876 258 4329 DPP4 0 . GRCh38 2 162008615 162008615 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1934G>C p.Gly645Ala p.G645A ENST00000360534 22/26 457 386 71 341 341 0 strelka-varscan-mutect DPP4,missense_variant,p.Gly645Ala,ENST00000360534,NM_001935.3;DPP4,non_coding_transcript_exon_variant,,ENST00000491591,;DPP4,3_prime_UTR_variant,,ENST00000434918,;DPP4,non_coding_transcript_exon_variant,,ENST00000490286,;DPP4,non_coding_transcript_exon_variant,,ENST00000494507,; G ENST00000360534 Transcript missense_variant 2495/3904 1934/2301 645/766 G/A gGc/gCc 1 -1 DPP4 HGNC HGNC:3009 protein_coding YES CCDS2216.1 ENSP00000353731 P27487 UPI000004F7BF NM_001935.3 deleterious(0.04) 22/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF128,Pfam_domain:PF00326,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 162008615 162008615 C G 1 0 0 0 0 1 0 0 0 4544 739 26 4 4 DPP4 2 162008615 Missense_Mutation SNP C C3L-00144_T 584962 162008615 80184914 259 4330 IFIH1 0 . GRCh38 2 162317878 162317878 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.430T>C p.= p.L144L ENST00000263642 1/16 76 64 12 55 55 0 strelka-varscan-mutect IFIH1,synonymous_variant,p.=,ENST00000263642,NM_022168.3;IFIH1,synonymous_variant,p.=,ENST00000421365,;GCA,upstream_gene_variant,,ENST00000429691,;GCA,upstream_gene_variant,,ENST00000446271,;GCA,upstream_gene_variant,,ENST00000473240,; G ENST00000263642 Transcript synonymous_variant 826/3595 430/3078 144/1025 L Ttg/Ctg 1 -1 IFIH1 HGNC HGNC:18873 protein_coding YES CCDS2217.1 ENSP00000263642 Q9BYX4 UPI000013D436 NM_022168.3 1/16 Gene3D:1.10.533.10,Pfam_domain:PF16739,hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF14,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 2 3 12 162317878 162317878 A G 1 0 0 0 0 0 0 0 1 7420 40 2 5 5 IFIH1 2 162317878 Silent SNP A C3L-00144_T 309263 162317878 79875651 260 4331 KCNH7 0 . GRCh38 2 162371968 162371968 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3452C>A p.Ser1151Tyr p.S1151Y ENST00000332142 16/16 341 256 85 294 293 1 strelka-varscan-mutect KCNH7,missense_variant,p.Ser1151Tyr,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Ser1051Tyr,ENST00000618399,;GCA,downstream_gene_variant,,ENST00000414723,; T ENST00000332142 Transcript missense_variant 3552/4113 3452/3591 1151/1196 S/Y tCt/tAt 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 deleterious_low_confidence(0.01) 16/16 MODERATE 1 SNV 1 1 PASS rs1274532863 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 162371968 162371968 G T 1 0 0 0 0 1 0 0 0 7953 942 33 2 2 KCNH7 2 162371968 Missense_Mutation SNP G C3L-00144_T 54090 162371968 79821561 261 4332 SCN3A 0 . GRCh38 2 165095568 165095568 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.4374C>A p.Phe1458Leu p.F1458L ENST00000283254 25/28 236 184 52 208 206 2 strelka-varscan-mutect SCN3A,missense_variant,p.Phe1458Leu,ENST00000360093,;SCN3A,missense_variant,p.Phe1458Leu,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Phe1409Leu,ENST00000409101,NM_001081677.1;SCN3A,downstream_gene_variant,,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000431341,;SCN3A,upstream_gene_variant,,ENST00000465043,;SCN3A,non_coding_transcript_exon_variant,,ENST00000471697,; T ENST00000283254 Transcript missense_variant 4842/9091 4374/6003 1458/2000 F/L ttC/ttA COSM3568708,COSM3568709 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0.02) 25/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 165095568 165095568 G T 1 0 0 0 0 1 0 0 0 14187 1281 45 2 2 SCN3A 2 165095568 Missense_Mutation SNP G C3L-00144_T 2723600 165095568 77097961 262 4333 SCN2A 0 . GRCh38 2 165344569 165344569 + Silent SNP G G A C3L-00144_T C3L-00144_N G G c.2577G>A p.= p.K859K ENST00000636071 17/28 262 237 25 195 195 0 strelka-varscan-mutect SCN2A,synonymous_variant,p.=,ENST00000636071,;SCN2A,synonymous_variant,p.=,ENST00000636985,;SCN2A,synonymous_variant,p.=,ENST00000637266,;SCN2A,synonymous_variant,p.=,ENST00000375437,NM_001040142.1;SCN2A,synonymous_variant,p.=,ENST00000283256,NM_021007.2;SCN2A,synonymous_variant,p.=,ENST00000375427,NM_001040143.1;SCN2A,synonymous_variant,p.=,ENST00000631182,;SCN2A,3_prime_UTR_variant,,ENST00000636662,;SCN2A,3_prime_UTR_variant,,ENST00000636384,;SCN2A,3_prime_UTR_variant,,ENST00000636769,;SCN2A,3_prime_UTR_variant,,ENST00000636135,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,; A ENST00000636071 Transcript synonymous_variant 2954/9303 2577/6018 859/2005 K aaG/aaA COSM5474359,COSM5474360 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 17/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 1,1 LOW 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 165344569 165344569 G A 1 0 0 0 0 0 0 0 1 14185 1020 36 3 3 SCN2A 2 165344569 Silent SNP G C3L-00144_T 249001 165344569 76848960 263 4334 SCN1A 0 . GRCh38 2 166058658 166058658 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.295A>G p.Ile99Val p.I99V ENST00000303395 4/28 267 203 64 226 226 0 strelka-varscan-mutect SCN1A,missense_variant,p.Ile99Val,ENST00000635776,;SCN1A,missense_variant,p.Ile99Val,ENST00000637988,;SCN1A,missense_variant,p.Ile99Val,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Ile99Val,ENST00000635750,;SCN1A,missense_variant,p.Ile99Val,ENST00000423058,;SCN1A,missense_variant,p.Ile99Val,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Ile99Val,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;SCN1A,missense_variant,p.Ile99Val,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000636759,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,; C ENST00000303395 Transcript missense_variant 713/8533 295/6030 99/2009 I/V Atc/Gtc 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 deleterious(0.02) 4/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 166058658 166058658 T C 1 0 0 0 0 1 0 0 0 14183 1464 51 5 5 SCN1A 2 166058658 Missense_Mutation SNP T C3L-00144_T 714089 166058658 76134871 264 4335 SCN9A 0 . GRCh38 2 166306542 166306542 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.435G>T p.Met145Ile p.M145I ENST00000409672 4/27 469 394 75 295 293 2 strelka-varscan-mutect SCN9A,missense_variant,p.Met145Ile,ENST00000303354,;SCN9A,missense_variant,p.Met145Ile,ENST00000409672,NM_002977.3;SCN9A,missense_variant,p.Met145Ile,ENST00000409435,;SCN9A,missense_variant,p.Met10Ile,ENST00000452182,;SCN9A,missense_variant,p.Met10Ile,ENST00000454569,;AC010127.3,downstream_gene_variant,,ENST00000447809,;SCN9A,upstream_gene_variant,,ENST00000472119,; A ENST00000409672 Transcript missense_variant 782/9768 435/5934 145/1977 M/I atG/atT 1 -1 SCN9A HGNC HGNC:10597 protein_coding YES CCDS46441.1 ENSP00000386306 Q15858 UPI0000140AC7 NM_002977.3 tolerated(0.11) 4/27 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF221,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS rs1352403629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 166306542 166306542 C A 1 0 0 0 0 1 0 0 0 14194 826 29 2 2 SCN9A 2 166306542 Missense_Mutation SNP C C3L-00144_T 247884 166306542 75886987 265 4336 XIRP2 0 . GRCh38 2 167243511 167243511 + Missense_Mutation SNP C C A rs775118091 C3L-00144_T C3L-00144_N C C c.2119C>A p.Leu707Ile p.L707I ENST00000409195 9/11 130 96 34 107 107 0 strelka-varscan-mutect XIRP2,missense_variant,p.Leu707Ile,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Leu485Ile,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Leu532Ile,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; A ENST00000409195 Transcript missense_variant 2208/12675 2119/10650 707/3549 L/I Ctt/Att rs775118091 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.03) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS rs775118091 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 167243511 167243511 C A 1 0 0 0 0 1 0 0 0 17989 797 28 2 2 XIRP2 2 167243511 Missense_Mutation SNP C C3L-00144_T 936969 167243511 74950018 266 4337 XIRP2 0 . GRCh38 2 167247493 167247493 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.6101A>G p.Gln2034Arg p.Q2034R ENST00000409195 9/11 255 208 47 201 201 0 strelka-varscan-mutect XIRP2,missense_variant,p.Gln2034Arg,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Gln1812Arg,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Gln1859Arg,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; G ENST00000409195 Transcript missense_variant 6190/12675 6101/10650 2034/3549 Q/R cAa/cGa 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious_low_confidence(0.03) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 167247493 167247493 A G 1 0 0 0 0 1 0 0 0 17989 130 5 5 5 XIRP2 2 167247493 Missense_Mutation SNP A C3L-00144_T 3982 167247493 74946036 267 4338 XIRP2 0 . GRCh38 2 167248794 167248794 + Missense_Mutation SNP G G T rs540282598 C3L-00144_T C3L-00144_N G G c.7402G>T p.Val2468Leu p.V2468L ENST00000409195 9/11 166 135 31 145 144 1 strelka-varscan-mutect XIRP2,missense_variant,p.Val2468Leu,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Val2246Leu,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Val2293Leu,ENST00000628543,;XIRP2,5_prime_UTR_variant,,ENST00000295237,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript missense_variant 7491/12675 7402/10650 2468/3549 V/L Gtg/Ttg rs540282598 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated_low_confidence(0.43) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS rs540282598 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 167248794 167248794 G T 1 0 0 0 0 1 0 0 0 17989 1261 44 2 2 XIRP2 2 167248794 Missense_Mutation SNP G C3L-00144_T 1301 167248794 74944735 268 4339 LRP2 0 . GRCh38 2 169165951 169165951 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.11739T>C p.= p.T3913T ENST00000263816 62/79 615 465 150 454 454 0 strelka-varscan-mutect LRP2,synonymous_variant,p.=,ENST00000263816,NM_004525.2; G ENST00000263816 Transcript synonymous_variant 12025/15808 11739/13968 3913/4655 T acT/acC 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 62/79 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,Low_complexity_(Seg):seg,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 169165951 169165951 A G 1 0 0 0 0 0 0 0 1 8851 175 7 5 5 LRP2 2 169165951 Silent SNP A C3L-00144_T 1917157 169165951 73027578 269 4340 EVX2 0 . GRCh38 2 176083379 176083379 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.398C>A p.Ala133Asp p.A133D ENST00000308618 1/3 178 142 36 157 157 0 strelka-varscan-mutect EVX2,missense_variant,p.Ala133Asp,ENST00000308618,NM_001080458.1; T ENST00000308618 Transcript missense_variant 535/4203 398/1431 133/476 A/D gCc/gAc 1 -1 EVX2 HGNC HGNC:3507 protein_coding YES CCDS33333.1 ENSP00000312385 Q03828 UPI000012A2AF NM_001080458.1 tolerated(0.06) 1/3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 176083379 176083379 G T 1 0 0 0 0 1 0 0 0 5162 1203 42 2 2 EVX2 2 176083379 Missense_Mutation SNP G C3L-00144_T 6917428 176083379 66110150 270 4341 HOXD8 0 . GRCh38 2 176131324 176131324 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.585T>A p.= p.P195P ENST00000313173 2/2 82 67 15 70 70 0 strelka-varscan-mutect HOXD8,synonymous_variant,p.=,ENST00000313173,NM_019558.3;HOXD8,synonymous_variant,p.=,ENST00000429017,NM_001199747.1;HOXD8,synonymous_variant,p.=,ENST00000450510,NM_001199746.1;HOXD8,synonymous_variant,p.=,ENST00000544999,;HOXD-AS2,intron_variant,,ENST00000440016,;HOXD-AS2,downstream_gene_variant,,ENST00000426965,; A ENST00000313173 Transcript synonymous_variant 1212/1917 585/873 195/290 P ccT/ccA 1 1 HOXD8 HGNC HGNC:5139 protein_coding YES CCDS2268.1 ENSP00000315949 P13378 UPI000012CF8B NM_019558.3 2/2 Gene3D:1.10.10.60,PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF110,Low_complexity_(Seg):seg,Superfamily_domains:SSF46689 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 176131324 176131324 T A 1 0 0 0 0 0 0 0 1 7219 1567 55 4 4 HOXD8 2 176131324 Silent SNP T C3L-00144_T 47945 176131324 66062205 271 4342 RBM45 0 . GRCh38 2 178124196 178124196 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1138A>G p.Lys380Glu p.K380E ENST00000286070 8/10 156 129 27 138 138 0 strelka-varscan-mutect RBM45,missense_variant,p.Lys41Glu,ENST00000455903,;RBM45,missense_variant,p.Lys382Glu,ENST00000616198,;RBM45,missense_variant,p.Lys380Glu,ENST00000286070,NM_152945.2;RBM45,upstream_gene_variant,,ENST00000424099,;RBM45,upstream_gene_variant,,ENST00000464647,;RBM45,non_coding_transcript_exon_variant,,ENST00000424000,;RBM45,non_coding_transcript_exon_variant,,ENST00000493048,; G ENST00000286070 Transcript missense_variant 1230/1785 1138/1425 380/474 K/E Aaa/Gaa 1 1 RBM45 HGNC HGNC:24468 protein_coding YES CCDS33335.1 ENSP00000286070 Q8IUH3 UPI00001AEAD8 NM_152945.2 tolerated(0.1) 8/10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 178124196 178124196 A G 1 0 0 0 0 1 0 0 0 13305 15 1 5 5 RBM45 2 178124196 Missense_Mutation SNP A C3L-00144_T 1992872 178124196 64069333 272 4343 PLEKHA3 0 . GRCh38 2 178501117 178501117 + Missense_Mutation SNP G G T rs755002136 C3L-00144_T C3L-00144_N G G c.716G>T p.Arg239Leu p.R239L ENST00000234453 7/8 265 217 48 217 217 0 strelka-varscan-mutect PLEKHA3,missense_variant,p.Arg239Leu,ENST00000234453,NM_019091.3;PLEKHA3,missense_variant,p.Arg48Leu,ENST00000421187,; T ENST00000234453 Transcript missense_variant 1118/13880 716/903 239/300 R/L cGc/cTc rs755002136 1 1 PLEKHA3 HGNC HGNC:14338 protein_coding YES CCDS33336.1 ENSP00000234453 Q9HB20 UPI000000DA8A NM_019091.3 deleterious(0.01) 7/8 MODERATE 1 SNV 1 1 PASS rs755002136 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178501117 178501117 G T 1 0 0 0 0 1 0 0 0 12150 1087 38 1 1 PLEKHA3 2 178501117 Missense_Mutation SNP G C3L-00144_T 376921 178501117 63692412 273 4344 TTN 0 . GRCh38 2 178544052 178544052 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.96092C>A p.Ser32031Tyr p.S32031Y ENST00000589042 346/363 144 110 34 125 123 2 strelka-varscan-mutect TTN,missense_variant,p.Ser32031Tyr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser30390Tyr,ENST00000591111,;TTN,missense_variant,p.Ser30390Tyr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser29463Tyr,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ser22966Tyr,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ser23158Tyr,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ser23091Tyr,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,upstream_gene_variant,,ENST00000603415,;TTN-AS1,downstream_gene_variant,,ENST00000431259,;TTN-AS1,downstream_gene_variant,,ENST00000588804,;TTN-AS1,downstream_gene_variant,,ENST00000589434,;TTN-AS1,downstream_gene_variant,,ENST00000590040,;RP11-65L3.4,downstream_gene_variant,,ENST00000604692,; T ENST00000589042 Transcript missense_variant 96317/109224 96092/107976 32031/35991 S/Y tCc/tAc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 346/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178544052 178544052 G T 1 0 0 0 0 1 0 0 0 17245 1174 41 2 2 TTN 2 178544052 Missense_Mutation SNP G C3L-00144_T 42935 178544052 63649477 274 4345 TTN 0 . GRCh38 2 178552920 178552920 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.89980C>A p.Leu29994Ile p.L29994I ENST00000589042 335/363 296 256 40 258 257 1 strelka-varscan-mutect TTN,missense_variant,p.Leu29994Ile,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu28353Ile,ENST00000591111,;TTN,missense_variant,p.Leu28353Ile,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu27426Ile,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Leu20929Ile,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Leu21121Ile,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Leu21054Ile,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; T ENST00000589042 Transcript missense_variant 90205/109224 89980/107976 29994/35991 L/I Cta/Ata 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 335/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178552920 178552920 G T 1 0 0 0 0 1 0 0 0 17245 962 34 2 2 TTN 2 178552920 Missense_Mutation SNP G C3L-00144_T 8868 178552920 63640609 275 4346 TTN 0 . GRCh38 2 178552933 178552933 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.89967C>A p.Ser29989Arg p.S29989R ENST00000589042 335/363 310 270 40 250 250 0 strelka-varscan-mutect TTN,missense_variant,p.Ser29989Arg,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser28348Arg,ENST00000591111,;TTN,missense_variant,p.Ser28348Arg,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser27421Arg,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ser20924Arg,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ser21116Arg,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ser21049Arg,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; T ENST00000589042 Transcript missense_variant 90192/109224 89967/107976 29989/35991 S/R agC/agA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 335/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178552933 178552933 G T 1 0 0 0 0 1 0 0 0 17245 1310 46 2 2 TTN 2 178552933 Missense_Mutation SNP G C3L-00144_T 13 178552933 63640596 276 4347 TTN 0 . GRCh38 2 178612410 178612410 + Silent SNP G G C C3L-00144_T C3L-00144_N G G c.50115C>G p.= p.V16705V ENST00000589042 266/363 510 378 132 364 364 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;RP11-171I2.4,upstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000627527,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,; C ENST00000589042 Transcript synonymous_variant 50340/109224 50115/107976 16705/35991 V gtC/gtG COSM1482397,COSM1482398,COSM1482399,COSM1482400 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 266/363 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1,1 LOW 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 178612410 178612410 G C 1 0 0 0 0 0 0 0 1 17245 1277 45 4 4 TTN 2 178612410 Silent SNP G C3L-00144_T 59477 178612410 63581119 277 4348 TTN 0 . GRCh38 2 178652271 178652271 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.39204C>A p.= p.P13068P ENST00000589042 203/363 523 386 137 433 433 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN,upstream_gene_variant,,ENST00000446966,;TTN,upstream_gene_variant,,ENST00000426232,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript synonymous_variant 39429/109224 39204/107976 13068/35991 P ccC/ccA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 203/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 LOW 1 SNV 5 1 PASS rs748388695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 178652271 178652271 G T 1 0 0 0 0 0 0 0 1 17245 1335 47 2 2 TTN 2 178652271 Silent SNP G C3L-00144_T 39861 178652271 63541258 278 4349 TTN 0 . GRCh38 2 178672082 178672082 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.35116G>C p.Glu11706Gln p.E11706Q ENST00000589042 155/363 412 335 77 331 331 0 strelka-varscan-mutect TTN,missense_variant,p.Glu11706Gln,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Glu11332Gln,ENST00000591111,;TTN,missense_variant,p.Glu11332Gln,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Glu10405Gln,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Glu67Gln,ENST00000448510,;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN,upstream_gene_variant,,ENST00000425332,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; G ENST00000589042 Transcript missense_variant 35341/109224 35116/107976 11706/35991 E/Q Gaa/Caa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 155/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 178672082 178672082 C G 1 0 0 0 0 1 0 0 0 17245 922 32 4 4 TTN 2 178672082 Missense_Mutation SNP C C3L-00144_T 19811 178672082 63521447 279 4350 TTN 0 . GRCh38 2 178709625 178709625 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.28694C>A p.Thr9565Lys p.T9565K ENST00000589042 99/363 209 158 51 125 125 0 strelka-varscan-mutect TTN,missense_variant,p.Thr9565Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Thr9248Lys,ENST00000591111,;TTN,missense_variant,p.Thr9248Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Thr8321Lys,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 28919/109224 28694/107976 9565/35991 T/K aCa/aAa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 99/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1423863240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178709625 178709625 G T 1 0 0 0 0 1 0 0 0 17245 1377 48 2 2 TTN 2 178709625 Missense_Mutation SNP G C3L-00144_T 37543 178709625 63483904 280 4351 TTN 0 . GRCh38 2 178709772 178709772 + Missense_Mutation SNP C C A rs374156904 C3L-00144_T C3L-00144_N C C c.28547G>T p.Arg9516Leu p.R9516L ENST00000589042 99/363 288 243 45 192 192 0 strelka-varscan-mutect TTN,missense_variant,p.Arg9516Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Arg9199Leu,ENST00000591111,;TTN,missense_variant,p.Arg9199Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Arg8272Leu,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; A ENST00000589042 Transcript missense_variant 28772/109224 28547/107976 9516/35991 R/L cGt/cTt rs374156904 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 99/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 not_provided,likely_benign MODERATE 1 SNV 5 1 1 PASS rs374156904 . 0 208 0 0 0 0 0 2 -3.510754 0 0 1 0 0 A 3 1 12 178709772 178709772 C A 1 0 0 0 0 1 0 0 0 17245 536 19 1 1 TTN 2 178709772 Missense_Mutation SNP C C3L-00144_T 147 178709772 63483757 281 4352 TTN 0 . GRCh38 2 178719237 178719237 + Missense_Mutation SNP G G T rs368438797 C3L-00144_T C3L-00144_N G G c.24153C>A p.Asp8051Glu p.D8051E ENST00000589042 83/363 203 159 44 119 119 0 strelka-varscan-mutect TTN,missense_variant,p.Asp8051Glu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Asp7734Glu,ENST00000591111,;TTN,missense_variant,p.Asp7734Glu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Asp6807Glu,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,;TTN-AS1,downstream_gene_variant,,ENST00000431752,; T ENST00000589042 Transcript missense_variant 24378/109224 24153/107976 8051/35991 D/E gaC/gaA rs368438797 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 83/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs368438797 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178719237 178719237 G T 1 0 0 0 0 1 0 0 0 17245 1368 48 2 2 TTN 2 178719237 Missense_Mutation SNP G C3L-00144_T 9465 178719237 63474292 282 4353 TTN 0 . GRCh38 2 178719408 178719408 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.23982G>T p.= p.V7994V ENST00000589042 83/363 107 78 29 104 104 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,; A ENST00000589042 Transcript synonymous_variant 24207/109224 23982/107976 7994/35991 V gtG/gtT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 83/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 178719408 178719408 C A 1 0 0 0 0 0 0 0 1 17245 813 29 2 2 TTN 2 178719408 Silent SNP C C3L-00144_T 171 178719408 63474121 283 4354 TTN 0 . GRCh38 2 178727782 178727782 + Frame_Shift_Del DEL C C - C3L-00144_T C3L-00144_N C C c.19796delG p.Gly6599GlufsTer7 p.G6599Efs*7 ENST00000589042 68/363 113 93 20 91 91 0 sindel-varindel-pindel TTN,frameshift_variant,p.Gly6599GlufsTer7,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Gly6282GlufsTer7,ENST00000591111,;TTN,frameshift_variant,p.Gly6282GlufsTer7,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Gly5355GlufsTer7,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,; - ENST00000589042 Transcript frameshift_variant 20021/109224 19796/107976 6599/35991 G/X gGa/ga COSM5395467,COSM5395468 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 68/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 HIGH 1 deletion 5 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 178727782 178727782 C - 1 0 1 0 1 0 0 0 0 17245 855 30 0 0 TTN 2 178727782 Frame_Shift_Del DEL C C3L-00144_T 8374 178727782 63465747 284 4355 TTN 0 . GRCh38 2 178732446 178732446 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.16615G>T p.Val5539Leu p.V5539L ENST00000589042 56/363 71 57 14 71 71 0 strelka-varscan-mutect TTN,missense_variant,p.Val5539Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Val5222Leu,ENST00000591111,;TTN,missense_variant,p.Val5222Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Val4295Leu,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,upstream_gene_variant,,ENST00000582847,;TTN-AS1,upstream_gene_variant,,ENST00000627661,; A ENST00000589042 Transcript missense_variant 16840/109224 16615/107976 5539/35991 V/L Gta/Tta 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 56/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999964 1 1 1 0 A 3 1 12 178732446 178732446 C A 1 0 0 0 0 1 0 0 0 17245 478 17 2 2 TTN 2 178732446 Missense_Mutation SNP C C3L-00144_T 4664 178732446 63461083 285 4356 TTN 0 . GRCh38 2 178758983 178758983 + Splice_Site SNP C C T novel C3L-00144_T C3L-00144_N C C c.10303+1G>A p.X3435_splice ENST00000589042 341 270 71 292 292 0 strelka-varscan-mutect TTN,splice_donor_variant,,ENST00000589042,NM_001267550.2;TTN,splice_donor_variant,,ENST00000591111,;TTN,splice_donor_variant,,ENST00000615779,NM_001256850.1;TTN,splice_donor_variant,,ENST00000342992,NM_133378.4;TTN,splice_donor_variant,,ENST00000460472,NM_003319.4;TTN,splice_donor_variant,,ENST00000342175,NM_133437.4;TTN,splice_donor_variant,,ENST00000359218,NM_133432.3;TTN,splice_donor_variant,,ENST00000360870,NM_133379.4;TTN,splice_donor_variant,,ENST00000634225,;TTN-AS1,splice_region_variant,,ENST00000627661,;TTN-AS1,splice_region_variant,,ENST00000578746,;TTN-AS1,splice_region_variant,,ENST00000590773,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000610005,;TTN-AS1,intron_variant,,ENST00000585451,; T ENST00000589042 Transcript splice_donor_variant -/109224 10303/107976 3435/35991 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 44/362 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 178758983 178758983 C T 1 0 0 0 0 0 0 1 0 17245 521 18 3 3 TTN 2 178758983 Splice_Site SNP C C3L-00144_T 26537 178758983 63434546 286 4357 TTN 0 . GRCh38 2 178769747 178769747 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.8834C>A p.Thr2945Lys p.T2945K ENST00000589042 37/363 366 293 73 254 254 0 strelka-varscan-mutect TTN,missense_variant,p.Thr2945Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Thr2945Lys,ENST00000591111,;TTN,missense_variant,p.Thr2945Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Thr2945Lys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Thr2899Lys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Thr2899Lys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Thr2899Lys,ENST00000359218,NM_133432.3;TTN,missense_variant,p.Thr2945Lys,ENST00000360870,NM_133379.4;TTN,upstream_gene_variant,,ENST00000634225,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000610005,;TTN-AS1,upstream_gene_variant,,ENST00000584485,;TTN-AS1,upstream_gene_variant,,ENST00000629094,; T ENST00000589042 Transcript missense_variant 9059/109224 8834/107976 2945/35991 T/K aCa/aAa COSM5694197,COSM5694198,COSM5694199,COSM5694200,COSM5694202 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 37/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 178769747 178769747 G T 1 0 0 0 0 1 0 0 0 17245 1377 48 2 2 TTN 2 178769747 Missense_Mutation SNP G C3L-00144_T 10764 178769747 63423782 287 4358 ITGA4 0 . GRCh38 2 181475834 181475834 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.571T>G p.Tyr191Asp p.Y191D ENST00000339307 5/5 189 159 30 140 140 0 strelka-varscan-mutect ITGA4,missense_variant,p.Tyr191Asp,ENST00000339307,;ITGA4,intron_variant,,ENST00000397033,NM_000885.4;ITGA4,intron_variant,,ENST00000233573,;ITGA4,intron_variant,,ENST00000478440,;ITGA4,intron_variant,,ENST00000465522,;ITGA4,downstream_gene_variant,,ENST00000484404,; G ENST00000339307 Transcript missense_variant 1019/1403 571/588 191/195 Y/D Tac/Gac 1 1 ITGA4 HGNC HGNC:6140 protein_coding ENSP00000340149 P13612 UPI00001B5D25 deleterious(0) 5/5 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 181475834 181475834 T G 1 0 0 0 0 1 0 0 0 7785 1638 57 5 5 ITGA4 2 181475834 Missense_Mutation SNP T C3L-00144_T 2706087 181475834 60717695 288 4359 FSIP2 0 . GRCh38 2 185743218 185743218 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.578A>T p.His193Leu p.H193L ENST00000343098 3/23 168 140 28 119 117 2 strelka-varscan-mutect FSIP2,missense_variant,p.His193Leu,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.His104Leu,ENST00000424728,;AC007966.1,upstream_gene_variant,,ENST00000421998,;AC007966.1,upstream_gene_variant,,ENST00000427269,;AC007966.1,upstream_gene_variant,,ENST00000437717,;FSIP2,non_coding_transcript_exon_variant,,ENST00000465275,;FSIP2,non_coding_transcript_exon_variant,,ENST00000469367,;FSIP2,upstream_gene_variant,,ENST00000429412,; T ENST00000343098 Transcript missense_variant 578/21054 578/20991 193/6996 H/L cAt/cTt 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 3/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 185743218 185743218 A T 1 0 0 0 0 1 0 0 0 5949 217 8 4 4 FSIP2 2 185743218 Missense_Mutation SNP A C3L-00144_T 4267384 185743218 56450311 289 4360 FSIP2 0 . GRCh38 2 185756249 185756249 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1316G>T p.Gly439Val p.G439V ENST00000343098 9/23 72 61 11 95 95 0 strelka-varscan-mutect FSIP2,missense_variant,p.Gly439Val,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Gly350Val,ENST00000424728,;FSIP2,intron_variant,,ENST00000429412,; T ENST00000343098 Transcript missense_variant 1316/21054 1316/20991 439/6996 G/V gGa/gTa 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0.01) 9/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE 1 SNV 5 1 PASS . . 3 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 185756249 185756249 G T 1 0 0 0 0 1 0 0 0 5949 1174 41 2 2 FSIP2 2 185756249 Missense_Mutation SNP G C3L-00144_T 13031 185756249 56437280 290 4361 FSIP2 0 . GRCh38 2 185788726 185788726 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1857C>A p.= p.A619A ENST00000343098 16/23 103 83 20 80 80 0 strelka-varscan-mutect FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,; A ENST00000343098 Transcript synonymous_variant 1857/21054 1857/20991 619/6996 A gcC/gcA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 185788726 185788726 C A 1 0 0 0 0 0 0 0 1 5949 581 21 2 2 FSIP2 2 185788726 Silent SNP C C3L-00144_T 32477 185788726 56404803 291 4362 FSIP2 0 . GRCh38 2 185792897 185792897 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.6028G>T p.Val2010Leu p.V2010L ENST00000343098 16/23 106 88 18 93 93 0 strelka-varscan-mutect FSIP2,missense_variant,p.Val2010Leu,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Val1921Leu,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,; T ENST00000343098 Transcript missense_variant 6028/21054 6028/20991 2010/6996 V/L Gta/Tta 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 185792897 185792897 G T 1 0 0 0 0 1 0 0 0 5949 1377 48 2 2 FSIP2 2 185792897 Missense_Mutation SNP G C3L-00144_T 4171 185792897 56400632 292 4363 FSIP2 0 . GRCh38 2 185804511 185804511 + Nonsense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.15472C>T p.Gln5158Ter p.Q5158* ENST00000343098 17/23 77 69 8 73 73 0 strelka-varscan-mutect FSIP2,stop_gained,p.Gln5158Ter,ENST00000343098,NM_173651.2;FSIP2,stop_gained,p.Gln5069Ter,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; T ENST00000343098 Transcript stop_gained 15472/21054 15472/20991 5158/6996 Q/* Caa/Taa 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 17/23 Pfam_domain:PF15783,Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 HIGH SNV 5 1 PASS . . 1 197 11 0 0 0 0 0 -17.04638 0.9999106 1 1 1 0 T 4 4 12 185804511 185804511 C T 1 0 0 0 0 0 1 0 0 5949 827 29 3 3 FSIP2 2 185804511 Nonsense_Mutation SNP C C3L-00144_T 11614 185804511 56389018 293 4364 FSIP2 0 . GRCh38 2 185806945 185806945 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.17906C>A p.Ser5969Tyr p.S5969Y ENST00000343098 17/23 146 114 32 153 153 0 strelka-varscan-mutect FSIP2,missense_variant,p.Ser5969Tyr,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Ser5880Tyr,ENST00000424728,;FSIP2,missense_variant,p.Ser87Tyr,ENST00000611759,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 17906/21054 17906/20991 5969/6996 S/Y tCc/tAc 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 tolerated(0.11) 17/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 185806945 185806945 C A 1 0 0 0 0 1 0 0 0 5949 855 30 2 2 FSIP2 2 185806945 Missense_Mutation SNP C C3L-00144_T 2434 185806945 56386584 294 4365 COL3A1 0 . GRCh38 2 188997701 188997701 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1871G>T p.Gly624Val p.G624V ENST00000304636 27/51 274 219 55 269 268 1 strelka-varscan-mutect COL3A1,missense_variant,p.Gly624Val,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Gly624Val,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000450867,;COL3A1,downstream_gene_variant,,ENST00000637672,; T ENST00000304636 Transcript missense_variant,splice_region_variant 2041/5543 1871/4401 624/1466 G/V gGg/gTg 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0) 27/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 188997701 188997701 G T 1 0 0 0 0 1 0 0 0 3477 1246 43 2 2 COL3A1 2 188997701 Missense_Mutation SNP G C3L-00144_T 3190756 188997701 53195828 295 4366 SLC40A1 0 . GRCh38 2 189561928 189561928 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1666G>T p.Asp556Tyr p.D556Y ENST00000261024 8/8 319 264 55 222 221 1 strelka-varscan-mutect SLC40A1,missense_variant,p.Asp556Tyr,ENST00000261024,NM_014585.5;SLC40A1,downstream_gene_variant,,ENST00000427241,; A ENST00000261024 Transcript missense_variant 2093/3442 1666/1716 556/571 D/Y Gat/Tat 1 -1 SLC40A1 HGNC HGNC:10909 protein_coding YES CCDS2299.1 ENSP00000261024 Q9NP59 UPI0000034CC2 NM_014585.5 deleterious_low_confidence(0.02) 8/8 hmmpanther:PTHR11660,hmmpanther:PTHR11660:SF47 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 189561928 189561928 C A 1 0 0 0 0 1 0 0 0 14906 826 29 2 2 SLC40A1 2 189561928 Missense_Mutation SNP C C3L-00144_T 564227 189561928 52631601 296 4367 DNAH7 0 . GRCh38 2 195910149 195910149 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3982G>T p.Gly1328Cys p.G1328C ENST00000312428 25/65 212 155 57 181 181 0 strelka-varscan-mutect DNAH7,missense_variant,p.Gly1328Cys,ENST00000312428,NM_018897.2;DNAH7,upstream_gene_variant,,ENST00000475293,; A ENST00000312428 Transcript missense_variant 4083/12394 3982/12075 1328/4024 G/C Ggt/Tgt 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0) 25/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12774,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 195910149 195910149 C A 1 0 0 0 0 1 0 0 0 4421 623 22 2 2 DNAH7 2 195910149 Missense_Mutation SNP C C3L-00144_T 6348221 195910149 46283380 297 4368 DNAH7 0 . GRCh38 2 196012872 196012872 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.904A>T p.Asn302Tyr p.N302Y ENST00000312428 10/65 123 99 24 116 116 0 strelka-varscan-mutect DNAH7,missense_variant,p.Asn302Tyr,ENST00000312428,NM_018897.2;DNAH7,missense_variant,p.Asn302Tyr,ENST00000410072,; A ENST00000312428 Transcript missense_variant 1005/12394 904/12075 302/4024 N/Y Aat/Tat 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.02) 10/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 196012872 196012872 T A 1 0 0 0 0 1 0 0 0 4421 1754 61 4 4 DNAH7 2 196012872 Missense_Mutation SNP T C3L-00144_T 102723 196012872 46180657 298 4369 SF3B1 0 . GRCh38 2 197398117 197398117 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.3135-1G>T p.X1045_splice ENST00000335508 176 148 28 114 114 0 strelka-varscan-mutect SF3B1,splice_acceptor_variant,,ENST00000335508,NM_012433.2;SF3B1,splice_acceptor_variant,,ENST00000424674,;SF3B1,downstream_gene_variant,,ENST00000462613,;SF3B1,splice_acceptor_variant,,ENST00000496458,;SF3B1,upstream_gene_variant,,ENST00000479532,; A ENST00000335508 Transcript splice_acceptor_variant -/6526 3135/3915 1045/1304 1 -1 SF3B1 HGNC HGNC:10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 UPI000013D493 NM_012433.2 21/24 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 197398117 197398117 C A 1 0 0 0 0 0 0 1 0 14428 695 24 2 2 SF3B1 2 197398117 Splice_Site SNP C C3L-00144_T 1385245 197398117 44795412 299 4370 PLCL1 0 . GRCh38 2 198084007 198084007 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.490A>G p.Lys164Glu p.K164E ENST00000428675 2/6 293 238 55 225 225 0 strelka-varscan-mutect PLCL1,missense_variant,p.Lys87Glu,ENST00000437704,;PLCL1,missense_variant,p.Lys164Glu,ENST00000428675,NM_006226.3;PLCL1,missense_variant,p.Lys90Glu,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; G ENST00000428675 Transcript missense_variant 888/5125 490/3288 164/1095 K/E Aaa/Gaa 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 deleterious(0) 2/6 PROSITE_profiles:PS50003,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF16457,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 198084007 198084007 A G 1 0 0 0 0 1 0 0 0 12133 15 1 5 5 PLCL1 2 198084007 Missense_Mutation SNP A C3L-00144_T 685890 198084007 44109522 300 4371 AOX1 0 . GRCh38 2 200615974 200615974 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1615C>A p.Pro539Thr p.P539T ENST00000374700 16/35 120 94 26 63 63 0 varscan-mutect AOX1,missense_variant,p.Pro539Thr,ENST00000374700,NM_001159.3;AOX1,non_coding_transcript_exon_variant,,ENST00000485106,;AOX1,non_coding_transcript_exon_variant,,ENST00000465297,;AOX1,downstream_gene_variant,,ENST00000485965,; A ENST00000374700 Transcript missense_variant 1856/5074 1615/4017 539/1338 P/T Cca/Aca 1 1 AOX1 HGNC HGNC:553 protein_coding YES CCDS33360.1 ENSP00000363832 Q06278 UPI0000071863 NM_001159.3 tolerated(0.12) 16/35 hmmpanther:PTHR11908:SF86,hmmpanther:PTHR11908,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02969 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 200615974 200615974 C A 1 0 0 0 0 1 0 0 0 839 869 30 2 2 AOX1 2 200615974 Missense_Mutation SNP C C3L-00144_T 2531967 200615974 41577555 301 4372 AOX1 0 . GRCh38 2 200669632 200669632 + Missense_Mutation SNP G G C rs371463224 C3L-00144_T C3L-00144_N G G c.3856G>C p.Ala1286Pro p.A1286P ENST00000374700 34/35 235 175 60 172 172 0 strelka-varscan-mutect AOX1,missense_variant,p.Ala1286Pro,ENST00000374700,NM_001159.3;AOX1,missense_variant,p.Ala126Pro,ENST00000439380,;AOX1,missense_variant,p.Ala150Pro,ENST00000260930,;AOX1,non_coding_transcript_exon_variant,,ENST00000485106,;AOX1,non_coding_transcript_exon_variant,,ENST00000465297,; C ENST00000374700 Transcript missense_variant 4097/5074 3856/4017 1286/1338 A/P Gca/Cca rs371463224 1 1 AOX1 HGNC HGNC:553 protein_coding YES CCDS33360.1 ENSP00000363832 Q06278 UPI0000071863 NM_001159.3 deleterious(0) 34/35 hmmpanther:PTHR11908:SF86,hmmpanther:PTHR11908,Gene3D:3.30.365.10,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02969,Superfamily_domains:SSF56003 MODERATE 1 SNV 1 1 PASS rs371463224 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 200669632 200669632 G C 1 0 0 0 0 1 0 0 0 839 1087 38 4 4 AOX1 2 200669632 Missense_Mutation SNP G C3L-00144_T 53658 200669632 41523897 302 4373 BMPR2 0 . GRCh38 2 202556092 202556092 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2427G>T p.= p.V809V ENST00000374580 12/13 302 247 55 250 250 0 strelka-varscan-mutect BMPR2,synonymous_variant,p.=,ENST00000374580,NM_001204.6;BMPR2,intron_variant,,ENST00000374574,; T ENST00000374580 Transcript synonymous_variant 2966/11461 2427/3117 809/1038 V gtG/gtT 1 1 BMPR2 HGNC HGNC:1078 protein_coding YES CCDS33361.1 ENSP00000363708 Q13873 UPI0000126A3B NM_001204.6 12/13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 202556092 202556092 G T 1 0 0 0 0 0 0 0 1 1626 1335 47 2 2 BMPR2 2 202556092 Silent SNP G C3L-00144_T 1886460 202556092 39637437 303 4374 KLF7 0 . GRCh38 2 207124070 207124070 + Missense_Mutation SNP C C A rs747043061 C3L-00144_T C3L-00144_N C C c.437G>T p.Arg146Leu p.R146L ENST00000309446 2/4 389 236 153 307 307 0 strelka-varscan-mutect KLF7,missense_variant,p.Arg146Leu,ENST00000309446,NM_003709.3;KLF7,missense_variant,p.Arg118Leu,ENST00000412414,NM_001270944.1;KLF7,missense_variant,p.Arg113Leu,ENST00000421199,NM_001270943.1;KLF7,missense_variant,p.Arg146Leu,ENST00000423015,NM_001270942.1;KLF7,missense_variant,p.Arg118Leu,ENST00000435602,;KLF7,intron_variant,,ENST00000458272,;KLF7,downstream_gene_variant,,ENST00000426163,;KLF7,downstream_gene_variant,,ENST00000457962,;KLF7-IT1,upstream_gene_variant,,ENST00000428777,;KLF7,intron_variant,,ENST00000467833,;KLF7,downstream_gene_variant,,ENST00000451244,; A ENST00000309446 Transcript missense_variant 814/8362 437/909 146/302 R/L cGc/cTc rs747043061 1 -1 KLF7 HGNC HGNC:6350 protein_coding YES CCDS2373.1 ENSP00000309570 O75840 A0A024R3X8 UPI0000042958 NM_003709.3 deleterious(0.03) 2/4 MODERATE 1 SNV 1 1 PASS rs747043061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 207124070 207124070 C A 1 0 0 0 0 1 0 0 0 8216 768 27 1 1 KLF7 2 207124070 Missense_Mutation SNP C C3L-00144_T 4567978 207124070 35069459 304 4375 MAP2 0 . GRCh38 2 209695552 209695552 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.3382G>C p.Glu1128Gln p.E1128Q ENST00000360351 7/15 83 41 42 74 74 0 strelka-varscan-mutect MAP2,missense_variant,p.Glu1128Gln,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Glu1124Gln,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; C ENST00000360351 Transcript missense_variant 3888/9711 3382/5484 1128/1827 E/Q Gag/Cag 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0) 7/15 Low_complexity_(Seg):seg,hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 209695552 209695552 G C 1 0 0 0 0 1 0 0 0 9157 1175 41 4 4 MAP2 2 209695552 Missense_Mutation SNP G C3L-00144_T 2571482 209695552 32497977 305 4376 MAP2 0 . GRCh38 2 209697040 209697040 + Frame_Shift_Del DEL G G - rs149033530 C3L-00144_T C3L-00144_N G G c.4512delG p.Thr1506ProfsTer26 p.T1506Pfs*26 ENST00000360351 9/15 101 87 14 92 92 0 sindel-pindel MAP2,frameshift_variant,p.Thr1506ProfsTer26,ENST00000360351,NM_002374.3;MAP2,frameshift_variant,p.Thr1502ProfsTer26,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000475600,;MAP2,intron_variant,,ENST00000471619,;MAP2,downstream_gene_variant,,ENST00000482864,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; - ENST00000360351 Transcript frameshift_variant 5017/9711 4511/5484 1504/1827 R/X cGg/cg rs149033530 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 9/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 HIGH 1 deletion 5 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.99998 1 1 1 0 - 7 5 12 209697040 209697040 G - 1 0 1 0 1 0 0 0 0 9157 1116 39 0 0 MAP2 2 209697040 Frame_Shift_Del DEL G C3L-00144_T 1488 209697040 32496489 306 4377 UNC80 0 . GRCh38 2 209918541 209918541 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.5023C>G p.Pro1675Ala p.P1675A ENST00000439458 32/64 112 67 45 80 80 0 strelka-varscan-mutect UNC80,missense_variant,p.Pro1675Ala,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Pro1670Ala,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; G ENST00000439458 Transcript missense_variant 5103/13562 5023/9777 1675/3258 P/A Ccc/Gcc 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0.01) 32/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 209918541 209918541 C G 1 0 0 0 0 1 0 0 0 17521 855 30 4 4 UNC80 2 209918541 Missense_Mutation SNP C C3L-00144_T 221501 209918541 32274988 307 4378 UNC80 0 . GRCh38 2 209926987 209926987 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.5608+1G>T p.X1870_splice ENST00000439458 111 84 27 111 111 0 strelka-varscan-mutect UNC80,splice_donor_variant,,ENST00000439458,NM_032504.1;UNC80,splice_donor_variant,,ENST00000272845,NM_182587.3;UNC80,splice_donor_variant,,ENST00000489023,; T ENST00000439458 Transcript splice_donor_variant -/13562 5608/9777 1870/3258 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 35/63 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 209926987 209926987 G T 1 0 0 0 0 0 0 1 0 17521 1275 44 2 2 UNC80 2 209926987 Splice_Site SNP G C3L-00144_T 8446 209926987 32266542 308 4379 UNC80 0 . GRCh38 2 209978699 209978699 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.8911G>T p.Asp2971Tyr p.D2971Y ENST00000439458 58/64 81 67 14 81 81 0 strelka-varscan-mutect UNC80,missense_variant,p.Asp2971Tyr,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Asp2966Tyr,ENST00000272845,NM_182587.3;UNC80,missense_variant,p.Asp497Tyr,ENST00000333907,;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,; T ENST00000439458 Transcript missense_variant 8991/13562 8911/9777 2971/3258 D/Y Gat/Tat 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious_low_confidence(0) 58/64 hmmpanther:PTHR31781:SF1,hmmpanther:PTHR31781 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 209978699 209978699 G T 1 0 0 0 0 1 0 0 0 17521 942 33 2 2 UNC80 2 209978699 Missense_Mutation SNP G C3L-00144_T 51712 209978699 32214830 309 4380 KANSL1L 0 . GRCh38 2 210153571 210153571 + Missense_Mutation SNP C C A rs762421124 C3L-00144_T C3L-00144_N C C c.1012G>T p.Gly338Cys p.G338C ENST00000281772 2/15 300 258 42 255 252 3 strelka-varscan-mutect KANSL1L,missense_variant,p.Gly338Cys,ENST00000281772,NM_152519.2;KANSL1L,missense_variant,p.Gly338Cys,ENST00000418791,NM_001307976.1;KANSL1L,missense_variant,p.Gly338Cys,ENST00000452086,;KANSL1L,missense_variant,p.Gly338Cys,ENST00000457374,;KANSL1L,missense_variant,p.Gly33Cys,ENST00000428655,;KANSL1L,missense_variant,p.Gly12Cys,ENST00000438563,;KANSL1L,missense_variant,p.Gly57Cys,ENST00000415553,;KANSL1L,downstream_gene_variant,,ENST00000429908,;KANSL1L,non_coding_transcript_exon_variant,,ENST00000453904,; A ENST00000281772 Transcript missense_variant 1276/4754 1012/2964 338/987 G/C Ggt/Tgt rs762421124,COSM3668925 1 -1 KANSL1L HGNC HGNC:26310 protein_coding YES CCDS33370.1 ENSP00000281772 A0AUZ9 UPI00002094A9 NM_152519.2 deleterious(0.01) 2/15 hmmpanther:PTHR22443:SF16,hmmpanther:PTHR22443 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs762421124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 210153571 210153571 C A 1 0 0 0 0 1 0 0 0 7890 623 22 2 2 KANSL1L 2 210153571 Missense_Mutation SNP C C3L-00144_T 174872 210153571 32039958 310 4381 ABCA12 0 . GRCh38 2 214986677 214986677 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.4028C>T p.Thr1343Ile p.T1343I ENST00000272895 28/53 413 363 50 367 367 0 strelka-varscan-mutect ABCA12,missense_variant,p.Thr1343Ile,ENST00000272895,NM_173076.2;ABCA12,missense_variant,p.Thr1025Ile,ENST00000389661,NM_015657.3; A ENST00000272895 Transcript missense_variant 4248/9100 4028/7788 1343/2595 T/I aCa/aTa 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 tolerated(0.05) 28/53 Gene3D:3.40.50.300,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF29,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 214986677 214986677 G A 1 0 0 0 0 1 0 0 0 34 1377 48 3 3 ABCA12 2 214986677 Missense_Mutation SNP G C3L-00144_T 4833106 214986677 27206852 311 4382 XRCC5 0 . GRCh38 2 216119115 216119115 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.441G>C p.= p.L147L ENST00000392133 7/23 281 244 37 179 179 0 strelka-varscan-mutect XRCC5,synonymous_variant,p.=,ENST00000392133,;XRCC5,synonymous_variant,p.=,ENST00000392132,NM_021141.3;XRCC5,downstream_gene_variant,,ENST00000417391,;XRCC5,non_coding_transcript_exon_variant,,ENST00000429133,;XRCC5,3_prime_UTR_variant,,ENST00000451695,;XRCC5,non_coding_transcript_exon_variant,,ENST00000460284,;XRCC5,downstream_gene_variant,,ENST00000476360,; C ENST00000392133 Transcript synonymous_variant 902/3761 441/2199 147/732 L ctG/ctC 1 1 XRCC5 HGNC HGNC:12833 protein_coding YES CCDS2402.1 ENSP00000375978 P13010 UPI0000034133 7/23 hmmpanther:PTHR12604:SF4,hmmpanther:PTHR12604,Pfam_domain:PF03731,PIRSF_domain:PIRSF016570,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 12 216119115 216119115 G C 1 0 0 0 0 0 0 0 1 18015 1335 47 4 4 XRCC5 2 216119115 Silent SNP G C3L-00144_T 1132438 216119115 26074414 312 4383 MARCH4 0 . GRCh38 2 216370008 216370008 + Missense_Mutation SNP C C A rs756413699 C3L-00144_T C3L-00144_N C C c.253G>T p.Gly85Trp p.G85W ENST00000273067 1/4 92 55 37 67 67 0 strelka-varscan-mutect MARCH4,missense_variant,p.Gly85Trp,ENST00000273067,NM_020814.2; A ENST00000273067 Transcript missense_variant 2020/4447 253/1233 85/410 G/W Ggg/Tgg rs756413699 1 -1 MARCH4 HGNC HGNC:29269 protein_coding YES CCDS33376.1 ENSP00000273067 Q9P2E8 UPI00001C1DB9 NM_020814.2 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF51,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs756413699 . 0 198 11 0 0 0 0 0 -20 0.9999939 1 1 1 0 A 3 1 12 216370008 216370008 C A 1 0 0 0 0 1 0 0 0 9228 652 23 1 1 MARCH4 2 216370008 Missense_Mutation SNP C C3L-00144_T 250893 216370008 25823521 313 4384 PRKAG3 0 . GRCh38 2 218827286 218827286 + Missense_Mutation SNP G G C rs748055391 C3L-00144_T C3L-00144_N G G c.963C>G p.Ile321Met p.I321M ENST00000439262 9/14 564 336 228 426 426 0 strelka-varscan-mutect PRKAG3,missense_variant,p.Ile321Met,ENST00000439262,NM_017431.2;PRKAG3,missense_variant,p.Ile321Met,ENST00000529249,;PRKAG3,downstream_gene_variant,,ENST00000430489,;MIR9500,downstream_gene_variant,,ENST00000635985,;PRKAG3,missense_variant,p.Ile321Met,ENST00000233944,;PRKAG3,missense_variant,p.Ser306Cys,ENST00000470307,;PRKAG3,non_coding_transcript_exon_variant,,ENST00000490971,; C ENST00000439262 Transcript missense_variant 984/2301 963/1470 321/489 I/M atC/atG rs748055391 1 -1 PRKAG3 HGNC HGNC:9387 protein_coding YES CCDS2424.1 ENSP00000397133 Q9UGI9 A0A024R426 UPI0000043D98 NM_017431.2 deleterious(0.03) 9/14 PROSITE_profiles:PS51371,hmmpanther:PTHR13780:SF31,hmmpanther:PTHR13780,Gene3D:3.10.580.10,Pfam_domain:PF00571,SMART_domains:SM00116,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS rs748055391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 218827286 218827286 G C 1 0 0 0 0 1 0 0 0 12635 1164 41 4 4 PRKAG3 2 218827286 Missense_Mutation SNP G C3L-00144_T 2457278 218827286 23366243 314 4385 PTPRN 0 . GRCh38 2 219300027 219300027 + Missense_Mutation SNP C C A rs139530025 C3L-00144_T C3L-00144_N C C c.1394G>T p.Arg465Leu p.R465L ENST00000295718 9/23 294 225 69 216 216 0 strelka-varscan-mutect PTPRN,missense_variant,p.Arg465Leu,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Arg465Leu,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Arg375Leu,ENST00000423636,NM_001199764.1;PTPRN,upstream_gene_variant,,ENST00000443981,;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,upstream_gene_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,; A ENST00000295718 Transcript missense_variant 1635/3784 1394/2940 465/979 R/L cGc/cTc rs139530025 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 deleterious(0.02) 9/23 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2 MODERATE 1 SNV 1 1 PASS rs139530025 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 219300027 219300027 C A 1 0 0 0 0 1 0 0 0 12961 768 27 1 1 PTPRN 2 219300027 Missense_Mutation SNP C C3L-00144_T 472741 219300027 22893502 315 4386 SPEG 0 . GRCh38 2 219477963 219477963 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.4885G>T p.Ala1629Ser p.A1629S ENST00000312358 22/41 368 272 96 253 253 0 strelka-varscan-mutect SPEG,missense_variant,p.Ala1629Ser,ENST00000312358,NM_005876.4;AC053503.11,downstream_gene_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,downstream_gene_variant,,ENST00000485069,; T ENST00000312358 Transcript missense_variant 5017/10782 4885/9804 1629/3267 A/S Gcc/Tcc COSM1752371 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 22/41 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 219477963 219477963 G T 1 0 0 0 0 1 0 0 0 15387 1203 42 2 2 SPEG 2 219477963 Missense_Mutation SNP G C3L-00144_T 177936 219477963 22715566 316 4387 ASIC4 0 . GRCh38 2 219514903 219514903 + Missense_Mutation SNP C C A rs752696438 C3L-00144_T C3L-00144_N C C c.560C>A p.Pro187Gln p.P187Q ENST00000347842 1/9 260 157 103 183 183 0 strelka-varscan-mutect ASIC4,missense_variant,p.Pro187Gln,ENST00000358078,;ASIC4,missense_variant,p.Pro187Gln,ENST00000347842,NM_182847.2;AC053503.11,intron_variant,,ENST00000429882,;ASIC4,upstream_gene_variant,,ENST00000473709,;ASIC4,non_coding_transcript_exon_variant,,ENST00000461395,;ASIC4,upstream_gene_variant,,ENST00000474489,; A ENST00000347842 Transcript missense_variant 574/2684 560/1944 187/647 P/Q cCa/cAa rs752696438 1 1 ASIC4 HGNC HGNC:21263 protein_coding YES CCDS2442.1 ENSP00000326627 Q96FT7 UPI0000456EFC NM_182847.2 tolerated(0.17) 1/9 Pfam_domain:PF00858,hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF13 MODERATE 1 SNV 1 1 PASS rs752696438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 219514903 219514903 C A 1 0 0 0 0 1 0 0 0 1188 594 21 2 2 ASIC4 2 219514903 Missense_Mutation SNP C C3L-00144_T 36940 219514903 22678626 317 4388 PAX3 0 . GRCh38 2 222297030 222297030 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.269A>T p.Tyr90Phe p.Y90F ENST00000392069 2/10 514 288 226 432 432 0 strelka-varscan-mutect PAX3,missense_variant,p.Tyr90Phe,ENST00000350526,NM_181457.3;PAX3,missense_variant,p.Tyr90Phe,ENST00000392069,NM_181459.3;PAX3,missense_variant,p.Tyr90Phe,ENST00000344493,NM_181461.3;PAX3,missense_variant,p.Tyr90Phe,ENST00000392070,NM_181458.3;PAX3,missense_variant,p.Tyr90Phe,ENST00000336840,NM_181460.3;PAX3,missense_variant,p.Tyr90Phe,ENST00000409551,NM_001127366.2;PAX3,missense_variant,p.Tyr90Phe,ENST00000409828,NM_000438.5;PAX3,missense_variant,p.Tyr90Phe,ENST00000258387,NM_013942.4;CCDC140,upstream_gene_variant,,ENST00000295226,NM_153038.1; A ENST00000392069 Transcript missense_variant 635/3170 269/1518 90/505 Y/F tAc/tTc 1 -1 PAX3 HGNC HGNC:8617 protein_coding YES CCDS2448.1 ENSP00000375921 P23760 UPI00001A8BF0 NM_181459.3 tolerated(0.05) 2/10 Gene3D:1.10.10.10,Pfam_domain:PF00292,Prints_domain:PR00027,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF307,SMART_domains:SM00351,Superfamily_domains:SSF46689 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 222297030 222297030 T A 1 0 0 0 0 1 0 0 0 11565 1638 57 4 4 PAX3 2 222297030 Missense_Mutation SNP T C3L-00144_T 2782127 222297030 19896499 318 4389 COL4A3 0 . GRCh38 2 227253300 227253300 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.650A>T p.His217Leu p.H217L ENST00000396578 12/52 365 209 156 220 220 0 strelka-varscan-mutect COL4A3,missense_variant,p.His217Leu,ENST00000396578,NM_000091.4;AC097662.2,intron_variant,,ENST00000439598,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000437673,;AC097662.2,intron_variant,,ENST00000606119,; T ENST00000396578 Transcript missense_variant 812/8097 650/5013 217/1670 H/L cAc/cTc 1 1 COL4A3 HGNC HGNC:2204 protein_coding YES CCDS42829.1 ENSP00000379823 Q01955 UPI000013E9F3 NM_000091.4 tolerated(0.72) 12/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF598,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 227253300 227253300 A T 1 0 0 0 0 1 0 0 0 3480 173 6 4 4 COL4A3 2 227253300 Missense_Mutation SNP A C3L-00144_T 4956270 227253300 14940229 319 4390 SPATA3 0 . GRCh38 2 230996365 230996365 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.132C>A p.= p.S44S ENST00000452881 1/9 348 320 28 245 245 0 varscan-mutect SPATA3,synonymous_variant,p.=,ENST00000452881,;SPATA3,synonymous_variant,p.=,ENST00000424440,;SPATA3,synonymous_variant,p.=,ENST00000433428,NM_139073.3;SPATA3,synonymous_variant,p.=,ENST00000612823,;SPATA3,synonymous_variant,p.=,ENST00000455816,;SPATA3,synonymous_variant,p.=,ENST00000440792,;SPATA3,upstream_gene_variant,,ENST00000423134,;SPATA3-AS1,upstream_gene_variant,,ENST00000414876,;SPATA3-AS1,upstream_gene_variant,,ENST00000446741,;SPATA3-AS1,upstream_gene_variant,,ENST00000434094,;SPATA3-AS1,upstream_gene_variant,,ENST00000426904,;SPATA3-AS1,upstream_gene_variant,,ENST00000457803,;SPATA3-AS1,upstream_gene_variant,,ENST00000418330,;SPATA3-AS1,upstream_gene_variant,,ENST00000441063,;SPATA3,upstream_gene_variant,,ENST00000409956,;SPATA3,intron_variant,,ENST00000454918,; A ENST00000452881 Transcript synonymous_variant 240/1618 132/579 44/192 S tcC/tcA 1 1 SPATA3 HGNC HGNC:17884 protein_coding YES CCDS2481.1 ENSP00000388895 Q8NHX4 UPI000006E910 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR22234,Pfam_domain:PF15662 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 230996365 230996365 C A 1 0 0 0 0 0 0 0 1 15342 581 21 2 2 SPATA3 2 230996365 Silent SNP C C3L-00144_T 3743065 230996365 11197164 320 4391 SPATA3 0 . GRCh38 2 230996392 230996392 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.159C>A p.= p.S53S ENST00000452881 1/9 489 361 128 369 369 0 strelka-varscan-mutect SPATA3,synonymous_variant,p.=,ENST00000452881,;SPATA3,synonymous_variant,p.=,ENST00000424440,;SPATA3,synonymous_variant,p.=,ENST00000433428,NM_139073.3;SPATA3,synonymous_variant,p.=,ENST00000612823,;SPATA3,synonymous_variant,p.=,ENST00000455816,;SPATA3,synonymous_variant,p.=,ENST00000423134,;SPATA3,synonymous_variant,p.=,ENST00000440792,;SPATA3-AS1,upstream_gene_variant,,ENST00000414876,;SPATA3-AS1,upstream_gene_variant,,ENST00000446741,;SPATA3-AS1,upstream_gene_variant,,ENST00000434094,;SPATA3-AS1,upstream_gene_variant,,ENST00000426904,;SPATA3-AS1,upstream_gene_variant,,ENST00000457803,;SPATA3-AS1,upstream_gene_variant,,ENST00000418330,;SPATA3-AS1,upstream_gene_variant,,ENST00000441063,;SPATA3,upstream_gene_variant,,ENST00000409956,;SPATA3,intron_variant,,ENST00000454918,; A ENST00000452881 Transcript synonymous_variant 267/1618 159/579 53/192 S tcC/tcA 1 1 SPATA3 HGNC HGNC:17884 protein_coding YES CCDS2481.1 ENSP00000388895 Q8NHX4 UPI000006E910 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR22234,Pfam_domain:PF15662 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 230996392 230996392 C A 1 0 0 0 0 0 0 0 1 15342 581 21 2 2 SPATA3 2 230996392 Silent SNP C C3L-00144_T 27 230996392 11197137 321 4392 UGT1A1 0 . GRCh38 2 233772448 233772448 + Silent SNP C C A rs199539868 C3L-00144_T C3L-00144_N C C c.1488C>A p.= p.A496A ENST00000305139 5/5 521 396 125 365 364 1 strelka-varscan-mutect UGT1A6,synonymous_variant,p.=,ENST00000305139,NM_001072.3;UGT1A9,synonymous_variant,p.=,ENST00000354728,NM_021027.2;UGT1A10,synonymous_variant,p.=,ENST00000344644,NM_019075.2;UGT1A8,synonymous_variant,p.=,ENST00000373450,NM_019076.4;UGT1A4,synonymous_variant,p.=,ENST00000373409,NM_007120.2;UGT1A1,synonymous_variant,p.=,ENST00000305208,NM_000463.2;UGT1A3,synonymous_variant,p.=,ENST00000482026,NM_019093.2;UGT1A5,synonymous_variant,p.=,ENST00000373414,NM_019078.1;UGT1A7,synonymous_variant,p.=,ENST00000373426,NM_019077.2;UGT1A6,synonymous_variant,p.=,ENST00000373424,NM_205862.1;MROH2A,upstream_gene_variant,,ENST00000610772,NM_001287395.1;UGT1A1,downstream_gene_variant,,ENST00000360418,;UGT1A10,downstream_gene_variant,,ENST00000373445,;UGT1A6,downstream_gene_variant,,ENST00000406651,;MROH2A,upstream_gene_variant,,ENST00000430892,;MROH2A,upstream_gene_variant,,ENST00000428446,;MROH2A,upstream_gene_variant,,ENST00000454283,;UGT1A4,3_prime_UTR_variant,,ENST00000450233,;UGT1A6,downstream_gene_variant,,ENST00000446481,; A ENST00000305139 Transcript synonymous_variant 1627/2479 1488/1599 496/532 A gcC/gcA rs199539868 1 1 UGT1A6 HGNC HGNC:12538 protein_coding YES CCDS2507.1 ENSP00000303174 P19224 Q5DSZ8 UPI000007021F NM_001072.3 5/5 Pfam_domain:PF00201,Transmembrane_helices:TMhelix LOW SNV 1 1 PASS rs199539868 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 233772448 233772448 C A 1 0 0 0 0 0 0 0 1 17469 639 23 1 1 UGT1A1 2 233772448 Silent SNP C C3L-00144_T 2776056 233772448 8421081 322 4393 ASB18 0 . GRCh38 2 236241350 236241350 + Missense_Mutation SNP G G T rs371669046 C3L-00144_T C3L-00144_N G G c.258C>A p.Asn86Lys p.N86K ENST00000409749 2/6 442 273 169 283 283 0 strelka-varscan-mutect ASB18,missense_variant,p.Asn86Lys,ENST00000409749,NM_212556.2;ASB18,intron_variant,,ENST00000430053,;AC079135.1,intron_variant,,ENST00000415226,; T ENST00000409749 Transcript missense_variant 258/1401 258/1401 86/466 N/K aaC/aaA rs371669046 1 -1 ASB18 HGNC HGNC:19770 protein_coding YES CCDS46548.1 ENSP00000386532 Q6ZVZ8 UPI00015D60A6 NM_212556.2 deleterious(0) 2/6 Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs371669046 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 236241350 236241350 G T 1 0 0 0 0 1 0 0 0 1164 1136 40 1 1 ASB18 2 236241350 Missense_Mutation SNP G C3L-00144_T 2468902 236241350 5952179 323 4394 CHL1 0 . GRCh38 3 343016 343016 + Nonsense_Mutation SNP G G T rs761520990 C3L-00144_T C3L-00144_N G G c.712G>T p.Glu238Ter p.E238* ENST00000256509 8/28 135 128 7 106 106 0 strelka-mutect CHL1,stop_gained,p.Glu238Ter,ENST00000256509,NM_006614.3;CHL1,stop_gained,p.Glu238Ter,ENST00000620033,NM_001253388.1;CHL1,intron_variant,,ENST00000397491,NM_001253387.1;CHL1,downstream_gene_variant,,ENST00000435603,;CHL1,intron_variant,,ENST00000453040,; T ENST00000256509 Transcript stop_gained 1354/8023 712/3675 238/1224 E/* Gaa/Taa rs761520990,COSM3593213 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 8/28 0,1 HIGH 1 SNV 1 0,1 1 PASS rs761520990 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 343016 343016 G T 1 0 0 0 0 0 1 0 0 3108 943 33 2 2 CHL1 3 343016 Nonsense_Mutation SNP G C3L-00144_T 343016 197952543 324 4395 CHL1 0 . GRCh38 3 361704 361704 + Missense_Mutation SNP C C G rs771129031 C3L-00144_T C3L-00144_N C C c.1312C>G p.Arg438Gly p.R438G ENST00000256509 13/28 154 111 43 132 132 0 strelka-varscan-mutect CHL1,missense_variant,p.Arg438Gly,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Arg438Gly,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Arg422Gly,ENST00000397491,NM_001253387.1;CHL1-AS1,downstream_gene_variant,,ENST00000417612,;CHL1-AS1,downstream_gene_variant,,ENST00000608098,;CHL1,non_coding_transcript_exon_variant,,ENST00000471332,;CHL1,3_prime_UTR_variant,,ENST00000453040,; G ENST00000256509 Transcript missense_variant 1954/8023 1312/3675 438/1224 R/G Cgt/Ggt rs771129031 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(0.19) 13/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653 MODERATE 1 SNV 1 1 PASS rs771129031 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 361704 361704 C G 1 0 0 0 0 1 0 0 0 3108 666 23 4 4 CHL1 3 361704 Missense_Mutation SNP C C3L-00144_T 18688 361704 197933855 325 4396 CNTN4 0 . GRCh38 3 3053833 3053833 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2838C>A p.Ser946Arg p.S946R ENST00000397461 23/24 256 235 21 281 279 2 strelka-varscan-mutect CNTN4,missense_variant,p.Ser946Arg,ENST00000397461,NM_001206955.1;CNTN4,missense_variant,p.Ser946Arg,ENST00000418658,NM_175607.2;CNTN4,missense_variant,p.Ser946Arg,ENST00000427331,;CNTN4,missense_variant,p.Ser618Arg,ENST00000397459,NM_001206956.1,NM_175613.2;CNTN4-AS1,intron_variant,,ENST00000442749,;CNTN4-AS1,intron_variant,,ENST00000629672,;CNTN4,non_coding_transcript_exon_variant,,ENST00000484686,; A ENST00000397461 Transcript missense_variant 3222/5198 2838/3081 946/1026 S/R agC/agA 1 1 CNTN4 HGNC HGNC:2174 protein_coding YES CCDS43041.1 ENSP00000380602 Q8IWV2 A0A024R2E5 UPI000007446C NM_001206955.1 tolerated(0.11) 23/24 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF568,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3053833 3053833 C A 1 0 0 0 0 1 0 0 0 3424 709 25 2 2 CNTN4 3 3053833 Missense_Mutation SNP C C3L-00144_T 2692129 3053833 195241726 326 4397 IL5RA 0 . GRCh38 3 3092235 3092235 + Missense_Mutation SNP G G T rs750574625 C3L-00144_T C3L-00144_N G G c.983C>A p.Pro328His p.P328H ENST00000446632 9/12 112 97 15 86 86 0 strelka-varscan-mutect IL5RA,missense_variant,p.Pro328His,ENST00000446632,NM_175726.3;IL5RA,missense_variant,p.Pro328His,ENST00000438560,NM_001243099.1;IL5RA,missense_variant,p.Pro328His,ENST00000256452,NM_000564.4;IL5RA,missense_variant,p.Pro328His,ENST00000383846,NM_175728.2;IL5RA,missense_variant,p.Pro328His,ENST00000430514,NM_175724.2;IL5RA,missense_variant,p.Pro328His,ENST00000456302,NM_175727.2;IL5RA,missense_variant,p.Pro328His,ENST00000311981,NM_175725.2;IL5RA,intron_variant,,ENST00000418488,; T ENST00000446632 Transcript missense_variant 1558/2514 983/1263 328/420 P/H cCt/cAt rs750574625 1 -1 IL5RA HGNC HGNC:6017 protein_coding YES CCDS2559.1 ENSP00000412209 Q01344 A0A024R2C8 UPI000013C656 NM_175726.3 deleterious(0.01) 9/12 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF17,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs750574625 . 0 207 0 3 0 0 0 0 -19.99977 0.999992 1 1 1 0 T 3 4 12 3092235 3092235 G T 1 0 0 0 0 1 0 0 0 7604 1000 35 2 2 IL5RA 3 3092235 Missense_Mutation SNP G C3L-00144_T 38402 3092235 195203324 327 4398 GRM7 0 . GRCh38 3 7298793 7298793 + Silent SNP C C A rs761307351 C3L-00144_T C3L-00144_N C C c.846C>A p.= p.A282A ENST00000357716 3/10 326 294 32 285 284 1 strelka-varscan-mutect GRM7,synonymous_variant,p.=,ENST00000486284,NM_181874.2;GRM7,synonymous_variant,p.=,ENST00000357716,NM_000844.3;GRM7,synonymous_variant,p.=,ENST00000389336,;GRM7,synonymous_variant,p.=,ENST00000402647,;GRM7,synonymous_variant,p.=,ENST00000448328,;GRM7,synonymous_variant,p.=,ENST00000467425,;GRM7,synonymous_variant,p.=,ENST00000440923,;GRM7,synonymous_variant,p.=,ENST00000389335,;GRM7,3_prime_UTR_variant,,ENST00000435689,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,;GRM7,non_coding_transcript_exon_variant,,ENST00000461677,; A ENST00000357716 Transcript synonymous_variant 1120/4127 846/2748 282/915 A gcC/gcA rs761307351 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 3/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS rs761307351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 7298793 7298793 C A 1 0 0 0 0 0 0 0 1 6684 639 23 1 1 GRM7 3 7298793 Silent SNP C C3L-00144_T 4206558 7298793 190996766 328 4399 GRM7 0 . GRCh38 3 7306512 7306512 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.893C>A p.Ala298Glu p.A298E ENST00000357716 4/10 299 241 58 244 243 1 strelka-varscan-mutect GRM7,missense_variant,p.Ala298Glu,ENST00000486284,NM_181874.2;GRM7,missense_variant,p.Ala298Glu,ENST00000357716,NM_000844.3;GRM7,missense_variant,p.Ala298Glu,ENST00000389336,;GRM7,missense_variant,p.Ala53Glu,ENST00000402647,;GRM7,missense_variant,p.Ala90Glu,ENST00000448328,;GRM7,missense_variant,p.Ala298Glu,ENST00000467425,;GRM7,missense_variant,p.Ala298Glu,ENST00000440923,;GRM7,missense_variant,p.Ala298Glu,ENST00000389335,;GRM7,3_prime_UTR_variant,,ENST00000435689,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,;GRM7,non_coding_transcript_exon_variant,,ENST00000461677,; A ENST00000357716 Transcript missense_variant 1167/4127 893/2748 298/915 A/E gCa/gAa 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 deleterious(0) 4/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7306512 7306512 C A 1 0 0 0 0 1 0 0 0 6684 710 25 2 2 GRM7 3 7306512 Missense_Mutation SNP C C3L-00144_T 7719 7306512 190989047 329 4400 BRPF1 0 . GRCh38 3 9734670 9734670 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.530C>G p.Pro177Arg p.P177R ENST00000383829 2/14 271 246 25 253 253 0 strelka-varscan-mutect BRPF1,missense_variant,p.Pro177Arg,ENST00000383829,NM_001003694.1;BRPF1,missense_variant,p.Pro177Arg,ENST00000424362,NM_001319050.1;BRPF1,missense_variant,p.Pro177Arg,ENST00000457855,NM_004634.2;BRPF1,missense_variant,p.Pro177Arg,ENST00000433861,NM_001319049.1;CPNE9,downstream_gene_variant,,ENST00000383832,NM_153635.2;BRPF1,downstream_gene_variant,,ENST00000420291,;BRPF1,downstream_gene_variant,,ENST00000426583,; G ENST00000383829 Transcript missense_variant 934/4736 530/3663 177/1220 P/R cCa/cGa 1 1 BRPF1 HGNC HGNC:14255 protein_coding YES CCDS33692.1 ENSP00000373340 P55201 UPI00001A9CA3 NM_001003694.1 deleterious(0) 2/14 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF85,Pfam_domain:PF10513 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 9734670 9734670 C G 1 0 0 0 0 1 0 0 0 1694 594 21 4 4 BRPF1 3 9734670 Missense_Mutation SNP C C3L-00144_T 2428158 9734670 188560889 330 4401 SLC6A1 0 . GRCh38 3 11034624 11034624 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1621G>A p.Ala541Thr p.A541T ENST00000287766 15/16 189 173 16 202 202 0 strelka-varscan-mutect SLC6A1,missense_variant,p.Ala541Thr,ENST00000287766,NM_003042.3;SLC6A1,non_coding_transcript_exon_variant,,ENST00000495636,; A ENST00000287766 Transcript missense_variant 2042/4502 1621/1800 541/599 A/T Gct/Act 1 1 SLC6A1 HGNC HGNC:11042 protein_coding YES CCDS2603.1 ENSP00000287766 P30531 A0A024R2G0 UPI000013DECF NM_003042.3 tolerated(0.12) 15/16 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF138,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -6.18203 0.9906613 1 1 1 0 A 3 1 12 11034624 11034624 G A 1 0 0 0 0 1 0 0 0 14956 1203 42 3 3 SLC6A1 3 11034624 Missense_Mutation SNP G C3L-00144_T 1299954 11034624 187260935 331 4402 FGD5 0 . GRCh38 3 14820698 14820698 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1627G>T p.Ala543Ser p.A543S ENST00000285046 1/20 47 38 9 43 43 0 strelka-varscan-mutect FGD5,missense_variant,p.Ala302Ser,ENST00000543601,NM_001320276.1;FGD5,missense_variant,p.Ala543Ser,ENST00000285046,NM_152536.3;FGD5,upstream_gene_variant,,ENST00000457774,; T ENST00000285046 Transcript missense_variant 1737/5720 1627/4389 543/1462 A/S Gcc/Tcc 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 tolerated(0.63) 1/20 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF13 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.98967 0.9999988 1 1 1 0 T 3 4 12 14820698 14820698 G T 1 0 0 0 0 1 0 0 0 5700 1203 42 2 2 FGD5 3 14820698 Missense_Mutation SNP G C3L-00144_T 3786074 14820698 183474861 332 4403 KCNH8 0 . GRCh38 3 19513009 19513009 + Missense_Mutation SNP C C A rs747522897 C3L-00144_T C3L-00144_N C C c.2119C>A p.Pro707Thr p.P707T ENST00000328405 13/16 190 167 23 189 189 0 strelka-varscan-mutect KCNH8,missense_variant,p.Pro707Thr,ENST00000328405,NM_144633.2;KCNH8,3_prime_UTR_variant,,ENST00000452398,; A ENST00000328405 Transcript missense_variant 2385/5137 2119/3324 707/1107 P/T Cca/Aca rs747522897 1 1 KCNH8 HGNC HGNC:18864 protein_coding YES CCDS2632.1 ENSP00000328813 Q96L42 UPI0000167D12 NM_144633.2 deleterious(0.02) 13/16 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF380 MODERATE 1 SNV 1 1 PASS rs747522897 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 19513009 19513009 C A 1 0 0 0 0 1 0 0 0 7954 623 22 2 2 KCNH8 3 19513009 Missense_Mutation SNP C C3L-00144_T 4692311 19513009 178782550 333 4404 KAT2B 0 . GRCh38 3 20101445 20101445 + Silent SNP T T G novel C3L-00144_T C3L-00144_N T T c.828T>G p.= p.S276S ENST00000263754 5/18 119 95 24 103 103 0 strelka-mutect KAT2B,synonymous_variant,p.=,ENST00000263754,NM_003884.4;KAT2B,downstream_gene_variant,,ENST00000426228,; G ENST00000263754 Transcript synonymous_variant 1283/4833 828/2499 276/832 S tcT/tcG 1 1 KAT2B HGNC HGNC:8638 protein_coding YES CCDS2634.1 ENSP00000263754 Q92831 UPI00002132DE NM_003884.4 5/18 Pfam_domain:PF06466,PIRSF_domain:PIRSF003048,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF116 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 20101445 20101445 T G 1 0 0 0 0 0 0 0 1 7896 1567 55 5 5 KAT2B 3 20101445 Silent SNP T C3L-00144_T 588436 20101445 178194114 334 4405 ZNF385D 0 . GRCh38 3 21665015 21665015 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.36G>T p.Gln12His p.Q12H ENST00000281523 2/8 97 81 16 77 77 0 strelka-varscan-mutect ZNF385D,missense_variant,p.Gln12His,ENST00000281523,NM_024697.2;ZNF385D,non_coding_transcript_exon_variant,,ENST00000494108,;ZNF385D,non_coding_transcript_exon_variant,,ENST00000478967,;ZNF385D,intron_variant,,ENST00000494118,;ZNF385D,missense_variant,p.Gln12His,ENST00000446749,; A ENST00000281523 Transcript missense_variant 555/10699 36/1188 12/395 Q/H caG/caT 1 -1 ZNF385D HGNC HGNC:26191 protein_coding YES CCDS2636.1 ENSP00000281523 Q9H6B1 UPI00000724AC NM_024697.2 tolerated(0.4) 2/8 hmmpanther:PTHR23067:SF12,hmmpanther:PTHR23067 MODERATE 1 SNV 1 1 PASS rs1293896581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 21665015 21665015 C A 1 0 0 0 0 1 0 0 0 18451 912 32 2 2 ZNF385D 3 21665015 Missense_Mutation SNP C C3L-00144_T 1563570 21665015 176630544 335 4406 NEK10 0 . GRCh38 3 27162531 27162531 + Missense_Mutation SNP C C A rs138337780 C3L-00144_T C3L-00144_N C C c.2940G>T p.Glu980Asp p.E980D ENST00000429845 32/39 169 153 16 119 119 0 strelka-varscan-mutect NEK10,missense_variant,p.Glu980Asp,ENST00000429845,NM_152534.4;NEK10,missense_variant,p.Glu292Asp,ENST00000295720,NM_001304384.1;NEK10,missense_variant,p.Glu292Asp,ENST00000383771,NM_001031741.3;NEK10,intron_variant,,ENST00000383770,;NEK10,intron_variant,,ENST00000498182,;NEK10,non_coding_transcript_exon_variant,,ENST00000574215,; A ENST00000429845 Transcript missense_variant 3303/4250 2940/3519 980/1172 E/D gaG/gaT rs138337780 1 -1 NEK10 HGNC HGNC:18592 protein_coding ENSP00000395849 Q6ZWH5 UPI0000EE2A86 NM_152534.4 tolerated(0.31) 32/39 MODERATE SNV 5 1 PASS rs138337780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 27162531 27162531 C A 1 0 0 0 0 1 0 0 0 10350 680 24 2 2 NEK10 3 27162531 Missense_Mutation SNP C C3L-00144_T 5497516 27162531 171133028 336 4407 STT3B 0 . GRCh38 3 31623707 31623707 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1573G>A p.Glu525Lys p.E525K ENST00000295770 11/16 104 85 19 91 91 0 strelka-varscan-mutect STT3B,missense_variant,p.Glu525Lys,ENST00000295770,NM_178862.2;STT3B,downstream_gene_variant,,ENST00000453168,;STT3B,downstream_gene_variant,,ENST00000423527,;STT3B,upstream_gene_variant,,ENST00000463044,;STT3B,downstream_gene_variant,,ENST00000436236,; A ENST00000295770 Transcript missense_variant 1782/4248 1573/2481 525/826 E/K Gaa/Aaa 1 1 STT3B HGNC HGNC:30611 protein_coding YES CCDS2650.1 ENSP00000295770 Q8TCJ2 UPI000006D7FB NM_178862.2 tolerated(0.77) 11/16 hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF25,Pfam_domain:PF02516 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31623707 31623707 G A 1 0 0 0 0 1 0 0 0 15717 1175 41 3 3 STT3B 3 31623707 Missense_Mutation SNP G C3L-00144_T 4461176 31623707 166671852 337 4408 CLASP2 0 . GRCh38 3 33577235 33577235 + Missense_Mutation SNP C C G rs764598812 C3L-00144_T C3L-00144_N C C c.1678G>C p.Ala560Pro p.A560P ENST00000480013 18/33 217 198 19 192 192 0 strelka-varscan-mutect CLASP2,missense_variant,p.Ala560Pro,ENST00000480013,NM_001207044.1;CLASP2,missense_variant,p.Ala63Pro,ENST00000475576,;CLASP2,intron_variant,,ENST00000399362,;CLASP2,intron_variant,,ENST00000359576,;CLASP2,intron_variant,,ENST00000468888,NM_015097.2;CLASP2,intron_variant,,ENST00000461133,;CLASP2,intron_variant,,ENST00000635664,;CLASP2,upstream_gene_variant,,ENST00000491045,; G ENST00000480013 Transcript missense_variant 2130/5972 1678/3882 560/1293 A/P Gcc/Ccc rs764598812 1 -1 CLASP2 HGNC HGNC:17078 protein_coding YES ENSP00000417518 J3KR49 UPI0001B7944D NM_001207044.1 deleterious(0.02) 18/33 MODERATE 1 SNV 5 1 PASS rs764598812 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 33577235 33577235 C G 1 0 0 0 0 1 0 0 0 3218 710 25 4 4 CLASP2 3 33577235 Missense_Mutation SNP C C3L-00144_T 1953528 33577235 164718324 338 4409 ARPP21 0 . GRCh38 3 35690131 35690131 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.536C>T p.Ala179Val p.A179V ENST00000417925 7/19 151 138 13 115 114 1 strelka-varscan-mutect ARPP21,missense_variant,p.Ala179Val,ENST00000187397,NM_016300.4;ARPP21,missense_variant,p.Ala179Val,ENST00000444190,NM_001267617.1;ARPP21,missense_variant,p.Ala179Val,ENST00000417925,NM_001267619.1;ARPP21,missense_variant,p.Ala21Val,ENST00000425289,;ARPP21,downstream_gene_variant,,ENST00000428373,NM_001267616.1;ARPP21,downstream_gene_variant,,ENST00000441454,;ARPP21,downstream_gene_variant,,ENST00000412048,NM_001267618.1;ARPP21,downstream_gene_variant,,ENST00000396482,NM_001025069.1,NM_001025068.1;ARPP21,downstream_gene_variant,,ENST00000450234,;ARPP21,downstream_gene_variant,,ENST00000438577,;ARPP21,downstream_gene_variant,,ENST00000413378,;ARPP21,upstream_gene_variant,,ENST00000476327,;ARPP21,missense_variant,p.Ala20Val,ENST00000427590,;ARPP21,missense_variant,p.Ala42Val,ENST00000446068,;ARPP21,3_prime_UTR_variant,,ENST00000414496,;ARPP21,downstream_gene_variant,,ENST00000434383,; T ENST00000417925 Transcript missense_variant 750/3086 536/2442 179/813 A/V gCt/gTt COSM4117000,COSM4117001 1 1 ARPP21 HGNC HGNC:16968 protein_coding YES CCDS58823.1 ENSP00000412326 Q9UBL0 UPI0000209B3D NM_001267619.1 deleterious(0) 7/19 Gene3D:3.30.1370.50,Pfam_domain:PF01424,PROSITE_profiles:PS51061,hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF14,SMART_domains:SM00393,Superfamily_domains:SSF82708 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35690131 35690131 C T 1 0 0 0 0 1 0 0 0 1121 797 28 3 3 ARPP21 3 35690131 Missense_Mutation SNP C C3L-00144_T 2112896 35690131 162605428 339 4410 ARPP21 0 . GRCh38 3 35729438 35729438 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1259G>T p.Gly420Val p.G420V ENST00000417925 13/19 342 267 75 313 311 2 strelka-varscan-mutect ARPP21,missense_variant,p.Gly454Val,ENST00000187397,NM_016300.4;ARPP21,missense_variant,p.Gly400Val,ENST00000444190,NM_001267617.1;ARPP21,missense_variant,p.Gly420Val,ENST00000417925,NM_001267619.1;ARPP21,missense_variant,p.Gly227Val,ENST00000425289,;ARPP21,non_coding_transcript_exon_variant,,ENST00000476327,;ARPP21,missense_variant,p.Gly112Val,ENST00000457165,;ARPP21,3_prime_UTR_variant,,ENST00000427590,;ARPP21,downstream_gene_variant,,ENST00000481854,; T ENST00000417925 Transcript missense_variant 1473/3086 1259/2442 420/813 G/V gGg/gTg 1 1 ARPP21 HGNC HGNC:16968 protein_coding YES CCDS58823.1 ENSP00000412326 Q9UBL0 UPI0000209B3D NM_001267619.1 deleterious(0.03) 13/19 hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35729438 35729438 G T 1 0 0 0 0 1 0 0 0 1121 1232 43 2 2 ARPP21 3 35729438 Missense_Mutation SNP G C3L-00144_T 39307 35729438 162566121 340 4411 ARPP21 0 . GRCh38 3 35739495 35739495 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1826G>T p.Gly609Val p.G609V ENST00000417925 16/19 282 251 31 238 238 0 strelka-varscan-mutect ARPP21,missense_variant,p.Gly608Val,ENST00000187397,NM_016300.4;ARPP21,missense_variant,p.Gly589Val,ENST00000444190,NM_001267617.1;ARPP21,missense_variant,p.Gly609Val,ENST00000417925,NM_001267619.1;MIR128-2,upstream_gene_variant,,ENST00000384893,;ARPP21,intron_variant,,ENST00000462173,;ARPP21,3_prime_UTR_variant,,ENST00000457165,;ARPP21,downstream_gene_variant,,ENST00000427590,; T ENST00000417925 Transcript missense_variant 2040/3086 1826/2442 609/813 G/V gGc/gTc 1 1 ARPP21 HGNC HGNC:16968 protein_coding YES CCDS58823.1 ENSP00000412326 Q9UBL0 UPI0000209B3D NM_001267619.1 tolerated(0.1) 16/19 hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF14 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35739495 35739495 G T 1 0 0 0 0 1 0 0 0 1121 1203 42 2 2 ARPP21 3 35739495 Missense_Mutation SNP G C3L-00144_T 10057 35739495 162556064 341 4412 GOLGA4 0 . GRCh38 3 37323915 37323915 + Nonsense_Mutation SNP G G T rs772532911 C3L-00144_T C3L-00144_N G G c.2095G>T p.Glu699Ter p.E699* ENST00000356847 15/23 165 155 10 166 163 3 strelka-varscan-mutect GOLGA4,stop_gained,p.Glu677Ter,ENST00000361924,NM_002078.4;GOLGA4,stop_gained,p.Glu699Ter,ENST00000356847,NM_001172713.1;GOLGA4,stop_gained,p.Glu548Ter,ENST00000437131,;GOLGA4,stop_gained,p.Glu238Ter,ENST00000429018,;GOLGA4,intron_variant,,ENST00000444882,;GOLGA4,downstream_gene_variant,,ENST00000435830,;GOLGA4,upstream_gene_variant,,ENST00000498250,;GOLGA4,downstream_gene_variant,,ENST00000497537,; T ENST00000356847 Transcript stop_gained 2394/7673 2095/6732 699/2243 E/* Gaa/Taa rs772532911 1 1 GOLGA4 HGNC HGNC:4427 protein_coding YES CCDS54564.1 ENSP00000349305 Q13439 UPI000198C9CA NM_001172713.1 15/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19327 HIGH 1 SNV 1 1 PASS rs772532911 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 37323915 37323915 G T 1 0 0 0 0 0 1 0 0 6433 943 33 2 2 GOLGA4 3 37323915 Nonsense_Mutation SNP G C3L-00144_T 1584420 37323915 160971644 342 4413 GOLGA4 0 . GRCh38 3 37326250 37326250 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.4430A>T p.Gln1477Leu p.Q1477L ENST00000356847 15/23 205 165 40 185 185 0 strelka-varscan-mutect GOLGA4,missense_variant,p.Gln1455Leu,ENST00000361924,NM_002078.4;GOLGA4,missense_variant,p.Gln1477Leu,ENST00000356847,NM_001172713.1;GOLGA4,missense_variant,p.Gln1326Leu,ENST00000437131,;GOLGA4,intron_variant,,ENST00000444882,;GOLGA4,downstream_gene_variant,,ENST00000429018,;GOLGA4,upstream_gene_variant,,ENST00000498250,;GOLGA4,downstream_gene_variant,,ENST00000497537,; T ENST00000356847 Transcript missense_variant 4729/7673 4430/6732 1477/2243 Q/L cAg/cTg 1 1 GOLGA4 HGNC HGNC:4427 protein_coding YES CCDS54564.1 ENSP00000349305 Q13439 UPI000198C9CA NM_001172713.1 deleterious(0.03) 15/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19327 MODERATE 1 SNV 1 1 PASS rs1281035493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 37326250 37326250 A T 1 0 0 0 0 1 0 0 0 6433 188 7 4 4 GOLGA4 3 37326250 Missense_Mutation SNP A C3L-00144_T 2335 37326250 160969309 343 4414 TTC21A 0 . GRCh38 3 39128914 39128914 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1899C>A p.= p.L633L ENST00000431162 14/29 209 161 48 175 175 0 strelka-varscan-mutect TTC21A,synonymous_variant,p.=,ENST00000431162,NM_145755.2;TTC21A,synonymous_variant,p.=,ENST00000440121,NM_001105513.2;TTC21A,non_coding_transcript_exon_variant,,ENST00000466875,;TTC21A,upstream_gene_variant,,ENST00000493856,;TTC21A,upstream_gene_variant,,ENST00000472866,;TTC21A,upstream_gene_variant,,ENST00000481734,;TTC21A,upstream_gene_variant,,ENST00000471025,;TTC21A,synonymous_variant,p.=,ENST00000430597,;TTC21A,upstream_gene_variant,,ENST00000473587,; A ENST00000431162 Transcript synonymous_variant 2033/4209 1899/3963 633/1320 L ctC/ctA 1 1 TTC21A HGNC HGNC:30761 protein_coding YES CCDS46800.1 ENSP00000398211 Q8NDW8 UPI00015D46B9 NM_145755.2 14/29 hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF2,Gene3D:1.25.40.10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 39128914 39128914 C A 1 0 0 0 0 0 0 0 1 17195 842 30 2 2 TTC21A 3 39128914 Silent SNP C C3L-00144_T 1802664 39128914 159166645 344 4415 ACKR2 0 . GRCh38 3 42864686 42864686 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.184A>T p.Ser62Cys p.S62C ENST00000422265 3/3 227 206 21 196 196 0 strelka-varscan-mutect ACKR2,missense_variant,p.Ser62Cys,ENST00000422265,NM_001296.4;ACKR2,missense_variant,p.Ser62Cys,ENST00000442925,;ACKR2,missense_variant,p.Ser62Cys,ENST00000493193,;ACKR2,missense_variant,p.Ser62Cys,ENST00000494619,;ACKR2,missense_variant,p.Ser62Cys,ENST00000497921,;ACKR2,missense_variant,p.Ser62Cys,ENST00000492609,;CYP8B1,intron_variant,,ENST00000437102,;KRBOX1,intron_variant,,ENST00000426937,;ACKR2,non_coding_transcript_exon_variant,,ENST00000498111,;ACKR2,non_coding_transcript_exon_variant,,ENST00000460855,;RP11-141M3.6,intron_variant,,ENST00000471537,;RP11-141M3.6,intron_variant,,ENST00000496604,;RP11-136C24.3,intron_variant,,ENST00000451200,;RP11-141M3.6,intron_variant,,ENST00000487368,;ACKR2,downstream_gene_variant,,ENST00000463699,; T ENST00000422265 Transcript missense_variant 359/2956 184/1155 62/384 S/C Agc/Tgc 1 1 ACKR2 HGNC HGNC:1565 protein_coding YES CCDS2706.1 ENSP00000416996 O00590 A0A024R2X7 UPI000004358E NM_001296.4 deleterious(0.03) 3/3 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF735,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42864686 42864686 A T 1 0 0 0 0 1 0 0 0 182 188 7 4 4 ACKR2 3 42864686 Missense_Mutation SNP A C3L-00144_T 3735772 42864686 155430873 345 4416 KIF15 0 . GRCh38 3 44838372 44838372 + Missense_Mutation SNP A A C rs753025763 C3L-00144_T C3L-00144_N A A c.3269A>C p.Gln1090Pro p.Q1090P ENST00000326047 27/35 101 93 8 94 94 0 strelka-varscan-mutect KIF15,missense_variant,p.Gln1090Pro,ENST00000326047,NM_020242.2;KIF15,missense_variant,p.Gln725Pro,ENST00000425755,;KIF15,3_prime_UTR_variant,,ENST00000438321,;KIF15,3_prime_UTR_variant,,ENST00000453693,;KIF15,upstream_gene_variant,,ENST00000422209,; C ENST00000326047 Transcript missense_variant 3418/4842 3269/4167 1090/1388 Q/P cAg/cCg rs753025763 1 1 KIF15 HGNC HGNC:17273 protein_coding YES CCDS33744.1 ENSP00000324020 Q9NS87 UPI000006DB0E NM_020242.2 deleterious(0) 27/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF502,hmmpanther:PTHR24115 MODERATE 1 SNV 1 1 PASS rs753025763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 44838372 44838372 A C 1 0 0 0 0 1 0 0 0 8141 188 7 5 5 KIF15 3 44838372 Missense_Mutation SNP A C3L-00144_T 1973686 44838372 153457187 346 4417 EXOSC7 0 . GRCh38 3 45011247 45011247 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.784G>T p.Val262Leu p.V262L ENST00000265564 8/8 123 101 22 132 132 0 strelka-varscan-mutect EXOSC7,missense_variant,p.Val262Leu,ENST00000265564,NM_015004.3;EXOSC7,non_coding_transcript_exon_variant,,ENST00000461361,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000491476,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000468667,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000459856,;EXOSC7,intron_variant,,ENST00000481405,;CLEC3B,intron_variant,,ENST00000490386,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000486727,; T ENST00000265564 Transcript missense_variant 832/1055 784/876 262/291 V/L Gtg/Ttg 1 1 EXOSC7 HGNC HGNC:28112 protein_coding YES CCDS2725.1 ENSP00000265564 Q15024 A0A024R2P7 UPI000020A5E9 NM_015004.3 deleterious(0.02) 8/8 hmmpanther:PTHR11097,hmmpanther:PTHR11097:SF8,Superfamily_domains:SSF55666 MODERATE 1 SNV 1 1 PASS rs1166502441 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 45011247 45011247 G T 1 0 0 0 0 1 0 0 0 5187 1377 48 2 2 EXOSC7 3 45011247 Missense_Mutation SNP G C3L-00144_T 172875 45011247 153284312 347 4418 XCR1 0 . GRCh38 3 46021507 46021507 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.441G>T p.= p.V147V ENST00000309285 2/2 231 200 31 244 244 0 strelka-varscan-mutect XCR1,synonymous_variant,p.=,ENST00000309285,NM_005283.2,NM_001024644.1;XCR1,downstream_gene_variant,,ENST00000395946,;NRBF2P2,upstream_gene_variant,,ENST00000413087,; A ENST00000309285 Transcript synonymous_variant 798/5281 441/1002 147/333 V gtG/gtT 1 -1 XCR1 HGNC HGNC:1625 protein_coding YES CCDS2736.1 ENSP00000310405 P46094 UPI000004358D NM_005283.2,NM_001024644.1 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF730,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 46021507 46021507 C A 1 0 0 0 0 0 0 0 1 17984 697 25 2 2 XCR1 3 46021507 Silent SNP C C3L-00144_T 1010260 46021507 152274052 348 4419 CCR1 0 . GRCh38 3 46203377 46203377 + Silent SNP G G T rs745406212 C3L-00144_T C3L-00144_N G G c.937C>A p.= p.R313R ENST00000296140 2/2 274 214 60 247 247 0 strelka-varscan-mutect CCR1,synonymous_variant,p.=,ENST00000296140,NM_001295.2;CCR3,intron_variant,,ENST00000357422,; T ENST00000296140 Transcript synonymous_variant 1063/2731 937/1068 313/355 R Cgg/Agg rs745406212 1 -1 CCR1 HGNC HGNC:1602 protein_coding YES CCDS2737.1 ENSP00000296140 P32246 Q5U003 UPI0000043584 NM_001295.2 2/2 hmmpanther:PTHR10489:SF711,hmmpanther:PTHR10489,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01106,Prints_domain:PR00657 LOW 1 SNV 1 1 PASS rs745406212 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 46203377 46203377 G T 1 0 0 0 0 0 0 0 1 2639 1086 38 1 1 CCR1 3 46203377 Silent SNP G C3L-00144_T 181870 46203377 152092182 349 4420 NBEAL2 0 . GRCh38 3 46991627 46991627 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.864G>T p.Trp288Cys p.W288C ENST00000450053 8/54 268 227 41 221 221 0 strelka-varscan-mutect NBEAL2,missense_variant,p.Trp288Cys,ENST00000450053,NM_015175.2;NBEAL2,upstream_gene_variant,,ENST00000416683,; T ENST00000450053 Transcript missense_variant 1043/8827 864/8265 288/2754 W/C tgG/tgT 1 1 NBEAL2 HGNC HGNC:31928 protein_coding YES CCDS46817.1 ENSP00000415034 Q6ZNJ1 UPI000022C020 NM_015175.2 tolerated(0.18) 8/54 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF50 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 12 46991627 46991627 G T 1 0 0 0 0 1 0 0 0 10200 1212 42 2 2 NBEAL2 3 46991627 Missense_Mutation SNP G C3L-00144_T 788250 46991627 151303932 350 4421 SPINK8 0 . GRCh38 3 48309917 48309917 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.269A>G p.Tyr90Cys p.Y90C ENST00000434006 4/5 58 45 13 83 83 0 strelka-mutect SPINK8,missense_variant,p.Tyr90Cys,ENST00000434006,NM_001080525.1; C ENST00000434006 Transcript missense_variant 269/444 269/294 90/97 Y/C tAt/tGt 1 -1 SPINK8 HGNC HGNC:33160 protein_coding YES CCDS46822.1 ENSP00000407497 P0C7L1 UPI00006C0662 NM_001080525.1 deleterious(0) 4/5 PROSITE_profiles:PS51465,hmmpanther:PTHR21312:SF37,hmmpanther:PTHR21312,Gene3D:3.30.60.30,Pfam_domain:PF00050,SMART_domains:SM00280,Superfamily_domains:SSF100895 MODERATE 1 SNV 3 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 48309917 48309917 T C 1 0 0 0 0 1 0 0 0 15418 1406 49 5 5 SPINK8 3 48309917 Missense_Mutation SNP T C3L-00144_T 1318290 48309917 149985642 351 4422 ATRIP 0 . GRCh38 3 48450171 48450171 + Splice_Site SNP G G A novel C3L-00144_T C3L-00144_N G G c.381+1G>A p.X127_splice ENST00000320211 92 85 7 85 84 1 strelka-varscan-mutect ATRIP,splice_donor_variant,,ENST00000412052,NM_001271023.1;ATRIP,splice_donor_variant,,ENST00000320211,NM_130384.2;ATRIP,splice_donor_variant,,ENST00000346691,NM_032166.3;ATRIP,splice_donor_variant,,ENST00000357105,NM_001271022.1;ATRIP,splice_donor_variant,,ENST00000635099,;RP11-24C3.2,upstream_gene_variant,,ENST00000438872,;RP11-24C3.2,upstream_gene_variant,,ENST00000435578,;ATRIP,splice_donor_variant,,ENST00000634384,;ATRIP,splice_donor_variant,,ENST00000635464,;ATRIP,splice_donor_variant,,ENST00000635082,;ATRIP,upstream_gene_variant,,ENST00000635084,; A ENST00000320211 Transcript splice_donor_variant -/2590 381/2376 127/791 1 1 ATRIP HGNC HGNC:33499 protein_coding YES CCDS2768.1 ENSP00000323099 Q8WXE1 A0A024R2U4 UPI0000070A6A NM_130384.2 2/12 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -14.64814 1 1 1 1 0 A 5 1 12 48450171 48450171 G A 1 0 0 0 0 0 0 1 0 1358 1275 44 3 3 ATRIP 3 48450171 Splice_Site SNP G C3L-00144_T 140254 48450171 149845388 352 4423 COL7A1 0 . GRCh38 3 48581704 48581704 + Splice_Site SNP A A G novel C3L-00144_T C3L-00144_N A A c.4722+2T>C p.X1574_splice ENST00000328333 670 527 143 631 631 0 strelka-varscan-mutect COL7A1,splice_donor_variant,,ENST00000328333,NM_000094.3;COL7A1,upstream_gene_variant,,ENST00000390201,;COL7A1,splice_donor_variant,,ENST00000487017,; G ENST00000328333 Transcript splice_donor_variant -/9276 4722/8835 1574/2944 1 -1 COL7A1 HGNC HGNC:2214 protein_coding YES CCDS2773.1 ENSP00000332371 Q02388 UPI0000126D20 NM_000094.3 48/117 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 12 48581704 48581704 A G 1 0 0 0 0 0 0 1 0 3493 405 14 5 5 COL7A1 3 48581704 Splice_Site SNP A C3L-00144_T 131533 48581704 149713855 353 4424 SLC26A6 0 . GRCh38 3 48628702 48628702 + Silent SNP G G T rs747181205 C3L-00144_T C3L-00144_N G G c.1612C>A p.= p.R538R ENST00000395550 15/21 247 222 25 220 219 1 strelka-varscan-mutect SLC26A6,synonymous_variant,p.=,ENST00000358747,NM_001040454.1;SLC26A6,synonymous_variant,p.=,ENST00000420764,NM_134263.2;SLC26A6,synonymous_variant,p.=,ENST00000395550,NM_022911.2;SLC26A6,synonymous_variant,p.=,ENST00000383733,NM_134426.2;SLC26A6,synonymous_variant,p.=,ENST00000455886,NM_001281732.1;SLC26A6,synonymous_variant,p.=,ENST00000337000,NM_001281733.1;SLC26A6,downstream_gene_variant,,ENST00000421649,;SLC26A6,downstream_gene_variant,,ENST00000431739,;SLC26A6,downstream_gene_variant,,ENST00000426599,;SLC26A6,downstream_gene_variant,,ENST00000611478,;SLC26A6,downstream_gene_variant,,ENST00000482282,;SLC26A6,3_prime_UTR_variant,,ENST00000307364,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000480524,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000496469,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000462009,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000469693,;SLC26A6,intron_variant,,ENST00000489483,;SLC26A6,downstream_gene_variant,,ENST00000444531,;SLC26A6,downstream_gene_variant,,ENST00000414944,;SLC26A6,upstream_gene_variant,,ENST00000466257,;SLC26A6,downstream_gene_variant,,ENST00000485361,;SLC26A6,downstream_gene_variant,,ENST00000431213,;SLC26A6,downstream_gene_variant,,ENST00000494717,; T ENST00000395550 Transcript synonymous_variant 1660/2589 1612/2280 538/759 R Cgg/Agg rs747181205 1 -1 SLC26A6 HGNC HGNC:14472 protein_coding YES CCDS43087.1 ENSP00000378920 Q9BXS9 UPI0000135460 NM_022911.2 15/21 PROSITE_profiles:PS50801,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF113,Gene3D:3.30.750.24,Pfam_domain:PF01740,TIGRFAM_domain:TIGR00815,Superfamily_domains:SSF52091 LOW 1 SNV 1 1 PASS rs747181205 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 48628702 48628702 G T 1 0 0 0 0 0 0 0 1 14791 1115 39 1 1 SLC26A6 3 48628702 Silent SNP G C3L-00144_T 46998 48628702 149666857 354 4425 ARIH2OS 0 . GRCh38 3 48918850 48918851 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.299_300insA p.Thr101HisfsTer34 p.T101Hfs*34 ENST00000408959 1/1 169 149 20 139 139 0 sindel-varindel-pindel ARIH2OS,frameshift_variant,p.Thr101HisfsTer34,ENST00000408959,NM_001123040.1;ARIH2,5_prime_UTR_variant,,ENST00000356401,NM_006321.2;ARIH2,5_prime_UTR_variant,,ENST00000449376,;ARIH2,5_prime_UTR_variant,,ENST00000430423,;ARIH2,5_prime_UTR_variant,,ENST00000452882,;ARIH2,upstream_gene_variant,,ENST00000420814,;ARIH2,upstream_gene_variant,,ENST00000449729,;ARIH2,upstream_gene_variant,,ENST00000433170,;ARIH2,non_coding_transcript_exon_variant,,ENST00000490095,;ARIH2,non_coding_transcript_exon_variant,,ENST00000483333,;ARIH2,non_coding_transcript_exon_variant,,ENST00000498314,;ARIH2,non_coding_transcript_exon_variant,,ENST00000495761,;ARIH2,non_coding_transcript_exon_variant,,ENST00000474618,;ARIH2,non_coding_transcript_exon_variant,,ENST00000482427,;ARIH2,non_coding_transcript_exon_variant,,ENST00000488963,;ARIH2,non_coding_transcript_exon_variant,,ENST00000478224,;ARIH2,upstream_gene_variant,,ENST00000484999,;ARIH2,upstream_gene_variant,,ENST00000474936,;ARIH2,upstream_gene_variant,,ENST00000470296,;ARIH2,upstream_gene_variant,,ENST00000486316,;ARIH2,non_coding_transcript_exon_variant,,ENST00000492077,;ARIH2,non_coding_transcript_exon_variant,,ENST00000463738,;ARIH2,upstream_gene_variant,,ENST00000466850,; T ENST00000408959 Transcript frameshift_variant 535-536/1598 299-300/873 100/290 P/PX ccc/ccAc 1 -1 ARIH2OS HGNC HGNC:34425 protein_coding YES CCDS43088.1 ENSP00000386193 Q8N7S6 UPI00000710A2 NM_001123040.1 1/1 HIGH insertion 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 7 5 12 48918850 48918850 - T 1 0 1 1 0 0 0 0 0 1061 1335 47 0 0 ARIH2OS 3 48918850 Frame_Shift_Ins INS - C3L-00144_T 290148 48918850 149376709 355 4426 USP19 0 . GRCh38 3 49116790 49116790 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000434032 7/27 91 59 32 66 66 0 strelka-varscan-mutect USP19,missense_variant,p.Gly345Trp,ENST00000453664,NM_001199162.1;USP19,missense_variant,p.Gly355Trp,ENST00000417901,NM_001199161.1;USP19,missense_variant,p.Gly355Trp,ENST00000434032,NM_001199160.1;USP19,missense_variant,p.Gly292Trp,ENST00000398892,;USP19,missense_variant,p.Gly254Trp,ENST00000398888,NM_006677.2;USP19,missense_variant,p.Gly292Trp,ENST00000398898,;USP19,missense_variant,p.Gly151Trp,ENST00000398896,;USP19,missense_variant,p.Gly340Trp,ENST00000306026,;USP19,missense_variant,p.Gly102Trp,ENST00000479073,;LAMB2,downstream_gene_variant,,ENST00000418109,NM_002292.3;LAMB2,downstream_gene_variant,,ENST00000305544,;USP19,non_coding_transcript_exon_variant,,ENST00000464931,;USP19,downstream_gene_variant,,ENST00000488993,;USP19,downstream_gene_variant,,ENST00000491859,;USP19,downstream_gene_variant,,ENST00000465902,;USP19,downstream_gene_variant,,ENST00000480163,;LAMB2,downstream_gene_variant,,ENST00000498377,;LAMB2,downstream_gene_variant,,ENST00000467506,;LAMB2,downstream_gene_variant,,ENST00000484713,; A ENST00000434032 Transcript missense_variant 1275/4677 1063/4260 355/1419 G/W Ggg/Tgg 1 -1 USP19 HGNC HGNC:12617 protein_coding YES CCDS56254.1 ENSP00000401197 O94966 UPI000198CAB3 NM_001199160.1 deleterious_low_confidence(0) 7/27 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49116790 49116790 C A 1 0 0 0 0 1 0 0 0 17591 594 21 2 2 USP19 3 49116790 Missense_Mutation SNP C C3L-00144_T 197940 49116790 149178769 356 4427 LAMB2 0 . GRCh38 3 49132821 49132821 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.47G>T p.Trp16Leu p.W16L ENST00000418109 2/33 264 237 27 226 226 0 strelka-varscan-mutect LAMB2,missense_variant,p.Trp16Leu,ENST00000418109,NM_002292.3;LAMB2,missense_variant,p.Trp16Leu,ENST00000305544,;LAMB2,intron_variant,,ENST00000494831,;LAMB2,upstream_gene_variant,,ENST00000486298,;LAMB2,upstream_gene_variant,,ENST00000483321,;LAMB2,upstream_gene_variant,,ENST00000488638,; A ENST00000418109 Transcript missense_variant 212/5674 47/5397 16/1798 W/L tGg/tTg 1 -1 LAMB2 HGNC HGNC:6487 protein_coding YES CCDS2789.1 ENSP00000388325 P55268 A0A024R319 UPI000013EA62 NM_002292.3 tolerated(0.44) 2/33 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF36,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1051360734 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49132821 49132821 C A 1 0 0 0 0 1 0 0 0 8515 595 21 2 2 LAMB2 3 49132821 Missense_Mutation SNP C C3L-00144_T 16031 49132821 149162738 357 4428 KLHDC8B 0 . GRCh38 3 49175135 49175135 + Silent SNP G G T C3L-00144_T C3L-00144_N G G c.840G>T p.= p.G280G ENST00000332780 5/6 153 134 19 108 108 0 strelka-varscan-mutect KLHDC8B,synonymous_variant,p.=,ENST00000332780,NM_173546.2;C3orf84,downstream_gene_variant,,ENST00000545770,NM_001080528.2;C3orf84,downstream_gene_variant,,ENST00000432035,;KLHDC8B,non_coding_transcript_exon_variant,,ENST00000459846,;KLHDC8B,intron_variant,,ENST00000462582,;KLHDC8B,downstream_gene_variant,,ENST00000476495,;C3orf84,downstream_gene_variant,,ENST00000443990,;KLHDC8B,non_coding_transcript_exon_variant,,ENST00000471811,; T ENST00000332780 Transcript synonymous_variant 1049/1959 840/1065 280/354 G ggG/ggT COSM3595249 1 1 KLHDC8B HGNC HGNC:28557 protein_coding YES CCDS2791.1 ENSP00000327468 Q8IXV7 A0A024R2X4 UPI000004EE01 NM_173546.2 5/6 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,SMART_domains:SM00612 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 12 49175135 49175135 G T 1 0 0 0 0 0 0 0 1 8227 1219 43 2 2 KLHDC8B 3 49175135 Silent SNP G C3L-00144_T 42314 49175135 149120424 358 4429 RNF123 0 . GRCh38 3 49697940 49697940 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.397+1G>T p.X133_splice ENST00000327697 309 273 36 245 245 0 strelka-varscan-mutect RNF123,splice_donor_variant,,ENST00000327697,NM_022064.3;RNF123,splice_donor_variant,,ENST00000432042,;RNF123,downstream_gene_variant,,ENST00000454491,;RNF123,downstream_gene_variant,,ENST00000629802,;RNF123,splice_donor_variant,,ENST00000487805,;RNF123,splice_donor_variant,,ENST00000486102,;RNF123,splice_donor_variant,,ENST00000457726,;RNF123,upstream_gene_variant,,ENST00000494005,;RNF123,downstream_gene_variant,,ENST00000443204,; T ENST00000327697 Transcript splice_donor_variant -/4311 397/3945 133/1314 1 1 RNF123 HGNC HGNC:21148 protein_coding YES CCDS33758.1 ENSP00000328287 Q5XPI4 UPI00001D6A07 NM_022064.3 6/38 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 49697940 49697940 G T 1 0 0 0 0 0 0 1 0 13611 1275 44 2 2 RNF123 3 49697940 Splice_Site SNP G C3L-00144_T 522805 49697940 148597619 359 4430 SEMA3F 0 . GRCh38 3 50182391 50182401 + Frame_Shift_Del DEL CGGTGGCTGAA CGGTGGCTGAA - novel C3L-00144_T C3L-00144_N CGGTGGCTGAA CGGTGGCTGAA c.755_763+2delGGCTGAACGGT ENST00000002829 8/19 254 229 25 201 201 0 sindel-pindel SEMA3F,frameshift_variant,,ENST00000002829,NM_004186.3;SEMA3F,frameshift_variant,,ENST00000434342,NM_001318800.1;SEMA3F,frameshift_variant,,ENST00000413852,NM_001318798.1;SEMA3F,frameshift_variant,,ENST00000450338,;SEMA3F,frameshift_variant,,ENST00000414301,;SEMA3F,upstream_gene_variant,,ENST00000470737,;SEMA3F,upstream_gene_variant,,ENST00000493743,; - ENST00000002829 Transcript frameshift_variant,splice_region_variant 1235-1245/3802 751-761/2358 251-254/785 RWLN/X CGGTGGCTGAAc/c 1 1 SEMA3F HGNC HGNC:10728 protein_coding YES CCDS2811.1 ENSP00000002829 Q13275 UPI0000135A69 NM_004186.3 8/19 PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF27,hmmpanther:PTHR11036,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 50182391 50182391 CGGTGGCTGAA - 1 0 1 0 1 0 0 0 0 14305 643 23 0 0 SEMA3F 3 50182391 Frame_Shift_Del DEL CGGTGGCTGAA C3L-00144_T 484451 50182391 148113168 360 4431 SEMA3B 0 . GRCh38 3 50275319 50275319 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.1524C>G p.= p.A508A ENST00000611067 14/17 68 52 16 39 39 0 strelka-varscan-mutect SEMA3B,synonymous_variant,p.=,ENST00000616701,NM_001290060.1;SEMA3B,synonymous_variant,p.=,ENST00000618865,NM_004636.3;SEMA3B,synonymous_variant,p.=,ENST00000433753,NM_001005914.2;SEMA3B,synonymous_variant,p.=,ENST00000611067,NM_001290061.1;SEMA3B,synonymous_variant,p.=,ENST00000456560,NM_001290063.1,NM_001290062.1;SEMA3B,synonymous_variant,p.=,ENST00000418576,;LSMEM2,upstream_gene_variant,,ENST00000316436,NM_153215.2,NM_001304385.1;SEMA3B,downstream_gene_variant,,ENST00000621029,;SEMA3B,downstream_gene_variant,,ENST00000612981,;SEMA3B,intron_variant,,ENST00000456210,;SEMA3B,non_coding_transcript_exon_variant,,ENST00000419007,;SEMA3B,non_coding_transcript_exon_variant,,ENST00000619119,;SEMA3B,non_coding_transcript_exon_variant,,ENST00000441915,;SEMA3B,non_coding_transcript_exon_variant,,ENST00000416295,;SEMA3B,downstream_gene_variant,,ENST00000612509,;SEMA3B,downstream_gene_variant,,ENST00000434030,;SEMA3B,downstream_gene_variant,,ENST00000439487,; G ENST00000611067 Transcript synonymous_variant 1551/2292 1524/2265 508/754 A gcC/gcG 1 1 SEMA3B HGNC HGNC:10724 protein_coding YES CCDS77743.1 ENSP00000480680 A0A0C4DGV8 UPI000007272A NM_001290061.1 14/17 Gene3D:2.130.10.10,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF37,Superfamily_domains:SSF101912 LOW 1 SNV 1 1 PASS rs1444261661 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 50275319 50275319 C G 1 0 0 0 0 0 0 0 1 14301 668 24 4 4 SEMA3B 3 50275319 Silent SNP C C3L-00144_T 92928 50275319 148020240 361 4432 RBM15B 0 . GRCh38 3 51391843 51391843 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.444C>T p.= p.P148P ENST00000563281 1/1 290 261 29 208 208 0 strelka-varscan-mutect RBM15B,synonymous_variant,p.=,ENST00000563281,NM_013286.4;DCAF1,downstream_gene_variant,,ENST00000504652,NM_001171904.1;DCAF1,downstream_gene_variant,,ENST00000423656,NM_014703.2;MANF,downstream_gene_variant,,ENST00000528157,NM_006010.5;MANF,downstream_gene_variant,,ENST00000470900,;MANF,downstream_gene_variant,,ENST00000446668,;MANF,downstream_gene_variant,,ENST00000482262,; T ENST00000563281 Transcript synonymous_variant 576/6641 444/2673 148/890 P ccC/ccT 1 1 RBM15B HGNC HGNC:24303 protein_coding YES CCDS33764.1 ENSP00000454545 Q8NDT2 UPI0000160BDE NM_013286.4 1/1 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF40,Low_complexity_(Seg):seg,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 51391843 51391843 C T 1 0 0 0 0 0 0 0 1 13283 639 23 1 1 RBM15B 3 51391843 Silent SNP C C3L-00144_T 1116524 51391843 146903716 362 4433 RAD54L2 0 . GRCh38 3 51590463 51590463 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.43C>G p.Pro15Ala p.P15A ENST00000409535 2/22 133 122 11 100 100 0 strelka-varscan-mutect RAD54L2,missense_variant,p.Pro15Ala,ENST00000409535,NM_001322253.1,NM_001322256.1,NM_015106.2;RAD54L2,non_coding_transcript_exon_variant,,ENST00000487093,; G ENST00000409535 Transcript missense_variant 168/9776 43/4404 15/1467 P/A Ccg/Gcg COSM4494810 1 1 RAD54L2 HGNC HGNC:29123 protein_coding YES CCDS33765.2 ENSP00000386520 Q9Y4B4 UPI000022C0AA NM_001322253.1,NM_001322256.1,NM_015106.2 deleterious_low_confidence(0.03) 2/22 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.96993 1 1 1 1 0 G 3 3 12 51590463 51590463 C G 1 0 0 0 0 1 0 0 0 13155 623 22 4 4 RAD54L2 3 51590463 Missense_Mutation SNP C C3L-00144_T 198620 51590463 146705096 363 4434 PCBP4 0 . GRCh38 3 51961229 51961229 + Silent SNP C C A rs143679967 C3L-00144_T C3L-00144_N C C c.12G>T p.= p.S4S ENST00000461554 3/14 141 110 31 135 135 0 strelka-varscan-mutect PCBP4,synonymous_variant,p.=,ENST00000461554,NM_001174100.1;PCBP4,synonymous_variant,p.=,ENST00000355852,NM_033008.2;PCBP4,synonymous_variant,p.=,ENST00000484633,NM_020418.3;PCBP4,synonymous_variant,p.=,ENST00000322099,NM_033010.2;PCBP4,synonymous_variant,p.=,ENST00000428823,;PCBP4,synonymous_variant,p.=,ENST00000471622,;PCBP4,synonymous_variant,p.=,ENST00000395014,;PCBP4,synonymous_variant,p.=,ENST00000466412,;PCBP4,synonymous_variant,p.=,ENST00000468324,;PCBP4,synonymous_variant,p.=,ENST00000483411,;PCBP4,synonymous_variant,p.=,ENST00000461544,;PCBP4,synonymous_variant,p.=,ENST00000497653,;PCBP4,synonymous_variant,p.=,ENST00000489595,;PCBP4,synonymous_variant,p.=,ENST00000490063,;GPR62,downstream_gene_variant,,ENST00000322241,NM_080865.3;RP11-155D18.12,non_coding_transcript_exon_variant,,ENST00000488257,;PCBP4,synonymous_variant,p.=,ENST00000471308,;PCBP4,non_coding_transcript_exon_variant,,ENST00000492809,;PCBP4,non_coding_transcript_exon_variant,,ENST00000498822,;PCBP4,non_coding_transcript_exon_variant,,ENST00000497390,;PCBP4,non_coding_transcript_exon_variant,,ENST00000471358,; A ENST00000461554 Transcript synonymous_variant 344/2147 12/1212 4/403 S tcG/tcT rs143679967 1 -1 PCBP4 HGNC HGNC:8652 protein_coding YES CCDS2839.1 ENSP00000417196 P57723 A0A024R320 UPI00001313CB NM_001174100.1 3/14 hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF166 LOW 1 SNV 1 1 PASS rs143679967 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 51961229 51961229 C A 1 0 0 0 0 0 0 0 1 11590 639 23 1 1 PCBP4 3 51961229 Silent SNP C C3L-00144_T 370766 51961229 146334330 364 4435 NISCH 0 . GRCh38 3 52488533 52488533 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.3041C>T p.Ala1014Val p.A1014V ENST00000345716 16/21 138 103 35 139 139 0 strelka-varscan-mutect NISCH,missense_variant,p.Ala1014Val,ENST00000345716,NM_007184.3;NISCH,missense_variant,p.Ala1014Val,ENST00000479054,;NISCH,downstream_gene_variant,,ENST00000488243,;NISCH,non_coding_transcript_exon_variant,,ENST00000489895,;NISCH,upstream_gene_variant,,ENST00000467594,;NISCH,downstream_gene_variant,,ENST00000460759,;NISCH,downstream_gene_variant,,ENST00000485765,; T ENST00000345716 Transcript missense_variant 3175/5238 3041/4515 1014/1504 A/V gCc/gTc 1 1 NISCH HGNC HGNC:18006 protein_coding YES CCDS33767.1 ENSP00000339958 Q9Y2I1 UPI000036715D NM_007184.3 tolerated(0.51) 16/21 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 52488533 52488533 C T 1 0 0 0 0 1 0 0 0 10467 739 26 3 3 NISCH 3 52488533 Missense_Mutation SNP C C3L-00144_T 527304 52488533 145807026 365 4436 ITIH1 0 . GRCh38 3 52789651 52789651 + Splice_Site SNP A A T novel C3L-00144_T C3L-00144_N A A c.2120-2A>T p.X707_splice ENST00000273283 106 92 14 117 117 0 strelka-varscan-mutect ITIH1,splice_acceptor_variant,,ENST00000273283,NM_002215.3,NM_001166434.2;ITIH1,splice_acceptor_variant,,ENST00000537050,NM_001166435.2,NM_001166436.2;ITIH1,splice_acceptor_variant,,ENST00000428133,;ITIH1,splice_acceptor_variant,,ENST00000405128,;ITIH1,splice_acceptor_variant,,ENST00000628722,;ITIH1,splice_acceptor_variant,,ENST00000482836,;ITIH1,splice_acceptor_variant,,ENST00000484844,;ITIH1,upstream_gene_variant,,ENST00000494705,; T ENST00000273283 Transcript splice_acceptor_variant -/2911 2120/2736 707/911 1 1 ITIH1 HGNC HGNC:6166 protein_coding YES CCDS2864.1 ENSP00000273283 P19827 UPI000012DA1C NM_002215.3,NM_001166434.2 18/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 52789651 52789651 A T 1 0 0 0 0 0 0 1 0 7809 202 7 4 4 ITIH1 3 52789651 Splice_Site SNP A C3L-00144_T 301118 52789651 145505908 366 4437 ERC2 0 . GRCh38 3 56296315 56296315 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.778G>T p.Glu260Ter p.E260* ENST00000288221 3/18 275 219 56 250 250 0 strelka-varscan-mutect ERC2,stop_gained,p.Glu260Ter,ENST00000288221,NM_015576.1;ERC2,stop_gained,p.Glu260Ter,ENST00000612797,;ERC2,stop_gained,p.Glu260Ter,ENST00000460849,; A ENST00000288221 Transcript stop_gained 1034/6138 778/2874 260/957 E/* Gag/Tag 1 -1 ERC2 HGNC HGNC:31922 protein_coding YES CCDS46851.1 ENSP00000288221 O15083 UPI00001C1572 NM_015576.1 3/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10174,hmmpanther:PTHR18861 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 56296315 56296315 C A 1 0 0 0 0 0 1 0 0 5060 893 31 1 1 ERC2 3 56296315 Nonsense_Mutation SNP C C3L-00144_T 3506664 56296315 141999244 367 4438 FLNB 0 . GRCh38 3 58134743 58134743 + Missense_Mutation SNP G G T rs372932282 C3L-00144_T C3L-00144_N G G c.4735G>T p.Gly1579Trp p.G1579W ENST00000490882 28/47 186 146 40 171 171 0 strelka-varscan-mutect FLNB,missense_variant,p.Gly1548Trp,ENST00000295956,NM_001457.3;FLNB,missense_variant,p.Gly1548Trp,ENST00000429972,NM_001164318.1;FLNB,missense_variant,p.Gly1548Trp,ENST00000358537,NM_001164319.1;FLNB,missense_variant,p.Gly1579Trp,ENST00000490882,NM_001164317.1;FLNB,missense_variant,p.Gly1379Trp,ENST00000493452,;FLNB,non_coding_transcript_exon_variant,,ENST00000481470,; T ENST00000490882 Transcript missense_variant 4900/8079 4735/7902 1579/2633 G/W Ggg/Tgg rs372932282 1 1 FLNB HGNC HGNC:3755 protein_coding YES CCDS54599.1 ENSP00000420213 O75369 UPI0001765F91 NM_001164317.1 deleterious(0) 28/47 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF238,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs372932282 . 0 206 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 T 3 4 12 58134743 58134743 G T 1 0 0 0 0 1 0 0 0 5790 1116 39 1 1 FLNB 3 58134743 Missense_Mutation SNP G C3L-00144_T 1838428 58134743 140160816 368 4439 FEZF2 0 . GRCh38 3 62372191 62372191 + Missense_Mutation SNP G G T rs759549742 C3L-00144_T C3L-00144_N G G c.678C>A p.Phe226Leu p.F226L ENST00000283268 2/5 106 87 19 85 84 1 strelka-varscan-mutect FEZF2,missense_variant,p.Phe226Leu,ENST00000283268,NM_018008.3;FEZF2,missense_variant,p.Phe226Leu,ENST00000486811,;FEZF2,missense_variant,p.Phe226Leu,ENST00000475839,;PTPRG-AS1,upstream_gene_variant,,ENST00000490916,;PTPRG-AS1,upstream_gene_variant,,ENST00000495542,; T ENST00000283268 Transcript missense_variant 973/2074 678/1380 226/459 F/L ttC/ttA rs759549742,COSM302225 1 -1 FEZF2 HGNC HGNC:13506 protein_coding YES CCDS2897.1 ENSP00000283268 Q8TBJ5 A0A140VKG3 UPI0000071A13 NM_018008.3 tolerated(0.49) 2/5 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF287 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759549742 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 62372191 62372191 G T 1 0 0 0 0 1 0 0 0 5689 1165 41 2 2 FEZF2 3 62372191 Missense_Mutation SNP G C3L-00144_T 4237448 62372191 135923368 369 4440 ATXN7 0 . GRCh38 3 63913220 63913220 + Frame_Shift_Del DEL G G - rs774868672 C3L-00144_T C3L-00144_N G G c.391delG p.Glu131LysfsTer92 p.E131Kfs*92 ENST00000538065 3/13 155 126 29 141 141 0 sindel-varindel-pindel ATXN7,frameshift_variant,p.Glu131LysfsTer92,ENST00000295900,NM_000333.3;ATXN7,frameshift_variant,p.Glu131LysfsTer92,ENST00000538065,NM_001177387.1;ATXN7,frameshift_variant,p.Glu131LysfsTer92,ENST00000487717,;ATXN7,downstream_gene_variant,,ENST00000474513,;SCAANT1,upstream_gene_variant,,ENST00000626439,;ATXN7,non_coding_transcript_exon_variant,,ENST00000474112,; - ENST00000538065 Transcript frameshift_variant 499/6842 389/2838 130/945 R/X cGg/cg rs774868672 1 1 ATXN7 HGNC HGNC:10560 protein_coding YES CCDS54603.1 ENSP00000439585 O15265 UPI00001B07C4 NM_001177387.1 3/13 hmmpanther:PTHR15117:SF2,hmmpanther:PTHR15117 HIGH 1 deletion 1 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999996 1 1 1 0 - 7 5 12 63913220 63913220 G - 1 0 1 0 1 0 0 0 0 1369 1130 39 0 0 ATXN7 3 63913220 Frame_Shift_Del DEL G C3L-00144_T 1541029 63913220 134382339 370 4441 PRICKLE2 0 . GRCh38 3 64146849 64146849 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1641G>T p.= p.L547L ENST00000295902 7/8 214 194 20 174 174 0 strelka-varscan-mutect PRICKLE2,synonymous_variant,p.=,ENST00000295902,NM_198859.3;PRICKLE2,synonymous_variant,p.=,ENST00000564377,; A ENST00000295902 Transcript synonymous_variant 2227/8305 1641/2535 547/844 L ctG/ctT 1 -1 PRICKLE2 HGNC HGNC:20340 protein_coding YES CCDS2902.1 ENSP00000295902 Q7Z3G6 A0A024R368 UPI0000160A8B NM_198859.3 7/8 hmmpanther:PTHR24211:SF18,hmmpanther:PTHR24211 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 64146849 64146849 C A 1 0 0 0 0 0 0 0 1 12619 581 21 2 2 PRICKLE2 3 64146849 Silent SNP C C3L-00144_T 233629 64146849 134148710 371 4442 KBTBD8 0 . GRCh38 3 67003903 67003903 + Frame_Shift_Del DEL A A - novel C3L-00144_T C3L-00144_N A A c.937delA p.Arg313GlyfsTer12 p.R313Gfs*12 ENST00000417314 3/4 205 184 21 176 176 0 sindel-varindel-pindel KBTBD8,frameshift_variant,p.Arg313GlyfsTer12,ENST00000417314,NM_032505.2;KBTBD8,intron_variant,,ENST00000460576,;KBTBD8,downstream_gene_variant,,ENST00000484414,;KBTBD8,downstream_gene_variant,,ENST00000460784,;KBTBD8,downstream_gene_variant,,ENST00000469661,; - ENST00000417314 Transcript frameshift_variant 985/4680 936/1806 312/601 G/X ggA/gg 1 1 KBTBD8 HGNC HGNC:30691 protein_coding YES CCDS2906.2 ENSP00000401878 Q8NFY9 UPI0000209974 NM_032505.2 3/4 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF24 HIGH 1 deletion 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 67003903 67003903 A - 1 0 1 0 1 0 0 0 0 7915 233 9 0 0 KBTBD8 3 67003903 Frame_Shift_Del DEL A C3L-00144_T 2857054 67003903 131291656 372 4443 FAM19A4 0 . GRCh38 3 68880741 68880741 + Missense_Mutation SNP C C A rs751781952 C3L-00144_T C3L-00144_N C C c.119G>T p.Arg40Leu p.R40L ENST00000295569 3/6 143 123 20 116 116 0 strelka-varscan-mutect FAM19A4,missense_variant,p.Arg40Leu,ENST00000295569,NM_001005527.2,NM_182522.4;FAM19A4,missense_variant,p.Arg40Leu,ENST00000634242,;FAM19A4,missense_variant,p.Arg40Leu,ENST00000495737,;RNA5SP135,upstream_gene_variant,,ENST00000517019,; A ENST00000295569 Transcript missense_variant 612/2292 119/423 40/140 R/L cGg/cTg rs751781952 1 -1 FAM19A4 HGNC HGNC:21591 protein_coding YES CCDS2907.1 ENSP00000295569 Q96LR4 A0A024R369 UPI0000071129 NM_001005527.2,NM_182522.4 tolerated(0.16) 3/6 hmmpanther:PTHR31770,hmmpanther:PTHR31770:SF7 MODERATE 1 SNV 1 1 PASS rs751781952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 68880741 68880741 C A 1 0 0 0 0 1 0 0 0 5381 652 23 1 1 FAM19A4 3 68880741 Missense_Mutation SNP C C3L-00144_T 1876838 68880741 129414818 373 4444 FRMD4B 0 . GRCh38 3 69181285 69181285 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2465G>T p.Gly822Val p.G822V ENST00000398540 21/23 341 312 29 268 268 0 strelka-varscan-mutect FRMD4B,missense_variant,p.Gly822Val,ENST00000398540,NM_015123.2;FRMD4B,missense_variant,p.Gly474Val,ENST00000478263,; A ENST00000398540 Transcript missense_variant 2549/5060 2465/3105 822/1034 G/V gGt/gTt 1 -1 FRMD4B HGNC HGNC:24886 protein_coding YES CCDS46863.1 ENSP00000381549 Q9Y2L6 UPI00001C1DF1 NM_015123.2 tolerated(0.35) 21/23 hmmpanther:PTHR23281:SF16,hmmpanther:PTHR23281 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 69181285 69181285 C A 1 0 0 0 0 1 0 0 0 5922 507 18 2 2 FRMD4B 3 69181285 Missense_Mutation SNP C C3L-00144_T 300544 69181285 129114274 374 4445 PDZRN3 0 . GRCh38 3 73383659 73383659 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2907G>A p.Met969Ile p.M969I ENST00000263666 10/10 466 418 48 436 436 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Met969Ile,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Met626Ile,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Met686Ile,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Met626Ile,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Met285Ile,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000492909,NM_001303139.1;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,; T ENST00000263666 Transcript missense_variant 3022/4248 2907/3201 969/1066 M/I atG/atA 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 10/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 73383659 73383659 C T 1 0 0 0 0 1 0 0 0 11797 594 21 3 3 PDZRN3 3 73383659 Missense_Mutation SNP C C3L-00144_T 4202374 73383659 124911900 375 4446 CADM2 0 . GRCh38 3 85935791 85935791 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.704C>A p.Pro235Gln p.P235Q ENST00000405615 6/10 155 118 37 124 124 0 strelka-varscan-mutect CADM2,missense_variant,p.Pro242Gln,ENST00000383699,NM_001256504.1,NM_001256505.1,NM_001167675.1;CADM2,missense_variant,p.Pro233Gln,ENST00000407528,NM_001167674.1;CADM2,missense_variant,p.Pro235Gln,ENST00000405615,NM_153184.3; A ENST00000405615 Transcript missense_variant 704/1314 704/1314 235/437 P/Q cCa/cAa 1 1 CADM2 HGNC HGNC:29849 protein_coding YES CCDS33792.1 ENSP00000384193 Q8N3J6 UPI000013F077 NM_153184.3 tolerated(0.09) 6/10 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 1 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 85935791 85935791 C A 1 0 0 0 0 1 0 0 0 2257 594 21 2 2 CADM2 3 85935791 Missense_Mutation SNP C C3L-00144_T 12552132 85935791 112359768 376 4447 C3orf38 0 . GRCh38 3 88156163 88156163 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.518G>T p.Trp173Leu p.W173L ENST00000318887 3/3 74 69 5 54 54 0 strelka-mutect C3orf38,missense_variant,p.Trp173Leu,ENST00000318887,NM_173824.3;C3orf38,missense_variant,p.Gly138Cys,ENST00000486971,;C3orf38,downstream_gene_variant,,ENST00000464919,;C3orf38,upstream_gene_variant,,ENST00000485219,; T ENST00000318887 Transcript missense_variant 828/2633 518/990 173/329 W/L tGg/tTg 1 1 C3orf38 HGNC HGNC:28384 protein_coding YES CCDS2921.2 ENSP00000322469 Q5JPI3 UPI000004D308 NM_173824.3 deleterious(0) 3/3 hmmpanther:PTHR21084,Pfam_domain:PF15008,Superfamily_domains:SSF54427 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -11.34496 1 1 1 1 0 T 3 4 12 88156163 88156163 G T 1 0 0 0 0 1 0 0 0 2066 1357 47 2 2 C3orf38 3 88156163 Missense_Mutation SNP G C3L-00144_T 2220372 88156163 110139396 377 4448 EPHA3 0 . GRCh38 3 89210097 89210097 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.391C>G p.His131Asp p.H131D ENST00000336596 3/17 242 198 44 207 207 0 strelka-varscan-mutect EPHA3,missense_variant,p.His131Asp,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.His131Asp,ENST00000494014,;EPHA3,missense_variant,p.His131Asp,ENST00000452448,NM_182644.2; G ENST00000336596 Transcript missense_variant 616/5809 391/2952 131/983 H/D Cat/Gat 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 tolerated(0.63) 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS rs1370363055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 89210097 89210097 C G 1 0 0 0 0 1 0 0 0 5015 826 29 4 4 EPHA3 3 89210097 Missense_Mutation SNP C C3L-00144_T 1053934 89210097 109085462 378 4449 EPHA6 0 . GRCh38 3 97244207 97244207 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1526T>A p.Ile509Lys p.I509K ENST00000389672 5/18 311 263 48 209 209 0 strelka-varscan-mutect EPHA6,missense_variant,p.Ile509Lys,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Ile509Lys,ENST00000470610,; A ENST00000389672 Transcript missense_variant 1564/3971 1526/3393 509/1130 I/K aTa/aAa 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 5/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 97244207 97244207 T A 1 0 0 0 0 1 0 0 0 5018 1406 49 4 4 EPHA6 3 97244207 Missense_Mutation SNP T C3L-00144_T 8034110 97244207 101051352 379 4450 EPHA6 0 . GRCh38 3 97637996 97637996 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2698G>T p.Val900Phe p.V900F ENST00000389672 14/18 250 190 60 172 172 0 strelka-varscan-mutect EPHA6,missense_variant,p.Val900Phe,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Val292Phe,ENST00000514100,NM_001278300.1;EPHA6,missense_variant,p.Val292Phe,ENST00000502694,NM_173655.3;EPHA6,missense_variant,p.Val224Phe,ENST00000477384,;EPHA6,3_prime_UTR_variant,,ENST00000508345,; T ENST00000389672 Transcript missense_variant 2736/3971 2698/3393 900/1130 V/F Gtc/Ttc 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0.01) 14/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 97637996 97637996 G T 1 0 0 0 0 1 0 0 0 5018 1261 44 2 2 EPHA6 3 97637996 Missense_Mutation SNP G C3L-00144_T 393789 97637996 100657563 380 4451 OR5H1 0 . GRCh38 3 98133026 98133026 + Missense_Mutation SNP C C A rs145926344 C3L-00144_T C3L-00144_N C C c.329C>A p.Thr110Lys p.T110K ENST00000354565 1/1 380 315 65 295 293 2 strelka-varscan-mutect OR5H1,missense_variant,p.Thr110Lys,ENST00000354565,NM_001005338.1;RP11-343D2.11,intron_variant,,ENST00000508964,; A ENST00000354565 Transcript missense_variant 329/942 329/942 110/313 T/K aCg/aAg rs145926344,COSM2950045 1 1 OR5H1 HGNC HGNC:8346 protein_coding YES CCDS33797.1 ENSP00000346575 A6NKK0 A0A126GW79 UPI0000197652 NM_001005338.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE SNV 0,1 1 PASS rs145926344 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 98133026 98133026 C A 1 0 0 0 0 1 0 0 0 11229 536 19 1 1 OR5H1 3 98133026 Missense_Mutation SNP C C3L-00144_T 495030 98133026 100162533 381 4452 OR5H1 0 . GRCh38 3 98133425 98133425 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.728C>A p.Ala243Asp p.A243D ENST00000354565 1/1 443 330 113 282 281 1 strelka-varscan-mutect OR5H1,missense_variant,p.Ala243Asp,ENST00000354565,NM_001005338.1;RP11-343D2.11,intron_variant,,ENST00000508964,; A ENST00000354565 Transcript missense_variant 728/942 728/942 243/313 A/D gCc/gAc 1 1 OR5H1 HGNC HGNC:8346 protein_coding YES CCDS33797.1 ENSP00000346575 A6NKK0 A0A126GW79 UPI0000197652 NM_001005338.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 98133425 98133425 C A 1 0 0 0 0 1 0 0 0 11229 739 26 2 2 OR5H1 3 98133425 Missense_Mutation SNP C C3L-00144_T 399 98133425 100162134 382 4453 FILIP1L 0 . GRCh38 3 99850262 99850262 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1414C>A p.Leu472Ile p.L472I ENST00000354552 5/6 249 232 17 171 171 0 strelka-varscan-mutect FILIP1L,missense_variant,p.Leu472Ile,ENST00000331335,NM_001042459.2;FILIP1L,missense_variant,p.Leu472Ile,ENST00000354552,NM_182909.3;FILIP1L,missense_variant,p.Leu232Ile,ENST00000383694,NM_014890.3;FILIP1L,missense_variant,p.Leu232Ile,ENST00000495625,;FILIP1L,missense_variant,p.Leu232Ile,ENST00000471562,NM_001282794.1;FILIP1L,missense_variant,p.Leu48Ile,ENST00000487087,NM_001282793.1;CMSS1,intron_variant,,ENST00000421999,NM_032359.3;CMSS1,intron_variant,,ENST00000463526,;FILIP1L,upstream_gene_variant,,ENST00000477258,;CMSS1,intron_variant,,ENST00000496116,;FILIP1L,intron_variant,,ENST00000476723,;CMSS1,intron_variant,,ENST00000491299,; T ENST00000354552 Transcript missense_variant 1885/3970 1414/3408 472/1135 L/I Cta/Ata 1 -1 FILIP1L HGNC HGNC:24589 protein_coding YES CCDS43117.1 ENSP00000346560 Q4L180 UPI00001B24B2 NM_182909.3 deleterious(0.03) 5/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF4 MODERATE 1 SNV 1 1 PASS rs1255987357 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 99850262 99850262 G T 1 0 0 0 0 1 0 0 0 5758 962 34 2 2 FILIP1L 3 99850262 Missense_Mutation SNP G C3L-00144_T 1716837 99850262 98445297 383 4454 MORC1 0 . GRCh38 3 109069681 109069681 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.766G>T p.Ala256Ser p.A256S ENST00000232603 9/28 175 140 35 142 142 0 strelka-varscan-mutect MORC1,missense_variant,p.Ala256Ser,ENST00000232603,NM_014429.3;MORC1,missense_variant,p.Ala256Ser,ENST00000483760,; A ENST00000232603 Transcript missense_variant 849/3764 766/2955 256/984 A/S Gcc/Tcc 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 tolerated(0.14) 9/28 hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337,Superfamily_domains:SSF55874 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 109069681 109069681 C A 1 0 0 0 0 1 0 0 0 9665 797 28 2 2 MORC1 3 109069681 Missense_Mutation SNP C C3L-00144_T 9219419 109069681 89225878 384 4455 DPPA2 0 . GRCh38 3 109304595 109304595 + Missense_Mutation SNP G G C C3L-00144_T C3L-00144_N G G c.734C>G p.Ala245Gly p.A245G ENST00000478945 7/9 143 110 33 118 118 0 strelka-varscan-mutect DPPA2,missense_variant,p.Ala245Gly,ENST00000478945,NM_138815.3; C ENST00000478945 Transcript missense_variant 981/1383 734/897 245/298 A/G gCa/gGa COSM4773631 1 -1 DPPA2 HGNC HGNC:19197 protein_coding YES CCDS2956.1 ENSP00000417710 Q7Z7J5 UPI000007143F NM_138815.3 tolerated(0.08) 7/9 Pfam_domain:PF14047,hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF10 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 109304595 109304595 G C 1 0 0 0 0 1 0 0 0 4549 1319 46 4 4 DPPA2 3 109304595 Missense_Mutation SNP G C3L-00144_T 234914 109304595 88990964 385 4456 SLC9C1 0 . GRCh38 3 112278806 112278806 + Missense_Mutation SNP G G T rs749177716 C3L-00144_T C3L-00144_N G G c.241C>A p.Arg81Ser p.R81S ENST00000305815 4/29 274 200 74 231 230 1 strelka-varscan-mutect SLC9C1,missense_variant,p.Arg81Ser,ENST00000305815,NM_183061.1;SLC9C1,missense_variant,p.Arg81Ser,ENST00000487372,NM_001320531.1;SLC9C1,missense_variant,p.Arg8Ser,ENST00000486574,;SLC9C1,non_coding_transcript_exon_variant,,ENST00000467397,;SLC9C1,missense_variant,p.Arg81Ser,ENST00000471295,; T ENST00000305815 Transcript missense_variant 494/4172 241/3534 81/1177 R/S Cgt/Agt rs749177716,COSM3408137 1 -1 SLC9C1 HGNC HGNC:31401 protein_coding YES CCDS33817.1 ENSP00000306627 Q4G0N8 UPI00002372C5 NM_183061.1 tolerated(0.47) 4/29 Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF87,Pfam_domain:PF00999 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs749177716 . 0 204 0 2 4 0 0 0 -20 0.9092115 1 1 1 0 T 3 4 12 112278806 112278806 G T 1 0 0 0 0 1 0 0 0 15006 1058 37 1 1 SLC9C1 3 112278806 Missense_Mutation SNP G C3L-00144_T 2974211 112278806 86016753 386 4457 BTLA 0 . GRCh38 3 112479758 112479758 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.100T>C p.Cys34Arg p.C34R ENST00000334529 2/5 58 52 6 51 51 0 strelka-varscan-mutect BTLA,missense_variant,p.Cys34Arg,ENST00000334529,NM_181780.3;BTLA,missense_variant,p.Cys34Arg,ENST00000383680,NM_001085357.1; G ENST00000334529 Transcript missense_variant 303/3213 100/870 34/289 C/R Tgt/Cgt 1 -1 BTLA HGNC HGNC:21087 protein_coding YES CCDS33819.1 ENSP00000333919 Q7Z6A9 UPI0000209F49 NM_181780.3 deleterious(0) 2/5 PROSITE_profiles:PS50835,hmmpanther:PTHR37996,hmmpanther:PTHR37996:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.50801 1 1 1 1 0 G 3 3 12 112479758 112479758 A G 1 0 0 0 0 1 0 0 0 1734 217 8 5 5 BTLA 3 112479758 Missense_Mutation SNP A C3L-00144_T 200952 112479758 85815801 387 4458 TIGIT 0 . GRCh38 3 114294074 114294074 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.13C>T p.Leu5Phe p.L5F ENST00000486257 2/5 231 195 36 173 172 1 strelka-varscan-mutect TIGIT,missense_variant,p.Leu72Phe,ENST00000481065,;TIGIT,missense_variant,p.Leu5Phe,ENST00000486257,;TIGIT,missense_variant,p.Leu5Phe,ENST00000383671,NM_173799.3;TIGIT,intron_variant,,ENST00000461158,;TIGIT,upstream_gene_variant,,ENST00000484319,;TIGIT,non_coding_transcript_exon_variant,,ENST00000485814,; T ENST00000486257 Transcript missense_variant 270/3149 13/735 5/244 L/F Ctc/Ttc 1 1 TIGIT HGNC HGNC:26838 protein_coding YES CCDS2980.1 ENSP00000419085 Q495A1 UPI000013F7B8 tolerated(0.08) 2/5 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF49,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 114294074 114294074 C T 1 0 0 0 0 1 0 0 0 16340 913 32 3 3 TIGIT 3 114294074 Missense_Mutation SNP C C3L-00144_T 1814316 114294074 84001485 388 4459 ZBTB20 0 . GRCh38 3 114351455 114351455 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.623G>T p.Gly208Val p.G208V ENST00000474710 4/5 276 227 49 189 189 0 strelka-varscan-mutect ZBTB20,missense_variant,p.Gly135Val,ENST00000357258,NM_015642.5;ZBTB20,missense_variant,p.Gly135Val,ENST00000462705,NM_001164343.2;ZBTB20,missense_variant,p.Gly135Val,ENST00000393785,NM_001164346.2;ZBTB20,missense_variant,p.Gly135Val,ENST00000471418,NM_001164345.2;ZBTB20,missense_variant,p.Gly135Val,ENST00000464560,NM_001164344.2;ZBTB20,missense_variant,p.Gly135Val,ENST00000481632,NM_001164347.2;ZBTB20,missense_variant,p.Gly208Val,ENST00000474710,NM_001164342.2;ZBTB20,downstream_gene_variant,,ENST00000470311,;ZBTB20-AS1,upstream_gene_variant,,ENST00000475939,;ZBTB20-AS1,upstream_gene_variant,,ENST00000467304,;ZBTB20-AS1,upstream_gene_variant,,ENST00000496219,;ZBTB20,intron_variant,,ENST00000479879,; A ENST00000474710 Transcript missense_variant 802/2757 623/2226 208/741 G/V gGc/gTc 1 -1 ZBTB20 HGNC HGNC:13503 protein_coding YES CCDS54626.1 ENSP00000419153 Q9HC78 UPI0000141957 NM_001164342.2 deleterious(0) 4/5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 114351455 114351455 C A 1 0 0 0 0 1 0 0 0 18097 739 26 2 2 ZBTB20 3 114351455 Missense_Mutation SNP C C3L-00144_T 57381 114351455 83944104 389 4460 UPK1B 0 . GRCh38 3 119187876 119187876 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.171G>T p.= p.G57G ENST00000264234 3/8 615 459 156 471 470 1 strelka-varscan-mutect UPK1B,synonymous_variant,p.=,ENST00000264234,NM_006952.3;UPK1B,synonymous_variant,p.=,ENST00000460625,;UPK1B,synonymous_variant,p.=,ENST00000479520,;UPK1B,synonymous_variant,p.=,ENST00000494855,;UPK1B,5_prime_UTR_variant,,ENST00000497685,;RP11-484M3.5,downstream_gene_variant,,ENST00000490594,; T ENST00000264234 Transcript synonymous_variant 320/2118 171/783 57/260 G ggG/ggT 1 1 UPK1B HGNC HGNC:12578 protein_coding YES CCDS2985.1 ENSP00000264234 O75841 UPI000013D4E8 NM_006952.3 3/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR19282:SF24,hmmpanther:PTHR19282,Pfam_domain:PF00335,Prints_domain:PR00259 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 119187876 119187876 G T 1 0 0 0 0 0 0 0 1 17534 1219 43 2 2 UPK1B 3 119187876 Silent SNP G C3L-00144_T 4836421 119187876 79107683 390 4461 ARHGAP31 0 . GRCh38 3 119415731 119415731 + Nonsense_Mutation SNP G G T rs149658506 C3L-00144_T C3L-00144_N G G c.3802G>T p.Gly1268Ter p.G1268* ENST00000264245 12/12 304 241 63 238 238 0 strelka-varscan-mutect ARHGAP31,stop_gained,p.Gly1268Ter,ENST00000264245,NM_020754.3; T ENST00000264245 Transcript stop_gained 4334/9317 3802/4335 1268/1444 G/* Gga/Tga rs149658506 1 1 ARHGAP31 HGNC HGNC:29216 protein_coding YES CCDS43135.1 ENSP00000264245 Q2M1Z3 UPI00001C1DFD NM_020754.3 12/12 hmmpanther:PTHR15729:SF3,hmmpanther:PTHR15729 HIGH 1 SNV 1 1 PASS rs149658506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 119415731 119415731 G T 1 0 0 0 0 0 1 0 0 1005 1117 39 1 1 ARHGAP31 3 119415731 Nonsense_Mutation SNP G C3L-00144_T 227855 119415731 78879828 391 4462 MAATS1 0 . GRCh38 3 119707549 119707549 + Missense_Mutation SNP G G T rs751536588,rs760911940 C3L-00144_T C3L-00144_N G G c.347G>T p.Arg116Leu p.R116L ENST00000273390 3/18 146 106 40 112 112 0 strelka-varscan-mutect MAATS1,missense_variant,p.Arg116Leu,ENST00000273390,NM_001320318.1,NM_001320316.1,NM_033364.3;MAATS1,missense_variant,p.Arg116Leu,ENST00000463700,;MAATS1,missense_variant,p.Arg14Leu,ENST00000498167,;MAATS1,3_prime_UTR_variant,,ENST00000482573,NM_001320318.1,NM_001320317.1;MAATS1,3_prime_UTR_variant,,ENST00000482927,;MAATS1,non_coding_transcript_exon_variant,,ENST00000483134,;MAATS1,non_coding_transcript_exon_variant,,ENST00000468630,;MAATS1,non_coding_transcript_exon_variant,,ENST00000469659,;MAATS1,intron_variant,,ENST00000475093,;MAATS1,downstream_gene_variant,,ENST00000488533,; T ENST00000273390 Transcript missense_variant 424/4433 347/2304 116/767 R/L cGg/cTg rs751536588,rs760911940 1 1 MAATS1 HGNC HGNC:24010 protein_coding YES CCDS2994.1 ENSP00000273390 Q7Z4T9 UPI00001C1DFE NM_001320318.1,NM_001320316.1,NM_033364.3 tolerated(0.41) 3/18 hmmpanther:PTHR22455,hmmpanther:PTHR22455:SF10 MODERATE 1 SNV 1 1 PASS rs760911940 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 119707549 119707549 G T 1 0 0 0 0 1 0 0 0 9055 1116 39 1 1 MAATS1 3 119707549 Missense_Mutation SNP G C3L-00144_T 291818 119707549 78588010 392 4463 GPR156 0 . GRCh38 3 120193426 120193426 + Splice_Site SNP T T A novel C3L-00144_T C3L-00144_N T T c.234-2A>T p.X78_splice ENST00000464295 234 177 57 177 177 0 strelka-varscan-mutect GPR156,splice_acceptor_variant,,ENST00000464295,;GPR156,splice_acceptor_variant,,ENST00000315843,NM_153002.2;GPR156,splice_acceptor_variant,,ENST00000461057,NM_001168271.1;GPR156,intron_variant,,ENST00000495912,; A ENST00000464295 Transcript splice_acceptor_variant -/4442 234/2445 78/814 1 -1 GPR156 HGNC HGNC:20844 protein_coding YES CCDS2997.1 ENSP00000417261 Q8NFN8 UPI000004731C 3/9 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 120193426 120193426 T A 1 0 0 0 0 0 0 1 0 6547 1536 53 4 4 GPR156 3 120193426 Splice_Site SNP T C3L-00144_T 485877 120193426 78102133 393 4464 HGD 0 . GRCh38 3 120633195 120633195 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1140G>A p.= p.K380K ENST00000283871 13/14 386 323 63 281 281 0 strelka-varscan-mutect HGD,synonymous_variant,p.=,ENST00000283871,NM_000187.3;HGD,downstream_gene_variant,,ENST00000494453,;HGD,downstream_gene_variant,,ENST00000475447,;HGD,3_prime_UTR_variant,,ENST00000492108,;HGD,non_coding_transcript_exon_variant,,ENST00000470321,; T ENST00000283871 Transcript synonymous_variant 1600/2005 1140/1338 380/445 K aaG/aaA 1 -1 HGD HGNC HGNC:4892 protein_coding YES CCDS3000.1 ENSP00000283871 Q93099 UPI000020A025 NM_000187.3 13/14 Gene3D:2.60.120.10,Pfam_domain:PF04209,hmmpanther:PTHR11056,Superfamily_domains:SSF51182,TIGRFAM_domain:TIGR01015 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 120633195 120633195 C T 1 0 0 0 0 0 0 0 1 6968 680 24 3 3 HGD 3 120633195 Silent SNP C C3L-00144_T 439769 120633195 77662364 394 4465 STXBP5L 0 . GRCh38 3 120909709 120909709 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.131G>C p.Gly44Ala p.G44A ENST00000273666 2/28 294 246 48 282 282 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Gly44Ala,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Gly44Ala,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Gly44Ala,ENST00000471262,;STXBP5L,missense_variant,p.Gly44Ala,ENST00000492541,;STXBP5L,missense_variant,p.Gly44Ala,ENST00000472879,;STXBP5L,missense_variant,p.Gly44Ala,ENST00000497029,;STXBP5L,missense_variant,p.Gly44Ala,ENST00000495504,;STXBP5L,missense_variant,p.Gly44Ala,ENST00000461772,; C ENST00000273666 Transcript missense_variant 402/9496 131/3561 44/1186 G/A gGg/gCg 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 tolerated(0.71) 2/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 120909709 120909709 G C 1 0 0 0 0 1 0 0 0 15741 1232 43 4 4 STXBP5L 3 120909709 Missense_Mutation SNP G C3L-00144_T 276514 120909709 77385850 395 4466 STXBP5L 0 . GRCh38 3 121239071 121239071 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1285C>A p.Leu429Met p.L429M ENST00000273666 13/28 223 189 34 160 160 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Leu429Met,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Leu429Met,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Leu429Met,ENST00000471262,;STXBP5L,missense_variant,p.Leu429Met,ENST00000492541,;STXBP5L,missense_variant,p.Leu429Met,ENST00000472879,;STXBP5L,missense_variant,p.Leu429Met,ENST00000497029,; A ENST00000273666 Transcript missense_variant 1556/9496 1285/3561 429/1186 L/M Ctg/Atg 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 deleterious(0) 13/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 121239071 121239071 C A 1 0 0 0 0 1 0 0 0 15741 564 20 2 2 STXBP5L 3 121239071 Missense_Mutation SNP C C3L-00144_T 329362 121239071 77056488 396 4467 STXBP5L 0 . GRCh38 3 121324558 121324558 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2314C>A p.Gln772Lys p.Q772K ENST00000497029 22/24 206 180 26 135 135 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Gln772Lys,ENST00000497029,;STXBP5L,intron_variant,,ENST00000273666,NM_014980.2;STXBP5L,intron_variant,,ENST00000471454,NM_001308330.1;STXBP5L,intron_variant,,ENST00000471262,;STXBP5L,intron_variant,,ENST00000492541,;STXBP5L,intron_variant,,ENST00000472879,; A ENST00000497029 Transcript missense_variant 2343/3036 2314/3003 772/1000 Q/K Cag/Aag 1 1 STXBP5L HGNC HGNC:30757 protein_coding ENSP00000420287 C9JPK3 UPI0001B797C0 tolerated(0.94) 22/24 MODERATE SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999973 1 1 1 0 A 3 1 12 121324558 121324558 C A 1 0 0 0 0 1 0 0 0 15741 479 17 2 2 STXBP5L 3 121324558 Missense_Mutation SNP C C3L-00144_T 85487 121324558 76971001 397 4468 STXBP5L 0 . GRCh38 3 121381509 121381509 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.2636A>G p.Glu879Gly p.E879G ENST00000273666 23/28 221 184 37 175 175 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Glu879Gly,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Glu855Gly,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Glu822Gly,ENST00000471262,;STXBP5L,missense_variant,p.Glu879Gly,ENST00000492541,;STXBP5L,missense_variant,p.Glu855Gly,ENST00000472879,;STXBP5L,missense_variant,p.Glu853Gly,ENST00000497029,; G ENST00000273666 Transcript missense_variant 2907/9496 2636/3561 879/1186 E/G gAg/gGg 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 deleterious(0.01) 23/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 121381509 121381509 A G 1 0 0 0 0 1 0 0 0 15741 304 11 5 5 STXBP5L 3 121381509 Missense_Mutation SNP A C3L-00144_T 56951 121381509 76914050 398 4469 POLQ 0 . GRCh38 3 121490267 121490267 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2664G>T p.Gln888His p.Q888H ENST00000264233 16/30 257 188 69 210 210 0 strelka-varscan-mutect POLQ,missense_variant,p.Gln1023His,ENST00000621776,;POLQ,missense_variant,p.Gln888His,ENST00000264233,NM_199420.3;RPL7AP11,upstream_gene_variant,,ENST00000486538,; A ENST00000264233 Transcript missense_variant 2793/8775 2664/7773 888/2590 Q/H caG/caT 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious(0.02) 16/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 121490267 121490267 C A 1 0 0 0 0 1 0 0 0 12318 796 28 2 2 POLQ 3 121490267 Missense_Mutation SNP C C3L-00144_T 108758 121490267 76805292 399 4470 POLQ 0 . GRCh38 3 121490343 121490344 + Frame_Shift_Ins INS - - A novel C3L-00144_T C3L-00144_N - - c.2587dupT p.Trp863LeufsTer10 p.W863Lfs*10 ENST00000264233 16/30 289 212 77 270 270 0 sindel-varindel-pindel POLQ,frameshift_variant,p.Trp998LeufsTer10,ENST00000621776,;POLQ,frameshift_variant,p.Trp863LeufsTer10,ENST00000264233,NM_199420.3;RPL7AP11,upstream_gene_variant,,ENST00000486538,; A ENST00000264233 Transcript frameshift_variant 2716-2717/8775 2587-2588/7773 863/2590 W/LX tgg/tTgg 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 16/30 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 12 121490343 121490343 - A 1 0 1 1 0 0 0 0 0 12318 595 21 0 0 POLQ 3 121490343 Frame_Shift_Ins INS - C3L-00144_T 76 121490343 76805216 400 4471 MUC13 0 . GRCh38 3 124913598 124913598 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1048C>A p.Leu350Met p.L350M ENST00000616727 7/12 416 346 70 305 305 0 strelka-varscan-mutect MUC13,missense_variant,p.Leu350Met,ENST00000616727,NM_033049.3;MUC13,downstream_gene_variant,,ENST00000478191,;MUC13,upstream_gene_variant,,ENST00000462728,; T ENST00000616727 Transcript missense_variant 1087/2879 1048/1539 350/512 L/M Ctg/Atg 1 -1 MUC13 HGNC HGNC:7511 protein_coding YES ENSP00000485028 Q9H3R2 UPI00000730EB NM_033049.3 tolerated(0.23) 7/12 hmmpanther:PTHR24041:SF24,hmmpanther:PTHR24041,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs1459845526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 124913598 124913598 G T 1 0 0 0 0 1 0 0 0 9970 991 35 2 2 MUC13 3 124913598 Missense_Mutation SNP G C3L-00144_T 3423255 124913598 73381961 401 4472 PLXNA1 0 . GRCh38 3 126989104 126989104 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.511G>T p.Gly171Cys p.G171C ENST00000393409 1/31 273 193 80 200 200 0 strelka-varscan-mutect PLXNA1,missense_variant,p.Gly171Cys,ENST00000393409,NM_032242.3; T ENST00000393409 Transcript missense_variant 511/9066 511/5691 171/1896 G/C Ggc/Tgc 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 deleterious(0) 1/31 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 126989104 126989104 G T 1 0 0 0 0 1 0 0 0 12225 1232 43 2 2 PLXNA1 3 126989104 Missense_Mutation SNP G C3L-00144_T 2075506 126989104 71306455 402 4473 PLXNA1 0 . GRCh38 3 127006150 127006150 + Missense_Mutation SNP G G T rs138310005 C3L-00144_T C3L-00144_N G G c.1969G>T p.Val657Phe p.V657F ENST00000393409 7/31 359 313 46 262 262 0 strelka-varscan-mutect PLXNA1,missense_variant,p.Val657Phe,ENST00000393409,NM_032242.3; T ENST00000393409 Transcript missense_variant 1969/9066 1969/5691 657/1896 V/F Gtc/Ttc rs138310005,COSM1418677 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 deleterious(0.01) 7/31 hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs138310005 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 127006150 127006150 G T 1 0 0 0 0 1 0 0 0 12225 1145 40 1 1 PLXNA1 3 127006150 Missense_Mutation SNP G C3L-00144_T 17046 127006150 71289409 403 4474 COL6A5 0 . GRCh38 3 130385157 130385157 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1654G>A p.Asp552Asn p.D552N ENST00000265379 5/43 451 325 126 320 320 0 strelka-varscan-mutect COL6A5,missense_variant,p.Asp552Asn,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Asp552Asn,ENST00000312481,; A ENST00000265379 Transcript missense_variant 2148/9214 1654/7836 552/2611 D/N Gat/Aat 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 tolerated(0.22) 5/43 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 130385157 130385157 G A 1 0 0 0 0 1 0 0 0 3491 1290 45 3 3 COL6A5 3 130385157 Missense_Mutation SNP G C3L-00144_T 3379007 130385157 67910402 404 4475 COL6A5 0 . GRCh38 3 130409363 130409363 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.4517G>A p.Gly1506Glu p.G1506E ENST00000265379 18/43 132 91 41 103 103 0 strelka-varscan-mutect COL6A5,missense_variant,p.Gly1506Glu,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Gly1506Glu,ENST00000312481,; A ENST00000265379 Transcript missense_variant 5011/9214 4517/7836 1506/2611 G/E gGa/gAa COSM4548600,COSM4969120 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0.01) 18/43 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF01391 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 130409363 130409363 G A 1 0 0 0 0 1 0 0 0 3491 1174 41 3 3 COL6A5 3 130409363 Missense_Mutation SNP G C3L-00144_T 24206 130409363 67886196 405 4476 COL6A5 0 . GRCh38 3 130410470 130410470 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.4609-1G>T p.X1537_splice ENST00000265379 119 89 30 96 96 0 strelka-varscan-mutect COL6A5,splice_acceptor_variant,,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,splice_acceptor_variant,,ENST00000312481,; T ENST00000265379 Transcript splice_acceptor_variant -/9214 4609/7836 1537/2611 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 19/42 HIGH 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 130410470 130410470 G T 1 0 0 0 0 0 0 1 0 3491 1014 35 2 2 COL6A5 3 130410470 Splice_Site SNP G C3L-00144_T 1107 130410470 67885089 406 4477 COL6A5 0 . GRCh38 3 130423874 130423874 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5137G>T p.Gly1713Ter p.G1713* ENST00000265379 29/43 257 181 76 185 185 0 strelka-varscan-mutect COL6A5,stop_gained,p.Gly1713Ter,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,stop_gained,p.Gly1713Ter,ENST00000312481,; T ENST00000265379 Transcript stop_gained 5631/9214 5137/7836 1713/2611 G/* Gga/Tga 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 29/43 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 130423874 130423874 G T 1 0 0 0 0 0 1 0 0 3491 1001 35 2 2 COL6A5 3 130423874 Nonsense_Mutation SNP G C3L-00144_T 13404 130423874 67871685 407 4478 DNAJC13 0 . GRCh38 3 132456662 132456662 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.1180-1G>T p.X394_splice ENST00000260818 136 102 34 123 122 1 strelka-varscan-mutect DNAJC13,splice_acceptor_variant,,ENST00000260818,NM_015268.3;DNAJC13,splice_acceptor_variant,,ENST00000486798,;DNAJC13,splice_acceptor_variant,,ENST00000471925,; T ENST00000260818 Transcript splice_acceptor_variant -/7730 1180/6732 394/2243 1 1 DNAJC13 HGNC HGNC:30343 protein_coding YES CCDS33857.1 ENSP00000260818 O75165 UPI000022C1FD NM_015268.3 11/55 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 132456662 132456662 G T 1 0 0 0 0 0 0 1 0 4446 1014 35 2 2 DNAJC13 3 132456662 Splice_Site SNP G C3L-00144_T 2032788 132456662 65838897 408 4479 KY 0 . GRCh38 3 134603584 134603584 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1981C>A p.Gln661Lys p.Q661K ENST00000423778 11/11 40 35 5 14 14 0 strelka-mutect KY,missense_variant,p.Gln640Lys,ENST00000508956,;KY,missense_variant,p.Gln661Lys,ENST00000423778,NM_178554.4;KY,3_prime_UTR_variant,,ENST00000503669,;EPHB1,intron_variant,,ENST00000472904,;EPHB1,intron_variant,,ENST00000467708,;EPHB1,downstream_gene_variant,,ENST00000467013,;KY,downstream_gene_variant,,ENST00000506319,; T ENST00000423778 Transcript missense_variant 2043/2345 1981/1986 661/661 Q/K Cag/Aag 1 -1 KY HGNC HGNC:26576 protein_coding YES CCDS46920.1 ENSP00000397598 Q8NBH2 UPI0000EE2109 NM_178554.4 tolerated_low_confidence(0.12) 11/11 hmmpanther:PTHR11039 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -12.7793 0.9999972 1 1 1 0 T 3 4 12 134603584 134603584 G T 1 0 0 0 0 1 0 0 0 8485 1357 47 2 2 KY 3 134603584 Missense_Mutation SNP G C3L-00144_T 2146922 134603584 63691975 409 4480 FOXL2 0 . GRCh38 3 138945999 138945999 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.724delG p.Ala242ProfsTer29 p.A242Pfs*29 ENST00000330315 1/1 52 44 8 48 48 0 sindel-varindel-pindel FOXL2,frameshift_variant,p.Ala242ProfsTer29,ENST00000330315,NM_023067.3;FOXL2NB,upstream_gene_variant,,ENST00000383165,NM_001040061.2;LINC01391,upstream_gene_variant,,ENST00000495287,;LINC01391,upstream_gene_variant,,ENST00000483650,;LINC01391,upstream_gene_variant,,ENST00000477059,;FOXL2NB,upstream_gene_variant,,ENST00000498709,;FOXL2NB,upstream_gene_variant,,ENST00000470680,; - ENST00000330315 Transcript frameshift_variant 1142/2917 724/1131 242/376 A/X Gcc/cc 1 -1 FOXL2 HGNC HGNC:1092 protein_coding YES CCDS3105.1 ENSP00000333188 P58012 Q53ZD3 UPI0000050DB3 NM_023067.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF177,hmmpanther:PTHR11829 HIGH deletion 1 PASS . . 0 203 7 0 0 0 0 0 -18.8182 0.9999996 1 1 1 0 - 7 5 12 138945999 138945999 C - 1 0 1 0 1 0 0 0 0 5880 739 26 0 0 FOXL2 3 138945999 Frame_Shift_Del DEL C C3L-00144_T 4342415 138945999 59349560 410 4481 TRIM42 0 . GRCh38 3 140682528 140682528 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.408C>A p.= p.A136A ENST00000286349 2/5 181 121 60 129 129 0 strelka-varscan-mutect TRIM42,synonymous_variant,p.=,ENST00000286349,NM_152616.4; A ENST00000286349 Transcript synonymous_variant 599/2539 408/2172 136/723 A gcC/gcA 1 1 TRIM42 HGNC HGNC:19014 protein_coding YES CCDS3113.1 ENSP00000286349 Q8IWZ5 UPI00001AEAE0 NM_152616.4 2/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF269 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 140682528 140682528 C A 1 0 0 0 0 0 0 0 1 17007 581 21 2 2 TRIM42 3 140682528 Silent SNP C C3L-00144_T 1736529 140682528 57613031 411 4482 TRIM42 0 . GRCh38 3 140688321 140688321 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1639A>C p.Lys547Gln p.K547Q ENST00000286349 3/5 305 223 82 228 228 0 strelka-varscan-mutect TRIM42,missense_variant,p.Lys547Gln,ENST00000286349,NM_152616.4; C ENST00000286349 Transcript missense_variant 1830/2539 1639/2172 547/723 K/Q Aag/Cag 1 1 TRIM42 HGNC HGNC:19014 protein_coding YES CCDS3113.1 ENSP00000286349 Q8IWZ5 UPI00001AEAE0 NM_152616.4 tolerated(0.55) 3/5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 140688321 140688321 A C 1 0 0 0 0 1 0 0 0 17007 131 5 5 5 TRIM42 3 140688321 Missense_Mutation SNP A C3L-00144_T 5793 140688321 57607238 412 4483 PAQR9 0 . GRCh38 3 142962575 142962575 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.762C>A p.= p.A254A ENST00000340634 1/1 224 185 39 159 159 0 strelka-varscan-mutect PAQR9,synonymous_variant,p.=,ENST00000340634,NM_198504.2;PAQR9,upstream_gene_variant,,ENST00000492509,;U2SURP,upstream_gene_variant,,ENST00000600150,;PAQR9,upstream_gene_variant,,ENST00000498470,;PAQR9-AS1,non_coding_transcript_exon_variant,,ENST00000625937,;PAQR9-AS1,intron_variant,,ENST00000627207,;PAQR9-AS1,upstream_gene_variant,,ENST00000595248,;PAQR9-AS1,upstream_gene_variant,,ENST00000595774,;PAQR9-AS1,upstream_gene_variant,,ENST00000598139,;PAQR9-AS1,upstream_gene_variant,,ENST00000593321,;PAQR9-AS1,upstream_gene_variant,,ENST00000478823,;PAQR9-AS1,upstream_gene_variant,,ENST00000493825,;PAQR9-AS1,upstream_gene_variant,,ENST00000625677,;PAQR9-AS1,upstream_gene_variant,,ENST00000594095,;PAQR9-AS1,upstream_gene_variant,,ENST00000497652,;PAQR9-AS1,upstream_gene_variant,,ENST00000598787,;PAQR9-AS1,upstream_gene_variant,,ENST00000607937,;PAQR9-AS1,upstream_gene_variant,,ENST00000608686,;PAQR9-AS1,upstream_gene_variant,,ENST00000608349,;RP11-372E1.7,downstream_gene_variant,,ENST00000468434,; T ENST00000340634 Transcript synonymous_variant 1108/2452 762/1134 254/377 A gcC/gcA 1 -1 PAQR9 HGNC HGNC:30131 protein_coding YES CCDS3128.1 ENSP00000341564 Q6ZVX9 UPI00000620A1 NM_198504.2 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR20855:SF58,hmmpanther:PTHR20855,Pfam_domain:PF03006 LOW SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 142962575 142962575 G T 1 0 0 0 0 0 0 0 1 11522 987 35 2 2 PAQR9 3 142962575 Silent SNP G C3L-00144_T 2274254 142962575 55332984 413 4484 SLC9A9 0 . GRCh38 3 143652289 143652289 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.721G>A p.Val241Met p.V241M ENST00000316549 6/16 384 359 25 300 300 0 strelka-varscan-mutect SLC9A9,missense_variant,p.Val241Met,ENST00000316549,NM_173653.3;SLC9A9,non_coding_transcript_exon_variant,,ENST00000483124,; T ENST00000316549 Transcript missense_variant 930/3627 721/1938 241/645 V/M Gtg/Atg 1 -1 SLC9A9 HGNC HGNC:20653 protein_coding YES CCDS33872.1 ENSP00000320246 Q8IVB4 UPI0000074664 NM_173653.3 deleterious(0) 6/16 Pfam_domain:PF00999,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF61,TIGRFAM_domain:TIGR00840,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 143652289 143652289 C T 1 0 0 0 0 1 0 0 0 15003 478 17 3 3 SLC9A9 3 143652289 Missense_Mutation SNP C C3L-00144_T 689714 143652289 54643270 414 4485 P2RY13 0 . GRCh38 3 151328208 151328208 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.848C>A p.Thr283Asn p.T283N ENST00000325602 2/2 191 157 34 148 147 1 strelka-varscan-mutect P2RY13,missense_variant,p.Thr283Asn,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; T ENST00000325602 Transcript missense_variant 868/2764 848/1065 283/354 T/N aCc/aAc 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 151328208 151328208 G T 1 0 0 0 0 1 0 0 0 11423 1261 44 2 2 P2RY13 3 151328208 Missense_Mutation SNP G C3L-00144_T 7675919 151328208 46967351 415 4486 IGSF10 0 . GRCh38 3 151443808 151443808 + Silent SNP C C A rs148647913 C3L-00144_T C3L-00144_N C C c.5139G>T p.= p.V1713V ENST00000282466 5/6 193 140 53 106 106 0 strelka-varscan-mutect IGSF10,synonymous_variant,p.=,ENST00000282466,NM_178822.4;IGSF10,upstream_gene_variant,,ENST00000489791,;IGSF10,upstream_gene_variant,,ENST00000495443,;IGSF10,upstream_gene_variant,,ENST00000493841,; A ENST00000282466 Transcript synonymous_variant 5139/11067 5139/7872 1713/2623 V gtG/gtT rs148647913 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 5/6 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs148647913 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 151443808 151443808 C A 1 0 0 0 0 0 0 0 1 7504 581 21 2 2 IGSF10 3 151443808 Silent SNP C C3L-00144_T 115600 151443808 46851751 416 4487 ARHGEF26 0 . GRCh38 3 154194643 154194643 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.1771-1G>T p.X591_splice ENST00000356448 161 130 31 122 122 0 strelka-varscan-mutect ARHGEF26,splice_acceptor_variant,,ENST00000356448,NM_001251962.1;ARHGEF26,splice_acceptor_variant,,ENST00000465093,NM_015595.3;ARHGEF26,splice_acceptor_variant,,ENST00000496710,NM_001251963.1;ARHGEF26,intron_variant,,ENST00000465817,; T ENST00000356448 Transcript splice_acceptor_variant -/5254 1771/2616 591/871 1 1 ARHGEF26 HGNC HGNC:24490 protein_coding YES CCDS46938.1 ENSP00000348828 Q96DR7 A0A140VJU4 UPI00001410D0 NM_001251962.1 8/14 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 154194643 154194643 G T 1 0 0 0 0 0 0 1 0 1035 956 33 2 2 ARHGEF26 3 154194643 Splice_Site SNP G C3L-00144_T 2750835 154194643 44100916 417 4488 SHOX2 0 . GRCh38 3 158105124 158105124 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.352A>T p.Arg118Trp p.R118W ENST00000389589 2/6 328 273 55 254 253 1 strelka-varscan-mutect SHOX2,missense_variant,p.Arg118Trp,ENST00000389589,NM_003030.4;SHOX2,missense_variant,p.Arg15Trp,ENST00000554685,;SHOX2,intron_variant,,ENST00000441443,NM_006884.3;SHOX2,intron_variant,,ENST00000483851,NM_001163678.1;RSRC1,upstream_gene_variant,,ENST00000464171,;RSRC1,upstream_gene_variant,,ENST00000611884,NM_001271838.1;RSRC1,upstream_gene_variant,,ENST00000295930,NM_016625.3;SHOX2,upstream_gene_variant,,ENST00000425436,;RSRC1,upstream_gene_variant,,ENST00000312179,NM_001271834.1;RSRC1,upstream_gene_variant,,ENST00000480820,;RSRC1,upstream_gene_variant,,ENST00000475278,;RSRC1,upstream_gene_variant,,ENST00000471994,;RSRC1,upstream_gene_variant,,ENST00000494002,;SHOX2,non_coding_transcript_exon_variant,,ENST00000490689,; A ENST00000389589 Transcript missense_variant 488/2072 352/1068 118/355 R/W Agg/Tgg 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 tolerated_low_confidence(0.18) 2/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 158105124 158105124 T A 1 0 0 0 0 1 0 0 0 14552 1623 56 4 4 SHOX2 3 158105124 Missense_Mutation SNP T C3L-00144_T 3910481 158105124 40190435 418 4489 SHOX2 0 . GRCh38 3 158105685 158105685 + Missense_Mutation SNP T T A C3L-00144_T C3L-00144_N T T c.340A>T p.Thr114Ser p.T114S ENST00000389589 1/6 321 277 44 271 271 0 strelka-varscan-mutect SHOX2,missense_variant,p.Thr114Ser,ENST00000441443,NM_006884.3;SHOX2,missense_variant,p.Thr114Ser,ENST00000389589,NM_003030.4;SHOX2,missense_variant,p.Thr114Ser,ENST00000483851,NM_001163678.1;SHOX2,missense_variant,p.Asp12Val,ENST00000554685,;RSRC1,upstream_gene_variant,,ENST00000464171,;RSRC1,upstream_gene_variant,,ENST00000611884,NM_001271838.1;RSRC1,upstream_gene_variant,,ENST00000295930,NM_016625.3;SHOX2,upstream_gene_variant,,ENST00000425436,;RSRC1,upstream_gene_variant,,ENST00000312179,NM_001271834.1;RSRC1,upstream_gene_variant,,ENST00000480820,;RSRC1,upstream_gene_variant,,ENST00000475278,;RSRC1,upstream_gene_variant,,ENST00000476899,;RSRC1,upstream_gene_variant,,ENST00000471994,;RSRC1,upstream_gene_variant,,ENST00000494002,;RSRC1,upstream_gene_variant,,ENST00000471911,;RSRC1,upstream_gene_variant,,ENST00000468344,;SHOX2,upstream_gene_variant,,ENST00000490689,;RSRC1,upstream_gene_variant,,ENST00000480119,; A ENST00000389589 Transcript missense_variant 476/2072 340/1068 114/355 T/S Acg/Tcg COSM3660303 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 tolerated_low_confidence(0.44) 1/6 1 MODERATE 1 SNV 1 1 1 PASS rs1377607419 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 158105685 158105685 T A 1 0 0 0 0 1 0 0 0 14552 1667 58 4 4 SHOX2 3 158105685 Missense_Mutation SNP T C3L-00144_T 561 158105685 40189874 419 4490 SI 0 . GRCh38 3 164991434 164991434 + Missense_Mutation SNP G G C C3L-00144_T C3L-00144_N G G c.5027C>G p.Ala1676Gly p.A1676G ENST00000264382 44/48 385 308 77 280 280 0 strelka-varscan-mutect SI,missense_variant,p.Ala1676Gly,ENST00000264382,NM_001041.3; C ENST00000264382 Transcript missense_variant 5090/6011 5027/5484 1676/1827 A/G gCt/gGt COSM1040734 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 44/48 Pfam_domain:PF01055,Superfamily_domains:SSF51011 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 164991434 164991434 G C 1 0 0 0 0 1 0 0 0 14561 971 34 4 4 SI 3 164991434 Missense_Mutation SNP G C3L-00144_T 6885749 164991434 33304125 420 4491 SI 0 . GRCh38 3 165013009 165013009 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.4033A>G p.Lys1345Glu p.K1345E ENST00000264382 34/48 442 356 86 361 360 1 strelka-varscan-mutect SI,missense_variant,p.Lys1345Glu,ENST00000264382,NM_001041.3; C ENST00000264382 Transcript missense_variant 4096/6011 4033/5484 1345/1827 K/E Aaa/Gaa 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(1) 34/48 Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 165013009 165013009 T C 1 0 0 0 0 1 0 0 0 14561 1763 61 5 5 SI 3 165013009 Missense_Mutation SNP T C3L-00144_T 21575 165013009 33282550 421 4492 SI 0 . GRCh38 3 165055205 165055205 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.1501G>A p.Gly501Arg p.G501R ENST00000264382 13/48 331 276 55 250 250 0 strelka-varscan-mutect SI,missense_variant,p.Gly501Arg,ENST00000264382,NM_001041.3; T ENST00000264382 Transcript missense_variant 1564/6011 1501/5484 501/1827 G/R Gga/Aga COSM3589591 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 13/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,PROSITE_patterns:PS00129,Pfam_domain:PF01055,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 165055205 165055205 C T 1 0 0 0 0 1 0 0 0 14561 603 21 3 3 SI 3 165055205 Missense_Mutation SNP C C3L-00144_T 42196 165055205 33240354 422 4493 SI 0 . GRCh38 3 165059027 165059027 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.1334A>G p.Glu445Gly p.E445G ENST00000264382 12/48 548 510 38 434 434 0 strelka-varscan-mutect SI,missense_variant,p.Glu445Gly,ENST00000264382,NM_001041.3; C ENST00000264382 Transcript missense_variant 1397/6011 1334/5484 445/1827 E/G gAg/gGg 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0.02) 12/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 165059027 165059027 T C 1 0 0 0 0 1 0 0 0 14561 1551 54 5 5 SI 3 165059027 Missense_Mutation SNP T C3L-00144_T 3822 165059027 33236532 423 4494 SERPINI2 0 . GRCh38 3 167471654 167471654 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.211C>A p.Leu71Met p.L71M ENST00000616363 3/10 337 240 97 260 260 0 strelka-varscan-mutect SERPINI2,missense_variant,p.Leu61Met,ENST00000476257,;SERPINI2,missense_variant,p.Leu71Met,ENST00000616363,NM_001012303.2;SERPINI2,missense_variant,p.Leu61Met,ENST00000264677,NM_006217.4;SERPINI2,missense_variant,p.Leu61Met,ENST00000461846,;SERPINI2,missense_variant,p.Leu61Met,ENST00000471111,;SERPINI2,missense_variant,p.Leu61Met,ENST00000466903,;SERPINI2,missense_variant,p.Leu61Met,ENST00000467583,;SERPINI2,non_coding_transcript_exon_variant,,ENST00000465031,; T ENST00000616363 Transcript missense_variant 412/1769 211/1248 71/415 L/M Ctg/Atg 1 -1 SERPINI2 HGNC HGNC:8945 protein_coding YES CCDS75047.1 ENSP00000481699 A0A0C4DGW9 UPI00004CEC5E NM_001012303.2 deleterious(0.04) 3/10 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF51,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 167471654 167471654 G T 1 0 0 0 0 1 0 0 0 14395 1020 36 2 2 SERPINI2 3 167471654 Missense_Mutation SNP G C3L-00144_T 2412627 167471654 30823905 424 4495 WDR49 0 . GRCh38 3 167522384 167522384 + Missense_Mutation SNP T T A C3L-00144_T C3L-00144_N T T c.1649A>T p.Glu550Val p.E550V ENST00000308378 12/15 191 140 51 171 171 0 strelka-varscan-mutect WDR49,missense_variant,p.Glu550Val,ENST00000308378,NM_178824.3;WDR49,missense_variant,p.Glu527Val,ENST00000472600,;WDR49,missense_variant,p.Glu122Val,ENST00000493061,;WDR49,intron_variant,,ENST00000479765,;WDR49,non_coding_transcript_exon_variant,,ENST00000476376,; A ENST00000308378 Transcript missense_variant 1955/2594 1649/2094 550/697 E/V gAg/gTg COSM4740979,COSM4740980 1 -1 WDR49 HGNC HGNC:26587 protein_coding YES CCDS3201.1 ENSP00000311343 Q8IV35 UPI00000746AD NM_178824.3 deleterious(0.03) 12/15 hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF219 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 167522384 167522384 T A 1 0 0 0 0 1 0 0 0 17862 1551 54 4 4 WDR49 3 167522384 Missense_Mutation SNP T C3L-00144_T 50730 167522384 30773175 425 4496 PRKCI 0 . GRCh38 3 170270455 170270455 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.488delG p.Gly163AspfsTer38 p.G163Dfs*38 ENST00000295797 6/18 167 132 35 160 160 0 sindel-varindel-pindel PRKCI,frameshift_variant,p.Gly163AspfsTer38,ENST00000295797,NM_002740.5; - ENST00000295797 Transcript frameshift_variant 790/4950 485/1791 162/596 W/X tGg/tg 1 1 PRKCI HGNC HGNC:9404 protein_coding YES CCDS3212.2 ENSP00000295797 P41743 UPI000020A798 NM_002740.5 6/18 Gene3D:3.30.60.20,Pfam_domain:PF00130,PIRSF_domain:PIRSF000554,Prints_domain:PR00008,PROSITE_patterns:PS00479,PROSITE_profiles:PS50081,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF214,SMART_domains:SM00109,Superfamily_domains:SSF57889 HIGH 1 deletion 1 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 170270455 170270455 G - 1 0 1 0 1 0 0 0 0 12647 1357 47 0 0 PRKCI 3 170270455 Frame_Shift_Del DEL G C3L-00144_T 2748071 170270455 28025104 426 4497 SLC7A14 0 . GRCh38 3 170526745 170526745 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.192C>A p.= p.G64G ENST00000231706 2/8 609 447 162 448 448 0 strelka-varscan-mutect SLC7A14,synonymous_variant,p.=,ENST00000231706,NM_020949.2;CLDN11,intron_variant,,ENST00000486975,;CLDN11,intron_variant,,ENST00000480067,; T ENST00000231706 Transcript synonymous_variant 508/10103 192/2316 64/771 G ggC/ggA 1 -1 SLC7A14 HGNC HGNC:29326 protein_coding YES CCDS33892.1 ENSP00000231706 Q8TBB6 UPI0000051F6B NM_020949.2 2/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF361,Pfam_domain:PF13520 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 170526745 170526745 G T 1 0 0 0 0 0 0 0 1 14979 1306 46 2 2 SLC7A14 3 170526745 Silent SNP G C3L-00144_T 256290 170526745 27768814 427 4498 SPATA16 0 . GRCh38 3 173019545 173019545 + Silent SNP C C A C3L-00144_T C3L-00144_N C C c.789G>T p.= p.R263R ENST00000351008 4/11 568 463 105 403 402 1 strelka-varscan-mutect SPATA16,synonymous_variant,p.=,ENST00000351008,NM_031955.5; A ENST00000351008 Transcript synonymous_variant 973/2106 789/1710 263/569 R cgG/cgT COSM4559040 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 4/11 Gene3D:1.25.40.10,Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336,Superfamily_domains:SSF48452 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 173019545 173019545 C A 1 0 0 0 0 0 0 0 1 15331 842 30 2 2 SPATA16 3 173019545 Silent SNP C C3L-00144_T 2492800 173019545 25276014 428 4499 CCDC39 0 . GRCh38 3 180651460 180651460 + Frame_Shift_Del DEL C C - rs757040004 C3L-00144_T C3L-00144_N C C c.1108delG p.Val370Ter p.V370* ENST00000442201 9/20 202 158 44 243 243 0 sindel-varindel-pindel CCDC39,frameshift_variant,p.Val370Ter,ENST00000442201,NM_181426.1;CCDC39,frameshift_variant,p.Val370Ter,ENST00000476379,; - ENST00000442201 Transcript frameshift_variant 1228/3279 1108/2826 370/941 V/X Gta/ta rs757040004 1 -1 CCDC39 HGNC HGNC:25244 protein_coding YES CCDS46964.1 ENSP00000405708 Q9UFE4 UPI00015D7298 NM_181426.1 9/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18962,hmmpanther:PTHR18962:SF0 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 180651460 180651460 C - 1 0 1 0 1 0 0 0 0 2520 478 17 0 0 CCDC39 3 180651460 Frame_Shift_Del DEL C C3L-00144_T 7631915 180651460 17644099 429 4500 KLHL24 0 . GRCh38 3 183650425 183650425 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.69G>A p.= p.K23K ENST00000454652 4/9 218 159 59 170 170 0 strelka-varscan-mutect KLHL24,synonymous_variant,p.=,ENST00000454652,NM_017644.3;KLHL24,synonymous_variant,p.=,ENST00000242810,;KLHL24,synonymous_variant,p.=,ENST00000476808,;KLHL24,synonymous_variant,p.=,ENST00000493074,;KLHL24,synonymous_variant,p.=,ENST00000468001,;KLHL24,synonymous_variant,p.=,ENST00000454495,;KLHL24,synonymous_variant,p.=,ENST00000482138,;KLHL24,synonymous_variant,p.=,ENST00000468101,;KLHL24,synonymous_variant,p.=,ENST00000437402,;KLHL24,synonymous_variant,p.=,ENST00000427201,;KLHL24,synonymous_variant,p.=,ENST00000473045,;KLHL24,intron_variant,,ENST00000475827,; A ENST00000454652 Transcript synonymous_variant 455/7380 69/1803 23/600 K aaG/aaA 1 1 KLHL24 HGNC HGNC:25947 protein_coding YES CCDS3246.1 ENSP00000395012 Q6TFL4 UPI000020A86F NM_017644.3 4/9 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF257 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 183650425 183650425 G A 1 0 0 0 0 0 0 0 1 8243 962 34 3 3 KLHL24 3 183650425 Silent SNP G C3L-00144_T 2998965 183650425 14645134 430 4501 HTR3C 0 . GRCh38 3 184054731 184054731 + Missense_Mutation SNP C C A rs143289420 C3L-00144_T C3L-00144_N C C c.78C>A p.Asp26Glu p.D26E ENST00000318351 2/9 42 33 9 36 36 0 strelka-varscan-mutect HTR3C,missense_variant,p.Asp26Glu,ENST00000318351,NM_130770.2; A ENST00000318351 Transcript missense_variant 112/1697 78/1344 26/447 D/E gaC/gaA rs143289420 1 1 HTR3C HGNC HGNC:24003 protein_coding YES CCDS3250.1 ENSP00000322617 Q8WXA8 UPI00001402D6 NM_130770.2 tolerated(0.29) 2/9 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF565 MODERATE 1 SNV 1 1 PASS rs143289420 . 0 200 10 0 0 0 0 0 -19.99617 0.9999916 1 1 1 0 A 3 1 12 184054731 184054731 C A 1 0 0 0 0 1 0 0 0 7342 535 19 1 1 HTR3C 3 184054731 Missense_Mutation SNP C C3L-00144_T 404306 184054731 14240828 431 4502 EIF4G1 0 . GRCh38 3 184321971 184321971 + Missense_Mutation SNP G G C C3L-00144_T C3L-00144_N G G c.1408G>C p.Glu470Gln p.E470Q ENST00000424196 9/32 250 208 42 188 188 0 strelka-varscan-mutect EIF4G1,missense_variant,p.Glu463Gln,ENST00000342981,NM_182917.4;EIF4G1,missense_variant,p.Glu470Gln,ENST00000424196,;EIF4G1,missense_variant,p.Glu423Gln,ENST00000414031,NM_001291157.1;EIF4G1,missense_variant,p.Glu463Gln,ENST00000346169,NM_198241.2;EIF4G1,missense_variant,p.Glu470Gln,ENST00000352767,NM_001194947.1;EIF4G1,missense_variant,p.Glu376Gln,ENST00000392537,NM_198244.2;EIF4G1,missense_variant,p.Glu470Gln,ENST00000382330,NM_001194946.1;EIF4G1,missense_variant,p.Glu376Gln,ENST00000427845,;EIF4G1,missense_variant,p.Glu267Gln,ENST00000434061,NM_004953.4;EIF4G1,missense_variant,p.Glu299Gln,ENST00000350481,NM_198242.2;EIF4G1,missense_variant,p.Glu423Gln,ENST00000411531,;EIF4G1,missense_variant,p.Glu267Gln,ENST00000435046,;EIF4G1,missense_variant,p.Glu299Gln,ENST00000441154,;EIF4G1,missense_variant,p.Glu404Gln,ENST00000426123,;EIF4G1,missense_variant,p.Glu470Gln,ENST00000421110,;EIF4G1,missense_variant,p.Glu463Gln,ENST00000450424,;EIF4G1,missense_variant,p.Glu299Gln,ENST00000444861,;EIF4G1,missense_variant,p.Glu267Gln,ENST00000457456,;EIF4G1,downstream_gene_variant,,ENST00000427141,;EIF4G1,downstream_gene_variant,,ENST00000456033,;EIF4G1,upstream_gene_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000440448,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000455679,;EIF4G1,downstream_gene_variant,,ENST00000428387,;SNORD66,upstream_gene_variant,,ENST00000390856,;EIF4G1,3_prime_UTR_variant,,ENST00000442406,;EIF4G1,3_prime_UTR_variant,,ENST00000413967,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,upstream_gene_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000493299,; C ENST00000424196 Transcript missense_variant 1797/5653 1408/4821 470/1606 E/Q Gag/Cag COSM402406 1 1 EIF4G1 HGNC HGNC:3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 tolerated(0.28) 9/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF10,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 2 1 1 PASS rs1355098520 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 184321971 184321971 G C 1 0 0 0 0 1 0 0 0 4870 943 33 4 4 EIF4G1 3 184321971 Missense_Mutation SNP G C3L-00144_T 267240 184321971 13973588 432 4503 IL1RAP 0 . GRCh38 3 190648374 190648374 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1382G>A p.Ser461Asn p.S461N ENST00000412504 10/10 57 39 18 57 57 0 strelka-varscan-mutect IL1RAP,missense_variant,p.Ser461Asn,ENST00000412504,;IL1RAP,missense_variant,p.Ser461Asn,ENST00000447382,NM_002182.3;IL1RAP,missense_variant,p.Ser461Asn,ENST00000072516,NM_001167929.1;IL1RAP,missense_variant,p.Ser461Asn,ENST00000439062,NM_001167928.1;IL1RAP,intron_variant,,ENST00000317757,NM_001167931.1;IL1RAP,intron_variant,,ENST00000443369,;IL1RAP,3_prime_UTR_variant,,ENST00000413869,;IL1RAP,3_prime_UTR_variant,,ENST00000342550,; A ENST00000412504 Transcript missense_variant 1731/4875 1382/1713 461/570 S/N aGc/aAc 1 1 IL1RAP HGNC HGNC:5995 protein_coding CCDS3298.1 ENSP00000412053 Q9NPH3 UPI000005416D deleterious(0) 10/10 Gene3D:3.40.50.10140,Pfam_domain:PF01582,Prints_domain:PR01537,PROSITE_profiles:PS50104,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF20,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 190648374 190648374 G A 1 0 0 0 0 1 0 0 0 7563 971 34 3 3 IL1RAP 3 190648374 Missense_Mutation SNP G C3L-00144_T 6326403 190648374 7647185 433 4504 MUC20 0 . GRCh38 3 195726399 195726399 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1796C>A p.Pro599His p.P599H ENST00000447234 2/4 432 404 28 302 301 1 varscan-mutect MUC20,missense_variant,p.Pro564His,ENST00000445522,;MUC20,missense_variant,p.Pro599His,ENST00000447234,NM_001282506.1;MUC20,missense_variant,p.Pro599His,ENST00000436408,;MUC20,missense_variant,p.Pro428His,ENST00000320736,;MUC20,missense_variant,p.Pro11His,ENST00000423938,;LINC00969,intron_variant,,ENST00000600197,;LINC00969,intron_variant,,ENST00000628392,;LINC00969,intron_variant,,ENST00000629721,;LINC00969,intron_variant,,ENST00000594446,;LINC00969,intron_variant,,ENST00000627297,;LINC00969,intron_variant,,ENST00000595086,;LINC00969,intron_variant,,ENST00000631359,;LINC00969,intron_variant,,ENST00000628125,;LINC00969,intron_variant,,ENST00000629537,;LINC00969,intron_variant,,ENST00000627993,;LINC00969,intron_variant,,ENST00000597662,;LINC00969,intron_variant,,ENST00000628982,;LINC00969,intron_variant,,ENST00000629807,;LINC00969,intron_variant,,ENST00000627035,;LINC00969,intron_variant,,ENST00000626093,;LINC00969,downstream_gene_variant,,ENST00000627609,;LINC00969,downstream_gene_variant,,ENST00000627471,;LINC00969,downstream_gene_variant,,ENST00000630197,;LINC00969,downstream_gene_variant,,ENST00000455807,;LINC00969,downstream_gene_variant,,ENST00000594976,;LINC00969,downstream_gene_variant,,ENST00000630874,;LINC00969,downstream_gene_variant,,ENST00000600288,;LINC00969,downstream_gene_variant,,ENST00000599566,;LINC00969,downstream_gene_variant,,ENST00000626979,;LINC00969,downstream_gene_variant,,ENST00000626872,;LINC00969,downstream_gene_variant,,ENST00000625383,;LINC00969,downstream_gene_variant,,ENST00000612098,;LINC00969,downstream_gene_variant,,ENST00000626566,;LINC00969,downstream_gene_variant,,ENST00000626852,;LINC00969,downstream_gene_variant,,ENST00000432194,;LINC00969,downstream_gene_variant,,ENST00000625665,;LINC00969,downstream_gene_variant,,ENST00000625531,;MUC20,downstream_gene_variant,,ENST00000485430,;MUC20,downstream_gene_variant,,ENST00000480350,;MUC20,non_coding_transcript_exon_variant,,ENST00000498018,; A ENST00000447234 Transcript missense_variant 1922/2589 1796/2130 599/709 P/H cCc/cAc 1 1 MUC20 HGNC HGNC:23282 protein_coding YES CCDS63877.1 ENSP00000414350 Q8N307 UPI000198CC5A NM_001282506.1 deleterious(0.03) 2/4 hmmpanther:PTHR37358,hmmpanther:PTHR37358:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 195726399 195726399 C A 1 0 0 0 0 1 0 0 0 9974 623 22 2 2 MUC20 3 195726399 Missense_Mutation SNP C C3L-00144_T 5078025 195726399 2569160 434 4505 MUC4 0 . GRCh38 3 195780980 195780980 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.10600G>T p.Ala3534Ser p.A3534S ENST00000463781 2/25 291 178 113 273 273 0 strelka-varscan MUC4,missense_variant,p.Ala3534Ser,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Ala3534Ser,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Ala3534Ser,ENST00000478156,;MUC4,missense_variant,p.Ala3534Ser,ENST00000466475,;MUC4,missense_variant,p.Ala3534Ser,ENST00000477756,;MUC4,missense_variant,p.Ala3534Ser,ENST00000477086,;MUC4,missense_variant,p.Ala3534Ser,ENST00000480843,;MUC4,missense_variant,p.Ala3534Ser,ENST00000462323,;MUC4,missense_variant,p.Ala3534Ser,ENST00000470451,;MUC4,missense_variant,p.Ala3534Ser,ENST00000479406,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,; A ENST00000463781 Transcript missense_variant 11060/17110 10600/16239 3534/5412 A/S Gcc/Tcc 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 tolerated_low_confidence(0.25) 2/25 MODERATE 1 SNV 5 1 PASS . . 0 178 0 0 15 17 0 0 -14.30476 0 0 1 0 0 A 3 1 12 195780980 195780980 C A 1 0 0 0 0 1 0 0 0 9977 768 27 1 1 MUC4 3 195780980 Missense_Mutation SNP C C3L-00144_T 54581 195780980 2514579 435 4506 SENP5 0 . GRCh38 3 196899673 196899673 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.1521A>T p.= p.L507L ENST00000323460 3/10 174 149 25 160 160 0 strelka-varscan-mutect SENP5,synonymous_variant,p.=,ENST00000323460,NM_152699.4;SENP5,synonymous_variant,p.=,ENST00000445299,NM_001308045.1;SENP5,5_prime_UTR_variant,,ENST00000419026,;SENP5,upstream_gene_variant,,ENST00000489744,; T ENST00000323460 Transcript synonymous_variant 1770/6308 1521/2268 507/755 L ctA/ctT 1 1 SENP5 HGNC HGNC:28407 protein_coding YES CCDS3322.1 ENSP00000327197 Q96HI0 UPI00001AF3BE NM_152699.4 3/10 hmmpanther:PTHR12606:SF10,hmmpanther:PTHR12606 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 196899673 196899673 A T 1 0 0 0 0 0 0 0 1 14325 407 15 4 4 SENP5 3 196899673 Silent SNP A C3L-00144_T 1118693 196899673 1395886 436 4507 FYTTD1 0 . GRCh38 3 197781834 197781834 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.882G>T p.= p.R294R ENST00000241502 9/9 262 210 52 194 193 1 strelka-varscan-mutect FYTTD1,synonymous_variant,p.=,ENST00000241502,NM_032288.6;FYTTD1,synonymous_variant,p.=,ENST00000424384,;FYTTD1,synonymous_variant,p.=,ENST00000415708,NM_001011537.2;FYTTD1,downstream_gene_variant,,ENST00000428738,;FYTTD1,non_coding_transcript_exon_variant,,ENST00000492360,;FYTTD1,downstream_gene_variant,,ENST00000412924,;FYTTD1,downstream_gene_variant,,ENST00000418169,; T ENST00000241502 Transcript synonymous_variant 1104/6866 882/957 294/318 R cgG/cgT 1 1 FYTTD1 HGNC HGNC:25407 protein_coding YES CCDS3329.1 ENSP00000241502 Q96QD9 A0A024R9K4 UPI0000073CEC NM_032288.6 9/9 hmmpanther:PTHR21038:SF2,hmmpanther:PTHR21038,Pfam_domain:PF07078 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 197781834 197781834 G T 1 0 0 0 0 0 0 0 1 5998 1248 44 2 2 FYTTD1 3 197781834 Silent SNP G C3L-00144_T 882161 197781834 513725 437 4508 GAK 0 . GRCh38 4 904694 904694 + Missense_Mutation SNP G G C rs754771509 C3L-00144_T C3L-00144_N G G c.468C>G p.Cys156Trp p.C156W ENST00000314167 5/28 117 103 14 117 117 0 strelka-varscan-mutect GAK,missense_variant,p.Cys156Trp,ENST00000314167,NM_005255.2;GAK,missense_variant,p.Cys77Trp,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,missense_variant,p.Cys68Trp,ENST00000511229,;GAK,intron_variant,,ENST00000618573,;GAK,intron_variant,,ENST00000502656,;GAK,non_coding_transcript_exon_variant,,ENST00000510022,;GAK,3_prime_UTR_variant,,ENST00000505819,;GAK,3_prime_UTR_variant,,ENST00000512325,;GAK,non_coding_transcript_exon_variant,,ENST00000507991,;GAK,intron_variant,,ENST00000507580,; C ENST00000314167 Transcript missense_variant 579/4442 468/3936 156/1311 C/W tgC/tgG rs754771509 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 deleterious(0) 5/28 PROSITE_profiles:PS50011,hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs754771509 . 0 201 7 2 0 0 0 0 -19.98422 0.99976 1 1 1 0 C 3 2 12 904694 904694 G C 1 0 0 0 0 1 0 0 0 6063 1195 42 4 4 GAK 4 904694 Missense_Mutation SNP G C3L-00144_T 904694 189309861 438 4509 JAKMIP1 0 . GRCh38 4 6035937 6035937 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2346G>T p.= p.R782R ENST00000409021 19/21 111 74 37 88 88 0 strelka-mutect JAKMIP1,synonymous_variant,p.=,ENST00000409021,NM_001099433.1;JAKMIP1,synonymous_variant,p.=,ENST00000409371,;JAKMIP1,synonymous_variant,p.=,ENST00000637373,; A ENST00000409021 Transcript synonymous_variant 2796/2975 2346/2496 782/831 R cgG/cgT 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 19/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 6035937 6035937 C A 1 0 0 0 0 0 0 0 1 7853 610 22 2 2 JAKMIP1 4 6035937 Silent SNP C C3L-00144_T 5131243 6035937 184178618 439 4510 WFS1 0 . GRCh38 4 6300992 6300992 + Missense_Mutation SNP G G C rs780762268 C3L-00144_T C3L-00144_N G G c.1197G>C p.Trp399Cys p.W399C ENST00000226760 8/8 399 319 80 356 356 0 strelka-varscan-mutect WFS1,missense_variant,p.Trp399Cys,ENST00000226760,NM_001145853.1,NM_006005.3;WFS1,missense_variant,p.Trp399Cys,ENST00000503569,;WFS1,downstream_gene_variant,,ENST00000506362,;WFS1,non_coding_transcript_exon_variant,,ENST00000507765,;WFS1,downstream_gene_variant,,ENST00000513395,; C ENST00000226760 Transcript missense_variant 1367/3640 1197/2673 399/890 W/C tgG/tgC rs780762268 1 1 WFS1 HGNC HGNC:12762 protein_coding YES CCDS3386.1 ENSP00000226760 O76024 A0A0S2Z4V6 UPI00000715C3 NM_001145853.1,NM_006005.3 deleterious(0) 8/8 hmmpanther:PTHR13098 MODERATE 1 SNV 1 1 PASS rs780762268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 6300992 6300992 G C 1 0 0 0 0 1 0 0 0 17917 1183 41 4 4 WFS1 4 6300992 Missense_Mutation SNP G C3L-00144_T 265055 6300992 183913563 440 4511 SORCS2 0 . GRCh38 4 7726845 7726845 + Silent SNP G G C rs529978013 C3L-00144_T C3L-00144_N G G c.2811G>C p.= p.T937T ENST00000507866 21/27 191 176 15 186 186 0 strelka-varscan-mutect SORCS2,synonymous_variant,p.=,ENST00000507866,NM_020777.2;SORCS2,synonymous_variant,p.=,ENST00000329016,; C ENST00000507866 Transcript synonymous_variant 2920/6152 2811/3480 937/1159 T acG/acC rs529978013 1 1 SORCS2 HGNC HGNC:16698 protein_coding YES CCDS47008.1 ENSP00000422185 Q96PQ0 UPI0000EE6E4F NM_020777.2 21/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF9 LOW 1 SNV 2 1 PASS rs529978013 . 0 206 0 2 2 0 0 0 -5.619869 0.9534606 1 1 1 0 C 2 2 12 7726845 7726845 G C 1 0 0 0 0 0 0 0 1 15253 1103 39 4 4 SORCS2 4 7726845 Silent SNP G C3L-00144_T 1425853 7726845 182487710 441 4512 SORCS2 0 . GRCh38 4 7729631 7729631 + Silent SNP G G C rs772636271 C3L-00144_T C3L-00144_N G G c.3027G>C p.= p.P1009P ENST00000507866 23/27 230 201 29 202 202 0 strelka-varscan-mutect SORCS2,synonymous_variant,p.=,ENST00000507866,NM_020777.2;SORCS2,synonymous_variant,p.=,ENST00000329016,;SORCS2,upstream_gene_variant,,ENST00000505529,; C ENST00000507866 Transcript synonymous_variant 3136/6152 3027/3480 1009/1159 P ccG/ccC rs772636271 1 1 SORCS2 HGNC HGNC:16698 protein_coding YES CCDS47008.1 ENSP00000422185 Q96PQ0 UPI0000EE6E4F NM_020777.2 23/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF9 LOW 1 SNV 2 1 PASS rs772636271 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 12 7729631 7729631 G C 1 0 0 0 0 0 0 0 1 15253 1103 39 4 4 SORCS2 4 7729631 Silent SNP G C3L-00144_T 2786 7729631 182484924 442 4513 SH3TC1 0 . GRCh38 4 8227890 8227890 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2196G>T p.= p.V732V ENST00000245105 12/18 376 299 77 331 331 0 strelka-varscan-mutect SH3TC1,synonymous_variant,p.=,ENST00000245105,NM_018986.3;SH3TC1,downstream_gene_variant,,ENST00000508641,;SH3TC1,downstream_gene_variant,,ENST00000514274,;SH3TC1,upstream_gene_variant,,ENST00000507801,;SH3TC1,3_prime_UTR_variant,,ENST00000515682,NM_001318480.1;SH3TC1,3_prime_UTR_variant,,ENST00000502669,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000506360,;SH3TC1,upstream_gene_variant,,ENST00000502559,;SH3TC1,upstream_gene_variant,,ENST00000502350,;SH3TC1,upstream_gene_variant,,ENST00000508183,;SH3TC1,upstream_gene_variant,,ENST00000511002,;SH3TC1,downstream_gene_variant,,ENST00000509553,;SH3TC1,upstream_gene_variant,,ENST00000513495,;SH3TC1,downstream_gene_variant,,ENST00000508438,; T ENST00000245105 Transcript synonymous_variant 2263/4226 2196/4011 732/1336 V gtG/gtT 1 1 SH3TC1 HGNC HGNC:26009 protein_coding YES CCDS3399.1 ENSP00000245105 Q8TE82 UPI000013CB93 NM_018986.3 12/18 hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 8227890 8227890 G T 1 0 0 0 0 0 0 0 1 14520 1335 47 2 2 SH3TC1 4 8227890 Silent SNP G C3L-00144_T 498259 8227890 181986665 443 4514 DRD5 0 . GRCh38 4 9783229 9783229 + Silent SNP C C A rs866493427 C3L-00144_T C3L-00144_N C C c.1200C>A p.= p.I400I ENST00000304374 1/1 329 290 39 301 301 0 strelka-varscan-mutect DRD5,synonymous_variant,p.=,ENST00000304374,NM_000798.4;SLC2A9,intron_variant,,ENST00000503803,;SLC2A9,intron_variant,,ENST00000508585,; A ENST00000304374 Transcript synonymous_variant 1550/2330 1200/1434 400/477 I atC/atA rs866493427,COSM5516297 1 1 DRD5 HGNC HGNC:3026 protein_coding YES CCDS3405.1 ENSP00000306129 P21918 UPI000004E905 NM_000798.4 1/1 0,1 LOW 1 SNV 0,1 1 PASS rs866493427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 9783229 9783229 C A 1 0 0 0 0 0 0 0 1 4579 874 31 1 1 DRD5 4 9783229 Silent SNP C C3L-00144_T 1555339 9783229 180431326 444 4515 ZNF518B 0 . GRCh38 4 10445827 10445827 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.502A>T p.Ser168Cys p.S168C ENST00000326756 3/3 186 159 27 155 155 0 strelka-varscan-mutect ZNF518B,missense_variant,p.Ser168Cys,ENST00000326756,NM_053042.2;ZNF518B,downstream_gene_variant,,ENST00000507515,; A ENST00000326756 Transcript missense_variant 941/6894 502/3225 168/1074 S/C Agc/Tgc 1 -1 ZNF518B HGNC HGNC:29365 protein_coding YES CCDS33960.1 ENSP00000317614 Q9C0D4 UPI0000160B97 NM_053042.2 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF188,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 10445827 10445827 T A 1 0 0 0 0 1 0 0 0 18535 1580 55 4 4 ZNF518B 4 10445827 Missense_Mutation SNP T C3L-00144_T 662598 10445827 179768728 445 4516 BOD1L1 0 . GRCh38 4 13601273 13601273 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.5627G>T p.Arg1876Ile p.R1876I ENST00000040738 10/26 212 168 44 215 215 0 strelka-varscan-mutect BOD1L1,missense_variant,p.Arg1876Ile,ENST00000040738,NM_148894.2; A ENST00000040738 Transcript missense_variant 5763/10565 5627/9156 1876/3051 R/I aGa/aTa 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 deleterious(0) 10/26 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 13601273 13601273 C A 1 0 0 0 0 1 0 0 0 1639 913 32 2 2 BOD1L1 4 13601273 Missense_Mutation SNP C C3L-00144_T 3155446 13601273 176613282 446 4517 BOD1L1 0 . GRCh38 4 13601766 13601766 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.5134G>T p.Gly1712Ter p.G1712* ENST00000040738 10/26 249 213 36 282 282 0 strelka-varscan-mutect BOD1L1,stop_gained,p.Gly1712Ter,ENST00000040738,NM_148894.2; A ENST00000040738 Transcript stop_gained 5270/10565 5134/9156 1712/3051 G/* Gga/Tga 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 10/26 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 13601766 13601766 C A 1 0 0 0 0 0 1 0 0 1639 632 22 2 2 BOD1L1 4 13601766 Nonsense_Mutation SNP C C3L-00144_T 493 13601766 176612789 447 4518 BOD1L1 0 . GRCh38 4 13614223 13614223 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1147G>T p.Ala383Ser p.A383S ENST00000040738 4/26 74 69 5 65 65 0 strelka-varscan-mutect BOD1L1,missense_variant,p.Ala383Ser,ENST00000040738,NM_148894.2;BOD1L1,3_prime_UTR_variant,,ENST00000482713,; A ENST00000040738 Transcript missense_variant 1283/10565 1147/9156 383/3051 A/S Gct/Tct 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 tolerated(0.48) 4/26 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 MODERATE 1 SNV 2 1 PASS . . 1 201 7 0 0 0 0 0 -11.19883 0.9999973 1 1 1 0 A 3 1 12 13614223 13614223 C A 1 0 0 0 0 1 0 0 0 1639 797 28 2 2 BOD1L1 4 13614223 Missense_Mutation SNP C C3L-00144_T 12457 13614223 176600332 448 4519 BST1 0 . GRCh38 4 15731756 15731756 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.868C>G p.Gln290Glu p.Q290E ENST00000265016 9/9 146 135 11 115 115 0 strelka-varscan-mutect BST1,missense_variant,p.Gln305Glu,ENST00000382346,;BST1,missense_variant,p.Gln290Glu,ENST00000265016,NM_004334.2;BST1,intron_variant,,ENST00000514445,;BST1,intron_variant,,ENST00000514989,;RP11-115L11.1,upstream_gene_variant,,ENST00000498116,; G ENST00000265016 Transcript missense_variant 1063/1480 868/957 290/318 Q/E Caa/Gaa 1 1 BST1 HGNC HGNC:1118 protein_coding YES CCDS3416.1 ENSP00000265016 Q10588 UPI0000072318 NM_004334.2 tolerated(0.14) 9/9 Gene3D:3.40.50.720,hmmpanther:PTHR10912,hmmpanther:PTHR10912:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 15731756 15731756 C G 1 0 0 0 0 1 0 0 0 1708 827 29 4 4 BST1 4 15731756 Missense_Mutation SNP C C3L-00144_T 2117533 15731756 174482799 449 4520 KCNIP4 0 . GRCh38 4 20730112 20730112 + Silent SNP G G T rs781507352 C3L-00144_T C3L-00144_N G G c.723C>A p.= p.R241R ENST00000382152 9/9 125 106 19 96 96 0 strelka-varscan-mutect KCNIP4,synonymous_variant,p.=,ENST00000382148,NM_001035003.1;KCNIP4,synonymous_variant,p.=,ENST00000359001,NM_147182.3;KCNIP4,synonymous_variant,p.=,ENST00000382152,NM_025221.5;KCNIP4,synonymous_variant,p.=,ENST00000382150,NM_147183.3;KCNIP4,synonymous_variant,p.=,ENST00000447367,NM_147181.3;KCNIP4,synonymous_variant,p.=,ENST00000509207,NM_001035004.1;PACRGL,intron_variant,,ENST00000507634,;PACRGL,downstream_gene_variant,,ENST00000360916,NM_145048.3;PACRGL,downstream_gene_variant,,ENST00000295290,;PACRGL,downstream_gene_variant,,ENST00000513459,NM_001317849.1;PACRGL,downstream_gene_variant,,ENST00000444671,NM_001130727.1;PACRGL,downstream_gene_variant,,ENST00000503585,NM_001258345.1;PACRGL,downstream_gene_variant,,ENST00000502374,NM_001258346.1;PACRGL,downstream_gene_variant,,ENST00000502938,;KCNIP4,non_coding_transcript_exon_variant,,ENST00000382149,;KCNIP4,3_prime_UTR_variant,,ENST00000515786,;PACRGL,intron_variant,,ENST00000471979,;PACRGL,intron_variant,,ENST00000467997,;PACRGL,intron_variant,,ENST00000506702,;PACRGL,downstream_gene_variant,,ENST00000508952,;PACRGL,downstream_gene_variant,,ENST00000506648,; T ENST00000382152 Transcript synonymous_variant 891/1767 723/753 241/250 R cgC/cgA rs781507352 1 -1 KCNIP4 HGNC HGNC:30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 9/9 hmmpanther:PTHR23055:SF30,hmmpanther:PTHR23055,Gene3D:1.10.238.10,Superfamily_domains:SSF47473,Prints_domain:PR00450 LOW SNV 5 1 PASS rs781507352 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 20730112 20730112 G T 1 0 0 0 0 0 0 0 1 7958 958 34 2 2 KCNIP4 4 20730112 Silent SNP G C3L-00144_T 4998356 20730112 169484443 450 4521 NWD2 0 . GRCh38 4 37245075 37245075 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.8C>A p.Pro3Gln p.P3Q ENST00000309447 1/7 311 242 69 336 335 1 strelka-varscan-mutect NWD2,missense_variant,p.Pro3Gln,ENST00000309447,NM_001144990.1;MIR4801,upstream_gene_variant,,ENST00000582704,; A ENST00000309447 Transcript missense_variant 856/8325 8/5229 3/1742 P/Q cCg/cAg 1 1 NWD2 HGNC HGNC:29229 protein_coding YES CCDS47040.1 ENSP00000309501 Q9ULI1 UPI00006C0875 NM_001144990.1 deleterious_low_confidence(0.02) 1/7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 37245075 37245075 C A 1 0 0 0 0 1 0 0 0 10855 652 23 1 1 NWD2 4 37245075 Missense_Mutation SNP C C3L-00144_T 16514963 37245075 152969480 451 4522 PDS5A 0 . GRCh38 4 39863030 39863030 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2810A>G p.His937Arg p.H937R ENST00000303538 25/33 221 196 25 166 166 0 strelka-mutect PDS5A,missense_variant,p.His937Arg,ENST00000303538,NM_001100399.1;PDS5A,3_prime_UTR_variant,,ENST00000507020,; C ENST00000303538 Transcript missense_variant 3350/7176 2810/4014 937/1337 H/R cAt/cGt 1 -1 PDS5A HGNC HGNC:29088 protein_coding YES CCDS47045.1 ENSP00000303427 Q29RF7 G1UI16 UPI00006C6A7E NM_001100399.1 deleterious(0.01) 25/33 Low_complexity_(Seg):seg,hmmpanther:PTHR12663:SF2,hmmpanther:PTHR12663,Gene3D:1.25.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 39863030 39863030 T C 1 0 0 0 0 1 0 0 0 11779 1464 51 5 5 PDS5A 4 39863030 Missense_Mutation SNP T C3L-00144_T 2617955 39863030 150351525 452 4523 BEND4 0 . GRCh38 4 42151864 42151864 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.280G>T p.Ala94Ser p.A94S ENST00000502486 2/6 34 27 7 34 34 0 strelka-varscan-mutect BEND4,missense_variant,p.Ala94Ser,ENST00000502486,NM_207406.3;BEND4,missense_variant,p.Ala90Ser,ENST00000504360,NM_001159547.1;BEND4,intron_variant,,ENST00000611697,; A ENST00000502486 Transcript missense_variant 860/8765 280/1605 94/534 A/S Gcc/Tcc 1 -1 BEND4 HGNC HGNC:23815 protein_coding YES CCDS47048.1 ENSP00000421169 Q6ZU67 UPI00015386AF NM_207406.3 tolerated_low_confidence(0.7) 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR35082 MODERATE 1 SNV 1 1 PASS rs1359953255 . 0 196 14 0 0 0 0 0 -17.81196 0.9998518 1 1 1 0 A 3 1 12 42151864 42151864 C A 1 0 0 0 0 1 0 0 0 1548 768 27 1 1 BEND4 4 42151864 Missense_Mutation SNP C C3L-00144_T 2288834 42151864 148062691 453 4524 YIPF7 0 . GRCh38 4 44651552 44651552 + Splice_Site SNP A A T novel C3L-00144_T C3L-00144_N A A c.71+2T>A p.X24_splice ENST00000332990 57 52 5 58 58 0 strelka-varscan-mutect YIPF7,splice_donor_variant,,ENST00000415895,;YIPF7,splice_donor_variant,,ENST00000332990,NM_182592.2;YIPF7,intron_variant,,ENST00000508947,;YIPF7,splice_donor_variant,,ENST00000510035,;YIPF7,splice_donor_variant,,ENST00000502794,; T ENST00000332990 Transcript splice_donor_variant -/937 71/843 24/280 1 -1 YIPF7 HGNC HGNC:26825 protein_coding YES CCDS54766.1 ENSP00000332772 Q8N8F6 UPI00015347BF NM_182592.2 1/5 HIGH 1 SNV 5 1 PASS . . 1 205 4 0 0 0 0 0 -12.13233 1 1 1 1 0 T 5 4 12 44651552 44651552 A T 1 0 0 0 0 0 0 1 0 18045 405 14 4 4 YIPF7 4 44651552 Splice_Site SNP A C3L-00144_T 2499688 44651552 145563003 454 4525 GABRA2 0 . GRCh38 4 46388650 46388650 + Silent SNP C C T C3L-00144_T C3L-00144_N C C c.57G>A p.= p.V19V ENST00000510861 2/10 128 116 12 121 121 0 strelka-mutect GABRA2,synonymous_variant,p.=,ENST00000507460,;GABRA2,synonymous_variant,p.=,ENST00000510861,;GABRA2,synonymous_variant,p.=,ENST00000514090,;GABRA2,synonymous_variant,p.=,ENST00000356504,NM_001114175.1;GABRA2,synonymous_variant,p.=,ENST00000381620,NM_000807.2;GABRA2,synonymous_variant,p.=,ENST00000515082,;GABRA2,synonymous_variant,p.=,ENST00000507069,;GABRA2,synonymous_variant,p.=,ENST00000503806,;GABRA2,synonymous_variant,p.=,ENST00000506961,;GABRA2,5_prime_UTR_variant,,ENST00000540012,NM_001286827.1;RP11-436F23.1,upstream_gene_variant,,ENST00000502455,;GABRA2,non_coding_transcript_exon_variant,,ENST00000509716,;GABRA2,synonymous_variant,p.=,ENST00000630416,;GABRA2,synonymous_variant,p.=,ENST00000510233,;GABRA2,synonymous_variant,p.=,ENST00000513005,;GABRA2,synonymous_variant,p.=,ENST00000514193,; T ENST00000510861 Transcript synonymous_variant 231/3411 57/1356 19/451 V gtG/gtA COSM5293665 1 -1 GABRA2 HGNC HGNC:4076 protein_coding YES CCDS3471.1 ENSP00000421828 P47869 A0A024R9X6 UPI000013DC88 2/10 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF218,Prints_domain:PR01615 1 LOW SNV 5 1 1 PASS . . 0 206 0 3 0 0 0 0 -17.40995 0.9999825 1 1 1 0 T 2 4 12 46388650 46388650 C T 1 0 0 0 0 0 0 0 1 6032 465 17 3 3 GABRA2 4 46388650 Silent SNP C C3L-00144_T 1737098 46388650 143825905 455 4526 GABRB1 0 . GRCh38 4 47425835 47425835 + Nonsense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1242C>A p.Tyr414Ter p.Y414* ENST00000295454 9/9 140 114 26 129 129 0 strelka-varscan-mutect GABRB1,stop_gained,p.Tyr414Ter,ENST00000295454,NM_000812.3; A ENST00000295454 Transcript stop_gained 1534/2143 1242/1425 414/474 Y/* taC/taA COSM2848611 1 1 GABRB1 HGNC HGNC:4081 protein_coding YES CCDS3474.1 ENSP00000295454 P18505 X5DNL6 UPI000012AFAC NM_000812.3 9/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF429,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 1 HIGH 1 SNV 1 1 1 PASS rs1422494010 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 47425835 47425835 C A 1 0 0 0 0 0 1 0 0 6037 547 19 1 1 GABRB1 4 47425835 Nonsense_Mutation SNP C C3L-00144_T 1037185 47425835 142788720 456 4527 CWH43 0 . GRCh38 4 49038137 49038137 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1760G>C p.Gly587Ala p.G587A ENST00000226432 13/16 163 150 13 142 142 0 strelka-varscan-mutect CWH43,missense_variant,p.Gly587Ala,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Gly560Ala,ENST00000513409,NM_001286791.1;CWH43,3_prime_UTR_variant,,ENST00000514053,; C ENST00000226432 Transcript missense_variant 1943/2472 1760/2100 587/699 G/A gGc/gCc 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.03) 13/16 hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99996 1 1 1 1 0 C 3 2 12 49038137 49038137 G C 1 0 0 0 0 1 0 0 0 3883 1203 42 4 4 CWH43 4 49038137 Missense_Mutation SNP G C3L-00144_T 1612302 49038137 141176418 457 4528 KIAA1211 0 . GRCh38 4 56315887 56315887 + Silent SNP C C A rs757540931 C3L-00144_T C3L-00144_N C C c.2385C>A p.= p.L795L ENST00000504228 6/9 468 416 52 366 365 1 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,;MRPL22P1,downstream_gene_variant,,ENST00000505398,; A ENST00000504228 Transcript synonymous_variant 2490/4628 2385/3702 795/1233 L ctC/ctA rs757540931,COSM4480073 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 0,1 LOW 1 SNV 5 0,1 1 PASS rs757540931 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 56315887 56315887 C A 1 0 0 0 0 0 0 0 1 8107 842 30 2 2 KIAA1211 4 56315887 Silent SNP C C3L-00144_T 7277750 56315887 133898668 458 4529 EPHA5 0 . GRCh38 4 65602286 65602286 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.265G>T p.Val89Leu p.V89L ENST00000622150 3/18 57 46 11 57 57 0 strelka-varscan-mutect EPHA5,missense_variant,p.Val89Leu,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Val89Leu,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Val89Leu,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Val89Leu,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Val89Leu,ENST00000432638,;EPHA5,missense_variant,p.Val89Leu,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 1018/8421 265/3117 89/1038 V/L Gtg/Ttg 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.41) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 65602286 65602286 C A 1 0 0 0 0 1 0 0 0 5017 565 20 2 2 EPHA5 4 65602286 Missense_Mutation SNP C C3L-00144_T 9286399 65602286 124612269 459 4530 UGT2B4 0 . GRCh38 4 69480796 69480796 + Silent SNP G G A C3L-00144_T C3L-00144_N G G c.1425C>T p.= p.H475H ENST00000305107 6/6 378 306 72 414 414 0 strelka-varscan-mutect UGT2B4,synonymous_variant,p.=,ENST00000305107,NM_021139.2;UGT2B4,3_prime_UTR_variant,,ENST00000512583,NM_001297615.1;UGT2B4,non_coding_transcript_exon_variant,,ENST00000506580,;UGT2B4,downstream_gene_variant,,ENST00000502655,; A ENST00000305107 Transcript synonymous_variant 1472/2103 1425/1587 475/528 H caC/caT COSM4635152 1 -1 UGT2B4 HGNC HGNC:12553 protein_coding YES CCDS43234.1 ENSP00000305221 P06133 UPI000000087F NM_021139.2 6/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF198,Pfam_domain:PF00201 1 LOW 1 SNV 1 1 1 PASS rs1365190372 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 69480796 69480796 G A 1 0 0 0 0 0 0 0 1 17485 1252 44 3 3 UGT2B4 4 69480796 Silent SNP G C3L-00144_T 3878510 69480796 120733759 460 4531 UGT2A1 0 . GRCh38 4 69639360 69639360 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.884C>T p.Ser295Phe p.S295F ENST00000514019 3/7 166 127 39 169 169 0 strelka-varscan-mutect UGT2A1,missense_variant,p.Ser295Phe,ENST00000514019,NM_001252274.2;UGT2A2,missense_variant,p.Ser94Phe,ENST00000604629,NM_001105677.2;UGT2A2,missense_variant,p.Ser94Phe,ENST00000604021,NM_001301233.1;UGT2A1,intron_variant,,ENST00000503640,NM_006798.4;UGT2A1,intron_variant,,ENST00000512704,NM_001301239.1;UGT2A1,intron_variant,,ENST00000286604,NM_001252275.2; A ENST00000514019 Transcript missense_variant 1000/2376 884/2082 295/693 S/F tCc/tTc COSM3605344,COSM5326501 1 -1 UGT2A1 HGNC HGNC:12542 protein_coding YES CCDS58902.1 ENSP00000425497 A0A140T9Z0 UPI0004620AF5 NM_001252274.2 tolerated(0.07) 3/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF229,Superfamily_domains:SSF53756 1,1 MODERATE SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 69639360 69639360 G A 1 0 0 0 0 1 0 0 0 17478 1174 41 3 3 UGT2A1 4 69639360 Missense_Mutation SNP G C3L-00144_T 158564 69639360 120575195 461 4532 SULT1E1 0 . GRCh38 4 69857549 69857549 + Silent SNP C C A rs138937330 C3L-00144_T C3L-00144_N C C c.96G>T p.= p.A32A ENST00000226444 2/8 148 126 22 140 140 0 strelka-varscan-mutect SULT1E1,synonymous_variant,p.=,ENST00000226444,NM_005420.2;SULT1E1,non_coding_transcript_exon_variant,,ENST00000504002,; A ENST00000226444 Transcript synonymous_variant 209/1780 96/885 32/294 A gcG/gcT rs138937330,COSM4125719 1 -1 SULT1E1 HGNC HGNC:11377 protein_coding YES CCDS3531.1 ENSP00000226444 P49888 Q53X91 UPI00000623C8 NM_005420.2 2/8 Gene3D:3.40.50.300,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF53,Superfamily_domains:SSF52540 0,1 LOW 1 SNV 1 0,1 1 PASS rs138937330 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 69857549 69857549 C A 1 0 0 0 0 0 0 0 1 15766 523 19 1 1 SULT1E1 4 69857549 Silent SNP C C3L-00144_T 218189 69857549 120357006 462 4533 NPFFR2 0 . GRCh38 4 72147158 72147158 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.915C>A p.= p.V305V ENST00000308744 4/4 121 96 25 124 124 0 strelka-varscan-mutect NPFFR2,synonymous_variant,p.=,ENST00000308744,NM_004885.2;NPFFR2,synonymous_variant,p.=,ENST00000395999,NM_001144756.1;NPFFR2,synonymous_variant,p.=,ENST00000358749,NM_053036.2;NPFFR2,3_prime_UTR_variant,,ENST00000344413,;NPFFR2,non_coding_transcript_exon_variant,,ENST00000506359,; A ENST00000308744 Transcript synonymous_variant 1013/1922 915/1569 305/522 V gtC/gtA 1 1 NPFFR2 HGNC HGNC:4525 protein_coding YES CCDS3551.1 ENSP00000307822 Q9Y5X5 UPI000012FFBD NM_004885.2 4/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF3,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 72147158 72147158 C A 1 0 0 0 0 0 0 0 1 10626 900 32 2 2 NPFFR2 4 72147158 Silent SNP C C3L-00144_T 2289609 72147158 118067397 463 4534 SCARB2 0 . GRCh38 4 76175792 76175792 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.823A>T p.Arg275Trp p.R275W ENST00000264896 6/12 232 170 62 249 249 0 strelka-varscan-mutect SCARB2,missense_variant,p.Arg275Trp,ENST00000264896,NM_005506.3;SCARB2,missense_variant,p.Arg132Trp,ENST00000452464,NM_001204255.1;SCARB2,downstream_gene_variant,,ENST00000502908,; A ENST00000264896 Transcript missense_variant,splice_region_variant 1173/4763 823/1437 275/478 R/W Agg/Tgg 1 -1 SCARB2 HGNC HGNC:1665 protein_coding YES CCDS3577.1 ENSP00000264896 Q14108 A0A024RDG6 UPI0000032D38 NM_005506.3 deleterious(0) 6/12 hmmpanther:PTHR11923:SF61,hmmpanther:PTHR11923,Pfam_domain:PF01130 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 76175792 76175792 T A 1 0 0 0 0 1 0 0 0 14148 1594 55 4 4 SCARB2 4 76175792 Missense_Mutation SNP T C3L-00144_T 4028634 76175792 114038763 464 4535 CCDC158 0 . GRCh38 4 76331391 76331391 + Silent SNP C C A rs376345467 C3L-00144_T C3L-00144_N C C c.2883G>T p.= p.S961S ENST00000388914 20/24 195 144 51 188 188 0 strelka-varscan-mutect CCDC158,synonymous_variant,p.=,ENST00000388914,NM_001042784.1;CCDC158,non_coding_transcript_exon_variant,,ENST00000504667,; A ENST00000388914 Transcript synonymous_variant 3036/3663 2883/3342 961/1113 S tcG/tcT rs376345467,COSM2151068 1 -1 CCDC158 HGNC HGNC:26374 protein_coding YES CCDS43242.1 ENSP00000373566 Q5M9N0 UPI00004DF23B NM_001042784.1 20/24 Pfam_domain:PF15921 0,1 LOW 1 SNV 5 0,1 1 PASS rs376345467 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 76331391 76331391 C A 1 0 0 0 0 0 0 0 1 2478 523 19 1 1 CCDC158 4 76331391 Silent SNP C C3L-00144_T 155599 76331391 113883164 465 4536 GK2 0 . GRCh38 4 79408046 79408046 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.155G>T p.Trp52Leu p.W52L ENST00000358842 1/1 133 108 25 120 120 0 strelka-varscan-mutect GK2,missense_variant,p.Trp52Leu,ENST00000358842,NM_033214.2; A ENST00000358842 Transcript missense_variant 248/1942 155/1662 52/553 W/L tGg/tTg 1 -1 GK2 HGNC HGNC:4291 protein_coding YES CCDS3585.1 ENSP00000351706 Q14410 A0A140VKG0 UPI000011E629 NM_033214.2 deleterious(0) 1/1 hmmpanther:PTHR10196:SF46,hmmpanther:PTHR10196,TIGRFAM_domain:TIGR01311,Pfam_domain:PF00370,Gene3D:3.30.420.40,PIRSF_domain:PIRSF000538,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 79408046 79408046 C A 1 0 0 0 0 1 0 0 0 6299 595 21 2 2 GK2 4 79408046 Missense_Mutation SNP C C3L-00144_T 3076655 79408046 110806509 466 4537 SNCA 0 . GRCh38 4 89822298 89822298 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.254C>A p.Ala85Glu p.A85E ENST00000336904 4/6 356 271 85 382 381 1 strelka-varscan-mutect SNCA,missense_variant,p.Ala71Glu,ENST00000394989,;SNCA,missense_variant,p.Ala85Glu,ENST00000420646,NM_007308.2;SNCA,missense_variant,p.Ala85Glu,ENST00000336904,NM_001146055.1;SNCA,missense_variant,p.Ala71Glu,ENST00000618500,;SNCA,missense_variant,p.Ala85Glu,ENST00000394986,NM_001146054.1;SNCA,missense_variant,p.Ala85Glu,ENST00000394991,NM_000345.3;SNCA,missense_variant,p.Ala85Glu,ENST00000345009,;SNCA,missense_variant,p.Ala85Glu,ENST00000508895,;SNCA,missense_variant,p.Ala85Glu,ENST00000502987,;SNCA,missense_variant,p.Ala85Glu,ENST00000506244,;SNCA,missense_variant,p.Ala71Glu,ENST00000505199,;SNCA,missense_variant,p.Ala71Glu,ENST00000611107,;SNCA,downstream_gene_variant,,ENST00000506691,; T ENST00000336904 Transcript missense_variant 343/3041 254/423 85/140 A/E gCa/gAa 1 -1 SNCA HGNC HGNC:11138 protein_coding YES CCDS3634.1 ENSP00000338345 P37840 UPI000003173B NM_001146055.1 deleterious(0) 4/6 Superfamily_domains:0053543,Gene3D:1xq8A00,Pfam_domain:PF01387,Prints_domain:PR01211,hmmpanther:PTHR13820,hmmpanther:PTHR13820:SF5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 89822298 89822298 G T 1 0 0 0 0 1 0 0 0 15161 1319 46 2 2 SNCA 4 89822298 Missense_Mutation SNP G C3L-00144_T 10414252 89822298 100392257 467 4538 SMARCAD1 0 . GRCh38 4 94285021 94285021 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2977A>T p.Asn993Tyr p.N993Y ENST00000359052 23/24 175 128 47 209 209 0 strelka-varscan-mutect SMARCAD1,missense_variant,p.Asn993Tyr,ENST00000359052,NM_001128430.1;SMARCAD1,missense_variant,p.Asn991Tyr,ENST00000354268,NM_020159.4;SMARCAD1,missense_variant,p.Asn993Tyr,ENST00000457823,NM_001128429.2;SMARCAD1,missense_variant,p.Asn561Tyr,ENST00000509418,NM_001254949.1;SMARCAD1,3_prime_UTR_variant,,ENST00000394961,; T ENST00000359052 Transcript missense_variant 3151/5017 2977/3087 993/1028 N/Y Aac/Tac 1 1 SMARCAD1 HGNC HGNC:18398 protein_coding YES CCDS47101.1 ENSP00000351947 Q9H4L7 UPI000020B1CF NM_001128430.1 deleterious(0.02) 23/24 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 94285021 94285021 A T 1 0 0 0 0 1 0 0 0 15065 362 13 4 4 SMARCAD1 4 94285021 Missense_Mutation SNP A C3L-00144_T 4462723 94285021 95929534 468 4539 ADH1B 0 . GRCh38 4 99318044 99318044 + Splice_Site SNP A A G novel C3L-00144_T C3L-00144_N A A c.259+2T>C p.X87_splice ENST00000305046 125 93 32 126 126 0 varscan-mutect ADH1B,splice_donor_variant,,ENST00000305046,NM_000668.5;ADH1B,splice_donor_variant,,ENST00000625860,;ADH1B,splice_donor_variant,,ENST00000506651,NM_001286650.1;ADH1B,splice_donor_variant,,ENST00000515694,;ADH1B,non_coding_transcript_exon_variant,,ENST00000632775,;ADH1B,non_coding_transcript_exon_variant,,ENST00000504498,; G ENST00000305046 Transcript splice_donor_variant -/4072 259/1128 87/375 1 -1 ADH1B HGNC HGNC:250 protein_coding YES CCDS34033.1 ENSP00000306606 P00325 V9HW50 UPI00001699B5 NM_000668.5 3/8 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 12 99318044 99318044 A G 1 0 0 0 0 0 0 1 0 381 405 14 5 5 ADH1B 4 99318044 Splice_Site SNP A C3L-00144_T 5033023 99318044 90896511 469 4540 RP11-766F14.2 0 . GRCh38 4 99650260 99650260 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.4389C>T p.= p.S1463S ENST00000511828 1/2 215 197 18 205 205 0 strelka-varscan-mutect RP11-766F14.2,synonymous_variant,p.=,ENST00000511828,; A ENST00000511828 Transcript synonymous_variant 4389/10086 4389/5382 1463/1793 S agC/agT 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE 1/2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 99650260 99650260 G A 1 0 0 0 0 0 0 0 1 13762 1310 46 3 3 RP11-766F14.2 4 99650260 Silent SNP G C3L-00144_T 332216 99650260 90564295 470 4541 RP11-766F14.2 0 . GRCh38 4 99651221 99651221 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.3428G>C p.Gly1143Ala p.G1143A ENST00000511828 1/2 142 106 36 147 147 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Gly1143Ala,ENST00000511828,; G ENST00000511828 Transcript missense_variant 3428/10086 3428/5382 1143/1793 G/A gGc/gCc 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE tolerated(0.4) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 99651221 99651221 C G 1 0 0 0 0 1 0 0 0 13762 739 26 4 4 RP11-766F14.2 4 99651221 Missense_Mutation SNP C C3L-00144_T 961 99651221 90563334 471 4542 PPP3CA 0 . GRCh38 4 101026002 101026002 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1429G>T p.Asp477Tyr p.D477Y ENST00000394854 14/14 182 146 36 194 194 0 strelka-varscan-mutect PPP3CA,missense_variant,p.Asp477Tyr,ENST00000394854,NM_000944.4;PPP3CA,missense_variant,p.Asp425Tyr,ENST00000323055,NM_001130692.1;PPP3CA,missense_variant,p.Asp245Tyr,ENST00000512215,;PPP3CA,missense_variant,p.Asp467Tyr,ENST00000394853,NM_001130691.1;PPP3CA,missense_variant,p.Asp379Tyr,ENST00000507176,; A ENST00000394854 Transcript missense_variant 2113/4685 1429/1566 477/521 D/Y Gac/Tac COSM336205,COSM5289767 1 -1 PPP3CA HGNC HGNC:9314 protein_coding YES CCDS34037.1 ENSP00000378323 Q08209 A0A0S2Z4C6 UPI0000110660 NM_000944.4 deleterious(0) 14/14 Superfamily_domains:SSF56300 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101026002 101026002 C A 1 0 0 0 0 1 0 0 0 12519 913 32 2 2 PPP3CA 4 101026002 Missense_Mutation SNP C C3L-00144_T 1374781 101026002 89188553 472 4543 TBCK 0 . GRCh38 4 106171255 106171255 + Missense_Mutation SNP C C A rs376380860 C3L-00144_T C3L-00144_N C C c.2075G>T p.Arg692Leu p.R692L ENST00000273980 24/27 187 153 34 223 222 1 strelka-varscan-mutect TBCK,missense_variant,p.Arg692Leu,ENST00000273980,;TBCK,missense_variant,p.Arg692Leu,ENST00000432496,NM_001163436.2;TBCK,missense_variant,p.Arg653Leu,ENST00000394706,NM_001163437.2;TBCK,missense_variant,p.Arg629Leu,ENST00000361687,NM_033115.4,NM_001290768.1;TBCK,missense_variant,p.Arg692Leu,ENST00000394708,NM_001163435.2;TBCK,non_coding_transcript_exon_variant,,ENST00000514689,;TBCK,non_coding_transcript_exon_variant,,ENST00000515705,;TBCK,non_coding_transcript_exon_variant,,ENST00000511011,;TBCK,upstream_gene_variant,,ENST00000506384,;TBCK,3_prime_UTR_variant,,ENST00000467183,;TBCK,non_coding_transcript_exon_variant,,ENST00000510927,; A ENST00000273980 Transcript missense_variant 2523/8101 2075/2682 692/893 R/L cGc/cTc rs376380860,COSM1426252 1 -1 TBCK HGNC HGNC:28261 protein_coding YES CCDS54788.1 ENSP00000273980 Q8TEA7 UPI000013EF70 tolerated(0.25) 24/27 hmmpanther:PTHR22957:SF168,hmmpanther:PTHR22957,Superfamily_domains:SSF47923 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs376380860 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 106171255 106171255 C A 1 0 0 0 0 1 0 0 0 16041 768 27 1 1 TBCK 4 106171255 Missense_Mutation SNP C C3L-00144_T 5145253 106171255 84043300 473 4544 LEF1 0 . GRCh38 4 108070769 108070769 + Nonsense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1010G>A p.Trp337Ter p.W337* ENST00000265165 9/12 143 103 40 115 115 0 strelka-varscan-mutect LEF1,stop_gained,p.Trp309Ter,ENST00000379951,NM_001130714.2;LEF1,stop_gained,p.Trp337Ter,ENST00000265165,NM_016269.4;LEF1,stop_gained,p.Trp309Ter,ENST00000438313,NM_001130713.2;LEF1,stop_gained,p.Trp241Ter,ENST00000510624,NM_001166119.1;LEF1,splice_region_variant,,ENST00000503879,;LEF1,splice_region_variant,,ENST00000504426,;LEF1,splice_region_variant,,ENST00000510135,;LEF1,splice_region_variant,,ENST00000509428,;LEF1,splice_region_variant,,ENST00000505379,;LEF1,splice_region_variant,,ENST00000514444,;LEF1,splice_region_variant,,ENST00000505297,;LEF1,splice_region_variant,,ENST00000504775,;LEF1,splice_region_variant,,ENST00000512407,;LEF1,splice_region_variant,,ENST00000506680,;LEF1,splice_region_variant,,ENST00000505328,;LEF1,non_coding_transcript_exon_variant,,ENST00000507470,; T ENST00000265165 Transcript stop_gained,splice_region_variant 1665/3068 1010/1200 337/399 W/* tGg/tAg 1 -1 LEF1 HGNC HGNC:6551 protein_coding YES CCDS3679.1 ENSP00000265165 Q9UJU2 A0A024RDI7 UPI0000052242 NM_016269.4 9/12 PROSITE_profiles:PS50118,hmmpanther:PTHR10373,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 108070769 108070769 C T 1 0 0 0 0 0 1 0 0 8622 608 21 3 3 LEF1 4 108070769 Nonsense_Mutation SNP C C3L-00144_T 1899514 108070769 82143786 474 4545 ZGRF1 0 . GRCh38 4 112558258 112558258 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.5012T>A p.Phe1671Tyr p.F1671Y ENST00000505019 20/28 122 87 35 111 111 0 strelka-varscan-mutect ZGRF1,missense_variant,p.Phe1671Tyr,ENST00000505019,NM_018392.4;ZGRF1,missense_variant,p.Phe1671Tyr,ENST00000445203,;ZGRF1,5_prime_UTR_variant,,ENST00000612287,;ZGRF1,missense_variant,p.Phe569Tyr,ENST00000445413,;ZGRF1,non_coding_transcript_exon_variant,,ENST00000506675,;ZGRF1,downstream_gene_variant,,ENST00000473015,; T ENST00000505019 Transcript missense_variant 5138/6652 5012/6315 1671/2104 F/Y tTt/tAt 1 -1 ZGRF1 HGNC HGNC:25654 protein_coding YES CCDS3700.2 ENSP00000424737 Q86YA3 UPI0000EE2F8F NM_018392.4 deleterious(0.03) 20/28 Gene3D:3.40.50.300,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 112558258 112558258 A T 1 0 0 0 0 1 0 0 0 18253 14 1 4 4 ZGRF1 4 112558258 Missense_Mutation SNP A C3L-00144_T 4487489 112558258 77656297 475 4546 TRPC3 0 . GRCh38 4 121914845 121914845 + Missense_Mutation SNP C C A rs758648981 C3L-00144_T C3L-00144_N C C c.1276G>T p.Val426Leu p.V426L ENST00000379645 4/12 145 109 36 138 138 0 strelka-varscan-mutect TRPC3,missense_variant,p.Val353Leu,ENST00000264811,NM_003305.2;TRPC3,missense_variant,p.Val426Leu,ENST00000379645,NM_001130698.1;TRPC3,intron_variant,,ENST00000513531,;TRPC3,3_prime_UTR_variant,,ENST00000506449,; A ENST00000379645 Transcript missense_variant 1350/3548 1276/2766 426/921 V/L Gtg/Ttg rs758648981 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 tolerated(0.07) 4/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs758648981 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 121914845 121914845 C A 1 0 0 0 0 1 0 0 0 17084 478 17 2 2 TRPC3 4 121914845 Missense_Mutation SNP C C3L-00144_T 9356587 121914845 68299710 476 4547 PCDH10 0 . GRCh38 4 133152709 133152709 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2569G>T p.Val857Phe p.V857F ENST00000264360 1/5 262 212 50 235 234 1 strelka-varscan-mutect PCDH10,missense_variant,p.Val857Phe,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Val857Phe,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; T ENST00000264360 Transcript missense_variant 3395/8489 2569/3123 857/1040 V/F Gtc/Ttc COSM3010532 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 tolerated(0.48) 1/5 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 133152709 133152709 G T 1 0 0 0 0 1 0 0 0 11594 1145 40 1 1 PCDH10 4 133152709 Missense_Mutation SNP G C3L-00144_T 11237864 133152709 57061846 477 4548 RAB33B 0 . GRCh38 4 139472703 139472703 + Silent SNP A A G C3L-00144_T C3L-00144_N A A c.267A>G p.= p.T89T ENST00000305626 2/2 66 51 15 68 68 0 strelka-varscan-mutect RAB33B,synonymous_variant,p.=,ENST00000305626,NM_031296.1; G ENST00000305626 Transcript synonymous_variant 656/4562 267/690 89/229 T acA/acG COSM732538 1 1 RAB33B HGNC HGNC:16075 protein_coding YES CCDS3747.1 ENSP00000306496 Q9H082 UPI000000123D NM_031296.1 2/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF378,hmmpanther:PTHR24073,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449 1 LOW 1 SNV 1 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 139472703 139472703 A G 1 0 0 0 0 0 0 0 1 13082 175 7 5 5 RAB33B 4 139472703 Silent SNP A C3L-00144_T 6319994 139472703 50741852 478 4549 MAML3 0 . GRCh38 4 139889836 139889836 + Missense_Mutation SNP C C G rs745581763 C3L-00144_T C3L-00144_N C C c.1600G>C p.Ala534Pro p.A534P ENST00000509479 2/5 242 184 58 243 243 0 strelka-varscan-mutect MAML3,missense_variant,p.Ala534Pro,ENST00000509479,NM_018717.4;MAML3,missense_variant,p.Ala62Pro,ENST00000398940,;MAML3,intron_variant,,ENST00000502696,; G ENST00000509479 Transcript missense_variant 2457/6844 1600/3417 534/1138 A/P Gca/Cca rs745581763 1 -1 MAML3 HGNC HGNC:16272 protein_coding YES CCDS54805.1 ENSP00000421180 Q96JK9 UPI00001C1E1E NM_018717.4 tolerated(0.32) 2/5 hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF8 MODERATE 1 SNV 1 1 PASS rs745581763 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 139889836 139889836 C G 1 0 0 0 0 1 0 0 0 9128 710 25 4 4 MAML3 4 139889836 Missense_Mutation SNP C C3L-00144_T 417133 139889836 50324719 479 4550 SCOC 0 . GRCh38 4 140373643 140373643 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.107G>T p.Arg36Leu p.R36L ENST00000608372 1/4 287 187 100 296 295 1 strelka-varscan-mutect SCOC,missense_variant,p.Arg36Leu,ENST00000608372,;SCOC,missense_variant,p.Arg36Leu,ENST00000614192,NM_001153484.1,NM_001153663.1;SCOC,missense_variant,p.Arg36Leu,ENST00000506597,NM_001153552.1;SCOC,5_prime_UTR_variant,,ENST00000394201,;SCOC,intron_variant,,ENST00000394203,NM_001153585.1;SCOC,intron_variant,,ENST00000394205,NM_032547.2;SCOC,intron_variant,,ENST00000338517,NM_001153635.1,NM_001153446.1;SCOC,intron_variant,,ENST00000512749,;SCOC,intron_variant,,ENST00000506322,;SCOC,upstream_gene_variant,,ENST00000510586,;SCOC,upstream_gene_variant,,ENST00000502535,;SCOC-AS1,upstream_gene_variant,,ENST00000512692,;SCOC-AS1,upstream_gene_variant,,ENST00000608178,;SCOC-AS1,upstream_gene_variant,,ENST00000609616,; T ENST00000608372 Transcript missense_variant 134/5129 107/480 36/159 R/L cGg/cTg 1 1 SCOC HGNC HGNC:20335 protein_coding YES CCDS54806.1 ENSP00000477352 Q9UIL1 UPI0000E5AC43 tolerated_low_confidence(0.07) 1/4 hmmpanther:PTHR21614 MODERATE 1 SNV 1 1 PASS rs1310272627 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 140373643 140373643 G T 1 0 0 0 0 1 0 0 0 14202 1116 39 1 1 SCOC 4 140373643 Missense_Mutation SNP G C3L-00144_T 483807 140373643 49840912 480 4551 CLGN 0 . GRCh38 4 140410608 140410608 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.163C>A p.Gln55Lys p.Q55K ENST00000325617 3/15 182 141 41 224 221 3 strelka-varscan-mutect CLGN,missense_variant,p.Gln55Lys,ENST00000325617,NM_004362.2;CLGN,missense_variant,p.Gln55Lys,ENST00000414773,NM_001130675.1;CLGN,missense_variant,p.Gln55Lys,ENST00000509477,; T ENST00000325617 Transcript missense_variant 604/3043 163/1833 55/610 Q/K Caa/Aaa 1 -1 CLGN HGNC HGNC:2060 protein_coding YES CCDS3751.1 ENSP00000326699 O14967 A0A140VKG2 UPI0000126E4A NM_004362.2 tolerated(0.94) 3/15 hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF7,Gene3D:2.60.120.200,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 140410608 140410608 G T 1 0 0 0 0 1 0 0 0 3292 1299 45 2 2 CLGN 4 140410608 Missense_Mutation SNP G C3L-00144_T 36965 140410608 49803947 481 4552 MGAT4D 0 . GRCh38 4 140498209 140498209 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.14A>T p.Gln5Leu p.Q5L ENST00000511113 1/11 154 114 40 136 136 0 strelka-varscan-mutect MGAT4D,missense_variant,p.Gln5Leu,ENST00000515354,;MGAT4D,missense_variant,p.Gln5Leu,ENST00000503109,;MGAT4D,missense_variant,p.Gln5Leu,ENST00000511113,NM_001277353.1;MGAT4D,missense_variant,p.Gln5Leu,ENST00000515402,;MGAT4D,non_coding_transcript_exon_variant,,ENST00000511632,;MGAT4D,non_coding_transcript_exon_variant,,ENST00000509091,;RP11-542P2.2,upstream_gene_variant,,ENST00000624981,;MGAT4D,missense_variant,p.Gln5Leu,ENST00000515121,;MGAT4D,non_coding_transcript_exon_variant,,ENST00000513106,; A ENST00000511113 Transcript missense_variant 14/1125 14/1125 5/374 Q/L cAg/cTg 1 -1 MGAT4D HGNC HGNC:43619 protein_coding YES CCDS64066.1 ENSP00000421185 A6NG13 UPI0001BFFEBB NM_001277353.1 tolerated(0.15) 1/11 PROSITE_profiles:PS51257,hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 140498209 140498209 T A 1 0 0 0 0 1 0 0 0 9508 1580 55 4 4 MGAT4D 4 140498209 Missense_Mutation SNP T C3L-00144_T 87601 140498209 49716346 482 4553 RNF175 0 . GRCh38 4 153712576 153712576 + Frame_Shift_Del DEL G G - rs201149369 C3L-00144_T C3L-00144_N G G c.765delC p.His257MetfsTer26 p.H257Mfs*26 ENST00000347063 8/9 106 74 32 110 110 0 sindel-varindel-pindel RNF175,frameshift_variant,p.His257MetfsTer26,ENST00000347063,NM_173662.2;RNF175,splice_region_variant,,ENST00000513656,;RNF175,downstream_gene_variant,,ENST00000503694,; - ENST00000347063 Transcript frameshift_variant,splice_region_variant 1138/1604 765/987 255/328 V/X gtC/gt rs201149369 1 -1 RNF175 HGNC HGNC:27735 protein_coding YES CCDS47149.1 ENSP00000340979 Q8N4F7 UPI0001AE7525 NM_173662.2 8/9 PROSITE_profiles:PS50089,hmmpanther:PTHR13407:SF2,hmmpanther:PTHR13407,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 153712576 153712576 G - 1 0 1 0 1 0 0 0 0 13640 985 34 0 0 RNF175 4 153712576 Frame_Shift_Del DEL G C3L-00144_T 13214367 153712576 36501979 483 4554 DCHS2 0 . GRCh38 4 154235331 154235331 + Silent SNP G G T rs760003334 C3L-00144_T C3L-00144_N G G c.7956C>A p.= p.I2652I ENST00000623607 25/25 152 118 34 185 185 0 strelka-varscan-mutect DCHS2,synonymous_variant,p.=,ENST00000357232,;DCHS2,synonymous_variant,p.=,ENST00000623607,NM_017639.3;RP11-290O12.2,intron_variant,,ENST00000624941,;RP11-290O12.2,intron_variant,,ENST00000623325,;RP11-9N12.2,upstream_gene_variant,,ENST00000625026,; T ENST00000623607 Transcript synonymous_variant 7956/8912 7956/8751 2652/2916 I atC/atA rs760003334,COSM3128713 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 25/25 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305 0,1 LOW 1 SNV 1 0,1 1 PASS rs760003334 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 154235331 154235331 G T 1 0 0 0 0 0 0 0 1 4091 1164 41 2 2 DCHS2 4 154235331 Silent SNP G C3L-00144_T 522755 154235331 35979224 484 4555 DCHS2 0 . GRCh38 4 154366330 154366330 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.574C>A p.Pro192Thr p.P192T ENST00000623607 5/25 394 308 86 383 382 1 strelka-varscan-mutect DCHS2,missense_variant,p.Pro192Thr,ENST00000357232,;DCHS2,missense_variant,p.Pro192Thr,ENST00000623607,NM_017639.3;DCHS2,missense_variant,p.Pro786Thr,ENST00000339452,NM_001142552.1; T ENST00000623607 Transcript missense_variant 574/8912 574/8751 192/2916 P/T Cca/Aca 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 tolerated(0.07) 5/25 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 154366330 154366330 G T 1 0 0 0 0 1 0 0 0 4091 1203 42 2 2 DCHS2 4 154366330 Missense_Mutation SNP G C3L-00144_T 130999 154366330 35848225 485 4556 FGA 0 . GRCh38 4 154589504 154589504 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.113G>T p.Arg38Met p.R38M ENST00000302053 2/6 442 330 112 467 467 0 strelka-varscan-mutect FGA,missense_variant,p.Arg38Met,ENST00000302053,NM_000508.3;FGA,missense_variant,p.Arg38Met,ENST00000403106,NM_021871.2;FGA,missense_variant,p.Arg38Met,ENST00000622532,; A ENST00000302053 Transcript missense_variant 192/3678 113/2601 38/866 R/M aGg/aTg COSM5652974,COSM5652975 1 -1 FGA HGNC HGNC:3661 protein_coding YES CCDS3787.1 ENSP00000306361 P02671 UPI000012A75A NM_000508.3 deleterious(0) 2/6 Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 154589504 154589504 C A 1 0 0 0 0 1 0 0 0 5694 681 24 2 2 FGA 4 154589504 Missense_Mutation SNP C C3L-00144_T 223174 154589504 35625051 486 4557 GRIA2 0 . GRCh38 4 157312699 157312699 + Missense_Mutation SNP G G T rs144288333 C3L-00144_T C3L-00144_N G G c.490G>T p.Val164Leu p.V164L ENST00000296526 4/16 41 35 6 52 52 0 strelka-varscan-mutect GRIA2,missense_variant,p.Val164Leu,ENST00000296526,NM_000826.3;GRIA2,missense_variant,p.Val117Leu,ENST00000393815,NM_001083620.1;GRIA2,missense_variant,p.Val164Leu,ENST00000264426,NM_001083619.1;GRIA2,missense_variant,p.Val117Leu,ENST00000507898,;GRIA2,missense_variant,p.Val117Leu,ENST00000505888,;GRIA2,missense_variant,p.Val37Leu,ENST00000503437,;GRIA2,missense_variant,p.Val117Leu,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; T ENST00000296526 Transcript missense_variant 815/5621 490/2652 164/883 V/L Gtg/Ttg rs144288333 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 tolerated(0.44) 4/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs144288333 . 0 200 10 0 0 0 0 0 -14.9045 0.9999821 1 1 1 0 T 3 4 12 157312699 157312699 G T 1 0 0 0 0 1 0 0 0 6648 1377 48 2 2 GRIA2 4 157312699 Missense_Mutation SNP G C3L-00144_T 2723195 157312699 32901856 487 4558 TKTL2 0 . GRCh38 4 163471911 163471911 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1824G>T p.Met608Ile p.M608I ENST00000280605 1/1 18 12 6 18 18 0 strelka-varscan-mutect TKTL2,missense_variant,p.Met608Ile,ENST00000280605,NM_032136.4; A ENST00000280605 Transcript missense_variant 1836/2654 1824/1881 608/626 M/I atG/atT 1 -1 TKTL2 HGNC HGNC:25313 protein_coding YES CCDS3805.1 ENSP00000280605 Q9H0I9 A0A140VKC2 UPI0000037C67 NM_032136.4 tolerated(0.41) 1/1 hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF49,Pfam_domain:PF02780,Gene3D:3.40.50.920,Superfamily_domains:SSF52922 MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -17.84326 1 1 1 1 0 A 3 1 12 163471911 163471911 C A 1 0 0 0 0 1 0 0 0 16379 478 17 2 2 TKTL2 4 163471911 Missense_Mutation SNP C C3L-00144_T 6159212 163471911 26742644 488 4559 TENM3 0 . GRCh38 4 182792957 182792957 + Missense_Mutation SNP C C G rs746800423 C3L-00144_T C3L-00144_N C C c.6285C>G p.Phe2095Leu p.F2095L ENST00000511685 26/28 205 163 42 219 219 0 strelka-varscan-mutect TENM3,missense_variant,p.Phe2095Leu,ENST00000511685,NM_001080477.2; G ENST00000511685 Transcript missense_variant 6408/10896 6285/8100 2095/2699 F/L ttC/ttG rs746800423 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 tolerated(0.49) 26/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 MODERATE 1 SNV 5 1 PASS rs746800423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 182792957 182792957 C G 1 0 0 0 0 1 0 0 0 16173 825 29 4 4 TENM3 4 182792957 Missense_Mutation SNP C C3L-00144_T 19321046 182792957 7421598 489 4560 TENM3 0 . GRCh38 4 182799674 182799674 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.7423G>T p.Val2475Leu p.V2475L ENST00000511685 28/28 263 205 58 273 272 1 strelka-varscan-mutect TENM3,missense_variant,p.Val2475Leu,ENST00000511685,NM_001080477.2; T ENST00000511685 Transcript missense_variant 7546/10896 7423/8100 2475/2699 V/L Gtg/Ttg 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 tolerated(0.9) 28/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 MODERATE 1 SNV 5 1 PASS rs1332303141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 182799674 182799674 G T 1 0 0 0 0 1 0 0 0 16173 1261 44 2 2 TENM3 4 182799674 Missense_Mutation SNP G C3L-00144_T 6717 182799674 7414881 490 4561 LRP2BP 0 . GRCh38 4 185378092 185378092 + Frame_Shift_Del DEL T T - novel C3L-00144_T C3L-00144_N T T c.95delA p.Lys32ArgfsTer19 p.K32Rfs*19 ENST00000328559 1/8 135 93 42 114 114 0 sindel-varindel-pindel LRP2BP,frameshift_variant,p.Lys32ArgfsTer19,ENST00000328559,NM_018409.3;LRP2BP,frameshift_variant,p.Lys32ArgfsTer19,ENST00000505916,;LRP2BP,frameshift_variant,p.Lys32ArgfsTer19,ENST00000511404,;LRP2BP,5_prime_UTR_variant,,ENST00000510776,;RP11-714G18.1,intron_variant,,ENST00000514884,; - ENST00000328559 Transcript frameshift_variant 907/5157 95/1044 32/347 K/X aAg/ag 1 -1 LRP2BP HGNC HGNC:25434 protein_coding YES CCDS3840.1 ENSP00000332681 Q9P2M1 UPI00001BB2BB NM_018409.3 1/8 HIGH 1 deletion 1 1 PASS . . 0 204 0 4 0 0 0 0 -20 0.9999784 1 1 1 0 - 7 5 12 185378092 185378092 T - 1 0 1 0 1 0 0 0 0 8852 1609 56 0 0 LRP2BP 4 185378092 Frame_Shift_Del DEL T C3L-00144_T 2578418 185378092 4836463 491 4562 FAT1 0 . GRCh38 4 186618886 186618886 + Missense_Mutation SNP C C T rs116784674 C3L-00144_T C3L-00144_N C C c.7700G>A p.Arg2567His p.R2567H ENST00000441802 10/27 129 118 11 134 134 0 strelka-varscan-mutect FAT1,missense_variant,p.Arg2567His,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Arg2569His,ENST00000614102,; T ENST00000441802 Transcript missense_variant 7910/14786 7700/13767 2567/4588 R/H cGt/cAt rs116784674 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 tolerated(0.56) 10/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs116784674 . 0 202 0 0 0 0 0 8 -4.990508 0 0 1 0 0 T 3 4 12 186618886 186618886 C T 1 0 0 0 0 1 0 0 0 5549 536 19 1 1 FAT1 4 186618886 Missense_Mutation SNP C C3L-00144_T 1240794 186618886 3595669 492 4563 FAT1 0 . GRCh38 4 186706777 186706777 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.3051T>C p.= p.Y1017Y ENST00000441802 2/27 154 119 35 165 165 0 strelka-varscan-mutect FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,;FAT1,downstream_gene_variant,,ENST00000509647,; G ENST00000441802 Transcript synonymous_variant 3261/14786 3051/13767 1017/4588 Y taT/taC 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 2/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 186706777 186706777 A G 1 0 0 0 0 0 0 0 1 5549 224 8 5 5 FAT1 4 186706777 Silent SNP A C3L-00144_T 87891 186706777 3507778 493 4564 LRRC14B 0 . GRCh38 5 195232 195232 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1424C>G p.Pro475Arg p.P475R ENST00000328278 2/2 765 670 95 332 332 0 strelka-varscan-mutect LRRC14B,missense_variant,p.Pro475Arg,ENST00000328278,NM_001080478.1;CCDC127,downstream_gene_variant,,ENST00000296824,NM_145265.2;CTD-2083E4.7,upstream_gene_variant,,ENST00000563761,; G ENST00000328278 Transcript missense_variant 1452/1573 1424/1545 475/514 P/R cCt/cGt 1 1 LRRC14B HGNC HGNC:37268 protein_coding YES CCDS47184.1 ENSP00000327675 A6NHZ5 UPI0000237324 NM_001080478.1 deleterious(0) 2/2 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF27 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 195232 195232 C G 1 0 0 0 0 1 0 0 0 8865 681 24 4 4 LRRC14B 5 195232 Missense_Mutation SNP C C3L-00144_T 195232 181343027 494 4565 EXOC3 0 . GRCh38 5 453445 453445 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.440A>T p.Asp147Val p.D147V ENST00000512944 4/13 405 377 28 161 161 0 strelka-mutect EXOC3,missense_variant,p.Asp147Val,ENST00000512944,NM_007277.4;EXOC3,missense_variant,p.Asp147Val,ENST00000315013,;EXOC3,missense_variant,p.Asp147Val,ENST00000515601,;EXOC3,missense_variant,p.Asp17Val,ENST00000503889,;EXOC3,upstream_gene_variant,,ENST00000510028,; T ENST00000512944 Transcript missense_variant 629/2825 440/2238 147/745 D/V gAc/gTc 1 1 EXOC3 HGNC HGNC:30378 protein_coding YES CCDS54830.1 ENSP00000425587 O60645 A0A024QYZ6 UPI000004A021 NM_007277.4 deleterious(0) 4/13 hmmpanther:PTHR21292:SF13,hmmpanther:PTHR21292 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 453445 453445 A T 1 0 0 0 0 1 0 0 0 5170 275 10 4 4 EXOC3 5 453445 Missense_Mutation SNP A C3L-00144_T 258213 453445 181084814 495 4566 TERT 0 . GRCh38 5 1294516 1294516 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.370C>T p.Pro124Ser p.P124S ENST00000310581 2/16 479 449 30 251 251 0 strelka-varscan-mutect TERT,missense_variant,p.Pro124Ser,ENST00000310581,NM_198253.2;TERT,missense_variant,p.Pro124Ser,ENST00000334602,NM_001193376.1;TERT,missense_variant,p.Pro124Ser,ENST00000508104,;TERT,downstream_gene_variant,,ENST00000522877,;TERT,missense_variant,p.Pro124Ser,ENST00000460137,; A ENST00000310581 Transcript missense_variant 428/4018 370/3399 124/1132 P/S Ccc/Tcc 1 -1 TERT HGNC HGNC:11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 UPI0000031309 NM_198253.2 tolerated(0.09) 2/16 hmmpanther:PTHR12066,hmmpanther:PTHR12066:SF0 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 12 1294516 1294516 G A 1 0 0 0 0 1 0 0 0 16183 1203 42 3 3 TERT 5 1294516 Missense_Mutation SNP G C3L-00144_T 841071 1294516 180243743 496 4567 SLC6A3 0 . GRCh38 5 1414815 1414815 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1032G>T p.Arg344Ser p.R344S ENST00000270349 8/15 922 865 57 455 455 0 strelka-varscan-mutect SLC6A3,missense_variant,p.Arg344Ser,ENST00000270349,NM_001044.4;SLC6A3,splice_region_variant,,ENST00000511750,; A ENST00000270349 Transcript missense_variant,splice_region_variant 1160/3936 1032/1863 344/620 R/S agG/agT 1 -1 SLC6A3 HGNC HGNC:11049 protein_coding YES CCDS3863.1 ENSP00000270349 Q01959 UPI000013548F NM_001044.4 deleterious(0.04) 8/15 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF38,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1414815 1414815 C A 1 0 0 0 0 1 0 0 0 14968 637 22 2 2 SLC6A3 5 1414815 Missense_Mutation SNP C C3L-00144_T 120299 1414815 180123444 497 4568 IRX1 0 . GRCh38 5 3599332 3599332 + Silent SNP C C T rs763266040 C3L-00144_T C3L-00144_N C C c.384C>T p.= p.P128P ENST00000302006 2/4 740 661 79 313 313 0 strelka-varscan-mutect IRX1,synonymous_variant,p.=,ENST00000302006,NM_024337.3;CTD-2012M11.3,intron_variant,,ENST00000559410,; T ENST00000302006 Transcript synonymous_variant 436/1858 384/1443 128/480 P ccC/ccT rs763266040,COSM1067564 1 1 IRX1 HGNC HGNC:14358 protein_coding YES CCDS34132.1 ENSP00000305244 P78414 UPI00001B6455 NM_024337.3 2/4 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF13,SMART_domains:SM00389 0,1 LOW 1 SNV 1 0,1 1 PASS rs763266040 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 3599332 3599332 C T 1 0 0 0 0 0 0 0 1 7751 639 23 1 1 IRX1 5 3599332 Silent SNP C C3L-00144_T 2184517 3599332 177938927 498 4569 ADAMTS16 0 . GRCh38 5 5140518 5140518 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.51G>T p.= p.L17L ENST00000274181 1/23 283 242 41 124 124 0 strelka-varscan-mutect ADAMTS16,synonymous_variant,p.=,ENST00000274181,NM_139056.2;ADAMTS16,synonymous_variant,p.=,ENST00000511368,;CTD-2297D10.2,upstream_gene_variant,,ENST00000512155,;CTD-2297D10.1,downstream_gene_variant,,ENST00000514848,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript synonymous_variant 189/4979 51/3675 17/1224 L ctG/ctT 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 1/23 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 5140518 5140518 G T 1 0 0 0 0 0 0 0 1 305 1364 48 2 2 ADAMTS16 5 5140518 Silent SNP G C3L-00144_T 1541186 5140518 176397741 499 4570 ADCY2 0 . GRCh38 5 7695775 7695775 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.893G>T p.Gly298Val p.G298V ENST00000338316 6/25 294 225 69 115 115 0 strelka-varscan-mutect ADCY2,missense_variant,p.Gly298Val,ENST00000338316,NM_020546.2;ADCY2,missense_variant,p.Gly87Val,ENST00000515681,;ADCY2,downstream_gene_variant,,ENST00000513693,; T ENST00000338316 Transcript missense_variant 982/6575 893/3276 298/1091 G/V gGc/gTc 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0.02) 6/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7695775 7695775 G T 1 0 0 0 0 1 0 0 0 338 1203 42 2 2 ADCY2 5 7695775 Missense_Mutation SNP G C3L-00144_T 2555257 7695775 173842484 500 4571 CTNND2 0 . GRCh38 5 11364701 11364701 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1367G>T p.Ser456Ile p.S456I ENST00000304623 8/22 266 226 40 123 123 0 strelka-varscan-mutect CTNND2,missense_variant,p.Ser456Ile,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Ser365Ile,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Ser119Ile,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Ser196Ile,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000504354,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506735,;CTNND2,downstream_gene_variant,,ENST00000511278,;CTNND2,missense_variant,p.Ser210Ile,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,;CTNND2,non_coding_transcript_exon_variant,,ENST00000507430,; A ENST00000304623 Transcript missense_variant 1557/5481 1367/3678 456/1225 S/I aGc/aTc COSM4675423 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.1) 8/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 11364701 11364701 C A 1 0 0 0 0 1 0 0 0 3829 811 28 2 2 CTNND2 5 11364701 Missense_Mutation SNP C C3L-00144_T 3668926 11364701 170173558 501 4572 DNAH5 0 . GRCh38 5 13735915 13735915 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.11473A>G p.Ile3825Val p.I3825V ENST00000265104 67/79 1119 974 145 461 460 1 strelka-varscan-mutect DNAH5,missense_variant,p.Ile3825Val,ENST00000265104,NM_001369.2; C ENST00000265104 Transcript missense_variant 11578/15633 11473/13875 3825/4624 I/V Atc/Gtc 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 tolerated(0.3) 67/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 13735915 13735915 T C 1 0 0 0 0 1 0 0 0 4419 1464 51 5 5 DNAH5 5 13735915 Missense_Mutation SNP T C3L-00144_T 2371214 13735915 167802344 502 4573 ANKH 0 . GRCh38 5 14758480 14758480 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.432G>T p.Met144Ile p.M144I ENST00000284268 3/12 755 711 44 299 296 3 strelka-varscan-mutect ANKH,missense_variant,p.Met144Ile,ENST00000284268,NM_054027.4;ANKH,upstream_gene_variant,,ENST00000503939,; A ENST00000284268 Transcript missense_variant,splice_region_variant 763/8203 432/1479 144/492 M/I atG/atT COSM3612200 1 -1 ANKH HGNC HGNC:15492 protein_coding YES CCDS3885.1 ENSP00000284268 Q9HCJ1 UPI000003F535 NM_054027.4 tolerated(0.22) 3/12 Pfam_domain:PF07260,hmmpanther:PTHR28384,hmmpanther:PTHR28384:SF1,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 14758480 14758480 C A 1 0 0 0 0 1 0 0 0 729 608 21 2 2 ANKH 5 14758480 Missense_Mutation SNP C C3L-00144_T 1022565 14758480 166779779 503 4574 FBXL7 0 . GRCh38 5 15928392 15928392 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.630C>A p.Cys210Ter p.C210* ENST00000504595 3/4 870 757 113 404 404 0 strelka-varscan-mutect FBXL7,stop_gained,p.Cys210Ter,ENST00000504595,NM_012304.4;FBXL7,stop_gained,p.Cys168Ter,ENST00000329673,;FBXL7,stop_gained,p.Cys163Ter,ENST00000510662,NM_001278317.1; A ENST00000504595 Transcript stop_gained 1111/4562 630/1476 210/491 C/* tgC/tgA 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 3/4 Gene3D:3.80.10.10,hmmpanther:PTHR24006,SMART_domains:SM00367,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 15928392 15928392 C A 1 0 0 0 0 0 1 0 0 5587 805 28 2 2 FBXL7 5 15928392 Nonsense_Mutation SNP C C3L-00144_T 1169912 15928392 165609867 504 4575 CDH18 0 . GRCh38 5 19473598 19473598 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2001C>A p.Asp667Glu p.D667E ENST00000507958 15/15 488 327 161 222 222 0 strelka-varscan-mutect CDH18,missense_variant,p.Asp667Glu,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Asp667Glu,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Asp667Glu,ENST00000274170,;CDH18,3_prime_UTR_variant,,ENST00000506372,NM_001291957.1;CDH18,3_prime_UTR_variant,,ENST00000502796,NM_001167667.1;CDH18,downstream_gene_variant,,ENST00000515257,;CDH18,non_coding_transcript_exon_variant,,ENST00000510297,; T ENST00000507958 Transcript missense_variant 2992/3542 2001/2373 667/790 D/E gaC/gaA COSM591974,COSM591975 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 15/15 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Pfam_domain:PF01049 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 19473598 19473598 G T 1 0 0 0 0 1 0 0 0 2806 1368 48 2 2 CDH18 5 19473598 Missense_Mutation SNP G C3L-00144_T 3545206 19473598 162064661 505 4576 CDH18 0 . GRCh38 5 19483396 19483396 + Missense_Mutation SNP C C A rs781255308 C3L-00144_T C3L-00144_N C C c.1787G>T p.Arg596Leu p.R596L ENST00000507958 14/15 596 456 140 222 222 0 strelka-varscan-mutect CDH18,missense_variant,p.Arg596Leu,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Arg596Leu,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Arg596Leu,ENST00000274170,;CDH18,missense_variant,p.Val561Leu,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Val560Leu,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Val427Leu,ENST00000515257,;CDH18,upstream_gene_variant,,ENST00000510297,; A ENST00000507958 Transcript missense_variant 2778/3542 1787/2373 596/790 R/L cGt/cTt rs781255308,COSM182511,COSM4421262,COSM5615523,COSM5615524 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 tolerated(0.41) 14/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,SMART_domains:SM00112 0,1,1,1,1 MODERATE 1 SNV 2 0,1,1,1,1 1 PASS rs781255308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 19483396 19483396 C A 1 0 0 0 0 1 0 0 0 2806 536 19 1 1 CDH18 5 19483396 Missense_Mutation SNP C C3L-00144_T 9798 19483396 162054863 506 4577 CDH18 0 . GRCh38 5 19483525 19483525 + Missense_Mutation SNP C C A rs775306740 C3L-00144_T C3L-00144_N C C c.1658G>T p.Arg553Leu p.R553L ENST00000507958 14/15 217 202 15 105 105 0 strelka-varscan-mutect CDH18,missense_variant,p.Arg553Leu,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Arg553Leu,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Arg553Leu,ENST00000274170,;CDH18,intron_variant,,ENST00000506372,NM_001291957.1;CDH18,intron_variant,,ENST00000502796,NM_001167667.1;CDH18,intron_variant,,ENST00000515257,;CDH18,upstream_gene_variant,,ENST00000510297,; A ENST00000507958 Transcript missense_variant 2649/3542 1658/2373 553/790 R/L cGg/cTg rs775306740 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0.02) 14/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS rs775306740 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 19483525 19483525 C A 1 0 0 0 0 1 0 0 0 2806 652 23 1 1 CDH18 5 19483525 Missense_Mutation SNP C C3L-00144_T 129 19483525 162054734 507 4578 CDH12 0 . GRCh38 5 21755833 21755833 + Missense_Mutation SNP G G T rs745634405 C3L-00144_T C3L-00144_N G G c.1643C>A p.Ala548Glu p.A548E ENST00000382254 14/15 272 194 78 111 111 0 strelka-varscan-mutect CDH12,missense_variant,p.Ala548Glu,ENST00000382254,NM_004061.3;CDH12,missense_variant,p.Ala548Glu,ENST00000504376,;CDH12,missense_variant,p.Ala508Glu,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript missense_variant 2730/4164 1643/2385 548/794 A/E gCg/gAg rs745634405 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 deleterious(0) 14/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs745634405 . 0 206 0 4 0 0 0 0 -20 0.9999767 1 1 1 0 T 3 4 12 21755833 21755833 G T 1 0 0 0 0 1 0 0 0 2801 1087 38 1 1 CDH12 5 21755833 Missense_Mutation SNP G C3L-00144_T 2272308 21755833 159782426 508 4579 CDH12 0 . GRCh38 5 21760600 21760600 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1591G>T p.Glu531Ter p.E531* ENST00000382254 13/15 497 464 33 225 225 0 strelka-varscan-mutect CDH12,stop_gained,p.Glu531Ter,ENST00000382254,NM_004061.3;CDH12,stop_gained,p.Glu531Ter,ENST00000504376,;CDH12,stop_gained,p.Glu491Ter,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; A ENST00000382254 Transcript stop_gained 2678/4164 1591/2385 531/794 E/* Gag/Tag 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 13/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 21760600 21760600 C A 1 0 0 0 0 0 1 0 0 2801 835 29 2 2 CDH12 5 21760600 Nonsense_Mutation SNP C C3L-00144_T 4767 21760600 159777659 509 4580 CDH10 0 . GRCh38 5 24537482 24537482 + Missense_Mutation SNP G G T rs779300580 C3L-00144_T C3L-00144_N G G c.424C>A p.Pro142Thr p.P142T ENST00000264463 3/12 466 326 140 211 211 0 strelka-varscan-mutect CDH10,missense_variant,p.Pro142Thr,ENST00000264463,NM_006727.3;CDH10,missense_variant,p.Pro142Thr,ENST00000510477,; T ENST00000264463 Transcript missense_variant 932/3438 424/2367 142/788 P/T Cca/Aca rs779300580,COSM1186749 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 deleterious(0) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779300580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 24537482 24537482 G T 1 0 0 0 0 1 0 0 0 2799 1203 42 2 2 CDH10 5 24537482 Missense_Mutation SNP G C3L-00144_T 2776882 24537482 157000777 510 4581 CDH9 0 . GRCh38 5 26885724 26885724 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1772G>T p.Cys591Phe p.C591F ENST00000231021 11/12 947 678 269 381 379 2 strelka-varscan-mutect CDH9,missense_variant,p.Cys591Phe,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505020,; A ENST00000231021 Transcript missense_variant 1945/3079 1772/2370 591/789 C/F tGc/tTc 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0) 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS rs1465472197 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 26885724 26885724 C A 1 0 0 0 0 1 0 0 0 2820 710 25 2 2 CDH9 5 26885724 Missense_Mutation SNP C C3L-00144_T 2348242 26885724 154652535 511 4582 CDH9 0 . GRCh38 5 26915773 26915773 + Missense_Mutation SNP C C A rs367589604 C3L-00144_T C3L-00144_N C C c.380G>T p.Arg127Leu p.R127L ENST00000231021 3/12 853 750 103 367 367 0 strelka-varscan-mutect CDH9,missense_variant,p.Arg127Leu,ENST00000231021,NM_016279.3;CDH9,missense_variant,p.Arg127Leu,ENST00000513289,;CDH9,downstream_gene_variant,,ENST00000511822,;CDH9,non_coding_transcript_exon_variant,,ENST00000505045,; A ENST00000231021 Transcript missense_variant 553/3079 380/2370 127/789 R/L cGt/cTt rs367589604 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 tolerated(0.07) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs367589604 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 26915773 26915773 C A 1 0 0 0 0 1 0 0 0 2820 536 19 1 1 CDH9 5 26915773 Missense_Mutation SNP C C3L-00144_T 30049 26915773 154622486 512 4583 NPR3 0 . GRCh38 5 32780785 32780785 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1259C>A p.Ala420Asp p.A420D ENST00000265074 5/8 316 179 137 165 165 0 strelka-varscan-mutect NPR3,missense_variant,p.Ala420Asp,ENST00000265074,NM_001204375.1;NPR3,missense_variant,p.Ala204Asp,ENST00000326958,NM_001204376.1;NPR3,missense_variant,p.Ala204Asp,ENST00000434067,;NPR3,missense_variant,p.Ala420Asp,ENST00000415167,NM_000908.3;NPR3,missense_variant,p.Ala197Asp,ENST00000509104,;NPR3,non_coding_transcript_exon_variant,,ENST00000506712,; A ENST00000265074 Transcript missense_variant 1602/7344 1259/1626 420/541 A/D gCc/gAc 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 tolerated(0.78) 5/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 32780785 32780785 C A 1 0 0 0 0 1 0 0 0 10652 739 26 2 2 NPR3 5 32780785 Missense_Mutation SNP C C3L-00144_T 5865012 32780785 148757474 513 4584 NPR3 0 . GRCh38 5 32786327 32786327 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1608C>A p.= p.S536S ENST00000265074 8/8 649 431 218 319 319 0 strelka-varscan-mutect NPR3,synonymous_variant,p.=,ENST00000265074,NM_001204375.1;NPR3,synonymous_variant,p.=,ENST00000326958,NM_001204376.1;NPR3,synonymous_variant,p.=,ENST00000434067,;NPR3,synonymous_variant,p.=,ENST00000415167,NM_000908.3;NPR3,downstream_gene_variant,,ENST00000509104,;NPR3,downstream_gene_variant,,ENST00000506712,; A ENST00000265074 Transcript synonymous_variant 1951/7344 1608/1626 536/541 S tcC/tcA 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 8/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 32786327 32786327 C A 1 0 0 0 0 0 0 0 1 10652 610 22 2 2 NPR3 5 32786327 Silent SNP C C3L-00144_T 5542 32786327 148751932 514 4585 ADAMTS12 0 . GRCh38 5 33549362 33549362 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4147G>T p.Gly1383Cys p.G1383C ENST00000504830 21/24 210 174 36 106 106 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Gly1383Cys,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Gly1298Cys,ENST00000352040,; A ENST00000504830 Transcript missense_variant 4483/8774 4147/4785 1383/1594 G/C Ggc/Tgc 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 21/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS rs1436110386 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 33549362 33549362 C A 1 0 0 0 0 1 0 0 0 301 623 22 2 2 ADAMTS12 5 33549362 Missense_Mutation SNP C C3L-00144_T 763035 33549362 147988897 515 4586 ADAMTS12 0 . GRCh38 5 33630833 33630833 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1969C>A p.Pro657Thr p.P657T ENST00000504830 13/24 549 508 41 258 256 2 strelka-varscan-mutect ADAMTS12,missense_variant,p.Pro657Thr,ENST00000504830,NM_030955.2;ADAMTS12,intron_variant,,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 2305/8774 1969/4785 657/1594 P/T Cct/Act 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 13/24 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 MODERATE 1 SNV 1 1 PASS rs924325130 . 0 207 0 3 0 0 0 0 -20 0.999973 1 1 1 0 T 3 4 12 33630833 33630833 G T 1 0 0 0 0 1 0 0 0 301 1232 43 2 2 ADAMTS12 5 33630833 Missense_Mutation SNP G C3L-00144_T 81471 33630833 147907426 516 4587 ADAMTS12 0 . GRCh38 5 33683945 33683945 + Missense_Mutation SNP C C T rs765900765 C3L-00144_T C3L-00144_N C C c.745G>A p.Glu249Lys p.E249K ENST00000504830 4/24 132 115 17 88 88 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Glu249Lys,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Glu249Lys,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 1081/8774 745/4785 249/1594 E/K Gag/Aag rs765900765,COSM592065 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 4/24 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,Superfamily_domains:SSF55486 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765900765 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 33683945 33683945 C T 1 0 0 0 0 1 0 0 0 301 864 30 3 3 ADAMTS12 5 33683945 Missense_Mutation SNP C C3L-00144_T 53112 33683945 147854314 517 4588 ADAMTS12 0 . GRCh38 5 33751453 33751453 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.585C>A p.Tyr195Ter p.Y195* ENST00000504830 3/24 713 672 41 296 296 0 strelka-varscan-mutect ADAMTS12,stop_gained,p.Tyr195Ter,ENST00000504830,NM_030955.2;ADAMTS12,stop_gained,p.Tyr195Ter,ENST00000352040,;ADAMTS12,stop_gained,p.Tyr195Ter,ENST00000515401,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript stop_gained 921/8774 585/4785 195/1594 Y/* taC/taA 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 3/24 Pfam_domain:PF01562,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 33751453 33751453 G T 1 0 0 0 0 0 1 0 0 301 1372 48 2 2 ADAMTS12 5 33751453 Nonsense_Mutation SNP G C3L-00144_T 67508 33751453 147786806 518 4589 RXFP3 0 . GRCh38 5 33937266 33937266 + Missense_Mutation SNP A A G C3L-00144_T C3L-00144_N A A c.526A>G p.Met176Val p.M176V ENST00000330120 1/1 299 171 128 151 151 0 strelka-varscan-mutect RXFP3,missense_variant,p.Met176Val,ENST00000330120,NM_016568.3; G ENST00000330120 Transcript missense_variant 881/1852 526/1410 176/469 M/V Atg/Gtg COSM1178089 1 1 RXFP3 HGNC HGNC:24883 protein_coding YES CCDS3900.1 ENSP00000328708 Q9NSD7 UPI0000046AEB NM_016568.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF70,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 33937266 33937266 A G 1 0 0 0 0 1 0 0 0 14022 217 8 5 5 RXFP3 5 33937266 Missense_Mutation SNP A C3L-00144_T 185813 33937266 147600993 519 4590 SPEF2 0 . GRCh38 5 35712865 35712865 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2893G>T p.Glu965Ter p.E965* ENST00000356031 20/37 403 328 75 174 173 1 strelka-varscan-mutect SPEF2,stop_gained,p.Glu965Ter,ENST00000637569,;SPEF2,stop_gained,p.Glu960Ter,ENST00000440995,;SPEF2,stop_gained,p.Glu965Ter,ENST00000356031,NM_024867.3;SPEF2,downstream_gene_variant,,ENST00000509059,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,downstream_gene_variant,,ENST00000503074,; T ENST00000356031 Transcript stop_gained 3047/5681 2893/5469 965/1822 E/* Gag/Tag 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 20/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 35712865 35712865 G T 1 0 0 0 0 0 1 0 0 15386 1291 45 2 2 SPEF2 5 35712865 Nonsense_Mutation SNP G C3L-00144_T 1775599 35712865 145825394 520 4591 SPEF2 0 . GRCh38 5 35792338 35792338 + Splice_Site SNP A A T novel C3L-00144_T C3L-00144_N A A c.4448-2A>T p.X1483_splice ENST00000356031 210 176 34 104 104 0 strelka-varscan-mutect SPEF2,splice_acceptor_variant,,ENST00000440995,;SPEF2,splice_acceptor_variant,,ENST00000356031,NM_024867.3;SPEF2,downstream_gene_variant,,ENST00000637569,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,downstream_gene_variant,,ENST00000635995,;SPEF2,splice_acceptor_variant,,ENST00000506526,;SPEF2,splice_acceptor_variant,,ENST00000513078,;SPEF2,splice_acceptor_variant,,ENST00000637061,; T ENST00000356031 Transcript splice_acceptor_variant -/5681 4448/5469 1483/1822 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 30/36 HIGH 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 35792338 35792338 A T 1 0 0 0 0 0 0 1 0 15386 434 15 4 4 SPEF2 5 35792338 Splice_Site SNP A C3L-00144_T 79473 35792338 145745921 521 4592 IL7R 0 . GRCh38 5 35867350 35867350 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.266A>T p.Gln89Leu p.Q89L ENST00000303115 3/8 470 294 176 237 237 0 strelka-varscan-mutect IL7R,missense_variant,p.Gln89Leu,ENST00000303115,NM_002185.3;IL7R,missense_variant,p.Gln89Leu,ENST00000506850,;IL7R,missense_variant,p.Gln89Leu,ENST00000511982,;IL7R,non_coding_transcript_exon_variant,,ENST00000511031,;IL7R,missense_variant,p.Gln89Leu,ENST00000514217,; T ENST00000303115 Transcript missense_variant 395/4626 266/1380 89/459 Q/L cAa/cTa 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 deleterious(0.01) 3/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35867350 35867350 A T 1 0 0 0 0 1 0 0 0 7609 130 5 4 4 IL7R 5 35867350 Missense_Mutation SNP A C3L-00144_T 75012 35867350 145670909 522 4593 NIPBL 0 . GRCh38 5 36975838 36975838 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.931C>T p.Pro311Ser p.P311S ENST00000282516 9/47 164 150 14 88 88 0 strelka-mutect NIPBL,missense_variant,p.Pro311Ser,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Pro311Ser,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,;NIPBL,non_coding_transcript_exon_variant,,ENST00000505998,; T ENST00000282516 Transcript missense_variant 1430/10435 931/8415 311/2804 P/S Cca/Tca 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated_low_confidence(0.06) 9/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 36975838 36975838 C T 1 0 0 0 0 1 0 0 0 10463 855 30 3 3 NIPBL 5 36975838 Missense_Mutation SNP C C3L-00144_T 1108488 36975838 144562421 523 4594 C5orf42 0 . GRCh38 5 37107618 37107618 + Nonsense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.9578G>A p.Trp3193Ter p.W3193* ENST00000425232 52/52 132 78 54 82 82 0 strelka-varscan-mutect C5orf42,stop_gained,p.Trp3193Ter,ENST00000425232,NM_023073.3;C5orf42,stop_gained,p.Trp3193Ter,ENST00000508244,;C5orf42,stop_gained,p.Trp2259Ter,ENST00000514429,;C5orf42,3_prime_UTR_variant,,ENST00000509849,; T ENST00000425232 Transcript stop_gained 9809/11199 9578/9594 3193/3197 W/* tGg/tAg COSM5334267,COSM5334268 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 52/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 37107618 37107618 C T 1 0 0 0 0 0 1 0 0 2100 595 21 3 3 C5orf42 5 37107618 Nonsense_Mutation SNP C C3L-00144_T 131780 37107618 144430641 524 4595 CARD6 0 . GRCh38 5 40852825 40852825 + Frame_Shift_Del DEL G G - rs756806898 C3L-00144_T C3L-00144_N G G c.1494delG p.Gln499LysfsTer9 p.Q499Kfs*9 ENST00000254691 3/3 308 254 54 150 150 0 sindel-varindel-pindel CARD6,frameshift_variant,p.Gln499LysfsTer9,ENST00000254691,NM_032587.3;CARD6,intron_variant,,ENST00000381677,; - ENST00000254691 Transcript frameshift_variant 1692/4221 1493/3114 498/1037 R/X cGg/cg rs756806898,COSM309854 1 1 CARD6 HGNC HGNC:16394 protein_coding YES CCDS3935.1 ENSP00000254691 Q9BX69 UPI000013CE50 NM_032587.3 3/3 hmmpanther:PTHR22797,hmmpanther:PTHR22797:SF36 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 40852825 40852825 G - 1 0 1 0 1 0 0 0 0 2346 1116 39 0 0 CARD6 5 40852825 Frame_Shift_Del DEL G C3L-00144_T 3745207 40852825 140685434 525 4596 C6 0 . GRCh38 5 41153838 41153838 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.2262C>G p.= p.P754P ENST00000263413 15/18 275 237 38 144 144 0 strelka-varscan-mutect C6,synonymous_variant,p.=,ENST00000263413,NM_001115131.2;C6,synonymous_variant,p.=,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000461473,;C6,downstream_gene_variant,,ENST00000511470,; C ENST00000263413 Transcript synonymous_variant 2527/3661 2262/2805 754/934 P ccC/ccG 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 15/18 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS rs1169273331 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 41153838 41153838 G C 1 0 0 0 0 0 0 0 1 2111 1335 47 4 4 C6 5 41153838 Silent SNP G C3L-00144_T 301013 41153838 140384421 526 4597 PARP8 0 . GRCh38 5 50833427 50833427 + Splice_Site SNP G G T rs78857756 C3L-00144_T C3L-00144_N G G c.1447+1G>T p.X483_splice ENST00000514342 81 61 20 99 99 0 strelka-varscan-mutect PARP8,splice_donor_variant,,ENST00000514342,;PARP8,intron_variant,,ENST00000281631,NM_024615.3;PARP8,intron_variant,,ENST00000505554,;PARP8,intron_variant,,ENST00000514067,NM_001178056.1;PARP8,intron_variant,,ENST00000505697,NM_001178055.1;PARP8,intron_variant,,ENST00000511363,;PARP8,intron_variant,,ENST00000503561,;PARP8,intron_variant,,ENST00000515166,; T ENST00000514342 Transcript splice_donor_variant -/2384 1447/1485 483/494 rs78857756 1 1 PARP8 HGNC HGNC:26124 protein_coding ENSP00000439022 F5H3X8 UPI0002065869 23/23 HIGH SNV 5 1 PASS rs78857756 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 50833427 50833427 G T 1 0 0 0 0 0 0 1 0 11545 1043 36 2 2 PARP8 5 50833427 Splice_Site SNP G C3L-00144_T 9679589 50833427 130704832 527 4598 HTR1A 0 . GRCh38 5 63961714 63961714 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.6T>A p.Asp2Glu p.D2E ENST00000323865 1/1 386 265 121 363 363 0 strelka-varscan-mutect HTR1A,missense_variant,p.Asp2Glu,ENST00000323865,NM_000524.3;HTR1A,missense_variant,p.Asp2Glu,ENST00000506598,;RP11-158J3.2,intron_variant,,ENST00000502882,; T ENST00000323865 Transcript missense_variant 420/1778 6/1269 2/422 D/E gaT/gaA 1 -1 HTR1A HGNC HGNC:5286 protein_coding YES CCDS34168.1 ENSP00000316244 P08908 Q5ZGX3 UPI0000124F1A NM_000524.3 tolerated_low_confidence(0.21) 1/1 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF20 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 63961714 63961714 A T 1 0 0 0 0 1 0 0 0 7332 214 8 4 4 HTR1A 5 63961714 Missense_Mutation SNP A C3L-00144_T 13128287 63961714 117576545 528 4599 ADAMTS6 0 . GRCh38 5 65197088 65197088 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2639A>T p.Tyr880Phe p.Y880F ENST00000381055 21/25 174 135 39 183 183 0 strelka-varscan-mutect ADAMTS6,missense_variant,p.Tyr880Phe,ENST00000381055,NM_197941.2;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000314351,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000417396,;ADAMTS6,3_prime_UTR_variant,,ENST00000381052,; A ENST00000381055 Transcript missense_variant 3496/7311 2639/3354 880/1117 Y/F tAc/tTc 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 tolerated(0.58) 21/25 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 65197088 65197088 T A 1 0 0 0 0 1 0 0 0 314 1638 57 4 4 ADAMTS6 5 65197088 Missense_Mutation SNP T C3L-00144_T 1235374 65197088 116341171 529 4600 TRIM23 0 . GRCh38 5 65596533 65596533 + Splice_Site SNP T T A novel C3L-00144_T C3L-00144_N T T c.1310-2A>T p.X437_splice ENST00000231524 114 105 9 116 116 0 strelka-varscan-mutect TRIM23,splice_acceptor_variant,,ENST00000231524,NM_001656.3;TRIM23,splice_acceptor_variant,,ENST00000381018,NM_033227.2;TRIM23,splice_acceptor_variant,,ENST00000274327,NM_033228.2; A ENST00000231524 Transcript splice_acceptor_variant -/4186 1310/1725 437/574 1 -1 TRIM23 HGNC HGNC:660 protein_coding YES CCDS3987.1 ENSP00000231524 P36406 UPI0000125DB3 NM_001656.3 8/10 HIGH 1 SNV 1 1 PASS . . 0 180 15 13 0 0 0 0 -12.68906 0.3646434 0 1 0 0 A 5 1 12 65596533 65596533 T A 1 0 0 0 0 0 0 1 0 16986 1594 55 4 4 TRIM23 5 65596533 Splice_Site SNP T C3L-00144_T 399445 65596533 115941726 530 4601 NLN 0 . GRCh38 5 65758656 65758656 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.131G>T p.Gly44Val p.G44V ENST00000380985 2/13 383 262 121 348 347 1 strelka-varscan-mutect NLN,missense_variant,p.Gly44Val,ENST00000380985,NM_020726.4;NLN,intron_variant,,ENST00000502464,;NLN,3_prime_UTR_variant,,ENST00000514991,;NLN,non_coding_transcript_exon_variant,,ENST00000506539,; T ENST00000380985 Transcript missense_variant 309/8661 131/2115 44/704 G/V gGc/gTc 1 1 NLN HGNC HGNC:16058 protein_coding YES CCDS3989.1 ENSP00000370372 Q9BYT8 UPI000003989D NM_020726.4 tolerated(0.09) 2/13 hmmpanther:PTHR11804,hmmpanther:PTHR11804:SF44,Gene3D:2o36A01,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 65758656 65758656 G T 1 0 0 0 0 1 0 0 0 10504 1203 42 2 2 NLN 5 65758656 Missense_Mutation SNP G C3L-00144_T 162123 65758656 115779603 531 4602 ENC1 0 . GRCh38 5 74636284 74636284 + Missense_Mutation SNP T T C C3L-00144_T C3L-00144_N T T c.202A>G p.Ser68Gly p.S68G ENST00000618628 3/4 197 126 71 158 158 0 strelka-varscan-mutect ENC1,missense_variant,p.Ser68Gly,ENST00000618628,NM_001256574.1;ENC1,missense_variant,p.Ser68Gly,ENST00000302351,NM_003633.3,NM_001256575.1;ENC1,missense_variant,p.Ser68Gly,ENST00000537006,;ENC1,5_prime_UTR_variant,,ENST00000510316,NM_001256576.1;HEXB,upstream_gene_variant,,ENST00000511181,NM_001292004.1;ENC1,downstream_gene_variant,,ENST00000508331,;ENC1,downstream_gene_variant,,ENST00000509127,;ENC1,upstream_gene_variant,,ENST00000509284,; C ENST00000618628 Transcript missense_variant 1470/5657 202/1770 68/589 S/G Agt/Ggt COSM4969529 1 -1 ENC1 HGNC HGNC:3345 protein_coding YES CCDS4021.1 ENSP00000479101 O14682 Q53XS2 UPI0000129EBB NM_001256574.1 deleterious(0) 3/4 PROSITE_profiles:PS50097,hmmpanther:PTHR24410:SF5,hmmpanther:PTHR24410,PIRSF_domain:PIRSF037037,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 74636284 74636284 T C 1 0 0 0 0 1 0 0 0 4955 1580 55 5 5 ENC1 5 74636284 Missense_Mutation SNP T C3L-00144_T 8877628 74636284 106901975 532 4603 ANKRD31 0 . GRCh38 5 75146119 75146119 + Frame_Shift_Del DEL T T - novel C3L-00144_T C3L-00144_N T T c.3292delA p.Arg1098GlyfsTer6 p.R1098Gfs*6 ENST00000274361 14/25 90 66 24 131 131 0 sindel-varindel ANKRD31,frameshift_variant,p.Arg1098GlyfsTer6,ENST00000506364,;ANKRD31,frameshift_variant,p.Arg1098GlyfsTer6,ENST00000274361,NM_001164443.1;ANKRD31,intron_variant,,ENST00000504022,; - ENST00000274361 Transcript frameshift_variant 3484/6036 3292/5622 1098/1873 R/X Agg/gg 1 -1 ANKRD31 HGNC HGNC:26853 protein_coding YES CCDS47233.1 ENSP00000274361 Q8N7Z5 UPI00001D7FAE NM_001164443.1 14/25 hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF14 HIGH 1 deletion 5 1 PASS . . 0 203 0 5 0 0 0 0 -20 0.9998367 1 1 1 0 - 7 5 12 75146119 75146119 T - 1 0 1 0 1 0 0 0 0 764 1608 56 0 0 ANKRD31 5 75146119 Frame_Shift_Del DEL T C3L-00144_T 509835 75146119 106392140 533 4604 SV2C 0 . GRCh38 5 76295839 76295839 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1399G>T p.Ala467Ser p.A467S ENST00000502798 9/13 147 92 55 132 132 0 strelka-varscan-mutect SV2C,missense_variant,p.Ala467Ser,ENST00000502798,NM_014979.3;SV2C,missense_variant,p.Ala467Ser,ENST00000322285,NM_001297716.1;RP11-466P24.6,intron_variant,,ENST00000502589,;SV2C,non_coding_transcript_exon_variant,,ENST00000506257,; T ENST00000502798 Transcript missense_variant 1841/11035 1399/2184 467/727 A/S Gca/Tca 1 1 SV2C HGNC HGNC:30670 protein_coding YES CCDS43331.1 ENSP00000423541 Q496J9 UPI000011DDBB NM_014979.3 tolerated(0.57) 9/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23511:SF6,hmmpanther:PTHR23511,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 76295839 76295839 G T 1 0 0 0 0 1 0 0 0 15803 1319 46 2 2 SV2C 5 76295839 Missense_Mutation SNP G C3L-00144_T 1149720 76295839 105242420 534 4605 VCAN 0 . GRCh38 5 83539323 83539323 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.6320G>T p.Arg2107Ile p.R2107I ENST00000265077 8/15 325 225 100 289 289 0 strelka-varscan-mutect VCAN,missense_variant,p.Arg2107Ile,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Arg1120Ile,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Arg1120Ile,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; T ENST00000265077 Transcript missense_variant 6885/12625 6320/10191 2107/3396 R/I aGa/aTa 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.15) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS rs1442972594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 83539323 83539323 G T 1 0 0 0 0 1 0 0 0 17683 942 33 2 2 VCAN 5 83539323 Missense_Mutation SNP G C3L-00144_T 7243484 83539323 97998936 535 4606 GPR150 0 . GRCh38 5 95620899 95620899 + Silent SNP C C A rs778183807 C3L-00144_T C3L-00144_N C C c.624C>A p.= p.A208A ENST00000380007 1/1 86 59 27 69 69 0 strelka-varscan-mutect GPR150,synonymous_variant,p.=,ENST00000380007,NM_199243.1; A ENST00000380007 Transcript synonymous_variant 822/2065 624/1305 208/434 A gcC/gcA rs778183807 1 1 GPR150 HGNC HGNC:23628 protein_coding YES CCDS4074.1 ENSP00000369344 Q8NGU9 G4XH61 UPI000003BCD0 NM_199243.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF650,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs778183807 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 95620899 95620899 C A 1 0 0 0 0 0 0 0 1 6542 610 22 2 2 GPR150 5 95620899 Silent SNP C C3L-00144_T 12081576 95620899 85917360 536 4607 LIX1 0 . GRCh38 5 97094954 97094954 + Silent SNP G G T rs373055209 C3L-00144_T C3L-00144_N G G c.643C>A p.= p.R215R ENST00000274382 6/6 362 250 112 329 328 1 strelka-varscan-mutect LIX1,synonymous_variant,p.=,ENST00000274382,NM_153234.4;CTD-2215E18.1,intron_variant,,ENST00000504578,; T ENST00000274382 Transcript synonymous_variant 939/4026 643/849 215/282 R Cgg/Agg rs373055209,COSM1071509 1 -1 LIX1 HGNC HGNC:18581 protein_coding YES CCDS4088.1 ENSP00000274382 Q8N485 UPI000007388A NM_153234.4 6/6 Pfam_domain:PF14954,hmmpanther:PTHR31139 0,1 LOW 1 SNV 1 0,1 1 PASS rs373055209 . 0 208 0 0 2 0 0 0 -20 0.9991644 1 1 1 0 T 2 4 12 97094954 97094954 G T 1 0 0 0 0 0 0 0 1 8754 1086 38 1 1 LIX1 5 97094954 Silent SNP G C3L-00144_T 1474055 97094954 84443305 537 4608 EFNA5 0 . GRCh38 5 107427216 107427216 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.418+1G>T p.X140_splice ENST00000333274 156 114 42 179 179 0 strelka-varscan-mutect EFNA5,splice_donor_variant,,ENST00000333274,NM_001962.2;EFNA5,splice_donor_variant,,ENST00000611503,;EFNA5,splice_donor_variant,,ENST00000509503,;EFNA5,downstream_gene_variant,,ENST00000505499,;EFNA5,non_coding_transcript_exon_variant,,ENST00000504941,; A ENST00000333274 Transcript splice_donor_variant -/5335 418/687 140/228 1 -1 EFNA5 HGNC HGNC:3225 protein_coding YES CCDS4097.1 ENSP00000328777 P52803 UPI0000129C93 NM_001962.2 2/4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 107427216 107427216 C A 1 0 0 0 0 0 0 1 0 4790 492 17 2 2 EFNA5 5 107427216 Splice_Site SNP C C3L-00144_T 10332262 107427216 74111043 538 4609 PJA2 0 . GRCh38 5 109378621 109378621 + Missense_Mutation SNP C C A rs866537162 C3L-00144_T C3L-00144_N C C c.866G>T p.Gly289Val p.G289V ENST00000361189 4/10 177 138 39 206 206 0 strelka-varscan-mutect PJA2,missense_variant,p.Gly289Val,ENST00000361189,NM_014819.4;PJA2,missense_variant,p.Gly289Val,ENST00000361557,;PJA2,downstream_gene_variant,,ENST00000511624,;PJA2,downstream_gene_variant,,ENST00000512822,; A ENST00000361189 Transcript missense_variant 1106/4889 866/2127 289/708 G/V gGt/gTt rs866537162 1 -1 PJA2 HGNC HGNC:17481 protein_coding YES CCDS4099.1 ENSP00000354775 O43164 UPI000013D192 NM_014819.4 tolerated(0.41) 4/10 hmmpanther:PTHR15710,hmmpanther:PTHR15710:SF5 MODERATE 1 SNV 1 1 PASS rs866537162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 109378621 109378621 C A 1 0 0 0 0 1 0 0 0 12058 507 18 2 2 PJA2 5 109378621 Missense_Mutation SNP C C3L-00144_T 1951405 109378621 72159638 539 4610 CAMK4 0 . GRCh38 5 111484148 111484148 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1104C>G p.Asp368Glu p.D368E ENST00000282356 11/11 94 72 22 82 82 0 strelka-varscan-mutect CAMK4,missense_variant,p.Asp368Glu,ENST00000282356,NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4;CAMK4,missense_variant,p.Asp368Glu,ENST00000512453,;CAMK4,non_coding_transcript_exon_variant,,ENST00000512890,;CAMK4,non_coding_transcript_exon_variant,,ENST00000510858,;CAMK4,3_prime_UTR_variant,,ENST00000515231,;CAMK4,non_coding_transcript_exon_variant,,ENST00000509645,;CAMK4,downstream_gene_variant,,ENST00000514007,; G ENST00000282356 Transcript missense_variant 1502/12240 1104/1422 368/473 D/E gaC/gaG 1 1 CAMK4 HGNC HGNC:1464 protein_coding YES CCDS4103.1 ENSP00000282356 Q16566 UPI000000128E NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4 tolerated(0.23) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 111484148 111484148 C G 1 0 0 0 0 1 0 0 0 2296 477 17 4 4 CAMK4 5 111484148 Missense_Mutation SNP C C3L-00144_T 2105527 111484148 70054111 540 4611 FEM1C 0 . GRCh38 5 115524599 115524599 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1563G>A p.= p.V521V ENST00000274457 3/3 86 71 15 88 88 0 strelka-varscan-mutect FEM1C,synonymous_variant,p.=,ENST00000274457,NM_020177.2; T ENST00000274457 Transcript synonymous_variant 2125/5816 1563/1854 521/617 V gtG/gtA 1 -1 FEM1C HGNC HGNC:16933 protein_coding YES CCDS4118.1 ENSP00000274457 Q96JP0 UPI0000046A79 NM_020177.2 3/3 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24173:SF14,hmmpanther:PTHR24173,Gene3D:1.25.40.20,Pfam_domain:PF13857,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 115524599 115524599 C T 1 0 0 0 0 0 0 0 1 5674 813 29 3 3 FEM1C 5 115524599 Silent SNP C C3L-00144_T 4040451 115524599 66013660 541 4612 SNCAIP 0 . GRCh38 5 122451576 122451576 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2870C>A p.Ser957Tyr p.S957Y ENST00000261367 12/14 169 121 48 187 187 0 strelka-varscan-mutect SNCAIP,missense_variant,p.Ser957Tyr,ENST00000261367,NM_001308100.1;SNCAIP,missense_variant,p.Ser910Tyr,ENST00000261368,NM_005460.2;SNCAIP,missense_variant,p.Ser850Tyr,ENST00000509154,;SNCAIP,missense_variant,p.Ser544Tyr,ENST00000379538,NM_001242935.1;SNCAIP,3_prime_UTR_variant,,ENST00000542191,;SNCAIP,3_prime_UTR_variant,,ENST00000504884,;SNCAIP,3_prime_UTR_variant,,ENST00000414317,;MGC32805,intron_variant,,ENST00000510972,;MGC32805,intron_variant,,ENST00000509993,;MGC32805,intron_variant,,ENST00000506053,;MGC32805,intron_variant,,ENST00000503529,;MGC32805,intron_variant,,ENST00000505546,;SNCAIP,3_prime_UTR_variant,,ENST00000395469,;SNCAIP,3_prime_UTR_variant,,ENST00000512385,;SNCAIP,3_prime_UTR_variant,,ENST00000508017,;SNCAIP,3_prime_UTR_variant,,ENST00000510658,;SNCAIP,3_prime_UTR_variant,,ENST00000509023,;SNCAIP,3_prime_UTR_variant,,ENST00000395466,;SNCAIP,3_prime_UTR_variant,,ENST00000512146,;SNCAIP,3_prime_UTR_variant,,ENST00000515215,;SNCAIP,non_coding_transcript_exon_variant,,ENST00000513719,; A ENST00000261367 Transcript missense_variant 4298/4986 2870/3051 957/1016 S/Y tCc/tAc 1 1 SNCAIP HGNC HGNC:11139 protein_coding YES CCDS78054.1 ENSP00000261367 Q9Y6H5 UPI000023272B NM_001308100.1 tolerated(0.27) 12/14 hmmpanther:PTHR22882 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 122451576 122451576 C A 1 0 0 0 0 1 0 0 0 15162 855 30 2 2 SNCAIP 5 122451576 Missense_Mutation SNP C C3L-00144_T 6926977 122451576 59086683 542 4613 PRDM6 0 . GRCh38 5 123090225 123090225 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.211C>A p.Pro71Thr p.P71T ENST00000407847 2/8 207 134 73 180 180 0 strelka-varscan-mutect PRDM6,missense_variant,p.Pro71Thr,ENST00000407847,NM_001136239.1;AC106786.1,non_coding_transcript_exon_variant,,ENST00000458103,;AC106786.1,upstream_gene_variant,,ENST00000442777,; A ENST00000407847 Transcript missense_variant 625/9267 211/1788 71/595 P/T Ccg/Acg 1 1 PRDM6 HGNC HGNC:9350 protein_coding YES CCDS47259.1 ENSP00000384725 Q9NQX0 UPI0001610E83 NM_001136239.1 tolerated_low_confidence(0.07) 2/8 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 123090225 123090225 C A 1 0 0 0 0 1 0 0 0 12592 623 22 2 2 PRDM6 5 123090225 Missense_Mutation SNP C C3L-00144_T 638649 123090225 58448034 543 4614 MEGF10 0 . GRCh38 5 127410504 127410504 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1033T>A p.Phe345Ile p.F345I ENST00000274473 10/26 482 336 146 406 406 0 strelka-varscan-mutect MEGF10,missense_variant,p.Phe345Ile,ENST00000274473,NM_032446.2;MEGF10,missense_variant,p.Phe345Ile,ENST00000503335,NM_001256545.1;MEGF10,missense_variant,p.Phe345Ile,ENST00000508365,NM_001308121.1;MEGF10,missense_variant,p.Phe345Ile,ENST00000418761,;MEGF10,non_coding_transcript_exon_variant,,ENST00000515002,; A ENST00000274473 Transcript missense_variant 1300/7594 1033/3423 345/1140 F/I Ttt/Att 1 1 MEGF10 HGNC HGNC:29634 protein_coding YES CCDS4142.1 ENSP00000274473 Q96KG7 UPI000006F868 NM_032446.2 deleterious(0) 10/26 Gene3D:2gy5A03,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,SMART_domains:SM00180,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 127410504 127410504 T A 1 0 0 0 0 1 0 0 0 9400 1609 56 4 4 MEGF10 5 127410504 Missense_Mutation SNP T C3L-00144_T 4320279 127410504 54127755 544 4615 SLC12A2 0 . GRCh38 5 128148761 128148761 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1889G>A p.Cys630Tyr p.C630Y ENST00000262461 12/27 128 88 40 112 112 0 strelka-varscan-mutect SLC12A2,missense_variant,p.Cys630Tyr,ENST00000262461,NM_001046.2;SLC12A2,missense_variant,p.Cys630Tyr,ENST00000343225,NM_001256461.1;SLC12A2,missense_variant,p.Cys630Tyr,ENST00000628403,;SLC12A2,missense_variant,p.Cys630Tyr,ENST00000509205,; A ENST00000262461 Transcript missense_variant 2078/6885 1889/3639 630/1212 C/Y tGt/tAt 1 1 SLC12A2 HGNC HGNC:10911 protein_coding YES CCDS4144.1 ENSP00000262461 P55011 Q53ZR1 UPI000013541A NM_001046.2 deleterious(0) 12/27 Pfam_domain:PF00324,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF58,TIGRFAM_domain:TIGR00930 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 128148761 128148761 G A 1 0 0 0 0 1 0 0 0 14648 1377 48 3 3 SLC12A2 5 128148761 Missense_Mutation SNP G C3L-00144_T 738257 128148761 53389498 545 4616 SLC27A6 0 . GRCh38 5 129029691 129029691 + Missense_Mutation SNP G G C rs1898548 C3L-00144_T C3L-00144_N G G c.1667G>C p.Arg556Pro p.R556P ENST00000262462 9/10 163 123 40 171 171 0 strelka-varscan-mutect SLC27A6,missense_variant,p.Arg556Pro,ENST00000262462,;SLC27A6,missense_variant,p.Arg556Pro,ENST00000395266,NM_014031.3,NM_001017372.1;SLC27A6,missense_variant,p.Arg556Pro,ENST00000506176,; C ENST00000262462 Transcript missense_variant 2677/3219 1667/1860 556/619 R/P cGa/cCa rs1898548 1 1 SLC27A6 HGNC HGNC:11000 protein_coding YES CCDS4145.1 ENSP00000262462 Q9Y2P4 UPI0000038E83 deleterious(0.01) 9/10 hmmpanther:PTHR24096:SF98,hmmpanther:PTHR24096,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS rs1898548 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 129029691 129029691 G C 1 0 0 0 0 1 0 0 0 14800 1058 37 4 4 SLC27A6 5 129029691 Missense_Mutation SNP G C3L-00144_T 880930 129029691 52508568 546 4617 ADAMTS19 0 . GRCh38 5 129509230 129509230 + Missense_Mutation SNP G G T rs767913138 C3L-00144_T C3L-00144_N G G c.883G>T p.Gly295Cys p.G295C ENST00000274487 3/23 111 74 37 123 123 0 strelka-varscan-mutect ADAMTS19,missense_variant,p.Gly295Cys,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,;ADAMTS19,missense_variant,p.Gly80Cys,ENST00000502709,;ADAMTS19,3_prime_UTR_variant,,ENST00000505791,; T ENST00000274487 Transcript missense_variant 1028/5234 883/3624 295/1207 G/C Ggt/Tgt rs767913138,COSM3136507,COSM5368242 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 deleterious(0) 3/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs767913138 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 129509230 129509230 G T 1 0 0 0 0 1 0 0 0 308 1348 47 2 2 ADAMTS19 5 129509230 Missense_Mutation SNP G C3L-00144_T 479539 129509230 52029029 547 4618 ADAMTS19 0 . GRCh38 5 129679893 129679893 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2618G>T p.Gly873Val p.G873V ENST00000274487 17/23 68 49 19 82 82 0 strelka-varscan-mutect ADAMTS19,missense_variant,p.Gly873Val,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,; T ENST00000274487 Transcript missense_variant 2763/5234 2618/3624 873/1207 G/V gGt/gTt 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 deleterious(0) 17/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 129679893 129679893 G T 1 0 0 0 0 1 0 0 0 308 1261 44 2 2 ADAMTS19 5 129679893 Missense_Mutation SNP G C3L-00144_T 170663 129679893 51858366 548 4619 RAPGEF6 0 . GRCh38 5 131464114 131464114 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2407G>T p.Glu803Ter p.E803* ENST00000296859 18/29 124 83 41 114 114 0 strelka-varscan-mutect RAPGEF6,stop_gained,p.Glu803Ter,ENST00000509018,NM_016340.5;CTC-432M15.3,stop_gained,p.Glu853Ter,ENST00000514667,;RAPGEF6,stop_gained,p.Glu808Ter,ENST00000507093,NM_001164387.1;RAPGEF6,stop_gained,p.Glu803Ter,ENST00000296859,NM_001164386.1;RAPGEF6,stop_gained,p.Glu803Ter,ENST00000627212,NM_001164388.1;RAPGEF6,stop_gained,p.Glu803Ter,ENST00000308008,NM_001164389.1;RAPGEF6,stop_gained,p.Glu518Ter,ENST00000512052,;RAPGEF6,stop_gained,p.Glu803Ter,ENST00000510071,NM_001164390.1;RAPGEF6,stop_gained,p.Glu803Ter,ENST00000515170,;RAPGEF6,non_coding_transcript_exon_variant,,ENST00000504919,; A ENST00000296859 Transcript stop_gained 2488/5618 2407/4830 803/1609 E/* Gag/Tag 1 -1 RAPGEF6 HGNC HGNC:20655 protein_coding YES CCDS54900.1 ENSP00000296859 Q8TEU7 UPI000189A836 NM_001164386.1 18/29 Pfam_domain:PF00788,PROSITE_profiles:PS50200,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF222,SMART_domains:SM00314 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 131464114 131464114 C A 1 0 0 0 0 0 1 0 0 13207 835 29 2 2 RAPGEF6 5 131464114 Nonsense_Mutation SNP C C3L-00144_T 1784221 131464114 50074145 549 4620 SLC22A5 0 . GRCh38 5 132370198 132370198 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.226G>T p.Glu76Ter p.E76* ENST00000435065 1/11 161 99 62 182 181 1 strelka-varscan-mutect SLC22A5,stop_gained,p.Glu76Ter,ENST00000245407,NM_003060.3;SLC22A5,stop_gained,p.Glu76Ter,ENST00000435065,NM_001308122.1;SLC22A5,upstream_gene_variant,,ENST00000415928,;MIR3936,upstream_gene_variant,,ENST00000584304,;AC034220.3,upstream_gene_variant,,ENST00000621103,;AC034220.3,upstream_gene_variant,,ENST00000457998,;SLC22A5,stop_gained,p.Glu76Ter,ENST00000437841,; T ENST00000435065 Transcript stop_gained 226/1746 226/1746 76/581 E/* Gag/Tag 1 1 SLC22A5 HGNC HGNC:10969 protein_coding YES CCDS78058.1 ENSP00000402760 O76082 UPI0000EFD9B4 NM_001308122.1 1/11 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF283 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 132370198 132370198 G T 1 0 0 0 0 0 1 0 0 14723 1059 37 1 1 SLC22A5 5 132370198 Nonsense_Mutation SNP G C3L-00144_T 906084 132370198 49168061 550 4621 SLC25A48 0 . GRCh38 5 135874097 135874097 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.594C>A p.Asn198Lys p.N198K ENST00000433282 6/7 75 57 18 82 82 0 strelka-varscan-mutect SLC25A48,missense_variant,p.Asn198Lys,ENST00000433282,;SLC25A48,intron_variant,,ENST00000425402,;SLC25A48,intron_variant,,ENST00000412661,NM_145282.4;SLC25A48,downstream_gene_variant,,ENST00000274513,;SLC25A48,downstream_gene_variant,,ENST00000462340,; A ENST00000433282 Transcript missense_variant 890/1111 594/774 198/257 N/K aaC/aaA 1 1 SLC25A48 HGNC HGNC:30451 protein_coding ENSP00000399834 J3KQI1 UPI0001D3B7D8 tolerated(0.77) 6/7 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF270,hmmpanther:PTHR24089,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588 MODERATE SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 12 135874097 135874097 C A 1 0 0 0 0 1 0 0 0 14778 477 17 2 2 SLC25A48 5 135874097 Missense_Mutation SNP C C3L-00144_T 3503899 135874097 45664162 551 4622 KLHL3 0 . GRCh38 5 137628382 137628382 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1506G>T p.Leu502Phe p.L502F ENST00000309755 13/15 303 217 86 252 252 0 strelka-varscan-mutect KLHL3,missense_variant,p.Leu470Phe,ENST00000508657,NM_001257194.1;KLHL3,missense_variant,p.Leu502Phe,ENST00000309755,NM_017415.2;KLHL3,missense_variant,p.Leu420Phe,ENST00000506491,NM_001257195.1;KLHL3,non_coding_transcript_exon_variant,,ENST00000506873,;KLHL3,3_prime_UTR_variant,,ENST00000504208,;KLHL3,non_coding_transcript_exon_variant,,ENST00000447439,;KLHL3,non_coding_transcript_exon_variant,,ENST00000509694,; A ENST00000309755 Transcript missense_variant 1950/6806 1506/1764 502/587 L/F ttG/ttT 1 -1 KLHL3 HGNC HGNC:6354 protein_coding YES CCDS4192.1 ENSP00000312397 Q9UH77 UPI000012DE05 NM_017415.2 tolerated(0.14) 13/15 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF179,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 137628382 137628382 C A 1 0 0 0 0 1 0 0 0 8248 593 21 2 2 KLHL3 5 137628382 Missense_Mutation SNP C C3L-00144_T 1754285 137628382 43909877 552 4623 KDM3B 0 . GRCh38 5 138391372 138391372 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1740G>T p.Lys580Asn p.K580N ENST00000314358 8/24 73 58 15 73 73 0 strelka-varscan-mutect KDM3B,missense_variant,p.Lys580Asn,ENST00000314358,NM_016604.3;KDM3B,intron_variant,,ENST00000542866,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,intron_variant,,ENST00000507996,; T ENST00000314358 Transcript missense_variant 1940/6813 1740/5286 580/1761 K/N aaG/aaT 1 1 KDM3B HGNC HGNC:1337 protein_coding YES CCDS34242.1 ENSP00000326563 Q7LBC6 UPI000020C6A8 NM_016604.3 tolerated_low_confidence(0.15) 8/24 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8 MODERATE 1 SNV 1 1 PASS rs1275402657 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 138391372 138391372 G T 1 0 0 0 0 1 0 0 0 8045 962 34 2 2 KDM3B 5 138391372 Missense_Mutation SNP G C3L-00144_T 762990 138391372 43146887 553 4624 KDM3B 0 . GRCh38 5 138431517 138431517 + Silent SNP G G A C3L-00144_T C3L-00144_N G G c.5163G>A p.= p.R1721R ENST00000314358 23/24 126 83 43 99 99 0 strelka-varscan-mutect KDM3B,synonymous_variant,p.=,ENST00000314358,NM_016604.3;KDM3B,synonymous_variant,p.=,ENST00000542866,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;KDM3B,downstream_gene_variant,,ENST00000509468,; A ENST00000314358 Transcript synonymous_variant 5363/6813 5163/5286 1721/1761 R agG/agA COSM4953478 1 1 KDM3B HGNC HGNC:1337 protein_coding YES CCDS34242.1 ENSP00000326563 Q7LBC6 UPI000020C6A8 NM_016604.3 23/24 PROSITE_profiles:PS51184,hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8,SMART_domains:SM00558,Superfamily_domains:SSF51197 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 138431517 138431517 G A 1 0 0 0 0 0 0 0 1 8045 1194 42 3 3 KDM3B 5 138431517 Silent SNP G C3L-00144_T 40145 138431517 43106742 554 4625 SLC35A4 0 . GRCh38 5 140567539 140567539 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.370G>A p.Gly124Arg p.G124R ENST00000514199 2/2 326 307 19 302 302 0 strelka-varscan-mutect SLC35A4,missense_variant,p.Gly124Arg,ENST00000514199,;SLC35A4,missense_variant,p.Gly124Arg,ENST00000323146,NM_080670.3;SLC35A4,missense_variant,p.Gly124Arg,ENST00000612662,;APBB3,upstream_gene_variant,,ENST00000357560,NM_133173.2;APBB3,upstream_gene_variant,,ENST00000358580,;APBB3,upstream_gene_variant,,ENST00000354402,NM_006051.3;APBB3,upstream_gene_variant,,ENST00000356738,NM_133172.2;APBB3,upstream_gene_variant,,ENST00000412920,NM_133174.2;APBB3,upstream_gene_variant,,ENST00000511201,;SLC35A4,downstream_gene_variant,,ENST00000623481,;APBB3,upstream_gene_variant,,ENST00000617240,;AC011380.9,intron_variant,,ENST00000507279,;AC011380.9,intron_variant,,ENST00000513766,;APBB3,upstream_gene_variant,,ENST00000505617,;AC011380.8,downstream_gene_variant,,ENST00000636851,;APBB3,upstream_gene_variant,,ENST00000510241,;APBB3,upstream_gene_variant,,ENST00000515056,;APBB3,upstream_gene_variant,,ENST00000511896,;APBB3,upstream_gene_variant,,ENST00000509914,;APBB3,upstream_gene_variant,,ENST00000467078,;APBB3,upstream_gene_variant,,ENST00000506958,;APBB3,upstream_gene_variant,,ENST00000506289,;APBB3,upstream_gene_variant,,ENST00000503979,;APBB3,upstream_gene_variant,,ENST00000513507,;APBB3,upstream_gene_variant,,ENST00000503850,;APBB3,upstream_gene_variant,,ENST00000506165,;APBB3,upstream_gene_variant,,ENST00000511459,;AC011380.8,downstream_gene_variant,,ENST00000638148,; A ENST00000514199 Transcript missense_variant 2056/3617 370/975 124/324 G/R Gga/Aga COSM448700 1 1 SLC35A4 HGNC HGNC:20753 protein_coding YES CCDS4231.1 ENSP00000424566 Q96G79 UPI0000036D2F deleterious(0.03) 2/2 hmmpanther:PTHR10231:SF25,hmmpanther:PTHR10231,PIRSF_domain:PIRSF005799,Pfam_domain:PF04142,Superfamily_domains:0043518 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 140567539 140567539 G A 1 0 0 0 0 1 0 0 0 14843 1349 47 3 3 SLC35A4 5 140567539 Missense_Mutation SNP G C3L-00144_T 2136022 140567539 40970720 555 4626 ZMAT2 0 . GRCh38 5 140702129 140702129 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.236G>T p.Gly79Val p.G79V ENST00000274712 3/6 99 61 38 98 97 1 strelka-varscan ZMAT2,missense_variant,p.Gly79Val,ENST00000274712,NM_144723.1;ZMAT2,missense_variant,p.Gly3Val,ENST00000519913,;HARS2,downstream_gene_variant,,ENST00000230771,NM_012208.3;HARS2,downstream_gene_variant,,ENST00000508522,NM_001278731.1;HARS2,downstream_gene_variant,,ENST00000448069,;ZMAT2,missense_variant,p.Gly78Val,ENST00000506644,; T ENST00000274712 Transcript missense_variant,splice_region_variant 363/1647 236/600 79/199 G/V gGa/gTa 1 1 ZMAT2 HGNC HGNC:26433 protein_coding YES CCDS4239.1 ENSP00000274712 Q96NC0 UPI0000029931 NM_144723.1 deleterious(0) 3/6 hmmpanther:PTHR23067,SMART_domains:SM00451,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 140702129 140702129 G T 1 0 0 0 0 1 0 0 0 18272 1246 43 2 2 ZMAT2 5 140702129 Missense_Mutation SNP G C3L-00144_T 134590 140702129 40836130 556 4627 PCDHA2 0 . GRCh38 5 140795065 140795065 + Frame_Shift_Del DEL C C - C3L-00144_T C3L-00144_N C C c.102delC p.Val35SerfsTer43 p.V35Sfs*43 ENST00000526136 1/4 321 231 90 425 425 0 sindel-varindel PCDHA2,frameshift_variant,p.Val35SerfsTer43,ENST00000526136,NM_018905.2;PCDHA2,frameshift_variant,p.Val35SerfsTer43,ENST00000520672,NM_031496.1;PCDHA2,frameshift_variant,p.Val35SerfsTer43,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; - ENST00000526136 Transcript frameshift_variant 101/5254 101/2847 34/948 S/X tCc/tc COSM5301598,COSM5301599 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 HIGH 1 deletion 1 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 140795065 140795065 C - 1 0 1 0 1 0 0 0 0 11611 855 30 0 0 PCDHA2 5 140795065 Frame_Shift_Del DEL C C3L-00144_T 92936 140795065 40743194 557 4628 PCDHA2 0 . GRCh38 5 140797083 140797083 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2119G>T p.Val707Leu p.V707L ENST00000526136 1/4 502 338 164 524 523 1 strelka-varscan-mutect PCDHA2,missense_variant,p.Val707Leu,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Val707Leu,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Val707Leu,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,upstream_gene_variant,,ENST00000522353,NM_018906.2;PCDHA3,upstream_gene_variant,,ENST00000532566,NM_031497.1;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; T ENST00000526136 Transcript missense_variant 2119/5254 2119/2847 707/948 V/L Gta/Tta COSM362370,COSM362371 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 deleterious_low_confidence(0.02) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 140797083 140797083 G T 1 0 0 0 0 1 0 0 0 11611 1261 44 2 2 PCDHA2 5 140797083 Missense_Mutation SNP G C3L-00144_T 2018 140797083 40741176 558 4629 PCDHA4 0 . GRCh38 5 140808477 140808477 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1290G>T p.= p.G430G ENST00000530339 1/4 505 349 156 496 494 2 strelka-varscan-mutect PCDHA4,synonymous_variant,p.=,ENST00000618834,NM_031500.2;PCDHA4,synonymous_variant,p.=,ENST00000530339,NM_018907.3;PCDHA4,synonymous_variant,p.=,ENST00000512229,;PCDHA4,synonymous_variant,p.=,ENST00000378125,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,downstream_gene_variant,,ENST00000532566,NM_031497.1;PCDHA2,downstream_gene_variant,,ENST00000520672,NM_031496.1;AC005609.16,intron_variant,,ENST00000624712,; T ENST00000530339 Transcript synonymous_variant 1290/5251 1290/2844 430/947 G ggG/ggT 1 1 PCDHA4 HGNC HGNC:8670 protein_coding YES CCDS54916.1 ENSP00000435300 Q9UN74 UPI00001273CC NM_018907.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 140808477 140808477 G T 1 0 0 0 0 0 0 0 1 11613 1219 43 2 2 PCDHA4 5 140808477 Silent SNP G C3L-00144_T 11394 140808477 40729782 559 4630 PCDHA5 0 . GRCh38 5 140823977 140823977 + Silent SNP C C A rs563481836 C3L-00144_T C3L-00144_N C C c.2202C>A p.= p.G734G ENST00000529859 1/4 194 137 57 200 200 0 strelka-varscan-mutect PCDHA5,synonymous_variant,p.=,ENST00000529859,NM_018908.2;PCDHA5,synonymous_variant,p.=,ENST00000614258,NM_031501.1;PCDHA5,synonymous_variant,p.=,ENST00000529619,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA4,intron_variant,,ENST00000512229,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA6,upstream_gene_variant,,ENST00000529310,NM_018909.3;PCDHA6,upstream_gene_variant,,ENST00000378126,NM_031848.2;PCDHA6,upstream_gene_variant,,ENST00000527624,NM_031849.2;AC005609.16,upstream_gene_variant,,ENST00000624712,; A ENST00000529859 Transcript synonymous_variant 2202/5218 2202/2811 734/936 G ggC/ggA rs563481836 1 1 PCDHA5 HGNC HGNC:8671 protein_coding YES CCDS54917.1 ENSP00000436557 Q9Y5H7 UPI00001273CD NM_018908.2 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111 LOW 1 SNV 1 1 PASS rs563481836 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 140823977 140823977 C A 1 0 0 0 0 0 0 0 1 11614 697 25 2 2 PCDHA5 5 140823977 Silent SNP C C3L-00144_T 15500 140823977 40714282 560 4631 PCDHB1 0 . GRCh38 5 141053567 141053567 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.2097C>T p.= p.S699S ENST00000306549 1/1 174 122 52 183 183 0 strelka-varscan-mutect PCDHB1,synonymous_variant,p.=,ENST00000306549,NM_013340.3;CTC-270D5.1,intron_variant,,ENST00000624139,;CTC-270D5.1,intron_variant,,ENST00000624778,;CTC-270D5.1,intron_variant,,ENST00000623741,;CTC-270D5.1,downstream_gene_variant,,ENST00000623109,; T ENST00000306549 Transcript synonymous_variant 2433/8210 2097/2457 699/818 S tcC/tcT 1 1 PCDHB1 HGNC HGNC:8680 protein_coding YES CCDS4243.1 ENSP00000307234 Q9Y5F3 UPI000013EB56 NM_013340.3 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF12,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 141053567 141053567 C T 1 0 0 0 0 0 0 0 1 11621 668 24 3 3 PCDHB1 5 141053567 Silent SNP C C3L-00144_T 229590 141053567 40484692 561 4632 PCDHB2 0 . GRCh38 5 141095509 141095509 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.719A>G p.Asn240Ser p.N240S ENST00000194155 1/1 141 122 19 135 135 0 strelka-varscan-mutect PCDHB2,missense_variant,p.Asn240Ser,ENST00000194155,NM_018936.3;PCDHB2,3_prime_UTR_variant,,ENST00000622947,;PCDHB2,3_prime_UTR_variant,,ENST00000624874,;PCDHB2,3_prime_UTR_variant,,ENST00000625033,;PCDHB3,upstream_gene_variant,,ENST00000231130,NM_018937.4;PCDHB2,upstream_gene_variant,,ENST00000624994,;CTC-270D5.1,intron_variant,,ENST00000623741,;AC005754.7,downstream_gene_variant,,ENST00000607216,;CTC-270D5.1,downstream_gene_variant,,ENST00000623615,;AC005754.7,downstream_gene_variant,,ENST00000625128,;AC005754.7,downstream_gene_variant,,ENST00000625066,; G ENST00000194155 Transcript missense_variant 932/4126 719/2397 240/798 N/S aAc/aGc 1 1 PCDHB2 HGNC HGNC:8687 protein_coding YES CCDS4244.1 ENSP00000194155 Q9Y5E7 UPI00001273DC NM_018936.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 141095509 141095509 A G 1 0 0 0 0 1 0 0 0 11629 43 2 5 5 PCDHB2 5 141095509 Missense_Mutation SNP A C3L-00144_T 41942 141095509 40442750 562 4633 PCDHB8 0 . GRCh38 5 141178232 141178232 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.198G>T p.Arg66Ser p.R66S ENST00000239444 1/1 51 31 20 64 64 0 strelka-varscan-mutect PCDHB8,missense_variant,p.Arg66Ser,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; T ENST00000239444 Transcript missense_variant 443/2740 198/2406 66/801 R/S agG/agT 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Pfam_domain:PF08266,SMART_domains:SM00112 MODERATE SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 141178232 141178232 G T 1 0 0 0 0 1 0 0 0 11635 1223 43 2 2 PCDHB8 5 141178232 Missense_Mutation SNP G C3L-00144_T 82723 141178232 40360027 563 4634 PCDHB14 0 . GRCh38 5 141224319 141224319 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.814G>T p.Gly272Ter p.G272* ENST00000239449 1/1 161 127 34 130 128 2 strelka-varscan-mutect PCDHB14,stop_gained,p.Gly272Ter,ENST00000239449,NM_018934.3;PCDHB14,stop_gained,p.Gly119Ter,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239449 Transcript stop_gained 1388/4828 814/2397 272/798 G/* Gga/Tga 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 141224319 141224319 G T 1 0 0 0 0 0 1 0 0 11626 1001 35 2 2 PCDHB14 5 141224319 Nonsense_Mutation SNP G C3L-00144_T 46087 141224319 40313940 564 4635 PCDHB14 0 . GRCh38 5 141225355 141225355 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1850T>A p.Val617Glu p.V617E ENST00000239449 1/1 296 239 57 283 283 0 strelka-varscan-mutect PCDHB14,missense_variant,p.Val617Glu,ENST00000239449,NM_018934.3;PCDHB14,missense_variant,p.Val464Glu,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239449 Transcript missense_variant 2424/4828 1850/2397 617/798 V/E gTg/gAg 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 141225355 141225355 T A 1 0 0 0 0 1 0 0 0 11626 1696 59 4 4 PCDHB14 5 141225355 Missense_Mutation SNP T C3L-00144_T 1036 141225355 40312904 565 4636 PCDHGB3 0 . GRCh38 5 141371281 141371281 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.887G>T p.Ser296Ile p.S296I ENST00000576222 1/4 229 161 68 190 190 0 strelka-varscan-mutect PCDHGB3,missense_variant,p.Ser296Ile,ENST00000576222,NM_018924.4;PCDHGB3,missense_variant,p.Ser296Ile,ENST00000618934,NM_032097.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,upstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGA6,upstream_gene_variant,,ENST00000517434,NM_018919.2;PCDHGA5,downstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000576222 Transcript missense_variant 1018/4727 887/2790 296/929 S/I aGt/aTt 1 1 PCDHGB3 HGNC HGNC:8710 protein_coding YES CCDS58980.1 ENSP00000461862 Q9Y5G1 UPI0000EE35B5 NM_018924.4 tolerated(0.06) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 141371281 141371281 G T 1 0 0 0 0 1 0 0 0 11651 1029 36 2 2 PCDHGB3 5 141371281 Missense_Mutation SNP G C3L-00144_T 145926 141371281 40166978 566 4637 PCDHGA6 0 . GRCh38 5 141376126 141376126 + Silent SNP C C A rs770848918 C3L-00144_T C3L-00144_N C C c.2043C>A p.= p.S681S ENST00000517434 1/4 266 181 85 292 292 0 strelka-varscan-mutect PCDHGA6,synonymous_variant,p.=,ENST00000610583,NM_032086.1;PCDHGA6,synonymous_variant,p.=,ENST00000517434,NM_018919.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000517434 Transcript synonymous_variant 2213/4775 2043/2799 681/932 S tcC/tcA rs770848918,COSM3975268,COSM3975269 1 1 PCDHGA6 HGNC HGNC:8704 protein_coding YES CCDS54926.1 ENSP00000429601 Q9Y5G7 UPI00000715C8 NM_018919.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF107,hmmpanther:PTHR24028 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs770848918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 141376126 141376126 C A 1 0 0 0 0 0 0 0 1 11645 639 23 1 1 PCDHGA6 5 141376126 Silent SNP C C3L-00144_T 4845 141376126 40162133 567 4638 PCDHGB5 0 . GRCh38 5 141399192 141399192 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1065C>T p.= p.N355N ENST00000617380 1/4 165 106 59 171 171 0 strelka-varscan-mutect PCDHGB5,synonymous_variant,p.=,ENST00000617380,NM_018925.2;PCDHGB5,synonymous_variant,p.=,ENST00000621169,NM_032099.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGA8,downstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA9,upstream_gene_variant,,ENST00000573521,NM_018921.2;PCDHGA9,upstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000617380 Transcript synonymous_variant 1065/4578 1065/2772 355/923 N aaC/aaT 1 1 PCDHGB5 HGNC HGNC:8712 protein_coding YES CCDS75339.1 ENSP00000478258 Q9Y5G0 UPI000007279C NM_018925.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF126,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 141399192 141399192 C T 1 0 0 0 0 0 0 0 1 11653 535 19 1 1 PCDHGB5 5 141399192 Silent SNP C C3L-00144_T 23066 141399192 40139067 568 4639 DIAPH1 0 . GRCh38 5 141578324 141578324 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.1064A>G p.Asn355Ser p.N355S ENST00000389054 11/28 407 380 27 364 364 0 strelka-varscan-mutect DIAPH1,missense_variant,p.Asn355Ser,ENST00000389054,NM_005219.4;DIAPH1,missense_variant,p.Asn311Ser,ENST00000253811,;DIAPH1,missense_variant,p.Asn355Ser,ENST00000398557,;DIAPH1,missense_variant,p.Asn346Ser,ENST00000389057,;DIAPH1,missense_variant,p.Asn346Ser,ENST00000518047,NM_001079812.2;DIAPH1,3_prime_UTR_variant,,ENST00000523100,;DIAPH1,non_coding_transcript_exon_variant,,ENST00000472516,; C ENST00000389054 Transcript missense_variant 1205/5795 1064/3819 355/1272 N/S aAt/aGt 1 -1 DIAPH1 HGNC HGNC:2876 protein_coding YES CCDS43374.1 ENSP00000373706 O60610 UPI0000EA87E6 NM_005219.4 deleterious(0.03) 11/28 Pfam_domain:PF06367,PROSITE_profiles:PS51232,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF17,SMART_domains:SM01139,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 141578324 141578324 T C 1 0 0 0 0 1 0 0 0 4322 1493 52 5 5 DIAPH1 5 141578324 Missense_Mutation SNP T C3L-00144_T 179132 141578324 39959935 569 4640 AFAP1L1 0 . GRCh38 5 149307595 149307595 + Silent SNP C C A rs144791179 C3L-00144_T C3L-00144_N C C c.729C>A p.= p.I243I ENST00000296721 7/19 194 134 60 160 159 1 strelka-varscan-mutect AFAP1L1,synonymous_variant,p.=,ENST00000296721,NM_152406.2;AFAP1L1,synonymous_variant,p.=,ENST00000515000,NM_001146337.1;AFAP1L1,non_coding_transcript_exon_variant,,ENST00000522492,;AFAP1L1,non_coding_transcript_exon_variant,,ENST00000455574,;AFAP1L1,downstream_gene_variant,,ENST00000508444,; A ENST00000296721 Transcript synonymous_variant 827/4177 729/2307 243/768 I atC/atA rs144791179 1 1 AFAP1L1 HGNC HGNC:26714 protein_coding YES CCDS34274.1 ENSP00000296721 Q8TED9 UPI00001C1E2F NM_152406.2 7/19 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF1,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS rs144791179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 149307595 149307595 C A 1 0 0 0 0 0 0 0 1 431 816 29 2 2 AFAP1L1 5 149307595 Silent SNP C C3L-00144_T 7729271 149307595 32230664 570 4641 SLC36A2 0 . GRCh38 5 151322051 151322051 + Missense_Mutation SNP A A T rs774837574 C3L-00144_T C3L-00144_N A A c.1175T>A p.Leu392Gln p.L392Q ENST00000335244 9/10 261 168 93 264 264 0 strelka-varscan-mutect SLC36A2,missense_variant,p.Leu392Gln,ENST00000335244,NM_181776.2;SLC36A2,missense_variant,p.Leu392Gln,ENST00000521967,;SLC36A2,downstream_gene_variant,,ENST00000523044,;SLC36A2,3_prime_UTR_variant,,ENST00000518617,;SLC36A2,3_prime_UTR_variant,,ENST00000518280,;CTC-224D3.1,downstream_gene_variant,,ENST00000604421,; T ENST00000335244 Transcript missense_variant 1305/3421 1175/1452 392/483 L/Q cTg/cAg rs774837574 1 -1 SLC36A2 HGNC HGNC:18762 protein_coding YES CCDS4315.1 ENSP00000334223 Q495M3 UPI000020D008 NM_181776.2 deleterious(0) 9/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF185,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs774837574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 151322051 151322051 A T 1 0 0 0 0 1 0 0 0 14872 202 7 4 4 SLC36A2 5 151322051 Missense_Mutation SNP A C3L-00144_T 2014456 151322051 30216208 571 4642 SAP30L 0 . GRCh38 5 154446720 154446720 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.116T>A p.Val39Asp p.V39D ENST00000297109 1/4 153 104 49 132 132 0 strelka-varscan-mutect SAP30L,missense_variant,p.Val39Asp,ENST00000297109,NM_024632.5;SAP30L,missense_variant,p.Val39Asp,ENST00000440364,NM_001131062.1;SAP30L,missense_variant,p.Val39Asp,ENST00000426761,NM_001131063.1;SAP30L-AS1,upstream_gene_variant,,ENST00000524264,;SAP30L-AS1,upstream_gene_variant,,ENST00000522312,;SAP30L-AS1,upstream_gene_variant,,ENST00000501280,;SAP30L-AS1,upstream_gene_variant,,ENST00000519727,;SAP30L,non_coding_transcript_exon_variant,,ENST00000523198,;SAP30L,non_coding_transcript_exon_variant,,ENST00000520159,;SAP30L,non_coding_transcript_exon_variant,,ENST00000519683,; A ENST00000297109 Transcript missense_variant 764/6226 116/552 39/183 V/D gTc/gAc 1 1 SAP30L HGNC HGNC:25663 protein_coding YES CCDS4326.1 ENSP00000297109 Q9HAJ7 UPI000007275D NM_024632.5 tolerated(0.62) 1/4 hmmpanther:PTHR13286,hmmpanther:PTHR13286:SF5,Pfam_domain:PF13866 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 154446720 154446720 T A 1 0 0 0 0 1 0 0 0 14096 1667 58 4 4 SAP30L 5 154446720 Missense_Mutation SNP T C3L-00144_T 3124669 154446720 27091539 572 4643 SOX30 0 . GRCh38 5 157638268 157638268 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1842C>T p.= p.H614H ENST00000265007 4/5 24 14 10 26 26 0 strelka-varscan-mutect SOX30,synonymous_variant,p.=,ENST00000265007,NM_178424.1;SOX30,synonymous_variant,p.=,ENST00000519442,NM_001308165.1;SOX30,intron_variant,,ENST00000311371,NM_007017.2; A ENST00000265007 Transcript synonymous_variant 2184/3265 1842/2262 614/753 H caC/caT 1 -1 SOX30 HGNC HGNC:30635 protein_coding YES CCDS4339.1 ENSP00000265007 O94993 UPI00001362BA NM_178424.1 4/5 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF10 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 157638268 157638268 G A 1 0 0 0 0 0 0 0 1 15278 1252 44 3 3 SOX30 5 157638268 Silent SNP G C3L-00144_T 3191548 157638268 23899991 573 4644 GABRA1 0 . GRCh38 5 161854234 161854234 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.151G>T p.Asp51Tyr p.D51Y ENST00000393943 3/10 319 233 86 252 252 0 strelka-varscan-mutect GABRA1,missense_variant,p.Asp51Tyr,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Asp51Tyr,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Asp66Tyr,ENST00000638159,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Asp51Tyr,ENST00000638112,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000636573,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Asp51Tyr,ENST00000637827,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000635880,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000634335,;GABRA1,missense_variant,p.Asp72Tyr,ENST00000522651,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000519621,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000521339,;GABRA1,downstream_gene_variant,,ENST00000635096,;GABRA1,downstream_gene_variant,,ENST00000637620,;GABRA1,stop_lost,p.Ter71TyrextTer7,ENST00000636340,;GABRA1,missense_variant,p.Asp51Tyr,ENST00000637044,; T ENST00000393943 Transcript missense_variant 934/4686 151/1371 51/456 D/Y Gat/Tat 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 deleterious(0) 3/10 Superfamily_domains:0038932,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 161854234 161854234 G T 1 0 0 0 0 1 0 0 0 6031 942 33 2 2 GABRA1 5 161854234 Missense_Mutation SNP G C3L-00144_T 4215966 161854234 19684025 574 4645 TENM2 0 . GRCh38 5 167284911 167284911 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.74C>A p.Ser25Tyr p.S25Y ENST00000518659 1/29 396 287 109 401 399 2 strelka-varscan-mutect TENM2,missense_variant,p.Ser25Tyr,ENST00000518659,NM_001122679.1;CTB-180C19.1,downstream_gene_variant,,ENST00000521697,; A ENST00000518659 Transcript missense_variant 113/8550 74/8325 25/2774 S/Y tCc/tAc 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious_low_confidence(0) 1/29 PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Pfam_domain:PF06484 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 167284911 167284911 C A 1 0 0 0 0 1 0 0 0 16172 855 30 2 2 TENM2 5 167284911 Missense_Mutation SNP C C3L-00144_T 5430677 167284911 14253348 575 4646 SH3PXD2B 0 . GRCh38 5 172382083 172382083 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.354G>T p.= p.V118V ENST00000311601 5/13 105 79 26 101 101 0 strelka-varscan-mutect SH3PXD2B,synonymous_variant,p.=,ENST00000311601,NM_001017995.2;SH3PXD2B,synonymous_variant,p.=,ENST00000636523,;SH3PXD2B,synonymous_variant,p.=,ENST00000519643,NM_001308175.1; A ENST00000311601 Transcript synonymous_variant 525/7777 354/2736 118/911 V gtG/gtT 1 -1 SH3PXD2B HGNC HGNC:29242 protein_coding YES CCDS34291.1 ENSP00000309714 A1X283 UPI000020C12E NM_001017995.2 5/13 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF8,SMART_domains:SM00312,Superfamily_domains:SSF64268 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 172382083 172382083 C A 1 0 0 0 0 0 0 0 1 14516 697 25 2 2 SH3PXD2B 5 172382083 Silent SNP C C3L-00144_T 5097172 172382083 9156176 576 4647 MSX2 0 . GRCh38 5 174729219 174729219 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.440C>A p.Thr147Lys p.T147K ENST00000239243 2/2 220 155 65 152 152 0 strelka-varscan-mutect MSX2,missense_variant,p.Thr147Lys,ENST00000239243,NM_002449.4;MSX2,3_prime_UTR_variant,,ENST00000507785,; A ENST00000239243 Transcript missense_variant 567/2241 440/804 147/267 T/K aCg/aAg 1 1 MSX2 HGNC HGNC:7392 protein_coding YES CCDS4392.1 ENSP00000239243 P35548 UPI000013CA79 NM_002449.4 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24338:SF10,hmmpanther:PTHR24338,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1484486574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 174729219 174729219 C A 1 0 0 0 0 1 0 0 0 9880 536 19 1 1 MSX2 5 174729219 Missense_Mutation SNP C C3L-00144_T 2347136 174729219 6809040 577 4648 ARL10 0 . GRCh38 5 176368859 176368859 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.438G>T p.= p.V146V ENST00000310389 3/4 154 135 19 108 108 0 strelka-varscan-mutect ARL10,synonymous_variant,p.=,ENST00000310389,NM_173664.4;ARL10,synonymous_variant,p.=,ENST00000514533,;ARL10,upstream_gene_variant,,ENST00000503175,;MIR1271,downstream_gene_variant,,ENST00000408537,;ARL10,non_coding_transcript_exon_variant,,ENST00000507151,; T ENST00000310389 Transcript synonymous_variant 534/10845 438/735 146/244 V gtG/gtT 1 1 ARL10 HGNC HGNC:22042 protein_coding YES CCDS4400.1 ENSP00000308496 Q8N8L6 UPI000006FEF9 NM_173664.4 3/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF158,Gene3D:3.40.50.300,Pfam_domain:PF00025,SMART_domains:SM00178,SMART_domains:SM00177,Superfamily_domains:SSF52540,Prints_domain:PR00328 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 176368859 176368859 G T 1 0 0 0 0 0 0 0 1 1063 1335 47 2 2 ARL10 5 176368859 Silent SNP G C3L-00144_T 1639640 176368859 5169400 578 4649 NSD1 0 . GRCh38 5 177135809 177135809 + Nonsense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.706C>T p.Gln236Ter p.Q236* ENST00000439151 2/23 67 60 7 56 56 0 strelka-varscan-mutect NSD1,stop_gained,p.Gln236Ter,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000511258,;NSD1,intron_variant,,ENST00000508896,;NSD1,intron_variant,,ENST00000510954,;NSD1,non_coding_transcript_exon_variant,,ENST00000602285,;NSD1,downstream_gene_variant,,ENST00000512992,; T ENST00000439151 Transcript stop_gained 751/12892 706/8091 236/2696 Q/* Cag/Tag 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 2/23 HIGH 1 SNV 1 1 PASS . . 0 181 25 4 0 0 0 0 -12.10355 0.8468205 0 1 1 0 T 4 4 12 177135809 177135809 C T 1 0 0 0 0 0 1 0 0 10728 479 17 3 3 NSD1 5 177135809 Nonsense_Mutation SNP C C3L-00144_T 766950 177135809 4402450 579 4650 DBN1 0 . GRCh38 5 177458064 177458064 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1776G>T p.= p.G592G ENST00000292385 13/15 401 291 110 342 341 1 strelka-varscan-mutect DBN1,synonymous_variant,p.=,ENST00000292385,NM_080881.2;DBN1,synonymous_variant,p.=,ENST00000309007,NM_004395.3;DBN1,synonymous_variant,p.=,ENST00000393565,;DBN1,synonymous_variant,p.=,ENST00000512501,;PRR7,downstream_gene_variant,,ENST00000323249,NM_030567.4;PRR7,downstream_gene_variant,,ENST00000502922,NM_001174101.1;PRR7,downstream_gene_variant,,ENST00000510492,NM_001174102.1;DBN1,downstream_gene_variant,,ENST00000477391,;PRR7,downstream_gene_variant,,ENST00000507881,;DBN1,non_coding_transcript_exon_variant,,ENST00000472831,;DBN1,downstream_gene_variant,,ENST00000467054,; A ENST00000292385 Transcript synonymous_variant 2386/3072 1776/1956 592/651 G ggG/ggT 1 -1 DBN1 HGNC HGNC:2695 protein_coding YES CCDS4421.1 ENSP00000292385 Q16643 UPI0000457395 NM_080881.2 13/15 hmmpanther:PTHR10829,hmmpanther:PTHR10829:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 177458064 177458064 C A 1 0 0 0 0 0 0 0 1 4052 842 30 2 2 DBN1 5 177458064 Silent SNP C C3L-00144_T 322255 177458064 4080195 580 4651 N4BP3 0 . GRCh38 5 178120505 178120505 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.658G>A p.Gly220Ser p.G220S ENST00000274605 3/5 355 264 91 274 274 0 strelka-varscan-mutect N4BP3,missense_variant,p.Gly220Ser,ENST00000274605,NM_015111.1; A ENST00000274605 Transcript missense_variant 1017/6080 658/1635 220/544 G/S Ggc/Agc 1 1 N4BP3 HGNC HGNC:29852 protein_coding YES CCDS34307.1 ENSP00000274605 O15049 UPI00001C1E2A NM_015111.1 tolerated(0.17) 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR32274 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 178120505 178120505 G A 1 0 0 0 0 1 0 0 0 10117 1232 43 3 3 N4BP3 5 178120505 Missense_Mutation SNP G C3L-00144_T 662441 178120505 3417754 581 4652 HNRNPAB 0 . GRCh38 5 178210591 178210591 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.967G>A p.Gly323Ser p.G323S ENST00000358344 8/8 325 298 27 230 230 0 strelka-varscan-mutect HNRNPAB,missense_variant,p.Gly323Ser,ENST00000358344,NM_031266.2;HNRNPAB,missense_variant,p.Gly323Ser,ENST00000504898,;HNRNPAB,missense_variant,p.Gly318Ser,ENST00000506339,;HNRNPAB,missense_variant,p.Gly276Ser,ENST00000506259,;HNRNPAB,missense_variant,p.Gly276Ser,ENST00000355836,NM_004499.3;HNRNPAB,missense_variant,p.Gly271Ser,ENST00000515193,;HNRNPAB,missense_variant,p.Gly274Ser,ENST00000514633,;PHYKPL,intron_variant,,ENST00000308158,NM_153373.3,NM_001278346.1;PHYKPL,intron_variant,,ENST00000481811,;PHYKPL,intron_variant,,ENST00000489262,;PHYKPL,intron_variant,,ENST00000494126,;PHYKPL,intron_variant,,ENST00000481436,;PHYKPL,intron_variant,,ENST00000493197,;PHYKPL,intron_variant,,ENST00000474052,;PHYKPL,intron_variant,,ENST00000393488,;PHYKPL,intron_variant,,ENST00000510991,;PHYKPL,downstream_gene_variant,,ENST00000476487,;PHYKPL,downstream_gene_variant,,ENST00000506045,;HNRNPAB,downstream_gene_variant,,ENST00000504796,; A ENST00000358344 Transcript missense_variant 1224/1796 967/999 323/332 G/S Ggt/Agt 1 1 HNRNPAB HGNC HGNC:5034 protein_coding YES CCDS34309.1 ENSP00000351108 Q99729 UPI0000070026 NM_031266.2 deleterious(0) 8/8 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF461 MODERATE 1 SNV 1 1 PASS . . 0 206 0 0 0 0 0 4 -10.04068 0 0 1 0 0 A 3 1 12 178210591 178210591 G A 1 0 0 0 0 1 0 0 0 7152 1348 47 3 3 HNRNPAB 5 178210591 Missense_Mutation SNP G C3L-00144_T 90086 178210591 3327668 582 4653 MGAT4B 0 . GRCh38 5 179798211 179798211 + Missense_Mutation SNP C C A rs374415178 C3L-00144_T C3L-00144_N C C c.1622G>T p.Arg541Leu p.R541L ENST00000337755 13/14 95 84 11 83 83 0 strelka-varscan-mutect MGAT4B,missense_variant,p.Arg541Leu,ENST00000337755,NM_054013.3;MGAT4B,missense_variant,p.Arg526Leu,ENST00000292591,NM_014275.4;MGAT4B,missense_variant,p.Arg351Leu,ENST00000518778,;MGAT4B,missense_variant,p.Arg218Leu,ENST00000520969,;MGAT4B,missense_variant,p.Arg307Leu,ENST00000520875,;MGAT4B,synonymous_variant,p.=,ENST00000519836,;MGAT4B,synonymous_variant,p.=,ENST00000518980,;MGAT4B,downstream_gene_variant,,ENST00000523108,;MGAT4B,downstream_gene_variant,,ENST00000518867,;LTC4S,downstream_gene_variant,,ENST00000292596,NM_145867.1;LTC4S,downstream_gene_variant,,ENST00000401985,;MIR1229,downstream_gene_variant,,ENST00000408467,;MGAT4B,non_coding_transcript_exon_variant,,ENST00000523382,;MGAT4B,non_coding_transcript_exon_variant,,ENST00000522293,;MAML1,downstream_gene_variant,,ENST00000503050,;MGAT4B,downstream_gene_variant,,ENST00000521305,;MGAT4B,downstream_gene_variant,,ENST00000520019,;MGAT4B,downstream_gene_variant,,ENST00000520134,;MGAT4B,downstream_gene_variant,,ENST00000519965,;MGAT4B,downstream_gene_variant,,ENST00000519616,;MGAT4B,non_coding_transcript_exon_variant,,ENST00000522451,;MGAT4B,downstream_gene_variant,,ENST00000518168,;LTC4S,downstream_gene_variant,,ENST00000465572,;MGAT4B,downstream_gene_variant,,ENST00000520918,;MGAT4B,downstream_gene_variant,,ENST00000520822,;MGAT4B,downstream_gene_variant,,ENST00000521855,;LTC4S,downstream_gene_variant,,ENST00000505170,;LTC4S,downstream_gene_variant,,ENST00000466071,;MGAT4B,downstream_gene_variant,,ENST00000523329,;MGAT4B,downstream_gene_variant,,ENST00000518702,;LTC4S,downstream_gene_variant,,ENST00000509898,;LTC4S,downstream_gene_variant,,ENST00000486713,;LTC4S,downstream_gene_variant,,ENST00000510544,; A ENST00000337755 Transcript missense_variant 2509/3027 1622/1692 541/563 R/L cGc/cTc rs374415178 1 -1 MGAT4B HGNC HGNC:7048 protein_coding YES CCDS4449.1 ENSP00000338487 Q9UQ53 UPI000015F50B NM_054013.3 deleterious(0) 13/14 hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF1 MODERATE SNV 2 1 PASS rs374415178 . 0 193 15 2 0 0 0 0 -17.59944 0.9932105 1 1 1 0 A 3 1 12 179798211 179798211 C A 1 0 0 0 0 1 0 0 0 9506 768 27 1 1 MGAT4B 5 179798211 Missense_Mutation SNP C C3L-00144_T 1587620 179798211 1740048 583 4654 RREB1 0 . GRCh38 6 7230614 7230614 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2515G>T p.Ala839Ser p.A839S ENST00000379938 10/13 113 107 6 97 97 0 strelka-varscan-mutect RREB1,missense_variant,p.Ala839Ser,ENST00000379938,NM_001003699.3;RREB1,missense_variant,p.Ala839Ser,ENST00000349384,NM_001003698.3;RREB1,missense_variant,p.Ala839Ser,ENST00000379933,NM_001168344.1;RREB1,missense_variant,p.Ala839Ser,ENST00000334984,NM_001003700.1;RREB1,upstream_gene_variant,,ENST00000611109,;RREB1,downstream_gene_variant,,ENST00000483150,; T ENST00000379938 Transcript missense_variant 3052/8778 2515/5229 839/1742 A/S Gct/Tct 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 tolerated(0.54) 10/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1036649369 . 0 205 3 2 0 0 0 0 -9.188752 0.9999441 1 1 1 0 T 3 4 12 7230614 7230614 G T 1 0 0 0 0 1 0 0 0 13933 1087 38 1 1 RREB1 6 7230614 Missense_Mutation SNP G C3L-00144_T 7230614 163575365 584 4655 DSP 0 . GRCh38 6 7576351 7576351 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2688G>T p.Gln896His p.Q896H ENST00000379802 19/24 336 215 121 235 235 0 strelka-varscan-mutect DSP,missense_variant,p.Gln896His,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Gln896His,ENST00000418664,NM_001008844.1; T ENST00000379802 Transcript missense_variant 3029/9796 2688/8616 896/2871 Q/H caG/caT 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 tolerated(0.1) 19/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs1195740147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7576351 7576351 G T 1 0 0 0 0 1 0 0 0 4602 991 35 2 2 DSP 6 7576351 Missense_Mutation SNP G C3L-00144_T 345737 7576351 163229628 585 4656 DSP 0 . GRCh38 6 7585079 7585079 + Missense_Mutation SNP G G T rs199597935 C3L-00144_T C3L-00144_N G G c.7817G>T p.Ser2606Ile p.S2606I ENST00000379802 24/24 422 267 155 302 302 0 strelka-varscan-mutect DSP,missense_variant,p.Ser2606Ile,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Ser2007Ile,ENST00000418664,NM_001008844.1; T ENST00000379802 Transcript missense_variant 8158/9796 7817/8616 2606/2871 S/I aGc/aTc rs199597935 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 deleterious(0.03) 24/24 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs199597935 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7585079 7585079 G T 1 0 0 0 0 1 0 0 0 4602 971 34 2 2 DSP 6 7585079 Missense_Mutation SNP G C3L-00144_T 8728 7585079 163220900 586 4657 DSP 0 . GRCh38 6 7585816 7585816 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.8554G>T p.Ala2852Ser p.A2852S ENST00000379802 24/24 141 86 55 81 81 0 strelka-varscan-mutect DSP,missense_variant,p.Ala2852Ser,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Ala2253Ser,ENST00000418664,NM_001008844.1;SNRNP48,upstream_gene_variant,,ENST00000342415,NM_152551.3;SNRNP48,upstream_gene_variant,,ENST00000634363,; T ENST00000379802 Transcript missense_variant 8895/9796 8554/8616 2852/2871 A/S Gcc/Tcc COSM362806 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 deleterious_low_confidence(0.02) 24/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999938 1 1 1 0 T 3 4 12 7585816 7585816 G T 1 0 0 0 0 1 0 0 0 4602 1087 38 1 1 DSP 6 7585816 Missense_Mutation SNP G C3L-00144_T 737 7585816 163220163 587 4658 NEDD9 0 . GRCh38 6 11213684 11213684 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.56C>T p.Ala19Val p.A19V ENST00000379446 2/7 145 135 10 106 106 0 strelka-varscan-mutect NEDD9,missense_variant,p.Ala19Val,ENST00000379446,NM_006403.3;NEDD9,missense_variant,p.Ala19Val,ENST00000379433,NM_182966.3;NEDD9,missense_variant,p.Ala19Val,ENST00000504387,NM_001142393.1;NEDD9,missense_variant,p.Ala13Val,ENST00000513989,;NEDD9,missense_variant,p.Ala19Val,ENST00000397378,;NEDD9,intron_variant,,ENST00000620854,NM_001271033.1;NEDD9,downstream_gene_variant,,ENST00000508546,;RP3-510L9.1,intron_variant,,ENST00000500636,;NEDD9,3_prime_UTR_variant,,ENST00000448183,; A ENST00000379446 Transcript missense_variant 223/4536 56/2505 19/834 A/V gCc/gTc 1 -1 NEDD9 HGNC HGNC:7733 protein_coding YES CCDS4520.1 ENSP00000368759 Q14511 UPI000000D981 NM_006403.3 deleterious(0) 2/7 Gene3D:2.30.30.40,Pfam_domain:PF14604,PROSITE_profiles:PS50002,hmmpanther:PTHR10654,hmmpanther:PTHR10654:SF20,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 11213684 11213684 G A 1 0 0 0 0 1 0 0 0 10341 1203 42 3 3 NEDD9 6 11213684 Missense_Mutation SNP G C3L-00144_T 3627868 11213684 159592295 588 4659 MBOAT1 0 . GRCh38 6 20152757 20152757 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.112G>T p.Val38Leu p.V38L ENST00000324607 2/13 173 154 19 124 124 0 strelka-varscan-mutect MBOAT1,missense_variant,p.Val38Leu,ENST00000324607,NM_001080480.2; A ENST00000324607 Transcript missense_variant 277/1794 112/1488 38/495 V/L Gta/Tta 1 -1 MBOAT1 HGNC HGNC:21579 protein_coding YES CCDS34346.1 ENSP00000324944 Q6ZNC8 UPI000020D5D0 NM_001080480.2 tolerated(0.19) 2/13 hmmpanther:PTHR13906,hmmpanther:PTHR13906:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 20152757 20152757 C A 1 0 0 0 0 1 0 0 0 9288 507 18 2 2 MBOAT1 6 20152757 Missense_Mutation SNP C C3L-00144_T 8939073 20152757 150653222 589 4660 PRL 0 . GRCh38 6 22292630 22292630 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.220C>A p.His74Asn p.H74N ENST00000306482 3/5 219 198 21 155 154 1 strelka-varscan-mutect PRL,missense_variant,p.His75Asn,ENST00000617911,;PRL,missense_variant,p.His74Asn,ENST00000306482,NM_001163558.2,NM_000948.5;PRL,missense_variant,p.His43Asn,ENST00000615510,;CASC15,intron_variant,,ENST00000561912,; T ENST00000306482 Transcript missense_variant 739/1354 220/684 74/227 H/N Cat/Aat 1 -1 PRL HGNC HGNC:9445 protein_coding YES CCDS4548.1 ENSP00000302150 P01236 Q5THQ0 UPI0000001C13 NM_001163558.2,NM_000948.5 tolerated(0.06) 3/5 hmmpanther:PTHR11417,hmmpanther:PTHR11417:SF5,Gene3D:1.20.1250.10,Pfam_domain:PF00103,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 12 22292630 22292630 G T 1 0 0 0 0 1 0 0 0 12660 1348 47 2 2 PRL 6 22292630 Missense_Mutation SNP G C3L-00144_T 2139873 22292630 148513349 590 4661 NRSN1 0 . GRCh38 6 24141095 24141095 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.361C>G p.Pro121Ala p.P121A ENST00000378475 2/2 41 26 15 23 23 0 strelka-varscan-mutect NRSN1,missense_variant,p.Pro121Ala,ENST00000378475,;NRSN1,intron_variant,,ENST00000378478,NM_080723.4;NRSN1,intron_variant,,ENST00000378491,;NRSN1,intron_variant,,ENST00000378477,;NRSN1,intron_variant,,ENST00000468195,; G ENST00000378475 Transcript missense_variant 372/800 361/441 121/146 P/A Cct/Gct 1 1 NRSN1 HGNC HGNC:17881 protein_coding ENSP00000367736 Q5VTS2 UPI0000458AA7 2/2 MODERATE SNV 3 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 24141095 24141095 C G 1 0 0 0 0 1 0 0 0 10721 739 26 4 4 NRSN1 6 24141095 Missense_Mutation SNP C C3L-00144_T 1848465 24141095 146664884 591 4662 KIAA0319 0 . GRCh38 6 24595965 24595965 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.709C>A p.Pro237Thr p.P237T ENST00000378214 3/21 179 115 64 155 155 0 strelka-varscan-mutect KIAA0319,missense_variant,p.Pro228Thr,ENST00000535378,NM_001168374.1;KIAA0319,missense_variant,p.Pro237Thr,ENST00000378214,NM_001168375.1,NM_014809.3;KIAA0319,missense_variant,p.Pro237Thr,ENST00000537886,NM_001168377.1;KIAA0319,missense_variant,p.Pro192Thr,ENST00000430948,NM_001168376.1;KIAA0319,missense_variant,p.Pro237Thr,ENST00000543707,;KRT8P43,upstream_gene_variant,,ENST00000406052,; T ENST00000378214 Transcript missense_variant 1234/6802 709/3219 237/1072 P/T Ccc/Acc 1 -1 KIAA0319 HGNC HGNC:21580 protein_coding YES CCDS34348.1 ENSP00000367459 Q5VV43 UPI000020D61A NM_001168375.1,NM_014809.3 tolerated(0.11) 3/21 hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF194 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 24595965 24595965 G T 1 0 0 0 0 1 0 0 0 8080 1174 41 2 2 KIAA0319 6 24595965 Missense_Mutation SNP G C3L-00144_T 454870 24595965 146210014 592 4663 SLC17A3 0 . GRCh38 6 25861670 25861670 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.579G>T p.Trp193Cys p.W193C ENST00000397060 5/13 532 482 50 371 371 0 strelka-varscan-mutect SLC17A3,missense_variant,p.Trp193Cys,ENST00000397060,NM_001098486.1;SLC17A3,missense_variant,p.Trp115Cys,ENST00000360657,;SLC17A3,missense_variant,p.Trp115Cys,ENST00000361703,NM_006632.3;SLC17A3,non_coding_transcript_exon_variant,,ENST00000509714,;SLC17A3,non_coding_transcript_exon_variant,,ENST00000503922,;SLC17A3,non_coding_transcript_exon_variant,,ENST00000308453,;SLC17A3,intron_variant,,ENST00000506105,;SLC17A3,intron_variant,,ENST00000449356,; A ENST00000397060 Transcript missense_variant 689/2052 579/1497 193/498 W/C tgG/tgT 1 -1 SLC17A3 HGNC HGNC:10931 protein_coding YES CCDS47385.1 ENSP00000380250 O00476 UPI0001536779 NM_001098486.1 deleterious(0) 5/13 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF134,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 25861670 25861670 C A 1 0 0 0 0 1 0 0 0 14683 624 22 2 2 SLC17A3 6 25861670 Missense_Mutation SNP C C3L-00144_T 1265705 25861670 144944309 593 4664 HIST1H2BK 0 . GRCh38 6 27146777 27146777 + Missense_Mutation SNP C C A rs373240509 C3L-00144_T C3L-00144_N C C c.22G>T p.Ala8Ser p.A8S ENST00000356950 1/1 172 114 58 126 126 0 varscan-mutect HIST1H2BK,missense_variant,p.Ala8Ser,ENST00000356950,NM_080593.2;HIST1H2AH,upstream_gene_variant,,ENST00000377459,NM_080596.2;MIR3143,upstream_gene_variant,,ENST00000584253,; A ENST00000356950 Transcript missense_variant 22/381 22/381 8/126 A/S Gct/Tct rs373240509 1 -1 HIST1H2BK HGNC HGNC:13954 protein_coding YES CCDS4621.1 ENSP00000349430 O60814 A0A024RCL8 UPI0000073CF8 NM_080593.2 tolerated_low_confidence(0.06) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23428,Gene3D:1.10.20.10,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS rs373240509 . 0 203 0 0 0 6 0 0 -6.539291 0.06526688 1 1 0 0 A 3 1 12 27146777 27146777 C A 1 0 0 0 0 1 0 0 0 7038 768 27 1 1 HIST1H2BK 6 27146777 Missense_Mutation SNP C C3L-00144_T 1285107 27146777 143659202 594 4665 POM121L2 0 . GRCh38 6 27310497 27310497 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.1674T>A p.= p.A558A ENST00000444565 1/1 247 154 93 170 170 0 strelka-varscan-mutect POM121L2,synonymous_variant,p.=,ENST00000444565,NM_033482.3;POM121L2,intron_variant,,ENST00000429945,; T ENST00000444565 Transcript synonymous_variant 1674/3108 1674/3108 558/1035 A gcT/gcA 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 27310497 27310497 A T 1 0 0 0 0 0 0 0 1 12353 175 7 4 4 POM121L2 6 27310497 Silent SNP A C3L-00144_T 163720 27310497 143495482 595 4666 HIST1H2BO 0 . GRCh38 6 27893680 27893680 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.218G>T p.Arg73Leu p.R73L ENST00000616182 1/1 462 415 47 301 301 0 strelka-varscan-mutect HIST1H2BO,missense_variant,p.Arg73Leu,ENST00000616182,NM_003527.4;HIST1H3J,upstream_gene_variant,,ENST00000359303,NM_003535.2;HIST1H2AM,upstream_gene_variant,,ENST00000359611,NM_003514.2;RNU7-26P,downstream_gene_variant,,ENST00000458980,;HIST1H3J,upstream_gene_variant,,ENST00000479986,; T ENST00000616182 Transcript missense_variant 218/381 218/381 73/126 R/L cGc/cTc 1 1 HIST1H2BO HGNC HGNC:4758 protein_coding YES CCDS4640.1 ENSP00000477527 P23527 UPI0000073C3C NM_003527.4 deleterious_low_confidence(0.01) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00621,hmmpanther:PTHR23428,SMART_domains:SM00427,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS rs990218942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27893680 27893680 G T 1 0 0 0 0 1 0 0 0 7042 1087 38 1 1 HIST1H2BO 6 27893680 Missense_Mutation SNP G C3L-00144_T 583183 27893680 142912299 596 4667 OR2B6 0 . GRCh38 6 27957937 27957937 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.697G>T p.Gly233Cys p.G233C ENST00000244623 1/1 117 108 9 96 96 0 strelka-varscan-mutect OR2B6,missense_variant,p.Gly233Cys,ENST00000244623,NM_012367.1; T ENST00000244623 Transcript missense_variant 697/942 697/942 233/313 G/C Ggt/Tgt 1 1 OR2B6 HGNC HGNC:8241 protein_coding YES CCDS4642.1 ENSP00000244623 P58173 A0A126GW55 UPI000003F061 NM_012367.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF202,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1358866464 . 0 201 2 5 2 0 0 0 -4.539156 0.7611155 1 1 1 0 T 3 4 12 27957937 27957937 G T 1 0 0 0 0 1 0 0 0 11070 1000 35 2 2 OR2B6 6 27957937 Missense_Mutation SNP G C3L-00144_T 64257 27957937 142848042 597 4668 ZKSCAN4 0 . GRCh38 6 28245493 28245493 + Nonsense_Mutation SNP C C A rs751143499 C3L-00144_T C3L-00144_N C C c.1261G>T p.Glu421Ter p.E421* ENST00000377294 5/5 152 92 60 116 116 0 strelka-varscan-mutect ZKSCAN4,stop_gained,p.Glu421Ter,ENST00000377294,NM_019110.4; A ENST00000377294 Transcript stop_gained 1505/2375 1261/1638 421/545 E/* Gaa/Taa rs751143499 1 -1 ZKSCAN4 HGNC HGNC:13854 protein_coding YES CCDS4647.1 ENSP00000366509 Q969J2 A0A0S2Z658 UPI000013C355 NM_019110.4 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF72,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS rs751143499 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 28245493 28245493 C A 1 0 0 0 0 0 1 0 0 18267 835 29 2 2 ZKSCAN4 6 28245493 Nonsense_Mutation SNP C C3L-00144_T 287556 28245493 142560486 598 4669 OR10C1 0 . GRCh38 6 29440376 29440376 + Missense_Mutation SNP C C A rs17177639 C3L-00144_T C3L-00144_N C C c.361C>A p.Arg121Ser p.R121S ENST00000444197 1/1 250 219 31 175 175 0 strelka-varscan-mutect OR10C1,missense_variant,p.Arg121Ser,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Arg123Ser,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; A ENST00000444197 Transcript missense_variant 1071/1649 361/939 121/312 R/S Cgc/Agc rs17177639 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321 19833159 MODERATE 1 SNV 1 PASS rs17177639 . 0 204 0 0 0 0 0 6 -4.560455 0 0 1 0 0 A 3 1 12 29440376 29440376 C A 1 0 0 0 0 1 0 0 0 10973 652 23 1 1 OR10C1 6 29440376 Missense_Mutation SNP C C3L-00144_T 1194883 29440376 141365603 599 4670 OR10C1 0 . GRCh38 6 29440734 29440734 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.719G>T p.Cys240Phe p.C240F ENST00000444197 1/1 345 209 136 264 264 0 strelka-varscan-mutect OR10C1,missense_variant,p.Cys240Phe,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Cys242Phe,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript missense_variant 1429/1649 719/939 240/312 C/F tGc/tTc 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs755081985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 29440734 29440734 G T 1 0 0 0 0 1 0 0 0 10973 1319 46 2 2 OR10C1 6 29440734 Missense_Mutation SNP G C3L-00144_T 358 29440734 141365245 600 4671 RPP21 0 . GRCh38 6 30345399 30345399 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.1205+1G>T p.X402_splice ENST00000623385 237 142 95 192 192 0 strelka-varscan-mutect TRIM39-RPP21,splice_donor_variant,,ENST00000623385,NM_001199119.1;RPP21,splice_donor_variant,,ENST00000428040,;RPP21,splice_donor_variant,,ENST00000433076,NM_001199120.1;RPP21,splice_donor_variant,,ENST00000442966,NM_024839.2;RPP21,splice_donor_variant,,ENST00000436442,NM_001199121.1;TRIM39,downstream_gene_variant,,ENST00000376659,NM_172016.2;TRIM39,downstream_gene_variant,,ENST00000376656,NM_021253.3;TRIM39,downstream_gene_variant,,ENST00000396551,;TRIM39,downstream_gene_variant,,ENST00000396548,;TRIM39,downstream_gene_variant,,ENST00000396547,;TRIM39,downstream_gene_variant,,ENST00000420746,;RPP21,splice_donor_variant,,ENST00000466327,;RPP21,splice_donor_variant,,ENST00000489124,;RPP21,intron_variant,,ENST00000491477,;RPP21,non_coding_transcript_exon_variant,,ENST00000498414,;RPP21,non_coding_transcript_exon_variant,,ENST00000473266,; T ENST00000623385 Transcript splice_donor_variant -/1698 1205/1512 402/503 1 1 TRIM39-RPP21 HGNC HGNC:38845 protein_coding YES CCDS78121.1 ENSP00000485378 A0A096LP39 UPI0001E92A3E NM_001199119.1 8/10 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 30345399 30345399 G T 1 0 0 0 0 0 0 1 0 13863 1275 44 2 2 RPP21 6 30345399 Splice_Site SNP G C3L-00144_T 904665 30345399 140460580 601 4672 ABCF1 0 . GRCh38 6 30586209 30586209 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1789G>T p.Glu597Ter p.E597* ENST00000326195 18/25 151 89 62 110 110 0 strelka-varscan-mutect ABCF1,stop_gained,p.Glu597Ter,ENST00000326195,NM_001025091.1;ABCF1,stop_gained,p.Glu559Ter,ENST00000376545,NM_001090.2;ABCF1,downstream_gene_variant,,ENST00000441867,;MIR877,downstream_gene_variant,,ENST00000401282,;ABCF1,stop_gained,p.Glu348Ter,ENST00000475993,;ABCF1,upstream_gene_variant,,ENST00000479542,; T ENST00000326195 Transcript stop_gained 1901/3481 1789/2538 597/845 E/* Gag/Tag 1 1 ABCF1 HGNC HGNC:70 protein_coding YES CCDS34380.1 ENSP00000313603 Q8NE71 UPI0000141876 NM_001025091.1 18/25 hmmpanther:PTHR19211,hmmpanther:PTHR19211:SF14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 30586209 30586209 G T 1 0 0 0 0 0 1 0 0 69 1175 41 2 2 ABCF1 6 30586209 Nonsense_Mutation SNP G C3L-00144_T 240810 30586209 140219770 602 4673 DHX16 0 . GRCh38 6 30656229 30656229 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2467A>T p.Met823Leu p.M823L ENST00000376442 16/20 288 185 103 156 156 0 strelka-varscan-mutect DHX16,missense_variant,p.Met823Leu,ENST00000376442,NM_003587.4,NM_001164239.1;DHX16,missense_variant,p.Met342Leu,ENST00000376437,;C6orf136,downstream_gene_variant,,ENST00000293604,NM_001161376.1;C6orf136,downstream_gene_variant,,ENST00000446773,;C6orf136,downstream_gene_variant,,ENST00000376473,NM_001109938.2;C6orf136,downstream_gene_variant,,ENST00000465699,;C6orf136,downstream_gene_variant,,ENST00000376471,NM_145029.3;C6orf136,downstream_gene_variant,,ENST00000467801,;C6orf136,downstream_gene_variant,,ENST00000468785,;DHX16,downstream_gene_variant,,ENST00000480966,;C6orf136,downstream_gene_variant,,ENST00000488383,;C6orf136,downstream_gene_variant,,ENST00000484551,;C6orf136,downstream_gene_variant,,ENST00000487873,;C6orf136,downstream_gene_variant,,ENST00000463794,;C6orf136,downstream_gene_variant,,ENST00000460172,; A ENST00000376442 Transcript missense_variant 2663/3445 2467/3126 823/1041 M/L Atg/Ttg 1 -1 DHX16 HGNC HGNC:2739 protein_coding YES CCDS4685.1 ENSP00000365625 O60231 Q5SQH4 UPI000000D73D NM_003587.4,NM_001164239.1 deleterious(0.01) 16/20 hmmpanther:PTHR18934:SF83,hmmpanther:PTHR18934,Pfam_domain:PF04408,SMART_domains:SM00847,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 30656229 30656229 T A 1 0 0 0 0 1 0 0 0 4306 1464 51 4 4 DHX16 6 30656229 Missense_Mutation SNP T C3L-00144_T 70020 30656229 140149750 603 4674 MDC1 0 . GRCh38 6 30705089 30705089 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4094C>A p.Ser1365Ter p.S1365* ENST00000376406 10/15 188 174 14 157 156 1 strelka-varscan-mutect MDC1,stop_gained,p.Ser1365Ter,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; T ENST00000376406 Transcript stop_gained 4742/7576 4094/6270 1365/2089 S/* tCa/tAa 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 10/15 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 30705089 30705089 G T 1 0 0 0 0 0 1 0 0 9341 1294 45 2 2 MDC1 6 30705089 Nonsense_Mutation SNP G C3L-00144_T 48860 30705089 140100890 604 4675 DDX39B 0 . GRCh38 6 31536561 31536561 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.555C>T p.= p.L185L ENST00000396172 5/11 245 224 21 139 139 0 strelka-varscan-mutect DDX39B,synonymous_variant,p.=,ENST00000396172,NM_004640.6;DDX39B,synonymous_variant,p.=,ENST00000458640,NM_080598.5;DDX39B,synonymous_variant,p.=,ENST00000376177,;DDX39B,synonymous_variant,p.=,ENST00000427214,;DDX39B,synonymous_variant,p.=,ENST00000456662,;DDX39B,synonymous_variant,p.=,ENST00000419338,;DDX39B,synonymous_variant,p.=,ENST00000431908,;DDX39B,synonymous_variant,p.=,ENST00000428098,;DDX39B,downstream_gene_variant,,ENST00000456976,;DDX39B,downstream_gene_variant,,ENST00000428450,;DDX39B,downstream_gene_variant,,ENST00000449757,;DDX39B,downstream_gene_variant,,ENST00000418897,;DDX39B,downstream_gene_variant,,ENST00000419020,;DDX39B,upstream_gene_variant,,ENST00000417023,;SNORD84,downstream_gene_variant,,ENST00000584275,;SNORD117,upstream_gene_variant,,ENST00000364915,;ATP6V1G2-DDX39B,3_prime_UTR_variant,,ENST00000376185,;DDX39B,non_coding_transcript_exon_variant,,ENST00000481456,;DDX39B,non_coding_transcript_exon_variant,,ENST00000462256,;DDX39B,non_coding_transcript_exon_variant,,ENST00000482195,;DDX39B,upstream_gene_variant,,ENST00000474961,;DDX39B,upstream_gene_variant,,ENST00000484566,;ATP6V1G2-DDX39B,downstream_gene_variant,,ENST00000480131,;DDX39B,upstream_gene_variant,,ENST00000478365,; A ENST00000396172 Transcript synonymous_variant 1186/2133 555/1287 185/428 L ctC/ctT 1 -1 DDX39B HGNC HGNC:13917 protein_coding YES CCDS4697.1 ENSP00000379475 Q13838 A0A024RCM3 UPI0000001D0B NM_004640.6 5/11 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF204,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 31536561 31536561 G A 1 0 0 0 0 0 0 0 1 4160 1277 45 3 3 DDX39B 6 31536561 Silent SNP G C3L-00144_T 831472 31536561 139269418 605 4676 BAG6 0 . GRCh38 6 31641362 31641362 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.2530delG p.Glu844SerfsTer36 p.E844Sfs*36 ENST00000375964 18/25 183 116 67 150 150 0 sindel-varindel BAG6,frameshift_variant,p.Glu844SerfsTer36,ENST00000375964,NM_004639.3;BAG6,frameshift_variant,p.Glu838SerfsTer36,ENST00000211379,NM_080703.2,NM_080702.2;BAG6,frameshift_variant,p.Glu838SerfsTer36,ENST00000375976,NM_001098534.1;BAG6,frameshift_variant,p.Glu838SerfsTer36,ENST00000362049,NM_001199698.1;BAG6,frameshift_variant,p.Glu712SerfsTer36,ENST00000439687,NM_001199697.1;PRRC2A,downstream_gene_variant,,ENST00000376033,NM_004638.3;PRRC2A,downstream_gene_variant,,ENST00000376007,NM_080686.2;BAG6,downstream_gene_variant,,ENST00000437771,;BAG6,downstream_gene_variant,,ENST00000435080,;BAG6,upstream_gene_variant,,ENST00000441793,;BAG6,downstream_gene_variant,,ENST00000438149,;BAG6,downstream_gene_variant,,ENST00000453833,;BAG6,upstream_gene_variant,,ENST00000422948,;BAG6,downstream_gene_variant,,ENST00000470875,;BAG6,downstream_gene_variant,,ENST00000469182,;BAG6,downstream_gene_variant,,ENST00000465348,;BAG6,upstream_gene_variant,,ENST00000464126,;BAG6,upstream_gene_variant,,ENST00000464869,;BAG6,downstream_gene_variant,,ENST00000462682,;BAG6,non_coding_transcript_exon_variant,,ENST00000462875,;PRRC2A,downstream_gene_variant,,ENST00000492691,;PRRC2A,downstream_gene_variant,,ENST00000487839,;PRRC2A,downstream_gene_variant,,ENST00000462617,;PRRC2A,downstream_gene_variant,,ENST00000482441,; - ENST00000375964 Transcript frameshift_variant 2844/3815 2530/3399 844/1132 E/X Gag/ag 1 -1 BAG6 HGNC HGNC:13919 protein_coding YES CCDS47403.1 ENSP00000365131 P46379 UPI000047029D NM_004639.3 18/25 hmmpanther:PTHR15204:SF0,hmmpanther:PTHR15204 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 31641362 31641362 C - 1 0 1 0 1 0 0 0 0 1449 922 32 0 0 BAG6 6 31641362 Frame_Shift_Del DEL C C3L-00144_T 104801 31641362 139164617 606 4677 BAG6 0 . GRCh38 6 31649315 31649315 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.307G>T p.Gly103Trp p.G103W ENST00000375964 4/25 220 120 100 126 126 0 strelka-varscan-mutect BAG6,missense_variant,p.Gly103Trp,ENST00000375964,NM_004639.3;BAG6,missense_variant,p.Gly103Trp,ENST00000211379,NM_080703.2,NM_080702.2;BAG6,missense_variant,p.Gly103Trp,ENST00000375976,NM_001098534.1;BAG6,missense_variant,p.Gly103Trp,ENST00000362049,NM_001199698.1;BAG6,missense_variant,p.Gly103Trp,ENST00000439687,NM_001199697.1;BAG6,missense_variant,p.Gly103Trp,ENST00000437771,;BAG6,missense_variant,p.Gly103Trp,ENST00000435080,;BAG6,missense_variant,p.Gly103Trp,ENST00000424480,;BAG6,missense_variant,p.Gly103Trp,ENST00000428326,;BAG6,missense_variant,p.Gly103Trp,ENST00000451898,;BAG6,missense_variant,p.Gly103Trp,ENST00000433828,;BAG6,missense_variant,p.Gly103Trp,ENST00000452994,;BAG6,missense_variant,p.Gly103Trp,ENST00000456622,;BAG6,missense_variant,p.Gly103Trp,ENST00000456286,;BAG6,missense_variant,p.Gly103Trp,ENST00000434444,;BAG6,missense_variant,p.Gly103Trp,ENST00000424176,;BAG6,missense_variant,p.Gly103Trp,ENST00000441054,;BAG6,missense_variant,p.Gly103Trp,ENST00000454165,;APOM,upstream_gene_variant,,ENST00000375918,;BAG6,upstream_gene_variant,,ENST00000438149,;APOM,upstream_gene_variant,,ENST00000375920,NM_001256169.1;BAG6,upstream_gene_variant,,ENST00000453833,;BAG6,upstream_gene_variant,,ENST00000470875,;BAG6,upstream_gene_variant,,ENST00000469182,;BAG6,upstream_gene_variant,,ENST00000462682,; A ENST00000375964 Transcript missense_variant 621/3815 307/3399 103/1132 G/W Ggg/Tgg COSM5640465,COSM5640466 1 -1 BAG6 HGNC HGNC:13919 protein_coding YES CCDS47403.1 ENSP00000365131 P46379 UPI000047029D NM_004639.3 deleterious(0) 4/25 Low_complexity_(Seg):seg,hmmpanther:PTHR15204:SF0,hmmpanther:PTHR15204,Superfamily_domains:SSF54236 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31649315 31649315 C A 1 0 0 0 0 1 0 0 0 1449 623 22 2 2 BAG6 6 31649315 Missense_Mutation SNP C C3L-00144_T 7953 31649315 139156664 607 4678 TNXB 0 . GRCh38 6 32042309 32042309 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1551C>A p.Asp517Glu p.D517E ENST00000451343 10/13 339 306 33 247 247 0 varscan-mutect TNXB,missense_variant,p.Asp4088Glu,ENST00000375244,NM_019105.6;TNXB,missense_variant,p.Asp1806Glu,ENST00000611016,;TNXB,missense_variant,p.Asp517Glu,ENST00000451343,NM_032470.3;CYP21A2,downstream_gene_variant,,ENST00000418967,NM_000500.7;CYP21A2,downstream_gene_variant,,ENST00000435122,NM_001128590.3;CYP21A2,downstream_gene_variant,,ENST00000478281,;CYP21A2,downstream_gene_variant,,ENST00000471671,;TNXB,non_coding_transcript_exon_variant,,ENST00000490077,;TNXB,non_coding_transcript_exon_variant,,ENST00000498094,;CYP21A2,downstream_gene_variant,,ENST00000479074,;CYP21A2,downstream_gene_variant,,ENST00000479730,;CYP21A2,downstream_gene_variant,,ENST00000486063,;CYP21A2,downstream_gene_variant,,ENST00000483041,;CYP21A2,downstream_gene_variant,,ENST00000466779,;CYP21A2,downstream_gene_variant,,ENST00000466879,;CYP21A2,downstream_gene_variant,,ENST00000480027,;CYP21A2,downstream_gene_variant,,ENST00000488465,;CYP21A2,downstream_gene_variant,,ENST00000464325,;CYP21A2,downstream_gene_variant,,ENST00000469053,;CYP21A2,downstream_gene_variant,,ENST00000462278,; T ENST00000451343 Transcript missense_variant 2460/3125 1551/2022 517/673 D/E gaC/gaA 1 -1 TNXB HGNC HGNC:11976 protein_coding YES CCDS4736.1 ENSP00000407685 P22105 UPI0000000E8E NM_032470.3 tolerated(0.45) 10/13 PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF244,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS rs1444918443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 32042309 32042309 G T 1 0 0 0 0 1 0 0 0 16820 1020 36 2 2 TNXB 6 32042309 Missense_Mutation SNP G C3L-00144_T 392994 32042309 138763670 608 4679 EGFL8 0 . GRCh38 6 32166699 32166699 + Splice_Site SNP A A C novel C3L-00144_T C3L-00144_N A A c.225-2A>C p.X75_splice ENST00000395512 64 31 33 57 57 0 strelka-mutect EGFL8,splice_acceptor_variant,,ENST00000395512,;EGFL8,splice_acceptor_variant,,ENST00000333845,NM_030652.3;EGFL8,splice_acceptor_variant,,ENST00000432129,;AGPAT1,downstream_gene_variant,,ENST00000395499,;AGPAT1,downstream_gene_variant,,ENST00000375107,NM_006411.3;AGPAT1,downstream_gene_variant,,ENST00000395497,;PPT2,downstream_gene_variant,,ENST00000395523,;AGPAT1,downstream_gene_variant,,ENST00000395496,;PPT2,downstream_gene_variant,,ENST00000324816,NM_001204103.1,NM_005155.6;AGPAT1,downstream_gene_variant,,ENST00000336984,NM_032741.4;AGPAT1,downstream_gene_variant,,ENST00000375104,;PPT2,downstream_gene_variant,,ENST00000375137,;PPT2,downstream_gene_variant,,ENST00000361568,NM_138717.2;PPT2,downstream_gene_variant,,ENST00000375143,;AGPAT1,downstream_gene_variant,,ENST00000617181,;AGPAT1,downstream_gene_variant,,ENST00000490711,;PPT2-EGFL8,downstream_gene_variant,,ENST00000453656,;PPT2,downstream_gene_variant,,ENST00000493548,;AGPAT1,downstream_gene_variant,,ENST00000476663,;EGFL8,upstream_gene_variant,,ENST00000489721,;PPT2-EGFL8,splice_acceptor_variant,,ENST00000422437,;PPT2-EGFL8,splice_acceptor_variant,,ENST00000428388,;EGFL8,splice_acceptor_variant,,ENST00000466239,;PPT2-EGFL8,splice_acceptor_variant,,ENST00000583227,;PPT2-EGFL8,splice_acceptor_variant,,ENST00000421600,;EGFL8,splice_acceptor_variant,,ENST00000482938,;PPT2-EGFL8,downstream_gene_variant,,ENST00000585246,;PPT2-EGFL8,downstream_gene_variant,,ENST00000479001,; C ENST00000395512 Transcript splice_acceptor_variant -/1312 225/882 75/293 1 1 EGFL8 HGNC HGNC:13944 protein_coding YES CCDS4743.1 ENSP00000378888 Q99944 UPI000006FB40 3/8 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 12 32166699 32166699 A C 1 0 0 0 0 0 0 1 0 4801 202 7 5 5 EGFL8 6 32166699 Splice_Site SNP A C3L-00144_T 124390 32166699 138639280 609 4680 COL11A2 0 . GRCh38 6 33165662 33165662 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4379C>A p.Ser1460Ter p.S1460* ENST00000374708 61/64 579 541 38 531 531 0 strelka-varscan-mutect COL11A2,stop_gained,p.Ser1546Ter,ENST00000341947,NM_080680.2;COL11A2,stop_gained,p.Ser1460Ter,ENST00000374708,NM_080681.2;COL11A2,stop_gained,p.Ser1439Ter,ENST00000361917,NM_080679.2;COL11A2,non_coding_transcript_exon_variant,,ENST00000477772,; T ENST00000374708 Transcript stop_gained 4638/6209 4379/4953 1460/1650 S/* tCa/tAa 1 -1 COL11A2 HGNC HGNC:2187 protein_coding YES CCDS43452.1 ENSP00000363840 Q4VXY6 UPI000013E9A5 NM_080681.2 61/64 Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF509,SMART_domains:SM00038 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 33165662 33165662 G T 1 0 0 0 0 0 1 0 0 3456 1294 45 2 2 COL11A2 6 33165662 Nonsense_Mutation SNP G C3L-00144_T 998963 33165662 137640317 610 4681 ITPR3 0 . GRCh38 6 33672102 33672102 + Silent SNP C C A rs370555491 C3L-00144_T C3L-00144_N C C c.2802C>A p.= p.S934S ENST00000374316 23/59 140 124 16 93 93 0 strelka-varscan-mutect ITPR3,synonymous_variant,p.=,ENST00000374316,;ITPR3,synonymous_variant,p.=,ENST00000605930,NM_002224.3; A ENST00000374316 Transcript synonymous_variant 3862/9870 2802/8016 934/2671 S tcC/tcA rs370555491,COSM483952 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 23/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 0,1 LOW 1 SNV 5 0,1 1 PASS rs370555491 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 33672102 33672102 C A 1 0 0 0 0 0 0 0 1 7828 639 23 1 1 ITPR3 6 33672102 Silent SNP C C3L-00144_T 506440 33672102 137133877 611 4682 CPNE5 0 . GRCh38 6 36798191 36798191 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.378T>A p.= p.P126P ENST00000244751 6/21 195 163 32 166 166 0 strelka-varscan-mutect CPNE5,synonymous_variant,p.=,ENST00000244751,NM_020939.1;CPNE5,synonymous_variant,p.=,ENST00000633136,;CPNE5,synonymous_variant,p.=,ENST00000633280,; T ENST00000244751 Transcript synonymous_variant 1003/3897 378/1782 126/593 P ccT/ccA 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 6/21 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF51,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 36798191 36798191 A T 1 0 0 0 0 0 0 0 1 3610 175 7 4 4 CPNE5 6 36798191 Silent SNP A C3L-00144_T 3126089 36798191 134007788 612 4683 ZFAND3 0 . GRCh38 6 38116581 38116581 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.371C>G p.Ser124Cys p.S124C ENST00000287218 5/6 63 49 14 59 59 0 strelka-varscan-mutect ZFAND3,missense_variant,p.Ser124Cys,ENST00000287218,NM_021943.2;ZFAND3,missense_variant,p.Ser102Cys,ENST00000373391,;ZFAND3,missense_variant,p.Ser155Cys,ENST00000474522,;ZFAND3,missense_variant,p.Ser101Cys,ENST00000373389,;ZFAND3,non_coding_transcript_exon_variant,,ENST00000440482,; G ENST00000287218 Transcript missense_variant 818/3366 371/684 124/227 S/C tCt/tGt 1 1 ZFAND3 HGNC HGNC:18019 protein_coding YES CCDS4836.1 ENSP00000287218 Q9H8U3 A0A024RD12 UPI000006E3A4 NM_021943.2 deleterious(0.02) 5/6 hmmpanther:PTHR10634,hmmpanther:PTHR10634:SF28 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 38116581 38116581 C G 1 0 0 0 0 1 0 0 0 18205 913 32 4 4 ZFAND3 6 38116581 Missense_Mutation SNP C C3L-00144_T 1318390 38116581 132689398 613 4684 DNAH8 0 . GRCh38 6 38929538 38929538 + Missense_Mutation SNP C C T rs758179326 C3L-00144_T C3L-00144_N C C c.11146C>T p.Arg3716Cys p.R3716C ENST00000327475 75/93 133 99 34 95 95 0 strelka-varscan-mutect DNAH8,missense_variant,p.Arg3716Cys,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Arg3499Cys,ENST00000359357,;DNAH8,missense_variant,p.Arg3716Cys,ENST00000449981,;RP1-207H1.3,non_coding_transcript_exon_variant,,ENST00000453417,;RP1-207H1.3,intron_variant,,ENST00000416948,;RP1-207H1.3,intron_variant,,ENST00000418399,;RP1-207H1.2,downstream_gene_variant,,ENST00000407768,; T ENST00000327475 Transcript missense_variant 11255/14360 11146/14124 3716/4707 R/C Cgc/Tgc rs758179326,COSM232188,COSM232189,COSM4355211 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 75/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF12781 0,1,1,1 MODERATE SNV 5 0,1,1,1 1 PASS rs758179326 . 0 205 2 3 0 0 0 0 -20 0.9999861 1 1 1 0 T 3 4 12 38929538 38929538 C T 1 0 0 0 0 1 0 0 0 4422 884 31 1 1 DNAH8 6 38929538 Missense_Mutation SNP C C3L-00144_T 812957 38929538 131876441 614 4685 GLP1R 0 . GRCh38 6 39073689 39073689 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.743G>T p.Gly248Val p.G248V ENST00000373256 7/13 189 169 20 161 161 0 strelka-varscan-mutect GLP1R,missense_variant,p.Gly248Val,ENST00000373256,NM_002062.3; T ENST00000373256 Transcript missense_variant 786/3105 743/1392 248/463 G/V gGc/gTc 1 1 GLP1R HGNC HGNC:4324 protein_coding YES CCDS4839.1 ENSP00000362353 P43220 UPI0000061F20 NM_002062.3 deleterious(0) 7/13 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF245,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249 MODERATE 1 SNV 1 1 PASS rs1388310962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 39073689 39073689 G T 1 0 0 0 0 1 0 0 0 6331 1203 42 2 2 GLP1R 6 39073689 Missense_Mutation SNP G C3L-00144_T 144151 39073689 131732290 615 4686 FOXP4 0 . GRCh38 6 41587893 41587893 + Missense_Mutation SNP A A T rs767996269 C3L-00144_T C3L-00144_N A A c.973A>T p.Ile325Phe p.I325F ENST00000373060 8/17 185 163 22 100 100 0 strelka-varscan-mutect FOXP4,missense_variant,p.Ile325Phe,ENST00000373060,NM_001012426.1;FOXP4,missense_variant,p.Ile324Phe,ENST00000373063,NM_138457.2;FOXP4,missense_variant,p.Ile325Phe,ENST00000307972,;FOXP4,missense_variant,p.Ile325Phe,ENST00000409208,;FOXP4,missense_variant,p.Ile323Phe,ENST00000373057,NM_001012427.1;FOXP4,downstream_gene_variant,,ENST00000451305,; T ENST00000373060 Transcript missense_variant 1431/5948 973/2043 325/680 I/F Atc/Ttc rs767996269 1 1 FOXP4 HGNC HGNC:20842 protein_coding YES CCDS34447.1 ENSP00000362151 Q8IVH2 UPI000007462D NM_001012426.1 deleterious(0.01) 8/17 hmmpanther:PTHR11829:SF171,hmmpanther:PTHR11829,Pfam_domain:PF16159 MODERATE 1 SNV 5 1 PASS rs767996269 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41587893 41587893 A T 1 0 0 0 0 1 0 0 0 5894 463 16 4 4 FOXP4 6 41587893 Missense_Mutation SNP A C3L-00144_T 2514204 41587893 129218086 616 4687 ABCC10 0 . GRCh38 6 43447353 43447353 + Missense_Mutation SNP G G C rs369147311 C3L-00144_T C3L-00144_N G G c.3650G>C p.Arg1217Pro p.R1217P ENST00000372530 17/22 370 351 19 206 206 0 strelka-varscan-mutect ABCC10,missense_variant,p.Arg1189Pro,ENST00000244533,NM_033450.2;ABCC10,missense_variant,p.Arg1217Pro,ENST00000372530,NM_001198934.1;DLK2,downstream_gene_variant,,ENST00000357338,NM_206539.2;DLK2,downstream_gene_variant,,ENST00000372488,NM_023932.3;DLK2,downstream_gene_variant,,ENST00000372485,NM_001286656.1,NM_001286655.1;DLK2,downstream_gene_variant,,ENST00000430324,;ABCC10,upstream_gene_variant,,ENST00000505344,;ABCC10,non_coding_transcript_exon_variant,,ENST00000463024,;ABCC10,non_coding_transcript_exon_variant,,ENST00000437104,;ABCC10,non_coding_transcript_exon_variant,,ENST00000372512,; C ENST00000372530 Transcript missense_variant 3865/5033 3650/4479 1217/1492 R/P cGg/cCg rs369147311 1 1 ABCC10 HGNC HGNC:52 protein_coding YES CCDS56430.1 ENSP00000361608 Q5T3U5 A0A024RD21 UPI000004A062 NM_001198934.1 deleterious(0) 17/22 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF235,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 2 1 PASS rs369147311 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 43447353 43447353 G C 1 0 0 0 0 1 0 0 0 54 1116 39 4 4 ABCC10 6 43447353 Missense_Mutation SNP G C3L-00144_T 1859460 43447353 127358626 617 4688 PLA2G7 0 . GRCh38 6 46716495 46716495 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.265G>T p.Asp89Tyr p.D89Y ENST00000274793 4/12 417 320 97 248 248 0 strelka-varscan-mutect PLA2G7,missense_variant,p.Asp89Tyr,ENST00000274793,NM_005084.3;PLA2G7,missense_variant,p.Asp89Tyr,ENST00000537365,NM_001168357.1; A ENST00000274793 Transcript missense_variant 462/1882 265/1326 89/441 D/Y Gat/Tat 1 -1 PLA2G7 HGNC HGNC:9040 protein_coding YES CCDS4917.1 ENSP00000274793 Q13093 UPI000002FED1 NM_005084.3 deleterious(0) 4/12 Gene3D:3.40.50.1820,Pfam_domain:PF03403,PIRSF_domain:PIRSF018169,hmmpanther:PTHR10272,hmmpanther:PTHR10272:SF12 MODERATE 1 SNV 1 1 PASS rs1210877518 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 46716495 46716495 C A 1 0 0 0 0 1 0 0 0 12105 913 32 2 2 PLA2G7 6 46716495 Missense_Mutation SNP C C3L-00144_T 3269142 46716495 124089484 618 4689 MEP1A 0 . GRCh38 6 46825466 46825466 + Nonsense_Mutation SNP G G T rs755741706 C3L-00144_T C3L-00144_N G G c.751G>T p.Glu251Ter p.E251* ENST00000230588 8/14 243 184 59 145 144 1 strelka-varscan-mutect MEP1A,stop_gained,p.Glu279Ter,ENST00000611727,;MEP1A,stop_gained,p.Glu251Ter,ENST00000230588,NM_005588.2; T ENST00000230588 Transcript stop_gained 760/2892 751/2241 251/746 E/* Gag/Tag rs755741706 1 1 MEP1A HGNC HGNC:7015 protein_coding YES CCDS4918.1 ENSP00000230588 Q16819 UPI000006E4E9 NM_005588.2 8/14 Gene3D:3.40.390.10,Pfam_domain:PF01400,PIRSF_domain:PIRSF001196,Prints_domain:PR00480,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF311,Superfamily_domains:SSF55486 HIGH 1 SNV 1 1 PASS rs755741706 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 46825466 46825466 G T 1 0 0 0 0 0 1 0 0 9420 943 33 2 2 MEP1A 6 46825466 Nonsense_Mutation SNP G C3L-00144_T 108971 46825466 123980513 619 4690 CENPQ 0 . GRCh38 6 49481043 49481043 + Missense_Mutation SNP G G T rs367615344 C3L-00144_T C3L-00144_N G G c.440G>T p.Arg147Leu p.R147L ENST00000335783 6/9 284 219 65 153 153 0 strelka-varscan-mutect CENPQ,missense_variant,p.Arg147Leu,ENST00000335783,NM_018132.3; T ENST00000335783 Transcript missense_variant 534/1733 440/807 147/268 R/L cGa/cTa rs367615344,COSM4769356 1 1 CENPQ HGNC HGNC:21347 protein_coding YES CCDS4925.1 ENSP00000337289 Q7L2Z9 UPI000020DE7B NM_018132.3 tolerated(0.09) 6/9 Pfam_domain:PF13094,hmmpanther:PTHR31345,hmmpanther:PTHR31345:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367615344 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 49481043 49481043 G T 1 0 0 0 0 1 0 0 0 2949 1058 37 1 1 CENPQ 6 49481043 Missense_Mutation SNP G C3L-00144_T 2655577 49481043 121324936 620 4691 PGK2 0 . GRCh38 6 49786360 49786360 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.828T>C p.= p.N276N ENST00000304801 1/1 421 340 81 282 282 0 strelka-varscan-mutect PGK2,synonymous_variant,p.=,ENST00000304801,NM_138733.4; G ENST00000304801 Transcript synonymous_variant 948/1657 828/1254 276/417 N aaT/aaC 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 49786360 49786360 A G 1 0 0 0 0 0 0 0 1 11880 214 8 5 5 PGK2 6 49786360 Silent SNP A C3L-00144_T 305317 49786360 121019619 621 4692 TFAP2D 0 . GRCh38 6 50745211 50745211 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.988G>T p.Glu330Ter p.E330* ENST00000008391 6/8 585 555 30 358 358 0 strelka-varscan-mutect TFAP2D,stop_gained,p.Glu330Ter,ENST00000008391,NM_172238.3;TFAP2D,non_coding_transcript_exon_variant,,ENST00000492804,; T ENST00000008391 Transcript stop_gained 1216/1711 988/1359 330/452 E/* Gaa/Taa 1 1 TFAP2D HGNC HGNC:15581 protein_coding YES CCDS4933.1 ENSP00000008391 Q7Z6R9 UPI00001A3A89 NM_172238.3 6/8 hmmpanther:PTHR10812:SF5,hmmpanther:PTHR10812,Pfam_domain:PF03299 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 50745211 50745211 G T 1 0 0 0 0 0 1 0 0 16223 943 33 2 2 TFAP2D 6 50745211 Nonsense_Mutation SNP G C3L-00144_T 958851 50745211 120060768 622 4693 TFAP2B 0 . GRCh38 6 50838070 50838070 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.917C>G p.Thr306Arg p.T306R ENST00000393655 5/7 725 511 214 428 428 0 strelka-varscan-mutect TFAP2B,missense_variant,p.Thr306Arg,ENST00000393655,NM_003221.3; G ENST00000393655 Transcript missense_variant 1086/5773 917/1383 306/460 T/R aCg/aGg 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 deleterious(0) 5/7 Pfam_domain:PF03299,Prints_domain:PR01748,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 MODERATE 1 SNV 1 1 PASS rs1232197674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 50838070 50838070 C G 1 0 0 0 0 1 0 0 0 16221 536 19 4 4 TFAP2B 6 50838070 Missense_Mutation SNP C C3L-00144_T 92859 50838070 119967909 623 4694 PKHD1 0 . GRCh38 6 51748403 51748403 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.9213A>T p.= p.P3071P ENST00000371117 58/67 238 161 77 154 154 0 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript synonymous_variant 9489/16282 9213/12225 3071/4074 P ccA/ccT 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 58/67 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF299,Gene3D:2.160.20.10,Pfam_domain:PF13229,Superfamily_domains:SSF51126 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 51748403 51748403 T A 1 0 0 0 0 0 0 0 1 12067 1567 55 4 4 PKHD1 6 51748403 Silent SNP T C3L-00144_T 910333 51748403 119057576 624 4695 IL17A 0 . GRCh38 6 52189247 52189247 + Silent SNP C C G rs17878530 C3L-00144_T C3L-00144_N C C c.423C>G p.= p.S141S ENST00000340057 3/3 228 175 53 136 136 0 strelka-varscan-mutect IL17A,synonymous_variant,p.=,ENST00000340057,NM_002190.2; G ENST00000340057 Transcript synonymous_variant 468/1859 423/468 141/155 S tcC/tcG rs17878530 1 1 IL17A HGNC HGNC:5981 protein_coding YES CCDS4937.1 ENSP00000344192 Q16552 UPI0000047D95 NM_002190.2 3/3 hmmpanther:PTHR21295:SF2,hmmpanther:PTHR21295,Pfam_domain:PF06083,Gene3D:2.10.90.10,Superfamily_domains:SSF57501,Prints_domain:PR01932 LOW 1 SNV 1 1 PASS rs17878530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 52189247 52189247 C G 1 0 0 0 0 0 0 0 1 7542 639 23 4 4 IL17A 6 52189247 Silent SNP C C3L-00144_T 440844 52189247 118616732 625 4696 TINAG 0 . GRCh38 6 54308834 54308834 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.284G>T p.Cys95Phe p.C95F ENST00000259782 1/11 277 183 94 159 159 0 strelka-varscan-mutect TINAG,missense_variant,p.Cys95Phe,ENST00000259782,NM_014464.3;TINAG,missense_variant,p.Cys91Phe,ENST00000370869,;TINAG,missense_variant,p.Cys77Phe,ENST00000370864,;TINAG,non_coding_transcript_exon_variant,,ENST00000486436,; T ENST00000259782 Transcript missense_variant 380/1754 284/1431 95/476 C/F tGt/tTt 1 1 TINAG HGNC HGNC:14599 protein_coding YES CCDS4955.1 ENSP00000259782 Q9UJW2 UPI000013D078 NM_014464.3 deleterious(0) 1/11 Pfam_domain:PF01033,PROSITE_patterns:PS00524,PROSITE_profiles:PS50958,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF274,SMART_domains:SM00201 MODERATE 1 SNV 1 1 PASS rs1263777188 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54308834 54308834 G T 1 0 0 0 0 1 0 0 0 16362 1377 48 2 2 TINAG 6 54308834 Missense_Mutation SNP G C3L-00144_T 2119587 54308834 116497145 626 4697 FAM83B 0 . GRCh38 6 54940905 54940905 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1934A>C p.Asn645Thr p.N645T ENST00000306858 5/5 145 120 25 100 100 0 strelka-varscan-mutect FAM83B,missense_variant,p.Asn645Thr,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; C ENST00000306858 Transcript missense_variant 2050/3167 1934/3036 645/1011 N/T aAt/aCt 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 tolerated(0.18) 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 54940905 54940905 A C 1 0 0 0 0 1 0 0 0 5492 101 4 5 5 FAM83B 6 54940905 Missense_Mutation SNP A C3L-00144_T 632071 54940905 115865074 627 4698 DST 0 . GRCh38 6 56628140 56628140 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.3984T>A p.= p.I1328I ENST00000312431 30/95 367 249 118 240 240 0 strelka-varscan-mutect DST,synonymous_variant,p.=,ENST00000361203,;DST,synonymous_variant,p.=,ENST00000421834,NM_183380.3;DST,synonymous_variant,p.=,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,synonymous_variant,p.=,ENST00000370788,;DST,synonymous_variant,p.=,ENST00000244364,NM_015548.4;DST,synonymous_variant,p.=,ENST00000439203,;DST,synonymous_variant,p.=,ENST00000370765,NM_001723.5;DST,synonymous_variant,p.=,ENST00000520645,;DST,synonymous_variant,p.=,ENST00000518935,;DST,upstream_gene_variant,,ENST00000522360,; T ENST00000312431 Transcript synonymous_variant 4110/17756 3984/16614 1328/5537 I atT/atA 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 30/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Superfamily_domains:SSF46966 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 56628140 56628140 A T 1 0 0 0 0 0 0 0 1 4604 126 5 4 4 DST 6 56628140 Silent SNP A C3L-00144_T 1687235 56628140 114177839 628 4699 LGSN 0 . GRCh38 6 63280565 63280565 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.986G>A p.Cys329Tyr p.C329Y ENST00000370657 4/4 233 194 39 130 130 0 strelka-varscan-mutect LGSN,missense_variant,p.Ala189Thr,ENST00000370658,NM_001143940.1;LGSN,missense_variant,p.Cys329Tyr,ENST00000370657,NM_016571.2;LGSN,3_prime_UTR_variant,,ENST00000622415,;LGSN,intron_variant,,ENST00000485906,; T ENST00000370657 Transcript missense_variant 1020/1949 986/1530 329/509 C/Y tGc/tAc 1 -1 LGSN HGNC HGNC:21016 protein_coding YES CCDS4964.1 ENSP00000359691 Q5TDP6 UPI000013DA35 NM_016571.2 tolerated(1) 4/4 hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF7,Gene3D:3.30.590.10,Pfam_domain:PF00120,SMART_domains:SM01230,Superfamily_domains:SSF55931 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 63280565 63280565 C T 1 0 0 0 0 1 0 0 0 8669 710 25 3 3 LGSN 6 63280565 Missense_Mutation SNP C C3L-00144_T 6652425 63280565 107525414 629 4700 EYS 0 . GRCh38 6 63984518 63984518 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.6920G>T p.Gly2307Val p.G2307V ENST00000370621 35/44 677 527 150 400 400 0 strelka-varscan-mutect EYS,missense_variant,p.Gly2307Val,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Gly2307Val,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Gly79Val,ENST00000398580,; A ENST00000370621 Transcript missense_variant 7447/10485 6920/9498 2307/3165 G/V gGc/gTc COSM5699935 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0) 35/44 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS rs1171456122 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 63984518 63984518 C A 1 0 0 0 0 1 0 0 0 5200 739 26 2 2 EYS 6 63984518 Missense_Mutation SNP C C3L-00144_T 703953 63984518 106821461 630 4701 COL9A1 0 . GRCh38 6 70234841 70234841 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2212C>A p.Gln738Lys p.Q738K ENST00000357250 34/38 466 304 162 429 428 1 strelka-varscan-mutect COL9A1,missense_variant,p.Gln738Lys,ENST00000357250,NM_001851.4;COL9A1,missense_variant,p.Gln495Lys,ENST00000320755,NM_078485.3;RP1-149L1.1,intron_variant,,ENST00000522264,;COL9A1,non_coding_transcript_exon_variant,,ENST00000489611,;COL9A1,non_coding_transcript_exon_variant,,ENST00000486080,;COL9A1,non_coding_transcript_exon_variant,,ENST00000447041,;COL9A1,downstream_gene_variant,,ENST00000493682,; T ENST00000357250 Transcript missense_variant 2371/4761 2212/2766 738/921 Q/K Cag/Aag 1 -1 COL9A1 HGNC HGNC:2217 protein_coding YES CCDS4971.1 ENSP00000349790 P20849 UPI000020D14B NM_001851.4 34/38 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF523,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 70234841 70234841 G T 1 0 0 0 0 1 0 0 0 3496 1328 46 2 2 COL9A1 6 70234841 Missense_Mutation SNP G C3L-00144_T 6250323 70234841 100571138 631 4702 SNAP91 0 . GRCh38 6 83594432 83594432 + Silent SNP G G A rs764376228 C3L-00144_T C3L-00144_N G G c.1374C>T p.= p.A458A ENST00000439399 17/30 190 136 54 126 125 1 strelka-varscan-mutect SNAP91,synonymous_variant,p.=,ENST00000521485,;SNAP91,synonymous_variant,p.=,ENST00000439399,NM_014841.2;SNAP91,synonymous_variant,p.=,ENST00000369694,NM_001242792.1;SNAP91,synonymous_variant,p.=,ENST00000195649,NM_001256718.1;SNAP91,synonymous_variant,p.=,ENST00000521743,;SNAP91,synonymous_variant,p.=,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,intron_variant,,ENST00000520213,NM_001242794.1;SNAP91,intron_variant,,ENST00000521931,;SNAP91,intron_variant,,ENST00000369691,;SNAP91,upstream_gene_variant,,ENST00000523448,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,;SNAP91,non_coding_transcript_exon_variant,,ENST00000523780,; A ENST00000439399 Transcript synonymous_variant 1691/4452 1374/2724 458/907 A gcC/gcT rs764376228,COSM5100598,COSM5100599 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 17/30 Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs764376228 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 83594432 83594432 G A 1 0 0 0 0 0 0 0 1 15154 1103 39 1 1 SNAP91 6 83594432 Silent SNP G C3L-00144_T 13359591 83594432 87211547 632 4703 ZNF292 0 . GRCh38 6 87218710 87218710 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.517G>T p.Glu173Ter p.E173* ENST00000369577 4/8 246 172 74 277 275 2 strelka-varscan-mutect ZNF292,stop_gained,p.Glu173Ter,ENST00000369577,NM_015021.1;ZNF292,stop_gained,p.Glu173Ter,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,intron_variant,,ENST00000518845,;ZNF292,non_coding_transcript_exon_variant,,ENST00000369578,;ZNF292,non_coding_transcript_exon_variant,,ENST00000524067,;ZNF292,non_coding_transcript_exon_variant,,ENST00000485016,; T ENST00000369577 Transcript stop_gained 560/10610 517/8172 173/2723 E/* Gaa/Taa 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 4/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 87218710 87218710 G T 1 0 0 0 0 0 1 0 0 18402 1175 41 2 2 ZNF292 6 87218710 Nonsense_Mutation SNP G C3L-00144_T 3624278 87218710 83587269 633 4704 MDN1 0 . GRCh38 6 89747364 89747364 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.3869A>G p.Lys1290Arg p.K1290R ENST00000369393 27/102 122 76 46 132 132 0 strelka-varscan-mutect MDN1,missense_variant,p.Lys1290Arg,ENST00000369393,NM_014611.2;MDN1,missense_variant,p.Lys1290Arg,ENST00000629399,;MDN1,downstream_gene_variant,,ENST00000439638,; C ENST00000369393 Transcript missense_variant 3985/18413 3869/16791 1290/5596 K/R aAg/aGg 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 tolerated(0.07) 27/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 89747364 89747364 T C 1 0 0 0 0 1 0 0 0 9353 1609 56 5 5 MDN1 6 89747364 Missense_Mutation SNP T C3L-00144_T 2528654 89747364 81058615 634 4705 SIM1 0 . GRCh38 6 100449370 100449370 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.536G>T p.Gly179Val p.G179V ENST00000369208 6/12 165 112 53 192 191 1 strelka-varscan-mutect SIM1,missense_variant,p.Gly179Val,ENST00000369208,;SIM1,missense_variant,p.Gly179Val,ENST00000262901,NM_005068.2; A ENST00000369208 Transcript missense_variant 1319/8430 536/2301 179/766 G/V gGc/gTc 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 deleterious(0) 6/12 hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29,Superfamily_domains:SSF55785 MODERATE 1 SNV 1 1 PASS rs1463030120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 100449370 100449370 C A 1 0 0 0 0 1 0 0 0 14586 739 26 2 2 SIM1 6 100449370 Missense_Mutation SNP C C3L-00144_T 10702006 100449370 70356609 635 4706 GRIK2 0 . GRCh38 6 101924626 101924626 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.1774C>G p.Pro592Ala p.P592A ENST00000421544 12/16 247 182 65 197 197 0 strelka-varscan-mutect GRIK2,missense_variant,p.Pro592Ala,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Pro592Ala,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Pro592Ala,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Pro554Ala,ENST00000318991,;GRIK2,missense_variant,p.Pro554Ala,ENST00000369137,;GRIK2,missense_variant,p.Pro554Ala,ENST00000369134,;GRIK2,upstream_gene_variant,,ENST00000487395,;GRIK2,upstream_gene_variant,,ENST00000487161,; G ENST00000421544 Transcript missense_variant 2264/4789 1774/2727 592/908 P/A Cca/Gca COSM1544821,COSM1544822,COSM5270536 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 tolerated(0.25) 12/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,SMART_domains:SM00079 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 101924626 101924626 C G 1 0 0 0 0 1 0 0 0 6656 855 30 4 4 GRIK2 6 101924626 Missense_Mutation SNP C C3L-00144_T 1475256 101924626 68881353 636 4707 AIM1 0 . GRCh38 6 106539488 106539488 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.3580A>T p.Thr1194Ser p.T1194S ENST00000369066 7/20 245 160 85 180 180 0 strelka-varscan-mutect AIM1,missense_variant,p.Thr1602Ser,ENST00000633556,;AIM1,missense_variant,p.Thr1194Ser,ENST00000369066,NM_001624.3;AIM1,upstream_gene_variant,,ENST00000457437,; T ENST00000369066 Transcript missense_variant 4067/7553 3580/5172 1194/1723 T/S Aca/Tca 1 1 AIM1 HGNC HGNC:356 protein_coding YES CCDS34506.1 ENSP00000358062 Q9Y4K1 UPI000013C91D NM_001624.3 tolerated(0.4) 7/20 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF2,Pfam_domain:PF00030,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 1 1 PASS rs1321140538 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 106539488 106539488 A T 1 0 0 0 0 1 0 0 0 507 391 14 4 4 AIM1 6 106539488 Missense_Mutation SNP A C3L-00144_T 4614862 106539488 64266491 637 4708 FIG4 0 . GRCh38 6 109776956 109776956 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1785G>T p.= p.L595L ENST00000230124 16/23 292 182 110 285 285 0 strelka-varscan-mutect FIG4,synonymous_variant,p.=,ENST00000230124,NM_014845.5;FIG4,synonymous_variant,p.=,ENST00000415980,; T ENST00000230124 Transcript synonymous_variant 1909/3011 1785/2724 595/907 L ctG/ctT 1 1 FIG4 HGNC HGNC:16873 protein_coding YES CCDS5078.1 ENSP00000230124 Q92562 UPI000000D9A3 NM_014845.5 16/23 hmmpanther:PTHR11200:SF9,hmmpanther:PTHR11200 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 109776956 109776956 G T 1 0 0 0 0 0 0 0 1 5753 1335 47 2 2 FIG4 6 109776956 Silent SNP G C3L-00144_T 3237468 109776956 61029023 638 4709 COL10A1 0 . GRCh38 6 116120794 116120794 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1322C>A p.Pro441Gln p.P441Q ENST00000327673 2/2 206 135 71 182 182 0 strelka-varscan-mutect COL10A1,missense_variant,p.Pro441Gln,ENST00000327673,;COL10A1,missense_variant,p.Pro441Gln,ENST00000243222,NM_000493.3;NT5DC1,intron_variant,,ENST00000319550,NM_152729.2;NT5DC1,intron_variant,,ENST00000419791,;COL10A1,downstream_gene_variant,,ENST00000452729,;COL10A1,downstream_gene_variant,,ENST00000418500,;NT5DC1,intron_variant,,ENST00000460749,;NT5DC1,downstream_gene_variant,,ENST00000417846,; T ENST00000327673 Transcript missense_variant 1730/3498 1322/2043 441/680 P/Q cCa/cAa 1 -1 COL10A1 HGNC HGNC:2185 protein_coding YES CCDS5105.1 ENSP00000327368 Q03692 UPI0000126D28 tolerated(0.17) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF570 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 116120794 116120794 G T 1 0 0 0 0 1 0 0 0 3454 1348 47 2 2 COL10A1 6 116120794 Missense_Mutation SNP G C3L-00144_T 6343838 116120794 54685185 639 4710 GPRC6A 0 . GRCh38 6 116809608 116809608 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.204A>T p.= p.I68I ENST00000310357 2/6 75 53 22 90 90 0 strelka-varscan-mutect GPRC6A,synonymous_variant,p.=,ENST00000310357,NM_148963.3;GPRC6A,synonymous_variant,p.=,ENST00000368549,NM_001286355.1;GPRC6A,synonymous_variant,p.=,ENST00000530250,NM_001286354.1; A ENST00000310357 Transcript synonymous_variant 226/2860 204/2781 68/926 I atA/atT 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 2/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 116809608 116809608 T A 1 0 0 0 0 0 0 0 1 6607 1396 49 4 4 GPRC6A 6 116809608 Silent SNP T C3L-00144_T 688814 116809608 53996371 640 4711 TBC1D32 0 . GRCh38 6 121241544 121241544 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2166G>T p.Arg722Ser p.R722S ENST00000398212 19/32 387 254 133 365 365 0 strelka-varscan-mutect TBC1D32,missense_variant,p.Arg722Ser,ENST00000275159,;TBC1D32,missense_variant,p.Arg722Ser,ENST00000398212,NM_152730.5;TBC1D32,upstream_gene_variant,,ENST00000398197,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,; A ENST00000398212 Transcript missense_variant 2216/3824 2166/3774 722/1257 R/S agG/agT 1 -1 TBC1D32 HGNC HGNC:21485 protein_coding YES CCDS43501.1 ENSP00000381270 Q96NH3 UPI0000E67203 NM_152730.5 tolerated(0.05) 19/32 Pfam_domain:PF14961,hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 121241544 121241544 C A 1 0 0 0 0 1 0 0 0 16022 738 26 2 2 TBC1D32 6 121241544 Missense_Mutation SNP C C3L-00144_T 4431936 121241544 49564435 641 4712 CLVS2 0 . GRCh38 6 123055817 123055817 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.687T>C p.= p.H229H ENST00000275162 5/6 179 115 64 158 158 0 strelka-varscan-mutect CLVS2,synonymous_variant,p.=,ENST00000275162,NM_001010852.3;CLVS2,synonymous_variant,p.=,ENST00000368438,; C ENST00000275162 Transcript synonymous_variant 2022/11485 687/984 229/327 H caT/caC 1 1 CLVS2 HGNC HGNC:23046 protein_coding YES CCDS34525.1 ENSP00000275162 Q5SYC1 UPI000013DA49 NM_001010852.3 5/6 PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF73,Pfam_domain:PF00650,Gene3D:3.40.525.10,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180 LOW 1 SNV 1 1 PASS rs1267913426 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 123055817 123055817 T C 1 0 0 0 0 0 0 0 1 3345 1461 51 5 5 CLVS2 6 123055817 Silent SNP T C3L-00144_T 1814273 123055817 47750162 642 4713 HDDC2 0 . GRCh38 6 125292862 125292862 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.357G>T p.Lys119Asn p.K119N ENST00000398153 4/6 307 208 99 243 243 0 strelka-varscan-mutect HDDC2,missense_variant,p.Lys119Asn,ENST00000398153,NM_016063.2;HDDC2,intron_variant,,ENST00000608295,;HDDC2,downstream_gene_variant,,ENST00000608284,;HDDC2,3_prime_UTR_variant,,ENST00000318787,;HDDC2,3_prime_UTR_variant,,ENST00000609477,;HDDC2,non_coding_transcript_exon_variant,,ENST00000608461,;HDDC2,non_coding_transcript_exon_variant,,ENST00000608532,; A ENST00000398153 Transcript missense_variant 400/918 357/615 119/204 K/N aaG/aaT 1 -1 HDDC2 HGNC HGNC:21078 protein_coding YES CCDS43503.1 ENSP00000381220 Q7Z4H3 A0A140VJK7 UPI0000070B81 NM_016063.2 tolerated(0.08) 4/6 Gene3D:1.10.3210.10,Pfam_domain:PF13023,hmmpanther:PTHR11845,SMART_domains:SM00471,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 125292862 125292862 C A 1 0 0 0 0 1 0 0 0 6903 680 24 2 2 HDDC2 6 125292862 Missense_Mutation SNP C C3L-00144_T 2237045 125292862 45513117 643 4714 HEY2 0 . GRCh38 6 125754537 125754537 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.319G>A p.Gly107Arg p.G107R ENST00000368364 4/5 116 78 38 85 85 0 strelka-varscan-mutect HEY2,missense_variant,p.Gly107Arg,ENST00000368364,NM_012259.2;HEY2,missense_variant,p.Gly61Arg,ENST00000368365,; A ENST00000368364 Transcript missense_variant 516/2678 319/1014 107/337 G/R Ggg/Agg 1 1 HEY2 HGNC HGNC:4881 protein_coding YES CCDS5131.1 ENSP00000357348 Q9UBP5 UPI0000037AFE NM_012259.2 deleterious(0) 4/5 hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF88,SMART_domains:SM00353 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 125754537 125754537 G A 1 0 0 0 0 1 0 0 0 6963 1000 35 3 3 HEY2 6 125754537 Missense_Mutation SNP G C3L-00144_T 461675 125754537 45051442 644 4715 GRM1 0 . GRCh38 6 146399564 146399564 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2525C>T p.Pro842Leu p.P842L ENST00000361719 8/9 177 120 57 201 201 0 strelka-varscan-mutect GRM1,missense_variant,p.Pro842Leu,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,missense_variant,p.Pro842Leu,ENST00000361719,;GRM1,missense_variant,p.Pro842Leu,ENST00000282753,NM_001278064.1;GRM1,missense_variant,p.Pro842Leu,ENST00000355289,NM_001278067.1;GRM1,missense_variant,p.Pro842Leu,ENST00000507907,; T ENST00000361719 Transcript missense_variant 2892/6754 2525/3585 842/1194 P/L cCt/cTt 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD deleterious(0) 8/9 PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 146399564 146399564 C T 1 0 0 0 0 1 0 0 0 6678 681 24 3 3 GRM1 6 146399564 Missense_Mutation SNP C C3L-00144_T 20645027 146399564 24406415 645 4716 STXBP5 0 . GRCh38 6 147267168 147267168 + Splice_Site SNP G G C novel C3L-00144_T C3L-00144_N G G c.714+1G>C p.X238_splice ENST00000321680 159 110 49 136 136 0 strelka-varscan-mutect STXBP5,splice_donor_variant,,ENST00000367481,NM_139244.4;STXBP5,splice_donor_variant,,ENST00000321680,NM_001127715.2;STXBP5,splice_donor_variant,,ENST00000367480,;STXBP5,splice_donor_variant,,ENST00000546097,; C ENST00000321680 Transcript splice_donor_variant -/3456 714/3456 238/1151 1 1 STXBP5 HGNC HGNC:19665 protein_coding YES CCDS47499.1 ENSP00000321826 Q5T5C0 UPI0000199FE0 NM_001127715.2 7/27 HIGH 1 SNV 5 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999797 1 1 1 0 C 5 2 12 147267168 147267168 G C 1 0 0 0 0 0 0 1 0 15740 1275 44 4 4 STXBP5 6 147267168 Splice_Site SNP G C3L-00144_T 867604 147267168 23538811 646 4717 IGF2R 0 . GRCh38 6 160071908 160071908 + Splice_Site SNP A A G novel C3L-00144_T C3L-00144_N A A c.4444-2A>G p.X1482_splice ENST00000356956 140 88 52 127 127 0 strelka-varscan-mutect IGF2R,splice_acceptor_variant,,ENST00000356956,NM_000876.2;IGF2R,upstream_gene_variant,,ENST00000487607,; G ENST00000356956 Transcript splice_acceptor_variant -/14044 4444/7476 1482/2491 1 1 IGF2R HGNC HGNC:5467 protein_coding YES CCDS5273.1 ENSP00000349437 P11717 UPI0000072478 NM_000876.2 31/47 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 12 160071908 160071908 A G 1 0 0 0 0 0 0 1 0 7482 434 15 5 5 IGF2R 6 160071908 Splice_Site SNP A C3L-00144_T 12804740 160071908 10734071 647 4718 C6orf118 0 . GRCh38 6 165298074 165298074 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.964G>C p.Gly322Arg p.G322R ENST00000230301 5/9 95 89 6 75 75 0 strelka-varscan-mutect C6orf118,missense_variant,p.Gly322Arg,ENST00000230301,NM_144980.3;C6orf118,upstream_gene_variant,,ENST00000494696,; G ENST00000230301 Transcript missense_variant 985/1812 964/1410 322/469 G/R Ggg/Cgg COSM319109 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 tolerated(0.09) 5/9 hmmpanther:PTHR34916,Pfam_domain:PF15739 1 MODERATE 1 SNV 1 1 1 PASS rs1199314816 . 0 206 4 0 0 0 0 0 -12.67773 1 1 1 1 0 G 3 3 12 165298074 165298074 C G 1 0 0 0 0 1 0 0 0 2115 623 22 4 4 C6orf118 6 165298074 Missense_Mutation SNP C C3L-00144_T 5226166 165298074 5507905 648 4719 PDE10A 0 . GRCh38 6 165418763 165418763 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.870C>A p.Asn290Lys p.N290K ENST00000539869 11/22 357 251 106 346 343 3 strelka-varscan-mutect PDE10A,missense_variant,p.Asn280Lys,ENST00000366882,NM_006661.3;PDE10A,missense_variant,p.Asn290Lys,ENST00000539869,NM_001130690.2; T ENST00000539869 Transcript missense_variant 926/4401 870/2370 290/789 N/K aaC/aaA 1 -1 PDE10A HGNC HGNC:8772 protein_coding YES CCDS47513.1 ENSP00000438284 Q9Y233 UPI000006F80E NM_001130690.2 tolerated(0.95) 11/22 Gene3D:3.30.450.40,Pfam_domain:PF01590,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF111,SMART_domains:SM00065,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 165418763 165418763 G T 1 0 0 0 0 1 0 0 0 11718 1252 44 2 2 PDE10A 6 165418763 Missense_Mutation SNP G C3L-00144_T 120689 165418763 5387216 649 4720 PRR18 0 . GRCh38 6 166307654 166307654 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.489C>T p.= p.P163P ENST00000322583 1/1 50 32 18 63 63 0 strelka-varscan-mutect PRR18,synonymous_variant,p.=,ENST00000322583,NM_175922.3;PRR18,downstream_gene_variant,,ENST00000529616,; A ENST00000322583 Transcript synonymous_variant 730/3084 489/888 163/295 P ccC/ccT 1 -1 PRR18 HGNC HGNC:28574 protein_coding YES CCDS5291.1 ENSP00000319590 Q8N4B5 UPI0000140E82 NM_175922.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR10994,Pfam_domain:PF15671 LOW 1 SNV 1 PASS rs1055125661 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 166307654 166307654 G A 1 0 0 0 0 0 0 0 1 12726 987 35 3 3 PRR18 6 166307654 Silent SNP G C3L-00144_T 888891 166307654 4498325 650 4721 FGFR1OP 0 . GRCh38 6 167024785 167024785 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.810G>T p.Arg270Ser p.R270S ENST00000366847 9/13 162 110 52 129 128 1 strelka-varscan-mutect FGFR1OP,missense_variant,p.Arg270Ser,ENST00000366847,NM_007045.3;FGFR1OP,missense_variant,p.Arg223Ser,ENST00000622353,NM_001278690.1;FGFR1OP,missense_variant,p.Arg250Ser,ENST00000349556,NM_194429.2;FGFR1OP,non_coding_transcript_exon_variant,,ENST00000496181,;FGFR1OP,upstream_gene_variant,,ENST00000488525,;RP11-517H2.6,splice_region_variant,,ENST00000609590,; T ENST00000366847 Transcript missense_variant 1041/14166 810/1200 270/399 R/S agG/agT 1 1 FGFR1OP HGNC HGNC:17012 protein_coding YES CCDS5296.1 ENSP00000355812 O95684 UPI0000071446 NM_007045.3 deleterious(0.05) 9/13 hmmpanther:PTHR15431 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 167024785 167024785 G T 1 0 0 0 0 1 0 0 0 5728 1188 41 2 2 FGFR1OP 6 167024785 Missense_Mutation SNP G C3L-00144_T 717131 167024785 3781194 651 4722 TNRC18 0 . GRCh38 7 5389227 5389227 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.597G>T p.= p.S199S ENST00000430969 5/30 71 51 20 34 34 0 strelka-varscan-mutect TNRC18,synonymous_variant,p.=,ENST00000399537,;TNRC18,synonymous_variant,p.=,ENST00000430969,NM_001080495.2;TNRC18,downstream_gene_variant,,ENST00000399434,;TNRC18,upstream_gene_variant,,ENST00000413081,;TNRC18,downstream_gene_variant,,ENST00000434361,; A ENST00000430969 Transcript synonymous_variant 946/10562 597/8907 199/2968 S tcG/tcT 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 5/30 LOW 1 SNV 5 1 PASS rs1327774698 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 5389227 5389227 C A 1 0 0 0 0 0 0 0 1 16812 523 19 1 1 TNRC18 7 5389227 Silent SNP C C3L-00144_T 5389227 153956746 652 4723 THSD7A 0 . GRCh38 7 11590520 11590520 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1393T>C p.Tyr465His p.Y465H ENST00000423059 4/28 309 242 67 180 180 0 strelka-varscan-mutect THSD7A,missense_variant,p.Tyr465His,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Tyr465His,ENST00000617773,; G ENST00000423059 Transcript missense_variant 1645/10663 1393/4974 465/1657 Y/H Tac/Cac 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 deleterious(0.01) 4/28 PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 11590520 11590520 A G 1 0 0 0 0 1 0 0 0 16313 391 14 5 5 THSD7A 7 11590520 Missense_Mutation SNP A C3L-00144_T 6201293 11590520 147755453 653 4724 VWDE 0 . GRCh38 7 12367409 12367409 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2846G>T p.Gly949Val p.G949V ENST00000275358 13/29 148 116 32 108 108 0 strelka-varscan-mutect VWDE,missense_variant,p.Gly949Val,ENST00000275358,NM_001135924.1;VWDE,missense_variant,p.Gly403Val,ENST00000614403,;VWDE,missense_variant,p.Gly949Val,ENST00000452576,;VWDE,3_prime_UTR_variant,,ENST00000521169,; A ENST00000275358 Transcript missense_variant 3035/5260 2846/4773 949/1590 G/V gGc/gTc 1 -1 VWDE HGNC HGNC:21897 protein_coding YES CCDS47544.1 ENSP00000275358 Q8N2E2 UPI00006C0B98 NM_001135924.1 deleterious(0) 13/29 MODERATE 1 SNV 5 1 PASS rs1286488448 . 0 206 2 2 0 0 0 0 -20 0.9999991 1 1 1 0 A 3 1 12 12367409 12367409 C A 1 0 0 0 0 1 0 0 0 17805 739 26 2 2 VWDE 7 12367409 Missense_Mutation SNP C C3L-00144_T 776889 12367409 146978564 654 4725 SNX13 0 . GRCh38 7 17845633 17845633 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1127G>A p.Ser376Asn p.S376N ENST00000428135 12/26 161 133 28 84 84 0 strelka-varscan-mutect SNX13,missense_variant,p.Ser376Asn,ENST00000611725,;SNX13,missense_variant,p.Ser376Asn,ENST00000428135,NM_015132.4;SNX13,3_prime_UTR_variant,,ENST00000409076,;SNX13,3_prime_UTR_variant,,ENST00000444712,; T ENST00000428135 Transcript missense_variant 1326/6357 1127/2874 376/957 S/N aGc/aAc 1 -1 SNX13 HGNC HGNC:21335 protein_coding YES CCDS47551.1 ENSP00000398789 Q9Y5W8 A0A024R9Z9 UPI000002B3E8 NM_015132.4 tolerated(0.47) 12/26 Pfam_domain:PF00615,PROSITE_profiles:PS50132,hmmpanther:PTHR22775,SMART_domains:SM00315,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999389 1 1 1 0 T 3 4 12 17845633 17845633 C T 1 0 0 0 0 1 0 0 0 15205 797 28 3 3 SNX13 7 17845633 Missense_Mutation SNP C C3L-00144_T 5478224 17845633 141500340 655 4726 HDAC9 0 . GRCh38 7 18647971 18647971 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1222A>T p.Met408Leu p.M408L ENST00000441542 9/25 206 149 57 138 138 0 strelka-varscan-mutect HDAC9,missense_variant,p.Met405Leu,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Met364Leu,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,missense_variant,p.Met405Leu,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Met392Leu,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,missense_variant,p.Met364Leu,ENST00000401921,;HDAC9,missense_variant,p.Met408Leu,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Met405Leu,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Met403Leu,ENST00000417496,NM_001204144.1;HDAC9,missense_variant,p.Met361Leu,ENST00000428307,NM_001204145.1;HDAC9,missense_variant,p.Met377Leu,ENST00000456174,NM_001204148.1;HDAC9,missense_variant,p.Met328Leu,ENST00000524023,NM_001204147.1;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; T ENST00000441542 Transcript missense_variant 1222/3210 1222/3210 408/1069 M/L Atg/Ttg 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 tolerated(0.47) 9/25 PIRSF_domain:PIRSF037911 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 18647971 18647971 A T 1 0 0 0 0 1 0 0 0 6901 101 4 4 4 HDAC9 7 18647971 Missense_Mutation SNP A C3L-00144_T 802338 18647971 140698002 656 4727 DNAH11 0 . GRCh38 7 21900007 21900007 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.13190A>C p.Asn4397Thr p.N4397T ENST00000409508 81/82 157 121 36 82 82 0 strelka-varscan-mutect DNAH11,missense_variant,p.Asn4397Thr,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.Asn4404Thr,ENST00000328843,;DNAH11,missense_variant,p.Asn4404Thr,ENST00000620169,;CDCA7L,downstream_gene_variant,,ENST00000406877,NM_018719.4;CDCA7L,downstream_gene_variant,,ENST00000356195,NM_001127370.2;CDCA7L,downstream_gene_variant,,ENST00000373934,NM_001127371.2;CDCA7L,downstream_gene_variant,,ENST00000435717,;CDCA7L,downstream_gene_variant,,ENST00000465490,;DNAH11,non_coding_transcript_exon_variant,,ENST00000479878,;CDCA7L,downstream_gene_variant,,ENST00000488845,;CDCA7L,downstream_gene_variant,,ENST00000489669,; C ENST00000409508 Transcript missense_variant 13221/14167 13190/13551 4397/4516 N/T aAt/aCt 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 deleterious(0) 81/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 21900007 21900007 A C 1 0 0 0 0 1 0 0 0 4413 101 4 5 5 DNAH11 7 21900007 Missense_Mutation SNP A C3L-00144_T 3252036 21900007 137445966 657 4728 HOXA6 0 . GRCh38 7 27147361 27147361 + Missense_Mutation SNP C C A rs756210185 C3L-00144_T C3L-00144_N C C c.389G>T p.Arg130Leu p.R130L ENST00000222728 1/2 240 158 82 149 149 0 strelka-varscan-mutect HOXA6,missense_variant,p.Arg130Leu,ENST00000222728,NM_024014.3;HOXA5,upstream_gene_variant,,ENST00000222726,NM_019102.3;HOXA-AS3,non_coding_transcript_exon_variant,,ENST00000518947,;HOXA-AS3,intron_variant,,ENST00000521197,;HOXA-AS3,intron_variant,,ENST00000518848,;HOXA-AS3,upstream_gene_variant,,ENST00000524304,;HOXA-AS3,upstream_gene_variant,,ENST00000521231,;HOXA6,non_coding_transcript_exon_variant,,ENST00000521478,;RP1-170O19.22,intron_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000518451,;RP1-170O19.23,downstream_gene_variant,,ENST00000498652,;HOXA5,upstream_gene_variant,,ENST00000520854,; A ENST00000222728 Transcript missense_variant 414/989 389/702 130/233 R/L cGg/cTg rs756210185 1 -1 HOXA6 HGNC HGNC:5107 protein_coding YES CCDS5407.1 ENSP00000222728 P31267 UPI000012CF32 NM_024014.3 tolerated(0.07) 1/2 hmmpanther:PTHR24326:SF223,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS rs756210185 . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 12 27147361 27147361 C A 1 0 0 0 0 1 0 0 0 7190 652 23 1 1 HOXA6 7 27147361 Missense_Mutation SNP C C3L-00144_T 5247354 27147361 132198612 658 4729 HOXA11 0 . GRCh38 7 27184586 27184586 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.559C>A p.Pro187Thr p.P187T ENST00000006015 1/2 303 277 26 242 241 1 strelka-varscan-mutect HOXA11,missense_variant,p.Pro187Thr,ENST00000006015,NM_005523.5;HOXA11,missense_variant,p.Pro157Thr,ENST00000517402,;HOXA10,upstream_gene_variant,,ENST00000396344,;HOXA10-HOXA9,upstream_gene_variant,,ENST00000470747,;RP1-170O19.14,downstream_gene_variant,,ENST00000523331,;HOXA11-AS,non_coding_transcript_exon_variant,,ENST00000520360,;HOXA11-AS,upstream_gene_variant,,ENST00000522863,;HOXA11-AS,upstream_gene_variant,,ENST00000522674,;HOXA11-AS,upstream_gene_variant,,ENST00000520395,;HOXA11-AS,upstream_gene_variant,,ENST00000479766,;HOXA11-AS1_4,upstream_gene_variant,,ENST00000620901,;HOXA11-AS1_5,upstream_gene_variant,,ENST00000620211,;HOXA11-AS1_2,upstream_gene_variant,,ENST00000615604,;HOXA11-AS1_6,upstream_gene_variant,,ENST00000620092,;HOXA11-AS1_3,upstream_gene_variant,,ENST00000613383,;HOXA11-AS1_1,upstream_gene_variant,,ENST00000613939,; T ENST00000006015 Transcript missense_variant 631/2295 559/942 187/313 P/T Ccg/Acg 1 -1 HOXA11 HGNC HGNC:5101 protein_coding YES CCDS5411.1 ENSP00000006015 P31270 UPI000000D992 NM_005523.5 deleterious(0.03) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27184586 27184586 G T 1 0 0 0 0 1 0 0 0 7184 1203 42 2 2 HOXA11 7 27184586 Missense_Mutation SNP G C3L-00144_T 37225 27184586 132161387 659 4730 HIBADH 0 . GRCh38 7 27632446 27632446 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.253-1G>T p.X85_splice ENST00000265395 263 173 90 172 171 1 strelka-varscan-mutect HIBADH,splice_acceptor_variant,,ENST00000265395,NM_152740.3;HIBADH,splice_region_variant,,ENST00000425715,;HIBADH,splice_acceptor_variant,,ENST00000428288,; A ENST00000265395 Transcript splice_acceptor_variant -/1990 253/1011 85/336 1 -1 HIBADH HGNC HGNC:4907 protein_coding YES CCDS5414.1 ENSP00000265395 P31937 A0A024RA75 UPI000000160A NM_152740.3 2/7 HIGH 1 SNV 1 1 PASS . . 0 196 0 11 2 0 0 0 -20 0.8830905 1 1 1 0 A 5 1 12 27632446 27632446 C A 1 0 0 0 0 0 0 1 0 6983 695 24 2 2 HIBADH 7 27632446 Splice_Site SNP C C3L-00144_T 447860 27632446 131713527 660 4731 CHN2 0 . GRCh38 7 29512642 29512642 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1314C>A p.= p.P438P ENST00000222792 13/13 420 307 113 253 253 0 strelka-varscan-mutect CHN2,splice_region_variant,,ENST00000495789,;CHN2,synonymous_variant,p.=,ENST00000222792,NM_004067.3,NM_001293071.1,NM_001293070.1,NM_001293072.1;CHN2,synonymous_variant,p.=,ENST00000412711,NM_001039936.2,NM_001293073.1,NM_001293075.1,NM_001293080.1;CHN2,synonymous_variant,p.=,ENST00000435288,;CHN2,synonymous_variant,p.=,ENST00000409041,NM_001293077.1;CHN2,synonymous_variant,p.=,ENST00000424025,NM_001293078.1;CHN2,synonymous_variant,p.=,ENST00000421775,NM_001293076.1;CHN2,synonymous_variant,p.=,ENST00000539389,;CHN2,synonymous_variant,p.=,ENST00000539406,;CHN2,3_prime_UTR_variant,,ENST00000439711,NM_001293079.1;CHN2,downstream_gene_variant,,ENST00000433720,;AC007255.8,downstream_gene_variant,,ENST00000450540,;AC007255.8,downstream_gene_variant,,ENST00000447171,;CHN2,non_coding_transcript_exon_variant,,ENST00000410098,; A ENST00000222792 Transcript synonymous_variant 1844/3530 1314/1407 438/468 P ccC/ccA 1 1 CHN2 HGNC HGNC:1944 protein_coding YES CCDS5420.1 ENSP00000222792 P52757 UPI000012781F NM_004067.3,NM_001293071.1,NM_001293070.1,NM_001293072.1 13/13 PROSITE_profiles:PS50238,hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF35,Pfam_domain:PF00620,PIRSF_domain:PIRSF038015,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 29512642 29512642 C A 1 0 0 0 0 0 0 0 1 3123 637 22 2 2 CHN2 7 29512642 Silent SNP C C3L-00144_T 1880196 29512642 129833331 661 4732 GARS 0 . GRCh38 7 30632247 30632247 + Missense_Mutation SNP C C T rs201358272 C3L-00144_T C3L-00144_N C C c.1904C>T p.Ser635Leu p.S635L ENST00000389266 16/17 574 450 124 349 348 1 strelka-varscan-mutect GARS,missense_variant,p.Ser635Leu,ENST00000389266,NM_001316772.1,NM_002047.2;GARS,splice_region_variant,,ENST00000485784,;GARS,splice_region_variant,,ENST00000444666,;GARS,splice_region_variant,,ENST00000465748,;GARS,non_coding_transcript_exon_variant,,ENST00000496643,;GARS,downstream_gene_variant,,ENST00000470392,; T ENST00000389266 Transcript missense_variant,splice_region_variant 2145/2634 1904/2220 635/739 S/L tCg/tTg rs201358272,CM065213,IPNMDB_828,COSM1089085 1 1 GARS HGNC HGNC:4162 protein_coding YES CCDS43564.1 ENSP00000373918 P41250 UPI00005A885C NM_001316772.1,NM_002047.2 deleterious(0) 16/17 Gene3D:3.40.50.800,Pfam_domain:PF03129,hmmpanther:PTHR10745,hmmpanther:PTHR10745:SF0,Superfamily_domains:SSF52954,TIGRFAM_domain:TIGR00389 pathogenic 0,0,0,1 MODERATE 1 SNV 1 1,1,0,1 1 PASS rs201358272 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 30632247 30632247 C T 1 0 0 0 0 1 0 0 0 6112 782 27 1 1 GARS 7 30632247 Missense_Mutation SNP C C3L-00144_T 1119605 30632247 128713726 662 4733 BMPER 0 . GRCh38 7 34079126 34079127 + Frame_Shift_Del DEL CG CG - novel C3L-00144_T C3L-00144_N CG CG c.1353_1354delGC p.Pro452ThrfsTer52 p.P452Tfs*52 ENST00000297161 13/16 213 142 71 146 146 0 sindel-varindel-pindel BMPER,frameshift_variant,p.Pro452ThrfsTer52,ENST00000297161,NM_133468.4;BMPER,intron_variant,,ENST00000476525,; - ENST00000297161 Transcript frameshift_variant 1722-1723/5031 1348-1349/2058 450/685 R/X CGc/c 1 1 BMPER HGNC HGNC:24154 protein_coding YES CCDS5442.1 ENSP00000297161 Q8N8U9 A0A090N7U6 UPI000006D462 NM_133468.4 13/16 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF272,Pfam_domain:PF00094,SMART_domains:SM00216 HIGH 1 deletion 1 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 34079126 34079126 CG - 1 0 1 0 1 0 0 0 0 1623 652 23 0 0 BMPER 7 34079126 Frame_Shift_Del DEL CG C3L-00144_T 3446879 34079126 125266847 663 4734 TBX20 0 . GRCh38 7 35204500 35204500 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.973G>T p.Gly325Trp p.G325W ENST00000408931 7/8 604 491 113 401 401 0 strelka-varscan-mutect TBX20,missense_variant,p.Gly325Trp,ENST00000408931,NM_001077653.2; A ENST00000408931 Transcript missense_variant 1500/1871 973/1344 325/447 G/W Ggg/Tgg 1 -1 TBX20 HGNC HGNC:11598 protein_coding YES CCDS43568.1 ENSP00000386170 Q9UMR3 UPI00004B23D3 NM_001077653.2 deleterious(0.03) 7/8 hmmpanther:PTHR11267 MODERATE 1 SNV 1 1 PASS rs1175494481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 35204500 35204500 C A 1 0 0 0 0 1 0 0 0 16061 623 22 2 2 TBX20 7 35204500 Missense_Mutation SNP C C3L-00144_T 1125374 35204500 124141473 664 4735 TBX20 0 . GRCh38 7 35248775 35248775 + Silent SNP C C A C3L-00144_T C3L-00144_N C C c.447G>T p.= p.L149L ENST00000408931 3/8 602 471 131 433 432 1 strelka-varscan-mutect TBX20,synonymous_variant,p.=,ENST00000408931,NM_001077653.2;TBX20,non_coding_transcript_exon_variant,,ENST00000492961,; A ENST00000408931 Transcript synonymous_variant 974/1871 447/1344 149/447 L ctG/ctT COSM4548445,COSM4548446 1 -1 TBX20 HGNC HGNC:11598 protein_coding YES CCDS43568.1 ENSP00000386170 Q9UMR3 UPI00004B23D3 NM_001077653.2 3/8 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,Gene3D:1h6fA00,Pfam_domain:PF00907,SMART_domains:SM00425,Superfamily_domains:SSF49417 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 35248775 35248775 C A 1 0 0 0 0 0 0 0 1 16061 813 29 2 2 TBX20 7 35248775 Silent SNP C C3L-00144_T 44275 35248775 124097198 665 4736 HECW1 0 . GRCh38 7 43444791 43444791 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1619C>A p.Ser540Tyr p.S540Y ENST00000395891 11/30 228 168 60 170 170 0 strelka-varscan-mutect HECW1,missense_variant,p.Ser540Tyr,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Ser540Tyr,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript missense_variant 2224/9501 1619/4821 540/1606 S/Y tCc/tAc 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious_low_confidence(0) 11/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43444791 43444791 C A 1 0 0 0 0 1 0 0 0 6924 855 30 2 2 HECW1 7 43444791 Missense_Mutation SNP C C3L-00144_T 8196016 43444791 115901182 666 4737 HECW1 0 . GRCh38 7 43468998 43468998 + Missense_Mutation SNP G G C rs773668081 C3L-00144_T C3L-00144_N G G c.2992G>C p.Glu998Gln p.E998Q ENST00000395891 16/30 480 386 94 305 305 0 strelka-varscan-mutect HECW1,missense_variant,p.Glu998Gln,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Glu964Gln,ENST00000453890,NM_001287059.1; C ENST00000395891 Transcript missense_variant 3597/9501 2992/4821 998/1606 E/Q Gaa/Caa rs773668081,COSM1549808,COSM1549809 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated(0.06) 16/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs773668081 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 43468998 43468998 G C 1 0 0 0 0 1 0 0 0 6924 1291 45 4 4 HECW1 7 43468998 Missense_Mutation SNP G C3L-00144_T 24207 43468998 115876975 667 4738 OGDH 0 . GRCh38 7 44697717 44697717 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2293G>T p.Gly765Ter p.G765* ENST00000222673 17/23 333 230 103 199 198 1 strelka-varscan-mutect OGDH,stop_gained,p.Gly765Ter,ENST00000222673,NM_002541.3;OGDH,stop_gained,p.Gly764Ter,ENST00000631326,;OGDH,stop_gained,p.Gly761Ter,ENST00000449767,NM_001165036.1;OGDH,stop_gained,p.Gly776Ter,ENST00000447398,;OGDH,stop_gained,p.Gly780Ter,ENST00000444676,;OGDH,stop_gained,p.Gly615Ter,ENST00000439616,; T ENST00000222673 Transcript stop_gained 2335/4181 2293/3072 765/1023 G/* Gga/Tga 1 1 OGDH HGNC HGNC:8124 protein_coding YES CCDS34627.1 ENSP00000222673 Q02218 UPI000006D5FE NM_002541.3 17/23 Gene3D:3.40.50.970,Pfam_domain:PF02779,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF7,SMART_domains:SM00861,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 44697717 44697717 G T 1 0 0 0 0 0 1 0 0 10913 1233 43 2 2 OGDH 7 44697717 Nonsense_Mutation SNP G C3L-00144_T 1228719 44697717 114648256 668 4739 PKD1L1 0 . GRCh38 7 47855176 47855176 + Missense_Mutation SNP C C A rs574906854 C3L-00144_T C3L-00144_N C C c.4680G>T p.Glu1560Asp p.E1560D ENST00000289672 29/57 153 134 19 97 97 0 strelka-varscan-mutect PKD1L1,missense_variant,p.Glu1560Asp,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; A ENST00000289672 Transcript missense_variant 4731/9092 4680/8550 1560/2849 E/D gaG/gaT rs574906854 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 deleterious(0.03) 29/57 PROSITE_profiles:PS51111,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF145 MODERATE 1 SNV 1 1 PASS rs574906854 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 47855176 47855176 C A 1 0 0 0 0 1 0 0 0 12060 564 20 2 2 PKD1L1 7 47855176 Missense_Mutation SNP C C3L-00144_T 3157459 47855176 111490797 669 4740 ABCA13 0 . GRCh38 7 48271993 48271993 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2327A>T p.Asn776Ile p.N776I ENST00000435803 17/62 404 301 103 343 343 0 strelka-varscan-mutect ABCA13,missense_variant,p.Asn776Ile,ENST00000435803,NM_152701.4;ABCA13,3_prime_UTR_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant 2351/17184 2327/15177 776/5058 N/I aAt/aTt 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0) 17/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 48271993 48271993 A T 1 0 0 0 0 1 0 0 0 35 101 4 4 4 ABCA13 7 48271993 Missense_Mutation SNP A C3L-00144_T 416817 48271993 111073980 670 4741 ABCA13 0 . GRCh38 7 48272089 48272089 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2423G>T p.Gly808Val p.G808V ENST00000435803 17/62 419 357 62 380 379 1 strelka-varscan-mutect ABCA13,missense_variant,p.Gly808Val,ENST00000435803,NM_152701.4;ABCA13,3_prime_UTR_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant 2447/17184 2423/15177 808/5058 G/V gGa/gTa 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.1) 17/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 48272089 48272089 G T 1 0 0 0 0 1 0 0 0 35 1174 41 2 2 ABCA13 7 48272089 Missense_Mutation SNP G C3L-00144_T 96 48272089 111073884 671 4742 ABCA13 0 . GRCh38 7 48587210 48587210 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.14562G>T p.= p.V4854V ENST00000435803 57/62 241 210 31 189 188 1 strelka-varscan-mutect ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000544596,;ABCA13,synonymous_variant,p.=,ENST00000411975,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,synonymous_variant,p.=,ENST00000453246,; T ENST00000435803 Transcript synonymous_variant 14586/17184 14562/15177 4854/5058 V gtG/gtT 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 57/62 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs1439016148 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 48587210 48587210 G T 1 0 0 0 0 0 0 0 1 35 1335 47 2 2 ABCA13 7 48587210 Silent SNP G C3L-00144_T 315121 48587210 110758763 672 4743 VOPP1 0 . GRCh38 7 55497629 55497629 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.175A>G p.Arg59Gly p.R59G ENST00000285279 3/5 244 185 59 211 211 0 strelka-varscan-mutect VOPP1,missense_variant,p.Arg59Gly,ENST00000285279,NM_001321242.1,NM_001321251.1,NM_030796.3;VOPP1,missense_variant,p.Arg50Gly,ENST00000433959,NM_001284284.1;VOPP1,missense_variant,p.Arg56Gly,ENST00000625836,NM_001284283.1;VOPP1,missense_variant,p.Arg42Gly,ENST00000418904,NM_001284282.1;VOPP1,missense_variant,p.Arg57Gly,ENST00000427700,;VOPP1,5_prime_UTR_variant,,ENST00000428648,NM_001321250.1,NM_001321249.1;VOPP1,5_prime_UTR_variant,,ENST00000428097,;VOPP1,5_prime_UTR_variant,,ENST00000453256,;VOPP1,5_prime_UTR_variant,,ENST00000417399,;VOPP1,5_prime_UTR_variant,,ENST00000455023,;VOPP1,5_prime_UTR_variant,,ENST00000414113,;VOPP1,5_prime_UTR_variant,,ENST00000452832,;VOPP1,intron_variant,,ENST00000454227,;VOPP1,non_coding_transcript_exon_variant,,ENST00000471168,;VOPP1,non_coding_transcript_exon_variant,,ENST00000453112,;VOPP1,non_coding_transcript_exon_variant,,ENST00000462326,;VOPP1,non_coding_transcript_exon_variant,,ENST00000481197,; C ENST00000285279 Transcript missense_variant 376/2962 175/519 59/172 R/G Agg/Ggg 1 -1 VOPP1 HGNC HGNC:34518 protein_coding YES CCDS47588.1 ENSP00000285279 Q96AW1 UPI000006F3B3 NM_001321242.1,NM_001321251.1,NM_030796.3 deleterious(0) 3/5 Prints_domain:PR02068,Prints_domain:PR02068,hmmpanther:PTHR14971,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 55497629 55497629 T C 1 0 0 0 0 1 0 0 0 17732 1550 54 5 5 VOPP1 7 55497629 Missense_Mutation SNP T C3L-00144_T 6910419 55497629 103848344 673 4744 ZNF713 0 . GRCh38 7 55939100 55939100 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.426C>T p.= p.I142I ENST00000429591 7/7 195 145 50 118 117 1 strelka-varscan-mutect ZNF713,synonymous_variant,p.=,ENST00000429591,NM_182633.2;ZNF713,synonymous_variant,p.=,ENST00000633730,;RP11-15K19.2,intron_variant,,ENST00000426595,; T ENST00000429591 Transcript synonymous_variant 1214/4339 426/1332 142/443 I atC/atT 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 7/7 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 55939100 55939100 C T 1 0 0 0 0 0 0 0 1 18692 845 30 3 3 ZNF713 7 55939100 Silent SNP C C3L-00144_T 441471 55939100 103406873 674 4745 ZNF713 0 . GRCh38 7 55939750 55939750 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1076A>G p.Glu359Gly p.E359G ENST00000429591 7/7 147 102 45 124 124 0 strelka-varscan-mutect ZNF713,missense_variant,p.Glu359Gly,ENST00000429591,NM_182633.2;ZNF713,missense_variant,p.Glu346Gly,ENST00000633730,;RP11-15K19.2,intron_variant,,ENST00000426595,; G ENST00000429591 Transcript missense_variant 1864/4339 1076/1332 359/443 E/G gAa/gGa 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 deleterious(0.03) 7/7 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 55939750 55939750 A G 1 0 0 0 0 1 0 0 0 18692 246 9 5 5 ZNF713 7 55939750 Missense_Mutation SNP A C3L-00144_T 650 55939750 103406223 675 4746 ZNF479 0 . GRCh38 7 57119940 57119940 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.1475C>A p.Pro492His p.P492H ENST00000331162 5/5 305 224 81 239 239 0 strelka-varscan-mutect ZNF479,missense_variant,p.Pro492His,ENST00000331162,NM_033273.2;ZNF479,missense_variant,p.Pro492His,ENST00000319636,;ZNF479,missense_variant,p.Pro380His,ENST00000620639,; T ENST00000331162 Transcript missense_variant 1746/2072 1475/1575 492/524 P/H cCc/cAc COSM3881927 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 deleterious(0.01) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 57119940 57119940 G T 1 0 0 0 0 1 0 0 0 18505 1232 43 2 2 ZNF479 7 57119940 Missense_Mutation SNP G C3L-00144_T 1180190 57119940 102226033 676 4747 ZNF679 0 . GRCh38 7 64266489 64266489 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.856C>A p.His286Asn p.H286N ENST00000421025 5/5 219 155 64 174 174 0 strelka-varscan-mutect ZNF679,missense_variant,p.His286Asn,ENST00000421025,NM_153363.2;ZNF679,missense_variant,p.His286Asn,ENST00000255746,; A ENST00000421025 Transcript missense_variant 1125/1567 856/1236 286/411 H/N Cac/Aac 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 deleterious(0.01) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF91,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 64266489 64266489 C A 1 0 0 0 0 1 0 0 0 18659 594 21 2 2 ZNF679 7 64266489 Missense_Mutation SNP C C3L-00144_T 7146549 64266489 95079484 677 4748 ZNF107 0 . GRCh38 7 64706443 64706443 + Missense_Mutation SNP G G T rs144739473 C3L-00144_T C3L-00144_N G G c.346G>T p.Gly116Cys p.G116C ENST00000620827 4/4 103 74 29 93 93 0 strelka-varscan-mutect ZNF107,missense_variant,p.Gly47Cys,ENST00000395391,;ZNF107,missense_variant,p.Gly47Cys,ENST00000423627,NM_016220.4;ZNF107,missense_variant,p.Gly116Cys,ENST00000620827,NM_001282359.1;ZNF107,missense_variant,p.Gly84Cys,ENST00000613690,NM_001282360.1;ZNF107,missense_variant,p.Gly47Cys,ENST00000344930,NM_001013746.2;ZNF107,missense_variant,p.Gly47Cys,ENST00000360117,; T ENST00000620827 Transcript missense_variant 546/5685 346/2559 116/852 G/C Ggc/Tgc rs144739473 1 1 ZNF107 HGNC HGNC:12887 protein_coding YES CCDS75605.1 ENSP00000483720 A0A0B4J2G0 UPI0000049C52 NM_001282359.1 deleterious(0.05) 4/4 MODERATE 1 SNV 4 1 PASS rs144739473 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 64706443 64706443 G T 1 0 0 0 0 1 0 0 0 18295 1000 35 2 2 ZNF107 7 64706443 Missense_Mutation SNP G C3L-00144_T 439954 64706443 94639530 678 4749 ZNF107 0 . GRCh38 7 64708369 64708369 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.2272G>C p.Glu758Gln p.E758Q ENST00000620827 4/4 274 233 41 243 243 0 strelka-varscan-mutect ZNF107,missense_variant,p.Glu689Gln,ENST00000395391,;ZNF107,missense_variant,p.Glu689Gln,ENST00000423627,NM_016220.4;ZNF107,missense_variant,p.Glu758Gln,ENST00000620827,NM_001282359.1;ZNF107,missense_variant,p.Glu726Gln,ENST00000613690,NM_001282360.1;ZNF107,missense_variant,p.Glu689Gln,ENST00000344930,NM_001013746.2;ZNF107,downstream_gene_variant,,ENST00000360117,; C ENST00000620827 Transcript missense_variant 2472/5685 2272/2559 758/852 E/Q Gag/Cag 1 1 ZNF107 HGNC HGNC:12887 protein_coding YES CCDS75605.1 ENSP00000483720 A0A0B4J2G0 UPI0000049C52 NM_001282359.1 deleterious(0.02) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF121,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 64708369 64708369 G C 1 0 0 0 0 1 0 0 0 18295 943 33 4 4 ZNF107 7 64708369 Missense_Mutation SNP G C3L-00144_T 1926 64708369 94637604 679 4750 ASL 0 . GRCh38 7 66086818 66086818 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.599G>T p.Gly200Val p.G200V ENST00000304874 8/17 185 135 50 125 124 1 strelka-varscan-mutect ASL,missense_variant,p.Gly200Val,ENST00000304874,NM_000048.3;ASL,missense_variant,p.Gly200Val,ENST00000395332,NM_001024943.1;ASL,missense_variant,p.Gly200Val,ENST00000395331,NM_001024944.1;ASL,missense_variant,p.Gly135Val,ENST00000362000,;ASL,intron_variant,,ENST00000380839,NM_001024946.1;AC068533.7,upstream_gene_variant,,ENST00000450043,;ASL,upstream_gene_variant,,ENST00000464970,;ASL,upstream_gene_variant,,ENST00000488343,;ASL,non_coding_transcript_exon_variant,,ENST00000487982,;ASL,downstream_gene_variant,,ENST00000496336,;ASL,upstream_gene_variant,,ENST00000493708,; T ENST00000304874 Transcript missense_variant 701/2143 599/1395 200/464 G/V gGg/gTg COSM33230 1 1 ASL HGNC HGNC:746 protein_coding YES CCDS5531.1 ENSP00000307188 P04424 A0A024RDL8 UPI0000001634 NM_000048.3 deleterious(0) 8/17 HAMAP:MF_00006,hmmpanther:PTHR11444:SF3,hmmpanther:PTHR11444,Gene3D:1.20.200.10,TIGRFAM_domain:TIGR00838,Pfam_domain:PF00206,Superfamily_domains:SSF48557,Prints_domain:PR00145 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 66086818 66086818 G T 1 0 0 0 0 1 0 0 0 1191 1246 43 2 2 ASL 7 66086818 Missense_Mutation SNP G C3L-00144_T 1378449 66086818 93259155 680 4751 RABGEF1 0 . GRCh38 7 66772056 66772056 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.199G>T p.Glu67Ter p.E67* ENST00000380828 2/9 53 35 18 28 28 0 varscan-mutect RABGEF1,stop_gained,p.Glu67Ter,ENST00000380828,NM_001287061.1;RABGEF1,stop_gained,p.Glu53Ter,ENST00000284957,NM_014504.2;RABGEF1,stop_gained,p.Glu53Ter,ENST00000510829,;RABGEF1,stop_gained,p.Glu66Ter,ENST00000439720,;RABGEF1,stop_gained,p.Glu53Ter,ENST00000450873,NM_001287062.1;RABGEF1,5_prime_UTR_variant,,ENST00000437078,NM_001287060.1;RABGEF1,downstream_gene_variant,,ENST00000442563,;RABGEF1,non_coding_transcript_exon_variant,,ENST00000484547,;KCTD7,stop_gained,p.Glu191Ter,ENST00000503687,;RABGEF1,stop_gained,p.Glu53Ter,ENST00000607882,; T ENST00000380828 Transcript stop_gained 370/3864 199/1518 67/505 E/* Gag/Tag 1 1 RABGEF1 HGNC HGNC:17676 protein_coding YES CCDS69308.1 ENSP00000370208 Q9UJ41 UPI00017A848C NM_001287061.1 2/9 hmmpanther:PTHR23101,hmmpanther:PTHR23101:SF69,Superfamily_domains:SSF57716 HIGH 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 12 66772056 66772056 G T 1 0 0 0 0 0 1 0 0 13125 1175 41 2 2 RABGEF1 7 66772056 Nonsense_Mutation SNP G C3L-00144_T 685238 66772056 92573917 681 4752 CALN1 0 . GRCh38 7 71787791 71787791 + Missense_Mutation SNP C C T rs370771019 C3L-00144_T C3L-00144_N C C c.770G>A p.Arg257Gln p.R257Q ENST00000395275 7/7 186 167 19 134 134 0 strelka-varscan-mutect CALN1,missense_variant,p.Arg257Gln,ENST00000395275,NM_031468.3;CALN1,missense_variant,p.Arg215Gln,ENST00000329008,NM_001017440.2;CALN1,missense_variant,p.Arg215Gln,ENST00000395276,;CALN1,missense_variant,p.Arg91Gln,ENST00000405452,;CALN1,missense_variant,p.Arg215Gln,ENST00000431984,; T ENST00000395275 Transcript missense_variant 1159/9459 770/786 257/261 R/Q cGg/cAg rs370771019,COSM3086485,COSM3086486 1 -1 CALN1 HGNC HGNC:13248 protein_coding YES CCDS47603.1 ENSP00000378690 Q9BXU9 UPI0000D4B903 NM_031468.3 deleterious_low_confidence(0) 7/7 hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF51 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs370771019 . 0 203 5 2 0 0 0 0 -20 0.9999147 1 1 1 0 T 3 4 12 71787791 71787791 C T 1 0 0 0 0 1 0 0 0 2282 652 23 1 1 CALN1 7 71787791 Missense_Mutation SNP C C3L-00144_T 5015735 71787791 87558182 682 4753 TRIM50 0 . GRCh38 7 73324404 73324404 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.384C>A p.= p.V128V ENST00000333149 2/7 460 413 47 344 344 0 strelka-varscan-mutect TRIM50,synonymous_variant,p.=,ENST00000333149,NM_178125.3,NM_001281450.1;TRIM50,synonymous_variant,p.=,ENST00000453152,NM_001281451.1;FKBP6,upstream_gene_variant,,ENST00000413573,NM_001281304.1;FKBP6,upstream_gene_variant,,ENST00000252037,NM_003602.4;FKBP6,upstream_gene_variant,,ENST00000431982,NM_001135211.2;FKBP6,upstream_gene_variant,,ENST00000442793,;TRIM50,non_coding_transcript_exon_variant,,ENST00000493498,;FKBP6,upstream_gene_variant,,ENST00000445032,;FKBP6,upstream_gene_variant,,ENST00000429879,;FKBP6,upstream_gene_variant,,ENST00000437013,; T ENST00000333149 Transcript synonymous_variant 585/2047 384/1464 128/487 V gtC/gtA 1 -1 TRIM50 HGNC HGNC:19017 protein_coding YES CCDS34654.1 ENSP00000327994 Q86XT4 Q2M204 UPI0000684286 NM_178125.3,NM_001281450.1 2/7 hmmpanther:PTHR24103:SF399,hmmpanther:PTHR24103,Superfamily_domains:SSF57845 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 73324404 73324404 G T 1 0 0 0 0 0 0 0 1 17018 929 33 2 2 TRIM50 7 73324404 Silent SNP G C3L-00144_T 1536613 73324404 86021569 683 4754 CLDN3 0 . GRCh38 7 73769596 73769596 + Missense_Mutation SNP G G A rs782810492 C3L-00144_T C3L-00144_N G G c.454C>T p.Pro152Ser p.P152S ENST00000395145 1/1 80 57 23 70 70 0 strelka-varscan-mutect CLDN3,missense_variant,p.Pro152Ser,ENST00000395145,NM_001306.3; A ENST00000395145 Transcript missense_variant 675/1274 454/663 152/220 P/S Ccc/Tcc rs782810492 1 -1 CLDN3 HGNC HGNC:2045 protein_coding YES CCDS5559.1 ENSP00000378577 O15551 Q75L79 UPI0000044942 NM_001306.3 tolerated(0.34) 1/1 hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF112,Pfam_domain:PF00822 MODERATE 1 SNV 1 PASS rs782810492 . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 12 73769596 73769596 G A 1 0 0 0 0 1 0 0 0 3251 1203 42 3 3 CLDN3 7 73769596 Missense_Mutation SNP G C3L-00144_T 445192 73769596 85576377 684 4755 GTF2IRD2B 0 . GRCh38 7 75148148 75148148 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1701C>T p.= p.I567I ENST00000472837 16/16 205 190 15 141 141 0 varscan-mutect GTF2IRD2B,synonymous_variant,p.=,ENST00000472837,NM_001003795.2;GTF2IRD2B,downstream_gene_variant,,ENST00000619142,;GTF2IRD2B,downstream_gene_variant,,ENST00000629105,;GTF2IRD2B,3_prime_UTR_variant,,ENST00000418185,;GTF2IRD2B,non_coding_transcript_exon_variant,,ENST00000611835,;GTF2IRD2B,downstream_gene_variant,,ENST00000394939,; T ENST00000472837 Transcript synonymous_variant 1891/3560 1701/2850 567/949 I atC/atT 1 1 GTF2IRD2B HGNC HGNC:33125 protein_coding YES CCDS34659.1 ENSP00000480524 Q6EKJ0 UPI0000251DF5 NM_001003795.2 16/16 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF35,Superfamily_domains:SSF53098 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 75148148 75148148 C T 1 0 0 0 0 0 0 0 1 6751 845 30 3 3 GTF2IRD2B 7 75148148 Silent SNP C C3L-00144_T 1378552 75148148 84197825 685 4756 GNAT3 0 . GRCh38 7 80462197 80462197 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.836C>A p.Thr279Asn p.T279N ENST00000398291 7/8 213 156 57 172 172 0 strelka-mutect GNAT3,missense_variant,p.Thr279Asn,ENST00000398291,NM_001102386.1;CD36,intron_variant,,ENST00000435819,; T ENST00000398291 Transcript missense_variant 930/1159 836/1065 279/354 T/N aCc/aAc 1 -1 GNAT3 HGNC HGNC:22800 protein_coding YES CCDS47625.1 ENSP00000381339 A8MTJ3 UPI0000198E14 NM_001102386.1 tolerated(0.19) 7/8 hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF66,Pfam_domain:PF00503,Gene3D:3.40.50.300,SMART_domains:SM00275,Superfamily_domains:SSF52540,Prints_domain:PR00441 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 80462197 80462197 G T 1 0 0 0 0 1 0 0 0 6393 1261 44 2 2 GNAT3 7 80462197 Missense_Mutation SNP G C3L-00144_T 5314049 80462197 78883776 686 4757 HGF 0 . GRCh38 7 81745095 81745095 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.651G>T p.Glu217Asp p.E217D ENST00000222390 6/18 368 289 79 308 308 0 strelka-varscan-mutect HGF,missense_variant,p.Glu217Asp,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Glu212Asp,ENST00000457544,NM_001010932.1;HGF,missense_variant,p.Glu217Asp,ENST00000444829,NM_001010931.1;HGF,missense_variant,p.Glu212Asp,ENST00000453411,NM_001010933.1; A ENST00000222390 Transcript missense_variant 878/5989 651/2187 217/728 E/D gaG/gaT 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 deleterious(0.03) 6/18 PROSITE_profiles:PS50070,hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 81745095 81745095 C A 1 0 0 0 0 1 0 0 0 6969 912 32 2 2 HGF 7 81745095 Missense_Mutation SNP C C3L-00144_T 1282898 81745095 77600878 687 4758 CACNA2D1 0 . GRCh38 7 81964301 81964301 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.2633C>T p.Ser878Leu p.S878L ENST00000356860 33/39 199 173 26 179 179 0 strelka-varscan-mutect CACNA2D1,missense_variant,p.Ser878Leu,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Ser890Leu,ENST00000356253,;CACNA2D1,downstream_gene_variant,,ENST00000486539,;CACNA2D1,upstream_gene_variant,,ENST00000469297,; A ENST00000356860 Transcript missense_variant 2972/7563 2633/3276 878/1091 S/L tCa/tTa 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 deleterious(0) 33/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 81964301 81964301 G A 1 0 0 0 0 1 0 0 0 2236 1294 45 3 3 CACNA2D1 7 81964301 Missense_Mutation SNP G C3L-00144_T 219206 81964301 77381672 688 4759 CACNA2D1 0 . GRCh38 7 81984659 81984659 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1849G>C p.Glu617Gln p.E617Q ENST00000356860 22/39 387 321 66 327 327 0 strelka-varscan-mutect CACNA2D1,missense_variant,p.Glu617Gln,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Glu636Gln,ENST00000356253,;CACNA2D1,missense_variant,p.Glu135Gln,ENST00000443883,; G ENST00000356860 Transcript missense_variant 2188/7563 1849/3276 617/1091 E/Q Gaa/Caa 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 tolerated(0.26) 22/39 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 81984659 81984659 C G 1 0 0 0 0 1 0 0 0 2236 922 32 4 4 CACNA2D1 7 81984659 Missense_Mutation SNP C C3L-00144_T 20358 81984659 77361314 689 4760 PCLO 0 . GRCh38 7 82914866 82914866 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.13120G>C p.Ala4374Pro p.A4374P ENST00000333891 7/25 191 137 54 175 175 0 strelka-varscan-mutect PCLO,missense_variant,p.Ala4374Pro,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Ala4374Pro,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Ala1094Pro,ENST00000437081,; G ENST00000333891 Transcript missense_variant 13458/20329 13120/15429 4374/5142 A/P Gcc/Ccc 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.02) 7/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 82914866 82914866 C G 1 0 0 0 0 1 0 0 0 11671 739 26 4 4 PCLO 7 82914866 Missense_Mutation SNP C C3L-00144_T 930207 82914866 76431107 690 4761 PCLO 0 . GRCh38 7 82954786 82954786 + Missense_Mutation SNP C C A rs189561105 C3L-00144_T C3L-00144_N C C c.6167G>T p.Arg2056Met p.R2056M ENST00000333891 5/25 149 129 20 99 99 0 strelka-varscan-mutect PCLO,missense_variant,p.Arg2056Met,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Arg2056Met,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript missense_variant 6505/20329 6167/15429 2056/5142 R/M aGg/aTg rs189561105,COSM1623182,COSM1623183,COSM1623184 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.02) 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 0,1,1,1 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs189561105 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 82954786 82954786 C A 1 0 0 0 0 1 0 0 0 11671 681 24 2 2 PCLO 7 82954786 Missense_Mutation SNP C C3L-00144_T 39920 82954786 76391187 691 4762 RUNDC3B 0 . GRCh38 7 87830016 87830016 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1408C>A p.Leu470Ile p.L470I ENST00000338056 12/12 51 43 8 41 41 0 strelka-varscan-mutect RUNDC3B,missense_variant,p.Leu470Ile,ENST00000338056,NM_138290.2;RUNDC3B,missense_variant,p.Leu453Ile,ENST00000394654,NM_001134405.1;RUNDC3B,missense_variant,p.Leu404Ile,ENST00000493037,NM_001134406.1;SLC25A40,downstream_gene_variant,,ENST00000341119,NM_018843.3;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000312373,; A ENST00000338056 Transcript missense_variant 1819/4099 1408/1422 470/473 L/I Cta/Ata 1 1 RUNDC3B HGNC HGNC:30286 protein_coding YES CCDS5609.1 ENSP00000337732 Q96NL0 UPI0000071425 NM_138290.2 tolerated(0.06) 12/12 hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835 MODERATE SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -19.11117 1 1 1 1 0 A 3 1 12 87830016 87830016 C A 1 0 0 0 0 1 0 0 0 14006 680 24 2 2 RUNDC3B 7 87830016 Missense_Mutation SNP C C3L-00144_T 4875230 87830016 71515957 692 4763 SRI 0 . GRCh38 7 88217187 88217187 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.140G>T p.Gly47Val p.G47V ENST00000265729 3/8 352 326 26 246 244 2 strelka-varscan-mutect SRI,missense_variant,p.Gly47Val,ENST00000265729,NM_003130.3,NM_001256891.1;SRI,missense_variant,p.Gly32Val,ENST00000431660,NM_001256892.1;SRI,missense_variant,p.Gly47Val,ENST00000419179,;SRI,missense_variant,p.Gly32Val,ENST00000394641,NM_198901.1;SRI,missense_variant,p.Gly4Val,ENST00000490437,;CTB-167B5.1,intron_variant,,ENST00000520993,;AC003991.3,upstream_gene_variant,,ENST00000594469,;SRI,missense_variant,p.Gly47Val,ENST00000457606,;SRI,non_coding_transcript_exon_variant,,ENST00000486860,;SRI,non_coding_transcript_exon_variant,,ENST00000488015,;SRI,non_coding_transcript_exon_variant,,ENST00000489079,; A ENST00000265729 Transcript missense_variant 193/2010 140/597 47/198 G/V gGg/gTg 1 -1 SRI HGNC HGNC:11292 protein_coding YES CCDS5612.1 ENSP00000265729 P30626 UPI0000112055 NM_003130.3,NM_001256891.1 deleterious(0) 3/8 Gene3D:1.10.238.10,Pfam_domain:PF13833,PROSITE_profiles:PS50222,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF297,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 88217187 88217187 C A 1 0 0 0 0 1 0 0 0 15510 637 22 2 2 SRI 7 88217187 Missense_Mutation SNP C C3L-00144_T 387171 88217187 71128786 693 4764 STEAP1 0 . GRCh38 7 90159843 90159843 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.55A>T p.Arg19Trp p.R19W ENST00000297205 2/5 149 131 18 159 159 0 strelka-varscan-mutect STEAP1,missense_variant,p.Arg19Trp,ENST00000297205,NM_012449.2;STEAP2-AS1,intron_variant,,ENST00000478318,;STEAP1,non_coding_transcript_exon_variant,,ENST00000475789,;STEAP1,upstream_gene_variant,,ENST00000412573,; T ENST00000297205 Transcript missense_variant 255/1313 55/1020 19/339 R/W Agg/Tgg 1 1 STEAP1 HGNC HGNC:11378 protein_coding YES CCDS5614.1 ENSP00000297205 Q9UHE8 UPI000003C398 NM_012449.2 tolerated_low_confidence(0.11) 2/5 hmmpanther:PTHR14239:SF3,hmmpanther:PTHR14239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 90159843 90159843 A T 1 0 0 0 0 1 0 0 0 15653 411 15 4 4 STEAP1 7 90159843 Missense_Mutation SNP A C3L-00144_T 1942656 90159843 69186130 694 4765 CFAP69 0 . GRCh38 7 90262050 90262051 + Frame_Shift_Del DEL TG TG - novel C3L-00144_T C3L-00144_N TG TG c.354_355delTG p.Cys118TrpfsTer12 p.C118Wfs*12 ENST00000389297 4/23 145 119 26 196 196 0 sindel-varindel-pindel CFAP69,frameshift_variant,p.Cys118TrpfsTer12,ENST00000389297,NM_001039706.2;CFAP69,frameshift_variant,p.Cys118TrpfsTer12,ENST00000497910,NM_001160138.1;CFAP69,frameshift_variant,p.Cys58TrpfsTer12,ENST00000457170,;AC002064.4,downstream_gene_variant,,ENST00000420245,;CFAP69,splice_donor_variant,,ENST00000463311,;CFAP69,intron_variant,,ENST00000485791,;CFAP69,frameshift_variant,p.Cys118TrpfsTer12,ENST00000451029,;CFAP69,frameshift_variant,p.Cys118TrpfsTer4,ENST00000427396,; - ENST00000389297 Transcript frameshift_variant 601-602/3902 350-351/2826 117/941 L/X cTG/c 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 4/23 hmmpanther:PTHR14716:SF0,hmmpanther:PTHR14716 HIGH 1 deletion 1 4 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 90262050 90262050 TG - 1 0 1 0 1 0 0 0 0 3030 1580 55 0 0 CFAP69 7 90262050 Frame_Shift_Del DEL TG C3L-00144_T 102207 90262050 69083923 695 4766 HEPACAM2 0 . GRCh38 7 93208658 93208658 + Missense_Mutation SNP C C A rs141573896 C3L-00144_T C3L-00144_N C C c.1003G>T p.Asp335Tyr p.D335Y ENST00000453812 5/11 305 274 31 244 244 0 strelka-varscan-mutect HEPACAM2,missense_variant,p.Asp312Tyr,ENST00000394468,NM_001039372.2;HEPACAM2,missense_variant,p.Asp300Tyr,ENST00000341723,NM_198151.2;HEPACAM2,missense_variant,p.Asp300Tyr,ENST00000440868,NM_001288810.1;HEPACAM2,missense_variant,p.Asp335Tyr,ENST00000453812,NM_001288804.1;HEPACAM2,upstream_gene_variant,,ENST00000492616,; A ENST00000453812 Transcript missense_variant 1026/1869 1003/1458 335/485 D/Y Gac/Tac rs141573896 1 -1 HEPACAM2 HGNC HGNC:27364 protein_coding YES CCDS75632.1 ENSP00000390204 A8MVW5 UPI000198CEF3 NM_001288804.1 deleterious(0) 5/11 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS rs141573896 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 93208658 93208658 C A 1 0 0 0 0 1 0 0 0 6937 855 30 2 2 HEPACAM2 7 93208658 Missense_Mutation SNP C C3L-00144_T 2946608 93208658 66137315 696 4767 COL1A2 0 . GRCh38 7 94408342 94408342 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.700C>T p.Arg234Cys p.R234C ENST00000297268 15/52 464 338 126 338 338 0 strelka-varscan-mutect COL1A2,missense_variant,p.Arg234Cys,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Arg232Cys,ENST00000620463,; T ENST00000297268 Transcript missense_variant 1171/5411 700/4101 234/1366 R/C Cgt/Tgt CM090272,COSM4505760 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 deleterious(0) 15/52 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs1206388800 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 94408342 94408342 C T 1 0 0 0 0 1 0 0 0 3466 652 23 1 1 COL1A2 7 94408342 Missense_Mutation SNP C C3L-00144_T 1199684 94408342 64937631 697 4768 PEG10 0 . GRCh38 7 94664110 94664110 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.782C>A p.Ser261Tyr p.S261Y ENST00000488574 2/2 263 176 87 176 175 1 strelka-varscan-mutect PEG10,missense_variant,p.Ser185Tyr,ENST00000482108,NM_015068.3,NM_001184961.1,NM_001172437.2,NM_001040152.1;PEG10,missense_variant,p.Ser219Tyr,ENST00000615790,NM_001184962.1;PEG10,missense_variant,p.Ser219Tyr,ENST00000612941,;PEG10,missense_variant,p.Ser185Tyr,ENST00000617526,;PEG10,missense_variant,p.Ser261Tyr,ENST00000488574,NM_001172438.2;PEG10,missense_variant,p.Ser261Tyr,ENST00000612748,;PEG10,downstream_gene_variant,,ENST00000613043,;PEG10,intron_variant,,ENST00000493935,;PEG10,upstream_gene_variant,,ENST00000465184,; A ENST00000488574 Transcript missense_variant 999/2587 782/1206 261/401 S/Y tCc/tAc 1 1 PEG10 HGNC HGNC:14005 protein_coding YES CCDS75636.1 ENSP00000418944 B4DSP0 UPI0000037665 NM_001172438.2 tolerated(0.06) 2/2 hmmpanther:PTHR15503:SF10,hmmpanther:PTHR15503 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 94664110 94664110 C A 1 0 0 0 0 1 0 0 0 11807 855 30 2 2 PEG10 7 94664110 Missense_Mutation SNP C C3L-00144_T 255768 94664110 64681863 698 4769 LMTK2 0 . GRCh38 7 98141517 98141517 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.352C>T p.Pro118Ser p.P118S ENST00000297293 3/14 154 133 21 111 111 0 strelka-varscan-mutect LMTK2,missense_variant,p.Pro118Ser,ENST00000297293,NM_014916.3;LMTK2,non_coding_transcript_exon_variant,,ENST00000493372,; T ENST00000297293 Transcript missense_variant 645/8946 352/4512 118/1503 P/S Ccc/Tcc 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 tolerated(0.12) 3/14 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF357 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 98141517 98141517 C T 1 0 0 0 0 1 0 0 0 8786 855 30 3 3 LMTK2 7 98141517 Missense_Mutation SNP C C3L-00144_T 3477407 98141517 61204456 699 4770 AZGP1 0 . GRCh38 7 99968088 99968088 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.671A>T p.Gln224Leu p.Q224L ENST00000411734 3/3 358 256 102 206 206 0 strelka-varscan-mutect AZGP1,missense_variant,p.Gln224Leu,ENST00000411734,;AZGP1,intron_variant,,ENST00000292401,NM_001185.3;AZGP1,intron_variant,,ENST00000419575,;AZGP1,upstream_gene_variant,,ENST00000483612,;AZGP1,intron_variant,,ENST00000477251,;AZGP1,downstream_gene_variant,,ENST00000495765,; A ENST00000411734 Transcript missense_variant 677/2027 671/684 224/227 Q/L cAg/cTg 1 -1 AZGP1 HGNC HGNC:910 protein_coding ENSP00000396093 C9JEV0 UPI0000D4BCFF deleterious_low_confidence(0) 3/3 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 99968088 99968088 T A 1 0 0 0 0 1 0 0 0 1396 1580 55 4 4 AZGP1 7 99968088 Missense_Mutation SNP T C3L-00144_T 1826571 99968088 59377885 700 4771 NYAP1 0 . GRCh38 7 100488928 100488934 + Frame_Shift_Del DEL GCCCGGA GCCCGGA - novel C3L-00144_T C3L-00144_N GCCCGGA GCCCGGA c.1210_1216delCGGAGCC p.Arg404ThrfsTer25 p.R404Tfs*25 ENST00000300179 4/7 64 58 6 60 60 0 sindel-varindel NYAP1,frameshift_variant,p.Arg404ThrfsTer25,ENST00000300179,NM_173564.3;NYAP1,frameshift_variant,p.Arg347ThrfsTer25,ENST00000454988,;NYAP1,upstream_gene_variant,,ENST00000496985,;NYAP1,upstream_gene_variant,,ENST00000489641,; - ENST00000300179 Transcript frameshift_variant 1366-1372/3581 1207-1213/2526 403-405/841 ARS/X GCCCGGAgc/gc 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 4/7 Pfam_domain:PF15439,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 HIGH 1 deletion 2 3 1 PASS . . 0 199 11 0 0 0 0 0 -13.46014 0.9998984 1 1 1 0 - 7 5 12 100488928 100488928 GCCCGGA - 1 0 1 0 1 0 0 0 0 10872 1203 42 0 0 NYAP1 7 100488928 Frame_Shift_Del DEL GCCCGGA C3L-00144_T 520840 100488928 58857045 701 4772 AGFG2 0 . GRCh38 7 100562271 100562271 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.890G>T p.Gly297Val p.G297V ENST00000300176 7/12 134 114 20 92 92 0 strelka-varscan-mutect AGFG2,missense_variant,p.Gly297Val,ENST00000300176,NM_006076.4;AGFG2,missense_variant,p.Gly39Val,ENST00000429987,;AGFG2,non_coding_transcript_exon_variant,,ENST00000474713,;AGFG2,3_prime_UTR_variant,,ENST00000430857,; T ENST00000300176 Transcript missense_variant 1012/4796 890/1446 297/481 G/V gGg/gTg 1 1 AGFG2 HGNC HGNC:5177 protein_coding YES CCDS5697.1 ENSP00000300176 O95081 A4D2D6 UPI000003E7D5 NM_006076.4 tolerated(0.35) 7/12 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF233 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 100562271 100562271 G T 1 0 0 0 0 1 0 0 0 458 1232 43 2 2 AGFG2 7 100562271 Missense_Mutation SNP G C3L-00144_T 73343 100562271 58783702 702 4773 ZAN 0 . GRCh38 7 100765439 100765439 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4355G>T p.Cys1452Phe p.C1452F ENST00000613979 23/48 564 424 140 487 485 2 strelka-varscan-mutect ZAN,missense_variant,p.Cys1452Phe,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Cys1452Phe,ENST00000618565,;ZAN,missense_variant,p.Cys1452Phe,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Cys1452Phe,ENST00000546292,;ZAN,missense_variant,p.Cys1452Phe,ENST00000542585,;ZAN,missense_variant,p.Cys1452Phe,ENST00000538115,;ZAN,missense_variant,p.Cys1452Phe,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; T ENST00000613979 Transcript missense_variant 4520/8669 4355/8439 1452/2812 C/F tGc/tTc 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 deleterious(0) 23/48 Gene3D:2.10.25.10,Pfam_domain:PF01826,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221,SMART_domains:SM00181,Superfamily_domains:SSF57567 MODERATE 1 SNV 1 1 PASS rs1416699213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 100765439 100765439 G T 1 0 0 0 0 1 0 0 0 18074 1319 46 2 2 ZAN 7 100765439 Missense_Mutation SNP G C3L-00144_T 203168 100765439 58580534 703 4774 SLC12A9 0 . GRCh38 7 100857062 100857062 + Missense_Mutation SNP G G T rs775068338 C3L-00144_T C3L-00144_N G G c.643G>T p.Gly215Trp p.G215W ENST00000354161 5/14 314 278 36 265 265 0 strelka-varscan-mutect SLC12A9,missense_variant,p.Gly215Trp,ENST00000354161,NM_020246.3;SLC12A9,missense_variant,p.Gly215Trp,ENST00000540482,NM_001267812.1;SLC12A9,missense_variant,p.Gly126Trp,ENST00000415287,NM_001267814.1;SLC12A9,5_prime_UTR_variant,,ENST00000418037,;SLC12A9,intron_variant,,ENST00000416675,;SLC12A9,downstream_gene_variant,,ENST00000434158,;RP11-126L15.4,upstream_gene_variant,,ENST00000412754,;SLC12A9,intron_variant,,ENST00000461016,;SLC12A9,upstream_gene_variant,,ENST00000475623,;SLC12A9,upstream_gene_variant,,ENST00000482184,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000497958,;SLC12A9,intron_variant,,ENST00000448342,;SLC12A9,upstream_gene_variant,,ENST00000487651,;SLC12A9,downstream_gene_variant,,ENST00000462106,; T ENST00000354161 Transcript missense_variant 768/3273 643/2745 215/914 G/W Ggg/Tgg rs775068338,COSM1225905 1 1 SLC12A9 HGNC HGNC:17435 protein_coding YES CCDS5707.1 ENSP00000275730 Q9BXP2 UPI000006CD28 NM_020246.3 deleterious(0) 5/14 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF52,Pfam_domain:PF00324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775068338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 100857062 100857062 G T 1 0 0 0 0 1 0 0 0 14655 1232 43 2 2 SLC12A9 7 100857062 Missense_Mutation SNP G C3L-00144_T 91623 100857062 58488911 704 4775 MUC12 0 . GRCh38 7 100990844 100990844 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.281C>A p.Thr94Lys p.T94K ENST00000536621 2/12 500 449 51 403 403 0 strelka-varscan-mutect MUC12,missense_variant,p.Thr237Lys,ENST00000379442,;MUC12,missense_variant,p.Thr94Lys,ENST00000536621,NM_001164462.1; A ENST00000536621 Transcript missense_variant 281/16321 281/16008 94/5335 T/K aCa/aAa 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 deleterious_low_confidence(0) 2/12 MODERATE 1 SNV 5 1 PASS rs1433284178 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 100990844 100990844 C A 1 0 0 0 0 1 0 0 0 9969 478 17 2 2 MUC12 7 100990844 Missense_Mutation SNP C C3L-00144_T 133782 100990844 58355129 705 4776 MUC12 0 . GRCh38 7 100992801 100992801 + Silent SNP G G T rs778671820 C3L-00144_T C3L-00144_N G G c.2238G>T p.= p.P746P ENST00000536621 2/12 724 644 80 663 662 1 varscan-mutect MUC12,synonymous_variant,p.=,ENST00000379442,;MUC12,synonymous_variant,p.=,ENST00000536621,NM_001164462.1; T ENST00000536621 Transcript synonymous_variant 2238/16321 2238/16008 746/5335 P ccG/ccT rs778671820 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 2/12 LOW 1 SNV 5 1 PASS rs778671820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 100992801 100992801 G T 1 0 0 0 0 0 0 0 1 9969 1103 39 1 1 MUC12 7 100992801 Silent SNP G C3L-00144_T 1957 100992801 58353172 706 4777 MUC12 0 . GRCh38 7 100993101 100993101 + Silent SNP C C A rs538991481 C3L-00144_T C3L-00144_N C C c.2538C>A p.= p.G846G ENST00000536621 2/12 530 468 62 442 442 0 varscan-mutect MUC12,synonymous_variant,p.=,ENST00000379442,;MUC12,synonymous_variant,p.=,ENST00000536621,NM_001164462.1; A ENST00000536621 Transcript synonymous_variant 2538/16321 2538/16008 846/5335 G ggC/ggA rs538991481,COSM4412405,COSM4412406 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 2/12 Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs538991481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 100993101 100993101 C A 1 0 0 0 0 0 0 0 1 9969 755 27 1 1 MUC12 7 100993101 Silent SNP C C3L-00144_T 300 100993101 58352872 707 4778 MUC12 0 . GRCh38 7 101005217 101005217 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.14654C>T p.Pro4885Leu p.P4885L ENST00000536621 2/12 347 239 108 254 254 0 strelka-varscan-mutect MUC12,missense_variant,p.Pro5028Leu,ENST00000379442,;MUC12,missense_variant,p.Pro4885Leu,ENST00000536621,NM_001164462.1; T ENST00000536621 Transcript missense_variant 14654/16321 14654/16008 4885/5335 P/L cCa/cTa 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 tolerated(0.1) 2/12 MODERATE 1 SNV 5 1 PASS rs962369951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101005217 101005217 C T 1 0 0 0 0 1 0 0 0 9969 594 21 3 3 MUC12 7 101005217 Missense_Mutation SNP C C3L-00144_T 12116 101005217 58340756 708 4779 MUC17 0 . GRCh38 7 101040342 101040342 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.8926A>T p.Ser2976Cys p.S2976C ENST00000306151 3/13 139 104 35 99 99 0 strelka-varscan-mutect MUC17,missense_variant,p.Ser2976Cys,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ser2976Cys,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; T ENST00000306151 Transcript missense_variant 8990/14247 8926/13482 2976/4493 S/C Agc/Tgc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101040342 101040342 A T 1 0 0 0 0 1 0 0 0 9973 188 7 4 4 MUC17 7 101040342 Missense_Mutation SNP A C3L-00144_T 35125 101040342 58305631 709 4780 FBXL13 0 . GRCh38 7 103025128 103025128 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.430G>A p.Val144Ile p.V144I ENST00000313221 6/20 272 202 70 215 215 0 strelka-varscan-mutect FBXL13,missense_variant,p.Val144Ile,ENST00000313221,NM_145032.3;FBXL13,missense_variant,p.Val234Ile,ENST00000379308,;FBXL13,missense_variant,p.Val144Ile,ENST00000436908,;FBXL13,missense_variant,p.Val144Ile,ENST00000379305,NM_001287150.1;FBXL13,missense_variant,p.Val144Ile,ENST00000455112,NM_001111038.1;FBXL13,missense_variant,p.Val144Ile,ENST00000456695,;FBXL13,downstream_gene_variant,,ENST00000440067,;RP11-645N11.3,upstream_gene_variant,,ENST00000447336,;FBXL13,non_coding_transcript_exon_variant,,ENST00000471074,;FBXL13,missense_variant,p.Val234Ile,ENST00000448002,; T ENST00000313221 Transcript missense_variant 857/2744 430/2208 144/735 V/I Gtc/Atc 1 -1 FBXL13 HGNC HGNC:21658 protein_coding YES CCDS5726.1 ENSP00000321927 Q8NEE6 UPI000020F830 NM_145032.3 tolerated(0.43) 6/20 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF485 MODERATE 1 SNV 2 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999994 1 1 1 0 T 3 4 12 103025128 103025128 C T 1 0 0 0 0 1 0 0 0 5573 565 20 3 3 FBXL13 7 103025128 Missense_Mutation SNP C C3L-00144_T 1984786 103025128 56320845 710 4781 RELN 0 . GRCh38 7 103551076 103551076 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.6293A>T p.His2098Leu p.H2098L ENST00000428762 41/65 615 544 71 508 507 1 strelka-varscan-mutect RELN,missense_variant,p.His2098Leu,ENST00000424685,;RELN,missense_variant,p.His2098Leu,ENST00000428762,NM_005045.3;RELN,missense_variant,p.His2098Leu,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 6453/11571 6293/10383 2098/3460 H/L cAc/cTc 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.12) 41/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 103551076 103551076 T A 1 0 0 0 0 1 0 0 0 13390 1696 59 4 4 RELN 7 103551076 Missense_Mutation SNP T C3L-00144_T 525948 103551076 55794897 711 4782 RELN 0 . GRCh38 7 103917096 103917096 + Missense_Mutation SNP C C A rs761478356 C3L-00144_T C3L-00144_N C C c.316G>T p.Gly106Cys p.G106C ENST00000428762 2/65 392 353 39 316 315 1 strelka-varscan-mutect RELN,missense_variant,p.Gly106Cys,ENST00000424685,;RELN,missense_variant,p.Gly106Cys,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Gly106Cys,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 476/11571 316/10383 106/3460 G/C Ggt/Tgt rs761478356 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious_low_confidence(0.03) 2/65 Low_complexity_(Seg):seg,PROSITE_profiles:PS51019,Pfam_domain:PF02014 MODERATE 1 SNV 5 1 PASS rs761478356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 103917096 103917096 C A 1 0 0 0 0 1 0 0 0 13390 681 24 2 2 RELN 7 103917096 Missense_Mutation SNP C C3L-00144_T 366020 103917096 55428877 712 4783 PIK3CG 0 . GRCh38 7 106867687 106867687 + Silent SNP C C T rs796408783 C3L-00144_T C3L-00144_N C C c.126C>T p.= p.F42F ENST00000359195 2/11 207 187 20 149 149 0 strelka-varscan-mutect PIK3CG,synonymous_variant,p.=,ENST00000359195,NM_002649.3;PIK3CG,synonymous_variant,p.=,ENST00000496166,NM_001282426.1;PIK3CG,synonymous_variant,p.=,ENST00000440650,NM_001282427.1;PIK3CG,intron_variant,,ENST00000473541,; T ENST00000359195 Transcript synonymous_variant 436/5377 126/3309 42/1102 F ttC/ttT rs796408783,COSM3254552 1 1 PIK3CG HGNC HGNC:8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 A0A024R720 UPI00000746B8 NM_002649.3 2/11 PROSITE_profiles:PS51544,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34 0,1 LOW 1 SNV 1 0,1 1 PASS rs796408783 . 0 207 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 12 106867687 106867687 C T 1 0 0 0 0 0 0 0 1 12011 883 31 1 1 PIK3CG 7 106867687 Silent SNP C C3L-00144_T 2950591 106867687 52478286 713 4784 LAMB1 0 . GRCh38 7 107961266 107961266 + Missense_Mutation SNP C C G rs773534292 C3L-00144_T C3L-00144_N C C c.2049G>C p.Glu683Asp p.E683D ENST00000222399 17/34 264 202 62 201 201 0 strelka-varscan-mutect LAMB1,missense_variant,p.Glu707Asp,ENST00000393561,;LAMB1,missense_variant,p.Glu683Asp,ENST00000222399,NM_002291.2;LAMB1,missense_variant,p.Glu683Asp,ENST00000393560,; G ENST00000222399 Transcript missense_variant 2280/5725 2049/5361 683/1786 E/D gaG/gaC rs773534292 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 tolerated(0.08) 17/34 PROSITE_profiles:PS51116 MODERATE 1 SNV 1 1 PASS rs773534292 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 107961266 107961266 C G 1 0 0 0 0 1 0 0 0 8514 796 28 4 4 LAMB1 7 107961266 Missense_Mutation SNP C C3L-00144_T 1093579 107961266 51384707 714 4785 GPR85 0 . GRCh38 7 113084021 113084021 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.701G>T p.Gly234Val p.G234V ENST00000297146 3/3 138 99 39 101 100 1 strelka-varscan-mutect GPR85,missense_variant,p.Gly234Val,ENST00000297146,NM_001146265.1,NM_018970.6;GPR85,missense_variant,p.Gly234Val,ENST00000424100,NM_001146267.1;GPR85,missense_variant,p.Gly234Val,ENST00000449591,NM_001146266.1;GPR85,downstream_gene_variant,,ENST00000438062,;GPR85,downstream_gene_variant,,ENST00000449735,;GPR85,downstream_gene_variant,,ENST00000487573,;GPR85,missense_variant,p.Gly234Val,ENST00000610164,; A ENST00000297146 Transcript missense_variant 1305/5079 701/1113 234/370 G/V gGa/gTa 1 -1 GPR85 HGNC HGNC:4536 protein_coding YES CCDS5758.1 ENSP00000297146 P60893 A4D0T8 UPI0000004048 NM_001146265.1,NM_018970.6 deleterious(0) 3/3 Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 113084021 113084021 C A 1 0 0 0 0 1 0 0 0 6596 855 30 2 2 GPR85 7 113084021 Missense_Mutation SNP C C3L-00144_T 5122755 113084021 46261952 715 4786 CAPZA2 0 . GRCh38 7 116904377 116904377 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.420C>T p.= p.V140V ENST00000361183 5/10 154 112 42 138 138 0 strelka-varscan-mutect CAPZA2,synonymous_variant,p.=,ENST00000361183,NM_006136.2;CAPZA2,synonymous_variant,p.=,ENST00000490693,;CAPZA2,synonymous_variant,p.=,ENST00000628758,;CAPZA2,non_coding_transcript_exon_variant,,ENST00000417431,;CAPZA2,downstream_gene_variant,,ENST00000414148,;CAPZA2,synonymous_variant,p.=,ENST00000426421,;CAPZA2,3_prime_UTR_variant,,ENST00000449080,;CAPZA2,non_coding_transcript_exon_variant,,ENST00000464669,; T ENST00000361183 Transcript synonymous_variant 559/5182 420/861 140/286 V gtC/gtT 1 1 CAPZA2 HGNC HGNC:1490 protein_coding YES CCDS5768.1 ENSP00000354947 P47755 A4D0V4 UPI00001270FC NM_006136.2 5/10 hmmpanther:PTHR10653:SF2,hmmpanther:PTHR10653,Pfam_domain:PF01267,Superfamily_domains:SSF90096 LOW 1 SNV 1 1 PASS rs1022490148 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 116904377 116904377 C T 1 0 0 0 0 0 0 0 1 2336 900 32 3 3 CAPZA2 7 116904377 Silent SNP C C3L-00144_T 3820356 116904377 42441596 716 4787 KCND2 0 . GRCh38 7 120275562 120275562 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.930G>T p.= p.L310L ENST00000331113 1/6 78 59 19 74 74 0 strelka-varscan-mutect KCND2,synonymous_variant,p.=,ENST00000331113,NM_012281.2; T ENST00000331113 Transcript synonymous_variant 1895/5331 930/1893 310/630 L ctG/ctT 1 1 KCND2 HGNC HGNC:6238 protein_coding YES CCDS5776.1 ENSP00000333496 Q9NZV8 A4D0V9 UPI0000073D37 NM_012281.2 1/6 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF159,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00169 LOW 1 SNV 1 1 PASS rs1359896450 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 120275562 120275562 G T 1 0 0 0 0 0 0 0 1 7935 1306 46 2 2 KCND2 7 120275562 Silent SNP G C3L-00144_T 3371185 120275562 39070411 717 4788 CPED1 0 . GRCh38 7 121271378 121271378 + Missense_Mutation SNP T T G rs371287806 C3L-00144_T C3L-00144_N T T c.2816T>G p.Met939Arg p.M939R ENST00000310396 22/23 252 200 52 189 189 0 strelka-varscan-mutect CPED1,missense_variant,p.Met939Arg,ENST00000310396,NM_024913.4; G ENST00000310396 Transcript missense_variant 3283/5340 2816/3081 939/1026 M/R aTg/aGg rs371287806 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 deleterious(0) 22/23 hmmpanther:PTHR14776 MODERATE 1 SNV 1 1 PASS rs371287806 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 121271378 121271378 T G 1 0 0 0 0 1 0 0 0 3598 1464 51 5 5 CPED1 7 121271378 Missense_Mutation SNP T C3L-00144_T 995816 121271378 38074595 718 4789 GRM8 0 . GRCh38 7 126532961 126532961 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.2421A>T p.= p.S807S ENST00000339582 9/11 42 33 9 46 46 0 strelka-varscan-mutect GRM8,synonymous_variant,p.=,ENST00000339582,NM_000845.2;GRM8,synonymous_variant,p.=,ENST00000358373,NM_001127323.1;GRM8,synonymous_variant,p.=,ENST00000444921,;GRM8,downstream_gene_variant,,ENST00000480995,;GRM8,synonymous_variant,p.=,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; A ENST00000339582 Transcript synonymous_variant 3230/4057 2421/2727 807/908 S tcA/tcT 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 9/11 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99923 1 1 1 1 0 A 2 1 12 126532961 126532961 T A 1 0 0 0 0 0 0 0 1 6685 1567 55 4 4 GRM8 7 126532961 Silent SNP T C3L-00144_T 5261583 126532961 32813012 719 4790 ZNF800 0 . GRCh38 7 127374581 127374581 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.755T>A p.Val252Glu p.V252E ENST00000393313 5/6 242 214 28 230 230 0 strelka-varscan-mutect ZNF800,missense_variant,p.Val252Glu,ENST00000393313,;ZNF800,missense_variant,p.Val252Glu,ENST00000265827,NM_176814.4;ZNF800,missense_variant,p.Val252Glu,ENST00000393312,;ZNF800,missense_variant,p.Val252Glu,ENST00000619291,;ZNF800,downstream_gene_variant,,ENST00000434602,;ZNF800,downstream_gene_variant,,ENST00000436992,;ZNF800,downstream_gene_variant,,ENST00000439506,;ZNF800,upstream_gene_variant,,ENST00000485577,; T ENST00000393313 Transcript missense_variant 1347/4358 755/1995 252/664 V/E gTa/gAa 1 -1 ZNF800 HGNC HGNC:27267 protein_coding YES CCDS5795.1 ENSP00000376989 Q2TB10 UPI000020FA03 deleterious(0.01) 5/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50157,hmmpanther:PTHR21020,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 12 127374581 127374581 A T 1 0 0 0 0 1 0 0 0 18754 391 14 4 4 ZNF800 7 127374581 Missense_Mutation SNP A C3L-00144_T 841620 127374581 31971392 720 4791 CCDC136 0 . GRCh38 7 128812106 128812106 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2335A>T p.Thr779Ser p.T779S ENST00000297788 13/18 511 459 52 438 437 1 strelka-varscan-mutect CCDC136,missense_variant,p.Thr779Ser,ENST00000297788,NM_022742.4;CCDC136,missense_variant,p.Thr656Ser,ENST00000494552,;CCDC136,missense_variant,p.Thr370Ser,ENST00000464672,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000378685,NM_001201372.1;CCDC136,upstream_gene_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000485832,;CCDC136,downstream_gene_variant,,ENST00000460941,; T ENST00000297788 Transcript missense_variant 2702/4169 2335/3465 779/1154 T/S Acc/Tcc 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 tolerated_low_confidence(0.75) 13/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 128812106 128812106 A T 1 0 0 0 0 1 0 0 0 2459 159 6 4 4 CCDC136 7 128812106 Missense_Mutation SNP A C3L-00144_T 1437525 128812106 30533867 721 4792 KCP 0 . GRCh38 7 128884003 128884003 + Frame_Shift_Del DEL G G - rs757433051 C3L-00144_T C3L-00144_N G G c.3243delC p.Glu1082ArgfsTer3 p.E1082Rfs*3 ENST00000610776 29/40 128 101 27 132 132 0 sindel-varindel-pindel KCP,frameshift_variant,p.Glu1082ArgfsTer3,ENST00000610776,;KCP,frameshift_variant,p.Glu1086ArgfsTer3,ENST00000613019,;KCP,frameshift_variant,p.Glu1022ArgfsTer3,ENST00000620378,NM_001135914.1;KCP,frameshift_variant,p.Glu1086ArgfsTer3,ENST00000611280,;KCP,upstream_gene_variant,,ENST00000492679,;KCP,upstream_gene_variant,,ENST00000460528,; - ENST00000610776 Transcript frameshift_variant,splice_region_variant 3286/5108 3243/4887 1081/1628 A/X gcC/gc rs757433051 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 29/40 PROSITE_profiles:PS50184,PROSITE_profiles:PS50184,Superfamily_domains:SSF57603 HIGH 1 deletion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 128884003 128884003 G - 1 0 1 0 1 0 0 0 0 8012 1130 39 0 0 KCP 7 128884003 Frame_Shift_Del DEL G C3L-00144_T 71897 128884003 30461970 722 4793 CPA4 0 . GRCh38 7 130298827 130298827 + Missense_Mutation SNP G G T rs759503907 C3L-00144_T C3L-00144_N G G c.150G>T p.Lys50Asn p.K50N ENST00000222482 2/11 196 161 35 159 158 1 strelka-varscan-mutect CPA4,missense_variant,p.Lys50Asn,ENST00000222482,NM_016352.3;CPA4,missense_variant,p.Lys50Asn,ENST00000445470,NM_001163446.1;CPA4,missense_variant,p.Lys50Asn,ENST00000473956,;CPA4,missense_variant,p.Lys50Asn,ENST00000492072,;CPA4,splice_region_variant,,ENST00000486598,;CPA4,intron_variant,,ENST00000493259,;CPA4,splice_region_variant,,ENST00000470542,;CPA4,splice_region_variant,,ENST00000474254,;CPA4,splice_region_variant,,ENST00000490117,;CPA4,splice_region_variant,,ENST00000497388,; T ENST00000222482 Transcript missense_variant,splice_region_variant 178/2797 150/1266 50/421 K/N aaG/aaT rs759503907 1 1 CPA4 HGNC HGNC:15740 protein_coding YES CCDS5818.1 ENSP00000222482 Q9UI42 A4D1M3 UPI0000048F00 NM_016352.3 deleterious(0.01) 2/11 Gene3D:3.30.70.340,Pfam_domain:PF02244,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF50,Superfamily_domains:SSF54897 MODERATE 1 SNV 1 1 PASS rs759503907 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 130298827 130298827 G T 1 0 0 0 0 1 0 0 0 3586 1014 35 2 2 CPA4 7 130298827 Missense_Mutation SNP G C3L-00144_T 1414824 130298827 29047146 723 4794 CPA4 0 . GRCh38 7 130322495 130322495 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1085C>A p.Ala362Asp p.A362D ENST00000222482 11/11 86 68 18 74 73 1 strelka-varscan-mutect CPA4,missense_variant,p.Ala362Asp,ENST00000222482,NM_016352.3;CPA4,missense_variant,p.Ala329Asp,ENST00000445470,NM_001163446.1;CPA4,missense_variant,p.Ala258Asp,ENST00000493259,; A ENST00000222482 Transcript missense_variant 1113/2797 1085/1266 362/421 A/D gCt/gAt 1 1 CPA4 HGNC HGNC:15740 protein_coding YES CCDS5818.1 ENSP00000222482 Q9UI42 A4D1M3 UPI0000048F00 NM_016352.3 deleterious(0) 11/11 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF50,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999912 1 1 1 0 A 3 1 12 130322495 130322495 C A 1 0 0 0 0 1 0 0 0 3586 797 28 2 2 CPA4 7 130322495 Missense_Mutation SNP C C3L-00144_T 23668 130322495 29023478 724 4795 MKLN1 0 . GRCh38 7 131399391 131399391 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.661G>T p.Asp221Tyr p.D221Y ENST00000352689 6/18 171 132 39 187 187 0 strelka-varscan-mutect MKLN1,missense_variant,p.Asp221Tyr,ENST00000352689,NM_001321316.1,NM_001145354.1,NM_013255.4;MKLN1,missense_variant,p.Asp129Tyr,ENST00000421797,;MKLN1,downstream_gene_variant,,ENST00000416992,;MKLN1,downstream_gene_variant,,ENST00000429546,;MKLN1,downstream_gene_variant,,ENST00000446815,;MKLN1,non_coding_transcript_exon_variant,,ENST00000494286,;MKLN1,3_prime_UTR_variant,,ENST00000458153,;MKLN1,non_coding_transcript_exon_variant,,ENST00000494785,; T ENST00000352689 Transcript missense_variant 701/11156 661/2208 221/735 D/Y Gat/Tat 1 1 MKLN1 HGNC HGNC:7109 protein_coding YES CCDS34754.1 ENSP00000323527 Q9UL63 UPI0000034CB0 NM_001321316.1,NM_001145354.1,NM_013255.4 deleterious(0) 6/18 PROSITE_profiles:PS50897,hmmpanther:PTHR15526,hmmpanther:PTHR15526:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 131399391 131399391 G T 1 0 0 0 0 1 0 0 0 9570 1290 45 2 2 MKLN1 7 131399391 Missense_Mutation SNP G C3L-00144_T 1076896 131399391 27946582 725 4796 PLXNA4 0 . GRCh38 7 132133082 132133082 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.5556G>T p.Glu1852Asp p.E1852D ENST00000359827 31/32 190 167 23 144 144 0 strelka-varscan-mutect PLXNA4,missense_variant,p.Glu1852Asp,ENST00000359827,;PLXNA4,missense_variant,p.Glu1852Asp,ENST00000321063,NM_020911.1; A ENST00000359827 Transcript missense_variant 6519/13786 5556/5685 1852/1894 E/D gaG/gaT 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B deleterious(0.01) 31/32 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,Superfamily_domains:SSF48350 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 132133082 132133082 C A 1 0 0 0 0 1 0 0 0 12228 912 32 2 2 PLXNA4 7 132133082 Missense_Mutation SNP C C3L-00144_T 733691 132133082 27212891 726 4797 WDR91 0 . GRCh38 7 135188486 135188486 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1828G>T p.Val610Leu p.V610L ENST00000354475 13/15 232 208 24 245 245 0 strelka-varscan-mutect WDR91,missense_variant,p.Val610Leu,ENST00000354475,NM_014149.3;WDR91,missense_variant,p.Val575Leu,ENST00000423565,;WDR91,non_coding_transcript_exon_variant,,ENST00000466182,;WDR91,non_coding_transcript_exon_variant,,ENST00000462707,;WDR91,non_coding_transcript_exon_variant,,ENST00000497853,;WDR91,downstream_gene_variant,,ENST00000479698,;WDR91,downstream_gene_variant,,ENST00000474411,; A ENST00000354475 Transcript missense_variant 1860/4588 1828/2244 610/747 V/L Gtg/Ttg 1 -1 WDR91 HGNC HGNC:24997 protein_coding YES CCDS34758.1 ENSP00000346466 A4D1P6 UPI000006F2DE NM_014149.3 deleterious(0.02) 13/15 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13083,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 135188486 135188486 C A 1 0 0 0 0 1 0 0 0 17894 478 17 2 2 WDR91 7 135188486 Missense_Mutation SNP C C3L-00144_T 3055404 135188486 24157487 727 4798 NUP205 0 . GRCh38 7 135635633 135635633 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.5112A>G p.= p.L1704L ENST00000285968 36/43 136 119 17 116 115 1 strelka-mutect NUP205,synonymous_variant,p.=,ENST00000285968,NM_015135.2;NUP205,3_prime_UTR_variant,,ENST00000477620,;NUP205,non_coding_transcript_exon_variant,,ENST00000607647,;NUP205,non_coding_transcript_exon_variant,,ENST00000461255,; G ENST00000285968 Transcript synonymous_variant 5138/6266 5112/6039 1704/2012 L ctA/ctG 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 36/43 hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 135635633 135635633 A G 1 0 0 0 0 0 0 0 1 10824 378 14 5 5 NUP205 7 135635633 Silent SNP A C3L-00144_T 447147 135635633 23710340 728 4799 DGKI 0 . GRCh38 7 137487615 137487615 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2377C>A p.Gln793Lys p.Q793K ENST00000288490 23/34 200 171 29 166 166 0 strelka-varscan-mutect DGKI,missense_variant,p.Gln493Lys,ENST00000453654,;DGKI,missense_variant,p.Gln796Lys,ENST00000424189,;DGKI,missense_variant,p.Gln775Lys,ENST00000446122,;DGKI,missense_variant,p.Gln793Lys,ENST00000288490,NM_004717.2;DGKI,missense_variant,p.Gln660Lys,ENST00000614521,;DGKI,non_coding_transcript_exon_variant,,ENST00000460662,; T ENST00000288490 Transcript missense_variant 2378/3895 2377/3198 793/1065 Q/K Cag/Aag COSM1144417,COSM5300562,COSM599107 1 -1 DGKI HGNC HGNC:2855 protein_coding YES CCDS5845.1 ENSP00000288490 O75912 UPI000012DD23 NM_004717.2 tolerated(0.07) 23/34 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 207 0 0 2 0 0 0 -14.20636 0.9965863 1 1 1 0 T 3 4 12 137487615 137487615 G T 1 0 0 0 0 1 0 0 0 4277 1391 48 2 2 DGKI 7 137487615 Missense_Mutation SNP G C3L-00144_T 1851982 137487615 21858358 729 4800 KIAA1549 0 . GRCh38 7 138871185 138871185 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.4523T>C p.Val1508Ala p.V1508A ENST00000422774 13/20 253 223 30 212 212 0 strelka-varscan-mutect KIAA1549,missense_variant,p.Val1508Ala,ENST00000440172,NM_020910.2;KIAA1549,missense_variant,p.Val1508Ala,ENST00000422774,NM_001164665.1; G ENST00000422774 Transcript missense_variant 4572/6283 4523/5853 1508/1950 V/A gTg/gCg 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 deleterious(0.01) 13/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590,Pfam_domain:PF12877 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 138871185 138871185 A G 1 0 0 0 0 1 0 0 0 8120 159 6 5 5 KIAA1549 7 138871185 Missense_Mutation SNP A C3L-00144_T 1383570 138871185 20474788 730 4801 KIAA1549 0 . GRCh38 7 138894398 138894398 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.3976A>T p.Thr1326Ser p.T1326S ENST00000422774 10/20 254 207 47 227 227 0 strelka-varscan-mutect KIAA1549,missense_variant,p.Thr1326Ser,ENST00000440172,NM_020910.2;KIAA1549,missense_variant,p.Thr1326Ser,ENST00000422774,NM_001164665.1; A ENST00000422774 Transcript missense_variant 4025/6283 3976/5853 1326/1950 T/S Aca/Tca 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 tolerated(0.15) 10/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590,Pfam_domain:PF12877 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 138894398 138894398 T A 1 0 0 0 0 1 0 0 0 8120 1696 59 4 4 KIAA1549 7 138894398 Missense_Mutation SNP T C3L-00144_T 23213 138894398 20451575 731 4802 KIAA1549 0 . GRCh38 7 138918367 138918367 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1259G>T p.Trp420Leu p.W420L ENST00000422774 2/20 186 151 35 172 172 0 strelka-varscan-mutect KIAA1549,missense_variant,p.Trp420Leu,ENST00000440172,NM_020910.2;KIAA1549,missense_variant,p.Trp420Leu,ENST00000422774,NM_001164665.1; A ENST00000422774 Transcript missense_variant 1308/6283 1259/5853 420/1950 W/L tGg/tTg 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 tolerated(0.55) 2/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590 MODERATE 1 SNV 1 1 PASS rs35969647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 138918367 138918367 C A 1 0 0 0 0 1 0 0 0 8120 595 21 2 2 KIAA1549 7 138918367 Missense_Mutation SNP C C3L-00144_T 23969 138918367 20427606 732 4803 TTC26 0 . GRCh38 7 139178518 139178518 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.1162T>G p.Tyr388Asp p.Y388D ENST00000464848 14/18 172 136 36 118 117 1 strelka-varscan-mutect TTC26,missense_variant,p.Tyr388Asp,ENST00000464848,NM_024926.3;TTC26,missense_variant,p.Tyr388Asp,ENST00000430935,NM_001144920.2;TTC26,missense_variant,p.Tyr357Asp,ENST00000343187,NM_001144923.2,NM_001287513.1;TTC26,missense_variant,p.Tyr281Asp,ENST00000478836,;TTC26,missense_variant,p.Tyr257Asp,ENST00000495038,NM_001287512.1;TTC26,3_prime_UTR_variant,,ENST00000476296,;RP11-365F18.3,upstream_gene_variant,,ENST00000489759,; G ENST00000464848 Transcript missense_variant 1242/4299 1162/1665 388/554 Y/D Tac/Gac 1 1 TTC26 HGNC HGNC:21882 protein_coding YES CCDS5852.1 ENSP00000419279 A0AVF1 UPI000020FBAD NM_024926.3 deleterious(0) 14/18 hmmpanther:PTHR14781:SF0,hmmpanther:PTHR14781,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 139178518 139178518 T G 1 0 0 0 0 1 0 0 0 17202 1768 61 5 5 TTC26 7 139178518 Missense_Mutation SNP T C3L-00144_T 260151 139178518 20167455 733 4804 KLRG2 0 . GRCh38 7 139480222 139480222 + Silent SNP C C A rs754933783 C3L-00144_T C3L-00144_N C C c.783G>T p.= p.L261L ENST00000340940 2/5 186 159 27 190 190 0 strelka-varscan-mutect KLRG2,synonymous_variant,p.=,ENST00000340940,NM_198508.2;KLRG2,intron_variant,,ENST00000393039,; A ENST00000340940 Transcript synonymous_variant 853/2197 783/1230 261/409 L ctG/ctT rs754933783 1 -1 KLRG2 HGNC HGNC:24778 protein_coding YES CCDS5854.1 ENSP00000339356 A4D1S0 UPI00001C0C37 NM_198508.2 2/5 hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF133,Superfamily_domains:SSF56436,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs754933783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 139480222 139480222 C A 1 0 0 0 0 0 0 0 1 8292 465 17 2 2 KLRG2 7 139480222 Silent SNP C C3L-00144_T 301704 139480222 19865751 734 4805 TBXAS1 0 . GRCh38 7 139957667 139957667 + Missense_Mutation SNP G G T rs568328354 C3L-00144_T C3L-00144_N G G c.863G>T p.Arg288Leu p.R288L ENST00000416849 13/18 439 360 79 392 391 1 strelka-varscan-mutect TBXAS1,missense_variant,p.Arg288Leu,ENST00000416849,NM_001166253.1;TBXAS1,missense_variant,p.Arg242Leu,ENST00000263552,NM_001130966.2,NM_001061.4;TBXAS1,missense_variant,p.Arg241Leu,ENST00000336425,;TBXAS1,missense_variant,p.Arg174Leu,ENST00000425687,NM_001166254.1;TBXAS1,missense_variant,p.Arg287Leu,ENST00000458722,;TBXAS1,missense_variant,p.Arg241Leu,ENST00000448866,;TBXAS1,missense_variant,p.Arg242Leu,ENST00000414508,NM_030984.3;TBXAS1,missense_variant,p.Arg241Leu,ENST00000411653,;TBXAS1,non_coding_transcript_exon_variant,,ENST00000462275,;TBXAS1,3_prime_UTR_variant,,ENST00000422328,NM_001314028.1;TBXAS1,non_coding_transcript_exon_variant,,ENST00000469630,;TBXAS1,non_coding_transcript_exon_variant,,ENST00000494876,;TBXAS1,downstream_gene_variant,,ENST00000476637,; T ENST00000416849 Transcript missense_variant 1401/2505 863/1743 288/580 R/L cGg/cTg rs568328354 1 1 TBXAS1 HGNC HGNC:11609 protein_coding YES CCDS55174.1 ENSP00000389414 A0A0C4DH47 UPI00017A722C NM_001166253.1 deleterious(0.01) 13/18 hmmpanther:PTHR24301,hmmpanther:PTHR24301:SF3,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 5 1 PASS rs568328354 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 139957667 139957667 G T 1 0 0 0 0 1 0 0 0 16068 1116 39 1 1 TBXAS1 7 139957667 Missense_Mutation SNP G C3L-00144_T 477445 139957667 19388306 735 4806 OR9A4 0 . GRCh38 7 141919508 141919508 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.633G>T p.Leu211Phe p.L211F ENST00000548136 1/1 286 256 30 260 258 2 strelka-varscan-mutect OR9A4,missense_variant,p.Leu211Phe,ENST00000548136,NM_001001656.1;MGAM,intron_variant,,ENST00000465654,;MGAM,intron_variant,,ENST00000497554,; T ENST00000548136 Transcript missense_variant 692/1093 633/945 211/314 L/F ttG/ttT 1 1 OR9A4 HGNC HGNC:15095 protein_coding YES CCDS43661.1 ENSP00000448789 Q8NGU2 A0A126GVB1 UPI0000041D24 NM_001001656.1 deleterious(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF216,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 141919508 141919508 G T 1 0 0 0 0 1 0 0 0 11316 1281 45 2 2 OR9A4 7 141919508 Missense_Mutation SNP G C3L-00144_T 1961841 141919508 17426465 736 4807 MGAM 0 . GRCh38 7 142027642 142027642 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1128G>T p.Trp376Cys p.W376C ENST00000549489 10/48 223 188 35 194 194 0 strelka-varscan-mutect MGAM,missense_variant,p.Trp376Cys,ENST00000475668,;MGAM,missense_variant,p.Trp376Cys,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Trp376Cys,ENST00000620571,;MGAM,upstream_gene_variant,,ENST00000495045,; T ENST00000549489 Transcript missense_variant 1223/6525 1128/5574 376/1857 W/C tgG/tgT 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 10/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142027642 142027642 G T 1 0 0 0 0 1 0 0 0 9499 1241 43 2 2 MGAM 7 142027642 Missense_Mutation SNP G C3L-00144_T 108134 142027642 17318331 737 4808 MGAM 0 . GRCh38 7 142065350 142065350 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.4500G>C p.= p.V1500V ENST00000549489 38/48 214 187 27 201 201 0 strelka-varscan-mutect MGAM,synonymous_variant,p.=,ENST00000475668,;MGAM,synonymous_variant,p.=,ENST00000549489,NM_004668.2;MGAM,synonymous_variant,p.=,ENST00000620571,; C ENST00000549489 Transcript synonymous_variant 4595/6525 4500/5574 1500/1857 V gtG/gtC 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 38/48 Pfam_domain:PF01055,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 142065350 142065350 G C 1 0 0 0 0 0 0 0 1 9499 1277 45 4 4 MGAM 7 142065350 Silent SNP G C3L-00144_T 37708 142065350 17280623 738 4809 MGAM 0 . GRCh38 7 142085944 142085944 + Silent SNP C C A rs762414046 C3L-00144_T C3L-00144_N C C c.6619C>A p.= p.R2207R ENST00000475668 55/71 138 120 18 110 110 0 strelka-varscan-mutect MGAM,synonymous_variant,p.=,ENST00000475668,;MGAM,intron_variant,,ENST00000549489,NM_004668.2;MGAM,intron_variant,,ENST00000620571,; A ENST00000475668 Transcript synonymous_variant 6673/9172 6619/8262 2207/2753 R Cgg/Agg rs762414046,COSM1596852 1 1 MGAM HGNC HGNC:7043 protein_coding ENSP00000417515 E7ER45 UPI0002B832FC 55/71 Pfam_domain:PF01055,Superfamily_domains:SSF51445 0,1 LOW SNV 5 0,1 1 PASS rs762414046 . 10 197 0 3 0 0 0 0 -20 0.9999866 1 1 1 0 A 2 1 12 142085944 142085944 C A 1 0 0 0 0 0 0 0 1 9499 759 27 1 1 MGAM 7 142085944 Silent SNP C C3L-00144_T 20594 142085944 17260029 739 4810 MGAM2 0 . GRCh38 7 142137453 142137453 + Missense_Mutation SNP C C A rs560004161 C3L-00144_T C3L-00144_N C C c.868C>A p.Pro290Thr p.P290T ENST00000477922 9/48 99 85 14 91 91 0 strelka-varscan-mutect MGAM2,missense_variant,p.Pro290Thr,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Pro290Thr,ENST00000550469,; A ENST00000477922 Transcript missense_variant 922/7867 868/7548 290/2515 P/T Cct/Act rs560004161,COSM2862677 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 9/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF74650 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs560004161 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 142137453 142137453 C A 1 0 0 0 0 1 0 0 0 9500 855 30 2 2 MGAM2 7 142137453 Missense_Mutation SNP C C3L-00144_T 51509 142137453 17208520 740 4811 MGAM2 0 . GRCh38 7 142158285 142158285 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2116C>A p.Gln706Lys p.Q706K ENST00000477922 19/48 208 180 28 208 207 1 strelka-varscan-mutect MGAM2,missense_variant,p.Gln706Lys,ENST00000477922,NM_001293626.1; A ENST00000477922 Transcript missense_variant 2170/7867 2116/7548 706/2515 Q/K Cag/Aag 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 19/48 Pfam_domain:PF01055,Superfamily_domains:SSF51011 MODERATE 1 SNV 5 1 PASS rs1331520067 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 142158285 142158285 C A 1 0 0 0 0 1 0 0 0 9500 711 25 2 2 MGAM2 7 142158285 Missense_Mutation SNP C C3L-00144_T 20832 142158285 17187688 741 4812 MGAM2 0 . GRCh38 7 142159318 142159318 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2195A>T p.Asp732Val p.D732V ENST00000477922 20/48 220 195 25 197 197 0 strelka-varscan-mutect MGAM2,missense_variant,p.Asp732Val,ENST00000477922,NM_001293626.1; T ENST00000477922 Transcript missense_variant 2249/7867 2195/7548 732/2515 D/V gAt/gTt 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.01) 20/48 Pfam_domain:PF01055,Superfamily_domains:SSF51011 MODERATE 1 SNV 5 1 PASS rs1313498849 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142159318 142159318 A T 1 0 0 0 0 1 0 0 0 9500 333 12 4 4 MGAM2 7 142159318 Missense_Mutation SNP A C3L-00144_T 1033 142159318 17186655 742 4813 MGAM2 0 . GRCh38 7 142197532 142197532 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.4765C>A p.= p.R1589R ENST00000477922 41/48 141 127 14 161 161 0 strelka-varscan-mutect MGAM2,synonymous_variant,p.=,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript synonymous_variant 4819/7867 4765/7548 1589/2515 R Cgg/Agg 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 41/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51011 LOW 1 SNV 5 1 PASS rs1256930355 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 142197532 142197532 C A 1 0 0 0 0 0 0 0 1 9500 643 23 1 1 MGAM2 7 142197532 Silent SNP C C3L-00144_T 38214 142197532 17148441 743 4814 PRSS1 0 . GRCh38 7 142752530 142752530 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.554G>T p.Cys185Phe p.C185F ENST00000311737 4/5 415 355 60 353 353 0 strelka-varscan-mutect PRSS1,missense_variant,p.Cys199Phe,ENST00000486171,;PRSS1,missense_variant,p.Cys185Phe,ENST00000612126,;PRSS1,missense_variant,p.Cys185Phe,ENST00000311737,NM_002769.4;PRSS1,missense_variant,p.Cys175Phe,ENST00000619214,;PRSS1,missense_variant,p.Cys135Phe,ENST00000492062,;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS1,non_coding_transcript_exon_variant,,ENST00000463701,;PRSS1,downstream_gene_variant,,ENST00000485223,;PRSS1,downstream_gene_variant,,ENST00000497041,; T ENST00000311737 Transcript missense_variant 560/800 554/744 185/247 C/F tGt/tTt 1 1 PRSS1 HGNC HGNC:9475 protein_coding YES CCDS5872.1 ENSP00000308720 P07477 UPI0000001309 NM_002769.4 deleterious(0) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24264:SF12,hmmpanther:PTHR24264,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142752530 142752530 G T 1 0 0 0 0 1 0 0 0 12761 1377 48 2 2 PRSS1 7 142752530 Missense_Mutation SNP G C3L-00144_T 554998 142752530 16593443 744 4815 PRSS2 0 . GRCh38 7 142773392 142773392 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.369G>T p.= p.L123L ENST00000633969 4/6 322 261 61 292 292 0 strelka-varscan-mutect PRSS2,synonymous_variant,p.=,ENST00000633969,NM_001303414.1;PRSS2,synonymous_variant,p.=,ENST00000632998,;PRSS2,synonymous_variant,p.=,ENST00000632805,;PRSS2,synonymous_variant,p.=,ENST00000539842,NM_002770.3;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS2,non_coding_transcript_exon_variant,,ENST00000618750,;PRSS2,downstream_gene_variant,,ENST00000610835,; T ENST00000633969 Transcript synonymous_variant 385/852 369/786 123/261 L ctG/ctT 1 1 PRSS2 HGNC HGNC:9483 protein_coding YES ENSP00000488437 A6XMV9 UPI0001578AE2 NM_001303414.1 4/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF21,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 142773392 142773392 G T 1 0 0 0 0 0 0 0 1 12764 1306 46 2 2 PRSS2 7 142773392 Silent SNP G C3L-00144_T 20862 142773392 16572581 745 4816 TRPV6 0 . GRCh38 7 142873453 142873453 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1903G>T p.Ala635Ser p.A635S ENST00000359396 13/15 132 109 23 130 129 1 strelka-varscan-mutect TRPV6,missense_variant,p.Ala635Ser,ENST00000359396,NM_018646.5;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;TRPV6,downstream_gene_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000619250,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; A ENST00000359396 Transcript missense_variant 2029/2928 1903/2298 635/765 A/S Gcc/Tcc 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 tolerated(0.07) 13/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 142873453 142873453 C A 1 0 0 0 0 1 0 0 0 17106 753 26 2 2 TRPV6 7 142873453 Missense_Mutation SNP C C3L-00144_T 100061 142873453 16472520 746 4817 TRPV6 0 . GRCh38 7 142874557 142874557 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1506G>T p.Trp502Cys p.W502C ENST00000359396 11/15 288 255 33 280 280 0 strelka-varscan-mutect TRPV6,missense_variant,p.Trp502Cys,ENST00000359396,NM_018646.5;TRPV6,missense_variant,p.Trp85Cys,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;TRPV6,non_coding_transcript_exon_variant,,ENST00000619250,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; A ENST00000359396 Transcript missense_variant 1632/2928 1506/2298 502/765 W/C tgG/tgT 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 deleterious(0) 11/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,Transmembrane_helices:TMhelix,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 142874557 142874557 C A 1 0 0 0 0 1 0 0 0 17106 508 18 2 2 TRPV6 7 142874557 Missense_Mutation SNP C C3L-00144_T 1104 142874557 16471416 747 4818 TRPV6 0 . GRCh38 7 142875576 142875576 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.1134G>C p.= p.L378L ENST00000359396 8/15 74 65 9 67 67 0 strelka-varscan-mutect TRPV6,synonymous_variant,p.=,ENST00000359396,NM_018646.5;TRPV6,intron_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;TRPV6,non_coding_transcript_exon_variant,,ENST00000619250,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; G ENST00000359396 Transcript synonymous_variant 1260/2928 1134/2298 378/765 L ctG/ctC 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 8/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,Transmembrane_helices:TMhelix,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 142875576 142875576 C G 1 0 0 0 0 0 0 0 1 17106 465 17 4 4 TRPV6 7 142875576 Silent SNP C C3L-00144_T 1019 142875576 16470397 748 4819 TRPV5 0 . GRCh38 7 142912551 142912551 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1719G>A p.= p.L573L ENST00000265310 13/15 194 171 23 212 212 0 strelka-varscan-mutect TRPV5,synonymous_variant,p.=,ENST00000265310,NM_019841.6;TRPV5,synonymous_variant,p.=,ENST00000439304,; T ENST00000265310 Transcript synonymous_variant 2068/2952 1719/2190 573/729 L ttG/ttA 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 13/15 Pfam_domain:PF00520,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 142912551 142912551 C T 1 0 0 0 0 0 0 0 1 17105 477 17 3 3 TRPV5 7 142912551 Silent SNP C C3L-00144_T 36975 142912551 16433422 749 4820 KEL 0 . GRCh38 7 142941256 142941256 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2195G>T p.Trp732Leu p.W732L ENST00000355265 19/19 229 197 32 241 240 1 strelka-varscan-mutect KEL,missense_variant,p.Trp732Leu,ENST00000355265,NM_000420.2;C7orf34,downstream_gene_variant,,ENST00000409607,NM_178829.4;C7orf34,downstream_gene_variant,,ENST00000458732,;KEL,downstream_gene_variant,,ENST00000479768,;KEL,downstream_gene_variant,,ENST00000470850,;KEL,downstream_gene_variant,,ENST00000465697,;KEL,downstream_gene_variant,,ENST00000478969,; A ENST00000355265 Transcript missense_variant 2670/2812 2195/2199 732/732 W/L tGg/tTg 1 -1 KEL HGNC HGNC:6308 protein_coding YES CCDS34766.1 ENSP00000347409 P23276 A0A077QP03 UPI000000D923 NM_000420.2 deleterious(0) 19/19 hmmpanther:PTHR11733:SF128,hmmpanther:PTHR11733,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 142941256 142941256 C A 1 0 0 0 0 1 0 0 0 8062 595 21 2 2 KEL 7 142941256 Missense_Mutation SNP C C3L-00144_T 28705 142941256 16404717 750 4821 OR6V1 0 . GRCh38 7 143052771 143052771 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.431G>T p.Gly144Val p.G144V ENST00000418316 1/1 229 193 36 186 185 1 strelka-varscan-mutect OR6V1,missense_variant,p.Gly144Val,ENST00000418316,NM_001001667.1; T ENST00000418316 Transcript missense_variant 452/1028 431/942 144/313 G/V gGg/gTg 1 1 OR6V1 HGNC HGNC:15090 protein_coding YES CCDS47728.1 ENSP00000396085 Q8N148 A0A126GWQ4 UPI0000041C19 NM_001001667.1 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF10,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 143052771 143052771 G T 1 0 0 0 0 1 0 0 0 11281 1232 43 2 2 OR6V1 7 143052771 Missense_Mutation SNP G C3L-00144_T 111515 143052771 16293202 751 4822 CASP2 0 . GRCh38 7 143303841 143303841 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1025G>T p.Gly342Val p.G342V ENST00000310447 9/11 402 329 73 363 363 0 strelka-varscan-mutect CASP2,missense_variant,p.Gly342Val,ENST00000310447,NM_032982.3;CASP2,3_prime_UTR_variant,,ENST00000619992,NM_032983.3;CASP2,non_coding_transcript_exon_variant,,ENST00000493642,;CASP2,3_prime_UTR_variant,,ENST00000350623,;CASP2,non_coding_transcript_exon_variant,,ENST00000472067,; T ENST00000310447 Transcript missense_variant 1266/4225 1025/1359 342/452 G/V gGg/gTg 1 1 CASP2 HGNC HGNC:1503 protein_coding YES CCDS5879.1 ENSP00000312664 P42575 A0A0S2Z3H1 UPI000020F1E8 NM_032982.3 deleterious(0.03) 9/11 hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF151,Pfam_domain:PF00656,PIRSF_domain:PIRSF038001,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 143303841 143303841 G T 1 0 0 0 0 1 0 0 0 2371 1232 43 2 2 CASP2 7 143303841 Missense_Mutation SNP G C3L-00144_T 251070 143303841 16042132 752 4823 OR2A25 0 . GRCh38 7 144074514 144074514 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.295C>A p.Gln99Lys p.Q99K ENST00000408898 1/1 473 406 67 499 498 1 strelka-varscan-mutect OR2A25,missense_variant,p.Gln99Lys,ENST00000408898,NM_001004488.1;OR2A41P,upstream_gene_variant,,ENST00000473586,; A ENST00000408898 Transcript missense_variant 333/1014 295/933 99/310 Q/K Cag/Aag 1 1 OR2A25 HGNC HGNC:19562 protein_coding YES CCDS43669.1 ENSP00000386167 A4D2G3 A0A126GVV5 UPI00002373C5 NM_001004488.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF146,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 144074514 144074514 C A 1 0 0 0 0 1 0 0 0 11055 595 21 2 2 OR2A25 7 144074514 Missense_Mutation SNP C C3L-00144_T 770673 144074514 15271459 753 4824 OR2A2 0 . GRCh38 7 144109702 144109702 + Silent SNP G G T C3L-00144_T C3L-00144_N G G c.120G>T p.= p.G40G ENST00000408979 1/1 232 191 41 209 209 0 strelka-varscan-mutect OR2A2,synonymous_variant,p.=,ENST00000408979,NM_001005480.2;OR2A14,synonymous_variant,p.=,ENST00000627593,; T ENST00000408979 Transcript synonymous_variant 189/1051 120/957 40/318 G ggG/ggT COSM3635481 1 1 OR2A2 HGNC HGNC:8230 protein_coding YES CCDS43671.1 ENSP00000386209 Q6IF42 A0A126GW45 UPI0000061E70 NM_001005480.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF82,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 144109702 144109702 G T 1 0 0 0 0 0 0 0 1 11054 1161 41 2 2 OR2A2 7 144109702 Silent SNP G C3L-00144_T 35188 144109702 15236271 754 4825 OR2A2 0 . GRCh38 7 144110028 144110028 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.446C>A p.Ser149Ter p.S149* ENST00000408979 1/1 166 139 27 182 182 0 strelka-varscan-mutect OR2A2,stop_gained,p.Ser149Ter,ENST00000408979,NM_001005480.2;OR2A14,intron_variant,,ENST00000627593,; A ENST00000408979 Transcript stop_gained 515/1051 446/957 149/318 S/* tCa/tAa 1 1 OR2A2 HGNC HGNC:8230 protein_coding YES CCDS43671.1 ENSP00000386209 Q6IF42 A0A126GW45 UPI0000061E70 NM_001005480.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF82,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 144110028 144110028 C A 1 0 0 0 0 0 1 0 0 11054 838 29 2 2 OR2A2 7 144110028 Nonsense_Mutation SNP C C3L-00144_T 326 144110028 15235945 755 4826 CNTNAP2 0 . GRCh38 7 146116892 146116892 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.16C>A p.Arg6Ser p.R6S ENST00000361727 1/24 88 76 12 102 102 0 strelka-mutect CNTNAP2,missense_variant,p.Arg6Ser,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Arg6Ser,ENST00000625365,;CNTNAP2,upstream_gene_variant,,ENST00000637150,;CNTNAP2,upstream_gene_variant,,ENST00000637105,; A ENST00000361727 Transcript missense_variant 534/9896 16/3996 6/1331 R/S Cgc/Agc 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated_low_confidence(0.06) 1/24 PROSITE_profiles:PS51257,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 146116892 146116892 C A 1 0 0 0 0 1 0 0 0 3428 768 27 1 1 CNTNAP2 7 146116892 Missense_Mutation SNP C C3L-00144_T 2006864 146116892 13229081 756 4827 CNTNAP2 0 . GRCh38 7 146774304 146774304 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.131C>G p.Pro44Arg p.P44R ENST00000361727 2/24 333 291 42 307 307 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Pro44Arg,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Pro44Arg,ENST00000625365,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,;CNTNAP2,upstream_gene_variant,,ENST00000636277,;CNTNAP2,upstream_gene_variant,,ENST00000636600,; G ENST00000361727 Transcript missense_variant 649/9896 131/3996 44/1331 P/R cCc/cGc COSM396243 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 2/24 Gene3D:2.60.120.260,PROSITE_profiles:PS50022,SMART_domains:SM00231,Superfamily_domains:SSF49785 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 146774304 146774304 C G 1 0 0 0 0 1 0 0 0 3428 623 22 4 4 CNTNAP2 7 146774304 Missense_Mutation SNP C C3L-00144_T 657412 146774304 12571669 757 4828 ZNF783 0 . GRCh38 7 149278409 149278409 + Silent SNP G G T rs746987451 C3L-00144_T C3L-00144_N G G c.684G>T p.= p.P228P ENST00000434415 5/6 182 166 16 184 184 0 strelka-varscan-mutect ZNF783,synonymous_variant,p.=,ENST00000434415,NM_001195220.1;ZNF783,non_coding_transcript_exon_variant,,ENST00000489518,;ZNF783,synonymous_variant,p.=,ENST00000378052,;ZNF783,synonymous_variant,p.=,ENST00000476295,;ZNF783,5_prime_UTR_variant,,ENST00000481519,;RP4-800G7.3,upstream_gene_variant,,ENST00000605566,; T ENST00000434415 Transcript synonymous_variant 847/4452 684/1641 228/546 P ccG/ccT rs746987451,COSM295660 1 1 ZNF783 HGNC HGNC:27222 protein_coding YES CCDS56519.1 ENSP00000410890 Q6ZMS7 UPI0000ED938D NM_001195220.1 5/6 hmmpanther:PTHR24390:SF40,hmmpanther:PTHR24390 0,1 LOW 1 SNV 5 0,1 1 PASS rs746987451 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 149278409 149278409 G T 1 0 0 0 0 0 0 0 1 18739 1132 40 1 1 ZNF783 7 149278409 Silent SNP G C3L-00144_T 2504105 149278409 10067564 758 4829 SSPO 0 . GRCh38 7 149806810 149806810 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.8729G>T p.Cys2910Phe p.C2910F ENST00000378016 58/107 232 195 37 180 180 0 strelka-varscan-mutect SSPO,missense_variant,p.Cys2910Phe,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,upstream_gene_variant,,ENST00000481772,; T ENST00000378016 Transcript missense_variant 8729/15589 8729/15453 2910/5150 C/F tGc/tTc 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 58/107 Gene3D:2.10.25.10,Pfam_domain:PF01826,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS rs1295053014 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 149806810 149806810 G T 1 0 0 0 0 1 0 0 0 15566 1319 46 2 2 SSPO 7 149806810 Missense_Mutation SNP G C3L-00144_T 528401 149806810 9539163 759 4830 KCNH2 0 . GRCh38 7 150951532 150951532 + Missense_Mutation SNP T T A C3L-00144_T C3L-00144_N T T c.1861A>T p.Ser621Cys p.S621C ENST00000262186 7/15 274 229 45 244 244 0 strelka-varscan-mutect KCNH2,missense_variant,p.Ser621Cys,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Ser281Cys,ENST00000330883,NM_172057.2;KCNH2,missense_variant,p.Ser505Cys,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; A ENST00000262186 Transcript missense_variant 2263/4286 1861/3480 621/1159 S/C Agc/Tgc CM057116 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0) 7/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR01463,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 150951532 150951532 T A 1 0 0 0 0 1 0 0 0 7948 1580 55 4 4 KCNH2 7 150951532 Missense_Mutation SNP T C3L-00144_T 1144722 150951532 8394441 760 4831 NOS3 0 . GRCh38 7 150998966 150998966 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.837G>T p.Trp279Cys p.W279C ENST00000297494 8/27 125 110 15 94 94 0 strelka-varscan-mutect NOS3,missense_variant,p.Trp279Cys,ENST00000297494,NM_000603.4;NOS3,missense_variant,p.Trp73Cys,ENST00000461406,;NOS3,missense_variant,p.Trp279Cys,ENST00000484524,NM_001160111.1;NOS3,missense_variant,p.Trp279Cys,ENST00000467517,NM_001160109.1,NM_001160110.1;NOS3,upstream_gene_variant,,ENST00000460603,; T ENST00000297494 Transcript missense_variant 1194/4388 837/3612 279/1203 W/C tgG/tgT 1 1 NOS3 HGNC HGNC:7876 protein_coding YES CCDS5912.1 ENSP00000297494 P29474 UPI000013E417 NM_000603.4 deleterious(0) 8/27 Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 150998966 150998966 G T 1 0 0 0 0 1 0 0 0 10589 1183 41 2 2 NOS3 7 150998966 Missense_Mutation SNP G C3L-00144_T 47434 150998966 8347007 761 4832 ATG9B 0 . GRCh38 7 151018345 151018345 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1821C>T p.= p.G607G ENST00000605952 7/17 35 26 9 30 30 0 strelka-varscan-mutect ATG9B,synonymous_variant,p.=,ENST00000469530,NM_173681.5;NOS3,downstream_gene_variant,,ENST00000297494,NM_000603.4;NOS3,downstream_gene_variant,,ENST00000461406,;ATG9B,non_coding_transcript_exon_variant,,ENST00000617967,;ATG9B,non_coding_transcript_exon_variant,,ENST00000611177,;ATG9B,downstream_gene_variant,,ENST00000473409,;NOS3,downstream_gene_variant,,ENST00000477227,;NOS3,downstream_gene_variant,,ENST00000468293,;ATG9B,upstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000466157,;ATG9B,synonymous_variant,p.=,ENST00000605952,;ATG9B,upstream_gene_variant,,ENST00000404733,;ATG9B,downstream_gene_variant,,ENST00000473134,;ATG9B,upstream_gene_variant,,ENST00000471797,;NOS3,downstream_gene_variant,,ENST00000475454,; A ENST00000605952 Transcript synonymous_variant,NMD_transcript_variant 1897/4572 1821/2775 607/924 G ggC/ggT 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 7/17 hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038,Pfam_domain:PF04109 LOW SNV 1 1 PASS rs1326616364 . 0 199 9 2 0 0 0 0 -18.84418 0.9998371 1 1 1 0 A 2 1 12 151018345 151018345 G A 1 0 0 0 0 0 0 0 1 1255 1074 38 1 1 ATG9B 7 151018345 Silent SNP G C3L-00144_T 19379 151018345 8327628 762 4833 NCAPG2 0 . GRCh38 7 158693492 158693492 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.84G>A p.= p.E28E ENST00000409339 3/28 128 105 23 115 115 0 strelka-varscan-mutect NCAPG2,synonymous_variant,p.=,ENST00000409339,NM_001281933.1;NCAPG2,synonymous_variant,p.=,ENST00000409423,NM_001281932.1;NCAPG2,synonymous_variant,p.=,ENST00000356309,NM_017760.6;NCAPG2,upstream_gene_variant,,ENST00000441982,;NCAPG2,non_coding_transcript_exon_variant,,ENST00000621338,;NCAPG2,synonymous_variant,p.=,ENST00000432615,;NCAPG2,upstream_gene_variant,,ENST00000467785,; T ENST00000409339 Transcript synonymous_variant 198/5253 84/3471 28/1156 E gaG/gaA 1 -1 NCAPG2 HGNC HGNC:21904 protein_coding YES CCDS64816.1 ENSP00000387007 Q86XI2 UPI00001A9CF1 NM_001281933.1 3/28 hmmpanther:PTHR16199,hmmpanther:PTHR16199:SF4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 158693492 158693492 C T 1 0 0 0 0 0 0 0 1 10224 695 24 3 3 NCAPG2 7 158693492 Silent SNP C C3L-00144_T 7675147 158693492 652481 763 4834 ARHGEF10 0 . GRCh38 8 1880116 1880116 + Silent SNP G G T rs758139509 C3L-00144_T C3L-00144_N G G c.987G>T p.= p.T329T ENST00000518288 10/30 365 324 41 273 273 0 strelka-varscan-mutect ARHGEF10,synonymous_variant,p.=,ENST00000518288,NM_001308153.1;ARHGEF10,synonymous_variant,p.=,ENST00000349830,NM_014629.2;ARHGEF10,synonymous_variant,p.=,ENST00000398564,;ARHGEF10,intron_variant,,ENST00000520359,NM_001308152.1;ARHGEF10,intron_variant,,ENST00000398560,;ARHGEF10,upstream_gene_variant,,ENST00000522435,;KBTBD11-OT1,3_prime_UTR_variant,,ENST00000635855,;KBTBD11-OT1,3_prime_UTR_variant,,ENST00000635773,;ARHGEF10,intron_variant,,ENST00000523711,;ARHGEF10,intron_variant,,ENST00000520972,; T ENST00000518288 Transcript synonymous_variant 1150/5648 987/4107 329/1368 T acG/acT rs758139509 1 1 ARHGEF10 HGNC HGNC:14103 protein_coding YES CCDS78296.1 ENSP00000431012 O15013 UPI0001E8F10F NM_001308153.1 10/30 hmmpanther:PTHR12877,hmmpanther:PTHR12877:SF14 LOW 1 SNV 1 1 PASS rs758139509 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 1880116 1880116 G T 1 0 0 0 0 0 0 0 1 1024 1103 39 1 1 ARHGEF10 8 1880116 Silent SNP G C3L-00144_T 1880116 143258520 764 4835 MYOM2 0 . GRCh38 8 2096338 2096338 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2217C>A p.= p.G739G ENST00000262113 18/37 210 185 25 196 196 0 strelka-varscan-mutect MYOM2,synonymous_variant,p.=,ENST00000262113,NM_003970.3;MYOM2,synonymous_variant,p.=,ENST00000523438,;MYOM2,upstream_gene_variant,,ENST00000518203,;MYOM2,downstream_gene_variant,,ENST00000518803,;MYOM2,upstream_gene_variant,,ENST00000519372,; A ENST00000262113 Transcript synonymous_variant 2358/5014 2217/4398 739/1465 G ggC/ggA 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 18/37 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 2096338 2096338 C A 1 0 0 0 0 0 0 0 1 10093 784 28 2 2 MYOM2 8 2096338 Silent SNP C C3L-00144_T 216222 2096338 143042298 765 4836 CSMD1 0 . GRCh38 8 2998071 2998071 + Missense_Mutation SNP C C A rs371234513 C3L-00144_T C3L-00144_N C C c.8320G>T p.Val2774Leu p.V2774L ENST00000520002 55/71 215 183 32 192 192 0 strelka-varscan-mutect CSMD1,missense_variant,p.Val2635Leu,ENST00000537824,;CSMD1,missense_variant,p.Val2191Leu,ENST00000335551,;CSMD1,missense_variant,p.Val2774Leu,ENST00000520002,;CSMD1,missense_variant,p.Val2774Leu,ENST00000602557,;CSMD1,missense_variant,p.Val2773Leu,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Val2716Leu,ENST00000400186,;CSMD1,missense_variant,p.Val2716Leu,ENST00000602723,;CSMD1,downstream_gene_variant,,ENST00000519623,; A ENST00000520002 Transcript missense_variant 8876/11740 8320/10698 2774/3565 V/L Gtg/Ttg rs371234513,COSM3719397,COSM3719398 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.16) 55/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs371234513 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 2998071 2998071 C A 1 0 0 0 0 1 0 0 0 3745 536 19 1 1 CSMD1 8 2998071 Missense_Mutation SNP C C3L-00144_T 901733 2998071 142140565 766 4837 CSMD1 0 . GRCh38 8 3000027 3000027 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.8137delC p.Val2714TrpfsTer5 p.V2714Wfs*5 ENST00000520002 54/71 186 162 24 221 221 0 sindel-varindel-pindel CSMD1,frameshift_variant,p.Val2575TrpfsTer5,ENST00000537824,;CSMD1,frameshift_variant,p.Val2131TrpfsTer5,ENST00000335551,;CSMD1,frameshift_variant,p.Val2714TrpfsTer5,ENST00000520002,;CSMD1,frameshift_variant,p.Val2714TrpfsTer5,ENST00000602557,;CSMD1,frameshift_variant,p.Val2713TrpfsTer5,ENST00000635120,NM_033225.5;CSMD1,frameshift_variant,p.Val2656TrpfsTer5,ENST00000400186,;CSMD1,frameshift_variant,p.Val2656TrpfsTer5,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000519623,; - ENST00000520002 Transcript frameshift_variant 8693/11740 8137/10698 2713/3565 L/X Ctt/tt 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 54/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 deletion 5 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999914 1 1 1 0 - 7 5 12 3000027 3000027 G - 1 0 1 0 1 0 0 0 0 3745 971 34 0 0 CSMD1 8 3000027 Frame_Shift_Del DEL G C3L-00144_T 1956 3000027 142138609 767 4838 CSMD1 0 . GRCh38 8 3052579 3052579 + Missense_Mutation SNP T T A rs573086063 C3L-00144_T C3L-00144_N T T c.7546A>T p.Ser2516Cys p.S2516C ENST00000520002 51/71 140 126 14 108 108 0 strelka-varscan-mutect CSMD1,missense_variant,p.Ser2377Cys,ENST00000537824,;CSMD1,missense_variant,p.Ser1933Cys,ENST00000335551,;CSMD1,missense_variant,p.Ser2516Cys,ENST00000520002,;CSMD1,missense_variant,p.Ser2516Cys,ENST00000602557,;CSMD1,missense_variant,p.Ser2515Cys,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Ser2516Cys,ENST00000400186,;CSMD1,missense_variant,p.Ser2516Cys,ENST00000602723,; A ENST00000520002 Transcript missense_variant 8102/11740 7546/10698 2516/3565 S/C Agt/Tgt rs573086063 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 51/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs573086063 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3052579 3052579 T A 1 0 0 0 0 1 0 0 0 3745 1580 55 4 4 CSMD1 8 3052579 Missense_Mutation SNP T C3L-00144_T 52552 3052579 142086057 768 4839 CSMD1 0 . GRCh38 8 3108626 3108626 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.6734G>A p.Gly2245Asp p.G2245D ENST00000520002 45/71 158 141 17 135 135 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly2106Asp,ENST00000537824,;CSMD1,missense_variant,p.Gly1725Asp,ENST00000335551,;CSMD1,missense_variant,p.Gly2245Asp,ENST00000520002,;CSMD1,missense_variant,p.Gly2245Asp,ENST00000602557,;CSMD1,missense_variant,p.Gly2244Asp,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly2245Asp,ENST00000400186,;CSMD1,missense_variant,p.Gly2245Asp,ENST00000602723,;CSMD1,downstream_gene_variant,,ENST00000520561,;CSMD1,upstream_gene_variant,,ENST00000523062,; T ENST00000520002 Transcript missense_variant 7290/11740 6734/10698 2245/3565 G/D gGc/gAc 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 45/71 PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 3108626 3108626 C T 1 0 0 0 0 1 0 0 0 3745 739 26 3 3 CSMD1 8 3108626 Missense_Mutation SNP C C3L-00144_T 56047 3108626 142030010 769 4840 XKR5 0 . GRCh38 8 6811852 6811852 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.1407T>C p.= p.S469S ENST00000618742 7/7 365 303 62 261 261 0 strelka-varscan-mutect XKR5,synonymous_variant,p.=,ENST00000618742,NM_207411.4,NM_001289973.1;XKR5,3_prime_UTR_variant,,ENST00000618990,; G ENST00000618742 Transcript synonymous_variant 1558/4893 1407/2061 469/686 S tcT/tcC 1 -1 XKR5 HGNC HGNC:20782 protein_coding YES ENSP00000483879 A0A087X143 UPI0000EE786F NM_207411.4,NM_001289973.1 7/7 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF21 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 6811852 6811852 A G 1 0 0 0 0 0 0 0 1 17993 175 7 5 5 XKR5 8 6811852 Silent SNP A C3L-00144_T 3703226 6811852 138326784 770 4841 DEFB106A 0 . GRCh38 8 7828867 7828867 + Missense_Mutation SNP G G C rs755413890 C3L-00144_T C3L-00144_N G G c.112G>C p.Gly38Arg p.G38R ENST00000335186 2/2 100 86 14 104 104 0 strelka-varscan-mutect DEFB106A,missense_variant,p.Gly38Arg,ENST00000335186,NM_152251.3;DEFB105A,upstream_gene_variant,,ENST00000334773,NM_152250.2; C ENST00000335186 Transcript missense_variant 117/303 112/198 38/65 G/R Ggg/Cgg rs755413890 1 1 DEFB106A HGNC HGNC:18088 protein_coding YES CCDS34833.1 ENSP00000335307 Q8N104 UPI0000128D8F NM_152251.3 tolerated(0.62) 2/2 hmmpanther:PTHR15001:SF22,hmmpanther:PTHR15001,Pfam_domain:PF13841,PD692757 MODERATE 1 SNV 1 1 PASS rs755413890 . 0 192 9 6 3 0 0 0 -8.274572 0.5603472 1 1 1 0 C 3 2 12 7828867 7828867 G C 1 0 0 0 0 1 0 0 0 4199 1116 39 4 4 DEFB106A 8 7828867 Missense_Mutation SNP G C3L-00144_T 1017015 7828867 137309769 771 4842 SGK223 0 . GRCh38 8 8376912 8376912 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1497G>T p.= p.V499V ENST00000615670 3/6 100 75 25 95 95 0 strelka-varscan-mutect SGK223,synonymous_variant,p.=,ENST00000615670,;SGK223,synonymous_variant,p.=,ENST00000622241,NM_001080826.2; A ENST00000615670 Transcript synonymous_variant 1762/4903 1497/4221 499/1406 V gtG/gtT 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F 3/6 hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972 LOW 1 SNV 5 1 PASS rs1352434266 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 8376912 8376912 C A 1 0 0 0 0 0 0 0 1 14469 697 25 2 2 SGK223 8 8376912 Silent SNP C C3L-00144_T 548045 8376912 136761724 772 4843 XKR6 0 . GRCh38 8 10898894 10898894 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.984G>C p.= p.L328L ENST00000416569 3/3 64 50 14 85 85 0 strelka-varscan-mutect XKR6,synonymous_variant,p.=,ENST00000416569,NM_173683.3;XKR6,synonymous_variant,p.=,ENST00000382461,; G ENST00000416569 Transcript synonymous_variant 1011/3382 984/1926 328/641 L ctG/ctC 1 -1 XKR6 HGNC HGNC:27806 protein_coding YES CCDS5978.2 ENSP00000416707 Q5GH73 UPI00004C7A9D NM_173683.3 3/3 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF7 LOW 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999812 1 1 1 0 G 2 3 12 10898894 10898894 C G 1 0 0 0 0 0 0 0 1 17994 813 29 4 4 XKR6 8 10898894 Silent SNP C C3L-00144_T 2521982 10898894 134239742 773 4844 XKR6 0 . GRCh38 8 10924661 10924661 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.934C>T p.Gln312Ter p.Q312* ENST00000416569 2/3 86 72 14 73 73 0 strelka-varscan-mutect XKR6,stop_gained,p.Gln312Ter,ENST00000416569,NM_173683.3;XKR6,stop_gained,p.Gln89Ter,ENST00000382461,; A ENST00000416569 Transcript stop_gained 961/3382 934/1926 312/641 Q/* Cag/Tag 1 -1 XKR6 HGNC HGNC:27806 protein_coding YES CCDS5978.2 ENSP00000416707 Q5GH73 UPI00004C7A9D NM_173683.3 2/3 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF7 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 12 10924661 10924661 G A 1 0 0 0 0 0 1 0 0 17994 1357 47 3 3 XKR6 8 10924661 Nonsense_Mutation SNP G C3L-00144_T 25767 10924661 134213975 774 4845 BLK 0 . GRCh38 8 11556705 11556705 + Nonsense_Mutation SNP G G T rs538418869 C3L-00144_T C3L-00144_N G G c.820G>T p.Gly274Ter p.G274* ENST00000259089 9/13 372 300 72 373 372 1 strelka-varscan-mutect BLK,stop_gained,p.Gly274Ter,ENST00000259089,NM_001715.2;BLK,stop_gained,p.Gly203Ter,ENST00000529894,;RP11-148O21.6,upstream_gene_variant,,ENST00000602626,;RP11-148O21.4,intron_variant,,ENST00000528629,;RP11-148O21.2,downstream_gene_variant,,ENST00000533322,;RP11-148O21.3,upstream_gene_variant,,ENST00000527922,;BLK,non_coding_transcript_exon_variant,,ENST00000526778,;BLK,upstream_gene_variant,,ENST00000526097,; T ENST00000259089 Transcript stop_gained 1412/2606 820/1518 274/505 G/* Gga/Tga rs538418869,COSM3644423 1 1 BLK HGNC HGNC:1057 protein_coding YES CCDS5982.1 ENSP00000259089 P51451 UPI000006EA28 NM_001715.2 9/13 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF181,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1 HIGH 1 SNV 1 0,1 1 PASS rs538418869 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 11556705 11556705 G T 1 0 0 0 0 0 1 0 0 1596 1233 43 2 2 BLK 8 11556705 Nonsense_Mutation SNP G C3L-00144_T 632044 11556705 133581931 775 4846 MTMR7 0 . GRCh38 8 17361230 17361230 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.355G>T p.Asp119Tyr p.D119Y ENST00000180173 4/14 290 244 46 216 216 0 strelka-varscan-mutect MTMR7,missense_variant,p.Asp119Tyr,ENST00000180173,NM_004686.4;MTMR7,missense_variant,p.Asp119Tyr,ENST00000521857,;MTMR7,intron_variant,,ENST00000517317,; A ENST00000180173 Transcript missense_variant 390/3850 355/1983 119/660 D/Y Gat/Tat 1 -1 MTMR7 HGNC HGNC:7454 protein_coding YES CCDS34851.1 ENSP00000180173 Q9Y216 UPI00004DFD27 NM_004686.4 deleterious(0) 4/14 hmmpanther:PTHR10807:SF35,hmmpanther:PTHR10807,Pfam_domain:PF06602 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17361230 17361230 C A 1 0 0 0 0 1 0 0 0 9935 855 30 2 2 MTMR7 8 17361230 Missense_Mutation SNP C C3L-00144_T 5804525 17361230 127777406 776 4847 PSD3 0 . GRCh38 8 18572528 18572528 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2784G>T p.Gln928His p.Q928H ENST00000327040 14/16 101 85 16 90 90 0 strelka-varscan-mutect PSD3,missense_variant,p.Gln929His,ENST00000440756,;PSD3,missense_variant,p.Gln928His,ENST00000327040,NM_015310.3;PSD3,missense_variant,p.Gln863His,ENST00000523619,;PSD3,missense_variant,p.Gln394His,ENST00000286485,NM_206909.2;PSD3,missense_variant,p.Gln257His,ENST00000428502,;PSD3,intron_variant,,ENST00000614430,;PSD3,intron_variant,,ENST00000615573,;PSD3,splice_region_variant,,ENST00000521878,;PSD3,splice_region_variant,,ENST00000518315,; A ENST00000327040 Transcript missense_variant,splice_region_variant 2887/11689 2784/3144 928/1047 Q/H caG/caT 1 -1 PSD3 HGNC HGNC:19093 protein_coding YES CCDS43720.1 ENSP00000324127 Q9NYI0 UPI0000210A46 NM_015310.3 deleterious(0.01) 14/16 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF106,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999983 1 1 1 0 A 3 1 12 18572528 18572528 C A 1 0 0 0 0 1 0 0 0 12799 695 24 2 2 PSD3 8 18572528 Missense_Mutation SNP C C3L-00144_T 1211298 18572528 126566108 777 4848 NPM2 0 . GRCh38 8 22034182 22034182 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.438T>A p.Asp146Glu p.D146E ENST00000397940 6/9 140 120 20 126 126 0 strelka-varscan-mutect NPM2,missense_variant,p.Asp146Glu,ENST00000397940,;NPM2,missense_variant,p.Asp146Glu,ENST00000521157,;NPM2,missense_variant,p.Asp146Glu,ENST00000518119,NM_001286680.1;NPM2,missense_variant,p.Asp146Glu,ENST00000289820,NM_182795.1;NPM2,missense_variant,p.Asp146Glu,ENST00000621538,;NPM2,intron_variant,,ENST00000381530,NM_001286681.1;NPM2,intron_variant,,ENST00000615914,;NPM2,downstream_gene_variant,,ENST00000520125,;NPM2,downstream_gene_variant,,ENST00000522813,;NPM2,downstream_gene_variant,,ENST00000520180,;NPM2,non_coding_transcript_exon_variant,,ENST00000520456,;NPM2,non_coding_transcript_exon_variant,,ENST00000522953,;NPM2,upstream_gene_variant,,ENST00000519373,;NPM2,upstream_gene_variant,,ENST00000524322,; A ENST00000397940 Transcript missense_variant 1453/1874 438/645 146/214 D/E gaT/gaA 1 1 NPM2 HGNC HGNC:7930 protein_coding YES CCDS6018.1 ENSP00000381032 Q86SE8 UPI000019A1BE tolerated(0.9) 6/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF03066,hmmpanther:PTHR22747,hmmpanther:PTHR22747:SF14,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999978 1 1 1 0 A 3 1 12 22034182 22034182 T A 1 0 0 0 0 1 0 0 0 10644 1461 51 4 4 NPM2 8 22034182 Missense_Mutation SNP T C3L-00144_T 3461654 22034182 123104454 778 4849 PIWIL2 0 . GRCh38 8 22281397 22281397 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.307G>C p.Gly103Arg p.G103R ENST00000356766 4/23 281 261 20 252 252 0 strelka-varscan-mutect PIWIL2,missense_variant,p.Gly103Arg,ENST00000356766,NM_018068.3;PIWIL2,missense_variant,p.Gly103Arg,ENST00000521356,;PIWIL2,missense_variant,p.Gly103Arg,ENST00000454009,NM_001135721.1;PIWIL2,missense_variant,p.Gly103Arg,ENST00000611073,; C ENST00000356766 Transcript missense_variant 455/5128 307/2922 103/973 G/R Ggc/Cgc 1 1 PIWIL2 HGNC HGNC:17644 protein_coding YES CCDS6029.1 ENSP00000349208 Q8TC59 W0HK13 UPI000006E98E NM_018068.3 deleterious_low_confidence(0.01) 4/23 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 22281397 22281397 G C 1 0 0 0 0 1 0 0 0 12054 1000 35 4 4 PIWIL2 8 22281397 Missense_Mutation SNP G C3L-00144_T 247215 22281397 122857239 779 4850 EGR3 0 . GRCh38 8 22692344 22692344 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.165G>T p.= p.P55P ENST00000519492 2/3 83 70 13 70 70 0 strelka-mutect EGR3,synonymous_variant,p.=,ENST00000519492,;EGR3,5_prime_UTR_variant,,ENST00000522910,NM_001199880.1;EGR3,intron_variant,,ENST00000317216,NM_004430.2;RP11-459E5.1,intron_variant,,ENST00000523627,;EGR3,intron_variant,,ENST00000524088,;EGR3,upstream_gene_variant,,ENST00000518773,; A ENST00000519492 Transcript synonymous_variant 399/1500 165/216 55/71 P ccG/ccT 1 -1 EGR3 HGNC HGNC:3240 protein_coding ENSP00000429370 E5RIM5 UPI0001E8EF26 2/3 LOW SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 12 22692344 22692344 C A 1 0 0 0 0 0 0 0 1 4809 639 23 1 1 EGR3 8 22692344 Silent SNP C C3L-00144_T 410947 22692344 122446292 780 4851 NEFM 0 . GRCh38 8 24914195 24914195 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.402G>T p.Gln134His p.Q134H ENST00000221166 1/3 536 467 69 460 460 0 strelka-varscan-mutect NEFM,missense_variant,p.Gln134His,ENST00000221166,NM_005382.2;NEFM,missense_variant,p.Gln134His,ENST00000437366,;NEFM,missense_variant,p.Gln134His,ENST00000518131,;NEFM,upstream_gene_variant,,ENST00000433454,NM_001105541.1;GS1-72M22.1,non_coding_transcript_exon_variant,,ENST00000607058,;RP11-624C23.1,upstream_gene_variant,,ENST00000519689,;NEFM,non_coding_transcript_exon_variant,,ENST00000521540,;NEFM,intron_variant,,ENST00000523467,; T ENST00000221166 Transcript missense_variant 1184/4020 402/2751 134/916 Q/H caG/caT 1 1 NEFM HGNC HGNC:7734 protein_coding YES CCDS6046.1 ENSP00000221166 P07197 UPI000013C7A9 NM_005382.2 tolerated(0.19) 1/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF19,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 24914195 24914195 G T 1 0 0 0 0 1 0 0 0 10344 991 35 2 2 NEFM 8 24914195 Missense_Mutation SNP G C3L-00144_T 2221851 24914195 120224441 781 4852 KCTD9 0 . GRCh38 8 25446148 25446148 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.151G>C p.Asp51His p.D51H ENST00000221200 2/12 93 79 14 91 91 0 strelka-varscan-mutect KCTD9,missense_variant,p.Asp51His,ENST00000221200,NM_017634.3;KCTD9,non_coding_transcript_exon_variant,,ENST00000518067,;KCTD9,non_coding_transcript_exon_variant,,ENST00000518997,;KCTD9,non_coding_transcript_exon_variant,,ENST00000524217,;KCTD9,intron_variant,,ENST00000522493,;KCTD9,downstream_gene_variant,,ENST00000517914,;KCTD9,missense_variant,p.Asp51His,ENST00000519665,;KCTD9,missense_variant,p.Asp51His,ENST00000523140,;KCTD9,non_coding_transcript_exon_variant,,ENST00000521458,;KCTD9,non_coding_transcript_exon_variant,,ENST00000523294,;KCTD9,downstream_gene_variant,,ENST00000520405,; G ENST00000221200 Transcript missense_variant 372/3401 151/1170 51/389 D/H Gat/Cat 1 -1 KCTD9 HGNC HGNC:22401 protein_coding YES CCDS6048.1 ENSP00000221200 Q7L273 UPI00001540AF NM_017634.3 deleterious(0.03) 2/12 Pfam_domain:PF11834,PROSITE_profiles:PS51490,hmmpanther:PTHR14958,hmmpanther:PTHR14958:SF31,Low_complexity_(Seg):seg,Superfamily_domains:SSF89837 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 25446148 25446148 C G 1 0 0 0 0 1 0 0 0 8033 826 29 4 4 KCTD9 8 25446148 Missense_Mutation SNP C C3L-00144_T 531953 25446148 119692488 782 4853 TEX15 0 . GRCh38 8 30847267 30847267 + Missense_Mutation SNP G G T rs367731089 C3L-00144_T C3L-00144_N G G c.1751C>A p.Thr584Lys p.T584K ENST00000256246 1/4 148 126 22 122 122 0 strelka-varscan-mutect TEX15,missense_variant,p.Thr584Lys,ENST00000256246,NM_031271.3;TEX15,downstream_gene_variant,,ENST00000523186,; T ENST00000256246 Transcript missense_variant 1826/10187 1751/8370 584/2789 T/K aCg/aAg rs367731089 1 -1 TEX15 HGNC HGNC:11738 protein_coding YES CCDS6080.1 ENSP00000256246 Q9BXT5 UPI000013CEF9 NM_031271.3 deleterious(0.01) 1/4 hmmpanther:PTHR22380,hmmpanther:PTHR22380:SF1 MODERATE 1 SNV 1 1 PASS rs367731089 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 30847267 30847267 G T 1 0 0 0 0 1 0 0 0 16201 1145 40 1 1 TEX15 8 30847267 Missense_Mutation SNP G C3L-00144_T 5401119 30847267 114291369 783 4854 WRN 0 . GRCh38 8 31080895 31080895 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.868G>T p.Glu290Ter p.E290* ENST00000298139 9/35 104 91 13 96 96 0 strelka-varscan-mutect WRN,stop_gained,p.Glu290Ter,ENST00000298139,NM_000553.4; T ENST00000298139 Transcript stop_gained 1117/5215 868/4299 290/1432 E/* Gaa/Taa 1 1 WRN HGNC HGNC:12791 protein_coding YES CCDS6082.1 ENSP00000298139 Q14191 UPI000013E49D NM_000553.4 9/35 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 31080895 31080895 G T 1 0 0 0 0 0 1 0 0 17959 943 33 2 2 WRN 8 31080895 Nonsense_Mutation SNP G C3L-00144_T 233628 31080895 114057741 784 4855 ADGRA2 0 . GRCh38 8 37797374 37797374 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.106G>T p.Gly36Cys p.G36C ENST00000412232 1/19 39 32 7 30 30 0 strelka-varscan-mutect ADGRA2,missense_variant,p.Gly36Cys,ENST00000315215,;ADGRA2,missense_variant,p.Gly36Cys,ENST00000412232,NM_032777.9;ADGRA2,intron_variant,,ENST00000428068,; T ENST00000412232 Transcript missense_variant 119/5651 106/4017 36/1338 G/C Ggc/Tgc 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 deleterious(0.01) 1/19 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.14153 1 1 1 1 0 T 3 4 12 37797374 37797374 G T 1 0 0 0 0 1 0 0 0 353 1116 39 1 1 ADGRA2 8 37797374 Missense_Mutation SNP G C3L-00144_T 6716479 37797374 107341262 785 4856 SNTG1 0 . GRCh38 8 50752060 50752060 + Silent SNP C C T C3L-00144_T C3L-00144_N C C c.1344C>T p.= p.S448S ENST00000522124 18/19 109 96 13 119 119 0 strelka-varscan-mutect SNTG1,synonymous_variant,p.=,ENST00000522124,NM_018967.3;SNTG1,synonymous_variant,p.=,ENST00000518864,NM_001287813.1;SNTG1,intron_variant,,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,; T ENST00000522124 Transcript synonymous_variant 2005/3504 1344/1554 448/517 S agC/agT COSM393837,COSM393838,COSM5300872,COSM5300873 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 18/19 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,Low_complexity_(Seg):seg 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS rs1325866719 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 50752060 50752060 C T 1 0 0 0 0 0 0 0 1 15194 709 25 3 3 SNTG1 8 50752060 Silent SNP C C3L-00144_T 12954686 50752060 94386576 786 4857 PXDNL 0 . GRCh38 8 51411304 51411304 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2008C>A p.Gln670Lys p.Q670K ENST00000356297 16/23 60 49 11 45 45 0 strelka-varscan-mutect PXDNL,missense_variant,p.Gln670Lys,ENST00000356297,NM_144651.4;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,upstream_gene_variant,,ENST00000522628,; T ENST00000356297 Transcript missense_variant 2109/4805 2008/4392 670/1463 Q/K Cag/Aag 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 tolerated(0.24) 16/23 hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 51411304 51411304 G T 1 0 0 0 0 1 0 0 0 13002 1328 46 2 2 PXDNL 8 51411304 Missense_Mutation SNP G C3L-00144_T 659244 51411304 93727332 787 4858 PXDNL 0 . GRCh38 8 51457641 51457641 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.839C>G p.Thr280Ser p.T280S ENST00000356297 9/23 139 111 28 109 109 0 strelka-varscan-mutect PXDNL,missense_variant,p.Thr280Ser,ENST00000356297,NM_144651.4; C ENST00000356297 Transcript missense_variant 940/4805 839/4392 280/1463 T/S aCt/aGt 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 tolerated(1) 9/23 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 51457641 51457641 G C 1 0 0 0 0 1 0 0 0 13002 1029 36 4 4 PXDNL 8 51457641 Missense_Mutation SNP G C3L-00144_T 46337 51457641 93680995 788 4859 OPRK1 0 . GRCh38 8 53229398 53229398 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1042C>T p.= p.L348L ENST00000265572 4/4 215 189 26 179 179 0 strelka-varscan-mutect OPRK1,synonymous_variant,p.=,ENST00000612786,NM_001282904.1;OPRK1,synonymous_variant,p.=,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,synonymous_variant,p.=,ENST00000613482,;OPRK1,synonymous_variant,p.=,ENST00000520287,;OPRK1,synonymous_variant,p.=,ENST00000524278,;RP11-162D9.3,intron_variant,,ENST00000524425,;OPRK1,3_prime_UTR_variant,,ENST00000522508,; A ENST00000265572 Transcript synonymous_variant 1340/5014 1042/1143 348/380 L Ctg/Ttg 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 4/4 Gene3D:1.20.1070.10,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF1,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 53229398 53229398 G A 1 0 0 0 0 0 0 0 1 10961 1020 36 3 3 OPRK1 8 53229398 Silent SNP G C3L-00144_T 1771757 53229398 91909238 789 4860 OPRK1 0 . GRCh38 8 53251009 53251009 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.29G>C p.Gly10Ala p.G10A ENST00000265572 2/4 67 61 6 64 64 0 strelka-varscan-mutect OPRK1,missense_variant,p.Gly10Ala,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,missense_variant,p.Gly10Ala,ENST00000613482,;OPRK1,missense_variant,p.Gly10Ala,ENST00000520287,;OPRK1,5_prime_UTR_variant,,ENST00000612786,NM_001282904.1;OPRK1,missense_variant,p.Gly10Ala,ENST00000522508,; G ENST00000265572 Transcript missense_variant 327/5014 29/1143 10/380 G/A gGg/gCg 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 tolerated_low_confidence(0.4) 2/4 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.75682 1 1 1 1 0 G 3 3 12 53251009 53251009 C G 1 0 0 0 0 1 0 0 0 10961 623 22 4 4 OPRK1 8 53251009 Missense_Mutation SNP C C3L-00144_T 21611 53251009 91887627 790 4861 RP1 0 . GRCh38 8 54629175 54629175 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5293G>T p.Gly1765Cys p.G1765C ENST00000220676 4/4 316 285 31 266 265 1 strelka-varscan-mutect RP1,missense_variant,p.Gly1765Cys,ENST00000220676,NM_006269.1;RP1,intron_variant,,ENST00000637698,;RP1,intron_variant,,ENST00000636932,; T ENST00000220676 Transcript missense_variant 5441/7100 5293/6471 1765/2156 G/C Ggc/Tgc 1 1 RP1 HGNC HGNC:10263 protein_coding YES CCDS6160.1 ENSP00000220676 P56715 UPI000013455B NM_006269.1 deleterious(0) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54629175 54629175 G T 1 0 0 0 0 1 0 0 0 13709 1348 47 2 2 RP1 8 54629175 Missense_Mutation SNP G C3L-00144_T 1378166 54629175 90509461 791 4862 LYN 0 . GRCh38 8 55950722 55950722 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.425A>T p.Gln142Leu p.Q142L ENST00000519728 6/13 231 195 36 198 197 1 strelka-varscan-mutect LYN,missense_variant,p.Gln121Leu,ENST00000520220,NM_001111097.2;LYN,missense_variant,p.Gln142Leu,ENST00000519728,NM_002350.3;LYN,missense_variant,p.Gln142Leu,ENST00000520050,;LYN,upstream_gene_variant,,ENST00000420292,; T ENST00000519728 Transcript missense_variant 721/2297 425/1539 142/512 Q/L cAg/cTg 1 1 LYN HGNC HGNC:6735 protein_coding YES CCDS6162.1 ENSP00000428924 P07948 UPI000013DACD NM_002350.3 tolerated(0.5) 6/13 PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF42,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550,Superfamily_domains:SSF50044,Prints_domain:PR00401 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 55950722 55950722 A T 1 0 0 0 0 1 0 0 0 9018 188 7 4 4 LYN 8 55950722 Missense_Mutation SNP A C3L-00144_T 1321547 55950722 89187914 792 4863 CHD7 0 . GRCh38 8 60865591 60865591 + Silent SNP C C T rs761229966 C3L-00144_T C3L-00144_N C C c.8652C>T p.= p.P2884P ENST00000423902 38/38 112 93 19 103 103 0 strelka-varscan-mutect CHD7,synonymous_variant,p.=,ENST00000423902,NM_017780.3;CHD7,synonymous_variant,p.=,ENST00000524602,;CHD7,downstream_gene_variant,,ENST00000618450,;CHD7,downstream_gene_variant,,ENST00000532149,;CHD7,downstream_gene_variant,,ENST00000528280,;CHD7,downstream_gene_variant,,ENST00000531695,; T ENST00000423902 Transcript synonymous_variant 9131/11568 8652/8994 2884/2997 P ccC/ccT rs761229966 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 38/38 LOW 1 SNV 5 1 PASS rs761229966 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 60865591 60865591 C T 1 0 0 0 0 0 0 0 1 3089 668 24 3 3 CHD7 8 60865591 Silent SNP C C3L-00144_T 4914869 60865591 84273045 793 4864 CLVS1 0 . GRCh38 8 61299909 61299909 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.82G>T p.Ala28Ser p.A28S ENST00000519846 3/7 196 167 29 168 168 0 strelka-varscan-mutect CLVS1,missense_variant,p.Ala28Ser,ENST00000519846,;CLVS1,missense_variant,p.Ala28Ser,ENST00000325897,NM_173519.2;CLVS1,missense_variant,p.Ala28Ser,ENST00000522621,;CLVS1,intron_variant,,ENST00000518592,;CLVS1,downstream_gene_variant,,ENST00000523868,;RP11-787D18.1,downstream_gene_variant,,ENST00000518064,;RP11-787D18.1,downstream_gene_variant,,ENST00000521801,;CLVS1,non_coding_transcript_exon_variant,,ENST00000521189,; T ENST00000519846 Transcript missense_variant 554/3622 82/1065 28/354 A/S Gct/Tct 1 1 CLVS1 HGNC HGNC:23139 protein_coding YES CCDS6176.1 ENSP00000428402 Q8IUQ0 UPI000007472D tolerated(0.35) 3/7 hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF72,Superfamily_domains:SSF46938 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 61299909 61299909 G T 1 0 0 0 0 1 0 0 0 3344 1203 42 2 2 CLVS1 8 61299909 Missense_Mutation SNP G C3L-00144_T 434318 61299909 83838727 794 4865 CLVS1 0 . GRCh38 8 61300177 61300177 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.350G>T p.Gly117Val p.G117V ENST00000519846 3/7 187 161 26 173 173 0 strelka-varscan-mutect CLVS1,missense_variant,p.Gly117Val,ENST00000519846,;CLVS1,missense_variant,p.Gly117Val,ENST00000325897,NM_173519.2;CLVS1,intron_variant,,ENST00000518592,;CLVS1,downstream_gene_variant,,ENST00000523868,;CLVS1,downstream_gene_variant,,ENST00000522621,;RP11-787D18.1,non_coding_transcript_exon_variant,,ENST00000518064,;RP11-787D18.1,downstream_gene_variant,,ENST00000521801,;CLVS1,non_coding_transcript_exon_variant,,ENST00000521189,; T ENST00000519846 Transcript missense_variant 822/3622 350/1065 117/354 G/V gGc/gTc 1 1 CLVS1 HGNC HGNC:23139 protein_coding YES CCDS6176.1 ENSP00000428402 Q8IUQ0 UPI000007472D deleterious(0.02) 3/7 Gene3D:3.40.525.10,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF72 MODERATE SNV 5 1 PASS rs1296695398 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 61300177 61300177 G T 1 0 0 0 0 1 0 0 0 3344 1203 42 2 2 CLVS1 8 61300177 Missense_Mutation SNP G C3L-00144_T 268 61300177 83838459 795 4866 CRH 0 . GRCh38 8 66177380 66177380 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.98G>T p.Gly33Val p.G33V ENST00000276571 2/2 178 129 49 194 194 0 strelka-varscan-mutect CRH,missense_variant,p.Gly33Val,ENST00000276571,NM_000756.2;TRIM55,downstream_gene_variant,,ENST00000315962,NM_184085.1;TRIM55,downstream_gene_variant,,ENST00000353317,NM_184086.1;TRIM55,downstream_gene_variant,,ENST00000276573,NM_033058.2;TRIM55,downstream_gene_variant,,ENST00000350034,NM_184087.1;TRIM55,downstream_gene_variant,,ENST00000517647,; A ENST00000276571 Transcript missense_variant 545/1543 98/591 33/196 G/V gGa/gTa 1 -1 CRH HGNC HGNC:2355 protein_coding YES CCDS6188.1 ENSP00000276571 P06850 A0A0S2Z478 UPI0000128435 NM_000756.2 deleterious(0.01) 2/2 hmmpanther:PTHR15035,hmmpanther:PTHR15035:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 66177380 66177380 C A 1 0 0 0 0 1 0 0 0 3670 855 30 2 2 CRH 8 66177380 Missense_Mutation SNP C C3L-00144_T 4877203 66177380 78961256 796 4867 PREX2 0 . GRCh38 8 68053197 68053197 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.1044delG p.Lys349SerfsTer9 p.K349Sfs*9 ENST00000288368 9/40 137 108 29 131 131 0 sindel-varindel-pindel PREX2,frameshift_variant,p.Lys349SerfsTer9,ENST00000288368,NM_024870.2;PREX2,non_coding_transcript_exon_variant,,ENST00000529398,;PREX2,non_coding_transcript_exon_variant,,ENST00000517617,; - ENST00000288368 Transcript frameshift_variant 1321/10750 1044/4821 348/1606 E/X gaG/ga 1 1 PREX2 HGNC HGNC:22950 protein_coding YES CCDS6201.1 ENSP00000288368 Q70Z35 UPI0000375435 NM_024870.2 9/40 PROSITE_profiles:PS50003,hmmpanther:PTHR22829:SF1,hmmpanther:PTHR22829,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 68053197 68053197 G - 1 0 1 0 1 0 0 0 0 12611 933 33 0 0 PREX2 8 68053197 Frame_Shift_Del DEL G C3L-00144_T 1875817 68053197 77085439 797 4868 EYA1 0 . GRCh38 8 71299702 71299702 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.575C>A p.Ser192Ter p.S192* ENST00000340726 8/18 179 159 20 216 216 0 strelka-varscan-mutect EYA1,stop_gained,p.Ser192Ter,ENST00000340726,NM_000503.5;EYA1,stop_gained,p.Ser186Ter,ENST00000303824,NM_001288575.1,NM_001288574.1;EYA1,stop_gained,p.Ser192Ter,ENST00000388742,NM_172058.3;EYA1,stop_gained,p.Ser159Ter,ENST00000388740,NM_172060.3;EYA1,stop_gained,p.Ser158Ter,ENST00000388741,;EYA1,stop_gained,p.Ser191Ter,ENST00000388743,;EYA1,stop_gained,p.Ser187Ter,ENST00000419131,NM_172059.3;EYA1,missense_variant,p.His165Asn,ENST00000465115,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,;EYA1,upstream_gene_variant,,ENST00000493349,; T ENST00000340726 Transcript stop_gained 1215/4326 575/1779 192/592 S/* tCa/tAa 1 -1 EYA1 HGNC HGNC:3519 protein_coding YES CCDS34906.1 ENSP00000342626 Q99502 A0A024R813 UPI000012A3B3 NM_000503.5 8/18 hmmpanther:PTHR10190,hmmpanther:PTHR10190:SF11 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 71299702 71299702 G T 1 0 0 0 0 0 1 0 0 5196 1294 45 2 2 EYA1 8 71299702 Nonsense_Mutation SNP G C3L-00144_T 3246505 71299702 73838934 798 4869 MSC 0 . GRCh38 8 71844025 71844025 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.154C>G p.Pro52Ala p.P52A ENST00000325509 1/2 79 64 15 77 77 0 strelka-varscan-mutect MSC,missense_variant,p.Pro52Ala,ENST00000325509,NM_005098.3;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000521467,;MSC-AS1,upstream_gene_variant,,ENST00000457356,;MSC-AS1,upstream_gene_variant,,ENST00000518916,;MSC-AS1,upstream_gene_variant,,ENST00000519751,;MSC,upstream_gene_variant,,ENST00000518440,;MSC,upstream_gene_variant,,ENST00000521739,; C ENST00000325509 Transcript missense_variant 444/2023 154/621 52/206 P/A Ccc/Gcc 1 -1 MSC HGNC HGNC:7321 protein_coding YES CCDS43746.1 ENSP00000321445 O60682 UPI000012FA29 NM_005098.3 tolerated(0.39) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23349:SF62,hmmpanther:PTHR23349 MODERATE 1 SNV 1 1 PASS rs1303022259 . 0 201 8 0 0 0 0 0 -20 0.9999988 1 1 1 0 C 3 2 12 71844025 71844025 G C 1 0 0 0 0 1 0 0 0 9851 1232 43 4 4 MSC 8 71844025 Missense_Mutation SNP G C3L-00144_T 544323 71844025 73294611 799 4870 TRPA1 0 . GRCh38 8 72052764 72052764 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.1646A>G p.Asn549Ser p.N549S ENST00000262209 14/27 328 286 42 296 295 1 strelka-varscan-mutect TRPA1,missense_variant,p.Asn549Ser,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Asn401Ser,ENST00000523582,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000457356,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000522519,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000512290,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,downstream_gene_variant,,ENST00000519751,;MSC-AS1,downstream_gene_variant,,ENST00000524152,;TRPA1,downstream_gene_variant,,ENST00000520788,; C ENST00000262209 Transcript missense_variant,splice_region_variant 1854/5223 1646/3360 549/1119 N/S aAc/aGc 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 14/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 72052764 72052764 T C 1 0 0 0 0 1 0 0 0 17082 1739 60 5 5 TRPA1 8 72052764 Missense_Mutation SNP T C3L-00144_T 208739 72052764 73085872 800 4871 SBSPON 0 . GRCh38 8 73081043 73081043 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.385G>C p.Gly129Arg p.G129R ENST00000297354 2/5 48 39 9 26 26 0 strelka-varscan-mutect SBSPON,missense_variant,p.Gly129Arg,ENST00000297354,NM_153225.3;RP11-956J14.1,downstream_gene_variant,,ENST00000442274,;SBSPON,non_coding_transcript_exon_variant,,ENST00000519697,; G ENST00000297354 Transcript missense_variant 590/3801 385/795 129/264 G/R Ggc/Cgc COSM338391 1 -1 SBSPON HGNC HGNC:30362 protein_coding YES CCDS43747.2 ENSP00000297354 Q8IVN8 UPI0000D47CF3 NM_153225.3 tolerated(0.07) 2/5 hmmpanther:PTHR20920,hmmpanther:PTHR20920:SF2,SMART_domains:SM00209 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99349 1 1 1 1 0 G 3 3 12 73081043 73081043 C G 1 0 0 0 0 1 0 0 0 14130 623 22 4 4 SBSPON 8 73081043 Missense_Mutation SNP C C3L-00144_T 1028279 73081043 72057593 801 4872 CRISPLD1 0 . GRCh38 8 75016600 75016600 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.763G>T p.Glu255Ter p.E255* ENST00000262207 7/15 146 127 19 129 129 0 strelka-mutect CRISPLD1,stop_gained,p.Glu255Ter,ENST00000262207,NM_031461.5;CRISPLD1,stop_gained,p.Glu67Ter,ENST00000523524,NM_001286778.1;CRISPLD1,stop_gained,p.Glu69Ter,ENST00000517786,NM_001286777.1;CRISPLD1,downstream_gene_variant,,ENST00000520277,;CRISPLD1,downstream_gene_variant,,ENST00000519798,; T ENST00000262207 Transcript stop_gained 1231/4287 763/1503 255/500 E/* Gaa/Taa 1 1 CRISPLD1 HGNC HGNC:18206 protein_coding YES CCDS6219.1 ENSP00000262207 Q9H336 UPI00000422F5 NM_031461.5 7/15 hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF73 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 75016600 75016600 G T 1 0 0 0 0 0 1 0 0 3683 1175 41 2 2 CRISPLD1 8 75016600 Nonsense_Mutation SNP G C3L-00144_T 1935557 75016600 70122036 802 4873 HNF4G 0 . GRCh38 8 75543942 75543942 + Nonsense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.220A>T p.Arg74Ter p.R74* ENST00000396423 2/10 106 83 23 119 119 0 strelka-varscan-mutect HNF4G,stop_gained,p.Arg74Ter,ENST00000396423,NM_004133.4;HNF4G,stop_gained,p.Arg37Ter,ENST00000354370,;HNF4G,intron_variant,,ENST00000396419,; T ENST00000396423 Transcript stop_gained 344/4209 220/1338 74/445 R/* Aga/Tga 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 2/10 PROSITE_profiles:PS51030,hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 75543942 75543942 A T 1 0 0 0 0 0 1 0 0 7145 180 7 4 4 HNF4G 8 75543942 Nonsense_Mutation SNP A C3L-00144_T 527342 75543942 69594694 803 4874 ZFHX4 0 . GRCh38 8 76704523 76704524 + Frame_Shift_Ins INS - - A novel C3L-00144_T C3L-00144_N - - c.438dupA p.Glu147ArgfsTer12 p.E147Rfs*12 ENST00000521891 2/11 298 254 44 294 294 0 sindel-varindel-pindel ZFHX4,frameshift_variant,p.Glu147ArgfsTer12,ENST00000521891,NM_024721.4;ZFHX4,frameshift_variant,p.Glu147ArgfsTer12,ENST00000518282,;ZFHX4,frameshift_variant,p.Glu147ArgfsTer?,ENST00000520307,;ZFHX4,frameshift_variant,p.Glu147ArgfsTer?,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript frameshift_variant 883-884/14019 435-436/10851 145-146/3616 -/X -/A 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 HIGH 1 insertion 5 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 12 76704523 76704523 - A 1 0 1 1 0 0 0 0 0 18213 581 21 0 0 ZFHX4 8 76704523 Frame_Shift_Ins INS - C3L-00144_T 1160581 76704523 68434113 804 4875 ZFHX4 0 . GRCh38 8 76707767 76707767 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2812G>T p.Val938Leu p.V938L ENST00000521891 3/11 253 193 60 241 241 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Val938Leu,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Val912Leu,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; T ENST00000521891 Transcript missense_variant 3260/14019 2812/10851 938/3616 V/L Gta/Tta 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(0.09) 3/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 76707767 76707767 G T 1 0 0 0 0 1 0 0 0 18213 1029 36 2 2 ZFHX4 8 76707767 Missense_Mutation SNP G C3L-00144_T 3244 76707767 68430869 805 4876 ZFHX4 0 . GRCh38 8 76855038 76855038 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.8117G>T p.Gly2706Val p.G2706V ENST00000521891 10/11 180 154 26 120 120 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Gly2706Val,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Gly2680Val,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; T ENST00000521891 Transcript missense_variant 8565/14019 8117/10851 2706/3616 G/V gGt/gTt 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS rs1255294073 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 76855038 76855038 G T 1 0 0 0 0 1 0 0 0 18213 1261 44 2 2 ZFHX4 8 76855038 Missense_Mutation SNP G C3L-00144_T 147271 76855038 68283598 806 4877 SNX16 0 . GRCh38 8 81823868 81823868 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.535G>T p.Asp179Tyr p.D179Y ENST00000396330 5/9 244 206 38 207 207 0 strelka-varscan-mutect SNX16,missense_variant,p.Asp179Tyr,ENST00000396330,NM_022133.3;SNX16,missense_variant,p.Asp150Tyr,ENST00000353788,NM_152837.2;SNX16,missense_variant,p.Asp179Tyr,ENST00000615066,;SNX16,missense_variant,p.Asp179Tyr,ENST00000345957,NM_152836.2;SNX16,missense_variant,p.Asp179Tyr,ENST00000521810,;SNX16,missense_variant,p.Asp150Tyr,ENST00000523757,;SNX16,intron_variant,,ENST00000520618,;SNX16,upstream_gene_variant,,ENST00000519212,; A ENST00000396330 Transcript missense_variant 1042/3452 535/1035 179/344 D/Y Gac/Tac 1 -1 SNX16 HGNC HGNC:14980 protein_coding YES CCDS6234.1 ENSP00000379621 P57768 UPI000004D24C NM_022133.3 deleterious(0) 5/9 PROSITE_profiles:PS50195,hmmpanther:PTHR22999,Pfam_domain:PF00787,Gene3D:3.30.1520.10,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 81823868 81823868 C A 1 0 0 0 0 1 0 0 0 15208 826 29 2 2 SNX16 8 81823868 Missense_Mutation SNP C C3L-00144_T 4968830 81823868 63314768 807 4878 ATP6V0D2 0 . GRCh38 8 86152946 86152946 + Missense_Mutation SNP C C G rs752246824 C3L-00144_T C3L-00144_N C C c.1022C>G p.Thr341Ser p.T341S ENST00000285393 8/8 58 50 8 50 50 0 strelka-varscan-mutect ATP6V0D2,missense_variant,p.Thr341Ser,ENST00000285393,NM_152565.1;CTD-3118D11.2,intron_variant,,ENST00000522679,;CTD-3118D11.2,downstream_gene_variant,,ENST00000524253,; G ENST00000285393 Transcript missense_variant 1164/2446 1022/1053 341/350 T/S aCt/aGt rs752246824 1 1 ATP6V0D2 HGNC HGNC:18266 protein_coding YES CCDS6241.1 ENSP00000285393 Q8N8Y2 A0A024R991 UPI0000051F69 NM_152565.1 tolerated(0.54) 8/8 Superfamily_domains:0044678,Pfam_domain:PF01992,PIRSF_domain:PIRSF018497,hmmpanther:PTHR11028,hmmpanther:PTHR11028:SF2 MODERATE 1 SNV 1 1 PASS rs752246824 . 0 208 2 0 0 0 0 0 -18.90516 1 1 1 1 0 G 3 3 12 86152946 86152946 C G 1 0 0 0 0 1 0 0 0 1327 565 20 4 4 ATP6V0D2 8 86152946 Missense_Mutation SNP C C3L-00144_T 4329078 86152946 58985690 808 4879 CALB1 0 . GRCh38 8 90082647 90082647 + Silent SNP G G A C3L-00144_T C3L-00144_N G G c.51C>T p.= p.F17F ENST00000265431 1/11 315 280 35 259 259 0 strelka-varscan-mutect CALB1,synonymous_variant,p.=,ENST00000265431,NM_004929.3;CALB1,intron_variant,,ENST00000523716,;CALB1,intron_variant,,ENST00000514406,;CALB1,intron_variant,,ENST00000520613,;CALB1,upstream_gene_variant,,ENST00000518457,;CALB1,non_coding_transcript_exon_variant,,ENST00000482702,;CALB1,upstream_gene_variant,,ENST00000473670,;CALB1,upstream_gene_variant,,ENST00000476853,; A ENST00000265431 Transcript synonymous_variant 233/2533 51/786 17/261 F ttC/ttT COSM5642861 1 -1 CALB1 HGNC HGNC:1434 protein_coding YES CCDS6251.1 ENSP00000265431 P05937 UPI000013D620 NM_004929.3 1/11 PROSITE_profiles:PS50222,hmmpanther:PTHR19972:SF3,hmmpanther:PTHR19972,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 90082647 90082647 G A 1 0 0 0 0 0 0 0 1 2263 1049 37 1 1 CALB1 8 90082647 Silent SNP G C3L-00144_T 3929701 90082647 55055989 809 4880 RUNX1T1 0 . GRCh38 8 91960415 91960415 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1819C>A p.His607Asn p.H607N ENST00000436581 12/12 385 337 48 414 413 1 strelka-varscan-mutect RUNX1T1,missense_variant,p.His548Asn,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.His548Asn,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.His548Asn,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.His548Asn,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.His607Asn,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.His521Asn,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.His528Asn,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.His548Asn,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.His521Asn,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.His521Asn,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.His511Asn,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.His511Asn,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.His559Asn,ENST00000520724,NM_001198634.1;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000521078,;RUNX1T1,downstream_gene_variant,,ENST00000521751,; T ENST00000436581 Transcript missense_variant 2006/7454 1819/1992 607/663 H/N Cat/Aat 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 deleterious(0) 12/12 PROSITE_profiles:PS50865,hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,PROSITE_patterns:PS01360,Pfam_domain:PF01753,Superfamily_domains:SSF144232,Prints_domain:PR01875 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 91960415 91960415 G T 1 0 0 0 0 1 0 0 0 14008 1348 47 2 2 RUNX1T1 8 91960415 Missense_Mutation SNP G C3L-00144_T 1877768 91960415 53178221 810 4881 RUNX1T1 0 . GRCh38 8 91986244 91986244 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.1336delG p.Glu446LysfsTer3 p.E446Kfs*3 ENST00000436581 9/12 418 344 74 426 426 0 sindel-varindel RUNX1T1,frameshift_variant,p.Glu387LysfsTer3,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,frameshift_variant,p.Glu387LysfsTer3,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,frameshift_variant,p.Glu387LysfsTer3,ENST00000523629,NM_175634.2;RUNX1T1,frameshift_variant,p.Glu387LysfsTer3,ENST00000614812,NM_001198631.1;RUNX1T1,frameshift_variant,p.Glu446LysfsTer3,ENST00000436581,NM_001198679.1;RUNX1T1,frameshift_variant,p.Glu360LysfsTer3,ENST00000613886,NM_001198632.1;RUNX1T1,frameshift_variant,p.Glu367LysfsTer3,ENST00000615601,NM_001198633.1;RUNX1T1,frameshift_variant,p.Glu387LysfsTer3,ENST00000265814,NM_001198628.1;RUNX1T1,frameshift_variant,p.Glu360LysfsTer3,ENST00000396218,NM_004349.3;RUNX1T1,frameshift_variant,p.Glu360LysfsTer3,ENST00000518844,NM_001198625.1;RUNX1T1,frameshift_variant,p.Glu350LysfsTer3,ENST00000422361,NM_175636.2;RUNX1T1,frameshift_variant,p.Glu350LysfsTer3,ENST00000360348,NM_175635.2;RUNX1T1,frameshift_variant,p.Glu398LysfsTer3,ENST00000520724,NM_001198634.1;RUNX1T1,frameshift_variant,p.Glu87LysfsTer3,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,downstream_gene_variant,,ENST00000518361,; - ENST00000436581 Transcript frameshift_variant 1523/7454 1336/1992 446/663 E/X Gaa/aa 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 9/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,Pfam_domain:PF08788 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 91986244 91986244 C - 1 0 1 0 1 0 0 0 0 14008 864 30 0 0 RUNX1T1 8 91986244 Frame_Shift_Del DEL C C3L-00144_T 25829 91986244 53152392 811 4882 GEM 0 . GRCh38 8 94250398 94250398 + Missense_Mutation SNP C C A rs145789382 C3L-00144_T C3L-00144_N C C c.803G>T p.Arg268Leu p.R268L ENST00000297596 5/5 350 282 68 260 259 1 strelka-varscan-mutect GEM,missense_variant,p.Arg268Leu,ENST00000297596,NM_005261.3;GEM,missense_variant,p.Arg268Leu,ENST00000396194,NM_181702.2; A ENST00000297596 Transcript missense_variant 1068/2208 803/891 268/296 R/L cGc/cTc rs145789382,COSM1102546,COSM356516 1 -1 GEM HGNC HGNC:4234 protein_coding YES CCDS6261.1 ENSP00000297596 P55040 A0A024R9F5 UPI000012B3BC NM_005261.3 deleterious(0.01) 5/5 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF192,PIRSF_domain:PIRSF038017 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs145789382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 94250398 94250398 C A 1 0 0 0 0 1 0 0 0 6202 768 27 1 1 GEM 8 94250398 Missense_Mutation SNP C C3L-00144_T 2264154 94250398 50888238 812 4883 INTS8 0 . GRCh38 8 94827775 94827775 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.500G>T p.Gly167Val p.G167V ENST00000523731 4/27 350 313 37 219 219 0 strelka-varscan-mutect INTS8,missense_variant,p.Gly167Val,ENST00000523731,NM_017864.3;INTS8,missense_variant,p.Gly126Val,ENST00000522171,;INTS8,missense_variant,p.Gly120Val,ENST00000519457,;INTS8,missense_variant,p.Gly58Val,ENST00000519053,;INTS8,missense_variant,p.Gly155Val,ENST00000521860,;INTS8,upstream_gene_variant,,ENST00000520526,;INTS8,downstream_gene_variant,,ENST00000523808,;INTS8,missense_variant,p.Gly167Val,ENST00000343161,;INTS8,missense_variant,p.Gly167Val,ENST00000523206,;INTS8,missense_variant,p.Gly167Val,ENST00000524333,;INTS8,non_coding_transcript_exon_variant,,ENST00000523321,; T ENST00000523731 Transcript missense_variant 633/4633 500/2988 167/995 G/V gGa/gTa 1 1 INTS8 HGNC HGNC:26048 protein_coding YES CCDS34925.1 ENSP00000430338 Q75QN2 UPI000023B7D0 NM_017864.3 tolerated(0.08) 4/27 hmmpanther:PTHR13350 MODERATE 1 SNV 1 1 PASS rs1385835112 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 94827775 94827775 G T 1 0 0 0 0 1 0 0 0 7687 1174 41 2 2 INTS8 8 94827775 Missense_Mutation SNP G C3L-00144_T 577377 94827775 50310861 813 4884 GDF6 0 . GRCh38 8 96144594 96144594 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1337A>T p.Asp446Val p.D446V ENST00000287020 2/2 228 179 49 194 194 0 strelka-varscan-mutect GDF6,missense_variant,p.Asp446Val,ENST00000287020,NM_001001557.2;GDF6,3_prime_UTR_variant,,ENST00000621429,;GDF6,3_prime_UTR_variant,,ENST00000620978,;KB-1043D8.8,upstream_gene_variant,,ENST00000602571,; A ENST00000287020 Transcript missense_variant 1437/3701 1337/1368 446/455 D/V gAc/gTc 1 -1 GDF6 HGNC HGNC:4221 protein_coding YES CCDS34926.1 ENSP00000287020 Q6KF10 A0A0S2A5D6 UPI0000047253 NM_001001557.2 deleterious(0) 2/2 Gene3D:2.10.90.10,Pfam_domain:PF00019,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF43,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 96144594 96144594 T A 1 0 0 0 0 1 0 0 0 6190 1667 58 4 4 GDF6 8 96144594 Missense_Mutation SNP T C3L-00144_T 1316819 96144594 48994042 814 4885 SDC2 0 . GRCh38 8 96602522 96602522 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.300G>T p.Gln100His p.Q100H ENST00000302190 3/5 141 120 21 71 71 0 strelka-varscan-mutect SDC2,missense_variant,p.Gln100His,ENST00000302190,NM_002998.3;SDC2,missense_variant,p.Gln64His,ENST00000518385,;SDC2,missense_variant,p.Gln71His,ENST00000519914,;SDC2,missense_variant,p.Gln71His,ENST00000522911,;SDC2,missense_variant,p.Gln71His,ENST00000523877,;SDC2,missense_variant,p.Gln71His,ENST00000521590,; T ENST00000302190 Transcript missense_variant 1221/3759 300/606 100/201 Q/H caG/caT 1 1 SDC2 HGNC HGNC:10659 protein_coding YES CCDS6272.1 ENSP00000307046 P34741 A0A024R9D1 UPI000013E7A4 NM_002998.3 deleterious(0.01) 3/5 hmmpanther:PTHR10915,hmmpanther:PTHR10915:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 96602522 96602522 G T 1 0 0 0 0 1 0 0 0 14224 933 33 2 2 SDC2 8 96602522 Missense_Mutation SNP G C3L-00144_T 457928 96602522 48536114 815 4886 DCAF13 0 . GRCh38 8 103415330 103415330 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.340G>A p.Ala114Thr p.A114T ENST00000297579 1/11 336 288 48 250 250 0 strelka-varscan-mutect DCAF13,missense_variant,p.Ala114Thr,ENST00000297579,NM_015420.6;DCAF13,missense_variant,p.Ala114Thr,ENST00000616836,;SLC25A32,upstream_gene_variant,,ENST00000297578,NM_030780.4;DCAF13,upstream_gene_variant,,ENST00000521971,;DCAF13,upstream_gene_variant,,ENST00000618975,;DCAF13,upstream_gene_variant,,ENST00000612750,;DCAF13,upstream_gene_variant,,ENST00000519682,;DCAF13,upstream_gene_variant,,ENST00000521999,;DCAF13,upstream_gene_variant,,ENST00000518554,;SLC25A32,upstream_gene_variant,,ENST00000521645,;SLC25A32,upstream_gene_variant,,ENST00000523256,;SLC25A32,upstream_gene_variant,,ENST00000523866,;DCAF13,upstream_gene_variant,,ENST00000521716,; A ENST00000297579 Transcript missense_variant 617/2642 340/1794 114/597 A/T Gcg/Acg 1 1 DCAF13 HGNC HGNC:24535 protein_coding YES CCDS34934.1 ENSP00000297579 A0A087WT20 UPI0000DBEF2A NM_015420.6 deleterious_low_confidence(0.01) 1/11 MODERATE 1 SNV 1 1 PASS rs1197041745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 103415330 103415330 G A 1 0 0 0 0 1 0 0 0 4067 1087 38 1 1 DCAF13 8 103415330 Missense_Mutation SNP G C3L-00144_T 6812808 103415330 41723306 816 4887 RIMS2 0 . GRCh38 8 103886090 103886090 + Missense_Mutation SNP G G C C3L-00144_T C3L-00144_N G G c.1491G>C p.Lys497Asn p.K497N ENST00000504942 4/24 387 328 59 332 332 0 strelka-varscan-mutect RIMS2,missense_variant,p.Lys305Asn,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Lys275Asn,ENST00000436393,;RIMS2,missense_variant,p.Lys497Asn,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Lys439Asn,ENST00000626043,;RIMS2,missense_variant,p.Lys305Asn,ENST00000408894,;RIMS2,missense_variant,p.Lys305Asn,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Lys501Asn,ENST00000632716,;RIMS2,missense_variant,p.Lys305Asn,ENST00000515551,; C ENST00000504942 Transcript missense_variant 1630/4228 1491/4050 497/1349 K/N aaG/aaC COSM1287627,COSM1287628,COSM1287629,COSM1287630,COSM1287631 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Low_complexity_(Seg):seg 1,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 103886090 103886090 G C 1 0 0 0 0 1 0 0 0 13543 962 34 4 4 RIMS2 8 103886090 Missense_Mutation SNP G C3L-00144_T 470760 103886090 41252546 817 4888 RIMS2 0 . GRCh38 8 104251090 104251090 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3758C>A p.Ala1253Glu p.A1253E ENST00000504942 23/24 231 202 29 176 175 1 strelka-varscan-mutect RIMS2,missense_variant,p.Ala1067Glu,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Ala1271Glu,ENST00000436393,;RIMS2,missense_variant,p.Ala1253Glu,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Ala1092Glu,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Ala189Glu,ENST00000339750,NM_001282882.1;RIMS2,missense_variant,p.Ala189Glu,ENST00000523362,;RIMS2,downstream_gene_variant,,ENST00000626043,;RIMS2,downstream_gene_variant,,ENST00000408894,; A ENST00000504942 Transcript missense_variant 3897/4228 3758/4050 1253/1349 A/E gCa/gAa 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 23/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS rs1432389650 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 104251090 104251090 C A 1 0 0 0 0 1 0 0 0 13543 710 25 2 2 RIMS2 8 104251090 Missense_Mutation SNP C C3L-00144_T 365000 104251090 40887546 818 4889 DPYS 0 . GRCh38 8 104424383 104424383 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1099G>A p.Gly367Ser p.G367S ENST00000351513 7/10 237 196 41 244 244 0 strelka-varscan-mutect DPYS,missense_variant,p.Gly367Ser,ENST00000351513,NM_001385.2;KB-1552D7.2,upstream_gene_variant,,ENST00000622091,;DPYS,downstream_gene_variant,,ENST00000519217,;KB-1552D7.2,upstream_gene_variant,,ENST00000319051,; T ENST00000351513 Transcript missense_variant 1232/2127 1099/1560 367/519 G/S Ggt/Agt 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 deleterious(0.01) 7/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,TIGRFAM_domain:TIGR02033,Pfam_domain:PF01979,Gene3D:3.20.20.140,Superfamily_domains:SSF51338,Superfamily_domains:SSF51556 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 104424383 104424383 C T 1 0 0 0 0 1 0 0 0 4561 594 21 3 3 DPYS 8 104424383 Missense_Mutation SNP C C3L-00144_T 173293 104424383 40714253 819 4890 DPYS 0 . GRCh38 8 104427983 104427983 + Silent SNP G G T rs373819650 C3L-00144_T C3L-00144_N G G c.1089C>A p.= p.G363G ENST00000351513 6/10 438 375 63 411 410 1 strelka-varscan-mutect DPYS,synonymous_variant,p.=,ENST00000351513,NM_001385.2;DPYS,downstream_gene_variant,,ENST00000519217,; T ENST00000351513 Transcript synonymous_variant 1222/2127 1089/1560 363/519 G ggC/ggA rs373819650,COSM3431995 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 6/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,TIGRFAM_domain:TIGR02033,Pfam_domain:PF01979,Gene3D:3.20.20.140,Superfamily_domains:SSF51338,Superfamily_domains:SSF51556 0,1 LOW 1 SNV 1 0,1 1 PASS rs373819650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 104427983 104427983 G T 1 0 0 0 0 0 0 0 1 4561 1101 38 1 1 DPYS 8 104427983 Silent SNP G C3L-00144_T 3600 104427983 40710653 820 4891 TMEM74 0 . GRCh38 8 108785054 108785054 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.45C>G p.= p.L15L ENST00000297459 2/2 62 58 4 59 59 0 strelka-mutect TMEM74,synonymous_variant,p.=,ENST00000297459,NM_153015.1;TMEM74,intron_variant,,ENST00000518838,; C ENST00000297459 Transcript synonymous_variant 224/1741 45/918 15/305 L ctC/ctG 1 -1 TMEM74 HGNC HGNC:26409 protein_coding YES CCDS6310.1 ENSP00000297459 Q96NL1 A0A024R9D4 UPI000006E80B NM_153015.1 2/2 hmmpanther:PTHR16125,hmmpanther:PTHR16125:SF3 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -10.0192 1 1 1 1 0 C 2 2 12 108785054 108785054 G C 1 0 0 0 0 0 0 0 1 16677 929 33 4 4 TMEM74 8 108785054 Silent SNP G C3L-00144_T 4357071 108785054 36353582 821 4892 TRHR 0 . GRCh38 8 109119393 109119393 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1135G>T p.Ala379Ser p.A379S ENST00000518632 3/3 86 75 11 99 99 0 strelka-varscan-mutect TRHR,missense_variant,p.Ala379Ser,ENST00000518632,;TRHR,missense_variant,p.Ala379Ser,ENST00000311762,NM_003301.5; T ENST00000518632 Transcript missense_variant 1486/1660 1135/1197 379/398 A/S Gcc/Tcc 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 tolerated_low_confidence(0.86) 3/3 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99993 1 1 1 1 0 T 3 4 12 109119393 109119393 G T 1 0 0 0 0 1 0 0 0 16969 1319 46 2 2 TRHR 8 109119393 Missense_Mutation SNP G C3L-00144_T 334339 109119393 36019243 822 4893 CSMD3 0 . GRCh38 8 112319901 112319901 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.7246G>T p.Gly2416Cys p.G2416C ENST00000297405 46/71 238 220 18 261 260 1 strelka-varscan-mutect CSMD3,missense_variant,p.Gly2416Cys,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly2376Cys,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly2312Cys,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gly1686Cys,ENST00000339701,;CSMD3,splice_region_variant,,ENST00000492692,; A ENST00000297405 Transcript missense_variant,splice_region_variant 7491/13212 7246/11124 2416/3707 G/C Ggt/Tgt COSM1150926,COSM748660 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 46/71 PROSITE_profiles:PS50923,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs904909497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 112319901 112319901 C A 1 0 0 0 0 1 0 0 0 3747 695 24 2 2 CSMD3 8 112319901 Missense_Mutation SNP C C3L-00144_T 3200508 112319901 32818735 823 4894 CSMD3 0 . GRCh38 8 112492578 112492578 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.5189G>T p.Gly1730Val p.G1730V ENST00000297405 31/71 182 153 29 164 163 1 strelka-varscan-mutect CSMD3,missense_variant,p.Gly1730Val,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly1690Val,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly1626Val,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gly1070Val,ENST00000339701,; A ENST00000297405 Transcript missense_variant 5434/13212 5189/11124 1730/3707 G/V gGt/gTt COSM1144846,COSM603819 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 31/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 112492578 112492578 C A 1 0 0 0 0 1 0 0 0 3747 507 18 2 2 CSMD3 8 112492578 Missense_Mutation SNP C C3L-00144_T 172677 112492578 32646058 824 4895 CSMD3 0 . GRCh38 8 112829711 112829711 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1834G>T p.Gly612Ter p.G612* ENST00000297405 12/71 467 403 64 393 393 0 strelka-varscan-mutect CSMD3,stop_gained,p.Gly612Ter,ENST00000297405,NM_198123.1;CSMD3,stop_gained,p.Gly572Ter,ENST00000343508,NM_198124.1;CSMD3,stop_gained,p.Gly508Ter,ENST00000455883,NM_052900.2; A ENST00000297405 Transcript stop_gained 2079/13212 1834/11124 612/3707 G/* Gga/Tga 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 12/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 112829711 112829711 C A 1 0 0 0 0 0 1 0 0 3747 603 21 2 2 CSMD3 8 112829711 Nonsense_Mutation SNP C C3L-00144_T 337133 112829711 32308925 825 4896 CSMD3 0 . GRCh38 8 113173877 113173877 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.554C>A p.Pro185His p.P185H ENST00000297405 4/71 231 206 25 220 220 0 strelka-varscan-mutect CSMD3,missense_variant,p.Pro185His,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro145His,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro185His,ENST00000455883,NM_052900.2;CSMD3,upstream_gene_variant,,ENST00000519485,;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,;CSMD3,non_coding_transcript_exon_variant,,ENST00000462254,; T ENST00000297405 Transcript missense_variant 799/13212 554/11124 185/3707 P/H cCc/cAc 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.51) 4/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 113173877 113173877 G T 1 0 0 0 0 1 0 0 0 3747 1232 43 2 2 CSMD3 8 113173877 Missense_Mutation SNP G C3L-00144_T 344166 113173877 31964759 826 4897 COL14A1 0 . GRCh38 8 120278561 120278561 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3464G>T p.Arg1155Met p.R1155M ENST00000297848 28/48 119 99 20 93 92 1 strelka-varscan-mutect COL14A1,missense_variant,p.Arg1155Met,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Arg1155Met,ENST00000309791,;COL14A1,missense_variant,p.Arg116Met,ENST00000247781,;COL14A1,downstream_gene_variant,,ENST00000432943,; T ENST00000297848 Transcript missense_variant 3734/6466 3464/5391 1155/1796 R/M aGg/aTg 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 tolerated(0.05) 28/48 PROSITE_profiles:PS50234,hmmpanther:PTHR11132:SF53,hmmpanther:PTHR11132,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 120278561 120278561 G T 1 0 0 0 0 1 0 0 0 3459 1000 35 2 2 COL14A1 8 120278561 Missense_Mutation SNP G C3L-00144_T 7104684 120278561 24860075 827 4898 COL14A1 0 . GRCh38 8 120315560 120315560 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4579G>T p.Gly1527Ter p.G1527* ENST00000297848 39/48 187 162 25 155 155 0 strelka-varscan-mutect COL14A1,stop_gained,p.Gly1527Ter,ENST00000297848,NM_021110.2;COL14A1,stop_gained,p.Gly1527Ter,ENST00000309791,;COL14A1,stop_gained,p.Gly488Ter,ENST00000247781,; T ENST00000297848 Transcript stop_gained 4849/6466 4579/5391 1527/1796 G/* Gga/Tga 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 39/48 hmmpanther:PTHR11132:SF53,hmmpanther:PTHR11132,Pfam_domain:PF01391 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 120315560 120315560 G T 1 0 0 0 0 0 1 0 0 3459 1001 35 2 2 COL14A1 8 120315560 Nonsense_Mutation SNP G C3L-00144_T 36999 120315560 24823076 828 4899 TBC1D31 0 . GRCh38 8 123105382 123105382 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1127A>T p.Gln376Leu p.Q376L ENST00000287380 8/22 206 181 25 174 174 0 strelka-varscan-mutect TBC1D31,missense_variant,p.Gln376Leu,ENST00000287380,NM_145647.3;TBC1D31,missense_variant,p.Gln271Leu,ENST00000521676,;TBC1D31,missense_variant,p.Gln271Leu,ENST00000522420,;TBC1D31,missense_variant,p.Gln376Leu,ENST00000327098,NM_001145088.1;TBC1D31,missense_variant,p.Gln9Leu,ENST00000518805,;TBC1D31,missense_variant,p.Gln44Leu,ENST00000519418,;TBC1D31,downstream_gene_variant,,ENST00000521914,;TBC1D31,3_prime_UTR_variant,,ENST00000524307,;TBC1D31,downstream_gene_variant,,ENST00000518099,;TBC1D31,upstream_gene_variant,,ENST00000518577,; T ENST00000287380 Transcript missense_variant 1217/3502 1127/3201 376/1066 Q/L cAg/cTg 1 1 TBC1D31 HGNC HGNC:30888 protein_coding YES CCDS6338.1 ENSP00000287380 Q96DN5 UPI000013DEAB NM_145647.3 tolerated(0.14) 8/22 hmmpanther:PTHR19853:SF1,hmmpanther:PTHR19853 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 123105382 123105382 A T 1 0 0 0 0 1 0 0 0 16021 188 7 4 4 TBC1D31 8 123105382 Missense_Mutation SNP A C3L-00144_T 2789822 123105382 22033254 829 4900 ZNF572 0 . GRCh38 8 124976545 124976545 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.277G>C p.Glu93Gln p.E93Q ENST00000319286 3/3 142 130 12 145 145 0 strelka-varscan-mutect ZNF572,missense_variant,p.Glu93Gln,ENST00000319286,NM_152412.2; C ENST00000319286 Transcript missense_variant 431/3275 277/1590 93/529 E/Q Gag/Cag 1 1 ZNF572 HGNC HGNC:26758 protein_coding YES CCDS6354.1 ENSP00000319305 Q7Z3I7 UPI0000140576 NM_152412.2 tolerated(0.28) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 124976545 124976545 G C 1 0 0 0 0 1 0 0 0 18578 943 33 4 4 ZNF572 8 124976545 Missense_Mutation SNP G C3L-00144_T 1871163 124976545 20162091 830 4901 ADCY8 0 . GRCh38 8 130867905 130867905 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2151C>A p.= p.V717V ENST00000286355 9/18 110 99 11 123 122 1 strelka-varscan-mutect ADCY8,synonymous_variant,p.=,ENST00000286355,NM_001115.2;ADCY8,intron_variant,,ENST00000377928,; T ENST00000286355 Transcript synonymous_variant 4244/5938 2151/3756 717/1251 V gtC/gtA 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 9/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 LOW 1 SNV 1 1 PASS rs1175097089 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 130867905 130867905 G T 1 0 0 0 0 0 0 0 1 344 929 33 2 2 ADCY8 8 130867905 Silent SNP G C3L-00144_T 5891360 130867905 14270731 831 4902 TG 0 . GRCh38 8 132983349 132983350 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.6201dupT p.Ala2068CysfsTer4 p.A2068Cfs*4 ENST00000220616 384 308 76 336 336 0 sindel-varindel-pindel TG,frameshift_variant,p.Ala2068CysfsTer4,ENST00000220616,NM_003235.4;TG,frameshift_variant,p.Ala524CysfsTer4,ENST00000519178,;TG,intron_variant,,ENST00000519543,;TG,splice_region_variant,,ENST00000522523,;TG,splice_region_variant,,ENST00000524151,;TG,splice_region_variant,,ENST00000520197,;TG,splice_region_variant,,ENST00000519294,;TG,frameshift_variant,p.Ala39CysfsTer4,ENST00000522797,;TG,splice_region_variant,,ENST00000523756,;TG,splice_region_variant,,ENST00000520089,; T ENST00000220616 Transcript frameshift_variant,splice_region_variant 6239-6240/8450 6199-6200/8307 2067/2768 I/IX att/aTtt 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 PIRSF_domain:PIRSF001831 HIGH 1 insertion 1 2 1 PASS . . 0 140 0 0 69 0 0 0 -20 0 0 1 0 0 T 7 5 12 132983349 132983349 - T 1 0 1 1 0 0 0 0 0 16246 1043 36 0 0 TG 8 132983349 Frame_Shift_Ins INS - C3L-00144_T 2115444 132983349 12155287 832 4903 ZFAT 0 . GRCh38 8 134637673 134637673 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.236G>A p.Gly79Glu p.G79E ENST00000377838 3/16 166 139 27 141 141 0 strelka-varscan-mutect ZFAT,missense_variant,p.Gly67Glu,ENST00000520727,NM_001029939.3,NM_001289394.1;ZFAT,missense_variant,p.Gly79Glu,ENST00000377838,NM_020863.3;ZFAT,missense_variant,p.Gly67Glu,ENST00000429442,;ZFAT,missense_variant,p.Gly67Glu,ENST00000520214,NM_001167583.2;ZFAT,missense_variant,p.Gly67Glu,ENST00000520356,NM_001174158.1;ZFAT,missense_variant,p.Gly79Glu,ENST00000523399,NM_001174157.1;ZFAT,missense_variant,p.Gly17Glu,ENST00000522257,;ZFAT,missense_variant,p.Gly67Glu,ENST00000518191,;ZFAT,upstream_gene_variant,,ENST00000523040,;ZFAT,missense_variant,p.Gly79Glu,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000522974,; T ENST00000377838 Transcript missense_variant 411/4597 236/3732 79/1243 G/E gGg/gAg 1 -1 ZFAT HGNC HGNC:19899 protein_coding YES CCDS47924.1 ENSP00000367069 Q9P243 UPI0000210061 NM_020863.3 deleterious(0) 3/16 hmmpanther:PTHR24387:SF218,hmmpanther:PTHR24387 MODERATE 1 SNV 1 1 PASS rs1183953847 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 134637673 134637673 C T 1 0 0 0 0 1 0 0 0 18209 623 22 3 3 ZFAT 8 134637673 Missense_Mutation SNP C C3L-00144_T 1654324 134637673 10500963 833 4904 FAM135B 0 . GRCh38 8 138132753 138132753 + Missense_Mutation SNP A A T rs371168199 C3L-00144_T C3L-00144_N A A c.4061T>A p.Val1354Asp p.V1354D ENST00000395297 20/20 324 256 68 346 345 1 strelka-varscan-mutect FAM135B,missense_variant,p.Val1354Asp,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,; T ENST00000395297 Transcript missense_variant 4232/6962 4061/4221 1354/1406 V/D gTt/gAt rs371168199 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 20/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS rs371168199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 138132753 138132753 A T 1 0 0 0 0 1 0 0 0 5299 43 2 4 4 FAM135B 8 138132753 Missense_Mutation SNP A C3L-00144_T 3495080 138132753 7005883 834 4905 FAM135B 0 . GRCh38 8 138151548 138151548 + Missense_Mutation SNP G G T rs147601721 C3L-00144_T C3L-00144_N G G c.2927C>A p.Pro976Gln p.P976Q ENST00000395297 13/20 163 140 23 157 157 0 strelka-varscan-mutect FAM135B,missense_variant,p.Pro976Gln,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Pro976Gln,ENST00000276737,;FAM135B,missense_variant,p.Pro286Gln,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,; T ENST00000395297 Transcript missense_variant 3098/6962 2927/4221 976/1406 P/Q cCg/cAg rs147601721,COSM363095,COSM363096 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated_low_confidence(0.82) 13/20 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs147601721 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 138151548 138151548 G T 1 0 0 0 0 1 0 0 0 5299 1116 39 1 1 FAM135B 8 138151548 Missense_Mutation SNP G C3L-00144_T 18795 138151548 6987088 835 4906 TSNARE1 0 . GRCh38 8 142229531 142229531 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1495G>A p.Ala499Thr p.A499T ENST00000524325 13/14 204 176 28 193 193 0 strelka-varscan-mutect TSNARE1,missense_variant,p.Ala499Thr,ENST00000524325,NM_145003.4;TSNARE1,missense_variant,p.Ala500Thr,ENST00000307180,;TSNARE1,missense_variant,p.Ala500Thr,ENST00000520166,; T ENST00000524325 Transcript missense_variant 1671/1963 1495/1542 499/513 A/T Gcc/Acc 1 -1 TSNARE1 HGNC HGNC:26437 protein_coding YES CCDS6384.1 ENSP00000428763 Q96NA8 UPI00001AEE5E NM_145003.4 tolerated(0.39) 13/14 Pfam_domain:PF05739,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF38,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142229531 142229531 C T 1 0 0 0 0 1 0 0 0 17135 710 25 3 3 TSNARE1 8 142229531 Missense_Mutation SNP C C3L-00144_T 4077983 142229531 2909105 836 4907 ADGRB1 0 . GRCh38 8 142477244 142477244 + Missense_Mutation SNP G G T rs574367163 C3L-00144_T C3L-00144_N G G c.1188G>T p.Glu396Asp p.E396D ENST00000517894 5/31 85 69 16 82 82 0 strelka-varscan-mutect ADGRB1,missense_variant,p.Glu396Asp,ENST00000517894,;ADGRB1,missense_variant,p.Glu396Asp,ENST00000323289,NM_001702.2;ADGRB1,missense_variant,p.Glu396Asp,ENST00000521208,;ADGRB1,upstream_gene_variant,,ENST00000518820,; T ENST00000517894 Transcript missense_variant 2082/6241 1188/4755 396/1584 E/D gaG/gaT rs574367163 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 deleterious(0) 5/31 PROSITE_profiles:PS50092,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF39,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS rs574367163 . 0 201 9 0 0 0 0 0 -20 0.999996 1 1 1 0 T 3 4 12 142477244 142477244 G T 1 0 0 0 0 1 0 0 0 355 962 34 2 2 ADGRB1 8 142477244 Missense_Mutation SNP G C3L-00144_T 247713 142477244 2661392 837 4908 LYNX1 0 . GRCh38 8 142775340 142775340 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.177+1G>T p.X59_splice ENST00000523332 115 88 27 125 125 0 strelka-varscan-mutect LYNX1,splice_donor_variant,,ENST00000523332,;LYNX1,missense_variant,p.Val60Phe,ENST00000614491,NM_177477.3;LYNX1,missense_variant,p.Val60Phe,ENST00000621401,NM_177457.4;LYNX1,missense_variant,p.Val60Phe,ENST00000620006,NM_177476.3;LYNX1,missense_variant,p.Val60Phe,ENST00000613110,;LYNX1,missense_variant,p.Val60Phe,ENST00000614268,;LYNX1,intron_variant,,ENST00000615007,NM_023946.3;LYNX1,downstream_gene_variant,,ENST00000522906,; A ENST00000523332 Transcript splice_donor_variant -/600 177/249 59/82 1 -1 LYNX1 HGNC HGNC:29604 protein_coding ENSP00000428713 G3V0Z9 UPI000021064F 3/4 HIGH SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 142775340 142775340 C A 1 0 0 0 0 0 0 1 0 9019 521 18 2 2 LYNX1 8 142775340 Splice_Site SNP C C3L-00144_T 298096 142775340 2363296 838 4909 CYP11B1 0 . GRCh38 8 142875022 142875022 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1333T>A p.Phe445Ile p.F445I ENST00000292427 8/9 401 336 65 355 355 0 strelka-varscan-mutect CYP11B1,missense_variant,p.Phe445Ile,ENST00000292427,NM_000497.3;CYP11B1,missense_variant,p.Phe123Ile,ENST00000519285,;CYP11B1,missense_variant,p.Phe516Ile,ENST00000377675,;CYP11B1,intron_variant,,ENST00000517471,NM_001026213.1;GML,intron_variant,,ENST00000522728,;CYP11B1,intron_variant,,ENST00000314111,; T ENST00000292427 Transcript missense_variant 1366/2664 1333/1512 445/503 F/I Ttt/Att 1 -1 CYP11B1 HGNC HGNC:2591 protein_coding YES CCDS6392.1 ENSP00000292427 P15538 UPI000013E0BA NM_000497.3 deleterious(0) 8/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,PROSITE_patterns:PS00086,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00385 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142875022 142875022 A T 1 0 0 0 0 1 0 0 0 3948 72 3 4 4 CYP11B1 8 142875022 Missense_Mutation SNP A C3L-00144_T 99682 142875022 2263614 839 4910 CYP11B2 0 . GRCh38 8 142915072 142915072 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.569C>A p.Pro190His p.P190H ENST00000323110 3/9 495 386 109 426 425 1 strelka-varscan-mutect CYP11B2,missense_variant,p.Pro190His,ENST00000323110,NM_000498.3;GML,intron_variant,,ENST00000522728,; T ENST00000323110 Transcript missense_variant 572/2936 569/1512 190/503 P/H cCc/cAc 1 -1 CYP11B2 HGNC HGNC:2592 protein_coding YES CCDS6393.1 ENSP00000325822 P19099 UPI00001282CF NM_000498.3 tolerated(0.09) 3/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 142915072 142915072 G T 1 0 0 0 0 1 0 0 0 3949 1232 43 2 2 CYP11B2 8 142915072 Missense_Mutation SNP G C3L-00144_T 40050 142915072 2223564 840 4911 ZC3H3 0 . GRCh38 8 143538488 143538488 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.879G>A p.= p.R293R ENST00000262577 2/12 299 243 56 251 250 1 strelka-varscan-mutect ZC3H3,synonymous_variant,p.=,ENST00000262577,NM_015117.2;RP11-661A12.5,downstream_gene_variant,,ENST00000530600,;RP11-661A12.4,upstream_gene_variant,,ENST00000517300,;RN7SKP175,upstream_gene_variant,,ENST00000408472,; T ENST00000262577 Transcript synonymous_variant 911/3280 879/2847 293/948 R cgG/cgA 1 -1 ZC3H3 HGNC HGNC:28972 protein_coding YES CCDS6402.1 ENSP00000262577 Q8IXZ2 UPI0000160D96 NM_015117.2 2/12 hmmpanther:PTHR23102 LOW 1 SNV 1 1 PASS rs1170009503 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 143538488 143538488 C T 1 0 0 0 0 0 0 0 1 18144 610 22 3 3 ZC3H3 8 143538488 Silent SNP C C3L-00144_T 623416 143538488 1600148 841 4912 ZC3H3 0 . GRCh38 8 143539068 143539068 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.299G>T p.Gly100Val p.G100V ENST00000262577 2/12 329 259 70 283 282 1 strelka-varscan-mutect ZC3H3,missense_variant,p.Gly100Val,ENST00000262577,NM_015117.2;RP11-661A12.5,downstream_gene_variant,,ENST00000530600,;RP11-661A12.4,upstream_gene_variant,,ENST00000517300,;RN7SKP175,upstream_gene_variant,,ENST00000408472,; A ENST00000262577 Transcript missense_variant 331/3280 299/2847 100/948 G/V gGg/gTg 1 -1 ZC3H3 HGNC HGNC:28972 protein_coding YES CCDS6402.1 ENSP00000262577 Q8IXZ2 UPI0000160D96 NM_015117.2 deleterious(0.04) 2/12 hmmpanther:PTHR23102 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 143539068 143539068 C A 1 0 0 0 0 1 0 0 0 18144 623 22 2 2 ZC3H3 8 143539068 Missense_Mutation SNP C C3L-00144_T 580 143539068 1599568 842 4913 WDR97 0 . GRCh38 8 144111206 144111206 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2410G>T p.Gly804Trp p.G804W ENST00000323662 10/24 523 415 108 440 440 0 strelka-varscan-mutect WDR97,missense_variant,p.Gly804Trp,ENST00000323662,;MAF1,downstream_gene_variant,,ENST00000534585,;MAF1,downstream_gene_variant,,ENST00000322428,NM_032272.4;MAF1,downstream_gene_variant,,ENST00000532522,;MAF1,downstream_gene_variant,,ENST00000527058,;MAF1,downstream_gene_variant,,ENST00000534811,;WDR97,downstream_gene_variant,,ENST00000533108,;SHARPIN,upstream_gene_variant,,ENST00000533184,;WDR97,missense_variant,p.Gly804Trp,ENST00000534167,;WDR97,non_coding_transcript_exon_variant,,ENST00000528691,;WDR97,non_coding_transcript_exon_variant,,ENST00000525150,;WDR97,upstream_gene_variant,,ENST00000529209,; T ENST00000323662 Transcript missense_variant 2435/6916 2410/4869 804/1622 G/W Ggg/Tgg 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 deleterious(0) 10/24 MODERATE SNV 5 1 PASS rs1017308155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 144111206 144111206 G T 1 0 0 0 0 1 0 0 0 17897 1348 47 2 2 WDR97 8 144111206 Missense_Mutation SNP G C3L-00144_T 572138 144111206 1027430 843 4914 HGH1 0 . GRCh38 8 144137896 144137896 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.61G>C p.Glu21Gln p.E21Q ENST00000347708 1/6 23 18 5 18 18 0 strelka-mutect HGH1,missense_variant,p.Glu21Gln,ENST00000347708,NM_016458.3;HGH1,missense_variant,p.Glu21Gln,ENST00000628266,;HGH1,non_coding_transcript_exon_variant,,ENST00000530074,;HGH1,missense_variant,p.Glu21Gln,ENST00000533266,;HGH1,upstream_gene_variant,,ENST00000534255,;HGH1,upstream_gene_variant,,ENST00000525101,;HGH1,upstream_gene_variant,,ENST00000530409,;TSSK5P,downstream_gene_variant,,ENST00000423978,; C ENST00000347708 Transcript missense_variant 128/2531 61/1173 21/390 E/Q Gag/Cag 1 1 HGH1 HGNC HGNC:24161 protein_coding YES CCDS6417.1 ENSP00000321320 Q9BTY7 UPI0000073A95 NM_016458.3 tolerated(0.16) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR13387 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 144137896 144137896 G C 1 0 0 0 0 1 0 0 0 6971 943 33 4 4 HGH1 8 144137896 Missense_Mutation SNP G C3L-00144_T 26690 144137896 1000740 844 4915 DGAT1 0 . GRCh38 8 144317038 144317038 + Missense_Mutation SNP G G A rs573410614 C3L-00144_T C3L-00144_N G G c.1232C>T p.Ser411Leu p.S411L ENST00000528718 15/17 197 176 21 169 169 0 strelka-varscan-mutect DGAT1,missense_variant,p.Ser411Leu,ENST00000528718,NM_012079.5;DGAT1,synonymous_variant,p.=,ENST00000332324,;HSF1,downstream_gene_variant,,ENST00000528838,NM_005526.2;HSF1,downstream_gene_variant,,ENST00000400780,;DGAT1,downstream_gene_variant,,ENST00000611213,;GS1-393G12.12,upstream_gene_variant,,ENST00000525023,;DGAT1,upstream_gene_variant,,ENST00000620428,;DGAT1,downstream_gene_variant,,ENST00000524844,;DGAT1,non_coding_transcript_exon_variant,,ENST00000524965,;DGAT1,non_coding_transcript_exon_variant,,ENST00000527885,;HSF1,downstream_gene_variant,,ENST00000532338,;HSF1,downstream_gene_variant,,ENST00000527328,;HSF1,downstream_gene_variant,,ENST00000614796,;DGAT1,downstream_gene_variant,,ENST00000531896,;HSF1,downstream_gene_variant,,ENST00000528842,;DGAT1,downstream_gene_variant,,ENST00000525371,;HSF1,downstream_gene_variant,,ENST00000534314,;HSF1,downstream_gene_variant,,ENST00000530661,; A ENST00000528718 Transcript missense_variant 1506/3711 1232/1467 411/488 S/L tCg/tTg rs573410614,COSM3834272 1 -1 DGAT1 HGNC HGNC:2843 protein_coding YES CCDS6420.1 ENSP00000482264 O75907 UPI0000061DF4 NM_012079.5 deleterious(0) 15/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF13,Pfam_domain:PF03062,PIRSF_domain:PIRSF500231,PIRSF_domain:PIRSF000439 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs573410614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 144317038 144317038 G A 1 0 0 0 0 1 0 0 0 4264 1059 37 1 1 DGAT1 8 144317038 Missense_Mutation SNP G C3L-00144_T 179142 144317038 821598 845 4916 FOXH1 0 . GRCh38 8 144475168 144475168 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.268T>A p.Cys90Ser p.C90S ENST00000377317 2/3 551 449 102 463 462 1 strelka-varscan-mutect FOXH1,missense_variant,p.Cys90Ser,ENST00000377317,NM_003923.2;KIFC2,downstream_gene_variant,,ENST00000301332,NM_145754.3;FOXH1,non_coding_transcript_exon_variant,,ENST00000525197,;KIFC2,downstream_gene_variant,,ENST00000531423,;PPP1R16A,upstream_gene_variant,,ENST00000529283,;PPP1R16A,upstream_gene_variant,,ENST00000533088,;PPP1R16A,upstream_gene_variant,,ENST00000526183,;KIFC2,downstream_gene_variant,,ENST00000531425,;PPP1R16A,upstream_gene_variant,,ENST00000526643,; T ENST00000377317 Transcript missense_variant 847/2503 268/1098 90/365 C/S Tgc/Agc 1 -1 FOXH1 HGNC HGNC:3814 protein_coding YES CCDS6428.1 ENSP00000366534 O75593 UPI0000053417 NM_003923.2 deleterious(0) 2/3 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF191,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 144475168 144475168 A T 1 0 0 0 0 1 0 0 0 5870 217 8 4 4 FOXH1 8 144475168 Missense_Mutation SNP A C3L-00144_T 158130 144475168 663468 846 4917 WASH1 0 . GRCh38 9 24990 24990 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.10G>T p.Val4Leu p.V4L ENST00000442898 2/11 101 67 34 57 57 0 strelka-varscan-mutect WASH1,missense_variant,p.Val4Leu,ENST00000442898,NM_182905.4;MIR1302-9,upstream_gene_variant,,ENST00000422679,; A ENST00000442898 Transcript missense_variant 153/1827 10/1398 4/465 V/L Gtg/Ttg 1 -1 WASH1 HGNC HGNC:24361 protein_coding YES CCDS78375.1 ENSP00000485627 A8K0Z3 UPI0000251DC1 NM_182905.4 tolerated_low_confidence(0.06) 2/11 hmmpanther:PTHR23331,hmmpanther:PTHR23331:SF1 MODERATE 1 SNV 2 1 PASS . . 57 149 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 24990 24990 C A 1 0 0 0 0 1 0 0 0 17815 478 17 2 2 WASH1 9 24990 Missense_Mutation SNP C C3L-00144_T 24990 138369727 847 4918 DMRT3 0 . GRCh38 9 990197 990197 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.611G>T p.Gly204Val p.G204V ENST00000190165 2/2 123 82 41 123 123 0 strelka-varscan-mutect DMRT3,missense_variant,p.Gly204Val,ENST00000190165,NM_021240.3;DMRT3,missense_variant,p.Gly67Val,ENST00000417254,; T ENST00000190165 Transcript missense_variant 649/2183 611/1419 204/472 G/V gGa/gTa 1 1 DMRT3 HGNC HGNC:13909 protein_coding YES CCDS6443.1 ENSP00000190165 Q9NQL9 UPI0000073634 NM_021240.3 tolerated(0.09) 2/2 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF73 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 990197 990197 G T 1 0 0 0 0 1 0 0 0 4394 1174 41 2 2 DMRT3 9 990197 Missense_Mutation SNP G C3L-00144_T 965207 990197 137404520 848 4919 KCNV2 0 . GRCh38 9 2717845 2717845 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.106C>A p.Arg36Ser p.R36S ENST00000382082 1/2 212 140 72 174 174 0 strelka-varscan-mutect KCNV2,missense_variant,p.Arg36Ser,ENST00000382082,NM_133497.3;PUM3,downstream_gene_variant,,ENST00000490444,; A ENST00000382082 Transcript missense_variant 344/2186 106/1638 36/545 R/S Cgt/Agt 1 1 KCNV2 HGNC HGNC:19698 protein_coding YES CCDS6447.1 ENSP00000371514 Q8TDN2 UPI0000048D8E NM_133497.3 tolerated_low_confidence(0.24) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 2717845 2717845 C A 1 0 0 0 0 1 0 0 0 8011 652 23 1 1 KCNV2 9 2717845 Missense_Mutation SNP C C3L-00144_T 1727648 2717845 135676872 849 4920 MLANA 0 . GRCh38 9 5897569 5897569 + Silent SNP C C A rs756181750 C3L-00144_T C3L-00144_N C C c.90C>A p.= p.I30I ENST00000381477 3/5 255 193 62 201 200 1 strelka-varscan-mutect MLANA,synonymous_variant,p.=,ENST00000381477,NM_005511.1;MLANA,synonymous_variant,p.=,ENST00000381471,;MLANA,synonymous_variant,p.=,ENST00000381476,;MLANA,non_coding_transcript_exon_variant,,ENST00000490518,;MLANA,non_coding_transcript_exon_variant,,ENST00000482341,;KIAA2026,downstream_gene_variant,,ENST00000443149,;KIAA2026,intron_variant,,ENST00000436015,; A ENST00000381477 Transcript synonymous_variant 250/2415 90/357 30/118 I atC/atA rs756181750 1 1 MLANA HGNC HGNC:7124 protein_coding YES CCDS6466.1 ENSP00000370886 Q16655 UPI0000039DCC NM_005511.1 3/5 Pfam_domain:PF14991,hmmpanther:PTHR15305,hmmpanther:PTHR15305:SF0,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs756181750 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 5897569 5897569 C A 1 0 0 0 0 0 0 0 1 9579 874 31 1 1 MLANA 9 5897569 Silent SNP C C3L-00144_T 3179724 5897569 132497148 850 4921 KIAA2026 0 . GRCh38 9 5919954 5919954 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.6042G>A p.= p.L2014L ENST00000399933 8/8 231 166 65 232 232 0 strelka-varscan-mutect KIAA2026,synonymous_variant,p.=,ENST00000399933,NM_001017969.2;KIAA2026,synonymous_variant,p.=,ENST00000381461,;KIAA2026,3_prime_UTR_variant,,ENST00000540714,;KIAA2026,intron_variant,,ENST00000436015,; T ENST00000399933 Transcript synonymous_variant 6042/6988 6042/6312 2014/2103 L ttG/ttA 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 8/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 5919954 5919954 C T 1 0 0 0 0 0 0 0 1 8134 593 21 3 3 KIAA2026 9 5919954 Silent SNP C C3L-00144_T 22385 5919954 132474763 851 4922 CNTLN 0 . GRCh38 9 17457703 17457703 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3294G>T p.Gln1098His p.Q1098H ENST00000380647 19/26 130 72 58 115 115 0 strelka-varscan-mutect CNTLN,missense_variant,p.Gln1098His,ENST00000380647,NM_017738.3;CNTLN,intron_variant,,ENST00000461247,; T ENST00000380647 Transcript missense_variant 3378/5576 3294/4221 1098/1406 Q/H caG/caT 1 1 CNTLN HGNC HGNC:23432 protein_coding YES CCDS43789.1 ENSP00000370021 Q9NXG0 UPI0000458809 NM_017738.3 tolerated(0.06) 19/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18957,hmmpanther:PTHR18957:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 17457703 17457703 G T 1 0 0 0 0 1 0 0 0 3420 1020 36 2 2 CNTLN 9 17457703 Missense_Mutation SNP G C3L-00144_T 11537749 17457703 120937014 852 4923 IFNA10 0 . GRCh38 9 21206613 21206613 + Frame_Shift_Del DEL C C - rs769439907 C3L-00144_T C3L-00144_N C C c.485delG p.Cys162LeufsTer11 p.C162Lfs*11 ENST00000357374 1/1 408 279 129 346 346 0 sindel-varindel-pindel IFNA10,frameshift_variant,p.Cys162LeufsTer11,ENST00000357374,NM_002171.2;IFNA7,upstream_gene_variant,,ENST00000239347,NM_021057.2;IFNWP18,downstream_gene_variant,,ENST00000437472,; - ENST00000357374 Transcript frameshift_variant 531/963 485/570 162/189 C/X tGt/tt rs769439907 1 -1 IFNA10 HGNC HGNC:5418 protein_coding YES CCDS6499.1 ENSP00000369566 P01566 UPI0000047765 NM_002171.2 1/1 Gene3D:1.20.1250.10,Pfam_domain:PF00143,Prints_domain:PR00266,PROSITE_patterns:PS00252,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF29,SMART_domains:SM00076,Superfamily_domains:SSF47266 HIGH 1 deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 21206613 21206613 C - 1 0 1 0 1 0 0 0 0 7432 478 17 0 0 IFNA10 9 21206613 Frame_Shift_Del DEL C C3L-00144_T 3748910 21206613 117188104 853 4924 IZUMO3 0 . GRCh38 9 24543229 24543229 + Nonstop_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.702A>T p.Ter234TyrextTer? p.*234Yext*? ENST00000604921 6/6 62 35 27 84 84 0 strelka-varscan-mutect IZUMO3,stop_lost,p.Ter240TyrextTer16,ENST00000543880,;IZUMO3,stop_lost,p.Ter234TyrextTer?,ENST00000604921,NM_001271706.1;IZUMO3,downstream_gene_variant,,ENST00000418122,;RP11-20A20.2,upstream_gene_variant,,ENST00000602851,;RP11-20A20.2,upstream_gene_variant,,ENST00000602614,; A ENST00000604921 Transcript stop_lost 729/743 702/702 234/233 */Y taA/taT 1 -1 IZUMO3 HGNC HGNC:31421 protein_coding YES CCDS65020.1 ENSP00000474246 S4R3E6 UPI0002742D6C NM_001271706.1 6/6 HIGH 1 SNV 5 1 PASS rs1223893251 . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 24543229 24543229 T A 1 0 0 0 0 0 0 0 0 7842 1848 64 4 4 IZUMO3 9 24543229 Nonstop_Mutation SNP T C3L-00144_T 3336616 24543229 113851488 854 4925 19 2 IZUMO3 0 . GRCh38 9 24543231 24543231 + Nonstop_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.700T>A p.Ter234LysextTer? p.*234Kext*? ENST00000604921 6/6 66 37 29 88 88 0 strelka-varscan-mutect IZUMO3,stop_lost,p.Ter240LysextTer16,ENST00000543880,;IZUMO3,stop_lost,p.Ter234LysextTer?,ENST00000604921,NM_001271706.1;IZUMO3,downstream_gene_variant,,ENST00000418122,;RP11-20A20.2,upstream_gene_variant,,ENST00000602851,;RP11-20A20.2,upstream_gene_variant,,ENST00000602614,; T ENST00000604921 Transcript stop_lost 727/743 700/702 234/233 */K Taa/Aaa 1 -1 IZUMO3 HGNC HGNC:31421 protein_coding YES CCDS65020.1 ENSP00000474246 S4R3E6 UPI0002742D6C NM_001271706.1 6/6 HIGH 1 SNV 5 1 PASS . . 1 201 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 4 4 12 24543231 24543231 A T 1 0 0 0 0 0 0 0 0 7842 462 16 4 4 IZUMO3 9 24543231 Nonstop_Mutation SNP A C3L-00144_T 2 24543231 113851486 855 4926 19 2 SPAG8 0 . GRCh38 9 35811410 35811410 + Nonsense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.636T>A p.Cys212Ter p.C212* ENST00000340291 2/8 356 319 37 313 313 0 strelka-varscan-mutect SPAG8,stop_gained,p.Cys212Ter,ENST00000340291,NM_172312.1;SPAG8,stop_gained,p.Cys210Ter,ENST00000484764,;SPAG8,stop_gained,p.Cys212Ter,ENST00000396638,NM_001039592.1;SPAG8,stop_gained,p.Cys210Ter,ENST00000497810,;NPR2,downstream_gene_variant,,ENST00000342694,NM_003995.3;TMEM8B,upstream_gene_variant,,ENST00000377996,;NPR2,downstream_gene_variant,,ENST00000421267,;HINT2,downstream_gene_variant,,ENST00000259667,NM_032593.2;NPR2,downstream_gene_variant,,ENST00000447210,;SPAG8,non_coding_transcript_exon_variant,,ENST00000479751,;SPAG8,intron_variant,,ENST00000463889,;HINT2,downstream_gene_variant,,ENST00000474908,;HINT2,downstream_gene_variant,,ENST00000474848,;HINT2,downstream_gene_variant,,ENST00000461169,;HINT2,downstream_gene_variant,,ENST00000490578,;SPAG8,upstream_gene_variant,,ENST00000489063,;HINT2,downstream_gene_variant,,ENST00000472085,;HINT2,downstream_gene_variant,,ENST00000471774,;SPAG8,stop_gained,p.Cys212Ter,ENST00000475644,;SPAG8,intron_variant,,ENST00000472605,;SPAG8,intron_variant,,ENST00000495667,;SPAG8,intron_variant,,ENST00000471631,;FAM221B,downstream_gene_variant,,ENST00000388950,;NPR2,downstream_gene_variant,,ENST00000464810,;NPR2,downstream_gene_variant,,ENST00000448821,;SPAG8,upstream_gene_variant,,ENST00000460836,;NPR2,downstream_gene_variant,,ENST00000469249,; T ENST00000340291 Transcript stop_gained 761/1759 636/1506 212/501 C/* tgT/tgA 1 -1 SPAG8 HGNC HGNC:14105 protein_coding YES CCDS6592.1 ENSP00000340982 Q99932 UPI000013E78B NM_172312.1 2/8 hmmpanther:PTHR15510 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 35811410 35811410 A T 1 0 0 0 0 0 1 0 0 15315 389 14 4 4 SPAG8 9 35811410 Nonsense_Mutation SNP A C3L-00144_T 11268179 35811410 102583307 856 4927 OR2S2 0 . GRCh38 9 35957963 35957963 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.136C>G p.Leu46Val p.L46V ENST00000341959 1/1 266 174 92 255 255 0 strelka-varscan-mutect OR2S2,missense_variant,p.Leu46Val,ENST00000341959,NM_019897.2; C ENST00000341959 Transcript missense_variant 192/1047 136/960 46/319 L/V Ctc/Gtc 1 -1 OR2S2 HGNC HGNC:8276 protein_coding YES CCDS6596.2 ENSP00000344040 Q9NQN1 UPI000003FF74 NM_019897.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF176,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 35957963 35957963 G C 1 0 0 0 0 1 0 0 0 11093 1000 35 4 4 OR2S2 9 35957963 Missense_Mutation SNP G C3L-00144_T 146553 35957963 102436754 857 4928 FRMPD1 0 . GRCh38 9 37740403 37740403 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1875C>A p.= p.S625S ENST00000539465 15/16 249 227 22 251 251 0 strelka-varscan-mutect FRMPD1,synonymous_variant,p.=,ENST00000539465,;FRMPD1,synonymous_variant,p.=,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; A ENST00000539465 Transcript synonymous_variant 2468/5465 1875/4737 625/1578 S tcC/tcA 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC 15/16 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 37740403 37740403 C A 1 0 0 0 0 0 0 0 1 5927 581 21 2 2 FRMPD1 9 37740403 Silent SNP C C3L-00144_T 1782440 37740403 100654314 858 4929 ANKRD18A 0 . GRCh38 9 38596192 38596192 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1148C>A p.Thr383Lys p.T383K ENST00000399703 9/16 80 69 11 56 56 0 strelka-mutect ANKRD18A,missense_variant,p.Thr383Lys,ENST00000399703,NM_147195.2;ANKRD18A,upstream_gene_variant,,ENST00000602295,;ANKRD18A,downstream_gene_variant,,ENST00000475234,; T ENST00000399703 Transcript missense_variant 1523/4041 1148/2979 383/992 T/K aCa/aAa 1 -1 ANKRD18A HGNC HGNC:23643 protein_coding YES CCDS55311.1 ENSP00000382610 Q8IVF6 UPI00001AF4AF NM_147195.2 deleterious(0.05) 9/16 hmmpanther:PTHR24147:SF27,hmmpanther:PTHR24147,Pfam_domain:PF14915 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.9999 0.9999995 1 1 1 0 T 3 4 12 38596192 38596192 G T 1 0 0 0 0 1 0 0 0 748 1377 48 2 2 ANKRD18A 9 38596192 Missense_Mutation SNP G C3L-00144_T 855789 38596192 99798525 859 4930 SPATA31A1 0 . GRCh38 9 39358128 39358128 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.410delC p.Pro137GlnfsTer30 p.P137Qfs*30 ENST00000377647 4/4 448 363 85 448 447 1 sindel-varindel-pindel SPATA31A1,frameshift_variant,p.Pro137GlnfsTer30,ENST00000377647,NM_001085452.2;SPATA31A1,non_coding_transcript_exon_variant,,ENST00000473440,;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,; - ENST00000377647 Transcript frameshift_variant 425/4256 405/4086 135/1361 D/X gaC/ga 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF15371 HIGH 1 deletion 1 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 39358128 39358128 C - 1 0 1 0 1 0 0 0 0 15343 506 18 0 0 SPATA31A1 9 39358128 Frame_Shift_Del DEL C C3L-00144_T 761936 39358128 99036589 860 4931 SPATA31A1 0 . GRCh38 9 39358609 39358609 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.886C>A p.= p.R296R ENST00000377647 4/4 322 265 57 324 324 0 strelka-varscan-mutect SPATA31A1,synonymous_variant,p.=,ENST00000377647,NM_001085452.2;SPATA31A1,non_coding_transcript_exon_variant,,ENST00000473440,;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,; A ENST00000377647 Transcript synonymous_variant 906/4256 886/4086 296/1361 R Cgg/Agg 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 LOW 1 SNV 1 1 PASS rs1351573408 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 39358609 39358609 C A 1 0 0 0 0 0 0 0 1 15343 643 23 1 1 SPATA31A1 9 39358609 Silent SNP C C3L-00144_T 481 39358609 99036108 861 4932 SPATA31A1 0 . GRCh38 9 39361490 39361490 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3767C>A p.Pro1256Gln p.P1256Q ENST00000377647 4/4 396 331 65 432 430 2 strelka-varscan-mutect SPATA31A1,missense_variant,p.Pro1256Gln,ENST00000377647,NM_001085452.2;RP11-347J14.4,intron_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 3787/4256 3767/4086 1256/1361 P/Q cCa/cAa 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 deleterious(0.01) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 39361490 39361490 C A 1 0 0 0 0 1 0 0 0 15343 594 21 2 2 SPATA31A1 9 39361490 Missense_Mutation SNP C C3L-00144_T 2881 39361490 99033227 862 4933 SPATA31A1 0 . GRCh38 9 39361783 39361783 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4060C>A p.His1354Asn p.H1354N ENST00000377647 4/4 281 251 30 255 255 0 varscan-mutect SPATA31A1,missense_variant,p.His1354Asn,ENST00000377647,NM_001085452.2;RP11-347J14.4,intron_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 4080/4256 4060/4086 1354/1361 H/N Cac/Aac 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 deleterious(0) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS rs1422179682 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 39361783 39361783 C A 1 0 0 0 0 1 0 0 0 15343 710 25 2 2 SPATA31A1 9 39361783 Missense_Mutation SNP C C3L-00144_T 293 39361783 99032934 863 4934 CNTNAP3B 0 . GRCh38 9 41964632 41964632 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1662C>A p.Ser554Arg p.S554R ENST00000377561 11/24 28 20 8 30 30 0 varscan-mutect CNTNAP3B,missense_variant,p.Ser554Arg,ENST00000612828,;CNTNAP3B,missense_variant,p.Ser554Arg,ENST00000377561,NM_001201380.2;CNTNAP3B,missense_variant,p.Ser554Arg,ENST00000341990,;CNTNAP3B,intron_variant,,ENST00000617422,;CNTNAP3B,upstream_gene_variant,,ENST00000491438,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,;CNTNAP3B,intron_variant,,ENST00000619138,;CNTNAP3B,intron_variant,,ENST00000479351,; T ENST00000377561 Transcript missense_variant 2055/5379 1662/3867 554/1288 S/R agC/agA 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 deleterious(0) 11/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1167641441 . 1 207 2 0 0 0 0 0 -19.99595 1 1 1 1 0 T 3 4 12 41964632 41964632 G T 1 0 0 0 0 1 0 0 0 3430 962 34 2 2 CNTNAP3B 9 41964632 Missense_Mutation SNP G C3L-00144_T 2602849 41964632 96430085 864 4935 SPATA31A6 0 . GRCh38 9 42187337 42187337 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1635G>T p.Arg545Ser p.R545S ENST00000332857 4/4 462 277 185 368 368 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Arg545Ser,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; T ENST00000332857 Transcript missense_variant 1664/4209 1635/4032 545/1343 R/S agG/agT 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(0.32) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS rs1316089062 . 11 199 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42187337 42187337 G T 1 0 0 0 0 1 0 0 0 15345 1165 41 2 2 SPATA31A6 9 42187337 Missense_Mutation SNP G C3L-00144_T 222705 42187337 96207380 865 4936 FP325317.1 0 . GRCh38 9 43110611 43110611 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.367G>T p.Val123Leu p.V123L ENST00000539936 6/7 162 143 19 144 144 0 strelka-varscan-mutect FP325317.1,missense_variant,p.Val123Leu,ENST00000539936,; A ENST00000539936 Transcript missense_variant 699/1681 367/498 123/165 V/L Gtg/Ttg 1 -1 FP325317.1 Clone_based_ensembl_gene protein_coding YES ENSP00000439534 F6QWF9 UPI000514C5D5 tolerated(1) 6/7 Gene3D:1.20.1080.10,Pfam_domain:PF00230,Prints_domain:PR00783,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF16,Low_complexity_(Seg):seg,Superfamily_domains:SSF81338,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43110611 43110611 C A 1 0 0 0 0 1 0 0 0 5901 507 18 2 2 FP325317.1 9 43110611 Missense_Mutation SNP C C3L-00144_T 923274 43110611 95284106 866 4937 ANKRD20A1 0 . GRCh38 9 67900527 67900527 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.1532T>G p.Met511Arg p.M511R ENST00000562196 15/15 89 75 14 116 116 0 strelka-varscan-mutect ANKRD20A1,missense_variant,p.Met511Arg,ENST00000562196,NM_032250.3;ANKRD20A1,downstream_gene_variant,,ENST00000622129,;ANKRD20A1,downstream_gene_variant,,ENST00000616155,;RP11-195B21.3,upstream_gene_variant,,ENST00000427989,; G ENST00000562196 Transcript missense_variant 1812/3379 1532/2472 511/823 M/R aTg/aGg 1 1 ANKRD20A1 HGNC HGNC:23665 protein_coding YES CCDS6620.1 ENSP00000477695 Q5TYW2 UPI0000457755 NM_032250.3 deleterious(0) 15/15 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF1 MODERATE 1 SNV 1 1 PASS . . 103 106 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 67900527 67900527 T G 1 0 0 0 0 1 0 0 0 751 1464 51 5 5 ANKRD20A1 9 67900527 Missense_Mutation SNP T C3L-00144_T 24789916 67900527 70494190 867 4938 SMC5 0 . GRCh38 9 70300175 70300175 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1439G>T p.Arg480Ile p.R480I ENST00000361138 10/25 156 133 23 132 132 0 strelka-varscan-mutect SMC5,missense_variant,p.Arg480Ile,ENST00000361138,NM_015110.3; T ENST00000361138 Transcript missense_variant 1556/5980 1439/3306 480/1101 R/I aGa/aTa 1 1 SMC5 HGNC HGNC:20465 protein_coding YES CCDS6632.1 ENSP00000354957 Q8IY18 UPI000036763A NM_015110.3 tolerated(0.16) 10/25 hmmpanther:PTHR19306:SF1,hmmpanther:PTHR19306,Pfam_domain:PF02463 MODERATE 1 SNV 1 1 PASS rs1288752425 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 70300175 70300175 G T 1 0 0 0 0 1 0 0 0 15079 942 33 2 2 SMC5 9 70300175 Missense_Mutation SNP G C3L-00144_T 2399648 70300175 68094542 868 4939 ZCCHC6 0 . GRCh38 9 86353165 86353165 + Missense_Mutation SNP C C G rs201201332 C3L-00144_T C3L-00144_N C C c.35G>C p.Arg12Pro p.R12P ENST00000375963 2/27 87 74 13 93 93 0 strelka-varscan-mutect ZCCHC6,missense_variant,p.Arg12Pro,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,missense_variant,p.Arg12Pro,ENST00000375960,NM_001185074.1;ZCCHC6,5_prime_UTR_variant,,ENST00000277141,;ZCCHC6,upstream_gene_variant,,ENST00000375947,; G ENST00000375963 Transcript missense_variant 208/5379 35/4488 12/1495 R/P cGc/cCc rs201201332 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 tolerated_low_confidence(0.09) 2/27 MODERATE 1 SNV 5 1 PASS rs201201332 . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 G 3 3 12 86353165 86353165 C G 1 0 0 0 0 1 0 0 0 18167 768 27 4 4 ZCCHC6 9 86353165 Missense_Mutation SNP C C3L-00144_T 16052990 86353165 52041552 869 4940 GAS1 0 . GRCh38 9 86946131 86946131 + Missense_Mutation SNP C C A rs757093506 C3L-00144_T C3L-00144_N C C c.649G>T p.Ala217Ser p.A217S ENST00000298743 1/1 471 390 81 435 434 1 strelka-varscan-mutect GAS1,missense_variant,p.Ala217Ser,ENST00000298743,NM_002048.2;GAS1RR,upstream_gene_variant,,ENST00000415801,; A ENST00000298743 Transcript missense_variant 1059/2827 649/1038 217/345 A/S Gcg/Tcg rs757093506 1 -1 GAS1 HGNC HGNC:4165 protein_coding YES CCDS6674.1 ENSP00000298743 P54826 UPI0000140B67 NM_002048.2 tolerated(0.22) 1/1 Pfam_domain:PF02351,hmmpanther:PTHR16840,hmmpanther:PTHR16840:SF3,SMART_domains:SM00907 MODERATE SNV 1 PASS rs757093506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 86946131 86946131 C A 1 0 0 0 0 1 0 0 0 6114 739 26 2 2 GAS1 9 86946131 Missense_Mutation SNP C C3L-00144_T 592966 86946131 51448586 870 4941 GAS1 0 . GRCh38 9 86946724 86946724 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.56G>T p.Gly19Val p.G19V ENST00000298743 1/1 101 84 17 73 73 0 strelka-varscan-mutect GAS1,missense_variant,p.Gly19Val,ENST00000298743,NM_002048.2;GAS1RR,upstream_gene_variant,,ENST00000415801,; A ENST00000298743 Transcript missense_variant 466/2827 56/1038 19/345 G/V gGc/gTc 1 -1 GAS1 HGNC HGNC:4165 protein_coding YES CCDS6674.1 ENSP00000298743 P54826 UPI0000140B67 NM_002048.2 tolerated_low_confidence(0.17) 1/1 hmmpanther:PTHR16840,hmmpanther:PTHR16840:SF3,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 86946724 86946724 C A 1 0 0 0 0 1 0 0 0 6114 739 26 2 2 GAS1 9 86946724 Missense_Mutation SNP C C3L-00144_T 593 86946724 51447993 871 4942 SEMA4D 0 . GRCh38 9 89379467 89379467 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1826T>C p.Leu609Ser p.L609S ENST00000450295 16/16 226 183 43 206 206 0 strelka-varscan-mutect SEMA4D,missense_variant,p.Leu609Ser,ENST00000450295,;SEMA4D,missense_variant,p.Leu609Ser,ENST00000438547,NM_006378.3;SEMA4D,missense_variant,p.Leu609Ser,ENST00000356444,;SEMA4D,missense_variant,p.Leu609Ser,ENST00000422704,;SEMA4D,intron_variant,,ENST00000420987,NM_001142287.1;SEMA4D,intron_variant,,ENST00000339861,;SEMA4D,intron_variant,,ENST00000455551,;SEMA4D,non_coding_transcript_exon_variant,,ENST00000486935,;SEMA4D,intron_variant,,ENST00000429836,;SEMA4D,intron_variant,,ENST00000537934,;SEMA4D,upstream_gene_variant,,ENST00000492386,;SEMA4D,downstream_gene_variant,,ENST00000544513,;SEMA4D,downstream_gene_variant,,ENST00000540183,; G ENST00000450295 Transcript missense_variant 2603/5684 1826/2589 609/862 L/S tTg/tCg 1 -1 SEMA4D HGNC HGNC:10732 protein_coding YES CCDS6685.1 ENSP00000416523 Q92854 UPI0000135A6C deleterious(0) 16/16 PROSITE_profiles:PS50835,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF18,Pfam_domain:PF00047,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 89379467 89379467 A G 1 0 0 0 0 1 0 0 0 14310 131 5 5 5 SEMA4D 9 89379467 Missense_Mutation SNP A C3L-00144_T 2432743 89379467 49015250 872 4943 WNK2 0 . GRCh38 9 93293066 93293066 + Silent SNP G G T rs775397503 C3L-00144_T C3L-00144_N G G c.5712G>T p.= p.T1904T ENST00000297954 23/30 96 83 13 81 81 0 strelka-varscan-mutect WNK2,synonymous_variant,p.=,ENST00000432730,;WNK2,synonymous_variant,p.=,ENST00000297954,NM_001282394.1;WNK2,synonymous_variant,p.=,ENST00000395477,NM_006648.3;WNK2,synonymous_variant,p.=,ENST00000411624,;WNK2,synonymous_variant,p.=,ENST00000427277,;WNK2,synonymous_variant,p.=,ENST00000448251,;WNK2,synonymous_variant,p.=,ENST00000453718,;WNK2,upstream_gene_variant,,ENST00000474009,;WNK2,upstream_gene_variant,,ENST00000479696,; T ENST00000297954 Transcript synonymous_variant 5712/7138 5712/6894 1904/2297 T acG/acT rs775397503 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 23/30 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF10 LOW 1 SNV 1 1 PASS rs775397503 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 93293066 93293066 G T 1 0 0 0 0 0 0 0 1 17934 1045 37 1 1 WNK2 9 93293066 Silent SNP G C3L-00144_T 3913599 93293066 45101651 873 4944 FOXE1 0 . GRCh38 9 97854806 97854806 + Missense_Mutation SNP G G T rs187232918 C3L-00144_T C3L-00144_N G G c.892G>T p.Ala298Ser p.A298S ENST00000375123 1/1 149 122 27 130 130 0 strelka-varscan-mutect FOXE1,missense_variant,p.Ala298Ser,ENST00000375123,NM_004473.3; T ENST00000375123 Transcript missense_variant 1553/3462 892/1122 298/373 A/S Gcc/Tcc rs187232918 1 1 FOXE1 HGNC HGNC:3806 protein_coding YES CCDS35078.1 ENSP00000364265 O00358 UPI0000167B2F NM_004473.3 tolerated(0.15) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF156 MODERATE 1 SNV 1 PASS rs187232918 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 97854806 97854806 G T 1 0 0 0 0 1 0 0 0 5865 1319 46 2 2 FOXE1 9 97854806 Missense_Mutation SNP G C3L-00144_T 4561740 97854806 40539911 874 4945 TBC1D2 0 . GRCh38 9 98199438 98199438 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2730G>T p.= p.R910R ENST00000465784 13/13 438 391 47 367 365 2 strelka-mutect TBC1D2,synonymous_variant,p.=,ENST00000465784,NM_001267571.1;TBC1D2,synonymous_variant,p.=,ENST00000375066,NM_018421.3;TBC1D2,synonymous_variant,p.=,ENST00000342112,;TBC1D2,synonymous_variant,p.=,ENST00000375063,NM_001267572.1;TBC1D2,3_prime_UTR_variant,,ENST00000375064,; A ENST00000465784 Transcript synonymous_variant 2910/3349 2730/2787 910/928 R cgG/cgT 1 -1 TBC1D2 HGNC HGNC:18026 protein_coding YES CCDS75865.1 ENSP00000481721 Q9BYX2 UPI000022D946 NM_001267571.1 13/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22957:SF249,hmmpanther:PTHR22957 LOW 1 SNV 1 1 PASS rs1295278062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 98199438 98199438 C A 1 0 0 0 0 0 0 0 1 16008 726 26 2 2 TBC1D2 9 98199438 Silent SNP C C3L-00144_T 344632 98199438 40195279 875 4946 INVS 0 . GRCh38 9 100292693 100292693 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2436C>A p.= p.G812G ENST00000262457 14/17 301 267 34 276 276 0 strelka-varscan-mutect INVS,synonymous_variant,p.=,ENST00000262457,NM_014425.3;INVS,intron_variant,,ENST00000262456,NM_183245.2; A ENST00000262457 Transcript synonymous_variant 2621/3709 2436/3198 812/1065 G ggC/ggA 1 1 INVS HGNC HGNC:17870 protein_coding YES CCDS6746.1 ENSP00000262457 Q9Y283 A0A024R153 UPI000013D2BB NM_014425.3 14/17 hmmpanther:PTHR24178 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 100292693 100292693 C A 1 0 0 0 0 0 0 0 1 7690 697 25 2 2 INVS 9 100292693 Silent SNP C C3L-00144_T 2093255 100292693 38102024 876 4947 PPP3R2 0 . GRCh38 9 101594414 101594414 + Missense_Mutation SNP C C A rs151037849 C3L-00144_T C3L-00144_N C C c.517G>T p.Val173Leu p.V173L ENST00000374806 1/1 81 65 16 48 48 0 strelka-varscan-mutect PPP3R2,missense_variant,p.Val173Leu,ENST00000374806,NM_147180.3;PPP3R2,missense_variant,p.Val70Leu,ENST00000636434,;GRIN3A,intron_variant,,ENST00000361820,NM_133445.2; A ENST00000374806 Transcript missense_variant 588/3387 517/522 173/173 V/L Gta/Tta rs151037849 1 -1 PPP3R2 HGNC HGNC:9318 protein_coding YES CCDS6759.1 ENSP00000363939 Q96LZ3 UPI0000035DAE NM_147180.3 tolerated_low_confidence(0.1) 1/1 hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF42 MODERATE SNV 1 PASS rs151037849 . 0 201 9 0 0 0 0 0 -20 0.9999964 1 1 1 0 A 3 1 12 101594414 101594414 C A 1 0 0 0 0 1 0 0 0 12523 536 19 1 1 PPP3R2 9 101594414 Missense_Mutation SNP C C3L-00144_T 1301721 101594414 36800303 877 4948 GRIN3A 0 . GRCh38 9 101670133 101670133 + Missense_Mutation SNP T T A rs757931023 C3L-00144_T C3L-00144_N T T c.2279A>T p.Tyr760Phe p.Y760F ENST00000361820 3/9 78 61 17 90 90 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Tyr760Phe,ENST00000361820,NM_133445.2; A ENST00000361820 Transcript missense_variant 2880/7770 2279/3348 760/1115 Y/F tAc/tTc rs757931023 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 deleterious(0) 3/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF00060,Gene3D:1.10.287.70,SMART_domains:SM00079,Prints_domain:PR00177 MODERATE 1 SNV 1 1 PASS rs757931023 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101670133 101670133 T A 1 0 0 0 0 1 0 0 0 6665 1638 57 4 4 GRIN3A 9 101670133 Missense_Mutation SNP T C3L-00144_T 75719 101670133 36724584 878 4949 OR13F1 0 . GRCh38 9 104504573 104504573 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.311C>A p.Ser104Tyr p.S104Y ENST00000334726 1/1 295 261 34 265 264 1 strelka-varscan-mutect OR13F1,missense_variant,p.Ser104Tyr,ENST00000334726,NM_001004485.1; A ENST00000334726 Transcript missense_variant 311/960 311/960 104/319 S/Y tCc/tAc COSM4486936 1 1 OR13F1 HGNC HGNC:14723 protein_coding YES CCDS35087.1 ENSP00000334452 Q8NGS4 UPI0000041B47 NM_001004485.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF61,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS rs1208351099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 104504573 104504573 C A 1 0 0 0 0 1 0 0 0 11017 855 30 2 2 OR13F1 9 104504573 Missense_Mutation SNP C C3L-00144_T 2834440 104504573 33890144 879 4950 OR13D1 0 . GRCh38 9 104695317 104695317 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.896C>G p.Thr299Ser p.T299S ENST00000318763 1/1 131 103 28 114 114 0 strelka-varscan-mutect OR13D1,missense_variant,p.Thr299Ser,ENST00000318763,NM_001004484.1; G ENST00000318763 Transcript missense_variant 896/1041 896/1041 299/346 T/S aCt/aGt 1 1 OR13D1 HGNC HGNC:14695 protein_coding YES CCDS35094.1 ENSP00000317357 Q8NGV5 UPI0000061E68 NM_001004484.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF268,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 104695317 104695317 C G 1 0 0 0 0 1 0 0 0 11016 565 20 4 4 OR13D1 9 104695317 Missense_Mutation SNP C C3L-00144_T 190744 104695317 33699400 880 4951 EPB41L4B 0 . GRCh38 9 109255521 109255521 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1159T>G p.Phe387Val p.F387V ENST00000374566 11/26 129 112 17 124 124 0 strelka-varscan-mutect EPB41L4B,missense_variant,p.Phe387Val,ENST00000374566,NM_019114.4;EPB41L4B,missense_variant,p.Phe387Val,ENST00000374557,NM_018424.3; C ENST00000374566 Transcript missense_variant 1677/5800 1159/2703 387/900 F/V Ttc/Gtc 1 -1 EPB41L4B HGNC HGNC:19818 protein_coding YES CCDS43859.1 ENSP00000363694 Q9H329 UPI0000458994 NM_019114.4 deleterious(0) 11/26 Pfam_domain:PF08736,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF18,SMART_domains:SM01195,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1385520366 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 109255521 109255521 A C 1 0 0 0 0 1 0 0 0 5003 72 3 5 5 EPB41L4B 9 109255521 Missense_Mutation SNP A C3L-00144_T 4560204 109255521 29139196 881 4952 ZNF883 0 . GRCh38 9 112998214 112998214 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.46A>T p.Thr16Ser p.T16S ENST00000619044 2/2 88 74 14 83 83 0 strelka-varscan-mutect ZNF883,missense_variant,p.Thr16Ser,ENST00000619044,NM_001101338.1; A ENST00000619044 Transcript missense_variant 957/2051 46/1140 16/379 T/S Act/Tct 1 -1 ZNF883 HGNC HGNC:27271 protein_coding YES ENSP00000490059 P0CG24 UPI00001D76EC NM_001101338.1 tolerated(0.34) 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 112998214 112998214 T A 1 0 0 0 0 1 0 0 0 18790 1638 57 4 4 ZNF883 9 112998214 Missense_Mutation SNP T C3L-00144_T 3742693 112998214 25396503 882 4953 TNFSF15 0 . GRCh38 9 114790584 114790584 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.624G>T p.Trp208Cys p.W208C ENST00000374045 4/4 265 226 39 194 194 0 strelka-varscan-mutect TNFSF15,missense_variant,p.Trp208Cys,ENST00000374045,NM_001204344.1,NM_005118.3;TNFSF15,missense_variant,p.Trp131Cys,ENST00000374044,; A ENST00000374045 Transcript missense_variant 738/6687 624/756 208/251 W/C tgG/tgT 1 -1 TNFSF15 HGNC HGNC:11931 protein_coding YES CCDS6809.1 ENSP00000363157 O95150 A0A0U5JA19 UPI000006F8DF NM_001204344.1,NM_005118.3 deleterious(0) 4/4 Gene3D:2.60.120.40,Pfam_domain:PF00229,Prints_domain:PR01234,PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF24,SMART_domains:SM00207,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 114790584 114790584 C A 1 0 0 0 0 1 0 0 0 16781 508 18 2 2 TNFSF15 9 114790584 Missense_Mutation SNP C C3L-00144_T 1792370 114790584 23604133 883 4954 TNC 0 . GRCh38 9 115063897 115063897 + Missense_Mutation SNP G G A rs746469774 C3L-00144_T C3L-00144_N G G c.3659C>T p.Thr1220Ile p.T1220I ENST00000350763 12/28 281 219 62 264 264 0 strelka-varscan-mutect TNC,missense_variant,p.Thr1220Ile,ENST00000350763,NM_002160.3;TNC,missense_variant,p.Thr1220Ile,ENST00000341037,;TNC,missense_variant,p.Thr1220Ile,ENST00000423613,;TNC,intron_variant,,ENST00000535648,;TNC,intron_variant,,ENST00000542877,;TNC,intron_variant,,ENST00000537320,;TNC,intron_variant,,ENST00000544972,;TNC,upstream_gene_variant,,ENST00000635336,;TNC,intron_variant,,ENST00000498724,;TNC,intron_variant,,ENST00000473855,;TNC,upstream_gene_variant,,ENST00000476680,; A ENST00000350763 Transcript missense_variant 4071/7641 3659/6606 1220/2201 T/I aCa/aTa rs746469774 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 tolerated(0.07) 12/28 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs746469774 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 115063897 115063897 G A 1 0 0 0 0 1 0 0 0 16744 1377 48 3 3 TNC 9 115063897 Missense_Mutation SNP G C3L-00144_T 273313 115063897 23330820 884 4955 TNC 0 . GRCh38 9 115085984 115085984 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1747G>A p.Gly583Ser p.G583S ENST00000350763 3/28 234 191 43 235 234 1 strelka-varscan-mutect TNC,missense_variant,p.Gly583Ser,ENST00000350763,NM_002160.3;TNC,missense_variant,p.Gly583Ser,ENST00000535648,;TNC,missense_variant,p.Gly583Ser,ENST00000341037,;TNC,missense_variant,p.Gly583Ser,ENST00000423613,;TNC,missense_variant,p.Gly583Ser,ENST00000542877,;TNC,missense_variant,p.Gly583Ser,ENST00000537320,;TNC,downstream_gene_variant,,ENST00000534839,; T ENST00000350763 Transcript missense_variant 2159/7641 1747/6606 583/2201 G/S Ggc/Agc 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 deleterious(0) 3/28 PROSITE_profiles:PS50026,hmmpanther:PTHR19143:SF38,hmmpanther:PTHR19143,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2gy5A03,SMART_domains:SM00181,PD936484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 115085984 115085984 C T 1 0 0 0 0 1 0 0 0 16744 623 22 3 3 TNC 9 115085984 Missense_Mutation SNP C C3L-00144_T 22087 115085984 23308733 885 4956 PAPPA 0 . GRCh38 9 116207554 116207554 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1577C>A p.Ala526Glu p.A526E ENST00000328252 3/22 158 144 14 102 102 0 strelka-varscan-mutect PAPPA,missense_variant,p.Ala526Glu,ENST00000328252,NM_002581.3; A ENST00000328252 Transcript missense_variant 1946/10959 1577/4884 526/1627 A/E gCa/gAa 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 3/22 Gene3D:3.40.390.10,Pfam_domain:PF05572,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -19.07576 0.9997583 1 1 1 0 A 3 1 12 116207554 116207554 C A 1 0 0 0 0 1 0 0 0 11512 710 25 2 2 PAPPA 9 116207554 Missense_Mutation SNP C C3L-00144_T 1121570 116207554 22187163 886 4957 PAPPA 0 . GRCh38 9 116235584 116235584 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.2679T>C p.= p.P893P ENST00000328252 7/22 322 273 49 316 316 0 strelka-varscan-mutect PAPPA,synonymous_variant,p.=,ENST00000328252,NM_002581.3; C ENST00000328252 Transcript synonymous_variant 3048/10959 2679/4884 893/1627 P ccT/ccC 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 7/22 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 116235584 116235584 T C 1 0 0 0 0 0 0 0 1 11512 1538 54 5 5 PAPPA 9 116235584 Silent SNP T C3L-00144_T 28030 116235584 22159133 887 4958 PAPPA 0 . GRCh38 9 116382433 116382433 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4716C>A p.Asn1572Lys p.N1572K ENST00000328252 21/22 188 177 11 174 174 0 strelka-varscan-mutect PAPPA,missense_variant,p.Asn1572Lys,ENST00000328252,NM_002581.3;PAPPA,non_coding_transcript_exon_variant,,ENST00000483254,; A ENST00000328252 Transcript missense_variant 5085/10959 4716/4884 1572/1627 N/K aaC/aaA 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 21/22 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347,SMART_domains:SM00004 MODERATE 1 SNV 1 1 PASS rs1355864464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 116382433 116382433 C A 1 0 0 0 0 1 0 0 0 11512 506 18 2 2 PAPPA 9 116382433 Missense_Mutation SNP C C3L-00144_T 146849 116382433 22012284 888 4959 ASTN2 0 . GRCh38 9 116805672 116805672 + Nonsense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.2203C>T p.Gln735Ter p.Q735* ENST00000361209 12/22 136 126 10 117 117 0 strelka-mutect ASTN2,stop_gained,p.Gln786Ter,ENST00000313400,;ASTN2,stop_gained,p.Gln735Ter,ENST00000361209,NM_014010.4;ASTN2,stop_gained,p.Gln509Ter,ENST00000373986,;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; A ENST00000361209 Transcript stop_gained 2335/4622 2203/3867 735/1288 Q/* Cag/Tag COSM1701600,COSM1701601 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 12/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 116805672 116805672 G A 1 0 0 0 0 0 1 0 0 1212 1357 47 3 3 ASTN2 9 116805672 Nonsense_Mutation SNP G C3L-00144_T 423239 116805672 21589045 889 4960 OR1J1 0 . GRCh38 9 122477309 122477309 + Silent SNP G G T rs780844209 C3L-00144_T C3L-00144_N G G c.618C>A p.= p.A206A ENST00000259357 1/1 303 249 54 292 292 0 strelka-varscan-mutect OR1J1,synonymous_variant,p.=,ENST00000259357,NM_001004451.1;RP11-542K23.9,downstream_gene_variant,,ENST00000412262,; T ENST00000259357 Transcript synonymous_variant 618/969 618/969 206/322 A gcC/gcA rs780844209,COSM1459828 1 -1 OR1J1 HGNC HGNC:8208 protein_coding YES CCDS35120.1 ENSP00000259357 Q8NGS3 A0A126GWP9 UPI0000061E79 NM_001004451.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF213,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW SNV 0,1 1 PASS rs780844209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 122477309 122477309 G T 1 0 0 0 0 0 0 0 1 11037 1335 47 2 2 OR1J1 9 122477309 Silent SNP G C3L-00144_T 5671637 122477309 15917408 890 4961 GARNL3 0 . GRCh38 9 127339668 127339668 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1052G>T p.Ser351Ile p.S351I ENST00000373387 13/28 292 252 40 210 210 0 strelka-varscan-mutect GARNL3,missense_variant,p.Ser351Ile,ENST00000373387,NM_032293.4;GARNL3,missense_variant,p.Ser329Ile,ENST00000435213,NM_001286779.1;GARNL3,non_coding_transcript_exon_variant,,ENST00000464616,;GARNL3,missense_variant,p.Ser333Ile,ENST00000373386,;GARNL3,downstream_gene_variant,,ENST00000495172,;GARNL3,upstream_gene_variant,,ENST00000460176,; T ENST00000373387 Transcript missense_variant 1404/3800 1052/3042 351/1013 S/I aGc/aTc 1 1 GARNL3 HGNC HGNC:25425 protein_coding YES CCDS6869.2 ENSP00000362485 Q5VVW2 UPI0000EE56F2 NM_032293.4 deleterious(0) 13/28 PROSITE_profiles:PS50085,hmmpanther:PTHR15711:SF24,hmmpanther:PTHR15711,Pfam_domain:PF02145,Superfamily_domains:0043732 MODERATE 1 SNV 1 1 PASS rs995695949 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 127339668 127339668 G T 1 0 0 0 0 1 0 0 0 6111 971 34 2 2 GARNL3 9 127339668 Missense_Mutation SNP G C3L-00144_T 4862359 127339668 11055049 891 4962 FAM129B 0 . GRCh38 9 127506873 127506873 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2213A>G p.Asp738Gly p.D738G ENST00000373312 14/14 126 117 9 119 119 0 strelka-mutect FAM129B,missense_variant,p.Asp738Gly,ENST00000373312,NM_022833.3;FAM129B,missense_variant,p.Asp725Gly,ENST00000373314,NM_001035534.2;LRSAM1,downstream_gene_variant,,ENST00000323301,NM_138361.5;LRSAM1,downstream_gene_variant,,ENST00000300417,NM_001005373.3;LRSAM1,downstream_gene_variant,,ENST00000373324,NM_001190723.2;LRSAM1,downstream_gene_variant,,ENST00000373322,NM_001005374.3;FAM129B,intron_variant,,ENST00000478917,;LRSAM1,downstream_gene_variant,,ENST00000483302,;FAM129B,downstream_gene_variant,,ENST00000468379,;FAM129B,downstream_gene_variant,,ENST00000484348,;FAM129B,downstream_gene_variant,,ENST00000465154,; C ENST00000373312 Transcript missense_variant 2427/3957 2213/2241 738/746 D/G gAc/gGc 1 -1 FAM129B HGNC HGNC:25282 protein_coding YES CCDS35145.1 ENSP00000362409 Q96TA1 UPI00001592F0 NM_022833.3 tolerated_low_confidence(0.18) 14/14 hmmpanther:PTHR14392:SF2,hmmpanther:PTHR14392 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -17.56927 1 1 1 1 0 C 3 2 12 127506873 127506873 T C 1 0 0 0 0 1 0 0 0 5287 1667 58 5 5 FAM129B 9 127506873 Missense_Mutation SNP T C3L-00144_T 167205 127506873 10887844 892 4963 URM1 0 . GRCh38 9 128371399 128371399 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.19G>T p.Val7Leu p.V7L ENST00000452446 1/4 177 158 19 171 170 1 strelka-varscan-mutect URM1,missense_variant,p.Val7Leu,ENST00000372850,NM_001265582.1;URM1,missense_variant,p.Val7Leu,ENST00000452446,NM_001135947.2;URM1,missense_variant,p.Val7Leu,ENST00000372853,NM_030914.3;URM1,missense_variant,p.Val7Leu,ENST00000372847,;URM1,missense_variant,p.Val7Leu,ENST00000470840,; T ENST00000452446 Transcript missense_variant 19/2944 19/441 7/146 V/L Gtg/Ttg COSM4916750,COSM4916751 1 1 URM1 HGNC HGNC:28378 protein_coding YES CCDS48035.1 ENSP00000412922 Q9BTM9 UPI00017A7D83 NM_001135947.2 tolerated(0.51) 1/4 Gene3D:3.10.20.30,HAMAP:MF_03048,Pfam_domain:PF09138,hmmpanther:PTHR14986,hmmpanther:PTHR14986:SF4,Superfamily_domains:SSF54285 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 128371399 128371399 G T 1 0 0 0 0 1 0 0 0 17559 1029 36 2 2 URM1 9 128371399 Missense_Mutation SNP G C3L-00144_T 864526 128371399 10023318 893 4964 HMCN2 0 . GRCh38 9 130349652 130349652 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.4416C>A p.= p.T1472T ENST00000624552 29/98 92 77 15 92 92 0 strelka-varscan-mutect HMCN2,synonymous_variant,p.=,ENST00000624552,NM_001291815.1; A ENST00000624552 Transcript synonymous_variant 4416/15610 4416/15180 1472/5059 T acC/acA 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 29/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS rs934945599 . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 2 1 12 130349652 130349652 C A 1 0 0 0 0 0 0 0 1 7112 581 21 2 2 HMCN2 9 130349652 Silent SNP C C3L-00144_T 1978253 130349652 8045065 894 4965 TTF1 0 . GRCh38 9 132402640 132402640 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.182A>G p.His61Arg p.H61R ENST00000334270 2/11 146 131 15 142 142 0 strelka-varscan-mutect TTF1,missense_variant,p.His61Arg,ENST00000334270,NM_007344.3;TTF1,intron_variant,,ENST00000612514,NM_001205296.1; C ENST00000334270 Transcript missense_variant 222/3052 182/2718 61/905 H/R cAt/cGt 1 -1 TTF1 HGNC HGNC:12397 protein_coding YES CCDS6948.1 ENSP00000333920 Q15361 A0A024R8C1 UPI00001B55A7 NM_007344.3 tolerated(0.14) 2/11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 132402640 132402640 T C 1 0 0 0 0 1 0 0 0 17228 1464 51 5 5 TTF1 9 132402640 Missense_Mutation SNP T C3L-00144_T 2052988 132402640 5992077 895 4966 COL5A1 0 . GRCh38 9 134766454 134766454 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2089G>T p.Gly697Cys p.G697C ENST00000371817 22/66 193 170 23 200 200 0 strelka-varscan-mutect COL5A1,missense_variant,p.Gly697Cys,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly697Cys,ENST00000618395,NM_001278074.1; T ENST00000371817 Transcript missense_variant,splice_region_variant 2503/8471 2089/5517 697/1838 G/C Ggt/Tgt 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0) 22/66 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 134766454 134766454 G T 1 0 0 0 0 1 0 0 0 3485 1246 43 2 2 COL5A1 9 134766454 Missense_Mutation SNP G C3L-00144_T 2363814 134766454 3628263 896 4967 FCN2 0 . GRCh38 9 134885317 134885317 + Missense_Mutation SNP G G T rs575801515 C3L-00144_T C3L-00144_N G G c.380G>T p.Arg127Leu p.R127L ENST00000291744 5/8 260 230 30 292 292 0 varscan-mutect FCN2,missense_variant,p.Arg127Leu,ENST00000291744,NM_004108.2;FCN2,missense_variant,p.Arg89Leu,ENST00000350339,NM_015837.2; T ENST00000291744 Transcript missense_variant 390/1057 380/942 127/313 R/L cGg/cTg rs575801515,COSM3214424,COSM4684223 1 1 FCN2 HGNC HGNC:3624 protein_coding YES CCDS6983.1 ENSP00000291744 Q15485 UPI000013E075 NM_004108.2 tolerated(0.1) 5/8 PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF165,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs575801515 . 0 206 0 0 0 0 0 4 -5.452302 0 0 1 0 0 T 3 4 12 134885317 134885317 G T 1 0 0 0 0 1 0 0 0 5655 1116 39 1 1 FCN2 9 134885317 Missense_Mutation SNP G C3L-00144_T 118863 134885317 3509400 897 4968 LCN1 0 . GRCh38 9 135523991 135523991 + Splice_Site SNP G G T rs776394912 C3L-00144_T C3L-00144_N G G c.403+1G>T p.X135_splice ENST00000263598 130 103 27 120 120 0 strelka-varscan-mutect LCN1,splice_donor_variant,,ENST00000263598,NM_001252619.1,NM_001252618.1,NM_002297.3,NM_001252617.1;LCN1,splice_donor_variant,,ENST00000371781,; T ENST00000263598 Transcript splice_donor_variant -/776 403/531 135/176 rs776394912 1 1 LCN1 HGNC HGNC:6525 protein_coding YES CCDS6991.1 ENSP00000263598 P31025 A0A024R8D7 UPI0000040631 NM_001252619.1,NM_001252618.1,NM_002297.3,NM_001252617.1 4/6 HIGH 1 SNV 1 1 PASS rs776394912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 135523991 135523991 G T 1 0 0 0 0 0 0 1 0 8586 1275 44 2 2 LCN1 9 135523991 Splice_Site SNP G C3L-00144_T 638674 135523991 2870726 898 4969 EXD3 0 . GRCh38 9 137306993 137306993 + Missense_Mutation SNP C C A rs750524262 C3L-00144_T C3L-00144_N C C c.2588G>T p.Cys863Phe p.C863F ENST00000340951 22/22 53 43 10 44 44 0 strelka-varscan-mutect EXD3,missense_variant,p.Cys863Phe,ENST00000340951,NM_017820.4;NRARP,upstream_gene_variant,,ENST00000356628,NM_001004354.2;EXD3,3_prime_UTR_variant,,ENST00000491734,;EXD3,non_coding_transcript_exon_variant,,ENST00000487745,; A ENST00000340951 Transcript missense_variant 2784/2872 2588/2631 863/876 C/F tGc/tTc rs750524262 1 -1 EXD3 HGNC HGNC:26023 protein_coding YES CCDS48066.1 ENSP00000340474 Q8N9H8 A0A140VJP9 UPI00003676BC NM_017820.4 tolerated(0.7) 22/22 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs750524262 . 0 200 10 0 0 0 0 0 -19.99981 0.9999892 1 1 1 0 A 3 1 12 137306993 137306993 C A 1 0 0 0 0 1 0 0 0 5166 710 25 2 2 EXD3 9 137306993 Missense_Mutation SNP C C3L-00144_T 1783002 137306993 1087724 899 4970 CACNA1B 0 . GRCh38 9 138023694 138023694 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.2951A>G p.Lys984Arg p.K984R ENST00000371372 19/47 331 298 33 291 290 1 strelka-varscan-mutect CACNA1B,missense_variant,p.Lys984Arg,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Lys984Arg,ENST00000371363,;CACNA1B,missense_variant,p.Lys985Arg,ENST00000371355,;CACNA1B,missense_variant,p.Lys985Arg,ENST00000371357,;CACNA1B,missense_variant,p.Lys984Arg,ENST00000277549,;CACNA1B,missense_variant,p.Lys984Arg,ENST00000277551,NM_001243812.1; G ENST00000371372 Transcript missense_variant 3096/9790 2951/7020 984/2339 K/R aAg/aGg 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 tolerated(0.56) 19/47 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 138023694 138023694 A G 1 0 0 0 0 1 0 0 0 2227 72 3 5 5 CACNA1B 9 138023694 Missense_Mutation SNP A C3L-00144_T 716701 138023694 371023 900 4971 CACNA1B 0 . GRCh38 9 138112453 138112453 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.5484G>T p.= p.V1828V ENST00000371372 40/47 290 229 61 209 209 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript synonymous_variant 5629/9790 5484/7020 1828/2339 V gtG/gtT 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 40/47 Pfam_domain:PF08763,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 138112453 138112453 G T 1 0 0 0 0 0 0 0 1 2227 1364 48 2 2 CACNA1B 9 138112453 Silent SNP G C3L-00144_T 88759 138112453 282264 901 4972 CACNA1B 0 . GRCh38 9 138112498 138112498 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.5529C>A p.= p.P1843P ENST00000371372 40/47 209 167 42 147 147 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; A ENST00000371372 Transcript synonymous_variant 5674/9790 5529/7020 1843/2339 P ccC/ccA 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 40/47 Pfam_domain:PF08763,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 LOW 1 SNV 5 1 PASS rs1258959076 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 138112498 138112498 C A 1 0 0 0 0 0 0 0 1 2227 610 22 2 2 CACNA1B 9 138112498 Silent SNP C C3L-00144_T 45 138112498 282219 902 4973 CACNA1B 0 . GRCh38 9 138121848 138121848 + Missense_Mutation SNP G G A rs76756995 C3L-00144_T C3L-00144_N G G c.6869G>A p.Arg2290His p.R2290H ENST00000371372 47/47 311 280 31 267 266 1 strelka-varscan-mutect CACNA1B,missense_variant,p.Arg2290His,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Arg2288His,ENST00000371363,;CACNA1B,missense_variant,p.Arg2291His,ENST00000371355,;CACNA1B,missense_variant,p.Arg2289His,ENST00000371357,;CACNA1B,missense_variant,p.Ala2228Thr,ENST00000277549,;CACNA1B,missense_variant,p.Ala2228Thr,ENST00000277551,NM_001243812.1; A ENST00000371372 Transcript missense_variant 7014/9790 6869/7020 2290/2339 R/H cGc/cAc rs76756995 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 deleterious(0.04) 47/47 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs76756995 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 138121848 138121848 G A 1 0 0 0 0 1 0 0 0 2227 1087 38 1 1 CACNA1B 9 138121848 Missense_Mutation SNP G C3L-00144_T 9350 138121848 272869 903 4974 ZMYND11 0 . GRCh38 10 239509 239509 + Silent SNP C C A rs761293702 C3L-00144_T C3L-00144_N C C c.681C>A p.= p.T227T ENST00000397962 7/15 128 115 13 100 100 0 varscan-mutect ZMYND11,synonymous_variant,p.=,ENST00000397962,NM_006624.5;ZMYND11,synonymous_variant,p.=,ENST00000381591,;ZMYND11,synonymous_variant,p.=,ENST00000309776,NM_001202466.1;ZMYND11,synonymous_variant,p.=,ENST00000397959,NM_001202465.1;ZMYND11,synonymous_variant,p.=,ENST00000381604,;ZMYND11,synonymous_variant,p.=,ENST00000402736,;ZMYND11,synonymous_variant,p.=,ENST00000627286,;ZMYND11,synonymous_variant,p.=,ENST00000381607,NM_001202464.1;ZMYND11,synonymous_variant,p.=,ENST00000381584,;ZMYND11,synonymous_variant,p.=,ENST00000509513,NM_212479.3;ZMYND11,synonymous_variant,p.=,ENST00000558098,NM_001202467.1,NM_001202468.1;ZMYND11,synonymous_variant,p.=,ENST00000602682,;ZMYND11,synonymous_variant,p.=,ENST00000403354,;ZMYND11,downstream_gene_variant,,ENST00000439456,;ZMYND11,downstream_gene_variant,,ENST00000397955,;ZMYND11,upstream_gene_variant,,ENST00000473115,;ZMYND11,upstream_gene_variant,,ENST00000488275,; A ENST00000397962 Transcript synonymous_variant 1022/4306 681/1809 227/602 T acC/acA rs761293702 1 1 ZMYND11 HGNC HGNC:16966 protein_coding YES CCDS7052.2 ENSP00000381053 Q15326 UPI0000458A5F NM_006624.5 7/15 PROSITE_profiles:PS50014,hmmpanther:PTHR24102,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370 LOW 1 SNV 1 1 PASS rs761293702 . 0 206 2 2 0 0 0 0 -19.12853 0.9999957 1 1 1 0 A 2 1 12 239509 239509 C A 1 0 0 0 0 0 0 0 1 18286 639 23 1 1 ZMYND11 10 239509 Silent SNP C C3L-00144_T 239509 133557913 904 4975 LARP4B 0 . GRCh38 10 825252 825252 + Nonsense_Mutation SNP C C A rs765670503 C3L-00144_T C3L-00144_N C C c.1297G>T p.Glu433Ter p.E433* ENST00000612396 13/18 311 284 27 295 295 0 strelka-varscan-mutect LARP4B,stop_gained,p.Glu433Ter,ENST00000612396,NM_015155.2;LARP4B,stop_gained,p.Glu433Ter,ENST00000316157,;LARP4B,upstream_gene_variant,,ENST00000448368,;LARP4B,upstream_gene_variant,,ENST00000609318,; A ENST00000612396 Transcript stop_gained 1614/8546 1297/2217 433/738 E/* Gaa/Taa rs765670503 1 -1 LARP4B HGNC HGNC:28987 protein_coding YES CCDS31131.1 ENSP00000482767 Q92615 UPI00001F8C87 NM_015155.2 13/18 hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF43 HIGH 1 SNV 5 1 PASS rs765670503 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 825252 825252 C A 1 0 0 0 0 0 1 0 0 8542 922 32 2 2 LARP4B 10 825252 Nonsense_Mutation SNP C C3L-00144_T 585743 825252 132972170 905 4976 ADARB2 0 . GRCh38 10 1363488 1363488 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.617C>A p.Pro206Gln p.P206Q ENST00000381312 3/10 39 26 13 28 28 0 strelka-varscan-mutect ADARB2,missense_variant,p.Pro206Gln,ENST00000381312,NM_018702.3;RP11-398B16.2,upstream_gene_variant,,ENST00000432987,; T ENST00000381312 Transcript missense_variant 943/8421 617/2220 206/739 P/Q cCg/cAg 1 -1 ADARB2 HGNC HGNC:227 protein_coding YES CCDS7058.1 ENSP00000370713 Q9NS39 UPI0000071776 NM_018702.3 tolerated(0.44) 3/10 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF17 MODERATE 1 SNV 1 1 PASS rs1175021884 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 1363488 1363488 G T 1 0 0 0 0 1 0 0 0 327 1116 39 1 1 ADARB2 10 1363488 Missense_Mutation SNP G C3L-00144_T 538236 1363488 132433934 906 4977 ADARB2 0 . GRCh38 10 1363562 1363563 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.542_543insA p.Ala182GlyfsTer207 p.A182Gfs*207 ENST00000381312 3/10 37 32 5 48 48 0 sindel-varindel-pindel ADARB2,frameshift_variant,p.Ala182GlyfsTer207,ENST00000381312,NM_018702.3;RP11-398B16.2,upstream_gene_variant,,ENST00000432987,; T ENST00000381312 Transcript frameshift_variant 868-869/8421 542-543/2220 181/739 A/AX gcg/gcAg 1 -1 ADARB2 HGNC HGNC:227 protein_coding YES CCDS7058.1 ENSP00000370713 Q9NS39 UPI0000071776 NM_018702.3 3/10 PROSITE_profiles:PS50137,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF17,Pfam_domain:PF00035,Gene3D:3.30.160.20,SMART_domains:SM00358,Superfamily_domains:SSF54768 HIGH 1 insertion 1 1 PASS . . 0 201 9 0 0 0 0 0 -12.93887 0.9999922 1 1 1 0 T 7 5 12 1363562 1363562 - T 1 0 1 1 0 0 0 0 0 327 639 23 0 0 ADARB2 10 1363562 Frame_Shift_Ins INS - C3L-00144_T 74 1363562 132433860 907 4978 AKR1C2 0 . GRCh38 10 4995754 4995754 + Splice_Site SNP A A T novel C3L-00144_T C3L-00144_N A A c.680+2T>A p.X227_splice ENST00000380753 184 167 17 151 151 0 varscan-mutect AKR1C2,splice_donor_variant,,ENST00000380753,NM_205845.2,NM_001354.5;AKR1C2,splice_donor_variant,,ENST00000421196,;AKR1C2,downstream_gene_variant,,ENST00000455190,NM_001135241.2;AKR1C2,downstream_gene_variant,,ENST00000604507,;RP11-499O7.7,intron_variant,,ENST00000451575,;RP11-499O7.7,upstream_gene_variant,,ENST00000440414,;AKR1C2,downstream_gene_variant,,ENST00000604184,;AKR1C2,splice_donor_variant,,ENST00000460124,; T ENST00000380753 Transcript splice_donor_variant -/3756 680/972 227/323 1 -1 AKR1C2 HGNC HGNC:385 protein_coding YES CCDS7062.1 ENSP00000370129 P52895 UPI0000111D9F NM_205845.2,NM_001354.5 6/8 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 4995754 4995754 A T 1 0 0 0 0 0 0 1 0 554 405 14 4 4 AKR1C2 10 4995754 Splice_Site SNP A C3L-00144_T 3632192 4995754 128801668 908 4979 IL15RA 0 . GRCh38 10 5960445 5960445 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.763G>T p.Glu255Ter p.E255* ENST00000397248 5/8 359 282 77 343 343 0 strelka-varscan-mutect IL15RA,stop_gained,p.Glu133Ter,ENST00000525219,NM_001243539.1;IL15RA,stop_gained,p.Glu255Ter,ENST00000397248,NM_001256765.1;IL15RA,stop_gained,p.Glu169Ter,ENST00000379977,NM_002189.3;IL15RA,stop_gained,p.Glu220Ter,ENST00000622442,;IL15RA,stop_gained,p.Glu220Ter,ENST00000620345,;IL15RA,stop_gained,p.Glu220Ter,ENST00000397251,;IL15RA,stop_gained,p.Glu136Ter,ENST00000528354,NM_172200.2;IL15RA,stop_gained,p.Glu220Ter,ENST00000620865,;IL15RA,stop_gained,p.Glu72Ter,ENST00000447291,;IL15RA,stop_gained,p.Glu100Ter,ENST00000397246,;IL15RA,stop_gained,p.Glu169Ter,ENST00000397255,;IL15RA,stop_gained,p.Glu132Ter,ENST00000453922,;IL15RA,stop_gained,p.Glu74Ter,ENST00000532039,;IL15RA,stop_gained,p.Glu136Ter,ENST00000530685,;IL15RA,stop_gained,p.Glu42Ter,ENST00000435171,;IL15RA,stop_gained,p.Glu71Ter,ENST00000379971,;IL15RA,stop_gained,p.Glu71Ter,ENST00000397250,;IL15RA,stop_gained,p.Glu136Ter,ENST00000429135,;IL15RA,non_coding_transcript_exon_variant,,ENST00000534292,;IL15RA,non_coding_transcript_exon_variant,,ENST00000379972,;IL15RA,non_coding_transcript_exon_variant,,ENST00000532948,;IL15RA,non_coding_transcript_exon_variant,,ENST00000379974,; A ENST00000397248 Transcript stop_gained 777/1799 763/1062 255/353 E/* Gag/Tag 1 -1 IL15RA HGNC HGNC:5978 protein_coding YES CCDS73065.1 ENSP00000380421 A0A0A0MS77 UPI00024F9753 NM_001256765.1 5/8 hmmpanther:PTHR15060,hmmpanther:PTHR15060:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 5960445 5960445 C A 1 0 0 0 0 0 1 0 0 7540 835 29 2 2 IL15RA 10 5960445 Nonsense_Mutation SNP C C3L-00144_T 964691 5960445 127836977 909 4980 PRKCQ 0 . GRCh38 10 6497235 6497235 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.559G>T p.Gly187Cys p.G187C ENST00000263125 6/18 334 299 35 267 266 1 strelka-varscan-mutect PRKCQ,missense_variant,p.Gly187Cys,ENST00000263125,NM_001323265.1,NM_006257.4,NM_001282644.1;PRKCQ,missense_variant,p.Gly62Cys,ENST00000539722,NM_001323266.1,NM_001282645.1;PRKCQ,missense_variant,p.Gly187Cys,ENST00000397176,NM_001242413.2;PRKCQ,missense_variant,p.Gly151Cys,ENST00000610727,; A ENST00000263125 Transcript missense_variant 659/3285 559/2121 187/706 G/C Ggc/Tgc 1 -1 PRKCQ HGNC HGNC:9410 protein_coding YES CCDS7079.1 ENSP00000263125 Q04759 UPI000012DF74 NM_001323265.1,NM_006257.4,NM_001282644.1 deleterious(0) 6/18 Gene3D:3.30.60.20,Pfam_domain:PF00130,PIRSF_domain:PIRSF000551,PIRSF_domain:PIRSF501105,PROSITE_patterns:PS00479,PROSITE_profiles:PS50081,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF181,SMART_domains:SM00109,Superfamily_domains:SSF57889 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 6497235 6497235 C A 1 0 0 0 0 1 0 0 0 12648 623 22 2 2 PRKCQ 10 6497235 Missense_Mutation SNP C C3L-00144_T 536790 6497235 127300187 910 4981 ITIH5 0 . GRCh38 10 7569776 7569776 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2041G>T p.Asp681Tyr p.D681Y ENST00000397146 12/14 101 73 28 78 78 0 strelka-varscan-mutect ITIH5,missense_variant,p.Asp681Tyr,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Asp467Tyr,ENST00000613909,NM_032817.5;ITIH5,downstream_gene_variant,,ENST00000397145,NM_001001851.2;ITIH5,non_coding_transcript_exon_variant,,ENST00000473591,;ITIH5,downstream_gene_variant,,ENST00000434980,;ITIH5,non_coding_transcript_exon_variant,,ENST00000492668,;ITIH5,downstream_gene_variant,,ENST00000476417,;ITIH5,downstream_gene_variant,,ENST00000468389,; A ENST00000397146 Transcript missense_variant 2120/6721 2041/2829 681/942 D/Y Gat/Tat 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 deleterious(0) 12/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7569776 7569776 C A 1 0 0 0 0 1 0 0 0 7813 826 29 2 2 ITIH5 10 7569776 Missense_Mutation SNP C C3L-00144_T 1072541 7569776 126227646 911 4982 MCM10 0 . GRCh38 10 13175642 13175642 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.728A>C p.Gln243Pro p.Q243P ENST00000484800 6/20 120 112 8 108 108 0 strelka-varscan-mutect MCM10,missense_variant,p.Gln242Pro,ENST00000378694,;MCM10,missense_variant,p.Gln242Pro,ENST00000378714,NM_018518.4;MCM10,missense_variant,p.Gln243Pro,ENST00000484800,NM_182751.2;MCM10,downstream_gene_variant,,ENST00000479669,; C ENST00000484800 Transcript missense_variant 831/3157 728/2628 243/875 Q/P cAa/cCa 1 1 MCM10 HGNC HGNC:18043 protein_coding YES CCDS7096.1 ENSP00000418268 Q7L590 UPI000013C5E2 NM_182751.2 tolerated(0.13) 6/20 hmmpanther:PTHR13454 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 13175642 13175642 A C 1 0 0 0 0 1 0 0 0 9317 130 5 5 5 MCM10 10 13175642 Missense_Mutation SNP A C3L-00144_T 5605866 13175642 120621780 912 4983 ITGA8 0 . GRCh38 10 15558177 15558177 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.2663C>G p.Pro888Arg p.P888R ENST00000378076 26/30 193 171 22 137 137 0 strelka-varscan-mutect ITGA8,missense_variant,p.Pro888Arg,ENST00000378076,NM_003638.2,NM_001291494.1; C ENST00000378076 Transcript missense_variant 3017/6755 2663/3192 888/1063 P/R cCt/cGt 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 tolerated(0.05) 26/30 Gene3D:1jv2A04,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 12 15558177 15558177 G C 1 0 0 0 0 1 0 0 0 7789 1000 35 4 4 ITGA8 10 15558177 Missense_Mutation SNP G C3L-00144_T 2382535 15558177 118239245 913 4984 ITGA8 0 . GRCh38 10 15604290 15604290 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2036A>T p.Glu679Val p.E679V ENST00000378076 20/30 214 167 47 205 204 1 strelka-varscan-mutect ITGA8,missense_variant,p.Glu679Val,ENST00000378076,NM_003638.2,NM_001291494.1;ITGA8,upstream_gene_variant,,ENST00000477064,; A ENST00000378076 Transcript missense_variant 2390/6755 2036/3192 679/1063 E/V gAa/gTa 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 tolerated(0.32) 20/30 Gene3D:2.60.40.1510,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs1338527059 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 15604290 15604290 T A 1 0 0 0 0 1 0 0 0 7789 1783 62 4 4 ITGA8 10 15604290 Missense_Mutation SNP T C3L-00144_T 46113 15604290 118193132 914 4985 MRC1 0 . GRCh38 10 17863653 17863653 + Missense_Mutation SNP G G T rs781837322 C3L-00144_T C3L-00144_N G G c.1754G>T p.Arg585Leu p.R585L ENST00000569591 11/30 265 205 60 220 220 0 strelka-varscan-mutect MRC1,missense_variant,p.Arg585Leu,ENST00000569591,NM_002438.3;RP11-457D2.3,intron_variant,,ENST00000442231,; T ENST00000569591 Transcript missense_variant 1876/5198 1754/4371 585/1456 R/L cGg/cTg rs781837322 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 tolerated(1) 11/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs781837322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 17863653 17863653 G T 1 0 0 0 0 1 0 0 0 9722 1116 39 1 1 MRC1 10 17863653 Missense_Mutation SNP G C3L-00144_T 2259363 17863653 115933769 915 4986 MALRD1 0 . GRCh38 10 19567688 19567688 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5665G>T p.Glu1889Ter p.E1889* ENST00000454679 33/40 162 127 35 147 146 1 strelka-varscan-mutect MALRD1,stop_gained,p.Glu1889Ter,ENST00000454679,NM_001142308.2;MALRD1,stop_gained,p.Glu1268Ter,ENST00000377266,;MALRD1,stop_gained,p.Glu240Ter,ENST00000377265,; T ENST00000454679 Transcript stop_gained 5833/6880 5665/6471 1889/2156 E/* Gag/Tag 1 1 MALRD1 HGNC HGNC:24331 protein_coding YES CCDS73071.1 ENSP00000412763 Q5VYJ5 UPI000387C99A NM_001142308.2 33/40 PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF86,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 19567688 19567688 G T 1 0 0 0 0 0 1 0 0 9121 943 33 2 2 MALRD1 10 19567688 Nonsense_Mutation SNP G C3L-00144_T 1704035 19567688 114229734 916 4987 PLXDC2 0 . GRCh38 10 20279729 20279729 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1500G>A p.Met500Ile p.M500I ENST00000377252 14/14 293 270 23 234 234 0 strelka-varscan-mutect PLXDC2,missense_variant,p.Met500Ile,ENST00000377252,NM_032812.8;PLXDC2,missense_variant,p.Met451Ile,ENST00000377242,NM_001282736.1;PLXDC2,non_coding_transcript_exon_variant,,ENST00000377238,; A ENST00000377252 Transcript missense_variant 2341/12468 1500/1590 500/529 M/I atG/atA 1 1 PLXDC2 HGNC HGNC:21013 protein_coding YES CCDS7132.1 ENSP00000366460 Q6UX71 UPI0000048F2C NM_032812.8 deleterious(0.01) 14/14 hmmpanther:PTHR13055:SF11,hmmpanther:PTHR13055 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 20279729 20279729 G A 1 0 0 0 0 1 0 0 0 12224 1290 45 3 3 PLXDC2 10 20279729 Missense_Mutation SNP G C3L-00144_T 712041 20279729 113517693 917 4988 SKIDA1 0 . GRCh38 10 21517525 21517525 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.298G>T p.Val100Phe p.V100F ENST00000449193 4/4 110 104 6 95 95 0 strelka-mutect SKIDA1,missense_variant,p.Val100Phe,ENST00000449193,NM_207371.3;SKIDA1,missense_variant,p.Val100Phe,ENST00000444772,;SKIDA1,downstream_gene_variant,,ENST00000633225,;SKIDA1,downstream_gene_variant,,ENST00000487107,; A ENST00000449193 Transcript missense_variant 2551/6598 298/2727 100/908 V/F Gtc/Ttc 1 -1 SKIDA1 HGNC HGNC:32697 protein_coding YES CCDS44363.1 ENSP00000410041 E9PAX1 UPI00015386B3 NM_207371.3 deleterious(0) 4/4 hmmpanther:PTHR23187:SF2,hmmpanther:PTHR23187 MODERATE 1 SNV 3 1 PASS . . 0 208 0 2 0 0 0 0 -9.269023 0.9999994 1 1 1 0 A 3 1 12 21517525 21517525 C A 1 0 0 0 0 1 0 0 0 14620 536 19 1 1 SKIDA1 10 21517525 Missense_Mutation SNP C C3L-00144_T 1237796 21517525 112279897 918 4989 GPR158 0 . GRCh38 10 25598125 25598125 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2499C>G p.Ser833Arg p.S833R ENST00000376351 11/11 205 156 49 176 176 0 strelka-varscan-mutect GPR158,missense_variant,p.Ser833Arg,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; G ENST00000376351 Transcript missense_variant 2858/6959 2499/3648 833/1215 S/R agC/agG 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 tolerated(0.1) 11/11 Low_complexity_(Seg):seg,hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 25598125 25598125 C G 1 0 0 0 0 1 0 0 0 6549 738 26 4 4 GPR158 10 25598125 Missense_Mutation SNP C C3L-00144_T 4080600 25598125 108199297 919 4990 GPR158 0 . GRCh38 10 25598270 25598270 + Missense_Mutation SNP G G T rs141827771 C3L-00144_T C3L-00144_N G G c.2644G>T p.Ala882Ser p.A882S ENST00000376351 11/11 177 132 45 177 177 0 strelka-varscan-mutect GPR158,missense_variant,p.Ala882Ser,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; T ENST00000376351 Transcript missense_variant 3003/6959 2644/3648 882/1215 A/S Gct/Tct rs141827771,COSM1603344,COSM2133819 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0) 11/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs141827771 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 25598270 25598270 G T 1 0 0 0 0 1 0 0 0 6549 1087 38 1 1 GPR158 10 25598270 Missense_Mutation SNP G C3L-00144_T 145 25598270 108199152 920 4991 MYO3A 0 . GRCh38 10 26125552 26125552 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.2058C>T p.= p.L686L ENST00000265944 19/35 373 293 80 338 338 0 strelka-varscan-mutect MYO3A,synonymous_variant,p.=,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; T ENST00000265944 Transcript synonymous_variant 2224/5581 2058/4851 686/1616 L ctC/ctT 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 19/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 26125552 26125552 C T 1 0 0 0 0 0 0 0 1 10077 900 32 3 3 MYO3A 10 26125552 Silent SNP C C3L-00144_T 527282 26125552 107671870 921 4992 APBB1IP 0 . GRCh38 10 26492375 26492375 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.49G>T p.Gly17Ter p.G17* ENST00000376236 3/15 122 107 15 105 104 1 strelka-varscan-mutect APBB1IP,stop_gained,p.Gly17Ter,ENST00000376236,NM_019043.3;APBB1IP,stop_gained,p.Gly17Ter,ENST00000356785,; T ENST00000376236 Transcript stop_gained 504/2771 49/2001 17/666 G/* Gga/Tga 1 1 APBB1IP HGNC HGNC:17379 protein_coding YES CCDS31167.1 ENSP00000365411 Q7Z5R6 UPI00001AF165 NM_019043.3 3/15 hmmpanther:PTHR11243,hmmpanther:PTHR11243:SF14 HIGH 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -19.99938 0.9999999 1 1 1 0 T 4 4 12 26492375 26492375 G T 1 0 0 0 0 0 1 0 0 880 1233 43 2 2 APBB1IP 10 26492375 Nonsense_Mutation SNP G C3L-00144_T 366823 26492375 107305047 922 4993 PDSS1 0 . GRCh38 10 26704734 26704734 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.220A>T p.Ile74Leu p.I74L ENST00000376215 3/12 306 283 23 314 314 0 strelka-varscan-mutect PDSS1,missense_variant,p.Ile74Leu,ENST00000376215,NM_014317.3;PDSS1,upstream_gene_variant,,ENST00000473224,; T ENST00000376215 Transcript missense_variant 273/1626 220/1248 74/415 I/L Ata/Tta 1 1 PDSS1 HGNC HGNC:17759 protein_coding YES CCDS31168.1 ENSP00000365388 Q5T2R2 UPI000013DB22 NM_014317.3 tolerated(0.42) 3/12 hmmpanther:PTHR12001,hmmpanther:PTHR12001:SF47 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 26704734 26704734 A T 1 0 0 0 0 1 0 0 0 11781 449 16 4 4 PDSS1 10 26704734 Missense_Mutation SNP A C3L-00144_T 212359 26704734 107092688 923 4994 ANKRD26 0 . GRCh38 10 27043526 27043526 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.2061A>G p.= p.L687L ENST00000376087 20/34 179 164 15 135 135 0 strelka-varscan-mutect ANKRD26,synonymous_variant,p.=,ENST00000436985,;ANKRD26,synonymous_variant,p.=,ENST00000376087,NM_014915.2,NM_001256053.1;ANKRD26,non_coding_transcript_exon_variant,,ENST00000490015,; C ENST00000376087 Transcript synonymous_variant 2227/6591 2061/5133 687/1710 L ttA/ttG 1 -1 ANKRD26 HGNC HGNC:29186 protein_coding YES CCDS41499.1 ENSP00000365255 Q9UPS8 UPI000006FC41 NM_014915.2,NM_001256053.1 20/34 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF24 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 27043526 27043526 T C 1 0 0 0 0 0 0 0 1 757 1751 61 5 5 ANKRD26 10 27043526 Silent SNP T C3L-00144_T 338792 27043526 106753896 924 4995 PTCHD3 0 . GRCh38 10 27413712 27413712 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.539C>A p.Ala180Glu p.A180E ENST00000438700 1/4 129 103 26 120 120 0 strelka-varscan-mutect PTCHD3,missense_variant,p.Ala180Glu,ENST00000438700,NM_001034842.3;PTCHD3,missense_variant,p.Ala180Glu,ENST00000622555,; T ENST00000438700 Transcript missense_variant 657/2529 539/2304 180/767 A/E gCg/gAg 1 -1 PTCHD3 HGNC HGNC:24776 protein_coding YES CCDS31173.1 ENSP00000417658 Q3KNS1 UPI000004E892 NM_001034842.3 tolerated(0.13) 1/4 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF60 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27413712 27413712 G T 1 0 0 0 0 1 0 0 0 12886 1087 38 1 1 PTCHD3 10 27413712 Missense_Mutation SNP G C3L-00144_T 370186 27413712 106383710 925 4996 KIAA1462 0 . GRCh38 10 30028655 30028655 + Missense_Mutation SNP C C A rs150974148 C3L-00144_T C3L-00144_N C C c.1493G>T p.Arg498Leu p.R498L ENST00000375377 3/4 41 32 9 48 48 0 strelka-varscan-mutect KIAA1462,missense_variant,p.Arg498Leu,ENST00000375377,NM_020848.2; A ENST00000375377 Transcript missense_variant 1595/9265 1493/4080 498/1359 R/L cGg/cTg rs150974148 1 -1 KIAA1462 HGNC HGNC:29283 protein_coding YES CCDS41500.1 ENSP00000364526 Q9P266 UPI00001D8117 NM_020848.2 tolerated(0.31) 3/4 hmmpanther:PTHR34757,hmmpanther:PTHR34757:SF1,Pfam_domain:PF15351 MODERATE 1 SNV 5 1 PASS rs150974148 . 0 201 8 0 0 0 0 0 -19.99764 0.9999991 1 1 1 0 A 3 1 12 30028655 30028655 C A 1 0 0 0 0 1 0 0 0 8116 652 23 1 1 KIAA1462 10 30028655 Missense_Mutation SNP C C3L-00144_T 2614943 30028655 103768767 926 4997 ZNF438 0 . GRCh38 10 30849095 30849095 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1310T>C p.Met437Thr p.M437T ENST00000442986 7/8 429 375 54 391 391 0 strelka-varscan-mutect ZNF438,start_lost,p.Met1?,ENST00000375311,;ZNF438,missense_variant,p.Met427Thr,ENST00000452305,NM_001143770.1,NM_001143771.1;ZNF438,missense_variant,p.Met388Thr,ENST00000538351,NM_001143769.1;ZNF438,missense_variant,p.Met437Thr,ENST00000442986,NM_182755.2;ZNF438,missense_variant,p.Met427Thr,ENST00000331737,;ZNF438,missense_variant,p.Met437Thr,ENST00000436087,NM_001143766.1,NM_001143768.1;ZNF438,missense_variant,p.Met437Thr,ENST00000361310,;ZNF438,missense_variant,p.Met437Thr,ENST00000413025,NM_001143767.1;ZNF438,intron_variant,,ENST00000609683,; G ENST00000442986 Transcript missense_variant 1745/3245 1310/2487 437/828 M/T aTg/aCg 1 -1 ZNF438 HGNC HGNC:21029 protein_coding YES CCDS7168.1 ENSP00000412363 Q7Z4V0 UPI00001B3D8F NM_182755.2 deleterious(0.05) 7/8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 30849095 30849095 A G 1 0 0 0 0 1 0 0 0 18481 217 8 5 5 ZNF438 10 30849095 Missense_Mutation SNP A C3L-00144_T 820440 30849095 102948327 927 4998 ARHGAP12 0 . GRCh38 10 31908748 31908748 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.108A>T p.Gln36His p.Q36H ENST00000344936 3/20 189 168 21 178 178 0 strelka-varscan-mutect ARHGAP12,missense_variant,p.Gln36His,ENST00000396144,NM_001270695.1;ARHGAP12,missense_variant,p.Gln36His,ENST00000375245,NM_001270697.1;ARHGAP12,missense_variant,p.Gln36His,ENST00000375250,NM_001270696.1,NM_001270698.1;ARHGAP12,missense_variant,p.Gln36His,ENST00000311380,NM_001270699.1;ARHGAP12,missense_variant,p.Gln36His,ENST00000344936,NM_018287.6;HMGB1P7,upstream_gene_variant,,ENST00000450921,; A ENST00000344936 Transcript missense_variant 343/4128 108/2541 36/846 Q/H caA/caT 1 -1 ARHGAP12 HGNC HGNC:16348 protein_coding YES CCDS7170.1 ENSP00000345808 Q8IWW6 UPI000007445E NM_018287.6 tolerated(0.06) 3/20 PROSITE_profiles:PS50002,hmmpanther:PTHR23181,hmmpanther:PTHR23181:SF3,Pfam_domain:PF14604,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31908748 31908748 T A 1 0 0 0 0 1 0 0 0 989 1606 56 4 4 ARHGAP12 10 31908748 Missense_Mutation SNP T C3L-00144_T 1059653 31908748 101888674 928 4999 AGAP14P 0 . GRCh38 10 46357312 46357312 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.656C>A p.Ser219Ter p.S219* ENST00000624701 9/9 168 137 31 166 163 3 strelka-varscan-mutect AGAP14P,stop_gained,p.Ser219Ter,ENST00000624701,; A ENST00000624701 Transcript stop_gained 656/2058 656/2058 219/685 S/* tCg/tAg 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213 HIGH 1 SNV 5 1 PASS rs1454501521 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 46357312 46357312 C A 1 0 0 0 0 0 1 0 0 444 893 31 1 1 AGAP14P 10 46357312 Nonsense_Mutation SNP C C3L-00144_T 14448564 46357312 87440110 929 5000 RBP3 0 . GRCh38 10 47349651 47349651 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1167C>T p.= p.A389A ENST00000584701 1/4 364 332 32 337 336 1 strelka-varscan-mutect RBP3,synonymous_variant,p.=,ENST00000584701,NM_002900.2; T ENST00000584701 Transcript synonymous_variant 1281/4276 1167/3744 389/1247 A gcC/gcT 1 1 RBP3 HGNC HGNC:9921 protein_coding YES CCDS73119.1 ENSP00000463151 P10745 UPI000012D87A NM_002900.2 1/4 Gene3D:3.30.750.44,Pfam_domain:PF11918,hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF3,Superfamily_domains:SSF52096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 47349651 47349651 C T 1 0 0 0 0 0 0 0 1 13325 581 21 3 3 RBP3 10 47349651 Silent SNP C C3L-00144_T 992339 47349651 86447771 930 5001 ZNF488 0 . GRCh38 10 47368022 47368022 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.808G>T p.Gly270Cys p.G270C ENST00000585316 2/2 88 72 16 75 75 0 strelka-varscan-mutect ZNF488,missense_variant,p.Gly270Cys,ENST00000585316,NM_153034.2;ZNF488,missense_variant,p.Gly163Cys,ENST00000591025,; A ENST00000585316 Transcript missense_variant 970/3496 808/1023 270/340 G/C Ggc/Tgc 1 -1 ZNF488 HGNC HGNC:23535 protein_coding YES CCDS73120.1 ENSP00000462269 Q96MN9 UPI00000736CF NM_153034.2 deleterious(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR16516:SF5,hmmpanther:PTHR16516 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 47368022 47368022 C A 1 0 0 0 0 1 0 0 0 18513 623 22 2 2 ZNF488 10 47368022 Missense_Mutation SNP C C3L-00144_T 18371 47368022 86429400 931 5002 FRMPD2 0 . GRCh38 10 48163474 48163474 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3735G>T p.Trp1245Cys p.W1245C ENST00000374201 28/29 114 104 10 126 126 0 varscan-mutect FRMPD2,missense_variant,p.Trp1245Cys,ENST00000374201,NM_001018071.3;FRMPD2,missense_variant,p.Trp1220Cys,ENST00000305531,NM_001318191.1;FRMPD2,missense_variant,p.Trp1245Cys,ENST00000636244,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000474573,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000463706,;FRMPD2,3_prime_UTR_variant,,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000635925,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000491130,; A ENST00000374201 Transcript missense_variant 4038/4997 3735/3930 1245/1309 W/C tgG/tgT 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 tolerated(0.2) 28/29 hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF42 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48163474 48163474 C A 1 0 0 0 0 1 0 0 0 5928 624 22 2 2 FRMPD2 10 48163474 Missense_Mutation SNP C C3L-00144_T 795452 48163474 85633948 932 5003 FRMPD2 0 . GRCh38 10 48171022 48171022 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3410G>T p.Gly1137Val p.G1137V ENST00000374201 26/29 90 77 13 90 90 0 varscan-mutect FRMPD2,missense_variant,p.Gly1137Val,ENST00000374201,NM_001018071.3;FRMPD2,missense_variant,p.Gly1112Val,ENST00000305531,NM_001318191.1;FRMPD2,missense_variant,p.Gly1137Val,ENST00000636244,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000474573,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000463706,;FRMPD2,3_prime_UTR_variant,,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000635925,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000491130,;FRMPD2,downstream_gene_variant,,ENST00000477710,; A ENST00000374201 Transcript missense_variant 3713/4997 3410/3930 1137/1309 G/V gGa/gTa 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 deleterious(0) 26/29 PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF42,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48171022 48171022 C A 1 0 0 0 0 1 0 0 0 5928 855 30 2 2 FRMPD2 10 48171022 Missense_Mutation SNP C C3L-00144_T 7548 48171022 85626400 933 5004 WDFY4 0 . GRCh38 10 48976967 48976967 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.9279C>A p.Asp3093Glu p.D3093E ENST00000325239 58/61 34 28 6 19 19 0 strelka-mutect WDFY4,missense_variant,p.Asp3093Glu,ENST00000325239,NM_020945.1;WDFY4,missense_variant,p.Asp1180Glu,ENST00000265453,;RP11-523O18.5,non_coding_transcript_exon_variant,,ENST00000428825,;WDFY4,non_coding_transcript_exon_variant,,ENST00000465910,;WDFY4,downstream_gene_variant,,ENST00000497480,;WDFY4,upstream_gene_variant,,ENST00000490507,;RP11-523O18.5,non_coding_transcript_exon_variant,,ENST00000610464,; A ENST00000325239 Transcript missense_variant 9279/9555 9279/9555 3093/3184 D/E gaC/gaA COSM5050201,COSM5050202 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 deleterious(0) 58/61 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,SMART_domains:SM00320,Superfamily_domains:SSF50978 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1015218230 . 0 206 4 0 0 0 0 0 -15.90311 1 1 1 1 0 A 3 1 12 48976967 48976967 C A 1 0 0 0 0 1 0 0 0 17831 535 19 1 1 WDFY4 10 48976967 Missense_Mutation SNP C C3L-00144_T 805945 48976967 84820455 934 5005 CHAT 0 . GRCh38 10 49646641 49646641 + Missense_Mutation SNP C C A rs116071049 C3L-00144_T C3L-00144_N C C c.1248C>A p.Asn416Lys p.N416K ENST00000337653 8/15 272 241 31 187 186 1 strelka-varscan-mutect CHAT,missense_variant,p.Asn334Lys,ENST00000395562,NM_001142933.1;CHAT,missense_variant,p.Asn416Lys,ENST00000337653,NM_020549.4;CHAT,missense_variant,p.Asn298Lys,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,missense_variant,p.Asn298Lys,ENST00000339797,NM_020984.3;CHAT,missense_variant,p.Asn298Lys,ENST00000395559,NM_020986.3;CHAT,3_prime_UTR_variant,,ENST00000466590,; A ENST00000337653 Transcript missense_variant 1401/2458 1248/2247 416/748 N/K aaC/aaA rs116071049 1 1 CHAT HGNC HGNC:1912 protein_coding YES CCDS7232.1 ENSP00000337103 P28329 UPI000013F1B9 NM_020549.4 deleterious(0) 8/15 Pfam_domain:PF00755,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF14,Superfamily_domains:SSF52777 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs116071049 . 0 208 0 0 0 0 0 2 -6.009022 0 0 1 0 0 A 3 1 12 49646641 49646641 C A 1 0 0 0 0 1 0 0 0 3073 535 19 1 1 CHAT 10 49646641 Missense_Mutation SNP C C3L-00144_T 669674 49646641 84150781 935 5006 C10orf53 0 . GRCh38 10 49708428 49708428 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.285C>T p.= p.S95S ENST00000374112 3/3 158 123 35 149 149 0 strelka-varscan-mutect C10orf53,synonymous_variant,p.=,ENST00000374112,NM_182554.2;C10orf53,synonymous_variant,p.=,ENST00000535836,; T ENST00000374112 Transcript synonymous_variant 297/2130 285/474 95/157 S agC/agT 1 1 C10orf53 HGNC HGNC:27421 protein_coding YES CCDS31202.1 ENSP00000363226 Q8N6V4 UPI00001406B3 NM_182554.2 3/3 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 49708428 49708428 C T 1 0 0 0 0 0 0 0 1 1764 709 25 3 3 C10orf53 10 49708428 Silent SNP C C3L-00144_T 61787 49708428 84088994 936 5007 PCDH15 0 . GRCh38 10 53808712 53808712 + Missense_Mutation SNP C C A rs751022451 C3L-00144_T C3L-00144_N C C c.5353G>T p.Gly1785Cys p.G1785C ENST00000613657 37/37 128 112 16 92 92 0 strelka-varscan-mutect PCDH15,missense_variant,p.Gly1785Cys,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Gly1778Cys,ENST00000395445,;PCDH15,missense_variant,p.Gly1784Cys,ENST00000612394,;PCDH15,missense_variant,p.Gly976Cys,ENST00000395446,;PCDH15,missense_variant,p.Gly714Cys,ENST00000395440,;PCDH15,missense_variant,p.Gly645Cys,ENST00000395442,;PCDH15,3_prime_UTR_variant,,ENST00000617271,NM_001142770.1;PCDH15,3_prime_UTR_variant,,ENST00000395438,;PCDH15,3_prime_UTR_variant,,ENST00000409834,;PCDH15,3_prime_UTR_variant,,ENST00000615043,;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,3_prime_UTR_variant,,ENST00000414367,;PCDH15,intron_variant,,ENST00000476074,; A ENST00000613657 Transcript missense_variant 5748/6329 5353/5373 1785/1790 G/C Ggt/Tgt rs751022451 1 -1 PCDH15 HGNC HGNC:14674 protein_coding CCDS73138.1 ENSP00000482794 A0A087WZN9 UPI0001884905 NM_001142769.1 deleterious_low_confidence(0) 37/37 MODERATE SNV 5 1 PASS rs751022451 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 53808712 53808712 C A 1 0 0 0 0 1 0 0 0 11598 681 24 2 2 PCDH15 10 53808712 Missense_Mutation SNP C C3L-00144_T 4100284 53808712 79988710 937 5008 BICC1 0 . GRCh38 10 58789709 58789709 + Missense_Mutation SNP C C A rs778393440 C3L-00144_T C3L-00144_N C C c.823C>A p.Leu275Ile p.L275I ENST00000373886 8/21 206 187 19 182 182 0 strelka-varscan-mutect BICC1,missense_variant,p.Leu275Ile,ENST00000373886,NM_001080512.2;BICC1,upstream_gene_variant,,ENST00000263103,; A ENST00000373886 Transcript missense_variant 827/5475 823/2925 275/974 L/I Ctt/Att rs778393440 1 1 BICC1 HGNC HGNC:19351 protein_coding YES CCDS31206.1 ENSP00000362993 Q9H694 UPI000059D156 NM_001080512.2 deleterious(0.01) 8/21 hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF38,Superfamily_domains:SSF54791 MODERATE 1 SNV 2 1 PASS rs778393440 . 0 207 0 3 0 0 0 0 -20 0.9999827 1 1 1 0 A 3 1 12 58789709 58789709 C A 1 0 0 0 0 1 0 0 0 1576 913 32 2 2 BICC1 10 58789709 Missense_Mutation SNP C C3L-00144_T 4980997 58789709 75007713 938 5009 FAM13C 0 . GRCh38 10 59355886 59355886 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.119+1G>T p.X40_splice ENST00000618804 250 194 56 207 207 0 strelka-varscan-mutect FAM13C,splice_donor_variant,,ENST00000618427,NM_001166698.1;FAM13C,splice_donor_variant,,ENST00000621119,;FAM13C,splice_donor_variant,,ENST00000614220,;FAM13C,splice_donor_variant,,ENST00000618804,NM_198215.3;FAM13C,splice_donor_variant,,ENST00000611933,NM_001001971.2;FAM13C,splice_donor_variant,,ENST00000468840,NM_001143773.1;FAM13C,splice_donor_variant,,ENST00000435852,;FAM13C,splice_donor_variant,,ENST00000422313,;FAM13C,splice_donor_variant,,ENST00000503444,;FAM13C,splice_donor_variant,,ENST00000512919,;FAM13C,splice_donor_variant,,ENST00000470220,;FAM13C,upstream_gene_variant,,ENST00000507862,;FAM13C,splice_donor_variant,,ENST00000622363,;FAM13C,splice_donor_variant,,ENST00000619059,; A ENST00000618804 Transcript splice_donor_variant -/3333 119/1758 40/585 1 -1 FAM13C HGNC HGNC:19371 protein_coding YES CCDS7255.1 ENSP00000481854 Q8NE31 UPI00001AEA18 NM_198215.3 2/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 59355886 59355886 C A 1 0 0 0 0 0 0 1 0 5303 521 18 2 2 FAM13C 10 59355886 Splice_Site SNP C C3L-00144_T 566177 59355886 74441536 939 5010 ANK3 0 . GRCh38 10 60071399 60071399 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.9482G>T p.Ser3161Ile p.S3161I ENST00000280772 37/44 262 241 21 266 265 1 strelka-varscan-mutect ANK3,missense_variant,p.Ser3161Ile,ENST00000280772,NM_020987.3;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000610321,;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000616444,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000511043,;ANK3,upstream_gene_variant,,ENST00000610901,;ANK3,upstream_gene_variant,,ENST00000613207,;ANK3,missense_variant,p.Ser391Ile,ENST00000621739,; A ENST00000280772 Transcript missense_variant 9674/16874 9482/13134 3161/4377 S/I aGc/aTc 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 deleterious_low_confidence(0) 37/44 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 60071399 60071399 C A 1 0 0 0 0 1 0 0 0 722 797 28 2 2 ANK3 10 60071399 Missense_Mutation SNP C C3L-00144_T 715513 60071399 73726023 940 5011 CDH23 0 . GRCh38 10 71682543 71682543 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1972A>T p.Ser658Cys p.S658C ENST00000224721 18/70 257 223 34 240 240 0 strelka-varscan-mutect CDH23,missense_variant,p.Ser658Cys,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Ser653Cys,ENST00000622827,;CDH23,missense_variant,p.Ser245Cys,ENST00000442677,;CDH23,missense_variant,p.Ser653Cys,ENST00000616684,NM_001171930.1;CDH23,missense_variant,p.Ser653Cys,ENST00000398809,;CDH23,missense_variant,p.Ser464Cys,ENST00000466757,;CDH23,missense_variant,p.Ser653Cys,ENST00000299366,NM_001171931.1; T ENST00000224721 Transcript missense_variant 2362/11139 1972/10080 658/3359 S/C Agc/Tgc 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 deleterious(0.01) 18/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 71682543 71682543 A T 1 0 0 0 0 1 0 0 0 2811 188 7 4 4 CDH23 10 71682543 Missense_Mutation SNP A C3L-00144_T 11611144 71682543 62114879 941 5012 FUT11 0 . GRCh38 10 73772548 73772548 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.215C>A p.Ala72Glu p.A72E ENST00000372841 1/3 41 36 5 35 35 0 strelka-varscan-mutect FUT11,missense_variant,p.Ala72Glu,ENST00000394790,NM_001284194.1;FUT11,missense_variant,p.Ala72Glu,ENST00000372841,NM_173540.2;SEC24C,downstream_gene_variant,,ENST00000339365,NM_004922.3;SEC24C,downstream_gene_variant,,ENST00000345254,NM_198597.2;RP11-574K11.32,non_coding_transcript_exon_variant,,ENST00000623453,;FUT11,upstream_gene_variant,,ENST00000465695,;FUT11,upstream_gene_variant,,ENST00000489264,;SEC24C,downstream_gene_variant,,ENST00000496827,;SEC24C,downstream_gene_variant,,ENST00000465076,;SEC24C,downstream_gene_variant,,ENST00000635550,; A ENST00000372841 Transcript missense_variant 258/2056 215/1479 72/492 A/E gCg/gAg 1 1 FUT11 HGNC HGNC:19233 protein_coding YES CCDS7333.1 ENSP00000361932 Q495W5 UPI00000474D6 NM_173540.2 tolerated(0.82) 1/3 PIRSF_domain:PIRSF037332,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF156 MODERATE 1 SNV 1 1 PASS rs1178002449 . 0 198 12 0 0 0 0 0 -12.53663 0.9998772 1 1 1 0 A 3 1 12 73772548 73772548 C A 1 0 0 0 0 1 0 0 0 5975 768 27 1 1 FUT11 10 73772548 Missense_Mutation SNP C C3L-00144_T 2090005 73772548 60024874 942 5013 LDB3 0 . GRCh38 10 86717990 86717990 + Missense_Mutation SNP G G T rs769156627 C3L-00144_T C3L-00144_N G G c.1718G>T p.Arg573Leu p.R573L ENST00000429277 11/14 169 154 15 132 132 0 strelka-varscan-mutect LDB3,missense_variant,p.Arg573Leu,ENST00000429277,NM_001171610.1;LDB3,missense_variant,p.Arg568Leu,ENST00000361373,NM_007078.2;LDB3,missense_variant,p.Arg458Leu,ENST00000263066,NM_001080114.1;LDB3,missense_variant,p.Arg573Leu,ENST00000623056,;LDB3,upstream_gene_variant,,ENST00000477489,; T ENST00000429277 Transcript missense_variant 1863/5436 1718/2199 573/732 R/L cGt/cTt rs769156627 1 1 LDB3 HGNC HGNC:15710 protein_coding YES CCDS53550.1 ENSP00000401437 O75112 UPI00017A876A NM_001171610.1 deleterious(0) 11/14 PROSITE_profiles:PS50023,hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF9,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 2 1 PASS rs769156627 . 0 204 0 4 0 0 0 2 -6.262595 0 0 1 0 0 T 3 4 12 86717990 86717990 G T 1 0 0 0 0 1 0 0 0 8604 1145 40 1 1 LDB3 10 86717990 Missense_Mutation SNP G C3L-00144_T 12945442 86717990 47079432 943 5014 RNLS 0 . GRCh38 10 88581614 88581614 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.320C>A p.Ala107Glu p.A107E ENST00000331772 3/7 112 94 18 86 86 0 strelka-mutect RNLS,missense_variant,p.Ala107Glu,ENST00000371947,NM_018363.3;RNLS,missense_variant,p.Ala107Glu,ENST00000331772,NM_001031709.2;RNLS,missense_variant,p.Ala107Glu,ENST00000437752,;Y_RNA,downstream_gene_variant,,ENST00000364678,;RNLS,non_coding_transcript_exon_variant,,ENST00000466945,;RNLS,intron_variant,,ENST00000481793,; T ENST00000331772 Transcript missense_variant 343/1447 320/1029 107/342 A/E gCa/gAa 1 -1 RNLS HGNC HGNC:25641 protein_coding YES CCDS31239.1 ENSP00000332530 Q5VYX0 UPI00001AFF46 NM_001031709.2 deleterious(0) 3/7 hmmpanther:PTHR23357,Gene3D:3.90.660.10,Pfam_domain:PF01593,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 88581614 88581614 G T 1 0 0 0 0 1 0 0 0 13685 1319 46 2 2 RNLS 10 88581614 Missense_Mutation SNP G C3L-00144_T 1863624 88581614 45215808 944 5015 IFIT3 0 . GRCh38 10 89339936 89339936 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.1281G>T p.Gln427His p.Q427H ENST00000371818 2/2 111 80 31 89 88 1 strelka-varscan-mutect IFIT3,missense_variant,p.Gln427His,ENST00000371818,NM_001549.5;IFIT3,missense_variant,p.Gln427His,ENST00000371811,NM_001031683.3;LIPA,intron_variant,,ENST00000371837,;LIPA,intron_variant,,ENST00000282673,;LIPA,intron_variant,,ENST00000487618,;LIPA,intron_variant,,ENST00000463623,;LIPA,intron_variant,,ENST00000489359,; T ENST00000371818 Transcript missense_variant 1461/2496 1281/1473 427/490 Q/H caG/caT COSM3791018 1 1 IFIT3 HGNC HGNC:5411 protein_coding YES CCDS7402.1 ENSP00000360883 O14879 Q5T765 UPI000012D3E5 NM_001549.5 deleterious(0.04) 2/2 Gene3D:1.25.40.10,Pfam_domain:PF13181,PROSITE_profiles:PS50005,hmmpanther:PTHR10271,hmmpanther:PTHR10271:SF3,SMART_domains:SM00028 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 89339936 89339936 G T 1 0 0 0 0 1 0 0 0 7424 933 33 2 2 IFIT3 10 89339936 Missense_Mutation SNP G C3L-00144_T 758322 89339936 44457486 945 5016 KIF20B 0 . GRCh38 10 89732968 89732968 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.2457A>G p.= p.V819V ENST00000371728 19/33 114 89 25 120 120 0 strelka-varscan-mutect KIF20B,synonymous_variant,p.=,ENST00000371728,NM_001284259.1;KIF20B,synonymous_variant,p.=,ENST00000260753,NM_016195.3;KIF20B,non_coding_transcript_exon_variant,,ENST00000478929,; G ENST00000371728 Transcript synonymous_variant 2522/6419 2457/5463 819/1820 V gtA/gtG 1 1 KIF20B HGNC HGNC:7212 protein_coding YES CCDS60590.1 ENSP00000360793 Q96Q89 UPI000013D104 NM_001284259.1 19/33 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 89732968 89732968 A G 1 0 0 0 0 0 0 0 1 8152 378 14 5 5 KIF20B 10 89732968 Silent SNP A C3L-00144_T 393032 89732968 44064454 946 5017 DNTT 0 . GRCh38 10 96319324 96319324 + Silent SNP A A T rs760485586 C3L-00144_T C3L-00144_N A A c.441A>T p.= p.V147V ENST00000371174 3/11 268 203 65 246 246 0 strelka-varscan-mutect DNTT,synonymous_variant,p.=,ENST00000371174,NM_004088.3;DNTT,synonymous_variant,p.=,ENST00000630152,NM_001017520.1; T ENST00000371174 Transcript synonymous_variant 543/1972 441/1530 147/509 V gtA/gtT rs760485586 1 1 DNTT HGNC HGNC:2983 protein_coding YES CCDS7447.1 ENSP00000360216 P04053 UPI000013C84B NM_004088.3 3/11 PIRSF_domain:PIRSF000817,PIRSF_domain:PIRSF501175,hmmpanther:PTHR11276,hmmpanther:PTHR11276:SF21 LOW 1 SNV 1 1 PASS rs760485586 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 96319324 96319324 A T 1 0 0 0 0 0 0 0 1 4494 378 14 4 4 DNTT 10 96319324 Silent SNP A C3L-00144_T 6586356 96319324 37478098 947 5018 TLL2 0 . GRCh38 10 96480415 96480415 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.220C>A p.Leu74Met p.L74M ENST00000357947 2/21 262 205 57 232 230 2 strelka-varscan-mutect TLL2,missense_variant,p.Leu74Met,ENST00000357947,NM_012465.3;TLL2,non_coding_transcript_exon_variant,,ENST00000469598,; T ENST00000357947 Transcript missense_variant 446/6756 220/3048 74/1015 L/M Ctg/Atg 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 tolerated(0.57) 2/21 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF638,PIRSF_domain:PIRSF001199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 96480415 96480415 G T 1 0 0 0 0 1 0 0 0 16392 962 34 2 2 TLL2 10 96480415 Missense_Mutation SNP G C3L-00144_T 161091 96480415 37317007 948 5019 FRAT1 0 . GRCh38 10 97319945 97319945 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.492G>T p.= p.L164L ENST00000371021 1/1 133 109 24 136 136 0 strelka-varscan-mutect FRAT1,synonymous_variant,p.=,ENST00000371021,NM_005479.3;FRAT1,upstream_gene_variant,,ENST00000490980,; T ENST00000371021 Transcript synonymous_variant 679/2649 492/840 164/279 L ctG/ctT 1 1 FRAT1 HGNC HGNC:3944 protein_coding YES CCDS7455.1 ENSP00000360060 Q92837 UPI000006D6B7 NM_005479.3 1/1 hmmpanther:PTHR35154,hmmpanther:PTHR35154:SF1,Pfam_domain:PF05350 LOW 1 SNV 1 PASS rs1477958435 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 97319945 97319945 G T 1 0 0 0 0 0 0 0 1 5909 1364 48 2 2 FRAT1 10 97319945 Silent SNP G C3L-00144_T 839530 97319945 36477477 949 5020 HPSE2 0 . GRCh38 10 98721789 98721789 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.824A>T p.Asn275Ile p.N275I ENST00000370552 5/12 427 322 105 367 367 0 strelka-varscan-mutect HPSE2,missense_variant,p.Asn72Ile,ENST00000404542,;HPSE2,missense_variant,p.Asn275Ile,ENST00000370552,NM_021828.4;HPSE2,missense_variant,p.Asn217Ile,ENST00000370549,NM_001166244.1;HPSE2,missense_variant,p.Asn275Ile,ENST00000370546,NM_001166246.1;HPSE2,missense_variant,p.Asn163Ile,ENST00000628193,NM_001166245.1; A ENST00000370552 Transcript missense_variant 884/2295 824/1779 275/592 N/I aAt/aTt 1 -1 HPSE2 HGNC HGNC:18374 protein_coding YES CCDS7477.1 ENSP00000359583 Q8WWQ2 UPI00001AEEC0 NM_021828.4 deleterious(0) 5/12 Gene3D:3.20.20.80,Pfam_domain:PF03662,hmmpanther:PTHR14363,hmmpanther:PTHR14363:SF15,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 98721789 98721789 T A 1 0 0 0 0 1 0 0 0 7240 1493 52 4 4 HPSE2 10 98721789 Missense_Mutation SNP T C3L-00144_T 1401844 98721789 35075633 950 5021 PKD2L1 0 . GRCh38 10 100292977 100292977 + Missense_Mutation SNP C C A rs776718992 C3L-00144_T C3L-00144_N C C c.1851G>T p.Gln617His p.Q617H ENST00000318222 11/16 85 61 24 108 108 0 strelka-varscan-mutect PKD2L1,missense_variant,p.Gln617His,ENST00000318222,NM_001253837.1,NM_016112.2;PKD2L1,intron_variant,,ENST00000465680,;PKD2L1,3_prime_UTR_variant,,ENST00000528248,; A ENST00000318222 Transcript missense_variant 2234/3043 1851/2418 617/805 Q/H caG/caT rs776718992 1 -1 PKD2L1 HGNC HGNC:9011 protein_coding YES CCDS7492.1 ENSP00000325296 Q9P0L9 UPI0000130FED NM_001253837.1,NM_016112.2 deleterious(0.02) 11/16 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF105,Gene3D:1.10.238.10 MODERATE 1 SNV 1 1 PASS rs776718992 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 100292977 100292977 C A 1 0 0 0 0 1 0 0 0 12063 564 20 2 2 PKD2L1 10 100292977 Missense_Mutation SNP C C3L-00144_T 1571188 100292977 33504445 951 5022 PAX2 0 . GRCh38 10 100749845 100749845 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.143G>C p.Gly48Ala p.G48A ENST00000370296 2/11 67 45 22 86 86 0 strelka-varscan-mutect PAX2,missense_variant,p.Gly48Ala,ENST00000370296,NM_003988.3;PAX2,missense_variant,p.Gly48Ala,ENST00000428433,NM_003987.3,NM_003990.3;PAX2,missense_variant,p.Gly48Ala,ENST00000355243,NM_001304569.1,NM_000278.3,NM_003989.3;PAX2,missense_variant,p.Gly47Ala,ENST00000361791,;PAX2,missense_variant,p.Gly52Ala,ENST00000554172,;PAX2,missense_variant,p.Gly48Ala,ENST00000427256,;PAX2,intron_variant,,ENST00000554363,;PAX2,intron_variant,,ENST00000553492,;PAX2,non_coding_transcript_exon_variant,,ENST00000483202,; C ENST00000370296 Transcript missense_variant 693/4140 143/1191 48/396 G/A gGt/gCt 1 1 PAX2 HGNC HGNC:8616 protein_coding YES CCDS7499.1 ENSP00000359319 Q02962 UPI000016AE71 NM_003988.3 deleterious(0) 2/11 PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF172,Gene3D:1.10.10.10,Pfam_domain:PF00292,SMART_domains:SM00351,Superfamily_domains:SSF46689,Prints_domain:PR00027 MODERATE 1 SNV 1 1 PASS rs1454668545 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 100749845 100749845 G C 1 0 0 0 0 1 0 0 0 11564 1261 44 4 4 PAX2 10 100749845 Missense_Mutation SNP G C3L-00144_T 456868 100749845 33047577 952 5023 COL17A1 0 . GRCh38 10 104061447 104061447 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.937C>A p.Gln313Lys p.Q313K ENST00000353479 13/56 213 164 49 158 158 0 strelka-varscan-mutect COL17A1,missense_variant,p.Gln313Lys,ENST00000353479,NM_000494.3;COL17A1,missense_variant,p.Gln313Lys,ENST00000369733,;COL17A1,missense_variant,p.Gln313Lys,ENST00000393211,;COL17A1,non_coding_transcript_exon_variant,,ENST00000488320,; T ENST00000353479 Transcript missense_variant 1228/5734 937/4494 313/1497 Q/K Cag/Aag 1 -1 COL17A1 HGNC HGNC:2194 protein_coding YES CCDS7554.1 ENSP00000340937 Q9UMD9 UPI000006DB58 NM_000494.3 deleterious(0.01) 13/56 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 104061447 104061447 G T 1 0 0 0 0 1 0 0 0 3462 1357 47 2 2 COL17A1 10 104061447 Missense_Mutation SNP G C3L-00144_T 3311602 104061447 29735975 953 5024 SORCS3 0 . GRCh38 10 105217111 105217111 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2723T>A p.Leu908Gln p.L908Q ENST00000369701 19/27 113 90 23 125 125 0 strelka-varscan-mutect SORCS3,missense_variant,p.Leu908Gln,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Leu908Gln,ENST00000369699,; A ENST00000369701 Transcript missense_variant 2950/5757 2723/3669 908/1222 L/Q cTg/cAg 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0) 19/27 Gene3D:2.60.40.670,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Superfamily_domains:SSF49299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 105217111 105217111 T A 1 0 0 0 0 1 0 0 0 15254 1580 55 4 4 SORCS3 10 105217111 Missense_Mutation SNP T C3L-00144_T 1155664 105217111 28580311 954 5025 SORCS3 0 . GRCh38 10 105263310 105263310 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.3605G>A p.Gly1202Glu p.G1202E ENST00000369701 27/27 185 142 43 135 135 0 strelka-mutect SORCS3,missense_variant,p.Gly1202Glu,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Gly1202Glu,ENST00000369699,; A ENST00000369701 Transcript missense_variant,splice_region_variant 3832/5757 3605/3669 1202/1222 G/E gGa/gAa 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 tolerated(0.07) 27/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 105263310 105263310 G A 1 0 0 0 0 1 0 0 0 15254 1188 41 3 3 SORCS3 10 105263310 Missense_Mutation SNP G C3L-00144_T 46199 105263310 28534112 955 5026 SORCS1 0 . GRCh38 10 106607261 106607261 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3070G>T p.Val1024Leu p.V1024L ENST00000263054 23/26 122 103 19 117 117 0 strelka-varscan-mutect SORCS1,missense_variant,p.Val1024Leu,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,missense_variant,p.Val782Leu,ENST00000612154,;SORCS1,missense_variant,p.Val782Leu,ENST00000622431,;SORCS1,missense_variant,p.Val782Leu,ENST00000344440,;SORCS1,missense_variant,p.Val559Leu,ENST00000369698,;SORCS1,missense_variant,p.Val39Leu,ENST00000452214,;SORCS1,non_coding_transcript_exon_variant,,ENST00000478809,;SORCS1,upstream_gene_variant,,ENST00000473866,; A ENST00000263054 Transcript missense_variant 3078/7272 3070/3507 1024/1168 V/L Gtg/Ttg 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 tolerated(0.12) 23/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 106607261 106607261 C A 1 0 0 0 0 1 0 0 0 15252 507 18 2 2 SORCS1 10 106607261 Missense_Mutation SNP C C3L-00144_T 1343951 106607261 27190161 956 5027 SORCS1 0 . GRCh38 10 107164300 107164300 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.227C>T p.Pro76Leu p.P76L ENST00000263054 1/26 106 93 13 61 61 0 strelka-varscan-mutect SORCS1,missense_variant,p.Pro76Leu,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1; A ENST00000263054 Transcript missense_variant 235/7272 227/3507 76/1168 P/L cCc/cTc 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 deleterious_low_confidence(0.03) 1/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8 MODERATE 1 SNV 1 1 PASS rs1478059066 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 107164300 107164300 G A 1 0 0 0 0 1 0 0 0 15252 1232 43 3 3 SORCS1 10 107164300 Missense_Mutation SNP G C3L-00144_T 557039 107164300 26633122 957 5028 GPAM 0 . GRCh38 10 112163728 112163728 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1396G>T p.Ala466Ser p.A466S ENST00000348367 14/22 372 291 81 341 341 0 strelka-varscan-mutect GPAM,missense_variant,p.Ala466Ser,ENST00000348367,NM_001244949.1,NM_020918.5;GPAM,missense_variant,p.Ala466Ser,ENST00000369425,; A ENST00000348367 Transcript missense_variant 1594/6371 1396/2487 466/828 A/S Gca/Tca 1 -1 GPAM HGNC HGNC:24865 protein_coding YES CCDS7570.1 ENSP00000265276 Q9HCL2 UPI000004AC02 NM_001244949.1,NM_020918.5 tolerated(0.59) 14/22 hmmpanther:PTHR12563,hmmpanther:PTHR12563:SF16,PIRSF_domain:PIRSF500064,PIRSF_domain:PIRSF000437 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 112163728 112163728 C A 1 0 0 0 0 1 0 0 0 6484 710 25 2 2 GPAM 10 112163728 Missense_Mutation SNP C C3L-00144_T 4999428 112163728 21633694 958 5029 NHLRC2 0 . GRCh38 10 113904850 113904850 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1738G>T p.Asp580Tyr p.D580Y ENST00000369301 10/11 244 199 45 214 214 0 strelka-varscan-mutect NHLRC2,missense_variant,p.Asp580Tyr,ENST00000369301,NM_198514.3; T ENST00000369301 Transcript missense_variant 1950/11051 1738/2181 580/726 D/Y Gat/Tat 1 1 NHLRC2 HGNC HGNC:24731 protein_coding YES CCDS7585.1 ENSP00000358307 Q8NBF2 UPI0000071EAF NM_198514.3 deleterious(0) 10/11 hmmpanther:PTHR13833,hmmpanther:PTHR13833:SF49 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 113904850 113904850 G T 1 0 0 0 0 1 0 0 0 10439 942 33 2 2 NHLRC2 10 113904850 Missense_Mutation SNP G C3L-00144_T 1741122 113904850 19892572 959 5030 ATRNL1 0 . GRCh38 10 115286249 115286249 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2267G>T p.Gly756Val p.G756V ENST00000355044 15/29 242 219 23 266 266 0 strelka-mutect ATRNL1,missense_variant,p.Gly756Val,ENST00000355044,NM_207303.4; T ENST00000355044 Transcript missense_variant 2393/8479 2267/4140 756/1379 G/V gGg/gTg 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 deleterious(0.01) 15/29 PROSITE_profiles:PS50041,hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,Gene3D:3.10.100.10,SMART_domains:SM00423,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 205 0 3 0 0 0 0 -20 0.9999822 1 1 1 0 T 3 4 12 115286249 115286249 G T 1 0 0 0 0 1 0 0 0 1360 1232 43 2 2 ATRNL1 10 115286249 Missense_Mutation SNP G C3L-00144_T 1381399 115286249 18511173 960 5031 ATRNL1 0 . GRCh38 10 115286310 115286310 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2328C>A p.Cys776Ter p.C776* ENST00000355044 15/29 183 152 31 244 244 0 strelka-varscan-mutect ATRNL1,stop_gained,p.Cys776Ter,ENST00000355044,NM_207303.4; A ENST00000355044 Transcript stop_gained 2454/8479 2328/4140 776/1379 C/* tgC/tgA 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 15/29 PROSITE_profiles:PS50041,hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 115286310 115286310 C A 1 0 0 0 0 0 1 0 0 1360 805 28 2 2 ATRNL1 10 115286310 Nonsense_Mutation SNP C C3L-00144_T 61 115286310 18511112 961 5032 HSPA12A 0 . GRCh38 10 116674940 116674940 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1869G>T p.= p.T623T ENST00000369209 12/12 433 358 75 450 450 0 strelka-varscan-mutect HSPA12A,synonymous_variant,p.=,ENST00000635765,;HSPA12A,synonymous_variant,p.=,ENST00000369209,NM_025015.2;C10orf82,upstream_gene_variant,,ENST00000369210,NM_144661.2;C10orf82,upstream_gene_variant,,ENST00000588184,;RP11-498B4.5,downstream_gene_variant,,ENST00000433600,;C10orf82,upstream_gene_variant,,ENST00000588224,;C10orf82,upstream_gene_variant,,ENST00000467153,; A ENST00000369209 Transcript synonymous_variant 1974/5722 1869/2028 623/675 T acG/acT 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 12/12 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 116674940 116674940 C A 1 0 0 0 0 0 0 0 1 7300 755 27 1 1 HSPA12A 10 116674940 Silent SNP C C3L-00144_T 1388630 116674940 17122482 962 5033 HSPA12A 0 . GRCh38 10 116683828 116683828 + Silent SNP G G A rs782420092 C3L-00144_T C3L-00144_N G G c.798C>T p.= p.Y266Y ENST00000369209 7/12 75 66 9 77 77 0 strelka-varscan-mutect HSPA12A,synonymous_variant,p.=,ENST00000635765,;HSPA12A,synonymous_variant,p.=,ENST00000369209,NM_025015.2;HSPA12A,synonymous_variant,p.=,ENST00000480802,; A ENST00000369209 Transcript synonymous_variant 903/5722 798/2028 266/675 Y taC/taT rs782420092 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 7/12 Gene3D:3.30.420.40,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46 LOW 1 SNV 1 1 PASS rs782420092 . 0 205 4 0 0 0 0 0 -19.56667 1 1 1 1 0 A 2 1 12 116683828 116683828 G A 1 0 0 0 0 0 0 0 1 7300 1372 48 3 3 HSPA12A 10 116683828 Silent SNP G C3L-00144_T 8888 116683828 17113594 963 5034 PRLHR 0 . GRCh38 10 118594578 118594578 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.667C>A p.Gln223Lys p.Q223K ENST00000239032 2/2 50 39 11 46 46 0 strelka-varscan-mutect PRLHR,missense_variant,p.Gln223Lys,ENST00000239032,NM_004248.2;PRLHR,missense_variant,p.Gln223Lys,ENST00000636925,; T ENST00000239032 Transcript missense_variant 857/5446 667/1113 223/370 Q/K Cag/Aag 1 -1 PRLHR HGNC HGNC:4464 protein_coding YES CCDS7606.1 ENSP00000239032 P49683 UPI000013CA6F NM_004248.2 tolerated(0.22) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 118594578 118594578 G T 1 0 0 0 0 1 0 0 0 12662 1357 47 2 2 PRLHR 10 118594578 Missense_Mutation SNP G C3L-00144_T 1910750 118594578 15202844 964 5035 PRLHR 0 . GRCh38 10 118594705 118594705 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.540G>T p.= p.V180V ENST00000239032 2/2 62 48 14 54 54 0 strelka-varscan-mutect PRLHR,synonymous_variant,p.=,ENST00000239032,NM_004248.2;PRLHR,synonymous_variant,p.=,ENST00000636925,; A ENST00000239032 Transcript synonymous_variant 730/5446 540/1113 180/370 V gtG/gtT 1 -1 PRLHR HGNC HGNC:4464 protein_coding YES CCDS7606.1 ENSP00000239032 P49683 UPI000013CA6F NM_004248.2 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 12 118594705 118594705 C A 1 0 0 0 0 0 0 0 1 12662 697 25 2 2 PRLHR 10 118594705 Silent SNP C C3L-00144_T 127 118594705 15202717 965 5036 CACUL1 0 . GRCh38 10 118686641 118686641 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1026G>T p.Arg342Ser p.R342S ENST00000369151 8/9 201 157 44 183 182 1 strelka-varscan-mutect CACUL1,missense_variant,p.Arg342Ser,ENST00000369151,NM_153810.4;CACUL1,splice_region_variant,,ENST00000544392,;CACUL1,splice_region_variant,,ENST00000493518,;CACUL1,splice_region_variant,,ENST00000489169,;CACUL1,non_coding_transcript_exon_variant,,ENST00000490610,; A ENST00000369151 Transcript missense_variant,splice_region_variant 1510/11311 1026/1110 342/369 R/S agG/agT 1 -1 CACUL1 HGNC HGNC:23727 protein_coding YES CCDS41570.1 ENSP00000358147 Q86Y37 UPI000000DCD0 NM_153810.4 tolerated(0.26) 8/9 hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF78 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 118686641 118686641 C A 1 0 0 0 0 1 0 0 0 2253 637 22 2 2 CACUL1 10 118686641 Missense_Mutation SNP C C3L-00144_T 91936 118686641 15110781 966 5037 SEC23IP 0 . GRCh38 10 119909089 119909089 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1150G>C p.Glu384Gln p.E384Q ENST00000369075 5/19 167 141 26 168 168 0 strelka-varscan-mutect SEC23IP,missense_variant,p.Glu384Gln,ENST00000369075,NM_007190.3;SEC23IP,missense_variant,p.Glu384Gln,ENST00000543134,;SEC23IP,intron_variant,,ENST00000446561,;SEC23IP,downstream_gene_variant,,ENST00000442952,; C ENST00000369075 Transcript missense_variant 1222/7168 1150/3003 384/1000 E/Q Gag/Cag 1 1 SEC23IP HGNC HGNC:17018 protein_coding YES CCDS7618.1 ENSP00000358071 Q9Y6Y8 UPI000006FCCE NM_007190.3 deleterious(0.01) 5/19 hmmpanther:PTHR23509:SF4,hmmpanther:PTHR23509 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 119909089 119909089 G C 1 0 0 0 0 1 0 0 0 14270 943 33 4 4 SEC23IP 10 119909089 Missense_Mutation SNP G C3L-00144_T 1222448 119909089 13888333 967 5038 TACC2 0 . GRCh38 10 122085869 122085869 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.3369A>C p.Gln1123His p.Q1123H ENST00000369005 4/23 67 61 6 49 49 0 strelka-mutect TACC2,missense_variant,p.Gln1123His,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Gln1123His,ENST00000334433,;TACC2,missense_variant,p.Gln1123His,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Gln1123His,ENST00000453444,;TACC2,missense_variant,p.Gln1123His,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; C ENST00000369005 Transcript missense_variant 3709/9673 3369/8847 1123/2948 Q/H caA/caC 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious(0) 4/23 Low_complexity_(Seg):seg,hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 122085869 122085869 A C 1 0 0 0 0 1 0 0 0 15898 69 3 5 5 TACC2 10 122085869 Missense_Mutation SNP A C3L-00144_T 2176780 122085869 11711553 968 5039 CPXM2 0 . GRCh38 10 123746885 123746885 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2150C>A p.Thr717Lys p.T717K ENST00000241305 14/14 348 270 78 304 304 0 strelka-varscan-mutect CPXM2,missense_variant,p.Thr717Lys,ENST00000241305,NM_198148.2;CPXM2,intron_variant,,ENST00000615851,;CPXM2,intron_variant,,ENST00000368854,; T ENST00000241305 Transcript missense_variant 2305/3554 2150/2271 717/756 T/K aCa/aAa 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 tolerated(0.23) 14/14 hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Pfam_domain:PF13620,Gene3D:2.60.40.1120,SMART_domains:SM00631,Superfamily_domains:SSF49464 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 123746885 123746885 G T 1 0 0 0 0 1 0 0 0 3636 1377 48 2 2 CPXM2 10 123746885 Missense_Mutation SNP G C3L-00144_T 1661016 123746885 10050537 969 5040 CPXM2 0 . GRCh38 10 123761982 123761982 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1667C>G p.Ala556Gly p.A556G ENST00000241305 11/14 128 111 17 127 127 0 strelka-varscan-mutect CPXM2,missense_variant,p.Ala556Gly,ENST00000241305,NM_198148.2;CPXM2,missense_variant,p.Ala52Gly,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; C ENST00000241305 Transcript missense_variant 1822/3554 1667/2271 556/756 A/G gCc/gGc 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 deleterious(0) 11/14 hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 123761982 123761982 G C 1 0 0 0 0 1 0 0 0 3636 1203 42 4 4 CPXM2 10 123761982 Missense_Mutation SNP G C3L-00144_T 15097 123761982 10035440 970 5041 CPXM2 0 . GRCh38 10 123768618 123768618 + Silent SNP G G T rs140548347 C3L-00144_T C3L-00144_N G G c.1207C>A p.= p.R403R ENST00000241305 9/14 166 145 21 164 164 0 strelka-varscan-mutect CPXM2,synonymous_variant,p.=,ENST00000241305,NM_198148.2;CPXM2,5_prime_UTR_variant,,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; T ENST00000241305 Transcript synonymous_variant 1362/3554 1207/2271 403/756 R Cgg/Agg rs140548347 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 9/14 hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS rs140548347 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 123768618 123768618 G T 1 0 0 0 0 0 0 0 1 3636 1115 39 1 1 CPXM2 10 123768618 Silent SNP G C3L-00144_T 6636 123768618 10028804 971 5042 FAM53B 0 . GRCh38 10 124682170 124682170 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.343C>A p.Arg115Ser p.R115S ENST00000337318 4/5 171 149 22 163 162 1 strelka-varscan-mutect FAM53B,missense_variant,p.Arg115Ser,ENST00000337318,NM_014661.3;FAM53B,missense_variant,p.Arg115Ser,ENST00000392754,;FAM53B,missense_variant,p.Arg115Ser,ENST00000280780,;RP11-12J10.3,3_prime_UTR_variant,,ENST00000494792,; T ENST00000337318 Transcript missense_variant 555/5431 343/1269 115/422 R/S Cgc/Agc 1 -1 FAM53B HGNC HGNC:28968 protein_coding YES CCDS7641.1 ENSP00000338532 Q14153 UPI000013DC3C NM_014661.3 deleterious(0) 4/5 hmmpanther:PTHR28567:SF1,hmmpanther:PTHR28567,Pfam_domain:PF15242 MODERATE 1 SNV 1 1 PASS rs953554433 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 124682170 124682170 G T 1 0 0 0 0 1 0 0 0 5456 1116 39 1 1 FAM53B 10 124682170 Missense_Mutation SNP G C3L-00144_T 913552 124682170 9115252 972 5043 C10orf90 0 . GRCh38 10 126504397 126504397 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.803A>T p.Asp268Val p.D268V ENST00000284694 3/9 275 208 67 244 244 0 strelka-varscan-mutect C10orf90,missense_variant,p.Asp268Val,ENST00000284694,NM_001004298.2;C10orf90,missense_variant,p.Asp221Val,ENST00000356858,;C10orf90,missense_variant,p.Asp268Val,ENST00000432642,;C10orf90,upstream_gene_variant,,ENST00000424927,;C10orf90,downstream_gene_variant,,ENST00000488181,;C10orf90,non_coding_transcript_exon_variant,,ENST00000368674,;C10orf90,downstream_gene_variant,,ENST00000463082,; A ENST00000284694 Transcript missense_variant 924/3076 803/2100 268/699 D/V gAc/gTc 1 -1 C10orf90 HGNC HGNC:26563 protein_coding YES CCDS31310.1 ENSP00000284694 Q96M02 UPI00001D808F NM_001004298.2 deleterious(0) 3/9 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 126504397 126504397 T A 1 0 0 0 0 1 0 0 0 1773 1667 58 4 4 C10orf90 10 126504397 Missense_Mutation SNP T C3L-00144_T 1822227 126504397 7293025 973 5044 DOCK1 0 . GRCh38 10 127384879 127384879 + Frame_Shift_Del DEL G G - rs780031433 C3L-00144_T C3L-00144_N G G c.3898delG p.Glu1300LysfsTer22 p.E1300Kfs*22 ENST00000623213 38/52 97 73 24 81 81 0 sindel-varindel-pindel DOCK1,frameshift_variant,p.Glu1279LysfsTer22,ENST00000280333,NM_001380.4;DOCK1,frameshift_variant,p.Glu1300LysfsTer22,ENST00000623213,NM_001290223.1; - ENST00000623213 Transcript frameshift_variant 3959/5761 3897/5661 1299/1886 Q/X caG/ca rs780031433 1 1 DOCK1 HGNC HGNC:2987 protein_coding YES CCDS76359.1 ENSP00000485033 A0A096LNH6 UPI0003EAEE97 NM_001290223.1 38/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF79,hmmpanther:PTHR23317,Pfam_domain:PF06920 HIGH 1 deletion 1 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 127384879 127384879 G - 1 0 1 0 1 0 0 0 0 4499 991 35 0 0 DOCK1 10 127384879 Frame_Shift_Del DEL G C3L-00144_T 880482 127384879 6412543 974 5045 MGMT 0 . GRCh38 10 129708016 129708016 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.340G>T p.Ala114Ser p.A114S ENST00000306010 3/5 138 125 13 152 151 1 strelka-varscan-mutect MGMT,missense_variant,p.Ala114Ser,ENST00000306010,NM_002412.3;MGMT,non_coding_transcript_exon_variant,,ENST00000462672,; T ENST00000306010 Transcript missense_variant 372/1759 340/717 114/238 A/S Gct/Tct 1 1 MGMT HGNC HGNC:7059 protein_coding YES CCDS7660.2 ENSP00000302111 P16455 B4DEE8 UPI00017A6D43 NM_002412.3 tolerated(0.09) 3/5 Gene3D:3l00A01,Pfam_domain:PF02870,hmmpanther:PTHR10815,hmmpanther:PTHR10815:SF5,Superfamily_domains:SSF53155 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 129708016 129708016 G T 1 0 0 0 0 1 0 0 0 9514 1203 42 2 2 MGMT 10 129708016 Missense_Mutation SNP G C3L-00144_T 2323137 129708016 4089406 975 5046 CFAP46 0 . GRCh38 10 132919319 132919319 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1854G>T p.= p.R618R ENST00000368586 15/58 95 75 20 66 66 0 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2;CFAP46,upstream_gene_variant,,ENST00000486104,; A ENST00000368586 Transcript synonymous_variant 1955/8278 1854/8148 618/2715 R cgG/cgT 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 15/58 Low_complexity_(Seg):seg,hmmpanther:PTHR15977,hmmpanther:PTHR15977:SF15 LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 132919319 132919319 C A 1 0 0 0 0 0 0 0 1 3021 753 26 2 2 CFAP46 10 132919319 Silent SNP C C3L-00144_T 3211303 132919319 878103 976 5047 LMNTD2 0 . GRCh38 11 558708 558708 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.217C>A p.Leu73Met p.L73M ENST00000329451 3/14 131 120 11 142 141 1 strelka-varscan-mutect LMNTD2,missense_variant,p.Leu73Met,ENST00000329451,NM_173573.2;LMNTD2,missense_variant,p.Leu80Met,ENST00000441853,;LMNTD2,missense_variant,p.Leu83Met,ENST00000486629,;LRRC56,downstream_gene_variant,,ENST00000270115,NM_198075.3;RASSF7,upstream_gene_variant,,ENST00000397583,NM_003475.3;RASSF7,upstream_gene_variant,,ENST00000431809,;RASSF7,upstream_gene_variant,,ENST00000397582,NM_001143993.1;RASSF7,upstream_gene_variant,,ENST00000454668,NM_001143994.1;RASSF7,upstream_gene_variant,,ENST00000528736,;RP11-496I9.1,non_coding_transcript_exon_variant,,ENST00000527620,;RP11-496I9.1,upstream_gene_variant,,ENST00000533844,;RP11-496I9.1,upstream_gene_variant,,ENST00000527113,;RASSF7,upstream_gene_variant,,ENST00000524468,;LMNTD2,non_coding_transcript_exon_variant,,ENST00000492515,;RASSF7,upstream_gene_variant,,ENST00000414138,;LMNTD2,upstream_gene_variant,,ENST00000469990,;RASSF7,upstream_gene_variant,,ENST00000531112,; T ENST00000329451 Transcript missense_variant 280/2084 217/1905 73/634 L/M Ctg/Atg COSM4666607 1 -1 LMNTD2 HGNC HGNC:28561 protein_coding YES CCDS7701.1 ENSP00000331167 Q8IXW0 UPI0000456441 NM_173573.2 deleterious(0) 3/14 hmmpanther:PTHR19956,hmmpanther:PTHR19956:SF5 1 MODERATE 1 SNV 1 1 1 PASS rs1459243090 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 558708 558708 G T 1 0 0 0 0 1 0 0 0 8776 1020 36 2 2 LMNTD2 11 558708 Missense_Mutation SNP G C3L-00144_T 558708 134527914 977 5048 RASSF7 0 . GRCh38 11 562622 562622 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.668T>C p.Leu223Pro p.L223P ENST00000397583 3/6 153 138 15 122 122 0 strelka-mutect RASSF7,missense_variant,p.Leu223Pro,ENST00000397583,NM_003475.3;RASSF7,missense_variant,p.Leu223Pro,ENST00000431809,;RASSF7,missense_variant,p.Leu223Pro,ENST00000397582,NM_001143993.1;RASSF7,missense_variant,p.Leu223Pro,ENST00000454668,NM_001143994.1;LMNTD2,upstream_gene_variant,,ENST00000329451,NM_173573.2;LMNTD2,upstream_gene_variant,,ENST00000441853,;LMNTD2,upstream_gene_variant,,ENST00000486629,;RASSF7,downstream_gene_variant,,ENST00000528736,;MIR210HG,downstream_gene_variant,,ENST00000500447,;MIR210HG,downstream_gene_variant,,ENST00000533920,;MIR210HG,downstream_gene_variant,,ENST00000528245,;MIR210HG,downstream_gene_variant,,ENST00000534540,;RP11-496I9.1,downstream_gene_variant,,ENST00000527620,;RP11-496I9.1,downstream_gene_variant,,ENST00000533844,;RP11-496I9.1,downstream_gene_variant,,ENST00000527113,;RASSF7,downstream_gene_variant,,ENST00000524468,;RASSF7,missense_variant,p.Leu80Pro,ENST00000531112,;RASSF7,3_prime_UTR_variant,,ENST00000414138,;LMNTD2,upstream_gene_variant,,ENST00000492515,; C ENST00000397583 Transcript missense_variant 1101/1928 668/1122 223/373 L/P cTg/cCg 1 1 RASSF7 HGNC HGNC:1166 protein_coding YES CCDS7702.1 ENSP00000380713 Q02833 A0A024RCE4 UPI0000127A61 NM_003475.3 deleterious(0.05) 3/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 562622 562622 T C 1 0 0 0 0 1 0 0 0 13252 1580 55 5 5 RASSF7 11 562622 Missense_Mutation SNP T C3L-00144_T 3914 562622 134524000 978 5049 PHRF1 0 . GRCh38 11 601696 601696 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1147G>T p.Val383Leu p.V383L ENST00000264555 10/18 146 138 8 105 105 0 strelka-mutect PHRF1,missense_variant,p.Val383Leu,ENST00000264555,NM_001286581.1;PHRF1,missense_variant,p.Val383Leu,ENST00000416188,NM_020901.3;PHRF1,missense_variant,p.Val382Leu,ENST00000413872,NM_001286582.1;PHRF1,missense_variant,p.Val379Leu,ENST00000533464,NM_001286583.1;PHRF1,missense_variant,p.Val383Leu,ENST00000534320,;PHRF1,non_coding_transcript_exon_variant,,ENST00000532550,; T ENST00000264555 Transcript missense_variant 1275/5523 1147/4950 383/1649 V/L Gta/Tta 1 1 PHRF1 HGNC HGNC:24351 protein_coding YES CCDS65988.1 ENSP00000264555 Q9P1Y6 A0A024RCA1 UPI000041A715 NM_001286581.1 tolerated(0.48) 10/18 Low_complexity_(Seg):seg,hmmpanther:PTHR12618:SF5,hmmpanther:PTHR12618 MODERATE 1 SNV 1 1 PASS . . 0 196 2 10 2 0 0 0 -3.491006 0.2680166 1 1 0 0 T 3 4 12 601696 601696 G T 1 0 0 0 0 1 0 0 0 11949 1275 44 2 2 PHRF1 11 601696 Missense_Mutation SNP G C3L-00144_T 39074 601696 134484926 979 5050 SLC25A22 0 . GRCh38 11 794489 794489 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.171C>G p.= p.V57V ENST00000320230 4/10 389 298 91 335 335 0 strelka-varscan-mutect SLC25A22,synonymous_variant,p.=,ENST00000320230,NM_024698.5;SLC25A22,synonymous_variant,p.=,ENST00000628067,NM_001191061.1;SLC25A22,synonymous_variant,p.=,ENST00000531214,NM_001191060.1;SLC25A22,synonymous_variant,p.=,ENST00000481290,;SLC25A22,synonymous_variant,p.=,ENST00000627843,;SLC25A22,synonymous_variant,p.=,ENST00000532484,;SLC25A22,synonymous_variant,p.=,ENST00000531534,;SLC25A22,synonymous_variant,p.=,ENST00000625419,;SLC25A22,synonymous_variant,p.=,ENST00000531437,;SLC25A22,synonymous_variant,p.=,ENST00000533385,;SLC25A22,synonymous_variant,p.=,ENST00000528606,;SLC25A22,synonymous_variant,p.=,ENST00000530360,;SLC25A22,synonymous_variant,p.=,ENST00000625752,;SLC25A22,synonymous_variant,p.=,ENST00000527723,;SLC25A22,synonymous_variant,p.=,ENST00000456706,;SLC25A22,synonymous_variant,p.=,ENST00000629634,;SLC25A22,synonymous_variant,p.=,ENST00000528936,;SLC25A22,synonymous_variant,p.=,ENST00000526152,;SLC25A22,synonymous_variant,p.=,ENST00000529066,;PIDD1,downstream_gene_variant,,ENST00000347755,NM_145886.3;PIDD1,downstream_gene_variant,,ENST00000411829,NM_145887.3;PANO1,upstream_gene_variant,,ENST00000620120,NM_001293167.1;CEND1,upstream_gene_variant,,ENST00000330106,NM_016564.3;SLC25A22,non_coding_transcript_exon_variant,,ENST00000625316,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000629602,;PIDD1,downstream_gene_variant,,ENST00000527812,;CEND1,upstream_gene_variant,,ENST00000524587,;SLC25A22,synonymous_variant,p.=,ENST00000529351,;SLC25A22,synonymous_variant,p.=,ENST00000531514,;SLC25A22,synonymous_variant,p.=,ENST00000527734,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000532361,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000527127,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000532459,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000524891,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000525010,;SLC25A22,non_coding_transcript_exon_variant,,ENST00000525644,;PIDD1,downstream_gene_variant,,ENST00000527357,;PIDD1,downstream_gene_variant,,ENST00000534525,;PIDD1,downstream_gene_variant,,ENST00000524486,;PIDD1,downstream_gene_variant,,ENST00000525028,;PIDD1,downstream_gene_variant,,ENST00000531286,;SLC25A22,upstream_gene_variant,,ENST00000630809,; C ENST00000320230 Transcript synonymous_variant 555/2796 171/972 57/323 V gtC/gtG 1 -1 SLC25A22 HGNC HGNC:19954 protein_coding YES CCDS7715.1 ENSP00000322020 Q9H936 UPI0000073CD3 NM_024698.5 4/10 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF380 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 794489 794489 G C 1 0 0 0 0 0 0 0 1 14750 1161 41 4 4 SLC25A22 11 794489 Silent SNP G C3L-00144_T 192793 794489 134292133 980 5051 AP2A2 0 . GRCh38 11 1008113 1008113 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2401C>G p.Pro801Ala p.P801A ENST00000332231 18/22 121 111 10 124 124 0 strelka-varscan-mutect AP2A2,missense_variant,p.Pro801Ala,ENST00000332231,NM_001242837.1;AP2A2,missense_variant,p.Pro800Ala,ENST00000448903,NM_012305.3;AP2A2,intron_variant,,ENST00000534328,;MUC6,downstream_gene_variant,,ENST00000421673,NM_005961.2;AP2A2,non_coding_transcript_exon_variant,,ENST00000525891,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529438,;AP2A2,3_prime_UTR_variant,,ENST00000528815,;AP2A2,non_coding_transcript_exon_variant,,ENST00000531497,;AP2A2,non_coding_transcript_exon_variant,,ENST00000526401,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529427,;AP2A2,upstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526376,; G ENST00000332231 Transcript missense_variant 2614/4656 2401/2823 801/940 P/A Cca/Gca 1 1 AP2A2 HGNC HGNC:562 protein_coding YES CCDS73234.1 ENSP00000327694 O94973 UPI000050AA18 NM_001242837.1 deleterious(0) 18/22 hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF24,Gene3D:1kyfA01,PIRSF_domain:PIRSF037091,Pfam_domain:PF02883,SMART_domains:SM00809,Superfamily_domains:SSF49348 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 1008113 1008113 C G 1 0 0 0 0 1 0 0 0 856 739 26 4 4 AP2A2 11 1008113 Missense_Mutation SNP C C3L-00144_T 213624 1008113 134078509 981 5052 MUC6 0 . GRCh38 11 1026129 1026129 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2559G>T p.Arg853Ser p.R853S ENST00000421673 21/33 86 64 22 93 93 0 strelka-varscan-mutect MUC6,missense_variant,p.Arg853Ser,ENST00000421673,NM_005961.2; A ENST00000421673 Transcript missense_variant 2610/8006 2559/7320 853/2439 R/S agG/agT 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 tolerated(0.2) 21/33 hmmpanther:PTHR11339:SF264,hmmpanther:PTHR11339,SMART_domains:SM00215 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1026129 1026129 C A 1 0 0 0 0 1 0 0 0 9980 622 22 2 2 MUC6 11 1026129 Missense_Mutation SNP C C3L-00144_T 18016 1026129 134060493 982 5053 MUC5AC 0 . GRCh38 11 1187003 1187003 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.8858C>A p.Thr2953Asn p.T2953N ENST00000621226 31/49 195 180 15 233 233 0 varscan-mutect MUC5AC,missense_variant,p.Thr2953Asn,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 8905/17448 8858/16965 2953/5654 T/N aCc/aAc 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated_low_confidence(0.24) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1365799715 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1187003 1187003 C A 1 0 0 0 0 1 0 0 0 9978 507 18 2 2 MUC5AC 11 1187003 Missense_Mutation SNP C C3L-00144_T 160874 1187003 133899619 983 5054 MUC5AC 0 . GRCh38 11 1192916 1192916 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.14514C>A p.= p.S4838S ENST00000621226 32/49 122 111 11 142 141 1 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript synonymous_variant 14561/17448 14514/16965 4838/5654 S tcC/tcA 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 32/49 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -16.27134 0.9999819 1 1 1 0 A 2 1 12 1192916 1192916 C A 1 0 0 0 0 0 0 0 1 9978 610 22 2 2 MUC5AC 11 1192916 Silent SNP C C3L-00144_T 5913 1192916 133893706 984 5055 MUC5B 0 . GRCh38 11 1226644 1226644 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.229T>A p.Cys77Ser p.C77S ENST00000529681 4/49 171 159 12 180 180 0 strelka-varscan-mutect MUC5B,missense_variant,p.Cys77Ser,ENST00000529681,NM_002458.2;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;MUC5B,upstream_gene_variant,,ENST00000531082,; A ENST00000529681 Transcript missense_variant 287/17911 229/17289 77/5762 C/S Tgc/Agc 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 deleterious(0) 4/49 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF269,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1226644 1226644 T A 1 0 0 0 0 1 0 0 0 9979 1696 59 4 4 MUC5B 11 1226644 Missense_Mutation SNP T C3L-00144_T 33728 1226644 133859978 985 5056 MUC5B 0 . GRCh38 11 1233241 1233241 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2294A>T p.Glu765Val p.E765V ENST00000529681 18/49 93 69 24 94 94 0 strelka-varscan-mutect MUC5B,missense_variant,p.Glu765Val,ENST00000529681,NM_002458.2;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;MUC5B,downstream_gene_variant,,ENST00000531082,; T ENST00000529681 Transcript missense_variant 2352/17911 2294/17289 765/5762 E/V gAg/gTg 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 deleterious(0) 18/49 Gene3D:2.10.25.10,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF269,SMART_domains:SM00214 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 1233241 1233241 A T 1 0 0 0 0 1 0 0 0 9979 304 11 4 4 MUC5B 11 1233241 Missense_Mutation SNP A C3L-00144_T 6597 1233241 133853381 986 5057 KRTAP5-4 0 . GRCh38 11 1621528 1621528 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.566G>T p.Cys189Phe p.C189F ENST00000399682 1/1 614 581 33 567 567 0 varscan-mutect KRTAP5-4,missense_variant,p.Cys189Phe,ENST00000399682,;KRTAP5-4,missense_variant,p.Cys180Phe,ENST00000616115,; A ENST00000399682 Transcript missense_variant 611/1181 566/687 189/228 C/F tGc/tTc 1 -1 KRTAP5-4 HGNC HGNC:23599 protein_coding YES ENSP00000382590 A8MUN0 UPI0000E592E4 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1621528 1621528 C A 1 0 0 0 0 1 0 0 0 8458 710 25 2 2 KRTAP5-4 11 1621528 Missense_Mutation SNP C C3L-00144_T 388287 1621528 133465094 987 5058 TH 0 . GRCh38 11 2168506 2168506 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.565C>A p.Pro189Thr p.P189T ENST00000381178 4/14 326 258 68 301 301 0 strelka-varscan-mutect TH,missense_variant,p.Pro189Thr,ENST00000381178,NM_199292.2;TH,missense_variant,p.Pro185Thr,ENST00000381175,NM_199293.2;TH,missense_variant,p.Pro158Thr,ENST00000352909,NM_000360.3;TH,missense_variant,p.Pro158Thr,ENST00000333684,;TH,upstream_gene_variant,,ENST00000412076,;MIR4686,upstream_gene_variant,,ENST00000584128,;TH,3_prime_UTR_variant,,ENST00000324155,;TH,3_prime_UTR_variant,,ENST00000381168,;TH,non_coding_transcript_exon_variant,,ENST00000469226,;TH,upstream_gene_variant,,ENST00000461172,;TH,upstream_gene_variant,,ENST00000479437,;TH,upstream_gene_variant,,ENST00000416223,; T ENST00000381178 Transcript missense_variant 584/1910 565/1587 189/528 P/T Ccc/Acc 1 -1 TH HGNC HGNC:11782 protein_coding YES CCDS7731.1 ENSP00000370571 P07101 UPI00001412DD NM_199292.2 tolerated(0.85) 4/14 PROSITE_profiles:PS51410,hmmpanther:PTHR11473,hmmpanther:PTHR11473:SF18,PIRSF_domain:PIRSF000336,TIGRFAM_domain:TIGR01269,Gene3D:1.10.800.10,Superfamily_domains:SSF55021 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 2168506 2168506 G T 1 0 0 0 0 1 0 0 0 16271 1232 43 2 2 TH 11 2168506 Missense_Mutation SNP G C3L-00144_T 546978 2168506 132918116 988 5059 TSPAN32 0 . GRCh38 11 2302912 2302912 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.135C>G p.= p.R45R ENST00000182290 2/10 148 127 21 115 115 0 strelka-varscan-mutect TSPAN32,synonymous_variant,p.=,ENST00000182290,NM_139022.2;TSPAN32,synonymous_variant,p.=,ENST00000612299,;TSPAN32,synonymous_variant,p.=,ENST00000451520,;TSPAN32,synonymous_variant,p.=,ENST00000381121,;TSPAN32,synonymous_variant,p.=,ENST00000381117,;C11orf21,upstream_gene_variant,,ENST00000381153,;C11orf21,upstream_gene_variant,,ENST00000456145,NM_001142946.1;TSPAN32,non_coding_transcript_exon_variant,,ENST00000483227,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000479508,;C11orf21,non_coding_transcript_exon_variant,,ENST00000495467,;C11orf21,upstream_gene_variant,,ENST00000470369,;TSPAN32,upstream_gene_variant,,ENST00000484523,;TSPAN32,missense_variant,p.Pro48Ala,ENST00000437313,;TSPAN32,synonymous_variant,p.=,ENST00000446063,;TSPAN32,synonymous_variant,p.=,ENST00000339046,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000461200,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000493924,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000498313,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000484104,;TSPAN32,non_coding_transcript_exon_variant,,ENST00000493948,; G ENST00000182290 Transcript synonymous_variant 272/1318 135/963 45/320 R cgC/cgG 1 1 TSPAN32 HGNC HGNC:13410 protein_coding YES CCDS7733.1 ENSP00000182290 Q96QS1 UPI000013198B NM_139022.2 2/10 Pfam_domain:PF00335,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF197 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 2302912 2302912 C G 1 0 0 0 0 0 0 0 1 17152 726 26 4 4 TSPAN32 11 2302912 Silent SNP C C3L-00144_T 134406 2302912 132783710 989 5060 CHRNA10 0 . GRCh38 11 3666259 3666259 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1201A>T p.Thr401Ser p.T401S ENST00000250699 5/5 149 131 18 128 127 1 strelka-varscan-mutect CHRNA10,missense_variant,p.Thr401Ser,ENST00000250699,NM_020402.3;CHRNA10,3_prime_UTR_variant,,ENST00000534359,NM_001303034.1,NM_001303035.1;ART1,downstream_gene_variant,,ENST00000250693,NM_004314.2;NUP98,downstream_gene_variant,,ENST00000533346,;Y_RNA,upstream_gene_variant,,ENST00000364409,;Y_RNA,upstream_gene_variant,,ENST00000363331,;CHRNA10,downstream_gene_variant,,ENST00000493827,;CHRNA10,3_prime_UTR_variant,,ENST00000526599,; A ENST00000250699 Transcript missense_variant 1273/1945 1201/1353 401/450 T/S Acc/Tcc 1 -1 CHRNA10 HGNC HGNC:13800 protein_coding YES CCDS7745.1 ENSP00000250699 Q9GZZ6 UPI0000038CF1 NM_020402.3 tolerated(0.17) 5/5 hmmpanther:PTHR18945:SF566,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3666259 3666259 T A 1 0 0 0 0 1 0 0 0 3142 1696 59 4 4 CHRNA10 11 3666259 Missense_Mutation SNP T C3L-00144_T 1363347 3666259 131420363 990 5061 OR52I1 0 . GRCh38 11 4594635 4594635 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.597C>A p.Ser199Arg p.S199R ENST00000530443 1/1 238 182 56 199 198 1 strelka-varscan-mutect OR52I1,missense_variant,p.Ser224Arg,ENST00000450052,;OR52I1,missense_variant,p.Ser199Arg,ENST00000530443,NM_001005169.1;TRIM68,downstream_gene_variant,,ENST00000300747,NM_018073.7;TRIM68,downstream_gene_variant,,ENST00000531101,; A ENST00000530443 Transcript missense_variant 597/975 597/975 199/324 S/R agC/agA COSM4032958 1 1 OR52I1 HGNC HGNC:15220 protein_coding YES CCDS59223.1 ENSP00000436453 Q8NGK6 UPI0000046AE5 NM_001005169.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF86,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 4594635 4594635 C A 1 0 0 0 0 1 0 0 0 11193 709 25 2 2 OR52I1 11 4594635 Missense_Mutation SNP C C3L-00144_T 928376 4594635 130491987 991 5062 OR52A5 0 . GRCh38 11 5132183 5132183 + Missense_Mutation SNP C C A rs771107155 C3L-00144_T C3L-00144_N C C c.460G>T p.Ala154Ser p.A154S ENST00000307388 1/1 149 110 39 107 107 0 strelka-varscan-mutect OR52A5,missense_variant,p.Ala154Ser,ENST00000307388,NM_001005160.2; A ENST00000307388 Transcript missense_variant 460/951 460/951 154/316 A/S Gct/Tct rs771107155 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 tolerated(0.24) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 5132183 5132183 C A 1 0 0 0 0 1 0 0 0 11183 739 26 2 2 OR52A5 11 5132183 Missense_Mutation SNP C C3L-00144_T 537548 5132183 129954439 992 5063 UBQLNL 0 . GRCh38 11 5515649 5515649 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.793G>T p.Gly265Cys p.G265C ENST00000380184 1/1 237 218 19 224 224 0 strelka-varscan-mutect UBQLNL,missense_variant,p.Gly265Cys,ENST00000380184,NM_145053.4;HBG2,intron_variant,,ENST00000380259,;OLFM5P,downstream_gene_variant,,ENST00000411807,; A ENST00000380184 Transcript missense_variant 1057/2313 793/1428 265/475 G/C Ggt/Tgt 1 -1 UBQLNL HGNC HGNC:28294 protein_coding YES CCDS31385.1 ENSP00000369531 Q8IYU4 UPI000066D8EC NM_145053.4 deleterious(0.03) 1/1 hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF9 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 5515649 5515649 C A 1 0 0 0 0 1 0 0 0 17424 681 24 2 2 UBQLNL 11 5515649 Missense_Mutation SNP C C3L-00144_T 383466 5515649 129570973 993 5064 OR52N1 0 . GRCh38 11 5788722 5788722 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.95C>A p.Pro32Gln p.P32Q ENST00000317078 1/1 166 137 29 106 105 1 strelka-varscan-mutect OR52N1,missense_variant,p.Pro32Gln,ENST00000317078,NM_001001913.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000317078 Transcript missense_variant 95/963 95/963 32/320 P/Q cCa/cAa 1 -1 OR52N1 HGNC HGNC:14853 protein_coding YES CCDS31398.1 ENSP00000322823 Q8NH53 UPI0000041BDD NM_001001913.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF145,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1338831953 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 5788722 5788722 G T 1 0 0 0 0 1 0 0 0 11200 1348 47 2 2 OR52N1 11 5788722 Missense_Mutation SNP G C3L-00144_T 273073 5788722 129297900 994 5065 OR56A3 0 . GRCh38 11 5947887 5947887 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.541T>A p.Cys181Ser p.C181S ENST00000329564 1/1 166 157 9 144 144 0 strelka-varscan-mutect OR56A3,missense_variant,p.Cys181Ser,ENST00000329564,NM_001003443.2;AC025016.1,downstream_gene_variant,,ENST00000528915,; A ENST00000329564 Transcript missense_variant 548/1022 541/948 181/315 C/S Tgc/Agc 1 1 OR56A3 HGNC HGNC:14786 protein_coding YES CCDS41614.1 ENSP00000331572 Q8NH54 A0A126GWL6 UPI0000041BF7 NM_001003443.2 tolerated(0.05) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF40,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 5947887 5947887 T A 1 0 0 0 0 1 0 0 0 11206 1580 55 4 4 OR56A3 11 5947887 Missense_Mutation SNP T C3L-00144_T 159165 5947887 129138735 995 5066 OR52L1 0 . GRCh38 11 5986083 5986083 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.848G>A p.Gly283Asp p.G283D ENST00000332249 1/1 322 304 18 279 279 0 strelka-varscan-mutect OR52L1,missense_variant,p.Gly283Asp,ENST00000332249,NM_001005173.3; T ENST00000332249 Transcript missense_variant 903/1094 848/990 283/329 G/D gGt/gAt 1 -1 OR52L1 HGNC HGNC:14785 protein_coding YES CCDS44529.1 ENSP00000330338 Q8NGH7 UPI000004B20D NM_001005173.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF96,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 5986083 5986083 C T 1 0 0 0 0 1 0 0 0 11198 507 18 3 3 OR52L1 11 5986083 Missense_Mutation SNP C C3L-00144_T 38196 5986083 129100539 996 5067 OR56A1 0 . GRCh38 11 6027279 6027279 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.426C>A p.= p.I142I ENST00000316650 1/1 301 230 71 304 304 0 strelka-varscan-mutect OR56A1,synonymous_variant,p.=,ENST00000316650,NM_001001917.2; T ENST00000316650 Transcript synonymous_variant 463/1071 426/957 142/318 I atC/atA 1 -1 OR56A1 HGNC HGNC:14781 protein_coding YES CCDS31405.1 ENSP00000321246 Q8NGH5 A0A126GVB5 UPI000013FE4B NM_001001917.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248:SF62,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 6027279 6027279 G T 1 0 0 0 0 0 0 0 1 11205 1280 45 2 2 OR56A1 11 6027279 Silent SNP G C3L-00144_T 41196 6027279 129059343 997 5068 CNGA4 0 . GRCh38 11 6240133 6240133 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.339G>T p.Trp113Cys p.W113C ENST00000379936 4/6 136 118 18 119 119 0 strelka-mutect CNGA4,missense_variant,p.Trp113Cys,ENST00000379936,NM_001037329.3;CNGA4,intron_variant,,ENST00000533426,; T ENST00000379936 Transcript missense_variant 454/1863 339/1728 113/575 W/C tgG/tgT 1 1 CNGA4 HGNC HGNC:2152 protein_coding YES CCDS31408.1 ENSP00000369268 Q8IV77 UPI000004C7EC NM_001037329.3 tolerated(0.18) 4/6 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF388,Superfamily_domains:SSF81324 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 6240133 6240133 G T 1 0 0 0 0 1 0 0 0 3379 1183 41 2 2 CNGA4 11 6240133 Missense_Mutation SNP G C3L-00144_T 212854 6240133 128846489 998 5069 CNGA4 0 . GRCh38 11 6240193 6240193 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.399C>T p.= p.G133G ENST00000379936 4/6 259 232 27 175 175 0 strelka-varscan-mutect CNGA4,synonymous_variant,p.=,ENST00000379936,NM_001037329.3;CNGA4,intron_variant,,ENST00000533426,; T ENST00000379936 Transcript synonymous_variant 514/1863 399/1728 133/575 G ggC/ggT 1 1 CNGA4 HGNC HGNC:2152 protein_coding YES CCDS31408.1 ENSP00000369268 Q8IV77 UPI000004C7EC NM_001037329.3 4/6 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF388,Superfamily_domains:SSF81324 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 6240193 6240193 C T 1 0 0 0 0 0 0 0 1 3379 726 26 3 3 CNGA4 11 6240193 Silent SNP C C3L-00144_T 60 6240193 128846429 999 5070 SMPD1 0 . GRCh38 11 6390734 6390734 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.136G>T p.Ala46Ser p.A46S ENST00000342245 1/6 192 169 23 207 207 0 varscan-mutect SMPD1,missense_variant,p.Ala46Ser,ENST00000342245,NM_001318087.1,NM_000543.4;SMPD1,missense_variant,p.Ala46Ser,ENST00000527275,NM_001007593.2;SMPD1,intron_variant,,ENST00000530395,;APBB1,downstream_gene_variant,,ENST00000389906,;APBB1,downstream_gene_variant,,ENST00000609360,NM_001164.4;APBB1,downstream_gene_variant,,ENST00000299402,;APBB1,downstream_gene_variant,,ENST00000311051,NM_145689.2;APBB1,downstream_gene_variant,,ENST00000610474,;APBB1,downstream_gene_variant,,ENST00000608394,NM_001257321.2;APBB1,downstream_gene_variant,,ENST00000618005,;APBB1,downstream_gene_variant,,ENST00000608704,NM_001257320.2;APBB1,downstream_gene_variant,,ENST00000608645,NM_001257326.2;APBB1,downstream_gene_variant,,ENST00000608655,NM_001257319.2;APBB1,downstream_gene_variant,,ENST00000621678,;APBB1,downstream_gene_variant,,ENST00000530885,NM_001257323.2;APBB1,downstream_gene_variant,,ENST00000609331,NM_001257325.2;APBB1,downstream_gene_variant,,ENST00000529519,;SMPD1,upstream_gene_variant,,ENST00000526280,;SMPD1,non_coding_transcript_exon_variant,,ENST00000533196,;APBB1,downstream_gene_variant,,ENST00000526240,;SMPD1,missense_variant,p.Ala46Ser,ENST00000534405,NM_001318088.1;SMPD1,missense_variant,p.Ala46Ser,ENST00000533123,;SMPD1,missense_variant,p.Ala46Ser,ENST00000531303,;APBB1,downstream_gene_variant,,ENST00000608435,;APBB1,downstream_gene_variant,,ENST00000524626,;SMPD1,upstream_gene_variant,,ENST00000531336,;SMPD1,upstream_gene_variant,,ENST00000532367,; T ENST00000342245 Transcript missense_variant 304/2452 136/1896 46/631 A/S Gcg/Tcg 1 1 SMPD1 HGNC HGNC:11120 protein_coding YES CCDS44531.1 ENSP00000340409 P17405 UPI000013E592 NM_001318087.1,NM_000543.4 tolerated_low_confidence(0.23) 1/6 PIRSF_domain:PIRSF000948,hmmpanther:PTHR10340,hmmpanther:PTHR10340:SF34,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -10.29253 0.9952766 1 1 1 0 T 3 4 12 6390734 6390734 G T 1 0 0 0 0 1 0 0 0 15125 1203 42 2 2 SMPD1 11 6390734 Missense_Mutation SNP G C3L-00144_T 150541 6390734 128695888 1000 5071 DCHS1 0 . GRCh38 11 6622564 6622564 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.9112G>C p.Ala3038Pro p.A3038P ENST00000299441 21/21 76 68 8 82 82 0 strelka-varscan-mutect DCHS1,missense_variant,p.Ala3038Pro,ENST00000299441,NM_003737.3;TPP1,upstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,upstream_gene_variant,,ENST00000533371,;TPP1,upstream_gene_variant,,ENST00000528657,;TPP1,upstream_gene_variant,,ENST00000436873,;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.9,downstream_gene_variant,,ENST00000545572,;TPP1,upstream_gene_variant,,ENST00000534644,;TPP1,upstream_gene_variant,,ENST00000524903,;TPP1,upstream_gene_variant,,ENST00000530040,;TPP1,upstream_gene_variant,,ENST00000428886,;TPP1,upstream_gene_variant,,ENST00000531754,;TPP1,upstream_gene_variant,,ENST00000528571,;TPP1,upstream_gene_variant,,ENST00000528917,; G ENST00000299441 Transcript missense_variant 9524/10765 9112/9897 3038/3298 A/P Gct/Cct 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0.01) 21/21 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -17.66199 1 1 1 1 0 G 3 3 12 6622564 6622564 C G 1 0 0 0 0 1 0 0 0 4090 739 26 4 4 DCHS1 11 6622564 Missense_Mutation SNP C C3L-00144_T 231830 6622564 128464058 1001 5072 DCHS1 0 . GRCh38 11 6626928 6626928 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.6111C>T p.= p.F2037F ENST00000299441 14/21 323 301 22 276 276 0 strelka-varscan-mutect DCHS1,synonymous_variant,p.=,ENST00000299441,NM_003737.3;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.6,upstream_gene_variant,,ENST00000526633,; A ENST00000299441 Transcript synonymous_variant 6523/10765 6111/9897 2037/3298 F ttC/ttT 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 14/21 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 6626928 6626928 G A 1 0 0 0 0 0 0 0 1 4090 1281 45 3 3 DCHS1 11 6626928 Silent SNP G C3L-00144_T 4364 6626928 128459694 1002 5073 OLFML1 0 . GRCh38 11 7485882 7485882 + Missense_Mutation SNP G G C rs776575251 C3L-00144_T C3L-00144_N G G c.7G>C p.Val3Leu p.V3L ENST00000329293 1/3 163 131 32 122 122 0 strelka-varscan-mutect OLFML1,missense_variant,p.Val3Leu,ENST00000329293,NM_198474.3;OLFML1,missense_variant,p.Val3Leu,ENST00000530135,;OLFML1,missense_variant,p.Val3Leu,ENST00000528758,;OLFML1,missense_variant,p.Val3Leu,ENST00000534244,;CTD-2516F10.2,intron_variant,,ENST00000622955,;CTD-2516F10.2,intron_variant,,ENST00000530201,;OLFML1,non_coding_transcript_exon_variant,,ENST00000528308,; C ENST00000329293 Transcript missense_variant 401/2792 7/1209 3/402 V/L Gtg/Ctg rs776575251 1 1 OLFML1 HGNC HGNC:24473 protein_coding YES CCDS7779.1 ENSP00000332511 Q6UWY5 UPI0000161991 NM_198474.3 tolerated_low_confidence(0.77) 1/3 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF13,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs776575251 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 7485882 7485882 G C 1 0 0 0 0 1 0 0 0 10931 1261 44 4 4 OLFML1 11 7485882 Missense_Mutation SNP G C3L-00144_T 858954 7485882 127600740 1003 5074 LMO1 0 . GRCh38 11 8227046 8227046 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.294C>A p.Phe98Leu p.F98L ENST00000335790 3/4 139 132 7 118 117 1 strelka-varscan LMO1,missense_variant,p.Phe98Leu,ENST00000335790,NM_002315.2;LMO1,missense_variant,p.Phe97Leu,ENST00000428101,NM_001270428.1;LMO1,missense_variant,p.Phe87Leu,ENST00000534484,;LMO1,non_coding_transcript_exon_variant,,ENST00000524379,; T ENST00000335790 Transcript missense_variant 790/1279 294/471 98/156 F/L ttC/ttA 1 -1 LMO1 HGNC HGNC:6641 protein_coding YES CCDS44534.1 ENSP00000338207 P25800 UPI0000133883 NM_002315.2 tolerated(0.12) 3/4 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8227046 8227046 G T 1 0 0 0 0 1 0 0 0 8777 1049 37 1 1 LMO1 11 8227046 Missense_Mutation SNP G C3L-00144_T 741164 8227046 126859576 1004 5075 ADM 0 . GRCh38 11 10305958 10305958 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.108G>T p.Lys36Asn p.K36N ENST00000528655 2/3 178 164 14 157 157 0 strelka-varscan-mutect ADM,missense_variant,p.Lys36Asn,ENST00000528655,;ADM,missense_variant,p.Lys36Asn,ENST00000278175,NM_001124.2;ADM,missense_variant,p.Lys36Asn,ENST00000525063,;ADM,missense_variant,p.Lys36Asn,ENST00000526492,;ADM,missense_variant,p.Lys36Asn,ENST00000528544,;ADM,missense_variant,p.Lys36Asn,ENST00000524948,;ADM,5_prime_UTR_variant,,ENST00000530439,;ADM,5_prime_UTR_variant,,ENST00000534464,;RP11-351I24.1,upstream_gene_variant,,ENST00000526906,;AMPD3,upstream_gene_variant,,ENST00000527261,; T ENST00000528655 Transcript missense_variant 725/1889 108/558 36/185 K/N aaG/aaT 1 1 ADM HGNC HGNC:259 protein_coding YES CCDS7801.1 ENSP00000436607 P35318 UPI00001255F0 tolerated(0.1) 2/3 hmmpanther:PTHR23414:SF3,hmmpanther:PTHR23414,Pfam_domain:PF00214,Prints_domain:PR00801 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 10305958 10305958 G T 1 0 0 0 0 1 0 0 0 395 1020 36 2 2 ADM 11 10305958 Missense_Mutation SNP G C3L-00144_T 2078912 10305958 124780664 1005 5076 CTR9 0 . GRCh38 11 10770255 10770255 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2155G>T p.Val719Phe p.V719F ENST00000361367 17/25 131 101 30 130 130 0 strelka-varscan-mutect CTR9,missense_variant,p.Val719Phe,ENST00000361367,NM_014633.4;CTR9,downstream_gene_variant,,ENST00000529355,;CTR9,upstream_gene_variant,,ENST00000529898,;CTR9,downstream_gene_variant,,ENST00000526874,; T ENST00000361367 Transcript missense_variant 2581/4586 2155/3522 719/1173 V/F Gtt/Ttt 1 1 CTR9 HGNC HGNC:16850 protein_coding YES CCDS7805.1 ENSP00000355013 Q6PD62 UPI000006F32A NM_014633.4 deleterious(0.01) 17/25 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR14027,hmmpanther:PTHR14027:SF2,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 10770255 10770255 G T 1 0 0 0 0 1 0 0 0 3833 1029 36 2 2 CTR9 11 10770255 Missense_Mutation SNP G C3L-00144_T 464297 10770255 124316367 1006 5077 PTH 0 . GRCh38 11 13492451 13492451 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.302C>A p.Ala101Glu p.A101E ENST00000282091 3/3 233 211 22 200 200 0 strelka-varscan-mutect PTH,missense_variant,p.Ala101Glu,ENST00000282091,NM_000315.2;PTH,missense_variant,p.Ala101Glu,ENST00000529816,NM_001316352.1;RP11-15D14.2,downstream_gene_variant,,ENST00000532318,; T ENST00000282091 Transcript missense_variant 417/813 302/348 101/115 A/E gCa/gAa 1 -1 PTH HGNC HGNC:9606 protein_coding YES CCDS7812.1 ENSP00000282091 P01270 UPI000013290A NM_000315.2 tolerated(0.26) 3/3 PIRSF_domain:PIRSF001832,hmmpanther:PTHR10541,hmmpanther:PTHR10541:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 13492451 13492451 G T 1 0 0 0 0 1 0 0 0 12913 1319 46 2 2 PTH 11 13492451 Missense_Mutation SNP G C3L-00144_T 2722196 13492451 121594171 1007 5078 RRAS2 0 . GRCh38 11 14358804 14358804 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.67G>T p.Gly23Cys p.G23C ENST00000256196 1/6 216 170 46 176 176 0 strelka-varscan-mutect RRAS2,missense_variant,p.Gly23Cys,ENST00000256196,NM_012250.5;RRAS2,intron_variant,,ENST00000537760,NM_001177314.1;RRAS2,intron_variant,,ENST00000529237,;RRAS2,upstream_gene_variant,,ENST00000534746,;RRAS2,upstream_gene_variant,,ENST00000532814,NM_001177315.1;RRAS2,upstream_gene_variant,,ENST00000526063,NM_001102669.2;RRAS2,missense_variant,p.Gly23Cys,ENST00000532950,;RRAS2,missense_variant,p.Gly23Cys,ENST00000526717,; A ENST00000256196 Transcript missense_variant 381/1516 67/615 23/204 G/C Ggc/Tgc 1 -1 RRAS2 HGNC HGNC:17271 protein_coding YES CCDS7814.1 ENSP00000256196 P62070 UPI0000029C08 NM_012250.5 deleterious(0) 1/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF245,hmmpanther:PTHR24070,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 14358804 14358804 C A 1 0 0 0 0 1 0 0 0 13931 623 22 2 2 RRAS2 11 14358804 Missense_Mutation SNP C C3L-00144_T 866353 14358804 120727818 1008 5079 MYOD1 0 . GRCh38 11 17720958 17720958 + Silent SNP C C A rs746400738 C3L-00144_T C3L-00144_N C C c.687C>A p.= p.A229A ENST00000250003 2/3 137 100 37 131 131 0 strelka-varscan-mutect MYOD1,synonymous_variant,p.=,ENST00000250003,NM_002478.4; A ENST00000250003 Transcript synonymous_variant 902/1801 687/963 229/320 A gcC/gcA rs746400738 1 1 MYOD1 HGNC HGNC:7611 protein_coding YES CCDS7826.1 ENSP00000250003 P15172 UPI000007280C NM_002478.4 2/3 Pfam_domain:PF12232,hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF2 LOW 1 SNV 1 1 PASS rs746400738 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 17720958 17720958 C A 1 0 0 0 0 0 0 0 1 10089 668 24 2 2 MYOD1 11 17720958 Silent SNP C C3L-00144_T 3362154 17720958 117365664 1009 5080 HTATIP2 0 . GRCh38 11 20383178 20383178 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.804G>T p.= p.G268G ENST00000419348 6/6 119 103 16 130 129 1 strelka-varscan-mutect HTATIP2,synonymous_variant,p.=,ENST00000451739,NM_001098522.1;HTATIP2,synonymous_variant,p.=,ENST00000419348,NM_001098520.1;HTATIP2,synonymous_variant,p.=,ENST00000531058,;HTATIP2,synonymous_variant,p.=,ENST00000443524,NM_001098521.1;HTATIP2,synonymous_variant,p.=,ENST00000421577,NM_006410.4;PRMT3,upstream_gene_variant,,ENST00000331079,NM_001145167.1,NM_005788.3;PRMT3,upstream_gene_variant,,ENST00000437750,NM_001145166.1;HTATIP2,non_coding_transcript_exon_variant,,ENST00000533914,;PRMT3,upstream_gene_variant,,ENST00000330796,;PRMT3,upstream_gene_variant,,ENST00000525188,;PRMT3,upstream_gene_variant,,ENST00000526583,; T ENST00000419348 Transcript synonymous_variant 873/1477 804/831 268/276 G ggG/ggT 1 1 HTATIP2 HGNC HGNC:16637 protein_coding YES CCDS44553.1 ENSP00000392985 Q9BUP3 UPI0001536775 NM_001098520.1 6/6 hmmpanther:PTHR14097:SF7,hmmpanther:PTHR14097 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 20383178 20383178 G T 1 0 0 0 0 0 0 0 1 7328 1161 41 2 2 HTATIP2 11 20383178 Silent SNP G C3L-00144_T 2662220 20383178 114703444 1010 5081 ANO5 0 . GRCh38 11 22227450 22227450 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.512G>T p.Gly171Val p.G171V ENST00000324559 7/22 320 296 24 299 297 2 strelka-varscan-mutect ANO5,missense_variant,p.Gly171Val,ENST00000324559,NM_001142649.1,NM_213599.2; T ENST00000324559 Transcript missense_variant 829/6651 512/2742 171/913 G/V gGa/gTa 1 1 ANO5 HGNC HGNC:27337 protein_coding YES CCDS31444.1 ENSP00000315371 Q75V66 UPI000035B19B NM_001142649.1,NM_213599.2 tolerated(0.12) 7/22 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF16178 MODERATE 1 SNV 1 1 PASS rs977056246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 22227450 22227450 G T 1 0 0 0 0 1 0 0 0 807 1174 41 2 2 ANO5 11 22227450 Missense_Mutation SNP G C3L-00144_T 1844272 22227450 112859172 1011 5082 DCDC1 0 . GRCh38 11 30906626 30906626 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1339C>A p.Pro447Thr p.P447T ENST00000406071 11/20 265 210 55 228 227 1 strelka-varscan-mutect DCDC1,missense_variant,p.Pro1340Thr,ENST00000597505,;DCDC1,missense_variant,p.Pro447Thr,ENST00000406071,NM_020869.3;DCDC1,missense_variant,p.Pro28Thr,ENST00000303697,;DCDC1,missense_variant,p.Pro375Thr,ENST00000444572,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;DCDC1,non_coding_transcript_exon_variant,,ENST00000429306,; T ENST00000406071 Transcript missense_variant 1655/4758 1339/2673 447/890 P/T Cca/Aca 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 tolerated(0.09) 11/20 hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 30906626 30906626 G T 1 0 0 0 0 1 0 0 0 4086 1174 41 2 2 DCDC1 11 30906626 Missense_Mutation SNP G C3L-00144_T 8679176 30906626 104179996 1012 5083 EIF3M 0 . GRCh38 11 32587045 32587045 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.76G>T p.Gly26Ter p.G26* ENST00000531120 2/11 125 112 13 95 95 0 strelka-varscan-mutect EIF3M,stop_gained,p.Gly26Ter,ENST00000531120,NM_006360.4;EIF3M,5_prime_UTR_variant,,ENST00000323213,;EIF3M,5_prime_UTR_variant,,ENST00000533439,;EIF3M,intron_variant,,ENST00000524896,NM_001307929.1;EIF3M,upstream_gene_variant,,ENST00000526267,;EIF3M,non_coding_transcript_exon_variant,,ENST00000532054,;EIF3M,splice_acceptor_variant,,ENST00000532444,;EIF3M,stop_gained,p.Gly26Ter,ENST00000531921,;EIF3M,stop_gained,p.Gly26Ter,ENST00000524711,;EIF3M,non_coding_transcript_exon_variant,,ENST00000530026,;EIF3M,non_coding_transcript_exon_variant,,ENST00000531186,;EIF3M,intron_variant,,ENST00000525782,;HNRNPA3P9,downstream_gene_variant,,ENST00000604913,; T ENST00000531120 Transcript stop_gained 139/5051 76/1125 26/374 G/* Gga/Tga 1 1 EIF3M HGNC HGNC:24460 protein_coding YES CCDS7880.1 ENSP00000436049 Q7L2H7 UPI0000070F8A NM_006360.4 2/11 HAMAP:MF_03012,hmmpanther:PTHR15350:SF2,hmmpanther:PTHR15350 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 32587045 32587045 G T 1 0 0 0 0 0 1 0 0 4857 1001 35 2 2 EIF3M 11 32587045 Nonsense_Mutation SNP G C3L-00144_T 1680419 32587045 102499577 1013 5084 QSER1 0 . GRCh38 11 32933356 32933356 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1711G>T p.Val571Leu p.V571L ENST00000399302 4/13 124 91 33 108 108 0 strelka-varscan-mutect QSER1,missense_variant,p.Val571Leu,ENST00000399302,NM_001076786.2;QSER1,missense_variant,p.Val332Leu,ENST00000527788,;QSER1,upstream_gene_variant,,ENST00000524678,;QSER1,downstream_gene_variant,,ENST00000528155,;QSER1,downstream_gene_variant,,ENST00000527250,; T ENST00000399302 Transcript missense_variant 2046/9335 1711/5208 571/1735 V/L Gtg/Ttg 1 1 QSER1 HGNC HGNC:26154 protein_coding YES CCDS41631.1 ENSP00000382241 Q2KHR3 UPI0000E467AF NM_001076786.2 deleterious(0.01) 4/13 hmmpanther:PTHR14709:SF2,hmmpanther:PTHR14709 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 32933356 32933356 G T 1 0 0 0 0 1 0 0 0 13037 1261 44 2 2 QSER1 11 32933356 Missense_Mutation SNP G C3L-00144_T 346311 32933356 102153266 1014 5085 LRRC4C 0 . GRCh38 11 40114401 40114401 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1892C>A p.Ser631Tyr p.S631Y ENST00000278198 2/2 77 73 4 70 70 0 strelka-mutect LRRC4C,missense_variant,p.Ser631Tyr,ENST00000278198,;LRRC4C,missense_variant,p.Ser631Tyr,ENST00000527150,;LRRC4C,missense_variant,p.Ser631Tyr,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Ser631Tyr,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Ser631Tyr,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript missense_variant 3856/4054 1892/1923 631/640 S/Y tCt/tAt 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious_low_confidence(0) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 40114401 40114401 G T 1 0 0 0 0 1 0 0 0 8903 942 33 2 2 LRRC4C 11 40114401 Missense_Mutation SNP G C3L-00144_T 7181045 40114401 94972221 1015 5086 LRP4 0 . GRCh38 11 46873579 46873579 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.4244A>T p.Asn1415Ile p.N1415I ENST00000378623 29/38 69 48 21 75 75 0 strelka-varscan-mutect LRP4,missense_variant,p.Asn1415Ile,ENST00000378623,NM_002334.3;LRP4-AS1,non_coding_transcript_exon_variant,,ENST00000502049,;LRP4-AS1,downstream_gene_variant,,ENST00000531719,;LRP4,non_coding_transcript_exon_variant,,ENST00000527656,; A ENST00000378623 Transcript missense_variant 4487/8076 4244/5718 1415/1905 N/I aAc/aTc 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 deleterious(0) 29/38 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,Pfam_domain:PF00058,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 46873579 46873579 T A 1 0 0 0 0 1 0 0 0 8854 1725 60 4 4 LRP4 11 46873579 Missense_Mutation SNP T C3L-00144_T 6759178 46873579 88213043 1016 5087 OR4C3 0 . GRCh38 11 48325054 48325054 + Missense_Mutation SNP C C A rs267602915 C3L-00144_T C3L-00144_N C C c.114C>A p.Phe38Leu p.F38L ENST00000319856 1/1 223 167 56 179 179 0 strelka-varscan-mutect OR4C3,missense_variant,p.Phe38Leu,ENST00000319856,NM_001004702.1;OR4C3,upstream_gene_variant,,ENST00000611380,; A ENST00000319856 Transcript missense_variant 135/1036 114/990 38/329 F/L ttC/ttA rs267602915,COSM1703901,COSM5496575 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs267602915 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48325054 48325054 C A 1 0 0 0 0 1 0 0 0 11126 825 29 2 2 OR4C3 11 48325054 Missense_Mutation SNP C C3L-00144_T 1451475 48325054 86761568 1017 5088 TRIM49B 0 . GRCh38 11 49037628 49037628 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1010C>A p.Thr337Asn p.T337N ENST00000622138 8/8 505 429 76 441 440 1 strelka-varscan-mutect TRIM49B,missense_variant,p.Thr337Asn,ENST00000622138,;TRIM49B,missense_variant,p.Thr337Asn,ENST00000332682,NM_001206626.1; A ENST00000622138 Transcript missense_variant 1339/2162 1010/1359 337/452 T/N aCc/aAc 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 tolerated(0.07) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49037628 49037628 C A 1 0 0 0 0 1 0 0 0 17015 507 18 2 2 TRIM49B 11 49037628 Missense_Mutation SNP C C3L-00144_T 712574 49037628 86048994 1018 5089 FOLH1 0 . GRCh38 11 49169228 49169228 + Missense_Mutation SNP C C A rs375484734 C3L-00144_T C3L-00144_N C C c.1339G>T p.Val447Leu p.V447L ENST00000256999 12/19 313 263 50 200 199 1 strelka-varscan-mutect FOLH1,missense_variant,p.Val432Leu,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Val447Leu,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Val447Leu,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Val139Leu,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Val432Leu,ENST00000533034,NM_001193472.1;FOLH1,non_coding_transcript_exon_variant,,ENST00000525629,;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,; A ENST00000256999 Transcript missense_variant 1600/2635 1339/2253 447/750 V/L Gtg/Ttg rs375484734 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 12/19 Gene3D:3.40.630.10,Pfam_domain:PF04389,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs375484734 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49169228 49169228 C A 1 0 0 0 0 1 0 0 0 5840 536 19 1 1 FOLH1 11 49169228 Missense_Mutation SNP C C3L-00144_T 131600 49169228 85917394 1019 5090 FOLH1 0 . GRCh38 11 49186651 49186651 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.632G>T p.Gly211Val p.G211V ENST00000256999 5/19 135 127 8 104 104 0 varscan-mutect FOLH1,missense_variant,p.Gly196Val,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Gly211Val,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Gly211Val,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Gly196Val,ENST00000533034,NM_001193472.1;FOLH1,5_prime_UTR_variant,,ENST00000343844,NM_001193473.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000526226,;FOLH1,upstream_gene_variant,,ENST00000458311,; A ENST00000256999 Transcript missense_variant 893/2635 632/2253 211/750 G/V gGa/gTa COSM1718900,COSM4033409 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 5/19 Gene3D:3.50.30.30,Pfam_domain:PF02225,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF52025 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49186651 49186651 C A 1 0 0 0 0 1 0 0 0 5840 855 30 2 2 FOLH1 11 49186651 Missense_Mutation SNP C C3L-00144_T 17423 49186651 85899971 1020 5091 OR4C46 0 . GRCh38 11 54603126 54603126 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.873G>T p.Gln291His p.Q291H ENST00000328188 1/1 40 32 8 34 34 0 varscan-mutect OR4C46,missense_variant,p.Gln291His,ENST00000328188,NM_001004703.1; A ENST00000328188 Transcript missense_variant 873/930 873/930 291/309 Q/H caG/caT 1 -1 OR4C46 HGNC HGNC:31271 protein_coding YES CCDS73288.1 ENSP00000329056 A6NHA9 UPI000013F6F8 NM_001004703.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR26451:SF284,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 202 7 0 0 0 0 0 -19.67067 0.9999998 1 1 1 0 A 3 1 12 54603126 54603126 C A 1 0 0 0 0 1 0 0 0 11127 912 32 2 2 OR4C46 11 54603126 Missense_Mutation SNP C C3L-00144_T 5416475 54603126 80483496 1021 5092 OR4S2 0 . GRCh38 11 55651519 55651520 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.617dupT p.Ser208GlufsTer53 p.S208Efs*53 ENST00000312422 1/1 231 200 31 181 181 0 sindel-varindel-pindel OR4S2,frameshift_variant,p.Ser208GlufsTer53,ENST00000312422,NM_001004059.2; T ENST00000312422 Transcript frameshift_variant 616-617/936 616-617/936 206/311 L/LX ctg/cTtg 1 1 OR4S2 HGNC HGNC:15183 protein_coding YES CCDS31505.1 ENSP00000310337 Q8NH73 A0A126GVG1 UPI00001D77D2 NM_001004059.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 insertion 1 1 PASS . . 23 185 2 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 12 55651519 55651519 - T 1 0 1 1 0 0 0 0 0 11159 912 32 0 0 OR4S2 11 55651519 Frame_Shift_Ins INS - C3L-00144_T 1048393 55651519 79435103 1022 5093 OR5D18 0 . GRCh38 11 55819934 55819934 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.305T>A p.Phe102Tyr p.F102Y ENST00000333976 1/1 338 291 47 248 247 1 strelka-varscan-mutect OR5D18,missense_variant,p.Phe102Tyr,ENST00000333976,NM_001001952.1; A ENST00000333976 Transcript missense_variant 305/942 305/942 102/313 F/Y tTc/tAc 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 tolerated(0.18) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 55819934 55819934 T A 1 0 0 0 0 1 0 0 0 11227 1783 62 4 4 OR5D18 11 55819934 Missense_Mutation SNP T C3L-00144_T 168415 55819934 79266688 1023 5094 OR5L2 0 . GRCh38 11 55827331 55827331 + Missense_Mutation SNP C C A rs752225092 C3L-00144_T C3L-00144_N C C c.113C>A p.Thr38Lys p.T38K ENST00000378397 1/1 286 221 65 220 219 1 strelka-varscan-mutect OR5L2,missense_variant,p.Thr38Lys,ENST00000378397,NM_001004739.1; A ENST00000378397 Transcript missense_variant 113/936 113/936 38/311 T/K aCg/aAg rs752225092,COSM543398 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs752225092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 55827331 55827331 C A 1 0 0 0 0 1 0 0 0 11240 536 19 1 1 OR5L2 11 55827331 Missense_Mutation SNP C C3L-00144_T 7397 55827331 79259291 1024 5095 OR8I2 0 . GRCh38 11 56093546 56093546 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.239A>T p.Lys80Met p.K80M ENST00000302124 1/1 177 125 52 103 102 1 strelka-varscan-mutect OR8I2,missense_variant,p.Lys80Met,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; T ENST00000302124 Transcript missense_variant 239/933 239/933 80/310 K/M aAg/aTg 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 56093546 56093546 A T 1 0 0 0 0 1 0 0 0 11308 72 3 4 4 OR8I2 11 56093546 Missense_Mutation SNP A C3L-00144_T 266215 56093546 78993076 1025 5096 OR8H3 0 . GRCh38 11 56123040 56123040 + Missense_Mutation SNP C C G rs769797689 C3L-00144_T C3L-00144_N C C c.668C>G p.Ser223Cys p.S223C ENST00000313472 1/1 203 163 40 198 198 0 strelka-varscan-mutect OR8H3,missense_variant,p.Ser223Cys,ENST00000313472,NM_001005201.1; G ENST00000313472 Transcript missense_variant 668/939 668/939 223/312 S/C tCt/tGt rs769797689,COSM1298161,COSM4710288 1 1 OR8H3 HGNC HGNC:15309 protein_coding YES CCDS31519.1 ENSP00000323928 Q8N146 UPI0000041D25 NM_001005201.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs769797689 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 56123040 56123040 C G 1 0 0 0 0 1 0 0 0 11307 913 32 4 4 OR8H3 11 56123040 Missense_Mutation SNP C C3L-00144_T 29494 56123040 78963582 1026 5097 OR5T2 0 . GRCh38 11 56232241 56232241 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.945A>G p.Ile315Met p.I315M ENST00000313264 1/1 125 103 22 94 94 0 strelka-varscan-mutect OR5T2,missense_variant,p.Ile315Met,ENST00000313264,NM_001004746.1; C ENST00000313264 Transcript missense_variant 945/1080 945/1080 315/359 I/M atA/atG 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 deleterious(0.05) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1409749509 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 56232241 56232241 T C 1 0 0 0 0 1 0 0 0 11250 1396 49 5 5 OR5T2 11 56232241 Missense_Mutation SNP T C3L-00144_T 109201 56232241 78854381 1027 5098 OR9G4 0 . GRCh38 11 56743278 56743278 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.534A>G p.= p.T178T ENST00000302957 1/1 308 249 59 237 237 0 strelka-varscan-mutect OR9G4,synonymous_variant,p.=,ENST00000302957,NM_001005284.1;MIR6128,upstream_gene_variant,,ENST00000615528,;OR9G3P,downstream_gene_variant,,ENST00000525553,; C ENST00000302957 Transcript synonymous_variant 534/985 534/984 178/327 T acA/acG 1 -1 OR9G4 HGNC HGNC:15322 protein_coding YES CCDS31537.1 ENSP00000307515 Q8NGQ1 UPI00001D77DB NM_001005284.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF141,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 56743278 56743278 T C 1 0 0 0 0 0 0 0 1 11318 1451 51 5 5 OR9G4 11 56743278 Silent SNP T C3L-00144_T 511037 56743278 78343344 1028 5099 APLNR 0 . GRCh38 11 57235949 57235949 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1056G>T p.Gln352His p.Q352H ENST00000606794 1/1 173 134 39 124 123 1 strelka-varscan-mutect APLNR,missense_variant,p.Gln352His,ENST00000606794,NM_005161.4;APLNR,missense_variant,p.Gln352His,ENST00000611099,;APLNR,missense_variant,p.Gln352His,ENST00000257254,; A ENST00000606794 Transcript missense_variant 1253/3609 1056/1143 352/380 Q/H caG/caT 1 -1 APLNR HGNC HGNC:339 protein_coding YES CCDS7950.1 ENSP00000475344 P35414 UPI0000001622 NM_005161.4 tolerated(0.09) 1/1 hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF31,Prints_domain:PR01416,PD061381 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 57235949 57235949 C A 1 0 0 0 0 1 0 0 0 899 680 24 2 2 APLNR 11 57235949 Missense_Mutation SNP C C3L-00144_T 492671 57235949 77850673 1029 5100 YPEL4 0 . GRCh38 11 57647001 57647001 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.107C>A p.Ala36Glu p.A36E ENST00000524669 2/5 82 66 16 58 58 0 strelka-varscan-mutect YPEL4,missense_variant,p.Ala36Glu,ENST00000524669,;YPEL4,missense_variant,p.Ala36Glu,ENST00000300022,NM_145008.2;YPEL4,missense_variant,p.Ala36Glu,ENST00000534711,;YPEL4,missense_variant,p.Ala36Glu,ENST00000534810,;CLP1,upstream_gene_variant,,ENST00000529773,;AP000662.4,non_coding_transcript_exon_variant,,ENST00000525988,;AP000662.4,intron_variant,,ENST00000530595,;AP000662.4,intron_variant,,ENST00000528466,;AP000662.4,upstream_gene_variant,,ENST00000529908,;AP000662.4,upstream_gene_variant,,ENST00000526243,;YPEL4,non_coding_transcript_exon_variant,,ENST00000529776,;YPEL4,downstream_gene_variant,,ENST00000531442,;YPEL4,downstream_gene_variant,,ENST00000533025,;YPEL4,missense_variant,p.Ala36Glu,ENST00000532314,;YPEL4,non_coding_transcript_exon_variant,,ENST00000528797,;YPEL4,non_coding_transcript_exon_variant,,ENST00000524592,; T ENST00000524669 Transcript missense_variant 2830/4000 107/384 36/127 A/E gCa/gAa 1 -1 YPEL4 HGNC HGNC:18328 protein_coding YES CCDS7963.1 ENSP00000432648 Q96NS1 A0A024R4Y8 UPI000013BE0B deleterious(0.02) 2/5 hmmpanther:PTHR13848,hmmpanther:PTHR13848:SF17,Pfam_domain:PF03226 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 12 57647001 57647001 G T 1 0 0 0 0 1 0 0 0 18054 1319 46 2 2 YPEL4 11 57647001 Missense_Mutation SNP G C3L-00144_T 411052 57647001 77439621 1030 5101 OR9I1 0 . GRCh38 11 58119010 58119010 + Silent SNP C C A rs149011210 C3L-00144_T C3L-00144_N C C c.435G>T p.= p.V145V ENST00000302610 1/1 150 119 31 96 96 0 strelka-varscan-mutect OR9I1,synonymous_variant,p.=,ENST00000302610,NM_001005211.1;OR9Q1,intron_variant,,ENST00000335397,NM_001005212.3; A ENST00000302610 Transcript synonymous_variant 435/945 435/945 145/314 V gtG/gtT rs149011210 1 -1 OR9I1 HGNC HGNC:14718 protein_coding YES CCDS31542.1 ENSP00000302606 Q8NGQ6 A0A126GVJ4 UPI0000041B43 NM_001005211.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF232,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs149011210 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 58119010 58119010 C A 1 0 0 0 0 0 0 0 1 11319 581 21 2 2 OR9I1 11 58119010 Silent SNP C C3L-00144_T 472009 58119010 76967612 1031 5102 OR10W1 0 . GRCh38 11 58267840 58267840 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.19G>C p.Ala7Pro p.A7P ENST00000395079 1/1 115 85 30 66 66 0 strelka-varscan-mutect OR10W1,missense_variant,p.Ala7Pro,ENST00000395079,NM_207374.3; G ENST00000395079 Transcript missense_variant 421/1469 19/918 7/305 A/P Gcc/Ccc 1 -1 OR10W1 HGNC HGNC:15139 protein_coding YES CCDS7968.1 ENSP00000378516 Q8NGF6 UPI000004B229 NM_207374.3 tolerated(0.46) 1/1 hmmpanther:PTHR26452:SF165,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1225180631 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 58267840 58267840 C G 1 0 0 0 0 1 0 0 0 10998 739 26 4 4 OR10W1 11 58267840 Missense_Mutation SNP C C3L-00144_T 148830 58267840 76818782 1032 5103 OR5B2 0 . GRCh38 11 58422358 58422358 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.904G>T p.Val302Leu p.V302L ENST00000302581 1/1 131 94 37 124 123 1 strelka-varscan-mutect OR5B2,missense_variant,p.Val302Leu,ENST00000302581,NM_001005566.2; A ENST00000302581 Transcript missense_variant 956/1049 904/930 302/309 V/L Gtg/Ttg 1 -1 OR5B2 HGNC HGNC:8323 protein_coding YES CCDS31550.1 ENSP00000303076 Q96R09 UPI000004B227 NM_001005566.2 tolerated_low_confidence(0.12) 1/1 hmmpanther:PTHR26452:SF3,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 58422358 58422358 C A 1 0 0 0 0 1 0 0 0 11221 565 20 2 2 OR5B2 11 58422358 Missense_Mutation SNP C C3L-00144_T 154518 58422358 76664264 1033 5104 FAM111B 0 . GRCh38 11 59124381 59124382 + Frame_Shift_Del DEL GT GT - novel C3L-00144_T C3L-00144_N GT GT c.288_289delGT p.Phe97TyrfsTer5 p.F97Yfs*5 ENST00000343597 4/4 194 180 14 140 140 0 sindel-pindel FAM111B,frameshift_variant,p.Phe97TyrfsTer5,ENST00000343597,NM_198947.3;FAM111B,frameshift_variant,p.Phe97TyrfsTer5,ENST00000620384,;FAM111B,frameshift_variant,p.Phe67TyrfsTer5,ENST00000411426,NM_001142704.1;FAM111B,frameshift_variant,p.Phe67TyrfsTer5,ENST00000529618,NM_001142703.1;FAM111B,frameshift_variant,p.Phe67TyrfsTer5,ENST00000534403,; - ENST00000343597 Transcript frameshift_variant 475-476/3488 284-285/2205 95/734 S/X aGT/a 1 1 FAM111B HGNC HGNC:24200 protein_coding YES CCDS7972.1 ENSP00000341565 Q6SJ93 UPI00001D77B8 NM_198947.3 4/4 hmmpanther:PTHR14389,hmmpanther:PTHR14389:SF4 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 59124381 59124381 GT - 1 0 1 0 1 0 0 0 0 5265 1029 36 0 0 FAM111B 11 59124381 Frame_Shift_Del DEL GT C3L-00144_T 702023 59124381 75962241 1034 5105 OR5AN1 0 . GRCh38 11 59364871 59364871 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.413C>A p.Ser138Ter p.S138* ENST00000313940 1/1 122 97 25 90 90 0 strelka-varscan-mutect OR5AN1,stop_gained,p.Ser138Ter,ENST00000313940,NM_001004729.1; A ENST00000313940 Transcript stop_gained 460/1037 413/936 138/311 S/* tCa/tAa 1 1 OR5AN1 HGNC HGNC:15255 protein_coding YES CCDS31559.1 ENSP00000320302 Q8NGI8 A0A126GVP9 UPI000004B1FD NM_001004729.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF262,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 59364871 59364871 C A 1 0 0 0 0 0 1 0 0 11215 838 29 2 2 OR5AN1 11 59364871 Nonsense_Mutation SNP C C3L-00144_T 240490 59364871 75721751 1035 5106 OR5A1 0 . GRCh38 11 59443910 59443910 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.742C>T p.= p.L248L ENST00000302030 1/1 195 159 36 113 113 0 strelka-varscan-mutect OR5A1,synonymous_variant,p.=,ENST00000302030,NM_001004728.1; T ENST00000302030 Transcript synonymous_variant 767/1051 742/948 248/315 L Ctg/Ttg 1 1 OR5A1 HGNC HGNC:8319 protein_coding YES CCDS31561.1 ENSP00000303096 Q8NGJ0 UPI0000041C97 NM_001004728.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF354,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 59443910 59443910 C T 1 0 0 0 0 0 0 0 1 11211 912 32 3 3 OR5A1 11 59443910 Silent SNP C C3L-00144_T 79039 59443910 75642712 1036 5107 MS4A8 0 . GRCh38 11 60708744 60708744 + Missense_Mutation SNP A A G rs773486448 C3L-00144_T C3L-00144_N A A c.497A>G p.Tyr166Cys p.Y166C ENST00000300226 5/7 173 137 36 124 124 0 strelka-varscan-mutect MS4A8,missense_variant,p.Tyr166Cys,ENST00000300226,NM_031457.1;MS4A8,missense_variant,p.Tyr148Cys,ENST00000525458,;MS4A8,intron_variant,,ENST00000529752,;MS4A8,non_coding_transcript_exon_variant,,ENST00000533691,;MS4A8,non_coding_transcript_exon_variant,,ENST00000532953,;MS4A8,non_coding_transcript_exon_variant,,ENST00000533354,;MS4A8,non_coding_transcript_exon_variant,,ENST00000450141,; G ENST00000300226 Transcript missense_variant 700/1353 497/753 166/250 Y/C tAt/tGt rs773486448 1 1 MS4A8 HGNC HGNC:13380 protein_coding YES CCDS7990.1 ENSP00000300226 Q9BY19 UPI0000047F97 NM_031457.1 tolerated(0.07) 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23320:SF56,hmmpanther:PTHR23320,Pfam_domain:PF04103 MODERATE 1 SNV 1 1 PASS rs773486448 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 60708744 60708744 A G 1 0 0 0 0 1 0 0 0 9846 449 16 5 5 MS4A8 11 60708744 Missense_Mutation SNP A C3L-00144_T 1264834 60708744 74377878 1037 5108 MS4A8 0 . GRCh38 11 60715366 60715366 + Silent SNP G G C rs371352560 C3L-00144_T C3L-00144_N G G c.705G>C p.= p.P235P ENST00000300226 7/7 317 271 46 192 192 0 strelka-varscan-mutect MS4A8,missense_variant,p.Gly218Arg,ENST00000529752,;MS4A8,synonymous_variant,p.=,ENST00000300226,NM_031457.1;MS4A8,downstream_gene_variant,,ENST00000525458,; C ENST00000300226 Transcript synonymous_variant 908/1353 705/753 235/250 P ccG/ccC rs371352560 1 1 MS4A8 HGNC HGNC:13380 protein_coding YES CCDS7990.1 ENSP00000300226 Q9BY19 UPI0000047F97 NM_031457.1 7/7 hmmpanther:PTHR23320:SF56,hmmpanther:PTHR23320 LOW 1 SNV 1 1 PASS rs371352560 . 0 208 0 0 2 0 0 0 -19.86841 0.9966914 1 1 1 0 C 2 2 12 60715366 60715366 G C 1 0 0 0 0 0 0 0 1 9846 1103 39 4 4 MS4A8 11 60715366 Silent SNP G C3L-00144_T 6622 60715366 74371256 1038 5109 SLC15A3 0 . GRCh38 11 60951061 60951061 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.491G>T p.Gly164Val p.G164V ENST00000227880 1/8 142 104 38 76 76 0 strelka-varscan-mutect SLC15A3,missense_variant,p.Gly164Val,ENST00000227880,NM_016582.2;SLC15A3,missense_variant,p.Gly31Val,ENST00000538739,;SLC15A3,upstream_gene_variant,,ENST00000536491,;SLC15A3,missense_variant,p.Gly164Val,ENST00000541505,;SLC15A3,upstream_gene_variant,,ENST00000540272,; A ENST00000227880 Transcript missense_variant 725/2115 491/1746 164/581 G/V gGc/gTc 1 -1 SLC15A3 HGNC HGNC:18068 protein_coding YES CCDS7998.1 ENSP00000227880 Q8IY34 UPI000004433B NM_016582.2 tolerated(0.2) 1/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF95,Pfam_domain:PF00854,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs1301145621 . 0 201 6 2 0 0 0 0 -20 0.9999723 1 1 1 0 A 3 1 12 60951061 60951061 C A 1 0 0 0 0 1 0 0 0 14665 739 26 2 2 SLC15A3 11 60951061 Missense_Mutation SNP C C3L-00144_T 235695 60951061 74135561 1039 5110 SCGB1D2 0 . GRCh38 11 62243410 62243410 + Missense_Mutation SNP G G C rs139603186 C3L-00144_T C3L-00144_N G G c.177G>C p.Lys59Asn p.K59N ENST00000244926 2/3 219 178 41 152 152 0 strelka-varscan-mutect SCGB1D2,missense_variant,p.Lys59Asn,ENST00000244926,NM_006551.3;RP11-703H8.9,intron_variant,,ENST00000529875,; C ENST00000244926 Transcript missense_variant 275/480 177/273 59/90 K/N aaG/aaC rs139603186 1 1 SCGB1D2 HGNC HGNC:18396 protein_coding YES CCDS8017.1 ENSP00000244926 O95969 UPI00000403D8 NM_006551.3 deleterious(0.04) 2/3 Gene3D:1utgA00,Pfam_domain:PF01099,PROSITE_profiles:PS51311,hmmpanther:PTHR11332,Superfamily_domains:SSF48201 MODERATE 1 SNV 1 1 PASS rs139603186 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 62243410 62243410 G C 1 0 0 0 0 1 0 0 0 14164 1020 36 4 4 SCGB1D2 11 62243410 Missense_Mutation SNP G C3L-00144_T 1292349 62243410 72843212 1040 5111 MTA2 0 . GRCh38 11 62595013 62595013 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1541G>T p.Arg514Leu p.R514L ENST00000278823 15/18 280 228 52 164 164 0 strelka-varscan-mutect MTA2,missense_variant,p.Arg514Leu,ENST00000278823,NM_004739.3;MTA2,missense_variant,p.Arg341Leu,ENST00000524902,;MTA2,missense_variant,p.Arg341Leu,ENST00000527204,;TUT1,upstream_gene_variant,,ENST00000476907,;TUT1,upstream_gene_variant,,ENST00000308436,NM_022830.2;TUT1,upstream_gene_variant,,ENST00000494385,;TUT1,upstream_gene_variant,,ENST00000278279,;RP11-864I4.1,upstream_gene_variant,,ENST00000496634,;TUT1,upstream_gene_variant,,ENST00000478537,;MTA2,downstream_gene_variant,,ENST00000526844,;MTA2,downstream_gene_variant,,ENST00000531179,;MTA2,downstream_gene_variant,,ENST00000531261,;MTA2,downstream_gene_variant,,ENST00000532239,; A ENST00000278823 Transcript missense_variant 1931/3058 1541/2007 514/668 R/L cGg/cTg 1 -1 MTA2 HGNC HGNC:7411 protein_coding YES CCDS8022.1 ENSP00000278823 O94776 A0A024R534 UPI000012F743 NM_004739.3 deleterious(0.02) 15/18 hmmpanther:PTHR10865:SF4,hmmpanther:PTHR10865 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 62595013 62595013 C A 1 0 0 0 0 1 0 0 0 9894 652 23 1 1 MTA2 11 62595013 Missense_Mutation SNP C C3L-00144_T 351603 62595013 72491609 1041 5112 STX5 0 . GRCh38 11 62824551 62824551 + Missense_Mutation SNP C C A rs531466952 C3L-00144_T C3L-00144_N C C c.694G>T p.Val232Phe p.V232F ENST00000294179 9/11 267 206 61 226 226 0 strelka-varscan-mutect STX5,missense_variant,p.Val232Phe,ENST00000294179,NM_003164.4;STX5,missense_variant,p.Val232Phe,ENST00000377897,NM_001244666.1;STX5,missense_variant,p.Val178Phe,ENST00000394690,;STX5,missense_variant,p.Val87Phe,ENST00000431400,;STX5,missense_variant,p.Trp235Cys,ENST00000491231,;STX5,3_prime_UTR_variant,,ENST00000492066,;STX5,downstream_gene_variant,,ENST00000488303,;STX5,downstream_gene_variant,,ENST00000486437,; A ENST00000294179 Transcript missense_variant 848/1794 694/1068 232/355 V/F Gtt/Ttt rs531466952 1 -1 STX5 HGNC HGNC:11440 protein_coding YES CCDS8038.2 ENSP00000294179 Q13190 UPI00001FA9B0 NM_003164.4 tolerated(0.06) 9/11 hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF3,Gene3D:1.20.58.70,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS rs531466952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 62824551 62824551 C A 1 0 0 0 0 1 0 0 0 15732 507 18 2 2 STX5 11 62824551 Missense_Mutation SNP C C3L-00144_T 229538 62824551 72262071 1042 5113 SLC22A9 0 . GRCh38 11 63373974 63373974 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.742C>A p.Leu248Met p.L248M ENST00000279178 4/10 238 204 34 170 168 2 strelka-varscan-mutect SLC22A9,missense_variant,p.Leu248Met,ENST00000279178,NM_080866.2;SLC22A10,downstream_gene_variant,,ENST00000525620,;SLC22A9,missense_variant,p.Pro196His,ENST00000536333,; A ENST00000279178 Transcript missense_variant 991/2343 742/1662 248/553 L/M Ctg/Atg 1 1 SLC22A9 HGNC HGNC:16261 protein_coding YES CCDS8043.1 ENSP00000279178 Q8IVM8 UPI00000745FF NM_080866.2 tolerated(0.18) 4/10 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF288,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 63373974 63373974 C A 1 0 0 0 0 1 0 0 0 14727 680 24 2 2 SLC22A9 11 63373974 Missense_Mutation SNP C C3L-00144_T 549423 63373974 71712648 1043 5114 PLA2G16 0 . GRCh38 11 63598143 63598143 + Silent SNP G G A rs766854304 C3L-00144_T C3L-00144_N G G c.36C>T p.= p.D12D ENST00000323646 2/4 248 196 52 183 183 0 strelka-varscan-mutect PLA2G16,synonymous_variant,p.=,ENST00000323646,NM_007069.3;PLA2G16,synonymous_variant,p.=,ENST00000415826,NM_001128203.1;PLA2G16,intron_variant,,ENST00000540943,;PLA2G16,non_coding_transcript_exon_variant,,ENST00000544269,;PLA2G16,intron_variant,,ENST00000394613,; A ENST00000323646 Transcript synonymous_variant 391/2594 36/489 12/162 D gaC/gaT rs766854304 1 -1 PLA2G16 HGNC HGNC:17825 protein_coding YES CCDS8047.1 ENSP00000320337 P53816 A0A024R561 UPI000012CBE4 NM_007069.3 2/4 Pfam_domain:PF04970,hmmpanther:PTHR13943,hmmpanther:PTHR13943:SF33 LOW 1 SNV 1 1 PASS rs766854304 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 63598143 63598143 G A 1 0 0 0 0 0 0 0 1 12089 1252 44 3 3 PLA2G16 11 63598143 Silent SNP G C3L-00144_T 224169 63598143 71488479 1044 5115 BAD 0 . GRCh38 11 64270250 64270250 + Missense_Mutation SNP C C A rs771173599 C3L-00144_T C3L-00144_N C C c.466G>T p.Asp156Tyr p.D156Y ENST00000394532 3/3 78 58 20 59 59 0 strelka-varscan-mutect BAD,missense_variant,p.Asp156Tyr,ENST00000394532,NM_004322.3;BAD,missense_variant,p.Asp156Tyr,ENST00000309032,NM_032989.2;BAD,missense_variant,p.Gly92Val,ENST00000544785,;GPR137,5_prime_UTR_variant,,ENST00000546139,;PLCB3,downstream_gene_variant,,ENST00000540288,NM_001316314.1,NM_000932.2;PLCB3,downstream_gene_variant,,ENST00000279230,;PLCB3,downstream_gene_variant,,ENST00000325234,NM_001184883.1;BAD,downstream_gene_variant,,ENST00000394531,;BAD,downstream_gene_variant,,ENST00000492141,;BAD,downstream_gene_variant,,ENST00000493798,; A ENST00000394532 Transcript missense_variant 737/1157 466/507 156/168 D/Y Gat/Tat rs771173599 1 -1 BAD HGNC HGNC:936 protein_coding YES CCDS8065.1 ENSP00000378040 Q92934 A0A024R562 UPI0000035C7F NM_004322.3 tolerated_low_confidence(0.06) 3/3 Pfam_domain:PF10514,hmmpanther:PTHR28540,hmmpanther:PTHR28540:SF1 MODERATE 1 SNV 1 1 PASS rs745596312 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 64270250 64270250 C A 1 0 0 0 0 1 0 0 0 1443 855 30 2 2 BAD 11 64270250 Missense_Mutation SNP C C3L-00144_T 672107 64270250 70816372 1045 5116 RASGRP2 0 . GRCh38 11 64739669 64739669 + Silent SNP G G T rs140968954 C3L-00144_T C3L-00144_N G G c.663C>A p.= p.A221A ENST00000354024 7/17 160 114 46 121 121 0 strelka-varscan-mutect RASGRP2,synonymous_variant,p.=,ENST00000377494,;RASGRP2,synonymous_variant,p.=,ENST00000354024,NM_153819.1;RASGRP2,synonymous_variant,p.=,ENST00000394432,NM_001098671.1;RASGRP2,synonymous_variant,p.=,ENST00000377497,NM_001098670.1;RASGRP2,synonymous_variant,p.=,ENST00000431822,;RASGRP2,downstream_gene_variant,,ENST00000394430,;RASGRP2,downstream_gene_variant,,ENST00000377486,;RASGRP2,downstream_gene_variant,,ENST00000377487,;RASGRP2,downstream_gene_variant,,ENST00000430645,;RASGRP2,downstream_gene_variant,,ENST00000377489,;RASGRP2,downstream_gene_variant,,ENST00000394429,;RASGRP2,downstream_gene_variant,,ENST00000394428,;RASGRP2,downstream_gene_variant,,ENST00000377485,;RASGRP2,downstream_gene_variant,,ENST00000419843,;RASGRP2,3_prime_UTR_variant,,ENST00000421556,NM_001318398.1;RASGRP2,3_prime_UTR_variant,,ENST00000445445,;RASGRP2,non_coding_transcript_exon_variant,,ENST00000464324,;RASGRP2,upstream_gene_variant,,ENST00000488071,;RASGRP2,upstream_gene_variant,,ENST00000465852,;RASGRP2,upstream_gene_variant,,ENST00000494001,;RASGRP2,upstream_gene_variant,,ENST00000497441,;RASGRP2,downstream_gene_variant,,ENST00000441258,;RASGRP2,downstream_gene_variant,,ENST00000480443,; T ENST00000354024 Transcript synonymous_variant 916/2310 663/1830 221/609 A gcC/gcA rs140968954 1 -1 RASGRP2 HGNC HGNC:9879 protein_coding YES CCDS31598.1 ENSP00000338864 Q7LDG7 UPI0000161186 NM_153819.1 7/17 PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF16,hmmpanther:PTHR23113,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 LOW 1 SNV 1 1 PASS rs140968954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 64739669 64739669 G T 1 0 0 0 0 0 0 0 1 13236 1219 43 2 2 RASGRP2 11 64739669 Silent SNP G C3L-00144_T 469419 64739669 70346953 1046 5117 BATF2 0 . GRCh38 11 64989170 64989170 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.784C>A p.Leu262Met p.L262M ENST00000301887 3/3 245 189 56 149 149 0 strelka-varscan-mutect BATF2,missense_variant,p.Leu262Met,ENST00000301887,NM_138456.3;BATF2,missense_variant,p.Leu177Met,ENST00000435842,NM_001300808.1;BATF2,missense_variant,p.Leu238Met,ENST00000527716,NM_001300807.1;BATF2,downstream_gene_variant,,ENST00000534177,;BATF2,non_coding_transcript_exon_variant,,ENST00000527454,; T ENST00000301887 Transcript missense_variant 915/2142 784/825 262/274 L/M Ctg/Atg 1 -1 BATF2 HGNC HGNC:25163 protein_coding YES CCDS8087.1 ENSP00000301887 Q8N1L9 UPI000006E749 NM_138456.3 deleterious(0.04) 3/3 MODERATE 1 SNV 1 1 PASS rs1288524345 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 64989170 64989170 G T 1 0 0 0 0 1 0 0 0 1471 991 35 2 2 BATF2 11 64989170 Missense_Mutation SNP G C3L-00144_T 249501 64989170 70097452 1047 5118 SYVN1 0 . GRCh38 11 65128601 65128601 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1709G>A p.Gly570Glu p.G570E ENST00000377190 15/16 286 260 26 166 165 1 strelka-varscan-mutect SYVN1,missense_variant,p.Gly569Glu,ENST00000526060,;SYVN1,missense_variant,p.Gly570Glu,ENST00000377190,NM_172230.2;SYVN1,missense_variant,p.Gly569Glu,ENST00000294256,NM_032431.2;SYVN1,missense_variant,p.Gly518Glu,ENST00000307289,;MRPL49,downstream_gene_variant,,ENST00000279242,NM_004927.3;SYVN1,downstream_gene_variant,,ENST00000531018,;SYVN1,downstream_gene_variant,,ENST00000528487,;MRPL49,downstream_gene_variant,,ENST00000533943,;MRPL49,downstream_gene_variant,,ENST00000534078,;MRPL49,downstream_gene_variant,,ENST00000526171,;MRPL49,downstream_gene_variant,,ENST00000531705,;SYVN1,downstream_gene_variant,,ENST00000610479,;MRPL49,downstream_gene_variant,,ENST00000524482,;MRPL49,downstream_gene_variant,,ENST00000528529,;SYVN1,downstream_gene_variant,,ENST00000526121,;SYVN1,downstream_gene_variant,,ENST00000527765,;SYVN1,non_coding_transcript_exon_variant,,ENST00000449943,;SYVN1,intron_variant,,ENST00000530451,;MRPL49,downstream_gene_variant,,ENST00000532671,;MRPL49,downstream_gene_variant,,ENST00000526319,;SYVN1,downstream_gene_variant,,ENST00000529207,;SYVN1,downstream_gene_variant,,ENST00000527142,;SYVN1,downstream_gene_variant,,ENST00000532771,;SYVN1,downstream_gene_variant,,ENST00000533685,;SYVN1,downstream_gene_variant,,ENST00000525874,; T ENST00000377190 Transcript missense_variant 1804/3052 1709/1854 570/617 G/E gGa/gAa 1 -1 SYVN1 HGNC HGNC:20738 protein_coding YES CCDS31605.1 ENSP00000366395 Q86TM6 UPI000004EE90 NM_172230.2 tolerated(0.61) 15/16 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 65128601 65128601 C T 1 0 0 0 0 1 0 0 0 15881 855 30 3 3 SYVN1 11 65128601 Missense_Mutation SNP C C3L-00144_T 139431 65128601 69958021 1048 5119 MUS81 0 . GRCh38 11 65860884 65860884 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.131A>T p.Gln44Leu p.Q44L ENST00000308110 1/16 63 53 10 52 52 0 strelka-varscan-mutect MUS81,missense_variant,p.Gln44Leu,ENST00000308110,NM_025128.4;MUS81,missense_variant,p.Gln109Leu,ENST00000529857,;MUS81,5_prime_UTR_variant,,ENST00000525768,;MUS81,intron_variant,,ENST00000533035,;CFL1,intron_variant,,ENST00000532134,;CFL1,intron_variant,,ENST00000534769,;CFL1,upstream_gene_variant,,ENST00000525451,;CFL1,upstream_gene_variant,,ENST00000308162,NM_005507.2;MUS81,upstream_gene_variant,,ENST00000529374,;CFL1,upstream_gene_variant,,ENST00000531407,;CFL1,upstream_gene_variant,,ENST00000527344,;CFL1,upstream_gene_variant,,ENST00000524553,;CFL1,upstream_gene_variant,,ENST00000534784,;MUS81,upstream_gene_variant,,ENST00000529742,;MUS81,upstream_gene_variant,,ENST00000530111,;CFL1,upstream_gene_variant,,ENST00000530413,;CFL1,upstream_gene_variant,,ENST00000531413,;CFL1,upstream_gene_variant,,ENST00000526975,;CFL1,upstream_gene_variant,,ENST00000527752,;MUS81,upstream_gene_variant,,ENST00000525006,;MUS81,upstream_gene_variant,,ENST00000525224,;MUS81,missense_variant,p.Gln9Leu,ENST00000524647,;MUS81,upstream_gene_variant,,ENST00000531905,;SNX32,downstream_gene_variant,,ENST00000530101,;MUS81,upstream_gene_variant,,ENST00000530928,;CFL1,upstream_gene_variant,,ENST00000530945,;MUS81,upstream_gene_variant,,ENST00000529786,;MUS81,upstream_gene_variant,,ENST00000530282,;MUS81,upstream_gene_variant,,ENST00000533519,;MUS81,upstream_gene_variant,,ENST00000533555,;MUS81,upstream_gene_variant,,ENST00000525147,; T ENST00000308110 Transcript missense_variant 480/2392 131/1656 44/551 Q/L cAg/cTg 1 1 MUS81 HGNC HGNC:29814 protein_coding YES CCDS8115.1 ENSP00000307853 Q96NY9 UPI000013ECCB NM_025128.4 tolerated(0.07) 1/16 Gene3D:1bpeA01,hmmpanther:PTHR13451,hmmpanther:PTHR13451:SF0,Superfamily_domains:SSF47802 MODERATE 1 SNV 1 1 PASS rs1340892035 . 0 204 5 0 0 0 0 0 -19.99927 1 1 1 1 0 T 3 4 12 65860884 65860884 A T 1 0 0 0 0 1 0 0 0 9986 202 7 4 4 MUS81 11 65860884 Missense_Mutation SNP A C3L-00144_T 732283 65860884 69225738 1049 5120 BRMS1 0 . GRCh38 11 66342128 66342128 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.107G>T p.Gly36Val p.G36V ENST00000425825 2/10 283 216 67 149 149 0 strelka-varscan-mutect BRMS1,missense_variant,p.Gly36Val,ENST00000359957,NM_015399.3;BRMS1,missense_variant,p.Gly36Val,ENST00000425825,NM_001024957.1;BRMS1,missense_variant,p.Gly36Val,ENST00000530756,;B4GAT1,downstream_gene_variant,,ENST00000311181,NM_006876.2;BRMS1,upstream_gene_variant,,ENST00000524699,;RP11-867G23.12,downstream_gene_variant,,ENST00000526655,;BRMS1,missense_variant,p.Gly36Val,ENST00000527375,;BRMS1,non_coding_transcript_exon_variant,,ENST00000530238,;BRMS1,non_coding_transcript_exon_variant,,ENST00000534617,;BRMS1,non_coding_transcript_exon_variant,,ENST00000525127,;BRMS1,non_coding_transcript_exon_variant,,ENST00000529544,; A ENST00000425825 Transcript missense_variant 262/1363 107/873 36/290 G/V gGc/gTc 1 -1 BRMS1 HGNC HGNC:17262 protein_coding YES CCDS44654.1 ENSP00000396052 G5E9I4 UPI0000545267 NM_001024957.1 tolerated(0.06) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR21964:SF15,hmmpanther:PTHR21964 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 66342128 66342128 C A 1 0 0 0 0 1 0 0 0 1691 739 26 2 2 BRMS1 11 66342128 Missense_Mutation SNP C C3L-00144_T 481244 66342128 68744494 1050 5121 SYT12 0 . GRCh38 11 67048716 67048716 + Missense_Mutation SNP C C G rs760875835 C3L-00144_T C3L-00144_N C C c.1225C>G p.Arg409Gly p.R409G ENST00000393946 11/11 215 162 53 140 140 0 strelka-varscan-mutect SYT12,missense_variant,p.Arg409Gly,ENST00000393946,;SYT12,missense_variant,p.Arg409Gly,ENST00000525457,NM_001177880.1;SYT12,missense_variant,p.Arg409Gly,ENST00000527043,NM_177963.3;MIR6860,downstream_gene_variant,,ENST00000635882,; G ENST00000393946 Transcript missense_variant 2387/4534 1225/1266 409/421 R/G Cgc/Ggc rs760875835,COSM3383760 1 1 SYT12 HGNC HGNC:18381 protein_coding YES CCDS8154.1 ENSP00000377520 Q8IV01 UPI00000746CD deleterious(0) 11/11 Gene3D:2.60.40.150,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF252,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs760875835 . 0 201 9 0 0 0 0 0 -20 0.9999977 1 1 1 0 G 3 3 12 67048716 67048716 C G 1 0 0 0 0 1 0 0 0 15862 768 27 4 4 SYT12 11 67048716 Missense_Mutation SNP C C3L-00144_T 706588 67048716 68037906 1051 5122 CPT1A 0 . GRCh38 11 68762634 68762634 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1868C>G p.Ala623Gly p.A623G ENST00000265641 15/19 444 326 118 322 322 0 strelka-varscan-mutect CPT1A,missense_variant,p.Ala623Gly,ENST00000265641,NM_001876.3;CPT1A,missense_variant,p.Ala623Gly,ENST00000376618,NM_001031847.2;CPT1A,missense_variant,p.Ala623Gly,ENST00000540367,;CPT1A,missense_variant,p.Ala623Gly,ENST00000539743,;CPT1A,non_coding_transcript_exon_variant,,ENST00000537756,; C ENST00000265641 Transcript missense_variant 2023/5232 1868/2322 623/773 A/G gCc/gGc 1 -1 CPT1A HGNC HGNC:2328 protein_coding YES CCDS8185.1 ENSP00000265641 P50416 A0A024R5F4 UPI000013D658 NM_001876.3 tolerated(0.55) 15/19 Pfam_domain:PF00755,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF74,Superfamily_domains:SSF52777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 68762634 68762634 G C 1 0 0 0 0 1 0 0 0 3628 1203 42 4 4 CPT1A 11 68762634 Missense_Mutation SNP G C3L-00144_T 1713918 68762634 66323988 1052 5123 IGHMBP2 0 . GRCh38 11 68935352 68935352 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1686G>T p.Lys562Asn p.K562N ENST00000255078 12/15 598 431 167 429 429 0 strelka-varscan-mutect IGHMBP2,missense_variant,p.Lys562Asn,ENST00000255078,NM_002180.2;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000541229,;IGHMBP2,downstream_gene_variant,,ENST00000568742,;IGHMBP2,downstream_gene_variant,,ENST00000536803,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000539064,;IGHMBP2,non_coding_transcript_exon_variant,,ENST00000545475,;IGHMBP2,intron_variant,,ENST00000543739,;IGHMBP2,upstream_gene_variant,,ENST00000544521,;IGHMBP2,downstream_gene_variant,,ENST00000537458,; T ENST00000255078 Transcript missense_variant 1797/3961 1686/2982 562/993 K/N aaG/aaT 1 1 IGHMBP2 HGNC HGNC:5542 protein_coding YES CCDS8187.1 ENSP00000255078 P38935 UPI000013CE82 NM_002180.2 tolerated(0.08) 12/15 Gene3D:3.40.50.300,Pfam_domain:PF13087,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF375,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00376 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 68935352 68935352 G T 1 0 0 0 0 1 0 0 0 7498 1020 36 2 2 IGHMBP2 11 68935352 Missense_Mutation SNP G C3L-00144_T 172718 68935352 66151270 1053 5124 FGF4 0 . GRCh38 11 69774920 69774920 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.165G>T p.Leu55Phe p.L55F ENST00000168712 1/3 223 174 49 148 148 0 strelka-varscan-mutect FGF4,missense_variant,p.Leu55Phe,ENST00000168712,NM_002007.2;FGF4,non_coding_transcript_exon_variant,,ENST00000538040,; A ENST00000168712 Transcript missense_variant 484/3233 165/621 55/206 L/F ttG/ttT 1 -1 FGF4 HGNC HGNC:3682 protein_coding YES CCDS8194.1 ENSP00000168712 P08620 UPI0000040662 NM_002007.2 tolerated(0.12) 1/3 hmmpanther:PTHR11486:SF31,hmmpanther:PTHR11486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 69774920 69774920 C A 1 0 0 0 0 1 0 0 0 5718 593 21 2 2 FGF4 11 69774920 Missense_Mutation SNP C C3L-00144_T 839568 69774920 65311702 1054 5125 ANO1 0 . GRCh38 11 70124407 70124407 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.955C>A p.Leu319Met p.L319M ENST00000355303 9/26 241 205 36 178 178 0 strelka-varscan-mutect ANO1,missense_variant,p.Leu319Met,ENST00000355303,NM_018043.5;ANO1,missense_variant,p.Leu54Met,ENST00000531349,;ANO1,missense_variant,p.Leu203Met,ENST00000530676,;ANO1,missense_variant,p.Leu291Met,ENST00000316296,;ANO1,missense_variant,p.Leu184Met,ENST00000530480,;RP11-805J14.3,upstream_gene_variant,,ENST00000530525,; A ENST00000355303 Transcript missense_variant 1260/4790 955/2961 319/986 L/M Ctg/Atg 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 deleterious(0) 9/26 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 70124407 70124407 C A 1 0 0 0 0 1 0 0 0 802 680 24 2 2 ANO1 11 70124407 Missense_Mutation SNP C C3L-00144_T 349487 70124407 64962215 1055 5126 ARAP1 0 . GRCh38 11 72699443 72699443 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2412G>T p.= p.L804L ENST00000393609 17/35 197 147 50 147 146 1 strelka-varscan-mutect ARAP1,synonymous_variant,p.=,ENST00000359373,;ARAP1,synonymous_variant,p.=,ENST00000393609,NM_001040118.2;ARAP1,synonymous_variant,p.=,ENST00000334211,NM_015242.4;ARAP1,synonymous_variant,p.=,ENST00000393605,;ARAP1,synonymous_variant,p.=,ENST00000426523,;ARAP1,synonymous_variant,p.=,ENST00000429686,NM_001135190.1;ARAP1,synonymous_variant,p.=,ENST00000455638,;ARAP1,synonymous_variant,p.=,ENST00000427971,;ARAP1,synonymous_variant,p.=,ENST00000452383,;ARAP1,upstream_gene_variant,,ENST00000542596,;ARAP1-AS2,upstream_gene_variant,,ENST00000500163,;ARAP1,non_coding_transcript_exon_variant,,ENST00000495878,;ARAP1,upstream_gene_variant,,ENST00000544958,;ARAP1,non_coding_transcript_exon_variant,,ENST00000465814,;ARAP1,upstream_gene_variant,,ENST00000546293,;ARAP1,upstream_gene_variant,,ENST00000543868,;ARAP1,upstream_gene_variant,,ENST00000536993,; A ENST00000393609 Transcript synonymous_variant 2615/5145 2412/4353 804/1450 L ctG/ctT 1 -1 ARAP1 HGNC HGNC:16925 protein_coding YES CCDS41687.1 ENSP00000377233 Q96P48 UPI000053F81B NM_001040118.2 17/35 PROSITE_profiles:PS50003,hmmpanther:PTHR23180:SF195,hmmpanther:PTHR23180,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 2 1 PASS rs1469305671 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 72699443 72699443 C A 1 0 0 0 0 0 0 0 1 960 581 21 2 2 ARAP1 11 72699443 Silent SNP C C3L-00144_T 2575036 72699443 62387179 1056 5127 PPME1 0 . GRCh38 11 74203819 74203819 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.193G>T p.Asp65Tyr p.D65Y ENST00000398427 2/14 160 128 32 129 128 1 strelka-varscan-mutect PPME1,missense_variant,p.Asp65Tyr,ENST00000328257,NM_016147.2;PPME1,missense_variant,p.Asp65Tyr,ENST00000398427,NM_001271593.1;RNA5SP343,upstream_gene_variant,,ENST00000363779,;PPME1,splice_region_variant,,ENST00000542710,;PPME1,splice_region_variant,,ENST00000544401,;AP000577.2,upstream_gene_variant,,ENST00000624366,; T ENST00000398427 Transcript missense_variant,splice_region_variant 293/2496 193/1203 65/400 D/Y Gat/Tat 1 1 PPME1 HGNC HGNC:30178 protein_coding YES CCDS60891.1 ENSP00000381461 Q9Y570 UPI0001639863 NM_001271593.1 deleterious(0.04) 2/14 hmmpanther:PTHR14189,PIRSF_domain:PIRSF022950 MODERATE 1 SNV 1 1 PASS rs1345039884 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 74203819 74203819 G T 1 0 0 0 0 1 0 0 0 12457 1188 41 2 2 PPME1 11 74203819 Missense_Mutation SNP G C3L-00144_T 1504376 74203819 60882803 1057 5128 MYO7A 0 . GRCh38 11 77172781 77172781 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1831A>T p.Ser611Cys p.S611C ENST00000409709 16/49 442 365 77 275 275 0 strelka-varscan-mutect MYO7A,missense_variant,p.Ser611Cys,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Ser611Cys,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Ser600Cys,ENST00000409619,;MYO7A,missense_variant,p.Ser611Cys,ENST00000409893,NM_001127179.2;MYO7A,missense_variant,p.Ser611Cys,ENST00000620575,; T ENST00000409709 Transcript missense_variant 2103/7462 1831/6648 611/2215 S/C Agc/Tgc 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.1) 16/49 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF369,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 77172781 77172781 A T 1 0 0 0 0 1 0 0 0 10083 420 15 4 4 MYO7A 11 77172781 Missense_Mutation SNP A C3L-00144_T 2968962 77172781 57913841 1058 5129 DDIAS 0 . GRCh38 11 82933735 82933735 + Silent SNP A A T rs373304578 C3L-00144_T C3L-00144_N A A c.2397A>T p.= p.S799S ENST00000533655 6/6 176 142 34 138 137 1 strelka-varscan-mutect DDIAS,synonymous_variant,p.=,ENST00000533655,NM_145018.3;DDIAS,synonymous_variant,p.=,ENST00000329143,;DDIAS,3_prime_UTR_variant,,ENST00000528759,;DDIAS,intron_variant,,ENST00000525361,;PRCP,intron_variant,,ENST00000534396,;DDIAS,downstream_gene_variant,,ENST00000525388,;DDIAS,downstream_gene_variant,,ENST00000532277,;DDIAS,downstream_gene_variant,,ENST00000532764,;DDIAS,downstream_gene_variant,,ENST00000524921,;DDIAS,downstream_gene_variant,,ENST00000528262,;DDIAS,downstream_gene_variant,,ENST00000532589,;DDIAS,downstream_gene_variant,,ENST00000533750,;DDIAS,downstream_gene_variant,,ENST00000528189,; T ENST00000533655 Transcript synonymous_variant 2609/3533 2397/2997 799/998 S tcA/tcT rs373304578 1 1 DDIAS HGNC HGNC:26351 protein_coding YES CCDS8263.1 ENSP00000435421 Q8IXT1 UPI00001AF966 NM_145018.3 6/6 hmmpanther:PTHR35537,hmmpanther:PTHR35537:SF1 LOW 1 SNV 1 1 PASS rs373304578 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 82933735 82933735 A T 1 0 0 0 0 0 0 0 1 4133 175 7 4 4 DDIAS 11 82933735 Silent SNP A C3L-00144_T 5760954 82933735 52152887 1059 5130 PCF11 0 . GRCh38 11 83169463 83169463 + Missense_Mutation SNP C C T rs760922239 C3L-00144_T C3L-00144_N C C c.3128C>T p.Pro1043Leu p.P1043L ENST00000298281 8/16 253 180 73 198 198 0 strelka-varscan-mutect PCF11,missense_variant,p.Pro1043Leu,ENST00000298281,NM_015885.3;PCF11,downstream_gene_variant,,ENST00000530660,;PCF11,downstream_gene_variant,,ENST00000530304,;PCF11,upstream_gene_variant,,ENST00000530906,; T ENST00000298281 Transcript missense_variant 3580/7677 3128/4668 1043/1555 P/L cCa/cTa rs760922239 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 deleterious(0.05) 8/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 MODERATE 1 SNV 1 1 PASS rs760922239 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 83169463 83169463 C T 1 0 0 0 0 1 0 0 0 11661 594 21 3 3 PCF11 11 83169463 Missense_Mutation SNP C C3L-00144_T 235728 83169463 51917159 1060 5131 TMEM126B 0 . GRCh38 11 85628620 85628620 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.13G>C p.Gly5Arg p.G5R ENST00000358867 1/5 292 241 51 186 186 0 strelka-varscan-mutect TMEM126B,missense_variant,p.Gly5Arg,ENST00000534341,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000358867,NM_018480.4;TMEM126B,5_prime_UTR_variant,,ENST00000393375,NM_001256546.1,NM_001193538.2;DLG2,upstream_gene_variant,,ENST00000376104,NM_001142699.1;TMEM126B,upstream_gene_variant,,ENST00000531274,;DLG2,upstream_gene_variant,,ENST00000472545,;DLG2,upstream_gene_variant,,ENST00000526147,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000528361,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000529197,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000526822,NM_001256547.1;TMEM126B,missense_variant,p.Gly5Arg,ENST00000531477,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000530783,;TMEM126B,missense_variant,p.Gly5Arg,ENST00000531718,;TMEM126B,missense_variant,p.Gly2Arg,ENST00000530901,; C ENST00000358867 Transcript missense_variant 36/989 13/693 5/230 G/R Ggg/Cgg 1 1 TMEM126B HGNC HGNC:30883 protein_coding YES CCDS8267.2 ENSP00000351737 Q8IUX1 UPI00003D5F21 NM_018480.4 tolerated_low_confidence(0.31) 1/5 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 85628620 85628620 G C 1 0 0 0 0 1 0 0 0 16483 1116 39 4 4 TMEM126B 11 85628620 Missense_Mutation SNP G C3L-00144_T 2459157 85628620 49458002 1061 5132 PRSS23 0 . GRCh38 11 86807898 86807898 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.255G>T p.= p.L85L ENST00000280258 2/2 370 305 65 229 228 1 strelka-varscan-mutect PRSS23,synonymous_variant,p.=,ENST00000280258,NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1;PRSS23,synonymous_variant,p.=,ENST00000527521,;PRSS23,intron_variant,,ENST00000533902,;PRSS23,intron_variant,,ENST00000531475,;PRSS23,intron_variant,,ENST00000533880,;PRSS23,intron_variant,,ENST00000532234,; T ENST00000280258 Transcript synonymous_variant 680/4015 255/1152 85/383 L ctG/ctT 1 1 PRSS23 HGNC HGNC:14370 protein_coding YES CCDS8278.1 ENSP00000280258 O95084 UPI0000048EBC NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1 2/2 hmmpanther:PTHR15462,hmmpanther:PTHR15462:SF10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 86807898 86807898 G T 1 0 0 0 0 0 0 0 1 12767 1364 48 2 2 PRSS23 11 86807898 Silent SNP G C3L-00144_T 1179278 86807898 48278724 1062 5133 TRIM77 0 . GRCh38 11 89710460 89710460 + Silent SNP G G T rs769499016 C3L-00144_T C3L-00144_N G G c.162G>T p.= p.V54V ENST00000398290 1/6 228 185 43 152 152 0 strelka-varscan-mutect TRIM77,synonymous_variant,p.=,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,upstream_gene_variant,,ENST00000534392,; T ENST00000398290 Transcript synonymous_variant 162/1353 162/1353 54/450 V gtG/gtT rs769499016 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 1/6 PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353,Pfam_domain:PF00097,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 LOW 1 SNV 5 1 PASS rs769499016 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 89710460 89710460 G T 1 0 0 0 0 0 0 0 1 17044 1364 48 2 2 TRIM77 11 89710460 Silent SNP G C3L-00144_T 2902562 89710460 45376162 1063 5134 TRIM77 0 . GRCh38 11 89710544 89710544 + Silent SNP C C A rs773753410 C3L-00144_T C3L-00144_N C C c.246C>A p.= p.P82P ENST00000398290 1/6 182 148 34 137 137 0 strelka-varscan-mutect TRIM77,synonymous_variant,p.=,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,upstream_gene_variant,,ENST00000534392,; A ENST00000398290 Transcript synonymous_variant 246/1353 246/1353 82/450 P ccC/ccA rs773753410 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 1/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353 LOW 1 SNV 5 1 PASS rs773753410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 89710544 89710544 C A 1 0 0 0 0 0 0 0 1 17044 668 24 2 2 TRIM77 11 89710544 Silent SNP C C3L-00144_T 84 89710544 45376078 1064 5135 TRIM49 0 . GRCh38 11 89798400 89798400 + Missense_Mutation SNP T T A rs560492199 C3L-00144_T C3L-00144_N T T c.1089A>T p.Lys363Asn p.K363N ENST00000329758 8/8 563 491 72 422 422 0 strelka-varscan-mutect TRIM49,missense_variant,p.Lys363Asn,ENST00000329758,NM_020358.2;TRIM49,missense_variant,p.Lys286Asn,ENST00000532501,; A ENST00000329758 Transcript missense_variant 1418/2163 1089/1359 363/452 K/N aaA/aaT rs560492199,COSM932923 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 tolerated(0.38) 8/8 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00449,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs560492199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 89798400 89798400 T A 1 0 0 0 0 1 0 0 0 17014 1606 56 4 4 TRIM49 11 89798400 Missense_Mutation SNP T C3L-00144_T 87856 89798400 45288222 1065 5136 TRIM64 0 . GRCh38 11 89970322 89970322 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.583C>T p.Arg195Trp p.R195W ENST00000533122 3/6 143 132 11 112 112 0 varscan-mutect TRIM64,missense_variant,p.Arg195Trp,ENST00000533122,NM_001136486.1; T ENST00000533122 Transcript missense_variant 585/2691 583/1350 195/449 R/W Cgg/Tgg 1 1 TRIM64 HGNC HGNC:14663 protein_coding YES CCDS73363.1 ENSP00000483764 A6NGJ6 UPI0001662601 NM_001136486.1 deleterious(0.02) 3/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103:SF354,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS . . 146 61 3 0 0 0 0 0 -19.94652 0.999942 0 1 1 0 T 3 4 12 89970322 89970322 C T 1 0 0 0 0 1 0 0 0 17031 527 19 1 1 TRIM64 11 89970322 Missense_Mutation SNP C C3L-00144_T 171922 89970322 45116300 1066 5137 NAALAD2 0 . GRCh38 11 90134773 90134773 + Missense_Mutation SNP G G T rs775781175 C3L-00144_T C3L-00144_N G G c.15G>T p.Arg5Ser p.R5S ENST00000534061 1/19 338 254 84 296 296 0 strelka-varscan-mutect NAALAD2,missense_variant,p.Arg5Ser,ENST00000534061,NM_005467.3;NAALAD2,missense_variant,p.Arg5Ser,ENST00000321955,NM_001300930.1;NAALAD2,missense_variant,p.Arg5Ser,ENST00000525171,;NAALAD2,missense_variant,p.Arg5Ser,ENST00000375944,;NAALAD2,missense_variant,p.Arg5Ser,ENST00000525497,;NAALAD2,upstream_gene_variant,,ENST00000526637,;NAALAD2,missense_variant,p.Arg5Ser,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,; T ENST00000534061 Transcript missense_variant 245/3600 15/2223 5/740 R/S agG/agT rs775781175 1 1 NAALAD2 HGNC HGNC:14526 protein_coding YES CCDS8288.1 ENSP00000432481 Q9Y3Q0 UPI0000031A85 NM_005467.3 tolerated_low_confidence(0.08) 1/19 hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF38 MODERATE 1 SNV 1 1 PASS rs775781175 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 90134773 90134773 G T 1 0 0 0 0 1 0 0 0 10132 1223 43 2 2 NAALAD2 11 90134773 Missense_Mutation SNP G C3L-00144_T 164451 90134773 44951849 1067 5138 HEPHL1 0 . GRCh38 11 94110959 94110959 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.3102C>A p.= p.T1034T ENST00000315765 18/20 234 180 54 163 163 0 strelka-varscan-mutect HEPHL1,synonymous_variant,p.=,ENST00000315765,NM_001098672.1; A ENST00000315765 Transcript synonymous_variant 3110/5345 3102/3480 1034/1159 T acC/acA 1 1 HEPHL1 HGNC HGNC:30477 protein_coding YES CCDS44710.1 ENSP00000313699 Q6MZM0 UPI0000237563 NM_001098672.1 18/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF655,Gene3D:2.60.40.420,Pfam_domain:PF07731,Superfamily_domains:SSF49503 LOW 1 SNV 5 1 PASS rs1196014982 . 0 205 0 5 0 0 0 0 -20 0.9998006 1 1 1 0 A 2 1 12 94110959 94110959 C A 1 0 0 0 0 0 0 0 1 6939 581 21 2 2 HEPHL1 11 94110959 Silent SNP C C3L-00144_T 3976186 94110959 40975663 1068 5139 CNTN5 0 . GRCh38 11 99956863 99956863 + Missense_Mutation SNP G G T rs201219815 C3L-00144_T C3L-00144_N G G c.731G>T p.Arg244Leu p.R244L ENST00000524871 8/25 370 301 69 308 308 0 strelka-varscan-mutect CNTN5,missense_variant,p.Arg244Leu,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Arg228Leu,ENST00000279463,;CNTN5,missense_variant,p.Arg166Leu,ENST00000619298,;CNTN5,missense_variant,p.Arg244Leu,ENST00000527185,NM_001243271.1;CNTN5,missense_variant,p.Arg244Leu,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Arg170Leu,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000525236,;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; T ENST00000524871 Transcript missense_variant 1021/6258 731/3303 244/1100 R/L cGg/cTg rs201219815 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 deleterious(0.01) 8/25 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs201219815 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 99956863 99956863 G T 1 0 0 0 0 1 0 0 0 3425 1116 39 1 1 CNTN5 11 99956863 Missense_Mutation SNP G C3L-00144_T 5845904 99956863 35129759 1069 5140 ARHGAP42 0 . GRCh38 11 100988730 100988730 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2554C>A p.Pro852Thr p.P852T ENST00000298815 24/24 216 149 67 158 158 0 strelka-varscan-mutect ARHGAP42,missense_variant,p.Pro818Thr,ENST00000524892,;ARHGAP42,missense_variant,p.Pro852Thr,ENST00000298815,NM_152432.2;TMEM133,upstream_gene_variant,,ENST00000303130,NM_032021.2;ARHGAP42,3_prime_UTR_variant,,ENST00000529535,; A ENST00000298815 Transcript missense_variant 2557/4752 2554/2625 852/874 P/T Cca/Aca 1 1 ARHGAP42 HGNC HGNC:26545 protein_coding YES ENSP00000298815 A6NI28 UPI00005778C9 NM_152432.2 deleterious(0) 24/24 PROSITE_profiles:PS50002,hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF3,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 100988730 100988730 C A 1 0 0 0 0 1 0 0 0 1013 507 18 2 2 ARHGAP42 11 100988730 Missense_Mutation SNP C C3L-00144_T 1031867 100988730 34097892 1070 5141 PGR 0 . GRCh38 11 101051490 101051490 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2291G>A p.Gly764Glu p.G764E ENST00000325455 5/8 288 225 63 223 223 0 strelka-varscan-mutect PGR,missense_variant,p.Gly764Glu,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,missense_variant,p.Gly725Glu,ENST00000619228,;PGR,missense_variant,p.Gly662Glu,ENST00000617858,;PGR,missense_variant,p.Gly662Glu,ENST00000263463,NM_001271161.2;PGR,missense_variant,p.Gly170Glu,ENST00000534013,NM_001271162.1;PGR,missense_variant,p.Gly764Glu,ENST00000534780,;PGR,missense_variant,p.Gly725Glu,ENST00000528960,;PGR,missense_variant,p.Gly662Glu,ENST00000526300,;PGR,non_coding_transcript_exon_variant,,ENST00000533207,;PGR,upstream_gene_variant,,ENST00000530764,; T ENST00000325455 Transcript missense_variant 3745/13748 2291/2802 764/933 G/E gGa/gAa 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 deleterious(0) 5/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101051490 101051490 C T 1 0 0 0 0 1 0 0 0 11894 855 30 3 3 PGR 11 101051490 Missense_Mutation SNP C C3L-00144_T 62760 101051490 34035132 1071 5142 PGR 0 . GRCh38 11 101051503 101051503 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2278G>T p.Val760Leu p.V760L ENST00000325455 5/8 292 228 64 226 226 0 strelka-varscan-mutect PGR,missense_variant,p.Val760Leu,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,missense_variant,p.Val721Leu,ENST00000619228,;PGR,missense_variant,p.Val658Leu,ENST00000617858,;PGR,missense_variant,p.Val658Leu,ENST00000263463,NM_001271161.2;PGR,missense_variant,p.Val166Leu,ENST00000534013,NM_001271162.1;PGR,missense_variant,p.Val760Leu,ENST00000534780,;PGR,missense_variant,p.Val721Leu,ENST00000528960,;PGR,missense_variant,p.Val658Leu,ENST00000526300,;PGR,non_coding_transcript_exon_variant,,ENST00000533207,;PGR,upstream_gene_variant,,ENST00000530764,; A ENST00000325455 Transcript missense_variant 3732/13748 2278/2802 760/933 V/L Gtg/Ttg 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 deleterious(0.03) 5/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS rs1368811016 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101051503 101051503 C A 1 0 0 0 0 1 0 0 0 11894 507 18 2 2 PGR 11 101051503 Missense_Mutation SNP C C3L-00144_T 13 101051503 34035119 1072 5143 TRPC6 0 . GRCh38 11 101476380 101476380 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1665G>T p.Gln555His p.Q555H ENST00000344327 6/13 266 196 70 198 196 2 strelka-varscan-mutect TRPC6,missense_variant,p.Gln555His,ENST00000344327,NM_004621.5;TRPC6,missense_variant,p.Gln500His,ENST00000360497,;TRPC6,missense_variant,p.Gln439His,ENST00000348423,;TRPC6,intron_variant,,ENST00000532133,; A ENST00000344327 Transcript missense_variant 2090/4612 1665/2796 555/931 Q/H caG/caT COSM3442572 1 -1 TRPC6 HGNC HGNC:12338 protein_coding YES CCDS8311.1 ENSP00000340913 Q9Y210 UPI00001374BA NM_004621.5 deleterious(0.03) 6/13 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870,Prints_domain:PR01647 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101476380 101476380 C A 1 0 0 0 0 1 0 0 0 17089 912 32 2 2 TRPC6 11 101476380 Missense_Mutation SNP C C3L-00144_T 424877 101476380 33610242 1073 5144 CEP126 0 . GRCh38 11 101962765 101962765 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1730G>T p.Ser577Ile p.S577I ENST00000263468 6/11 79 63 16 86 86 0 strelka-varscan-mutect CEP126,missense_variant,p.Ser577Ile,ENST00000263468,NM_020802.3;CEP126,3_prime_UTR_variant,,ENST00000532529,; T ENST00000263468 Transcript missense_variant 2000/7039 1730/3354 577/1117 S/I aGt/aTt 1 1 CEP126 HGNC HGNC:29264 protein_coding YES CCDS31658.1 ENSP00000263468 Q9P2H0 UPI0004433B8D NM_020802.3 deleterious(0) 6/11 hmmpanther:PTHR31191:SF4,hmmpanther:PTHR31191,Pfam_domain:PF15352 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101962765 101962765 G T 1 0 0 0 0 1 0 0 0 2957 1029 36 2 2 CEP126 11 101962765 Missense_Mutation SNP G C3L-00144_T 486385 101962765 33123857 1074 5145 MMP12 0 . GRCh38 11 102873019 102873019 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.196G>T p.Glu66Ter p.E66* ENST00000571244 2/10 509 411 98 326 325 1 strelka-varscan-mutect MMP12,stop_gained,p.Glu66Ter,ENST00000571244,NM_002426.4; A ENST00000571244 Transcript stop_gained 293/1874 196/1413 66/470 E/* Gaa/Taa 1 -1 MMP12 HGNC HGNC:7158 protein_coding YES CCDS73375.1 ENSP00000458585 P39900 UPI00000422BE NM_002426.4 2/10 Gene3D:3.40.390.10,Pfam_domain:PF01471,PIRSF_domain:PIRSF001191,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF32,Superfamily_domains:SSF47090 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 102873019 102873019 C A 1 0 0 0 0 0 1 0 0 9614 922 32 2 2 MMP12 11 102873019 Nonsense_Mutation SNP C C3L-00144_T 910254 102873019 32213603 1075 5146 GRIA4 0 . GRCh38 11 105924765 105924765 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1843C>A p.Pro615Thr p.P615T ENST00000282499 12/17 50 29 21 54 54 0 strelka-varscan-mutect GRIA4,missense_variant,p.Pro615Thr,ENST00000393127,NM_001077243.2;GRIA4,missense_variant,p.Pro615Thr,ENST00000282499,NM_000829.3;GRIA4,missense_variant,p.Pro615Thr,ENST00000530497,;GRIA4,missense_variant,p.Pro615Thr,ENST00000525187,; A ENST00000282499 Transcript missense_variant 2289/5508 1843/2709 615/902 P/T Ccc/Acc 1 1 GRIA4 HGNC HGNC:4574 protein_coding YES CCDS8333.1 ENSP00000282499 P48058 UPI000013DCE6 NM_000829.3 deleterious(0) 12/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF100,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 105924765 105924765 C A 1 0 0 0 0 1 0 0 0 6650 521 18 2 2 GRIA4 11 105924765 Missense_Mutation SNP C C3L-00144_T 3051746 105924765 29161857 1076 5147 MSANTD4 0 . GRCh38 11 106009590 106009590 + Missense_Mutation SNP C C G rs752235602 C3L-00144_T C3L-00144_N C C c.983G>C p.Arg328Pro p.R328P ENST00000301919 3/3 171 128 43 141 141 0 strelka-varscan-mutect MSANTD4,missense_variant,p.Arg328Pro,ENST00000301919,NM_032424.1;MSANTD4,downstream_gene_variant,,ENST00000530788,;MSANTD4,downstream_gene_variant,,ENST00000530108,;MSANTD4,downstream_gene_variant,,ENST00000534458,;MSANTD4,downstream_gene_variant,,ENST00000617528,;MSANTD4,non_coding_transcript_exon_variant,,ENST00000529805,; G ENST00000301919 Transcript missense_variant 2399/4087 983/1038 328/345 R/P cGc/cCc rs752235602,COSM4017476 1 -1 MSANTD4 HGNC HGNC:29383 protein_coding YES CCDS31663.1 ENSP00000304713 Q8NCY6 UPI0000073CF1 NM_032424.1 deleterious(0) 3/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21732 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752235602 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 106009590 106009590 C G 1 0 0 0 0 1 0 0 0 9850 768 27 4 4 MSANTD4 11 106009590 Missense_Mutation SNP C C3L-00144_T 84825 106009590 29077032 1077 5148 GUCY1A2 0 . GRCh38 11 106776570 106776570 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1705G>T p.Gly569Cys p.G569C ENST00000282249 6/9 170 120 50 134 134 0 strelka-varscan-mutect GUCY1A2,missense_variant,p.Gly569Cys,ENST00000526355,NM_000855.2;GUCY1A2,missense_variant,p.Gly569Cys,ENST00000282249,NM_001256424.1;GUCY1A2,missense_variant,p.Gly590Cys,ENST00000347596,; A ENST00000282249 Transcript missense_variant 2095/3047 1705/2292 569/763 G/C Ggt/Tgt 1 -1 GUCY1A2 HGNC HGNC:4684 protein_coding YES CCDS58170.1 ENSP00000282249 P33402 UPI000002A79C NM_001256424.1 deleterious(0) 6/9 PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF276,Pfam_domain:PF00211,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 106776570 106776570 C A 1 0 0 0 0 1 0 0 0 6775 681 24 2 2 GUCY1A2 11 106776570 Missense_Mutation SNP C C3L-00144_T 766980 106776570 28310052 1078 5149 ATM 0 . GRCh38 11 108244923 108244923 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.798G>T p.Trp266Cys p.W266C ENST00000278616 7/63 337 281 56 296 296 0 strelka-varscan-mutect ATM,missense_variant,p.Trp266Cys,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Trp266Cys,ENST00000452508,;ATM,missense_variant,p.Trp266Cys,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000527891,; T ENST00000278616 Transcript missense_variant 1183/13147 798/9171 266/3056 W/C tgG/tgT 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 deleterious(0) 7/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF72,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 108244923 108244923 G T 1 0 0 0 0 1 0 0 0 1261 1183 41 2 2 ATM 11 108244923 Missense_Mutation SNP G C3L-00144_T 1468353 108244923 26841699 1079 5150 EXPH5 0 . GRCh38 11 108514033 108514033 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1474G>T p.Asp492Tyr p.D492Y ENST00000265843 6/6 186 155 31 143 143 0 strelka-varscan-mutect EXPH5,missense_variant,p.Asp492Tyr,ENST00000265843,NM_001144764.1,NM_001144765.1,NM_001144763.1,NM_015065.2;EXPH5,missense_variant,p.Asp485Tyr,ENST00000525344,NM_001308019.1;EXPH5,missense_variant,p.Asp416Tyr,ENST00000526312,;EXPH5,missense_variant,p.Asp304Tyr,ENST00000533052,;EXPH5,missense_variant,p.Asp336Tyr,ENST00000524840,; A ENST00000265843 Transcript missense_variant 1585/10187 1474/5970 492/1989 D/Y Gac/Tac 1 -1 EXPH5 HGNC HGNC:30578 protein_coding YES CCDS8341.1 ENSP00000265843 Q8NEV8 UPI00018E24EB NM_001144764.1,NM_001144765.1,NM_001144763.1,NM_015065.2 deleterious(0) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR21469 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 108514033 108514033 C A 1 0 0 0 0 1 0 0 0 5190 826 29 2 2 EXPH5 11 108514033 Missense_Mutation SNP C C3L-00144_T 269110 108514033 26572589 1080 5151 DDX10 0 . GRCh38 11 108692031 108692031 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1131G>T p.Arg377Ser p.R377S ENST00000322536 8/18 108 86 22 83 83 0 strelka-varscan-mutect DDX10,missense_variant,p.Arg377Ser,ENST00000526794,;DDX10,missense_variant,p.Arg377Ser,ENST00000322536,NM_004398.3;RPS2P39,upstream_gene_variant,,ENST00000492327,; T ENST00000322536 Transcript missense_variant 1260/3264 1131/2628 377/875 R/S agG/agT 1 1 DDX10 HGNC HGNC:2735 protein_coding YES CCDS8342.1 ENSP00000314348 Q13206 UPI0000140E62 NM_004398.3 deleterious(0) 8/18 PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF281,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 108692031 108692031 G T 1 0 0 0 0 1 0 0 0 4146 1223 43 2 2 DDX10 11 108692031 Missense_Mutation SNP G C3L-00144_T 177998 108692031 26394591 1081 5152 C11orf87 0 . GRCh38 11 109424082 109424082 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.449C>A p.Ser150Tyr p.S150Y ENST00000327419 2/2 361 275 86 268 266 2 strelka-varscan-mutect C11orf87,missense_variant,p.Ser150Tyr,ENST00000327419,NM_207645.3;RP11-708B6.2,intron_variant,,ENST00000532929,;RP11-708B6.2,intron_variant,,ENST00000532992,; A ENST00000327419 Transcript missense_variant 852/5884 449/594 150/197 S/Y tCc/tAc 1 1 C11orf87 HGNC HGNC:33788 protein_coding YES CCDS31672.1 ENSP00000331581 Q6NUJ2 A0A158RFU1 UPI000013E5BC NM_207645.3 tolerated_low_confidence(0.06) 2/2 hmmpanther:PTHR31870,hmmpanther:PTHR31870:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 109424082 109424082 C A 1 0 0 0 0 1 0 0 0 1799 855 30 2 2 C11orf87 11 109424082 Missense_Mutation SNP C C3L-00144_T 732051 109424082 25662540 1082 5153 ARHGAP20 0 . GRCh38 11 110583616 110583616 + Missense_Mutation SNP C C A rs773385706 C3L-00144_T C3L-00144_N C C c.1537G>T p.Val513Phe p.V513F ENST00000260283 14/16 304 226 78 202 202 0 strelka-varscan-mutect ARHGAP20,missense_variant,p.Val513Phe,ENST00000260283,NM_020809.3;ARHGAP20,missense_variant,p.Val490Phe,ENST00000524756,NM_001258415.1;ARHGAP20,missense_variant,p.Val487Phe,ENST00000533353,NM_001258416.1;ARHGAP20,missense_variant,p.Val477Phe,ENST00000527598,NM_001258418.1;ARHGAP20,missense_variant,p.Val477Phe,ENST00000528829,NM_001258417.1;ARHGAP20,missense_variant,p.Val56Phe,ENST00000529591,; A ENST00000260283 Transcript missense_variant 1822/6189 1537/3576 513/1191 V/F Gtc/Ttc rs773385706 1 -1 ARHGAP20 HGNC HGNC:18357 protein_coding YES CCDS31673.1 ENSP00000260283 Q9P2F6 UPI000013D0BA NM_020809.3 deleterious(0.04) 14/16 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR23179,hmmpanther:PTHR23179:SF28,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS rs773385706 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 110583616 110583616 C A 1 0 0 0 0 1 0 0 0 994 478 17 2 2 ARHGAP20 11 110583616 Missense_Mutation SNP C C3L-00144_T 1159534 110583616 24503006 1083 5154 NCAM1 0 . GRCh38 11 113270396 113270396 + Splice_Site SNP G G T rs782039890 C3L-00144_T C3L-00144_N G G c.2417+1G>T p.X806_splice ENST00000619839 179 137 42 120 120 0 strelka-varscan-mutect NCAM1,splice_donor_variant,,ENST00000615285,;NCAM1,splice_donor_variant,,ENST00000615112,;NCAM1,splice_donor_variant,,ENST00000618266,;NCAM1,splice_donor_variant,,ENST00000316851,NM_181351.4;NCAM1,splice_donor_variant,,ENST00000619839,NM_001242607.1;NCAM1,splice_donor_variant,,ENST00000531044,NM_000615.6;NCAM1,splice_donor_variant,,ENST00000528158,;NCAM1,splice_donor_variant,,ENST00000533073,;NCAM1,splice_donor_variant,,ENST00000528590,;NCAM1,downstream_gene_variant,,ENST00000620046,;NCAM1-AS1,non_coding_transcript_exon_variant,,ENST00000526229,;NCAM1-AS1,non_coding_transcript_exon_variant,,ENST00000533638,;NCAM1,splice_donor_variant,,ENST00000611284,;NCAM1,splice_donor_variant,,ENST00000533226,; T ENST00000619839 Transcript splice_donor_variant -/2993 2417/2655 806/884 rs782039890 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 19/20 HIGH SNV 5 1 PASS rs782039890 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 113270396 113270396 G T 1 0 0 0 0 0 0 1 0 10218 1159 40 1 1 NCAM1 11 113270396 Splice_Site SNP G C3L-00144_T 2686780 113270396 21816226 1084 5155 RNF214 0 . GRCh38 11 117238869 117238869 + Nonsense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.376G>T p.Glu126Ter p.E126* ENST00000300650 3/15 334 234 100 269 267 2 strelka-varscan-mutect RNF214,stop_gained,p.Glu126Ter,ENST00000300650,NM_207343.3;RNF214,stop_gained,p.Glu126Ter,ENST00000531452,NM_001077239.1;RNF214,stop_gained,p.Glu126Ter,ENST00000534428,;RNF214,intron_variant,,ENST00000530849,;RNF214,intron_variant,,ENST00000531287,NM_001278249.1;RNF214,non_coding_transcript_exon_variant,,ENST00000529869,; T ENST00000300650 Transcript stop_gained 484/2755 376/2112 126/703 E/* Gag/Tag COSM253286 1 1 RNF214 HGNC HGNC:25335 protein_coding YES CCDS41720.1 ENSP00000300650 Q8ND24 A0A024R3D4 UPI00001D7749 NM_207343.3 3/15 hmmpanther:PTHR15727 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 117238869 117238869 G T 1 0 0 0 0 0 1 0 0 13657 1175 41 2 2 RNF214 11 117238869 Nonsense_Mutation SNP G C3L-00144_T 3968473 117238869 17847753 1085 5156 CD3D 0 . GRCh38 11 118339884 118339884 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.297G>T p.= p.L99L ENST00000300692 3/5 508 386 122 381 381 0 strelka-varscan-mutect CD3D,synonymous_variant,p.=,ENST00000300692,NM_000732.4;CD3D,synonymous_variant,p.=,ENST00000529594,;CD3D,intron_variant,,ENST00000534687,;CD3D,intron_variant,,ENST00000392884,NM_001040651.1;CD3G,upstream_gene_variant,,ENST00000532917,NM_000073.2;CD3G,upstream_gene_variant,,ENST00000392883,;CD3G,upstream_gene_variant,,ENST00000532903,;CD3G,upstream_gene_variant,,ENST00000528540,;CD3D,intron_variant,,ENST00000526561,;CD3G,upstream_gene_variant,,ENST00000292144,;CD3G,upstream_gene_variant,,ENST00000533462,;CD3G,upstream_gene_variant,,ENST00000527777,; A ENST00000300692 Transcript synonymous_variant 434/861 297/516 99/171 L ctG/ctT 1 -1 CD3D HGNC HGNC:1673 protein_coding YES CCDS8394.1 ENSP00000300692 P04234 B0YIY4 UPI0000127356 NM_000732.4 3/5 Gene3D:2.60.40.10,Pfam_domain:PF16680,hmmpanther:PTHR10570,hmmpanther:PTHR10570:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 118339884 118339884 C A 1 0 0 0 0 0 0 0 1 2714 581 21 2 2 CD3D 11 118339884 Silent SNP C C3L-00144_T 1101015 118339884 16746738 1086 5157 CD3G 0 . GRCh38 11 118350683 118350683 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.439G>T p.Ala147Ser p.A147S ENST00000532917 4/7 391 321 70 262 259 3 strelka-varscan-mutect CD3G,missense_variant,p.Ala147Ser,ENST00000532917,NM_000073.2;CD3G,intron_variant,,ENST00000392883,;CD3G,splice_region_variant,,ENST00000532903,;CD3G,downstream_gene_variant,,ENST00000528540,;CD3G,splice_region_variant,,ENST00000292144,;CD3G,non_coding_transcript_exon_variant,,ENST00000527777,;CD3G,downstream_gene_variant,,ENST00000533462,; T ENST00000532917 Transcript missense_variant,splice_region_variant 507/2678 439/549 147/182 A/S Gct/Tct 1 1 CD3G HGNC HGNC:1675 protein_coding YES CCDS8395.1 ENSP00000431445 P09693 B0YIY5 UPI000012735F NM_000073.2 deleterious(0.02) 4/7 hmmpanther:PTHR10570,hmmpanther:PTHR10570:SF8 MODERATE 1 SNV 1 1 PASS rs1352779607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 118350683 118350683 G T 1 0 0 0 0 1 0 0 0 2717 1014 35 2 2 CD3G 11 118350683 Missense_Mutation SNP G C3L-00144_T 10799 118350683 16735939 1087 5158 POU2F3 0 . GRCh38 11 120299726 120299726 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.367G>T p.Gly123Cys p.G123C ENST00000260264 5/13 161 127 34 103 102 1 strelka-varscan-mutect POU2F3,missense_variant,p.Gly123Cys,ENST00000260264,NM_001244682.1;POU2F3,missense_variant,p.Gly121Cys,ENST00000543440,NM_014352.3;POU2F3,stop_gained,p.Glu121Ter,ENST00000533620,;POU2F3,upstream_gene_variant,,ENST00000606153,; T ENST00000260264 Transcript missense_variant,splice_region_variant 401/2903 367/1317 123/438 G/C Ggt/Tgt 1 1 POU2F3 HGNC HGNC:19864 protein_coding YES CCDS58190.1 ENSP00000260264 Q9UKI9 UPI0002064EE0 NM_001244682.1 deleterious(0) 5/13 Low_complexity_(Seg):seg,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF81,Prints_domain:PR00029 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 120299726 120299726 G T 1 0 0 0 0 1 0 0 0 12389 1014 35 2 2 POU2F3 11 120299726 Missense_Mutation SNP G C3L-00144_T 1949043 120299726 14786896 1088 5159 TECTA 0 . GRCh38 11 121168926 121168926 + Splice_Site SNP G G A novel C3L-00144_T C3L-00144_N G G c.5999+1G>A p.X2000_splice ENST00000392793 322 238 84 252 250 2 strelka-varscan-mutect TECTA,splice_donor_variant,,ENST00000392793,;TECTA,splice_donor_variant,,ENST00000264037,NM_005422.2; A ENST00000392793 Transcript splice_donor_variant -/7426 5999/6468 2000/2155 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D 20/23 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 121168926 121168926 G A 1 0 0 0 0 0 0 1 0 16158 1275 44 3 3 TECTA 11 121168926 Splice_Site SNP G C3L-00144_T 869200 121168926 13917696 1089 5160 C11orf63 0 . GRCh38 11 122946704 122946704 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1841A>T p.Asn614Ile p.N614I ENST00000227349 6/9 245 193 52 177 177 0 strelka-varscan-mutect C11orf63,missense_variant,p.Asn614Ile,ENST00000227349,NM_024806.3;C11orf63,missense_variant,p.Asn614Ile,ENST00000531316,;C11orf63,non_coding_transcript_exon_variant,,ENST00000534362,; T ENST00000227349 Transcript missense_variant 2375/3147 1841/2337 614/778 N/I aAc/aTc 1 1 C11orf63 HGNC HGNC:26288 protein_coding YES CCDS8438.1 ENSP00000227349 Q6NUN7 UPI00001FA5AB NM_024806.3 tolerated(0.06) 6/9 hmmpanther:PTHR14726,hmmpanther:PTHR14726:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 122946704 122946704 A T 1 0 0 0 0 1 0 0 0 1790 43 2 4 4 C11orf63 11 122946704 Missense_Mutation SNP A C3L-00144_T 1777778 122946704 12139918 1090 5161 C11orf63 0 . GRCh38 11 122957402 122957402 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2050G>T p.Val684Phe p.V684F ENST00000227349 8/9 144 107 37 98 98 0 strelka-varscan-mutect C11orf63,missense_variant,p.Val684Phe,ENST00000227349,NM_024806.3;C11orf63,missense_variant,p.Val684Phe,ENST00000531316,;ATP5F1P5,upstream_gene_variant,,ENST00000526403,; T ENST00000227349 Transcript missense_variant 2584/3147 2050/2337 684/778 V/F Gtc/Ttc 1 1 C11orf63 HGNC HGNC:26288 protein_coding YES CCDS8438.1 ENSP00000227349 Q6NUN7 UPI00001FA5AB NM_024806.3 deleterious(0) 8/9 Pfam_domain:PF15261,hmmpanther:PTHR14726,hmmpanther:PTHR14726:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 122957402 122957402 G T 1 0 0 0 0 1 0 0 0 1790 1029 36 2 2 C11orf63 11 122957402 Missense_Mutation SNP G C3L-00144_T 10698 122957402 12129220 1091 5162 OR10G4 0 . GRCh38 11 124016248 124016248 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.674T>G p.Leu225Arg p.L225R ENST00000320891 1/1 229 179 50 197 197 0 strelka-varscan-mutect OR10G4,missense_variant,p.Leu225Arg,ENST00000320891,NM_001004462.1; G ENST00000320891 Transcript missense_variant 674/936 674/936 225/311 L/R cTg/cGg 1 1 OR10G4 HGNC HGNC:14809 protein_coding YES CCDS31702.1 ENSP00000325076 Q8NGN3 A0A126GWS5 UPI0000041BAD NM_001004462.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF6,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 124016248 124016248 T G 1 0 0 0 0 1 0 0 0 10977 1580 55 5 5 OR10G4 11 124016248 Missense_Mutation SNP T C3L-00144_T 1058846 124016248 11070374 1092 5163 OR8B2 0 . GRCh38 11 124383301 124383301 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.43G>T p.Ala15Ser p.A15S ENST00000375013 1/1 132 97 35 103 103 0 strelka-varscan-mutect OR8B2,missense_variant,p.Ala15Ser,ENST00000375013,NM_001005468.1; A ENST00000375013 Transcript missense_variant 62/968 43/942 15/313 A/S Gct/Tct 1 -1 OR8B2 HGNC HGNC:8471 protein_coding YES CCDS31708.1 ENSP00000364152 Q96RD0 A0A126GVQ4 UPI000004B1E5 NM_001005468.1 tolerated_low_confidence(0.2) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF258,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 124383301 124383301 C A 1 0 0 0 0 1 0 0 0 11297 710 25 2 2 OR8B2 11 124383301 Missense_Mutation SNP C C3L-00144_T 367053 124383301 10703321 1093 5164 OR8B8 0 . GRCh38 11 124440928 124440928 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.158C>A p.Ser53Tyr p.S53Y ENST00000328064 1/1 354 263 91 234 234 0 strelka-varscan-mutect OR8B8,missense_variant,p.Ser53Tyr,ENST00000328064,NM_012378.1; T ENST00000328064 Transcript missense_variant 231/1033 158/936 53/311 S/Y tCt/tAt 1 -1 OR8B8 HGNC HGNC:8477 protein_coding YES CCDS8446.1 ENSP00000330280 Q15620 A0A126GW73 UPI00000015B1 NM_012378.1 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF214,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 124440928 124440928 G T 1 0 0 0 0 1 0 0 0 11300 942 33 2 2 OR8B8 11 124440928 Missense_Mutation SNP G C3L-00144_T 57627 124440928 10645694 1094 5165 OR8B12 0 . GRCh38 11 124542740 124542740 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.915C>T p.= p.G305G ENST00000306842 1/1 68 50 18 51 51 0 strelka-varscan-mutect OR8B12,synonymous_variant,p.=,ENST00000306842,NM_001005195.1;RP11-728D14.6,upstream_gene_variant,,ENST00000533869,; A ENST00000306842 Transcript synonymous_variant 940/998 915/933 305/310 G ggC/ggT 1 -1 OR8B12 HGNC HGNC:15307 protein_coding YES CCDS31711.1 ENSP00000307159 Q8NGG6 A0A126GWS7 UPI0000041E25 NM_001005195.1 1/1 hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF267,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1379631539 . 0 179 29 2 0 0 0 0 -20 0.9736021 0 1 1 0 A 2 1 12 124542740 124542740 G A 1 0 0 0 0 0 0 0 1 11296 1306 46 3 3 OR8B12 11 124542740 Silent SNP G C3L-00144_T 101812 124542740 10543882 1095 5166 ROBO3 0 . GRCh38 11 124876445 124876445 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2764C>T p.Leu922Phe p.L922F ENST00000397801 17/28 46 35 11 12 12 0 strelka-mutect ROBO3,missense_variant,p.Leu922Phe,ENST00000397801,NM_022370.3;ROBO3,missense_variant,p.Leu900Phe,ENST00000538940,;ROBO3,upstream_gene_variant,,ENST00000543966,;ROBO3,upstream_gene_variant,,ENST00000525482,;ROBO3,upstream_gene_variant,,ENST00000528820,;ROBO3,upstream_gene_variant,,ENST00000528144,;ROBO3,upstream_gene_variant,,ENST00000531075,;ROBO3,upstream_gene_variant,,ENST00000526551,;ROBO3,upstream_gene_variant,,ENST00000532472,;ROBO3,upstream_gene_variant,,ENST00000531545,;ROBO3,non_coding_transcript_exon_variant,,ENST00000527196,;ROBO3,upstream_gene_variant,,ENST00000527245,;ROBO3,upstream_gene_variant,,ENST00000529658,;ROBO3,upstream_gene_variant,,ENST00000525448,;ROBO3,upstream_gene_variant,,ENST00000534598,;ROBO3,upstream_gene_variant,,ENST00000524971,;ROBO3,upstream_gene_variant,,ENST00000525304,;ROBO3,upstream_gene_variant,,ENST00000528068,;ROBO3,upstream_gene_variant,,ENST00000531888,;ROBO3,upstream_gene_variant,,ENST00000530647,;ROBO3,upstream_gene_variant,,ENST00000531119,; T ENST00000397801 Transcript missense_variant 2956/4569 2764/4161 922/1386 L/F Ctc/Ttc 1 1 ROBO3 HGNC HGNC:13433 protein_coding YES CCDS44755.1 ENSP00000380903 Q96MS0 UPI000035AA82 NM_022370.3 deleterious(0.01) 17/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF724 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 124876445 124876445 C T 1 0 0 0 0 1 0 0 0 13693 797 28 3 3 ROBO3 11 124876445 Missense_Mutation SNP C C3L-00144_T 333705 124876445 10210177 1096 5167 HEPN1 0 . GRCh38 11 124919992 124919992 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.242G>T p.Ser81Ile p.S81I ENST00000408930 1/1 144 97 47 135 135 0 strelka-varscan-mutect HEPN1,missense_variant,p.Ser81Ile,ENST00000408930,NM_001037558.2;HEPACAM,3_prime_UTR_variant,,ENST00000298251,NM_152722.4;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; T ENST00000408930 Transcript missense_variant 749/1434 242/267 81/88 S/I aGc/aTc 1 1 HEPN1 HGNC HGNC:34400 protein_coding YES CCDS41729.1 ENSP00000386143 Q6WQI6 UPI0000D6269C NM_001037558.2 deleterious_low_confidence(0.02) 1/1 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 124919992 124919992 G T 1 0 0 0 0 1 0 0 0 6940 971 34 2 2 HEPN1 11 124919992 Missense_Mutation SNP G C3L-00144_T 43547 124919992 10166630 1097 5168 HEPACAM 0 . GRCh38 11 124921229 124921229 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1160G>A p.Arg387His p.R387H ENST00000298251 7/7 196 185 11 125 125 0 strelka-varscan-mutect HEPACAM,missense_variant,p.Arg387His,ENST00000298251,NM_152722.4;HEPN1,downstream_gene_variant,,ENST00000408930,NM_001037558.2;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; T ENST00000298251 Transcript missense_variant 1566/3602 1160/1251 387/416 R/H cGc/cAc 1 -1 HEPACAM HGNC HGNC:26361 protein_coding YES CCDS8456.1 ENSP00000298251 Q14CZ8 UPI000013E4B5 NM_152722.4 tolerated_low_confidence(0.14) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1182107619 . 0 199 7 3 0 0 0 0 -13.63725 0.9950296 1 1 1 0 T 3 4 12 124921229 124921229 C T 1 0 0 0 0 1 0 0 0 6936 768 27 1 1 HEPACAM 11 124921229 Missense_Mutation SNP C C3L-00144_T 1237 124921229 10165393 1098 5169 CCDC15 0 . GRCh38 11 125040599 125040599 + Missense_Mutation SNP G G T rs749849352 C3L-00144_T C3L-00144_N G G c.2744G>T p.Arg915Leu p.R915L ENST00000344762 16/16 176 143 33 114 114 0 strelka-varscan-mutect CCDC15,missense_variant,p.Arg926Leu,ENST00000529051,;CCDC15,missense_variant,p.Arg915Leu,ENST00000344762,NM_025004.2;CCDC15,non_coding_transcript_exon_variant,,ENST00000530061,;CCDC15,downstream_gene_variant,,ENST00000524471,; T ENST00000344762 Transcript missense_variant 3003/3893 2744/2856 915/951 R/L cGg/cTg rs749849352 1 1 CCDC15 HGNC HGNC:25798 protein_coding YES CCDS44756.1 ENSP00000341684 Q0P6D6 UPI0000EE3BEA NM_025004.2 deleterious(0) 16/16 hmmpanther:PTHR14817 MODERATE 1 SNV 5 1 PASS rs749849352 . 0 206 0 3 0 0 0 0 -20 0.9999958 1 1 1 0 T 3 4 12 125040599 125040599 G T 1 0 0 0 0 1 0 0 0 2470 1116 39 1 1 CCDC15 11 125040599 Missense_Mutation SNP G C3L-00144_T 119370 125040599 10046023 1099 5170 CDON 0 . GRCh38 11 126010417 126010417 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1476G>C p.Gln492His p.Q492H ENST00000392693 8/20 185 156 29 147 147 0 strelka-varscan-mutect CDON,missense_variant,p.Gln492His,ENST00000392693,NM_001243597.1;CDON,missense_variant,p.Gln492His,ENST00000263577,NM_016952.4;CDON,missense_variant,p.Gln468His,ENST00000534661,;CDON,3_prime_UTR_variant,,ENST00000531830,;CDON,downstream_gene_variant,,ENST00000525625,; G ENST00000392693 Transcript missense_variant 1604/9138 1476/3864 492/1287 Q/H caG/caC 1 -1 CDON HGNC HGNC:17104 protein_coding YES CCDS58192.1 ENSP00000376458 Q4KMG0 UPI0000E0013A NM_001243597.1 tolerated(0.22) 8/20 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF12,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 126010417 126010417 C G 1 0 0 0 0 1 0 0 0 2874 680 24 4 4 CDON 11 126010417 Missense_Mutation SNP C C3L-00144_T 969818 126010417 9076205 1100 5171 KCNJ1 0 . GRCh38 11 128839539 128839539 + Missense_Mutation SNP G G C rs142030262 C3L-00144_T C3L-00144_N G G c.762C>G p.Asp254Glu p.D254E ENST00000392664 2/2 399 303 96 308 308 0 strelka-varscan-mutect KCNJ1,missense_variant,p.Asp235Glu,ENST00000392665,;KCNJ1,missense_variant,p.Asp235Glu,ENST00000392666,NM_153766.2,NM_153764.2;KCNJ1,missense_variant,p.Asp235Glu,ENST00000324036,NM_153767.3;KCNJ1,missense_variant,p.Asp235Glu,ENST00000440599,NM_153765.2;KCNJ1,missense_variant,p.Asp254Glu,ENST00000392664,NM_000220.4;KCNJ1,downstream_gene_variant,,ENST00000324003,;KCNJ1,downstream_gene_variant,,ENST00000531562,; C ENST00000392664 Transcript missense_variant 879/1674 762/1176 254/391 D/E gaC/gaG rs142030262 1 -1 KCNJ1 HGNC HGNC:6255 protein_coding YES CCDS8476.1 ENSP00000376432 P48048 UPI000012D891 NM_000220.4 deleterious(0.04) 2/2 hmmpanther:PTHR11767:SF6,hmmpanther:PTHR11767,Gene3D:2.60.40.1400,Pfam_domain:PF01007,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81296,Prints_domain:PR01321 MODERATE 1 SNV 1 1 PASS rs142030262 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 128839539 128839539 G C 1 0 0 0 0 1 0 0 0 7959 1136 40 4 4 KCNJ1 11 128839539 Missense_Mutation SNP G C3L-00144_T 2829122 128839539 6247083 1101 5172 ARHGAP32 0 . GRCh38 11 129064876 129064876 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.685A>G p.Lys229Glu p.K229E ENST00000310343 7/22 320 255 65 206 205 1 strelka-varscan-mutect ARHGAP32,missense_variant,p.Lys229Glu,ENST00000310343,NM_001142685.1;ARHGAP32,missense_variant,p.Lys155Glu,ENST00000524655,;ARHGAP32,downstream_gene_variant,,ENST00000525234,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000533509,; C ENST00000310343 Transcript missense_variant 685/10111 685/6264 229/2087 K/E Aag/Gag 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 deleterious(0.02) 7/22 hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 129064876 129064876 T C 1 0 0 0 0 1 0 0 0 1006 1821 63 5 5 ARHGAP32 11 129064876 Missense_Mutation SNP T C3L-00144_T 225337 129064876 6021746 1102 5173 ADAMTS8 0 . GRCh38 11 130416214 130416214 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1213T>A p.Trp405Arg p.W405R ENST00000257359 4/9 146 124 22 133 133 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Trp405Arg,ENST00000257359,NM_007037.4;ADAMTS8,upstream_gene_variant,,ENST00000531752,; T ENST00000257359 Transcript missense_variant 1920/4010 1213/2670 405/889 W/R Tgg/Agg 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 deleterious(0) 4/9 PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486,Prints_domain:PR01861 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 130416214 130416214 A T 1 0 0 0 0 1 0 0 0 316 188 7 4 4 ADAMTS8 11 130416214 Missense_Mutation SNP A C3L-00144_T 1351338 130416214 4670408 1103 5174 ADAMTS15 0 . GRCh38 11 130473185 130473185 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2217G>T p.= p.G739G ENST00000299164 8/8 399 325 74 318 317 1 strelka-varscan-mutect ADAMTS15,synonymous_variant,p.=,ENST00000299164,NM_139055.2; T ENST00000299164 Transcript synonymous_variant 2217/5673 2217/2853 739/950 G ggG/ggT 1 1 ADAMTS15 HGNC HGNC:16305 protein_coding YES CCDS8488.1 ENSP00000299164 Q8TE58 UPI000004F277 NM_139055.2 8/8 Pfam_domain:PF05986,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF39 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 130473185 130473185 G T 1 0 0 0 0 0 0 0 1 304 1190 42 2 2 ADAMTS15 11 130473185 Silent SNP G C3L-00144_T 56971 130473185 4613437 1104 5175 ADAMTS15 0 . GRCh38 11 130473512 130473512 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2544G>T p.Trp848Cys p.W848C ENST00000299164 8/8 99 81 18 81 81 0 strelka-varscan-mutect ADAMTS15,missense_variant,p.Trp848Cys,ENST00000299164,NM_139055.2; T ENST00000299164 Transcript missense_variant 2544/5673 2544/2853 848/950 W/C tgG/tgT 1 1 ADAMTS15 HGNC HGNC:16305 protein_coding YES CCDS8488.1 ENSP00000299164 Q8TE58 UPI000004F277 NM_139055.2 deleterious(0) 8/8 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF39,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 130473512 130473512 G T 1 0 0 0 0 1 0 0 0 304 1241 43 2 2 ADAMTS15 11 130473512 Missense_Mutation SNP G C3L-00144_T 327 130473512 4613110 1105 5176 CACNA1C 0 . GRCh38 12 2601884 2601884 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2944G>T p.Gly982Cys p.G982C ENST00000347598 23/49 207 188 19 198 198 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Gly962Cys,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000406454,;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Gly987Cys,ENST00000335762,;CACNA1C,missense_variant,p.Gly962Cys,ENST00000480911,;CACNA1C,missense_variant,p.Gly982Cys,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Gly962Cys,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Gly982Cys,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Gly962Cys,ENST00000399644,NM_001129841.1;CACNA1C-AS3,downstream_gene_variant,,ENST00000543559,; T ENST00000347598 Transcript missense_variant 2944/6655 2944/6561 982/2186 G/C Ggt/Tgt 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0.01) 23/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 2601884 2601884 G T 1 0 0 0 0 1 0 0 0 2228 1232 43 2 2 CACNA1C 12 2601884 Missense_Mutation SNP G C3L-00144_T 2601884 130673425 1106 5177 RP4-816N1.8 0 . GRCh38 12 2854928 2854928 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.591G>T p.Gln197His p.Q197H ENST00000637658 2/3 92 79 13 88 87 1 strelka-varscan-mutect RP4-816N1.8,missense_variant,p.Gln197His,ENST00000637658,;FOXM1,downstream_gene_variant,,ENST00000627656,NM_001243088.1;FOXM1,downstream_gene_variant,,ENST00000342628,NM_202002.2;FOXM1,downstream_gene_variant,,ENST00000361953,NM_202003.2,NM_001243089.1;FOXM1,downstream_gene_variant,,ENST00000359843,NM_021953.3;FOXM1,downstream_gene_variant,,ENST00000535350,;ITFG2,intron_variant,,ENST00000537710,;ITFG2,upstream_gene_variant,,ENST00000545509,;ITFG2,upstream_gene_variant,,ENST00000540300,;FOXM1,downstream_gene_variant,,ENST00000536066,; A ENST00000637658 Transcript missense_variant 648/1167 591/918 197/305 Q/H caG/caT 1 -1 RP4-816N1.8 Clone_based_vega_gene protein_coding YES ENSP00000489863 A6NCN8 UPI00017BE937 tolerated(0.77) 2/3 Pfam_domain:PF15046,hmmpanther:PTHR35156,hmmpanther:PTHR35156:SF1 MODERATE SNV 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999928 1 1 1 0 A 3 1 12 2854928 2854928 C A 1 0 0 0 0 1 0 0 0 13779 680 24 2 2 RP4-816N1.8 12 2854928 Missense_Mutation SNP C C3L-00144_T 253044 2854928 130420381 1107 5178 CCND2 0 . GRCh38 12 4278907 4278907 + Missense_Mutation SNP C C A rs751104155 C3L-00144_T C3L-00144_N C C c.559C>A p.Leu187Met p.L187M ENST00000261254 3/5 78 67 11 68 68 0 strelka-varscan-mutect CCND2,missense_variant,p.Leu187Met,ENST00000261254,NM_001759.3;CCND2,missense_variant,p.Leu103Met,ENST00000536537,;CCND2-AS1,upstream_gene_variant,,ENST00000539135,;CCND2-AS2,upstream_gene_variant,,ENST00000537370,;CCND2,non_coding_transcript_exon_variant,,ENST00000541542,;CCND2,non_coding_transcript_exon_variant,,ENST00000536795,; A ENST00000261254 Transcript missense_variant 828/6480 559/870 187/289 L/M Ctg/Atg rs751104155,COSM324944 1 1 CCND2 HGNC HGNC:1583 protein_coding YES CCDS8524.1 ENSP00000261254 P30279 UPI00001275C5 NM_001759.3 deleterious(0.03) 3/5 hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF66,Gene3D:1.10.472.10,Pfam_domain:PF02984,SMART_domains:SM01332,Superfamily_domains:SSF47954 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751104155 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 4278907 4278907 C A 1 0 0 0 0 1 0 0 0 2616 912 32 2 2 CCND2 12 4278907 Missense_Mutation SNP C C3L-00144_T 1423979 4278907 128996402 1108 5179 GALNT8 0 . GRCh38 12 4810420 4810420 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.379G>T p.Gly127Trp p.G127W ENST00000280684 1/1 156 135 21 153 152 1 strelka-varscan-mutect GALNT8,missense_variant,p.Gly127Trp,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Gly127Trp,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; T ENST00000280684 Transcript missense_variant 1245/4237 379/1590 127/529 G/W Ggg/Tgg 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD deleterious(0) 1/1 Gene3D:3.30.710.10,Pfam_domain:PF02214,Prints_domain:PR01496,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 4810420 4810420 G T 1 0 0 0 0 1 0 0 0 6090 1232 43 2 2 GALNT8 12 4810420 Missense_Mutation SNP G C3L-00144_T 531513 4810420 128464889 1109 5180 KCNA5 0 . GRCh38 12 5045551 5045551 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.1404T>C p.= p.P468P ENST00000252321 1/1 374 305 69 299 299 0 strelka-varscan-mutect KCNA5,synonymous_variant,p.=,ENST00000252321,NM_002234.3; C ENST00000252321 Transcript synonymous_variant 1563/2800 1404/1842 468/613 P ccT/ccC 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,Superfamily_domains:SSF81324 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 5045551 5045551 T C 1 0 0 0 0 0 0 0 1 7922 1567 55 5 5 KCNA5 12 5045551 Silent SNP T C3L-00144_T 235131 5045551 128229758 1110 5181 VWF 0 . GRCh38 12 5983163 5983163 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.7068C>A p.= p.P2356P ENST00000261405 41/52 387 317 70 318 318 0 strelka-varscan-mutect VWF,synonymous_variant,p.=,ENST00000261405,NM_000552.3; T ENST00000261405 Transcript synonymous_variant 7323/8838 7068/8442 2356/2813 P ccC/ccA 1 -1 VWF HGNC HGNC:12726 protein_coding YES CCDS8539.1 ENSP00000261405 P04275 UPI00001AE7EE NM_000552.3 41/52 PIRSF_domain:PIRSF002495 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 5983163 5983163 G T 1 0 0 0 0 0 0 0 1 17806 1335 47 2 2 VWF 12 5983163 Silent SNP G C3L-00144_T 937612 5983163 127292146 1111 5182 ACSM4 0 . GRCh38 12 7324354 7324354 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1390T>A p.Tyr464Asn p.Y464N ENST00000399422 10/13 266 241 25 212 212 0 strelka-varscan-mutect ACSM4,missense_variant,p.Tyr464Asn,ENST00000399422,NM_001080454.1; A ENST00000399422 Transcript missense_variant 1438/2142 1390/1743 464/580 Y/N Tat/Aat 1 1 ACSM4 HGNC HGNC:32016 protein_coding YES CCDS44825.1 ENSP00000382349 P0C7M7 UPI0000DD812A NM_001080454.1 deleterious(0.01) 10/13 hmmpanther:PTHR24095:SF127,hmmpanther:PTHR24095,Pfam_domain:PF00501,Gene3D:2.30.38.10,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7324354 7324354 T A 1 0 0 0 0 1 0 0 0 228 1638 57 4 4 ACSM4 12 7324354 Missense_Mutation SNP T C3L-00144_T 1341191 7324354 125950955 1112 5183 CD163L1 0 . GRCh38 12 7403804 7403804 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1169G>T p.Gly390Val p.G390V ENST00000416109 6/20 186 155 31 188 188 0 strelka-varscan-mutect CD163L1,missense_variant,p.Gly380Val,ENST00000313599,NM_174941.5;CD163L1,missense_variant,p.Gly390Val,ENST00000416109,NM_001297650.1;CD163L1,missense_variant,p.Gly26Val,ENST00000545926,; A ENST00000416109 Transcript missense_variant 1188/4603 1169/4392 390/1463 G/V gGg/gTg 1 -1 CD163L1 HGNC HGNC:30375 protein_coding YES CCDS73434.1 ENSP00000393474 Q9NR16 UPI0001AE6A76 NM_001297650.1 deleterious(0) 6/20 PROSITE_profiles:PS50287,Gene3D:3.10.250.10,Pfam_domain:PF00530,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7403804 7403804 C A 1 0 0 0 0 1 0 0 0 2671 623 22 2 2 CD163L1 12 7403804 Missense_Mutation SNP C C3L-00144_T 79450 7403804 125871505 1113 5184 CD163 0 . GRCh38 12 7495273 7495273 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1228G>T p.Val410Phe p.V410F ENST00000359156 6/17 525 447 78 426 426 0 strelka-varscan-mutect CD163,missense_variant,p.Val410Phe,ENST00000359156,NM_004244.5;CD163,missense_variant,p.Val410Phe,ENST00000396620,;CD163,missense_variant,p.Val410Phe,ENST00000432237,NM_203416.3;CD163,missense_variant,p.Val398Phe,ENST00000541972,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,; A ENST00000359156 Transcript missense_variant 1431/4268 1228/3471 410/1156 V/F Gtt/Ttt 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 deleterious(0) 6/17 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7495273 7495273 C A 1 0 0 0 0 1 0 0 0 2670 507 18 2 2 CD163 12 7495273 Missense_Mutation SNP C C3L-00144_T 91469 7495273 125780036 1114 5185 PRB3 0 . GRCh38 12 11267869 11267869 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.380G>C p.Gly127Ala p.G127A ENST00000538488 3/4 74 56 18 70 70 0 varscan-mutect PRB3,missense_variant,p.Gly127Ala,ENST00000538488,NM_006249.5;PRB3,missense_variant,p.Gly127Ala,ENST00000381842,;PRB3,non_coding_transcript_exon_variant,,ENST00000539835,; G ENST00000538488 Transcript missense_variant 516/1283 380/1056 127/351 G/A gGa/gCa 1 -1 PRB3 HGNC HGNC:9339 protein_coding YES ENSP00000442626 F5H7C1 UPI00002371BA NM_006249.5 tolerated(0.64) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23203:SF2,hmmpanther:PTHR23203,Pfam_domain:PF15240,Pfam_domain:PF15240,Pfam_domain:PF15240,SMART_domains:SM01412 MODERATE 1 SNV 5 1 PASS rs1428858364 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 11267869 11267869 C G 1 0 0 0 0 1 0 0 0 12575 855 30 4 4 PRB3 12 11267869 Missense_Mutation SNP C C3L-00144_T 3772596 11267869 122007440 1115 5186 GRIN2B 0 . GRCh38 12 13608651 13608651 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1962G>T p.Met654Ile p.M654I ENST00000609686 9/13 402 347 55 379 375 4 strelka-varscan-mutect GRIN2B,missense_variant,p.Met654Ile,ENST00000609686,NM_000834.3;GRIN2B,missense_variant,p.Met7Ile,ENST00000637214,;GRIN2B,non_coding_transcript_exon_variant,,ENST00000628166,; A ENST00000609686 Transcript missense_variant 2416/30355 1962/4455 654/1484 M/I atG/atT 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 deleterious(0.01) 9/13 Gene3D:1.10.287.70,Pfam_domain:PF00060,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF192,SMART_domains:SM00079 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 13608651 13608651 C A 1 0 0 0 0 1 0 0 0 6662 826 29 2 2 GRIN2B 12 13608651 Missense_Mutation SNP C C3L-00144_T 2340782 13608651 119666658 1116 5187 PTPRO 0 . GRCh38 12 15526161 15526161 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2063C>A p.Thr688Asn p.T688N ENST00000281171 12/27 400 363 37 368 368 0 strelka-varscan-mutect PTPRO,missense_variant,p.Thr688Asn,ENST00000281171,NM_030667.2;PTPRO,missense_variant,p.Thr688Asn,ENST00000348962,NM_002848.3; A ENST00000281171 Transcript missense_variant 2393/5301 2063/3651 688/1216 T/N aCt/aAt 1 1 PTPRO HGNC HGNC:9678 protein_coding YES CCDS8675.1 ENSP00000281171 Q16827 UPI000013DC62 NM_030667.2 tolerated(0.29) 12/27 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF315,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 15526161 15526161 C A 1 0 0 0 0 1 0 0 0 12963 565 20 2 2 PTPRO 12 15526161 Missense_Mutation SNP C C3L-00144_T 1917510 15526161 117749148 1117 5188 SLC15A5 0 . GRCh38 12 16272721 16272721 + Missense_Mutation SNP C C A rs764937676 C3L-00144_T C3L-00144_N C C c.424G>T p.Ala142Ser p.A142S ENST00000344941 2/9 416 330 86 340 340 0 strelka-varscan-mutect SLC15A5,missense_variant,p.Ala142Ser,ENST00000344941,NM_001170798.1; A ENST00000344941 Transcript missense_variant 424/2923 424/1740 142/579 A/S Gca/Tca rs764937676 1 -1 SLC15A5 HGNC HGNC:33455 protein_coding YES ENSP00000340402 A6NIM6 UPI0000DD8132 NM_001170798.1 deleterious(0.01) 2/9 Pfam_domain:PF00854,hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF91,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS rs764937676 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 16272721 16272721 C A 1 0 0 0 0 1 0 0 0 14667 710 25 2 2 SLC15A5 12 16272721 Missense_Mutation SNP C C3L-00144_T 746560 16272721 117002588 1118 5189 SLCO1C1 0 . GRCh38 12 20723254 20723254 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1186G>C p.Gly396Arg p.G396R ENST00000545604 10/16 220 178 42 245 245 0 strelka-varscan-mutect SLCO1C1,missense_variant,p.Gly396Arg,ENST00000266509,NM_017435.4;SLCO1C1,missense_variant,p.Gly278Arg,ENST00000545102,NM_001145944.1;SLCO1C1,missense_variant,p.Gly396Arg,ENST00000545604,NM_001145946.1;SLCO1C1,missense_variant,p.Gly347Arg,ENST00000540354,NM_001145945.1;SLCO1C1,splice_region_variant,,ENST00000539415,; C ENST00000545604 Transcript missense_variant,splice_region_variant 1416/2557 1186/2193 396/730 G/R Ggg/Cgg 1 1 SLCO1C1 HGNC HGNC:13819 protein_coding YES CCDS53757.1 ENSP00000444149 Q9NYB5 UPI00004C3E1B NM_001145946.1 deleterious(0) 10/16 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF99,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs1391930843 . 0 208 0 0 2 0 0 0 -19.99991 0.9980011 1 1 1 0 C 3 2 12 20723254 20723254 G C 1 0 0 0 0 1 0 0 0 15012 1130 39 4 4 SLCO1C1 12 20723254 Missense_Mutation SNP G C3L-00144_T 4450533 20723254 112552055 1119 5190 ABCC9 0 . GRCh38 12 21882831 21882831 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1954C>A p.Leu652Met p.L652M ENST00000261200 14/38 241 204 37 224 224 0 strelka-varscan-mutect ABCC9,missense_variant,p.Leu652Met,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Leu652Met,ENST00000261201,NM_005691.3;ABCC9,intron_variant,,ENST00000544039,;RP11-729I10.2,intron_variant,,ENST00000539874,; T ENST00000261200 Transcript missense_variant 1954/8293 1954/4650 652/1549 L/M Ctg/Atg 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 tolerated(0.39) 14/38 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 21882831 21882831 G T 1 0 0 0 0 1 0 0 0 63 991 35 2 2 ABCC9 12 21882831 Missense_Mutation SNP G C3L-00144_T 1159577 21882831 111392478 1120 5191 ITPR2 0 . GRCh38 12 26561823 26561823 + Missense_Mutation SNP C C G rs774885630 C3L-00144_T C3L-00144_N C C c.4760G>C p.Arg1587Pro p.R1587P ENST00000381340 35/57 400 349 51 317 317 0 strelka-varscan-mutect ITPR2,missense_variant,p.Arg1587Pro,ENST00000381340,NM_002223.2; G ENST00000381340 Transcript missense_variant 5177/11405 4760/8106 1587/2701 R/P cGc/cCc rs774885630,COSM4206232 1 -1 ITPR2 HGNC HGNC:6181 protein_coding YES CCDS41764.1 ENSP00000370744 Q14571 UPI00001FB7D2 NM_002223.2 deleterious(0) 35/57 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF53,Superfamily_domains:SSF48371 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774885630 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 26561823 26561823 C G 1 0 0 0 0 1 0 0 0 7827 768 27 4 4 ITPR2 12 26561823 Missense_Mutation SNP C C3L-00144_T 4678992 26561823 106713486 1121 5192 OVCH1 0 . GRCh38 12 29471854 29471854 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1804G>T p.Gly602Cys p.G602C ENST00000318184 16/28 239 207 32 243 243 0 strelka-varscan-mutect OVCH1,missense_variant,p.Gly602Cys,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; A ENST00000318184 Transcript missense_variant 1804/3405 1804/3405 602/1134 G/C Ggt/Tgt 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 deleterious(0) 16/28 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 2 1 PASS rs1385011999 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 29471854 29471854 C A 1 0 0 0 0 1 0 0 0 11393 681 24 2 2 OVCH1 12 29471854 Missense_Mutation SNP C C3L-00144_T 2910031 29471854 103803455 1122 5193 DENND5B 0 . GRCh38 12 31409355 31409355 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2816G>T p.Arg939Leu p.R939L ENST00000536562 16/23 84 70 14 72 72 0 strelka-varscan-mutect DENND5B,missense_variant,p.Arg904Leu,ENST00000389082,NM_144973.3;DENND5B,missense_variant,p.Arg939Leu,ENST00000536562,NM_001308339.1; A ENST00000536562 Transcript missense_variant 2967/4291 2816/3930 939/1309 R/L cGt/cTt 1 -1 DENND5B HGNC HGNC:28338 protein_coding YES CCDS76542.1 ENSP00000444889 G3V1S3 UPI0000D621CB NM_001308339.1 tolerated(0.13) 16/23 PROSITE_profiles:PS50826,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF45,Pfam_domain:PF02759,SMART_domains:SM00593,Superfamily_domains:0052343 MODERATE 1 SNV 2 1 PASS rs1276257487 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31409355 31409355 C A 1 0 0 0 0 1 0 0 0 4241 536 19 1 1 DENND5B 12 31409355 Missense_Mutation SNP C C3L-00144_T 1937501 31409355 101865954 1123 5194 PKP2 0 . GRCh38 12 32792493 32792493 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.2578-1G>T p.X860_splice ENST00000070846 683 612 71 580 579 1 strelka-varscan-mutect PKP2,splice_acceptor_variant,,ENST00000340811,NM_001005242.2;PKP2,splice_acceptor_variant,,ENST00000070846,NM_004572.3;PKP2,splice_acceptor_variant,,ENST00000546769,; A ENST00000070846 Transcript splice_acceptor_variant -/4241 2578/2646 860/881 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 13/13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 32792493 32792493 C A 1 0 0 0 0 0 0 1 0 12081 695 24 2 2 PKP2 12 32792493 Splice_Site SNP C C3L-00144_T 1383138 32792493 100482816 1124 5195 C12orf40 0 . GRCh38 12 39721077 39721077 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1785G>T p.= p.G595G ENST00000324616 13/13 415 328 87 422 420 2 strelka-varscan-mutect C12orf40,synonymous_variant,p.=,ENST00000324616,NM_001031748.2;C12orf40,intron_variant,,ENST00000468200,; T ENST00000324616 Transcript synonymous_variant 1939/2776 1785/1959 595/652 G ggG/ggT 1 1 C12orf40 HGNC HGNC:26846 protein_coding YES CCDS41770.1 ENSP00000317671 Q86WS4 UPI000069A925 NM_001031748.2 13/13 hmmpanther:PTHR35158:SF1,hmmpanther:PTHR35158,Pfam_domain:PF15089 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 39721077 39721077 G T 1 0 0 0 0 0 0 0 1 1809 1161 41 2 2 C12orf40 12 39721077 Silent SNP G C3L-00144_T 6928584 39721077 93554232 1125 5196 SLC2A13 0 . GRCh38 12 39951300 39951300 + Missense_Mutation SNP C C A rs543033286 C3L-00144_T C3L-00144_N C C c.991G>T p.Gly331Cys p.G331C ENST00000280871 4/10 227 208 19 189 188 1 strelka-varscan-mutect SLC2A13,missense_variant,p.Gly331Cys,ENST00000280871,NM_052885.3;SLC2A13,missense_variant,p.Gly331Cys,ENST00000380858,; A ENST00000280871 Transcript missense_variant 1042/7003 991/1947 331/648 G/C Ggc/Tgc rs543033286 1 -1 SLC2A13 HGNC HGNC:15956 protein_coding YES CCDS8736.2 ENSP00000280871 Q96QE2 UPI000066D913 NM_052885.3 tolerated(0.07) 4/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF89,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs543033286 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 39951300 39951300 C A 1 0 0 0 0 1 0 0 0 14812 594 21 2 2 SLC2A13 12 39951300 Missense_Mutation SNP C C3L-00144_T 230223 39951300 93324009 1126 5197 CNTN1 0 . GRCh38 12 40933704 40933704 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.811C>T p.Pro271Ser p.P271S ENST00000551295 9/24 231 203 28 202 202 0 strelka-varscan-mutect CNTN1,missense_variant,p.Pro271Ser,ENST00000551295,NM_001843.3;CNTN1,missense_variant,p.Pro271Ser,ENST00000347616,;CNTN1,missense_variant,p.Pro260Ser,ENST00000348761,NM_175038.2;CNTN1,missense_variant,p.Pro271Ser,ENST00000547849,NM_001256064.1;CNTN1,missense_variant,p.Pro271Ser,ENST00000547702,NM_001256063.1; T ENST00000551295 Transcript missense_variant 928/5557 811/3057 271/1018 P/S Ccg/Tcg 1 1 CNTN1 HGNC HGNC:2171 protein_coding YES CCDS8737.1 ENSP00000447006 Q12860 A0A024R104 UPI0000127EBA NM_001843.3 deleterious(0) 9/24 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 40933704 40933704 C T 1 0 0 0 0 1 0 0 0 3421 855 30 3 3 CNTN1 12 40933704 Missense_Mutation SNP C C3L-00144_T 982404 40933704 92341605 1127 5198 PDZRN4 0 . GRCh38 12 41563562 41563562 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.1380T>C p.= p.D460D ENST00000402685 8/10 182 162 20 159 159 0 strelka-varscan-mutect PDZRN4,synonymous_variant,p.=,ENST00000298919,;PDZRN4,synonymous_variant,p.=,ENST00000402685,NM_001164595.1;PDZRN4,synonymous_variant,p.=,ENST00000539469,NM_013377.3;PDZRN4,non_coding_transcript_exon_variant,,ENST00000548316,; C ENST00000402685 Transcript synonymous_variant 1388/3347 1380/3111 460/1036 D gaT/gaC 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 8/10 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF6,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 2 1 PASS rs1429268147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 41563562 41563562 T C 1 0 0 0 0 0 0 0 1 11798 1461 51 5 5 PDZRN4 12 41563562 Silent SNP T C3L-00144_T 629858 41563562 91711747 1128 5199 PDZRN4 0 . GRCh38 12 41573803 41573803 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.3024G>A p.Met1008Ile p.M1008I ENST00000402685 10/10 71 61 10 55 55 0 strelka-varscan-mutect PDZRN4,missense_variant,p.Met748Ile,ENST00000298919,;PDZRN4,missense_variant,p.Met1008Ile,ENST00000402685,NM_001164595.1;PDZRN4,missense_variant,p.Met750Ile,ENST00000539469,NM_013377.3;PDZRN4,non_coding_transcript_exon_variant,,ENST00000548316,; A ENST00000402685 Transcript missense_variant 3032/3347 3024/3111 1008/1036 M/I atG/atA 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 tolerated(0.37) 10/10 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF6 MODERATE 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -19.99705 1 1 1 1 0 A 3 1 12 41573803 41573803 G A 1 0 0 0 0 1 0 0 0 11798 1290 45 3 3 PDZRN4 12 41573803 Missense_Mutation SNP G C3L-00144_T 10241 41573803 91701506 1129 5200 ADAMTS20 0 . GRCh38 12 43377471 43377471 + Missense_Mutation SNP C C A rs112430320 C3L-00144_T C3L-00144_N C C c.4889G>T p.Arg1630Leu p.R1630L ENST00000389420 32/39 224 184 40 202 201 1 strelka-varscan-mutect ADAMTS20,missense_variant,p.Arg1630Leu,ENST00000389420,NM_025003.3; A ENST00000389420 Transcript missense_variant 4889/6076 4889/5733 1630/1910 R/L cGg/cTg rs112430320,COSM3416837,COSM3416838 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(0.56) 32/39 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs112430320 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43377471 43377471 C A 1 0 0 0 0 1 0 0 0 310 652 23 1 1 ADAMTS20 12 43377471 Missense_Mutation SNP C C3L-00144_T 1803668 43377471 89897838 1130 5201 ADAMTS20 0 . GRCh38 12 43428462 43428462 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3724G>T p.Asp1242Tyr p.D1242Y ENST00000389420 26/39 261 219 42 210 210 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Asp1242Tyr,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Asp1242Tyr,ENST00000395541,;ADAMTS20,missense_variant,p.Asp1242Tyr,ENST00000553158,;ADAMTS20,missense_variant,p.Asp372Tyr,ENST00000549670,; A ENST00000389420 Transcript missense_variant 3724/6076 3724/5733 1242/1910 D/Y Gat/Tat 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0.02) 26/39 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43428462 43428462 C A 1 0 0 0 0 1 0 0 0 310 826 29 2 2 ADAMTS20 12 43428462 Missense_Mutation SNP C C3L-00144_T 50991 43428462 89846847 1131 5202 DBX2 0 . GRCh38 12 45016522 45016522 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.784G>C p.Glu262Gln p.E262Q ENST00000332700 4/4 92 72 20 112 112 0 strelka-varscan-mutect DBX2,missense_variant,p.Glu262Gln,ENST00000332700,NM_001004329.2; G ENST00000332700 Transcript missense_variant 956/2806 784/1020 262/339 E/Q Gag/Cag 1 -1 DBX2 HGNC HGNC:33186 protein_coding YES CCDS31781.1 ENSP00000331470 Q6ZNG2 UPI000041A784 NM_001004329.2 tolerated(0.09) 4/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4 MODERATE 1 SNV 2 1 PASS rs1246450969 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 45016522 45016522 C G 1 0 0 0 0 1 0 0 0 4060 922 32 4 4 DBX2 12 45016522 Missense_Mutation SNP C C3L-00144_T 1588060 45016522 88258787 1132 5203 SLC38A1 0 . GRCh38 12 46197800 46197800 + Missense_Mutation SNP T T A rs201058166 C3L-00144_T C3L-00144_N T T c.1282A>T p.Met428Leu p.M428L ENST00000552197 16/17 137 118 19 122 122 0 strelka-varscan-mutect SLC38A1,missense_variant,p.Met428Leu,ENST00000398637,NM_001077484.1,NM_001278389.1,NM_030674.3;SLC38A1,missense_variant,p.Met428Leu,ENST00000439706,NM_001278387.1;SLC38A1,missense_variant,p.Met428Leu,ENST00000549049,NM_001278388.1;SLC38A1,missense_variant,p.Met428Leu,ENST00000552197,NM_001278390.1;SLC38A1,missense_variant,p.Met428Leu,ENST00000546893,;SLC38A1,missense_variant,p.Met428Leu,ENST00000612161,;SLC38A1,downstream_gene_variant,,ENST00000549633,;SLC38A1,non_coding_transcript_exon_variant,,ENST00000548979,; A ENST00000552197 Transcript missense_variant 1967/2599 1282/1512 428/503 M/L Atg/Ttg rs201058166 1 -1 SLC38A1 HGNC HGNC:13447 protein_coding YES CCDS61106.1 ENSP00000449756 F8VX04 UPI00018923FA NM_001278390.1 tolerated(1) 16/17 hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF184,Pfam_domain:PF01490,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs201058166 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 46197800 46197800 T A 1 0 0 0 0 1 0 0 0 14879 1464 51 4 4 SLC38A1 12 46197800 Missense_Mutation SNP T C3L-00144_T 1181278 46197800 87077509 1133 5204 PFKM 0 . GRCh38 12 48141325 48141325 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1569C>A p.= p.G523G ENST00000340802 17/25 262 233 29 223 223 0 strelka-varscan-mutect PFKM,synonymous_variant,p.=,ENST00000359794,NM_000289.5;PFKM,synonymous_variant,p.=,ENST00000340802,NM_001166686.1;PFKM,synonymous_variant,p.=,ENST00000312352,NM_001166687.1;PFKM,synonymous_variant,p.=,ENST00000547587,NM_001166688.1;PFKM,synonymous_variant,p.=,ENST00000551804,;PFKM,synonymous_variant,p.=,ENST00000546465,;PFKM,upstream_gene_variant,,ENST00000553055,;PFKM,3_prime_UTR_variant,,ENST00000547581,;PFKM,3_prime_UTR_variant,,ENST00000552752,;PFKM,non_coding_transcript_exon_variant,,ENST00000546964,;PFKM,downstream_gene_variant,,ENST00000547148,;PFKM,upstream_gene_variant,,ENST00000550802,;PFKM,upstream_gene_variant,,ENST00000552818,;PFKM,downstream_gene_variant,,ENST00000552989,;PFKM,upstream_gene_variant,,ENST00000552214,; A ENST00000340802 Transcript synonymous_variant 1793/3176 1569/2556 523/851 G ggC/ggA 1 1 PFKM HGNC HGNC:8877 protein_coding YES CCDS53786.1 ENSP00000345771 P08237 UPI0000D621DC NM_001166686.1 17/25 HAMAP:MF_03184,hmmpanther:PTHR13697,hmmpanther:PTHR13697:SF13,Pfam_domain:PF00365,PIRSF_domain:PIRSF000533,Gene3D:3.40.50.450,TIGRFAM_domain:TIGR02478,Superfamily_domains:SSF53784 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 48141325 48141325 C A 1 0 0 0 0 0 0 0 1 11855 784 28 2 2 PFKM 12 48141325 Silent SNP C C3L-00144_T 1943525 48141325 85133984 1134 5205 KMT2D 0 . GRCh38 12 49031271 49031271 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.13434G>T p.= p.R4478R ENST00000301067 39/54 185 156 29 151 151 0 strelka-varscan-mutect KMT2D,synonymous_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,non_coding_transcript_exon_variant,,ENST00000552391,; A ENST00000301067 Transcript synonymous_variant 13434/19419 13434/16614 4478/5537 R cgG/cgT 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 39/54 LOW 1 SNV 5 1 PASS rs1170892210 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 49031271 49031271 C A 1 0 0 0 0 0 0 0 1 8298 610 22 2 2 KMT2D 12 49031271 Silent SNP C C3L-00144_T 889946 49031271 84244038 1135 5206 KMT2D 0 . GRCh38 12 49031975 49031975 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.12730C>T p.Gln4244Ter p.Q4244* ENST00000301067 39/54 29 23 6 38 38 0 strelka-varscan-mutect KMT2D,stop_gained,p.Gln4244Ter,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,; A ENST00000301067 Transcript stop_gained 12730/19419 12730/16614 4244/5537 Q/* Cag/Tag 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 39/54 HIGH 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -16.54495 1 1 1 1 0 A 4 1 12 49031975 49031975 G A 1 0 0 0 0 0 1 0 0 8298 1357 47 3 3 KMT2D 12 49031975 Nonsense_Mutation SNP G C3L-00144_T 704 49031975 84243334 1136 5207 KMT2D 0 . GRCh38 12 49044935 49044935 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4772G>T p.Trp1591Leu p.W1591L ENST00000301067 19/54 146 116 30 117 117 0 strelka-varscan-mutect KMT2D,missense_variant,p.Trp1591Leu,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; A ENST00000301067 Transcript missense_variant 4772/19419 4772/16614 1591/5537 W/L tGg/tTg 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 deleterious(0.01) 19/54 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF380 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 49044935 49044935 C A 1 0 0 0 0 1 0 0 0 8298 595 21 2 2 KMT2D 12 49044935 Missense_Mutation SNP C C3L-00144_T 12960 49044935 84230374 1137 5208 KRT7 0 . GRCh38 12 52248204 52248204 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1233G>A p.= p.V411V ENST00000331817 8/9 239 220 19 205 204 1 strelka-varscan-mutect KRT7,synonymous_variant,p.=,ENST00000331817,NM_005556.3;KRT86,upstream_gene_variant,,ENST00000553310,;RP3-416H24.1,upstream_gene_variant,,ENST00000546686,;KRT7,non_coding_transcript_exon_variant,,ENST00000552322,;KRT7,non_coding_transcript_exon_variant,,ENST00000548657,;KRT7,non_coding_transcript_exon_variant,,ENST00000550153,;KRT7,non_coding_transcript_exon_variant,,ENST00000549127,;KRT87P,downstream_gene_variant,,ENST00000529785,;KRT7,downstream_gene_variant,,ENST00000546856,;KRT7,downstream_gene_variant,,ENST00000552183,;KRT7,non_coding_transcript_exon_variant,,ENST00000549638,;KRT7,downstream_gene_variant,,ENST00000551130,;KRT87P,downstream_gene_variant,,ENST00000534226,; A ENST00000331817 Transcript synonymous_variant 1416/1754 1233/1410 411/469 V gtG/gtA 1 1 KRT7 HGNC HGNC:6445 protein_coding YES CCDS8822.1 ENSP00000329243 P08729 UPI000013CF9E NM_005556.3 8/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 52248204 52248204 G A 1 0 0 0 0 0 0 0 1 8365 1277 45 3 3 KRT7 12 52248204 Silent SNP G C3L-00144_T 3203269 52248204 81027105 1138 5209 KRT6C 0 . GRCh38 12 52469851 52469851 + Missense_Mutation SNP G G T rs759012703 C3L-00144_T C3L-00144_N G G c.1243C>A p.Arg415Ser p.R415S ENST00000252250 7/9 497 415 82 433 431 2 strelka-varscan-mutect KRT6C,missense_variant,p.Arg415Ser,ENST00000252250,NM_173086.4;KRT6C,downstream_gene_variant,,ENST00000553087,; T ENST00000252250 Transcript missense_variant 1291/2289 1243/1695 415/564 R/S Cgt/Agt rs759012703 1 -1 KRT6C HGNC HGNC:20406 protein_coding YES CCDS8829.1 ENSP00000252250 P48668 UPI00001AE73F NM_173086.4 deleterious(0) 7/9 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01276,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs759012703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 52469851 52469851 G T 1 0 0 0 0 1 0 0 0 8364 1087 38 1 1 KRT6C 12 52469851 Missense_Mutation SNP G C3L-00144_T 221647 52469851 80805458 1139 5210 KRT6A 0 . GRCh38 12 52490592 52490592 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1054G>T p.Ala352Ser p.A352S ENST00000330722 5/9 591 484 107 558 558 0 strelka-varscan-mutect KRT6A,missense_variant,p.Ala352Ser,ENST00000330722,NM_005554.3;KRT6A,non_coding_transcript_exon_variant,,ENST00000549898,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549754,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549600,;KRT6A,non_coding_transcript_exon_variant,,ENST00000548735,; A ENST00000330722 Transcript missense_variant 1123/2310 1054/1695 352/564 A/S Gct/Tct 1 -1 KRT6A HGNC HGNC:6443 protein_coding YES CCDS41786.1 ENSP00000369317 P02538 A0A0S2Z428 UPI000013CD4C NM_005554.3 deleterious(0.01) 5/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52490592 52490592 C A 1 0 0 0 0 1 0 0 0 8362 739 26 2 2 KRT6A 12 52490592 Missense_Mutation SNP C C3L-00144_T 20741 52490592 80784717 1140 5211 KRT6A 0 . GRCh38 12 52490608 52490608 + Missense_Mutation SNP C C A rs772528079 C3L-00144_T C3L-00144_N C C c.1038G>T p.Gln346His p.Q346H ENST00000330722 5/9 615 502 113 591 590 1 strelka-varscan-mutect KRT6A,missense_variant,p.Gln346His,ENST00000330722,NM_005554.3;KRT6A,non_coding_transcript_exon_variant,,ENST00000549898,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549754,;KRT6A,non_coding_transcript_exon_variant,,ENST00000549600,;KRT6A,non_coding_transcript_exon_variant,,ENST00000548735,; A ENST00000330722 Transcript missense_variant 1107/2310 1038/1695 346/564 Q/H caG/caT rs772528079 1 -1 KRT6A HGNC HGNC:6443 protein_coding YES CCDS41786.1 ENSP00000369317 P02538 A0A0S2Z428 UPI000013CD4C NM_005554.3 deleterious(0.03) 5/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs772528079 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52490608 52490608 C A 1 0 0 0 0 1 0 0 0 8362 912 32 2 2 KRT6A 12 52490608 Missense_Mutation SNP C C3L-00144_T 16 52490608 80784701 1141 5212 KRT5 0 . GRCh38 12 52519921 52519921 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.376G>T p.Gly126Cys p.G126C ENST00000252242 1/9 295 253 42 287 285 2 strelka-varscan-mutect KRT5,missense_variant,p.Gly126Cys,ENST00000252242,NM_000424.3;KRT5,missense_variant,p.Gly16Cys,ENST00000549420,;KRT5,missense_variant,p.Gly126Cys,ENST00000546577,;KRT5,missense_variant,p.Gly91Cys,ENST00000551275,;KRT5,upstream_gene_variant,,ENST00000548409,;KRT5,upstream_gene_variant,,ENST00000551188,;KRT5,non_coding_transcript_exon_variant,,ENST00000552629,;KRT5,upstream_gene_variant,,ENST00000549511,;KRT5,upstream_gene_variant,,ENST00000551013,;KRT5,upstream_gene_variant,,ENST00000547890,;KRT5,upstream_gene_variant,,ENST00000552952,; A ENST00000252242 Transcript missense_variant 767/2531 376/1773 126/590 G/C Ggc/Tgc 1 -1 KRT5 HGNC HGNC:6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 UPI000013CD4B NM_000424.3 deleterious(0.01) 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF205,hmmpanther:PTHR23239,Pfam_domain:PF16208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52519921 52519921 C A 1 0 0 0 0 1 0 0 0 8361 594 21 2 2 KRT5 12 52519921 Missense_Mutation SNP C C3L-00144_T 29313 52519921 80755388 1142 5213 KRT2 0 . GRCh38 12 52645122 52645122 + Missense_Mutation SNP G G C rs746933813 C3L-00144_T C3L-00144_N G G c.1817C>G p.Ser606Cys p.S606C ENST00000309680 9/9 384 288 96 301 301 0 strelka-varscan-mutect KRT2,missense_variant,p.Ser606Cys,ENST00000309680,NM_000423.2;KRT2,downstream_gene_variant,,ENST00000547106,; C ENST00000309680 Transcript missense_variant 1839/2403 1817/1920 606/639 S/C tCc/tGc rs746933813 1 -1 KRT2 HGNC HGNC:6439 protein_coding YES CCDS8835.1 ENSP00000310861 P35908 UPI0000367804 NM_000423.2 deleterious_low_confidence(0) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF134 MODERATE 1 SNV 1 1 PASS rs746933813 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 52645122 52645122 G C 1 0 0 0 0 1 0 0 0 8339 1174 41 4 4 KRT2 12 52645122 Missense_Mutation SNP G C3L-00144_T 125201 52645122 80630187 1143 5214 SOAT2 0 . GRCh38 12 53105600 53105600 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.315C>G p.Ile105Met p.I105M ENST00000301466 4/15 196 157 39 159 159 0 strelka-varscan-mutect SOAT2,missense_variant,p.Ile105Met,ENST00000301466,NM_003578.3;SOAT2,intron_variant,,ENST00000551896,;IGFBP6,downstream_gene_variant,,ENST00000548547,;IGFBP6,downstream_gene_variant,,ENST00000301464,NM_002178.2;IGFBP6,downstream_gene_variant,,ENST00000549628,;SOAT2,missense_variant,p.Ile105Met,ENST00000542365,;IGFBP6,downstream_gene_variant,,ENST00000548176,; G ENST00000301466 Transcript missense_variant 375/2044 315/1569 105/522 I/M atC/atG COSM3812355 1 1 SOAT2 HGNC HGNC:11178 protein_coding YES CCDS8847.1 ENSP00000301466 O75908 UPI0000135B61 NM_003578.3 tolerated(0.18) 4/15 PIRSF_domain:PIRSF000439,PIRSF_domain:PIRSF500230,hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF10 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 53105600 53105600 C G 1 0 0 0 0 1 0 0 0 15232 816 29 4 4 SOAT2 12 53105600 Missense_Mutation SNP C C3L-00144_T 460478 53105600 80169709 1144 5215 HOXC11 0 . GRCh38 12 53973392 53973392 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.151C>A p.Leu51Met p.L51M ENST00000546378 1/2 231 192 39 197 196 1 strelka-varscan-mutect HOXC11,missense_variant,p.Leu51Met,ENST00000546378,NM_014212.3;HOXC11,missense_variant,p.Leu51Met,ENST00000243082,;HOTAIR,intron_variant,,ENST00000424518,;HOTAIR,intron_variant,,ENST00000455246,;HOTAIR,upstream_gene_variant,,ENST00000439545,;AC012531.2,downstream_gene_variant,,ENST00000611375,; A ENST00000546378 Transcript missense_variant 267/3261 151/915 51/304 L/M Ctg/Atg 1 1 HOXC11 HGNC HGNC:5123 protein_coding YES CCDS8867.1 ENSP00000446680 O43248 UPI000012CF7D NM_014212.3 deleterious(0) 1/2 hmmpanther:PTHR24326:SF172,hmmpanther:PTHR24326,Pfam_domain:PF12045 MODERATE 1 SNV 1 1 PASS rs1389429092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 53973392 53973392 C A 1 0 0 0 0 1 0 0 0 7204 680 24 2 2 HOXC11 12 53973392 Missense_Mutation SNP C C3L-00144_T 867792 53973392 79301917 1145 5216 TAC3 0 . GRCh38 12 57013372 57013372 + Silent SNP T T C novel C3L-00144_T C3L-00144_N T T c.225A>G p.= p.T75T ENST00000615887 4/9 325 253 72 368 368 0 strelka-varscan-mutect TAC3,synonymous_variant,p.=,ENST00000615887,;TAC3,synonymous_variant,p.=,ENST00000458521,NM_013251.3;TAC3,synonymous_variant,p.=,ENST00000441881,NM_001178054.1;TAC3,synonymous_variant,p.=,ENST00000415231,;TAC3,synonymous_variant,p.=,ENST00000393867,;TAC3,synonymous_variant,p.=,ENST00000300108,;TAC3,synonymous_variant,p.=,ENST00000379411,;TAC3,synonymous_variant,p.=,ENST00000438756,;TAC3,synonymous_variant,p.=,ENST00000357616,;TAC3,synonymous_variant,p.=,ENST00000423597,;TAC3,non_coding_transcript_exon_variant,,ENST00000496757,; C ENST00000615887 Transcript synonymous_variant 364/1120 225/366 75/121 T acA/acG 1 -1 TAC3 HGNC HGNC:11521 protein_coding YES CCDS8928.1 ENSP00000483110 Q9UHF0 A0A024RB47 UPI00000312E8 4/9 hmmpanther:PTHR15536,hmmpanther:PTHR15536:SF1,PIRSF_domain:PIRSF001843,Prints_domain:PR01828 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 57013372 57013372 T C 1 0 0 0 0 0 0 0 1 15895 1451 51 5 5 TAC3 12 57013372 Silent SNP T C3L-00144_T 3039980 57013372 76261937 1146 5217 MYO1A 0 . GRCh38 12 57047381 57047381 + Missense_Mutation SNP C C A rs768857384 C3L-00144_T C3L-00144_N C C c.352G>T p.Val118Leu p.V118L ENST00000442789 6/29 322 302 20 277 277 0 strelka-varscan-mutect MYO1A,missense_variant,p.Val118Leu,ENST00000442789,NM_001256041.1;MYO1A,missense_variant,p.Val118Leu,ENST00000300119,NM_005379.3;MYO1A,intron_variant,,ENST00000492945,;MYO1A,downstream_gene_variant,,ENST00000433964,;MYO1A,downstream_gene_variant,,ENST00000471791,;MYO1A,5_prime_UTR_variant,,ENST00000554234,; A ENST00000442789 Transcript missense_variant 640/3658 352/3132 118/1043 V/L Gtg/Ttg rs768857384 1 -1 MYO1A HGNC HGNC:7595 protein_coding YES CCDS8929.1 ENSP00000393392 Q9UBC5 UPI000012FAC2 NM_001256041.1 tolerated(0.11) 6/29 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF291,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193 MODERATE 1 SNV 1 1 PASS rs768857384 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 57047381 57047381 C A 1 0 0 0 0 1 0 0 0 10069 478 17 2 2 MYO1A 12 57047381 Missense_Mutation SNP C C3L-00144_T 34009 57047381 76227928 1147 5218 MYO1A 0 . GRCh38 12 57048041 57048041 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.178G>T p.Glu60Ter p.E60* ENST00000442789 4/29 290 257 33 258 258 0 strelka-varscan-mutect MYO1A,stop_gained,p.Glu60Ter,ENST00000442789,NM_001256041.1;MYO1A,stop_gained,p.Glu60Ter,ENST00000300119,NM_005379.3;MYO1A,stop_gained,p.Glu60Ter,ENST00000433964,;MYO1A,intron_variant,,ENST00000492945,;MYO1A,non_coding_transcript_exon_variant,,ENST00000471791,;MYO1A,upstream_gene_variant,,ENST00000554234,; A ENST00000442789 Transcript stop_gained 466/3658 178/3132 60/1043 E/* Gag/Tag 1 -1 MYO1A HGNC HGNC:7595 protein_coding YES CCDS8929.1 ENSP00000393392 Q9UBC5 UPI000012FAC2 NM_001256041.1 4/29 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF291,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 57048041 57048041 C A 1 0 0 0 0 0 1 0 0 10069 922 32 2 2 MYO1A 12 57048041 Nonsense_Mutation SNP C C3L-00144_T 660 57048041 76227268 1148 5219 GLI1 0 . GRCh38 12 57466292 57466292 + Frame_Shift_Del DEL G G - rs368789621,rs759448855 C3L-00144_T C3L-00144_N G G c.821delG p.Gly274AlafsTer6 p.G274Afs*6 ENST00000228682 8/12 126 104 22 117 116 1 sindel-varindel GLI1,frameshift_variant,p.Gly274AlafsTer6,ENST00000228682,NM_005269.2;GLI1,frameshift_variant,p.Gly233AlafsTer6,ENST00000546141,NM_001167609.1;GLI1,frameshift_variant,p.Gly146AlafsTer6,ENST00000543426,NM_001160045.1;GLI1,frameshift_variant,p.Gly233AlafsTer6,ENST00000528467,;GLI1,frameshift_variant,p.Gly146AlafsTer6,ENST00000532291,;GLI1,downstream_gene_variant,,ENST00000528432,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; - ENST00000228682 Transcript frameshift_variant 906/3613 815/3321 272/1106 W/X tGg/tg rs368789621,rs759448855,COSM1180784 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 8/12 PROSITE_profiles:PS50157,hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818,Gene3D:3.30.160.60,SMART_domains:SM00355 0,0,1 HIGH 1 deletion 1 6 0,0,1 1 PASS . . 0 196 3 7 3 0 0 0 -13.13139 0.6960022 1 1 1 0 - 7 5 12 57466292 57466292 G - 1 0 1 0 1 0 0 0 0 6315 1357 47 0 0 GLI1 12 57466292 Frame_Shift_Del DEL G C3L-00144_T 418251 57466292 75809017 1149 5220 GLI1 0 . GRCh38 12 57470991 57470991 + Missense_Mutation SNP C C A rs192168783 C3L-00144_T C3L-00144_N C C c.2251C>A p.Leu751Met p.L751M ENST00000228682 12/12 56 48 8 37 37 0 strelka-varscan-mutect GLI1,missense_variant,p.Leu751Met,ENST00000228682,NM_005269.2;GLI1,missense_variant,p.Leu710Met,ENST00000546141,NM_001167609.1;GLI1,missense_variant,p.Leu623Met,ENST00000543426,NM_001160045.1;GLI1,missense_variant,p.Leu710Met,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,downstream_gene_variant,,ENST00000548139,;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;MARS,upstream_gene_variant,,ENST00000549133,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;GLI1,downstream_gene_variant,,ENST00000527742,;ARHGAP9,downstream_gene_variant,,ENST00000546704,; A ENST00000228682 Transcript missense_variant 2342/3613 2251/3321 751/1106 L/M Ctg/Atg rs192168783,COSM4827335 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 tolerated(0.2) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs192168783 . 0 207 3 0 0 0 0 0 -18.87587 1 1 1 1 0 A 3 1 12 57470991 57470991 C A 1 0 0 0 0 1 0 0 0 6315 912 32 2 2 GLI1 12 57470991 Missense_Mutation SNP C C3L-00144_T 4699 57470991 75804318 1150 5221 B4GALNT1 0 . GRCh38 12 57626903 57626903 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.1443G>A p.= p.V481V ENST00000341156 11/11 258 200 58 259 259 0 strelka-varscan-mutect B4GALNT1,synonymous_variant,p.=,ENST00000341156,NM_001478.4;B4GALNT1,synonymous_variant,p.=,ENST00000418555,NM_001276468.1;SLC26A10,downstream_gene_variant,,ENST00000320442,NM_133489.2;B4GALNT1,downstream_gene_variant,,ENST00000550764,NM_001276469.1;B4GALNT1,downstream_gene_variant,,ENST00000552350,;B4GALNT1,downstream_gene_variant,,ENST00000449184,;B4GALNT1,downstream_gene_variant,,ENST00000548888,;B4GALNT1,downstream_gene_variant,,ENST00000551220,;B4GALNT1,downstream_gene_variant,,ENST00000547741,;SLC26A10,downstream_gene_variant,,ENST00000490243,;SLC26A10,downstream_gene_variant,,ENST00000483647,;B4GALNT1,downstream_gene_variant,,ENST00000550943,;B4GALNT1,3_prime_UTR_variant,,ENST00000552798,;B4GALNT1,non_coding_transcript_exon_variant,,ENST00000553142,;B4GALNT1,non_coding_transcript_exon_variant,,ENST00000552468,;SLC26A10,downstream_gene_variant,,ENST00000474359,;SLC26A10,downstream_gene_variant,,ENST00000440686,;SLC26A10,downstream_gene_variant,,ENST00000487816,;B4GALNT1,downstream_gene_variant,,ENST00000551925,;B4GALNT1,downstream_gene_variant,,ENST00000549391,;SLC26A10,downstream_gene_variant,,ENST00000474791,;SLC26A10,downstream_gene_variant,,ENST00000463802,;B4GALNT1,downstream_gene_variant,,ENST00000548487,;B4GALNT1,downstream_gene_variant,,ENST00000552219,; T ENST00000341156 Transcript synonymous_variant 2028/3036 1443/1602 481/533 V gtG/gtA 1 -1 B4GALNT1 HGNC HGNC:4117 protein_coding YES CCDS8950.1 ENSP00000341562 Q00973 UPI0000126DD5 NM_001478.4 11/11 Gene3D:3.90.550.10,PIRSF_domain:PIRSF000474,hmmpanther:PTHR15046,hmmpanther:PTHR15046:SF1,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 57626903 57626903 C T 1 0 0 0 0 0 0 0 1 1422 581 21 3 3 B4GALNT1 12 57626903 Silent SNP C C3L-00144_T 155912 57626903 75648406 1151 5222 AGAP2 0 . GRCh38 12 57732873 57732873 + Silent SNP C C G rs545156621 C3L-00144_T C3L-00144_N C C c.1656G>C p.= p.G552G ENST00000547588 6/19 227 197 30 177 177 0 strelka-varscan-mutect AGAP2,synonymous_variant,p.=,ENST00000257897,NM_014770.3;AGAP2,synonymous_variant,p.=,ENST00000328568,;AGAP2,synonymous_variant,p.=,ENST00000547588,NM_001122772.2;AGAP2,upstream_gene_variant,,ENST00000549129,;AGAP2-AS1,downstream_gene_variant,,ENST00000542466,; G ENST00000547588 Transcript synonymous_variant 1656/3579 1656/3579 552/1192 G ggG/ggC rs545156621 1 -1 AGAP2 HGNC HGNC:16921 protein_coding YES CCDS44932.1 ENSP00000449241 F8VVT9 UPI00001AF80C NM_001122772.2 6/19 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51419,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF256,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs545156621 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 2 3 12 57732873 57732873 C G 1 0 0 0 0 0 0 0 1 445 726 26 4 4 AGAP2 12 57732873 Silent SNP C C3L-00144_T 105970 57732873 75542436 1152 5223 AGAP2 0 . GRCh38 12 57742038 57742038 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.34G>T p.Val12Leu p.V12L ENST00000257897 1/18 126 106 20 134 134 0 strelka-varscan-mutect AGAP2,missense_variant,p.Val12Leu,ENST00000257897,NM_014770.3;AGAP2,upstream_gene_variant,,ENST00000328568,;AGAP2,upstream_gene_variant,,ENST00000547588,NM_001122772.2;TSPAN31,upstream_gene_variant,,ENST00000547992,;TSPAN31,upstream_gene_variant,,ENST00000257910,NM_005981.3;TSPAN31,upstream_gene_variant,,ENST00000552816,;TSPAN31,upstream_gene_variant,,ENST00000548167,;TSPAN31,upstream_gene_variant,,ENST00000547472,;TSPAN31,intron_variant,,ENST00000553221,;TSPAN31,intron_variant,,ENST00000550528,;TSPAN31,intron_variant,,ENST00000547311,;TSPAN31,upstream_gene_variant,,ENST00000548093,;TSPAN31,upstream_gene_variant,,ENST00000550791,;TSPAN31,upstream_gene_variant,,ENST00000546993,;TSPAN31,upstream_gene_variant,,ENST00000549052,;TSPAN31,upstream_gene_variant,,ENST00000546922,;TSPAN31,upstream_gene_variant,,ENST00000553089,; A ENST00000257897 Transcript missense_variant 120/5388 34/2511 12/836 V/L Gtg/Ttg 1 -1 AGAP2 HGNC HGNC:16921 protein_coding CCDS8951.1 ENSP00000257897 Q99490 A0A024RB55 UPI00000012B8 NM_014770.3 deleterious(0.01) 1/18 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 57742038 57742038 C A 1 0 0 0 0 1 0 0 0 445 565 20 2 2 AGAP2 12 57742038 Missense_Mutation SNP C C3L-00144_T 9165 57742038 75533271 1153 5224 AVPR1A 0 . GRCh38 12 63150095 63150095 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.742C>T p.Arg248Cys p.R248C ENST00000299178 1/2 365 287 78 328 328 0 strelka-varscan-mutect AVPR1A,missense_variant,p.Arg248Cys,ENST00000299178,NM_000706.4;AVPR1A,missense_variant,p.Arg29Cys,ENST00000550940,;RP11-715H19.2,upstream_gene_variant,,ENST00000624438,; A ENST00000299178 Transcript missense_variant 848/5963 742/1257 248/418 R/C Cgc/Tgc COSM1747188 1 -1 AVPR1A HGNC HGNC:895 protein_coding YES CCDS8965.1 ENSP00000299178 P37288 X5D2B0 UPI0000050439 NM_000706.4 deleterious(0.01) 1/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF17,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 63150095 63150095 G A 1 0 0 0 0 1 0 0 0 1387 1116 39 1 1 AVPR1A 12 63150095 Missense_Mutation SNP G C3L-00144_T 5408057 63150095 70125214 1154 5225 AVPR1A 0 . GRCh38 12 63150728 63150728 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.109G>T p.Glu37Ter p.E37* ENST00000299178 1/2 209 178 31 201 201 0 strelka-varscan-mutect AVPR1A,stop_gained,p.Glu37Ter,ENST00000299178,NM_000706.4;AVPR1A,upstream_gene_variant,,ENST00000550940,;RP11-715H19.2,upstream_gene_variant,,ENST00000624438,; A ENST00000299178 Transcript stop_gained 215/5963 109/1257 37/418 E/* Gag/Tag 1 -1 AVPR1A HGNC HGNC:895 protein_coding YES CCDS8965.1 ENSP00000299178 P37288 X5D2B0 UPI0000050439 NM_000706.4 1/2 hmmpanther:PTHR24241:SF17,hmmpanther:PTHR24241,Prints_domain:PR00752 HIGH 1 SNV 1 1 PASS rs1297557645 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 63150728 63150728 C A 1 0 0 0 0 0 1 0 0 1387 864 30 2 2 AVPR1A 12 63150728 Nonsense_Mutation SNP C C3L-00144_T 633 63150728 70124581 1155 5226 TBK1 0 . GRCh38 12 64466926 64466926 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.384G>T p.Glu128Asp p.E128D ENST00000331710 5/21 80 67 13 72 72 0 strelka-varscan-mutect TBK1,missense_variant,p.Glu128Asp,ENST00000331710,NM_013254.3;TBK1,downstream_gene_variant,,ENST00000538890,;TBK1,downstream_gene_variant,,ENST00000540417,;TBK1,downstream_gene_variant,,ENST00000539810,; T ENST00000331710 Transcript missense_variant 723/3256 384/2190 128/729 E/D gaG/gaT 1 1 TBK1 HGNC HGNC:11584 protein_coding YES CCDS8968.1 ENSP00000329967 Q9UHD2 UPI0000035B47 NM_013254.3 deleterious(0.03) 5/21 PROSITE_profiles:PS50011,hmmpanther:PTHR22969:SF14,hmmpanther:PTHR22969,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 64466926 64466926 G T 1 0 0 0 0 1 0 0 0 16042 933 33 2 2 TBK1 12 64466926 Missense_Mutation SNP G C3L-00144_T 1316198 64466926 68808383 1156 5227 NUP107 0 . GRCh38 12 68690694 68690694 + Missense_Mutation SNP G G C rs779902780 C3L-00144_T C3L-00144_N G G c.251G>C p.Gly84Ala p.G84A ENST00000229179 4/28 220 198 22 160 160 0 strelka-varscan-mutect NUP107,missense_variant,p.Gly84Ala,ENST00000229179,NM_020401.2;NUP107,missense_variant,p.Gly55Ala,ENST00000539906,;NUP107,5_prime_UTR_variant,,ENST00000378905,;NUP107,5_prime_UTR_variant,,ENST00000538549,;RP11-637A17.2,upstream_gene_variant,,ENST00000500695,;RP11-637A17.2,upstream_gene_variant,,ENST00000502102,;RP11-637A17.2,upstream_gene_variant,,ENST00000433116,;NUP107,non_coding_transcript_exon_variant,,ENST00000537598,;NUP107,non_coding_transcript_exon_variant,,ENST00000535333,;NUP107,missense_variant,p.Gly84Ala,ENST00000535718,;NUP107,non_coding_transcript_exon_variant,,ENST00000545140,;NUP107,non_coding_transcript_exon_variant,,ENST00000539373,;NUP107,downstream_gene_variant,,ENST00000540453,;RPL7P42,downstream_gene_variant,,ENST00000481005,; C ENST00000229179 Transcript missense_variant 583/6457 251/2778 84/925 G/A gGg/gCg rs779902780 1 1 NUP107 HGNC HGNC:29914 protein_coding YES CCDS8985.1 ENSP00000229179 P57740 UPI000012FC0B NM_020401.2 tolerated_low_confidence(0.65) 4/28 hmmpanther:PTHR13003 MODERATE 1 SNV 1 1 PASS rs779902780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 68690694 68690694 G C 1 0 0 0 0 1 0 0 0 10818 1232 43 4 4 NUP107 12 68690694 Missense_Mutation SNP G C3L-00144_T 4223768 68690694 64584615 1157 5228 LRRC10 0 . GRCh38 12 69610355 69610355 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.484C>A p.Gln162Lys p.Q162K ENST00000361484 1/1 136 119 17 135 135 0 strelka-varscan-mutect LRRC10,missense_variant,p.Gln162Lys,ENST00000361484,NM_201550.3; T ENST00000361484 Transcript missense_variant 808/2599 484/834 162/277 Q/K Cag/Aag 1 -1 LRRC10 HGNC HGNC:20264 protein_coding YES CCDS31856.1 ENSP00000355166 Q5BKY1 UPI00001D79A1 NM_201550.3 tolerated(0.27) 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,Low_complexity_(Seg):seg,SMART_domains:SM00364,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 69610355 69610355 G T 1 0 0 0 0 1 0 0 0 8863 1357 47 2 2 LRRC10 12 69610355 Missense_Mutation SNP G C3L-00144_T 919661 69610355 63664954 1158 5229 PTPRB 0 . GRCh38 12 70622598 70622598 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.500C>A p.Pro167Gln p.P167Q ENST00000334414 3/34 145 115 30 176 175 1 strelka-varscan-mutect PTPRB,missense_variant,p.Pro167Gln,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Pro167Gln,ENST00000550358,;PTPRB,missense_variant,p.Pro166Gln,ENST00000551525,;PTPRB,intron_variant,,ENST00000548122,;PTPRB,non_coding_transcript_exon_variant,,ENST00000538174,;PTPRB,non_coding_transcript_exon_variant,,ENST00000552253,; T ENST00000334414 Transcript missense_variant 545/12316 500/6648 167/2215 P/Q cCa/cAa 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious_low_confidence(0.02) 3/34 MODERATE 1 SNV 1 1 PASS rs1203383436 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 70622598 70622598 G T 1 0 0 0 0 1 0 0 0 12950 1348 47 2 2 PTPRB 12 70622598 Missense_Mutation SNP G C3L-00144_T 1012243 70622598 62652711 1159 5230 LGR5 0 . GRCh38 12 71584629 71584629 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2619C>A p.Ser873Arg p.S873R ENST00000266674 18/18 280 249 31 240 240 0 strelka-varscan-mutect LGR5,missense_variant,p.Ser873Arg,ENST00000266674,NM_003667.3;LGR5,missense_variant,p.Ser849Arg,ENST00000540815,NM_001277226.1;LGR5,missense_variant,p.Ser801Arg,ENST00000536515,NM_001277227.1;RP11-186F10.2,upstream_gene_variant,,ENST00000546601,;LGR5,non_coding_transcript_exon_variant,,ENST00000550851,; A ENST00000266674 Transcript missense_variant 2930/4611 2619/2724 873/907 S/R agC/agA 1 1 LGR5 HGNC HGNC:4504 protein_coding YES CCDS9000.1 ENSP00000266674 O75473 A0A0A8K8C7 UPI000004B65C NM_003667.3 tolerated(0.13) 18/18 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF259 MODERATE 1 SNV 1 1 PASS rs1157226820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 71584629 71584629 C A 1 0 0 0 0 1 0 0 0 8667 796 28 2 2 LGR5 12 71584629 Missense_Mutation SNP C C3L-00144_T 962031 71584629 61690680 1160 5231 TMEM19 0 . GRCh38 12 71697302 71697302 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.405G>T p.Gln135His p.Q135H ENST00000266673 4/6 361 321 40 304 301 3 strelka-varscan-mutect TMEM19,missense_variant,p.Gln135His,ENST00000266673,NM_018279.3;TMEM19,missense_variant,p.Gln135His,ENST00000549735,;TMEM19,missense_variant,p.Gln135His,ENST00000550524,;TMEM19,missense_variant,p.Gln34His,ENST00000546677,;TMEM19,upstream_gene_variant,,ENST00000550787,;TMEM19,upstream_gene_variant,,ENST00000546795,;RP11-293I14.2,3_prime_UTR_variant,,ENST00000548802,; T ENST00000266673 Transcript missense_variant 999/5656 405/1011 135/336 Q/H caG/caT 1 1 TMEM19 HGNC HGNC:25605 protein_coding YES CCDS9002.1 ENSP00000266673 Q96HH6 A0A024RBA1 UPI000006EFAF NM_018279.3 deleterious(0.02) 4/6 Pfam_domain:PF01940,hmmpanther:PTHR13353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 71697302 71697302 G T 1 0 0 0 0 1 0 0 0 16555 991 35 2 2 TMEM19 12 71697302 Missense_Mutation SNP G C3L-00144_T 112673 71697302 61578007 1161 5232 TMEM19 0 . GRCh38 12 71700836 71700836 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.852G>T p.Leu284Phe p.L284F ENST00000266673 6/6 100 90 10 101 101 0 strelka-varscan-mutect TMEM19,missense_variant,p.Leu284Phe,ENST00000266673,NM_018279.3;TMEM19,missense_variant,p.Leu100Phe,ENST00000550787,;TMEM19,missense_variant,p.Leu128Phe,ENST00000546795,;TMEM19,downstream_gene_variant,,ENST00000549735,;TMEM19,downstream_gene_variant,,ENST00000550524,;TMEM19,downstream_gene_variant,,ENST00000546677,;RP11-293I14.2,downstream_gene_variant,,ENST00000548802,; T ENST00000266673 Transcript missense_variant 1446/5656 852/1011 284/336 L/F ttG/ttT 1 1 TMEM19 HGNC HGNC:25605 protein_coding YES CCDS9002.1 ENSP00000266673 Q96HH6 A0A024RBA1 UPI000006EFAF NM_018279.3 tolerated(0.87) 6/6 Pfam_domain:PF01940,hmmpanther:PTHR13353 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 71700836 71700836 G T 1 0 0 0 0 1 0 0 0 16555 1362 47 2 2 TMEM19 12 71700836 Missense_Mutation SNP G C3L-00144_T 3534 71700836 61574473 1162 5233 TRHDE 0 . GRCh38 12 72378044 72378044 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1103A>C p.Tyr368Ser p.Y368S ENST00000261180 3/19 248 206 42 214 214 0 strelka-varscan-mutect TRHDE,missense_variant,p.Tyr368Ser,ENST00000261180,NM_013381.2;TRHDE,intron_variant,,ENST00000547300,;TRHDE,non_coding_transcript_exon_variant,,ENST00000548156,; C ENST00000261180 Transcript missense_variant 1199/10733 1103/3075 368/1024 Y/S tAt/tCt 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0) 3/19 Pfam_domain:PF01433,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 72378044 72378044 A C 1 0 0 0 0 1 0 0 0 16968 449 16 5 5 TRHDE 12 72378044 Missense_Mutation SNP A C3L-00144_T 677208 72378044 60897265 1163 5234 NAP1L1 0 . GRCh38 12 76060155 76060155 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.331C>T p.Gln111Ter p.Q111* ENST00000618691 5/15 140 112 28 115 114 1 strelka-varscan-mutect NAP1L1,stop_gained,p.Gln111Ter,ENST00000618691,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000261182,NM_139207.2,NM_004537.4;NAP1L1,stop_gained,p.Gln70Ter,ENST00000431879,;NAP1L1,stop_gained,p.Gln105Ter,ENST00000552056,;NAP1L1,stop_gained,p.Gln48Ter,ENST00000547773,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000393263,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000549596,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000535020,NM_001307924.1;NAP1L1,stop_gained,p.Gln70Ter,ENST00000542344,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000552342,;NAP1L1,stop_gained,p.Gln70Ter,ENST00000548044,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000551992,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000550934,;NAP1L1,stop_gained,p.Gln70Ter,ENST00000548273,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000551600,;NAP1L1,stop_gained,p.Gln111Ter,ENST00000547704,;NAP1L1,stop_gained,p.Gln137Ter,ENST00000547479,;NAP1L1,stop_gained,p.Gln70Ter,ENST00000551524,;NAP1L1,5_prime_UTR_variant,,ENST00000544816,;NAP1L1,stop_gained,p.Gln73Ter,ENST00000552147,;NAP1L1,stop_gained,p.Gln51Ter,ENST00000547529,;NAP1L1,non_coding_transcript_exon_variant,,ENST00000549988,;NAP1L1,upstream_gene_variant,,ENST00000547993,;RP11-290L1.4,downstream_gene_variant,,ENST00000552477,; A ENST00000618691 Transcript stop_gained 818/13505 331/1176 111/391 Q/* Cag/Tag 1 -1 NAP1L1 HGNC HGNC:7637 protein_coding YES CCDS9013.1 ENSP00000477538 P55209 A0A024RBB7 UPI0000052A55 5/15 hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF70,Pfam_domain:PF00956,Superfamily_domains:SSF143113 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 76060155 76060155 G A 1 0 0 0 0 0 1 0 0 10165 1299 45 3 3 NAP1L1 12 76060155 Nonsense_Mutation SNP G C3L-00144_T 3682111 76060155 57215154 1164 5235 NAV3 0 . GRCh38 12 78050049 78050049 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2080C>A p.Gln694Lys p.Q694K ENST00000397909 10/40 260 230 30 237 237 0 strelka-varscan-mutect NAV3,missense_variant,p.Gln694Lys,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Gln694Lys,ENST00000536525,NM_014903.5;NAV3,downstream_gene_variant,,ENST00000549464,;RP11-136F16.1,downstream_gene_variant,,ENST00000549103,; A ENST00000397909 Transcript missense_variant 2253/9821 2080/7158 694/2385 Q/K Cag/Aag 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 10/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 78050049 78050049 C A 1 0 0 0 0 1 0 0 0 10194 711 25 2 2 NAV3 12 78050049 Missense_Mutation SNP C C3L-00144_T 1989894 78050049 55225260 1165 5236 TMTC2 0 . GRCh38 12 82857527 82857527 + Missense_Mutation SNP G G C rs764991903 C3L-00144_T C3L-00144_N G G c.601G>C p.Val201Leu p.V201L ENST00000321196 2/12 92 82 10 122 122 0 strelka-varscan-mutect TMTC2,missense_variant,p.Val195Leu,ENST00000549919,;TMTC2,missense_variant,p.Val201Leu,ENST00000321196,NM_152588.1;TMTC2,missense_variant,p.Val201Leu,ENST00000548305,NM_001320322.1;TMTC2,non_coding_transcript_exon_variant,,ENST00000551915,;TMTC2,intron_variant,,ENST00000546590,NM_001320321.1; C ENST00000321196 Transcript missense_variant 1308/5681 601/2511 201/836 V/L Gtc/Ctc rs764991903 1 1 TMTC2 HGNC HGNC:25440 protein_coding YES CCDS9025.1 ENSP00000322300 Q8N394 UPI0000073F0F NM_152588.1 tolerated(0.62) 2/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF390 MODERATE 1 SNV 1 1 PASS rs764991903 . 0 202 6 2 0 0 0 0 -16.08572 0.9998456 1 1 1 0 C 3 2 12 82857527 82857527 G C 1 0 0 0 0 1 0 0 0 16735 1377 48 4 4 TMTC2 12 82857527 Missense_Mutation SNP G C3L-00144_T 4807478 82857527 50417782 1166 5237 MGAT4C 0 . GRCh38 12 85980197 85980197 + Nonsense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.529G>T p.Glu177Ter p.E177* ENST00000611864 4/4 155 126 29 126 125 1 strelka-varscan-mutect MGAT4C,stop_gained,p.Glu177Ter,ENST00000611864,;MGAT4C,stop_gained,p.Glu177Ter,ENST00000620241,;MGAT4C,stop_gained,p.Glu177Ter,ENST00000621808,NM_013244.3;MGAT4C,stop_gained,p.Glu177Ter,ENST00000548651,;MGAT4C,stop_gained,p.Glu177Ter,ENST00000552808,;MGAT4C,stop_gained,p.Glu177Ter,ENST00000547225,;MGAT4C,intron_variant,,ENST00000552435,; A ENST00000611864 Transcript stop_gained 585/25116 529/1437 177/478 E/* Gag/Tag COSM3466177,COSM4897993 1 -1 MGAT4C HGNC HGNC:30871 protein_coding YES CCDS9030.1 ENSP00000481096 Q9UBM8 UPI00001B002C 4/4 Pfam_domain:PF04666,hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF14 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 85980197 85980197 C A 1 0 0 0 0 0 1 0 0 9507 864 30 2 2 MGAT4C 12 85980197 Nonsense_Mutation SNP C C3L-00144_T 3122670 85980197 47295112 1167 5238 DCN 0 . GRCh38 12 91151789 91151790 + Frame_Shift_Ins INS - - A novel C3L-00144_T C3L-00144_N - - c.749dupT p.Leu250PhefsTer12 p.L250Ffs*12 ENST00000052754 7/8 353 300 53 345 345 0 sindel-varindel-pindel DCN,frameshift_variant,p.Leu250PhefsTer12,ENST00000052754,NM_001920.3;DCN,frameshift_variant,p.Leu250PhefsTer12,ENST00000393155,NM_133503.2;DCN,frameshift_variant,p.Leu250PhefsTer12,ENST00000552962,;DCN,frameshift_variant,p.Leu103PhefsTer12,ENST00000425043,NM_133505.2;DCN,frameshift_variant,p.Leu20PhefsTer12,ENST00000550758,;DCN,frameshift_variant,p.Leu103PhefsTer12,ENST00000547568,;DCN,frameshift_variant,p.Leu141PhefsTer12,ENST00000420120,NM_133504.2;DCN,frameshift_variant,p.Leu103PhefsTer12,ENST00000546391,;DCN,intron_variant,,ENST00000441303,NM_133506.2;DCN,intron_variant,,ENST00000456569,NM_133507.2; A ENST00000052754 Transcript frameshift_variant 1251-1252/7156 749-750/1080 250/359 L/FX ttg/ttTg 1 -1 DCN HGNC HGNC:2705 protein_coding YES CCDS9039.1 ENSP00000052754 P07585 Q6FH10 UPI000013187E NM_001920.3 7/8 Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF5,PIRSF_domain:PIRSF002490,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 12 91151789 91151789 - A 1 0 1 1 0 0 0 0 0 4099 608 21 0 0 DCN 12 91151789 Frame_Shift_Ins INS - C3L-00144_T 5171592 91151789 42123520 1168 5239 C12orf74 0 . GRCh38 12 92707138 92707138 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.507G>T p.Gln169His p.Q169H ENST00000397833 2/3 92 69 23 73 73 0 strelka-varscan-mutect C12orf74,missense_variant,p.Gln169His,ENST00000544406,NM_001178097.2;C12orf74,missense_variant,p.Gln169His,ENST00000397833,NM_001037671.3; T ENST00000397833 Transcript missense_variant,splice_region_variant 958/1856 507/573 169/190 Q/H caG/caT 1 1 C12orf74 HGNC HGNC:27887 protein_coding YES CCDS41819.1 ENSP00000380933 Q32Q52 UPI00005DB386 NM_001037671.3 deleterious(0) 2/3 Pfam_domain:PF15720,hmmpanther:PTHR41399 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 92707138 92707138 G T 1 0 0 0 0 1 0 0 0 1823 1014 35 2 2 C12orf74 12 92707138 Missense_Mutation SNP G C3L-00144_T 1555349 92707138 40568171 1169 5240 FGD6 0 . GRCh38 12 95209020 95209020 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2264A>T p.Glu755Val p.E755V ENST00000343958 2/21 385 335 50 361 361 0 strelka-varscan-mutect FGD6,missense_variant,p.Glu755Val,ENST00000343958,NM_018351.3;FGD6,missense_variant,p.Glu755Val,ENST00000546711,;FGD6,missense_variant,p.Glu755Val,ENST00000549499,;FGD6,upstream_gene_variant,,ENST00000550368,;FGD6,intron_variant,,ENST00000451107,; A ENST00000343958 Transcript missense_variant 2488/9288 2264/4293 755/1430 E/V gAg/gTg 1 -1 FGD6 HGNC HGNC:21740 protein_coding YES CCDS31878.1 ENSP00000344446 Q6ZV73 UPI00001FB2F4 NM_018351.3 deleterious(0) 2/21 hmmpanther:PTHR12673:SF12,hmmpanther:PTHR12673 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 95209020 95209020 T A 1 0 0 0 0 1 0 0 0 5701 1551 54 4 4 FGD6 12 95209020 Missense_Mutation SNP T C3L-00144_T 2501882 95209020 38066289 1170 5241 ANKS1B 0 . GRCh38 12 98781193 98781193 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.3290A>T p.Glu1097Val p.E1097V ENST00000547776 23/26 159 130 29 113 113 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Glu1097Val,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Glu287Val,ENST00000550693,NM_001204069.1;ANKS1B,missense_variant,p.Glu347Val,ENST00000549493,NM_181670.3;ANKS1B,missense_variant,p.Glu195Val,ENST00000549025,NM_001204066.1;ANKS1B,missense_variant,p.Glu613Val,ENST00000547010,;ANKS1B,missense_variant,p.Glu263Val,ENST00000549558,NM_020140.3;ANKS1B,missense_variant,p.Glu103Val,ENST00000341752,NM_001204081.1;ANKS1B,missense_variant,p.Glu369Val,ENST00000550778,;ANKS1B,missense_variant,p.Glu232Val,ENST00000547446,NM_001204067.1;ANKS1B,missense_variant,p.Glu127Val,ENST00000333732,NM_001204079.1,NM_001204080.1,NM_001204065.1;ANKS1B,missense_variant,p.Glu323Val,ENST00000546960,NM_001204068.1;ANKS1B,missense_variant,p.Glu263Val,ENST00000546568,NM_001204070.1;ANKS1B,missense_variant,p.Glu126Val,ENST00000546364,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000549315,;ANKS1B,missense_variant,p.Ser106Cys,ENST00000547362,; A ENST00000547776 Transcript missense_variant 3290/3885 3290/3747 1097/1248 E/V gAg/gTg 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 deleterious(0) 23/26 Gene3D:2.30.29.30,Pfam_domain:PF00640,PROSITE_profiles:PS01179,hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 98781193 98781193 T A 1 0 0 0 0 1 0 0 0 795 1551 54 4 4 ANKS1B 12 98781193 Missense_Mutation SNP T C3L-00144_T 3572173 98781193 34494116 1171 5242 ANO4 0 . GRCh38 12 100971352 100971352 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.503C>G p.Pro168Arg p.P168R ENST00000392977 6/28 233 215 18 166 166 0 strelka-varscan-mutect ANO4,missense_variant,p.Pro133Arg,ENST00000392979,NM_178826.3;ANO4,missense_variant,p.Pro168Arg,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,missense_variant,p.Pro168Arg,ENST00000549155,; G ENST00000392977 Transcript missense_variant 713/3509 503/2868 168/955 P/R cCa/cGa 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 deleterious(0) 6/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF16178 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 100971352 100971352 C G 1 0 0 0 0 1 0 0 0 806 594 21 4 4 ANO4 12 100971352 Missense_Mutation SNP C C3L-00144_T 2190159 100971352 32303957 1172 5243 MYBPC1 0 . GRCh38 12 101629437 101629437 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.107G>T p.Trp36Leu p.W36L ENST00000452455 4/30 448 410 38 393 391 2 strelka-varscan-mutect MYBPC1,missense_variant,p.Trp49Leu,ENST00000549145,;MYBPC1,missense_variant,p.Trp61Leu,ENST00000361466,NM_002465.3;MYBPC1,missense_variant,p.Trp61Leu,ENST00000361685,NM_206819.2;MYBPC1,missense_variant,p.Trp36Leu,ENST00000452455,NM_001254718.1;MYBPC1,missense_variant,p.Trp10Leu,ENST00000547405,NM_001254722.1;MYBPC1,missense_variant,p.Trp36Leu,ENST00000553190,NM_206821.2;MYBPC1,missense_variant,p.Trp22Leu,ENST00000547509,;MYBPC1,missense_variant,p.Trp23Leu,ENST00000392934,NM_001254723.1;MYBPC1,missense_variant,p.Trp36Leu,ENST00000545503,NM_001254719.1;MYBPC1,missense_variant,p.Trp24Leu,ENST00000541119,NM_001254720.1;MYBPC1,missense_variant,p.Trp36Leu,ENST00000536007,NM_001254721.1;MYBPC1,missense_variant,p.Trp36Leu,ENST00000550270,NM_206820.2;MYBPC1,5_prime_UTR_variant,,ENST00000551300,;MYBPC1,5_prime_UTR_variant,,ENST00000550514,;MYBPC1,intron_variant,,ENST00000550501,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000550312,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000548834,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000552198,;MYBPC1,downstream_gene_variant,,ENST00000547627,; T ENST00000452455 Transcript missense_variant 209/3861 107/3522 36/1173 W/L tGg/tTg 1 1 MYBPC1 HGNC HGNC:7549 protein_coding YES CCDS58268.1 ENSP00000400908 Q00872 UPI0001AE6B26 NM_001254718.1 tolerated(0.31) 4/30 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101629437 101629437 G T 1 0 0 0 0 1 0 0 0 10011 1362 47 2 2 MYBPC1 12 101629437 Missense_Mutation SNP G C3L-00144_T 658085 101629437 31645872 1173 5244 STAB2 0 . GRCh38 12 103758238 103758238 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.7056C>A p.= p.S2352S ENST00000388887 64/69 262 247 15 262 261 1 strelka-varscan-mutect STAB2,synonymous_variant,p.=,ENST00000388887,NM_017564.9;RP11-341G23.4,intron_variant,,ENST00000551299,;STAB2,non_coding_transcript_exon_variant,,ENST00000548073,;STAB2,non_coding_transcript_exon_variant,,ENST00000548579,; A ENST00000388887 Transcript synonymous_variant 7260/8251 7056/7656 2352/2551 S tcC/tcA 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 64/69 PROSITE_profiles:PS50213,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Superfamily_domains:SSF82153 LOW 1 SNV 1 1 PASS rs960154535 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 103758238 103758238 C A 1 0 0 0 0 0 0 0 1 15616 581 21 2 2 STAB2 12 103758238 Silent SNP C C3L-00144_T 2128801 103758238 29517071 1174 5245 SLC41A2 0 . GRCh38 12 104805168 104805168 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1706G>A p.Gly569Glu p.G569E ENST00000258538 10/10 65 51 14 63 63 0 strelka-varscan-mutect SLC41A2,missense_variant,p.Gly569Glu,ENST00000258538,NM_032148.3;SLC41A2,non_coding_transcript_exon_variant,,ENST00000549713,; T ENST00000258538 Transcript missense_variant 1834/4449 1706/1722 569/573 G/E gGa/gAa 1 -1 SLC41A2 HGNC HGNC:31045 protein_coding YES CCDS9100.2 ENSP00000258538 Q96JW4 UPI00001FB431 NM_032148.3 tolerated(0.06) 10/10 hmmpanther:PTHR16228,hmmpanther:PTHR16228:SF25 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 104805168 104805168 C T 1 0 0 0 0 1 0 0 0 14908 855 30 3 3 SLC41A2 12 104805168 Missense_Mutation SNP C C3L-00144_T 1046930 104805168 28470141 1175 5246 RFX4 0 . GRCh38 12 106720041 106720041 + Missense_Mutation SNP G G A rs773180417 C3L-00144_T C3L-00144_N G G c.1247G>A p.Arg416His p.R416H ENST00000357881 12/18 150 130 20 133 132 1 strelka-varscan-mutect RFX4,missense_variant,p.Arg407His,ENST00000392842,NM_213594.2;RFX4,missense_variant,p.Arg313His,ENST00000229387,NM_032491.5;RFX4,missense_variant,p.Arg416His,ENST00000357881,NM_001206691.1;RFX4,downstream_gene_variant,,ENST00000539967,;RP11-482D24.3,intron_variant,,ENST00000552415,;RP11-144F15.1,intron_variant,,ENST00000551505,;RP11-144F15.1,intron_variant,,ENST00000549203,;RFX4,non_coding_transcript_exon_variant,,ENST00000536688,;RFX4,downstream_gene_variant,,ENST00000536722,; A ENST00000357881 Transcript missense_variant 1387/2565 1247/2235 416/744 R/H cGc/cAc rs773180417 1 1 RFX4 HGNC HGNC:9985 protein_coding YES CCDS55880.1 ENSP00000350552 Q33E94 UPI00001FB460 NM_001206691.1 tolerated(0.13) 12/18 hmmpanther:PTHR12619:SF25,hmmpanther:PTHR12619 MODERATE 1 SNV 1 1 PASS rs773180417 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 106720041 106720041 G A 1 0 0 0 0 1 0 0 0 13439 1087 38 1 1 RFX4 12 106720041 Missense_Mutation SNP G C3L-00144_T 1914873 106720041 26555268 1176 5247 PWP1 0 . GRCh38 12 107710501 107710501 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1387G>T p.Val463Phe p.V463F ENST00000412830 14/15 174 163 11 115 115 0 strelka-varscan-mutect PWP1,missense_variant,p.Val463Phe,ENST00000412830,NM_001317962.1,NM_007062.1;PWP1,missense_variant,p.Val401Phe,ENST00000541166,; T ENST00000412830 Transcript missense_variant 1555/2621 1387/1506 463/501 V/F Gtc/Ttc 1 1 PWP1 HGNC HGNC:17015 protein_coding YES CCDS9114.1 ENSP00000387365 Q13610 A0A024RBH5 UPI0000132B9C NM_001317962.1,NM_007062.1 tolerated(0.11) 14/15 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR14091 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 107710501 107710501 G T 1 0 0 0 0 1 0 0 0 12997 1029 36 2 2 PWP1 12 107710501 Missense_Mutation SNP G C3L-00144_T 990460 107710501 25564808 1177 5248 ASCL4 0 . GRCh38 12 107775278 107775278 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.63C>A p.= p.P21P ENST00000342331 1/1 209 166 43 185 184 1 strelka-varscan-mutect ASCL4,synonymous_variant,p.=,ENST00000342331,NM_203436.2; A ENST00000342331 Transcript synonymous_variant 894/2260 63/522 21/173 P ccC/ccA 1 1 ASCL4 HGNC HGNC:24311 protein_coding YES CCDS31894.2 ENSP00000345420 Q6XD76 UPI00001973FA NM_203436.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR13935,hmmpanther:PTHR13935:SF51 LOW 1 SNV 1 PASS rs1262408633 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 107775278 107775278 C A 1 0 0 0 0 0 0 0 1 1178 610 22 2 2 ASCL4 12 107775278 Silent SNP C C3L-00144_T 64777 107775278 25500031 1178 5249 CMKLR1 0 . GRCh38 12 108292477 108292477 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.486C>G p.= p.V162V ENST00000312143 3/3 141 131 10 108 108 0 strelka-varscan-mutect CMKLR1,synonymous_variant,p.=,ENST00000312143,NM_001142344.1;CMKLR1,synonymous_variant,p.=,ENST00000412676,NM_001142345.1;CMKLR1,synonymous_variant,p.=,ENST00000550402,NM_001142343.1;CMKLR1,synonymous_variant,p.=,ENST00000552995,NM_004072.2;CMKLR1,downstream_gene_variant,,ENST00000550573,;CMKLR1,downstream_gene_variant,,ENST00000549466,; C ENST00000312143 Transcript synonymous_variant 850/5283 486/1122 162/373 V gtC/gtG 1 -1 CMKLR1 HGNC HGNC:2121 protein_coding YES CCDS44965.1 ENSP00000311733 Q99788 UPI0000127BD4 NM_001142344.1 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF696,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 108292477 108292477 G C 1 0 0 0 0 0 0 0 1 3354 1277 45 4 4 CMKLR1 12 108292477 Silent SNP G C3L-00144_T 517199 108292477 24982832 1179 5250 SDS 0 . GRCh38 12 113398835 113398835 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.205G>T p.Gly69Cys p.G69C ENST00000257549 4/8 65 55 10 88 88 0 strelka-varscan-mutect SDS,missense_variant,p.Gly69Cys,ENST00000257549,NM_006843.2;SDS,missense_variant,p.Gly163Cys,ENST00000547342,;SDS,intron_variant,,ENST00000552280,;SDS,non_coding_transcript_exon_variant,,ENST00000553112,;SDS,downstream_gene_variant,,ENST00000546639,;SDS,downstream_gene_variant,,ENST00000546785,; A ENST00000257549 Transcript missense_variant 328/1606 205/987 69/328 G/C Ggc/Tgc 1 -1 SDS HGNC HGNC:10691 protein_coding YES CCDS9169.1 ENSP00000257549 P20132 UPI000013CF6B NM_006843.2 deleterious(0) 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10314:SF103,hmmpanther:PTHR10314,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 MODERATE 1 SNV 2 1 PASS rs1232014554 . 0 208 2 0 0 0 0 0 -19.99958 1 1 1 1 0 A 3 1 12 113398835 113398835 C A 1 0 0 0 0 1 0 0 0 14251 681 24 2 2 SDS 12 113398835 Missense_Mutation SNP C C3L-00144_T 5106358 113398835 19876474 1180 5251 20 2 SDS 0 . GRCh38 12 113398837 113398837 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.203C>A p.Ala68Glu p.A68E ENST00000257549 4/8 68 57 11 86 85 1 strelka-varscan-mutect SDS,missense_variant,p.Ala68Glu,ENST00000257549,NM_006843.2;SDS,missense_variant,p.Ala162Glu,ENST00000547342,;SDS,intron_variant,,ENST00000552280,;SDS,non_coding_transcript_exon_variant,,ENST00000553112,;SDS,non_coding_transcript_exon_variant,,ENST00000546639,;SDS,downstream_gene_variant,,ENST00000546785,; T ENST00000257549 Transcript missense_variant 326/1606 203/987 68/328 A/E gCa/gAa 1 -1 SDS HGNC HGNC:10691 protein_coding YES CCDS9169.1 ENSP00000257549 P20132 UPI000013CF6B NM_006843.2 deleterious(0) 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10314:SF103,hmmpanther:PTHR10314,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 12 113398837 113398837 G T 1 0 0 0 0 1 0 0 0 14251 1319 46 2 2 SDS 12 113398837 Missense_Mutation SNP G C3L-00144_T 2 113398837 19876472 1181 5252 20 2 TBX5 0 . GRCh38 12 114356087 114356087 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.1002A>T p.= p.T334T ENST00000310346 9/9 381 334 47 351 350 1 strelka-varscan-mutect TBX5,synonymous_variant,p.=,ENST00000310346,NM_000192.3;TBX5,synonymous_variant,p.=,ENST00000349716,NM_080717.2;TBX5,synonymous_variant,p.=,ENST00000405440,NM_181486.2; A ENST00000310346 Transcript synonymous_variant 1669/3825 1002/1557 334/518 T acA/acT 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 9/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 114356087 114356087 T A 1 0 0 0 0 0 0 0 1 16065 1567 55 4 4 TBX5 12 114356087 Silent SNP T C3L-00144_T 957250 114356087 18919222 1182 5253 NOS1 0 . GRCh38 12 117280863 117280863 + Silent SNP A A T rs777714218 C3L-00144_T C3L-00144_N A A c.1386T>A p.= p.S462S ENST00000618760 8/30 112 98 14 120 120 0 strelka-varscan-mutect NOS1,synonymous_variant,p.=,ENST00000618760,NM_001204218.1;NOS1,synonymous_variant,p.=,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,synonymous_variant,p.=,ENST00000338101,;NOS1,synonymous_variant,p.=,ENST00000344089,; T ENST00000618760 Transcript synonymous_variant 2097/12283 1386/4407 462/1468 S tcT/tcA rs777714218 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 8/30 Pfam_domain:PF02898,Gene3D:3.90.340.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 LOW 1 SNV 5 1 PASS rs777714218 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 117280863 117280863 A T 1 0 0 0 0 0 0 0 1 10586 202 7 4 4 NOS1 12 117280863 Silent SNP A C3L-00144_T 2924776 117280863 15994446 1183 5254 HSPB8 0 . GRCh38 12 119193816 119193816 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.549C>T p.= p.N183N ENST00000281938 3/3 563 490 73 468 468 0 strelka-varscan-mutect HSPB8,synonymous_variant,p.=,ENST00000281938,NM_014365.2;HSPB8,intron_variant,,ENST00000541798,;HSPB8,non_coding_transcript_exon_variant,,ENST00000542496,;RP11-64B16.2,upstream_gene_variant,,ENST00000392530,; T ENST00000281938 Transcript synonymous_variant 1220/2152 549/591 183/196 N aaC/aaT 1 1 HSPB8 HGNC HGNC:30171 protein_coding YES CCDS9189.1 ENSP00000281938 Q9UJY1 UPI0000037C1B NM_014365.2 3/3 hmmpanther:PTHR11527,hmmpanther:PTHR11527:SF157 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 119193816 119193816 C T 1 0 0 0 0 0 0 0 1 7320 477 17 3 3 HSPB8 12 119193816 Silent SNP C C3L-00144_T 1912953 119193816 14081493 1184 5255 CIT 0 . GRCh38 12 119690317 119690317 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.6020A>T p.Glu2007Val p.E2007V ENST00000392521 47/48 188 149 39 193 193 0 strelka-varscan-mutect CIT,missense_variant,p.Glu2007Val,ENST00000392521,NM_001206999.1;CIT,missense_variant,p.Glu1965Val,ENST00000261833,NM_007174.2;CIT,missense_variant,p.Glu1578Val,ENST00000392520,;CIT,intron_variant,,ENST00000612548,;CIT,non_coding_transcript_exon_variant,,ENST00000537607,;CIT,downstream_gene_variant,,ENST00000469414,;CIT,non_coding_transcript_exon_variant,,ENST00000545913,;CIT,downstream_gene_variant,,ENST00000544872,; A ENST00000392521 Transcript missense_variant 6076/8708 6020/6210 2007/2069 E/V gAg/gTg 1 -1 CIT HGNC HGNC:1985 protein_coding YES CCDS55891.1 ENSP00000376306 O14578 UPI0000683C41 NM_001206999.1 deleterious_low_confidence(0) 47/48 PIRSF_domain:PIRSF038145,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 119690317 119690317 T A 1 0 0 0 0 1 0 0 0 3201 1551 54 4 4 CIT 12 119690317 Missense_Mutation SNP T C3L-00144_T 496501 119690317 13584992 1185 5256 SETD1B 0 . GRCh38 12 121814258 121814258 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2043G>T p.= p.L681L ENST00000542440 7/18 71 65 6 65 65 0 strelka-mutect SETD1B,synonymous_variant,p.=,ENST00000542440,NM_015048.1;SETD1B,synonymous_variant,p.=,ENST00000604567,;SETD1B,synonymous_variant,p.=,ENST00000619791,;SETD1B,synonymous_variant,p.=,ENST00000267197,; T ENST00000542440 Transcript synonymous_variant 2111/8185 2043/5772 681/1923 L ctG/ctT 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 7/18 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 190 19 0 0 0 0 0 -12.89993 0.9931781 1 1 1 0 T 2 4 12 121814258 121814258 G T 1 0 0 0 0 0 0 0 1 14408 1306 46 2 2 SETD1B 12 121814258 Silent SNP G C3L-00144_T 2123941 121814258 11461051 1186 5257 IL31 0 . GRCh38 12 122172717 122172717 + Missense_Mutation SNP C C G rs148866660 C3L-00144_T C3L-00144_N C C c.190G>C p.Val64Leu p.V64L ENST00000377035 3/3 81 73 8 93 93 0 strelka-varscan-mutect IL31,missense_variant,p.Val64Leu,ENST00000377035,NM_001014336.1;LRRC43,intron_variant,,ENST00000537729,; G ENST00000377035 Transcript missense_variant 217/904 190/495 64/164 V/L Gtg/Ctg rs148866660 1 -1 IL31 HGNC HGNC:19372 protein_coding YES CCDS31919.1 ENSP00000366234 Q6EBC2 UPI00003BF6FE NM_001014336.1 tolerated(0.24) 3/3 hmmpanther:PTHR38652:SF1,hmmpanther:PTHR38652,Pfam_domain:PF15209 MODERATE 1 SNV 1 1 PASS rs148866660 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 122172717 122172717 C G 1 0 0 0 0 1 0 0 0 7589 536 19 4 4 IL31 12 122172717 Missense_Mutation SNP C C3L-00144_T 358459 122172717 11102592 1187 5258 DHX37 0 . GRCh38 12 124964954 124964954 + Silent SNP C C A rs759736418 C3L-00144_T C3L-00144_N C C c.1788G>T p.= p.L596L ENST00000308736 14/27 136 126 10 131 130 1 strelka-varscan-mutect DHX37,missense_variant,p.Cys48Phe,ENST00000543962,;DHX37,synonymous_variant,p.=,ENST00000308736,NM_032656.3;DHX37,synonymous_variant,p.=,ENST00000544745,;DHX37,non_coding_transcript_exon_variant,,ENST00000539298,; A ENST00000308736 Transcript synonymous_variant 1887/4550 1788/3474 596/1157 L ctG/ctT rs759736418 1 -1 DHX37 HGNC HGNC:17210 protein_coding YES CCDS9261.1 ENSP00000311135 Q8IY37 UPI00000742DC NM_032656.3 14/27 Low_complexity_(Seg):seg,PROSITE_profiles:PS51194,hmmpanther:PTHR18934:SF99,hmmpanther:PTHR18934,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs759736418 . 0 207 2 0 0 0 0 0 -19.26028 1 1 1 1 0 A 2 1 12 124964954 124964954 C A 1 0 0 0 0 0 0 0 1 4314 697 25 2 2 DHX37 12 124964954 Silent SNP C C3L-00144_T 2792237 124964954 8310355 1188 5259 BRI3BP 0 . GRCh38 12 125025183 125025183 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.509G>T p.Cys170Phe p.C170F ENST00000341446 3/3 444 390 54 451 448 3 strelka-varscan-mutect BRI3BP,missense_variant,p.Cys170Phe,ENST00000341446,NM_080626.5;THRIL,downstream_gene_variant,,ENST00000627370,; T ENST00000341446 Transcript missense_variant 600/6648 509/756 170/251 C/F tGc/tTc COSM4039988 1 1 BRI3BP HGNC HGNC:14251 protein_coding YES CCDS9262.1 ENSP00000340761 Q8WY22 UPI000006D8B0 NM_080626.5 tolerated(0.09) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR31253,hmmpanther:PTHR31253:SF0,Pfam_domain:PF14965 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 125025183 125025183 G T 1 0 0 0 0 1 0 0 0 1683 1319 46 2 2 BRI3BP 12 125025183 Missense_Mutation SNP G C3L-00144_T 60229 125025183 8250126 1189 5260 TMEM132B 0 . GRCh38 12 125583994 125583994 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1422G>T p.Lys474Asn p.K474N ENST00000299308 5/9 332 295 37 310 306 4 strelka-varscan-mutect TMEM132B,missense_variant,p.Lys474Asn,ENST00000299308,NM_052907.3;TMEM132B,non_coding_transcript_exon_variant,,ENST00000534945,; T ENST00000299308 Transcript missense_variant,splice_region_variant 1430/10906 1422/3237 474/1078 K/N aaG/aaT 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 deleterious(0) 5/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388,Pfam_domain:PF16070 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 125583994 125583994 G T 1 0 0 0 0 1 0 0 0 16490 1014 35 2 2 TMEM132B 12 125583994 Missense_Mutation SNP G C3L-00144_T 558811 125583994 7691315 1190 5261 TMEM132C 0 . GRCh38 12 128706208 128706208 + Silent SNP G G A C3L-00144_T C3L-00144_N G G c.3240G>A p.= p.E1080E ENST00000435159 9/9 137 110 27 128 128 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript synonymous_variant 3240/4947 3240/3327 1080/1108 E gaG/gaA COSM936897,COSM936898 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 128706208 128706208 G A 1 0 0 0 0 0 0 0 1 16491 991 35 3 3 TMEM132C 12 128706208 Silent SNP G C3L-00144_T 3122214 128706208 4569101 1191 5262 GLT1D1 0 . GRCh38 12 128899246 128899246 + Missense_Mutation SNP G G T rs768702559 C3L-00144_T C3L-00144_N G G c.334G>T p.Ala112Ser p.A112S ENST00000281703 4/8 224 200 24 242 241 1 strelka-varscan-mutect GLT1D1,missense_variant,p.Ala112Ser,ENST00000442111,;GLT1D1,missense_variant,p.Ala112Ser,ENST00000281703,NM_144669.1;GLT1D1,missense_variant,p.Ala101Ser,ENST00000537468,;GLT1D1,missense_variant,p.Ala105Ser,ENST00000413816,;GLT1D1,intron_variant,,ENST00000441390,;GLT1D1,intron_variant,,ENST00000539044,; T ENST00000281703 Transcript missense_variant 380/2725 334/801 112/266 A/S Gct/Tct rs768702559 1 1 GLT1D1 HGNC HGNC:26483 protein_coding YES CCDS9265.1 ENSP00000281703 Q96MS3 UPI0000070E33 NM_144669.1 deleterious(0.03) 4/8 MODERATE 1 SNV 2 1 PASS rs768702559 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 12 128899246 128899246 G T 1 0 0 0 0 1 0 0 0 6344 1087 38 1 1 GLT1D1 12 128899246 Missense_Mutation SNP G C3L-00144_T 193038 128899246 4376063 1192 5263 TMEM132D 0 . GRCh38 12 129074211 129074211 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2964C>A p.= p.I988I ENST00000422113 9/9 287 262 25 222 222 0 strelka-varscan-mutect TMEM132D,synonymous_variant,p.=,ENST00000422113,NM_133448.2;TMEM132D,synonymous_variant,p.=,ENST00000389441,; T ENST00000422113 Transcript synonymous_variant 3291/5776 2964/3300 988/1099 I atC/atA 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 129074211 129074211 G T 1 0 0 0 0 0 0 0 1 16492 1280 45 2 2 TMEM132D 12 129074211 Silent SNP G C3L-00144_T 174965 129074211 4201098 1193 5264 TMEM132D 0 . GRCh38 12 129700071 129700071 + Missense_Mutation SNP C C A rs560334536 C3L-00144_T C3L-00144_N C C c.707G>T p.Arg236Ile p.R236I ENST00000422113 2/9 325 280 45 327 326 1 strelka-varscan-mutect TMEM132D,missense_variant,p.Arg236Ile,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript missense_variant 1034/5776 707/3300 236/1099 R/I aGa/aTa rs560334536 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 tolerated(0.08) 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS rs560334536 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 129700071 129700071 C A 1 0 0 0 0 1 0 0 0 16492 913 32 2 2 TMEM132D 12 129700071 Missense_Mutation SNP C C3L-00144_T 625860 129700071 3575238 1194 5265 TMEM132D 0 . GRCh38 12 129700121 129700121 + Silent SNP C C A rs143084996 C3L-00144_T C3L-00144_N C C c.657G>T p.= p.P219P ENST00000422113 2/9 207 167 40 188 188 0 strelka-varscan-mutect TMEM132D,synonymous_variant,p.=,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript synonymous_variant 984/5776 657/3300 219/1099 P ccG/ccT rs143084996,COSM122066 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 0,1 LOW 1 SNV 1 0,1 1 PASS rs143084996 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 129700121 129700121 C A 1 0 0 0 0 0 0 0 1 16492 639 23 1 1 TMEM132D 12 129700121 Silent SNP C C3L-00144_T 50 129700121 3575188 1195 5266 RIMBP2 0 . GRCh38 12 130441904 130441904 + Missense_Mutation SNP G G C rs777554273 C3L-00144_T C3L-00144_N G G c.1397C>G p.Pro466Arg p.P466R ENST00000261655 8/19 211 166 45 178 178 0 strelka-varscan-mutect RIMBP2,missense_variant,p.Pro466Arg,ENST00000261655,NM_015347.4;RIMBP2,missense_variant,p.Pro374Arg,ENST00000535703,; C ENST00000261655 Transcript missense_variant 1561/6321 1397/3159 466/1052 P/R cCg/cGg rs777554273 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 deleterious(0) 8/19 PROSITE_profiles:PS50853,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18 MODERATE 1 SNV 1 1 PASS rs777554273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 130441904 130441904 G C 1 0 0 0 0 1 0 0 0 13538 1116 39 4 4 RIMBP2 12 130441904 Missense_Mutation SNP G C3L-00144_T 741783 130441904 2833405 1196 5267 FBRSL1 0 . GRCh38 12 132572592 132572592 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1554C>A p.Phe518Leu p.F518L ENST00000434748 11/17 235 223 12 212 212 0 strelka-mutect FBRSL1,missense_variant,p.Phe518Leu,ENST00000434748,NM_001142641.1;FBRSL1,non_coding_transcript_exon_variant,,ENST00000537804,;FBRSL1,non_coding_transcript_exon_variant,,ENST00000543453,;FBRSL1,intron_variant,,ENST00000536075,;FBRSL1,downstream_gene_variant,,ENST00000539264,;FBRSL1,downstream_gene_variant,,ENST00000543360,;FBRSL1,non_coding_transcript_exon_variant,,ENST00000542306,; A ENST00000434748 Transcript missense_variant 2574/5568 1554/3138 518/1045 F/L ttC/ttA COSM937232,COSM937233 1 1 FBRSL1 HGNC HGNC:29308 protein_coding YES CCDS45010.1 ENSP00000396160 Q9HCM7 UPI00018830C3 NM_001142641.1 deleterious(0.02) 11/17 hmmpanther:PTHR14429,hmmpanther:PTHR14429:SF20,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs987647453 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 132572592 132572592 C A 1 0 0 0 0 1 0 0 0 5571 883 31 1 1 FBRSL1 12 132572592 Missense_Mutation SNP C C3L-00144_T 2130688 132572592 702717 1197 5268 CHFR 0 . GRCh38 12 132862372 132862372 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.457G>T p.Asp153Tyr p.D153Y ENST00000266880 6/18 69 54 15 62 62 0 strelka-varscan-mutect CHFR,missense_variant,p.Asp153Tyr,ENST00000266880,NM_018223.2;CHFR,intron_variant,,ENST00000450056,NM_001161346.1;CHFR,intron_variant,,ENST00000443047,NM_001161347.1;CHFR,intron_variant,,ENST00000432561,NM_001161344.1,NM_001161345.1;CHFR,intron_variant,,ENST00000540963,;CHFR,intron_variant,,ENST00000541817,;RP11-46H11.11,downstream_gene_variant,,ENST00000623177,;CHFR,intron_variant,,ENST00000315585,;CHFR,upstream_gene_variant,,ENST00000535897,; A ENST00000266880 Transcript missense_variant 521/11133 457/1872 153/623 D/Y Gat/Tat 1 -1 CHFR HGNC HGNC:20455 protein_coding CCDS31937.1 ENSP00000266880 Q96EP1 UPI0000236D67 NM_018223.2 deleterious(0.01) 6/18 MODERATE SNV 2 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999991 1 1 1 0 A 3 1 12 132862372 132862372 C A 1 0 0 0 0 1 0 0 0 3096 826 29 2 2 CHFR 12 132862372 Missense_Mutation SNP C C3L-00144_T 289780 132862372 412937 1198 5269 ANHX 0 . GRCh38 12 133227121 133227121 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.533C>A p.Pro178His p.P178H ENST00000545940 4/8 125 99 26 82 82 0 strelka-varscan-mutect ANHX,missense_variant,p.Pro178His,ENST00000545940,;ANHX,missense_variant,p.Pro178His,ENST00000419717,NM_001191054.1; T ENST00000545940 Transcript missense_variant 2272/3452 533/1140 178/379 P/H cCt/cAt 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 tolerated(0.16) 4/8 PROSITE_profiles:PS50071,hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 133227121 133227121 G T 1 0 0 0 0 1 0 0 0 719 1000 35 2 2 ANHX 12 133227121 Missense_Mutation SNP G C3L-00144_T 364749 133227121 48188 1199 5270 ZMYM5 0 . GRCh38 13 19824773 19824773 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1714G>C p.Glu572Gln p.E572Q ENST00000337963 8/8 194 174 20 163 163 0 strelka-varscan-mutect ZMYM5,missense_variant,p.Glu572Gln,ENST00000337963,NM_001142684.1;ZMYM5,missense_variant,p.Glu562Gln,ENST00000502168,;ZMYM5,non_coding_transcript_exon_variant,,ENST00000535942,;ZMYM5,non_coding_transcript_exon_variant,,ENST00000382909,; G ENST00000337963 Transcript missense_variant 1979/3268 1714/2010 572/669 E/Q Gaa/Caa 1 -1 ZMYM5 HGNC HGNC:13029 protein_coding ENSP00000337034 Q9UJ78 UPI000178DE9C NM_001142684.1 deleterious(0) 8/8 MODERATE SNV 5 1 PASS rs950018107 . 0 188 2 10 10 0 0 0 -7.58728 0.03058901 0 1 0 0 G 3 3 12 19824773 19824773 C G 1 0 0 0 0 1 0 0 0 18283 835 29 4 4 ZMYM5 13 19824773 Missense_Mutation SNP C C3L-00144_T 19824773 94539555 1200 5271 XPO4 0 . GRCh38 13 20902706 20902706 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.33G>T p.= p.V11V ENST00000255305 1/23 63 54 9 58 58 0 strelka-varscan-mutect XPO4,synonymous_variant,p.=,ENST00000255305,NM_022459.4;XPO4,synonymous_variant,p.=,ENST00000400602,;XPO4,non_coding_transcript_exon_variant,,ENST00000490513,;XPO4,non_coding_transcript_exon_variant,,ENST00000465018,; A ENST00000255305 Transcript synonymous_variant 105/9921 33/3456 11/1151 V gtG/gtT 1 -1 XPO4 HGNC HGNC:17796 protein_coding YES CCDS41872.1 ENSP00000255305 Q9C0E2 UPI0000139018 NM_022459.4 1/23 hmmpanther:PTHR12596,hmmpanther:PTHR12596:SF1 LOW 1 SNV 1 1 PASS rs1313692426 . 0 205 4 0 0 0 0 0 -19.89459 1 1 1 1 0 A 2 1 12 20902706 20902706 C A 1 0 0 0 0 0 0 0 1 18005 813 29 2 2 XPO4 13 20902706 Silent SNP C C3L-00144_T 1077933 20902706 93461622 1201 5272 LATS2 0 . GRCh38 13 20983394 20983394 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2312A>G p.Tyr771Cys p.Y771C ENST00000382592 5/8 248 186 62 228 228 0 strelka-varscan-mutect LATS2,missense_variant,p.Tyr771Cys,ENST00000382592,NM_014572.2; C ENST00000382592 Transcript missense_variant 2718/5511 2312/3267 771/1088 Y/C tAc/tGc 1 -1 LATS2 HGNC HGNC:6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 A0A024RDM3 UPI000013DBF5 NM_014572.2 deleterious(0) 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF149,hmmpanther:PTHR24356,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 20983394 20983394 T C 1 0 0 0 0 1 0 0 0 8552 1638 57 5 5 LATS2 13 20983394 Missense_Mutation SNP T C3L-00144_T 80688 20983394 93380934 1202 5273 PARP4 0 . GRCh38 13 24503644 24503644 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.132+1G>T p.X44_splice ENST00000381989 138 113 25 129 129 0 strelka-varscan-mutect PARP4,splice_donor_variant,,ENST00000381989,NM_006437.3;TPTE2P6,intron_variant,,ENST00000445572,; A ENST00000381989 Transcript splice_donor_variant -/5474 132/5175 44/1724 1 -1 PARP4 HGNC HGNC:271 protein_coding YES CCDS9307.1 ENSP00000371419 Q9UKK3 UPI000013C76E NM_006437.3 2/33 HIGH 1 SNV 1 1 PASS rs1003491928 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 24503644 24503644 C A 1 0 0 0 0 0 0 1 0 11543 521 18 2 2 PARP4 13 24503644 Splice_Site SNP C C3L-00144_T 3520250 24503644 89860684 1203 5274 AMER2 0 . GRCh38 13 25169694 25169694 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1926C>A p.= p.S642S ENST00000515384 1/1 68 53 15 60 60 0 strelka-varscan-mutect AMER2,synonymous_variant,p.=,ENST00000357816,NM_199138.2;AMER2,synonymous_variant,p.=,ENST00000515384,NM_152704.3;LINC00463,downstream_gene_variant,,ENST00000413501,; T ENST00000515384 Transcript synonymous_variant 2594/3197 1926/2016 642/671 S tcC/tcA 1 -1 AMER2 HGNC HGNC:26360 protein_coding YES CCDS53859.1 ENSP00000426528 Q8N7J2 UPI0000231C76 NM_152704.3 1/1 hmmpanther:PTHR22237:SF1,hmmpanther:PTHR22237 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 25169694 25169694 G T 1 0 0 0 0 0 0 0 1 668 1335 47 2 2 AMER2 13 25169694 Silent SNP G C3L-00144_T 666050 25169694 89194634 1204 5275 CDX2 0 . GRCh38 13 27964996 27964996 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.561C>A p.Asp187Glu p.D187E ENST00000381020 2/3 160 145 15 148 148 0 strelka-varscan-mutect CDX2,missense_variant,p.Asp187Glu,ENST00000381020,NM_001265.4;CDX2,non_coding_transcript_exon_variant,,ENST00000548877,; T ENST00000381020 Transcript missense_variant 2694/4053 561/942 187/313 D/E gaC/gaA 1 -1 CDX2 HGNC HGNC:1806 protein_coding YES CCDS9328.1 ENSP00000370408 Q99626 UPI000013E4C8 NM_001265.4 tolerated(0.55) 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24332,hmmpanther:PTHR24332:SF16,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1397725727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27964996 27964996 G T 1 0 0 0 0 1 0 0 0 2889 1368 48 2 2 CDX2 13 27964996 Missense_Mutation SNP G C3L-00144_T 2795302 27964996 86399332 1205 5276 PDS5B 0 . GRCh38 13 32694256 32694256 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1503G>T p.= p.L501L ENST00000315596 14/35 261 196 65 250 249 1 strelka-varscan-mutect PDS5B,synonymous_variant,p.=,ENST00000315596,NM_015032.3;PDS5B,synonymous_variant,p.=,ENST00000450460,;PDS5B,downstream_gene_variant,,ENST00000498550,; T ENST00000315596 Transcript synonymous_variant 1689/7497 1503/4344 501/1447 L ctG/ctT 1 1 PDS5B HGNC HGNC:20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 NM_015032.3 14/35 hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 32694256 32694256 G T 1 0 0 0 0 0 0 0 1 11780 1306 46 2 2 PDS5B 13 32694256 Silent SNP G C3L-00144_T 4729260 32694256 81670072 1206 5277 RFC3 0 . GRCh38 13 33821236 33821236 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.192G>T p.= p.V64V ENST00000380071 2/9 163 129 34 189 187 2 strelka-varscan-mutect RFC3,synonymous_variant,p.=,ENST00000380071,NM_002915.3;RFC3,synonymous_variant,p.=,ENST00000434425,NM_181558.2; T ENST00000380071 Transcript synonymous_variant 322/2402 192/1071 64/356 V gtG/gtT 1 1 RFC3 HGNC HGNC:9971 protein_coding YES CCDS9352.1 ENSP00000369411 P40938 A0A024RDQ8 UPI0000125168 NM_002915.3 2/9 hmmpanther:PTHR11669,hmmpanther:PTHR11669:SF1,Pfam_domain:PF13177,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 33821236 33821236 G T 1 0 0 0 0 0 0 0 1 13417 1335 47 2 2 RFC3 13 33821236 Silent SNP G C3L-00144_T 1126980 33821236 80543092 1207 5278 NBEA 0 . GRCh38 13 35098310 35098310 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1585G>T p.Ala529Ser p.A529S ENST00000400445 11/58 104 79 25 103 103 0 strelka-varscan-mutect NBEA,missense_variant,p.Ala529Ser,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Ala529Ser,ENST00000310336,;NBEA,missense_variant,p.Ala529Ser,ENST00000629018,;NBEA,missense_variant,p.Ala529Ser,ENST00000379939,; T ENST00000400445 Transcript missense_variant 2119/11119 1585/8841 529/2946 A/S Gca/Tca 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 tolerated(0.53) 11/58 Pfam_domain:PF15787,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF62,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35098310 35098310 G T 1 0 0 0 0 1 0 0 0 10198 1203 42 2 2 NBEA 13 35098310 Missense_Mutation SNP G C3L-00144_T 1277074 35098310 79266018 1208 5279 SOHLH2 0 . GRCh38 13 36190008 36190008 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.579G>T p.Leu193Phe p.L193F ENST00000379881 6/11 96 85 11 79 78 1 strelka-varscan-mutect SOHLH2,missense_variant,p.Leu193Phe,ENST00000379881,NM_017826.2;CCDC169-SOHLH2,missense_variant,p.Leu270Phe,ENST00000511166,NM_001198910.1;SOHLH2,missense_variant,p.Leu193Phe,ENST00000317764,NM_001282147.1; A ENST00000379881 Transcript missense_variant 668/2193 579/1278 193/425 L/F ttG/ttT COSM4802927 1 -1 SOHLH2 HGNC HGNC:26026 protein_coding YES CCDS9355.1 ENSP00000369210 Q9NX45 UPI000006D052 NM_017826.2 tolerated(0.05) 6/11 hmmpanther:PTHR16223,hmmpanther:PTHR16223:SF16 1 MODERATE SNV 2 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.54351 0.9999999 1 1 1 0 A 3 1 12 36190008 36190008 C A 1 0 0 0 0 1 0 0 0 15247 477 17 2 2 SOHLH2 13 36190008 Missense_Mutation SNP C C3L-00144_T 1091698 36190008 78174320 1209 5280 TRPC4 0 . GRCh38 13 37746091 37746091 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.743G>T p.Cys248Phe p.C248F ENST00000625583 2/10 347 309 38 347 346 1 strelka-varscan-mutect TRPC4,missense_variant,p.Cys248Phe,ENST00000379705,NM_016179.2;TRPC4,missense_variant,p.Cys248Phe,ENST00000625583,NM_003306.1;TRPC4,missense_variant,p.Cys248Phe,ENST00000358477,NM_001135955.1;TRPC4,missense_variant,p.Cys248Phe,ENST00000355779,NM_001135957.1;TRPC4,missense_variant,p.Cys248Phe,ENST00000379673,NM_001135956.1;TRPC4,missense_variant,p.Cys248Phe,ENST00000426868,;TRPC4,intron_variant,,ENST00000338947,NM_001135958.1;TRPC4,intron_variant,,ENST00000379679,;TRPC4,missense_variant,p.Cys248Phe,ENST00000488717,; A ENST00000625583 Transcript missense_variant 743/3009 743/2949 248/982 C/F tGc/tTc 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 deleterious(0) 2/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS rs1231465398 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 37746091 37746091 C A 1 0 0 0 0 1 0 0 0 17085 710 25 2 2 TRPC4 13 37746091 Missense_Mutation SNP C C3L-00144_T 1556083 37746091 76618237 1210 5281 FREM2 0 . GRCh38 13 38850120 38850120 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.6462G>T p.= p.G2154G ENST00000280481 9/24 253 218 35 239 239 0 strelka-varscan-mutect FREM2,synonymous_variant,p.=,ENST00000280481,NM_207361.5;FREM2,non_coding_transcript_exon_variant,,ENST00000482551,; T ENST00000280481 Transcript synonymous_variant 6678/16070 6462/9510 2154/3169 G ggG/ggT 1 1 FREM2 HGNC HGNC:25396 protein_coding YES CCDS31960.1 ENSP00000280481 Q5SZK8 UPI000443805C NM_207361.5 9/24 hmmpanther:PTHR11878:SF32,hmmpanther:PTHR11878,Pfam_domain:PF03160,SMART_domains:SM00237,Superfamily_domains:SSF141072 LOW 1 SNV 2 1 PASS rs1306132213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 38850120 38850120 G T 1 0 0 0 0 0 0 0 1 5912 1219 43 2 2 FREM2 13 38850120 Silent SNP G C3L-00144_T 1104029 38850120 75514208 1211 5282 STOML3 0 . GRCh38 13 38976539 38976539 + Splice_Site SNP C C T novel C3L-00144_T C3L-00144_N C C c.229+1G>A p.X77_splice ENST00000379631 204 156 48 172 172 0 strelka-varscan-mutect STOML3,splice_donor_variant,,ENST00000379631,NM_145286.2;STOML3,splice_donor_variant,,ENST00000423210,NM_001144033.1; T ENST00000379631 Transcript splice_donor_variant -/2121 229/876 77/291 1 -1 STOML3 HGNC HGNC:19420 protein_coding YES CCDS9367.1 ENSP00000368952 Q8TAV4 UPI000003615B NM_145286.2 3/6 HIGH 1 SNV 1 1 PASS rs1295821118 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 38976539 38976539 C T 1 0 0 0 0 0 0 1 0 15694 521 18 3 3 STOML3 13 38976539 Splice_Site SNP C C3L-00144_T 126419 38976539 75387789 1212 5283 LRRC63 0 . GRCh38 13 46213067 46213067 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.33C>A p.= p.P11P ENST00000595396 1/9 249 198 51 201 200 1 strelka-varscan-mutect LRRC63,synonymous_variant,p.=,ENST00000595396,;LRRC63,synonymous_variant,p.=,ENST00000446175,NM_001282460.1;LCP1,upstream_gene_variant,,ENST00000398576,;LCP1,upstream_gene_variant,,ENST00000442275,;LRRC63,synonymous_variant,p.=,ENST00000378805,; A ENST00000595396 Transcript synonymous_variant 33/2327 33/1764 11/587 P ccC/ccA 1 1 LRRC63 HGNC HGNC:34296 protein_coding YES CCDS61325.1 ENSP00000469337 J3KQU2 UPI0002742DC2 1/9 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs987162191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 46213067 46213067 C A 1 0 0 0 0 0 0 0 1 8913 668 24 2 2 LRRC63 13 46213067 Silent SNP C C3L-00144_T 7236528 46213067 68151261 1213 5284 DLEU7 0 . GRCh38 13 50843320 50843320 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.327C>A p.= p.P109P ENST00000504404 1/2 63 51 12 40 40 0 strelka-varscan-mutect DLEU7,synonymous_variant,p.=,ENST00000400393,NM_198989.2;DLEU7,synonymous_variant,p.=,ENST00000504404,NM_001306135.1;DLEU7-AS1,intron_variant,,ENST00000413510,; T ENST00000504404 Transcript synonymous_variant 377/1122 327/666 109/221 P ccC/ccA 1 -1 DLEU7 HGNC HGNC:17567 protein_coding YES CCDS76635.1 ENSP00000427177 Q6UYE1 UPI0000225CA2 NM_001306135.1 1/2 hmmpanther:PTHR36961:SF1,hmmpanther:PTHR36961,Pfam_domain:PF15760 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 50843320 50843320 G T 1 0 0 0 0 0 0 0 1 4360 987 35 2 2 DLEU7 13 50843320 Silent SNP G C3L-00144_T 4630253 50843320 63521008 1214 5285 ATP7B 0 . GRCh38 13 51973949 51973949 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1271C>A p.Ala424Asp p.A424D ENST00000242839 2/21 347 290 57 303 303 0 strelka-varscan-mutect ATP7B,missense_variant,p.Ala424Asp,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Ala424Asp,ENST00000448424,;ATP7B,missense_variant,p.Ala313Asp,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Ala424Asp,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Ala424Asp,ENST00000634844,;ATP7B,missense_variant,p.Ala424Asp,ENST00000418097,;ATP7B,missense_variant,p.Ala424Asp,ENST00000400370,;ATP7B,non_coding_transcript_exon_variant,,ENST00000482841,;ATP7B,non_coding_transcript_exon_variant,,ENST00000483772,;ATP7B,intron_variant,,ENST00000635406,;ATP7B,missense_variant,p.Ala424Asp,ENST00000634308,;ATP7B,upstream_gene_variant,,ENST00000634620,; T ENST00000242839 Transcript missense_variant 1428/6638 1271/4398 424/1465 A/D gCt/gAt 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 deleterious(0) 2/21 PROSITE_profiles:PS50846,Gene3D:3.30.70.100,TIGRFAM_domain:TIGR00003,Superfamily_domains:SSF55008 MODERATE 1 SNV 1 1 PASS rs1257774863 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 51973949 51973949 G T 1 0 0 0 0 1 0 0 0 1344 971 34 2 2 ATP7B 13 51973949 Missense_Mutation SNP G C3L-00144_T 1130629 51973949 62390379 1215 5286 PCDH8 0 . GRCh38 13 52847746 52847746 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.691C>A p.Leu231Ile p.L231I ENST00000377942 1/3 39 32 7 48 48 0 strelka-mutect PCDH8,missense_variant,p.Leu231Ile,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Leu231Ile,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; T ENST00000377942 Transcript missense_variant 895/5088 691/3213 231/1070 L/I Ctc/Atc 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 tolerated(0.58) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -17.84352 1 1 1 1 0 T 3 4 12 52847746 52847746 G T 1 0 0 0 0 1 0 0 0 11604 1000 35 2 2 PCDH8 13 52847746 Missense_Mutation SNP G C3L-00144_T 873797 52847746 61516582 1216 5287 PCDH17 0 . GRCh38 13 57632936 57632936 + Silent SNP C C A rs751268818 C3L-00144_T C3L-00144_N C C c.390C>A p.= p.P130P ENST00000377918 1/4 537 487 50 509 506 3 strelka-varscan-mutect PCDH17,synonymous_variant,p.=,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,intron_variant,,ENST00000610846,;PCDH17,synonymous_variant,p.=,ENST00000484979,; A ENST00000377918 Transcript synonymous_variant 1125/8232 390/3480 130/1159 P ccC/ccA rs751268818 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 1/4 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs751268818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 57632936 57632936 C A 1 0 0 0 0 0 0 0 1 11599 668 24 2 2 PCDH17 13 57632936 Silent SNP C C3L-00144_T 4785190 57632936 56731392 1217 5288 PCDH17 0 . GRCh38 13 57633153 57633153 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.607C>A p.Arg203Ser p.R203S ENST00000377918 1/4 278 253 25 264 263 1 strelka-varscan-mutect PCDH17,missense_variant,p.Arg203Ser,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,non_coding_transcript_exon_variant,,ENST00000610846,;PCDH17,missense_variant,p.Arg203Ser,ENST00000484979,; A ENST00000377918 Transcript missense_variant 1342/8232 607/3480 203/1159 R/S Cgc/Agc COSM4768936 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 deleterious(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 57633153 57633153 C A 1 0 0 0 0 1 0 0 0 11599 652 23 1 1 PCDH17 13 57633153 Missense_Mutation SNP C C3L-00144_T 217 57633153 56731175 1218 5289 DACH1 0 . GRCh38 13 71681846 71681846 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.913A>T p.Met305Leu p.M305L ENST00000613252 2/11 207 188 19 180 180 0 strelka-varscan-mutect DACH1,missense_variant,p.Met305Leu,ENST00000613252,NM_080759.5;DACH1,missense_variant,p.Met305Leu,ENST00000611519,NM_080760.5;DACH1,missense_variant,p.Met305Leu,ENST00000620444,NM_004392.6;DACH1,missense_variant,p.Met305Leu,ENST00000619232,; A ENST00000613252 Transcript missense_variant 1336/5233 913/2121 305/706 M/L Atg/Ttg 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 tolerated_low_confidence(1) 2/11 hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577 MODERATE 1 SNV 1 1 PASS rs888954628 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 71681846 71681846 T A 1 0 0 0 0 1 0 0 0 4021 1464 51 4 4 DACH1 13 71681846 Missense_Mutation SNP T C3L-00144_T 14048693 71681846 42682482 1219 5290 DACH1 0 . GRCh38 13 71866239 71866239 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.531C>A p.= p.S177S ENST00000613252 1/11 96 85 11 98 98 0 strelka-varscan-mutect DACH1,synonymous_variant,p.=,ENST00000613252,NM_080759.5;DACH1,synonymous_variant,p.=,ENST00000611519,NM_080760.5;DACH1,synonymous_variant,p.=,ENST00000620444,NM_004392.6;DACH1,synonymous_variant,p.=,ENST00000619232,; T ENST00000613252 Transcript synonymous_variant 954/5233 531/2121 177/706 S tcC/tcA 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 1/11 hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577,Pfam_domain:PF02437 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 71866239 71866239 G T 1 0 0 0 0 0 0 0 1 4021 1219 43 2 2 DACH1 13 71866239 Silent SNP G C3L-00144_T 184393 71866239 42498089 1220 5291 TBC1D4 0 . GRCh38 13 75362089 75362089 + Silent SNP G G A rs763365007 C3L-00144_T C3L-00144_N G G c.1017C>T p.= p.H339H ENST00000377636 2/21 161 116 45 141 141 0 strelka-varscan-mutect TBC1D4,synonymous_variant,p.=,ENST00000377636,NM_014832.3;TBC1D4,synonymous_variant,p.=,ENST00000431480,NM_001286658.1;TBC1D4,synonymous_variant,p.=,ENST00000377625,NM_001286659.1; A ENST00000377636 Transcript synonymous_variant 1364/6364 1017/3897 339/1298 H caC/caT rs763365007 1 -1 TBC1D4 HGNC HGNC:19165 protein_coding YES CCDS41901.1 ENSP00000366863 O60343 UPI00001AE7B3 NM_014832.3 2/21 SMART_domains:SM00462,Superfamily_domains:SSF50729 LOW 1 SNV 2 1 PASS rs763365007 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 75362089 75362089 G A 1 0 0 0 0 0 0 0 1 16027 1136 40 1 1 TBC1D4 13 75362089 Silent SNP G C3L-00144_T 3495850 75362089 39002239 1221 5292 UCHL3 0 . GRCh38 13 75569499 75569499 + Nonsense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.466C>T p.Gln156Ter p.Q156* ENST00000377595 6/9 153 145 8 135 135 0 strelka-varscan-mutect UCHL3,stop_gained,p.Gln120Ter,ENST00000618773,NM_001270952.1;UCHL3,stop_gained,p.Gln156Ter,ENST00000377595,NM_006002.4;UCHL3,stop_gained,p.Gln90Ter,ENST00000419068,;RP11-29G8.3,non_coding_transcript_exon_variant,,ENST00000563635,;UCHL3,non_coding_transcript_exon_variant,,ENST00000606347,;UCHL3,non_coding_transcript_exon_variant,,ENST00000471792,;RP11-29G8.3,non_coding_transcript_exon_variant,,ENST00000570285,; T ENST00000377595 Transcript stop_gained 496/844 466/693 156/230 Q/* Cag/Tag 1 1 UCHL3 HGNC HGNC:12515 protein_coding YES CCDS9453.1 ENSP00000366819 P15374 A0A140VJZ4 UPI000004D00E NM_006002.4 6/9 hmmpanther:PTHR10589:SF24,hmmpanther:PTHR10589,Pfam_domain:PF01088,Gene3D:3.40.532.10,Superfamily_domains:SSF54001 HIGH 1 SNV 1 1 PASS . . 0 204 0 6 0 0 0 0 -10.39544 0.988059 1 1 1 0 T 4 4 12 75569499 75569499 C T 1 0 0 0 0 0 1 0 0 17445 827 29 3 3 UCHL3 13 75569499 Nonsense_Mutation SNP C C3L-00144_T 207410 75569499 38794829 1222 5293 ACOD1 0 . GRCh38 13 76957524 76957524 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.985G>A p.Glu329Lys p.E329K ENST00000377462 5/5 371 294 77 297 296 1 strelka-varscan-mutect ACOD1,missense_variant,p.Glu329Lys,ENST00000377462,NM_001258406.1;ACOD1,missense_variant,p.Glu329Lys,ENST00000449753,; A ENST00000377462 Transcript missense_variant 1047/2165 985/1446 329/481 E/K Gaa/Aaa 1 1 ACOD1 HGNC HGNC:33904 protein_coding YES CCDS58299.1 ENSP00000366682 A6NK06 UPI000015C60D NM_001258406.1 deleterious(0) 5/5 hmmpanther:PTHR16943:SF11,hmmpanther:PTHR16943,Gene3D:1szqA02,Pfam_domain:PF03972,Superfamily_domains:0043815 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 76957524 76957524 G A 1 0 0 0 0 1 0 0 0 189 1291 45 3 3 ACOD1 13 76957524 Missense_Mutation SNP G C3L-00144_T 1388025 76957524 37406804 1223 5294 SLITRK1 0 . GRCh38 13 83880158 83880158 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1350G>T p.Glu450Asp p.E450D ENST00000377084 1/1 176 160 16 174 174 0 strelka-mutect SLITRK1,missense_variant,p.Glu450Asp,ENST00000377084,NM_052910.2,NM_001281503.1; A ENST00000377084 Transcript missense_variant 2236/5189 1350/2091 450/696 E/D gaG/gaT 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 deleterious(0) 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 83880158 83880158 C A 1 0 0 0 0 1 0 0 0 15033 564 20 2 2 SLITRK1 13 83880158 Missense_Mutation SNP C C3L-00144_T 6922634 83880158 30484170 1224 5295 SLITRK6 0 . GRCh38 13 85794980 85794980 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.1529C>T p.Thr510Ile p.T510I ENST00000400286 2/2 230 177 53 221 221 0 strelka-varscan-mutect SLITRK6,missense_variant,p.Thr510Ile,ENST00000400286,NM_032229.2; A ENST00000400286 Transcript missense_variant 2128/4318 1529/2526 510/841 T/I aCc/aTc COSM5282698 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 tolerated(0.51) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF5,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 85794980 85794980 G A 1 0 0 0 0 1 0 0 0 15038 1261 44 3 3 SLITRK6 13 85794980 Missense_Mutation SNP G C3L-00144_T 1914822 85794980 28569348 1225 5296 DZIP1 0 . GRCh38 13 95641645 95641645 + Frame_Shift_Del DEL C C - rs781323042 C3L-00144_T C3L-00144_N C C c.247delG p.Ala83LeufsTer5 p.A83Lfs*5 ENST00000347108 3/21 219 179 40 192 192 0 sindel-varindel-pindel DZIP1,frameshift_variant,p.Ala83LeufsTer5,ENST00000361396,NM_014934.4;DZIP1,frameshift_variant,p.Ala83LeufsTer5,ENST00000347108,;DZIP1,frameshift_variant,p.Ala83LeufsTer5,ENST00000361156,;DZIP1,frameshift_variant,p.Ala83LeufsTer5,ENST00000376829,NM_198968.3;DZIP1,non_coding_transcript_exon_variant,,ENST00000466027,;DZIP1,frameshift_variant,p.Ala129LeufsTer5,ENST00000466569,; - ENST00000347108 Transcript frameshift_variant 680/7068 247/2604 83/867 A/X Gct/ct rs781323042 1 -1 DZIP1 HGNC HGNC:20908 protein_coding YES CCDS9478.1 ENSP00000257312 Q86YF9 UPI000000D9B8 3/21 hmmpanther:PTHR21502,hmmpanther:PTHR21502:SF5,Pfam_domain:PF13815 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 95641645 95641645 C - 1 0 1 0 1 0 0 0 0 4687 739 26 0 0 DZIP1 13 95641645 Frame_Shift_Del DEL C C3L-00144_T 9846665 95641645 18722683 1226 5297 DNAJC3 0 . GRCh38 13 95725220 95725220 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.361C>G p.Leu121Val p.L121V ENST00000602402 4/12 127 113 14 139 139 0 strelka-varscan-mutect DNAJC3,missense_variant,p.Leu121Val,ENST00000602402,NM_006260.4;DNAJC3,missense_variant,p.Leu121Val,ENST00000376795,; G ENST00000602402 Transcript missense_variant 478/5591 361/1515 121/504 L/V Ctt/Gtt 1 1 DNAJC3 HGNC HGNC:9439 protein_coding YES CCDS9479.1 ENSP00000473631 Q13217 A8KA82 UPI000006F088 NM_006260.4 tolerated(0.07) 4/12 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,Pfam_domain:PF09976,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs1226556031 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 95725220 95725220 C G 1 0 0 0 0 1 0 0 0 4460 565 20 4 4 DNAJC3 13 95725220 Missense_Mutation SNP C C3L-00144_T 83575 95725220 18639108 1227 5298 ITGBL1 0 . GRCh38 13 101567741 101567741 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.359G>T p.Gly120Val p.G120V ENST00000376180 3/11 121 112 9 113 113 0 strelka-mutect ITGBL1,missense_variant,p.Gly120Val,ENST00000376180,NM_004791.2;ITGBL1,missense_variant,p.Gly27Val,ENST00000622834,;ITGBL1,missense_variant,p.Gly27Val,ENST00000376162,NM_001271756.1;ITGBL1,5_prime_UTR_variant,,ENST00000545560,NM_001271754.1;ITGBL1,intron_variant,,ENST00000618057,NM_001271755.1; T ENST00000376180 Transcript missense_variant 578/2494 359/1485 120/494 G/V gGa/gTa 1 1 ITGBL1 HGNC HGNC:6164 protein_coding YES CCDS9499.1 ENSP00000365351 O95965 A0A024RDW7 UPI0000073C95 NM_004791.2 deleterious(0) 3/11 hmmpanther:PTHR10082:SF3,hmmpanther:PTHR10082,Gene3D:2.10.25.10,Pfam_domain:PF07974,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 101567741 101567741 G T 1 0 0 0 0 1 0 0 0 7808 1174 41 2 2 ITGBL1 13 101567741 Missense_Mutation SNP G C3L-00144_T 5842521 101567741 12796587 1228 5299 FGF14 0 . GRCh38 13 101916453 101916453 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.193G>T p.Asp65Tyr p.D65Y ENST00000376143 1/5 380 340 40 419 418 1 strelka-varscan-mutect FGF14,missense_variant,p.Asp65Tyr,ENST00000376143,NM_004115.3;FGF14,intron_variant,,ENST00000376131,NM_175929.2; A ENST00000376143 Transcript missense_variant,splice_region_variant 193/744 193/744 65/247 D/Y Gat/Tat COSM4841746 1 -1 FGF14 HGNC HGNC:3671 protein_coding CCDS9501.1 ENSP00000365313 Q92915 UPI000003C0F2 NM_004115.3 deleterious(0.02) 1/5 hmmpanther:PTHR11486:SF18,hmmpanther:PTHR11486,Gene3D:2.80.10.50 1 MODERATE SNV 1 1 1 PASS rs1199591646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 101916453 101916453 C A 1 0 0 0 0 1 0 0 0 5707 695 24 2 2 FGF14 13 101916453 Missense_Mutation SNP C C3L-00144_T 348712 101916453 12447875 1229 5300 TPP2 0 . GRCh38 13 102627068 102627068 + Nonsense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.841G>T p.Glu281Ter p.E281* ENST00000376065 7/29 76 71 5 53 52 1 strelka-mutect TPP2,stop_gained,p.Glu281Ter,ENST00000376052,;TPP2,stop_gained,p.Glu281Ter,ENST00000376065,NM_003291.2;TPP2,non_coding_transcript_exon_variant,,ENST00000496126,;TPP2,upstream_gene_variant,,ENST00000493770,; T ENST00000376065 Transcript stop_gained 877/3931 841/3750 281/1249 E/* Gaa/Taa COSM696119 1 1 TPP2 HGNC HGNC:12016 protein_coding YES CCDS9502.1 ENSP00000365233 P29144 UPI0000001C91 NM_003291.2 7/29 hmmpanther:PTHR10795,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 102627068 102627068 G T 1 0 0 0 0 0 1 0 0 16893 1291 45 2 2 TPP2 13 102627068 Nonsense_Mutation SNP G C3L-00144_T 710615 102627068 11737260 1230 5301 CCDC168 0 . GRCh38 13 102730888 102730888 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.19809delG p.Leu6603PhefsTer12 p.L6603Ffs*12 ENST00000322527 4/4 129 110 19 152 152 0 sindel-varindel CCDC168,frameshift_variant,p.Leu6603PhefsTer12,ENST00000322527,NM_001146197.1; - ENST00000322527 Transcript frameshift_variant 19947/21466 19809/21246 6603/7081 L/X ttG/tt 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 HIGH 1 deletion 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 102730888 102730888 C - 1 0 1 0 1 0 0 0 0 2484 477 17 0 0 CCDC168 13 102730888 Frame_Shift_Del DEL C C3L-00144_T 103820 102730888 11633440 1231 5302 CCDC168 0 . GRCh38 13 102742503 102742503 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.8194C>A p.Leu2732Ile p.L2732I ENST00000322527 4/4 109 95 14 135 134 1 strelka-varscan-mutect CCDC168,missense_variant,p.Leu2732Ile,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; T ENST00000322527 Transcript missense_variant 8332/21466 8194/21246 2732/7081 L/I Ctt/Att 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.62) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 208 0 2 0 0 0 0 -19.99469 0.9999999 1 1 1 0 T 3 4 12 102742503 102742503 G T 1 0 0 0 0 1 0 0 0 2484 1029 36 2 2 CCDC168 13 102742503 Missense_Mutation SNP G C3L-00144_T 11615 102742503 11621825 1232 5303 CCDC168 0 . GRCh38 13 102744106 102744106 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.6591G>C p.Trp2197Cys p.W2197C ENST00000322527 4/4 226 179 47 217 217 0 strelka-varscan-mutect CCDC168,missense_variant,p.Trp2197Cys,ENST00000322527,NM_001146197.1;LINC00283,non_coding_transcript_exon_variant,,ENST00000430111,; G ENST00000322527 Transcript missense_variant 6729/21466 6591/21246 2197/7081 W/C tgG/tgC 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious_low_confidence(0.01) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 102744106 102744106 C G 1 0 0 0 0 1 0 0 0 2484 508 18 4 4 CCDC168 13 102744106 Missense_Mutation SNP C C3L-00144_T 1603 102744106 11620222 1233 5304 KDELC1 0 . GRCh38 13 102789011 102789012 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.1293_1293+1insA p.Ala432SerfsTer15 p.A432Sfs*15 ENST00000376004 117 102 15 130 130 0 sindel-varindel-pindel KDELC1,frameshift_variant,p.Ala432SerfsTer15,ENST00000376004,NM_024089.2;KDELC1,splice_region_variant,,ENST00000460338,;KDELC1,intron_variant,,ENST00000484943,;KDELC1,downstream_gene_variant,,ENST00000486540,; T ENST00000376004 Transcript frameshift_variant,splice_region_variant 1630-1631/2060 1293-1294/1509 431-432/502 -/X -/A 1 -1 KDELC1 HGNC HGNC:19350 protein_coding YES CCDS9504.1 ENSP00000365172 Q6UW63 UPI000004C663 NM_024089.2 hmmpanther:PTHR12203,hmmpanther:PTHR12203:SF21,Pfam_domain:PF05686,SMART_domains:SM00672 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 12 102789011 102789011 - T 1 0 1 1 0 0 0 0 0 8034 521 18 0 0 KDELC1 13 102789011 Frame_Shift_Ins INS - C3L-00144_T 44905 102789011 11575317 1234 5305 TMEM255B 0 . GRCh38 13 113804948 113804948 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.733C>A p.Gln245Lys p.Q245K ENST00000375353 8/9 103 96 7 85 84 1 strelka-mutect TMEM255B,missense_variant,p.Gln245Lys,ENST00000375353,NM_182614.2;TMEM255B,non_coding_transcript_exon_variant,,ENST00000467169,;TMEM255B,downstream_gene_variant,,ENST00000498692,; A ENST00000375353 Transcript missense_variant 760/6100 733/981 245/326 Q/K Cag/Aag COSM3417399 1 1 TMEM255B HGNC HGNC:28297 protein_coding YES CCDS45071.1 ENSP00000364502 Q8WV15 UPI0000071C2C NM_182614.2 tolerated(0.11) 8/9 hmmpanther:PTHR33721:SF3,hmmpanther:PTHR33721,Pfam_domain:PF14967 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 113804948 113804948 C A 1 0 0 0 0 1 0 0 0 16615 595 21 2 2 TMEM255B 13 113804948 Missense_Mutation SNP C C3L-00144_T 11015937 113804948 559380 1235 5306 POTEM 0 . GRCh38 14 18967984 18967984 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.499A>T p.Asn167Tyr p.N167Y ENST00000547889 1/11 170 155 15 178 177 1 varscan-mutect POTEM,missense_variant,p.Asn167Tyr,ENST00000547889,NM_001145442.1;POTEM,missense_variant,p.Asn167Tyr,ENST00000552966,;POTEM,missense_variant,p.Asn167Tyr,ENST00000616847,; T ENST00000547889 Transcript missense_variant 551/1817 499/1527 167/508 N/Y Aac/Tac 1 1 POTEM HGNC HGNC:37096 protein_coding YES CCDS73609.1 ENSP00000448062 A6NI47 UPI00006C1407 NM_001145442.1 deleterious(0.01) 1/11 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 18967984 18967984 A T 1 0 0 0 0 1 0 0 0 12384 246 9 4 4 POTEM 14 18967984 Missense_Mutation SNP A C3L-00144_T 18967984 88075734 1236 5307 POTEG 0 . GRCh38 14 19425689 19425689 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.834T>A p.= p.L278L ENST00000547848 4/11 119 109 10 142 142 0 varscan-mutect POTEG,synonymous_variant,p.=,ENST00000547848,NM_001005356.2;RNU6-1268P,upstream_gene_variant,,ENST00000391214,;RP11-244H18.1,downstream_gene_variant,,ENST00000621705,;POTEG,synonymous_variant,p.=,ENST00000622767,;POTEG,3_prime_UTR_variant,,ENST00000547722,; T ENST00000547848 Transcript synonymous_variant 886/2204 834/1527 278/508 L ctT/ctA 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 4/11 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 65 144 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 19425689 19425689 A T 1 0 0 0 0 0 0 0 1 12380 117 5 4 4 POTEG 14 19425689 Silent SNP A C3L-00144_T 457705 19425689 87618029 1237 5308 OR4N2 0 . GRCh38 14 19828082 19828082 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.634C>A p.Leu212Met p.L212M ENST00000315947 1/1 344 326 18 372 372 0 varscan-mutect OR4N2,missense_variant,p.Leu212Met,ENST00000315947,NM_001004723.2;OR4N2,downstream_gene_variant,,ENST00000557414,;OR4N2,downstream_gene_variant,,ENST00000557677,; A ENST00000315947 Transcript missense_variant 634/924 634/924 212/307 L/M Ctg/Atg COSM954077 1 1 OR4N2 HGNC HGNC:14742 protein_coding YES CCDS32022.1 ENSP00000319601 Q8NGD1 A0A126GVT2 UPI000004A5DF NM_001004723.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF439,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 19828082 19828082 C A 1 0 0 0 0 1 0 0 0 11153 912 32 2 2 OR4N2 14 19828082 Missense_Mutation SNP C C3L-00144_T 402393 19828082 87215636 1238 5309 OR4N2 0 . GRCh38 14 19828321 19828321 + Missense_Mutation SNP C C A rs778283039 C3L-00144_T C3L-00144_N C C c.873C>A p.Asn291Lys p.N291K ENST00000315947 1/1 232 213 19 250 250 0 strelka-varscan-mutect OR4N2,missense_variant,p.Asn291Lys,ENST00000315947,NM_001004723.2;OR4N2,downstream_gene_variant,,ENST00000557414,;OR4N2,downstream_gene_variant,,ENST00000557677,; A ENST00000315947 Transcript missense_variant 873/924 873/924 291/307 N/K aaC/aaA rs778283039 1 1 OR4N2 HGNC HGNC:14742 protein_coding YES CCDS32022.1 ENSP00000319601 Q8NGD1 A0A126GVT2 UPI000004A5DF NM_001004723.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF439,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs778283039 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 19828321 19828321 C A 1 0 0 0 0 1 0 0 0 11153 506 18 2 2 OR4N2 14 19828321 Missense_Mutation SNP C C3L-00144_T 239 19828321 87215397 1239 5310 OR4K5 0 . GRCh38 14 19921554 19921554 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.948A>G p.= p.L316L ENST00000315915 1/1 113 96 17 113 113 0 strelka-varscan-mutect OR4K5,synonymous_variant,p.=,ENST00000315915,NM_001005483.1; G ENST00000315915 Transcript synonymous_variant 973/1078 948/972 316/323 L ctA/ctG 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 1/1 Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 19921554 19921554 A G 1 0 0 0 0 0 0 0 1 11150 407 15 5 5 OR4K5 14 19921554 Silent SNP A C3L-00144_T 93233 19921554 87122164 1240 5311 OR4K1 0 . GRCh38 14 19935927 19935927 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.261T>A p.= p.I87I ENST00000285600 1/1 412 378 34 390 390 0 strelka-varscan-mutect OR4K1,synonymous_variant,p.=,ENST00000285600,NM_001004063.2; A ENST00000285600 Transcript synonymous_variant 320/1076 261/936 87/311 I atT/atA 1 1 OR4K1 HGNC HGNC:14726 protein_coding YES CCDS32025.1 ENSP00000285600 Q8NGD4 UPI0000041B4A NM_001004063.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF182,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1478663859 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 19935927 19935927 T A 1 0 0 0 0 0 0 0 1 11144 1800 63 4 4 OR4K1 14 19935927 Silent SNP T C3L-00144_T 14373 19935927 87107791 1241 5312 OR4K15 0 . GRCh38 14 19976180 19976180 + Nonsense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.662T>A p.Leu221Ter p.L221* ENST00000305051 1/1 298 265 33 233 233 0 strelka-varscan-mutect OR4K15,stop_gained,p.Leu221Ter,ENST00000305051,NM_001005486.1; A ENST00000305051 Transcript stop_gained 737/1216 662/1047 221/348 L/* tTa/tAa 1 1 OR4K15 HGNC HGNC:15353 protein_coding YES CCDS32026.1 ENSP00000304077 Q8NH41 UPI000015F249 NM_001005486.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF287,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 19976180 19976180 T A 1 0 0 0 0 0 1 0 0 11147 1764 61 4 4 OR4K15 14 19976180 Nonsense_Mutation SNP T C3L-00144_T 40253 19976180 87067538 1242 5313 OR4K17 0 . GRCh38 14 20118120 20118120 + Silent SNP C C A C3L-00144_T C3L-00144_N C C c.714C>A p.= p.S238S ENST00000315543 1/1 233 205 28 209 208 1 strelka-varscan-mutect OR4K17,synonymous_variant,p.=,ENST00000315543,NM_001004715.1; A ENST00000315543 Transcript synonymous_variant 714/1032 714/1032 238/343 S tcC/tcA COSM697646 1 1 OR4K17 HGNC HGNC:15355 protein_coding YES CCDS32030.1 ENSP00000319197 Q8NGC6 A0A126GVZ4 UPI000004B1EA NM_001004715.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF322,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS rs1229323000 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 20118120 20118120 C A 1 0 0 0 0 0 0 0 1 11148 610 22 2 2 OR4K17 14 20118120 Silent SNP C C3L-00144_T 141940 20118120 86925598 1243 5314 NDRG2 0 . GRCh38 14 21018794 21018795 + Frame_Shift_Ins INS - - C novel C3L-00144_T C3L-00144_N - - c.781dupG p.Val261GlyfsTer8 p.V261Gfs*8 ENST00000556147 12/16 110 94 16 94 94 0 sindel-varindel-pindel NDRG2,splice_donor_variant,,ENST00000397847,NM_001282215.1;NDRG2,frameshift_variant,p.Val261GlyfsTer8,ENST00000556147,NM_001320329.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000555158,NM_001282214.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000553503,NM_001282213.1;NDRG2,frameshift_variant,p.Val174GlyfsTer8,ENST00000554104,NM_001282216.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000350792,NM_016250.2;NDRG2,frameshift_variant,p.Val261GlyfsTer8,ENST00000298687,NM_201535.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000397844,NM_001282212.1;NDRG2,frameshift_variant,p.Val261GlyfsTer8,ENST00000397853,NM_201540.1;NDRG2,frameshift_variant,p.Val261GlyfsTer8,ENST00000397858,NM_201537.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000360463,NM_201536.1;NDRG2,frameshift_variant,p.Val261GlyfsTer8,ENST00000397851,NM_201539.1;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000554143,NM_201541.1,NM_201538.1;NDRG2,frameshift_variant,p.Val218GlyfsTer8,ENST00000298684,;NDRG2,frameshift_variant,p.Val257GlyfsTer8,ENST00000403829,NM_001282211.1;NDRG2,frameshift_variant,p.Val246GlyfsTer8,ENST00000397856,;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000555026,;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000556008,;NDRG2,frameshift_variant,p.Val247GlyfsTer8,ENST00000556974,;NDRG2,frameshift_variant,p.Val177GlyfsTer8,ENST00000553593,;NDRG2,frameshift_variant,p.Val174GlyfsTer8,ENST00000556366,;NDRG2,frameshift_variant,p.Val187GlyfsTer8,ENST00000635386,;NDRG2,intron_variant,,ENST00000557633,;NDRG2,downstream_gene_variant,,ENST00000553784,;NDRG2,downstream_gene_variant,,ENST00000555733,;NDRG2,downstream_gene_variant,,ENST00000555869,;NDRG2,downstream_gene_variant,,ENST00000557169,;NDRG2,downstream_gene_variant,,ENST00000553867,;NDRG2,downstream_gene_variant,,ENST00000555384,;NDRG2,downstream_gene_variant,,ENST00000556420,;NDRG2,downstream_gene_variant,,ENST00000554531,;NDRG2,downstream_gene_variant,,ENST00000553442,;NDRG2,downstream_gene_variant,,ENST00000556457,;NDRG2,downstream_gene_variant,,ENST00000557676,;NDRG2,downstream_gene_variant,,ENST00000554561,;NDRG2,downstream_gene_variant,,ENST00000555142,;NDRG2,downstream_gene_variant,,ENST00000556329,;NDRG2,downstream_gene_variant,,ENST00000556924,;NDRG2,downstream_gene_variant,,ENST00000554094,;NDRG2,downstream_gene_variant,,ENST00000557264,;NDRG2,downstream_gene_variant,,ENST00000554472,;NDRG2,downstream_gene_variant,,ENST00000554419,;NDRG2,downstream_gene_variant,,ENST00000556688,;NDRG2,downstream_gene_variant,,ENST00000557149,;NDRG2,downstream_gene_variant,,ENST00000556561,;NDRG2,downstream_gene_variant,,ENST00000554893,;NDRG2,downstream_gene_variant,,ENST00000555657,;NDRG2,downstream_gene_variant,,ENST00000554489,;NDRG2,downstream_gene_variant,,ENST00000554833,;NDRG2,downstream_gene_variant,,ENST00000557274,;NDRG2,downstream_gene_variant,,ENST00000554398,;NDRG2,downstream_gene_variant,,ENST00000554483,;NDRG2,downstream_gene_variant,,ENST00000557182,;NDRG2,downstream_gene_variant,,ENST00000554415,;NDRG2,downstream_gene_variant,,ENST00000449431,;NDRG2,downstream_gene_variant,,ENST00000553563,;NDRG2,downstream_gene_variant,,ENST00000622747,;NDRG2,downstream_gene_variant,,ENST00000554277,;NDRG2,3_prime_UTR_variant,,ENST00000557353,;NDRG2,non_coding_transcript_exon_variant,,ENST00000556716,;NDRG2,non_coding_transcript_exon_variant,,ENST00000555650,;NDRG2,non_coding_transcript_exon_variant,,ENST00000553793,;NDRG2,non_coding_transcript_exon_variant,,ENST00000557416,;NDRG2,downstream_gene_variant,,ENST00000553741,;NDRG2,downstream_gene_variant,,ENST00000555695,;NDRG2,downstream_gene_variant,,ENST00000553862,;NDRG2,downstream_gene_variant,,ENST00000557669,;NDRG2,downstream_gene_variant,,ENST00000557305,;NDRG2,downstream_gene_variant,,ENST00000557728,;NDRG2,downstream_gene_variant,,ENST00000557198,;NDRG2,downstream_gene_variant,,ENST00000557616,;NDRG2,downstream_gene_variant,,ENST00000553900,;NDRG2,downstream_gene_variant,,ENST00000366204,;NDRG2,downstream_gene_variant,,ENST00000555767,;NDRG2,downstream_gene_variant,,ENST00000557113,;NDRG2,downstream_gene_variant,,ENST00000557167,;NDRG2,downstream_gene_variant,,ENST00000553567,;NDRG2,downstream_gene_variant,,ENST00000554379,;NDRG2,downstream_gene_variant,,ENST00000557318,; C ENST00000556147 Transcript frameshift_variant 1722-1723/2880 781-782/1116 261/371 V/GX gta/gGta 1 -1 NDRG2 HGNC HGNC:14460 protein_coding YES CCDS9565.1 ENSP00000451712 Q9UN36 UPI000012FEDE NM_001320329.1 12/16 Gene3D:3.40.50.1820,Pfam_domain:PF03096,hmmpanther:PTHR11034,hmmpanther:PTHR11034:SF17,Superfamily_domains:SSF53474 HIGH 1 insertion 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 12 21018794 21018794 - C 1 0 1 1 0 0 0 0 0 10273 405 14 0 0 NDRG2 14 21018794 Frame_Shift_Ins INS - C3L-00144_T 900674 21018794 86024924 1244 5315 OR10G3 0 . GRCh38 14 21570596 21570597 + Frame_Shift_Ins INS - - A novel C3L-00144_T C3L-00144_N - - c.148dupT p.Trp50LeufsTer22 p.W50Lfs*22 ENST00000303532 1/1 224 206 18 191 191 0 sindel-varindel-pindel OR10G3,frameshift_variant,p.Trp50LeufsTer22,ENST00000303532,NM_001005465.1; A ENST00000303532 Transcript frameshift_variant 148-149/942 148-149/942 50/313 W/LX tgg/tTgg 1 -1 OR10G3 HGNC HGNC:8171 protein_coding YES CCDS32046.1 ENSP00000302437 Q8NGC4 A0A126GWE3 UPI000003CAB2 NM_001005465.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF69,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 insertion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 12 21570596 21570596 - A 1 0 1 1 0 0 0 0 0 10976 595 21 0 0 OR10G3 14 21570596 Frame_Shift_Ins INS - C3L-00144_T 551802 21570596 85473122 1245 5316 OR6J1 0 . GRCh38 14 22634026 22634026 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.786C>A p.= p.S262S ENST00000540461 1/1 219 179 40 211 211 0 strelka-varscan-mutect OR6J1,synonymous_variant,p.=,ENST00000540461,;AC243945.1,downstream_gene_variant,,ENST00000623775,; T ENST00000540461 Transcript synonymous_variant 786/1044 786/1044 262/347 S tcC/tcA 1 -1 OR6J1 HGNC HGNC:14707 protein_coding YES ENSP00000437629 Q8NGC5 UPI000462094B 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF53,hmmpanther:PTHR26454,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 22634026 22634026 G T 1 0 0 0 0 0 0 0 1 11270 1219 43 2 2 OR6J1 14 22634026 Silent SNP G C3L-00144_T 1063430 22634026 84409692 1246 5317 PCK2 0 . GRCh38 14 24099582 24099582 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.877G>T p.Gly293Trp p.G293W ENST00000216780 6/10 72 57 15 51 51 0 strelka-varscan-mutect PCK2,missense_variant,p.Gly159Trp,ENST00000545054,NM_001308054.1;PCK2,missense_variant,p.Gly159Trp,ENST00000558096,;PCK2,missense_variant,p.Gly293Trp,ENST00000216780,NM_004563.3;PCK2,missense_variant,p.Gly159Trp,ENST00000561286,NM_001291556.1;PCK2,missense_variant,p.Gly293Trp,ENST00000396973,NM_001018073.2;PCK2,missense_variant,p.Gly305Trp,ENST00000559250,;NRL,intron_variant,,ENST00000561028,;NRL,intron_variant,,ENST00000558280,;NRL,upstream_gene_variant,,ENST00000396997,;PCK2,downstream_gene_variant,,ENST00000560736,;PCK2,downstream_gene_variant,,ENST00000559837,;PCK2,upstream_gene_variant,,ENST00000559171,;PCK2,downstream_gene_variant,,ENST00000560657,;PCK2,3_prime_UTR_variant,,ENST00000559503,;PCK2,non_coding_transcript_exon_variant,,ENST00000558674,;PCK2,non_coding_transcript_exon_variant,,ENST00000561050,;PCK2,downstream_gene_variant,,ENST00000560106,;PCK2,downstream_gene_variant,,ENST00000559584,;PCK2,upstream_gene_variant,,ENST00000557969,; T ENST00000216780 Transcript missense_variant 1145/2357 877/1923 293/640 G/W Ggg/Tgg 1 1 PCK2 HGNC HGNC:8725 protein_coding YES CCDS9609.1 ENSP00000216780 Q16822 UPI0000169DF3 NM_004563.3 deleterious(0) 6/10 HAMAP:MF_00452,hmmpanther:PTHR11561,hmmpanther:PTHR11561:SF5,Gene3D:3.90.228.20,PIRSF_domain:PIRSF001348,Pfam_domain:PF00821,Superfamily_domains:SSF53795 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 24099582 24099582 G T 1 0 0 0 0 1 0 0 0 11670 1000 35 2 2 PCK2 14 24099582 Missense_Mutation SNP G C3L-00144_T 1465556 24099582 82944136 1247 5318 ADCY4 0 . GRCh38 14 24330199 24330199 + Missense_Mutation SNP G G A rs140776899 C3L-00144_T C3L-00144_N G G c.1027C>T p.Arg343Cys p.R343C ENST00000310677 8/26 157 112 45 131 131 0 strelka-mutect ADCY4,missense_variant,p.Arg343Cys,ENST00000310677,NM_139247.3,NM_001198568.1,NM_001198592.1;ADCY4,missense_variant,p.Arg343Cys,ENST00000554068,;ADCY4,missense_variant,p.Arg343Cys,ENST00000418030,;RP11-934B9.3,downstream_gene_variant,,ENST00000555591,;ADCY4,downstream_gene_variant,,ENST00000559167,;ADCY4,downstream_gene_variant,,ENST00000561138,;ADCY4,upstream_gene_variant,,ENST00000556932,;ADCY4,downstream_gene_variant,,ENST00000558563,;ADCY4,downstream_gene_variant,,ENST00000558125,;ADCY4,synonymous_variant,p.=,ENST00000554781,;ADCY4,non_coding_transcript_exon_variant,,ENST00000554577,;ADCY4,non_coding_transcript_exon_variant,,ENST00000545213,;ADCY4,intron_variant,,ENST00000557056,;ADCY4,downstream_gene_variant,,ENST00000557099,;ADCY4,downstream_gene_variant,,ENST00000554674,;ADCY4,upstream_gene_variant,,ENST00000554959,; A ENST00000310677 Transcript missense_variant 1141/3415 1027/3234 343/1077 R/C Cgc/Tgc rs140776899 1 -1 ADCY4 HGNC HGNC:235 protein_coding YES CCDS9627.1 ENSP00000312126 Q8NFM4 UPI00000398CC NM_139247.3,NM_001198568.1,NM_001198592.1 deleterious(0) 8/26 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF286,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 2 1 PASS rs140776899 . 0 202 5 3 0 0 0 0 -20 0.9999205 1 1 1 0 A 3 1 12 24330199 24330199 G A 1 0 0 0 0 1 0 0 0 340 1087 38 1 1 ADCY4 14 24330199 Missense_Mutation SNP G C3L-00144_T 230617 24330199 82713519 1248 5319 KHNYN 0 . GRCh38 14 24431515 24431515 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.254C>T p.Pro85Leu p.P85L ENST00000251343 3/8 56 52 4 68 68 0 strelka-varscan-mutect KHNYN,missense_variant,p.Pro85Leu,ENST00000251343,NM_001290256.1;KHNYN,missense_variant,p.Pro85Leu,ENST00000553935,NM_015299.2;KHNYN,missense_variant,p.Pro85Leu,ENST00000556842,NM_001290257.1;KHNYN,missense_variant,p.Pro85Leu,ENST00000556510,;CBLN3,upstream_gene_variant,,ENST00000267406,NM_001039771.2;KHNYN,upstream_gene_variant,,ENST00000554268,;CBLN3,upstream_gene_variant,,ENST00000555436,;KHNYN,upstream_gene_variant,,ENST00000556255,; T ENST00000251343 Transcript missense_variant 393/6725 254/2037 85/678 P/L cCg/cTg COSM4695105 1 1 KHNYN HGNC HGNC:20166 protein_coding YES CCDS32058.1 ENSP00000251343 O15037 UPI000000CC1F NM_001290256.1 deleterious(0) 3/8 hmmpanther:PTHR12876:SF28,hmmpanther:PTHR12876,Superfamily_domains:SSF54791 1 MODERATE 1 SNV 1 1 1 PASS rs1264990848 . 0 202 8 0 0 0 0 0 -9.816031 0.9999908 1 1 1 0 T 3 4 12 24431515 24431515 C T 1 0 0 0 0 1 0 0 0 8071 652 23 1 1 KHNYN 14 24431515 Missense_Mutation SNP C C3L-00144_T 101316 24431515 82612203 1249 5320 FOXG1 0 . GRCh38 14 28768585 28768585 + Missense_Mutation SNP G G C C3L-00144_T C3L-00144_N G G c.1306G>C p.Ala436Pro p.A436P ENST00000313071 1/1 404 321 83 351 351 0 strelka-varscan-mutect FOXG1,missense_variant,p.Ala436Pro,ENST00000313071,NM_005249.4;LINC01551,upstream_gene_variant,,ENST00000399387,;LINC01551,upstream_gene_variant,,ENST00000552957,;LINC01551,upstream_gene_variant,,ENST00000548213,;FOXG1-AS1,upstream_gene_variant,,ENST00000551395,;FOXG1-AS1,upstream_gene_variant,,ENST00000546560,;FOXG1-AS1,upstream_gene_variant,,ENST00000549487,;FOXG1,downstream_gene_variant,,ENST00000637817,;FOXG1,downstream_gene_variant,,ENST00000636893,;FOXG1,downstream_gene_variant,,ENST00000636353,;FOXG1,downstream_gene_variant,,ENST00000637220,;FOXG1,downstream_gene_variant,,ENST00000636346,;FOXG1,downstream_gene_variant,,ENST00000636604,;FOXG1,downstream_gene_variant,,ENST00000637351,; C ENST00000313071 Transcript missense_variant 3198/4890 1306/1470 436/489 A/P Gcc/Ccc COSM1207418 1 1 FOXG1 HGNC HGNC:3811 protein_coding YES CCDS9636.1 ENSP00000339004 P55316 UPI00001AE46C NM_005249.4 tolerated_low_confidence(0.18) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF165,Low_complexity_(Seg):seg 1 MODERATE SNV 1 1 PASS rs1301757713 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 28768585 28768585 G C 1 0 0 0 0 1 0 0 0 5869 1087 38 4 4 FOXG1 14 28768585 Missense_Mutation SNP G C3L-00144_T 4337070 28768585 78275133 1250 5321 GPR33 0 . GRCh38 14 31483027 31483027 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.939C>A p.= p.S313S ENST00000399285 2/2 55 48 7 57 57 0 strelka-varscan-mutect GPR33,synonymous_variant,p.=,ENST00000399285,NM_001197184.2; T ENST00000399285 Transcript synonymous_variant 994/1057 939/1002 313/333 S tcC/tcA 1 -1 GPR33 HGNC HGNC:4489 protein_coding YES CCDS73628.1 ENSP00000421557 Q49SQ1 UPI0000585CCE NM_001197184.2 2/2 hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF5,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.88695 1 1 1 1 0 T 2 4 12 31483027 31483027 G T 1 0 0 0 0 0 0 0 1 6573 1335 47 2 2 GPR33 14 31483027 Silent SNP G C3L-00144_T 2714442 31483027 75560691 1251 5322 NPAS3 0 . GRCh38 14 33215228 33215228 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.187C>A p.Arg63Ser p.R63S ENST00000356141 3/12 168 117 51 121 119 2 strelka-varscan-mutect NPAS3,missense_variant,p.Arg33Ser,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Arg33Ser,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Arg70Ser,ENST00000551492,;NPAS3,missense_variant,p.Arg63Ser,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Arg33Ser,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Arg40Ser,ENST00000551634,;NPAS3,5_prime_UTR_variant,,ENST00000547068,;NPAS3,5_prime_UTR_variant,,ENST00000551008,;NPAS3,upstream_gene_variant,,ENST00000546849,;NPAS3,non_coding_transcript_exon_variant,,ENST00000549770,; A ENST00000356141 Transcript missense_variant 187/2802 187/2802 63/933 R/S Cgc/Agc COSM5298451,COSM5298452,COSM5298453,COSM5298454 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious(0) 3/12 PROSITE_profiles:PS50888,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 33215228 33215228 C A 1 0 0 0 0 1 0 0 0 10612 652 23 1 1 NPAS3 14 33215228 Missense_Mutation SNP C C3L-00144_T 1732201 33215228 73828490 1252 5323 NPAS3 0 . GRCh38 14 33778493 33778493 + Silent SNP T T A novel C3L-00144_T C3L-00144_N T T c.1074T>A p.= p.P358P ENST00000356141 9/12 245 188 57 209 209 0 strelka-varscan-mutect NPAS3,synonymous_variant,p.=,ENST00000346562,NM_022123.2;NPAS3,synonymous_variant,p.=,ENST00000548645,NM_001165893.1;NPAS3,synonymous_variant,p.=,ENST00000551492,;NPAS3,synonymous_variant,p.=,ENST00000356141,NM_001164749.1;NPAS3,synonymous_variant,p.=,ENST00000357798,NM_173159.2;NPAS3,synonymous_variant,p.=,ENST00000551634,;NPAS3,synonymous_variant,p.=,ENST00000552874,; A ENST00000356141 Transcript synonymous_variant 1074/2802 1074/2802 358/933 P ccT/ccA 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 9/12 PROSITE_profiles:PS50112,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043,Pfam_domain:PF08447,Gene3D:3.30.450.20,SMART_domains:SM00091,Superfamily_domains:SSF55785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 33778493 33778493 T A 1 0 0 0 0 0 0 0 1 10612 1567 55 4 4 NPAS3 14 33778493 Silent SNP T C3L-00144_T 563265 33778493 73265225 1253 5324 NPAS3 0 . GRCh38 14 33800275 33800275 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1968C>A p.= p.I656I ENST00000356141 12/12 280 205 75 254 254 0 strelka-varscan-mutect NPAS3,synonymous_variant,p.=,ENST00000346562,NM_022123.2;NPAS3,synonymous_variant,p.=,ENST00000548645,NM_001165893.1;NPAS3,synonymous_variant,p.=,ENST00000551492,;NPAS3,synonymous_variant,p.=,ENST00000356141,NM_001164749.1;NPAS3,synonymous_variant,p.=,ENST00000357798,NM_173159.2;NPAS3,synonymous_variant,p.=,ENST00000551634,; A ENST00000356141 Transcript synonymous_variant 1968/2802 1968/2802 656/933 I atC/atA 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 12/12 hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 33800275 33800275 C A 1 0 0 0 0 0 0 0 1 10612 816 29 2 2 NPAS3 14 33800275 Silent SNP C C3L-00144_T 21782 33800275 73243443 1254 5325 BAZ1A 0 . GRCh38 14 34826031 34826031 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.518delG p.Ser173ThrfsTer52 p.S173Tfs*52 ENST00000360310 4/27 141 126 15 151 151 0 sindel-varindel-pindel BAZ1A,frameshift_variant,p.Ser173ThrfsTer52,ENST00000360310,NM_013448.2;BAZ1A,frameshift_variant,p.Ser173ThrfsTer52,ENST00000358716,NM_182648.1;BAZ1A,frameshift_variant,p.Ser173ThrfsTer52,ENST00000382422,;BAZ1A,downstream_gene_variant,,ENST00000553853,;BAZ1A,frameshift_variant,p.Ser64ThrfsTer11,ENST00000553573,; - ENST00000360310 Transcript frameshift_variant 1086/6010 518/4671 173/1556 S/X aGc/ac 1 -1 BAZ1A HGNC HGNC:960 protein_coding YES CCDS9651.1 ENSP00000353458 Q9NRL2 UPI00001584D3 NM_013448.2 4/27 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF173 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 34826031 34826031 C - 1 0 1 0 1 0 0 0 0 1474 797 28 0 0 BAZ1A 14 34826031 Frame_Shift_Del DEL C C3L-00144_T 1025756 34826031 72217687 1255 5326 MIA2 0 . GRCh38 14 39247892 39247892 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1318G>T p.Asp440Tyr p.D440Y ENST00000553728 4/28 127 92 35 122 121 1 strelka-varscan-mutect RP11-407N17.3,missense_variant,p.Asp440Tyr,ENST00000553728,;MIA2,missense_variant,p.Asp440Tyr,ENST00000280082,NM_054024.3;MIA2,non_coding_transcript_exon_variant,,ENST00000556784,; T ENST00000553728 Transcript missense_variant 1531/4392 1318/4020 440/1339 D/Y Gac/Tac 1 1 RP11-407N17.3 Clone_based_vega_gene protein_coding YES ENSP00000452252 G3V599 UPI00021CF1EF tolerated(0.58) 4/28 Low_complexity_(Seg):seg,hmmpanther:PTHR23158:SF38,hmmpanther:PTHR23158 MODERATE SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 39247892 39247892 G T 1 0 0 0 0 1 0 0 0 9521 942 33 2 2 MIA2 14 39247892 Missense_Mutation SNP G C3L-00144_T 4421861 39247892 67795826 1256 5327 FANCM 0 . GRCh38 14 45170589 45170589 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2003G>T p.Gly668Val p.G668V ENST00000267430 12/23 144 131 13 168 168 0 strelka-varscan-mutect FANCM,missense_variant,p.Gly668Val,ENST00000267430,NM_020937.2;FANCM,missense_variant,p.Gly642Val,ENST00000542564,NM_001308133.1;FANCM,missense_variant,p.Gly184Val,ENST00000556250,;FANCM,downstream_gene_variant,,ENST00000556036,NM_001308134.1; T ENST00000267430 Transcript missense_variant,splice_region_variant 2088/7111 2003/6147 668/2048 G/V gGa/gTa 1 1 FANCM HGNC HGNC:23168 protein_coding YES CCDS32070.1 ENSP00000267430 Q8IYD8 UPI000059F032 NM_020937.2 deleterious(0) 12/23 hmmpanther:PTHR14025:SF20,hmmpanther:PTHR14025 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.45112 0.9999998 1 1 1 0 T 3 4 12 45170589 45170589 G T 1 0 0 0 0 1 0 0 0 5531 1188 41 2 2 FANCM 14 45170589 Missense_Mutation SNP G C3L-00144_T 5922697 45170589 61873129 1257 5328 PYGL 0 . GRCh38 14 50909935 50909935 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2137G>T p.Gly713Cys p.G713C ENST00000216392 17/20 449 326 123 405 404 1 strelka-varscan-mutect PYGL,missense_variant,p.Gly713Cys,ENST00000216392,NM_002863.4;PYGL,missense_variant,p.Gly713Cys,ENST00000532462,;PYGL,missense_variant,p.Gly679Cys,ENST00000544180,NM_001163940.1;ABHD12B,downstream_gene_variant,,ENST00000337334,NM_001206673.1;ABHD12B,downstream_gene_variant,,ENST00000353130,NM_181814.1;RP11-218E20.5,upstream_gene_variant,,ENST00000557343,;PYGL,non_coding_transcript_exon_variant,,ENST00000532107,;ABHD12B,downstream_gene_variant,,ENST00000382029,NM_181533.3;ABHD12B,downstream_gene_variant,,ENST00000557345,; A ENST00000216392 Transcript missense_variant 2470/3048 2137/2544 713/847 G/C Ggc/Tgc 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 deleterious(0) 17/20 hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF12,TIGRFAM_domain:TIGR02093,Gene3D:3.40.50.2000,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 50909935 50909935 C A 1 0 0 0 0 1 0 0 0 13015 594 21 2 2 PYGL 14 50909935 Missense_Mutation SNP C C3L-00144_T 5739346 50909935 56133783 1258 5329 PYGL 0 . GRCh38 14 50944239 50944239 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.165G>T p.= p.A55A ENST00000216392 1/20 260 207 53 225 225 0 strelka-varscan-mutect PYGL,synonymous_variant,p.=,ENST00000216392,NM_002863.4;PYGL,synonymous_variant,p.=,ENST00000532462,;PYGL,synonymous_variant,p.=,ENST00000544180,NM_001163940.1;PYGL,non_coding_transcript_exon_variant,,ENST00000530336,; A ENST00000216392 Transcript synonymous_variant 498/3048 165/2544 55/847 A gcG/gcT 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 1/20 hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF12,TIGRFAM_domain:TIGR02093,Gene3D:3.40.50.2000,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS rs1462467753 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 50944239 50944239 C A 1 0 0 0 0 0 0 0 1 13015 755 27 1 1 PYGL 14 50944239 Silent SNP C C3L-00144_T 34304 50944239 56099479 1259 5330 NID2 0 . GRCh38 14 52060164 52060164 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.727A>C p.Ser243Arg p.S243R ENST00000216286 3/22 139 109 30 114 114 0 strelka-varscan-mutect NID2,missense_variant,p.Ser243Arg,ENST00000216286,NM_007361.3;NID2,intron_variant,,ENST00000617139,; G ENST00000216286 Transcript missense_variant 727/4811 727/4128 243/1375 S/R Agc/Cgc 1 -1 NID2 HGNC HGNC:13389 protein_coding YES CCDS9706.1 ENSP00000216286 Q14112 UPI000013C6E1 NM_007361.3 tolerated(0.05) 3/22 Pfam_domain:PF06119,PROSITE_profiles:PS51220,SMART_domains:SM00539 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 52060164 52060164 T G 1 0 0 0 0 1 0 0 0 10448 1580 55 5 5 NID2 14 52060164 Missense_Mutation SNP T C3L-00144_T 1115925 52060164 54983554 1260 5331 SYT16 0 . GRCh38 14 62075173 62075173 + Missense_Mutation SNP C C A rs773110798 C3L-00144_T C3L-00144_N C C c.775C>A p.Leu259Ile p.L259I ENST00000568344 3/6 185 138 47 190 189 1 strelka-varscan-mutect SYT16,missense_variant,p.Leu259Ile,ENST00000568344,NM_031914.2;SYT16,missense_variant,p.Leu149Ile,ENST00000636133,;SYT16,upstream_gene_variant,,ENST00000430451,;RP11-355I22.5,intron_variant,,ENST00000553990,;SYT16,missense_variant,p.Leu259Ile,ENST00000555409,; A ENST00000568344 Transcript missense_variant 972/13978 775/1938 259/645 L/I Ctc/Atc rs773110798 1 1 SYT16 HGNC HGNC:23142 protein_coding YES CCDS45121.1 ENSP00000478637 Q17RD7 UPI0000EE1AC0 NM_031914.2 tolerated(0.06) 3/6 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF113 MODERATE 1 SNV 1 1 PASS rs773110798 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 62075173 62075173 C A 1 0 0 0 0 1 0 0 0 15866 913 32 2 2 SYT16 14 62075173 Missense_Mutation SNP C C3L-00144_T 10015009 62075173 44968545 1261 5332 PPP1R36 0 . GRCh38 14 64587272 64587272 + Missense_Mutation SNP G G T rs768722132 C3L-00144_T C3L-00144_N G G c.790G>T p.Gly264Trp p.G264W ENST00000298705 10/12 109 99 10 112 112 0 strelka-varscan-mutect PPP1R36,missense_variant,p.Gly264Trp,ENST00000298705,NM_172365.2;RP11-973N13.3,intron_variant,,ENST00000556634,;RP11-973N13.3,intron_variant,,ENST00000554454,;PPP1R36,3_prime_UTR_variant,,ENST00000467261,;PPP1R36,non_coding_transcript_exon_variant,,ENST00000554400,;PPP1R36,non_coding_transcript_exon_variant,,ENST00000556023,; T ENST00000298705 Transcript missense_variant 886/1405 790/1269 264/422 G/W Ggg/Tgg rs768722132 1 1 PPP1R36 HGNC HGNC:20097 protein_coding YES CCDS9767.1 ENSP00000298705 Q96LQ0 UPI0000070446 NM_172365.2 deleterious(0) 10/12 hmmpanther:PTHR21055,Pfam_domain:PF14895 MODERATE 1 SNV 1 1 PASS rs768722132 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 64587272 64587272 G T 1 0 0 0 0 1 0 0 0 12490 1000 35 2 2 PPP1R36 14 64587272 Missense_Mutation SNP G C3L-00144_T 2512099 64587272 42456446 1262 5333 PLEK2 0 . GRCh38 14 67392745 67392745 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.586G>T p.Val196Leu p.V196L ENST00000216446 5/9 221 196 25 193 192 1 strelka-varscan-mutect PLEK2,missense_variant,p.Val196Leu,ENST00000216446,NM_016445.1;PLEK2,missense_variant,p.Val130Leu,ENST00000554395,;PLEK2,upstream_gene_variant,,ENST00000556532,;PLEK2,3_prime_UTR_variant,,ENST00000553387,;PLEK2,intron_variant,,ENST00000555803,; A ENST00000216446 Transcript missense_variant 727/1549 586/1062 196/353 V/L Gtg/Ttg 1 -1 PLEK2 HGNC HGNC:19238 protein_coding YES CCDS9782.1 ENSP00000216446 Q9NYT0 UPI0000035D89 NM_016445.1 tolerated(0.13) 5/9 PROSITE_profiles:PS50186,hmmpanther:PTHR12092,hmmpanther:PTHR12092:SF2,Pfam_domain:PF00610,Gene3D:1.10.10.10,SMART_domains:SM00049,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 67392745 67392745 C A 1 0 0 0 0 1 0 0 0 12147 478 17 2 2 PLEK2 14 67392745 Missense_Mutation SNP C C3L-00144_T 2805473 67392745 39650973 1263 5334 SMOC1 0 . GRCh38 14 70023363 70023363 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1207C>A p.Arg403Ser p.R403S ENST00000361956 11/12 337 257 80 288 287 1 strelka-varscan-mutect SMOC1,missense_variant,p.Arg403Ser,ENST00000381280,NM_022137.5;SMOC1,missense_variant,p.Arg403Ser,ENST00000361956,NM_001034852.2; A ENST00000361956 Transcript missense_variant 1470/2040 1207/1308 403/435 R/S Cgt/Agt 1 1 SMOC1 HGNC HGNC:20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF NM_001034852.2 deleterious(0) 11/12 hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF13,Gene3D:1.10.238.10,Pfam_domain:PF10591,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs1322307106 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 70023363 70023363 C A 1 0 0 0 0 1 0 0 0 15122 768 27 1 1 SMOC1 14 70023363 Missense_Mutation SNP C C3L-00144_T 2630618 70023363 37020355 1264 5335 HEATR4 0 . GRCh38 14 73520936 73520936 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.985C>T p.Gln329Ter p.Q329* ENST00000553558 4/18 199 176 23 157 157 0 strelka-varscan-mutect HEATR4,stop_gained,p.Gln329Ter,ENST00000553558,NM_001220484.1;HEATR4,stop_gained,p.Gln329Ter,ENST00000334988,NM_203309.2;HEATR4,downstream_gene_variant,,ENST00000556455,;HEATR4,downstream_gene_variant,,ENST00000563329,;HEATR4,downstream_gene_variant,,ENST00000557603,;RP3-414A15.11,upstream_gene_variant,,ENST00000553394,;RP3-414A15.2,upstream_gene_variant,,ENST00000555972,; A ENST00000553558 Transcript stop_gained 1307/3523 985/3081 329/1026 Q/* Cag/Tag 1 -1 HEATR4 HGNC HGNC:16761 protein_coding YES CCDS9815.2 ENSP00000450444 Q86WZ0 UPI00001FD7FD NM_001220484.1 4/18 hmmpanther:PTHR12697,hmmpanther:PTHR12697:SF20 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 73520936 73520936 G A 1 0 0 0 0 0 1 0 0 6912 1357 47 3 3 HEATR4 14 73520936 Nonsense_Mutation SNP G C3L-00144_T 3497573 73520936 33522782 1265 5336 ENTPD5 0 . GRCh38 14 73976352 73976352 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.614C>A p.Thr205Asn p.T205N ENST00000334696 9/16 278 239 39 227 227 0 strelka-varscan-mutect ENTPD5,missense_variant,p.Thr205Asn,ENST00000334696,NM_001249.2;ENTPD5,missense_variant,p.Thr205Asn,ENST00000557325,;ENTPD5,missense_variant,p.Thr205Asn,ENST00000553284,;ENTPD5,upstream_gene_variant,,ENST00000555829,; T ENST00000334696 Transcript missense_variant 934/5842 614/1287 205/428 T/N aCc/aAc 1 -1 ENTPD5 HGNC HGNC:3367 protein_coding YES CCDS9825.1 ENSP00000335246 O75356 A0A024R6D3 UPI0000052B69 NM_001249.2 deleterious(0) 9/16 hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF35,Pfam_domain:PF01150 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 12 73976352 73976352 G T 1 0 0 0 0 1 0 0 0 4987 1261 44 2 2 ENTPD5 14 73976352 Missense_Mutation SNP G C3L-00144_T 455416 73976352 33067366 1266 5337 YLPM1 0 . GRCh38 14 74799215 74799215 + Missense_Mutation SNP T T A rs751081719 C3L-00144_T C3L-00144_N T T c.3918T>A p.Asn1306Lys p.N1306K ENST00000325680 5/21 238 197 41 230 228 2 strelka-varscan-mutect YLPM1,missense_variant,p.Asn1306Lys,ENST00000325680,NM_019589.2;YLPM1,intron_variant,,ENST00000552421,;YLPM1,missense_variant,p.Asn859Lys,ENST00000549293,; A ENST00000325680 Transcript missense_variant 4042/7108 3918/6441 1306/2146 N/K aaT/aaA rs751081719 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 tolerated_low_confidence(0.17) 5/21 hmmpanther:PTHR13413,hmmpanther:PTHR13413:SF0 MODERATE 1 SNV 5 1 PASS rs751081719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 74799215 74799215 T A 1 0 0 0 0 1 0 0 0 18048 1461 51 4 4 YLPM1 14 74799215 Missense_Mutation SNP T C3L-00144_T 822863 74799215 32244503 1267 5338 GPATCH2L 0 . GRCh38 14 76195961 76195961 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1277G>T p.Ser426Ile p.S426I ENST00000261530 9/10 326 298 28 340 340 0 strelka-varscan-mutect GPATCH2L,missense_variant,p.Ser426Ile,ENST00000261530,NM_017926.3;GPATCH2L,missense_variant,p.Ser421Ile,ENST00000621494,NM_017972.3;GPATCH2L,missense_variant,p.Ser421Ile,ENST00000312858,;GPATCH2L,missense_variant,p.Ala47Ser,ENST00000554799,;GPATCH2L,missense_variant,p.Ala47Ser,ENST00000553588,;GPATCH2L,non_coding_transcript_exon_variant,,ENST00000556675,;GPATCH2L,missense_variant,p.Ser19Ile,ENST00000556372,;GPATCH2L,3_prime_UTR_variant,,ENST00000554375,; T ENST00000261530 Transcript missense_variant 1343/14007 1277/1449 426/482 S/I aGc/aTc 1 1 GPATCH2L HGNC HGNC:20210 protein_coding YES CCDS9848.1 ENSP00000261530 Q9NWQ4 A0A024R6E4 UPI000006FA38 NM_017926.3 deleterious(0.02) 9/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 76195961 76195961 G T 1 0 0 0 0 1 0 0 0 6492 971 34 2 2 GPATCH2L 14 76195961 Missense_Mutation SNP G C3L-00144_T 1396746 76195961 30847757 1268 5339 ADCK1 0 . GRCh38 14 77907833 77907833 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.772G>C p.Glu258Gln p.E258Q ENST00000238561 7/11 203 149 54 153 153 0 strelka-varscan-mutect ADCK1,missense_variant,p.Glu258Gln,ENST00000238561,NM_020421.3;ADCK1,missense_variant,p.Glu190Gln,ENST00000341211,NM_001142545.1;ADCK1,intron_variant,,ENST00000557501,;ADCK1,non_coding_transcript_exon_variant,,ENST00000555333,;ADCK1,upstream_gene_variant,,ENST00000556560,;ADCK1,3_prime_UTR_variant,,ENST00000393639,; C ENST00000238561 Transcript missense_variant 871/2234 772/1572 258/523 E/Q Gag/Cag 1 1 ADCK1 HGNC HGNC:19038 protein_coding YES CCDS9869.1 ENSP00000238561 Q86TW2 UPI000014035F NM_020421.3 tolerated(0.19) 7/11 Gene3D:3.90.1200.10,hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF58,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 77907833 77907833 G C 1 0 0 0 0 1 0 0 0 331 1175 41 4 4 ADCK1 14 77907833 Missense_Mutation SNP G C3L-00144_T 1711872 77907833 29135885 1269 5340 NRXN3 0 . GRCh38 14 79861541 79861541 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.4572C>T p.= p.N1524N ENST00000634499 20/20 193 152 41 218 218 0 strelka-varscan-mutect NRXN3,synonymous_variant,p.=,ENST00000634499,;NRXN3,synonymous_variant,p.=,ENST00000635466,;NRXN3,synonymous_variant,p.=,ENST00000557594,NM_001272020.1;NRXN3,intron_variant,,ENST00000281127,NM_138970.4;NRXN3,intron_variant,,ENST00000428277,NM_001105250.2;NRXN3,intron_variant,,ENST00000554719,NM_004796.5;NRXN3,intron_variant,,ENST00000556003,;NRXN3,3_prime_UTR_variant,,ENST00000554738,;NRXN3,3_prime_UTR_variant,,ENST00000555387,; T ENST00000634499 Transcript synonymous_variant 5577/6069 4572/4995 1524/1664 N aaC/aaT 1 1 NRXN3 HGNC HGNC:8010 protein_coding ENSP00000488920 A0A0U1RQC5 UPI000719A152 20/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 79861541 79861541 C T 1 0 0 0 0 0 0 0 1 10726 506 18 3 3 NRXN3 14 79861541 Silent SNP C C3L-00144_T 1953708 79861541 27182177 1270 5341 DIO2 0 . GRCh38 14 80206325 80206325 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.236C>A p.Pro79Gln p.P79Q ENST00000555750 2/3 180 162 18 195 192 3 strelka-varscan-mutect DIO2,missense_variant,p.Pro79Gln,ENST00000422005,NM_001242503.2,NM_001242502.1;DIO2,missense_variant,p.Pro79Gln,ENST00000555750,NM_001007023.3;DIO2,intron_variant,,ENST00000557010,NM_001324462.1,NM_000793.5;DIO2,intron_variant,,ENST00000438257,NM_013989.4;DIO2,intron_variant,,ENST00000556811,;DIO2,intron_variant,,ENST00000557125,;DIO2,downstream_gene_variant,,ENST00000554188,;DIO2,missense_variant,p.Pro27Gln,ENST00000555844,; T ENST00000555750 Transcript missense_variant 264/1049 236/930 79/309 P/Q cCa/cAa 1 -1 DIO2 HGNC HGNC:2884 protein_coding YES CCDS55934.1 ENSP00000450980 A0A0A0MTQ2 UPI000046D384 NM_001007023.3 tolerated_low_confidence(0.06) 2/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 80206325 80206325 G T 1 0 0 0 0 1 0 0 0 4330 1348 47 2 2 DIO2 14 80206325 Missense_Mutation SNP G C3L-00144_T 344784 80206325 26837393 1271 5342 EML5 0 . GRCh38 14 88738966 88738966 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.760G>T p.Gly254Cys p.G254C ENST00000554922 6/44 274 223 51 229 229 0 strelka-varscan-mutect EML5,missense_variant,p.Gly254Cys,ENST00000554922,NM_183387.2;EML5,missense_variant,p.Gly254Cys,ENST00000380664,; A ENST00000554922 Transcript missense_variant 1009/9570 760/5934 254/1977 G/C Ggc/Tgc 1 -1 EML5 HGNC HGNC:18197 protein_coding YES CCDS45148.1 ENSP00000451998 Q05BV3 UPI00001C0438 NM_183387.2 deleterious(0) 6/44 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF16,SMART_domains:SM00320,Superfamily_domains:SSF50978,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 88738966 88738966 C A 1 0 0 0 0 1 0 0 0 4943 594 21 2 2 EML5 14 88738966 Missense_Mutation SNP C C3L-00144_T 8532641 88738966 18304752 1272 5343 SLC24A4 0 . GRCh38 14 92325934 92325934 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.197C>G p.Ala66Gly p.A66G ENST00000532405 2/17 149 133 16 173 173 0 strelka-varscan-mutect SLC24A4,missense_variant,p.Ala66Gly,ENST00000532405,NM_153646.3;SLC24A4,missense_variant,p.Ala66Gly,ENST00000531433,NM_153647.3;SLC24A4,missense_variant,p.Ala2Gly,ENST00000393265,NM_153648.3; G ENST00000532405 Transcript missense_variant 423/9950 197/1869 66/622 A/G gCc/gGc 1 1 SLC24A4 HGNC HGNC:10978 protein_coding YES CCDS9903.2 ENSP00000431840 Q8NFF2 UPI000044C5DE NM_153646.3 tolerated(0.21) 2/17 hmmpanther:PTHR10846:SF21,hmmpanther:PTHR10846 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 92325934 92325934 C G 1 0 0 0 0 1 0 0 0 14734 739 26 4 4 SLC24A4 14 92325934 Missense_Mutation SNP C C3L-00144_T 3586968 92325934 14717784 1273 5344 UNC79 0 . GRCh38 14 93643656 93643656 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.5589G>T p.= p.L1863L ENST00000256339 35/50 341 275 66 318 317 1 strelka-varscan-mutect UNC79,synonymous_variant,p.=,ENST00000553484,;UNC79,synonymous_variant,p.=,ENST00000555664,;UNC79,synonymous_variant,p.=,ENST00000256339,NM_020818.3;UNC79,synonymous_variant,p.=,ENST00000393151,;UNC79,synonymous_variant,p.=,ENST00000621021,; T ENST00000256339 Transcript synonymous_variant 6244/8400 5589/7377 1863/2458 L ctG/ctT 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 35/50 Low_complexity_(Seg):seg,hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 93643656 93643656 G T 1 0 0 0 0 0 0 0 1 17520 1335 47 2 2 UNC79 14 93643656 Silent SNP G C3L-00144_T 1317722 93643656 13400062 1274 5345 SERPINA4 0 . GRCh38 14 94569453 94569453 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1142C>A p.Thr381Asn p.T381N ENST00000557004 5/5 243 215 28 230 230 0 strelka-varscan-mutect SERPINA4,missense_variant,p.Thr381Asn,ENST00000557004,NM_006215.3;SERPINA4,missense_variant,p.Thr381Asn,ENST00000555095,NM_001289032.1;SERPINA4,missense_variant,p.Thr381Asn,ENST00000298841,NM_001289033.1;SERPINA5,intron_variant,,ENST00000553780,;SERPINA5,intron_variant,,ENST00000554220,; A ENST00000557004 Transcript missense_variant 1563/2012 1142/1284 381/427 T/N aCc/aAc 1 1 SERPINA4 HGNC HGNC:8948 protein_coding YES CCDS9927.1 ENSP00000450838 P29622 A0A024R6I9 UPI000000CBEF NM_006215.3 deleterious(0) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF194,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 94569453 94569453 C A 1 0 0 0 0 1 0 0 0 14367 507 18 2 2 SERPINA4 14 94569453 Missense_Mutation SNP C C3L-00144_T 925797 94569453 12474265 1275 5346 SYNE3 0 . GRCh38 14 95444607 95444607 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1654G>T p.Asp552Tyr p.D552Y ENST00000334258 9/17 98 82 16 88 88 0 strelka-mutect SYNE3,missense_variant,p.Asp552Tyr,ENST00000557275,;SYNE3,missense_variant,p.Asp552Tyr,ENST00000334258,NM_152592.3;SYNE3,missense_variant,p.Asp309Tyr,ENST00000554873,;SYNE3,missense_variant,p.Asp552Tyr,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,; A ENST00000334258 Transcript missense_variant 1669/3275 1654/2928 552/975 D/Y Gac/Tac 1 -1 SYNE3 HGNC HGNC:19861 protein_coding YES CCDS9935.1 ENSP00000334308 Q6ZMZ3 UPI0000246F54 NM_152592.3 deleterious(0) 9/17 hmmpanther:PTHR11915,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 95444607 95444607 C A 1 0 0 0 0 1 0 0 0 15839 913 32 2 2 SYNE3 14 95444607 Missense_Mutation SNP C C3L-00144_T 875154 95444607 11599111 1276 5347 VRK1 0 . GRCh38 14 96876029 96876029 + Splice_Site SNP G G C C3L-00144_T C3L-00144_N G G c.1069-1G>C p.X357_splice ENST00000216639 340 283 57 320 320 0 strelka-varscan-mutect VRK1,splice_acceptor_variant,,ENST00000216639,NM_003384.2;VRK1,coding_sequence_variant,p.=,ENST00000553683,;VRK1,intron_variant,,ENST00000557222,;VRK1,splice_acceptor_variant,,ENST00000555067,;VRK1,upstream_gene_variant,,ENST00000555402,; C ENST00000216639 Transcript splice_acceptor_variant -/1745 1069/1191 357/396 COSM4952776 1 1 VRK1 HGNC HGNC:12718 protein_coding YES CCDS9947.1 ENSP00000216639 Q99986 UPI0000073867 NM_003384.2 11/12 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 12 96876029 96876029 G C 1 0 0 0 0 0 0 1 0 17768 956 33 4 4 VRK1 14 96876029 Splice_Site SNP G C3L-00144_T 1431422 96876029 10167689 1277 5348 CYP46A1 0 . GRCh38 14 99725410 99725410 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1196G>T p.Gly399Val p.G399V ENST00000261835 13/15 216 181 35 179 179 0 strelka-varscan-mutect CYP46A1,missense_variant,p.Gly399Val,ENST00000261835,NM_006668.1;CYP46A1,missense_variant,p.Gly302Val,ENST00000380228,;CYP46A1,downstream_gene_variant,,ENST00000556313,;CYP46A1,3_prime_UTR_variant,,ENST00000554917,;CYP46A1,non_coding_transcript_exon_variant,,ENST00000554176,;CYP46A1,downstream_gene_variant,,ENST00000556822,; T ENST00000261835 Transcript missense_variant 1300/2181 1196/1503 399/500 G/V gGg/gTg 1 1 CYP46A1 HGNC HGNC:2641 protein_coding YES CCDS9954.1 ENSP00000261835 Q9Y6A2 UPI00001281DC NM_006668.1 deleterious(0) 13/15 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24293,hmmpanther:PTHR24293:SF2,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 99725410 99725410 G T 1 0 0 0 0 1 0 0 0 3985 1232 43 2 2 CYP46A1 14 99725410 Missense_Mutation SNP G C3L-00144_T 2849381 99725410 7318308 1278 5349 TECPR2 0 . GRCh38 14 102434998 102434998 + Silent SNP G G T rs765050564 C3L-00144_T C3L-00144_N G G c.2181G>T p.= p.P727P ENST00000359520 9/20 155 119 36 158 158 0 strelka-varscan-mutect TECPR2,synonymous_variant,p.=,ENST00000359520,NM_014844.3;TECPR2,synonymous_variant,p.=,ENST00000558678,NM_001172631.1;TECPR2,intron_variant,,ENST00000560060,;TECPR2,upstream_gene_variant,,ENST00000557786,; T ENST00000359520 Transcript synonymous_variant 2407/8686 2181/4236 727/1411 P ccG/ccT rs765050564 1 1 TECPR2 HGNC HGNC:19957 protein_coding YES CCDS32162.1 ENSP00000352510 O15040 UPI00001FDC38 NM_014844.3 9/20 hmmpanther:PTHR23287,hmmpanther:PTHR23287:SF16 LOW 1 SNV 1 1 PASS rs765050564 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 102434998 102434998 G T 1 0 0 0 0 0 0 0 1 16155 1103 39 1 1 TECPR2 14 102434998 Silent SNP G C3L-00144_T 2709588 102434998 4608720 1279 5350 TNFAIP2 0 . GRCh38 14 103127043 103127043 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.274G>T p.Glu92Ter p.E92* ENST00000560869 3/12 23 17 6 21 21 0 strelka-mutect TNFAIP2,stop_gained,p.Glu92Ter,ENST00000560869,;TNFAIP2,stop_gained,p.Glu92Ter,ENST00000333007,NM_006291.2;TNFAIP2,upstream_gene_variant,,ENST00000560670,;TNFAIP2,downstream_gene_variant,,ENST00000558056,;LINC00677,upstream_gene_variant,,ENST00000558224,;LINC00677,upstream_gene_variant,,ENST00000560742,;TNFAIP2,intron_variant,,ENST00000559195,;TNFAIP2,intron_variant,,ENST00000559406,;TNFAIP2,intron_variant,,ENST00000560562,;TNFAIP2,upstream_gene_variant,,ENST00000560428,;TNFAIP2,upstream_gene_variant,,ENST00000561156,; T ENST00000560869 Transcript stop_gained 913/4683 274/1965 92/654 E/* Gag/Tag 1 1 TNFAIP2 HGNC HGNC:11895 protein_coding YES CCDS9979.1 ENSP00000452634 Q03169 UPI0000164A41 3/12 Low_complexity_(Seg):seg,hmmpanther:PTHR21292:SF4,hmmpanther:PTHR21292 HIGH SNV 5 1 PASS rs935901268 . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 103127043 103127043 G T 1 0 0 0 0 0 1 0 0 16747 1175 41 2 2 TNFAIP2 14 103127043 Nonsense_Mutation SNP G C3L-00144_T 692045 103127043 3916675 1280 5351 AHNAK2 0 . GRCh38 14 104942406 104942406 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.13045C>A p.Gln4349Lys p.Q4349K ENST00000333244 7/7 500 455 45 441 441 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Gln4349Lys,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;PLD4,downstream_gene_variant,,ENST00000392593,NM_138790.2;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; T ENST00000333244 Transcript missense_variant 13165/18254 13045/17388 4349/5795 Q/K Cag/Aag 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.13) 7/7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 104942406 104942406 G T 1 0 0 0 0 1 0 0 0 492 1299 45 2 2 AHNAK2 14 104942406 Missense_Mutation SNP G C3L-00144_T 1815363 104942406 2101312 1281 5352 NIPA1 0 . GRCh38 15 22823783 22823783 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.534G>T p.Trp178Cys p.W178C ENST00000337435 5/5 238 182 56 202 202 0 strelka-varscan-mutect NIPA1,missense_variant,p.Trp103Cys,ENST00000437912,;NIPA1,missense_variant,p.Trp178Cys,ENST00000337435,NM_144599.4;NIPA1,missense_variant,p.Trp103Cys,ENST00000561183,NM_001142275.1;NIPA1,downstream_gene_variant,,ENST00000560069,;NIPA1,3_prime_UTR_variant,,ENST00000559448,;NIPA1,3_prime_UTR_variant,,ENST00000557930,; T ENST00000337435 Transcript missense_variant 559/6567 534/990 178/329 W/C tgG/tgT 1 1 NIPA1 HGNC HGNC:17043 protein_coding YES CCDS73691.1 ENSP00000337452 Q7RTP0 UPI00001D9756 NM_144599.4 tolerated(0.16) 5/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR12570:SF17,hmmpanther:PTHR12570,Pfam_domain:PF05653 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 22823783 22823783 G T 1 0 0 0 0 1 0 0 0 10457 1183 41 2 2 NIPA1 15 22823783 Missense_Mutation SNP G C3L-00144_T 22823783 79167406 1282 5353 MKRN3 0 . GRCh38 15 23565939 23565939 + Silent SNP A A C novel C3L-00144_T C3L-00144_N A A c.157A>C p.= p.R53R ENST00000314520 1/1 221 177 44 256 256 0 strelka-varscan-mutect MKRN3,synonymous_variant,p.=,ENST00000314520,NM_005664.3;MKRN3,synonymous_variant,p.=,ENST00000568252,;MKRN3,synonymous_variant,p.=,ENST00000564592,;AC126407.1,intron_variant,,ENST00000626930,;MIR4508,upstream_gene_variant,,ENST00000584178,;MKRN3-AS1,downstream_gene_variant,,ENST00000563044,;MKRN3,upstream_gene_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,; C ENST00000314520 Transcript synonymous_variant 256/2337 157/1524 53/507 R Agg/Cgg 1 1 MKRN3 HGNC HGNC:7114 protein_coding YES CCDS10013.1 ENSP00000313881 Q13064 UPI000000DAA1 NM_005664.3 1/1 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 23565939 23565939 A C 1 0 0 0 0 0 0 0 1 9576 63 3 5 5 MKRN3 15 23565939 Silent SNP A C3L-00144_T 742156 23565939 78425250 1283 5354 OCA2 0 . GRCh38 15 27844975 27844975 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.2416T>A p.Phe806Ile p.F806I ENST00000354638 23/24 350 283 67 368 368 0 strelka-varscan-mutect OCA2,missense_variant,p.Phe806Ile,ENST00000354638,NM_000275.2;OCA2,missense_variant,p.Phe782Ile,ENST00000353809,NM_001300984.1; T ENST00000354638 Transcript missense_variant 2572/3186 2416/2517 806/838 F/I Ttc/Atc 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 deleterious(0) 23/24 hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27844975 27844975 A T 1 0 0 0 0 1 0 0 0 10892 72 3 4 4 OCA2 15 27844975 Missense_Mutation SNP A C3L-00144_T 4279036 27844975 74146214 1284 5355 21 2 OCA2 0 . GRCh38 15 27844977 27844977 + Missense_Mutation SNP G G C rs758859062 C3L-00144_T C3L-00144_N G G c.2414C>G p.Ser805Cys p.S805C ENST00000354638 23/24 358 288 70 377 377 0 strelka-varscan-mutect OCA2,missense_variant,p.Ser805Cys,ENST00000354638,NM_000275.2;OCA2,missense_variant,p.Ser781Cys,ENST00000353809,NM_001300984.1; C ENST00000354638 Transcript missense_variant 2570/3186 2414/2517 805/838 S/C tCc/tGc rs758859062 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 deleterious(0) 23/24 hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283 MODERATE 1 SNV 1 1 PASS rs758859062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 27844977 27844977 G C 1 0 0 0 0 1 0 0 0 10892 1174 41 4 4 OCA2 15 27844977 Missense_Mutation SNP G C3L-00144_T 2 27844977 74146212 1285 5356 21 2 GOLGA8Q 0 . GRCh38 15 30562210 30562210 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1693C>A p.Gln565Lys p.Q565K ENST00000562783 18/19 163 93 70 176 176 0 strelka-varscan-mutect GOLGA8Q,missense_variant,p.Gln565Lys,ENST00000562783,;RN7SL796P,downstream_gene_variant,,ENST00000613991,;GOLGA8Q,downstream_gene_variant,,ENST00000565941,; A ENST00000562783 Transcript missense_variant 1693/1899 1693/1899 565/632 Q/K Cag/Aag 1 1 GOLGA8Q HGNC HGNC:44408 protein_coding YES ENSP00000457904 H3BV12 UPI0000DD8290 deleterious(0) 18/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS . . 36 174 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 30562210 30562210 C A 1 0 0 0 0 1 0 0 0 6456 595 21 2 2 GOLGA8Q 15 30562210 Missense_Mutation SNP C C3L-00144_T 2717233 30562210 71428979 1286 5357 CHRNA7 0 . GRCh38 15 32031015 32031015 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.260G>T p.Ser87Ile p.S87I ENST00000454250 2/10 138 103 35 134 134 0 strelka-varscan-mutect CHRNA7,missense_variant,p.Ser58Ile,ENST00000306901,NM_000746.5;CHRNA7,missense_variant,p.Ser87Ile,ENST00000454250,NM_001190455.2;CHRNA7,missense_variant,p.Ser58Ile,ENST00000637552,;CHRNA7,missense_variant,p.Ser65Ile,ENST00000636440,;CHRNA7,5_prime_UTR_variant,,ENST00000637033,;CHRNA7,5_prime_UTR_variant,,ENST00000636603,;CHRNA7,5_prime_UTR_variant,,ENST00000635884,;CHRNA7,5_prime_UTR_variant,,ENST00000638106,;CHRNA7,intron_variant,,ENST00000637183,;CHRNA7,intron_variant,,ENST00000635978,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000637350,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000637519,;CHRNA7,missense_variant,p.Ser6Ile,ENST00000636271,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000437966,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000637971,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000638031,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000635722,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000636850,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000636044,;CHRNA7,missense_variant,p.Ser58Ile,ENST00000637786,;CHRNA7,missense_variant,p.Ser14Ile,ENST00000635759,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636295,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636647,; T ENST00000454250 Transcript missense_variant 367/2093 260/1596 87/531 S/I aGc/aTc 1 1 CHRNA7 HGNC HGNC:1960 protein_coding YES CCDS53924.1 ENSP00000407546 P36544 UPI0000E23BA6 NM_001190455.2 tolerated(0.12) 2/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF572,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 32031015 32031015 G T 1 0 0 0 0 1 0 0 0 3148 971 34 2 2 CHRNA7 15 32031015 Missense_Mutation SNP G C3L-00144_T 1468805 32031015 69960174 1287 5358 FMN1 0 . GRCh38 15 32902028 32902028 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3390G>T p.Glu1130Asp p.E1130D ENST00000616417 13/21 66 54 12 80 80 0 strelka-varscan-mutect FMN1,missense_variant,p.Glu1130Asp,ENST00000616417,NM_001277313.1;FMN1,missense_variant,p.Glu907Asp,ENST00000334528,NM_001103184.3;FMN1,missense_variant,p.Glu1130Asp,ENST00000559047,;FMN1,missense_variant,p.Glu1032Asp,ENST00000561249,;FMN1,missense_variant,p.Glu84Asp,ENST00000560317,;FMN1,missense_variant,p.Glu5Asp,ENST00000558711,; A ENST00000616417 Transcript missense_variant 3894/13529 3390/4260 1130/1419 E/D gaG/gaT 1 -1 FMN1 HGNC HGNC:3768 protein_coding YES CCDS61581.1 ENSP00000479134 Q68DA7 UPI0001AE68B4 NM_001277313.1 deleterious(0.02) 13/21 PROSITE_profiles:PS51444,hmmpanther:PTHR13037:SF11,hmmpanther:PTHR13037,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 32902028 32902028 C A 1 0 0 0 0 1 0 0 0 5805 564 20 2 2 FMN1 15 32902028 Missense_Mutation SNP C C3L-00144_T 871013 32902028 69089161 1288 5359 FMN1 0 . GRCh38 15 33154424 33154424 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.491G>T p.Gly164Val p.G164V ENST00000616417 4/21 170 118 52 188 187 1 strelka-varscan-mutect FMN1,missense_variant,p.Gly164Val,ENST00000616417,NM_001277313.1;FMN1,missense_variant,p.Gly164Val,ENST00000559047,;FMN1,missense_variant,p.Gly164Val,ENST00000561249,;FMN1,missense_variant,p.Gly164Val,ENST00000320930,NM_001277314.1; A ENST00000616417 Transcript missense_variant 995/13529 491/4260 164/1419 G/V gGa/gTa 1 -1 FMN1 HGNC HGNC:3768 protein_coding YES CCDS61581.1 ENSP00000479134 Q68DA7 UPI0001AE68B4 NM_001277313.1 tolerated(0.05) 4/21 hmmpanther:PTHR13037:SF11,hmmpanther:PTHR13037 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 33154424 33154424 C A 1 0 0 0 0 1 0 0 0 5805 855 30 2 2 FMN1 15 33154424 Missense_Mutation SNP C C3L-00144_T 252396 33154424 68836765 1289 5360 BUB1B 0 . GRCh38 15 40217602 40217602 + Missense_Mutation SNP G G T rs143232848 C3L-00144_T C3L-00144_N G G c.2785G>T p.Gly929Cys p.G929C ENST00000287598 21/23 353 257 96 364 361 3 strelka-varscan-mutect BUB1B,missense_variant,p.Gly929Cys,ENST00000287598,NM_001211.5;BUB1B,missense_variant,p.Gly943Cys,ENST00000412359,;BUB1B-PAK6,5_prime_UTR_variant,,ENST00000441369,NM_001128628.2;BUB1B-PAK6,missense_variant,p.Gly6Cys,ENST00000558658,;BUB1B-PAK6,synonymous_variant,p.=,ENST00000453867,;BUB1B,non_coding_transcript_exon_variant,,ENST00000558151,;BUB1B-PAK6,upstream_gene_variant,,ENST00000559435,; T ENST00000287598 Transcript missense_variant 2980/3725 2785/3153 929/1050 G/C Ggc/Tgc rs143232848 1 1 BUB1B HGNC HGNC:1149 protein_coding YES CCDS10053.1 ENSP00000287598 O60566 UPI000006E699 NM_001211.5 deleterious(0) 21/23 hmmpanther:PTHR14030:SF4,hmmpanther:PTHR14030,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs143232848 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 40217602 40217602 G T 1 0 0 0 0 1 0 0 0 1747 1116 39 1 1 BUB1B 15 40217602 Missense_Mutation SNP G C3L-00144_T 7063178 40217602 61773587 1290 5361 CASC5 0 . GRCh38 15 40657371 40657371 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.6689C>T p.Ser2230Leu p.S2230L ENST00000346991 25/27 135 104 31 104 104 0 strelka-varscan-mutect CASC5,missense_variant,p.Ser2230Leu,ENST00000346991,NM_170589.4;CASC5,missense_variant,p.Ser2204Leu,ENST00000399668,NM_144508.4;CASC5,missense_variant,p.Ser1249Leu,ENST00000526913,;CASC5,downstream_gene_variant,,ENST00000532347,; T ENST00000346991 Transcript missense_variant 7079/9573 6689/7029 2230/2342 S/L tCa/tTa COSM699921 1 1 CASC5 HGNC HGNC:24054 protein_coding YES CCDS42023.1 ENSP00000335463 Q8NG31 UPI0000E59BD3 NM_170589.4 deleterious(0) 25/27 hmmpanther:PTHR16520,hmmpanther:PTHR16520:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 40657371 40657371 C T 1 0 0 0 0 1 0 0 0 2363 838 29 3 3 CASC5 15 40657371 Missense_Mutation SNP C C3L-00144_T 439769 40657371 61333818 1291 5362 LTK 0 . GRCh38 15 41511325 41511325 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.836C>A p.Ser279Ter p.S279* ENST00000263800 7/20 27 17 10 43 43 0 strelka-varscan-mutect LTK,stop_gained,p.Ser279Ter,ENST00000263800,NM_002344.5;LTK,intron_variant,,ENST00000355166,NM_206961.3;LTK,intron_variant,,ENST00000453182,NM_001135685.1;LTK,intron_variant,,ENST00000561619,;LTK,non_coding_transcript_exon_variant,,ENST00000563518,;LTK,upstream_gene_variant,,ENST00000569283,; T ENST00000263800 Transcript stop_gained 933/3046 836/2595 279/864 S/* tCg/tAg 1 -1 LTK HGNC HGNC:6721 protein_coding YES CCDS10077.1 ENSP00000263800 P29376 UPI000013D463 NM_002344.5 7/20 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF294,Pfam_domain:PF12810 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 41511325 41511325 G T 1 0 0 0 0 0 1 0 0 8986 1059 37 1 1 LTK 15 41511325 Nonsense_Mutation SNP G C3L-00144_T 853954 41511325 60479864 1292 5363 PLA2G4D 0 . GRCh38 15 42079644 42079644 + Missense_Mutation SNP G G T rs780118874 C3L-00144_T C3L-00144_N G G c.1210C>A p.Arg404Ser p.R404S ENST00000290472 13/20 114 80 34 134 134 0 strelka-varscan-mutect PLA2G4D,missense_variant,p.Arg404Ser,ENST00000290472,NM_178034.3;PLA2G4D,downstream_gene_variant,,ENST00000560132,; T ENST00000290472 Transcript missense_variant 1305/3584 1210/2457 404/818 R/S Cgc/Agc rs780118874,COSM5362876 1 -1 PLA2G4D HGNC HGNC:30038 protein_coding YES CCDS32203.1 ENSP00000290472 Q86XP0 UPI00001FE2F2 NM_178034.3 tolerated(0.15) 13/20 Gene3D:3.40.1090.10,Pfam_domain:PF01735,PROSITE_profiles:PS51210,hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF31,SMART_domains:SM00022,Superfamily_domains:SSF52151 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780118874 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42079644 42079644 G T 1 0 0 0 0 1 0 0 0 12100 1087 38 1 1 PLA2G4D 15 42079644 Missense_Mutation SNP G C3L-00144_T 568319 42079644 59911545 1293 5364 PLA2G4F 0 . GRCh38 15 42156440 42156440 + Missense_Mutation SNP C C A rs752946660 C3L-00144_T C3L-00144_N C C c.110G>T p.Arg37Leu p.R37L ENST00000397272 1/20 178 137 41 181 181 0 strelka-varscan-mutect PLA2G4F,missense_variant,p.Arg37Leu,ENST00000397272,NM_213600.3;VPS39,downstream_gene_variant,,ENST00000318006,NM_015289.3;VPS39,downstream_gene_variant,,ENST00000348544,NM_001301138.1;PLA2G4F,missense_variant,p.Arg37Leu,ENST00000569985,;PLA2G4F,missense_variant,p.Arg37Leu,ENST00000290497,;PLA2G4F,missense_variant,p.Arg37Leu,ENST00000561627,;PLA2G4F,missense_variant,p.Arg37Leu,ENST00000565553,;VPS39,downstream_gene_variant,,ENST00000562258,;VPS39,downstream_gene_variant,,ENST00000614932,;VPS39,downstream_gene_variant,,ENST00000564994,; A ENST00000397272 Transcript missense_variant,splice_region_variant 197/5587 110/2550 37/849 R/L cGg/cTg rs752946660 1 -1 PLA2G4F HGNC HGNC:27396 protein_coding YES CCDS32204.1 ENSP00000380442 Q68DD2 UPI0000160965 NM_213600.3 deleterious(0.02) 1/20 MODERATE 1 SNV 1 1 PASS rs752946660 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 42156440 42156440 C A 1 0 0 0 0 1 0 0 0 12102 666 23 1 1 PLA2G4F 15 42156440 Missense_Mutation SNP C C3L-00144_T 76796 42156440 59834749 1294 5365 STARD9 0 . GRCh38 15 42669181 42669181 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1341G>T p.Trp447Cys p.W447C ENST00000290607 16/33 79 57 22 73 73 0 strelka-varscan-mutect STARD9,missense_variant,p.Trp447Cys,ENST00000290607,NM_020759.2;STARD9,missense_variant,p.Trp22Cys,ENST00000569419,;STARD9,non_coding_transcript_exon_variant,,ENST00000564158,;STARD9,non_coding_transcript_exon_variant,,ENST00000568493,; T ENST00000290607 Transcript missense_variant 1398/15567 1341/14103 447/4700 W/C tgG/tgT 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 deleterious(0) 16/33 MODERATE 1 SNV 5 1 PASS rs1320231619 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42669181 42669181 G T 1 0 0 0 0 1 0 0 0 15639 1183 41 2 2 STARD9 15 42669181 Missense_Mutation SNP G C3L-00144_T 512741 42669181 59322008 1295 5366 CDAN1 0 . GRCh38 15 42734276 42734276 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1207C>T p.Pro403Ser p.P403S ENST00000356231 7/28 485 345 140 448 448 0 strelka-varscan-mutect CDAN1,missense_variant,p.Pro403Ser,ENST00000356231,NM_138477.2;TTBK2,downstream_gene_variant,,ENST00000267890,NM_173500.3;CDAN1,downstream_gene_variant,,ENST00000563260,;CTD-2036P10.3,upstream_gene_variant,,ENST00000567456,;CDAN1,upstream_gene_variant,,ENST00000562465,; A ENST00000356231 Transcript missense_variant 1231/4637 1207/3684 403/1227 P/S Cca/Tca 1 -1 CDAN1 HGNC HGNC:1713 protein_coding YES CCDS32209.1 ENSP00000348564 Q8IWY9 UPI0000229BCB NM_138477.2 tolerated(0.08) 7/28 hmmpanther:PTHR28678 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 42734276 42734276 G A 1 0 0 0 0 1 0 0 0 2757 1261 44 3 3 CDAN1 15 42734276 Missense_Mutation SNP G C3L-00144_T 65095 42734276 59256913 1296 5367 STRC 0 . GRCh38 15 43609321 43609321 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3512G>T p.Trp1171Leu p.W1171L ENST00000450892 16/29 363 283 80 408 408 0 strelka-varscan-mutect STRC,missense_variant,p.Trp1171Leu,ENST00000450892,NM_153700.2;STRC,missense_variant,p.Trp398Leu,ENST00000541030,;CKMT1B,downstream_gene_variant,,ENST00000411560,;STRC,3_prime_UTR_variant,,ENST00000428650,;STRC,3_prime_UTR_variant,,ENST00000440125,;STRC,3_prime_UTR_variant,,ENST00000455136,;STRC,non_coding_transcript_exon_variant,,ENST00000485556,;STRC,non_coding_transcript_exon_variant,,ENST00000471703,;STRC,non_coding_transcript_exon_variant,,ENST00000448437,;STRC,downstream_gene_variant,,ENST00000483250,;STRC,downstream_gene_variant,,ENST00000470279,; A ENST00000450892 Transcript missense_variant 3590/5680 3512/5328 1171/1775 W/L tGg/tTg 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 tolerated(0.05) 16/29 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF14 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43609321 43609321 C A 1 0 0 0 0 1 0 0 0 15709 595 21 2 2 STRC 15 43609321 Missense_Mutation SNP C C3L-00144_T 875045 43609321 58381868 1297 5368 MYO5C 0 . GRCh38 15 52237531 52237531 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2819G>T p.Arg940Met p.R940M ENST00000261839 22/41 185 132 53 215 215 0 strelka-varscan-mutect MYO5C,missense_variant,p.Arg940Met,ENST00000261839,NM_018728.3;MYO5C,3_prime_UTR_variant,,ENST00000560809,;MYO5C,3_prime_UTR_variant,,ENST00000558902,;MYO5C,non_coding_transcript_exon_variant,,ENST00000559434,; A ENST00000261839 Transcript missense_variant 2981/6971 2819/5229 940/1742 R/M aGg/aTg 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 deleterious(0.02) 22/41 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52237531 52237531 C A 1 0 0 0 0 1 0 0 0 10081 681 24 2 2 MYO5C 15 52237531 Missense_Mutation SNP C C3L-00144_T 8628210 52237531 49753658 1298 5369 UNC13C 0 . GRCh38 15 54321976 54321976 + Missense_Mutation SNP G G T rs780996626 C3L-00144_T C3L-00144_N G G c.4306G>T p.Gly1436Cys p.G1436C ENST00000260323 13/32 374 264 110 331 331 0 strelka-varscan-mutect UNC13C,missense_variant,p.Gly1436Cys,ENST00000260323,NM_001080534.1;UNC13C,non_coding_transcript_exon_variant,,ENST00000561210,;HNRNPA1P74,upstream_gene_variant,,ENST00000560782,; T ENST00000260323 Transcript missense_variant 4306/12946 4306/6645 1436/2214 G/C Ggt/Tgt rs780996626 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0) 13/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 MODERATE 1 SNV 5 1 PASS rs780996626 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54321976 54321976 G T 1 0 0 0 0 1 0 0 0 17510 1116 39 1 1 UNC13C 15 54321976 Missense_Mutation SNP G C3L-00144_T 2084445 54321976 47669213 1299 5370 ISLR2 0 . GRCh38 15 74133106 74133106 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.352G>T p.Asp118Tyr p.D118Y ENST00000361742 4/4 154 115 39 188 188 0 strelka-varscan-mutect ISLR2,missense_variant,p.Asp118Tyr,ENST00000361742,NM_001130136.1;ISLR2,missense_variant,p.Asp118Tyr,ENST00000435464,NM_001130138.1;ISLR2,missense_variant,p.Asp118Tyr,ENST00000565159,NM_001130137.1;ISLR2,missense_variant,p.Asp118Tyr,ENST00000453268,NM_020851.2;ISLR2,missense_variant,p.Asp118Tyr,ENST00000565540,;ISLR2,missense_variant,p.Asp118Tyr,ENST00000419208,;ISLR2,missense_variant,p.Asp118Tyr,ENST00000561740,;ISLR2,downstream_gene_variant,,ENST00000569886,;ISLR2,downstream_gene_variant,,ENST00000567206,;ISLR2,downstream_gene_variant,,ENST00000565332,;RP11-247C2.2,upstream_gene_variant,,ENST00000563727,;RP11-247C2.2,upstream_gene_variant,,ENST00000514871,;ISLR2,intron_variant,,ENST00000561975,;ISLR2,downstream_gene_variant,,ENST00000565068,; T ENST00000361742 Transcript missense_variant 1121/4817 352/2238 118/745 D/Y Gac/Tac COSM964762 1 1 ISLR2 HGNC HGNC:29286 protein_coding YES CCDS10259.1 ENSP00000355402 Q6UXK2 UPI000004C60F NM_001130136.1 deleterious(0) 4/4 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF15,SMART_domains:SM00369,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 74133106 74133106 G T 1 0 0 0 0 1 0 0 0 7766 1058 37 1 1 ISLR2 15 74133106 Missense_Mutation SNP G C3L-00144_T 19811130 74133106 27858083 1300 5371 LINGO1 0 . GRCh38 15 77614710 77614710 + Silent SNP G G T rs573844311 C3L-00144_T C3L-00144_N G G c.1197C>A p.= p.P399P ENST00000355300 2/2 298 213 85 276 275 1 strelka-varscan-mutect LINGO1,synonymous_variant,p.=,ENST00000355300,NM_032808.6;LINGO1,synonymous_variant,p.=,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,downstream_gene_variant,,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000561686,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000564472,; T ENST00000355300 Transcript synonymous_variant 1372/3055 1197/1863 399/620 P ccC/ccA rs573844311 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31 LOW 1 SNV 1 1 PASS rs573844311 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 77614710 77614710 G T 1 0 0 0 0 0 0 0 1 8735 1103 39 1 1 LINGO1 15 77614710 Silent SNP G C3L-00144_T 3481604 77614710 24376479 1301 5372 ANKRD34C 0 . GRCh38 15 79293318 79293318 + Nonsense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.34G>T p.Gly12Ter p.G12* ENST00000421388 1/1 57 44 13 49 49 0 strelka-varscan-mutect ANKRD34C,stop_gained,p.Gly12Ter,ENST00000421388,NM_001146341.1; T ENST00000421388 Transcript stop_gained 34/4951 34/1608 12/535 G/* Gga/Tga COSM4825465 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 1/1 PROSITE_profiles:PS50297,hmmpanther:PTHR24157,SMART_domains:SM00248,Superfamily_domains:SSF48403 1 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 79293318 79293318 G T 1 0 0 0 0 0 1 0 0 769 1349 47 2 2 ANKRD34C 15 79293318 Nonsense_Mutation SNP G C3L-00144_T 1678608 79293318 22697871 1302 5373 ANKRD34C 0 . GRCh38 15 79293604 79293604 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.320A>T p.Glu107Val p.E107V ENST00000421388 1/1 177 142 35 182 182 0 strelka-varscan-mutect ANKRD34C,missense_variant,p.Glu107Val,ENST00000421388,NM_001146341.1; T ENST00000421388 Transcript missense_variant 320/4951 320/1608 107/535 E/V gAg/gTg 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 tolerated(0.05) 1/1 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24157,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 79293604 79293604 A T 1 0 0 0 0 1 0 0 0 769 304 11 4 4 ANKRD34C 15 79293604 Missense_Mutation SNP A C3L-00144_T 286 79293604 22697585 1303 5374 IL16 0 . GRCh38 15 81292963 81292963 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1828G>T p.Asp610Tyr p.D610Y ENST00000302987 11/18 180 135 45 163 163 0 strelka-varscan-mutect IL16,missense_variant,p.Asp610Tyr,ENST00000394660,NM_001172128.1;IL16,missense_variant,p.Asp610Tyr,ENST00000302987,NM_172217.3;IL16,upstream_gene_variant,,ENST00000394652,NM_004513.5;IL16,downstream_gene_variant,,ENST00000559383,;IL16,upstream_gene_variant,,ENST00000560230,;IL16,3_prime_UTR_variant,,ENST00000360547,;IL16,3_prime_UTR_variant,,ENST00000560115,;IL16,downstream_gene_variant,,ENST00000560241,;IL16,upstream_gene_variant,,ENST00000558857,; T ENST00000302987 Transcript missense_variant 1828/3999 1828/3999 610/1332 D/Y Gac/Tac 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 deleterious(0) 11/18 hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 81292963 81292963 G T 1 0 0 0 0 1 0 0 0 7541 1290 45 2 2 IL16 15 81292963 Missense_Mutation SNP G C3L-00144_T 1999359 81292963 20698226 1304 5375 AGBL1 0 . GRCh38 15 86674413 86674413 + Missense_Mutation SNP C C G rs377271003 C3L-00144_T C3L-00144_N C C c.3198C>G p.Asp1066Glu p.D1066E ENST00000441037 23/25 103 74 29 92 92 0 strelka-varscan-mutect AGBL1,missense_variant,p.Asp206Glu,ENST00000614907,;AGBL1,missense_variant,p.Asp1066Glu,ENST00000441037,;AGBL1,missense_variant,p.Asp1020Glu,ENST00000635782,NM_152336.2;AGBL1,missense_variant,p.Asp1020Glu,ENST00000421325,; G ENST00000441037 Transcript missense_variant 3198/3551 3198/3339 1066/1112 D/E gaC/gaG rs377271003 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 tolerated(0.97) 23/25 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5 MODERATE 1 SNV 5 1 PASS rs377271003 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 12 86674413 86674413 C G 1 0 0 0 0 1 0 0 0 451 535 19 4 4 AGBL1 15 86674413 Missense_Mutation SNP C C3L-00144_T 5381450 86674413 15316776 1305 5376 ANPEP 0 . GRCh38 15 89792485 89792485 + Frame_Shift_Del DEL A A - novel C3L-00144_T C3L-00144_N A A c.2327delT p.Phe776SerfsTer66 p.F776Sfs*66 ENST00000300060 17/21 131 92 39 142 142 0 sindel-varindel-pindel ANPEP,frameshift_variant,p.Phe776SerfsTer66,ENST00000300060,NM_001150.2;ANPEP,non_coding_transcript_exon_variant,,ENST00000558740,;ANPEP,downstream_gene_variant,,ENST00000559761,; - ENST00000300060 Transcript frameshift_variant 2641/3678 2327/2904 776/967 F/X tTc/tc 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 17/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Pfam_domain:PF11838 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 89792485 89792485 A - 1 0 1 0 1 0 0 0 0 817 246 9 0 0 ANPEP 15 89792485 Frame_Shift_Del DEL A C3L-00144_T 3118072 89792485 12198704 1306 5377 SYNGR3 0 . GRCh38 16 1992884 1992884 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.502C>T p.= p.L168L ENST00000248121 4/4 69 62 7 69 69 0 strelka-varscan-mutect SYNGR3,missense_variant,p.Pro145Leu,ENST00000563869,;SYNGR3,synonymous_variant,p.=,ENST00000248121,NM_004209.5;SYNGR3,3_prime_UTR_variant,,ENST00000562045,;SYNGR3,intron_variant,,ENST00000618464,;ZNF598,downstream_gene_variant,,ENST00000563630,NM_178167.3;SYNGR3,downstream_gene_variant,,ENST00000568896,;AC005606.14,upstream_gene_variant,,ENST00000565041,;AC005606.15,upstream_gene_variant,,ENST00000567515,;SYNGR3,non_coding_transcript_exon_variant,,ENST00000564642,;ZNF598,downstream_gene_variant,,ENST00000565396,;ZNF598,downstream_gene_variant,,ENST00000562988,; T ENST00000248121 Transcript synonymous_variant 660/2051 502/690 168/229 L Ctg/Ttg 1 1 SYNGR3 HGNC HGNC:11501 protein_coding YES CCDS10456.1 ENSP00000248121 O43761 UPI0000135B32 NM_004209.5 4/4 PIRSF_domain:PIRSF011282,PROSITE_profiles:PS51225,hmmpanther:PTHR10838,hmmpanther:PTHR10838:SF8,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.76908 1 1 1 1 0 T 2 4 12 1992884 1992884 C T 1 0 0 0 0 0 0 0 1 15844 680 24 3 3 SYNGR3 16 1992884 Silent SNP C C3L-00144_T 1992884 88345461 1307 5378 PKD1 0 . GRCh38 16 2092058 2092058 + Silent SNP C C A rs780113152 C3L-00144_T C3L-00144_N C C c.11400G>T p.= p.P3800P ENST00000262304 40/46 468 359 109 470 470 0 strelka-varscan-mutect PKD1,synonymous_variant,p.=,ENST00000262304,NM_001009944.2;PKD1,synonymous_variant,p.=,ENST00000423118,NM_000296.3;TSC2,downstream_gene_variant,,ENST00000219476,NM_000548.3;TSC2,downstream_gene_variant,,ENST00000350773,NM_001114382.1;TSC2,downstream_gene_variant,,ENST00000568454,NM_001318832.1;TSC2,downstream_gene_variant,,ENST00000401874,NM_001077183.1;TSC2,downstream_gene_variant,,ENST00000439673,NM_001318827.1;TSC2,downstream_gene_variant,,ENST00000382538,NM_001318829.1;TSC2,downstream_gene_variant,,ENST00000569110,;MIR1225,upstream_gene_variant,,ENST00000408729,;RP11-304L19.1,intron_variant,,ENST00000570072,;RP11-304L19.1,intron_variant,,ENST00000563284,;RP11-304L19.3,downstream_gene_variant,,ENST00000565937,;PKD1,synonymous_variant,p.=,ENST00000561668,;PKD1,3_prime_UTR_variant,,ENST00000487932,;PKD1,3_prime_UTR_variant,,ENST00000562425,;PKD1,non_coding_transcript_exon_variant,,ENST00000485120,;PKD1,non_coding_transcript_exon_variant,,ENST00000567355,;TSC2,downstream_gene_variant,,ENST00000439117,NM_001318831.1;TSC2,downstream_gene_variant,,ENST00000497886,;TSC2,downstream_gene_variant,,ENST00000569930,;PKD1,upstream_gene_variant,,ENST00000472577,;PKD1,downstream_gene_variant,,ENST00000472659,;PKD1,upstream_gene_variant,,ENST00000564313,;PKD1,downstream_gene_variant,,ENST00000568796,; A ENST00000262304 Transcript synonymous_variant 11609/14138 11400/12912 3800/4303 P ccG/ccT rs780113152 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 40/46 Pfam_domain:PF08016,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143 LOW 1 SNV 1 1 PASS rs780113152 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 2092058 2092058 C A 1 0 0 0 0 0 0 0 1 12059 639 23 1 1 PKD1 16 2092058 Silent SNP C C3L-00144_T 99174 2092058 88246287 1308 5379 PKD1 0 . GRCh38 16 2117929 2117929 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1063G>C p.Ala355Pro p.A355P ENST00000262304 5/46 172 130 42 162 162 0 strelka-varscan-mutect PKD1,missense_variant,p.Ala355Pro,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Ala355Pro,ENST00000423118,NM_000296.3;PKD1,missense_variant,p.Ala51Pro,ENST00000488185,;RP11-304L19.2,upstream_gene_variant,,ENST00000562027,;RP11-304L19.4,downstream_gene_variant,,ENST00000568795,;PKD1,non_coding_transcript_exon_variant,,ENST00000570150,;PKD1,upstream_gene_variant,,ENST00000468674,;PKD1,missense_variant,p.Ala11Pro,ENST00000568591,;PKD1,upstream_gene_variant,,ENST00000483731,;PKD1,upstream_gene_variant,,ENST00000415938,;PKD1,upstream_gene_variant,,ENST00000565639,;PKD1,upstream_gene_variant,,ENST00000569983,; G ENST00000262304 Transcript missense_variant 1272/14138 1063/12912 355/4303 A/P Gca/Cca 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 tolerated(0.22) 5/46 PROSITE_profiles:PS50093,SMART_domains:SM00089,Superfamily_domains:SSF49299,TIGRFAM_domain:TIGR00864 MODERATE 1 SNV 1 1 PASS rs1303352586 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 2117929 2117929 C G 1 0 0 0 0 1 0 0 0 12059 739 26 4 4 PKD1 16 2117929 Missense_Mutation SNP C C3L-00144_T 25871 2117929 88220416 1309 5380 E4F1 0 . GRCh38 16 2223689 2223689 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.76G>C p.Gly26Arg p.G26R ENST00000301727 1/14 164 111 53 147 147 0 strelka-varscan-mutect E4F1,missense_variant,p.Gly26Arg,ENST00000301727,NM_004424.4;E4F1,missense_variant,p.Gly26Arg,ENST00000564139,NM_001288776.1;E4F1,missense_variant,p.Gly26Arg,ENST00000565090,NM_001288778.1;E4F1,upstream_gene_variant,,ENST00000565413,;E4F1,missense_variant,p.Gly26Arg,ENST00000562589,;E4F1,upstream_gene_variant,,ENST00000569796,; C ENST00000301727 Transcript missense_variant 124/2573 76/2355 26/784 G/R Ggc/Cgc 1 1 E4F1 HGNC HGNC:3121 protein_coding YES CCDS32370.1 ENSP00000301727 Q66K89 UPI00001AED0F NM_004424.4 deleterious_low_confidence(0.01) 1/14 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 2223689 2223689 G C 1 0 0 0 0 1 0 0 0 4698 1232 43 4 4 E4F1 16 2223689 Missense_Mutation SNP G C3L-00144_T 105760 2223689 88114656 1310 5381 E4F1 0 . GRCh38 16 2234969 2234969 + Missense_Mutation SNP G G T rs372658146 C3L-00144_T C3L-00144_N G G c.1903G>T p.Val635Leu p.V635L ENST00000301727 12/14 222 189 33 181 181 0 strelka-varscan-mutect E4F1,missense_variant,p.Val635Leu,ENST00000301727,NM_004424.4;E4F1,missense_variant,p.Val458Leu,ENST00000565090,NM_001288778.1;E4F1,intron_variant,,ENST00000564139,NM_001288776.1;DNASE1L2,upstream_gene_variant,,ENST00000564065,;ECI1,downstream_gene_variant,,ENST00000301729,NM_001919.3;ECI1,downstream_gene_variant,,ENST00000570258,;DNASE1L2,upstream_gene_variant,,ENST00000320700,NM_001374.2;DNASE1L2,upstream_gene_variant,,ENST00000567494,NM_001301680.1;DNASE1L2,upstream_gene_variant,,ENST00000613572,;DNASE1L2,upstream_gene_variant,,ENST00000382437,;ECI1,downstream_gene_variant,,ENST00000562238,NM_001178029.1;E4F1,downstream_gene_variant,,ENST00000565413,;DNASE1L2,upstream_gene_variant,,ENST00000569184,;RP11-304L19.12,downstream_gene_variant,,ENST00000564055,;E4F1,non_coding_transcript_exon_variant,,ENST00000569796,;E4F1,non_coding_transcript_exon_variant,,ENST00000567111,;E4F1,downstream_gene_variant,,ENST00000562589,;E4F1,downstream_gene_variant,,ENST00000563643,;E4F1,downstream_gene_variant,,ENST00000564930,; T ENST00000301727 Transcript missense_variant 1951/2573 1903/2355 635/784 V/L Gtg/Ttg rs372658146 1 1 E4F1 HGNC HGNC:3121 protein_coding YES CCDS32370.1 ENSP00000301727 Q66K89 UPI00001AED0F NM_004424.4 deleterious(0.01) 12/14 MODERATE 1 SNV 1 1 PASS rs372658146 . 0 207 0 3 0 0 0 0 -20 0.9999936 1 1 1 0 T 3 4 12 2234969 2234969 G T 1 0 0 0 0 1 0 0 0 4698 1145 40 1 1 E4F1 16 2234969 Missense_Mutation SNP G C3L-00144_T 11280 2234969 88103376 1311 5382 NUDT16L1 0 . GRCh38 16 4694464 4694464 + Missense_Mutation SNP G G T rs758779340 C3L-00144_T C3L-00144_N G G c.640G>T p.Ala214Ser p.A214S ENST00000405142 2/2 76 67 9 49 49 0 strelka-varscan-mutect NUDT16L1,missense_variant,p.Ala214Ser,ENST00000405142,;NUDT16L1,intron_variant,,ENST00000586536,NM_001193452.1;NUDT16L1,intron_variant,,ENST00000304301,NM_032349.3;NUDT16L1,intron_variant,,ENST00000586252,;NUDT16L1,intron_variant,,ENST00000590460,;MGRN1,downstream_gene_variant,,ENST00000399577,NM_001142290.2;MGRN1,downstream_gene_variant,,ENST00000415496,NM_001142291.2;MGRN1,downstream_gene_variant,,ENST00000262370,NM_015246.3;ANKS3,downstream_gene_variant,,ENST00000304283,NM_133450.3;ANKS3,downstream_gene_variant,,ENST00000614075,;ANKS3,downstream_gene_variant,,ENST00000450067,NM_001242929.1;ANKS3,downstream_gene_variant,,ENST00000446014,NM_001308089.1;ANKS3,downstream_gene_variant,,ENST00000585773,;ANKS3,downstream_gene_variant,,ENST00000588513,;ANKS3,downstream_gene_variant,,ENST00000591653,;ANKS3,downstream_gene_variant,,ENST00000590803,;ANKS3,downstream_gene_variant,,ENST00000592077,;ANKS3,downstream_gene_variant,,ENST00000590193,;ANKS3,downstream_gene_variant,,ENST00000589035,;ANKS3,downstream_gene_variant,,ENST00000591185,;ANKS3,downstream_gene_variant,,ENST00000588398,; T ENST00000405142 Transcript missense_variant 649/2040 640/744 214/247 A/S Gcc/Tcc rs758779340 1 1 NUDT16L1 HGNC HGNC:28154 protein_coding ENSP00000458144 Q9BRJ7 UPI000006F550 deleterious_low_confidence(0.03) 2/2 MODERATE SNV 1 1 PASS rs758779340 . 0 205 3 2 0 0 0 0 -15.28917 0.9999897 1 1 1 0 T 3 4 12 4694464 4694464 G T 1 0 0 0 0 1 0 0 0 10797 1087 38 1 1 NUDT16L1 16 4694464 Missense_Mutation SNP G C3L-00144_T 2459495 4694464 85643881 1312 5383 ZNF500 0 . GRCh38 16 4752536 4752536 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1283G>T p.Arg428Leu p.R428L ENST00000219478 6/6 161 142 19 125 125 0 strelka-varscan-mutect ZNF500,missense_variant,p.Arg428Leu,ENST00000219478,NM_021646.2;ZNF500,missense_variant,p.Arg428Leu,ENST00000545009,NM_001303450.1;ZNF500,missense_variant,p.Ala33Ser,ENST00000588942,;C16orf71,downstream_gene_variant,,ENST00000299320,NM_139170.2;C16orf71,downstream_gene_variant,,ENST00000590191,;ZNF500,downstream_gene_variant,,ENST00000592425,;Metazoa_SRP,upstream_gene_variant,,ENST00000622471,;ZNF500,non_coding_transcript_exon_variant,,ENST00000591026,;RP11-127I20.7,non_coding_transcript_exon_variant,,ENST00000588099,;ZNF500,3_prime_UTR_variant,,ENST00000589422,;C16orf71,downstream_gene_variant,,ENST00000586256,; A ENST00000219478 Transcript missense_variant 1583/5880 1283/1443 428/480 R/L cGc/cTc 1 -1 ZNF500 HGNC HGNC:23716 protein_coding YES CCDS32383.1 ENSP00000219478 O60304 UPI00001C1FB0 NM_021646.2 deleterious(0.01) 6/6 Gene3D:3.30.160.60,Pfam_domain:PF13894,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF74,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS rs1280452143 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 4752536 4752536 C A 1 0 0 0 0 1 0 0 0 18520 768 27 1 1 ZNF500 16 4752536 Missense_Mutation SNP C C3L-00144_T 58072 4752536 85585809 1313 5384 USP7 0 . GRCh38 16 8900566 8900566 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.2273A>G p.Asp758Gly p.D758G ENST00000344836 21/31 169 123 46 145 145 0 strelka-varscan-mutect USP7,missense_variant,p.Asp758Gly,ENST00000344836,NM_001321858.1,NM_003470.2;USP7,missense_variant,p.Asp742Gly,ENST00000381886,NM_001286458.1,NM_001286457.1;USP7,missense_variant,p.Asp659Gly,ENST00000563085,;USP7,3_prime_UTR_variant,,ENST00000563961,;USP7,3_prime_UTR_variant,,ENST00000565455,;USP7,3_prime_UTR_variant,,ENST00000567692,;USP7,non_coding_transcript_exon_variant,,ENST00000569448,;USP7,non_coding_transcript_exon_variant,,ENST00000566131,;USP7,intron_variant,,ENST00000563043,;USP7,downstream_gene_variant,,ENST00000542333,;USP7,downstream_gene_variant,,ENST00000570256,;USP7,upstream_gene_variant,,ENST00000562051,;USP7,downstream_gene_variant,,ENST00000567329,;USP7,upstream_gene_variant,,ENST00000565883,;USP7,upstream_gene_variant,,ENST00000567113,;USP7,upstream_gene_variant,,ENST00000562615,; C ENST00000344836 Transcript missense_variant 2472/5412 2273/3309 758/1102 D/G gAt/gGt 1 -1 USP7 HGNC HGNC:12630 protein_coding YES CCDS32385.1 ENSP00000343535 Q93009 UPI000013F0BE NM_001321858.1,NM_003470.2 tolerated(0.3) 21/31 Pfam_domain:PF12436 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 8900566 8900566 T C 1 0 0 0 0 1 0 0 0 17631 1435 50 5 5 USP7 16 8900566 Missense_Mutation SNP T C3L-00144_T 4148030 8900566 81437779 1314 5385 USP7 0 . GRCh38 16 8904482 8904482 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1657C>T p.Gln553Ter p.Q553* ENST00000344836 15/31 160 151 9 116 116 0 strelka-varscan-mutect USP7,stop_gained,p.Gln553Ter,ENST00000344836,NM_001321858.1,NM_003470.2;USP7,stop_gained,p.Gln537Ter,ENST00000381886,NM_001286458.1,NM_001286457.1;USP7,stop_gained,p.Gln454Ter,ENST00000563085,;USP7,missense_variant,p.Ser481Leu,ENST00000542333,;USP7,3_prime_UTR_variant,,ENST00000563961,;USP7,3_prime_UTR_variant,,ENST00000565455,;USP7,non_coding_transcript_exon_variant,,ENST00000570256,;USP7,non_coding_transcript_exon_variant,,ENST00000567329,;USP7,upstream_gene_variant,,ENST00000569448,;USP7,upstream_gene_variant,,ENST00000566131,;USP7,upstream_gene_variant,,ENST00000562051,;USP7,upstream_gene_variant,,ENST00000563043,;USP7,upstream_gene_variant,,ENST00000567692,; A ENST00000344836 Transcript stop_gained 1856/5412 1657/3309 553/1102 Q/* Cag/Tag 1 -1 USP7 HGNC HGNC:12630 protein_coding YES CCDS32385.1 ENSP00000343535 Q93009 UPI000013F0BE NM_001321858.1,NM_003470.2 15/31 Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 8904482 8904482 G A 1 0 0 0 0 0 1 0 0 17631 1299 45 3 3 USP7 16 8904482 Nonsense_Mutation SNP G C3L-00144_T 3916 8904482 81433863 1315 5386 CPPED1 0 . GRCh38 16 12664985 12664985 + Silent SNP C C G C3L-00144_T C3L-00144_N C C c.846G>C p.= p.V282V ENST00000381774 4/4 143 99 44 155 155 0 strelka-varscan-mutect CPPED1,missense_variant,p.Gly109Arg,ENST00000261660,;CPPED1,synonymous_variant,p.=,ENST00000381774,NM_018340.2;CPPED1,synonymous_variant,p.=,ENST00000433677,NM_001099455.1; G ENST00000381774 Transcript synonymous_variant 1087/6273 846/945 282/314 V gtG/gtC COSM365070 1 -1 CPPED1 HGNC HGNC:25632 protein_coding YES CCDS42120.1 ENSP00000371193 Q9BRF8 UPI000013D1D1 NM_018340.2 4/4 hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF34,Gene3D:3.60.21.10,Superfamily_domains:SSF56300 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 12664985 12664985 C G 1 0 0 0 0 0 0 0 1 3617 594 21 4 4 CPPED1 16 12664985 Silent SNP C C3L-00144_T 3760503 12664985 77673360 1316 5387 PDZD9 0 . GRCh38 16 21984355 21984355 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.527C>G p.Ser176Cys p.S176C ENST00000537222 3/3 269 228 41 205 205 0 strelka-mutect PDZD9,missense_variant,p.Ser236Cys,ENST00000424898,;PDZD9,missense_variant,p.Ser176Cys,ENST00000537222,NM_173806.3;UQCRC2,downstream_gene_variant,,ENST00000268379,NM_003366.2;UQCRC2,downstream_gene_variant,,ENST00000561553,;PDZD9,3_prime_UTR_variant,,ENST00000523914,;UQCRC2,downstream_gene_variant,,ENST00000563898,;UQCRC2,downstream_gene_variant,,ENST00000561798,; C ENST00000537222 Transcript missense_variant 578/1068 527/615 176/204 S/C tCt/tGt 1 -1 PDZD9 HGNC HGNC:28740 protein_coding YES CCDS10602.2 ENSP00000441685 Q8IXQ8 UPI0000E24140 NM_173806.3 deleterious(0.03) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22698 MODERATE SNV 3 1 PASS rs1293350658 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 21984355 21984355 G C 1 0 0 0 0 1 0 0 0 11794 942 33 4 4 PDZD9 16 21984355 Missense_Mutation SNP G C3L-00144_T 9319370 21984355 68353990 1317 5388 PALB2 0 . GRCh38 16 23636137 23636137 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.409G>T p.Gly137Cys p.G137C ENST00000261584 4/13 138 110 28 94 93 1 strelka-varscan-mutect PALB2,missense_variant,p.Gly137Cys,ENST00000261584,NM_024675.3;PALB2,5_prime_UTR_variant,,ENST00000568219,;PALB2,downstream_gene_variant,,ENST00000561514,;PALB2,non_coding_transcript_exon_variant,,ENST00000567003,;PALB2,intron_variant,,ENST00000565038,; A ENST00000261584 Transcript missense_variant 562/4003 409/3561 137/1186 G/C Ggt/Tgt 1 -1 PALB2 HGNC HGNC:26144 protein_coding YES CCDS32406.1 ENSP00000261584 Q86YC2 UPI000000DA86 NM_024675.3 deleterious(0.03) 4/13 hmmpanther:PTHR14662,hmmpanther:PTHR14662:SF2 MODERATE 1 SNV 1 1 PASS rs1397816581 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 23636137 23636137 C A 1 0 0 0 0 1 0 0 0 11485 594 21 2 2 PALB2 16 23636137 Missense_Mutation SNP C C3L-00144_T 1651782 23636137 66702208 1318 5389 CHP2 0 . GRCh38 16 23757320 23757320 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.534C>A p.= p.T178T ENST00000300113 6/7 87 81 6 70 70 0 strelka-varscan-mutect CHP2,synonymous_variant,p.=,ENST00000300113,NM_022097.3;CTD-2385L22.2,upstream_gene_variant,,ENST00000623305,; A ENST00000300113 Transcript synonymous_variant 957/2382 534/591 178/196 T acC/acA 1 1 CHP2 HGNC HGNC:24927 protein_coding YES CCDS10617.1 ENSP00000300113 O43745 UPI000013E626 NM_022097.3 6/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF49,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -12.77218 0.9999997 1 1 1 0 A 2 1 12 23757320 23757320 C A 1 0 0 0 0 0 0 0 1 3127 608 21 2 2 CHP2 16 23757320 Silent SNP C C3L-00144_T 121183 23757320 66581025 1319 5390 PRKCB 0 . GRCh38 16 24214718 24214718 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1924C>A p.Pro642Thr p.P642T ENST00000303531 17/17 279 252 27 225 225 0 strelka-varscan-mutect PRKCB,missense_variant,p.Pro642Thr,ENST00000303531,NM_002738.6;PRKCB,intron_variant,,ENST00000321728,NM_212535.2; A ENST00000303531 Transcript missense_variant 2076/7969 1924/2022 642/673 P/T Cct/Act 1 1 PRKCB HGNC HGNC:9395 protein_coding YES CCDS10619.1 ENSP00000305355 P05771 UPI000002ACF9 NM_002738.6 deleterious(0) 17/17 Pfam_domain:PF00433,PIRSF_domain:PIRSF000550,PROSITE_profiles:PS51285,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF188,SMART_domains:SM00133,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 24214718 24214718 C A 1 0 0 0 0 1 0 0 0 12641 507 18 2 2 PRKCB 16 24214718 Missense_Mutation SNP C C3L-00144_T 457398 24214718 66123627 1320 5391 HS3ST4 0 . GRCh38 16 25692752 25692752 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.335C>G p.Pro112Arg p.P112R ENST00000331351 1/2 34 28 6 29 29 0 strelka-mutect HS3ST4,missense_variant,p.Pro112Arg,ENST00000331351,NM_006040.2; G ENST00000331351 Transcript missense_variant 727/3203 335/1371 112/456 P/R cCc/cGc 1 1 HS3ST4 HGNC HGNC:5200 protein_coding YES CCDS53995.1 ENSP00000330606 Q9Y661 UPI000040938A NM_006040.2 tolerated_low_confidence(0.37) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1385567443 . 0 208 2 0 0 0 0 0 -16.2041 1 1 1 1 0 G 3 3 12 25692752 25692752 C G 1 0 0 0 0 1 0 0 0 7261 623 22 4 4 HS3ST4 16 25692752 Missense_Mutation SNP C C3L-00144_T 1478034 25692752 64645593 1321 5392 GTF3C1 0 . GRCh38 16 27483126 27483126 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.4002-1G>T p.X1334_splice ENST00000356183 203 164 39 142 142 0 strelka-varscan-mutect GTF3C1,splice_acceptor_variant,,ENST00000356183,NM_001520.3;GTF3C1,splice_acceptor_variant,,ENST00000561623,NM_001286242.1;GTF3C1,splice_acceptor_variant,,ENST00000568569,;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,downstream_gene_variant,,ENST00000570129,;GTF3C1,splice_acceptor_variant,,ENST00000566779,;GTF3C1,intron_variant,,ENST00000564664,;GTF3C1,upstream_gene_variant,,ENST00000569394,; A ENST00000356183 Transcript splice_acceptor_variant -/7018 4002/6330 1334/2109 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 25/36 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 27483126 27483126 C A 1 0 0 0 0 0 0 1 0 6753 927 32 2 2 GTF3C1 16 27483126 Splice_Site SNP C C3L-00144_T 1790374 27483126 62855219 1322 5393 GTF3C1 0 . GRCh38 16 27492405 27492405 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.3084G>T p.= p.L1028L ENST00000356183 19/37 187 171 16 160 160 0 strelka-varscan-mutect GTF3C1,synonymous_variant,p.=,ENST00000356183,NM_001520.3;GTF3C1,synonymous_variant,p.=,ENST00000561623,NM_001286242.1;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,upstream_gene_variant,,ENST00000568569,;GTF3C1,upstream_gene_variant,,ENST00000564664,; A ENST00000356183 Transcript synonymous_variant 3100/7018 3084/6330 1028/2109 L ctG/ctT 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 19/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 27492405 27492405 C A 1 0 0 0 0 0 0 0 1 6753 813 29 2 2 GTF3C1 16 27492405 Silent SNP C C3L-00144_T 9279 27492405 62845940 1323 5394 KIAA0556 0 . GRCh38 16 27761440 27761440 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.3659G>A p.Trp1220Ter p.W1220* ENST00000261588 19/28 105 85 20 90 90 0 strelka-varscan-mutect KIAA0556,stop_gained,p.Trp1220Ter,ENST00000261588,NM_015202.2; A ENST00000261588 Transcript stop_gained 3678/6616 3659/4857 1220/1618 W/* tGg/tAg 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 19/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534,Pfam_domain:PF14652 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 27761440 27761440 G A 1 0 0 0 0 0 1 0 0 8088 1357 47 3 3 KIAA0556 16 27761440 Nonsense_Mutation SNP G C3L-00144_T 269035 27761440 62576905 1324 5395 IL27 0 . GRCh38 16 28499717 28499717 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.666G>T p.= p.L222L ENST00000356897 5/5 273 211 62 277 275 2 strelka-varscan-mutect IL27,synonymous_variant,p.=,ENST00000356897,NM_145659.3;CLN3,upstream_gene_variant,,ENST00000569430,;APOBR,downstream_gene_variant,,ENST00000564831,NM_018690.3;APOBR,downstream_gene_variant,,ENST00000431282,;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,; A ENST00000356897 Transcript synonymous_variant 689/1044 666/732 222/243 L ctG/ctT 1 -1 IL27 HGNC HGNC:19157 protein_coding YES CCDS10633.1 ENSP00000349365 Q8NEV9 UPI0000141330 NM_145659.3 5/5 hmmpanther:PTHR20879,hmmpanther:PTHR20879:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 28499717 28499717 C A 1 0 0 0 0 0 0 0 1 7583 697 25 2 2 IL27 16 28499717 Silent SNP C C3L-00144_T 738277 28499717 61838628 1325 5396 CD19 0 . GRCh38 16 28937291 28937291 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1219G>T p.Glu407Ter p.E407* ENST00000538922 9/15 262 195 67 271 271 0 strelka-varscan-mutect CD19,stop_gained,p.Glu407Ter,ENST00000538922,NM_001178098.1;CD19,stop_gained,p.Glu407Ter,ENST00000324662,NM_001770.5;CD19,stop_gained,p.Glu407Ter,ENST00000567541,;RABEP2,upstream_gene_variant,,ENST00000566762,;CD19,non_coding_transcript_exon_variant,,ENST00000565089,;CD19,non_coding_transcript_exon_variant,,ENST00000567368,;CD19,downstream_gene_variant,,ENST00000566890,; T ENST00000538922 Transcript stop_gained 1281/1957 1219/1674 407/557 E/* Gag/Tag 1 1 CD19 HGNC HGNC:1633 protein_coding YES CCDS53998.1 ENSP00000437940 P15391 UPI0000E02929 NM_001178098.1 9/15 hmmpanther:PTHR16674,hmmpanther:PTHR16674:SF2,Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS rs886948983 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 28937291 28937291 G T 1 0 0 0 0 0 1 0 0 2676 1175 41 2 2 CD19 16 28937291 Nonsense_Mutation SNP G C3L-00144_T 437574 28937291 61401054 1326 5397 C16orf54 0 . GRCh38 16 29744466 29744466 + Silent SNP G G T rs551608693,rs779355314 C3L-00144_T C3L-00144_N G G c.486C>A p.= p.P162P ENST00000329410 2/2 135 118 17 146 146 0 strelka-varscan-mutect C16orf54,synonymous_variant,p.=,ENST00000329410,NM_175900.3;AC009133.17,upstream_gene_variant,,ENST00000565600,; T ENST00000329410 Transcript synonymous_variant 582/2585 486/675 162/224 P ccC/ccA rs551608693,rs779355314 1 -1 C16orf54 HGNC HGNC:26649 protein_coding YES CCDS10652.1 ENSP00000327506 Q6UWD8 UPI0000141B48 NM_175900.3 2/2 hmmpanther:PTHR36134,Pfam_domain:PF15755 LOW 1 SNV 1 1 PASS rs551608693 . 0 204 0 5 0 0 0 0 -20 0.9993483 1 1 1 0 T 2 4 12 29744466 29744466 G T 1 0 0 0 0 0 0 0 1 1858 1103 39 1 1 C16orf54 16 29744466 Silent SNP G C3L-00144_T 807175 29744466 60593879 1327 5398 ZNF689 0 . GRCh38 16 30604715 30604715 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1052A>T p.Glu351Val p.E351V ENST00000287461 3/3 100 91 9 91 91 0 strelka-varscan-mutect ZNF689,missense_variant,p.Glu351Val,ENST00000287461,NM_138447.2;RP11-146F11.5,intron_variant,,ENST00000563540,;ZNF689,non_coding_transcript_exon_variant,,ENST00000566673,;ZNF689,non_coding_transcript_exon_variant,,ENST00000563304,;ZNF689,non_coding_transcript_exon_variant,,ENST00000565440,;ZNF689,downstream_gene_variant,,ENST00000564262,;ZNF689,downstream_gene_variant,,ENST00000565710,; A ENST00000287461 Transcript missense_variant 1390/3547 1052/1503 351/500 E/V gAg/gTg 1 -1 ZNF689 HGNC HGNC:25173 protein_coding YES CCDS10686.1 ENSP00000287461 Q96CS4 UPI000006CDAD NM_138447.2 deleterious(0.01) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF23,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 194 13 3 0 0 0 0 -13.89809 0.9856912 1 1 1 0 A 3 1 12 30604715 30604715 T A 1 0 0 0 0 1 0 0 0 18667 1551 54 4 4 ZNF689 16 30604715 Missense_Mutation SNP T C3L-00144_T 860249 30604715 59733630 1328 5399 PRSS36 0 . GRCh38 16 31143345 31143345 + Missense_Mutation SNP A A C novel C3L-00144_T C3L-00144_N A A c.1097T>G p.Leu366Arg p.L366R ENST00000268281 8/15 69 47 22 83 83 0 strelka-varscan-mutect PRSS36,missense_variant,p.Leu366Arg,ENST00000268281,NM_173502.4;PRSS36,missense_variant,p.Leu366Arg,ENST00000569305,NM_001258290.1;PRSS36,missense_variant,p.Leu366Arg,ENST00000418068,NM_001258291.1;PRSS36,non_coding_transcript_exon_variant,,ENST00000562368,;PRSS36,upstream_gene_variant,,ENST00000563693,;PRSS36,upstream_gene_variant,,ENST00000571878,; C ENST00000268281 Transcript missense_variant 1156/2840 1097/2568 366/855 L/R cTg/cGg 1 -1 PRSS36 HGNC HGNC:26906 protein_coding YES CCDS32436.1 ENSP00000268281 Q5K4E3 UPI00001FFF6A NM_173502.4 tolerated(0.07) 8/15 PROSITE_profiles:PS50240,hmmpanther:PTHR24276,hmmpanther:PTHR24276:SF62,Gene3D:2.40.10.10,PIRSF_domain:PIRSF037933,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs1364686683 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 31143345 31143345 A C 1 0 0 0 0 1 0 0 0 12772 202 7 5 5 PRSS36 16 31143345 Missense_Mutation SNP A C3L-00144_T 538630 31143345 59195000 1329 5400 ITGAX 0 . GRCh38 16 31363365 31363365 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1701C>A p.= p.S567S ENST00000562522 14/31 395 313 82 326 326 0 strelka-varscan-mutect ITGAX,synonymous_variant,p.=,ENST00000268296,NM_000887.4;ITGAX,synonymous_variant,p.=,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,; A ENST00000562522 Transcript synonymous_variant 1734/3990 1701/3510 567/1169 S tcC/tcA 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 14/31 Gene3D:3nigC00,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 31363365 31363365 C A 1 0 0 0 0 0 0 0 1 7796 610 22 2 2 ITGAX 16 31363365 Silent SNP C C3L-00144_T 220020 31363365 58974980 1330 5401 ITGAX 0 . GRCh38 16 31381852 31381852 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3437G>T p.Gly1146Val p.G1146V ENST00000562522 30/31 196 162 34 157 157 0 strelka-varscan-mutect ITGAX,missense_variant,p.Gly1146Val,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Gly1146Val,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,; T ENST00000562522 Transcript missense_variant 3470/3990 3437/3510 1146/1169 G/V gGa/gTa 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.16) 30/31 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 31381852 31381852 G T 1 0 0 0 0 1 0 0 0 7796 1174 41 2 2 ITGAX 16 31381852 Missense_Mutation SNP G C3L-00144_T 18487 31381852 58956493 1331 5402 SALL1 0 . GRCh38 16 51139490 51139490 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2732G>T p.Ser911Ile p.S911I ENST00000251020 2/3 293 233 60 293 292 1 strelka-varscan-mutect SALL1,missense_variant,p.Ser814Ile,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Ser911Ile,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Ser814Ile,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 2766/5146 2732/3975 911/1324 S/I aGc/aTc 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51139490 51139490 C A 1 0 0 0 0 1 0 0 0 14069 797 28 2 2 SALL1 16 51139490 Missense_Mutation SNP C C3L-00144_T 19757638 51139490 39198855 1332 5403 MMP2 0 . GRCh38 16 55488630 55488630 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.920C>T p.Thr307Ile p.T307I ENST00000219070 6/13 249 191 58 306 306 0 strelka-varscan-mutect MMP2,missense_variant,p.Thr307Ile,ENST00000219070,NM_004530.5;MMP2,missense_variant,p.Thr231Ile,ENST00000570308,;MMP2,missense_variant,p.Thr257Ile,ENST00000437642,NM_001127891.2;MMP2,missense_variant,p.Thr231Ile,ENST00000543485,NM_001302508.1,NM_001302510.1,NM_001302509.1;MMP2,upstream_gene_variant,,ENST00000570283,;MMP2,downstream_gene_variant,,ENST00000564864,;MMP2,downstream_gene_variant,,ENST00000568715,;RP11-212I21.3,non_coding_transcript_exon_variant,,ENST00000623886,; T ENST00000219070 Transcript missense_variant 1429/3741 920/1983 307/660 T/I aCt/aTt 1 1 MMP2 HGNC HGNC:7166 protein_coding YES CCDS10752.1 ENSP00000219070 P08253 A0A024R6R4 UPI00000422C4 NM_004530.5 deleterious(0) 6/13 Gene3D:2.10.10.10,Pfam_domain:PF00040,Pfam_domain:PF00413,PROSITE_patterns:PS00023,PROSITE_profiles:PS51092,SMART_domains:SM00059,SMART_domains:SM00235,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 55488630 55488630 C T 1 0 0 0 0 1 0 0 0 9621 565 20 3 3 MMP2 16 55488630 Missense_Mutation SNP C C3L-00144_T 4349140 55488630 34849715 1333 5404 CDH5 0 . GRCh38 16 66403074 66403074 + Missense_Mutation SNP G G T rs758376963 C3L-00144_T C3L-00144_N G G c.2260G>T p.Asp754Tyr p.D754Y ENST00000341529 12/12 302 240 62 322 322 0 strelka-varscan-mutect CDH5,missense_variant,p.Asp754Tyr,ENST00000341529,NM_001795.3;CDH5,missense_variant,p.Asp639Tyr,ENST00000614547,;CDH5,missense_variant,p.Asp193Tyr,ENST00000539168,;CDH5,3_prime_UTR_variant,,ENST00000565334,; T ENST00000341529 Transcript missense_variant 2408/4120 2260/2355 754/784 D/Y Gac/Tac rs758376963 1 1 CDH5 HGNC HGNC:1764 protein_coding YES CCDS10804.1 ENSP00000344115 P33151 UPI000016B272 NM_001795.3 deleterious(0) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF89,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 MODERATE 1 SNV 1 1 PASS rs758376963 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 66403074 66403074 G T 1 0 0 0 0 1 0 0 0 2816 1290 45 2 2 CDH5 16 66403074 Missense_Mutation SNP G C3L-00144_T 10914444 66403074 23935271 1334 5405 TRADD 0 . GRCh38 16 67155488 67155488 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.318G>T p.= p.A106A ENST00000345057 3/5 138 106 32 146 146 0 strelka-varscan-mutect TRADD,synonymous_variant,p.=,ENST00000345057,NM_003789.3;TRADD,synonymous_variant,p.=,ENST00000486556,;B3GNT9,upstream_gene_variant,,ENST00000449549,NM_033309.2;FBXL8,upstream_gene_variant,,ENST00000258200,;FBXL8,upstream_gene_variant,,ENST00000519917,NM_018378.2;FBXL8,upstream_gene_variant,,ENST00000518148,;FBXL8,upstream_gene_variant,,ENST00000521920,;FBXL8,upstream_gene_variant,,ENST00000517382,;TRADD,downstream_gene_variant,,ENST00000566104,;TRADD,downstream_gene_variant,,ENST00000563348,;FBXL8,upstream_gene_variant,,ENST00000519945,;TRADD,upstream_gene_variant,,ENST00000566247,; A ENST00000345057 Transcript synonymous_variant 787/1877 318/939 106/312 A gcG/gcT 1 -1 TRADD HGNC HGNC:12030 protein_coding YES CCDS10829.1 ENSP00000341268 Q15628 UPI00001372E3 NM_003789.3 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR14913,Gene3D:1f3vA00,Pfam_domain:PF09034,Superfamily_domains:0046699,PD182470 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 67155488 67155488 C A 1 0 0 0 0 0 0 0 1 16919 755 27 1 1 TRADD 16 67155488 Silent SNP C C3L-00144_T 752414 67155488 23182857 1335 5406 PKD1L3 0 . GRCh38 16 71990331 71990331 + Splice_Site SNP T T C novel C3L-00144_T C3L-00144_N T T c.536-2A>G p.X179_splice ENST00000620267 87 76 11 68 68 0 strelka-varscan-mutect PKD1L3,splice_acceptor_variant,,ENST00000620267,NM_181536.1;RPL39P31,downstream_gene_variant,,ENST00000467090,; C ENST00000620267 Transcript splice_acceptor_variant -/5199 536/5199 179/1732 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 3/29 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.06954 0.9999999 1 1 1 0 C 5 2 12 71990331 71990331 T C 1 0 0 0 0 0 0 1 0 12061 1536 53 5 5 PKD1L3 16 71990331 Splice_Site SNP T C3L-00144_T 4834843 71990331 18348014 1336 5407 WDR59 0 . GRCh38 16 74888302 74888302 + Missense_Mutation SNP C C A rs144238663 C3L-00144_T C3L-00144_N C C c.2213G>T p.Arg738Leu p.R738L ENST00000262144 22/26 98 72 26 79 79 0 strelka-varscan-mutect WDR59,missense_variant,p.Arg738Leu,ENST00000262144,NM_030581.3;WDR59,intron_variant,,ENST00000563797,;WDR59,downstream_gene_variant,,ENST00000569229,;WDR59,non_coding_transcript_exon_variant,,ENST00000569788,;WDR59,non_coding_transcript_exon_variant,,ENST00000567018,;WDR59,upstream_gene_variant,,ENST00000569183,;WDR59,downstream_gene_variant,,ENST00000563381,;WDR59,downstream_gene_variant,,ENST00000566924,;WDR59,upstream_gene_variant,,ENST00000569968,; A ENST00000262144 Transcript missense_variant 2344/5898 2213/2925 738/974 R/L cGg/cTg rs144238663 1 -1 WDR59 HGNC HGNC:25706 protein_coding YES CCDS32488.1 ENSP00000262144 Q6PJI9 UPI000019839C NM_030581.3 deleterious(0.05) 22/26 hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF116 MODERATE 1 SNV 5 1 PASS rs144238663 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 74888302 74888302 C A 1 0 0 0 0 1 0 0 0 17867 652 23 1 1 WDR59 16 74888302 Missense_Mutation SNP C C3L-00144_T 2897971 74888302 15450043 1337 5408 CTRB1 0 . GRCh38 16 75219055 75219055 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.48C>A p.= p.A16A ENST00000361017 1/7 192 149 43 170 169 1 strelka-varscan-mutect CTRB1,synonymous_variant,p.=,ENST00000361017,NM_001906.4;CTRB1,upstream_gene_variant,,ENST00000495583,; A ENST00000361017 Transcript synonymous_variant 56/858 48/792 16/263 A gcC/gcA 1 1 CTRB1 HGNC HGNC:2521 protein_coding YES CCDS32490.1 ENSP00000354294 P17538 UPI000013E843 NM_001906.4 1/7 hmmpanther:PTHR24250,hmmpanther:PTHR24250:SF23,Superfamily_domains:SSF50494,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 75219055 75219055 C A 1 0 0 0 0 0 0 0 1 3834 695 24 2 2 CTRB1 16 75219055 Silent SNP C C3L-00144_T 330753 75219055 15119290 1338 5409 CNTNAP4 0 . GRCh38 16 76521187 76521187 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.2413C>G p.His805Asp p.H805D ENST00000611870 16/24 243 193 50 253 253 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.His805Asp,ENST00000307431,;CNTNAP4,missense_variant,p.His805Asp,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.His757Asp,ENST00000377504,;CNTNAP4,missense_variant,p.His808Asp,ENST00000476707,;CNTNAP4,missense_variant,p.His757Asp,ENST00000622250,;CNTNAP4,missense_variant,p.His732Asp,ENST00000478060,NM_138994.3; G ENST00000611870 Transcript missense_variant 2798/4867 2413/3927 805/1308 H/D Cat/Gat COSM5363274,COSM5363275 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0) 16/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,Superfamily_domains:SSF49899 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 76521187 76521187 C G 1 0 0 0 0 1 0 0 0 3431 826 29 4 4 CNTNAP4 16 76521187 Missense_Mutation SNP C C3L-00144_T 1302132 76521187 13817158 1339 5410 CBFA2T3 0 . GRCh38 16 88901618 88901618 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.190G>T p.Asp64Tyr p.D64Y ENST00000268679 2/12 198 171 27 163 161 2 strelka-varscan-mutect CBFA2T3,missense_variant,p.Asp64Tyr,ENST00000268679,NM_005187.5;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000327483,NM_175931.2;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000569464,;CBFA2T3,missense_variant,p.Asp64Tyr,ENST00000563640,;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000562719,;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000569443,;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000564416,;CBFA2T3,missense_variant,p.Asp3Tyr,ENST00000570046,; A ENST00000268679 Transcript missense_variant 587/4477 190/1962 64/653 D/Y Gac/Tac COSM3513244 1 -1 CBFA2T3 HGNC HGNC:1537 protein_coding YES CCDS10972.1 ENSP00000268679 O75081 UPI0000167F93 NM_005187.5 deleterious_low_confidence(0.01) 2/12 hmmpanther:PTHR10379,hmmpanther:PTHR10379:SF6 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 88901618 88901618 C A 1 0 0 0 0 1 0 0 0 2399 855 30 2 2 CBFA2T3 16 88901618 Missense_Mutation SNP C C3L-00144_T 12380431 88901618 1436727 1340 5411 ZZEF1 0 . GRCh38 17 4016381 4016381 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.8087G>C p.Gly2696Ala p.G2696A ENST00000381638 49/55 189 139 50 211 211 0 strelka-varscan-mutect ZZEF1,missense_variant,p.Gly2696Ala,ENST00000381638,NM_015113.3;ZZEF1,3_prime_UTR_variant,,ENST00000572831,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000573536,;ZZEF1,downstream_gene_variant,,ENST00000575428,; G ENST00000381638 Transcript missense_variant 8212/11456 8087/8886 2696/2961 G/A gGa/gCa 1 -1 ZZEF1 HGNC HGNC:29027 protein_coding YES CCDS11043.1 ENSP00000371051 O43149 UPI00004569F7 NM_015113.3 tolerated(0.13) 49/55 hmmpanther:PTHR22772:SF4,hmmpanther:PTHR22772 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 4016381 4016381 C G 1 0 0 0 0 1 0 0 0 18859 855 30 4 4 ZZEF1 17 4016381 Missense_Mutation SNP C C3L-00144_T 4016381 79241060 1341 5412 ANKFY1 0 . GRCh38 17 4207957 4207957 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.834G>C p.= p.L278L ENST00000570535 6/25 32 24 8 43 43 0 strelka-mutect ANKFY1,synonymous_variant,p.=,ENST00000341657,;ANKFY1,synonymous_variant,p.=,ENST00000570535,NM_001257999.1;ANKFY1,synonymous_variant,p.=,ENST00000574367,NM_016376.3;ANKFY1,3_prime_UTR_variant,,ENST00000572412,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000570934,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000573250,; G ENST00000570535 Transcript synonymous_variant 951/6458 834/3636 278/1211 L ctG/ctC 1 -1 ANKFY1 HGNC HGNC:20763 protein_coding YES CCDS58502.1 ENSP00000459943 Q9P2R3 UPI00003FECB0 NM_001257999.1 6/25 PROSITE_profiles:PS50297,hmmpanther:PTHR24189,hmmpanther:PTHR24189:SF34,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS rs1280472043 . 0 205 4 0 0 0 0 0 -19.96985 1 1 1 1 0 G 2 3 12 4207957 4207957 C G 1 0 0 0 0 0 0 0 1 728 465 17 4 4 ANKFY1 17 4207957 Silent SNP C C3L-00144_T 191576 4207957 79049484 1342 5413 VMO1 0 . GRCh38 17 4785455 4785455 + Silent SNP G G A rs867305384 C3L-00144_T C3L-00144_N G G c.516C>T p.= p.G172G ENST00000328739 3/3 224 162 62 246 246 0 strelka-varscan-mutect VMO1,synonymous_variant,p.=,ENST00000328739,NM_182566.2;VMO1,3_prime_UTR_variant,,ENST00000441199,NM_001144939.1;VMO1,3_prime_UTR_variant,,ENST00000416307,NM_001144940.1;VMO1,3_prime_UTR_variant,,ENST00000354194,NM_001144941.1;GLTPD2,upstream_gene_variant,,ENST00000331264,NM_001014985.2;TM4SF5,downstream_gene_variant,,ENST00000270560,NM_003963.2;RP11-81A22.4,upstream_gene_variant,,ENST00000623798,;TM4SF5,downstream_gene_variant,,ENST00000576530,; A ENST00000328739 Transcript synonymous_variant 596/766 516/609 172/202 G ggC/ggT rs867305384,COSM980662 1 -1 VMO1 HGNC HGNC:30387 protein_coding YES CCDS11055.1 ENSP00000328397 Q7Z5L0 UPI000004BA7A NM_182566.2 3/3 hmmpanther:PTHR18841:SF3,hmmpanther:PTHR18841,Pfam_domain:PF03762,Gene3D:1vmoA00,Superfamily_domains:0050258 0,1 LOW 1 SNV 1 0,1 1 PASS rs867305384 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 4785455 4785455 G A 1 0 0 0 0 0 0 0 1 17724 1074 38 1 1 VMO1 17 4785455 Silent SNP G C3L-00144_T 577498 4785455 78471986 1343 5414 AIPL1 0 . GRCh38 17 6428361 6428361 + Missense_Mutation SNP T T A rs773661686 C3L-00144_T C3L-00144_N T T c.422A>T p.Gln141Leu p.Q141L ENST00000381129 3/6 401 302 99 434 433 1 strelka-varscan-mutect AIPL1,missense_variant,p.Gln141Leu,ENST00000381129,NM_014336.4;AIPL1,missense_variant,p.Gln141Leu,ENST00000575265,;AIPL1,missense_variant,p.Gln129Leu,ENST00000574506,NM_001285399.2,NM_001285402.1;AIPL1,missense_variant,p.Gln141Leu,ENST00000571740,NM_001285403.2;AIPL1,missense_variant,p.Gln119Leu,ENST00000570466,NM_001285400.2;AIPL1,missense_variant,p.Gln141Leu,ENST00000576776,NM_001285401.2;AIPL1,missense_variant,p.Gln81Leu,ENST00000576307,NM_001033055.2;AIPL1,missense_variant,p.Gln141Leu,ENST00000574913,;AIPL1,intron_variant,,ENST00000250087,NM_001033054.2;AIPL1,intron_variant,,ENST00000570584,;AIPL1,3_prime_UTR_variant,,ENST00000381128,; A ENST00000381129 Transcript missense_variant 503/2959 422/1155 141/384 Q/L cAg/cTg rs773661686 1 -1 AIPL1 HGNC HGNC:359 protein_coding YES CCDS11075.1 ENSP00000370521 Q9NZN9 F1T0B6 UPI0000125741 NM_014336.4 tolerated(0.48) 3/6 Gene3D:3.10.50.40,hmmpanther:PTHR11242,hmmpanther:PTHR11242:SF2,Superfamily_domains:SSF54534 MODERATE 1 SNV 1 1 PASS rs773661686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 6428361 6428361 T A 1 0 0 0 0 1 0 0 0 513 1580 55 4 4 AIPL1 17 6428361 Missense_Mutation SNP T C3L-00144_T 1642906 6428361 76829080 1344 5415 TP53 0 . GRCh38 17 7675151 7675151 + Missense_Mutation SNP C C A rs762846821 C3L-00144_T C3L-00144_N C C c.461G>T p.Gly154Val p.G154V ENST00000269305 5/11 248 175 73 244 243 1 strelka-varscan-mutect TP53,missense_variant,p.Gly154Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly154Val,ENST00000420246,;TP53,missense_variant,p.Gly115Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly115Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly154Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly115Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly154Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly115Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly154Val,ENST00000445888,;TP53,missense_variant,p.Gly115Val,ENST00000619485,;TP53,missense_variant,p.Gly22Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly22Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly22Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly154Val,ENST00000359597,;TP53,missense_variant,p.Gly143Val,ENST00000615910,;TP53,missense_variant,p.Gly154Val,ENST00000413465,;TP53,missense_variant,p.Gly22Val,ENST00000509690,;TP53,missense_variant,p.Gly154Val,ENST00000508793,;TP53,missense_variant,p.Gly61Val,ENST00000514944,;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly115Val,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 651/2579 461/1182 154/393 G/V gGc/gTc rs762846821,CM951223,TP53_g.12449G>C,TP53_g.12449G>T,TP53_g.12449G>A,COSM1649372,COSM342243,COSM342244,COSM342245,COSM342246,COSM4271946,COSM45622,COSM46378,COSM5315967,COSM5315968,COSM5315969,COSM5315970,COSM5315971,COSM5315972,COSM5315973,COSM6815 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs762846821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7675151 7675151 C A 1 0 0 0 0 1 0 0 0 16859 739 26 2 2 TP53 17 7675151 Missense_Mutation SNP C C3L-00144_T 1246790 7675151 75582290 1345 5416 ALOXE3 0 . GRCh38 17 8117995 8117995 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.392C>G p.Pro131Arg p.P131R ENST00000318227 2/16 351 264 87 366 366 0 strelka-varscan-mutect ALOXE3,missense_variant,p.Pro155Arg,ENST00000380149,;ALOXE3,missense_variant,p.Pro131Arg,ENST00000318227,NM_001165960.1;ALOXE3,5_prime_UTR_variant,,ENST00000448843,NM_021628.2;HES7,downstream_gene_variant,,ENST00000541682,NM_001165967.1;HES7,downstream_gene_variant,,ENST00000317814,NM_032580.3;HES7,downstream_gene_variant,,ENST00000577735,; C ENST00000318227 Transcript missense_variant 661/3053 392/2532 131/843 P/R cCc/cGc 1 -1 ALOXE3 HGNC HGNC:13743 protein_coding YES CCDS54084.1 ENSP00000314879 Q9BYJ1 UPI0000EE63AA NM_001165960.1 deleterious_low_confidence(0) 2/16 MODERATE SNV 2 1 PASS rs1218247458 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 8117995 8117995 G C 1 0 0 0 0 1 0 0 0 642 1232 43 4 4 ALOXE3 17 8117995 Missense_Mutation SNP G C3L-00144_T 442844 8117995 75139446 1346 5417 PFAS 0 . GRCh38 17 8255074 8255074 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.326G>T p.Arg109Leu p.R109L ENST00000314666 4/28 186 140 46 167 167 0 strelka-varscan-mutect PFAS,missense_variant,p.Arg109Leu,ENST00000314666,NM_012393.2;PFAS,missense_variant,p.Arg109Leu,ENST00000584044,;PFAS,missense_variant,p.Arg109Leu,ENST00000625942,;PFAS,downstream_gene_variant,,ENST00000585183,;PFAS,downstream_gene_variant,,ENST00000581242,;PFAS,missense_variant,p.Arg109Leu,ENST00000580356,; T ENST00000314666 Transcript missense_variant 459/5371 326/4017 109/1338 R/L cGc/cTc 1 1 PFAS HGNC HGNC:8863 protein_coding YES CCDS11136.1 ENSP00000313490 O15067 UPI00001A95E5 NM_012393.2 tolerated(0.08) 4/28 HAMAP:MF_00419,hmmpanther:PTHR10099,hmmpanther:PTHR10099:SF1,TIGRFAM_domain:TIGR01735,Superfamily_domains:SSF82697 MODERATE 1 SNV 1 1 PASS rs1192661049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8255074 8255074 G T 1 0 0 0 0 1 0 0 0 11844 1087 38 1 1 PFAS 17 8255074 Missense_Mutation SNP G C3L-00144_T 137079 8255074 75002367 1347 5418 PIK3R6 0 . GRCh38 17 8832908 8832908 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.783C>A p.= p.P261P ENST00000619866 9/20 353 264 89 352 351 1 strelka-varscan-mutect PIK3R6,synonymous_variant,p.=,ENST00000619866,NM_001010855.3,NM_001290211.1;PIK3R6,synonymous_variant,p.=,ENST00000614407,;PIK3R6,3_prime_UTR_variant,,ENST00000611951,;PIK3R6,intron_variant,,ENST00000613555,; T ENST00000619866 Transcript synonymous_variant 1023/3041 783/2265 261/754 P ccC/ccA 1 -1 PIK3R6 HGNC HGNC:27101 protein_coding YES CCDS73985.1 ENSP00000480157 Q5UE93 UPI0000043463 NM_001010855.3,NM_001290211.1 9/20 hmmpanther:PTHR15593:SF1,hmmpanther:PTHR15593,Pfam_domain:PF10486 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 8832908 8832908 G T 1 0 0 0 0 0 0 0 1 12018 1103 39 1 1 PIK3R6 17 8832908 Silent SNP G C3L-00144_T 577834 8832908 74424533 1348 5419 PIK3R5 0 . GRCh38 17 8887555 8887555 + Missense_Mutation SNP G G C rs773805061 C3L-00144_T C3L-00144_N G G c.1745C>G p.Pro582Arg p.P582R ENST00000447110 11/19 177 128 49 165 165 0 strelka-varscan-mutect PIK3R5,missense_variant,p.Pro582Arg,ENST00000447110,NM_001142633.2;PIK3R5,missense_variant,p.Pro196Arg,ENST00000616147,NM_001251852.1;PIK3R5,missense_variant,p.Pro196Arg,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,missense_variant,p.Pro196Arg,ENST00000623421,NM_001251855.1;PIK3R5,missense_variant,p.Pro582Arg,ENST00000581552,NM_014308.3;PIK3R5,missense_variant,p.Pro582Arg,ENST00000584803,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,; C ENST00000447110 Transcript missense_variant 1875/4495 1745/2643 582/880 P/R cCc/cGc rs773805061 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 tolerated(0.54) 11/19 Low_complexity_(Seg):seg,hmmpanther:PTHR15593,hmmpanther:PTHR15593:SF2,Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS rs773805061 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 8887555 8887555 G C 1 0 0 0 0 1 0 0 0 12017 1232 43 4 4 PIK3R5 17 8887555 Missense_Mutation SNP G C3L-00144_T 54647 8887555 74369886 1349 5420 GLP2R 0 . GRCh38 17 9861159 9861159 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.946G>C p.Val316Leu p.V316L ENST00000262441 8/13 221 172 49 206 206 0 strelka-varscan-mutect GLP2R,missense_variant,p.Val316Leu,ENST00000262441,NM_004246.2;GLP2R,missense_variant,p.Val136Leu,ENST00000574745,;GLP2R,downstream_gene_variant,,ENST00000304773,;GLP2R,3_prime_UTR_variant,,ENST00000458005,; C ENST00000262441 Transcript missense_variant 1459/4572 946/1662 316/553 V/L Gta/Cta 1 1 GLP2R HGNC HGNC:4325 protein_coding YES CCDS11150.1 ENSP00000262441 O95838 UPI0000050469 NM_004246.2 tolerated(0.06) 8/13 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF269,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249 MODERATE 1 SNV 1 1 PASS rs1289368447 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 9861159 9861159 G C 1 0 0 0 0 1 0 0 0 6332 1377 48 4 4 GLP2R 17 9861159 Missense_Mutation SNP G C3L-00144_T 973604 9861159 73396282 1350 5421 GAS7 0 . GRCh38 17 9926671 9926671 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.984G>A p.= p.Q328Q ENST00000432992 10/14 226 164 62 209 209 0 strelka-varscan-mutect GAS7,synonymous_variant,p.=,ENST00000323816,;GAS7,synonymous_variant,p.=,ENST00000437099,NM_001130831.1;GAS7,synonymous_variant,p.=,ENST00000432992,NM_201433.1;GAS7,synonymous_variant,p.=,ENST00000585266,NM_201432.1;GAS7,synonymous_variant,p.=,ENST00000580865,NM_003644.2;GAS7,synonymous_variant,p.=,ENST00000542249,;GAS7,synonymous_variant,p.=,ENST00000579158,;GAS7,intron_variant,,ENST00000396115,;GAS7,intron_variant,,ENST00000583882,;GAS7,non_coding_transcript_exon_variant,,ENST00000581871,;GAS7,downstream_gene_variant,,ENST00000580811,;GAS7,upstream_gene_variant,,ENST00000581112,;GAS7,non_coding_transcript_exon_variant,,ENST00000578456,; T ENST00000432992 Transcript synonymous_variant 1145/4970 984/1431 328/476 Q caG/caA 1 -1 GAS7 HGNC HGNC:4169 protein_coding YES CCDS11152.1 ENSP00000407552 O60861 UPI00001B4B17 NM_201433.1 10/14 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51741,hmmpanther:PTHR23065,Superfamily_domains:SSF103657 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 9926671 9926671 C T 1 0 0 0 0 0 0 0 1 6120 796 28 3 3 GAS7 17 9926671 Silent SNP C C3L-00144_T 65512 9926671 73330770 1351 5422 MYH4 0 . GRCh38 17 10445063 10445063 + Silent SNP G G T rs199974986 C3L-00144_T C3L-00144_N G G c.5379C>A p.= p.T1793T ENST00000255381 37/40 413 316 97 415 415 0 strelka-varscan-mutect MYH4,synonymous_variant,p.=,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000255381 Transcript synonymous_variant 5490/6016 5379/5820 1793/1939 T acC/acA rs199974986 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 37/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271 LOW 1 SNV 1 1 PASS rs199974986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 10445063 10445063 G T 1 0 0 0 0 0 0 0 1 10037 1103 39 1 1 MYH4 17 10445063 Silent SNP G C3L-00144_T 518392 10445063 72812378 1352 5423 MYH4 0 . GRCh38 17 10452478 10452478 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.3286G>A p.Gly1096Ser p.G1096S ENST00000255381 26/40 243 198 45 229 229 0 strelka-varscan-mutect MYH4,missense_variant,p.Gly1096Ser,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000255381 Transcript missense_variant 3397/6016 3286/5820 1096/1939 G/S Ggc/Agc 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 tolerated(1) 26/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 10452478 10452478 C T 1 0 0 0 0 1 0 0 0 10037 681 24 3 3 MYH4 17 10452478 Missense_Mutation SNP C C3L-00144_T 7415 10452478 72804963 1353 5424 MYH4 0 . GRCh38 17 10453260 10453260 + Missense_Mutation SNP C C A rs138556802 C3L-00144_T C3L-00144_N C C c.3003G>T p.Lys1001Asn p.K1001N ENST00000255381 24/40 356 274 82 342 341 1 strelka-varscan-mutect MYH4,missense_variant,p.Lys1001Asn,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript missense_variant 3114/6016 3003/5820 1001/1939 K/N aaG/aaT rs138556802 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0) 24/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS rs138556802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 10453260 10453260 C A 1 0 0 0 0 1 0 0 0 10037 680 24 2 2 MYH4 17 10453260 Missense_Mutation SNP C C3L-00144_T 782 10453260 72804181 1354 5425 MYH4 0 . GRCh38 17 10454951 10454951 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2425A>T p.Met809Leu p.M809L ENST00000255381 21/40 160 117 43 145 144 1 strelka-varscan-mutect MYH4,missense_variant,p.Met809Leu,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript missense_variant 2536/6016 2425/5820 809/1939 M/L Atg/Ttg 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 tolerated(1) 21/40 Gene3D:1wdcA00,PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 10454951 10454951 T A 1 0 0 0 0 1 0 0 0 10037 1435 50 4 4 MYH4 17 10454951 Missense_Mutation SNP T C3L-00144_T 1691 10454951 72802490 1355 5426 MYH1 0 . GRCh38 17 10505884 10505884 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2102G>T p.Gly701Val p.G701V ENST00000226207 19/40 238 183 55 216 216 0 strelka-varscan-mutect MYH1,missense_variant,p.Gly701Val,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 2197/6024 2102/5820 701/1939 G/V gGt/gTt 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 19/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 10505884 10505884 C A 1 0 0 0 0 1 0 0 0 10029 507 18 2 2 MYH1 17 10505884 Missense_Mutation SNP C C3L-00144_T 50933 10505884 72751557 1356 5427 MYH2 0 . GRCh38 17 10529040 10529040 + Silent SNP G G T rs745807547 C3L-00144_T C3L-00144_N G G c.3394C>A p.= p.R1132R ENST00000245503 27/40 471 349 122 403 403 0 strelka-varscan-mutect MYH2,synonymous_variant,p.=,ENST00000245503,NM_017534.5;MYH2,synonymous_variant,p.=,ENST00000397183,NM_001100112.1;MYH2,intron_variant,,ENST00000532183,;MYH2,intron_variant,,ENST00000622564,;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000245503 Transcript synonymous_variant 3779/6339 3394/5826 1132/1941 R Cgg/Agg rs745807547,COSM3783016 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,Low_complexity_(Seg):seg,Superfamily_domains:SSF90257 0,1 LOW 1 SNV 1 0,1 1 PASS rs745807547 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 10529040 10529040 G T 1 0 0 0 0 0 0 0 1 10035 1086 38 1 1 MYH2 17 10529040 Silent SNP G C3L-00144_T 23156 10529040 72728401 1357 5428 DNAH9 0 . GRCh38 17 11647079 11647079 + Missense_Mutation SNP A A T C3L-00144_T C3L-00144_N A A c.1978A>T p.Thr660Ser p.T660S ENST00000262442 12/69 93 77 16 80 80 0 strelka-varscan-mutect DNAH9,missense_variant,p.Thr660Ser,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Thr660Ser,ENST00000454412,; T ENST00000262442 Transcript missense_variant 2046/13750 1978/13461 660/4486 T/S Aca/Tca COSM3771264 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 tolerated(0.33) 12/69 Pfam_domain:PF08385,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 11647079 11647079 A T 1 0 0 0 0 1 0 0 0 4423 275 10 4 4 DNAH9 17 11647079 Missense_Mutation SNP A C3L-00144_T 1118039 11647079 71610362 1358 5429 FLII 0 . GRCh38 17 18253628 18253628 + Missense_Mutation SNP C C A rs547560301 C3L-00144_T C3L-00144_N C C c.771G>T p.Gln257His p.Q257H ENST00000327031 8/30 139 103 36 171 171 0 strelka-varscan-mutect FLII,missense_variant,p.Gln257His,ENST00000327031,NM_002018.3;FLII,missense_variant,p.Gln203His,ENST00000545457,NM_001256265.1;FLII,missense_variant,p.Gln246His,ENST00000579294,NM_001256264.1;FLII,missense_variant,p.Gln257His,ENST00000578558,;FLII,missense_variant,p.Gln140His,ENST00000488932,;FLII,intron_variant,,ENST00000577485,;FLII,downstream_gene_variant,,ENST00000473425,;FLII,downstream_gene_variant,,ENST00000581349,;FLII,downstream_gene_variant,,ENST00000628188,;FLII,intron_variant,,ENST00000584444,;FLII,missense_variant,p.Gln102His,ENST00000577626,;FLII,3_prime_UTR_variant,,ENST00000578101,;FLII,3_prime_UTR_variant,,ENST00000581401,;FLII,non_coding_transcript_exon_variant,,ENST00000461110,;FLII,non_coding_transcript_exon_variant,,ENST00000488221,;FLII,downstream_gene_variant,,ENST00000478416,;FLII,upstream_gene_variant,,ENST00000496727,;FLII,upstream_gene_variant,,ENST00000577402,;FLII,downstream_gene_variant,,ENST00000582626,; A ENST00000327031 Transcript missense_variant 997/4338 771/3810 257/1269 Q/H caG/caT rs547560301 1 -1 FLII HGNC HGNC:3750 protein_coding YES CCDS11192.1 ENSP00000324573 Q13045 UPI0000001284 NM_002018.3 deleterious(0.04) 8/30 PROSITE_profiles:PS51450,hmmpanther:PTHR11977:SF42,hmmpanther:PTHR11977,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058,Prints_domain:PR00019 MODERATE 1 SNV 1 1 PASS rs547560301 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 18253628 18253628 C A 1 0 0 0 0 1 0 0 0 5787 912 32 2 2 FLII 17 18253628 Missense_Mutation SNP C C3L-00144_T 6606549 18253628 65003813 1359 5430 FBXW10 0 . GRCh38 17 18772658 18772658 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2253C>A p.= p.L751L ENST00000395665 12/14 169 124 45 135 135 0 strelka-varscan-mutect FBXW10,synonymous_variant,p.=,ENST00000308799,;FBXW10,synonymous_variant,p.=,ENST00000395665,NM_001267585.1;FBXW10,synonymous_variant,p.=,ENST00000301938,NM_001267586.1;FBXW10,downstream_gene_variant,,ENST00000573605,;FBXW10,3_prime_UTR_variant,,ENST00000574478,; A ENST00000395665 Transcript synonymous_variant 2474/3431 2253/3159 751/1052 L ctC/ctA 1 1 FBXW10 HGNC HGNC:1211 protein_coding YES CCDS11199.3 ENSP00000379025 Q5XX13 UPI0000200B30 NM_001267585.1 12/14 hmmpanther:PTHR19872,hmmpanther:PTHR19872:SF7 LOW 1 SNV 1 1 PASS rs1405694972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 18772658 18772658 C A 1 0 0 0 0 0 0 0 1 5626 842 30 2 2 FBXW10 17 18772658 Silent SNP C C3L-00144_T 519030 18772658 64484783 1360 5431 VTN 0 . GRCh38 17 28368642 28368643 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.857dupA p.His286GlnfsTer9 p.H286Qfs*9 ENST00000226218 6/8 245 193 52 195 195 0 sindel-varindel-pindel VTN,frameshift_variant,p.His286GlnfsTer9,ENST00000226218,NM_000638.3;SARM1,upstream_gene_variant,,ENST00000585482,NM_015077.3;TMEM199,downstream_gene_variant,,ENST00000292114,NM_152464.2;CTB-96E2.2,upstream_gene_variant,,ENST00000555059,;SEBOX,upstream_gene_variant,,ENST00000536498,NM_001080837.3;VTN,downstream_gene_variant,,ENST00000542029,;CTB-96E2.10,upstream_gene_variant,,ENST00000613598,;SARM1,intron_variant,,ENST00000379061,;CTB-96E2.3,intron_variant,,ENST00000591482,;VTN,non_coding_transcript_exon_variant,,ENST00000539746,; T ENST00000226218 Transcript frameshift_variant 1476-1477/2149 857-858/1437 286/478 H/QX cac/caAc 1 -1 VTN HGNC HGNC:12724 protein_coding YES CCDS11229.1 ENSP00000226218 P04004 D9ZGG2 UPI0000138E65 NM_000638.3 6/8 Pfam_domain:PF00045,PROSITE_profiles:PS51642,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF3,SMART_domains:SM00120,Superfamily_domains:SSF50923 HIGH 1 insertion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999969 1 1 1 0 T 7 5 12 28368642 28368642 - T 1 0 1 1 0 0 0 0 0 17791 1252 44 0 0 VTN 17 28368642 Frame_Shift_Ins INS - C3L-00144_T 9595984 28368642 54888799 1361 5432 PIGS 0 . GRCh38 17 28571125 28571125 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.98C>A p.Pro33Gln p.P33Q ENST00000308360 2/12 305 250 55 238 237 1 strelka-varscan-mutect PIGS,missense_variant,p.Pro33Gln,ENST00000308360,NM_033198.3;PIGS,missense_variant,p.Pro25Gln,ENST00000395346,;ALDOC,downstream_gene_variant,,ENST00000226253,NM_005165.2;ALDOC,downstream_gene_variant,,ENST00000395321,;ALDOC,downstream_gene_variant,,ENST00000395319,;ALDOC,downstream_gene_variant,,ENST00000460201,;ALDOC,downstream_gene_variant,,ENST00000578590,;ALDOC,downstream_gene_variant,,ENST00000584086,;ALDOC,downstream_gene_variant,,ENST00000581807,;ALDOC,downstream_gene_variant,,ENST00000435638,;RP11-192H23.5,upstream_gene_variant,,ENST00000585189,;PIGS,non_coding_transcript_exon_variant,,ENST00000584413,;PIGS,missense_variant,p.Pro33Gln,ENST00000582721,;PIGS,non_coding_transcript_exon_variant,,ENST00000583631,;PIGS,non_coding_transcript_exon_variant,,ENST00000577594,;PIGS,intron_variant,,ENST00000268758,;RP11-192H23.4,intron_variant,,ENST00000481916,;PIGS,intron_variant,,ENST00000584080,;ALDOC,downstream_gene_variant,,ENST00000582381,; T ENST00000308360 Transcript missense_variant 474/2877 98/1668 33/555 P/Q cCg/cAg 1 -1 PIGS HGNC HGNC:14937 protein_coding YES CCDS11235.1 ENSP00000309430 Q96S52 UPI000013D7D9 NM_033198.3 deleterious(0) 2/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR21072,Pfam_domain:PF10510 MODERATE 1 SNV 1 1 PASS rs1421876778 . 0 207 0 3 0 0 0 0 -20 0.9999956 1 1 1 0 T 3 4 12 28571125 28571125 G T 1 0 0 0 0 1 0 0 0 11992 1116 39 1 1 PIGS 17 28571125 Missense_Mutation SNP G C3L-00144_T 202483 28571125 54686316 1362 5433 KIAA0100 0 . GRCh38 17 28643289 28643290 + Frame_Shift_Ins INS - - A novel C3L-00144_T C3L-00144_N - - c.270dupT p.Gly91TrpfsTer14 p.G91Wfs*14 ENST00000528896 4/39 158 124 34 144 144 0 sindel-varindel-pindel KIAA0100,frameshift_variant,p.Gly91TrpfsTer14,ENST00000528896,NM_014680.3;KIAA0100,5_prime_UTR_variant,,ENST00000544884,;KIAA0100,5_prime_UTR_variant,,ENST00000389003,;KIAA0100,frameshift_variant,p.Trp74LeufsTer38,ENST00000583403,;KIAA0100,non_coding_transcript_exon_variant,,ENST00000577417,;KIAA0100,non_coding_transcript_exon_variant,,ENST00000580882,;KIAA0100,upstream_gene_variant,,ENST00000577580,;KIAA0100,upstream_gene_variant,,ENST00000582901,;KIAA0100,upstream_gene_variant,,ENST00000581267,;KIAA0100,upstream_gene_variant,,ENST00000579253,; A ENST00000528896 Transcript frameshift_variant 345-346/7407 270-271/6708 90-91/2235 -/X -/T 1 -1 KIAA0100 HGNC HGNC:28960 protein_coding YES CCDS32595.1 ENSP00000436773 Q14667 UPI00004B4130 NM_014680.3 4/39 hmmpanther:PTHR15678,Pfam_domain:PF10344 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 7 5 12 28643289 28643289 - A 1 0 1 1 0 0 0 0 0 8074 603 21 0 0 KIAA0100 17 28643289 Frame_Shift_Ins INS - C3L-00144_T 72164 28643289 54614152 1363 5434 MYO18A 0 . GRCh38 17 29094838 29094838 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4522G>T p.Asp1508Tyr p.D1508Y ENST00000527372 30/42 250 209 41 216 216 0 strelka-varscan-mutect MYO18A,missense_variant,p.Asp1508Tyr,ENST00000527372,NM_078471.3;MYO18A,missense_variant,p.Asp1508Tyr,ENST00000533112,;MYO18A,missense_variant,p.Asp1508Tyr,ENST00000531253,NM_203318.1;MYO18A,missense_variant,p.Asp1507Tyr,ENST00000628822,;MYO18A,upstream_gene_variant,,ENST00000529578,;MYO18A,upstream_gene_variant,,ENST00000546105,;MYO18A,upstream_gene_variant,,ENST00000531892,;MYO18A,3_prime_UTR_variant,,ENST00000530254,;MYO18A,non_coding_transcript_exon_variant,,ENST00000530557,;MYO18A,intron_variant,,ENST00000533652,;MYO18A,downstream_gene_variant,,ENST00000532143,;MYO18A,upstream_gene_variant,,ENST00000529889,;MYO18A,upstream_gene_variant,,ENST00000531438,; A ENST00000527372 Transcript missense_variant 4703/9992 4522/6165 1508/2054 D/Y Gac/Tac 1 -1 MYO18A HGNC HGNC:31104 protein_coding YES CCDS45642.1 ENSP00000437073 Q92614 UPI0000167F32 NM_078471.3 deleterious(0) 30/42 Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF421,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 29094838 29094838 C A 1 0 0 0 0 1 0 0 0 10066 855 30 2 2 MYO18A 17 29094838 Missense_Mutation SNP C C3L-00144_T 451549 29094838 54162603 1364 5435 SSH2 0 . GRCh38 17 29632101 29632101 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.3093C>T p.= p.P1031P ENST00000540801 16/16 194 167 27 139 139 0 strelka-varscan-mutect SSH2,synonymous_variant,p.=,ENST00000269033,NM_033389.3;SSH2,synonymous_variant,p.=,ENST00000540801,NM_001282129.1;SSH2,upstream_gene_variant,,ENST00000577991,;ABHD15-AS1,intron_variant,,ENST00000581474,; A ENST00000540801 Transcript synonymous_variant 3186/4538 3093/4353 1031/1450 P ccC/ccT 1 -1 SSH2 HGNC HGNC:30580 protein_coding YES CCDS74024.1 ENSP00000444743 F5H527 UPI0002065A97 NM_001282129.1 16/16 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 29632101 29632101 G A 1 0 0 0 0 0 0 0 1 15561 1219 43 3 3 SSH2 17 29632101 Silent SNP G C3L-00144_T 537263 29632101 53625340 1365 5436 EFCAB5 0 . GRCh38 17 30080223 30080223 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.3179G>A p.Arg1060Lys p.R1060K ENST00000394835 16/23 114 92 22 78 78 0 strelka-varscan-mutect EFCAB5,missense_variant,p.Arg1060Lys,ENST00000394835,NM_198529.3;EFCAB5,missense_variant,p.Arg742Lys,ENST00000419434,;EFCAB5,intron_variant,,ENST00000588978,; A ENST00000394835 Transcript missense_variant 3371/5132 3179/4512 1060/1503 R/K aGg/aAg 1 1 EFCAB5 HGNC HGNC:24801 protein_coding YES CCDS11254.2 ENSP00000378312 A4FU69 UPI0000E59EF5 NM_198529.3 deleterious(0.05) 16/23 hmmpanther:PTHR31938,hmmpanther:PTHR31938:SF6,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 30080223 30080223 G A 1 0 0 0 0 1 0 0 0 4772 1000 35 3 3 EFCAB5 17 30080223 Missense_Mutation SNP G C3L-00144_T 448122 30080223 53177218 1366 5437 UNC45B 0 . GRCh38 17 35183487 35183487 + Missense_Mutation SNP G G T rs750532284 C3L-00144_T C3L-00144_N G G c.2440G>T p.Gly814Trp p.G814W ENST00000268876 19/20 131 106 25 89 88 1 strelka-varscan-mutect UNC45B,missense_variant,p.Gly814Trp,ENST00000268876,NM_173167.2;UNC45B,missense_variant,p.Gly812Trp,ENST00000394570,NM_001267052.1,NM_001033576.1;UNC45B,missense_variant,p.Gly733Trp,ENST00000591048,NM_001308281.1; T ENST00000268876 Transcript missense_variant 2537/5679 2440/2796 814/931 G/W Ggg/Tgg rs750532284 1 1 UNC45B HGNC HGNC:14304 protein_coding YES CCDS11292.1 ENSP00000268876 Q8IWX7 UPI0000074455 NM_173167.2 deleterious(0) 19/20 Gene3D:1.25.10.10,SMART_domains:SM00185,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs750532284 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 35183487 35183487 G T 1 0 0 0 0 1 0 0 0 17513 1116 39 1 1 UNC45B 17 35183487 Missense_Mutation SNP G C3L-00144_T 5103264 35183487 48073954 1367 5438 CCL23 0 . GRCh38 17 36013206 36013206 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.405G>C p.Arg135Ser p.R135S ENST00000615050 4/4 200 130 70 123 123 0 strelka-varscan-mutect CCL23,missense_variant,p.Arg135Ser,ENST00000615050,NM_005064.5;CCL23,missense_variant,p.Arg118Ser,ENST00000612516,NM_145898.3;RP11-104J23.2,downstream_gene_variant,,ENST00000617747,;RP11-104J23.1,downstream_gene_variant,,ENST00000617328,;RP11-104J23.1,downstream_gene_variant,,ENST00000619334,;CCL23,3_prime_UTR_variant,,ENST00000613876,; G ENST00000615050 Transcript missense_variant 476/624 405/414 135/137 R/S agG/agC 1 -1 CCL23 HGNC HGNC:10622 protein_coding YES CCDS11305.1 ENSP00000481357 P55773 UPI000002B480 NM_005064.5 deleterious_low_confidence(0.02) 4/4 hmmpanther:PTHR12015:SF77,hmmpanther:PTHR12015 MODERATE 1 SNV 1 1 PASS rs989537125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 36013206 36013206 C G 1 0 0 0 0 1 0 0 0 2593 854 30 4 4 CCL23 17 36013206 Missense_Mutation SNP C C3L-00144_T 829719 36013206 47244235 1368 5439 CCL4L2 0 . GRCh38 17 36211217 36211217 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.76A>T p.Met26Leu p.M26L ENST00000617405 1/3 478 372 106 353 352 1 strelka-varscan-mutect CCL4L2,stop_gained,p.Lys26Ter,ENST00000620055,;CCL4L2,missense_variant,p.Met26Leu,ENST00000617416,NM_001291470.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000615418,NM_001291472.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000620732,NM_001291469.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000617405,NM_001291475.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000620098,NM_001291471.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000610565,NM_001291473.1;CCL4L2,missense_variant,p.Thr26Ser,ENST00000613173,NM_001291474.1;CCL4L2,missense_variant,p.Met26Leu,ENST00000620250,;CCL4L2,missense_variant,p.Met26Leu,ENST00000620576,NM_001291468.1; T ENST00000617405 Transcript missense_variant,splice_region_variant 155/846 76/312 26/103 M/L Atg/Ttg 1 1 CCL4L2 HGNC HGNC:24066 protein_coding YES CCDS77000.1 ENSP00000483330 Q8NHW4 UPI000050BF29 NM_001291475.1 tolerated(0.6) 1/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF103,Gene3D:2.40.50.40,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS . . 6 204 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 36211217 36211217 A T 1 0 0 0 0 1 0 0 0 2602 86 3 4 4 CCL4L2 17 36211217 Missense_Mutation SNP A C3L-00144_T 198011 36211217 47046224 1369 5440 MYO19 0 . GRCh38 17 36507058 36507058 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1549G>T p.Gly517Cys p.G517C ENST00000614623 17/26 99 82 17 72 72 0 strelka-varscan-mutect MYO19,missense_variant,p.Gly517Cys,ENST00000614623,NM_001163735.1;MYO19,intron_variant,,ENST00000610930,NM_025109.5;MYO19,missense_variant,p.Gly517Cys,ENST00000610992,;MYO19,3_prime_UTR_variant,,ENST00000621550,;MYO19,non_coding_transcript_exon_variant,,ENST00000611622,;MYO19,non_coding_transcript_exon_variant,,ENST00000611125,;MYO19,non_coding_transcript_exon_variant,,ENST00000614416,;MYO19,upstream_gene_variant,,ENST00000611794,;MYO19,upstream_gene_variant,,ENST00000620943,;MYO19,downstream_gene_variant,,ENST00000611063,;MYO19,downstream_gene_variant,,ENST00000612097,;MYO19,upstream_gene_variant,,ENST00000610576,;MYO19,downstream_gene_variant,,ENST00000615902,;MYO19,downstream_gene_variant,,ENST00000620413,; A ENST00000614623 Transcript missense_variant 2072/4054 1549/2913 517/970 G/C Ggc/Tgc 1 -1 MYO19 HGNC HGNC:26234 protein_coding YES CCDS54112.1 ENSP00000479518 Q96H55 UPI000173AA19 NM_001163735.1 deleterious(0.05) 17/26 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF289,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 36507058 36507058 C A 1 0 0 0 0 1 0 0 0 10068 623 22 2 2 MYO19 17 36507058 Missense_Mutation SNP C C3L-00144_T 295841 36507058 46750383 1370 5441 TBC1D3L 0 . GRCh38 17 37978661 37978661 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1459G>T p.Asp487Tyr p.D487Y ENST00000612727 13/13 104 60 44 92 92 0 varscan-mutect TBC1D3L,missense_variant,p.Asp487Tyr,ENST00000612727,;TBC1D3L,missense_variant,p.Asp487Tyr,ENST00000617678,NM_001291459.1; A ENST00000612727 Transcript missense_variant 1459/2148 1459/1650 487/549 D/Y Gac/Tac 1 -1 TBC1D3L HGNC HGNC:51246 protein_coding YES CCDS74043.1 ENSP00000481508 B9A6J9 UPI00019145CA deleterious(0) 13/13 hmmpanther:PTHR22957:SF233,hmmpanther:PTHR22957 MODERATE 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 37978661 37978661 C A 1 0 0 0 0 1 0 0 0 16026 855 30 2 2 TBC1D3L 17 37978661 Missense_Mutation SNP C C3L-00144_T 1471603 37978661 45278780 1371 5442 TBC1D3L 0 . GRCh38 17 37978733 37978733 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.1387G>C p.Asp463His p.D463H ENST00000612727 13/13 39 28 11 40 40 0 varscan-mutect TBC1D3L,missense_variant,p.Asp463His,ENST00000612727,;TBC1D3L,missense_variant,p.Asp463His,ENST00000617678,NM_001291459.1; G ENST00000612727 Transcript missense_variant 1387/2148 1387/1650 463/549 D/H Gac/Cac 1 -1 TBC1D3L HGNC HGNC:51246 protein_coding YES CCDS74043.1 ENSP00000481508 B9A6J9 UPI00019145CA deleterious(0.05) 13/13 hmmpanther:PTHR22957:SF233,hmmpanther:PTHR22957 MODERATE 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 37978733 37978733 C G 1 0 0 0 0 1 0 0 0 16026 855 30 4 4 TBC1D3L 17 37978733 Missense_Mutation SNP C C3L-00144_T 72 37978733 45278708 1372 5443 CACNB1 0 . GRCh38 17 39175298 39175298 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1692C>T p.= p.N564N ENST00000394303 14/14 303 235 68 187 187 0 strelka-varscan-mutect CACNB1,synonymous_variant,p.=,ENST00000394303,NM_000723.4;CACNB1,3_prime_UTR_variant,,ENST00000622445,;CACNB1,downstream_gene_variant,,ENST00000344140,NM_199247.2;CACNB1,downstream_gene_variant,,ENST00000394310,NM_199248.2;RP5-906A24.2,intron_variant,,ENST00000579256,;CACNB1,non_coding_transcript_exon_variant,,ENST00000539338,;CACNB1,downstream_gene_variant,,ENST00000582544,; A ENST00000394303 Transcript synonymous_variant 1900/3742 1692/1797 564/598 N aaC/aaT 1 -1 CACNB1 HGNC HGNC:1401 protein_coding YES CCDS42311.1 ENSP00000377840 Q02641 UPI0000127290 NM_000723.4 14/14 hmmpanther:PTHR11824,hmmpanther:PTHR11824:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 39175298 39175298 G A 1 0 0 0 0 0 0 0 1 2240 1252 44 3 3 CACNB1 17 39175298 Silent SNP G C3L-00144_T 1196565 39175298 44082143 1373 5444 STARD3 0 . GRCh38 17 39658516 39658516 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.541G>T p.Glu181Ter p.E181* ENST00000336308 6/15 96 75 21 55 55 0 strelka-varscan-mutect STARD3,stop_gained,p.Glu181Ter,ENST00000336308,NM_006804.3;STARD3,stop_gained,p.Glu155Ter,ENST00000580611,;STARD3,stop_gained,p.Glu163Ter,ENST00000394250,NM_001165938.1;STARD3,stop_gained,p.Glu181Ter,ENST00000443521,;STARD3,missense_variant,p.Arg176Ser,ENST00000544210,NM_001165937.1;STARD3,downstream_gene_variant,,ENST00000581894,;STARD3,downstream_gene_variant,,ENST00000583419,;STARD3,downstream_gene_variant,,ENST00000577248,;STARD3,downstream_gene_variant,,ENST00000579479,;STARD3,downstream_gene_variant,,ENST00000580331,;STARD3,downstream_gene_variant,,ENST00000583718,;STARD3,non_coding_transcript_exon_variant,,ENST00000578232,;STARD3,non_coding_transcript_exon_variant,,ENST00000582874,;STARD3,downstream_gene_variant,,ENST00000460894,;STARD3,downstream_gene_variant,,ENST00000585214,;STARD3,downstream_gene_variant,,ENST00000578254,;STARD3,upstream_gene_variant,,ENST00000583639,;STARD3,missense_variant,p.Arg158Ser,ENST00000578577,;STARD3,non_coding_transcript_exon_variant,,ENST00000481171,;STARD3,non_coding_transcript_exon_variant,,ENST00000584850,;STARD3,non_coding_transcript_exon_variant,,ENST00000488876,;STARD3,non_coding_transcript_exon_variant,,ENST00000583582,;STARD3,non_coding_transcript_exon_variant,,ENST00000585269,;STARD3,non_coding_transcript_exon_variant,,ENST00000484773,;STARD3,upstream_gene_variant,,ENST00000471896,;STARD3,upstream_gene_variant,,ENST00000578384,;STARD3,upstream_gene_variant,,ENST00000578686,;STARD3,upstream_gene_variant,,ENST00000583884,;STARD3,downstream_gene_variant,,ENST00000580551,; T ENST00000336308 Transcript stop_gained 759/2132 541/1338 181/445 E/* Gag/Tag 1 1 STARD3 HGNC HGNC:17579 protein_coding YES CCDS11341.1 ENSP00000337446 Q14849 UPI000013CE10 NM_006804.3 6/15 PROSITE_profiles:PS51439,hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF51,Pfam_domain:PF10457 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 39658516 39658516 G T 1 0 0 0 0 0 1 0 0 15632 1175 41 2 2 STARD3 17 39658516 Nonsense_Mutation SNP G C3L-00144_T 483218 39658516 43598925 1374 5445 ORMDL3 0 . GRCh38 17 39922551 39922551 + Nonstop_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.461G>T p.Ter154LeuextTer39 p.*154Lext*39 ENST00000394169 6/6 80 65 15 79 79 0 strelka-varscan-mutect ORMDL3,stop_lost,p.Ter154LeuextTer39,ENST00000394169,;ORMDL3,stop_lost,p.Ter154LeuextTer39,ENST00000304046,NM_001320803.1,NM_139280.2;ORMDL3,stop_lost,p.Ter154LeuextTer39,ENST00000579695,NM_001320802.1;ORMDL3,stop_lost,p.Ter138LeuextTer?,ENST00000584220,;GSDMB,upstream_gene_variant,,ENST00000418519,NM_001165958.1;GSDMB,upstream_gene_variant,,ENST00000520542,NM_001165959.1;GSDMB,upstream_gene_variant,,ENST00000309481,NM_001042471.1;ORMDL3,downstream_gene_variant,,ENST00000584000,;ORMDL3,downstream_gene_variant,,ENST00000582052,;ORMDL3,upstream_gene_variant,,ENST00000579287,;ORMDL3,stop_lost,p.Ter103LeuextTer64,ENST00000581284,;GSDMB,upstream_gene_variant,,ENST00000477054,; A ENST00000394169 Transcript stop_lost 1956/2230 461/462 154/153 */L tGa/tTa COSM382014,COSM5204026 1 -1 ORMDL3 HGNC HGNC:16038 protein_coding YES CCDS11355.1 ENSP00000377724 Q8N138 A0A024R1W6 UPI0000035F64 6/6 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 39922551 39922551 C A 1 0 0 0 0 0 0 0 0 11337 840 29 2 2 ORMDL3 17 39922551 Nonstop_Mutation SNP C C3L-00144_T 264035 39922551 43334890 1375 5446 KRT20 0 . GRCh38 17 40880234 40880234 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.658G>T p.Gly220Cys p.G220C ENST00000167588 4/8 101 85 16 63 63 0 strelka-varscan-mutect KRT20,missense_variant,p.Gly220Cys,ENST00000167588,NM_019010.2;KRT20,downstream_gene_variant,,ENST00000482529,; A ENST00000167588 Transcript missense_variant 700/1737 658/1275 220/424 G/C Ggc/Tgc 1 -1 KRT20 HGNC HGNC:20412 protein_coding YES CCDS11379.1 ENSP00000167588 P35900 UPI000012DAF1 NM_019010.2 deleterious(0) 4/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF167,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 12 40880234 40880234 C A 1 0 0 0 0 1 0 0 0 8340 623 22 2 2 KRT20 17 40880234 Missense_Mutation SNP C C3L-00144_T 957683 40880234 42377207 1376 5447 KRTAP4-9 0 . GRCh38 17 41105642 41105642 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.254G>T p.Cys85Phe p.C85F ENST00000391415 1/1 405 340 65 283 282 1 strelka-varscan-mutect KRTAP4-9,missense_variant,p.Cys85Phe,ENST00000391415,NM_001146041.1;KRTAP4-9,missense_variant,p.Cys70Phe,ENST00000617453,;KRTAP4-7,intron_variant,,ENST00000612231,;KRTAP4-16,upstream_gene_variant,,ENST00000440582,; T ENST00000391415 Transcript missense_variant 311/1157 254/633 85/210 C/F tGt/tTt 1 1 KRTAP4-9 HGNC HGNC:18910 protein_coding YES CCDS54124.1 ENSP00000375234 Q9BYQ8 UPI000021D2D3 NM_001146041.1 deleterious(0.01) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF1,Pfam_domain:PF01500 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41105642 41105642 G T 1 0 0 0 0 1 0 0 0 8452 1377 48 2 2 KRTAP4-9 17 41105642 Missense_Mutation SNP G C3L-00144_T 225408 41105642 42151799 1377 5448 KRTAP9-2 0 . GRCh38 17 41227145 41227145 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.491G>T p.Cys164Phe p.C164F ENST00000377721 1/1 177 122 55 167 167 0 strelka-varscan-mutect KRTAP9-2,missense_variant,p.Cys164Phe,ENST00000377721,NM_031961.2; T ENST00000377721 Transcript missense_variant 498/1005 491/525 164/174 C/F tGt/tTt 1 1 KRTAP9-2 HGNC HGNC:16926 protein_coding YES CCDS32651.1 ENSP00000366950 Q9BYQ4 UPI000013CE13 NM_031961.2 deleterious(0) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF56 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41227145 41227145 G T 1 0 0 0 0 1 0 0 0 8470 1377 48 2 2 KRTAP9-2 17 41227145 Missense_Mutation SNP G C3L-00144_T 121503 41227145 42030296 1378 5449 KRTAP16-1 0 . GRCh38 17 41308302 41308302 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.952C>A p.Pro318Thr p.P318T ENST00000391352 1/1 142 113 29 122 122 0 strelka-varscan-mutect KRTAP16-1,missense_variant,p.Pro318Thr,ENST00000391352,NM_001146182.1; T ENST00000391352 Transcript missense_variant 952/1554 952/1554 318/517 P/T Ccc/Acc 1 -1 KRTAP16-1 HGNC HGNC:18916 protein_coding YES CCDS56032.1 ENSP00000375147 A8MUX0 UPI000015FD61 NM_001146182.1 tolerated(0.65) 1/1 Pfam_domain:PF13885,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs1352668688 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41308302 41308302 G T 1 0 0 0 0 1 0 0 0 8410 1232 43 2 2 KRTAP16-1 17 41308302 Missense_Mutation SNP G C3L-00144_T 81157 41308302 41949139 1379 5450 KRT13 0 . GRCh38 17 41502575 41502575 + Missense_Mutation SNP G G A rs759178223 C3L-00144_T C3L-00144_N G G c.1043C>T p.Thr348Met p.T348M ENST00000246635 6/8 570 468 102 427 427 0 strelka-varscan-mutect KRT13,missense_variant,p.Thr348Met,ENST00000246635,NM_153490.2;KRT13,missense_variant,p.Thr348Met,ENST00000336861,NM_002274.3;KRT13,missense_variant,p.Thr348Met,ENST00000587544,;KRT13,downstream_gene_variant,,ENST00000590425,;KRT13,downstream_gene_variant,,ENST00000587435,;AC019349.5,downstream_gene_variant,,ENST00000411759,;KRT13,downstream_gene_variant,,ENST00000587118,;KRT13,upstream_gene_variant,,ENST00000475217,;KRT13,3_prime_UTR_variant,,ENST00000464634,;KRT13,non_coding_transcript_exon_variant,,ENST00000468313,; A ENST00000246635 Transcript missense_variant 1090/1699 1043/1377 348/458 T/M aCg/aTg rs759178223,COSM3989015 1 -1 KRT13 HGNC HGNC:6415 protein_coding YES CCDS11396.1 ENSP00000246635 P13646 UPI000013CBF6 NM_153490.2 deleterious(0.01) 6/8 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF121,SMART_domains:SM01391,Superfamily_domains:SSF64593 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759178223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 41502575 41502575 G A 1 0 0 0 0 1 0 0 0 8332 1145 40 1 1 KRT13 17 41502575 Missense_Mutation SNP G C3L-00144_T 194273 41502575 41754866 1380 5451 HSD17B1 0 . GRCh38 17 42553196 42553196 + Missense_Mutation SNP C C A rs61738807 C3L-00144_T C3L-00144_N C C c.170C>A p.Pro57Gln p.P57Q ENST00000585807 2/6 295 201 94 260 260 0 strelka-varscan-mutect HSD17B1,missense_variant,p.Pro57Gln,ENST00000585807,NM_000413.2;HSD17B1,missense_variant,p.Pro57Gln,ENST00000225929,;RP11-400F19.6,non_coding_transcript_exon_variant,,ENST00000590513,;RP11-400F19.8,intron_variant,,ENST00000585572,;HSD17B1,missense_variant,p.Pro57Gln,ENST00000590299,;HSD17B1,non_coding_transcript_exon_variant,,ENST00000593215,;HSD17B1,non_coding_transcript_exon_variant,,ENST00000587280,;HSD17B1P1,downstream_gene_variant,,ENST00000590052,; A ENST00000585807 Transcript missense_variant 3890/4982 170/987 57/328 P/Q cCg/cAg rs61738807,COSM4066578 1 1 HSD17B1 HGNC HGNC:5210 protein_coding YES CCDS11428.1 ENSP00000466799 P14061 UPI00001AE658 NM_000413.2 tolerated(0.11) 2/6 hmmpanther:PTHR24322:SF577,hmmpanther:PTHR24322,Gene3D:3.40.50.720,Pfam_domain:PF00106,PIRSF_domain:PIRSF000095,Superfamily_domains:SSF51735 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs61738807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 42553196 42553196 C A 1 0 0 0 0 1 0 0 0 7273 652 23 1 1 HSD17B1 17 42553196 Missense_Mutation SNP C C3L-00144_T 1050621 42553196 40704245 1381 5452 VAT1 0 . GRCh38 17 43022059 43022059 + Silent SNP G G C novel C3L-00144_T C3L-00144_N G G c.264C>G p.= p.L88L ENST00000355653 1/6 449 332 117 324 324 0 strelka-varscan-mutect VAT1,synonymous_variant,p.=,ENST00000355653,NM_006373.3;VAT1,synonymous_variant,p.=,ENST00000587062,;VAT1,intron_variant,,ENST00000587173,;VAT1,intron_variant,,ENST00000590924,;RND2,upstream_gene_variant,,ENST00000587250,NM_005440.4;VAT1,upstream_gene_variant,,ENST00000420567,;VAT1,upstream_gene_variant,,ENST00000587147,;VAT1,upstream_gene_variant,,ENST00000589709,;VAT1,upstream_gene_variant,,ENST00000589828,;RND2,upstream_gene_variant,,ENST00000587117,; C ENST00000355653 Transcript synonymous_variant 360/2734 264/1182 88/393 L ctC/ctG 1 -1 VAT1 HGNC HGNC:16919 protein_coding YES CCDS11451.1 ENSP00000347872 Q99536 A0A024R1Z6 UPI000006DA93 NM_006373.3 1/6 Gene3D:3.90.180.10,Pfam_domain:PF08240,hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF503,SMART_domains:SM00829,Superfamily_domains:SSF50129 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 43022059 43022059 G C 1 0 0 0 0 0 0 0 1 17674 1277 45 4 4 VAT1 17 43022059 Silent SNP G C3L-00144_T 468863 43022059 40235382 1382 5453 CD300LG 0 . GRCh38 17 43848859 43848859 + Missense_Mutation SNP T T A rs367773909 C3L-00144_T C3L-00144_N T T c.345T>A p.Asp115Glu p.D115E ENST00000317310 2/7 157 124 33 171 171 0 strelka-varscan-mutect CD300LG,missense_variant,p.Asp115Glu,ENST00000317310,NM_145273.3;CD300LG,missense_variant,p.Asp115Glu,ENST00000588884,;CD300LG,missense_variant,p.Asp115Glu,ENST00000539718,NM_001168322.1;CD300LG,missense_variant,p.Asp115Glu,ENST00000377203,NM_001168323.1;CD300LG,missense_variant,p.Asp115Glu,ENST00000293396,NM_001168324.1;CD300LG,missense_variant,p.Asp115Glu,ENST00000586233,; A ENST00000317310 Transcript missense_variant 386/2758 345/999 115/332 D/E gaT/gaA rs367773909 1 1 CD300LG HGNC HGNC:30455 protein_coding YES CCDS11470.1 ENSP00000321005 Q6UXG3 UPI000013E104 NM_145273.3 deleterious(0.04) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR11860:SF22,hmmpanther:PTHR11860,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs367773909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43848859 43848859 T A 1 0 0 0 0 1 0 0 0 2706 1461 51 4 4 CD300LG 17 43848859 Missense_Mutation SNP T C3L-00144_T 826800 43848859 39408582 1383 5454 MPP2 0 . GRCh38 17 43881488 43881488 + Silent SNP G G A rs76832034 C3L-00144_T C3L-00144_N G G c.918C>T p.= p.I306I ENST00000518766 7/13 308 285 23 203 203 0 strelka-varscan-mutect MPP2,synonymous_variant,p.=,ENST00000612133,NM_001278381.1;MPP2,synonymous_variant,p.=,ENST00000625880,;MPP2,synonymous_variant,p.=,ENST00000269095,NM_005374.4;MPP2,synonymous_variant,p.=,ENST00000536246,NM_001278375.1;MPP2,synonymous_variant,p.=,ENST00000622681,NM_001278371.1;MPP2,synonymous_variant,p.=,ENST00000377184,NM_001278376.2;MPP2,synonymous_variant,p.=,ENST00000461854,NM_001278372.1;MPP2,synonymous_variant,p.=,ENST00000523501,NM_001278373.1;MPP2,synonymous_variant,p.=,ENST00000520305,NM_001278374.1;MPP2,synonymous_variant,p.=,ENST00000518766,NM_001278370.1;MPP2,downstream_gene_variant,,ENST00000523220,;MPP2,downstream_gene_variant,,ENST00000473246,;MPP2,downstream_gene_variant,,ENST00000520406,;MPP2,downstream_gene_variant,,ENST00000524294,;MPP2,downstream_gene_variant,,ENST00000522172,;MPP2,downstream_gene_variant,,ENST00000523934,;MPP2,downstream_gene_variant,,ENST00000523762,;MPP2,downstream_gene_variant,,ENST00000521178,;MPP2,downstream_gene_variant,,ENST00000520241,;MPP2,downstream_gene_variant,,ENST00000520319,; A ENST00000518766 Transcript synonymous_variant 975/1896 918/1794 306/597 I atC/atT rs76832034 1 -1 MPP2 HGNC HGNC:7220 protein_coding YES CCDS62210.1 ENSP00000428182 A0A0C4DH75 UPI0001914C39 NM_001278370.1 7/13 PROSITE_profiles:PS50002,hmmpanther:PTHR23122:SF35,hmmpanther:PTHR23122,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 2 1 PASS rs76832034 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 43881488 43881488 G A 1 0 0 0 0 0 0 0 1 9700 1048 37 1 1 MPP2 17 43881488 Silent SNP G C3L-00144_T 32629 43881488 39375953 1384 5455 SLC4A1 0 . GRCh38 17 44251194 44251194 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2620C>A p.Leu874Met p.L874M ENST00000262418 19/20 521 371 150 361 359 2 strelka-varscan-mutect SLC4A1,missense_variant,p.Leu874Met,ENST00000262418,NM_000342.3;SLC4A1,missense_variant,p.Leu508Met,ENST00000399246,;SLC4A1,upstream_gene_variant,,ENST00000631130,; T ENST00000262418 Transcript missense_variant 2776/4965 2620/2736 874/911 L/M Ctg/Atg 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 tolerated(0.16) 19/20 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00834,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 44251194 44251194 G T 1 0 0 0 0 1 0 0 0 14927 962 34 2 2 SLC4A1 17 44251194 Missense_Mutation SNP G C3L-00144_T 369706 44251194 39006247 1385 5456 ITGA2B 0 . GRCh38 17 44377749 44377749 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.2136G>A p.= p.E712E ENST00000262407 21/30 556 459 97 426 425 1 strelka-varscan-mutect ITGA2B,synonymous_variant,p.=,ENST00000262407,NM_000419.3;ITGA2B,upstream_gene_variant,,ENST00000587295,;ITGA2B,upstream_gene_variant,,ENST00000588098,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592462,;ITGA2B,downstream_gene_variant,,ENST00000592226,; T ENST00000262407 Transcript synonymous_variant 2168/3333 2136/3120 712/1039 E gaG/gaA 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 21/30 hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Pfam_domain:PF08441,Gene3D:2.60.40.1510,Superfamily_domains:SSF69179 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 44377749 44377749 C T 1 0 0 0 0 0 0 0 1 7783 912 32 3 3 ITGA2B 17 44377749 Silent SNP C C3L-00144_T 126555 44377749 38879692 1386 5457 ADAM11 0 . GRCh38 17 44769747 44769747 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.267C>T p.= p.V89V ENST00000200557 3/27 252 205 47 188 188 0 strelka-varscan-mutect ADAM11,synonymous_variant,p.=,ENST00000200557,NM_001318933.1,NM_002390.4;ADAM11,5_prime_UTR_variant,,ENST00000535346,;ADAM11,synonymous_variant,p.=,ENST00000355638,;ADAM11,upstream_gene_variant,,ENST00000587773,; T ENST00000200557 Transcript synonymous_variant 436/4571 267/2310 89/769 V gtC/gtT 1 1 ADAM11 HGNC HGNC:189 protein_coding YES CCDS11486.1 ENSP00000200557 O75078 UPI000013C629 NM_001318933.1,NM_002390.4 3/27 Pfam_domain:PF01562,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF114 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 44769747 44769747 C T 1 0 0 0 0 0 0 0 1 279 813 29 3 3 ADAM11 17 44769747 Silent SNP C C3L-00144_T 391998 44769747 38487694 1387 5458 MYL4 0 . GRCh38 17 47219990 47219990 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.250G>T p.Ala84Ser p.A84S ENST00000354968 4/8 299 234 65 194 194 0 strelka-varscan-mutect MYL4,missense_variant,p.Ala84Ser,ENST00000354968,NM_001002841.1;MYL4,missense_variant,p.Ala84Ser,ENST00000393450,NM_002476.2;MYL4,missense_variant,p.Ala84Ser,ENST00000572316,;MYL4,missense_variant,p.Ala84Ser,ENST00000536623,;MYL4,missense_variant,p.Ala84Ser,ENST00000576874,;MYL4,missense_variant,p.Ala115Ser,ENST00000572303,;MYL4,upstream_gene_variant,,ENST00000570671,;MYL4,missense_variant,p.Ala84Ser,ENST00000573747,;MYL4,3_prime_UTR_variant,,ENST00000571981,;MYL4,3_prime_UTR_variant,,ENST00000570772,; T ENST00000354968 Transcript missense_variant 378/907 250/594 84/197 A/S Gcc/Tcc 1 1 MYL4 HGNC HGNC:7585 protein_coding YES CCDS11510.1 ENSP00000347055 P12829 UPI000013C60D NM_001002841.1 deleterious(0.02) 4/8 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR23048,hmmpanther:PTHR23048:SF1,Superfamily_domains:SSF47473 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 47219990 47219990 G T 1 0 0 0 0 1 0 0 0 10049 1203 42 2 2 MYL4 17 47219990 Missense_Mutation SNP G C3L-00144_T 2450243 47219990 36037451 1388 5459 NFE2L1 0 . GRCh38 17 48056514 48056514 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.639G>T p.Gln213His p.Q213H ENST00000362042 3/6 417 343 74 279 277 2 strelka-varscan-mutect NFE2L1,missense_variant,p.Gln213His,ENST00000362042,NM_003204.2;NFE2L1,missense_variant,p.Gln202His,ENST00000361665,;NFE2L1,missense_variant,p.Gln213His,ENST00000357480,;NFE2L1,missense_variant,p.Gln213His,ENST00000585291,;NFE2L1,missense_variant,p.Gln87His,ENST00000536222,;NFE2L1,missense_variant,p.Gln44His,ENST00000583378,;NFE2L1,missense_variant,p.Gln55His,ENST00000582155,;NFE2L1,missense_variant,p.Gln76His,ENST00000577431,;NFE2L1,missense_variant,p.Gln87His,ENST00000580050,;NFE2L1,5_prime_UTR_variant,,ENST00000584634,;NFE2L1,5_prime_UTR_variant,,ENST00000580037,;NFE2L1,5_prime_UTR_variant,,ENST00000577411,;NFE2L1,5_prime_UTR_variant,,ENST00000583210,;NFE2L1,upstream_gene_variant,,ENST00000581319,;NFE2L1,downstream_gene_variant,,ENST00000579537,;RP5-890E16.4,downstream_gene_variant,,ENST00000583349,; T ENST00000362042 Transcript missense_variant 1255/4774 639/2319 213/772 Q/H caG/caT 1 1 NFE2L1 HGNC HGNC:7781 protein_coding YES CCDS11524.1 ENSP00000354855 Q14494 UPI000012FFCF NM_003204.2 tolerated(0.43) 3/6 hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF31 MODERATE 1 SNV 1 1 PASS rs1379352022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 48056514 48056514 G T 1 0 0 0 0 1 0 0 0 10404 991 35 2 2 NFE2L1 17 48056514 Missense_Mutation SNP G C3L-00144_T 836524 48056514 35200927 1389 5460 HOXB3 0 . GRCh38 17 48555586 48555586 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.82G>T p.Gly28Trp p.G28W ENST00000465120 4/5 478 375 103 322 320 2 strelka-varscan-mutect HOXB3,missense_variant,p.Gly28Trp,ENST00000465120,;HOXB3,5_prime_UTR_variant,,ENST00000311626,NM_002146.4;HOXB3,5_prime_UTR_variant,,ENST00000498678,;HOXB3,5_prime_UTR_variant,,ENST00000472863,;HOXB3,5_prime_UTR_variant,,ENST00000489475,;HOXB3,5_prime_UTR_variant,,ENST00000460160,;HOXB3,5_prime_UTR_variant,,ENST00000471459,;HOXB3,intron_variant,,ENST00000476342,;HOXB3,intron_variant,,ENST00000490677,;HOXB3,upstream_gene_variant,,ENST00000470495,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS2,upstream_gene_variant,,ENST00000464382,;HOXB-AS1,downstream_gene_variant,,ENST00000435312,;HOXB-AS1,downstream_gene_variant,,ENST00000502764,;HOXB-AS1,downstream_gene_variant,,ENST00000508688,;HOXB3,non_coding_transcript_exon_variant,,ENST00000478644,; A ENST00000465120 Transcript missense_variant 332/943 82/360 28/119 G/W Ggg/Tgg 1 -1 HOXB3 HGNC HGNC:5114 protein_coding ENSP00000446783 F8W1L2 UPI00020CDF89 deleterious_low_confidence(0) 4/5 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48555586 48555586 C A 1 0 0 0 0 1 0 0 0 7196 623 22 2 2 HOXB3 17 48555586 Missense_Mutation SNP C C3L-00144_T 499072 48555586 34701855 1390 5461 HOXB3 0 . GRCh38 17 48573859 48573859 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.27G>T p.= p.A9A ENST00000490677 1/2 381 328 53 248 248 0 strelka-varscan-mutect HOXB3,synonymous_variant,p.=,ENST00000490677,;HOXB3,synonymous_variant,p.=,ENST00000465120,;HOXB3,5_prime_UTR_variant,,ENST00000311626,NM_002146.4;HOXB3,5_prime_UTR_variant,,ENST00000498678,;HOXB3,5_prime_UTR_variant,,ENST00000489475,;HOXB3,5_prime_UTR_variant,,ENST00000460160,;HOXB3,intron_variant,,ENST00000472863,;HOXB3,intron_variant,,ENST00000476342,;HOXB4,downstream_gene_variant,,ENST00000332503,NM_024015.4;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB3,downstream_gene_variant,,ENST00000552000,;HOXB3,downstream_gene_variant,,ENST00000464266,; A ENST00000490677 Transcript synonymous_variant 165/1109 27/894 9/297 A gcG/gcT 1 -1 HOXB3 HGNC HGNC:5114 protein_coding ENSP00000449977 F8VXG0 UPI00018921FB 1/2 LOW SNV 1 1 PASS rs1333549721 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 48573859 48573859 C A 1 0 0 0 0 0 0 0 1 7196 871 31 1 1 HOXB3 17 48573859 Silent SNP C C3L-00144_T 18273 48573859 34683582 1391 5462 HOXB8 0 . GRCh38 17 48614345 48614345 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.360G>T p.Glu120Asp p.E120D ENST00000239144 1/2 95 71 24 68 68 0 strelka-varscan-mutect HOXB8,missense_variant,p.Glu120Asp,ENST00000239144,NM_024016.3;HOXB8,missense_variant,p.Glu120Asp,ENST00000576562,;HOXB7,upstream_gene_variant,,ENST00000239165,NM_004502.3;HOXB8,upstream_gene_variant,,ENST00000498634,;HOXB7,intron_variant,,ENST00000567101,; A ENST00000239144 Transcript missense_variant 595/1823 360/732 120/243 E/D gaG/gaT 1 -1 HOXB8 HGNC HGNC:5119 protein_coding YES CCDS11533.1 ENSP00000239144 P17481 UPI000012CF63 NM_024016.3 tolerated(0.3) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF46,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48614345 48614345 C A 1 0 0 0 0 1 0 0 0 7201 680 24 2 2 HOXB8 17 48614345 Missense_Mutation SNP C C3L-00144_T 40486 48614345 34643096 1392 5463 TTLL6 0 . GRCh38 17 48804860 48804860 + Missense_Mutation SNP C C G rs866808413 C3L-00144_T C3L-00144_N C C c.235G>C p.Ala79Pro p.A79P ENST00000393382 2/16 712 598 114 540 540 0 strelka-varscan-mutect TTLL6,missense_variant,p.Ala79Pro,ENST00000393382,NM_001130918.1;TTLL6,downstream_gene_variant,,ENST00000470462,;TTLL6,missense_variant,p.Ala81Pro,ENST00000376681,;TTLL6,3_prime_UTR_variant,,ENST00000456415,;TTLL6,non_coding_transcript_exon_variant,,ENST00000490027,;TTLL6,upstream_gene_variant,,ENST00000509809,; G ENST00000393382 Transcript missense_variant 377/3551 235/2676 79/891 A/P Gcg/Ccg rs866808413,COSM5149441 1 -1 TTLL6 HGNC HGNC:26664 protein_coding YES CCDS45724.1 ENSP00000377043 Q8N841 UPI00017BCE80 NM_001130918.1 deleterious(0.01) 2/16 hmmpanther:PTHR12241:SF96,hmmpanther:PTHR12241 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs866808413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 48804860 48804860 C G 1 0 0 0 0 1 0 0 0 17242 768 27 4 4 TTLL6 17 48804860 Missense_Mutation SNP C C3L-00144_T 190515 48804860 34452581 1393 5464 UBE2Z 0 . GRCh38 17 48926976 48926976 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.907G>A p.Glu303Lys p.E303K ENST00000360943 7/7 122 102 20 86 86 0 strelka-varscan-mutect UBE2Z,missense_variant,p.Glu303Lys,ENST00000360943,NM_023079.4;SNF8,downstream_gene_variant,,ENST00000502492,NM_007241.2;SNF8,downstream_gene_variant,,ENST00000290330,;UBE2Z,downstream_gene_variant,,ENST00000514948,;AC091133.1,upstream_gene_variant,,ENST00000435491,;SNF8,downstream_gene_variant,,ENST00000514089,;UBE2Z,3_prime_UTR_variant,,ENST00000506498,;UBE2Z,3_prime_UTR_variant,,ENST00000504684,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000513342,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000506271,;SNF8,downstream_gene_variant,,ENST00000504000,;SNF8,downstream_gene_variant,,ENST00000510558,;SNF8,downstream_gene_variant,,ENST00000514929,;SNF8,downstream_gene_variant,,ENST00000507302,;SNF8,downstream_gene_variant,,ENST00000576353,;SNF8,downstream_gene_variant,,ENST00000515572,;SNF8,downstream_gene_variant,,ENST00000509989,;SNF8,downstream_gene_variant,,ENST00000573795,;SNF8,downstream_gene_variant,,ENST00000509995,; A ENST00000360943 Transcript missense_variant 1042/3122 907/1065 303/354 E/K Gag/Aag 1 1 UBE2Z HGNC HGNC:25847 protein_coding YES CCDS11540.2 ENSP00000354201 Q9H832 UPI00005A774B NM_023079.4 tolerated(0.1) 7/7 Gene3D:3.10.110.10,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF22 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 48926976 48926976 G A 1 0 0 0 0 1 0 0 0 17401 943 33 3 3 UBE2Z 17 48926976 Missense_Mutation SNP G C3L-00144_T 122116 48926976 34330465 1394 5465 ABI3 0 . GRCh38 17 49222562 49222562 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.948G>T p.= p.L316L ENST00000225941 8/8 149 106 43 113 113 0 strelka-varscan-mutect ABI3,synonymous_variant,p.=,ENST00000225941,NM_016428.2;ABI3,synonymous_variant,p.=,ENST00000419580,NM_001135186.1;ABI3,synonymous_variant,p.=,ENST00000571035,;ABI3,3_prime_UTR_variant,,ENST00000573347,;PHOSPHO1,downstream_gene_variant,,ENST00000413580,NM_001143804.1;PHOSPHO1,downstream_gene_variant,,ENST00000310544,NM_178500.3;PHOSPHO1,downstream_gene_variant,,ENST00000514112,;PHOSPHO1,downstream_gene_variant,,ENST00000511066,;PHOSPHO1,downstream_gene_variant,,ENST00000503902,;PHOSPHO1,downstream_gene_variant,,ENST00000512250,;PHOSPHO1,downstream_gene_variant,,ENST00000574638,; T ENST00000225941 Transcript synonymous_variant 1446/2109 948/1101 316/366 L ctG/ctT 1 1 ABI3 HGNC HGNC:29859 protein_coding YES CCDS11546.1 ENSP00000225941 Q9P2A4 UPI000013C888 NM_016428.2 8/8 PROSITE_profiles:PS50002,hmmpanther:PTHR10460:SF7,hmmpanther:PTHR10460,Pfam_domain:PF14604,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00452 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 49222562 49222562 G T 1 0 0 0 0 0 0 0 1 100 1364 48 2 2 ABI3 17 49222562 Silent SNP G C3L-00144_T 295586 49222562 34034879 1395 5466 SPOP 0 . GRCh38 17 49611448 49611448 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.490G>A p.Val164Met p.V164M ENST00000393328 7/11 378 298 80 250 250 0 strelka-varscan-mutect SPOP,missense_variant,p.Val164Met,ENST00000393328,NM_003563.3,NM_001007226.1;SPOP,missense_variant,p.Val164Met,ENST00000347630,NM_001007227.1,NM_001007229.1,NM_001007230.1;SPOP,missense_variant,p.Val164Met,ENST00000503676,;SPOP,missense_variant,p.Val164Met,ENST00000504102,NM_001007228.1;SPOP,missense_variant,p.Val164Met,ENST00000509079,;SPOP,missense_variant,p.Val164Met,ENST00000505581,;SPOP,missense_variant,p.Val164Met,ENST00000507970,;SPOP,3_prime_UTR_variant,,ENST00000506399,;SPOP,3_prime_UTR_variant,,ENST00000509869,;SPOP,upstream_gene_variant,,ENST00000504889,; T ENST00000393328 Transcript missense_variant 856/2985 490/1125 164/374 V/M Gtg/Atg 1 -1 SPOP HGNC HGNC:11254 protein_coding YES CCDS11551.1 ENSP00000377001 O43791 UPI0000003F5C NM_003563.3,NM_001007226.1 deleterious(0.02) 7/11 Gene3D:2.60.210.10,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF97,Superfamily_domains:SSF49599 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 49611448 49611448 C T 1 0 0 0 0 1 0 0 0 15437 478 17 3 3 SPOP 17 49611448 Missense_Mutation SNP C C3L-00144_T 388886 49611448 33645993 1396 5467 CA10 0 . GRCh38 17 51633522 51633522 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.918G>T p.Gln306His p.Q306H ENST00000451037 8/9 149 99 50 112 112 0 strelka-varscan-mutect CA10,missense_variant,p.Gln306His,ENST00000451037,NM_020178.4;CA10,missense_variant,p.Gln306His,ENST00000442502,NM_001082534.1;CA10,missense_variant,p.Gln306His,ENST00000285273,NM_001082533.1;CA10,missense_variant,p.Gln231His,ENST00000570565,;CA10,downstream_gene_variant,,ENST00000575181,;CA10,downstream_gene_variant,,ENST00000571918,;CA10,3_prime_UTR_variant,,ENST00000571371,; A ENST00000451037 Transcript missense_variant 1859/3189 918/987 306/328 Q/H caG/caT 1 -1 CA10 HGNC HGNC:1369 protein_coding YES CCDS32684.1 ENSP00000405388 Q9NS85 UPI000000167C NM_020178.4 tolerated(0.12) 8/9 hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51633522 51633522 C A 1 0 0 0 0 1 0 0 0 2197 680 24 2 2 CA10 17 51633522 Missense_Mutation SNP C C3L-00144_T 2022074 51633522 31623919 1397 5468 CA10 0 . GRCh38 17 52157739 52157739 + Silent SNP G G T C3L-00144_T C3L-00144_N G G c.48C>A p.= p.I16I ENST00000451037 1/9 263 199 64 197 197 0 strelka-varscan-mutect CA10,synonymous_variant,p.=,ENST00000451037,NM_020178.4;CA10,synonymous_variant,p.=,ENST00000442502,NM_001082534.1;CA10,synonymous_variant,p.=,ENST00000285273,NM_001082533.1;CA10,synonymous_variant,p.=,ENST00000575181,;CA10,intron_variant,,ENST00000570565,;CA10,non_coding_transcript_exon_variant,,ENST00000573294,;CA10,synonymous_variant,p.=,ENST00000571371,; T ENST00000451037 Transcript synonymous_variant 989/3189 48/987 16/328 I atC/atA COSM1521686 1 -1 CA10 HGNC HGNC:1369 protein_coding YES CCDS32684.1 ENSP00000405388 Q9NS85 UPI000000167C NM_020178.4 1/9 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 52157739 52157739 G T 1 0 0 0 0 0 0 0 1 2197 1048 37 1 1 CA10 17 52157739 Silent SNP G C3L-00144_T 524217 52157739 31099702 1398 5469 KIF2B 0 . GRCh38 17 53823891 53823891 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.858A>T p.= p.P286P ENST00000268919 1/1 123 94 29 131 131 0 strelka-varscan-mutect KIF2B,synonymous_variant,p.=,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript synonymous_variant 991/2313 858/2022 286/673 P ccA/ccT 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 1/1 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 53823891 53823891 A T 1 0 0 0 0 0 0 0 1 8163 146 6 4 4 KIF2B 17 53823891 Silent SNP A C3L-00144_T 1666152 53823891 29433550 1399 5470 C17orf64 0 . GRCh38 17 60426273 60426273 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.266G>T p.Gly89Val p.G89V ENST00000269127 3/6 291 218 73 155 154 1 strelka-varscan-mutect C17orf64,missense_variant,p.Gly89Val,ENST00000269127,NM_181707.2;C17orf64,missense_variant,p.Gly52Val,ENST00000474834,;USP32,upstream_gene_variant,,ENST00000588898,;USP32,upstream_gene_variant,,ENST00000590297,;C17orf64,downstream_gene_variant,,ENST00000461535,;C17orf64,non_coding_transcript_exon_variant,,ENST00000464714,; T ENST00000269127 Transcript missense_variant 350/950 266/711 89/236 G/V gGg/gTg 1 1 C17orf64 HGNC HGNC:26990 protein_coding YES CCDS32698.2 ENSP00000269127 Q86WR6 UPI0000161125 NM_181707.2 deleterious(0) 3/6 Pfam_domain:PF13907,hmmpanther:PTHR21765,SMART_domains:SM01176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 60426273 60426273 G T 1 0 0 0 0 1 0 0 0 1886 1232 43 2 2 C17orf64 17 60426273 Missense_Mutation SNP G C3L-00144_T 6602382 60426273 22831168 1400 5471 EFCAB3 0 . GRCh38 17 62406619 62406619 + Silent SNP C C A rs756722182 C3L-00144_T C3L-00144_N C C c.784C>A p.= p.R262R ENST00000450662 9/12 348 256 92 225 225 0 strelka-varscan-mutect EFCAB3,synonymous_variant,p.=,ENST00000450662,NM_001144933.1;EFCAB3,synonymous_variant,p.=,ENST00000305286,NM_173503.3;EFCAB3,downstream_gene_variant,,ENST00000520404,;EFCAB3,non_coding_transcript_exon_variant,,ENST00000636041,; A ENST00000450662 Transcript synonymous_variant 855/1694 784/1473 262/490 R Cgg/Agg rs756722182 1 1 EFCAB3 HGNC HGNC:26379 protein_coding YES CCDS45751.1 ENSP00000403932 Q8N7B9 UPI0001929531 NM_001144933.1 9/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23050:SF158,hmmpanther:PTHR23050 LOW 1 SNV 5 1 PASS rs756722182 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 62406619 62406619 C A 1 0 0 0 0 0 0 0 1 4771 643 23 1 1 EFCAB3 17 62406619 Silent SNP C C3L-00144_T 1980346 62406619 20850822 1401 5472 TLK2 0 . GRCh38 17 62576737 62576737 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1216G>C p.Glu406Gln p.E406Q ENST00000326270 14/23 256 184 72 158 158 0 strelka-varscan-mutect TLK2,missense_variant,p.Glu235Gln,ENST00000582809,;TLK2,missense_variant,p.Glu406Gln,ENST00000326270,NM_001284333.1;TLK2,missense_variant,p.Glu384Gln,ENST00000346027,NM_006852.3;TLK2,missense_variant,p.Glu352Gln,ENST00000343388,NM_001284363.1;TLK2,missense_variant,p.Glu320Gln,ENST00000581041,;TLK2,missense_variant,p.Glu175Gln,ENST00000578697,;TLK2,downstream_gene_variant,,ENST00000584367,; C ENST00000326270 Transcript missense_variant 1484/3512 1216/2319 406/772 E/Q Gaa/Caa 1 1 TLK2 HGNC HGNC:11842 protein_coding YES CCDS62283.1 ENSP00000316512 Q86UE8 UPI00001B6B0E NM_001284333.1 deleterious(0.01) 14/23 hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 62576737 62576737 G C 1 0 0 0 0 1 0 0 0 16390 943 33 4 4 TLK2 17 62576737 Missense_Mutation SNP G C3L-00144_T 170118 62576737 20680704 1402 5473 ACE 0 . GRCh38 17 63486603 63486603 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.2107delC p.Gln703ArgfsTer7 p.Q703Rfs*7 ENST00000290866 14/25 672 627 45 474 474 0 varindel-pindel ACE,frameshift_variant,p.Gln703ArgfsTer7,ENST00000428043,;ACE,frameshift_variant,p.Gln703ArgfsTer7,ENST00000290866,NM_000789.3;ACE,frameshift_variant,p.Gln129ArgfsTer7,ENST00000290863,NM_152830.2;ACE,frameshift_variant,p.Gln129ArgfsTer7,ENST00000413513,NM_001178057.1;ACE,upstream_gene_variant,,ENST00000582761,;ACE,downstream_gene_variant,,ENST00000584529,;ACE,upstream_gene_variant,,ENST00000577418,;CTD-2501B8.1,frameshift_variant,p.Gln129ArgfsTer7,ENST00000577647,;ACE,frameshift_variant,p.Gln129ArgfsTer7,ENST00000579314,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,3_prime_UTR_variant,,ENST00000582005,;ACE,3_prime_UTR_variant,,ENST00000579726,;ACE,3_prime_UTR_variant,,ENST00000579204,;ACE,downstream_gene_variant,,ENST00000582678,;ACE,upstream_gene_variant,,ENST00000584865,;ACE,upstream_gene_variant,,ENST00000583645,; - ENST00000290866 Transcript frameshift_variant 2129/4959 2105/3921 702/1306 T/X aCc/ac 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 14/25 hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 63486603 63486603 C - 1 0 1 0 1 0 0 0 0 174 507 18 0 0 ACE 17 63486603 Frame_Shift_Del DEL C C3L-00144_T 909866 63486603 19770838 1403 5474 KCNH6 0 . GRCh38 17 63544034 63544034 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.2256C>A p.= p.P752P ENST00000583023 11/14 108 85 23 73 72 1 strelka-varscan-mutect KCNH6,synonymous_variant,p.=,ENST00000583023,NM_030779.3;KCNH6,intron_variant,,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,intron_variant,,ENST00000581784,NM_173092.2;KCNH6,intron_variant,,ENST00000456941,;KCNH6,intron_variant,,ENST00000583465,; A ENST00000583023 Transcript synonymous_variant 2267/3821 2256/2985 752/994 P ccC/ccA 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 11/14 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 63544034 63544034 C A 1 0 0 0 0 0 0 0 1 7952 610 22 2 2 KCNH6 17 63544034 Silent SNP C C3L-00144_T 57431 63544034 19713407 1404 5475 GH2 0 . GRCh38 17 63880771 63880771 + Frame_Shift_Del DEL C C - novel C3L-00144_T C3L-00144_N C C c.457delG p.Val153Ter p.V153* ENST00000332800 4/4 390 303 87 291 291 0 sindel-varindel-pindel GH2,splice_donor_variant,,ENST00000423893,NM_002059.4;GH2,splice_donor_variant,,ENST00000449787,NM_022556.3;GH2,splice_donor_variant,,ENST00000622506,;GH2,frameshift_variant,p.Val153Ter,ENST00000332800,NM_022557.3;GH2,splice_region_variant,,ENST00000456543,NM_022558.3;CSH2,intron_variant,,ENST00000620751,; - ENST00000332800 Transcript frameshift_variant 591/1138 457/771 153/256 V/X Gtg/tg 1 -1 GH2 HGNC HGNC:4262 protein_coding YES CCDS11648.1 ENSP00000333157 P01242 UPI000002B3EF NM_022557.3 4/4 Gene3D:1.20.1250.10,Superfamily_domains:SSF47266 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 63880771 63880771 C - 1 0 1 0 1 0 0 0 0 6246 521 18 0 0 GH2 17 63880771 Frame_Shift_Del DEL C C3L-00144_T 336737 63880771 19376670 1405 5476 GNA13 0 . GRCh38 17 65056377 65056377 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.217G>T p.Gly73Trp p.G73W ENST00000439174 1/4 473 347 126 324 322 2 strelka-varscan-mutect GNA13,missense_variant,p.Gly73Trp,ENST00000439174,NM_006572.5;GNA13,upstream_gene_variant,,ENST00000541118,NM_001282425.1;RP11-583F2.5,downstream_gene_variant,,ENST00000581796,; A ENST00000439174 Transcript missense_variant 463/4922 217/1134 73/377 G/W Ggg/Tgg 1 -1 GNA13 HGNC HGNC:4381 protein_coding YES CCDS11661.1 ENSP00000400717 Q14344 A0A024R8M0 UPI0000073EBA NM_006572.5 deleterious(0) 1/4 hmmpanther:PTHR10218:SF85,hmmpanther:PTHR10218,Pfam_domain:PF00503,Gene3D:1.10.400.10,SMART_domains:SM00275 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 65056377 65056377 C A 1 0 0 0 0 1 0 0 0 6381 652 23 1 1 GNA13 17 65056377 Missense_Mutation SNP C C3L-00144_T 1175606 65056377 18201064 1406 5477 CEP112 0 . GRCh38 17 65852035 65852035 + Splice_Site SNP C C T rs762903928 C3L-00144_T C3L-00144_N C C c.2164-1G>A p.X722_splice ENST00000392769 101 68 33 75 75 0 strelka-varscan-mutect CEP112,splice_acceptor_variant,,ENST00000392769,;CEP112,splice_acceptor_variant,,ENST00000535342,NM_001199165.2;CEP112,splice_acceptor_variant,,ENST00000537949,NM_001302891.1;CEP112,splice_acceptor_variant,,ENST00000580482,;CEP112,splice_acceptor_variant,,ENST00000580694,;CEP112,splice_acceptor_variant,,ENST00000584627,;CEP112,splice_acceptor_variant,,ENST00000582795,;CEP112,splice_acceptor_variant,,ENST00000584987,;CEP112,splice_acceptor_variant,,ENST00000582861,; T ENST00000392769 Transcript splice_acceptor_variant -/3517 2164/2868 722/955 rs762903928 1 -1 CEP112 HGNC HGNC:28514 protein_coding YES CCDS32710.1 ENSP00000376522 Q8N8E3 UPI0000603C26 20/26 HIGH 1 SNV 5 1 PASS rs762903928 . 0 200 9 0 0 0 0 0 -20 0.9999986 1 1 1 0 T 5 4 12 65852035 65852035 C T 1 0 0 0 0 0 0 1 0 2955 695 24 3 3 CEP112 17 65852035 Splice_Site SNP C C3L-00144_T 795658 65852035 17405406 1407 5478 PRKCA 0 . GRCh38 17 66738854 66738854 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1321G>T p.Val441Leu p.V441L ENST00000413366 11/17 354 268 86 230 229 1 strelka-varscan-mutect PRKCA,missense_variant,p.Val441Leu,ENST00000413366,NM_002737.2;PRKCA,splice_region_variant,,ENST00000284384,; T ENST00000413366 Transcript missense_variant,splice_region_variant 1347/8751 1321/2019 441/672 V/L Gta/Tta 1 1 PRKCA HGNC HGNC:9393 protein_coding YES CCDS11664.1 ENSP00000408695 P17252 L7RSM7 UPI000013DD98 NM_002737.2 tolerated(0.19) 11/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF193,Pfam_domain:PF00069,PIRSF_domain:PIRSF000550,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 66738854 66738854 G T 1 0 0 0 0 1 0 0 0 12640 1043 36 2 2 PRKCA 17 66738854 Missense_Mutation SNP G C3L-00144_T 886819 66738854 16518587 1408 5479 CACNG4 0 . GRCh38 17 67030778 67030778 + Nonsense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.758C>A p.Ser253Ter p.S253* ENST00000262138 4/4 259 191 68 197 197 0 strelka-varscan-mutect CACNG4,stop_gained,p.Ser253Ter,ENST00000262138,NM_014405.3;RP11-74H8.1,downstream_gene_variant,,ENST00000579138,; A ENST00000262138 Transcript stop_gained 760/3380 758/984 253/327 S/* tCg/tAg COSM380914 1 1 CACNG4 HGNC HGNC:1408 protein_coding YES CCDS11667.1 ENSP00000262138 Q9UBN1 A0A024R8J8 UPI0000001649 NM_014405.3 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR12107,hmmpanther:PTHR12107:SF7 1 HIGH 1 SNV 1 1 1 PASS rs1230291904 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 67030778 67030778 C A 1 0 0 0 0 0 1 0 0 2247 893 31 1 1 CACNG4 17 67030778 Nonsense_Mutation SNP C C3L-00144_T 291924 67030778 16226663 1409 5480 SOX9 0 . GRCh38 17 72122836 72122836 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.549G>T p.Lys183Asn p.K183N ENST00000245479 2/3 496 368 128 299 298 1 strelka-varscan-mutect SOX9,missense_variant,p.Lys183Asn,ENST00000245479,NM_000346.3;SOX9-AS1,intron_variant,,ENST00000414600,;SOX9-AS1,intron_variant,,ENST00000628742,;SOX9-AS1,upstream_gene_variant,,ENST00000440093,;SOX9-AS1,upstream_gene_variant,,ENST00000533179,;SOX9-AS1,upstream_gene_variant,,ENST00000529667,;SOX9-AS1,upstream_gene_variant,,ENST00000533232,; T ENST00000245479 Transcript missense_variant 921/3935 549/1530 183/509 K/N aaG/aaT 1 1 SOX9 HGNC HGNC:11204 protein_coding YES CCDS11689.1 ENSP00000245479 P48436 UPI00000009D8 NM_000346.3 deleterious(0.01) 2/3 hmmpanther:PTHR10270:SF212,hmmpanther:PTHR10270,Gene3D:1.10.30.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 72122836 72122836 G T 1 0 0 0 0 1 0 0 0 15284 933 33 2 2 SOX9 17 72122836 Missense_Mutation SNP G C3L-00144_T 5092058 72122836 11134605 1410 5481 SOX9 0 . GRCh38 17 72123793 72123793 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.936G>T p.Gln312His p.Q312H ENST00000245479 3/3 318 300 18 228 228 0 strelka-varscan-mutect SOX9,missense_variant,p.Gln312His,ENST00000245479,NM_000346.3;SOX9-AS1,intron_variant,,ENST00000414600,;SOX9-AS1,intron_variant,,ENST00000628742,;SOX9-AS1,upstream_gene_variant,,ENST00000440093,;SOX9-AS1,upstream_gene_variant,,ENST00000533179,;SOX9-AS1,upstream_gene_variant,,ENST00000529667,;SOX9-AS1,upstream_gene_variant,,ENST00000533232,; T ENST00000245479 Transcript missense_variant 1308/3935 936/1530 312/509 Q/H caG/caT 1 1 SOX9 HGNC HGNC:11204 protein_coding YES CCDS11689.1 ENSP00000245479 P48436 UPI00000009D8 NM_000346.3 tolerated(0.13) 3/3 hmmpanther:PTHR10270:SF212,hmmpanther:PTHR10270 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 72123793 72123793 G T 1 0 0 0 0 1 0 0 0 15284 991 35 2 2 SOX9 17 72123793 Missense_Mutation SNP G C3L-00144_T 957 72123793 11133648 1411 5482 SDK2 0 . GRCh38 17 73358127 73358127 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5545C>A p.Pro1849Thr p.P1849T ENST00000392650 40/45 387 283 104 265 264 1 strelka-varscan-mutect SDK2,missense_variant,p.Pro1849Thr,ENST00000392650,NM_001144952.1;SDK2,missense_variant,p.Pro1006Thr,ENST00000424778,;SDK2,non_coding_transcript_exon_variant,,ENST00000410094,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; T ENST00000392650 Transcript missense_variant 5546/10723 5545/6519 1849/2172 P/T Ccg/Acg 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 tolerated(0.58) 40/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 73358127 73358127 G T 1 0 0 0 0 1 0 0 0 14244 1232 43 2 2 SDK2 17 73358127 Missense_Mutation SNP G C3L-00144_T 1234334 73358127 9899314 1412 5483 KIF19 0 . GRCh38 17 74350511 74350511 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1324G>A p.Glu442Lys p.E442K ENST00000389916 11/20 194 138 56 126 126 0 strelka-varscan-mutect KIF19,missense_variant,p.Glu442Lys,ENST00000389916,NM_153209.3;KIF19,missense_variant,p.Glu400Lys,ENST00000551294,;KIF19,non_coding_transcript_exon_variant,,ENST00000547389,;KIF19,non_coding_transcript_exon_variant,,ENST00000359939,;KIF19,downstream_gene_variant,,ENST00000549637,; A ENST00000389916 Transcript missense_variant 1462/3643 1324/2997 442/998 E/K Gag/Aag 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 deleterious(0.01) 11/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF434 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 74350511 74350511 G A 1 0 0 0 0 1 0 0 0 8146 1175 41 3 3 KIF19 17 74350511 Missense_Mutation SNP G C3L-00144_T 992384 74350511 8906930 1413 5484 KIF19 0 . GRCh38 17 74353299 74353299 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2218G>T p.Glu740Ter p.E740* ENST00000389916 16/20 242 181 61 157 157 0 strelka-varscan-mutect KIF19,stop_gained,p.Glu740Ter,ENST00000389916,NM_153209.3;KIF19,downstream_gene_variant,,ENST00000551294,;BTBD17,downstream_gene_variant,,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000547389,;KIF19,downstream_gene_variant,,ENST00000359939,;KIF19,downstream_gene_variant,,ENST00000549637,; T ENST00000389916 Transcript stop_gained,splice_region_variant 2356/3643 2218/2997 740/998 E/* Gag/Tag 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 16/20 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 74353299 74353299 G T 1 0 0 0 0 0 1 0 0 8146 1188 41 2 2 KIF19 17 74353299 Nonsense_Mutation SNP G C3L-00144_T 2788 74353299 8904142 1414 5485 GPRC5C 0 . GRCh38 17 74440735 74440735 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1094G>T p.Arg365Leu p.R365L ENST00000392627 2/4 77 55 22 49 49 0 strelka-varscan-mutect GPRC5C,missense_variant,p.Arg365Leu,ENST00000392627,NM_022036.2;GPRC5C,missense_variant,p.Arg340Leu,ENST00000392628,;GPRC5C,missense_variant,p.Arg332Leu,ENST00000392629,NM_018653.3;GPRC5C,missense_variant,p.Arg5Leu,ENST00000342648,;GPRC5C,intron_variant,,ENST00000481232,;GPRC5C,intron_variant,,ENST00000581590,;GPRC5C,downstream_gene_variant,,ENST00000582473,;GPRC5C,downstream_gene_variant,,ENST00000582444,;GPRC5C,upstream_gene_variant,,ENST00000582873,;GPRC5C,upstream_gene_variant,,ENST00000482723,;GPRC5C,upstream_gene_variant,,ENST00000577663,; T ENST00000392627 Transcript missense_variant 2220/2988 1094/1461 365/486 R/L cGg/cTg 1 1 GPRC5C HGNC HGNC:13309 protein_coding YES CCDS11699.1 ENSP00000376403 A0A0C4DFY5 UPI0000231CB2 NM_022036.2 deleterious(0) 2/4 hmmpanther:PTHR14511,hmmpanther:PTHR14511:SF15 MODERATE 1 SNV 1 1 PASS rs1022287414 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 74440735 74440735 G T 1 0 0 0 0 1 0 0 0 6605 1116 39 1 1 GPRC5C 17 74440735 Missense_Mutation SNP G C3L-00144_T 87436 74440735 8816706 1415 5486 OTOP2 0 . GRCh38 17 74930357 74930357 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.722T>G p.Phe241Cys p.F241C ENST00000331427 6/7 340 245 95 261 261 0 strelka-varscan-mutect OTOP2,missense_variant,p.Phe241Cys,ENST00000331427,NM_178160.2;OTOP2,missense_variant,p.Phe241Cys,ENST00000580223,;OTOP2,downstream_gene_variant,,ENST00000584711,; G ENST00000331427 Transcript missense_variant 814/2147 722/1689 241/562 F/C tTc/tGc 1 1 OTOP2 HGNC HGNC:19657 protein_coding YES CCDS11708.1 ENSP00000332528 Q7RTS6 UPI000018F613 NM_178160.2 deleterious(0) 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF35,Pfam_domain:PF03189 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 74930357 74930357 T G 1 0 0 0 0 1 0 0 0 11374 1783 62 5 5 OTOP2 17 74930357 Missense_Mutation SNP T C3L-00144_T 489622 74930357 8327084 1416 5487 UNC13D 0 . GRCh38 17 75840069 75840069 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.900G>A p.= p.V300V ENST00000207549 11/32 624 468 156 385 385 0 strelka-varscan-mutect UNC13D,synonymous_variant,p.=,ENST00000207549,NM_199242.2;UNC13D,synonymous_variant,p.=,ENST00000412096,;UNC13D,synonymous_variant,p.=,ENST00000592386,;UNC13D,intron_variant,,ENST00000586147,;UNC13D,downstream_gene_variant,,ENST00000590762,;UNC13D,downstream_gene_variant,,ENST00000586108,;UNC13D,non_coding_transcript_exon_variant,,ENST00000587504,;UNC13D,downstream_gene_variant,,ENST00000585574,;UNC13D,synonymous_variant,p.=,ENST00000587105,;UNC13D,non_coding_transcript_exon_variant,,ENST00000591563,;UNC13D,downstream_gene_variant,,ENST00000588774,;UNC13D,upstream_gene_variant,,ENST00000591616,;UNC13D,downstream_gene_variant,,ENST00000587495,; T ENST00000207549 Transcript synonymous_variant 1280/4393 900/3273 300/1090 V gtG/gtA 1 -1 UNC13D HGNC HGNC:23147 protein_coding YES CCDS11730.1 ENSP00000207549 Q70J99 UPI000015FC91 NM_199242.2 11/32 Low_complexity_(Seg):seg,hmmpanther:PTHR10774:SF98,hmmpanther:PTHR10774 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 75840069 75840069 C T 1 0 0 0 0 0 0 0 1 17511 697 25 3 3 UNC13D 17 75840069 Silent SNP C C3L-00144_T 909712 75840069 7417372 1417 5488 MXRA7 0 . GRCh38 17 76677604 76677604 + Missense_Mutation SNP C C A rs202238128 C3L-00144_T C3L-00144_N C C c.599G>T p.Arg200Leu p.R200L ENST00000355797 4/4 214 150 64 131 129 2 strelka-varscan-mutect MXRA7,missense_variant,p.Arg200Leu,ENST00000355797,NM_001008528.2;MXRA7,downstream_gene_variant,,ENST00000592148,;MXRA7,downstream_gene_variant,,ENST00000375036,NM_001008529.2;MXRA7,downstream_gene_variant,,ENST00000449428,NM_198530.3;MXRA7,downstream_gene_variant,,ENST00000589082,;MXRA7,downstream_gene_variant,,ENST00000585519,;MXRA7,downstream_gene_variant,,ENST00000588114,;RP11-318A15.2,downstream_gene_variant,,ENST00000565271,; A ENST00000355797 Transcript missense_variant 608/5661 599/615 200/204 R/L cGg/cTg rs202238128 1 -1 MXRA7 HGNC HGNC:7541 protein_coding YES CCDS32745.1 ENSP00000348050 P84157 UPI000023765A NM_001008528.2 4/4 hmmpanther:PTHR21845 MODERATE 1 SNV 2 1 PASS rs202238128 . 0 205 0 4 0 0 0 0 -20 0.9999776 1 1 1 0 A 3 1 12 76677604 76677604 C A 1 0 0 0 0 1 0 0 0 10003 652 23 1 1 MXRA7 17 76677604 Missense_Mutation SNP C C3L-00144_T 837535 76677604 6579837 1418 5489 MGAT5B 0 . GRCh38 17 76904392 76904392 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.693G>A p.= p.Q231Q ENST00000428789 5/16 163 129 34 78 78 0 strelka-varscan-mutect MGAT5B,synonymous_variant,p.=,ENST00000569840,NM_001199172.1;MGAT5B,synonymous_variant,p.=,ENST00000301618,NM_144677.2;MGAT5B,synonymous_variant,p.=,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,synonymous_variant,p.=,ENST00000565043,; A ENST00000428789 Transcript synonymous_variant 796/4053 693/2406 231/801 Q caG/caA 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 5/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 76904392 76904392 G A 1 0 0 0 0 0 0 0 1 9510 933 33 3 3 MGAT5B 17 76904392 Silent SNP G C3L-00144_T 226788 76904392 6353049 1419 5490 MGAT5B 0 . GRCh38 17 76946446 76946446 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.1946A>G p.His649Arg p.H649R ENST00000428789 14/16 80 52 28 39 39 0 strelka-mutect MGAT5B,missense_variant,p.His640Arg,ENST00000569840,NM_001199172.1;MGAT5B,missense_variant,p.His638Arg,ENST00000301618,NM_144677.2;MGAT5B,missense_variant,p.His649Arg,ENST00000428789,NM_198955.1;RP11-87G24.3,downstream_gene_variant,,ENST00000585902,;RP11-87G24.3,downstream_gene_variant,,ENST00000564292,;MGAT5B,non_coding_transcript_exon_variant,,ENST00000563153,;MGAT5B,3_prime_UTR_variant,,ENST00000565043,;MGAT5B,non_coding_transcript_exon_variant,,ENST00000568598,; G ENST00000428789 Transcript missense_variant 2049/4053 1946/2406 649/801 H/R cAc/cGc 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 tolerated(0.06) 14/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 76946446 76946446 A G 1 0 0 0 0 1 0 0 0 9510 173 6 5 5 MGAT5B 17 76946446 Missense_Mutation SNP A C3L-00144_T 42054 76946446 6310995 1420 5491 DNAH17 0 . GRCh38 17 78566683 78566683 + Silent SNP C C A rs754988436 C3L-00144_T C3L-00144_N C C c.1500G>T p.= p.L500L ENST00000389840 11/81 340 270 70 231 231 0 strelka-varscan-mutect DNAH17,synonymous_variant,p.=,ENST00000389840,NM_173628.3;DNAH17,synonymous_variant,p.=,ENST00000585328,;DNAH17,non_coding_transcript_exon_variant,,ENST00000589793,; A ENST00000389840 Transcript synonymous_variant 1625/13723 1500/13389 500/4462 L ctG/ctT rs754988436 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 11/81 Pfam_domain:PF08385,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 LOW 1 SNV 5 1 PASS rs754988436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 78566683 78566683 C A 1 0 0 0 0 0 0 0 1 4416 581 21 2 2 DNAH17 17 78566683 Silent SNP C C3L-00144_T 1620237 78566683 4690758 1421 5492 CEP295NL 0 . GRCh38 17 78890778 78890778 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1726G>T p.Gly576Cys p.G576C ENST00000322630 3/3 558 440 118 334 332 2 strelka-varscan-mutect CEP295NL,missense_variant,p.Gly576Cys,ENST00000322630,NM_001243541.1,NM_001243540.1;CEP295NL,missense_variant,p.Gly576Cys,ENST00000619342,;TIMP2,intron_variant,,ENST00000262768,NM_003255.4;TIMP2,intron_variant,,ENST00000536189,;CEP295NL,intron_variant,,ENST00000586713,;CEP295NL,downstream_gene_variant,,ENST00000590267,;CEP295NL,downstream_gene_variant,,ENST00000587052,; A ENST00000322630 Transcript missense_variant 1892/2090 1726/1866 576/621 G/C Ggc/Tgc 1 -1 CEP295NL HGNC HGNC:44659 protein_coding YES CCDS58603.1 ENSP00000312767 Q96MC4 UPI0000071A46 NM_001243541.1,NM_001243540.1 tolerated(0.12) 3/3 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF2 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 78890778 78890778 C A 1 0 0 0 0 1 0 0 0 2971 623 22 2 2 CEP295NL 17 78890778 Missense_Mutation SNP C C3L-00144_T 324095 78890778 4366663 1422 5493 CBX4 0 . GRCh38 17 79834853 79834853 + Silent SNP C C A rs772029545 C3L-00144_T C3L-00144_N C C c.789G>T p.= p.V263V ENST00000269397 5/5 93 70 23 68 68 0 strelka-varscan-mutect CBX4,synonymous_variant,p.=,ENST00000269397,NM_003655.2;CBX4,downstream_gene_variant,,ENST00000448310,;CBX4,downstream_gene_variant,,ENST00000495122,;CBX4,downstream_gene_variant,,ENST00000494546,; A ENST00000269397 Transcript synonymous_variant 967/2664 789/1683 263/560 V gtG/gtT rs772029545 1 -1 CBX4 HGNC HGNC:1554 protein_coding YES CCDS32758.1 ENSP00000269397 O00257 A0A0S2Z5B2 UPI000013D82E NM_003655.2 5/5 hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF10 LOW 1 SNV 1 1 PASS rs772029545 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 79834853 79834853 C A 1 0 0 0 0 0 0 0 1 2420 813 29 2 2 CBX4 17 79834853 Silent SNP C C3L-00144_T 944075 79834853 3422588 1423 5494 CCDC40 0 . GRCh38 17 80087626 80087626 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.2469G>A p.= p.K823K ENST00000397545 15/20 725 686 39 513 513 0 strelka-varscan-mutect CCDC40,synonymous_variant,p.=,ENST00000397545,NM_017950.3;CCDC40,synonymous_variant,p.=,ENST00000374877,NM_001243342.1;CCDC40,upstream_gene_variant,,ENST00000573903,;CCDC40,non_coding_transcript_exon_variant,,ENST00000572253,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;CCDC40,non_coding_transcript_exon_variant,,ENST00000575431,;CCDC40,upstream_gene_variant,,ENST00000574933,; A ENST00000397545 Transcript synonymous_variant 2496/4294 2469/3429 823/1142 K aaG/aaA 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 15/20 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF08647,hmmpanther:PTHR16275,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 80087626 80087626 G A 1 0 0 0 0 0 0 0 1 2521 933 33 3 3 CCDC40 17 80087626 Silent SNP G C3L-00144_T 252773 80087626 3169815 1424 5495 LRRC45 0 . GRCh38 17 82024764 82024764 + Splice_Site SNP G G A novel C3L-00144_T C3L-00144_N G G c.353+1G>A p.X118_splice ENST00000306688 68 52 16 39 39 0 strelka-varscan-mutect LRRC45,splice_donor_variant,,ENST00000306688,NM_144999.3;LRRC45,splice_donor_variant,,ENST00000577638,;STRA13,upstream_gene_variant,,ENST00000392359,NM_001271006.1;STRA13,upstream_gene_variant,,ENST00000584347,;STRA13,upstream_gene_variant,,ENST00000306704,NM_144998.3;STRA13,upstream_gene_variant,,ENST00000584600,;STRA13,upstream_gene_variant,,ENST00000580435,NM_001271007.1;STRA13,upstream_gene_variant,,ENST00000579520,;LRRC45,splice_donor_variant,,ENST00000583383,;STRA13,upstream_gene_variant,,ENST00000583767,;STRA13,upstream_gene_variant,,ENST00000584514,;STRA13,upstream_gene_variant,,ENST00000577379,;STRA13,upstream_gene_variant,,ENST00000580090,;LRRC45,upstream_gene_variant,,ENST00000583302,;LRRC45,upstream_gene_variant,,ENST00000581227,;STRA13,upstream_gene_variant,,ENST00000585091,;LRRC45,upstream_gene_variant,,ENST00000582083,; A ENST00000306688 Transcript splice_donor_variant -/2701 353/2013 118/670 1 1 LRRC45 HGNC HGNC:28302 protein_coding YES CCDS11797.1 ENSP00000306760 Q96CN5 UPI000006EF33 NM_144999.3 3/16 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 82024764 82024764 G A 1 0 0 0 0 0 0 1 0 8898 1275 44 3 3 LRRC45 17 82024764 Splice_Site SNP G C3L-00144_T 1937138 82024764 1232677 1425 5496 COLEC12 0 . GRCh38 18 334803 334803 + Silent SNP T T A rs148864903 C3L-00144_T C3L-00144_N T T c.1755A>T p.= p.P585P ENST00000400256 6/10 42 34 8 38 38 0 strelka-varscan-mutect COLEC12,synonymous_variant,p.=,ENST00000400256,NM_130386.2;COLEC12,non_coding_transcript_exon_variant,,ENST00000582147,; A ENST00000400256 Transcript synonymous_variant 1963/5742 1755/2229 585/742 P ccA/ccT rs148864903 1 -1 COLEC12 HGNC HGNC:16016 protein_coding YES CCDS32782.1 ENSP00000383115 Q5KU26 UPI00002018EC NM_130386.2 6/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF597,hmmpanther:PTHR24023,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS rs148864903 . 0 207 3 0 0 0 0 0 -19.74926 1 1 1 1 0 A 2 1 12 334803 334803 T A 1 0 0 0 0 0 0 0 1 3502 1451 51 4 4 COLEC12 18 334803 Silent SNP T C3L-00144_T 334803 80038482 1426 5497 YES1 0 . GRCh38 18 745737 745737 + Missense_Mutation SNP G G T rs746080500 C3L-00144_T C3L-00144_N G G c.695C>A p.Thr232Asn p.T232N ENST00000584307 6/12 110 61 49 86 86 0 strelka-varscan-mutect YES1,missense_variant,p.Thr232Asn,ENST00000584307,;YES1,missense_variant,p.Thr237Asn,ENST00000577961,;YES1,missense_variant,p.Thr232Asn,ENST00000314574,NM_005433.3; T ENST00000584307 Transcript missense_variant 866/4639 695/1632 232/543 T/N aCt/aAt rs746080500 1 -1 YES1 HGNC HGNC:12841 protein_coding YES CCDS11824.1 ENSP00000462468 P07947 UPI0000062316 tolerated(0.06) 6/12 Gene3D:3.30.505.10,Pfam_domain:PF00017,Prints_domain:PR00401,PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF224,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs746080500 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 745737 745737 G T 1 0 0 0 0 1 0 0 0 18036 1029 36 2 2 YES1 18 745737 Missense_Mutation SNP G C3L-00144_T 410934 745737 79627548 1427 5498 SMCHD1 0 . GRCh38 18 2705718 2705718 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1867C>T p.Leu623Phe p.L623F ENST00000320876 14/48 143 99 44 139 139 0 strelka-varscan-mutect SMCHD1,missense_variant,p.Leu623Phe,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,missense_variant,p.Leu94Phe,ENST00000577880,;SMCHD1,non_coding_transcript_exon_variant,,ENST00000577300,;SMCHD1,upstream_gene_variant,,ENST00000584897,;SMCHD1,downstream_gene_variant,,ENST00000585229,;SMCHD1,upstream_gene_variant,,ENST00000581711,; T ENST00000320876 Transcript missense_variant 2205/8821 1867/6018 623/2005 L/F Ctc/Ttc 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 deleterious(0.02) 14/48 hmmpanther:PTHR22640,hmmpanther:PTHR22640:SF2 MODERATE SNV 5 1 PASS rs886042326 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 2705718 2705718 C T 1 0 0 0 0 1 0 0 0 15081 681 24 3 3 SMCHD1 18 2705718 Missense_Mutation SNP C C3L-00144_T 1959981 2705718 77667567 1428 5499 LPIN2 0 . GRCh38 18 2922095 2922095 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.2279G>T p.Arg760Leu p.R760L ENST00000261596 17/20 205 141 64 170 170 0 strelka-varscan-mutect LPIN2,missense_variant,p.Arg760Leu,ENST00000261596,NM_014646.2;RP11-737O24.5,downstream_gene_variant,,ENST00000608032,; A ENST00000261596 Transcript missense_variant 2518/6229 2279/2691 760/896 R/L cGg/cTg COSM240516 1 -1 LPIN2 HGNC HGNC:14450 protein_coding YES CCDS11829.1 ENSP00000261596 Q92539 UPI000012E865 NM_014646.2 tolerated(0.07) 17/20 hmmpanther:PTHR12181,hmmpanther:PTHR12181:SF11,Gene3D:3.40.50.1000,Pfam_domain:PF08235,SMART_domains:SM00775,Superfamily_domains:SSF56784 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 2922095 2922095 C A 1 0 0 0 0 1 0 0 0 8819 652 23 1 1 LPIN2 18 2922095 Missense_Mutation SNP C C3L-00144_T 216377 2922095 77451190 1429 5500 DLGAP1 0 . GRCh38 18 3879472 3879472 + Silent SNP C C A rs558598498 C3L-00144_T C3L-00144_N C C c.597G>T p.= p.P199P ENST00000315677 4/13 106 65 41 95 95 0 strelka-varscan-mutect DLGAP1,synonymous_variant,p.=,ENST00000315677,NM_004746.3;DLGAP1,synonymous_variant,p.=,ENST00000581527,NM_001242761.1;DLGAP1,upstream_gene_variant,,ENST00000515196,NM_001242763.1;DLGAP1,upstream_gene_variant,,ENST00000534970,NM_001242762.1;DLGAP1-AS3,intron_variant,,ENST00000577649,;DLGAP1,non_coding_transcript_exon_variant,,ENST00000498188,;DLGAP1,upstream_gene_variant,,ENST00000478161,; A ENST00000315677 Transcript synonymous_variant 1193/6683 597/2934 199/977 P ccG/ccT rs558598498 1 -1 DLGAP1 HGNC HGNC:2905 protein_coding YES CCDS11836.1 ENSP00000316377 O14490 UPI0000129490 NM_004746.3 4/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF7 LOW SNV 5 1 PASS rs558598498 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 3879472 3879472 C A 1 0 0 0 0 0 0 0 1 4366 639 23 1 1 DLGAP1 18 3879472 Silent SNP C C3L-00144_T 957377 3879472 76493813 1430 5501 EPB41L3 0 . GRCh38 18 5478263 5478263 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.359C>A p.Ser120Ter p.S120* ENST00000341928 3/23 200 149 51 180 180 0 strelka-varscan-mutect EPB41L3,stop_gained,p.Ser120Ter,ENST00000341928,NM_012307.3;EPB41L3,stop_gained,p.Ser120Ter,ENST00000342933,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000400111,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000544123,NM_001281533.1;EPB41L3,stop_gained,p.Ser120Ter,ENST00000540638,NM_001281534.1;EPB41L3,stop_gained,p.Ser11Ter,ENST00000545076,NM_001281535.1;EPB41L3,stop_gained,p.Ser120Ter,ENST00000578503,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000580989,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000584651,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000584015,;EPB41L3,stop_gained,p.Ser120Ter,ENST00000580308,;EPB41L3,intron_variant,,ENST00000584670,;EPB41L3,downstream_gene_variant,,ENST00000581833,;EPB41L3,downstream_gene_variant,,ENST00000585142,;EPB41L3,downstream_gene_variant,,ENST00000582592,;EPB41L3,downstream_gene_variant,,ENST00000582703,;EPB41L3,downstream_gene_variant,,ENST00000580179,;RP11-286N3.1,intron_variant,,ENST00000577527,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000581454,;EPB41L3,downstream_gene_variant,,ENST00000578431,;EPB41L3,stop_gained,p.Ser11Ter,ENST00000637651,;EPB41L3,3_prime_UTR_variant,,ENST00000580866,; T ENST00000341928 Transcript stop_gained 700/4706 359/3264 120/1087 S/* tCa/tAa 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 3/23 PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF20,Pfam_domain:PF09379,Gene3D:3.10.20.90,SMART_domains:SM00295,Superfamily_domains:SSF54236 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 5478263 5478263 G T 1 0 0 0 0 0 1 0 0 5001 1294 45 2 2 EPB41L3 18 5478263 Nonsense_Mutation SNP G C3L-00144_T 1598791 5478263 74895022 1431 5502 MTCL1 0 . GRCh38 18 8783787 8783787 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.675C>A p.= p.I225I ENST00000359865 6/17 126 87 39 91 91 0 strelka-varscan-mutect MTCL1,synonymous_variant,p.=,ENST00000359865,NM_015210.3;MTCL1,synonymous_variant,p.=,ENST00000400050,;MTCL1,synonymous_variant,p.=,ENST00000517570,;MTCL1,synonymous_variant,p.=,ENST00000306329,;MTCL1,upstream_gene_variant,,ENST00000521018,;MTCL1,upstream_gene_variant,,ENST00000523811,;MTCL1,synonymous_variant,p.=,ENST00000520495,;MTCL1,upstream_gene_variant,,ENST00000517554,; A ENST00000359865 Transcript synonymous_variant 817/6093 675/4761 225/1586 I atC/atA 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 6/17 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF11365,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3 LOW 1 SNV 2 1 PASS rs894694031 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 8783787 8783787 C A 1 0 0 0 0 0 0 0 1 9900 874 31 1 1 MTCL1 18 8783787 Silent SNP C C3L-00144_T 3305524 8783787 71589498 1432 5503 APCDD1 0 . GRCh38 18 10487846 10487846 + Missense_Mutation SNP G G T rs560171977 C3L-00144_T C3L-00144_N G G c.1353G>T p.Arg451Ser p.R451S ENST00000355285 5/5 152 99 53 158 157 1 strelka-varscan-mutect APCDD1,missense_variant,p.Arg451Ser,ENST00000355285,NM_153000.4;APCDD1,downstream_gene_variant,,ENST00000578882,;APCDD1,3_prime_UTR_variant,,ENST00000423585,;APCDD1,downstream_gene_variant,,ENST00000579685,;APCDD1,downstream_gene_variant,,ENST00000582723,; T ENST00000355285 Transcript missense_variant 1707/3809 1353/1545 451/514 R/S agG/agT rs560171977 1 1 APCDD1 HGNC HGNC:15718 protein_coding YES CCDS11849.1 ENSP00000347433 Q8J025 UPI000000D766 NM_153000.4 tolerated(0.18) 5/5 Pfam_domain:PF14921,hmmpanther:PTHR31021,hmmpanther:PTHR31021:SF2,SMART_domains:SM01352 MODERATE 1 SNV 1 1 PASS rs560171977 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 10487846 10487846 G T 1 0 0 0 0 1 0 0 0 885 1194 42 2 2 APCDD1 18 10487846 Missense_Mutation SNP G C3L-00144_T 1704059 10487846 69885439 1433 5504 GREB1L 0 . GRCh38 18 21508465 21508465 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.4609G>T p.Ala1537Ser p.A1537S ENST00000580732 27/33 454 314 140 385 385 0 strelka-varscan-mutect GREB1L,missense_variant,p.Ala1537Ser,ENST00000580732,;GREB1L,missense_variant,p.Ala1537Ser,ENST00000424526,NM_001142966.1;GREB1L,missense_variant,p.Ala1428Ser,ENST00000269218,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578955,; T ENST00000580732 Transcript missense_variant 4990/8749 4609/5772 1537/1923 A/S Gcc/Tcc 1 1 GREB1L HGNC HGNC:31042 protein_coding YES CCDS45836.1 ENSP00000464162 Q9C091 UPI0001642876 deleterious(0) 27/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF12 MODERATE 1 SNV 5 1 PASS rs1211371878 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 21508465 21508465 G T 1 0 0 0 0 1 0 0 0 6640 1087 38 1 1 GREB1L 18 21508465 Missense_Mutation SNP G C3L-00144_T 11020619 21508465 58864820 1434 5505 DSC1 0 . GRCh38 18 31154800 31154800 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.601G>T p.Asp201Tyr p.D201Y ENST00000257198 5/16 145 99 46 155 154 1 strelka-varscan-mutect DSC1,missense_variant,p.Asp201Tyr,ENST00000257197,NM_004948.3;DSC1,missense_variant,p.Asp201Tyr,ENST00000257198,NM_024421.2;DSCAS,intron_variant,,ENST00000581836,; A ENST00000257198 Transcript missense_variant 863/4225 601/2685 201/894 D/Y Gac/Tac 1 -1 DSC1 HGNC HGNC:3035 protein_coding YES CCDS11894.1 ENSP00000257198 Q08554 UPI000006DF10 NM_024421.2 deleterious(0) 5/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF8,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31154800 31154800 C A 1 0 0 0 0 1 0 0 0 4586 826 29 2 2 DSC1 18 31154800 Missense_Mutation SNP C C3L-00144_T 9646335 31154800 49218485 1435 5506 RNF165 0 . GRCh38 18 46433380 46433380 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.252G>T p.= p.P84P ENST00000269439 2/8 353 232 121 290 288 2 strelka-varscan-mutect RNF165,synonymous_variant,p.=,ENST00000269439,NM_152470.2;RNF165,synonymous_variant,p.=,ENST00000593230,;RNF165,intron_variant,,ENST00000543885,NM_001256758.1;RNF165,intron_variant,,ENST00000586604,; T ENST00000269439 Transcript synonymous_variant 303/7596 252/1041 84/346 P ccG/ccT 1 1 RNF165 HGNC HGNC:31696 protein_coding YES CCDS32823.1 ENSP00000269439 Q6ZSG1 A0A059NXK6 UPI00001C0E38 NM_152470.2 2/8 hmmpanther:PTHR22763:SF76,hmmpanther:PTHR22763 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 46433380 46433380 G T 1 0 0 0 0 0 0 0 1 13633 1074 38 1 1 RNF165 18 46433380 Silent SNP G C3L-00144_T 15278580 46433380 33939905 1436 5507 CTIF 0 . GRCh38 18 48663800 48663800 + Missense_Mutation SNP G G C rs539460174 C3L-00144_T C3L-00144_N G G c.301G>C p.Ala101Pro p.A101P ENST00000382998 5/13 252 175 77 252 252 0 strelka-varscan-mutect CTIF,missense_variant,p.Ala101Pro,ENST00000256413,NM_014772.2;CTIF,missense_variant,p.Ala101Pro,ENST00000382998,NM_001142397.1;CTIF,missense_variant,p.Ala101Pro,ENST00000591387,;CTIF,missense_variant,p.Ala101Pro,ENST00000587752,;CTIF,missense_variant,p.Ala101Pro,ENST00000588345,;CTIF,missense_variant,p.Ala117Pro,ENST00000591412,;CTIF,non_coding_transcript_exon_variant,,ENST00000589585,;RP11-426J5.1,upstream_gene_variant,,ENST00000623145,; C ENST00000382998 Transcript missense_variant 558/4407 301/1803 101/600 A/P Gcg/Ccg rs539460174 1 1 CTIF HGNC HGNC:23925 protein_coding YES CCDS45864.1 ENSP00000372459 O43310 UPI0000074650 NM_001142397.1 deleterious_low_confidence(0) 5/13 MODERATE 1 SNV 1 1 PASS rs539460174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 48663800 48663800 G C 1 0 0 0 0 1 0 0 0 3819 1203 42 4 4 CTIF 18 48663800 Missense_Mutation SNP G C3L-00144_T 2230420 48663800 31709485 1437 5508 C18orf54 0 . GRCh38 18 54362325 54362325 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.966G>T p.Leu322Phe p.L322F ENST00000620105 4/9 117 86 31 103 103 0 strelka-varscan-mutect C18orf54,missense_variant,p.Leu322Phe,ENST00000620105,NM_001288981.1,NM_001288980.1;C18orf54,missense_variant,p.Leu322Phe,ENST00000382911,;C18orf54,intron_variant,,ENST00000300091,NM_173529.5,NM_001288982.1;C18orf54,intron_variant,,ENST00000578138,;STARD6,upstream_gene_variant,,ENST00000581310,;STARD6,upstream_gene_variant,,ENST00000577499,;STARD6,upstream_gene_variant,,ENST00000584040,;C18orf54,upstream_gene_variant,,ENST00000582188,; T ENST00000620105 Transcript missense_variant 1268/5693 966/1602 322/533 L/F ttG/ttT 1 1 C18orf54 HGNC HGNC:13796 protein_coding YES CCDS74223.1 ENSP00000477654 Q8IYD9 UPI000022A74A NM_001288981.1,NM_001288980.1 tolerated(0.34) 4/9 hmmpanther:PTHR35079:SF1,hmmpanther:PTHR35079 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54362325 54362325 G T 1 0 0 0 0 1 0 0 0 1900 1281 45 2 2 C18orf54 18 54362325 Missense_Mutation SNP G C3L-00144_T 5698525 54362325 26010960 1438 5509 BOD1L2 0 . GRCh38 18 57147559 57147559 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.247C>A p.His83Asn p.H83N ENST00000585477 1/1 265 187 78 241 241 0 strelka-varscan-mutect BOD1L2,missense_variant,p.His83Asn,ENST00000585477,NM_001257964.1;CTD-2526M8.3,upstream_gene_variant,,ENST00000590942,; A ENST00000585477 Transcript missense_variant 498/3239 247/519 83/172 H/N Cat/Aat 1 1 BOD1L2 HGNC HGNC:28505 protein_coding YES CCDS59322.1 ENSP00000467843 Q8IYS8 UPI000006F702 NM_001257964.1 deleterious(0.02) 1/1 PD486480,Pfam_domain:PF05205,hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF5 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 57147559 57147559 C A 1 0 0 0 0 1 0 0 0 1640 478 17 2 2 BOD1L2 18 57147559 Missense_Mutation SNP C C3L-00144_T 2785234 57147559 23225726 1439 5510 PHLPP1 0 . GRCh38 18 62972519 62972519 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3566G>T p.Cys1189Phe p.C1189F ENST00000262719 15/17 62 44 18 59 59 0 strelka-varscan-mutect PHLPP1,missense_variant,p.Cys1189Phe,ENST00000262719,NM_194449.3; T ENST00000262719 Transcript missense_variant 3800/6390 3566/5154 1189/1717 C/F tGt/tTt 1 1 PHLPP1 HGNC HGNC:20610 protein_coding YES CCDS45881.2 ENSP00000262719 O60346 UPI000051AE2E NM_194449.3 deleterious(0) 15/17 Gene3D:3.60.40.10,Pfam_domain:PF00481,PROSITE_profiles:PS51746,SMART_domains:SM00332,Superfamily_domains:SSF81606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 62972519 62972519 G T 1 0 0 0 0 1 0 0 0 11942 1391 48 2 2 PHLPP1 18 62972519 Missense_Mutation SNP G C3L-00144_T 5824960 62972519 17400766 1440 5511 SERPINB5 0 . GRCh38 18 63503376 63503376 + Missense_Mutation SNP C C A rs780437142 C3L-00144_T C3L-00144_N C C c.782C>A p.Pro261His p.P261H ENST00000382771 7/7 308 234 74 284 284 0 strelka-varscan-mutect SERPINB5,missense_variant,p.Pro261His,ENST00000382771,NM_002639.4;SERPINB5,non_coding_transcript_exon_variant,,ENST00000464346,;SERPINB5,downstream_gene_variant,,ENST00000465652,; A ENST00000382771 Transcript missense_variant 1074/2783 782/1128 261/375 P/H cCc/cAc rs780437142 1 1 SERPINB5 HGNC HGNC:8949 protein_coding YES CCDS32839.1 ENSP00000372221 P36952 A0A024R2B6 UPI0000201E51 NM_002639.4 deleterious(0) 7/7 Gene3D:2.30.39.10,Pfam_domain:PF00079,Prints_domain:PR00676,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF55,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs780437142 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 63503376 63503376 C A 1 0 0 0 0 1 0 0 0 14380 623 22 2 2 SERPINB5 18 63503376 Missense_Mutation SNP C C3L-00144_T 530857 63503376 16869909 1441 5512 CDH19 0 . GRCh38 18 66505131 66505132 + Frame_Shift_Ins INS - - C novel C3L-00144_T C3L-00144_N - - c.1999dupG p.Glu667GlyfsTer11 p.E667Gfs*11 ENST00000262150 12/12 110 83 27 106 106 0 sindel-varindel-pindel CDH19,frameshift_variant,p.Glu667GlyfsTer11,ENST00000262150,NM_021153.3;CDH19,3_prime_UTR_variant,,ENST00000540086,NM_001271028.1;CDH19,3_prime_UTR_variant,,ENST00000579658,; C ENST00000262150 Transcript frameshift_variant 2292-2293/6341 1999-2000/2319 667/772 E/GX gaa/gGaa 1 -1 CDH19 HGNC HGNC:1758 protein_coding YES CCDS11994.1 ENSP00000262150 Q9H159 UPI0000048ECF NM_021153.3 12/12 Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF323 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 12 66505131 66505131 - C 1 0 1 1 0 0 0 0 0 2807 1783 62 0 0 CDH19 18 66505131 Frame_Shift_Ins INS - C3L-00144_T 3001755 66505131 13868154 1442 5513 CDH19 0 . GRCh38 18 66572061 66572061 + Missense_Mutation SNP G G T rs759627014 C3L-00144_T C3L-00144_N G G c.144C>A p.Asn48Lys p.N48K ENST00000262150 2/12 148 100 48 114 114 0 strelka-varscan-mutect CDH19,missense_variant,p.Asn48Lys,ENST00000262150,NM_021153.3;CDH19,missense_variant,p.Asn48Lys,ENST00000540086,NM_001271028.1;CDH19,missense_variant,p.Asn37Lys,ENST00000454642,;CDH19,missense_variant,p.Asn48Lys,ENST00000580157,;CDH19,missense_variant,p.Asn48Lys,ENST00000579658,; T ENST00000262150 Transcript missense_variant 437/6341 144/2319 48/772 N/K aaC/aaA rs759627014,COSM1523503,COSM5201509 1 -1 CDH19 HGNC HGNC:1758 protein_coding YES CCDS11994.1 ENSP00000262150 Q9H159 UPI0000048ECF NM_021153.3 deleterious(0.04) 2/12 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF323 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs759627014 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 66572061 66572061 G T 1 0 0 0 0 1 0 0 0 2807 1252 44 2 2 CDH19 18 66572061 Missense_Mutation SNP G C3L-00144_T 66930 66572061 13801224 1443 5514 CBLN2 0 . GRCh38 18 72538655 72538655 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.475C>G p.Gln159Glu p.Q159E ENST00000269503 4/5 155 116 39 126 126 0 strelka-varscan-mutect CBLN2,missense_variant,p.Gln159Glu,ENST00000269503,NM_182511.3;CBLN2,missense_variant,p.Gln159Glu,ENST00000585159,;CBLN2,missense_variant,p.Gln43Glu,ENST00000584764,;CBLN2,missense_variant,p.Gln45Glu,ENST00000581073,;CBLN2,splice_region_variant,,ENST00000583651,;CBLN2,splice_region_variant,,ENST00000581425,; C ENST00000269503 Transcript missense_variant,splice_region_variant 1249/2945 475/675 159/224 Q/E Cag/Gag 1 -1 CBLN2 HGNC HGNC:1544 protein_coding YES CCDS11999.1 ENSP00000269503 Q8IUK8 A0A024R380 UPI0000032E73 NM_182511.3 tolerated(0.08) 4/5 PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF50,hmmpanther:PTHR22923,Gene3D:2.60.120.40,Pfam_domain:PF00386,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 72538655 72538655 G C 1 0 0 0 0 1 0 0 0 2406 1362 47 4 4 CBLN2 18 72538655 Missense_Mutation SNP G C3L-00144_T 5966594 72538655 7834630 1444 5515 AP3D1 0 . GRCh38 19 2132578 2132578 + Missense_Mutation SNP C C A rs374552258 C3L-00144_T C3L-00144_N C C c.355G>T p.Asp119Tyr p.D119Y ENST00000355272 5/32 221 170 51 158 157 1 strelka-varscan-mutect AP3D1,missense_variant,p.Asp119Tyr,ENST00000355272,NM_001261826.1;AP3D1,missense_variant,p.Asp119Tyr,ENST00000345016,NM_003938.6;AP3D1,splice_region_variant,,ENST00000591284,;AP3D1,upstream_gene_variant,,ENST00000590683,; A ENST00000355272 Transcript missense_variant,splice_region_variant 562/5034 355/3648 119/1215 D/Y Gac/Tac rs374552258 1 -1 AP3D1 HGNC HGNC:568 protein_coding YES CCDS58638.1 ENSP00000347416 O14617 UPI0000202F99 NM_001261826.1 deleterious(0) 5/32 hmmpanther:PTHR22781,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037092,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs374552258 . 0 201 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 3 1 12 2132578 2132578 C A 1 0 0 0 0 1 0 0 0 862 869 30 2 2 AP3D1 19 2132578 Missense_Mutation SNP C C3L-00144_T 2132578 56485038 1445 5516 TMPRSS9 0 . GRCh38 19 2399070 2399070 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.289C>A p.Pro97Thr p.P97T ENST00000332578 3/17 237 219 18 208 207 1 strelka-varscan-mutect TMPRSS9,missense_variant,p.Pro97Thr,ENST00000332578,NM_182973.1;TMPRSS9,missense_variant,p.Pro97Thr,ENST00000613480,;TMPRSS9,downstream_gene_variant,,ENST00000592650,;TMPRSS9,non_coding_transcript_exon_variant,,ENST00000395264,; A ENST00000332578 Transcript missense_variant 289/3331 289/3180 97/1059 P/T Ccc/Acc 1 1 TMPRSS9 HGNC HGNC:30079 protein_coding YES CCDS12088.1 ENSP00000330264 Q7Z410 UPI00001B4EC6 NM_182973.1 tolerated(0.47) 3/17 PIRSF_domain:PIRSF037931 MODERATE 1 SNV 1 1 PASS rs1329684326 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 2399070 2399070 C A 1 0 0 0 0 1 0 0 0 16729 507 18 2 2 TMPRSS9 19 2399070 Missense_Mutation SNP C C3L-00144_T 266492 2399070 56218546 1446 5517 ZNF554 0 . GRCh38 19 2834192 2834192 + Frame_Shift_Del DEL G G - rs200374686 C3L-00144_T C3L-00144_N G G c.958delG p.Ala320GlnfsTer20 p.A320Qfs*20 ENST00000317243 5/5 184 162 22 173 173 0 sindel-varindel-pindel ZNF554,frameshift_variant,p.Ala320GlnfsTer20,ENST00000317243,NM_001102651.1;ZNF554,downstream_gene_variant,,ENST00000591265,;ZNF554,3_prime_UTR_variant,,ENST00000590116,;ZNF554,non_coding_transcript_exon_variant,,ENST00000588534,; - ENST00000317243 Transcript frameshift_variant 1155/2736 957/1617 319/538 T/X acG/ac rs200374686 1 1 ZNF554 HGNC HGNC:26629 protein_coding YES CCDS42462.1 ENSP00000321132 Q86TJ5 UPI000000DC5D NM_001102651.1 5/5 Gene3D:3.30.160.60,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF56,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 2834192 2834192 G - 1 0 1 0 1 0 0 0 0 18559 1103 39 0 0 ZNF554 19 2834192 Frame_Shift_Del DEL G C3L-00144_T 435122 2834192 55783424 1447 5518 SMIM24 0 . GRCh38 19 3480417 3480417 + Missense_Mutation SNP G G T rs750433493 C3L-00144_T C3L-00144_N G G c.47C>A p.Ser16Tyr p.S16Y ENST00000215531 1/4 83 71 12 95 95 0 strelka-varscan-mutect SMIM24,missense_variant,p.Ser16Tyr,ENST00000215531,NM_001136503.1;SMIM24,upstream_gene_variant,,ENST00000587847,;SMIM24,upstream_gene_variant,,ENST00000591708,;SMIM24,non_coding_transcript_exon_variant,,ENST00000586804,; T ENST00000215531 Transcript missense_variant 126/1329 47/393 16/130 S/Y tCc/tAc rs750433493 1 -1 SMIM24 HGNC HGNC:37244 protein_coding YES CCDS45915.1 ENSP00000215531 O75264 UPI000015B2DA NM_001136503.1 deleterious(0.01) 1/4 Pfam_domain:PF15807,hmmpanther:PTHR15296,hmmpanther:PTHR15296:SF2,Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 1 1 PASS rs750433493 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 3480417 3480417 G T 1 0 0 0 0 1 0 0 0 15110 1174 41 2 2 SMIM24 19 3480417 Missense_Mutation SNP G C3L-00144_T 646225 3480417 55137199 1448 5519 SHD 0 . GRCh38 19 4290539 4290539 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.929C>A p.Pro310His p.P310H ENST00000543264 6/6 224 138 86 192 192 0 strelka-varscan-mutect SHD,missense_variant,p.Pro310His,ENST00000543264,NM_020209.3;SHD,missense_variant,p.Pro270His,ENST00000599689,;TMIGD2,downstream_gene_variant,,ENST00000301272,NM_144615.2;TMIGD2,downstream_gene_variant,,ENST00000595645,NM_001169126.1;TMIGD2,downstream_gene_variant,,ENST00000600114,NM_001308232.1;TMIGD2,downstream_gene_variant,,ENST00000600349,;SHD,downstream_gene_variant,,ENST00000600475,;SHD,3_prime_UTR_variant,,ENST00000593383,;SHD,non_coding_transcript_exon_variant,,ENST00000597466,; A ENST00000543264 Transcript missense_variant 2392/2577 929/1023 310/340 P/H cCc/cAc 1 1 SHD HGNC HGNC:30633 protein_coding YES CCDS12125.1 ENSP00000446058 Q96IW2 UPI000007030D NM_020209.3 deleterious(0) 6/6 PROSITE_profiles:PS50001,hmmpanther:PTHR15127,hmmpanther:PTHR15127:SF33,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 4290539 4290539 C A 1 0 0 0 0 1 0 0 0 14535 623 22 2 2 SHD 19 4290539 Missense_Mutation SNP C C3L-00144_T 810122 4290539 54327077 1449 5520 KDM4B 0 . GRCh38 19 5150358 5150358 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3022G>T p.Val1008Leu p.V1008L ENST00000159111 22/23 156 121 35 128 128 0 strelka-varscan-mutect KDM4B,missense_variant,p.Val1042Leu,ENST00000611640,;KDM4B,missense_variant,p.Val1008Leu,ENST00000159111,NM_015015.2;KDM4B,missense_variant,p.Val1042Leu,ENST00000536461,;KDM4B,splice_region_variant,,ENST00000589104,; T ENST00000159111 Transcript missense_variant,splice_region_variant 3240/5593 3022/3291 1008/1096 V/L Gtg/Ttg 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 deleterious(0.01) 22/23 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30,SMART_domains:SM00333,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 5150358 5150358 G T 1 0 0 0 0 1 0 0 0 8047 1275 44 2 2 KDM4B 19 5150358 Missense_Mutation SNP G C3L-00144_T 859819 5150358 53467258 1450 5521 ARHGEF18 0 . GRCh38 19 7444324 7444324 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.917G>T p.Cys306Phe p.C306F ENST00000359920 4/20 399 253 146 351 349 2 strelka-varscan-mutect ARHGEF18,missense_variant,p.Cys306Phe,ENST00000359920,NM_001130955.1;ARHGEF18,missense_variant,p.Cys148Phe,ENST00000319670,NM_015318.3;CTD-2207O23.3,missense_variant,p.Cys240Phe,ENST00000617428,;ARHGEF18,upstream_gene_variant,,ENST00000594665,;ARHGEF18,downstream_gene_variant,,ENST00000599752,;ARHGEF18,non_coding_transcript_exon_variant,,ENST00000595600,; T ENST00000359920 Transcript missense_variant 1170/5733 917/3522 306/1173 C/F tGc/tTc 1 1 ARHGEF18 HGNC HGNC:17090 protein_coding YES CCDS45946.1 ENSP00000352995 Q6ZSZ5 UPI0000D6170D NM_001130955.1 deleterious(0.01) 4/20 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF120,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7444324 7444324 G T 1 0 0 0 0 1 0 0 0 1031 1319 46 2 2 ARHGEF18 19 7444324 Missense_Mutation SNP G C3L-00144_T 2293966 7444324 51173292 1451 5522 CLEC4G 0 . GRCh38 19 7731302 7731302 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.184G>A p.Ala62Thr p.A62T ENST00000328853 3/9 182 154 28 134 134 0 strelka-varscan-mutect CLEC4G,missense_variant,p.Ala62Thr,ENST00000328853,NM_198492.3,NM_001244856.1;CLEC4G,missense_variant,p.Ala104Thr,ENST00000599020,;CLEC4G,non_coding_transcript_exon_variant,,ENST00000598081,; T ENST00000328853 Transcript missense_variant 253/1360 184/882 62/293 A/T Gcg/Acg 1 -1 CLEC4G HGNC HGNC:24591 protein_coding YES CCDS12185.1 ENSP00000327599 Q6UXB4 Q08G24 UPI000004C65D NM_198492.3,NM_001244856.1 tolerated(0.33) 3/9 hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF245 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7731302 7731302 C T 1 0 0 0 0 1 0 0 0 3285 739 26 3 3 CLEC4G 19 7731302 Missense_Mutation SNP C C3L-00144_T 286978 7731302 50886314 1452 5523 ELAVL1 0 . GRCh38 19 7963656 7963656 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.808G>T p.Val270Phe p.V270F ENST00000407627 6/6 360 237 123 306 305 1 strelka-varscan-mutect ELAVL1,missense_variant,p.Val270Phe,ENST00000407627,NM_001419.2;ELAVL1,missense_variant,p.Val270Phe,ENST00000596459,;ELAVL1,3_prime_UTR_variant,,ENST00000593807,;ELAVL1,intron_variant,,ENST00000596154,;CTD-3193O13.14,downstream_gene_variant,,ENST00000595107,; A ENST00000407627 Transcript missense_variant 938/6015 808/981 270/326 V/F Gtc/Ttc 1 -1 ELAVL1 HGNC HGNC:3312 protein_coding YES CCDS12193.1 ENSP00000385269 Q15717 UPI0000129E74 NM_001419.2 deleterious(0) 6/6 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF351,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 7963656 7963656 C A 1 0 0 0 0 1 0 0 0 4882 536 19 1 1 ELAVL1 19 7963656 Missense_Mutation SNP C C3L-00144_T 232354 7963656 50653960 1453 5524 MUC16 0 . GRCh38 19 8903193 8903193 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.38521C>A p.Pro12841Thr p.P12841T ENST00000397910 33/84 157 114 43 155 155 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro12841Thr,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 38725/43816 38521/43524 12841/14507 P/T Cca/Aca 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 33/84 Low_complexity_(Seg):seg,hmmpanther:PTHR14672 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8903193 8903193 G T 1 0 0 0 0 1 0 0 0 9972 1174 41 2 2 MUC16 19 8903193 Missense_Mutation SNP G C3L-00144_T 939537 8903193 49714423 1454 5525 MUC16 0 . GRCh38 19 8937108 8937108 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.33847A>T p.Arg11283Trp p.R11283W ENST00000397910 5/84 202 147 55 165 164 1 strelka-varscan-mutect MUC16,missense_variant,p.Arg11283Trp,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 34051/43816 33847/43524 11283/14507 R/W Agg/Tgg 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 MODERATE 1 SNV 5 1 PASS rs1230555820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 8937108 8937108 T A 1 0 0 0 0 1 0 0 0 9972 1608 56 4 4 MUC16 19 8937108 Missense_Mutation SNP T C3L-00144_T 33915 8937108 49680508 1455 5526 MUC16 0 . GRCh38 19 8946055 8946055 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.30715G>A p.Glu10239Lys p.E10239K ENST00000397910 3/84 104 56 48 92 91 1 strelka-varscan-mutect MUC16,missense_variant,p.Glu10239Lys,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 30919/43816 30715/43524 10239/14507 E/K Gag/Aag COSM384915,COSM384916 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8946055 8946055 C T 1 0 0 0 0 1 0 0 0 9972 864 30 3 3 MUC16 19 8946055 Missense_Mutation SNP C C3L-00144_T 8947 8946055 49671561 1456 5527 MUC16 0 . GRCh38 19 8952762 8952762 + Nonsense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.24008C>A p.Ser8003Ter p.S8003* ENST00000397910 3/84 141 122 19 145 145 0 strelka-varscan-mutect MUC16,stop_gained,p.Ser8003Ter,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript stop_gained 24212/43816 24008/43524 8003/14507 S/* tCa/tAa COSM3542522,COSM3542523,COSM3542524 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg 1,1,1 HIGH 1 SNV 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 8952762 8952762 G T 1 0 0 0 0 0 1 0 0 9972 1294 45 2 2 MUC16 19 8952762 Nonsense_Mutation SNP G C3L-00144_T 6707 8952762 49664854 1457 5528 MUC16 0 . GRCh38 19 8955222 8955222 + Missense_Mutation SNP G G T rs370133928 C3L-00144_T C3L-00144_N G G c.21548C>A p.Ala7183Glu p.A7183E ENST00000397910 3/84 103 72 31 91 91 0 strelka-varscan-mutect MUC16,missense_variant,p.Ala7183Glu,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 21752/43816 21548/43524 7183/14507 A/E gCg/gAg rs370133928,COSM4138277,COSM4138278,COSM4138279 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs370133928 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8955222 8955222 G T 1 0 0 0 0 1 0 0 0 9972 1087 38 1 1 MUC16 19 8955222 Missense_Mutation SNP G C3L-00144_T 2460 8955222 49662394 1458 5529 OR1M1 0 . GRCh38 19 9093446 9093446 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.202C>A p.Leu68Met p.L68M ENST00000429566 1/1 128 80 48 98 98 0 strelka-varscan-mutect OR1M1,missense_variant,p.Leu68Met,ENST00000429566,NM_001004456.1; A ENST00000429566 Transcript missense_variant 268/1035 202/942 68/313 L/M Ctg/Atg 1 1 OR1M1 HGNC HGNC:8220 protein_coding YES CCDS32896.1 ENSP00000401966 Q8NGA1 UPI0000041C29 NM_001004456.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF295,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 9093446 9093446 C A 1 0 0 0 0 1 0 0 0 11046 680 24 2 2 OR1M1 19 9093446 Missense_Mutation SNP C C3L-00144_T 138224 9093446 49524170 1459 5530 OR7G1 0 . GRCh38 19 9115483 9115483 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.281A>T p.Tyr94Phe p.Y94F ENST00000541538 1/1 207 128 79 167 167 0 strelka-varscan-mutect OR7G1,missense_variant,p.Tyr94Phe,ENST00000541538,NM_001005192.2; A ENST00000541538 Transcript missense_variant 281/936 281/936 94/311 Y/F tAc/tTc 1 -1 OR7G1 HGNC HGNC:8465 protein_coding YES CCDS32898.2 ENSP00000444134 Q8NGA0 A0A126GVS6 UPI0000041C27 NM_001005192.2 deleterious(0.03) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF320,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs151211604 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 9115483 9115483 T A 1 0 0 0 0 1 0 0 0 11292 1638 57 4 4 OR7G1 19 9115483 Missense_Mutation SNP T C3L-00144_T 22037 9115483 49502133 1460 5531 ZNF560 0 . GRCh38 19 9469117 9469117 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.600T>A p.Asn200Lys p.N200K ENST00000301480 9/10 191 135 56 213 211 2 strelka-varscan-mutect ZNF560,missense_variant,p.Asn200Lys,ENST00000301480,NM_152476.2;ZNF560,non_coding_transcript_exon_variant,,ENST00000585974,; T ENST00000301480 Transcript missense_variant 814/2654 600/2373 200/790 N/K aaT/aaA 1 -1 ZNF560 HGNC HGNC:26484 protein_coding YES CCDS12214.1 ENSP00000301480 Q96MR9 UPI000013E720 NM_152476.2 deleterious(0.02) 9/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 9469117 9469117 A T 1 0 0 0 0 1 0 0 0 18565 214 8 4 4 ZNF560 19 9469117 Missense_Mutation SNP A C3L-00144_T 353634 9469117 49148499 1461 5532 COL5A3 0 . GRCh38 19 9985859 9985859 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2389G>T p.Gly797Ter p.G797* ENST00000264828 31/67 136 94 42 102 102 0 strelka-varscan-mutect COL5A3,stop_gained,p.Gly797Ter,ENST00000264828,NM_015719.3; A ENST00000264828 Transcript stop_gained 2475/6174 2389/5238 797/1745 G/* Gga/Tga 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 31/67 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 9985859 9985859 C A 1 0 0 0 0 0 1 0 0 3487 690 24 2 2 COL5A3 19 9985859 Nonsense_Mutation SNP C C3L-00144_T 516742 9985859 48631757 1462 5533 RDH8 0 . GRCh38 19 10018761 10018761 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.353C>A p.Pro118His p.P118H ENST00000591589 3/6 92 71 21 78 77 1 strelka-varscan-mutect RDH8,missense_variant,p.Pro118His,ENST00000591589,NM_015725.2;RDH8,upstream_gene_variant,,ENST00000587782,;RDH8,intron_variant,,ENST00000589570,; A ENST00000591589 Transcript missense_variant 542/1715 353/996 118/331 P/H cCc/cAc COSM4489847,COSM4489848 1 1 RDH8 HGNC HGNC:14423 protein_coding YES CCDS12223.2 ENSP00000466058 K7ELF7 UPI000059D661 NM_015725.2 deleterious(0) 3/6 hmmpanther:PTHR24322:SF323,hmmpanther:PTHR24322,Pfam_domain:PF00106,PIRSF_domain:PIRSF000095,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 10018761 10018761 C A 1 0 0 0 0 1 0 0 0 13365 623 22 2 2 RDH8 19 10018761 Missense_Mutation SNP C C3L-00144_T 32902 10018761 48598855 1463 5534 CACNA1A 0 . GRCh38 19 13298683 13298683 + Missense_Mutation SNP G G A rs768873463 C3L-00144_T C3L-00144_N G G c.2950C>T p.Arg984Trp p.R984W ENST00000360228 19/47 134 102 32 141 141 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Arg985Trp,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Arg985Trp,ENST00000635895,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000637769,;CACNA1A,missense_variant,p.Arg984Trp,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Arg988Trp,ENST00000614285,;CACNA1A,missense_variant,p.Arg938Trp,ENST00000637736,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000636389,;CACNA1A,missense_variant,p.Arg988Trp,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Arg988Trp,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Arg986Trp,ENST00000573710,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000635727,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000636012,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000637276,;CACNA1A,missense_variant,p.Arg986Trp,ENST00000637927,;CACNA1A,missense_variant,p.Arg985Trp,ENST00000636549,NM_001174080.1; A ENST00000360228 Transcript missense_variant 3185/8627 2950/7521 984/2506 R/W Cgg/Tgg rs768873463 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0) 19/47 Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59 MODERATE 1 SNV 1 1 PASS rs768873463 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 13298683 13298683 G A 1 0 0 0 0 1 0 0 0 2226 1115 39 1 1 CACNA1A 19 13298683 Missense_Mutation SNP G C3L-00144_T 3279922 13298683 45318933 1464 5535 NANOS3 0 . GRCh38 19 13877321 13877321 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.73G>T p.Gly25Cys p.G25C ENST00000339133 1/2 173 131 42 187 187 0 strelka-varscan-mutect NANOS3,missense_variant,p.Gly25Cys,ENST00000397555,;NANOS3,missense_variant,p.Gly25Cys,ENST00000339133,NM_001098622.2;MIR181D,downstream_gene_variant,,ENST00000384853,;MIR181C,downstream_gene_variant,,ENST00000384881,;NANOS3,intron_variant,,ENST00000591727,;NANOS3,intron_variant,,ENST00000591161,; T ENST00000339133 Transcript missense_variant 75/581 73/579 25/192 G/C Ggt/Tgt 1 1 NANOS3 HGNC HGNC:22048 protein_coding YES CCDS42511.1 ENSP00000341992 P60323 UPI0000366D46 NM_001098622.2 deleterious(0.04) 1/2 hmmpanther:PTHR12887 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 13877321 13877321 G T 1 0 0 0 0 1 0 0 0 10162 1232 43 2 2 NANOS3 19 13877321 Missense_Mutation SNP G C3L-00144_T 578638 13877321 44740295 1465 5536 OR10H1 0 . GRCh38 19 15807199 15807199 + Missense_Mutation SNP G G T rs375583661 C3L-00144_T C3L-00144_N G G c.839C>A p.Thr280Lys p.T280K ENST00000334920 1/1 165 147 18 154 154 0 varscan-mutect OR10H1,missense_variant,p.Thr280Lys,ENST00000334920,NM_013940.2; T ENST00000334920 Transcript missense_variant 928/1124 839/957 280/318 T/K aCg/aAg rs375583661 1 -1 OR10H1 HGNC HGNC:8172 protein_coding YES CCDS12335.1 ENSP00000335596 Q9Y4A9 A0A126GVU5 UPI000004CA3D NM_013940.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF122,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs375583661 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 15807199 15807199 G T 1 0 0 0 0 1 0 0 0 10982 1145 40 1 1 OR10H1 19 15807199 Missense_Mutation SNP G C3L-00144_T 1929878 15807199 42810417 1466 5537 CYP4F2 0 . GRCh38 19 15879848 15879848 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1165C>A p.Leu389Met p.L389M ENST00000221700 10/13 359 271 88 287 287 0 strelka-varscan-mutect CYP4F2,missense_variant,p.Leu389Met,ENST00000221700,NM_001082.4;CYP4F2,missense_variant,p.Leu389Met,ENST00000011989,;CYP4F2,intron_variant,,ENST00000589654,;CYP4F2,non_coding_transcript_exon_variant,,ENST00000392846,;CYP4F2,non_coding_transcript_exon_variant,,ENST00000592710,;CYP4F2,downstream_gene_variant,,ENST00000587671,; T ENST00000221700 Transcript missense_variant 1261/2407 1165/1563 389/520 L/M Ctg/Atg 1 -1 CYP4F2 HGNC HGNC:2645 protein_coding YES CCDS12336.1 ENSP00000221700 P78329 UPI0000052BE6 NM_001082.4 deleterious(0.03) 10/13 hmmpanther:PTHR24291:SF45,hmmpanther:PTHR24291,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00385 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 15879848 15879848 G T 1 0 0 0 0 1 0 0 0 3991 991 35 2 2 CYP4F2 19 15879848 Missense_Mutation SNP G C3L-00144_T 72649 15879848 42737768 1467 5538 MYO9B 0 . GRCh38 19 17206001 17206001 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.5106A>T p.= p.V1702V ENST00000595618 32/40 60 55 5 59 59 0 strelka-varscan-mutect MYO9B,synonymous_variant,p.=,ENST00000595618,NM_001130065.1;MYO9B,synonymous_variant,p.=,ENST00000594824,NM_004145.3;MYO9B,synonymous_variant,p.=,ENST00000397274,;MYO9B,synonymous_variant,p.=,ENST00000595641,;MYO9B,upstream_gene_variant,,ENST00000597073,;MYO9B,upstream_gene_variant,,ENST00000596942,;MYO9B,upstream_gene_variant,,ENST00000598419,;CTD-3032J10.3,downstream_gene_variant,,ENST00000601929,;MYO9B,3_prime_UTR_variant,,ENST00000602158,;MYO9B,non_coding_transcript_exon_variant,,ENST00000599420,;MYO9B,intron_variant,,ENST00000593533,;MYO9B,upstream_gene_variant,,ENST00000597572,;MYO9B,upstream_gene_variant,,ENST00000597881,; T ENST00000595618 Transcript synonymous_variant 5258/7623 5106/6069 1702/2022 V gtA/gtT 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 32/40 Gene3D:1.10.555.10,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.29717 1 1 1 1 0 T 2 4 12 17206001 17206001 A T 1 0 0 0 0 0 0 0 1 10086 407 15 4 4 MYO9B 19 17206001 Silent SNP A C3L-00144_T 1326153 17206001 41411615 1468 5539 FAM129C 0 . GRCh38 19 17539357 17539357 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.815C>A p.Ala272Glu p.A272E ENST00000335393 8/16 131 118 13 110 110 0 strelka-varscan-mutect FAM129C,missense_variant,p.Ala272Glu,ENST00000335393,NM_001321826.1,NM_173544.4;FAM129C,missense_variant,p.Ala272Glu,ENST00000595684,;FAM129C,missense_variant,p.Ala272Glu,ENST00000332386,NM_001098524.1;FAM129C,missense_variant,p.Ala241Glu,ENST00000601861,;FAM129C,missense_variant,p.Ala241Glu,ENST00000599164,NM_001321827.1;FAM129C,missense_variant,p.Ala241Glu,ENST00000599124,;FAM129C,missense_variant,p.Ala218Glu,ENST00000600871,;FAM129C,5_prime_UTR_variant,,ENST00000449408,;FAM129C,downstream_gene_variant,,ENST00000597887,;FAM129C,missense_variant,p.Ala241Glu,ENST00000600519,;FAM129C,upstream_gene_variant,,ENST00000595601,;FAM129C,downstream_gene_variant,,ENST00000599819,; A ENST00000335393 Transcript missense_variant 953/2508 815/2094 272/697 A/E gCg/gAg 1 1 FAM129C HGNC HGNC:24130 protein_coding YES CCDS12362.1 ENSP00000335040 Q86XR2 UPI0000246FFF NM_001321826.1,NM_173544.4 tolerated(0.69) 8/16 hmmpanther:PTHR14392:SF4,hmmpanther:PTHR14392 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17539357 17539357 C A 1 0 0 0 0 1 0 0 0 5288 768 27 1 1 FAM129C 19 17539357 Missense_Mutation SNP C C3L-00144_T 333356 17539357 41078259 1469 5540 MAP1S 0 . GRCh38 19 17727969 17727969 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2585C>T p.Thr862Ile p.T862I ENST00000324096 5/7 117 104 13 79 79 0 strelka-varscan-mutect MAP1S,missense_variant,p.Thr862Ile,ENST00000324096,NM_018174.4;MAP1S,missense_variant,p.Thr836Ile,ENST00000544059,NM_001308363.1;MAP1S,intron_variant,,ENST00000597735,;MAP1S,intron_variant,,ENST00000597000,;MAP1S,downstream_gene_variant,,ENST00000600186,;MAP1S,downstream_gene_variant,,ENST00000594625,;CTD-3149D2.4,non_coding_transcript_exon_variant,,ENST00000595363,;MAP1S,non_coding_transcript_exon_variant,,ENST00000597681,;MAP1S,downstream_gene_variant,,ENST00000601544,;MAP1S,downstream_gene_variant,,ENST00000599494,;MAP1S,upstream_gene_variant,,ENST00000598756,;MAP1S,downstream_gene_variant,,ENST00000594340,;MAP1S,downstream_gene_variant,,ENST00000595338,;MAP1S,downstream_gene_variant,,ENST00000598916,;MAP1S,downstream_gene_variant,,ENST00000597067,;MAP1S,downstream_gene_variant,,ENST00000594212,;MAP1S,downstream_gene_variant,,ENST00000594365,;MAP1S,downstream_gene_variant,,ENST00000598769,;MAP1S,downstream_gene_variant,,ENST00000596637,;MAP1S,downstream_gene_variant,,ENST00000593593,;MAP1S,downstream_gene_variant,,ENST00000600608,; T ENST00000324096 Transcript missense_variant 2736/3419 2585/3180 862/1059 T/I aCc/aTc 1 1 MAP1S HGNC HGNC:15715 protein_coding YES CCDS32954.1 ENSP00000325313 Q66K74 UPI00002036F9 NM_018174.4 tolerated(0.08) 5/7 hmmpanther:PTHR13843 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999883 1 1 1 0 T 3 4 12 17727969 17727969 C T 1 0 0 0 0 1 0 0 0 9156 507 18 3 3 MAP1S 19 17727969 Missense_Mutation SNP C C3L-00144_T 188612 17727969 40889647 1470 5541 FCHO1 0 . GRCh38 19 17784141 17784141 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2132G>T p.Trp711Leu p.W711L ENST00000594202 25/29 191 135 56 176 175 1 strelka-varscan-mutect FCHO1,missense_variant,p.Trp711Leu,ENST00000594202,NM_001161357.1;FCHO1,missense_variant,p.Trp711Leu,ENST00000596536,NM_015122.2;FCHO1,missense_variant,p.Trp711Leu,ENST00000252771,;FCHO1,missense_variant,p.Trp711Leu,ENST00000600676,NM_001161358.1;FCHO1,missense_variant,p.Trp711Leu,ENST00000596951,;FCHO1,missense_variant,p.Trp718Leu,ENST00000597512,;FCHO1,missense_variant,p.Trp661Leu,ENST00000595033,NM_001161359.1;FCHO1,non_coding_transcript_exon_variant,,ENST00000595594,;FCHO1,downstream_gene_variant,,ENST00000600058,;FCHO1,downstream_gene_variant,,ENST00000602111,;FCHO1,downstream_gene_variant,,ENST00000599766,; T ENST00000594202 Transcript missense_variant 2411/3214 2132/2676 711/891 W/L tGg/tTg 1 1 FCHO1 HGNC HGNC:29002 protein_coding YES CCDS59365.1 ENSP00000473001 A0A0C3SFZ9 UPI000059D6B0 NM_001161357.1 deleterious(0.02) 25/29 Pfam_domain:PF10291,PROSITE_profiles:PS51072,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 17784141 17784141 G T 1 0 0 0 0 1 0 0 0 5649 1357 47 2 2 FCHO1 19 17784141 Missense_Mutation SNP G C3L-00144_T 56172 17784141 40833475 1471 5542 SLC5A5 0 . GRCh38 19 17890889 17890889 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1655C>A p.Pro552His p.P552H ENST00000222248 14/15 471 415 56 363 361 2 strelka-varscan-mutect SLC5A5,missense_variant,p.Pro552His,ENST00000222248,NM_000453.2;SLC5A5,downstream_gene_variant,,ENST00000597109,; A ENST00000222248 Transcript missense_variant 2002/3576 1655/1932 552/643 P/H cCc/cAc 1 1 SLC5A5 HGNC HGNC:11040 protein_coding YES CCDS12368.1 ENSP00000222248 Q92911 UPI00001359F6 NM_000453.2 tolerated(0.21) 14/15 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17890889 17890889 C A 1 0 0 0 0 1 0 0 0 14951 637 22 2 2 SLC5A5 19 17890889 Missense_Mutation SNP C C3L-00144_T 106748 17890889 40726727 1472 5543 CCDC124 0 . GRCh38 19 17943326 17943326 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.415G>C p.Glu139Gln p.E139Q ENST00000597436 4/5 417 361 56 355 355 0 strelka-varscan-mutect CCDC124,missense_variant,p.Glu139Gln,ENST00000597436,NM_138442.3;CCDC124,missense_variant,p.Glu139Gln,ENST00000445755,NM_001136203.1;CCDC124,downstream_gene_variant,,ENST00000596123,; C ENST00000597436 Transcript missense_variant 522/1055 415/672 139/223 E/Q Gag/Cag 1 1 CCDC124 HGNC HGNC:25171 protein_coding YES CCDS12369.1 ENSP00000471455 Q96CT7 A0A024R7M8 UPI000006D46F NM_138442.3 tolerated(0.19) 4/5 hmmpanther:PTHR21680:SF0,hmmpanther:PTHR21680,Pfam_domain:PF06244 MODERATE 1 SNV 1 1 PASS rs1284975868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 17943326 17943326 G C 1 0 0 0 0 1 0 0 0 2452 1175 41 4 4 CCDC124 19 17943326 Missense_Mutation SNP G C3L-00144_T 52437 17943326 40674290 1473 5544 KIAA1683 0 . GRCh38 19 18267425 18267425 + Missense_Mutation SNP C C T rs111708098 C3L-00144_T C3L-00144_N C C c.115G>A p.Ala39Thr p.A39T ENST00000392413 3/4 35 30 5 21 21 0 strelka-mutect KIAA1683,missense_variant,p.Ala39Thr,ENST00000392413,NM_001145304.1;KIAA1683,missense_variant,p.Ala39Thr,ENST00000600328,NM_025249.3;KIAA1683,missense_variant,p.Ala39Thr,ENST00000612316,;KIAA1683,missense_variant,p.Ala39Thr,ENST00000608950,;KIAA1683,5_prime_UTR_variant,,ENST00000600359,NM_001145305.1;KIAA1683,5_prime_UTR_variant,,ENST00000593659,;KIAA1683,5_prime_UTR_variant,,ENST00000595654,;KIAA1683,5_prime_UTR_variant,,ENST00000599528,;KIAA1683,upstream_gene_variant,,ENST00000599638,; T ENST00000392413 Transcript missense_variant 331/4402 115/4104 39/1367 A/T Gct/Act rs111708098 1 -1 KIAA1683 HGNC HGNC:29350 protein_coding YES CCDS46017.1 ENSP00000376213 Q9H0B3 UPI000194EC26 NM_001145304.1 tolerated(0.34) 3/4 hmmpanther:PTHR22590,hmmpanther:PTHR22590:SF2 MODERATE 1 SNV 1 1 PASS rs111708098 . 0 198 12 0 0 0 0 0 -12.96466 0.9999101 1 1 1 0 T 3 4 12 18267425 18267425 C T 1 0 0 0 0 1 0 0 0 8126 768 27 1 1 KIAA1683 19 18267425 Missense_Mutation SNP C C3L-00144_T 324099 18267425 40350191 1474 5545 NCAN 0 . GRCh38 19 19228578 19228578 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2958G>T p.Glu986Asp p.E986D ENST00000252575 8/15 207 147 60 160 159 1 strelka-varscan-mutect NCAN,missense_variant,p.Glu986Asp,ENST00000252575,NM_004386.2;RNU6-1028P,upstream_gene_variant,,ENST00000517164,;NCAN,non_coding_transcript_exon_variant,,ENST00000590187,; T ENST00000252575 Transcript missense_variant 3057/6387 2958/3966 986/1321 E/D gaG/gaT 1 1 NCAN HGNC HGNC:2465 protein_coding YES CCDS12397.1 ENSP00000252575 O14594 A0A024R7M3 UPI000013CD70 NM_004386.2 deleterious(0.01) 8/15 hmmpanther:PTHR22804:SF24,hmmpanther:PTHR22804 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 19228578 19228578 G T 1 0 0 0 0 1 0 0 0 10220 991 35 2 2 NCAN 19 19228578 Missense_Mutation SNP G C3L-00144_T 961153 19228578 39389038 1475 5546 CILP2 0 . GRCh38 19 19543959 19543959 + Silent SNP C C A C3L-00144_T C3L-00144_N C C c.1414C>A p.= p.R472R ENST00000291495 8/8 316 280 36 227 227 0 strelka-varscan-mutect CILP2,synonymous_variant,p.=,ENST00000586018,;CILP2,synonymous_variant,p.=,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; A ENST00000291495 Transcript synonymous_variant 1499/4199 1414/3471 472/1156 R Cgg/Agg COSM1242130 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 1 LOW 1 SNV 1 1 1 PASS rs1227767281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 19543959 19543959 C A 1 0 0 0 0 0 0 0 1 3192 875 31 1 1 CILP2 19 19543959 Silent SNP C C3L-00144_T 315381 19543959 39073657 1476 5547 ZNF14 0 . GRCh38 19 19712595 19712595 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.686G>T p.Gly229Val p.G229V ENST00000344099 4/4 188 136 52 154 154 0 strelka-varscan-mutect ZNF14,missense_variant,p.Gly229Val,ENST00000344099,NM_021030.2;CTC-412M14.5,downstream_gene_variant,,ENST00000604034,; A ENST00000344099 Transcript missense_variant 825/2949 686/1929 229/642 G/V gGg/gTg 1 -1 ZNF14 HGNC HGNC:12924 protein_coding YES CCDS12409.1 ENSP00000340514 P17017 UPI00001E058E NM_021030.2 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF31,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 19712595 19712595 C A 1 0 0 0 0 1 0 0 0 18309 623 22 2 2 ZNF14 19 19712595 Missense_Mutation SNP C C3L-00144_T 168636 19712595 38905021 1477 5548 ZNF492 0 . GRCh38 19 22663809 22663809 + Missense_Mutation SNP C C A rs370256405 C3L-00144_T C3L-00144_N C C c.140C>A p.Ser47Tyr p.S47Y ENST00000456783 4/4 34 21 13 41 41 0 strelka-varscan-mutect ZNF492,missense_variant,p.Ser47Tyr,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; A ENST00000456783 Transcript missense_variant 384/4245 140/1596 47/531 S/Y tCt/tAt rs370256405 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.04) 4/4 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108 MODERATE 1 SNV 1 1 PASS rs370256405 . 2 203 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 22663809 22663809 C A 1 0 0 0 0 1 0 0 0 18516 913 32 2 2 ZNF492 19 22663809 Missense_Mutation SNP C C3L-00144_T 2951214 22663809 35953807 1478 5549 ZNF681 0 . GRCh38 19 23744606 23744606 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.944G>T p.Cys315Phe p.C315F ENST00000402377 4/4 218 198 20 216 216 0 strelka-varscan-mutect ZNF681,missense_variant,p.Cys315Phe,ENST00000402377,NM_138286.2;ZNF681,downstream_gene_variant,,ENST00000528059,;ZNF681,downstream_gene_variant,,ENST00000531570,; A ENST00000402377 Transcript missense_variant 1086/6497 944/1938 315/645 C/F tGt/tTt 1 -1 ZNF681 HGNC HGNC:26457 protein_coding YES CCDS12414.2 ENSP00000384000 Q96N22 UPI000022ABC8 NM_138286.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF356,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 23744606 23744606 C A 1 0 0 0 0 1 0 0 0 18661 478 17 2 2 ZNF681 19 23744606 Missense_Mutation SNP C C3L-00144_T 1080797 23744606 34873010 1479 5550 ZNF681 0 . GRCh38 19 23745248 23745248 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.302G>T p.Arg101Ile p.R101I ENST00000402377 4/4 112 100 12 96 96 0 strelka-varscan-mutect ZNF681,missense_variant,p.Arg101Ile,ENST00000402377,NM_138286.2;ZNF681,missense_variant,p.Arg32Ile,ENST00000528059,;ZNF681,missense_variant,p.Arg32Ile,ENST00000531570,; A ENST00000402377 Transcript missense_variant 444/6497 302/1938 101/645 R/I aGa/aTa 1 -1 ZNF681 HGNC HGNC:26457 protein_coding YES CCDS12414.2 ENSP00000384000 Q96N22 UPI000022ABC8 NM_138286.2 deleterious(0) 4/4 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF356 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99998 1 1 1 1 0 A 3 1 12 23745248 23745248 C A 1 0 0 0 0 1 0 0 0 18661 913 32 2 2 ZNF681 19 23745248 Missense_Mutation SNP C C3L-00144_T 642 23745248 34872368 1480 5551 URI1 0 . GRCh38 19 30007484 30007484 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.532G>T p.Ala178Ser p.A178S ENST00000392271 7/11 292 218 74 230 229 1 strelka-varscan-mutect URI1,missense_variant,p.Ala178Ser,ENST00000392271,NM_003796.3;URI1,missense_variant,p.Ala160Ser,ENST00000360605,NM_001252641.1;URI1,missense_variant,p.Ala102Ser,ENST00000576442,;URI1,upstream_gene_variant,,ENST00000575242,;URI1,downstream_gene_variant,,ENST00000574233,;URI1,upstream_gene_variant,,ENST00000573052,;URI1,non_coding_transcript_exon_variant,,ENST00000574176,;URI1,non_coding_transcript_exon_variant,,ENST00000570704,;URI1,3_prime_UTR_variant,,ENST00000574110,;URI1,downstream_gene_variant,,ENST00000574666,; T ENST00000392271 Transcript missense_variant 829/3444 532/1608 178/535 A/S Gct/Tct 1 1 URI1 HGNC HGNC:13236 protein_coding YES CCDS12420.1 ENSP00000376097 O94763 UPI00001604C8 NM_003796.3 tolerated(0.15) 7/11 hmmpanther:PTHR15111,hmmpanther:PTHR15111:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 30007484 30007484 G T 1 0 0 0 0 1 0 0 0 17558 1319 46 2 2 URI1 19 30007484 Missense_Mutation SNP G C3L-00144_T 6262236 30007484 28610132 1481 5552 ZNF536 0 . GRCh38 19 30444052 30444052 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.490G>T p.Asp164Tyr p.D164Y ENST00000355537 2/5 260 236 24 280 280 0 strelka-varscan-mutect ZNF536,missense_variant,p.Asp164Tyr,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Asp164Tyr,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript missense_variant 637/4945 490/3903 164/1300 D/Y Gac/Tac 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated(0.08) 2/5 Gene3D:3.30.160.60,Pfam_domain:PF13909,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 30444052 30444052 G T 1 0 0 0 0 1 0 0 0 18547 1058 37 1 1 ZNF536 19 30444052 Missense_Mutation SNP G C3L-00144_T 436568 30444052 28173564 1482 5553 SLC7A9 0 . GRCh38 19 32858509 32858509 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.908G>T p.Trp303Leu p.W303L ENST00000023064 9/13 653 595 58 487 486 1 strelka-varscan-mutect SLC7A9,missense_variant,p.Trp303Leu,ENST00000023064,NM_001243036.1,NM_001126335.1,NM_014270.4;SLC7A9,missense_variant,p.Trp303Leu,ENST00000590341,;SLC7A9,missense_variant,p.Trp303Leu,ENST00000587772,;RN7SKP22,downstream_gene_variant,,ENST00000365097,;SLC7A9,3_prime_UTR_variant,,ENST00000590465,;SLC7A9,3_prime_UTR_variant,,ENST00000592232,;SLC7A9,non_coding_transcript_exon_variant,,ENST00000589659,; A ENST00000023064 Transcript missense_variant 1100/1761 908/1464 303/487 W/L tGg/tTg 1 -1 SLC7A9 HGNC HGNC:11067 protein_coding YES CCDS12425.1 ENSP00000023064 P82251 UPI0000037773 NM_001243036.1,NM_001126335.1,NM_014270.4 deleterious(0.01) 9/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785:SF354,hmmpanther:PTHR11785,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 32858509 32858509 C A 1 0 0 0 0 1 0 0 0 14988 595 21 2 2 SLC7A9 19 32858509 Missense_Mutation SNP C C3L-00144_T 2414457 32858509 25759107 1483 5554 CHST8 0 . GRCh38 19 33771968 33771968 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.180A>T p.= p.P60P ENST00000262622 4/4 67 60 7 47 47 0 strelka-varscan-mutect CHST8,synonymous_variant,p.=,ENST00000262622,NM_022467.3;CHST8,synonymous_variant,p.=,ENST00000434302,NM_001127895.1;CHST8,synonymous_variant,p.=,ENST00000438847,NM_001127896.1;CHST8,synonymous_variant,p.=,ENST00000591231,; T ENST00000262622 Transcript synonymous_variant 938/2479 180/1275 60/424 P ccA/ccT 1 1 CHST8 HGNC HGNC:15993 protein_coding YES CCDS12433.1 ENSP00000262622 Q9H2A9 UPI000006F966 NM_022467.3 4/4 hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF7 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -15.99946 1 1 1 1 0 T 2 4 12 33771968 33771968 A T 1 0 0 0 0 0 0 0 1 3170 175 7 4 4 CHST8 19 33771968 Silent SNP A C3L-00144_T 913459 33771968 24845648 1484 5555 GAPDHS 0 . GRCh38 19 35536822 35536822 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.77C>G p.Ala26Gly p.A26G ENST00000222286 2/11 88 61 27 58 58 0 strelka-varscan-mutect GAPDHS,missense_variant,p.Ala26Gly,ENST00000222286,NM_014364.4;GAPDHS,5_prime_UTR_variant,,ENST00000585510,;TMEM147-AS1,downstream_gene_variant,,ENST00000588286,;TMEM147-AS1,downstream_gene_variant,,ENST00000590717,;TMEM147-AS1,downstream_gene_variant,,ENST00000589137,;TMEM147-AS1,downstream_gene_variant,,ENST00000590125,;GAPDHS,intron_variant,,ENST00000586334,; G ENST00000222286 Transcript missense_variant 193/1489 77/1227 26/408 A/G gCa/gGa 1 1 GAPDHS HGNC HGNC:24864 protein_coding YES CCDS12465.1 ENSP00000222286 O14556 A0A0K0K1K1 UPI000012AE83 NM_014364.4 tolerated_low_confidence(0.35) 2/11 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999902 1 1 1 0 G 3 3 12 35536822 35536822 C G 1 0 0 0 0 1 0 0 0 6105 710 25 4 4 GAPDHS 19 35536822 Missense_Mutation SNP C C3L-00144_T 1764854 35536822 23080794 1485 5556 ETV2 0 . GRCh38 19 35642468 35642468 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.8T>A p.Leu3Gln p.L3Q ENST00000402764 2/7 49 40 9 32 32 0 strelka-varscan-mutect ETV2,missense_variant,p.Leu3Gln,ENST00000379026,;ETV2,missense_variant,p.Leu3Gln,ENST00000402764,NM_014209.3;ETV2,missense_variant,p.Leu3Gln,ENST00000403402,;ETV2,missense_variant,p.Leu3Gln,ENST00000619399,;ETV2,missense_variant,p.Leu3Gln,ENST00000621247,;ETV2,missense_variant,p.Leu3Gln,ENST00000379023,NM_001304549.1;ETV2,intron_variant,,ENST00000479824,NM_001300974.1;RBM42,downstream_gene_variant,,ENST00000262633,NM_024321.3;RBM42,downstream_gene_variant,,ENST00000588161,NM_001319113.1;RBM42,downstream_gene_variant,,ENST00000589871,;RBM42,downstream_gene_variant,,ENST00000592202,;RBM42,downstream_gene_variant,,ENST00000589559,;RBM42,downstream_gene_variant,,ENST00000586618,;ETV2,upstream_gene_variant,,ENST00000591135,; A ENST00000402764 Transcript missense_variant 447/1487 8/1029 3/342 L/Q cTg/cAg 1 1 ETV2 HGNC HGNC:3491 protein_coding YES CCDS32995.2 ENSP00000384524 O00321 UPI000013C7F7 NM_014209.3 deleterious(0.03) 2/7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 35642468 35642468 T A 1 0 0 0 0 1 0 0 0 5142 1580 55 4 4 ETV2 19 35642468 Missense_Mutation SNP T C3L-00144_T 105646 35642468 22975148 1486 5557 ZFP82 0 . GRCh38 19 36393809 36393809 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.531G>T p.Lys177Asn p.K177N ENST00000392161 5/5 277 198 79 215 215 0 strelka-varscan-mutect ZFP82,missense_variant,p.Lys177Asn,ENST00000392161,NM_133466.2;ZFP82,intron_variant,,ENST00000445543,;ZFP82,non_coding_transcript_exon_variant,,ENST00000590993,; A ENST00000392161 Transcript missense_variant 774/2623 531/1599 177/532 K/N aaG/aaT 1 -1 ZFP82 HGNC HGNC:28682 protein_coding YES CCDS12493.1 ENSP00000431265 Q8N141 D3Y299 UPI0000071159 NM_133466.2 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF252,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 36393809 36393809 C A 1 0 0 0 0 1 0 0 0 18230 680 24 2 2 ZFP82 19 36393809 Missense_Mutation SNP C C3L-00144_T 751341 36393809 22223807 1487 5558 ZNF568 0 . GRCh38 19 36997019 36997019 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.1328G>T p.Arg443Ile p.R443I ENST00000617745 8/8 110 99 11 103 102 1 strelka-mutect ZNF568,missense_variant,p.Arg443Ile,ENST00000617745,NM_001204838.1;ZNF568,missense_variant,p.Arg379Ile,ENST00000455427,NM_001204839.1;ZNF568,missense_variant,p.Arg443Ile,ENST00000444991,;ZNF568,missense_variant,p.Arg311Ile,ENST00000433993,;ZNF568,downstream_gene_variant,,ENST00000455817,;ZNF568,downstream_gene_variant,,ENST00000588596,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,; T ENST00000617745 Transcript missense_variant 1528/2441 1328/1908 443/635 R/I aGa/aTa COSM5464532 1 1 ZNF568 HGNC HGNC:25392 protein_coding CCDS74351.1 ENSP00000482444 A0A087WZ84 UPI0001FD28F8 NM_001204838.1 deleterious(0.01) 8/8 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF107,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 36997019 36997019 G T 1 0 0 0 0 1 0 0 0 18573 942 33 2 2 ZNF568 19 36997019 Missense_Mutation SNP G C3L-00144_T 603210 36997019 21620597 1488 5559 ZNF607 0 . GRCh38 19 37699145 37699145 + Missense_Mutation SNP C C G C3L-00144_T C3L-00144_N C C c.986G>C p.Arg329Thr p.R329T ENST00000355202 5/5 255 234 21 215 215 0 strelka-varscan-mutect ZNF607,missense_variant,p.Arg329Thr,ENST00000355202,NM_032689.4;ZNF607,missense_variant,p.Arg328Thr,ENST00000395835,NM_001172677.1;ZNF607,downstream_gene_variant,,ENST00000591664,;ZNF607,downstream_gene_variant,,ENST00000590670,;CTD-2528L19.4,intron_variant,,ENST00000586606,;CTD-2528L19.4,intron_variant,,ENST00000585547,;CTD-2528L19.4,intron_variant,,ENST00000591114,;ZNF607,downstream_gene_variant,,ENST00000586559,; G ENST00000355202 Transcript missense_variant 1582/4364 986/2091 329/696 R/T aGa/aCa COSM995814 1 -1 ZNF607 HGNC HGNC:28192 protein_coding YES CCDS33006.1 ENSP00000347338 Q96SK3 UPI000040BC07 NM_032689.4 deleterious(0.01) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF319,hmmpanther:PTHR24377,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS rs1041881636 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 37699145 37699145 C G 1 0 0 0 0 1 0 0 0 18608 913 32 4 4 ZNF607 19 37699145 Missense_Mutation SNP C C3L-00144_T 702126 37699145 20918471 1489 5560 WDR87 0 . GRCh38 19 37886656 37886656 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.7015delC p.Gln2339ArgfsTer14 p.Q2339Rfs*14 ENST00000447313 6/6 83 59 24 75 75 0 sindel-varindel-pindel WDR87,frameshift_variant,p.Gln2339ArgfsTer14,ENST00000447313,NM_001291088.1;WDR87,frameshift_variant,p.Gln2300ArgfsTer14,ENST00000303868,NM_031951.4; - ENST00000447313 Transcript frameshift_variant 7176/9009 7015/8739 2339/2912 Q/X Cag/ag 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 6/6 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg HIGH 1 deletion 2 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 12 37886656 37886656 G - 1 0 1 0 1 0 0 0 0 17890 1299 45 0 0 WDR87 19 37886656 Frame_Shift_Del DEL G C3L-00144_T 187511 37886656 20730960 1490 5561 WDR87 0 . GRCh38 19 37890140 37890140 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.3531C>A p.= p.S1177S ENST00000447313 6/6 297 195 102 196 195 1 strelka-varscan-mutect WDR87,synonymous_variant,p.=,ENST00000447313,NM_001291088.1;WDR87,synonymous_variant,p.=,ENST00000303868,NM_031951.4; T ENST00000447313 Transcript synonymous_variant 3692/9009 3531/8739 1177/2912 S tcC/tcA 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 6/6 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 37890140 37890140 G T 1 0 0 0 0 0 0 0 1 17890 1219 43 2 2 WDR87 19 37890140 Silent SNP G C3L-00144_T 3484 37890140 20727476 1491 5562 WDR87 0 . GRCh38 19 37891689 37891689 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.3257C>G p.Pro1086Arg p.P1086R ENST00000447313 5/6 520 352 168 406 406 0 strelka-varscan-mutect WDR87,missense_variant,p.Pro1086Arg,ENST00000447313,NM_001291088.1;WDR87,missense_variant,p.Pro1047Arg,ENST00000303868,NM_031951.4;WDR87,downstream_gene_variant,,ENST00000473328,; C ENST00000447313 Transcript missense_variant 3418/9009 3257/8739 1086/2912 P/R cCg/cGg 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 tolerated(0.07) 5/6 MODERATE 1 SNV 2 1 PASS rs1489429611 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 37891689 37891689 G C 1 0 0 0 0 1 0 0 0 17890 1116 39 4 4 WDR87 19 37891689 Missense_Mutation SNP G C3L-00144_T 1549 37891689 20725927 1492 5563 RASGRP4 0 . GRCh38 19 38412968 38412968 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1498T>A p.Phe500Ile p.F500I ENST00000615439 12/17 358 252 106 269 269 0 strelka-varscan-mutect RASGRP4,missense_variant,p.Phe500Ile,ENST00000618320,;RASGRP4,missense_variant,p.Phe500Ile,ENST00000615439,NM_170604.2;RASGRP4,missense_variant,p.Phe466Ile,ENST00000454404,NM_001146205.1;RASGRP4,missense_variant,p.Phe486Ile,ENST00000586305,NM_001146202.1;RASGRP4,missense_variant,p.Phe431Ile,ENST00000587753,NM_001146204.1;RASGRP4,missense_variant,p.Phe408Ile,ENST00000614135,;RASGRP4,missense_variant,p.Phe408Ile,ENST00000433821,NM_001146203.1;RASGRP4,missense_variant,p.Phe403Ile,ENST00000617966,;RASGRP4,missense_variant,p.Phe403Ile,ENST00000293062,NM_001146207.1;RASGRP4,missense_variant,p.Phe311Ile,ENST00000622174,;RASGRP4,missense_variant,p.Phe311Ile,ENST00000426920,NM_001146206.1;RASGRP4,missense_variant,p.Phe500Ile,ENST00000587738,;FAM98C,downstream_gene_variant,,ENST00000252530,NM_174905.3;FAM98C,downstream_gene_variant,,ENST00000343358,;FAM98C,downstream_gene_variant,,ENST00000588262,;RASGRP4,missense_variant,p.Phe500Ile,ENST00000589358,;RASGRP4,missense_variant,p.Phe486Ile,ENST00000589474,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000615340,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588708,;FAM98C,downstream_gene_variant,,ENST00000586372,;FAM98C,downstream_gene_variant,,ENST00000588348,;RASGRP4,upstream_gene_variant,,ENST00000587287,;FAM98C,downstream_gene_variant,,ENST00000589027,; T ENST00000615439 Transcript missense_variant 1712/3217 1498/2022 500/673 F/I Ttc/Atc 1 -1 RASGRP4 HGNC HGNC:18958 protein_coding YES CCDS46068.1 ENSP00000479844 Q8TDF6 UPI0000050F40 NM_170604.2 deleterious(0) 12/17 PROSITE_profiles:PS50222,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF157 MODERATE 1 SNV 1 1 PASS rs1292354546 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 38412968 38412968 A T 1 0 0 0 0 1 0 0 0 13238 72 3 4 4 RASGRP4 19 38412968 Missense_Mutation SNP A C3L-00144_T 521279 38412968 20204648 1493 5564 RASGRP4 0 . GRCh38 19 38415066 38415066 + Missense_Mutation SNP G G T rs751201302 C3L-00144_T C3L-00144_N G G c.1012C>A p.Arg338Ser p.R338S ENST00000615439 9/17 206 142 64 178 178 0 strelka-varscan-mutect RASGRP4,missense_variant,p.Arg338Ser,ENST00000618320,;RASGRP4,missense_variant,p.Arg338Ser,ENST00000615439,NM_170604.2;RASGRP4,missense_variant,p.Arg304Ser,ENST00000454404,NM_001146205.1;RASGRP4,missense_variant,p.Arg324Ser,ENST00000586305,NM_001146202.1;RASGRP4,missense_variant,p.Arg241Ser,ENST00000617966,;RASGRP4,missense_variant,p.Arg241Ser,ENST00000293062,NM_001146207.1;RASGRP4,missense_variant,p.Arg338Ser,ENST00000587738,;RASGRP4,intron_variant,,ENST00000587753,NM_001146204.1;RASGRP4,intron_variant,,ENST00000614135,;RASGRP4,intron_variant,,ENST00000433821,NM_001146203.1;RASGRP4,intron_variant,,ENST00000622174,;RASGRP4,intron_variant,,ENST00000426920,NM_001146206.1;RASGRP4,missense_variant,p.Arg338Ser,ENST00000589358,;RASGRP4,missense_variant,p.Arg324Ser,ENST00000589474,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000615340,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588708,;RASGRP4,upstream_gene_variant,,ENST00000587287,; T ENST00000615439 Transcript missense_variant 1226/3217 1012/2022 338/673 R/S Cgc/Agc rs751201302 1 -1 RASGRP4 HGNC HGNC:18958 protein_coding YES CCDS46068.1 ENSP00000479844 Q8TDF6 UPI0000050F40 NM_170604.2 deleterious(0) 9/17 PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF157,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS rs751201302 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 38415066 38415066 G T 1 0 0 0 0 1 0 0 0 13238 1116 39 1 1 RASGRP4 19 38415066 Missense_Mutation SNP G C3L-00144_T 2098 38415066 20202550 1494 5565 MAP4K1 0 . GRCh38 19 38609642 38609642 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.960C>A p.= p.S320S ENST00000591517 13/32 164 149 15 138 137 1 strelka-varscan-mutect MAP4K1,synonymous_variant,p.=,ENST00000591517,NM_007181.5;MAP4K1,synonymous_variant,p.=,ENST00000589130,;MAP4K1,synonymous_variant,p.=,ENST00000396857,NM_001042600.2;MAP4K1,synonymous_variant,p.=,ENST00000586296,;MAP4K1,upstream_gene_variant,,ENST00000591921,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000589002,;MAP4K1,3_prime_UTR_variant,,ENST00000585583,;MAP4K1,downstream_gene_variant,,ENST00000591707,;MAP4K1,downstream_gene_variant,,ENST00000592888,;MAP4K1,downstream_gene_variant,,ENST00000592225,;MAP4K1,downstream_gene_variant,,ENST00000588083,; T ENST00000591517 Transcript synonymous_variant 989/2700 960/2502 320/833 S tcC/tcA 1 -1 MAP4K1 HGNC HGNC:6863 protein_coding YES CCDS59385.1 ENSP00000465039 Q92918 UPI00000747ED NM_007181.5 13/32 hmmpanther:PTHR24361:SF88,hmmpanther:PTHR24361,PIRSF_domain:PIRSF038172 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 38609642 38609642 G T 1 0 0 0 0 0 0 0 1 9183 1335 47 2 2 MAP4K1 19 38609642 Silent SNP G C3L-00144_T 194576 38609642 20007974 1495 5566 FCGBP 0 . GRCh38 19 39914166 39914166 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.2921A>T p.Asp974Val p.D974V ENST00000616721 6/28 317 287 30 229 229 0 strelka-varscan-mutect FCGBP,missense_variant,p.Asp974Val,ENST00000616721,NM_003890.2; A ENST00000616721 Transcript missense_variant 2929/12787 2921/12615 974/4204 D/V gAc/gTc 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 deleterious(0) 6/28 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF244,SMART_domains:SM00216 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 39914166 39914166 T A 1 0 0 0 0 1 0 0 0 5641 1667 58 4 4 FCGBP 19 39914166 Missense_Mutation SNP T C3L-00144_T 1304524 39914166 18703450 1496 5567 MAP3K10 0 . GRCh38 19 40204530 40204530 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.909C>A p.Tyr303Ter p.Y303* ENST00000253055 3/10 118 104 14 99 99 0 strelka-varscan-mutect MAP3K10,stop_gained,p.Tyr303Ter,ENST00000253055,NM_002446.3;MAP3K10,non_coding_transcript_exon_variant,,ENST00000593906,;MAP3K10,stop_gained,p.Tyr53Ter,ENST00000597986,;MAP3K10,intron_variant,,ENST00000593502,;MAP3K10,intron_variant,,ENST00000594951,;MAP3K10,upstream_gene_variant,,ENST00000594791,;MAP3K10,upstream_gene_variant,,ENST00000601702,;MAP3K10,upstream_gene_variant,,ENST00000594569,; A ENST00000253055 Transcript stop_gained 1197/3436 909/2865 303/954 Y/* taC/taA 1 1 MAP3K10 HGNC HGNC:6849 protein_coding YES CCDS12549.1 ENSP00000253055 Q02779 UPI000013CDAC NM_002446.3 3/10 PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF515,Pfam_domain:PF07714,PIRSF_domain:PIRSF000556,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR00109 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 40204530 40204530 C A 1 0 0 0 0 0 1 0 0 9166 518 18 2 2 MAP3K10 19 40204530 Nonsense_Mutation SNP C C3L-00144_T 290364 40204530 18413086 1497 5568 PRR19 0 . GRCh38 19 42310705 42310705 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1036G>A p.Glu346Lys p.E346K ENST00000499536 2/2 30 18 12 21 21 0 strelka-varscan-mutect PRR19,missense_variant,p.Glu346Lys,ENST00000499536,;PRR19,missense_variant,p.Glu346Lys,ENST00000341747,NM_199285.2;PRR19,3_prime_UTR_variant,,ENST00000598490,;TMEM145,upstream_gene_variant,,ENST00000598766,;TMEM145,upstream_gene_variant,,ENST00000301204,NM_173633.2;PRR19,downstream_gene_variant,,ENST00000595750,;TMEM145,upstream_gene_variant,,ENST00000601020,;TMEM145,upstream_gene_variant,,ENST00000595775,; A ENST00000499536 Transcript missense_variant 1847/1956 1036/1071 346/356 E/K Gaa/Aaa 1 1 PRR19 HGNC HGNC:33728 protein_coding YES CCDS33036.1 ENSP00000445247 A6NJB7 UPI000016101F deleterious(0) 2/2 hmmpanther:PTHR37346,Pfam_domain:PF15455 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 42310705 42310705 G A 1 0 0 0 0 1 0 0 0 12727 1175 41 3 3 PRR19 19 42310705 Missense_Mutation SNP G C3L-00144_T 2106175 42310705 16306911 1498 5569 MEGF8 0 . GRCh38 19 42355787 42355787 + Missense_Mutation SNP G G T rs778640003 C3L-00144_T C3L-00144_N G G c.4174G>T p.Gly1392Cys p.G1392C ENST00000251268 24/42 142 98 44 96 96 0 strelka-varscan-mutect MEGF8,missense_variant,p.Gly1325Cys,ENST00000334370,NM_001410.2;MEGF8,missense_variant,p.Gly1392Cys,ENST00000251268,NM_001271938.1;MEGF8,5_prime_UTR_variant,,ENST00000378073,;MIR8077,downstream_gene_variant,,ENST00000618566,;MEGF8,downstream_gene_variant,,ENST00000593840,; T ENST00000251268 Transcript missense_variant 4174/9549 4174/8538 1392/2845 G/C Ggc/Tgc rs778640003 1 1 MEGF8 HGNC HGNC:3233 protein_coding YES CCDS62693.1 ENSP00000251268 Q7Z7M0 UPI00005788D1 NM_001271938.1 tolerated(0.05) 24/42 PROSITE_profiles:PS01180 MODERATE 1 SNV 5 1 PASS rs778640003 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42355787 42355787 G T 1 0 0 0 0 1 0 0 0 9403 1348 47 2 2 MEGF8 19 42355787 Missense_Mutation SNP G C3L-00144_T 45082 42355787 16261829 1499 5570 PSG1 0 . GRCh38 19 42878087 42878087 + Missense_Mutation SNP C C A rs532735187 C3L-00144_T C3L-00144_N C C c.256G>T p.Gly86Cys p.G86C ENST00000312439 2/6 344 318 26 231 231 0 varscan-mutect PSG1,missense_variant,p.Gly86Cys,ENST00000244296,NM_006905.2;PSG1,missense_variant,p.Gly86Cys,ENST00000436291,NM_001184825.1;PSG1,missense_variant,p.Gly86Cys,ENST00000595356,NM_001184826.1;PSG1,missense_variant,p.Gly86Cys,ENST00000312439,NM_001297773.1;PSG1,missense_variant,p.Gly86Cys,ENST00000403380,;PSG1,missense_variant,p.Gly86Cys,ENST00000595124,;PSG1,missense_variant,p.Gly15Cys,ENST00000595930,;PSG1,missense_variant,p.Gly7Cys,ENST00000597058,;PSG1,non_coding_transcript_exon_variant,,ENST00000601073,;PSG1,non_coding_transcript_exon_variant,,ENST00000601456,; A ENST00000312439 Transcript missense_variant 342/1882 256/1287 86/428 G/C Ggt/Tgt rs532735187 1 -1 PSG1 HGNC HGNC:9514 protein_coding YES CCDS74380.1 ENSP00000308970 P11464 UPI000006DB43 NM_001297773.1 deleterious(0.03) 2/6 Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs532735187 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 42878087 42878087 C A 1 0 0 0 0 1 0 0 0 12804 652 23 1 1 PSG1 19 42878087 Missense_Mutation SNP C C3L-00144_T 522300 42878087 15739529 1500 5571 PSG7 0 . GRCh38 19 42929720 42929720 + Missense_Mutation SNP A A T rs745772540 C3L-00144_T C3L-00144_N A A c.65T>A p.Val22Glu p.V22E ENST00000623675 2/5 112 84 28 102 101 1 strelka-varscan-mutect PSG7,missense_variant,p.Leu144Gln,ENST00000446844,;PSG7,missense_variant,p.Leu144Gln,ENST00000406070,NM_002783.2,NM_001290042.1;PSG7,missense_variant,p.Leu144Gln,ENST00000617049,;PSG7,missense_variant,p.Val22Glu,ENST00000623675,NM_001206650.1;PSG7,splice_region_variant,,ENST00000599620,;PSG7,upstream_gene_variant,,ENST00000599226,; T ENST00000623675 Transcript missense_variant,splice_region_variant 87/1392 65/894 22/297 V/E gTg/gAg rs745772540 1 -1 PSG7 HGNC HGNC:9524 protein_coding YES CCDS77310.1 ENSP00000485117 A0A096LNM5 UPI000209A891 NM_001206650.1 deleterious(0.02) 2/5 MODERATE 1 SNV 1 1 PASS rs745772540 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 42929720 42929720 A T 1 0 0 0 0 1 0 0 0 12811 173 6 4 4 PSG7 19 42929720 Missense_Mutation SNP A C3L-00144_T 51633 42929720 15687896 1501 5572 PSG4 0 . GRCh38 19 43204041 43204041 + Missense_Mutation SNP C C G rs758535731 C3L-00144_T C3L-00144_N C C c.275G>C p.Gly92Ala p.G92A ENST00000405312 2/6 345 313 32 267 267 0 strelka-varscan-mutect PSG4,missense_variant,p.Gly92Ala,ENST00000405312,NM_002780.4;PSG4,missense_variant,p.Gly92Ala,ENST00000433626,NM_001276495.1;PSG4,missense_variant,p.Gly92Ala,ENST00000244295,NM_213633.2;PSG4,missense_variant,p.Gly108Ala,ENST00000451895,;PSG4,missense_variant,p.Gly71Ala,ENST00000599746,;PSG4,missense_variant,p.Gly21Ala,ENST00000600572,;PSG4,intron_variant,,ENST00000596907,;PSG4,intron_variant,,ENST00000599391,;PSG4,non_coding_transcript_exon_variant,,ENST00000597912,;PSG4,non_coding_transcript_exon_variant,,ENST00000495316,;PSG4,intron_variant,,ENST00000595949,;PSG4,intron_variant,,ENST00000601041,;PSG4,intron_variant,,ENST00000596199,; G ENST00000405312 Transcript missense_variant 513/2168 275/1260 92/419 G/A gGg/gCg rs758535731 1 -1 PSG4 HGNC HGNC:9521 protein_coding YES CCDS46093.1 ENSP00000384770 Q00888 UPI000034ECBA NM_002780.4 deleterious(0) 2/6 hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs758535731 . 14 196 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 43204041 43204041 C G 1 0 0 0 0 1 0 0 0 12808 623 22 4 4 PSG4 19 43204041 Missense_Mutation SNP C C3L-00144_T 274321 43204041 15413575 1502 5573 CD177 0 . GRCh38 19 43362116 43362116 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1110G>A p.= p.Q370Q ENST00000618265 9/9 127 112 15 75 75 0 varscan-mutect CD177,synonymous_variant,p.=,ENST00000618265,NM_020406.3;CTC-490G23.4,intron_variant,,ENST00000607109,;CD177,3_prime_UTR_variant,,ENST00000378012,; A ENST00000618265 Transcript synonymous_variant 1166/2222 1110/1314 370/437 Q caG/caA 1 1 CD177 HGNC HGNC:30072 protein_coding YES CCDS62700.1 ENSP00000479536 A0A087WVM2 UPI0000DB6A71 NM_020406.3 9/9 hmmpanther:PTHR16529,hmmpanther:PTHR16529:SF8,Pfam_domain:PF00021,Superfamily_domains:SSF57302 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 43362116 43362116 G A 1 0 0 0 0 0 0 0 1 2674 991 35 3 3 CD177 19 43362116 Silent SNP G C3L-00144_T 158075 43362116 15255500 1503 5574 ZNF230 0 . GRCh38 19 44010727 44010727 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.688G>T p.Gly230Trp p.G230W ENST00000429154 5/5 439 401 38 317 316 1 strelka-varscan-mutect ZNF230,missense_variant,p.Gly230Trp,ENST00000429154,NM_006300.3;ZNF230,downstream_gene_variant,,ENST00000585491,;ZNF230,downstream_gene_variant,,ENST00000585632,;ZNF230,3_prime_UTR_variant,,ENST00000585568,; T ENST00000429154 Transcript missense_variant 916/4115 688/1425 230/474 G/W Ggg/Tgg 1 1 ZNF230 HGNC HGNC:13024 protein_coding YES CCDS33044.1 ENSP00000409318 Q9UIE0 UPI000016960C NM_006300.3 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF176,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 44010727 44010727 G T 1 0 0 0 0 1 0 0 0 18361 1348 47 2 2 ZNF230 19 44010727 Missense_Mutation SNP G C3L-00144_T 648611 44010727 14606889 1504 5575 CEACAM20 0 . GRCh38 19 44517074 44517074 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1181G>A p.Gly394Glu p.G394E ENST00000614924 6/12 632 583 49 480 480 0 strelka-varscan-mutect CEACAM20,missense_variant,p.Gly394Glu,ENST00000621342,;CEACAM20,missense_variant,p.Gly394Glu,ENST00000617951,;CEACAM20,missense_variant,p.Gly394Glu,ENST00000614924,NM_001102597.2;CEACAM20,missense_variant,p.Gly394Glu,ENST00000611497,NM_001102600.2;CEACAM20,intron_variant,,ENST00000614577,NM_001102599.2;CEACAM20,intron_variant,,ENST00000620096,NM_001102598.2; T ENST00000614924 Transcript missense_variant 1197/1809 1181/1791 394/596 G/E gGg/gAg 1 -1 CEACAM20 HGNC HGNC:24879 protein_coding YES CCDS74393.1 ENSP00000481937 A0A087WYM6 UPI0003EC04B5 NM_001102597.2 tolerated(1) 6/12 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 44517074 44517074 C T 1 0 0 0 0 1 0 0 0 2897 623 22 3 3 CEACAM20 19 44517074 Missense_Mutation SNP C C3L-00144_T 506347 44517074 14100542 1505 5576 MARK4 0 . GRCh38 19 45294405 45294405 + Frame_Shift_Del DEL C C - C3L-00144_T C3L-00144_N C C c.1553delC p.Pro518ArgfsTer102 p.P518Rfs*102 ENST00000262891 14/17 286 195 91 241 241 0 sindel-varindel-pindel MARK4,frameshift_variant,p.Pro518ArgfsTer102,ENST00000300843,NM_031417.3;MARK4,frameshift_variant,p.Pro518ArgfsTer102,ENST00000262891,NM_001199867.1;MARK4,intron_variant,,ENST00000620044,;MARK4,intron_variant,,ENST00000622871,; - ENST00000262891 Transcript frameshift_variant 1882/3573 1551/2259 517/752 R/X cgC/cg COSM4700743,COSM4700744 1 1 MARK4 HGNC HGNC:13538 protein_coding YES CCDS56097.1 ENSP00000262891 Q96L34 UPI0000044D47 NM_001199867.1 14/17 hmmpanther:PTHR24346 1,1 HIGH 1 deletion 1 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 45294405 45294405 C - 1 0 1 0 1 0 0 0 0 9240 726 26 0 0 MARK4 19 45294405 Frame_Shift_Del DEL C C3L-00144_T 777331 45294405 13323211 1506 5577 IRF2BP1 0 . GRCh38 19 45884313 45884313 + Missense_Mutation SNP C C G rs773353053 C3L-00144_T C3L-00144_N C C c.1462G>C p.Gly488Arg p.G488R ENST00000302165 1/1 187 128 59 146 146 0 strelka-varscan-mutect IRF2BP1,missense_variant,p.Gly488Arg,ENST00000302165,NM_015649.2; G ENST00000302165 Transcript missense_variant 1858/2564 1462/1755 488/584 G/R Ggg/Cgg rs773353053,COSM1579926 1 -1 IRF2BP1 HGNC HGNC:21728 protein_coding YES CCDS12678.1 ENSP00000307265 Q8IU81 UPI00000747C7 NM_015649.2 tolerated(0.54) 1/1 hmmpanther:PTHR10816,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 PASS rs773353053 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 45884313 45884313 C G 1 0 0 0 0 1 0 0 0 7735 652 23 4 4 IRF2BP1 19 45884313 Missense_Mutation SNP C C3L-00144_T 589908 45884313 12733303 1507 5578 IGFL3 0 . GRCh38 19 46124036 46124036 + Missense_Mutation SNP C C A rs759215266 C3L-00144_T C3L-00144_N C C c.200G>T p.Arg67Leu p.R67L ENST00000341415 3/4 259 222 37 217 217 0 strelka-varscan-mutect IGFL3,missense_variant,p.Arg67Leu,ENST00000341415,NM_207393.1;AC007193.6,intron_variant,,ENST00000597989,; A ENST00000341415 Transcript missense_variant 225/662 200/378 67/125 R/L cGc/cTc rs759215266 1 -1 IGFL3 HGNC HGNC:32930 protein_coding YES CCDS33058.1 ENSP00000344860 Q6UXB1 UPI000003597A NM_207393.1 deleterious(0.01) 3/4 hmmpanther:PTHR34827:SF1,hmmpanther:PTHR34827,Pfam_domain:PF14653 MODERATE 1 SNV 1 1 PASS rs759215266 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 12 46124036 46124036 C A 1 0 0 0 0 1 0 0 0 7494 768 27 1 1 IGFL3 19 46124036 Missense_Mutation SNP C C3L-00144_T 239723 46124036 12493580 1508 5579 PTGIR 0 . GRCh38 19 46623875 46623875 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.351C>A p.= p.R117R ENST00000291294 2/3 142 126 16 118 118 0 strelka-varscan-mutect PTGIR,synonymous_variant,p.=,ENST00000291294,NM_000960.3;PTGIR,synonymous_variant,p.=,ENST00000596260,;PTGIR,intron_variant,,ENST00000597185,;PTGIR,intron_variant,,ENST00000598865,;PTGIR,intron_variant,,ENST00000594275,;PTGIR,non_coding_transcript_exon_variant,,ENST00000595460,; T ENST00000291294 Transcript synonymous_variant 485/2107 351/1161 117/386 R cgC/cgA 1 -1 PTGIR HGNC HGNC:9602 protein_coding YES CCDS12686.1 ENSP00000291294 P43119 UPI000005042B NM_000960.3 2/3 PROSITE_profiles:PS50262,hmmpanther:PTHR11866:SF7,hmmpanther:PTHR11866,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 46623875 46623875 G T 1 0 0 0 0 0 0 0 1 12907 958 34 2 2 PTGIR 19 46623875 Silent SNP G C3L-00144_T 499839 46623875 11993741 1509 5580 DACT3 0 . GRCh38 19 46649474 46649474 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.898C>A p.= p.R300R ENST00000391916 4/4 26 21 5 20 20 0 strelka-mutect DACT3,synonymous_variant,p.=,ENST00000391916,NM_145056.2;DACT3,synonymous_variant,p.=,ENST00000300875,NM_001301046.1;DACT3,downstream_gene_variant,,ENST00000410105,; T ENST00000391916 Transcript synonymous_variant 972/2834 898/1890 300/629 R Cga/Aga 1 -1 DACT3 HGNC HGNC:30745 protein_coding YES CCDS12688.2 ENSP00000375783 Q96B18 UPI0000202707 NM_145056.2 4/4 hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF1 LOW 1 SNV 5 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 46649474 46649474 G T 1 0 0 0 0 0 0 0 1 4025 1095 38 1 1 DACT3 19 46649474 Silent SNP G C3L-00144_T 25599 46649474 11968142 1510 5581 NPAS1 0 . GRCh38 19 47039443 47039443 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.841C>G p.Leu281Val p.L281V ENST00000602212 8/12 199 189 10 129 129 0 strelka-varscan-mutect NPAS1,missense_variant,p.Leu281Val,ENST00000602212,;NPAS1,missense_variant,p.Leu281Val,ENST00000449844,NM_002517.2;NPAS1,missense_variant,p.Leu106Val,ENST00000602189,;NPAS1,missense_variant,p.Leu105Val,ENST00000439365,NM_001321086.1;NPAS1,missense_variant,p.Leu105Val,ENST00000594670,;NPAS1,non_coding_transcript_exon_variant,,ENST00000600352,;NPAS1,intron_variant,,ENST00000601169,;NPAS1,intron_variant,,ENST00000594257,; G ENST00000602212 Transcript missense_variant 1061/2117 841/1773 281/590 L/V Ctg/Gtg 1 1 NPAS1 HGNC HGNC:7894 protein_coding YES CCDS12694.1 ENSP00000469142 Q99742 UPI0000073CD1 tolerated(0.42) 8/12 hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF25 MODERATE 1 SNV 1 1 PASS rs753683869 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 47039443 47039443 C G 1 0 0 0 0 1 0 0 0 10610 680 24 4 4 NPAS1 19 47039443 Missense_Mutation SNP C C3L-00144_T 389969 47039443 11578173 1511 5582 RASIP1 0 . GRCh38 19 48724920 48724920 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2168C>A p.Pro723His p.P723H ENST00000222145 9/12 260 172 88 224 223 1 strelka-varscan-mutect RASIP1,missense_variant,p.Pro723His,ENST00000222145,NM_017805.2;RASIP1,missense_variant,p.Pro153His,ENST00000599291,;RASIP1,downstream_gene_variant,,ENST00000594232,;RASIP1,non_coding_transcript_exon_variant,,ENST00000601530,; T ENST00000222145 Transcript missense_variant 2373/3308 2168/2892 723/963 P/H cCt/cAt 1 -1 RASIP1 HGNC HGNC:24716 protein_coding YES CCDS12731.1 ENSP00000222145 Q5U651 UPI000020283D NM_017805.2 deleterious(0.03) 9/12 PROSITE_profiles:PS51126,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 48724920 48724920 G T 1 0 0 0 0 1 0 0 0 13239 1000 35 2 2 RASIP1 19 48724920 Missense_Mutation SNP G C3L-00144_T 1685477 48724920 9892696 1512 5583 CGB5 0 . GRCh38 19 49045079 49045079 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.283G>T p.Gly95Cys p.G95C ENST00000301408 3/3 86 75 11 77 77 0 varscan-mutect CGB5,missense_variant,p.Gly95Cys,ENST00000301408,NM_033043.1;CGB8,downstream_gene_variant,,ENST00000448456,NM_033183.2;CTB-60B18.17,downstream_gene_variant,,ENST00000593746,; T ENST00000301408 Transcript missense_variant 609/841 283/498 95/165 G/C Ggc/Tgc 1 1 CGB5 HGNC HGNC:16452 protein_coding YES CCDS12752.1 ENSP00000301408 P0DN86 A0A0F7RQP8 UPI0000035497 NM_033043.1 deleterious(0) 3/3 hmmpanther:PTHR11515:SF16,hmmpanther:PTHR11515,Gene3D:2.10.90.10,Pfam_domain:PF00007,SMART_domains:SM00068,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS rs1380257856 . 0 204 6 0 0 0 0 0 -19.99979 0.9999999 1 1 1 0 T 3 4 12 49045079 49045079 G T 1 0 0 0 0 1 0 0 0 3057 1116 39 1 1 CGB5 19 49045079 Missense_Mutation SNP G C3L-00144_T 320159 49045079 9572537 1513 5584 TRPM4 0 . GRCh38 19 49190209 49190209 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2021C>G p.Ser674Cys p.S674C ENST00000252826 15/25 282 261 21 196 196 0 strelka-varscan-mutect TRPM4,missense_variant,p.Ser674Cys,ENST00000252826,NM_017636.3;TRPM4,missense_variant,p.Ser674Cys,ENST00000427978,NM_001195227.1;TRPM4,splice_region_variant,,ENST00000596338,;TRPM4,splice_region_variant,,ENST00000595519,NM_001321283.1;TRPM4,splice_region_variant,,ENST00000598502,NM_001321282.1;TRPM4,splice_region_variant,,ENST00000598697,NM_001321285.1;TRPM4,splice_region_variant,,ENST00000595071,;TRPM4,intron_variant,,ENST00000595882,; G ENST00000252826 Transcript missense_variant,splice_region_variant 2147/4109 2021/3645 674/1214 S/C tCt/tGt 1 1 TRPM4 HGNC HGNC:17993 protein_coding YES CCDS33073.1 ENSP00000252826 Q8TD43 UPI0000070598 NM_017636.3 deleterious(0) 15/25 hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 49190209 49190209 C G 1 0 0 0 0 1 0 0 0 17094 927 32 4 4 TRPM4 19 49190209 Missense_Mutation SNP C C3L-00144_T 145130 49190209 9427407 1514 5585 ASPDH 0 . GRCh38 19 50512577 50512577 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.436C>A p.Leu146Ile p.L146I ENST00000389208 5/7 27 17 10 14 14 0 strelka-varscan-mutect ASPDH,missense_variant,p.Leu146Ile,ENST00000389208,NM_001114598.1;ASPDH,missense_variant,p.Leu41Ile,ENST00000376916,NM_001024656.2;ASPDH,5_prime_UTR_variant,,ENST00000601207,;LRRC4B,downstream_gene_variant,,ENST00000599957,;LRRC4B,downstream_gene_variant,,ENST00000389201,NM_001080457.1;JOSD2,upstream_gene_variant,,ENST00000598418,NM_001270640.1,NM_001270639.1;JOSD2,upstream_gene_variant,,ENST00000601423,NM_138334.3,NM_001270686.1;JOSD2,upstream_gene_variant,,ENST00000595669,NM_001270641.1;JOSD2,upstream_gene_variant,,ENST00000594350,;ASPDH,downstream_gene_variant,,ENST00000598657,;ASPDH,non_coding_transcript_exon_variant,,ENST00000597030,;ASPDH,intron_variant,,ENST00000601287,;JOSD2,upstream_gene_variant,,ENST00000602146,;ASPDH,upstream_gene_variant,,ENST00000597232,;ASPDH,downstream_gene_variant,,ENST00000593569,;JOSD2,upstream_gene_variant,,ENST00000595718,; T ENST00000389208 Transcript missense_variant 498/1040 436/852 146/283 L/I Ctt/Att 1 -1 ASPDH HGNC HGNC:33856 protein_coding YES CCDS46153.1 ENSP00000373860 A6ND91 UPI00015B3C66 NM_001114598.1 deleterious(0.01) 5/7 Gene3D:3.30.360.10,PIRSF_domain:PIRSF005227,hmmpanther:PTHR31873,Superfamily_domains:SSF51735,Superfamily_domains:SSF55347 MODERATE SNV 5 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 50512577 50512577 G T 1 0 0 0 0 1 0 0 0 1198 1014 35 2 2 ASPDH 19 50512577 Missense_Mutation SNP G C3L-00144_T 1322368 50512577 8105039 1515 5586 KLK3 0 . GRCh38 19 50859995 50859995 + Silent SNP C C G C3L-00144_T C3L-00144_N C C c.654C>G p.= p.V218V ENST00000326003 5/5 93 67 26 95 95 0 strelka-varscan-mutect KLK3,synonymous_variant,p.=,ENST00000326003,NM_001648.2;KLK3,synonymous_variant,p.=,ENST00000617027,;KLK3,synonymous_variant,p.=,ENST00000595952,NM_001030048.1;KLK3,synonymous_variant,p.=,ENST00000598145,;KLK3,3_prime_UTR_variant,,ENST00000360617,NM_001030047.1;KLK3,downstream_gene_variant,,ENST00000593997,;KLK3,downstream_gene_variant,,ENST00000597483,;KLK3,downstream_gene_variant,,ENST00000601503,;KLK3,downstream_gene_variant,,ENST00000597286,;KLK2,upstream_gene_variant,,ENST00000593493,;KLK3,3_prime_UTR_variant,,ENST00000422986,;KLK3,3_prime_UTR_variant,,ENST00000596185,;KLK3,3_prime_UTR_variant,,ENST00000595392,;KLK3,non_coding_transcript_exon_variant,,ENST00000601349,;KLK3,non_coding_transcript_exon_variant,,ENST00000596333,;KLK3,non_coding_transcript_exon_variant,,ENST00000601812,;KLK3,downstream_gene_variant,,ENST00000595151,; G ENST00000326003 Transcript synonymous_variant 695/1463 654/786 218/261 V gtC/gtG COSM5390452 1 1 KLK3 HGNC HGNC:6364 protein_coding YES CCDS12807.1 ENSP00000314151 P07288 Q546G3 UPI0000001C9E NM_001648.2 5/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_patterns:PS00135,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF139,SMART_domains:SM00020,Superfamily_domains:SSF50494 1 LOW 1 SNV 1 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 G 2 3 12 50859995 50859995 C G 1 0 0 0 0 0 0 0 1 8274 900 32 4 4 KLK3 19 50859995 Silent SNP C C3L-00144_T 347418 50859995 7757621 1516 5587 KLK5 0 . GRCh38 19 50949049 50949049 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.402C>A p.Phe134Leu p.F134L ENST00000336334 4/6 301 212 89 269 268 1 strelka-varscan-mutect KLK5,missense_variant,p.Phe134Leu,ENST00000336334,NM_012427.4;KLK5,missense_variant,p.Phe134Leu,ENST00000391809,NM_001077491.1;KLK5,missense_variant,p.Phe134Leu,ENST00000593428,NM_001077492.1;KLK5,missense_variant,p.Phe134Leu,ENST00000594846,;CTB-147C22.8,upstream_gene_variant,,ENST00000601506,;CTB-147C22.8,upstream_gene_variant,,ENST00000594939,;KLK5,non_coding_transcript_exon_variant,,ENST00000595585,; T ENST00000336334 Transcript missense_variant 755/1563 402/882 134/293 F/L ttC/ttA 1 -1 KLK5 HGNC HGNC:6366 protein_coding YES CCDS12810.1 ENSP00000337733 Q9Y337 A0A024R4G4 UPI000003751F NM_012427.4 tolerated(0.77) 4/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF270,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 50949049 50949049 G T 1 0 0 0 0 1 0 0 0 8276 1165 41 2 2 KLK5 19 50949049 Missense_Mutation SNP G C3L-00144_T 89054 50949049 7668567 1517 5588 KLK12 0 . GRCh38 19 51032116 51032116 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.217G>T p.Gly73Trp p.G73W ENST00000250351 4/7 510 455 55 405 404 1 strelka-varscan-mutect KLK12,missense_variant,p.Gly73Trp,ENST00000525263,;KLK12,missense_variant,p.Gly73Trp,ENST00000319590,NM_145894.1;KLK12,missense_variant,p.Gly73Trp,ENST00000250351,NM_019598.2;KLK12,intron_variant,,ENST00000529888,NM_145895.1;KLK11,upstream_gene_variant,,ENST00000594768,NM_144947.1;KLK11,upstream_gene_variant,,ENST00000319720,NM_006853.2;KLK11,upstream_gene_variant,,ENST00000391804,NM_001167605.1;CTC-518B2.9,intron_variant,,ENST00000594910,;KLK11,upstream_gene_variant,,ENST00000594458,;KLK12,missense_variant,p.Gly73Trp,ENST00000531374,;KLK12,intron_variant,,ENST00000526824,;KLK12,intron_variant,,ENST00000530943,;KLK11,upstream_gene_variant,,ENST00000319756,; A ENST00000250351 Transcript missense_variant 334/882 217/765 73/254 G/W Ggg/Tgg 1 -1 KLK12 HGNC HGNC:6360 protein_coding YES CCDS12820.1 ENSP00000250351 Q9UKR0 UPI000002ACDD NM_019598.2 deleterious(0) 4/7 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF217,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51032116 51032116 C A 1 0 0 0 0 1 0 0 0 8269 623 22 2 2 KLK12 19 51032116 Missense_Mutation SNP C C3L-00144_T 83067 51032116 7585500 1518 5589 SIGLEC9 0 . GRCh38 19 51127145 51127145 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.864C>T p.= p.S288S ENST00000440804 4/7 457 336 121 346 345 1 strelka-varscan-mutect SIGLEC9,synonymous_variant,p.=,ENST00000440804,NM_001198558.1;SIGLEC9,synonymous_variant,p.=,ENST00000250360,NM_014441.2;SIGLEC9,synonymous_variant,p.=,ENST00000599948,;SIGLEC18P,downstream_gene_variant,,ENST00000602271,; T ENST00000440804 Transcript synonymous_variant 931/1960 864/1440 288/479 S agC/agT 1 1 SIGLEC9 HGNC HGNC:10878 protein_coding YES CCDS56100.1 ENSP00000413861 Q9Y336 UPI00017A75A8 NM_001198558.1 4/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF43,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 51127145 51127145 C T 1 0 0 0 0 0 0 0 1 14579 796 28 3 3 SIGLEC9 19 51127145 Silent SNP C C3L-00144_T 95029 51127145 7490471 1519 5590 SIGLEC7 0 . GRCh38 19 51142605 51142605 + Missense_Mutation SNP C C A rs773967401 C3L-00144_T C3L-00144_N C C c.236C>A p.Ala79Asp p.A79D ENST00000317643 1/7 418 370 48 314 314 0 strelka-varscan-mutect SIGLEC7,missense_variant,p.Ala79Asp,ENST00000317643,NM_014385.3;SIGLEC7,missense_variant,p.Ala79Asp,ENST00000305628,NM_016543.3;SIGLEC7,missense_variant,p.Ala79Asp,ENST00000601682,;SIGLEC7,missense_variant,p.Ala79Asp,ENST00000600577,NM_001277201.1;SIGLEC7,missense_variant,p.Ala79Asp,ENST00000536156,;SIGLEC7,upstream_gene_variant,,ENST00000599250,;CTD-3187F8.15,downstream_gene_variant,,ENST00000601996,;SIGLEC19P,upstream_gene_variant,,ENST00000600623,; A ENST00000317643 Transcript missense_variant 305/1754 236/1404 79/467 A/D gCc/gAc rs773967401 1 1 SIGLEC7 HGNC HGNC:10876 protein_coding YES CCDS12826.1 ENSP00000323328 Q9Y286 UPI000011B40B NM_014385.3 deleterious(0) 1/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF43,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs773967401 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51142605 51142605 C A 1 0 0 0 0 1 0 0 0 14577 739 26 2 2 SIGLEC7 19 51142605 Missense_Mutation SNP C C3L-00144_T 15460 51142605 7475011 1520 5591 IGLON5 0 . GRCh38 19 51323780 51323780 + Nonsense_Mutation SNP G G T rs527872132 C3L-00144_T C3L-00144_N G G c.277G>T p.Glu93Ter p.E93* ENST00000270642 3/8 185 171 14 151 151 0 varscan-mutect IGLON5,stop_gained,p.Glu93Ter,ENST00000270642,NM_001101372.1; T ENST00000270642 Transcript stop_gained 277/2606 277/1011 93/336 E/* Gag/Tag rs527872132,COSM287159 1 1 IGLON5 HGNC HGNC:34550 protein_coding YES CCDS46158.1 ENSP00000270642 A6NGN9 UPI000058F1A8 NM_001101372.1 3/8 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF148,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 HIGH 1 SNV 5 0,1 1 PASS rs527872132 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 51323780 51323780 G T 1 0 0 0 0 0 1 0 0 7502 1059 37 1 1 IGLON5 19 51323780 Nonsense_Mutation SNP G C3L-00144_T 181175 51323780 7293836 1521 5592 NKG7 0 . GRCh38 19 51371972 51371972 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.407G>C p.Gly136Ala p.G136A ENST00000221978 3/4 119 82 37 96 96 0 strelka-varscan-mutect NKG7,missense_variant,p.Gly136Ala,ENST00000221978,NM_005601.3;NKG7,missense_variant,p.Ala130Pro,ENST00000595217,;NKG7,missense_variant,p.Gly43Ala,ENST00000593572,;NKG7,missense_variant,p.Gly60Ala,ENST00000595157,;NKG7,intron_variant,,ENST00000600427,;CLDND2,upstream_gene_variant,,ENST00000291715,NM_152353.2;CLDND2,upstream_gene_variant,,ENST00000601435,;CLDND2,upstream_gene_variant,,ENST00000593841,;CTD-2616J11.11,upstream_gene_variant,,ENST00000600067,; G ENST00000221978 Transcript missense_variant 587/843 407/498 136/165 G/A gGc/gCc 1 -1 NKG7 HGNC HGNC:7830 protein_coding YES CCDS12830.1 ENSP00000221978 Q16617 UPI00001301FE NM_005601.3 tolerated(0.08) 3/4 Pfam_domain:PF00822,hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF34,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 12 51371972 51371972 C G 1 0 0 0 0 1 0 0 0 10478 739 26 4 4 NKG7 19 51371972 Missense_Mutation SNP C C3L-00144_T 48192 51371972 7245644 1522 5593 AC018755.18 0 . GRCh38 19 51646303 51646303 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.375T>A p.Asp125Glu p.D125E ENST00000360844 2/7 151 136 15 114 114 0 varscan-mutect SIGLEC14,missense_variant,p.Asp125Glu,ENST00000360844,NM_001098612.1;AC018755.18,missense_variant,p.Asp125Glu,ENST00000599649,;AC018755.18,intron_variant,,ENST00000429354,;SIGLEC5,upstream_gene_variant,,ENST00000534261,NM_003830.3;SIGLEC14,upstream_gene_variant,,ENST00000533866,;RPL7P51,upstream_gene_variant,,ENST00000490532,; T ENST00000360844 Transcript missense_variant 417/2035 375/1191 125/396 D/E gaT/gaA 1 -1 SIGLEC14 HGNC HGNC:32926 protein_coding YES CCDS42604.1 ENSP00000354090 Q08ET2 UPI0000E44158 NM_001098612.1 tolerated(0.42) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF67,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1233286194 . 65 144 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 51646303 51646303 A T 1 0 0 0 0 1 0 0 0 125 214 8 4 4 AC018755.18 19 51646303 Missense_Mutation SNP A C3L-00144_T 274331 51646303 6971313 1523 5594 HAS1 0 . GRCh38 19 51713701 51713701 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1463G>T p.Trp488Leu p.W488L ENST00000222115 5/5 257 169 88 231 230 1 strelka-varscan-mutect HAS1,missense_variant,p.Trp487Leu,ENST00000540069,NM_001297436.1;HAS1,missense_variant,p.Trp488Leu,ENST00000222115,NM_001523.3;HAS1,missense_variant,p.Trp495Leu,ENST00000601714,;HAS1,downstream_gene_variant,,ENST00000594621,;HAS1,downstream_gene_variant,,ENST00000601667,;SPACA6,downstream_gene_variant,,ENST00000573896,; A ENST00000222115 Transcript missense_variant 1498/2087 1463/1737 488/578 W/L tGg/tTg 1 -1 HAS1 HGNC HGNC:4818 protein_coding YES CCDS12838.1 ENSP00000222115 Q92839 UPI000006D531 NM_001523.3 deleterious(0) 5/5 hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF4 MODERATE 1 SNV 1 1 PASS rs755563438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51713701 51713701 C A 1 0 0 0 0 1 0 0 0 6847 595 21 2 2 HAS1 19 51713701 Missense_Mutation SNP C C3L-00144_T 67398 51713701 6903915 1524 5595 ZNF577 0 . GRCh38 19 51873535 51873535 + Missense_Mutation SNP C C A rs766397069 C3L-00144_T C3L-00144_N C C c.455G>T p.Cys152Phe p.C152F ENST00000301399 7/7 271 182 89 197 196 1 strelka-varscan-mutect ZNF577,missense_variant,p.Cys152Phe,ENST00000301399,NM_032679.2;AC074141.1,splice_region_variant,,ENST00000451628,NM_001135590.1; A ENST00000301399 Transcript missense_variant 846/3079 455/1458 152/485 C/F tGt/tTt rs766397069 1 -1 ZNF577 HGNC HGNC:28673 protein_coding YES CCDS12842.2 ENSP00000301399 Q9BSK1 A0A024R4N6 UPI000059D778 NM_032679.2 tolerated(0.43) 7/7 hmmpanther:PTHR24377:SF327,hmmpanther:PTHR24377,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs766397069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 51873535 51873535 C A 1 0 0 0 0 1 0 0 0 18583 492 17 2 2 ZNF577 19 51873535 Missense_Mutation SNP C C3L-00144_T 159834 51873535 6744081 1525 5596 ZNF649 0 . GRCh38 19 51891874 51891874 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.262C>T p.= p.L88L ENST00000354957 5/5 62 51 11 40 40 0 strelka-varscan-mutect ZNF649,synonymous_variant,p.=,ENST00000354957,NM_023074.3;ZNF649,synonymous_variant,p.=,ENST00000600738,;ZNF577,upstream_gene_variant,,ENST00000301399,NM_032679.2;ZNF649,downstream_gene_variant,,ENST00000599530,;ZNF649,downstream_gene_variant,,ENST00000596690,;ZNF649,downstream_gene_variant,,ENST00000595418,;ZNF649-AS1,intron_variant,,ENST00000600329,;ZNF649,downstream_gene_variant,,ENST00000599671,;ZNF649,downstream_gene_variant,,ENST00000597882,; A ENST00000354957 Transcript synonymous_variant 547/3197 262/1518 88/505 L Ctg/Ttg 1 -1 ZNF649 HGNC HGNC:25741 protein_coding YES CCDS12843.1 ENSP00000347043 Q9BS31 UPI000006D442 NM_023074.3 5/5 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF34 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999955 1 1 1 0 A 2 1 12 51891874 51891874 G A 1 0 0 0 0 0 0 0 1 18637 933 33 3 3 ZNF649 19 51891874 Silent SNP G C3L-00144_T 18339 51891874 6725742 1526 5597 ZNF350 0 . GRCh38 19 51965807 51965807 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.646A>C p.Ile216Leu p.I216L ENST00000243644 5/5 283 197 86 215 215 0 strelka-varscan-mutect ZNF350,missense_variant,p.Ile216Leu,ENST00000243644,NM_021632.3;ZNF350,downstream_gene_variant,,ENST00000601430,;ZNF350,downstream_gene_variant,,ENST00000594929,;ZNF350,downstream_gene_variant,,ENST00000597788,;ZNF350,downstream_gene_variant,,ENST00000593596,;ZNF350-AS1,intron_variant,,ENST00000595010,;ZNF350-AS1,intron_variant,,ENST00000600253,;ZNF350,downstream_gene_variant,,ENST00000600703,;ZNF350,downstream_gene_variant,,ENST00000598254,; G ENST00000243644 Transcript missense_variant 874/2338 646/1599 216/532 I/L Atc/Ctc 1 -1 ZNF350 HGNC HGNC:16656 protein_coding YES CCDS12845.1 ENSP00000243644 Q9GZX5 UPI00000721F1 NM_021632.3 tolerated(0.4) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF11,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 51965807 51965807 T G 1 0 0 0 0 1 0 0 0 18435 1464 51 5 5 ZNF350 19 51965807 Missense_Mutation SNP T C3L-00144_T 73933 51965807 6651809 1527 5598 PPP2R1A 0 . GRCh38 19 52212988 52212988 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.685G>A p.Val229Met p.V229M ENST00000322088 6/15 96 64 32 70 70 0 strelka-varscan-mutect PPP2R1A,missense_variant,p.Val229Met,ENST00000322088,NM_014225.5;PPP2R1A,missense_variant,p.Val50Met,ENST00000462990,;PPP2R1A,missense_variant,p.Val269Met,ENST00000454220,;PPP2R1A,downstream_gene_variant,,ENST00000473455,;PPP2R1A,downstream_gene_variant,,ENST00000495876,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000473820,;PPP2R1A,non_coding_transcript_exon_variant,,ENST00000462047,;PPP2R1A,downstream_gene_variant,,ENST00000468280,;PPP2R1A,downstream_gene_variant,,ENST00000490868,; A ENST00000322088 Transcript missense_variant 743/5380 685/1770 229/589 V/M Gtg/Atg COSM371369,COSM5347055 1 1 PPP2R1A HGNC HGNC:9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 A8K7B7 UPI000006EB9C NM_014225.5 deleterious(0) 6/15 PROSITE_profiles:PS50077,hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Gene3D:1.25.10.10,Pfam_domain:PF13646,Superfamily_domains:SSF48371 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 52212988 52212988 G A 1 0 0 0 0 1 0 0 0 12505 1145 40 1 1 PPP2R1A 19 52212988 Missense_Mutation SNP G C3L-00144_T 247181 52212988 6404628 1528 5599 ZNF534 0 . GRCh38 19 52438235 52438235 + Missense_Mutation SNP C C G rs371740379 C3L-00144_T C3L-00144_N C C c.814C>G p.Gln272Glu p.Q272E ENST00000332323 4/4 235 167 68 198 198 0 strelka-varscan-mutect ZNF534,missense_variant,p.Gln272Glu,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Gln259Glu,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; G ENST00000332323 Transcript missense_variant 875/2086 814/2025 272/674 Q/E Caa/Gaa rs371740379 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 tolerated(1) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs371740379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 52438235 52438235 C G 1 0 0 0 0 1 0 0 0 18546 479 17 4 4 ZNF534 19 52438235 Missense_Mutation SNP C C3L-00144_T 225247 52438235 6179381 1529 5600 ZNF415 0 . GRCh38 19 53109265 53109265 + Silent SNP C C G rs142864555 C3L-00144_T C3L-00144_N C C c.780G>C p.= p.A260A ENST00000500065 4/4 184 149 35 172 172 0 strelka-varscan-mutect ZNF415,synonymous_variant,p.=,ENST00000500065,NM_001136038.2;ZNF415,synonymous_variant,p.=,ENST00000421033,NM_001164309.1;ZNF415,synonymous_variant,p.=,ENST00000243643,NM_018355.3;ZNF415,synonymous_variant,p.=,ENST00000601493,;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; G ENST00000500065 Transcript synonymous_variant 1114/2496 780/1668 260/555 A gcG/gcC rs142864555,COSM4080968 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,SMART_domains:SM00614,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 0,1 LOW 1 SNV 4 0,1 1 PASS rs142864555 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 53109265 53109265 C G 1 0 0 0 0 0 0 0 1 18464 755 27 4 4 ZNF415 19 53109265 Silent SNP C C3L-00144_T 671030 53109265 5508351 1530 5601 ZNF845 0 . GRCh38 19 53352452 53352452 + Missense_Mutation SNP A A G rs774098620 C3L-00144_T C3L-00144_N A A c.1777A>G p.Thr593Ala p.T593A ENST00000458035 4/4 287 227 60 260 260 0 strelka-varscan-mutect ZNF845,missense_variant,p.Thr593Ala,ENST00000458035,NM_138374.1;ZNF845,missense_variant,p.Thr593Ala,ENST00000595091,;ZNF525,intron_variant,,ENST00000635711,;ZNF845,downstream_gene_variant,,ENST00000601857,; G ENST00000458035 Transcript missense_variant 1894/4311 1777/2913 593/970 T/A Acc/Gcc rs774098620 1 1 ZNF845 HGNC HGNC:25112 protein_coding YES CCDS46170.1 ENSP00000388311 Q96IR2 UPI0001662BAC NM_138374.1 tolerated(0.59) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS rs774098620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 53352452 53352452 A G 1 0 0 0 0 1 0 0 0 18779 43 2 5 5 ZNF845 19 53352452 Missense_Mutation SNP A C3L-00144_T 243187 53352452 5265164 1531 5602 ZNF813 0 . GRCh38 19 53491074 53491074 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.842G>T p.Ser281Ile p.S281I ENST00000396403 4/4 327 230 97 279 278 1 strelka-varscan-mutect ZNF813,missense_variant,p.Ser281Ile,ENST00000396403,NM_001004301.3;ZNF813,downstream_gene_variant,,ENST00000490956,;ZNF813,downstream_gene_variant,,ENST00000468450,;CTD-2224J9.4,upstream_gene_variant,,ENST00000483735,; T ENST00000396403 Transcript missense_variant 970/6151 842/1854 281/617 S/I aGt/aTt 1 1 ZNF813 HGNC HGNC:33257 protein_coding YES CCDS46172.1 ENSP00000379684 Q6ZN06 UPI000040C511 NM_001004301.3 tolerated(0.17) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 53491074 53491074 G T 1 0 0 0 0 1 0 0 0 18761 1029 36 2 2 ZNF813 19 53491074 Missense_Mutation SNP G C3L-00144_T 138622 53491074 5126542 1532 5603 LILRB1 0 . GRCh38 19 54633671 54633671 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1295G>T p.Gly432Val p.G432V ENST00000324602 8/15 112 84 28 77 77 0 strelka-varscan-mutect LILRB1,missense_variant,p.Gly432Val,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Gly432Val,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Gly432Val,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Gly432Val,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Gly468Val,ENST00000427581,;LILRB1,missense_variant,p.Gly432Val,ENST00000396315,;LILRB1,intron_variant,,ENST00000396317,NM_001278398.2;AC009892.10,downstream_gene_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,non_coding_transcript_exon_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,missense_variant,p.Gly432Val,ENST00000421584,;LILRB1,upstream_gene_variant,,ENST00000480375,;LILRB1,upstream_gene_variant,,ENST00000487425,; T ENST00000324602 Transcript missense_variant 1460/2774 1295/1959 432/652 G/V gGc/gTc 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 deleterious(0.04) 8/15 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54633671 54633671 G T 1 0 0 0 0 1 0 0 0 8698 1203 42 2 2 LILRB1 19 54633671 Missense_Mutation SNP G C3L-00144_T 1142597 54633671 3983945 1533 5604 LILRB1 0 . GRCh38 19 54634657 54634657 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1380G>T p.= p.L460L ENST00000324602 10/15 154 127 27 90 90 0 strelka-varscan-mutect LILRB1,synonymous_variant,p.=,ENST00000396331,NM_006669.6;LILRB1,synonymous_variant,p.=,ENST00000396327,NM_001081638.3;LILRB1,synonymous_variant,p.=,ENST00000396332,NM_001081639.3;LILRB1,synonymous_variant,p.=,ENST00000324602,NM_001081637.2;LILRB1,synonymous_variant,p.=,ENST00000427581,;LILRB1,synonymous_variant,p.=,ENST00000396315,;LILRB1,synonymous_variant,p.=,ENST00000396317,NM_001278398.2;AC009892.10,downstream_gene_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,synonymous_variant,p.=,ENST00000421584,;LILRB1,non_coding_transcript_exon_variant,,ENST00000487425,;LILRB1,upstream_gene_variant,,ENST00000480375,; T ENST00000324602 Transcript synonymous_variant 1545/2774 1380/1959 460/652 L ctG/ctT 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 10/15 Low_complexity_(Seg):seg,hmmpanther:PTHR11738:SF117,hmmpanther:PTHR11738 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 54634657 54634657 G T 1 0 0 0 0 0 0 0 1 8698 1335 47 2 2 LILRB1 19 54634657 Silent SNP G C3L-00144_T 986 54634657 3982959 1534 5605 LILRB4 0 . GRCh38 19 54666721 54666721 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1013C>A p.Pro338His p.P338H ENST00000391736 12/14 258 236 22 206 205 1 strelka-varscan-mutect LILRB4,missense_variant,p.Pro338His,ENST00000391736,NM_001278426.3;LILRB4,missense_variant,p.Pro338His,ENST00000430952,NM_001278427.3;LILRB4,missense_variant,p.Pro339His,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,missense_variant,p.Pro338His,ENST00000391734,;LILRB4,missense_variant,p.Pro337His,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,non_coding_transcript_exon_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,non_coding_transcript_exon_variant,,ENST00000470943,;AC011515.2,upstream_gene_variant,,ENST00000441512,; A ENST00000391736 Transcript missense_variant 1328/4002 1013/1347 338/448 P/H cCt/cAt 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 deleterious(0.02) 12/14 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 54666721 54666721 C A 1 0 0 0 0 1 0 0 0 8701 681 24 2 2 LILRB4 19 54666721 Missense_Mutation SNP C C3L-00144_T 32064 54666721 3950895 1535 5606 KIR3DL3 0 . GRCh38 19 54727801 54727801 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.546G>T p.Met182Ile p.M182I ENST00000291860 4/8 388 350 38 252 252 0 strelka-mutect KIR3DL3,missense_variant,p.Met182Ile,ENST00000291860,NM_153443.4;CTB-61M7.1,intron_variant,,ENST00000400864,; T ENST00000291860 Transcript missense_variant 564/1691 546/1233 182/410 M/I atG/atT 1 1 KIR3DL3 HGNC HGNC:16312 protein_coding YES CCDS12903.1 ENSP00000291860 A0A0B4J1R5 UPI00005056C3 NM_153443.4 tolerated(1) 4/8 hmmpanther:PTHR11738:SF91,hmmpanther:PTHR11738,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1230115617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 54727801 54727801 G T 1 0 0 0 0 1 0 0 0 8186 1348 47 2 2 KIR3DL3 19 54727801 Missense_Mutation SNP G C3L-00144_T 61080 54727801 3889815 1536 5607 KIR2DL4 0 . GRCh38 19 54805057 54805057 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.341C>A p.Pro114His p.P114H ENST00000345540 3/7 81 71 10 70 70 0 strelka-varscan-mutect KIR2DL4,missense_variant,p.Pro153His,ENST00000396284,;KIR2DL4,missense_variant,p.Pro113His,ENST00000396289,;KIR2DL4,missense_variant,p.Pro114His,ENST00000359085,NM_001080772.1;KIR2DL4,missense_variant,p.Pro114His,ENST00000345540,NM_001080770.1;KIR2DL4,missense_variant,p.Pro114His,ENST00000357494,;KIR2DL4,intron_variant,,ENST00000346587,;KIR2DL4,intron_variant,,ENST00000396293,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000463062,;KIR2DL4,non_coding_transcript_exon_variant,,ENST00000486965,; A ENST00000345540 Transcript missense_variant 353/1447 341/1029 114/342 P/H cCc/cAc 1 1 KIR2DL4 HGNC HGNC:6332 protein_coding YES CCDS42619.1 ENSP00000339634 Q99706 UPI000013E082 NM_001080770.1 deleterious(0) 3/7 Gene3D:2.60.40.10,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF91,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.98664 1 1 1 1 0 A 3 1 12 54805057 54805057 C A 1 0 0 0 0 1 0 0 0 8183 623 22 2 2 KIR2DL4 19 54805057 Missense_Mutation SNP C C3L-00144_T 77256 54805057 3812559 1537 5608 EPS8L1 0 . GRCh38 19 55081390 55081390 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.672G>C p.Gln224His p.Q224H ENST00000201647 8/20 255 219 36 191 191 0 strelka-varscan-mutect EPS8L1,missense_variant,p.Gln224His,ENST00000201647,NM_133180.2;EPS8L1,missense_variant,p.Gln160His,ENST00000540810,;EPS8L1,missense_variant,p.Gln97His,ENST00000245618,NM_017729.3;EPS8L1,missense_variant,p.Gln206His,ENST00000586329,;EPS8L1,intron_variant,,ENST00000588359,;EPS8L1,non_coding_transcript_exon_variant,,ENST00000592824,;EPS8L1,upstream_gene_variant,,ENST00000585347,;EPS8L1,missense_variant,p.Gln186His,ENST00000587786,;EPS8L1,non_coding_transcript_exon_variant,,ENST00000590232,;EPS8L1,upstream_gene_variant,,ENST00000592102,;EPS8L1,upstream_gene_variant,,ENST00000589362,;EPS8L1,upstream_gene_variant,,ENST00000592284,;EPS8L1,downstream_gene_variant,,ENST00000591219,;EPS8L1,upstream_gene_variant,,ENST00000590610,;EPS8L1,downstream_gene_variant,,ENST00000592044,;EPS8L1,upstream_gene_variant,,ENST00000589694,;EPS8L1,downstream_gene_variant,,ENST00000592318,; C ENST00000201647 Transcript missense_variant 728/2536 672/2172 224/723 Q/H caG/caC 1 1 EPS8L1 HGNC HGNC:21295 protein_coding YES CCDS12914.1 ENSP00000201647 Q8TE68 UPI000013C630 NM_133180.2 tolerated(0.54) 8/20 hmmpanther:PTHR12287,hmmpanther:PTHR12287:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 12 55081390 55081390 G C 1 0 0 0 0 1 0 0 0 5043 933 33 4 4 EPS8L1 19 55081390 Missense_Mutation SNP G C3L-00144_T 276333 55081390 3536226 1538 5609 SBK2 0 . GRCh38 19 55529809 55529809 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.971A>T p.His324Leu p.H324L ENST00000413299 4/4 268 189 79 242 242 0 strelka-varscan-mutect SBK2,missense_variant,p.His324Leu,ENST00000413299,NM_001101401.2;SBK2,missense_variant,p.His324Leu,ENST00000344158,; A ENST00000413299 Transcript missense_variant 1009/1085 971/1047 324/348 H/L cAc/cTc 1 -1 SBK2 HGNC HGNC:34416 protein_coding YES CCDS42631.1 ENSP00000389015 P0C263 UPI00015DFA43 NM_001101401.2 deleterious(0) 4/4 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 55529809 55529809 T A 1 0 0 0 0 1 0 0 0 14125 1696 59 4 4 SBK2 19 55529809 Missense_Mutation SNP T C3L-00144_T 448419 55529809 3087807 1539 5610 ZNF579 0 . GRCh38 19 55579109 55579109 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.531G>T p.= p.G177G ENST00000325421 2/2 326 248 78 251 250 1 strelka-varscan-mutect ZNF579,synonymous_variant,p.=,ENST00000325421,NM_152600.2;ZNF579,downstream_gene_variant,,ENST00000592239,; A ENST00000325421 Transcript synonymous_variant 560/2899 531/1689 177/562 G ggG/ggT 1 -1 ZNF579 HGNC HGNC:26646 protein_coding YES CCDS12927.1 ENSP00000320188 Q8NAF0 UPI0000141657 NM_152600.2 2/2 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 55579109 55579109 C A 1 0 0 0 0 0 0 0 1 18585 610 22 2 2 ZNF579 19 55579109 Silent SNP C C3L-00144_T 49300 55579109 3038507 1540 5611 NLRP9 0 . GRCh38 19 55715166 55715166 + Missense_Mutation SNP C C A rs761525281 C3L-00144_T C3L-00144_N C C c.2390G>T p.Cys797Phe p.C797F ENST00000332836 6/9 227 210 17 147 147 0 strelka-varscan-mutect NLRP9,missense_variant,p.Cys797Phe,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Cys797Phe,ENST00000590200,; A ENST00000332836 Transcript missense_variant 2418/3484 2390/2976 797/991 C/F tGc/tTc rs761525281 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 tolerated(0.68) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs761525281 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 55715166 55715166 C A 1 0 0 0 0 1 0 0 0 10522 710 25 2 2 NLRP9 19 55715166 Missense_Mutation SNP C C3L-00144_T 136057 55715166 2902450 1541 5612 NLRP9 0 . GRCh38 19 55733200 55733200 + Nonsense_Mutation SNP C C A rs150929335 C3L-00144_T C3L-00144_N C C c.631G>T p.Glu211Ter p.E211* ENST00000332836 2/9 141 97 44 95 95 0 strelka-varscan-mutect NLRP9,stop_gained,p.Glu211Ter,ENST00000332836,NM_176820.3;NLRP9,stop_gained,p.Glu211Ter,ENST00000590200,;RN7SKP109,upstream_gene_variant,,ENST00000410592,; A ENST00000332836 Transcript stop_gained 659/3484 631/2976 211/991 E/* Gag/Tag rs150929335 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 2/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS rs150929335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 55733200 55733200 C A 1 0 0 0 0 0 1 0 0 10522 922 32 2 2 NLRP9 19 55733200 Nonsense_Mutation SNP C C3L-00144_T 18034 55733200 2884416 1542 5613 NLRP11 0 . GRCh38 19 55809722 55809722 + Silent SNP C C A rs745959992 C3L-00144_T C3L-00144_N C C c.888G>T p.= p.T296T ENST00000589093 3/10 204 186 18 128 128 0 strelka-varscan-mutect NLRP11,synonymous_variant,p.=,ENST00000589093,NM_145007.3;NLRP11,synonymous_variant,p.=,ENST00000589824,;NLRP11,synonymous_variant,p.=,ENST00000592953,NM_001297743.1;NLRP11,downstream_gene_variant,,ENST00000593208,;NLRP11,synonymous_variant,p.=,ENST00000590409,;NLRP11,synonymous_variant,p.=,ENST00000593244,; A ENST00000589093 Transcript synonymous_variant 982/3417 888/3102 296/1033 T acG/acT rs745959992 1 -1 NLRP11 HGNC HGNC:22945 protein_coding YES CCDS12935.1 ENSP00000466285 P59045 UPI000013ED9D NM_145007.3 3/10 hmmpanther:PTHR24106:SF62,hmmpanther:PTHR24106,Pfam_domain:PF05729 LOW 1 SNV 1 1 PASS rs745959992 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 55809722 55809722 C A 1 0 0 0 0 0 0 0 1 10510 871 31 1 1 NLRP11 19 55809722 Silent SNP C C3L-00144_T 76522 55809722 2807894 1543 5614 NLRP8 0 . GRCh38 19 55948089 55948089 + Nonsense_Mutation SNP G G T rs200578165 C3L-00144_T C3L-00144_N G G c.187G>T p.Glu63Ter p.E63* ENST00000291971 1/10 188 161 27 181 181 0 strelka-varscan-mutect NLRP8,stop_gained,p.Glu63Ter,ENST00000291971,NM_176811.2;NLRP8,stop_gained,p.Glu63Ter,ENST00000590542,; T ENST00000291971 Transcript stop_gained 258/3934 187/3147 63/1048 E/* Gag/Tag rs200578165 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 1/10 PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF54,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Pfam_domain:PF02758,SMART_domains:SM01289,Superfamily_domains:SSF47986 HIGH 1 SNV 2 1 PASS rs200578165 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 55948089 55948089 G T 1 0 0 0 0 0 1 0 0 10521 1291 45 2 2 NLRP8 19 55948089 Nonsense_Mutation SNP G C3L-00144_T 138367 55948089 2669527 1544 5615 NLRP8 0 . GRCh38 19 55955400 55955400 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1342C>A p.Gln448Lys p.Q448K ENST00000291971 3/10 238 167 71 216 216 0 strelka-varscan-mutect NLRP8,missense_variant,p.Gln448Lys,ENST00000291971,NM_176811.2;NLRP8,missense_variant,p.Gln448Lys,ENST00000590542,; A ENST00000291971 Transcript missense_variant 1413/3934 1342/3147 448/1048 Q/K Caa/Aaa 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 deleterious(0.02) 3/10 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF54 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 55955400 55955400 C A 1 0 0 0 0 1 0 0 0 10521 595 21 2 2 NLRP8 19 55955400 Missense_Mutation SNP C C3L-00144_T 7311 55955400 2662216 1545 5616 NLRP5 0 . GRCh38 19 56015797 56015797 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.564A>T p.Gln188His p.Q188H ENST00000390649 4/15 109 96 13 79 79 0 strelka-varscan-mutect NLRP5,missense_variant,p.Gln188His,ENST00000390649,NM_153447.4;NLRP5,intron_variant,,ENST00000621651,;NLRP5,missense_variant,p.Gln161His,ENST00000597673,; T ENST00000390649 Transcript missense_variant,splice_region_variant 564/3888 564/3603 188/1200 Q/H caA/caT 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 tolerated(0.11) 4/15 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 56015797 56015797 A T 1 0 0 0 0 1 0 0 0 10518 86 3 4 4 NLRP5 19 56015797 Missense_Mutation SNP A C3L-00144_T 60397 56015797 2601819 1546 5617 NLRP5 0 . GRCh38 19 56033681 56033681 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2587C>A p.His863Asn p.H863N ENST00000390649 9/15 100 87 13 83 83 0 strelka-varscan-mutect NLRP5,missense_variant,p.His863Asn,ENST00000390649,NM_153447.4;NLRP5,missense_variant,p.His863Asn,ENST00000621651,; A ENST00000390649 Transcript missense_variant 2587/3888 2587/3603 863/1200 H/N Cac/Aac 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 deleterious(0.04) 9/15 hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.92697 0.9999999 1 1 1 0 A 3 1 12 56033681 56033681 C A 1 0 0 0 0 1 0 0 0 10518 478 17 2 2 NLRP5 19 56033681 Missense_Mutation SNP C C3L-00144_T 17884 56033681 2583935 1547 5618 GALP 0 . GRCh38 19 56183203 56183203 + Nonsense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.286G>T p.Glu96Ter p.E96* ENST00000357330 5/6 269 250 19 188 188 0 strelka-varscan-mutect GALP,stop_gained,p.Glu96Ter,ENST00000357330,NM_033106.3;GALP,3_prime_UTR_variant,,ENST00000440823,NM_001145546.1;GALP,downstream_gene_variant,,ENST00000590002,; T ENST00000357330 Transcript stop_gained 368/938 286/351 96/116 E/* Gag/Tag 1 1 GALP HGNC HGNC:24840 protein_coding YES CCDS12940.1 ENSP00000349884 Q9UBC7 UPI0000039C09 NM_033106.3 5/6 hmmpanther:PTHR20950,hmmpanther:PTHR20950:SF1 HIGH 1 SNV 1 1 PASS rs1173168886 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 56183203 56183203 G T 1 0 0 0 0 0 1 0 0 6094 943 33 2 2 GALP 19 56183203 Nonsense_Mutation SNP G C3L-00144_T 149522 56183203 2434413 1548 5619 ZSCAN5CP 0 . GRCh38 19 56208514 56208514 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.805G>C p.Ala269Pro p.A269P ENST00000534327 5/5 190 171 19 154 153 1 varscan-mutect ZSCAN5CP,missense_variant,p.Ala269Pro,ENST00000534327,;ZSCAN5CP,missense_variant,p.Ala269Pro,ENST00000376267,; C ENST00000534327 Transcript missense_variant 954/1892 805/1491 269/496 A/P Gct/Cct 1 1 ZSCAN5CP HGNC HGNC:34294 protein_coding YES ENSP00000435234 A6NGD5 UPI000041AA91 deleterious(0.01) 5/5 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF223 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 56208514 56208514 G C 1 0 0 0 0 1 0 0 0 18839 1319 46 4 4 ZSCAN5CP 19 56208514 Missense_Mutation SNP G C3L-00144_T 25311 56208514 2409102 1549 5620 ZNF667 0 . GRCh38 19 56442256 56442256 + Missense_Mutation SNP G G T rs750443644 C3L-00144_T C3L-00144_N G G c.739C>A p.His247Asn p.H247N ENST00000504904 7/7 215 203 12 162 161 1 strelka-varscan-mutect ZNF667,missense_variant,p.His247Asn,ENST00000504904,NM_001321356.1;ZNF667,missense_variant,p.His247Asn,ENST00000292069,NM_022103.3;ZNF667,missense_variant,p.His29Asn,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; T ENST00000504904 Transcript missense_variant 1459/4390 739/1833 247/610 H/N Cat/Aat rs750443644,COSM1001870,COSM3540030,COSM3540031,COSM4870267 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 deleterious(0.03) 7/7 hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,SMART_domains:SM00355 0,1,1,1,1 MODERATE 1 SNV 2 0,1,1,1,1 1 PASS rs750443644 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 56442256 56442256 G T 1 0 0 0 0 1 0 0 0 18648 1290 45 2 2 ZNF667 19 56442256 Missense_Mutation SNP G C3L-00144_T 233742 56442256 2175360 1550 5621 ZNF835 0 . GRCh38 19 56665036 56665036 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.163G>T p.Asp55Tyr p.D55Y ENST00000537055 2/2 515 364 151 471 470 1 strelka-varscan-mutect ZNF835,missense_variant,p.Asp55Tyr,ENST00000537055,NM_001005850.2;ZNF835,missense_variant,p.Asp55Tyr,ENST00000601659,; A ENST00000537055 Transcript missense_variant 395/3450 163/1614 55/537 D/Y Gat/Tat COSM1001961 1 -1 ZNF835 HGNC HGNC:34332 protein_coding YES CCDS56105.1 ENSP00000444747 Q9Y2P0 UPI0000EE7244 NM_001005850.2 deleterious(0.02) 2/2 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF368 1 MODERATE 1 SNV 2 1 1 PASS rs980585605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 56665036 56665036 C A 1 0 0 0 0 1 0 0 0 18771 884 31 1 1 ZNF835 19 56665036 Missense_Mutation SNP C C3L-00144_T 222780 56665036 1952580 1551 5622 ZIM2 0 . GRCh38 19 56779434 56779434 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.685G>A p.Glu229Lys p.E229K ENST00000629319 11/12 241 223 18 187 186 1 strelka-varscan-mutect ZIM2,missense_variant,p.Glu229Lys,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,missense_variant,p.Glu229Lys,ENST00000599935,;ZIM2,missense_variant,p.Glu229Lys,ENST00000593711,NM_015363.4;ZIM2,missense_variant,p.Glu229Lys,ENST00000601070,;ZIM2-AS1,intron_variant,,ENST00000595954,;ZIM2-AS1,intron_variant,,ENST00000594400,;ZIM2-AS1,intron_variant,,ENST00000597946,;ZIM2,3_prime_UTR_variant,,ENST00000595671,;ZIM2,3_prime_UTR_variant,,ENST00000597281,;ZIM2,non_coding_transcript_exon_variant,,ENST00000596270,; T ENST00000629319 Transcript missense_variant 1228/2253 685/1584 229/527 E/K Gaa/Aaa 1 -1 ZIM2 HGNC HGNC:12875 protein_coding YES CCDS33123.1 ENSP00000486502 Q9NZV7 A0A024R4S8 UPI000013C3DF NM_001146326.1,NM_001146327.1 deleterious(0.01) 11/12 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF354,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE SNV 5 1 PASS rs1309297904 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 56779434 56779434 C T 1 0 0 0 0 1 0 0 0 18262 864 30 3 3 ZIM2 19 56779434 Missense_Mutation SNP C C3L-00144_T 114398 56779434 1838182 1552 5623 PEG3 0 . GRCh38 19 56814508 56814508 + Missense_Mutation SNP C C A rs752946677 C3L-00144_T C3L-00144_N C C c.3934G>T p.Gly1312Trp p.G1312W ENST00000326441 10/10 102 94 8 97 97 0 strelka-varscan-mutect PEG3,missense_variant,p.Gly1312Trp,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Gly1188Trp,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Gly1312Trp,ENST00000599534,;PEG3,missense_variant,p.Gly1312Trp,ENST00000599577,;PEG3,missense_variant,p.Gly1186Trp,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 4298/8723 3934/4767 1312/1588 G/W Ggg/Tgg rs752946677 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0) 10/10 MODERATE 1 SNV 1 1 PASS rs752946677 . 0 204 6 0 0 0 0 0 -16.18112 0.9999997 1 1 1 0 A 3 1 12 56814508 56814508 C A 1 0 0 0 0 1 0 0 0 11808 652 23 1 1 PEG3 19 56814508 Missense_Mutation SNP C C3L-00144_T 35074 56814508 1803108 1553 5624 PEG3 0 . GRCh38 19 56816975 56816975 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.1467T>C p.= p.S489S ENST00000326441 10/10 225 201 24 204 204 0 strelka-varscan-mutect PEG3,synonymous_variant,p.=,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,synonymous_variant,p.=,ENST00000598410,NM_001146187.1;PEG3,synonymous_variant,p.=,ENST00000599534,;PEG3,synonymous_variant,p.=,ENST00000599577,;PEG3,synonymous_variant,p.=,ENST00000593695,NM_001146185.1;PEG3,synonymous_variant,p.=,ENST00000600833,;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; G ENST00000326441 Transcript synonymous_variant 1831/8723 1467/4767 489/1588 S agT/agC 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 10/10 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 56816975 56816975 A G 1 0 0 0 0 0 0 0 1 11808 156 6 5 5 PEG3 19 56816975 Silent SNP A C3L-00144_T 2467 56816975 1800641 1554 5625 ZIM3 0 . GRCh38 19 57134978 57134978 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.1359T>A p.= p.G453G ENST00000269834 5/5 175 159 16 165 165 0 strelka-varscan-mutect ZIM3,synonymous_variant,p.=,ENST00000269834,NM_052882.1;USP29,downstream_gene_variant,,ENST00000254181,NM_020903.2;USP29,downstream_gene_variant,,ENST00000598197,; T ENST00000269834 Transcript synonymous_variant 1745/2627 1359/1419 453/472 G ggT/ggA 1 -1 ZIM3 HGNC HGNC:16366 protein_coding YES CCDS33125.1 ENSP00000269834 Q96PE6 UPI000013C3E0 NM_052882.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF30,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 57134978 57134978 A T 1 0 0 0 0 0 0 0 1 18263 378 14 4 4 ZIM3 19 57134978 Silent SNP A C3L-00144_T 318003 57134978 1482638 1555 5626 ZIK1 0 . GRCh38 19 57590169 57590169 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.358G>T p.Gly120Trp p.G120W ENST00000597850 4/4 310 210 100 225 224 1 strelka-varscan-mutect ZIK1,missense_variant,p.Gly120Trp,ENST00000597850,NM_001010879.2;ZIK1,missense_variant,p.Gly107Trp,ENST00000536878,NM_001321145.1;ZIK1,missense_variant,p.Gly65Trp,ENST00000599456,;ZIK1,missense_variant,p.Gly101Trp,ENST00000600053,;ZIK1,missense_variant,p.Gly93Trp,ENST00000598689,;ZIK1,3_prime_UTR_variant,,ENST00000307468,;ZIK1,downstream_gene_variant,,ENST00000597219,;ZIK1,downstream_gene_variant,,ENST00000598726,; T ENST00000597850 Transcript missense_variant 573/4181 358/1464 120/487 G/W Ggg/Tgg 1 1 ZIK1 HGNC HGNC:33104 protein_coding YES CCDS33135.1 ENSP00000472867 Q3SY52 UPI00001609B2 NM_001010879.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 57590169 57590169 G T 1 0 0 0 0 1 0 0 0 18261 1348 47 2 2 ZIK1 19 57590169 Missense_Mutation SNP G C3L-00144_T 455191 57590169 1027447 1556 5627 ZNF530 0 . GRCh38 19 57606038 57606038 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.513G>T p.= p.G171G ENST00000332854 3/3 216 188 28 223 222 1 strelka-varscan-mutect ZNF530,synonymous_variant,p.=,ENST00000332854,NM_020880.3;ZNF530,intron_variant,,ENST00000597864,;ZNF530,downstream_gene_variant,,ENST00000597700,;ZNF530,synonymous_variant,p.=,ENST00000600619,;ZNF530,non_coding_transcript_exon_variant,,ENST00000598297,; T ENST00000332854 Transcript synonymous_variant 733/2962 513/1800 171/599 G ggG/ggT 1 1 ZNF530 HGNC HGNC:29297 protein_coding YES CCDS12955.1 ENSP00000332861 Q6P9A1 UPI0000199017 NM_020880.3 3/3 LOW 1 SNV 1 1 PASS rs1215933782 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 57606038 57606038 G T 1 0 0 0 0 0 0 0 1 18544 1219 43 2 2 ZNF530 19 57606038 Silent SNP G C3L-00144_T 15869 57606038 1011578 1557 5628 ZNF154 0 . GRCh38 19 57702577 57702577 + Silent SNP G G C rs201612246 C3L-00144_T C3L-00144_N G G c.372C>G p.= p.A124A ENST00000512439 3/4 212 157 55 190 190 0 strelka-varscan-mutect ZNF154,synonymous_variant,p.=,ENST00000512439,NM_001085384.2;AC003006.7,intron_variant,,ENST00000594684,;ZNF551,intron_variant,,ENST00000596085,;AC003006.7,intron_variant,,ENST00000599221,;ZNF154,synonymous_variant,p.=,ENST00000451275,; C ENST00000512439 Transcript synonymous_variant 569/5687 372/1314 124/437 A gcC/gcG rs201612246 1 -1 ZNF154 HGNC HGNC:12939 protein_coding YES CCDS42639.1 ENSP00000421258 Q13106 A0A024R4Q0 UPI00001D819A NM_001085384.2 3/4 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF75 LOW 1 SNV 1 1 PASS rs201612246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 57702577 57702577 G C 1 0 0 0 0 0 0 0 1 18316 1335 47 4 4 ZNF154 19 57702577 Silent SNP G C3L-00144_T 96539 57702577 915039 1558 5629 ZNF552 0 . GRCh38 19 57808396 57808396 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.868C>A p.His290Asn p.H290N ENST00000391701 3/3 87 78 9 68 68 0 strelka-varscan-mutect ZNF552,missense_variant,p.His290Asn,ENST00000391701,NM_024762.3;ZNF586,intron_variant,,ENST00000599802,;ZNF586,intron_variant,,ENST00000598885,;ZNF552,intron_variant,,ENST00000594473,;ZNF552,3_prime_UTR_variant,,ENST00000596248,;ZNF552,downstream_gene_variant,,ENST00000600397,; T ENST00000391701 Transcript missense_variant 1038/2352 868/1224 290/407 H/N Cac/Aac 1 -1 ZNF552 HGNC HGNC:26135 protein_coding YES CCDS12963.1 ENSP00000375582 Q9H707 UPI0000202D72 NM_024762.3 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF209,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.30065 1 1 1 1 0 T 3 4 12 57808396 57808396 G T 1 0 0 0 0 1 0 0 0 18558 1290 45 2 2 ZNF552 19 57808396 Missense_Mutation SNP G C3L-00144_T 105819 57808396 809220 1559 5630 ZNF135 0 . GRCh38 19 58063493 58063493 + Missense_Mutation SNP G G T rs778065252 C3L-00144_T C3L-00144_N G G c.244G>T p.Ala82Ser p.A82S ENST00000401053 3/4 440 404 36 322 322 0 strelka-varscan-mutect ZNF135,missense_variant,p.Ala28Ser,ENST00000506786,NM_001289402.1;ZNF135,missense_variant,p.Ala82Ser,ENST00000401053,NM_001164529.1,NM_007134.1;ZNF135,missense_variant,p.Ala70Ser,ENST00000313434,NM_001289401.1;ZNF135,missense_variant,p.Ala70Ser,ENST00000511556,NM_003436.3;ZNF135,missense_variant,p.Ala82Ser,ENST00000359978,NM_001164530.1;ZNF135,intron_variant,,ENST00000515535,; T ENST00000401053 Transcript missense_variant 247/3346 244/2049 82/682 A/S Gca/Tca rs778065252 1 1 ZNF135 HGNC HGNC:12919 protein_coding YES CCDS54329.1 ENSP00000441410 P52742 UPI0001B3CB2A NM_001164529.1,NM_007134.1 tolerated(0.25) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF250,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS rs778065252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 58063493 58063493 G T 1 0 0 0 0 1 0 0 0 18306 1203 42 2 2 ZNF135 19 58063493 Missense_Mutation SNP G C3L-00144_T 255097 58063493 554123 1560 5631 A1BG 0 . GRCh38 19 58352939 58352939 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.329T>A p.Leu110Gln p.L110Q ENST00000263100 3/8 116 105 11 99 98 1 strelka-varscan-mutect A1BG,missense_variant,p.Leu110Gln,ENST00000263100,NM_130786.3;A1BG,missense_variant,p.Leu64Gln,ENST00000600966,;ZNF497,downstream_gene_variant,,ENST00000311044,NM_198458.2;ZNF497,downstream_gene_variant,,ENST00000425453,NM_001207009.1;ZNF497,downstream_gene_variant,,ENST00000595763,;A1BG-AS1,non_coding_transcript_exon_variant,,ENST00000595302,;A1BG-AS1,intron_variant,,ENST00000594950,;A1BG-AS1,intron_variant,,ENST00000600686,;A1BG-AS1,intron_variant,,ENST00000593960,;A1BG-AS1,intron_variant,,ENST00000593374,;A1BG-AS1,intron_variant,,ENST00000600379,;A1BG-AS1,intron_variant,,ENST00000599728,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000599109,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000600123,;CTD-2619J13.5,downstream_gene_variant,,ENST00000623509,;CTD-2619J13.8,downstream_gene_variant,,ENST00000596636,;A1BG,non_coding_transcript_exon_variant,,ENST00000595014,; T ENST00000263100 Transcript missense_variant 391/1722 329/1488 110/495 L/Q cTg/cAg 1 -1 A1BG HGNC HGNC:5 protein_coding YES CCDS12976.1 ENSP00000263100 P04217 V9HWD8 UPI0000167B10 NM_130786.3 deleterious(0) 3/8 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF3,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -16.53747 0.9999008 1 1 1 0 T 3 4 12 58352939 58352939 A T 1 0 0 0 0 1 0 0 0 1 188 7 4 4 A1BG 19 58352939 Missense_Mutation SNP A C3L-00144_T 289446 58352939 264677 1561 5632 ZNF497 0 . GRCh38 19 58356210 58356210 + Missense_Mutation SNP C C G rs772405314 C3L-00144_T C3L-00144_N C C c.1426G>C p.Gly476Arg p.G476R ENST00000311044 3/3 115 102 13 87 87 0 strelka-mutect ZNF497,missense_variant,p.Gly476Arg,ENST00000311044,NM_198458.2;ZNF497,missense_variant,p.Gly476Arg,ENST00000425453,NM_001207009.1;A1BG,upstream_gene_variant,,ENST00000263100,NM_130786.3;A1BG,upstream_gene_variant,,ENST00000600966,;ZNF497,downstream_gene_variant,,ENST00000595763,;A1BG-AS1,downstream_gene_variant,,ENST00000595302,;A1BG-AS1,downstream_gene_variant,,ENST00000594950,;CTD-2619J13.9,upstream_gene_variant,,ENST00000599952,;A1BG-AS1,downstream_gene_variant,,ENST00000600686,;A1BG-AS1,downstream_gene_variant,,ENST00000593960,;A1BG-AS1,downstream_gene_variant,,ENST00000593374,;A1BG-AS1,downstream_gene_variant,,ENST00000600379,;A1BG-AS1,downstream_gene_variant,,ENST00000599728,;CTD-2619J13.8,non_coding_transcript_exon_variant,,ENST00000600123,;CTD-2619J13.8,intron_variant,,ENST00000599109,;CTD-2619J13.5,downstream_gene_variant,,ENST00000623509,;CTD-2619J13.8,upstream_gene_variant,,ENST00000596636,;A1BG,upstream_gene_variant,,ENST00000595014,; G ENST00000311044 Transcript missense_variant 1615/3468 1426/1497 476/498 G/R Ggg/Cgg rs772405314 1 -1 ZNF497 HGNC HGNC:23714 protein_coding YES CCDS12977.1 ENSP00000311183 Q6ZNH5 UPI00001D819C NM_198458.2 deleterious(0.05) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF30,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS rs772405314 . 0 200 10 0 0 0 0 0 -20 0.9999698 1 1 1 0 G 3 3 12 58356210 58356210 C G 1 0 0 0 0 1 0 0 0 18519 652 23 4 4 ZNF497 19 58356210 Missense_Mutation SNP C C3L-00144_T 3271 58356210 261406 1562 5633 ZNF446 0 . GRCh38 19 58480221 58480221 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.848C>A p.Pro283His p.P283H ENST00000594369 7/7 157 118 39 123 121 2 strelka-varscan-mutect ZNF446,missense_variant,p.Pro283His,ENST00000594369,NM_017908.3;ZNF446,missense_variant,p.Pro255Thr,ENST00000335841,;ZNF446,missense_variant,p.Pro255His,ENST00000622313,;ZNF446,missense_variant,p.Pro283His,ENST00000610298,;ZNF446,intron_variant,,ENST00000596341,;ZNF324,downstream_gene_variant,,ENST00000536459,;ZNF446,downstream_gene_variant,,ENST00000600013,;RNU6-1337P,downstream_gene_variant,,ENST00000516525,;CTD-2619J13.23,upstream_gene_variant,,ENST00000598051,;SLC27A5,3_prime_UTR_variant,,ENST00000595851,;ZNF446,non_coding_transcript_exon_variant,,ENST00000391694,;ZNF446,downstream_gene_variant,,ENST00000594468,; A ENST00000594369 Transcript missense_variant 1229/2238 848/1353 283/450 P/H cCc/cAc 1 1 ZNF446 HGNC HGNC:21036 protein_coding YES CCDS12982.1 ENSP00000472802 Q9NWS9 UPI0000071779 NM_017908.3 deleterious(0.03) 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF73 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 58480221 58480221 C A 1 0 0 0 0 1 0 0 0 18490 623 22 2 2 ZNF446 19 58480221 Missense_Mutation SNP C C3L-00144_T 124011 58480221 137395 1563 5634 SLC52A3 0 . GRCh38 20 761776 761776 + Silent SNP C C T rs755616826 C3L-00144_T C3L-00144_N C C c.1122G>A p.= p.G374G ENST00000632431 4/5 425 397 28 330 330 0 strelka-varscan-mutect SLC52A3,synonymous_variant,p.=,ENST00000381944,;SLC52A3,synonymous_variant,p.=,ENST00000632431,NM_033409.3;SLC52A3,synonymous_variant,p.=,ENST00000217254,;SLC52A3,non_coding_transcript_exon_variant,,ENST00000473664,;SLC52A3,downstream_gene_variant,,ENST00000488495,; T ENST00000632431 Transcript synonymous_variant 1461/2694 1122/1410 374/469 G ggG/ggA rs755616826,COSM3549316,COSM3549317 1 -1 SLC52A3 HGNC HGNC:16187 protein_coding YES CCDS13007.1 ENSP00000488723 Q9NQ40 K0A6P4 UPI000002A74E NM_033409.3 4/5 Pfam_domain:PF06237,hmmpanther:PTHR12929,hmmpanther:PTHR12929:SF4,Transmembrane_helices:TMhelix 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs755616826 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 761776 761776 C T 1 0 0 0 0 0 0 0 1 14943 610 22 3 3 SLC52A3 20 761776 Silent SNP C C3L-00144_T 761776 63682391 1564 5635 C20orf202 0 . GRCh38 20 1206928 1206928 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.195C>A p.= p.V65V ENST00000400633 2/2 129 113 16 112 112 0 strelka-varscan-mutect C20orf202,synonymous_variant,p.=,ENST00000400633,NM_001009612.2;RP4-545L17.12,non_coding_transcript_exon_variant,,ENST00000619766,; A ENST00000400633 Transcript synonymous_variant 258/1604 195/369 65/122 V gtC/gtA 1 1 C20orf202 HGNC HGNC:37254 protein_coding YES CCDS46567.1 ENSP00000383474 A1L168 UPI0000141828 NM_001009612.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR32289:SF5,hmmpanther:PTHR32289 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 1206928 1206928 C A 1 0 0 0 0 0 0 0 1 2007 842 30 2 2 C20orf202 20 1206928 Silent SNP C C3L-00144_T 445152 1206928 63237239 1565 5636 SIRPB2 0 . GRCh38 20 1477380 1477380 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.817G>T p.Ala273Ser p.A273S ENST00000359801 4/5 152 120 32 142 142 0 strelka-varscan-mutect SIRPB2,missense_variant,p.Ala273Ser,ENST00000359801,NM_001122962.1;SIRPB2,missense_variant,p.Ala175Ser,ENST00000444444,NM_001134836.1;NSFL1C,upstream_gene_variant,,ENST00000553571,;SIRPB2,downstream_gene_variant,,ENST00000608747,;SIRPB2,missense_variant,p.Ala273Ser,ENST00000481731,;SIRPB2,missense_variant,p.Ala273Ser,ENST00000486775,;SIRPB2,non_coding_transcript_exon_variant,,ENST00000381630,;SIRPB2,downstream_gene_variant,,ENST00000609796,;SIRPB2,downstream_gene_variant,,ENST00000608073,; A ENST00000359801 Transcript missense_variant 854/2642 817/1029 273/342 A/S Gca/Tca COSM4862923,COSM4862924,COSM723602,COSM723603 1 -1 SIRPB2 HGNC HGNC:16247 protein_coding YES CCDS42849.1 ENSP00000352849 Q5JXA9 UPI00001D8311 NM_001122962.1 tolerated(0.43) 4/5 hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF9 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 1477380 1477380 C A 1 0 0 0 0 1 0 0 0 14597 739 26 2 2 SIRPB2 20 1477380 Missense_Mutation SNP C C3L-00144_T 270452 1477380 62966787 1566 5637 TGM3 0 . GRCh38 20 2317131 2317131 + Silent SNP C C A rs202051623 C3L-00144_T C3L-00144_N C C c.733C>A p.= p.R245R ENST00000381458 6/13 259 212 47 214 214 0 strelka-varscan-mutect TGM3,synonymous_variant,p.=,ENST00000381458,NM_003245.3;TGM3,non_coding_transcript_exon_variant,,ENST00000463090,; A ENST00000381458 Transcript synonymous_variant 796/2642 733/2082 245/693 R Cgg/Agg rs202051623 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 6/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS rs202051623 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 2317131 2317131 C A 1 0 0 0 0 0 0 0 1 16264 643 23 1 1 TGM3 20 2317131 Silent SNP C C3L-00144_T 839751 2317131 62127036 1567 5638 TGM3 0 . GRCh38 20 2335198 2335198 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1725G>T p.= p.V575V ENST00000381458 11/13 372 308 64 301 300 1 strelka-varscan-mutect TGM3,synonymous_variant,p.=,ENST00000381458,NM_003245.3; T ENST00000381458 Transcript synonymous_variant 1788/2642 1725/2082 575/693 V gtG/gtT 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 11/13 Gene3D:2.60.40.10,Pfam_domain:PF00927,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 2335198 2335198 G T 1 0 0 0 0 0 0 0 1 16264 1364 48 2 2 TGM3 20 2335198 Silent SNP G C3L-00144_T 18067 2335198 62108969 1568 5639 TGM6 0 . GRCh38 20 2403467 2403467 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1060G>T p.Val354Phe p.V354F ENST00000202625 8/13 666 517 149 534 532 2 strelka-varscan-mutect TGM6,missense_variant,p.Val354Phe,ENST00000202625,NM_198994.2;TGM6,missense_variant,p.Val354Phe,ENST00000381423,NM_001254734.1;TGM6,downstream_gene_variant,,ENST00000477505,; T ENST00000202625 Transcript missense_variant 1121/2292 1060/2121 354/706 V/F Gtt/Ttt 1 1 TGM6 HGNC HGNC:16255 protein_coding YES CCDS13025.1 ENSP00000202625 O95932 UPI0000367011 NM_198994.2 deleterious(0) 8/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF50,PIRSF_domain:PIRSF000459,Gene3D:1ex0A02,Pfam_domain:PF01841,SMART_domains:SM00460,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs979829530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 2403467 2403467 G T 1 0 0 0 0 1 0 0 0 16267 1261 44 2 2 TGM6 20 2403467 Missense_Mutation SNP G C3L-00144_T 68269 2403467 62040700 1569 5640 CPXM1 0 . GRCh38 20 2795609 2795609 + Silent SNP C C G rs374663889 C3L-00144_T C3L-00144_N C C c.1710G>C p.= p.T570T ENST00000380605 11/14 110 80 30 106 106 0 strelka-varscan-mutect CPXM1,synonymous_variant,p.=,ENST00000380605,NM_019609.4,NM_001184699.1; G ENST00000380605 Transcript synonymous_variant 1775/2391 1710/2205 570/734 T acG/acC rs374663889 1 -1 CPXM1 HGNC HGNC:15771 protein_coding YES CCDS13033.1 ENSP00000369979 Q96SM3 UPI0000039DD0 NM_019609.4,NM_001184699.1 11/14 hmmpanther:PTHR11532:SF43,hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS rs374663889 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 2795609 2795609 C G 1 0 0 0 0 0 0 0 1 3635 639 23 4 4 CPXM1 20 2795609 Silent SNP C C3L-00144_T 392142 2795609 61648558 1570 5641 CPXM1 0 . GRCh38 20 2797095 2797095 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.833-1G>T p.X278_splice ENST00000380605 162 128 34 128 127 1 strelka-varscan-mutect CPXM1,splice_acceptor_variant,,ENST00000380605,NM_019609.4,NM_001184699.1; A ENST00000380605 Transcript splice_acceptor_variant -/2391 833/2205 278/734 1 -1 CPXM1 HGNC HGNC:15771 protein_coding YES CCDS13033.1 ENSP00000369979 Q96SM3 UPI0000039DD0 NM_019609.4,NM_001184699.1 6/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 2797095 2797095 C A 1 0 0 0 0 0 0 1 0 3635 927 32 2 2 CPXM1 20 2797095 Splice_Site SNP C C3L-00144_T 1486 2797095 61647072 1571 5642 UBOX5 0 . GRCh38 20 3122280 3122280 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.359A>C p.Lys120Thr p.K120T ENST00000217173 3/5 383 317 66 295 295 0 strelka-varscan-mutect UBOX5,missense_variant,p.Lys120Thr,ENST00000217173,NM_001267584.1,NM_014948.3;UBOX5,missense_variant,p.Lys120Thr,ENST00000348031,NM_199415.2;UBOX5,downstream_gene_variant,,ENST00000449731,;UBOX5-AS1,intron_variant,,ENST00000446537,; G ENST00000217173 Transcript missense_variant 831/4631 359/1626 120/541 K/T aAa/aCa 1 -1 UBOX5 HGNC HGNC:17777 protein_coding YES CCDS13046.1 ENSP00000217173 O94941 UPI0000137935 NM_001267584.1,NM_014948.3 deleterious(0) 3/5 hmmpanther:PTHR13492:SF2,hmmpanther:PTHR13492 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 3122280 3122280 T G 1 0 0 0 0 1 0 0 0 17418 1841 64 5 5 UBOX5 20 3122280 Missense_Mutation SNP T C3L-00144_T 325185 3122280 61321887 1572 5643 FASTKD5 0 . GRCh38 20 3148758 3148758 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.313G>T p.Asp105Tyr p.D105Y ENST00000380266 2/2 310 269 41 270 270 0 strelka-varscan-mutect FASTKD5,missense_variant,p.Asp105Tyr,ENST00000380266,NM_021826.4;UBOX5,intron_variant,,ENST00000217173,NM_001267584.1,NM_014948.3;UBOX5,intron_variant,,ENST00000348031,NM_199415.2;UBOX5,intron_variant,,ENST00000449731,;UBOX5-AS1,intron_variant,,ENST00000446537,; A ENST00000380266 Transcript missense_variant 635/2874 313/2295 105/764 D/Y Gac/Tac 1 -1 FASTKD5 HGNC HGNC:25790 protein_coding YES CCDS13048.1 ENSP00000369618 Q7L8L6 UPI000015F514 NM_021826.4 deleterious(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR21228:SF30,hmmpanther:PTHR21228 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3148758 3148758 C A 1 0 0 0 0 1 0 0 0 5548 855 30 2 2 FASTKD5 20 3148758 Missense_Mutation SNP C C3L-00144_T 26478 3148758 61295409 1573 5644 C20orf194 0 . GRCh38 20 3324969 3324969 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.1189-1G>T p.X397_splice ENST00000252032 234 196 38 145 145 0 strelka-varscan-mutect C20orf194,splice_acceptor_variant,,ENST00000252032,NM_001009984.2; A ENST00000252032 Transcript splice_acceptor_variant -/6869 1189/3534 397/1177 1 -1 C20orf194 HGNC HGNC:17721 protein_coding YES CCDS42851.1 ENSP00000252032 Q5TEA3 UPI0000470A8D NM_001009984.2 13/36 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 3324969 3324969 C A 1 0 0 0 0 0 0 1 0 2005 695 24 2 2 C20orf194 20 3324969 Splice_Site SNP C C3L-00144_T 176211 3324969 61119198 1574 5645 MAVS 0 . GRCh38 20 3865967 3865980 + Frame_Shift_Del DEL CAACCCTGGGCCAC CAACCCTGGGCCAC - novel C3L-00144_T C3L-00144_N CAACCCTGGGCCAC CAACCCTGGGCCAC c.1444_1457delAACCCTGGGCCACC p.Asn482CysfsTer95 p.N482Cfs*95 ENST00000428216 7/7 170 136 34 173 173 0 sindel-varindel-pindel MAVS,frameshift_variant,p.Asn482CysfsTer95,ENST00000428216,NM_020746.4;MAVS,frameshift_variant,p.Asn341CysfsTer95,ENST00000416600,NM_001206491.1; - ENST00000428216 Transcript frameshift_variant 1571-1584/11714 1443-1456/1623 481-486/540 GNPGPP/GX ggCAACCCTGGGCCACct/ggct 1 1 MAVS HGNC HGNC:29233 protein_coding YES CCDS33437.1 ENSP00000401980 Q7Z434 UPI000015F983 NM_020746.4 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR21446:SF6,hmmpanther:PTHR21446 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 3865967 3865967 CAACCCTGGGCCAC - 1 0 1 0 1 0 0 0 0 9265 697 25 0 0 MAVS 20 3865967 Frame_Shift_Del DEL CAACCCTGGGCCAC C3L-00144_T 540998 3865967 60578200 1575 5646 ADRA1D 0 . GRCh38 20 4247935 4247935 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1023C>T p.= p.S341S ENST00000379453 1/2 153 120 33 96 96 0 strelka-varscan-mutect ADRA1D,synonymous_variant,p.=,ENST00000379453,NM_000678.3; A ENST00000379453 Transcript synonymous_variant 1140/2728 1023/1719 341/572 S tcC/tcT 1 -1 ADRA1D HGNC HGNC:280 protein_coding YES CCDS13079.1 ENSP00000368766 P25100 B0ZBE0 UPI000003B078 NM_000678.3 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF14,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 4247935 4247935 G A 1 0 0 0 0 0 0 0 1 412 1219 43 3 3 ADRA1D 20 4247935 Silent SNP G C3L-00144_T 381968 4247935 60196232 1576 5647 PLCB4 0 . GRCh38 20 9453379 9453379 + Silent SNP G G T rs749780243 C3L-00144_T C3L-00144_N G G c.2877G>T p.= p.T959T ENST00000378501 29/36 199 168 31 195 194 1 strelka-varscan-mutect PLCB4,synonymous_variant,p.=,ENST00000378501,NM_000933.3;PLCB4,synonymous_variant,p.=,ENST00000378493,;PLCB4,synonymous_variant,p.=,ENST00000378473,NM_001172646.1;PLCB4,synonymous_variant,p.=,ENST00000278655,NM_182797.2;PLCB4,synonymous_variant,p.=,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,; T ENST00000378501 Transcript synonymous_variant 2892/5833 2877/3585 959/1194 T acG/acT rs749780243,COSM724635 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 29/36 Superfamily_domains:0053448,Gene3D:1jadA00,PIRSF_domain:PIRSF000956,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106 0,1 LOW 1 SNV 5 0,1 1 PASS rs749780243 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 12 9453379 9453379 G T 1 0 0 0 0 0 0 0 1 12124 1074 38 1 1 PLCB4 20 9453379 Silent SNP G C3L-00144_T 5205444 9453379 54990788 1577 5648 SNAP25 0 . GRCh38 20 10299413 10299413 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.552+1G>T p.X184_splice ENST00000254976 69 55 14 59 59 0 strelka-varscan-mutect SNAP25,splice_donor_variant,,ENST00000254976,NM_130811.2;SNAP25,splice_donor_variant,,ENST00000304886,NM_003081.3;SNAP25-AS1,intron_variant,,ENST00000421143,;SNAP25-AS1,intron_variant,,ENST00000453544,;SNAP25,splice_donor_variant,,ENST00000495883,; T ENST00000254976 Transcript splice_donor_variant -/2053 552/621 184/206 1 1 SNAP25 HGNC HGNC:11132 protein_coding YES CCDS13110.1 ENSP00000254976 P60880 UPI0000001103 NM_130811.2 7/7 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.999999 1 1 1 0 T 5 4 12 10299413 10299413 G T 1 0 0 0 0 0 0 1 0 15151 1275 44 2 2 SNAP25 20 10299413 Splice_Site SNP G C3L-00144_T 846034 10299413 54144754 1578 5649 MACROD2 0 . GRCh38 20 15862744 15862744 + Splice_Site SNP G G T novel C3L-00144_T C3L-00144_N G G c.646-1G>T p.X216_splice ENST00000217246 180 165 15 158 158 0 strelka-varscan-mutect MACROD2,splice_acceptor_variant,,ENST00000217246,NM_080676.5;MACROD2,splice_acceptor_variant,,ENST00000402914,NM_001033087.1;MACROD2,5_prime_UTR_variant,,ENST00000378058,; T ENST00000217246 Transcript splice_acceptor_variant -/4994 646/1278 216/425 1 1 MACROD2 HGNC HGNC:16126 protein_coding YES CCDS13120.2 ENSP00000217246 A1Z1Q3 UPI00005B2E12 NM_080676.5 8/16 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 12 15862744 15862744 G T 1 0 0 0 0 0 0 1 0 9062 1014 35 2 2 MACROD2 20 15862744 Splice_Site SNP G C3L-00144_T 5563331 15862744 48581423 1579 5650 THBD 0 . GRCh38 20 23049142 23049142 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.363G>T p.Arg121Ser p.R121S ENST00000377103 1/1 281 220 61 185 185 0 strelka-varscan-mutect THBD,missense_variant,p.Arg121Ser,ENST00000377103,NM_000361.2; A ENST00000377103 Transcript missense_variant 600/4109 363/1728 121/575 R/S agG/agT 1 -1 THBD HGNC HGNC:11784 protein_coding YES CCDS13148.1 ENSP00000366307 P07204 UPI00000002BD NM_000361.2 deleterious(0.01) 1/1 PROSITE_profiles:PS50041,hmmpanther:PTHR24036,Pfam_domain:PF00059,PIRSF_domain:PIRSF001775,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 23049142 23049142 C A 1 0 0 0 0 1 0 0 0 16285 506 18 2 2 THBD 20 23049142 Missense_Mutation SNP C C3L-00144_T 7186398 23049142 41395025 1580 5651 GINS1 0 . GRCh38 20 25407856 25407856 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.36G>A p.= p.E12E ENST00000262460 1/7 198 154 44 184 184 0 strelka-varscan-mutect GINS1,synonymous_variant,p.=,ENST00000262460,NM_021067.3;GINS1,non_coding_transcript_exon_variant,,ENST00000484893,; A ENST00000262460 Transcript synonymous_variant 130/3249 36/591 12/196 E gaG/gaA 1 1 GINS1 HGNC HGNC:28980 protein_coding YES CCDS33451.1 ENSP00000262460 Q14691 UPI00001393F9 NM_021067.3 1/7 hmmpanther:PTHR12914,hmmpanther:PTHR12914:SF2,Superfamily_domains:SSF158573 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 25407856 25407856 G A 1 0 0 0 0 0 0 0 1 6269 962 34 3 3 GINS1 20 25407856 Silent SNP G C3L-00144_T 2358714 25407856 39036311 1581 5652 FAM182B 0 . GRCh38 20 25775222 25775222 + Frame_Shift_Del DEL G G - novel C3L-00144_T C3L-00144_N G G c.98delC p.Pro33GlnfsTer22 p.P33Qfs*22 ENST00000376403 3/3 512 459 53 406 406 0 sindel-varindel-pindel FAM182B,frameshift_variant,p.Pro33GlnfsTer22,ENST00000376403,;FAM182B,frameshift_variant,p.Pro41GlnfsTer22,ENST00000584071,;FAM182B,frameshift_variant,p.Pro32GlnfsTer22,ENST00000376404,;FAM182B,non_coding_transcript_exon_variant,,ENST00000478164,;FAM182B,non_coding_transcript_exon_variant,,ENST00000582267,;FAM182B,non_coding_transcript_exon_variant,,ENST00000485279,;FAM182B,non_coding_transcript_exon_variant,,ENST00000453481,;FAM182B,downstream_gene_variant,,ENST00000584356,; - ENST00000376403 Transcript frameshift_variant 477/1681 98/459 33/152 P/X cCa/ca 1 -1 FAM182B HGNC HGNC:34503 protein_coding YES ENSP00000365585 Q5T319 UPI000047001E 3/3 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 25775222 25775222 G - 1 0 1 0 1 0 0 0 0 5356 1348 47 0 0 FAM182B 20 25775222 Frame_Shift_Del DEL G C3L-00144_T 367366 25775222 38668945 1582 5653 DEFB119 0 . GRCh38 20 31377433 31377433 + Missense_Mutation SNP C C A rs746865254 C3L-00144_T C3L-00144_N C C c.68G>T p.Arg23Leu p.R23L ENST00000376321 2/2 60 48 12 40 40 0 strelka-varscan-mutect DEFB119,missense_variant,p.Arg23Leu,ENST00000376321,NM_153289.3;DEFB119,synonymous_variant,p.=,ENST00000339144,;DEFB118,downstream_gene_variant,,ENST00000253381,NM_054112.2;SNORA40,downstream_gene_variant,,ENST00000390832,;DEFB119,non_coding_transcript_exon_variant,,ENST00000492344,; A ENST00000376321 Transcript missense_variant 188/457 68/255 23/84 R/L cGc/cTc rs746865254,COSM274767,COSM3693356,COSM4440949,COSM4440950 1 -1 DEFB119 HGNC HGNC:18099 protein_coding CCDS13178.1 ENSP00000365499 Q8N690 UPI000003D7C7 NM_153289.3 tolerated_low_confidence(0.08) 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF6 0,1,1,1,1 MODERATE SNV 1 0,1,1,1,1 1 PASS rs746865254 . 0 201 9 0 0 0 0 0 -20 0.9999965 1 1 1 0 A 3 1 12 31377433 31377433 C A 1 0 0 0 0 1 0 0 0 4210 768 27 1 1 DEFB119 20 31377433 Missense_Mutation SNP C C3L-00144_T 5602211 31377433 33066734 1583 5654 TM9SF4 0 . GRCh38 20 32165351 32165351 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.1836G>C p.Met612Ile p.M612I ENST00000398022 18/18 294 229 65 219 219 0 strelka-varscan-mutect TM9SF4,missense_variant,p.Met595Ile,ENST00000217315,;TM9SF4,missense_variant,p.Met612Ile,ENST00000398022,NM_014742.3;TM9SF4,non_coding_transcript_exon_variant,,ENST00000495749,;TM9SF4,non_coding_transcript_exon_variant,,ENST00000479591,; C ENST00000398022 Transcript missense_variant 2071/3978 1836/1929 612/642 M/I atG/atC 1 1 TM9SF4 HGNC HGNC:30797 protein_coding YES CCDS13196.2 ENSP00000381104 Q92544 A0A024QYR3 UPI0000206163 NM_014742.3 tolerated(0.82) 18/18 hmmpanther:PTHR10766,hmmpanther:PTHR10766:SF55,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 32165351 32165351 G C 1 0 0 0 0 1 0 0 0 16424 1348 47 4 4 TM9SF4 20 32165351 Missense_Mutation SNP G C3L-00144_T 787918 32165351 32278816 1584 5655 BPIFB2 0 . GRCh38 20 33019657 33019657 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.987C>G p.His329Gln p.H329Q ENST00000170150 11/16 124 105 19 114 114 0 strelka-varscan-mutect BPIFB2,missense_variant,p.His329Gln,ENST00000170150,NM_025227.2; G ENST00000170150 Transcript missense_variant 1182/1898 987/1377 329/458 H/Q caC/caG 1 1 BPIFB2 HGNC HGNC:16177 protein_coding YES CCDS13210.1 ENSP00000170150 Q8N4F0 UPI00000377B0 NM_025227.2 tolerated(0.29) 11/16 hmmpanther:PTHR10504:SF92,hmmpanther:PTHR10504,Gene3D:1ewfA02,Pfam_domain:PF02886,PIRSF_domain:PIRSF002417,SMART_domains:SM00329,Superfamily_domains:SSF55394 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 33019657 33019657 C G 1 0 0 0 0 1 0 0 0 1658 477 17 4 4 BPIFB2 20 33019657 Missense_Mutation SNP C C3L-00144_T 854306 33019657 31424510 1585 5656 BPIFB6 0 . GRCh38 20 33031746 33031746 + Splice_Site SNP T T A novel C3L-00144_T C3L-00144_N T T c.97+2T>A p.X33_splice ENST00000349552 207 165 42 162 162 0 strelka-varscan-mutect BPIFB6,splice_donor_variant,,ENST00000349552,NM_174897.2;BPIFB6,splice_region_variant,p.=,ENST00000542375,; A ENST00000349552 Transcript splice_donor_variant -/1362 97/1362 33/453 1 1 BPIFB6 HGNC HGNC:16504 protein_coding YES CCDS13211.1 ENSP00000344929 Q8NFQ5 UPI000003C8F3 NM_174897.2 1/14 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 33031746 33031746 T A 1 0 0 0 0 0 0 1 0 1661 1710 59 4 4 BPIFB6 20 33031746 Splice_Site SNP T C3L-00144_T 12089 33031746 31412421 1586 5657 SLA2 0 . GRCh38 20 36641325 36641325 + Missense_Mutation SNP A A G novel C3L-00144_T C3L-00144_N A A c.11T>C p.Leu4Pro p.L4P ENST00000262866 2/8 204 178 26 165 165 0 strelka-varscan-mutect SLA2,missense_variant,p.Leu4Pro,ENST00000262866,NM_032214.3;SLA2,missense_variant,p.Leu4Pro,ENST00000360672,NM_175077.2; G ENST00000262866 Transcript missense_variant 434/2757 11/786 4/261 L/P cTg/cCg 1 -1 SLA2 HGNC HGNC:17329 protein_coding YES CCDS13282.1 ENSP00000262866 Q9H6Q3 UPI000004B142 NM_032214.3 tolerated(0.16) 2/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 36641325 36641325 A G 1 0 0 0 0 1 0 0 0 14629 188 7 5 5 SLA2 20 36641325 Missense_Mutation SNP A C3L-00144_T 3609579 36641325 27802842 1587 5658 KIAA1755 0 . GRCh38 20 38228182 38228182 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1930C>A p.Gln644Lys p.Q644K ENST00000279024 6/14 139 111 28 114 114 0 strelka-varscan-mutect KIAA1755,missense_variant,p.Gln644Lys,ENST00000279024,NM_001029864.1;KIAA1755,missense_variant,p.Gln644Lys,ENST00000496900,;KIAA1755,upstream_gene_variant,,ENST00000435901,; T ENST00000279024 Transcript missense_variant 2202/6429 1930/3603 644/1200 Q/K Cag/Aag 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 tolerated(0.93) 6/14 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.999999 1 1 1 0 T 3 4 12 38228182 38228182 G T 1 0 0 0 0 1 0 0 0 8128 1386 48 2 2 KIAA1755 20 38228182 Missense_Mutation SNP G C3L-00144_T 1586857 38228182 26215985 1588 5659 EMILIN3 0 . GRCh38 20 41362908 41362908 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.661G>A p.Ala221Thr p.A221T ENST00000332312 4/4 163 140 23 139 139 0 strelka-varscan-mutect EMILIN3,missense_variant,p.Ala221Thr,ENST00000332312,NM_052846.1;LPIN3,downstream_gene_variant,,ENST00000373257,;LPIN3,downstream_gene_variant,,ENST00000632009,NM_001301860.1;LPIN3,downstream_gene_variant,,ENST00000445975,;LPIN3,downstream_gene_variant,,ENST00000491528,;LPIN3,downstream_gene_variant,,ENST00000496565,; T ENST00000332312 Transcript missense_variant 854/3796 661/2301 221/766 A/T Gct/Act 1 -1 EMILIN3 HGNC HGNC:16123 protein_coding YES CCDS13316.1 ENSP00000332806 Q9NT22 UPI00001D82E8 NM_052846.1 tolerated(0.31) 4/4 hmmpanther:PTHR15427:SF2,hmmpanther:PTHR15427 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41362908 41362908 C T 1 0 0 0 0 1 0 0 0 4938 710 25 3 3 EMILIN3 20 41362908 Missense_Mutation SNP C C3L-00144_T 3134726 41362908 23081259 1589 5660 PTPRT 0 . GRCh38 20 42282498 42282498 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2167G>T p.Ala723Ser p.A723S ENST00000373198 13/32 218 174 44 157 156 1 strelka-varscan-mutect PTPRT,missense_variant,p.Ala723Ser,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Ala723Ser,ENST00000373193,;PTPRT,missense_variant,p.Ala723Ser,ENST00000373201,;PTPRT,missense_variant,p.Ala723Ser,ENST00000373190,;PTPRT,missense_variant,p.Ala723Ser,ENST00000373184,;PTPRT,missense_variant,p.Ala723Ser,ENST00000356100,;PTPRT,missense_variant,p.Ala723Ser,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Ala341Ser,ENST00000612229,;PTPRT,missense_variant,p.Ala339Ser,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 2403/12746 2167/4383 723/1460 A/S Gct/Tct 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0.04) 13/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 MODERATE 1 SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999965 1 1 1 0 A 3 1 12 42282498 42282498 C A 1 0 0 0 0 1 0 0 0 12967 739 26 2 2 PTPRT 20 42282498 Missense_Mutation SNP C C3L-00144_T 919590 42282498 22161669 1590 5661 TOX2 0 . GRCh38 20 44065881 44065881 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.1130T>C p.Leu377Pro p.L377P ENST00000341197 7/9 125 101 24 100 100 0 strelka-varscan-mutect TOX2,missense_variant,p.Leu359Pro,ENST00000358131,NM_001098798.1;TOX2,missense_variant,p.Leu335Pro,ENST00000372999,NM_032883.2;TOX2,missense_variant,p.Leu377Pro,ENST00000341197,NM_001098797.1;TOX2,missense_variant,p.Leu335Pro,ENST00000423191,NM_001098796.1;TOX2,intron_variant,,ENST00000413823,;TOX2,non_coding_transcript_exon_variant,,ENST00000435864,; C ENST00000341197 Transcript missense_variant 1158/1880 1130/1521 377/506 L/P cTg/cCg 1 1 TOX2 HGNC HGNC:16095 protein_coding YES CCDS46603.1 ENSP00000344724 Q96NM4 UPI000040F535 NM_001098797.1 tolerated(0.05) 7/9 Low_complexity_(Seg):seg,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF220 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 44065881 44065881 T C 1 0 0 0 0 1 0 0 0 16856 1580 55 5 5 TOX2 20 44065881 Missense_Mutation SNP T C3L-00144_T 1783383 44065881 20378286 1591 5662 JPH2 0 . GRCh38 20 44159804 44159804 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.983G>A p.Cys328Tyr p.C328Y ENST00000372980 2/6 447 357 90 368 368 0 strelka-varscan-mutect JPH2,missense_variant,p.Cys328Tyr,ENST00000372980,NM_020433.4; T ENST00000372980 Transcript missense_variant 1856/4787 983/2091 328/696 C/Y tGc/tAc 1 -1 JPH2 HGNC HGNC:14202 protein_coding YES CCDS13325.1 ENSP00000362071 Q9BR39 UPI000012DAC2 NM_020433.4 deleterious(0) 2/6 hmmpanther:PTHR23085:SF5,hmmpanther:PTHR23085,PIRSF_domain:PIRSF037387,Gene3D:1h3iA01,Pfam_domain:PF02493,SMART_domains:SM00698,Superfamily_domains:0038399 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 44159804 44159804 C T 1 0 0 0 0 1 0 0 0 7873 710 25 3 3 JPH2 20 44159804 Missense_Mutation SNP C C3L-00144_T 93923 44159804 20284363 1592 5663 STK4 0 . GRCh38 20 45025054 45025054 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.1229G>A p.Ser410Asn p.S410N ENST00000372806 10/11 165 152 13 114 113 1 strelka-varscan-mutect STK4,missense_variant,p.Ser410Asn,ENST00000372806,NM_006282.2;STK4,missense_variant,p.Ser355Asn,ENST00000499879,;STK4,missense_variant,p.Ser410Asn,ENST00000372801,; A ENST00000372806 Transcript missense_variant 1324/6342 1229/1464 410/487 S/N aGc/aAc 1 1 STK4 HGNC HGNC:11408 protein_coding YES CCDS13341.1 ENSP00000361892 Q13043 UPI00001360FF NM_006282.2 tolerated(0.49) 10/11 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF425 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 45025054 45025054 G A 1 0 0 0 0 1 0 0 0 15683 971 34 3 3 STK4 20 45025054 Missense_Mutation SNP G C3L-00144_T 865250 45025054 19419113 1593 5664 CDH22 0 . GRCh38 20 46174932 46174932 + Silent SNP C C G novel C3L-00144_T C3L-00144_N C C c.2061G>C p.= p.A687A ENST00000537909 12/12 239 196 43 225 225 0 strelka-varscan-mutect CDH22,synonymous_variant,p.=,ENST00000537909,NM_021248.2;CDH22,synonymous_variant,p.=,ENST00000372262,;RP5-998H6.2,upstream_gene_variant,,ENST00000450586,; G ENST00000537909 Transcript synonymous_variant 2704/3902 2061/2487 687/828 A gcG/gcC 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 12/12 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF01049 LOW 1 SNV 2 1 PASS rs1310127802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 46174932 46174932 C G 1 0 0 0 0 0 0 0 1 2810 755 27 4 4 CDH22 20 46174932 Silent SNP C C3L-00144_T 1149878 46174932 18269235 1594 5665 CDH22 0 . GRCh38 20 46241051 46241051 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.462C>A p.Phe154Leu p.F154L ENST00000537909 3/12 267 217 50 256 256 0 strelka-varscan-mutect CDH22,missense_variant,p.Phe154Leu,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Phe154Leu,ENST00000372262,; T ENST00000537909 Transcript missense_variant 1105/3902 462/2487 154/828 F/L ttC/ttA 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 deleterious(0) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 46241051 46241051 G T 1 0 0 0 0 1 0 0 0 2810 1281 45 2 2 CDH22 20 46241051 Missense_Mutation SNP G C3L-00144_T 66119 46241051 18203116 1595 5666 NFATC2 0 . GRCh38 20 51391438 51391438 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2736C>A p.= p.I912I ENST00000396009 10/10 286 260 26 202 200 2 strelka-varscan-mutect NFATC2,synonymous_variant,p.=,ENST00000396009,NM_001258297.1,NM_173091.3;NFATC2,synonymous_variant,p.=,ENST00000609943,NM_001258295.1,NM_001258292.1;NFATC2,3_prime_UTR_variant,,ENST00000371564,NM_012340.4;NFATC2,3_prime_UTR_variant,,ENST00000414705,NM_001136021.2;NFATC2,3_prime_UTR_variant,,ENST00000610033,NM_001258296.1;NFATC2,3_prime_UTR_variant,,ENST00000609507,NM_001258294.1;NFATC2,non_coding_transcript_exon_variant,,ENST00000496054,; T ENST00000396009 Transcript synonymous_variant 2956/7437 2736/2778 912/925 I atC/atA 1 -1 NFATC2 HGNC HGNC:7776 protein_coding YES CCDS13437.1 ENSP00000379330 Q13469 UPI0000167D0F NM_001258297.1,NM_173091.3 10/10 hmmpanther:PTHR12533:SF4,hmmpanther:PTHR12533 LOW 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.999779 1 1 1 0 T 2 4 12 51391438 51391438 G T 1 0 0 0 0 0 0 0 1 10399 1280 45 2 2 NFATC2 20 51391438 Silent SNP G C3L-00144_T 5150387 51391438 13052729 1596 5667 TSHZ2 0 . GRCh38 20 53253842 53253842 + Silent SNP C C A rs141908704 C3L-00144_T C3L-00144_N C C c.384C>A p.= p.V128V ENST00000371497 2/3 165 132 33 114 112 2 strelka-varscan-mutect TSHZ2,synonymous_variant,p.=,ENST00000371497,NM_173485.5;TSHZ2,synonymous_variant,p.=,ENST00000603338,NM_001193421.1;TSHZ2,synonymous_variant,p.=,ENST00000329613,;RP4-678D15.1,downstream_gene_variant,,ENST00000606932,;TSHZ2,upstream_gene_variant,,ENST00000605656,; A ENST00000371497 Transcript synonymous_variant 1271/12187 384/3105 128/1034 V gtC/gtA rs141908704 1 1 TSHZ2 HGNC HGNC:13010 protein_coding YES CCDS33490.1 ENSP00000360552 Q9NRE2 UPI0000206747 NM_173485.5 2/3 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF3 LOW 1 SNV 1 1 PASS rs141908704 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 53253842 53253842 C A 1 0 0 0 0 0 0 0 1 17129 900 32 2 2 TSHZ2 20 53253842 Silent SNP C C3L-00144_T 1862404 53253842 11190325 1597 5668 CASS4 0 . GRCh38 20 56452958 56452958 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.1782G>A p.= p.K594K ENST00000360314 6/7 241 202 39 208 208 0 strelka-varscan-mutect CASS4,synonymous_variant,p.=,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,intron_variant,,ENST00000434344,NM_001164115.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; A ENST00000360314 Transcript synonymous_variant 2007/2619 1782/2361 594/786 K aaG/aaA 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 6/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 56452958 56452958 G A 1 0 0 0 0 0 0 0 1 2382 991 35 3 3 CASS4 20 56452958 Silent SNP G C3L-00144_T 3199116 56452958 7991209 1598 5669 BHLHE23 0 . GRCh38 20 63006129 63006129 + Missense_Mutation SNP G G T rs746566653,rs780915763 C3L-00144_T C3L-00144_N G G c.646C>A p.Leu216Met p.L216M ENST00000612929 1/1 124 103 21 129 128 1 strelka-varscan-mutect BHLHE23,missense_variant,p.Leu216Met,ENST00000612929,NM_080606.3;BHLHE23,missense_variant,p.Leu200Met,ENST00000370346,;RP11-305P22.9,upstream_gene_variant,,ENST00000607802,;RP11-305P22.9,upstream_gene_variant,,ENST00000606208,; T ENST00000612929 Transcript missense_variant 907/1109 646/726 216/241 L/M Ctg/Atg rs746566653,rs780915763 1 -1 BHLHE23 HGNC HGNC:16093 protein_coding YES CCDS33507.2 ENSP00000480998 A0A087WXG3 UPI00024D1415 NM_080606.3 deleterious(0.01) 1/1 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF53 MODERATE SNV 1 PASS rs746566653 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 63006129 63006129 G T 1 0 0 0 0 1 0 0 0 1570 991 35 2 2 BHLHE23 20 63006129 Missense_Mutation SNP G C3L-00144_T 6553171 63006129 1438038 1599 5670 HELZ2 0 . GRCh38 20 63565242 63565242 + Missense_Mutation SNP C C A rs749056408 C3L-00144_T C3L-00144_N C C c.3580G>T p.Val1194Leu p.V1194L ENST00000467148 8/19 331 281 50 260 260 0 strelka-varscan-mutect HELZ2,missense_variant,p.Val1194Leu,ENST00000467148,NM_001037335.2;HELZ2,missense_variant,p.Val625Leu,ENST00000427522,NM_033405.3;HELZ2,downstream_gene_variant,,ENST00000479540,;HELZ2,upstream_gene_variant,,ENST00000478861,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,downstream_gene_variant,,ENST00000370082,; A ENST00000467148 Transcript missense_variant 3650/8064 3580/7950 1194/2649 V/L Gtg/Ttg rs749056408 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 deleterious(0.01) 8/19 Low_complexity_(Seg):seg,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS rs749056408 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 63565242 63565242 C A 1 0 0 0 0 1 0 0 0 6932 536 19 1 1 HELZ2 20 63565242 Missense_Mutation SNP C C3L-00144_T 559113 63565242 878925 1600 5671 PCMTD2 0 . GRCh38 20 64260239 64260239 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.274G>T p.Gly92Trp p.G92W ENST00000308824 2/6 156 121 35 132 132 0 strelka-varscan-mutect PCMTD2,missense_variant,p.Gly92Trp,ENST00000308824,NM_018257.2;PCMTD2,missense_variant,p.Gly92Trp,ENST00000369758,NM_001104925.1;PCMTD2,missense_variant,p.Gly92Trp,ENST00000299468,;PCMTD2,missense_variant,p.Gly92Trp,ENST00000609764,;PCMTD2,missense_variant,p.Gly92Trp,ENST00000610074,;PCMTD2,missense_variant,p.Gly92Trp,ENST00000610196,;PCMTD2,intron_variant,,ENST00000609372,;PCMTD2,downstream_gene_variant,,ENST00000609297,;PCMTD2,missense_variant,p.Gly53Trp,ENST00000608844,; T ENST00000308824 Transcript missense_variant 401/3843 274/1086 92/361 G/W Ggg/Tgg 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 deleterious(0) 2/6 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2,Superfamily_domains:SSF53335 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 64260239 64260239 G T 1 0 0 0 0 1 0 0 0 11675 1348 47 2 2 PCMTD2 20 64260239 Missense_Mutation SNP G C3L-00144_T 694997 64260239 183928 1601 5672 AF165138.7 0 . GRCh38 21 14643093 14643093 + Missense_Mutation SNP T T G novel C3L-00144_T C3L-00144_N T T c.41A>C p.Gln14Pro p.Q14P ENST00000435732 1/7 193 176 17 171 171 0 strelka-varscan-mutect AF165138.7,missense_variant,p.Gln14Pro,ENST00000435732,NM_001256579.2;AF165138.7,missense_variant,p.Gln22Pro,ENST00000400562,; G ENST00000435732 Transcript missense_variant 41/1151 41/459 14/152 Q/P cAa/cCa 1 -1 AF165138.7 Clone_based_vega_gene protein_coding YES ENSP00000401381 H7C1N6 UPI0004620D9C NM_001256579.2 deleterious(0.02) 1/7 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 14643093 14643093 T G 1 0 0 0 0 1 0 0 0 429 1812 63 5 5 AF165138.7 21 14643093 Missense_Mutation SNP T C3L-00144_T 14643093 32066890 1602 5673 TMPRSS15 0 . GRCh38 21 18332165 18332165 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1573G>T p.Gly525Ter p.G525* ENST00000284885 14/25 397 365 32 377 377 0 strelka-varscan-mutect TMPRSS15,stop_gained,p.Gly525Ter,ENST00000284885,NM_002772.2; A ENST00000284885 Transcript stop_gained 1607/3947 1573/3060 525/1019 G/* Gga/Tga 1 -1 TMPRSS15 HGNC HGNC:9490 protein_coding YES CCDS13571.1 ENSP00000284885 P98073 UPI000013DDBE NM_002772.2 14/25 PROSITE_profiles:PS01180,Pfam_domain:PF00431,PIRSF_domain:PIRSF001138,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 18332165 18332165 C A 1 0 0 0 0 0 1 0 0 16722 603 21 2 2 TMPRSS15 21 18332165 Nonsense_Mutation SNP C C3L-00144_T 3689072 18332165 28377818 1603 5674 ADAMTS5 0 . GRCh38 21 26924277 26924277 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.2569C>A p.Pro857Thr p.P857T ENST00000284987 8/8 237 200 37 208 207 1 strelka-varscan-mutect ADAMTS5,missense_variant,p.Pro857Thr,ENST00000284987,NM_007038.3;AP001601.2,intron_variant,,ENST00000426771,; T ENST00000284987 Transcript missense_variant 2691/9056 2569/2793 857/930 P/T Cca/Aca 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 tolerated(0.48) 8/8 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 26924277 26924277 G T 1 0 0 0 0 1 0 0 0 313 1174 41 2 2 ADAMTS5 21 26924277 Missense_Mutation SNP G C3L-00144_T 8592112 26924277 19785706 1604 5675 ADAMTS5 0 . GRCh38 21 26965625 26965625 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.767G>T p.Trp256Leu p.W256L ENST00000284987 1/8 103 76 27 118 118 0 strelka-varscan-mutect ADAMTS5,missense_variant,p.Trp256Leu,ENST00000284987,NM_007038.3; A ENST00000284987 Transcript missense_variant 889/9056 767/2793 256/930 W/L tGg/tTg 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 tolerated(0.52) 1/8 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 26965625 26965625 C A 1 0 0 0 0 1 0 0 0 313 595 21 2 2 ADAMTS5 21 26965625 Missense_Mutation SNP C C3L-00144_T 41348 26965625 19744358 1605 5676 GRIK1 0 . GRCh38 21 29577145 29577145 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.1949T>A p.Ile650Lys p.I650K ENST00000399907 14/17 165 134 31 152 152 0 strelka-varscan-mutect GRIK1,missense_variant,p.Ile635Lys,ENST00000399914,;GRIK1,missense_variant,p.Ile650Lys,ENST00000399907,NM_000830.3;GRIK1,missense_variant,p.Ile635Lys,ENST00000399909,;GRIK1,missense_variant,p.Ile650Lys,ENST00000399913,;GRIK1,missense_variant,p.Ile650Lys,ENST00000327783,;GRIK1,missense_variant,p.Ile635Lys,ENST00000389125,NM_175611.2;GRIK1,missense_variant,p.Ile650Lys,ENST00000389124,;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; T ENST00000399907 Transcript missense_variant 2361/3472 1949/2757 650/918 I/K aTa/aAa 1 -1 GRIK1 HGNC HGNC:4579 protein_coding YES CCDS42913.1 ENSP00000382791 P39086 UPI000012B612 NM_000830.3 deleterious(0) 14/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF36,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Prints_domain:PR00177 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 29577145 29577145 A T 1 0 0 0 0 1 0 0 0 6655 449 16 4 4 GRIK1 21 29577145 Missense_Mutation SNP A C3L-00144_T 2611520 29577145 17132838 1606 5677 KRTAP6-3 0 . GRCh38 21 30592676 30592676 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.231C>A p.Asp77Glu p.D77E ENST00000391624 1/1 278 234 44 252 252 0 strelka-varscan-mutect KRTAP6-3,missense_variant,p.Asp77Glu,ENST00000391624,NM_181605.3;KRTAP22-2,upstream_gene_variant,,ENST00000382830,NM_001164434.1; A ENST00000391624 Transcript missense_variant 237/636 231/333 77/110 D/E gaC/gaA COSM1662531 1 1 KRTAP6-3 HGNC HGNC:18933 protein_coding YES CCDS77622.1 ENSP00000375482 Q3LI67 UPI00003D4D73 NM_181605.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31678,hmmpanther:PTHR31678:SF4 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 30592676 30592676 C A 1 0 0 0 0 1 0 0 0 8466 564 20 2 2 KRTAP6-3 21 30592676 Missense_Mutation SNP C C3L-00144_T 1015531 30592676 16117307 1607 5678 ITSN1 0 . GRCh38 21 33888192 33888192 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.5058G>T p.Lys1686Asn p.K1686N ENST00000381318 40/40 143 101 42 100 100 0 strelka-varscan-mutect ITSN1,missense_variant,p.Lys1686Asn,ENST00000381318,NM_003024.2;ITSN1,missense_variant,p.Lys1681Asn,ENST00000399367,;ITSN1,3_prime_UTR_variant,,ENST00000381285,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,downstream_gene_variant,,ENST00000381284,;ITSN1,downstream_gene_variant,,ENST00000415023,;ITSN1,downstream_gene_variant,,ENST00000420666,; T ENST00000381318 Transcript missense_variant 5346/17015 5058/5166 1686/1721 K/N aaG/aaT 1 1 ITSN1 HGNC HGNC:6183 protein_coding YES CCDS33545.1 ENSP00000370719 Q15811 UPI00001403C6 NM_003024.2 deleterious(0.01) 40/40 Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 33888192 33888192 G T 1 0 0 0 0 1 0 0 0 7832 933 33 2 2 ITSN1 21 33888192 Missense_Mutation SNP G C3L-00144_T 3295516 33888192 12821791 1608 5679 KCNJ6 0 . GRCh38 21 37625397 37625397 + Missense_Mutation SNP C C A C3L-00144_T C3L-00144_N C C c.1034G>T p.Gly345Val p.G345V ENST00000609713 4/4 304 237 67 275 275 0 strelka-varscan-mutect KCNJ6,missense_variant,p.Gly345Val,ENST00000609713,NM_002240.3; A ENST00000609713 Transcript missense_variant 1624/19645 1034/1272 345/423 G/V gGg/gTg COSM3912083 1 -1 KCNJ6 HGNC HGNC:6267 protein_coding YES CCDS42927.1 ENSP00000477437 P48051 UPI0000000B10 NM_002240.3 deleterious(0) 4/4 hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF19,Pfam_domain:PF01007,Gene3D:2.60.40.1400,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81296 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 37625397 37625397 C A 1 0 0 0 0 1 0 0 0 7972 623 22 2 2 KCNJ6 21 37625397 Missense_Mutation SNP C C3L-00144_T 3737205 37625397 9084586 1609 5680 ETS2 0 . GRCh38 21 38819653 38819653 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.962C>T p.Ser321Phe p.S321F ENST00000360214 9/11 555 514 41 453 452 1 strelka-varscan-mutect ETS2,missense_variant,p.Ser321Phe,ENST00000360214,NM_001256295.1;ETS2,missense_variant,p.Ser321Phe,ENST00000360938,NM_005239.5;ETS2,downstream_gene_variant,,ENST00000432278,;ETS2,downstream_gene_variant,,ENST00000456966,; T ENST00000360214 Transcript missense_variant 1422/3936 962/1410 321/469 S/F tCt/tTt 1 1 ETS2 HGNC HGNC:3489 protein_coding YES CCDS13659.1 ENSP00000353344 P15036 UPI0000000E04 NM_001256295.1 tolerated(0.08) 9/11 PIRSF_domain:PIRSF001698,PIRSF_domain:PIRSF501032 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 38819653 38819653 C T 1 0 0 0 0 1 0 0 0 5140 913 32 3 3 ETS2 21 38819653 Missense_Mutation SNP C C3L-00144_T 1194256 38819653 7890330 1610 5681 DSCAM 0 . GRCh38 21 40347713 40347713 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1167G>T p.Lys389Asn p.K389N ENST00000400454 6/33 239 196 43 217 217 0 strelka-varscan-mutect DSCAM,missense_variant,p.Lys389Asn,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Lys224Asn,ENST00000617870,;DSCAM,missense_variant,p.Lys141Asn,ENST00000404019,; A ENST00000400454 Transcript missense_variant 1645/8552 1167/6039 389/2012 K/N aaG/aaT 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 tolerated(0.67) 6/33 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 40347713 40347713 C A 1 0 0 0 0 1 0 0 0 4589 680 24 2 2 DSCAM 21 40347713 Missense_Mutation SNP C C3L-00144_T 1528060 40347713 6362270 1611 5682 RIPK4 0 . GRCh38 21 41741506 41741506 + Missense_Mutation SNP C C G rs148030694 C3L-00144_T C3L-00144_N C C c.1687G>C p.Val563Leu p.V563L ENST00000332512 8/8 138 110 28 132 132 0 strelka-varscan-mutect RIPK4,missense_variant,p.Val611Leu,ENST00000352483,;RIPK4,missense_variant,p.Val563Leu,ENST00000332512,NM_020639.2;AP001615.9,downstream_gene_variant,,ENST00000423276,; G ENST00000332512 Transcript missense_variant 1752/3889 1687/2355 563/784 V/L Gtg/Ctg rs148030694 1 -1 RIPK4 HGNC HGNC:496 protein_coding YES CCDS13675.1 ENSP00000332454 P57078 UPI000002A3C9 NM_020639.2 tolerated(0.52) 8/8 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF65,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs148030694 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 41741506 41741506 C G 1 0 0 0 0 1 0 0 0 13557 536 19 4 4 RIPK4 21 41741506 Missense_Mutation SNP C C3L-00144_T 1393793 41741506 4968477 1612 5683 ZBTB21 0 . GRCh38 21 41992163 41992163 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.1933G>A p.Gly645Ser p.G645S ENST00000310826 3/3 244 189 55 203 203 0 strelka-varscan-mutect ZBTB21,missense_variant,p.Gly645Ser,ENST00000310826,NM_001320731.1,NM_001098402.1;ZBTB21,missense_variant,p.Gly645Ser,ENST00000398499,;ZBTB21,missense_variant,p.Gly645Ser,ENST00000398511,NM_020727.4;ZBTB21,intron_variant,,ENST00000398505,NM_001320729.1,NM_001098403.1;ZBTB21,downstream_gene_variant,,ENST00000425521,;ZBTB21,downstream_gene_variant,,ENST00000398497,;ZBTB21,downstream_gene_variant,,ENST00000449949,;ZBTB21,intron_variant,,ENST00000465968,; T ENST00000310826 Transcript missense_variant 2117/7449 1933/3201 645/1066 G/S Ggt/Agt 1 -1 ZBTB21 HGNC HGNC:13083 protein_coding YES CCDS13678.1 ENSP00000308759 Q9ULJ3 UPI000013C34D NM_001320731.1,NM_001098402.1 tolerated(0.06) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 41992163 41992163 C T 1 0 0 0 0 1 0 0 0 18098 594 21 3 3 ZBTB21 21 41992163 Missense_Mutation SNP C C3L-00144_T 250657 41992163 4717820 1613 5684 AIRE 0 . GRCh38 21 44294426 44294426 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1426T>A p.Ser476Thr p.S476T ENST00000291582 12/14 96 88 8 99 99 0 strelka-varscan-mutect AIRE,missense_variant,p.Ser476Thr,ENST00000291582,NM_000383.3;AIRE,non_coding_transcript_exon_variant,,ENST00000530812,;AIRE,non_coding_transcript_exon_variant,,ENST00000527919,;AIRE,non_coding_transcript_exon_variant,,ENST00000337909,;AIRE,non_coding_transcript_exon_variant,,ENST00000397994,; A ENST00000291582 Transcript missense_variant 1553/2257 1426/1638 476/545 S/T Tca/Aca 1 1 AIRE HGNC HGNC:360 protein_coding YES CCDS13706.1 ENSP00000291582 O43918 UPI0000030FA6 NM_000383.3 tolerated(0.13) 12/14 Gene3D:3.30.40.10,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF15,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -16.90017 1 1 1 1 0 A 3 1 12 44294426 44294426 T A 1 0 0 0 0 1 0 0 0 514 1551 54 4 4 AIRE 21 44294426 Missense_Mutation SNP T C3L-00144_T 2302263 44294426 2415557 1614 5685 KRTAP10-4 0 . GRCh38 21 44574306 44574306 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.548C>A p.Ser183Tyr p.S183Y ENST00000400374 1/1 645 545 100 705 704 1 strelka-varscan-mutect KRTAP10-4,missense_variant,p.Ser183Tyr,ENST00000400374,NM_198687.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,upstream_gene_variant,,ENST00000397916,; A ENST00000400374 Transcript missense_variant 578/1643 548/1206 183/401 S/Y tCc/tAc 1 1 KRTAP10-4 HGNC HGNC:20521 protein_coding YES CCDS42957.1 ENSP00000383225 P60372 UPI00003D4D6E NM_198687.2 tolerated(0.18) 1/1 Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 44574306 44574306 C A 1 0 0 0 0 1 0 0 0 8394 855 30 2 2 KRTAP10-4 21 44574306 Missense_Mutation SNP C C3L-00144_T 279880 44574306 2135677 1615 5686 FTCD 0 . GRCh38 21 46145441 46145441 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1236C>A p.Asp412Glu p.D412E ENST00000291670 10/15 104 81 23 95 95 0 strelka-varscan-mutect FTCD,missense_variant,p.Asp412Glu,ENST00000397748,NM_001320412.1;FTCD,missense_variant,p.Asp412Glu,ENST00000291670,NM_006657.2;FTCD,missense_variant,p.Asp412Glu,ENST00000397746,NM_206965.1;FTCD,missense_variant,p.Asp412Glu,ENST00000397743,;FTCD,non_coding_transcript_exon_variant,,ENST00000498355,;FTCD,non_coding_transcript_exon_variant,,ENST00000488577,;FTCD,upstream_gene_variant,,ENST00000460011,;FTCD,upstream_gene_variant,,ENST00000494498,;FTCD,downstream_gene_variant,,ENST00000480950,;FTCD,downstream_gene_variant,,ENST00000469240,; T ENST00000291670 Transcript missense_variant 1280/1905 1236/1626 412/541 D/E gaC/gaA 1 -1 FTCD HGNC HGNC:3974 protein_coding YES CCDS13731.1 ENSP00000291670 O95954 UPI000012AC75 NM_006657.2 deleterious(0) 10/15 Superfamily_domains:0041691,Pfam_domain:PF04961,hmmpanther:PTHR12234,hmmpanther:PTHR12234:SF0 MODERATE 1 SNV 1 1 PASS rs1183507055 . 0 202 8 0 0 0 0 0 -20 0.9999991 1 1 1 0 T 3 4 12 46145441 46145441 G T 1 0 0 0 0 1 0 0 0 5955 1136 40 1 1 FTCD 21 46145441 Missense_Mutation SNP G C3L-00144_T 1571135 46145441 564542 1616 5687 PCNT 0 . GRCh38 21 46349180 46349180 + Missense_Mutation SNP G G C rs149949585 C3L-00144_T C3L-00144_N G G c.1201G>C p.Ala401Pro p.A401P ENST00000359568 7/47 331 306 25 272 272 0 strelka-varscan-mutect PCNT,missense_variant,p.Ala401Pro,ENST00000359568,NM_006031.5;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,non_coding_transcript_exon_variant,,ENST00000490468,;PCNT,non_coding_transcript_exon_variant,,ENST00000466474,;PCNT,non_coding_transcript_exon_variant,,ENST00000483844,; C ENST00000359568 Transcript missense_variant 1308/10560 1201/10011 401/3336 A/P Gct/Cct rs149949585 1 1 PCNT HGNC HGNC:16068 protein_coding YES CCDS33592.1 ENSP00000352572 O95613 UPI00001AEB88 NM_006031.5 deleterious(0.01) 7/47 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS rs149949585 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 46349180 46349180 G C 1 0 0 0 0 1 0 0 0 11678 1203 42 4 4 PCNT 21 46349180 Missense_Mutation SNP G C3L-00144_T 203739 46349180 360803 1617 5688 CCT8L2 0 . GRCh38 22 16592153 16592153 + Missense_Mutation SNP C C A rs149623775 C3L-00144_T C3L-00144_N C C c.398G>T p.Arg133Leu p.R133L ENST00000359963 1/1 144 107 37 136 136 0 strelka-varscan-mutect CCT8L2,missense_variant,p.Arg133Leu,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; A ENST00000359963 Transcript missense_variant 658/2060 398/1674 133/557 R/L cGg/cTg rs149623775,COSM1200213 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 tolerated(1) 1/1 Gene3D:1.10.560.10,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100,Superfamily_domains:SSF48592 0,1 MODERATE 1 SNV 0,1 1 PASS rs149623775 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 16592153 16592153 C A 1 0 0 0 0 1 0 0 0 2662 652 23 1 1 CCT8L2 22 16592153 Missense_Mutation SNP C C3L-00144_T 16592153 34226315 1618 5689 GAB4 0 . GRCh38 22 16988109 16988109 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.537C>A p.= p.P179P ENST00000400588 3/10 124 88 36 95 94 1 strelka-varscan-mutect GAB4,synonymous_variant,p.=,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,intron_variant,,ENST00000523144,;GAB4,synonymous_variant,p.=,ENST00000465611,; T ENST00000400588 Transcript synonymous_variant 645/2630 537/1725 179/574 P ccC/ccA 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 3/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 16988109 16988109 G T 1 0 0 0 0 0 0 0 1 6022 1335 47 2 2 GAB4 22 16988109 Silent SNP G C3L-00144_T 395956 16988109 33830359 1619 5690 IL17RA 0 . GRCh38 22 17102148 17102148 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.608G>T p.Trp203Leu p.W203L ENST00000319363 7/13 621 472 149 566 565 1 strelka-varscan-mutect IL17RA,missense_variant,p.Trp203Leu,ENST00000319363,NM_014339.6;IL17RA,missense_variant,p.Trp203Leu,ENST00000612619,NM_001289905.1;IL17RA,downstream_gene_variant,,ENST00000477874,;IL17RA,downstream_gene_variant,,ENST00000459971,; T ENST00000319363 Transcript missense_variant 741/8607 608/2601 203/866 W/L tGg/tTg 1 1 IL17RA HGNC HGNC:5985 protein_coding YES CCDS13739.1 ENSP00000320936 Q96F46 UPI000005031F NM_014339.6 deleterious(0) 7/13 Pfam_domain:PF16578,hmmpanther:PTHR15583,hmmpanther:PTHR15583:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 17102148 17102148 G T 1 0 0 0 0 1 0 0 0 7547 1357 47 2 2 IL17RA 22 17102148 Missense_Mutation SNP G C3L-00144_T 114039 17102148 33716320 1620 5691 CECR1 0 . GRCh38 22 17209633 17209633 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.45G>T p.Leu15Phe p.L15F ENST00000399837 2/10 136 110 26 120 120 0 strelka-varscan-mutect CECR1,missense_variant,p.Leu15Phe,ENST00000399837,NM_001282226.1,NM_001282225.1;CECR1,missense_variant,p.Leu15Phe,ENST00000399839,;CECR1,missense_variant,p.Leu15Phe,ENST00000262607,;CECR1,missense_variant,p.Leu15Phe,ENST00000441548,;CECR1,missense_variant,p.Leu15Phe,ENST00000543038,;CECR1,intron_variant,,ENST00000449907,NM_001282228.1,NM_001282227.1;CECR1,intron_variant,,ENST00000610390,NM_001282229.1;FAM32BP,upstream_gene_variant,,ENST00000344033,; A ENST00000399837 Transcript missense_variant 321/4505 45/1536 15/511 L/F ttG/ttT 1 -1 CECR1 HGNC HGNC:1839 protein_coding YES CCDS13742.1 ENSP00000382731 Q9NZK5 UPI000013D2E8 NM_001282226.1,NM_001282225.1 tolerated(0.09) 2/10 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17209633 17209633 C A 1 0 0 0 0 1 0 0 0 2912 709 25 2 2 CECR1 22 17209633 Missense_Mutation SNP C C3L-00144_T 107485 17209633 33608835 1621 5692 MICAL3 0 . GRCh38 22 17900853 17900853 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.836G>T p.Arg279Met p.R279M ENST00000441493 6/32 162 128 34 147 147 0 strelka-varscan-mutect MICAL3,missense_variant,p.Arg279Met,ENST00000441493,NM_015241.2;MICAL3,missense_variant,p.Arg279Met,ENST00000414725,;MICAL3,missense_variant,p.Arg279Met,ENST00000585038,NM_001136004.3;MICAL3,missense_variant,p.Arg279Met,ENST00000400561,NM_001122731.2;MICAL3,missense_variant,p.Arg279Met,ENST00000383094,;MICAL3,downstream_gene_variant,,ENST00000424046,;MICAL3,missense_variant,p.Arg279Met,ENST00000495076,; A ENST00000441493 Transcript missense_variant 1189/9445 836/6009 279/2002 R/M aGg/aTg 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 deleterious(0) 6/32 hmmpanther:PTHR11915:SF239,hmmpanther:PTHR11915,Gene3D:3.50.50.60 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 17900853 17900853 C A 1 0 0 0 0 1 0 0 0 9528 681 24 2 2 MICAL3 22 17900853 Missense_Mutation SNP C C3L-00144_T 691220 17900853 32917615 1622 5693 RIMBP3 0 . GRCh38 22 18608921 18608921 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.2514G>A p.Met838Ile p.M838I ENST00000619918 1/1 166 147 19 152 152 0 varscan-mutect RIMBP3,missense_variant,p.Met838Ile,ENST00000619918,NM_015672.1;SCARNA17,downstream_gene_variant,,ENST00000614296,;RN7SKP131,upstream_gene_variant,,ENST00000410698,; T ENST00000619918 Transcript missense_variant 2999/6105 2514/4920 838/1639 M/I atG/atA 1 -1 RIMBP3 HGNC HGNC:29344 protein_coding YES CCDS46665.1 ENSP00000483386 Q9UFD9 UPI0000237729 NM_015672.1 tolerated(0.08) 1/1 Gene3D:2.30.30.40,PROSITE_profiles:PS50002,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF21,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 18608921 18608921 C T 1 0 0 0 0 1 0 0 0 13539 594 21 3 3 RIMBP3 22 18608921 Missense_Mutation SNP C C3L-00144_T 708068 18608921 32209547 1623 5694 CCDC188 0 . GRCh38 22 20149586 20149586 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.844C>A p.Leu282Ile p.L282I ENST00000439765 5/9 308 254 54 267 267 0 strelka-varscan-mutect CCDC188,missense_variant,p.Leu282Ile,ENST00000439765,;ZDHHC8,downstream_gene_variant,,ENST00000334554,NM_013373.3;ZDHHC8,downstream_gene_variant,,ENST00000405930,NM_001185024.1;ZDHHC8,downstream_gene_variant,,ENST00000320602,;CCDC188,non_coding_transcript_exon_variant,,ENST00000444532,; T ENST00000439765 Transcript missense_variant 923/1475 844/1209 282/402 L/I Ctc/Atc 1 -1 CCDC188 HGNC HGNC:51899 protein_coding YES ENSP00000409542 H7C350 UPI000387C900 deleterious_low_confidence(0.01) 5/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22422:SF6,hmmpanther:PTHR22422,Pfam_domain:PF14992 MODERATE SNV 5 1 PASS rs1314470133 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 20149586 20149586 G T 1 0 0 0 0 1 0 0 0 2503 985 34 2 2 CCDC188 22 20149586 Missense_Mutation SNP G C3L-00144_T 1540665 20149586 30668882 1624 5695 CCDC116 0 . GRCh38 22 21635019 21635019 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.956A>T p.Gln319Leu p.Q319L ENST00000292779 4/5 235 199 36 210 210 0 strelka-varscan-mutect CCDC116,missense_variant,p.Gln319Leu,ENST00000292779,NM_152612.2;CCDC116,missense_variant,p.Gln319Leu,ENST00000607942,;YDJC,upstream_gene_variant,,ENST00000292778,NM_001017964.1;YDJC,upstream_gene_variant,,ENST00000398873,;CCDC116,downstream_gene_variant,,ENST00000425975,;YDJC,upstream_gene_variant,,ENST00000473985,;YDJC,upstream_gene_variant,,ENST00000468686,;YDJC,upstream_gene_variant,,ENST00000415762,; T ENST00000292779 Transcript missense_variant 1117/2260 956/1842 319/613 Q/L cAg/cTg 1 1 CCDC116 HGNC HGNC:26688 protein_coding YES CCDS13791.1 ENSP00000292779 Q8IYX3 UPI00000741C9 NM_152612.2 deleterious(0) 4/5 hmmpanther:PTHR36861,Pfam_domain:PF15774 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 21635019 21635019 A T 1 0 0 0 0 1 0 0 0 2446 188 7 4 4 CCDC116 22 21635019 Missense_Mutation SNP A C3L-00144_T 1485433 21635019 29183449 1625 5696 RSPH14 0 . GRCh38 22 23061841 23061841 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.758G>T p.Gly253Val p.G253V ENST00000216036 6/7 312 266 46 215 215 0 strelka-varscan-mutect RSPH14,missense_variant,p.Gly253Val,ENST00000216036,NM_014433.2; A ENST00000216036 Transcript missense_variant 955/1291 758/1047 253/348 G/V gGt/gTt 1 -1 RSPH14 HGNC HGNC:13437 protein_coding YES CCDS13803.1 ENSP00000216036 Q9UHP6 UPI000004A0CE NM_014433.2 deleterious(0) 6/7 Gene3D:1.25.10.10,Pfam_domain:PF00514,hmmpanther:PTHR15599,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 23061841 23061841 C A 1 0 0 0 0 1 0 0 0 13962 507 18 2 2 RSPH14 22 23061841 Missense_Mutation SNP C C3L-00144_T 1426822 23061841 27756627 1626 5697 TMEM211 0 . GRCh38 22 24935491 24935491 + Silent SNP G G T C3L-00144_T C3L-00144_N G G c.232C>A p.= p.R78R ENST00000407886 4/4 268 214 54 201 200 1 strelka-varscan-mutect TMEM211,synonymous_variant,p.=,ENST00000407886,NM_001001663.1;TMEM211,synonymous_variant,p.=,ENST00000423535,; T ENST00000407886 Transcript synonymous_variant 485/866 232/390 78/129 R Cgg/Agg COSM1032781,COSM3357322 1 -1 TMEM211 HGNC HGNC:33725 protein_coding YES CCDS33624.1 ENSP00000385494 A0A0C4DG04 UPI0000160696 NM_001001663.1 4/4 hmmpanther:PTHR12489,hmmpanther:PTHR12489:SF20,Pfam_domain:PF10242 1,1 LOW 1 SNV 3 1,1 1 PASS rs1024236807 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 24935491 24935491 G T 1 0 0 0 0 0 0 0 1 16575 1115 39 1 1 TMEM211 22 24935491 Silent SNP G C3L-00144_T 1873650 24935491 25882977 1627 5698 KIAA1671 0 . GRCh38 22 25040644 25040644 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.3514G>T p.Asp1172Tyr p.D1172Y ENST00000358431 3/11 281 225 56 248 248 0 strelka-varscan-mutect KIAA1671,missense_variant,p.Asp1172Tyr,ENST00000358431,NM_001145206.1;KIAA1671,missense_variant,p.Asp1172Tyr,ENST00000406486,;KIAA1671,non_coding_transcript_exon_variant,,ENST00000494730,;KIAA1671,upstream_gene_variant,,ENST00000461374,; T ENST00000358431 Transcript missense_variant 3540/10490 3514/5421 1172/1806 D/Y Gat/Tat 1 1 KIAA1671 HGNC HGNC:29345 protein_coding YES CCDS46676.1 ENSP00000351207 Q9BY89 UPI00002073DC NM_001145206.1 deleterious(0.01) 3/11 hmmpanther:PTHR22042,hmmpanther:PTHR22042:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 25040644 25040644 G T 1 0 0 0 0 1 0 0 0 8125 942 33 2 2 KIAA1671 22 25040644 Missense_Mutation SNP G C3L-00144_T 105153 25040644 25777824 1628 5699 MYO18B 0 . GRCh38 22 25843823 25843823 + Silent SNP G G T rs369215277 C3L-00144_T C3L-00144_N G G c.3297G>T p.= p.T1099T ENST00000335473 18/44 200 149 51 170 170 0 strelka-varscan-mutect MYO18B,synonymous_variant,p.=,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,synonymous_variant,p.=,ENST00000407587,;MYO18B,synonymous_variant,p.=,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript synonymous_variant 3547/8565 3297/7704 1099/2567 T acG/acT rs369215277 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 18/44 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs369215277 . 0 207 0 0 2 0 0 0 -20 0.9987811 1 1 1 0 T 2 4 12 25843823 25843823 G T 1 0 0 0 0 0 0 0 1 10067 1103 39 1 1 MYO18B 22 25843823 Silent SNP G C3L-00144_T 803179 25843823 24974645 1629 5700 RFPL2 0 . GRCh38 22 32193046 32193046 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.412C>A p.Leu138Ile p.L138I ENST00000400237 4/5 225 202 23 218 218 0 varscan-mutect RFPL2,missense_variant,p.Leu138Ile,ENST00000400237,NM_001098527.2;RFPL2,missense_variant,p.Leu77Ile,ENST00000248980,NM_001159545.1,NM_006605.3,NM_001159546.1;RFPL2,missense_variant,p.Leu138Ile,ENST00000248983,;AL008723.1,downstream_gene_variant,,ENST00000623133,;RFPL3-AS1_1,upstream_gene_variant,,ENST00000618747,;RFPL2,non_coding_transcript_exon_variant,,ENST00000489846,;RFPL2,3_prime_UTR_variant,,ENST00000626996,;RFPL2,3_prime_UTR_variant,,ENST00000628378,; T ENST00000400237 Transcript missense_variant 1348/2407 412/1137 138/378 L/I Ctt/Att 1 -1 RFPL2 HGNC HGNC:9979 protein_coding YES CCDS43009.2 ENSP00000383096 O75678 UPI000013CC66 NM_001098527.2 tolerated(0.16) 4/5 Gene3D:3.30.40.10,Pfam_domain:PF15227,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF225,Superfamily_domains:SSF57850 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 32193046 32193046 G T 1 0 0 0 0 1 0 0 0 13425 1029 36 2 2 RFPL2 22 32193046 Missense_Mutation SNP G C3L-00144_T 6349223 32193046 18625422 1630 5701 MYH9 0 . GRCh38 22 36306034 36306034 + Silent SNP C C A rs756137861 C3L-00144_T C3L-00144_N C C c.2055G>T p.= p.P685P ENST00000216181 17/41 367 302 65 277 277 0 strelka-varscan-mutect MYH9,synonymous_variant,p.=,ENST00000216181,NM_002473.5;MYH9,upstream_gene_variant,,ENST00000495928,;MYH9,upstream_gene_variant,,ENST00000473022,; A ENST00000216181 Transcript synonymous_variant 2286/7501 2055/5883 685/1960 P ccG/ccT rs756137861 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 17/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF317,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs756137861 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 36306034 36306034 C A 1 0 0 0 0 0 0 0 1 10042 755 27 1 1 MYH9 22 36306034 Silent SNP C C3L-00144_T 4112988 36306034 14512434 1631 5702 CSF2RB 0 . GRCh38 22 36938316 36938316 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.2508G>T p.= p.R836R ENST00000403662 14/14 504 394 110 410 409 1 strelka-varscan-mutect CSF2RB,synonymous_variant,p.=,ENST00000403662,NM_000395.2;CSF2RB,synonymous_variant,p.=,ENST00000262825,;CSF2RB,synonymous_variant,p.=,ENST00000406230,; T ENST00000403662 Transcript synonymous_variant 2730/4863 2508/2694 836/897 R cgG/cgT 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF22,PIRSF_domain:PIRSF001956 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 36938316 36938316 G T 1 0 0 0 0 0 0 0 1 3736 1161 41 2 2 CSF2RB 22 36938316 Silent SNP G C3L-00144_T 632282 36938316 13880152 1632 5703 GCAT 0 . GRCh38 22 37812968 37812968 + Missense_Mutation SNP G G C rs371002709 C3L-00144_T C3L-00144_N G G c.487G>C p.Ala163Pro p.A163P ENST00000323205 3/10 172 133 39 166 166 0 strelka-varscan-mutect GCAT,missense_variant,p.Ala163Pro,ENST00000323205,NM_001171690.1;GCAT,missense_variant,p.Ala137Pro,ENST00000248924,NM_014291.3;GCAT,missense_variant,p.Ala122Pro,ENST00000451984,;GCAT,missense_variant,p.Ala163Pro,ENST00000445195,;GCAT,non_coding_transcript_exon_variant,,ENST00000415371,;GCAT,3_prime_UTR_variant,,ENST00000426858,;GCAT,non_coding_transcript_exon_variant,,ENST00000478203,; C ENST00000323205 Transcript missense_variant 550/1656 487/1338 163/445 A/P Gcc/Ccc rs371002709 1 1 GCAT HGNC HGNC:4188 protein_coding YES CCDS54527.1 ENSP00000371110 O75600 UPI000020770F NM_001171690.1 deleterious(0) 3/10 Gene3D:3.40.640.10,HAMAP:MF_00985,Pfam_domain:PF00155,hmmpanther:PTHR13693,hmmpanther:PTHR13693:SF60,Superfamily_domains:SSF53383,TIGRFAM_domain:TIGR01822 MODERATE 1 SNV 2 1 PASS rs371002709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 37812968 37812968 G C 1 0 0 0 0 1 0 0 0 6154 1087 38 4 4 GCAT 22 37812968 Missense_Mutation SNP G C3L-00144_T 874652 37812968 13005500 1633 5704 GCAT 0 . GRCh38 22 37816279 37816279 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1144G>T p.Ala382Ser p.A382S ENST00000323205 8/10 275 247 28 199 199 0 strelka-varscan-mutect GCAT,missense_variant,p.Ala382Ser,ENST00000323205,NM_001171690.1;GCAT,missense_variant,p.Ala356Ser,ENST00000248924,NM_014291.3;GCAT,downstream_gene_variant,,ENST00000451984,;GCAT,downstream_gene_variant,,ENST00000445195,;GCAT,downstream_gene_variant,,ENST00000415371,;GCAT,downstream_gene_variant,,ENST00000426858,;GCAT,downstream_gene_variant,,ENST00000478203,; T ENST00000323205 Transcript missense_variant 1207/1656 1144/1338 382/445 A/S Gcc/Tcc 1 1 GCAT HGNC HGNC:4188 protein_coding YES CCDS54527.1 ENSP00000371110 O75600 UPI000020770F NM_001171690.1 deleterious(0.01) 8/10 Gene3D:3.90.1150.10,HAMAP:MF_00985,Pfam_domain:PF00155,hmmpanther:PTHR13693,hmmpanther:PTHR13693:SF60,Superfamily_domains:SSF53383,TIGRFAM_domain:TIGR01822 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 37816279 37816279 G T 1 0 0 0 0 1 0 0 0 6154 1319 46 2 2 GCAT 22 37816279 Missense_Mutation SNP G C3L-00144_T 3311 37816279 13002189 1634 5705 DMC1 0 . GRCh38 22 38538613 38538613 + Splice_Site SNP C C A novel C3L-00144_T C3L-00144_N C C c.587-1G>T p.X196_splice ENST00000216024 450 386 64 340 340 0 strelka-varscan-mutect DMC1,splice_acceptor_variant,,ENST00000216024,NM_007068.3;DMC1,splice_acceptor_variant,,ENST00000428462,NM_001278208.1;DMC1,splice_acceptor_variant,,ENST00000439567,; A ENST00000216024 Transcript splice_acceptor_variant -/2371 587/1023 196/340 1 -1 DMC1 HGNC HGNC:2927 protein_coding YES CCDS13973.1 ENSP00000216024 Q14565 UPI00001294D1 NM_007068.3 9/13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 12 38538613 38538613 C A 1 0 0 0 0 0 0 1 0 4386 695 24 2 2 DMC1 22 38538613 Splice_Site SNP C C3L-00144_T 722334 38538613 12279855 1635 5706 FAM227A 0 . GRCh38 22 38599902 38599902 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1226G>T p.Ser409Ile p.S409I ENST00000355830 14/19 72 58 14 65 65 0 strelka-varscan-mutect FAM227A,missense_variant,p.Ser414Ile,ENST00000535113,NM_001291030.1,NM_001013647.1;FAM227A,missense_variant,p.Ser409Ile,ENST00000355830,;FAM227A,non_coding_transcript_exon_variant,,ENST00000540952,;FAM227A,non_coding_transcript_exon_variant,,ENST00000544346,;FAM227A,non_coding_transcript_exon_variant,,ENST00000541689,; A ENST00000355830 Transcript missense_variant 1522/2417 1226/1941 409/646 S/I aGc/aTc 1 -1 FAM227A HGNC HGNC:44197 protein_coding YES ENSP00000348086 A0A0A0MRD0 UPI000165DBC2 tolerated(0.18) 14/19 hmmpanther:PTHR33560,hmmpanther:PTHR33560:SF1 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 38599902 38599902 C A 1 0 0 0 0 1 0 0 0 5418 797 28 2 2 FAM227A 22 38599902 Missense_Mutation SNP C C3L-00144_T 61289 38599902 12218566 1636 5707 NPTXR 0 . GRCh38 22 38843342 38843342 + Missense_Mutation SNP C C A rs775179493 C3L-00144_T C3L-00144_N C C c.517G>T p.Gly173Trp p.G173W ENST00000333039 1/5 89 67 22 75 75 0 strelka-varscan-mutect NPTXR,missense_variant,p.Gly173Trp,ENST00000333039,NM_014293.3; A ENST00000333039 Transcript missense_variant 641/5784 517/1503 173/500 G/W Ggg/Tgg rs775179493 1 -1 NPTXR HGNC HGNC:7954 protein_coding YES CCDS33647.1 ENSP00000327545 O95502 UPI00001B0258 NM_014293.3 deleterious(0.01) 1/5 hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF94 MODERATE 1 SNV 1 1 PASS rs775179493 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 38843342 38843342 C A 1 0 0 0 0 1 0 0 0 10660 652 23 1 1 NPTXR 22 38843342 Missense_Mutation SNP C C3L-00144_T 243440 38843342 11975126 1637 5708 APOBEC3A 0 . GRCh38 22 38962211 38962211 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.583C>A p.Gln195Lys p.Q195K ENST00000402255 5/6 270 224 46 240 240 0 strelka-varscan-mutect APOBEC3A,missense_variant,p.Gln195Lys,ENST00000402255,;APOBEC3A,missense_variant,p.Gln195Lys,ENST00000249116,NM_001270406.1,NM_145699.3;APOBEC3A,missense_variant,p.Gln195Lys,ENST00000618553,;APOBEC3A,downstream_gene_variant,,ENST00000488758,; A ENST00000402255 Transcript missense_variant,splice_region_variant 787/1478 583/600 195/199 Q/K Cag/Aag 1 1 APOBEC3A HGNC HGNC:17343 protein_coding YES CCDS13981.1 ENSP00000384359 P31941 A0A0K0MJ49 UPI00001318F4 tolerated(0.08) 5/6 hmmpanther:PTHR13857:SF14,hmmpanther:PTHR13857 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 38962211 38962211 C A 1 0 0 0 0 1 0 0 0 910 608 21 2 2 APOBEC3A 22 38962211 Missense_Mutation SNP C C3L-00144_T 118869 38962211 11856257 1638 5709 CACNA1I 0 . GRCh38 22 39658995 39658995 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.2209C>G p.Arg737Gly p.R737G ENST00000402142 12/37 385 321 64 298 298 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Arg737Gly,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Arg702Gly,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Arg737Gly,ENST00000401624,;CACNA1I,missense_variant,p.Arg702Gly,ENST00000407673,; G ENST00000402142 Transcript missense_variant 2209/10004 2209/6672 737/2223 R/G Cgc/Ggc 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0) 12/37 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 39658995 39658995 C G 1 0 0 0 0 1 0 0 0 2234 768 27 4 4 CACNA1I 22 39658995 Missense_Mutation SNP C C3L-00144_T 696784 39658995 11159473 1639 5710 CACNA1I 0 . GRCh38 22 39659846 39659846 + Missense_Mutation SNP G G T C3L-00144_T C3L-00144_N G G c.2598G>T p.Gln866His p.Q866H ENST00000402142 14/37 178 149 29 194 194 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Gln866His,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Gln831His,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Gln866His,ENST00000401624,;CACNA1I,missense_variant,p.Gln831His,ENST00000407673,; T ENST00000402142 Transcript missense_variant 2598/10004 2598/6672 866/2223 Q/H caG/caT COSM3554625,COSM3554626,COSM3554627,COSM3554628 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0.01) 14/37 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Superfamily_domains:SSF81324 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 39659846 39659846 G T 1 0 0 0 0 1 0 0 0 2234 991 35 2 2 CACNA1I 22 39659846 Missense_Mutation SNP G C3L-00144_T 851 39659846 11158622 1640 5711 CACNA1I 0 . GRCh38 22 39686156 39686156 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.6423G>T p.= p.P2141P ENST00000402142 37/37 74 62 12 61 61 0 strelka-varscan-mutect CACNA1I,synonymous_variant,p.=,ENST00000402142,NM_021096.3;CACNA1I,synonymous_variant,p.=,ENST00000404898,NM_001003406.1;CACNA1I,downstream_gene_variant,,ENST00000401624,;CACNA1I,downstream_gene_variant,,ENST00000407673,; T ENST00000402142 Transcript synonymous_variant 6423/10004 6423/6672 2141/2223 P ccG/ccT 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 37/37 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 196 11 2 0 0 0 0 -19.9349 0.999037 1 1 1 0 T 2 4 12 39686156 39686156 G T 1 0 0 0 0 0 0 0 1 2234 1074 38 1 1 CACNA1I 22 39686156 Silent SNP G C3L-00144_T 26310 39686156 11132312 1641 5712 ZC3H7B 0 . GRCh38 22 41356740 41356740 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.2613C>T p.= p.F871F ENST00000352645 22/23 300 265 35 239 239 0 strelka-varscan-mutect ZC3H7B,synonymous_variant,p.=,ENST00000352645,NM_017590.5; T ENST00000352645 Transcript synonymous_variant 2870/5909 2613/2934 871/977 F ttC/ttT 1 1 ZC3H7B HGNC HGNC:30869 protein_coding YES CCDS14013.1 ENSP00000345793 Q9UGR2 UPI000002B2AD NM_017590.5 22/23 hmmpanther:PTHR14928,hmmpanther:PTHR14928:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 41356740 41356740 C T 1 0 0 0 0 0 0 0 1 18148 825 29 3 3 ZC3H7B 22 41356740 Silent SNP C C3L-00144_T 1670584 41356740 9461728 1642 5713 PACSIN2 0 . GRCh38 22 42891049 42891049 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.351G>C p.Lys117Asn p.K117N ENST00000263246 4/11 497 389 108 406 406 0 strelka-varscan-mutect PACSIN2,missense_variant,p.Lys117Asn,ENST00000263246,NM_001184970.1;PACSIN2,missense_variant,p.Lys117Asn,ENST00000337959,;PACSIN2,missense_variant,p.Lys117Asn,ENST00000407585,NM_001184971.1;PACSIN2,missense_variant,p.Lys117Asn,ENST00000403744,NM_007229.3;PACSIN2,missense_variant,p.Lys117Asn,ENST00000402229,;PACSIN2,missense_variant,p.Lys117Asn,ENST00000634914,;PACSIN2,missense_variant,p.Lys117Asn,ENST00000453643,;PACSIN2,missense_variant,p.Lys117Asn,ENST00000422336,;PACSIN2,missense_variant,p.Lys117Asn,ENST00000418133,;PACSIN2,downstream_gene_variant,,ENST00000453079,;PACSIN2,downstream_gene_variant,,ENST00000445706,; G ENST00000263246 Transcript missense_variant 553/3249 351/1461 117/486 K/N aaG/aaC 1 -1 PACSIN2 HGNC HGNC:8571 protein_coding YES CCDS43023.1 ENSP00000263246 Q9UNF0 UPI00001311CA NM_001184970.1 deleterious(0) 4/11 PROSITE_profiles:PS51741,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF14,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 42891049 42891049 C G 1 0 0 0 0 1 0 0 0 11453 680 24 4 4 PACSIN2 22 42891049 Missense_Mutation SNP C C3L-00144_T 1534309 42891049 7927419 1643 5714 SCUBE1 0 . GRCh38 22 43227418 43227418 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1163G>T p.Cys388Phe p.C388F ENST00000360835 10/22 252 156 96 221 220 1 strelka-varscan-mutect SCUBE1,missense_variant,p.Cys388Phe,ENST00000360835,NM_173050.3;SCUBE1,intron_variant,,ENST00000615096,;SCUBE1,downstream_gene_variant,,ENST00000449304,;Z82214.2,upstream_gene_variant,,ENST00000419643,; A ENST00000360835 Transcript missense_variant 1290/9808 1163/2967 388/988 C/F tGt/tTt 1 -1 SCUBE1 HGNC HGNC:13441 protein_coding YES CCDS14048.1 ENSP00000354080 Q8IWY4 UPI000020790F NM_173050.3 deleterious(0.01) 10/22 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS00010,PROSITE_profiles:PS50026,hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF4,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 43227418 43227418 C A 1 0 0 0 0 1 0 0 0 14215 478 17 2 2 SCUBE1 22 43227418 Missense_Mutation SNP C C3L-00144_T 336369 43227418 7591050 1644 5715 SCUBE1 0 . GRCh38 22 43262826 43262826 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.504C>A p.Asn168Lys p.N168K ENST00000360835 5/22 191 128 63 131 129 2 strelka-varscan-mutect SCUBE1,missense_variant,p.Asn168Lys,ENST00000360835,NM_173050.3;SCUBE1,missense_variant,p.Asn168Lys,ENST00000290460,;SCUBE1,missense_variant,p.Asn168Lys,ENST00000615096,;SCUBE1,upstream_gene_variant,,ENST00000449304,; T ENST00000360835 Transcript missense_variant 631/9808 504/2967 168/988 N/K aaC/aaA 1 -1 SCUBE1 HGNC HGNC:13441 protein_coding YES CCDS14048.1 ENSP00000354080 Q8IWY4 UPI000020790F NM_173050.3 deleterious(0.01) 5/22 Gene3D:2.10.25.10,hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF4,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 43262826 43262826 G T 1 0 0 0 0 1 0 0 0 14215 1368 48 2 2 SCUBE1 22 43262826 Missense_Mutation SNP G C3L-00144_T 35408 43262826 7555642 1645 5716 TBC1D22A 0 . GRCh38 22 46912080 46912080 + Missense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.907G>A p.Glu303Lys p.E303K ENST00000337137 8/13 121 113 8 98 98 0 strelka-varscan-mutect TBC1D22A,missense_variant,p.Glu273Lys,ENST00000380995,NM_001284304.1;TBC1D22A,missense_variant,p.Glu303Lys,ENST00000337137,NM_014346.3;TBC1D22A,missense_variant,p.Glu256Lys,ENST00000406733,NM_001284305.1;TBC1D22A,missense_variant,p.Glu244Lys,ENST00000407381,;TBC1D22A,missense_variant,p.Glu225Lys,ENST00000355704,NM_001284303.1;U51561.1,downstream_gene_variant,,ENST00000625149,;TBC1D22A,missense_variant,p.Glu256Lys,ENST00000441162,;TBC1D22A,3_prime_UTR_variant,,ENST00000394449,; A ENST00000337137 Transcript missense_variant 1073/3787 907/1554 303/517 E/K Gaa/Aaa 1 1 TBC1D22A HGNC HGNC:1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 UPI0000128722 NM_014346.3 deleterious(0) 8/13 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF255,Gene3D:2qq8A02,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 201 2 5 2 0 0 0 -3.959041 0.7073004 1 1 1 0 A 3 1 12 46912080 46912080 G A 1 0 0 0 0 1 0 0 0 16011 1291 45 3 3 TBC1D22A 22 46912080 Missense_Mutation SNP G C3L-00144_T 3649254 46912080 3906388 1646 5717 PLXNB2 0 . GRCh38 22 50278993 50278993 + Nonsense_Mutation SNP G G A novel C3L-00144_T C3L-00144_N G G c.4408C>T p.Gln1470Ter p.Q1470* ENST00000449103 28/37 56 36 20 59 59 0 strelka-mutect PLXNB2,stop_gained,p.Gln1470Ter,ENST00000449103,;PLXNB2,stop_gained,p.Gln1470Ter,ENST00000359337,NM_012401.3;PLXNB2,stop_gained,p.Gln102Ter,ENST00000614805,;PLXNB2,5_prime_UTR_variant,,ENST00000610984,;PLXNB2,intron_variant,,ENST00000411680,;PLXNB2,downstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000496720,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,;PLXNB2,upstream_gene_variant,,ENST00000479818,;PLXNB2,downstream_gene_variant,,ENST00000492578,; A ENST00000449103 Transcript stop_gained 4549/6383 4408/5517 1470/1838 Q/* Cag/Tag 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D 28/37 hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625,Pfam_domain:PF08337,Gene3D:3.10.20.90 HIGH 1 SNV 5 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999927 1 1 1 0 A 4 1 12 50278993 50278993 G A 1 0 0 0 0 0 1 0 0 12230 1328 46 3 3 PLXNB2 22 50278993 Nonsense_Mutation SNP G C3L-00144_T 3366913 50278993 539475 1647 5718 PLXNB2 0 . GRCh38 22 50290346 50290346 + Missense_Mutation SNP G G A C3L-00144_T C3L-00144_N G G c.239C>T p.Pro80Leu p.P80L ENST00000449103 3/37 227 135 92 187 187 0 strelka-varscan-mutect PLXNB2,missense_variant,p.Pro80Leu,ENST00000449103,;PLXNB2,missense_variant,p.Pro80Leu,ENST00000359337,NM_012401.3;PLXNB2,missense_variant,p.Pro80Leu,ENST00000432455,;PLXNB2,missense_variant,p.Pro80Leu,ENST00000425954,;PLXNB2,upstream_gene_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000434732,;PLXNB2,upstream_gene_variant,,ENST00000496720,; A ENST00000449103 Transcript missense_variant 380/6383 239/5517 80/1838 P/L cCg/cTg COSM726727 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D deleterious(0) 3/37 PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912 1 MODERATE 1 SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 50290346 50290346 G A 1 0 0 0 0 1 0 0 0 12230 1116 39 1 1 PLXNB2 22 50290346 Missense_Mutation SNP G C3L-00144_T 11353 50290346 528122 1648 5719 ARSH 0 . GRCh38 X 3033334 3033334 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1638C>A p.Phe546Leu p.F546L ENST00000381130 9/9 71 44 27 42 42 0 strelka-varscan-mutect ARSH,missense_variant,p.Phe546Leu,ENST00000381130,NM_001011719.1; A ENST00000381130 Transcript missense_variant 1638/1875 1638/1689 546/562 F/L ttC/ttA 1 1 ARSH HGNC HGNC:32488 protein_coding YES CCDS35198.1 ENSP00000370522 Q5FYA8 UPI00001D7C2E NM_001011719.1 tolerated(0.08) 9/9 Pfam_domain:PF14707,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF240,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3033334 3033334 C A 1 0 0 0 0 1 0 0 0 1136 854 30 2 2 ARSH 23 3033334 Missense_Mutation SNP C C3L-00144_T 3033334 153007561 1649 5720 MXRA5 0 . GRCh38 X 3311560 3311560 + Missense_Mutation SNP C C G novel C3L-00144_T C3L-00144_N C C c.6643G>C p.Asp2215His p.D2215H ENST00000217939 7/7 88 56 32 69 69 0 strelka-varscan-mutect MXRA5,missense_variant,p.Asp2215His,ENST00000217939,NM_015419.3; G ENST00000217939 Transcript missense_variant 6798/9793 6643/8487 2215/2828 D/H Gat/Cat 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 12 3311560 3311560 C G 1 0 0 0 0 1 0 0 0 10002 913 32 4 4 MXRA5 23 3311560 Missense_Mutation SNP C C3L-00144_T 278226 3311560 152729335 1650 5721 MXRA5 0 . GRCh38 X 3320774 3320774 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.4911G>T p.Gln1637His p.Q1637H ENST00000217939 5/7 182 116 66 158 158 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gln1637His,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 5066/9793 4911/8487 1637/2828 Q/H caG/caT 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0.05) 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3320774 3320774 C A 1 0 0 0 0 1 0 0 0 10002 564 20 2 2 MXRA5 23 3320774 Missense_Mutation SNP C C3L-00144_T 9214 3320774 152720121 1651 5722 MXRA5 0 . GRCh38 X 3322062 3322062 + Missense_Mutation SNP T T C novel C3L-00144_T C3L-00144_N T T c.3623A>G p.Asn1208Ser p.N1208S ENST00000217939 5/7 104 63 41 83 83 0 strelka-varscan-mutect MXRA5,missense_variant,p.Asn1208Ser,ENST00000217939,NM_015419.3; C ENST00000217939 Transcript missense_variant 3778/9793 3623/8487 1208/2828 N/S aAc/aGc 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.92) 5/7 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF680 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 3322062 3322062 T C 1 0 0 0 0 1 0 0 0 10002 1725 60 5 5 MXRA5 23 3322062 Missense_Mutation SNP T C3L-00144_T 1288 3322062 152718833 1652 5723 MXRA5 0 . GRCh38 X 3322871 3322871 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.2814G>T p.Glu938Asp p.E938D ENST00000217939 5/7 98 63 35 76 76 0 strelka-varscan-mutect MXRA5,missense_variant,p.Glu938Asp,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 2969/9793 2814/8487 938/2828 E/D gaG/gaT 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.32) 5/7 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 3322871 3322871 C A 1 0 0 0 0 1 0 0 0 10002 912 32 2 2 MXRA5 23 3322871 Missense_Mutation SNP C C3L-00144_T 809 3322871 152718024 1653 5724 VCX 0 . GRCh38 X 7843227 7843227 + Silent SNP G G C rs751198308 C3L-00144_T C3L-00144_N G G c.24G>C p.= p.S8S ENST00000381059 2/3 471 394 77 416 416 0 strelka-varscan-mutect VCX,synonymous_variant,p.=,ENST00000381059,NM_013452.2;VCX,synonymous_variant,p.=,ENST00000620630,;VCX,synonymous_variant,p.=,ENST00000341408,; C ENST00000381059 Transcript synonymous_variant 243/967 24/621 8/206 S tcG/tcC rs751198308 1 1 VCX HGNC HGNC:12667 protein_coding YES CCDS14128.1 ENSP00000370447 Q9H320 UPI0000138291 NM_013452.2 2/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0 LOW 1 SNV 1 1 PASS rs751198308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 12 7843227 7843227 G C 1 0 0 0 0 0 0 0 1 17688 1103 39 4 4 VCX 23 7843227 Silent SNP G C3L-00144_T 4520356 7843227 148197668 1654 5725 22 2 VCX 0 . GRCh38 X 7843229 7843229 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.26G>T p.Gly9Val p.G9V ENST00000381059 2/3 488 443 45 427 427 0 varscan-mutect VCX,missense_variant,p.Gly9Val,ENST00000381059,NM_013452.2;VCX,missense_variant,p.Gly9Val,ENST00000620630,;VCX,missense_variant,p.Gly9Val,ENST00000341408,; T ENST00000381059 Transcript missense_variant 245/967 26/621 9/206 G/V gGa/gTa 1 1 VCX HGNC HGNC:12667 protein_coding YES CCDS14128.1 ENSP00000370447 Q9H320 UPI0000138291 NM_013452.2 deleterious_low_confidence(0) 2/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 7843229 7843229 G T 1 0 0 0 0 1 0 0 0 17688 1174 41 2 2 VCX 23 7843229 Missense_Mutation SNP G C3L-00144_T 2 7843229 148197666 1655 5726 22 2 VCX3B 0 . GRCh38 X 8465476 8465476 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.26G>T p.Gly9Val p.G9V ENST00000381032 2/3 512 433 79 411 410 1 strelka-varscan-mutect VCX3B,missense_variant,p.Gly9Val,ENST00000381032,NM_001001888.3;VCX3B,missense_variant,p.Gly9Val,ENST00000453306,;VCX3B,missense_variant,p.Gly9Val,ENST00000444481,;VCX3B,missense_variant,p.Gly9Val,ENST00000381029,; T ENST00000381032 Transcript missense_variant 333/1171 26/741 9/246 G/V gGa/gTa 1 1 VCX3B HGNC HGNC:31838 protein_coding YES CCDS48077.2 ENSP00000370420 Q9H321 UPI000057A469 NM_001001888.3 deleterious_low_confidence(0) 2/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0 MODERATE 1 SNV 5 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 8465476 8465476 G T 1 0 0 0 0 1 0 0 0 17690 1174 41 2 2 VCX3B 23 8465476 Missense_Mutation SNP G C3L-00144_T 622247 8465476 147575419 1656 5727 VCX3B 0 . GRCh38 X 8465791 8465791 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.149G>T p.Arg50Leu p.R50L ENST00000381032 3/3 103 92 11 121 121 0 varscan-mutect VCX3B,missense_variant,p.Arg50Leu,ENST00000381032,NM_001001888.3;VCX3B,missense_variant,p.Arg50Leu,ENST00000453306,;VCX3B,missense_variant,p.Arg50Leu,ENST00000444481,;VCX3B,missense_variant,p.Arg50Leu,ENST00000381029,; T ENST00000381032 Transcript missense_variant 456/1171 149/741 50/246 R/L cGc/cTc 1 1 VCX3B HGNC HGNC:31838 protein_coding YES CCDS48077.2 ENSP00000370420 Q9H321 UPI000057A469 NM_001001888.3 tolerated_low_confidence(0.16) 3/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1283270507 . 1 206 3 0 0 0 0 0 -19.99902 1 1 1 1 0 T 3 4 12 8465791 8465791 G T 1 0 0 0 0 1 0 0 0 17690 1087 38 1 1 VCX3B 23 8465791 Missense_Mutation SNP G C3L-00144_T 315 8465791 147575104 1657 5728 FANCB 0 . GRCh38 X 14850617 14850617 + Nonsense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1384G>T p.Glu462Ter p.E462* ENST00000398334 7/10 67 54 13 88 88 0 strelka-varscan-mutect FANCB,stop_gained,p.Glu462Ter,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,stop_gained,p.Glu462Ter,ENST00000324138,NM_152633.2;FANCB,stop_gained,p.Glu462Ter,ENST00000452869,; A ENST00000398334 Transcript stop_gained 1652/3008 1384/2580 462/859 E/* Gaa/Taa 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 7/10 hmmpanther:PTHR28450 HIGH 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 14850617 14850617 C A 1 0 0 0 0 0 1 0 0 5522 835 29 2 2 FANCB 23 14850617 Nonsense_Mutation SNP C C3L-00144_T 6384826 14850617 141190278 1658 5729 PIR 0 . GRCh38 X 15459687 15459687 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.243C>G p.His81Gln p.H81Q ENST00000380421 4/10 123 81 42 109 109 0 strelka-varscan-mutect PIR,missense_variant,p.His81Gln,ENST00000380421,NM_003662.3,NM_001018109.2;PIR,missense_variant,p.His81Gln,ENST00000380420,;BMX,upstream_gene_variant,,ENST00000357607,;PIR,non_coding_transcript_exon_variant,,ENST00000476381,; C ENST00000380421 Transcript missense_variant 704/1539 243/873 81/290 H/Q caC/caG 1 -1 PIR HGNC HGNC:30048 protein_coding YES CCDS14167.1 ENSP00000369786 O00625 A0A024RBX6 UPI0000049C30 NM_003662.3,NM_001018109.2 deleterious(0.01) 4/10 Gene3D:2.60.120.10,Pfam_domain:PF02678,PIRSF_domain:PIRSF006232,hmmpanther:PTHR13903,hmmpanther:PTHR13903:SF8,Superfamily_domains:SSF51182 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 15459687 15459687 G C 1 0 0 0 0 1 0 0 0 12039 1368 48 4 4 PIR 23 15459687 Missense_Mutation SNP G C3L-00144_T 609070 15459687 140581208 1659 5730 CDKL5 0 . GRCh38 X 18604206 18604206 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1282G>T p.Gly428Cys p.G428C ENST00000379989 13/22 339 207 132 332 332 0 strelka-varscan-mutect CDKL5,missense_variant,p.Gly428Cys,ENST00000623535,;CDKL5,missense_variant,p.Gly428Cys,ENST00000635828,;CDKL5,missense_variant,p.Gly428Cys,ENST00000379989,NM_001037343.1;CDKL5,missense_variant,p.Gly428Cys,ENST00000379996,NM_003159.2;CDKL5,missense_variant,p.Gly428Cys,ENST00000463994,;CDKL5,missense_variant,p.Gly428Cys,ENST00000637881,; T ENST00000379989 Transcript missense_variant 1567/3463 1282/3093 428/1030 G/C Ggc/Tgc 1 1 CDKL5 HGNC HGNC:11411 protein_coding YES CCDS14186.1 ENSP00000369325 O76039 UPI0000136103 NM_001037343.1 deleterious_low_confidence(0) 13/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 18604206 18604206 G T 1 0 0 0 0 1 0 0 0 2861 1000 35 2 2 CDKL5 23 18604206 Missense_Mutation SNP G C3L-00144_T 3144519 18604206 137436689 1660 5731 PHEX 0 . GRCh38 X 22077685 22077685 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.646A>T p.Asn216Tyr p.N216Y ENST00000379374 5/22 190 129 61 157 157 0 strelka-varscan-mutect PHEX,missense_variant,p.Asn216Tyr,ENST00000379374,NM_001282754.1,NM_000444.5; T ENST00000379374 Transcript missense_variant 1211/6172 646/2250 216/749 N/Y Aat/Tat 1 1 PHEX HGNC HGNC:8918 protein_coding YES CCDS14204.1 ENSP00000368682 P78562 UPI0000033C42 NM_001282754.1,NM_000444.5 deleterious(0.01) 5/22 Pfam_domain:PF05649,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF149,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 22077685 22077685 A T 1 0 0 0 0 1 0 0 0 11908 130 5 4 4 PHEX 23 22077685 Missense_Mutation SNP A C3L-00144_T 3473479 22077685 133963210 1661 5732 MAGEB18 0 . GRCh38 X 26139403 26139403 + Frame_Shift_Del DEL A A - rs751715961 C3L-00144_T C3L-00144_N A A c.419delA p.Lys140ArgfsTer25 p.K140Rfs*25 ENST00000325250 2/3 144 125 19 140 140 0 sindel-varindel-pindel MAGEB18,frameshift_variant,p.Lys140ArgfsTer25,ENST00000325250,NM_173699.3; - ENST00000325250 Transcript frameshift_variant 605/1811 418/1032 140/343 K/X Aag/ag rs751715961 1 1 MAGEB18 HGNC HGNC:28515 protein_coding YES CCDS14216.1 ENSP00000314543 Q96M61 UPI00001415E3 NM_173699.3 2/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF23,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 26139403 26139403 A - 1 0 1 0 1 0 0 0 0 9091 247 9 0 0 MAGEB18 23 26139403 Frame_Shift_Del DEL A C3L-00144_T 4061718 26139403 129901492 1662 5733 MAGEB6 0 . GRCh38 X 26194662 26194662 + Missense_Mutation SNP T T A C3L-00144_T C3L-00144_N T T c.816T>A p.Ser272Arg p.S272R ENST00000379034 2/2 85 58 27 94 94 0 strelka-varscan-mutect MAGEB6,missense_variant,p.Ser272Arg,ENST00000379034,NM_173523.2; A ENST00000379034 Transcript missense_variant 965/1949 816/1224 272/407 S/R agT/agA COSM4876874 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 tolerated(0.31) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 12 26194662 26194662 T A 1 0 0 0 0 1 0 0 0 9096 1693 59 4 4 MAGEB6 23 26194662 Missense_Mutation SNP T C3L-00144_T 55259 26194662 129846233 1663 5734 PPP4R3CP 0 . GRCh38 X 27462802 27462802 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.495C>T p.= p.I165I ENST00000412172 1/1 175 130 45 140 140 0 strelka-varscan-mutect PPP4R3CP,synonymous_variant,p.=,ENST00000412172,; A ENST00000412172 Transcript synonymous_variant 540/3131 495/2499 165/832 I atC/atT 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 27462802 27462802 G A 1 0 0 0 0 0 0 0 1 12529 932 33 3 3 PPP4R3CP 23 27462802 Silent SNP G C3L-00144_T 1268140 27462802 128578093 1664 5735 PPP4R3CP 0 . GRCh38 X 27463066 27463066 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.231C>A p.Asn77Lys p.N77K ENST00000412172 1/1 121 71 50 79 79 0 strelka-varscan-mutect PPP4R3CP,missense_variant,p.Asn77Lys,ENST00000412172,; T ENST00000412172 Transcript missense_variant 276/3131 231/2499 77/832 N/K aaC/aaA 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 27463066 27463066 G T 1 0 0 0 0 1 0 0 0 12529 1252 44 2 2 PPP4R3CP 23 27463066 Missense_Mutation SNP G C3L-00144_T 264 27463066 128577829 1665 5736 MAGEB3 0 . GRCh38 X 30236938 30236938 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.1014C>A p.= p.A338A ENST00000361644 5/5 36 23 13 38 38 0 strelka-varscan-mutect MAGEB3,synonymous_variant,p.=,ENST00000361644,NM_002365.4;MAGEB3,synonymous_variant,p.=,ENST00000620842,; A ENST00000361644 Transcript synonymous_variant 1751/2305 1014/1041 338/346 A gcC/gcA 1 1 MAGEB3 HGNC HGNC:6810 protein_coding YES CCDS14220.1 ENSP00000355198 O15480 UPI000013E79F NM_002365.4 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11736:SF53,hmmpanther:PTHR11736 LOW 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 30236938 30236938 C A 1 0 0 0 0 0 0 0 1 9093 581 21 2 2 MAGEB3 23 30236938 Silent SNP C C3L-00144_T 2773872 30236938 125803957 1666 5737 DMD 0 . GRCh38 X 31182783 31182783 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.9929A>T p.Gln3310Leu p.Q3310L ENST00000357033 68/79 152 95 57 124 124 0 strelka-varscan-mutect DMD,missense_variant,p.Gln3310Leu,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Gln3306Leu,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Gln3309Leu,ENST00000620040,;DMD,missense_variant,p.Gln3305Leu,ENST00000619831,;DMD,missense_variant,p.Gln850Leu,ENST00000378707,NM_004013.2;DMD,missense_variant,p.Gln850Leu,ENST00000359836,NM_004022.2;DMD,missense_variant,p.Gln850Leu,ENST00000541735,NM_004020.3,NM_004023.2;DMD,missense_variant,p.Gln1006Leu,ENST00000358062,;DMD,missense_variant,p.Gln581Leu,ENST00000343523,NM_004014.2;DMD,missense_variant,p.Gln850Leu,ENST00000474231,NM_004021.2;DMD,missense_variant,p.Gln242Leu,ENST00000378723,NM_004016.2;DMD,missense_variant,p.Gln242Leu,ENST00000378702,NM_004015.2,NM_004017.2;DMD,missense_variant,p.Gln242Leu,ENST00000361471,NM_004018.2;DMD,missense_variant,p.Gln242Leu,ENST00000378680,;DMD,missense_variant,p.Gln100Leu,ENST00000378705,;DMD,non_coding_transcript_exon_variant,,ENST00000475732,; A ENST00000357033 Transcript missense_variant 10136/13956 9929/11058 3310/3685 Q/L cAg/cTg 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0) 68/79 PROSITE_profiles:PS50135,hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Pfam_domain:PF00569,SMART_domains:SM00291,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs886044071 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 31182783 31182783 T A 1 0 0 0 0 1 0 0 0 4387 1580 55 4 4 DMD 23 31182783 Missense_Mutation SNP T C3L-00144_T 945845 31182783 124858112 1667 5738 FAM47A 0 . GRCh38 X 34131218 34131218 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1061C>A p.Pro354His p.P354H ENST00000346193 1/1 71 47 24 56 56 0 strelka-varscan-mutect FAM47A,missense_variant,p.Pro354His,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.Pro354His,ENST00000613251,; T ENST00000346193 Transcript missense_variant 1094/2556 1061/2376 354/791 P/H cCt/cAt 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 deleterious(0) 1/1 Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 34131218 34131218 G T 1 0 0 0 0 1 0 0 0 5447 1000 35 2 2 FAM47A 23 34131218 Missense_Mutation SNP G C3L-00144_T 2948435 34131218 121909677 1668 5739 CFAP47 0 . GRCh38 X 36144605 36144605 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.1305T>A p.Ser435Arg p.S435R ENST00000313548 10/10 92 62 30 88 88 0 strelka-varscan-mutect CFAP47,missense_variant,p.Ser435Arg,ENST00000313548,;CFAP47,intron_variant,,ENST00000378653,NM_001304548.1;CFAP47,non_coding_transcript_exon_variant,,ENST00000378660,; A ENST00000313548 Transcript missense_variant 1345/1549 1305/1509 435/502 S/R agT/agA 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000324767 UPI000006F5CD deleterious_low_confidence(0) 10/10 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999987 1 1 1 0 A 3 1 12 36144605 36144605 T A 1 0 0 0 0 1 0 0 0 3022 1693 59 4 4 CFAP47 23 36144605 Missense_Mutation SNP T C3L-00144_T 2013387 36144605 119896290 1669 5740 OTC 0 . GRCh38 X 38411914 38411914 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.920A>T p.Lys307Met p.K307M ENST00000039007 9/10 348 195 153 286 286 0 strelka-varscan-mutect OTC,missense_variant,p.Lys307Met,ENST00000039007,NM_000531.5;RP5-972B16.2,intron_variant,,ENST00000465127,; T ENST00000039007 Transcript missense_variant 1072/1585 920/1065 307/354 K/M aAg/aTg 1 1 OTC HGNC HGNC:8512 protein_coding YES CCDS14247.1 ENSP00000039007 P00480 UPI000013C550 NM_000531.5 deleterious(0.01) 9/10 Gene3D:3.40.50.1370,Pfam_domain:PF00185,Prints_domain:PR00100,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF1,Superfamily_domains:SSF53671,TIGRFAM_domain:TIGR00658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 38411914 38411914 A T 1 0 0 0 0 1 0 0 0 11367 72 3 4 4 OTC 23 38411914 Missense_Mutation SNP A C3L-00144_T 2267309 38411914 117628981 1670 5741 CXorf38 0 . GRCh38 X 40647512 40647512 + Silent SNP C C T novel C3L-00144_T C3L-00144_N C C c.9G>A p.= p.L3L ENST00000327877 1/7 91 62 29 75 75 0 strelka-varscan-mutect CXorf38,synonymous_variant,p.=,ENST00000327877,NM_144970.2;CXorf38,5_prime_UTR_variant,,ENST00000378426,;CXorf38,5_prime_UTR_variant,,ENST00000378421,;MED14,downstream_gene_variant,,ENST00000324817,NM_004229.3;MED14,downstream_gene_variant,,ENST00000416199,; T ENST00000327877 Transcript synonymous_variant 36/2118 9/960 3/319 L ctG/ctA 1 -1 CXorf38 HGNC HGNC:28589 protein_coding YES CCDS14253.1 ENSP00000330488 Q8TB03 UPI000007293E NM_144970.2 1/7 PD661243,hmmpanther:PTHR35083 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 40647512 40647512 C T 1 0 0 0 0 0 0 0 1 3913 465 17 3 3 CXorf38 23 40647512 Silent SNP C C3L-00144_T 2235598 40647512 115393383 1671 5742 WNK3 0 . GRCh38 X 54237470 54237470 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.4096C>G p.His1366Asp p.H1366D ENST00000354646 20/24 52 26 26 55 55 0 strelka-varscan-mutect WNK3,missense_variant,p.His1366Asp,ENST00000354646,NM_020922.4;WNK3,missense_variant,p.His1319Asp,ENST00000375169,NM_001002838.3;WNK3,missense_variant,p.His1366Asp,ENST00000375159,;WNK3,missense_variant,p.His1366Asp,ENST00000620763,; C ENST00000354646 Transcript missense_variant 4535/11341 4096/5403 1366/1800 H/D Cat/Gat 1 -1 WNK3 HGNC HGNC:14543 protein_coding YES CCDS14357.1 ENSP00000346667 Q9BYP7 UPI00001AF003 NM_020922.4 tolerated(0.25) 20/24 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF47 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 54237470 54237470 G C 1 0 0 0 0 1 0 0 0 17935 1348 47 4 4 WNK3 23 54237470 Missense_Mutation SNP G C3L-00144_T 13589958 54237470 101803425 1672 5743 PAGE3 0 . GRCh38 X 55258520 55258520 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.328C>G p.Gln110Glu p.Q110E ENST00000374951 5/5 139 90 49 134 134 0 strelka-varscan-mutect PAGE3,missense_variant,p.Gln110Glu,ENST00000374951,NM_001171252.1,NM_001017931.2,NM_001303613.1;PAGE3,missense_variant,p.Gln110Glu,ENST00000519203,; C ENST00000374951 Transcript missense_variant 637/745 328/342 110/113 Q/E Caa/Gaa 1 -1 PAGE3 HGNC HGNC:4110 protein_coding YES ENSP00000364089 Q5JUK9 UPI0000161132 NM_001171252.1,NM_001017931.2,NM_001303613.1 tolerated(0.21) 5/5 hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF1,SMART_domains:SM01379 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 55258520 55258520 G C 1 0 0 0 0 1 0 0 0 11470 1328 46 4 4 PAGE3 23 55258520 Missense_Mutation SNP G C3L-00144_T 1021050 55258520 100782375 1673 5744 EDA2R 0 . GRCh38 X 66599533 66599533 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.908C>G p.Thr303Ser p.T303S ENST00000396050 6/7 23 15 8 16 16 0 strelka-varscan-mutect EDA2R,missense_variant,p.Thr282Ser,ENST00000451436,NM_001199687.2;EDA2R,missense_variant,p.Thr303Ser,ENST00000396050,NM_001242310.1;EDA2R,missense_variant,p.Thr282Ser,ENST00000374719,NM_001324206.1,NM_021783.3;EDA2R,missense_variant,p.Thr303Ser,ENST00000253392,; C ENST00000396050 Transcript missense_variant 918/3429 908/957 303/318 T/S aCt/aGt 1 -1 EDA2R HGNC HGNC:17756 protein_coding YES CCDS56603.1 ENSP00000379365 Q9HAV5 UPI00001B037F NM_001242310.1 tolerated(1) 6/7 hmmpanther:PTHR12120:SF8,hmmpanther:PTHR12120 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.9992 1 1 1 1 0 C 3 2 12 66599533 66599533 G C 1 0 0 0 0 1 0 0 0 4732 1029 36 4 4 EDA2R 23 66599533 Missense_Mutation SNP G C3L-00144_T 11341013 66599533 89441362 1674 5745 YIPF6 0 . GRCh38 X 68513390 68513390 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.250A>T p.Thr84Ser p.T84S ENST00000462683 3/7 38 22 16 35 35 0 strelka-varscan-mutect YIPF6,missense_variant,p.Thr84Ser,ENST00000462683,NM_173834.3;YIPF6,missense_variant,p.Thr41Ser,ENST00000374622,NM_001195214.1;YIPF6,missense_variant,p.Thr41Ser,ENST00000451537,;YIPF6,non_coding_transcript_exon_variant,,ENST00000470730,;YIPF6,non_coding_transcript_exon_variant,,ENST00000374643,;YIPF6,non_coding_transcript_exon_variant,,ENST00000496576,;YIPF6,non_coding_transcript_exon_variant,,ENST00000462972,; T ENST00000462683 Transcript missense_variant 994/6741 250/711 84/236 T/S Act/Tct 1 1 YIPF6 HGNC HGNC:28304 protein_coding YES CCDS14389.1 ENSP00000417573 Q96EC8 UPI000003778F NM_173834.3 tolerated(0.77) 3/7 hmmpanther:PTHR21236:SF1,hmmpanther:PTHR21236,Pfam_domain:PF04893 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 68513390 68513390 A T 1 0 0 0 0 1 0 0 0 18044 391 14 4 4 YIPF6 23 68513390 Missense_Mutation SNP A C3L-00144_T 1913857 68513390 87527505 1675 5746 FAM155B 0 . GRCh38 X 69529008 69529008 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.877T>A p.Trp293Arg p.W293R ENST00000252338 2/3 47 27 20 38 38 0 strelka-varscan-mutect FAM155B,missense_variant,p.Trp293Arg,ENST00000252338,NM_015686.2; A ENST00000252338 Transcript missense_variant 919/4013 877/1419 293/472 W/R Tgg/Agg 1 1 FAM155B HGNC HGNC:30701 protein_coding YES CCDS35317.1 ENSP00000252338 O75949 UPI0000070EAA NM_015686.2 deleterious(0) 2/3 hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 69529008 69529008 T A 1 0 0 0 0 1 0 0 0 5314 1580 55 4 4 FAM155B 23 69529008 Missense_Mutation SNP T C3L-00144_T 1015618 69529008 86511887 1676 5747 UPRT 0 . GRCh38 X 75299865 75299865 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.693G>T p.= p.R231R ENST00000373383 5/7 79 47 32 77 77 0 strelka-varscan-mutect UPRT,synonymous_variant,p.=,ENST00000373379,NM_001307944.1;UPRT,synonymous_variant,p.=,ENST00000373383,NM_145052.3;UPRT,synonymous_variant,p.=,ENST00000530743,;UPRT,non_coding_transcript_exon_variant,,ENST00000474175,;UPRT,non_coding_transcript_exon_variant,,ENST00000526850,;UPRT,downstream_gene_variant,,ENST00000531704,;UPRT,3_prime_UTR_variant,,ENST00000462237,; T ENST00000373383 Transcript synonymous_variant 860/2186 693/930 231/309 R cgG/cgT 1 1 UPRT HGNC HGNC:28334 protein_coding YES CCDS14429.1 ENSP00000362481 Q96BW1 A8KAF9 UPI000004B62E NM_145052.3 5/7 Gene3D:3.40.50.2020,Pfam_domain:PF14681,hmmpanther:PTHR10285,Superfamily_domains:SSF53271 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 75299865 75299865 G T 1 0 0 0 0 0 0 0 1 17540 1161 41 2 2 UPRT 23 75299865 Silent SNP G C3L-00144_T 5770857 75299865 80741030 1677 5748 FAM46D 0 . GRCh38 X 80443698 80443698 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.1159G>T p.Gly387Cys p.G387C ENST00000538312 5/5 26 15 11 38 38 0 strelka-varscan-mutect FAM46D,missense_variant,p.Gly387Cys,ENST00000538312,NM_001170574.1;FAM46D,missense_variant,p.Gly387Cys,ENST00000308293,NM_152630.4; T ENST00000538312 Transcript missense_variant 1493/3106 1159/1170 387/389 G/C Ggt/Tgt 1 1 FAM46D HGNC HGNC:28399 protein_coding YES CCDS14446.1 ENSP00000443410 Q8NEK8 UPI0000073CF3 NM_001170574.1 deleterious_low_confidence(0) 5/5 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 80443698 80443698 G T 1 0 0 0 0 1 0 0 0 5446 1348 47 2 2 FAM46D 23 80443698 Missense_Mutation SNP G C3L-00144_T 5143833 80443698 75597197 1678 5749 CYLC1 0 . GRCh38 X 83872908 83872908 + Missense_Mutation SNP A A T rs775989724 C3L-00144_T C3L-00144_N A A c.200A>T p.Glu67Val p.E67V ENST00000329312 4/5 25 15 10 34 34 0 strelka-varscan-mutect CYLC1,missense_variant,p.Glu67Val,ENST00000329312,NM_021118.2;CYLC1,intron_variant,,ENST00000621735,NM_001271680.1; T ENST00000329312 Transcript missense_variant 237/2106 200/1956 67/651 E/V gAa/gTa rs775989724 1 1 CYLC1 HGNC HGNC:2582 protein_coding YES CCDS35341.1 ENSP00000331556 P35663 UPI0000251E1D NM_021118.2 deleterious(0) 4/5 hmmpanther:PTHR16742,hmmpanther:PTHR16742:SF1,Pfam_domain:PF15241 MODERATE 1 SNV 1 1 PASS rs775989724 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 83872908 83872908 A T 1 0 0 0 0 1 0 0 0 3944 246 9 4 4 CYLC1 23 83872908 Missense_Mutation SNP A C3L-00144_T 3429210 83872908 72167987 1679 5750 PCDH11X 0 . GRCh38 X 92618870 92618870 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.3974C>A p.Thr1325Asn p.T1325N ENST00000373094 7/7 279 180 99 272 272 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Thr1325Asn,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Thr1315Asn,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Thr1317Asn,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Thr1307Asn,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Thr1288Asn,ENST00000373088,NM_001168362.1;PCDH11X,3_prime_UTR_variant,,ENST00000504220,NM_001168361.1; A ENST00000373094 Transcript missense_variant 4819/9179 3974/4044 1325/1347 T/N aCc/aAc 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious_low_confidence(0) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 92618870 92618870 C A 1 0 0 0 0 1 0 0 0 11595 507 18 2 2 PCDH11X 23 92618870 Missense_Mutation SNP C C3L-00144_T 8745962 92618870 63422025 1680 5751 FAM133A 0 . GRCh38 X 93709729 93709729 + Missense_Mutation SNP T T A novel C3L-00144_T C3L-00144_N T T c.310T>A p.Ser104Thr p.S104T ENST00000322139 3/3 115 68 47 126 125 1 strelka-varscan-mutect FAM133A,missense_variant,p.Ser104Thr,ENST00000322139,NM_001171111.1;FAM133A,missense_variant,p.Ser104Thr,ENST00000332647,NM_173698.2,NM_001171110.1,NM_001171109.1; A ENST00000322139 Transcript missense_variant 747/3292 310/747 104/248 S/T Tct/Act 1 1 FAM133A HGNC HGNC:26748 protein_coding YES CCDS14466.1 ENSP00000318974 Q8N9E0 UPI000006FB0A NM_001171111.1 tolerated_low_confidence(0.1) 3/3 hmmpanther:PTHR31911,hmmpanther:PTHR31911:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 93709729 93709729 T A 1 0 0 0 0 1 0 0 0 5293 1667 58 4 4 FAM133A 23 93709729 Missense_Mutation SNP T C3L-00144_T 1090859 93709729 62331166 1681 5752 ARMCX5 0 . GRCh38 X 102603096 102603096 + Missense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.955C>T p.Leu319Phe p.L319F ENST00000604957 1/1 88 63 25 86 86 0 strelka-varscan-mutect ARMCX5,missense_variant,p.Leu319Phe,ENST00000604957,NM_001168482.1,NM_001168478.1,NM_022838.3;ARMCX5,missense_variant,p.Leu319Phe,ENST00000246174,NM_001168479.1,NM_001168480.1,NM_001168485.1;ARMCX5,missense_variant,p.Leu319Phe,ENST00000372742,;ARMCX5,downstream_gene_variant,,ENST00000477663,;ARMCX5,downstream_gene_variant,,ENST00000479502,;ARMCX5,downstream_gene_variant,,ENST00000473968,;RP4-769N13.7,intron_variant,,ENST00000602441,;ARMCX5-GPRASP2,intron_variant,,ENST00000476910,;ARMCX5-GPRASP2,intron_variant,,ENST00000466616,;ARMCX5-GPRASP2,intron_variant,,ENST00000460793,;ARMCX5-GPRASP2,intron_variant,,ENST00000486740,;ARMCX5-GPRASP2,intron_variant,,ENST00000475738,;ARMCX5-GPRASP2,intron_variant,,ENST00000460026,;ARMCX5-GPRASP2,intron_variant,,ENST00000465548,;ARMCX5-GPRASP2,intron_variant,,ENST00000602366,;ARMCX5-GPRASP2,intron_variant,,ENST00000602463,; T ENST00000604957 Transcript missense_variant 3577/4640 955/1677 319/558 L/F Ctt/Ttt 1 1 ARMCX5 HGNC HGNC:25772 protein_coding YES CCDS14500.1 ENSP00000474720 Q6P1M9 UPI000013CBDB NM_001168482.1,NM_001168478.1,NM_022838.3 deleterious(0.01) 1/1 hmmpanther:PTHR15712,hmmpanther:PTHR15712:SF12,Pfam_domain:PF04826,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 102603096 102603096 C T 1 0 0 0 0 1 0 0 0 1103 681 24 3 3 ARMCX5 23 102603096 Missense_Mutation SNP C C3L-00144_T 8893367 102603096 53437799 1682 5753 NXF3 0 . GRCh38 X 103077683 103077683 + Silent SNP G G T novel C3L-00144_T C3L-00144_N G G c.1515C>A p.= p.A505A ENST00000395065 18/20 134 97 37 105 105 0 strelka-varscan-mutect NXF3,synonymous_variant,p.=,ENST00000395065,NM_022052.1;NXF3,downstream_gene_variant,,ENST00000427570,;NXF3,non_coding_transcript_exon_variant,,ENST00000497850,;NXF3,non_coding_transcript_exon_variant,,ENST00000470724,;NXF3,non_coding_transcript_exon_variant,,ENST00000468528,;NXF3,downstream_gene_variant,,ENST00000460791,;NXF3,downstream_gene_variant,,ENST00000494300,; T ENST00000395065 Transcript synonymous_variant 1617/1938 1515/1596 505/531 A gcC/gcA 1 -1 NXF3 HGNC HGNC:8073 protein_coding YES CCDS14503.1 ENSP00000378504 Q9H4D5 UPI00000015F8 NM_022052.1 18/20 hmmpanther:PTHR10662,hmmpanther:PTHR10662:SF12,Gene3D:3.10.450.50,Superfamily_domains:SSF54427 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 103077683 103077683 G T 1 0 0 0 0 0 0 0 1 10857 987 35 2 2 NXF3 23 103077683 Silent SNP G C3L-00144_T 474587 103077683 52963212 1683 5754 PLP1 0 . GRCh38 X 103786584 103786584 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.311A>T p.Tyr104Phe p.Y104F ENST00000612423 4/8 218 149 69 183 183 0 strelka-varscan-mutect PLP1,missense_variant,p.Tyr104Phe,ENST00000612423,NM_001128834.2;PLP1,missense_variant,p.Tyr104Phe,ENST00000621218,NM_000533.4,NM_001305004.1;PLP1,missense_variant,p.Tyr104Phe,ENST00000619236,NM_199478.2;PLP1,missense_variant,p.Tyr104Phe,ENST00000434483,;PLP1,missense_variant,p.Tyr104Phe,ENST00000494475,;PLP1,missense_variant,p.Tyr104Phe,ENST00000443502,;PLP1,missense_variant,p.Tyr104Phe,ENST00000422393,;PLP1,missense_variant,p.Tyr104Phe,ENST00000455268,;PLP1,downstream_gene_variant,,ENST00000433491,;PLP1,non_coding_transcript_exon_variant,,ENST00000479569,;PLP1,non_coding_transcript_exon_variant,,ENST00000478642,;PLP1,non_coding_transcript_exon_variant,,ENST00000619257,;PLP1,non_coding_transcript_exon_variant,,ENST00000485688,;PLP1,non_coding_transcript_exon_variant,,ENST00000461231,;PLP1,intron_variant,,ENST00000465975,;PLP1,upstream_gene_variant,,ENST00000466486,;PLP1,downstream_gene_variant,,ENST00000495678,;PLP1,downstream_gene_variant,,ENST00000464776,;PLP1,upstream_gene_variant,,ENST00000494119,;PLP1,non_coding_transcript_exon_variant,,ENST00000485931,;PLP1,non_coding_transcript_exon_variant,,ENST00000476160,;PLP1,upstream_gene_variant,,ENST00000496836,;PLP1,downstream_gene_variant,,ENST00000480325,; T ENST00000612423 Transcript missense_variant 591/3132 311/834 104/277 Y/F tAc/tTc 1 1 PLP1 HGNC HGNC:9086 protein_coding YES CCDS14513.1 ENSP00000481006 P60201 A8K9L3 UPI000000031E NM_001128834.2 tolerated(1) 4/8 Pfam_domain:PF01275,Prints_domain:PR00214,hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF11 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 103786584 103786584 A T 1 0 0 0 0 1 0 0 0 12200 391 14 4 4 PLP1 23 103786584 Missense_Mutation SNP A C3L-00144_T 708901 103786584 52254311 1684 5755 FAM199X 0 . GRCh38 X 104186619 104186619 + Nonsense_Mutation SNP C C T novel C3L-00144_T C3L-00144_N C C c.727C>T p.Gln243Ter p.Q243* ENST00000493442 4/6 41 28 13 29 29 0 strelka-varscan-mutect FAM199X,stop_gained,p.Gln243Ter,ENST00000493442,NM_207318.3;FAM199X,splice_region_variant,,ENST00000299906,; T ENST00000493442 Transcript stop_gained,splice_region_variant 893/7457 727/1167 243/388 Q/* Cag/Tag 1 1 FAM199X HGNC HGNC:25195 protein_coding YES CCDS35364.1 ENSP00000417581 Q6PEV8 B0QYU2 UPI00001C2069 NM_207318.3 4/6 Pfam_domain:PF15814,hmmpanther:PTHR32003,hmmpanther:PTHR32003:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 12 104186619 104186619 C T 1 0 0 0 0 0 1 0 0 5377 724 25 3 3 FAM199X 23 104186619 Nonsense_Mutation SNP C C3L-00144_T 400035 104186619 51854276 1685 5756 COL4A6 0 . GRCh38 X 108210001 108210001 + Missense_Mutation SNP C C G rs752125609 C3L-00144_T C3L-00144_N C C c.514G>C p.Asp172His p.D172H ENST00000394872 8/46 62 41 21 67 67 0 strelka-varscan-mutect COL4A6,missense_variant,p.Asp172His,ENST00000394872,NM_001287758.1;COL4A6,missense_variant,p.Asp172His,ENST00000334504,NM_033641.3;COL4A6,missense_variant,p.Asp172His,ENST00000621266,NM_001287759.1;COL4A6,missense_variant,p.Asp173His,ENST00000372216,NM_001847.3;COL4A6,missense_variant,p.Asp172His,ENST00000538570,NM_001287760.1;COL4A6,missense_variant,p.Asp172His,ENST00000545689,;COL4A6,downstream_gene_variant,,ENST00000468338,; G ENST00000394872 Transcript missense_variant 748/6750 514/5124 172/1707 D/H Gat/Cat rs752125609 1 -1 COL4A6 HGNC HGNC:2208 protein_coding YES CCDS76010.1 ENSP00000378340 A8MXH5 UPI000387C996 NM_001287758.1 deleterious(0) 8/46 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF533 MODERATE 1 SNV 5 1 PASS rs752125609 . 0 206 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 G 3 3 12 108210001 108210001 C G 1 0 0 0 0 1 0 0 0 3484 869 30 4 4 COL4A6 23 108210001 Missense_Mutation SNP C C3L-00144_T 4023382 108210001 47830894 1686 5757 TRPC5 0 . GRCh38 X 111912521 111912521 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.670G>T p.Gly224Cys p.G224C ENST00000262839 3/11 81 51 30 84 84 0 strelka-varscan-mutect TRPC5,missense_variant,p.Gly224Cys,ENST00000262839,NM_012471.2; A ENST00000262839 Transcript missense_variant 1589/5839 670/2922 224/973 G/C Ggc/Tgc 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 deleterious(0) 3/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,TIGRFAM_domain:TIGR00870,Pfam_domain:PF08344 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 12 111912521 111912521 C A 1 0 0 0 0 1 0 0 0 17087 623 22 2 2 TRPC5 23 111912521 Missense_Mutation SNP C C3L-00144_T 3702520 111912521 44128374 1687 5758 TRPC5 0 . GRCh38 X 111912655 111912655 + Missense_Mutation SNP A A T novel C3L-00144_T C3L-00144_N A A c.536T>A p.Val179Glu p.V179E ENST00000262839 3/11 140 85 55 126 125 1 strelka-varscan-mutect TRPC5,missense_variant,p.Val179Glu,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript missense_variant 1455/5839 536/2922 179/973 V/E gTg/gAg 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 tolerated(1) 3/11 Low_complexity_(Seg):seg,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,TIGRFAM_domain:TIGR00870,Pfam_domain:PF08344 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 111912655 111912655 A T 1 0 0 0 0 1 0 0 0 17087 159 6 4 4 TRPC5 23 111912655 Missense_Mutation SNP A C3L-00144_T 134 111912655 44128240 1688 5759 LUZP4 0 . GRCh38 X 115303312 115303312 + Missense_Mutation SNP G G T novel C3L-00144_T C3L-00144_N G G c.236G>T p.Cys79Phe p.C79F ENST00000371920 3/4 74 44 30 73 73 0 strelka-varscan-mutect LUZP4,missense_variant,p.Cys79Phe,ENST00000371920,NM_016383.4;LUZP4,intron_variant,,ENST00000371921,NM_001318840.1; T ENST00000371920 Transcript missense_variant 243/1701 236/942 79/313 C/F tGc/tTc 1 1 LUZP4 HGNC HGNC:24971 protein_coding YES CCDS14567.1 ENSP00000360988 Q9P127 UPI0000036093 NM_016383.4 tolerated(1) 3/4 hmmpanther:PTHR22550,hmmpanther:PTHR22550:SF11 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 115303312 115303312 G T 1 0 0 0 0 1 0 0 0 8997 1319 46 2 2 LUZP4 23 115303312 Missense_Mutation SNP G C3L-00144_T 3390657 115303312 40737583 1689 5760 KIAA1210 0 . GRCh38 X 119104998 119104998 + Silent SNP C C A rs764251121 C3L-00144_T C3L-00144_N C C c.1062G>T p.= p.A354A ENST00000402510 7/14 166 109 57 135 134 1 strelka-varscan-mutect KIAA1210,synonymous_variant,p.=,ENST00000402510,NM_020721.1; A ENST00000402510 Transcript synonymous_variant 1062/7824 1062/5130 354/1709 A gcG/gcT rs764251121 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 7/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118,Pfam_domain:PF15262 LOW 1 SNV 5 1 PASS rs764251121 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 119104998 119104998 C A 1 0 0 0 0 0 0 0 1 8106 871 31 1 1 KIAA1210 23 119104998 Silent SNP C C3L-00144_T 3801686 119104998 36935897 1690 5761 CT47B1 0 . GRCh38 X 120875642 120875642 + Missense_Mutation SNP G G C rs773988367 C3L-00144_T C3L-00144_N G G c.29C>G p.Thr10Ser p.T10S ENST00000371311 1/3 153 98 55 149 149 0 varscan-mutect CT47B1,missense_variant,p.Thr10Ser,ENST00000371311,NM_001145718.1;RP1-321E8.5,downstream_gene_variant,,ENST00000613352,;RP1-321E8.4,upstream_gene_variant,,ENST00000604718,; C ENST00000371311 Transcript missense_variant 288/1328 29/900 10/299 T/S aCc/aGc rs773988367 1 -1 CT47B1 HGNC HGNC:33293 protein_coding YES CCDS48161.1 ENSP00000360360 P0C2W7 UPI000036776D NM_001145718.1 tolerated(0.26) 1/3 hmmpanther:PTHR32157:SF4,hmmpanther:PTHR32157,Pfam_domain:PF15623 MODERATE SNV 5 1 PASS rs773988367 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 120875642 120875642 G C 1 0 0 0 0 1 0 0 0 3791 1261 44 4 4 CT47B1 23 120875642 Missense_Mutation SNP G C3L-00144_T 1770644 120875642 35165253 1691 5762 DCAF12L1 0 . GRCh38 X 126551269 126551269 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.1340G>T p.Gly447Val p.G447V ENST00000371126 1/2 74 52 22 46 46 0 strelka-varscan-mutect DCAF12L1,missense_variant,p.Gly447Val,ENST00000371126,NM_178470.4; A ENST00000371126 Transcript missense_variant 1583/3382 1340/1392 447/463 G/V gGg/gTg 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 deleterious(0) 1/2 hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 126551269 126551269 C A 1 0 0 0 0 1 0 0 0 4065 623 22 2 2 DCAF12L1 23 126551269 Missense_Mutation SNP C C3L-00144_T 5675627 126551269 29489626 1692 5763 DCAF12L1 0 . GRCh38 X 126552046 126552046 + Missense_Mutation SNP C C A novel C3L-00144_T C3L-00144_N C C c.563G>T p.Gly188Val p.G188V ENST00000371126 1/2 132 88 44 128 128 0 strelka-varscan-mutect DCAF12L1,missense_variant,p.Gly188Val,ENST00000371126,NM_178470.4; A ENST00000371126 Transcript missense_variant 806/3382 563/1392 188/463 G/V gGc/gTc 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 deleterious(0.03) 1/2 Gene3D:2.130.10.10,hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 12 126552046 126552046 C A 1 0 0 0 0 1 0 0 0 4065 739 26 2 2 DCAF12L1 23 126552046 Missense_Mutation SNP C C3L-00144_T 777 126552046 29488849 1693 5764 ACTRT1 0 . GRCh38 X 128051654 128051654 + Missense_Mutation SNP C C T C3L-00144_T C3L-00144_N C C c.553G>A p.Gly185Arg p.G185R ENST00000371124 1/1 77 41 36 65 65 0 strelka-varscan-mutect ACTRT1,missense_variant,p.Gly185Arg,ENST00000371124,NM_138289.3; T ENST00000371124 Transcript missense_variant 745/1437 553/1131 185/376 G/R Ggg/Agg COSM308855 1 -1 ACTRT1 HGNC HGNC:24027 protein_coding YES CCDS14611.1 ENSP00000360165 Q8TDG2 UPI0000072276 NM_138289.3 deleterious(0) 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF153,SMART_domains:SM00268,Superfamily_domains:SSF53067 1 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 12 128051654 128051654 C T 1 0 0 0 0 1 0 0 0 261 681 24 3 3 ACTRT1 23 128051654 Missense_Mutation SNP C C3L-00144_T 1499608 128051654 27989241 1694 5765 ZDHHC9 0 . GRCh38 X 129823689 129823689 + Silent SNP G G A novel C3L-00144_T C3L-00144_N G G c.477C>T p.= p.D159D ENST00000357166 5/11 180 126 54 160 159 1 strelka-varscan-mutect ZDHHC9,synonymous_variant,p.=,ENST00000357166,NM_016032.3;ZDHHC9,synonymous_variant,p.=,ENST00000371064,NM_001008222.2;ZDHHC9,synonymous_variant,p.=,ENST00000406492,;ZDHHC9,synonymous_variant,p.=,ENST00000433917,;ZDHHC9,non_coding_transcript_exon_variant,,ENST00000491039,; A ENST00000357166 Transcript synonymous_variant 869/4569 477/1095 159/364 D gaC/gaT 1 -1 ZDHHC9 HGNC HGNC:18475 protein_coding YES CCDS35395.1 ENSP00000349689 Q9Y397 UPI0000048EB7 NM_016032.3 5/11 Pfam_domain:PF01529,PROSITE_profiles:PS50216,hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 129823689 129823689 G A 1 0 0 0 0 0 0 0 1 18198 1368 48 3 3 ZDHHC9 23 129823689 Silent SNP G C3L-00144_T 1772035 129823689 26217206 1695 5766 STK26 0 . GRCh38 X 132072871 132072872 + Frame_Shift_Ins INS - - T novel C3L-00144_T C3L-00144_N - - c.1086dupT p.Glu363Ter p.E363* ENST00000394334 10/12 73 48 25 84 84 0 sindel-varindel-pindel STK26,frameshift_variant,p.Glu363Ter,ENST00000394334,NM_016542.3;STK26,frameshift_variant,p.Glu286Ter,ENST00000394335,NM_001042453.1;STK26,frameshift_variant,p.Glu385Ter,ENST00000481105,;STK26,frameshift_variant,p.Glu301Ter,ENST00000496850,NM_001042452.1;STK26,intron_variant,,ENST00000354719,;FRMD7,downstream_gene_variant,,ENST00000298542,NM_194277.2;FRMD7,downstream_gene_variant,,ENST00000370879,; T ENST00000394334 Transcript frameshift_variant 1338-1339/3288 1085-1086/1251 362/416 A/AX gct/gcTt 1 1 STK26 HGNC HGNC:18174 protein_coding YES CCDS14631.1 ENSP00000377867 Q9P289 UPI0000030CB8 NM_016542.3 10/12 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF206 HIGH 1 insertion 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 T 7 5 12 132072871 132072871 - T 1 0 1 1 0 0 0 0 0 15671 811 28 0 0 STK26 23 132072871 Frame_Shift_Ins INS - C3L-00144_T 2249182 132072871 23968024 1696 5767 CT55 0 . GRCh38 X 135160503 135160503 + Missense_Mutation SNP G G C novel C3L-00144_T C3L-00144_N G G c.332C>G p.Thr111Ser p.T111S ENST00000276241 3/6 70 47 23 64 64 0 strelka-varscan-mutect CT55,missense_variant,p.Thr111Ser,ENST00000344129,NM_017863.2;CT55,missense_variant,p.Thr111Ser,ENST00000276241,NM_001031705.2; C ENST00000276241 Transcript missense_variant 559/1445 332/795 111/264 T/S aCc/aGc 1 -1 CT55 HGNC HGNC:26047 protein_coding YES CCDS35400.1 ENSP00000276241 Q8WUE5 UPI000006D94A NM_001031705.2 tolerated(0.38) 3/6 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF354 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 12 135160503 135160503 G C 1 0 0 0 0 1 0 0 0 3792 1261 44 4 4 CT55 23 135160503 Missense_Mutation SNP G C3L-00144_T 3087632 135160503 20880392 1697 5768 ARHGEF6 0 . GRCh38 X 136745336 136745336 + Nonsense_Mutation SNP C C A rs754597402 C3L-00144_T C3L-00144_N C C c.346G>T p.Glu116Ter p.E116* ENST00000250617 4/22 177 111 66 182 182 0 strelka-varscan-mutect ARHGEF6,stop_gained,p.Glu116Ter,ENST00000250617,NM_004840.2;ARHGEF6,5_prime_UTR_variant,,ENST00000370622,;ARHGEF6,5_prime_UTR_variant,,ENST00000370620,NM_001306177.1; A ENST00000250617 Transcript stop_gained 1552/6019 346/2331 116/776 E/* Gaa/Taa rs754597402,COSM3558323 1 -1 ARHGEF6 HGNC HGNC:685 protein_coding YES CCDS14660.1 ENSP00000250617 Q15052 UPI0000001C8E NM_004840.2 4/22 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF123,Pfam_domain:PF16615,Superfamily_domains:SSF47576 0,1 HIGH 1 SNV 1 0,1 1 PASS rs754597402 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 12 136745336 136745336 C A 1 0 0 0 0 0 1 0 0 1046 922 32 2 2 ARHGEF6 23 136745336 Nonsense_Mutation SNP C C3L-00144_T 1584833 136745336 19295559 1698 5769 MAGEC2 0 . GRCh38 X 142203184 142203184 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.804G>T p.= p.G268G ENST00000247452 3/3 72 44 28 75 75 0 strelka-varscan-mutect MAGEC2,synonymous_variant,p.=,ENST00000247452,NM_016249.3; A ENST00000247452 Transcript synonymous_variant 1152/1991 804/1122 268/373 G ggG/ggT 1 -1 MAGEC2 HGNC HGNC:13574 protein_coding YES CCDS14678.1 ENSP00000354660 Q9UBF1 UPI000012F059 NM_016249.3 3/3 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29,SMART_domains:SM01373 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 142203184 142203184 C A 1 0 0 0 0 0 0 0 1 9099 610 22 2 2 MAGEC2 23 142203184 Silent SNP C C3L-00144_T 5457848 142203184 13837711 1699 5770 SLITRK4 0 . GRCh38 X 143630046 143630046 + Silent SNP A A G novel C3L-00144_T C3L-00144_N A A c.1063T>C p.= p.L355L ENST00000596188 2/2 109 95 14 93 93 0 strelka-varscan-mutect SLITRK4,synonymous_variant,p.=,ENST00000596188,NM_001184750.2;SLITRK4,synonymous_variant,p.=,ENST00000338017,NM_173078.4;SLITRK4,synonymous_variant,p.=,ENST00000356928,NM_001184749.2; G ENST00000596188 Transcript synonymous_variant 1289/8545 1063/2514 355/837 L Ttg/Ctg 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 2/2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 12 143630046 143630046 A G 1 0 0 0 0 0 0 0 1 15036 11 1 5 5 SLITRK4 23 143630046 Silent SNP A C3L-00144_T 1426862 143630046 12410849 1700 5771 FMR1NB 0 . GRCh38 X 147981636 147981636 + Silent SNP C C A novel C3L-00144_T C3L-00144_N C C c.234C>A p.= p.I78I ENST00000370467 1/6 96 56 40 82 82 0 strelka-varscan-mutect FMR1NB,synonymous_variant,p.=,ENST00000370467,NM_152578.2; A ENST00000370467 Transcript synonymous_variant 308/1021 234/768 78/255 I atC/atA 1 1 FMR1NB HGNC HGNC:26372 protein_coding YES CCDS14683.1 ENSP00000359498 Q8N0W7 UPI0000062299 NM_152578.2 1/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR37360:SF1,hmmpanther:PTHR37360 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 12 147981636 147981636 C A 1 0 0 0 0 0 0 0 1 5817 845 30 2 2 FMR1NB 23 147981636 Silent SNP C C3L-00144_T 4351590 147981636 8059259 1701 5772 AVPR2 0 . GRCh38 X 153906000 153906000 + Frame_Shift_Del DEL C C - C3L-00144_T C3L-00144_N C C c.495delC p.Phe166SerfsTer46 p.F166Sfs*46 ENST00000358927 3/4 246 138 108 203 203 0 sindel-varindel-pindel AVPR2,frameshift_variant,p.Phe166SerfsTer46,ENST00000358927,;AVPR2,frameshift_variant,p.Phe166SerfsTer46,ENST00000337474,NM_000054.4;AVPR2,frameshift_variant,p.Phe166SerfsTer46,ENST00000370049,NM_001146151.1;AVPR2,frameshift_variant,p.Phe166SerfsTer46,ENST00000430697,;ARHGAP4,downstream_gene_variant,,ENST00000370028,NM_001164741.1;ARHGAP4,downstream_gene_variant,,ENST00000350060,NM_001666.4;ARHGAP4,downstream_gene_variant,,ENST00000370016,;ARHGAP4,downstream_gene_variant,,ENST00000393721,;ARHGAP4,downstream_gene_variant,,ENST00000442172,;ARHGAP4,downstream_gene_variant,,ENST00000454164,;ARHGAP4,downstream_gene_variant,,ENST00000467421,;AVPR2,intron_variant,,ENST00000434679,;L1CAM,intron_variant,,ENST00000464967,;ARHGAP4,downstream_gene_variant,,ENST00000404127,;ARHGAP4,downstream_gene_variant,,ENST00000470209,;ARHGAP4,downstream_gene_variant,,ENST00000420383,;ARHGAP4,downstream_gene_variant,,ENST00000494302,;ARHGAP4,downstream_gene_variant,,ENST00000494397,;ARHGAP4,downstream_gene_variant,,ENST00000466928,;ARHGAP4,downstream_gene_variant,,ENST00000461739,; - ENST00000358927 Transcript frameshift_variant 703/1763 494/1116 165/371 A/X gCc/gc CM025909 1 1 AVPR2 HGNC HGNC:897 protein_coding YES CCDS14735.1 ENSP00000351805 P30518 UPI000005043B 3/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF20,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH deletion 5 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 12 153906000 153906000 C - 1 0 1 0 1 0 0 0 0 1389 739 26 0 0 AVPR2 23 153906000 Frame_Shift_Del DEL C C3L-00144_T 5924364 153906000 2134895 1702 5773 HCFC1 0 . GRCh38 X 153959908 153959908 + Silent SNP C C A rs782668582 C3L-00144_T C3L-00144_N C C c.1338G>T p.= p.T446T ENST00000310441 8/26 48 27 21 39 39 0 strelka-mutect HCFC1,synonymous_variant,p.=,ENST00000310441,NM_005334.2;HCFC1,synonymous_variant,p.=,ENST00000369984,;HCFC1,downstream_gene_variant,,ENST00000461098,; A ENST00000310441 Transcript synonymous_variant 2305/8869 1338/6108 446/2035 T acG/acT rs782668582 1 -1 HCFC1 HGNC HGNC:4839 protein_coding YES CCDS44020.1 ENSP00000309555 P51610 UPI0000142F1F NM_005334.2 8/26 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,SMART_domains:SM00060 LOW 1 SNV 1 1 PASS rs782668582 . 0 200 9 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 2 1 12 153959908 153959908 C A 1 0 0 0 0 0 0 0 1 6879 755 27 1 1 HCFC1 23 153959908 Silent SNP C C3L-00144_T 53908 153959908 2080987 1703 5774 PCDH11Y 0 . GRCh38 Y 5099900 5099900 + Silent SNP A A T novel C3L-00144_T C3L-00144_N A A c.2322A>T p.= p.T774T ENST00000362095 2/3 86 77 9 128 128 0 varscan-mutect PCDH11Y,synonymous_variant,p.=,ENST00000400457,NM_032973.2;PCDH11Y,synonymous_variant,p.=,ENST00000622698,NM_001278619.1;PCDH11Y,synonymous_variant,p.=,ENST00000333703,NM_032971.2;PCDH11Y,synonymous_variant,p.=,ENST00000215473,;PCDH11Y,synonymous_variant,p.=,ENST00000362095,NM_032972.2; T ENST00000362095 Transcript synonymous_variant 3056/4220 2322/3147 774/1048 T acA/acT 1 1 PCDH11Y HGNC HGNC:15813 protein_coding YES CCDS14777.1 ENSP00000355419 Q9BZA8 UPI000006EF4D NM_032972.2 2/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 12 5099900 5099900 A T 1 0 0 0 0 0 0 0 1 11596 175 7 4 4 PCDH11Y 24 5099900 Silent SNP A C3L-00144_T 5099900 52127515 1704 5775 SENP7 0 . GRCh38 3 101332897 101332897 + Missense_Mutation SNP A A T rs774147547 C3L-00263_T C3L-00263_N A A c.10T>A p.Phe4Ile p.F4I ENST00000394085 1/7 102 95 7 117 117 0 strelka-varscan-mutect SENP7,missense_variant,p.Phe4Ile,ENST00000394085,;SENP7,intron_variant,,ENST00000394095,NM_020654.4;SENP7,intron_variant,,ENST00000314261,NM_001282801.1;SENP7,intron_variant,,ENST00000394094,NM_001077203.2;SENP7,intron_variant,,ENST00000394091,NM_001282803.1;SENP7,intron_variant,,ENST00000348610,NM_001282802.1;SENP7,downstream_gene_variant,,ENST00000460107,; T ENST00000394085 Transcript missense_variant 373/1483 10/717 4/238 F/I Ttt/Att rs774147547 1 -1 SENP7 HGNC HGNC:30402 protein_coding ENSP00000377647 Q9BQF6 UPI000002B362 1/7 PROSITE_profiles:PS50600 MODERATE SNV 1 1 PASS rs774147547 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 13 101332897 101332897 A T 1 0 0 0 0 1 0 0 0 14327 101 4 4 4 SENP7 3 101332897 Missense_Mutation SNP A C3L-00263_T 101332897 96962662 1 5776 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3L-00263_T C3L-00263_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 307 287 20 267 267 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 11111111 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 13 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3L-00263_T 25245351 108029958 2 5777 PHLPP1 0 . GRCh38 18 62975429 62975429 + Missense_Mutation SNP G G A novel C3L-00263_T C3L-00263_N G G c.3788G>A p.Gly1263Asp p.G1263D ENST00000262719 16/17 183 170 13 173 171 2 strelka-varscan-mutect PHLPP1,missense_variant,p.Gly1263Asp,ENST00000262719,NM_194449.3; A ENST00000262719 Transcript missense_variant 4022/6390 3788/5154 1263/1717 G/D gGt/gAt 1 1 PHLPP1 HGNC HGNC:20610 protein_coding YES CCDS45881.2 ENSP00000262719 O60346 UPI000051AE2E NM_194449.3 deleterious(0.01) 16/17 Gene3D:3.60.40.10,Pfam_domain:PF00481,PROSITE_profiles:PS51746,SMART_domains:SM00332,Superfamily_domains:SSF81606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 13 62975429 62975429 G A 1 0 0 0 0 1 0 0 0 11942 1261 44 3 3 PHLPP1 18 62975429 Missense_Mutation SNP G C3L-00263_T 62975429 17397856 3 5778 AGRN 0 . GRCh38 1 1022206 1022206 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.207G>T p.= p.R69R ENST00000379370 2/36 385 346 39 306 306 0 strelka-varscan-mutect AGRN,synonymous_variant,p.=,ENST00000379370,NM_198576.3;AGRN,5_prime_UTR_variant,,ENST00000620552,NM_001305275.1; T ENST00000379370 Transcript synonymous_variant 257/7323 207/6138 69/2045 R cgG/cgT 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 2/36 Gene3D:2.40.50.120,Pfam_domain:PF03146,PROSITE_profiles:PS51121,Superfamily_domains:SSF50242 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 1022206 1022206 G T 1 0 0 0 0 0 0 0 1 476 1246 43 2 2 AGRN 1 1022206 Silent SNP G C3L-00279_T 1022206 247934216 1 5779 CCDC27 0 . GRCh38 1 3763756 3763756 + Nonsense_Mutation SNP C C T rs762081181 C3L-00279_T C3L-00279_N C C c.1372C>T p.Arg458Ter p.R458* ENST00000294600 8/12 242 221 21 188 188 0 strelka-varscan-mutect CCDC27,stop_gained,p.Arg458Ter,ENST00000294600,NM_152492.2;CCDC27,3_prime_UTR_variant,,ENST00000462521,; T ENST00000294600 Transcript stop_gained 1456/2176 1372/1971 458/656 R/* Cga/Tga rs762081181 1 1 CCDC27 HGNC HGNC:26546 protein_coding YES CCDS50.1 ENSP00000294600 Q2M243 UPI000013E186 NM_152492.2 8/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18853:SF8,hmmpanther:PTHR18853 HIGH 1 SNV 1 1 PASS rs762081181 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 3763756 3763756 C T 1 0 0 0 0 0 1 0 0 2511 760 27 1 1 CCDC27 1 3763756 Nonsense_Mutation SNP C C3L-00279_T 2741550 3763756 245192666 2 5780 PLEKHG5 0 . GRCh38 1 6471539 6471539 + Silent SNP C C T rs775775743 C3L-00279_T C3L-00279_N C C c.1467G>A p.= p.R489R ENST00000537245 13/22 188 168 20 181 181 0 strelka-varscan-mutect PLEKHG5,synonymous_variant,p.=,ENST00000377748,NM_198681.3;PLEKHG5,synonymous_variant,p.=,ENST00000537245,NM_001265592.1;PLEKHG5,synonymous_variant,p.=,ENST00000535355,NM_001265593.1;PLEKHG5,synonymous_variant,p.=,ENST00000340850,NM_001042664.1;PLEKHG5,synonymous_variant,p.=,ENST00000400913,NM_001042665.1;PLEKHG5,synonymous_variant,p.=,ENST00000377732,;PLEKHG5,synonymous_variant,p.=,ENST00000400915,NM_001042663.1;PLEKHG5,synonymous_variant,p.=,ENST00000377728,NM_020631.4;PLEKHG5,synonymous_variant,p.=,ENST00000377740,;PLEKHG5,synonymous_variant,p.=,ENST00000377725,NM_001265594.1;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000487949,; T ENST00000537245 Transcript synonymous_variant 1532/4794 1467/3258 489/1085 R cgG/cgA rs775775743 1 -1 PLEKHG5 HGNC HGNC:29105 protein_coding YES CCDS57969.1 ENSP00000439625 O94827 UPI000206539E NM_001265592.1 13/22 PROSITE_profiles:PS50010,hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF9,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 2 1 PASS rs775775743 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 6471539 6471539 C T 1 0 0 0 0 0 0 0 1 12166 726 26 3 3 PLEKHG5 1 6471539 Silent SNP C C3L-00279_T 2707783 6471539 242484883 3 5781 PRAMEF2 0 . GRCh38 1 12860273 12860273 + Splice_Site SNP T T G C3L-00279_T C3L-00279_N T T c.866+2T>G p.X289_splice ENST00000240189 301 256 45 264 264 0 strelka-varscan-mutect PRAMEF2,splice_donor_variant,,ENST00000240189,NM_023014.1; G ENST00000240189 Transcript splice_donor_variant -/1642 866/1425 289/474 COSM4021493 1 1 PRAMEF2 HGNC HGNC:28841 protein_coding YES CCDS149.1 ENSP00000240189 O60811 UPI0000139EF9 NM_023014.1 3/3 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 14 12860273 12860273 T G 1 0 0 0 0 0 0 1 0 12562 1710 59 5 5 PRAMEF2 1 12860273 Splice_Site SNP T C3L-00279_T 6388734 12860273 236096149 4 5782 ATP13A2 0 . GRCh38 1 17005700 17005700 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.89C>A p.Ser30Tyr p.S30Y ENST00000326735 2/29 503 443 60 423 423 0 strelka-varscan-mutect ATP13A2,missense_variant,p.Ser30Tyr,ENST00000452699,NM_001141973.2;ATP13A2,missense_variant,p.Ser30Tyr,ENST00000326735,NM_022089.3;ATP13A2,missense_variant,p.Ser30Tyr,ENST00000341676,NM_001141974.2;ATP13A2,missense_variant,p.Ser6Tyr,ENST00000510069,;ATP13A2,missense_variant,p.Ser23Tyr,ENST00000509619,;ATP13A2,5_prime_UTR_variant,,ENST00000617114,;ATP13A2,upstream_gene_variant,,ENST00000511957,;ATP13A2,upstream_gene_variant,,ENST00000508222,;RP1-37C10.3,downstream_gene_variant,,ENST00000446261,;ATP13A2,upstream_gene_variant,,ENST00000463860,; T ENST00000326735 Transcript missense_variant 123/3840 89/3543 30/1180 S/Y tCc/tAc 1 -1 ATP13A2 HGNC HGNC:30213 protein_coding YES CCDS175.1 ENSP00000327214 Q9NQ11 UPI0000049724 NM_022089.3 deleterious(0) 2/29 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF86,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 17005700 17005700 G T 1 0 0 0 0 1 0 0 0 1276 1174 41 2 2 ATP13A2 1 17005700 Missense_Mutation SNP G C3L-00279_T 4145427 17005700 231950722 5 5783 UBR4 0 . GRCh38 1 19081705 19081705 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.102G>T p.= p.V34V ENST00000375225 1/4 294 256 38 213 213 0 strelka-varscan-mutect UBR4,synonymous_variant,p.=,ENST00000375225,;UBR4,intron_variant,,ENST00000375254,NM_020765.2;UBR4,intron_variant,,ENST00000375224,;UBR4,upstream_gene_variant,,ENST00000486515,;UBR4,upstream_gene_variant,,ENST00000459947,; A ENST00000375225 Transcript synonymous_variant 536/1533 102/777 34/258 V gtG/gtT 1 -1 UBR4 HGNC HGNC:30313 protein_coding ENSP00000364373 Q5TBN9 UPI000040DD3B 1/4 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 19081705 19081705 C A 1 0 0 0 0 0 0 0 1 17428 581 21 2 2 UBR4 1 19081705 Silent SNP C C3L-00279_T 2076005 19081705 229874717 6 5784 KIF17 0 . GRCh38 1 20684928 20684928 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.2112G>T p.= p.V704V ENST00000247986 10/15 406 354 52 332 331 1 strelka-varscan-mutect KIF17,synonymous_variant,p.=,ENST00000247986,NM_020816.3;KIF17,synonymous_variant,p.=,ENST00000400463,NM_001122819.2;KIF17,synonymous_variant,p.=,ENST00000375044,NM_001287212.1;KIF17,non_coding_transcript_exon_variant,,ENST00000490034,;KIF17,non_coding_transcript_exon_variant,,ENST00000477167,;KIF17,non_coding_transcript_exon_variant,,ENST00000462858,;KIF17,non_coding_transcript_exon_variant,,ENST00000498225,; A ENST00000247986 Transcript synonymous_variant 2423/3969 2112/3090 704/1029 V gtG/gtT 1 -1 KIF17 HGNC HGNC:19167 protein_coding YES CCDS213.1 ENSP00000247986 Q9P2E2 UPI0000185F1A NM_020816.3 10/15 hmmpanther:PTHR24115:SF355,hmmpanther:PTHR24115 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 20684928 20684928 C A 1 0 0 0 0 0 0 0 1 8143 581 21 2 2 KIF17 1 20684928 Silent SNP C C3L-00279_T 1603223 20684928 228271494 7 5785 EPHB2 0 . GRCh38 1 22865035 22865035 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.1126G>A p.Gly376Arg p.G376R ENST00000374632 5/16 168 142 26 131 131 0 strelka-varscan-mutect EPHB2,missense_variant,p.Gly376Arg,ENST00000400191,NM_001309193.1;EPHB2,missense_variant,p.Gly370Arg,ENST00000374627,;EPHB2,missense_variant,p.Gly376Arg,ENST00000374632,NM_004442.6;EPHB2,missense_variant,p.Gly376Arg,ENST00000374630,NM_017449.3;EPHB2,missense_variant,p.Gly376Arg,ENST00000544305,;MIR4253,upstream_gene_variant,,ENST00000581187,;EPHB2,non_coding_transcript_exon_variant,,ENST00000465676,;EPHB2,upstream_gene_variant,,ENST00000490436,; A ENST00000374632 Transcript missense_variant 1139/3677 1126/2964 376/987 G/R Ggg/Agg COSM3864746,COSM3864747,COSM3864748 1 1 EPHB2 HGNC HGNC:3393 protein_coding YES CCDS230.1 ENSP00000363763 P29323 UPI000016135C NM_004442.6 tolerated(0.09) 5/16 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF123,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF57184 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1444928620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 22865035 22865035 G A 1 0 0 0 0 1 0 0 0 5022 1116 39 1 1 EPHB2 1 22865035 Missense_Mutation SNP G C3L-00279_T 2180107 22865035 226091387 8 5786 MAN1C1 0 . GRCh38 1 25758593 25758593 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.931G>T p.Gly311Trp p.G311W ENST00000374332 6/12 255 217 38 187 186 1 strelka-varscan-mutect MAN1C1,missense_variant,p.Gly101Trp,ENST00000611903,;MAN1C1,missense_variant,p.Gly311Trp,ENST00000374332,NM_020379.3,NM_001289010.1;MAN1C1,missense_variant,p.Gly131Trp,ENST00000263979,;MAN1C1,missense_variant,p.Gly82Trp,ENST00000374329,;MAN1C1,splice_region_variant,,ENST00000473891,; T ENST00000374332 Transcript missense_variant,splice_region_variant 1261/4641 931/1893 311/630 G/W Ggg/Tgg 1 1 MAN1C1 HGNC HGNC:19080 protein_coding YES CCDS265.1 ENSP00000363452 Q9NR34 UPI000012EABD NM_020379.3,NM_001289010.1 deleterious(0.02) 6/12 hmmpanther:PTHR11742:SF28,hmmpanther:PTHR11742,Gene3D:1.50.10.50,Pfam_domain:PF01532,Superfamily_domains:SSF48225,Prints_domain:PR00747 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 25758593 25758593 G T 1 0 0 0 0 1 0 0 0 9134 1362 47 2 2 MAN1C1 1 25758593 Missense_Mutation SNP G C3L-00279_T 2893558 25758593 223197829 9 5787 TRIM63 0 . GRCh38 1 26057228 26057228 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.954C>T p.= p.A318A ENST00000374272 7/9 199 174 25 161 161 0 strelka-varscan-mutect TRIM63,synonymous_variant,p.=,ENST00000374272,NM_032588.3;TRIM63,downstream_gene_variant,,ENST00000483052,; A ENST00000374272 Transcript synonymous_variant 1093/1770 954/1062 318/353 A gcC/gcT 1 -1 TRIM63 HGNC HGNC:16007 protein_coding YES CCDS273.1 ENSP00000363390 Q969Q1 UPI00000437F6 NM_032588.3 7/9 PROSITE_profiles:PS51262,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF279 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 26057228 26057228 G A 1 0 0 0 0 0 0 0 1 17030 1219 43 3 3 TRIM63 1 26057228 Silent SNP G C3L-00279_T 298635 26057228 222899194 10 5788 ZNF683 0 . GRCh38 1 26368532 26368532 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.40A>T p.Arg14Trp p.R14W ENST00000436292 2/7 147 129 18 101 101 0 strelka-varscan-mutect ZNF683,missense_variant,p.Arg14Trp,ENST00000436292,NM_001307925.1;ZNF683,missense_variant,p.Arg14Trp,ENST00000403843,;ZNF683,missense_variant,p.Arg14Trp,ENST00000349618,NM_001114759.1,NM_173574.2;ZNF683,missense_variant,p.Arg22Trp,ENST00000455900,;ZNF683,missense_variant,p.Arg14Trp,ENST00000451801,;ZNF683,missense_variant,p.Arg14Trp,ENST00000416125,;ZNF683,missense_variant,p.Arg22Trp,ENST00000423508,;ZNF683,missense_variant,p.Arg14Trp,ENST00000453132,;ZNF683,missense_variant,p.Arg14Trp,ENST00000454975,; A ENST00000436292 Transcript missense_variant 161/1712 40/1575 14/524 R/W Agg/Tgg 1 -1 ZNF683 HGNC HGNC:28495 protein_coding YES CCDS76126.1 ENSP00000388792 Q8IZ20 UPI0000EE2F2D NM_001307925.1 deleterious_low_confidence(0) 2/7 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 26368532 26368532 T A 1 0 0 0 0 1 0 0 0 18663 1521 53 4 4 ZNF683 1 26368532 Missense_Mutation SNP T C3L-00279_T 311304 26368532 222587890 11 5789 OPRD1 0 . GRCh38 1 28812515 28812515 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.132G>T p.= p.S44S ENST00000234961 1/3 223 187 36 188 187 1 strelka-varscan-mutect OPRD1,synonymous_variant,p.=,ENST00000234961,NM_000911.3;OPRD1,synonymous_variant,p.=,ENST00000621425,; T ENST00000234961 Transcript synonymous_variant 374/9345 132/1119 44/372 S tcG/tcT 1 1 OPRD1 HGNC HGNC:8153 protein_coding YES CCDS329.1 ENSP00000234961 P41143 UPI0000130D94 NM_000911.3 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24229:SF2,hmmpanther:PTHR24229,Gene3D:1.20.1070.10,Prints_domain:PR00525 LOW 1 SNV 1 1 PASS rs1393775005 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 28812515 28812515 G T 1 0 0 0 0 0 0 0 1 10960 1132 40 1 1 OPRD1 1 28812515 Silent SNP G C3L-00279_T 2443983 28812515 220143907 12 5790 AGO1 0 . GRCh38 1 35917699 35917699 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.2135G>T p.Arg712Leu p.R712L ENST00000373204 16/19 166 148 18 154 154 0 strelka-varscan-mutect AGO1,missense_variant,p.Arg712Leu,ENST00000373204,NM_012199.2;AGO1,missense_variant,p.Arg637Leu,ENST00000373206,;AGO1,3_prime_UTR_variant,,ENST00000635259,; T ENST00000373204 Transcript missense_variant 2348/13708 2135/2574 712/857 R/L cGc/cTc COSM1205108 1 1 AGO1 HGNC HGNC:3262 protein_coding YES CCDS398.1 ENSP00000362300 Q9UL18 UPI000012D07D NM_012199.2 deleterious(0) 16/19 PROSITE_profiles:PS50822,hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891,Pfam_domain:PF02171,Gene3D:3.30.420.10,SMART_domains:SM00950,Superfamily_domains:SSF53098 1 MODERATE 1 SNV 1 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999656 1 1 1 0 T 3 4 14 35917699 35917699 G T 1 0 0 0 0 1 0 0 0 464 1087 38 1 1 AGO1 1 35917699 Missense_Mutation SNP G C3L-00279_T 7105184 35917699 213038723 13 5791 HEYL 0 . GRCh38 1 39627057 39627057 + Missense_Mutation SNP C C A rs367972512 C3L-00279_T C3L-00279_N C C c.437G>T p.Arg146Leu p.R146L ENST00000372852 5/5 348 318 30 265 265 0 strelka-varscan-mutect HEYL,missense_variant,p.Arg146Leu,ENST00000372852,NM_014571.3; A ENST00000372852 Transcript missense_variant 757/3661 437/987 146/328 R/L cGg/cTg rs367972512,COSM4985793 1 -1 HEYL HGNC HGNC:4882 protein_coding YES CCDS439.1 ENSP00000361943 Q9NQ87 UPI000013E317 NM_014571.3 deleterious(0) 5/5 Superfamily_domains:0053813,Pfam_domain:PF07527,PROSITE_profiles:PS51054,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF79,SMART_domains:SM00511 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367972512 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 39627057 39627057 C A 1 0 0 0 0 1 0 0 0 6964 652 23 1 1 HEYL 1 39627057 Missense_Mutation SNP C C3L-00279_T 3709358 39627057 209329365 14 5792 P3H1 0 . GRCh38 1 42766813 42766813 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.159G>T p.= p.G53G ENST00000236040 1/14 410 343 67 320 320 0 strelka-mutect P3H1,synonymous_variant,p.=,ENST00000236040,NM_001243246.1;P3H1,synonymous_variant,p.=,ENST00000397054,NM_001146289.1;P3H1,synonymous_variant,p.=,ENST00000296388,NM_022356.3;P3H1,synonymous_variant,p.=,ENST00000372526,;C1orf50,upstream_gene_variant,,ENST00000372525,NM_024097.3;C1orf50,upstream_gene_variant,,ENST00000468913,;P3H1,non_coding_transcript_exon_variant,,ENST00000492956,;P3H1,non_coding_transcript_exon_variant,,ENST00000495874,;P3H1,non_coding_transcript_exon_variant,,ENST00000460031,;RP5-994D16.12,upstream_gene_variant,,ENST00000603943,;P3H1,upstream_gene_variant,,ENST00000463465,;RP5-994D16.12,upstream_gene_variant,,ENST00000464081,; A ENST00000236040 Transcript synonymous_variant 200/2993 159/2415 53/804 G ggG/ggT 1 -1 P3H1 HGNC HGNC:19316 protein_coding YES CCDS57986.1 ENSP00000236040 Q32P28 UPI000013E32E NM_001243246.1 1/14 hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF5 LOW SNV 2 1 PASS rs1484901390 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 42766813 42766813 C A 1 0 0 0 0 0 0 0 1 11429 610 22 2 2 P3H1 1 42766813 Silent SNP C C3L-00279_T 3139756 42766813 206189609 15 5793 RPS8 0 . GRCh38 1 44777679 44777679 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.277A>T p.Thr93Ser p.T93S ENST00000396651 4/6 286 249 37 214 214 0 strelka-mutect RPS8,missense_variant,p.Thr93Ser,ENST00000396651,NM_001012.1;RPS8,missense_variant,p.Thr73Ser,ENST00000372209,;SNORD46,downstream_gene_variant,,ENST00000364043,;SNORD55,downstream_gene_variant,,ENST00000581525,;SNORD38A,upstream_gene_variant,,ENST00000365161,;SNORD38B,upstream_gene_variant,,ENST00000625943,;SNORD38B,upstream_gene_variant,,ENST00000384690,;RP11-269F19.2,upstream_gene_variant,,ENST00000428791,;RPS8,non_coding_transcript_exon_variant,,ENST00000485390,;RPS8,non_coding_transcript_exon_variant,,ENST00000464658,;RPS8,non_coding_transcript_exon_variant,,ENST00000484599,;RPS8,non_coding_transcript_exon_variant,,ENST00000497035,;RPS8,downstream_gene_variant,,ENST00000470475,;RPS8,upstream_gene_variant,,ENST00000474582,;RPS15AP11,downstream_gene_variant,,ENST00000594193,; T ENST00000396651 Transcript missense_variant 437/881 277/627 93/208 T/S Acc/Tcc 1 1 RPS8 HGNC HGNC:10441 protein_coding YES CCDS513.1 ENSP00000379888 P62241 Q5JR94 UPI000015D557 NM_001012.1 deleterious(0) 4/6 Pfam_domain:PF01201,hmmpanther:PTHR10394,TIGRFAM_domain:TIGR00307 MODERATE 1 SNV 1 1 PASS rs900337622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 44777679 44777679 A T 1 0 0 0 0 1 0 0 0 13916 391 14 4 4 RPS8 1 44777679 Missense_Mutation SNP A C3L-00279_T 2010866 44777679 204178743 16 5794 UROD 0 . GRCh38 1 45014811 45014811 + Missense_Mutation SNP T T G C3L-00279_T C3L-00279_N T T c.850T>G p.Trp284Gly p.W284G ENST00000246337 8/10 303 260 43 247 246 1 strelka-varscan-mutect UROD,missense_variant,p.Trp284Gly,ENST00000246337,NM_000374.4;UROD,missense_variant,p.Trp284Gly,ENST00000636836,;UROD,missense_variant,p.Trp238Gly,ENST00000636293,;UROD,missense_variant,p.Trp224Gly,ENST00000428106,;ZSWIM5,downstream_gene_variant,,ENST00000359600,NM_020883.1;HECTD3,upstream_gene_variant,,ENST00000372172,NM_024602.5;UROD,downstream_gene_variant,,ENST00000434478,;UROD,non_coding_transcript_exon_variant,,ENST00000494399,;UROD,non_coding_transcript_exon_variant,,ENST00000472254,;UROD,non_coding_transcript_exon_variant,,ENST00000478467,;UROD,non_coding_transcript_exon_variant,,ENST00000465678,;UROD,non_coding_transcript_exon_variant,,ENST00000466193,;UROD,downstream_gene_variant,,ENST00000469548,;UROD,downstream_gene_variant,,ENST00000463092,;UROD,downstream_gene_variant,,ENST00000486699,;UROD,downstream_gene_variant,,ENST00000462688,;UROD,downstream_gene_variant,,ENST00000491300,;UROD,downstream_gene_variant,,ENST00000490385,;UROD,downstream_gene_variant,,ENST00000460906,;UROD,downstream_gene_variant,,ENST00000496439,;UROD,downstream_gene_variant,,ENST00000491773,;UROD,downstream_gene_variant,,ENST00000460334,;UROD,downstream_gene_variant,,ENST00000473012,;UROD,downstream_gene_variant,,ENST00000461035,; G ENST00000246337 Transcript missense_variant 969/1300 850/1104 284/367 W/G Tgg/Ggg CM091819 1 1 UROD HGNC HGNC:12591 protein_coding YES CCDS518.1 ENSP00000246337 P06132 UPI0000112E85 NM_000374.4 deleterious(0) 8/10 Gene3D:3.20.20.210,HAMAP:MF_00218,Pfam_domain:PF01208,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF2,Superfamily_domains:SSF51726,TIGRFAM_domain:TIGR01464 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 45014811 45014811 T G 1 0 0 0 0 1 0 0 0 17561 1580 55 5 5 UROD 1 45014811 Missense_Mutation SNP T C3L-00279_T 237132 45014811 203941611 17 5795 CYP4X1 0 . GRCh38 1 47036151 47036151 + Missense_Mutation SNP G G T rs114619570 C3L-00279_T C3L-00279_N G G c.755G>T p.Arg252Leu p.R252L ENST00000371901 6/12 97 87 10 67 67 0 strelka-varscan-mutect CYP4X1,missense_variant,p.Arg252Leu,ENST00000371901,NM_178033.1;CYP4X1,non_coding_transcript_exon_variant,,ENST00000466294,; T ENST00000371901 Transcript missense_variant 1005/2357 755/1530 252/509 R/L cGa/cTa rs114619570 1 1 CYP4X1 HGNC HGNC:20244 protein_coding YES CCDS544.1 ENSP00000360968 Q8N118 UPI000003F043 NM_178033.1 deleterious(0) 6/12 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF55,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs114619570 . 0 203 6 0 0 0 0 0 -19.88753 0.9999998 1 1 1 0 T 3 4 14 47036151 47036151 G T 1 0 0 0 0 1 0 0 0 3996 1058 37 1 1 CYP4X1 1 47036151 Missense_Mutation SNP G C3L-00279_T 2021340 47036151 201920271 18 5796 SLC5A9 0 . GRCh38 1 48239451 48239451 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.1666C>A p.Leu556Met p.L556M ENST00000236495 13/15 254 219 35 281 281 0 strelka-varscan-mutect SLC5A9,missense_variant,p.Leu556Met,ENST00000236495,NM_001135181.1;SLC5A9,missense_variant,p.Leu531Met,ENST00000438567,NM_001011547.2;SLC5A9,missense_variant,p.Leu552Met,ENST00000533824,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000525901,;SLC5A9,upstream_gene_variant,,ENST00000471020,;SLC5A9,missense_variant,p.Leu23Met,ENST00000532322,;SLC5A9,3_prime_UTR_variant,,ENST00000425816,;SLC5A9,non_coding_transcript_exon_variant,,ENST00000493837,;SLC5A9,downstream_gene_variant,,ENST00000441260,; A ENST00000236495 Transcript missense_variant 1716/3272 1666/2121 556/706 L/M Ctg/Atg COSM3805485 1 1 SLC5A9 HGNC HGNC:22146 protein_coding YES CCDS44136.1 ENSP00000236495 Q2M3M2 UPI0000251D94 NM_001135181.1 tolerated(0.06) 13/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF96 1 MODERATE 1 SNV 1 1 1 PASS rs1306615062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 48239451 48239451 C A 1 0 0 0 0 1 0 0 0 14955 680 24 2 2 SLC5A9 1 48239451 Missense_Mutation SNP C C3L-00279_T 1203300 48239451 200716971 19 5797 BSND 0 . GRCh38 1 55007180 55007180 + Silent SNP C C G rs774504119 C3L-00279_T C3L-00279_N C C c.456C>G p.= p.G152G ENST00000371265 3/4 244 207 37 214 214 0 strelka-varscan-mutect BSND,synonymous_variant,p.=,ENST00000371265,NM_057176.2; G ENST00000371265 Transcript synonymous_variant 710/3472 456/963 152/320 G ggC/ggG rs774504119,COSM4009011 1 1 BSND HGNC HGNC:16512 protein_coding YES CCDS602.1 ENSP00000360312 Q8WZ55 Q5VU50 UPI000006DC8D NM_057176.2 3/4 PD968187,Pfam_domain:PF15462,hmmpanther:PTHR28399,hmmpanther:PTHR28399:SF1,Low_complexity_(Seg):seg 0,1 LOW 1 SNV 1 0,1 1 PASS rs774504119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 55007180 55007180 C G 1 0 0 0 0 0 0 0 1 1705 755 27 4 4 BSND 1 55007180 Silent SNP C C3L-00279_T 6767729 55007180 193949242 20 5798 SERBP1 0 . GRCh38 1 67420155 67420155 + Missense_Mutation SNP C C A rs749718037 C3L-00279_T C3L-00279_N C C c.850G>T p.Gly284Cys p.G284C ENST00000370995 6/8 167 135 32 58 58 0 strelka-varscan-mutect SERBP1,missense_variant,p.Gly263Cys,ENST00000370994,NM_015640.3;SERBP1,missense_variant,p.Gly284Cys,ENST00000370995,NM_001018067.1;SERBP1,missense_variant,p.Gly269Cys,ENST00000361219,NM_001018069.1;SERBP1,missense_variant,p.Gly278Cys,ENST00000370990,NM_001018068.1;RNU6-387P,downstream_gene_variant,,ENST00000411331,;SERBP1,non_coding_transcript_exon_variant,,ENST00000484880,;SERBP1,non_coding_transcript_exon_variant,,ENST00000462814,;SERBP1,non_coding_transcript_exon_variant,,ENST00000493607,;SERBP1,downstream_gene_variant,,ENST00000490406,; A ENST00000370995 Transcript missense_variant 936/3482 850/1227 284/408 G/C Ggt/Tgt rs749718037 1 -1 SERBP1 HGNC HGNC:17860 protein_coding YES CCDS30746.1 ENSP00000360034 Q8NC51 UPI0000036970 NM_001018067.1 deleterious(0.02) 6/8 hmmpanther:PTHR12299:SF29,hmmpanther:PTHR12299,Pfam_domain:PF04774,SMART_domains:SM01233 MODERATE 1 SNV 1 1 PASS rs749718037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 67420155 67420155 C A 1 0 0 0 0 1 0 0 0 14350 623 22 2 2 SERBP1 1 67420155 Missense_Mutation SNP C C3L-00279_T 12412975 67420155 181536267 21 5799 LRRC7 0 . GRCh38 1 69760359 69760359 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.155A>T p.Tyr52Phe p.Y52F ENST00000035383 1/25 333 288 45 211 211 0 strelka-varscan-mutect LRRC7,missense_variant,p.Tyr57Phe,ENST00000310961,;LRRC7,missense_variant,p.Tyr52Phe,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Tyr90Phe,ENST00000370958,;LRRC7,5_prime_UTR_variant,,ENST00000415775,; T ENST00000035383 Transcript missense_variant 185/5000 155/4614 52/1537 Y/F tAt/tTt 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious(0.03) 1/25 PROSITE_profiles:PS51450,hmmpanther:PTHR23155:SF459,hmmpanther:PTHR23155,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 69760359 69760359 A T 1 0 0 0 0 1 0 0 0 8916 449 16 4 4 LRRC7 1 69760359 Missense_Mutation SNP A C3L-00279_T 2340204 69760359 179196063 22 5800 TNNI3K 0 . GRCh38 1 74439501 74439501 + Nonsense_Mutation SNP G G A rs779354276 C3L-00279_T C3L-00279_N G G c.1890G>A p.Trp630Ter p.W630* ENST00000326637 20/25 178 152 26 137 137 0 strelka-varscan-mutect TNNI3K,stop_gained,p.Trp630Ter,ENST00000326637,NM_015978.2;FPGT-TNNI3K,stop_gained,p.Trp744Ter,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,stop_gained,p.Trp731Ter,ENST00000370899,NM_001199327.1;TNNI3K,stop_gained,p.Trp176Ter,ENST00000534020,;TNNI3K,non_coding_transcript_exon_variant,,ENST00000370889,; A ENST00000326637 Transcript stop_gained 1941/3001 1890/2508 630/835 W/* tgG/tgA rs779354276 1 1 TNNI3K HGNC HGNC:19661 protein_coding YES CCDS664.1 ENSP00000322251 Q59H18 UPI0000035B8F NM_015978.2 20/25 PROSITE_profiles:PS50011,hmmpanther:PTHR23257:SF477,hmmpanther:PTHR23257,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS rs779354276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 74439501 74439501 G A 1 0 0 0 0 0 1 0 0 16802 1183 41 3 3 TNNI3K 1 74439501 Nonsense_Mutation SNP G C3L-00279_T 4679142 74439501 174516921 23 5801 WDR63 0 . GRCh38 1 85071988 85071988 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.47T>A p.Leu16Gln p.L16Q ENST00000294664 2/23 104 85 19 61 61 0 strelka-varscan-mutect WDR63,missense_variant,p.Leu16Gln,ENST00000294664,NM_145172.4;WDR63,missense_variant,p.Leu16Gln,ENST00000370596,;WDR63,missense_variant,p.Leu16Gln,ENST00000326813,NM_001288563.1;WDR63,missense_variant,p.Leu16Gln,ENST00000528899,;WDR63,missense_variant,p.Leu16Gln,ENST00000464801,; A ENST00000294664 Transcript missense_variant 227/2995 47/2676 16/891 L/Q cTa/cAa 1 1 WDR63 HGNC HGNC:30711 protein_coding YES CCDS702.1 ENSP00000294664 Q8IWG1 A0A140VJZ8 UPI00000744F1 NM_145172.4 tolerated(0.61) 2/23 hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 85071988 85071988 T A 1 0 0 0 0 1 0 0 0 17873 1522 53 4 4 WDR63 1 85071988 Missense_Mutation SNP T C3L-00279_T 10632487 85071988 163884434 24 5802 SYDE2 0 . GRCh38 1 85169082 85169082 + Missense_Mutation SNP T T A rs751155174 C3L-00279_T C3L-00279_N T T c.2815A>T p.Thr939Ser p.T939S ENST00000341460 5/7 255 224 31 137 137 0 strelka-varscan-mutect SYDE2,missense_variant,p.Thr939Ser,ENST00000341460,NM_032184.1; A ENST00000341460 Transcript missense_variant 2865/5512 2815/3585 939/1194 T/S Act/Tct rs751155174 1 -1 SYDE2 HGNC HGNC:25841 protein_coding YES CCDS44169.1 ENSP00000340594 Q5VT97 UPI0001553B04 NM_032184.1 deleterious(0.02) 5/7 PROSITE_profiles:PS50238,hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF47,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 5 1 PASS rs751155174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 85169082 85169082 T A 1 0 0 0 0 1 0 0 0 15826 1696 59 4 4 SYDE2 1 85169082 Missense_Mutation SNP T C3L-00279_T 97094 85169082 163787340 25 5803 TGFBR3 0 . GRCh38 1 91758612 91758612 + Splice_Site SNP C C A novel C3L-00279_T C3L-00279_N C C c.384+1G>T p.X128_splice ENST00000212355 341 286 55 358 358 0 strelka-varscan-mutect TGFBR3,splice_donor_variant,,ENST00000212355,NM_003243.4;TGFBR3,splice_donor_variant,,ENST00000370399,NM_001195684.1;TGFBR3,splice_donor_variant,,ENST00000525962,;TGFBR3,splice_donor_variant,,ENST00000465892,NM_001195683.1;TGFBR3,splice_donor_variant,,ENST00000468996,;TGFBR3,splice_donor_variant,,ENST00000533089,;TGFBR3,splice_donor_variant,,ENST00000532540,; A ENST00000212355 Transcript splice_donor_variant -/6465 384/2556 128/851 1 -1 TGFBR3 HGNC HGNC:11774 protein_coding YES CCDS30770.1 ENSP00000212355 Q03167 UPI000049D997 NM_003243.4 4/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 14 91758612 91758612 C A 1 0 0 0 0 0 0 1 0 16256 521 18 2 2 TGFBR3 1 91758612 Splice_Site SNP C C3L-00279_T 6589530 91758612 157197810 26 5804 NTNG1 0 . GRCh38 1 107324567 107324567 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.532T>A p.Tyr178Asn p.Y178N ENST00000370068 3/8 259 215 44 171 171 0 strelka-varscan-mutect NTNG1,missense_variant,p.Tyr178Asn,ENST00000370067,;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370068,;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370065,;NTNG1,missense_variant,p.Tyr178Asn,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; A ENST00000370068 Transcript missense_variant 1378/4034 532/1620 178/539 Y/N Tat/Aat 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.60.120.260,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 107324567 107324567 T A 1 0 0 0 0 1 0 0 0 10769 1754 61 4 4 NTNG1 1 107324567 Missense_Mutation SNP T C3L-00279_T 15565955 107324567 141631855 27 5805 VAV3 0 . GRCh38 1 107642630 107642630 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1903C>A p.Leu635Met p.L635M ENST00000370056 20/27 203 173 30 241 241 0 strelka-varscan-mutect VAV3,missense_variant,p.Leu635Met,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Leu635Met,ENST00000527011,;VAV3,missense_variant,p.Leu75Met,ENST00000415432,NM_001079874.1;VAV3,missense_variant,p.Leu163Met,ENST00000529809,;VAV3,non_coding_transcript_exon_variant,,ENST00000343258,;VAV3,non_coding_transcript_exon_variant,,ENST00000525460,;VAV3,non_coding_transcript_exon_variant,,ENST00000533398,;VAV3,non_coding_transcript_exon_variant,,ENST00000529033,;VAV3,3_prime_UTR_variant,,ENST00000529413,;VAV3,3_prime_UTR_variant,,ENST00000525231,;VAV3,non_coding_transcript_exon_variant,,ENST00000479977,; T ENST00000370056 Transcript missense_variant 2178/4990 1903/2544 635/847 L/M Ctg/Atg 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 tolerated(0.14) 20/27 PROSITE_profiles:PS50002,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 107642630 107642630 G T 1 0 0 0 0 1 0 0 0 17678 933 33 2 2 VAV3 1 107642630 Missense_Mutation SNP G C3L-00279_T 318063 107642630 141313792 28 5806 SYT6 0 . GRCh38 1 114097855 114097855 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1132G>T p.Gly378Ter p.G378* ENST00000609117 6/8 151 132 19 146 146 0 strelka-varscan-mutect SYT6,stop_gained,p.Gly378Ter,ENST00000609117,;SYT6,stop_gained,p.Gly378Ter,ENST00000369547,NM_001270805.1;SYT6,stop_gained,p.Gly378Ter,ENST00000607941,NM_205848.3;SYT6,stop_gained,p.Gly463Ter,ENST00000610222,;SYT6,3_prime_UTR_variant,,ENST00000610121,;SYT6,3_prime_UTR_variant,,ENST00000610096,; A ENST00000609117 Transcript stop_gained 1436/4424 1132/1278 378/425 G/* Gga/Tga 1 -1 SYT6 HGNC HGNC:18638 protein_coding YES CCDS871.1 ENSP00000477344 Q5T7P8 I6L9C3 UPI000000DACA 6/8 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF45,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 114097855 114097855 C A 1 0 0 0 0 0 1 0 0 15872 690 24 2 2 SYT6 1 114097855 Nonsense_Mutation SNP C C3L-00279_T 6455225 114097855 134858567 29 5807 SPAG17 0 . GRCh38 1 118040795 118040795 + Nonsense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.3101C>A p.Ser1034Ter p.S1034* ENST00000336338 22/49 237 194 43 75 75 0 strelka-varscan-mutect SPAG17,stop_gained,p.Ser1034Ter,ENST00000336338,NM_206996.2;SPAG17,upstream_gene_variant,,ENST00000470550,;SPAG17,upstream_gene_variant,,ENST00000486589,; T ENST00000336338 Transcript stop_gained 3167/6924 3101/6672 1034/2223 S/* tCa/tAa 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 22/49 hmmpanther:PTHR21963 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 118040795 118040795 G T 1 0 0 0 0 0 1 0 0 15310 1294 45 2 2 SPAG17 1 118040795 Nonsense_Mutation SNP G C3L-00279_T 3942940 118040795 130915627 30 5808 MTMR11 0 . GRCh38 1 149935621 149935621 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.227G>A p.Arg76Lys p.R76K ENST00000439741 3/17 259 220 39 211 211 0 strelka-varscan-mutect MTMR11,splice_acceptor_variant,,ENST00000369140,NM_181873.3;MTMR11,missense_variant,p.Arg76Lys,ENST00000439741,NM_001145862.1;OTUD7B,downstream_gene_variant,,ENST00000581312,NM_020205.3;MTMR11,non_coding_transcript_exon_variant,,ENST00000492824,;MTMR11,non_coding_transcript_exon_variant,,ENST00000482025,;MTMR11,intron_variant,,ENST00000466496,;MTMR11,upstream_gene_variant,,ENST00000490310,;MTMR11,upstream_gene_variant,,ENST00000495054,;MTMR11,upstream_gene_variant,,ENST00000493562,;MTMR11,upstream_gene_variant,,ENST00000479272,;MTMR11,non_coding_transcript_exon_variant,,ENST00000482343,; T ENST00000439741 Transcript missense_variant 478/2856 227/2130 76/709 R/K aGg/aAg 1 -1 MTMR11 HGNC HGNC:24307 protein_coding YES CCDS72902.1 ENSP00000391668 A4FU01 UPI000173AA17 NM_001145862.1 tolerated(0.08) 3/17 hmmpanther:PTHR10807:SF51,hmmpanther:PTHR10807,Superfamily_domains:SSF50729 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 149935621 149935621 C T 1 0 0 0 0 1 0 0 0 9928 681 24 3 3 MTMR11 1 149935621 Missense_Mutation SNP C C3L-00279_T 31894826 149935621 99020801 31 5809 NPR1 0 . GRCh38 1 153688171 153688171 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2367G>T p.Gln789His p.Q789H ENST00000368680 15/22 177 151 26 144 144 0 strelka-varscan-mutect NPR1,missense_variant,p.Gln789His,ENST00000368680,NM_000906.3;MIR8083,downstream_gene_variant,,ENST00000620823,;NPR1,upstream_gene_variant,,ENST00000368677,; T ENST00000368680 Transcript missense_variant 2839/4236 2367/3186 789/1061 Q/H caG/caT 1 1 NPR1 HGNC HGNC:7943 protein_coding YES CCDS1051.1 ENSP00000357669 P16066 A0A140VJE6 UPI0000125B3D NM_000906.3 tolerated(0.14) 15/22 PROSITE_profiles:PS50011,hmmpanther:PTHR11920:SF300,hmmpanther:PTHR11920,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 153688171 153688171 G T 1 0 0 0 0 1 0 0 0 10650 991 35 2 2 NPR1 1 153688171 Missense_Mutation SNP G C3L-00279_T 3752550 153688171 95268251 32 5810 OR10J3 0 . GRCh38 1 159314540 159314540 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.120C>A p.= p.L40L ENST00000332217 1/1 409 367 42 278 278 0 strelka-varscan-mutect OR10J3,synonymous_variant,p.=,ENST00000332217,NM_001004467.1; T ENST00000332217 Transcript synonymous_variant 120/990 120/990 40/329 L ctC/ctA 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 159314540 159314540 G T 1 0 0 0 0 0 0 0 1 10988 929 33 2 2 OR10J3 1 159314540 Silent SNP G C3L-00279_T 5626369 159314540 89641882 33 5811 ADAMTS4 0 . GRCh38 1 161196175 161196175 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1086A>T p.Glu362Asp p.E362D ENST00000367996 3/9 55 46 9 51 51 0 strelka-varscan-mutect ADAMTS4,missense_variant,p.Glu362Asp,ENST00000367996,NM_005099.4;ADAMTS4,3_prime_UTR_variant,,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000367993,NM_004550.4;NDUFS2,upstream_gene_variant,,ENST00000496133,;NDUFS2,upstream_gene_variant,,ENST00000479948,;ADAMTS4,upstream_gene_variant,,ENST00000478394,; A ENST00000367996 Transcript missense_variant 1515/9773 1086/2514 362/837 E/D gaA/gaT 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 deleterious(0) 3/9 PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.9861 1 1 1 1 0 A 3 1 14 161196175 161196175 T A 1 0 0 0 0 1 0 0 0 312 1739 60 4 4 ADAMTS4 1 161196175 Missense_Mutation SNP T C3L-00279_T 1881635 161196175 87760247 34 5812 FCRLB 0 . GRCh38 1 161725989 161725989 + Missense_Mutation SNP G G T rs748049975 C3L-00279_T C3L-00279_N G G c.476G>T p.Arg159Leu p.R159L ENST00000367948 6/8 232 208 24 152 152 0 strelka-mutect FCRLB,missense_variant,p.Arg159Leu,ENST00000367948,NM_001320241.1,NM_001002901.3;FCRLB,missense_variant,p.Arg159Leu,ENST00000336830,NM_001288831.1;FCRLB,missense_variant,p.Arg152Leu,ENST00000367944,NM_001288832.1;FCRLB,missense_variant,p.Arg159Leu,ENST00000367946,NM_001288829.1;FCRLB,missense_variant,p.Arg152Leu,ENST00000367945,NM_001288830.1;FCRLB,non_coding_transcript_exon_variant,,ENST00000495397,; T ENST00000367948 Transcript missense_variant 691/1977 476/1281 159/426 R/L cGt/cTt rs748049975 1 1 FCRLB HGNC HGNC:26431 protein_coding YES CCDS30927.1 ENSP00000356925 Q6BAA4 UPI00003FF782 NM_001320241.1,NM_001002901.3 tolerated(0.11) 6/8 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF65,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs748049975 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 161725989 161725989 G T 1 0 0 0 0 1 0 0 0 5663 1145 40 1 1 FCRLB 1 161725989 Missense_Mutation SNP G C3L-00279_T 529814 161725989 87230433 35 5813 POU2F1 0 . GRCh38 1 167220934 167220934 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.37T>A p.Ser13Thr p.S13T ENST00000367866 1/16 245 220 25 185 184 1 strelka-varscan-mutect POU2F1,missense_variant,p.Ser13Thr,ENST00000367866,NM_002697.3;POU2F1,missense_variant,p.Ser13Thr,ENST00000429375,NM_001198786.1;POU2F1,5_prime_UTR_variant,,ENST00000541643,;RP11-277B15.3,upstream_gene_variant,,ENST00000606967,;POU2F1,non_coding_transcript_exon_variant,,ENST00000367865,;POU2F1,non_coding_transcript_exon_variant,,ENST00000492850,;POU2F1,non_coding_transcript_exon_variant,,ENST00000557909,;POU2F1,non_coding_transcript_exon_variant,,ENST00000559038,;POU2F1,missense_variant,p.Ser13Thr,ENST00000271411,;POU2F1,missense_variant,p.Ser13Thr,ENST00000560232,;POU2F1,missense_variant,p.Ser13Thr,ENST00000442313,; A ENST00000367866 Transcript missense_variant 106/13905 37/2301 13/766 S/T Tca/Aca 1 1 POU2F1 HGNC HGNC:9212 protein_coding YES CCDS1259.2 ENSP00000356840 P14859 UPI0000EE3C74 NM_002697.3 tolerated_low_confidence(0.43) 1/16 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF47,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 167220934 167220934 T A 1 0 0 0 0 1 0 0 0 12387 1783 62 4 4 POU2F1 1 167220934 Missense_Mutation SNP T C3L-00279_T 5494945 167220934 81735488 36 5814 MYOC 0 . GRCh38 1 171636175 171636175 + Missense_Mutation SNP C C A rs201573718 C3L-00279_T C3L-00279_N C C c.1265G>T p.Arg422Leu p.R422L ENST00000037502 3/3 790 637 153 604 603 1 strelka-varscan-mutect MYOC,missense_variant,p.Arg422Leu,ENST00000037502,NM_000261.1;RP3-454G6.2,intron_variant,,ENST00000637303,; A ENST00000037502 Transcript missense_variant 1337/2095 1265/1515 422/504 R/L cGt/cTt rs201573718,CM981347 1 -1 MYOC HGNC HGNC:7610 protein_coding YES CCDS1297.1 ENSP00000037502 Q99972 A0A0S2Z421 UPI00000012D6 NM_000261.1 deleterious(0.01) 3/3 Pfam_domain:PF02191,PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF33,SMART_domains:SM00284 MODERATE 1 SNV 1 1,1 1 PASS rs201573718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 171636175 171636175 C A 1 0 0 0 0 1 0 0 0 10087 536 19 1 1 MYOC 1 171636175 Missense_Mutation SNP C C3L-00279_T 4415241 171636175 77320247 37 5815 PAPPA2 0 . GRCh38 1 176595159 176595159 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1555C>A p.Leu519Ile p.L519I ENST00000367662 3/23 408 340 68 335 335 0 strelka-varscan-mutect PAPPA2,missense_variant,p.Leu519Ile,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Leu519Ile,ENST00000367661,NM_021936.2; A ENST00000367662 Transcript missense_variant 2719/9691 1555/5376 519/1791 L/I Ctt/Att 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 deleterious(0.02) 3/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 176595159 176595159 C A 1 0 0 0 0 1 0 0 0 11513 681 24 2 2 PAPPA2 1 176595159 Missense_Mutation SNP C C3L-00279_T 4958984 176595159 72361263 38 5816 AXDND1 0 . GRCh38 1 179534822 179534822 + Missense_Mutation SNP A A C C3L-00279_T C3L-00279_N A A c.2891A>C p.Glu964Ala p.E964A ENST00000367618 25/26 121 103 18 39 39 0 strelka-varscan-mutect AXDND1,missense_variant,p.Glu964Ala,ENST00000367618,NM_144696.5;AXDND1,missense_variant,p.Glu824Ala,ENST00000434088,;AXDND1,3_prime_UTR_variant,,ENST00000617277,;AXDND1,non_coding_transcript_exon_variant,,ENST00000484883,;AXDND1,non_coding_transcript_exon_variant,,ENST00000484455,;AXDND1,3_prime_UTR_variant,,ENST00000511157,; C ENST00000367618 Transcript missense_variant 3278/3642 2891/3039 964/1012 E/A gAg/gCg COSM677856 1 1 AXDND1 HGNC HGNC:26564 protein_coding YES CCDS30948.1 ENSP00000356590 Q5T1B0 UPI000022AC91 NM_144696.5 deleterious(0) 25/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23052 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 179534822 179534822 A C 1 0 0 0 0 1 0 0 0 1392 304 11 5 5 AXDND1 1 179534822 Missense_Mutation SNP A C3L-00279_T 2939663 179534822 69421600 39 5817 CACNA1E 0 . GRCh38 1 181757960 181757960 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.4343A>T p.Asp1448Val p.D1448V ENST00000367573 31/48 196 170 26 165 164 1 strelka-varscan-mutect CACNA1E,missense_variant,p.Asp1429Val,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Asp1448Val,ENST00000621551,;CACNA1E,missense_variant,p.Asp1448Val,ENST00000367567,;CACNA1E,missense_variant,p.Asp1429Val,ENST00000358338,;CACNA1E,missense_variant,p.Asp1448Val,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Asp1448Val,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Asp1447Val,ENST00000357570,;CACNA1E,missense_variant,p.Asp1429Val,ENST00000360108,; T ENST00000367573 Transcript missense_variant 4343/7067 4343/6942 1448/2313 D/V gAc/gTc 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0) 31/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 181757960 181757960 A T 1 0 0 0 0 1 0 0 0 2230 275 10 4 4 CACNA1E 1 181757960 Missense_Mutation SNP A C3L-00279_T 2223138 181757960 67198462 40 5818 TRMT1L 0 . GRCh38 1 185143437 185143437 + Splice_Site SNP C C T novel C3L-00279_T C3L-00279_N C C c.780-1G>A p.X260_splice ENST00000367506 205 173 32 89 89 0 strelka-varscan-mutect TRMT1L,splice_acceptor_variant,,ENST00000367506,NM_030934.4,NM_001202423.1;TRMT1L,upstream_gene_variant,,ENST00000458395,;TRMT1L,downstream_gene_variant,,ENST00000487028,; T ENST00000367506 Transcript splice_acceptor_variant -/4392 780/2202 260/733 1 -1 TRMT1L HGNC HGNC:16782 protein_coding YES CCDS1366.1 ENSP00000356476 Q7Z2T5 UPI000000DADB NM_030934.4,NM_001202423.1 6/14 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 14 185143437 185143437 C T 1 0 0 0 0 0 0 1 0 17068 695 24 3 3 TRMT1L 1 185143437 Splice_Site SNP C C3L-00279_T 3385477 185143437 63812985 41 5819 TPR 0 . GRCh38 1 186313999 186313999 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.7064G>T p.Gly2355Val p.G2355V ENST00000367478 51/51 115 95 20 30 30 0 strelka-varscan-mutect TPR,missense_variant,p.Gly2355Val,ENST00000367478,NM_003292.2;PRG4,3_prime_UTR_variant,,ENST00000445192,NM_005807.4;PRG4,3_prime_UTR_variant,,ENST00000367483,NM_001127708.2;PRG4,3_prime_UTR_variant,,ENST00000635041,NM_001303232.1;PRG4,3_prime_UTR_variant,,ENST00000367485,NM_001127709.2,NM_001127710.2;RNU6-1240P,upstream_gene_variant,,ENST00000365155,;TPR,downstream_gene_variant,,ENST00000467810,; A ENST00000367478 Transcript missense_variant 7361/9708 7064/7092 2355/2363 G/V gGa/gTa 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 deleterious_low_confidence(0.03) 51/51 hmmpanther:PTHR18898,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 186313999 186313999 C A 1 0 0 0 0 1 0 0 0 16897 855 30 2 2 TPR 1 186313999 Missense_Mutation SNP C C3L-00279_T 1170562 186313999 62642423 42 5820 KCNT2 0 . GRCh38 1 196258250 196258250 + Missense_Mutation SNP A A T rs769341865 C3L-00279_T C3L-00279_N A A c.3155T>A p.Leu1052His p.L1052H ENST00000294725 26/28 250 210 40 161 161 0 strelka-varscan-mutect KCNT2,missense_variant,p.Leu1028His,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Leu1052His,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Leu985His,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; T ENST00000294725 Transcript missense_variant 4071/4409 3155/3408 1052/1135 L/H cTt/cAt rs769341865 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious(0) 26/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 MODERATE 1 SNV 1 1 PASS rs769341865 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 196258250 196258250 A T 1 0 0 0 0 1 0 0 0 8008 72 3 4 4 KCNT2 1 196258250 Missense_Mutation SNP A C3L-00279_T 9944251 196258250 52698172 43 5821 KCNT2 0 . GRCh38 1 196429584 196429584 + Missense_Mutation SNP G G T rs373151987 C3L-00279_T C3L-00279_N G G c.812C>A p.Pro271His p.P271H ENST00000294725 9/28 127 117 10 76 76 0 strelka-varscan-mutect KCNT2,missense_variant,p.Pro271His,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Pro271His,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Pro271His,ENST00000609185,NM_001287820.1;KCNT2,intron_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,;KCNT2,upstream_gene_variant,,ENST00000466914,; T ENST00000294725 Transcript missense_variant 1728/4409 812/3408 271/1135 P/H cCc/cAc rs373151987 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious(0) 9/28 Gene3D:1.10.287.70,Pfam_domain:PF07885,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs373151987 . 0 208 2 0 0 0 0 0 -19.51119 1 1 1 1 0 T 3 4 14 196429584 196429584 G T 1 0 0 0 0 1 0 0 0 8008 1232 43 2 2 KCNT2 1 196429584 Missense_Mutation SNP G C3L-00279_T 171334 196429584 52526838 44 5822 ASPM 0 . GRCh38 1 197146322 197146322 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.116T>A p.Leu39Gln p.L39Q ENST00000367409 1/28 558 492 66 450 449 1 strelka-varscan-mutect ASPM,missense_variant,p.Leu39Gln,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Leu39Gln,ENST00000294732,NM_001206846.1;ASPM,missense_variant,p.Leu39Gln,ENST00000612785,; T ENST00000367409 Transcript missense_variant 373/10887 116/10434 39/3477 L/Q cTg/cAg 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 deleterious(0) 1/28 Pfam_domain:PF15780 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 197146322 197146322 A T 1 0 0 0 0 1 0 0 0 1203 188 7 4 4 ASPM 1 197146322 Missense_Mutation SNP A C3L-00279_T 716738 197146322 51810100 45 5823 NEK7 0 . GRCh38 1 198297135 198297135 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.693A>T p.= p.A231A ENST00000367385 9/10 126 107 19 44 44 0 strelka-varscan-mutect NEK7,synonymous_variant,p.=,ENST00000367385,NM_133494.2;NEK7,synonymous_variant,p.=,ENST00000538004,;NEK7,non_coding_transcript_exon_variant,,ENST00000493790,; T ENST00000367385 Transcript synonymous_variant 1035/4149 693/909 231/302 A gcA/gcT 1 1 NEK7 HGNC HGNC:13386 protein_coding YES CCDS1394.1 ENSP00000356355 Q8TDX7 A0A024R964 UPI0000073180 NM_133494.2 9/10 PROSITE_profiles:PS50011,hmmpanther:PTHR24362,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000654,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR00109 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 198297135 198297135 A T 1 0 0 0 0 0 0 0 1 10357 204 8 4 4 NEK7 1 198297135 Silent SNP A C3L-00279_T 1150813 198297135 50659287 46 5824 IGFN1 0 . GRCh38 1 201206455 201206455 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1562G>T p.Arg521Met p.R521M ENST00000335211 12/24 243 192 51 185 185 0 strelka-varscan-mutect IGFN1,missense_variant,p.Arg521Met,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,non_coding_transcript_exon_variant,,ENST00000444705,;IGFN1,intron_variant,,ENST00000437879,; T ENST00000335211 Transcript missense_variant 1692/11810 1562/11127 521/3708 R/M aGg/aTg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0.01) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 201206455 201206455 G T 1 0 0 0 0 1 0 0 0 7497 1000 35 2 2 IGFN1 1 201206455 Missense_Mutation SNP G C3L-00279_T 2909320 201206455 47749967 47 5825 IGFN1 0 . GRCh38 1 201211134 201211134 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.6241G>T p.Gly2081Cys p.G2081C ENST00000335211 12/24 618 511 107 312 312 0 strelka-varscan-mutect IGFN1,missense_variant,p.Gly2081Cys,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,;IGFN1,downstream_gene_variant,,ENST00000444705,; T ENST00000335211 Transcript missense_variant 6371/11810 6241/11127 2081/3708 G/C Ggt/Tgt 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 201211134 201211134 G T 1 0 0 0 0 1 0 0 0 7497 1232 43 2 2 IGFN1 1 201211134 Missense_Mutation SNP G C3L-00279_T 4679 201211134 47745288 48 5826 PTPN7 0 . GRCh38 1 202152672 202152672 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1060C>A p.His354Asn p.H354N ENST00000309017 8/10 189 167 22 144 144 0 strelka-varscan-mutect PTPN7,missense_variant,p.His354Asn,ENST00000309017,NM_002832.3;PTPN7,missense_variant,p.His288Asn,ENST00000367279,NM_080588.2;PTPN7,missense_variant,p.His330Asn,ENST00000477554,NM_001199797.1;PTPN7,missense_variant,p.His78Asn,ENST00000477625,;PTPN7,downstream_gene_variant,,ENST00000467283,;PTPN7,downstream_gene_variant,,ENST00000435759,;PTPN7,downstream_gene_variant,,ENST00000486116,;PTPN7,downstream_gene_variant,,ENST00000476061,;PTPN7,downstream_gene_variant,,ENST00000464870,;PTPN7,downstream_gene_variant,,ENST00000629151,;PTPN7,non_coding_transcript_exon_variant,,ENST00000492977,;PTPN7,downstream_gene_variant,,ENST00000479092,;PTPN7,missense_variant,p.His249Asn,ENST00000495688,;PTPN7,3_prime_UTR_variant,,ENST00000496197,;PTPN7,3_prime_UTR_variant,,ENST00000480836,;PTPN7,3_prime_UTR_variant,,ENST00000462815,; T ENST00000309017 Transcript missense_variant 1834/3765 1060/1398 354/465 H/N Cac/Aac 1 -1 PTPN7 HGNC HGNC:9659 protein_coding YES CCDS1423.2 ENSP00000309116 P35236 UPI00004701F6 NM_002832.3 deleterious(0.01) 8/10 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF41,hmmpanther:PTHR19134,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799,Prints_domain:PR00700 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 202152672 202152672 G T 1 0 0 0 0 1 0 0 0 12947 1319 46 2 2 PTPN7 1 202152672 Missense_Mutation SNP G C3L-00279_T 941538 202152672 46803750 49 5827 PTPN7 0 . GRCh38 1 202157798 202157798 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.647C>A p.Pro216His p.P216H ENST00000309017 4/10 267 221 46 233 233 0 strelka-varscan-mutect PTPN7,missense_variant,p.Pro216His,ENST00000309017,NM_002832.3;PTPN7,missense_variant,p.Pro150His,ENST00000367279,NM_080588.2;PTPN7,missense_variant,p.Pro192His,ENST00000477554,NM_001199797.1;PTPN7,missense_variant,p.Pro110His,ENST00000467283,;PTPN7,missense_variant,p.Pro111His,ENST00000486116,;PTPN7,missense_variant,p.Pro90His,ENST00000476061,;PTPN7,missense_variant,p.Pro111His,ENST00000464870,;PTPN7,synonymous_variant,p.=,ENST00000435759,;PTPN7,5_prime_UTR_variant,,ENST00000477625,;PTPN7,intron_variant,,ENST00000629151,;PTPN7,downstream_gene_variant,,ENST00000492451,;PTPN7,non_coding_transcript_exon_variant,,ENST00000492977,;PTPN7,non_coding_transcript_exon_variant,,ENST00000479092,;PTPN7,missense_variant,p.Pro111His,ENST00000495688,;PTPN7,missense_variant,p.Pro50Thr,ENST00000480836,;PTPN7,synonymous_variant,p.=,ENST00000496197,;PTPN7,intron_variant,,ENST00000462815,;PTPN7,downstream_gene_variant,,ENST00000468385,;PTPN7,downstream_gene_variant,,ENST00000491584,; T ENST00000309017 Transcript missense_variant 1421/3765 647/1398 216/465 P/H cCc/cAc 1 -1 PTPN7 HGNC HGNC:9659 protein_coding YES CCDS1423.2 ENSP00000309116 P35236 UPI00004701F6 NM_002832.3 deleterious(0.03) 4/10 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF41,hmmpanther:PTHR19134,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 202157798 202157798 G T 1 0 0 0 0 1 0 0 0 12947 1232 43 2 2 PTPN7 1 202157798 Missense_Mutation SNP G C3L-00279_T 5126 202157798 46798624 50 5828 NFASC 0 . GRCh38 1 204974185 204974185 + Missense_Mutation SNP C C A rs367856348 C3L-00279_T C3L-00279_N C C c.1286C>A p.Pro429Gln p.P429Q ENST00000339876 13/30 181 150 31 164 163 1 strelka-mutect NFASC,missense_variant,p.Pro429Gln,ENST00000339876,NM_001005388.2;NFASC,missense_variant,p.Pro429Gln,ENST00000401399,;NFASC,missense_variant,p.Pro440Gln,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Pro440Gln,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Pro423Gln,ENST00000404076,;NFASC,missense_variant,p.Pro440Gln,ENST00000404907,;NFASC,missense_variant,p.Pro416Gln,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Pro399Gln,ENST00000367173,;NFASC,missense_variant,p.Pro440Gln,ENST00000513543,;NFASC,missense_variant,p.Pro429Gln,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,missense_variant,p.Pro446Gln,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000512826,;NFASC,non_coding_transcript_exon_variant,,ENST00000514644,; A ENST00000339876 Transcript missense_variant 1614/10333 1286/3723 429/1240 P/Q cCg/cAg rs367856348 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 deleterious(0.01) 13/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs367856348 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 204974185 204974185 C A 1 0 0 0 0 1 0 0 0 10396 652 23 1 1 NFASC 1 204974185 Missense_Mutation SNP C C3L-00279_T 2816387 204974185 43982237 51 5829 AVPR1B 0 . GRCh38 1 206116032 206116032 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.859G>T p.Val287Leu p.V287L ENST00000367126 1/2 139 127 12 100 100 0 strelka-mutect AVPR1B,missense_variant,p.Val287Leu,ENST00000367126,NM_000707.3;RP11-38J22.3,upstream_gene_variant,,ENST00000425896,;AVPR1B,intron_variant,,ENST00000612906,; A ENST00000367126 Transcript missense_variant 1324/2237 859/1275 287/424 V/L Gtg/Ttg COSM902900 1 -1 AVPR1B HGNC HGNC:896 protein_coding YES CCDS73015.1 ENSP00000356094 P47901 UPI000005043A NM_000707.3 deleterious(0) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF18,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS rs1023144913 . 0 206 3 0 0 0 0 0 -19.9996 1 1 1 1 0 A 3 1 14 206116032 206116032 C A 1 0 0 0 0 1 0 0 0 1388 536 19 1 1 AVPR1B 1 206116032 Missense_Mutation SNP C C3L-00279_T 1141847 206116032 42840390 52 5830 PROX1 0 . GRCh38 1 213998023 213998023 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.1488A>T p.= p.P496P ENST00000366958 2/5 94 86 8 57 57 0 strelka-varscan-mutect PROX1,synonymous_variant,p.=,ENST00000498508,;PROX1,synonymous_variant,p.=,ENST00000366958,NM_001270616.1;PROX1,synonymous_variant,p.=,ENST00000261454,;PROX1,synonymous_variant,p.=,ENST00000435016,NM_002763.4;PROX1,downstream_gene_variant,,ENST00000471129,;PROX1,downstream_gene_variant,,ENST00000607425,; T ENST00000366958 Transcript synonymous_variant 2096/8240 1488/2214 496/737 P ccA/ccT 1 1 PROX1 HGNC HGNC:9459 protein_coding YES CCDS31021.1 ENSP00000355925 Q92786 UPI0000071D14 NM_001270616.1 2/5 hmmpanther:PTHR12198 LOW 1 SNV 1 1 PASS rs1399935358 . 0 208 2 0 0 0 0 0 -16.98435 1 1 1 1 0 T 2 4 14 213998023 213998023 A T 1 0 0 0 0 0 0 0 1 12696 204 8 4 4 PROX1 1 213998023 Silent SNP A C3L-00279_T 7881991 213998023 34958399 53 5831 USH2A 0 . GRCh38 1 215782858 215782858 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.10465G>A p.Ala3489Thr p.A3489T ENST00000307340 53/72 278 218 60 185 185 0 strelka-varscan-mutect USH2A,missense_variant,p.Ala3489Thr,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 10852/18883 10465/15609 3489/5202 A/T Gct/Act 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.43) 53/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 215782858 215782858 C T 1 0 0 0 0 1 0 0 0 17570 797 28 3 3 USH2A 1 215782858 Missense_Mutation SNP C C3L-00279_T 1784835 215782858 33173564 54 5832 23 2 USH2A 0 . GRCh38 1 215782862 215782862 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.10461C>A p.Ser3487Arg p.S3487R ENST00000307340 53/72 265 206 59 184 183 1 strelka-varscan-mutect USH2A,missense_variant,p.Ser3487Arg,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 10848/18883 10461/15609 3487/5202 S/R agC/agA COSM358329 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 53/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 215782862 215782862 G T 1 0 0 0 0 1 0 0 0 17570 1310 46 2 2 USH2A 1 215782862 Missense_Mutation SNP G C3L-00279_T 4 215782862 33173560 55 5833 23 2 USH2A 0 . GRCh38 1 216199920 216199920 + Nonsense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.3518C>A p.Ser1173Ter p.S1173* ENST00000307340 17/72 620 540 80 404 404 0 strelka-varscan-mutect USH2A,stop_gained,p.Ser1173Ter,ENST00000307340,NM_206933.2;USH2A,stop_gained,p.Ser1173Ter,ENST00000366942,NM_007123.5;RP5-1099E6.3,intron_variant,,ENST00000420867,;MRPS18BP1,downstream_gene_variant,,ENST00000414228,; T ENST00000307340 Transcript stop_gained 3905/18883 3518/15609 1173/5202 S/* tCa/tAa CM1110190,COSM425319,COSM4813028,COSM4813029 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 17/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1,1 HIGH 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 216199920 216199920 G T 1 0 0 0 0 0 1 0 0 17570 1294 45 2 2 USH2A 1 216199920 Nonsense_Mutation SNP G C3L-00279_T 417058 216199920 32756502 56 5834 RAB3GAP2 0 . GRCh38 1 220195153 220195153 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1055G>T p.Trp352Leu p.W352L ENST00000358951 12/35 636 571 65 428 428 0 strelka-varscan-mutect RAB3GAP2,missense_variant,p.Trp352Leu,ENST00000358951,NM_012414.3;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,downstream_gene_variant,,ENST00000237724,; A ENST00000358951 Transcript missense_variant 1172/7257 1055/4182 352/1393 W/L tGg/tTg 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 tolerated(0.09) 12/35 Pfam_domain:PF14655,hmmpanther:PTHR12472 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 220195153 220195153 C A 1 0 0 0 0 1 0 0 0 13095 595 21 2 2 RAB3GAP2 1 220195153 Missense_Mutation SNP C C3L-00279_T 3995233 220195153 28761269 57 5835 LIN9 0 . GRCh38 1 226239018 226239018 + Nonsense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1246A>T p.Lys416Ter p.K416* ENST00000328205 12/15 228 197 31 58 58 0 strelka-varscan-mutect LIN9,stop_gained,p.Lys416Ter,ENST00000328205,NM_173083.3;LIN9,stop_gained,p.Lys471Ter,ENST00000366808,NM_001270410.1;LIN9,stop_gained,p.Lys376Ter,ENST00000460719,NM_001270409.1;LIN9,stop_gained,p.Lys381Ter,ENST00000481685,; A ENST00000328205 Transcript stop_gained 1792/3567 1246/1677 416/558 K/* Aag/Tag 1 -1 LIN9 HGNC HGNC:30830 protein_coding YES CCDS1553.1 ENSP00000329102 Q5TKA1 UPI00001B2F3C NM_173083.3 12/15 hmmpanther:PTHR21689 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 226239018 226239018 T A 1 0 0 0 0 0 1 0 0 8721 1821 63 4 4 LIN9 1 226239018 Nonsense_Mutation SNP T C3L-00279_T 6043865 226239018 22717404 58 5836 SNAP47 0 . GRCh38 1 227759361 227759361 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.999A>G p.= p.P333P ENST00000315781 3/5 654 543 111 484 484 0 strelka-varscan-mutect SNAP47,synonymous_variant,p.=,ENST00000426344,;SNAP47,synonymous_variant,p.=,ENST00000315781,NM_053052.3;SNAP47,synonymous_variant,p.=,ENST00000366759,;SNAP47,synonymous_variant,p.=,ENST00000617596,;SNAP47,synonymous_variant,p.=,ENST00000418653,;SNAP47,synonymous_variant,p.=,ENST00000366760,;SNAP47,synonymous_variant,p.=,ENST00000478768,;SNAP47,synonymous_variant,p.=,ENST00000606873,;SNAP47,non_coding_transcript_exon_variant,,ENST00000491439,; G ENST00000315781 Transcript synonymous_variant 1413/2367 999/1395 333/464 P ccA/ccG 1 1 SNAP47 HGNC HGNC:30669 protein_coding YES CCDS1562.1 ENSP00000314157 Q5SQN1 UPI000036662E NM_053052.3 3/5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 227759361 227759361 A G 1 0 0 0 0 0 0 0 1 15153 175 7 5 5 SNAP47 1 227759361 Silent SNP A C3L-00279_T 1520343 227759361 21197061 59 5837 ERO1B 0 . GRCh38 1 236226419 236226419 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.902A>C p.Lys301Thr p.K301T ENST00000354619 12/16 484 397 87 278 278 0 strelka-varscan-mutect ERO1B,missense_variant,p.Lys301Thr,ENST00000354619,NM_019891.3;ERO1B,missense_variant,p.Lys26Thr,ENST00000264181,;GPR137B,downstream_gene_variant,,ENST00000477559,; G ENST00000354619 Transcript missense_variant 1104/4567 902/1404 301/467 K/T aAg/aCg 1 -1 ERO1B HGNC HGNC:14355 protein_coding YES CCDS31064.1 ENSP00000346635 Q86YB8 UPI00004700B5 NM_019891.3 deleterious(0) 12/16 Superfamily_domains:0043331,Pfam_domain:PF04137,PIRSF_domain:PIRSF017205,hmmpanther:PTHR12613,hmmpanther:PTHR12613:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 236226419 236226419 T G 1 0 0 0 0 1 0 0 0 5098 1609 56 5 5 ERO1B 1 236226419 Missense_Mutation SNP T C3L-00279_T 8467058 236226419 12730003 60 5838 HEATR1 0 . GRCh38 1 236574808 236574808 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.3180G>A p.= p.L1060L ENST00000366582 23/45 355 306 49 254 254 0 strelka-varscan-mutect HEATR1,synonymous_variant,p.=,ENST00000366582,NM_018072.5;HEATR1,intron_variant,,ENST00000366581,;HEATR1,upstream_gene_variant,,ENST00000490339,; T ENST00000366582 Transcript synonymous_variant 3295/8447 3180/6435 1060/2144 L ctG/ctA 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 23/45 hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 236574808 236574808 C T 1 0 0 0 0 0 0 0 1 6910 697 25 3 3 HEATR1 1 236574808 Silent SNP C C3L-00279_T 348389 236574808 12381614 61 5839 ACTN2 0 . GRCh38 1 236739518 236739518 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1093G>T p.Gly365Cys p.G365C ENST00000542672 10/21 672 544 128 505 505 0 strelka-varscan-mutect ACTN2,missense_variant,p.Gly157Cys,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Gly365Cys,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Gly365Cys,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000492634,;ACTN2,non_coding_transcript_exon_variant,,ENST00000494762,; T ENST00000542672 Transcript missense_variant 1313/4906 1093/2685 365/894 G/C Ggc/Tgc 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0) 10/21 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 236739518 236739518 G T 1 0 0 0 0 1 0 0 0 249 1232 43 2 2 ACTN2 1 236739518 Missense_Mutation SNP G C3L-00279_T 164710 236739518 12216904 62 5840 ZP4 0 . GRCh38 1 237886840 237886840 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.770A>C p.Asn257Thr p.N257T ENST00000611898 6/13 216 176 40 203 203 0 strelka-varscan-mutect ZP4,missense_variant,p.Asn257Thr,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Asn257Thr,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; G ENST00000611898 Transcript missense_variant 1057/2474 770/1623 257/540 N/T aAt/aCt 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0.02) 6/13 Pfam_domain:PF00100,Prints_domain:PR00023,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 237886840 237886840 T G 1 0 0 0 0 1 0 0 0 18810 1493 52 5 5 ZP4 1 237886840 Missense_Mutation SNP T C3L-00279_T 1147322 237886840 11069582 63 5841 CHRM3 0 . GRCh38 1 239908785 239908785 + Missense_Mutation SNP C C A rs143159997 C3L-00279_T C3L-00279_N C C c.1334C>A p.Ser445Tyr p.S445Y ENST00000255380 5/5 433 340 93 348 348 0 strelka-varscan-mutect CHRM3,missense_variant,p.Ser445Tyr,ENST00000255380,NM_000740.2;CHRM3,missense_variant,p.Ser445Tyr,ENST00000615928,;CHRM3,downstream_gene_variant,,ENST00000448020,; A ENST00000255380 Transcript missense_variant 2113/8780 1334/1773 445/590 S/Y tCc/tAc rs143159997 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 deleterious(0) 5/5 Pfam_domain:PF00001,PROSITE_profiles:PS50262,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS rs143159997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 239908785 239908785 C A 1 0 0 0 0 1 0 0 0 3138 855 30 2 2 CHRM3 1 239908785 Missense_Mutation SNP C C3L-00279_T 2021945 239908785 9047637 64 5842 FMN2 0 . GRCh38 1 240178000 240178000 + Missense_Mutation SNP G G C rs777504752 C3L-00279_T C3L-00279_N G G c.1862G>C p.Arg621Pro p.R621P ENST00000319653 3/18 144 132 12 118 118 0 strelka-varscan-mutect FMN2,missense_variant,p.Arg621Pro,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,missense_variant,p.Arg54Pro,ENST00000447095,;RP11-567G24.3,non_coding_transcript_exon_variant,,ENST00000412311,;RP11-567G24.3,non_coding_transcript_exon_variant,,ENST00000444308,; C ENST00000319653 Transcript missense_variant 2092/6434 1862/5169 621/1722 R/P cGa/cCa rs777504752,COSM311242,COSM4401885,COSM5212414 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious(0) 3/18 0,1,1,1 MODERATE SNV 5 0,1,1,1 1 PASS rs777504752 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 240178000 240178000 G C 1 0 0 0 0 1 0 0 0 5806 1058 37 4 4 FMN2 1 240178000 Missense_Mutation SNP G C3L-00279_T 269215 240178000 8778422 65 5843 RGS7 0 . GRCh38 1 240806270 240806270 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.1139G>C p.Arg380Thr p.R380T ENST00000366565 15/18 424 350 74 323 323 0 strelka-varscan-mutect RGS7,missense_variant,p.Arg380Thr,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Arg380Thr,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Arg380Thr,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Arg327Thr,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Arg211Thr,ENST00000440928,; G ENST00000366565 Transcript missense_variant 1521/2494 1139/1464 380/487 R/T aGa/aCa 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 tolerated(0.23) 15/18 PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26,Pfam_domain:PF00615,Gene3D:1.10.167.10,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 240806270 240806270 C G 1 0 0 0 0 1 0 0 0 13481 913 32 4 4 RGS7 1 240806270 Missense_Mutation SNP C C3L-00279_T 628270 240806270 8150152 66 5844 RGS7 0 . GRCh38 1 240816363 240816363 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.737C>A p.Pro246His p.P246H ENST00000366565 11/18 443 369 74 123 123 0 strelka-varscan-mutect RGS7,missense_variant,p.Pro246His,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Pro246His,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Pro246His,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Pro193His,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Pro77His,ENST00000440928,; T ENST00000366565 Transcript missense_variant 1119/2494 737/1464 246/487 P/H cCc/cAc COSM5095239,COSM5095240,COSM5095241 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 deleterious(0) 11/18 Low_complexity_(Seg):seg,Gene3D:4.10.260.10 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1427324166 . 0 198 0 0 11 0 0 0 -20 0.1130198 1 1 0 0 T 3 4 14 240816363 240816363 G T 1 0 0 0 0 1 0 0 0 13481 1232 43 2 2 RGS7 1 240816363 Missense_Mutation SNP G C3L-00279_T 10093 240816363 8140059 67 5845 ADSS 0 . GRCh38 1 244420169 244420169 + Splice_Site SNP C C A novel C3L-00279_T C3L-00279_N C C c.790+1G>T p.X264_splice ENST00000366535 111 90 21 22 22 0 strelka-varscan-mutect ADSS,splice_donor_variant,,ENST00000366535,NM_001126.3;ADSS,splice_donor_variant,,ENST00000462358,;ADSS,upstream_gene_variant,,ENST00000468215,; A ENST00000366535 Transcript splice_donor_variant -/2780 790/1371 264/456 1 -1 ADSS HGNC HGNC:292 protein_coding YES CCDS1624.1 ENSP00000355493 P30520 A0A024R5Q7 UPI0000132AF5 NM_001126.3 8/12 HIGH 1 SNV 1 1 PASS . . 0 200 7 3 0 0 0 0 -20 0.9995406 1 1 1 0 A 5 1 14 244420169 244420169 C A 1 0 0 0 0 0 0 1 0 421 521 18 2 2 ADSS 1 244420169 Splice_Site SNP C C3L-00279_T 3603806 244420169 4536253 68 5846 C1orf101 0 . GRCh38 1 244572527 244572527 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1705C>A p.His569Asn p.H569N ENST00000366534 11/22 332 288 44 98 98 0 strelka-varscan-mutect C1orf101,missense_variant,p.His569Asn,ENST00000366534,NM_001130957.1;C1orf101,missense_variant,p.His418Asn,ENST00000366531,NM_001242340.1;C1orf101,missense_variant,p.His569Asn,ENST00000366533,NM_173807.4;C1orf101,missense_variant,p.His489Asn,ENST00000428042,;C1orf101,non_coding_transcript_exon_variant,,ENST00000473875,; A ENST00000366534 Transcript missense_variant 1759/3333 1705/2856 569/951 H/N Cat/Aat 1 1 C1orf101 HGNC HGNC:28491 protein_coding YES CCDS44340.1 ENSP00000355492 Q5SY80 UPI00004701CD NM_001130957.1 tolerated(0.37) 11/22 hmmpanther:PTHR33722:SF3,hmmpanther:PTHR33722,Pfam_domain:PF15020 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 244572527 244572527 C A 1 0 0 0 0 1 0 0 0 1954 478 17 2 2 C1orf101 1 244572527 Missense_Mutation SNP C C3L-00279_T 152358 244572527 4383895 69 5847 NLRP3 0 . GRCh38 1 247444695 247444695 + Frame_Shift_Del DEL C C - novel C3L-00279_T C3L-00279_N C C c.2886delC p.Thr963HisfsTer3 p.T963Hfs*3 ENST00000336119 8/9 558 491 67 468 467 1 sindel-varindel-pindel NLRP3,frameshift_variant,p.Thr906HisfsTer3,ENST00000366497,NM_001127461.2;NLRP3,frameshift_variant,p.Thr963HisfsTer3,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,frameshift_variant,p.Thr906HisfsTer3,ENST00000366496,;NLRP3,frameshift_variant,p.Thr963HisfsTer3,ENST00000391828,NM_001079821.2;NLRP3,frameshift_variant,p.Thr849HisfsTer3,ENST00000348069,NM_183395.2;NLRP3,frameshift_variant,p.Thr906HisfsTer3,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000532083,; - ENST00000336119 Transcript frameshift_variant 3631/4170 2885/3111 962/1036 S/X tCc/tc 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR24106:SF4,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 247444695 247444695 C - 1 0 1 0 1 0 0 0 0 10516 855 30 0 0 NLRP3 1 247444695 Frame_Shift_Del DEL C C3L-00279_T 2872168 247444695 1511727 70 5848 OR2M5 0 . GRCh38 1 248145532 248145532 + Missense_Mutation SNP C C G rs150844237 C3L-00279_T C3L-00279_N C C c.385C>G p.Pro129Ala p.P129A ENST00000366476 1/1 484 392 92 303 302 1 strelka-varscan-mutect OR2M5,missense_variant,p.Pro129Ala,ENST00000366476,NM_001004690.1; G ENST00000366476 Transcript missense_variant 385/939 385/939 129/312 P/A Cct/Gct rs150844237,COSM3486986,COSM4913165 1 1 OR2M5 HGNC HGNC:19576 protein_coding YES CCDS31105.1 ENSP00000355432 A3KFT3 UPI00001612E2 NM_001004690.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs150844237 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 248145532 248145532 C G 1 0 0 0 0 1 0 0 0 11091 623 22 4 4 OR2M5 1 248145532 Missense_Mutation SNP C C3L-00279_T 700837 248145532 810890 71 5849 OR2M3 0 . GRCh38 1 248203973 248203973 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.906G>T p.Met302Ile p.M302I ENST00000456743 1/1 286 236 50 203 203 0 strelka-mutect OR2M3,missense_variant,p.Met302Ile,ENST00000456743,NM_001004689.1; T ENST00000456743 Transcript missense_variant 906/939 906/939 302/312 M/I atG/atT 1 1 OR2M3 HGNC HGNC:8269 protein_coding YES CCDS31107.1 ENSP00000389625 Q8NG83 A0A126GV67 UPI000004B234 NM_001004689.1 deleterious(0.01) 1/1 hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 248203973 248203973 G T 1 0 0 0 0 1 0 0 0 11089 1290 45 2 2 OR2M3 1 248203973 Missense_Mutation SNP G C3L-00279_T 58441 248203973 752449 72 5850 OR2T1 0 . GRCh38 1 248406860 248406860 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.866C>G p.Ala289Gly p.A289G ENST00000366474 1/1 206 158 48 175 175 0 strelka-varscan-mutect OR2T1,missense_variant,p.Ala289Gly,ENST00000366474,NM_030904.1; G ENST00000366474 Transcript missense_variant 866/1110 866/1110 289/369 A/G gCc/gGc 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 248406860 248406860 C G 1 0 0 0 0 1 0 0 0 11094 739 26 4 4 OR2T1 1 248406860 Missense_Mutation SNP C C3L-00279_T 202887 248406860 549562 73 5851 GREB1 0 . GRCh38 2 11618734 11618734 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3859C>A p.Pro1287Thr p.P1287T ENST00000381486 22/33 132 105 27 84 84 0 strelka-varscan-mutect GREB1,missense_variant,p.Pro1287Thr,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Pro1287Thr,ENST00000234142,;GREB1,missense_variant,p.Pro285Thr,ENST00000396123,;GREB1,downstream_gene_variant,,ENST00000472040,; A ENST00000381486 Transcript missense_variant 4159/8484 3859/5850 1287/1949 P/T Ccc/Acc 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 tolerated(0.4) 22/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS rs1459858496 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 11618734 11618734 C A 1 0 0 0 0 1 0 0 0 6639 623 22 2 2 GREB1 2 11618734 Missense_Mutation SNP C C3L-00279_T 11618734 230574795 74 5852 RAD51AP2 0 . GRCh38 2 17515654 17515654 + Missense_Mutation SNP T T C rs766415253 C3L-00279_T C3L-00279_N T T c.2762A>G p.Asn921Ser p.N921S ENST00000399080 1/3 70 57 13 21 21 0 strelka-varscan-mutect RAD51AP2,missense_variant,p.Asn921Ser,ENST00000399080,NM_001321233.1,NM_001099218.2; C ENST00000399080 Transcript missense_variant 2786/3724 2762/3480 921/1159 N/S aAt/aGt rs766415253 1 -1 RAD51AP2 HGNC HGNC:34417 protein_coding YES CCDS42656.1 ENSP00000382030 Q09MP3 UPI0000418FD4 NM_001321233.1,NM_001099218.2 deleterious(0.01) 1/3 hmmpanther:PTHR15361,hmmpanther:PTHR15361:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 17515654 17515654 T C 1 0 0 0 0 1 0 0 0 13148 1493 52 5 5 RAD51AP2 2 17515654 Missense_Mutation SNP T C3L-00279_T 5896920 17515654 224677875 75 5853 ITSN2 0 . GRCh38 2 24246826 24246826 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.3356G>A p.Ser1119Asn p.S1119N ENST00000355123 28/40 256 226 30 157 157 0 strelka-varscan-mutect ITSN2,missense_variant,p.Ser1119Asn,ENST00000355123,NM_006277.2;ITSN2,missense_variant,p.Ser1092Asn,ENST00000361999,NM_019595.3;ITSN2,missense_variant,p.Ser1102Asn,ENST00000622089,;ITSN2,missense_variant,p.Ser1119Asn,ENST00000406921,NM_147152.2;ITSN2,missense_variant,p.Ser47Asn,ENST00000416160,; T ENST00000355123 Transcript missense_variant 3800/6300 3356/5094 1119/1697 S/N aGt/aAt 1 -1 ITSN2 HGNC HGNC:6184 protein_coding YES CCDS1710.2 ENSP00000347244 Q9NZM3 UPI000013D415 NM_006277.2 tolerated(0.08) 28/40 hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF29,Gene3D:2.30.30.40,Superfamily_domains:SSF50044,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 24246826 24246826 C T 1 0 0 0 0 1 0 0 0 7833 565 20 3 3 ITSN2 2 24246826 Missense_Mutation SNP C C3L-00279_T 6731172 24246826 217946703 76 5854 DNMT3A 0 . GRCh38 2 25282431 25282431 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.458C>T p.Ser153Leu p.S153L ENST00000406659 4/4 282 240 42 249 249 0 strelka-varscan-mutect DNMT3A,missense_variant,p.Ser153Leu,ENST00000406659,NM_001320892.1,NM_175630.1;DNMT3A,intron_variant,,ENST00000264709,NM_175629.2;DNMT3A,intron_variant,,ENST00000321117,NM_022552.4;DNMT3A,intron_variant,,ENST00000380756,; A ENST00000406659 Transcript missense_variant 796/1775 458/501 153/166 S/L tCa/tTa 1 -1 DNMT3A HGNC HGNC:2978 protein_coding CCDS46232.1 ENSP00000384852 Q9Y6K1 UPI00001602D1 NM_001320892.1,NM_175630.1 tolerated_low_confidence(0.73) 4/4 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 25282431 25282431 G A 1 0 0 0 0 1 0 0 0 4489 1294 45 3 3 DNMT3A 2 25282431 Missense_Mutation SNP G C3L-00279_T 1035605 25282431 216911098 77 5855 DTNB 0 . GRCh38 2 25388277 25388277 + Missense_Mutation SNP C C T rs202036284 C3L-00279_T C3L-00279_N C C c.1660G>A p.Gly554Ser p.G554S ENST00000406818 17/21 229 193 36 168 168 0 strelka-varscan-mutect DTNB,missense_variant,p.Gly554Ser,ENST00000406818,NM_021907.4;DTNB,missense_variant,p.Gly547Ser,ENST00000288642,NM_001256303.1;DTNB,missense_variant,p.Gly554Ser,ENST00000407661,NM_183360.2,NM_001256304.1;DTNB,missense_variant,p.Gly554Ser,ENST00000404103,NM_033147.3;DTNB,missense_variant,p.Gly490Ser,ENST00000496972,NM_001256308.1;DTNB,missense_variant,p.Gly524Ser,ENST00000407038,NM_033148.3;DTNB,missense_variant,p.Gly517Ser,ENST00000407186,NM_001320933.1,NM_001320934.1;DTNB,missense_variant,p.Gly517Ser,ENST00000405222,NM_183361.2;DTNB,downstream_gene_variant,,ENST00000481841,;DTNB,upstream_gene_variant,,ENST00000497476,;DTNB,3_prime_UTR_variant,,ENST00000398951,NM_001320932.1;DTNB,3_prime_UTR_variant,,ENST00000356599,;DTNB,non_coding_transcript_exon_variant,,ENST00000479898,;DTNB,non_coding_transcript_exon_variant,,ENST00000489949,;DTNB,non_coding_transcript_exon_variant,,ENST00000482145,;DTNB,non_coding_transcript_exon_variant,,ENST00000498437,; T ENST00000406818 Transcript missense_variant 1910/2474 1660/1884 554/627 G/S Ggc/Agc rs202036284 1 -1 DTNB HGNC HGNC:3058 protein_coding YES CCDS46237.1 ENSP00000384084 O60941 UPI0000129949 NM_021907.4 tolerated(0.6) 17/21 PIRSF_domain:PIRSF038204,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF309 MODERATE 1 SNV 1 1 PASS rs202036284 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 25388277 25388277 C T 1 0 0 0 0 1 0 0 0 4612 652 23 1 1 DTNB 2 25388277 Missense_Mutation SNP C C3L-00279_T 105846 25388277 216805252 78 5856 YPEL5 0 . GRCh38 2 30158781 30158781 + Nonsense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.304G>T p.Glu102Ter p.E102* ENST00000379520 5/5 429 381 48 374 374 0 strelka-varscan YPEL5,stop_gained,p.Glu102Ter,ENST00000379520,NM_001127401.1;YPEL5,stop_gained,p.Glu102Ter,ENST00000379519,NM_001127400.1;YPEL5,stop_gained,p.Glu102Ter,ENST00000402003,NM_001127399.1;YPEL5,stop_gained,p.Glu102Ter,ENST00000261353,NM_016061.2;YPEL5,stop_gained,p.Glu102Ter,ENST00000402708,;YPEL5,non_coding_transcript_exon_variant,,ENST00000495673,;YPEL5,non_coding_transcript_exon_variant,,ENST00000470120,;YPEL5,downstream_gene_variant,,ENST00000492439,;YPEL5,downstream_gene_variant,,ENST00000490211,; T ENST00000379520 Transcript stop_gained 808/2560 304/366 102/121 E/* Gaa/Taa 1 1 YPEL5 HGNC HGNC:18329 protein_coding YES CCDS1771.1 ENSP00000368835 P62699 UPI000000407C NM_001127401.1 5/5 Pfam_domain:PF03226,hmmpanther:PTHR13848 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 30158781 30158781 G T 1 0 0 0 0 0 1 0 0 18055 1175 41 2 2 YPEL5 2 30158781 Nonsense_Mutation SNP G C3L-00279_T 4770504 30158781 212034748 79 5857 SLC8A1 0 . GRCh38 2 40160805 40160805 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.2229C>G p.Ser743Arg p.S743R ENST00000403092 9/11 411 370 41 282 282 0 strelka-varscan SLC8A1,missense_variant,p.Ser707Arg,ENST00000406785,;SLC8A1,missense_variant,p.Ser743Arg,ENST00000403092,;SLC8A1,missense_variant,p.Ser738Arg,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Ser707Arg,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Ser707Arg,ENST00000405269,;SLC8A1,missense_variant,p.Ser743Arg,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Ser735Arg,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Ser707Arg,ENST00000406391,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000625324,;SLC8A1-AS1,intron_variant,,ENST00000593848,;SLC8A1-AS1,intron_variant,,ENST00000625780,;SLC8A1-AS1,intron_variant,,ENST00000598247,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000625234,;SLC8A1-AS1,intron_variant,,ENST00000631022,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000631142,;SLC8A1-AS1,intron_variant,,ENST00000628471,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000435515,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000627219,;SLC8A1-AS1,intron_variant,,ENST00000629329,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000629180,;SLC8A1-AS1,intron_variant,,ENST00000629157,;SLC8A1-AS1,intron_variant,,ENST00000631204,;SLC8A1-AS1,intron_variant,,ENST00000630783,;SLC8A1-AS1,intron_variant,,ENST00000625381,;SLC8A1-AS1,intron_variant,,ENST00000631137,;SLC8A1-AS1,intron_variant,,ENST00000627108,;SLC8A1-AS1,intron_variant,,ENST00000626098,;SLC8A1-AS1,intron_variant,,ENST00000631330,;SLC8A1-AS1,intron_variant,,ENST00000630006,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1,3_prime_UTR_variant,,ENST00000407929,; C ENST00000403092 Transcript missense_variant 2263/3178 2229/2922 743/973 S/R agC/agG 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 deleterious(0) 9/11 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 40160805 40160805 G C 1 0 0 0 0 1 0 0 0 14989 962 34 4 4 SLC8A1 2 40160805 Missense_Mutation SNP G C3L-00279_T 10002024 40160805 202032724 80 5858 BCL11A 0 . GRCh38 2 60460802 60460802 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2110G>T p.Gly704Trp p.G704W ENST00000335712 4/4 279 243 36 272 271 1 strelka-varscan BCL11A,missense_variant,p.Gly704Trp,ENST00000335712,NM_022893.3;BCL11A,missense_variant,p.Gly704Trp,ENST00000356842,NM_018014.3;BCL11A,missense_variant,p.Gly670Trp,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,3_prime_UTR_variant,,ENST00000631857,; A ENST00000335712 Transcript missense_variant 2338/5942 2110/2508 704/835 G/W Ggg/Tgg 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 deleterious(0) 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 60460802 60460802 C A 1 0 0 0 0 1 0 0 0 1510 652 23 1 1 BCL11A 2 60460802 Missense_Mutation SNP C C3L-00279_T 20299997 60460802 181732727 81 5859 PLEK 0 . GRCh38 2 68386607 68386607 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.578C>T p.Ala193Val p.A193V ENST00000234313 5/9 218 197 21 217 216 1 strelka-varscan PLEK,missense_variant,p.Ala193Val,ENST00000234313,NM_002664.2;PLEK,upstream_gene_variant,,ENST00000474788,; T ENST00000234313 Transcript missense_variant 757/2869 578/1053 193/350 A/V gCt/gTt 1 1 PLEK HGNC HGNC:9070 protein_coding YES CCDS1887.1 ENSP00000234313 P08567 UPI00002085C1 NM_002664.2 tolerated(1) 5/9 PROSITE_profiles:PS50186,hmmpanther:PTHR12092,hmmpanther:PTHR12092:SF1,Gene3D:1.10.10.10,Pfam_domain:PF00610,SMART_domains:SM00049,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 68386607 68386607 C T 1 0 0 0 0 1 0 0 0 12146 797 28 3 3 PLEK 2 68386607 Missense_Mutation SNP C C3L-00279_T 7925805 68386607 173806922 82 5860 FIGLA 0 . GRCh38 2 70787782 70787782 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.251G>T p.Gly84Val p.G84V ENST00000332372 2/5 284 254 30 233 233 0 strelka-varscan FIGLA,missense_variant,p.Gly84Val,ENST00000332372,NM_001004311.3; A ENST00000332372 Transcript missense_variant 256/722 251/660 84/219 G/V gGt/gTt 1 -1 FIGLA HGNC HGNC:24669 protein_coding YES CCDS46320.1 ENSP00000333097 Q6QHK4 UPI000041902B NM_001004311.3 deleterious(0.01) 2/5 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF57,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 70787782 70787782 C A 1 0 0 0 0 1 0 0 0 5754 507 18 2 2 FIGLA 2 70787782 Missense_Mutation SNP C C3L-00279_T 2401175 70787782 171405747 83 5861 24 2 FIGLA 0 . GRCh38 2 70787785 70787785 + Missense_Mutation SNP C C A rs199702150 C3L-00279_T C3L-00279_N C C c.248G>T p.Arg83Leu p.R83L ENST00000332372 2/5 276 246 30 231 231 0 strelka-varscan FIGLA,missense_variant,p.Arg83Leu,ENST00000332372,NM_001004311.3; A ENST00000332372 Transcript missense_variant 253/722 248/660 83/219 R/L cGt/cTt rs199702150 1 -1 FIGLA HGNC HGNC:24669 protein_coding YES CCDS46320.1 ENSP00000333097 Q6QHK4 UPI000041902B NM_001004311.3 deleterious(0.02) 2/5 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF57,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 70787785 70787785 C A 1 0 0 0 0 1 0 0 0 5754 536 19 1 1 FIGLA 2 70787785 Missense_Mutation SNP C C3L-00279_T 3 70787785 171405744 84 5862 24 2 ALMS1 0 . GRCh38 2 73572932 73572932 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.11055C>A p.Ser3685Arg p.S3685R ENST00000613296 16/23 328 289 39 205 204 1 strelka-varscan ALMS1,missense_variant,p.Ser3685Arg,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Ser3643Arg,ENST00000484298,;ALMS1,missense_variant,p.Ser3685Arg,ENST00000614410,;ALMS1,3_prime_UTR_variant,,ENST00000423048,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,; A ENST00000613296 Transcript missense_variant 11166/12925 11055/12507 3685/4168 S/R agC/agA 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 tolerated(0.36) 16/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 73572932 73572932 C A 1 0 0 0 0 1 0 0 0 635 738 26 2 2 ALMS1 2 73572932 Missense_Mutation SNP C C3L-00279_T 2785147 73572932 168620597 85 5863 SEMA4F 0 . GRCh38 2 74656585 74656585 + Missense_Mutation SNP C C G C3L-00279_T C3L-00279_N C C c.197C>G p.Ser66Cys p.S66C ENST00000357877 2/14 185 157 28 136 136 0 strelka-varscan SEMA4F,missense_variant,p.Ser66Cys,ENST00000611975,NM_001271662.1;SEMA4F,missense_variant,p.Ser66Cys,ENST00000357877,NM_004263.4;SEMA4F,missense_variant,p.Ser66Cys,ENST00000339773,NM_001271661.1;SEMA4F,missense_variant,p.Ser66Cys,ENST00000453930,;SEMA4F,missense_variant,p.Ser66Cys,ENST00000434486,;SEMA4F,missense_variant,p.Ser66Cys,ENST00000446927,;SEMA4F,missense_variant,p.Ser66Cys,ENST00000420077,;SEMA4F,3_prime_UTR_variant,,ENST00000416236,;SEMA4F,intron_variant,,ENST00000458114,; G ENST00000357877 Transcript missense_variant 346/4312 197/2313 66/770 S/C tCt/tGt COSM4923953 1 1 SEMA4F HGNC HGNC:10734 protein_coding YES CCDS1955.1 ENSP00000350547 O95754 UPI0000001BF5 NM_004263.4 deleterious(0) 2/14 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF72,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 74656585 74656585 C G 1 0 0 0 0 1 0 0 0 14311 913 32 4 4 SEMA4F 2 74656585 Missense_Mutation SNP C C3L-00279_T 1083653 74656585 167536944 86 5864 DUSP2 0 . GRCh38 2 96144333 96144333 + Missense_Mutation SNP C C A rs369325506 C3L-00279_T C3L-00279_N C C c.551G>T p.Ser184Ile p.S184I ENST00000288943 3/4 280 234 46 231 231 0 strelka-varscan DUSP2,missense_variant,p.Ser184Ile,ENST00000288943,NM_004418.3;AC012307.2,downstream_gene_variant,,ENST00000449242,;DUSP2,non_coding_transcript_exon_variant,,ENST00000488952,; A ENST00000288943 Transcript missense_variant 637/1688 551/945 184/314 S/I aGc/aTc rs369325506 1 -1 DUSP2 HGNC HGNC:3068 protein_coding YES CCDS2016.1 ENSP00000288943 Q05923 UPI000012995D NM_004418.3 deleterious(0) 3/4 Gene3D:3.90.190.10,Pfam_domain:PF00782,PIRSF_domain:PIRSF000939,PROSITE_profiles:PS50054,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF109,SMART_domains:SM00195,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 96144333 96144333 C A 1 0 0 0 0 1 0 0 0 4641 797 28 2 2 DUSP2 2 96144333 Missense_Mutation SNP C C3L-00279_T 21487748 96144333 146049196 87 5865 AFF3 0 . GRCh38 2 99593290 99593290 + Missense_Mutation SNP C C A rs200976815 C3L-00279_T C3L-00279_N C C c.2446G>T p.Ala816Ser p.A816S ENST00000409579 15/25 176 151 25 118 118 0 strelka-varscan AFF3,missense_variant,p.Ala791Ser,ENST00000409236,;AFF3,missense_variant,p.Ala791Ser,ENST00000317233,NM_002285.2;AFF3,missense_variant,p.Ala816Ser,ENST00000409579,NM_001025108.1; A ENST00000409579 Transcript missense_variant 2679/4342 2446/3756 816/1251 A/S Gcc/Tcc rs200976815 1 -1 AFF3 HGNC HGNC:6473 protein_coding YES CCDS33258.1 ENSP00000386834 P51826 UPI0000545269 NM_001025108.1 tolerated(0.32) 15/25 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999979 1 1 1 0 A 3 1 14 99593290 99593290 C A 1 0 0 0 0 1 0 0 0 435 768 27 1 1 AFF3 2 99593290 Missense_Mutation SNP C C3L-00279_T 3448957 99593290 142600239 88 5866 SLC9A2 0 . GRCh38 2 102657562 102657562 + Splice_Site SNP A A T novel C3L-00279_T C3L-00279_N A A c.290-2A>T p.X97_splice ENST00000233969 96 79 17 57 57 0 strelka-varscan SLC9A2,splice_acceptor_variant,,ENST00000233969,NM_003048.4; T ENST00000233969 Transcript splice_acceptor_variant -/5410 290/2439 97/812 1 1 SLC9A2 HGNC HGNC:11072 protein_coding YES CCDS2062.1 ENSP00000233969 Q9UBY0 UPI000012FD21 NM_003048.4 1/11 HIGH 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999878 1 1 1 0 T 5 4 14 102657562 102657562 A T 1 0 0 0 0 0 0 1 0 14994 202 7 4 4 SLC9A2 2 102657562 Splice_Site SNP A C3L-00279_T 3064272 102657562 139535967 89 5867 ZC3H6 0 . GRCh38 2 112331346 112331346 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2428G>T p.Ala810Ser p.A810S ENST00000409871 12/12 239 213 26 165 164 1 strelka-varscan ZC3H6,missense_variant,p.Ala810Ser,ENST00000409871,NM_198581.2;ZC3H6,missense_variant,p.Ala810Ser,ENST00000343936,;ZC3H6,upstream_gene_variant,,ENST00000502881,; T ENST00000409871 Transcript missense_variant 2829/11542 2428/3570 810/1189 A/S Gca/Tca 1 1 ZC3H6 HGNC HGNC:24762 protein_coding YES CCDS46393.1 ENSP00000386764 P61129 UPI00004215E8 NM_198581.2 tolerated(0.99) 12/12 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF22 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 112331346 112331346 G T 1 0 0 0 0 1 0 0 0 18146 1319 46 2 2 ZC3H6 2 112331346 Missense_Mutation SNP G C3L-00279_T 9673784 112331346 129862183 90 5868 CNTNAP5 0 . GRCh38 2 124747248 124747248 + Nonsense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.2094G>A p.Trp698Ter p.W698* ENST00000431078 14/24 203 166 37 185 185 0 strelka-varscan CNTNAP5,stop_gained,p.Trp698Ter,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript stop_gained 2458/5284 2094/3921 698/1306 W/* tgG/tgA 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 14/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 124747248 124747248 G A 1 0 0 0 0 0 1 0 0 3432 1270 44 3 3 CNTNAP5 2 124747248 Nonsense_Mutation SNP G C3L-00279_T 12415902 124747248 117446281 91 5869 GPR148 0 . GRCh38 2 130729158 130729158 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.7G>T p.Asp3Tyr p.D3Y ENST00000309926 1/1 18 11 7 14 14 0 strelka-varscan GPR148,missense_variant,p.Asp3Tyr,ENST00000309926,NM_207364.2; T ENST00000309926 Transcript missense_variant 89/1267 7/1044 3/347 D/Y Gat/Tat 1 1 GPR148 HGNC HGNC:23623 protein_coding YES CCDS2163.1 ENSP00000308908 Q8TDV2 UPI0000048E0D NM_207364.2 deleterious(0.05) 1/1 MODERATE 1 SNV 1 PASS . . 10 199 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 130729158 130729158 G T 1 0 0 0 0 1 0 0 0 6539 1174 41 2 2 GPR148 2 130729158 Missense_Mutation SNP G C3L-00279_T 5981910 130729158 111464371 92 5870 MAP3K19 0 . GRCh38 2 134980949 134980949 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3792G>T p.Lys1264Asn p.K1264N ENST00000392915 12/13 459 400 59 366 364 2 strelka-varscan MAP3K19,missense_variant,p.Lys1264Asn,ENST00000392915,;MAP3K19,missense_variant,p.Lys1264Asn,ENST00000375845,NM_025052.4;MAP3K19,missense_variant,p.Lys1151Asn,ENST00000358371,NM_001018044.2;MAP3K19,missense_variant,p.Lys654Asn,ENST00000437365,;MAP3K19,missense_variant,p.Lys396Asn,ENST00000392917,NM_001282883.1;MAP3K19,missense_variant,p.Lys446Asn,ENST00000375844,NM_001018046.2;MAP3K19,missense_variant,p.Lys398Asn,ENST00000392918,NM_001018047.2;MAP3K19,downstream_gene_variant,,ENST00000637841,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000478805,; A ENST00000392915 Transcript missense_variant 4476/5030 3792/3987 1264/1328 K/N aaG/aaT 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 deleterious(0) 12/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 134980949 134980949 C A 1 0 0 0 0 1 0 0 0 9172 796 28 2 2 MAP3K19 2 134980949 Missense_Mutation SNP C C3L-00279_T 4251791 134980949 107212580 93 5871 LRP1B 0 . GRCh38 2 140907957 140907957 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.3440C>T p.Thr1147Ile p.T1147I ENST00000389484 22/91 340 302 38 232 230 2 strelka-varscan LRP1B,missense_variant,p.Thr1147Ile,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Thr292Ile,ENST00000434794,; A ENST00000389484 Transcript missense_variant 4412/16535 3440/13800 1147/4599 T/I aCc/aTc COSM370021 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 22/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF105,hmmpanther:PTHR10529,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 140907957 140907957 G A 1 0 0 0 0 1 0 0 0 8850 1261 44 3 3 LRP1B 2 140907957 Missense_Mutation SNP G C3L-00279_T 5927008 140907957 101285572 94 5872 LY75 0 . GRCh38 2 159840857 159840857 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.3379G>C p.Ala1127Pro p.A1127P ENST00000263636 25/35 556 481 75 430 430 0 strelka-varscan LY75,missense_variant,p.Ala1127Pro,ENST00000263636,NM_002349.3;LY75-CD302,missense_variant,p.Ala1127Pro,ENST00000504764,NM_001198759.1;LY75-CD302,missense_variant,p.Ala1127Pro,ENST00000505052,NM_001198760.1; G ENST00000263636 Transcript missense_variant 3407/6886 3379/5169 1127/1722 A/P Gct/Cct 1 -1 LY75 HGNC HGNC:6729 protein_coding YES CCDS2211.1 ENSP00000263636 O60449 UPI00001AE885 NM_002349.3 deleterious(0) 25/35 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF65,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 159840857 159840857 C G 1 0 0 0 0 1 0 0 0 9010 710 25 4 4 LY75 2 159840857 Missense_Mutation SNP C C3L-00279_T 18932900 159840857 82352672 95 5873 SLC4A10 0 . GRCh38 2 161957033 161957033 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2586G>T p.Met862Ile p.M862I ENST00000446997 20/27 331 277 54 284 284 0 strelka-varscan SLC4A10,missense_variant,p.Met843Ile,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Met832Ile,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Met862Ile,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Met832Ile,ENST00000272716,;SLC4A10,missense_variant,p.Met862Ile,ENST00000421911,;SLC4A10,3_prime_UTR_variant,,ENST00000446228,; T ENST00000446997 Transcript missense_variant 2679/5551 2586/3357 862/1118 M/I atG/atT 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 deleterious(0.03) 20/27 Transmembrane_helices:TMhelix,hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 161957033 161957033 G T 1 0 0 0 0 1 0 0 0 14928 1319 46 2 2 SLC4A10 2 161957033 Missense_Mutation SNP G C3L-00279_T 2116176 161957033 80236496 96 5874 XIRP2 0 . GRCh38 2 166903634 166903634 + Missense_Mutation SNP T T A rs775164919 C3L-00279_T C3L-00279_N T T c.152T>A p.Val51Glu p.V51E ENST00000409195 2/11 345 301 44 279 279 0 strelka-varscan XIRP2,missense_variant,p.Val51Glu,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Val51Glu,ENST00000409728,NM_001199143.1;XIRP2,missense_variant,p.Val51Glu,ENST00000409043,NM_001079810.3; A ENST00000409195 Transcript missense_variant 241/12675 152/10650 51/3549 V/E gTa/gAa rs775164919 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious_low_confidence(0.04) 2/11 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 166903634 166903634 T A 1 0 0 0 0 1 0 0 0 17989 1638 57 4 4 XIRP2 2 166903634 Missense_Mutation SNP T C3L-00279_T 4946601 166903634 75289895 97 5875 XIRP2 0 . GRCh38 2 167244780 167244780 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3388C>A p.Leu1130Ile p.L1130I ENST00000409195 9/11 179 152 27 55 55 0 strelka-varscan XIRP2,missense_variant,p.Leu1130Ile,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Leu908Ile,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Leu955Ile,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 3477/12675 3388/10650 1130/3549 L/I Ctc/Atc 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.01) 9/11 Pfam_domain:PF08043,PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 167244780 167244780 C A 1 0 0 0 0 1 0 0 0 17989 797 28 2 2 XIRP2 2 167244780 Missense_Mutation SNP C C3L-00279_T 341146 167244780 74948749 98 5876 NOSTRIN 0 . GRCh38 2 168843078 168843078 + Silent SNP C C G novel C3L-00279_T C3L-00279_N C C c.591C>G p.= p.T197T ENST00000444448 10/19 97 86 11 41 41 0 strelka-varscan NOSTRIN,synonymous_variant,p.=,ENST00000444448,;NOSTRIN,synonymous_variant,p.=,ENST00000458381,NM_001171631.1;NOSTRIN,synonymous_variant,p.=,ENST00000317647,NM_001039724.3;NOSTRIN,synonymous_variant,p.=,ENST00000445023,NM_052946.3;NOSTRIN,synonymous_variant,p.=,ENST00000397206,;NOSTRIN,synonymous_variant,p.=,ENST00000397209,NM_001171632.1;NOSTRIN,synonymous_variant,p.=,ENST00000447264,;SPC25,intron_variant,,ENST00000479309,;NOSTRIN,non_coding_transcript_exon_variant,,ENST00000486873,; G ENST00000444448 Transcript synonymous_variant 1067/2537 591/1692 197/563 T acC/acG 1 1 NOSTRIN HGNC HGNC:20203 protein_coding YES CCDS54415.1 ENSP00000394051 Q8IVI9 UPI00001400FD 10/19 PROSITE_profiles:PS51741,hmmpanther:PTHR14167,Superfamily_domains:SSF103657 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 168843078 168843078 C G 1 0 0 0 0 0 0 0 1 10591 581 21 4 4 NOSTRIN 2 168843078 Silent SNP C C3L-00279_T 1598298 168843078 73350451 99 5877 FASTKD1 0 . GRCh38 2 169540130 169540130 + Silent SNP T T C novel C3L-00279_T C3L-00279_N T T c.1866A>G p.= p.T622T ENST00000453153 10/15 91 79 12 33 33 0 strelka-varscan FASTKD1,synonymous_variant,p.=,ENST00000453153,NM_024622.4;FASTKD1,synonymous_variant,p.=,ENST00000453929,NM_001281476.1;FASTKD1,upstream_gene_variant,,ENST00000495505,;FASTKD1,upstream_gene_variant,,ENST00000490590,;FASTKD1,upstream_gene_variant,,ENST00000488516,; C ENST00000453153 Transcript synonymous_variant 2213/2967 1866/2544 622/847 T acA/acG 1 -1 FASTKD1 HGNC HGNC:26150 protein_coding YES CCDS33318.1 ENSP00000400513 Q53R41 UPI000050BC4D NM_024622.4 10/15 hmmpanther:PTHR21228:SF29,hmmpanther:PTHR21228,Pfam_domain:PF06743 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 14 169540130 169540130 T C 1 0 0 0 0 0 0 0 1 5545 1683 59 5 5 FASTKD1 2 169540130 Silent SNP T C3L-00279_T 697052 169540130 72653399 100 5878 DCAF17 0 . GRCh38 2 171468960 171468960 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.911A>G p.Tyr304Cys p.Y304C ENST00000375255 9/14 554 482 72 327 327 0 strelka-varscan DCAF17,missense_variant,p.Tyr304Cys,ENST00000375255,NM_025000.3;DCAF17,missense_variant,p.Tyr304Cys,ENST00000539783,NM_001164821.1;DCAF17,missense_variant,p.Tyr24Cys,ENST00000611110,;DCAF17,missense_variant,p.Tyr55Cys,ENST00000339506,;DCAF17,upstream_gene_variant,,ENST00000431110,;DCAF17,non_coding_transcript_exon_variant,,ENST00000468592,;DCAF17,upstream_gene_variant,,ENST00000493106,; G ENST00000375255 Transcript missense_variant 1238/5828 911/1563 304/520 Y/C tAc/tGc 1 1 DCAF17 HGNC HGNC:25784 protein_coding YES CCDS2243.2 ENSP00000364404 Q5H9S7 UPI00004C429A NM_025000.3 deleterious(0.01) 9/14 hmmpanther:PTHR14815,Pfam_domain:PF15802 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 171468960 171468960 A G 1 0 0 0 0 1 0 0 0 4070 391 14 5 5 DCAF17 2 171468960 Missense_Mutation SNP A C3L-00279_T 1928830 171468960 70724569 101 5879 RAPGEF4 0 . GRCh38 2 172988765 172988765 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1300G>T p.Ala434Ser p.A434S ENST00000397081 14/31 281 246 35 217 217 0 strelka-varscan RAPGEF4,missense_variant,p.Ala434Ser,ENST00000397081,NM_007023.3;RAPGEF4,missense_variant,p.Ala290Ser,ENST00000397087,NM_001100397.1;RAPGEF4,missense_variant,p.Ala434Ser,ENST00000409036,;RAPGEF4,missense_variant,p.Ala281Ser,ENST00000540783,NM_001282899.1;RAPGEF4,missense_variant,p.Ala263Ser,ENST00000538974,NM_001282900.1;RAPGEF4,missense_variant,p.Ala214Ser,ENST00000535187,NM_001282901.1;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000473043,;RAPGEF4,downstream_gene_variant,,ENST00000459852,; T ENST00000397081 Transcript missense_variant 1443/4299 1300/3036 434/1011 A/S Gcc/Tcc 1 1 RAPGEF4 HGNC HGNC:16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 UPI000006D4C7 NM_007023.3 deleterious(0) 14/31 Gene3D:2.60.120.10,Pfam_domain:PF00027,Prints_domain:PR00103,PROSITE_profiles:PS50042,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 172988765 172988765 G T 1 0 0 0 0 1 0 0 0 13205 1319 46 2 2 RAPGEF4 2 172988765 Missense_Mutation SNP G C3L-00279_T 1519805 172988765 69204764 102 5880 HOXD13 0 . GRCh38 2 176093635 176093635 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.745C>A p.Pro249Thr p.P249T ENST00000392539 1/2 100 83 17 71 71 0 strelka-varscan HOXD13,missense_variant,p.Pro249Thr,ENST00000392539,NM_000523.3; A ENST00000392539 Transcript missense_variant 745/2240 745/1032 249/343 P/T Cca/Aca 1 1 HOXD13 HGNC HGNC:5136 protein_coding YES CCDS2264.2 ENSP00000376322 P35453 UPI000020912A NM_000523.3 tolerated(1) 1/2 hmmpanther:PTHR24326:SF182,hmmpanther:PTHR24326 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 176093635 176093635 C A 1 0 0 0 0 1 0 0 0 7216 739 26 2 2 HOXD13 2 176093635 Missense_Mutation SNP C C3L-00279_T 3104870 176093635 66099894 103 5881 TTN 0 . GRCh38 2 178593862 178593862 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.58438C>A p.Pro19480Thr p.P19480T ENST00000589042 298/363 296 256 40 201 201 0 strelka-varscan TTN,missense_variant,p.Pro19480Thr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro17839Thr,ENST00000591111,;TTN,missense_variant,p.Pro17839Thr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro16912Thr,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Pro10415Thr,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Pro10607Thr,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Pro10540Thr,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000629117,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000626517,;TTN-AS1,downstream_gene_variant,,ENST00000590743,;TTN-AS1,upstream_gene_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 58663/109224 58438/107976 19480/35991 P/T Cct/Act 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 298/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 178593862 178593862 G T 1 0 0 0 0 1 0 0 0 17245 1188 41 2 2 TTN 2 178593862 Missense_Mutation SNP G C3L-00279_T 2500227 178593862 63599667 104 5882 TTN 0 . GRCh38 2 178605162 178605162 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.54015T>C p.= p.T18005T ENST00000589042 280/363 217 189 28 142 142 0 strelka-varscan TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000586452,;TTN-AS1,upstream_gene_variant,,ENST00000627527,;TTN-AS1,downstream_gene_variant,,ENST00000626517,; G ENST00000589042 Transcript synonymous_variant 54240/109224 54015/107976 18005/35991 T acT/acC 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 280/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999914 1 1 1 0 G 2 3 14 178605162 178605162 A G 1 0 0 0 0 0 0 0 1 17245 175 7 5 5 TTN 2 178605162 Silent SNP A C3L-00279_T 11300 178605162 63588367 105 5883 TTN 0 . GRCh38 2 178612080 178612080 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.50331T>A p.Asn16777Lys p.N16777K ENST00000589042 267/363 232 202 30 219 218 1 strelka-varscan TTN,missense_variant,p.Asn16777Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Asn15136Lys,ENST00000591111,;TTN,missense_variant,p.Asn15136Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Asn14209Lys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Asn7712Lys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Asn7904Lys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Asn7837Lys,ENST00000359218,NM_133432.3;RP11-171I2.4,upstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000627527,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 50556/109224 50331/107976 16777/35991 N/K aaT/aaA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 267/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 178612080 178612080 A T 1 0 0 0 0 1 0 0 0 17245 214 8 4 4 TTN 2 178612080 Missense_Mutation SNP A C3L-00279_T 6918 178612080 63581449 106 5884 TTN 0 . GRCh38 2 178684347 178684347 + Missense_Mutation SNP G G C rs778076110 C3L-00279_T C3L-00279_N G G c.32705C>G p.Ala10902Gly p.A10902G ENST00000589042 132/363 183 165 18 86 86 0 strelka-varscan TTN,missense_variant,p.Ala10902Gly,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ala10585Gly,ENST00000591111,;TTN,missense_variant,p.Ala10585Gly,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ala9658Gly,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; C ENST00000589042 Transcript missense_variant 32930/109224 32705/107976 10902/35991 A/G gCg/gGg rs778076110,COSM4088702,COSM4088703 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 132/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 not_provided 0,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 207 0 3 0 0 0 0 -19.99998 0.9999849 1 1 1 0 C 3 2 14 178684347 178684347 G C 1 0 0 0 0 1 0 0 0 17245 1087 38 4 4 TTN 2 178684347 Missense_Mutation SNP G C3L-00279_T 72267 178684347 63509182 107 5885 FSIP2 0 . GRCh38 2 185789530 185789530 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.2661A>G p.= p.T887T ENST00000343098 16/23 220 186 34 61 61 0 strelka-varscan FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,; G ENST00000343098 Transcript synonymous_variant 2661/21054 2661/20991 887/6996 T acA/acG 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 185789530 185789530 A G 1 0 0 0 0 0 0 0 1 5949 204 8 5 5 FSIP2 2 185789530 Silent SNP A C3L-00279_T 7105183 185789530 56403999 108 5886 COL3A1 0 . GRCh38 2 188997219 188997219 + Splice_Site SNP G G C novel C3L-00279_T C3L-00279_N G G c.1815+1G>C p.X605_splice ENST00000304636 575 517 58 460 460 0 strelka-varscan COL3A1,splice_donor_variant,,ENST00000304636,NM_000090.3;COL3A1,splice_donor_variant,,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000450867,;COL3A1,downstream_gene_variant,,ENST00000637672,; C ENST00000304636 Transcript splice_donor_variant -/5543 1815/4401 605/1466 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 25/50 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 14 188997219 188997219 G C 1 0 0 0 0 0 0 1 0 3477 1275 44 4 4 COL3A1 2 188997219 Splice_Site SNP G C3L-00279_T 3207689 188997219 53196310 109 5887 COL3A1 0 . GRCh38 2 188999333 188999333 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2071G>T p.Ala691Ser p.A691S ENST00000304636 30/51 533 468 65 452 452 0 strelka-varscan COL3A1,missense_variant,p.Ala691Ser,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Ala691Ser,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000637672,;COL3A1,upstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript missense_variant 2241/5543 2071/4401 691/1466 A/S Gcc/Tcc 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 tolerated(0.54) 30/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 188999333 188999333 G T 1 0 0 0 0 1 0 0 0 3477 1203 42 2 2 COL3A1 2 188999333 Missense_Mutation SNP G C3L-00279_T 2114 188999333 53194196 110 5888 PLCL1 0 . GRCh38 2 198089029 198089029 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2887G>T p.Val963Leu p.V963L ENST00000428675 3/6 375 334 41 335 335 0 strelka-varscan PLCL1,missense_variant,p.Val886Leu,ENST00000437704,;PLCL1,missense_variant,p.Val963Leu,ENST00000428675,NM_006226.3;PLCL1,missense_variant,p.Val889Leu,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript missense_variant 3285/5125 2887/3288 963/1095 V/L Gtg/Ttg 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 tolerated(0.47) 3/6 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 198089029 198089029 G T 1 0 0 0 0 1 0 0 0 12133 1377 48 2 2 PLCL1 2 198089029 Missense_Mutation SNP G C3L-00279_T 9089696 198089029 44104500 111 5889 MAP2 0 . GRCh38 2 209730211 209730211 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.5298G>C p.Glu1766Asp p.E1766D ENST00000360351 15/15 263 220 43 262 262 0 strelka-varscan MAP2,missense_variant,p.Glu1766Asp,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Glu1762Asp,ENST00000447185,;MAP2,missense_variant,p.Glu410Asp,ENST00000392194,NM_031845.2;MAP2,missense_variant,p.Glu498Asp,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,missense_variant,p.Glu410Asp,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,; C ENST00000360351 Transcript missense_variant 5804/9711 5298/5484 1766/1827 E/D gaG/gaC 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 tolerated(0.12) 15/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 209730211 209730211 G C 1 0 0 0 0 1 0 0 0 9157 962 34 4 4 MAP2 2 209730211 Missense_Mutation SNP G C3L-00279_T 11641182 209730211 32463318 112 5890 UNC80 0 . GRCh38 2 209973234 209973234 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.8353G>T p.Gly2785Trp p.G2785W ENST00000439458 55/64 195 170 25 168 168 0 strelka-varscan UNC80,missense_variant,p.Gly2785Trp,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Gly2780Trp,ENST00000272845,NM_182587.3;UNC80,missense_variant,p.Gly311Trp,ENST00000333907,;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,;UNC80,downstream_gene_variant,,ENST00000489023,; T ENST00000439458 Transcript missense_variant 8433/13562 8353/9777 2785/3258 G/W Ggg/Tgg 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0) 55/64 hmmpanther:PTHR31781:SF1,hmmpanther:PTHR31781 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 209973234 209973234 G T 1 0 0 0 0 1 0 0 0 17521 1000 35 2 2 UNC80 2 209973234 Missense_Mutation SNP G C3L-00279_T 243023 209973234 32220295 113 5891 SPEG 0 . GRCh38 2 219435268 219435268 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.291C>A p.= p.R97R ENST00000312358 1/41 138 113 25 148 148 0 strelka-varscan SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000498378,; A ENST00000312358 Transcript synonymous_variant 423/10782 291/9804 97/3267 R cgC/cgA 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 1/41 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 219435268 219435268 C A 1 0 0 0 0 0 0 0 1 15387 784 28 2 2 SPEG 2 219435268 Silent SNP C C3L-00279_T 9462034 219435268 22758261 114 5892 SPEG 0 . GRCh38 2 219483160 219483160 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.5697C>T p.= p.A1899A ENST00000312358 30/41 250 200 50 218 218 0 strelka-varscan SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript synonymous_variant 5829/10782 5697/9804 1899/3267 A gcC/gcT 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 219483160 219483160 C T 1 0 0 0 0 0 0 0 1 15387 610 22 3 3 SPEG 2 219483160 Silent SNP C C3L-00279_T 47892 219483160 22710369 115 5893 COL4A4 0 . GRCh38 2 227059469 227059469 + Missense_Mutation SNP C C A rs200920187 C3L-00279_T C3L-00279_N C C c.2319G>T p.Arg773Ser p.R773S ENST00000396625 28/48 569 502 67 506 506 0 strelka-varscan-mutect COL4A4,missense_variant,p.Arg773Ser,ENST00000396625,NM_000092.4; A ENST00000396625 Transcript missense_variant 2527/9895 2319/5073 773/1690 R/S agG/agT rs200920187 1 -1 COL4A4 HGNC HGNC:2206 protein_coding YES CCDS42828.1 ENSP00000379866 P53420 UPI000013D987 NM_000092.4 tolerated(0.07) 28/48 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF533 MODERATE 1 SNV 5 1 PASS rs200920187 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 227059469 227059469 C A 1 0 0 0 0 1 0 0 0 3482 622 22 2 2 COL4A4 2 227059469 Missense_Mutation SNP C C3L-00279_T 7576309 227059469 15134060 116 5894 COL6A3 0 . GRCh38 2 237387884 237387884 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.1010C>T p.Ala337Val p.A337V ENST00000295550 4/44 295 259 36 217 217 0 strelka-varscan-mutect COL6A3,missense_variant,p.Ala337Val,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Ala131Val,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Ala131Val,ENST00000409809,;COL6A3,missense_variant,p.Ala131Val,ENST00000392004,NM_057165.4;COL6A3,missense_variant,p.Ala337Val,ENST00000433762,;COL6A3,missense_variant,p.Ala65Val,ENST00000491233,;COL6A3,intron_variant,,ENST00000472056,NM_057166.4;COL6A3,intron_variant,,ENST00000347401,;COL6A3,intron_variant,,ENST00000392003,NM_057164.4; A ENST00000295550 Transcript missense_variant 1463/10749 1010/9534 337/3177 A/V gCa/gTa 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 tolerated(0.05) 4/44 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 237387884 237387884 G A 1 0 0 0 0 1 0 0 0 3490 1319 46 3 3 COL6A3 2 237387884 Missense_Mutation SNP G C3L-00279_T 10328415 237387884 4805645 117 5895 NDUFA10 0 . GRCh38 2 240018536 240018536 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.564G>T p.Gln188His p.Q188H ENST00000307300 4/11 562 505 57 456 455 1 strelka-varscan-mutect NDUFA10,missense_variant,p.Gln188His,ENST00000307300,;NDUFA10,missense_variant,p.Gln188His,ENST00000407129,;NDUFA10,intron_variant,,ENST00000252711,NM_004544.3;NDUFA10,intron_variant,,ENST00000404554,;NDUFA10,intron_variant,,ENST00000620965,;NDUFA10,intron_variant,,ENST00000443626,;NDUFA10,intron_variant,,ENST00000485344,;NDUFA10,intron_variant,,ENST00000414580,;NDUFA10,downstream_gene_variant,,ENST00000497536,; A ENST00000307300 Transcript missense_variant 587/1313 564/1290 188/429 Q/H caG/caT 1 -1 NDUFA10 HGNC HGNC:7684 protein_coding ENSP00000302321 O95299 UPI000006FC2B deleterious_low_confidence(0.01) 4/11 Gene3D:3.40.50.300 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 240018536 240018536 C A 1 0 0 0 0 1 0 0 0 10281 912 32 2 2 NDUFA10 2 240018536 Missense_Mutation SNP C C3L-00279_T 2630652 240018536 2174993 118 5896 AGXT 0 . GRCh38 2 240870653 240870653 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.368T>A p.Val123Glu p.V123E ENST00000307503 3/11 276 238 38 268 268 0 strelka-varscan-mutect AGXT,missense_variant,p.Val123Glu,ENST00000307503,NM_000030.2;AGXT,non_coding_transcript_exon_variant,,ENST00000472436,;AGXT,upstream_gene_variant,,ENST00000476698,; A ENST00000307503 Transcript missense_variant 755/1865 368/1179 123/392 V/E gTg/gAg 1 1 AGXT HGNC HGNC:341 protein_coding YES CCDS2543.1 ENSP00000302620 P21549 UPI0000135E9B NM_000030.2 deleterious(0) 3/11 Gene3D:3.40.640.10,Pfam_domain:PF00266,PIRSF_domain:PIRSF000524,hmmpanther:PTHR21152,hmmpanther:PTHR21152:SF22,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs1311612079 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 240870653 240870653 T A 1 0 0 0 0 1 0 0 0 483 1696 59 4 4 AGXT 2 240870653 Missense_Mutation SNP T C3L-00279_T 852117 240870653 1322876 119 5897 ATG4B 0 . GRCh38 2 241654549 241654549 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.287G>T p.Trp96Leu p.W96L ENST00000404914 5/13 209 181 28 183 183 0 strelka-mutect ATG4B,missense_variant,p.Trp96Leu,ENST00000405546,NM_178326.2;ATG4B,missense_variant,p.Trp96Leu,ENST00000404914,NM_013325.4;ATG4B,missense_variant,p.Trp22Leu,ENST00000402096,;ATG4B,missense_variant,p.Trp96Leu,ENST00000425239,;ATG4B,missense_variant,p.Trp96Leu,ENST00000400771,;ATG4B,missense_variant,p.Trp22Leu,ENST00000430617,;ATG4B,missense_variant,p.Trp22Leu,ENST00000419606,;ATG4B,missense_variant,p.Trp22Leu,ENST00000429899,;ATG4B,downstream_gene_variant,,ENST00000625810,;ATG4B,downstream_gene_variant,,ENST00000491867,;ATG4B,3_prime_UTR_variant,,ENST00000344376,;ATG4B,3_prime_UTR_variant,,ENST00000400772,;ATG4B,non_coding_transcript_exon_variant,,ENST00000482507,;ATG4B,non_coding_transcript_exon_variant,,ENST00000494465,;ATG4B,non_coding_transcript_exon_variant,,ENST00000483778,;ATG4B,non_coding_transcript_exon_variant,,ENST00000493618,;ATG4B,non_coding_transcript_exon_variant,,ENST00000475195,;ATG4B,non_coding_transcript_exon_variant,,ENST00000468018,;ATG4B,non_coding_transcript_exon_variant,,ENST00000465399,;ATG4B,non_coding_transcript_exon_variant,,ENST00000479554,;ATG4B,downstream_gene_variant,,ENST00000415107,; T ENST00000404914 Transcript missense_variant 390/2878 287/1182 96/393 W/L tGg/tTg 1 1 ATG4B HGNC HGNC:20790 protein_coding YES CCDS46564.1 ENSP00000384259 Q9Y4P1 UPI00001AF16F NM_013325.4 deleterious(0) 5/13 Pfam_domain:PF03416,hmmpanther:PTHR22624,hmmpanther:PTHR22624:SF39,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 241654549 241654549 G T 1 0 0 0 0 1 0 0 0 1249 1362 47 2 2 ATG4B 2 241654549 Missense_Mutation SNP G C3L-00279_T 783896 241654549 538980 120 5898 PDCD1 0 . GRCh38 2 241851213 241851213 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.712C>A p.Pro238Thr p.P238T ENST00000334409 5/5 190 167 23 172 171 1 strelka-varscan-mutect PDCD1,missense_variant,p.Pro238Thr,ENST00000334409,NM_005018.2;PDCD1,downstream_gene_variant,,ENST00000343705,;PDCD1,3_prime_UTR_variant,,ENST00000418831,; T ENST00000334409 Transcript missense_variant 782/2114 712/867 238/288 P/T Ccc/Acc 1 -1 PDCD1 HGNC HGNC:8760 protein_coding YES CCDS33428.1 ENSP00000335062 Q15116 A0A0M3M0G7 UPI0000061E11 NM_005018.2 deleterious(0.01) 5/5 hmmpanther:PTHR15264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 241851213 241851213 G T 1 0 0 0 0 1 0 0 0 11703 1232 43 2 2 PDCD1 2 241851213 Missense_Mutation SNP G C3L-00279_T 196664 241851213 342316 121 5899 SYN2 0 . GRCh38 3 12145783 12145783 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.632C>A p.Pro211His p.P211H ENST00000621198 4/13 198 165 33 206 206 0 strelka-varscan-mutect SYN2,missense_variant,p.Pro211His,ENST00000620175,NM_003178.5;SYN2,missense_variant,p.Pro211His,ENST00000621198,NM_133625.4;SYN2,non_coding_transcript_exon_variant,,ENST00000424884,;SYN2,upstream_gene_variant,,ENST00000439861,; A ENST00000621198 Transcript missense_variant 782/2674 632/1749 211/582 P/H cCc/cAc 1 1 SYN2 HGNC HGNC:11495 protein_coding YES CCDS74900.1 ENSP00000480050 A0A087WW96 UPI0000167B8A NM_133625.4 deleterious(0.02) 4/13 hmmpanther:PTHR10841:SF20,hmmpanther:PTHR10841,Pfam_domain:PF02078,Gene3D:3.40.50.20,Superfamily_domains:SSF52440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 12145783 12145783 C A 1 0 0 0 0 1 0 0 0 15831 623 22 2 2 SYN2 3 12145783 Missense_Mutation SNP C C3L-00279_T 12145783 186149776 122 5900 TGFBR2 0 . GRCh38 3 30672111 30672111 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1003G>T p.Ala335Ser p.A335S ENST00000359013 5/8 362 307 55 371 371 0 strelka-varscan-mutect TGFBR2,missense_variant,p.Ala310Ser,ENST00000295754,NM_003242.5;TGFBR2,missense_variant,p.Ala335Ser,ENST00000359013,NM_001024847.2; T ENST00000359013 Transcript missense_variant 1286/4605 1003/1779 335/592 A/S Gct/Tct 1 1 TGFBR2 HGNC HGNC:11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 deleterious(0.03) 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,Gene3D:3.30.200.20,PIRSF_domain:PIRSF037393,Pfam_domain:PF07714,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30672111 30672111 G T 1 0 0 0 0 1 0 0 0 16255 1203 42 2 2 TGFBR2 3 30672111 Missense_Mutation SNP G C3L-00279_T 18526328 30672111 167623448 123 5901 SCN10A 0 . GRCh38 3 38728714 38728714 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2468C>A p.Pro823His p.P823H ENST00000449082 15/27 188 164 24 157 157 0 strelka-varscan-mutect SCN10A,missense_variant,p.Pro823His,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; T ENST00000449082 Transcript missense_variant 2468/6418 2468/5871 823/1956 P/H cCc/cAc 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 deleterious(0.04) 15/27 hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 38728714 38728714 G T 1 0 0 0 0 1 0 0 0 14181 1232 43 2 2 SCN10A 3 38728714 Missense_Mutation SNP G C3L-00279_T 8056603 38728714 159566845 124 5902 TTC21A 0 . GRCh38 3 39126347 39126347 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.1503G>T p.= p.L501L ENST00000431162 12/29 266 240 26 246 246 0 strelka-varscan-mutect TTC21A,synonymous_variant,p.=,ENST00000431162,NM_145755.2;TTC21A,synonymous_variant,p.=,ENST00000440121,NM_001105513.2;TTC21A,upstream_gene_variant,,ENST00000466875,;TTC21A,upstream_gene_variant,,ENST00000471025,;TTC21A,synonymous_variant,p.=,ENST00000430597,;TTC21A,upstream_gene_variant,,ENST00000473587,; T ENST00000431162 Transcript synonymous_variant 1637/4209 1503/3963 501/1320 L ctG/ctT 1 1 TTC21A HGNC HGNC:30761 protein_coding YES CCDS46800.1 ENSP00000398211 Q8NDW8 UPI00015D46B9 NM_145755.2 12/29 hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF2,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 39126347 39126347 G T 1 0 0 0 0 0 0 0 1 17195 1277 45 2 2 TTC21A 3 39126347 Silent SNP G C3L-00279_T 397633 39126347 159169212 125 5903 ZNF197 0 . GRCh38 3 44642862 44642862 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1732A>T p.Ser578Cys p.S578C ENST00000396058 5/5 245 205 40 108 108 0 strelka-varscan-mutect ZNF197,missense_variant,p.Ser578Cys,ENST00000396058,;ZNF197,missense_variant,p.Ser578Cys,ENST00000344387,NM_006991.3;ZNF197,intron_variant,,ENST00000383745,NM_001024855.1;ZNF197,intron_variant,,ENST00000383744,;RP11-944L7.4,intron_variant,,ENST00000457331,;ZNF197,intron_variant,,ENST00000334075,; T ENST00000396058 Transcript missense_variant 1899/4299 1732/3090 578/1029 S/C Agc/Tgc 1 1 ZNF197 HGNC HGNC:12988 protein_coding YES CCDS2717.1 ENSP00000379370 O14709 UPI000013C317 deleterious(0.03) 5/5 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 44642862 44642862 A T 1 0 0 0 0 1 0 0 0 18336 72 3 4 4 ZNF197 3 44642862 Missense_Mutation SNP A C3L-00279_T 5516515 44642862 153652697 126 5904 DNAH12 0 . GRCh38 3 57408448 57408448 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.6108A>T p.= p.P2036P ENST00000495027 40/74 128 113 15 102 102 0 strelka-varscan-mutect DNAH12,synonymous_variant,p.=,ENST00000495027,NM_001291661.1;DNAH12,synonymous_variant,p.=,ENST00000351747,; A ENST00000495027 Transcript synonymous_variant 6289/12146 6108/11883 2036/3960 P ccA/ccT 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 40/74 Gene3D:3.40.50.300,Pfam_domain:PF12775,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -19.99794 0.9999895 1 1 1 0 A 2 1 14 57408448 57408448 T A 1 0 0 0 0 0 0 0 1 4414 1567 55 4 4 DNAH12 3 57408448 Silent SNP T C3L-00279_T 12765586 57408448 140887111 127 5905 C3orf67 0 . GRCh38 3 58870287 58870287 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.363A>T p.= p.T121T ENST00000295966 8/16 133 109 24 78 78 0 strelka-varscan-mutect C3orf67,synonymous_variant,p.=,ENST00000472469,;C3orf67,synonymous_variant,p.=,ENST00000295966,NM_198463.2;C3orf67,synonymous_variant,p.=,ENST00000482387,;C3orf67-AS1,intron_variant,,ENST00000482372,;C3orf67-AS1,intron_variant,,ENST00000493123,;C3orf67-AS1,intron_variant,,ENST00000492031,;C3orf67-AS1,intron_variant,,ENST00000463703,;C3orf67,3_prime_UTR_variant,,ENST00000468415,; A ENST00000295966 Transcript synonymous_variant 867/2650 363/1692 121/563 T acA/acT 1 -1 C3orf67 HGNC HGNC:24763 protein_coding YES CCDS33776.1 ENSP00000295966 Q6ZVT6 UPI00001C098C NM_198463.2 8/16 hmmpanther:PTHR12458 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 58870287 58870287 T A 1 0 0 0 0 0 0 0 1 2071 1799 63 4 4 C3orf67 3 58870287 Silent SNP T C3L-00279_T 1461839 58870287 139425272 128 5906 CADPS 0 . GRCh38 3 62550086 62550086 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1783G>T p.Ala595Ser p.A595S ENST00000383710 11/30 231 196 35 232 232 0 strelka-varscan-mutect CADPS,missense_variant,p.Ala595Ser,ENST00000383710,NM_003716.3;CADPS,missense_variant,p.Ala595Ser,ENST00000612439,;CADPS,missense_variant,p.Ala595Ser,ENST00000357948,NM_183393.2;CADPS,missense_variant,p.Ala595Ser,ENST00000283269,NM_183394.2;CADPS,missense_variant,p.Ala90Ser,ENST00000542833,;CADPS,non_coding_transcript_exon_variant,,ENST00000478434,;CADPS,non_coding_transcript_exon_variant,,ENST00000490424,; A ENST00000383710 Transcript missense_variant 2133/5471 1783/4062 595/1353 A/S Gct/Tct 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 deleterious(0.02) 11/30 PROSITE_profiles:PS50003,hmmpanther:PTHR12166:SF6,hmmpanther:PTHR12166,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 62550086 62550086 C A 1 0 0 0 0 1 0 0 0 2260 710 25 2 2 CADPS 3 62550086 Missense_Mutation SNP C C3L-00279_T 3679799 62550086 135745473 129 5907 CADM2 0 . GRCh38 3 85912449 85912449 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.585C>T p.= p.D195D ENST00000405615 5/10 280 249 31 310 310 0 strelka-varscan-mutect CADM2,synonymous_variant,p.=,ENST00000383699,NM_001256504.1,NM_001256505.1,NM_001167675.1;CADM2,synonymous_variant,p.=,ENST00000407528,NM_001167674.1;CADM2,synonymous_variant,p.=,ENST00000405615,NM_153184.3; T ENST00000405615 Transcript synonymous_variant 585/1314 585/1314 195/437 D gaC/gaT 1 1 CADM2 HGNC HGNC:29849 protein_coding YES CCDS33792.1 ENSP00000384193 Q8N3J6 UPI000013F077 NM_153184.3 5/10 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Gene3D:2.60.40.10,Pfam_domain:PF08205,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 85912449 85912449 C T 1 0 0 0 0 0 0 0 1 2257 506 18 3 3 CADM2 3 85912449 Silent SNP C C3L-00279_T 23362363 85912449 112383110 130 5908 EPHA3 0 . GRCh38 3 89209964 89209964 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.258G>C p.Trp86Cys p.W86C ENST00000336596 3/17 196 172 24 159 159 0 strelka-varscan-mutect EPHA3,missense_variant,p.Trp86Cys,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.Trp86Cys,ENST00000494014,;EPHA3,missense_variant,p.Trp86Cys,ENST00000452448,NM_182644.2; C ENST00000336596 Transcript missense_variant 483/5809 258/2952 86/983 W/C tgG/tgC 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 deleterious(0.01) 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 89209964 89209964 G C 1 0 0 0 0 1 0 0 0 5015 1241 43 4 4 EPHA3 3 89209964 Missense_Mutation SNP G C3L-00279_T 3297515 89209964 109085595 131 5909 EPHA6 0 . GRCh38 3 97475375 97475375 + Nonsense_Mutation SNP G G T rs747807400 C3L-00279_T C3L-00279_N G G c.1918G>T p.Gly640Ter p.G640* ENST00000389672 8/18 217 195 22 200 199 1 strelka-varscan-mutect EPHA6,stop_gained,p.Gly640Ter,ENST00000389672,NM_001080448.2;EPHA6,stop_gained,p.Gly32Ter,ENST00000514100,NM_001278300.1;EPHA6,stop_gained,p.Gly32Ter,ENST00000502694,NM_173655.3;EPHA6,stop_gained,p.Gly6Ter,ENST00000477384,;EPHA6,stop_gained,p.Gly32Ter,ENST00000503760,;EPHA6,stop_gained,p.Gly6Ter,ENST00000508345,; T ENST00000389672 Transcript stop_gained 1956/3971 1918/3393 640/1130 G/* Gga/Tga rs747807400 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 8/18 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364 HIGH 1 SNV 2 1 PASS rs747807400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 97475375 97475375 G T 1 0 0 0 0 0 1 0 0 5018 1001 35 2 2 EPHA6 3 97475375 Nonsense_Mutation SNP G C3L-00279_T 8265411 97475375 100820184 132 5910 EPHA6 0 . GRCh38 3 97747550 97747550 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3256C>A p.Leu1086Met p.L1086M ENST00000389672 17/18 125 97 28 55 55 0 strelka-varscan-mutect EPHA6,missense_variant,p.Leu1086Met,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Leu11Met,ENST00000506349,;EPHA6,downstream_gene_variant,,ENST00000477384,; A ENST00000389672 Transcript missense_variant 3294/3971 3256/3393 1086/1130 L/M Ctg/Atg 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 tolerated(0.26) 17/18 Gene3D:1.10.150.50,Pfam_domain:PF00536,PROSITE_profiles:PS50105,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 97747550 97747550 C A 1 0 0 0 0 1 0 0 0 5018 680 24 2 2 EPHA6 3 97747550 Missense_Mutation SNP C C3L-00279_T 272175 97747550 100548009 133 5911 OR5H6 0 . GRCh38 3 98265143 98265143 + Missense_Mutation SNP G G T rs774037160 C3L-00279_T C3L-00279_N G G c.859G>T p.Asp287Tyr p.D287Y ENST00000383696 1/1 188 171 17 145 145 0 varscan-mutect OR5H6,missense_variant,p.Asp287Tyr,ENST00000383696,NM_001005479.1;RP11-325B23.2,intron_variant,,ENST00000508616,; T ENST00000383696 Transcript missense_variant 859/978 859/978 287/325 D/Y Gat/Tat rs774037160 1 1 OR5H6 HGNC HGNC:14767 protein_coding YES CCDS33800.1 ENSP00000373196 Q8NGV6 UPI000004B1EC NM_001005479.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF301,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs774037160 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 98265143 98265143 G T 1 0 0 0 0 1 0 0 0 11233 942 33 2 2 OR5H6 3 98265143 Missense_Mutation SNP G C3L-00279_T 517593 98265143 100030416 134 5912 ABI3BP 0 . GRCh38 3 100792757 100792757 + Nonsense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.1900C>T p.Gln634Ter p.Q634* ENST00000284322 23/35 253 225 28 65 65 0 strelka-varscan-mutect ABI3BP,stop_gained,p.Gln1311Ter,ENST00000471714,;ABI3BP,stop_gained,p.Gln634Ter,ENST00000284322,NM_015429.3;ABI3BP,stop_gained,p.Gln690Ter,ENST00000495591,;ABI3BP,stop_gained,p.Gln214Ter,ENST00000471901,;ABI3BP,stop_gained,p.Gln50Ter,ENST00000497395,;ABI3BP,intron_variant,,ENST00000486770,;ABI3BP,downstream_gene_variant,,ENST00000478235,;ABI3BP,downstream_gene_variant,,ENST00000466947,;ABI3BP,downstream_gene_variant,,ENST00000482765,;ABI3BP,downstream_gene_variant,,ENST00000527943,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000470336,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,; A ENST00000284322 Transcript stop_gained 2010/4498 1900/3228 634/1075 Q/* Caa/Taa 1 -1 ABI3BP HGNC HGNC:17265 protein_coding YES CCDS46880.1 ENSP00000284322 Q7Z7G0 UPI000011C136 NM_015429.3 23/35 Low_complexity_(Seg):seg,hmmpanther:PTHR23197:SF10,hmmpanther:PTHR23197 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 100792757 100792757 G A 1 0 0 0 0 0 1 0 0 101 1357 47 3 3 ABI3BP 3 100792757 Nonsense_Mutation SNP G C3L-00279_T 2527614 100792757 97502802 135 5913 CBLB 0 . GRCh38 3 105678569 105678569 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2431G>T p.Glu811Ter p.E811* ENST00000264122 17/19 638 575 63 438 438 0 strelka-varscan-mutect CBLB,stop_gained,p.Glu811Ter,ENST00000264122,NM_001321786.1,NM_001321788.1,NM_170662.3;CBLB,stop_gained,p.Glu150Ter,ENST00000394030,;CBLB,stop_gained,p.Glu26Ter,ENST00000407712,;CBLB,downstream_gene_variant,,ENST00000403724,;CBLB,downstream_gene_variant,,ENST00000405772,;CBLB,upstream_gene_variant,,ENST00000476370,; A ENST00000264122 Transcript stop_gained,splice_region_variant 2753/6780 2431/2949 811/982 E/* Gaa/Taa 1 -1 CBLB HGNC HGNC:1542 protein_coding YES CCDS2948.1 ENSP00000264122 Q13191 UPI00001AE89F NM_001321786.1,NM_001321788.1,NM_170662.3 17/19 hmmpanther:PTHR23007:SF3,hmmpanther:PTHR23007 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 105678569 105678569 C A 1 0 0 0 0 0 1 0 0 2402 840 29 2 2 CBLB 3 105678569 Nonsense_Mutation SNP C C3L-00279_T 4885812 105678569 92616990 136 5914 PHLDB2 0 . GRCh38 3 111949046 111949046 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2602G>T p.Val868Leu p.V868L ENST00000431670 10/18 302 262 40 210 210 0 strelka-varscan-mutect PHLDB2,missense_variant,p.Val868Leu,ENST00000431670,NM_001134438.1;PHLDB2,missense_variant,p.Val825Leu,ENST00000412622,NM_145753.2;PHLDB2,missense_variant,p.Val852Leu,ENST00000393923,NM_001134437.1;PHLDB2,missense_variant,p.Val868Leu,ENST00000393925,NM_001134439.1;PHLDB2,missense_variant,p.Val825Leu,ENST00000481953,;PHLDB2,missense_variant,p.Val825Leu,ENST00000498699,;PHLDB2,intron_variant,,ENST00000495180,;PHLDB2,non_coding_transcript_exon_variant,,ENST00000478733,;PHLDB2,upstream_gene_variant,,ENST00000478584,;PHLDB2,upstream_gene_variant,,ENST00000460365,;PHLDB2,downstream_gene_variant,,ENST00000491694,; T ENST00000431670 Transcript missense_variant 3013/6127 2602/3762 868/1253 V/L Gtg/Ttg 1 1 PHLDB2 HGNC HGNC:29573 protein_coding YES CCDS46886.1 ENSP00000405405 Q86SQ0 UPI0000457152 NM_001134438.1 tolerated(0.54) 10/18 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF21 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999918 1 1 1 0 T 3 4 14 111949046 111949046 G T 1 0 0 0 0 1 0 0 0 11940 1377 48 2 2 PHLDB2 3 111949046 Missense_Mutation SNP G C3L-00279_T 6270477 111949046 86346513 137 5915 CASR 0 . GRCh38 3 122284086 122284087 + Frame_Shift_Ins INS - - A novel C3L-00279_T C3L-00279_N - - c.2162_2163insA p.Thr722HisfsTer48 p.T722Hfs*48 ENST00000498619 7/7 124 107 17 118 118 0 sindel-varindel CASR,frameshift_variant,p.Thr722HisfsTer48,ENST00000498619,NM_001178065.1;CASR,frameshift_variant,p.Thr712HisfsTer48,ENST00000490131,NM_000388.3; A ENST00000498619 Transcript frameshift_variant 2600-2601/5011 2162-2163/3267 721/1088 P/PX ccc/ccAc 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 7/7 Pfam_domain:PF00003,Prints_domain:PR00592,PROSITE_profiles:PS50259,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF358 HIGH 1 insertion 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 14 122284086 122284086 - A 1 0 1 1 0 0 0 0 0 2381 623 22 0 0 CASR 3 122284086 Frame_Shift_Ins INS - C3L-00279_T 10335040 122284086 76011473 138 5916 MYLK 0 . GRCh38 3 123707945 123707945 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.2199C>A p.= p.S733S ENST00000360304 15/33 392 333 59 323 323 0 strelka-varscan-mutect MYLK,synonymous_variant,p.=,ENST00000360772,;MYLK,synonymous_variant,p.=,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,synonymous_variant,p.=,ENST00000359169,NM_053027.3;MYLK,synonymous_variant,p.=,ENST00000354792,;MYLK,synonymous_variant,p.=,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,synonymous_variant,p.=,ENST00000475616,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,downstream_gene_variant,,ENST00000514623,; T ENST00000360304 Transcript synonymous_variant 2385/7738 2199/5745 733/1914 S tcC/tcA 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 15/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 123707945 123707945 G T 1 0 0 0 0 0 0 0 1 10056 1219 43 2 2 MYLK 3 123707945 Silent SNP G C3L-00279_T 1423859 123707945 74587614 139 5917 MYLK 0 . GRCh38 3 123733057 123733057 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1355C>A p.Thr452Asn p.T452N ENST00000360304 10/33 505 437 68 449 449 0 strelka-varscan-mutect MYLK,missense_variant,p.Thr452Asn,ENST00000360772,;MYLK,missense_variant,p.Thr452Asn,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,missense_variant,p.Thr452Asn,ENST00000359169,NM_053027.3;MYLK,missense_variant,p.Thr452Asn,ENST00000475616,;MYLK,intron_variant,,ENST00000354792,;MYLK,intron_variant,,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,intron_variant,,ENST00000514623,;MYLK,downstream_gene_variant,,ENST00000506361,; T ENST00000360304 Transcript missense_variant 1541/7738 1355/5745 452/1914 T/N aCc/aAc 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 tolerated(0.5) 10/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs769458226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 123733057 123733057 G T 1 0 0 0 0 1 0 0 0 10056 1261 44 2 2 MYLK 3 123733057 Missense_Mutation SNP G C3L-00279_T 25112 123733057 74562502 140 5918 ALDH1L1 0 . GRCh38 3 126160856 126160856 + Frame_Shift_Del DEL G G - novel C3L-00279_T C3L-00279_N G G c.154delC p.Leu52TrpfsTer53 p.L52Wfs*53 ENST00000273450 2/23 113 94 19 116 116 0 sindel-varindel-pindel ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000393434,NM_012190.3;ALDH1L1,frameshift_variant,p.Leu52TrpfsTer53,ENST00000273450,NM_001270364.1;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000472186,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000455064,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000393431,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000452905,NM_001270365.1;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000460368,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000488356,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000490367,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer53,ENST00000509952,;RNU1-30P,upstream_gene_variant,,ENST00000606575,;ALDH1L1,upstream_gene_variant,,ENST00000413612,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer566,ENST00000473607,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer8,ENST00000493803,;ALDH1L1,frameshift_variant,p.Leu42TrpfsTer?,ENST00000511283,;ALDH1L1,upstream_gene_variant,,ENST00000476245,;ALDH1L1,upstream_gene_variant,,ENST00000484724,; - ENST00000273450 Transcript frameshift_variant 372/3179 154/2739 52/912 L/X Ctg/tg 1 -1 ALDH1L1 HGNC HGNC:3978 protein_coding YES CCDS58851.1 ENSP00000273450 O75891 UPI0000425C57 NM_001270364.1 2/23 Gene3D:3.40.50.170,Pfam_domain:PF00551,PIRSF_domain:PIRSF036489,Superfamily_domains:SSF53328 HIGH 1 deletion 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999984 1 1 1 0 - 7 5 14 126160856 126160856 G - 1 0 1 0 1 0 0 0 0 594 1014 35 0 0 ALDH1L1 3 126160856 Frame_Shift_Del DEL G C3L-00279_T 2427799 126160856 72134703 141 5919 UROC1 0 . GRCh38 3 126500843 126500843 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.1177G>A p.Gly393Arg p.G393R ENST00000383579 12/21 539 452 87 524 524 0 strelka-varscan-mutect UROC1,missense_variant,p.Gly333Arg,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.Gly393Arg,ENST00000383579,NM_001165974.1; T ENST00000383579 Transcript missense_variant 1211/2735 1177/2211 393/736 G/R Ggg/Agg 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 deleterious(0.02) 12/21 Gene3D:1x87B01,HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 126500843 126500843 C T 1 0 0 0 0 1 0 0 0 17560 623 22 3 3 UROC1 3 126500843 Missense_Mutation SNP C C3L-00279_T 339987 126500843 71794716 142 5920 COL6A5 0 . GRCh38 3 130406157 130406157 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.4407T>A p.Asp1469Glu p.D1469E ENST00000265379 16/43 297 273 24 156 156 0 strelka-varscan-mutect COL6A5,missense_variant,p.Asp1469Glu,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Asp1469Glu,ENST00000312481,; A ENST00000265379 Transcript missense_variant 4901/9214 4407/7836 1469/2611 D/E gaT/gaA 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0.04) 16/43 Low_complexity_(Seg):seg,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF01391 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 130406157 130406157 T A 1 0 0 0 0 1 0 0 0 3491 1461 51 4 4 COL6A5 3 130406157 Missense_Mutation SNP T C3L-00279_T 3905314 130406157 67889402 143 5921 EPHB1 0 . GRCh38 3 135132840 135132840 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1088G>T p.Cys363Phe p.C363F ENST00000398015 5/16 262 227 35 248 248 0 strelka-varscan-mutect EPHB1,missense_variant,p.Cys363Phe,ENST00000398015,NM_004441.4;EPHB1,5_prime_UTR_variant,,ENST00000493838,;EPHB1,downstream_gene_variant,,ENST00000488154,;EPHB1,non_coding_transcript_exon_variant,,ENST00000488992,;EPHB1,downstream_gene_variant,,ENST00000482618,; T ENST00000398015 Transcript missense_variant 1458/4672 1088/2955 363/984 C/F tGc/tTc 1 1 EPHB1 HGNC HGNC:3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 UPI000012A07E NM_004441.4 deleterious(0) 5/16 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,Low_complexity_(Seg):seg,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 135132840 135132840 G T 1 0 0 0 0 1 0 0 0 5021 1319 46 2 2 EPHB1 3 135132840 Missense_Mutation SNP G C3L-00279_T 4726683 135132840 63162719 144 5922 U2SURP 0 . GRCh38 3 143016290 143016290 + Nonsense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.355G>T p.Glu119Ter p.E119* ENST00000473835 5/28 175 155 20 46 46 0 strelka-varscan-mutect U2SURP,stop_gained,p.Glu119Ter,ENST00000473835,NM_001320219.1,NM_001080415.1;U2SURP,stop_gained,p.Glu119Ter,ENST00000493598,;U2SURP,stop_gained,p.Glu99Ter,ENST00000600150,;U2SURP,stop_gained,p.Glu119Ter,ENST00000493782,;U2SURP,stop_gained,p.Glu89Ter,ENST00000465175,;U2SURP,non_coding_transcript_exon_variant,,ENST00000485374,;U2SURP,stop_gained,p.Glu121Ter,ENST00000463563,;U2SURP,stop_gained,p.Glu119Ter,ENST00000488497,;U2SURP,non_coding_transcript_exon_variant,,ENST00000461591,;U2SURP,non_coding_transcript_exon_variant,,ENST00000470400,;U2SURP,non_coding_transcript_exon_variant,,ENST00000491827,;U2SURP,upstream_gene_variant,,ENST00000488587,; T ENST00000473835 Transcript stop_gained 445/7276 355/3090 119/1029 E/* Gag/Tag 1 1 U2SURP HGNC HGNC:30855 protein_coding YES CCDS46928.1 ENSP00000418563 O15042 UPI0000160746 NM_001320219.1,NM_001080415.1 5/28 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23140:SF1,hmmpanther:PTHR23140 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 143016290 143016290 G T 1 0 0 0 0 0 1 0 0 17341 1175 41 2 2 U2SURP 3 143016290 Nonsense_Mutation SNP G C3L-00279_T 7883450 143016290 55279269 145 5923 ZIC1 0 . GRCh38 3 147410697 147410697 + Missense_Mutation SNP C C G rs775474959 C3L-00279_T C3L-00279_N C C c.585C>G p.His195Gln p.H195Q ENST00000282928 1/3 356 310 46 293 293 0 strelka-varscan-mutect ZIC1,missense_variant,p.His195Gln,ENST00000282928,NM_003412.3;ZIC1,intron_variant,,ENST00000488404,;ZIC4,upstream_gene_variant,,ENST00000383075,NM_032153.5;ZIC4,upstream_gene_variant,,ENST00000462748,;ZIC4,upstream_gene_variant,,ENST00000491672,NM_001243256.1;ZIC4,upstream_gene_variant,,ENST00000463250,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,upstream_gene_variant,,ENST00000464144,; G ENST00000282928 Transcript missense_variant 1314/5241 585/1344 195/447 H/Q caC/caG rs775474959 1 1 ZIC1 HGNC HGNC:12872 protein_coding YES CCDS3136.1 ENSP00000282928 Q15915 UPI000013DD09 NM_003412.3 tolerated(0.07) 1/3 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26 MODERATE 1 SNV 1 1 PASS rs775474959 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 147410697 147410697 C G 1 0 0 0 0 1 0 0 0 18257 535 19 4 4 ZIC1 3 147410697 Missense_Mutation SNP C C3L-00279_T 4394407 147410697 50884862 146 5924 SI 0 . GRCh38 3 165062457 165062457 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.934G>T p.Val312Leu p.V312L ENST00000264382 9/48 187 161 26 63 63 0 strelka-varscan-mutect SI,missense_variant,p.Val312Leu,ENST00000264382,NM_001041.3; A ENST00000264382 Transcript missense_variant 997/6011 934/5484 312/1827 V/L Gta/Tta 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.77) 9/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 165062457 165062457 C A 1 0 0 0 0 1 0 0 0 14561 565 20 2 2 SI 3 165062457 Missense_Mutation SNP C C3L-00279_T 17651760 165062457 33233102 147 5925 TNIK 0 . GRCh38 3 171126101 171126101 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.1824C>T p.= p.S608S ENST00000436636 17/33 95 78 17 80 80 0 strelka-varscan-mutect TNIK,synonymous_variant,p.=,ENST00000436636,NM_015028.2;TNIK,synonymous_variant,p.=,ENST00000341852,NM_001161565.1;TNIK,synonymous_variant,p.=,ENST00000284483,NM_001161560.1;TNIK,synonymous_variant,p.=,ENST00000357327,NM_001161561.1;TNIK,synonymous_variant,p.=,ENST00000470834,NM_001161562.1;TNIK,synonymous_variant,p.=,ENST00000488470,NM_001161563.1;TNIK,synonymous_variant,p.=,ENST00000460047,NM_001161564.1;TNIK,synonymous_variant,p.=,ENST00000475336,NM_001161566.1; A ENST00000436636 Transcript synonymous_variant 2169/6970 1824/4083 608/1360 S tcC/tcT 1 -1 TNIK HGNC HGNC:30765 protein_coding YES CCDS46956.1 ENSP00000399511 Q9UKE5 UPI000003ABDF NM_015028.2 17/33 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999987 1 1 1 0 A 2 1 14 171126101 171126101 G A 1 0 0 0 0 0 0 0 1 16786 1219 43 3 3 TNIK 3 171126101 Silent SNP G C3L-00279_T 6063644 171126101 27169458 148 5926 TNIK 0 . GRCh38 3 171138351 171138351 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1448A>T p.Gln483Leu p.Q483L ENST00000436636 15/33 79 70 9 65 65 0 strelka-varscan-mutect TNIK,missense_variant,p.Gln483Leu,ENST00000436636,NM_015028.2;TNIK,missense_variant,p.Gln454Leu,ENST00000341852,NM_001161565.1;TNIK,missense_variant,p.Gln483Leu,ENST00000284483,NM_001161560.1;TNIK,missense_variant,p.Gln454Leu,ENST00000357327,NM_001161561.1;TNIK,missense_variant,p.Gln454Leu,ENST00000470834,NM_001161562.1;TNIK,missense_variant,p.Gln483Leu,ENST00000488470,NM_001161563.1;TNIK,missense_variant,p.Gln483Leu,ENST00000460047,NM_001161564.1;TNIK,missense_variant,p.Gln454Leu,ENST00000475336,NM_001161566.1; A ENST00000436636 Transcript missense_variant 1793/6970 1448/4083 483/1360 Q/L cAg/cTg 1 -1 TNIK HGNC HGNC:30765 protein_coding YES CCDS46956.1 ENSP00000399511 Q9UKE5 UPI000003ABDF NM_015028.2 tolerated(0.09) 15/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF308,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -19.04131 0.9999315 1 1 1 0 A 3 1 14 171138351 171138351 T A 1 0 0 0 0 1 0 0 0 16786 1580 55 4 4 TNIK 3 171138351 Missense_Mutation SNP T C3L-00279_T 12250 171138351 27157208 149 5927 CEP19 0 . GRCh38 3 196707800 196707800 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.255G>T p.Leu85Phe p.L85F ENST00000409690 3/3 474 404 70 292 292 0 strelka-varscan-mutect CEP19,missense_variant,p.Leu85Phe,ENST00000409690,NM_032898.4;CEP19,missense_variant,p.Leu46Phe,ENST00000399942,;PIGX,intron_variant,,ENST00000426755,;PIGX,upstream_gene_variant,,ENST00000392391,NM_017861.3;PIGX,upstream_gene_variant,,ENST00000296333,NM_001166304.1;PIGX,upstream_gene_variant,,ENST00000451319,;PIGX,upstream_gene_variant,,ENST00000421265,;RNU6-646P,downstream_gene_variant,,ENST00000364571,;PIGX,upstream_gene_variant,,ENST00000495440,;PIGX,upstream_gene_variant,,ENST00000415832,;PIGX,upstream_gene_variant,,ENST00000453218,;PIGX,upstream_gene_variant,,ENST00000457284,; A ENST00000409690 Transcript missense_variant 678/2201 255/504 85/167 L/F ttG/ttT 1 -1 CEP19 HGNC HGNC:28209 protein_coding YES CCDS43193.2 ENSP00000387209 Q96LK0 UPI0000071B37 NM_032898.4 deleterious(0.01) 3/3 Pfam_domain:PF14933,hmmpanther:PTHR31539 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 196707800 196707800 C A 1 0 0 0 0 1 0 0 0 2966 477 17 2 2 CEP19 3 196707800 Missense_Mutation SNP C C3L-00279_T 25569449 196707800 1587759 150 5928 RGS12 0 . GRCh38 4 3316430 3316430 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.260G>T p.Cys87Phe p.C87F ENST00000344733 2/18 335 312 23 306 306 0 strelka-varscan-mutect RGS12,missense_variant,p.Cys87Phe,ENST00000382788,NM_002926.3;RGS12,missense_variant,p.Cys87Phe,ENST00000344733,NM_198229.2;RGS12,missense_variant,p.Cys87Phe,ENST00000336727,;RGS12,upstream_gene_variant,,ENST00000511805,;RP11-357G3.2,downstream_gene_variant,,ENST00000600073,;RGS12,missense_variant,p.Cys87Phe,ENST00000514268,;RGS12,non_coding_transcript_exon_variant,,ENST00000502947,;RGS12,intron_variant,,ENST00000506631,;RP11-357G3.2,downstream_gene_variant,,ENST00000510094,; T ENST00000344733 Transcript missense_variant 1164/5469 260/4344 87/1447 C/F tGc/tTc 1 1 RGS12 HGNC HGNC:9994 protein_coding YES CCDS3366.1 ENSP00000339381 O14924 UPI0000133830 NM_198229.2 deleterious(0) 2/18 PROSITE_profiles:PS50106,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF149,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 3316430 3316430 G T 1 0 0 0 0 1 0 0 0 13466 1319 46 2 2 RGS12 4 3316430 Missense_Mutation SNP G C3L-00279_T 3316430 186898125 151 5929 EVC2 0 . GRCh38 4 5663202 5663202 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.1050A>T p.= p.S350S ENST00000344408 9/22 516 437 79 465 465 0 strelka-varscan-mutect EVC2,synonymous_variant,p.=,ENST00000310917,NM_001166136.1;EVC2,synonymous_variant,p.=,ENST00000344408,NM_147127.4;EVC2,synonymous_variant,p.=,ENST00000475313,;EVC2,synonymous_variant,p.=,ENST00000509670,; A ENST00000344408 Transcript synonymous_variant 1104/4390 1050/3927 350/1308 S tcA/tcT 1 -1 EVC2 HGNC HGNC:19747 protein_coding YES CCDS3382.2 ENSP00000342144 Q86UK5 UPI00001910B5 NM_147127.4 9/22 Pfam_domain:PF12297,hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 5663202 5663202 T A 1 0 0 0 0 0 0 0 1 5153 1567 55 4 4 EVC2 4 5663202 Silent SNP T C3L-00279_T 2346772 5663202 184551353 152 5930 EVC 0 . GRCh38 4 5753011 5753011 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1274A>T p.Gln425Leu p.Q425L ENST00000264956 9/21 343 298 45 298 298 0 strelka-varscan-mutect EVC,missense_variant,p.Gln425Leu,ENST00000264956,NM_001306090.1,NM_153717.2;EVC,missense_variant,p.Gln425Leu,ENST00000509451,NM_001306092.1;EVC,non_coding_transcript_exon_variant,,ENST00000514919,;CRMP1,intron_variant,,ENST00000506216,; T ENST00000264956 Transcript missense_variant 1458/6431 1274/2979 425/992 Q/L cAg/cTg 1 1 EVC HGNC HGNC:3497 protein_coding YES CCDS3383.1 ENSP00000264956 P57679 UPI000012A2A5 NM_001306090.1,NM_153717.2 tolerated(1) 9/21 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 5753011 5753011 A T 1 0 0 0 0 1 0 0 0 5152 188 7 4 4 EVC 4 5753011 Missense_Mutation SNP A C3L-00279_T 89809 5753011 184461544 153 5931 C4orf50 0 . GRCh38 4 5973803 5973803 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.3960G>C p.Arg1320Ser p.R1320S ENST00000531445 9/12 149 138 11 126 126 0 strelka-mutect C4orf50,missense_variant,p.Arg1320Ser,ENST00000531445,;C4orf50,missense_variant,p.Arg88Ser,ENST00000324058,; G ENST00000531445 Transcript missense_variant 4036/6860 3960/4527 1320/1508 R/S agG/agC 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 deleterious(0) 9/12 hmmpanther:PTHR36866,Pfam_domain:PF15030 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 5973803 5973803 C G 1 0 0 0 0 1 0 0 0 2089 854 30 4 4 C4orf50 4 5973803 Missense_Mutation SNP C C3L-00279_T 220792 5973803 184240752 154 5932 SLC2A9 0 . GRCh38 4 9908298 9908298 + Silent SNP C C A rs576420234 C3L-00279_T C3L-00279_N C C c.1050G>T p.= p.P350P ENST00000264784 8/12 361 313 48 341 341 0 strelka-varscan-mutect SLC2A9,synonymous_variant,p.=,ENST00000506583,;SLC2A9,synonymous_variant,p.=,ENST00000309065,NM_001001290.1;SLC2A9,synonymous_variant,p.=,ENST00000264784,NM_020041.2;SLC2A9,non_coding_transcript_exon_variant,,ENST00000505104,;SLC2A9,non_coding_transcript_exon_variant,,ENST00000503280,; A ENST00000264784 Transcript synonymous_variant 1104/1850 1050/1623 350/540 P ccG/ccT rs576420234,COSM3927450,COSM3927451 1 -1 SLC2A9 HGNC HGNC:13446 protein_coding YES CCDS3407.1 ENSP00000264784 Q9NRM0 UPI000013D56E NM_020041.2 8/12 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF35,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs576420234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 9908298 9908298 C A 1 0 0 0 0 0 0 0 1 14822 639 23 1 1 SLC2A9 4 9908298 Silent SNP C C3L-00279_T 3934495 9908298 180306257 155 5933 FAM184B 0 . GRCh38 4 17636610 17636610 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2702C>A p.Ala901Glu p.A901E ENST00000265018 15/18 163 153 10 185 184 1 strelka-varscan-mutect FAM184B,missense_variant,p.Ala901Glu,ENST00000265018,NM_015688.1;MED28,downstream_gene_variant,,ENST00000237380,NM_025205.4;MED28,downstream_gene_variant,,ENST00000499786,; T ENST00000265018 Transcript missense_variant 2915/6622 2702/3183 901/1060 A/E gCg/gAg 1 -1 FAM184B HGNC HGNC:29235 protein_coding YES CCDS47033.1 ENSP00000265018 Q9ULE4 UPI000020BD7C NM_015688.1 tolerated(0.47) 15/18 hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870 MODERATE 1 SNV 1 1 PASS rs1483292394 . 0 205 0 5 0 0 0 0 -12.94436 0.997414 1 1 1 0 T 3 4 14 17636610 17636610 G T 1 0 0 0 0 1 0 0 0 5359 1087 38 1 1 FAM184B 4 17636610 Missense_Mutation SNP G C3L-00279_T 7728312 17636610 172577945 156 5934 ADGRA3 0 . GRCh38 4 22387939 22387939 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.3732C>T p.= p.S1244S ENST00000334304 19/19 196 178 18 192 192 0 strelka-varscan-mutect ADGRA3,synonymous_variant,p.=,ENST00000334304,NM_145290.3;ADGRA3,non_coding_transcript_exon_variant,,ENST00000282943,;ADGRA3,downstream_gene_variant,,ENST00000504617,;ADGRA3,non_coding_transcript_exon_variant,,ENST00000499527,;ADGRA3,intron_variant,,ENST00000511051,; A ENST00000334304 Transcript synonymous_variant 4002/4566 3732/3966 1244/1321 S agC/agT 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 19/19 LOW 1 SNV 1 1 PASS rs1169737414 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 22387939 22387939 G A 1 0 0 0 0 0 0 0 1 354 1310 46 3 3 ADGRA3 4 22387939 Silent SNP G C3L-00279_T 4751329 22387939 167826616 157 5935 ADGRA3 0 . GRCh38 4 22401471 22401471 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2441G>T p.Gly814Val p.G814V ENST00000334304 16/19 226 195 31 130 130 0 strelka-varscan-mutect ADGRA3,missense_variant,p.Gly814Val,ENST00000334304,NM_145290.3;ADGRA3,non_coding_transcript_exon_variant,,ENST00000282943,;ADGRA3,intron_variant,,ENST00000504617,;ADGRA3,5_prime_UTR_variant,,ENST00000511051,; A ENST00000334304 Transcript missense_variant 2711/4566 2441/3966 814/1321 G/V gGa/gTa 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 deleterious(0) 16/19 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF35,hmmpanther:PTHR12011,Pfam_domain:PF00002 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 22401471 22401471 C A 1 0 0 0 0 1 0 0 0 354 855 30 2 2 ADGRA3 4 22401471 Missense_Mutation SNP C C3L-00279_T 13532 22401471 167813084 158 5936 STIM2 0 . GRCh38 4 27002997 27002997 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.874G>C p.Asp292His p.D292H ENST00000465503 7/13 130 114 16 127 127 0 strelka-mutect STIM2,missense_variant,p.Asp292His,ENST00000467087,NM_020860.3;STIM2,missense_variant,p.Asp292His,ENST00000467011,NM_001169117.1;STIM2,missense_variant,p.Asp292His,ENST00000465503,NM_001169118.1;STIM2,upstream_gene_variant,,ENST00000473519,;STIM2,downstream_gene_variant,,ENST00000463501,;STIM2,downstream_gene_variant,,ENST00000494628,; C ENST00000465503 Transcript missense_variant 1252/3613 874/2265 292/754 D/H Gat/Cat 1 1 STIM2 HGNC HGNC:19205 protein_coding YES CCDS54751.1 ENSP00000417569 H0Y860 UPI0001B79443 NM_001169118.1 deleterious(0.02) 7/13 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 27002997 27002997 G C 1 0 0 0 0 1 0 0 0 15661 1174 41 4 4 STIM2 4 27002997 Missense_Mutation SNP G C3L-00279_T 4601526 27002997 163211558 159 5937 PCDH7 0 . GRCh38 4 30721589 30721589 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.167G>T p.Gly56Val p.G56V ENST00000543491 1/1 153 124 29 154 154 0 strelka-varscan-mutect PCDH7,missense_variant,p.Gly56Val,ENST00000361762,NM_002589.2;PCDH7,missense_variant,p.Gly56Val,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; T ENST00000543491 Transcript missense_variant 737/4457 167/3219 56/1072 G/V gGc/gTc 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 deleterious(0.03) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF321,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS rs1225973318 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30721589 30721589 G T 1 0 0 0 0 1 0 0 0 11603 1203 42 2 2 PCDH7 4 30721589 Missense_Mutation SNP G C3L-00279_T 3718592 30721589 159492966 160 5938 GABRG1 0 . GRCh38 4 46097216 46097216 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.238C>A p.Arg80Ser p.R80S ENST00000295452 2/9 65 53 12 33 33 0 strelka-varscan-mutect GABRG1,missense_variant,p.Arg80Ser,ENST00000295452,NM_173536.3; T ENST00000295452 Transcript missense_variant 406/6785 238/1398 80/465 R/S Cgt/Agt COSM1429842 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 deleterious(0) 2/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR01620,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,TIGRFAM_domain:TIGR00860 1 MODERATE 1 SNV 1 1 1 PASS rs1239800695 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 46097216 46097216 G T 1 0 0 0 0 1 0 0 0 6042 1058 37 1 1 GABRG1 4 46097216 Missense_Mutation SNP G C3L-00279_T 15375627 46097216 144117339 161 5939 FRYL 0 . GRCh38 4 48570853 48570853 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.2970G>A p.= p.L990L ENST00000358350 27/64 165 147 18 148 147 1 strelka-varscan-mutect FRYL,synonymous_variant,p.=,ENST00000358350,NM_015030.1;FRYL,synonymous_variant,p.=,ENST00000503238,;FRYL,synonymous_variant,p.=,ENST00000507711,;RNU5E-3P,downstream_gene_variant,,ENST00000515913,;FRYL,non_coding_transcript_exon_variant,,ENST00000511343,; T ENST00000358350 Transcript synonymous_variant 3575/11706 2970/9042 990/3013 L ctG/ctA 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 27/64 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 48570853 48570853 C T 1 0 0 0 0 0 0 0 1 5936 581 21 3 3 FRYL 4 48570853 Silent SNP C C3L-00279_T 2473637 48570853 141643702 162 5940 PDGFRA 0 . GRCh38 4 54261325 54261325 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.280C>A p.His94Asn p.H94N ENST00000257290 3/23 325 263 62 281 281 0 strelka-varscan-mutect PDGFRA,missense_variant,p.His94Asn,ENST00000257290,NM_006206.4;PDGFRA,missense_variant,p.His94Asn,ENST00000508170,;PDGFRA,missense_variant,p.His94Asn,ENST00000504461,;PDGFRA,missense_variant,p.His94Asn,ENST00000503856,;PDGFRA,missense_variant,p.His119Asn,ENST00000512143,;PDGFRA,missense_variant,p.His94Asn,ENST00000512522,;RP11-231C18.3,intron_variant,,ENST00000507166,;PDGFRA,missense_variant,p.His94Asn,ENST00000509490,;PDGFRA,intron_variant,,ENST00000509092,; A ENST00000257290 Transcript missense_variant 611/6576 280/3270 94/1089 H/N Cac/Aac 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 tolerated(0.79) 3/23 PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726,Prints_domain:PR01832 MODERATE 1 SNV 1 1 PASS rs1418656533 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 54261325 54261325 C A 1 0 0 0 0 1 0 0 0 11749 594 21 2 2 PDGFRA 4 54261325 Missense_Mutation SNP C C3L-00279_T 5690472 54261325 135953230 163 5941 PDGFRA 0 . GRCh38 4 54285482 54285482 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.2435A>T p.Lys812Ile p.K812I ENST00000257290 17/23 427 373 54 272 272 0 strelka-varscan-mutect PDGFRA,missense_variant,p.Lys812Ile,ENST00000257290,NM_006206.4;RP11-231C18.3,missense_variant,p.Lys572Ile,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000509490,;PDGFRA,downstream_gene_variant,,ENST00000509092,;PDGFRA,downstream_gene_variant,,ENST00000507536,; T ENST00000257290 Transcript missense_variant 2766/6576 2435/3270 812/1089 K/I aAa/aTa 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 deleterious(0) 17/23 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00220,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 54285482 54285482 A T 1 0 0 0 0 1 0 0 0 11749 28 1 4 4 PDGFRA 4 54285482 Missense_Mutation SNP A C3L-00279_T 24157 54285482 135929073 164 5942 TMPRSS11D 0 . GRCh38 4 67827277 67827277 + Silent SNP G G T rs368640864 C3L-00279_T C3L-00279_N G G c.936C>A p.= p.G312G ENST00000283916 8/10 139 113 26 97 97 0 strelka-varscan-mutect TMPRSS11D,synonymous_variant,p.=,ENST00000283916,NM_004262.2;TMPRSS11D,intron_variant,,ENST00000514868,;UBA6-AS1,intron_variant,,ENST00000500538,;TMPRSS11D,downstream_gene_variant,,ENST00000502573,;TMPRSS11D,non_coding_transcript_exon_variant,,ENST00000505533,; T ENST00000283916 Transcript synonymous_variant 1035/2817 936/1257 312/418 G ggC/ggA rs368640864,COSM1430607 1 -1 TMPRSS11D HGNC HGNC:24059 protein_coding YES CCDS3518.1 ENSP00000283916 O60235 UPI000003FE66 NM_004262.2 8/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF20,hmmpanther:PTHR24256,Gene3D:2.40.10.10,PIRSF_domain:PIRSF037941,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 LOW 1 SNV 1 0,1 1 PASS rs368640864 . 0 201 8 0 0 0 0 0 -20 0.9999987 1 1 1 0 T 2 4 14 67827277 67827277 G T 1 0 0 0 0 0 0 0 1 16717 1074 38 1 1 TMPRSS11D 4 67827277 Silent SNP G C3L-00279_T 13541795 67827277 122387278 165 5943 RUFY3 0 . GRCh38 4 70789517 70789517 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1262A>T p.Gln421Leu p.Q421L ENST00000381006 12/18 112 96 16 40 40 0 strelka-varscan-mutect RUFY3,missense_variant,p.Gln421Leu,ENST00000226328,NM_001291994.1,NM_014961.4;RUFY3,missense_variant,p.Gln421Leu,ENST00000381006,NM_001037442.3;RUFY3,missense_variant,p.Gln368Leu,ENST00000502653,NM_001291993.1;RUFY3,missense_variant,p.Gln481Leu,ENST00000417478,NM_001130709.1;RUFY3,upstream_gene_variant,,ENST00000507333,;RUFY3,missense_variant,p.Gln20Leu,ENST00000512103,;RUFY3,missense_variant,p.Gln69Leu,ENST00000504805,; T ENST00000381006 Transcript missense_variant 1841/3098 1262/1863 421/620 Q/L cAg/cTg 1 1 RUFY3 HGNC HGNC:30285 protein_coding YES CCDS34001.1 ENSP00000370394 Q7L099 UPI00005FB126 NM_001037442.3 deleterious(0) 12/18 hmmpanther:PTHR22835:SF37,hmmpanther:PTHR22835 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 70789517 70789517 A T 1 0 0 0 0 1 0 0 0 14002 188 7 4 4 RUFY3 4 70789517 Missense_Mutation SNP A C3L-00279_T 2962240 70789517 119425038 166 5944 MMRN1 0 . GRCh38 4 89935407 89935407 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1727A>T p.Asn576Ile p.N576I ENST00000394980 7/9 164 153 11 49 49 0 strelka-mutect MMRN1,missense_variant,p.Asn576Ile,ENST00000394980,;MMRN1,missense_variant,p.Asn576Ile,ENST00000264790,NM_007351.2;MMRN1,missense_variant,p.Asn318Ile,ENST00000508372,; T ENST00000394980 Transcript missense_variant 2046/5217 1727/3687 576/1228 N/I aAt/aTt 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 deleterious(0) 7/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 MODERATE 1 SNV 5 1 PASS rs1245775900 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 89935407 89935407 A T 1 0 0 0 0 1 0 0 0 9633 101 4 4 4 MMRN1 4 89935407 Missense_Mutation SNP A C3L-00279_T 19145890 89935407 100279148 167 5945 CCSER1 0 . GRCh38 4 91598651 91598651 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.2297G>C p.Arg766Pro p.R766P ENST00000509176 11/11 273 231 42 256 256 0 strelka-varscan-mutect CCSER1,missense_variant,p.Arg766Pro,ENST00000509176,NM_001145065.1;RP11-254A24.2,upstream_gene_variant,,ENST00000623567,; C ENST00000509176 Transcript missense_variant 2585/5847 2297/2703 766/900 R/P cGt/cCt 1 1 CCSER1 HGNC HGNC:29349 protein_coding YES CCDS47099.1 ENSP00000425040 Q9C0I3 UPI00005A6104 NM_001145065.1 tolerated_low_confidence(0.3) 11/11 hmmpanther:PTHR22461,hmmpanther:PTHR22461:SF1 MODERATE 1 SNV 1 1 PASS rs1259840333 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 14 91598651 91598651 G C 1 0 0 0 0 1 0 0 0 2652 1145 40 4 4 CCSER1 4 91598651 Missense_Mutation SNP G C3L-00279_T 1663244 91598651 98615904 168 5946 UNC5C 0 . GRCh38 4 95335592 95335592 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.164C>T p.Ser55Phe p.S55F ENST00000453304 2/16 132 114 18 54 54 0 strelka-varscan-mutect UNC5C,missense_variant,p.Ser55Phe,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Ser14Phe,ENST00000610318,;UNC5C,missense_variant,p.Ser55Phe,ENST00000513796,;UNC5C,missense_variant,p.Ser55Phe,ENST00000506749,;UNC5C,missense_variant,p.Ser55Phe,ENST00000504962,; A ENST00000453304 Transcript missense_variant 513/9875 164/2796 55/931 S/F tCt/tTt 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 deleterious(0) 2/16 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 95335592 95335592 G A 1 0 0 0 0 1 0 0 0 17517 942 33 3 3 UNC5C 4 95335592 Missense_Mutation SNP G C3L-00279_T 3736941 95335592 94878963 169 5947 TACR3 0 . GRCh38 4 103589768 103589768 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1312G>T p.Gly438Cys p.G438C ENST00000304883 5/5 508 428 80 483 483 0 strelka-varscan-mutect TACR3,missense_variant,p.Gly438Cys,ENST00000304883,NM_001059.2;RP11-297P16.3,intron_variant,,ENST00000502936,;RP11-297P16.3,intron_variant,,ENST00000512401,; A ENST00000304883 Transcript missense_variant 1453/5190 1312/1398 438/465 G/C Ggc/Tgc 1 -1 TACR3 HGNC HGNC:11528 protein_coding YES CCDS3664.1 ENSP00000303325 P29371 UPI0000050413 NM_001059.2 deleterious(0.01) 5/5 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF46 MODERATE 1 SNV 1 1 PASS rs1308179178 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 103589768 103589768 C A 1 0 0 0 0 1 0 0 0 15903 594 21 2 2 TACR3 4 103589768 Missense_Mutation SNP C C3L-00279_T 8254176 103589768 86624787 170 5948 DKK2 0 . GRCh38 4 107035416 107035416 + Missense_Mutation SNP T T A C3L-00279_T C3L-00279_N T T c.176A>T p.Gln59Leu p.Q59L ENST00000285311 1/4 363 342 21 301 300 1 varscan-mutect DKK2,missense_variant,p.Gln59Leu,ENST00000285311,NM_014421.2;DKK2,intron_variant,,ENST00000513208,;DKK2,intron_variant,,ENST00000510463,;DKK2,non_coding_transcript_exon_variant,,ENST00000510534,; A ENST00000285311 Transcript missense_variant 882/3638 176/780 59/259 Q/L cAa/cTa COSM4452306 1 -1 DKK2 HGNC HGNC:2892 protein_coding YES CCDS3675.1 ENSP00000285311 Q9UBU2 UPI0000048EF2 NM_014421.2 tolerated(0.29) 1/4 hmmpanther:PTHR12113:SF12,hmmpanther:PTHR12113 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 107035416 107035416 T A 1 0 0 0 0 1 0 0 0 4351 1812 63 4 4 DKK2 4 107035416 Missense_Mutation SNP T C3L-00279_T 3445648 107035416 83179139 171 5949 GAR1 0 . GRCh38 4 109816292 109816292 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.128G>T p.Gly43Val p.G43V ENST00000226796 2/7 131 106 25 137 137 0 strelka-varscan-mutect GAR1,missense_variant,p.Gly43Val,ENST00000226796,NM_018983.3;GAR1,missense_variant,p.Gly43Val,ENST00000394631,NM_032993.2;RP11-602N24.3,upstream_gene_variant,,ENST00000609440,;GAR1,non_coding_transcript_exon_variant,,ENST00000503671,;GAR1,non_coding_transcript_exon_variant,,ENST00000506840,; T ENST00000226796 Transcript missense_variant 392/1224 128/654 43/217 G/V gGc/gTc 1 1 GAR1 HGNC HGNC:14264 protein_coding YES CCDS34050.1 ENSP00000226796 Q9NY12 A0A024RDJ3 UPI0000070C13 NM_018983.3 deleterious_low_confidence(0.01) 2/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 109816292 109816292 G T 1 0 0 0 0 1 0 0 0 6108 1203 42 2 2 GAR1 4 109816292 Missense_Mutation SNP G C3L-00279_T 2780876 109816292 80398263 172 5950 ANK2 0 . GRCh38 4 113242186 113242186 + Missense_Mutation SNP G G A rs761620495 C3L-00279_T C3L-00279_N G G c.868G>A p.Gly290Ser p.G290S ENST00000357077 9/46 538 509 29 451 450 1 strelka-varscan-mutect ANK2,missense_variant,p.Gly290Ser,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Gly290Ser,ENST00000264366,;ANK2,missense_variant,p.Gly269Ser,ENST00000506722,NM_001127493.1;ANK2,missense_variant,p.Gly290Ser,ENST00000394537,NM_020977.3;ANK2,missense_variant,p.Gly305Ser,ENST00000504454,;ANK2,missense_variant,p.Gly269Ser,ENST00000503423,;ANK2,missense_variant,p.Gly262Ser,ENST00000634436,;ANK2,missense_variant,p.Gly269Ser,ENST00000503271,; A ENST00000357077 Transcript missense_variant 921/14196 868/11874 290/3957 G/S Ggt/Agt rs761620495,COSM4661560,COSM4661561 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated(0.35) 9/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs761620495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 113242186 113242186 G A 1 0 0 0 0 1 0 0 0 721 1116 39 1 1 ANK2 4 113242186 Missense_Mutation SNP G C3L-00279_T 3425894 113242186 76972369 173 5951 ANK2 0 . GRCh38 4 113357397 113357397 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.8779C>A p.Pro2927Thr p.P2927T ENST00000357077 38/46 735 679 56 216 216 0 strelka-varscan-mutect ANK2,missense_variant,p.Pro2927Thr,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Pro2894Thr,ENST00000264366,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript missense_variant 8832/14196 8779/11874 2927/3957 P/T Cct/Act 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 113357397 113357397 C A 1 0 0 0 0 1 0 0 0 721 623 22 2 2 ANK2 4 113357397 Missense_Mutation SNP C C3L-00279_T 115211 113357397 76857158 174 5952 FAT4 0 . GRCh38 4 125490363 125490363 + Frame_Shift_Del DEL C C - C3L-00279_T C3L-00279_N C C c.13542delC p.Val4515SerfsTer9 p.V4515Sfs*9 ENST00000394329 17/17 391 348 43 473 473 0 sindel-varindel-pindel FAT4,frameshift_variant,p.Val4515SerfsTer9,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,frameshift_variant,p.Val2756SerfsTer9,ENST00000335110,; - ENST00000394329 Transcript frameshift_variant 13554/16123 13541/14946 4514/4981 T/X aCc/ac COSM3600101,COSM3600102 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 17/17 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 1,1 HIGH 1 deletion 5 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 125490363 125490363 C - 1 0 1 0 1 0 0 0 0 5552 507 18 0 0 FAT4 4 125490363 Frame_Shift_Del DEL C C3L-00279_T 12132966 125490363 64724192 175 5953 PCDH10 0 . GRCh38 4 133151324 133151324 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1184G>T p.Cys395Phe p.C395F ENST00000264360 1/5 316 276 40 351 351 0 strelka-varscan-mutect PCDH10,missense_variant,p.Cys395Phe,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Cys395Phe,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; T ENST00000264360 Transcript missense_variant 2010/8489 1184/3123 395/1040 C/F tGc/tTc 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 deleterious(0) 1/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 133151324 133151324 G T 1 0 0 0 0 1 0 0 0 11594 1319 46 2 2 PCDH10 4 133151324 Missense_Mutation SNP G C3L-00279_T 7660961 133151324 57063231 176 5954 MAML3 0 . GRCh38 4 139719709 139719709 + Missense_Mutation SNP C C A rs373700602 C3L-00279_T C3L-00279_N C C c.3031G>T p.Val1011Leu p.V1011L ENST00000509479 5/5 231 188 43 207 207 0 strelka-varscan-mutect MAML3,missense_variant,p.Val1011Leu,ENST00000509479,NM_018717.4;MGST2,intron_variant,,ENST00000616265,NM_001204367.1,NM_001204366.1;MAML3,downstream_gene_variant,,ENST00000502696,;MGST2,intron_variant,,ENST00000515137,;MGST2,intron_variant,,ENST00000503816,; A ENST00000509479 Transcript missense_variant 3888/6844 3031/3417 1011/1138 V/L Gtg/Ttg rs373700602,COSM4122412,COSM4122413 1 -1 MAML3 HGNC HGNC:16272 protein_coding YES CCDS54805.1 ENSP00000421180 Q96JK9 UPI00001C1E1E NM_018717.4 tolerated(0.56) 5/5 hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF8 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs373700602 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 139719709 139719709 C A 1 0 0 0 0 1 0 0 0 9128 536 19 1 1 MAML3 4 139719709 Missense_Mutation SNP C C3L-00279_T 6568385 139719709 50494846 177 5955 SMARCA5 0 . GRCh38 4 143548079 143548079 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.2924A>T p.Gln975Leu p.Q975L ENST00000283131 22/24 99 92 7 37 37 0 strelka-mutect SMARCA5,missense_variant,p.Gln975Leu,ENST00000283131,NM_003601.3;SMARCA5,non_coding_transcript_exon_variant,,ENST00000508573,;SMARCA5,downstream_gene_variant,,ENST00000515531,; T ENST00000283131 Transcript missense_variant 3386/7923 2924/3159 975/1052 Q/L cAg/cTg 1 1 SMARCA5 HGNC HGNC:11101 protein_coding YES CCDS3761.1 ENSP00000283131 O60264 UPI000006E693 NM_003601.3 tolerated(0.13) 22/24 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF691,Pfam_domain:PF09111,Gene3D:1.10.10.60,SMART_domains:SM00717,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -14.38904 1 1 1 1 0 T 3 4 14 143548079 143548079 A T 1 0 0 0 0 1 0 0 0 15064 188 7 4 4 SMARCA5 4 143548079 Missense_Mutation SNP A C3L-00279_T 3828370 143548079 46666476 178 5956 GYPE 0 . GRCh38 4 143876855 143876855 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.137G>A p.Gly46Glu p.G46E ENST00000358615 3/4 276 226 50 82 82 0 strelka-varscan-mutect GYPE,missense_variant,p.Gly46Glu,ENST00000358615,NM_198682.2;GYPE,missense_variant,p.Gly46Glu,ENST00000437468,NM_002102.3;GYPE,intron_variant,,ENST00000506264,; T ENST00000358615 Transcript missense_variant,splice_region_variant 189/1684 137/237 46/78 G/E gGg/gAg 1 -1 GYPE HGNC HGNC:4705 protein_coding YES CCDS47138.1 ENSP00000351430 P15421 UPI000012B76B NM_198682.2 tolerated_low_confidence(0.12) 3/4 hmmpanther:PTHR13813 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 143876855 143876855 C T 1 0 0 0 0 1 0 0 0 6793 637 22 3 3 GYPE 4 143876855 Missense_Mutation SNP C C3L-00279_T 328776 143876855 46337700 179 5957 DCHS2 0 . GRCh38 4 154320598 154320598 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.3436C>A p.Leu1146Met p.L1146M ENST00000623607 14/25 547 475 72 484 482 2 strelka-varscan DCHS2,missense_variant,p.Leu1146Met,ENST00000357232,;DCHS2,missense_variant,p.Leu1146Met,ENST00000623607,NM_017639.3;DCHS2,downstream_gene_variant,,ENST00000339452,NM_001142552.1; T ENST00000623607 Transcript missense_variant 3436/8912 3436/8751 1146/2916 L/M Ctg/Atg 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 tolerated(0.09) 14/25 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 154320598 154320598 G T 1 0 0 0 0 1 0 0 0 4091 1020 36 2 2 DCHS2 4 154320598 Missense_Mutation SNP G C3L-00279_T 10443743 154320598 35893957 180 5958 FSTL5 0 . GRCh38 4 161481035 161481035 + Silent SNP G G C novel C3L-00279_T C3L-00279_N G G c.1593C>G p.= p.S531S ENST00000306100 13/16 197 158 39 130 130 0 strelka-varscan FSTL5,synonymous_variant,p.=,ENST00000306100,NM_020116.4;FSTL5,synonymous_variant,p.=,ENST00000379164,NM_001128427.2;FSTL5,synonymous_variant,p.=,ENST00000427802,NM_001128428.2; C ENST00000306100 Transcript synonymous_variant 2030/4831 1593/2544 531/847 S tcC/tcG 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 13/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Gene3D:2.130.10.10,Superfamily_domains:0047643 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 14 161481035 161481035 G C 1 0 0 0 0 0 0 0 1 5954 1219 43 4 4 FSTL5 4 161481035 Silent SNP G C3L-00279_T 7160437 161481035 28733520 181 5959 TRIML2 0 . GRCh38 4 188091443 188091443 + Missense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.1244G>A p.Gly415Glu p.G415E ENST00000512729 7/7 199 162 37 164 164 0 strelka-varscan TRIML2,missense_variant,p.Gly415Glu,ENST00000512729,NM_173553.2;TRIML2,missense_variant,p.Gly400Glu,ENST00000326754,NM_001303419.1;TRIML2,3_prime_UTR_variant,,ENST00000503141,;TRIML2,3_prime_UTR_variant,,ENST00000503475,; T ENST00000512729 Transcript missense_variant 1469/1639 1244/1314 415/437 G/E gGa/gAa COSM3131976 1 -1 TRIML2 HGNC HGNC:26378 protein_coding YES ENSP00000422581 Q8N7C3 UPI000020B818 NM_173553.2 tolerated(0.76) 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF347,hmmpanther:PTHR24103,SMART_domains:SM00449,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 188091443 188091443 C T 1 0 0 0 0 1 0 0 0 17048 855 30 3 3 TRIML2 4 188091443 Missense_Mutation SNP C C3L-00279_T 26610408 188091443 2123112 182 5960 TRIML1 0 . GRCh38 4 188140593 188140593 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.474C>A p.= p.T158T ENST00000332517 2/6 239 211 28 185 185 0 strelka-varscan TRIML1,synonymous_variant,p.=,ENST00000332517,NM_178556.3;RP11-366H4.3,downstream_gene_variant,,ENST00000501322,;TRIML1,upstream_gene_variant,,ENST00000507581,;TRIML1,upstream_gene_variant,,ENST00000512233,; A ENST00000332517 Transcript synonymous_variant 614/1797 474/1407 158/468 T acC/acA 1 1 TRIML1 HGNC HGNC:26698 protein_coding YES CCDS3851.1 ENSP00000327738 Q8N9V2 UPI000006FC8A NM_178556.3 2/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF350 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 188140593 188140593 C A 1 0 0 0 0 0 0 0 1 17047 610 22 2 2 TRIML1 4 188140593 Silent SNP C C3L-00279_T 49150 188140593 2073962 183 5961 IRX2 0 . GRCh38 5 2748882 2748882 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.826G>T p.Gly276Cys p.G276C ENST00000382611 3/5 261 222 39 288 288 0 strelka-varscan-mutect IRX2,missense_variant,p.Gly276Cys,ENST00000382611,NM_001134222.1;IRX2,missense_variant,p.Gly276Cys,ENST00000302057,NM_033267.4;C5orf38,upstream_gene_variant,,ENST00000515640,NM_001306150.1;C5orf38,upstream_gene_variant,,ENST00000334000,NM_001306149.1,NM_178569.3;C5orf38,upstream_gene_variant,,ENST00000397835,;C5orf38,upstream_gene_variant,,ENST00000505778,;C5orf38,upstream_gene_variant,,ENST00000457752,NM_001294337.1;C5orf38,upstream_gene_variant,,ENST00000503940,;C5orf38,upstream_gene_variant,,ENST00000505106,; A ENST00000382611 Transcript missense_variant 1075/2630 826/1416 276/471 G/C Ggc/Tgc COSM4790519,COSM5332780 1 -1 IRX2 HGNC HGNC:14359 protein_coding YES CCDS3868.1 ENSP00000372056 Q9BZI1 UPI00001B6456 NM_001134222.1 tolerated(0.05) 3/5 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF15 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 2748882 2748882 C A 1 0 0 0 0 1 0 0 0 7752 623 22 2 2 IRX2 5 2748882 Missense_Mutation SNP C C3L-00279_T 2748882 178789377 184 5962 ADCY2 0 . GRCh38 5 7773015 7773015 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2298G>T p.Met766Ile p.M766I ENST00000338316 18/25 289 264 25 281 280 1 strelka-varscan-mutect ADCY2,missense_variant,p.Met766Ile,ENST00000338316,NM_020546.2;ADCY2,upstream_gene_variant,,ENST00000493243,; T ENST00000338316 Transcript missense_variant 2387/6575 2298/3276 766/1091 M/I atG/atT 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0) 18/25 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 7773015 7773015 G T 1 0 0 0 0 1 0 0 0 338 1290 45 2 2 ADCY2 5 7773015 Missense_Mutation SNP G C3L-00279_T 5024133 7773015 173765244 185 5963 SEMA5A 0 . GRCh38 5 9054150 9054150 + Nonsense_Mutation SNP C C A rs868830163 C3L-00279_T C3L-00279_N C C c.2626G>T p.Gly876Ter p.G876* ENST00000382496 19/23 193 167 26 188 188 0 strelka-varscan-mutect SEMA5A,stop_gained,p.Gly876Ter,ENST00000382496,NM_003966.2;MIR4636,upstream_gene_variant,,ENST00000582271,; A ENST00000382496 Transcript stop_gained 3292/11762 2626/3225 876/1074 G/* Gga/Tga rs868830163,COSM5538748 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 19/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1 HIGH 1 SNV 1 0,1 1 PASS rs868830163 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 14 9054150 9054150 C A 1 0 0 0 0 0 1 0 0 14313 603 21 2 2 SEMA5A 5 9054150 Nonsense_Mutation SNP C C3L-00279_T 1281135 9054150 172484109 186 5964 CTNND2 0 . GRCh38 5 11397201 11397201 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.442C>A p.Pro148Thr p.P148T ENST00000304623 6/22 147 123 24 123 123 0 strelka-varscan-mutect CTNND2,missense_variant,p.Pro148Thr,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Pro57Thr,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Pro134Thr,ENST00000508761,;CTNND2,missense_variant,p.Pro57Thr,ENST00000513598,;CTNND2,intron_variant,,ENST00000503622,NM_001288716.1;CTNND2,intron_variant,,ENST00000502551,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,intron_variant,,ENST00000511278,;CTNND2,missense_variant,p.Pro148Thr,ENST00000504499,;CTNND2,intron_variant,,ENST00000513588,; T ENST00000304623 Transcript missense_variant,splice_region_variant 632/5481 442/3678 148/1225 P/T Ccc/Acc 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0.01) 6/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS rs1166866077 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 11397201 11397201 G T 1 0 0 0 0 1 0 0 0 3829 1217 42 2 2 CTNND2 5 11397201 Missense_Mutation SNP G C3L-00279_T 2343051 11397201 170141058 187 5965 PRDM9 0 . GRCh38 5 23510025 23510026 + Frame_Shift_Ins INS - - G novel C3L-00279_T C3L-00279_N - - c.299_300insG p.Val101SerfsTer14 p.V101Sfs*14 ENST00000296682 4/11 544 473 71 395 395 0 varindel-pindel PRDM9,frameshift_variant,p.Val101SerfsTer14,ENST00000296682,NM_020227.2;PRDM9,frameshift_variant,p.Val42SerfsTer14,ENST00000635252,;PRDM9,frameshift_variant,p.Gln101GlnfsTer?,ENST00000502755,; G ENST00000296682 Transcript frameshift_variant,splice_region_variant 481-482/3691 299-300/2685 100/894 Q/QX caa/caGa 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 4/11 HIGH 1 insertion 1 1 PASS . . 0 207 0 0 3 0 0 0 -20 0.9599046 1 1 1 0 G 7 5 14 23510025 23510025 - G 1 0 1 1 0 0 0 0 0 12595 144 5 0 0 PRDM9 5 23510025 Frame_Shift_Ins INS - C3L-00279_T 12112824 23510025 158028234 188 5966 PRDM9 0 . GRCh38 5 23522845 23522845 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.842C>A p.Thr281Lys p.T281K ENST00000296682 8/11 572 497 75 493 493 0 strelka-varscan-mutect PRDM9,missense_variant,p.Thr281Lys,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Thr222Lys,ENST00000635252,; A ENST00000296682 Transcript missense_variant 1024/3691 842/2685 281/894 T/K aCa/aAa 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 8/11 PROSITE_profiles:PS50280,hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Pfam_domain:PF00856,Gene3D:2.170.270.10,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 23522845 23522845 C A 1 0 0 0 0 1 0 0 0 12595 478 17 2 2 PRDM9 5 23522845 Missense_Mutation SNP C C3L-00279_T 12820 23522845 158015414 189 5967 ADAMTS12 0 . GRCh38 5 33576998 33576998 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.3028A>T p.Ile1010Phe p.I1010F ENST00000504830 19/24 411 362 49 396 396 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Ile1010Phe,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Ile925Phe,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; A ENST00000504830 Transcript missense_variant 3364/8774 3028/4785 1010/1594 I/F Att/Ttt 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.08) 19/24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 33576998 33576998 T A 1 0 0 0 0 1 0 0 0 301 1406 49 4 4 ADAMTS12 5 33576998 Missense_Mutation SNP T C3L-00279_T 10054153 33576998 147961261 190 5968 AGXT2 0 . GRCh38 5 35032809 35032809 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.692T>A p.Val231Asp p.V231D ENST00000231420 7/14 566 509 57 556 555 1 strelka-varscan-mutect AGXT2,missense_variant,p.Val231Asp,ENST00000231420,NM_031900.3;AGXT2,missense_variant,p.Val231Asp,ENST00000618015,;AGXT2,missense_variant,p.Val231Asp,ENST00000510428,;AGXT2,downstream_gene_variant,,ENST00000505542,; T ENST00000231420 Transcript missense_variant 893/2364 692/1545 231/514 V/D gTt/gAt 1 -1 AGXT2 HGNC HGNC:14412 protein_coding YES CCDS3908.1 ENSP00000231420 Q9BYV1 UPI0000125709 NM_031900.3 tolerated(0.12) 7/14 Gene3D:3.40.640.10,Pfam_domain:PF00202,hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF58,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 35032809 35032809 A T 1 0 0 0 0 1 0 0 0 484 43 2 4 4 AGXT2 5 35032809 Missense_Mutation SNP A C3L-00279_T 1455811 35032809 146505450 191 5969 OSMR 0 . GRCh38 5 38881666 38881666 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.320G>C p.Cys107Ser p.C107S ENST00000274276 4/18 408 340 68 298 298 0 strelka-varscan-mutect OSMR,missense_variant,p.Cys107Ser,ENST00000274276,NM_001323505.1,NM_001323506.1,NM_003999.2;OSMR,missense_variant,p.Cys107Ser,ENST00000502536,NM_001168355.1; C ENST00000274276 Transcript missense_variant 722/5539 320/2940 107/979 C/S tGt/tCt 1 1 OSMR HGNC HGNC:8507 protein_coding YES CCDS3928.1 ENSP00000274276 Q99650 UPI000004CAC3 NM_001323505.1,NM_001323506.1,NM_003999.2 deleterious(0) 4/18 hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF95 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 38881666 38881666 G C 1 0 0 0 0 1 0 0 0 11359 1377 48 4 4 OSMR 5 38881666 Missense_Mutation SNP G C3L-00279_T 3848857 38881666 142656593 192 5970 C9 0 . GRCh38 5 39316028 39316028 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.617C>A p.Thr206Asn p.T206N ENST00000263408 6/11 126 109 17 35 35 0 strelka-varscan C9,missense_variant,p.Thr206Asn,ENST00000263408,NM_001737.3;C9,splice_region_variant,,ENST00000509186,; T ENST00000263408 Transcript missense_variant,splice_region_variant 713/2713 617/1680 206/559 T/N aCc/aAc 1 -1 C9 HGNC HGNC:1358 protein_coding YES CCDS3929.1 ENSP00000263408 P02748 UPI0000001065 NM_001737.3 deleterious(0) 6/11 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF362,hmmpanther:PTHR19325 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 39316028 39316028 G T 1 0 0 0 0 1 0 0 0 2169 1275 44 2 2 C9 5 39316028 Missense_Mutation SNP G C3L-00279_T 434362 39316028 142222231 193 5971 MROH2B 0 . GRCh38 5 41033103 41033103 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2299C>A p.Gln767Lys p.Q767K ENST00000399564 23/42 373 332 41 183 183 0 strelka-varscan-mutect MROH2B,missense_variant,p.Gln767Lys,ENST00000399564,NM_173489.4;MROH2B,missense_variant,p.Gln322Lys,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,; T ENST00000399564 Transcript missense_variant 2750/5239 2299/4758 767/1585 Q/K Caa/Aaa 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 tolerated(1) 23/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 41033103 41033103 G T 1 0 0 0 0 1 0 0 0 9745 1357 47 2 2 MROH2B 5 41033103 Missense_Mutation SNP G C3L-00279_T 1717075 41033103 140505156 194 5972 HCN1 0 . GRCh38 5 45303666 45303666 + Missense_Mutation SNP G G C C3L-00279_T C3L-00279_N G G c.1551C>G p.His517Gln p.H517Q ENST00000303230 6/8 507 450 57 229 229 0 strelka-varscan-mutect HCN1,missense_variant,p.His517Gln,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; C ENST00000303230 Transcript missense_variant 1792/9885 1551/2673 517/890 H/Q caC/caG COSM257091 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 deleterious(0.02) 6/8 Gene3D:2.60.120.10,Pfam_domain:PF00027,PROSITE_patterns:PS00888,PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,SMART_domains:SM00100,Superfamily_domains:SSF51206 1 MODERATE 1 SNV 1 1 1 PASS rs1007416378 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 45303666 45303666 G C 1 0 0 0 0 1 0 0 0 6883 1136 40 4 4 HCN1 5 45303666 Missense_Mutation SNP G C3L-00279_T 4270563 45303666 136234593 195 5973 IL6ST 0 . GRCh38 5 55951993 55951993 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1635T>A p.Asp545Glu p.D545E ENST00000381298 13/17 128 109 19 66 66 0 strelka-varscan-mutect IL6ST,missense_variant,p.Asp545Glu,ENST00000381298,NM_002184.3;IL6ST,missense_variant,p.Asp545Glu,ENST00000336909,;IL6ST,missense_variant,p.Asp545Glu,ENST00000502326,;IL6ST,missense_variant,p.Asp484Glu,ENST00000381294,NM_001190981.1;IL6ST,3_prime_UTR_variant,,ENST00000381287,NM_175767.2;IL6ST,3_prime_UTR_variant,,ENST00000522633,;IL6ST,intron_variant,,ENST00000381293,;IL6ST,intron_variant,,ENST00000381286,;IL6ST,upstream_gene_variant,,ENST00000423954,;IL6ST,3_prime_UTR_variant,,ENST00000503773,;IL6ST,upstream_gene_variant,,ENST00000523039,;IL6ST,upstream_gene_variant,,ENST00000583149,;IL6ST,downstream_gene_variant,,ENST00000506241,; T ENST00000381298 Transcript missense_variant 1948/9057 1635/2757 545/918 D/E gaT/gaA 1 -1 IL6ST HGNC HGNC:6021 protein_coding YES CCDS3971.1 ENSP00000370698 P40189 UPI000013CF29 NM_002184.3 tolerated(0.31) 13/17 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF83,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1180867411 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 55951993 55951993 A T 1 0 0 0 0 1 0 0 0 7607 214 8 4 4 IL6ST 5 55951993 Missense_Mutation SNP A C3L-00279_T 10648327 55951993 125586266 196 5974 VCAN 0 . GRCh38 5 83542180 83542180 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.9177A>G p.= p.P3059P ENST00000265077 8/15 408 356 52 268 268 0 strelka-varscan-mutect VCAN,synonymous_variant,p.=,ENST00000265077,NM_004385.4;VCAN,synonymous_variant,p.=,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,non_coding_transcript_exon_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; G ENST00000265077 Transcript synonymous_variant 9742/12625 9177/10191 3059/3396 P ccA/ccG 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 83542180 83542180 A G 1 0 0 0 0 0 0 0 1 17683 204 8 5 5 VCAN 5 83542180 Silent SNP A C3L-00279_T 27590187 83542180 97996079 197 5975 FBN2 0 . GRCh38 5 128277929 128277929 + Nonsense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.7422C>A p.Cys2474Ter p.C2474* ENST00000508053 64/71 540 454 86 501 501 0 strelka-varscan-mutect FBN2,stop_gained,p.Cys2474Ter,ENST00000508053,;FBN2,stop_gained,p.Cys2474Ter,ENST00000262464,NM_001999.3;FBN2,stop_gained,p.Cys2473Ter,ENST00000619499,; T ENST00000508053 Transcript stop_gained 8397/11132 7422/8739 2474/2912 C/* tgC/tgA COSM1060312,COSM1060313 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 64/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS00010,PROSITE_patterns:PS01186,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 1,1 HIGH 1 SNV 5 1,1 1 PASS rs1223904235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 128277929 128277929 G T 1 0 0 0 0 0 1 0 0 5566 963 34 2 2 FBN2 5 128277929 Nonsense_Mutation SNP G C3L-00279_T 44735749 128277929 53260330 198 5976 FBN2 0 . GRCh38 5 128290795 128290795 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.6382T>A p.Cys2128Ser p.C2128S ENST00000508053 56/71 347 296 51 269 268 1 strelka-varscan-mutect FBN2,missense_variant,p.Cys2128Ser,ENST00000508053,;FBN2,missense_variant,p.Cys2128Ser,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Cys2127Ser,ENST00000619499,; T ENST00000508053 Transcript missense_variant 7357/11132 6382/8739 2128/2912 C/S Tgt/Agt 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 56/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 128290795 128290795 A T 1 0 0 0 0 1 0 0 0 5566 188 7 4 4 FBN2 5 128290795 Missense_Mutation SNP A C3L-00279_T 12866 128290795 53247464 199 5977 SLC27A6 0 . GRCh38 5 128988748 128988748 + Nonsense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.834T>A p.Cys278Ter p.C278* ENST00000262462 3/10 152 125 27 102 102 0 strelka-varscan-mutect SLC27A6,stop_gained,p.Cys278Ter,ENST00000262462,;SLC27A6,stop_gained,p.Cys278Ter,ENST00000395266,NM_014031.3,NM_001017372.1;SLC27A6,stop_gained,p.Cys278Ter,ENST00000506176,;SLC27A6,stop_gained,p.Cys97Ter,ENST00000508645,; A ENST00000262462 Transcript stop_gained 1844/3219 834/1860 278/619 C/* tgT/tgA 1 1 SLC27A6 HGNC HGNC:11000 protein_coding YES CCDS4145.1 ENSP00000262462 Q9Y2P4 UPI0000038E83 3/10 hmmpanther:PTHR24096:SF98,hmmpanther:PTHR24096,Pfam_domain:PF00501,Gene3D:3.40.50.980,Superfamily_domains:SSF56801 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 128988748 128988748 T A 1 0 0 0 0 0 1 0 0 14800 1702 59 4 4 SLC27A6 5 128988748 Nonsense_Mutation SNP T C3L-00279_T 697953 128988748 52549511 200 5978 PCDHA3 0 . GRCh38 5 140803492 140803492 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.2295C>A p.= p.P765P ENST00000522353 1/4 239 202 37 222 221 1 strelka-varscan-mutect PCDHA3,synonymous_variant,p.=,ENST00000522353,NM_018906.2;PCDHA3,synonymous_variant,p.=,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000530339,NM_018907.3;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; A ENST00000522353 Transcript synonymous_variant 2295/5260 2295/2853 765/950 P ccC/ccA 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 140803492 140803492 C A 1 0 0 0 0 0 0 0 1 11612 581 21 2 2 PCDHA3 5 140803492 Silent SNP C C3L-00279_T 11814744 140803492 40734767 201 5979 PCDHB2 0 . GRCh38 5 141096342 141096342 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1552C>A p.Leu518Ile p.L518I ENST00000194155 1/1 880 766 114 1041 1041 0 strelka-varscan-mutect PCDHB2,missense_variant,p.Leu518Ile,ENST00000194155,NM_018936.3;PCDHB2,3_prime_UTR_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000624874,;PCDHB2,downstream_gene_variant,,ENST00000625033,;PCDHB2,upstream_gene_variant,,ENST00000624994,;CTC-270D5.1,non_coding_transcript_exon_variant,,ENST00000623615,;CTC-270D5.1,non_coding_transcript_exon_variant,,ENST00000623741,;AC005754.7,downstream_gene_variant,,ENST00000607216,;AC005754.7,downstream_gene_variant,,ENST00000625128,;AC005754.7,downstream_gene_variant,,ENST00000625066,;AC005754.7,downstream_gene_variant,,ENST00000624802,; A ENST00000194155 Transcript missense_variant 1765/4126 1552/2397 518/798 L/I Ctc/Atc 1 1 PCDHB2 HGNC HGNC:8687 protein_coding YES CCDS4244.1 ENSP00000194155 Q9Y5E7 UPI00001273DC NM_018936.3 deleterious_low_confidence(0.01) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 141096342 141096342 C A 1 0 0 0 0 1 0 0 0 11629 913 32 2 2 PCDHB2 5 141096342 Missense_Mutation SNP C C3L-00279_T 292850 141096342 40441917 202 5980 PCDHB3 0 . GRCh38 5 141102213 141102213 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.1564G>A p.Glu522Lys p.E522K ENST00000231130 1/1 905 790 115 876 876 0 varscan-mutect PCDHB3,missense_variant,p.Glu522Lys,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000194155,NM_018936.3;PCDHB2,downstream_gene_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000624513,;AC005754.7,non_coding_transcript_exon_variant,,ENST00000607216,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; A ENST00000231130 Transcript missense_variant 1741/3355 1564/2391 522/796 E/K Gag/Aag COSM3610570 1 1 PCDHB3 HGNC HGNC:8688 protein_coding YES CCDS4245.1 ENSP00000231130 Q9Y5E6 UPI0003CC25DF NM_018937.4 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE SNV 1 1 PASS rs1440048692 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 141102213 141102213 G A 1 0 0 0 0 1 0 0 0 11630 1059 37 1 1 PCDHB3 5 141102213 Missense_Mutation SNP G C3L-00279_T 5871 141102213 40436046 203 5981 PCDHB6 0 . GRCh38 5 141151987 141151987 + Missense_Mutation SNP C C A rs782167344 C3L-00279_T C3L-00279_N C C c.1730C>A p.Ala577Glu p.A577E ENST00000231136 1/1 761 661 100 817 815 2 varscan-mutect PCDHB6,missense_variant,p.Ala577Glu,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Ala441Glu,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; A ENST00000231136 Transcript missense_variant 1966/3266 1730/2385 577/794 A/E gCg/gAg rs782167344 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 deleterious(0.01) 1/1 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS rs782167344 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 141151987 141151987 C A 1 0 0 0 0 1 0 0 0 11633 768 27 1 1 PCDHB6 5 141151987 Missense_Mutation SNP C C3L-00279_T 49774 141151987 40386272 204 5982 PCDHB12 0 . GRCh38 5 141211059 141211059 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.2152A>T p.Arg718Trp p.R718W ENST00000239450 1/1 376 312 64 386 386 0 strelka-varscan-mutect PCDHB12,missense_variant,p.Arg718Trp,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Arg381Trp,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239450 Transcript missense_variant 2341/3853 2152/2388 718/795 R/W Agg/Tgg 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Pfam_domain:PF16492 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 141211059 141211059 A T 1 0 0 0 0 1 0 0 0 11624 179 7 4 4 PCDHB12 5 141211059 Missense_Mutation SNP A C3L-00279_T 59072 141211059 40327200 205 5983 PCDHGB2 0 . GRCh38 5 141360839 141360839 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.704C>A p.Ala235Asp p.A235D ENST00000522605 1/4 168 143 25 164 164 0 strelka-varscan-mutect PCDHGB2,missense_variant,p.Ala235Asp,ENST00000522605,NM_018923.2;PCDHGB2,missense_variant,p.Ala235Asp,ENST00000622527,NM_032096.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA5,upstream_gene_variant,,ENST00000518069,NM_018918.2;PCDHGA5,upstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA4,downstream_gene_variant,,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000522605 Transcript missense_variant 704/4602 704/2796 235/931 A/D gCc/gAc 1 1 PCDHGB2 HGNC HGNC:8709 protein_coding YES CCDS54924.1 ENSP00000429018 Q9Y5G2 UPI000006EE67 NM_018923.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF73,hmmpanther:PTHR24028,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS rs1337655560 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 141360839 141360839 C A 1 0 0 0 0 1 0 0 0 11650 739 26 2 2 PCDHGB2 5 141360839 Missense_Mutation SNP C C3L-00279_T 149780 141360839 40177420 206 5984 KCTD16 0 . GRCh38 5 144206924 144206924 + Frame_Shift_Del DEL G G - novel C3L-00279_T C3L-00279_N G G c.212delG p.Gly71GlufsTer36 p.G71Efs*36 ENST00000507359 2/3 111 99 12 98 98 0 sindel-varindel-pindel KCTD16,frameshift_variant,p.Gly71GlufsTer36,ENST00000507359,;KCTD16,frameshift_variant,p.Gly71GlufsTer36,ENST00000512467,NM_020768.3; - ENST00000507359 Transcript frameshift_variant 1301/13950 210/1287 70/428 K/X aaG/aa 1 1 KCTD16 HGNC HGNC:29244 protein_coding YES CCDS34260.1 ENSP00000426548 Q68DU8 UPI000004A046 2/3 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF28,Pfam_domain:PF02214,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 HIGH 1 deletion 1 2 1 PASS . . 0 206 2 2 0 0 0 0 -18.39634 0.9999962 1 1 1 0 - 7 5 14 144206924 144206924 G - 1 0 1 0 1 0 0 0 0 8020 991 35 0 0 KCTD16 5 144206924 Frame_Shift_Del DEL G C3L-00279_T 2846085 144206924 37331335 207 5985 PDGFRB 0 . GRCh38 5 150115939 150115939 + Missense_Mutation SNP G G T rs529787907 C3L-00279_T C3L-00279_N G G c.3145C>A p.Leu1049Met p.L1049M ENST00000261799 23/23 101 86 15 105 105 0 strelka-varscan-mutect PDGFRB,missense_variant,p.Leu1049Met,ENST00000261799,NM_002609.3;CSF1R,upstream_gene_variant,,ENST00000286301,NM_001288705.1,NM_005211.3;CSF1R,upstream_gene_variant,,ENST00000511344,;PDGFRB,downstream_gene_variant,,ENST00000519575,;PDGFRB,upstream_gene_variant,,ENST00000520851,;PDGFRB,downstream_gene_variant,,ENST00000521723,;PDGFRB,3_prime_UTR_variant,,ENST00000520579,; T ENST00000261799 Transcript missense_variant 3615/5717 3145/3321 1049/1106 L/M Ctg/Atg rs529787907 1 -1 PDGFRB HGNC HGNC:8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 UPI0000131791 NM_002609.3 tolerated(0.1) 23/23 PIRSF_domain:PIRSF000615,PIRSF_domain:PIRSF500948,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF53 MODERATE 1 SNV 1 1 PASS rs529787907 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 150115939 150115939 G T 1 0 0 0 0 1 0 0 0 11750 991 35 2 2 PDGFRB 5 150115939 Missense_Mutation SNP G C3L-00279_T 5909015 150115939 31422320 208 5986 SLC36A1 0 . GRCh38 5 151458847 151458847 + Missense_Mutation SNP G G T rs752896616 C3L-00279_T C3L-00279_N G G c.55G>T p.Val19Leu p.V19L ENST00000243389 2/11 157 138 19 163 163 0 strelka-varscan-mutect SLC36A1,missense_variant,p.Val19Leu,ENST00000243389,NM_078483.2;SLC36A1,missense_variant,p.Val19Leu,ENST00000520701,;SLC36A1,missense_variant,p.Val19Leu,ENST00000521925,;SLC36A1,missense_variant,p.Val19Leu,ENST00000616007,;SLC36A1,missense_variant,p.Val19Leu,ENST00000429484,NM_001308151.1;SLC36A1,missense_variant,p.Val19Leu,ENST00000520111,;SLC36A1,missense_variant,p.Val19Leu,ENST00000517945,;SLC36A1,missense_variant,p.Val19Leu,ENST00000519829,;SLC36A1,non_coding_transcript_exon_variant,,ENST00000521351,; T ENST00000243389 Transcript missense_variant 278/5781 55/1431 19/476 V/L Gtg/Ttg rs752896616 1 1 SLC36A1 HGNC HGNC:18761 protein_coding YES CCDS4316.1 ENSP00000243389 Q7Z2H8 UPI00001A9D3C NM_078483.2 tolerated(0.71) 2/11 hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF188 MODERATE 1 SNV 1 1 PASS rs752896616 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 151458847 151458847 G T 1 0 0 0 0 1 0 0 0 14871 1145 40 1 1 SLC36A1 5 151458847 Missense_Mutation SNP G C3L-00279_T 1342908 151458847 30079412 209 5987 ITK 0 . GRCh38 5 157244454 157244454 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1425G>T p.Glu475Asp p.E475D ENST00000422843 13/17 423 356 67 451 451 0 strelka-varscan-mutect ITK,missense_variant,p.Glu475Asp,ENST00000422843,NM_005546.3;ITK,non_coding_transcript_exon_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,upstream_gene_variant,,ENST00000523926,;ITK,downstream_gene_variant,,ENST00000520173,;ITK,downstream_gene_variant,,ENST00000519759,; T ENST00000422843 Transcript missense_variant 1577/4528 1425/1863 475/620 E/D gaG/gaT 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 tolerated(0.1) 13/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 157244454 157244454 G T 1 0 0 0 0 1 0 0 0 7815 991 35 2 2 ITK 5 157244454 Missense_Mutation SNP G C3L-00279_T 5785607 157244454 24293805 210 5988 DOCK2 0 . GRCh38 5 170034490 170034490 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.3559G>C p.Asp1187His p.D1187H ENST00000256935 35/52 319 271 48 370 370 0 strelka-varscan-mutect DOCK2,missense_variant,p.Asp1187His,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Asp679His,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,3_prime_UTR_variant,,ENST00000433448,; C ENST00000256935 Transcript missense_variant 3639/6097 3559/5493 1187/1830 D/H Gat/Cat 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0) 35/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 170034490 170034490 G C 1 0 0 0 0 1 0 0 0 4502 1174 41 4 4 DOCK2 5 170034490 Missense_Mutation SNP G C3L-00279_T 12790036 170034490 11503769 211 5989 HK3 0 . GRCh38 5 176889691 176889691 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.684G>T p.Met228Ile p.M228I ENST00000292432 7/19 306 263 43 305 304 1 strelka-varscan-mutect HK3,missense_variant,p.Met228Ile,ENST00000292432,NM_002115.2;HK3,3_prime_UTR_variant,,ENST00000504910,;HK3,intron_variant,,ENST00000509717,;HK3,upstream_gene_variant,,ENST00000506834,; A ENST00000292432 Transcript missense_variant 776/3066 684/2772 228/923 M/I atG/atT 1 -1 HK3 HGNC HGNC:4925 protein_coding YES CCDS4407.1 ENSP00000292432 P52790 A0A024R7R1 UPI000006E237 NM_002115.2 tolerated(0.19) 7/19 PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF1,Gene3D:3.40.367.20,Pfam_domain:PF00349,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 176889691 176889691 C A 1 0 0 0 0 1 0 0 0 7081 594 21 2 2 HK3 5 176889691 Missense_Mutation SNP C C3L-00279_T 6855201 176889691 4648568 212 5990 CANX 0 . GRCh38 5 179719709 179719709 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.953C>T p.Thr318Ile p.T318I ENST00000247461 9/15 206 184 22 184 184 0 strelka-varscan-mutect CANX,missense_variant,p.Thr318Ile,ENST00000247461,NM_001746.3;CANX,missense_variant,p.Thr318Ile,ENST00000452673,NM_001024649.1;CANX,missense_variant,p.Thr318Ile,ENST00000504734,;CANX,missense_variant,p.Thr254Ile,ENST00000502673,;CANX,downstream_gene_variant,,ENST00000508787,;CANX,downstream_gene_variant,,ENST00000503126,;CANX,3_prime_UTR_variant,,ENST00000514032,;CANX,downstream_gene_variant,,ENST00000506298,;CANX,upstream_gene_variant,,ENST00000505090,; T ENST00000247461 Transcript missense_variant 1153/4260 953/1779 318/592 T/I aCa/aTa 1 1 CANX HGNC HGNC:1473 protein_coding YES CCDS4447.1 ENSP00000247461 P27824 UPI000000D9F9 NM_001746.3 tolerated(0.15) 9/15 Gene3D:2.10.250.10,Pfam_domain:PF00262,hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF11,Superfamily_domains:SSF63887 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 179719709 179719709 C T 1 0 0 0 0 1 0 0 0 2311 478 17 3 3 CANX 5 179719709 Missense_Mutation SNP C C3L-00279_T 2830018 179719709 1818550 213 5991 BTNL8 0 . GRCh38 5 180911487 180911487 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.546C>T p.= p.N182N ENST00000340184 3/8 367 321 46 414 414 0 strelka-varscan-mutect BTNL8,synonymous_variant,p.=,ENST00000231229,NM_024850.2;BTNL8,synonymous_variant,p.=,ENST00000340184,NM_001040462.2;BTNL8,synonymous_variant,p.=,ENST00000508408,NM_001159708.1;BTNL8,synonymous_variant,p.=,ENST00000400707,NM_001159709.1;BTNL8,synonymous_variant,p.=,ENST00000610640,;BTNL8,synonymous_variant,p.=,ENST00000511704,NM_001159707.1;BTNL8,5_prime_UTR_variant,,ENST00000533815,NM_001159710.1;BTNL8,5_prime_UTR_variant,,ENST00000505126,;Y_RNA,downstream_gene_variant,,ENST00000410920,;BTNL8,non_coding_transcript_exon_variant,,ENST00000514448,;BTNL8,non_coding_transcript_exon_variant,,ENST00000513442,;BTNL8,upstream_gene_variant,,ENST00000503543,; T ENST00000340184 Transcript synonymous_variant 752/2071 546/1503 182/500 N aaC/aaT 1 1 BTNL8 HGNC HGNC:26131 protein_coding YES CCDS43413.1 ENSP00000342197 Q6UX41 UPI00000389ED NM_001040462.2 3/8 PROSITE_profiles:PS50835,hmmpanther:PTHR24100:SF73,hmmpanther:PTHR24100,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 180911487 180911487 C T 1 0 0 0 0 0 0 0 1 1743 477 17 3 3 BTNL8 5 180911487 Silent SNP C C3L-00279_T 1191778 180911487 626772 214 5992 OR2V2 0 . GRCh38 5 181155804 181155804 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.862C>A p.Pro288Thr p.P288T ENST00000328275 1/1 224 197 27 185 185 0 strelka-varscan-mutect OR2V2,missense_variant,p.Pro288Thr,ENST00000328275,NM_206880.1; A ENST00000328275 Transcript missense_variant 862/948 862/948 288/315 P/T Ccc/Acc COSM3615039,COSM4422191 1 1 OR2V2 HGNC HGNC:15341 protein_coding YES CCDS4461.1 ENSP00000332185 Q96R30 UPI0000041C79 NM_206880.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF235,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 181155804 181155804 C A 1 0 0 0 0 1 0 0 0 11109 623 22 2 2 OR2V2 5 181155804 Missense_Mutation SNP C C3L-00279_T 244317 181155804 382455 215 5993 EXOC2 0 . GRCh38 6 633079 633079 + Nonsense_Mutation SNP C C A rs551076085 C3L-00279_T C3L-00279_N C C c.157G>T p.Glu53Ter p.E53* ENST00000230449 3/28 227 188 39 119 119 0 strelka-varscan-mutect EXOC2,stop_gained,p.Glu53Ter,ENST00000230449,NM_018303.5;EXOC2,stop_gained,p.Glu53Ter,ENST00000443083,; A ENST00000230449 Transcript stop_gained 293/4449 157/2775 53/924 E/* Gaa/Taa rs551076085 1 -1 EXOC2 HGNC HGNC:24968 protein_coding YES CCDS34327.1 ENSP00000230449 Q96KP1 A0A024QZT2 UPI000003E7E3 NM_018303.5 3/28 hmmpanther:PTHR13043,Pfam_domain:PF01833,Gene3D:2.60.40.10,Superfamily_domains:SSF81296 HIGH 1 SNV 1 1 PASS rs551076085 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 633079 633079 C A 1 0 0 0 0 0 1 0 0 5169 922 32 2 2 EXOC2 6 633079 Nonsense_Mutation SNP C C3L-00279_T 633079 170172900 216 5994 ECI2 0 . GRCh38 6 4117416 4117416 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.921A>T p.= p.T307T ENST00000380118 9/10 199 170 29 111 111 0 strelka-varscan-mutect ECI2,synonymous_variant,p.=,ENST00000465828,;ECI2,synonymous_variant,p.=,ENST00000380118,NM_206836.2;ECI2,synonymous_variant,p.=,ENST00000380125,NM_001166010.1;ECI2,synonymous_variant,p.=,ENST00000361538,NM_006117.2;C6orf201,intron_variant,,ENST00000380175,NM_001085401.2;C6orf201,downstream_gene_variant,,ENST00000360378,;C6orf201,upstream_gene_variant,,ENST00000496987,;ECI2,3_prime_UTR_variant,,ENST00000380120,;ECI2,3_prime_UTR_variant,,ENST00000496241,;ECI2,3_prime_UTR_variant,,ENST00000478266,;ECI2,non_coding_transcript_exon_variant,,ENST00000464583,;ECI2,non_coding_transcript_exon_variant,,ENST00000464057,;C6orf201,intron_variant,,ENST00000436110,;C6orf201,intron_variant,,ENST00000427996,;C6orf201,intron_variant,,ENST00000451679,; A ENST00000380118 Transcript synonymous_variant 958/1407 921/1185 307/394 T acA/acT 1 -1 ECI2 HGNC HGNC:14601 protein_coding YES CCDS43420.2 ENSP00000369461 O75521 UPI000004ECA9 NM_206836.2 9/10 hmmpanther:PTHR23310:SF72,hmmpanther:PTHR23310,Gene3D:3.90.226.10,Pfam_domain:PF00378,Superfamily_domains:SSF52096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 4117416 4117416 T A 1 0 0 0 0 0 0 0 1 4724 1567 55 4 4 ECI2 6 4117416 Silent SNP T C3L-00279_T 3484337 4117416 166688563 217 5995 RPP40 0 . GRCh38 6 4995261 4995261 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.909A>C p.Glu303Asp p.E303D ENST00000380051 8/8 238 213 25 127 127 0 strelka-varscan-mutect RPP40,missense_variant,p.Glu303Asp,ENST00000380051,NM_006638.3;RPP40,missense_variant,p.Glu280Asp,ENST00000319533,NM_001286132.1;RPP40,missense_variant,p.Glu261Asp,ENST00000618533,NM_001286133.1;RPP40,missense_variant,p.Glu243Asp,ENST00000464646,;RPP40,downstream_gene_variant,,ENST00000468105,;RPP40,downstream_gene_variant,,ENST00000479782,; G ENST00000380051 Transcript missense_variant 954/1483 909/1092 303/363 E/D gaA/gaC 1 -1 RPP40 HGNC HGNC:20992 protein_coding YES CCDS34333.1 ENSP00000369391 O75818 UPI000020E473 NM_006638.3 tolerated(0.08) 8/8 Pfam_domain:PF08584,hmmpanther:PTHR15396,hmmpanther:PTHR15396:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 4995261 4995261 T G 1 0 0 0 0 1 0 0 0 13868 1722 60 5 5 RPP40 6 4995261 Missense_Mutation SNP T C3L-00279_T 877845 4995261 165810718 218 5996 TRIM39 0 . GRCh38 6 30341991 30341991 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.1289G>T p.Arg430Leu p.R430L ENST00000376656 9/9 349 267 82 282 282 0 strelka-varscan-mutect TRIM39,missense_variant,p.Arg400Leu,ENST00000376659,NM_172016.2;TRIM39,missense_variant,p.Arg430Leu,ENST00000376656,NM_021253.3;TRIM39,missense_variant,p.Arg400Leu,ENST00000396551,;TRIM39,missense_variant,p.Arg400Leu,ENST00000396548,;TRIM39,missense_variant,p.Arg430Leu,ENST00000396547,;TRIM39-RPP21,intron_variant,,ENST00000623385,NM_001199119.1;TRIM39,downstream_gene_variant,,ENST00000420746,;RPP21,upstream_gene_variant,,ENST00000428040,;RPP21,upstream_gene_variant,,ENST00000433076,NM_001199120.1;RPP21,upstream_gene_variant,,ENST00000442966,NM_024839.2;RPP21,upstream_gene_variant,,ENST00000436442,NM_001199121.1;RPP21,upstream_gene_variant,,ENST00000466327,;RPP21,upstream_gene_variant,,ENST00000491477,;RPP21,upstream_gene_variant,,ENST00000489124,;RPP21,upstream_gene_variant,,ENST00000498414,;RPP21,upstream_gene_variant,,ENST00000473266,; T ENST00000376656 Transcript missense_variant 1601/3338 1289/1557 430/518 R/L cGg/cTg COSM4654074,COSM4654075,COSM4654076 1 1 TRIM39 HGNC HGNC:10065 protein_coding YES CCDS34377.1 ENSP00000365844 Q9HCM9 A0A024RCP5 UPI000013D097 NM_021253.3 tolerated(0.32) 9/9 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF368,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30341991 30341991 G T 1 0 0 0 0 1 0 0 0 17002 1116 39 1 1 TRIM39 6 30341991 Missense_Mutation SNP G C3L-00279_T 25346730 30341991 140463988 219 5997 BTNL2 0 . GRCh38 6 32403065 32403065 + Silent SNP G G T C3L-00279_T C3L-00279_N G G c.579C>A p.= p.I193I ENST00000454136 3/7 588 471 117 529 529 0 strelka-varscan-mutect BTNL2,synonymous_variant,p.=,ENST00000454136,NM_001304561.1;BTNL2,synonymous_variant,p.=,ENST00000374993,;BTNL2,intron_variant,,ENST00000544175,;BTNL2,downstream_gene_variant,,ENST00000446536,;BTNL2,intron_variant,,ENST00000465865,; T ENST00000454136 Transcript synonymous_variant 584/1460 579/1449 193/482 I atC/atA COSM5259998,COSM5259999 1 -1 BTNL2 HGNC HGNC:1142 protein_coding YES CCDS78126.1 ENSP00000390613 F8WBA1 UPI0001B79374 NM_001304561.1 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF15,Gene3D:2.60.40.10,SMART_domains:SM00407,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 32403065 32403065 G T 1 0 0 0 0 0 0 0 1 1741 1164 41 2 2 BTNL2 6 32403065 Silent SNP G C3L-00279_T 2061074 32403065 138402914 220 5998 ADGRF1 0 . GRCh38 6 47009842 47009842 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1593G>T p.Gln531His p.Q531H ENST00000371253 11/15 215 172 43 178 178 0 strelka-varscan-mutect ADGRF1,missense_variant,p.Gln531His,ENST00000371253,NM_153840.3;ADGRF1,missense_variant,p.Gln334His,ENST00000283297,;ADGRF1,non_coding_transcript_exon_variant,,ENST00000449332,;ADGRF1,non_coding_transcript_exon_variant,,ENST00000419892,;ADGRF1,downstream_gene_variant,,ENST00000471487,;ADGRF1,downstream_gene_variant,,ENST00000475745,; A ENST00000371253 Transcript missense_variant 1809/5468 1593/2733 531/910 Q/H caG/caT 1 -1 ADGRF1 HGNC HGNC:18990 protein_coding YES CCDS34471.1 ENSP00000360299 Q5T601 UPI00000474ED NM_153840.3 deleterious(0.05) 11/15 PROSITE_profiles:PS50221,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF310,SMART_domains:SM00303 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 47009842 47009842 C A 1 0 0 0 0 1 0 0 0 363 796 28 2 2 ADGRF1 6 47009842 Missense_Mutation SNP C C3L-00279_T 14606777 47009842 123796137 221 5999 PKHD1 0 . GRCh38 6 52056759 52056759 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.1632A>T p.= p.A544A ENST00000371117 18/67 552 464 88 427 426 1 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript synonymous_variant 1908/16282 1632/12225 544/4074 A gcA/gcT 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 18/67 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 52056759 52056759 T A 1 0 0 0 0 0 0 0 1 12067 1567 55 4 4 PKHD1 6 52056759 Silent SNP T C3L-00279_T 5046917 52056759 118749220 222 6000 EYS 0 . GRCh38 6 64813504 64813504 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.3317C>A p.Pro1106Gln p.P1106Q ENST00000370621 22/44 257 223 34 154 154 0 strelka-varscan-mutect EYS,missense_variant,p.Pro1106Gln,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Pro1106Gln,ENST00000370621,NM_001292009.1; T ENST00000370621 Transcript missense_variant 3844/10485 3317/9498 1106/3165 P/Q cCa/cAa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.52) 22/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 64813504 64813504 G T 1 0 0 0 0 1 0 0 0 5200 1348 47 2 2 EYS 6 64813504 Missense_Mutation SNP G C3L-00279_T 12756745 64813504 105992475 223 6001 EYS 0 . GRCh38 6 65405292 65405292 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.938G>A p.Ser313Asn p.S313N ENST00000370621 6/44 251 221 30 85 85 0 strelka-varscan-mutect EYS,missense_variant,p.Ser313Asn,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Ser313Asn,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Ser313Asn,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Ser313Asn,ENST00000342421,NM_198283.1; T ENST00000370621 Transcript missense_variant 1465/10485 938/9498 313/3165 S/N aGt/aAt 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.49) 6/44 hmmpanther:PTHR24033 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 65405292 65405292 C T 1 0 0 0 0 1 0 0 0 5200 565 20 3 3 EYS 6 65405292 Missense_Mutation SNP C C3L-00279_T 591788 65405292 105400687 224 6002 COL9A1 0 . GRCh38 6 70294385 70294385 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.478C>A p.Leu160Met p.L160M ENST00000357250 5/38 437 388 49 283 283 0 strelka-varscan-mutect COL9A1,missense_variant,p.Leu160Met,ENST00000357250,NM_001851.4;COL9A1,missense_variant,p.Leu160Met,ENST00000370496,; T ENST00000357250 Transcript missense_variant 637/4761 478/2766 160/921 L/M Ctg/Atg 1 -1 COL9A1 HGNC HGNC:2217 protein_coding YES CCDS4971.1 ENSP00000349790 P20849 UPI000020D14B NM_001851.4 5/38 Gene3D:2.60.120.200,SMART_domains:SM00210,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 70294385 70294385 G T 1 0 0 0 0 1 0 0 0 3496 1020 36 2 2 COL9A1 6 70294385 Missense_Mutation SNP G C3L-00279_T 4889093 70294385 100511594 225 6003 KHDC1L 0 . GRCh38 6 73223784 73223784 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.351C>T p.= p.V117V ENST00000370388 3/3 231 209 22 227 227 0 strelka-varscan-mutect KHDC1L,synonymous_variant,p.=,ENST00000370388,NM_001126063.2;KHDC1L,downstream_gene_variant,,ENST00000471312,;RP11-257K9.8,3_prime_UTR_variant,,ENST00000423730,; A ENST00000370388 Transcript synonymous_variant 395/635 351/387 117/128 V gtC/gtT 1 -1 KHDC1L HGNC HGNC:37274 protein_coding YES CCDS47450.1 ENSP00000359415 Q5JSQ8 UPI0000070CED NM_001126063.2 3/3 hmmpanther:PTHR31368,hmmpanther:PTHR31368:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 73223784 73223784 G A 1 0 0 0 0 0 0 0 1 8065 1277 45 3 3 KHDC1L 6 73223784 Silent SNP G C3L-00279_T 2929399 73223784 97582195 226 6004 COL12A1 0 . GRCh38 6 75134823 75134823 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.5427C>A p.= p.V1809V ENST00000322507 32/66 207 190 17 158 158 0 strelka-varscan-mutect COL12A1,synonymous_variant,p.=,ENST00000322507,NM_004370.5;COL12A1,synonymous_variant,p.=,ENST00000615798,;COL12A1,synonymous_variant,p.=,ENST00000483888,;COL12A1,synonymous_variant,p.=,ENST00000416123,;COL12A1,synonymous_variant,p.=,ENST00000345356,NM_080645.2;COL12A1,synonymous_variant,p.=,ENST00000419671,; T ENST00000322507 Transcript synonymous_variant 5737/11723 5427/9192 1809/3063 V gtC/gtA 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 32/66 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs1452235912 . 0 207 0 2 0 0 0 0 -19.99638 0.9999998 1 1 1 0 T 2 4 14 75134823 75134823 G T 1 0 0 0 0 0 0 0 1 3457 1161 41 2 2 COL12A1 6 75134823 Silent SNP G C3L-00279_T 1911039 75134823 95671156 227 6005 SENP6 0 . GRCh38 6 75695825 75695825 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.2097G>A p.= p.L699L ENST00000447266 17/24 67 61 6 34 34 0 strelka-mutect SENP6,synonymous_variant,p.=,ENST00000447266,NM_015571.3;SENP6,synonymous_variant,p.=,ENST00000370010,NM_001100409.2;SENP6,synonymous_variant,p.=,ENST00000503501,;SENP6,non_coding_transcript_exon_variant,,ENST00000474906,; A ENST00000447266 Transcript synonymous_variant 2575/6501 2097/3339 699/1112 L ctG/ctA 1 1 SENP6 HGNC HGNC:20944 protein_coding YES CCDS47454.1 ENSP00000402527 Q9GZR1 UPI0000141B65 NM_015571.3 17/24 Pfam_domain:PF02902,PROSITE_profiles:PS50600,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF350,Low_complexity_(Seg):seg,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 75695825 75695825 G A 1 0 0 0 0 0 0 0 1 14326 1277 45 3 3 SENP6 6 75695825 Silent SNP G C3L-00279_T 561002 75695825 95110154 228 6006 PHIP 0 . GRCh38 6 79016554 79016554 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.1225C>A p.Arg409Ser p.R409S ENST00000275034 13/40 140 121 19 99 98 1 strelka-varscan-mutect PHIP,missense_variant,p.Arg409Ser,ENST00000275034,NM_017934.5; T ENST00000275034 Transcript missense_variant 1393/10460 1225/5466 409/1821 R/S Cgt/Agt COSM5032130 1 -1 PHIP HGNC HGNC:15673 protein_coding YES CCDS4987.1 ENSP00000275034 Q8WWQ0 UPI000013DA40 NM_017934.5 deleterious(0.01) 13/40 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR16266,hmmpanther:PTHR16266:SF4,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 MODERATE 1 SNV 1 1 1 PASS rs1486010928 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 79016554 79016554 G T 1 0 0 0 0 1 0 0 0 11930 1058 37 1 1 PHIP 6 79016554 Missense_Mutation SNP G C3L-00279_T 3320729 79016554 91789425 229 6007 ANKRD6 0 . GRCh38 6 89595970 89595970 + Missense_Mutation SNP C C A rs765628094 C3L-00279_T C3L-00279_N C C c.175C>A p.Gln59Lys p.Q59K ENST00000522441 3/16 319 288 31 339 339 0 strelka-varscan-mutect ANKRD6,missense_variant,p.Gln59Lys,ENST00000369408,NM_001242813.1;ANKRD6,missense_variant,p.Gln59Lys,ENST00000522441,NM_001242811.1;ANKRD6,missense_variant,p.Gln59Lys,ENST00000339746,NM_001242809.1;ANKRD6,missense_variant,p.Gln59Lys,ENST00000447838,NM_014942.4;ANKRD6,missense_variant,p.Gln59Lys,ENST00000520793,NM_001242814.1;ANKRD6,missense_variant,p.Gln59Lys,ENST00000485637,;ANKRD6,missense_variant,p.Gln59Lys,ENST00000465722,;ANKRD6,missense_variant,p.Gln59Lys,ENST00000522705,;ANKRD6,missense_variant,p.Gln59Lys,ENST00000523798,;ANKRD6,missense_variant,p.Gln59Lys,ENST00000520458,;ANKRD6,intron_variant,,ENST00000518150,;LYRM2,intron_variant,,ENST00000626778,;ANKRD6,intron_variant,,ENST00000522779,;ANKRD6,non_coding_transcript_exon_variant,,ENST00000520886,;LYRM2,intron_variant,,ENST00000520897,; A ENST00000522441 Transcript missense_variant 816/3157 175/2184 59/727 Q/K Cag/Aag rs765628094 1 1 ANKRD6 HGNC HGNC:17280 protein_coding YES CCDS56441.1 ENSP00000430985 Q9Y2G4 UPI000020D325 NM_001242811.1 tolerated(0.09) 3/16 Gene3D:1.25.40.20,Pfam_domain:PF13857,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24203,hmmpanther:PTHR24203:SF7,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs765628094 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 89595970 89595970 C A 1 0 0 0 0 1 0 0 0 786 595 21 2 2 ANKRD6 6 89595970 Missense_Mutation SNP C C3L-00279_T 10579416 89595970 81210009 230 6008 SNX3 0 . GRCh38 6 108214609 108214609 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.272C>A p.Pro91Gln p.P91Q ENST00000230085 3/4 146 126 20 141 141 0 strelka-varscan-mutect SNX3,missense_variant,p.Pro91Gln,ENST00000230085,NM_003795.5;SNX3,missense_variant,p.Pro59Gln,ENST00000426155,NM_152827.3;SNX3,missense_variant,p.Pro69Gln,ENST00000349379,NM_001300929.1;SNX3,3_prime_UTR_variant,,ENST00000368979,; T ENST00000230085 Transcript missense_variant 611/1755 272/489 91/162 P/Q cCg/cAg 1 -1 SNX3 HGNC HGNC:11174 protein_coding YES CCDS5064.1 ENSP00000230085 O60493 UPI00000013A7 NM_003795.5 deleterious(0.04) 3/4 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF145,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS rs923109909 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 108214609 108214609 G T 1 0 0 0 0 1 0 0 0 15220 1116 39 1 1 SNX3 6 108214609 Missense_Mutation SNP G C3L-00279_T 18618639 108214609 62591370 231 6009 LACE1 0 . GRCh38 6 108324019 108324019 + Missense_Mutation SNP A A T rs376944723 C3L-00279_T C3L-00279_N A A c.334A>T p.Asn112Tyr p.N112Y ENST00000368977 2/13 222 201 21 124 124 0 strelka-varscan-mutect LACE1,missense_variant,p.Asn112Tyr,ENST00000368977,NM_145315.3;LACE1,missense_variant,p.Asn79Tyr,ENST00000437715,;LACE1,intron_variant,,ENST00000421954,;LACE1,non_coding_transcript_exon_variant,,ENST00000430458,; T ENST00000368977 Transcript missense_variant 520/5208 334/1446 112/481 N/Y Aat/Tat rs376944723 1 1 LACE1 HGNC HGNC:16411 protein_coding YES CCDS5067.1 ENSP00000357973 Q8WV93 UPI0000072226 NM_145315.3 deleterious(0.01) 2/13 Pfam_domain:PF03969,hmmpanther:PTHR12169,hmmpanther:PTHR12169:SF6 MODERATE 1 SNV 1 1 PASS rs376944723 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 108324019 108324019 A T 1 0 0 0 0 1 0 0 0 8498 130 5 4 4 LACE1 6 108324019 Missense_Mutation SNP A C3L-00279_T 109410 108324019 62481960 232 6010 DSE 0 . GRCh38 6 116436083 116436083 + Nonsense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.1615G>T p.Gly539Ter p.G539* ENST00000452085 6/6 243 221 22 179 179 0 strelka-varscan-mutect DSE,stop_gained,p.Gly539Ter,ENST00000452085,NM_001080976.1;DSE,stop_gained,p.Gly539Ter,ENST00000331677,;DSE,stop_gained,p.Gly539Ter,ENST00000359564,NM_013352.2;DSE,non_coding_transcript_exon_variant,,ENST00000606712,; T ENST00000452085 Transcript stop_gained 1809/10586 1615/2877 539/958 G/* Gga/Tga COSM5555697 1 1 DSE HGNC HGNC:21144 protein_coding YES CCDS5107.1 ENSP00000404049 Q9UL01 UPI0000073CB8 NM_001080976.1 6/6 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF3 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 116436083 116436083 G T 1 0 0 0 0 0 1 0 0 4595 1001 35 2 2 DSE 6 116436083 Nonsense_Mutation SNP G C3L-00279_T 8112064 116436083 54369896 233 6011 GJA1 0 . GRCh38 6 121447683 121447683 + Nonsense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.836C>A p.Ser279Ter p.S279* ENST00000282561 2/2 663 591 72 587 584 3 strelka-varscan-mutect GJA1,stop_gained,p.Ser279Ter,ENST00000282561,NM_000165.4; A ENST00000282561 Transcript stop_gained 993/3037 836/1149 279/382 S/* tCg/tAg COSM168629 1 1 GJA1 HGNC HGNC:4274 protein_coding YES CCDS5123.1 ENSP00000282561 P17302 UPI000013DCEC NM_000165.4 2/2 hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF33,Superfamily_domains:0049114 1 HIGH 1 SNV 1 1 1 PASS rs1265740574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 121447683 121447683 C A 1 0 0 0 0 0 1 0 0 6280 893 31 1 1 GJA1 6 121447683 Nonsense_Mutation SNP C C3L-00279_T 5011600 121447683 49358296 234 6012 HDDC2 0 . GRCh38 6 125292880 125292880 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.339A>T p.= p.L113L ENST00000398153 4/6 339 309 30 118 118 0 strelka-varscan-mutect HDDC2,synonymous_variant,p.=,ENST00000398153,NM_016063.2;HDDC2,intron_variant,,ENST00000608295,;HDDC2,downstream_gene_variant,,ENST00000608284,;HDDC2,3_prime_UTR_variant,,ENST00000318787,;HDDC2,3_prime_UTR_variant,,ENST00000609477,;HDDC2,non_coding_transcript_exon_variant,,ENST00000608461,;HDDC2,non_coding_transcript_exon_variant,,ENST00000608532,; A ENST00000398153 Transcript synonymous_variant 382/918 339/615 113/204 L ctA/ctT 1 -1 HDDC2 HGNC HGNC:21078 protein_coding YES CCDS43503.1 ENSP00000381220 Q7Z4H3 A0A140VJK7 UPI0000070B81 NM_016063.2 4/6 Gene3D:1.10.3210.10,Pfam_domain:PF13023,hmmpanther:PTHR11845,SMART_domains:SM00471,Superfamily_domains:SSF109604 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 125292880 125292880 T A 1 0 0 0 0 0 0 0 1 6903 1625 57 4 4 HDDC2 6 125292880 Silent SNP T C3L-00279_T 3845197 125292880 45513099 235 6013 EPB41L2 0 . GRCh38 6 130901049 130901049 + Missense_Mutation SNP C C A rs778911472 C3L-00279_T C3L-00279_N C C c.1061G>T p.Gly354Val p.G354V ENST00000337057 7/20 346 322 24 299 299 0 strelka-varscan-mutect EPB41L2,missense_variant,p.Gly354Val,ENST00000337057,NM_001431.3;EPB41L2,missense_variant,p.Gly354Val,ENST00000368128,;EPB41L2,missense_variant,p.Gly354Val,ENST00000628542,;EPB41L2,missense_variant,p.Gly354Val,ENST00000527411,;EPB41L2,missense_variant,p.Gly354Val,ENST00000530481,NM_001199388.2;EPB41L2,missense_variant,p.Gly354Val,ENST00000445890,;EPB41L2,missense_variant,p.Gly354Val,ENST00000528282,NM_001252660.1;EPB41L2,missense_variant,p.Gly354Val,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,missense_variant,p.Gly354Val,ENST00000529208,;EPB41L2,missense_variant,p.Gly354Val,ENST00000525271,;EPB41L2,missense_variant,p.Gly354Val,ENST00000527659,;EPB41L2,missense_variant,p.Gly354Val,ENST00000525193,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000530148,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000528179,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000526333,; A ENST00000337057 Transcript missense_variant 1243/4457 1061/3018 354/1005 G/V gGc/gTc rs778911472,COSM3829032 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 deleterious(0.02) 7/20 Gene3D:1.20.80.10,Pfam_domain:PF00373,PIRSF_domain:PIRSF002304,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF17,SMART_domains:SM00295,Superfamily_domains:SSF47031 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778911472 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 130901049 130901049 C A 1 0 0 0 0 1 0 0 0 5000 739 26 2 2 EPB41L2 6 130901049 Missense_Mutation SNP C C3L-00279_T 5608169 130901049 39904930 236 6014 SLC18B1 0 . GRCh38 6 132779283 132779283 + Silent SNP G G C novel C3L-00279_T C3L-00279_N G G c.780C>G p.= p.L260L ENST00000275227 7/14 221 206 15 172 172 0 strelka-varscan-mutect SLC18B1,synonymous_variant,p.=,ENST00000275227,NM_052831.2;SLC18B1,intron_variant,,ENST00000367918,; C ENST00000275227 Transcript synonymous_variant 877/2368 780/1371 260/456 L ctC/ctG 1 -1 SLC18B1 HGNC HGNC:21573 protein_coding YES CCDS5163.1 ENSP00000275227 Q6NT16 UPI000013DA50 NM_052831.2 7/14 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF2,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 14 132779283 132779283 G C 1 0 0 0 0 0 0 0 1 14693 929 33 4 4 SLC18B1 6 132779283 Silent SNP G C3L-00279_T 1878234 132779283 38026696 237 6015 NHSL1 0 . GRCh38 6 138496259 138496259 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.315G>T p.= p.L105L ENST00000427025 2/7 253 216 37 298 298 0 strelka-varscan-mutect NHSL1,synonymous_variant,p.=,ENST00000427025,NM_020464.1;NHSL1,synonymous_variant,p.=,ENST00000343505,NM_001144060.1;NHSL1,synonymous_variant,p.=,ENST00000342260,;NHSL1,synonymous_variant,p.=,ENST00000533765,;NHSL1,synonymous_variant,p.=,ENST00000491526,;NHSL1,non_coding_transcript_exon_variant,,ENST00000479393,;NHSL1,non_coding_transcript_exon_variant,,ENST00000426841,; A ENST00000427025 Transcript synonymous_variant 944/7500 315/4833 105/1610 L ctG/ctT 1 -1 NHSL1 HGNC HGNC:21021 protein_coding YES CCDS55063.1 ENSP00000394546 Q5SYE7 UPI0001750345 NM_020464.1 2/7 hmmpanther:PTHR23039:SF3,hmmpanther:PTHR23039 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 138496259 138496259 C A 1 0 0 0 0 0 0 0 1 10444 697 25 2 2 NHSL1 6 138496259 Silent SNP C C3L-00279_T 5716976 138496259 32309720 238 6016 ADGB 0 . GRCh38 6 146717056 146717056 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1915T>A p.Cys639Ser p.C639S ENST00000397944 15/36 55 48 7 29 29 0 strelka-varscan-mutect ADGB,missense_variant,p.Cys639Ser,ENST00000397944,NM_024694.3;ADGB,missense_variant,p.Cys59Ser,ENST00000480328,;ADGB,3_prime_UTR_variant,,ENST00000493950,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,; A ENST00000397944 Transcript missense_variant 1991/5325 1915/5004 639/1667 C/S Tgt/Agt 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 tolerated(0.11) 15/36 hmmpanther:PTHR10183:SF304,hmmpanther:PTHR10183,SMART_domains:SM00230 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 146717056 146717056 T A 1 0 0 0 0 1 0 0 0 351 1580 55 4 4 ADGB 6 146717056 Missense_Mutation SNP T C3L-00279_T 8220797 146717056 24088923 239 6017 TIAM2 0 . GRCh38 6 155137432 155137432 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.1450G>A p.Glu484Lys p.E484K ENST00000461783 7/29 321 291 30 272 272 0 strelka-varscan-mutect TIAM2,missense_variant,p.Glu484Lys,ENST00000461783,;TIAM2,missense_variant,p.Glu484Lys,ENST00000318981,NM_012454.3;TIAM2,missense_variant,p.Glu484Lys,ENST00000360366,;TIAM2,missense_variant,p.Glu484Lys,ENST00000529824,;TIAM2,missense_variant,p.Glu484Lys,ENST00000528535,; A ENST00000461783 Transcript missense_variant 2723/6981 1450/5106 484/1701 E/K Gag/Aag COSM3622220 1 1 TIAM2 HGNC HGNC:11806 protein_coding YES CCDS34558.1 ENSP00000437188 Q8IVF5 UPI00004DF8BE deleterious(0.02) 7/29 Low_complexity_(Seg):seg,hmmpanther:PTHR22826:SF118,hmmpanther:PTHR22826 1 MODERATE 1 SNV 2 1 1 PASS rs1031872527 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 155137432 155137432 G A 1 0 0 0 0 1 0 0 0 16325 1059 37 1 1 TIAM2 6 155137432 Missense_Mutation SNP G C3L-00279_T 8420376 155137432 15668547 240 6018 RSPH3 0 . GRCh38 6 158999801 158999801 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.176C>A p.Thr59Asn p.T59N ENST00000252655 1/8 136 129 7 134 134 0 strelka-varscan-mutect RSPH3,missense_variant,p.Thr59Asn,ENST00000252655,NM_031924.4;RSPH3,5_prime_UTR_variant,,ENST00000367069,;RSPH3,upstream_gene_variant,,ENST00000449822,;RP1-111C20.4,intron_variant,,ENST00000607391,;RP1-111C20.4,upstream_gene_variant,,ENST00000607796,;RP1-111C20.4,upstream_gene_variant,,ENST00000606470,; T ENST00000252655 Transcript missense_variant 366/2175 176/1683 59/560 T/N aCc/aAc 1 -1 RSPH3 HGNC HGNC:21054 protein_coding YES CCDS5260.1 ENSP00000252655 Q86UC2 UPI000013CD78 NM_031924.4 tolerated_low_confidence(0.11) 1/8 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -13.19604 0.9999993 1 1 1 0 T 3 4 14 158999801 158999801 G T 1 0 0 0 0 1 0 0 0 13963 1261 44 2 2 RSPH3 6 158999801 Missense_Mutation SNP G C3L-00279_T 3862369 158999801 11806178 241 6019 C6orf118 0 . GRCh38 6 165301824 165301824 + Silent SNP C C A C3L-00279_T C3L-00279_N C C c.498G>T p.= p.R166R ENST00000230301 2/9 229 213 16 190 190 0 strelka-varscan-mutect C6orf118,synonymous_variant,p.=,ENST00000230301,NM_144980.3; A ENST00000230301 Transcript synonymous_variant 519/1812 498/1410 166/469 R cgG/cgT COSM3622741,COSM3622742 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 2/9 Low_complexity_(Seg):seg,hmmpanther:PTHR34916 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 165301824 165301824 C A 1 0 0 0 0 0 0 0 1 2115 610 22 2 2 C6orf118 6 165301824 Silent SNP C C3L-00279_T 6302023 165301824 5504155 242 6020 PDE10A 0 . GRCh38 6 165435351 165435351 + Frame_Shift_Del DEL C C - rs373361582 C3L-00279_T C3L-00279_N C C c.423delG p.Ile142Ter p.I142* ENST00000539869 6/22 144 131 13 150 150 0 sindel-varindel-pindel PDE10A,frameshift_variant,p.Ile132Ter,ENST00000366882,NM_006661.3;PDE10A,frameshift_variant,p.Ile142Ter,ENST00000539869,NM_001130690.2; - ENST00000539869 Transcript frameshift_variant 479/4401 423/2370 141/789 G/X ggG/gg rs373361582 1 -1 PDE10A HGNC HGNC:8772 protein_coding YES CCDS47513.1 ENSP00000438284 Q9Y233 UPI000006F80E NM_001130690.2 6/22 Gene3D:3.30.450.40,Pfam_domain:PF01590,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF111,SMART_domains:SM00065,Superfamily_domains:SSF55781 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.45112 0.9999998 1 1 1 0 - 7 5 14 165435351 165435351 C - 1 0 1 0 1 0 0 0 0 11718 842 30 0 0 PDE10A 6 165435351 Frame_Shift_Del DEL C C3L-00279_T 133527 165435351 5370628 243 6021 SMOC2 0 . GRCh38 6 168510018 168510018 + Missense_Mutation SNP G G T rs138763725 C3L-00279_T C3L-00279_N G G c.188G>T p.Arg63Leu p.R63L ENST00000354536 2/13 296 242 54 254 254 0 strelka-varscan-mutect SMOC2,missense_variant,p.Arg63Leu,ENST00000354536,NM_022138.2;SMOC2,missense_variant,p.Arg63Leu,ENST00000356284,NM_001166412.1; T ENST00000354536 Transcript missense_variant 408/3150 188/1374 63/457 R/L cGt/cTt rs138763725 1 1 SMOC2 HGNC HGNC:20323 protein_coding YES CCDS5307.1 ENSP00000346537 Q9H3U7 UPI0000072A56 NM_022138.2 tolerated(0.43) 2/13 PROSITE_profiles:PS51465,hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF14,Gene3D:3.30.60.30,Pfam_domain:PF07648,SMART_domains:SM00280,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS rs138763725 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 168510018 168510018 G T 1 0 0 0 0 1 0 0 0 15123 1145 40 1 1 SMOC2 6 168510018 Missense_Mutation SNP G C3L-00279_T 3074667 168510018 2295961 244 6022 ELFN1 0 . GRCh38 7 1746319 1746319 + Missense_Mutation SNP G G T rs774563944 C3L-00279_T C3L-00279_N G G c.1723G>T p.Ala575Ser p.A575S ENST00000424383 3/3 116 101 15 115 115 0 strelka-varscan-mutect ELFN1,missense_variant,p.Ala575Ser,ENST00000424383,;ELFN1,missense_variant,p.Ala575Ser,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; T ENST00000424383 Transcript missense_variant 2210/3845 1723/2487 575/828 A/S Gcg/Tcg rs774563944 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 deleterious(0.01) 3/3 hmmpanther:PTHR24367:SF34,hmmpanther:PTHR24367 MODERATE SNV 5 1 PASS rs774563944 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 1746319 1746319 G T 1 0 0 0 0 1 0 0 0 4891 1087 38 1 1 ELFN1 7 1746319 Missense_Mutation SNP G C3L-00279_T 1746319 157599654 245 6023 IQCE 0 . GRCh38 7 2572303 2572303 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.371A>G p.His124Arg p.H124R ENST00000476665 5/21 187 169 18 167 167 0 strelka-varscan-mutect IQCE,missense_variant,p.His124Arg,ENST00000402050,NM_152558.4;IQCE,missense_variant,p.His59Arg,ENST00000623361,NM_001287501.1,NM_001287502.1;IQCE,missense_variant,p.His124Arg,ENST00000476665,NM_001287499.1;IQCE,missense_variant,p.His108Arg,ENST00000611775,NM_001287500.1;IQCE,missense_variant,p.His59Arg,ENST00000325979,;IQCE,missense_variant,p.His108Arg,ENST00000438376,;IQCE,missense_variant,p.His73Arg,ENST00000404984,;IQCE,missense_variant,p.His124Arg,ENST00000415271,;IQCE,missense_variant,p.His59Arg,ENST00000423395,;IQCE,missense_variant,p.His59Arg,ENST00000422276,;IQCE,3_prime_UTR_variant,,ENST00000325997,;IQCE,non_coding_transcript_exon_variant,,ENST00000470731,; G ENST00000476665 Transcript missense_variant 474/2400 371/2109 124/702 H/R cAt/cGt 1 1 IQCE HGNC HGNC:29171 protein_coding YES CCDS75559.1 ENSP00000480715 A0A087WX45 UPI0000EE76A1 NM_001287499.1 tolerated(0.08) 5/21 hmmpanther:PTHR22590 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 2572303 2572303 A G 1 0 0 0 0 1 0 0 0 7710 217 8 5 5 IQCE 7 2572303 Missense_Mutation SNP A C3L-00279_T 825984 2572303 156773670 246 6024 COL28A1 0 . GRCh38 7 7531583 7531583 + Missense_Mutation SNP C C T rs371960243 C3L-00279_T C3L-00279_N C C c.446G>A p.Arg149His p.R149H ENST00000399429 3/35 155 135 20 99 98 1 strelka-varscan-mutect COL28A1,missense_variant,p.Arg149His,ENST00000399429,NM_001037763.2; T ENST00000399429 Transcript missense_variant 587/4277 446/3378 149/1125 R/H cGt/cAt rs371960243,COSM1284227 1 -1 COL28A1 HGNC HGNC:22442 protein_coding YES CCDS43553.1 ENSP00000382356 Q2UY09 UPI000155D64E NM_001037763.2 tolerated(0.07) 3/35 PROSITE_profiles:PS50234,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF578,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371960243 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 7531583 7531583 C T 1 0 0 0 0 1 0 0 0 3475 536 19 1 1 COL28A1 7 7531583 Missense_Mutation SNP C C3L-00279_T 4959280 7531583 151814390 247 6025 GLCCI1 0 . GRCh38 7 7969436 7969436 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.86G>T p.Gly29Val p.G29V ENST00000223145 1/8 85 68 17 78 78 0 strelka-mutect GLCCI1,missense_variant,p.Gly29Val,ENST00000223145,NM_138426.3;GLCCI1,upstream_gene_variant,,ENST00000430798,;GLCCI1,upstream_gene_variant,,ENST00000414914,;UMAD1,downstream_gene_variant,,ENST00000482067,;AC006042.7,intron_variant,,ENST00000428660,;RP11-505D17.1,intron_variant,,ENST00000469183,;GLCCI1,upstream_gene_variant,,ENST00000474269,;GLCCI1,upstream_gene_variant,,ENST00000470583,;GLCCI1,upstream_gene_variant,,ENST00000492797,;GLCCI1,upstream_gene_variant,,ENST00000460897,; T ENST00000223145 Transcript missense_variant 643/4743 86/1644 29/547 G/V gGg/gTg 1 1 GLCCI1 HGNC HGNC:18713 protein_coding YES CCDS34601.1 ENSP00000223145 Q86VQ1 UPI00001907F7 NM_138426.3 deleterious_low_confidence(0) 1/8 hmmpanther:PTHR14972,hmmpanther:PTHR14972:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1343403963 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 7969436 7969436 G T 1 0 0 0 0 1 0 0 0 6309 1232 43 2 2 GLCCI1 7 7969436 Missense_Mutation SNP G C3L-00279_T 437853 7969436 151376537 248 6026 THSD7A 0 . GRCh38 7 11379175 11379175 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.4696G>T p.Asp1566Tyr p.D1566Y ENST00000423059 26/28 397 342 55 323 322 1 strelka-varscan-mutect THSD7A,missense_variant,p.Asp1566Tyr,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Asp1566Tyr,ENST00000617773,;AC004538.3,non_coding_transcript_exon_variant,,ENST00000595972,;AC004538.3,intron_variant,,ENST00000421121,;AC004538.3,intron_variant,,ENST00000428533,;AC004538.3,intron_variant,,ENST00000428967,;AC004538.3,intron_variant,,ENST00000445839,;AC004538.3,intron_variant,,ENST00000616268,;AC004538.3,downstream_gene_variant,,ENST00000599875,;THSD7A,non_coding_transcript_exon_variant,,ENST00000408005,; A ENST00000423059 Transcript missense_variant 4948/10663 4696/4974 1566/1657 D/Y Gac/Tac 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 deleterious(0.03) 26/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 11379175 11379175 C A 1 0 0 0 0 1 0 0 0 16313 855 30 2 2 THSD7A 7 11379175 Missense_Mutation SNP C C3L-00279_T 3409739 11379175 147966798 249 6027 THSD7A 0 . GRCh38 7 11407388 11407388 + Silent SNP G G T rs755988902 C3L-00279_T C3L-00279_N G G c.3834C>A p.= p.S1278S ENST00000423059 20/28 257 223 34 205 205 0 strelka-varscan-mutect THSD7A,synonymous_variant,p.=,ENST00000423059,NM_015204.2;THSD7A,synonymous_variant,p.=,ENST00000617773,;AC004538.3,intron_variant,,ENST00000445839,;AC004160.4,intron_variant,,ENST00000425837,; T ENST00000423059 Transcript synonymous_variant 4086/10663 3834/4974 1278/1657 S tcC/tcA rs755988902 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 20/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209 LOW SNV 5 1 PASS rs755988902 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 11407388 11407388 G T 1 0 0 0 0 0 0 0 1 16313 987 35 2 2 THSD7A 7 11407388 Silent SNP G C3L-00279_T 28213 11407388 147938585 250 6028 EVX1 0 . GRCh38 7 27245169 27245169 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.549G>A p.Met183Ile p.M183I ENST00000496902 2/3 489 429 60 492 492 0 strelka-varscan EVX1,missense_variant,p.Met183Ile,ENST00000496902,NM_001989.4,NM_001304519.1;EVX1,missense_variant,p.Cys70Tyr,ENST00000580535,;EVX1,missense_variant,p.Cys165Tyr,ENST00000222761,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1-AS,upstream_gene_variant,,ENST00000519218,;EVX1,upstream_gene_variant,,ENST00000518886,; A ENST00000496902 Transcript missense_variant 880/2955 549/1224 183/407 M/I atG/atA 1 1 EVX1 HGNC HGNC:3506 protein_coding YES CCDS5413.1 ENSP00000419266 P49640 UPI000012A2AD NM_001989.4,NM_001304519.1 tolerated(0.27) 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF246,hmmpanther:PTHR24329,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 27245169 27245169 G A 1 0 0 0 0 1 0 0 0 5161 1319 46 3 3 EVX1 7 27245169 Missense_Mutation SNP G C3L-00279_T 15837781 27245169 132100804 251 6029 BBS9 0 . GRCh38 7 33336568 33336568 + Missense_Mutation SNP G G C rs745384211 C3L-00279_T C3L-00279_N G G c.1144G>C p.Asp382His p.D382H ENST00000242067 10/23 314 274 40 151 151 0 strelka-varscan BBS9,missense_variant,p.Asp382His,ENST00000242067,NM_198428.2;BBS9,missense_variant,p.Asp382His,ENST00000355070,NM_001033605.1;BBS9,missense_variant,p.Asp382His,ENST00000396127,NM_001033604.1;BBS9,missense_variant,p.Asp382His,ENST00000350941,NM_014451.3;BBS9,missense_variant,p.Asp382His,ENST00000433714,; C ENST00000242067 Transcript missense_variant 1665/4027 1144/2664 382/887 D/H Gat/Cat rs745384211 1 1 BBS9 HGNC HGNC:30000 protein_coding YES CCDS43566.1 ENSP00000242067 Q3SYG4 A0A090N8P4 UPI000020ED57 NM_198428.2 deleterious(0) 10/23 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14727,hmmpanther:PTHR20991,hmmpanther:PTHR20991:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 33336568 33336568 G C 1 0 0 0 0 1 0 0 0 1489 1290 45 4 4 BBS9 7 33336568 Missense_Mutation SNP G C3L-00279_T 6091399 33336568 126009405 252 6030 BMPER 0 . GRCh38 7 33966547 33966547 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.388C>G p.Leu130Val p.L130V ENST00000297161 5/16 587 512 75 450 450 0 strelka-varscan BMPER,missense_variant,p.Leu130Val,ENST00000297161,NM_133468.4;BMPER,missense_variant,p.Phe96Leu,ENST00000436222,;BMPER,3_prime_UTR_variant,,ENST00000444773,; G ENST00000297161 Transcript missense_variant 762/5031 388/2058 130/685 L/V Cta/Gta 1 1 BMPER HGNC HGNC:24154 protein_coding YES CCDS5442.1 ENSP00000297161 Q8N8U9 A0A090N7U6 UPI000006D462 NM_133468.4 tolerated(0.19) 5/16 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF272,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 33966547 33966547 C G 1 0 0 0 0 1 0 0 0 1623 912 32 4 4 BMPER 7 33966547 Missense_Mutation SNP C C3L-00279_T 629979 33966547 125379426 253 6031 HECW1 0 . GRCh38 7 43445154 43445154 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1982G>T p.Ser661Ile p.S661I ENST00000395891 11/30 112 95 17 112 112 0 strelka-varscan HECW1,missense_variant,p.Ser661Ile,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Ser661Ile,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; T ENST00000395891 Transcript missense_variant 2587/9501 1982/4821 661/1606 S/I aGc/aTc 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious_low_confidence(0) 11/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 43445154 43445154 G T 1 0 0 0 0 1 0 0 0 6924 971 34 2 2 HECW1 7 43445154 Missense_Mutation SNP G C3L-00279_T 9478607 43445154 115900819 254 6032 HECW1 0 . GRCh38 7 43450923 43450923 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2494C>A p.Pro832Thr p.P832T ENST00000395891 12/30 289 255 34 213 213 0 strelka-varscan HECW1,missense_variant,p.Pro832Thr,ENST00000395891,NM_015052.4;HECW1,intron_variant,,ENST00000453890,NM_001287059.1; A ENST00000395891 Transcript missense_variant 3099/9501 2494/4821 832/1606 P/T Cca/Aca 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious(0) 12/30 PROSITE_profiles:PS50020,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,Pfam_domain:PF00397,Gene3D:2.20.70.10,SMART_domains:SM00456,Superfamily_domains:SSF51045 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 43450923 43450923 C A 1 0 0 0 0 1 0 0 0 6924 855 30 2 2 HECW1 7 43450923 Missense_Mutation SNP C C3L-00279_T 5769 43450923 115895050 255 6033 FIGNL1 0 . GRCh38 7 50445721 50445721 + Missense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.1567G>A p.Glu523Lys p.E523K ENST00000419119 2/2 232 206 26 141 141 0 strelka-varscan FIGNL1,missense_variant,p.Glu523Lys,ENST00000419119,;FIGNL1,missense_variant,p.Glu523Lys,ENST00000433017,NM_001287492.1;FIGNL1,missense_variant,p.Glu523Lys,ENST00000611938,;FIGNL1,missense_variant,p.Glu523Lys,ENST00000395556,NM_001042762.2,NM_022116.4;FIGNL1,missense_variant,p.Glu523Lys,ENST00000356889,;FIGNL1,missense_variant,p.Glu523Lys,ENST00000615084,NM_001287496.1,NM_001287494.1,NM_001287493.1;FIGNL1,missense_variant,p.Glu523Lys,ENST00000617389,NM_001287495.1;FIGNL1,missense_variant,p.Glu523Lys,ENST00000613602,;FIGNL1,downstream_gene_variant,,ENST00000440350,;FIGNL1,downstream_gene_variant,,ENST00000435566,;FIGNL1,downstream_gene_variant,,ENST00000420829,;FIGNL1,downstream_gene_variant,,ENST00000422854,;FIGNL1,downstream_gene_variant,,ENST00000448788,;FIGNL1,downstream_gene_variant,,ENST00000436590,; T ENST00000419119 Transcript missense_variant 3121/3700 1567/2025 523/674 E/K Gaa/Aaa COSM1313161 1 -1 FIGNL1 HGNC HGNC:13286 protein_coding YES CCDS5510.1 ENSP00000410811 Q6PIW4 UPI000013CE5D deleterious(0) 2/2 hmmpanther:PTHR23074:SF75,hmmpanther:PTHR23074,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 50445721 50445721 C T 1 0 0 0 0 1 0 0 0 5756 922 32 3 3 FIGNL1 7 50445721 Missense_Mutation SNP C C3L-00279_T 6994798 50445721 108900252 256 6034 ZNF679 0 . GRCh38 7 64266284 64266284 + Nonsense_Mutation SNP C C A rs376022989 C3L-00279_T C3L-00279_N C C c.651C>A p.Cys217Ter p.C217* ENST00000421025 5/5 105 94 11 44 44 0 strelka-varscan ZNF679,stop_gained,p.Cys217Ter,ENST00000421025,NM_153363.2;ZNF679,stop_gained,p.Cys217Ter,ENST00000255746,; A ENST00000421025 Transcript stop_gained 920/1567 651/1236 217/411 C/* tgC/tgA rs376022989,COSM3085054 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF91,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 HIGH 1 SNV 1 0,1 1 PASS . . 0 201 2 6 0 0 0 0 -16.58899 0.9937488 1 1 1 0 A 4 1 14 64266284 64266284 C A 1 0 0 0 0 0 1 0 0 18659 776 27 1 1 ZNF679 7 64266284 Nonsense_Mutation SNP C C3L-00279_T 13820563 64266284 95079689 257 6035 AUTS2 0 . GRCh38 7 70790783 70790784 + Frame_Shift_Del DEL CC CC - novel C3L-00279_T C3L-00279_N CC CC c.3569_3570delCC p.Pro1190GlnfsTer91 p.P1190Qfs*91 ENST00000342771 19/19 104 90 14 115 115 0 sindel-varindel-pindel AUTS2,frameshift_variant,p.Pro1190GlnfsTer91,ENST00000342771,NM_015570.3;AUTS2,frameshift_variant,p.Pro1166GlnfsTer91,ENST00000406775,NM_001127231.2;AUTS2,frameshift_variant,p.Pro942GlnfsTer91,ENST00000611706,;AUTS2,frameshift_variant,p.Pro918GlnfsTer91,ENST00000615871,;AUTS2,downstream_gene_variant,,ENST00000418686,;AUTS2,downstream_gene_variant,,ENST00000498384,;AUTS2,downstream_gene_variant,,ENST00000449547,;AUTS2,downstream_gene_variant,,ENST00000439256,; - ENST00000342771 Transcript frameshift_variant 3888-3889/6173 3567-3568/3780 1189-1190/1259 LP/LX ctCCcc/ctcc 1 1 AUTS2 HGNC HGNC:14262 protein_coding YES CCDS5539.1 ENSP00000344087 Q8WXX7 UPI0000126665 NM_015570.3 19/19 hmmpanther:PTHR14429,hmmpanther:PTHR14429:SF5 HIGH 1 deletion 1 2 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999921 1 1 1 0 - 7 5 14 70790783 70790783 CC - 1 0 1 0 1 0 0 0 0 1381 842 30 0 0 AUTS2 7 70790783 Frame_Shift_Del DEL CC C3L-00279_T 6524499 70790783 88555190 258 6036 PCLO 0 . GRCh38 7 82949574 82949574 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.11014G>A p.Ala3672Thr p.A3672T ENST00000333891 6/25 175 152 23 130 130 0 strelka-varscan-mutect PCLO,missense_variant,p.Ala3672Thr,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Ala3672Thr,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Ala392Thr,ENST00000437081,; T ENST00000333891 Transcript missense_variant 11352/20329 11014/15429 3672/5142 A/T Gcc/Acc 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.45) 6/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 82949574 82949574 C T 1 0 0 0 0 1 0 0 0 11671 797 28 3 3 PCLO 7 82949574 Missense_Mutation SNP C C3L-00279_T 12158791 82949574 76396399 259 6037 PCLO 0 . GRCh38 7 82955268 82955268 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.5685A>T p.= p.P1895P ENST00000333891 5/25 173 153 20 62 62 0 strelka-varscan-mutect PCLO,synonymous_variant,p.=,ENST00000333891,NM_033026.5;PCLO,synonymous_variant,p.=,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript synonymous_variant 6023/20329 5685/15429 1895/5142 P ccA/ccT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 82955268 82955268 T A 1 0 0 0 0 0 0 0 1 11671 1799 63 4 4 PCLO 7 82955268 Silent SNP T C3L-00279_T 5694 82955268 76390705 260 6038 SEMA3E 0 . GRCh38 7 83418434 83418434 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.506G>T p.Arg169Ile p.R169I ENST00000307792 5/17 428 365 63 277 277 0 strelka-varscan-mutect SEMA3E,missense_variant,p.Arg169Ile,ENST00000307792,NM_012431.2;SEMA3E,missense_variant,p.Arg109Ile,ENST00000427262,NM_001178129.1;SEMA3E,missense_variant,p.Arg109Ile,ENST00000442159,; A ENST00000307792 Transcript missense_variant 974/6476 506/2328 169/775 R/I aGa/aTa 1 -1 SEMA3E HGNC HGNC:10727 protein_coding YES CCDS34674.1 ENSP00000303212 O15041 UPI0000135A68 NM_012431.2 deleterious(0) 5/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 83418434 83418434 C A 1 0 0 0 0 1 0 0 0 14304 913 32 2 2 SEMA3E 7 83418434 Missense_Mutation SNP C C3L-00279_T 463166 83418434 75927539 261 6039 ZNF804B 0 . GRCh38 7 89335848 89335848 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.2866G>A p.Glu956Lys p.E956K ENST00000333190 4/4 283 254 29 181 181 0 strelka-varscan-mutect ZNF804B,missense_variant,p.Glu956Lys,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Glu873Lys,ENST00000611114,; A ENST00000333190 Transcript missense_variant 3475/4659 2866/4050 956/1349 E/K Gag/Aag 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 tolerated(0.65) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 89335848 89335848 G A 1 0 0 0 0 1 0 0 0 18756 943 33 3 3 ZNF804B 7 89335848 Missense_Mutation SNP G C3L-00279_T 5917414 89335848 70010125 262 6040 STEAP2 0 . GRCh38 7 90225090 90225090 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.8C>A p.Ser3Ter p.S3* ENST00000394621 3/6 120 105 15 49 49 0 strelka-varscan-mutect STEAP2,stop_gained,p.Ser3Ter,ENST00000394621,NM_001244944.1;STEAP2,stop_gained,p.Ser3Ter,ENST00000287908,NM_152999.3;STEAP2,stop_gained,p.Ser3Ter,ENST00000394622,NM_001040665.1;STEAP2,stop_gained,p.Ser3Ter,ENST00000394626,NM_001244945.1;STEAP2,stop_gained,p.Ser3Ter,ENST00000394629,NM_001040666.1;STEAP2,stop_gained,p.Ser3Ter,ENST00000394632,NM_001244946.1;STEAP2,stop_gained,p.Ser3Ter,ENST00000402625,;STEAP2,stop_gained,p.Ser3Ter,ENST00000428074,;STEAP2,stop_gained,p.Ser3Ter,ENST00000426158,;STEAP2,non_coding_transcript_exon_variant,,ENST00000482369,; A ENST00000394621 Transcript stop_gained 514/7033 8/1473 3/490 S/* tCa/tAa 1 1 STEAP2 HGNC HGNC:17885 protein_coding YES CCDS5615.1 ENSP00000378119 Q8NFT2 UPI000013DEE0 NM_001244944.1 3/6 hmmpanther:PTHR14239:SF6,hmmpanther:PTHR14239 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 14 90225090 90225090 C A 1 0 0 0 0 0 1 0 0 15655 838 29 2 2 STEAP2 7 90225090 Nonsense_Mutation SNP C C3L-00279_T 889242 90225090 69120883 263 6041 CDK6 0 . GRCh38 7 92833166 92833166 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.158G>T p.Gly53Val p.G53V ENST00000265734 2/8 394 351 43 320 320 0 strelka-varscan-mutect CDK6,missense_variant,p.Gly53Val,ENST00000265734,NM_001259.6;CDK6,missense_variant,p.Gly53Val,ENST00000424848,NM_001145306.1;AC002454.1,upstream_gene_variant,,ENST00000435695,;AC002454.1,upstream_gene_variant,,ENST00000452050,;CDK6,downstream_gene_variant,,ENST00000491250,; A ENST00000265734 Transcript missense_variant 570/11612 158/981 53/326 G/V gGc/gTc 1 -1 CDK6 HGNC HGNC:1777 protein_coding YES CCDS5628.1 ENSP00000265734 Q00534 UPI00001108FA NM_001259.6 deleterious(0) 2/8 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF130,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 92833166 92833166 C A 1 0 0 0 0 1 0 0 0 2852 739 26 2 2 CDK6 7 92833166 Missense_Mutation SNP C C3L-00279_T 2608076 92833166 66512807 264 6042 COL1A2 0 . GRCh38 7 94395035 94395035 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.4C>A p.Leu2Ile p.L2I ENST00000297268 1/52 486 421 65 434 434 0 strelka-varscan-mutect COL1A2,missense_variant,p.Leu2Ile,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Leu2Ile,ENST00000620463,; A ENST00000297268 Transcript missense_variant 475/5411 4/4101 2/1366 L/I Ctc/Atc 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 tolerated_low_confidence(0.43) 1/52 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 94395035 94395035 C A 1 0 0 0 0 1 0 0 0 3466 797 28 2 2 COL1A2 7 94395035 Missense_Mutation SNP C C3L-00279_T 1561869 94395035 64950938 265 6043 COL1A2 0 . GRCh38 7 94420562 94420562 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2209G>T p.Ala737Ser p.A737S ENST00000297268 37/52 911 790 121 766 762 4 strelka-varscan-mutect COL1A2,missense_variant,p.Ala737Ser,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Ala735Ser,ENST00000620463,;COL1A2,non_coding_transcript_exon_variant,,ENST00000497316,;COL1A2,non_coding_transcript_exon_variant,,ENST00000473573,;COL1A2,non_coding_transcript_exon_variant,,ENST00000461525,;COL1A2,non_coding_transcript_exon_variant,,ENST00000467931,;COL1A2,upstream_gene_variant,,ENST00000481570,;COL1A2,upstream_gene_variant,,ENST00000478215,;COL1A2,upstream_gene_variant,,ENST00000469732,;COL1A2,downstream_gene_variant,,ENST00000488298,; T ENST00000297268 Transcript missense_variant 2680/5411 2209/4101 737/1366 A/S Gct/Tct 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 tolerated(0.06) 37/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 94420562 94420562 G T 1 0 0 0 0 1 0 0 0 3466 1319 46 2 2 COL1A2 7 94420562 Missense_Mutation SNP G C3L-00279_T 25527 94420562 64925411 266 6044 DYNC1I1 0 . GRCh38 7 95984867 95984867 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.684G>T p.Glu228Asp p.E228D ENST00000324972 8/17 318 287 31 181 181 0 strelka-varscan-mutect DYNC1I1,missense_variant,p.Glu228Asp,ENST00000324972,NM_004411.4;DYNC1I1,missense_variant,p.Glu211Asp,ENST00000447467,NM_001135556.1;DYNC1I1,missense_variant,p.Glu208Asp,ENST00000437599,NM_001278421.1;DYNC1I1,missense_variant,p.Glu191Asp,ENST00000359388,NM_001135557.1;DYNC1I1,missense_variant,p.Glu211Asp,ENST00000457059,;DYNC1I1,missense_variant,p.Glu191Asp,ENST00000630942,NM_001278422.1;DYNC1I1,missense_variant,p.Glu133Asp,ENST00000537881,;DYNC1I1,non_coding_transcript_exon_variant,,ENST00000519371,; T ENST00000324972 Transcript missense_variant 877/2950 684/1938 228/645 E/D gaG/gaT 1 1 DYNC1I1 HGNC HGNC:2963 protein_coding YES CCDS5644.1 ENSP00000320130 O14576 A4D1I7 UPI0000129A01 NM_004411.4 tolerated(0.19) 8/17 hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 95984867 95984867 G T 1 0 0 0 0 1 0 0 0 4666 991 35 2 2 DYNC1I1 7 95984867 Missense_Mutation SNP G C3L-00279_T 1564305 95984867 63361106 267 6045 NYAP1 0 . GRCh38 7 100493823 100493823 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.2446C>A p.= p.R816R ENST00000300179 7/7 175 147 28 164 164 0 strelka-varscan-mutect NYAP1,synonymous_variant,p.=,ENST00000300179,NM_173564.3;NYAP1,synonymous_variant,p.=,ENST00000454988,;NYAP1,non_coding_transcript_exon_variant,,ENST00000496985,;NYAP1,non_coding_transcript_exon_variant,,ENST00000489641,; A ENST00000300179 Transcript synonymous_variant 2605/3581 2446/2526 816/841 R Cgg/Agg 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 7/7 Pfam_domain:PF15452,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 LOW 1 SNV 2 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999983 1 1 1 0 A 2 1 14 100493823 100493823 C A 1 0 0 0 0 0 0 0 1 10872 759 27 1 1 NYAP1 7 100493823 Silent SNP C C3L-00279_T 4508956 100493823 58852150 268 6046 ZAN 0 . GRCh38 7 100790988 100790988 + Nonsense_Mutation SNP C C A rs552182725 C3L-00279_T C3L-00279_N C C c.7404C>A p.Cys2468Ter p.C2468* ENST00000613979 40/48 197 167 30 150 150 0 strelka-varscan-mutect ZAN,stop_gained,p.Cys2468Ter,ENST00000613979,NM_003386.2;ZAN,stop_gained,p.Cys2468Ter,ENST00000618565,;ZAN,stop_gained,p.Cys2468Ter,ENST00000620596,NM_173059.2;ZAN,stop_gained,p.Cys2468Ter,ENST00000546292,;ZAN,stop_gained,p.Cys2468Ter,ENST00000542585,;ZAN,stop_gained,p.Cys2468Ter,ENST00000538115,;ZAN,stop_gained,p.Cys2468Ter,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; A ENST00000613979 Transcript stop_gained 7569/8669 7404/8439 2468/2812 C/* tgC/tgA rs552182725,COSM1233070 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 40/48 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221,SMART_domains:SM00216 0,1 HIGH 1 SNV 1 0,1 1 PASS rs552182725 . 0 202 0 5 2 0 0 0 -15.15882 0.9326297 1 1 1 0 A 4 1 14 100790988 100790988 C A 1 0 0 0 0 0 1 0 0 18074 776 27 1 1 ZAN 7 100790988 Nonsense_Mutation SNP C C3L-00279_T 297165 100790988 58554985 269 6047 MUC17 0 . GRCh38 7 101035129 101035129 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.3713C>T p.Thr1238Ile p.T1238I ENST00000306151 3/13 163 145 18 124 124 0 strelka-varscan MUC17,missense_variant,p.Thr1238Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Thr1238Ile,ENST00000379439,; T ENST00000306151 Transcript missense_variant 3777/14247 3713/13482 1238/4493 T/I aCc/aTc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 101035129 101035129 C T 1 0 0 0 0 1 0 0 0 9973 507 18 3 3 MUC17 7 101035129 Missense_Mutation SNP C C3L-00279_T 244141 101035129 58310844 270 6048 NRCAM 0 . GRCh38 7 108150122 108150122 + Missense_Mutation SNP T T C novel C3L-00279_T C3L-00279_N T T c.3703A>G p.Lys1235Glu p.K1235E ENST00000379028 33/33 174 142 32 95 95 0 strelka-varscan NRCAM,missense_variant,p.Lys1235Glu,ENST00000379028,;NRCAM,missense_variant,p.Lys1142Glu,ENST00000413765,NM_001193582.1;NRCAM,missense_variant,p.Lys1114Glu,ENST00000351718,NM_005010.4;NRCAM,missense_variant,p.Lys1123Glu,ENST00000379024,NM_001193583.1,NM_001193584.1;NRCAM,missense_variant,p.Lys1235Glu,ENST00000425651,NM_001037132.2;NRCAM,missense_variant,p.Lys1230Glu,ENST00000379022,;NRCAM,missense_variant,p.Lys134Glu,ENST00000445634,;NRCAM,non_coding_transcript_exon_variant,,ENST00000522550,;NRCAM,non_coding_transcript_exon_variant,,ENST00000415105,; C ENST00000379028 Transcript missense_variant 4189/6685 3703/3915 1235/1304 K/E Aaa/Gaa 1 -1 NRCAM HGNC HGNC:7994 protein_coding YES CCDS47686.1 ENSP00000368314 Q92823 UPI00005E2661 tolerated(0.06) 33/33 Pfam_domain:PF13882,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 108150122 108150122 T C 1 0 0 0 0 1 0 0 0 10700 1792 62 5 5 NRCAM 7 108150122 Missense_Mutation SNP T C3L-00279_T 7114993 108150122 51195851 271 6049 PPP1R3A 0 . GRCh38 7 113879926 113879927 + Frame_Shift_Ins INS - - A novel C3L-00279_T C3L-00279_N - - c.1165dupT p.Tyr389LeufsTer4 p.Y389Lfs*4 ENST00000284601 4/4 196 183 13 74 74 0 varindel-pindel PPP1R3A,frameshift_variant,p.Tyr389LeufsTer4,ENST00000284601,NM_002711.3;PPP1R3A,frameshift_variant,p.Tyr68LeufsTer4,ENST00000449795,;PPP1R3A,3_prime_UTR_variant,,ENST00000284602,; A ENST00000284601 Transcript frameshift_variant 1234-1235/4384 1165-1166/3369 389/1122 Y/LX tac/tTac 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 HIGH 1 insertion 1 1 PASS . . 0 203 4 3 0 0 0 0 -16.41111 0.9992203 1 1 1 0 A 7 5 14 113879926 113879926 - A 1 0 1 1 0 0 0 0 0 12492 1638 57 0 0 PPP1R3A 7 113879926 Frame_Shift_Ins INS - C3L-00279_T 5729804 113879926 45466047 272 6050 PTPRZ1 0 . GRCh38 7 122054001 122054001 + Missense_Mutation SNP C C A rs147791375 C3L-00279_T C3L-00279_N C C c.6344C>A p.Ala2115Asp p.A2115D ENST00000393386 26/30 217 196 21 101 101 0 strelka-varscan PTPRZ1,missense_variant,p.Ala2115Asp,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.Ala1248Asp,ENST00000449182,NM_001206839.1; A ENST00000393386 Transcript missense_variant 6755/8175 6344/6948 2115/2315 A/D gCc/gAc rs147791375 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0) 26/30 PROSITE_profiles:PS50055,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 14 122054001 122054001 C A 1 0 0 0 0 1 0 0 0 12969 739 26 2 2 PTPRZ1 7 122054001 Missense_Mutation SNP C C3L-00279_T 8174075 122054001 37291972 273 6051 FLNC 0 . GRCh38 7 128856546 128856546 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.7280C>A p.Ala2427Glu p.A2427E ENST00000325888 44/48 428 380 48 386 386 0 strelka-varscan FLNC,missense_variant,p.Ala2427Glu,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Ala2394Glu,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; A ENST00000325888 Transcript missense_variant 7541/9188 7280/8178 2427/2725 A/E gCg/gAg 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.25) 44/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 128856546 128856546 C A 1 0 0 0 0 1 0 0 0 5791 768 27 1 1 FLNC 7 128856546 Missense_Mutation SNP C C3L-00279_T 6802545 128856546 30489427 274 6052 CPA5 0 . GRCh38 7 130350100 130350100 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.324G>A p.= p.K108K ENST00000485477 4/12 101 82 19 81 81 0 strelka-varscan CPA5,synonymous_variant,p.=,ENST00000485477,;CPA5,synonymous_variant,p.=,ENST00000466363,;CPA5,synonymous_variant,p.=,ENST00000474905,NM_080385.4,NM_001127441.1;CPA5,synonymous_variant,p.=,ENST00000431780,NM_001127442.1;CPA5,synonymous_variant,p.=,ENST00000461828,NM_001318223.1;CPA5,synonymous_variant,p.=,ENST00000393213,;CPA5,synonymous_variant,p.=,ENST00000463587,;CPA5,downstream_gene_variant,,ENST00000494311,;CPA5,downstream_gene_variant,,ENST00000497503,;CPA5,non_coding_transcript_exon_variant,,ENST00000495736,; A ENST00000485477 Transcript synonymous_variant 1453/2573 324/1311 108/436 K aaG/aaA 1 1 CPA5 HGNC HGNC:15722 protein_coding YES CCDS5819.1 ENSP00000420237 Q8WXQ8 A4D1M2 UPI000000D837 4/12 hmmpanther:PTHR11705:SF16,hmmpanther:PTHR11705,Gene3D:3.30.70.340,Pfam_domain:PF02244,Superfamily_domains:SSF54897 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 130350100 130350100 G A 1 0 0 0 0 0 0 0 1 3587 991 35 3 3 CPA5 7 130350100 Silent SNP G C3L-00279_T 1493554 130350100 28995873 275 6053 PLXNA4 0 . GRCh38 7 132227599 132227599 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.1734C>A p.= p.V578V ENST00000359827 7/32 254 220 34 177 176 1 strelka-varscan PLXNA4,synonymous_variant,p.=,ENST00000359827,;PLXNA4,synonymous_variant,p.=,ENST00000321063,NM_020911.1; T ENST00000359827 Transcript synonymous_variant 2697/13786 1734/5685 578/1894 V gtC/gtA 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 7/32 hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 132227599 132227599 G T 1 0 0 0 0 0 0 0 1 12228 1188 41 2 2 PLXNA4 7 132227599 Silent SNP G C3L-00279_T 1877499 132227599 27118374 276 6054 CALD1 0 . GRCh38 7 134891635 134891635 + Silent SNP C C A C3L-00279_T C3L-00279_N C C c.15C>A p.= p.S5S ENST00000393118 1/13 167 147 20 112 112 0 strelka-varscan CALD1,synonymous_variant,p.=,ENST00000393118,NM_033139.3;CALD1,synonymous_variant,p.=,ENST00000495522,;CALD1,synonymous_variant,p.=,ENST00000424922,NM_033140.3;CALD1,intron_variant,,ENST00000361901,NM_004342.6;CALD1,intron_variant,,ENST00000361675,NM_033138.3;CALD1,intron_variant,,ENST00000422748,NM_033157.3;CALD1,intron_variant,,ENST00000417172,;CALD1,intron_variant,,ENST00000436461,;CALD1,intron_variant,,ENST00000454108,;CALD1,intron_variant,,ENST00000445569,;CALD1,intron_variant,,ENST00000435928,;CALD1,intron_variant,,ENST00000489019,;CALD1,synonymous_variant,p.=,ENST00000443197,;CALD1,intron_variant,,ENST00000482470,;CALD1,intron_variant,,ENST00000430085,; A ENST00000393118 Transcript synonymous_variant 236/4281 15/1677 5/558 S tcC/tcA COSM1247257 1 1 CALD1 HGNC HGNC:1441 protein_coding CCDS47716.1 ENSP00000376826 Q05682 UPI000002A558 NM_033139.3 1/13 Low_complexity_(Seg):seg 1 LOW SNV 1 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 2 1 14 134891635 134891635 C A 1 0 0 0 0 0 0 0 1 2271 639 23 1 1 CALD1 7 134891635 Silent SNP C C3L-00279_T 2664036 134891635 24454338 277 6055 KIAA1549 0 . GRCh38 7 138871223 138871223 + Silent SNP C C A rs538170892 C3L-00279_T C3L-00279_N C C c.4485G>T p.= p.P1495P ENST00000422774 13/20 160 140 20 128 128 0 strelka-varscan KIAA1549,synonymous_variant,p.=,ENST00000440172,NM_020910.2;KIAA1549,synonymous_variant,p.=,ENST00000422774,NM_001164665.1; A ENST00000422774 Transcript synonymous_variant 4534/6283 4485/5853 1495/1950 P ccG/ccT rs538170892 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 13/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590,Pfam_domain:PF12877 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 138871223 138871223 C A 1 0 0 0 0 0 0 0 1 8120 639 23 1 1 KIAA1549 7 138871223 Silent SNP C C3L-00279_T 3979588 138871223 20474750 278 6056 TMEM178B 0 . GRCh38 7 141470715 141470715 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.814G>T p.Ala272Ser p.A272S ENST00000565468 4/4 240 216 24 171 171 0 strelka-varscan TMEM178B,missense_variant,p.Ala272Ser,ENST00000565468,NM_001195278.1;TMEM178B,missense_variant,p.Ala270Ser,ENST00000610315,; T ENST00000565468 Transcript missense_variant 893/10558 814/885 272/294 A/S Gcc/Tcc 1 1 TMEM178B HGNC HGNC:44112 protein_coding YES CCDS59086.1 ENSP00000456594 H3BS89 UPI0000E217DE NM_001195278.1 tolerated(0.43) 4/4 hmmpanther:PTHR32005,hmmpanther:PTHR32005:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 141470715 141470715 G T 1 0 0 0 0 1 0 0 0 16540 971 34 2 2 TMEM178B 7 141470715 Missense_Mutation SNP G C3L-00279_T 2599492 141470715 17875258 279 6057 MGAM2 0 . GRCh38 7 142131583 142131583 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.376C>A p.Leu126Ile p.L126I ENST00000477922 5/48 226 196 30 198 198 0 strelka-varscan MGAM2,missense_variant,p.Leu126Ile,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Leu126Ile,ENST00000550469,; A ENST00000477922 Transcript missense_variant 430/7867 376/7548 126/2515 L/I Ctt/Att 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated(0.12) 5/48 Pfam_domain:PF16863,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF74650 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 142131583 142131583 C A 1 0 0 0 0 1 0 0 0 9500 681 24 2 2 MGAM2 7 142131583 Missense_Mutation SNP C C3L-00279_T 660868 142131583 17214390 280 6058 CLCN1 0 . GRCh38 7 143321747 143321747 + Missense_Mutation SNP C C A rs143506735 C3L-00279_T C3L-00279_N C C c.595C>A p.Arg199Ser p.R199S ENST00000343257 5/23 561 490 71 416 415 1 strelka-varscan CLCN1,missense_variant,p.Arg199Ser,ENST00000343257,NM_000083.2;CLCN1,non_coding_transcript_exon_variant,,ENST00000495612,;CLCN1,missense_variant,p.Arg19Ser,ENST00000455478,;CLCN1,missense_variant,p.Arg19Ser,ENST00000432192,; A ENST00000343257 Transcript missense_variant 682/3172 595/2967 199/988 R/S Cgt/Agt rs143506735,COSM1201276 1 1 CLCN1 HGNC HGNC:2019 protein_coding YES CCDS5881.1 ENSP00000339867 P35523 UPI000020F1EC NM_000083.2 deleterious(0) 5/23 hmmpanther:PTHR11689:SF29,hmmpanther:PTHR11689,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340,Prints_domain:PR00762 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 143321747 143321747 C A 1 0 0 0 0 1 0 0 0 3226 884 31 1 1 CLCN1 7 143321747 Missense_Mutation SNP C C3L-00279_T 1190164 143321747 16024226 281 6059 OR6B1 0 . GRCh38 7 144004049 144004049 + Missense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.53C>T p.Pro18Leu p.P18L ENST00000408922 1/1 86 72 14 108 108 0 strelka-varscan OR6B1,missense_variant,p.Pro18Leu,ENST00000408922,NM_001005281.1; T ENST00000408922 Transcript missense_variant 121/1055 53/936 18/311 P/L cCt/cTt COSM4984041 1 1 OR6B1 HGNC HGNC:8354 protein_coding YES CCDS43667.1 ENSP00000386151 O95007 UPI0000041B18 NM_001005281.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF284,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 144004049 144004049 C T 1 0 0 0 0 1 0 0 0 11255 681 24 3 3 OR6B1 7 144004049 Missense_Mutation SNP C C3L-00279_T 682302 144004049 15341924 282 6060 GIMAP6 0 . GRCh38 7 150628049 150628049 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.759G>T p.Gln253His p.Q253H ENST00000618759 3/3 391 346 45 348 348 0 strelka-varscan GIMAP6,missense_variant,p.Gln253His,ENST00000618759,NM_001244072.1;GIMAP6,missense_variant,p.Gln183His,ENST00000328902,NM_024711.5;GIMAP6,3_prime_UTR_variant,,ENST00000493969,NM_001244071.1; A ENST00000618759 Transcript missense_variant 1239/3910 759/1089 253/362 Q/H caG/caT COSM1600139 1 -1 GIMAP6 HGNC HGNC:21918 protein_coding YES CCDS75676.1 ENSP00000479580 B4DH95 UPI00017A6DF2 NM_001244072.1 tolerated(0.22) 3/3 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF51,hmmpanther:PTHR10903,Pfam_domain:PF04548,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 150628049 150628049 C A 1 0 0 0 0 1 0 0 0 6263 680 24 2 2 GIMAP6 7 150628049 Missense_Mutation SNP C C3L-00279_T 6624000 150628049 8717924 283 6061 NEFM 0 . GRCh38 8 24917117 24917117 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1262G>T p.Gly421Val p.G421V ENST00000221166 3/3 337 309 28 210 210 0 strelka-varscan NEFM,missense_variant,p.Gly421Val,ENST00000221166,NM_005382.2;NEFM,missense_variant,p.Gly421Val,ENST00000437366,;NEFM,missense_variant,p.Gly45Val,ENST00000433454,NM_001105541.1;NEFM,missense_variant,p.Gly421Val,ENST00000518131,;GS1-72M22.1,upstream_gene_variant,,ENST00000607058,;NEFM,non_coding_transcript_exon_variant,,ENST00000521540,;NEFM,downstream_gene_variant,,ENST00000523467,; T ENST00000221166 Transcript missense_variant 2044/4020 1262/2751 421/916 G/V gGg/gTg 1 1 NEFM HGNC HGNC:7734 protein_coding YES CCDS6046.1 ENSP00000221166 P07197 UPI000013C7A9 NM_005382.2 tolerated(0.09) 3/3 hmmpanther:PTHR23239:SF19,hmmpanther:PTHR23239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 24917117 24917117 G T 1 0 0 0 0 1 0 0 0 10344 1232 43 2 2 NEFM 8 24917117 Missense_Mutation SNP G C3L-00279_T 24917117 120221519 284 6062 NUGGC 0 . GRCh38 8 28064523 28064523 + Frame_Shift_Del DEL T T - novel C3L-00279_T C3L-00279_N T T c.920delA p.Lys307ArgfsTer8 p.K307Rfs*8 ENST00000413272 7/19 157 145 12 145 145 0 sindel-varindel-pindel NUGGC,frameshift_variant,p.Lys307ArgfsTer8,ENST00000413272,NM_001010906.1; - ENST00000413272 Transcript frameshift_variant,splice_region_variant 1063/3887 920/2391 307/796 K/X aAg/ag 1 -1 NUGGC HGNC HGNC:33550 protein_coding YES CCDS47833.1 ENSP00000408697 Q68CJ6 UPI0000237454 NM_001010906.1 7/19 hmmpanther:PTHR19331,Gene3D:3.40.50.300,Pfam_domain:PF00350,Superfamily_domains:SSF52540 HIGH 1 deletion 2 1 PASS . . 0 189 0 16 4 0 0 0 -4.706149 0.0734877 1 1 0 0 - 7 5 14 28064523 28064523 T - 1 0 1 0 1 0 0 0 0 10814 1623 56 0 0 NUGGC 8 28064523 Frame_Shift_Del DEL T C3L-00279_T 3147406 28064523 117074113 285 6063 EXTL3 0 . GRCh38 8 28716547 28716547 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.488A>G p.Lys163Arg p.K163R ENST00000220562 3/7 518 461 57 462 462 0 strelka-varscan EXTL3,missense_variant,p.Lys163Arg,ENST00000220562,NM_001440.3;EXTL3,intron_variant,,ENST00000523149,;EXTL3,intron_variant,,ENST00000521532,;EXTL3,upstream_gene_variant,,ENST00000521473,;EXTL3,intron_variant,,ENST00000519886,;EXTL3,downstream_gene_variant,,ENST00000518223,;EXTL3,downstream_gene_variant,,ENST00000522725,;EXTL3,downstream_gene_variant,,ENST00000520940,;EXTL3,downstream_gene_variant,,ENST00000454906,;EXTL3,downstream_gene_variant,,ENST00000519288,;EXTL3,upstream_gene_variant,,ENST00000522698,; G ENST00000220562 Transcript missense_variant 1390/6483 488/2760 163/919 K/R aAg/aGg 1 1 EXTL3 HGNC HGNC:3518 protein_coding YES CCDS6070.1 ENSP00000220562 O43909 UPI000012A35D NM_001440.3 tolerated(0.53) 3/7 hmmpanther:PTHR11062:SF73,hmmpanther:PTHR11062 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 28716547 28716547 A G 1 0 0 0 0 1 0 0 0 5195 72 3 5 5 EXTL3 8 28716547 Missense_Mutation SNP A C3L-00279_T 652024 28716547 116422089 286 6064 TEX15 0 . GRCh38 8 30846671 30846671 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2347C>A p.Pro783Thr p.P783T ENST00000256246 1/4 227 206 21 144 144 0 strelka-varscan TEX15,missense_variant,p.Pro783Thr,ENST00000256246,NM_031271.3;TEX15,downstream_gene_variant,,ENST00000523186,; T ENST00000256246 Transcript missense_variant 2422/10187 2347/8370 783/2789 P/T Cca/Aca 1 -1 TEX15 HGNC HGNC:11738 protein_coding YES CCDS6080.1 ENSP00000256246 Q9BXT5 UPI000013CEF9 NM_031271.3 tolerated(1) 1/4 hmmpanther:PTHR22380,hmmpanther:PTHR22380:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30846671 30846671 G T 1 0 0 0 0 1 0 0 0 16201 1203 42 2 2 TEX15 8 30846671 Missense_Mutation SNP G C3L-00279_T 2130124 30846671 114291965 287 6065 WRN 0 . GRCh38 8 31120242 31120242 + Splice_Site SNP G G T novel C3L-00279_T C3L-00279_N G G c.2449-1G>T p.X817_splice ENST00000298139 306 266 40 210 210 0 strelka-varscan WRN,splice_acceptor_variant,,ENST00000298139,NM_000553.4;WRN,splice_acceptor_variant,,ENST00000521620,;WRN,non_coding_transcript_exon_variant,,ENST00000520169,; T ENST00000298139 Transcript splice_acceptor_variant -/5215 2449/4299 817/1432 1 1 WRN HGNC HGNC:12791 protein_coding YES CCDS6082.1 ENSP00000298139 Q14191 UPI000013E49D NM_000553.4 20/34 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 14 31120242 31120242 G T 1 0 0 0 0 0 0 1 0 17959 1043 36 2 2 WRN 8 31120242 Splice_Site SNP G C3L-00279_T 273571 31120242 114018394 288 6066 PRKDC 0 . GRCh38 8 47794390 47794390 + Missense_Mutation SNP T T A rs374286545 C3L-00279_T C3L-00279_N T T c.10570A>T p.Asn3524Tyr p.N3524Y ENST00000314191 74/86 268 231 37 158 158 0 strelka-varscan PRKDC,missense_variant,p.Asn3524Tyr,ENST00000314191,NM_006904.6;PRKDC,missense_variant,p.Asn3524Tyr,ENST00000338368,NM_001081640.1; A ENST00000314191 Transcript missense_variant 10627/13509 10570/12387 3524/4128 N/Y Aac/Tac rs374286545 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 tolerated(0.06) 74/86 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF68 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 47794390 47794390 T A 1 0 0 0 0 1 0 0 0 12654 1754 61 4 4 PRKDC 8 47794390 Missense_Mutation SNP T C3L-00279_T 16674148 47794390 97344246 289 6067 RGS20 0 . GRCh38 8 53879267 53879267 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.175C>A p.Pro59Thr p.P59T ENST00000297313 2/6 224 190 34 260 260 0 strelka-varscan RGS20,missense_variant,p.Pro59Thr,ENST00000297313,NM_170587.3;RGS20,intron_variant,,ENST00000344277,NM_001286673.1;RGS20,upstream_gene_variant,,ENST00000276500,NM_003702.4;RGS20,upstream_gene_variant,,ENST00000522225,;RP11-1070A24.2,upstream_gene_variant,,ENST00000606037,;RGS20,upstream_gene_variant,,ENST00000523414,;RGS20,upstream_gene_variant,,ENST00000523064,;RGS20,upstream_gene_variant,,ENST00000518286,;RGS20,intron_variant,,ENST00000517659,NM_001286675.1;RGS20,intron_variant,,ENST00000523280,NM_001286674.1; A ENST00000297313 Transcript missense_variant 267/2104 175/1167 59/388 P/T Cct/Act 1 1 RGS20 HGNC HGNC:14600 protein_coding YES CCDS6155.1 ENSP00000297313 O76081 UPI000013383C NM_170587.3 deleterious_low_confidence(0) 2/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 53879267 53879267 C A 1 0 0 0 0 1 0 0 0 13474 739 26 2 2 RGS20 8 53879267 Missense_Mutation SNP C C3L-00279_T 6084877 53879267 91259369 290 6068 MOS 0 . GRCh38 8 56113599 56113599 + Frame_Shift_Del DEL G G - C3L-00279_T C3L-00279_N G G c.384delC p.Ala129GlnfsTer6 p.A129Qfs*6 ENST00000311923 1/1 159 142 17 211 211 0 sindel-varindel-pindel MOS,frameshift_variant,p.Ala129GlnfsTer6,ENST00000311923,NM_005372.1; - ENST00000311923 Transcript frameshift_variant 384/1041 384/1041 128/346 P/X ccC/cc COSM5457933 1 -1 MOS HGNC HGNC:7199 protein_coding YES CCDS6164.1 ENSP00000310722 P00540 UPI000012DF0C NM_005372.1 1/1 Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF000654,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 56113599 56113599 G - 1 0 1 0 1 0 0 0 0 9676 1103 39 0 0 MOS 8 56113599 Frame_Shift_Del DEL G C3L-00279_T 2234332 56113599 89025037 291 6069 ADHFE1 0 . GRCh38 8 66451985 66451985 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.767A>G p.Tyr256Cys p.Y256C ENST00000396623 9/14 193 165 28 173 173 0 strelka-varscan ADHFE1,missense_variant,p.Tyr256Cys,ENST00000396623,NM_144650.2;ADHFE1,missense_variant,p.Tyr208Cys,ENST00000415254,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000496501,;ADHFE1,upstream_gene_variant,,ENST00000480040,;ADHFE1,missense_variant,p.Tyr256Cys,ENST00000424777,;ADHFE1,3_prime_UTR_variant,,ENST00000426810,;ADHFE1,3_prime_UTR_variant,,ENST00000419955,;ADHFE1,3_prime_UTR_variant,,ENST00000276576,;ADHFE1,3_prime_UTR_variant,,ENST00000396621,;ADHFE1,3_prime_UTR_variant,,ENST00000422166,;ADHFE1,3_prime_UTR_variant,,ENST00000443372,;ADHFE1,downstream_gene_variant,,ENST00000449512,; G ENST00000396623 Transcript missense_variant 798/1990 767/1404 256/467 Y/C tAc/tGc 1 1 ADHFE1 HGNC HGNC:16354 protein_coding YES CCDS6190.2 ENSP00000379865 Q8IWW8 UPI000004966C NM_144650.2 deleterious(0) 9/14 Gene3D:1.20.1090.10,Pfam_domain:PF00465,Superfamily_domains:SSF56796 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 66451985 66451985 A G 1 0 0 0 0 1 0 0 0 387 391 14 5 5 ADHFE1 8 66451985 Missense_Mutation SNP A C3L-00279_T 10338386 66451985 78686651 292 6070 EYA1 0 . GRCh38 8 71321761 71321761 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.391G>C p.Gly131Arg p.G131R ENST00000340726 6/18 301 260 41 247 247 0 strelka-varscan EYA1,missense_variant,p.Gly131Arg,ENST00000340726,NM_000503.5;EYA1,missense_variant,p.Gly130Arg,ENST00000303824,NM_001288575.1,NM_001288574.1;EYA1,missense_variant,p.Gly131Arg,ENST00000388742,NM_172058.3;EYA1,missense_variant,p.Gly98Arg,ENST00000388740,NM_172060.3;EYA1,missense_variant,p.Gly97Arg,ENST00000388741,;EYA1,missense_variant,p.Gly130Arg,ENST00000388743,;EYA1,missense_variant,p.Gly131Arg,ENST00000419131,NM_172059.3;EYA1,missense_variant,p.Gln108His,ENST00000465115,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,;EYA1,non_coding_transcript_exon_variant,,ENST00000422295,; G ENST00000340726 Transcript missense_variant 1031/4326 391/1779 131/592 G/R Gga/Cga 1 -1 EYA1 HGNC HGNC:3519 protein_coding YES CCDS34906.1 ENSP00000342626 Q99502 A0A024R813 UPI000012A3B3 NM_000503.5 deleterious(0) 6/18 hmmpanther:PTHR10190,hmmpanther:PTHR10190:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 71321761 71321761 C G 1 0 0 0 0 1 0 0 0 5196 690 24 4 4 EYA1 8 71321761 Missense_Mutation SNP C C3L-00279_T 4869776 71321761 73816875 293 6071 ZFHX4 0 . GRCh38 8 76706063 76706063 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.1975C>A p.Leu659Met p.L659M ENST00000521891 2/11 158 137 21 172 172 0 strelka-varscan ZFHX4,missense_variant,p.Leu659Met,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Leu659Met,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript missense_variant 2423/14019 1975/10851 659/3616 L/M Ctg/Atg COSM3901576,COSM3901577 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 2/11 PROSITE_patterns:PS00028,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 76706063 76706063 C A 1 0 0 0 0 1 0 0 0 18213 680 24 2 2 ZFHX4 8 76706063 Missense_Mutation SNP C C3L-00279_T 5384302 76706063 68432573 294 6072 ATP6V0D2 0 . GRCh38 8 86141483 86141483 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.515C>A p.Ala172Asp p.A172D ENST00000285393 4/8 72 63 9 35 35 0 strelka-varscan ATP6V0D2,missense_variant,p.Ala172Asp,ENST00000285393,NM_152565.1;CTD-3118D11.2,intron_variant,,ENST00000522679,; A ENST00000285393 Transcript missense_variant 657/2446 515/1053 172/350 A/D gCt/gAt 1 1 ATP6V0D2 HGNC HGNC:18266 protein_coding YES CCDS6241.1 ENSP00000285393 Q8N8Y2 A0A024R991 UPI0000051F69 NM_152565.1 tolerated(1) 4/8 Superfamily_domains:0044678,Pfam_domain:PF01992,PIRSF_domain:PIRSF018497,hmmpanther:PTHR11028,hmmpanther:PTHR11028:SF2 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.62034 1 1 1 1 0 A 3 1 14 86141483 86141483 C A 1 0 0 0 0 1 0 0 0 1327 797 28 2 2 ATP6V0D2 8 86141483 Missense_Mutation SNP C C3L-00279_T 9435420 86141483 58997153 295 6073 SLC7A13 0 . GRCh38 8 86217689 86217689 + Missense_Mutation SNP C C A rs527670230 C3L-00279_T C3L-00279_N C C c.960G>T p.Glu320Asp p.E320D ENST00000297524 3/4 215 186 29 89 89 0 strelka-varscan SLC7A13,missense_variant,p.Glu320Asp,ENST00000297524,NM_138817.2;SLC7A13,missense_variant,p.Glu311Asp,ENST00000419776,;SLC7A13,non_coding_transcript_exon_variant,,ENST00000520624,; A ENST00000297524 Transcript missense_variant 1064/1878 960/1413 320/470 E/D gaG/gaT rs527670230 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 tolerated(0.07) 3/4 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 86217689 86217689 C A 1 0 0 0 0 1 0 0 0 14978 680 24 2 2 SLC7A13 8 86217689 Missense_Mutation SNP C C3L-00279_T 76206 86217689 58920947 296 6074 CDH17 0 . GRCh38 8 94177650 94177650 + Silent SNP C C A C3L-00279_T C3L-00279_N C C c.222G>T p.= p.R74R ENST00000027335 4/18 256 231 25 137 137 0 strelka-varscan CDH17,synonymous_variant,p.=,ENST00000027335,NM_004063.3;CDH17,synonymous_variant,p.=,ENST00000450165,NM_001144663.1;CDH17,synonymous_variant,p.=,ENST00000441892,;CDH17,synonymous_variant,p.=,ENST00000521491,; A ENST00000027335 Transcript synonymous_variant 347/3693 222/2499 74/832 R cgG/cgT COSM4405634 1 -1 CDH17 HGNC HGNC:1756 protein_coding YES CCDS6260.1 ENSP00000027335 Q12864 UPI000013C546 NM_004063.3 4/18 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF292,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 94177650 94177650 C A 1 0 0 0 0 0 0 0 1 2805 610 22 2 2 CDH17 8 94177650 Silent SNP C C3L-00279_T 7959961 94177650 50960986 297 6075 CPQ 0 . GRCh38 8 96879924 96879924 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.768A>T p.= p.L256L ENST00000220763 4/8 403 349 54 256 256 0 strelka-varscan CPQ,synonymous_variant,p.=,ENST00000220763,NM_016134.3; T ENST00000220763 Transcript synonymous_variant 978/1947 768/1419 256/472 L ctA/ctT 1 1 CPQ HGNC HGNC:16910 protein_coding YES CCDS6273.1 ENSP00000220763 Q9Y646 A0A024R9B8 UPI00000706B8 NM_016134.3 4/8 hmmpanther:PTHR12053,hmmpanther:PTHR12053:SF3,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 96879924 96879924 A T 1 0 0 0 0 0 0 0 1 3618 349 13 4 4 CPQ 8 96879924 Silent SNP A C3L-00279_T 2702274 96879924 48258712 298 6076 CPQ 0 . GRCh38 8 97066197 97066197 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1242A>T p.Gln414His p.Q414H ENST00000220763 7/8 191 163 28 176 176 0 strelka-varscan CPQ,missense_variant,p.Gln414His,ENST00000220763,NM_016134.3;CPQ,missense_variant,p.Gln72His,ENST00000522617,;CPQ,non_coding_transcript_exon_variant,,ENST00000529551,;CPQ,non_coding_transcript_exon_variant,,ENST00000532528,; T ENST00000220763 Transcript missense_variant 1452/1947 1242/1419 414/472 Q/H caA/caT 1 1 CPQ HGNC HGNC:16910 protein_coding YES CCDS6273.1 ENSP00000220763 Q9Y646 A0A024R9B8 UPI00000706B8 NM_016134.3 tolerated(0.11) 7/8 Gene3D:3.40.630.10,Pfam_domain:PF04389,hmmpanther:PTHR12053,hmmpanther:PTHR12053:SF3,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 97066197 97066197 A T 1 0 0 0 0 1 0 0 0 3618 69 3 4 4 CPQ 8 97066197 Missense_Mutation SNP A C3L-00279_T 186273 97066197 48072439 299 6077 ZFPM2 0 . GRCh38 8 105803015 105803015 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2933C>A p.Ala978Asp p.A978D ENST00000407775 8/8 382 326 56 209 209 0 strelka-varscan-mutect ZFPM2,missense_variant,p.Ala978Asp,ENST00000407775,NM_012082.3;ZFPM2,missense_variant,p.Ala846Asp,ENST00000520492,;ZFPM2,missense_variant,p.Ala846Asp,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; A ENST00000407775 Transcript missense_variant 3183/4700 2933/3456 978/1151 A/D gCc/gAc 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 tolerated(0.3) 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 105803015 105803015 C A 1 0 0 0 0 1 0 0 0 18236 739 26 2 2 ZFPM2 8 105803015 Missense_Mutation SNP C C3L-00279_T 8736818 105803015 39335621 300 6078 RSPO2 0 . GRCh38 8 107989077 107989077 + Missense_Mutation SNP G G T rs774354810 C3L-00279_T C3L-00279_N G G c.262C>A p.Pro88Thr p.P88T ENST00000276659 3/6 211 190 21 265 265 0 strelka-varscan-mutect RSPO2,missense_variant,p.Pro88Thr,ENST00000276659,NM_178565.4;RSPO2,missense_variant,p.Pro21Thr,ENST00000517939,NM_001317942.1;RSPO2,missense_variant,p.Pro21Thr,ENST00000521502,;RSPO2,missense_variant,p.Pro60Thr,ENST00000520026,;RSPO2,missense_variant,p.Pro21Thr,ENST00000521757,;RSPO2,missense_variant,p.Pro88Thr,ENST00000521956,;RSPO2,intron_variant,,ENST00000517781,NM_001282863.1;RSPO2,downstream_gene_variant,,ENST00000522333,; T ENST00000276659 Transcript missense_variant 883/3111 262/732 88/243 P/T Cca/Aca rs774354810 1 -1 RSPO2 HGNC HGNC:28583 protein_coding YES CCDS6307.1 ENSP00000276659 Q6UXX9 UPI000021046F NM_178565.4 tolerated(0.08) 3/6 hmmpanther:PTHR23275:SF40,hmmpanther:PTHR23275,Gene3D:2.10.220.10,Pfam_domain:PF15913,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs774354810 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 107989077 107989077 G T 1 0 0 0 0 1 0 0 0 13968 1232 43 2 2 RSPO2 8 107989077 Missense_Mutation SNP G C3L-00279_T 2186062 107989077 37149559 301 6079 PKHD1L1 0 . GRCh38 8 109430038 109430038 + Splice_Site SNP G G T novel C3L-00279_T C3L-00279_N G G c.3229+1G>T p.X1077_splice ENST00000378402 109 101 8 49 49 0 strelka-mutect PKHD1L1,splice_donor_variant,,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript splice_donor_variant -/13076 3229/12732 1077/4243 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 27/77 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 14 109430038 109430038 G T 1 0 0 0 0 0 0 1 0 12068 1275 44 2 2 PKHD1L1 8 109430038 Splice_Site SNP G C3L-00279_T 1440961 109430038 35708598 302 6080 PKHD1L1 0 . GRCh38 8 109464503 109464503 + Silent SNP G G C novel C3L-00279_T C3L-00279_N G G c.7671G>C p.= p.V2557V ENST00000378402 49/78 314 285 29 241 241 0 strelka-varscan-mutect PKHD1L1,synonymous_variant,p.=,ENST00000378402,NM_177531.4; C ENST00000378402 Transcript synonymous_variant 7775/13076 7671/12732 2557/4243 V gtG/gtC 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 49/78 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 14 109464503 109464503 G C 1 0 0 0 0 0 0 0 1 12068 1277 45 4 4 PKHD1L1 8 109464503 Silent SNP G C3L-00279_T 34465 109464503 35674133 303 6081 CSMD3 0 . GRCh38 8 112292652 112292652 + Missense_Mutation SNP G G T rs777412084 C3L-00279_T C3L-00279_N G G c.8673C>A p.Phe2891Leu p.F2891L ENST00000297405 55/71 469 415 54 300 300 0 strelka-varscan-mutect CSMD3,missense_variant,p.Phe2891Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Phe2851Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Phe2722Leu,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Phe2161Leu,ENST00000339701,; T ENST00000297405 Transcript missense_variant 8918/13212 8673/11124 2891/3707 F/L ttC/ttA rs777412084 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 55/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs777412084 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 112292652 112292652 G T 1 0 0 0 0 1 0 0 0 3747 1281 45 2 2 CSMD3 8 112292652 Missense_Mutation SNP G C3L-00279_T 2828149 112292652 32845984 304 6082 CSMD3 0 . GRCh38 8 112301943 112301943 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.8290A>T p.Thr2764Ser p.T2764S ENST00000297405 53/71 312 275 37 203 203 0 strelka-varscan-mutect CSMD3,missense_variant,p.Thr2764Ser,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Thr2724Ser,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Thr2595Ser,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Thr2034Ser,ENST00000339701,; A ENST00000297405 Transcript missense_variant 8535/13212 8290/11124 2764/3707 T/S Aca/Tca 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.57) 53/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 112301943 112301943 T A 1 0 0 0 0 1 0 0 0 3747 1638 57 4 4 CSMD3 8 112301943 Missense_Mutation SNP T C3L-00279_T 9291 112301943 32836693 305 6083 COL14A1 0 . GRCh38 8 120147846 120147846 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.4A>G p.Lys2Glu p.K2E ENST00000297848 2/48 226 188 38 136 136 0 strelka-varscan-mutect COL14A1,missense_variant,p.Lys2Glu,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Lys2Glu,ENST00000309791,;COL14A1,missense_variant,p.Lys2Glu,ENST00000537875,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,;COL14A1,missense_variant,p.Lys2Glu,ENST00000498051,; G ENST00000297848 Transcript missense_variant 274/6466 4/5391 2/1796 K/E Aag/Gag 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 tolerated_low_confidence(0.06) 2/48 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 120147846 120147846 A G 1 0 0 0 0 1 0 0 0 3459 247 9 5 5 COL14A1 8 120147846 Missense_Mutation SNP A C3L-00279_T 7845903 120147846 24990790 306 6084 FER1L6 0 . GRCh38 8 124049720 124049720 + Silent SNP T T C novel C3L-00279_T C3L-00279_N T T c.2838T>C p.= p.S946S ENST00000522917 22/41 286 258 28 238 238 0 strelka-varscan-mutect FER1L6,synonymous_variant,p.=,ENST00000522917,NM_001039112.2;FER1L6-AS2,intron_variant,,ENST00000520031,; C ENST00000522917 Transcript synonymous_variant 3044/6051 2838/5574 946/1857 S tcT/tcC 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 22/41 hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 14 124049720 124049720 T C 1 0 0 0 0 0 0 0 1 5678 1567 55 5 5 FER1L6 8 124049720 Silent SNP T C3L-00279_T 3901874 124049720 21088916 307 6085 LRRC6 0 . GRCh38 8 132625294 132625294 + Silent SNP G G T rs780609401 C3L-00279_T C3L-00279_N G G c.814C>A p.= p.R272R ENST00000620350 6/12 98 84 14 28 28 0 strelka-varscan-mutect LRRC6,synonymous_variant,p.=,ENST00000620350,NM_012472.4;LRRC6,synonymous_variant,p.=,ENST00000618342,;LRRC6,synonymous_variant,p.=,ENST00000519595,;LRRC6,synonymous_variant,p.=,ENST00000518642,;LRRC6,synonymous_variant,p.=,ENST00000250173,;LRRC6,synonymous_variant,p.=,ENST00000522789,;LRRC6,upstream_gene_variant,,ENST00000519085,;LRRC6,non_coding_transcript_exon_variant,,ENST00000520446,;LRRC6,downstream_gene_variant,,ENST00000523503,;LRRC6,upstream_gene_variant,,ENST00000522597,; T ENST00000620350 Transcript synonymous_variant 938/1878 814/1401 272/466 R Cgg/Agg rs780609401 1 -1 LRRC6 HGNC HGNC:16725 protein_coding YES CCDS6365.1 ENSP00000484634 Q86X45 UPI000000DBC5 NM_012472.4 6/12 hmmpanther:PTHR24365,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs780609401 . 0 200 9 0 0 0 0 0 -20 0.9999927 1 1 1 0 T 2 4 14 132625294 132625294 G T 1 0 0 0 0 0 0 0 1 8911 1144 40 1 1 LRRC6 8 132625294 Silent SNP G C3L-00279_T 8575574 132625294 12513342 308 6086 TG 0 . GRCh38 8 133096242 133096242 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.7441C>A p.Pro2481Thr p.P2481T ENST00000220616 43/48 280 248 32 247 247 0 strelka-varscan-mutect TG,missense_variant,p.Pro2481Thr,ENST00000220616,NM_003235.4;TG,missense_variant,p.Pro937Thr,ENST00000519178,;TG,missense_variant,p.Pro614Thr,ENST00000519543,;SLA,intron_variant,,ENST00000338087,NM_001045556.2;SLA,intron_variant,,ENST00000395352,NM_001045557.2;SLA,intron_variant,,ENST00000524345,NM_001282965.1;SLA,intron_variant,,ENST00000517648,NM_001282964.1;SLA,intron_variant,,ENST00000519341,;SLA,intron_variant,,ENST00000522119,;SLA,intron_variant,,ENST00000521302,;SLA,intron_variant,,ENST00000523610,;SLA,intron_variant,,ENST00000519558,;SLA,intron_variant,,ENST00000519747,;SLA,intron_variant,,ENST00000518565,;SLA,intron_variant,,ENST00000521823,;SLA,intron_variant,,ENST00000517932,;SLA,intron_variant,,ENST00000522946,;TG,3_prime_UTR_variant,,ENST00000523756,;TG,non_coding_transcript_exon_variant,,ENST00000522996,;TG,non_coding_transcript_exon_variant,,ENST00000522809,; A ENST00000220616 Transcript missense_variant 7481/8450 7441/8307 2481/2768 P/T Cct/Act 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 deleterious(0) 43/48 Gene3D:3.40.50.1820,Pfam_domain:PF00135,PIRSF_domain:PIRSF001831,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 133096242 133096242 C A 1 0 0 0 0 1 0 0 0 16246 855 30 2 2 TG 8 133096242 Missense_Mutation SNP C C3L-00279_T 470948 133096242 12042394 309 6087 MAFA 0 . GRCh38 8 143429414 143429414 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.993C>A p.Phe331Leu p.F331L ENST00000333480 1/1 176 152 24 176 176 0 strelka-varscan-mutect MAFA,missense_variant,p.Phe331Leu,ENST00000333480,NM_201589.3;MAFA,intron_variant,,ENST00000528185,; T ENST00000333480 Transcript missense_variant 993/2347 993/1062 331/353 F/L ttC/ttA 1 -1 MAFA HGNC HGNC:23145 protein_coding YES CCDS34955.1 ENSP00000328364 Q8NHW3 UPI00001B0366 NM_201589.3 tolerated(0.65) 1/1 hmmpanther:PTHR10129:SF30,hmmpanther:PTHR10129 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 143429414 143429414 G T 1 0 0 0 0 1 0 0 0 9073 1165 41 2 2 MAFA 8 143429414 Missense_Mutation SNP G C3L-00279_T 10333172 143429414 1709222 310 6088 EPPK1 0 . GRCh38 8 143867533 143867533 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.5721C>T p.= p.T1907T ENST00000615648 2/2 200 157 43 207 206 1 strelka-varscan-mutect EPPK1,synonymous_variant,p.=,ENST00000615648,NM_031308.3;EPPK1,synonymous_variant,p.=,ENST00000568225,; A ENST00000615648 Transcript synonymous_variant 5793/16002 5721/15267 1907/5088 T acC/acT 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 2/2 Gene3D:3.90.1290.10,Pfam_domain:PF00681,SMART_domains:SM00250,Superfamily_domains:SSF75399 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 143867533 143867533 G A 1 0 0 0 0 0 0 0 1 5038 1335 47 3 3 EPPK1 8 143867533 Silent SNP G C3L-00279_T 438119 143867533 1271103 311 6089 KIFC2 0 . GRCh38 8 144468551 144468551 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.904G>T p.Val302Leu p.V302L ENST00000301332 9/17 137 114 23 85 84 1 strelka-varscan-mutect KIFC2,missense_variant,p.Val302Leu,ENST00000301332,NM_145754.3;FOXH1,downstream_gene_variant,,ENST00000377317,NM_003923.2;CYHR1,upstream_gene_variant,,ENST00000438911,NM_138496.1;CYHR1,upstream_gene_variant,,ENST00000403000,NM_032687.3;CYHR1,upstream_gene_variant,,ENST00000306145,;CYHR1,upstream_gene_variant,,ENST00000424149,NM_001129888.1;CYHR1,upstream_gene_variant,,ENST00000526887,;CYHR1,upstream_gene_variant,,ENST00000533764,;CYHR1,upstream_gene_variant,,ENST00000530637,;CTD-2517M22.16,downstream_gene_variant,,ENST00000525461,;KIFC2,upstream_gene_variant,,ENST00000531423,;KIFC2,upstream_gene_variant,,ENST00000531425,;KIFC2,downstream_gene_variant,,ENST00000533114,;KIFC2,downstream_gene_variant,,ENST00000529644,;CYHR1,upstream_gene_variant,,ENST00000524623,;KIFC2,upstream_gene_variant,,ENST00000529864,; T ENST00000301332 Transcript missense_variant 1281/3646 904/2517 302/838 V/L Gtg/Ttg 1 1 KIFC2 HGNC HGNC:29530 protein_coding YES CCDS6427.1 ENSP00000301332 Q96AC6 UPI000006D3B2 NM_145754.3 tolerated(0.45) 9/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 144468551 144468551 G T 1 0 0 0 0 1 0 0 0 8178 1261 44 2 2 KIFC2 8 144468551 Missense_Mutation SNP G C3L-00279_T 601018 144468551 670085 312 6090 RFX3 0 . GRCh38 9 3257101 3257101 + Missense_Mutation SNP C C A rs780925118 C3L-00279_T C3L-00279_N C C c.1704G>T p.Gln568His p.Q568H ENST00000382004 15/18 500 443 57 453 453 0 strelka-varscan-mutect RFX3,missense_variant,p.Gln568His,ENST00000382004,NM_134428.2;RFX3,missense_variant,p.Gln568His,ENST00000617270,NM_001282116.1;RFX3,missense_variant,p.Gln568His,ENST00000358730,NM_002919.3;RFX3,missense_variant,p.Gln141His,ENST00000458034,;RFX3,missense_variant,p.Gln33His,ENST00000449234,; A ENST00000382004 Transcript missense_variant 2016/9307 1704/2250 568/749 Q/H caG/caT rs780925118 1 -1 RFX3 HGNC HGNC:9984 protein_coding YES CCDS6449.1 ENSP00000371434 P48380 UPI0000070BFB NM_134428.2 deleterious(0) 15/18 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF20 MODERATE 1 SNV 1 1 PASS rs780925118 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 3257101 3257101 C A 1 0 0 0 0 1 0 0 0 13438 564 20 2 2 RFX3 9 3257101 Missense_Mutation SNP C C3L-00279_T 3257101 135137616 313 6091 SPATA31A1 0 . GRCh38 9 39361655 39361655 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.3932A>G p.Asn1311Ser p.N1311S ENST00000377647 4/4 606 569 37 614 614 0 varscan-mutect SPATA31A1,missense_variant,p.Asn1311Ser,ENST00000377647,NM_001085452.2;RP11-347J14.4,intron_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; G ENST00000377647 Transcript missense_variant 3952/4256 3932/4086 1311/1361 N/S aAc/aGc 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 tolerated(0.25) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 39361655 39361655 A G 1 0 0 0 0 1 0 0 0 15343 43 2 5 5 SPATA31A1 9 39361655 Missense_Mutation SNP A C3L-00279_T 36104554 39361655 99033062 314 6092 TRPM3 0 . GRCh38 9 70625299 70625299 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.1665G>T p.= p.L555L ENST00000377110 13/25 272 246 26 244 244 0 strelka-varscan-mutect TRPM3,synonymous_variant,p.=,ENST00000377110,NM_001007471.2;TRPM3,synonymous_variant,p.=,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,synonymous_variant,p.=,ENST00000377105,NM_024971.5;TRPM3,synonymous_variant,p.=,ENST00000357533,;TRPM3,synonymous_variant,p.=,ENST00000396292,NM_206946.3;TRPM3,synonymous_variant,p.=,ENST00000358082,;TRPM3,synonymous_variant,p.=,ENST00000396285,NM_020952.4;TRPM3,synonymous_variant,p.=,ENST00000408909,;TRPM3,synonymous_variant,p.=,ENST00000396280,NM_206945.3;TRPM3,synonymous_variant,p.=,ENST00000377111,; A ENST00000377110 Transcript synonymous_variant 1909/12258 1665/5124 555/1707 L ctG/ctT 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 13/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 70625299 70625299 C A 1 0 0 0 0 0 0 0 1 17093 813 29 2 2 TRPM3 9 70625299 Silent SNP C C3L-00279_T 31263644 70625299 67769418 315 6093 TMEM2 0 . GRCh38 9 71729914 71729914 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1980G>T p.Met660Ile p.M660I ENST00000377044 10/24 189 173 16 85 85 0 strelka-varscan-mutect TMEM2,missense_variant,p.Met660Ile,ENST00000377044,NM_013390.2;TMEM2,missense_variant,p.Met597Ile,ENST00000377066,NM_001135820.1;TMEM2,splice_region_variant,,ENST00000542935,;TMEM2,downstream_gene_variant,,ENST00000546219,; A ENST00000377044 Transcript missense_variant,splice_region_variant 2520/6523 1980/4152 660/1383 M/I atG/atT 1 -1 TMEM2 HGNC HGNC:11869 protein_coding YES CCDS6638.1 ENSP00000366243 Q9UHN6 A0A024R229 UPI0000071E8D NM_013390.2 tolerated(0.42) 10/24 hmmpanther:PTHR15535,hmmpanther:PTHR15535:SF17 MODERATE 1 SNV 1 1 PASS rs1385395303 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 71729914 71729914 C A 1 0 0 0 0 1 0 0 0 16561 637 22 2 2 TMEM2 9 71729914 Missense_Mutation SNP C C3L-00279_T 1104615 71729914 66664803 316 6094 PCSK5 0 . GRCh38 9 76023877 76023877 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.551A>T p.Asn184Ile p.N184I ENST00000545128 4/37 88 77 11 78 78 0 strelka-varscan-mutect PCSK5,missense_variant,p.Asn184Ile,ENST00000545128,NM_001190482.1;PCSK5,missense_variant,p.Asn184Ile,ENST00000376752,NM_006200.5;PCSK5,missense_variant,p.Asn184Ile,ENST00000376767,; T ENST00000545128 Transcript missense_variant 1089/9538 551/5583 184/1860 N/I aAc/aTc 1 1 PCSK5 HGNC HGNC:8747 protein_coding YES CCDS55320.1 ENSP00000446280 Q92824 UPI0001DAD817 NM_001190482.1 deleterious(0) 4/37 hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF378,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -19.99977 1 1 1 1 0 T 3 4 14 76023877 76023877 A T 1 0 0 0 0 1 0 0 0 11691 57 2 4 4 PCSK5 9 76023877 Missense_Mutation SNP A C3L-00279_T 4293963 76023877 62370840 317 6095 SPATA31D1 0 . GRCh38 9 81993697 81993697 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.3227C>A p.Thr1076Lys p.T1076K ENST00000344803 4/4 227 215 12 193 193 0 strelka-varscan-mutect SPATA31D1,missense_variant,p.Thr1076Lys,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; A ENST00000344803 Transcript missense_variant 3274/4833 3227/4731 1076/1576 T/K aCa/aAa COSM4164055,COSM4164056 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.81) 4/4 hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 81993697 81993697 C A 1 0 0 0 0 1 0 0 0 15347 478 17 2 2 SPATA31D1 9 81993697 Missense_Mutation SNP C C3L-00279_T 5969820 81993697 56401020 318 6096 AUH 0 . GRCh38 9 91325334 91325334 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.489A>T p.= p.A163A ENST00000375731 4/10 339 311 28 124 124 0 strelka-varscan-mutect AUH,synonymous_variant,p.=,ENST00000375731,NM_001698.2;AUH,intron_variant,,ENST00000303617,NM_001306190.1;AUH,non_coding_transcript_exon_variant,,ENST00000478465,; A ENST00000375731 Transcript synonymous_variant 513/1577 489/1020 163/339 A gcA/gcT 1 -1 AUH HGNC HGNC:890 protein_coding YES CCDS6689.1 ENSP00000364883 Q13825 UPI0000072F64 NM_001698.2 4/10 hmmpanther:PTHR11941:SF12,hmmpanther:PTHR11941,Pfam_domain:PF00378,Gene3D:3.90.226.10,Superfamily_domains:SSF52096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 91325334 91325334 T A 1 0 0 0 0 0 0 0 1 1374 1567 55 4 4 AUH 9 91325334 Silent SNP T C3L-00279_T 9331637 91325334 47069383 319 6097 PTPDC1 0 . GRCh38 9 94097985 94097985 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.1419G>C p.Leu473Phe p.L473F ENST00000620992 6/9 332 294 38 332 332 0 strelka-varscan-mutect PTPDC1,missense_variant,p.Leu419Phe,ENST00000375360,NM_177995.2,NM_001253830.1;PTPDC1,missense_variant,p.Leu473Phe,ENST00000620992,NM_001253829.1;PTPDC1,missense_variant,p.Leu471Phe,ENST00000288976,NM_152422.4;PTPDC1,upstream_gene_variant,,ENST00000467049,; C ENST00000620992 Transcript missense_variant 1521/4437 1419/2427 473/808 L/F ttG/ttC 1 1 PTPDC1 HGNC HGNC:30184 protein_coding YES CCDS75860.1 ENSP00000477817 A0A087WTF0 UPI0000E0BDFA NM_001253829.1 tolerated(0.17) 6/9 hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF72 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 94097985 94097985 G C 1 0 0 0 0 1 0 0 0 12930 1339 47 4 4 PTPDC1 9 94097985 Missense_Mutation SNP G C3L-00279_T 2772651 94097985 44296732 320 6098 TRIM14 0 . GRCh38 9 98094892 98094892 + Silent SNP C C G rs760786474 C3L-00279_T C3L-00279_N C C c.675G>C p.= p.T225T ENST00000341469 4/6 133 120 13 139 139 0 strelka-varscan-mutect TRIM14,synonymous_variant,p.=,ENST00000341469,NM_014788.3;TRIM14,synonymous_variant,p.=,ENST00000375098,;TRIM14,synonymous_variant,p.=,ENST00000342043,NM_033219.2;TRIM14,non_coding_transcript_exon_variant,,ENST00000478401,;TRIM14,3_prime_UTR_variant,,ENST00000475147,; G ENST00000341469 Transcript synonymous_variant 685/4454 675/1329 225/442 T acG/acC rs760786474 1 -1 TRIM14 HGNC HGNC:16283 protein_coding YES CCDS6734.1 ENSP00000344208 Q14142 A0A024R165 UPI0000137065 NM_014788.3 4/6 hmmpanther:PTHR24103:SF35,hmmpanther:PTHR24103 LOW 1 SNV 1 1 PASS rs760786474 . 0 207 0 2 0 0 0 0 -18.91643 0.9999998 1 1 1 0 G 2 3 14 98094892 98094892 C G 1 0 0 0 0 0 0 0 1 16978 755 27 4 4 TRIM14 9 98094892 Silent SNP C C3L-00279_T 3996907 98094892 40299825 321 6099 GABBR2 0 . GRCh38 9 98306339 98306339 + Missense_Mutation SNP C C G C3L-00279_T C3L-00279_N C C c.2011G>C p.Gly671Arg p.G671R ENST00000259455 15/19 238 222 16 260 260 0 strelka-varscan-mutect GABBR2,missense_variant,p.Gly671Arg,ENST00000259455,NM_005458.7;GABBR2,missense_variant,p.Gly80Arg,ENST00000634457,;GABBR2,non_coding_transcript_exon_variant,,ENST00000637410,;GABBR2,non_coding_transcript_exon_variant,,ENST00000635462,;GABBR2,upstream_gene_variant,,ENST00000636575,;GABBR2,non_coding_transcript_exon_variant,,ENST00000634354,; G ENST00000259455 Transcript missense_variant 2471/5788 2011/2826 671/941 G/R Ggt/Cgt COSM3652218 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 deleterious(0) 15/19 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF40,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS rs1388019965 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 98306339 98306339 C G 1 0 0 0 0 1 0 0 0 6027 652 23 4 4 GABBR2 9 98306339 Missense_Mutation SNP C C3L-00279_T 211447 98306339 40088378 322 6100 ANKS6 0 . GRCh38 9 98783954 98783954 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1111G>T p.Gly371Trp p.G371W ENST00000353234 4/15 67 61 6 54 54 0 strelka-varscan-mutect ANKS6,missense_variant,p.Gly371Trp,ENST00000353234,NM_173551.3;ANKS6,missense_variant,p.Gly70Trp,ENST00000375019,;ANKS6,splice_region_variant,,ENST00000634393,;ANKS6,non_coding_transcript_exon_variant,,ENST00000486778,;ANKS6,non_coding_transcript_exon_variant,,ENST00000466120,; A ENST00000353234 Transcript missense_variant,splice_region_variant 1159/7164 1111/2616 371/871 G/W Ggg/Tgg 1 -1 ANKS6 HGNC HGNC:26724 protein_coding YES CCDS43856.1 ENSP00000297837 Q68DC2 UPI0000530317 NM_173551.3 deleterious(0) 4/15 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR10627:SF39,hmmpanther:PTHR10627,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs898782506 . 0 206 4 0 0 0 0 0 -13.75682 1 1 1 1 0 A 3 1 14 98783954 98783954 C A 1 0 0 0 0 1 0 0 0 798 608 21 2 2 ANKS6 9 98783954 Missense_Mutation SNP C C3L-00279_T 477615 98783954 39610763 323 6101 OR13F1 0 . GRCh38 9 104504475 104504475 + Silent SNP C C A C3L-00279_T C3L-00279_N C C c.213C>A p.= p.I71I ENST00000334726 1/1 217 202 15 180 180 0 strelka-varscan-mutect OR13F1,synonymous_variant,p.=,ENST00000334726,NM_001004485.1; A ENST00000334726 Transcript synonymous_variant 213/960 213/960 71/319 I atC/atA COSM752210 1 1 OR13F1 HGNC HGNC:14723 protein_coding YES CCDS35087.1 ENSP00000334452 Q8NGS4 UPI0000041B47 NM_001004485.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF61,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 104504475 104504475 C A 1 0 0 0 0 0 0 0 1 11017 903 32 2 2 OR13F1 9 104504475 Silent SNP C C3L-00279_T 5720521 104504475 33890242 324 6102 OR13C5 0 . GRCh38 9 104598806 104598806 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.608C>A p.Thr203Lys p.T203K ENST00000374779 1/1 258 239 19 164 164 0 strelka-varscan-mutect OR13C5,missense_variant,p.Thr203Lys,ENST00000374779,NM_001004482.1; T ENST00000374779 Transcript missense_variant 608/957 608/957 203/318 T/K aCa/aAa 1 -1 OR13C5 HGNC HGNC:15100 protein_coding YES CCDS35091.1 ENSP00000363911 Q8NGS8 UPI0000041D12 NM_001004482.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF121,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 104598806 104598806 G T 1 0 0 0 0 1 0 0 0 11013 1377 48 2 2 OR13C5 9 104598806 Missense_Mutation SNP G C3L-00279_T 94331 104598806 33795911 325 6103 OR13C2 0 . GRCh38 9 104605158 104605158 + Missense_Mutation SNP G G T rs768722886 C3L-00279_T C3L-00279_N G G c.470C>A p.Ala157Glu p.A157E ENST00000542196 1/1 224 195 29 180 180 0 varscan-mutect OR13C2,missense_variant,p.Ala157Glu,ENST00000542196,NM_001004481.1; T ENST00000542196 Transcript missense_variant 470/957 470/957 157/318 A/E gCa/gAa rs768722886 1 -1 OR13C2 HGNC HGNC:14701 protein_coding YES CCDS35092.1 ENSP00000438815 Q8NGS9 A0A126GWR7 UPI0000041B29 NM_001004481.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF279,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs768722886 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 104605158 104605158 G T 1 0 0 0 0 1 0 0 0 11010 1319 46 2 2 OR13C2 9 104605158 Missense_Mutation SNP G C3L-00279_T 6352 104605158 33789559 326 6104 HDHD3 0 . GRCh38 9 113373937 113373937 + Missense_Mutation SNP G G A rs76975306 C3L-00279_T C3L-00279_N G G c.418C>T p.Arg140Trp p.R140W ENST00000238379 2/2 243 227 16 196 196 0 strelka-varscan-mutect HDHD3,missense_variant,p.Arg140Trp,ENST00000238379,NM_031219.3;HDHD3,missense_variant,p.Arg140Trp,ENST00000374180,NM_001304509.1,NM_001304510.1,NM_001304511.1;BSPRY,downstream_gene_variant,,ENST00000374183,NM_001317943.1,NM_017688.2;HDHD3,non_coding_transcript_exon_variant,,ENST00000485934,;BSPRY,downstream_gene_variant,,ENST00000462085,; A ENST00000238379 Transcript missense_variant 1316/1834 418/756 140/251 R/W Cgg/Tgg rs76975306 1 -1 HDHD3 HGNC HGNC:28171 protein_coding YES CCDS6793.1 ENSP00000238379 Q9BSH5 UPI0000073CC1 NM_031219.3 deleterious(0) 2/2 Gene3D:3.40.50.1000,Pfam_domain:PF13419,hmmpanther:PTHR12725,hmmpanther:PTHR12725:SF74,Low_complexity_(Seg):seg,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01549,TIGRFAM_domain:TIGR02252 MODERATE 1 SNV 1 1 PASS rs76975306 . 0 208 0 2 0 0 0 0 -19.30485 0.9999996 1 1 1 0 A 3 1 14 113373937 113373937 G A 1 0 0 0 0 1 0 0 0 6907 1144 40 1 1 HDHD3 9 113373937 Missense_Mutation SNP G C3L-00279_T 8768779 113373937 25020780 327 6105 ASTN2 0 . GRCh38 9 116620328 116620328 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3035G>T p.Ser1012Ile p.S1012I ENST00000361209 17/22 287 262 25 243 242 1 strelka-varscan-mutect ASTN2,missense_variant,p.Ser1063Ile,ENST00000313400,;ASTN2,missense_variant,p.Ser1012Ile,ENST00000361209,NM_014010.4;ASTN2,missense_variant,p.Ser115Ile,ENST00000361477,NM_198187.3;ASTN2,missense_variant,p.Ser786Ile,ENST00000373986,;ASTN2,missense_variant,p.Ser115Ile,ENST00000358637,NM_001184735.1;ASTN2,missense_variant,p.Ser164Ile,ENST00000288520,NM_198186.3;ASTN2,missense_variant,p.Ser115Ile,ENST00000341734,NM_001184734.1,NM_198188.2; A ENST00000361209 Transcript missense_variant 3167/4622 3035/3867 1012/1288 S/I aGc/aTc 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 deleterious(0) 17/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 116620328 116620328 C A 1 0 0 0 0 1 0 0 0 1212 797 28 2 2 ASTN2 9 116620328 Missense_Mutation SNP C C3L-00279_T 3246391 116620328 21774389 328 6106 TLR4 0 . GRCh38 9 117713628 117713628 + Missense_Mutation SNP C C A rs556171096 C3L-00279_T C3L-00279_N C C c.1500C>A p.Phe500Leu p.F500L ENST00000355622 3/3 285 262 23 166 166 0 strelka-varscan-mutect TLR4,missense_variant,p.Phe500Leu,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Phe460Leu,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; A ENST00000355622 Transcript missense_variant 1601/4844 1500/2520 500/839 F/L ttC/ttA rs556171096 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 tolerated(0.45) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs556171096 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 117713628 117713628 C A 1 0 0 0 0 1 0 0 0 16399 854 30 2 2 TLR4 9 117713628 Missense_Mutation SNP C C3L-00279_T 1093300 117713628 20681089 329 6107 CDK5RAP2 0 . GRCh38 9 120439585 120439585 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.3536A>T p.Tyr1179Phe p.Y1179F ENST00000349780 24/38 318 286 32 295 295 0 strelka-varscan-mutect CDK5RAP2,missense_variant,p.Tyr1179Phe,ENST00000349780,NM_018249.5;CDK5RAP2,missense_variant,p.Tyr1179Phe,ENST00000360190,NM_001011649.2;CDK5RAP2,missense_variant,p.Tyr949Phe,ENST00000360822,NM_001272039.1;CDK5RAP2,missense_variant,p.Tyr573Phe,ENST00000416449,;CDK5RAP2,missense_variant,p.Tyr189Phe,ENST00000425647,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000468989,;CDK5RAP2,downstream_gene_variant,,ENST00000479584,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,; A ENST00000349780 Transcript missense_variant 3716/6228 3536/5682 1179/1893 Y/F tAc/tTc 1 -1 CDK5RAP2 HGNC HGNC:18672 protein_coding YES CCDS6823.1 ENSP00000343818 Q96SN8 UPI0000367673 NM_018249.5 deleterious(0.04) 24/38 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 120439585 120439585 T A 1 0 0 0 0 1 0 0 0 2850 1638 57 4 4 CDK5RAP2 9 120439585 Missense_Mutation SNP T C3L-00279_T 2725957 120439585 17955132 330 6108 AL513122.1 0 . GRCh38 9 121329282 121329282 + Silent SNP G G T rs759980004 C3L-00279_T C3L-00279_N G G c.2085G>T p.= p.T695T ENST00000373818 15/17 673 615 58 612 611 1 strelka-varscan-mutect GSN,synonymous_variant,p.=,ENST00000373823,NM_001127664.1,NM_198252.2,NM_001127662.1,NM_001127665.1;GSN,synonymous_variant,p.=,ENST00000373818,NM_000177.4;GSN,synonymous_variant,p.=,ENST00000545652,NM_001258030.1;GSN,synonymous_variant,p.=,ENST00000394353,NM_001258029.1;AL513122.1,synonymous_variant,p.=,ENST00000449733,NM_001127663.1;AL513122.2,synonymous_variant,p.=,ENST00000373808,NM_001127667.1,NM_001127666.1;GSN,3_prime_UTR_variant,,ENST00000373806,;GSN,non_coding_transcript_exon_variant,,ENST00000373807,;GSN,non_coding_transcript_exon_variant,,ENST00000477553,; T ENST00000373818 Transcript synonymous_variant 2154/2657 2085/2349 695/782 T acG/acT rs759980004,COSM4643299,COSM4643300,COSM4643301 1 1 GSN HGNC HGNC:4620 protein_coding YES CCDS6828.1 ENSP00000362924 P06396 UPI000012B3B4 NM_000177.4 15/17 hmmpanther:PTHR11977:SF29,hmmpanther:PTHR11977,Gene3D:3.40.20.10,Pfam_domain:PF00626,SMART_domains:SM00262,Superfamily_domains:SSF55753,Prints_domain:PR00597 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs759980004 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 121329282 121329282 G T 1 0 0 0 0 0 0 0 1 579 1103 39 1 1 AL513122.1 9 121329282 Silent SNP G C3L-00279_T 889697 121329282 17065435 331 6109 OR1K1 0 . GRCh38 9 122800476 122800476 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.354C>A p.= p.A118A ENST00000277309 1/1 253 224 29 222 222 0 strelka-varscan-mutect OR1K1,synonymous_variant,p.=,ENST00000277309,NM_080859.1;PDCL,intron_variant,,ENST00000436632,; A ENST00000277309 Transcript synonymous_variant 354/951 354/951 118/316 A gcC/gcA 1 1 OR1K1 HGNC HGNC:8212 protein_coding YES CCDS35132.1 ENSP00000277309 Q8NGR3 A0A126GVB9 UPI000004B1FE NM_080859.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF331,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs1455504694 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 122800476 122800476 C A 1 0 0 0 0 0 0 0 1 11040 581 21 2 2 OR1K1 9 122800476 Silent SNP C C3L-00279_T 1471194 122800476 15594241 332 6110 LHX2 0 . GRCh38 9 124015356 124015356 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.558G>T p.= p.V186V ENST00000373615 3/5 210 191 19 203 202 1 strelka-varscan-mutect LHX2,synonymous_variant,p.=,ENST00000373615,NM_004789.3;LHX2,synonymous_variant,p.=,ENST00000446480,;LHX2,synonymous_variant,p.=,ENST00000560961,;LHX2,upstream_gene_variant,,ENST00000488674,;RP11-85O21.4,downstream_gene_variant,,ENST00000421041,; T ENST00000373615 Transcript synonymous_variant 1297/2554 558/1221 186/406 V gtG/gtT 1 1 LHX2 HGNC HGNC:6594 protein_coding YES CCDS6853.1 ENSP00000362717 P50458 UPI000012E659 NM_004789.3 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF90 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 124015356 124015356 G T 1 0 0 0 0 0 0 0 1 8680 1335 47 2 2 LHX2 9 124015356 Silent SNP G C3L-00279_T 1214880 124015356 14379361 333 6111 LMX1B 0 . GRCh38 9 126693244 126693244 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.662G>T p.Arg221Leu p.R221L ENST00000355497 4/8 461 427 34 485 483 2 strelka-varscan-mutect LMX1B,missense_variant,p.Arg221Leu,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Arg221Leu,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Arg198Leu,ENST00000561065,;LMX1B,missense_variant,p.Arg221Leu,ENST00000526117,NM_002316.3; T ENST00000355497 Transcript missense_variant 669/5809 662/1221 221/406 R/L cGa/cTa 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 deleterious(0) 4/8 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96,Low_complexity_(Seg):seg,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1329660584 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 126693244 126693244 G T 1 0 0 0 0 1 0 0 0 8789 1058 37 1 1 LMX1B 9 126693244 Missense_Mutation SNP G C3L-00279_T 2677888 126693244 11701473 334 6112 LMX1B 0 . GRCh38 9 126695896 126695896 + Missense_Mutation SNP C C A rs756003941 C3L-00279_T C3L-00279_N C C c.977C>A p.Pro326Gln p.P326Q ENST00000355497 7/8 227 206 21 184 184 0 strelka-varscan-mutect LMX1B,missense_variant,p.Pro326Gln,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Pro315Gln,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Pro303Gln,ENST00000561065,;LMX1B,missense_variant,p.Pro315Gln,ENST00000526117,NM_002316.3; A ENST00000355497 Transcript missense_variant 984/5809 977/1221 326/406 P/Q cCa/cAa rs756003941,COSM390693 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 tolerated(0.09) 7/8 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs756003941 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 126695896 126695896 C A 1 0 0 0 0 1 0 0 0 8789 594 21 2 2 LMX1B 9 126695896 Missense_Mutation SNP C C3L-00279_T 2652 126695896 11698821 335 6113 RALGPS1 0 . GRCh38 9 126962305 126962305 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.16G>C p.Gly6Arg p.G6R ENST00000259351 2/19 275 252 23 318 318 0 strelka-varscan-mutect RALGPS1,missense_variant,p.Gly6Arg,ENST00000259351,NM_014636.2;RALGPS1,missense_variant,p.Gly6Arg,ENST00000373434,NM_001190728.1;RALGPS1,missense_variant,p.Gly6Arg,ENST00000424082,NM_001322320.1,NM_001190729.1;RALGPS1,missense_variant,p.Gly6Arg,ENST00000394022,;RALGPS1,missense_variant,p.Gly6Arg,ENST00000373436,NM_001190730.1;RALGPS1,missense_variant,p.Gly6Arg,ENST00000394011,;RALGPS1,missense_variant,p.Gly6Arg,ENST00000319107,;RALGPS1,non_coding_transcript_exon_variant,,ENST00000480993,;RALGPS1,non_coding_transcript_exon_variant,,ENST00000472427,;RALGPS1,non_coding_transcript_exon_variant,,ENST00000373439,; C ENST00000259351 Transcript missense_variant 283/6336 16/1674 6/557 G/R Ggt/Cgt 1 1 RALGPS1 HGNC HGNC:16851 protein_coding YES CCDS35143.1 ENSP00000259351 Q5JS13 UPI000006D3AF NM_014636.2 deleterious_low_confidence(0) 2/19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 126962305 126962305 G C 1 0 0 0 0 1 0 0 0 13176 1348 47 4 4 RALGPS1 9 126962305 Missense_Mutation SNP G C3L-00279_T 266409 126962305 11432412 336 6114 ANGPTL2 0 . GRCh38 9 127108141 127108141 + Silent SNP G G T rs777044764 C3L-00279_T C3L-00279_N G G c.591C>A p.= p.I197I ENST00000373425 2/5 163 138 25 156 155 1 strelka-varscan-mutect ANGPTL2,synonymous_variant,p.=,ENST00000373425,NM_012098.2;RALGPS1,intron_variant,,ENST00000259351,NM_014636.2;ANGPTL2,intron_variant,,ENST00000373417,;RALGPS1,intron_variant,,ENST00000373434,NM_001190728.1;RALGPS1,intron_variant,,ENST00000424082,NM_001322320.1,NM_001190729.1;RALGPS1,intron_variant,,ENST00000394022,;RALGPS1,intron_variant,,ENST00000373436,NM_001190730.1;ANGPTL2,upstream_gene_variant,,ENST00000491991,;ANGPTL2,upstream_gene_variant,,ENST00000470194,; T ENST00000373425 Transcript synonymous_variant 1209/3707 591/1482 197/493 I atC/atA rs777044764 1 -1 ANGPTL2 HGNC HGNC:490 protein_coding YES CCDS6868.1 ENSP00000362524 Q9UKU9 A0A024R868 UPI0000049E07 NM_012098.2 2/5 hmmpanther:PTHR19143:SF24,hmmpanther:PTHR19143 LOW 1 SNV 1 1 PASS rs777044764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 127108141 127108141 G T 1 0 0 0 0 0 0 0 1 712 1048 37 1 1 ANGPTL2 9 127108141 Silent SNP G C3L-00279_T 145836 127108141 11286576 337 6115 RALGDS 0 . GRCh38 9 133108264 133108264 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.921A>T p.= p.V307V ENST00000372050 6/18 156 140 16 104 104 0 strelka-varscan-mutect RALGDS,synonymous_variant,p.=,ENST00000393160,NM_001042368.2;RALGDS,synonymous_variant,p.=,ENST00000393157,NM_001271775.1;RALGDS,synonymous_variant,p.=,ENST00000372050,NM_006266.3;RALGDS,synonymous_variant,p.=,ENST00000372047,NM_001271776.1;RALGDS,synonymous_variant,p.=,ENST00000372062,NM_001271774.1;RALGDS,upstream_gene_variant,,ENST00000424572,;RALGDS,upstream_gene_variant,,ENST00000460587,;RALGDS,synonymous_variant,p.=,ENST00000493438,;RALGDS,non_coding_transcript_exon_variant,,ENST00000469972,;RALGDS,non_coding_transcript_exon_variant,,ENST00000482648,;RALGDS,upstream_gene_variant,,ENST00000471109,;RALGDS,upstream_gene_variant,,ENST00000493067,; A ENST00000372050 Transcript synonymous_variant 943/3634 921/2745 307/914 V gtA/gtT 1 -1 RALGDS HGNC HGNC:9842 protein_coding YES CCDS6959.1 ENSP00000361120 Q12967 UPI000012B8BC NM_006266.3 6/18 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF35,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 133108264 133108264 T A 1 0 0 0 0 0 0 0 1 13175 1509 53 4 4 RALGDS 9 133108264 Silent SNP T C3L-00279_T 6000123 133108264 5286453 338 6116 PMPCA 0 . GRCh38 9 136418576 136418576 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1012G>T p.Ala338Ser p.A338S ENST00000371717 9/13 133 117 16 124 124 0 strelka-mutect PMPCA,missense_variant,p.Ala46Ser,ENST00000444897,;PMPCA,missense_variant,p.Ala338Ser,ENST00000371717,NM_015160.2;PMPCA,missense_variant,p.Ala207Ser,ENST00000399219,NM_001282946.1,NM_001282944.1;PMPCA,downstream_gene_variant,,ENST00000610649,;PMPCA,non_coding_transcript_exon_variant,,ENST00000462616,;PMPCA,downstream_gene_variant,,ENST00000612553,;PMPCA,downstream_gene_variant,,ENST00000622209,;PMPCA,downstream_gene_variant,,ENST00000371720,;PMPCA,downstream_gene_variant,,ENST00000620895,; T ENST00000371717 Transcript missense_variant 1111/2174 1012/1578 338/525 A/S Gca/Tca 1 1 PMPCA HGNC HGNC:18667 protein_coding YES CCDS35180.1 ENSP00000360782 Q10713 UPI00000703D3 NM_015160.2 deleterious(0) 9/13 Gene3D:3.30.830.10,Pfam_domain:PF05193,hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF49,Superfamily_domains:SSF63411 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99995 0.9999999 1 1 1 0 T 3 4 14 136418576 136418576 G T 1 0 0 0 0 1 0 0 0 12247 1319 46 2 2 PMPCA 9 136418576 Missense_Mutation SNP G C3L-00279_T 3310312 136418576 1976141 339 6117 IL2RA 0 . GRCh38 10 6025958 6025958 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.132A>T p.= p.G44G ENST00000379959 2/8 383 359 24 328 328 0 strelka-varscan-mutect IL2RA,synonymous_variant,p.=,ENST00000379959,NM_000417.2;IL2RA,synonymous_variant,p.=,ENST00000379954,NM_001308242.1;IL2RA,synonymous_variant,p.=,ENST00000256876,;IL2RA,synonymous_variant,p.=,ENST00000447847,;RP11-536K7.5,upstream_gene_variant,,ENST00000440436,; A ENST00000379959 Transcript synonymous_variant 306/3176 132/819 44/272 G ggA/ggT 1 -1 IL2RA HGNC HGNC:6008 protein_coding YES CCDS7076.1 ENSP00000369293 P01589 UPI000012D4A3 NM_000417.2 2/8 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR10573,hmmpanther:PTHR10573:SF0,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 6025958 6025958 T A 1 0 0 0 0 0 0 0 1 7585 1770 62 4 4 IL2RA 10 6025958 Silent SNP T C3L-00279_T 6025958 127771464 340 6118 SFMBT2 0 . GRCh38 10 7243615 7243615 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000397167 9/21 231 216 15 137 136 1 strelka-varscan-mutect SFMBT2,missense_variant,p.Gly355Trp,ENST00000397167,NM_001029880.2;SFMBT2,missense_variant,p.Gly355Trp,ENST00000361972,NM_001018039.1; A ENST00000397167 Transcript missense_variant 1256/8024 1063/2685 355/894 G/W Ggg/Tgg 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 deleterious(0) 9/21 PROSITE_profiles:PS51079,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF02820,Gene3D:2.30.30.160,SMART_domains:SM00561,Superfamily_domains:SSF63748 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 7243615 7243615 C A 1 0 0 0 0 1 0 0 0 14436 623 22 2 2 SFMBT2 10 7243615 Missense_Mutation SNP C C3L-00279_T 1217657 7243615 126553807 341 6119 DHTKD1 0 . GRCh38 10 12084589 12084589 + Silent SNP C C G novel C3L-00279_T C3L-00279_N C C c.360C>G p.= p.V120V ENST00000263035 3/17 370 342 28 271 271 0 strelka-varscan-mutect DHTKD1,synonymous_variant,p.=,ENST00000263035,NM_018706.6;DHTKD1,synonymous_variant,p.=,ENST00000437298,;DHTKD1,upstream_gene_variant,,ENST00000415935,;DHTKD1,intron_variant,,ENST00000465617,; G ENST00000263035 Transcript synonymous_variant 422/5159 360/2760 120/919 V gtC/gtG 1 1 DHTKD1 HGNC HGNC:23537 protein_coding YES CCDS7087.1 ENSP00000263035 Q96HY7 UPI000013D38C NM_018706.6 3/17 hmmpanther:PTHR23152:SF11,hmmpanther:PTHR23152,PIRSF_domain:PIRSF000157,TIGRFAM_domain:TIGR00239,Superfamily_domains:SSF52518 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 12084589 12084589 C G 1 0 0 0 0 0 0 0 1 4304 900 32 4 4 DHTKD1 10 12084589 Silent SNP C C3L-00279_T 4840974 12084589 121712833 342 6120 SEPHS1 0 . GRCh38 10 13344859 13344859 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.92G>T p.Cys31Phe p.C31F ENST00000327347 2/9 132 125 7 126 126 0 varscan-mutect SEPHS1,missense_variant,p.Cys31Phe,ENST00000327347,NM_012247.4;SEPHS1,missense_variant,p.Cys31Phe,ENST00000378614,NM_001195604.1;SEPHS1,missense_variant,p.Cys31Phe,ENST00000413411,;SEPHS1,intron_variant,,ENST00000545675,NM_001195602.1;SEPHS1,upstream_gene_variant,,ENST00000425947,;SEPHS1,non_coding_transcript_exon_variant,,ENST00000494329,; A ENST00000327347 Transcript missense_variant 468/3273 92/1179 31/392 C/F tGc/tTc 1 -1 SEPHS1 HGNC HGNC:19685 protein_coding YES CCDS7098.1 ENSP00000367893 P49903 UPI0000135E82 NM_012247.4 deleterious(0) 2/9 PIRSF_domain:PIRSF036407,hmmpanther:PTHR10256,hmmpanther:PTHR10256:SF2,Superfamily_domains:SSF55326,TIGRFAM_domain:TIGR00476 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -10.05686 0.9999993 1 1 1 0 A 3 1 14 13344859 13344859 C A 1 0 0 0 0 1 0 0 0 14330 710 25 2 2 SEPHS1 10 13344859 Missense_Mutation SNP C C3L-00279_T 1260270 13344859 120452563 343 6121 CUBN 0 . GRCh38 10 16877038 16877038 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.8965A>T p.Ser2989Cys p.S2989C ENST00000377833 57/67 684 609 75 680 680 0 strelka-varscan-mutect CUBN,missense_variant,p.Ser2989Cys,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript missense_variant 9031/11949 8965/10872 2989/3623 S/C Agc/Tgc 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 deleterious(0.02) 57/67 PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs1466992790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 16877038 16877038 T A 1 0 0 0 0 1 0 0 0 3861 1580 55 4 4 CUBN 10 16877038 Missense_Mutation SNP T C3L-00279_T 3532179 16877038 116920384 344 6122 VIM 0 . GRCh38 10 17234767 17234767 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.957C>T p.= p.Y319Y ENST00000544301 6/10 556 502 54 534 534 0 strelka-varscan-mutect VIM,synonymous_variant,p.=,ENST00000544301,NM_003380.3;VIM,synonymous_variant,p.=,ENST00000224237,;VIM,synonymous_variant,p.=,ENST00000421459,;VIM,downstream_gene_variant,,ENST00000478317,;VIM,downstream_gene_variant,,ENST00000478746,;RP11-124N14.3,non_coding_transcript_exon_variant,,ENST00000456355,;VIM-AS1,upstream_gene_variant,,ENST00000605833,;VIM,non_coding_transcript_exon_variant,,ENST00000495528,;VIM,downstream_gene_variant,,ENST00000485947,;VIM,downstream_gene_variant,,ENST00000637053,;VIM,synonymous_variant,p.=,ENST00000469543,;VIM,synonymous_variant,p.=,ENST00000487938,; T ENST00000544301 Transcript synonymous_variant 1370/2128 957/1401 319/466 Y taC/taT 1 1 VIM HGNC HGNC:12692 protein_coding YES CCDS7120.1 ENSP00000446007 P08670 V9HWE1 UPI00000012EB NM_003380.3 6/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF27,Pfam_domain:PF00038,SMART_domains:SM01391 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 17234767 17234767 C T 1 0 0 0 0 0 0 0 1 17712 518 18 3 3 VIM 10 17234767 Silent SNP C C3L-00279_T 357729 17234767 116562655 345 6123 SKIDA1 0 . GRCh38 10 21517443 21517443 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.380C>A p.Pro127His p.P127H ENST00000449193 4/4 65 56 9 76 76 0 strelka-varscan-mutect SKIDA1,missense_variant,p.Pro127His,ENST00000449193,NM_207371.3;SKIDA1,missense_variant,p.Pro127His,ENST00000444772,;SKIDA1,downstream_gene_variant,,ENST00000633225,;SKIDA1,downstream_gene_variant,,ENST00000487107,; T ENST00000449193 Transcript missense_variant 2633/6598 380/2727 127/908 P/H cCc/cAc 1 -1 SKIDA1 HGNC HGNC:32697 protein_coding YES CCDS44363.1 ENSP00000410041 E9PAX1 UPI00015386B3 NM_207371.3 tolerated(0.1) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23187:SF2,hmmpanther:PTHR23187 MODERATE 1 SNV 3 1 PASS . . 0 205 5 0 0 0 0 0 -19.8305 1 1 1 1 0 T 3 4 14 21517443 21517443 G T 1 0 0 0 0 1 0 0 0 14620 1232 43 2 2 SKIDA1 10 21517443 Missense_Mutation SNP G C3L-00279_T 4282676 21517443 112279979 346 6124 KIAA1217 0 . GRCh38 10 24546104 24546104 + Missense_Mutation SNP G G T rs768673575 C3L-00279_T C3L-00279_N G G c.5612G>T p.Gly1871Val p.G1871V ENST00000376454 21/21 319 276 43 292 290 2 strelka-varscan-mutect KIAA1217,missense_variant,p.Gly1871Val,ENST00000376454,NM_019590.4;KIAA1217,missense_variant,p.Gly1192Val,ENST00000376462,NM_001098500.2;KIAA1217,missense_variant,p.Gly1302Val,ENST00000376452,NM_001282767.1;KIAA1217,missense_variant,p.Gly1277Val,ENST00000458595,NM_001282768.1;KIAA1217,missense_variant,p.Gly1192Val,ENST00000430453,;KIAA1217,3_prime_UTR_variant,,ENST00000376451,;KIAA1217,3_prime_UTR_variant,,ENST00000396445,;KIAA1217,downstream_gene_variant,,ENST00000307544,NM_001282769.1;KIAA1217,downstream_gene_variant,,ENST00000396446,NM_001282770.1;KIAA1217,downstream_gene_variant,,ENST00000635163,;KIAA1217,downstream_gene_variant,,ENST00000492009,; T ENST00000376454 Transcript missense_variant 5642/7381 5612/5832 1871/1943 G/V gGt/gTt rs768673575 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 deleterious(0.01) 21/21 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4 MODERATE 1 SNV 1 1 PASS rs768673575 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 24546104 24546104 G T 1 0 0 0 0 1 0 0 0 8109 1261 44 2 2 KIAA1217 10 24546104 Missense_Mutation SNP G C3L-00279_T 3028661 24546104 109251318 347 6125 GPR158 0 . GRCh38 10 25598085 25598085 + Missense_Mutation SNP C C A rs748910742 C3L-00279_T C3L-00279_N C C c.2459C>A p.Thr820Asn p.T820N ENST00000376351 11/11 307 279 28 225 225 0 strelka-varscan-mutect GPR158,missense_variant,p.Thr820Asn,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; A ENST00000376351 Transcript missense_variant 2818/6959 2459/3648 820/1215 T/N aCt/aAt rs748910742 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0.01) 11/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS rs748910742 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 25598085 25598085 C A 1 0 0 0 0 1 0 0 0 6549 565 20 2 2 GPR158 10 25598085 Missense_Mutation SNP C C3L-00279_T 1051981 25598085 108199337 348 6126 MYO3A 0 . GRCh38 10 26125496 26125496 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.2002G>A p.Val668Ile p.V668I ENST00000265944 19/35 549 512 37 323 323 0 strelka-varscan-mutect MYO3A,missense_variant,p.Val668Ile,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; A ENST00000265944 Transcript missense_variant 2168/5581 2002/4851 668/1616 V/I Gta/Ata 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0.04) 19/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 26125496 26125496 G A 1 0 0 0 0 1 0 0 0 10077 1377 48 3 3 MYO3A 10 26125496 Missense_Mutation SNP G C3L-00279_T 527411 26125496 107671926 349 6127 AGAP4 0 . GRCh38 10 45847239 45847239 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.109G>T p.Gly37Trp p.G37W ENST00000448048 1/7 967 883 84 1043 1043 0 varscan-mutect AGAP4,missense_variant,p.Gly37Trp,ENST00000616763,;AGAP4,missense_variant,p.Gly37Trp,ENST00000311652,;AGAP4,missense_variant,p.Gly37Trp,ENST00000448048,NM_133446.3;AGAP4,missense_variant,p.Gly37Trp,ENST00000618171,NM_001276343.2;AGAP4,upstream_gene_variant,,ENST00000492347,;AGAP4,non_coding_transcript_exon_variant,,ENST00000430779,;AGAP4,non_coding_transcript_exon_variant,,ENST00000490752,;AGAP4,upstream_gene_variant,,ENST00000495243,; A ENST00000448048 Transcript missense_variant 235/2439 109/1992 37/663 G/W Ggg/Tgg 1 -1 AGAP4 HGNC HGNC:23459 protein_coding YES CCDS7215.1 ENSP00000392513 Q96P64 UPI000013ED67 NM_133446.3 deleterious_low_confidence(0) 1/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23180:SF213,hmmpanther:PTHR23180 MODERATE 1 SNV 1 1 PASS rs1371059894 . 0 179 0 0 30 0 0 0 -18.1009 0 0 1 0 0 A 3 1 14 45847239 45847239 C A 1 0 0 0 0 1 0 0 0 447 594 21 2 2 AGAP4 10 45847239 Missense_Mutation SNP C C3L-00279_T 19721743 45847239 87950183 350 6128 C10orf71 0 . GRCh38 10 49325301 49325301 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2756C>A p.Pro919His p.P919H ENST00000374144 3/3 340 314 26 339 339 0 strelka-varscan-mutect C10orf71,missense_variant,p.Pro919His,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript missense_variant 3044/5230 2756/4308 919/1435 P/H cCc/cAc 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 tolerated(0.11) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 49325301 49325301 C A 1 0 0 0 0 1 0 0 0 1769 623 22 2 2 C10orf71 10 49325301 Missense_Mutation SNP C C3L-00279_T 3478062 49325301 84472121 351 6129 FAM21A 0 . GRCh38 10 50078676 50078676 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.293G>T p.Arg98Leu p.R98L ENST00000282633 4/31 359 333 26 283 283 0 varscan-mutect FAM21A,missense_variant,p.Arg98Leu,ENST00000351071,NM_001291398.1;FAM21A,missense_variant,p.Arg98Leu,ENST00000314664,;FAM21A,missense_variant,p.Arg98Leu,ENST00000611324,;FAM21A,missense_variant,p.Arg10Leu,ENST00000399339,;FAM21A,missense_variant,p.Arg98Leu,ENST00000282633,NM_001005751.2;FAM21A,splice_region_variant,,ENST00000492914,;FAM21A,upstream_gene_variant,,ENST00000476514,;FAM21A,missense_variant,p.Arg98Leu,ENST00000434114,; T ENST00000282633 Transcript missense_variant,splice_region_variant 338/4272 293/4026 98/1341 R/L cGt/cTt 1 1 FAM21A HGNC HGNC:23416 protein_coding YES CCDS41527.1 ENSP00000282633 Q641Q2 UPI000044FEAB NM_001005751.2 deleterious(0) 4/31 hmmpanther:PTHR21669,hmmpanther:PTHR21669:SF4 MODERATE 1 SNV 1 1 PASS rs1487596302 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 50078676 50078676 G T 1 0 0 0 0 1 0 0 0 5411 1159 40 1 1 FAM21A 10 50078676 Missense_Mutation SNP G C3L-00279_T 753375 50078676 83718746 352 6130 A1CF 0 . GRCh38 10 50816141 50816141 + Missense_Mutation SNP C C A rs574044306 C3L-00279_T C3L-00279_N C C c.1030G>T p.Asp344Tyr p.D344Y ENST00000395489 11/15 369 327 42 412 411 1 strelka-varscan-mutect A1CF,missense_variant,p.Asp344Tyr,ENST00000395489,NM_001198819.1;A1CF,missense_variant,p.Asp344Tyr,ENST00000395495,NM_001198820.1;A1CF,missense_variant,p.Asp336Tyr,ENST00000282641,NM_001198818.1;A1CF,missense_variant,p.Asp336Tyr,ENST00000374001,;A1CF,missense_variant,p.Asp344Tyr,ENST00000373995,NM_138933.2;A1CF,missense_variant,p.Asp336Tyr,ENST00000373997,NM_014576.3;A1CF,missense_variant,p.Asp336Tyr,ENST00000373993,NM_138932.2;A1CF,non_coding_transcript_exon_variant,,ENST00000493415,;ASAH2B,intron_variant,,ENST00000483649,; A ENST00000395489 Transcript missense_variant 1430/9517 1030/1809 344/602 D/Y Gat/Tat rs574044306,COSM1702386,COSM1702387,COSM1702388 1 -1 A1CF HGNC HGNC:24086 protein_coding YES CCDS73133.1 ENSP00000378868 F8W9F8 UPI0001E92A39 NM_001198819.1 deleterious(0.05) 11/15 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF313,TIGRFAM_domain:TIGR01648 0,1,1,1 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs574044306 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 50816141 50816141 C A 1 0 0 0 0 1 0 0 0 2 826 29 2 2 A1CF 10 50816141 Missense_Mutation SNP C C3L-00279_T 737465 50816141 82981281 353 6131 PCDH15 0 . GRCh38 10 53822974 53822974 + Silent SNP C C T C3L-00279_T C3L-00279_N C C c.4773G>A p.= p.L1591L ENST00000373957 35/35 435 395 40 360 359 1 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000617271,NM_001142770.1;PCDH15,intron_variant,,ENST00000613657,NM_001142769.1;PCDH15,intron_variant,,ENST00000395445,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000395438,;PCDH15,intron_variant,,ENST00000612394,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,;PCDH15,upstream_gene_variant,,ENST00000476074,; T ENST00000373957 Transcript synonymous_variant 5168/7032 4773/5889 1591/1962 L ctG/ctA COSM4846291,COSM4846292 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 35/35 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 53822974 53822974 C T 1 0 0 0 0 0 0 0 1 11598 813 29 3 3 PCDH15 10 53822974 Silent SNP C C3L-00279_T 3006833 53822974 79974448 354 6132 TMEM26 0 . GRCh38 10 61452919 61452919 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.163A>C p.Lys55Gln p.K55Q ENST00000399298 1/6 173 160 13 154 154 0 strelka-varscan-mutect TMEM26,missense_variant,p.Lys55Gln,ENST00000399298,NM_178505.6;TMEM26-AS1,non_coding_transcript_exon_variant,,ENST00000389640,;TMEM26,missense_variant,p.Lys55Gln,ENST00000503886,;TMEM26,missense_variant,p.Lys55Gln,ENST00000488505,; G ENST00000399298 Transcript missense_variant 532/5151 163/1107 55/368 K/Q Aag/Cag 1 -1 TMEM26 HGNC HGNC:28550 protein_coding YES CCDS41530.1 ENSP00000382237 Q6ZUK4 UPI00001C0B3F NM_178505.6 deleterious(0.01) 1/6 Pfam_domain:PF09772,hmmpanther:PTHR22168,hmmpanther:PTHR22168:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1028462711 . 0 206 4 0 0 0 0 0 -19.99989 1 1 1 1 0 G 3 3 14 61452919 61452919 T G 1 0 0 0 0 1 0 0 0 16620 1821 63 5 5 TMEM26 10 61452919 Missense_Mutation SNP T C3L-00279_T 7629945 61452919 72344503 355 6133 TBATA 0 . GRCh38 10 70774319 70774319 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.811G>T p.Ala271Ser p.A271S ENST00000299290 9/11 275 252 23 249 249 0 strelka-mutect TBATA,missense_variant,p.Ala272Ser,ENST00000456372,NM_001318241.1;TBATA,missense_variant,p.Ala271Ser,ENST00000299290,NM_001318243.1,NM_152710.2;TBATA,upstream_gene_variant,,ENST00000394982,; A ENST00000299290 Transcript missense_variant 1201/1583 811/1056 271/351 A/S Gct/Tct 1 -1 TBATA HGNC HGNC:23511 protein_coding YES CCDS7308.1 ENSP00000299290 Q96M53 UPI000013E57C NM_001318243.1,NM_152710.2 tolerated(0.15) 9/11 hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF3,Pfam_domain:PF15256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 70774319 70774319 C A 1 0 0 0 0 1 0 0 0 15996 739 26 2 2 TBATA 10 70774319 Missense_Mutation SNP C C3L-00279_T 9321400 70774319 63023103 356 6134 CDH23 0 . GRCh38 10 71677642 71677642 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.1716G>T p.= p.V572V ENST00000224721 16/70 277 260 17 298 298 0 strelka-varscan-mutect CDH23,synonymous_variant,p.=,ENST00000224721,NM_022124.5;CDH23,synonymous_variant,p.=,ENST00000622827,;CDH23,synonymous_variant,p.=,ENST00000442677,;CDH23,synonymous_variant,p.=,ENST00000616684,NM_001171930.1;CDH23,synonymous_variant,p.=,ENST00000398809,;CDH23,synonymous_variant,p.=,ENST00000466757,;CDH23,synonymous_variant,p.=,ENST00000299366,NM_001171931.1; T ENST00000224721 Transcript synonymous_variant 2106/11139 1716/10080 572/3359 V gtG/gtT 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 16/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 71677642 71677642 G T 1 0 0 0 0 0 0 0 1 2811 1335 47 2 2 CDH23 10 71677642 Silent SNP G C3L-00279_T 903323 71677642 62119780 357 6135 CDH23 0 . GRCh38 10 71799170 71799170 + Missense_Mutation SNP G G T rs550770402 C3L-00279_T C3L-00279_N G G c.394G>T p.Val132Leu p.V132L ENST00000398788 4/23 161 148 13 138 138 0 strelka-varscan-mutect CDH23,missense_variant,p.Val2377Leu,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Val2372Leu,ENST00000622827,;CDH23,missense_variant,p.Val132Leu,ENST00000398788,NM_001171933.1;CDH23,missense_variant,p.Val132Leu,ENST00000619887,NM_001171934.1;CDH23,non_coding_transcript_exon_variant,,ENST00000475158,; T ENST00000398788 Transcript missense_variant 711/4329 394/3345 132/1114 V/L Gtg/Ttg rs550770402,COSM5186097 1 1 CDH23 HGNC HGNC:13733 protein_coding YES CCDS53540.1 ENSP00000381768 Q9H251 UPI0000496839 NM_001171933.1 tolerated(0.07) 4/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs550770402 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 71799170 71799170 G T 1 0 0 0 0 1 0 0 0 2811 1145 40 1 1 CDH23 10 71799170 Missense_Mutation SNP G C3L-00279_T 121528 71799170 61998252 358 6136 CFAP70 0 . GRCh38 10 73312475 73312475 + Missense_Mutation SNP C C A rs147595147 C3L-00279_T C3L-00279_N C C c.1291G>T p.Val431Leu p.V431L ENST00000310715 11/28 57 52 5 20 20 0 strelka-mutect CFAP70,missense_variant,p.Val431Leu,ENST00000310715,NM_145170.3;CFAP70,splice_region_variant,,ENST00000355577,;CFAP70,intron_variant,,ENST00000340329,;CFAP70,splice_region_variant,,ENST00000493787,; A ENST00000310715 Transcript missense_variant,splice_region_variant 1412/3703 1291/3366 431/1121 V/L Gtg/Ttg rs147595147 1 -1 CFAP70 HGNC HGNC:30726 protein_coding YES CCDS7324.3 ENSP00000310829 Q5T0N1 UPI00001AEF7A NM_145170.3 tolerated(0.7) 11/28 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF394 MODERATE 1 SNV 5 1 PASS rs147595147 . 0 206 4 0 0 0 0 0 -12.13233 1 1 1 1 0 A 3 1 14 73312475 73312475 C A 1 0 0 0 0 1 0 0 0 3031 492 17 2 2 CFAP70 10 73312475 Missense_Mutation SNP C C3L-00279_T 1513305 73312475 60484947 359 6137 KAT6B 0 . GRCh38 10 74976000 74976000 + Missense_Mutation SNP G G A rs146395020 C3L-00279_T C3L-00279_N G G c.1663G>A p.Gly555Arg p.G555R ENST00000287239 8/18 692 631 61 619 618 1 strelka-varscan-mutect KAT6B,missense_variant,p.Gly555Arg,ENST00000287239,NM_012330.3;KAT6B,intron_variant,,ENST00000372711,NM_001256468.1;KAT6B,intron_variant,,ENST00000372724,NM_001256469.1;KAT6B,intron_variant,,ENST00000372725,;KAT6B,intron_variant,,ENST00000372714,;KAT6B,upstream_gene_variant,,ENST00000490365,; A ENST00000287239 Transcript missense_variant 2152/8287 1663/6222 555/2073 G/R Gga/Aga rs146395020,COSM3397253 1 1 KAT6B HGNC HGNC:17582 protein_coding YES CCDS7345.1 ENSP00000287239 Q8WYB5 UPI000013DEA0 NM_012330.3 deleterious(0) 8/18 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs146395020 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 74976000 74976000 G A 1 0 0 0 0 1 0 0 0 7899 1233 43 3 3 KAT6B 10 74976000 Missense_Mutation SNP G C3L-00279_T 1663525 74976000 58821422 360 6138 POLR3A 0 . GRCh38 10 78004729 78004729 + Frame_Shift_Del DEL T T - novel C3L-00279_T C3L-00279_N T T c.2234delA p.Glu745GlyfsTer7 p.E745Gfs*7 ENST00000372371 16/31 392 362 30 394 393 1 sindel-varindel-pindel POLR3A,frameshift_variant,p.Glu745GlyfsTer7,ENST00000372371,NM_007055.3;POLR3A,non_coding_transcript_exon_variant,,ENST00000472014,;POLR3A,3_prime_UTR_variant,,ENST00000473588,; - ENST00000372371 Transcript frameshift_variant 2372/6640 2234/4173 745/1390 E/X gAg/gg 1 -1 POLR3A HGNC HGNC:30074 protein_coding YES CCDS7354.1 ENSP00000361446 O14802 UPI000007456A NM_007055.3 16/31 hmmpanther:PTHR19376:SF32,hmmpanther:PTHR19376,Pfam_domain:PF05000,Superfamily_domains:SSF64484 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 78004729 78004729 T - 1 0 1 0 1 0 0 0 0 12339 1551 54 0 0 POLR3A 10 78004729 Frame_Shift_Del DEL T C3L-00279_T 3028729 78004729 55792693 361 6139 DNMBP 0 . GRCh38 10 99880208 99880208 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.4151C>T p.Thr1384Ile p.T1384I ENST00000324109 16/17 233 217 16 170 170 0 strelka-varscan-mutect DNMBP,missense_variant,p.Thr1384Ile,ENST00000324109,NM_015221.2;DNMBP,missense_variant,p.Thr1016Ile,ENST00000636706,NM_001318326.1;DNMBP,missense_variant,p.Thr672Ile,ENST00000543621,NM_001318327.1; A ENST00000324109 Transcript missense_variant 4243/6400 4151/4734 1384/1577 T/I aCc/aTc 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 deleterious(0.04) 16/17 hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.53035 0.9999996 1 1 1 0 A 3 1 14 99880208 99880208 G A 1 0 0 0 0 1 0 0 0 4487 1261 44 3 3 DNMBP 10 99880208 Missense_Mutation SNP G C3L-00279_T 21875479 99880208 33917214 362 6140 INPP5F 0 . GRCh38 10 119808005 119808005 + Frame_Shift_Del DEL G G - novel C3L-00279_T C3L-00279_N G G c.1516delG p.Ala506ProfsTer17 p.A506Pfs*17 ENST00000361976 13/20 154 142 12 136 136 0 sindel-varindel-pindel INPP5F,frameshift_variant,p.Ala506ProfsTer17,ENST00000361976,NM_014937.3;PHACTR2P1,intron_variant,,ENST00000636592,; - ENST00000361976 Transcript frameshift_variant 1680/5063 1514/3399 505/1132 W/X tGg/tg 1 1 INPP5F HGNC HGNC:17054 protein_coding YES CCDS7616.1 ENSP00000354519 Q9Y2H2 UPI000006FBCA NM_014937.3 13/20 PROSITE_profiles:PS50275,hmmpanther:PTHR11200:SF167,hmmpanther:PTHR11200 HIGH 1 deletion 1 2 1 PASS . . 0 208 0 2 0 0 0 0 -16.53496 0.9999997 1 1 1 0 - 7 5 14 119808005 119808005 G - 1 0 1 0 1 0 0 0 0 7661 1357 47 0 0 INPP5F 10 119808005 Frame_Shift_Del DEL G C3L-00279_T 19927797 119808005 13989417 363 6141 BTBD16 0 . GRCh38 10 122276934 122276934 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.162A>T p.= p.P54P ENST00000260723 3/16 140 126 14 131 130 1 strelka-varscan-mutect BTBD16,synonymous_variant,p.=,ENST00000260723,NM_001318189.1,NM_144587.2; T ENST00000260723 Transcript synonymous_variant 413/1849 162/1521 54/506 P ccA/ccT 1 1 BTBD16 HGNC HGNC:26340 protein_coding YES CCDS31301.1 ENSP00000260723 Q32M84 UPI00003CEFB9 NM_001318189.1,NM_144587.2 3/16 hmmpanther:PTHR23231,hmmpanther:PTHR23231:SF4 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 122276934 122276934 A T 1 0 0 0 0 0 0 0 1 1715 202 7 4 4 BTBD16 10 122276934 Silent SNP A C3L-00279_T 2468929 122276934 11520488 364 6142 HTRA1 0 . GRCh38 10 122488970 122488970 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.541C>G p.Pro181Ala p.P181A ENST00000368984 2/9 520 473 47 493 493 0 strelka-varscan-mutect HTRA1,missense_variant,p.Pro181Ala,ENST00000368984,NM_002775.4; G ENST00000368984 Transcript missense_variant 669/2120 541/1443 181/480 P/A Cct/Gct 1 1 HTRA1 HGNC HGNC:9476 protein_coding YES CCDS7630.1 ENSP00000357980 Q92743 UPI0000114888 NM_002775.4 deleterious(0) 2/9 Gene3D:2.40.10.10,hmmpanther:PTHR22939,hmmpanther:PTHR22939:SF13,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 122488970 122488970 C G 1 0 0 0 0 1 0 0 0 7349 623 22 4 4 HTRA1 10 122488970 Missense_Mutation SNP C C3L-00279_T 212036 122488970 11308452 365 6143 HTRA1 0 . GRCh38 10 122510104 122510104 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.1129A>G p.Ile377Val p.I377V ENST00000368984 7/9 505 468 37 491 491 0 strelka-varscan-mutect HTRA1,missense_variant,p.Ile377Val,ENST00000368984,NM_002775.4;HTRA1,missense_variant,p.Ile118Val,ENST00000420892,; G ENST00000368984 Transcript missense_variant 1257/2120 1129/1443 377/480 I/V Atc/Gtc 1 1 HTRA1 HGNC HGNC:9476 protein_coding YES CCDS7630.1 ENSP00000357980 Q92743 UPI0000114888 NM_002775.4 tolerated(0.67) 7/9 PROSITE_profiles:PS50106,hmmpanther:PTHR22939,hmmpanther:PTHR22939:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 122510104 122510104 A G 1 0 0 0 0 1 0 0 0 7349 217 8 5 5 HTRA1 10 122510104 Missense_Mutation SNP A C3L-00279_T 21134 122510104 11287318 366 6144 STK32C 0 . GRCh38 10 132331645 132331645 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.92A>T p.His31Leu p.H31L ENST00000368620 1/4 136 126 10 133 133 0 strelka-varscan-mutect STK32C,missense_variant,p.His31Leu,ENST00000368620,;STK32C,missense_variant,p.His31Leu,ENST00000368619,;STK32C,missense_variant,p.His31Leu,ENST00000456004,NM_001318880.1;LRRC27,upstream_gene_variant,,ENST00000368614,NM_030626.2;LRRC27,upstream_gene_variant,,ENST00000368613,NM_001143757.1;LRRC27,upstream_gene_variant,,ENST00000344079,NM_001143759.1;LRRC27,upstream_gene_variant,,ENST00000368612,;LRRC27,upstream_gene_variant,,ENST00000625755,NM_001143758.1;LRRC27,upstream_gene_variant,,ENST00000462656,; A ENST00000368620 Transcript missense_variant 203/830 92/719 31/239 H/L cAc/cTc 1 -1 STK32C HGNC HGNC:21332 protein_coding ENSP00000357609 A0A0A0MRK9 UPI0006644D0A 1/4 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 132331645 132331645 T A 1 0 0 0 0 1 0 0 0 15676 1696 59 4 4 STK32C 10 132331645 Missense_Mutation SNP T C3L-00279_T 9821541 132331645 1465777 367 6145 NLRP6 0 . GRCh38 11 281143 281143 + Missense_Mutation SNP T T C novel C3L-00279_T C3L-00279_N T T c.1409T>C p.Leu470Pro p.L470P ENST00000312165 4/8 200 174 26 182 182 0 strelka-varscan-mutect NLRP6,missense_variant,p.Leu470Pro,ENST00000534750,NM_001276700.1;NLRP6,missense_variant,p.Leu470Pro,ENST00000312165,NM_138329.2;NLRP6,downstream_gene_variant,,ENST00000527946,; C ENST00000312165 Transcript missense_variant 1409/2679 1409/2679 470/892 L/P cTt/cCt 1 1 NLRP6 HGNC HGNC:22944 protein_coding YES CCDS7693.1 ENSP00000309767 P59044 UPI00001AEFE1 NM_138329.2 deleterious(0) 4/8 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF3 MODERATE 1 SNV 1 1 PASS rs1409041110 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 281143 281143 T C 1 0 0 0 0 1 0 0 0 10519 1609 56 5 5 NLRP6 11 281143 Missense_Mutation SNP T C3L-00279_T 281143 134805479 368 6146 LMNTD2 0 . GRCh38 11 557988 557988 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.451G>C p.Glu151Gln p.E151Q ENST00000329451 5/14 66 54 12 65 65 0 strelka-varscan-mutect LMNTD2,missense_variant,p.Glu151Gln,ENST00000329451,NM_173573.2;LMNTD2,missense_variant,p.Glu158Gln,ENST00000441853,;LMNTD2,missense_variant,p.Glu161Gln,ENST00000486629,;LRRC56,downstream_gene_variant,,ENST00000270115,NM_198075.3;RASSF7,upstream_gene_variant,,ENST00000397583,NM_003475.3;RASSF7,upstream_gene_variant,,ENST00000431809,;RASSF7,upstream_gene_variant,,ENST00000397582,NM_001143993.1;RASSF7,upstream_gene_variant,,ENST00000454668,NM_001143994.1;RASSF7,upstream_gene_variant,,ENST00000528736,;RP11-496I9.1,non_coding_transcript_exon_variant,,ENST00000527620,;RP11-496I9.1,upstream_gene_variant,,ENST00000533844,;RP11-496I9.1,upstream_gene_variant,,ENST00000527113,;RASSF7,upstream_gene_variant,,ENST00000524468,;RASSF7,upstream_gene_variant,,ENST00000414138,;LMNTD2,upstream_gene_variant,,ENST00000469990,;RASSF7,upstream_gene_variant,,ENST00000531112,;LMNTD2,downstream_gene_variant,,ENST00000492515,; G ENST00000329451 Transcript missense_variant 514/2084 451/1905 151/634 E/Q Gag/Cag 1 -1 LMNTD2 HGNC HGNC:28561 protein_coding YES CCDS7701.1 ENSP00000331167 Q8IXW0 UPI0000456441 NM_173573.2 tolerated(1) 5/14 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19956,hmmpanther:PTHR19956:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1212389087 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 557988 557988 C G 1 0 0 0 0 1 0 0 0 8776 864 30 4 4 LMNTD2 11 557988 Missense_Mutation SNP C C3L-00279_T 276845 557988 134528634 369 6147 SLC22A18AS 0 . GRCh38 11 2899669 2899669 + Nonsense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.33G>A p.Trp11Ter p.W11* ENST00000625099 3/4 63 53 10 57 57 0 strelka-varscan-mutect SLC22A18AS,stop_gained,p.Trp11Ter,ENST00000625099,NM_007105.3;SLC22A18AS,intron_variant,,ENST00000455942,NM_001302862.1;SLC22A18,upstream_gene_variant,,ENST00000380574,NM_001315501.1;SLC22A18,upstream_gene_variant,,ENST00000312221,NM_002555.5;SLC22A18,upstream_gene_variant,,ENST00000347936,NM_183233.2;SLC22A18,upstream_gene_variant,,ENST00000449793,NM_001315502.1;SLC22A18,upstream_gene_variant,,ENST00000485423,;SLC22A18,upstream_gene_variant,,ENST00000492567,; T ENST00000625099 Transcript stop_gained 530/1659 33/762 11/253 W/* tgG/tgA 1 -1 SLC22A18AS HGNC HGNC:10965 protein_coding YES ENSP00000487968 Q8N1D0 UPI000013FBB8 NM_007105.3 3/4 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99912 0.9999999 1 1 1 0 T 4 4 14 2899669 2899669 C T 1 0 0 0 0 0 1 0 0 14715 624 22 3 3 SLC22A18AS 11 2899669 Nonsense_Mutation SNP C C3L-00279_T 2341681 2899669 132186953 370 6148 SLC22A18 0 . GRCh38 11 2909672 2909672 + Silent SNP C C T rs760431741 C3L-00279_T C3L-00279_N C C c.498C>T p.= p.L166L ENST00000380574 5/11 163 143 20 139 139 0 strelka-varscan-mutect SLC22A18,synonymous_variant,p.=,ENST00000380574,NM_001315501.1;SLC22A18,synonymous_variant,p.=,ENST00000312221,NM_002555.5;SLC22A18,synonymous_variant,p.=,ENST00000347936,NM_183233.2;SLC22A18,intron_variant,,ENST00000449793,NM_001315502.1;SLC22A18,downstream_gene_variant,,ENST00000485423,;SLC22A18,non_coding_transcript_exon_variant,,ENST00000492567,;SLC22A18,non_coding_transcript_exon_variant,,ENST00000498244,; T ENST00000380574 Transcript synonymous_variant 929/1755 498/1275 166/424 L ctC/ctT rs760431741 1 1 SLC22A18 HGNC HGNC:10964 protein_coding YES CCDS7740.1 ENSP00000369948 Q96BI1 UPI0000070F3F NM_001315501.1 5/11 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24002,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Prints_domain:PR01035 LOW 1 SNV 5 1 PASS rs760431741 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 2909672 2909672 C T 1 0 0 0 0 0 0 0 1 14714 871 31 1 1 SLC22A18 11 2909672 Silent SNP C C3L-00279_T 10003 2909672 132176950 371 6149 OR51L1 0 . GRCh38 11 4999369 4999369 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.387C>A p.Cys129Ter p.C129* ENST00000321543 1/1 293 253 40 262 262 0 strelka-varscan-mutect OR51L1,stop_gained,p.Cys129Ter,ENST00000321543,NM_001004755.1; A ENST00000321543 Transcript stop_gained 387/948 387/948 129/315 C/* tgC/tgA 1 1 OR51L1 HGNC HGNC:14759 protein_coding YES CCDS31369.1 ENSP00000322156 Q8NGJ5 A0A126GVJ8 UPI0000041B76 NM_001004755.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF37,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 4999369 4999369 C A 1 0 0 0 0 0 1 0 0 11176 747 26 2 2 OR51L1 11 4999369 Nonsense_Mutation SNP C C3L-00279_T 2089697 4999369 130087253 372 6150 OR51B5 0 . GRCh38 11 5342851 5342851 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.674G>A p.Ser225Asn p.S225N ENST00000300773 1/1 154 139 15 134 134 0 strelka-varscan-mutect OR51B5,missense_variant,p.Ser225Asn,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;AC104389.28,downstream_gene_variant,,ENST00000418729,; T ENST00000300773 Transcript missense_variant 674/939 674/939 225/312 S/N aGc/aAc 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 tolerated(0.14) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -19.97229 0.9999998 1 1 1 0 T 3 4 14 5342851 5342851 C T 1 0 0 0 0 1 0 0 0 11165 797 28 3 3 OR51B5 11 5342851 Missense_Mutation SNP C C3L-00279_T 343482 5342851 129743771 373 6151 OR52D1 0 . GRCh38 11 5488718 5488718 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.12C>A p.= p.S4S ENST00000322641 1/1 97 86 11 89 88 1 strelka-varscan-mutect OR52D1,synonymous_variant,p.=,ENST00000322641,NM_001005163.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000322641 Transcript synonymous_variant 34/1065 12/957 4/318 S tcC/tcA 1 1 OR52D1 HGNC HGNC:15212 protein_coding YES CCDS31384.1 ENSP00000326232 Q9H346 A0A126GVG9 UPI0000041DD3 NM_001005163.2 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF75,Superfamily_domains:SSF81321 LOW SNV 1 PASS rs1309925653 . 0 198 12 0 0 0 0 0 -19.99814 0.9998581 1 1 1 0 A 2 1 14 5488718 5488718 C A 1 0 0 0 0 0 0 0 1 11186 581 21 2 2 OR52D1 11 5488718 Silent SNP C C3L-00279_T 145867 5488718 129597904 374 6152 OR56A3 0 . GRCh38 11 5947916 5947916 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.570A>T p.Arg190Ser p.R190S ENST00000329564 1/1 251 221 30 166 166 0 strelka-varscan-mutect OR56A3,missense_variant,p.Arg190Ser,ENST00000329564,NM_001003443.2;AC025016.1,downstream_gene_variant,,ENST00000528915,; T ENST00000329564 Transcript missense_variant 577/1022 570/948 190/315 R/S agA/agT 1 1 OR56A3 HGNC HGNC:14786 protein_coding YES CCDS41614.1 ENSP00000331572 Q8NH54 A0A126GWL6 UPI0000041BF7 NM_001003443.2 tolerated(0.82) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF40,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 5947916 5947916 A T 1 0 0 0 0 1 0 0 0 11206 272 10 4 4 OR56A3 11 5947916 Missense_Mutation SNP A C3L-00279_T 459198 5947916 129138706 375 6153 OR56A4 0 . GRCh38 11 6002127 6002127 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.1022C>G p.Ala341Gly p.A341G ENST00000330728 1/1 117 96 21 97 97 0 strelka-varscan-mutect OR56A4,missense_variant,p.Ala341Gly,ENST00000330728,NM_001005179.2; C ENST00000330728 Transcript missense_variant 1068/1209 1022/1098 341/365 A/G gCt/gGt 1 -1 OR56A4 HGNC HGNC:14791 protein_coding YES CCDS31404.1 ENSP00000328215 Q8NGH8 UPI000041A756 NM_001005179.2 deleterious(0.01) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF81,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 6002127 6002127 G C 1 0 0 0 0 1 0 0 0 11207 971 34 4 4 OR56A4 11 6002127 Missense_Mutation SNP G C3L-00279_T 54211 6002127 129084495 376 6154 CCKBR 0 . GRCh38 11 6260069 6260069 + Silent SNP C C A rs765920167 C3L-00279_T C3L-00279_N C C c.141C>A p.= p.A47A ENST00000334619 1/5 224 193 31 257 257 0 strelka-varscan-mutect CCKBR,synonymous_variant,p.=,ENST00000525462,;CCKBR,synonymous_variant,p.=,ENST00000334619,NM_176875.3;CCKBR,synonymous_variant,p.=,ENST00000532715,;CCKBR,synonymous_variant,p.=,ENST00000525014,;CCKBR,synonymous_variant,p.=,ENST00000531712,; A ENST00000334619 Transcript synonymous_variant 334/2121 141/1344 47/447 A gcC/gcA rs765920167,COSM1355482,COSM1355483 1 1 CCKBR HGNC HGNC:1571 protein_coding YES CCDS7761.1 ENSP00000335544 P32239 UPI0000000C18 NM_176875.3 1/5 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF45,Superfamily_domains:SSF81321,Prints_domain:PR00527 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs765920167 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 6260069 6260069 C A 1 0 0 0 0 0 0 0 1 2579 639 23 1 1 CCKBR 11 6260069 Silent SNP C C3L-00279_T 257942 6260069 128826553 377 6155 DCHS1 0 . GRCh38 11 6624044 6624044 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.7632T>A p.= p.A2544A ENST00000299441 21/21 232 201 31 168 168 0 strelka-varscan-mutect DCHS1,synonymous_variant,p.=,ENST00000299441,NM_003737.3;TPP1,upstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,upstream_gene_variant,,ENST00000533371,;TPP1,upstream_gene_variant,,ENST00000528657,;TPP1,upstream_gene_variant,,ENST00000436873,;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.9,downstream_gene_variant,,ENST00000545572,;TPP1,upstream_gene_variant,,ENST00000534644,;TPP1,upstream_gene_variant,,ENST00000524903,;TPP1,upstream_gene_variant,,ENST00000530040,;TPP1,upstream_gene_variant,,ENST00000428886,;TPP1,upstream_gene_variant,,ENST00000531754,;TPP1,upstream_gene_variant,,ENST00000528571,;TPP1,upstream_gene_variant,,ENST00000528917,; T ENST00000299441 Transcript synonymous_variant 8044/10765 7632/9897 2544/3298 A gcT/gcA 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 21/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 6624044 6624044 A T 1 0 0 0 0 0 0 0 1 4090 175 7 4 4 DCHS1 11 6624044 Silent SNP A C3L-00279_T 363975 6624044 128462578 378 6156 DCHS1 0 . GRCh38 11 6629548 6629548 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.5065G>T p.Val1689Phe p.V1689F ENST00000299441 12/21 279 235 44 235 235 0 strelka-varscan-mutect DCHS1,missense_variant,p.Val1689Phe,ENST00000299441,NM_003737.3;RP11-732A19.6,upstream_gene_variant,,ENST00000526633,; A ENST00000299441 Transcript missense_variant 5477/10765 5065/9897 1689/3298 V/F Gtc/Ttc 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0.01) 12/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1289410605 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 6629548 6629548 C A 1 0 0 0 0 1 0 0 0 4090 536 19 1 1 DCHS1 11 6629548 Missense_Mutation SNP C C3L-00279_T 5504 6629548 128457074 379 6157 DCHS1 0 . GRCh38 11 6640795 6640795 + Silent SNP A A T rs750151822 C3L-00279_T C3L-00279_N A A c.819T>A p.= p.P273P ENST00000299441 2/21 358 306 52 279 279 0 strelka-varscan-mutect DCHS1,synonymous_variant,p.=,ENST00000299441,NM_003737.3; T ENST00000299441 Transcript synonymous_variant 1231/10765 819/9897 273/3298 P ccT/ccA rs750151822 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 2/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs750151822 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 6640795 6640795 A T 1 0 0 0 0 0 0 0 1 4090 175 7 4 4 DCHS1 11 6640795 Silent SNP A C3L-00279_T 11247 6640795 128445827 380 6158 IPO7 0 . GRCh38 11 9423776 9423776 + Splice_Site SNP G G A novel C3L-00279_T C3L-00279_N G G c.1042-1G>A p.X348_splice ENST00000379719 82 75 7 25 25 0 strelka-mutect IPO7,splice_acceptor_variant,,ENST00000379719,NM_006391.2;SNORA23,upstream_gene_variant,,ENST00000365128,;IPO7,upstream_gene_variant,,ENST00000530037,;IPO7,downstream_gene_variant,,ENST00000531235,; A ENST00000379719 Transcript splice_acceptor_variant -/6191 1042/3117 348/1038 1 1 IPO7 HGNC HGNC:9852 protein_coding YES CCDS31425.1 ENSP00000369042 O95373 UPI0000072C06 NM_006391.2 9/24 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 14 9423776 9423776 G A 1 0 0 0 0 0 0 1 0 7700 1014 35 3 3 IPO7 11 9423776 Splice_Site SNP G C3L-00279_T 2782981 9423776 125662846 381 6159 SBF2 0 . GRCh38 11 10028470 10028470 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.601C>T p.Leu201Phe p.L201F ENST00000256190 6/40 482 416 66 280 280 0 strelka-varscan-mutect SBF2,missense_variant,p.Leu201Phe,ENST00000256190,NM_030962.3;SBF2,non_coding_transcript_exon_variant,,ENST00000527019,;SBF2,non_coding_transcript_exon_variant,,ENST00000533770,;SBF2,non_coding_transcript_exon_variant,,ENST00000533661,; A ENST00000256190 Transcript missense_variant 739/7439 601/5550 201/1849 L/F Ctc/Ttc 1 -1 SBF2 HGNC HGNC:2135 protein_coding YES CCDS31427.1 ENSP00000256190 Q86WG5 UPI00000622D5 NM_030962.3 tolerated(0.12) 6/40 Pfam_domain:PF02141,PROSITE_profiles:PS50211,SMART_domains:SM00799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 10028470 10028470 G A 1 0 0 0 0 1 0 0 0 14123 942 33 3 3 SBF2 11 10028470 Missense_Mutation SNP G C3L-00279_T 604694 10028470 125058152 382 6160 PIK3C2A 0 . GRCh38 11 17097056 17097056 + Splice_Site SNP C C G novel C3L-00279_T C3L-00279_N C C c.4326+1G>C p.X1442_splice ENST00000265970 120 104 16 38 38 0 strelka-varscan-mutect PIK3C2A,splice_donor_variant,,ENST00000265970,NM_001321378.1,NM_002645.2;PIK3C2A,splice_donor_variant,,ENST00000531428,; G ENST00000265970 Transcript splice_donor_variant -/8227 4326/5061 1442/1686 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 26/31 HIGH 1 SNV 1 1 PASS rs772083223 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 14 17097056 17097056 C G 1 0 0 0 0 0 0 1 0 12004 492 17 4 4 PIK3C2A 11 17097056 Splice_Site SNP C C3L-00279_T 7068586 17097056 117989566 383 6161 PIK3C2A 0 . GRCh38 11 17105300 17105300 + Missense_Mutation SNP C C A rs201770470 C3L-00279_T C3L-00279_N C C c.3550G>T p.Val1184Leu p.V1184L ENST00000265970 22/32 244 214 30 169 168 1 strelka-mutect PIK3C2A,missense_variant,p.Val1184Leu,ENST00000265970,NM_001321378.1,NM_002645.2;PIK3C2A,non_coding_transcript_exon_variant,,ENST00000531428,; A ENST00000265970 Transcript missense_variant 3550/8227 3550/5061 1184/1686 V/L Gtg/Ttg rs201770470 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 deleterious(0) 22/32 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF28,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs201770470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 17105300 17105300 C A 1 0 0 0 0 1 0 0 0 12004 521 18 2 2 PIK3C2A 11 17105300 Missense_Mutation SNP C C3L-00279_T 8244 17105300 117981322 384 6162 SERGEF 0 . GRCh38 11 17788258 17788258 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1204C>A p.Leu402Met p.L402M ENST00000265965 11/11 190 172 18 120 120 0 strelka-varscan-mutect SERGEF,missense_variant,p.Leu402Met,ENST00000265965,NM_012139.3;SERGEF,missense_variant,p.Leu266Met,ENST00000529151,;SERGEF,3_prime_UTR_variant,,ENST00000528200,;SERGEF,3_prime_UTR_variant,,ENST00000525920,;SERGEF,non_coding_transcript_exon_variant,,ENST00000528369,;SERGEF,non_coding_transcript_exon_variant,,ENST00000524589,;SERGEF,non_coding_transcript_exon_variant,,ENST00000531299,;SERGEF,non_coding_transcript_exon_variant,,ENST00000529440,;SERGEF,non_coding_transcript_exon_variant,,ENST00000531926,;SERGEF,3_prime_UTR_variant,,ENST00000525422,;SERGEF,3_prime_UTR_variant,,ENST00000527494,;SERGEF,3_prime_UTR_variant,,ENST00000532546,; T ENST00000265965 Transcript missense_variant 1356/1566 1204/1377 402/458 L/M Ctg/Atg 1 -1 SERGEF HGNC HGNC:17499 protein_coding YES CCDS7828.1 ENSP00000265965 Q9UGK8 UPI000007326C NM_012139.3 tolerated(0.06) 11/11 PROSITE_profiles:PS50012,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF208 MODERATE 1 SNV 1 1 PASS rs1224191328 . 0 207 0 2 0 0 0 0 -19.99998 0.9999998 1 1 1 0 T 3 4 14 17788258 17788258 G T 1 0 0 0 0 1 0 0 0 14353 962 34 2 2 SERGEF 11 17788258 Missense_Mutation SNP G C3L-00279_T 682958 17788258 117298364 385 6163 PTPN5 0 . GRCh38 11 18740655 18740655 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.863A>T p.Glu288Val p.E288V ENST00000358540 8/15 56 50 6 51 51 0 strelka-varscan-mutect PTPN5,missense_variant,p.Glu256Val,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,missense_variant,p.Glu288Val,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,missense_variant,p.Glu92Val,ENST00000477854,;PTPN5,missense_variant,p.Glu264Val,ENST00000396168,NM_001278238.1,NM_001278239.1;RP11-1081L13.4,downstream_gene_variant,,ENST00000527285,;PTPN5,downstream_gene_variant,,ENST00000496201,; A ENST00000358540 Transcript missense_variant 1294/3135 863/1698 288/565 E/V gAa/gTa 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 tolerated(0.07) 8/15 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF40,PIRSF_domain:PIRSF001997,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.31692 1 1 1 1 0 A 3 1 14 18740655 18740655 T A 1 0 0 0 0 1 0 0 0 12945 1783 62 4 4 PTPN5 11 18740655 Missense_Mutation SNP T C3L-00279_T 952397 18740655 116345967 386 6164 QSER1 0 . GRCh38 11 32933329 32933329 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1684G>T p.Asp562Tyr p.D562Y ENST00000399302 4/13 96 84 12 54 54 0 strelka-varscan-mutect QSER1,missense_variant,p.Asp562Tyr,ENST00000399302,NM_001076786.2;QSER1,missense_variant,p.Asp323Tyr,ENST00000527788,;QSER1,upstream_gene_variant,,ENST00000524678,;QSER1,downstream_gene_variant,,ENST00000528155,;QSER1,downstream_gene_variant,,ENST00000527250,; T ENST00000399302 Transcript missense_variant 2019/9335 1684/5208 562/1735 D/Y Gat/Tat 1 1 QSER1 HGNC HGNC:26154 protein_coding YES CCDS41631.1 ENSP00000382241 Q2KHR3 UPI0000E467AF NM_001076786.2 deleterious(0) 4/13 hmmpanther:PTHR14709:SF2,hmmpanther:PTHR14709 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 32933329 32933329 G T 1 0 0 0 0 1 0 0 0 13037 942 33 2 2 QSER1 11 32933329 Missense_Mutation SNP G C3L-00279_T 14192674 32933329 102153293 387 6165 NAT10 0 . GRCh38 11 34134533 34134533 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1858G>T p.Gly620Cys p.G620C ENST00000257829 18/29 346 323 23 288 287 1 strelka-varscan-mutect NAT10,missense_variant,p.Gly620Cys,ENST00000257829,NM_024662.2;NAT10,missense_variant,p.Gly548Cys,ENST00000531159,NM_001144030.1;NAT10,missense_variant,p.Gly467Cys,ENST00000615292,;NAT10,intron_variant,,ENST00000527971,;NAT10,upstream_gene_variant,,ENST00000530017,; T ENST00000257829 Transcript missense_variant 2064/4002 1858/3078 620/1025 G/C Ggt/Tgt 1 1 NAT10 HGNC HGNC:29830 protein_coding YES CCDS7889.1 ENSP00000257829 Q9H0A0 UPI000013CF8E NM_024662.2 deleterious(0.01) 18/29 PROSITE_profiles:PS51186,hmmpanther:PTHR10925,Pfam_domain:PF13718,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 34134533 34134533 G T 1 0 0 0 0 1 0 0 0 10183 1348 47 2 2 NAT10 11 34134533 Missense_Mutation SNP G C3L-00279_T 1201204 34134533 100952089 388 6166 PDHX 0 . GRCh38 11 34994981 34994981 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1315A>T p.Ile439Phe p.I439F ENST00000227868 11/11 443 387 56 360 360 0 strelka-varscan-mutect PDHX,missense_variant,p.Ile424Phe,ENST00000448838,NM_001135024.1;PDHX,missense_variant,p.Ile439Phe,ENST00000227868,NM_003477.2;PDHX,missense_variant,p.Ile212Phe,ENST00000430469,NM_001166158.1;PDHX,missense_variant,p.Ile127Phe,ENST00000526309,;PDHX,intron_variant,,ENST00000477173,; T ENST00000227868 Transcript missense_variant 1399/2389 1315/1506 439/501 I/F Att/Ttt 1 1 PDHX HGNC HGNC:21350 protein_coding YES CCDS7896.1 ENSP00000227868 O00330 UPI0000130C34 NM_003477.2 deleterious(0) 11/11 hmmpanther:PTHR23151:SF57,hmmpanther:PTHR23151,Gene3D:3.30.559.10,Pfam_domain:PF00198,Superfamily_domains:SSF52777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 34994981 34994981 A T 1 0 0 0 0 1 0 0 0 11755 217 8 4 4 PDHX 11 34994981 Missense_Mutation SNP A C3L-00279_T 860448 34994981 100091641 389 6167 RAG2 0 . GRCh38 11 36592712 36592712 + Missense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.1457G>A p.Arg486Lys p.R486K ENST00000618712 3/3 578 511 67 320 320 0 strelka-varscan-mutect RAG2,missense_variant,p.Arg486Lys,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,missense_variant,p.Arg486Lys,ENST00000311485,NM_000536.3;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000529083,;RAG2,downstream_gene_variant,,ENST00000527033,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,intron_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; T ENST00000618712 Transcript missense_variant 2051/2818 1457/1584 486/527 R/K aGa/aAa COSM5321763 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 tolerated(0.55) 3/3 Pfam_domain:PF13341,hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0,Superfamily_domains:SSF57903 1 MODERATE 1 SNV 4 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 36592712 36592712 C T 1 0 0 0 0 1 0 0 0 13165 913 32 3 3 RAG2 11 36592712 Missense_Mutation SNP C C3L-00279_T 1597731 36592712 98493910 390 6168 DGKZ 0 . GRCh38 11 46372823 46372823 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.1688C>T p.Pro563Leu p.P563L ENST00000454345 14/32 228 188 40 157 157 0 strelka-varscan-mutect DGKZ,missense_variant,p.Pro563Leu,ENST00000454345,NM_001105540.1;DGKZ,missense_variant,p.Pro391Leu,ENST00000343674,NM_201532.2;DGKZ,missense_variant,p.Pro374Leu,ENST00000456247,NM_001199267.1;DGKZ,missense_variant,p.Pro375Leu,ENST00000527911,NM_001199266.1;DGKZ,missense_variant,p.Pro352Leu,ENST00000318201,NM_001199268.1;DGKZ,missense_variant,p.Pro379Leu,ENST00000532868,NM_201533.3;DGKZ,missense_variant,p.Pro375Leu,ENST00000421244,NM_003646.3;DGKZ,missense_variant,p.Pro153Leu,ENST00000528615,;DGKZ,upstream_gene_variant,,ENST00000524869,;DGKZ,downstream_gene_variant,,ENST00000525242,;DGKZ,downstream_gene_variant,,ENST00000524448,;MIR4688,upstream_gene_variant,,ENST00000577966,;DGKZ,downstream_gene_variant,,ENST00000534215,;DGKZ,upstream_gene_variant,,ENST00000529660,;DGKZ,3_prime_UTR_variant,,ENST00000524984,;DGKZ,non_coding_transcript_exon_variant,,ENST00000528173,;DGKZ,non_coding_transcript_exon_variant,,ENST00000531879,;DGKZ,non_coding_transcript_exon_variant,,ENST00000527903,;DGKZ,upstream_gene_variant,,ENST00000527211,;DGKZ,downstream_gene_variant,,ENST00000527674,;DGKZ,upstream_gene_variant,,ENST00000529698,;DGKZ,downstream_gene_variant,,ENST00000533376,; T ENST00000454345 Transcript missense_variant 1813/4086 1688/3354 563/1117 P/L cCt/cTt 1 1 DGKZ HGNC HGNC:2857 protein_coding YES CCDS41640.1 ENSP00000412178 Q13574 UPI000013DB71 NM_001105540.1 deleterious(0) 14/32 Pfam_domain:PF00781,PROSITE_profiles:PS50146,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF43,SMART_domains:SM00046,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 46372823 46372823 C T 1 0 0 0 0 1 0 0 0 4280 681 24 3 3 DGKZ 11 46372823 Missense_Mutation SNP C C3L-00279_T 9780111 46372823 88713799 391 6169 MTCH2 0 . GRCh38 11 47634717 47634717 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.324T>A p.Asn108Lys p.N108K ENST00000302503 5/13 143 124 19 93 93 0 strelka-varscan-mutect MTCH2,missense_variant,p.Asn108Lys,ENST00000302503,NM_001317231.1,NM_014342.3;MTCH2,missense_variant,p.Asn99Lys,ENST00000530428,;MTCH2,non_coding_transcript_exon_variant,,ENST00000539759,;MTCH2,non_coding_transcript_exon_variant,,ENST00000533571,;MTCH2,intron_variant,,ENST00000525649,; T ENST00000302503 Transcript missense_variant 482/2587 324/912 108/303 N/K aaT/aaA 1 -1 MTCH2 HGNC HGNC:17587 protein_coding YES CCDS7943.1 ENSP00000303222 Q9Y6C9 UPI000006E280 NM_001317231.1,NM_014342.3 tolerated(0.24) 5/13 Superfamily_domains:0048588,Gene3D:1okcA00,hmmpanther:PTHR10780,hmmpanther:PTHR10780:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 47634717 47634717 A T 1 0 0 0 0 1 0 0 0 9899 214 8 4 4 MTCH2 11 47634717 Missense_Mutation SNP A C3L-00279_T 1261894 47634717 87451905 392 6170 PTPRJ 0 . GRCh38 11 48145038 48145038 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2825C>A p.Pro942His p.P942H ENST00000418331 14/25 289 249 40 190 189 1 strelka-varscan-mutect PTPRJ,missense_variant,p.Pro942His,ENST00000613246,;PTPRJ,missense_variant,p.Pro942His,ENST00000418331,NM_002843.3;PTPRJ,missense_variant,p.Pro946His,ENST00000615445,;PTPRJ,upstream_gene_variant,,ENST00000527026,; A ENST00000418331 Transcript missense_variant 3177/5122 2825/4014 942/1337 P/H cCt/cAt 1 1 PTPRJ HGNC HGNC:9673 protein_coding YES CCDS7945.1 ENSP00000400010 Q12913 UPI00004564C8 NM_002843.3 tolerated(0.13) 14/25 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF211 MODERATE 1 SNV 1 1 PASS rs1051417875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 48145038 48145038 C A 1 0 0 0 0 1 0 0 0 12958 681 24 2 2 PTPRJ 11 48145038 Missense_Mutation SNP C C3L-00279_T 510321 48145038 86941584 393 6171 OR5F1 0 . GRCh38 11 55994133 55994133 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.493A>T p.Ser165Cys p.S165C ENST00000278409 1/1 296 266 30 273 273 0 strelka-varscan-mutect OR5F1,missense_variant,p.Ser165Cys,ENST00000278409,NM_003697.1; A ENST00000278409 Transcript missense_variant 493/945 493/945 165/314 S/C Agc/Tgc 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 deleterious(0.05) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 55994133 55994133 T A 1 0 0 0 0 1 0 0 0 11228 1580 55 4 4 OR5F1 11 55994133 Missense_Mutation SNP T C3L-00279_T 7849095 55994133 79092489 394 6172 OR5M8 0 . GRCh38 11 56490585 56490585 + Silent SNP G G A rs760237003 C3L-00279_T C3L-00279_N G G c.786C>T p.= p.P262P ENST00000327216 1/1 177 155 22 65 65 0 strelka-varscan-mutect OR5M8,synonymous_variant,p.=,ENST00000327216,NM_001005282.1; A ENST00000327216 Transcript synonymous_variant 786/936 786/936 262/311 P ccC/ccT rs760237003 1 -1 OR5M8 HGNC HGNC:14846 protein_coding YES CCDS31533.1 ENSP00000323354 Q8NGP6 A0A126GWD6 UPI00000405CC NM_001005282.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF146,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1481959010 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 56490585 56490585 G A 1 0 0 0 0 0 0 0 1 11245 987 35 3 3 OR5M8 11 56490585 Silent SNP G C3L-00279_T 496452 56490585 78596037 395 6173 APLNR 0 . GRCh38 11 57236276 57236276 + Silent SNP C C G novel C3L-00279_T C3L-00279_N C C c.729G>C p.= p.R243R ENST00000606794 1/1 132 122 10 140 140 0 strelka-varscan-mutect APLNR,synonymous_variant,p.=,ENST00000606794,NM_005161.4;APLNR,synonymous_variant,p.=,ENST00000611099,;APLNR,synonymous_variant,p.=,ENST00000257254,; G ENST00000606794 Transcript synonymous_variant 926/3609 729/1143 243/380 R cgG/cgC 1 -1 APLNR HGNC HGNC:339 protein_coding YES CCDS7950.1 ENSP00000475344 P35414 UPI0000001622 NM_005161.4 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF31,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 57236276 57236276 C G 1 0 0 0 0 0 0 0 1 899 726 26 4 4 APLNR 11 57236276 Silent SNP C C3L-00279_T 745691 57236276 77850346 396 6174 OR5B12 0 . GRCh38 11 58439585 58439585 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.567C>A p.Asp189Glu p.D189E ENST00000302572 1/1 166 155 11 104 104 0 strelka-varscan-mutect OR5B12,missense_variant,p.Asp189Glu,ENST00000302572,NM_001004733.2; T ENST00000302572 Transcript missense_variant 589/1054 567/945 189/314 D/E gaC/gaA 1 -1 OR5B12 HGNC HGNC:15432 protein_coding YES CCDS31551.1 ENSP00000306657 Q96R08 UPI00000015B2 NM_001004733.2 tolerated_low_confidence(0.06) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 58439585 58439585 G T 1 0 0 0 0 1 0 0 0 11219 1368 48 2 2 OR5B12 11 58439585 Missense_Mutation SNP G C3L-00279_T 1203309 58439585 76647037 397 6175 MS4A1 0 . GRCh38 11 60464308 60464308 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.300C>A p.= p.L100L ENST00000534668 4/7 415 383 32 247 246 1 strelka-varscan-mutect MS4A1,synonymous_variant,p.=,ENST00000534668,NM_152866.2;MS4A1,synonymous_variant,p.=,ENST00000389939,;MS4A1,synonymous_variant,p.=,ENST00000345732,NM_021950.3;MS4A1,synonymous_variant,p.=,ENST00000532073,;MS4A1,synonymous_variant,p.=,ENST00000533306,;MS4A1,intron_variant,,ENST00000528313,;MS4A1,downstream_gene_variant,,ENST00000532491,;MS4A1,downstream_gene_variant,,ENST00000524807,;MS4A1,non_coding_transcript_exon_variant,,ENST00000534503,;MS4A1,downstream_gene_variant,,ENST00000527101,;MS4A1,upstream_gene_variant,,ENST00000532418,;MS4A1,upstream_gene_variant,,ENST00000530482,; A ENST00000534668 Transcript synonymous_variant 589/3475 300/894 100/297 L ctC/ctA 1 1 MS4A1 HGNC HGNC:7315 protein_coding YES CCDS31570.1 ENSP00000433277 P11836 A0A024R507 UPI000012733B NM_152866.2 4/7 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF79,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 60464308 60464308 C A 1 0 0 0 0 0 0 0 1 9831 842 30 2 2 MS4A1 11 60464308 Silent SNP C C3L-00279_T 2024723 60464308 74622314 398 6176 DDB1 0 . GRCh38 11 61316314 61316314 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1381G>T p.Gly461Cys p.G461C ENST00000301764 12/27 170 157 13 148 148 0 strelka-varscan-mutect DDB1,missense_variant,p.Gly461Cys,ENST00000301764,NM_001923.4;DDB1,intron_variant,,ENST00000543658,;DDB1,non_coding_transcript_exon_variant,,ENST00000545930,;DDB1,intron_variant,,ENST00000538280,;DDB1,missense_variant,p.Gly461Cys,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000539739,;DDB1,non_coding_transcript_exon_variant,,ENST00000535967,;DDB1,non_coding_transcript_exon_variant,,ENST00000537877,;DDB1,non_coding_transcript_exon_variant,,ENST00000540784,;DDB1,non_coding_transcript_exon_variant,,ENST00000535174,;DDB1,upstream_gene_variant,,ENST00000535147,;DDB1,upstream_gene_variant,,ENST00000414411,;DDB1,upstream_gene_variant,,ENST00000539332,;DDB1,downstream_gene_variant,,ENST00000539712,; A ENST00000301764 Transcript missense_variant 1779/4506 1381/3423 461/1140 G/C Ggc/Tgc 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 deleterious(0.04) 12/27 hmmpanther:PTHR10644,Gene3D:2.130.10.10,Pfam_domain:PF10433 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 61316314 61316314 C A 1 0 0 0 0 1 0 0 0 4126 594 21 2 2 DDB1 11 61316314 Missense_Mutation SNP C C3L-00279_T 852006 61316314 73770308 399 6177 AHNAK 0 . GRCh38 11 62517840 62517840 + Missense_Mutation SNP C C G C3L-00279_T C3L-00279_N C C c.16577G>C p.Gly5526Ala p.G5526A ENST00000378024 5/5 242 215 27 224 224 0 strelka-varscan-mutect AHNAK,missense_variant,p.Gly5526Ala,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; G ENST00000378024 Transcript missense_variant 16852/18787 16577/17673 5526/5890 G/A gGt/gCt COSM5263852,COSM5263853 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0.02) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 62517840 62517840 C G 1 0 0 0 0 1 0 0 0 491 507 18 4 4 AHNAK 11 62517840 Missense_Mutation SNP C C3L-00279_T 1201526 62517840 72568782 400 6178 SLC22A8 0 . GRCh38 11 62999786 62999786 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.494C>A p.Ser165Tyr p.S165Y ENST00000336232 4/11 84 72 12 85 85 0 strelka-varscan-mutect SLC22A8,missense_variant,p.Ser165Tyr,ENST00000336232,NM_001184732.1,NM_004254.3;SLC22A8,missense_variant,p.Ser165Tyr,ENST00000430500,;SLC22A8,missense_variant,p.Ser165Tyr,ENST00000311438,;SLC22A8,missense_variant,p.Ser74Tyr,ENST00000545207,NM_001184733.1;SLC22A8,missense_variant,p.Ser42Tyr,ENST00000535878,NM_001184736.1;SLC22A8,non_coding_transcript_exon_variant,,ENST00000542795,;SLC22A8,non_coding_transcript_exon_variant,,ENST00000542904,;SLC22A8,upstream_gene_variant,,ENST00000539841,;SLC22A8,upstream_gene_variant,,ENST00000451262,; T ENST00000336232 Transcript missense_variant 630/2178 494/1629 165/542 S/Y tCc/tAc 1 -1 SLC22A8 HGNC HGNC:10972 protein_coding YES CCDS8042.1 ENSP00000337335 Q8TCC7 UPI0000036DF2 NM_001184732.1,NM_004254.3 deleterious(0) 4/11 Low_complexity_(Seg):seg,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF294,TIGRFAM_domain:TIGR00898,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs1489921809 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 62999786 62999786 G T 1 0 0 0 0 1 0 0 0 14726 1174 41 2 2 SLC22A8 11 62999786 Missense_Mutation SNP G C3L-00279_T 481946 62999786 72086836 401 6179 MARK2 0 . GRCh38 11 63900664 63900664 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.874A>G p.Arg292Gly p.R292G ENST00000402010 9/19 145 126 19 102 102 0 strelka-varscan-mutect MARK2,missense_variant,p.Arg292Gly,ENST00000402010,NM_001039469.2;MARK2,missense_variant,p.Arg259Gly,ENST00000377810,;MARK2,missense_variant,p.Arg292Gly,ENST00000361128,NM_001163296.1;MARK2,missense_variant,p.Arg292Gly,ENST00000508192,NM_004954.4;MARK2,missense_variant,p.Arg292Gly,ENST00000350490,NM_001163297.1;MARK2,missense_variant,p.Arg292Gly,ENST00000502399,;MARK2,missense_variant,p.Arg259Gly,ENST00000509502,NM_017490.3;MARK2,missense_variant,p.Arg259Gly,ENST00000513765,;MARK2,missense_variant,p.Arg259Gly,ENST00000408948,;MARK2,missense_variant,p.Arg259Gly,ENST00000425897,;MARK2,downstream_gene_variant,,ENST00000543220,;MARK2,downstream_gene_variant,,ENST00000540169,;MARK2,upstream_gene_variant,,ENST00000535116,; G ENST00000402010 Transcript missense_variant 1453/4728 874/2367 292/788 R/G Aga/Gga 1 1 MARK2 HGNC HGNC:3332 protein_coding YES CCDS53649.1 ENSP00000385751 Q7KZI7 UPI00004F6F00 NM_001039469.2 deleterious(0) 9/19 PROSITE_profiles:PS50011,hmmpanther:PTHR24346,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 63900664 63900664 A G 1 0 0 0 0 1 0 0 0 9238 296 11 5 5 MARK2 11 63900664 Missense_Mutation SNP A C3L-00279_T 900878 63900664 71185958 402 6180 EHBP1L1 0 . GRCh38 11 65585002 65585002 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.3344A>T p.Glu1115Val p.E1115V ENST00000309295 12/19 217 192 25 245 245 0 strelka-varscan-mutect EHBP1L1,missense_variant,p.Glu1115Val,ENST00000309295,NM_001099409.1;EHBP1L1,missense_variant,p.Glu532Val,ENST00000533237,;EHBP1L1,missense_variant,p.Glu344Val,ENST00000634639,;EHBP1L1,missense_variant,p.Glu165Val,ENST00000533465,;EHBP1L1,intron_variant,,ENST00000529099,;EHBP1L1,downstream_gene_variant,,ENST00000526990,; T ENST00000309295 Transcript missense_variant 3609/5185 3344/4572 1115/1523 E/V gAg/gTg 1 1 EHBP1L1 HGNC HGNC:30682 protein_coding YES CCDS44649.1 ENSP00000312671 Q8N3D4 UPI00001605A9 NM_001099409.1 deleterious(0.02) 12/19 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF295,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 65585002 65585002 A T 1 0 0 0 0 1 0 0 0 4812 304 11 4 4 EHBP1L1 11 65585002 Missense_Mutation SNP A C3L-00279_T 1684338 65585002 69501620 403 6181 NPAS4 0 . GRCh38 11 66424630 66424630 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1740C>A p.Ser580Arg p.S580R ENST00000311034 7/8 223 204 19 212 212 0 strelka-varscan-mutect NPAS4,missense_variant,p.Ser580Arg,ENST00000311034,NM_178864.3;NPAS4,3_prime_UTR_variant,,ENST00000525148,;NPAS4,downstream_gene_variant,,ENST00000524617,; A ENST00000311034 Transcript missense_variant 1916/3303 1740/2409 580/802 S/R agC/agA 1 1 NPAS4 HGNC HGNC:18983 protein_coding YES CCDS8138.1 ENSP00000311196 Q8IUM7 UPI0000074744 NM_178864.3 deleterious(0) 7/8 hmmpanther:PTHR23043:SF24,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 66424630 66424630 C A 1 0 0 0 0 1 0 0 0 10613 738 26 2 2 NPAS4 11 66424630 Missense_Mutation SNP C C3L-00279_T 839628 66424630 68661992 404 6182 NADSYN1 0 . GRCh38 11 71458456 71458456 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.175G>C p.Glu59Gln p.E59Q ENST00000319023 3/21 185 165 20 169 169 0 strelka-varscan-mutect NADSYN1,missense_variant,p.Glu59Gln,ENST00000319023,NM_018161.4;NADSYN1,non_coding_transcript_exon_variant,,ENST00000527538,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000525245,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000533769,;NADSYN1,missense_variant,p.Glu26Gln,ENST00000525200,;NADSYN1,missense_variant,p.Glu59Gln,ENST00000528509,;NADSYN1,missense_variant,p.Glu59Gln,ENST00000529120,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000534634,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000524949,;NADSYN1,downstream_gene_variant,,ENST00000533612,; C ENST00000319023 Transcript missense_variant 363/2773 175/2121 59/706 E/Q Gag/Cag 1 1 NADSYN1 HGNC HGNC:29832 protein_coding YES CCDS8201.1 ENSP00000326424 Q6IA69 UPI00001404C2 NM_018161.4 deleterious(0) 3/21 PROSITE_profiles:PS50263,hmmpanther:PTHR23090:SF9,hmmpanther:PTHR23090,PIRSF_domain:PIRSF006630,Gene3D:3.60.110.10,Pfam_domain:PF00795,Superfamily_domains:SSF56317 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 71458456 71458456 G C 1 0 0 0 0 1 0 0 0 10145 1059 37 4 4 NADSYN1 11 71458456 Missense_Mutation SNP G C3L-00279_T 5033826 71458456 63628166 405 6183 INPPL1 0 . GRCh38 11 72238055 72238055 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.3566A>T p.Gln1189Leu p.Q1189L ENST00000298229 27/28 49 43 6 36 36 0 strelka-varscan-mutect INPPL1,missense_variant,p.Gln1189Leu,ENST00000298229,NM_001567.3;INPPL1,missense_variant,p.Gln947Leu,ENST00000538751,;INPPL1,missense_variant,p.Gln51Leu,ENST00000320683,;INPPL1,synonymous_variant,p.=,ENST00000541756,;INPPL1,intron_variant,,ENST00000541752,;PHOX2A,downstream_gene_variant,,ENST00000298231,NM_005169.3;PHOX2A,downstream_gene_variant,,ENST00000546310,;PHOX2A,downstream_gene_variant,,ENST00000544057,;INPPL1,intron_variant,,ENST00000535985,;INPPL1,downstream_gene_variant,,ENST00000541303,;INPPL1,downstream_gene_variant,,ENST00000545355,; T ENST00000298229 Transcript missense_variant 3770/4733 3566/3777 1189/1258 Q/L cAg/cTg 1 1 INPPL1 HGNC HGNC:6080 protein_coding YES CCDS8213.1 ENSP00000298229 O15357 UPI000013E4AF NM_001567.3 tolerated(0.09) 27/28 MODERATE 1 SNV 1 1 PASS rs1369263812 . 0 206 4 0 0 0 0 0 -14.737 1 1 1 1 0 T 3 4 14 72238055 72238055 A T 1 0 0 0 0 1 0 0 0 7664 188 7 4 4 INPPL1 11 72238055 Missense_Mutation SNP A C3L-00279_T 779599 72238055 62848567 406 6184 CCDC83 0 . GRCh38 11 85916132 85916132 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.1072G>A p.Asp358Asn p.D358N ENST00000280245 11/12 136 127 9 53 53 0 strelka-mutect CCDC83,missense_variant,p.Asp358Asn,ENST00000280245,NM_173556.4;CCDC83,missense_variant,p.Asp327Asn,ENST00000342404,NM_001286159.1;CCDC83,missense_variant,p.Asp232Asn,ENST00000526729,;RP11-90K17.2,downstream_gene_variant,,ENST00000531414,;CCDC83,downstream_gene_variant,,ENST00000529676,; A ENST00000280245 Transcript missense_variant 1584/2358 1072/1335 358/444 D/N Gat/Aat 1 1 CCDC83 HGNC HGNC:28535 protein_coding YES CCDS8271.1 ENSP00000280245 Q8IWF9 UPI00001C098D NM_173556.4 tolerated(0.38) 11/12 hmmpanther:PTHR21468:SF1,hmmpanther:PTHR21468 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 85916132 85916132 G A 1 0 0 0 0 1 0 0 0 2555 942 33 3 3 CCDC83 11 85916132 Missense_Mutation SNP G C3L-00279_T 13678077 85916132 49170490 407 6185 GRM5 0 . GRCh38 11 88597221 88597221 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1526C>A p.Ser509Tyr p.S509Y ENST00000305447 5/9 92 83 9 47 47 0 strelka-varscan-mutect GRM5,missense_variant,p.Ser509Tyr,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Ser509Tyr,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Ser509Tyr,ENST00000305432,; T ENST00000305447 Transcript missense_variant 1676/4571 1526/3639 509/1212 S/Y tCt/tAt 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 5/9 Pfam_domain:PF07562,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 88597221 88597221 G T 1 0 0 0 0 1 0 0 0 6682 942 33 2 2 GRM5 11 88597221 Missense_Mutation SNP G C3L-00279_T 2681089 88597221 46489401 408 6186 TRIM49 0 . GRCh38 11 89798519 89798519 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.970A>T p.Thr324Ser p.T324S ENST00000329758 8/8 208 190 18 154 154 0 varscan-mutect TRIM49,missense_variant,p.Thr324Ser,ENST00000329758,NM_020358.2;TRIM49,missense_variant,p.Thr247Ser,ENST00000532501,; A ENST00000329758 Transcript missense_variant 1299/2163 970/1359 324/452 T/S Aca/Tca 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 tolerated(0.48) 8/8 Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 89798519 89798519 T A 1 0 0 0 0 1 0 0 0 17014 1725 60 4 4 TRIM49 11 89798519 Missense_Mutation SNP T C3L-00279_T 1201298 89798519 45288103 409 6187 KDM4E 0 . GRCh38 11 95026275 95026275 + Silent SNP C C A rs782053839 C3L-00279_T C3L-00279_N C C c.718C>A p.= p.R240R ENST00000450979 1/1 537 463 74 505 504 1 strelka-varscan-mutect KDM4E,synonymous_variant,p.=,ENST00000450979,NM_001161630.1;RP11-60C6.8,upstream_gene_variant,,ENST00000616726,; A ENST00000450979 Transcript synonymous_variant 1018/2339 718/1521 240/506 R Cgg/Agg rs782053839,COSM5316192,COSM5316193 1 1 KDM4E HGNC HGNC:37098 protein_coding YES CCDS44713.1 ENSP00000397239 B2RXH2 UPI00001607E8 NM_001161630.1 1/1 PROSITE_profiles:PS51184,hmmpanther:PTHR10694:SF34,hmmpanther:PTHR10694,Pfam_domain:PF02373,SMART_domains:SM00558,Superfamily_domains:SSF51197 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs782053839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 95026275 95026275 C A 1 0 0 0 0 0 0 0 1 8050 759 27 1 1 KDM4E 11 95026275 Silent SNP C C3L-00279_T 5227756 95026275 40060347 410 6188 DYNC2H1 0 . GRCh38 11 103479122 103479122 + Nonsense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.12814G>T p.Glu4272Ter p.E4272* ENST00000398093 90/90 241 217 24 186 185 1 strelka-varscan-mutect DYNC2H1,stop_gained,p.Glu4265Ter,ENST00000375735,NM_001377.2;DYNC2H1,stop_gained,p.Glu4272Ter,ENST00000398093,NM_001080463.1;DYNC2H1,stop_gained,p.Glu878Ter,ENST00000334267,;DYNC2H1,stop_gained,p.Glu182Ter,ENST00000533197,;DYNC2H1,3_prime_UTR_variant,,ENST00000528670,;DYNC2H1,non_coding_transcript_exon_variant,,ENST00000527252,;DYNC2H1,non_coding_transcript_exon_variant,,ENST00000530547,; T ENST00000398093 Transcript stop_gained 12814/12945 12814/12945 4272/4314 E/* Gag/Tag 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 90/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF03028 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 103479122 103479122 G T 1 0 0 0 0 0 1 0 0 4670 1291 45 2 2 DYNC2H1 11 103479122 Nonsense_Mutation SNP G C3L-00279_T 8452847 103479122 31607500 411 6189 ALG9 0 . GRCh38 11 111837491 111837491 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.1449C>T p.= p.P483P ENST00000616540 12/15 393 350 43 316 316 0 strelka-varscan-mutect ALG9,synonymous_variant,p.=,ENST00000532425,;RP11-108O10.8,synonymous_variant,p.=,ENST00000622211,;ALG9,synonymous_variant,p.=,ENST00000398006,NM_001077692.1;ALG9,synonymous_variant,p.=,ENST00000616540,NM_024740.2;ALG9,synonymous_variant,p.=,ENST00000614444,NM_001077690.1;ALG9,synonymous_variant,p.=,ENST00000531154,NM_001077691.1;ALG9,intron_variant,,ENST00000530851,;ALG9,downstream_gene_variant,,ENST00000527294,;ALG9,upstream_gene_variant,,ENST00000526272,;ALG9,3_prime_UTR_variant,,ENST00000619129,;ALG9,downstream_gene_variant,,ENST00000613181,;ALG9,downstream_gene_variant,,ENST00000527714,; A ENST00000616540 Transcript synonymous_variant 1548/2069 1449/1857 483/618 P ccC/ccT 1 -1 ALG9 HGNC HGNC:15672 protein_coding YES CCDS73380.1 ENSP00000482437 Q9H6U8 UPI000006ED01 NM_024740.2 12/15 Pfam_domain:PF03901,hmmpanther:PTHR22760,hmmpanther:PTHR22760:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 111837491 111837491 G A 1 0 0 0 0 0 0 0 1 624 1335 47 3 3 ALG9 11 111837491 Silent SNP G C3L-00279_T 8358369 111837491 23249131 412 6190 TMPRSS5 0 . GRCh38 11 113693185 113693185 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.850A>T p.Arg284Trp p.R284W ENST00000299882 9/13 112 95 17 105 105 0 strelka-varscan-mutect TMPRSS5,missense_variant,p.Arg284Trp,ENST00000299882,NM_030770.3;TMPRSS5,missense_variant,p.Arg275Trp,ENST00000545579,NM_001288751.1;TMPRSS5,missense_variant,p.Arg25Trp,ENST00000540540,;TMPRSS5,missense_variant,p.Arg240Trp,ENST00000538955,NM_001288750.1;TMPRSS5,missense_variant,p.Arg25Trp,ENST00000536856,;TMPRSS5,missense_variant,p.Arg215Trp,ENST00000544634,NM_001288752.1;TMPRSS5,missense_variant,p.Arg171Trp,ENST00000544476,NM_001288749.1;TMPRSS5,downstream_gene_variant,,ENST00000538770,;TMPRSS5,downstream_gene_variant,,ENST00000539732,;TMPRSS5,non_coding_transcript_exon_variant,,ENST00000545265,;TMPRSS5,non_coding_transcript_exon_variant,,ENST00000545412,; A ENST00000299882 Transcript missense_variant 999/2232 850/1374 284/457 R/W Agg/Tgg 1 -1 TMPRSS5 HGNC HGNC:14908 protein_coding YES CCDS44735.1 ENSP00000299882 Q9H3S3 UPI00001FA3AA NM_030770.3 deleterious(0.05) 9/13 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF144,hmmpanther:PTHR24256,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.999998 1 1 1 0 A 3 1 14 113693185 113693185 T A 1 0 0 0 0 1 0 0 0 16726 1579 55 4 4 TMPRSS5 11 113693185 Missense_Mutation SNP T C3L-00279_T 1855694 113693185 21393437 413 6191 DSCAML1 0 . GRCh38 11 117437208 117437208 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.4814C>A p.Thr1605Lys p.T1605K ENST00000321322 26/33 416 361 55 385 384 1 strelka-varscan-mutect DSCAML1,missense_variant,p.Thr1605Lys,ENST00000321322,NM_020693.3;DSCAML1,missense_variant,p.Thr1335Lys,ENST00000527706,; T ENST00000321322 Transcript missense_variant 4816/6899 4814/6342 1605/2113 T/K aCg/aAg 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 deleterious(0) 26/33 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 117437208 117437208 G T 1 0 0 0 0 1 0 0 0 4590 1145 40 1 1 DSCAML1 11 117437208 Missense_Mutation SNP G C3L-00279_T 3744023 117437208 17649414 414 6192 TRIM29 0 . GRCh38 11 120137656 120137656 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.376G>T p.Glu126Ter p.E126* ENST00000341846 1/9 577 503 74 456 456 0 strelka-varscan-mutect TRIM29,stop_gained,p.Glu126Ter,ENST00000341846,NM_012101.3;TRIM29,missense_variant,p.Arg75Leu,ENST00000627238,;TRIM29,downstream_gene_variant,,ENST00000532833,;TRIM29,downstream_gene_variant,,ENST00000529495,;TRIM29,downstream_gene_variant,,ENST00000529040,;TRIM29,downstream_gene_variant,,ENST00000529011,;TRIM29,missense_variant,p.Arg75Leu,ENST00000475051,; A ENST00000341846 Transcript stop_gained 798/3328 376/1767 126/588 E/* Gag/Tag 1 -1 TRIM29 HGNC HGNC:17274 protein_coding YES CCDS8428.1 ENSP00000343129 Q14134 A0A024R3J1 UPI0000073FDE NM_012101.3 1/9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 120137656 120137656 C A 1 0 0 0 0 0 1 0 0 16992 893 31 1 1 TRIM29 11 120137656 Nonsense_Mutation SNP C C3L-00279_T 2700448 120137656 14948966 415 6193 TECTA 0 . GRCh38 11 121165343 121165343 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.5343G>T p.Arg1781Ser p.R1781S ENST00000392793 17/24 217 189 28 228 228 0 strelka-varscan-mutect TECTA,missense_variant,p.Arg1781Ser,ENST00000392793,;TECTA,missense_variant,p.Arg1781Ser,ENST00000264037,NM_005422.2; T ENST00000392793 Transcript missense_variant 5614/7426 5343/6468 1781/2155 R/S agG/agT 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D tolerated(0.41) 17/24 hmmpanther:PTHR11339:SF235,hmmpanther:PTHR11339 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 121165343 121165343 G T 1 0 0 0 0 1 0 0 0 16158 1223 43 2 2 TECTA 11 121165343 Missense_Mutation SNP G C3L-00279_T 1027687 121165343 13921279 416 6194 VWA5A 0 . GRCh38 11 124123429 124123429 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.994G>A p.Gly332Ser p.G332S ENST00000456829 9/19 181 159 22 152 152 0 strelka-varscan-mutect VWA5A,missense_variant,p.Gly332Ser,ENST00000456829,NM_001130142.1;VWA5A,missense_variant,p.Gly332Ser,ENST00000392748,NM_014622.4;VWA5A,missense_variant,p.Gly348Ser,ENST00000392744,;VWA5A,missense_variant,p.Gly332Ser,ENST00000449321,;VWA5A,missense_variant,p.Gly332Ser,ENST00000361352,NM_198315.2; A ENST00000456829 Transcript missense_variant 1245/4388 994/2361 332/786 G/S Ggc/Agc 1 1 VWA5A HGNC HGNC:6658 protein_coding YES CCDS8444.1 ENSP00000407726 O00534 A0A024R3H3 UPI0000158B80 NM_001130142.1 deleterious(0) 9/19 PROSITE_profiles:PS50234,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF100,Pfam_domain:PF13768,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 124123429 124123429 G A 1 0 0 0 0 1 0 0 0 17796 1348 47 3 3 VWA5A 11 124123429 Missense_Mutation SNP G C3L-00279_T 2958086 124123429 10963193 417 6195 TBRG1 0 . GRCh38 11 124625783 124625783 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.334G>A p.Val112Met p.V112M ENST00000441174 3/9 291 263 28 323 323 0 strelka-varscan-mutect TBRG1,missense_variant,p.Val112Met,ENST00000441174,NM_032811.2;TBRG1,intron_variant,,ENST00000531667,;TBRG1,non_coding_transcript_exon_variant,,ENST00000438907,;TBRG1,non_coding_transcript_exon_variant,,ENST00000452080,;TBRG1,missense_variant,p.Val112Met,ENST00000284290,;TBRG1,missense_variant,p.Val112Met,ENST00000530731,;TBRG1,non_coding_transcript_exon_variant,,ENST00000473629,;TBRG1,intron_variant,,ENST00000529543,;TBRG1,upstream_gene_variant,,ENST00000491010,;TBRG1,upstream_gene_variant,,ENST00000531033,; A ENST00000441174 Transcript missense_variant 538/4004 334/1236 112/411 V/M Gtg/Atg 1 1 TBRG1 HGNC HGNC:29551 protein_coding YES CCDS8448.2 ENSP00000409016 Q3YBR2 UPI000059F045 NM_032811.2 tolerated(0.23) 3/9 hmmpanther:PTHR22715,hmmpanther:PTHR22715:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 124625783 124625783 G A 1 0 0 0 0 1 0 0 0 16053 1377 48 3 3 TBRG1 11 124625783 Missense_Mutation SNP G C3L-00279_T 502354 124625783 10460839 418 6196 ETS1 0 . GRCh38 11 128489297 128489297 + Silent SNP C C G rs202110839 C3L-00279_T C3L-00279_N C C c.528G>C p.= p.L176L ENST00000392668 5/10 183 166 17 154 154 0 strelka-varscan-mutect ETS1,synonymous_variant,p.=,ENST00000392668,NM_001143820.1;ETS1,synonymous_variant,p.=,ENST00000526145,;ETS1,synonymous_variant,p.=,ENST00000319397,NM_005238.3;ETS1,synonymous_variant,p.=,ENST00000531611,;ETS1,intron_variant,,ENST00000535549,NM_001162422.1;ETS1,downstream_gene_variant,,ENST00000608978,; G ENST00000392668 Transcript synonymous_variant 613/5139 528/1458 176/485 L ctG/ctC rs202110839 1 -1 ETS1 HGNC HGNC:3488 protein_coding YES CCDS44767.1 ENSP00000376436 P14921 UPI00001BDB62 NM_001143820.1 5/10 PROSITE_profiles:PS51433,hmmpanther:PTHR11849:SF209,hmmpanther:PTHR11849,PIRSF_domain:PIRSF001698,Pfam_domain:PF02198,Gene3D:1.10.150.50,SMART_domains:SM00251,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS rs202110839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 128489297 128489297 C G 1 0 0 0 0 0 0 0 1 5139 697 25 4 4 ETS1 11 128489297 Silent SNP C C3L-00279_T 3863514 128489297 6597325 419 6197 OPCML 0 . GRCh38 11 132437253 132437253 + Silent SNP G G T rs780275496 C3L-00279_T C3L-00279_N G G c.633C>A p.= p.P211P ENST00000331898 4/7 201 178 23 189 188 1 strelka-varscan-mutect OPCML,synonymous_variant,p.=,ENST00000331898,NM_001319106.1,NM_001319105.1,NM_002545.3;OPCML,synonymous_variant,p.=,ENST00000524381,NM_001012393.1;OPCML,synonymous_variant,p.=,ENST00000541867,;OPCML,synonymous_variant,p.=,ENST00000612177,;OPCML,synonymous_variant,p.=,ENST00000374778,;OPCML,non_coding_transcript_exon_variant,,ENST00000529038,; T ENST00000331898 Transcript synonymous_variant 1212/6833 633/1038 211/345 P ccC/ccA rs780275496,COSM1352679,COSM1352680 1 -1 OPCML HGNC HGNC:8143 protein_coding YES CCDS8492.1 ENSP00000330862 Q14982 A8K0Y0 UPI0000055AE0 NM_001319106.1,NM_001319105.1,NM_002545.3 4/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF107,SMART_domains:SM00409 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs780275496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 132437253 132437253 G T 1 0 0 0 0 0 0 0 1 10951 1103 39 1 1 OPCML 11 132437253 Silent SNP G C3L-00279_T 3947956 132437253 2649369 420 6198 PZP 0 . GRCh38 12 9202588 9202588 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.364C>A p.Leu122Met p.L122M ENST00000261336 3/36 230 208 22 217 217 0 strelka-varscan-mutect PZP,missense_variant,p.Leu122Met,ENST00000261336,NM_002864.2;PZP,missense_variant,p.Leu122Met,ENST00000535230,; T ENST00000261336 Transcript missense_variant 393/4610 364/4449 122/1482 L/M Ctg/Atg 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 deleterious(0.04) 3/36 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 9202588 9202588 G T 1 0 0 0 0 1 0 0 0 13025 1020 36 2 2 PZP 12 9202588 Missense_Mutation SNP G C3L-00279_T 9202588 124072721 421 6199 PDE3A 0 . GRCh38 12 20370145 20370145 + Missense_Mutation SNP G G T rs747321056 C3L-00279_T C3L-00279_N G G c.861G>T p.Lys287Asn p.K287N ENST00000359062 1/16 81 66 15 81 81 0 strelka-varscan-mutect PDE3A,missense_variant,p.Lys287Asn,ENST00000359062,NM_000921.4,NM_001244683.1;RP11-284H19.1,non_coding_transcript_exon_variant,,ENST00000535755,;PDE3A,non_coding_transcript_exon_variant,,ENST00000542675,; T ENST00000359062 Transcript missense_variant 901/7576 861/3426 287/1141 K/N aaG/aaT rs747321056 1 1 PDE3A HGNC HGNC:8778 protein_coding YES CCDS31754.1 ENSP00000351957 Q14432 UPI000014175F NM_000921.4,NM_001244683.1 deleterious(0) 1/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF104 MODERATE 1 SNV 1 1 PASS rs747321056 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 20370145 20370145 G T 1 0 0 0 0 1 0 0 0 11725 933 33 2 2 PDE3A 12 20370145 Missense_Mutation SNP G C3L-00279_T 11167557 20370145 112905164 422 6200 ABCC9 0 . GRCh38 12 21872643 21872643 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.2180G>T p.Gly727Val p.G727V ENST00000261200 16/38 280 244 36 219 219 0 strelka-varscan-mutect ABCC9,missense_variant,p.Gly727Val,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Gly727Val,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Gly354Val,ENST00000544039,;RP11-729I10.2,intron_variant,,ENST00000539874,; A ENST00000261200 Transcript missense_variant 2180/8293 2180/4650 727/1549 G/V gGa/gTa COSM5374868,COSM5374869 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 deleterious(0) 16/38 PROSITE_profiles:PS50893,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,Pfam_domain:PF00005,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 21872643 21872643 C A 1 0 0 0 0 1 0 0 0 63 855 30 2 2 ABCC9 12 21872643 Missense_Mutation SNP C C3L-00279_T 1502498 21872643 111402666 423 6201 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3L-00279_T C3L-00279_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 338 288 50 286 286 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3L-00279_T 3372707 25245350 108029959 424 6202 MMP19 0 . GRCh38 12 55837100 55837100 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.1463C>T p.Pro488Leu p.P488L ENST00000322569 9/9 84 68 16 86 86 0 strelka-varscan-mutect MMP19,missense_variant,p.Pro488Leu,ENST00000322569,NM_002429.5;MMP19,missense_variant,p.Pro465Leu,ENST00000548629,;MMP19,3_prime_UTR_variant,,ENST00000409200,NM_001272101.1;TMEM198B,downstream_gene_variant,,ENST00000478241,;TMEM198B,downstream_gene_variant,,ENST00000508246,;TMEM198B,downstream_gene_variant,,ENST00000482378,;TMEM198B,downstream_gene_variant,,ENST00000471276,;TMEM198B,downstream_gene_variant,,ENST00000487582,;TMEM198B,downstream_gene_variant,,ENST00000636428,;TMEM198B,downstream_gene_variant,,ENST00000636659,;TMEM198B,downstream_gene_variant,,ENST00000635938,;TMEM198B,downstream_gene_variant,,ENST00000637783,;TMEM198B,downstream_gene_variant,,ENST00000637951,;TMEM198B,downstream_gene_variant,,ENST00000636790,;MMP19,downstream_gene_variant,,ENST00000547487,;TMEM198B,downstream_gene_variant,,ENST00000637092,;TMEM198B,downstream_gene_variant,,ENST00000637087,;MMP19,downstream_gene_variant,,ENST00000547299,;MMP19,3_prime_UTR_variant,,ENST00000548882,;MMP19,3_prime_UTR_variant,,ENST00000552872,;MMP19,non_coding_transcript_exon_variant,,ENST00000547685,;MMP19,downstream_gene_variant,,ENST00000552763,;TMEM198B,downstream_gene_variant,,ENST00000484016,; A ENST00000322569 Transcript missense_variant 1555/2229 1463/1527 488/508 P/L cCc/cTc COSM3463270,COSM3463271 1 -1 MMP19 HGNC HGNC:7165 protein_coding YES CCDS8895.1 ENSP00000313437 Q99542 UPI0000030AE6 NM_002429.5 tolerated_low_confidence(0.06) 9/9 Low_complexity_(Seg):seg,PIRSF_domain:PIRSF001191 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 55837100 55837100 G A 1 0 0 0 0 1 0 0 0 9620 1232 43 3 3 MMP19 12 55837100 Missense_Mutation SNP G C3L-00279_T 30591750 55837100 77438209 425 6203 GLI1 0 . GRCh38 12 57464018 57464018 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.120C>A p.Phe40Leu p.F40L ENST00000228682 3/12 211 182 29 238 238 0 strelka-varscan-mutect GLI1,missense_variant,p.Phe40Leu,ENST00000228682,NM_005269.2;GLI1,missense_variant,p.Phe40Leu,ENST00000528432,;GLI1,intron_variant,,ENST00000546141,NM_001167609.1;GLI1,intron_variant,,ENST00000543426,NM_001160045.1;GLI1,intron_variant,,ENST00000528467,;GLI1,intron_variant,,ENST00000532291,;INHBE,downstream_gene_variant,,ENST00000551553,;GLI1,intron_variant,,ENST00000530789,;GLI1,upstream_gene_variant,,ENST00000527742,; A ENST00000228682 Transcript missense_variant 211/3613 120/3321 40/1106 F/L ttC/ttA COSM3812659 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 tolerated(0.38) 3/12 hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 57464018 57464018 C A 1 0 0 0 0 1 0 0 0 6315 912 32 2 2 GLI1 12 57464018 Missense_Mutation SNP C C3L-00279_T 1626918 57464018 75811291 426 6204 CDK4 0 . GRCh38 12 57751647 57751647 + Missense_Mutation SNP C C T rs104894340 C3L-00279_T C3L-00279_N C C c.71G>A p.Arg24His p.R24H ENST00000257904 2/8 702 601 101 660 658 2 strelka-varscan-mutect CDK4,missense_variant,p.Arg24His,ENST00000257904,NM_000075.3;CDK4,missense_variant,p.Arg24His,ENST00000312990,;CDK4,missense_variant,p.Arg24His,ENST00000552254,;CDK4,missense_variant,p.Arg24His,ENST00000552388,;CDK4,missense_variant,p.Arg24His,ENST00000552862,;CDK4,5_prime_UTR_variant,,ENST00000547281,;CDK4,5_prime_UTR_variant,,ENST00000551800,;CDK4,intron_variant,,ENST00000546489,;CDK4,intron_variant,,ENST00000549606,;TSPAN31,downstream_gene_variant,,ENST00000547992,;MARCH9,upstream_gene_variant,,ENST00000266643,NM_138396.5;TSPAN31,downstream_gene_variant,,ENST00000257910,NM_005981.3;TSPAN31,downstream_gene_variant,,ENST00000552816,;TSPAN31,downstream_gene_variant,,ENST00000548167,;TSPAN31,downstream_gene_variant,,ENST00000547472,;CDK4,downstream_gene_variant,,ENST00000547853,;MIR6759,upstream_gene_variant,,ENST00000638110,;CDK4,non_coding_transcript_exon_variant,,ENST00000551888,;TSPAN31,downstream_gene_variant,,ENST00000553221,;CDK4,missense_variant,p.Arg24His,ENST00000553237,;CDK4,missense_variant,p.Arg24His,ENST00000550419,;CDK4,non_coding_transcript_exon_variant,,ENST00000551706,;TSPAN31,downstream_gene_variant,,ENST00000550791,;TSPAN31,downstream_gene_variant,,ENST00000546993,;TSPAN31,downstream_gene_variant,,ENST00000549052,;TSPAN31,downstream_gene_variant,,ENST00000546922,;MARCH9,upstream_gene_variant,,ENST00000552279,;TSPAN31,downstream_gene_variant,,ENST00000553089,;CDK4,upstream_gene_variant,,ENST00000552713,; T ENST00000257904 Transcript missense_variant 437/2076 71/912 24/303 R/H cGt/cAt rs104894340,CM980320,KinMutBase_CDK4_DNA:g.1072G>A,COSM1989836 1 -1 CDK4 HGNC HGNC:1773 protein_coding YES CCDS8953.1 ENSP00000257904 P11802 A0A024RBB6 UPI0000113582 NM_000075.3 deleterious(0) 2/8 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF129,SMART_domains:SM00220,Superfamily_domains:SSF56112 risk_factor 0,0,0,1 MODERATE 1 SNV 1 1,1,0,1 1 PASS rs104894340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 57751647 57751647 C T 1 0 0 0 0 1 0 0 0 2845 536 19 1 1 CDK4 12 57751647 Missense_Mutation SNP C C3L-00279_T 287629 57751647 75523662 427 6205 NAP1L1 0 . GRCh38 12 76055084 76055084 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.565G>C p.Asp189His p.D189H ENST00000618691 8/15 70 57 13 32 32 0 strelka-varscan-mutect NAP1L1,missense_variant,p.Asp189His,ENST00000618691,;NAP1L1,missense_variant,p.Asp189His,ENST00000261182,NM_139207.2,NM_004537.4;NAP1L1,missense_variant,p.Asp121His,ENST00000431879,;NAP1L1,missense_variant,p.Asp183His,ENST00000552056,;NAP1L1,missense_variant,p.Asp126His,ENST00000547773,;NAP1L1,missense_variant,p.Asp189His,ENST00000393263,;NAP1L1,missense_variant,p.Asp189His,ENST00000549596,;NAP1L1,missense_variant,p.Asp189His,ENST00000535020,NM_001307924.1;NAP1L1,missense_variant,p.Asp147His,ENST00000542344,;NAP1L1,missense_variant,p.Asp6His,ENST00000544816,;NAP1L1,missense_variant,p.Asp200His,ENST00000552342,;NAP1L1,missense_variant,p.Asp148His,ENST00000548044,;NAP1L1,missense_variant,p.Asp189His,ENST00000551992,;NAP1L1,missense_variant,p.Asp162His,ENST00000550934,;NAP1L1,missense_variant,p.Asp148His,ENST00000548273,;NAP1L1,missense_variant,p.Asp195His,ENST00000551600,;NAP1L1,missense_variant,p.Asp196His,ENST00000547704,;NAP1L1,downstream_gene_variant,,ENST00000547479,;NAP1L1,downstream_gene_variant,,ENST00000551524,;NAP1L1,missense_variant,p.Asp150His,ENST00000552147,;NAP1L1,missense_variant,p.Asp129His,ENST00000547529,;NAP1L1,non_coding_transcript_exon_variant,,ENST00000547993,;NAP1L1,downstream_gene_variant,,ENST00000549988,;NAP1L1,upstream_gene_variant,,ENST00000547969,;RP11-290L1.4,upstream_gene_variant,,ENST00000552477,; G ENST00000618691 Transcript missense_variant 1052/13505 565/1176 189/391 D/H Gat/Cat 1 -1 NAP1L1 HGNC HGNC:7637 protein_coding YES CCDS9013.1 ENSP00000477538 P55209 A0A024RBB7 UPI0000052A55 deleterious(0) 8/15 hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF70,Pfam_domain:PF00956,Superfamily_domains:SSF143113 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 76055084 76055084 C G 1 0 0 0 0 1 0 0 0 10165 884 31 4 4 NAP1L1 12 76055084 Missense_Mutation SNP C C3L-00279_T 18303437 76055084 57220225 428 6206 NTS 0 . GRCh38 12 85878424 85878424 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.215C>G p.Ala72Gly p.A72G ENST00000256010 3/4 139 122 17 62 62 0 strelka-mutect NTS,missense_variant,p.Ala72Gly,ENST00000256010,NM_006183.4;NTS,intron_variant,,ENST00000551529,;NTS,non_coding_transcript_exon_variant,,ENST00000550879,; G ENST00000256010 Transcript missense_variant 322/1237 215/513 72/170 A/G gCt/gGt 1 1 NTS HGNC HGNC:8038 protein_coding YES CCDS9029.1 ENSP00000256010 P30990 Q6FH20 UPI0000000CAD NM_006183.4 tolerated(0.17) 3/4 PD016590,Pfam_domain:PF07421,Prints_domain:PR01668,hmmpanther:PTHR15356,hmmpanther:PTHR15356:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 85878424 85878424 C G 1 0 0 0 0 1 0 0 0 10775 797 28 4 4 NTS 12 85878424 Missense_Mutation SNP C C3L-00279_T 9823340 85878424 47396885 429 6207 GNPTAB 0 . GRCh38 12 101760145 101760145 + Splice_Site SNP T T C novel C3L-00279_T C3L-00279_N T T c.3136-2A>G p.X1046_splice ENST00000299314 260 222 38 98 98 0 strelka-varscan-mutect GNPTAB,splice_acceptor_variant,,ENST00000299314,NM_024312.4;GNPTAB,upstream_gene_variant,,ENST00000550718,;GNPTAB,upstream_gene_variant,,ENST00000549194,;GNPTAB,upstream_gene_variant,,ENST00000549738,; C ENST00000299314 Transcript splice_acceptor_variant -/5701 3136/3771 1046/1256 1 -1 GNPTAB HGNC HGNC:29670 protein_coding YES CCDS9088.1 ENSP00000299314 Q3T906 UPI000004CC0C NM_024312.4 15/20 HIGH 1 SNV 1 1 PASS rs1367040986 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 5 2 14 101760145 101760145 T C 1 0 0 0 0 0 0 1 0 6424 1536 53 5 5 GNPTAB 12 101760145 Splice_Site SNP T C3L-00279_T 15881721 101760145 31515164 430 6208 TCP11L2 0 . GRCh38 12 106329347 106329347 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.790G>T p.Gly264Cys p.G264C ENST00000547153 7/7 243 208 35 243 243 0 strelka-varscan-mutect TCP11L2,missense_variant,p.Gly264Cys,ENST00000547153,NM_001286262.1;TCP11L2,intron_variant,,ENST00000299045,NM_152772.2;TCP11L2,downstream_gene_variant,,ENST00000546625,; T ENST00000547153 Transcript missense_variant 964/1788 790/801 264/266 G/C Ggt/Tgt 1 1 TCP11L2 HGNC HGNC:28627 protein_coding CCDS66456.1 ENSP00000448952 Q8N4U5 UPI000013F7D0 NM_001286262.1 tolerated_low_confidence(0.11) 7/7 hmmpanther:PTHR12832,hmmpanther:PTHR12832:SF17 MODERATE SNV 2 1 PASS rs1001046838 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 106329347 106329347 G T 1 0 0 0 0 1 0 0 0 16122 1000 35 2 2 TCP11L2 12 106329347 Missense_Mutation SNP G C3L-00279_T 4569202 106329347 26945962 431 6209 MAPKAPK5 0 . GRCh38 12 111885932 111885932 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.865C>G p.Pro289Ala p.P289A ENST00000551404 10/14 205 168 37 176 176 0 strelka-varscan-mutect MAPKAPK5,missense_variant,p.Pro289Ala,ENST00000550735,NM_003668.3;MAPKAPK5,missense_variant,p.Pro289Ala,ENST00000551404,NM_139078.2;MAPKAPK5,missense_variant,p.Pro140Ala,ENST00000549875,;MAPKAPK5,3_prime_UTR_variant,,ENST00000553053,;MAPKAPK5,non_coding_transcript_exon_variant,,ENST00000552111,;MAPKAPK5,upstream_gene_variant,,ENST00000547067,;MAPKAPK5,upstream_gene_variant,,ENST00000547915,; G ENST00000551404 Transcript missense_variant 973/1630 865/1422 289/473 P/A Ccg/Gcg 1 1 MAPKAPK5 HGNC HGNC:6889 protein_coding YES CCDS44975.1 ENSP00000449381 Q8IW41 UPI0000161429 NM_139078.2 tolerated(0.07) 10/14 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24349,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs1028263034 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 111885932 111885932 C G 1 0 0 0 0 1 0 0 0 9215 507 18 4 4 MAPKAPK5 12 111885932 Missense_Mutation SNP C C3L-00279_T 5556585 111885932 21389377 432 6210 TMEM132D 0 . GRCh38 12 129074561 129074561 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.2614T>A p.Leu872Ile p.L872I ENST00000422113 9/9 330 283 47 321 321 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Leu872Ile,ENST00000422113,NM_133448.2;TMEM132D,missense_variant,p.Leu410Ile,ENST00000389441,; T ENST00000422113 Transcript missense_variant 2941/5776 2614/3300 872/1099 L/I Tta/Ata 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 tolerated(0.31) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 129074561 129074561 A T 1 0 0 0 0 1 0 0 0 16492 11 1 4 4 TMEM132D 12 129074561 Missense_Mutation SNP A C3L-00279_T 17188629 129074561 4200748 433 6211 TMEM132D 0 . GRCh38 12 129699937 129699937 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.841C>T p.= p.L281L ENST00000422113 2/9 426 358 68 431 431 0 strelka-varscan-mutect TMEM132D,synonymous_variant,p.=,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript synonymous_variant 1168/5776 841/3300 281/1099 L Ctg/Ttg 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 129699937 129699937 G A 1 0 0 0 0 0 0 0 1 16492 991 35 3 3 TMEM132D 12 129699937 Silent SNP G C3L-00279_T 625376 129699937 3575372 434 6212 RIMBP2 0 . GRCh38 12 130399721 130399721 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.3090C>A p.= p.S1030S ENST00000261655 18/19 205 187 18 167 167 0 strelka-varscan-mutect RIMBP2,synonymous_variant,p.=,ENST00000261655,NM_015347.4;RIMBP2,downstream_gene_variant,,ENST00000536632,;RIMBP2,3_prime_UTR_variant,,ENST00000540658,; T ENST00000261655 Transcript synonymous_variant 3254/6321 3090/3159 1030/1052 S tcC/tcA 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 18/19 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18 LOW 1 SNV 1 1 PASS rs1216897016 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 130399721 130399721 G T 1 0 0 0 0 0 0 0 1 13538 1219 43 2 2 RIMBP2 12 130399721 Silent SNP G C3L-00279_T 699784 130399721 2875588 435 6213 NUP58 0 . GRCh38 13 25315398 25315398 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.616G>T p.Ala206Ser p.A206S ENST00000381736 6/16 175 143 32 95 95 0 strelka-varscan-mutect NUP58,missense_variant,p.Ala206Ser,ENST00000463407,;NUP58,missense_variant,p.Ala206Ser,ENST00000381736,NM_014089.3;NUP58,missense_variant,p.Ala194Ser,ENST00000381718,NM_001008564.1;NUP58,missense_variant,p.Ala206Ser,ENST00000381747,;NUP58,missense_variant,p.Ala153Ser,ENST00000394327,;NUP58,non_coding_transcript_exon_variant,,ENST00000466694,;NUP58,non_coding_transcript_exon_variant,,ENST00000495460,;NUP58,upstream_gene_variant,,ENST00000476553,;NUP58,downstream_gene_variant,,ENST00000490231,;NUP58,downstream_gene_variant,,ENST00000465068,; T ENST00000381736 Transcript missense_variant 866/4332 616/1800 206/599 A/S Gca/Tca 1 1 NUP58 HGNC HGNC:20261 protein_coding YES CCDS9314.1 ENSP00000371155 Q9BVL2 UPI000006D9D4 NM_014089.3 tolerated(0.11) 6/16 Low_complexity_(Seg):seg,hmmpanther:PTHR13437,Pfam_domain:PF15967 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 25315398 25315398 G T 1 0 0 0 0 1 0 0 0 10833 971 34 2 2 NUP58 13 25315398 Missense_Mutation SNP G C3L-00279_T 25315398 89048930 436 6214 ALOX5AP 0 . GRCh38 13 30735550 30735550 + Splice_Site SNP G G T novel C3L-00279_T C3L-00279_N G G c.117-1G>T p.X39_splice ENST00000617770 188 162 26 138 138 0 strelka-varscan-mutect ALOX5AP,splice_acceptor_variant,,ENST00000617770,NM_001204406.1;ALOX5AP,5_prime_UTR_variant,,ENST00000380490,NM_001629.3; T ENST00000617770 Transcript splice_acceptor_variant -/1224 117/657 39/218 1 1 ALOX5AP HGNC HGNC:436 protein_coding YES CCDS73558.1 ENSP00000479870 A0A087WW23 UPI0000E00F64 NM_001204406.1 1/5 HIGH 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999536 1 1 1 0 T 5 4 14 30735550 30735550 G T 1 0 0 0 0 0 0 1 0 641 1014 35 2 2 ALOX5AP 13 30735550 Splice_Site SNP G C3L-00279_T 5420152 30735550 83628778 437 6215 HTR2A 0 . GRCh38 13 46835323 46835323 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.930G>T p.Arg310Ser p.R310S ENST00000542664 4/4 338 293 45 329 328 1 strelka-varscan-mutect HTR2A,missense_variant,p.Arg310Ser,ENST00000542664,NM_000621.4;HTR2A,missense_variant,p.Arg310Ser,ENST00000378688,;HTR2A,missense_variant,p.Arg226Ser,ENST00000543956,NM_001165947.2; A ENST00000542664 Transcript missense_variant 1661/5429 930/1416 310/471 R/S agG/agT 1 -1 HTR2A HGNC HGNC:5293 protein_coding YES CCDS9405.1 ENSP00000437737 P28223 UPI000000126E NM_000621.4 deleterious(0.02) 4/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF30,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 46835323 46835323 C A 1 0 0 0 0 1 0 0 0 7337 854 30 2 2 HTR2A 13 46835323 Missense_Mutation SNP C C3L-00279_T 16099773 46835323 67529005 438 6216 PCDH17 0 . GRCh38 13 57632591 57632591 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.45C>A p.= p.A15A ENST00000377918 1/4 317 280 37 416 412 4 strelka-varscan-mutect PCDH17,synonymous_variant,p.=,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,downstream_gene_variant,,ENST00000610846,;PCDH17,synonymous_variant,p.=,ENST00000484979,; A ENST00000377918 Transcript synonymous_variant 780/8232 45/3480 15/1159 A gcC/gcA 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 1/4 Gene3D:2.60.40.60,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,Cleavage_site_(Signalp):SignalP-noTM,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 57632591 57632591 C A 1 0 0 0 0 0 0 0 1 11599 610 22 2 2 PCDH17 13 57632591 Silent SNP C C3L-00279_T 10797268 57632591 56731737 439 6217 TBC1D4 0 . GRCh38 13 75362202 75362202 + Missense_Mutation SNP C C T rs766539297 C3L-00279_T C3L-00279_N C C c.904G>A p.Glu302Lys p.E302K ENST00000377636 2/21 462 409 53 448 448 0 strelka-varscan-mutect TBC1D4,missense_variant,p.Glu302Lys,ENST00000377636,NM_014832.3;TBC1D4,missense_variant,p.Glu302Lys,ENST00000431480,NM_001286658.1;TBC1D4,missense_variant,p.Glu302Lys,ENST00000377625,NM_001286659.1; T ENST00000377636 Transcript missense_variant 1251/6364 904/3897 302/1298 E/K Gaa/Aaa rs766539297,COSM4561933 1 -1 TBC1D4 HGNC HGNC:19165 protein_coding YES CCDS41901.1 ENSP00000366863 O60343 UPI00001AE7B3 NM_014832.3 deleterious(0.01) 2/21 SMART_domains:SM00462 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs766539297 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 75362202 75362202 C T 1 0 0 0 0 1 0 0 0 16027 864 30 3 3 TBC1D4 13 75362202 Missense_Mutation SNP C C3L-00279_T 17729611 75362202 39002126 440 6218 CCDC168 0 . GRCh38 13 102735250 102735250 + Silent SNP C C T rs111548184 C3L-00279_T C3L-00279_N C C c.15447G>A p.= p.A5149A ENST00000322527 4/4 283 237 46 143 143 0 strelka-varscan-mutect CCDC168,synonymous_variant,p.=,ENST00000322527,NM_001146197.1; T ENST00000322527 Transcript synonymous_variant 15585/21466 15447/21246 5149/7081 A gcG/gcA rs111548184,COSM3384710,COSM3384711 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 Pfam_domain:PF15804,hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 0,1,1 LOW 1 SNV 3 0,1,1 1 PASS rs111548184 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 102735250 102735250 C T 1 0 0 0 0 0 0 0 1 2484 639 23 1 1 CCDC168 13 102735250 Silent SNP C C3L-00279_T 27373048 102735250 11629078 441 6219 SLC10A2 0 . GRCh38 13 103051308 103051308 + Frame_Shift_Del DEL C C - rs758439886 C3L-00279_T C3L-00279_N C C c.710delG p.Gly237ValfsTer69 p.G237Vfs*69 ENST00000245312 4/6 362 305 57 362 362 0 sindel-varindel-pindel SLC10A2,frameshift_variant,p.Gly237ValfsTer69,ENST00000245312,NM_000452.2; - ENST00000245312 Transcript frameshift_variant 1307/3779 710/1047 237/348 G/X gGt/gt rs758439886 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 4/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 103051308 103051308 C - 1 0 1 0 1 0 0 0 0 14639 507 18 0 0 SLC10A2 13 103051308 Frame_Shift_Del DEL C C3L-00279_T 316058 103051308 11313020 442 6220 COL4A2 0 . GRCh38 13 110430571 110430571 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.612G>T p.= p.V204V ENST00000360467 10/48 443 388 55 462 462 0 strelka-varscan-mutect COL4A2,synonymous_variant,p.=,ENST00000360467,NM_001846.2;RP11-291I6.2,downstream_gene_variant,,ENST00000619688,;COL4A2,non_coding_transcript_exon_variant,,ENST00000462309,; T ENST00000360467 Transcript synonymous_variant 918/6281 612/5139 204/1712 V gtG/gtT 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 10/48 hmmpanther:PTHR24023:SF588,hmmpanther:PTHR24023,Pfam_domain:PF01391 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 110430571 110430571 G T 1 0 0 0 0 0 0 0 1 3479 1335 47 2 2 COL4A2 13 110430571 Silent SNP G C3L-00279_T 7379263 110430571 3933757 443 6221 OR4Q3 0 . GRCh38 14 19748029 19748029 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.602T>G p.Ile201Arg p.I201R ENST00000331723 1/1 398 354 44 327 327 0 strelka-varscan-mutect OR4Q3,missense_variant,p.Ile201Arg,ENST00000331723,NM_172194.1;OR4N2,intron_variant,,ENST00000557414,; G ENST00000331723 Transcript missense_variant 602/942 602/942 201/313 I/R aTa/aGa 1 1 OR4Q3 HGNC HGNC:15426 protein_coding YES CCDS32020.1 ENSP00000330049 Q8NH05 A0A126GW32 UPI0000061EF0 NM_172194.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF208,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 19748029 19748029 T G 1 0 0 0 0 1 0 0 0 11157 1406 49 5 5 OR4Q3 14 19748029 Missense_Mutation SNP T C3L-00279_T 19748029 87295689 444 6222 TTC5 0 . GRCh38 14 20299413 20299413 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.432G>T p.Met144Ile p.M144I ENST00000258821 4/10 348 312 36 418 416 2 strelka-varscan-mutect TTC5,missense_variant,p.Met144Ile,ENST00000258821,NM_138376.2;TTC5,downstream_gene_variant,,ENST00000553828,;TTC5,missense_variant,p.Gly122Cys,ENST00000383029,;TTC5,non_coding_transcript_exon_variant,,ENST00000554157,;TTC5,downstream_gene_variant,,ENST00000557379,; A ENST00000258821 Transcript missense_variant 489/4779 432/1323 144/440 M/I atG/atT 1 -1 TTC5 HGNC HGNC:19274 protein_coding YES CCDS9546.1 ENSP00000258821 Q8N0Z6 UPI000013D00B NM_138376.2 deleterious(0.01) 4/10 Gene3D:1.25.40.10,hmmpanther:PTHR26312,hmmpanther:PTHR26312:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 20299413 20299413 C A 1 0 0 0 0 1 0 0 0 17220 594 21 2 2 TTC5 14 20299413 Missense_Mutation SNP C C3L-00279_T 551384 20299413 86744305 445 6223 RPGRIP1 0 . GRCh38 14 21294705 21294705 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.114G>T p.Leu38Phe p.L38F ENST00000400017 2/24 228 207 21 158 158 0 strelka-varscan-mutect RPGRIP1,missense_variant,p.Leu38Phe,ENST00000400017,NM_020366.3;RPGRIP1,missense_variant,p.Leu38Phe,ENST00000557771,;RPGRIP1,missense_variant,p.Leu38Phe,ENST00000556336,; T ENST00000400017 Transcript missense_variant 114/3940 114/3861 38/1286 L/F ttG/ttT COSM416251,COSM4808846 1 1 RPGRIP1 HGNC HGNC:13436 protein_coding YES CCDS45080.1 ENSP00000382895 Q96KN7 UPI0000071B81 NM_020366.3 tolerated(0.05) 2/24 hmmpanther:PTHR14240:SF3,hmmpanther:PTHR14240 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 21294705 21294705 G T 1 0 0 0 0 1 0 0 0 13801 1281 45 2 2 RPGRIP1 14 21294705 Missense_Mutation SNP G C3L-00279_T 995292 21294705 85749013 446 6224 PABPN1 0 . GRCh38 14 23322255 23322255 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.426G>T p.Glu142Asp p.E142D ENST00000216727 2/7 372 319 53 333 333 0 strelka-varscan-mutect PABPN1,missense_variant,p.Glu142Asp,ENST00000397276,;PABPN1,missense_variant,p.Glu142Asp,ENST00000216727,NM_004643.3;BCL2L2-PABPN1,missense_variant,p.Glu169Asp,ENST00000557008,;BCL2L2-PABPN1,missense_variant,p.Glu169Asp,ENST00000553781,NM_001199864.1;PABPN1,missense_variant,p.Glu14Asp,ENST00000556821,;PABPN1,missense_variant,p.Glu14Asp,ENST00000557702,;PABPN1,upstream_gene_variant,,ENST00000555295,;BCL2L2-PABPN1,downstream_gene_variant,,ENST00000556100,;PABPN1,non_coding_transcript_exon_variant,,ENST00000556809,;PABPN1,upstream_gene_variant,,ENST00000553960,;PABPN1,upstream_gene_variant,,ENST00000554062,; T ENST00000216727 Transcript missense_variant 607/2001 426/921 142/306 E/D gaG/gaT 1 1 PABPN1 HGNC HGNC:8565 protein_coding YES CCDS9592.1 ENSP00000216727 Q86U42 UPI000006F6E7 NM_004643.3 tolerated(0.06) 2/7 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 23322255 23322255 G T 1 0 0 0 0 1 0 0 0 11446 991 35 2 2 PABPN1 14 23322255 Missense_Mutation SNP G C3L-00279_T 2027550 23322255 83721463 447 6225 JPH4 0 . GRCh38 14 23571283 23571283 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1448G>T p.Gly483Val p.G483V ENST00000397118 6/7 75 65 10 88 88 0 strelka-varscan-mutect JPH4,missense_variant,p.Gly483Val,ENST00000397118,NM_032452.2;JPH4,missense_variant,p.Gly483Val,ENST00000356300,NM_001146028.1;JPH4,missense_variant,p.Gly484Val,ENST00000622501,;JPH4,missense_variant,p.Gly148Val,ENST00000544177,;AP1G2,upstream_gene_variant,,ENST00000308724,NM_001282475.1;AP1G2,upstream_gene_variant,,ENST00000397120,NM_001282474.1,NM_003917.4;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000556843,;RP11-66N24.3,downstream_gene_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000460049,;AP1G2,upstream_gene_variant,,ENST00000465445,;AP1G2,upstream_gene_variant,,ENST00000535852,;JPH4,downstream_gene_variant,,ENST00000553505,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000554312,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000554816,; A ENST00000397118 Transcript missense_variant 2351/4386 1448/1887 483/628 G/V gGa/gTa 1 -1 JPH4 HGNC HGNC:20156 protein_coding YES CCDS9603.1 ENSP00000380307 Q96JJ6 UPI00001C1F68 NM_032452.2 tolerated(0.08) 6/7 hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF14,PIRSF_domain:PIRSF037387 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99667 1 1 1 1 0 A 3 1 14 23571283 23571283 C A 1 0 0 0 0 1 0 0 0 7875 855 30 2 2 JPH4 14 23571283 Missense_Mutation SNP C C3L-00279_T 249028 23571283 83472435 448 6226 DHRS2 0 . GRCh38 14 23639004 23639004 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.140G>T p.Gly47Val p.G47V ENST00000344777 2/9 123 110 13 129 129 0 strelka-varscan-mutect DHRS2,missense_variant,p.Gly47Val,ENST00000250383,NM_005794.3;DHRS2,missense_variant,p.Gly47Val,ENST00000344777,NM_182908.4;DHRS2,missense_variant,p.Gly47Val,ENST00000611765,;DHRS2,missense_variant,p.Gly47Val,ENST00000432832,;DHRS2,upstream_gene_variant,,ENST00000557535,;DHRS2,upstream_gene_variant,,ENST00000553600,;DHRS2,splice_region_variant,,ENST00000553896,;DHRS2,splice_region_variant,,ENST00000556729,;DHRS2,splice_region_variant,,ENST00000556701,;DHRS2,upstream_gene_variant,,ENST00000556550,; T ENST00000344777 Transcript missense_variant,splice_region_variant 578/1678 140/903 47/300 G/V gGg/gTg 1 1 DHRS2 HGNC HGNC:18349 protein_coding YES CCDS41927.1 ENSP00000344674 Q13268 UPI00001A3E34 NM_182908.4 deleterious(0) 2/9 hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF322,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735,Prints_domain:PR00081 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 23639004 23639004 G T 1 0 0 0 0 1 0 0 0 4295 1246 43 2 2 DHRS2 14 23639004 Missense_Mutation SNP G C3L-00279_T 67721 23639004 83404714 449 6227 SCFD1 0 . GRCh38 14 30633981 30633981 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.256G>T p.Val86Phe p.V86F ENST00000458591 4/25 96 89 7 52 52 0 strelka-mutect SCFD1,missense_variant,p.Val86Phe,ENST00000458591,NM_016106.3;SCFD1,missense_variant,p.Val19Phe,ENST00000544052,NM_182835.2;SCFD1,missense_variant,p.Val61Phe,ENST00000557076,;SCFD1,5_prime_UTR_variant,,ENST00000396629,NM_001283032.1,NM_001283033.1,NM_001283031.1,NM_001257376.1;SCFD1,intron_variant,,ENST00000553693,;SCFD1,missense_variant,p.Val19Phe,ENST00000484733,;SCFD1,missense_variant,p.Val86Phe,ENST00000311943,;SCFD1,missense_variant,p.Val66Phe,ENST00000554776,;SCFD1,missense_variant,p.Val61Phe,ENST00000557713,;SCFD1,3_prime_UTR_variant,,ENST00000463622,;SCFD1,intron_variant,,ENST00000556768,;SCFD1,intron_variant,,ENST00000555259,;SCFD1,upstream_gene_variant,,ENST00000556534,;SCFD1,downstream_gene_variant,,ENST00000556413,; T ENST00000458591 Transcript missense_variant 483/2359 256/1929 86/642 V/F Gtt/Ttt 1 1 SCFD1 HGNC HGNC:20726 protein_coding YES CCDS9639.1 ENSP00000390783 Q8WVM8 UPI000013C6E3 NM_016106.3 deleterious(0) 4/25 Gene3D:3.40.50.2060,Pfam_domain:PF00995,PIRSF_domain:PIRSF005715,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF2,Superfamily_domains:SSF56815 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30633981 30633981 G T 1 0 0 0 0 1 0 0 0 14155 1377 48 2 2 SCFD1 14 30633981 Missense_Mutation SNP G C3L-00279_T 6994977 30633981 76409737 450 6228 PYGL 0 . GRCh38 14 50910016 50910016 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2056G>T p.Gly686Trp p.G686W ENST00000216392 17/20 548 498 50 493 493 0 strelka-varscan-mutect PYGL,missense_variant,p.Gly686Trp,ENST00000216392,NM_002863.4;PYGL,missense_variant,p.Gly686Trp,ENST00000532462,;PYGL,missense_variant,p.Gly652Trp,ENST00000544180,NM_001163940.1;RP11-218E20.5,upstream_gene_variant,,ENST00000557343,;PYGL,non_coding_transcript_exon_variant,,ENST00000532107,; A ENST00000216392 Transcript missense_variant 2389/3048 2056/2544 686/847 G/W Ggg/Tgg 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 deleterious(0) 17/20 hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF12,TIGRFAM_domain:TIGR02093,Gene3D:3.40.50.2000,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 50910016 50910016 C A 1 0 0 0 0 1 0 0 0 13015 594 21 2 2 PYGL 14 50910016 Missense_Mutation SNP C C3L-00279_T 20276035 50910016 56133702 451 6229 DACT1 0 . GRCh38 14 58646706 58646706 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.2083C>A p.= p.R695R ENST00000335867 4/4 203 188 15 253 253 0 strelka-varscan-mutect DACT1,synonymous_variant,p.=,ENST00000395153,NM_001079520.1;DACT1,synonymous_variant,p.=,ENST00000541264,;DACT1,synonymous_variant,p.=,ENST00000335867,NM_016651.5;DACT1,synonymous_variant,p.=,ENST00000556859,;DACT1,downstream_gene_variant,,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,; A ENST00000335867 Transcript synonymous_variant 2107/2571 2083/2511 695/836 R Cgg/Agg 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 58646706 58646706 C A 1 0 0 0 0 0 0 0 1 4023 643 23 1 1 DACT1 14 58646706 Silent SNP C C3L-00279_T 7736690 58646706 48397012 452 6230 C14orf39 0 . GRCh38 14 60485072 60485072 + Missense_Mutation SNP C C G rs142135991 C3L-00279_T C3L-00279_N C C c.7G>C p.Asp3His p.D3H ENST00000321731 2/18 93 86 7 61 61 0 strelka-mutect C14orf39,missense_variant,p.Asp3His,ENST00000321731,NM_174978.2;C14orf39,missense_variant,p.Asp3His,ENST00000556799,;C14orf39,intron_variant,,ENST00000555476,;C14orf39,missense_variant,p.Asp3His,ENST00000557138,; G ENST00000321731 Transcript missense_variant 167/2813 7/1764 3/587 D/H Gac/Cac rs142135991 1 -1 C14orf39 HGNC HGNC:19849 protein_coding YES CCDS9746.1 ENSP00000324920 Q8N1H7 UPI0000140C15 NM_174978.2 deleterious(0.02) 2/18 hmmpanther:PTHR35449 MODERATE 1 SNV 1 1 PASS rs142135991 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 60485072 60485072 C G 1 0 0 0 0 1 0 0 0 1839 826 29 4 4 C14orf39 14 60485072 Missense_Mutation SNP C C3L-00279_T 1838366 60485072 46558646 453 6231 SYT16 0 . GRCh38 14 62100618 62100618 + Missense_Mutation SNP A A T rs769941155 C3L-00279_T C3L-00279_N A A c.1849A>T p.Ser617Cys p.S617C ENST00000568344 6/6 352 315 37 289 288 1 strelka-varscan-mutect SYT16,missense_variant,p.Ser617Cys,ENST00000568344,NM_031914.2;SYT16,missense_variant,p.Ser175Cys,ENST00000430451,;RP11-355I22.2,downstream_gene_variant,,ENST00000554252,;SYT16,3_prime_UTR_variant,,ENST00000555409,; T ENST00000568344 Transcript missense_variant 2046/13978 1849/1938 617/645 S/C Agt/Tgt rs769941155 1 1 SYT16 HGNC HGNC:23142 protein_coding YES CCDS45121.1 ENSP00000478637 Q17RD7 UPI0000EE1AC0 NM_031914.2 deleterious(0) 6/6 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF113,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs769941155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 62100618 62100618 A T 1 0 0 0 0 1 0 0 0 15866 188 7 4 4 SYT16 14 62100618 Missense_Mutation SNP A C3L-00279_T 1615546 62100618 44943100 454 6232 SYNE2 0 . GRCh38 14 64225035 64225035 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.20506A>T p.Thr6836Ser p.T6836S ENST00000358025 115/116 448 404 44 404 404 0 strelka-varscan-mutect SYNE2,missense_variant,p.Thr6836Ser,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Thr6814Ser,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Asp6740Val,ENST00000357395,;SYNE2,missense_variant,p.Asp6734Val,ENST00000554584,;SYNE2,missense_variant,p.Thr3470Ser,ENST00000555002,;SYNE2,missense_variant,p.Thr3199Ser,ENST00000394768,;SYNE2,missense_variant,p.Thr692Ser,ENST00000555022,;SYNE2,missense_variant,p.Thr597Ser,ENST00000554805,;SYNE2,missense_variant,p.Thr358Ser,ENST00000441438,NM_182910.2;SYNE2,missense_variant,p.Thr485Ser,ENST00000458046,NM_182913.2;ESR2,intron_variant,,ENST00000556275,;ESR2,downstream_gene_variant,,ENST00000554572,NM_001291712.1;ESR2,downstream_gene_variant,,ENST00000353772,NM_001040275.1;ESR2,downstream_gene_variant,,ENST00000358599,NM_001291723.1;ESR2,downstream_gene_variant,,ENST00000555278,NM_001214902.1;ESR2,downstream_gene_variant,,ENST00000553796,NM_001271876.1;SYNE2,3_prime_UTR_variant,,ENST00000555612,;SYNE2,3_prime_UTR_variant,,ENST00000553289,;ESR2,downstream_gene_variant,,ENST00000344288,;SYNE2,downstream_gene_variant,,ENST00000554928,; T ENST00000358025 Transcript missense_variant 20718/21842 20506/20724 6836/6907 T/S Aca/Tca 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(1) 115/116 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 64225035 64225035 A T 1 0 0 0 0 1 0 0 0 15838 275 10 4 4 SYNE2 14 64225035 Missense_Mutation SNP A C3L-00279_T 2124417 64225035 42818683 455 6233 SPTB 0 . GRCh38 14 64822984 64822984 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.111C>T p.= p.A37A ENST00000556626 2/36 624 562 62 591 591 0 strelka-varscan-mutect SPTB,synonymous_variant,p.=,ENST00000556626,;SPTB,synonymous_variant,p.=,ENST00000389722,NM_001024858.2;SPTB,synonymous_variant,p.=,ENST00000389721,NM_000347.5;SPTB,synonymous_variant,p.=,ENST00000389720,; A ENST00000556626 Transcript synonymous_variant 254/10153 111/6987 37/2328 A gcC/gcT 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D 2/36 PIRSF_domain:PIRSF002297,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 64822984 64822984 G A 1 0 0 0 0 0 0 0 1 15474 1335 47 3 3 SPTB 14 64822984 Silent SNP G C3L-00279_T 597949 64822984 42220734 456 6234 GALNT16 0 . GRCh38 14 69338677 69338677 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.994G>T p.Gly332Cys p.G332C ENST00000337827 10/16 222 197 25 169 169 0 strelka-mutect GALNT16,missense_variant,p.Gly332Cys,ENST00000337827,NM_001168368.1,NM_020692.2;GALNT16,missense_variant,p.Gly332Cys,ENST00000448469,;GALNT16,missense_variant,p.Gly332Cys,ENST00000553669,;GALNT16,non_coding_transcript_exon_variant,,ENST00000556677,;GALNT16,missense_variant,p.Gly332Cys,ENST00000553471,; T ENST00000337827 Transcript missense_variant 1321/5708 994/1677 332/558 G/C Ggt/Tgt 1 1 GALNT16 HGNC HGNC:23233 protein_coding YES CCDS32107.1 ENSP00000336729 Q8N428 Q68VJ8 UPI000004D296 NM_001168368.1,NM_020692.2 deleterious(0) 10/16 hmmpanther:PTHR11675:SF3,hmmpanther:PTHR11675,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 69338677 69338677 G T 1 0 0 0 0 1 0 0 0 6082 1348 47 2 2 GALNT16 14 69338677 Missense_Mutation SNP G C3L-00279_T 4515693 69338677 37705041 457 6235 SLC8A3 0 . GRCh38 14 70166933 70166933 + Missense_Mutation SNP C C G rs139479097 C3L-00279_T C3L-00279_N C C c.1490G>C p.Gly497Ala p.G497A ENST00000381269 2/8 314 283 31 288 288 0 strelka-varscan-mutect SLC8A3,missense_variant,p.Gly497Ala,ENST00000381269,NM_183002.2;SLC8A3,missense_variant,p.Gly497Ala,ENST00000357887,NM_033262.4;SLC8A3,missense_variant,p.Gly497Ala,ENST00000356921,NM_182932.2;SLC8A3,missense_variant,p.Gly497Ala,ENST00000528359,;SLC8A3,missense_variant,p.Gly497Ala,ENST00000534137,NM_058240.3;SLC8A3,missense_variant,p.Gly497Ala,ENST00000494208,; G ENST00000381269 Transcript missense_variant 2244/5268 1490/2784 497/927 G/A gGg/gCg rs139479097 1 -1 SLC8A3 HGNC HGNC:11070 protein_coding YES CCDS35498.1 ENSP00000370669 P57103 UPI0000073C9A NM_183002.2 tolerated(0.12) 2/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF7,TIGRFAM_domain:TIGR00845,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS rs139479097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 70166933 70166933 C G 1 0 0 0 0 1 0 0 0 14991 623 22 4 4 SLC8A3 14 70166933 Missense_Mutation SNP C C3L-00279_T 828256 70166933 36876785 458 6236 SIPA1L1 0 . GRCh38 14 71588040 71588040 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.168C>T p.= p.P56P ENST00000555818 2/22 287 256 31 207 207 0 strelka-varscan-mutect SIPA1L1,synonymous_variant,p.=,ENST00000555818,NM_015556.2,NM_001284247.1;SIPA1L1,synonymous_variant,p.=,ENST00000358550,NM_001284246.1;SIPA1L1,synonymous_variant,p.=,ENST00000381232,NM_001284245.1;SIPA1L1,downstream_gene_variant,,ENST00000557151,;SIPA1L1,downstream_gene_variant,,ENST00000555989,;SIPA1L1,downstream_gene_variant,,ENST00000554362,;SIPA1L1,downstream_gene_variant,,ENST00000555652,; T ENST00000555818 Transcript synonymous_variant 516/7831 168/5415 56/1804 P ccC/ccT 1 1 SIPA1L1 HGNC HGNC:20284 protein_coding YES CCDS9807.1 ENSP00000450832 O43166 UPI00000443CB NM_015556.2,NM_001284247.1 2/22 hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 71588040 71588040 C T 1 0 0 0 0 0 0 0 1 14592 610 22 3 3 SIPA1L1 14 71588040 Silent SNP C C3L-00279_T 1421107 71588040 35455678 459 6237 ITPK1 0 . GRCh38 14 92941651 92941651 + Frame_Shift_Del DEL C C - rs572318884 C3L-00279_T C3L-00279_N C C c.1155delG p.His386ThrfsTer72 p.H386Tfs*72 ENST00000267615 11/11 151 129 22 145 145 0 sindel-varindel-pindel ITPK1,frameshift_variant,p.His386ThrfsTer72,ENST00000267615,;ITPK1,frameshift_variant,p.His386ThrfsTer72,ENST00000556603,NM_001142593.1,NM_014216.4;ITPK1,frameshift_variant,p.His267ThrfsTer72,ENST00000555495,;ITPK1,intron_variant,,ENST00000354313,NM_001142594.1;ITPK1,downstream_gene_variant,,ENST00000556954,;ITPK1,downstream_gene_variant,,ENST00000553695,; - ENST00000267615 Transcript frameshift_variant 1329/6066 1155/1245 385/414 P/X ccG/cc rs572318884 1 -1 ITPK1 HGNC HGNC:6177 protein_coding YES CCDS9907.1 ENSP00000267615 Q13572 A0A024R6H3 UPI000006F88A 11/11 HIGH 1 deletion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999933 1 1 1 0 - 7 5 14 92941651 92941651 C - 1 0 1 0 1 0 0 0 0 7822 755 27 0 0 ITPK1 14 92941651 Frame_Shift_Del DEL C C3L-00279_T 21353611 92941651 14102067 460 6238 UNC79 0 . GRCh38 14 93600771 93600771 + Splice_Site SNP G G T novel C3L-00279_T C3L-00279_N G G c.3043+1G>T p.X1015_splice ENST00000256339 151 139 12 49 49 0 strelka-varscan-mutect UNC79,splice_donor_variant,,ENST00000553484,;UNC79,splice_donor_variant,,ENST00000555664,;UNC79,splice_donor_variant,,ENST00000256339,NM_020818.3;UNC79,splice_donor_variant,,ENST00000393151,;UNC79,splice_donor_variant,,ENST00000621021,; T ENST00000256339 Transcript splice_donor_variant -/8400 3043/7377 1015/2458 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 25/49 HIGH 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.9992 1 1 1 1 0 T 5 4 14 93600771 93600771 G T 1 0 0 0 0 0 0 1 0 17520 1043 36 2 2 UNC79 14 93600771 Splice_Site SNP G C3L-00279_T 659120 93600771 13442947 461 6239 UNC79 0 . GRCh38 14 93621713 93621713 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3949C>A p.Leu1317Ile p.L1317I ENST00000256339 30/50 143 125 18 99 98 1 strelka-varscan-mutect UNC79,missense_variant,p.Leu1516Ile,ENST00000553484,;UNC79,missense_variant,p.Leu1494Ile,ENST00000555664,;UNC79,missense_variant,p.Leu1317Ile,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Leu1494Ile,ENST00000393151,;UNC79,missense_variant,p.Leu1317Ile,ENST00000621021,; A ENST00000256339 Transcript missense_variant 4604/8400 3949/7377 1317/2458 L/I Cta/Ata 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious_low_confidence(0.01) 30/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 93621713 93621713 C A 1 0 0 0 0 1 0 0 0 17520 796 28 2 2 UNC79 14 93621713 Missense_Mutation SNP C C3L-00279_T 20942 93621713 13422005 462 6240 SERPINA5 0 . GRCh38 14 94592116 94592116 + Silent SNP G G T rs370278940 C3L-00279_T C3L-00279_N G G c.1098G>T p.= p.T366T ENST00000329597 6/6 186 160 26 190 190 0 strelka-varscan-mutect SERPINA5,synonymous_variant,p.=,ENST00000329597,NM_000624.5;SERPINA5,synonymous_variant,p.=,ENST00000554866,;SERPINA5,synonymous_variant,p.=,ENST00000554276,;SERPINA5,synonymous_variant,p.=,ENST00000553780,;SERPINA5,downstream_gene_variant,,ENST00000554760,;SERPINA5,downstream_gene_variant,,ENST00000556775,;SERPINA5,downstream_gene_variant,,ENST00000555681,;SERPINA5,downstream_gene_variant,,ENST00000557598,;SERPINA5,downstream_gene_variant,,ENST00000554220,;SERPINA5,downstream_gene_variant,,ENST00000553511,;SERPINA5,downstream_gene_variant,,ENST00000554633,;SERPINA5,downstream_gene_variant,,ENST00000556064,;SERPINA3,synonymous_variant,p.=,ENST00000553947,;SERPINA5,downstream_gene_variant,,ENST00000556730,; T ENST00000329597 Transcript synonymous_variant 1333/2337 1098/1221 366/406 T acG/acT rs370278940,COSM3499416 1 1 SERPINA5 HGNC HGNC:8723 protein_coding YES CCDS9928.1 ENSP00000333203 P05154 A0A024R6N9 UPI000013E52C NM_000624.5 6/6 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF176,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 0,1 LOW 1 SNV 1 0,1 1 PASS rs370278940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 94592116 94592116 G T 1 0 0 0 0 0 0 0 1 14368 1103 39 1 1 SERPINA5 14 94592116 Silent SNP G C3L-00279_T 970403 94592116 12451602 463 6241 BDKRB1 0 . GRCh38 14 96263784 96263784 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.102C>T p.= p.D34D ENST00000216629 3/3 266 227 39 305 305 0 strelka-varscan-mutect BDKRB1,synonymous_variant,p.=,ENST00000216629,NM_000710.3;BDKRB1,synonymous_variant,p.=,ENST00000553356,;BDKRB1,synonymous_variant,p.=,ENST00000611804,;RP11-404P21.8,3_prime_UTR_variant,,ENST00000553811,;RP11-404P21.3,intron_variant,,ENST00000553638,;RP11-404P21.8,non_coding_transcript_exon_variant,,ENST00000555847,;BDKRB1,upstream_gene_variant,,ENST00000557122,; T ENST00000216629 Transcript synonymous_variant 708/1687 102/1062 34/353 D gaC/gaT 1 1 BDKRB1 HGNC HGNC:1029 protein_coding YES CCDS9943.1 ENSP00000216629 P46663 UPI0000000348 NM_000710.3 3/3 hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF28,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00993,PD012188 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 96263784 96263784 C T 1 0 0 0 0 0 0 0 1 1539 506 18 3 3 BDKRB1 14 96263784 Silent SNP C C3L-00279_T 1671668 96263784 10779934 464 6242 ATG2B 0 . GRCh38 14 96306887 96306887 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.4333G>T p.Glu1445Ter p.E1445* ENST00000359933 30/42 207 181 26 219 219 0 strelka-varscan-mutect ATG2B,stop_gained,p.Glu1445Ter,ENST00000359933,NM_018036.5;ATG2B,non_coding_transcript_exon_variant,,ENST00000261834,; A ENST00000359933 Transcript stop_gained 5227/13684 4333/6237 1445/2078 E/* Gag/Tag 1 -1 ATG2B HGNC HGNC:20187 protein_coding YES CCDS9944.2 ENSP00000353010 Q96BY7 UPI000155D51F NM_018036.5 30/42 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF20 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 96306887 96306887 C A 1 0 0 0 0 0 1 0 0 1246 864 30 2 2 ATG2B 14 96306887 Nonsense_Mutation SNP C C3L-00279_T 43103 96306887 10736831 465 6243 CYP46A1 0 . GRCh38 14 99691856 99691856 + Missense_Mutation SNP G G T rs780458125 C3L-00279_T C3L-00279_N G G c.277G>T p.Val93Phe p.V93F ENST00000261835 3/15 265 240 25 215 215 0 strelka-varscan-mutect CYP46A1,missense_variant,p.Val93Phe,ENST00000261835,NM_006668.1;CYP46A1,5_prime_UTR_variant,,ENST00000380228,;RP11-543C4.3,intron_variant,,ENST00000555875,;CYP46A1,missense_variant,p.Val93Phe,ENST00000554611,; T ENST00000261835 Transcript missense_variant 381/2181 277/1503 93/500 V/F Gtt/Ttt rs780458125 1 1 CYP46A1 HGNC HGNC:2641 protein_coding YES CCDS9954.1 ENSP00000261835 Q9Y6A2 UPI00001281DC NM_006668.1 deleterious(0) 3/15 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24293,hmmpanther:PTHR24293:SF2,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs780458125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 99691856 99691856 G T 1 0 0 0 0 1 0 0 0 3985 1275 44 2 2 CYP46A1 14 99691856 Missense_Mutation SNP G C3L-00279_T 3384969 99691856 7351862 466 6244 DYNC1H1 0 . GRCh38 14 102038570 102038570 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.11019A>G p.= p.P3673P ENST00000360184 58/78 480 413 67 442 442 0 strelka-varscan-mutect DYNC1H1,synonymous_variant,p.=,ENST00000360184,NM_001376.4;DYNC1H1,intron_variant,,ENST00000553423,;RP11-1017G21.4,intron_variant,,ENST00000557551,;RP11-1017G21.4,intron_variant,,ENST00000557242,;RP11-1017G21.4,intron_variant,,ENST00000553701,;DYNC1H1,downstream_gene_variant,,ENST00000556791,;DYNC1H1,upstream_gene_variant,,ENST00000555102,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000555800,;DYNC1H1,upstream_gene_variant,,ENST00000556139,;DYNC1H1,upstream_gene_variant,,ENST00000556499,; G ENST00000360184 Transcript synonymous_variant 11183/14333 11019/13941 3673/4646 P ccA/ccG 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 58/78 Pfam_domain:PF12781,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 LOW 1 SNV 1 1 PASS rs1477864954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 14 102038570 102038570 A G 1 0 0 0 0 0 0 0 1 4665 204 8 5 5 DYNC1H1 14 102038570 Silent SNP A C3L-00279_T 2346714 102038570 5005148 467 6245 C14orf180 0 . GRCh38 14 104587842 104587842 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.205G>T p.Val69Leu p.V69L ENST00000331952 3/5 129 117 12 112 112 0 strelka-varscan-mutect C14orf180,missense_variant,p.Val69Leu,ENST00000557649,NM_001008404.2;C14orf180,missense_variant,p.Val69Leu,ENST00000410013,NM_001286400.1;C14orf180,missense_variant,p.Val69Leu,ENST00000331952,NM_001286399.1;TMEM179,intron_variant,,ENST00000415614,;TMEM179,downstream_gene_variant,,ENST00000616017,;TMEM179,downstream_gene_variant,,ENST00000556320,;RP11-614O9.1,downstream_gene_variant,,ENST00000556073,; T ENST00000331952 Transcript missense_variant 461/1455 205/534 69/177 V/L Gtg/Ttg 1 1 C14orf180 HGNC HGNC:33795 protein_coding YES CCDS66722.1 ENSP00000333041 J3KNP8 UPI00021CF38C NM_001286399.1 deleterious_low_confidence(0) 3/5 hmmpanther:PTHR36868:SF1,hmmpanther:PTHR36868,Pfam_domain:PF15555 MODERATE 1 SNV 2 1 PASS rs1484525910 . 0 206 4 0 0 0 0 0 -19.99981 1 1 1 1 0 T 3 4 14 104587842 104587842 G T 1 0 0 0 0 1 0 0 0 1835 1145 40 1 1 C14orf180 14 104587842 Missense_Mutation SNP G C3L-00279_T 2549272 104587842 2455876 468 6246 MAGEL2 0 . GRCh38 15 23647738 23647738 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.5C>T p.Ser2Leu p.S2L ENST00000532292 1/1 27 21 6 23 23 0 strelka-varscan-mutect MAGEL2,missense_variant,p.Ser2Leu,ENST00000532292,NM_019066.4; A ENST00000532292 Transcript missense_variant 104/4298 5/3750 2/1249 S/L tCg/tTg 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -16.47855 1 1 1 1 0 A 3 1 14 23647738 23647738 G A 1 0 0 0 0 1 0 0 0 9107 1059 37 1 1 MAGEL2 15 23647738 Missense_Mutation SNP G C3L-00279_T 23647738 78343451 469 6247 AQR 0 . GRCh38 15 34904376 34904376 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1961A>T p.Asn654Ile p.N654I ENST00000156471 19/35 102 91 11 38 38 0 strelka-varscan-mutect AQR,missense_variant,p.Asn654Ile,ENST00000156471,NM_014691.2;AQR,3_prime_UTR_variant,,ENST00000543879,; A ENST00000156471 Transcript missense_variant 2187/9694 1961/4458 654/1485 N/I aAt/aTt 1 -1 AQR HGNC HGNC:29513 protein_coding YES CCDS42013.1 ENSP00000156471 O60306 A0A024R9L1 UPI00001C1F85 NM_014691.2 deleterious(0) 19/35 hmmpanther:PTHR10887:SF5,hmmpanther:PTHR10887,Pfam_domain:PF16399,PIRSF_domain:PIRSF038901 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 34904376 34904376 T A 1 0 0 0 0 1 0 0 0 957 1493 52 4 4 AQR 15 34904376 Missense_Mutation SNP T C3L-00279_T 11256638 34904376 67086813 470 6248 SLTM 0 . GRCh38 15 58887290 58887290 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2626A>T p.Asn876Tyr p.N876Y ENST00000380516 18/21 234 196 38 226 226 0 strelka-varscan-mutect SLTM,missense_variant,p.Asn876Tyr,ENST00000380516,NM_024755.2,NM_001013843.1;SLTM,missense_variant,p.Asn442Tyr,ENST00000432750,;RNF111,intron_variant,,ENST00000559757,;SLTM,upstream_gene_variant,,ENST00000560494,;SLTM,downstream_gene_variant,,ENST00000557791,;AC025918.2,upstream_gene_variant,,ENST00000452467,;SLTM,3_prime_UTR_variant,,ENST00000492526,;SLTM,3_prime_UTR_variant,,ENST00000557924,;SLTM,non_coding_transcript_exon_variant,,ENST00000558052,;SLTM,upstream_gene_variant,,ENST00000493062,;SLTM,downstream_gene_variant,,ENST00000560695,;SLTM,downstream_gene_variant,,ENST00000558734,; A ENST00000380516 Transcript missense_variant 2714/4147 2626/3105 876/1034 N/Y Aat/Tat 1 -1 SLTM HGNC HGNC:20709 protein_coding YES CCDS10168.2 ENSP00000369887 Q9NWH9 UPI0000039EA4 NM_024755.2,NM_001013843.1 deleterious(0.05) 18/21 hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 58887290 58887290 T A 1 0 0 0 0 1 0 0 0 15043 1812 63 4 4 SLTM 15 58887290 Missense_Mutation SNP T C3L-00279_T 23982914 58887290 43103899 471 6249 RNF111 0 . GRCh38 15 59094886 59094886 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.2974C>T p.Pro992Ser p.P992S ENST00000559209 14/14 333 287 46 353 353 0 strelka-varscan-mutect RNF111,missense_variant,p.Pro983Ser,ENST00000348370,NM_001270529.1,NM_017610.7;RNF111,missense_variant,p.Pro992Ser,ENST00000559209,NM_001270528.1;RNF111,missense_variant,p.Pro991Ser,ENST00000557998,NM_001270530.1;RNF111,missense_variant,p.Pro1000Ser,ENST00000561186,;RNF111,non_coding_transcript_exon_variant,,ENST00000560080,;RNF111,non_coding_transcript_exon_variant,,ENST00000560952,;RNF111,downstream_gene_variant,,ENST00000560216,; T ENST00000559209 Transcript missense_variant 3110/5278 2974/2988 992/995 P/S Cca/Tca 1 1 RNF111 HGNC HGNC:17384 protein_coding YES CCDS58365.1 ENSP00000453872 Q6ZNA4 UPI0000EE4EBD NM_001270528.1 tolerated(1) 14/14 hmmpanther:PTHR22763:SF15,hmmpanther:PTHR22763 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 59094886 59094886 C T 1 0 0 0 0 1 0 0 0 13603 739 26 3 3 RNF111 15 59094886 Missense_Mutation SNP C C3L-00279_T 207596 59094886 42896303 472 6250 MYO9A 0 . GRCh38 15 71899958 71899958 + Missense_Mutation SNP C C A rs74687859 C3L-00279_T C3L-00279_N C C c.3199G>T p.Val1067Leu p.V1067L ENST00000356056 24/42 180 155 25 186 186 0 strelka-varscan-mutect MYO9A,missense_variant,p.Val1067Leu,ENST00000356056,NM_006901.3;MYO9A,missense_variant,p.Val1067Leu,ENST00000564571,;MYO9A,missense_variant,p.Val1067Leu,ENST00000444904,;MYO9A,missense_variant,p.Val687Leu,ENST00000566885,;MYO9A,upstream_gene_variant,,ENST00000561618,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,downstream_gene_variant,,ENST00000566744,;MYO9A,upstream_gene_variant,,ENST00000568781,; A ENST00000356056 Transcript missense_variant 3672/12411 3199/7647 1067/2548 V/L Gtg/Ttg rs74687859 1 -1 MYO9A HGNC HGNC:7608 protein_coding YES CCDS10239.1 ENSP00000348349 B2RTY4 UPI000013D213 NM_006901.3 tolerated(0.54) 24/42 PROSITE_profiles:PS50096,hmmpanther:PTHR13140:SF9,hmmpanther:PTHR13140,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs74687859 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 71899958 71899958 C A 1 0 0 0 0 1 0 0 0 10085 478 17 2 2 MYO9A 15 71899958 Missense_Mutation SNP C C3L-00279_T 12805072 71899958 30091231 473 6251 HCN4 0 . GRCh38 15 73322661 73322661 + Frame_Shift_Del DEL G G - novel C3L-00279_T C3L-00279_N G G c.3432delC p.Ile1145SerfsTer36 p.I1145Sfs*36 ENST00000261917 8/8 225 181 44 304 304 0 sindel-varindel-pindel HCN4,frameshift_variant,p.Ile1145SerfsTer36,ENST00000261917,NM_005477.2; - ENST00000261917 Transcript frameshift_variant 4426/7228 3432/3612 1144/1203 A/X gcC/gc 1 -1 HCN4 HGNC HGNC:16882 protein_coding YES CCDS10248.1 ENSP00000261917 Q9Y3Q4 UPI000003FFB5 NM_005477.2 8/8 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 73322661 73322661 G - 1 0 1 0 1 0 0 0 0 6886 1335 47 0 0 HCN4 15 73322661 Frame_Shift_Del DEL G C3L-00279_T 1422703 73322661 28668528 474 6252 ISLR 0 . GRCh38 15 74175367 74175367 + Missense_Mutation SNP C C A rs780036106 C3L-00279_T C3L-00279_N C C c.509C>A p.Thr170Asn p.T170N ENST00000249842 2/2 128 108 20 114 114 0 strelka-varscan-mutect ISLR,missense_variant,p.Thr170Asn,ENST00000249842,NM_005545.3;ISLR,missense_variant,p.Thr170Asn,ENST00000395118,NM_201526.1;ISLR,missense_variant,p.Thr170Asn,ENST00000560862,;STRA6,downstream_gene_variant,,ENST00000323940,NM_001142617.1;STRA6,downstream_gene_variant,,ENST00000616000,NM_001142618.1;STRA6,downstream_gene_variant,,ENST00000395105,NM_022369.3;STRA6,downstream_gene_variant,,ENST00000423167,NM_001142619.1;STRA6,downstream_gene_variant,,ENST00000416286,;STRA6,downstream_gene_variant,,ENST00000449139,;STRA6,downstream_gene_variant,,ENST00000535552,NM_001199040.1;STRA6,downstream_gene_variant,,ENST00000563965,NM_001199042.1;STRA6,downstream_gene_variant,,ENST00000574278,NM_001199041.1;STRA6,downstream_gene_variant,,ENST00000572785,;ISLR,downstream_gene_variant,,ENST00000559510,;RP11-665J16.1,intron_variant,,ENST00000561647,;STRA6,downstream_gene_variant,,ENST00000574439,;STRA6,downstream_gene_variant,,ENST00000545137,; A ENST00000249842 Transcript missense_variant 866/2371 509/1287 170/428 T/N aCc/aAc rs780036106,COSM555976 1 1 ISLR HGNC HGNC:6133 protein_coding YES CCDS10260.1 ENSP00000249842 O14498 A0A146E5L3 UPI0000049E09 NM_005545.3 tolerated(0.26) 2/2 hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF14,Pfam_domain:PF13855,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780036106 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 74175367 74175367 C A 1 0 0 0 0 1 0 0 0 7765 507 18 2 2 ISLR 15 74175367 Missense_Mutation SNP C C3L-00279_T 852706 74175367 27815822 475 6253 IGF1R 0 . GRCh38 15 98908823 98908823 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1386G>T p.Met462Ile p.M462I ENST00000268035 6/21 657 578 79 624 621 3 strelka-varscan-mutect IGF1R,missense_variant,p.Met462Ile,ENST00000268035,NM_000875.4;IGF1R,missense_variant,p.Met462Ile,ENST00000558762,NM_001291858.1;IGF1R,missense_variant,p.Met159Ile,ENST00000558898,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559582,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,;IGF1R,upstream_gene_variant,,ENST00000560144,; T ENST00000268035 Transcript missense_variant 1997/11803 1386/4104 462/1367 M/I atG/atT 1 1 IGF1R HGNC HGNC:5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 UPI000012D3EA NM_000875.4 deleterious(0.01) 6/21 hmmpanther:PTHR24416:SF106,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 98908823 98908823 G T 1 0 0 0 0 1 0 0 0 7477 1348 47 2 2 IGF1R 15 98908823 Missense_Mutation SNP G C3L-00279_T 24733456 98908823 3082366 476 6254 DECR2 0 . GRCh38 16 410277 410277 + Silent SNP C C T rs765659217 C3L-00279_T C3L-00279_N C C c.372C>T p.= p.A124A ENST00000219481 5/9 273 238 35 287 287 0 strelka-varscan-mutect DECR2,synonymous_variant,p.=,ENST00000219481,NM_020664.3;DECR2,synonymous_variant,p.=,ENST00000424398,;DECR2,synonymous_variant,p.=,ENST00000633348,;DECR2,synonymous_variant,p.=,ENST00000633923,;DECR2,downstream_gene_variant,,ENST00000627716,;DECR2,non_coding_transcript_exon_variant,,ENST00000461947,;DECR2,downstream_gene_variant,,ENST00000461802,;DECR2,downstream_gene_variant,,ENST00000632744,;DECR2,missense_variant,p.Leu187Phe,ENST00000439661,;DECR2,synonymous_variant,p.=,ENST00000429116,;DECR2,3_prime_UTR_variant,,ENST00000437024,;NME4,3_prime_UTR_variant,,ENST00000444498,;DECR2,3_prime_UTR_variant,,ENST00000445291,;DECR2,non_coding_transcript_exon_variant,,ENST00000461749,;DECR2,non_coding_transcript_exon_variant,,ENST00000465166,;DECR2,non_coding_transcript_exon_variant,,ENST00000469922,;DECR2,downstream_gene_variant,,ENST00000633025,;DECR2,downstream_gene_variant,,ENST00000631605,; T ENST00000219481 Transcript synonymous_variant 510/1615 372/879 124/292 A gcC/gcT rs765659217 1 1 DECR2 HGNC HGNC:2754 protein_coding YES CCDS10409.1 ENSP00000219481 Q9NUI1 UPI000003BBDC NM_020664.3 5/9 hmmpanther:PTHR24322:SF539,hmmpanther:PTHR24322,Pfam_domain:PF13561,Gene3D:3.40.50.720,SMART_domains:SM00822,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS rs765659217 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 410277 410277 C T 1 0 0 0 0 0 0 0 1 4186 668 24 3 3 DECR2 16 410277 Silent SNP C C3L-00279_T 410277 89928068 477 6255 RPL3L 0 . GRCh38 16 1954097 1954097 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.55C>A p.His19Asn p.H19N ENST00000268661 2/10 78 70 8 60 60 0 strelka-varscan-mutect RPL3L,missense_variant,p.His19Asn,ENST00000268661,NM_005061.2;RPL3L,5_prime_UTR_variant,,ENST00000565426,;RPL3L,downstream_gene_variant,,ENST00000566484,; T ENST00000268661 Transcript missense_variant 150/2182 55/1224 19/407 H/N Cat/Aat COSM3506831 1 -1 RPL3L HGNC HGNC:10351 protein_coding YES CCDS10450.1 ENSP00000268661 Q92901 UPI0000161C28 NM_005061.2 deleterious(0) 2/10 hmmpanther:PTHR11363,hmmpanther:PTHR11363:SF7,Pfam_domain:PF00297,Superfamily_domains:SSF50447 1 MODERATE 1 SNV 1 1 1 PASS . . 0 202 8 0 0 0 0 0 -17.13243 0.9999958 1 1 1 0 T 3 4 14 1954097 1954097 G T 1 0 0 0 0 1 0 0 0 13847 1348 47 2 2 RPL3L 16 1954097 Missense_Mutation SNP G C3L-00279_T 1543820 1954097 88384248 478 6256 NTN3 0 . GRCh38 16 2473286 2473286 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1286C>A p.Pro429His p.P429H ENST00000293973 4/6 195 167 28 158 158 0 strelka-mutect NTN3,missense_variant,p.Pro429His,ENST00000293973,NM_006181.2;TBC1D24,upstream_gene_variant,,ENST00000567020,NM_020705.2;TBC1D24,upstream_gene_variant,,ENST00000293970,NM_001199107.1;RP11-715J22.6,upstream_gene_variant,,ENST00000561847,;TBC1D24,upstream_gene_variant,,ENST00000630263,;TBC1D24,upstream_gene_variant,,ENST00000569874,; A ENST00000293973 Transcript missense_variant 1489/1986 1286/1743 429/580 P/H cCc/cAc 1 1 NTN3 HGNC HGNC:8030 protein_coding YES CCDS10469.1 ENSP00000293973 O00634 UPI000006ED30 NM_006181.2 deleterious(0.01) 4/6 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF292 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 2473286 2473286 C A 1 0 0 0 0 1 0 0 0 10766 623 22 2 2 NTN3 16 2473286 Missense_Mutation SNP C C3L-00279_T 519189 2473286 87865059 479 6257 GRIN2A 0 . GRCh38 16 9763508 9763508 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.4036C>A p.Gln1346Lys p.Q1346K ENST00000396573 14/14 342 315 27 279 279 0 strelka-varscan-mutect GRIN2A,missense_variant,p.Gln1346Lys,ENST00000396573,NM_000833.4;GRIN2A,missense_variant,p.Gln1209Lys,ENST00000396575,;GRIN2A,missense_variant,p.Gln1346Lys,ENST00000330684,NM_001134407.2;GRIN2A,intron_variant,,ENST00000562109,NM_001134408.2;GRIN2A,intron_variant,,ENST00000535259,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,intron_variant,,ENST00000461292,;GRIN2A,downstream_gene_variant,,ENST00000463531,; T ENST00000396573 Transcript missense_variant 4346/14450 4036/4395 1346/1464 Q/K Caa/Aaa 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 tolerated(0.92) 14/14 Pfam_domain:PF10565 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 9763508 9763508 G T 1 0 0 0 0 1 0 0 0 6661 1357 47 2 2 GRIN2A 16 9763508 Missense_Mutation SNP G C3L-00279_T 7290222 9763508 80574837 480 6258 NOMO2 0 . GRCh38 16 18531491 18531491 + Silent SNP T T A rs143309872 C3L-00279_T C3L-00279_N T T c.1512A>T p.= p.S504S ENST00000621364 13/32 393 363 30 288 288 0 varscan-mutect NOMO2,synonymous_variant,p.=,ENST00000330537,;NOMO2,synonymous_variant,p.=,ENST00000622306,NM_173614.2;NOMO2,synonymous_variant,p.=,ENST00000621364,NM_001004060.1;NOMO2,synonymous_variant,p.=,ENST00000381474,;NOMO2,synonymous_variant,p.=,ENST00000543392,;NOMO2,synonymous_variant,p.=,ENST00000569051,;NOMO2,3_prime_UTR_variant,,ENST00000564991,;NOMO2,upstream_gene_variant,,ENST00000567831,;RP11-457I16.4,upstream_gene_variant,,ENST00000575091,; A ENST00000621364 Transcript synonymous_variant 1584/3921 1512/3804 504/1267 S tcA/tcT rs143309872 1 -1 NOMO2 HGNC HGNC:22652 protein_coding YES CCDS32394.1 ENSP00000477502 Q5JPE7 UPI00001AFC79 NM_001004060.1 13/32 hmmpanther:PTHR23303 LOW 1 SNV 1 1 PASS rs143309872 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 18531491 18531491 T A 1 0 0 0 0 0 0 0 1 10576 1567 55 4 4 NOMO2 16 18531491 Silent SNP T C3L-00279_T 8767983 18531491 71806854 481 6259 GPRC5B 0 . GRCh38 16 19872504 19872504 + Silent SNP G G A C3L-00279_T C3L-00279_N G G c.342C>T p.= p.I114I ENST00000300571 2/4 244 213 31 197 197 0 strelka-varscan-mutect GPRC5B,synonymous_variant,p.=,ENST00000300571,NM_016235.2;GPRC5B,synonymous_variant,p.=,ENST00000569479,;GPRC5B,synonymous_variant,p.=,ENST00000569847,;GPRC5B,synonymous_variant,p.=,ENST00000535671,;GPRC5B,synonymous_variant,p.=,ENST00000562469,;GPRC5B,synonymous_variant,p.=,ENST00000566822,;GPRC5B,downstream_gene_variant,,ENST00000564449,;GPRC5B,downstream_gene_variant,,ENST00000568214,;GPRC5B,downstream_gene_variant,,ENST00000570142,; A ENST00000300571 Transcript synonymous_variant 534/5213 342/1212 114/403 I atC/atT COSM3969426 1 -1 GPRC5B HGNC HGNC:13308 protein_coding YES CCDS10581.1 ENSP00000300571 Q9NZH0 A0A024QYX2 UPI0000032747 NM_016235.2 2/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR14511,hmmpanther:PTHR14511:SF9,Pfam_domain:PF00003 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 19872504 19872504 G A 1 0 0 0 0 0 0 0 1 6604 1280 45 3 3 GPRC5B 16 19872504 Silent SNP G C3L-00279_T 1341013 19872504 70465841 482 6260 UMOD 0 . GRCh38 16 20341187 20341187 + Frame_Shift_Del DEL C C - novel C3L-00279_T C3L-00279_N C C c.1580delG p.Gly527AlafsTer10 p.G527Afs*10 ENST00000396134 8/12 448 416 32 421 421 0 sindel-varindel-pindel UMOD,frameshift_variant,p.Gly494AlafsTer10,ENST00000302509,NM_001008389.2,NM_003361.3;UMOD,frameshift_variant,p.Gly527AlafsTer10,ENST00000396134,NM_001278614.1;UMOD,frameshift_variant,p.Gly543AlafsTer10,ENST00000396138,;UMOD,frameshift_variant,p.Gly494AlafsTer10,ENST00000570689,;UMOD,non_coding_transcript_exon_variant,,ENST00000570331,; - ENST00000396134 Transcript frameshift_variant 1704/2408 1580/2022 527/673 G/X gGc/gc 1 -1 UMOD HGNC HGNC:12559 protein_coding YES CCDS61876.1 ENSP00000379438 P07911 UPI000059D336 NM_001278614.1 8/12 PROSITE_profiles:PS51034,hmmpanther:PTHR24044:SF263,hmmpanther:PTHR24044,PROSITE_patterns:PS00682,Pfam_domain:PF00100,SMART_domains:SM00241 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 20341187 20341187 C - 1 0 1 0 1 0 0 0 0 17503 739 26 0 0 UMOD 16 20341187 Frame_Shift_Del DEL C C3L-00279_T 468683 20341187 69997158 483 6261 GTF3C1 0 . GRCh38 16 27497688 27497688 + Frame_Shift_Del DEL T T - C3L-00279_T C3L-00279_N T T c.2299delA p.Ser767ValfsTer7 p.S767Vfs*7 ENST00000356183 14/37 142 119 23 95 95 0 sindel-pindel GTF3C1,frameshift_variant,p.Ser767ValfsTer7,ENST00000356183,NM_001520.3;GTF3C1,frameshift_variant,p.Ser767ValfsTer7,ENST00000561623,NM_001286242.1;GTF3C1,intron_variant,,ENST00000569653,; - ENST00000356183 Transcript frameshift_variant 2315/7018 2299/6330 767/2109 S/X Agt/gt COSM1180827 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 14/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 1 HIGH 1 deletion 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999984 1 1 1 0 - 7 5 14 27497688 27497688 T - 1 0 1 0 1 0 0 0 0 6753 1609 56 0 0 GTF3C1 16 27497688 Frame_Shift_Del DEL T C3L-00279_T 7156501 27497688 62840657 484 6262 APOBR 0 . GRCh38 16 28495582 28495582 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.541G>A p.Glu181Lys p.E181K ENST00000564831 2/4 142 117 25 121 121 0 strelka-varscan-mutect APOBR,missense_variant,p.Glu181Lys,ENST00000564831,NM_018690.3;APOBR,missense_variant,p.Glu181Lys,ENST00000431282,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000636147,NM_001042432.1;CLN3,upstream_gene_variant,,ENST00000359984,NM_000086.2;CLN3,upstream_gene_variant,,ENST00000360019,NM_001286104.1;CLN3,upstream_gene_variant,,ENST00000357857,NM_001286110.1;CLN3,upstream_gene_variant,,ENST00000333496,;CLN3,upstream_gene_variant,,ENST00000631023,;CLN3,upstream_gene_variant,,ENST00000357806,;CLN3,upstream_gene_variant,,ENST00000567963,NM_001286109.1;CLN3,upstream_gene_variant,,ENST00000395653,;CLN3,upstream_gene_variant,,ENST00000565316,;CLN3,upstream_gene_variant,,ENST00000637100,;CLN3,upstream_gene_variant,,ENST00000636228,;CLN3,upstream_gene_variant,,ENST00000355477,;CLN3,upstream_gene_variant,,ENST00000635973,;IL27,downstream_gene_variant,,ENST00000356897,NM_145659.3;CLN3,upstream_gene_variant,,ENST00000568443,;CLN3,upstream_gene_variant,,ENST00000568497,;CLN3,upstream_gene_variant,,ENST00000565778,;CLN3,upstream_gene_variant,,ENST00000565688,;CLN3,upstream_gene_variant,,ENST00000568558,;CLN3,upstream_gene_variant,,ENST00000567804,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000565236,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566472,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,;CLN3,upstream_gene_variant,,ENST00000565047,;CLN3,upstream_gene_variant,,ENST00000563874,;CLN3,upstream_gene_variant,,ENST00000636977,;RP11-435I10.4,upstream_gene_variant,,ENST00000635887,;RP11-435I10.4,upstream_gene_variant,,ENST00000636503,;RP11-435I10.4,upstream_gene_variant,,ENST00000637376,;RP11-435I10.4,upstream_gene_variant,,ENST00000636866,;RP11-435I10.4,upstream_gene_variant,,ENST00000636078,;CLN3,upstream_gene_variant,,ENST00000636853,;RP11-435I10.4,upstream_gene_variant,,ENST00000636017,;RP11-435I10.4,upstream_gene_variant,,ENST00000636766,;CLN3,upstream_gene_variant,,ENST00000636839,;CLN3,upstream_gene_variant,,ENST00000568076,;CLN3,upstream_gene_variant,,ENST00000561689,;RP11-435I10.4,upstream_gene_variant,,ENST00000637299,;CLN3,upstream_gene_variant,,ENST00000637107,;CLN3,upstream_gene_variant,,ENST00000635958,;CLN3,upstream_gene_variant,,ENST00000637184,;RP11-435I10.4,upstream_gene_variant,,ENST00000568224,;CLN3,upstream_gene_variant,,ENST00000568452,;CLN3,upstream_gene_variant,,ENST00000637871,;CLN3,upstream_gene_variant,,ENST00000637578,;CLN3,upstream_gene_variant,,ENST00000636172,;CLN3,upstream_gene_variant,,ENST00000566083,;CLN3,upstream_gene_variant,,ENST00000635861,;CLN3,upstream_gene_variant,,ENST00000566824,;CLN3,upstream_gene_variant,,ENST00000637699,;CLN3,upstream_gene_variant,,ENST00000565140,;CLN3,upstream_gene_variant,,ENST00000628023,;CLN3,upstream_gene_variant,,ENST00000568422,;CLN3,upstream_gene_variant,,ENST00000564574,;CLN3,upstream_gene_variant,,ENST00000569030,;CLN3,upstream_gene_variant,,ENST00000568472,;CLN3,upstream_gene_variant,,ENST00000566057,;CLN3,upstream_gene_variant,,ENST00000567495,;CLN3,upstream_gene_variant,,ENST00000637985,;CLN3,upstream_gene_variant,,ENST00000561505,; A ENST00000564831 Transcript missense_variant 574/3792 541/3294 181/1097 E/K Gag/Aag 1 1 APOBR HGNC HGNC:24087 protein_coding YES CCDS58442.1 ENSP00000457539 Q0VD83 UPI000013EFFC NM_018690.3 deleterious(0.02) 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15964:SF0,hmmpanther:PTHR15964 MODERATE 1 SNV 1 1 PASS rs1186553609 . 0 207 0 3 0 0 0 0 -20 0.9999954 1 1 1 0 A 3 1 14 28495582 28495582 G A 1 0 0 0 0 1 0 0 0 918 1175 41 3 3 APOBR 16 28495582 Missense_Mutation SNP G C3L-00279_T 997894 28495582 61842763 485 6263 SRCAP 0 . GRCh38 16 30737307 30737307 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.7267A>T p.Thr2423Ser p.T2423S ENST00000262518 34/34 422 348 74 429 429 0 strelka-varscan-mutect SRCAP,missense_variant,p.Thr2423Ser,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Thr2164Ser,ENST00000395059,;TMEM265,upstream_gene_variant,,ENST00000615541,NM_001256829.1;RP11-2C24.4,upstream_gene_variant,,ENST00000483578,;RP11-2C24.9,missense_variant,p.Thr2246Ser,ENST00000380361,;SRCAP,downstream_gene_variant,,ENST00000474008,; T ENST00000262518 Transcript missense_variant 7652/11754 7267/9693 2423/3230 T/S Acc/Tcc 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 tolerated_low_confidence(0.16) 34/34 Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30737307 30737307 A T 1 0 0 0 0 1 0 0 0 15493 159 6 4 4 SRCAP 16 30737307 Missense_Mutation SNP A C3L-00279_T 2241725 30737307 59601038 486 6264 RNF40 0 . GRCh38 16 30766772 30766772 + Missense_Mutation SNP G G T rs146102570 C3L-00279_T C3L-00279_N G G c.1325G>T p.Arg442Leu p.R442L ENST00000324685 11/20 256 228 28 205 205 0 strelka-varscan-mutect RNF40,missense_variant,p.Arg442Leu,ENST00000324685,NM_014771.3,NM_001207033.1,NM_001286572.2;RNF40,missense_variant,p.Arg402Leu,ENST00000563683,;RNF40,missense_variant,p.Arg342Leu,ENST00000357890,NM_001207034.1;CCDC189,upstream_gene_variant,,ENST00000543610,NM_001014979.2;CCDC189,upstream_gene_variant,,ENST00000541260,;CCDC189,upstream_gene_variant,,ENST00000545825,NM_001195620.1;RNF40,downstream_gene_variant,,ENST00000563909,;RNF40,upstream_gene_variant,,ENST00000567365,;RNF40,downstream_gene_variant,,ENST00000565995,;RNF40,downstream_gene_variant,,ENST00000566811,;RNF40,downstream_gene_variant,,ENST00000565931,;RNF40,non_coding_transcript_exon_variant,,ENST00000493683,;RNF40,non_coding_transcript_exon_variant,,ENST00000566703,;CCDC189,upstream_gene_variant,,ENST00000544487,;CCDC189,upstream_gene_variant,,ENST00000543128,;CCDC189,upstream_gene_variant,,ENST00000544643,;CCDC189,upstream_gene_variant,,ENST00000546006,;CCDC189,upstream_gene_variant,,ENST00000545809,;RNF40,upstream_gene_variant,,ENST00000564260,; T ENST00000324685 Transcript missense_variant 1760/5634 1325/3006 442/1001 R/L cGc/cTc rs146102570,COSM185094 1 1 RNF40 HGNC HGNC:16867 protein_coding YES CCDS10691.1 ENSP00000325677 O75150 A0A024QZG0 UPI0000073F6C NM_014771.3,NM_001207033.1,NM_001286572.2 deleterious(0) 11/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23163,hmmpanther:PTHR23163:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs146102570 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 30766772 30766772 G T 1 0 0 0 0 1 0 0 0 13673 1087 38 1 1 RNF40 16 30766772 Missense_Mutation SNP G C3L-00279_T 29465 30766772 59571573 487 6265 ITGAX 0 . GRCh38 16 31362744 31362744 + Silent SNP G G T rs577520206 C3L-00279_T C3L-00279_N G G c.1350G>T p.= p.T450T ENST00000562522 12/31 179 163 16 166 166 0 strelka-varscan-mutect ITGAX,synonymous_variant,p.=,ENST00000268296,NM_000887.4;ITGAX,synonymous_variant,p.=,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,; T ENST00000562522 Transcript synonymous_variant 1383/3990 1350/3510 450/1169 T acG/acT rs577520206 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 12/31 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS rs577520206 . 0 205 0 4 0 0 0 0 -19.98144 0.9997625 1 1 1 0 T 2 4 14 31362744 31362744 G T 1 0 0 0 0 0 0 0 1 7796 1103 39 1 1 ITGAX 16 31362744 Silent SNP G C3L-00279_T 595972 31362744 58975601 488 6266 ITGAX 0 . GRCh38 16 31371210 31371210 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.1837C>T p.Leu613Phe p.L613F ENST00000562522 15/31 91 78 13 91 91 0 strelka-varscan-mutect ITGAX,missense_variant,p.Leu613Phe,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Leu613Phe,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,upstream_gene_variant,,ENST00000562138,; T ENST00000562522 Transcript missense_variant 1870/3990 1837/3510 613/1169 L/F Ctc/Ttc 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.08) 15/31 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 31371210 31371210 C T 1 0 0 0 0 1 0 0 0 7796 811 28 3 3 ITGAX 16 31371210 Missense_Mutation SNP C C3L-00279_T 8466 31371210 58967135 489 6267 ABCC11 0 . GRCh38 16 48187245 48187245 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.2889G>T p.= p.L963L ENST00000394747 20/29 324 272 52 270 270 0 strelka-varscan-mutect ABCC11,synonymous_variant,p.=,ENST00000394747,NM_033151.3;ABCC11,synonymous_variant,p.=,ENST00000356608,;ABCC11,synonymous_variant,p.=,ENST00000394748,NM_032583.3;ABCC11,synonymous_variant,p.=,ENST00000353782,NM_145186.2;ABCC11,non_coding_transcript_exon_variant,,ENST00000565329,;ABCC11,downstream_gene_variant,,ENST00000569172,; A ENST00000394747 Transcript synonymous_variant 3239/4862 2889/4149 963/1382 L ctG/ctT 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 20/29 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS rs1196687490 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 48187245 48187245 C A 1 0 0 0 0 0 0 0 1 55 465 17 2 2 ABCC11 16 48187245 Silent SNP C C3L-00279_T 16816035 48187245 42151100 490 6268 ZNF423 0 . GRCh38 16 49523699 49523699 + Silent SNP G G T rs767884892 C3L-00279_T C3L-00279_N G G c.3750C>A p.= p.A1250A ENST00000561648 8/9 235 219 16 258 258 0 strelka-varscan-mutect ZNF423,synonymous_variant,p.=,ENST00000561648,;ZNF423,synonymous_variant,p.=,ENST00000563137,;ZNF423,synonymous_variant,p.=,ENST00000262383,NM_015069.3;ZNF423,synonymous_variant,p.=,ENST00000562871,;ZNF423,synonymous_variant,p.=,ENST00000535559,;ZNF423,synonymous_variant,p.=,ENST00000562520,NM_001271620.1;ZNF423,synonymous_variant,p.=,ENST00000567169,; T ENST00000561648 Transcript synonymous_variant 4051/7907 3750/3855 1250/1284 A gcC/gcA rs767884892 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC 8/9 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS rs767884892 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 49523699 49523699 G T 1 0 0 0 0 0 0 0 1 18470 1103 39 1 1 ZNF423 16 49523699 Silent SNP G C3L-00279_T 1336454 49523699 40814646 491 6269 SALL1 0 . GRCh38 16 51138768 51138768 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.3454C>G p.His1152Asp p.H1152D ENST00000251020 2/3 212 191 21 197 197 0 strelka-varscan-mutect SALL1,missense_variant,p.His1055Asp,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.His1152Asp,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.His1055Asp,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; C ENST00000251020 Transcript missense_variant 3488/5146 3454/3975 1152/1324 H/D Cac/Gac 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0) 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF12874,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1250230086 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 51138768 51138768 G C 1 0 0 0 0 1 0 0 0 14069 1290 45 4 4 SALL1 16 51138768 Missense_Mutation SNP G C3L-00279_T 1615069 51138768 39199577 492 6270 IRX6 0 . GRCh38 16 55329307 55329307 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.1329A>T p.= p.A443A ENST00000290552 5/6 69 63 6 58 58 0 strelka-varscan-mutect IRX6,synonymous_variant,p.=,ENST00000290552,NM_024335.2;RP11-26L20.4,upstream_gene_variant,,ENST00000573934,;RP11-26L20.3,intron_variant,,ENST00000558730,;IRX6,downstream_gene_variant,,ENST00000558315,; T ENST00000290552 Transcript synonymous_variant 2661/3128 1329/1341 443/446 A gcA/gcT 1 1 IRX6 HGNC HGNC:14675 protein_coding YES CCDS32449.1 ENSP00000290552 P78412 UPI00001C0A88 NM_024335.2 5/6 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 55329307 55329307 A T 1 0 0 0 0 0 0 0 1 7756 202 7 4 4 IRX6 16 55329307 Silent SNP A C3L-00279_T 4190539 55329307 35009038 493 6271 COQ9 0 . GRCh38 16 57459592 57459592 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.739C>T p.= p.L247L ENST00000262507 7/9 517 470 47 462 462 0 strelka-varscan-mutect COQ9,synonymous_variant,p.=,ENST00000262507,NM_020312.3;COQ9,synonymous_variant,p.=,ENST00000567072,;COQ9,synonymous_variant,p.=,ENST00000564655,;COQ9,synonymous_variant,p.=,ENST00000567933,;COQ9,synonymous_variant,p.=,ENST00000565964,;COQ9,intron_variant,,ENST00000563166,;POLR2C,upstream_gene_variant,,ENST00000219252,NM_032940.2;COQ9,downstream_gene_variant,,ENST00000563391,;POLR2C,upstream_gene_variant,,ENST00000564651,;AC009052.12,upstream_gene_variant,,ENST00000567090,;COQ9,3_prime_UTR_variant,,ENST00000564115,;COQ9,non_coding_transcript_exon_variant,,ENST00000569980,;POLR2C,upstream_gene_variant,,ENST00000567982,;POLR2C,upstream_gene_variant,,ENST00000563115,;COQ9,downstream_gene_variant,,ENST00000562734,;COQ9,downstream_gene_variant,,ENST00000568790,;COQ9,downstream_gene_variant,,ENST00000562426,;POLR2C,upstream_gene_variant,,ENST00000562953,;POLR2C,upstream_gene_variant,,ENST00000562599,;COQ9,downstream_gene_variant,,ENST00000567576,;COQ9,downstream_gene_variant,,ENST00000567480,;POLR2C,upstream_gene_variant,,ENST00000564626,; T ENST00000262507 Transcript synonymous_variant 808/1677 739/957 247/318 L Ctg/Ttg 1 1 COQ9 HGNC HGNC:25302 protein_coding YES CCDS32459.1 ENSP00000262507 O75208 A0A024R6U3 UPI0000070ECA NM_020312.3 7/9 hmmpanther:PTHR21427,Pfam_domain:PF08511,TIGRFAM_domain:TIGR02396 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 57459592 57459592 C T 1 0 0 0 0 0 0 0 1 3545 796 28 3 3 COQ9 16 57459592 Silent SNP C C3L-00279_T 2130285 57459592 32878753 494 6272 CNGB1 0 . GRCh38 16 57962980 57962980 + Silent SNP C C A C3L-00279_T C3L-00279_N C C c.375G>T p.= p.P125P ENST00000251102 5/33 577 521 56 507 507 0 strelka-varscan-mutect CNGB1,synonymous_variant,p.=,ENST00000251102,NM_001297.4;CNGB1,synonymous_variant,p.=,ENST00000564448,NM_001286130.1;CNGB1,synonymous_variant,p.=,ENST00000311183,NM_001135639.1;CNGB1,synonymous_variant,p.=,ENST00000562761,;CNGB1,downstream_gene_variant,,ENST00000567568,; A ENST00000251102 Transcript synonymous_variant 436/5641 375/3756 125/1251 P ccG/ccT COSM1378614,COSM5167064 1 -1 CNGB1 HGNC HGNC:2151 protein_coding YES CCDS42169.1 ENSP00000251102 Q14028 UPI000013CCDF NM_001297.4 5/33 1,1 LOW 1 SNV 1 1,1 1 PASS rs1406243873 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 57962980 57962980 C A 1 0 0 0 0 0 0 0 1 3380 639 23 1 1 CNGB1 16 57962980 Silent SNP C C3L-00279_T 503388 57962980 32375365 495 6273 CARMIL2 0 . GRCh38 16 67648315 67648315 + Splice_Site SNP G G T rs780608299 C3L-00279_T C3L-00279_N G G c.1334+1G>T p.X445_splice ENST00000334583 116 101 15 134 134 0 strelka-varscan-mutect CARMIL2,splice_donor_variant,,ENST00000334583,NM_001013838.1;CARMIL2,splice_donor_variant,,ENST00000545661,NM_001317026.1;CARMIL2,splice_donor_variant,,ENST00000602742,;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602321,;CARMIL2,downstream_gene_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602931,;CARMIL2,upstream_gene_variant,,ENST00000602924,;CARMIL2,downstream_gene_variant,,ENST00000602467,; T ENST00000334583 Transcript splice_donor_variant -/4687 1334/4308 445/1435 rs780608299 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 14/37 HIGH 1 SNV 1 1 PASS rs780608299 . 0 206 2 2 0 0 0 0 -19.99973 0.9999974 1 1 1 0 T 5 4 14 67648315 67648315 G T 1 0 0 0 0 0 0 1 0 2352 1159 40 1 1 CARMIL2 16 67648315 Splice_Site SNP G C3L-00279_T 9685335 67648315 22690030 496 6274 CDH3 0 . GRCh38 16 68681092 68681092 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.992A>T p.Gln331Leu p.Q331L ENST00000264012 8/16 649 560 89 606 606 0 strelka-varscan-mutect CDH3,missense_variant,p.Gln331Leu,ENST00000264012,NM_001793.4;CDH3,missense_variant,p.Gln331Leu,ENST00000429102,NM_001317195.1;CDH3,3_prime_UTR_variant,,ENST00000542274,;CDH3,3_prime_UTR_variant,,ENST00000569036,;CDH3,downstream_gene_variant,,ENST00000566808,; T ENST00000264012 Transcript missense_variant 1536/4929 992/2490 331/829 Q/L cAg/cTg 1 1 CDH3 HGNC HGNC:1762 protein_coding YES CCDS10868.1 ENSP00000264012 P22223 UPI0000161BFF NM_001793.4 tolerated(0.23) 8/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF267,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS rs955742330 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 68681092 68681092 A T 1 0 0 0 0 1 0 0 0 2814 202 7 4 4 CDH3 16 68681092 Missense_Mutation SNP A C3L-00279_T 1032777 68681092 21657253 497 6275 GLG1 0 . GRCh38 16 74465793 74465793 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2550A>T p.Glu850Asp p.E850D ENST00000205061 19/27 213 188 25 181 181 0 strelka-varscan-mutect GLG1,missense_variant,p.Glu850Asp,ENST00000205061,NM_012201.5;GLG1,missense_variant,p.Glu850Asp,ENST00000422840,NM_001145667.1;GLG1,missense_variant,p.Glu839Asp,ENST00000447066,NM_001145666.1;Y_RNA,upstream_gene_variant,,ENST00000384794,;GLG1,3_prime_UTR_variant,,ENST00000562090,;GLG1,3_prime_UTR_variant,,ENST00000567951,;GLG1,non_coding_transcript_exon_variant,,ENST00000561481,;GLG1,downstream_gene_variant,,ENST00000566601,;GLG1,upstream_gene_variant,,ENST00000563646,;GLG1,downstream_gene_variant,,ENST00000563432,; A ENST00000205061 Transcript missense_variant 2570/8261 2550/3612 850/1203 E/D gaA/gaT 1 -1 GLG1 HGNC HGNC:4316 protein_coding YES CCDS32485.1 ENSP00000205061 Q92896 UPI00001FFBD9 NM_012201.5 tolerated(0.27) 19/27 PROSITE_profiles:PS51289,hmmpanther:PTHR11884:SF1,hmmpanther:PTHR11884,Pfam_domain:PF00839 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 74465793 74465793 T A 1 0 0 0 0 1 0 0 0 6314 1838 64 4 4 GLG1 16 74465793 Missense_Mutation SNP T C3L-00279_T 5784701 74465793 15872552 498 6276 ZNF469 0 . GRCh38 16 88429342 88429342 + Silent SNP G G A C3L-00279_T C3L-00279_N G G c.1872G>A p.= p.Q624Q ENST00000437464 1/2 590 507 83 531 530 1 strelka-varscan-mutect ZNF469,synonymous_variant,p.=,ENST00000565624,;ZNF469,synonymous_variant,p.=,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript synonymous_variant 1872/13203 1872/11778 624/3925 Q caG/caA COSM5641633 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 1/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 88429342 88429342 G A 1 0 0 0 0 0 0 0 1 18500 962 34 3 3 ZNF469 16 88429342 Silent SNP G C3L-00279_T 13963549 88429342 1909003 499 6277 NLRP1 0 . GRCh38 17 5530635 5530635 + Silent SNP C C A rs200040886 C3L-00279_T C3L-00279_N C C c.3366G>T p.= p.A1122A ENST00000617618 13/18 401 350 51 394 393 1 strelka-varscan-mutect NLRP1,synonymous_variant,p.=,ENST00000262467,NM_001033053.2;NLRP1,synonymous_variant,p.=,ENST00000269280,NM_014922.4;NLRP1,synonymous_variant,p.=,ENST00000617618,NM_033004.3;NLRP1,synonymous_variant,p.=,ENST00000619223,NM_033006.3;NLRP1,synonymous_variant,p.=,ENST00000345221,;NLRP1,synonymous_variant,p.=,ENST00000613500,;NLRP1,synonymous_variant,p.=,ENST00000572272,;NLRP1,synonymous_variant,p.=,ENST00000354411,;NLRP1,synonymous_variant,p.=,ENST00000577119,NM_033007.3;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,synonymous_variant,p.=,ENST00000544378,;NLRP1,3_prime_UTR_variant,,ENST00000571451,; A ENST00000617618 Transcript synonymous_variant 3732/4788 3366/4422 1122/1473 A gcG/gcT rs200040886 1 -1 NLRP1 HGNC HGNC:14374 protein_coding YES CCDS42246.1 ENSP00000478516 Q9C000 UPI0000038309 NM_033004.3 13/18 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13,Pfam_domain:PF13553 LOW 1 SNV 5 1 PASS rs200040886 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 5530635 5530635 C A 1 0 0 0 0 0 0 0 1 10508 639 23 1 1 NLRP1 17 5530635 Silent SNP C C3L-00279_T 5530635 77726806 500 6278 NLRP1 0 . GRCh38 17 5533980 5533980 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.2969G>C p.Ser990Thr p.S990T ENST00000617618 10/18 174 156 18 256 256 0 strelka-varscan-mutect NLRP1,missense_variant,p.Ser990Thr,ENST00000262467,NM_001033053.2;NLRP1,missense_variant,p.Ser990Thr,ENST00000269280,NM_014922.4;NLRP1,missense_variant,p.Ser990Thr,ENST00000617618,NM_033004.3;NLRP1,missense_variant,p.Ser960Thr,ENST00000619223,NM_033006.3;NLRP1,missense_variant,p.Ser990Thr,ENST00000345221,;NLRP1,missense_variant,p.Ser990Thr,ENST00000613500,;NLRP1,missense_variant,p.Ser990Thr,ENST00000572272,;NLRP1,missense_variant,p.Ser960Thr,ENST00000354411,;NLRP1,missense_variant,p.Ser960Thr,ENST00000577119,NM_033007.3;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,missense_variant,p.Ser990Thr,ENST00000571451,;NLRP1,missense_variant,p.Ser990Thr,ENST00000544378,; G ENST00000617618 Transcript missense_variant 3335/4788 2969/4422 990/1473 S/T aGt/aCt 1 -1 NLRP1 HGNC HGNC:14374 protein_coding YES CCDS42246.1 ENSP00000478516 Q9C000 UPI0000038309 NM_033004.3 tolerated(0.39) 10/18 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 5533980 5533980 C G 1 0 0 0 0 1 0 0 0 10508 565 20 4 4 NLRP1 17 5533980 Missense_Mutation SNP C C3L-00279_T 3345 5533980 77723461 501 6279 AIPL1 0 . GRCh38 17 6426679 6426679 + Frame_Shift_Del DEL C C - novel C3L-00279_T C3L-00279_N C C c.720delG p.Leu241Ter p.L241* ENST00000381129 5/6 298 258 40 314 314 0 sindel-varindel-pindel AIPL1,frameshift_variant,p.Leu241Ter,ENST00000381129,NM_014336.4;AIPL1,frameshift_variant,p.Leu178Ter,ENST00000250087,NM_001033054.2;AIPL1,frameshift_variant,p.Leu241Ter,ENST00000575265,;AIPL1,frameshift_variant,p.Leu229Ter,ENST00000574506,NM_001285399.2,NM_001285402.1;AIPL1,frameshift_variant,p.Leu233Ter,ENST00000571740,NM_001285403.2;AIPL1,frameshift_variant,p.Leu219Ter,ENST00000570466,NM_001285400.2;AIPL1,frameshift_variant,p.Leu217Ter,ENST00000576776,NM_001285401.2;AIPL1,frameshift_variant,p.Leu181Ter,ENST00000576307,NM_001033055.2;AIPL1,intron_variant,,ENST00000570584,;AIPL1,downstream_gene_variant,,ENST00000574913,;AIPL1,3_prime_UTR_variant,,ENST00000381128,; - ENST00000381129 Transcript frameshift_variant 801/2959 720/1155 240/384 L/X ctG/ct 1 -1 AIPL1 HGNC HGNC:359 protein_coding YES CCDS11075.1 ENSP00000370521 Q9NZN9 F1T0B6 UPI0000125741 NM_014336.4 5/6 Gene3D:1.25.40.10,PROSITE_profiles:PS50293,hmmpanther:PTHR11242,hmmpanther:PTHR11242:SF2,Low_complexity_(Seg):seg,Superfamily_domains:SSF48452 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 6426679 6426679 C - 1 0 1 0 1 0 0 0 0 513 724 25 0 0 AIPL1 17 6426679 Frame_Shift_Del DEL C C3L-00279_T 892699 6426679 76830762 502 6280 PITPNM3 0 . GRCh38 17 6464667 6464667 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.1995G>T p.= p.L665L ENST00000262483 15/20 139 125 14 117 117 0 strelka-varscan-mutect PITPNM3,synonymous_variant,p.=,ENST00000262483,NM_031220.3;PITPNM3,synonymous_variant,p.=,ENST00000421306,NM_001165966.1;PITPNM3,upstream_gene_variant,,ENST00000575201,;PITPNM3,non_coding_transcript_exon_variant,,ENST00000576664,;PITPNM3,non_coding_transcript_exon_variant,,ENST00000572795,; A ENST00000262483 Transcript synonymous_variant 2083/7086 1995/2925 665/974 L ctG/ctT 1 -1 PITPNM3 HGNC HGNC:21043 protein_coding YES CCDS11076.1 ENSP00000262483 Q9BZ71 UPI000022A281 NM_031220.3 15/20 hmmpanther:PTHR10658 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 6464667 6464667 C A 1 0 0 0 0 0 0 0 1 12048 813 29 2 2 PITPNM3 17 6464667 Silent SNP C C3L-00279_T 37988 6464667 76792774 503 6281 TP53 0 . GRCh38 17 7674947 7674947 + Missense_Mutation SNP A A G rs760043106 C3L-00279_T C3L-00279_N A A c.584T>C p.Ile195Thr p.I195T ENST00000269305 6/11 617 528 89 556 556 0 strelka-varscan-mutect TP53,missense_variant,p.Ile195Thr,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Ile195Thr,ENST00000420246,;TP53,missense_variant,p.Ile156Thr,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Ile156Thr,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Ile195Thr,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Ile156Thr,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Ile195Thr,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Ile156Thr,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Ile195Thr,ENST00000445888,;TP53,missense_variant,p.Ile156Thr,ENST00000619485,;TP53,missense_variant,p.Ile63Thr,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Ile36Thr,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Ile63Thr,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Ile36Thr,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Ile63Thr,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Ile36Thr,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Ile195Thr,ENST00000359597,;TP53,missense_variant,p.Ile184Thr,ENST00000615910,;TP53,missense_variant,p.Ile195Thr,ENST00000413465,;TP53,missense_variant,p.Ile63Thr,ENST00000509690,;TP53,missense_variant,p.Ile102Thr,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Ile156Thr,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 774/2579 584/1182 195/393 I/T aTc/aCc rs760043106,CM092575,TP53_g.12653T>G,TP53_g.12653T>C,TP53_g.12653T>A,COSM11089,COSM116921,COSM116922,COSM116923,COSM116924,COSM1645297,COSM1738250,COSM1738251,COSM1738252,COSM1738253,COSM1738254,COSM212744,COSM212745,COSM212746,COSM212747,COSM3403267,COSM3421936,COSM44539,COSM44877,COSM4858456,COSM4858457 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs760043106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 7674947 7674947 A G 1 0 0 0 0 1 0 0 0 16859 333 12 5 5 TP53 17 7674947 Missense_Mutation SNP A C3L-00279_T 1210280 7674947 75582494 504 6282 PIK3R5 0 . GRCh38 17 8904776 8904776 + Splice_Site SNP C C A novel C3L-00279_T C3L-00279_N C C c.412+1G>T p.X138_splice ENST00000447110 141 118 23 133 133 0 strelka-varscan-mutect PIK3R5,splice_donor_variant,,ENST00000447110,NM_001142633.2;PIK3R5,splice_donor_variant,,ENST00000616147,NM_001251852.1;PIK3R5,splice_donor_variant,,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,splice_donor_variant,,ENST00000623421,NM_001251855.1;PIK3R5,splice_donor_variant,,ENST00000581552,NM_014308.3;PIK3R5,splice_donor_variant,,ENST00000584803,;PIK3R5,downstream_gene_variant,,ENST00000581895,;PIK3R5,splice_donor_variant,,ENST00000578457,;PIK3R5,splice_donor_variant,,ENST00000580959,;PIK3R5,splice_donor_variant,,ENST00000577981,;PIK3R5,splice_donor_variant,,ENST00000269300,;PIK3R5,splice_donor_variant,,ENST00000578515,; A ENST00000447110 Transcript splice_donor_variant -/4495 412/2643 138/880 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 5/18 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 5 1 14 8904776 8904776 C A 1 0 0 0 0 0 0 1 0 12017 521 18 2 2 PIK3R5 17 8904776 Splice_Site SNP C C3L-00279_T 1229829 8904776 74352665 505 6283 DNAH9 0 . GRCh38 17 11690022 11690022 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.4200C>A p.Asp1400Glu p.D1400E ENST00000262442 20/69 460 397 63 599 599 0 strelka-varscan-mutect DNAH9,missense_variant,p.Asp1400Glu,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Asp1400Glu,ENST00000454412,; A ENST00000262442 Transcript missense_variant 4268/13750 4200/13461 1400/4486 D/E gaC/gaA 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 tolerated(0.05) 20/69 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 11690022 11690022 C A 1 0 0 0 0 1 0 0 0 4423 506 18 2 2 DNAH9 17 11690022 Missense_Mutation SNP C C3L-00279_T 2785246 11690022 71567419 506 6284 FBXW10 0 . GRCh38 17 18749747 18749747 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.696G>T p.= p.R232R ENST00000395665 3/14 237 214 23 224 224 0 varscan-mutect FBXW10,synonymous_variant,p.=,ENST00000308799,;FBXW10,synonymous_variant,p.=,ENST00000395665,NM_001267585.1;FBXW10,synonymous_variant,p.=,ENST00000301938,NM_001267586.1;FBXW10,3_prime_UTR_variant,,ENST00000574478,; T ENST00000395665 Transcript synonymous_variant 917/3431 696/3159 232/1052 R cgG/cgT 1 1 FBXW10 HGNC HGNC:1211 protein_coding YES CCDS11199.3 ENSP00000379025 Q5XX13 UPI0000200B30 NM_001267585.1 3/14 hmmpanther:PTHR19872,hmmpanther:PTHR19872:SF7 LOW 1 SNV 1 1 PASS rs1172318381 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 18749747 18749747 G T 1 0 0 0 0 0 0 0 1 5626 1248 44 2 2 FBXW10 17 18749747 Silent SNP G C3L-00279_T 7059725 18749747 64507694 507 6285 CCL3 0 . GRCh38 17 36088759 36088759 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.192C>A p.Phe64Leu p.F64L ENST00000613922 3/3 430 380 50 458 458 0 strelka-varscan-mutect CCL3,missense_variant,p.Phe64Leu,ENST00000613922,NM_002983.2;AC069363.1,intron_variant,,ENST00000616926,;AC069363.1,intron_variant,,ENST00000620056,;AC069363.1,intron_variant,,ENST00000615750,;CCL3,non_coding_transcript_exon_variant,,ENST00000614051,;CCL3,intron_variant,,ENST00000613928,; T ENST00000613922 Transcript missense_variant 275/778 192/279 64/92 F/L ttC/ttA 1 -1 CCL3 HGNC HGNC:10627 protein_coding YES CCDS11307.1 ENSP00000477908 P10147 UPI00001362C9 NM_002983.2 deleterious(0) 3/3 Gene3D:2.40.50.40,Pfam_domain:PF00048,PROSITE_patterns:PS00472,hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF94,SMART_domains:SM00199,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 36088759 36088759 G T 1 0 0 0 0 1 0 0 0 2599 1188 41 2 2 CCL3 17 36088759 Missense_Mutation SNP G C3L-00279_T 17339012 36088759 47168682 508 6286 SRCIN1 0 . GRCh38 17 38543855 38543855 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.3385G>T p.Ala1129Ser p.A1129S ENST00000617146 18/19 239 204 35 164 164 0 strelka-varscan-mutect SRCIN1,missense_variant,p.Ala1129Ser,ENST00000617146,NM_025248.2;SRCIN1,missense_variant,p.Ala1163Ser,ENST00000621492,;SRCIN1,missense_variant,p.Ala917Ser,ENST00000622190,;SRCIN1,downstream_gene_variant,,ENST00000613927,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000621763,;SRCIN1,downstream_gene_variant,,ENST00000621275,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000622519,; A ENST00000617146 Transcript missense_variant 3610/7058 3385/3552 1129/1183 A/S Gcc/Tcc 1 -1 SRCIN1 HGNC HGNC:29506 protein_coding YES CCDS45660.1 ENSP00000484715 Q9C0H9 UPI0000E27F82 NM_025248.2 tolerated(0.51) 18/19 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF5 MODERATE 1 SNV 2 1 PASS . . 0 205 0 2 3 0 0 0 -16.37029 0.9199781 1 1 1 0 A 3 1 14 38543855 38543855 C A 1 0 0 0 0 1 0 0 0 15494 739 26 2 2 SRCIN1 17 38543855 Missense_Mutation SNP C C3L-00279_T 2455096 38543855 44713586 509 6287 GSDMB 0 . GRCh38 17 39905904 39905904 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.970G>C p.Gly324Arg p.G324R ENST00000418519 9/11 262 247 15 259 259 0 strelka-varscan-mutect GSDMB,missense_variant,p.Gly302Arg,ENST00000394175,NM_018530.2;GSDMB,missense_variant,p.Gly324Arg,ENST00000418519,NM_001165958.1;GSDMB,missense_variant,p.Gly315Arg,ENST00000520542,NM_001165959.1;GSDMB,missense_variant,p.Gly311Arg,ENST00000309481,NM_001042471.1;GSDMB,missense_variant,p.Gly324Arg,ENST00000360317,;GSDMB,missense_variant,p.Gly311Arg,ENST00000394179,;GSDMB,3_prime_UTR_variant,,ENST00000523371,;GSDMB,3_prime_UTR_variant,,ENST00000524039,;GSDMB,3_prime_UTR_variant,,ENST00000522564,;GSDMB,non_coding_transcript_exon_variant,,ENST00000477054,;GSDMB,non_coding_transcript_exon_variant,,ENST00000479136,;GSDMB,non_coding_transcript_exon_variant,,ENST00000486560,;GSDMB,downstream_gene_variant,,ENST00000464556,;GSDMB,downstream_gene_variant,,ENST00000519429,;GSDMB,downstream_gene_variant,,ENST00000468820,; G ENST00000418519 Transcript missense_variant 1101/1597 970/1251 324/416 G/R Ggg/Cgg 1 -1 GSDMB HGNC HGNC:23690 protein_coding YES CCDS54120.1 ENSP00000415049 Q8TAX9 UPI0000200C24 NM_001165958.1 deleterious(0) 9/11 hmmpanther:PTHR16399,hmmpanther:PTHR16399:SF20,Pfam_domain:PF04598 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 39905904 39905904 C G 1 0 0 0 0 1 0 0 0 6699 594 21 4 4 GSDMB 17 39905904 Missense_Mutation SNP C C3L-00279_T 1362049 39905904 43351537 510 6288 LRRC3C 0 . GRCh38 17 39944569 39944569 + Silent SNP C C A rs145060487 C3L-00279_T C3L-00279_N C C c.663C>A p.= p.T221T ENST00000377924 2/2 86 74 12 92 91 1 strelka-varscan-mutect LRRC3C,synonymous_variant,p.=,ENST00000377924,NM_001195545.1;RP11-387H17.4,downstream_gene_variant,,ENST00000582263,; A ENST00000377924 Transcript synonymous_variant 713/891 663/828 221/275 T acC/acA rs145060487 1 1 LRRC3C HGNC HGNC:40034 protein_coding YES CCDS54121.1 ENSP00000367157 A6NJW4 UPI0000198ACC NM_001195545.1 2/2 LOW 1 SNV 3 1 PASS rs145060487 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 14 39944569 39944569 C A 1 0 0 0 0 0 0 0 1 8892 639 23 1 1 LRRC3C 17 39944569 Silent SNP C C3L-00279_T 38665 39944569 43312872 511 6289 KRT23 0 . GRCh38 17 40936481 40936481 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.123C>A p.= p.A41A ENST00000209718 2/9 76 66 10 48 48 0 strelka-varscan-mutect KRT23,synonymous_variant,p.=,ENST00000209718,NM_015515.4;KRT23,synonymous_variant,p.=,ENST00000485751,;KRT23,intron_variant,,ENST00000436344,NM_001282433.1;KRT23,upstream_gene_variant,,ENST00000584517,;AC004231.2,intron_variant,,ENST00000418393,;KRT23,downstream_gene_variant,,ENST00000582283,;KRT23,downstream_gene_variant,,ENST00000585006,;KRT23,non_coding_transcript_exon_variant,,ENST00000582754,;KRT23,intron_variant,,ENST00000462312,;KRT23,intron_variant,,ENST00000494691,; T ENST00000209718 Transcript synonymous_variant 548/1987 123/1269 41/422 A gcC/gcA 1 -1 KRT23 HGNC HGNC:6438 protein_coding YES CCDS11380.1 ENSP00000209718 Q9C075 A0A024R1X9 UPI000013C66F NM_015515.4 2/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF44 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.99354 1 1 1 1 0 T 2 4 14 40936481 40936481 G T 1 0 0 0 0 0 0 0 1 8342 1219 43 2 2 KRT23 17 40936481 Silent SNP G C3L-00279_T 991912 40936481 42320960 512 6290 KRT34 0 . GRCh38 17 41379068 41379068 + Missense_Mutation SNP G G T rs529354447 C3L-00279_T C3L-00279_N G G c.1111C>A p.Arg371Ser p.R371S ENST00000394001 6/7 544 475 69 513 513 0 strelka-varscan-mutect KRT34,missense_variant,p.Arg371Ser,ENST00000394001,NM_021013.3; T ENST00000394001 Transcript missense_variant 1142/1751 1111/1311 371/436 R/S Cgc/Agc rs529354447,COSM3517314 1 -1 KRT34 HGNC HGNC:6452 protein_coding YES CCDS11390.1 ENSP00000377570 O76011 UPI000013CD0C NM_021013.3 deleterious(0) 6/7 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01248,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF165,SMART_domains:SM01391,Superfamily_domains:SSF64593 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs529354447 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 41379068 41379068 G T 1 0 0 0 0 1 0 0 0 8353 1116 39 1 1 KRT34 17 41379068 Missense_Mutation SNP G C3L-00279_T 442587 41379068 41878373 513 6291 ADAM11 0 . GRCh38 17 44777251 44777251 + Silent SNP C C T C3L-00279_T C3L-00279_N C C c.1767C>T p.= p.V589V ENST00000200557 21/27 84 71 13 75 75 0 strelka-varscan-mutect ADAM11,synonymous_variant,p.=,ENST00000200557,NM_001318933.1,NM_002390.4;ADAM11,synonymous_variant,p.=,ENST00000535346,;ADAM11,synonymous_variant,p.=,ENST00000587773,;ADAM11,3_prime_UTR_variant,,ENST00000355638,;ADAM11,non_coding_transcript_exon_variant,,ENST00000588363,; T ENST00000200557 Transcript synonymous_variant 1936/4571 1767/2310 589/769 V gtC/gtT COSM5342941,COSM5342942 1 1 ADAM11 HGNC HGNC:189 protein_coding YES CCDS11486.1 ENSP00000200557 O75078 UPI000013C629 NM_001318933.1,NM_002390.4 21/27 Pfam_domain:PF08516,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF114,SMART_domains:SM00608 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 44777251 44777251 C T 1 0 0 0 0 0 0 0 1 279 842 30 3 3 ADAM11 17 44777251 Silent SNP C C3L-00279_T 3398183 44777251 38480190 514 6292 MAP3K14 0 . GRCh38 17 45286572 45286572 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.1011A>T p.= p.L337L ENST00000376926 4/15 315 269 46 218 217 1 strelka-varscan-mutect MAP3K14,synonymous_variant,p.=,ENST00000376926,;MAP3K14,synonymous_variant,p.=,ENST00000344686,NM_003954.4;MAP3K14,intron_variant,,ENST00000617331,; A ENST00000376926 Transcript synonymous_variant 1242/4583 1011/2844 337/947 L ctA/ctT 1 -1 MAP3K14 HGNC HGNC:6853 protein_coding YES CCDS74079.1 ENSP00000482657 Q99558 UPI0000074220 4/15 hmmpanther:PTHR24361:SF226,hmmpanther:PTHR24361,PIRSF_domain:PIRSF038175 LOW 1 SNV 1 1 PASS rs1346051042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 45286572 45286572 T A 1 0 0 0 0 0 0 0 1 9170 1509 53 4 4 MAP3K14 17 45286572 Silent SNP T C3L-00279_T 509321 45286572 37970869 515 6293 HOXB1 0 . GRCh38 17 48530502 48530502 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.403G>T p.Gly135Trp p.G135W ENST00000239174 1/2 190 170 20 132 132 0 strelka-varscan-mutect HOXB1,missense_variant,p.Gly135Trp,ENST00000239174,NM_002144.3;HOXB1,missense_variant,p.Gly135Trp,ENST00000577092,; A ENST00000239174 Transcript missense_variant 496/2020 403/906 135/301 G/W Ggg/Tgg 1 -1 HOXB1 HGNC HGNC:5111 protein_coding YES CCDS32675.1 ENSP00000355140 P14653 UPI0000163BFF NM_002144.3 deleterious(0.01) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF167,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 48530502 48530502 C A 1 0 0 0 0 1 0 0 0 7193 623 22 2 2 HOXB1 17 48530502 Missense_Mutation SNP C C3L-00279_T 3243930 48530502 34726939 516 6294 SEPT4 0 . GRCh38 17 58525145 58525145 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.640G>A p.Gly214Ser p.G214S ENST00000457347 6/13 263 241 22 199 199 0 strelka-varscan-mutect SEPT4,missense_variant,p.Gly180Ser,ENST00000426861,NM_080415.3;SEPT4,missense_variant,p.Gly214Ser,ENST00000457347,NM_001256782.1;SEPT4,missense_variant,p.Gly199Ser,ENST00000317268,NM_004574.4;SEPT4,missense_variant,p.Gly52Ser,ENST00000583114,NM_001256822.1;SEPT4,missense_variant,p.Gly191Ser,ENST00000412945,NM_001198713.1;SEPT4,missense_variant,p.Gly180Ser,ENST00000393086,;SEPT4,missense_variant,p.Gly180Ser,ENST00000317256,NM_080416.3;SEPT4,missense_variant,p.Gly100Ser,ENST00000580844,;SEPT4,missense_variant,p.Gly100Ser,ENST00000579371,;SEPT4,missense_variant,p.Gly81Ser,ENST00000580809,;SEPT4,missense_variant,p.Gly204Ser,ENST00000583291,;SEPT4,missense_variant,p.Gly105Ser,ENST00000577729,;SEPT4,downstream_gene_variant,,ENST00000581607,;SEPT4-AS1,intron_variant,,ENST00000580589,;SEPT4-AS1,upstream_gene_variant,,ENST00000580769,;SEPT4-AS1,upstream_gene_variant,,ENST00000578022,;SEPT4,downstream_gene_variant,,ENST00000580791,;SEPT4,downstream_gene_variant,,ENST00000584528,;SEPT4,downstream_gene_variant,,ENST00000580740,;SEPT4,downstream_gene_variant,,ENST00000581921,;SEPT4,3_prime_UTR_variant,,ENST00000581615,;SEPT4,3_prime_UTR_variant,,ENST00000578131,;SEPT4,non_coding_transcript_exon_variant,,ENST00000585170,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580796,;SEPT4,non_coding_transcript_exon_variant,,ENST00000582270,;SEPT4,non_coding_transcript_exon_variant,,ENST00000583273,;SEPT4,non_coding_transcript_exon_variant,,ENST00000577440,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584488,;SEPT4,downstream_gene_variant,,ENST00000582976,;SEPT4,downstream_gene_variant,,ENST00000584789,;SEPT4,downstream_gene_variant,,ENST00000582248,;SEPT4,downstream_gene_variant,,ENST00000578747,; T ENST00000457347 Transcript missense_variant 785/1795 640/1482 214/493 G/S Ggt/Agt 1 -1 SEPT4 HGNC HGNC:9165 protein_coding YES CCDS58582.1 ENSP00000402000 O43236 UPI00017A809C NM_001256782.1 deleterious(0.01) 6/13 Gene3D:3.40.50.300,Pfam_domain:PF00735,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF71,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 58525145 58525145 C T 1 0 0 0 0 1 0 0 0 14342 623 22 3 3 SEPT4 17 58525145 Missense_Mutation SNP C C3L-00279_T 9994643 58525145 24732296 517 6295 ACE 0 . GRCh38 17 63479804 63479804 + Missense_Mutation SNP G G T rs12720754 C3L-00279_T C3L-00279_N G G c.547G>T p.Ala183Ser p.A183S ENST00000290866 4/25 578 504 74 474 474 0 strelka-varscan-mutect ACE,missense_variant,p.Ala183Ser,ENST00000428043,;ACE,missense_variant,p.Ala183Ser,ENST00000290866,NM_000789.3;ACE,missense_variant,p.Ala183Ser,ENST00000582627,;ACE,non_coding_transcript_exon_variant,,ENST00000584529,;ACE,downstream_gene_variant,,ENST00000583336,;ACE,synonymous_variant,p.=,ENST00000582678,;ACE,non_coding_transcript_exon_variant,,ENST00000580318,;ACE,upstream_gene_variant,,ENST00000579726,;ACE,downstream_gene_variant,,ENST00000579462,; T ENST00000290866 Transcript missense_variant 571/4959 547/3921 183/1306 A/S Gcc/Tcc rs12720754 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 tolerated(0.25) 4/25 Pfam_domain:PF01401,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs12720754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 63479804 63479804 G T 1 0 0 0 0 1 0 0 0 174 1087 38 1 1 ACE 17 63479804 Missense_Mutation SNP G C3L-00279_T 4954659 63479804 19777637 518 6296 CSHL1 0 . GRCh38 17 63910878 63910878 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.57C>A p.= p.P19P ENST00000309894 2/5 635 555 80 546 546 0 varscan-mutect CSHL1,synonymous_variant,p.=,ENST00000392824,;CSHL1,synonymous_variant,p.=,ENST00000611417,;CSHL1,synonymous_variant,p.=,ENST00000259003,NM_001321068.1;CSHL1,synonymous_variant,p.=,ENST00000309894,NM_022581.1,NM_022579.1;CSHL1,intron_variant,,ENST00000450719,;CSHL1,intron_variant,,ENST00000561003,;CSHL1,intron_variant,,ENST00000346606,NM_001318.2;CSHL1,intron_variant,,ENST00000438387,NM_022580.1;CSHL1,non_coding_transcript_exon_variant,,ENST00000558099,;CSHL1,non_coding_transcript_exon_variant,,ENST00000560999,;CSHL1,non_coding_transcript_exon_variant,,ENST00000558609,; T ENST00000309894 Transcript synonymous_variant 57/669 57/669 19/222 P ccC/ccA 1 -1 CSHL1 HGNC HGNC:2442 protein_coding YES CCDS11652.1 ENSP00000309524 Q14406 UPI00001602B9 NM_022581.1,NM_022579.1 2/5 Pfam_domain:PF00103,hmmpanther:PTHR11417,hmmpanther:PTHR11417:SF40,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 63910878 63910878 G T 1 0 0 0 0 0 0 0 1 3743 987 35 2 2 CSHL1 17 63910878 Silent SNP G C3L-00279_T 431074 63910878 19346563 519 6297 TTYH2 0 . GRCh38 17 74215687 74215687 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.41G>T p.Cys14Phe p.C14F ENST00000529107 1/14 250 231 19 224 224 0 strelka-varscan-mutect TTYH2,missense_variant,p.Cys14Phe,ENST00000529107,;TTYH2,intron_variant,,ENST00000269346,NM_032646.5;MGC16275,upstream_gene_variant,,ENST00000499670,;MGC16275,upstream_gene_variant,,ENST00000532794,;MGC16275,upstream_gene_variant,,ENST00000531617,; T ENST00000529107 Transcript missense_variant 72/2015 41/1542 14/513 C/F tGt/tTt 1 1 TTYH2 HGNC HGNC:13877 protein_coding ENSP00000433089 B4DKD1 UPI00017A761E deleterious_low_confidence(0) 1/14 MODERATE SNV 2 1 PASS rs1216533687 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 74215687 74215687 G T 1 0 0 0 0 1 0 0 0 17250 1377 48 2 2 TTYH2 17 74215687 Missense_Mutation SNP G C3L-00279_T 10304809 74215687 9041754 520 6298 BTBD17 0 . GRCh38 17 74360099 74360099 + Silent SNP G G T rs775484462 C3L-00279_T C3L-00279_N G G c.232C>A p.= p.R78R ENST00000375366 2/3 393 340 53 329 329 0 strelka-varscan-mutect BTBD17,synonymous_variant,p.=,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000389916,NM_153209.3; T ENST00000375366 Transcript synonymous_variant 359/1805 232/1437 78/478 R Cgg/Agg rs775484462,COSM370788 1 -1 BTBD17 HGNC HGNC:33758 protein_coding YES CCDS32719.1 ENSP00000364515 A6NE02 UPI00001D7961 NM_001080466.1 2/3 PROSITE_profiles:PS50097,hmmpanther:PTHR24410:SF12,hmmpanther:PTHR24410,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 0,1 LOW 1 SNV 2 0,1 1 PASS rs775484462 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 74360099 74360099 G T 1 0 0 0 0 0 0 0 1 1716 1115 39 1 1 BTBD17 17 74360099 Silent SNP G C3L-00279_T 144412 74360099 8897342 521 6299 RECQL5 0 . GRCh38 17 75661681 75661681 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.799A>T p.Arg267Trp p.R267W ENST00000317905 5/20 208 186 22 218 218 0 strelka-varscan-mutect RECQL5,missense_variant,p.Arg267Trp,ENST00000420326,NM_001003716.3;RECQL5,missense_variant,p.Arg267Trp,ENST00000317905,NM_004259.6;RECQL5,missense_variant,p.Arg240Trp,ENST00000423245,;RECQL5,missense_variant,p.Arg267Trp,ENST00000578201,;RECQL5,missense_variant,p.Arg267Trp,ENST00000584999,;RECQL5,missense_variant,p.Arg267Trp,ENST00000340830,NM_001003715.3;RECQL5,intron_variant,,ENST00000580078,;RECQL5,upstream_gene_variant,,ENST00000579274,;RECQL5,upstream_gene_variant,,ENST00000582464,; A ENST00000317905 Transcript missense_variant 959/3704 799/2976 267/991 R/W Agg/Tgg 1 -1 RECQL5 HGNC HGNC:9950 protein_coding YES CCDS42380.1 ENSP00000317636 O94762 A0A024R8M9 UPI0000133477 NM_004259.6 deleterious(0) 5/20 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF85,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00614 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 75661681 75661681 T A 1 0 0 0 0 1 0 0 0 13373 1579 55 4 4 RECQL5 17 75661681 Missense_Mutation SNP T C3L-00279_T 1301582 75661681 7595760 522 6300 RNF157 0 . GRCh38 17 76159517 76159517 + Missense_Mutation SNP G G T rs753352670 C3L-00279_T C3L-00279_N G G c.1122C>A p.Asn374Lys p.N374K ENST00000269391 12/19 128 114 14 110 110 0 strelka-varscan-mutect RNF157,missense_variant,p.Asn374Lys,ENST00000269391,NM_052916.2;RNF157,missense_variant,p.Asn374Lys,ENST00000319945,;RNF157,downstream_gene_variant,,ENST00000591615,;RNF157,upstream_gene_variant,,ENST00000591355,;RP11-449J21.5,downstream_gene_variant,,ENST00000586661,;RP11-449J21.5,downstream_gene_variant,,ENST00000592748,;RNF157,upstream_gene_variant,,ENST00000592869,;RNF157,downstream_gene_variant,,ENST00000593155,; T ENST00000269391 Transcript missense_variant 1255/4955 1122/2040 374/679 N/K aaC/aaA rs753352670,COSM5519512,COSM5519513 1 -1 RNF157 HGNC HGNC:29402 protein_coding YES CCDS32740.1 ENSP00000269391 Q96PX1 UPI00001C1FDD NM_052916.2 deleterious(0) 12/19 hmmpanther:PTHR22996:SF1,hmmpanther:PTHR22996 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs753352670 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 76159517 76159517 G T 1 0 0 0 0 1 0 0 0 13632 1136 40 1 1 RNF157 17 76159517 Missense_Mutation SNP G C3L-00279_T 497836 76159517 7097924 523 6301 JMJD6 0 . GRCh38 17 76720483 76720483 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.957G>A p.= p.E319E ENST00000445478 5/7 206 175 31 182 182 0 strelka-varscan-mutect JMJD6,missense_variant,p.Ala351Thr,ENST00000617192,;JMJD6,synonymous_variant,p.=,ENST00000445478,NM_001081461.1;JMJD6,synonymous_variant,p.=,ENST00000397625,NM_015167.2;JMJD6,intron_variant,,ENST00000585429,;uc_338,downstream_gene_variant,,ENST00000613268,;JMJD6,missense_variant,p.Ala351Thr,ENST00000542934,;JMJD6,3_prime_UTR_variant,,ENST00000303996,;JMJD6,non_coding_transcript_exon_variant,,ENST00000591460,;JMJD6,non_coding_transcript_exon_variant,,ENST00000589982,; T ENST00000445478 Transcript synonymous_variant 1161/5303 957/1245 319/414 E gaG/gaA 1 -1 JMJD6 HGNC HGNC:19355 protein_coding YES CCDS42383.1 ENSP00000394085 Q6NYC1 UPI00003DFD0B NM_001081461.1 5/7 hmmpanther:PTHR12480,hmmpanther:PTHR12480:SF5,Superfamily_domains:SSF51197 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999607 1 1 1 0 T 2 4 14 76720483 76720483 C T 1 0 0 0 0 0 0 0 1 7866 797 28 3 3 JMJD6 17 76720483 Silent SNP C C3L-00279_T 560966 76720483 6536958 524 6302 TMC6 0 . GRCh38 17 78119359 78119359 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.1749G>T p.= p.R583R ENST00000590602 14/20 653 574 79 559 558 1 strelka-varscan-mutect TMC6,synonymous_variant,p.=,ENST00000590602,NM_001127198.1;TMC6,synonymous_variant,p.=,ENST00000392467,;TMC6,synonymous_variant,p.=,ENST00000322914,NM_007267.6;TMC6,synonymous_variant,p.=,ENST00000591436,;TMC6,intron_variant,,ENST00000306591,;TMC6,downstream_gene_variant,,ENST00000589553,;TMC6,non_coding_transcript_exon_variant,,ENST00000590934,;TMC6,intron_variant,,ENST00000592076,;TMC6,non_coding_transcript_exon_variant,,ENST00000593044,;TMC6,non_coding_transcript_exon_variant,,ENST00000591756,;TMC6,downstream_gene_variant,,ENST00000588087,;TMC6,downstream_gene_variant,,ENST00000586271,;TMC6,upstream_gene_variant,,ENST00000589933,;TMC6,downstream_gene_variant,,ENST00000585849,; A ENST00000590602 Transcript synonymous_variant 1909/5268 1749/2418 583/805 R cgG/cgT 1 -1 TMC6 HGNC HGNC:18021 protein_coding YES CCDS32748.1 ENSP00000465261 Q7Z403 A0A024R8V2 UPI000013D819 NM_001127198.1 14/20 hmmpanther:PTHR23302:SF4,hmmpanther:PTHR23302,Pfam_domain:PF07810 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 78119359 78119359 C A 1 0 0 0 0 0 0 0 1 16435 842 30 2 2 TMC6 17 78119359 Silent SNP C C3L-00279_T 1398876 78119359 5138082 525 6303 CBX2 0 . GRCh38 17 79784868 79784868 + Silent SNP G G T rs202081500 C3L-00279_T C3L-00279_N G G c.1425G>T p.= p.S475S ENST00000310942 5/5 330 289 41 252 252 0 strelka-varscan-mutect CBX2,synonymous_variant,p.=,ENST00000310942,NM_005189.2;CBX2,downstream_gene_variant,,ENST00000269399,NM_032647.3; T ENST00000310942 Transcript synonymous_variant 1529/4644 1425/1599 475/532 S tcG/tcT rs202081500,COSM2802782 1 1 CBX2 HGNC HGNC:1552 protein_coding YES CCDS32757.1 ENSP00000308750 Q14781 UPI000004C4E1 NM_005189.2 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF98 0,1 LOW 1 SNV 2 0,1 1 PASS rs202081500 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 79784868 79784868 G T 1 0 0 0 0 0 0 0 1 2418 1074 38 1 1 CBX2 17 79784868 Silent SNP G C3L-00279_T 1665509 79784868 3472573 526 6304 PIEZO2 0 . GRCh38 18 10705738 10705738 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.5258C>G p.Thr1753Arg p.T1753R ENST00000503781 37/52 89 74 15 101 101 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Thr1704Arg,ENST00000383408,;PIEZO2,missense_variant,p.Thr1753Arg,ENST00000302079,;PIEZO2,missense_variant,p.Thr1778Arg,ENST00000580640,;PIEZO2,missense_variant,p.Thr1753Arg,ENST00000503781,NM_022068.3;PIEZO2,upstream_gene_variant,,ENST00000538948,;RP11-856M7.2,intron_variant,,ENST00000584167,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; C ENST00000503781 Transcript missense_variant 5258/8259 5258/8259 1753/2752 T/R aCg/aGg 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 tolerated(0.06) 37/52 MODERATE 1 SNV 1 1 PASS rs1250272856 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 10705738 10705738 G C 1 0 0 0 0 1 0 0 0 11975 1145 40 4 4 PIEZO2 18 10705738 Missense_Mutation SNP G C3L-00279_T 10705738 69667547 527 6305 GREB1L 0 . GRCh38 18 21449617 21449617 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.1501C>T p.Pro501Ser p.P501S ENST00000580732 12/33 300 259 41 284 284 0 strelka-varscan-mutect GREB1L,missense_variant,p.Pro501Ser,ENST00000580732,;GREB1L,missense_variant,p.Pro501Ser,ENST00000424526,NM_001142966.1;GREB1L,intron_variant,,ENST00000269218,;GREB1L,upstream_gene_variant,,ENST00000581327,;SNORD23,downstream_gene_variant,,ENST00000408212,;RP11-296E23.1,intron_variant,,ENST00000584611,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578368,;GREB1L,non_coding_transcript_exon_variant,,ENST00000584446,;GREB1L,upstream_gene_variant,,ENST00000578955,;GREB1L,upstream_gene_variant,,ENST00000580683,; T ENST00000580732 Transcript missense_variant 1882/8749 1501/5772 501/1923 P/S Cct/Tct 1 1 GREB1L HGNC HGNC:31042 protein_coding YES CCDS45836.1 ENSP00000464162 Q9C091 UPI0001642876 tolerated(0.22) 12/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF12 MODERATE SNV 5 1 PASS rs1480242087 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 21449617 21449617 C T 1 0 0 0 0 1 0 0 0 6640 623 22 3 3 GREB1L 18 21449617 Missense_Mutation SNP C C3L-00279_T 10743879 21449617 58923668 528 6306 ZNF521 0 . GRCh38 18 25322188 25322188 + Splice_Site SNP C C A novel C3L-00279_T C3L-00279_N C C c.41-1G>T p.X14_splice ENST00000361524 239 193 46 162 161 1 strelka-varscan-mutect ZNF521,splice_acceptor_variant,,ENST00000361524,NM_015461.2;ZNF521,splice_acceptor_variant,,ENST00000584787,NM_001308225.1;ZNF521,splice_acceptor_variant,,ENST00000538137,;ZNF521,splice_acceptor_variant,,ENST00000577801,;ZNF521,splice_acceptor_variant,,ENST00000580488,;ZNF521,splice_acceptor_variant,,ENST00000577461,;ZNF521,splice_acceptor_variant,,ENST00000579111,;ZNF521,splice_acceptor_variant,,ENST00000582584,;ZNF521,splice_acceptor_variant,,ENST00000583005,;ZNF521,splice_acceptor_variant,,ENST00000399425,;ZNF521,non_coding_transcript_exon_variant,,ENST00000583398,; A ENST00000361524 Transcript splice_acceptor_variant -/4871 41/3936 14/1311 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 2/7 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 14 25322188 25322188 C A 1 0 0 0 0 0 0 1 0 18537 927 32 2 2 ZNF521 18 25322188 Splice_Site SNP C C3L-00279_T 3872571 25322188 55051097 529 6307 SS18 0 . GRCh38 18 26038555 26038555 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.880G>T p.Gly294Cys p.G294C ENST00000415083 7/11 182 158 24 130 130 0 strelka-varscan-mutect SS18,stop_gained,p.Gly294Ter,ENST00000269137,NM_005637.2;SS18,missense_variant,p.Gly294Cys,ENST00000415083,NM_001007559.1;SS18,missense_variant,p.Gly271Cys,ENST00000542420,NM_001308201.1;SS18,downstream_gene_variant,,ENST00000585241,;SS18,upstream_gene_variant,,ENST00000582092,;SS18,splice_region_variant,,ENST00000579640,;SS18,splice_region_variant,,ENST00000269138,;SS18,splice_region_variant,,ENST00000585121,;SS18,splice_region_variant,,ENST00000539244,;SS18,upstream_gene_variant,,ENST00000580958,; A ENST00000415083 Transcript missense_variant,splice_region_variant 936/3414 880/1257 294/418 G/C Ggt/Tgt 1 -1 SS18 HGNC HGNC:11340 protein_coding YES CCDS32807.1 ENSP00000414516 Q15532 A0A024RC40 UPI0000136056 NM_001007559.1 deleterious_low_confidence(0.01) 7/11 hmmpanther:PTHR23107,hmmpanther:PTHR23107:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 26038555 26038555 C A 1 0 0 0 0 1 0 0 0 15549 608 21 2 2 SS18 18 26038555 Missense_Mutation SNP C C3L-00279_T 716367 26038555 54334730 530 6308 DSG3 0 . GRCh38 18 31475954 31475954 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.2694C>G p.Cys898Trp p.C898W ENST00000257189 16/16 400 351 49 329 329 0 strelka-varscan-mutect DSG3,missense_variant,p.Cys898Trp,ENST00000257189,NM_001944.2; G ENST00000257189 Transcript missense_variant 2777/5525 2694/3000 898/999 C/W tgC/tgG 1 1 DSG3 HGNC HGNC:3050 protein_coding YES CCDS11898.1 ENSP00000257189 P32926 UPI000013CF4B NM_001944.2 tolerated(0.18) 16/16 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 31475954 31475954 C G 1 0 0 0 0 1 0 0 0 4599 747 26 4 4 DSG3 18 31475954 Missense_Mutation SNP C C3L-00279_T 5437399 31475954 48897331 531 6309 ASXL3 0 . GRCh38 18 33739545 33739545 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.2141C>T p.Ser714Leu p.S714L ENST00000269197 11/12 273 250 23 81 81 0 strelka-varscan-mutect ASXL3,missense_variant,p.Ser714Leu,ENST00000269197,NM_030632.1;ASXL3,3_prime_UTR_variant,,ENST00000592288,; T ENST00000269197 Transcript missense_variant 2196/11399 2141/6747 714/2248 S/L tCa/tTa 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 deleterious_low_confidence(0) 11/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF18 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 33739545 33739545 C T 1 0 0 0 0 1 0 0 0 1216 838 29 3 3 ASXL3 18 33739545 Missense_Mutation SNP C C3L-00279_T 2263591 33739545 46633740 532 6310 SETBP1 0 . GRCh38 18 44952262 44952262 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2922C>A p.Tyr974Ter p.Y974* ENST00000282030 4/6 793 717 76 623 623 0 strelka-varscan-mutect SETBP1,stop_gained,p.Tyr974Ter,ENST00000282030,NM_015559.2; A ENST00000282030 Transcript stop_gained 3218/9899 2922/4791 974/1596 Y/* taC/taA 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 HIGH 1 SNV 1 1 PASS rs1311498327 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 44952262 44952262 C A 1 0 0 0 0 0 1 0 0 14406 489 17 2 2 SETBP1 18 44952262 Nonsense_Mutation SNP C C3L-00279_T 11212717 44952262 35421023 533 6311 ST8SIA5 0 . GRCh38 18 46680409 46680409 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.872C>A p.Thr291Asn p.T291N ENST00000538168 8/8 289 253 36 349 349 0 strelka-varscan-mutect ST8SIA5,missense_variant,p.Thr291Asn,ENST00000538168,NM_001307986.1;ST8SIA5,missense_variant,p.Thr255Asn,ENST00000315087,NM_013305.4;ST8SIA5,missense_variant,p.Thr224Asn,ENST00000536490,NM_001307987.1;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000590497,;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000587428,; T ENST00000538168 Transcript missense_variant 1173/13761 872/1239 291/412 T/N aCc/aAc 1 -1 ST8SIA5 HGNC HGNC:17827 protein_coding YES CCDS77184.1 ENSP00000445492 O15466 UPI0000E03E3B NM_001307986.1 8/8 hmmpanther:PTHR11987:SF4,hmmpanther:PTHR11987,PIRSF_domain:PIRSF005557,Pfam_domain:PF00777 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 46680409 46680409 G T 1 0 0 0 0 1 0 0 0 15613 1261 44 2 2 ST8SIA5 18 46680409 Missense_Mutation SNP G C3L-00279_T 1728147 46680409 33692876 534 6312 PIAS2 0 . GRCh38 18 46855371 46855371 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.700G>A p.Val234Ile p.V234I ENST00000585916 5/14 67 62 5 32 32 0 strelka-mutect PIAS2,missense_variant,p.Val234Ile,ENST00000585916,NM_001324049.1,NM_001324048.1,NM_001324047.1,NM_004671.3;PIAS2,missense_variant,p.Val234Ile,ENST00000324794,NM_001324051.1,NM_001324054.1,NM_173206.3;PIAS2,missense_variant,p.Val263Ile,ENST00000592212,;PIAS2,5_prime_UTR_variant,,ENST00000545673,;PIAS2,3_prime_UTR_variant,,ENST00000398654,;PIAS2,non_coding_transcript_exon_variant,,ENST00000590127,;PIAS2,non_coding_transcript_exon_variant,,ENST00000592011,;PIAS2,non_coding_transcript_exon_variant,,ENST00000589819,;RP11-687F6.4,upstream_gene_variant,,ENST00000587732,; T ENST00000585916 Transcript missense_variant 700/11075 700/1866 234/621 V/I Gta/Ata 1 -1 PIAS2 HGNC HGNC:17311 protein_coding YES CCDS32824.1 ENSP00000465676 O75928 UPI0000201CB9 NM_001324049.1,NM_001324048.1,NM_001324047.1,NM_004671.3 tolerated(0.05) 5/14 Pfam_domain:PF14324,PROSITE_profiles:PS51466,hmmpanther:PTHR10782,hmmpanther:PTHR10782:SF12 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -9.188115 0.999973 1 1 1 0 T 3 4 14 46855371 46855371 C T 1 0 0 0 0 1 0 0 0 11966 565 20 3 3 PIAS2 18 46855371 Missense_Mutation SNP C C3L-00279_T 174962 46855371 33517914 535 6313 MISP 0 . GRCh38 19 757489 757489 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.543G>T p.= p.L181L ENST00000215582 2/5 250 198 52 280 280 0 strelka-varscan-mutect MISP,synonymous_variant,p.=,ENST00000215582,NM_173481.2;MISP,upstream_gene_variant,,ENST00000614180,; T ENST00000215582 Transcript synonymous_variant 646/2871 543/2040 181/679 L ctG/ctT 1 1 MISP HGNC HGNC:27000 protein_coding YES CCDS12042.1 ENSP00000215582 Q8IVT2 UPI00000745CD NM_173481.2 2/5 hmmpanther:PTHR18839,hmmpanther:PTHR18839:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 757489 757489 G T 1 0 0 0 0 0 0 0 1 9562 1335 47 2 2 MISP 19 757489 Silent SNP G C3L-00279_T 757489 57860127 536 6314 SAFB2 0 . GRCh38 19 5587891 5587907 + Frame_Shift_Del DEL CTAGCCGCGCCTGCGTC CTAGCCGCGCCTGCGTC - novel C3L-00279_T C3L-00279_N CTAGCCGCGCCTGCGTC CTAGCCGCGCCTGCGTC c.2599_2615delGACGCAGGCGCGGCTAG p.Asp867ProfsTer97 p.D867Pfs*97 ENST00000252542 19/21 160 144 16 169 169 0 sindel-varindel-pindel SAFB2,frameshift_variant,p.Asp867ProfsTer97,ENST00000252542,NM_014649.2;SAFB2,non_coding_transcript_exon_variant,,ENST00000587802,;SAFB2,non_coding_transcript_exon_variant,,ENST00000589925,;SAFB2,downstream_gene_variant,,ENST00000590000,; - ENST00000252542 Transcript frameshift_variant 2864-2880/3371 2599-2615/2862 867-872/953 DAGAAS/X GACGCAGGCGCGGCTAGc/c 1 -1 SAFB2 HGNC HGNC:21605 protein_coding YES CCDS32879.1 ENSP00000252542 Q14151 UPI0000071DB7 NM_014649.2 19/21 hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF4 HIGH 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 5587891 5587891 CTAGCCGCGCCTGCGTC - 1 0 1 0 1 0 0 0 0 14066 797 28 0 0 SAFB2 19 5587891 Frame_Shift_Del DEL CTAGCCGCGCCTGCGTC C3L-00279_T 4830402 5587891 53029725 537 6315 ACER1 0 . GRCh38 19 6306762 6306762 + Silent SNP G G T rs368149486 C3L-00279_T C3L-00279_N G G c.747C>A p.= p.P249P ENST00000301452 6/6 92 77 15 88 88 0 strelka-varscan-mutect ACER1,synonymous_variant,p.=,ENST00000301452,NM_133492.2; T ENST00000301452 Transcript synonymous_variant 825/1445 747/795 249/264 P ccC/ccA rs368149486 1 -1 ACER1 HGNC HGNC:18356 protein_coding YES CCDS12161.1 ENSP00000301452 Q8TDN7 UPI000003FD52 NM_133492.2 6/6 Pfam_domain:PF05875,hmmpanther:PTHR12956,hmmpanther:PTHR12956:SF18 LOW 1 SNV 1 1 PASS rs368149486 . 0 202 8 0 0 0 0 0 -20 0.9999984 1 1 1 0 T 2 4 14 6306762 6306762 G T 1 0 0 0 0 0 0 0 1 176 1103 39 1 1 ACER1 19 6306762 Silent SNP G C3L-00279_T 718871 6306762 52310854 538 6316 DENND1C 0 . GRCh38 19 6479895 6479895 + Silent SNP G G T rs757060526,rs770533838 C3L-00279_T C3L-00279_N G G c.90C>A p.= p.P30P ENST00000381480 3/23 218 192 26 210 210 0 strelka-varscan-mutect DENND1C,synonymous_variant,p.=,ENST00000381480,NM_024898.3;DENND1C,5_prime_UTR_variant,,ENST00000590173,;DENND1C,5_prime_UTR_variant,,ENST00000590473,;DENND1C,5_prime_UTR_variant,,ENST00000588421,;DENND1C,intron_variant,,ENST00000543576,NM_001290331.1;DENND1C,non_coding_transcript_exon_variant,,ENST00000591030,;DENND1C,missense_variant,p.Pro10Gln,ENST00000586046,;DENND1C,5_prime_UTR_variant,,ENST00000590867,;DENND1C,non_coding_transcript_exon_variant,,ENST00000592543,;DENND1C,upstream_gene_variant,,ENST00000590444,;DENND1C,upstream_gene_variant,,ENST00000590818,;DENND1C,upstream_gene_variant,,ENST00000589491,;DENND1C,upstream_gene_variant,,ENST00000588988,; T ENST00000381480 Transcript synonymous_variant 203/2816 90/2406 30/801 P ccC/ccA rs757060526,rs770533838,COSM2727724,COSM2727725 1 -1 DENND1C HGNC HGNC:26225 protein_coding YES CCDS45938.1 ENSP00000370889 Q8IV53 UPI000007469C NM_024898.3 3/23 Pfam_domain:PF03456,PROSITE_profiles:PS50946,hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF25,SMART_domains:SM00800 0,0,1,1 LOW 1 SNV 1 0,0,1,1 1 PASS rs770533838 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 6479895 6479895 G T 1 0 0 0 0 0 0 0 1 4232 1335 47 2 2 DENND1C 19 6479895 Silent SNP G C3L-00279_T 173133 6479895 52137721 539 6317 ELAVL1 0 . GRCh38 19 7963720 7963720 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.744C>G p.Ile248Met p.I248M ENST00000407627 6/6 387 345 42 405 405 0 strelka-varscan-mutect ELAVL1,missense_variant,p.Ile248Met,ENST00000407627,NM_001419.2;ELAVL1,missense_variant,p.Ile248Met,ENST00000596459,;ELAVL1,3_prime_UTR_variant,,ENST00000593807,;ELAVL1,intron_variant,,ENST00000596154,;CTD-3193O13.14,downstream_gene_variant,,ENST00000595107,; C ENST00000407627 Transcript missense_variant 874/6015 744/981 248/326 I/M atC/atG 1 -1 ELAVL1 HGNC HGNC:3312 protein_coding YES CCDS12193.1 ENSP00000385269 Q15717 UPI0000129E74 NM_001419.2 deleterious(0.01) 6/6 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF351,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 7963720 7963720 G C 1 0 0 0 0 1 0 0 0 4882 932 33 4 4 ELAVL1 19 7963720 Missense_Mutation SNP G C3L-00279_T 1483825 7963720 50653896 540 6318 ADAMTS10 0 . GRCh38 19 8586680 8586680 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.2281C>A p.Pro761Thr p.P761T ENST00000270328 19/25 351 289 62 275 275 0 strelka-varscan-mutect ADAMTS10,missense_variant,p.Pro761Thr,ENST00000270328,;ADAMTS10,missense_variant,p.Pro761Thr,ENST00000597188,NM_030957.3;ADAMTS10,missense_variant,p.Pro248Thr,ENST00000595838,NM_001282352.1;AC130469.2,downstream_gene_variant,,ENST00000597256,;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,;ADAMTS10,3_prime_UTR_variant,,ENST00000593826,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000596911,;ADAMTS10,downstream_gene_variant,,ENST00000603221,;ADAMTS10,downstream_gene_variant,,ENST00000596236,; T ENST00000270328 Transcript missense_variant 2512/4194 2281/3312 761/1103 P/T Cct/Act COSM1003577 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 tolerated(0.23) 19/25 Pfam_domain:PF05986,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26 1 MODERATE 1 SNV 5 1 1 PASS rs1314345152 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 8586680 8586680 G T 1 0 0 0 0 1 0 0 0 300 1203 42 2 2 ADAMTS10 19 8586680 Missense_Mutation SNP G C3L-00279_T 622960 8586680 50030936 541 6319 ADAMTS10 0 . GRCh38 19 8601050 8601050 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.688G>T p.Gly230Cys p.G230C ENST00000270328 5/25 448 390 58 474 474 0 strelka-varscan-mutect ADAMTS10,missense_variant,p.Gly230Cys,ENST00000270328,;ADAMTS10,missense_variant,p.Gly230Cys,ENST00000597188,NM_030957.3;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000596709,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000596466,;ADAMTS10,missense_variant,p.Gly230Cys,ENST00000596851,;ADAMTS10,missense_variant,p.Gly230Cys,ENST00000593913,;ADAMTS10,upstream_gene_variant,,ENST00000601163,;ADAMTS10,downstream_gene_variant,,ENST00000593534,;ADAMTS10,upstream_gene_variant,,ENST00000601872,; A ENST00000270328 Transcript missense_variant 919/4194 688/3312 230/1103 G/C Ggc/Tgc 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 tolerated(0.21) 5/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 8601050 8601050 C A 1 0 0 0 0 1 0 0 0 300 681 24 2 2 ADAMTS10 19 8601050 Missense_Mutation SNP C C3L-00279_T 14370 8601050 50016566 542 6320 MUC16 0 . GRCh38 19 8952436 8952436 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.24334C>A p.Gln8112Lys p.Q8112K ENST00000397910 3/84 114 91 23 95 94 1 strelka-varscan-mutect MUC16,missense_variant,p.Gln8112Lys,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 24538/43816 24334/43524 8112/14507 Q/K Cag/Aag 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 8952436 8952436 G T 1 0 0 0 0 1 0 0 0 9972 1299 45 2 2 MUC16 19 8952436 Missense_Mutation SNP G C3L-00279_T 351386 8952436 49665180 543 6321 MUC16 0 . GRCh38 19 8953910 8953910 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.22860C>A p.= p.T7620T ENST00000397910 3/84 237 207 30 190 189 1 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 23064/43816 22860/43524 7620/14507 T acC/acA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 LOW 1 SNV 5 1 PASS rs1407778815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 8953910 8953910 G T 1 0 0 0 0 0 0 0 1 9972 1335 47 2 2 MUC16 19 8953910 Silent SNP G C3L-00279_T 1474 8953910 49663706 544 6322 ZNF560 0 . GRCh38 19 9467938 9467938 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1009G>T p.Val337Leu p.V337L ENST00000301480 10/10 165 141 24 90 90 0 strelka-varscan-mutect ZNF560,missense_variant,p.Val337Leu,ENST00000301480,NM_152476.2;ZNF560,downstream_gene_variant,,ENST00000585974,; A ENST00000301480 Transcript missense_variant 1223/2654 1009/2373 337/790 V/L Gta/Tta 1 -1 ZNF560 HGNC HGNC:26484 protein_coding YES CCDS12214.1 ENSP00000301480 Q96MR9 UPI000013E720 NM_152476.2 tolerated(0.72) 10/10 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF44,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 9467938 9467938 C A 1 0 0 0 0 1 0 0 0 18565 478 17 2 2 ZNF560 19 9467938 Missense_Mutation SNP C C3L-00279_T 514028 9467938 49149678 545 6323 ZNF560 0 . GRCh38 19 9469660 9469660 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.499G>T p.Glu167Ter p.E167* ENST00000301480 8/10 228 191 37 181 181 0 strelka-varscan-mutect ZNF560,stop_gained,p.Glu167Ter,ENST00000301480,NM_152476.2;ZNF560,non_coding_transcript_exon_variant,,ENST00000585974,; A ENST00000301480 Transcript stop_gained 713/2654 499/2373 167/790 E/* Gag/Tag 1 -1 ZNF560 HGNC HGNC:26484 protein_coding YES CCDS12214.1 ENSP00000301480 Q96MR9 UPI000013E720 NM_152476.2 8/10 PROSITE_profiles:PS50805,Low_complexity_(Seg):seg,SMART_domains:SM00349 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 9469660 9469660 C A 1 0 0 0 0 0 1 0 0 18565 922 32 2 2 ZNF560 19 9469660 Nonsense_Mutation SNP C C3L-00279_T 1722 9469660 49147956 546 6324 PKN1 0 . GRCh38 19 14443534 14443534 + Silent SNP G G T rs2161287 C3L-00279_T C3L-00279_N G G c.405G>T p.= p.A135A ENST00000342216 3/22 136 118 18 147 146 1 strelka-varscan-mutect PKN1,synonymous_variant,p.=,ENST00000242783,NM_002741.3;PKN1,synonymous_variant,p.=,ENST00000342216,NM_213560.1;PKN1,synonymous_variant,p.=,ENST00000586557,;PKN1,synonymous_variant,p.=,ENST00000590097,;PKN1,5_prime_UTR_variant,,ENST00000585619,;PKN1,non_coding_transcript_exon_variant,,ENST00000587429,;PKN1,downstream_gene_variant,,ENST00000592794,;PKN1,non_coding_transcript_exon_variant,,ENST00000585839,; T ENST00000342216 Transcript synonymous_variant 436/2960 405/2847 135/948 A gcG/gcT rs2161287 1 1 PKN1 HGNC HGNC:9405 protein_coding YES CCDS42514.1 ENSP00000343325 Q16512 UPI0000366D4D NM_213560.1 3/22 Gene3D:1.10.287.160,Pfam_domain:PF02185,SMART_domains:SM00742,Superfamily_domains:SSF46585 LOW 1 SNV 2 1 PASS rs2161287 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 14 14443534 14443534 G T 1 0 0 0 0 0 0 0 1 12075 1103 39 1 1 PKN1 19 14443534 Silent SNP G C3L-00279_T 4973874 14443534 44174082 547 6325 OR10H2 0 . GRCh38 19 15728783 15728783 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.740T>A p.Ile247Asn p.I247N ENST00000305899 1/1 207 178 29 165 165 0 strelka-varscan-mutect OR10H2,missense_variant,p.Ile247Asn,ENST00000305899,NM_013939.2; A ENST00000305899 Transcript missense_variant 764/1041 740/948 247/315 I/N aTt/aAt 1 1 OR10H2 HGNC HGNC:8173 protein_coding YES CCDS12333.1 ENSP00000306095 O60403 A0A126GWJ7 UPI000004CA3E NM_013939.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF111,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 15728783 15728783 T A 1 0 0 0 0 1 0 0 0 10983 1493 52 4 4 OR10H2 19 15728783 Missense_Mutation SNP T C3L-00279_T 1285249 15728783 42888833 548 6326 ZNF430 0 . GRCh38 19 21057189 21057189 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.881G>T p.Cys294Phe p.C294F ENST00000261560 5/5 161 137 24 59 59 0 strelka-varscan-mutect ZNF430,missense_variant,p.Cys294Phe,ENST00000261560,NM_025189.3,NM_001172671.1;ZNF430,downstream_gene_variant,,ENST00000599548,;ZNF430,upstream_gene_variant,,ENST00000597922,; T ENST00000261560 Transcript missense_variant 1062/3923 881/1713 294/570 C/F tGt/tTt 1 1 ZNF430 HGNC HGNC:20808 protein_coding YES CCDS32978.1 ENSP00000261560 Q9H8G1 UPI000020389E NM_025189.3,NM_001172671.1 deleterious(0.01) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF131,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 21057189 21057189 G T 1 0 0 0 0 1 0 0 0 18476 1377 48 2 2 ZNF430 19 21057189 Missense_Mutation SNP G C3L-00279_T 5328406 21057189 37560427 549 6327 ZNF536 0 . GRCh38 19 30445493 30445493 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1931A>T p.His644Leu p.H644L ENST00000355537 2/5 256 234 22 194 194 0 strelka-varscan-mutect ZNF536,missense_variant,p.His644Leu,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.His644Leu,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript missense_variant 2078/4945 1931/3903 644/1300 H/L cAc/cTc 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 2/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 30445493 30445493 A T 1 0 0 0 0 1 0 0 0 18547 159 6 4 4 ZNF536 19 30445493 Missense_Mutation SNP A C3L-00279_T 9388304 30445493 28172123 550 6328 GPI 0 . GRCh38 19 34381490 34381490 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.808G>A p.Asp270Asn p.D270N ENST00000415930 9/18 415 362 53 298 298 0 strelka-varscan-mutect GPI,missense_variant,p.Asp270Asn,ENST00000415930,NM_001184722.1;GPI,missense_variant,p.Asp259Asn,ENST00000356487,NM_000175.3,NM_001289790.1;GPI,missense_variant,p.Asp274Asn,ENST00000588991,NM_001289789.1;GPI,missense_variant,p.Asp259Asn,ENST00000586425,;GPI,downstream_gene_variant,,ENST00000589640,;GPI,downstream_gene_variant,,ENST00000589399,;GPI,downstream_gene_variant,,ENST00000591204,;GPI,downstream_gene_variant,,ENST00000590375,;GPI,downstream_gene_variant,,ENST00000592144,;GPI,downstream_gene_variant,,ENST00000590362,; A ENST00000415930 Transcript missense_variant 978/4000 808/1710 270/569 D/N Gac/Aac 1 1 GPI HGNC HGNC:4458 protein_coding YES CCDS54246.1 ENSP00000405573 P06744 UPI00017A6DE4 NM_001184722.1 deleterious_low_confidence(0.04) 9/18 HAMAP:MF_00473,Pfam_domain:PF00342,PROSITE_profiles:PS51463,hmmpanther:PTHR11469,hmmpanther:PTHR11469:SF4,Superfamily_domains:SSF53697 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 34381490 34381490 G A 1 0 0 0 0 1 0 0 0 6513 1290 45 3 3 GPI 19 34381490 Missense_Mutation SNP G C3L-00279_T 3935997 34381490 24236126 551 6329 PRODH2 0 . GRCh38 19 35812170 35812170 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.702G>C p.Gln234His p.Q234H ENST00000301175 4/11 173 151 22 136 136 0 strelka-varscan-mutect PRODH2,missense_variant,p.Gln234His,ENST00000301175,NM_021232.1;PRODH2,non_coding_transcript_exon_variant,,ENST00000587695,;PRODH2,non_coding_transcript_exon_variant,,ENST00000591694,; G ENST00000301175 Transcript missense_variant 720/1677 702/1611 234/536 Q/H caG/caC 1 -1 PRODH2 HGNC HGNC:17325 protein_coding YES CCDS12478.1 ENSP00000301175 Q9UF12 UPI000006EE59 NM_021232.1 deleterious(0) 4/11 hmmpanther:PTHR13914,hmmpanther:PTHR13914:SF5,Gene3D:3.20.20.220,Superfamily_domains:SSF51730 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 35812170 35812170 C G 1 0 0 0 0 1 0 0 0 12682 796 28 4 4 PRODH2 19 35812170 Missense_Mutation SNP C C3L-00279_T 1430680 35812170 22805446 552 6330 ZNF568 0 . GRCh38 19 36997456 36997456 + Nonsense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1765A>T p.Arg589Ter p.R589* ENST00000617745 8/8 293 252 41 217 217 0 strelka-varscan-mutect ZNF568,stop_gained,p.Arg589Ter,ENST00000617745,NM_001204838.1;ZNF568,stop_gained,p.Arg525Ter,ENST00000455427,NM_001204839.1;ZNF568,downstream_gene_variant,,ENST00000444991,;ZNF568,downstream_gene_variant,,ENST00000433993,;ZNF568,downstream_gene_variant,,ENST00000455817,;ZNF568,downstream_gene_variant,,ENST00000588596,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,; T ENST00000617745 Transcript stop_gained 1965/2441 1765/1908 589/635 R/* Aga/Tga 1 1 ZNF568 HGNC HGNC:25392 protein_coding CCDS74351.1 ENSP00000482444 A0A087WZ84 UPI0001FD28F8 NM_001204838.1 8/8 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF107,Superfamily_domains:SSF57667 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 14 36997456 36997456 A T 1 0 0 0 0 0 1 0 0 18573 296 11 4 4 ZNF568 19 36997456 Nonsense_Mutation SNP A C3L-00279_T 1185286 36997456 21620160 553 6331 ZNF607 0 . GRCh38 19 37698439 37698439 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1692G>T p.Lys564Asn p.K564N ENST00000355202 5/5 247 192 55 173 173 0 strelka-varscan-mutect ZNF607,missense_variant,p.Lys564Asn,ENST00000355202,NM_032689.4;ZNF607,missense_variant,p.Lys563Asn,ENST00000395835,NM_001172677.1;ZNF607,downstream_gene_variant,,ENST00000591664,;ZNF607,downstream_gene_variant,,ENST00000590670,;CTD-2528L19.4,intron_variant,,ENST00000586606,;CTD-2528L19.4,intron_variant,,ENST00000585547,;CTD-2528L19.4,intron_variant,,ENST00000591114,;ZNF607,downstream_gene_variant,,ENST00000586559,;CTD-2528L19.3,upstream_gene_variant,,ENST00000589357,; A ENST00000355202 Transcript missense_variant 2288/4364 1692/2091 564/696 K/N aaG/aaT 1 -1 ZNF607 HGNC HGNC:28192 protein_coding YES CCDS33006.1 ENSP00000347338 Q96SK3 UPI000040BC07 NM_032689.4 tolerated(0.57) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF319,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 37698439 37698439 C A 1 0 0 0 0 1 0 0 0 18608 680 24 2 2 ZNF607 19 37698439 Missense_Mutation SNP C C3L-00279_T 700983 37698439 20919177 554 6332 WDR87 0 . GRCh38 19 37885403 37885403 + Silent SNP A A G novel C3L-00279_T C3L-00279_N A A c.8268T>C p.= p.S2756S ENST00000447313 6/6 376 338 38 127 127 0 strelka-varscan-mutect WDR87,synonymous_variant,p.=,ENST00000447313,NM_001291088.1;WDR87,synonymous_variant,p.=,ENST00000303868,NM_031951.4; G ENST00000447313 Transcript synonymous_variant 8429/9009 8268/8739 2756/2912 S tcT/tcC 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 6/6 LOW 1 SNV 2 1 PASS . . 0 202 0 2 6 0 0 0 -11.99388 0.2843796 1 1 0 0 G 2 3 14 37885403 37885403 A G 1 0 0 0 0 0 0 0 1 17890 407 15 5 5 WDR87 19 37885403 Silent SNP A C3L-00279_T 186964 37885403 20732213 555 6333 SIPA1L3 0 . GRCh38 19 38081597 38081597 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.32G>T p.Gly11Val p.G11V ENST00000222345 3/22 80 71 9 66 66 0 strelka-varscan-mutect SIPA1L3,missense_variant,p.Gly11Val,ENST00000222345,NM_015073.2;SIPA1L3,downstream_gene_variant,,ENST00000476317,; T ENST00000222345 Transcript missense_variant 541/7987 32/5346 11/1781 G/V gGt/gTt 1 1 SIPA1L3 HGNC HGNC:23801 protein_coding YES CCDS33007.1 ENSP00000222345 O60292 UPI00001D8160 NM_015073.2 deleterious_low_confidence(0.01) 3/22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 38081597 38081597 G T 1 0 0 0 0 1 0 0 0 14594 1261 44 2 2 SIPA1L3 19 38081597 Missense_Mutation SNP G C3L-00279_T 196194 38081597 20536019 556 6334 DYRK1B 0 . GRCh38 19 39830733 39830733 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.114G>T p.= p.R38R ENST00000593685 3/11 152 125 27 102 102 0 strelka-varscan-mutect DYRK1B,synonymous_variant,p.=,ENST00000593685,;DYRK1B,synonymous_variant,p.=,ENST00000323039,NM_004714.2;DYRK1B,synonymous_variant,p.=,ENST00000348817,NM_006484.2;DYRK1B,synonymous_variant,p.=,ENST00000430012,NM_006483.2;DYRK1B,synonymous_variant,p.=,ENST00000597639,;DYRK1B,synonymous_variant,p.=,ENST00000601972,;DYRK1B,synonymous_variant,p.=,ENST00000600611,;FBL,downstream_gene_variant,,ENST00000221801,NM_001436.3;FBL,downstream_gene_variant,,ENST00000595545,;FBL,downstream_gene_variant,,ENST00000601274,;FBL,downstream_gene_variant,,ENST00000597224,;MIR6719,upstream_gene_variant,,ENST00000622428,;FBL,downstream_gene_variant,,ENST00000593503,;FBL,downstream_gene_variant,,ENST00000594443,;DYRK1B,upstream_gene_variant,,ENST00000601696,; A ENST00000593685 Transcript synonymous_variant 583/2724 114/1890 38/629 R cgG/cgT 1 -1 DYRK1B HGNC HGNC:3092 protein_coding YES CCDS12543.1 ENSP00000469863 Q9Y463 A0A024R0I0 UPI0000001059 3/11 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF27 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 39830733 39830733 C A 1 0 0 0 0 0 0 0 1 4679 610 22 2 2 DYRK1B 19 39830733 Silent SNP C C3L-00279_T 1749136 39830733 18786883 557 6335 FCGBP 0 . GRCh38 19 39866990 39866990 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.12080G>T p.Cys4027Phe p.C4027F ENST00000616721 26/28 162 138 24 115 115 0 strelka-varscan-mutect FCGBP,missense_variant,p.Cys4027Phe,ENST00000616721,NM_003890.2; A ENST00000616721 Transcript missense_variant 12088/12787 12080/12615 4027/4204 C/F tGc/tTc 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 deleterious(0) 26/28 Pfam_domain:PF12714,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF244,SMART_domains:SM00215,SMART_domains:SM00216,SMART_domains:SM00274 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 39866990 39866990 C A 1 0 0 0 0 1 0 0 0 5641 710 25 2 2 FCGBP 19 39866990 Missense_Mutation SNP C C3L-00279_T 36257 39866990 18750626 558 6336 NUMBL 0 . GRCh38 19 40686995 40686995 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.25G>T p.Gly9Cys p.G9C ENST00000252891 2/10 112 80 32 58 58 0 strelka-varscan-mutect NUMBL,missense_variant,p.Gly9Cys,ENST00000252891,NM_004756.4;NUMBL,splice_region_variant,,ENST00000598773,;NUMBL,splice_region_variant,,ENST00000595741,;NUMBL,splice_region_variant,,ENST00000600636,;NUMBL,intron_variant,,ENST00000598779,NM_001289979.1;NUMBL,intron_variant,,ENST00000540131,NM_001289980.1;ADCK4,downstream_gene_variant,,ENST00000324464,NM_024876.3;ADCK4,downstream_gene_variant,,ENST00000243583,NM_001142555.2;NUMBL,upstream_gene_variant,,ENST00000600967,;NUMBL,splice_region_variant,,ENST00000599594,;ADCK4,downstream_gene_variant,,ENST00000593724,;NUMBL,upstream_gene_variant,,ENST00000598759,;NUMBL,upstream_gene_variant,,ENST00000599786,;NUMBL,upstream_gene_variant,,ENST00000593367,; A ENST00000252891 Transcript missense_variant,splice_region_variant 193/3561 25/1830 9/609 G/C Ggc/Tgc 1 -1 NUMBL HGNC HGNC:8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 UPI000003032B NM_004756.4 deleterious_low_confidence(0.01) 2/10 PIRSF_domain:PIRSF017607,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF32 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 40686995 40686995 C A 1 0 0 0 0 1 0 0 0 10817 637 22 2 2 NUMBL 19 40686995 Missense_Mutation SNP C C3L-00279_T 820005 40686995 17930621 559 6337 RAB4B 0 . GRCh38 19 40783818 40783818 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.253C>T p.= p.L85L ENST00000594800 4/8 61 52 9 32 32 0 strelka-varscan-mutect RAB4B,synonymous_variant,p.=,ENST00000594800,;RAB4B,synonymous_variant,p.=,ENST00000357052,NM_016154.4;RAB4B,intron_variant,,ENST00000602173,;CTC-490E21.14,intron_variant,,ENST00000595728,;RAB4B,intron_variant,,ENST00000602069,;RAB4B-EGLN2,intron_variant,,ENST00000601949,;RAB4B-EGLN2,synonymous_variant,p.=,ENST00000594136,;RAB4B,synonymous_variant,p.=,ENST00000378307,;MIA-RAB4B,3_prime_UTR_variant,,ENST00000600729,;RAB4B,non_coding_transcript_exon_variant,,ENST00000597476,;RAB4B,non_coding_transcript_exon_variant,,ENST00000600078,;RAB4B-EGLN2,non_coding_transcript_exon_variant,,ENST00000596216,;RAB4B,upstream_gene_variant,,ENST00000598430,; T ENST00000594800 Transcript synonymous_variant 413/1173 253/642 85/213 L Ctg/Ttg 1 1 RAB4B HGNC HGNC:9782 protein_coding YES CCDS33030.1 ENSP00000470246 P61018 A0A024R0K8 UPI000000125C 4/8 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF387,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.94062 1 1 1 1 0 T 2 4 14 40783818 40783818 C T 1 0 0 0 0 0 0 0 1 13107 680 24 3 3 RAB4B 19 40783818 Silent SNP C C3L-00279_T 96823 40783818 17833798 560 6338 ATP1A3 0 . GRCh38 19 41978242 41978242 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.1754A>T p.Asn585Ile p.N585I ENST00000545399 13/23 471 368 103 445 445 0 strelka-varscan-mutect ATP1A3,missense_variant,p.Asn585Ile,ENST00000545399,NM_001256214.1;ATP1A3,missense_variant,p.Asn572Ile,ENST00000302102,NM_152296.4;ATP1A3,missense_variant,p.Asn542Ile,ENST00000602133,;ATP1A3,missense_variant,p.Asn583Ile,ENST00000543770,NM_001256213.1;ATP1A3,missense_variant,p.Asn572Ile,ENST00000441343,; A ENST00000545399 Transcript missense_variant 1938/3618 1754/3081 585/1026 N/I aAc/aTc 1 -1 ATP1A3 HGNC HGNC:801 protein_coding YES CCDS58664.1 ENSP00000444688 P13637 UPI0001914BDE NM_001256214.1 deleterious(0) 13/23 Gene3D:3.40.1110.10,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660,TIGRFAM_domain:TIGR01106 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 41978242 41978242 T A 1 0 0 0 0 1 0 0 0 1282 1725 60 4 4 ATP1A3 19 41978242 Missense_Mutation SNP T C3L-00279_T 1194424 41978242 16639374 561 6339 PSG8 0 . GRCh38 19 42758070 42758070 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.641C>T p.Pro214Leu p.P214L ENST00000306511 3/5 308 240 68 319 319 0 strelka-varscan-mutect PSG8,missense_variant,p.Pro214Leu,ENST00000404209,NM_001130167.1;PSG8,missense_variant,p.Pro92Leu,ENST00000406636,NM_001130168.1;PSG8,missense_variant,p.Pro214Leu,ENST00000306511,NM_182707.2;PSG8,intron_variant,,ENST00000401467,;PSG8,non_coding_transcript_exon_variant,,ENST00000600709,;PSG8,non_coding_transcript_exon_variant,,ENST00000469260,;PSG8,3_prime_UTR_variant,,ENST00000478387,;PSG8,upstream_gene_variant,,ENST00000466163,; A ENST00000306511 Transcript missense_variant 739/1441 641/1281 214/426 P/L cCc/cTc 1 -1 PSG8 HGNC HGNC:9525 protein_coding YES CCDS33037.1 ENSP00000305005 Q9UQ74 UPI0000071471 NM_182707.2 tolerated(0.07) 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1217784155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 42758070 42758070 G A 1 0 0 0 0 1 0 0 0 12812 1232 43 3 3 PSG8 19 42758070 Missense_Mutation SNP G C3L-00279_T 779828 42758070 15859546 562 6340 PSG5 0 . GRCh38 19 43185049 43185049 + Missense_Mutation SNP C C A rs771257107 C3L-00279_T C3L-00279_N C C c.163G>T p.Val55Phe p.V55F ENST00000366175 2/6 259 213 46 153 153 0 strelka-varscan-mutect PSG5,missense_variant,p.Val55Phe,ENST00000404580,;PSG5,missense_variant,p.Val55Phe,ENST00000599812,;PSG5,missense_variant,p.Val55Phe,ENST00000366175,;PSG5,missense_variant,p.Val55Phe,ENST00000342951,NM_001130014.1,NM_002781.3;PSG5,missense_variant,p.Val55Phe,ENST00000407356,;PSG5,missense_variant,p.Val55Phe,ENST00000407568,;PSG5,non_coding_transcript_exon_variant,,ENST00000401992,;PSG5,upstream_gene_variant,,ENST00000489220,;PSG5,non_coding_transcript_exon_variant,,ENST00000600817,; A ENST00000366175 Transcript missense_variant 294/1766 163/1008 55/335 V/F Gtc/Ttc rs771257107,COSM3288697 1 -1 PSG5 HGNC HGNC:9522 protein_coding YES CCDS12617.1 ENSP00000382334 Q15238 A0A024R0S1 UPI000013C7B9 deleterious(0) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs771257107 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 43185049 43185049 C A 1 0 0 0 0 1 0 0 0 12809 478 17 2 2 PSG5 19 43185049 Missense_Mutation SNP C C3L-00279_T 426979 43185049 15432567 563 6341 CD177 0 . GRCh38 19 43360380 43360380 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.735G>T p.Gln245His p.Q245H ENST00000618265 6/9 173 140 33 147 147 0 strelka-varscan-mutect CD177,missense_variant,p.Gln245His,ENST00000618265,NM_020406.3;CTC-490G23.4,downstream_gene_variant,,ENST00000607109,;CD177,3_prime_UTR_variant,,ENST00000378012,; T ENST00000618265 Transcript missense_variant 791/2222 735/1314 245/437 Q/H caG/caT 1 1 CD177 HGNC HGNC:30072 protein_coding YES CCDS62700.1 ENSP00000479536 A0A087WVM2 UPI0000DB6A71 NM_020406.3 deleterious(0) 6/9 hmmpanther:PTHR16529,hmmpanther:PTHR16529:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 43360380 43360380 G T 1 0 0 0 0 1 0 0 0 2674 991 35 2 2 CD177 19 43360380 Missense_Mutation SNP G C3L-00279_T 175331 43360380 15257236 564 6342 ZNF284 0 . GRCh38 19 44085961 44085961 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.483C>T p.= p.I161I ENST00000421176 5/5 345 280 65 223 223 0 strelka-varscan-mutect ZNF284,synonymous_variant,p.=,ENST00000421176,NM_001037813.2;RNU6-902P,upstream_gene_variant,,ENST00000517212,;AC084219.2,3_prime_UTR_variant,,ENST00000591793,; T ENST00000421176 Transcript synonymous_variant 699/4351 483/1782 161/593 I atC/atT 1 1 ZNF284 HGNC HGNC:13078 protein_coding YES CCDS46099.1 ENSP00000411032 Q2VY69 UPI00005788EA NM_001037813.2 5/5 hmmpanther:PTHR24388,hmmpanther:PTHR24388:SF2,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 44085961 44085961 C T 1 0 0 0 0 0 0 0 1 18397 845 30 3 3 ZNF284 19 44085961 Silent SNP C C3L-00279_T 725581 44085961 14531655 565 6343 MARK4 0 . GRCh38 19 45280402 45280402 + Silent SNP G G T C3L-00279_T C3L-00279_N G G c.1035G>T p.= p.R345R ENST00000262891 11/17 230 197 33 226 226 0 strelka-varscan-mutect MARK4,synonymous_variant,p.=,ENST00000300843,NM_031417.3;MARK4,synonymous_variant,p.=,ENST00000262891,NM_001199867.1;MARK4,3_prime_UTR_variant,,ENST00000620044,;MARK4,3_prime_UTR_variant,,ENST00000592207,;MARK4,3_prime_UTR_variant,,ENST00000592762,;MARK4,non_coding_transcript_exon_variant,,ENST00000588621,;MARK4,non_coding_transcript_exon_variant,,ENST00000590897,; T ENST00000262891 Transcript synonymous_variant 1366/3573 1035/2259 345/752 R cgG/cgT COSM3664843,COSM3664844 1 1 MARK4 HGNC HGNC:13538 protein_coding YES CCDS56097.1 ENSP00000262891 Q96L34 UPI0000044D47 NM_001199867.1 11/17 PROSITE_profiles:PS50030,hmmpanther:PTHR24346,Gene3D:1.10.8.10,Pfam_domain:PF00627,SMART_domains:SM00165 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 45280402 45280402 G T 1 0 0 0 0 0 0 0 1 9240 1219 43 2 2 MARK4 19 45280402 Silent SNP G C3L-00279_T 1194441 45280402 13337214 566 6344 NPAS1 0 . GRCh38 19 47045542 47045542 + Missense_Mutation SNP A A C rs748739875 C3L-00279_T C3L-00279_N A A c.1664A>C p.His555Pro p.H555P ENST00000602212 12/12 78 69 9 146 146 0 strelka-mutect NPAS1,missense_variant,p.His555Pro,ENST00000602212,;NPAS1,missense_variant,p.His555Pro,ENST00000449844,NM_002517.2;NPAS1,missense_variant,p.His380Pro,ENST00000602189,;NPAS1,3_prime_UTR_variant,,ENST00000439365,NM_001321086.1;NPAS1,downstream_gene_variant,,ENST00000594670,;TMEM160,downstream_gene_variant,,ENST00000253047,NM_017854.1;NPAS1,downstream_gene_variant,,ENST00000600352,;NPAS1,downstream_gene_variant,,ENST00000601169,;NPAS1,downstream_gene_variant,,ENST00000594257,; C ENST00000602212 Transcript missense_variant 1884/2117 1664/1773 555/590 H/P cAc/cCc rs748739875 1 1 NPAS1 HGNC HGNC:7894 protein_coding YES CCDS12694.1 ENSP00000469142 Q99742 UPI0000073CD1 deleterious_low_confidence(0) 12/12 hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF25 MODERATE 1 SNV 1 1 PASS rs748739875 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 47045542 47045542 A C 1 0 0 0 0 1 0 0 0 10610 159 6 5 5 NPAS1 19 47045542 Missense_Mutation SNP A C3L-00279_T 1765140 47045542 11572074 567 6345 MED25 0 . GRCh38 19 49830124 49830124 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.725A>T p.Lys242Met p.K242M ENST00000312865 7/18 84 68 16 69 69 0 strelka-varscan-mutect MED25,missense_variant,p.Lys242Met,ENST00000312865,NM_030973.3;MED25,missense_variant,p.Lys242Met,ENST00000620467,;MED25,missense_variant,p.Lys241Asn,ENST00000612791,;MED25,intron_variant,,ENST00000538643,;MED25,intron_variant,,ENST00000617849,;MED25,intron_variant,,ENST00000618715,;MED25,intron_variant,,ENST00000612854,;MED25,intron_variant,,ENST00000595185,;MED25,intron_variant,,ENST00000622402,;MED25,upstream_gene_variant,,ENST00000593767,;MED25,upstream_gene_variant,,ENST00000614963,;MED25,upstream_gene_variant,,ENST00000594998,;MED25,upstream_gene_variant,,ENST00000599722,; T ENST00000312865 Transcript missense_variant 778/2332 725/2244 242/747 K/M aAg/aTg 1 1 MED25 HGNC HGNC:28845 protein_coding YES CCDS33075.1 ENSP00000326767 Q71SY5 UPI00002029A3 NM_030973.3 deleterious(0.02) 7/18 hmmpanther:PTHR12433,hmmpanther:PTHR12433:SF10,Pfam_domain:PF11235 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 49830124 49830124 A T 1 0 0 0 0 1 0 0 0 9382 72 3 4 4 MED25 19 49830124 Missense_Mutation SNP A C3L-00279_T 2784582 49830124 8787492 568 6346 MYH14 0 . GRCh38 19 50293279 50293279 + Missense_Mutation SNP G G T rs368770587 C3L-00279_T C3L-00279_N G G c.5303G>T p.Arg1768Leu p.R1768L ENST00000601313 38/43 383 331 52 448 448 0 strelka-varscan-mutect MYH14,missense_variant,p.Arg1768Leu,ENST00000601313,NM_001145809.1;MYH14,missense_variant,p.Arg1735Leu,ENST00000425460,NM_001077186.1;MYH14,missense_variant,p.Arg1727Leu,ENST00000376970,NM_024729.3;MYH14,missense_variant,p.Arg1735Leu,ENST00000598205,;MYH14,missense_variant,p.Arg1727Leu,ENST00000596571,;MYH14,missense_variant,p.Arg370Leu,ENST00000440075,;MYH14,3_prime_UTR_variant,,ENST00000262269,;MYH14,non_coding_transcript_exon_variant,,ENST00000595016,; T ENST00000601313 Transcript missense_variant 5333/6896 5303/6111 1768/2036 R/L cGg/cTg rs368770587 1 1 MYH14 HGNC HGNC:23212 protein_coding YES CCDS54295.1 ENSP00000470298 Q7Z406 UPI0001641C2F NM_001145809.1 tolerated(0.09) 38/43 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF462,Pfam_domain:PF01576 MODERATE 1 SNV 1 1 PASS rs368770587 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 50293279 50293279 G T 1 0 0 0 0 1 0 0 0 10033 1116 39 1 1 MYH14 19 50293279 Missense_Mutation SNP G C3L-00279_T 463155 50293279 8324337 569 6347 SIGLEC10 0 . GRCh38 19 51417230 51417230 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.273G>C p.Gln91His p.Q91H ENST00000339313 2/11 325 283 42 314 314 0 strelka-varscan-mutect SIGLEC10,missense_variant,p.Gln91His,ENST00000353836,NM_001171157.1;SIGLEC10,missense_variant,p.Gln91His,ENST00000441969,NM_001171159.1;SIGLEC10,missense_variant,p.Gln91His,ENST00000442846,NM_001171161.1;SIGLEC10,missense_variant,p.Gln91His,ENST00000339313,NM_033130.4;SIGLEC10,missense_variant,p.Gln91His,ENST00000439889,NM_001171156.1;SIGLEC10,missense_variant,p.Gln91His,ENST00000525998,;SIGLEC10,missense_variant,p.Gln91His,ENST00000436984,NM_001171158.1;SIGLEC10,missense_variant,p.Gln58His,ENST00000530476,;SIGLEC10,intron_variant,,ENST00000529627,;CTD-2616J11.2,non_coding_transcript_exon_variant,,ENST00000532688,;CTD-2616J11.2,downstream_gene_variant,,ENST00000526996,;CTD-2616J11.3,downstream_gene_variant,,ENST00000532473,;SIGLEC10,non_coding_transcript_exon_variant,,ENST00000524527,;SIGLEC10,intron_variant,,ENST00000357375,; G ENST00000339313 Transcript missense_variant 390/2256 273/2094 91/697 Q/H caG/caC 1 -1 SIGLEC10 HGNC HGNC:15620 protein_coding YES CCDS12832.1 ENSP00000345243 Q96LC7 UPI0000047E1A NM_033130.4 tolerated(0.07) 2/11 Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF68,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 51417230 51417230 C G 1 0 0 0 0 1 0 0 0 14570 796 28 4 4 SIGLEC10 19 51417230 Missense_Mutation SNP C C3L-00279_T 1123951 51417230 7200386 570 6348 ERVV-1 0 . GRCh38 19 53014201 53014201 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.111G>T p.= p.S37S ENST00000602168 1/1 101 88 13 57 57 0 varscan-mutect ERVV-1,synonymous_variant,p.=,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; T ENST00000602168 Transcript synonymous_variant 281/2202 111/1434 37/477 S tcG/tcT 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 1/1 hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF8 LOW SNV 1 PASS rs1420475982 . 0 199 11 0 0 0 0 0 -20 0.9999464 1 1 1 0 T 2 4 14 53014201 53014201 G T 1 0 0 0 0 0 0 0 1 5106 1103 39 1 1 ERVV-1 19 53014201 Silent SNP G C3L-00279_T 1596971 53014201 5603415 571 6349 KIR3DX1 0 . GRCh38 19 54533844 54533844 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.183C>A p.Phe61Leu p.F61L ENST00000221567 3/9 410 341 69 408 408 0 strelka-varscan-mutect KIR3DX1,missense_variant,p.Phe61Leu,ENST00000610811,;KIR3DX1,upstream_gene_variant,,ENST00000611588,;KIR3DX1,missense_variant,p.Phe61Leu,ENST00000221567,;KIR3DX1,missense_variant,p.Phe61Leu,ENST00000446586,;KIR3DX1,missense_variant,p.Phe61Leu,ENST00000447145,;KIR3DX1,missense_variant,p.Phe61Leu,ENST00000434659,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000613375,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000612759,; A ENST00000221567 Transcript missense_variant,NMD_transcript_variant 190/1378 183/1059 61/352 F/L ttC/ttA 1 1 KIR3DX1 HGNC HGNC:25043 nonsense_mediated_decay YES ENSP00000221567 Q9H7L2 UPI0000DE238B tolerated(0.15) 3/9 hmmpanther:PTHR11738:SF113,hmmpanther:PTHR11738,Pfam_domain:PF00047,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 54533844 54533844 C A 1 0 0 0 0 1 0 0 0 8187 854 30 2 2 KIR3DX1 19 54533844 Missense_Mutation SNP C C3L-00279_T 1519643 54533844 4083772 572 6350 PPP6R1 0 . GRCh38 19 55241607 55241607 + Missense_Mutation SNP C C A rs751463370 C3L-00279_T C3L-00279_N C C c.878G>T p.Ser293Ile p.S293I ENST00000412770 8/24 116 102 14 89 89 0 strelka-varscan-mutect PPP6R1,missense_variant,p.Ser293Ile,ENST00000412770,NM_014931.3;PPP6R1,missense_variant,p.Ser293Ile,ENST00000587283,;PPP6R1,downstream_gene_variant,,ENST00000592242,;MIR6803,downstream_gene_variant,,ENST00000615997,;MIR6802,upstream_gene_variant,,ENST00000617379,;PPP6R1,non_coding_transcript_exon_variant,,ENST00000591323,;PPP6R1,non_coding_transcript_exon_variant,,ENST00000591602,;PPP6R1,upstream_gene_variant,,ENST00000589343,;PPP6R1,upstream_gene_variant,,ENST00000586690,; A ENST00000412770 Transcript missense_variant 1445/3961 878/2646 293/881 S/I aGc/aTc rs751463370 1 -1 PPP6R1 HGNC HGNC:29195 protein_coding YES CCDS46186.1 ENSP00000414202 Q9UPN7 UPI0000202C6D NM_014931.3 tolerated(0.11) 8/24 hmmpanther:PTHR12634:SF13,hmmpanther:PTHR12634,Pfam_domain:PF04499 MODERATE 1 SNV 1 1 PASS rs751463370 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 55241607 55241607 C A 1 0 0 0 0 1 0 0 0 12534 797 28 2 2 PPP6R1 19 55241607 Missense_Mutation SNP C C3L-00279_T 707763 55241607 3376009 573 6351 FAM71E2 0 . GRCh38 19 55358314 55358314 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2554A>T p.Arg852Trp p.R852W ENST00000424985 9/11 61 44 17 52 52 0 strelka-varscan-mutect FAM71E2,missense_variant,p.Arg852Trp,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;COX6B2,upstream_gene_variant,,ENST00000589879,;COX6B2,upstream_gene_variant,,ENST00000586191,;CTD-2105E13.6,missense_variant,p.Arg402Trp,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; A ENST00000424985 Transcript missense_variant 2748/3191 2554/2769 852/922 R/W Agg/Tgg 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 deleterious(0.01) 9/11 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 55358314 55358314 T A 1 0 0 0 0 1 0 0 0 5476 1550 54 4 4 FAM71E2 19 55358314 Missense_Mutation SNP T C3L-00279_T 116707 55358314 3259302 574 6352 ZNF543 0 . GRCh38 19 57329000 57329000 + Missense_Mutation SNP G G T rs765099244 C3L-00279_T C3L-00279_N G G c.1538G>T p.Gly513Val p.G513V ENST00000321545 4/4 263 239 24 247 246 1 strelka-varscan-mutect ZNF543,missense_variant,p.Gly513Val,ENST00000321545,NM_213598.3; T ENST00000321545 Transcript missense_variant 1883/3659 1538/1803 513/600 G/V gGg/gTg rs765099244 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs765099244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 57329000 57329000 G T 1 0 0 0 0 1 0 0 0 18550 1232 43 2 2 ZNF543 19 57329000 Missense_Mutation SNP G C3L-00279_T 1970686 57329000 1288616 575 6353 TRMT6 0 . GRCh38 20 5942565 5942565 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.889G>A p.Ala297Thr p.A297T ENST00000203001 7/11 504 440 64 349 348 1 strelka-varscan-mutect TRMT6,missense_variant,p.Ala297Thr,ENST00000203001,NM_015939.4;TRMT6,missense_variant,p.Ala127Thr,ENST00000453074,NM_001281467.1;TRMT6,non_coding_transcript_exon_variant,,ENST00000473131,;TRMT6,non_coding_transcript_exon_variant,,ENST00000466974,;TRMT6,downstream_gene_variant,,ENST00000493972,; T ENST00000203001 Transcript missense_variant 1020/2327 889/1494 297/497 A/T Gct/Act 1 -1 TRMT6 HGNC HGNC:20900 protein_coding YES CCDS13093.1 ENSP00000203001 Q9UJA5 UPI000006D9E4 NM_015939.4 tolerated(0.66) 7/11 PIRSF_domain:PIRSF038170,hmmpanther:PTHR12945 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 5942565 5942565 C T 1 0 0 0 0 1 0 0 0 17073 739 26 3 3 TRMT6 20 5942565 Missense_Mutation SNP C C3L-00279_T 5942565 58501602 576 6354 HAO1 0 . GRCh38 20 7940289 7940289 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.134C>A p.Ser45Tyr p.S45Y ENST00000378789 1/8 87 77 10 29 29 0 strelka-varscan-mutect HAO1,missense_variant,p.Ser45Tyr,ENST00000378789,NM_017545.2; T ENST00000378789 Transcript missense_variant 186/1777 134/1113 45/370 S/Y tCc/tAc 1 -1 HAO1 HGNC HGNC:4809 protein_coding YES CCDS13100.1 ENSP00000368066 Q9UJM8 A8K058 UPI000012C08B NM_017545.2 deleterious(0.04) 1/8 PROSITE_profiles:PS51349,hmmpanther:PTHR10578,Gene3D:3.20.20.70,PIRSF_domain:PIRSF000138,Pfam_domain:PF01070,Superfamily_domains:SSF51395 MODERATE 1 SNV 1 1 PASS rs1281967601 . 0 208 2 0 0 0 0 0 -19.98784 1 1 1 1 0 T 3 4 14 7940289 7940289 G T 1 0 0 0 0 1 0 0 0 6837 1188 41 2 2 HAO1 20 7940289 Missense_Mutation SNP G C3L-00279_T 1997724 7940289 56503878 577 6355 PLCB4 0 . GRCh38 20 9476727 9476727 + Missense_Mutation SNP C C T rs760551309 C3L-00279_T C3L-00279_N C C c.3470C>T p.Ser1157Phe p.S1157F ENST00000378501 35/36 198 184 14 153 152 1 strelka-varscan-mutect PLCB4,missense_variant,p.Ser1157Phe,ENST00000378501,NM_000933.3;PLCB4,intron_variant,,ENST00000378493,;PLCB4,intron_variant,,ENST00000378473,NM_001172646.1;PLCB4,intron_variant,,ENST00000278655,NM_182797.2;PLCB4,intron_variant,,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,intron_variant,,ENST00000464199,;PLCB4,intron_variant,,ENST00000482123,;PLCB4,intron_variant,,ENST00000473151,; T ENST00000378501 Transcript missense_variant 3485/5833 3470/3585 1157/1194 S/F tCc/tTc rs760551309,COSM578635 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 deleterious(0.04) 35/36 Superfamily_domains:0053448,Gene3D:1jadA00,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF000956,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs760551309 . 0 208 0 2 0 0 0 0 -17.95391 0.9999997 1 1 1 0 T 3 4 14 9476727 9476727 C T 1 0 0 0 0 1 0 0 0 12124 855 30 3 3 PLCB4 20 9476727 Missense_Mutation SNP C C3L-00279_T 1536438 9476727 54967440 578 6356 KIF16B 0 . GRCh38 20 16379126 16379126 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2876A>T p.Tyr959Phe p.Y959F ENST00000408042 19/23 156 144 12 112 112 0 strelka-varscan-mutect KIF16B,missense_variant,p.Tyr959Phe,ENST00000354981,NM_024704.4;KIF16B,missense_variant,p.Tyr959Phe,ENST00000636835,NM_001199865.1;KIF16B,missense_variant,p.Tyr959Phe,ENST00000408042,NM_001199866.1;KIF16B,downstream_gene_variant,,ENST00000450176,; A ENST00000408042 Transcript missense_variant 3034/4640 2876/4179 959/1392 Y/F tAc/tTc 1 -1 KIF16B HGNC HGNC:15869 protein_coding YES CCDS56178.1 ENSP00000384164 Q96L93 UPI00003BF77C NM_001199866.1 deleterious_low_confidence(0.04) 19/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF400,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 16379126 16379126 T A 1 0 0 0 0 1 0 0 0 8142 1638 57 4 4 KIF16B 20 16379126 Missense_Mutation SNP T C3L-00279_T 6902399 16379126 48065041 579 6357 SEC23B 0 . GRCh38 20 18551157 18551157 + Silent SNP T T A novel C3L-00279_T C3L-00279_N T T c.1974T>A p.= p.I658I ENST00000336714 17/20 299 281 18 206 206 0 strelka-varscan-mutect SEC23B,synonymous_variant,p.=,ENST00000336714,NM_032986.3,NM_032985.4,NM_006363.4;SEC23B,synonymous_variant,p.=,ENST00000377475,NM_001172746.1;SEC23B,synonymous_variant,p.=,ENST00000377465,NM_001172745.1;SEC23B,synonymous_variant,p.=,ENST00000262544,;SEC23B,intron_variant,,ENST00000422877,; A ENST00000336714 Transcript synonymous_variant 2406/3411 1974/2304 658/767 I atT/atA 1 1 SEC23B HGNC HGNC:10702 protein_coding YES CCDS13137.1 ENSP00000338844 Q15437 UPI0000135455 NM_032986.3,NM_032985.4,NM_006363.4 17/20 hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF7,Gene3D:3.40.20.10,Pfam_domain:PF00626,Superfamily_domains:SSF82754 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 18551157 18551157 T A 1 0 0 0 0 0 0 0 1 14269 1800 63 4 4 SEC23B 20 18551157 Silent SNP T C3L-00279_T 2172031 18551157 45893010 580 6358 NKX2-2 0 . GRCh38 20 21512309 21512309 + Missense_Mutation SNP G G T rs760256898 C3L-00279_T C3L-00279_N G G c.436C>A p.Arg146Ser p.R146S ENST00000377142 2/2 417 381 36 417 416 1 strelka-varscan-mutect NKX2-2,missense_variant,p.Arg146Ser,ENST00000377142,NM_002509.3;NKX2-2-AS1,non_coding_transcript_exon_variant,,ENST00000549659,; T ENST00000377142 Transcript missense_variant 793/2092 436/822 146/273 R/S Cgc/Agc rs760256898,COSM4707078 1 -1 NKX2-2 HGNC HGNC:7835 protein_coding YES CCDS13145.1 ENSP00000366347 O95096 UPI00001301E6 NM_002509.3 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF24,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760256898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 21512309 21512309 G T 1 0 0 0 0 1 0 0 0 10486 1087 38 1 1 NKX2-2 20 21512309 Missense_Mutation SNP G C3L-00279_T 2961152 21512309 42931858 581 6359 PAX1 0 . GRCh38 20 21706620 21706620 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.469A>T p.Thr157Ser p.T157S ENST00000398485 2/5 425 393 32 371 371 0 strelka-varscan-mutect PAX1,missense_variant,p.Thr157Ser,ENST00000613128,NM_001257096.1;PAX1,missense_variant,p.Thr157Ser,ENST00000398485,NM_006192.4;PAX1,missense_variant,p.Thr133Ser,ENST00000444366,;RP5-1065O2.4,upstream_gene_variant,,ENST00000624692,;PAX1,intron_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,; T ENST00000398485 Transcript missense_variant 523/2838 469/1605 157/534 T/S Acc/Tcc 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious(0.01) 2/5 Gene3D:1.10.10.10,Pfam_domain:PF00292,Prints_domain:PR00027,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF262,SMART_domains:SM00351,Superfamily_domains:SSF46689 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 21706620 21706620 A T 1 0 0 0 0 1 0 0 0 11563 275 10 4 4 PAX1 20 21706620 Missense_Mutation SNP A C3L-00279_T 194311 21706620 42737547 582 6360 FOXA2 0 . GRCh38 20 22582224 22582224 + Nonsense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1018G>T p.Glu340Ter p.E340* ENST00000419308 2/2 115 107 8 68 68 0 strelka-varscan-mutect FOXA2,stop_gained,p.Glu340Ter,ENST00000419308,NM_021784.4;FOXA2,stop_gained,p.Glu334Ter,ENST00000377115,NM_153675.2;LINC00261,upstream_gene_variant,,ENST00000564492,; A ENST00000419308 Transcript stop_gained 1203/2422 1018/1392 340/463 E/* Gag/Tag 1 -1 FOXA2 HGNC HGNC:5022 protein_coding YES CCDS46585.1 ENSP00000400341 Q9Y261 B0ZTD4 UPI000040F9A0 NM_021784.4 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF167 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.18078 1 1 1 1 0 A 4 1 14 22582224 22582224 C A 1 0 0 0 0 0 1 0 0 5850 922 32 2 2 FOXA2 20 22582224 Nonsense_Mutation SNP C C3L-00279_T 875604 22582224 41861943 583 6361 SSTR4 0 . GRCh38 20 23036212 23036212 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.729G>A p.= p.L243L ENST00000255008 1/1 127 115 12 117 117 0 strelka-varscan-mutect SSTR4,synonymous_variant,p.=,ENST00000255008,NM_001052.2;RP4-753D10.3,intron_variant,,ENST00000440921,;RP4-753D10.3,upstream_gene_variant,,ENST00000419734,; A ENST00000255008 Transcript synonymous_variant 827/1427 729/1167 243/388 L ctG/ctA 1 1 SSTR4 HGNC HGNC:11333 protein_coding YES CCDS42856.1 ENSP00000255008 P31391 UPI000013CE7A NM_001052.2 1/1 Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF0,Prints_domain:PR00246 LOW SNV 1 PASS rs1473912681 . 0 207 3 0 0 0 0 0 -19.99988 1 1 1 1 0 A 2 1 14 23036212 23036212 G A 1 0 0 0 0 0 0 0 1 15577 1306 46 3 3 SSTR4 20 23036212 Silent SNP G C3L-00279_T 453988 23036212 41407955 584 6362 CST1 0 . GRCh38 20 23747848 23747848 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.394T>A p.Ser132Thr p.S132T ENST00000304749 3/3 237 214 23 204 204 0 strelka-mutect CST1,missense_variant,p.Ser132Thr,ENST00000304749,NM_001898.2;CST1,missense_variant,p.Ser132Thr,ENST00000398402,; T ENST00000304749 Transcript missense_variant 465/760 394/426 132/141 S/T Tcc/Acc 1 -1 CST1 HGNC HGNC:2473 protein_coding YES CCDS13160.1 ENSP00000305731 P01037 UPI000013E9BC NM_001898.2 tolerated(0.15) 3/3 hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF35,Gene3D:3.10.450.10,SMART_domains:SM00043,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 23747848 23747848 A T 1 0 0 0 0 1 0 0 0 3770 275 10 4 4 CST1 20 23747848 Missense_Mutation SNP A C3L-00279_T 711636 23747848 40696319 585 6363 SUN5 0 . GRCh38 20 32985771 32985771 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.862A>T p.Ser288Cys p.S288C ENST00000356173 11/13 187 170 17 142 142 0 strelka-varscan-mutect SUN5,missense_variant,p.Ser288Cys,ENST00000356173,NM_080675.3;SUN5,missense_variant,p.Ser263Cys,ENST00000375523,; A ENST00000356173 Transcript missense_variant 955/1254 862/1140 288/379 S/C Agc/Tgc 1 -1 SUN5 HGNC HGNC:16252 protein_coding YES CCDS13209.1 ENSP00000348496 Q8TC36 UPI0000135D7C NM_080675.3 deleterious(0.04) 11/13 Pfam_domain:PF07738,PROSITE_profiles:PS51469,hmmpanther:PTHR12911,hmmpanther:PTHR12911:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 32985771 32985771 T A 1 0 0 0 0 1 0 0 0 15780 1580 55 4 4 SUN5 20 32985771 Missense_Mutation SNP T C3L-00279_T 9237923 32985771 31458396 586 6364 EDEM2 0 . GRCh38 20 35115802 35115802 + Silent SNP C C A rs746681749 C3L-00279_T C3L-00279_N C C c.1368G>T p.= p.A456A ENST00000374492 11/11 326 288 38 299 299 0 strelka-varscan-mutect EDEM2,synonymous_variant,p.=,ENST00000374492,NM_018217.2;EDEM2,synonymous_variant,p.=,ENST00000374491,NM_001145025.1;SNORD56,downstream_gene_variant,,ENST00000364281,; A ENST00000374492 Transcript synonymous_variant 1474/1919 1368/1737 456/578 A gcG/gcT rs746681749 1 -1 EDEM2 HGNC HGNC:15877 protein_coding YES CCDS13247.1 ENSP00000363616 Q9BV94 UPI00001285D9 NM_018217.2 11/11 hmmpanther:PTHR11742:SF41,hmmpanther:PTHR11742,Gene3D:1.50.10.50,Pfam_domain:PF01532,Superfamily_domains:SSF48225 LOW 1 SNV 1 1 PASS rs746681749 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 35115802 35115802 C A 1 0 0 0 0 0 0 0 1 4740 639 23 1 1 EDEM2 20 35115802 Silent SNP C C3L-00279_T 2130031 35115802 29328365 587 6365 SOGA1 0 . GRCh38 20 36810104 36810104 + Nonsense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2461A>T p.Lys821Ter p.K821* ENST00000237536 7/15 169 160 9 138 138 0 strelka-varscan-mutect SOGA1,stop_gained,p.Lys821Ter,ENST00000237536,NM_080627.2;SOGA1,stop_gained,p.Lys583Ter,ENST00000279034,NM_199181.2;SOGA1,stop_gained,p.Lys435Ter,ENST00000465671,; A ENST00000237536 Transcript stop_gained 2803/14371 2461/4986 821/1661 K/* Aag/Tag 1 -1 SOGA1 HGNC HGNC:16111 protein_coding YES CCDS54459.1 ENSP00000237536 O94964 UPI0000E5A319 NM_080627.2 7/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF1 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 14 36810104 36810104 T A 1 0 0 0 0 0 1 0 0 15244 1826 63 4 4 SOGA1 20 36810104 Nonsense_Mutation SNP T C3L-00279_T 1694302 36810104 27634063 588 6366 ARHGAP40 0 . GRCh38 20 38649840 38649840 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1861C>A p.Pro621Thr p.P621T ENST00000373345 15/15 240 214 26 199 199 0 strelka-varscan-mutect ARHGAP40,missense_variant,p.Pro621Thr,ENST00000373345,NM_001164431.1;ARHGAP40,missense_variant,p.Pro153Thr,ENST00000373346,;ARHGAP40,intron_variant,,ENST00000243967,;ARHGAP40,intron_variant,,ENST00000414158,; A ENST00000373345 Transcript missense_variant 2029/2841 1861/1869 621/622 P/T Ccc/Acc 1 1 ARHGAP40 HGNC HGNC:16226 protein_coding YES ENSP00000362442 Q5TG30 UPI0000DD8570 NM_001164431.1 tolerated(0.07) 15/15 hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF4 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 38649840 38649840 C A 1 0 0 0 0 1 0 0 0 1012 623 22 2 2 ARHGAP40 20 38649840 Missense_Mutation SNP C C3L-00279_T 1839736 38649840 25794327 589 6367 FAM83D 0 . GRCh38 20 38926478 38926478 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.126C>A p.= p.P42P ENST00000619304 1/4 161 152 9 136 136 0 strelka-varscan-mutect FAM83D,synonymous_variant,p.=,ENST00000619304,;FAM83D,synonymous_variant,p.=,ENST00000217429,NM_030919.2;FAM83D,synonymous_variant,p.=,ENST00000619850,;PPP1R16B,downstream_gene_variant,,ENST00000299824,NM_015568.2;PPP1R16B,downstream_gene_variant,,ENST00000373331,NM_001172735.1; A ENST00000619304 Transcript synonymous_variant 167/2475 126/1848 42/615 P ccC/ccA 1 1 FAM83D HGNC HGNC:16122 protein_coding YES CCDS42872.1 ENSP00000481110 A0A087WXK8 UPI00004708E6 1/4 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 38926478 38926478 C A 1 0 0 0 0 0 0 0 1 5494 639 23 1 1 FAM83D 20 38926478 Silent SNP C C3L-00279_T 276638 38926478 25517689 590 6368 DHX35 0 . GRCh38 20 39023735 39023735 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.1639A>T p.Thr547Ser p.T547S ENST00000252011 17/22 171 154 17 123 123 0 strelka-varscan-mutect DHX35,missense_variant,p.Thr547Ser,ENST00000252011,NM_021931.3;DHX35,missense_variant,p.Thr547Ser,ENST00000373325,;DHX35,missense_variant,p.Thr516Ser,ENST00000373323,NM_001190809.1;DHX35,intron_variant,,ENST00000449559,;DHX35,3_prime_UTR_variant,,ENST00000484417,; T ENST00000252011 Transcript missense_variant 1672/3325 1639/2112 547/703 T/S Act/Tct 1 1 DHX35 HGNC HGNC:15861 protein_coding YES CCDS13310.1 ENSP00000252011 Q9H5Z1 UPI0000129088 NM_021931.3 deleterious(0.04) 17/22 Pfam_domain:PF04408,hmmpanther:PTHR18934,SMART_domains:SM00847,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 39023735 39023735 A T 1 0 0 0 0 1 0 0 0 4312 159 6 4 4 DHX35 20 39023735 Missense_Mutation SNP A C3L-00279_T 97257 39023735 25420432 591 6369 JPH2 0 . GRCh38 20 44160057 44160057 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.730A>T p.Ser244Cys p.S244C ENST00000372980 2/6 504 434 70 518 518 0 strelka-varscan-mutect JPH2,missense_variant,p.Ser244Cys,ENST00000372980,NM_020433.4; A ENST00000372980 Transcript missense_variant 1603/4787 730/2091 244/696 S/C Agc/Tgc 1 -1 JPH2 HGNC HGNC:14202 protein_coding YES CCDS13325.1 ENSP00000362071 Q9BR39 UPI000012DAC2 NM_020433.4 deleterious(0) 2/6 hmmpanther:PTHR23085:SF5,hmmpanther:PTHR23085,PIRSF_domain:PIRSF037387 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 44160057 44160057 T A 1 0 0 0 0 1 0 0 0 7873 1580 55 4 4 JPH2 20 44160057 Missense_Mutation SNP T C3L-00279_T 5136322 44160057 20284110 592 6370 SLC12A5 0 . GRCh38 20 46053687 46053687 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.2726C>A p.Ala909Glu p.A909E ENST00000454036 20/26 81 66 15 60 60 0 strelka-varscan-mutect SLC12A5,missense_variant,p.Ala886Glu,ENST00000243964,NM_020708.4;SLC12A5,missense_variant,p.Ala909Glu,ENST00000454036,NM_001134771.1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616201,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,upstream_gene_variant,,ENST00000637437,;SLC12A5,downstream_gene_variant,,ENST00000539566,;SLC12A5,upstream_gene_variant,,ENST00000628413,; A ENST00000454036 Transcript missense_variant 2802/3593 2726/3420 909/1139 A/E gCg/gAg 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 deleterious(0) 20/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF03522,TIGRFAM_domain:TIGR00930 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 46053687 46053687 C A 1 0 0 0 0 1 0 0 0 14651 768 27 1 1 SLC12A5 20 46053687 Missense_Mutation SNP C C3L-00279_T 1893630 46053687 18390480 593 6371 GNAS 0 . GRCh38 20 58910363 58910363 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2929G>T p.Val977Leu p.V977L ENST00000371100 12/13 530 486 44 448 448 0 strelka-varscan-mutect GNAS,missense_variant,p.Val977Leu,ENST00000371100,NM_080425.2;GNAS,missense_variant,p.Val963Leu,ENST00000371102,;GNAS,missense_variant,p.Val335Leu,ENST00000354359,NM_001077488.2;GNAS,missense_variant,p.Val334Leu,ENST00000371085,NM_000516.4;GNAS,missense_variant,p.Val320Leu,ENST00000371095,NM_080426.2;GNAS,missense_variant,p.Val319Leu,ENST00000265620,NM_001077489.2;GNAS,missense_variant,p.Val98Leu,ENST00000306090,;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,NM_016592.2;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000604005,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000488652,;GNAS,downstream_gene_variant,,ENST00000470512,;GNAS,downstream_gene_variant,,ENST00000472183,;GNAS,downstream_gene_variant,,ENST00000480232,;GNAS,downstream_gene_variant,,ENST00000476935,;GNAS,downstream_gene_variant,,ENST00000492907,;GNAS,downstream_gene_variant,,ENST00000481039,;GNAS,downstream_gene_variant,,ENST00000467321,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000482112,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000464788,;GNAS,downstream_gene_variant,,ENST00000468895,;GNAS,downstream_gene_variant,,ENST00000467227,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,downstream_gene_variant,,ENST00000493958,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000475610,;GNAS,downstream_gene_variant,,ENST00000487981,;GNAS,downstream_gene_variant,,ENST00000479025,; T ENST00000371100 Transcript missense_variant 3481/4029 2929/3114 977/1037 V/L Gtg/Ttg 1 1 GNAS HGNC HGNC:4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 UPI0000E444AE NM_080425.2 deleterious(0.01) 12/13 Gene3D:3.40.50.300,Pfam_domain:PF00503,Prints_domain:PR00443,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF36,SMART_domains:SM00275,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 58910363 58910363 G T 1 0 0 0 0 1 0 0 0 6390 1145 40 1 1 GNAS 20 58910363 Missense_Mutation SNP G C3L-00279_T 12856676 58910363 5533804 594 6372 ZNF831 0 . GRCh38 20 59191527 59191527 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.508A>T p.Arg170Trp p.R170W ENST00000637017 4/8 185 152 33 188 188 0 strelka-varscan-mutect ZNF831,missense_variant,p.Arg170Trp,ENST00000637017,;ZNF831,missense_variant,p.Arg170Trp,ENST00000371030,NM_178457.2; T ENST00000637017 Transcript missense_variant 2057/10953 508/5034 170/1677 R/W Agg/Tgg 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 deleterious(0) 4/8 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 59191527 59191527 A T 1 0 0 0 0 1 0 0 0 18770 295 11 4 4 ZNF831 20 59191527 Missense_Mutation SNP A C3L-00279_T 281164 59191527 5252640 595 6373 ZNF831 0 . GRCh38 20 59253028 59253028 + Missense_Mutation SNP T T G novel C3L-00279_T C3L-00279_N T T c.4078T>G p.Cys1360Gly p.C1360G ENST00000637017 7/8 196 179 17 157 157 0 strelka-varscan-mutect ZNF831,missense_variant,p.Cys1360Gly,ENST00000637017,;ZNF831,missense_variant,p.Cys1360Gly,ENST00000371030,NM_178457.2; G ENST00000637017 Transcript missense_variant 5627/10953 4078/5034 1360/1677 C/G Tgt/Ggt 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 tolerated(0.66) 7/8 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 59253028 59253028 T G 1 0 0 0 0 1 0 0 0 18770 1812 63 5 5 ZNF831 20 59253028 Missense_Mutation SNP T C3L-00279_T 61501 59253028 5191139 596 6374 EDN3 0 . GRCh38 20 59322412 59322412 + Frame_Shift_Del DEL G G - novel C3L-00279_T C3L-00279_N G G c.585delG p.Lys196ArgfsTer13 p.K196Rfs*13 ENST00000337938 4/5 452 409 43 340 340 0 sindel-varindel-pindel EDN3,frameshift_variant,p.Lys196ArgfsTer2,ENST00000311585,NM_207032.2;EDN3,frameshift_variant,p.Lys196ArgfsTer13,ENST00000337938,NM_001302455.1,NM_207034.2;EDN3,frameshift_variant,p.Lys196ArgfsTer13,ENST00000371028,;EDN3,intron_variant,,ENST00000395654,NM_207033.2;EDN3,intron_variant,,ENST00000371025,NM_001302456.1; - ENST00000337938 Transcript frameshift_variant 969/2636 583/717 195/238 G/X Ggg/gg 1 1 EDN3 HGNC HGNC:3178 protein_coding YES CCDS13477.1 ENSP00000337128 P14138 UPI000012A221 NM_001302455.1,NM_207034.2 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR13874,hmmpanther:PTHR13874:SF11 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 59322412 59322412 G - 1 0 1 0 1 0 0 0 0 4746 1014 35 0 0 EDN3 20 59322412 Frame_Shift_Del DEL G C3L-00279_T 69384 59322412 5121755 597 6375 KCNQ2 0 . GRCh38 20 63406799 63406799 + Missense_Mutation SNP C C A rs751425807 C3L-00279_T C3L-00279_N C C c.2464G>T p.Ala822Ser p.A822S ENST00000359125 17/17 670 545 125 583 583 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Ala804Ser,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Ala822Ser,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Ala621Ser,ENST00000637193,;KCNQ2,missense_variant,p.Ala794Ser,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Ala791Ser,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Ala678Ser,ENST00000357249,;KCNQ2,intron_variant,,ENST00000370224,;KCNQ2,intron_variant,,ENST00000625514,;KCNQ2,intron_variant,,ENST00000629241,;KCNQ2,intron_variant,,ENST00000629676,;KCNQ2,downstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000637063,;KCNQ2,downstream_gene_variant,,ENST00000637338,;KCNQ2,downstream_gene_variant,,ENST00000637656,; A ENST00000359125 Transcript missense_variant 2591/3253 2464/2619 822/872 A/S Gcg/Tcg rs751425807 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 tolerated_low_confidence(0.36) 17/17 Pfam_domain:PF11956 MODERATE 1 SNV 1 1 PASS rs751425807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 63406799 63406799 C A 1 0 0 0 0 1 0 0 0 7999 768 27 1 1 KCNQ2 20 63406799 Missense_Mutation SNP C C3L-00279_T 4084387 63406799 1037368 598 6376 NPBWR2 0 . GRCh38 20 64106806 64106806 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.26C>A p.Pro9His p.P9H ENST00000369768 1/1 168 153 15 130 130 0 strelka-varscan-mutect NPBWR2,missense_variant,p.Pro9His,ENST00000369768,NM_005286.2; T ENST00000369768 Transcript missense_variant 366/1352 26/1002 9/333 P/H cCc/cAc 1 -1 NPBWR2 HGNC HGNC:4530 protein_coding YES CCDS13557.1 ENSP00000358783 P48146 UPI000013CBB3 NM_005286.2 tolerated(0.07) 1/1 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF18 MODERATE 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 64106806 64106806 G T 1 0 0 0 0 1 0 0 0 10617 1232 43 2 2 NPBWR2 20 64106806 Missense_Mutation SNP G C3L-00279_T 700007 64106806 337361 599 6377 PCMTD2 0 . GRCh38 20 64273534 64273534 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1020G>T p.Gln340His p.Q340H ENST00000308824 6/6 55 47 8 42 42 0 strelka-varscan-mutect PCMTD2,missense_variant,p.Gln340His,ENST00000308824,NM_018257.2;PCMTD2,missense_variant,p.Gln313His,ENST00000369758,NM_001104925.1;PCMTD2,missense_variant,p.Gln190His,ENST00000609372,;PCMTD2,missense_variant,p.Gln180His,ENST00000609818,;PCMTD2,intron_variant,,ENST00000299468,;PCMTD2,non_coding_transcript_exon_variant,,ENST00000266078,;RP11-476I15.5,upstream_gene_variant,,ENST00000614601,; T ENST00000308824 Transcript missense_variant 1147/3843 1020/1086 340/361 Q/H caG/caT 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 64273534 64273534 G T 1 0 0 0 0 1 0 0 0 11675 933 33 2 2 PCMTD2 20 64273534 Missense_Mutation SNP G C3L-00279_T 166728 64273534 170633 600 6378 TIAM1 0 . GRCh38 21 31266717 31266717 + Missense_Mutation SNP C C A rs751635033 C3L-00279_T C3L-00279_N C C c.256G>T p.Gly86Trp p.G86W ENST00000286827 5/29 383 345 38 350 349 1 strelka-varscan-mutect TIAM1,missense_variant,p.Gly86Trp,ENST00000286827,NM_003253.2;TIAM1,missense_variant,p.Gly86Trp,ENST00000541036,;TIAM1,missense_variant,p.Gly86Trp,ENST00000455508,;TIAM1,intron_variant,,ENST00000469412,; A ENST00000286827 Transcript missense_variant 728/7200 256/4776 86/1591 G/W Ggg/Tgg rs751635033,COSM3389970,COSM3389971 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 deleterious_low_confidence(0) 5/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs751635033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 31266717 31266717 C A 1 0 0 0 0 1 0 0 0 16324 652 23 1 1 TIAM1 21 31266717 Missense_Mutation SNP C C3L-00279_T 31266717 15443266 601 6379 HUNK 0 . GRCh38 21 31924747 31924747 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.541G>T p.Gly181Trp p.G181W ENST00000270112 2/11 78 61 17 76 76 0 strelka-varscan-mutect HUNK,missense_variant,p.Gly181Trp,ENST00000270112,NM_014586.1;HUNK,missense_variant,p.Gly66Trp,ENST00000430354,; T ENST00000270112 Transcript missense_variant 901/7385 541/2145 181/714 G/W Ggg/Tgg 1 1 HUNK HGNC HGNC:13326 protein_coding YES CCDS13610.1 ENSP00000270112 P57058 UPI0000035B66 NM_014586.1 deleterious(0) 2/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF188,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1233238090 . 0 198 11 0 0 0 0 0 -20 0.9999803 1 1 1 0 T 3 4 14 31924747 31924747 G T 1 0 0 0 0 1 0 0 0 7354 1116 39 1 1 HUNK 21 31924747 Missense_Mutation SNP G C3L-00279_T 658030 31924747 14785236 602 6380 URB1 0 . GRCh38 21 32319239 32319239 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.5770A>T p.Ile1924Phe p.I1924F ENST00000382751 36/39 167 144 23 220 220 0 strelka-varscan-mutect URB1,missense_variant,p.Ile1924Phe,ENST00000382751,NM_014825.2;MRAP,downstream_gene_variant,,ENST00000339944,NM_206898.1; A ENST00000382751 Transcript missense_variant 5886/10832 5770/6816 1924/2271 I/F Atc/Ttc 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 deleterious(0.02) 36/39 hmmpanther:PTHR13500 MODERATE 1 SNV 1 1 PASS rs1363263282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 32319239 32319239 T A 1 0 0 0 0 1 0 0 0 17554 1464 51 4 4 URB1 21 32319239 Missense_Mutation SNP T C3L-00279_T 394492 32319239 14390744 603 6381 DSCAM 0 . GRCh38 21 40178981 40178981 + Missense_Mutation SNP G G A rs747965562 C3L-00279_T C3L-00279_N G G c.2893C>T p.Arg965Trp p.R965W ENST00000400454 15/33 512 474 38 494 493 1 strelka-varscan-mutect DSCAM,missense_variant,p.Arg965Trp,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Arg800Trp,ENST00000617870,;DSCAM,missense_variant,p.Arg717Trp,ENST00000404019,; A ENST00000400454 Transcript missense_variant 3371/8552 2893/6039 965/2012 R/W Cgg/Tgg rs747965562,COSM5434121 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 deleterious(0.01) 15/33 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs747965562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 40178981 40178981 G A 1 0 0 0 0 1 0 0 0 4589 1115 39 1 1 DSCAM 21 40178981 Missense_Mutation SNP G C3L-00279_T 7859742 40178981 6531002 604 6382 KRTAP10-9 0 . GRCh38 21 44627789 44627789 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.618C>A p.= p.S206S ENST00000397911 1/1 743 665 78 596 594 2 strelka-varscan-mutect KRTAP10-9,synonymous_variant,p.=,ENST00000397911,NM_198690.2;KRTAP10-9,synonymous_variant,p.=,ENST00000616529,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;KRTAP10-9,intron_variant,,ENST00000484861,; A ENST00000397911 Transcript synonymous_variant 667/1171 618/879 206/292 S tcC/tcA 1 1 KRTAP10-9 HGNC HGNC:22971 protein_coding YES CCDS42961.1 ENSP00000381009 P60411 UPI000036709D NM_198690.2 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 44627789 44627789 C A 1 0 0 0 0 0 0 0 1 8399 668 24 2 2 KRTAP10-9 21 44627789 Silent SNP C C3L-00279_T 4448808 44627789 2082194 605 6383 UBE2G2 0 . GRCh38 21 44773606 44773606 + Missense_Mutation SNP C C A rs782417629 C3L-00279_T C3L-00279_N C C c.326G>T p.Arg109Leu p.R109L ENST00000345496 5/6 260 229 31 191 191 0 strelka-varscan-mutect UBE2G2,missense_variant,p.Arg109Leu,ENST00000345496,NM_003343.5;UBE2G2,missense_variant,p.Arg81Leu,ENST00000330942,NM_182688.2;UBE2G2,non_coding_transcript_exon_variant,,ENST00000477954,;UBE2G2,non_coding_transcript_exon_variant,,ENST00000497630,;UBE2G2,downstream_gene_variant,,ENST00000497664,;UBE2G2,downstream_gene_variant,,ENST00000490450,;UBE2G2,downstream_gene_variant,,ENST00000496395,;UBE2G2,3_prime_UTR_variant,,ENST00000491513,;UBE2G2,3_prime_UTR_variant,,ENST00000478200,;UBE2G2,non_coding_transcript_exon_variant,,ENST00000481546,;UBE2G2,downstream_gene_variant,,ENST00000462569,; A ENST00000345496 Transcript missense_variant 597/3566 326/498 109/165 R/L cGg/cTg rs782417629 1 -1 UBE2G2 HGNC HGNC:12483 protein_coding YES CCDS13714.1 ENSP00000338348 P60604 UPI0000027925 NM_003343.5 deleterious(0) 5/6 Gene3D:3.10.110.10,Pfam_domain:PF00179,PROSITE_profiles:PS50127,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF154,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS rs782417629 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 44773606 44773606 C A 1 0 0 0 0 1 0 0 0 17378 652 23 1 1 UBE2G2 21 44773606 Missense_Mutation SNP C C3L-00279_T 145817 44773606 1936377 606 6384 PEX26 0 . GRCh38 22 18083579 18083579 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.514G>T p.Gly172Cys p.G172C ENST00000329627 4/6 544 477 67 484 484 0 strelka-varscan-mutect PEX26,missense_variant,p.Gly172Cys,ENST00000329627,NM_017929.5;PEX26,missense_variant,p.Gly172Cys,ENST00000610387,NM_001199319.1;PEX26,missense_variant,p.Gly172Cys,ENST00000399744,NM_001127649.2;PEX26,missense_variant,p.Gly172Cys,ENST00000428061,;XXbac-B476C20.9,upstream_gene_variant,,ENST00000607927,;XXbac-B476C20.9,upstream_gene_variant,,ENST00000622035,;PEX26,intron_variant,,ENST00000474897,;XXbac-B476C20.11,upstream_gene_variant,,ENST00000427227,; T ENST00000329627 Transcript missense_variant 720/18445 514/918 172/305 G/C Ggc/Tgc 1 1 PEX26 HGNC HGNC:22965 protein_coding YES CCDS13750.1 ENSP00000331106 Q7Z412 A0A024R100 UPI000000DBD1 NM_017929.5 deleterious(0) 4/6 hmmpanther:PTHR16262,hmmpanther:PTHR16262:SF2,Pfam_domain:PF07163 MODERATE 1 SNV 1 1 PASS rs773583223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 18083579 18083579 G T 1 0 0 0 0 1 0 0 0 11836 1232 43 2 2 PEX26 22 18083579 Missense_Mutation SNP G C3L-00279_T 18083579 32734889 607 6385 BCR 0 . GRCh38 22 23315456 23315456 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.3750G>T p.= p.L1250L ENST00000305877 23/23 274 243 31 271 271 0 strelka-varscan-mutect BCR,synonymous_variant,p.=,ENST00000305877,NM_004327.3;BCR,synonymous_variant,p.=,ENST00000359540,NM_021574.2;BCR,3_prime_UTR_variant,,ENST00000398512,;BCR,non_coding_transcript_exon_variant,,ENST00000436990,;BCR,downstream_gene_variant,,ENST00000458056,;BCR,downstream_gene_variant,,ENST00000475025,; T ENST00000305877 Transcript synonymous_variant 4501/7082 3750/3816 1250/1271 L ctG/ctT 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 23/23 hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 23315456 23315456 G T 1 0 0 0 0 0 0 0 1 1535 1306 46 2 2 BCR 22 23315456 Silent SNP G C3L-00279_T 5231877 23315456 27503012 608 6386 CRYBB1 0 . GRCh38 22 26616301 26616301 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.19G>T p.Ala7Ser p.A7S ENST00000215939 2/6 297 257 40 355 355 0 strelka-varscan-mutect CRYBB1,missense_variant,p.Ala7Ser,ENST00000215939,NM_001887.3; A ENST00000215939 Transcript missense_variant 150/1102 19/759 7/252 A/S Gcc/Tcc 1 -1 CRYBB1 HGNC HGNC:2397 protein_coding YES CCDS13840.1 ENSP00000215939 P53674 UPI000000165D NM_001887.3 tolerated_low_confidence(0.29) 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 26616301 26616301 C A 1 0 0 0 0 1 0 0 0 3712 739 26 2 2 CRYBB1 22 26616301 Missense_Mutation SNP C C3L-00279_T 3300845 26616301 24202167 609 6387 SFI1 0 . GRCh38 22 31528842 31528842 + Missense_Mutation SNP G G T rs368077396 C3L-00279_T C3L-00279_N G G c.245G>T p.Arg82Leu p.R82L ENST00000400288 3/33 112 100 12 102 102 0 strelka-mutect SFI1,missense_variant,p.Arg82Leu,ENST00000540643,NM_001258325.1;SFI1,missense_variant,p.Arg82Leu,ENST00000432498,NM_014775.3;SFI1,missense_variant,p.Arg82Leu,ENST00000400288,NM_001007467.2;SFI1,missense_variant,p.Arg33Leu,ENST00000450787,;SFI1,missense_variant,p.Arg82Leu,ENST00000629688,;SFI1,intron_variant,,ENST00000400289,NM_001258326.1,NM_001258327.1;SFI1,intron_variant,,ENST00000443011,;SFI1,downstream_gene_variant,,ENST00000444859,;SFI1,non_coding_transcript_exon_variant,,ENST00000465646,;SFI1,non_coding_transcript_exon_variant,,ENST00000465437,;SFI1,missense_variant,p.Arg82Leu,ENST00000524296,;SFI1,missense_variant,p.Arg82Leu,ENST00000411518,;SFI1,non_coding_transcript_exon_variant,,ENST00000382162,;SFI1,non_coding_transcript_exon_variant,,ENST00000486708,;DRG1,downstream_gene_variant,,ENST00000548143,; T ENST00000400288 Transcript missense_variant 350/4002 245/3729 82/1242 R/L cGg/cTg rs368077396 1 1 SFI1 HGNC HGNC:29064 protein_coding YES CCDS43004.1 ENSP00000383145 A8K8P3 UPI00004703B1 NM_001007467.2 deleterious(0) 3/33 hmmpanther:PTHR22028,hmmpanther:PTHR22028:SF4 MODERATE 1 SNV 2 1 PASS rs368077396 . 0 201 8 0 0 0 0 0 -19.99994 0.9999959 1 1 1 0 T 3 4 14 31528842 31528842 G T 1 0 0 0 0 1 0 0 0 14434 1116 39 1 1 SFI1 22 31528842 Missense_Mutation SNP G C3L-00279_T 4912541 31528842 19289626 610 6388 YWHAH 0 . GRCh38 22 31956690 31956690 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.639G>T p.Glu213Asp p.E213D ENST00000248975 2/2 289 235 54 302 301 1 strelka-varscan-mutect YWHAH,missense_variant,p.Glu213Asp,ENST00000248975,NM_003405.3;YWHAH,3_prime_UTR_variant,,ENST00000397492,;YWHAH,downstream_gene_variant,,ENST00000420430,;YWHAH,non_coding_transcript_exon_variant,,ENST00000471374,;YWHAH,downstream_gene_variant,,ENST00000479649,;YWHAH,downstream_gene_variant,,ENST00000443669,; T ENST00000248975 Transcript missense_variant 912/1825 639/741 213/246 E/D gaG/gaT 1 1 YWHAH HGNC HGNC:12853 protein_coding YES CCDS13901.1 ENSP00000248975 Q04917 A0A024R1K7 UPI000013CC64 NM_003405.3 deleterious_low_confidence(0.02) 2/2 hmmpanther:PTHR18860,hmmpanther:PTHR18860:SF16,Pfam_domain:PF00244,Gene3D:3iquA00,PIRSF_domain:PIRSF000868,SMART_domains:SM00101,Superfamily_domains:SSF48445,Prints_domain:PR00305 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 31956690 31956690 G T 1 0 0 0 0 1 0 0 0 18065 991 35 2 2 YWHAH 22 31956690 Missense_Mutation SNP G C3L-00279_T 427848 31956690 18861778 611 6389 MXRA5 0 . GRCh38 X 3311318 3311318 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.6885T>A p.= p.G2295G ENST00000217939 7/7 438 401 37 442 442 0 strelka-varscan-mutect MXRA5,synonymous_variant,p.=,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript synonymous_variant 7040/9793 6885/8487 2295/2828 G ggT/ggA 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS rs1276817050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 3311318 3311318 A T 1 0 0 0 0 0 0 0 1 10002 146 6 4 4 MXRA5 23 3311318 Silent SNP A C3L-00279_T 3311318 152729577 612 6390 EGFL6 0 . GRCh38 X 13617756 13617756 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.805G>T p.Val269Phe p.V269F ENST00000380602 8/12 115 101 14 65 65 0 strelka-varscan-mutect EGFL6,missense_variant,p.Val269Phe,ENST00000361306,NM_015507.3;EGFL6,missense_variant,p.Val269Phe,ENST00000380602,NM_001167890.1; T ENST00000380602 Transcript missense_variant 1045/2385 805/1665 269/554 V/F Gtc/Ttc 1 1 EGFL6 HGNC HGNC:3235 protein_coding YES CCDS55370.1 ENSP00000369976 Q8IUX8 UPI0000034CAE NM_001167890.1 tolerated(0.65) 8/12 hmmpanther:PTHR24050,hmmpanther:PTHR24050:SF18 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 13617756 13617756 G T 1 0 0 0 0 1 0 0 0 4799 1029 36 2 2 EGFL6 23 13617756 Missense_Mutation SNP G C3L-00279_T 10306438 13617756 142423139 613 6391 FANCB 0 . GRCh38 X 14843730 14843730 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.2417G>A p.Arg806Lys p.R806K ENST00000398334 10/10 283 266 17 134 134 0 strelka-varscan-mutect FANCB,missense_variant,p.Arg806Lys,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Arg806Lys,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Arg806Lys,ENST00000452869,; T ENST00000398334 Transcript missense_variant 2685/3008 2417/2580 806/859 R/K aGg/aAg 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 tolerated(0.49) 10/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 14843730 14843730 C T 1 0 0 0 0 1 0 0 0 5522 681 24 3 3 FANCB 23 14843730 Missense_Mutation SNP C C3L-00279_T 1225974 14843730 141197165 614 6392 BEND2 0 . GRCh38 X 18201925 18201925 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.923C>T p.Pro308Leu p.P308L ENST00000380033 6/14 187 175 12 135 135 0 strelka-varscan-mutect BEND2,missense_variant,p.Pro308Leu,ENST00000380033,NM_153346.4;BEND2,intron_variant,,ENST00000380030,NM_001184767.1; A ENST00000380033 Transcript missense_variant 1056/4611 923/2400 308/799 P/L cCa/cTa 1 -1 BEND2 HGNC HGNC:28509 protein_coding YES CCDS14184.1 ENSP00000369372 Q8NDZ0 UPI000013FE0F NM_153346.4 tolerated(0.06) 6/14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 18201925 18201925 G A 1 0 0 0 0 1 0 0 0 1546 1348 47 3 3 BEND2 23 18201925 Missense_Mutation SNP G C3L-00279_T 3358195 18201925 137838970 615 6393 MAGEB6 0 . GRCh38 X 26194041 26194041 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.195G>T p.Gln65His p.Q65H ENST00000379034 2/2 200 185 15 189 189 0 strelka-varscan-mutect MAGEB6,missense_variant,p.Gln65His,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript missense_variant 344/1949 195/1224 65/407 Q/H caG/caT 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 deleterious(0.03) 2/2 hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 MODERATE 1 SNV 1 1 PASS rs1053594324 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 26194041 26194041 G T 1 0 0 0 0 1 0 0 0 9096 991 35 2 2 MAGEB6 23 26194041 Missense_Mutation SNP G C3L-00279_T 7992116 26194041 129846854 616 6394 NR0B1 0 . GRCh38 X 30304739 30304739 + Missense_Mutation SNP G G A rs140730327 C3L-00279_T C3L-00279_N G G c.1253C>T p.Thr418Met p.T418M ENST00000378970 2/2 389 350 39 310 308 2 strelka-varscan-mutect NR0B1,missense_variant,p.Thr418Met,ENST00000378970,NM_000475.4;NR0B1,downstream_gene_variant,,ENST00000378963,; A ENST00000378970 Transcript missense_variant 1488/2021 1253/1413 418/470 T/M aCg/aTg rs140730327,COSM1119896 1 -1 NR0B1 HGNC HGNC:7960 protein_coding YES CCDS14223.1 ENSP00000368253 P51843 F1D8P4 UPI0000128ED4 NM_000475.4 tolerated(0.37) 2/2 hmmpanther:PTHR24081:SF1,hmmpanther:PTHR24081,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs140730327 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 14 30304739 30304739 G A 1 0 0 0 0 1 0 0 0 10669 1145 40 1 1 NR0B1 23 30304739 Missense_Mutation SNP G C3L-00279_T 4110698 30304739 125736156 617 6395 FAM47A 0 . GRCh38 X 34130838 34130838 + Missense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.1441G>A p.Glu481Lys p.E481K ENST00000346193 1/1 69 64 5 80 80 0 strelka-varscan-mutect FAM47A,missense_variant,p.Glu481Lys,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.Glu481Lys,ENST00000613251,; T ENST00000346193 Transcript missense_variant 1474/2556 1441/2376 481/791 E/K Gaa/Aaa COSM3561306 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 deleterious(0.01) 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 1 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -11.38329 0.9999979 1 1 1 0 T 3 4 14 34130838 34130838 C T 1 0 0 0 0 1 0 0 0 5447 864 30 3 3 FAM47A 23 34130838 Missense_Mutation SNP C C3L-00279_T 3826099 34130838 121910057 618 6396 CFAP47 0 . GRCh38 X 36236807 36236807 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.7280C>T p.Thr2427Ile p.T2427I ENST00000378653 48/64 111 92 19 83 83 0 strelka-varscan-mutect CFAP47,missense_variant,p.Thr2427Ile,ENST00000378653,NM_001304548.1; T ENST00000378653 Transcript missense_variant 7346/9943 7280/9564 2427/3187 T/I aCa/aTa 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 tolerated(0.38) 48/64 hmmpanther:PTHR23053 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 14 36236807 36236807 C T 1 0 0 0 0 1 0 0 0 3022 478 17 3 3 CFAP47 23 36236807 Missense_Mutation SNP C C3L-00279_T 2105969 36236807 119804088 619 6397 FAM47C 0 . GRCh38 X 37009485 37009485 + Frame_Shift_Del DEL C C - C3L-00279_T C3L-00279_N C C c.1076delC p.Pro359GlnfsTer466 p.P359Qfs*466 ENST00000358047 1/1 357 321 36 328 328 0 sindel-varindel-pindel FAM47C,frameshift_variant,p.Pro359GlnfsTer466,ENST00000358047,NM_001013736.2; - ENST00000358047 Transcript frameshift_variant 1089/3270 1075/3108 359/1035 P/X Cca/ca COSM1714861,COSM1714862 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 1,1 HIGH 1 deletion 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 14 37009485 37009485 C - 1 0 1 0 1 0 0 0 0 5449 855 30 0 0 FAM47C 23 37009485 Frame_Shift_Del DEL C C3L-00279_T 772678 37009485 119031410 620 6398 BCOR 0 . GRCh38 X 40053930 40053930 + Silent SNP G G T rs758816828 C3L-00279_T C3L-00279_N G G c.4932C>A p.= p.T1644T ENST00000378444 14/15 377 342 35 348 347 1 strelka-varscan-mutect BCOR,synonymous_variant,p.=,ENST00000342274,NM_001123383.1;BCOR,synonymous_variant,p.=,ENST00000378444,NM_001123385.1;BCOR,synonymous_variant,p.=,ENST00000378455,NM_001123384.1;BCOR,synonymous_variant,p.=,ENST00000397354,NM_017745.5;BCOR,synonymous_variant,p.=,ENST00000378463,;BCOR,synonymous_variant,p.=,ENST00000442018,;BCOR,synonymous_variant,p.=,ENST00000413905,;BCOR,intron_variant,,ENST00000427012,; T ENST00000378444 Transcript synonymous_variant 5161/6358 4932/5268 1644/1755 T acC/acA rs758816828 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 14/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117,Pfam_domain:PF16553 LOW 1 SNV 1 1 PASS rs758816828 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 40053930 40053930 G T 1 0 0 0 0 0 0 0 1 1533 1219 43 2 2 BCOR 23 40053930 Silent SNP G C3L-00279_T 3044445 40053930 115986965 621 6399 BCOR 0 . GRCh38 X 40063803 40063803 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.3652T>C p.Trp1218Arg p.W1218R ENST00000378444 8/15 370 342 28 340 340 0 strelka-varscan-mutect BCOR,missense_variant,p.Trp1184Arg,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Trp1218Arg,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Trp1166Arg,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Trp1184Arg,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Trp1184Arg,ENST00000406200,;BCOR,missense_variant,p.Trp61Arg,ENST00000378463,;BCOR,missense_variant,p.Trp88Arg,ENST00000413905,;BCOR,upstream_gene_variant,,ENST00000442018,;BCOR,upstream_gene_variant,,ENST00000427012,; G ENST00000378444 Transcript missense_variant 3881/6358 3652/5268 1218/1755 W/R Tgg/Cgg 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 deleterious(0) 8/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117,Pfam_domain:PF15808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 40063803 40063803 A G 1 0 0 0 0 1 0 0 0 1533 217 8 5 5 BCOR 23 40063803 Missense_Mutation SNP A C3L-00279_T 9873 40063803 115977092 622 6400 RBM10 0 . GRCh38 X 47179938 47179938 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.1155G>T p.= p.L385L ENST00000329236 10/24 421 386 35 386 386 0 strelka-varscan-mutect RBM10,synonymous_variant,p.=,ENST00000377604,NM_005676.4,NM_001204467.1;RBM10,synonymous_variant,p.=,ENST00000329236,NM_001204468.1;RBM10,synonymous_variant,p.=,ENST00000345781,NM_001204466.1;RBM10,synonymous_variant,p.=,ENST00000628161,NM_152856.2;RBM10,non_coding_transcript_exon_variant,,ENST00000478410,;RBM10,intron_variant,,ENST00000496012,; T ENST00000329236 Transcript synonymous_variant 1155/3201 1155/2988 385/995 L ctG/ctT 1 1 RBM10 HGNC HGNC:9896 protein_coding YES CCDS75969.1 ENSP00000328848 A0A0A0MR66 UPI0000211F0E NM_001204468.1 10/24 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF4,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 47179938 47179938 G T 1 0 0 0 0 0 0 0 1 13277 1335 47 2 2 RBM10 23 47179938 Silent SNP G C3L-00279_T 7116135 47179938 108860957 623 6401 TIMP1 0 . GRCh38 X 47585604 47585604 + Missense_Mutation SNP C C G rs754889950 C3L-00279_T C3L-00279_N C C c.390C>G p.Ser130Arg p.S130R ENST00000218388 5/6 88 76 12 80 80 0 strelka-varscan-mutect TIMP1,missense_variant,p.Ser130Arg,ENST00000218388,NM_003254.2;TIMP1,missense_variant,p.Ser66Arg,ENST00000377017,;TIMP1,missense_variant,p.Ser88Arg,ENST00000445623,;TIMP1,3_prime_UTR_variant,,ENST00000456754,;SYN1,intron_variant,,ENST00000295987,NM_006950.3;SYN1,intron_variant,,ENST00000340666,NM_133499.2;TIMP1,downstream_gene_variant,,ENST00000441738,;MIR4769,upstream_gene_variant,,ENST00000584126,; G ENST00000218388 Transcript missense_variant 560/892 390/624 130/207 S/R agC/agG rs754889950 1 1 TIMP1 HGNC HGNC:11820 protein_coding YES CCDS14281.1 ENSP00000218388 P01033 Q6FGX5 UPI00001135B1 NM_003254.2 tolerated(0.12) 5/6 PROSITE_profiles:PS50189,hmmpanther:PTHR11844,hmmpanther:PTHR11844:SF20,Gene3D:2e2dC01,Pfam_domain:PF00965,SMART_domains:SM00206,Superfamily_domains:SSF50242 MODERATE 1 SNV 1 1 PASS rs754889950 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 14 47585604 47585604 C G 1 0 0 0 0 1 0 0 0 16358 738 26 4 4 TIMP1 23 47585604 Missense_Mutation SNP C C3L-00279_T 405666 47585604 108455291 624 6402 CFP 0 . GRCh38 X 47627618 47627618 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.427G>T p.Gly143Trp p.G143W ENST00000247153 5/10 88 81 7 75 75 0 strelka-varscan-mutect CFP,missense_variant,p.Gly143Trp,ENST00000247153,NM_002621.2;CFP,missense_variant,p.Gly143Trp,ENST00000396992,NM_001145252.1;CFP,missense_variant,p.Gly143Trp,ENST00000377005,;CFP,missense_variant,p.Gly8Trp,ENST00000469388,;CFP,downstream_gene_variant,,ENST00000480317,;CFP,non_coding_transcript_exon_variant,,ENST00000485991,;CFP,upstream_gene_variant,,ENST00000478222,; A ENST00000247153 Transcript missense_variant 669/1713 427/1410 143/469 G/W Ggg/Tgg 1 -1 CFP HGNC HGNC:8864 protein_coding YES CCDS14282.1 ENSP00000247153 P27918 A0A0S2Z4I5 UPI0000132325 NM_002621.2 deleterious(0) 5/10 PROSITE_profiles:PS50092,hmmpanther:PTHR22906,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,Prints_domain:PR01705 MODERATE 1 SNV 5 1 PASS rs1190480861 . 0 207 3 0 0 0 0 0 -15.0274 1 1 1 1 0 A 3 1 14 47627618 47627618 C A 1 0 0 0 0 1 0 0 0 3051 623 22 2 2 CFP 23 47627618 Missense_Mutation SNP C C3L-00279_T 42014 47627618 108413277 625 6403 CCDC22 0 . GRCh38 X 49250163 49250163 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.1786G>A p.Gly596Ser p.G596S ENST00000376227 17/17 177 160 17 170 170 0 strelka-mutect CCDC22,missense_variant,p.Gly596Ser,ENST00000376227,NM_014008.4;FOXP3,downstream_gene_variant,,ENST00000455775,;FOXP3,downstream_gene_variant,,ENST00000376207,NM_014009.3;FOXP3,downstream_gene_variant,,ENST00000376199,NM_001114377.1;FOXP3,downstream_gene_variant,,ENST00000557224,;FOXP3,downstream_gene_variant,,ENST00000376197,;FOXP3,downstream_gene_variant,,ENST00000518685,; A ENST00000376227 Transcript missense_variant 1956/2319 1786/1884 596/627 G/S Ggc/Agc 1 1 CCDC22 HGNC HGNC:28909 protein_coding YES CCDS14322.1 ENSP00000365401 O60826 A0A024QZ03 UPI000006FFC7 NM_014008.4 tolerated(0.38) 17/17 hmmpanther:PTHR15668,Pfam_domain:PF05667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 49250163 49250163 G A 1 0 0 0 0 1 0 0 0 2508 1232 43 3 3 CCDC22 23 49250163 Missense_Mutation SNP G C3L-00279_T 1622545 49250163 106790732 626 6404 MAGED1 0 . GRCh38 X 51901866 51901866 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2441G>T p.Gly814Val p.G814V ENST00000375695 13/14 181 170 11 175 175 0 strelka-varscan-mutect MAGED1,missense_variant,p.Gly814Val,ENST00000375695,NM_001005333.1;MAGED1,missense_variant,p.Gly758Val,ENST00000375722,;MAGED1,missense_variant,p.Gly758Val,ENST00000326587,NM_006986.3;MAGED1,missense_variant,p.Gly758Val,ENST00000375772,NM_001005332.1;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,;MAGED1,non_coding_transcript_exon_variant,,ENST00000473931,;RP11-234P3.2,downstream_gene_variant,,ENST00000428250,; T ENST00000375695 Transcript missense_variant 2594/2875 2441/2505 814/834 G/V gGt/gTt 1 1 MAGED1 HGNC HGNC:6813 protein_coding YES CCDS35279.1 ENSP00000364847 Q9Y5V3 UPI0000074161 NM_001005333.1 deleterious_low_confidence(0) 13/14 Low_complexity_(Seg):seg,hmmpanther:PTHR11736:SF28,hmmpanther:PTHR11736 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.31208 1 1 1 1 0 T 3 4 14 51901866 51901866 G T 1 0 0 0 0 1 0 0 0 9101 1261 44 2 2 MAGED1 23 51901866 Missense_Mutation SNP G C3L-00279_T 2651703 51901866 104139029 627 6405 SPANXN5 0 . GRCh38 X 52796612 52796612 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.95G>A p.Arg32Lys p.R32K ENST00000375511 2/2 143 127 16 85 85 0 strelka-varscan-mutect SPANXN5,missense_variant,p.Arg32Lys,ENST00000375511,NM_001009616.3;RP13-77O11.12,downstream_gene_variant,,ENST00000452829,; T ENST00000375511 Transcript missense_variant 848/1316 95/219 32/72 R/K aGg/aAg 1 -1 SPANXN5 HGNC HGNC:33178 protein_coding YES CCDS35295.1 ENSP00000364661 Q5MJ07 UPI000023FDD3 NM_001009616.3 tolerated(0.9) 2/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF7 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 52796612 52796612 C T 1 0 0 0 0 1 0 0 0 15325 681 24 3 3 SPANXN5 23 52796612 Missense_Mutation SNP C C3L-00279_T 894746 52796612 103244283 628 6406 HUWE1 0 . GRCh38 X 53554812 53554812 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.8315C>A p.Pro2772Gln p.P2772Q ENST00000342160 60/83 206 187 19 144 144 0 strelka-varscan-mutect HUWE1,missense_variant,p.Pro2772Gln,ENST00000342160,;HUWE1,missense_variant,p.Pro2772Gln,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Pro2763Gln,ENST00000612484,;MIR98,downstream_gene_variant,,ENST00000606724,;MIRLET7F2,downstream_gene_variant,,ENST00000385277,; T ENST00000342160 Transcript missense_variant 8773/14796 8315/13125 2772/4374 P/Q cCa/cAa 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC tolerated_low_confidence(0.14) 60/83 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 14 53554812 53554812 G T 1 0 0 0 0 1 0 0 0 7357 1348 47 2 2 HUWE1 23 53554812 Missense_Mutation SNP G C3L-00279_T 758200 53554812 102486083 629 6407 TRO 0 . GRCh38 X 54930724 54930724 + Missense_Mutation SNP A A G novel C3L-00279_T C3L-00279_N A A c.4000A>G p.Ile1334Val p.I1334V ENST00000173898 12/13 277 256 21 269 269 0 strelka-varscan-mutect TRO,missense_variant,p.Ile1334Val,ENST00000173898,NM_001039705.2;TRO,missense_variant,p.Ile865Val,ENST00000420798,NM_001271183.1;TRO,missense_variant,p.Ile937Val,ENST00000375041,NM_001271184.1;TRO,intron_variant,,ENST00000319167,NM_016157.3;TRO,intron_variant,,ENST00000375022,NM_177556.2;TRO,intron_variant,,ENST00000622017,;TRO,intron_variant,,ENST00000399736,NM_177557.2;PFKFB1,downstream_gene_variant,,ENST00000375006,NM_001271804.1,NM_002625.3;PFKFB1,downstream_gene_variant,,ENST00000545676,NM_001271805.1;PFKFB1,downstream_gene_variant,,ENST00000614686,;PFKFB1,downstream_gene_variant,,ENST00000374992,;SNORA11,downstream_gene_variant,,ENST00000408823,;TRO,intron_variant,,ENST00000475183,;TRO,downstream_gene_variant,,ENST00000492142,;TRO,non_coding_transcript_exon_variant,,ENST00000492706,;TRO,intron_variant,,ENST00000445561,;TRO,downstream_gene_variant,,ENST00000469211,; G ENST00000173898 Transcript missense_variant 4112/4647 4000/4296 1334/1431 I/V Atc/Gtc 1 1 TRO HGNC HGNC:12326 protein_coding YES CCDS43959.1 ENSP00000173898 Q12816 UPI000021208F NM_001039705.2 tolerated_low_confidence(0.12) 12/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 54930724 54930724 A G 1 0 0 0 0 1 0 0 0 17079 217 8 5 5 TRO 23 54930724 Missense_Mutation SNP A C3L-00279_T 1375912 54930724 101110171 630 6408 AMER1 0 . GRCh38 X 64190080 64190081 + Frame_Shift_Ins INS - - A novel C3L-00279_T C3L-00279_N - - c.3206_3207insT p.Ser1070GlnfsTer24 p.S1070Qfs*24 ENST00000330258 2/2 78 70 8 91 91 0 sindel-varindel-pindel AMER1,frameshift_variant,p.Ser1070GlnfsTer24,ENST00000330258,NM_152424.3;AMER1,intron_variant,,ENST00000374869,; A ENST00000330258 Transcript frameshift_variant 3479-3480/8443 3206-3207/3408 1069/1135 P/PX ccc/ccTc 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 2/2 Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 202 7 0 0 0 0 0 -17.19034 0.999999 1 1 1 0 A 7 5 14 64190080 64190080 - A 1 0 1 1 0 0 0 0 0 667 1335 47 0 0 AMER1 23 64190080 Frame_Shift_Ins INS - C3L-00279_T 9259356 64190080 91850815 631 6409 ZC4H2 0 . GRCh38 X 64919177 64919177 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.426G>T p.Trp142Cys p.W142C ENST00000374839 4/5 180 162 18 179 179 0 strelka-varscan-mutect ZC4H2,missense_variant,p.Trp119Cys,ENST00000337990,NM_001178032.2,NM_001243804.1;ZC4H2,missense_variant,p.Trp142Cys,ENST00000374839,NM_018684.3;ZC4H2,intron_variant,,ENST00000447788,NM_001178033.2;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488608,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000476032,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000492653,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488831,;ZC4H2,intron_variant,,ENST00000488406,; A ENST00000374839 Transcript missense_variant 533/2184 426/675 142/224 W/C tgG/tgT 1 -1 ZC4H2 HGNC HGNC:24931 protein_coding YES CCDS14380.1 ENSP00000363972 Q9NQZ6 UPI0000025CAA NM_018684.3 tolerated(0.16) 4/5 Pfam_domain:PF10146,hmmpanther:PTHR31058 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 64919177 64919177 C A 1 0 0 0 0 1 0 0 0 18153 740 26 2 2 ZC4H2 23 64919177 Missense_Mutation SNP C C3L-00279_T 729097 64919177 91121718 632 6410 MED12 0 . GRCh38 X 71137793 71137793 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.5894C>A p.Pro1965His p.P1965H ENST00000374080 41/45 285 247 38 297 295 2 strelka-varscan-mutect MED12,missense_variant,p.Pro1815His,ENST00000333646,;MED12,missense_variant,p.Pro1964His,ENST00000374102,;MED12,missense_variant,p.Pro1965His,ENST00000374080,NM_005120.2;MED12,intron_variant,,ENST00000444034,; A ENST00000374080 Transcript missense_variant 5926/6795 5894/6534 1965/2177 P/H cCc/cAc 1 1 MED12 HGNC HGNC:11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 UPI00004257E2 NM_005120.2 deleterious_low_confidence(0) 41/45 Pfam_domain:PF12144,hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF24,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 14 71137793 71137793 C A 1 0 0 0 0 1 0 0 0 9367 623 22 2 2 MED12 23 71137793 Missense_Mutation SNP C C3L-00279_T 6218616 71137793 84903102 633 6411 TAF1 0 . GRCh38 X 71384964 71384964 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2201G>T p.Gly734Val p.G734V ENST00000423759 14/39 183 165 18 91 91 0 strelka-mutect TAF1,missense_variant,p.Gly734Val,ENST00000423759,NM_001286074.1;TAF1,missense_variant,p.Gly713Val,ENST00000373790,NM_138923.3;TAF1,missense_variant,p.Gly734Val,ENST00000276072,NM_004606.4;TAF1,upstream_gene_variant,,ENST00000478305,;TAF1,upstream_gene_variant,,ENST00000472567,;TAF1,upstream_gene_variant,,ENST00000474917,; T ENST00000423759 Transcript missense_variant 2277/7722 2201/5688 734/1895 G/V gGa/gTa 1 1 TAF1 HGNC HGNC:11535 protein_coding YES CCDS69783.1 ENSP00000406549 P21675 UPI000171708A NM_001286074.1 deleterious(0.04) 14/39 Pfam_domain:PF12157,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 71384964 71384964 G T 1 0 0 0 0 1 0 0 0 15909 1174 41 2 2 TAF1 23 71384964 Missense_Mutation SNP G C3L-00279_T 247171 71384964 84655931 634 6412 NHSL2 0 . GRCh38 X 72138905 72138905 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1357G>T p.Gly453Trp p.G453W ENST00000633930 6/8 258 226 32 235 235 0 strelka-varscan-mutect NHSL2,missense_variant,p.Gly453Trp,ENST00000633930,NM_001013627.2;NHSL2,missense_variant,p.Gly178Trp,ENST00000631375,;NHSL2,missense_variant,p.Gly87Trp,ENST00000510661,;NHSL2,missense_variant,p.Gly170Trp,ENST00000632230,;NHSL2,downstream_gene_variant,,ENST00000631833,;NHSL2,non_coding_transcript_exon_variant,,ENST00000373677,; T ENST00000633930 Transcript missense_variant 1627/13660 1357/3678 453/1225 G/W Ggg/Tgg 1 1 NHSL2 HGNC HGNC:33737 protein_coding YES ENSP00000488668 A0A0J9YY34 UPI0001B09231 NM_001013627.2 deleterious(0) 6/8 hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF2 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 14 72138905 72138905 G T 1 0 0 0 0 1 0 0 0 10445 1348 47 2 2 NHSL2 23 72138905 Missense_Mutation SNP G C3L-00279_T 753941 72138905 83901990 635 6413 ERCC6L 0 . GRCh38 X 72205400 72205400 + Missense_Mutation SNP G G T rs746653103 C3L-00279_T C3L-00279_N G G c.3367C>A p.Pro1123Thr p.P1123T ENST00000334463 2/2 181 161 20 113 113 0 strelka-varscan-mutect ERCC6L,missense_variant,p.Pro1000Thr,ENST00000373657,;ERCC6L,missense_variant,p.Pro1123Thr,ENST00000334463,NM_017669.2;PIN4,intron_variant,,ENST00000423432,NM_001170747.1;PIN4,intron_variant,,ENST00000496835,;PIN4,intron_variant,,ENST00000439980,; T ENST00000334463 Transcript missense_variant 3503/4243 3367/3753 1123/1250 P/T Cct/Act rs746653103 1 -1 ERCC6L HGNC HGNC:20794 protein_coding YES CCDS35329.1 ENSP00000334675 Q2NKX8 UPI000021233E NM_017669.2 tolerated(0.64) 2/2 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF756 MODERATE 1 SNV 1 1 PASS rs746653103 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 72205400 72205400 G T 1 0 0 0 0 1 0 0 0 5067 1174 41 2 2 ERCC6L 23 72205400 Missense_Mutation SNP G C3L-00279_T 66495 72205400 83835495 636 6414 KIAA2022 0 . GRCh38 X 74741355 74741355 + Missense_Mutation SNP G G A novel C3L-00279_T C3L-00279_N G G c.3202C>T p.Leu1068Phe p.L1068F ENST00000055682 3/4 317 295 22 274 274 0 strelka-varscan-mutect KIAA2022,missense_variant,p.Leu1068Phe,ENST00000055682,NM_001008537.2;KIAA2022,missense_variant,p.Leu1068Phe,ENST00000616200,;KIAA2022,upstream_gene_variant,,ENST00000424929,; A ENST00000055682 Transcript missense_variant 3814/11719 3202/4551 1068/1516 L/F Ctt/Ttt 1 -1 KIAA2022 HGNC HGNC:29433 protein_coding YES CCDS35337.1 ENSP00000055682 Q5QGS0 UPI00001C207B NM_001008537.2 deleterious(0.03) 3/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 74741355 74741355 G A 1 0 0 0 0 1 0 0 0 8133 1000 35 3 3 KIAA2022 23 74741355 Missense_Mutation SNP G C3L-00279_T 2535955 74741355 81299540 637 6415 UPRT 0 . GRCh38 X 75300868 75300868 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.726C>A p.Ser242Arg p.S242R ENST00000373383 6/7 89 77 12 57 57 0 strelka-varscan-mutect UPRT,missense_variant,p.Ser242Arg,ENST00000373379,NM_001307944.1;UPRT,missense_variant,p.Ser242Arg,ENST00000373383,NM_145052.3;UPRT,missense_variant,p.Ser106Arg,ENST00000530743,;UPRT,splice_region_variant,,ENST00000474175,;UPRT,splice_region_variant,,ENST00000526850,;UPRT,downstream_gene_variant,,ENST00000531704,;UPRT,splice_region_variant,,ENST00000462237,; A ENST00000373383 Transcript missense_variant,splice_region_variant 893/2186 726/930 242/309 S/R agC/agA 1 1 UPRT HGNC HGNC:28334 protein_coding YES CCDS14429.1 ENSP00000362481 Q96BW1 A8KAF9 UPI000004B62E NM_145052.3 deleterious(0) 6/7 Gene3D:3.40.50.2020,Pfam_domain:PF14681,hmmpanther:PTHR10285,Superfamily_domains:SSF53271 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999918 1 1 1 0 A 3 1 14 75300868 75300868 C A 1 0 0 0 0 1 0 0 0 17540 724 25 2 2 UPRT 23 75300868 Missense_Mutation SNP C C3L-00279_T 559513 75300868 80740027 638 6416 ZCCHC5 0 . GRCh38 X 78657759 78657759 + Missense_Mutation SNP G G T rs200454840 C3L-00279_T C3L-00279_N G G c.662C>A p.Ala221Asp p.A221D ENST00000321110 2/2 415 375 40 367 367 0 strelka-varscan-mutect ZCCHC5,missense_variant,p.Ala221Asp,ENST00000321110,NM_152694.2; T ENST00000321110 Transcript missense_variant 958/2648 662/1428 221/475 A/D gCt/gAt rs200454840 1 -1 ZCCHC5 HGNC HGNC:22997 protein_coding YES CCDS14440.1 ENSP00000316794 Q8N8U3 UPI00000710DD NM_152694.2 tolerated(0.06) 2/2 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF7 MODERATE 1 SNV 2 1 PASS rs200454840 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 78657759 78657759 G T 1 0 0 0 0 1 0 0 0 18166 971 34 2 2 ZCCHC5 23 78657759 Missense_Mutation SNP G C3L-00279_T 3356891 78657759 77383136 639 6417 BRWD3 0 . GRCh38 X 80704722 80704722 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.2677T>A p.Ser893Thr p.S893T ENST00000373275 23/41 396 361 35 132 132 0 strelka-varscan-mutect BRWD3,missense_variant,p.Ser893Thr,ENST00000373275,NM_153252.4;BRWD3,non_coding_transcript_exon_variant,,ENST00000473691,; T ENST00000373275 Transcript missense_variant 2894/11381 2677/5409 893/1802 S/T Tcc/Acc 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 tolerated(0.44) 23/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 80704722 80704722 A T 1 0 0 0 0 1 0 0 0 1700 275 10 4 4 BRWD3 23 80704722 Missense_Mutation SNP A C3L-00279_T 2046963 80704722 75336173 640 6418 BRWD3 0 . GRCh38 X 80704761 80704761 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.2638C>A p.Arg880Ser p.R880S ENST00000373275 23/41 361 326 35 136 136 0 strelka-varscan-mutect BRWD3,missense_variant,p.Arg880Ser,ENST00000373275,NM_153252.4;BRWD3,non_coding_transcript_exon_variant,,ENST00000473691,; T ENST00000373275 Transcript missense_variant 2855/11381 2638/5409 880/1802 R/S Cgt/Agt COSM3406620 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 tolerated(0.11) 23/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 80704761 80704761 G T 1 0 0 0 0 1 0 0 0 1700 1145 40 1 1 BRWD3 23 80704761 Missense_Mutation SNP G C3L-00279_T 39 80704761 75336134 641 6419 POU3F4 0 . GRCh38 X 83508696 83508696 + Silent SNP C C A rs765320605 C3L-00279_T C3L-00279_N C C c.372C>A p.= p.I124I ENST00000373200 1/1 286 261 25 245 245 0 strelka-varscan-mutect POU3F4,synonymous_variant,p.=,ENST00000373200,NM_000307.4;RP3-326L13.2,non_coding_transcript_exon_variant,,ENST00000625081,; A ENST00000373200 Transcript synonymous_variant 447/3878 372/1086 124/361 I atC/atA rs765320605,COSM3563695,COSM3563696 1 1 POU3F4 HGNC HGNC:9217 protein_coding YES CCDS14450.1 ENSP00000362296 P49335 UPI0000131D8A NM_000307.4 1/1 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF83,PIRSF_domain:PIRSF002629 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs765320605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 83508696 83508696 C A 1 0 0 0 0 0 0 0 1 12393 816 29 2 2 POU3F4 23 83508696 Silent SNP C C3L-00279_T 2803935 83508696 72532199 642 6420 APOOL 0 . GRCh38 X 85074020 85074020 + Missense_Mutation SNP C C A C3L-00279_T C3L-00279_N C C c.509C>A p.Ala170Asp p.A170D ENST00000373173 7/9 139 125 14 61 61 0 strelka-varscan-mutect APOOL,missense_variant,p.Leu165Ile,ENST00000622540,;APOOL,missense_variant,p.Ala170Asp,ENST00000613473,;APOOL,missense_variant,p.Ala170Asp,ENST00000373173,NM_198450.5; A ENST00000373173 Transcript missense_variant 596/1279 509/807 170/268 A/D gCt/gAt COSM1126056 1 1 APOOL HGNC HGNC:24009 protein_coding YES CCDS48138.1 ENSP00000362268 Q6UXV4 UPI00001D6936 NM_198450.5 tolerated(0.09) 7/9 Pfam_domain:PF09769,hmmpanther:PTHR14564,hmmpanther:PTHR14564:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 85074020 85074020 C A 1 0 0 0 0 1 0 0 0 936 797 28 2 2 APOOL 23 85074020 Missense_Mutation SNP C C3L-00279_T 1565324 85074020 70966875 643 6421 ZNF711 0 . GRCh38 X 85255336 85255336 + Missense_Mutation SNP G G A C3L-00279_T C3L-00279_N G G c.157G>A p.Asp53Asn p.D53N ENST00000373165 4/9 439 399 40 232 232 0 strelka-varscan-mutect ZNF711,missense_variant,p.Asp53Asn,ENST00000360700,;ZNF711,missense_variant,p.Asp53Asn,ENST00000373165,NM_021998.4;ZNF711,missense_variant,p.Asp53Asn,ENST00000276123,; A ENST00000373165 Transcript missense_variant 463/4124 157/2286 53/761 D/N Gat/Aat COSM1138216,COSM296391 1 1 ZNF711 HGNC HGNC:13128 protein_coding YES CCDS35344.1 ENSP00000362260 Q9Y462 UPI0000212114 NM_021998.4 tolerated_low_confidence(0.1) 4/9 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF1 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1427911141 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 85255336 85255336 G A 1 0 0 0 0 1 0 0 0 18691 1290 45 3 3 ZNF711 23 85255336 Missense_Mutation SNP G C3L-00279_T 181316 85255336 70785559 644 6422 PCDH11X 0 . GRCh38 X 91835761 91835761 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.257C>A p.Thr86Asn p.T86N ENST00000373094 1/7 665 599 66 623 623 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Thr86Asn,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Thr86Asn,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Thr86Asn,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Thr86Asn,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Thr86Asn,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Thr86Asn,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Thr86Asn,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; A ENST00000373094 Transcript missense_variant 1102/9179 257/4044 86/1347 T/N aCt/aAt 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0) 1/7 Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 91835761 91835761 C A 1 0 0 0 0 1 0 0 0 11595 565 20 2 2 PCDH11X 23 91835761 Missense_Mutation SNP C C3L-00279_T 6580425 91835761 64205134 645 6423 NOX1 0 . GRCh38 X 100843997 100843997 + Silent SNP C C T novel C3L-00279_T C3L-00279_N C C c.1650G>A p.= p.L550L ENST00000372966 13/13 198 185 13 168 168 0 strelka-mutect NOX1,synonymous_variant,p.=,ENST00000372966,NM_007052.4;NOX1,synonymous_variant,p.=,ENST00000372960,NM_001271815.1;NOX1,synonymous_variant,p.=,ENST00000217885,NM_013955.2;NOX1,synonymous_variant,p.=,ENST00000427768,;NOX1,intron_variant,,ENST00000372964,;CSTF2,downstream_gene_variant,,ENST00000415585,NM_001306206.1;CSTF2,downstream_gene_variant,,ENST00000372972,NM_001325.2;CSTF2,downstream_gene_variant,,ENST00000475126,; T ENST00000372966 Transcript synonymous_variant 1856/2529 1650/1695 550/564 L ctG/ctA 1 -1 NOX1 HGNC HGNC:7889 protein_coding YES CCDS14474.1 ENSP00000362057 Q9Y5S8 UPI00001303C1 NM_007052.4 13/13 hmmpanther:PTHR11972:SF71,hmmpanther:PTHR11972,Gene3D:3.40.50.80,Superfamily_domains:SSF52343 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99924 1 1 1 1 0 T 2 4 14 100843997 100843997 C T 1 0 0 0 0 0 0 0 1 10602 581 21 3 3 NOX1 23 100843997 Silent SNP C C3L-00279_T 9008236 100843997 55196898 646 6424 TBC1D8B 0 . GRCh38 X 106820982 106820982 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.347A>T p.Gln116Leu p.Q116L ENST00000357242 3/21 51 41 10 15 15 0 strelka-mutect TBC1D8B,missense_variant,p.Gln116Leu,ENST00000357242,NM_017752.2;TBC1D8B,missense_variant,p.Gln116Leu,ENST00000481617,;TBC1D8B,missense_variant,p.Gln116Leu,ENST00000276175,;TBC1D8B,missense_variant,p.Gln116Leu,ENST00000310452,NM_198881.1;TBC1D8B,missense_variant,p.Gln18Leu,ENST00000460545,;MORC4,intron_variant,,ENST00000604604,; T ENST00000357242 Transcript missense_variant 521/5717 347/3363 116/1120 Q/L cAa/cTa 1 1 TBC1D8B HGNC HGNC:24715 protein_coding YES CCDS14522.1 ENSP00000349781 Q0IIM8 UPI0000225CD5 NM_017752.2 tolerated(0.06) 3/21 hmmpanther:PTHR22957:SF320,hmmpanther:PTHR22957 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 14 106820982 106820982 A T 1 0 0 0 0 1 0 0 0 16031 130 5 4 4 TBC1D8B 23 106820982 Missense_Mutation SNP A C3L-00279_T 5976985 106820982 49219913 647 6425 MORC4 0 . GRCh38 X 106942852 106942852 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2039C>A p.Thr680Asn p.T680N ENST00000355610 15/17 332 296 36 261 261 0 strelka-varscan-mutect MORC4,missense_variant,p.Thr680Asn,ENST00000355610,NM_024657.4;MORC4,missense_variant,p.Thr680Asn,ENST00000255495,NM_001085354.2;MORC4,intron_variant,,ENST00000604604,;MORC4,upstream_gene_variant,,ENST00000478924,; T ENST00000355610 Transcript missense_variant 2314/3834 2039/2814 680/937 T/N aCc/aAc 1 -1 MORC4 HGNC HGNC:23485 protein_coding YES CCDS14525.2 ENSP00000347821 Q8TE76 UPI00003E75D3 NM_024657.4 tolerated(1) 15/17 hmmpanther:PTHR23336,hmmpanther:PTHR23336:SF22 MODERATE 1 SNV 2 1 PASS rs1328940608 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 106942852 106942852 G T 1 0 0 0 0 1 0 0 0 9668 1261 44 2 2 MORC4 23 106942852 Missense_Mutation SNP G C3L-00279_T 121870 106942852 49098043 648 6426 ACSL4 0 . GRCh38 X 109681007 109681007 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.769C>A p.Pro257Thr p.P257T ENST00000340800 7/17 204 185 19 72 72 0 strelka-varscan-mutect ACSL4,missense_variant,p.Pro257Thr,ENST00000340800,NM_001318509.1,NM_022977.2;ACSL4,missense_variant,p.Pro257Thr,ENST00000469796,;ACSL4,missense_variant,p.Pro216Thr,ENST00000348502,NM_001318510.1,NM_004458.2;ACSL4,downstream_gene_variant,,ENST00000502391,;ACSL4,downstream_gene_variant,,ENST00000508092,;ACSL4,downstream_gene_variant,,ENST00000505855,;ACSL4,downstream_gene_variant,,ENST00000504980,;ACSL4,downstream_gene_variant,,ENST00000469857,; T ENST00000340800 Transcript missense_variant 1274/5333 769/2136 257/711 P/T Cca/Aca 1 -1 ACSL4 HGNC HGNC:3571 protein_coding YES CCDS14548.1 ENSP00000339787 O60488 UPI000012E293 NM_001318509.1,NM_022977.2 tolerated(0.16) 7/17 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF241,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 109681007 109681007 G T 1 0 0 0 0 1 0 0 0 221 1232 43 2 2 ACSL4 23 109681007 Missense_Mutation SNP G C3L-00279_T 2738155 109681007 46359888 649 6427 RGAG1 0 . GRCh38 X 110451803 110451803 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1186G>T p.Gly396Trp p.G396W ENST00000465301 3/4 277 256 21 266 266 0 strelka-varscan-mutect RGAG1,missense_variant,p.Gly396Trp,ENST00000465301,NM_020769.2;RGAG1,missense_variant,p.Gly396Trp,ENST00000540313,;RGAG1,downstream_gene_variant,,ENST00000520821,; T ENST00000465301 Transcript missense_variant 1432/5426 1186/4167 396/1388 G/W Ggg/Tgg 1 1 RGAG1 HGNC HGNC:29245 protein_coding YES CCDS14552.1 ENSP00000419786 Q8NET4 UPI000006F841 NM_020769.2 deleterious(0) 3/4 hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF48 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 110451803 110451803 G T 1 0 0 0 0 1 0 0 0 13446 1348 47 2 2 RGAG1 23 110451803 Missense_Mutation SNP G C3L-00279_T 770796 110451803 45589092 650 6428 CAPN6 0 . GRCh38 X 111247936 111247936 + Missense_Mutation SNP G G C rs770534374 C3L-00279_T C3L-00279_N G G c.1541C>G p.Pro514Arg p.P514R ENST00000324068 11/13 332 295 37 250 250 0 strelka-varscan-mutect CAPN6,missense_variant,p.Pro514Arg,ENST00000324068,NM_014289.3; C ENST00000324068 Transcript missense_variant 1709/3568 1541/1926 514/641 P/R cCg/cGg rs770534374 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 deleterious(0.02) 11/13 hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183 MODERATE 1 SNV 1 1 PASS rs770534374 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 111247936 111247936 G C 1 0 0 0 0 1 0 0 0 2324 1116 39 4 4 CAPN6 23 111247936 Missense_Mutation SNP G C3L-00279_T 796133 111247936 44792959 651 6429 TRPC5 0 . GRCh38 X 111912338 111912338 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.853C>A p.His285Asn p.H285N ENST00000262839 3/11 112 106 6 75 75 0 strelka-varscan-mutect TRPC5,missense_variant,p.His285Asn,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript missense_variant 1772/5839 853/2922 285/973 H/N Cat/Aat 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 tolerated(0.92) 3/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,TIGRFAM_domain:TIGR00870,Prints_domain:PR01646 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.17361 1 1 1 1 0 T 3 4 14 111912338 111912338 G T 1 0 0 0 0 1 0 0 0 17087 1348 47 2 2 TRPC5 23 111912338 Missense_Mutation SNP G C3L-00279_T 664402 111912338 44128557 652 6430 RP13-347D8.7 0 . GRCh38 X 119073334 119073334 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.109G>T p.Gly37Cys p.G37C ENST00000620151 1/3 43 39 4 64 64 0 strelka-varscan-mutect RP13-347D8.7,missense_variant,p.Gly37Cys,ENST00000620151,; T ENST00000620151 Transcript missense_variant 109/1147 109/975 37/324 G/C Ggc/Tgc 1 1 RP13-347D8.7 Clone_based_vega_gene protein_coding YES ENSP00000488984 A0A0U1RQG5 UPI000719A0D1 deleterious(0.01) 1/3 hmmpanther:PTHR32157,hmmpanther:PTHR32157:SF2,Pfam_domain:PF15623 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -10.69844 1 1 1 1 0 T 3 4 14 119073334 119073334 G T 1 0 0 0 0 1 0 0 0 13772 1348 47 2 2 RP13-347D8.7 23 119073334 Missense_Mutation SNP G C3L-00279_T 7160996 119073334 36967561 653 6431 KIAA1210 0 . GRCh38 X 119123639 119123639 + Missense_Mutation SNP C C T novel C3L-00279_T C3L-00279_N C C c.424G>A p.Ala142Thr p.A142T ENST00000402510 3/14 203 191 12 84 84 0 varscan-mutect KIAA1210,missense_variant,p.Ala142Thr,ENST00000402510,NM_020721.1; T ENST00000402510 Transcript missense_variant 424/7824 424/5130 142/1709 A/T Gct/Act 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 tolerated(0.17) 3/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -14.98833 0.9999995 1 1 1 0 T 3 4 14 119123639 119123639 C T 1 0 0 0 0 1 0 0 0 8106 739 26 3 3 KIAA1210 23 119123639 Missense_Mutation SNP C C3L-00279_T 50305 119123639 36917256 654 6432 GRIA3 0 . GRCh38 X 123185919 123185919 + Missense_Mutation SNP A A T novel C3L-00279_T C3L-00279_N A A c.197A>T p.Glu66Val p.E66V ENST00000622768 2/16 1010 858 152 803 803 0 strelka-varscan-mutect GRIA3,missense_variant,p.Glu66Val,ENST00000622768,NM_000828.4;GRIA3,missense_variant,p.Glu66Val,ENST00000620443,NM_007325.4;GRIA3,missense_variant,p.Glu66Val,ENST00000620581,;GRIA3,missense_variant,p.Glu66Val,ENST00000541091,;GRIA3,missense_variant,p.Glu66Val,ENST00000611689,NM_001256743.1;GRIA3,missense_variant,p.Glu66Val,ENST00000616590,;GRIA3,non_coding_transcript_exon_variant,,ENST00000479118,; T ENST00000622768 Transcript missense_variant 490/5173 197/2685 66/894 E/V gAg/gTg 1 1 GRIA3 HGNC HGNC:4573 protein_coding YES CCDS14604.1 ENSP00000481554 P42263 UPI000013D503 NM_000828.4 deleterious(0.05) 2/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF151,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 123185919 123185919 A T 1 0 0 0 0 1 0 0 0 6649 304 11 4 4 GRIA3 23 123185919 Missense_Mutation SNP A C3L-00279_T 4062280 123185919 32854976 655 6433 TEX13C 0 . GRCh38 X 125320292 125320292 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.173G>C p.Arg58Pro p.R58P ENST00000632600 1/1 250 223 27 187 187 0 strelka-varscan-mutect TEX13C,missense_variant,p.Arg58Pro,ENST00000632600,NM_001195272.1; C ENST00000632600 Transcript missense_variant 173/5095 173/2982 58/993 R/P cGg/cCg 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 deleterious(0.02) 1/1 hmmpanther:PTHR23111,hmmpanther:PTHR23111:SF32,Pfam_domain:PF15186 MODERATE 1 SNV 1 PASS . . 0 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 14 125320292 125320292 G C 1 0 0 0 0 1 0 0 0 16199 1116 39 4 4 TEX13C 23 125320292 Missense_Mutation SNP G C3L-00279_T 2134373 125320292 30720603 656 6434 DCAF12L2 0 . GRCh38 X 126164539 126164539 + Nonsense_Mutation SNP C C T C3L-00279_T C3L-00279_N C C c.1386G>A p.Trp462Ter p.W462* ENST00000360028 1/1 116 110 6 94 94 0 strelka-varscan-mutect DCAF12L2,stop_gained,p.Trp462Ter,ENST00000360028,NM_001013628.2; T ENST00000360028 Transcript stop_gained 1559/2599 1386/1392 462/463 W/* tgG/tgA COSM227964 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 1/1 hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860 1 HIGH 1 SNV 1 1 PASS . . 2 202 6 0 0 0 0 0 -11.89042 0.9999992 1 1 1 0 T 4 4 14 126164539 126164539 C T 1 0 0 0 0 0 1 0 0 4066 856 30 3 3 DCAF12L2 23 126164539 Nonsense_Mutation SNP C C3L-00279_T 844247 126164539 29876356 657 6435 XPNPEP2 0 . GRCh38 X 129767646 129767646 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.1784C>A p.Pro595His p.P595H ENST00000371106 20/21 422 378 44 297 297 0 strelka-varscan-mutect XPNPEP2,missense_variant,p.Pro595His,ENST00000371106,NM_003399.5; A ENST00000371106 Transcript missense_variant 1976/3270 1784/2025 595/674 P/H cCc/cAc 1 1 XPNPEP2 HGNC HGNC:12823 protein_coding YES CCDS14613.1 ENSP00000360147 O43895 UPI000013901A NM_003399.5 deleterious(0) 20/21 hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF98,Gene3D:3.90.230.10,Pfam_domain:PF16188,Superfamily_domains:SSF55920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 129767646 129767646 C A 1 0 0 0 0 1 0 0 0 18002 623 22 2 2 XPNPEP2 23 129767646 Missense_Mutation SNP C C3L-00279_T 3603107 129767646 26273249 658 6436 BCORL1 0 . GRCh38 X 130013648 130013648 + Silent SNP A A T novel C3L-00279_T C3L-00279_N A A c.876A>T p.= p.S292S ENST00000540052 3/12 365 315 50 254 254 0 strelka-varscan-mutect BCORL1,synonymous_variant,p.=,ENST00000540052,NM_021946.4;BCORL1,synonymous_variant,p.=,ENST00000218147,;BCORL1,upstream_gene_variant,,ENST00000456822,;BCORL1,upstream_gene_variant,,ENST00000441294,;BCORL1,downstream_gene_variant,,ENST00000488135,; T ENST00000540052 Transcript synonymous_variant 920/7127 876/5136 292/1711 S tcA/tcT 1 1 BCORL1 HGNC HGNC:25657 protein_coding YES CCDS14616.1 ENSP00000437775 Q5H9F3 UPI0001D3414A NM_021946.4 3/12 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 130013648 130013648 A T 1 0 0 0 0 0 0 0 1 1534 175 7 4 4 BCORL1 23 130013648 Silent SNP A C3L-00279_T 246002 130013648 26027247 659 6437 ELF4 0 . GRCh38 X 130069530 130069530 + Silent SNP G G A novel C3L-00279_T C3L-00279_N G G c.957C>T p.= p.A319A ENST00000308167 8/9 213 194 19 177 177 0 strelka-varscan-mutect ELF4,synonymous_variant,p.=,ENST00000308167,NM_001421.3;ELF4,synonymous_variant,p.=,ENST00000335997,NM_001127197.1;ELF4,synonymous_variant,p.=,ENST00000615377,;ELF4,downstream_gene_variant,,ENST00000434609,; A ENST00000308167 Transcript synonymous_variant 1337/4165 957/1992 319/663 A gcC/gcT 1 -1 ELF4 HGNC HGNC:3319 protein_coding YES CCDS14617.1 ENSP00000311280 Q99607 UPI0000072B32 NM_001421.3 8/9 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF170,Low_complexity_(Seg):seg,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 130069530 130069530 G A 1 0 0 0 0 0 0 0 1 4889 987 35 3 3 ELF4 23 130069530 Silent SNP G C3L-00279_T 55882 130069530 25971365 660 6438 RAB33A 0 . GRCh38 X 130184476 130184476 + Silent SNP C C A novel C3L-00279_T C3L-00279_N C C c.450C>A p.= p.G150G ENST00000257017 2/2 443 407 36 337 337 0 strelka-varscan-mutect RAB33A,synonymous_variant,p.=,ENST00000257017,NM_004794.2; A ENST00000257017 Transcript synonymous_variant 864/1258 450/714 150/237 G ggC/ggA 1 1 RAB33A HGNC HGNC:9773 protein_coding YES CCDS14621.1 ENSP00000257017 Q14088 UPI000000126B NM_004794.2 2/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF326,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 14 130184476 130184476 C A 1 0 0 0 0 0 0 0 1 13081 697 25 2 2 RAB33A 23 130184476 Silent SNP C C3L-00279_T 114946 130184476 25856419 661 6439 IGSF1 0 . GRCh38 X 131275271 131275271 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.3215C>A p.Pro1072His p.P1072H ENST00000370903 17/20 227 200 27 169 169 0 strelka-varscan-mutect IGSF1,missense_variant,p.Pro1058His,ENST00000370904,;IGSF1,missense_variant,p.Pro1072His,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Pro1058His,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Pro1067His,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000467244,; T ENST00000370903 Transcript missense_variant 3498/4594 3215/4026 1072/1341 P/H cCc/cAc 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 deleterious(0) 17/20 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF102,Gene3D:2.60.40.10,Pfam_domain:PF13895,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 131275271 131275271 G T 1 0 0 0 0 1 0 0 0 7503 1232 43 2 2 IGSF1 23 131275271 Missense_Mutation SNP G C3L-00279_T 1090795 131275271 24765624 662 6440 IGSF1 0 . GRCh38 X 131277176 131277176 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.2386C>A p.Pro796Thr p.P796T ENST00000370903 14/20 269 231 38 197 196 1 varscan-mutect IGSF1,missense_variant,p.Pro782Thr,ENST00000370904,;IGSF1,missense_variant,p.Pro796Thr,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Pro782Thr,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Pro791Thr,ENST00000361420,NM_001555.4;IGSF1,non_coding_transcript_exon_variant,,ENST00000467244,;IGSF1,downstream_gene_variant,,ENST00000469836,; T ENST00000370903 Transcript missense_variant 2669/4594 2386/4026 796/1341 P/T Cct/Act 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 tolerated(0.05) 14/20 PROSITE_profiles:PS50835,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 131277176 131277176 G T 1 0 0 0 0 1 0 0 0 7503 1232 43 2 2 IGSF1 23 131277176 Missense_Mutation SNP G C3L-00279_T 1905 131277176 24763719 663 6441 IGSF1 0 . GRCh38 X 131285237 131285237 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.609C>G p.Ile203Met p.I203M ENST00000370903 5/20 126 117 9 99 99 0 strelka-varscan-mutect IGSF1,missense_variant,p.Ile194Met,ENST00000370904,;IGSF1,missense_variant,p.Ile203Met,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Ile194Met,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Ile203Met,ENST00000361420,NM_001555.4;IGSF1,missense_variant,p.Ile203Met,ENST00000370901,NM_205833.3;IGSF1,missense_variant,p.Ile203Met,ENST00000370900,NM_001170963.1;IGSF1,upstream_gene_variant,,ENST00000469836,; C ENST00000370903 Transcript missense_variant 892/4594 609/4026 203/1341 I/M atC/atG 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 tolerated(0.11) 5/20 Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.34807 1 1 1 1 0 C 3 2 14 131285237 131285237 G C 1 0 0 0 0 1 0 0 0 7503 1164 41 4 4 IGSF1 23 131285237 Missense_Mutation SNP G C3L-00279_T 8061 131285237 24755658 664 6442 FRMD7 0 . GRCh38 X 132078378 132078378 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.1639C>A p.Leu547Met p.L547M ENST00000298542 12/12 682 640 42 402 402 0 strelka-varscan-mutect FRMD7,missense_variant,p.Leu547Met,ENST00000298542,NM_194277.2;FRMD7,missense_variant,p.Leu427Met,ENST00000370879,;FRMD7,missense_variant,p.Leu532Met,ENST00000464296,NM_001306193.1;STK26,downstream_gene_variant,,ENST00000394334,NM_016542.3;STK26,downstream_gene_variant,,ENST00000354719,;STK26,downstream_gene_variant,,ENST00000394335,NM_001042453.1;STK26,downstream_gene_variant,,ENST00000481105,;STK26,downstream_gene_variant,,ENST00000496850,NM_001042452.1; T ENST00000298542 Transcript missense_variant 1815/3198 1639/2145 547/714 L/M Ctg/Atg 1 -1 FRMD7 HGNC HGNC:8079 protein_coding YES CCDS35397.1 ENSP00000298542 Q6ZUT3 UPI00001C0AED NM_194277.2 deleterious(0.04) 12/12 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 132078378 132078378 G T 1 0 0 0 0 1 0 0 0 5925 991 35 2 2 FRMD7 23 132078378 Missense_Mutation SNP G C3L-00279_T 793141 132078378 23962517 665 6443 ADGRG4 0 . GRCh38 X 136345234 136345234 + Missense_Mutation SNP C C T rs775821351 C3L-00279_T C3L-00279_N C C c.1528C>T p.Pro510Ser p.P510S ENST00000394143 6/26 326 309 17 168 168 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Pro510Ser,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Pro510Ser,ENST00000370652,;ADGRG4,missense_variant,p.Pro305Ser,ENST00000394141,; T ENST00000394143 Transcript missense_variant 1819/9931 1528/9243 510/3080 P/S Cca/Tca rs775821351,COSM1569686 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 tolerated(0.15) 6/26 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775821351 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 136345234 136345234 C T 1 0 0 0 0 1 0 0 0 371 623 22 3 3 ADGRG4 23 136345234 Missense_Mutation SNP C C3L-00279_T 4266856 136345234 19695661 666 6444 ADGRG4 0 . GRCh38 X 136345736 136345736 + Missense_Mutation SNP T T A novel C3L-00279_T C3L-00279_N T T c.2030T>A p.Val677Glu p.V677E ENST00000394143 6/26 341 315 26 234 234 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Val677Glu,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Val677Glu,ENST00000370652,;ADGRG4,missense_variant,p.Val472Glu,ENST00000394141,; A ENST00000394143 Transcript missense_variant 2321/9931 2030/9243 677/3080 V/E gTg/gAg 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 6/26 MODERATE 1 SNV 1 1 PASS rs956197378 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 136345736 136345736 T A 1 0 0 0 0 1 0 0 0 371 1696 59 4 4 ADGRG4 23 136345736 Missense_Mutation SNP T C3L-00279_T 502 136345736 19695159 667 6445 MAGEC2 0 . GRCh38 X 142203716 142203716 + Missense_Mutation SNP G G T rs746859287 C3L-00279_T C3L-00279_N G G c.272C>A p.Pro91His p.P91H ENST00000247452 3/3 168 128 40 133 132 1 strelka-varscan-mutect MAGEC2,missense_variant,p.Pro91His,ENST00000247452,NM_016249.3; T ENST00000247452 Transcript missense_variant 620/1991 272/1122 91/373 P/H cCt/cAt rs746859287 1 -1 MAGEC2 HGNC HGNC:13574 protein_coding YES CCDS14678.1 ENSP00000354660 Q9UBF1 UPI000012F059 NM_016249.3 deleterious(0.02) 3/3 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs746859287 . 0 201 9 0 0 0 0 0 -20 0.9999975 1 1 1 0 T 3 4 14 142203716 142203716 G T 1 0 0 0 0 1 0 0 0 9099 1000 35 2 2 MAGEC2 23 142203716 Missense_Mutation SNP G C3L-00279_T 5857980 142203716 13837179 668 6446 SLITRK4 0 . GRCh38 X 143629577 143629577 + Missense_Mutation SNP A A C novel C3L-00279_T C3L-00279_N A A c.1532T>G p.Leu511Arg p.L511R ENST00000596188 2/2 438 404 34 302 301 1 strelka-varscan-mutect SLITRK4,missense_variant,p.Leu511Arg,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.Leu511Arg,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.Leu511Arg,ENST00000356928,NM_001184749.2; C ENST00000596188 Transcript missense_variant 1758/8545 1532/2514 511/837 L/R cTg/cGg 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 deleterious(0) 2/2 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 143629577 143629577 A C 1 0 0 0 0 1 0 0 0 15036 188 7 5 5 SLITRK4 23 143629577 Missense_Mutation SNP A C3L-00279_T 1425861 143629577 12411318 669 6447 IDS 0 . GRCh38 X 149505095 149505095 + Missense_Mutation SNP G G T C3L-00279_T C3L-00279_N G G c.43C>A p.Leu15Met p.L15M ENST00000340855 1/9 228 215 13 171 171 0 strelka-varscan-mutect IDS,missense_variant,p.Leu15Met,ENST00000340855,NM_001166550.2,NM_000202.6;IDS,missense_variant,p.Leu15Met,ENST00000370441,NM_006123.4;IDS,missense_variant,p.Leu15Met,ENST00000428056,;IDS,missense_variant,p.Leu15Met,ENST00000521702,;AF011889.5,intron_variant,,ENST00000422081,;AF011889.5,intron_variant,,ENST00000427113,;AF011889.5,intron_variant,,ENST00000523759,;AF011889.5,intron_variant,,ENST00000441880,;IDS,upstream_gene_variant,,ENST00000490775,;IDS,missense_variant,p.Leu15Met,ENST00000466323,;IDS,upstream_gene_variant,,ENST00000464251,; T ENST00000340855 Transcript missense_variant 253/7619 43/1653 15/550 L/M Ctg/Atg CD931006 1 -1 IDS HGNC HGNC:5389 protein_coding YES CCDS14685.1 ENSP00000339801 P22304 UPI000012D213 NM_001166550.2,NM_000202.6 deleterious(0.02) 1/9 hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF207,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99719 1 1 1 1 0 T 3 4 14 149505095 149505095 G T 1 0 0 0 0 1 0 0 0 7404 933 33 2 2 IDS 23 149505095 Missense_Mutation SNP G C3L-00279_T 5875518 149505095 6535800 670 6448 GABRQ 0 . GRCh38 X 152652558 152652558 + Silent SNP G G T rs782246365 C3L-00279_T C3L-00279_N G G c.1176G>T p.= p.V392V ENST00000598523 9/9 120 105 15 93 93 0 strelka-varscan-mutect GABRQ,synonymous_variant,p.=,ENST00000598523,NM_018558.3; T ENST00000598523 Transcript synonymous_variant 1196/6172 1176/1899 392/632 V gtG/gtT rs782246365 1 1 GABRQ HGNC HGNC:14454 protein_coding YES CCDS14707.1 ENSP00000469332 Q9UN88 UPI000013DAC0 NM_018558.3 9/9 LOW 1 SNV 1 1 PASS rs782246365 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 152652558 152652558 G T 1 0 0 0 0 0 0 0 1 6046 1335 47 2 2 GABRQ 23 152652558 Silent SNP G C3L-00279_T 3147463 152652558 3388337 671 6449 MAGEA6 0 . GRCh38 X 152767319 152767319 + Missense_Mutation SNP C C G novel C3L-00279_T C3L-00279_N C C c.332G>C p.Arg111Thr p.R111T ENST00000616035 3/3 570 512 58 518 518 0 strelka-varscan-mutect MAGEA6,missense_variant,p.Arg111Thr,ENST00000616035,NM_175868.1;MAGEA6,missense_variant,p.Arg111Thr,ENST00000329342,NM_005363.2;MAGEA6,missense_variant,p.Arg111Thr,ENST00000457643,;MAGEA6,missense_variant,p.Arg111Thr,ENST00000412733,; G ENST00000616035 Transcript missense_variant 590/1762 332/945 111/314 R/T aGg/aCg 1 -1 MAGEA6 HGNC HGNC:6804 protein_coding YES CCDS76050.1 ENSP00000480637 P43360 UPI000000D9B0 NM_175868.1 tolerated(0.11) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 14 152767319 152767319 C G 1 0 0 0 0 1 0 0 0 9085 681 24 4 4 MAGEA6 23 152767319 Missense_Mutation SNP C C3L-00279_T 114761 152767319 3273576 672 6450 ZNF185 0 . GRCh38 X 152965445 152965445 + Splice_Site SNP A A T novel C3L-00279_T C3L-00279_N A A c.1812-2A>T p.X604_splice ENST00000535861 166 155 11 103 103 0 strelka-varscan-mutect ZNF185,splice_acceptor_variant,,ENST00000535861,NM_001178106.1;ZNF185,splice_acceptor_variant,,ENST00000539731,NM_001178107.1,NM_001178109.1;ZNF185,splice_acceptor_variant,,ENST00000449285,NM_001178108.1;ZNF185,splice_acceptor_variant,,ENST00000370268,NM_007150.3;ZNF185,splice_acceptor_variant,,ENST00000318504,NM_001178110.1;ZNF185,splice_acceptor_variant,,ENST00000318529,NM_001178113.1;ZNF185,splice_acceptor_variant,,ENST00000324823,;ZNF185,splice_acceptor_variant,,ENST00000426821,;ZNF185,splice_acceptor_variant,,ENST00000454925,NM_001178115.1;ZNF185,splice_acceptor_variant,,ENST00000370270,;ZNF185,splice_acceptor_variant,,ENST00000436731,; T ENST00000535861 Transcript splice_acceptor_variant -/4421 1812/2166 604/721 1 1 ZNF185 HGNC HGNC:12976 protein_coding YES CCDS55529.1 ENSP00000440847 O15231 UPI0001D27F7E NM_001178106.1 19/23 HIGH 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -19.74195 1 1 1 1 0 T 5 4 14 152965445 152965445 A T 1 0 0 0 0 0 0 1 0 18332 202 7 4 4 ZNF185 23 152965445 Splice_Site SNP A C3L-00279_T 198126 152965445 3075450 673 6451 TREX2 0 . GRCh38 X 153444890 153444890 + Silent SNP G G T rs141205509 C3L-00279_T C3L-00279_N G G c.541C>A p.= p.R181R ENST00000330912 13/13 347 321 26 262 260 2 strelka-varscan-mutect TREX2,synonymous_variant,p.=,ENST00000330912,;TREX2,synonymous_variant,p.=,ENST00000338525,;TREX2,synonymous_variant,p.=,ENST00000334497,;TREX2,synonymous_variant,p.=,ENST00000370232,;TREX2,synonymous_variant,p.=,ENST00000370231,NM_080701.3;TREX2,synonymous_variant,p.=,ENST00000393862,;TREX2,synonymous_variant,p.=,ENST00000370212,;HAUS7,downstream_gene_variant,,ENST00000370211,NM_017518.7;HAUS7,downstream_gene_variant,,ENST00000435662,;HAUS7,downstream_gene_variant,,ENST00000484394,;HAUS7,downstream_gene_variant,,ENST00000491286,;HAUS7,downstream_gene_variant,,ENST00000437046,;HAUS7,downstream_gene_variant,,ENST00000460898,; T ENST00000330912 Transcript synonymous_variant 2092/2262 541/711 181/236 R Cgg/Agg rs141205509 1 -1 TREX2 HGNC HGNC:12270 protein_coding YES CCDS35437.1 ENSP00000333441 Q9BQ50 UPI000006F0D9 13/13 Gene3D:3.30.420.10,hmmpanther:PTHR13058,hmmpanther:PTHR13058:SF20,SMART_domains:SM00479,Superfamily_domains:SSF53098 LOW 1 SNV 1 1 PASS rs141205509 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 153444890 153444890 G T 1 0 0 0 0 0 0 0 1 16966 1115 39 1 1 TREX2 23 153444890 Silent SNP G C3L-00279_T 479445 153444890 2596005 674 6452 ATP2B3 0 . GRCh38 X 153565064 153565064 + Missense_Mutation SNP G G T novel C3L-00279_T C3L-00279_N G G c.3303G>T p.Gln1101His p.Q1101H ENST00000263519 19/20 266 181 85 274 272 2 strelka-varscan-mutect ATP2B3,missense_variant,p.Gln1087His,ENST00000370186,;ATP2B3,missense_variant,p.Gln1101His,ENST00000263519,NM_001001344.2;ATP2B3,missense_variant,p.Gln1101His,ENST00000349466,;ATP2B3,missense_variant,p.Gln1101His,ENST00000359149,NM_021949.3;ATP2B3,missense_variant,p.Gln1087His,ENST00000393842,;ATP2B3,downstream_gene_variant,,ENST00000460549,;ATP2B3,upstream_gene_variant,,ENST00000496610,; T ENST00000263519 Transcript missense_variant 3429/6420 3303/3663 1101/1220 Q/H caG/caT 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 deleterious(0.03) 19/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Pfam_domain:PF12424 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 14 153565064 153565064 G T 1 0 0 0 0 1 0 0 0 1294 933 33 2 2 ATP2B3 23 153565064 Missense_Mutation SNP G C3L-00279_T 120174 153565064 2475831 675 6453 PNCK 0 . GRCh38 X 153670578 153670578 + Missense_Mutation SNP G G C novel C3L-00279_T C3L-00279_N G G c.1160C>G p.Thr387Ser p.T387S ENST00000447676 11/12 225 186 39 181 181 0 strelka-varscan-mutect PNCK,missense_variant,p.Thr304Ser,ENST00000370150,;PNCK,missense_variant,p.Thr387Ser,ENST00000447676,NM_001039582.3;PNCK,missense_variant,p.Thr327Ser,ENST00000370142,;PNCK,missense_variant,p.Thr304Ser,ENST00000340888,;PNCK,missense_variant,p.Thr321Ser,ENST00000370145,NM_001135740.1;PNCK,missense_variant,p.Thr36Ser,ENST00000438984,;PNCK,downstream_gene_variant,,ENST00000422811,;PNCK,downstream_gene_variant,,ENST00000439087,;PNCK,downstream_gene_variant,,ENST00000425526,;PNCK,downstream_gene_variant,,ENST00000418241,;PNCK,downstream_gene_variant,,ENST00000419804,;PNCK,downstream_gene_variant,,ENST00000458354,;PNCK,downstream_gene_variant,,ENST00000423545,;PNCK,downstream_gene_variant,,ENST00000434652,;RN7SL687P,downstream_gene_variant,,ENST00000480496,;PNCK,downstream_gene_variant,,ENST00000475172,;PNCK,downstream_gene_variant,,ENST00000462280,;PNCK,downstream_gene_variant,,ENST00000460106,;PNCK,non_coding_transcript_exon_variant,,ENST00000472324,;PNCK,non_coding_transcript_exon_variant,,ENST00000466074,;PNCK,non_coding_transcript_exon_variant,,ENST00000488994,;PNCK,downstream_gene_variant,,ENST00000473680,;PNCK,downstream_gene_variant,,ENST00000466638,;PNCK,downstream_gene_variant,,ENST00000488168,;PNCK,downstream_gene_variant,,ENST00000465303,;PNCK,downstream_gene_variant,,ENST00000489536,;PNCK,downstream_gene_variant,,ENST00000463548,;PNCK,downstream_gene_variant,,ENST00000433470,;PNCK,downstream_gene_variant,,ENST00000411968,;PNCK,downstream_gene_variant,,ENST00000466662,; C ENST00000447676 Transcript missense_variant 1346/1585 1160/1281 387/426 T/S aCc/aGc 1 -1 PNCK HGNC HGNC:13415 protein_coding YES CCDS35503.2 ENSP00000405950 Q6P2M8 UPI0000237966 NM_001039582.3 deleterious(0.03) 11/12 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF113,Gene3D:1.10.510.10 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 14 153670578 153670578 G C 1 0 0 0 0 1 0 0 0 12252 1261 44 4 4 PNCK 23 153670578 Missense_Mutation SNP G C3L-00279_T 105514 153670578 2370317 676 6454 PLXNB3 0 . GRCh38 X 153769813 153769813 + Silent SNP C C A rs782235610 C3L-00279_T C3L-00279_N C C c.1572C>A p.= p.T524T ENST00000538966 8/37 178 154 24 169 169 0 strelka-varscan-mutect PLXNB3,synonymous_variant,p.=,ENST00000538966,NM_001163257.1;PLXNB3,synonymous_variant,p.=,ENST00000361971,NM_005393.2;PLXNB3,upstream_gene_variant,,ENST00000411613,;U52111.14,upstream_gene_variant,,ENST00000434284,;U52111.14,upstream_gene_variant,,ENST00000416854,; A ENST00000538966 Transcript synonymous_variant 1843/6377 1572/5799 524/1932 T acC/acA rs782235610 1 1 PLXNB3 HGNC HGNC:9105 protein_coding YES CCDS55536.1 ENSP00000442736 Q9ULL4 UPI0001AFF680 NM_001163257.1 8/37 Gene3D:3.30.1680.10,Pfam_domain:PF01437,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF33,SMART_domains:SM00423,Superfamily_domains:SSF103575 LOW SNV 5 1 PASS rs782235610 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 14 153769813 153769813 C A 1 0 0 0 0 0 0 0 1 12231 610 22 2 2 PLXNB3 23 153769813 Silent SNP C C3L-00279_T 99235 153769813 2271082 677 6455 PDZD4 0 . GRCh38 X 153803743 153803743 + Silent SNP G G T rs375303161 C3L-00279_T C3L-00279_N G G c.1938C>A p.= p.P646P ENST00000393758 8/8 266 235 31 208 208 0 strelka-varscan-mutect PDZD4,synonymous_variant,p.=,ENST00000393758,NM_001303515.1,NM_001303513.1,NM_001303512.1;PDZD4,synonymous_variant,p.=,ENST00000164640,NM_001303516.1,NM_032512.3;PDZD4,synonymous_variant,p.=,ENST00000544474,NM_001303514.1;PDZD4,downstream_gene_variant,,ENST00000475140,;PDZD4,downstream_gene_variant,,ENST00000483693,;PDZD4,downstream_gene_variant,,ENST00000484792,;PDZD4,downstream_gene_variant,,ENST00000468491,;PDZD4,downstream_gene_variant,,ENST00000480418,;PDZD4,downstream_gene_variant,,ENST00000480650,; T ENST00000393758 Transcript synonymous_variant 2188/3763 1938/2328 646/775 P ccC/ccA rs375303161 1 -1 PDZD4 HGNC HGNC:21167 protein_coding YES CCDS78518.1 ENSP00000377355 Q17RL8 UPI0000211CB2 NM_001303515.1,NM_001303513.1,NM_001303512.1 8/8 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF4 LOW 1 SNV 1 1 PASS rs375303161 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 14 153803743 153803743 G T 1 0 0 0 0 0 0 0 1 11791 1103 39 1 1 PDZD4 23 153803743 Silent SNP G C3L-00279_T 33930 153803743 2237152 678 6456 L1CAM 0 . GRCh38 X 153864355 153864355 + Silent SNP G G T rs782807254 C3L-00279_T C3L-00279_N G G c.3289C>A p.= p.R1097R ENST00000370060 25/29 449 367 82 349 349 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,synonymous_variant,p.=,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000455590,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000484652,; T ENST00000370060 Transcript synonymous_variant 3479/5113 3289/3774 1097/1257 R Cgg/Agg rs782807254,COSM4107900 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 25/29 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489 0,1 LOW 1 SNV 5 0,1 1 PASS rs782807254 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 153864355 153864355 G T 1 0 0 0 0 0 0 0 1 8489 1115 39 1 1 L1CAM 23 153864355 Silent SNP G C3L-00279_T 60612 153864355 2176540 679 6457 L1CAM 0 . GRCh38 X 153875777 153875777 + Silent SNP G G T novel C3L-00279_T C3L-00279_N G G c.60C>A p.= p.I20I ENST00000370060 2/29 632 586 46 531 531 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,synonymous_variant,p.=,ENST00000439496,;L1CAM,synonymous_variant,p.=,ENST00000458029,;L1CAM,synonymous_variant,p.=,ENST00000407935,;L1CAM,synonymous_variant,p.=,ENST00000420165,;LCA10,upstream_gene_variant,,ENST00000618311,;L1CAM,non_coding_transcript_exon_variant,,ENST00000464967,;L1CAM,non_coding_transcript_exon_variant,,ENST00000460553,; T ENST00000370060 Transcript synonymous_variant 250/5113 60/3774 20/1257 I atC/atA 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 2/29 hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 14 153875777 153875777 G T 1 0 0 0 0 0 0 0 1 8489 1164 41 2 2 L1CAM 23 153875777 Silent SNP G C3L-00279_T 11422 153875777 2165118 680 6458 IRAK1 0 . GRCh38 X 154019248 154019248 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.385G>T p.Ala129Ser p.A129S ENST00000369980 3/14 147 137 10 136 136 0 strelka-varscan-mutect IRAK1,missense_variant,p.Ala129Ser,ENST00000369980,NM_001569.3;IRAK1,missense_variant,p.Ala129Ser,ENST00000369974,NM_001025243.1;IRAK1,missense_variant,p.Ala155Ser,ENST00000429936,;IRAK1,missense_variant,p.Ala129Ser,ENST00000393687,NM_001025242.1;IRAK1,missense_variant,p.Ala125Ser,ENST00000444230,;MECP2,downstream_gene_variant,,ENST00000303391,NM_004992.3;IRAK1,upstream_gene_variant,,ENST00000443220,;IRAK1,upstream_gene_variant,,ENST00000437278,;IRAK1,upstream_gene_variant,,ENST00000455690,;IRAK1,downstream_gene_variant,,ENST00000390190,;IRAK1,upstream_gene_variant,,ENST00000477274,;IRAK1,upstream_gene_variant,,ENST00000467236,;IRAK1,missense_variant,p.Ala155Ser,ENST00000369973,;IRAK1,upstream_gene_variant,,ENST00000463031,; A ENST00000369980 Transcript missense_variant 553/3666 385/2139 129/712 A/S Gcc/Tcc 1 -1 IRAK1 HGNC HGNC:6112 protein_coding YES CCDS14740.1 ENSP00000358997 P51617 UPI000012D873 NM_001569.3 tolerated(0.3) 3/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.76709 1 1 1 1 0 A 3 1 14 154019248 154019248 C A 1 0 0 0 0 1 0 0 0 7727 739 26 2 2 IRAK1 23 154019248 Missense_Mutation SNP C C3L-00279_T 143471 154019248 2021647 681 6459 F8 0 . GRCh38 X 154930554 154930554 + Missense_Mutation SNP C C A rs143174629 C3L-00279_T C3L-00279_N C C c.3236G>T p.Arg1079Met p.R1079M ENST00000360256 14/26 229 216 13 75 75 0 strelka-varscan-mutect F8,missense_variant,p.Arg1079Met,ENST00000360256,NM_000132.3; A ENST00000360256 Transcript missense_variant 3437/9059 3236/7056 1079/2351 R/M aGg/aTg rs143174629 1 -1 F8 HGNC HGNC:3546 protein_coding YES CCDS35457.1 ENSP00000353393 P00451 UPI000012A416 NM_000132.3 tolerated(0.09) 14/26 PIRSF_domain:PIRSF000354 MODERATE 1 SNV 1 1 PASS rs143174629 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 14 154930554 154930554 C A 1 0 0 0 0 1 0 0 0 5218 681 24 2 2 F8 23 154930554 Missense_Mutation SNP C C3L-00279_T 911306 154930554 1110341 682 6460 RAB39B 0 . GRCh38 X 155264146 155264146 + Missense_Mutation SNP C C A novel C3L-00279_T C3L-00279_N C C c.143G>T p.Arg48Leu p.R48L ENST00000369454 1/2 554 525 29 465 464 1 strelka-varscan-mutect RAB39B,missense_variant,p.Arg48Leu,ENST00000369454,NM_171998.3; A ENST00000369454 Transcript missense_variant 444/3505 143/642 48/213 R/L cGc/cTc 1 -1 RAB39B HGNC HGNC:16499 protein_coding YES CCDS14766.1 ENSP00000358466 Q96DA2 UPI00000412A6 NM_171998.3 deleterious(0) 1/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF395,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 14 155264146 155264146 C A 1 0 0 0 0 1 0 0 0 13089 768 27 1 1 RAB39B 23 155264146 Missense_Mutation SNP C C3L-00279_T 333592 155264146 776749 683 6461 TTC34 0 . GRCh38 1 2787614 2787614 + Missense_Mutation SNP T T A novel C3L-00368_T C3L-00368_N T T c.182A>T p.Tyr61Phe p.Y61F ENST00000637179 2/7 90 78 12 99 99 0 strelka-varscan-mutect TTC34,missense_variant,p.Tyr574Phe,ENST00000401095,;TTC34,missense_variant,p.Tyr61Phe,ENST00000637179,NM_001242672.1; A ENST00000637179 Transcript missense_variant 256/1775 182/1701 61/566 Y/F tAc/tTc 1 -1 TTC34 HGNC HGNC:34297 protein_coding YES CCDS55565.1 ENSP00000490537 UPI00017503B1 NM_001242672.1 deleterious(0.01) 2/7 PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF341,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 2787614 2787614 T A 1 0 0 0 0 1 0 0 0 17212 1638 57 4 4 TTC34 1 2787614 Missense_Mutation SNP T C3L-00368_T 2787614 246168808 1 6462 UBR4 0 . GRCh38 1 19081536 19081558 + Frame_Shift_Del DEL CTTGGAGGTTCTTCTCTTCTCGG CTTGGAGGTTCTTCTCTTCTCGG - novel C3L-00368_T C3L-00368_N CTTGGAGGTTCTTCTCTTCTCGG CTTGGAGGTTCTTCTCTTCTCGG c.15024_15046delCCGAGAAGAGAAGAACCTCCAAG p.Arg5009LeufsTer15 p.R5009Lfs*15 ENST00000375254 103/106 215 175 40 282 282 0 sindel-varindel-pindel UBR4,frameshift_variant,p.Arg5009LeufsTer15,ENST00000375254,NM_020765.2;UBR4,frameshift_variant,p.Arg716LeufsTer15,ENST00000375224,;UBR4,frameshift_variant,p.Arg84LeufsTer15,ENST00000375225,;UBR4,upstream_gene_variant,,ENST00000486515,;UBR4,upstream_gene_variant,,ENST00000459947,; - ENST00000375254 Transcript frameshift_variant 15052-15074/15906 15024-15046/15552 5008-5016/5183 SREEKNLQG/SX tcCCGAGAAGAGAAGAACCTCCAAGgc/tcgc 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 103/106 hmmpanther:PTHR21725,Pfam_domain:PF13764 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 15 19081536 19081536 CTTGGAGGTTCTTCTCTTCTCGG - 1 0 1 0 1 0 0 0 0 17428 681 24 0 0 UBR4 1 19081536 Frame_Shift_Del DEL CTTGGAGGTTCTTCTCTTCTCGG C3L-00368_T 16293922 19081536 229874886 2 6463 UBR4 0 . GRCh38 1 19187445 19187445 + Missense_Mutation SNP T T G novel C3L-00368_T C3L-00368_N T T c.1490A>C p.His497Pro p.H497P ENST00000375254 12/106 134 118 16 111 111 0 strelka-varscan-mutect UBR4,missense_variant,p.His497Pro,ENST00000375254,NM_020765.2; G ENST00000375254 Transcript missense_variant 1518/15906 1490/15552 497/5183 H/P cAc/cCc 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 tolerated(0.37) 12/106 hmmpanther:PTHR21725 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 19187445 19187445 T G 1 0 0 0 0 1 0 0 0 17428 1710 59 5 5 UBR4 1 19187445 Missense_Mutation SNP T C3L-00368_T 105909 19187445 229768977 3 6464 TBX15 0 . GRCh38 1 118885051 118885051 + Missense_Mutation SNP C C A rs754594223 C3L-00368_T C3L-00368_N C C c.1172G>T p.Gly391Val p.G391V ENST00000207157 8/8 673 549 124 636 635 1 strelka-varscan-mutect TBX15,missense_variant,p.Gly497Val,ENST00000369429,;TBX15,missense_variant,p.Gly391Val,ENST00000207157,NM_152380.2;TBX15,missense_variant,p.Gly225Val,ENST00000449873,; A ENST00000207157 Transcript missense_variant 1487/3492 1172/1491 391/496 G/V gGg/gTg rs754594223,COSM5234102,COSM5234103,COSM527887 1 -1 TBX15 HGNC HGNC:11594 protein_coding YES CCDS30816.1 ENSP00000207157 Q96SF7 UPI000046D38E NM_152380.2 tolerated(0.11) 8/8 hmmpanther:PTHR11267:SF98,hmmpanther:PTHR11267 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs754594223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 118885051 118885051 C A 1 0 0 0 0 1 0 0 0 16057 623 22 2 2 TBX15 1 118885051 Missense_Mutation SNP C C3L-00368_T 99697606 118885051 130071371 4 6465 SELP 0 . GRCh38 1 169609557 169609557 + Missense_Mutation SNP A A G novel C3L-00368_T C3L-00368_N A A c.1280T>C p.Ile427Thr p.I427T ENST00000263686 8/17 202 177 25 143 143 0 strelka-varscan-mutect SELP,missense_variant,p.Ile427Thr,ENST00000263686,NM_003005.3;SELP,missense_variant,p.Ile426Thr,ENST00000426706,;SELP,missense_variant,p.Ile365Thr,ENST00000367788,;SELP,missense_variant,p.Ile365Thr,ENST00000367786,;SELP,missense_variant,p.Ile365Thr,ENST00000458599,;SELP,intron_variant,,ENST00000367795,; G ENST00000263686 Transcript missense_variant 1318/3142 1280/2493 427/830 I/T aTa/aCa 1 -1 SELP HGNC HGNC:10721 protein_coding YES CCDS1282.1 ENSP00000263686 P16109 A0A024R8Y9 UPI0000204D4A NM_003005.3 tolerated(0.72) 8/17 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF19,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 169609557 169609557 A G 1 0 0 0 0 1 0 0 0 14296 449 16 5 5 SELP 1 169609557 Missense_Mutation SNP A C3L-00368_T 50724506 169609557 79346865 5 6466 EDARADD 0 . GRCh38 1 236482358 236482358 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.357G>T p.Gln119His p.Q119H ENST00000334232 6/6 220 119 101 169 169 0 strelka-varscan-mutect EDARADD,missense_variant,p.Gln109His,ENST00000359362,NM_080738.3;EDARADD,missense_variant,p.Gln97His,ENST00000637660,;EDARADD,missense_variant,p.Gln119His,ENST00000334232,NM_145861.2;EDARADD,downstream_gene_variant,,ENST00000439430,;ENO1P1,upstream_gene_variant,,ENST00000366587,; T ENST00000334232 Transcript missense_variant 524/858 357/648 119/215 Q/H caG/caT 1 1 EDARADD HGNC HGNC:14341 protein_coding YES CCDS1610.1 ENSP00000335076 Q8WWZ3 UPI0000456324 NM_145861.2 deleterious(0) 6/6 hmmpanther:PTHR28469,hmmpanther:PTHR28469:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 236482358 236482358 G T 1 0 0 0 0 1 0 0 0 4734 991 35 2 2 EDARADD 1 236482358 Missense_Mutation SNP G C3L-00368_T 66872801 236482358 12474064 6 6467 NBAS 0 . GRCh38 2 15309219 15309219 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.4611G>T p.Leu1537Phe p.L1537F ENST00000281513 39/52 423 336 87 432 431 1 strelka-varscan-mutect NBAS,missense_variant,p.Leu1537Phe,ENST00000281513,NM_015909.3;NBAS,missense_variant,p.Leu585Phe,ENST00000442506,; A ENST00000281513 Transcript missense_variant 4637/7281 4611/7116 1537/2371 L/F ttG/ttT 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 tolerated(0.46) 39/52 hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 15309219 15309219 C A 1 0 0 0 0 1 0 0 0 10197 709 25 2 2 NBAS 2 15309219 Missense_Mutation SNP C C3L-00368_T 15309219 226884310 7 6468 EHD3 0 . GRCh38 2 31266258 31266258 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.1162C>A p.His388Asn p.H388N ENST00000322054 6/6 136 116 20 151 151 0 strelka-varscan-mutect EHD3,missense_variant,p.His388Asn,ENST00000322054,NM_014600.2; A ENST00000322054 Transcript missense_variant 1447/4636 1162/1608 388/535 H/N Cat/Aat 1 1 EHD3 HGNC HGNC:3244 protein_coding YES CCDS1774.1 ENSP00000327116 Q9NZN3 UPI0000140D07 NM_014600.2 tolerated(1) 6/6 hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF67 MODERATE 1 SNV 1 1 PASS rs1393335932 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 31266258 31266258 C A 1 0 0 0 0 1 0 0 0 4815 594 21 2 2 EHD3 2 31266258 Missense_Mutation SNP C C3L-00368_T 15957039 31266258 210927271 8 6469 ARHGAP25 0 . GRCh38 2 68822669 68822669 + Silent SNP A A T novel C3L-00368_T C3L-00368_N A A c.1530A>T p.= p.P510P ENST00000409202 10/11 203 164 39 199 199 0 strelka-varscan-mutect ARHGAP25,synonymous_variant,p.=,ENST00000409202,NM_001007231.2;ARHGAP25,synonymous_variant,p.=,ENST00000409220,NM_001166276.1;ARHGAP25,synonymous_variant,p.=,ENST00000409030,NM_014882.2;ARHGAP25,synonymous_variant,p.=,ENST00000467265,NM_001166277.1;ARHGAP25,synonymous_variant,p.=,ENST00000497259,;ARHGAP25,synonymous_variant,p.=,ENST00000479844,;ARHGAP25,downstream_gene_variant,,ENST00000497079,;ARHGAP25,downstream_gene_variant,,ENST00000473986,; T ENST00000409202 Transcript synonymous_variant 1895/2945 1530/1941 510/646 P ccA/ccT 1 1 ARHGAP25 HGNC HGNC:28951 protein_coding YES CCDS33214.2 ENSP00000386911 P42331 UPI0000251EDD NM_001007231.2 10/11 hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF20 LOW 1 SNV 2 1 PASS rs1160136241 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 68822669 68822669 A T 1 0 0 0 0 0 0 0 1 999 175 7 4 4 ARHGAP25 2 68822669 Silent SNP A C3L-00368_T 37556411 68822669 173370860 9 6470 PLA2R1 0 . GRCh38 2 159949680 159949680 + Missense_Mutation SNP C C A rs751061892 C3L-00368_T C3L-00368_N C C c.3637G>T p.Asp1213Tyr p.D1213Y ENST00000283243 25/30 177 155 22 174 174 0 strelka-varscan-mutect PLA2R1,missense_variant,p.Asp1213Tyr,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.Asp1213Tyr,ENST00000392771,NM_001007267.2;PLA2R1,upstream_gene_variant,,ENST00000460710,; A ENST00000283243 Transcript missense_variant 3844/14371 3637/4392 1213/1463 D/Y Gac/Tac rs751061892,COSM5461787 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 deleterious(0) 25/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_patterns:PS00615,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,SMART_domains:SM00034,Superfamily_domains:SSF56436 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751061892 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 159949680 159949680 C A 1 0 0 0 0 1 0 0 0 12106 884 31 1 1 PLA2R1 2 159949680 Missense_Mutation SNP C C3L-00368_T 91127011 159949680 82243849 10 6471 KCNH7 0 . GRCh38 2 162373590 162373590 + Silent SNP G G T novel C3L-00368_T C3L-00368_N G G c.3204C>A p.= p.P1068P ENST00000332142 15/16 117 111 6 69 69 0 strelka-mutect KCNH7,synonymous_variant,p.=,ENST00000332142,NM_033272.3;KCNH7,synonymous_variant,p.=,ENST00000618399,;GCA,downstream_gene_variant,,ENST00000414723,; T ENST00000332142 Transcript synonymous_variant 3304/4113 3204/3591 1068/1196 P ccC/ccA 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 15/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.34136 1 1 1 1 0 T 2 4 15 162373590 162373590 G T 1 0 0 0 0 0 0 0 1 7953 1219 43 2 2 KCNH7 2 162373590 Silent SNP G C3L-00368_T 2423910 162373590 79819939 11 6472 ABCB11 0 . GRCh38 2 168935368 168935368 + Silent SNP G G T rs766744091 C3L-00368_T C3L-00368_N G G c.2872C>A p.= p.R958R ENST00000263817 23/28 150 126 24 165 165 0 strelka-varscan-mutect ABCB11,synonymous_variant,p.=,ENST00000263817,NM_003742.2;ABCB11,3_prime_UTR_variant,,ENST00000439188,; T ENST00000263817 Transcript synonymous_variant 2997/4775 2872/3966 958/1321 R Cgg/Agg rs766744091,COSM3314679,COSM4305553 1 -1 ABCB11 HGNC HGNC:42 protein_coding YES CCDS46444.1 ENSP00000263817 O95342 UPI0000163BFA NM_003742.2 23/28 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF165,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs766744091 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 168935368 168935368 G T 1 0 0 0 0 0 0 0 1 46 1086 38 1 1 ABCB11 2 168935368 Silent SNP G C3L-00368_T 6561778 168935368 73258161 12 6473 GIGYF2 0 . GRCh38 2 232839909 232839910 + Frame_Shift_Ins INS - - C novel C3L-00368_T C3L-00368_N - - c.2891dupC p.Leu965AlafsTer5 p.L965Afs*5 ENST00000409451 25/31 263 215 48 327 327 0 sindel-varindel-pindel GIGYF2,frameshift_variant,p.Leu966AlafsTer5,ENST00000629305,;GIGYF2,frameshift_variant,p.Leu944AlafsTer5,ENST00000409547,NM_015575.3;GIGYF2,frameshift_variant,p.Leu966AlafsTer5,ENST00000409480,;GIGYF2,frameshift_variant,p.Leu965AlafsTer5,ENST00000409451,NM_001103147.1;GIGYF2,frameshift_variant,p.Leu944AlafsTer5,ENST00000373563,NM_001103146.1;GIGYF2,frameshift_variant,p.Leu938AlafsTer5,ENST00000409196,NM_001103148.1;GIGYF2,upstream_gene_variant,,ENST00000426102,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000469843,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000474312,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000471011,; C ENST00000409451 Transcript frameshift_variant 3116-3117/5937 2890-2891/3963 964/1320 T/TX acg/aCcg 1 1 GIGYF2 HGNC HGNC:11960 protein_coding YES CCDS46542.1 ENSP00000387170 Q6Y7W6 UPI00003FEC8F NM_001103147.1 25/31 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14445,hmmpanther:PTHR14445:SF38 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 15 232839909 232839909 - C 1 0 1 1 0 0 0 0 0 6258 159 6 0 0 GIGYF2 2 232839909 Frame_Shift_Ins INS - C3L-00368_T 63904541 232839909 9353620 13 6474 NUP210 0 . GRCh38 3 13317759 13317759 + Silent SNP T T C novel C3L-00368_T C3L-00368_N T T c.5586A>G p.= p.T1862T ENST00000254508 40/40 128 109 19 172 172 0 strelka-varscan-mutect NUP210,synonymous_variant,p.=,ENST00000254508,NM_024923.3; C ENST00000254508 Transcript synonymous_variant 5669/7193 5586/5664 1862/1887 T acA/acG 1 -1 NUP210 HGNC HGNC:30052 protein_coding YES CCDS33704.1 ENSP00000254508 Q8TEM1 UPI00001600AF NM_024923.3 40/40 hmmpanther:PTHR23019,hmmpanther:PTHR23019:SF2 LOW 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 15 13317759 13317759 T C 1 0 0 0 0 0 0 0 1 10825 1451 51 5 5 NUP210 3 13317759 Silent SNP T C3L-00368_T 13317759 184977800 14 6475 COLQ 0 . GRCh38 3 15456566 15456566 + Missense_Mutation SNP T T C novel C3L-00368_T C3L-00368_N T T c.968A>G p.Asn323Ser p.N323S ENST00000383788 14/17 416 346 70 424 424 0 strelka-varscan-mutect COLQ,missense_variant,p.Asn323Ser,ENST00000383788,NM_005677.3;COLQ,missense_variant,p.Asn313Ser,ENST00000383781,NM_080538.2;COLQ,missense_variant,p.Asn323Ser,ENST00000603808,;COLQ,missense_variant,p.Asn289Ser,ENST00000383786,NM_080539.3;EAF1-AS1,upstream_gene_variant,,ENST00000629729,;EAF1-AS1,upstream_gene_variant,,ENST00000608408,; C ENST00000383788 Transcript missense_variant 1094/3005 968/1368 323/455 N/S aAc/aGc 1 -1 COLQ HGNC HGNC:2226 protein_coding YES CCDS33709.1 ENSP00000373298 Q9Y215 UPI000013F74C NM_005677.3 tolerated(0.18) 14/17 hmmpanther:PTHR24023:SF6,hmmpanther:PTHR24023 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 15456566 15456566 T C 1 0 0 0 0 1 0 0 0 3505 1725 60 5 5 COLQ 3 15456566 Missense_Mutation SNP T C3L-00368_T 2138807 15456566 182838993 15 6476 MST1R 0 . GRCh38 3 49895814 49895814 + Nonsense_Mutation SNP G G A novel C3L-00368_T C3L-00368_N G G c.2863C>T p.Gln955Ter p.Q955* ENST00000296474 12/20 160 139 21 207 207 0 strelka-varscan-mutect MST1R,stop_gained,p.Gln955Ter,ENST00000296474,NM_002447.2;MST1R,stop_gained,p.Gln849Ter,ENST00000621387,NM_001318913.1;MST1R,stop_gained,p.Gln906Ter,ENST00000344206,NM_001244937.1;MST1R,stop_gained,p.Gln2Ter,ENST00000434765,;MST1R,intron_variant,,ENST00000613534,;MST1R,intron_variant,,ENST00000612032,;MST1R,intron_variant,,ENST00000440292,;CTD-2330K9.2,upstream_gene_variant,,ENST00000435478,;MST1R,stop_gained,p.Gln955Ter,ENST00000411578,;MST1R,non_coding_transcript_exon_variant,,ENST00000467110,;MST1R,downstream_gene_variant,,ENST00000468525,;MST1R,downstream_gene_variant,,ENST00000485044,;MST1R,downstream_gene_variant,,ENST00000493535,;MST1R,downstream_gene_variant,,ENST00000497001,;MST1R,upstream_gene_variant,,ENST00000463789,;MST1R,upstream_gene_variant,,ENST00000490053,; A ENST00000296474 Transcript stop_gained 2891/4536 2863/4203 955/1400 Q/* Cag/Tag 1 -1 MST1R HGNC HGNC:7381 protein_coding YES CCDS2807.1 ENSP00000296474 Q04912 UPI000159688A NM_002447.2 12/20 PIRSF_domain:PIRSF000617,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF113 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 15 49895814 49895814 G A 1 0 0 0 0 0 1 0 0 9876 1386 48 3 3 MST1R 3 49895814 Nonsense_Mutation SNP G C3L-00368_T 34439248 49895814 148399745 16 6477 CPNE4 0 . GRCh38 3 131587515 131587515 + Frame_Shift_Del DEL T T - novel C3L-00368_T C3L-00368_N T T c.803delA p.Lys268ArgfsTer3 p.K268Rfs*3 ENST00000617767 8/16 137 117 20 155 155 0 sindel-varindel-pindel CPNE4,frameshift_variant,p.Lys250ArgfsTer3,ENST00000512055,;CPNE4,frameshift_variant,p.Lys250ArgfsTer3,ENST00000429747,NM_130808.2;CPNE4,frameshift_variant,p.Lys268ArgfsTer3,ENST00000617767,NM_001289112.1;CPNE4,frameshift_variant,p.Lys250ArgfsTer3,ENST00000511604,;CPNE4,frameshift_variant,p.Lys268ArgfsTer3,ENST00000512332,NM_153429.1;CPNE4,frameshift_variant,p.Lys268ArgfsTer3,ENST00000502818,;CPNE4,non_coding_transcript_exon_variant,,ENST00000515418,; - ENST00000617767 Transcript frameshift_variant 998/3556 803/1728 268/575 K/X aAg/ag 1 -1 CPNE4 HGNC HGNC:2317 protein_coding YES CCDS75010.1 ENSP00000478878 Q96A23 UPI000002A6F1 NM_001289112.1 8/16 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF4,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 HIGH 1 deletion 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 15 131587515 131587515 T - 1 0 1 0 1 0 0 0 0 3609 1609 56 0 0 CPNE4 3 131587515 Frame_Shift_Del DEL T C3L-00368_T 81691701 131587515 66708044 17 6478 DNAJC13 0 . GRCh38 3 132492583 132492586 + Frame_Shift_Del DEL CTCC CTCC - novel C3L-00368_T C3L-00368_N CTCC CTCC c.3793_3796delCTCC p.Leu1265GlyfsTer14 p.L1265Gfs*14 ENST00000260818 33/56 170 148 22 217 217 0 sindel-varindel DNAJC13,frameshift_variant,p.Leu1265GlyfsTer14,ENST00000260818,NM_015268.3;DNAJC13,downstream_gene_variant,,ENST00000506813,; - ENST00000260818 Transcript frameshift_variant 4041-4044/7730 3793-3796/6732 1265-1266/2243 LR/X CTCCgg/gg 1 1 DNAJC13 HGNC HGNC:30343 protein_coding YES CCDS33857.1 ENSP00000260818 O75165 UPI000022C1FD NM_015268.3 33/56 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 15 132492583 132492583 CTCC - 1 0 1 0 1 0 0 0 0 4446 565 20 0 0 DNAJC13 3 132492583 Frame_Shift_Del DEL CTCC C3L-00368_T 905068 132492583 65802976 18 6479 GRK7 0 . GRCh38 3 141780775 141780775 + Silent SNP C C A rs149043656 C3L-00368_T C3L-00368_N C C c.1014C>A p.= p.A338A ENST00000264952 2/4 157 130 27 167 167 0 strelka-varscan-mutect GRK7,synonymous_variant,p.=,ENST00000264952,NM_139209.2; A ENST00000264952 Transcript synonymous_variant 1151/3239 1014/1662 338/553 A gcC/gcA rs149043656 1 1 GRK7 HGNC HGNC:17031 protein_coding YES CCDS3120.1 ENSP00000264952 Q8WTQ7 UPI000004244D NM_139209.2 2/4 PROSITE_profiles:PS50011,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF12,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs149043656 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 141780775 141780775 C A 1 0 0 0 0 0 0 0 1 6677 639 23 1 1 GRK7 3 141780775 Silent SNP C C3L-00368_T 9288192 141780775 56514784 19 6480 U2SURP 0 . GRCh38 3 143024002 143024002 + Missense_Mutation SNP G G A novel C3L-00368_T C3L-00368_N G G c.1258G>A p.Val420Ile p.V420I ENST00000473835 13/28 142 127 15 185 185 0 strelka-varscan-mutect U2SURP,missense_variant,p.Val420Ile,ENST00000473835,NM_001320219.1,NM_001080415.1;U2SURP,missense_variant,p.Val419Ile,ENST00000493598,;U2SURP,missense_variant,p.Val422Ile,ENST00000463563,;U2SURP,intron_variant,,ENST00000488497,;U2SURP,intron_variant,,ENST00000488587,;U2SURP,upstream_gene_variant,,ENST00000480029,;U2SURP,downstream_gene_variant,,ENST00000461591,;U2SURP,upstream_gene_variant,,ENST00000472373,;U2SURP,downstream_gene_variant,,ENST00000470400,; A ENST00000473835 Transcript missense_variant 1348/7276 1258/3090 420/1029 V/I Gtt/Att 1 1 U2SURP HGNC HGNC:30855 protein_coding YES CCDS46928.1 ENSP00000418563 O15042 UPI0000160746 NM_001320219.1,NM_001080415.1 deleterious(0.03) 13/28 hmmpanther:PTHR23140:SF1,hmmpanther:PTHR23140,Superfamily_domains:SSF109905 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.98874 0.9999864 1 1 1 0 A 3 1 15 143024002 143024002 G A 1 0 0 0 0 1 0 0 0 17341 1261 44 3 3 U2SURP 3 143024002 Missense_Mutation SNP G C3L-00368_T 1243227 143024002 55271557 20 6481 GPR78 0 . GRCh38 4 8581505 8581505 + Missense_Mutation SNP A A C novel C3L-00368_T C3L-00368_N A A c.523A>C p.Thr175Pro p.T175P ENST00000382487 1/3 136 107 29 144 144 0 strelka-varscan-mutect GPR78,missense_variant,p.Thr175Pro,ENST00000382487,NM_080819.4;GPR78,intron_variant,,ENST00000509216,;GPR78,upstream_gene_variant,,ENST00000504255,;GPR78,downstream_gene_variant,,ENST00000503448,;GPR78,downstream_gene_variant,,ENST00000503981,;GPR78,missense_variant,p.Thr175Pro,ENST00000514302,; C ENST00000382487 Transcript missense_variant 940/1694 523/1092 175/363 T/P Acg/Ccg 1 1 GPR78 HGNC HGNC:4528 protein_coding YES CCDS3403.1 ENSP00000371927 Q96P69 B2R7M4 UPI0000037A5F NM_080819.4 tolerated(0.09) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs907348878 . 0 201 9 0 0 0 0 0 -20 0.9999969 1 1 1 0 C 3 2 15 8581505 8581505 A C 1 0 0 0 0 1 0 0 0 6592 159 6 5 5 GPR78 4 8581505 Missense_Mutation SNP A C3L-00368_T 8581505 181633050 21 6482 UGT8 0 . GRCh38 4 114622963 114622963 + Missense_Mutation SNP C C T novel C3L-00368_T C3L-00368_N C C c.83C>T p.Pro28Leu p.P28L ENST00000310836 2/6 167 133 34 176 176 0 strelka-varscan-mutect UGT8,missense_variant,p.Pro28Leu,ENST00000310836,NM_001128174.1;UGT8,missense_variant,p.Pro28Leu,ENST00000394511,NM_003360.3;UGT8,missense_variant,p.Pro28Leu,ENST00000507710,; T ENST00000310836 Transcript missense_variant 605/4084 83/1626 28/541 P/L cCa/cTa 1 1 UGT8 HGNC HGNC:12555 protein_coding YES CCDS3705.1 ENSP00000311648 Q16880 UPI000013F094 NM_001128174.1 deleterious(0) 2/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF313,Low_complexity_(Seg):seg,Superfamily_domains:SSF53756,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 114622963 114622963 C T 1 0 0 0 0 1 0 0 0 17489 594 21 3 3 UGT8 4 114622963 Missense_Mutation SNP C C3L-00368_T 106041458 114622963 75591592 22 6483 ADAD1 0 . GRCh38 4 122429680 122429680 + Missense_Mutation SNP C C A rs55924141 C3L-00368_T C3L-00368_N C C c.1672C>A p.Gln558Lys p.Q558K ENST00000296513 13/13 123 101 22 157 157 0 strelka-varscan-mutect ADAD1,missense_variant,p.Gln558Lys,ENST00000296513,NM_139243.3;ADAD1,missense_variant,p.Gln540Lys,ENST00000388725,NM_001159295.1;ADAD1,missense_variant,p.Gln547Lys,ENST00000388724,NM_001159285.1; A ENST00000296513 Transcript missense_variant 1857/1961 1672/1731 558/576 Q/K Caa/Aaa rs55924141 1 1 ADAD1 HGNC HGNC:30713 protein_coding YES CCDS34058.1 ENSP00000296513 Q96M93 UPI000006DF76 NM_139243.3 deleterious(0.01) 13/13 Pfam_domain:PF02137,PROSITE_profiles:PS50141,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF103,SMART_domains:SM00552 MODERATE 1 SNV 2 1 PASS rs55924141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 122429680 122429680 C A 1 0 0 0 0 1 0 0 0 275 479 17 2 2 ADAD1 4 122429680 Missense_Mutation SNP C C3L-00368_T 7806717 122429680 67784875 23 6484 ZDHHC11 0 . GRCh38 5 848654 848654 + Missense_Mutation SNP C C G rs752092268 C3L-00368_T C3L-00368_N C C c.229G>C p.Gly77Arg p.G77R ENST00000283441 2/13 43 38 5 42 42 0 varscan-mutect ZDHHC11,missense_variant,p.Gly77Arg,ENST00000283441,NM_024786.2;ZDHHC11,intron_variant,,ENST00000511193,;ZDHHC11,upstream_gene_variant,,ENST00000511539,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000512775,;ZDHHC11,intron_variant,,ENST00000508951,;ZDHHC11,upstream_gene_variant,,ENST00000507800,;BRD9,downstream_gene_variant,,ENST00000493082,;ZDHHC11,upstream_gene_variant,,ENST00000503880,;ZDHHC11,upstream_gene_variant,,ENST00000505815,;ZDHHC11,upstream_gene_variant,,ENST00000512190,; G ENST00000283441 Transcript missense_variant 613/2604 229/1239 77/412 G/R Ggg/Cgg rs752092268 1 -1 ZDHHC11 HGNC HGNC:19158 protein_coding YES CCDS3857.1 ENSP00000283441 Q9H8X9 UPI000013C384 NM_024786.2 deleterious(0) 2/13 hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF83,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs752092268 . 0 204 5 0 0 0 0 0 -12.78865 1 1 1 1 0 G 3 3 15 848654 848654 C G 1 0 0 0 0 1 0 0 0 18176 652 23 4 4 ZDHHC11 5 848654 Missense_Mutation SNP C C3L-00368_T 848654 180689605 24 6485 SRD5A1 0 . GRCh38 5 6656098 6656098 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.481G>T p.Gly161Cys p.G161C ENST00000274192 3/5 269 195 74 251 251 0 strelka-varscan-mutect SRD5A1,missense_variant,p.Gly161Cys,ENST00000274192,NM_001047.2;SRD5A1,downstream_gene_variant,,ENST00000504286,;SRD5A1,missense_variant,p.Gly105Val,ENST00000513117,;SRD5A1,3_prime_UTR_variant,,ENST00000510531,; T ENST00000274192 Transcript missense_variant 715/7132 481/780 161/259 G/C Ggc/Tgc 1 1 SRD5A1 HGNC HGNC:11284 protein_coding YES CCDS3870.1 ENSP00000274192 P18405 UPI00000534C8 NM_001047.2 deleterious(0) 3/5 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50244,hmmpanther:PTHR10556:SF41,hmmpanther:PTHR10556,Pfam_domain:PF02544,PIRSF_domain:PIRSF015596 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 6656098 6656098 G T 1 0 0 0 0 1 0 0 0 15495 1232 43 2 2 SRD5A1 5 6656098 Missense_Mutation SNP G C3L-00368_T 5807444 6656098 174882161 25 6486 MTRR 0 . GRCh38 5 7889116 7889116 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.1249G>T p.Asp417Tyr p.D417Y ENST00000264668 9/15 494 322 172 392 392 0 strelka-varscan-mutect MTRR,missense_variant,p.Asp417Tyr,ENST00000264668,NM_024010.2;MTRR,missense_variant,p.Asp390Tyr,ENST00000440940,NM_002454.2;MTRR,non_coding_transcript_exon_variant,,ENST00000508101,;MTRR,non_coding_transcript_exon_variant,,ENST00000509961,;MTRR,upstream_gene_variant,,ENST00000507414,;MTRR,missense_variant,p.Gly369Val,ENST00000510525,;MTRR,3_prime_UTR_variant,,ENST00000511461,;MTRR,3_prime_UTR_variant,,ENST00000513439,;MTRR,non_coding_transcript_exon_variant,,ENST00000512311,;MTRR,upstream_gene_variant,,ENST00000507202,; T ENST00000264668 Transcript missense_variant 1279/3274 1249/2178 417/725 D/Y Gac/Tac 1 1 MTRR HGNC HGNC:7473 protein_coding YES CCDS3874.1 ENSP00000264668 Q9UBK8 UPI000013D550 NM_024010.2 deleterious(0) 9/15 Gene3D:1.20.990.10,Pfam_domain:PF00667,PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF84,Superfamily_domains:SSF63380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 7889116 7889116 G T 1 0 0 0 0 1 0 0 0 9958 1174 41 2 2 MTRR 5 7889116 Missense_Mutation SNP G C3L-00368_T 1233018 7889116 173649143 26 6487 SEMA5A 0 . GRCh38 5 9224835 9224835 + Missense_Mutation SNP G G A novel C3L-00368_T C3L-00368_N G G c.485C>T p.Pro162Leu p.P162L ENST00000382496 8/23 168 158 10 176 176 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Pro162Leu,ENST00000382496,NM_003966.2;SEMA5A,missense_variant,p.Pro162Leu,ENST00000513968,;SEMA5A,non_coding_transcript_exon_variant,,ENST00000514923,; A ENST00000382496 Transcript missense_variant 1151/11762 485/3225 162/1074 P/L cCc/cTc 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0) 8/23 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 9224835 9224835 G A 1 0 0 0 0 1 0 0 0 14313 1232 43 3 3 SEMA5A 5 9224835 Missense_Mutation SNP G C3L-00368_T 1335719 9224835 172313424 27 6488 CDH9 0 . GRCh38 5 26915684 26915684 + Missense_Mutation SNP G G A novel C3L-00368_T C3L-00368_N G G c.469C>T p.Pro157Ser p.P157S ENST00000231021 3/12 180 135 45 207 207 0 strelka-varscan-mutect CDH9,missense_variant,p.Pro157Ser,ENST00000231021,NM_016279.3;CDH9,downstream_gene_variant,,ENST00000513289,;CDH9,downstream_gene_variant,,ENST00000511822,;CDH9,non_coding_transcript_exon_variant,,ENST00000505045,; A ENST00000231021 Transcript missense_variant 642/3079 469/2370 157/789 P/S Cca/Tca 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 26915684 26915684 G A 1 0 0 0 0 1 0 0 0 2820 1203 42 3 3 CDH9 5 26915684 Missense_Mutation SNP G C3L-00368_T 17690849 26915684 154622575 28 6489 C6 0 . GRCh38 5 41172228 41172228 + Nonsense_Mutation SNP C C A rs369653180 C3L-00368_T C3L-00368_N C C c.1288G>T p.Glu430Ter p.E430* ENST00000263413 9/18 419 349 70 442 441 1 strelka-varscan-mutect C6,stop_gained,p.Glu430Ter,ENST00000263413,NM_001115131.2;C6,stop_gained,p.Glu430Ter,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000475349,;C6,non_coding_transcript_exon_variant,,ENST00000473450,; A ENST00000263413 Transcript stop_gained 1553/3661 1288/2805 430/934 E/* Gaa/Taa rs369653180 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 9/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Pfam_domain:PF01823,SMART_domains:SM00457 HIGH 1 SNV 1 1 PASS rs369653180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 15 41172228 41172228 C A 1 0 0 0 0 0 1 0 0 2111 840 29 2 2 C6 5 41172228 Nonsense_Mutation SNP C C3L-00368_T 14256544 41172228 140366031 29 6490 MSH3 0 . GRCh38 5 80679007 80679007 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.1254G>T p.Met418Ile p.M418I ENST00000265081 8/24 463 384 79 408 408 0 strelka-varscan-mutect MSH3,missense_variant,p.Met418Ile,ENST00000265081,NM_002439.4; T ENST00000265081 Transcript missense_variant 1334/4092 1254/3414 418/1137 M/I atG/atT 1 1 MSH3 HGNC HGNC:7326 protein_coding YES CCDS34195.1 ENSP00000265081 P20585 UPI0000DBEE85 NM_002439.4 tolerated(1) 8/24 hmmpanther:PTHR11361:SF34,hmmpanther:PTHR11361,Pfam_domain:PF05188,Gene3D:3.30.420.110,Superfamily_domains:SSF53150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 80679007 80679007 G T 1 0 0 0 0 1 0 0 0 9854 1377 48 2 2 MSH3 5 80679007 Missense_Mutation SNP G C3L-00368_T 39506779 80679007 100859252 30 6491 ANKHD1 0 . GRCh38 5 140402054 140402054 + Silent SNP G G T novel C3L-00368_T C3L-00368_N G G c.87G>T p.= p.S29S ENST00000532219 1/36 31 21 10 34 34 0 strelka-varscan-mutect ANKHD1-EIF4EBP3,synonymous_variant,p.=,ENST00000532219,NM_020690.5;ANKHD1,synonymous_variant,p.=,ENST00000360839,NM_017747.2;ANKHD1,synonymous_variant,p.=,ENST00000421134,;ANKHD1,synonymous_variant,p.=,ENST00000394723,NM_024668.3;ANKHD1,synonymous_variant,p.=,ENST00000616482,NM_001197030.1;ANKHD1,synonymous_variant,p.=,ENST00000394722,NM_017978.2;ANKHD1,synonymous_variant,p.=,ENST00000511151,;ANKHD1,5_prime_UTR_variant,,ENST00000297183,;RNU4-14P,upstream_gene_variant,,ENST00000410858,;CTC-329D1.2,upstream_gene_variant,,ENST00000507521,; T ENST00000532219 Transcript synonymous_variant 147/8246 87/7854 29/2617 S tcG/tcT 1 1 ANKHD1-EIF4EBP3 HGNC HGNC:33530 protein_coding YES CCDS4224.1 ENSP00000432016 UPI0000074448 NM_020690.5 1/36 Low_complexity_(Seg):seg,hmmpanther:PTHR23206:SF5,hmmpanther:PTHR23206 LOW SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 140402054 140402054 G T 1 0 0 0 0 0 0 0 1 730 1103 39 1 1 ANKHD1 5 140402054 Silent SNP G C3L-00368_T 59723047 140402054 41136205 31 6492 PCDHB8 0 . GRCh38 5 141178582 141178582 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.548C>A p.Thr183Asn p.T183N ENST00000239444 1/1 1565 1455 110 1421 1421 0 varscan-mutect PCDHB8,missense_variant,p.Thr183Asn,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; A ENST00000239444 Transcript missense_variant 793/2740 548/2406 183/801 T/N aCc/aAc 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 141178582 141178582 C A 1 0 0 0 0 1 0 0 0 11635 507 18 2 2 PCDHB8 5 141178582 Missense_Mutation SNP C C3L-00368_T 776528 141178582 40359677 32 6493 FABP6 0 . GRCh38 5 160238633 160238633 + Missense_Mutation SNP G G A C3L-00368_T C3L-00368_N G G c.508G>A p.Glu170Lys p.E170K ENST00000393980 7/7 253 226 27 234 234 0 strelka-varscan-mutect FABP6,missense_variant,p.Glu170Lys,ENST00000393980,NM_001130958.1,NM_001040442.1;FABP6,missense_variant,p.Glu121Lys,ENST00000402432,NM_001445.2;FABP6,3_prime_UTR_variant,,ENST00000523955,;FABP6,non_coding_transcript_exon_variant,,ENST00000521362,; A ENST00000393980 Transcript missense_variant 654/756 508/534 170/177 E/K Gag/Aag COSM4550758,COSM4550759 1 1 FABP6 HGNC HGNC:3561 protein_coding YES CCDS43393.1 ENSP00000377549 P51161 UPI000020C072 NM_001130958.1,NM_001040442.1 tolerated(1) 7/7 Gene3D:2.40.128.20,Pfam_domain:PF14651,Prints_domain:PR00178,hmmpanther:PTHR11955,hmmpanther:PTHR11955:SF69,Superfamily_domains:SSF50814 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1379368786 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 160238633 160238633 G A 1 0 0 0 0 1 0 0 0 5233 1291 45 3 3 FABP6 5 160238633 Missense_Mutation SNP G C3L-00368_T 19060051 160238633 21299626 33 6494 CREBRF 0 . GRCh38 5 173090924 173090924 + Missense_Mutation SNP C C T rs377679411 C3L-00368_T C3L-00368_N C C c.745C>T p.Arg249Trp p.R249W ENST00000296953 4/9 268 254 14 233 233 0 strelka-varscan CREBRF,missense_variant,p.Arg249Trp,ENST00000296953,NM_153607.2;CREBRF,missense_variant,p.Arg249Trp,ENST00000522692,NM_001168393.1,NM_001168394.1;CREBRF,missense_variant,p.Arg249Trp,ENST00000520420,;CREBRF,downstream_gene_variant,,ENST00000523161,;CREBRF,non_coding_transcript_exon_variant,,ENST00000520464,;CDC42P5,upstream_gene_variant,,ENST00000518654,; T ENST00000296953 Transcript missense_variant 1064/7778 745/1920 249/639 R/W Cgg/Tgg rs377679411 1 1 CREBRF HGNC HGNC:24050 protein_coding YES CCDS34293.1 ENSP00000296953 Q8IUR6 UPI000049E01D NM_153607.2 deleterious_low_confidence(0) 4/9 hmmpanther:PTHR21552 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 173090924 173090924 C T 1 0 0 0 0 1 0 0 0 3663 643 23 1 1 CREBRF 5 173090924 Missense_Mutation SNP C C3L-00368_T 12852291 173090924 8447335 34 6495 GPLD1 0 . GRCh38 6 24466730 24466730 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.771G>T p.Trp257Cys p.W257C ENST00000230036 10/25 127 120 7 152 152 0 varscan-mutect GPLD1,missense_variant,p.Trp257Cys,ENST00000230036,NM_001503.3;GPLD1,non_coding_transcript_exon_variant,,ENST00000474784,; A ENST00000230036 Transcript missense_variant 882/3489 771/2523 257/840 W/C tgG/tgT 1 -1 GPLD1 HGNC HGNC:4459 protein_coding YES CCDS4553.1 ENSP00000230036 P80108 UPI000013C91C NM_001503.3 deleterious(0) 10/25 hmmpanther:PTHR23221 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 24466730 24466730 C A 1 0 0 0 0 1 0 0 0 6516 508 18 2 2 GPLD1 6 24466730 Missense_Mutation SNP C C3L-00368_T 24466730 146339249 35 6496 BTN3A3 0 . GRCh38 6 26452235 26452235 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.1579G>T p.Val527Leu p.V527L ENST00000244519 11/11 196 151 45 180 180 0 strelka-varscan-mutect BTN3A3,missense_variant,p.Val527Leu,ENST00000244519,NM_006994.4;BTN3A3,missense_variant,p.Val478Leu,ENST00000361232,NM_197974.2;BTN3A3,downstream_gene_variant,,ENST00000487272,;BTN3A3,downstream_gene_variant,,ENST00000490254,NM_001242803.1;BTN3A3,non_coding_transcript_exon_variant,,ENST00000480110,;BTN3A3,downstream_gene_variant,,ENST00000483179,;BTN3A3,downstream_gene_variant,,ENST00000477388,;BTN3A3,downstream_gene_variant,,ENST00000497681,; T ENST00000244519 Transcript missense_variant 1822/3002 1579/1755 527/584 V/L Gtg/Ttg 1 1 BTN3A3 HGNC HGNC:1140 protein_coding YES CCDS4611.1 ENSP00000244519 O00478 A0A024R042 UPI00000480EF NM_006994.4 tolerated(0.4) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 26452235 26452235 G T 1 0 0 0 0 1 0 0 0 1740 1029 36 2 2 BTN3A3 6 26452235 Missense_Mutation SNP G C3L-00368_T 1985505 26452235 144353744 36 6497 PPP1R10 0 . GRCh38 6 30609101 30609101 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.170C>A p.Thr57Asn p.T57N ENST00000376511 4/20 174 140 34 172 172 0 strelka-varscan-mutect PPP1R10,missense_variant,p.Thr57Asn,ENST00000376511,NM_002714.3;PPP1R10,downstream_gene_variant,,ENST00000484449,;PPP1R10,upstream_gene_variant,,ENST00000461593,;PPP1R10,upstream_gene_variant,,ENST00000476704,;PPP1R10,upstream_gene_variant,,ENST00000496955,;PPP1R10,upstream_gene_variant,,ENST00000468181,; T ENST00000376511 Transcript missense_variant 723/4525 170/2823 57/940 T/N aCc/aAc 1 -1 PPP1R10 HGNC HGNC:9284 protein_coding YES CCDS4681.1 ENSP00000365694 Q96QC0 Q2L6I0 UPI000000D73C NM_002714.3 deleterious(0) 4/20 hmmpanther:PTHR12506,hmmpanther:PTHR12506:SF18 MODERATE 1 SNV 1 1 PASS rs1473097433 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 30609101 30609101 G T 1 0 0 0 0 1 0 0 0 12462 1261 44 2 2 PPP1R10 6 30609101 Missense_Mutation SNP G C3L-00368_T 4156866 30609101 140196878 37 6498 NOTCH4 0 . GRCh38 6 32220569 32220569 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.995G>T p.Cys332Phe p.C332F ENST00000375023 6/30 295 267 28 287 287 0 strelka-varscan-mutect NOTCH4,missense_variant,p.Cys332Phe,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENST00000375023 Transcript missense_variant 1134/6745 995/6012 332/2003 C/F tGc/tTc 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0) 6/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF64,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,PROSITE_patterns:PS00010,Pfam_domain:PF07645,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 32220569 32220569 C A 1 0 0 0 0 1 0 0 0 10596 710 25 2 2 NOTCH4 6 32220569 Missense_Mutation SNP C C3L-00368_T 1611468 32220569 138585410 38 6499 XPO5 0 . GRCh38 6 43524566 43524567 + Frame_Shift_Ins INS - - T novel C3L-00368_T C3L-00368_N - - c.3381_3382insA p.Gln1128ThrfsTer3 p.Q1128Tfs*3 ENST00000265351 31/32 213 184 29 197 197 0 sindel-varindel-pindel XPO5,frameshift_variant,p.Gln1128ThrfsTer3,ENST00000265351,NM_020750.2;XPO5,frameshift_variant,p.Gln243ThrfsTer3,ENST00000455285,;POLR1C,intron_variant,,ENST00000304004,;POLR1C,downstream_gene_variant,,ENST00000372389,NM_203290.2;POLR1C,downstream_gene_variant,,ENST00000372344,;POLR1C,downstream_gene_variant,,ENST00000428025,;POLR1C,downstream_gene_variant,,ENST00000423780,;RP3-337H4.9,upstream_gene_variant,,ENST00000607571,;XPO5,3_prime_UTR_variant,,ENST00000486936,;XPO5,non_coding_transcript_exon_variant,,ENST00000455854,;XPO5,non_coding_transcript_exon_variant,,ENST00000488195,;POLR1C,downstream_gene_variant,,ENST00000455605,;POLR1C,downstream_gene_variant,,ENST00000481352,;POLR1C,downstream_gene_variant,,ENST00000488601,;XPO5,downstream_gene_variant,,ENST00000398835,;XPO5,downstream_gene_variant,,ENST00000450462,;POLR1C,downstream_gene_variant,,ENST00000512472,; T ENST00000265351 Transcript frameshift_variant 3592-3593/5364 3381-3382/3615 1127-1128/1204 -/X -/A 1 -1 XPO5 HGNC HGNC:17675 protein_coding YES CCDS47430.1 ENSP00000265351 Q9HAV4 UPI000006CC97 NM_020750.2 31/32 hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF3,Superfamily_domains:SSF48371 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 7 5 15 43524566 43524566 - T 1 0 1 1 0 0 0 0 0 18006 1357 47 0 0 XPO5 6 43524566 Frame_Shift_Ins INS - C3L-00368_T 11303997 43524566 127281413 39 6500 PHF3 0 . GRCh38 6 63684896 63684896 + Nonsense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.1174G>T p.Glu392Ter p.E392* ENST00000262043 4/16 205 173 32 247 246 1 strelka-varscan-mutect PHF3,stop_gained,p.Glu392Ter,ENST00000262043,NM_001290259.1;PHF3,stop_gained,p.Glu392Ter,ENST00000393387,NM_015153.3;PHF3,stop_gained,p.Glu206Ter,ENST00000506783,;PHF3,stop_gained,p.Glu392Ter,ENST00000509330,NM_001290260.1;PHF3,stop_gained,p.Glu345Ter,ENST00000494284,;PHF3,stop_gained,p.Glu304Ter,ENST00000481385,;PHF3,intron_variant,,ENST00000515594,;PHF3,downstream_gene_variant,,ENST00000514822,;PHF3,3_prime_UTR_variant,,ENST00000509876,; T ENST00000262043 Transcript stop_gained 1514/8233 1174/6120 392/2039 E/* Gaa/Taa 1 1 PHF3 HGNC HGNC:8921 protein_coding YES CCDS4966.1 ENSP00000262043 Q92576 UPI000007154D NM_001290259.1 4/16 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 15 63684896 63684896 G T 1 0 0 0 0 0 1 0 0 11923 1291 45 2 2 PHF3 6 63684896 Nonsense_Mutation SNP G C3L-00368_T 20160330 63684896 107121083 40 6501 QRSL1 0 . GRCh38 6 106654807 106654807 + Silent SNP G G T rs149046939 C3L-00368_T C3L-00368_N G G c.927G>T p.= p.G309G ENST00000369046 8/11 206 189 17 235 235 0 varscan-mutect QRSL1,synonymous_variant,p.=,ENST00000369046,NM_018292.4;QRSL1,downstream_gene_variant,,ENST00000369044,; T ENST00000369046 Transcript synonymous_variant 1031/4106 927/1587 309/528 G ggG/ggT rs149046939 1 1 QRSL1 HGNC HGNC:21020 protein_coding YES CCDS5057.1 ENSP00000358042 Q9H0R6 UPI0000047463 NM_018292.4 8/11 HAMAP:MF_00120,hmmpanther:PTHR11895:SF7,hmmpanther:PTHR11895,TIGRFAM_domain:TIGR00132,Gene3D:3.90.1300.10,Pfam_domain:PF01425,Superfamily_domains:SSF75304 LOW 1 SNV 1 1 PASS rs149046939 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 106654807 106654807 G T 1 0 0 0 0 0 0 0 1 13036 1219 43 2 2 QRSL1 6 106654807 Silent SNP G C3L-00368_T 42969911 106654807 64151172 41 6502 EYA4 0 . GRCh38 6 133462687 133462687 + Missense_Mutation SNP A A T rs751512877 C3L-00368_T C3L-00368_N A A c.647A>T p.Gln216Leu p.Q216L ENST00000531901 9/20 317 264 53 348 348 0 strelka-varscan-mutect EYA4,missense_variant,p.Gln216Leu,ENST00000367895,NM_004100.4;EYA4,missense_variant,p.Gln216Leu,ENST00000355167,NM_172105.3;EYA4,missense_variant,p.Gln193Leu,ENST00000355286,NM_172103.3;EYA4,missense_variant,p.Gln193Leu,ENST00000525849,;EYA4,missense_variant,p.Gln216Leu,ENST00000531901,NM_001301013.1;EYA4,missense_variant,p.Gln162Leu,ENST00000452339,NM_001301012.1;EYA4,missense_variant,p.Gln162Leu,ENST00000430974,;EYA4,missense_variant,p.Gln216Leu,ENST00000431403,;EYA4,non_coding_transcript_exon_variant,,ENST00000531861,;EYA4,non_coding_transcript_exon_variant,,ENST00000421413,;EYA4,upstream_gene_variant,,ENST00000532518,;EYA4,downstream_gene_variant,,ENST00000525614,;EYA4,non_coding_transcript_exon_variant,,ENST00000497350,; T ENST00000531901 Transcript missense_variant 876/2892 647/1938 216/645 Q/L cAg/cTg rs751512877 1 1 EYA4 HGNC HGNC:3522 protein_coding YES CCDS75521.1 ENSP00000432770 F2Z2Y1 UPI0001AE72E3 NM_001301013.1 deleterious(0.05) 9/20 hmmpanther:PTHR10190:SF17,hmmpanther:PTHR10190 MODERATE 1 SNV 2 1 PASS rs751512877 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 133462687 133462687 A T 1 0 0 0 0 1 0 0 0 5199 188 7 4 4 EYA4 6 133462687 Missense_Mutation SNP A C3L-00368_T 26807880 133462687 37343292 42 6503 DDX56 0 . GRCh38 7 44571572 44571572 + Silent SNP C C A rs746566080 C3L-00368_T C3L-00368_N C C c.810G>T p.= p.R270R ENST00000258772 6/14 407 362 45 362 361 1 strelka-mutect DDX56,synonymous_variant,p.=,ENST00000258772,NM_019082.3;DDX56,synonymous_variant,p.=,ENST00000431640,NM_001257189.1;DDX56,upstream_gene_variant,,ENST00000448192,;DDX56,non_coding_transcript_exon_variant,,ENST00000485367,;DDX56,non_coding_transcript_exon_variant,,ENST00000467318,;DDX56,upstream_gene_variant,,ENST00000479602,;DDX56,synonymous_variant,p.=,ENST00000421223,;DDX56,synonymous_variant,p.=,ENST00000433257,;DDX56,3_prime_UTR_variant,,ENST00000446987,;DDX56,3_prime_UTR_variant,,ENST00000415758,;DDX56,downstream_gene_variant,,ENST00000479440,;DDX56,upstream_gene_variant,,ENST00000473924,; A ENST00000258772 Transcript synonymous_variant 917/2336 810/1644 270/547 R cgG/cgT rs746566080 1 -1 DDX56 HGNC HGNC:18193 protein_coding YES CCDS5492.1 ENSP00000258772 Q9NY93 UPI0000037BB1 NM_019082.3 6/14 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF96,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs746566080 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 44571572 44571572 C A 1 0 0 0 0 0 0 0 1 4177 842 30 2 2 DDX56 7 44571572 Silent SNP C C3L-00368_T 44571572 114774401 43 6504 EGFR 0 . GRCh38 7 55174015 55174015 + Missense_Mutation SNP G G C rs121913428 C3L-00368_T C3L-00368_N G G c.2156G>C p.Gly719Ala p.G719A ENST00000275493 18/28 373 305 68 346 346 0 strelka-mutect EGFR,missense_variant,p.Gly719Ala,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Gly674Ala,ENST00000454757,;EGFR,missense_variant,p.Gly674Ala,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1; C ENST00000275493 Transcript missense_variant 2333/9821 2156/3633 719/1210 G/A gGc/gCc rs121913428,COSM18425,COSM20848,COSM6239 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 18/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913428 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 55174015 55174015 G C 1 0 0 0 0 1 0 0 0 4803 1203 42 4 4 EGFR 7 55174015 Missense_Mutation SNP G C3L-00368_T 10602443 55174015 104171958 44 6505 EGFR 0 . GRCh38 7 55181312 55181312 + Missense_Mutation SNP G G T rs121913465 C3L-00368_T C3L-00368_N G G c.2303G>T p.Ser768Ile p.S768I ENST00000275493 20/28 241 196 45 272 272 0 strelka-varscan-mutect EGFR,missense_variant,p.Ser768Ile,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Ser723Ile,ENST00000454757,;EGFR,missense_variant,p.Ser723Ile,ENST00000455089,;EGFR-AS1,non_coding_transcript_exon_variant,,ENST00000442411,; T ENST00000275493 Transcript missense_variant 2480/9821 2303/3633 768/1210 S/I aGc/aTc rs121913465,COSM12989,COSM291998,COSM6241 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 20/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs146024686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 55181312 55181312 G T 1 0 0 0 0 1 0 0 0 4803 971 34 2 2 EGFR 7 55181312 Missense_Mutation SNP G C3L-00368_T 7297 55181312 104164661 45 6506 ZNF679 0 . GRCh38 7 64249131 64249131 + Missense_Mutation SNP C C G rs559743213 C3L-00368_T C3L-00368_N C C c.14C>G p.Pro5Arg p.P5R ENST00000421025 2/5 291 239 52 318 318 0 strelka-varscan-mutect ZNF679,missense_variant,p.Pro5Arg,ENST00000421025,NM_153363.2;ZNF679,missense_variant,p.Pro5Arg,ENST00000255746,; G ENST00000421025 Transcript missense_variant 283/1567 14/1236 5/411 P/R cCg/cGg rs559743213,COSM3785741 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 deleterious_low_confidence(0.02) 2/5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs559743213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 64249131 64249131 C G 1 0 0 0 0 1 0 0 0 18659 652 23 4 4 ZNF679 7 64249131 Missense_Mutation SNP C C3L-00368_T 9067819 64249131 95096842 46 6507 FSCN3 0 . GRCh38 7 127595324 127595324 + Silent SNP G G T novel C3L-00368_T C3L-00368_N G G c.162G>T p.= p.V54V ENST00000265825 2/7 75 57 18 87 87 0 strelka-varscan-mutect FSCN3,synonymous_variant,p.=,ENST00000265825,NM_020369.2;FSCN3,5_prime_UTR_variant,,ENST00000478821,;ARF5,downstream_gene_variant,,ENST00000000233,NM_001662.3;ARF5,downstream_gene_variant,,ENST00000415666,;FSCN3,non_coding_transcript_exon_variant,,ENST00000478328,;GCC1,upstream_gene_variant,,ENST00000497650,;GCC1,upstream_gene_variant,,ENST00000473728,;FSCN3,3_prime_UTR_variant,,ENST00000421705,;ARF5,downstream_gene_variant,,ENST00000463733,;FSCN3,upstream_gene_variant,,ENST00000469242,;ARF5,downstream_gene_variant,,ENST00000489673,; T ENST00000265825 Transcript synonymous_variant 381/2238 162/1497 54/498 V gtG/gtT 1 1 FSCN3 HGNC HGNC:3961 protein_coding YES CCDS34746.1 ENSP00000265825 Q9NQT6 A0A140VK18 UPI000012AC5F NM_020369.2 2/7 hmmpanther:PTHR10551,hmmpanther:PTHR10551:SF1,PIRSF_domain:PIRSF005682,Gene3D:2.80.10.50,Pfam_domain:PF06268,Superfamily_domains:SSF50405 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 127595324 127595324 G T 1 0 0 0 0 0 0 0 1 5942 1277 45 2 2 FSCN3 7 127595324 Silent SNP G C3L-00368_T 63346193 127595324 31750649 47 6508 MGAM2 0 . GRCh38 7 142132048 142132048 + Missense_Mutation SNP A A G novel C3L-00368_T C3L-00368_N A A c.538A>G p.Ser180Gly p.S180G ENST00000477922 6/48 122 102 20 148 148 0 strelka-varscan-mutect MGAM2,missense_variant,p.Ser180Gly,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Ser180Gly,ENST00000550469,; G ENST00000477922 Transcript missense_variant 592/7867 538/7548 180/2515 S/G Agc/Ggc 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated(0.49) 6/48 Pfam_domain:PF16863,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF74650 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 142132048 142132048 A G 1 0 0 0 0 1 0 0 0 9500 188 7 5 5 MGAM2 7 142132048 Missense_Mutation SNP A C3L-00368_T 14536724 142132048 17213925 48 6509 KRBA1 0 . GRCh38 7 149733450 149733451 + Frame_Shift_Ins INS - - A novel C3L-00368_T C3L-00368_N - - c.2599dupA p.Thr867AsnfsTer52 p.T867Nfs*52 ENST00000496259 17/17 258 204 54 277 277 0 sindel-varindel-pindel KRBA1,frameshift_variant,p.Thr833AsnfsTer52,ENST00000319551,NM_032534.3;KRBA1,frameshift_variant,p.Thr867AsnfsTer52,ENST00000496259,NM_001290187.1;KRBA1,frameshift_variant,p.Thr772AsnfsTer52,ENST00000485033,;KRBA1,3_prime_UTR_variant,,ENST00000621069,;KRBA1,downstream_gene_variant,,ENST00000489951,; A ENST00000496259 Transcript frameshift_variant 2642-2643/3763 2598-2599/3195 866-867/1064 -/X -/A 1 1 KRBA1 HGNC HGNC:22228 protein_coding YES CCDS78285.1 ENSP00000418647 A0A0C4DH65 UPI0003F48BD7 NM_001290187.1 17/17 hmmpanther:PTHR22740 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 15 149733450 149733450 - A 1 0 1 1 0 0 0 0 0 8319 1165 41 0 0 KRBA1 7 149733450 Frame_Shift_Ins INS - C3L-00368_T 7601402 149733450 9612523 49 6510 PPP3CC 0 . GRCh38 8 22474961 22474961 + Silent SNP C C A novel C3L-00368_T C3L-00368_N C C c.57C>A p.= p.P19P ENST00000397775 2/15 153 133 20 174 174 0 strelka-varscan-mutect PPP3CC,synonymous_variant,p.=,ENST00000240139,NM_005605.4;PPP3CC,synonymous_variant,p.=,ENST00000289963,NM_001243975.1;PPP3CC,synonymous_variant,p.=,ENST00000397775,NM_001243974.1;PPP3CC,synonymous_variant,p.=,ENST00000518852,;PPP3CC,synonymous_variant,p.=,ENST00000522000,;PPP3CC,upstream_gene_variant,,ENST00000522034,; A ENST00000397775 Transcript synonymous_variant 331/2094 57/1566 19/521 P ccC/ccA 1 1 PPP3CC HGNC HGNC:9316 protein_coding YES CCDS59093.1 ENSP00000380878 P48454 UPI00017A7ABA NM_001243974.1 2/15 hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF186,Superfamily_domains:SSF56300 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 22474961 22474961 C A 1 0 0 0 0 0 0 0 1 12521 668 24 2 2 PPP3CC 8 22474961 Silent SNP C C3L-00368_T 22474961 122663675 50 6511 SNTG1 0 . GRCh38 8 50656961 50656961 + Missense_Mutation SNP G G T C3L-00368_T C3L-00368_N G G c.902G>T p.Arg301Ile p.R301I ENST00000522124 14/19 137 114 23 141 141 0 strelka-varscan-mutect SNTG1,missense_variant,p.Arg301Ile,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Arg301Ile,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Arg301Ile,ENST00000517473,NM_001287814.1;SNTG1,missense_variant,p.Arg301Ile,ENST00000520825,;SNTG1,missense_variant,p.Arg75Ile,ENST00000524004,; T ENST00000522124 Transcript missense_variant 1563/3504 902/1554 301/517 R/I aGa/aTa COSM5409666,COSM5409667 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 14/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1479918393 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 50656961 50656961 G T 1 0 0 0 0 1 0 0 0 15194 942 33 2 2 SNTG1 8 50656961 Missense_Mutation SNP G C3L-00368_T 28182000 50656961 94481675 51 6512 ZFHX4 0 . GRCh38 8 76842671 76842671 + Missense_Mutation SNP G G C novel C3L-00368_T C3L-00368_N G G c.3411G>C p.Glu1137Asp p.E1137D ENST00000521891 6/11 114 86 28 97 97 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Glu1137Asp,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Glu1111Asp,ENST00000518282,;ZFHX4,3_prime_UTR_variant,,ENST00000523625,;ZFHX4,3_prime_UTR_variant,,ENST00000519536,; C ENST00000521891 Transcript missense_variant 3859/14019 3411/10851 1137/3616 E/D gaG/gaC 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(1) 6/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 76842671 76842671 G C 1 0 0 0 0 1 0 0 0 18213 991 35 4 4 ZFHX4 8 76842671 Missense_Mutation SNP G C3L-00368_T 26185710 76842671 68295965 52 6513 GRHL2 0 . GRCh38 8 101644172 101644172 + Missense_Mutation SNP A A T novel C3L-00368_T C3L-00368_N A A c.1559A>T p.Glu520Val p.E520V ENST00000251808 13/16 484 413 71 465 465 0 strelka-varscan-mutect GRHL2,missense_variant,p.Glu520Val,ENST00000251808,NM_024915.3;GRHL2,missense_variant,p.Glu504Val,ENST00000395927,;GRHL2,non_coding_transcript_exon_variant,,ENST00000517674,;GRHL2,non_coding_transcript_exon_variant,,ENST00000474338,; T ENST00000251808 Transcript missense_variant 1897/5239 1559/1878 520/625 E/V gAg/gTg 1 1 GRHL2 HGNC HGNC:2799 protein_coding YES CCDS34931.1 ENSP00000251808 Q6ISB3 UPI000013CD16 NM_024915.3 deleterious(0.03) 13/16 hmmpanther:PTHR11037:SF17,hmmpanther:PTHR11037 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 101644172 101644172 A T 1 0 0 0 0 1 0 0 0 6644 304 11 4 4 GRHL2 8 101644172 Missense_Mutation SNP A C3L-00368_T 24801501 101644172 43494464 53 6514 ADCY8 0 . GRCh38 8 131039468 131039468 + Missense_Mutation SNP A A T novel C3L-00368_T C3L-00368_N A A c.866T>A p.Leu289His p.L289H ENST00000286355 1/18 244 197 47 302 302 0 strelka-varscan-mutect ADCY8,missense_variant,p.Leu289His,ENST00000286355,NM_001115.2;ADCY8,missense_variant,p.Leu289His,ENST00000377928,; T ENST00000286355 Transcript missense_variant 2959/5938 866/3756 289/1251 L/H cTc/cAc 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 deleterious(0) 1/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,Pfam_domain:PF16214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 131039468 131039468 A T 1 0 0 0 0 1 0 0 0 344 304 11 4 4 ADCY8 8 131039468 Missense_Mutation SNP A C3L-00368_T 29395296 131039468 14099168 54 6515 CDKN2A 0 . GRCh38 9 21971187 21971187 + Nonsense_Mutation SNP G G A rs121913387 C3L-00368_T C3L-00368_N G G c.172C>T p.Arg58Ter p.R58* ENST00000498124 2/4 332 269 63 430 430 0 strelka-varscan-mutect CDKN2A,stop_gained,p.Arg58Ter,ENST00000304494,NM_000077.4;CDKN2A,stop_gained,p.Arg7Ter,ENST00000494262,;CDKN2A,stop_gained,p.Arg7Ter,ENST00000498628,;CDKN2A,stop_gained,p.Arg58Ter,ENST00000498124,NM_001195132.1;CDKN2A,stop_gained,p.Arg7Ter,ENST00000578845,;CDKN2A,stop_gained,p.Arg58Ter,ENST00000579122,;CDKN2A,stop_gained,p.Arg7Ter,ENST00000497750,;CDKN2A,stop_gained,p.Arg7Ter,ENST00000479692,;CDKN2A,missense_variant,p.Pro72Leu,ENST00000579755,NM_058195.3;CDKN2A,missense_variant,p.Pro72Leu,ENST00000530628,;CDKN2A-AS1,downstream_gene_variant,,ENST00000441769,;CDKN2A,non_coding_transcript_exon_variant,,ENST00000380150,;CDKN2A,upstream_gene_variant,,ENST00000577854,;CDKN2A,3_prime_UTR_variant,,ENST00000380151,;RP11-145E5.5,intron_variant,,ENST00000404796,; A ENST00000498124 Transcript stop_gained 211/880 172/504 58/167 R/* Cga/Tga rs121913387,CM940227,COSM12473,COSM13641,COSM1624870,COSM231506,COSM231507,COSM231508,COSM5599280,COSM99730,COSM99731 1 -1 CDKN2A HGNC HGNC:1787 protein_coding YES CCDS56565.1 ENSP00000418915 P42771 UPI0001565711 NM_001195132.1 2/4 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR24148,hmmpanther:PTHR24148:SF38,Superfamily_domains:SSF48403 0,0,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 0,1,1,1,1,1,1,1,1,1,1 1 PASS rs121913387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 15 21971187 21971187 G A 1 0 0 0 0 0 1 0 0 2865 1125 39 1 1 CDKN2A 9 21971187 Nonsense_Mutation SNP G C3L-00368_T 21971187 116423530 55 6516 TAF1L 0 . GRCh38 9 32632263 32632263 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.3317C>A p.Thr1106Lys p.T1106K ENST00000242310 1/1 266 217 49 250 250 0 strelka-varscan-mutect TAF1L,missense_variant,p.Thr1106Lys,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; T ENST00000242310 Transcript missense_variant 3407/6216 3317/5481 1106/1826 T/K aCa/aAa 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 tolerated(0.07) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 32632263 32632263 G T 1 0 0 0 0 1 0 0 0 15919 1377 48 2 2 TAF1L 9 32632263 Missense_Mutation SNP G C3L-00368_T 10661076 32632263 105762454 56 6517 GDA 0 . GRCh38 9 72241192 72241192 + Silent SNP C C A novel C3L-00368_T C3L-00368_N C C c.1029C>A p.= p.I343I ENST00000238018 11/16 118 88 30 156 156 0 strelka-varscan-mutect GDA,synonymous_variant,p.=,ENST00000545168,NM_001242507.2,NM_001242506.2;GDA,synonymous_variant,p.=,ENST00000358399,NM_004293.4;GDA,synonymous_variant,p.=,ENST00000238018,NM_001242505.2;GDA,synonymous_variant,p.=,ENST00000376986,;GDA,synonymous_variant,p.=,ENST00000436438,;GDA,synonymous_variant,p.=,ENST00000475764,;GDA,synonymous_variant,p.=,ENST00000489618,; A ENST00000238018 Transcript synonymous_variant 1238/2074 1029/1416 343/471 I atC/atA 1 1 GDA HGNC HGNC:4212 protein_coding YES CCDS56576.1 ENSP00000238018 Q9Y2T3 UPI000015828B NM_001242505.2 11/16 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11271,hmmpanther:PTHR11271:SF6,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02967 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 72241192 72241192 C A 1 0 0 0 0 0 0 0 1 6178 816 29 2 2 GDA 9 72241192 Silent SNP C C3L-00368_T 39608929 72241192 66153525 57 6518 UBQLN1 0 . GRCh38 9 83679897 83679897 + Missense_Mutation SNP T T C novel C3L-00368_T C3L-00368_N T T c.589A>G p.Ser197Gly p.S197G ENST00000376395 4/11 297 280 17 325 324 1 strelka-varscan-mutect UBQLN1,missense_variant,p.Ser197Gly,ENST00000376395,NM_013438.4;UBQLN1,missense_variant,p.Ser197Gly,ENST00000257468,NM_053067.2;UBQLN1,intron_variant,,ENST00000529923,;UBQLN1,non_coding_transcript_exon_variant,,ENST00000533705,; C ENST00000376395 Transcript missense_variant 1113/4118 589/1770 197/589 S/G Agc/Ggc 1 -1 UBQLN1 HGNC HGNC:12508 protein_coding YES CCDS6663.1 ENSP00000365576 Q9UMX0 A0A024R284 UPI0000038DA1 NM_013438.4 tolerated(0.5) 4/11 hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF5,SMART_domains:SM00727 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 83679897 83679897 T C 1 0 0 0 0 1 0 0 0 17420 1551 54 5 5 UBQLN1 9 83679897 Missense_Mutation SNP T C3L-00368_T 11438705 83679897 54714820 58 6519 ZCCHC6 0 . GRCh38 9 86323608 86323608 + Missense_Mutation SNP A A C novel C3L-00368_T C3L-00368_N A A c.2142T>G p.Asn714Lys p.N714K ENST00000375963 13/27 247 205 42 289 289 0 strelka-varscan-mutect ZCCHC6,missense_variant,p.Asn3Lys,ENST00000277141,;ZCCHC6,missense_variant,p.Asn714Lys,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,missense_variant,p.Asn591Lys,ENST00000375960,NM_001185074.1;ZCCHC6,upstream_gene_variant,,ENST00000375957,;ZCCHC6,downstream_gene_variant,,ENST00000469004,; C ENST00000375963 Transcript missense_variant 2315/5379 2142/4488 714/1495 N/K aaT/aaG 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 tolerated_low_confidence(0.19) 13/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 86323608 86323608 A C 1 0 0 0 0 1 0 0 0 18167 214 8 5 5 ZCCHC6 9 86323608 Missense_Mutation SNP A C3L-00368_T 2643711 86323608 52071109 59 6520 WNK2 0 . GRCh38 9 93253019 93253019 + Missense_Mutation SNP C C A rs55672370 C3L-00368_T C3L-00368_N C C c.1971C>A p.Ser657Arg p.S657R ENST00000297954 8/30 83 66 17 87 86 1 strelka-varscan-mutect WNK2,missense_variant,p.Ser653Arg,ENST00000432730,;WNK2,missense_variant,p.Ser657Arg,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Ser657Arg,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Ser261Arg,ENST00000411624,;WNK2,missense_variant,p.Ser657Arg,ENST00000448039,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000464625,; A ENST00000297954 Transcript missense_variant 1971/7138 1971/6894 657/2297 S/R agC/agA rs55672370 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0.02) 8/30 hmmpanther:PTHR13902:SF10,hmmpanther:PTHR13902 MODERATE 1 SNV 1 1 PASS rs55672370 . 0 195 13 2 0 0 0 0 -20 0.9987345 1 1 1 0 A 3 1 15 93253019 93253019 C A 1 0 0 0 0 1 0 0 0 17934 767 27 1 1 WNK2 9 93253019 Missense_Mutation SNP C C3L-00368_T 6929411 93253019 45141698 60 6521 OR13C8 0 . GRCh38 9 104569191 104569191 + Silent SNP G G C rs78381147 C3L-00368_T C3L-00368_N G G c.24G>C p.= p.T8T ENST00000335040 1/1 83 67 16 81 81 0 strelka-varscan-mutect OR13C8,synonymous_variant,p.=,ENST00000335040,NM_001004483.1; C ENST00000335040 Transcript synonymous_variant 24/963 24/963 8/320 T acG/acC rs78381147 1 1 OR13C8 HGNC HGNC:15103 protein_coding YES CCDS35090.1 ENSP00000334068 Q8NGS7 A0A126GVC7 UPI000004B203 NM_001004483.1 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF87,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs78381147 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 15 104569191 104569191 G C 1 0 0 0 0 0 0 0 1 11014 1132 40 4 4 OR13C8 9 104569191 Silent SNP G C3L-00368_T 11316172 104569191 33825526 61 6522 SVEP1 0 . GRCh38 9 110379473 110379473 + Silent SNP G G T novel C3L-00368_T C3L-00368_N G G c.10282C>A p.= p.R3428R ENST00000374469 44/48 213 181 32 229 228 1 strelka-varscan-mutect SVEP1,synonymous_variant,p.=,ENST00000401783,;SVEP1,synonymous_variant,p.=,ENST00000374469,NM_153366.3;SVEP1,upstream_gene_variant,,ENST00000476205,; T ENST00000374469 Transcript synonymous_variant 10477/12194 10282/10716 3428/3571 R Cga/Aga 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 44/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 110379473 110379473 G T 1 0 0 0 0 0 0 0 1 15805 1066 37 1 1 SVEP1 9 110379473 Silent SNP G C3L-00368_T 5810282 110379473 28015244 62 6523 TLR4 0 . GRCh38 9 117713840 117713840 + Missense_Mutation SNP T T A novel C3L-00368_T C3L-00368_N T T c.1712T>A p.Leu571Gln p.L571Q ENST00000355622 3/3 213 202 11 247 246 1 strelka-mutect TLR4,missense_variant,p.Leu571Gln,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Leu531Gln,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; A ENST00000355622 Transcript missense_variant 1813/4844 1712/2520 571/839 L/Q cTa/cAa 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 deleterious(0.02) 3/3 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 117713840 117713840 T A 1 0 0 0 0 1 0 0 0 16399 1522 53 4 4 TLR4 9 117713840 Missense_Mutation SNP T C3L-00368_T 7334367 117713840 20680877 63 6524 BRINP1 0 . GRCh38 9 119168027 119168027 + Missense_Mutation SNP C C T novel C3L-00368_T C3L-00368_N C C c.1343G>A p.Gly448Asp p.G448D ENST00000265922 8/8 144 107 37 142 142 0 strelka-varscan-mutect BRINP1,missense_variant,p.Gly448Asp,ENST00000265922,NM_014618.2;BRINP1,intron_variant,,ENST00000482797,; T ENST00000265922 Transcript missense_variant 1805/3202 1343/2286 448/761 G/D gGc/gAc 1 -1 BRINP1 HGNC HGNC:2687 protein_coding YES CCDS6822.1 ENSP00000265922 O60477 UPI000013D6A7 NM_014618.2 deleterious(0) 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF7 MODERATE 1 SNV 1 1 PASS rs1181656311 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 119168027 119168027 C T 1 0 0 0 0 1 0 0 0 1685 739 26 3 3 BRINP1 9 119168027 Missense_Mutation SNP C C3L-00368_T 1454187 119168027 19226690 64 6525 SLC39A12 0 . GRCh38 10 17953309 17953309 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.33G>T p.Trp11Cys p.W11C ENST00000377369 2/13 178 145 33 166 166 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Trp11Cys,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Trp11Cys,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Trp11Cys,ENST00000377374,NM_152725.3;SLC39A12,intron_variant,,ENST00000539911,NM_001282734.1; T ENST00000377369 Transcript missense_variant 306/2808 33/2076 11/691 W/C tgG/tgT 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 tolerated_low_confidence(0.11) 2/13 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 17953309 17953309 G T 1 0 0 0 0 1 0 0 0 14893 1241 43 2 2 SLC39A12 10 17953309 Missense_Mutation SNP G C3L-00368_T 17953309 115844113 65 6526 PSD 0 . GRCh38 10 102415219 102415219 + Silent SNP G G A novel C3L-00368_T C3L-00368_N G G c.768C>T p.= p.P256P ENST00000020673 4/17 75 71 4 108 108 0 varscan-mutect PSD,synonymous_variant,p.=,ENST00000020673,NM_002779.4;PSD,synonymous_variant,p.=,ENST00000406432,NM_001270965.1;PSD,5_prime_UTR_variant,,ENST00000611678,NM_001270966.1;FBXL15,upstream_gene_variant,,ENST00000224862,NM_024326.3;FBXL15,upstream_gene_variant,,ENST00000369956,;FBXL15,upstream_gene_variant,,ENST00000432590,;FBXL15,upstream_gene_variant,,ENST00000457067,;PSD,downstream_gene_variant,,ENST00000492902,;FBXL15,upstream_gene_variant,,ENST00000481808,;PSD,downstream_gene_variant,,ENST00000472685,;PSD,upstream_gene_variant,,ENST00000488194,; A ENST00000020673 Transcript synonymous_variant 1295/4183 768/3075 256/1024 P ccC/ccT 1 -1 PSD HGNC HGNC:9507 protein_coding YES CCDS31272.1 ENSP00000020673 A5PKW4 UPI0000404928 NM_002779.4 4/17 Low_complexity_(Seg):seg,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -9.382354 1 1 1 1 0 A 2 1 15 102415219 102415219 G A 1 0 0 0 0 0 0 0 1 12797 1219 43 3 3 PSD 10 102415219 Silent SNP G C3L-00368_T 84461910 102415219 31382203 66 6527 PTDSS2 0 . GRCh38 11 490491 490492 + Frame_Shift_Del DEL TC TC - novel C3L-00368_T C3L-00368_N TC TC c.1373_1374delTC p.Val458GlyfsTer38 p.V458Gfs*38 ENST00000308020 12/12 302 261 41 324 324 0 sindel-varindel-pindel PTDSS2,frameshift_variant,p.Val458GlyfsTer38,ENST00000308020,NM_030783.1;RNH1,downstream_gene_variant,,ENST00000534797,;RNH1,downstream_gene_variant,,ENST00000397615,NM_203383.1,NM_002939.3;RNH1,downstream_gene_variant,,ENST00000354420,NM_203387.2;RNH1,downstream_gene_variant,,ENST00000397614,NM_203385.1;RNH1,downstream_gene_variant,,ENST00000533410,NM_203386.2;RNH1,downstream_gene_variant,,ENST00000356187,NM_203389.2;RNH1,downstream_gene_variant,,ENST00000438658,NM_203384.1;RNH1,downstream_gene_variant,,ENST00000397604,NM_203388.2;RNH1,downstream_gene_variant,,ENST00000529768,;PTDSS2,downstream_gene_variant,,ENST00000532614,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000526878,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000531411,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000530029,;RNH1,downstream_gene_variant,,ENST00000525522,;RNH1,downstream_gene_variant,,ENST00000525701,;PTDSS2,downstream_gene_variant,,ENST00000531520,;PTDSS2,downstream_gene_variant,,ENST00000527325,;RNH1,downstream_gene_variant,,ENST00000524464,; - ENST00000308020 Transcript frameshift_variant 1549-1550/2445 1373-1374/1464 458/487 V/X gTC/g 1 1 PTDSS2 HGNC HGNC:15463 protein_coding YES CCDS7696.1 ENSP00000308258 Q9BVG9 A0A024RC97 UPI000004124C NM_030783.1 12/12 hmmpanther:PTHR15362,hmmpanther:PTHR15362:SF12 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 15 490491 490491 TC - 1 0 1 0 1 0 0 0 0 12890 1667 58 0 0 PTDSS2 11 490491 Frame_Shift_Del DEL TC C3L-00368_T 490491 134596131 67 6528 PDE3B 0 . GRCh38 11 14644234 14644234 + Silent SNP C C T novel C3L-00368_T C3L-00368_N C C c.159C>T p.= p.R53R ENST00000282096 1/16 183 133 50 202 202 0 strelka-varscan-mutect PDE3B,synonymous_variant,p.=,ENST00000282096,NM_000922.3;PDE3B,synonymous_variant,p.=,ENST00000455098,;PSMA1,upstream_gene_variant,,ENST00000418988,NM_148976.2;PDE3B,upstream_gene_variant,,ENST00000534317,;PSMA1,upstream_gene_variant,,ENST00000528018,; T ENST00000282096 Transcript synonymous_variant 512/6076 159/3339 53/1112 R cgC/cgT 1 1 PDE3B HGNC HGNC:8779 protein_coding YES CCDS7817.1 ENSP00000282096 Q13370 UPI000013DCB7 NM_000922.3 1/16 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 14644234 14644234 C T 1 0 0 0 0 0 0 0 1 11726 784 28 3 3 PDE3B 11 14644234 Silent SNP C C3L-00368_T 14153743 14644234 120442388 68 6529 NAV2 0 . GRCh38 11 19933546 19933546 + Silent SNP C C T C3L-00368_T C3L-00368_N C C c.1371C>T p.= p.P457P ENST00000396087 8/41 67 56 11 63 63 0 strelka-varscan-mutect NAV2,synonymous_variant,p.=,ENST00000527559,;NAV2,synonymous_variant,p.=,ENST00000540292,;NAV2,synonymous_variant,p.=,ENST00000396085,NM_182964.5;NAV2,synonymous_variant,p.=,ENST00000349880,NM_145117.4;NAV2,synonymous_variant,p.=,ENST00000360655,NM_001111018.1;NAV2,synonymous_variant,p.=,ENST00000396087,NM_001244963.1;NAV2,non_coding_transcript_exon_variant,,ENST00000528008,; T ENST00000396087 Transcript synonymous_variant 1470/7882 1371/7467 457/2488 P ccC/ccT COSM5562437,COSM5562438 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 8/41 Low_complexity_(Seg):seg,hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99999 1 1 1 1 0 T 2 4 15 19933546 19933546 C T 1 0 0 0 0 0 0 0 1 10193 581 21 3 3 NAV2 11 19933546 Silent SNP C C3L-00368_T 5289312 19933546 115153076 69 6530 OR5A1 0 . GRCh38 11 59444055 59444055 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.887G>T p.Arg296Met p.R296M ENST00000302030 1/1 139 112 27 174 174 0 strelka-varscan-mutect OR5A1,missense_variant,p.Arg296Met,ENST00000302030,NM_001004728.1; T ENST00000302030 Transcript missense_variant 912/1051 887/948 296/315 R/M aGg/aTg 1 1 OR5A1 HGNC HGNC:8319 protein_coding YES CCDS31561.1 ENSP00000303096 Q8NGJ0 UPI0000041C97 NM_001004728.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF354,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999507 1 1 1 0 T 3 4 15 59444055 59444055 G T 1 0 0 0 0 1 0 0 0 11211 1000 35 2 2 OR5A1 11 59444055 Missense_Mutation SNP G C3L-00368_T 39510509 59444055 75642567 70 6531 DDB1 0 . GRCh38 11 61313538 61313538 + Missense_Mutation SNP T T C novel C3L-00368_T C3L-00368_N T T c.2030A>G p.Asn677Ser p.N677S ENST00000301764 16/27 183 152 31 182 182 0 strelka-varscan-mutect DDB1,missense_variant,p.Asn677Ser,ENST00000301764,NM_001923.4;DDB1,intron_variant,,ENST00000543658,;DDB1,downstream_gene_variant,,ENST00000545930,;DDB1,downstream_gene_variant,,ENST00000538280,;DDB1,missense_variant,p.Asn677Ser,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000535147,;DDB1,non_coding_transcript_exon_variant,,ENST00000537877,;DDB1,downstream_gene_variant,,ENST00000414411,;DDB1,upstream_gene_variant,,ENST00000539332,;DDB1,downstream_gene_variant,,ENST00000539739,;DDB1,downstream_gene_variant,,ENST00000535967,;DDB1,downstream_gene_variant,,ENST00000540784,;DDB1,downstream_gene_variant,,ENST00000535174,; C ENST00000301764 Transcript missense_variant 2428/4506 2030/3423 677/1140 N/S aAc/aGc 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 tolerated(0.52) 16/27 hmmpanther:PTHR10644 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 15 61313538 61313538 T C 1 0 0 0 0 1 0 0 0 4126 1725 60 5 5 DDB1 11 61313538 Missense_Mutation SNP T C3L-00368_T 1869483 61313538 73773084 71 6532 TKFC 0 . GRCh38 11 61339326 61339326 + Missense_Mutation SNP G G T rs750037556 C3L-00368_T C3L-00368_N G G c.377G>T p.Arg126Leu p.R126L ENST00000394900 5/18 153 132 21 155 155 0 strelka-varscan-mutect TKFC,missense_variant,p.Arg126Leu,ENST00000394900,NM_015533.3;TKFC,missense_variant,p.Arg125Leu,ENST00000529479,;TKFC,missense_variant,p.Arg126Leu,ENST00000532173,;TKFC,upstream_gene_variant,,ENST00000534084,;TKFC,downstream_gene_variant,,ENST00000524968,;TKFC,downstream_gene_variant,,ENST00000530057,;TKFC,downstream_gene_variant,,ENST00000533393,;TKFC,downstream_gene_variant,,ENST00000530456,;TKFC,downstream_gene_variant,,ENST00000525170,;TKFC,downstream_gene_variant,,ENST00000529620,;TKFC,non_coding_transcript_exon_variant,,ENST00000529092,;DDB1,intron_variant,,ENST00000540166,;TKFC,downstream_gene_variant,,ENST00000529121,;TKFC,upstream_gene_variant,,ENST00000534134,;TKFC,upstream_gene_variant,,ENST00000524953,;TKFC,upstream_gene_variant,,ENST00000528061,;TKFC,upstream_gene_variant,,ENST00000533853,;TKFC,upstream_gene_variant,,ENST00000534370,; T ENST00000394900 Transcript missense_variant 606/4696 377/1728 126/575 R/L cGg/cTg rs750037556 1 1 TKFC HGNC HGNC:24552 protein_coding YES CCDS8003.1 ENSP00000378360 Q3LXA3 A0A140VJH7 UPI00000718B9 NM_015533.3 deleterious(0) 5/18 PROSITE_profiles:PS51481,hmmpanther:PTHR28629:SF4,hmmpanther:PTHR28629,Gene3D:3.40.50.10440,TIGRFAM_domain:TIGR02361,Pfam_domain:PF02733,Superfamily_domains:SSF82549 MODERATE 1 SNV 1 1 PASS rs750037556 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 61339326 61339326 G T 1 0 0 0 0 1 0 0 0 16376 1116 39 1 1 TKFC 11 61339326 Missense_Mutation SNP G C3L-00368_T 25788 61339326 73747296 72 6533 CCDC87 0 . GRCh38 11 66590848 66590848 + Missense_Mutation SNP C C A rs201450672 C3L-00368_T C3L-00368_N C C c.2168G>T p.Arg723Leu p.R723L ENST00000333861 1/1 194 165 29 189 188 1 strelka-varscan-mutect CCDC87,missense_variant,p.Arg723Leu,ENST00000333861,NM_018219.2;CCS,upstream_gene_variant,,ENST00000533244,NM_005125.1;CCS,upstream_gene_variant,,ENST00000310190,;CCS,upstream_gene_variant,,ENST00000530961,;CCS,upstream_gene_variant,,ENST00000530384,;CCS,upstream_gene_variant,,ENST00000526066,;CCS,upstream_gene_variant,,ENST00000531990,;CCS,upstream_gene_variant,,ENST00000526058,; A ENST00000333861 Transcript missense_variant 2236/2908 2168/2550 723/849 R/L cGg/cTg rs201450672,COSM333528 1 -1 CCDC87 HGNC HGNC:25579 protein_coding YES CCDS8145.1 ENSP00000328487 Q9NVE4 UPI000013EFC2 NM_018219.2 tolerated(0.17) 1/1 hmmpanther:PTHR16078,hmmpanther:PTHR16078:SF1,Pfam_domain:PF03999 0,1 MODERATE SNV 0,1 1 PASS rs201450672 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 66590848 66590848 C A 1 0 0 0 0 1 0 0 0 2561 652 23 1 1 CCDC87 11 66590848 Missense_Mutation SNP C C3L-00368_T 5251522 66590848 68495774 73 6534 FAT3 0 . GRCh38 11 92797985 92797985 + Missense_Mutation SNP C C A rs201013393 C3L-00368_T C3L-00368_N C C c.4522C>A p.Arg1508Ser p.R1508S ENST00000525166 9/27 215 177 38 226 226 0 strelka-varscan-mutect FAT3,missense_variant,p.Arg1658Ser,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Arg1508Ser,ENST00000525166,; A ENST00000525166 Transcript missense_variant 4544/18699 4522/13320 1508/4439 R/S Cgc/Agc rs201013393,COSM4201756,COSM4201757 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.24) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs201013393 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 92797985 92797985 C A 1 0 0 0 0 1 0 0 0 5551 768 27 1 1 FAT3 11 92797985 Missense_Mutation SNP C C3L-00368_T 26207137 92797985 42288637 74 6535 DRD2 0 . GRCh38 11 113412632 113412632 + Silent SNP G G T rs149410294 C3L-00368_T C3L-00368_N G G c.1062C>A p.= p.S354S ENST00000362072 7/8 419 328 91 533 533 0 strelka-varscan-mutect DRD2,synonymous_variant,p.=,ENST00000362072,NM_000795.3;DRD2,synonymous_variant,p.=,ENST00000544518,;DRD2,synonymous_variant,p.=,ENST00000542968,;DRD2,synonymous_variant,p.=,ENST00000346454,NM_016574.3;DRD2,synonymous_variant,p.=,ENST00000538967,;DRD2,downstream_gene_variant,,ENST00000543292,;RP11-159N11.3,downstream_gene_variant,,ENST00000546284,;DRD2,downstream_gene_variant,,ENST00000535984,;DRD2,downstream_gene_variant,,ENST00000540600,;DRD2,downstream_gene_variant,,ENST00000539420,; T ENST00000362072 Transcript synonymous_variant 1407/2789 1062/1332 354/443 S tcC/tcA rs149410294 1 -1 DRD2 HGNC HGNC:3023 protein_coding YES CCDS8361.1 ENSP00000354859 P14416 A0A024R3C5 UPI0000001315 NM_000795.3 7/8 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF68,SMART_domains:SM01381 LOW 1 SNV 1 1 PASS rs149410294 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 113412632 113412632 G T 1 0 0 0 0 0 0 0 1 4576 1219 43 2 2 DRD2 11 113412632 Silent SNP G C3L-00368_T 20614647 113412632 21673990 75 6536 OR8B2 0 . GRCh38 11 124383050 124383050 + Missense_Mutation SNP C C T rs765029743 C3L-00368_T C3L-00368_N C C c.294G>A p.Met98Ile p.M98I ENST00000375013 1/1 270 220 50 379 379 0 strelka-varscan-mutect OR8B2,missense_variant,p.Met98Ile,ENST00000375013,NM_001005468.1; T ENST00000375013 Transcript missense_variant 313/968 294/942 98/313 M/I atG/atA rs765029743 1 -1 OR8B2 HGNC HGNC:8471 protein_coding YES CCDS31708.1 ENSP00000364152 Q96RD0 A0A126GVQ4 UPI000004B1E5 NM_001005468.1 deleterious_low_confidence(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF258,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs765029743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 124383050 124383050 C T 1 0 0 0 0 1 0 0 0 11297 826 29 3 3 OR8B2 11 124383050 Missense_Mutation SNP C C3L-00368_T 10970418 124383050 10703572 76 6537 TMTC1 0 . GRCh38 12 29556977 29556977 + Missense_Mutation SNP G G T C3L-00368_T C3L-00368_N G G c.1556C>A p.Ala519Glu p.A519E ENST00000539277 10/18 363 180 183 265 265 0 strelka-varscan-mutect TMTC1,missense_variant,p.Ala411Glu,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Ala581Glu,ENST00000551659,;TMTC1,missense_variant,p.Ala543Glu,ENST00000552618,;TMTC1,missense_variant,p.Ala519Glu,ENST00000539277,NM_001193451.1;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,non_coding_transcript_exon_variant,,ENST00000553189,; T ENST00000539277 Transcript missense_variant 1615/2758 1556/2649 519/882 A/E gCg/gAg COSM4041331,COSM4041332 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 deleterious(0) 10/18 Gene3D:1.25.40.10,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00028,Superfamily_domains:SSF48452 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1359298899 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 29556977 29556977 G T 1 0 0 0 0 1 0 0 0 16734 1087 38 1 1 TMTC1 12 29556977 Missense_Mutation SNP G C3L-00368_T 29556977 103718332 77 6538 TPH2 0 . GRCh38 12 72031521 72031521 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.1299G>T p.Arg433Ser p.R433S ENST00000333850 11/11 344 287 57 379 379 0 strelka-varscan-mutect TPH2,missense_variant,p.Arg433Ser,ENST00000333850,NM_173353.3;TPH2,intron_variant,,ENST00000550403,;TPH2,intron_variant,,ENST00000547348,;TPH2,intron_variant,,ENST00000547278,;TPH2,intron_variant,,ENST00000551074,; T ENST00000333850 Transcript missense_variant,splice_region_variant 1440/2360 1299/1473 433/490 R/S agG/agT 1 1 TPH2 HGNC HGNC:20692 protein_coding YES CCDS31859.1 ENSP00000329093 Q8IWU9 UPI000007446F NM_173353.3 deleterious(0) 11/11 Gene3D:1.10.800.10,Pfam_domain:PF00351,PIRSF_domain:PIRSF000336,PROSITE_profiles:PS51410,hmmpanther:PTHR11473,hmmpanther:PTHR11473:SF16,Superfamily_domains:SSF56534,TIGRFAM_domain:TIGR01270 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 72031521 72031521 G T 1 0 0 0 0 1 0 0 0 16883 1246 43 2 2 TPH2 12 72031521 Missense_Mutation SNP G C3L-00368_T 42474544 72031521 61243788 78 6539 NOS1 0 . GRCh38 12 117215313 117215313 + Missense_Mutation SNP G G C novel C3L-00368_T C3L-00368_N G G c.4403C>G p.Ser1468Cys p.S1468C ENST00000618760 30/30 27 23 4 42 42 0 strelka-varscan-mutect NOS1,missense_variant,p.Ser1468Cys,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Ser1434Cys,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Ser1468Cys,ENST00000338101,;NOS1,missense_variant,p.Ser1433Cys,ENST00000344089,; C ENST00000618760 Transcript missense_variant 5114/12283 4403/4407 1468/1468 S/C tCc/tGc 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 deleterious_low_confidence(0) 30/30 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -12.03705 1 1 1 1 0 C 3 2 15 117215313 117215313 G C 1 0 0 0 0 1 0 0 0 10586 1174 41 4 4 NOS1 12 117215313 Missense_Mutation SNP G C3L-00368_T 45183792 117215313 16059996 79 6540 OR4E2 0 . GRCh38 14 21665554 21665554 + Missense_Mutation SNP G G T C3L-00368_T C3L-00368_N G G c.472G>T p.Gly158Trp p.G158W ENST00000408935 1/1 122 104 18 117 116 1 strelka-varscan-mutect OR4E2,missense_variant,p.Gly158Trp,ENST00000408935,NM_001001912.2;OR4E1,downstream_gene_variant,,ENST00000610316,; T ENST00000408935 Transcript missense_variant 472/942 472/942 158/313 G/W Ggg/Tgg COSM552534 1 1 OR4E2 HGNC HGNC:8297 protein_coding YES CCDS41916.1 ENSP00000386195 Q8NGC2 A0A126GVR8 UPI0000EE498D NM_001001912.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF160,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 21665554 21665554 G T 1 0 0 0 0 1 0 0 0 11137 1000 35 2 2 OR4E2 14 21665554 Missense_Mutation SNP G C3L-00368_T 21665554 85378164 80 6541 NOVA1 0 . GRCh38 14 26448879 26448879 + Missense_Mutation SNP C C T novel C3L-00368_T C3L-00368_N C C c.604G>A p.Gly202Arg p.G202R ENST00000539517 5/5 216 175 41 200 200 0 strelka-varscan-mutect NOVA1,missense_variant,p.Gly202Arg,ENST00000539517,NM_002515.2;NOVA1,missense_variant,p.Gly178Arg,ENST00000465357,NM_006489.2;NOVA1,missense_variant,p.Gly165Arg,ENST00000549571,;NOVA1,missense_variant,p.Gly161Arg,ENST00000449198,;NOVA1,missense_variant,p.Gly80Arg,ENST00000549146,;NOVA1,missense_variant,p.Gly56Arg,ENST00000347476,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,3_prime_UTR_variant,,ENST00000546546,; T ENST00000539517 Transcript missense_variant 922/3912 604/1524 202/507 G/R Ggg/Agg 1 -1 NOVA1 HGNC HGNC:7886 protein_coding YES CCDS32061.1 ENSP00000438875 P51513 UPI000013D74E NM_002515.2 deleterious(0) 5/5 PROSITE_profiles:PS50084,hmmpanther:PTHR10288:SF150,hmmpanther:PTHR10288,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 26448879 26448879 C T 1 0 0 0 0 1 0 0 0 10600 681 24 3 3 NOVA1 14 26448879 Missense_Mutation SNP C C3L-00368_T 4783325 26448879 80594839 81 6542 BEGAIN 0 . GRCh38 14 100538100 100538100 + Missense_Mutation SNP C C T novel C3L-00368_T C3L-00368_N C C c.1651G>A p.Glu551Lys p.E551K ENST00000443071 6/6 56 44 12 68 68 0 strelka-varscan-mutect BEGAIN,missense_variant,p.Glu770Lys,ENST00000637716,;BEGAIN,missense_variant,p.Glu581Lys,ENST00000637646,;BEGAIN,missense_variant,p.Glu551Lys,ENST00000443071,NM_001159531.1;BEGAIN,missense_variant,p.Glu551Lys,ENST00000355173,NM_020836.3;BEGAIN,downstream_gene_variant,,ENST00000556188,;BEGAIN,downstream_gene_variant,,ENST00000553553,;BEGAIN,downstream_gene_variant,,ENST00000554356,;BEGAIN,downstream_gene_variant,,ENST00000557378,;BEGAIN,downstream_gene_variant,,ENST00000554140,;CTD-2062F14.3,upstream_gene_variant,,ENST00000553301,;BEGAIN,non_coding_transcript_exon_variant,,ENST00000556751,; T ENST00000443071 Transcript missense_variant 1797/2744 1651/1782 551/593 E/K Gag/Aag 1 -1 BEGAIN HGNC HGNC:24163 protein_coding YES CCDS9962.1 ENSP00000411124 Q9BUH8 UPI00000710B1 NM_001159531.1 deleterious(0.01) 6/6 hmmpanther:PTHR28664,hmmpanther:PTHR28664:SF2 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 100538100 100538100 C T 1 0 0 0 0 1 0 0 0 1545 864 30 3 3 BEGAIN 14 100538100 Missense_Mutation SNP C C3L-00368_T 74089221 100538100 6505618 82 6543 BRF1 0 . GRCh38 14 105228839 105228839 + Nonsense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.769G>T p.Glu257Ter p.E257* ENST00000547530 7/18 204 174 30 177 177 0 strelka-varscan-mutect BRF1,stop_gained,p.Glu53Ter,ENST00000392557,NM_145685.2;BRF1,stop_gained,p.Glu257Ter,ENST00000547530,NM_001519.3;BRF1,stop_gained,p.Glu230Ter,ENST00000379937,NM_001242788.1;BRF1,stop_gained,p.Glu19Ter,ENST00000446501,NM_001242789.1;BRF1,stop_gained,p.Glu142Ter,ENST00000440513,NM_001242786.1;BRF1,stop_gained,p.Glu142Ter,ENST00000327359,NM_001242787.1;BRF1,stop_gained,p.Glu53Ter,ENST00000549655,;BRF1,stop_gained,p.Glu53Ter,ENST00000619151,;BRF1,stop_gained,p.Glu53Ter,ENST00000379932,;BRF1,stop_gained,p.Glu53Ter,ENST00000551787,;BRF1,stop_gained,p.Glu53Ter,ENST00000552127,;BRF1,stop_gained,p.Glu111Ter,ENST00000546417,;BRF1,downstream_gene_variant,,ENST00000550208,;BRF1,upstream_gene_variant,,ENST00000547562,; A ENST00000547530 Transcript stop_gained 828/3358 769/2034 257/677 E/* Gag/Tag 1 -1 BRF1 HGNC HGNC:11551 protein_coding YES CCDS10001.1 ENSP00000448387 Q92994 F8VS36 UPI0000136C55 NM_001519.3 7/18 hmmpanther:PTHR11618,hmmpanther:PTHR11618:SF4,Pfam_domain:PF00382,Gene3D:1.10.472.10,SMART_domains:SM00385,Superfamily_domains:SSF47954,Prints_domain:PR00685 HIGH 1 SNV 1 1 PASS rs1491416469 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 15 105228839 105228839 C A 1 0 0 0 0 0 1 0 0 1680 835 29 2 2 BRF1 14 105228839 Nonsense_Mutation SNP C C3L-00368_T 4690739 105228839 1814879 83 6544 RYR3 0 . GRCh38 15 33586092 33586092 + Missense_Mutation SNP G G T rs761171982 C3L-00368_T C3L-00368_N G G c.1764G>T p.Leu588Phe p.L588F ENST00000634891 16/104 210 183 27 200 200 0 strelka-varscan-mutect RYR3,missense_variant,p.Leu588Phe,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Leu588Phe,ENST00000622037,;RYR3,missense_variant,p.Leu588Phe,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Leu588Phe,ENST00000389232,;RYR3,missense_variant,p.Leu588Phe,ENST00000634418,; T ENST00000634891 Transcript missense_variant 1865/15591 1764/14613 588/4870 L/F ttG/ttT rs761171982 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 16/104 Pfam_domain:PF01365,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs761171982 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 33586092 33586092 G T 1 0 0 0 0 1 0 0 0 14030 1339 47 2 2 RYR3 15 33586092 Missense_Mutation SNP G C3L-00368_T 33586092 68405097 84 6545 ARIH1 0 . GRCh38 15 72570175 72570175 + Splice_Site SNP A A T novel C3L-00368_T C3L-00368_N A A c.1027-2A>T p.X343_splice ENST00000379887 108 90 18 90 90 0 strelka-varscan-mutect ARIH1,splice_acceptor_variant,,ENST00000379887,NM_005744.3;ARIH1,non_coding_transcript_exon_variant,,ENST00000565950,;ARIH1,intron_variant,,ENST00000561987,;ARIH1,upstream_gene_variant,,ENST00000561770,; T ENST00000379887 Transcript splice_acceptor_variant -/21681 1027/1674 343/557 1 1 ARIH1 HGNC HGNC:689 protein_coding YES CCDS10244.1 ENSP00000369217 Q9Y4X5 UPI0000033466 NM_005744.3 9/13 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 15 72570175 72570175 A T 1 0 0 0 0 0 0 1 0 1059 434 15 4 4 ARIH1 15 72570175 Splice_Site SNP A C3L-00368_T 38984083 72570175 29421014 85 6546 CHD2 0 . GRCh38 15 92997371 92997377 + Frame_Shift_Del DEL AAAACAG AAAACAG - novel C3L-00368_T C3L-00368_N AAAACAG AAAACAG c.3854_3860delAAACAGA p.Lys1285ThrfsTer6 p.K1285Tfs*6 ENST00000394196 30/39 80 71 9 80 80 0 sindel-varindel-pindel CHD2,frameshift_variant,p.Lys1285ThrfsTer6,ENST00000394196,NM_001271.3;CHD2,frameshift_variant,p.Lys1285ThrfsTer6,ENST00000626874,;CHD2,non_coding_transcript_exon_variant,,ENST00000636306,;CHD2,non_coding_transcript_exon_variant,,ENST00000635922,;CHD2,downstream_gene_variant,,ENST00000635856,;CHD2,frameshift_variant,p.Lys49ThrfsTer6,ENST00000625662,;CHD2,frameshift_variant,p.Lys24ThrfsTer6,ENST00000629104,;CHD2,3_prime_UTR_variant,,ENST00000636881,;CHD2,3_prime_UTR_variant,,ENST00000637789,;CHD2,non_coding_transcript_exon_variant,,ENST00000627185,;CHD2,downstream_gene_variant,,ENST00000637572,; - ENST00000394196 Transcript frameshift_variant 4429-4435/9363 3853-3859/5487 1285-1287/1828 KTD/X AAAACAGac/ac 1 1 CHD2 HGNC HGNC:1917 protein_coding YES CCDS10374.2 ENSP00000377747 O14647 UPI0000E8A85C NM_001271.3 30/39 HIGH 1 deletion 5 1 1 PASS . . 0 200 9 0 0 0 0 0 -19.06819 0.999988 1 1 1 0 - 7 5 15 92997371 92997371 AAAACAG - 1 0 1 0 1 0 0 0 0 3084 363 13 0 0 CHD2 15 92997371 Frame_Shift_Del DEL AAAACAG C3L-00368_T 20427196 92997371 8993818 86 6547 CAPN15 0 . GRCh38 16 549011 549011 + Missense_Mutation SNP G G A novel C3L-00368_T C3L-00368_N G G c.1468G>A p.Asp490Asn p.D490N ENST00000219611 5/14 325 303 22 265 265 0 strelka-varscan-mutect CAPN15,missense_variant,p.Asp490Asn,ENST00000219611,NM_005632.2;CAPN15,downstream_gene_variant,,ENST00000637507,;CAPN15,downstream_gene_variant,,ENST00000562370,;CAPN15,downstream_gene_variant,,ENST00000568988,;CAPN15,upstream_gene_variant,,ENST00000566977,;LA16c-366D1.3,intron_variant,,ENST00000565879,;CAPN15,upstream_gene_variant,,ENST00000565010,; A ENST00000219611 Transcript missense_variant 1831/4744 1468/3261 490/1086 D/N Gat/Aat 1 1 CAPN15 HGNC HGNC:11182 protein_coding YES CCDS10410.1 ENSP00000219611 O75808 UPI0000071B68 NM_005632.2 deleterious(0) 5/14 Pfam_domain:PF00648,Prints_domain:PR00704,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF294,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 549011 549011 G A 1 0 0 0 0 1 0 0 0 2320 1174 41 3 3 CAPN15 16 549011 Missense_Mutation SNP G C3L-00368_T 549011 89789334 87 6548 RBFOX1 0 . GRCh38 16 7518353 7518353 + Silent SNP G G A C3L-00368_T C3L-00368_N G G c.363G>A p.= p.A121A ENST00000422070 5/16 145 111 34 113 113 0 strelka-mutect RBFOX1,synonymous_variant,p.=,ENST00000550418,NM_018723.3;RBFOX1,synonymous_variant,p.=,ENST00000340209,;RBFOX1,synonymous_variant,p.=,ENST00000620507,;RBFOX1,synonymous_variant,p.=,ENST00000547372,;RBFOX1,synonymous_variant,p.=,ENST00000355637,NM_145893.2;RBFOX1,synonymous_variant,p.=,ENST00000311745,NM_145891.2;RBFOX1,synonymous_variant,p.=,ENST00000553186,NM_001142333.1;RBFOX1,synonymous_variant,p.=,ENST00000547605,;RBFOX1,synonymous_variant,p.=,ENST00000422070,NM_001308117.1;RBFOX1,synonymous_variant,p.=,ENST00000535565,;RBFOX1,synonymous_variant,p.=,ENST00000436368,NM_145892.2;RBFOX1,synonymous_variant,p.=,ENST00000547338,NM_001142334.1;RBFOX1,synonymous_variant,p.=,ENST00000552089,;RBFOX1,synonymous_variant,p.=,ENST00000551752,;RBFOX1,synonymous_variant,p.=,ENST00000570626,;RBFOX1,non_coding_transcript_exon_variant,,ENST00000569889,; A ENST00000422070 Transcript synonymous_variant 559/1684 363/1278 121/425 A gcG/gcA COSM4062893,COSM4062894,COSM4062895,COSM4062896 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 5/16 hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932 1,1,1,1 LOW 1 SNV 2 1,1,1,1 1 PASS rs1490574094 . 0 204 4 2 0 0 0 0 -20 0.999993 1 1 1 0 A 2 1 15 7518353 7518353 G A 1 0 0 0 0 0 0 0 1 13271 1103 39 1 1 RBFOX1 16 7518353 Silent SNP G C3L-00368_T 6969342 7518353 82819992 88 6549 C16orf46 0 . GRCh38 16 81061521 81061521 + Missense_Mutation SNP G G T rs537023465 C3L-00368_T C3L-00368_N G G c.828C>A p.Asn276Lys p.N276K ENST00000299578 4/4 110 103 7 141 141 0 strelka-varscan-mutect C16orf46,missense_variant,p.Asn276Lys,ENST00000378611,NM_001100873.1;C16orf46,missense_variant,p.Asn276Lys,ENST00000299578,NM_152337.2;C16orf46,downstream_gene_variant,,ENST00000565253,;RP11-303E16.8,intron_variant,,ENST00000564536,;C16orf46,downstream_gene_variant,,ENST00000444657,; T ENST00000299578 Transcript missense_variant 1064/1605 828/1188 276/395 N/K aaC/aaA rs537023465,COSM3402494,COSM3402495 1 -1 C16orf46 HGNC HGNC:26525 protein_coding YES CCDS10932.1 ENSP00000299578 Q6P387 UPI000013E5BE NM_152337.2 tolerated(1) 4/4 hmmpanther:PTHR36869:SF1,hmmpanther:PTHR36869,Pfam_domain:PF15032 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs537023465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 81061521 81061521 G T 1 0 0 0 0 1 0 0 0 1856 1136 40 1 1 C16orf46 16 81061521 Missense_Mutation SNP G C3L-00368_T 73543168 81061521 9276824 89 6550 ZZEF1 0 . GRCh38 17 4021155 4021155 + Missense_Mutation SNP C C A novel C3L-00368_T C3L-00368_N C C c.7378G>T p.Asp2460Tyr p.D2460Y ENST00000381638 45/55 78 68 10 87 87 0 strelka-varscan-mutect ZZEF1,missense_variant,p.Asp2460Tyr,ENST00000381638,NM_015113.3;ZZEF1,downstream_gene_variant,,ENST00000573183,;ZZEF1,upstream_gene_variant,,ENST00000573536,;ZZEF1,downstream_gene_variant,,ENST00000571436,;ZZEF1,downstream_gene_variant,,ENST00000573606,;ZZEF1,upstream_gene_variant,,ENST00000575428,;ZZEF1,upstream_gene_variant,,ENST00000572831,; A ENST00000381638 Transcript missense_variant 7503/11456 7378/8886 2460/2961 D/Y Gat/Tat 1 -1 ZZEF1 HGNC HGNC:29027 protein_coding YES CCDS11043.1 ENSP00000371051 O43149 UPI00004569F7 NM_015113.3 deleterious(0) 45/55 hmmpanther:PTHR22772:SF4,hmmpanther:PTHR22772 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99476 1 1 1 1 0 A 3 1 15 4021155 4021155 C A 1 0 0 0 0 1 0 0 0 18859 855 30 2 2 ZZEF1 17 4021155 Missense_Mutation SNP C C3L-00368_T 4021155 79236286 90 6551 ALOXE3 0 . GRCh38 17 8096689 8096700 + In_Frame_Del DEL CCTGGTTCCGCT CCTGGTTCCGCT - novel C3L-00368_T C3L-00368_N CCTGGTTCCGCT CCTGGTTCCGCT c.2459_2470delAGCGGAACCAGG p.Glu820_Gln823del p.E820_Q823del ENST00000318227 16/16 244 210 34 308 308 0 sindel-varindel-pindel ALOXE3,inframe_deletion,p.Glu844_Gln847del,ENST00000380149,;ALOXE3,inframe_deletion,p.Glu688_Gln691del,ENST00000448843,NM_021628.2;ALOXE3,inframe_deletion,p.Glu820_Gln823del,ENST00000318227,NM_001165960.1;ALOXE3,non_coding_transcript_exon_variant,,ENST00000583808,; - ENST00000318227 Transcript inframe_deletion 2728-2739/3053 2459-2470/2532 820-824/843 ERNQG/G gAGCGGAACCAGGgt/ggt 1 -1 ALOXE3 HGNC HGNC:13743 protein_coding YES CCDS54084.1 ENSP00000314879 Q9BYJ1 UPI0000EE63AA NM_001165960.1 16/16 Gene3D:1.20.245.10,Pfam_domain:PF00305,PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF62,Superfamily_domains:SSF48484 MODERATE 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 15 8096689 8096689 CCTGGTTCCGCT - 1 0 1 0 1 0 0 0 0 642 623 22 0 0 ALOXE3 17 8096689 In_Frame_Del DEL CCTGGTTCCGCT C3L-00368_T 4075534 8096689 75160752 91 6552 DSG3 0 . GRCh38 18 31460919 31460919 + Silent SNP G G A novel C3L-00368_T C3L-00368_N G G c.771G>A p.= p.V257V ENST00000257189 7/16 96 82 14 113 113 0 strelka-varscan-mutect DSG3,synonymous_variant,p.=,ENST00000257189,NM_001944.2; A ENST00000257189 Transcript synonymous_variant 854/5525 771/3000 257/999 V gtG/gtA 1 1 DSG3 HGNC HGNC:3050 protein_coding YES CCDS11898.1 ENSP00000257189 P32926 UPI000013CF4B NM_001944.2 7/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF3,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 31460919 31460919 G A 1 0 0 0 0 0 0 0 1 4599 1277 45 3 3 DSG3 18 31460919 Silent SNP G C3L-00368_T 31460919 48912366 92 6553 DOT1L 0 . GRCh38 19 2191114 2191114 + Nonsense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.367G>T p.Glu123Ter p.E123* ENST00000398665 5/28 373 305 68 430 429 1 strelka-varscan-mutect DOT1L,stop_gained,p.Glu123Ter,ENST00000398665,NM_032482.2;DOT1L,stop_gained,p.Glu99Ter,ENST00000452696,;DOT1L,3_prime_UTR_variant,,ENST00000478937,; T ENST00000398665 Transcript stop_gained 403/7436 367/4614 123/1537 E/* Gag/Tag 1 1 DOT1L HGNC HGNC:24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 5/28 PROSITE_profiles:PS51569,hmmpanther:PTHR21451,hmmpanther:PTHR21451:SF0,Pfam_domain:PF08123,PIRSF_domain:PIRSF037123,Superfamily_domains:SSF53335 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 15 2191114 2191114 G T 1 0 0 0 0 0 1 0 0 4523 1059 37 1 1 DOT1L 19 2191114 Nonsense_Mutation SNP G C3L-00368_T 2191114 56426502 93 6554 MUC16 0 . GRCh38 19 8972534 8972534 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.8605C>A p.Pro2869Thr p.P2869T ENST00000397910 1/84 103 86 17 126 126 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro2869Thr,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 8809/43816 8605/43524 2869/14507 P/T Cca/Aca 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 8972534 8972534 G T 1 0 0 0 0 1 0 0 0 9972 1232 43 2 2 MUC16 19 8972534 Missense_Mutation SNP G C3L-00368_T 6781420 8972534 49645082 94 6555 PSG11 0 . GRCh38 19 43010012 43010012 + Missense_Mutation SNP T T A rs201933852 C3L-00368_T C3L-00368_N T T c.994A>T p.Asn332Tyr p.N332Y ENST00000320078 5/6 202 161 41 223 223 0 strelka-varscan-mutect PSG11,missense_variant,p.Asn332Tyr,ENST00000320078,NM_002785.2;PSG11,missense_variant,p.Asn210Tyr,ENST00000403486,NM_203287.1,NM_001113410.1;PSG11,missense_variant,p.Asn210Tyr,ENST00000306322,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG11,downstream_gene_variant,,ENST00000599976,;PSG11,3_prime_UTR_variant,,ENST00000593983,;PSG11,non_coding_transcript_exon_variant,,ENST00000593994,;PSG11,downstream_gene_variant,,ENST00000595138,;PSG11,downstream_gene_variant,,ENST00000594655,; A ENST00000320078 Transcript missense_variant 1134/1575 994/1008 332/335 N/Y Aat/Tat rs201933852 1 -1 PSG11 HGNC HGNC:9516 protein_coding YES CCDS12614.2 ENSP00000319140 Q9UQ72 UPI000004EE8C NM_002785.2 tolerated(0.07) 5/6 MODERATE 1 SNV 2 1 PASS rs201933852 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 15 43010012 43010012 T A 1 0 0 0 0 1 0 0 0 12805 1812 63 4 4 PSG11 19 43010012 Missense_Mutation SNP T C3L-00368_T 34037478 43010012 15607604 95 6556 KIAA1755 0 . GRCh38 20 38222504 38222504 + Missense_Mutation SNP T T G novel C3L-00368_T C3L-00368_N T T c.2362A>C p.Thr788Pro p.T788P ENST00000279024 10/14 269 218 51 268 268 0 strelka-varscan-mutect KIAA1755,missense_variant,p.Thr788Pro,ENST00000279024,NM_001029864.1;KIAA1755,missense_variant,p.Thr87Pro,ENST00000435901,;KIAA1755,downstream_gene_variant,,ENST00000496900,;KIAA1755,non_coding_transcript_exon_variant,,ENST00000484362,;KIAA1755,upstream_gene_variant,,ENST00000460881,;KIAA1755,upstream_gene_variant,,ENST00000487506,; G ENST00000279024 Transcript missense_variant 2634/6429 2362/3603 788/1200 T/P Acc/Ccc 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 deleterious(0.01) 10/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF125 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 38222504 38222504 T G 1 0 0 0 0 1 0 0 0 8128 1696 59 5 5 KIAA1755 20 38222504 Missense_Mutation SNP T C3L-00368_T 38222504 26221663 96 6557 ADA 0 . GRCh38 20 44629112 44629112 + Silent SNP G G T C3L-00368_T C3L-00368_N G G c.153C>A p.= p.G51G ENST00000372874 3/12 426 352 74 392 390 2 strelka-varscan-mutect ADA,synonymous_variant,p.=,ENST00000372874,NM_000022.2;ADA,synonymous_variant,p.=,ENST00000537820,;PKIG,downstream_gene_variant,,ENST00000372887,;ADA,non_coding_transcript_exon_variant,,ENST00000492931,;ADA,non_coding_transcript_exon_variant,,ENST00000536076,;ADA,upstream_gene_variant,,ENST00000464097,;ADA,synonymous_variant,p.=,ENST00000536532,;ADA,synonymous_variant,p.=,ENST00000539235,;ADA,non_coding_transcript_exon_variant,,ENST00000545776,; T ENST00000372874 Transcript synonymous_variant 288/1539 153/1092 51/363 G ggC/ggA COSM1495078 1 -1 ADA HGNC HGNC:186 protein_coding YES CCDS13335.1 ENSP00000361965 P00813 A0A0S2Z381 UPI000000D982 NM_000022.2 3/12 HAMAP:MF_00540,hmmpanther:PTHR11409:SF43,hmmpanther:PTHR11409,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR01430,Pfam_domain:PF00962,Superfamily_domains:SSF51556 1 LOW 1 SNV 1 1 1 PASS rs1018302697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 44629112 44629112 G T 1 0 0 0 0 0 0 0 1 274 1306 46 2 2 ADA 20 44629112 Silent SNP G C3L-00368_T 6406608 44629112 19815055 97 6558 CASS4 0 . GRCh38 20 56452755 56452755 + Missense_Mutation SNP T T G novel C3L-00368_T C3L-00368_N T T c.1579T>G p.Tyr527Asp p.Y527D ENST00000360314 6/7 224 178 46 235 235 0 strelka-varscan-mutect CASS4,missense_variant,p.Tyr527Asp,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,intron_variant,,ENST00000434344,NM_001164115.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; G ENST00000360314 Transcript missense_variant 1804/2619 1579/2361 527/786 Y/D Tac/Gac 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0) 6/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654,Pfam_domain:PF08824 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 15 56452755 56452755 T G 1 0 0 0 0 1 0 0 0 2382 1522 53 5 5 CASS4 20 56452755 Missense_Mutation SNP T C3L-00368_T 11823643 56452755 7991412 98 6559 NEFH 0 . GRCh38 22 29480945 29480945 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.683G>T p.Gly228Val p.G228V ENST00000310624 1/4 308 256 52 377 377 0 strelka-varscan-mutect NEFH,missense_variant,p.Gly228Val,ENST00000310624,NM_021076.3;AC000035.3,non_coding_transcript_exon_variant,,ENST00000634116,;RFPL1S,upstream_gene_variant,,ENST00000461286,;RFPL1S,upstream_gene_variant,,ENST00000419368,; T ENST00000310624 Transcript missense_variant 716/3783 683/3063 228/1020 G/V gGc/gTc 1 1 NEFH HGNC HGNC:7737 protein_coding YES CCDS13858.1 ENSP00000311997 P12036 UPI00001AEF71 NM_021076.3 tolerated(0.09) 1/4 hmmpanther:PTHR23214,hmmpanther:PTHR23214:SF1,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs1359147057 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 15 29480945 29480945 G T 1 0 0 0 0 1 0 0 0 10342 1203 42 2 2 NEFH 22 29480945 Missense_Mutation SNP G C3L-00368_T 29480945 21337523 99 6560 PARVB 0 . GRCh38 22 44024438 44024438 + Silent SNP G G A novel C3L-00368_T C3L-00368_N G G c.99G>A p.= p.R33R ENST00000338758 1/13 52 47 5 42 42 0 strelka-mutect PARVB,synonymous_variant,p.=,ENST00000338758,NM_013327.4;PARVB,intron_variant,,ENST00000406477,NM_001003828.2;PARVB,upstream_gene_variant,,ENST00000619710,NM_001243386.1;PARVB,non_coding_transcript_exon_variant,,ENST00000402876,; A ENST00000338758 Transcript synonymous_variant 162/5429 99/1095 33/364 R cgG/cgA 1 1 PARVB HGNC HGNC:14653 protein_coding CCDS14056.1 ENSP00000342492 Q9HBI1 UPI000013132A NM_013327.4 1/13 PIRSF_domain:PIRSF039131,hmmpanther:PTHR12114,hmmpanther:PTHR12114:SF7,Superfamily_domains:SSF47576 LOW SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 15 44024438 44024438 G A 1 0 0 0 0 0 0 0 1 11550 1161 41 3 3 PARVB 22 44024438 Silent SNP G C3L-00368_T 14543493 44024438 6794030 100 6561 CFAP47 0 . GRCh38 X 35948314 35948314 + Missense_Mutation SNP G G T novel C3L-00368_T C3L-00368_N G G c.518G>T p.Gly173Val p.G173V ENST00000297866 4/16 45 35 10 83 83 0 strelka-varscan-mutect CFAP47,missense_variant,p.Gly173Val,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Gly173Val,ENST00000297866,NM_152632.3;CFAP47,missense_variant,p.Gly173Val,ENST00000493930,; T ENST00000297866 Transcript missense_variant,splice_region_variant 584/3608 518/2931 173/976 G/V gGc/gTc 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 deleterious(0) 4/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 15 35948314 35948314 G T 1 0 0 0 0 1 0 0 0 3022 1217 42 2 2 CFAP47 23 35948314 Missense_Mutation SNP G C3L-00368_T 35948314 120092581 101 6562 OR13H1 0 . GRCh38 X 131544385 131544385 + Silent SNP C C T C3L-00368_T C3L-00368_N C C c.312C>T p.= p.S104S ENST00000338616 1/1 156 125 31 196 196 0 strelka-varscan-mutect OR13H1,synonymous_variant,p.=,ENST00000338616,NM_001004486.1;IGSF1,intron_variant,,ENST00000370904,; T ENST00000338616 Transcript synonymous_variant 312/927 312/927 104/308 S tcC/tcT COSM4106690 1 1 OR13H1 HGNC HGNC:14755 protein_coding YES CCDS35396.1 ENSP00000340748 Q8NG92 A0A126GW70 UPI000003CAC9 NM_001004486.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF76,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 15 131544385 131544385 C T 1 0 0 0 0 0 0 0 1 11019 668 24 3 3 OR13H1 23 131544385 Silent SNP C C3L-00368_T 95596071 131544385 24496510 102 6563 MIB2 0 . GRCh38 1 1629648 1629648 + Missense_Mutation SNP G G A novel C3L-00412_T C3L-00412_N G G c.2918G>A p.Arg973His p.R973H ENST00000505820 19/20 56 50 6 84 84 0 strelka-varscan-mutect MIB2,missense_variant,p.Arg969His,ENST00000520777,NM_001170686.1;MIB2,missense_variant,p.Arg872His,ENST00000504599,;MIB2,missense_variant,p.Arg973His,ENST00000505820,NM_080875.2;MIB2,missense_variant,p.Arg959His,ENST00000355826,NM_001170687.1;MIB2,missense_variant,p.Arg908His,ENST00000518681,NM_001170688.1;MIB2,missense_variant,p.Arg822His,ENST00000378708,;MIB2,missense_variant,p.Arg732His,ENST00000514234,;MIB2,missense_variant,p.Arg235His,ENST00000483015,;MIB2,synonymous_variant,p.=,ENST00000378712,NM_001170689.1;MMP23B,upstream_gene_variant,,ENST00000356026,NM_006983.1;MMP23B,upstream_gene_variant,,ENST00000378675,;MMP23B,upstream_gene_variant,,ENST00000479814,;MIB2,downstream_gene_variant,,ENST00000510793,;MMP23B,upstream_gene_variant,,ENST00000503792,;MMP23B,upstream_gene_variant,,ENST00000435358,;MIB2,downstream_gene_variant,,ENST00000503789,;MMP23B,upstream_gene_variant,,ENST00000472264,;MIB2,downstream_gene_variant,,ENST00000512004,;MIB2,3_prime_UTR_variant,,ENST00000487053,;MIB2,3_prime_UTR_variant,,ENST00000489635,;MIB2,3_prime_UTR_variant,,ENST00000506488,;MIB2,non_coding_transcript_exon_variant,,ENST00000479659,;MIB2,non_coding_transcript_exon_variant,,ENST00000511502,;MIB2,non_coding_transcript_exon_variant,,ENST00000511910,;MIB2,non_coding_transcript_exon_variant,,ENST00000470373,;MIB2,downstream_gene_variant,,ENST00000507229,;MMP23B,upstream_gene_variant,,ENST00000512731,;MIB2,downstream_gene_variant,,ENST00000473511,;MIB2,downstream_gene_variant,,ENST00000464570,;MIB2,downstream_gene_variant,,ENST00000505370,;MIB2,downstream_gene_variant,,ENST00000502470,;MIB2,downstream_gene_variant,,ENST00000467597,;MMP23B,upstream_gene_variant,,ENST00000489782,;MIB2,downstream_gene_variant,,ENST00000514363,;MIB2,downstream_gene_variant,,ENST00000508148,;MIB2,downstream_gene_variant,,ENST00000486072,;MMP23B,upstream_gene_variant,,ENST00000490017,;MMP23B,upstream_gene_variant,,ENST00000486400,; A ENST00000505820 Transcript missense_variant 2935/3305 2918/3213 973/1070 R/H cGc/cAc 1 1 MIB2 HGNC HGNC:30577 protein_coding YES CCDS41224.2 ENSP00000426103 Q96AX9 UPI0001C0B37A NM_080875.2 tolerated(0.37) 19/20 PROSITE_profiles:PS50089,hmmpanther:PTHR24202:SF4,hmmpanther:PTHR24202,Pfam_domain:PF13920,SMART_domains:SM00184 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -13.91898 0.9999648 1 1 1 0 A 3 1 16 1629648 1629648 G A 1 0 0 0 0 1 0 0 0 9524 1087 38 1 1 MIB2 1 1629648 Missense_Mutation SNP G C3L-00412_T 1629648 247326774 1 6564 25 2 MIB2 0 . GRCh38 1 1629650 1629650 + Missense_Mutation SNP A A T novel C3L-00412_T C3L-00412_N A A c.2920A>T p.Arg974Trp p.R974W ENST00000505820 19/20 55 49 6 84 84 0 strelka-varscan-mutect MIB2,missense_variant,p.Arg970Trp,ENST00000520777,NM_001170686.1;MIB2,missense_variant,p.Arg873Trp,ENST00000504599,;MIB2,missense_variant,p.Arg974Trp,ENST00000505820,NM_080875.2;MIB2,missense_variant,p.Arg960Trp,ENST00000355826,NM_001170687.1;MIB2,missense_variant,p.Arg909Trp,ENST00000518681,NM_001170688.1;MIB2,missense_variant,p.Arg823Trp,ENST00000378708,;MIB2,missense_variant,p.Gln733Leu,ENST00000378712,NM_001170689.1;MIB2,missense_variant,p.Arg733Trp,ENST00000514234,;MIB2,missense_variant,p.Arg236Trp,ENST00000483015,;MMP23B,upstream_gene_variant,,ENST00000356026,NM_006983.1;MMP23B,upstream_gene_variant,,ENST00000378675,;MMP23B,upstream_gene_variant,,ENST00000479814,;MIB2,downstream_gene_variant,,ENST00000510793,;MMP23B,upstream_gene_variant,,ENST00000503792,;MMP23B,upstream_gene_variant,,ENST00000435358,;MIB2,downstream_gene_variant,,ENST00000503789,;MMP23B,upstream_gene_variant,,ENST00000472264,;MIB2,downstream_gene_variant,,ENST00000512004,;MIB2,3_prime_UTR_variant,,ENST00000487053,;MIB2,3_prime_UTR_variant,,ENST00000489635,;MIB2,3_prime_UTR_variant,,ENST00000506488,;MIB2,non_coding_transcript_exon_variant,,ENST00000479659,;MIB2,non_coding_transcript_exon_variant,,ENST00000511502,;MIB2,non_coding_transcript_exon_variant,,ENST00000511910,;MIB2,non_coding_transcript_exon_variant,,ENST00000470373,;MIB2,downstream_gene_variant,,ENST00000507229,;MMP23B,upstream_gene_variant,,ENST00000512731,;MIB2,downstream_gene_variant,,ENST00000473511,;MIB2,downstream_gene_variant,,ENST00000464570,;MIB2,downstream_gene_variant,,ENST00000505370,;MIB2,downstream_gene_variant,,ENST00000502470,;MIB2,downstream_gene_variant,,ENST00000467597,;MMP23B,upstream_gene_variant,,ENST00000489782,;MIB2,downstream_gene_variant,,ENST00000514363,;MIB2,downstream_gene_variant,,ENST00000508148,;MIB2,downstream_gene_variant,,ENST00000486072,;MMP23B,upstream_gene_variant,,ENST00000490017,;MMP23B,upstream_gene_variant,,ENST00000486400,; T ENST00000505820 Transcript missense_variant 2937/3305 2920/3213 974/1070 R/W Agg/Tgg 1 1 MIB2 HGNC HGNC:30577 protein_coding YES CCDS41224.2 ENSP00000426103 Q96AX9 UPI0001C0B37A NM_080875.2 deleterious(0) 19/20 PROSITE_profiles:PS50089,hmmpanther:PTHR24202:SF4,hmmpanther:PTHR24202,Pfam_domain:PF13920,SMART_domains:SM00184 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.49839 1 1 1 1 0 T 3 4 16 1629650 1629650 A T 1 0 0 0 0 1 0 0 0 9524 188 7 4 4 MIB2 1 1629650 Missense_Mutation SNP A C3L-00412_T 2 1629650 247326772 2 6565 25 2 CROCC 0 . GRCh38 1 16929929 16929929 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.435G>T p.= p.R145R ENST00000375541 4/37 112 105 7 121 120 1 strelka-varscan-mutect CROCC,synonymous_variant,p.=,ENST00000375541,NM_014675.4;CROCC,synonymous_variant,p.=,ENST00000467938,;CROCC,intron_variant,,ENST00000445545,;CROCC,intron_variant,,ENST00000466256,;CROCC,upstream_gene_variant,,ENST00000492631,; T ENST00000375541 Transcript synonymous_variant 504/6656 435/6054 145/2017 R cgG/cgT 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 4/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 16929929 16929929 G T 1 0 0 0 0 0 0 0 1 3694 1161 41 2 2 CROCC 1 16929929 Silent SNP G C3L-00412_T 15300279 16929929 232026493 3 6566 TRIM63 0 . GRCh38 1 26058416 26058416 + Missense_Mutation SNP C C G rs61749355 C3L-00412_T C3L-00412_N C C c.805G>C p.Glu269Gln p.E269Q ENST00000374272 5/9 190 176 14 188 188 0 strelka-varscan-mutect TRIM63,missense_variant,p.Glu269Gln,ENST00000374272,NM_032588.3;TRIM63,downstream_gene_variant,,ENST00000483052,; G ENST00000374272 Transcript missense_variant 944/1770 805/1062 269/353 E/Q Gag/Cag rs61749355 1 -1 TRIM63 HGNC HGNC:16007 protein_coding YES CCDS273.1 ENSP00000363390 Q969Q1 UPI00000437F6 NM_032588.3 tolerated(0.08) 5/9 PROSITE_profiles:PS51262,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF279 22821932 MODERATE 1 SNV 1 1 PASS rs61749355 . 0 207 0 0 0 0 0 2 -8.020022 0 0 1 0 0 G 3 3 16 26058416 26058416 C G 1 0 0 0 0 1 0 0 0 17030 893 31 4 4 TRIM63 1 26058416 Missense_Mutation SNP C C3L-00412_T 9128487 26058416 222898006 4 6567 C8B 0 . GRCh38 1 56931852 56931852 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1579G>T p.Val527Phe p.V527F ENST00000371237 11/12 358 322 36 422 422 0 strelka-varscan-mutect C8B,missense_variant,p.Val475Phe,ENST00000543257,NM_001278543.1;C8B,missense_variant,p.Val465Phe,ENST00000535057,NM_001278544.1;C8B,missense_variant,p.Val527Phe,ENST00000371237,NM_000066.3;C8B,non_coding_transcript_exon_variant,,ENST00000465658,; A ENST00000371237 Transcript missense_variant 1646/2037 1579/1776 527/591 V/F Gtt/Ttt 1 -1 C8B HGNC HGNC:1353 protein_coding YES CCDS30730.1 ENSP00000360281 P07358 UPI000013C9B2 NM_000066.3 tolerated(0.41) 11/12 hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 56931852 56931852 C A 1 0 0 0 0 1 0 0 0 2151 478 17 2 2 C8B 1 56931852 Missense_Mutation SNP C C3L-00412_T 30873436 56931852 192024570 5 6568 CLCA1 0 . GRCh38 1 86482296 86482296 + Nonsense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.649G>T p.Gly217Ter p.G217* ENST00000234701 6/15 123 111 12 149 148 1 strelka-mutect CLCA1,stop_gained,p.Gly217Ter,ENST00000234701,;CLCA1,stop_gained,p.Gly217Ter,ENST00000394711,NM_001285.3; T ENST00000234701 Transcript stop_gained 1000/3310 649/2745 217/914 G/* Gga/Tga 1 1 CLCA1 HGNC HGNC:2015 protein_coding YES CCDS709.1 ENSP00000234701 A8K7I4 UPI00001AE689 6/15 hmmpanther:PTHR10579:SF52,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 16 86482296 86482296 G T 1 0 0 0 0 0 1 0 0 3221 1001 35 2 2 CLCA1 1 86482296 Nonsense_Mutation SNP G C3L-00412_T 29550444 86482296 162474126 6 6569 HFM1 0 . GRCh38 1 91385711 91385711 + Silent SNP A A G novel C3L-00412_T C3L-00412_N A A c.618T>C p.= p.Y206Y ENST00000370425 5/39 189 172 17 209 209 0 strelka-varscan-mutect HFM1,synonymous_variant,p.=,ENST00000370425,NM_001017975.4;HFM1,synonymous_variant,p.=,ENST00000427444,;HFM1,synonymous_variant,p.=,ENST00000448819,;HFM1,non_coding_transcript_exon_variant,,ENST00000481900,;HFM1,non_coding_transcript_exon_variant,,ENST00000488023,; G ENST00000370425 Transcript synonymous_variant 717/4931 618/4308 206/1435 Y taT/taC 1 -1 HFM1 HGNC HGNC:20193 protein_coding YES CCDS30769.2 ENSP00000359454 A2PYH4 UPI0000F51F79 NM_001017975.4 5/39 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 91385711 91385711 A G 1 0 0 0 0 0 0 0 1 6967 456 16 5 5 HFM1 1 91385711 Silent SNP A C3L-00412_T 4903415 91385711 157570711 7 6570 COL11A1 0 . GRCh38 1 102962694 102962694 + Nonsense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.2983G>T p.Glu995Ter p.E995* ENST00000370096 39/67 255 242 13 270 269 1 strelka-varscan-mutect COL11A1,stop_gained,p.Glu1007Ter,ENST00000358392,NM_080629.2;COL11A1,stop_gained,p.Glu995Ter,ENST00000370096,NM_001854.3;COL11A1,stop_gained,p.Glu956Ter,ENST00000353414,NM_001190709.1;COL11A1,stop_gained,p.Glu879Ter,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,;COL11A1,upstream_gene_variant,,ENST00000465209,; A ENST00000370096 Transcript stop_gained 3296/7286 2983/5421 995/1806 E/* Gag/Tag 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 39/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 16 102962694 102962694 C A 1 0 0 0 0 0 1 0 0 3455 835 29 2 2 COL11A1 1 102962694 Nonsense_Mutation SNP C C3L-00412_T 11576983 102962694 145993728 8 6571 SMG5 0 . GRCh38 1 156263476 156263476 + Missense_Mutation SNP C C G novel C3L-00412_T C3L-00412_N C C c.1950G>C p.Met650Ile p.M650I ENST00000361813 13/22 216 200 16 203 203 0 strelka-varscan-mutect SMG5,missense_variant,p.Met650Ile,ENST00000361813,NM_001323617.1,NM_001323616.1,NM_015327.2;SMG5,downstream_gene_variant,,ENST00000489907,; G ENST00000361813 Transcript missense_variant 2095/4559 1950/3051 650/1016 M/I atG/atC 1 -1 SMG5 HGNC HGNC:24644 protein_coding YES CCDS1137.1 ENSP00000355261 Q9UPR3 UPI0000050C24 NM_001323617.1,NM_001323616.1,NM_015327.2 deleterious(0.04) 13/22 hmmpanther:PTHR15696:SF8,hmmpanther:PTHR15696 MODERATE 1 SNV 1 1 PASS rs1436332107 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 156263476 156263476 C G 1 0 0 0 0 1 0 0 0 15090 594 21 4 4 SMG5 1 156263476 Missense_Mutation SNP C C3L-00412_T 53300782 156263476 92692946 9 6572 OR6N1 0 . GRCh38 1 158766197 158766197 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.486G>T p.Leu162Phe p.L162F ENST00000335094 1/1 186 149 37 205 204 1 strelka-varscan-mutect OR6N1,missense_variant,p.Leu162Phe,ENST00000335094,NM_001005185.1; A ENST00000335094 Transcript missense_variant 486/939 486/939 162/312 L/F ttG/ttT 1 -1 OR6N1 HGNC HGNC:15034 protein_coding YES CCDS30905.1 ENSP00000335535 Q8NGY5 UPI000003FE15 NM_001005185.1 tolerated(0.18) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF123,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs933466925 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 158766197 158766197 C A 1 0 0 0 0 1 0 0 0 11275 825 29 2 2 OR6N1 1 158766197 Missense_Mutation SNP C C3L-00412_T 2502721 158766197 90190225 10 6573 ACKR1 0 . GRCh38 1 159205814 159205814 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.381C>A p.Ser127Arg p.S127R ENST00000368121 1/1 83 78 5 112 112 0 strelka-varscan-mutect ACKR1,missense_variant,p.Ser125Arg,ENST00000537147,;ACKR1,missense_variant,p.Ser125Arg,ENST00000368122,NM_002036.3;ACKR1,missense_variant,p.Ser127Arg,ENST00000368121,NM_001122951.2;ACKR1,missense_variant,p.Ser127Arg,ENST00000435307,;CADM3,downstream_gene_variant,,ENST00000368125,NM_001127173.1;CADM3,downstream_gene_variant,,ENST00000368124,NM_021189.3;CADM3-AS1,intron_variant,,ENST00000609696,;CADM3-AS1,upstream_gene_variant,,ENST00000415675,; A ENST00000368121 Transcript missense_variant 556/1240 381/1017 127/338 S/R agC/agA 1 1 ACKR1 HGNC HGNC:4035 protein_coding YES CCDS44252.1 ENSP00000357103 Q16570 Q5Y7A1 UPI000013E1B0 NM_001122951.2 tolerated(0.35) 1/1 hmmpanther:PTHR14181 MODERATE SNV 1 PASS rs1046534263 . 0 207 3 0 0 0 0 0 -11.26509 1 1 1 1 0 A 3 1 16 159205814 159205814 C A 1 0 0 0 0 1 0 0 0 181 796 28 2 2 ACKR1 1 159205814 Missense_Mutation SNP C C3L-00412_T 439617 159205814 89750608 11 6574 BPNT1 0 . GRCh38 1 220079813 220079813 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.34G>T p.Val12Leu p.V12L ENST00000469520 3/10 192 178 14 154 154 0 strelka-varscan-mutect BPNT1,missense_variant,p.Val12Leu,ENST00000469520,;BPNT1,missense_variant,p.Val12Leu,ENST00000322067,NM_006085.5;BPNT1,missense_variant,p.Val12Leu,ENST00000414869,NM_001286150.1;BPNT1,missense_variant,p.Val12Leu,ENST00000354807,;BPNT1,missense_variant,p.Val12Leu,ENST00000463953,;BPNT1,missense_variant,p.Val12Leu,ENST00000498237,;BPNT1,missense_variant,p.Val12Leu,ENST00000498791,;BPNT1,intron_variant,,ENST00000544404,NM_001286151.1,NM_001286149.1;BPNT1,intron_variant,,ENST00000480959,;BPNT1,intron_variant,,ENST00000482136,; A ENST00000469520 Transcript missense_variant 484/2737 34/927 12/308 V/L Gta/Tta 1 -1 BPNT1 HGNC HGNC:1096 protein_coding YES CCDS41469.1 ENSP00000446828 O95861 V9HWF9 UPI000007212C tolerated(0.42) 3/10 hmmpanther:PTHR20854,hmmpanther:PTHR20854:SF5,Gene3D:3.30.540.10,Superfamily_domains:SSF56655 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 220079813 220079813 C A 1 0 0 0 0 1 0 0 0 1663 507 18 2 2 BPNT1 1 220079813 Missense_Mutation SNP C C3L-00412_T 60873999 220079813 28876609 12 6575 C1orf101 0 . GRCh38 1 244552326 244552326 + Missense_Mutation SNP T T C novel C3L-00412_T C3L-00412_N T T c.541T>C p.Trp181Arg p.W181R ENST00000366534 9/22 50 43 7 69 69 0 strelka-varscan-mutect C1orf101,missense_variant,p.Trp181Arg,ENST00000366534,NM_001130957.1;C1orf101,missense_variant,p.Trp30Arg,ENST00000366531,NM_001242340.1;C1orf101,missense_variant,p.Trp181Arg,ENST00000366533,NM_173807.4;C1orf101,missense_variant,p.Trp101Arg,ENST00000428042,;C1orf101,non_coding_transcript_exon_variant,,ENST00000464170,;C1orf101,non_coding_transcript_exon_variant,,ENST00000460986,;C1orf101,non_coding_transcript_exon_variant,,ENST00000478554,;C1orf101,intron_variant,,ENST00000473875,; C ENST00000366534 Transcript missense_variant 595/3333 541/2856 181/951 W/R Tgg/Cgg 1 1 C1orf101 HGNC HGNC:28491 protein_coding YES CCDS44340.1 ENSP00000355492 Q5SY80 UPI00004701CD NM_001130957.1 deleterious(0) 9/22 hmmpanther:PTHR33722:SF3,hmmpanther:PTHR33722 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -17.23307 1 1 1 1 0 C 3 2 16 244552326 244552326 T C 1 0 0 0 0 1 0 0 0 1954 1594 55 5 5 C1orf101 1 244552326 Missense_Mutation SNP T C3L-00412_T 24472513 244552326 4404096 13 6576 SOX11 0 . GRCh38 2 5693099 5693099 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.378G>T p.Met126Ile p.M126I ENST00000322002 1/1 268 248 20 245 244 1 strelka-varscan-mutect SOX11,missense_variant,p.Met126Ile,ENST00000322002,NM_003108.3;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC010729.1,upstream_gene_variant,,ENST00000455579,;LINC01248,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,; T ENST00000322002 Transcript missense_variant 433/8719 378/1326 126/441 M/I atG/atT 1 1 SOX11 HGNC HGNC:11191 protein_coding YES CCDS1654.1 ENSP00000322568 P35716 UPI00001362AD NM_003108.3 tolerated(0.23) 1/1 Gene3D:1.10.30.10,PIRSF_domain:PIRSF038098,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF113,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs1182148169 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 5693099 5693099 G T 1 0 0 0 0 1 0 0 0 15268 1348 47 2 2 SOX11 2 5693099 Missense_Mutation SNP G C3L-00412_T 5693099 236500430 14 6577 ASTL 0 . GRCh38 2 96124084 96124084 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.1062C>A p.= p.L354L ENST00000342380 9/9 78 72 6 131 130 1 strelka-varscan-mutect ASTL,synonymous_variant,p.=,ENST00000342380,NM_001002036.3; T ENST00000342380 Transcript synonymous_variant 1062/1296 1062/1296 354/431 L ctC/ctA 1 -1 ASTL HGNC HGNC:31704 protein_coding YES CCDS33249.1 ENSP00000343674 Q6HA08 UPI0000161978 NM_001002036.3 9/9 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 96124084 96124084 G T 1 0 0 0 0 0 0 0 1 1210 1277 45 2 2 ASTL 2 96124084 Silent SNP G C3L-00412_T 90430985 96124084 146069445 15 6578 GPD2 0 . GRCh38 2 156557419 156557419 + Silent SNP G G T rs756980310 C3L-00412_T C3L-00412_N G G c.1002G>T p.= p.A334A ENST00000310454 9/17 295 276 19 254 254 0 strelka-varscan-mutect GPD2,synonymous_variant,p.=,ENST00000310454,NM_001083112.2;GPD2,synonymous_variant,p.=,ENST00000409125,;GPD2,synonymous_variant,p.=,ENST00000438166,NM_000408.4;GPD2,synonymous_variant,p.=,ENST00000409674,;GPD2,synonymous_variant,p.=,ENST00000540309,;GPD2,synonymous_variant,p.=,ENST00000409861,; T ENST00000310454 Transcript synonymous_variant 1374/6041 1002/2184 334/727 A gcG/gcT rs756980310 1 1 GPD2 HGNC HGNC:4456 protein_coding YES CCDS2202.1 ENSP00000308610 P43304 UPI000013F012 NM_001083112.2 9/17 Gene3D:3.50.50.60,Pfam_domain:PF01266,hmmpanther:PTHR11985,hmmpanther:PTHR11985:SF15,Superfamily_domains:SSF54373 LOW 1 SNV 1 1 PASS rs756980310 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 156557419 156557419 G T 1 0 0 0 0 0 0 0 1 6508 1045 37 1 1 GPD2 2 156557419 Silent SNP G C3L-00412_T 60433335 156557419 85636110 16 6579 XIRP2 0 . GRCh38 2 167243129 167243129 + Missense_Mutation SNP G G T C3L-00412_T C3L-00412_N G G c.1737G>T p.Trp579Cys p.W579C ENST00000409195 9/11 139 130 9 159 159 0 strelka-varscan-mutect XIRP2,missense_variant,p.Trp579Cys,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Trp357Cys,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Trp404Cys,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript missense_variant 1826/12675 1737/10650 579/3549 W/C tgG/tgT COSM3569433 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 Pfam_domain:PF08043,PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 167243129 167243129 G T 1 0 0 0 0 1 0 0 0 17989 1183 41 2 2 XIRP2 2 167243129 Missense_Mutation SNP G C3L-00412_T 10685710 167243129 74950400 17 6580 GORASP2 0 . GRCh38 2 170966073 170966073 + Silent SNP A A T rs762866384 C3L-00412_T C3L-00412_N A A c.1302A>T p.= p.P434P ENST00000234160 10/10 350 326 24 323 323 0 strelka-varscan-mutect GORASP2,synonymous_variant,p.=,ENST00000234160,NM_001201428.1,NM_015530.4;GORASP2,downstream_gene_variant,,ENST00000493692,;GORASP2,3_prime_UTR_variant,,ENST00000442798,;GORASP2,non_coding_transcript_exon_variant,,ENST00000486498,; T ENST00000234160 Transcript synonymous_variant 2117/3173 1302/1359 434/452 P ccA/ccT rs762866384 1 1 GORASP2 HGNC HGNC:17500 protein_coding YES CCDS33325.1 ENSP00000234160 Q9H8Y8 UPI000007373B NM_001201428.1,NM_015530.4 10/10 hmmpanther:PTHR12893,hmmpanther:PTHR12893:SF1 LOW 1 SNV 1 1 PASS rs762866384 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 170966073 170966073 A T 1 0 0 0 0 0 0 0 1 6470 175 7 4 4 GORASP2 2 170966073 Silent SNP A C3L-00412_T 3722944 170966073 71227456 18 6581 FSIP2 0 . GRCh38 2 185833109 185833109 + Silent SNP C C A novel C3L-00412_T C3L-00412_N C C c.20874C>A p.= p.V6958V ENST00000343098 23/23 259 234 25 236 234 2 strelka-varscan-mutect FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2,3_prime_UTR_variant,,ENST00000611759,;FSIP2,3_prime_UTR_variant,,ENST00000415915,; A ENST00000343098 Transcript synonymous_variant 20874/21054 20874/20991 6958/6996 V gtC/gtA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 23/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 185833109 185833109 C A 1 0 0 0 0 0 0 0 1 5949 900 32 2 2 FSIP2 2 185833109 Silent SNP C C3L-00412_T 14867036 185833109 56360420 19 6582 COL5A2 0 . GRCh38 2 189078524 189078524 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1051G>T p.Gly351Cys p.G351C ENST00000374866 16/54 264 247 17 287 287 0 strelka-varscan-mutect COL5A2,missense_variant,p.Gly351Cys,ENST00000374866,NM_000393.3;COL5A2,intron_variant,,ENST00000618828,; A ENST00000374866 Transcript missense_variant 1326/6949 1051/4500 351/1499 G/C Ggt/Tgt 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 deleterious(0) 16/54 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 189078524 189078524 C A 1 0 0 0 0 1 0 0 0 3486 623 22 2 2 COL5A2 2 189078524 Missense_Mutation SNP C C3L-00412_T 3245415 189078524 53115005 20 6583 UNC80 0 . GRCh38 2 209913931 209913931 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.4822G>T p.Gly1608Trp p.G1608W ENST00000439458 30/64 75 69 6 80 80 0 strelka-varscan-mutect UNC80,missense_variant,p.Gly1608Trp,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Gly1603Trp,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; T ENST00000439458 Transcript missense_variant 4902/13562 4822/9777 1608/3258 G/W Ggg/Tgg 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0) 30/64 Low_complexity_(Seg):seg,hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -13.2306 0.9999998 1 1 1 0 T 3 4 16 209913931 209913931 G T 1 0 0 0 0 1 0 0 0 17521 1000 35 2 2 UNC80 2 209913931 Missense_Mutation SNP G C3L-00412_T 20835407 209913931 32279598 21 6584 MKRN2 0 . GRCh38 3 12574828 12574828 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.679G>C p.Ala227Pro p.A227P ENST00000170447 5/8 228 216 12 209 209 0 strelka-mutect MKRN2,missense_variant,p.Ala227Pro,ENST00000170447,NM_014160.4;MKRN2,missense_variant,p.Ala225Pro,ENST00000448482,;MKRN2,missense_variant,p.Ala184Pro,ENST00000411987,NM_001271707.1;Metazoa_SRP,downstream_gene_variant,,ENST00000621376,; C ENST00000170447 Transcript missense_variant 816/2848 679/1251 227/416 A/P Gcc/Ccc 1 1 MKRN2 HGNC HGNC:7113 protein_coding YES CCDS33702.1 ENSP00000170447 Q9H000 UPI000007116E NM_014160.4 deleterious(0.01) 5/8 hmmpanther:PTHR11224:SF17,hmmpanther:PTHR11224 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 12574828 12574828 G C 1 0 0 0 0 1 0 0 0 9574 1203 42 4 4 MKRN2 3 12574828 Missense_Mutation SNP G C3L-00412_T 12574828 185720731 22 6585 UGT2B7 0 . GRCh38 4 69098548 69098548 + Frame_Shift_Del DEL A A - rs778968369 C3L-00412_T C3L-00412_N A A c.730delA p.Thr244LeufsTer73 p.T244Lfs*73 ENST00000305231 2/6 137 129 8 147 147 0 varindel-pindel UGT2B7,frameshift_variant,p.Thr244LeufsTer73,ENST00000305231,NM_001074.2;UGT2B7,frameshift_variant,p.Thr244LeufsTer73,ENST00000508661,;UGT2B7,frameshift_variant,p.Thr244LeufsTer73,ENST00000622664,;UGT2B7,5_prime_UTR_variant,,ENST00000502942,;UGT2B7,non_coding_transcript_exon_variant,,ENST00000509763,; - ENST00000305231 Transcript frameshift_variant 776/1887 730/1590 244/529 T/X Act/ct rs778968369 1 1 UGT2B7 HGNC HGNC:12554 protein_coding YES CCDS3526.1 ENSP00000304811 P16662 UPI00000015EC NM_001074.2 2/6 hmmpanther:PTHR11926:SF382,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 16 69098548 69098548 A - 1 0 1 0 1 0 0 0 0 17486 159 6 0 0 UGT2B7 4 69098548 Frame_Shift_Del DEL A C3L-00412_T 69098548 121116007 23 6586 PDHA2 0 . GRCh38 4 95841001 95841001 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.851C>A p.Thr284Asn p.T284N ENST00000295266 1/1 234 216 18 297 297 0 strelka-varscan-mutect PDHA2,missense_variant,p.Thr284Asn,ENST00000295266,NM_005390.4; A ENST00000295266 Transcript missense_variant 983/1456 851/1167 284/388 T/N aCc/aAc 1 1 PDHA2 HGNC HGNC:8807 protein_coding YES CCDS3644.1 ENSP00000295266 P29803 UPI0000130C31 NM_005390.4 deleterious(0) 1/1 hmmpanther:PTHR11516:SF27,hmmpanther:PTHR11516,Pfam_domain:PF00676,TIGRFAM_domain:TIGR03182,Gene3D:3.40.50.970,Superfamily_domains:SSF52518 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 95841001 95841001 C A 1 0 0 0 0 1 0 0 0 11753 507 18 2 2 PDHA2 4 95841001 Missense_Mutation SNP C C3L-00412_T 26742453 95841001 94373554 24 6587 26 2 PDHA2 0 . GRCh38 4 95841002 95841002 + Silent SNP C C A novel C3L-00412_T C3L-00412_N C C c.852C>A p.= p.T284T ENST00000295266 1/1 236 219 17 300 299 1 strelka-varscan-mutect PDHA2,synonymous_variant,p.=,ENST00000295266,NM_005390.4; A ENST00000295266 Transcript synonymous_variant 984/1456 852/1167 284/388 T acC/acA 1 1 PDHA2 HGNC HGNC:8807 protein_coding YES CCDS3644.1 ENSP00000295266 P29803 UPI0000130C31 NM_005390.4 1/1 hmmpanther:PTHR11516:SF27,hmmpanther:PTHR11516,Pfam_domain:PF00676,TIGRFAM_domain:TIGR03182,Gene3D:3.40.50.970,Superfamily_domains:SSF52518 LOW 1 SNV 1 PASS rs1041605730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 95841002 95841002 C A 1 0 0 0 0 0 0 0 1 11753 668 24 2 2 PDHA2 4 95841002 Silent SNP C C3L-00412_T 1 95841002 94373553 25 6588 26 2 SYNPO2 0 . GRCh38 4 119027373 119027373 + Missense_Mutation SNP A A T novel C3L-00412_T C3L-00412_N A A c.1004A>T p.Gln335Leu p.Q335L ENST00000307142 3/5 87 81 6 105 105 0 strelka-varscan-mutect SYNPO2,missense_variant,p.Gln335Leu,ENST00000429713,NM_001128933.2;SYNPO2,missense_variant,p.Gln335Leu,ENST00000307142,NM_133477.2;SYNPO2,missense_variant,p.Gln287Leu,ENST00000504178,;SYNPO2,missense_variant,p.Gln304Leu,ENST00000610556,NM_001286754.1;SYNPO2,missense_variant,p.Gln335Leu,ENST00000434046,NM_001128934.2;SYNPO2,intron_variant,,ENST00000448416,NM_001286755.1; T ENST00000307142 Transcript missense_variant 1200/7295 1004/3786 335/1261 Q/L cAg/cTg 1 1 SYNPO2 HGNC HGNC:17732 protein_coding YES CCDS34054.1 ENSP00000306015 Q9UMS6 UPI00001D75EB NM_133477.2 deleterious(0.03) 3/5 MODERATE 1 SNV 1 1 PASS rs1341900721 . 0 206 3 0 0 0 0 0 -13.07321 1 1 1 1 0 T 3 4 16 119027373 119027373 A T 1 0 0 0 0 1 0 0 0 15851 188 7 4 4 SYNPO2 4 119027373 Missense_Mutation SNP A C3L-00412_T 23186371 119027373 71187182 26 6589 INPP4B 0 . GRCh38 4 142124619 142124619 + Missense_Mutation SNP G G A rs145209328 C3L-00412_T C3L-00412_N G G c.1862C>T p.Thr621Met p.T621M ENST00000513000 20/27 223 208 15 215 214 1 strelka-varscan-mutect INPP4B,missense_variant,p.Thr621Met,ENST00000513000,NM_003866.2;INPP4B,missense_variant,p.Thr621Met,ENST00000509777,;INPP4B,missense_variant,p.Thr621Met,ENST00000262992,NM_001101669.1;INPP4B,missense_variant,p.Thr621Met,ENST00000508116,;INPP4B,missense_variant,p.Thr621Met,ENST00000510812,;INPP4B,missense_variant,p.Thr436Met,ENST00000511838,;INPP4B,missense_variant,p.Thr492Met,ENST00000514525,;INPP4B,3_prime_UTR_variant,,ENST00000512630,; A ENST00000513000 Transcript missense_variant 2296/8831 1862/2775 621/924 T/M aCg/aTg rs145209328 1 -1 INPP4B HGNC HGNC:6075 protein_coding YES CCDS3757.1 ENSP00000425487 O15327 UPI000013D37A NM_003866.2 deleterious(0.04) 20/27 hmmpanther:PTHR12187,hmmpanther:PTHR12187:SF3 MODERATE 1 SNV 1 1 PASS rs145209328 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 142124619 142124619 G A 1 0 0 0 0 1 0 0 0 7656 1145 40 1 1 INPP4B 4 142124619 Missense_Mutation SNP G C3L-00412_T 23097246 142124619 48089936 27 6590 NEIL3 0 . GRCh38 4 177353586 177353586 + Missense_Mutation SNP A A G novel C3L-00412_T C3L-00412_N A A c.1318A>G p.Ile440Val p.I440V ENST00000264596 8/10 314 290 24 282 282 0 strelka-varscan-mutect NEIL3,missense_variant,p.Ile440Val,ENST00000264596,NM_018248.2;RP11-376O6.2,intron_variant,,ENST00000506895,;NEIL3,3_prime_UTR_variant,,ENST00000513321,; G ENST00000264596 Transcript missense_variant 1436/2408 1318/1818 440/605 I/V Ata/Gta 1 1 NEIL3 HGNC HGNC:24573 protein_coding YES CCDS3828.1 ENSP00000264596 Q8TAT5 UPI000013D53D NM_018248.2 tolerated(0.62) 8/10 hmmpanther:PTHR22993,hmmpanther:PTHR22993:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 177353586 177353586 A G 1 0 0 0 0 1 0 0 0 10348 449 16 5 5 NEIL3 4 177353586 Missense_Mutation SNP A C3L-00412_T 35228967 177353586 12860969 28 6591 SEMA5A 0 . GRCh38 5 9062985 9062985 + Missense_Mutation SNP C C A rs770636604 C3L-00412_T C3L-00412_N C C c.2420G>T p.Arg807Leu p.R807L ENST00000382496 18/23 559 523 36 477 476 1 strelka-varscan-mutect SEMA5A,missense_variant,p.Arg807Leu,ENST00000382496,NM_003966.2; A ENST00000382496 Transcript missense_variant 3086/11762 2420/3225 807/1074 R/L cGg/cTg rs770636604,COSM1311389 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0) 18/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,Prints_domain:PR01705 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770636604 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 9062985 9062985 C A 1 0 0 0 0 1 0 0 0 14313 652 23 1 1 SEMA5A 5 9062985 Missense_Mutation SNP C C3L-00412_T 9062985 172475274 29 6592 FBXL7 0 . GRCh38 5 15937028 15937028 + Missense_Mutation SNP A A T novel C3L-00412_T C3L-00412_N A A c.1318A>T p.Ser440Cys p.S440C ENST00000504595 4/4 191 181 10 184 184 0 strelka-varscan-mutect FBXL7,missense_variant,p.Ser440Cys,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Ser398Cys,ENST00000329673,;FBXL7,missense_variant,p.Ser393Cys,ENST00000510662,NM_001278317.1;MIR887,downstream_gene_variant,,ENST00000401258,; T ENST00000504595 Transcript missense_variant 1799/4562 1318/1476 440/491 S/C Agc/Tgc 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.2) 4/4 Gene3D:3.80.10.10,Pfam_domain:PF13516,hmmpanther:PTHR24006,SMART_domains:SM00367,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 15937028 15937028 A T 1 0 0 0 0 1 0 0 0 5587 304 11 4 4 FBXL7 5 15937028 Missense_Mutation SNP A C3L-00412_T 6874043 15937028 165601231 30 6593 DAB2 0 . GRCh38 5 39376791 39376791 + Frame_Shift_Del DEL C C - rs766009192 C3L-00412_T C3L-00412_N C C c.1996delG p.Val666CysfsTer14 p.V666Cfs*14 ENST00000320816 12/15 373 350 23 360 360 0 varindel-pindel DAB2,frameshift_variant,p.Val645CysfsTer14,ENST00000545653,NM_001244871.1;DAB2,frameshift_variant,p.Val666CysfsTer14,ENST00000320816,NM_001343.3;DAB2,frameshift_variant,p.Val448CysfsTer14,ENST00000339788,;DAB2,frameshift_variant,p.Val645CysfsTer14,ENST00000509337,;C9,intron_variant,,ENST00000483232,;DAB2,upstream_gene_variant,,ENST00000502879,; - ENST00000320816 Transcript frameshift_variant 2464/4534 1996/2313 666/770 V/X Gtg/tg rs766009192 1 -1 DAB2 HGNC HGNC:2662 protein_coding YES CCDS34149.1 ENSP00000313391 P98082 A0A024R036 UPI0000169E27 NM_001343.3 12/15 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF30 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 16 39376791 39376791 C - 1 0 1 0 1 0 0 0 0 4019 478 17 0 0 DAB2 5 39376791 Frame_Shift_Del DEL C C3L-00412_T 23439763 39376791 142161468 31 6594 SH3TC2 0 . GRCh38 5 149028157 149028157 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1575G>T p.Trp525Cys p.W525C ENST00000515425 11/17 431 404 27 430 429 1 strelka-varscan-mutect SH3TC2,missense_variant,p.Trp525Cys,ENST00000515425,NM_024577.3;SH3TC2,missense_variant,p.Trp518Cys,ENST00000512049,;SH3TC2,downstream_gene_variant,,ENST00000513340,;SH3TC2,downstream_gene_variant,,ENST00000503071,;SH3TC2,missense_variant,p.Trp525Cys,ENST00000504690,;SH3TC2,3_prime_UTR_variant,,ENST00000323829,;SH3TC2,3_prime_UTR_variant,,ENST00000504517,;SH3TC2,3_prime_UTR_variant,,ENST00000513604,;SH3TC2,3_prime_UTR_variant,,ENST00000511307,;SH3TC2,3_prime_UTR_variant,,ENST00000510779,; A ENST00000515425 Transcript missense_variant 1677/4059 1575/3867 525/1288 W/C tgG/tgT 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 deleterious(0) 11/17 Gene3D:1.25.40.10,hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 149028157 149028157 C A 1 0 0 0 0 1 0 0 0 14521 624 22 2 2 SH3TC2 5 149028157 Missense_Mutation SNP C C3L-00412_T 109651366 149028157 32510102 32 6595 HAVCR1 0 . GRCh38 5 157029747 157029747 + Silent SNP A A G novel C3L-00412_T C3L-00412_N A A c.1047T>C p.= p.F349F ENST00000625904 7/7 333 312 21 342 342 0 strelka-varscan-mutect HAVCR1,missense_variant,p.Tyr361His,ENST00000339252,NM_001099414.1,NM_012206.2;HAVCR1,missense_variant,p.Tyr361His,ENST00000523175,NM_001173393.1;HAVCR1,synonymous_variant,p.=,ENST00000625904,;HAVCR1,synonymous_variant,p.=,ENST00000522693,NM_001308156.1;HAVCR1,non_coding_transcript_exon_variant,,ENST00000517644,; G ENST00000625904 Transcript synonymous_variant 1580/1807 1047/1206 349/401 F ttT/ttC 1 -1 HAVCR1 HGNC HGNC:17866 protein_coding YES CCDS78076.1 ENSP00000487363 E9PFX0 UPI000020C020 7/7 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 157029747 157029747 A G 1 0 0 0 0 0 0 0 1 6859 362 13 5 5 HAVCR1 5 157029747 Silent SNP A C3L-00412_T 8001590 157029747 24508512 33 6596 RREB1 0 . GRCh38 6 7229296 7229296 + Missense_Mutation SNP G G T rs368120167 C3L-00412_T C3L-00412_N G G c.1197G>T p.Gln399His p.Q399H ENST00000379938 10/13 145 136 9 159 159 0 strelka-varscan-mutect RREB1,missense_variant,p.Gln399His,ENST00000379938,NM_001003699.3;RREB1,missense_variant,p.Gln399His,ENST00000349384,NM_001003698.3;RREB1,missense_variant,p.Gln399His,ENST00000379933,NM_001168344.1;RREB1,missense_variant,p.Gln399His,ENST00000334984,NM_001003700.1;RREB1,missense_variant,p.Gln399His,ENST00000483150,;RREB1,upstream_gene_variant,,ENST00000611109,; T ENST00000379938 Transcript missense_variant 1734/8778 1197/5229 399/1742 Q/H caG/caT rs368120167 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 tolerated(0.06) 10/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42 MODERATE 1 SNV 1 1 PASS rs368120167 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 7229296 7229296 G T 1 0 0 0 0 1 0 0 0 13933 962 34 2 2 RREB1 6 7229296 Missense_Mutation SNP G C3L-00412_T 7229296 163576683 34 6597 HIST1H3D 0 . GRCh38 6 26196983 26196983 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.268G>T p.Val90Leu p.V90L ENST00000356476 1/1 463 438 25 471 470 1 strelka-varscan-mutect HIST1H3D,missense_variant,p.Val90Leu,ENST00000356476,NM_003530.4;RP1-34B20.21,3_prime_UTR_variant,,ENST00000635200,;HIST1H2BF,upstream_gene_variant,,ENST00000356530,NM_003522.3;HIST1H2AD,downstream_gene_variant,,ENST00000341023,NM_021065.3;RP1-34B20.21,3_prime_UTR_variant,,ENST00000635641,;HIST1H1PS1,downstream_gene_variant,,ENST00000404269,; A ENST00000356476 Transcript missense_variant 268/411 268/411 90/136 V/L Gtg/Ttg 1 -1 HIST1H3D HGNC HGNC:4767 protein_coding YES CCDS4590.1 ENSP00000366999 P68431 UPI00000003C7 NM_003530.4 tolerated_low_confidence(0.12) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE SNV 1 PASS rs1281998710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 26196983 26196983 C A 1 0 0 0 0 1 0 0 0 7046 507 18 2 2 HIST1H3D 6 26196983 Missense_Mutation SNP C C3L-00412_T 18967687 26196983 144608996 35 6598 ITPR3 0 . GRCh38 6 33689242 33689242 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.6699G>T p.= p.V2233V ENST00000374316 51/59 73 67 6 104 104 0 strelka-varscan-mutect ITPR3,synonymous_variant,p.=,ENST00000374316,;ITPR3,synonymous_variant,p.=,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript synonymous_variant 7759/9870 6699/8016 2233/2671 V gtG/gtT 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 51/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 LOW 1 SNV 5 1 PASS rs1372770319 . 0 207 3 0 0 0 0 0 -13.61539 1 1 1 1 0 T 2 4 16 33689242 33689242 G T 1 0 0 0 0 0 0 0 1 7828 1333 46 2 2 ITPR3 6 33689242 Silent SNP G C3L-00412_T 7492259 33689242 137116737 36 6599 CPNE5 0 . GRCh38 6 36756297 36756297 + Missense_Mutation SNP A A T novel C3L-00412_T C3L-00412_N A A c.857T>A p.Val286Glu p.V286E ENST00000244751 13/21 153 138 15 145 145 0 strelka-varscan-mutect CPNE5,missense_variant,p.Val286Glu,ENST00000244751,NM_020939.1;CPNE5,missense_variant,p.Val287Glu,ENST00000633136,;CPNE5,splice_region_variant,,ENST00000393189,NM_001314018.1,NM_001314020.1;CPNE5,splice_region_variant,,ENST00000459703,;CPNE5,splice_region_variant,,ENST00000633929,;CPNE5,splice_region_variant,,ENST00000493411,;CPNE5,splice_region_variant,,ENST00000634222,; T ENST00000244751 Transcript missense_variant,splice_region_variant 1482/3897 857/1782 286/593 V/E gTg/gAg 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 deleterious(0.01) 13/21 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF51,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 36756297 36756297 A T 1 0 0 0 0 1 0 0 0 3610 173 6 4 4 CPNE5 6 36756297 Missense_Mutation SNP A C3L-00412_T 3067055 36756297 134049682 37 6600 GLYATL3 0 . GRCh38 6 49511994 49511994 + Missense_Mutation SNP T T A novel C3L-00412_T C3L-00412_N T T c.4T>A p.Leu2Met p.L2M ENST00000371197 2/6 112 103 9 93 93 0 strelka-varscan-mutect GLYATL3,missense_variant,p.Leu2Met,ENST00000371197,NM_001010904.1;GLYATL3,missense_variant,p.Leu2Met,ENST00000545705,; A ENST00000371197 Transcript missense_variant 117/1113 4/867 2/288 L/M Ttg/Atg 1 1 GLYATL3 HGNC HGNC:21349 protein_coding YES CCDS47440.1 ENSP00000360240 Q5SZD4 UPI000023780B NM_001010904.1 deleterious(0.02) 2/6 Pfam_domain:PF06021,hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF6 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 49511994 49511994 T A 1 0 0 0 0 1 0 0 0 6360 1722 60 4 4 GLYATL3 6 49511994 Missense_Mutation SNP T C3L-00412_T 12755697 49511994 121293985 38 6601 BEND6 0 . GRCh38 6 56992466 56992466 + Missense_Mutation SNP T T C novel C3L-00412_T C3L-00412_N T T c.209T>C p.Leu70Ser p.L70S ENST00000370746 3/7 241 227 14 208 208 0 strelka-varscan-mutect BEND6,missense_variant,p.Leu70Ser,ENST00000370748,NM_001318539.1;BEND6,missense_variant,p.Leu70Ser,ENST00000370746,NM_152731.2;BEND6,missense_variant,p.Leu70Ser,ENST00000370745,; C ENST00000370746 Transcript missense_variant 478/2379 209/840 70/279 L/S tTg/tCg 1 1 BEND6 HGNC HGNC:20871 protein_coding YES CCDS43476.1 ENSP00000359782 Q5SZJ8 UPI000020DF34 NM_152731.2 deleterious_low_confidence(0) 3/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR35346 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 56992466 56992466 T C 1 0 0 0 0 1 0 0 0 1550 1821 63 5 5 BEND6 6 56992466 Missense_Mutation SNP T C3L-00412_T 7480472 56992466 113813513 39 6602 LAMA2 0 . GRCh38 6 129353214 129353214 + Missense_Mutation SNP A A T novel C3L-00412_T C3L-00412_N A A c.4574A>T p.Gln1525Leu p.Q1525L ENST00000421865 32/65 153 143 10 174 174 0 strelka-mutect LAMA2,missense_variant,p.Gln1525Leu,ENST00000618192,;LAMA2,missense_variant,p.Gln1525Leu,ENST00000617695,;LAMA2,missense_variant,p.Gln1525Leu,ENST00000421865,NM_001079823.1,NM_000426.3; T ENST00000421865 Transcript missense_variant 4623/9640 4574/9369 1525/3122 Q/L cAa/cTa 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.05) 32/65 Gene3D:2.10.25.10,Prints_domain:PR00011,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 129353214 129353214 A T 1 0 0 0 0 1 0 0 0 8510 130 5 4 4 LAMA2 6 129353214 Missense_Mutation SNP A C3L-00412_T 72360748 129353214 41452765 40 6603 SASH1 0 . GRCh38 6 148548538 148548538 + Missense_Mutation SNP C C T novel C3L-00412_T C3L-00412_N C C c.3724C>T p.Pro1242Ser p.P1242S ENST00000367467 20/20 49 45 4 72 72 0 strelka-varscan-mutect SASH1,missense_variant,p.Pro1242Ser,ENST00000367467,NM_015278.3;SASH1,missense_variant,p.Pro652Ser,ENST00000622663,; T ENST00000367467 Transcript missense_variant 4199/7711 3724/3744 1242/1247 P/S Cca/Tca 1 1 SASH1 HGNC HGNC:19182 protein_coding YES CCDS5212.1 ENSP00000356437 O94885 UPI00003519AE NM_015278.3 tolerated_low_confidence(0.24) 20/20 hmmpanther:PTHR12301:SF3,hmmpanther:PTHR12301 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -10.23427 0.9999998 1 1 1 0 T 3 4 16 148548538 148548538 C T 1 0 0 0 0 1 0 0 0 14109 739 26 3 3 SASH1 6 148548538 Missense_Mutation SNP C C3L-00412_T 19195324 148548538 22257441 41 6604 GINM1 0 . GRCh38 6 149572529 149572529 + Missense_Mutation SNP A A G novel C3L-00412_T C3L-00412_N A A c.203A>G p.Glu68Gly p.E68G ENST00000367419 3/8 125 117 8 133 133 0 strelka-varscan-mutect GINM1,missense_variant,p.Glu68Gly,ENST00000367419,NM_138785.3;RP1-12G14.9,downstream_gene_variant,,ENST00000627304,; G ENST00000367419 Transcript missense_variant 324/2024 203/993 68/330 E/G gAg/gGg 1 1 GINM1 HGNC HGNC:21074 protein_coding YES CCDS5216.1 ENSP00000356389 Q9NU53 UPI0000049E0C NM_138785.3 tolerated(0.34) 3/8 hmmpanther:PTHR28549,hmmpanther:PTHR28549:SF1,PD320073 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 149572529 149572529 A G 1 0 0 0 0 1 0 0 0 6268 304 11 5 5 GINM1 6 149572529 Missense_Mutation SNP A C3L-00412_T 1023991 149572529 21233450 42 6605 ARID1B 0 . GRCh38 6 157196248 157196248 + Nonsense_Mutation SNP G G T rs199674889 C3L-00412_T C3L-00412_N G G c.3946G>T p.Gly1316Ter p.G1316* ENST00000346085 16/20 180 167 13 200 199 1 strelka-varscan-mutect ARID1B,stop_gained,p.Gly1316Ter,ENST00000346085,NM_020732.3;ARID1B,stop_gained,p.Gly1356Ter,ENST00000636930,;ARID1B,stop_gained,p.Gly1303Ter,ENST00000350026,NM_017519.2;ARID1B,stop_gained,p.Gly825Ter,ENST00000414678,;ARID1B,stop_gained,p.Gly606Ter,ENST00000637904,;ARID1B,stop_gained,p.Gly546Ter,ENST00000635849,;ARID1B,stop_gained,p.Gly562Ter,ENST00000637015,;ARID1B,stop_gained,p.Gly553Ter,ENST00000637810,;ARID1B,stop_gained,p.Gly423Ter,ENST00000635957,;ARID1B,non_coding_transcript_exon_variant,,ENST00000637741,;ARID1B,3_prime_UTR_variant,,ENST00000637568,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636227,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636940,;ARID1B,upstream_gene_variant,,ENST00000636254,; T ENST00000346085 Transcript stop_gained 4502/10194 3946/6750 1316/2249 G/* Gga/Tga rs199674889 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 16/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 HIGH 1 SNV 1 1 PASS rs199674889 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 16 157196248 157196248 G T 1 0 0 0 0 0 1 0 0 1050 1117 39 1 1 ARID1B 6 157196248 Nonsense_Mutation SNP G C3L-00412_T 7623719 157196248 13609731 43 6606 IGF2R 0 . GRCh38 6 160061610 160061610 + Missense_Mutation SNP G G A rs8191843 C3L-00412_T C3L-00412_N G G c.3370G>A p.Val1124Ile p.V1124I ENST00000356956 24/48 136 125 11 191 191 0 strelka-varscan-mutect IGF2R,missense_variant,p.Val1124Ile,ENST00000356956,NM_000876.2; A ENST00000356956 Transcript missense_variant 3518/14044 3370/7476 1124/2491 V/I Gtt/Att rs8191843,COSM1075596 1 1 IGF2R HGNC HGNC:5467 protein_coding YES CCDS5273.1 ENSP00000349437 P11717 UPI0000072478 NM_000876.2 deleterious(0.03) 24/48 Gene3D:2.70.130.10,Pfam_domain:PF00878,hmmpanther:PTHR15071,hmmpanther:PTHR15071:SF5,SMART_domains:SM01404,Superfamily_domains:SSF50911 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs8191843 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 160061610 160061610 G A 1 0 0 0 0 1 0 0 0 7482 1145 40 1 1 IGF2R 6 160061610 Missense_Mutation SNP G C3L-00412_T 2865362 160061610 10744369 44 6607 TTYH3 0 . GRCh38 7 2632184 2632184 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.29G>T p.Trp10Leu p.W10L ENST00000258796 1/14 112 100 12 118 118 0 strelka-varscan-mutect TTYH3,missense_variant,p.Trp10Leu,ENST00000258796,NM_025250.2;TTYH3,missense_variant,p.Trp10Leu,ENST00000407643,; T ENST00000258796 Transcript missense_variant 234/4840 29/1572 10/523 W/L tGg/tTg 1 1 TTYH3 HGNC HGNC:22222 protein_coding YES CCDS34588.1 ENSP00000258796 Q9C0H2 A0A024R816 UPI000020E9F9 NM_025250.2 deleterious(0.01) 1/14 hmmpanther:PTHR12424,hmmpanther:PTHR12424:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 16 2632184 2632184 G T 1 0 0 0 0 1 0 0 0 17251 1357 47 2 2 TTYH3 7 2632184 Missense_Mutation SNP G C3L-00412_T 2632184 156713789 45 6608 PHTF2 0 . GRCh38 7 77840280 77840280 + Missense_Mutation SNP A A G rs778356622 C3L-00412_T C3L-00412_N A A c.25A>G p.Ile9Val p.I9V ENST00000422959 2/19 143 135 8 151 151 0 strelka-varscan PHTF2,missense_variant,p.Ile9Val,ENST00000416283,;PHTF2,missense_variant,p.Ile9Val,ENST00000307305,NM_001127358.1,NM_020432.4;PHTF2,missense_variant,p.Ile9Val,ENST00000248550,;PHTF2,missense_variant,p.Ile9Val,ENST00000275575,;PHTF2,missense_variant,p.Ile9Val,ENST00000422959,NM_001127357.1;PHTF2,missense_variant,p.Ile9Val,ENST00000450574,NM_001127359.1;PHTF2,missense_variant,p.Ile9Val,ENST00000424760,;PHTF2,missense_variant,p.Ile9Val,ENST00000415251,NM_001127360.1; G ENST00000422959 Transcript missense_variant 227/3525 25/2256 9/751 I/V Ata/Gta rs778356622,COSM1132940,COSM1132941 1 1 PHTF2 HGNC HGNC:13411 protein_coding YES CCDS47621.1 ENSP00000403042 Q8N3S3 UPI0000E674D3 NM_001127357.1 tolerated(0.31) 2/19 Pfam_domain:PF12129,hmmpanther:PTHR12680,hmmpanther:PTHR12680:SF2 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 77840280 77840280 A G 1 0 0 0 0 1 0 0 0 11951 449 16 5 5 PHTF2 7 77840280 Missense_Mutation SNP A C3L-00412_T 75208096 77840280 81505693 46 6609 LRRC17 0 . GRCh38 7 102934235 102934235 + Missense_Mutation SNP A A G novel C3L-00412_T C3L-00412_N A A c.322A>G p.Lys108Glu p.K108E ENST00000339431 2/4 185 174 11 191 191 0 strelka-varscan LRRC17,missense_variant,p.Lys108Glu,ENST00000249377,NM_005824.2;LRRC17,missense_variant,p.Lys108Glu,ENST00000339431,NM_001031692.2;FBXL13,intron_variant,,ENST00000313221,NM_145032.3;FBXL13,intron_variant,,ENST00000379308,;FBXL13,intron_variant,,ENST00000436908,;FBXL13,intron_variant,,ENST00000379305,NM_001287150.1;FBXL13,intron_variant,,ENST00000455112,NM_001111038.1;FBXL13,intron_variant,,ENST00000456695,;LRRC17,downstream_gene_variant,,ENST00000455453,;FBXL13,intron_variant,,ENST00000477915,;LRRC17,upstream_gene_variant,,ENST00000485478,;FBXL13,upstream_gene_variant,,ENST00000468216,;LRRC17,downstream_gene_variant,,ENST00000498487,;FBXL13,intron_variant,,ENST00000448002,; G ENST00000339431 Transcript missense_variant 617/1963 322/1326 108/441 K/E Aaa/Gaa 1 1 LRRC17 HGNC HGNC:16895 protein_coding YES CCDS34721.1 ENSP00000344242 Q8N6Y2 UPI00000719CD NM_001031692.2 deleterious(0.03) 2/4 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF323,Low_complexity_(Seg):seg,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 102934235 102934235 A G 1 0 0 0 0 1 0 0 0 8868 247 9 5 5 LRRC17 7 102934235 Missense_Mutation SNP A C3L-00412_T 25093955 102934235 56411738 47 6610 PRRT4 0 . GRCh38 7 128352216 128352216 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1340G>T p.Gly447Val p.G447V ENST00000446477 6/6 182 166 16 176 176 0 strelka-varscan PRRT4,missense_variant,p.Gly447Val,ENST00000446477,NM_001174164.1;PRRT4,missense_variant,p.Gly447Val,ENST00000535159,;PRRT4,missense_variant,p.Gly447Val,ENST00000489517,;PRRT4,intron_variant,,ENST00000489835,NM_001114726.2;PRRT4,intron_variant,,ENST00000480290,; A ENST00000446477 Transcript missense_variant 1654/3544 1340/2700 447/899 G/V gGc/gTc 1 -1 PRRT4 HGNC HGNC:37280 protein_coding YES CCDS55160.1 ENSP00000415026 C9JH25 UPI0000DD7E1D NM_001174164.1 tolerated(0.26) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR35578,hmmpanther:PTHR35578:SF1,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 128352216 128352216 C A 1 0 0 0 0 1 0 0 0 12758 739 26 2 2 PRRT4 7 128352216 Missense_Mutation SNP C C3L-00412_T 25417981 128352216 30993757 48 6611 NOBOX 0 . GRCh38 7 144401211 144401211 + Missense_Mutation SNP G G T rs762139523 C3L-00412_T C3L-00412_N G G c.679C>A p.Arg227Ser p.R227S ENST00000467773 4/10 134 123 11 122 122 0 strelka-varscan NOBOX,missense_variant,p.Arg227Ser,ENST00000467773,NM_001080413.3;NOBOX,missense_variant,p.Arg227Ser,ENST00000483238,; T ENST00000467773 Transcript missense_variant 679/2076 679/2076 227/691 R/S Cgt/Agt rs762139523,COSM3879037,COSM3879038 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 tolerated(0.15) 4/10 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF282 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 144401211 144401211 G T 1 0 0 0 0 1 0 0 0 10554 1116 39 1 1 NOBOX 7 144401211 Missense_Mutation SNP G C3L-00412_T 16048995 144401211 14944762 49 6612 SFRP1 0 . GRCh38 8 41308844 41308844 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.316C>A p.His106Asn p.H106N ENST00000220772 1/3 124 110 14 161 160 1 strelka-varscan-mutect SFRP1,missense_variant,p.His106Asn,ENST00000220772,NM_003012.4;SFRP1,upstream_gene_variant,,ENST00000379845,; T ENST00000220772 Transcript missense_variant 654/4492 316/945 106/314 H/N Cac/Aac 1 -1 SFRP1 HGNC HGNC:10776 protein_coding YES CCDS34886.1 ENSP00000220772 Q8N474 UPI0000038CE3 NM_003012.4 deleterious(0) 1/3 PROSITE_profiles:PS50038,hmmpanther:PTHR11309:SF87,hmmpanther:PTHR11309,Gene3D:1ijyA00,Pfam_domain:PF01392,SMART_domains:SM00063,Superfamily_domains:SSF63501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 41308844 41308844 G T 1 0 0 0 0 1 0 0 0 14440 1348 47 2 2 SFRP1 8 41308844 Missense_Mutation SNP G C3L-00412_T 41308844 103829792 50 6613 PREX2 0 . GRCh38 8 68134276 68134276 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.3984G>T p.Leu1328Phe p.L1328F ENST00000288368 32/40 98 92 6 115 114 1 strelka-varscan-mutect PREX2,missense_variant,p.Leu1328Phe,ENST00000288368,NM_024870.2; T ENST00000288368 Transcript missense_variant,splice_region_variant 4261/10750 3984/4821 1328/1606 L/F ttG/ttT 1 1 PREX2 HGNC HGNC:22950 protein_coding YES CCDS6201.1 ENSP00000288368 Q70Z35 UPI0000375435 NM_024870.2 tolerated(0.06) 32/40 hmmpanther:PTHR22829:SF1,hmmpanther:PTHR22829 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.88333 1 1 1 1 0 T 3 4 16 68134276 68134276 G T 1 0 0 0 0 1 0 0 0 12611 1362 47 2 2 PREX2 8 68134276 Missense_Mutation SNP G C3L-00412_T 26825432 68134276 77004360 51 6614 KIAA1429 0 . GRCh38 8 94509750 94509750 + Missense_Mutation SNP T T G novel C3L-00412_T C3L-00412_N T T c.3817A>C p.Ser1273Arg p.S1273R ENST00000297591 15/24 177 165 12 179 179 0 strelka-varscan-mutect KIAA1429,missense_variant,p.Ser1273Arg,ENST00000297591,NM_015496.4;KIAA1429,downstream_gene_variant,,ENST00000421249,NM_183009.2;KIAA1429,downstream_gene_variant,,ENST00000523405,;KIAA1429,missense_variant,p.Ser626Arg,ENST00000522263,;KIAA1429,non_coding_transcript_exon_variant,,ENST00000521080,; G ENST00000297591 Transcript missense_variant 3893/6528 3817/5439 1273/1812 S/R Agt/Cgt 1 -1 KIAA1429 HGNC HGNC:24500 protein_coding YES CCDS34923.1 ENSP00000297591 Q69YN4 UPI00001BBB23 NM_015496.4 tolerated(0.05) 15/24 hmmpanther:PTHR23185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 94509750 94509750 T G 1 0 0 0 0 1 0 0 0 8114 1580 55 5 5 KIAA1429 8 94509750 Missense_Mutation SNP T C3L-00412_T 26375474 94509750 50628886 52 6615 PKHD1L1 0 . GRCh38 8 109445335 109445335 + Silent SNP T T A novel C3L-00412_T C3L-00412_N T T c.5466T>A p.= p.A1822A ENST00000378402 38/78 206 193 13 269 269 0 strelka-varscan-mutect PKHD1L1,synonymous_variant,p.=,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript synonymous_variant 5570/13076 5466/12732 1822/4243 A gcT/gcA 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 38/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 109445335 109445335 T A 1 0 0 0 0 0 0 0 1 12068 1538 54 4 4 PKHD1L1 8 109445335 Silent SNP T C3L-00412_T 14935585 109445335 35693301 53 6616 CSMD3 0 . GRCh38 8 112656178 112656178 + Missense_Mutation SNP T T A C3L-00412_T C3L-00412_N T T c.2980A>T p.Asn994Tyr p.N994Y ENST00000297405 18/71 128 115 13 148 147 1 strelka-varscan-mutect CSMD3,missense_variant,p.Asn994Tyr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Asn954Tyr,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Asn890Tyr,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Asn334Tyr,ENST00000339701,; A ENST00000297405 Transcript missense_variant 3225/13212 2980/11124 994/3707 N/Y Aat/Tat COSM5615934,COSM5615935 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.18) 18/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 112656178 112656178 T A 1 0 0 0 0 1 0 0 0 3747 1754 61 4 4 CSMD3 8 112656178 Missense_Mutation SNP T C3L-00412_T 3210843 112656178 32482458 54 6617 SLC30A8 0 . GRCh38 8 117172614 117172614 + Missense_Mutation SNP C C T C3L-00412_T C3L-00412_N C C c.1043C>T p.Thr348Ile p.T348I ENST00000456015 8/8 264 246 18 251 251 0 strelka-varscan-mutect SLC30A8,missense_variant,p.Thr299Ile,ENST00000427715,NM_001172815.1,NM_001172813.1;SLC30A8,missense_variant,p.Thr299Ile,ENST00000519688,NM_001172814.1;SLC30A8,missense_variant,p.Thr348Ile,ENST00000456015,NM_173851.2;SLC30A8,missense_variant,p.Thr299Ile,ENST00000521243,NM_001172811.1; T ENST00000456015 Transcript missense_variant 1043/2520 1043/1110 348/369 T/I aCc/aTc COSM3896334 1 1 SLC30A8 HGNC HGNC:20303 protein_coding YES CCDS6322.1 ENSP00000415011 Q8IWU4 UPI00001B00D6 NM_173851.2 deleterious(0) 8/8 hmmpanther:PTHR11562:SF37,hmmpanther:PTHR11562,TIGRFAM_domain:TIGR01297,Superfamily_domains:SSF160240 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 117172614 117172614 C T 1 0 0 0 0 1 0 0 0 14831 507 18 3 3 SLC30A8 8 117172614 Missense_Mutation SNP C C3L-00412_T 4516436 117172614 27966022 55 6618 CA9 0 . GRCh38 9 35679230 35679230 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.953C>A p.Pro318His p.P318H ENST00000378357 7/11 187 175 12 237 236 1 strelka-varscan-mutect CA9,missense_variant,p.Pro318His,ENST00000378357,NM_001216.2;CA9,missense_variant,p.Pro318His,ENST00000617161,;TPM2,downstream_gene_variant,,ENST00000378292,NM_213674.1;TPM2,downstream_gene_variant,,ENST00000378300,;TPM2,downstream_gene_variant,,ENST00000360958,NM_003289.3;TPM2,downstream_gene_variant,,ENST00000329305,NM_001301226.1;TPM2,downstream_gene_variant,,ENST00000607559,;CA9,non_coding_transcript_exon_variant,,ENST00000493245,;CA9,upstream_gene_variant,,ENST00000485665,;ARHGEF39,upstream_gene_variant,,ENST00000490638,; A ENST00000378357 Transcript missense_variant 1057/1618 953/1380 318/459 P/H cCc/cAc 1 1 CA9 HGNC HGNC:1383 protein_coding YES CCDS6585.1 ENSP00000367608 Q16790 A0A0S2Z3D0 UPI000013E02C NM_001216.2 deleterious(0) 7/11 Gene3D:3.10.200.10,Pfam_domain:PF00194,PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF18,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 35679230 35679230 C A 1 0 0 0 0 1 0 0 0 2210 623 22 2 2 CA9 9 35679230 Missense_Mutation SNP C C3L-00412_T 35679230 102715487 56 6619 FRMPD1 0 . GRCh38 9 37730994 37730994 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.749G>T p.Arg250Met p.R250M ENST00000539465 9/16 175 157 18 213 213 0 strelka-varscan-mutect FRMPD1,missense_variant,p.Arg250Met,ENST00000539465,;FRMPD1,missense_variant,p.Arg250Met,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; T ENST00000539465 Transcript missense_variant 1342/5465 749/4737 250/1578 R/M aGg/aTg 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC deleterious(0) 9/16 PROSITE_profiles:PS50057,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF346,SMART_domains:SM00295,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 37730994 37730994 G T 1 0 0 0 0 1 0 0 0 5927 1000 35 2 2 FRMPD1 9 37730994 Missense_Mutation SNP G C3L-00412_T 2051764 37730994 100663723 57 6620 TLR4 0 . GRCh38 9 117713562 117713562 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.1434G>C p.Met478Ile p.M478I ENST00000355622 3/3 153 144 9 173 173 0 strelka-varscan-mutect TLR4,missense_variant,p.Met478Ile,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Met438Ile,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; C ENST00000355622 Transcript missense_variant 1535/4844 1434/2520 478/839 M/I atG/atC 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 deleterious(0.03) 3/3 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 117713562 117713562 G C 1 0 0 0 0 1 0 0 0 16399 1348 47 4 4 TLR4 9 117713562 Missense_Mutation SNP G C3L-00412_T 79982568 117713562 20681155 58 6621 PTGS1 0 . GRCh38 9 122386583 122386583 + Missense_Mutation SNP C C G novel C3L-00412_T C3L-00412_N C C c.1147C>G p.Leu383Val p.L383V ENST00000362012 9/11 483 453 30 483 483 0 strelka-varscan-mutect PTGS1,missense_variant,p.Leu358Val,ENST00000540753,NM_001271368.1;PTGS1,missense_variant,p.Leu414Val,ENST00000619306,;PTGS1,missense_variant,p.Leu274Val,ENST00000373698,NM_001271166.1,NM_001271367.1,NM_001271165.1;PTGS1,missense_variant,p.Leu383Val,ENST00000362012,NM_000962.3;PTGS1,missense_variant,p.Leu335Val,ENST00000614910,NM_001271164.1;PTGS1,missense_variant,p.Leu383Val,ENST00000223423,NM_080591.2;PTGS1,downstream_gene_variant,,ENST00000426608,; G ENST00000362012 Transcript missense_variant 1152/4964 1147/1800 383/599 L/V Ctc/Gtc 1 1 PTGS1 HGNC HGNC:9604 protein_coding YES CCDS6842.1 ENSP00000354612 P23219 UPI0000161DAC NM_000962.3 deleterious(0.01) 9/11 PROSITE_profiles:PS50292,hmmpanther:PTHR11903:SF6,hmmpanther:PTHR11903,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 122386583 122386583 C G 1 0 0 0 0 1 0 0 0 12911 913 32 4 4 PTGS1 9 122386583 Missense_Mutation SNP C C3L-00412_T 4673021 122386583 16008134 59 6622 ITIH5 0 . GRCh38 10 7637436 7637436 + Silent SNP G G T C3L-00412_T C3L-00412_N G G c.444C>A p.= p.P148P ENST00000397146 5/14 163 146 17 202 202 0 varscan-mutect ITIH5,synonymous_variant,p.=,ENST00000397146,NM_030569.6;ITIH5,synonymous_variant,p.=,ENST00000397145,NM_001001851.2;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,; T ENST00000397146 Transcript synonymous_variant 523/6721 444/2829 148/942 P ccC/ccA COSM1506154,COSM5278921,COSM5278922,COSM5307762 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 5/14 PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,Pfam_domain:PF08487,SMART_domains:SM00609 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 7637436 7637436 G T 1 0 0 0 0 0 0 0 1 7813 1335 47 2 2 ITIH5 10 7637436 Silent SNP G C3L-00412_T 7637436 126159986 60 6623 ITGA8 0 . GRCh38 10 15647050 15647050 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.1003C>G p.Leu335Val p.L335V ENST00000378076 12/30 123 112 11 146 146 0 strelka-varscan-mutect ITGA8,missense_variant,p.Leu335Val,ENST00000378076,NM_003638.2,NM_001291494.1;ITGA8,upstream_gene_variant,,ENST00000468882,; C ENST00000378076 Transcript missense_variant,splice_region_variant 1357/6755 1003/3192 335/1063 L/V Ctg/Gtg 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 deleterious(0.02) 12/30 Gene3D:3nigC00,Pfam_domain:PF01839,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 15647050 15647050 G C 1 0 0 0 0 1 0 0 0 7789 1043 36 4 4 ITGA8 10 15647050 Missense_Mutation SNP G C3L-00412_T 8009614 15647050 118150372 61 6624 PCDH15 0 . GRCh38 10 54066820 54066820 + Silent SNP A A T novel C3L-00412_T C3L-00412_N A A c.2172T>A p.= p.P724P ENST00000373957 19/35 288 262 26 270 270 0 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000614895,;PCDH15,synonymous_variant,p.=,ENST00000373965,NM_001142772.1;PCDH15,synonymous_variant,p.=,ENST00000414778,;PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,synonymous_variant,p.=,ENST00000617271,NM_001142770.1;PCDH15,synonymous_variant,p.=,ENST00000613657,NM_001142769.1;PCDH15,synonymous_variant,p.=,ENST00000395445,;PCDH15,synonymous_variant,p.=,ENST00000616114,;PCDH15,synonymous_variant,p.=,ENST00000395438,;PCDH15,synonymous_variant,p.=,ENST00000612394,;PCDH15,synonymous_variant,p.=,ENST00000621708,NM_001142771.1;PCDH15,synonymous_variant,p.=,ENST00000409834,;PCDH15,synonymous_variant,p.=,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; T ENST00000373957 Transcript synonymous_variant 2567/7032 2172/5889 724/1962 P ccT/ccA 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 19/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 54066820 54066820 A T 1 0 0 0 0 0 0 0 1 11598 59 3 4 4 PCDH15 10 54066820 Silent SNP A C3L-00412_T 38419770 54066820 79730602 62 6625 LRIT1 0 . GRCh38 10 84232566 84232566 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1233G>T p.Gln411His p.Q411H ENST00000372105 4/4 99 91 8 145 144 1 strelka-mutect LRIT1,missense_variant,p.Gln411His,ENST00000372105,NM_015613.2; A ENST00000372105 Transcript missense_variant 1255/2228 1233/1872 411/623 Q/H caG/caT 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 tolerated(0.18) 4/4 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 84232566 84232566 C A 1 0 0 0 0 1 0 0 0 8842 912 32 2 2 LRIT1 10 84232566 Missense_Mutation SNP C C3L-00412_T 30165746 84232566 49564856 63 6626 TCERG1L 0 . GRCh38 10 131146585 131146585 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.1110C>A p.= p.P370P ENST00000368642 7/12 129 117 12 124 124 0 strelka-varscan-mutect TCERG1L,synonymous_variant,p.=,ENST00000368642,NM_174937.3;TCERG1L,non_coding_transcript_exon_variant,,ENST00000483040,; T ENST00000368642 Transcript synonymous_variant 1196/2618 1110/1761 370/586 P ccC/ccA 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 7/12 Gene3D:2.20.70.10,PROSITE_profiles:PS50020,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5,SMART_domains:SM00456,Superfamily_domains:SSF51045 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 131146585 131146585 G T 1 0 0 0 0 0 0 0 1 16093 1335 47 2 2 TCERG1L 10 131146585 Silent SNP G C3L-00412_T 46914019 131146585 2650837 64 6627 ADAM8 0 . GRCh38 10 133269454 133269454 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1939G>T p.Val647Leu p.V647L ENST00000445355 18/23 57 52 5 86 86 0 strelka-mutect ADAM8,missense_variant,p.Val647Leu,ENST00000445355,NM_001109.4;ADAM8,missense_variant,p.Val647Leu,ENST00000415217,NM_001164489.1;ADAM8,missense_variant,p.Val582Leu,ENST00000485491,NM_001164490.1;ADAM8,downstream_gene_variant,,ENST00000486609,;ADAM8,downstream_gene_variant,,ENST00000559180,;ADAM8,downstream_gene_variant,,ENST00000537099,;ADAM8,downstream_gene_variant,,ENST00000463298,;ADAM8,downstream_gene_variant,,ENST00000560135,;ADAM8,downstream_gene_variant,,ENST00000468964,;ADAM8,downstream_gene_variant,,ENST00000561175,; A ENST00000445355 Transcript missense_variant 1990/3279 1939/2475 647/824 V/L Gtg/Ttg 1 -1 ADAM8 HGNC HGNC:215 protein_coding YES CCDS31319.2 ENSP00000453302 P78325 UPI0001AE6E16 NM_001109.4 tolerated(0.31) 18/23 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF20 MODERATE 1 SNV 1 1 PASS rs1368170154 . 0 208 2 0 0 0 0 0 -12.43336 1 1 1 1 0 A 3 1 16 133269454 133269454 C A 1 0 0 0 0 1 0 0 0 296 507 18 2 2 ADAM8 10 133269454 Missense_Mutation SNP C C3L-00412_T 2122869 133269454 527968 65 6628 RASSF7 0 . GRCh38 11 562642 562642 + Frame_Shift_Del DEL C C - rs866584869 C3L-00412_T C3L-00412_N C C c.693delC p.Ser232HisfsTer31 p.S232Hfs*31 ENST00000397583 3/6 148 137 11 170 170 0 sindel-varindel-pindel RASSF7,frameshift_variant,p.Ser232HisfsTer31,ENST00000397583,NM_003475.3;RASSF7,frameshift_variant,p.Ser232HisfsTer31,ENST00000431809,;RASSF7,frameshift_variant,p.Ser232HisfsTer31,ENST00000397582,NM_001143993.1;RASSF7,frameshift_variant,p.Ser232HisfsTer31,ENST00000454668,NM_001143994.1;LMNTD2,upstream_gene_variant,,ENST00000329451,NM_173573.2;LMNTD2,upstream_gene_variant,,ENST00000441853,;LMNTD2,upstream_gene_variant,,ENST00000486629,;RASSF7,downstream_gene_variant,,ENST00000528736,;MIR210HG,downstream_gene_variant,,ENST00000500447,;MIR210HG,downstream_gene_variant,,ENST00000533920,;MIR210HG,downstream_gene_variant,,ENST00000528245,;MIR210HG,downstream_gene_variant,,ENST00000534540,;RP11-496I9.1,downstream_gene_variant,,ENST00000527620,;RP11-496I9.1,downstream_gene_variant,,ENST00000533844,;RP11-496I9.1,downstream_gene_variant,,ENST00000527113,;RASSF7,downstream_gene_variant,,ENST00000524468,;RASSF7,frameshift_variant,p.Ser89HisfsTer31,ENST00000531112,;RASSF7,3_prime_UTR_variant,,ENST00000414138,;LMNTD2,upstream_gene_variant,,ENST00000492515,; - ENST00000397583 Transcript frameshift_variant 1121/1928 688/1122 230/373 P/X Ccc/cc rs866584869 1 1 RASSF7 HGNC HGNC:1166 protein_coding YES CCDS7702.1 ENSP00000380713 Q02833 A0A024RCE4 UPI0000127A61 NM_003475.3 3/6 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF11 HIGH 1 deletion 1 5 1 PASS . . 0 207 0 3 0 0 0 0 -15.08407 0.9999728 1 1 1 0 - 7 5 16 562642 562642 C - 1 0 1 0 1 0 0 0 0 13252 739 26 0 0 RASSF7 11 562642 Frame_Shift_Del DEL C C3L-00412_T 562642 134523980 66 6629 ABCC8 0 . GRCh38 11 17397708 17397708 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.3846C>A p.= p.G1282G ENST00000302539 31/39 392 364 28 387 387 0 strelka-varscan-mutect ABCC8,synonymous_variant,p.=,ENST00000302539,NM_001287174.1;ABCC8,synonymous_variant,p.=,ENST00000389817,NM_000352.4;ABCC8,synonymous_variant,p.=,ENST00000528374,;ABCC8,3_prime_UTR_variant,,ENST00000527905,;ABCC8,3_prime_UTR_variant,,ENST00000531891,;ABCC8,non_coding_transcript_exon_variant,,ENST00000531137,;ABCC8,upstream_gene_variant,,ENST00000531642,;ABCC8,upstream_gene_variant,,ENST00000525022,;ABCC8,upstream_gene_variant,,ENST00000526037,;ABCC8,upstream_gene_variant,,ENST00000532220,;ABCC8,upstream_gene_variant,,ENST00000526168,; T ENST00000302539 Transcript synonymous_variant 3915/4923 3846/4749 1282/1582 G ggC/ggA 1 -1 ABCC8 HGNC HGNC:59 protein_coding YES CCDS73264.1 ENSP00000303960 Q09428 UPI00015DFF64 NM_001287174.1 31/39 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF187,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 17397708 17397708 G T 1 0 0 0 0 0 0 0 1 62 1190 42 2 2 ABCC8 11 17397708 Silent SNP G C3L-00412_T 16835066 17397708 117688914 67 6630 OR5J2 0 . GRCh38 11 56176779 56176779 + Silent SNP A A G C3L-00412_T C3L-00412_N A A c.162A>G p.= p.K54K ENST00000312298 1/1 128 116 12 118 118 0 strelka-varscan-mutect OR5J2,synonymous_variant,p.=,ENST00000312298,NM_001005492.1; G ENST00000312298 Transcript synonymous_variant 162/939 162/939 54/312 K aaA/aaG COSM4145825 1 1 OR5J2 HGNC HGNC:19612 protein_coding YES CCDS31522.1 ENSP00000310788 Q8NH18 A0A126GVP0 UPI000004B232 NM_001005492.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF343,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 56176779 56176779 A G 1 0 0 0 0 0 0 0 1 11235 40 2 5 5 OR5J2 11 56176779 Silent SNP A C3L-00412_T 38779071 56176779 78909843 68 6631 SLC22A6 0 . GRCh38 11 62977304 62977304 + Missense_Mutation SNP T T A novel C3L-00412_T C3L-00412_N T T c.1445A>T p.Tyr482Phe p.Y482F ENST00000377871 9/10 348 321 27 450 450 0 strelka-varscan-mutect SLC22A6,missense_variant,p.Tyr482Phe,ENST00000377871,NM_004790.4;SLC22A6,missense_variant,p.Tyr482Phe,ENST00000360421,NM_153276.2;SLC22A6,intron_variant,,ENST00000421062,NM_153278.2;SLC22A6,intron_variant,,ENST00000458333,NM_153277.2;SLC22A6,downstream_gene_variant,,ENST00000537349,;SLC22A6,3_prime_UTR_variant,,ENST00000540654,; A ENST00000377871 Transcript missense_variant 1712/2151 1445/1692 482/563 Y/F tAc/tTc 1 -1 SLC22A6 HGNC HGNC:10970 protein_coding YES CCDS31591.1 ENSP00000367102 Q4U2R8 UPI00000747EC NM_004790.4 tolerated(0.59) 9/10 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF231,Gene3D:1.20.1250.20,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs938308762 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 62977304 62977304 T A 1 0 0 0 0 1 0 0 0 14724 1638 57 4 4 SLC22A6 11 62977304 Missense_Mutation SNP T C3L-00412_T 6800525 62977304 72109318 69 6632 CCDC88B 0 . GRCh38 11 64343238 64343238 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.1122G>T p.= p.L374L ENST00000356786 11/27 123 114 9 139 139 0 strelka-varscan-mutect CCDC88B,synonymous_variant,p.=,ENST00000356786,NM_032251.5;MIR7155,upstream_gene_variant,,ENST00000615925,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000463837,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000494080,;CCDC88B,non_coding_transcript_exon_variant,,ENST00000494566,;CCDC88B,upstream_gene_variant,,ENST00000492980,; T ENST00000356786 Transcript synonymous_variant 1166/4915 1122/4431 374/1476 L ctG/ctT 1 1 CCDC88B HGNC HGNC:26757 protein_coding YES CCDS8072.2 ENSP00000349238 A6NC98 UPI00001FAAA6 NM_032251.5 11/27 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947:SF35,hmmpanther:PTHR18947,Pfam_domain:PF05622 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.17236 0.9999997 1 1 1 0 T 2 4 16 64343238 64343238 G T 1 0 0 0 0 0 0 0 1 2563 1335 47 2 2 CCDC88B 11 64343238 Silent SNP G C3L-00412_T 1365934 64343238 70743384 70 6633 ARHGAP42 0 . GRCh38 11 100913535 100913535 + Frame_Shift_Del DEL G G - novel C3L-00412_T C3L-00412_N G G c.469delG p.Glu157SerfsTer23 p.E157Sfs*23 ENST00000298815 5/24 97 92 5 93 93 0 varindel-pindel ARHGAP42,frameshift_variant,p.Glu157SerfsTer23,ENST00000298815,NM_152432.2;ARHGAP42,frameshift_variant,p.Glu13SerfsTer23,ENST00000531183,;ARHGAP42,intron_variant,,ENST00000524892,;ARHGAP42,downstream_gene_variant,,ENST00000534060,;ARHGAP42,downstream_gene_variant,,ENST00000529406,; - ENST00000298815 Transcript frameshift_variant 471/4752 468/2625 156/874 K/X aaG/aa 1 1 ARHGAP42 HGNC HGNC:26545 protein_coding YES ENSP00000298815 A6NI28 UPI00005778C9 NM_152432.2 5/24 hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF3,Gene3D:1y2oA00,Pfam_domain:PF16746,Superfamily_domains:SSF103657 HIGH 1 deletion 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.63521 1 1 1 1 0 - 7 5 16 100913535 100913535 G - 1 0 1 0 1 0 0 0 0 1013 991 35 0 0 ARHGAP42 11 100913535 Frame_Shift_Del DEL G C3L-00412_T 36570297 100913535 34173087 71 6634 OR8G5 0 . GRCh38 11 124265081 124265081 + Silent SNP G G T novel C3L-00412_T C3L-00412_N G G c.255G>T p.= p.G85G ENST00000524943 1/1 241 224 17 336 335 1 varscan-mutect OR8G5,synonymous_variant,p.=,ENST00000524943,NM_001005198.1; T ENST00000524943 Transcript synonymous_variant 255/1041 255/1041 85/346 G ggG/ggT 1 1 OR8G5 HGNC HGNC:19622 protein_coding YES CCDS66256.1 ENSP00000477014 Q8NG78 A0A126GVX5 UPI00003B286B NM_001005198.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 124265081 124265081 G T 1 0 0 0 0 0 0 0 1 11304 1190 42 2 2 OR8G5 11 124265081 Silent SNP G C3L-00412_T 23351546 124265081 10821541 72 6635 CACNA1C 0 . GRCh38 12 2653883 2653883 + Missense_Mutation SNP G G A novel C3L-00412_T C3L-00412_N G G c.4267G>A p.Ala1423Thr p.A1423T ENST00000347598 35/49 156 145 11 165 165 0 strelka-mutect CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000406454,;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Ala1400Thr,ENST00000335762,;CACNA1C,missense_variant,p.Ala1423Thr,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Ala1397Thr,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Ala1403Thr,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Ala1395Thr,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Ala1392Thr,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Ala1364Thr,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Ala1364Thr,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Ala1362Thr,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Ala1375Thr,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Ala66Thr,ENST00000616390,;CACNA1C,downstream_gene_variant,,ENST00000483136,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000492150,; A ENST00000347598 Transcript missense_variant 4267/6655 4267/6561 1423/2186 A/T Gcg/Acg 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0) 35/49 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 2653883 2653883 G A 1 0 0 0 0 1 0 0 0 2228 1087 38 1 1 CACNA1C 12 2653883 Missense_Mutation SNP G C3L-00412_T 2653883 130621426 73 6636 SLC15A5 0 . GRCh38 12 16257743 16257743 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.712C>A p.Leu238Ile p.L238I ENST00000344941 3/9 99 91 8 88 88 0 strelka-varscan-mutect SLC15A5,missense_variant,p.Leu238Ile,ENST00000344941,NM_001170798.1; T ENST00000344941 Transcript missense_variant 712/2923 712/1740 238/579 L/I Ctt/Att 1 -1 SLC15A5 HGNC HGNC:33455 protein_coding YES ENSP00000340402 A6NIM6 UPI0000DD8132 NM_001170798.1 tolerated(0.65) 3/9 Pfam_domain:PF00854,hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF91,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -16.77724 1 1 1 1 0 T 3 4 16 16257743 16257743 G T 1 0 0 0 0 1 0 0 0 14667 942 33 2 2 SLC15A5 12 16257743 Missense_Mutation SNP G C3L-00412_T 13603860 16257743 117017566 74 6637 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3L-00412_T C3L-00412_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 348 320 28 268 268 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3L-00412_T 8987608 25245351 108029958 75 6638 LGR5 0 . GRCh38 12 71583910 71583910 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.1900G>T p.Gly634Trp p.G634W ENST00000266674 18/18 254 240 14 282 281 1 strelka-varscan-mutect LGR5,missense_variant,p.Gly634Trp,ENST00000266674,NM_003667.3;LGR5,missense_variant,p.Gly610Trp,ENST00000540815,NM_001277226.1;LGR5,missense_variant,p.Gly562Trp,ENST00000536515,NM_001277227.1;RP11-186F10.2,upstream_gene_variant,,ENST00000546601,;LGR5,splice_region_variant,,ENST00000550851,;LGR5,downstream_gene_variant,,ENST00000547310,; T ENST00000266674 Transcript missense_variant 2211/4611 1900/2724 634/907 G/W Ggg/Tgg 1 1 LGR5 HGNC HGNC:4504 protein_coding YES CCDS9000.1 ENSP00000266674 O75473 A0A0A8K8C7 UPI000004B65C NM_003667.3 deleterious(0) 18/18 Gene3D:1.20.1070.10,Prints_domain:PR00373,PROSITE_profiles:PS50262,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF259,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 71583910 71583910 G T 1 0 0 0 0 1 0 0 0 8667 1348 47 2 2 LGR5 12 71583910 Missense_Mutation SNP G C3L-00412_T 46338559 71583910 61691399 76 6639 ACACB 0 . GRCh38 12 109167939 109167939 + Missense_Mutation SNP G G T rs773787420 C3L-00412_T C3L-00412_N G G c.830G>T p.Arg277Leu p.R277L ENST00000338432 4/53 219 205 14 190 190 0 strelka-varscan-mutect ACACB,missense_variant,p.Arg277Leu,ENST00000338432,;ACACB,missense_variant,p.Arg277Leu,ENST00000377848,NM_001093.3;ACACB,missense_variant,p.Arg75Leu,ENST00000544726,;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,downstream_gene_variant,,ENST00000546328,; T ENST00000338432 Transcript missense_variant 949/9360 830/7377 277/2458 R/L cGc/cTc rs773787420,COSM278567 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB deleterious(0) 4/53 PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF00289,Gene3D:3.40.50.20,Superfamily_domains:SSF52440 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773787420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 109167939 109167939 G T 1 0 0 0 0 1 0 0 0 150 1087 38 1 1 ACACB 12 109167939 Missense_Mutation SNP G C3L-00412_T 37584029 109167939 24107370 77 6640 EP400 0 . GRCh38 12 131982416 131982416 + Missense_Mutation SNP C C T novel C3L-00412_T C3L-00412_N C C c.1867C>T p.Leu623Phe p.L623F ENST00000389562 4/52 94 88 6 127 127 0 strelka-mutect EP400,missense_variant,p.Leu623Phe,ENST00000389562,;EP400,missense_variant,p.Leu623Phe,ENST00000389561,NM_015409.4;EP400,missense_variant,p.Leu659Phe,ENST00000333577,;EP400,missense_variant,p.Leu586Phe,ENST00000332482,; T ENST00000389562 Transcript missense_variant 1902/12836 1867/9372 623/3123 L/F Ctc/Ttc 1 1 EP400 HGNC HGNC:11958 protein_coding YES CCDS31929.2 ENSP00000374213 Q96L91 UPI00004566BC tolerated_low_confidence(0.07) 4/52 Low_complexity_(Seg):seg,hmmpanther:PTHR10799:SF599,hmmpanther:PTHR10799 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -13.01126 1 1 1 1 0 T 3 4 16 131982416 131982416 C T 1 0 0 0 0 1 0 0 0 4995 681 24 3 3 EP400 12 131982416 Missense_Mutation SNP C C3L-00412_T 22814477 131982416 1292893 78 6641 FARP1 0 . GRCh38 13 98213411 98213411 + Missense_Mutation SNP C C T C3L-00412_T C3L-00412_N C C c.169C>T p.Pro57Ser p.P57S ENST00000627049 2/28 120 114 6 89 89 0 strelka-varscan-mutect FARP1,missense_variant,p.Pro57Ser,ENST00000596580,;FARP1,missense_variant,p.Pro57Ser,ENST00000319562,NM_005766.3;FARP1,missense_variant,p.Pro57Ser,ENST00000627049,;FARP1,missense_variant,p.Pro57Ser,ENST00000595437,NM_001286839.1;FARP1,missense_variant,p.Pro57Ser,ENST00000376581,NM_001001715.3;FARP1,missense_variant,p.Pro57Ser,ENST00000598389,;MIR3170,downstream_gene_variant,,ENST00000582699,;FARP1,downstream_gene_variant,,ENST00000600648,; T ENST00000627049 Transcript missense_variant,splice_region_variant 587/5103 169/3231 57/1076 P/S Cca/Tca COSM1368142,COSM1368143,COSM1368144 1 1 FARP1 HGNC HGNC:3591 protein_coding YES CCDS66572.1 ENSP00000486285 C9JME2 UPI000041C6E3 tolerated(0.37) 2/28 PROSITE_profiles:PS50057,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF105,Pfam_domain:PF09379,Gene3D:3.10.20.90,SMART_domains:SM00295,Superfamily_domains:SSF54236,Prints_domain:PR00661 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 98213411 98213411 C T 1 0 0 0 0 1 0 0 0 5536 869 30 3 3 FARP1 13 98213411 Missense_Mutation SNP C C3L-00412_T 98213411 16150917 79 6642 COL4A1 0 . GRCh38 13 110186520 110186520 + Missense_Mutation SNP G G T rs760702058 C3L-00412_T C3L-00412_N G G c.1762C>A p.Pro588Thr p.P588T ENST00000375820 26/52 101 89 12 109 109 0 strelka-varscan-mutect COL4A1,missense_variant,p.Pro588Thr,ENST00000375820,NM_001845.5;COL4A1,downstream_gene_variant,,ENST00000543140,NM_001303110.1; T ENST00000375820 Transcript missense_variant 1884/6532 1762/5010 588/1669 P/T Cct/Act rs760702058 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 tolerated(0.09) 26/52 Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs760702058 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 110186520 110186520 G T 1 0 0 0 0 1 0 0 0 3478 1232 43 2 2 COL4A1 13 110186520 Missense_Mutation SNP G C3L-00412_T 11973109 110186520 4177808 80 6643 NUBPL 0 . GRCh38 14 31850178 31850178 + Missense_Mutation SNP T T C novel C3L-00412_T C3L-00412_N T T c.874T>C p.Phe292Leu p.F292L ENST00000281081 10/11 381 358 23 390 390 0 strelka-varscan-mutect NUBPL,missense_variant,p.Phe292Leu,ENST00000281081,NM_025152.2;NUBPL,missense_variant,p.Phe158Leu,ENST00000550649,;NUBPL,non_coding_transcript_exon_variant,,ENST00000418681,;NUBPL,downstream_gene_variant,,ENST00000551015,;NUBPL,3_prime_UTR_variant,,ENST00000547839,;NUBPL,non_coding_transcript_exon_variant,,ENST00000552888,; C ENST00000281081 Transcript missense_variant 919/3049 874/960 292/319 F/L Ttt/Ctt 1 1 NUBPL HGNC HGNC:20278 protein_coding YES CCDS41940.1 ENSP00000281081 Q8TB37 X5D2R5 UPI00003669AB NM_025152.2 tolerated(0.08) 10/11 HAMAP:MF_02040,hmmpanther:PTHR23264:SF31,hmmpanther:PTHR23264,Pfam_domain:PF10609,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 31850178 31850178 T C 1 0 0 0 0 1 0 0 0 10783 1725 60 5 5 NUBPL 14 31850178 Missense_Mutation SNP T C3L-00412_T 31850178 75193540 81 6644 YLPM1 0 . GRCh38 14 74817072 74817072 + Nonsense_Mutation SNP C C T rs752467058 C3L-00412_T C3L-00412_N C C c.5827C>T p.Gln1943Ter p.Q1943* ENST00000325680 14/21 82 76 6 58 58 0 strelka-varscan-mutect YLPM1,stop_gained,p.Gln1943Ter,ENST00000325680,NM_019589.2;YLPM1,stop_gained,p.Gln1237Ter,ENST00000552421,;YLPM1,stop_gained,p.Gln352Ter,ENST00000547879,;YLPM1,upstream_gene_variant,,ENST00000554107,;YLPM1,upstream_gene_variant,,ENST00000546901,;YLPM1,stop_gained,p.Gln1496Ter,ENST00000549293,; T ENST00000325680 Transcript stop_gained 5951/7108 5827/6441 1943/2146 Q/* Cag/Tag rs752467058 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 14/21 hmmpanther:PTHR13413,hmmpanther:PTHR13413:SF0,Pfam_domain:PF13671,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 HIGH 1 SNV 5 1 PASS rs752467058 . 0 202 8 0 0 0 0 0 -12.82976 0.9999913 1 1 1 0 T 4 4 16 74817072 74817072 C T 1 0 0 0 0 0 1 0 0 18048 595 21 3 3 YLPM1 14 74817072 Nonsense_Mutation SNP C C3L-00412_T 42966894 74817072 32226646 82 6645 GANC 0 . GRCh38 15 42310824 42310824 + Silent SNP C C T novel C3L-00412_T C3L-00412_N C C c.1035C>T p.= p.F345F ENST00000318010 10/24 138 121 17 149 149 0 strelka-mutect GANC,synonymous_variant,p.=,ENST00000318010,NM_198141.2;GANC,synonymous_variant,p.=,ENST00000566442,NM_001301409.1;GANC,non_coding_transcript_exon_variant,,ENST00000567421,;BNIP3P5,upstream_gene_variant,,ENST00000562290,; T ENST00000318010 Transcript synonymous_variant 1275/7781 1035/2745 345/914 F ttC/ttT 1 1 GANC HGNC HGNC:4139 protein_coding YES CCDS10084.1 ENSP00000326227 Q8TET4 UPI00001FE303 NM_198141.2 10/24 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF60,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 42310824 42310824 C T 1 0 0 0 0 0 0 0 1 6102 825 29 3 3 GANC 15 42310824 Silent SNP C C3L-00412_T 42310824 59680365 83 6646 ZNF609 0 . GRCh38 15 64675715 64675715 + Missense_Mutation SNP C C T novel C3L-00412_T C3L-00412_N C C c.2861C>T p.Ser954Phe p.S954F ENST00000326648 4/9 190 175 15 273 272 1 strelka-varscan-mutect ZNF609,missense_variant,p.Ser954Phe,ENST00000326648,NM_015042.1;RNU6-549P,downstream_gene_variant,,ENST00000384433,;ZNF609,downstream_gene_variant,,ENST00000559364,; T ENST00000326648 Transcript missense_variant 2989/8746 2861/4236 954/1411 S/F tCc/tTc 1 1 ZNF609 HGNC HGNC:29003 protein_coding YES CCDS32270.1 ENSP00000316527 O15014 UPI00001D7783 NM_015042.1 deleterious(0.02) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR21564:SF3,hmmpanther:PTHR21564 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 64675715 64675715 C T 1 0 0 0 0 1 0 0 0 18610 855 30 3 3 ZNF609 15 64675715 Missense_Mutation SNP C C3L-00412_T 22364891 64675715 37315474 84 6647 LINGO1 0 . GRCh38 15 77614893 77614893 + Silent SNP G G A rs770463478 C3L-00412_T C3L-00412_N G G c.1014C>T p.= p.R338R ENST00000355300 2/2 287 255 32 345 345 0 strelka-varscan-mutect LINGO1,synonymous_variant,p.=,ENST00000355300,NM_032808.6;LINGO1,synonymous_variant,p.=,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,downstream_gene_variant,,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000561686,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000564472,; A ENST00000355300 Transcript synonymous_variant 1189/3055 1014/1863 338/620 R cgC/cgT rs770463478,COSM5179618 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1 LOW 1 SNV 1 0,1 1 PASS rs770463478 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 77614893 77614893 G A 1 0 0 0 0 0 0 0 1 8735 1074 38 1 1 LINGO1 15 77614893 Silent SNP G C3L-00412_T 12939178 77614893 24376296 85 6648 TICRR 0 . GRCh38 15 89575751 89575751 + Silent SNP G G A novel C3L-00412_T C3L-00412_N G G c.165G>A p.= p.A55A ENST00000268138 1/22 248 233 15 287 287 0 strelka-varscan-mutect TICRR,synonymous_variant,p.=,ENST00000268138,NM_152259.3;TICRR,synonymous_variant,p.=,ENST00000560985,NM_001308025.1;RP11-429B14.1,intron_variant,,ENST00000559041,;RP11-429B14.3,downstream_gene_variant,,ENST00000560477,; A ENST00000268138 Transcript synonymous_variant 270/6775 165/5733 55/1910 A gcG/gcA 1 1 TICRR HGNC HGNC:28704 protein_coding YES CCDS10352.2 ENSP00000268138 Q7Z2Z1 UPI0000D61399 NM_152259.3 1/22 hmmpanther:PTHR21556 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 89575751 89575751 G A 1 0 0 0 0 0 0 0 1 16328 1074 38 1 1 TICRR 15 89575751 Silent SNP G C3L-00412_T 11960858 89575751 12415438 86 6649 TNRC6A 0 . GRCh38 16 24791082 24791082 + Missense_Mutation SNP G G A novel C3L-00412_T C3L-00412_N G G c.2440G>A p.Val814Ile p.V814I ENST00000395799 6/25 64 59 5 64 64 0 strelka-mutect TNRC6A,missense_variant,p.Val814Ile,ENST00000395799,NM_014494.2;TNRC6A,missense_variant,p.Val814Ile,ENST00000315183,;TNRC6A,upstream_gene_variant,,ENST00000450465,;TNRC6A,3_prime_UTR_variant,,ENST00000491718,;TNRC6A,upstream_gene_variant,,ENST00000568903,;TNRC6A,upstream_gene_variant,,ENST00000561726,;TNRC6A,upstream_gene_variant,,ENST00000567232,; A ENST00000395799 Transcript missense_variant 2569/8438 2440/5889 814/1962 V/I Gtc/Atc 1 1 TNRC6A HGNC HGNC:11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 UPI000059D33E NM_014494.2 tolerated(0.19) 6/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28 MODERATE 1 SNV 5 1 PASS . . 0 198 11 0 0 0 0 0 -11.38581 0.9998466 1 1 1 0 A 3 1 16 24791082 24791082 G A 1 0 0 0 0 1 0 0 0 16813 1261 44 3 3 TNRC6A 16 24791082 Missense_Mutation SNP G C3L-00412_T 24791082 65547263 87 6650 SETD1A 0 . GRCh38 16 30971437 30971437 + Nonsense_Mutation SNP G G T rs773277646 C3L-00412_T C3L-00412_N G G c.3076G>T p.Glu1026Ter p.E1026* ENST00000262519 13/19 95 84 11 96 96 0 strelka-varscan-mutect SETD1A,stop_gained,p.Glu1026Ter,ENST00000262519,NM_014712.2; T ENST00000262519 Transcript stop_gained 3762/6903 3076/5124 1026/1707 E/* Gaa/Taa rs773277646,COSM4060278 1 1 SETD1A HGNC HGNC:29010 protein_coding YES CCDS32435.1 ENSP00000262519 O15047 UPI00001C1FA9 NM_014712.2 13/19 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF295 0,1 HIGH 1 SNV 1 0,1 1 PASS rs773277646 . 0 202 8 0 0 0 0 0 -19.99904 0.9999967 1 1 1 0 T 4 4 16 30971437 30971437 G T 1 0 0 0 0 0 1 0 0 14407 1059 37 1 1 SETD1A 16 30971437 Nonsense_Mutation SNP G C3L-00412_T 6180355 30971437 59366908 88 6651 ITGAX 0 . GRCh38 16 31377255 31377255 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.2779G>C p.Val927Leu p.V927L ENST00000562522 23/31 143 135 8 176 176 0 strelka-varscan-mutect ITGAX,missense_variant,p.Val927Leu,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Val927Leu,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000562138,; C ENST00000562522 Transcript missense_variant 2812/3990 2779/3510 927/1169 V/L Gtg/Ctg 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.04) 23/31 Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 31377255 31377255 G C 1 0 0 0 0 1 0 0 0 7796 1377 48 4 4 ITGAX 16 31377255 Missense_Mutation SNP G C3L-00412_T 405818 31377255 58961090 89 6652 CDH8 0 . GRCh38 16 61652821 61652821 + Missense_Mutation SNP G G A novel C3L-00412_T C3L-00412_N G G c.2231C>T p.Thr744Ile p.T744I ENST00000577730 12/12 35 31 4 60 60 0 varscan-mutect CDH8,missense_variant,p.Thr744Ile,ENST00000577730,;CDH8,3_prime_UTR_variant,,ENST00000577390,NM_001796.4;CDH8,intron_variant,,ENST00000299345,;CDH8,downstream_gene_variant,,ENST00000583483,;CDH8,3_prime_UTR_variant,,ENST00000585315,; A ENST00000577730 Transcript missense_variant 2430/8009 2231/2235 744/744 T/I aCa/aTa 1 -1 CDH8 HGNC HGNC:1767 protein_coding ENSP00000462018 J3KRI5 UPI0002466E8E 12/12 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -11.45608 1 1 1 1 0 A 3 1 16 61652821 61652821 G A 1 0 0 0 0 1 0 0 0 2819 1377 48 3 3 CDH8 16 61652821 Missense_Mutation SNP G C3L-00412_T 30275566 61652821 28685524 90 6653 BANP 0 . GRCh38 16 88006104 88006104 + Missense_Mutation SNP G G T rs773807056 C3L-00412_T C3L-00412_N G G c.470G>T p.Arg157Leu p.R157L ENST00000393207 6/14 299 280 19 282 282 0 strelka-varscan-mutect BANP,missense_variant,p.Arg157Leu,ENST00000393207,NM_001173543.1;BANP,missense_variant,p.Arg165Leu,ENST00000538234,NM_001173539.1,NM_001173542.1;BANP,missense_variant,p.Arg157Leu,ENST00000286122,;BANP,missense_variant,p.Arg126Leu,ENST00000393208,NM_079837.2;BANP,missense_variant,p.Arg126Leu,ENST00000355022,NM_017869.3;BANP,missense_variant,p.Arg132Leu,ENST00000626016,NM_001173540.1;BANP,missense_variant,p.Arg126Leu,ENST00000479780,NM_001173541.1;BANP,missense_variant,p.Arg132Leu,ENST00000439677,;BANP,downstream_gene_variant,,ENST00000436970,;BANP,3_prime_UTR_variant,,ENST00000459966,;BANP,downstream_gene_variant,,ENST00000466197,;BANP,downstream_gene_variant,,ENST00000485772,; T ENST00000393207 Transcript missense_variant 691/2438 470/1560 157/519 R/L cGt/cTt rs773807056 1 1 BANP HGNC HGNC:13450 protein_coding YES CCDS54054.1 ENSP00000376902 Q8N9N5 UPI0000E59DA3 NM_001173543.1 tolerated_low_confidence(0.15) 6/14 hmmpanther:PTHR16243 MODERATE 1 SNV 2 1 PASS rs773807056 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 88006104 88006104 G T 1 0 0 0 0 1 0 0 0 1462 1145 40 1 1 BANP 16 88006104 Missense_Mutation SNP G C3L-00412_T 26353283 88006104 2332241 91 6654 OR1E1 0 . GRCh38 17 3397571 3397571 + Silent SNP C C A novel C3L-00412_T C3L-00412_N C C c.840G>T p.= p.V280V ENST00000322608 1/1 217 196 21 249 248 1 varscan-mutect OR1E1,synonymous_variant,p.=,ENST00000322608,NM_003553.2; A ENST00000322608 Transcript synonymous_variant 840/1307 840/945 280/314 V gtG/gtT 1 -1 OR1E1 HGNC HGNC:8189 protein_coding YES CCDS11024.1 ENSP00000313384 P30953 UPI0000041BB6 NM_003553.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF367,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 3397571 3397571 C A 1 0 0 0 0 0 0 0 1 11032 581 21 2 2 OR1E1 17 3397571 Silent SNP C C3L-00412_T 3397571 79859870 92 6655 PIK3R6 0 . GRCh38 17 8827271 8827271 + Silent SNP C C G rs755202323 C3L-00412_T C3L-00412_N C C c.1416G>C p.= p.P472P ENST00000619866 13/20 122 112 10 132 132 0 strelka-varscan-mutect PIK3R6,synonymous_variant,p.=,ENST00000619866,NM_001010855.3,NM_001290211.1;PIK3R6,synonymous_variant,p.=,ENST00000614407,;PIK3R6,3_prime_UTR_variant,,ENST00000611951,;PIK3R6,3_prime_UTR_variant,,ENST00000613555,; G ENST00000619866 Transcript synonymous_variant 1656/3041 1416/2265 472/754 P ccG/ccC rs755202323 1 -1 PIK3R6 HGNC HGNC:27101 protein_coding YES CCDS73985.1 ENSP00000480157 Q5UE93 UPI0000043463 NM_001010855.3,NM_001290211.1 13/20 hmmpanther:PTHR15593:SF1,hmmpanther:PTHR15593 LOW 1 SNV 5 1 PASS rs755202323 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 8827271 8827271 C G 1 0 0 0 0 0 0 0 1 12018 639 23 4 4 PIK3R6 17 8827271 Silent SNP C C3L-00412_T 5429700 8827271 74430170 93 6656 FLII 0 . GRCh38 17 18246013 18246013 + Missense_Mutation SNP C C A rs145565671 C3L-00412_T C3L-00412_N C C c.3317G>T p.Gly1106Val p.G1106V ENST00000327031 26/30 258 243 15 357 357 0 strelka-varscan-mutect FLII,missense_variant,p.Gly1106Val,ENST00000327031,NM_002018.3;FLII,missense_variant,p.Gly1051Val,ENST00000545457,NM_001256265.1;FLII,missense_variant,p.Gly1095Val,ENST00000579294,NM_001256264.1;FLII,missense_variant,p.Gly17Val,ENST00000577398,;FLII,intron_variant,,ENST00000578558,;FLII,intron_variant,,ENST00000577485,;LLGL1,downstream_gene_variant,,ENST00000316843,NM_004140.3;LLGL1,downstream_gene_variant,,ENST00000621229,;FLII,3_prime_UTR_variant,,ENST00000578101,;FLII,non_coding_transcript_exon_variant,,ENST00000487693,;FLII,non_coding_transcript_exon_variant,,ENST00000493600,;FLII,non_coding_transcript_exon_variant,,ENST00000474265,;FLII,non_coding_transcript_exon_variant,,ENST00000493401,;LLGL1,downstream_gene_variant,,ENST00000479155,;FLII,downstream_gene_variant,,ENST00000496727,;FLII,upstream_gene_variant,,ENST00000465046,;FLII,downstream_gene_variant,,ENST00000459958,;FLII,downstream_gene_variant,,ENST00000577402,;FLII,downstream_gene_variant,,ENST00000580453,;FLII,upstream_gene_variant,,ENST00000581858,;FLII,upstream_gene_variant,,ENST00000487369,;FLII,downstream_gene_variant,,ENST00000580966,; A ENST00000327031 Transcript missense_variant 3543/4338 3317/3810 1106/1269 G/V gGc/gTc rs145565671 1 -1 FLII HGNC HGNC:3750 protein_coding YES CCDS11192.1 ENSP00000324573 Q13045 UPI0000001284 NM_002018.3 deleterious(0) 26/30 hmmpanther:PTHR11977:SF42,hmmpanther:PTHR11977,Gene3D:3.40.20.10,SMART_domains:SM00262,Superfamily_domains:SSF55753 MODERATE 1 SNV 1 1 PASS rs145565671 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 18246013 18246013 C A 1 0 0 0 0 1 0 0 0 5787 739 26 2 2 FLII 17 18246013 Missense_Mutation SNP C C3L-00412_T 9418742 18246013 65011428 94 6657 FAM187A 0 . GRCh38 17 44904238 44904238 + Missense_Mutation SNP G G A novel C3L-00412_T C3L-00412_N G G c.409G>A p.Asp137Asn p.D137N ENST00000331733 4/4 134 118 16 136 136 0 strelka-varscan-mutect FAM187A,missense_variant,p.Asp137Asn,ENST00000331733,;CCDC103,3_prime_UTR_variant,,ENST00000417826,;EFTUD2,upstream_gene_variant,,ENST00000426333,NM_004247.3;EFTUD2,upstream_gene_variant,,ENST00000591382,NM_001258353.1;EFTUD2,upstream_gene_variant,,ENST00000592576,NM_001258354.1;GFAP,downstream_gene_variant,,ENST00000253408,NM_002055.4;EFTUD2,upstream_gene_variant,,ENST00000402521,NM_001142605.1;FAM187A,downstream_gene_variant,,ENST00000412523,NM_001258399.1,NM_001258396.1,NM_213607.2,NM_001258395.1;CCDC103,downstream_gene_variant,,ENST00000410006,;CCDC103,downstream_gene_variant,,ENST00000357776,NM_001258398.1;CCDC103,downstream_gene_variant,,ENST00000577339,;CCDC103,downstream_gene_variant,,ENST00000410027,NM_001258397.1;GFAP,downstream_gene_variant,,ENST00000588735,;EFTUD2,upstream_gene_variant,,ENST00000593072,;GFAP,downstream_gene_variant,,ENST00000591880,;GFAP,downstream_gene_variant,,ENST00000586125,;AC015936.3,intron_variant,,ENST00000441312,;GFAP,downstream_gene_variant,,ENST00000592706,;GFAP,downstream_gene_variant,,ENST00000588640,;GFAP,downstream_gene_variant,,ENST00000592065,;GFAP,downstream_gene_variant,,ENST00000589701,;EFTUD2,upstream_gene_variant,,ENST00000589825,;GFAP,downstream_gene_variant,,ENST00000585543,;EFTUD2,upstream_gene_variant,,ENST00000592408,;EFTUD2,upstream_gene_variant,,ENST00000590105,; A ENST00000331733 Transcript missense_variant 2245/3397 409/1242 137/413 D/N Gat/Aat 1 1 FAM187A HGNC HGNC:35153 protein_coding ENSP00000329499 A6NFU0 UPI000013E667 deleterious(0) 4/4 hmmpanther:PTHR32178,hmmpanther:PTHR32178:SF7 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 44904238 44904238 G A 1 0 0 0 0 1 0 0 0 5363 1058 37 1 1 FAM187A 17 44904238 Missense_Mutation SNP G C3L-00412_T 26658225 44904238 38353203 95 6658 MAP3K3 0 . GRCh38 17 63688556 63688556 + Missense_Mutation SNP G G T rs773083246 C3L-00412_T C3L-00412_N G G c.833G>T p.Arg278Leu p.R278L ENST00000361357 10/17 292 269 23 337 337 0 strelka-varscan-mutect MAP3K3,missense_variant,p.Arg278Leu,ENST00000361357,NM_203351.1;MAP3K3,missense_variant,p.Arg247Leu,ENST00000361733,NM_002401.3;MAP3K3,missense_variant,p.Arg278Leu,ENST00000579585,;MAP3K3,missense_variant,p.Arg274Leu,ENST00000584573,;MAP3K3,missense_variant,p.Arg243Leu,ENST00000577395,;MAP3K3,non_coding_transcript_exon_variant,,ENST00000577784,;MAP3K3,3_prime_UTR_variant,,ENST00000577597,;MAP3K3,3_prime_UTR_variant,,ENST00000585302,;MAP3K3,non_coding_transcript_exon_variant,,ENST00000578622,;MAP3K3,upstream_gene_variant,,ENST00000577839,;MAP3K3,upstream_gene_variant,,ENST00000581732,; T ENST00000361357 Transcript missense_variant 1151/4818 833/1974 278/657 R/L cGt/cTt rs773083246 1 1 MAP3K3 HGNC HGNC:6855 protein_coding YES CCDS32701.1 ENSP00000354927 Q99759 UPI0000074003 NM_203351.1 tolerated(0.06) 10/17 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF350 MODERATE 1 SNV 1 1 PASS rs773083246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 63688556 63688556 G T 1 0 0 0 0 1 0 0 0 9174 1145 40 1 1 MAP3K3 17 63688556 Missense_Mutation SNP G C3L-00412_T 18784318 63688556 19568885 96 6659 ANKRD12 0 . GRCh38 18 9254625 9254625 + Missense_Mutation SNP A A G C3L-00412_T C3L-00412_N A A c.1358A>G p.Asp453Gly p.D453G ENST00000262126 9/13 90 84 6 73 73 0 strelka-varscan-mutect ANKRD12,missense_variant,p.Asp453Gly,ENST00000262126,NM_015208.4;ANKRD12,missense_variant,p.Asp430Gly,ENST00000400020,NM_001083625.2,NM_001204056.1;ANKRD12,downstream_gene_variant,,ENST00000546007,;RP11-888D10.4,upstream_gene_variant,,ENST00000609701,;Y_RNA,downstream_gene_variant,,ENST00000384364,;Y_RNA,upstream_gene_variant,,ENST00000364013,;RP11-21J18.1,downstream_gene_variant,,ENST00000578850,;ANKRD12,3_prime_UTR_variant,,ENST00000359158,; G ENST00000262126 Transcript missense_variant 1598/11288 1358/6189 453/2062 D/G gAt/gGt COSM324712 1 1 ANKRD12 HGNC HGNC:29135 protein_coding YES CCDS11843.1 ENSP00000262126 Q6UB98 UPI0000073327 NM_015208.4 deleterious_low_confidence(0) 9/13 hmmpanther:PTHR24149,hmmpanther:PTHR24149:SF7 1 MODERATE 1 SNV 1 1 1 PASS rs1181808326 . 0 205 5 0 0 0 0 0 -12.747 1 1 1 1 0 G 3 3 16 9254625 9254625 A G 1 0 0 0 0 1 0 0 0 741 333 12 5 5 ANKRD12 18 9254625 Missense_Mutation SNP A C3L-00412_T 9254625 71118660 97 6660 ZNF521 0 . GRCh38 18 25226032 25226032 + Missense_Mutation SNP C C A rs779955981 C3L-00412_T C3L-00412_N C C c.1886G>T p.Arg629Leu p.R629L ENST00000361524 4/8 201 186 15 195 194 1 strelka-varscan-mutect ZNF521,missense_variant,p.Arg629Leu,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Arg409Leu,ENST00000584787,NM_001308225.1;ZNF521,missense_variant,p.Arg629Leu,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,missense_variant,p.Arg629Leu,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; A ENST00000361524 Transcript missense_variant 2035/4871 1886/3936 629/1311 R/L cGt/cTt rs779955981,COSM4580350 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 tolerated(0.76) 4/8 hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779955981 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 25226032 25226032 C A 1 0 0 0 0 1 0 0 0 18537 536 19 1 1 ZNF521 18 25226032 Missense_Mutation SNP C C3L-00412_T 15971407 25226032 55147253 98 6661 MBD1 0 . GRCh38 18 50269798 50269798 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.1799G>T p.Gly600Val p.G600V ENST00000590208 16/16 263 246 17 306 304 2 strelka-varscan-mutect MBD1,stop_gained,p.Glu496Ter,ENST00000587605,NM_001204143.1;MBD1,missense_variant,p.Gly531Val,ENST00000269471,NM_015845.3;MBD1,missense_variant,p.Gly600Val,ENST00000590208,NM_001204136.1;MBD1,missense_variant,p.Gly531Val,ENST00000588937,;MBD1,3_prime_UTR_variant,,ENST00000591416,;MBD1,3_prime_UTR_variant,,ENST00000269468,NM_015846.3;MBD1,3_prime_UTR_variant,,ENST00000347968,NM_015844.2;MBD1,3_prime_UTR_variant,,ENST00000339998,NM_001204142.1;MBD1,3_prime_UTR_variant,,ENST00000353909,NM_015847.3;MBD1,3_prime_UTR_variant,,ENST00000585595,;MBD1,3_prime_UTR_variant,,ENST00000589541,;MBD1,intron_variant,,ENST00000585672,NM_001204141.1;MBD1,intron_variant,,ENST00000382948,NM_001204139.1;MBD1,intron_variant,,ENST00000592060,;MBD1,downstream_gene_variant,,ENST00000457839,NM_001204137.1,NM_001204138.1;MBD1,downstream_gene_variant,,ENST00000398495,NM_001204140.1;CFAP53,upstream_gene_variant,,ENST00000398545,NM_145020.3;MBD1,downstream_gene_variant,,ENST00000398493,;MBD1,downstream_gene_variant,,ENST00000591535,NM_001204151.1;MBD1,downstream_gene_variant,,ENST00000398488,NM_002384.2;MBD1,downstream_gene_variant,,ENST00000589733,;MBD1,downstream_gene_variant,,ENST00000586884,; A ENST00000590208 Transcript missense_variant 2146/2913 1799/1968 600/655 G/V gGa/gTa 1 -1 MBD1 HGNC HGNC:6916 protein_coding YES CCDS59320.1 ENSP00000468785 Q9UIS9 UPI0001F995B6 NM_001204136.1 tolerated_low_confidence(0.19) 16/16 hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 50269798 50269798 C A 1 0 0 0 0 1 0 0 0 9271 864 30 2 2 MBD1 18 50269798 Missense_Mutation SNP C C3L-00412_T 25043766 50269798 30103487 99 6662 ALPK2 0 . GRCh38 18 58529209 58529209 + Missense_Mutation SNP C C G rs562011454 C3L-00412_T C3L-00412_N C C c.5383G>C p.Glu1795Gln p.E1795Q ENST00000361673 6/13 152 143 9 207 207 0 strelka-varscan-mutect ALPK2,missense_variant,p.Glu1795Gln,ENST00000361673,NM_052947.3;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; G ENST00000361673 Transcript missense_variant 5597/7303 5383/6513 1795/2170 E/Q Gag/Cag rs562011454 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0) 6/13 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS rs562011454 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 58529209 58529209 C G 1 0 0 0 0 1 0 0 0 645 835 29 4 4 ALPK2 18 58529209 Missense_Mutation SNP C C3L-00412_T 8259411 58529209 21844076 100 6663 STK11 0 . GRCh38 19 1220492 1220492 + Missense_Mutation SNP T T G novel C3L-00412_T C3L-00412_N T T c.584T>G p.Leu195Arg p.L195R ENST00000326873 4/10 69 61 8 78 77 1 strelka-mutect STK11,missense_variant,p.Leu195Arg,ENST00000586243,;STK11,missense_variant,p.Leu195Arg,ENST00000326873,NM_000455.4;STK11,missense_variant,p.Leu137Arg,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; G ENST00000326873 Transcript missense_variant 1034/2611 584/1302 195/433 L/R cTg/cGg 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 4/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 197 12 0 0 0 0 0 -17.45251 0.9998589 1 1 1 0 G 3 3 16 1220492 1220492 T G 1 0 0 0 0 1 0 0 0 15664 1580 55 5 5 STK11 19 1220492 Missense_Mutation SNP T C3L-00412_T 1220492 57397124 101 6664 CLEC4M 0 . GRCh38 19 7766017 7766017 + Silent SNP A A G novel C3L-00412_T C3L-00412_N A A c.594A>G p.= p.K198K ENST00000327325 4/7 101 92 9 85 84 1 varscan-mutect CLEC4M,synonymous_variant,p.=,ENST00000327325,NM_001144909.1,NM_001144905.1,NM_001144910.1,NM_014257.4;CLEC4M,synonymous_variant,p.=,ENST00000394122,;CLEC4M,synonymous_variant,p.=,ENST00000248228,;CLEC4M,synonymous_variant,p.=,ENST00000334806,NM_001144904.1;CLEC4M,synonymous_variant,p.=,ENST00000359059,NM_001144907.1;CLEC4M,synonymous_variant,p.=,ENST00000596363,NM_001144911.1;CLEC4M,synonymous_variant,p.=,ENST00000596707,;CLEC4M,synonymous_variant,p.=,ENST00000595751,;CLEC4M,intron_variant,,ENST00000597522,NM_001144908.1;CLEC4M,intron_variant,,ENST00000595496,NM_001144906.1;CLEC4M,non_coding_transcript_exon_variant,,ENST00000601089,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000598879,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000599333,;CLEC4M,upstream_gene_variant,,ENST00000602143,; G ENST00000327325 Transcript synonymous_variant 712/1935 594/1200 198/399 K aaA/aaG 1 1 CLEC4M HGNC HGNC:13523 protein_coding YES CCDS12187.1 ENSP00000316228 Q9H2X3 UPI0000073C48 NM_001144909.1,NM_001144905.1,NM_001144910.1,NM_014257.4 4/7 hmmpanther:PTHR22802:SF244,hmmpanther:PTHR22802 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -18.70645 1 1 1 1 0 G 2 3 16 7766017 7766017 A G 1 0 0 0 0 0 0 0 1 3286 98 4 5 5 CLEC4M 19 7766017 Silent SNP A C3L-00412_T 6545525 7766017 50851599 102 6665 SMARCA4 0 . GRCh38 19 10991154 10991154 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.1250G>T p.Arg417Leu p.R417L ENST00000429416 9/36 246 223 23 276 276 0 strelka-varscan-mutect SMARCA4,missense_variant,p.Arg417Leu,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Arg417Leu,ENST00000413806,;SMARCA4,missense_variant,p.Arg417Leu,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.Arg417Leu,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Arg417Leu,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.Arg417Leu,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.Arg417Leu,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.Arg417Leu,ENST00000444061,NM_001128848.1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,; T ENST00000429416 Transcript missense_variant 1531/5691 1250/4944 417/1647 R/L cGc/cTc 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 deleterious(0.02) 9/36 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 10991154 10991154 G T 1 0 0 0 0 1 0 0 0 15063 1101 38 1 1 SMARCA4 19 10991154 Missense_Mutation SNP G C3L-00412_T 3225137 10991154 47626462 103 6666 ZNF626 0 . GRCh38 19 20646405 20646405 + Missense_Mutation SNP C C G novel C3L-00412_T C3L-00412_N C C c.4G>C p.Gly2Arg p.G2R ENST00000601440 2/4 197 181 16 192 191 1 varscan-mutect ZNF626,missense_variant,p.Gly2Arg,ENST00000601440,NM_001076675.2;ZNF626,missense_variant,p.Gly2Arg,ENST00000612591,;ZNF626,missense_variant,p.Gly2Arg,ENST00000291750,NM_145297.3;ZNF626,intron_variant,,ENST00000595405,;CTC-513N18.7,splice_region_variant,,ENST00000595094,; G ENST00000601440 Transcript missense_variant,splice_region_variant 151/5963 4/1587 2/528 G/R Gga/Cga 1 -1 ZNF626 HGNC HGNC:30461 protein_coding YES CCDS42535.1 ENSP00000469958 Q68DY1 UPI000035E843 NM_001076675.2 deleterious(0.03) 2/4 hmmpanther:PTHR24384:SF129,hmmpanther:PTHR24384,Superfamily_domains:0044637 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 20646405 20646405 C G 1 0 0 0 0 1 0 0 0 18625 637 22 4 4 ZNF626 19 20646405 Missense_Mutation SNP C C3L-00412_T 9655251 20646405 37971211 104 6667 ZNF536 0 . GRCh38 19 30444811 30444811 + Missense_Mutation SNP G G T C3L-00412_T C3L-00412_N G G c.1249G>T p.Gly417Cys p.G417C ENST00000355537 2/5 165 147 18 194 194 0 strelka-varscan-mutect ZNF536,missense_variant,p.Gly417Cys,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Gly417Cys,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript missense_variant 1396/4945 1249/3903 417/1300 G/C Ggc/Tgc COSM5265916,COSM994430 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0.01) 2/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1433897311 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 30444811 30444811 G T 1 0 0 0 0 1 0 0 0 18547 1116 39 1 1 ZNF536 19 30444811 Missense_Mutation SNP G C3L-00412_T 9798406 30444811 28172805 105 6668 ZNF781 0 . GRCh38 19 37669934 37669934 + Missense_Mutation SNP C C G novel C3L-00412_T C3L-00412_N C C c.215G>C p.Cys72Ser p.C72S ENST00000358582 4/4 100 95 5 121 121 0 strelka-varscan-mutect ZNF781,missense_variant,p.Cys72Ser,ENST00000358582,NM_152605.3;ZNF781,missense_variant,p.Cys72Ser,ENST00000590008,;ZFP30,intron_variant,,ENST00000587199,;ZFP30,intron_variant,,ENST00000586732,;ZFP30,intron_variant,,ENST00000589676,;ZNF781,downstream_gene_variant,,ENST00000593040,; G ENST00000358582 Transcript missense_variant 964/3147 215/984 72/327 C/S tGt/tCt 1 -1 ZNF781 HGNC HGNC:26745 protein_coding YES CCDS12507.1 ENSP00000351391 Q8N8C0 A0A024R0G3 UPI0000351D6C NM_152605.3 tolerated(0.43) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.95365 1 1 1 1 0 G 3 3 16 37669934 37669934 C G 1 0 0 0 0 1 0 0 0 18737 478 17 4 4 ZNF781 19 37669934 Missense_Mutation SNP C C3L-00412_T 7225123 37669934 20947682 106 6669 CEACAM16 0 . GRCh38 19 44708075 44708075 + Missense_Mutation SNP C C A rs775387666 C3L-00412_T C3L-00412_N C C c.1155C>A p.Asn385Lys p.N385K ENST00000587331 6/7 141 132 9 130 130 0 strelka-varscan-mutect CEACAM16,missense_variant,p.Asn385Lys,ENST00000587331,NM_001039213.3;CEACAM16,missense_variant,p.Asn385Lys,ENST00000405314,;CTB-171A8.1,intron_variant,,ENST00000590796,; A ENST00000587331 Transcript missense_variant 1370/1701 1155/1278 385/425 N/K aaC/aaA rs775387666 1 1 CEACAM16 HGNC HGNC:31948 protein_coding YES CCDS54278.1 ENSP00000466561 Q2WEN9 UPI00001D8176 NM_001039213.3 deleterious(0) 6/7 Gene3D:2.60.40.10,hmmpanther:PTHR10489,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs775387666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 44708075 44708075 C A 1 0 0 0 0 1 0 0 0 2894 564 20 2 2 CEACAM16 19 44708075 Missense_Mutation SNP C C3L-00412_T 7038141 44708075 13909541 107 6670 TRPM4 0 . GRCh38 19 49171595 49171595 + Silent SNP C C G novel C3L-00412_T C3L-00412_N C C c.876C>G p.= p.T292T ENST00000252826 8/25 162 146 16 232 232 0 strelka-varscan-mutect TRPM4,synonymous_variant,p.=,ENST00000252826,NM_017636.3;TRPM4,synonymous_variant,p.=,ENST00000427978,NM_001195227.1;TRPM4,downstream_gene_variant,,ENST00000598691,;TRPM4,non_coding_transcript_exon_variant,,ENST00000601347,;TRPM4,3_prime_UTR_variant,,ENST00000595519,NM_001321283.1;TRPM4,3_prime_UTR_variant,,ENST00000598502,NM_001321282.1;TRPM4,3_prime_UTR_variant,,ENST00000598697,NM_001321285.1;TRPM4,non_coding_transcript_exon_variant,,ENST00000596338,;TRPM4,downstream_gene_variant,,ENST00000594568,; G ENST00000252826 Transcript synonymous_variant 1002/4109 876/3645 292/1214 T acC/acG 1 1 TRPM4 HGNC HGNC:17993 protein_coding YES CCDS33073.1 ENSP00000252826 Q8TD43 UPI0000070598 NM_017636.3 8/25 hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800,Superfamily_domains:0051779 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 49171595 49171595 C G 1 0 0 0 0 0 0 0 1 17094 610 22 4 4 TRPM4 19 49171595 Silent SNP C C3L-00412_T 4463520 49171595 9446021 108 6671 RFPL4AL1 0 . GRCh38 19 55772768 55772768 + Missense_Mutation SNP T T A novel C3L-00412_T C3L-00412_N T T c.453T>A p.His151Gln p.H151Q ENST00000341750 3/3 400 379 21 458 458 0 varscan-mutect RFPL4AL1,missense_variant,p.His151Gln,ENST00000341750,NM_001277397.1;RFPL4AP1,upstream_gene_variant,,ENST00000530883,; A ENST00000341750 Transcript missense_variant 497/908 453/864 151/287 H/Q caT/caA 1 1 RFPL4AL1 HGNC HGNC:45147 protein_coding YES CCDS59425.1 ENSP00000345151 F8VTS6 UPI000015FD78 NM_001277397.1 deleterious(0.02) 3/3 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 55772768 55772768 T A 1 0 0 0 0 1 0 0 0 13429 1490 52 4 4 RFPL4AL1 19 55772768 Missense_Mutation SNP T C3L-00412_T 6601173 55772768 2844848 109 6672 SIRPG 0 . GRCh38 20 1636472 1636472 + Missense_Mutation SNP G G T C3L-00412_T C3L-00412_N G G c.464C>A p.Ala155Glu p.A155E ENST00000303415 3/6 159 146 13 214 214 0 strelka-varscan-mutect SIRPG,missense_variant,p.Ala122Glu,ENST00000381580,;SIRPG,missense_variant,p.Ala155Glu,ENST00000303415,NM_018556.3;SIRPG,missense_variant,p.Ala155Glu,ENST00000381583,NM_001039508.1;SIRPG,missense_variant,p.Ala155Glu,ENST00000216927,;SIRPG,intron_variant,,ENST00000344103,NM_080816.2;SIRPG-AS1,intron_variant,,ENST00000456177,;SIRPG-AS1,intron_variant,,ENST00000437384,; T ENST00000303415 Transcript missense_variant 529/1716 464/1164 155/387 A/E gCg/gAg COSM4653257 1 -1 SIRPG HGNC HGNC:15757 protein_coding YES CCDS13020.2 ENSP00000305529 Q9P1W8 UPI00001AE5FD NM_018556.3 tolerated(0.22) 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6,Pfam_domain:PF07654,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS rs1290175888 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 1636472 1636472 G T 1 0 0 0 0 1 0 0 0 14599 1087 38 1 1 SIRPG 20 1636472 Missense_Mutation SNP G C3L-00412_T 1636472 62807695 110 6673 TGM6 0 . GRCh38 20 2397960 2397960 + Missense_Mutation SNP C C G rs575622127 C3L-00412_T C3L-00412_N C C c.586C>G p.Arg196Gly p.R196G ENST00000202625 5/13 472 446 26 452 452 0 strelka-varscan-mutect TGM6,missense_variant,p.Arg196Gly,ENST00000202625,NM_198994.2;TGM6,missense_variant,p.Arg196Gly,ENST00000381423,NM_001254734.1;TGM6,non_coding_transcript_exon_variant,,ENST00000477505,; G ENST00000202625 Transcript missense_variant 647/2292 586/2121 196/706 R/G Cga/Gga rs575622127 1 1 TGM6 HGNC HGNC:16255 protein_coding YES CCDS13025.1 ENSP00000202625 O95932 UPI0000367011 NM_198994.2 deleterious(0) 5/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF50,PIRSF_domain:PIRSF000459,Gene3D:1ex0A02,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs575622127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 16 2397960 2397960 C G 1 0 0 0 0 1 0 0 0 16267 876 31 4 4 TGM6 20 2397960 Missense_Mutation SNP C C3L-00412_T 761488 2397960 62046207 111 6674 GPCPD1 0 . GRCh38 20 5578612 5578612 + Splice_Site SNP C C A novel C3L-00412_T C3L-00412_N C C c.474-1G>T p.X158_splice ENST00000379019 138 126 12 190 190 0 strelka-varscan-mutect GPCPD1,splice_acceptor_variant,,ENST00000379019,NM_019593.3;GPCPD1,upstream_gene_variant,,ENST00000418646,;GPCPD1,splice_acceptor_variant,,ENST00000481038,;GPCPD1,splice_acceptor_variant,,ENST00000481690,;GPCPD1,upstream_gene_variant,,ENST00000633552,;GPCPD1,upstream_gene_variant,,ENST00000473797,; A ENST00000379019 Transcript splice_acceptor_variant -/5489 474/2019 158/672 1 -1 GPCPD1 HGNC HGNC:26957 protein_coding YES CCDS13090.1 ENSP00000368305 Q9NPB8 UPI0000062241 NM_019593.3 7/19 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 16 5578612 5578612 C A 1 0 0 0 0 0 0 1 0 6505 695 24 2 2 GPCPD1 20 5578612 Splice_Site SNP C C3L-00412_T 3180652 5578612 58865555 112 6675 FERMT1 0 . GRCh38 20 6107614 6107614 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.767C>G p.Ser256Cys p.S256C ENST00000217289 6/15 252 233 19 245 245 0 strelka-varscan-mutect FERMT1,missense_variant,p.Ser256Cys,ENST00000217289,NM_017671.4;FERMT1,5_prime_UTR_variant,,ENST00000536936,;FERMT1,downstream_gene_variant,,ENST00000378844,; C ENST00000217289 Transcript missense_variant 1556/5151 767/2034 256/677 S/C tCc/tGc 1 -1 FERMT1 HGNC HGNC:15889 protein_coding YES CCDS13098.1 ENSP00000217289 Q9BQL6 UPI00001285DD NM_017671.4 tolerated(0.14) 6/15 hmmpanther:PTHR16160:SF12,hmmpanther:PTHR16160,SMART_domains:SM00295 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 6107614 6107614 G C 1 0 0 0 0 1 0 0 0 5680 1174 41 4 4 FERMT1 20 6107614 Missense_Mutation SNP G C3L-00412_T 529002 6107614 58336553 113 6676 SLC32A1 0 . GRCh38 20 38727763 38727763 + Silent SNP G G T C3L-00412_T C3L-00412_N G G c.702G>T p.= p.P234P ENST00000217420 2/2 329 305 24 382 380 2 strelka-varscan-mutect SLC32A1,synonymous_variant,p.=,ENST00000217420,NM_080552.2; T ENST00000217420 Transcript synonymous_variant 965/2574 702/1578 234/525 P ccG/ccT COSM3546235 1 1 SLC32A1 HGNC HGNC:11018 protein_coding YES CCDS13307.1 ENSP00000217420 Q9H598 UPI0000043423 NM_080552.2 2/2 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF221 1 LOW 1 SNV 1 1 1 PASS rs1423783883 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 16 38727763 38727763 G T 1 0 0 0 0 0 0 0 1 14835 1103 39 1 1 SLC32A1 20 38727763 Silent SNP G C3L-00412_T 32620149 38727763 25716404 114 6677 GNAS 0 . GRCh38 20 58854632 58854632 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.1367G>C p.Gly456Ala p.G456A ENST00000371100 1/13 287 256 31 184 184 0 strelka-varscan-mutect GNAS,missense_variant,p.Gly456Ala,ENST00000371100,NM_080425.2;GNAS,missense_variant,p.Gly456Ala,ENST00000371099,;GNAS,missense_variant,p.Gly456Ala,ENST00000371102,;GNAS,missense_variant,p.Gly393Arg,ENST00000306120,NM_001077490.1;GNAS,intron_variant,,ENST00000313949,;GNAS,intron_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000371098,;GNAS,intron_variant,,ENST00000419558,;GNAS,intron_variant,,ENST00000453292,;GNAS,upstream_gene_variant,,ENST00000423897,;GNAS,upstream_gene_variant,,ENST00000450130,;GNAS,upstream_gene_variant,,ENST00000349036,;GNAS-AS1,upstream_gene_variant,,ENST00000424094,;GNAS-AS1,upstream_gene_variant,,ENST00000598163,;GNAS-AS1_5,downstream_gene_variant,,ENST00000614281,;GNAS-AS1_4,downstream_gene_variant,,ENST00000616546,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000481768,;GNAS,intron_variant,,ENST00000491348,;GNAS,intron_variant,,ENST00000472183,;GNAS,intron_variant,,ENST00000493744,;GNAS,intron_variant,,ENST00000482112,;GNAS,intron_variant,,ENST00000490374,;GNAS,intron_variant,,ENST00000467227,;GNAS,intron_variant,,ENST00000462499,; C ENST00000371100 Transcript missense_variant 1919/4029 1367/3114 456/1037 G/A gGg/gCg 1 1 GNAS HGNC HGNC:4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 UPI0000E444AE NM_080425.2 tolerated_low_confidence(1) 1/13 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 58854632 58854632 G C 1 0 0 0 0 1 0 0 0 6390 1232 43 4 4 GNAS 20 58854632 Missense_Mutation SNP G C3L-00412_T 20126869 58854632 5589535 115 6678 MRGBP 0 . GRCh38 20 62799617 62799617 + Missense_Mutation SNP A A T C3L-00412_T C3L-00412_N A A c.589A>T p.Ser197Cys p.S197C ENST00000370487 5/5 71 60 11 91 91 0 strelka-varscan-mutect MRGBP,missense_variant,p.Ser197Cys,ENST00000370487,NM_018270.4;OGFR-AS1,downstream_gene_variant,,ENST00000431361,; T ENST00000370487 Transcript missense_variant 660/2781 589/615 197/204 S/C Agt/Tgt COSM5057486 1 1 MRGBP HGNC HGNC:15866 protein_coding YES CCDS13503.1 ENSP00000359518 Q9NV56 UPI0000049FC0 NM_018270.4 deleterious(0.04) 5/5 hmmpanther:PTHR13581,hmmpanther:PTHR13581:SF5,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 16 62799617 62799617 A T 1 0 0 0 0 1 0 0 0 9728 188 7 4 4 MRGBP 20 62799617 Missense_Mutation SNP A C3L-00412_T 3944985 62799617 1644550 116 6679 PRPF6 0 . GRCh38 20 64028481 64028481 + Frame_Shift_Del DEL G G - novel C3L-00412_T C3L-00412_N G G c.2344delG p.Glu782SerfsTer11 p.E782Sfs*11 ENST00000266079 18/21 150 138 12 193 193 0 sindel-pindel PRPF6,frameshift_variant,p.Glu782SerfsTer11,ENST00000266079,NM_012469.3; - ENST00000266079 Transcript frameshift_variant 2454/3044 2343/2826 781/941 L/X ttG/tt 1 1 PRPF6 HGNC HGNC:15860 protein_coding YES CCDS13550.1 ENSP00000266079 O94906 UPI0000132356 NM_012469.3 18/21 Gene3D:1.25.40.10,PROSITE_profiles:PS50293,hmmpanther:PTHR11246,SMART_domains:SM00386,Superfamily_domains:SSF48452 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 16 64028481 64028481 G - 1 0 1 0 1 0 0 0 0 12710 1362 47 0 0 PRPF6 20 64028481 Frame_Shift_Del DEL G C3L-00412_T 1228864 64028481 415686 117 6680 RGS19 0 . GRCh38 20 64074044 64074044 + Missense_Mutation SNP C C A novel C3L-00412_T C3L-00412_N C C c.463G>T p.Val155Leu p.V155L ENST00000395042 6/6 57 51 6 94 94 0 strelka-varscan-mutect RGS19,missense_variant,p.Val155Leu,ENST00000395042,NM_005873.2;RGS19,missense_variant,p.Val155Leu,ENST00000332298,NM_001039467.1;TCEA2,downstream_gene_variant,,ENST00000395053,;TCEA2,downstream_gene_variant,,ENST00000361317,NM_198723.1;TCEA2,downstream_gene_variant,,ENST00000343484,NM_003195.4;TCEA2,downstream_gene_variant,,ENST00000440819,;TCEA2,downstream_gene_variant,,ENST00000339217,;TCEA2,downstream_gene_variant,,ENST00000458442,;MIR6813,downstream_gene_variant,,ENST00000621638,;TCEA2,downstream_gene_variant,,ENST00000465111,;TCEA2,downstream_gene_variant,,ENST00000487164,;TCEA2,downstream_gene_variant,,ENST00000461072,;RGS19,downstream_gene_variant,,ENST00000493165,;TCEA2,downstream_gene_variant,,ENST00000475236,;TCEA2,downstream_gene_variant,,ENST00000495168,;TCEA2,downstream_gene_variant,,ENST00000465433,;TCEA2,downstream_gene_variant,,ENST00000477783,;TCEA2,downstream_gene_variant,,ENST00000470559,;RGS19,downstream_gene_variant,,ENST00000479996,; A ENST00000395042 Transcript missense_variant,splice_region_variant 730/1593 463/654 155/217 V/L Gtg/Ttg 1 -1 RGS19 HGNC HGNC:13735 protein_coding YES CCDS13555.1 ENSP00000378483 P49795 UPI0000133838 NM_005873.2 deleterious(0) 6/6 Gene3D:1.10.167.10,Pfam_domain:PF00615,Prints_domain:PR01301,PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF145,SMART_domains:SM00315,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 16 64074044 64074044 C A 1 0 0 0 0 1 0 0 0 13472 521 18 2 2 RGS19 20 64074044 Missense_Mutation SNP C C3L-00412_T 45563 64074044 370123 118 6681 UMODL1 0 . GRCh38 21 42111140 42111140 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.1918G>T p.Gly640Cys p.G640C ENST00000408989 11/22 178 164 14 318 317 1 strelka-varscan-mutect UMODL1,missense_variant,p.Gly568Cys,ENST00000400427,NM_001199527.1;UMODL1,missense_variant,p.Gly640Cys,ENST00000408989,NM_173568.3;UMODL1,intron_variant,,ENST00000400424,NM_001199528.2;UMODL1,intron_variant,,ENST00000408910,NM_001004416.2;UMODL1-AS1,upstream_gene_variant,,ENST00000329015,;UMODL1,upstream_gene_variant,,ENST00000475047,; T ENST00000408989 Transcript missense_variant 1918/5262 1918/4341 640/1446 G/C Ggt/Tgt 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42935.1 ENSP00000386126 Q5DID0 UPI0000D6254B NM_173568.3 tolerated(0.1) 11/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 42111140 42111140 G T 1 0 0 0 0 1 0 0 0 17504 1232 43 2 2 UMODL1 21 42111140 Missense_Mutation SNP G C3L-00412_T 42111140 4598843 119 6682 CECR2 0 . GRCh38 22 17549040 17549040 + Silent SNP A A G novel C3L-00412_T C3L-00412_N A A c.3261A>G p.= p.T1087T ENST00000400585 17/19 156 142 14 171 170 1 strelka-varscan-mutect CECR2,synonymous_variant,p.=,ENST00000612582,;CECR2,synonymous_variant,p.=,ENST00000342247,NM_001290047.1;CECR2,synonymous_variant,p.=,ENST00000400585,NM_001290046.1;CECR2,synonymous_variant,p.=,ENST00000262608,;CECR2,synonymous_variant,p.=,ENST00000355219,; G ENST00000400585 Transcript synonymous_variant 3699/4833 3261/3903 1087/1300 T acA/acG 1 1 CECR2 HGNC HGNC:1840 protein_coding YES CCDS77646.1 ENSP00000383428 B7WPH3 UPI000198C520 NM_001290046.1 17/19 LOW 1 SNV 1 1 PASS rs1288722407 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 16 17549040 17549040 A G 1 0 0 0 0 0 0 0 1 2913 146 6 5 5 CECR2 22 17549040 Silent SNP A C3L-00412_T 17549040 33269428 120 6683 FRMPD4 0 . GRCh38 X 12717580 12717580 + Silent SNP G G A novel C3L-00412_T C3L-00412_N G G c.2754G>A p.= p.E918E ENST00000380682 16/17 87 75 12 93 93 0 strelka-mutect FRMPD4,synonymous_variant,p.=,ENST00000380682,NM_014728.3;FRMPD4,synonymous_variant,p.=,ENST00000616992,; A ENST00000380682 Transcript synonymous_variant 3260/8465 2754/3969 918/1322 E gaG/gaA 1 1 FRMPD4 HGNC HGNC:29007 protein_coding YES CCDS35201.1 ENSP00000370057 Q14CM0 UPI00001C2066 NM_014728.3 16/17 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 12717580 12717580 G A 1 0 0 0 0 0 0 0 1 5930 933 33 3 3 FRMPD4 23 12717580 Silent SNP G C3L-00412_T 12717580 143323315 121 6684 FAM120C 0 . GRCh38 X 54135030 54135030 + Missense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.1417C>A p.His473Asn p.H473N ENST00000375180 7/16 65 46 19 65 65 0 strelka-varscan-mutect FAM120C,missense_variant,p.His473Asn,ENST00000375180,NM_017848.5;FAM120C,missense_variant,p.His473Asn,ENST00000328235,NM_001300788.1; T ENST00000375180 Transcript missense_variant 1474/8057 1417/3291 473/1096 H/N Cat/Aat 1 -1 FAM120C HGNC HGNC:16949 protein_coding YES CCDS14356.1 ENSP00000364324 Q9NX05 UPI00001D68ED NM_017848.5 tolerated(0.39) 7/16 hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF15 MODERATE 1 SNV 1 1 PASS rs782380910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 16 54135030 54135030 G T 1 0 0 0 0 1 0 0 0 5275 1348 47 2 2 FAM120C 23 54135030 Missense_Mutation SNP G C3L-00412_T 41417450 54135030 101905865 122 6685 NRK 0 . GRCh38 X 105908257 105908257 + Nonsense_Mutation SNP G G T novel C3L-00412_T C3L-00412_N G G c.1039G>T p.Glu347Ter p.E347* ENST00000243300 12/29 54 44 10 50 50 0 strelka-varscan-mutect NRK,stop_gained,p.Glu347Ter,ENST00000243300,NM_198465.3;NRK,3_prime_UTR_variant,,ENST00000428173,; T ENST00000243300 Transcript stop_gained 1342/8062 1039/4749 347/1582 E/* Gaa/Taa 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 12/29 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF417,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99993 1 1 1 1 0 T 4 4 16 105908257 105908257 G T 1 0 0 0 0 0 1 0 0 10713 1291 45 2 2 NRK 23 105908257 Nonsense_Mutation SNP G C3L-00412_T 51773227 105908257 50132638 123 6686 LHFPL1 0 . GRCh38 X 112671187 112671187 + Frame_Shift_Del DEL C C - novel C3L-00412_T C3L-00412_N C C c.204delG p.Arg69AlafsTer19 p.R69Afs*19 ENST00000371968 2/4 91 81 10 105 105 0 sindel-varindel-pindel LHFPL1,frameshift_variant,p.Arg69AlafsTer19,ENST00000371968,NM_178175.3;LHFPL1,intron_variant,,ENST00000478229,; - ENST00000371968 Transcript frameshift_variant 444/1675 204/663 68/220 G/X ggG/gg 1 -1 LHFPL1 HGNC HGNC:6587 protein_coding YES CCDS14562.1 ENSP00000361036 Q86WI0 UPI00000622AD NM_178175.3 2/4 hmmpanther:PTHR12489:SF15,hmmpanther:PTHR12489,Pfam_domain:PF10242 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 16 112671187 112671187 C - 1 0 1 0 1 0 0 0 0 8673 726 26 0 0 LHFPL1 23 112671187 Frame_Shift_Del DEL C C3L-00412_T 6762930 112671187 43369708 124 6687 PRR32 0 . GRCh38 X 126821289 126821289 + Silent SNP C C A novel C3L-00412_T C3L-00412_N C C c.651C>A p.= p.G217G ENST00000371125 2/2 134 108 26 140 139 1 strelka-varscan-mutect PRR32,synonymous_variant,p.=,ENST00000371125,NM_001122716.1; A ENST00000371125 Transcript synonymous_variant 731/1228 651/897 217/298 G ggC/ggA 1 1 PRR32 HGNC HGNC:34498 protein_coding YES CCDS48163.1 ENSP00000360166 B1ATL7 UPI00004A3B00 NM_001122716.1 2/2 Pfam_domain:PF15488,hmmpanther:PTHR37343,hmmpanther:PTHR37343:SF1 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 16 126821289 126821289 C A 1 0 0 0 0 0 0 0 1 12738 726 26 2 2 PRR32 23 126821289 Silent SNP C C3L-00412_T 14150102 126821289 29219606 125 6688 ADGRG4 0 . GRCh38 X 136363494 136363494 + Missense_Mutation SNP C C A rs143014685 C3L-00412_T C3L-00412_N C C c.7295C>A p.Thr2432Lys p.T2432K ENST00000394143 13/26 128 117 11 92 92 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Thr2432Lys,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Thr2432Lys,ENST00000370652,;ADGRG4,missense_variant,p.Thr2227Lys,ENST00000394141,; A ENST00000394143 Transcript missense_variant 7586/9931 7295/9243 2432/3080 T/K aCg/aAg rs143014685 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 13/26 hmmpanther:PTHR12011:SF277,hmmpanther:PTHR12011 MODERATE 1 SNV 1 1 PASS rs143014685 . 0 208 2 0 0 0 0 0 -19.99039 1 1 1 1 0 A 3 1 16 136363494 136363494 C A 1 0 0 0 0 1 0 0 0 371 536 19 1 1 ADGRG4 23 136363494 Missense_Mutation SNP C C3L-00412_T 9542205 136363494 19677401 126 6689 CNGA2 0 . GRCh38 X 151738505 151738505 + Missense_Mutation SNP G G A rs773056408 C3L-00412_T C3L-00412_N G G c.22G>A p.Val8Met p.V8M ENST00000329903 1/6 92 85 7 82 82 0 strelka-varscan-mutect CNGA2,missense_variant,p.Val8Met,ENST00000329903,NM_005140.1; A ENST00000329903 Transcript missense_variant 55/2834 22/1995 8/664 V/M Gtg/Atg rs773056408,COSM4637553 1 1 CNGA2 HGNC HGNC:2149 protein_coding YES CCDS14701.1 ENSP00000328478 Q16280 UPI000003E7AE NM_005140.1 tolerated_low_confidence(0.19) 1/6 hmmpanther:PTHR10217:SF389,hmmpanther:PTHR10217 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773056408 . 0 207 3 0 0 0 0 0 -14.86998 1 1 1 1 0 A 3 1 16 151738505 151738505 G A 1 0 0 0 0 1 0 0 0 3377 1377 48 3 3 CNGA2 23 151738505 Missense_Mutation SNP G C3L-00412_T 15375011 151738505 4302390 127 6690 MAGEA3 0 . GRCh38 X 152701625 152701625 + Missense_Mutation SNP G G C novel C3L-00412_T C3L-00412_N G G c.793G>C p.Asp265His p.D265H ENST00000598245 3/3 109 99 10 137 137 0 varscan-mutect MAGEA3,missense_variant,p.Asp265His,ENST00000598245,;MAGEA3,missense_variant,p.Asp265His,ENST00000370278,NM_005362.3;MAGEA3,downstream_gene_variant,,ENST00000417212,; C ENST00000598245 Transcript missense_variant 1051/1762 793/945 265/314 D/H Gat/Cat 1 1 MAGEA3 HGNC HGNC:6801 protein_coding YES CCDS76045.1 ENSP00000473093 P43357 UPI0000062194 deleterious(0.01) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 2 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 16 152701625 152701625 G C 1 0 0 0 0 1 0 0 0 9083 1290 45 4 4 MAGEA3 23 152701625 Missense_Mutation SNP G C3L-00412_T 963120 152701625 3339270 128 6691 RAPGEF4 0 . GRCh38 2 172795157 172795157 + Frame_Shift_Del DEL G G - rs187369427 C3L-00422_T C3L-00422_N G G c.200delG p.Gly67GlufsTer2 p.G67Efs*2 ENST00000397081 2/31 38 34 4 99 99 0 varindel-pindel RAPGEF4,frameshift_variant,p.Gly67GlufsTer2,ENST00000397081,NM_007023.3;RAPGEF4,frameshift_variant,p.Gly67GlufsTer2,ENST00000409036,;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000464976,;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000484331,; - ENST00000397081 Transcript frameshift_variant 341/4299 198/3036 66/1011 K/X aaG/aa rs187369427 1 1 RAPGEF4 HGNC HGNC:16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 UPI000006D4C7 NM_007023.3 2/31 Gene3D:2.60.120.10,Pfam_domain:PF00027,PROSITE_profiles:PS50042,SMART_domains:SM00100,Superfamily_domains:SSF51206 HIGH 1 deletion 1 2 1 PASS . . 0 202 7 0 0 0 0 0 -10.72919 0.999999 1 1 1 0 - 7 5 17 172795157 172795157 G - 1 0 1 0 1 0 0 0 0 13205 991 35 0 0 RAPGEF4 2 172795157 Frame_Shift_Del DEL G C3L-00422_T 172795157 69398372 1 6692 HRH1 0 . GRCh38 3 11259609 11259609 + Missense_Mutation SNP A A G novel C3L-00422_T C3L-00422_N A A c.572A>G p.Lys191Arg p.K191R ENST00000397056 3/3 115 109 6 127 127 0 strelka-mutect HRH1,missense_variant,p.Lys191Arg,ENST00000397056,NM_000861.3;HRH1,missense_variant,p.Lys191Arg,ENST00000431010,NM_001098212.1,NM_001098211.1;HRH1,missense_variant,p.Lys191Arg,ENST00000438284,NM_001098213.1;HRH1,downstream_gene_variant,,ENST00000413416,; G ENST00000397056 Transcript missense_variant 763/4711 572/1464 191/487 K/R aAg/aGg 1 1 HRH1 HGNC HGNC:5182 protein_coding YES CCDS2604.1 ENSP00000380247 P35367 UPI0000050401 NM_000861.3 deleterious(0.01) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00530,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF239,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 17 11259609 11259609 A G 1 0 0 0 0 1 0 0 0 7250 72 3 5 5 HRH1 3 11259609 Missense_Mutation SNP A C3L-00422_T 11259609 187035950 2 6693 SVEP1 0 . GRCh38 9 110406786 110406786 + Missense_Mutation SNP A A C novel C3L-00422_T C3L-00422_N A A c.8814T>G p.Asp2938Glu p.D2938E ENST00000374469 38/48 152 133 19 184 183 1 strelka-varscan-mutect SVEP1,missense_variant,p.Asp2941Glu,ENST00000401783,;SVEP1,missense_variant,p.Asp2938Glu,ENST00000374469,NM_153366.3; C ENST00000374469 Transcript missense_variant 9009/12194 8814/10716 2938/3571 D/E gaT/gaG 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 deleterious(0.01) 38/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 17 110406786 110406786 A C 1 0 0 0 0 1 0 0 0 15805 214 8 5 5 SVEP1 9 110406786 Missense_Mutation SNP A C3L-00422_T 110406786 27987931 3 6694 FNBP4 0 . GRCh38 11 47754556 47754556 + Missense_Mutation SNP A A T C3L-00422_T C3L-00422_N A A c.422T>A p.Ile141Asn p.I141N ENST00000263773 3/17 95 76 19 91 91 0 strelka-varscan-mutect FNBP4,missense_variant,p.Ile141Asn,ENST00000263773,NM_001318339.1,NM_015308.2;FNBP4,intron_variant,,ENST00000540172,;FNBP4,non_coding_transcript_exon_variant,,ENST00000534003,;FNBP4,non_coding_transcript_exon_variant,,ENST00000542975,;FNBP4,non_coding_transcript_exon_variant,,ENST00000533707,; T ENST00000263773 Transcript missense_variant 435/3972 422/3054 141/1017 I/N aTt/aAt COSM927500 1 -1 FNBP4 HGNC HGNC:19752 protein_coding YES CCDS41644.1 ENSP00000263773 Q8N3X1 UPI0000DBEF37 NM_001318339.1,NM_015308.2 deleterious(0) 3/17 1 MODERATE 1 SNV 1 1 1 PASS rs1487583260 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 17 47754556 47754556 A T 1 0 0 0 0 1 0 0 0 5823 101 4 4 4 FNBP4 11 47754556 Missense_Mutation SNP A C3L-00422_T 47754556 87332066 4 6695 DDIAS 0 . GRCh38 11 82930261 82930261 + Frame_Shift_Del DEL T T - novel C3L-00422_T C3L-00422_N T T c.384delT p.Phe128LeufsTer3 p.F128Lfs*3 ENST00000533655 5/6 59 56 3 136 136 0 varindel-pindel DDIAS,frameshift_variant,p.Phe128LeufsTer3,ENST00000533655,NM_145018.3;DDIAS,frameshift_variant,p.Phe128LeufsTer3,ENST00000329143,;DDIAS,frameshift_variant,p.Phe128LeufsTer3,ENST00000525361,;DDIAS,frameshift_variant,p.Phe189LeufsTer3,ENST00000532764,;DDIAS,intron_variant,,ENST00000528759,;DDIAS,intron_variant,,ENST00000525388,;PRCP,intron_variant,,ENST00000534396,;DDIAS,intron_variant,,ENST00000524921,;DDIAS,downstream_gene_variant,,ENST00000532277,;DDIAS,downstream_gene_variant,,ENST00000528262,;DDIAS,downstream_gene_variant,,ENST00000532589,;DDIAS,non_coding_transcript_exon_variant,,ENST00000533750,;DDIAS,downstream_gene_variant,,ENST00000528189,; - ENST00000533655 Transcript frameshift_variant 592/3533 380/2997 127/998 I/X aTt/at 1 1 DDIAS HGNC HGNC:26351 protein_coding YES CCDS8263.1 ENSP00000435421 Q8IXT1 UPI00001AF966 NM_145018.3 5/6 hmmpanther:PTHR35537,hmmpanther:PTHR35537:SF1,Superfamily_domains:SSF50249 HIGH 1 deletion 1 4 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 17 82930261 82930261 T - 1 0 1 0 1 0 0 0 0 4133 1493 52 0 0 DDIAS 11 82930261 Frame_Shift_Del DEL T C3L-00422_T 35175705 82930261 52156361 5 6696 SLC26A10 0 . GRCh38 12 57622835 57622835 + Silent SNP G G A novel C3L-00422_T C3L-00422_N G G c.840G>A p.= p.L280L ENST00000320442 6/14 51 45 6 109 107 2 varscan-mutect SLC26A10,synonymous_variant,p.=,ENST00000320442,NM_133489.2;B4GALNT1,downstream_gene_variant,,ENST00000341156,NM_001478.4;B4GALNT1,downstream_gene_variant,,ENST00000418555,NM_001276468.1;B4GALNT1,downstream_gene_variant,,ENST00000547741,;SLC26A10,downstream_gene_variant,,ENST00000637859,;AC025165.8,upstream_gene_variant,,ENST00000356672,;AC025165.8,upstream_gene_variant,,ENST00000444467,;AC025165.8,upstream_gene_variant,,ENST00000593846,;ARHGEF25,downstream_gene_variant,,ENST00000477314,;SLC26A10,upstream_gene_variant,,ENST00000490243,;SLC26A10,upstream_gene_variant,,ENST00000483647,;SLC26A10,synonymous_variant,p.=,ENST00000474359,;SLC26A10,synonymous_variant,p.=,ENST00000440686,;B4GALNT1,downstream_gene_variant,,ENST00000553142,;B4GALNT1,downstream_gene_variant,,ENST00000552468,;B4GALNT1,downstream_gene_variant,,ENST00000552798,;SLC26A10,upstream_gene_variant,,ENST00000487816,;SLC26A10,upstream_gene_variant,,ENST00000474791,;SLC26A10,downstream_gene_variant,,ENST00000497297,;SLC26A10,downstream_gene_variant,,ENST00000463802,; A ENST00000320442 Transcript synonymous_variant 1151/2389 840/1692 280/563 L ctG/ctA 1 1 SLC26A10 HGNC HGNC:14470 protein_coding YES CCDS8949.2 ENSP00000320217 Q8NG04 UPI000007059E NM_133489.2 6/14 hmmpanther:PTHR11814:SF99,hmmpanther:PTHR11814,Pfam_domain:PF00916 LOW 1 SNV 1 1 PASS . . 0 205 0 0 0 0 0 4 -2.804847 0 0 1 0 0 A 2 1 17 57622835 57622835 G A 1 0 0 0 0 0 0 0 1 14785 1335 47 3 3 SLC26A10 12 57622835 Silent SNP G C3L-00422_T 57622835 75652474 6 6697 ATL1 0 . GRCh38 14 50628096 50628096 + Frame_Shift_Del DEL G G - C3L-00422_T C3L-00422_N G G c.1186delG p.Glu396LysfsTer4 p.E396Kfs*4 ENST00000358385 12/14 115 102 13 200 200 0 sindel-varindel-pindel ATL1,frameshift_variant,p.Glu396LysfsTer4,ENST00000441560,NM_001127713.1,NM_181598.3;ATL1,frameshift_variant,p.Glu396LysfsTer4,ENST00000358385,NM_015915.4;SAV1,downstream_gene_variant,,ENST00000555720,;ATL1,3_prime_UTR_variant,,ENST00000555266,;ATL1,upstream_gene_variant,,ENST00000556067,; - ENST00000358385 Transcript frameshift_variant 1426/2647 1185/1677 395/558 K/X aaG/aa COSM5644646 1 1 ATL1 HGNC HGNC:11231 protein_coding YES CCDS9700.1 ENSP00000351155 Q8WXF7 A0A0S2Z5B0 UPI0000073893 NM_015915.4 12/14 hmmpanther:PTHR10751:SF15,hmmpanther:PTHR10751,Gene3D:1f5nA01,Superfamily_domains:0037397 1 HIGH 1 deletion 1 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 17 50628096 50628096 G - 1 0 1 0 1 0 0 0 0 1258 991 35 0 0 ATL1 14 50628096 Frame_Shift_Del DEL G C3L-00422_T 50628096 56415622 7 6698 MGA 0 . GRCh38 15 41696714 41696714 + Missense_Mutation SNP T T G novel C3L-00422_T C3L-00422_N T T c.1704T>G p.Asp568Glu p.D568E ENST00000219905 3/24 69 56 13 178 178 0 strelka-varscan-mutect MGA,missense_variant,p.Asp568Glu,ENST00000566586,;MGA,missense_variant,p.Asp568Glu,ENST00000219905,NM_001164273.1;MGA,missense_variant,p.Asp568Glu,ENST00000570161,;MGA,missense_variant,p.Asp568Glu,ENST00000545763,NM_001080541.2;MGA,missense_variant,p.Asp568Glu,ENST00000563576,;MGA,missense_variant,p.Asp568Glu,ENST00000566718,;MGA,downstream_gene_variant,,ENST00000568630,; G ENST00000219905 Transcript missense_variant 1885/12042 1704/9198 568/3065 D/E gaT/gaG 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 tolerated(0.08) 3/24 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 17 41696714 41696714 T G 1 0 0 0 0 1 0 0 0 9498 1490 52 5 5 MGA 15 41696714 Missense_Mutation SNP T C3L-00422_T 41696714 60294475 8 6699 PANX2 0 . GRCh38 22 50177108 50177108 + Silent SNP C C T novel C3L-00422_T C3L-00422_N C C c.396C>T p.= p.A132A ENST00000395842 2/3 134 98 36 134 134 0 strelka-varscan-mutect PANX2,synonymous_variant,p.=,ENST00000395842,NM_052839.3;PANX2,synonymous_variant,p.=,ENST00000159647,NM_001160300.1;PANX2,3_prime_UTR_variant,,ENST00000402472,; T ENST00000395842 Transcript synonymous_variant 396/3051 396/2034 132/677 A gcC/gcT 1 1 PANX2 HGNC HGNC:8600 protein_coding YES CCDS14085.2 ENSP00000379183 Q96RD6 UPI0000E070D3 NM_052839.3 2/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF7,Pfam_domain:PF00876 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 17 50177108 50177108 C T 1 0 0 0 0 0 0 0 1 11502 639 23 1 1 PANX2 22 50177108 Silent SNP C C3L-00422_T 50177108 641360 9 6700 ARMCX4 0 . GRCh38 X 101493876 101493876 + Missense_Mutation SNP G G A novel C3L-00422_T C3L-00422_N G G c.5287G>A p.Asp1763Asn p.D1763N ENST00000423738 2/2 235 216 19 174 173 1 strelka-varscan-mutect ARMCX4,missense_variant,p.Asp1763Asn,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; A ENST00000423738 Transcript missense_variant 5489/7424 5287/6873 1763/2290 D/N Gat/Aat 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 tolerated(0.72) 2/2 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 17 101493876 101493876 G A 1 0 0 0 0 1 0 0 0 1102 942 33 3 3 ARMCX4 23 101493876 Missense_Mutation SNP G C3L-00422_T 101493876 54547019 10 6701 SRM 0 . GRCh38 1 11059911 11059911 + Silent SNP G G A novel C3L-00510_T C3L-00510_N G G c.33C>T p.= p.S11S ENST00000376957 1/8 61 57 4 77 77 0 strelka-mutect SRM,synonymous_variant,p.=,ENST00000376957,NM_003132.2;SRM,upstream_gene_variant,,ENST00000487300,;SRM,upstream_gene_variant,,ENST00000490101,;SRM,upstream_gene_variant,,ENST00000465788,;SRM,synonymous_variant,p.=,ENST00000459997,;SRM,upstream_gene_variant,,ENST00000475189,; A ENST00000376957 Transcript synonymous_variant 114/1266 33/909 11/302 S tcC/tcT 1 -1 SRM HGNC HGNC:11296 protein_coding YES CCDS125.1 ENSP00000366156 P19623 UPI0000049054 NM_003132.2 1/8 PIRSF_domain:PIRSF000502,hmmpanther:PTHR11558,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 197 10 3 0 0 0 0 -7.705798 0.9892265 1 1 1 0 A 2 1 18 11059911 11059911 G A 1 0 0 0 0 0 0 0 1 15512 1103 39 1 1 SRM 1 11059911 Silent SNP G C3L-00510_T 11059911 237896511 1 6702 CCDC17 0 . GRCh38 1 45622563 45622563 + Missense_Mutation SNP G G A novel C3L-00510_T C3L-00510_N G G c.845C>T p.Ser282Leu p.S282L ENST00000528266 6/13 125 77 48 179 179 0 strelka-mutect CCDC17,missense_variant,p.Ser273Leu,ENST00000421127,NM_001190182.1;CCDC17,missense_variant,p.Ser282Leu,ENST00000528266,NM_001114938.2;CCDC17,intron_variant,,ENST00000445048,;GPBP1L1,downstream_gene_variant,,ENST00000355105,NM_021639.4;GPBP1L1,downstream_gene_variant,,ENST00000290795,;NASP,downstream_gene_variant,,ENST00000350030,NM_002482.3;NASP,downstream_gene_variant,,ENST00000537798,NM_001195193.1;NASP,downstream_gene_variant,,ENST00000351223,NM_152298.3;NASP,downstream_gene_variant,,ENST00000372052,;NASP,downstream_gene_variant,,ENST00000531612,;NASP,downstream_gene_variant,,ENST00000534450,;CCDC17,non_coding_transcript_exon_variant,,ENST00000464739,;GPBP1L1,downstream_gene_variant,,ENST00000479235,;NASP,downstream_gene_variant,,ENST00000530073,;CCDC17,missense_variant,p.Ser250Leu,ENST00000479529,;CCDC17,3_prime_UTR_variant,,ENST00000372044,;CCDC17,non_coding_transcript_exon_variant,,ENST00000482416,;CCDC17,non_coding_transcript_exon_variant,,ENST00000491755,;CCDC17,non_coding_transcript_exon_variant,,ENST00000525599,;NASP,downstream_gene_variant,,ENST00000481782,;NASP,downstream_gene_variant,,ENST00000472408,; A ENST00000528266 Transcript missense_variant 993/2181 845/1869 282/622 S/L tCg/tTg 1 -1 CCDC17 HGNC HGNC:26574 protein_coding YES CCDS44131.2 ENSP00000432172 Q96LX7 UPI0001AE78A9 NM_001114938.2 tolerated(0.25) 6/13 hmmpanther:PTHR33820 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 45622563 45622563 G A 1 0 0 0 0 1 0 0 0 2486 1059 37 1 1 CCDC17 1 45622563 Missense_Mutation SNP G C3L-00510_T 34562652 45622563 203333859 2 6703 ZNF648 0 . GRCh38 1 182056586 182056586 + Silent SNP G G A novel C3L-00510_T C3L-00510_N G G c.1425C>T p.= p.P475P ENST00000339948 2/2 317 243 74 311 311 0 strelka-varscan-mutect ZNF648,synonymous_variant,p.=,ENST00000339948,NM_001009992.1; A ENST00000339948 Transcript synonymous_variant 1633/3649 1425/1707 475/568 P ccC/ccT 1 -1 ZNF648 HGNC HGNC:18190 protein_coding YES CCDS30952.1 ENSP00000344129 Q5T619 UPI0000161414 NM_001009992.1 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24376:SF1,hmmpanther:PTHR24376,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 18 182056586 182056586 G A 1 0 0 0 0 0 0 0 1 18636 987 35 3 3 ZNF648 1 182056586 Silent SNP G C3L-00510_T 136434023 182056586 66899836 3 6704 OR2L3 0 . GRCh38 1 248060759 248060759 + Silent SNP C C G novel C3L-00510_T C3L-00510_N C C c.78C>G p.= p.L26L ENST00000359959 1/1 231 210 21 157 157 0 varscan-mutect OR2L3,synonymous_variant,p.=,ENST00000359959,NM_001004687.1; G ENST00000359959 Transcript synonymous_variant 78/939 78/939 26/312 L ctC/ctG 1 1 OR2L3 HGNC HGNC:15009 protein_coding YES CCDS31104.1 ENSP00000353044 Q8NG85 UPI0000061EB8 NM_001004687.1 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26453:SF166,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 G 2 3 18 248060759 248060759 C G 1 0 0 0 0 0 0 0 1 11086 900 32 4 4 OR2L3 1 248060759 Silent SNP C C3L-00510_T 66004173 248060759 895663 4 6705 CBWD2 0 . GRCh38 2 113437884 113437884 + Frame_Shift_Del DEL G G - novel C3L-00510_T C3L-00510_N G G c.17delG p.Gly6AspfsTer46 p.G6Dfs*46 ENST00000259199 1/15 208 144 64 301 301 0 sindel-varindel-pindel CBWD2,frameshift_variant,p.Gly6AspfsTer46,ENST00000259199,NM_172003.3;CBWD2,frameshift_variant,p.Gly6AspfsTer46,ENST00000416503,;CBWD2,frameshift_variant,p.Gly6AspfsTer46,ENST00000433343,;RP11-480C16.1,downstream_gene_variant,,ENST00000608834,;CBWD2,frameshift_variant,p.Gly6AspfsTer46,ENST00000358604,;CBWD2,frameshift_variant,p.Gly6AspfsTer46,ENST00000456188,;CBWD2,non_coding_transcript_exon_variant,,ENST00000492566,;CBWD2,non_coding_transcript_exon_variant,,ENST00000490323,;CBWD2,non_coding_transcript_exon_variant,,ENST00000463627,; - ENST00000259199 Transcript frameshift_variant 194/1812 16/1188 6/395 G/X Gga/ga 1 1 CBWD2 HGNC HGNC:17907 protein_coding YES CCDS2116.1 ENSP00000259199 Q8IUF1 UPI000007478B NM_172003.3 1/15 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 18 113437884 113437884 G - 1 0 1 0 1 0 0 0 0 2413 1349 47 0 0 CBWD2 2 113437884 Frame_Shift_Del DEL G C3L-00510_T 113437884 128755645 5 6706 SCAP 0 . GRCh38 3 47419573 47419573 + Silent SNP A A G novel C3L-00510_T C3L-00510_N A A c.1695T>C p.= p.S565S ENST00000265565 13/23 65 35 30 112 112 0 strelka-varscan-mutect SCAP,synonymous_variant,p.=,ENST00000265565,NM_012235.2;SCAP,synonymous_variant,p.=,ENST00000545718,;SCAP,intron_variant,,ENST00000428413,;SCAP,3_prime_UTR_variant,,ENST00000441517,NM_001320044.1;SCAP,3_prime_UTR_variant,,ENST00000320017,;SCAP,3_prime_UTR_variant,,ENST00000416208,;SCAP,downstream_gene_variant,,ENST00000465628,;SCAP,downstream_gene_variant,,ENST00000468965,; G ENST00000265565 Transcript synonymous_variant 2108/4394 1695/3840 565/1279 S agT/agC 1 -1 SCAP HGNC HGNC:30634 protein_coding YES CCDS2755.2 ENSP00000265565 Q12770 UPI0000135624 NM_012235.2 13/23 hmmpanther:PTHR10796:SF127,hmmpanther:PTHR10796 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 18 47419573 47419573 A G 1 0 0 0 0 0 0 0 1 14143 156 6 5 5 SCAP 3 47419573 Silent SNP A C3L-00510_T 47419573 150875986 6 6707 PRR23C 0 . GRCh38 3 139044374 139044374 + Missense_Mutation SNP C C T rs770562080 C3L-00510_T C3L-00510_N C C c.247G>A p.Ala83Thr p.A83T ENST00000413199 1/1 125 65 60 150 150 0 strelka-varscan-mutect PRR23C,missense_variant,p.Ala83Thr,ENST00000413199,NM_001134657.1;MRPS22,intron_variant,,ENST00000495075,; T ENST00000413199 Transcript missense_variant 519/2791 247/789 83/262 A/T Gcg/Acg rs770562080,COSM3392086 1 -1 PRR23C HGNC HGNC:37173 protein_coding YES CCDS46924.1 ENSP00000396648 Q6ZRP0 UPI00001C0F48 NM_001134657.1 deleterious(0.04) 1/1 hmmpanther:PTHR31813:SF6,hmmpanther:PTHR31813,Pfam_domain:PF10630 0,1 MODERATE SNV 0,1 1 PASS rs770562080 . 0 207 0 3 0 0 0 0 -20 0.9999994 1 1 1 0 T 3 4 18 139044374 139044374 C T 1 0 0 0 0 1 0 0 0 12731 768 27 1 1 PRR23C 3 139044374 Missense_Mutation SNP C C3L-00510_T 91624801 139044374 59251185 7 6708 NAAA 0 . GRCh38 4 75921102 75921102 + Missense_Mutation SNP A A T rs756840514 C3L-00510_T C3L-00510_N A A c.688T>A p.Phe230Ile p.F230I ENST00000286733 6/11 43 24 19 75 75 0 strelka-varscan-mutect NAAA,missense_variant,p.Phe230Ile,ENST00000286733,NM_014435.3;NAAA,missense_variant,p.Phe129Ile,ENST00000505594,;NAAA,missense_variant,p.Phe230Ile,ENST00000507956,;NAAA,missense_variant,p.Phe105Ile,ENST00000602782,;NAAA,upstream_gene_variant,,ENST00000511606,;NAAA,missense_variant,p.Phe35Ile,ENST00000513045,; T ENST00000286733 Transcript missense_variant 790/1900 688/1080 230/359 F/I Ttc/Atc rs756840514 1 -1 NAAA HGNC HGNC:736 protein_coding YES CCDS43239.1 ENSP00000286733 Q02083 UPI00001AEAEE NM_014435.3 deleterious(0) 6/11 Pfam_domain:PF02275,PIRSF_domain:PIRSF017632,hmmpanther:PTHR28583,hmmpanther:PTHR28583:SF4 MODERATE 1 SNV 5 1 PASS rs756840514 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 18 75921102 75921102 A T 1 0 0 0 0 1 0 0 0 10131 72 3 4 4 NAAA 4 75921102 Missense_Mutation SNP A C3L-00510_T 75921102 114293453 8 6709 SEMA5A 0 . GRCh38 5 9108194 9108194 + Silent SNP A A G novel C3L-00510_T C3L-00510_N A A c.2019T>C p.= p.I673I ENST00000382496 16/23 162 149 13 160 160 0 strelka-varscan-mutect SEMA5A,synonymous_variant,p.=,ENST00000382496,NM_003966.2; G ENST00000382496 Transcript synonymous_variant 2685/11762 2019/3225 673/1074 I atT/atC 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 16/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.7396 0.9999998 1 1 1 0 G 2 3 18 9108194 9108194 A G 1 0 0 0 0 0 0 0 1 14313 242 9 5 5 SEMA5A 5 9108194 Silent SNP A C3L-00510_T 9108194 172430065 9 6710 VCAN 0 . GRCh38 5 83521784 83521784 + Missense_Mutation SNP C C A novel C3L-00510_T C3L-00510_N C C c.3478C>A p.His1160Asn p.H1160N ENST00000265077 7/15 138 128 10 154 153 1 strelka-varscan-mutect VCAN,missense_variant,p.His1160Asn,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.His1160Asn,ENST00000342785,NM_001164098.1;VCAN,missense_variant,p.His1112Asn,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 4043/12625 3478/10191 1160/3396 H/N Cac/Aac 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.48) 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 83521784 83521784 C A 1 0 0 0 0 1 0 0 0 17683 594 21 2 2 VCAN 5 83521784 Missense_Mutation SNP C C3L-00510_T 74413590 83521784 98016475 10 6711 ADGRV1 0 . GRCh38 5 90694510 90694510 + Missense_Mutation SNP T T G novel C3L-00510_T C3L-00510_N T T c.7754T>G p.Ile2585Ser p.I2585S ENST00000405460 33/90 353 243 110 388 388 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Ile2585Ser,ENST00000405460,NM_032119.3;ADGRV1,missense_variant,p.Ile151Ser,ENST00000509621,; G ENST00000405460 Transcript missense_variant 7850/19338 7754/18921 2585/6306 I/S aTt/aGt 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 tolerated(0.1) 33/90 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,SMART_domains:SM00237 MODERATE 1 SNV 1 1 PASS rs1229881653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 18 90694510 90694510 T G 1 0 0 0 0 1 0 0 0 379 1493 52 5 5 ADGRV1 5 90694510 Missense_Mutation SNP T C3L-00510_T 7172726 90694510 90843749 11 6712 TAAR1 0 . GRCh38 6 132645539 132645539 + Silent SNP T T C novel C3L-00510_T C3L-00510_N T T c.465A>G p.= p.A155A ENST00000275216 1/1 170 148 22 194 194 0 strelka-varscan-mutect TAAR1,synonymous_variant,p.=,ENST00000275216,NM_138327.1; C ENST00000275216 Transcript synonymous_variant 465/1020 465/1020 155/339 A gcA/gcG 1 -1 TAAR1 HGNC HGNC:17734 protein_coding YES CCDS5158.1 ENSP00000275216 Q96RJ0 UPI000000D874 NM_138327.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF220,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 18 132645539 132645539 T C 1 0 0 0 0 0 0 0 1 15885 1451 51 5 5 TAAR1 6 132645539 Silent SNP T C3L-00510_T 132645539 38160440 12 6713 27 2 TAAR1 0 . GRCh38 6 132645548 132645548 + Silent SNP A A G novel C3L-00510_T C3L-00510_N A A c.456T>C p.= p.A152A ENST00000275216 1/1 185 160 25 206 206 0 strelka-varscan-mutect TAAR1,synonymous_variant,p.=,ENST00000275216,NM_138327.1; G ENST00000275216 Transcript synonymous_variant 456/1020 456/1020 152/339 A gcT/gcC 1 -1 TAAR1 HGNC HGNC:17734 protein_coding YES CCDS5158.1 ENSP00000275216 Q96RJ0 UPI000000D874 NM_138327.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF220,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 18 132645548 132645548 A G 1 0 0 0 0 0 0 0 1 15885 175 7 5 5 TAAR1 6 132645548 Silent SNP A C3L-00510_T 9 132645548 38160431 13 6714 27 2 EGFR 0 . GRCh38 7 55142382 55142382 + Missense_Mutation SNP T T G C3L-00510_T C3L-00510_N T T c.185T>G p.Leu62Arg p.L62R ENST00000275493 2/28 363 232 131 427 427 0 strelka-varscan EGFR,missense_variant,p.Leu62Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu62Arg,ENST00000454757,;EGFR,missense_variant,p.Leu62Arg,ENST00000455089,;EGFR,missense_variant,p.Leu62Arg,ENST00000344576,NM_201284.1;EGFR,missense_variant,p.Leu62Arg,ENST00000342916,NM_201282.1;EGFR,missense_variant,p.Leu62Arg,ENST00000420316,NM_201283.1;EGFR,missense_variant,p.Leu9Arg,ENST00000450046,; G ENST00000275493 Transcript missense_variant 362/9821 185/3633 62/1210 L/R cTt/cGt COSM35602,COSM5253287,COSM601589 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0.01) 2/28 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Pfam_domain:PF01030,PIRSF_domain:PIRSF000619,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 18 55142382 55142382 T G 1 0 0 0 0 1 0 0 0 4803 1609 56 5 5 EGFR 7 55142382 Missense_Mutation SNP T C3L-00510_T 55142382 104203591 14 6715 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3L-00510_T C3L-00510_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 389 226 163 593 593 0 strelka-varscan EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 18 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3L-00510_T 49440 55191822 104154151 15 6716 RBPMS 0 . GRCh38 8 30479334 30479334 + Missense_Mutation SNP T T C novel C3L-00510_T C3L-00510_N T T c.203T>C p.Phe68Ser p.F68S ENST00000339877 4/7 160 98 62 155 155 0 strelka-varscan RBPMS,missense_variant,p.Phe68Ser,ENST00000320203,NM_006867.3;RBPMS,missense_variant,p.Phe68Ser,ENST00000287771,NM_001008711.2;RBPMS,missense_variant,p.Phe68Ser,ENST00000397323,NM_001008710.2;RBPMS,missense_variant,p.Phe68Ser,ENST00000339877,NM_001008712.2;RBPMS,missense_variant,p.Phe68Ser,ENST00000517860,;RBPMS,5_prime_UTR_variant,,ENST00000520191,;RBPMS,5_prime_UTR_variant,,ENST00000520161,;RBPMS,5_prime_UTR_variant,,ENST00000519647,;RBPMS,5_prime_UTR_variant,,ENST00000523115,;RBPMS,non_coding_transcript_exon_variant,,ENST00000523717,;RBPMS,non_coding_transcript_exon_variant,,ENST00000522708,;RBPMS,downstream_gene_variant,,ENST00000521816,;RBPMS,missense_variant,p.Phe44Ser,ENST00000519359,;RBPMS,missense_variant,p.Phe2Ser,ENST00000522694,; C ENST00000339877 Transcript missense_variant 785/1341 203/660 68/219 F/S tTt/tCt 1 1 RBPMS HGNC HGNC:19097 protein_coding YES CCDS34876.1 ENSP00000340176 Q93062 UPI000002B229 NM_001008712.2 deleterious(0) 4/7 PROSITE_profiles:PS50102,hmmpanther:PTHR10501,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 18 30479334 30479334 T C 1 0 0 0 0 1 0 0 0 13331 1841 64 5 5 RBPMS 8 30479334 Missense_Mutation SNP T C3L-00510_T 30479334 114659302 16 6717 SVEP1 0 . GRCh38 9 110465886 110465886 + Missense_Mutation SNP C C A rs773002647 C3L-00510_T C3L-00510_N C C c.3301G>T p.Val1101Leu p.V1101L ENST00000374469 18/48 91 74 17 141 140 1 strelka-varscan-mutect SVEP1,missense_variant,p.Val1101Leu,ENST00000401783,;SVEP1,missense_variant,p.Val1101Leu,ENST00000374469,NM_153366.3;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,; A ENST00000374469 Transcript missense_variant 3496/12194 3301/10716 1101/3571 V/L Gtg/Ttg rs773002647,COSM3413246,COSM3413247 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 tolerated(0.11) 18/48 Pfam_domain:PF07699,SMART_domains:SM01411,Superfamily_domains:SSF57184 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs773002647 . 0 202 0 5 2 0 0 0 -11.58778 0.9518512 1 1 1 0 A 3 1 18 110465886 110465886 C A 1 0 0 0 0 1 0 0 0 15805 536 19 1 1 SVEP1 9 110465886 Missense_Mutation SNP C C3L-00510_T 110465886 27928831 17 6718 XPNPEP1 0 . GRCh38 10 109882639 109882639 + Silent SNP G G C novel C3L-00510_T C3L-00510_N G G c.834C>G p.= p.L278L ENST00000502935 10/21 87 81 6 160 160 0 strelka-varscan-mutect XPNPEP1,synonymous_variant,p.=,ENST00000502935,NM_001324132.1,NM_020383.3;XPNPEP1,synonymous_variant,p.=,ENST00000322238,NM_001167604.1;XPNPEP1,synonymous_variant,p.=,ENST00000369683,NM_001324128.1;XPNPEP1,synonymous_variant,p.=,ENST00000403138,;XPNPEP1,synonymous_variant,p.=,ENST00000423625,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000430337,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000460523,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000443078,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000507328,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000508059,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000509646,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000512582,;XPNPEP1,downstream_gene_variant,,ENST00000506777,;XPNPEP1,downstream_gene_variant,,ENST00000490740,;XPNPEP1,upstream_gene_variant,,ENST00000494564,;XPNPEP1,upstream_gene_variant,,ENST00000510988,;XPNPEP1,downstream_gene_variant,,ENST00000451592,;XPNPEP1,downstream_gene_variant,,ENST00000505255,;XPNPEP1,upstream_gene_variant,,ENST00000460055,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000488118,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000513817,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000472336,;XPNPEP1,upstream_gene_variant,,ENST00000508525,; C ENST00000502935 Transcript synonymous_variant 954/2539 834/2001 278/666 L ctC/ctG 1 -1 XPNPEP1 HGNC HGNC:12822 protein_coding YES CCDS7560.2 ENSP00000421566 Q9NQW7 UPI00003D2EAD NM_001324132.1,NM_020383.3 10/21 Pfam_domain:PF16189,Gene3D:3.40.350.10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 18 109882639 109882639 G C 1 0 0 0 0 0 0 0 1 18001 956 33 4 4 XPNPEP1 10 109882639 Silent SNP G C3L-00510_T 109882639 23914783 18 6719 OR52E2 0 . GRCh38 11 5059332 5059332 + Missense_Mutation SNP C C A C3L-00510_T C3L-00510_N C C c.296G>T p.Cys99Phe p.C99F ENST00000321522 1/1 114 75 39 139 139 0 strelka-varscan-mutect OR52E2,missense_variant,p.Cys99Phe,ENST00000321522,NM_001005164.2; A ENST00000321522 Transcript missense_variant 296/978 296/978 99/325 C/F tGc/tTc COSM5613378 1 -1 OR52E2 HGNC HGNC:14769 protein_coding YES CCDS31371.1 ENSP00000322088 Q8NGJ4 UPI0000046AE3 NM_001005164.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF169,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs1421411535 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 5059332 5059332 C A 1 0 0 0 0 1 0 0 0 11187 710 25 2 2 OR52E2 11 5059332 Missense_Mutation SNP C C3L-00510_T 5059332 130027290 19 6720 ETS1 0 . GRCh38 11 128489411 128489411 + Silent SNP G G A novel C3L-00510_T C3L-00510_N G G c.414C>T p.= p.D138D ENST00000392668 5/10 267 159 108 424 424 0 strelka-varscan-mutect ETS1,synonymous_variant,p.=,ENST00000392668,NM_001143820.1;ETS1,synonymous_variant,p.=,ENST00000526145,;ETS1,synonymous_variant,p.=,ENST00000319397,NM_005238.3;ETS1,synonymous_variant,p.=,ENST00000531611,;ETS1,intron_variant,,ENST00000535549,NM_001162422.1;ETS1,downstream_gene_variant,,ENST00000608978,; A ENST00000392668 Transcript synonymous_variant 499/5139 414/1458 138/485 D gaC/gaT 1 -1 ETS1 HGNC HGNC:3488 protein_coding YES CCDS44767.1 ENSP00000376436 P14921 UPI00001BDB62 NM_001143820.1 5/10 PROSITE_profiles:PS51433,hmmpanther:PTHR11849:SF209,hmmpanther:PTHR11849,PIRSF_domain:PIRSF001698,Pfam_domain:PF02198,Gene3D:1.10.150.50,SMART_domains:SM00251,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 18 128489411 128489411 G A 1 0 0 0 0 0 0 0 1 5139 1020 36 3 3 ETS1 11 128489411 Silent SNP G C3L-00510_T 123430079 128489411 6597211 20 6721 CACNA1C 0 . GRCh38 12 2666737 2666737 + Silent SNP G G A rs376555924 C3L-00510_T C3L-00510_N G G c.4722G>A p.= p.P1574P ENST00000347598 39/49 158 93 65 240 240 0 strelka-varscan-mutect CACNA1C,synonymous_variant,p.=,ENST00000399655,NM_000719.6;CACNA1C,synonymous_variant,p.=,ENST00000399634,NM_001167625.1;CACNA1C,synonymous_variant,p.=,ENST00000406454,;CACNA1C,synonymous_variant,p.=,ENST00000399617,NM_001167624.2;CACNA1C,synonymous_variant,p.=,ENST00000399603,NM_001167623.1;CACNA1C,synonymous_variant,p.=,ENST00000335762,;CACNA1C,synonymous_variant,p.=,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,synonymous_variant,p.=,ENST00000344100,NM_001129829.1;CACNA1C,synonymous_variant,p.=,ENST00000327702,NM_001129830.2;CACNA1C,synonymous_variant,p.=,ENST00000399638,NM_001129831.1;CACNA1C,synonymous_variant,p.=,ENST00000399606,NM_001129832.1;CACNA1C,synonymous_variant,p.=,ENST00000399621,NM_001129834.1;CACNA1C,synonymous_variant,p.=,ENST00000399637,NM_001129835.1;CACNA1C,synonymous_variant,p.=,ENST00000402845,NM_001129833.1;CACNA1C,synonymous_variant,p.=,ENST00000399629,NM_001129836.1;CACNA1C,synonymous_variant,p.=,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,synonymous_variant,p.=,ENST00000399595,NM_001129837.1;CACNA1C,synonymous_variant,p.=,ENST00000399649,NM_001129839.1;CACNA1C,synonymous_variant,p.=,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,synonymous_variant,p.=,ENST00000399601,NM_001129843.1;CACNA1C,synonymous_variant,p.=,ENST00000399641,NM_001129840.1;CACNA1C,synonymous_variant,p.=,ENST00000399644,NM_001129841.1;CACNA1C,synonymous_variant,p.=,ENST00000616390,;CACNA1C-AS2,downstream_gene_variant,,ENST00000545526,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000465934,; A ENST00000347598 Transcript synonymous_variant 4722/6655 4722/6561 1574/2186 P ccG/ccA rs376555924,COSM430967,COSM430968,COSM430969,COSM430970,COSM430971 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 39/49 Pfam_domain:PF16905,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 0,1,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1,1 1 PASS rs376555924 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 18 2666737 2666737 G A 1 0 0 0 0 0 0 0 1 2228 1074 38 1 1 CACNA1C 12 2666737 Silent SNP G C3L-00510_T 2666737 130608572 21 6722 GAPDH 0 . GRCh38 12 6537377 6537377 + Missense_Mutation SNP T T C novel C3L-00510_T C3L-00510_N T T c.512T>C p.Val171Ala p.V171A ENST00000229239 7/9 253 78 175 169 169 0 strelka-varscan-mutect GAPDH,missense_variant,p.Val171Ala,ENST00000229239,NM_002046.5;GAPDH,missense_variant,p.Val171Ala,ENST00000396861,NM_001289745.1;GAPDH,missense_variant,p.Val129Ala,ENST00000396858,NM_001256799.2;GAPDH,missense_variant,p.Val96Ala,ENST00000396856,;GAPDH,missense_variant,p.Val171Ala,ENST00000396859,NM_001289746.1;GAPDH,missense_variant,p.Val129Ala,ENST00000619601,;IFFO1,downstream_gene_variant,,ENST00000436152,;IFFO1,downstream_gene_variant,,ENST00000465801,;IFFO1,downstream_gene_variant,,ENST00000615885,;IFFO1,downstream_gene_variant,,ENST00000619571,NM_001193457.1;IFFO1,downstream_gene_variant,,ENST00000336604,NM_080730.4;IFFO1,downstream_gene_variant,,ENST00000356896,NM_001039670.2;IFFO1,downstream_gene_variant,,ENST00000396840,;RP5-940J5.3,upstream_gene_variant,,ENST00000537921,;RP5-940J5.9,downstream_gene_variant,,ENST00000602946,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466525,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466588,;GAPDH,non_coding_transcript_exon_variant,,ENST00000474249,;GAPDH,non_coding_transcript_exon_variant,,ENST00000492719,;IFFO1,downstream_gene_variant,,ENST00000488007,;IFFO1,downstream_gene_variant,,ENST00000471408,;IFFO1,downstream_gene_variant,,ENST00000487279,;IFFO1,downstream_gene_variant,,ENST00000472558,;IFFO1,downstream_gene_variant,,ENST00000396830,;GAPDH,downstream_gene_variant,,ENST00000496049,; C ENST00000229239 Transcript missense_variant 1178/1875 512/1008 171/335 V/A gTg/gCg 1 1 GAPDH HGNC HGNC:4141 protein_coding YES CCDS8549.1 ENSP00000229239 P04406 V9HVZ4 UPI000013C8ED NM_002046.5 deleterious_low_confidence(0.03) 7/9 hmmpanther:PTHR10836,Pfam_domain:PF02800,Gene3D:3.30.360.10,PIRSF_domain:PIRSF000149,TIGRFAM_domain:TIGR01534,Superfamily_domains:SSF51735,Superfamily_domains:SSF55347 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 18 6537377 6537377 T C 1 0 0 0 0 1 0 0 0 6104 1696 59 5 5 GAPDH 12 6537377 Missense_Mutation SNP T C3L-00510_T 3870640 6537377 126737932 22 6723 1 5 3 3 608 N T_C_A 3.083855e-07 GAPDH 0 . GRCh38 12 6537764 6537764 + Missense_Mutation SNP C C T novel C3L-00510_T C3L-00510_N C C c.706C>T p.Pro236Ser p.P236S ENST00000229239 8/9 235 133 102 277 277 0 strelka-varscan-mutect GAPDH,missense_variant,p.Pro236Ser,ENST00000229239,NM_002046.5;GAPDH,missense_variant,p.Pro236Ser,ENST00000396861,NM_001289745.1;GAPDH,missense_variant,p.Pro194Ser,ENST00000396858,NM_001256799.2;GAPDH,missense_variant,p.Pro161Ser,ENST00000396856,;GAPDH,missense_variant,p.Pro236Ser,ENST00000396859,NM_001289746.1;GAPDH,missense_variant,p.Pro194Ser,ENST00000619601,;IFFO1,downstream_gene_variant,,ENST00000436152,;IFFO1,downstream_gene_variant,,ENST00000465801,;IFFO1,downstream_gene_variant,,ENST00000615885,;IFFO1,downstream_gene_variant,,ENST00000619571,NM_001193457.1;IFFO1,downstream_gene_variant,,ENST00000336604,NM_080730.4;IFFO1,downstream_gene_variant,,ENST00000356896,NM_001039670.2;IFFO1,downstream_gene_variant,,ENST00000396840,;RP5-940J5.3,upstream_gene_variant,,ENST00000537921,;RP5-940J5.9,downstream_gene_variant,,ENST00000602946,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466525,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466588,;GAPDH,non_coding_transcript_exon_variant,,ENST00000474249,;GAPDH,non_coding_transcript_exon_variant,,ENST00000492719,;IFFO1,downstream_gene_variant,,ENST00000488007,;IFFO1,downstream_gene_variant,,ENST00000471408,;IFFO1,downstream_gene_variant,,ENST00000487279,;IFFO1,downstream_gene_variant,,ENST00000472558,;IFFO1,downstream_gene_variant,,ENST00000396830,;GAPDH,downstream_gene_variant,,ENST00000496049,; T ENST00000229239 Transcript missense_variant 1372/1875 706/1008 236/335 P/S Ccc/Tcc 1 1 GAPDH HGNC HGNC:4141 protein_coding YES CCDS8549.1 ENSP00000229239 P04406 V9HVZ4 UPI000013C8ED NM_002046.5 deleterious_low_confidence(0.04) 8/9 hmmpanther:PTHR10836,Pfam_domain:PF02800,Gene3D:3.30.360.10,PIRSF_domain:PIRSF000149,TIGRFAM_domain:TIGR01534,Superfamily_domains:SSF55347,Prints_domain:PR00078 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 18 6537764 6537764 C T 1 0 0 0 0 1 0 0 0 6104 623 22 3 3 GAPDH 12 6537764 Missense_Mutation SNP C C3L-00510_T 387 6537764 126737545 23 6724 1 5 3 3 608 N T_C_A 3.083855e-07 GAPDH 0 . GRCh38 12 6537984 6537984 + Missense_Mutation SNP A A C novel C3L-00510_T C3L-00510_N A A c.926A>C p.Lys309Thr p.K309T ENST00000229239 8/9 81 43 38 121 121 0 strelka-varscan-mutect GAPDH,missense_variant,p.Lys309Thr,ENST00000229239,NM_002046.5;GAPDH,missense_variant,p.Lys309Thr,ENST00000396861,NM_001289745.1;GAPDH,missense_variant,p.Lys267Thr,ENST00000396858,NM_001256799.2;GAPDH,missense_variant,p.Lys234Thr,ENST00000396856,;GAPDH,missense_variant,p.Lys309Thr,ENST00000396859,NM_001289746.1;GAPDH,missense_variant,p.Lys267Thr,ENST00000619601,;IFFO1,downstream_gene_variant,,ENST00000436152,;IFFO1,downstream_gene_variant,,ENST00000465801,;IFFO1,downstream_gene_variant,,ENST00000615885,;IFFO1,downstream_gene_variant,,ENST00000619571,NM_001193457.1;IFFO1,downstream_gene_variant,,ENST00000336604,NM_080730.4;IFFO1,downstream_gene_variant,,ENST00000356896,NM_001039670.2;IFFO1,downstream_gene_variant,,ENST00000396840,;RP5-940J5.9,splice_region_variant,,ENST00000602946,;RP5-940J5.3,upstream_gene_variant,,ENST00000537921,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466525,;GAPDH,non_coding_transcript_exon_variant,,ENST00000466588,;GAPDH,non_coding_transcript_exon_variant,,ENST00000474249,;IFFO1,downstream_gene_variant,,ENST00000488007,;IFFO1,downstream_gene_variant,,ENST00000471408,;IFFO1,downstream_gene_variant,,ENST00000487279,;IFFO1,downstream_gene_variant,,ENST00000472558,;IFFO1,downstream_gene_variant,,ENST00000396830,;GAPDH,downstream_gene_variant,,ENST00000492719,;GAPDH,downstream_gene_variant,,ENST00000496049,; C ENST00000229239 Transcript missense_variant 1592/1875 926/1008 309/335 K/T aAg/aCg 1 1 GAPDH HGNC HGNC:4141 protein_coding YES CCDS8549.1 ENSP00000229239 P04406 V9HVZ4 UPI000013C8ED NM_002046.5 deleterious_low_confidence(0) 8/9 hmmpanther:PTHR10836,Pfam_domain:PF02800,Gene3D:3.30.360.10,PIRSF_domain:PIRSF000149,TIGRFAM_domain:TIGR01534,Superfamily_domains:SSF55347 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 18 6537984 6537984 A C 1 0 0 0 0 1 0 0 0 6104 72 3 5 5 GAPDH 12 6537984 Missense_Mutation SNP A C3L-00510_T 220 6537984 126737325 24 6725 1 5 3 3 608 N T_C_A 3.083855e-07 ACVR1B 0 . GRCh38 12 51975443 51975450 + Frame_Shift_Del DEL GCGCAACA GCGCAACA - novel C3L-00510_T C3L-00510_N GCGCAACA GCGCAACA c.270_277delGCGCAACA p.Arg91ProfsTer6 p.R91Pfs*6 ENST00000541224 2/10 192 129 63 355 355 0 sindel-pindel ACVR1B,frameshift_variant,p.Arg91ProfsTer6,ENST00000257963,NM_004302.4;ACVR1B,frameshift_variant,p.Arg39ProfsTer6,ENST00000542485,NM_020327.3;ACVR1B,frameshift_variant,p.Arg91ProfsTer6,ENST00000541224,NM_020328.3;ACVR1B,frameshift_variant,p.Arg91ProfsTer6,ENST00000426655,;ACVR1B,frameshift_variant,p.Arg91ProfsTer6,ENST00000415850,;ACVR1B,frameshift_variant,p.Arg39ProfsTer6,ENST00000536420,; - ENST00000541224 Transcript frameshift_variant 313-320/1791 270-277/1641 90-93/546 LRNT/LX ctGCGCAACAcc/ctcc 1 1 ACVR1B HGNC HGNC:172 protein_coding YES CCDS44894.2 ENSP00000442656 P36896 UPI0001915052 NM_020328.3 2/10 Gene3D:2.10.60.10,Pfam_domain:PF01064,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF22,Superfamily_domains:SSF57302 HIGH 1 deletion 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 18 51975443 51975443 GCGCAACA - 1 0 1 0 1 0 0 0 0 265 1306 46 0 0 ACVR1B 12 51975443 Frame_Shift_Del DEL GCGCAACA C3L-00510_T 45437459 51975443 81299866 25 6726 DUSP6 0 . GRCh38 12 89349255 89349255 + Nonstop_Mutation SNP C C A C3L-00510_T C3L-00510_N C C c.1145G>T p.Ter382LeuextTer36 p.*382Lext*36 ENST00000279488 3/3 39 21 18 61 61 0 strelka-varscan-mutect DUSP6,stop_lost,p.Ter382LeuextTer36,ENST00000279488,NM_001946.3;DUSP6,stop_lost,p.Ter236LeuextTer36,ENST00000308385,NM_022652.3;DUSP6,stop_lost,p.Ter257LeuextTer36,ENST00000547291,;DUSP6,downstream_gene_variant,,ENST00000548755,;RP11-823E8.3,upstream_gene_variant,,ENST00000611513,;DUSP6,downstream_gene_variant,,ENST00000547140,; A ENST00000279488 Transcript stop_lost 2377/4400 1145/1146 382/381 */L tGa/tTa COSM4937920 1 -1 DUSP6 HGNC HGNC:3072 protein_coding YES CCDS9033.1 ENSP00000279488 Q16828 A0A024RBC1 UPI000013ED2F NM_001946.3 3/3 1 HIGH 1 SNV 1 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 4 1 18 89349255 89349255 C A 1 0 0 0 0 0 0 0 0 4651 837 29 2 2 DUSP6 12 89349255 Nonstop_Mutation SNP C C3L-00510_T 37373812 89349255 43926054 26 6727 GALNT9 0 . GRCh38 12 132201204 132201206 + In_Frame_Del DEL TCA TCA - novel C3L-00510_T C3L-00510_N TCA TCA c.221_223delTGA p.Leu74_Lys75delinsGln p.L74_K75delinsQ ENST00000397325 4/7 159 121 38 265 265 0 sindel-varindel-pindel GALNT9,inframe_deletion,p.Leu440_Lys441delinsGln,ENST00000328957,;GALNT9,inframe_deletion,p.Leu74_Lys75delinsGln,ENST00000397325,NM_021808.3;GALNT9,inframe_deletion,p.Leu213_Lys214delinsGln,ENST00000411988,;GALNT9,inframe_deletion,p.Leu74_Lys75delinsGln,ENST00000541995,NM_001122636.1;GALNT9,inframe_deletion,p.Leu74_Lys75delinsGln,ENST00000538356,;GALNT9,downstream_gene_variant,,ENST00000542942,;RP13-977J11.3,non_coding_transcript_exon_variant,,ENST00000623965,; - ENST00000397325 Transcript inframe_deletion 499-501/1727 221-223/714 74-75/237 LK/Q cTGAag/cag 1 -1 GALNT9 HGNC HGNC:4131 protein_coding YES CCDS41866.1 ENSP00000380488 Q9HCQ5 UPI000006CCBE NM_021808.3 4/7 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF28,Superfamily_domains:SSF53448 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 18 132201204 132201204 TCA - 1 0 1 0 1 0 0 0 0 6091 1792 62 0 0 GALNT9 12 132201204 In_Frame_Del DEL TCA C3L-00510_T 42851949 132201204 1074105 27 6728 HECTD1 0 . GRCh38 14 31134983 31134983 + Missense_Mutation SNP C C T novel C3L-00510_T C3L-00510_N C C c.3467G>A p.Arg1156His p.R1156H ENST00000399332 22/43 254 169 85 314 313 1 strelka-mutect HECTD1,missense_variant,p.Arg1156His,ENST00000399332,NM_015382.3;HECTD1,missense_variant,p.Arg1156His,ENST00000553700,;HECTD1,missense_variant,p.Arg1160His,ENST00000611816,;HECTD1,missense_variant,p.Arg630His,ENST00000553957,;HECTD1,upstream_gene_variant,,ENST00000557369,;HECTD1,downstream_gene_variant,,ENST00000554850,; T ENST00000399332 Transcript missense_variant 3956/9134 3467/7833 1156/2610 R/H cGt/cAt 1 -1 HECTD1 HGNC HGNC:20157 protein_coding YES CCDS41939.1 ENSP00000382269 Q9ULT8 UPI0000D9BBA1 NM_015382.3 deleterious(0) 22/43 Gene3D:2.60.120.260,Pfam_domain:PF07738,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF322,Superfamily_domains:SSF49785 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 18 31134983 31134983 C T 1 0 0 0 0 1 0 0 0 6920 536 19 1 1 HECTD1 14 31134983 Missense_Mutation SNP C C3L-00510_T 31134983 75908735 28 6729 TLE3 0 . GRCh38 15 70054585 70054585 + Missense_Mutation SNP G G A C3L-00510_T C3L-00510_N G G c.1688C>T p.Ser563Leu p.S563L ENST00000558939 16/20 50 45 5 155 155 0 strelka-varscan-mutect TLE3,missense_variant,p.Ser563Leu,ENST00000558939,NM_005078.3;TLE3,missense_variant,p.Ser563Leu,ENST00000627388,;TLE3,missense_variant,p.Ser551Leu,ENST00000317509,NM_020908.2;TLE3,missense_variant,p.Ser555Leu,ENST00000557997,NM_001282979.1;TLE3,missense_variant,p.Ser507Leu,ENST00000560589,;TLE3,missense_variant,p.Ser573Leu,ENST00000559929,;TLE3,missense_variant,p.Ser565Leu,ENST00000560939,;TLE3,missense_variant,p.Ser563Leu,ENST00000559048,;TLE3,missense_variant,p.Ser569Leu,ENST00000558201,;TLE3,missense_variant,p.Ser553Leu,ENST00000440567,NM_001282981.1;TLE3,missense_variant,p.Ser490Leu,ENST00000539550,NM_001282982.1;TLE3,missense_variant,p.Ser560Leu,ENST00000451782,NM_001105192.2;TLE3,missense_variant,p.Ser558Leu,ENST00000558379,NM_001282980.1;TLE3,missense_variant,p.Ser555Leu,ENST00000557907,;TLE3,missense_variant,p.Ser144Leu,ENST00000559191,;TLE3,3_prime_UTR_variant,,ENST00000557919,;TLE3,3_prime_UTR_variant,,ENST00000561453,;TLE3,3_prime_UTR_variant,,ENST00000560525,;TLE3,non_coding_transcript_exon_variant,,ENST00000557815,;TLE3,non_coding_transcript_exon_variant,,ENST00000542329,;TLE3,upstream_gene_variant,,ENST00000559608,;TLE3,downstream_gene_variant,,ENST00000559826,; A ENST00000558939 Transcript missense_variant 3066/6004 1688/2319 563/772 S/L tCg/tTg COSM416842,COSM4812727 1 -1 TLE3 HGNC HGNC:11839 protein_coding YES CCDS45293.1 ENSP00000452871 Q04726 UPI000013703A NM_005078.3 deleterious(0) 16/20 PROSITE_profiles:PS50294,hmmpanther:PTHR10814,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1350882604 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 70054585 70054585 G A 1 0 0 0 0 1 0 0 0 16386 1059 37 1 1 TLE3 15 70054585 Missense_Mutation SNP G C3L-00510_T 70054585 31936604 29 6730 LOXL1 0 . GRCh38 15 73946505 73946505 + Missense_Mutation SNP T T C novel C3L-00510_T C3L-00510_N T T c.1300T>C p.Phe434Leu p.F434L ENST00000261921 3/7 124 30 94 304 304 0 strelka-varscan-mutect LOXL1,missense_variant,p.Phe434Leu,ENST00000261921,NM_005576.2;LOXL1,upstream_gene_variant,,ENST00000567675,;LOXL1,3_prime_UTR_variant,,ENST00000566011,;LOXL1,non_coding_transcript_exon_variant,,ENST00000566530,;LOXL1,upstream_gene_variant,,ENST00000562548,; C ENST00000261921 Transcript missense_variant 1626/2351 1300/1725 434/574 F/L Ttc/Ctc 1 1 LOXL1 HGNC HGNC:6665 protein_coding YES CCDS10253.1 ENSP00000261921 Q08397 UPI000013D224 NM_005576.2 deleterious(0) 3/7 hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF4,Pfam_domain:PF01186,Prints_domain:PR00074 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 18 73946505 73946505 T C 1 0 0 0 0 1 0 0 0 8802 1609 56 5 5 LOXL1 15 73946505 Missense_Mutation SNP T C3L-00510_T 3891920 73946505 28044684 30 6731 MSRB1 0 . GRCh38 16 1940962 1940962 + Missense_Mutation SNP G G C novel C3L-00510_T C3L-00510_N G G c.499C>G p.Pro167Ala p.P167A ENST00000399753 2/3 263 148 115 373 373 0 strelka-varscan-mutect MSRB1,missense_variant,p.Pro167Ala,ENST00000399753,;MSRB1,intron_variant,,ENST00000361871,NM_016332.2;MSRB1,intron_variant,,ENST00000622125,;MSRB1,intron_variant,,ENST00000564908,;MSRB1,intron_variant,,ENST00000473663,;RPL3L,downstream_gene_variant,,ENST00000268661,NM_005061.2;MSRB1,downstream_gene_variant,,ENST00000489198,; C ENST00000399753 Transcript missense_variant 538/847 499/681 167/226 P/A Ccc/Gcc 1 -1 MSRB1 HGNC HGNC:14133 protein_coding ENSP00000382657 A8MYR2 UPI0000E59D5E 2/3 MODERATE SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 18 1940962 1940962 G C 1 0 0 0 0 1 0 0 0 9871 1232 43 4 4 MSRB1 16 1940962 Missense_Mutation SNP G C3L-00510_T 1940962 88397383 31 6732 ABCC6 0 . GRCh38 16 16165823 16165823 + Missense_Mutation SNP A A T rs761996195 C3L-00510_T C3L-00510_N A A c.3106T>A p.Phe1036Ile p.F1036I ENST00000205557 23/31 354 231 123 497 497 0 strelka-varscan-mutect ABCC6,missense_variant,p.Phe1036Ile,ENST00000205557,NM_001171.5;ABCC6,3_prime_UTR_variant,,ENST00000622290,;ABCC6,3_prime_UTR_variant,,ENST00000456970,; T ENST00000205557 Transcript missense_variant 3136/5747 3106/4512 1036/1503 F/I Ttt/Att rs761996195 1 -1 ABCC6 HGNC HGNC:57 protein_coding YES CCDS10568.1 ENSP00000205557 O95255 UPI00001AE5CA NM_001171.5 deleterious(0) 23/31 PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF226,hmmpanther:PTHR24223,TIGRFAM_domain:TIGR00957,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS rs761996195 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 18 16165823 16165823 A T 1 0 0 0 0 1 0 0 0 61 72 3 4 4 ABCC6 16 16165823 Missense_Mutation SNP A C3L-00510_T 14224861 16165823 74172522 32 6733 DRC7 0 . GRCh38 16 57727332 57727332 + Missense_Mutation SNP G G A C3L-00510_T C3L-00510_N G G c.2119G>A p.Glu707Lys p.E707K ENST00000360716 16/19 245 231 14 327 327 0 strelka-mutect DRC7,missense_variant,p.Glu707Lys,ENST00000360716,NM_001289162.1;DRC7,missense_variant,p.Glu707Lys,ENST00000394337,NM_032269.5;DRC7,missense_variant,p.Glu642Lys,ENST00000336825,NM_001289163.1;DRC7,missense_variant,p.Glu260Lys,ENST00000562250,;DRC7,non_coding_transcript_exon_variant,,ENST00000565609,; A ENST00000360716 Transcript missense_variant 2340/3041 2119/2625 707/874 E/K Gag/Aag COSM1709227 1 1 DRC7 HGNC HGNC:25289 protein_coding YES CCDS10787.1 ENSP00000353942 Q8IY82 UPI00001AEB68 NM_001289162.1 deleterious(0) 16/19 hmmpanther:PTHR35249,hmmpanther:PTHR35249:SF1 1 MODERATE 1 SNV 1 1 1 PASS rs1267268672 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 57727332 57727332 G A 1 0 0 0 0 1 0 0 0 4574 1175 41 3 3 DRC7 16 57727332 Missense_Mutation SNP G C3L-00510_T 41561509 57727332 32611013 33 6734 ACADVL 0 . GRCh38 17 7224165 7224165 + Missense_Mutation SNP C C G novel C3L-00510_T C3L-00510_N C C c.1523C>G p.Ser508Cys p.S508C ENST00000543245 16/21 316 294 22 743 743 0 strelka-varscan-mutect ACADVL,missense_variant,p.Ser485Cys,ENST00000356839,NM_000018.3;ACADVL,missense_variant,p.Ser508Cys,ENST00000543245,NM_001270447.1;ACADVL,missense_variant,p.Ser463Cys,ENST00000350303,NM_001270448.1,NM_001033859.2;ACADVL,missense_variant,p.Ser105Cys,ENST00000542255,;ACADVL,intron_variant,,ENST00000579546,;DLG4,upstream_gene_variant,,ENST00000399510,NM_001321074.1,NM_001365.3;DVL2,downstream_gene_variant,,ENST00000005340,NM_004422.2;DVL2,downstream_gene_variant,,ENST00000575458,;DVL2,downstream_gene_variant,,ENST00000575756,;DVL2,downstream_gene_variant,,ENST00000574143,;DVL2,downstream_gene_variant,,ENST00000575086,;ACADVL,downstream_gene_variant,,ENST00000583312,;ACADVL,downstream_gene_variant,,ENST00000584103,;ACADVL,downstream_gene_variant,,ENST00000579886,;MIR324,upstream_gene_variant,,ENST00000362183,;ACADVL,intron_variant,,ENST00000583074,;DVL2,downstream_gene_variant,,ENST00000574642,;ACADVL,downstream_gene_variant,,ENST00000581562,;ACADVL,downstream_gene_variant,,ENST00000577857,;ACADVL,3_prime_UTR_variant,,ENST00000322910,;ACADVL,non_coding_transcript_exon_variant,,ENST00000578711,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579425,;ACADVL,non_coding_transcript_exon_variant,,ENST00000585203,;ACADVL,non_coding_transcript_exon_variant,,ENST00000583850,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579894,;ACADVL,non_coding_transcript_exon_variant,,ENST00000579391,;ACADVL,intron_variant,,ENST00000583858,;ACADVL,downstream_gene_variant,,ENST00000577191,;DVL2,downstream_gene_variant,,ENST00000576840,;ACADVL,downstream_gene_variant,,ENST00000579286,;ACADVL,downstream_gene_variant,,ENST00000582379,;ACADVL,downstream_gene_variant,,ENST00000577433,;ACADVL,downstream_gene_variant,,ENST00000581378,;ACADVL,downstream_gene_variant,,ENST00000582056,;ACADVL,downstream_gene_variant,,ENST00000578269,;ACADVL,downstream_gene_variant,,ENST00000578824,;ACADVL,upstream_gene_variant,,ENST00000578319,;ACADVL,upstream_gene_variant,,ENST00000578809,;DVL2,downstream_gene_variant,,ENST00000576285,;ACADVL,downstream_gene_variant,,ENST00000582356,;DVL2,downstream_gene_variant,,ENST00000574591,;ACADVL,downstream_gene_variant,,ENST00000583760,;ACADVL,upstream_gene_variant,,ENST00000578033,;DVL2,downstream_gene_variant,,ENST00000571745,;ACADVL,downstream_gene_variant,,ENST00000582166,;ACADVL,downstream_gene_variant,,ENST00000578421,;ACADVL,downstream_gene_variant,,ENST00000580263,;DVL2,downstream_gene_variant,,ENST00000577154,;ACADVL,upstream_gene_variant,,ENST00000583848,;ACADVL,downstream_gene_variant,,ENST00000580365,;ACADVL,downstream_gene_variant,,ENST00000578579,;DVL2,downstream_gene_variant,,ENST00000573354,;ACADVL,upstream_gene_variant,,ENST00000582450,; G ENST00000543245 Transcript missense_variant 1544/2227 1523/2037 508/678 S/C tCt/tGt 1 1 ACADVL HGNC HGNC:92 protein_coding YES CCDS58509.1 ENSP00000438689 P49748 UPI0002064F84 NM_001270447.1 deleterious(0) 16/21 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF292 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 18 7224165 7224165 C G 1 0 0 0 0 1 0 0 0 159 913 32 4 4 ACADVL 17 7224165 Missense_Mutation SNP C C3L-00510_T 7224165 76033276 34 6735 TP53 0 . GRCh38 17 7675085 7675085 + Missense_Mutation SNP C C T rs786202962 C3L-00510_T C3L-00510_N C C c.527G>A p.Cys176Tyr p.C176Y ENST00000269305 5/11 164 41 123 525 523 2 strelka-varscan-mutect TP53,missense_variant,p.Cys176Tyr,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Cys176Tyr,ENST00000420246,;TP53,missense_variant,p.Cys137Tyr,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Cys137Tyr,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Cys176Tyr,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Cys137Tyr,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Cys176Tyr,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Cys137Tyr,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Cys176Tyr,ENST00000445888,;TP53,missense_variant,p.Cys137Tyr,ENST00000619485,;TP53,missense_variant,p.Cys44Tyr,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Cys17Tyr,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Cys44Tyr,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Cys17Tyr,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Cys44Tyr,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Cys17Tyr,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Cys176Tyr,ENST00000359597,;TP53,missense_variant,p.Cys165Tyr,ENST00000615910,;TP53,missense_variant,p.Cys176Tyr,ENST00000413465,;TP53,missense_variant,p.Cys44Tyr,ENST00000509690,;TP53,missense_variant,p.Cys83Tyr,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.Cys137Tyr,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 717/2579 527/1182 176/393 C/Y tGc/tAc rs786202962,TP53_g.12515G>A,TP53_g.12515del,TP53_g.12515G>T,TP53_g.12515G>C,COSM10645,COSM10687,COSM117395,COSM117396,COSM117397,COSM117398,COSM1640850,COSM1649384,COSM3378352,COSM3388204,COSM44645,COSM99669,COSM99670,COSM99671,COSM99672 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs786202962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 18 7675085 7675085 C T 1 0 0 0 0 1 0 0 0 16859 710 25 3 3 TP53 17 7675085 Missense_Mutation SNP C C3L-00510_T 450920 7675085 75582356 35 6736 CFAP53 0 . GRCh38 18 50227540 50227540 + Missense_Mutation SNP T T A novel C3L-00510_T C3L-00510_N T T c.1386A>T p.Gln462His p.Q462H ENST00000398545 8/8 304 264 40 417 416 1 strelka-varscan-mutect CFAP53,missense_variant,p.Gln462His,ENST00000398545,NM_145020.3; A ENST00000398545 Transcript missense_variant 1504/1851 1386/1545 462/514 Q/H caA/caT 1 -1 CFAP53 HGNC HGNC:26530 protein_coding YES CCDS11940.2 ENSP00000381553 Q96M91 UPI000014C50D NM_145020.3 tolerated(0.16) 8/8 hmmpanther:PTHR31183,hmmpanther:PTHR31183:SF1,Pfam_domain:PF13868 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 50227540 50227540 T A 1 0 0 0 0 1 0 0 0 3024 1606 56 4 4 CFAP53 18 50227540 Missense_Mutation SNP T C3L-00510_T 50227540 30145745 36 6737 KEAP1 0 . GRCh38 19 10491967 10491969 + In_Frame_Del DEL TTG TTG - novel C3L-00510_T C3L-00510_N TTG TTG c.933_935delCAA p.His311_Lys312delinsGln p.H311_K312delinsQ ENST00000171111 3/6 143 53 90 374 374 0 sindel-varindel KEAP1,inframe_deletion,p.His311_Lys312delinsGln,ENST00000171111,NM_203500.1;KEAP1,inframe_deletion,p.His311_Lys312delinsGln,ENST00000393623,NM_012289.3;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590593,;KEAP1,upstream_gene_variant,,ENST00000590237,; - ENST00000171111 Transcript inframe_deletion 1481-1483/2955 933-935/1875 311-312/624 HK/Q caCAAg/cag 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 18 10491967 10491967 TTG - 1 0 1 0 1 0 0 0 0 8061 1609 56 0 0 KEAP1 19 10491967 In_Frame_Del DEL TTG C3L-00510_T 10491967 48125649 37 6738 PRPF6 0 . GRCh38 20 64026015 64026015 + Missense_Mutation SNP G G A novel C3L-00510_T C3L-00510_N G G c.1985G>A p.Arg662Gln p.R662Q ENST00000266079 15/21 611 568 43 596 593 3 strelka-varscan-mutect PRPF6,missense_variant,p.Arg662Gln,ENST00000266079,NM_012469.3; A ENST00000266079 Transcript missense_variant 2096/3044 1985/2826 662/941 R/Q cGg/cAg 1 1 PRPF6 HGNC HGNC:15860 protein_coding YES CCDS13550.1 ENSP00000266079 O94906 UPI0000132356 NM_012469.3 deleterious(0.01) 15/21 Gene3D:1.25.40.10,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14559,PROSITE_profiles:PS50293,hmmpanther:PTHR11246,Low_complexity_(Seg):seg,SMART_domains:SM00386,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 64026015 64026015 G A 1 0 0 0 0 1 0 0 0 12710 1116 39 1 1 PRPF6 20 64026015 Missense_Mutation SNP G C3L-00510_T 64026015 418152 38 6739 TRMT2A 0 . GRCh38 22 20116220 20116220 + Silent SNP G G A novel C3L-00510_T C3L-00510_N G G c.417C>T p.= p.L139L ENST00000252136 2/12 99 30 69 245 245 0 strelka-varscan-mutect TRMT2A,synonymous_variant,p.=,ENST00000252136,NM_022727.5,NM_182984.4;TRMT2A,synonymous_variant,p.=,ENST00000403707,;TRMT2A,synonymous_variant,p.=,ENST00000404751,NM_001257994.1;TRMT2A,synonymous_variant,p.=,ENST00000439169,;RANBP1,synonymous_variant,p.=,ENST00000430524,NM_001278639.1;RANBP1,synonymous_variant,p.=,ENST00000432879,;DGCR8,downstream_gene_variant,,ENST00000351989,NM_022720.6;DGCR8,downstream_gene_variant,,ENST00000383024,NM_001190326.1;DGCR8,downstream_gene_variant,,ENST00000407755,;RANBP1,upstream_gene_variant,,ENST00000402752,NM_001278640.1;RANBP1,upstream_gene_variant,,ENST00000418705,NM_001278641.1;RANBP1,upstream_gene_variant,,ENST00000331821,NM_002882.3;RANBP1,upstream_gene_variant,,ENST00000423859,;TRMT2A,upstream_gene_variant,,ENST00000444845,;RANBP1,upstream_gene_variant,,ENST00000416427,;RANBP1,upstream_gene_variant,,ENST00000411892,;TRMT2A,downstream_gene_variant,,ENST00000445045,;TRMT2A,upstream_gene_variant,,ENST00000444256,;RANBP1,upstream_gene_variant,,ENST00000421656,;MIR6816,upstream_gene_variant,,ENST00000620368,;AC006547.8,upstream_gene_variant,,ENST00000412713,;TRMT2A,upstream_gene_variant,,ENST00000492988,;RANBP1,upstream_gene_variant,,ENST00000467920,;TRMT2A,upstream_gene_variant,,ENST00000488335,;TRMT2A,upstream_gene_variant,,ENST00000480460,;RANBP1,synonymous_variant,p.=,ENST00000435265,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000494641,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000468917,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000464535,;DGCR8,downstream_gene_variant,,ENST00000495826,;DGCR8,downstream_gene_variant,,ENST00000498171,;DGCR8,downstream_gene_variant,,ENST00000475941,;TRMT2A,upstream_gene_variant,,ENST00000494820,;TRMT2A,upstream_gene_variant,,ENST00000487668,;TRMT2A,upstream_gene_variant,,ENST00000471040,;TRMT2A,upstream_gene_variant,,ENST00000480339,;TRMT2A,upstream_gene_variant,,ENST00000463710,;RANBP1,upstream_gene_variant,,ENST00000488484,;TRMT2A,upstream_gene_variant,,ENST00000487378,;TRMT2A,upstream_gene_variant,,ENST00000459644,; A ENST00000252136 Transcript synonymous_variant 806/2964 417/1878 139/625 L ctC/ctT 1 -1 TRMT2A HGNC HGNC:24974 protein_coding YES CCDS13774.1 ENSP00000252136 Q8IZ69 UPI00001BBFC5 NM_022727.5,NM_182984.4 2/12 PROSITE_profiles:PS50102,hmmpanther:PTHR11061:SF24,hmmpanther:PTHR11061,Gene3D:3.30.70.330,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 18 20116220 20116220 G A 1 0 0 0 0 0 0 0 1 17069 1277 45 3 3 TRMT2A 22 20116220 Silent SNP G C3L-00510_T 20116220 30702248 39 6740 FRMPD3 0 . GRCh38 X 107601527 107601527 + Missense_Mutation SNP C C A rs759791679 C3L-00510_T C3L-00510_N C C c.3587C>A p.Pro1196His p.P1196H ENST00000276185 16/16 195 128 67 246 246 0 strelka-varscan-mutect FRMPD3,missense_variant,p.Pro1196His,ENST00000276185,NM_032428.1;FRMPD3,missense_variant,p.Pro1144His,ENST00000439554,; A ENST00000276185 Transcript missense_variant 3587/7304 3587/5433 1196/1810 P/H cCc/cAc rs759791679 1 1 FRMPD3 HGNC HGNC:29382 protein_coding YES CCDS76006.1 ENSP00000276185 Q5JV73 UPI00006C1C33 NM_032428.1 deleterious_low_confidence(0) 16/16 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs759791679 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 18 107601527 107601527 C A 1 0 0 0 0 1 0 0 0 5929 623 22 2 2 FRMPD3 23 107601527 Missense_Mutation SNP C C3L-00510_T 107601527 48439368 40 6741 SLC10A3 0 . GRCh38 X 154488564 154488564 + Missense_Mutation SNP C C G novel C3L-00510_T C3L-00510_N C C c.377G>C p.Gly126Ala p.G126A ENST00000263512 2/2 99 60 39 159 159 0 strelka-varscan-mutect SLC10A3,missense_variant,p.Gly126Ala,ENST00000263512,NM_019848.4;SLC10A3,missense_variant,p.Gly181Ala,ENST00000393586,;SLC10A3,missense_variant,p.Gly126Ala,ENST00000393587,NM_001142392.2;SLC10A3,missense_variant,p.Gly126Ala,ENST00000453912,;SLC10A3,intron_variant,,ENST00000369649,NM_001142391.2;UBL4A,upstream_gene_variant,,ENST00000369660,NM_014235.4;UBL4A,upstream_gene_variant,,ENST00000369653,;UBL4A,upstream_gene_variant,,ENST00000630530,;UBL4A,upstream_gene_variant,,ENST00000477777,;UBL4A,upstream_gene_variant,,ENST00000421431,;UBL4A,upstream_gene_variant,,ENST00000417913,;UBL4A,upstream_gene_variant,,ENST00000481237,; G ENST00000263512 Transcript missense_variant 903/2161 377/1434 126/477 G/A gGa/gCa 1 -1 SLC10A3 HGNC HGNC:22979 protein_coding YES CCDS14755.1 ENSP00000263512 P09131 UPI0000131021 NM_019848.4 tolerated(0.26) 2/2 hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF3 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 18 154488564 154488564 C G 1 0 0 0 0 1 0 0 0 14640 855 30 4 4 SLC10A3 23 154488564 Missense_Mutation SNP C C3L-00510_T 46887037 154488564 1552331 41 6742 HES5 0 . GRCh38 1 2529642 2529642 + Missense_Mutation SNP C C G novel C3L-00604_T C3L-00604_N C C c.328G>C p.Asp110His p.D110H ENST00000378453 3/3 232 208 24 62 62 0 strelka-varscan-mutect HES5,missense_variant,p.Asp110His,ENST00000378453,NM_001010926.3;PANK4,upstream_gene_variant,,ENST00000378466,NM_018216.2;PANK4,upstream_gene_variant,,ENST00000435556,;PANK4,upstream_gene_variant,,ENST00000491212,;PANK4,upstream_gene_variant,,ENST00000502770,;PANK4,upstream_gene_variant,,ENST00000486396,;PANK4,upstream_gene_variant,,ENST00000514922,; G ENST00000378453 Transcript missense_variant 409/1306 328/501 110/166 D/H Gac/Cac 1 -1 HES5 HGNC HGNC:19764 protein_coding YES CCDS41233.1 ENSP00000367714 Q5TA89 UPI00001D7D69 NM_001010926.3 deleterious(0) 3/3 PROSITE_profiles:PS51054,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF13,Pfam_domain:PF07527,SMART_domains:SM00511 MODERATE 1 SNV 1 1 PASS rs986028820 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 19 2529642 2529642 C G 1 0 0 0 0 1 0 0 0 6953 884 31 4 4 HES5 1 2529642 Missense_Mutation SNP C C3L-00604_T 2529642 246426780 1 6743 PKN2 0 . GRCh38 1 88741216 88741216 + Missense_Mutation SNP T T A novel C3L-00604_T C3L-00604_N T T c.277T>A p.Leu93Ile p.L93I ENST00000370521 2/22 96 83 13 152 152 0 strelka-varscan-mutect PKN2,missense_variant,p.Leu93Ile,ENST00000370521,NM_006256.2;PKN2,missense_variant,p.Leu93Ile,ENST00000370513,;PKN2,missense_variant,p.Leu93Ile,ENST00000316005,; A ENST00000370521 Transcript missense_variant 636/6121 277/2955 93/984 L/I Tta/Ata 1 1 PKN2 HGNC HGNC:9406 protein_coding YES CCDS714.1 ENSP00000359552 Q16513 UPI000004D291 NM_006256.2 deleterious(0.03) 2/22 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Gene3D:1.10.287.160,Pfam_domain:PF02185,SMART_domains:SM00742,Superfamily_domains:SSF46585 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 88741216 88741216 T A 1 0 0 0 0 1 0 0 0 12076 1490 52 4 4 PKN2 1 88741216 Missense_Mutation SNP T C3L-00604_T 86211574 88741216 160215206 2 6744 ELF3 0 . GRCh38 1 202013188 202013188 + Missense_Mutation SNP T T C novel C3L-00604_T C3L-00604_N T T c.695T>C p.Phe232Ser p.F232S ENST00000359651 6/8 143 133 10 92 92 0 strelka-mutect ELF3,missense_variant,p.Phe232Ser,ENST00000359651,;ELF3,missense_variant,p.Phe232Ser,ENST00000367284,NM_001114309.1,NM_004433.4;ELF3,missense_variant,p.Phe232Ser,ENST00000367283,;ELF3,missense_variant,p.Phe230Ser,ENST00000446188,;RP11-510N19.5,intron_variant,,ENST00000504773,;RP11-465N4.4,upstream_gene_variant,,ENST00000419190,;ELF3,non_coding_transcript_exon_variant,,ENST00000490203,;ELF3,non_coding_transcript_exon_variant,,ENST00000470384,;ELF3,downstream_gene_variant,,ENST00000495848,;ELF3,upstream_gene_variant,,ENST00000475698,;ELF3,downstream_gene_variant,,ENST00000498017,;ELF3,downstream_gene_variant,,ENST00000479874,; C ENST00000359651 Transcript missense_variant 3887/4994 695/1116 232/371 F/S tTt/tCt 1 1 ELF3 HGNC HGNC:3318 protein_coding YES CCDS1419.1 ENSP00000352673 P78545 A0A024R974 UPI0000034E32 tolerated(0.09) 6/8 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -18.60826 0.9999996 1 1 1 0 C 3 2 19 202013188 202013188 T C 1 0 0 0 0 1 0 0 0 4888 1841 64 5 5 ELF3 1 202013188 Missense_Mutation SNP T C3L-00604_T 113271972 202013188 46943234 3 6745 DSTYK 0 . GRCh38 1 205211522 205211522 + Missense_Mutation SNP C C A novel C3L-00604_T C3L-00604_N C C c.14G>T p.Gly5Val p.G5V ENST00000367162 1/13 117 66 51 60 60 0 strelka-varscan-mutect DSTYK,missense_variant,p.Gly5Val,ENST00000367162,NM_015375.2;DSTYK,missense_variant,p.Gly5Val,ENST00000367161,NM_199462.2; A ENST00000367162 Transcript missense_variant 45/7874 14/2790 5/929 G/V gGg/gTg 1 -1 DSTYK HGNC HGNC:29043 protein_coding YES CCDS1451.1 ENSP00000356130 Q6XUX3 UPI00001D7D39 NM_015375.2 deleterious_low_confidence(0.04) 1/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1226609749 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 205211522 205211522 C A 1 0 0 0 0 1 0 0 0 4606 623 22 2 2 DSTYK 1 205211522 Missense_Mutation SNP C C3L-00604_T 3198334 205211522 43744900 4 6746 OR2C3 0 . GRCh38 1 247532242 247532242 + Silent SNP C C T novel C3L-00604_T C3L-00604_N C C c.270G>A p.= p.Q90Q ENST00000366487 2/2 491 376 115 321 321 0 strelka-varscan-mutect OR2C3,synonymous_variant,p.=,ENST00000366487,NM_198074.4;OR2C3,synonymous_variant,p.=,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; T ENST00000366487 Transcript synonymous_variant 632/2742 270/963 90/320 Q caG/caA 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 19 247532242 247532242 C T 1 0 0 0 0 0 0 0 1 11072 912 32 3 3 OR2C3 1 247532242 Silent SNP C C3L-00604_T 42320720 247532242 1424180 5 6747 SIX2 0 . GRCh38 2 45006218 45006218 + Missense_Mutation SNP G G C novel C3L-00604_T C3L-00604_N G G c.828C>G p.Asp276Glu p.D276E ENST00000303077 2/2 450 393 57 430 430 0 strelka-varscan-mutect SIX2,missense_variant,p.Asp276Glu,ENST00000303077,NM_016932.4; C ENST00000303077 Transcript missense_variant 1148/2205 828/876 276/291 D/E gaC/gaG 1 -1 SIX2 HGNC HGNC:10888 protein_coding YES CCDS1822.1 ENSP00000304502 Q9NPC8 UPI00001359C0 NM_016932.4 deleterious_low_confidence(0) 2/2 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF29 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 19 45006218 45006218 G C 1 0 0 0 0 1 0 0 0 14610 1020 36 4 4 SIX2 2 45006218 Missense_Mutation SNP G C3L-00604_T 45006218 197187311 6 6748 ADD2 0 . GRCh38 2 70683702 70683702 + Silent SNP C C T novel C3L-00604_T C3L-00604_N C C c.1014G>A p.= p.R338R ENST00000264436 10/16 120 102 18 105 105 0 strelka-varscan-mutect ADD2,synonymous_variant,p.=,ENST00000264436,NM_001617.3;ADD2,synonymous_variant,p.=,ENST00000413157,NM_017482.3;ADD2,synonymous_variant,p.=,ENST00000407644,NM_001185054.1;ADD2,synonymous_variant,p.=,ENST00000355733,NM_017488.3;ADD2,synonymous_variant,p.=,ENST00000430656,NM_001185055.1;ADD2,intron_variant,,ENST00000456320,;ADD2,intron_variant,,ENST00000522886,;AC007395.3,upstream_gene_variant,,ENST00000457851,;ADD2,synonymous_variant,p.=,ENST00000403045,; T ENST00000264436 Transcript synonymous_variant 1459/9267 1014/2181 338/726 R cgG/cgA 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 10/16 hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 19 70683702 70683702 C T 1 0 0 0 0 0 0 0 1 349 726 26 3 3 ADD2 2 70683702 Silent SNP C C3L-00604_T 25677484 70683702 171509827 7 6749 TRANK1 0 . GRCh38 3 36874145 36874145 + Silent SNP C C A novel C3L-00604_T C3L-00604_N C C c.927G>T p.= p.T309T ENST00000429976 8/23 71 57 14 78 78 0 strelka-varscan-mutect TRANK1,synonymous_variant,p.=,ENST00000429976,NM_014831.2; A ENST00000429976 Transcript synonymous_variant 1175/10481 927/8778 309/2925 T acG/acT 1 -1 TRANK1 HGNC HGNC:29011 protein_coding YES CCDS46789.2 ENSP00000416168 O15050 UPI00017BE82B NM_014831.2 8/23 hmmpanther:PTHR21529,hmmpanther:PTHR21529:SF4 LOW 1 SNV 5 1 PASS rs969787740 . 0 203 5 2 0 0 0 0 -19.99999 0.999977 1 1 1 0 A 2 1 19 36874145 36874145 C A 1 0 0 0 0 0 0 0 1 16937 523 19 1 1 TRANK1 3 36874145 Silent SNP C C3L-00604_T 36874145 161421414 8 6750 DPPA2 0 . GRCh38 3 109304596 109304596 + Missense_Mutation SNP C C T novel C3L-00604_T C3L-00604_N C C c.733G>A p.Ala245Thr p.A245T ENST00000478945 7/9 163 148 15 122 122 0 varscan-mutect DPPA2,missense_variant,p.Ala245Thr,ENST00000478945,NM_138815.3; T ENST00000478945 Transcript missense_variant 980/1383 733/897 245/298 A/T Gca/Aca 1 -1 DPPA2 HGNC HGNC:19197 protein_coding YES CCDS2956.1 ENSP00000417710 Q7Z7J5 UPI000007143F NM_138815.3 deleterious(0.05) 7/9 Pfam_domain:PF14047,hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 109304596 109304596 C T 1 0 0 0 0 1 0 0 0 4549 710 25 3 3 DPPA2 3 109304596 Missense_Mutation SNP C C3L-00604_T 72430451 109304596 88990963 9 6751 TOPBP1 0 . GRCh38 3 133611024 133611024 + Missense_Mutation SNP G G T novel C3L-00604_T C3L-00604_N G G c.4153C>A p.Gln1385Lys p.Q1385K ENST00000260810 25/28 118 105 13 70 70 0 strelka-mutect TOPBP1,missense_variant,p.Gln1385Lys,ENST00000260810,NM_007027.3;TOPBP1,upstream_gene_variant,,ENST00000503338,;TOPBP1,upstream_gene_variant,,ENST00000503464,; T ENST00000260810 Transcript missense_variant 4285/5378 4153/4569 1385/1522 Q/K Caa/Aaa 1 -1 TOPBP1 HGNC HGNC:17008 protein_coding YES CCDS46919.1 ENSP00000260810 Q92547 UPI000020A292 NM_007027.3 tolerated(0.2) 25/28 hmmpanther:PTHR13561:SF32,hmmpanther:PTHR13561 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 133611024 133611024 G T 1 0 0 0 0 1 0 0 0 16846 1386 48 2 2 TOPBP1 3 133611024 Missense_Mutation SNP G C3L-00604_T 24306428 133611024 64684535 10 6752 PIK3CA 0 . GRCh38 3 179218294 179218294 + Missense_Mutation SNP G G A rs121913273 C3L-00604_T C3L-00604_N G G c.1624G>A p.Glu542Lys p.E542K ENST00000263967 10/21 174 123 51 140 140 0 strelka-varscan-mutect PIK3CA,missense_variant,p.Glu542Lys,ENST00000263967,NM_006218.2;PIK3CA,upstream_gene_variant,,ENST00000462255,; A ENST00000263967 Transcript missense_variant 1781/9093 1624/3207 542/1068 E/K Gaa/Aaa rs121913273,COSM125369,COSM17442,COSM326157,COSM760 1 1 PIK3CA HGNC HGNC:8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 UPI000013D494 NM_006218.2 deleterious(0.04) 10/21 Gene3D:1.25.40.70,Pfam_domain:PF00613,PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF54,SMART_domains:SM00145,Superfamily_domains:SSF48371 pathogenic 0,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS rs121913273 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 179218294 179218294 G A 1 0 0 0 0 1 0 0 0 12008 1291 45 3 3 PIK3CA 3 179218294 Missense_Mutation SNP G C3L-00604_T 45607270 179218294 19077265 11 6753 ANKRD17 0 . GRCh38 4 73142767 73142767 + Missense_Mutation SNP C C A novel C3L-00604_T C3L-00604_N C C c.1958G>T p.Gly653Val p.G653V ENST00000358602 12/34 169 145 24 130 130 0 strelka-varscan-mutect ANKRD17,missense_variant,p.Gly653Val,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,missense_variant,p.Gly538Val,ENST00000558247,;ANKRD17,missense_variant,p.Gly540Val,ENST00000509867,NM_001286771.1;ANKRD17,missense_variant,p.Gly653Val,ENST00000330838,NM_198889.1;ANKRD17,intron_variant,,ENST00000561029,;ANKRD17,splice_region_variant,,ENST00000514252,; A ENST00000358602 Transcript missense_variant,splice_region_variant 2075/10784 1958/7812 653/2603 G/V gGa/gTa 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 deleterious(0) 12/34 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 73142767 73142767 C A 1 0 0 0 0 1 0 0 0 747 869 30 2 2 ANKRD17 4 73142767 Missense_Mutation SNP C C3L-00604_T 73142767 117071788 12 6754 RNF144B 0 . GRCh38 6 18439717 18439717 + Missense_Mutation SNP C C T novel C3L-00604_T C3L-00604_N C C c.304C>T p.Leu102Phe p.L102F ENST00000259939 4/8 170 125 45 130 130 0 strelka-varscan-mutect RNF144B,missense_variant,p.Leu102Phe,ENST00000259939,NM_182757.3; T ENST00000259939 Transcript missense_variant 621/5036 304/912 102/303 L/F Ctt/Ttt 1 1 RNF144B HGNC HGNC:21578 protein_coding YES CCDS34345.1 ENSP00000259939 Q7Z419 UPI00001B2DA3 NM_182757.3 deleterious(0.04) 4/8 hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF104,Pfam_domain:PF01485,SMART_domains:SM00647,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 18439717 18439717 C T 1 0 0 0 0 1 0 0 0 13624 565 20 3 3 RNF144B 6 18439717 Missense_Mutation SNP C C3L-00604_T 18439717 152366262 13 6755 HACE1 0 . GRCh38 6 104776793 104776793 + Silent SNP C C A C3L-00604_T C3L-00604_N C C c.1812G>T p.= p.L604L ENST00000262903 17/24 306 236 70 336 336 0 strelka-varscan-mutect HACE1,synonymous_variant,p.=,ENST00000262903,NM_001321083.1,NM_020771.3;HACE1,synonymous_variant,p.=,ENST00000518503,;HACE1,synonymous_variant,p.=,ENST00000518402,;HACE1,intron_variant,,ENST00000369125,;HACE1,non_coding_transcript_exon_variant,,ENST00000517995,;HACE1,3_prime_UTR_variant,,ENST00000416605,;HACE1,3_prime_UTR_variant,,ENST00000517424,;HACE1,non_coding_transcript_exon_variant,,ENST00000369127,; A ENST00000262903 Transcript synonymous_variant 2089/4576 1812/2730 604/909 L ctG/ctT COSM4531662 1 -1 HACE1 HGNC HGNC:21033 protein_coding YES CCDS5050.1 ENSP00000262903 Q8IYU2 UPI00001602DC NM_001321083.1,NM_020771.3 17/24 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,SMART_domains:SM00119,Superfamily_domains:SSF56204 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 19 104776793 104776793 C A 1 0 0 0 0 0 0 0 1 6826 465 17 2 2 HACE1 6 104776793 Silent SNP C C3L-00604_T 86337076 104776793 66029186 14 6756 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3L-00604_T C3L-00604_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 588 408 180 445 445 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 19 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3L-00604_T 55174772 104171201 15 6757 POM121C 0 . GRCh38 7 75437684 75437684 + Missense_Mutation SNP G G A novel C3L-00604_T C3L-00604_N G G c.311C>T p.Pro104Leu p.P104L ENST00000615331 7/15 58 37 21 43 43 0 strelka-varscan-mutect POM121C,missense_variant,p.Pro104Leu,ENST00000615331,NM_001099415.2;POM121C,missense_variant,p.Pro346Leu,ENST00000607367,;POM121C,splice_region_variant,,ENST00000439629,;POM121C,downstream_gene_variant,,ENST00000398379,;POM121C,upstream_gene_variant,,ENST00000473168,;POM121C,upstream_gene_variant,,ENST00000479864,; A ENST00000615331 Transcript missense_variant,splice_region_variant 1176/5835 311/2964 104/987 P/L cCt/cTt 1 -1 POM121C HGNC HGNC:34005 protein_coding YES CCDS47617.1 ENSP00000481575 A0A087WY75 UPI0003335169 NM_001099415.2 deleterious(0.02) 7/15 hmmpanther:PTHR23193:SF5,hmmpanther:PTHR23193,Pfam_domain:PF15229 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 75437684 75437684 G A 1 0 0 0 0 1 0 0 0 12351 1014 35 3 3 POM121C 7 75437684 Missense_Mutation SNP G C3L-00604_T 20262912 75437684 83908289 16 6758 CTTNBP2 0 . GRCh38 7 117735087 117735087 + Silent SNP G G A rs780731601 C3L-00604_T C3L-00604_N G G c.3702C>T p.= p.S1234S ENST00000160373 16/23 97 87 10 66 66 0 strelka-varscan-mutect CTTNBP2,synonymous_variant,p.=,ENST00000160373,NM_033427.2;CTTNBP2,synonymous_variant,p.=,ENST00000446636,;CTTNBP2,downstream_gene_variant,,ENST00000435233,;CTTNBP2,3_prime_UTR_variant,,ENST00000441556,; A ENST00000160373 Transcript synonymous_variant 3794/5970 3702/4992 1234/1663 S tcC/tcT rs780731601,COSM1622249 1 -1 CTTNBP2 HGNC HGNC:15679 protein_coding YES CCDS5774.1 ENSP00000160373 Q8WZ74 Q20BG9 UPI000006E94A NM_033427.2 16/23 0,1 LOW 1 SNV 1 0,1 1 PASS rs780731601 . 0 200 10 0 0 0 0 0 -19.82604 0.9999635 1 1 1 0 A 2 1 19 117735087 117735087 G A 1 0 0 0 0 0 0 0 1 3854 1103 39 1 1 CTTNBP2 7 117735087 Silent SNP G C3L-00604_T 42297403 117735087 41610886 17 6759 CCDC136 0 . GRCh38 7 128814834 128814834 + Missense_Mutation SNP T T G novel C3L-00604_T C3L-00604_N T T c.2960T>G p.Met987Arg p.M987R ENST00000297788 15/18 200 143 57 117 117 0 strelka-varscan-mutect CCDC136,missense_variant,p.Met987Arg,ENST00000297788,NM_022742.4;CCDC136,missense_variant,p.Met864Arg,ENST00000494552,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000464672,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000378685,NM_001201372.1;CCDC136,non_coding_transcript_exon_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000460941,; G ENST00000297788 Transcript missense_variant 3327/4169 2960/3465 987/1154 M/R aTg/aGg 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 deleterious(0.05) 15/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26 MODERATE 1 SNV 1 1 PASS rs1184844522 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 19 128814834 128814834 T G 1 0 0 0 0 1 0 0 0 2459 1464 51 5 5 CCDC136 7 128814834 Missense_Mutation SNP T C3L-00604_T 11079747 128814834 30531139 18 6760 COPG2 0 . GRCh38 7 130612237 130612237 + Missense_Mutation SNP T T A novel C3L-00604_T C3L-00604_N T T c.494A>T p.His165Leu p.H165L ENST00000425248 8/24 84 59 25 74 74 0 strelka-varscan-mutect COPG2,missense_variant,p.His165Leu,ENST00000425248,NM_012133.5;COPG2,missense_variant,p.His165Leu,ENST00000330992,NM_001290033.1; A ENST00000425248 Transcript missense_variant,splice_region_variant 574/3134 494/2616 165/871 H/L cAc/cTc 1 -1 COPG2 HGNC HGNC:2237 protein_coding YES CCDS75662.1 ENSP00000402346 Q9UBF2 A0A140VK12 UPI0000000960 NM_012133.5 deleterious(0) 8/24 hmmpanther:PTHR10261:SF4,hmmpanther:PTHR10261,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037093,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999956 1 1 1 0 A 3 1 19 130612237 130612237 T A 1 0 0 0 0 1 0 0 0 3524 1710 59 4 4 COPG2 7 130612237 Missense_Mutation SNP T C3L-00604_T 1797403 130612237 28733736 19 6761 EZH2 0 . GRCh38 7 148811666 148811666 + Missense_Mutation SNP G G A novel C3L-00604_T C3L-00604_N G G c.1906C>T p.Pro636Ser p.P636S ENST00000320356 16/20 178 139 39 111 111 0 strelka-varscan-mutect EZH2,missense_variant,p.Pro636Ser,ENST00000320356,NM_004456.4;EZH2,missense_variant,p.Pro631Ser,ENST00000460911,NM_001203247.1;EZH2,missense_variant,p.Pro580Ser,ENST00000476773,NM_001203249.1;EZH2,missense_variant,p.Pro580Ser,ENST00000478654,;EZH2,missense_variant,p.Pro592Ser,ENST00000350995,NM_152998.2;EZH2,missense_variant,p.Pro622Ser,ENST00000483967,NM_001203248.1;EZH2,3_prime_UTR_variant,,ENST00000492143,;EZH2,non_coding_transcript_exon_variant,,ENST00000469631,; A ENST00000320356 Transcript missense_variant 2028/2639 1906/2256 636/751 P/S Cct/Tct 1 -1 EZH2 HGNC HGNC:3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 A0A090N8E9 UPI000006D77C NM_004456.4 tolerated(1) 16/20 PROSITE_profiles:PS50280,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF287,Gene3D:2.170.270.10,Pfam_domain:PF00856,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 205 0 3 2 0 0 0 -19.99999 0.9862906 1 1 1 0 A 3 1 19 148811666 148811666 G A 1 0 0 0 0 1 0 0 0 5202 1174 41 3 3 EZH2 7 148811666 Missense_Mutation SNP G C3L-00604_T 18199429 148811666 10534307 20 6762 DLGAP2 0 . GRCh38 8 1678346 1678346 + Silent SNP C C T rs755621517 C3L-00604_T C3L-00604_N C C c.2139C>T p.= p.S713S ENST00000612087 8/11 254 238 16 197 197 0 strelka-varscan-mutect DLGAP2,synonymous_variant,p.=,ENST00000612087,NM_001277161.1;DLGAP2,synonymous_variant,p.=,ENST00000520901,;DLGAP2,synonymous_variant,p.=,ENST00000637795,;DLGAP2,synonymous_variant,p.=,ENST00000421627,;DLGAP2,synonymous_variant,p.=,ENST00000637152,NM_004745.4;DLGAP2,synonymous_variant,p.=,ENST00000522499,;DLGAP2,upstream_gene_variant,,ENST00000518530,;DLGAP2,non_coding_transcript_exon_variant,,ENST00000524065,; T ENST00000612087 Transcript synonymous_variant 2273/10088 2139/2886 713/961 S tcC/tcT rs755621517,COSM1097423,COSM1097424 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 8/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3,Pfam_domain:PF03359 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs755621517 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 19 1678346 1678346 C T 1 0 0 0 0 0 0 0 1 4367 639 23 1 1 DLGAP2 8 1678346 Silent SNP C C3L-00604_T 1678346 143460290 21 6763 HOOK3 0 . GRCh38 8 43007885 43007885 + Missense_Mutation SNP A A T novel C3L-00604_T C3L-00604_N A A c.1694A>T p.Lys565Met p.K565M ENST00000307602 18/22 186 133 53 153 153 0 strelka-varscan-mutect HOOK3,missense_variant,p.Lys565Met,ENST00000307602,NM_032410.3;HOOK3,missense_variant,p.Lys43Met,ENST00000533539,;HOOK3,non_coding_transcript_exon_variant,,ENST00000524839,;HOOK3,3_prime_UTR_variant,,ENST00000526882,; T ENST00000307602 Transcript missense_variant 1894/14398 1694/2157 565/718 K/M aAg/aTg 1 1 HOOK3 HGNC HGNC:23576 protein_coding YES CCDS6139.1 ENSP00000305699 Q86VS8 UPI000006DD7B NM_032410.3 deleterious(0) 18/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947:SF38,hmmpanther:PTHR18947,Pfam_domain:PF05622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 43007885 43007885 A T 1 0 0 0 0 1 0 0 0 7178 72 3 4 4 HOOK3 8 43007885 Missense_Mutation SNP A C3L-00604_T 41329539 43007885 102130751 22 6764 TAF1L 0 . GRCh38 9 32634703 32634703 + Missense_Mutation SNP G G T novel C3L-00604_T C3L-00604_N G G c.877C>A p.Gln293Lys p.Q293K ENST00000242310 1/1 227 134 93 288 288 0 strelka-varscan-mutect TAF1L,missense_variant,p.Gln293Lys,ENST00000242310,NM_153809.2;RP11-555J4.4,non_coding_transcript_exon_variant,,ENST00000430787,; T ENST00000242310 Transcript missense_variant 967/6216 877/5481 293/1826 Q/K Cag/Aag 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 tolerated(0.87) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs936487944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 32634703 32634703 G T 1 0 0 0 0 1 0 0 0 15919 1328 46 2 2 TAF1L 9 32634703 Missense_Mutation SNP G C3L-00604_T 32634703 105760014 23 6765 RECK 0 . GRCh38 9 36110020 36110020 + Missense_Mutation SNP G G T novel C3L-00604_T C3L-00604_N G G c.1829G>T p.Cys610Phe p.C610F ENST00000377966 15/21 232 184 48 164 164 0 strelka-varscan-mutect RECK,missense_variant,p.Cys610Phe,ENST00000377966,NM_021111.2; T ENST00000377966 Transcript missense_variant 2395/4888 1829/2916 610/971 C/F tGc/tTc 1 1 RECK HGNC HGNC:11345 protein_coding YES CCDS6597.1 ENSP00000367202 O95980 UPI0000133587 NM_021111.2 deleterious(0) 15/21 hmmpanther:PTHR13487 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 36110020 36110020 G T 1 0 0 0 0 1 0 0 0 13370 1319 46 2 2 RECK 9 36110020 Missense_Mutation SNP G C3L-00604_T 3475317 36110020 102284697 24 6766 TRPM6 0 . GRCh38 9 74739854 74739854 + Missense_Mutation SNP C C T rs142946646 C3L-00604_T C3L-00604_N C C c.5356G>A p.Val1786Ile p.V1786I ENST00000360774 34/39 524 402 122 429 429 0 strelka-varscan-mutect TRPM6,missense_variant,p.Val1786Ile,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Val1781Ile,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Val1781Ile,ENST00000449912,NM_001177310.1; T ENST00000360774 Transcript missense_variant 5594/8425 5356/6069 1786/2022 V/I Gtc/Atc rs142946646,COSM3216984,COSM3216985,COSM4374758 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 tolerated(1) 34/39 Gene3D:3.30.200.20,Pfam_domain:PF02816,PROSITE_profiles:PS51158,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15,SMART_domains:SM00811,Superfamily_domains:SSF56112 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs142946646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 74739854 74739854 C T 1 0 0 0 0 1 0 0 0 17096 536 19 1 1 TRPM6 9 74739854 Missense_Mutation SNP C C3L-00604_T 38629834 74739854 63654863 25 6767 GNA14 0 . GRCh38 9 77529102 77529102 + Silent SNP C C T rs781490674 C3L-00604_T C3L-00604_N C C c.276G>A p.= p.T92T ENST00000341700 2/7 217 162 55 173 173 0 strelka-varscan-mutect GNA14,synonymous_variant,p.=,ENST00000341700,NM_004297.3;GNA14-AS1,downstream_gene_variant,,ENST00000439145,; T ENST00000341700 Transcript synonymous_variant 790/2482 276/1068 92/355 T acG/acA rs781490674 1 -1 GNA14 HGNC HGNC:4382 protein_coding YES CCDS6657.1 ENSP00000365807 O95837 UPI000004D20C NM_004297.3 2/7 Gene3D:1.10.400.10,Pfam_domain:PF00503,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF213,SMART_domains:SM00275,Superfamily_domains:SSF47895 LOW 1 SNV 1 1 PASS rs781490674 . 0 207 0 3 0 0 0 0 -20 0.9999978 1 1 1 0 T 2 4 19 77529102 77529102 C T 1 0 0 0 0 0 0 0 1 6382 755 27 1 1 GNA14 9 77529102 Silent SNP C C3L-00604_T 2789248 77529102 60865615 26 6768 ERCC6 0 . GRCh38 10 49528507 49528507 + Missense_Mutation SNP T T A novel C3L-00604_T C3L-00604_N T T c.562A>T p.Ile188Phe p.I188F ENST00000355832 4/21 427 384 43 426 426 0 strelka-varscan-mutect ERCC6,missense_variant,p.Ile188Phe,ENST00000355832,NM_000124.3;ERCC6,missense_variant,p.Ile188Phe,ENST00000515869,NM_001277059.1;ERCC6,missense_variant,p.Ile188Phe,ENST00000447839,NM_001277058.1;ERCC6,downstream_gene_variant,,ENST00000462247,;ERCC6,non_coding_transcript_exon_variant,,ENST00000479652,; A ENST00000355832 Transcript missense_variant 641/8008 562/4482 188/1493 I/F Atc/Ttc 1 -1 ERCC6 HGNC HGNC:3438 protein_coding YES CCDS7229.1 ENSP00000348089 Q03468 UPI000000D8DA NM_000124.3 deleterious(0.01) 4/21 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 49528507 49528507 T A 1 0 0 0 0 1 0 0 0 5066 1435 50 4 4 ERCC6 10 49528507 Missense_Mutation SNP T C3L-00604_T 49528507 84268915 27 6769 ABCC8 0 . GRCh38 11 17430865 17430865 + Missense_Mutation SNP G G A C3L-00604_T C3L-00604_N G G c.1766C>T p.Pro589Leu p.P589L ENST00000302539 12/39 596 516 80 400 400 0 strelka-varscan-mutect ABCC8,missense_variant,p.Pro589Leu,ENST00000302539,NM_001287174.1;ABCC8,missense_variant,p.Pro589Leu,ENST00000389817,NM_000352.4;ABCC8,non_coding_transcript_exon_variant,,ENST00000528202,;ABCC8,missense_variant,p.Pro589Leu,ENST00000527905,;ABCC8,non_coding_transcript_exon_variant,,ENST00000532728,;ABCC8,non_coding_transcript_exon_variant,,ENST00000635881,;ABCC8,non_coding_transcript_exon_variant,,ENST00000526002,;ABCC8,upstream_gene_variant,,ENST00000531911,;SDHCP4,downstream_gene_variant,,ENST00000532834,; A ENST00000302539 Transcript missense_variant 1835/4923 1766/4749 589/1582 P/L cCg/cTg COSM925483 1 -1 ABCC8 HGNC HGNC:59 protein_coding YES CCDS73264.1 ENSP00000303960 Q09428 UPI00015DFF64 NM_001287174.1 deleterious(0) 12/39 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF187,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 17430865 17430865 G A 1 0 0 0 0 1 0 0 0 62 1116 39 1 1 ABCC8 11 17430865 Missense_Mutation SNP G C3L-00604_T 17430865 117655757 28 6770 TRIM64C 0 . GRCh38 11 49054121 49054121 + Missense_Mutation SNP G G A novel C3L-00604_T C3L-00604_N G G c.946C>T p.Arg316Cys p.R316C ENST00000617704 6/6 293 275 18 249 249 0 strelka-varscan-mutect TRIM64C,missense_variant,p.Arg316Cys,ENST00000617704,NM_001206631.1;TRIM64C,missense_variant,p.Arg313Cys,ENST00000530230,; A ENST00000617704 Transcript missense_variant 946/1353 946/1353 316/450 R/C Cgc/Tgc 1 -1 TRIM64C HGNC HGNC:37148 protein_coding YES CCDS73287.1 ENSP00000481815 A0A087WYH8 UPI00006C1130 NM_001206631.1 tolerated(0.08) 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF354,hmmpanther:PTHR24103,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 5 1 PASS rs1379722418 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 49054121 49054121 G A 1 0 0 0 0 1 0 0 0 17033 1058 37 1 1 TRIM64C 11 49054121 Missense_Mutation SNP G C3L-00604_T 31623256 49054121 86032501 29 6771 VPS51 0 . GRCh38 11 65107945 65107945 + Silent SNP G G T novel C3L-00604_T C3L-00604_N G G c.648G>T p.= p.L216L ENST00000279281 4/10 133 106 27 85 84 1 strelka-varscan-mutect VPS51,synonymous_variant,p.=,ENST00000279281,NM_013265.3;VPS51,synonymous_variant,p.=,ENST00000529180,;VPS51,synonymous_variant,p.=,ENST00000534557,;VPS51,synonymous_variant,p.=,ENST00000530773,;TM7SF2,upstream_gene_variant,,ENST00000279263,NM_003273.3;TM7SF2,upstream_gene_variant,,ENST00000345348,NM_001277233.1;TM7SF2,upstream_gene_variant,,ENST00000525385,;TM7SF2,upstream_gene_variant,,ENST00000531321,;TM7SF2,upstream_gene_variant,,ENST00000534371,;TM7SF2,upstream_gene_variant,,ENST00000526809,;TM7SF2,upstream_gene_variant,,ENST00000529414,;TM7SF2,upstream_gene_variant,,ENST00000524986,;VPS51,downstream_gene_variant,,ENST00000528588,;VPS51,upstream_gene_variant,,ENST00000526856,;VPS51,upstream_gene_variant,,ENST00000530673,;TM7SF2,upstream_gene_variant,,ENST00000526085,;VPS51,downstream_gene_variant,,ENST00000526578,;TM7SF2,upstream_gene_variant,,ENST00000530750,;AP003068.9,downstream_gene_variant,,ENST00000528887,;VPS51,non_coding_transcript_exon_variant,,ENST00000527646,;TM7SF2,upstream_gene_variant,,ENST00000531029,;TM7SF2,upstream_gene_variant,,ENST00000533646,;VPS51,3_prime_UTR_variant,,ENST00000534124,;VPS51,3_prime_UTR_variant,,ENST00000533487,;TM7SF2,upstream_gene_variant,,ENST00000530650,;TM7SF2,upstream_gene_variant,,ENST00000529601,;TM7SF2,upstream_gene_variant,,ENST00000533766,;VPS51,upstream_gene_variant,,ENST00000534591,;TM7SF2,upstream_gene_variant,,ENST00000529292,;VPS51,upstream_gene_variant,,ENST00000533827,;TM7SF2,upstream_gene_variant,,ENST00000527851,;VPS51,downstream_gene_variant,,ENST00000533656,;TM7SF2,upstream_gene_variant,,ENST00000524690,;TM7SF2,upstream_gene_variant,,ENST00000529233,;TM7SF2,upstream_gene_variant,,ENST00000530892,;VPS51,upstream_gene_variant,,ENST00000531146,;TM7SF2,upstream_gene_variant,,ENST00000528026,; T ENST00000279281 Transcript synonymous_variant 740/2714 648/2349 216/782 L ctG/ctT 1 1 VPS51 HGNC HGNC:1172 protein_coding YES CCDS8093.1 ENSP00000279281 Q9UID3 UPI000006D6D8 NM_013265.3 4/10 hmmpanther:PTHR15954,hmmpanther:PTHR15954:SF4,Superfamily_domains:SSF74788 LOW 1 SNV 1 1 PASS rs1266759247 . 0 205 3 2 0 0 0 0 -20 0.9999966 1 1 1 0 T 2 4 19 65107945 65107945 G T 1 0 0 0 0 0 0 0 1 17761 1306 46 2 2 VPS51 11 65107945 Silent SNP G C3L-00604_T 16053824 65107945 69978677 30 6772 KDM2A 0 . GRCh38 11 67246057 67246057 + Missense_Mutation SNP G G C novel C3L-00604_T C3L-00604_N G G c.1906G>C p.Glu636Gln p.E636Q ENST00000529006 15/21 244 231 13 193 193 0 strelka-varscan-mutect KDM2A,missense_variant,p.Glu636Gln,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Glu636Gln,ENST00000398645,;KDM2A,missense_variant,p.Glu619Gln,ENST00000308783,;KDM2A,missense_variant,p.Glu197Gln,ENST00000530342,NM_001256405.1;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000525041,;KDM2A,non_coding_transcript_exon_variant,,ENST00000534486,;KDM2A,non_coding_transcript_exon_variant,,ENST00000529124,;KDM2A,downstream_gene_variant,,ENST00000517637,; C ENST00000529006 Transcript missense_variant 2352/6967 1906/3489 636/1162 E/Q Gag/Cag 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 tolerated(0.43) 15/21 Gene3D:3.30.40.10,Pfam_domain:PF16866,PROSITE_patterns:PS01359,PROSITE_profiles:PS50016,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 19 67246057 67246057 G C 1 0 0 0 0 1 0 0 0 8042 1291 45 4 4 KDM2A 11 67246057 Missense_Mutation SNP G C3L-00604_T 2138112 67246057 67840565 31 6773 KLHL42 0 . GRCh38 12 27780501 27780501 + Silent SNP C C T novel C3L-00604_T C3L-00604_N C C c.171C>T p.= p.L57L ENST00000381271 1/3 113 88 25 146 145 1 varscan-mutect KLHL42,synonymous_variant,p.=,ENST00000381271,NM_020782.1;KLHL42,upstream_gene_variant,,ENST00000543254,;RP11-860B13.1,splice_region_variant,,ENST00000545904,;KLHL42,synonymous_variant,p.=,ENST00000539176,; T ENST00000381271 Transcript synonymous_variant 482/6703 171/1518 57/505 L ctC/ctT 1 1 KLHL42 HGNC HGNC:29252 protein_coding YES CCDS31763.1 ENSP00000370671 Q9P2K6 B2RNT7 UPI0000185FB1 NM_020782.1 1/3 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF54,hmmpanther:PTHR24412,Gene3D:3.30.710.10,Superfamily_domains:SSF54695 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 19 27780501 27780501 C T 1 0 0 0 0 0 0 0 1 8260 813 29 3 3 KLHL42 12 27780501 Silent SNP C C3L-00604_T 27780501 105494808 32 6774 PCED1B 0 . GRCh38 12 47235156 47235156 + Missense_Mutation SNP G G C novel C3L-00604_T C3L-00604_N G G c.93G>C p.Lys31Asn p.K31N ENST00000546455 4/4 24 18 6 23 23 0 strelka-mutect PCED1B,missense_variant,p.Lys31Asn,ENST00000546455,NM_138371.2;PCED1B,missense_variant,p.Lys31Asn,ENST00000432328,NM_001281429.1;PCED1B,missense_variant,p.Lys31Asn,ENST00000549500,;PCED1B,missense_variant,p.Lys31Asn,ENST00000549630,;PCED1B,missense_variant,p.Lys31Asn,ENST00000551777,;PCED1B,intron_variant,,ENST00000548348,;RP11-493L12.3,downstream_gene_variant,,ENST00000547748,; C ENST00000546455 Transcript missense_variant 824/2328 93/1299 31/432 K/N aaG/aaC 1 1 PCED1B HGNC HGNC:28255 protein_coding YES CCDS8752.1 ENSP00000446688 Q96HM7 A0A024R115 UPI000006E8D2 NM_138371.2 deleterious(0) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR14469,hmmpanther:PTHR14469:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 19 47235156 47235156 G C 1 0 0 0 0 1 0 0 0 11660 991 35 4 4 PCED1B 12 47235156 Missense_Mutation SNP G C3L-00604_T 19454655 47235156 86040153 33 6775 CYP1A2 0 . GRCh38 15 74751229 74751229 + Missense_Mutation SNP G G C C3L-00604_T C3L-00604_N G G c.872G>C p.Ser291Thr p.S291T ENST00000343932 3/7 149 78 71 178 178 0 strelka-varscan-mutect CYP1A2,missense_variant,p.Ser291Thr,ENST00000343932,NM_000761.4; C ENST00000343932 Transcript missense_variant 935/2728 872/1551 291/516 S/T aGc/aCc COSM4561158 1 1 CYP1A2 HGNC HGNC:2596 protein_coding YES CCDS32293.1 ENSP00000342007 P05177 UPI0000073775 NM_000761.4 tolerated(0.59) 3/7 hmmpanther:PTHR24299:SF7,hmmpanther:PTHR24299,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 19 74751229 74751229 G C 1 0 0 0 0 1 0 0 0 3953 971 34 4 4 CYP1A2 15 74751229 Missense_Mutation SNP G C3L-00604_T 74751229 27239960 34 6776 NPIPB4 0 . GRCh38 16 21837665 21837665 + Frame_Shift_Del DEL T T - novel C3L-00604_T C3L-00604_N T T c.722delA p.Asn241ThrfsTer16 p.N241Tfs*16 ENST00000415645 7/9 19 6 13 17 17 0 varindel-pindel NPIPB4,frameshift_variant,p.Asn241ThrfsTer16,ENST00000415645,NM_130464.2;NPIPB4,frameshift_variant,p.Asn25ThrfsTer16,ENST00000537951,;NPIPB4,downstream_gene_variant,,ENST00000614197,;NPIPB4,non_coding_transcript_exon_variant,,ENST00000165086,;NPIPB4,downstream_gene_variant,,ENST00000541329,;NPIPB4,3_prime_UTR_variant,,ENST00000542133,;NPIPB4,non_coding_transcript_exon_variant,,ENST00000545367,;NPIPB4,downstream_gene_variant,,ENST00000543660,;RP11-645C24.6,downstream_gene_variant,,ENST00000622730,; - ENST00000415645 Transcript frameshift_variant 762/3606 722/3417 241/1138 N/X aAc/ac 1 -1 NPIPB4 HGNC HGNC:41985 protein_coding YES ENSP00000404439 C9JG80 UPI00020651A0 NM_130464.2 7/9 Pfam_domain:PF06409,hmmpanther:PTHR15438,hmmpanther:PTHR15438:SF0 HIGH 1 deletion 5 1 PASS . . 6 198 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 19 21837665 21837665 T - 1 0 1 0 1 0 0 0 0 10638 1725 60 0 0 NPIPB4 16 21837665 Frame_Shift_Del DEL T C3L-00604_T 21837665 68500680 35 6777 HES7 0 . GRCh38 17 8121749 8121749 + Frame_Shift_Del DEL C C - rs778098548 C3L-00604_T C3L-00604_N C C c.515delG p.Gly172AlafsTer202 p.G172Afs*202 ENST00000541682 4/4 75 68 7 69 69 0 sindel-varindel-pindel HES7,frameshift_variant,p.Gly172AlafsTer202,ENST00000541682,NM_001165967.1;HES7,frameshift_variant,p.Gly167AlafsTer?,ENST00000317814,NM_032580.3;ALOXE3,upstream_gene_variant,,ENST00000380149,;ALOXE3,upstream_gene_variant,,ENST00000448843,NM_021628.2;ALOXE3,upstream_gene_variant,,ENST00000318227,NM_001165960.1;HES7,downstream_gene_variant,,ENST00000577735,; - ENST00000541682 Transcript frameshift_variant 515/1674 515/693 172/230 G/X gGc/gc rs778098548 1 -1 HES7 HGNC HGNC:15977 protein_coding YES CCDS54085.1 ENSP00000446205 Q9BYE0 UPI0000E59E09 NM_001165967.1 4/4 hmmpanther:PTHR10985:SF84,hmmpanther:PTHR10985 HIGH 1 deletion 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.37404 1 1 1 1 0 - 7 5 19 8121749 8121749 C - 1 0 1 0 1 0 0 0 0 6955 739 26 0 0 HES7 17 8121749 Frame_Shift_Del DEL C C3L-00604_T 8121749 75135692 36 6778 MUC16 0 . GRCh38 19 8885763 8885763 + Silent SNP A A G novel C3L-00604_T C3L-00604_N A A c.41133T>C p.= p.P13711P ENST00000397910 61/84 51 44 7 80 80 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2;MUC16,synonymous_variant,p.=,ENST00000599436,;MUC16,synonymous_variant,p.=,ENST00000601404,;MUC16,synonymous_variant,p.=,ENST00000596768,; G ENST00000397910 Transcript synonymous_variant 41337/43816 41133/43524 13711/14507 P ccT/ccC 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 61/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,Superfamily_domains:0047452 LOW 1 SNV 5 1 PASS rs35789580 . 0 206 4 0 0 0 0 0 -16.86031 1 1 1 1 0 G 2 3 19 8885763 8885763 A G 1 0 0 0 0 0 0 0 1 9972 175 7 5 5 MUC16 19 8885763 Silent SNP A C3L-00604_T 8885763 49731853 37 6779 ZNF257 0 . GRCh38 19 22088982 22088982 + Missense_Mutation SNP G G C novel C3L-00604_T C3L-00604_N G G c.1232G>C p.Trp411Ser p.W411S ENST00000594947 4/4 177 165 12 154 154 0 strelka-varscan-mutect ZNF257,missense_variant,p.Trp411Ser,ENST00000594947,NM_033468.2;ZNF257,downstream_gene_variant,,ENST00000600162,;ZNF257,downstream_gene_variant,,ENST00000597927,;ZNF257,3_prime_UTR_variant,,ENST00000435820,NM_001316996.1; C ENST00000594947 Transcript missense_variant 1376/3874 1232/1692 411/563 W/S tGg/tCg 1 1 ZNF257 HGNC HGNC:13498 protein_coding YES CCDS46030.1 ENSP00000470209 Q9Y2Q1 UPI0000E045CA NM_033468.2 tolerated(0.41) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF127,Gene3D:3.30.160.60,SMART_domains:SM00355 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 19 22088982 22088982 G C 1 0 0 0 0 1 0 0 0 18376 1357 47 4 4 ZNF257 19 22088982 Missense_Mutation SNP G C3L-00604_T 13203219 22088982 36528634 38 6780 TSHZ3 0 . GRCh38 19 31277205 31277205 + Missense_Mutation SNP G G A novel C3L-00604_T C3L-00604_N G G c.2588C>T p.Ser863Phe p.S863F ENST00000240587 2/2 86 78 8 61 61 0 strelka-mutect TSHZ3,missense_variant,p.Ser863Phe,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; A ENST00000240587 Transcript missense_variant 2916/5176 2588/3246 863/1081 S/F tCc/tTc 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 31277205 31277205 G A 1 0 0 0 0 1 0 0 0 17130 1174 41 3 3 TSHZ3 19 31277205 Missense_Mutation SNP G C3L-00604_T 9188223 31277205 27340411 39 6781 NUMBL 0 . GRCh38 19 40686966 40686966 + Silent SNP C C A novel C3L-00604_T C3L-00604_N C C c.54G>T p.= p.L18L ENST00000252891 2/10 90 75 15 80 80 0 strelka-varscan-mutect NUMBL,synonymous_variant,p.=,ENST00000252891,NM_004756.4;NUMBL,5_prime_UTR_variant,,ENST00000598773,;NUMBL,5_prime_UTR_variant,,ENST00000595741,;NUMBL,5_prime_UTR_variant,,ENST00000600636,;NUMBL,intron_variant,,ENST00000598779,NM_001289979.1;NUMBL,intron_variant,,ENST00000540131,NM_001289980.1;ADCK4,downstream_gene_variant,,ENST00000324464,NM_024876.3;ADCK4,downstream_gene_variant,,ENST00000243583,NM_001142555.2;NUMBL,upstream_gene_variant,,ENST00000600967,;NUMBL,non_coding_transcript_exon_variant,,ENST00000599594,;ADCK4,downstream_gene_variant,,ENST00000593724,;NUMBL,upstream_gene_variant,,ENST00000598759,;NUMBL,upstream_gene_variant,,ENST00000599786,;NUMBL,upstream_gene_variant,,ENST00000593367,; A ENST00000252891 Transcript synonymous_variant 222/3561 54/1830 18/609 L ctG/ctT 1 -1 NUMBL HGNC HGNC:8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 UPI000003032B NM_004756.4 2/10 PIRSF_domain:PIRSF017607,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF32 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 19 40686966 40686966 C A 1 0 0 0 0 0 0 0 1 10817 697 25 2 2 NUMBL 19 40686966 Silent SNP C C3L-00604_T 9409761 40686966 17930650 40 6782 RBM39 0 . GRCh38 20 35705257 35705257 + Missense_Mutation SNP T T A novel C3L-00604_T C3L-00604_N T T c.1381A>T p.Ile461Phe p.I461F ENST00000253363 15/17 115 86 29 79 79 0 strelka-varscan-mutect RBM39,missense_variant,p.Ile455Phe,ENST00000361162,NM_001323424.1,NM_004902.3;RBM39,missense_variant,p.Ile461Phe,ENST00000253363,NM_184234.2;RBM39,missense_variant,p.Ile439Phe,ENST00000528062,NM_001242600.1,NM_001242599.1;RBM39,missense_variant,p.Ile312Phe,ENST00000448303,;ROMO1,downstream_gene_variant,,ENST00000374078,NM_080748.2;ROMO1,downstream_gene_variant,,ENST00000336695,;ROMO1,downstream_gene_variant,,ENST00000374077,;ROMO1,downstream_gene_variant,,ENST00000374072,;ROMO1,downstream_gene_variant,,ENST00000397416,;RBM39,downstream_gene_variant,,ENST00000470563,;RBM39,3_prime_UTR_variant,,ENST00000403542,;RBM39,3_prime_UTR_variant,,ENST00000338163,;RBM39,3_prime_UTR_variant,,ENST00000429968,;RBM39,3_prime_UTR_variant,,ENST00000444878,;RBM39,3_prime_UTR_variant,,ENST00000476806,;RBM39,non_coding_transcript_exon_variant,,ENST00000463004,;RBM39,non_coding_transcript_exon_variant,,ENST00000461283,;RBM39,non_coding_transcript_exon_variant,,ENST00000492779,;RBM39,non_coding_transcript_exon_variant,,ENST00000482563,;RBM39,non_coding_transcript_exon_variant,,ENST00000465158,;RBM39,non_coding_transcript_exon_variant,,ENST00000495293,;RBM39,non_coding_transcript_exon_variant,,ENST00000496183,;RBM39,non_coding_transcript_exon_variant,,ENST00000490354,;RBM39,downstream_gene_variant,,ENST00000615771,;RBM39,downstream_gene_variant,,ENST00000475651,;RBM39,downstream_gene_variant,,ENST00000468086,;RBM39,downstream_gene_variant,,ENST00000471635,; A ENST00000253363 Transcript missense_variant 1405/2488 1381/1593 461/530 I/F Att/Ttt 1 -1 RBM39 HGNC HGNC:15923 protein_coding YES CCDS13266.1 ENSP00000253363 Q14498 UPI0000134418 NM_184234.2 deleterious(0.01) 15/17 Gene3D:3.30.70.330,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01622 MODERATE 1 SNV 1 1 PASS rs1176144841 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 19 35705257 35705257 T A 1 0 0 0 0 1 0 0 0 13299 1406 49 4 4 RBM39 20 35705257 Missense_Mutation SNP T C3L-00604_T 35705257 28738910 41 6783 SLC5A3 0 . GRCh38 21 34095545 34095545 + Missense_Mutation SNP G G T C3L-00604_T C3L-00604_N G G c.347G>T p.Arg116Leu p.R116L ENST00000381151 2/2 246 196 50 209 209 0 strelka-varscan-mutect SLC5A3,missense_variant,p.Arg116Leu,ENST00000381151,NM_006933.6;MRPS6,intron_variant,,ENST00000399312,NM_032476.3;MRPS6,intron_variant,,ENST00000477091,;MRPS6,intron_variant,,ENST00000488492,;AP000320.7,intron_variant,,ENST00000362077,; T ENST00000381151 Transcript missense_variant 859/11576 347/2157 116/718 R/L cGa/cTa COSM5016665 1 1 SLC5A3 HGNC HGNC:11038 protein_coding YES CCDS33549.1 ENSP00000370543 P53794 UPI0000465182 NM_006933.6 deleterious(0) 2/2 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF150,TIGRFAM_domain:TIGR00813 1 MODERATE 1 SNV 1 1 1 PASS rs1408574398 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 34095545 34095545 G T 1 0 0 0 0 1 0 0 0 14949 1058 37 1 1 SLC5A3 21 34095545 Missense_Mutation SNP G C3L-00604_T 34095545 12614438 42 6784 KRTAP10-4 0 . GRCh38 21 44574746 44574746 + Missense_Mutation SNP C C T novel C3L-00604_T C3L-00604_N C C c.988C>T p.Pro330Ser p.P330S ENST00000400374 1/1 611 537 74 495 494 1 strelka-varscan-mutect KRTAP10-4,missense_variant,p.Pro330Ser,ENST00000400374,NM_198687.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,upstream_gene_variant,,ENST00000397916,;KRTAP10-5,downstream_gene_variant,,ENST00000400372,NM_198694.3; T ENST00000400374 Transcript missense_variant 1018/1643 988/1206 330/401 P/S Cct/Tct 1 1 KRTAP10-4 HGNC HGNC:20521 protein_coding YES CCDS42957.1 ENSP00000383225 P60372 UPI00003D4D6E NM_198687.2 deleterious(0.04) 1/1 Pfam_domain:PF13885,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 44574746 44574746 C T 1 0 0 0 0 1 0 0 0 8394 739 26 3 3 KRTAP10-4 21 44574746 Missense_Mutation SNP C C3L-00604_T 10479201 44574746 2135237 43 6785 MICAL3 0 . GRCh38 22 17895311 17895311 + Silent SNP G G A novel C3L-00604_T C3L-00604_N G G c.1422C>T p.= p.I474I ENST00000441493 10/32 215 138 77 185 185 0 strelka-varscan-mutect MICAL3,synonymous_variant,p.=,ENST00000441493,NM_015241.2;MICAL3,synonymous_variant,p.=,ENST00000414725,;MICAL3,synonymous_variant,p.=,ENST00000585038,NM_001136004.3;MICAL3,synonymous_variant,p.=,ENST00000400561,NM_001122731.2;MICAL3,synonymous_variant,p.=,ENST00000383094,;MICAL3,upstream_gene_variant,,ENST00000461307,;MICAL3,3_prime_UTR_variant,,ENST00000495076,; A ENST00000441493 Transcript synonymous_variant 1775/9445 1422/6009 474/2002 I atC/atT 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 10/32 Superfamily_domains:SSF47576 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 19 17895311 17895311 G A 1 0 0 0 0 0 0 0 1 9528 1280 45 3 3 MICAL3 22 17895311 Silent SNP G C3L-00604_T 17895311 32923157 44 6786 MAGEB5 0 . GRCh38 X 26217518 26217518 + Missense_Mutation SNP A A G novel C3L-00604_T C3L-00604_N A A c.217A>G p.Arg73Gly p.R73G ENST00000602297 2/2 140 126 14 128 128 0 strelka-varscan-mutect MAGEB5,missense_variant,p.Arg73Gly,ENST00000602297,NM_001271752.1; G ENST00000602297 Transcript missense_variant 464/1216 217/828 73/275 R/G Aga/Gga 1 1 MAGEB5 HGNC HGNC:23795 protein_coding YES CCDS65233.1 ENSP00000473493 Q9BZ81 UPI0000237754 NM_001271752.1 deleterious(0.02) 2/2 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF35,SMART_domains:SM01373 MODERATE 1 SNV 3 1 PASS rs1197668527 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 19 26217518 26217518 A G 1 0 0 0 0 1 0 0 0 9095 64 3 5 5 MAGEB5 23 26217518 Missense_Mutation SNP A C3L-00604_T 26217518 129823377 45 6787 MAGEC2 0 . GRCh38 X 142203281 142203281 + Missense_Mutation SNP A A T C3L-00604_T C3L-00604_N A A c.707T>A p.Val236Glu p.V236E ENST00000247452 3/3 193 172 21 171 171 0 strelka-varscan-mutect MAGEC2,missense_variant,p.Val236Glu,ENST00000247452,NM_016249.3; T ENST00000247452 Transcript missense_variant 1055/1991 707/1122 236/373 V/E gTg/gAg COSM3379432 1 -1 MAGEC2 HGNC HGNC:13574 protein_coding YES CCDS14678.1 ENSP00000354660 Q9UBF1 UPI000012F059 NM_016249.3 deleterious(0) 3/3 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 19 142203281 142203281 A T 1 0 0 0 0 1 0 0 0 9099 159 6 4 4 MAGEC2 23 142203281 Missense_Mutation SNP A C3L-00604_T 115985763 142203281 13837614 46 6788 PIK3CD 0 . GRCh38 1 9721539 9721539 + Missense_Mutation SNP G G A rs748760424 C3L-00893_T C3L-00893_N G G c.1907G>A p.Arg636Gln p.R636Q ENST00000377346 15/24 611 451 160 399 399 0 strelka-varscan-mutect PIK3CD,missense_variant,p.Arg660Gln,ENST00000536656,;PIK3CD,missense_variant,p.Arg660Gln,ENST00000628140,;PIK3CD,missense_variant,p.Arg636Gln,ENST00000377346,NM_005026.3;PIK3CD,missense_variant,p.Arg660Gln,ENST00000361110,;PIK3CD,missense_variant,p.Arg660Gln,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,; A ENST00000377346 Transcript missense_variant 2102/5203 1907/3135 636/1044 R/Q cGg/cAg rs748760424 1 1 PIK3CD HGNC HGNC:8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 UPI000013E807 NM_005026.3 deleterious(0) 15/24 PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF35,Gene3D:1.25.40.70,Pfam_domain:PF00613,SMART_domains:SM00145,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs748760424 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 9721539 9721539 G A 1 0 0 0 0 1 0 0 0 12010 1116 39 1 1 PIK3CD 1 9721539 Missense_Mutation SNP G C3L-00893_T 9721539 239234883 1 6789 EPHA8 0 . GRCh38 1 22597345 22597345 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.1799C>A p.Pro600His p.P600H ENST00000166244 10/17 120 110 10 59 59 0 strelka-varscan-mutect EPHA8,missense_variant,p.Pro600His,ENST00000166244,NM_020526.3; A ENST00000166244 Transcript missense_variant 1871/4943 1799/3018 600/1005 P/H cCc/cAc 1 1 EPHA8 HGNC HGNC:3391 protein_coding YES CCDS225.1 ENSP00000166244 P29322 UPI000012A07B NM_020526.3 tolerated(0.08) 10/17 Low_complexity_(Seg):seg,hmmpanther:PTHR24416:SF339,hmmpanther:PTHR24416,Pfam_domain:PF14575,PIRSF_domain:PIRSF000666 MODERATE 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -19.42617 1 1 1 1 0 A 3 1 20 22597345 22597345 C A 1 0 0 0 0 1 0 0 0 5020 623 22 2 2 EPHA8 1 22597345 Missense_Mutation SNP C C3L-00893_T 12875806 22597345 226359077 2 6790 GRIK3 0 . GRCh38 1 36817213 36817213 + Silent SNP C C A rs144959883 C3L-00893_T C3L-00893_N C C c.1938G>T p.= p.T646T ENST00000373091 13/16 364 288 76 303 302 1 strelka-varscan-mutect GRIK3,synonymous_variant,p.=,ENST00000373091,NM_000831.3;GRIK3,synonymous_variant,p.=,ENST00000373093,; A ENST00000373091 Transcript synonymous_variant 1955/9101 1938/2760 646/919 T acG/acT rs144959883 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 13/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,SMART_domains:SM00079,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs144959883 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 20 36817213 36817213 C A 1 0 0 0 0 0 0 0 1 6657 755 27 1 1 GRIK3 1 36817213 Silent SNP C C3L-00893_T 14219868 36817213 212139209 3 6791 CACNA1S 0 . GRCh38 1 201077896 201077896 + Missense_Mutation SNP C C A rs372105058 C3L-00893_T C3L-00893_N C C c.1602G>T p.Arg534Ser p.R534S ENST00000362061 11/44 289 248 41 111 111 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Arg534Ser,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Arg534Ser,ENST00000367338,; A ENST00000362061 Transcript missense_variant 1829/6166 1602/5622 534/1873 R/S agG/agT rs372105058,COSM5235917 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 deleterious(0.01) 11/44 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Superfamily_domains:SSF81324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372105058 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 201077896 201077896 C A 1 0 0 0 0 1 0 0 0 2235 854 30 2 2 CACNA1S 1 201077896 Missense_Mutation SNP C C3L-00893_T 164260683 201077896 47878526 4 6792 IGFN1 0 . GRCh38 1 201226957 201226957 + Missense_Mutation SNP G G A rs371094909 C3L-00893_T C3L-00893_N G G c.10862G>A p.Arg3621Gln p.R3621Q ENST00000335211 23/24 306 285 21 132 132 0 strelka-varscan-mutect IGFN1,missense_variant,p.Arg3621Gln,ENST00000335211,NM_001164586.1;IGFN1,missense_variant,p.Arg1164Gln,ENST00000295591,;IGFN1,missense_variant,p.Arg1039Gln,ENST00000412892,;RP11-567E21.3,upstream_gene_variant,,ENST00000453155,;IGFN1,3_prime_UTR_variant,,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,; A ENST00000335211 Transcript missense_variant 10992/11810 10862/11127 3621/3708 R/Q cGg/cAg rs371094909 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0) 23/24 PROSITE_profiles:PS50835,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs371094909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 201226957 201226957 G A 1 0 0 0 0 1 0 0 0 7497 1116 39 1 1 IGFN1 1 201226957 Missense_Mutation SNP G C3L-00893_T 149061 201226957 47729465 5 6793 RYR2 0 . GRCh38 1 237631489 237631489 + Missense_Mutation SNP A A G novel C3L-00893_T C3L-00893_N A A c.6503A>G p.His2168Arg p.H2168R ENST00000366574 42/105 316 282 34 242 242 0 strelka-varscan RYR2,missense_variant,p.His2168Arg,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.His2152Arg,ENST00000360064,; G ENST00000366574 Transcript missense_variant 6820/16562 6503/14904 2168/4967 H/R cAc/cGc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 42/105 Superfamily_domains:0048280,Gene3D:1n4kA02,Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 20 237631489 237631489 A G 1 0 0 0 0 1 0 0 0 14029 159 6 5 5 RYR2 1 237631489 Missense_Mutation SNP A C3L-00893_T 36404532 237631489 11324933 6 6794 OR2G3 0 . GRCh38 1 247605595 247605595 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.10G>T p.Gly4Cys p.G4C ENST00000320002 1/1 100 85 15 50 50 0 strelka-varscan OR2G3,missense_variant,p.Gly4Cys,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; T ENST00000320002 Transcript missense_variant 10/930 10/930 4/309 G/C Ggc/Tgc 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 deleterious(0.03) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 247605595 247605595 G T 1 0 0 0 0 1 0 0 0 11077 1232 43 2 2 OR2G3 1 247605595 Missense_Mutation SNP G C3L-00893_T 9974106 247605595 1350827 7 6795 OR14I1 0 . GRCh38 1 248682205 248682205 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.100C>A p.Leu34Met p.L34M ENST00000342623 1/1 252 216 36 117 117 0 strelka-varscan OR14I1,missense_variant,p.Leu34Met,ENST00000342623,NM_001004734.1; T ENST00000342623 Transcript missense_variant 100/936 100/936 34/311 L/M Ctg/Atg 1 -1 OR14I1 HGNC HGNC:19575 protein_coding YES CCDS31125.1 ENSP00000339726 A6ND48 UPI0000199BC9 NM_001004734.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF316,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 248682205 248682205 G T 1 0 0 0 0 1 0 0 0 11024 933 33 2 2 OR14I1 1 248682205 Missense_Mutation SNP G C3L-00893_T 1076610 248682205 274217 8 6796 HADHA 0 . GRCh38 2 26191251 26191251 + Nonstop_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.2291G>T p.Ter764LeuextTer31 p.*764Lext*31 ENST00000380649 20/20 539 402 137 338 338 0 strelka-varscan-mutect HADHA,stop_lost,p.Ter764LeuextTer31,ENST00000380649,NM_000182.4;GAREM2,downstream_gene_variant,,ENST00000407684,NM_001191033.1;GAREM2,downstream_gene_variant,,ENST00000401533,NM_001168241.1;HADHA,downstream_gene_variant,,ENST00000492433,;GAREM2,downstream_gene_variant,,ENST00000496070,; A ENST00000380649 Transcript stop_lost 2421/3037 2291/2292 764/763 */L tGa/tTa 1 -1 HADHA HGNC HGNC:4801 protein_coding YES CCDS1721.1 ENSP00000370023 P40939 E9KL44 UPI0000129B6B NM_000182.4 20/20 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 20 26191251 26191251 C A 1 0 0 0 0 0 0 0 0 6829 837 29 2 2 HADHA 2 26191251 Nonstop_Mutation SNP C C3L-00893_T 26191251 216002278 9 6797 PLB1 0 . GRCh38 2 28540375 28540375 + Silent SNP A A G novel C3L-00893_T C3L-00893_N A A c.708A>G p.= p.P236P ENST00000327757 12/58 293 212 81 169 168 1 strelka-varscan-mutect PLB1,synonymous_variant,p.=,ENST00000422425,NM_001170585.1;PLB1,synonymous_variant,p.=,ENST00000327757,NM_153021.4;PLB1,synonymous_variant,p.=,ENST00000404858,;PLB1,downstream_gene_variant,,ENST00000416713,; G ENST00000327757 Transcript synonymous_variant 752/5107 708/4377 236/1458 P ccA/ccG 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 12/58 hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 20 28540375 28540375 A G 1 0 0 0 0 0 0 0 1 12118 175 7 5 5 PLB1 2 28540375 Silent SNP A C3L-00893_T 2349124 28540375 213653154 10 6798 CEP68 0 . GRCh38 2 65082632 65082632 + Missense_Mutation SNP T T C rs752528667 C3L-00893_T C3L-00893_N T T c.2201T>C p.Met734Thr p.M734T ENST00000377990 6/7 140 114 26 110 110 0 strelka-varscan CEP68,missense_variant,p.Met734Thr,ENST00000377990,NM_001319100.1,NM_015147.2;CEP68,missense_variant,p.Met597Thr,ENST00000260569,NM_001319101.1;RAB1A,downstream_gene_variant,,ENST00000409784,NM_004161.4;RAB1A,downstream_gene_variant,,ENST00000409892,;RAB1A,intron_variant,,ENST00000494188,; C ENST00000377990 Transcript missense_variant 2404/5847 2201/2274 734/757 M/T aTg/aCg rs752528667 1 1 CEP68 HGNC HGNC:29076 protein_coding YES CCDS1880.2 ENSP00000367229 Q76N32 UPI0000505465 NM_001319100.1,NM_015147.2 tolerated(0.68) 6/7 hmmpanther:PTHR14514 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 20 65082632 65082632 T C 1 0 0 0 0 1 0 0 0 2979 1464 51 5 5 CEP68 2 65082632 Missense_Mutation SNP T C3L-00893_T 36542257 65082632 177110897 11 6799 RAB11FIP5 0 . GRCh38 2 73075558 73075558 + Missense_Mutation SNP G G A novel C3L-00893_T C3L-00893_N G G c.1925C>T p.Pro642Leu p.P642L ENST00000258098 5/5 273 254 19 203 203 0 strelka-varscan RAB11FIP5,missense_variant,p.Pro1313Leu,ENST00000486777,;RAB11FIP5,missense_variant,p.Pro642Leu,ENST00000258098,NM_015470.2;SFXN5,upstream_gene_variant,,ENST00000272433,NM_144579.2;SFXN5,upstream_gene_variant,,ENST00000411783,;SFXN5,upstream_gene_variant,,ENST00000410065,;SFXN5,upstream_gene_variant,,ENST00000442582,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000482554,;SFXN5,intron_variant,,ENST00000485057,;SFXN5,upstream_gene_variant,,ENST00000479293,;SFXN5,upstream_gene_variant,,ENST00000472259,;SFXN5,upstream_gene_variant,,ENST00000416579,;SFXN5,upstream_gene_variant,,ENST00000497144,;SFXN5,upstream_gene_variant,,ENST00000475630,;SFXN5,upstream_gene_variant,,ENST00000484123,;SFXN5,upstream_gene_variant,,ENST00000450185,; A ENST00000258098 Transcript missense_variant 2166/4342 1925/1962 642/653 P/L cCc/cTc 1 -1 RAB11FIP5 HGNC HGNC:24845 protein_coding YES CCDS1923.1 ENSP00000258098 Q9BXF6 UPI000007079C NM_015470.2 deleterious(0) 5/5 PROSITE_profiles:PS51511,hmmpanther:PTHR15746:SF14,hmmpanther:PTHR15746,Pfam_domain:PF09457,Superfamily_domains:SSF144270 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.9992 0.9999996 1 1 1 0 A 3 1 20 73075558 73075558 G A 1 0 0 0 0 1 0 0 0 13055 1232 43 3 3 RAB11FIP5 2 73075558 Missense_Mutation SNP G C3L-00893_T 7992926 73075558 169117971 12 6800 SFTPB 0 . GRCh38 2 85668203 85668203 + Missense_Mutation SNP T T A novel C3L-00893_T C3L-00893_N T T c.17A>T p.Tyr6Phe p.Y6F ENST00000409383 2/12 229 174 55 167 167 0 strelka-varscan SFTPB,missense_variant,p.Tyr6Phe,ENST00000409383,NM_198843.2,NM_000542.3;SFTPB,5_prime_UTR_variant,,ENST00000393822,;SFTPB,5_prime_UTR_variant,,ENST00000519937,;SFTPB,upstream_gene_variant,,ENST00000428225,;SFTPB,upstream_gene_variant,,ENST00000494165,;SFTPB,upstream_gene_variant,,ENST00000473692,;SFTPB,upstream_gene_variant,,ENST00000491167,; A ENST00000409383 Transcript missense_variant 117/1867 17/1182 6/393 Y/F tAc/tTc 1 -1 SFTPB HGNC HGNC:10801 protein_coding YES CCDS1983.2 ENSP00000386346 D6W5L6 UPI0000421A06 NM_198843.2,NM_000542.3 tolerated_low_confidence(0.35) 2/12 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 85668203 85668203 T A 1 0 0 0 0 1 0 0 0 14451 1638 57 4 4 SFTPB 2 85668203 Missense_Mutation SNP T C3L-00893_T 12592645 85668203 156525326 13 6801 WDR33 0 . GRCh38 2 127765182 127765182 + Missense_Mutation SNP T T C novel C3L-00893_T C3L-00893_N T T c.466A>G p.Ile156Val p.I156V ENST00000322313 5/22 144 127 17 121 121 0 strelka-varscan WDR33,missense_variant,p.Ile156Val,ENST00000322313,NM_018383.4;WDR33,missense_variant,p.Ile156Val,ENST00000393006,NM_001006623.2;WDR33,missense_variant,p.Ile156Val,ENST00000409658,NM_001006622.2;WDR33,missense_variant,p.Ile78Val,ENST00000436787,;WDR33,downstream_gene_variant,,ENST00000408998,; C ENST00000322313 Transcript missense_variant 625/9471 466/4011 156/1336 I/V Ata/Gta 1 -1 WDR33 HGNC HGNC:25651 protein_coding YES CCDS2150.1 ENSP00000325377 Q9C0J8 UPI000013D032 NM_018383.4 deleterious(0.02) 5/22 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR22836,hmmpanther:PTHR22836:SF0,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 20 127765182 127765182 T C 1 0 0 0 0 1 0 0 0 17847 1493 52 5 5 WDR33 2 127765182 Missense_Mutation SNP T C3L-00893_T 42096979 127765182 114428347 14 6802 FRZB 0 . GRCh38 2 182838553 182838553 + Missense_Mutation SNP T T A novel C3L-00893_T C3L-00893_N T T c.653A>T p.Glu218Val p.E218V ENST00000295113 4/6 347 325 22 233 233 0 strelka-varscan FRZB,missense_variant,p.Glu218Val,ENST00000295113,NM_001463.3; A ENST00000295113 Transcript missense_variant 1263/3162 653/978 218/325 E/V gAg/gTg 1 -1 FRZB HGNC HGNC:3959 protein_coding YES CCDS2286.1 ENSP00000295113 Q92765 D9ZGF6 UPI0000051054 NM_001463.3 deleterious(0) 4/6 Gene3D:2.40.50.120,Pfam_domain:PF01759,PROSITE_profiles:PS50189,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF97,SMART_domains:SM00643,Superfamily_domains:SSF50242 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 182838553 182838553 T A 1 0 0 0 0 1 0 0 0 5937 1551 54 4 4 FRZB 2 182838553 Missense_Mutation SNP T C3L-00893_T 55073371 182838553 59354976 15 6803 SPEG 0 . GRCh38 2 219451144 219451144 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.2122G>T p.Asp708Tyr p.D708Y ENST00000312358 5/41 99 76 23 76 76 0 strelka-varscan-mutect SPEG,missense_variant,p.Asp708Tyr,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Asp604Tyr,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,non_coding_transcript_exon_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,missense_variant,p.Gly43Val,ENST00000409595,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,downstream_gene_variant,,ENST00000452101,; T ENST00000312358 Transcript missense_variant 2254/10782 2122/9804 708/3267 D/Y Gat/Tat 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 5/41 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 219451144 219451144 G T 1 0 0 0 0 1 0 0 0 15387 1174 41 2 2 SPEG 2 219451144 Missense_Mutation SNP G C3L-00893_T 36612591 219451144 22742385 16 6804 TGM4 0 . GRCh38 3 44901550 44901550 + Silent SNP G G T novel C3L-00893_T C3L-00893_N G G c.684G>T p.= p.V228V ENST00000296125 7/14 102 60 42 100 100 0 varscan-mutect TGM4,synonymous_variant,p.=,ENST00000296125,NM_003241.3;RP11-272D20.2,downstream_gene_variant,,ENST00000427258,;TGM4,3_prime_UTR_variant,,ENST00000422219,;TGM4,upstream_gene_variant,,ENST00000459830,;TGM4,downstream_gene_variant,,ENST00000495844,; T ENST00000296125 Transcript synonymous_variant 752/3388 684/2055 228/684 V gtG/gtT 1 1 TGM4 HGNC HGNC:11780 protein_coding YES CCDS2723.1 ENSP00000296125 P49221 UPI0000136CCD NM_003241.3 7/14 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF45,Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 44901550 44901550 G T 1 0 0 0 0 0 0 0 1 16265 1306 46 2 2 TGM4 3 44901550 Silent SNP G C3L-00893_T 44901550 153394009 17 6805 BOC 0 . GRCh38 3 113279879 113279879 + Silent SNP C C T novel C3L-00893_T C3L-00893_N C C c.2079C>T p.= p.P693P ENST00000273395 13/20 145 94 51 104 104 0 strelka-varscan-mutect BOC,synonymous_variant,p.=,ENST00000495514,NM_033254.3;BOC,synonymous_variant,p.=,ENST00000355385,;BOC,synonymous_variant,p.=,ENST00000273395,NM_001301861.1;BOC,upstream_gene_variant,,ENST00000473008,;BOC,downstream_gene_variant,,ENST00000497495,;BOC,non_coding_transcript_exon_variant,,ENST00000466059,;BOC,non_coding_transcript_exon_variant,,ENST00000479182,;BOC,non_coding_transcript_exon_variant,,ENST00000463971,;BOC,upstream_gene_variant,,ENST00000488486,; T ENST00000273395 Transcript synonymous_variant 2418/4276 2079/3348 693/1115 P ccC/ccT 1 1 BOC HGNC HGNC:17173 protein_coding YES CCDS77788.1 ENSP00000273395 Q9BWV1 UPI0000D61B53 NM_001301861.1 13/20 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF11,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 113279879 113279879 C T 1 0 0 0 0 0 0 0 1 1637 581 21 3 3 BOC 3 113279879 Silent SNP C C3L-00893_T 68378329 113279879 85015680 18 6806 HEG1 0 . GRCh38 3 125012821 125012821 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.2758G>T p.Val920Leu p.V920L ENST00000311127 6/17 349 324 25 257 257 0 strelka-varscan-mutect HEG1,missense_variant,p.Val920Leu,ENST00000311127,NM_020733.1;HEG1,downstream_gene_variant,,ENST00000477536,;HEG1,upstream_gene_variant,,ENST00000488654,; A ENST00000311127 Transcript missense_variant 2826/9156 2758/4146 920/1381 V/L Gta/Tta 1 -1 HEG1 HGNC HGNC:29227 protein_coding YES CCDS46898.1 ENSP00000311502 Q9ULI3 UPI00006C069B NM_020733.1 tolerated(0.11) 6/17 hmmpanther:PTHR24037:SF3,hmmpanther:PTHR24037 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 125012821 125012821 C A 1 0 0 0 0 1 0 0 0 6926 478 17 2 2 HEG1 3 125012821 Missense_Mutation SNP C C3L-00893_T 11732942 125012821 73282738 19 6807 EVC 0 . GRCh38 4 5748201 5748201 + Silent SNP G G A novel C3L-00893_T C3L-00893_N G G c.993G>A p.= p.Q331Q ENST00000264956 8/21 667 610 57 472 472 0 strelka-varscan-mutect EVC,synonymous_variant,p.=,ENST00000264956,NM_001306090.1,NM_153717.2;EVC,synonymous_variant,p.=,ENST00000509451,NM_001306092.1;CRMP1,non_coding_transcript_exon_variant,,ENST00000506216,;EVC,upstream_gene_variant,,ENST00000514919,; A ENST00000264956 Transcript synonymous_variant 1177/6431 993/2979 331/992 Q caG/caA 1 1 EVC HGNC HGNC:3497 protein_coding YES CCDS3383.1 ENSP00000264956 P57679 UPI000012A2A5 NM_001306090.1,NM_153717.2 8/21 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 20 5748201 5748201 G A 1 0 0 0 0 0 0 0 1 5152 1020 36 3 3 EVC 4 5748201 Silent SNP G C3L-00893_T 5748201 184466354 20 6808 PHOX2B 0 . GRCh38 4 41745903 41745903 + Silent SNP G G A novel C3L-00893_T C3L-00893_N G G c.849C>T p.= p.I283I ENST00000226382 3/3 280 214 66 221 221 0 strelka-varscan-mutect PHOX2B,synonymous_variant,p.=,ENST00000226382,NM_003924.3;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,;PHOX2B,downstream_gene_variant,,ENST00000510424,; A ENST00000226382 Transcript synonymous_variant 1209/3030 849/945 283/314 I atC/atT 1 -1 PHOX2B HGNC HGNC:9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 3/3 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF301 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 20 41745903 41745903 G A 1 0 0 0 0 0 0 0 1 11947 1164 41 3 3 PHOX2B 4 41745903 Silent SNP G C3L-00893_T 35997702 41745903 148468652 21 6809 PTPN13 0 . GRCh38 4 86799188 86799188 + Silent SNP T T C novel C3L-00893_T C3L-00893_N T T c.6504T>C p.= p.H2168H ENST00000436978 42/48 32 25 7 25 25 0 strelka-varscan PTPN13,synonymous_variant,p.=,ENST00000436978,NM_080685.2;PTPN13,synonymous_variant,p.=,ENST00000427191,NM_006264.2;PTPN13,synonymous_variant,p.=,ENST00000411767,NM_080683.2;PTPN13,synonymous_variant,p.=,ENST00000511467,;PTPN13,synonymous_variant,p.=,ENST00000316707,NM_080684.2; C ENST00000436978 Transcript synonymous_variant 6984/8573 6504/7473 2168/2490 H caT/caC 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 42/48 hmmpanther:PTHR19134:SF197,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000933 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 20 86799188 86799188 T C 1 0 0 0 0 0 0 0 1 12935 1461 51 5 5 PTPN13 4 86799188 Silent SNP T C3L-00893_T 45053285 86799188 103415367 22 6810 IBSP 0 . GRCh38 4 87810708 87810708 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.349G>T p.Asp117Tyr p.D117Y ENST00000226284 6/7 304 238 66 229 229 0 strelka-varscan IBSP,missense_variant,p.Asp117Tyr,ENST00000226284,NM_004967.3; T ENST00000226284 Transcript missense_variant 416/1546 349/954 117/317 D/Y Gac/Tac 1 1 IBSP HGNC HGNC:5341 protein_coding YES CCDS3624.1 ENSP00000226284 P21815 UPI000013C899 NM_004967.3 deleterious(0.01) 6/7 hmmpanther:PTHR10345:SF0,hmmpanther:PTHR10345,Pfam_domain:PF05432 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 87810708 87810708 G T 1 0 0 0 0 1 0 0 0 7375 1174 41 2 2 IBSP 4 87810708 Missense_Mutation SNP G C3L-00893_T 1011520 87810708 102403847 23 6811 TBCK 0 . GRCh38 4 106236461 106236461 + Missense_Mutation SNP G G A novel C3L-00893_T C3L-00893_N G G c.1279C>T p.Pro427Ser p.P427S ENST00000273980 15/27 81 67 14 49 49 0 strelka-varscan TBCK,missense_variant,p.Pro427Ser,ENST00000273980,;TBCK,missense_variant,p.Pro427Ser,ENST00000432496,NM_001163436.2;TBCK,missense_variant,p.Pro388Ser,ENST00000394706,NM_001163437.2;TBCK,missense_variant,p.Pro364Ser,ENST00000361687,NM_033115.4,NM_001290768.1;TBCK,missense_variant,p.Pro427Ser,ENST00000394708,NM_001163435.2;TBCK,5_prime_UTR_variant,,ENST00000503516,;TBCK,3_prime_UTR_variant,,ENST00000467183,;TBCK,3_prime_UTR_variant,,ENST00000508666,;TBCK,non_coding_transcript_exon_variant,,ENST00000510927,; A ENST00000273980 Transcript missense_variant 1727/8101 1279/2682 427/893 P/S Cct/Tct 1 -1 TBCK HGNC HGNC:28261 protein_coding YES CCDS54788.1 ENSP00000273980 Q8TEA7 UPI000013EF70 deleterious(0) 15/27 hmmpanther:PTHR22957:SF168,hmmpanther:PTHR22957 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 106236461 106236461 G A 1 0 0 0 0 1 0 0 0 16041 1232 43 3 3 TBCK 4 106236461 Missense_Mutation SNP G C3L-00893_T 18425753 106236461 83978094 24 6812 ADAMTS16 0 . GRCh38 5 5232499 5232499 + Silent SNP C C A novel C3L-00893_T C3L-00893_N C C c.1833C>A p.= p.R611R ENST00000274181 12/23 206 152 54 295 295 0 strelka-varscan-mutect ADAMTS16,synonymous_variant,p.=,ENST00000274181,NM_139056.2;ADAMTS16,upstream_gene_variant,,ENST00000513709,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript synonymous_variant 1971/4979 1833/3675 611/1224 R cgC/cgA 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 12/23 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,Prints_domain:PR01857 LOW 1 SNV 2 1 PASS rs1438866229 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 20 5232499 5232499 C A 1 0 0 0 0 0 0 0 1 305 726 26 2 2 ADAMTS16 5 5232499 Silent SNP C C3L-00893_T 5232499 176305760 25 6813 FAM134B 0 . GRCh38 5 16478048 16478048 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.859G>T p.Ala287Ser p.A287S ENST00000306320 7/9 60 56 4 30 30 0 strelka-mutect FAM134B,missense_variant,p.Ala287Ser,ENST00000306320,NM_001034850.2;FAM134B,missense_variant,p.Ala146Ser,ENST00000399793,NM_019000.4;FAM134B,non_coding_transcript_exon_variant,,ENST00000509977,;FAM134B,missense_variant,p.Ala7Ser,ENST00000510362,;FAM134B,downstream_gene_variant,,ENST00000506441,; A ENST00000306320 Transcript missense_variant 946/3268 859/1494 287/497 A/S Gct/Tct 1 -1 FAM134B HGNC HGNC:25964 protein_coding YES CCDS43304.1 ENSP00000304642 Q9H6L5 UPI000006D7DB NM_001034850.2 tolerated(0.22) 7/9 hmmpanther:PTHR28659,hmmpanther:PTHR28659:SF3 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -10.09091 1 1 1 1 0 A 3 1 20 16478048 16478048 C A 1 0 0 0 0 1 0 0 0 5296 797 28 2 2 FAM134B 5 16478048 Missense_Mutation SNP C C3L-00893_T 11245549 16478048 165060211 26 6814 PCDHA6 0 . GRCh38 5 140830410 140830410 + Missense_Mutation SNP C C A C3L-00893_T C3L-00893_N C C c.2319C>A p.Ser773Arg p.S773R ENST00000529310 1/4 193 152 41 164 164 0 strelka-mutect PCDHA6,missense_variant,p.Ser773Arg,ENST00000529310,NM_018909.3;PCDHA6,missense_variant,p.Ser773Arg,ENST00000378126,NM_031848.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA7,upstream_gene_variant,,ENST00000525929,NM_018910.2;PCDHA5,downstream_gene_variant,,ENST00000614258,NM_031501.1;PCDHA7,upstream_gene_variant,,ENST00000356878,NM_031852.1; A ENST00000529310 Transcript missense_variant 2433/5374 2319/2853 773/950 S/R agC/agA COSM5422176,COSM5422177 1 1 PCDHA6 HGNC HGNC:8672 protein_coding YES CCDS47281.1 ENSP00000433378 Q9UN73 UPI00001273CE NM_018909.3 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR24028:SF131,hmmpanther:PTHR24028 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 140830410 140830410 C A 1 0 0 0 0 1 0 0 0 11615 738 26 2 2 PCDHA6 5 140830410 Missense_Mutation SNP C C3L-00893_T 124352362 140830410 40707849 27 6815 PCDHA13 0 . GRCh38 5 140882272 140882272 + Silent SNP C C T rs782377951 C3L-00893_T C3L-00893_N C C c.4C>T p.= p.L2L ENST00000289272 1/4 109 87 22 91 91 0 strelka-varscan-mutect PCDHA13,synonymous_variant,p.=,ENST00000289272,NM_018904.2;PCDHA13,synonymous_variant,p.=,ENST00000409494,;PCDHA13,synonymous_variant,p.=,ENST00000617769,NM_031865.1;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;PCDHA12,downstream_gene_variant,,ENST00000613593,NM_031864.2;AC005609.17,non_coding_transcript_exon_variant,,ENST00000625195,; T ENST00000289272 Transcript synonymous_variant 4/5260 4/2853 2/950 L Ctg/Ttg rs782377951 1 1 PCDHA13 HGNC HGNC:8667 protein_coding YES CCDS4240.1 ENSP00000289272 Q9Y5I0 UPI00001273D6 NM_018904.2 1/4 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101 LOW 1 SNV 1 1 PASS rs782377951 . 0 201 9 0 0 0 0 0 -20 0.9999965 1 1 1 0 T 2 4 20 140882272 140882272 C T 1 0 0 0 0 0 0 0 1 11610 811 28 3 3 PCDHA13 5 140882272 Silent SNP C C3L-00893_T 51862 140882272 40655987 28 6816 PCDHGA7 0 . GRCh38 5 141385026 141385026 + Silent SNP C C T rs777670481 C3L-00893_T C3L-00893_N C C c.2127C>T p.= p.L709L ENST00000518325 1/4 460 396 64 311 311 0 strelka-varscan-mutect PCDHGA7,synonymous_variant,p.=,ENST00000518325,NM_018920.3;PCDHGA7,synonymous_variant,p.=,ENST00000617050,NM_032087.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,upstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB4,upstream_gene_variant,,ENST00000519479,NM_003736.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000518325 Transcript synonymous_variant 2127/4605 2127/2799 709/932 L ctC/ctT rs777670481,COSM1486423 1 1 PCDHGA7 HGNC HGNC:8705 protein_coding YES CCDS54927.1 ENSP00000430024 Q9Y5G6 UPI000007146F NM_018920.3 1/4 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs777670481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 141385026 141385026 C T 1 0 0 0 0 0 0 0 1 11646 871 31 1 1 PCDHGA7 5 141385026 Silent SNP C C3L-00893_T 502754 141385026 40153233 29 6817 ZNF354B 0 . GRCh38 5 178884148 178884148 + Missense_Mutation SNP A A G rs765748276 C3L-00893_T C3L-00893_N A A c.1696A>G p.Ile566Val p.I566V ENST00000322434 5/5 155 113 42 97 97 0 strelka-varscan-mutect ZNF354B,missense_variant,p.Ile566Val,ENST00000322434,NM_058230.2;ZNF354B,downstream_gene_variant,,ENST00000520377,;RNU1-39P,upstream_gene_variant,,ENST00000383897,;ZNF354B,non_coding_transcript_exon_variant,,ENST00000522714,;ZNF354B,upstream_gene_variant,,ENST00000522624,; G ENST00000322434 Transcript missense_variant 1922/2802 1696/1839 566/612 I/V Att/Gtt rs765748276,COSM4585757 1 1 ZNF354B HGNC HGNC:17197 protein_coding YES CCDS4439.1 ENSP00000327143 Q96LW1 UPI0000071A24 NM_058230.2 tolerated(0.21) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF87,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765748276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 20 178884148 178884148 A G 1 0 0 0 0 1 0 0 0 18437 449 16 5 5 ZNF354B 5 178884148 Missense_Mutation SNP A C3L-00893_T 37499122 178884148 2654111 30 6818 FLT4 0 . GRCh38 5 180621698 180621698 + Missense_Mutation SNP C C G rs771458044 C3L-00893_T C3L-00893_N C C c.1864G>C p.Ala622Pro p.A622P ENST00000261937 13/30 190 165 25 121 121 0 strelka-mutect FLT4,missense_variant,p.Ala622Pro,ENST00000261937,NM_182925.4;FLT4,missense_variant,p.Ala622Pro,ENST00000393347,NM_002020.4;FLT4,missense_variant,p.Ala622Pro,ENST00000502649,;FLT4,3_prime_UTR_variant,,ENST00000619105,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,non_coding_transcript_exon_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; G ENST00000261937 Transcript missense_variant 1943/5857 1864/4092 622/1363 A/P Gcc/Ccc rs771458044 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 tolerated(0.07) 13/30 PROSITE_profiles:PS50835,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs771458044 . 0 204 4 2 0 0 0 0 -20 0.9999778 1 1 1 0 G 3 3 20 180621698 180621698 C G 1 0 0 0 0 1 0 0 0 5800 768 27 4 4 FLT4 5 180621698 Missense_Mutation SNP C C3L-00893_T 1737550 180621698 916561 31 6819 FAM83B 0 . GRCh38 6 54940128 54940128 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.1157G>T p.Arg386Met p.R386M ENST00000306858 5/5 210 154 56 149 149 0 strelka-varscan-mutect FAM83B,missense_variant,p.Arg386Met,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; T ENST00000306858 Transcript missense_variant 1273/3167 1157/3036 386/1011 R/M aGg/aTg 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 deleterious(0) 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 54940128 54940128 G T 1 0 0 0 0 1 0 0 0 5492 1000 35 2 2 FAM83B 6 54940128 Missense_Mutation SNP G C3L-00893_T 54940128 115865851 32 6820 RIMS1 0 . GRCh38 6 72233796 72233796 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.1702G>T p.Asp568Tyr p.D568Y ENST00000521978 7/34 317 247 70 202 201 1 strelka-varscan-mutect RIMS1,missense_variant,p.Asp568Tyr,ENST00000264839,;RIMS1,missense_variant,p.Asp568Tyr,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Asp568Tyr,ENST00000491071,;RIMS1,missense_variant,p.Asp568Tyr,ENST00000520567,;RIMS1,missense_variant,p.Asp568Tyr,ENST00000517960,;RIMS1,missense_variant,p.Asp568Tyr,ENST00000518273,;RIMS1,missense_variant,p.Asp568Tyr,ENST00000522291,;RIMS1,missense_variant,p.Asp42Tyr,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Asp142Tyr,ENST00000517433,;RIMS1,missense_variant,p.Asp42Tyr,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Asp27Tyr,ENST00000517827,NM_001168410.1;RIMS1,5_prime_UTR_variant,,ENST00000425662,NM_001168409.1;RIMS1,5_prime_UTR_variant,,ENST00000453976,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,;RIMS1,non_coding_transcript_exon_variant,,ENST00000524197,; T ENST00000521978 Transcript missense_variant 1702/5079 1702/5079 568/1692 D/Y Gat/Tat 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious(0) 7/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 72233796 72233796 G T 1 0 0 0 0 1 0 0 0 13542 1174 41 2 2 RIMS1 6 72233796 Missense_Mutation SNP G C3L-00893_T 17293668 72233796 98572183 33 6821 AIM1 0 . GRCh38 6 106520704 106520704 + Missense_Mutation SNP G G C novel C3L-00893_T C3L-00893_N G G c.2272G>C p.Glu758Gln p.E758Q ENST00000369066 2/20 293 219 74 237 237 0 strelka-varscan-mutect AIM1,missense_variant,p.Glu1166Gln,ENST00000633556,;AIM1,missense_variant,p.Glu758Gln,ENST00000369066,NM_001624.3; C ENST00000369066 Transcript missense_variant 2759/7553 2272/5172 758/1723 E/Q Gaa/Caa 1 1 AIM1 HGNC HGNC:356 protein_coding YES CCDS34506.1 ENSP00000358062 Q9Y4K1 UPI000013C91D NM_001624.3 tolerated(0.14) 2/20 hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF2 MODERATE 1 SNV 1 1 PASS rs1239175400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 20 106520704 106520704 G C 1 0 0 0 0 1 0 0 0 507 1175 41 4 4 AIM1 6 106520704 Missense_Mutation SNP G C3L-00893_T 34286908 106520704 64285275 34 6822 AP5Z1 0 . GRCh38 7 4783346 4783346 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.397G>T p.Gly133Cys p.G133C ENST00000348624 4/17 144 108 36 92 92 0 strelka-varscan-mutect AP5Z1,missense_variant,p.Gly133Cys,ENST00000348624,NM_014855.2;AP5Z1,non_coding_transcript_exon_variant,,ENST00000496303,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000477680,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000491375,;AP5Z1,upstream_gene_variant,,ENST00000469614,;AP5Z1,upstream_gene_variant,,ENST00000477454,; T ENST00000348624 Transcript missense_variant 491/2901 397/2424 133/807 G/C Ggc/Tgc 1 1 AP5Z1 HGNC HGNC:22197 protein_coding YES CCDS47528.1 ENSP00000297562 O43299 UPI00003E5903 NM_014855.2 tolerated(0.28) 4/17 hmmpanther:PTHR12181:SF29,hmmpanther:PTHR12181 MODERATE 1 SNV 5 1 PASS rs1213712664 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 4783346 4783346 G T 1 0 0 0 0 1 0 0 0 874 1232 43 2 2 AP5Z1 7 4783346 Missense_Mutation SNP G C3L-00893_T 4783346 154562627 35 6823 RADIL 0 . GRCh38 7 4801727 4801727 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.2768G>T p.Gly923Val p.G923V ENST00000399583 12/15 284 208 76 275 275 0 strelka-varscan-mutect RADIL,missense_variant,p.Gly923Val,ENST00000399583,NM_018059.4;RADIL,3_prime_UTR_variant,,ENST00000445392,;RADIL,non_coding_transcript_exon_variant,,ENST00000473130,;RADIL,non_coding_transcript_exon_variant,,ENST00000472999,;RADIL,downstream_gene_variant,,ENST00000469399,; A ENST00000399583 Transcript missense_variant 2956/3689 2768/3228 923/1075 G/V gGc/gTc 1 -1 RADIL HGNC HGNC:22226 protein_coding YES CCDS43544.1 ENSP00000382492 Q96JH8 UPI0000E0A787 NM_018059.4 tolerated(0.21) 12/15 hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 4801727 4801727 C A 1 0 0 0 0 1 0 0 0 13158 739 26 2 2 RADIL 7 4801727 Missense_Mutation SNP C C3L-00893_T 18381 4801727 154544246 36 6824 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3L-00893_T C3L-00893_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 638 497 141 569 569 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 20 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3L-00893_T 50373045 55174772 104171201 37 6825 POT1 0 . GRCh38 7 124846978 124846978 + Missense_Mutation SNP A A C novel C3L-00893_T C3L-00893_N A A c.970T>G p.Tyr324Asp p.Y324D ENST00000357628 12/19 41 30 11 34 34 0 strelka-varscan-mutect POT1,missense_variant,p.Tyr324Asp,ENST00000357628,NM_015450.2;POT1,missense_variant,p.Tyr193Asp,ENST00000393329,NM_001042594.1;POT1,upstream_gene_variant,,ENST00000608200,;POT1,downstream_gene_variant,,ENST00000610141,;POT1,missense_variant,p.Tyr324Asp,ENST00000609106,;POT1,missense_variant,p.Tyr324Asp,ENST00000607932,;POT1,3_prime_UTR_variant,,ENST00000608057,;POT1,upstream_gene_variant,,ENST00000466483,;POT1,downstream_gene_variant,,ENST00000608126,; C ENST00000357628 Transcript missense_variant 1569/4080 970/1905 324/634 Y/D Tac/Gac 1 -1 POT1 HGNC HGNC:17284 protein_coding YES CCDS5793.1 ENSP00000350249 Q9NUX5 A0A024R739 UPI0000073E3F NM_015450.2 tolerated(0.1) 12/19 hmmpanther:PTHR14513,hmmpanther:PTHR14513:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 20 124846978 124846978 A C 1 0 0 0 0 1 0 0 0 12374 449 16 5 5 POT1 7 124846978 Missense_Mutation SNP A C3L-00893_T 69672206 124846978 34498995 38 6826 LZTS1 0 . GRCh38 8 20253385 20253385 + Silent SNP C C T novel C3L-00893_T C3L-00893_N C C c.546G>A p.= p.L182L ENST00000381569 3/4 105 74 31 98 98 0 strelka-varscan LZTS1,synonymous_variant,p.=,ENST00000381569,;LZTS1,synonymous_variant,p.=,ENST00000265801,NM_021020.3;LZTS1,synonymous_variant,p.=,ENST00000522290,;LZTS1,intron_variant,,ENST00000616228,; T ENST00000381569 Transcript synonymous_variant 904/5706 546/1791 182/596 L ctG/ctA 1 -1 LZTS1 HGNC HGNC:13861 protein_coding YES CCDS6015.1 ENSP00000370981 Q9Y250 UPI000006DEE8 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR19354:SF5,hmmpanther:PTHR19354 LOW 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 2 4 20 20253385 20253385 C T 1 0 0 0 0 0 0 0 1 9051 697 25 3 3 LZTS1 8 20253385 Silent SNP C C3L-00893_T 20253385 124885251 39 6827 KIAA1429 0 . GRCh38 8 94534946 94534946 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.377G>T p.Gly126Val p.G126V ENST00000297591 5/24 349 279 70 224 223 1 strelka-varscan-mutect KIAA1429,missense_variant,p.Gly126Val,ENST00000297591,NM_015496.4;KIAA1429,missense_variant,p.Gly126Val,ENST00000421249,NM_183009.2;RP11-267M23.3,downstream_gene_variant,,ENST00000521010,;KIAA1429,intron_variant,,ENST00000519001,; A ENST00000297591 Transcript missense_variant 453/6528 377/5439 126/1812 G/V gGa/gTa 1 -1 KIAA1429 HGNC HGNC:24500 protein_coding YES CCDS34923.1 ENSP00000297591 Q69YN4 UPI00001BBB23 NM_015496.4 deleterious(0) 5/24 Pfam_domain:PF15912,hmmpanther:PTHR23185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 94534946 94534946 C A 1 0 0 0 0 1 0 0 0 8114 855 30 2 2 KIAA1429 8 94534946 Missense_Mutation SNP C C3L-00893_T 74281561 94534946 50603690 40 6828 CYP11B2 0 . GRCh38 8 142917135 142917135 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.319C>A p.His107Asn p.H107N ENST00000323110 2/9 704 592 112 345 345 0 strelka-varscan-mutect CYP11B2,missense_variant,p.His107Asn,ENST00000323110,NM_000498.3;GML,downstream_gene_variant,,ENST00000522728,; T ENST00000323110 Transcript missense_variant 322/2936 319/1512 107/503 H/N Cat/Aat 1 -1 CYP11B2 HGNC HGNC:2592 protein_coding YES CCDS6393.1 ENSP00000325822 P19099 UPI00001282CF NM_000498.3 tolerated(0.07) 2/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 142917135 142917135 G T 1 0 0 0 0 1 0 0 0 3949 1319 46 2 2 CYP11B2 8 142917135 Missense_Mutation SNP G C3L-00893_T 48382189 142917135 2221501 41 6829 EQTN 0 . GRCh38 9 27284898 27284898 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.710G>T p.Gly237Val p.G237V ENST00000380032 8/8 306 240 66 272 272 0 strelka-varscan-mutect EQTN,missense_variant,p.Gly237Val,ENST00000380032,NM_020641.2;EQTN,missense_variant,p.Gly208Val,ENST00000537675,NM_001161585.1; A ENST00000380032 Transcript missense_variant 794/1033 710/885 237/294 G/V gGt/gTt 1 -1 EQTN HGNC HGNC:1359 protein_coding YES CCDS35001.1 ENSP00000369371 Q9NQ60 UPI000013CA7C NM_020641.2 deleterious(0) 8/8 Pfam_domain:PF15339,hmmpanther:PTHR36874 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 27284898 27284898 C A 1 0 0 0 0 1 0 0 0 5050 507 18 2 2 EQTN 9 27284898 Missense_Mutation SNP C C3L-00893_T 27284898 111109819 42 6830 TMC1 0 . GRCh38 9 72754872 72754872 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.729G>T p.Leu243Phe p.L243F ENST00000297784 12/24 605 484 121 462 462 0 strelka-varscan-mutect TMC1,missense_variant,p.Leu243Phe,ENST00000297784,NM_138691.2;TMC1,missense_variant,p.Leu243Phe,ENST00000340019,; T ENST00000297784 Transcript missense_variant 1269/3201 729/2283 243/760 L/F ttG/ttT 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 deleterious(0) 12/24 hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 72754872 72754872 G T 1 0 0 0 0 1 0 0 0 16430 1368 48 2 2 TMC1 9 72754872 Missense_Mutation SNP G C3L-00893_T 45469974 72754872 65639845 43 6831 TMC1 0 . GRCh38 9 72821014 72821014 + Silent SNP C C T novel C3L-00893_T C3L-00893_N C C c.1936C>T p.= p.L646L ENST00000297784 20/24 930 710 220 659 659 0 strelka-varscan-mutect TMC1,synonymous_variant,p.=,ENST00000297784,NM_138691.2;TMC1,synonymous_variant,p.=,ENST00000340019,;TMC1,non_coding_transcript_exon_variant,,ENST00000486417,;TMC1,non_coding_transcript_exon_variant,,ENST00000469455,; T ENST00000297784 Transcript synonymous_variant 2476/3201 1936/2283 646/760 L Ctg/Ttg 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 20/24 Low_complexity_(Seg):seg,hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 72821014 72821014 C T 1 0 0 0 0 0 0 0 1 16430 680 24 3 3 TMC1 9 72821014 Silent SNP C C3L-00893_T 66142 72821014 65573703 44 6832 AGTPBP1 0 . GRCh38 9 85655277 85655277 + Missense_Mutation SNP G G A novel C3L-00893_T C3L-00893_N G G c.1109C>T p.Ser370Phe p.S370F ENST00000337006 10/25 180 168 12 188 188 0 strelka-varscan-mutect AGTPBP1,missense_variant,p.Ser370Phe,ENST00000337006,NM_001286715.1;AGTPBP1,missense_variant,p.Ser318Phe,ENST00000357081,;AGTPBP1,intron_variant,,ENST00000628899,NM_001286717.1;AGTPBP1,intron_variant,,ENST00000376083,NM_015239.2;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000376081,;AGTPBP1,downstream_gene_variant,,ENST00000491784,;AGTPBP1,downstream_gene_variant,,ENST00000376080,; A ENST00000337006 Transcript missense_variant 1176/4473 1109/3837 370/1278 S/F tCc/tTc 1 -1 AGTPBP1 HGNC HGNC:17258 protein_coding YES CCDS75854.1 ENSP00000338512 J3KNS1 UPI000387D56E NM_001286715.1 deleterious(0.02) 10/25 hmmpanther:PTHR12756:SF24,hmmpanther:PTHR12756 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -15.65796 0.9999996 1 1 1 0 A 3 1 20 85655277 85655277 G A 1 0 0 0 0 1 0 0 0 479 1174 41 3 3 AGTPBP1 9 85655277 Missense_Mutation SNP G C3L-00893_T 12834263 85655277 52739440 45 6833 SVEP1 0 . GRCh38 9 110471414 110471414 + Missense_Mutation SNP T T C novel C3L-00893_T C3L-00893_N T T c.2948A>G p.Lys983Arg p.K983R ENST00000374469 16/48 249 178 71 162 162 0 strelka-varscan-mutect SVEP1,missense_variant,p.Lys983Arg,ENST00000401783,;SVEP1,missense_variant,p.Lys983Arg,ENST00000374469,NM_153366.3;SVEP1,downstream_gene_variant,,ENST00000374461,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,; C ENST00000374469 Transcript missense_variant 3143/12194 2948/10716 983/3571 K/R aAg/aGg 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 tolerated(0.11) 16/48 MODERATE 1 SNV 5 1 PASS . . 0 203 0 5 2 0 0 0 -20 0.9766679 1 1 1 0 C 3 2 20 110471414 110471414 T C 1 0 0 0 0 1 0 0 0 15805 1609 56 5 5 SVEP1 9 110471414 Missense_Mutation SNP T C3L-00893_T 24816137 110471414 27923303 46 6834 ITIH5 0 . GRCh38 10 7579764 7579764 + Missense_Mutation SNP T T A novel C3L-00893_T C3L-00893_N T T c.1409A>T p.Gln470Leu p.Q470L ENST00000397146 9/14 153 112 41 137 137 0 strelka-varscan-mutect ITIH5,missense_variant,p.Gln470Leu,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Gln470Leu,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Gln256Leu,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,3_prime_UTR_variant,,ENST00000461751,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,upstream_gene_variant,,ENST00000468389,;ITIH5,upstream_gene_variant,,ENST00000492668,; A ENST00000397146 Transcript missense_variant 1488/6721 1409/2829 470/942 Q/L cAg/cTg 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 tolerated(0.09) 9/14 PROSITE_profiles:PS50234,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 7579764 7579764 T A 1 0 0 0 0 1 0 0 0 7813 1580 55 4 4 ITIH5 10 7579764 Missense_Mutation SNP T C3L-00893_T 7579764 126217658 47 6835 CCSER2 0 . GRCh38 10 84513890 84513902 + Frame_Shift_Del DEL TTAAAGCCATCCA TTAAAGCCATCCA - novel C3L-00893_T C3L-00893_N TTAAAGCCATCCA TTAAAGCCATCCA c.2768_2780delTAAAGCCATCCAT p.Leu923TyrfsTer2 p.L923Yfs*2 ENST00000372088 10/10 407 332 75 353 353 0 sindel-varindel-pindel CCSER2,frameshift_variant,p.Leu923TyrfsTer2,ENST00000372088,NM_001284240.1;CCSER2,3_prime_UTR_variant,,ENST00000224756,NM_018999.3;CCSER2,3_prime_UTR_variant,,ENST00000543283,NM_001284243.1;CCSER2,non_coding_transcript_exon_variant,,ENST00000494144,;CCSER2,downstream_gene_variant,,ENST00000493409,;CCSER2,downstream_gene_variant,,ENST00000498300,;CCSER2,downstream_gene_variant,,ENST00000480006,;CCSER2,downstream_gene_variant,,ENST00000466105,; - ENST00000372088 Transcript frameshift_variant 3026-3038/7657 2767-2779/3144 923-927/1047 LKPSI/X TTAAAGCCATCCAta/ta 1 1 CCSER2 HGNC HGNC:29197 protein_coding YES CCDS60582.1 ENSP00000361160 Q9H7U1 UPI00001F92C7 NM_001284240.1 10/10 Low_complexity_(Seg):seg HIGH 1 deletion 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 20 84513890 84513890 TTAAAGCCATCCA - 1 0 1 0 1 0 0 0 0 2653 1838 64 0 0 CCSER2 10 84513890 Frame_Shift_Del DEL TTAAAGCCATCCA C3L-00893_T 76934126 84513890 49283532 48 6836 CYP2C9 0 . GRCh38 10 94981351 94981351 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.1130G>T p.Arg377Ile p.R377I ENST00000260682 7/9 508 350 158 331 331 0 strelka-varscan-mutect CYP2C9,missense_variant,p.Arg377Ile,ENST00000260682,NM_000771.3; T ENST00000260682 Transcript missense_variant 1142/1847 1130/1473 377/490 R/I aGa/aTa 1 1 CYP2C9 HGNC HGNC:2623 protein_coding YES CCDS7437.1 ENSP00000260682 P11712 S5RV20 UPI0000128258 NM_000771.3 deleterious(0) 7/9 hmmpanther:PTHR24300:SF175,hmmpanther:PTHR24300,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 94981351 94981351 G T 1 0 0 0 0 1 0 0 0 3971 942 33 2 2 CYP2C9 10 94981351 Missense_Mutation SNP G C3L-00893_T 10467461 94981351 38816071 49 6837 GSTO2 0 . GRCh38 10 104297676 104297676 + Silent SNP G G C novel C3L-00893_T C3L-00893_N G G c.567G>C p.= p.G189G ENST00000338595 6/7 146 101 45 88 88 0 strelka-varscan-mutect GSTO2,synonymous_variant,p.=,ENST00000369707,NM_001191014.1;GSTO2,synonymous_variant,p.=,ENST00000450629,NM_001191013.1;GSTO2,synonymous_variant,p.=,ENST00000338595,NM_183239.1;GSTO2,non_coding_transcript_exon_variant,,ENST00000473401,;GSTO2,non_coding_transcript_exon_variant,,ENST00000467629,;GSTO2,non_coding_transcript_exon_variant,,ENST00000498052,; C ENST00000338595 Transcript synonymous_variant 887/1179 567/732 189/243 G ggG/ggC 1 1 GSTO2 HGNC HGNC:23064 protein_coding YES CCDS7556.1 ENSP00000345023 Q9H4Y5 UPI000004D293 NM_183239.1 6/7 PROSITE_profiles:PS50405,hmmpanther:PTHR11260,hmmpanther:PTHR11260:SF197,Gene3D:1.20.1050.10,Pfam_domain:PF13410,Superfamily_domains:SSF47616 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 20 104297676 104297676 G C 1 0 0 0 0 0 0 0 1 6727 1161 41 4 4 GSTO2 10 104297676 Silent SNP G C3L-00893_T 9316325 104297676 29499746 50 6838 RRM1 0 . GRCh38 11 4111995 4111995 + Missense_Mutation SNP G G A novel C3L-00893_T C3L-00893_N G G c.583G>A p.Glu195Lys p.E195K ENST00000300738 7/19 148 124 24 97 97 0 strelka-varscan-mutect RRM1,missense_variant,p.Glu195Lys,ENST00000300738,NM_001033.3;RRM1,upstream_gene_variant,,ENST00000534285,;RRM1,downstream_gene_variant,,ENST00000532710,;RRM1,missense_variant,p.Glu8Lys,ENST00000528442,;RRM1,3_prime_UTR_variant,,ENST00000532170,;RRM1,3_prime_UTR_variant,,ENST00000533349,NM_001318064.1;RRM1,upstream_gene_variant,,ENST00000533495,NM_001318065.1;RRM1,downstream_gene_variant,,ENST00000526350,; A ENST00000300738 Transcript missense_variant 787/3076 583/2379 195/792 E/K Gag/Aag 1 1 RRM1 HGNC HGNC:10451 protein_coding YES CCDS7750.1 ENSP00000300738 P23921 UPI0000000C7C NM_001033.3 tolerated_low_confidence(0.17) 7/19 hmmpanther:PTHR11573,Pfam_domain:PF00317,Gene3D:3.20.70.20,TIGRFAM_domain:TIGR02506,Superfamily_domains:SSF48168 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 4111995 4111995 G A 1 0 0 0 0 1 0 0 0 13935 1291 45 3 3 RRM1 11 4111995 Missense_Mutation SNP G C3L-00893_T 4111995 130974627 51 6839 OR52A5 0 . GRCh38 11 5132438 5132438 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.205G>T p.Ala69Ser p.A69S ENST00000307388 1/1 126 100 26 107 107 0 strelka-varscan-mutect OR52A5,missense_variant,p.Ala69Ser,ENST00000307388,NM_001005160.2; A ENST00000307388 Transcript missense_variant 205/951 205/951 69/316 A/S Gca/Tca 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 tolerated(0.11) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1463532884 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 5132438 5132438 C A 1 0 0 0 0 1 0 0 0 11183 739 26 2 2 OR52A5 11 5132438 Missense_Mutation SNP C C3L-00893_T 1020443 5132438 129954184 52 6840 HBD 0 . GRCh38 11 5234012 5234012 + Missense_Mutation SNP G G T rs61746501 C3L-00893_T C3L-00893_N G G c.294C>A p.His98Gln p.H98Q ENST00000380299 2/3 574 425 149 476 476 0 strelka-varscan-mutect HBD,missense_variant,p.His98Gln,ENST00000380299,NM_000519.3;HBD,missense_variant,p.His98Gln,ENST00000429817,;HBD,missense_variant,p.His98Gln,ENST00000292901,;HBD,intron_variant,,ENST00000417377,;HBB,upstream_gene_variant,,ENST00000380315,; T ENST00000380299 Transcript missense_variant 509/785 294/444 98/147 H/Q caC/caA rs61746501 1 -1 HBD HGNC HGNC:4829 protein_coding YES CCDS31376.1 ENSP00000369654 P02042 A0N071 UPI0000161DC2 NM_000519.3 deleterious(0.02) 2/3 PROSITE_profiles:PS01033,hmmpanther:PTHR11442:SF50,hmmpanther:PTHR11442,Pfam_domain:PF00042,Gene3D:1.10.490.10,Superfamily_domains:SSF46458,Prints_domain:PR00814 MODERATE 1 SNV 1 1 PASS rs61746501 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 5234012 5234012 G T 1 0 0 0 0 1 0 0 0 6865 1136 40 1 1 HBD 11 5234012 Missense_Mutation SNP G C3L-00893_T 101574 5234012 129852610 53 6841 IGSF22 0 . GRCh38 11 18706935 18706935 + Missense_Mutation SNP A A T novel C3L-00893_T C3L-00893_N A A c.3559T>A p.Trp1187Arg p.W1187R ENST00000513874 21/23 47 30 17 34 34 0 strelka-varscan-mutect IGSF22,missense_variant,p.Trp1187Arg,ENST00000513874,NM_173588.3;TMEM86A,downstream_gene_variant,,ENST00000280734,NM_153347.2;RP11-1081L13.4,non_coding_transcript_exon_variant,,ENST00000527285,;IGSF22,upstream_gene_variant,,ENST00000510673,;IGSF22,3_prime_UTR_variant,,ENST00000319338,;IGSF22,downstream_gene_variant,,ENST00000504981,; T ENST00000513874 Transcript missense_variant 3699/4284 3559/3981 1187/1326 W/R Tgg/Agg 1 -1 IGSF22 HGNC HGNC:26750 protein_coding YES CCDS41625.2 ENSP00000421191 Q8N9C0 UPI0001D3B05B NM_173588.3 deleterious(0.01) 21/23 PROSITE_profiles:PS50853 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 18706935 18706935 A T 1 0 0 0 0 1 0 0 0 7507 188 7 4 4 IGSF22 11 18706935 Missense_Mutation SNP A C3L-00893_T 13472923 18706935 116379687 54 6842 DYNC2H1 0 . GRCh38 11 103253363 103253363 + Missense_Mutation SNP A A T novel C3L-00893_T C3L-00893_N A A c.10142A>T p.Asn3381Ile p.N3381I ENST00000398093 67/90 167 137 30 63 63 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Asn3374Ile,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Asn3381Ile,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,; T ENST00000398093 Transcript missense_variant 10142/12945 10142/12945 3381/4314 N/I aAc/aTc 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0) 67/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF12781 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 103253363 103253363 A T 1 0 0 0 0 1 0 0 0 4670 43 2 4 4 DYNC2H1 11 103253363 Missense_Mutation SNP A C3L-00893_T 84546428 103253363 31833259 55 6843 ANO2 0 . GRCh38 12 5922646 5922646 + Missense_Mutation SNP C C T C3L-00893_T C3L-00893_N C C c.169G>A p.Gly57Ser p.G57S ENST00000356134 2/27 124 111 13 134 134 0 strelka-varscan-mutect ANO2,missense_variant,p.Gly57Ser,ENST00000327087,;ANO2,missense_variant,p.Gly57Ser,ENST00000356134,NM_001278597.1,NM_001278596.1;ANO2,missense_variant,p.Gly61Ser,ENST00000546188,; T ENST00000356134 Transcript missense_variant 241/3717 169/3000 57/999 G/S Ggt/Agt COSM5375739,COSM5375740,COSM5375741 1 -1 ANO2 HGNC HGNC:1183 protein_coding YES CCDS44807.2 ENSP00000348453 Q9NQ90 UPI00000715DF NM_001278597.1,NM_001278596.1 tolerated_low_confidence(0.54) 2/27 hmmpanther:PTHR12308:SF20,hmmpanther:PTHR12308 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs943604098 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 5922646 5922646 C T 1 0 0 0 0 1 0 0 0 804 652 23 1 1 ANO2 12 5922646 Missense_Mutation SNP C C3L-00893_T 5922646 127352663 56 6844 ASIC1 0 . GRCh38 12 50059859 50059859 + Missense_Mutation SNP C C T novel C3L-00893_T C3L-00893_N C C c.463C>T p.Arg155Cys p.R155C ENST00000228468 3/12 338 275 63 233 233 0 strelka-varscan-mutect ASIC1,missense_variant,p.Arg155Cys,ENST00000228468,NM_020039.3;ASIC1,missense_variant,p.Arg155Cys,ENST00000447966,NM_001095.3;ASIC1,upstream_gene_variant,,ENST00000453327,;ASIC1,missense_variant,p.Arg155Cys,ENST00000550558,; T ENST00000228468 Transcript missense_variant 848/4072 463/1725 155/574 R/C Cgt/Tgt 1 1 ASIC1 HGNC HGNC:100 protein_coding YES CCDS8796.1 ENSP00000228468 P78348 UPI000013C8D6 NM_020039.3 tolerated(0.18) 3/12 hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF170,Gene3D:2qtsA03,Pfam_domain:PF00858 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 50059859 50059859 C T 1 0 0 0 0 1 0 0 0 1185 768 27 1 1 ASIC1 12 50059859 Missense_Mutation SNP C C3L-00893_T 44137213 50059859 83215450 57 6845 GALNT6 0 . GRCh38 12 51377344 51377344 + Missense_Mutation SNP C C G rs146516622 C3L-00893_T C3L-00893_N C C c.515G>C p.Arg172Pro p.R172P ENST00000543196 3/11 329 237 92 190 190 0 strelka-varscan-mutect GALNT6,missense_variant,p.Arg172Pro,ENST00000543196,;GALNT6,missense_variant,p.Arg172Pro,ENST00000356317,NM_007210.3;GALNT6,downstream_gene_variant,,ENST00000603563,;GALNT6,downstream_gene_variant,,ENST00000605138,;GALNT6,downstream_gene_variant,,ENST00000605617,;GALNT6,downstream_gene_variant,,ENST00000603188,;GALNT6,downstream_gene_variant,,ENST00000604506,;GALNT6,downstream_gene_variant,,ENST00000604381,;GALNT6,downstream_gene_variant,,ENST00000604847,;GALNT6,downstream_gene_variant,,ENST00000605055,;GALNT6,downstream_gene_variant,,ENST00000604426,;GALNT6,downstream_gene_variant,,ENST00000603203,;GALNT6,downstream_gene_variant,,ENST00000605089,;GALNT6,downstream_gene_variant,,ENST00000605822,;GALNT6,downstream_gene_variant,,ENST00000603482,;GALNT6,missense_variant,p.Arg172Pro,ENST00000603641,; G ENST00000543196 Transcript missense_variant 721/5207 515/1869 172/622 R/P cGc/cCc rs146516622 1 -1 GALNT6 HGNC HGNC:4128 protein_coding YES CCDS8813.1 ENSP00000444171 Q8NCL4 UPI000013D726 tolerated(0.1) 3/11 hmmpanther:PTHR11675:SF58,hmmpanther:PTHR11675,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs146516622 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 20 51377344 51377344 C G 1 0 0 0 0 1 0 0 0 6088 768 27 4 4 GALNT6 12 51377344 Missense_Mutation SNP C C3L-00893_T 1317485 51377344 81897965 58 6846 ALX1 0 . GRCh38 12 85283634 85283634 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.289G>T p.Asp97Tyr p.D97Y ENST00000316824 2/4 296 208 88 217 217 0 strelka-varscan-mutect ALX1,missense_variant,p.Asp97Tyr,ENST00000316824,NM_006982.2; T ENST00000316824 Transcript missense_variant 444/1445 289/981 97/326 D/Y Gac/Tac 1 1 ALX1 HGNC HGNC:1494 protein_coding YES CCDS9028.1 ENSP00000315417 Q15699 V9HWA7 UPI000013FEBD NM_006982.2 deleterious(0) 2/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF359 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 85283634 85283634 G T 1 0 0 0 0 1 0 0 0 654 1174 41 2 2 ALX1 12 85283634 Missense_Mutation SNP G C3L-00893_T 33906290 85283634 47991675 59 6847 GALNT9 0 . GRCh38 12 132261028 132261028 + Silent SNP G G T rs782365196 C3L-00893_T C3L-00893_N G G c.681C>A p.= p.R227R ENST00000328957 4/11 176 133 43 203 203 0 strelka-varscan-mutect GALNT9,synonymous_variant,p.=,ENST00000328957,;GALNT9,upstream_gene_variant,,ENST00000411988,;GALNT9,non_coding_transcript_exon_variant,,ENST00000535208,;GALNT9,non_coding_transcript_exon_variant,,ENST00000424720,; T ENST00000328957 Transcript synonymous_variant 681/2410 681/1812 227/603 R cgC/cgA rs782365196 1 -1 GALNT9 HGNC HGNC:4131 protein_coding ENSP00000329846 J3KNN1 UPI00004566BE 4/11 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF28,Gene3D:3.90.550.10,Pfam_domain:PF00535,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS rs782365196 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 132261028 132261028 G T 1 0 0 0 0 0 0 0 1 6091 1074 38 1 1 GALNT9 12 132261028 Silent SNP G C3L-00893_T 46977394 132261028 1014281 60 6848 DACH1 0 . GRCh38 13 71559867 71559867 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.1388G>T p.Ser463Ile p.S463I ENST00000613252 5/11 103 73 30 106 106 0 strelka-varscan-mutect DACH1,missense_variant,p.Ser463Ile,ENST00000613252,NM_080759.5;DACH1,missense_variant,p.Ser515Ile,ENST00000619232,;DACH1,intron_variant,,ENST00000611519,NM_080760.5;DACH1,intron_variant,,ENST00000620444,NM_004392.6; A ENST00000613252 Transcript missense_variant 1811/5233 1388/2121 463/706 S/I aGc/aTc 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 deleterious_low_confidence(0) 5/11 Low_complexity_(Seg):seg,hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 71559867 71559867 C A 1 0 0 0 0 1 0 0 0 4021 797 28 2 2 DACH1 13 71559867 Missense_Mutation SNP C C3L-00893_T 71559867 42804461 61 6849 OR4K17 0 . GRCh38 14 20118326 20118326 + Missense_Mutation SNP C C T novel C3L-00893_T C3L-00893_N C C c.920C>T p.Thr307Ile p.T307I ENST00000315543 1/1 201 162 39 159 158 1 strelka-varscan-mutect OR4K17,missense_variant,p.Thr307Ile,ENST00000315543,NM_001004715.1; T ENST00000315543 Transcript missense_variant 920/1032 920/1032 307/343 T/I aCc/aTc 1 1 OR4K17 HGNC HGNC:15355 protein_coding YES CCDS32030.1 ENSP00000319197 Q8NGC6 A0A126GVZ4 UPI000004B1EA NM_001004715.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF322,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1332380344 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 20118326 20118326 C T 1 0 0 0 0 1 0 0 0 11148 507 18 3 3 OR4K17 14 20118326 Missense_Mutation SNP C C3L-00893_T 20118326 86925392 62 6850 NKX2-1 0 . GRCh38 14 36517753 36517753 + Missense_Mutation SNP T T C novel C3L-00893_T C3L-00893_N T T c.731A>G p.Tyr244Cys p.Y244C ENST00000354822 3/3 826 756 70 639 639 0 strelka-varscan-mutect NKX2-1,missense_variant,p.Tyr214Cys,ENST00000518149,;NKX2-1,missense_variant,p.Tyr214Cys,ENST00000498187,NM_003317.3;NKX2-1,missense_variant,p.Tyr244Cys,ENST00000354822,NM_001079668.2;NKX2-1,missense_variant,p.Tyr214Cys,ENST00000522719,;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000546983,;RP11-964E11.3,intron_variant,,ENST00000634305,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; C ENST00000354822 Transcript missense_variant 830/2191 731/1206 244/401 Y/C tAc/tGc 1 -1 NKX2-1 HGNC HGNC:11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 UPI000007328C NM_001079668.2 deleterious(0) 3/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF33,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 20 36517753 36517753 T C 1 0 0 0 0 1 0 0 0 10485 1638 57 5 5 NKX2-1 14 36517753 Missense_Mutation SNP T C3L-00893_T 16399427 36517753 70525965 63 6851 SLC35F4 0 . GRCh38 14 57581350 57581350 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.671C>A p.Thr224Asn p.T224N ENST00000556826 4/8 174 136 38 137 137 0 strelka-varscan-mutect SLC35F4,missense_variant,p.Thr224Asn,ENST00000556826,NM_001306087.1,NM_001206920.1;SLC35F4,missense_variant,p.Thr260Asn,ENST00000339762,;SLC35F4,missense_variant,p.Thr101Asn,ENST00000554729,;RP11-409I10.2,downstream_gene_variant,,ENST00000555600,;SLC35F4,missense_variant,p.Thr101Asn,ENST00000557254,;SLC35F4,upstream_gene_variant,,ENST00000556306,; T ENST00000556826 Transcript missense_variant 908/1908 671/1458 224/485 T/N aCt/aAt 1 -1 SLC35F4 HGNC HGNC:19845 protein_coding YES CCDS76684.1 ENSP00000452086 G3V4Z9 UPI000045678B NM_001306087.1,NM_001206920.1 deleterious(0) 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR19346:SF2,hmmpanther:PTHR19346,Superfamily_domains:0043518,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 57581350 57581350 G T 1 0 0 0 0 1 0 0 0 14862 1029 36 2 2 SLC35F4 14 57581350 Missense_Mutation SNP G C3L-00893_T 21063597 57581350 49462368 64 6852 UNC79 0 . GRCh38 14 93477703 93477703 + Missense_Mutation SNP C C G novel C3L-00893_T C3L-00893_N C C c.63C>G p.Ser21Arg p.S21R ENST00000256339 4/50 69 53 16 37 37 0 strelka-varscan-mutect UNC79,missense_variant,p.Ser198Arg,ENST00000553484,;UNC79,missense_variant,p.Ser198Arg,ENST00000555664,;UNC79,missense_variant,p.Ser21Arg,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Ser198Arg,ENST00000393151,;UNC79,missense_variant,p.Ser21Arg,ENST00000621021,; G ENST00000256339 Transcript missense_variant 718/8400 63/7377 21/2458 S/R agC/agG 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious(0) 4/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696,Pfam_domain:PF14776 MODERATE 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999974 1 1 1 0 G 3 3 20 93477703 93477703 C G 1 0 0 0 0 1 0 0 0 17520 709 25 4 4 UNC79 14 93477703 Missense_Mutation SNP C C3L-00893_T 35896353 93477703 13566015 65 6853 AVEN 0 . GRCh38 15 34003157 34003157 + Missense_Mutation SNP C C T novel C3L-00893_T C3L-00893_N C C c.320G>A p.Gly107Glu p.G107E ENST00000306730 2/6 136 93 43 118 118 0 strelka-varscan-mutect AVEN,missense_variant,p.Gly107Glu,ENST00000306730,NM_020371.2;CHRM5,intron_variant,,ENST00000383263,NM_012125.3;CHRM5,intron_variant,,ENST00000560035,; T ENST00000306730 Transcript missense_variant 450/1605 320/1089 107/362 G/E gGa/gAa 1 -1 AVEN HGNC HGNC:13509 protein_coding YES CCDS10030.1 ENSP00000306822 Q9NQS1 UPI000012666A NM_020371.2 tolerated(0.33) 2/6 hmmpanther:PTHR16524 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 34003157 34003157 C T 1 0 0 0 0 1 0 0 0 1382 855 30 3 3 AVEN 15 34003157 Missense_Mutation SNP C C3L-00893_T 34003157 67988032 66 6854 CELF6 0 . GRCh38 15 72290226 72290226 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.424G>T p.Gly142Cys p.G142C ENST00000287202 4/13 182 135 47 153 153 0 strelka-varscan-mutect CELF6,missense_variant,p.Gly142Cys,ENST00000287202,NM_052840.4;CELF6,missense_variant,p.Gly29Cys,ENST00000395258,;CELF6,missense_variant,p.Gly27Cys,ENST00000543764,NM_001172685.1;CELF6,missense_variant,p.Gly142Cys,ENST00000567083,NM_001172684.1;RP11-106M3.3,intron_variant,,ENST00000570175,;CELF6,missense_variant,p.Trp96Cys,ENST00000437872,;RP11-106M3.5,missense_variant,p.Gly142Cys,ENST00000569547,;RP11-106M3.2,3_prime_UTR_variant,,ENST00000379915,; A ENST00000287202 Transcript missense_variant 679/3345 424/1446 142/481 G/C Ggc/Tgc 1 -1 CELF6 HGNC HGNC:14059 protein_coding YES CCDS10242.1 ENSP00000287202 Q96J87 UPI000006F0AA NM_052840.4 deleterious(0.04) 4/13 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF385,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 72290226 72290226 C A 1 0 0 0 0 1 0 0 0 2927 623 22 2 2 CELF6 15 72290226 Missense_Mutation SNP C C3L-00893_T 38287069 72290226 29700963 67 6855 ISL2 0 . GRCh38 15 76340542 76340542 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.778C>A p.Gln260Lys p.Q260K ENST00000290759 4/6 110 76 34 97 97 0 strelka-varscan-mutect ISL2,missense_variant,p.Gln260Lys,ENST00000290759,NM_145805.2;RP11-685G9.4,upstream_gene_variant,,ENST00000602530,;RP11-685G9.2,intron_variant,,ENST00000559539,;ISL2,missense_variant,p.Ala172Glu,ENST00000558656,;ISL2,downstream_gene_variant,,ENST00000558437,; A ENST00000290759 Transcript missense_variant 938/1881 778/1080 260/359 Q/K Cag/Aag 1 1 ISL2 HGNC HGNC:18524 protein_coding YES CCDS10290.1 ENSP00000290759 Q96A47 UPI000012D8FC NM_145805.2 tolerated(0.25) 4/6 hmmpanther:PTHR24204:SF2,hmmpanther:PTHR24204 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 76340542 76340542 C A 1 0 0 0 0 1 0 0 0 7764 711 25 2 2 ISL2 15 76340542 Missense_Mutation SNP C C3L-00893_T 4050316 76340542 25650647 68 6856 CACNA1H 0 . GRCh38 16 1209319 1209319 + Silent SNP C C T novel C3L-00893_T C3L-00893_N C C c.3651C>T p.= p.R1217R ENST00000348261 17/35 453 409 44 522 522 0 strelka-varscan-mutect CACNA1H,synonymous_variant,p.=,ENST00000348261,NM_021098.2;CACNA1H,synonymous_variant,p.=,ENST00000358590,NM_001005407.1;CACNA1H,synonymous_variant,p.=,ENST00000565831,;CACNA1H,upstream_gene_variant,,ENST00000569107,;CACNA1H,upstream_gene_variant,,ENST00000564231,;CACNA1H,upstream_gene_variant,,ENST00000562079,;RP11-616M22.3,upstream_gene_variant,,ENST00000564700,;CACNA1H,upstream_gene_variant,,ENST00000637236,;CACNA1H,upstream_gene_variant,,ENST00000569953,; T ENST00000348261 Transcript synonymous_variant 4019/8208 3651/7062 1217/2353 R cgC/cgT 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 17/35 LOW 1 SNV 1 1 PASS rs929083218 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 20 1209319 1209319 C T 1 0 0 0 0 0 0 0 1 2233 755 27 1 1 CACNA1H 16 1209319 Silent SNP C C3L-00893_T 1209319 89129026 69 6857 SALL1 0 . GRCh38 16 51138908 51138908 + Missense_Mutation SNP G G T novel C3L-00893_T C3L-00893_N G G c.3314C>A p.Thr1105Asn p.T1105N ENST00000251020 2/3 733 547 186 443 443 0 strelka-varscan-mutect SALL1,missense_variant,p.Thr1008Asn,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Thr1105Asn,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Thr1008Asn,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; T ENST00000251020 Transcript missense_variant 3348/5146 3314/3975 1105/1324 T/N aCc/aAc 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.19) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 51138908 51138908 G T 1 0 0 0 0 1 0 0 0 14069 1261 44 2 2 SALL1 16 51138908 Missense_Mutation SNP G C3L-00893_T 49929589 51138908 39199437 70 6858 WDR81 0 . GRCh38 17 1726296 1726296 + Missense_Mutation SNP C C G novel C3L-00893_T C3L-00893_N C C c.1337C>G p.Ser446Cys p.S446C ENST00000409644 1/10 74 59 15 48 48 0 strelka-varscan-mutect WDR81,missense_variant,p.Ser446Cys,ENST00000409644,NM_001163809.1;WDR81,intron_variant,,ENST00000309182,NM_152348.3;WDR81,intron_variant,,ENST00000419248,NM_001163811.1;WDR81,intron_variant,,ENST00000437219,NM_001163673.1;WDR81,intron_variant,,ENST00000446363,;WDR81,intron_variant,,ENST00000418841,;WDR81,intron_variant,,ENST00000455636,;WDR81,intron_variant,,ENST00000468539,;WDR81,upstream_gene_variant,,ENST00000575206,;RP11-961A15.1,intron_variant,,ENST00000576540,;WDR81,intron_variant,,ENST00000492901,;WDR81,upstream_gene_variant,,ENST00000464528,;WDR81,upstream_gene_variant,,ENST00000479966,;WDR81,upstream_gene_variant,,ENST00000474958,;WDR81,upstream_gene_variant,,ENST00000495411,; G ENST00000409644 Transcript missense_variant 1337/6733 1337/5826 446/1941 S/C tCc/tGc 1 1 WDR81 HGNC HGNC:26600 protein_coding YES CCDS54062.1 ENSP00000386609 Q562E7 UPI0001881A85 NM_001163809.1 deleterious(0) 1/10 PROSITE_profiles:PS50197,Pfam_domain:PF02138,Gene3D:1t77A02,SMART_domains:SM01026,Superfamily_domains:SSF81837 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 20 1726296 1726296 C G 1 0 0 0 0 1 0 0 0 17885 855 30 4 4 WDR81 17 1726296 Missense_Mutation SNP C C3L-00893_T 1726296 81531145 71 6859 PPM1D 0 . GRCh38 17 60663148 60663148 + Nonsense_Mutation SNP G G T C3L-00893_T C3L-00893_N G G c.1414G>T p.Glu472Ter p.E472* ENST00000305921 6/6 271 210 61 220 220 0 strelka-varscan-mutect PPM1D,stop_gained,p.Glu472Ter,ENST00000305921,NM_003620.3;AC110602.1,upstream_gene_variant,,ENST00000625901,;RNU6-623P,upstream_gene_variant,,ENST00000363143,;PPM1D,3_prime_UTR_variant,,ENST00000392995,; T ENST00000305921 Transcript stop_gained 1646/4778 1414/1818 472/605 E/* Gaa/Taa COSM1736844 1 1 PPM1D HGNC HGNC:9277 protein_coding YES CCDS11625.1 ENSP00000306682 O15297 A0A0S2Z4M2 UPI0000130FE8 NM_003620.3 6/6 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 20 60663148 60663148 G T 1 0 0 0 0 0 1 0 0 12447 943 33 2 2 PPM1D 17 60663148 Nonsense_Mutation SNP G C3L-00893_T 58936852 60663148 22594293 72 6860 DNAH17 0 . GRCh38 17 78507533 78507533 + Missense_Mutation SNP G G T rs780954162 C3L-00893_T C3L-00893_N G G c.4509C>A p.Phe1503Leu p.F1503L ENST00000389840 28/81 334 227 107 186 186 0 strelka-varscan-mutect DNAH17,missense_variant,p.Phe1503Leu,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Phe1500Leu,ENST00000585328,;DNAH17,non_coding_transcript_exon_variant,,ENST00000587177,;DNAH17-AS1,downstream_gene_variant,,ENST00000598378,; T ENST00000389840 Transcript missense_variant 4634/13723 4509/13389 1503/4462 F/L ttC/ttA rs780954162 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 28/81 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE SNV 5 1 PASS rs780954162 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 78507533 78507533 G T 1 0 0 0 0 1 0 0 0 4416 1281 45 2 2 DNAH17 17 78507533 Missense_Mutation SNP G C3L-00893_T 17844385 78507533 4749908 73 6861 YES1 0 . GRCh38 18 751806 751806 + Splice_Site SNP T T C novel C3L-00893_T C3L-00893_N T T c.272-2A>G p.X91_splice ENST00000584307 39 25 14 41 41 0 strelka-varscan-mutect YES1,splice_acceptor_variant,,ENST00000584307,;YES1,splice_acceptor_variant,,ENST00000577961,;YES1,splice_acceptor_variant,,ENST00000314574,NM_005433.3;YES1,splice_acceptor_variant,,ENST00000577611,;YES1,downstream_gene_variant,,ENST00000581960,; C ENST00000584307 Transcript splice_acceptor_variant -/4639 272/1632 91/543 1 -1 YES1 HGNC HGNC:12841 protein_coding YES CCDS11824.1 ENSP00000462468 P07947 UPI0000062316 2/11 HIGH 1 SNV 1 1 PASS rs542657377 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 20 751806 751806 T C 1 0 0 0 0 0 0 1 0 18036 1536 53 5 5 YES1 18 751806 Splice_Site SNP T C3L-00893_T 751806 79621479 74 6862 NFATC1 0 . GRCh38 18 79448897 79448897 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.1502C>A p.Thr501Asn p.T501N ENST00000427363 4/10 422 312 110 385 383 2 strelka-varscan-mutect NFATC1,missense_variant,p.Thr501Asn,ENST00000591814,NM_172390.2;NFATC1,missense_variant,p.Thr501Asn,ENST00000253506,NM_006162.4;NFATC1,missense_variant,p.Thr488Asn,ENST00000329101,NM_172387.2;NFATC1,missense_variant,p.Thr488Asn,ENST00000318065,NM_172389.2;NFATC1,missense_variant,p.Thr29Asn,ENST00000545796,NM_001278673.1;NFATC1,missense_variant,p.Thr29Asn,ENST00000397790,NM_172388.2;NFATC1,missense_variant,p.Thr501Asn,ENST00000427363,NM_001278669.1;NFATC1,missense_variant,p.Thr488Asn,ENST00000592223,NM_001278675.1;NFATC1,missense_variant,p.Thr501Asn,ENST00000587635,;NFATC1,missense_variant,p.Thr501Asn,ENST00000542384,NM_001278670.1;NFATC1,missense_variant,p.Thr488Asn,ENST00000586434,NM_001278672.1;NFATC1,non_coding_transcript_exon_variant,,ENST00000590224,;NFATC1,3_prime_UTR_variant,,ENST00000590313,;NFATC1,non_coding_transcript_exon_variant,,ENST00000591065,;NFATC1,upstream_gene_variant,,ENST00000591089,; A ENST00000427363 Transcript missense_variant 1502/2832 1502/2832 501/943 T/N aCc/aAc 1 1 NFATC1 HGNC HGNC:7775 protein_coding YES CCDS62467.1 ENSP00000389377 O95644 UPI000012FFB5 NM_001278669.1 deleterious(0) 4/10 PROSITE_profiles:PS50254,hmmpanther:PTHR12533:SF5,hmmpanther:PTHR12533,Gene3D:2.60.40.340,Pfam_domain:PF00554,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 79448897 79448897 C A 1 0 0 0 0 1 0 0 0 10398 507 18 2 2 NFATC1 18 79448897 Missense_Mutation SNP C C3L-00893_T 78697091 79448897 924388 75 6863 MUC16 0 . GRCh38 19 8938522 8938522 + Silent SNP C C T novel C3L-00893_T C3L-00893_N C C c.32433G>A p.= p.L10811L ENST00000397910 5/84 336 261 75 287 287 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 32637/43816 32433/43524 10811/14507 L ctG/ctA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 LOW 1 SNV 5 1 PASS rs1238667852 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 8938522 8938522 C T 1 0 0 0 0 0 0 0 1 9972 813 29 3 3 MUC16 19 8938522 Silent SNP C C3L-00893_T 8938522 49679094 76 6864 ELAVL3 0 . GRCh38 19 11458139 11458139 + Missense_Mutation SNP T T A novel C3L-00893_T C3L-00893_N T T c.635A>T p.Gln212Leu p.Q212L ENST00000359227 5/7 629 438 191 421 419 2 strelka-varscan-mutect ELAVL3,missense_variant,p.Gln212Leu,ENST00000359227,NM_001420.3;ELAVL3,missense_variant,p.Gln212Leu,ENST00000438662,NM_032281.2; A ENST00000359227 Transcript missense_variant 1060/4729 635/1104 212/367 Q/L cAg/cTg 1 -1 ELAVL3 HGNC HGNC:3314 protein_coding YES CCDS32912.1 ENSP00000352162 Q14576 UPI0000129E75 NM_001420.3 tolerated(0.23) 5/7 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF351,TIGRFAM_domain:TIGR01661,Superfamily_domains:SSF54928 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 11458139 11458139 T A 1 0 0 0 0 1 0 0 0 4884 1580 55 4 4 ELAVL3 19 11458139 Missense_Mutation SNP T C3L-00893_T 2519617 11458139 47159477 77 6865 EPS8L1 0 . GRCh38 19 55086881 55086881 + Missense_Mutation SNP A A C novel C3L-00893_T C3L-00893_N A A c.1945A>C p.Ser649Arg p.S649R ENST00000201647 18/20 43 33 10 44 44 0 strelka-varscan-mutect EPS8L1,missense_variant,p.Ser649Arg,ENST00000201647,NM_133180.2;EPS8L1,missense_variant,p.Ser585Arg,ENST00000540810,;EPS8L1,missense_variant,p.Ser522Arg,ENST00000245618,NM_017729.3;EPS8L1,missense_variant,p.Ser335Arg,ENST00000588359,;EPS8L1,intron_variant,,ENST00000586329,;PPP1R12C,downstream_gene_variant,,ENST00000263433,NM_017607.3,NM_001271618.1;PPP1R12C,downstream_gene_variant,,ENST00000435544,;PPP1R12C,downstream_gene_variant,,ENST00000592993,;PPP1R12C,downstream_gene_variant,,ENST00000591938,;EPS8L1,non_coding_transcript_exon_variant,,ENST00000587901,;EPS8L1,downstream_gene_variant,,ENST00000592824,;EPS8L1,downstream_gene_variant,,ENST00000585347,;EPS8L1,non_coding_transcript_exon_variant,,ENST00000592102,;EPS8L1,non_coding_transcript_exon_variant,,ENST00000589362,;EPS8L1,downstream_gene_variant,,ENST00000587786,;PPP1R12C,downstream_gene_variant,,ENST00000590268,;EPS8L1,upstream_gene_variant,,ENST00000587715,;EPS8L1,downstream_gene_variant,,ENST00000592284,;EPS8L1,downstream_gene_variant,,ENST00000590610,;EPS8L1,downstream_gene_variant,,ENST00000589694,; C ENST00000201647 Transcript missense_variant 2001/2536 1945/2172 649/723 S/R Agc/Cgc 1 1 EPS8L1 HGNC HGNC:21295 protein_coding YES CCDS12914.1 ENSP00000201647 Q8TE68 UPI000013C630 NM_133180.2 deleterious(0) 18/20 hmmpanther:PTHR12287,hmmpanther:PTHR12287:SF19 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99999 1 1 1 1 0 C 3 2 20 55086881 55086881 A C 1 0 0 0 0 1 0 0 0 5043 420 15 5 5 EPS8L1 19 55086881 Missense_Mutation SNP A C3L-00893_T 43628742 55086881 3530735 78 6866 ZNF304 0 . GRCh38 19 57356228 57356228 + Missense_Mutation SNP G G A novel C3L-00893_T C3L-00893_N G G c.500G>A p.Gly167Glu p.G167E ENST00000443917 4/4 232 182 50 152 152 0 strelka-varscan-mutect ZNF304,missense_variant,p.Gly120Glu,ENST00000391705,NM_020657.3;ZNF304,missense_variant,p.Gly120Glu,ENST00000282286,;ZNF304,missense_variant,p.Gly167Glu,ENST00000443917,NM_001290318.1;ZNF304,missense_variant,p.Gly78Glu,ENST00000598744,NM_001290319.1;CTC-444N24.13,upstream_gene_variant,,ENST00000597973,; A ENST00000443917 Transcript missense_variant 839/3391 500/2121 167/706 G/E gGg/gAg 1 1 ZNF304 HGNC HGNC:13505 protein_coding YES CCDS77365.1 ENSP00000401642 E7EQD3 UPI00015DFA73 NM_001290318.1 tolerated(0.25) 4/4 PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF205,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 57356228 57356228 G A 1 0 0 0 0 1 0 0 0 18408 1232 43 3 3 ZNF304 19 57356228 Missense_Mutation SNP G C3L-00893_T 2269347 57356228 1261388 79 6867 SIGLEC1 0 . GRCh38 20 3690135 3690135 + Missense_Mutation SNP G G T rs746740761 C3L-00893_T C3L-00893_N G G c.4721C>A p.Ala1574Asp p.A1574D ENST00000344754 18/21 347 248 99 271 271 0 strelka-varscan-mutect SIGLEC1,missense_variant,p.Ala1574Asp,ENST00000344754,NM_023068.3;SIGLEC1,missense_variant,p.Ala388Asp,ENST00000419548,; T ENST00000344754 Transcript missense_variant 4721/6720 4721/5130 1574/1709 A/D gCc/gAc rs746740761 1 -1 SIGLEC1 HGNC HGNC:11127 protein_coding YES CCDS13060.1 ENSP00000341141 Q9BZZ2 UPI0000049BA6 NM_023068.3 deleterious(0) 18/21 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF70,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs746740761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 3690135 3690135 G T 1 0 0 0 0 1 0 0 0 14569 1203 42 2 2 SIGLEC1 20 3690135 Missense_Mutation SNP G C3L-00893_T 3690135 60754032 80 6868 DTD1 0 . GRCh38 20 18744231 18744231 + Silent SNP G G T novel C3L-00893_T C3L-00893_N G G c.609G>T p.= p.V203V ENST00000377452 5/6 252 184 68 185 185 0 strelka-varscan-mutect DTD1,synonymous_variant,p.=,ENST00000377452,NM_080820.4;DTD1,downstream_gene_variant,,ENST00000618693,; T ENST00000377452 Transcript synonymous_variant 789/1387 609/630 203/209 V gtG/gtT 1 1 DTD1 HGNC HGNC:16219 protein_coding YES CCDS13138.1 ENSP00000366672 Q8TEA8 UPI000013D2D6 NM_080820.4 5/6 hmmpanther:PTHR10472 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 20 18744231 18744231 G T 1 0 0 0 0 0 0 0 1 4607 1364 48 2 2 DTD1 20 18744231 Silent SNP G C3L-00893_T 15054096 18744231 45699936 81 6869 MRPL39 0 . GRCh38 21 25601399 25601399 + Missense_Mutation SNP C C A novel C3L-00893_T C3L-00893_N C C c.489G>T p.Met163Ile p.M163I ENST00000307301 4/11 190 162 28 135 134 1 strelka-varscan-mutect MRPL39,missense_variant,p.Met163Ile,ENST00000307301,NM_080794.3;MRPL39,missense_variant,p.Met163Ile,ENST00000352957,NM_017446.3;MRPL39,missense_variant,p.Met163Ile,ENST00000419219,; A ENST00000307301 Transcript missense_variant 531/1199 489/1062 163/353 M/I atG/atT 1 -1 MRPL39 HGNC HGNC:14027 protein_coding YES CCDS33522.1 ENSP00000305682 Q9NYK5 UPI00001AEAC0 NM_080794.3 tolerated(0.39) 4/11 Gene3D:1tkeA02,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF34,Superfamily_domains:SSF55186 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 20 25601399 25601399 C A 1 0 0 0 0 1 0 0 0 9777 594 21 2 2 MRPL39 21 25601399 Missense_Mutation SNP C C3L-00893_T 25601399 21108584 82 6870 SIM2 0 . GRCh38 21 36747708 36747708 + Silent SNP C C A novel C3L-00893_T C3L-00893_N C C c.1620C>A p.= p.P540P ENST00000290399 11/11 31 22 9 65 65 0 strelka-varscan-mutect SIM2,synonymous_variant,p.=,ENST00000290399,NM_005069.4,NM_009586.3;HLCS,downstream_gene_variant,,ENST00000399120,NM_001242784.1;HLCS,downstream_gene_variant,,ENST00000612277,NM_001242785.1;HLCS,downstream_gene_variant,,ENST00000336648,NM_000411.6;SIM2,downstream_gene_variant,,ENST00000431229,;SIM2,downstream_gene_variant,,ENST00000481185,; A ENST00000290399 Transcript synonymous_variant 2233/4442 1620/2004 540/667 P ccC/ccA 1 1 SIM2 HGNC HGNC:10883 protein_coding YES CCDS13646.1 ENSP00000290399 Q14190 UPI000013599A NM_005069.4,NM_009586.3 11/11 PROSITE_profiles:PS51302,hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF19,Pfam_domain:PF06621 LOW 1 SNV 1 1 PASS rs1174942263 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 20 36747708 36747708 C A 1 0 0 0 0 0 0 0 1 14587 610 22 2 2 SIM2 21 36747708 Silent SNP C C3L-00893_T 11146309 36747708 9962275 83 6871 CBX6 0 . GRCh38 22 38866532 38866532 + Missense_Mutation SNP T T C novel C3L-00893_T C3L-00893_N T T c.916A>G p.Ser306Gly p.S306G ENST00000407418 5/5 185 151 34 144 144 0 strelka-varscan-mutect CBX6,missense_variant,p.Ser306Gly,ENST00000407418,NM_014292.4;CBX6,missense_variant,p.Ser288Gly,ENST00000216083,NM_001303494.1;CBX6,downstream_gene_variant,,ENST00000469420,; C ENST00000407418 Transcript missense_variant 1040/6122 916/1239 306/412 S/G Agc/Ggc 1 -1 CBX6 HGNC HGNC:1556 protein_coding YES CCDS13980.1 ENSP00000384490 O95503 UPI00001271FD NM_014292.4 tolerated_low_confidence(0.14) 5/5 hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF8 MODERATE 1 SNV 1 1 PASS . . 0 195 3 10 2 0 0 0 -19.24158 0.7344883 1 1 1 0 C 3 2 20 38866532 38866532 T C 1 0 0 0 0 1 0 0 0 2422 1580 55 5 5 CBX6 22 38866532 Missense_Mutation SNP T C3L-00893_T 38866532 11951936 84 6872 GK 0 . GRCh38 X 30720734 30720734 + Missense_Mutation SNP A A G novel C3L-00893_T C3L-00893_N A A c.1350A>G p.Ile450Met p.I450M ENST00000427190 17/21 248 109 139 175 175 0 strelka-varscan-mutect GK,missense_variant,p.Ile450Met,ENST00000427190,NM_001205019.1;GK,missense_variant,p.Ile444Met,ENST00000378943,NM_001128127.2;GK,missense_variant,p.Ile450Met,ENST00000378946,NM_203391.3;GK,missense_variant,p.Ile444Met,ENST00000378945,NM_000167.5;GK,missense_variant,p.Ile39Met,ENST00000378938,;GK-AS1,intron_variant,,ENST00000464659,;RP11-242C19.2,intron_variant,,ENST00000497961,;GK,3_prime_UTR_variant,,ENST00000481024,; G ENST00000427190 Transcript missense_variant 1529/4573 1350/1680 450/559 I/M atA/atG 1 1 GK HGNC HGNC:4289 protein_coding YES CCDS75963.1 ENSP00000401720 P32189 UPI000002AA8A NM_001205019.1 deleterious(0.04) 17/21 hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF63,Pfam_domain:PF02782,TIGRFAM_domain:TIGR01311,PIRSF_domain:PIRSF000538,Gene3D:3.30.420.40,Superfamily_domains:SSF53067 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 20 30720734 30720734 A G 1 0 0 0 0 1 0 0 0 6298 381 14 5 5 GK 23 30720734 Missense_Mutation SNP A C3L-00893_T 30720734 125320161 85 6873 MED12 0 . GRCh38 X 71129375 71129375 + Missense_Mutation SNP A A T novel C3L-00893_T C3L-00893_N A A c.3637A>T p.Asn1213Tyr p.N1213Y ENST00000374080 26/45 314 140 174 200 200 0 strelka-varscan-mutect MED12,missense_variant,p.Asn1060Tyr,ENST00000333646,;MED12,missense_variant,p.Asn1213Tyr,ENST00000374102,;MED12,missense_variant,p.Asn1213Tyr,ENST00000374080,NM_005120.2;MED12,non_coding_transcript_exon_variant,,ENST00000460771,;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000471663,;MED12,downstream_gene_variant,,ENST00000489199,; T ENST00000374080 Transcript missense_variant 3669/6795 3637/6534 1213/2177 N/Y Aac/Tac 1 1 MED12 HGNC HGNC:11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 UPI00004257E2 NM_005120.2 deleterious(0) 26/45 hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 20 71129375 71129375 A T 1 0 0 0 0 1 0 0 0 9367 246 9 4 4 MED12 23 71129375 Missense_Mutation SNP A C3L-00893_T 40408641 71129375 84911520 86 6874 CEP104 0 . GRCh38 1 3833893 3833897 + Frame_Shift_Del DEL CGGGC CGGGC - novel C3L-00913_T C3L-00913_N CGGGC CGGGC c.1624_1628delGCCCG p.Ala542ProfsTer16 p.A542Pfs*16 ENST00000378230 12/22 294 270 24 205 205 0 sindel-varindel-pindel CEP104,frameshift_variant,p.Ala542ProfsTer16,ENST00000378230,NM_014704.3;CEP104,upstream_gene_variant,,ENST00000461667,;CEP104,upstream_gene_variant,,ENST00000438539,;CEP104,downstream_gene_variant,,ENST00000443466,;CEP104,non_coding_transcript_exon_variant,,ENST00000460038,;CEP104,non_coding_transcript_exon_variant,,ENST00000494653,;CEP104,upstream_gene_variant,,ENST00000495701,; - ENST00000378230 Transcript frameshift_variant 1949-1953/6424 1624-1628/2778 542-543/925 AR/X GCCCGc/c 1 -1 CEP104 HGNC HGNC:24866 protein_coding YES CCDS30571.1 ENSP00000367476 O60308 UPI0000139AA8 NM_014704.3 12/22 hmmpanther:PTHR13371:SF0,hmmpanther:PTHR13371,Gene3D:1.25.10.10,SMART_domains:SM01349,Superfamily_domains:SSF48371 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 3833893 3833893 CGGGC - 1 0 1 0 1 0 0 0 0 2954 768 27 0 0 CEP104 1 3833893 Frame_Shift_Del DEL CGGGC C3L-00913_T 3833893 245122529 1 6875 MFN2 0 . GRCh38 1 11996195 11996195 + Silent SNP C C G novel C3L-00913_T C3L-00913_N C C c.351C>G p.= p.L117L ENST00000235329 5/19 587 552 35 371 371 0 strelka-varscan-mutect MFN2,synonymous_variant,p.=,ENST00000235329,NM_014874.3;MFN2,synonymous_variant,p.=,ENST00000444836,NM_001127660.1;MFN2,downstream_gene_variant,,ENST00000412236,;MFN2,downstream_gene_variant,,ENST00000497302,; G ENST00000235329 Transcript synonymous_variant 673/4539 351/2274 117/757 L ctC/ctG 1 1 MFN2 HGNC HGNC:16877 protein_coding YES CCDS30587.1 ENSP00000235329 O95140 UPI0000039854 NM_014874.3 5/19 Gene3D:3.40.50.300,Pfam_domain:PF00350,PROSITE_profiles:PS51718,hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF1,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs1468573342 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 11996195 11996195 C G 1 0 0 0 0 0 0 0 1 9476 900 32 4 4 MFN2 1 11996195 Silent SNP C C3L-00913_T 8162302 11996195 236960227 2 6876 VWA5B1 0 . GRCh38 1 20345495 20345495 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.2666G>A p.Ser889Asn p.S889N ENST00000375079 17/22 366 330 36 242 242 0 strelka-varscan-mutect VWA5B1,missense_variant,p.Ser889Asn,ENST00000289815,NM_001039500.2;VWA5B1,missense_variant,p.Ser889Asn,ENST00000375079,;VWA5B1,non_coding_transcript_exon_variant,,ENST00000525343,;VWA5B1,missense_variant,p.Ser316Asn,ENST00000467486,;VWA5B1,3_prime_UTR_variant,,ENST00000485375,; A ENST00000375079 Transcript missense_variant 2862/3859 2666/3663 889/1220 S/N aGc/aAc 1 1 VWA5B1 HGNC HGNC:26538 protein_coding YES ENSP00000364220 Q5TIE3 UPI000066D8B8 deleterious(0) 17/22 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF109 MODERATE 1 SNV 5 1 PASS rs1483336742 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 20345495 20345495 G A 1 0 0 0 0 1 0 0 0 17797 971 34 3 3 VWA5B1 1 20345495 Missense_Mutation SNP G C3L-00913_T 8349300 20345495 228610927 3 6877 ADGRB2 0 . GRCh38 1 31744667 31744667 + Silent SNP C C G novel C3L-00913_T C3L-00913_N C C c.903G>C p.= p.G301G ENST00000373655 5/33 323 288 35 242 242 0 strelka-varscan-mutect ADGRB2,synonymous_variant,p.=,ENST00000373658,;ADGRB2,synonymous_variant,p.=,ENST00000373655,NM_001294335.1;ADGRB2,synonymous_variant,p.=,ENST00000398542,;ADGRB2,synonymous_variant,p.=,ENST00000527361,NM_001294336.1;ADGRB2,synonymous_variant,p.=,ENST00000398556,;ADGRB2,synonymous_variant,p.=,ENST00000398547,;ADGRB2,synonymous_variant,p.=,ENST00000398538,;ADGRB2,synonymous_variant,p.=,ENST00000420125,;ADGRB2,synonymous_variant,p.=,ENST00000533175,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000530134,;ADGRB2,upstream_gene_variant,,ENST00000468430,; G ENST00000373655 Transcript synonymous_variant 1245/5400 903/4755 301/1584 G ggG/ggC 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 5/33 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 31744667 31744667 C G 1 0 0 0 0 0 0 0 1 356 726 26 4 4 ADGRB2 1 31744667 Silent SNP C C3L-00913_T 11399172 31744667 217211755 4 6878 AZIN2 0 . GRCh38 1 33094677 33094677 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.717C>T p.= p.F239F ENST00000373441 5/9 205 186 19 113 112 1 strelka-varscan-mutect AZIN2,synonymous_variant,p.=,ENST00000294517,NM_052998.3;AZIN2,synonymous_variant,p.=,ENST00000373443,NM_001293562.1,NM_001301823.1;AZIN2,synonymous_variant,p.=,ENST00000373441,NM_001301825.1;AZIN2,intron_variant,,ENST00000373440,;AZIN2,non_coding_transcript_exon_variant,,ENST00000484656,;AZIN2,non_coding_transcript_exon_variant,,ENST00000475935,;AZIN2,non_coding_transcript_exon_variant,,ENST00000478204,;AZIN2,non_coding_transcript_exon_variant,,ENST00000481886,;AZIN2,non_coding_transcript_exon_variant,,ENST00000471119,;AZIN2,non_coding_transcript_exon_variant,,ENST00000477570,;AZIN2,non_coding_transcript_exon_variant,,ENST00000483027,;AZIN2,non_coding_transcript_exon_variant,,ENST00000473089,;AZIN2,non_coding_transcript_exon_variant,,ENST00000497280,;AZIN2,non_coding_transcript_exon_variant,,ENST00000492521,;AZIN2,downstream_gene_variant,,ENST00000492420,;AZIN2,downstream_gene_variant,,ENST00000462920,;AZIN2,downstream_gene_variant,,ENST00000497710,;AZIN2,downstream_gene_variant,,ENST00000478635,; T ENST00000373441 Transcript synonymous_variant 717/1443 717/1443 239/480 F ttC/ttT 1 1 AZIN2 HGNC HGNC:29957 protein_coding YES CCDS76138.1 ENSP00000362540 Q96A70 UPI000002A7C5 NM_001301825.1 5/9 Gene3D:3.20.20.10,Pfam_domain:PF02784,PROSITE_patterns:PS00879,hmmpanther:PTHR11482,hmmpanther:PTHR11482:SF4,Superfamily_domains:SSF51419 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 33094677 33094677 C T 1 0 0 0 0 0 0 0 1 1399 854 30 3 3 AZIN2 1 33094677 Silent SNP C C3L-00913_T 1350010 33094677 215861745 5 6879 STIL 0 . GRCh38 1 47299919 47299919 + Silent SNP C C G novel C3L-00913_T C3L-00913_N C C c.687G>C p.= p.G229G ENST00000371877 6/17 287 263 24 205 205 0 strelka-mutect STIL,synonymous_variant,p.=,ENST00000360380,NM_001282936.1,NM_003035.2;STIL,synonymous_variant,p.=,ENST00000337817,NM_001282939.1,NM_001282938.1;STIL,synonymous_variant,p.=,ENST00000371877,NM_001048166.1;STIL,synonymous_variant,p.=,ENST00000396221,NM_001282937.1;STIL,synonymous_variant,p.=,ENST00000447475,;STIL,downstream_gene_variant,,ENST00000413565,;STIL,non_coding_transcript_exon_variant,,ENST00000433827,; G ENST00000371877 Transcript synonymous_variant 835/5009 687/3867 229/1288 G ggG/ggC 1 -1 STIL HGNC HGNC:10879 protein_coding YES CCDS41329.1 ENSP00000360944 Q15468 UPI00002042D5 NM_001048166.1 6/17 Pfam_domain:PF15253,hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 47299919 47299919 C G 1 0 0 0 0 0 0 0 1 15659 842 30 4 4 STIL 1 47299919 Silent SNP C C3L-00913_T 14205242 47299919 201656503 6 6880 WDR78 0 . GRCh38 1 66837657 66837657 + Missense_Mutation SNP G G A C3L-00913_T C3L-00913_N G G c.1634C>T p.Ser545Leu p.S545L ENST00000371023 10/10 208 183 25 126 126 0 strelka-varscan-mutect WDR78,missense_variant,p.Ser545Leu,ENST00000371023,NM_207014.2;WDR78,missense_variant,p.Ser167Leu,ENST00000531552,;WDR78,intron_variant,,ENST00000371026,NM_024763.4;WDR78,intron_variant,,ENST00000464352,;WDR78,intron_variant,,ENST00000491297,; A ENST00000371023 Transcript missense_variant 1643/1697 1634/1638 545/545 S/L tCa/tTa COSM5381450 1 -1 WDR78 HGNC HGNC:26252 protein_coding CCDS44157.1 ENSP00000360062 Q5VTH9 UPI0000366548 NM_207014.2 10/10 1 MODERATE SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 21 66837657 66837657 G A 1 0 0 0 0 1 0 0 0 17884 1294 45 3 3 WDR78 1 66837657 Missense_Mutation SNP G C3L-00913_T 19537738 66837657 182118765 7 6881 LRRC7 0 . GRCh38 1 69760200 69760200 + Missense_Mutation SNP T T A rs746453993 C3L-00913_T C3L-00913_N T T c.11T>A p.Leu4Gln p.L4Q ENST00000310961 4/27 219 192 27 161 160 1 strelka-varscan-mutect LRRC7,missense_variant,p.Leu4Gln,ENST00000310961,;LRRC7,missense_variant,p.Leu37Gln,ENST00000370958,;LRRC7,5_prime_UTR_variant,,ENST00000035383,NM_020794.2;LRRC7,5_prime_UTR_variant,,ENST00000415775,; A ENST00000310961 Transcript missense_variant 429/6507 11/4488 4/1495 L/Q cTg/cAg rs746453993 1 1 LRRC7 HGNC HGNC:18531 protein_coding ENSP00000309245 A0A075B6E9 UPI00004588A5 deleterious_low_confidence(0) 4/27 MODERATE SNV 5 1 PASS rs746453993 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 69760200 69760200 T A 1 0 0 0 0 1 0 0 0 8916 1580 55 4 4 LRRC7 1 69760200 Missense_Mutation SNP T C3L-00913_T 2922543 69760200 179196222 8 6882 GBP7 0 . GRCh38 1 89150351 89150351 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.850G>C p.Gly284Arg p.G284R ENST00000294671 6/11 184 155 29 132 132 0 strelka-varscan-mutect GBP7,missense_variant,p.Gly284Arg,ENST00000294671,NM_207398.2;GBP2,5_prime_UTR_variant,,ENST00000464839,; G ENST00000294671 Transcript missense_variant 989/2454 850/1917 284/638 G/R Gga/Cga 1 -1 GBP7 HGNC HGNC:29606 protein_coding YES CCDS720.1 ENSP00000294671 Q8N8V2 UPI000013E1A3 NM_207398.2 deleterious(0.01) 6/11 hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF17,Gene3D:1f5nA01,Pfam_domain:PF02841,Superfamily_domains:0037397 MODERATE 1 SNV 2 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999983 1 1 1 0 G 3 3 21 89150351 89150351 C G 1 0 0 0 0 1 0 0 0 6149 632 22 4 4 GBP7 1 89150351 Missense_Mutation SNP C C3L-00913_T 19390151 89150351 159806071 9 6883 EPHX4 0 . GRCh38 1 92063105 92063105 + Nonsense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.908G>A p.Trp303Ter p.W303* ENST00000370383 7/7 244 217 27 155 155 0 strelka-varscan-mutect EPHX4,stop_gained,p.Trp303Ter,ENST00000370383,NM_173567.4;LPCAT2BP,upstream_gene_variant,,ENST00000420263,; A ENST00000370383 Transcript stop_gained 1006/1437 908/1089 303/362 W/* tGg/tAg 1 1 EPHX4 HGNC HGNC:23758 protein_coding YES CCDS736.1 ENSP00000359410 Q8IUS5 UPI000013E9F5 NM_173567.4 7/7 Gene3D:3.40.50.1820,Prints_domain:PR00412,hmmpanther:PTHR10992,hmmpanther:PTHR10992:SF278,Superfamily_domains:SSF53474 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 21 92063105 92063105 G A 1 0 0 0 0 0 1 0 0 5029 1357 47 3 3 EPHX4 1 92063105 Nonsense_Mutation SNP G C3L-00913_T 2912754 92063105 156893317 10 6884 NBPF4 0 . GRCh38 1 108223743 108223743 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1879C>T p.Pro627Ser p.P627S ENST00000415641 15/15 189 171 18 140 139 1 varscan-mutect NBPF4,missense_variant,p.Pro627Ser,ENST00000415641,NM_001143989.2;NBPF4,missense_variant,p.Pro656Ser,ENST00000613157,; A ENST00000415641 Transcript missense_variant 2083/2485 1879/1917 627/638 P/S Cca/Tca 1 -1 NBPF4 HGNC HGNC:26550 protein_coding YES CCDS44182.1 ENSP00000389237 Q96M43 UPI000046FF97 NM_001143989.2 deleterious_low_confidence(0) 15/15 MODERATE 1 SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -19.99997 0.9999838 1 1 1 0 A 3 1 21 108223743 108223743 G A 1 0 0 0 0 1 0 0 0 10213 1275 44 3 3 NBPF4 1 108223743 Missense_Mutation SNP G C3L-00913_T 16160638 108223743 140732679 11 6885 SLC6A17 0 . GRCh38 1 110198246 110198246 + Missense_Mutation SNP G G T rs550485152 C3L-00913_T C3L-00913_N G G c.1986G>T p.Lys662Asn p.K662N ENST00000331565 12/12 322 281 41 198 197 1 strelka-varscan-mutect SLC6A17,missense_variant,p.Lys662Asn,ENST00000331565,NM_001010898.2;SLC6A17,downstream_gene_variant,,ENST00000465159,; T ENST00000331565 Transcript missense_variant 2471/6427 1986/2184 662/727 K/N aaG/aaT rs550485152 1 1 SLC6A17 HGNC HGNC:31399 protein_coding YES CCDS30799.1 ENSP00000330199 Q9H1V8 UPI0000470B3D NM_001010898.2 tolerated(0.05) 12/12 hmmpanther:PTHR11616:SF102,hmmpanther:PTHR11616 MODERATE 1 SNV 2 1 PASS rs550485152 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 110198246 110198246 G T 1 0 0 0 0 1 0 0 0 14963 991 35 2 2 SLC6A17 1 110198246 Missense_Mutation SNP G C3L-00913_T 1974503 110198246 138758176 12 6886 KCND3 0 . GRCh38 1 111982709 111982709 + Silent SNP C C G novel C3L-00913_T C3L-00913_N C C c.18G>C p.= p.A6A ENST00000315987 2/8 253 227 26 164 164 0 strelka-varscan-mutect KCND3,synonymous_variant,p.=,ENST00000369697,;KCND3,synonymous_variant,p.=,ENST00000315987,NM_004980.4;KCND3,synonymous_variant,p.=,ENST00000302127,NM_172198.2; G ENST00000315987 Transcript synonymous_variant 498/2716 18/1968 6/655 A gcG/gcC 1 -1 KCND3 HGNC HGNC:6239 protein_coding YES CCDS843.1 ENSP00000319591 Q9UK17 UPI000003050A NM_004980.4 2/8 Pfam_domain:PF11601,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs1222104971 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 111982709 111982709 C G 1 0 0 0 0 0 0 0 1 7936 639 23 4 4 KCND3 1 111982709 Silent SNP C C3L-00913_T 1784463 111982709 136973713 13 6887 BCAS2 0 . GRCh38 1 114576721 114576721 + Missense_Mutation SNP G G C novel C3L-00913_T C3L-00913_N G G c.224C>G p.Ala75Gly p.A75G ENST00000369541 3/7 241 222 19 174 174 0 strelka-varscan-mutect BCAS2,missense_variant,p.Ala75Gly,ENST00000369541,NM_005872.2;BCAS2,intron_variant,,ENST00000485021,; C ENST00000369541 Transcript missense_variant 272/1299 224/678 75/225 A/G gCt/gGt 1 -1 BCAS2 HGNC HGNC:975 protein_coding YES CCDS874.1 ENSP00000358554 O75934 B2R7W3 UPI0000029BC3 NM_005872.2 tolerated(0.29) 3/7 Pfam_domain:PF05700,hmmpanther:PTHR13296,hmmpanther:PTHR13296:SF0 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 114576721 114576721 G C 1 0 0 0 0 1 0 0 0 1498 971 34 4 4 BCAS2 1 114576721 Missense_Mutation SNP G C3L-00913_T 2594012 114576721 134379701 14 6888 VANGL1 0 . GRCh38 1 115664002 115664002 + Silent SNP G G T rs143094973 C3L-00913_T C3L-00913_N G G c.546G>T p.= p.V182V ENST00000355485 4/8 755 680 75 591 591 0 strelka-varscan-mutect VANGL1,synonymous_variant,p.=,ENST00000355485,NM_138959.2;VANGL1,synonymous_variant,p.=,ENST00000369510,NM_001172411.1;VANGL1,synonymous_variant,p.=,ENST00000310260,NM_001172412.1;VANGL1,synonymous_variant,p.=,ENST00000369509,; T ENST00000355485 Transcript synonymous_variant 817/8691 546/1575 182/524 V gtG/gtT rs143094973 1 1 VANGL1 HGNC HGNC:15512 protein_coding YES CCDS883.1 ENSP00000347672 Q8TAA9 A0A024R0E3 UPI0000070B72 NM_138959.2 4/8 Pfam_domain:PF06638,PIRSF_domain:PIRSF007991,hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF8,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs143094973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 115664002 115664002 G T 1 0 0 0 0 0 0 0 1 17664 1364 48 2 2 VANGL1 1 115664002 Silent SNP G C3L-00913_T 1087281 115664002 133292420 15 6889 NBPF12 0 . GRCh38 1 146978957 146978957 + Splice_Site SNP A A T novel C3L-00913_T C3L-00913_N A A c.2399-2A>T p.X800_splice ENST00000617931 70 60 10 66 66 0 varscan-mutect NBPF12,splice_acceptor_variant,,ENST00000617931,;NBPF12,splice_acceptor_variant,,ENST00000617844,NM_001278141.1;NBPF12,splice_acceptor_variant,,ENST00000611443,;NBPF12,splice_acceptor_variant,,ENST00000579935,;NBPF12,splice_acceptor_variant,,ENST00000617614,;NBPF12,splice_acceptor_variant,,ENST00000613714,;NBPF12,splice_acceptor_variant,,ENST00000617864,;NBPF12,splice_acceptor_variant,,ENST00000439206,; T ENST00000617931 Transcript splice_acceptor_variant -/7061 2399/4374 800/1457 1 1 NBPF12 HGNC HGNC:24297 protein_coding YES CCDS72881.1 ENSP00000478609 A0A087WUF1 UPI00032968BC 20/35 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 21 146978957 146978957 A T 1 0 0 0 0 0 0 1 0 10206 202 7 4 4 NBPF12 1 146978957 Splice_Site SNP A C3L-00913_T 31314955 146978957 101977465 16 6890 MR1 0 . GRCh38 1 181049296 181049296 + Missense_Mutation SNP G G T rs550176170 C3L-00913_T C3L-00913_N G G c.312G>T p.Arg104Ser p.R104S ENST00000614012 3/7 187 174 13 148 148 0 strelka-varscan-mutect MR1,missense_variant,p.Arg104Ser,ENST00000614012,NM_001531.2;MR1,missense_variant,p.Arg104Ser,ENST00000367580,;MR1,missense_variant,p.Arg104Ser,ENST00000617803,NM_001310213.1,NM_001195000.1;MR1,missense_variant,p.Arg104Ser,ENST00000434571,NM_001195035.1;MR1,missense_variant,p.Arg104Ser,ENST00000282990,;MR1,missense_variant,p.Arg104Ser,ENST00000367579,NM_001194999.1;MR1,non_coding_transcript_exon_variant,,ENST00000438435,;MR1,non_coding_transcript_exon_variant,,ENST00000367578,;MR1,non_coding_transcript_exon_variant,,ENST00000486453,; T ENST00000614012 Transcript missense_variant 473/7860 312/1026 104/341 R/S agG/agT rs550176170 1 1 MR1 HGNC HGNC:4975 protein_coding YES CCDS1342.1 ENSP00000477563 Q95460 UPI0000072BD9 NM_001531.2 tolerated(0.5) 3/7 hmmpanther:PTHR16675:SF141,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452,Prints_domain:PR01638 MODERATE 1 SNV 5 1 PASS rs550176170 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 181049296 181049296 G T 1 0 0 0 0 1 0 0 0 9718 1194 42 2 2 MR1 1 181049296 Missense_Mutation SNP G C3L-00913_T 34070339 181049296 67907126 17 6891 PTPRC 0 . GRCh38 1 198699687 198699687 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.422G>T p.Gly141Val p.G141V ENST00000442510 5/33 632 552 80 428 427 1 strelka-varscan-mutect PTPRC,missense_variant,p.Gly141Val,ENST00000442510,NM_002838.4;PTPRC,missense_variant,p.Gly75Val,ENST00000367367,;PTPRC,missense_variant,p.Gly75Val,ENST00000530727,;PTPRC,intron_variant,,ENST00000348564,NM_080921.3;PTPRC,intron_variant,,ENST00000367379,;PTPRC,downstream_gene_variant,,ENST00000413409,NM_001267798.1;PTPRC,downstream_gene_variant,,ENST00000418674,;PTPRC,non_coding_transcript_exon_variant,,ENST00000391970,;PTPRC,non_coding_transcript_exon_variant,,ENST00000427110,;PTPRC,missense_variant,p.Gly141Val,ENST00000529828,;PTPRC,non_coding_transcript_exon_variant,,ENST00000462363,;PTPRC,non_coding_transcript_exon_variant,,ENST00000484135,; T ENST00000442510 Transcript missense_variant 563/5164 422/3921 141/1306 G/V gGc/gTc 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 tolerated(0.38) 5/33 PIRSF_domain:PIRSF002004 MODERATE 1 SNV 1 1 PASS rs1170608605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 198699687 198699687 G T 1 0 0 0 0 1 0 0 0 12951 1203 42 2 2 PTPRC 1 198699687 Missense_Mutation SNP G C3L-00913_T 17650391 198699687 50256735 18 6892 RBBP5 0 . GRCh38 1 205105103 205105115 + Frame_Shift_Del DEL ACATCCCACTGTG ACATCCCACTGTG - novel C3L-00913_T C3L-00913_N ACATCCCACTGTG ACATCCCACTGTG c.272_284delCACAGTGGGATGT p.Ser91PhefsTer17 p.S91Ffs*17 ENST00000264515 4/14 230 216 14 180 180 0 sindel-pindel RBBP5,frameshift_variant,p.Ser91PhefsTer17,ENST00000264515,NM_001193273.1,NM_005057.3;RBBP5,frameshift_variant,p.Ser91PhefsTer17,ENST00000367164,NM_001193272.1;RBBP5,non_coding_transcript_exon_variant,,ENST00000484379,; - ENST00000264515 Transcript frameshift_variant 414-426/4404 272-284/1617 91-95/538 SQWDV/X tCACAGTGGGATGTt/tt 1 -1 RBBP5 HGNC HGNC:9888 protein_coding YES CCDS30983.1 ENSP00000264515 Q15291 A0A024R9B5 UPI00001A9CA5 NM_001193273.1,NM_005057.3 4/14 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF433,SMART_domains:SM00320,Superfamily_domains:SSF117289 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 205105103 205105103 ACATCCCACTGTG - 1 0 1 0 1 0 0 0 0 13263 43 2 0 0 RBBP5 1 205105103 Frame_Shift_Del DEL ACATCCCACTGTG C3L-00913_T 6405416 205105103 43851319 19 6893 USH2A 0 . GRCh38 1 216246992 216246992 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.2402G>T p.Gly801Val p.G801V ENST00000307340 13/72 242 215 27 173 172 1 strelka-varscan-mutect USH2A,missense_variant,p.Gly801Val,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Gly801Val,ENST00000366942,NM_007123.5; A ENST00000307340 Transcript missense_variant 2789/18883 2402/15609 801/5202 G/V gGa/gTa 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 13/72 Gene3D:2.10.25.10,Pfam_domain:PF00053,Prints_domain:PR00011,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 216246992 216246992 C A 1 0 0 0 0 1 0 0 0 17570 855 30 2 2 USH2A 1 216246992 Missense_Mutation SNP C C3L-00913_T 11141889 216246992 32709430 20 6894 SLC30A10 0 . GRCh38 1 219928351 219928351 + Nonsense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.90C>A p.Tyr30Ter p.Y30* ENST00000366926 1/4 347 320 27 303 303 0 strelka-varscan SLC30A10,stop_gained,p.Tyr30Ter,ENST00000366926,NM_018713.2;SLC30A10,intron_variant,,ENST00000484239,;SLC30A10,stop_gained,p.Tyr30Ter,ENST00000356609,; T ENST00000366926 Transcript stop_gained 252/1915 90/1458 30/485 Y/* taC/taA 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 1/4 Superfamily_domains:0054606,Gene3D:3h90A01,Pfam_domain:PF01545,hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF14,TIGRFAM_domain:TIGR01297,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 21 219928351 219928351 G T 1 0 0 0 0 0 1 0 0 14824 1256 44 2 2 SLC30A10 1 219928351 Nonsense_Mutation SNP G C3L-00913_T 3681359 219928351 29028071 21 6895 ACTN2 0 . GRCh38 1 236762485 236762485 + Missense_Mutation SNP C C A rs141563497 C3L-00913_T C3L-00913_N C C c.2551C>A p.Arg851Ser p.R851S ENST00000542672 21/21 458 429 29 339 338 1 strelka-varscan ACTN2,missense_variant,p.Arg643Ser,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Arg851Ser,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Arg851Ser,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; A ENST00000542672 Transcript missense_variant 2771/4906 2551/2685 851/894 R/S Cgt/Agt rs141563497,COSM1639758,COSM4233962 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0) 21/21 Gene3D:1.10.238.10,Pfam_domain:PF08726,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM01184,Superfamily_domains:SSF47473 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 236762485 236762485 C A 1 0 0 0 0 1 0 0 0 249 768 27 1 1 ACTN2 1 236762485 Missense_Mutation SNP C C3L-00913_T 16834134 236762485 12193937 22 6896 RYR2 0 . GRCh38 1 237590732 237590732 + Missense_Mutation SNP G G C rs762489681 C3L-00913_T C3L-00913_N G G c.3900G>C p.Met1300Ile p.M1300I ENST00000366574 31/105 89 75 14 78 78 0 strelka-varscan RYR2,missense_variant,p.Met1300Ile,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Met1284Ile,ENST00000360064,; C ENST00000366574 Transcript missense_variant 4217/16562 3900/14904 1300/4967 M/I atG/atC rs762489681 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.46) 31/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 237590732 237590732 G C 1 0 0 0 0 1 0 0 0 14029 1377 48 4 4 RYR2 1 237590732 Missense_Mutation SNP G C3L-00913_T 828247 237590732 11365690 23 6897 RYR2 0 . GRCh38 1 237650036 237650036 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.7672G>A p.Gly2558Ser p.G2558S ENST00000366574 50/105 409 386 23 292 291 1 strelka-varscan RYR2,missense_variant,p.Gly2558Ser,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly2542Ser,ENST00000360064,; A ENST00000366574 Transcript missense_variant 7989/16562 7672/14904 2558/4967 G/S Ggc/Agc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.06) 50/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 237650036 237650036 G A 1 0 0 0 0 1 0 0 0 14029 1232 43 3 3 RYR2 1 237650036 Missense_Mutation SNP G C3L-00913_T 59304 237650036 11306386 24 6898 ZP4 0 . GRCh38 1 237885433 237885433 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1118C>A p.Thr373Asn p.T373N ENST00000611898 8/13 155 134 21 138 138 0 strelka-varscan ZP4,missense_variant,p.Thr373Asn,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Thr373Asn,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; T ENST00000611898 Transcript missense_variant 1405/2474 1118/1623 373/540 T/N aCt/aAt 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 tolerated(0.19) 8/13 Pfam_domain:PF00100,Prints_domain:PR00023,PROSITE_patterns:PS00682,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 237885433 237885433 G T 1 0 0 0 0 1 0 0 0 18810 1029 36 2 2 ZP4 1 237885433 Missense_Mutation SNP G C3L-00913_T 235397 237885433 11070989 25 6899 MAP1LC3C 0 . GRCh38 1 241998954 241998954 + Missense_Mutation SNP A A T novel C3L-00913_T C3L-00913_N A A c.55T>A p.Leu19Met p.L19M ENST00000357246 1/4 129 109 20 122 122 0 strelka-varscan MAP1LC3C,missense_variant,p.Leu19Met,ENST00000357246,NM_001004343.2; T ENST00000357246 Transcript missense_variant 120/1182 55/444 19/147 L/M Ttg/Atg 1 -1 MAP1LC3C HGNC HGNC:13353 protein_coding YES CCDS31074.1 ENSP00000349785 Q9BXW4 UPI0000070E14 NM_001004343.2 deleterious(0.02) 1/4 Gene3D:3.10.20.90,hmmpanther:PTHR10969,hmmpanther:PTHR10969:SF41,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 241998954 241998954 A T 1 0 0 0 0 1 0 0 0 9155 86 3 4 4 MAP1LC3C 1 241998954 Missense_Mutation SNP A C3L-00913_T 4113521 241998954 6957468 26 6900 OR2G2 0 . GRCh38 1 247589133 247589133 + Silent SNP C C T rs865888004 C3L-00913_T C3L-00913_N C C c.774C>T p.= p.I258I ENST00000320065 1/1 327 310 17 247 247 0 strelka-varscan OR2G2,synonymous_variant,p.=,ENST00000320065,NM_001001915.1;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; T ENST00000320065 Transcript synonymous_variant 774/954 774/954 258/317 I atC/atT rs865888004,COSM5249562 1 1 OR2G2 HGNC HGNC:15007 protein_coding YES CCDS31092.1 ENSP00000326349 Q8NGZ5 UPI0000061EB9 NM_001001915.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF132,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 247589133 247589133 C T 1 0 0 0 0 0 0 0 1 11076 816 29 3 3 OR2G2 1 247589133 Silent SNP C C3L-00913_T 5590179 247589133 1367289 27 6901 OR1C1 0 . GRCh38 1 247757596 247757596 + Missense_Mutation SNP C C G rs774677753 C3L-00913_T C3L-00913_N C C c.811G>C p.Asp271His p.D271H ENST00000408896 1/1 309 293 16 229 229 0 strelka-varscan OR1C1,missense_variant,p.Asp271His,ENST00000408896,NM_012353.2; G ENST00000408896 Transcript missense_variant 811/945 811/945 271/314 D/H Gac/Cac rs774677753,COSM4559607 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 247757596 247757596 C G 1 0 0 0 0 1 0 0 0 11029 884 31 4 4 OR1C1 1 247757596 Missense_Mutation SNP C C3L-00913_T 168463 247757596 1198826 28 6902 OR2AJ1 0 . GRCh38 1 247934272 247934272 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.504C>A p.Phe168Leu p.F168L ENST00000318244 1/1 213 185 28 172 172 0 strelka-varscan OR2AJ1,missense_variant,p.Phe168Leu,ENST00000318244,;CLK3P2,downstream_gene_variant,,ENST00000427566,;OR2X1P,upstream_gene_variant,,ENST00000421144,; A ENST00000318244 Transcript missense_variant 504/987 504/987 168/328 F/L ttC/ttA 1 1 OR2AJ1 HGNC HGNC:15001 protein_coding YES ENSP00000325078 Q8NGZ0 UPI0000061E5C deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF214,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 247934272 247934272 C A 1 0 0 0 0 1 0 0 0 11063 912 32 2 2 OR2AJ1 1 247934272 Missense_Mutation SNP C C3L-00913_T 176676 247934272 1022150 29 6903 RHOB 0 . GRCh38 2 20447667 20447667 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.202C>T p.Arg68Cys p.R68C ENST00000272233 1/1 203 185 18 158 158 0 strelka-varscan-mutect RHOB,missense_variant,p.Arg68Cys,ENST00000272233,NM_004040.3;AC023137.2,upstream_gene_variant,,ENST00000448241,; T ENST00000272233 Transcript missense_variant 594/2372 202/591 68/196 R/C Cgc/Tgc 1 1 RHOB HGNC HGNC:668 protein_coding YES CCDS1699.1 ENSP00000272233 P62745 UPI0000021989 NM_004040.3 deleterious(0) 1/1 PROSITE_profiles:PS51420,hmmpanther:PTHR24072:SF100,hmmpanther:PTHR24072,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 20447667 20447667 C T 1 0 0 0 0 1 0 0 0 13505 652 23 1 1 RHOB 2 20447667 Missense_Mutation SNP C C3L-00913_T 20447667 221745862 30 6904 GDF7 0 . GRCh38 2 20671356 20671356 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.1284C>G p.Ile428Met p.I428M ENST00000272224 2/2 341 322 19 231 231 0 strelka-varscan-mutect GDF7,missense_variant,p.Ile428Met,ENST00000272224,NM_182828.2; G ENST00000272224 Transcript missense_variant 1860/9749 1284/1353 428/450 I/M atC/atG 1 1 GDF7 HGNC HGNC:4222 protein_coding YES CCDS1701.1 ENSP00000272224 Q7Z4P5 UPI0000208B29 NM_182828.2 deleterious(0) 2/2 PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF160,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 20671356 20671356 C G 1 0 0 0 0 1 0 0 0 6191 874 31 4 4 GDF7 2 20671356 Missense_Mutation SNP C C3L-00913_T 223689 20671356 221522173 31 6905 SLC8A1 0 . GRCh38 2 40115456 40115456 + Missense_Mutation SNP G G C novel C3L-00913_T C3L-00913_N G G c.2719C>G p.Leu907Val p.L907V ENST00000403092 11/11 292 264 28 221 221 0 strelka-varscan SLC8A1,missense_variant,p.Leu871Val,ENST00000406785,;SLC8A1,missense_variant,p.Leu907Val,ENST00000403092,;SLC8A1,missense_variant,p.Leu902Val,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Leu871Val,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Leu871Val,ENST00000405269,;SLC8A1,missense_variant,p.Leu907Val,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Leu899Val,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Leu871Val,ENST00000406391,;SLC8A1-AS1,intron_variant,,ENST00000610721,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000625324,;SLC8A1-AS1,intron_variant,,ENST00000593848,;SLC8A1-AS1,intron_variant,,ENST00000625780,;SLC8A1-AS1,intron_variant,,ENST00000598247,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000625234,;SLC8A1-AS1,intron_variant,,ENST00000631022,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000631142,;SLC8A1-AS1,intron_variant,,ENST00000628471,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000435515,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000627219,;SLC8A1-AS1,intron_variant,,ENST00000629329,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000629180,;SLC8A1-AS1,intron_variant,,ENST00000629157,;SLC8A1-AS1,intron_variant,,ENST00000631204,;SLC8A1-AS1,intron_variant,,ENST00000630783,;SLC8A1-AS1,intron_variant,,ENST00000625381,;SLC8A1-AS1,intron_variant,,ENST00000631137,;SLC8A1-AS1,intron_variant,,ENST00000627108,;SLC8A1-AS1,intron_variant,,ENST00000626098,;SLC8A1-AS1,intron_variant,,ENST00000631330,;SLC8A1-AS1,intron_variant,,ENST00000630006,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1,3_prime_UTR_variant,,ENST00000407929,; C ENST00000403092 Transcript missense_variant 2753/3178 2719/2922 907/973 L/V Cta/Gta 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 deleterious(0) 11/11 Pfam_domain:PF01699,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 40115456 40115456 G C 1 0 0 0 0 1 0 0 0 14989 1020 36 4 4 SLC8A1 2 40115456 Missense_Mutation SNP G C3L-00913_T 19444100 40115456 202078073 32 6906 LRPPRC 0 . GRCh38 2 43946155 43946155 + Missense_Mutation SNP C C A rs754760201 C3L-00913_T C3L-00913_N C C c.2168G>T p.Arg723Leu p.R723L ENST00000260665 21/38 573 503 70 383 383 0 strelka-varscan LRPPRC,missense_variant,p.Arg723Leu,ENST00000260665,NM_133259.3;LRPPRC,downstream_gene_variant,,ENST00000467058,; A ENST00000260665 Transcript missense_variant 2226/6335 2168/4185 723/1394 R/L cGa/cTa rs754760201 1 -1 LRPPRC HGNC HGNC:15714 protein_coding YES CCDS33189.1 ENSP00000260665 P42704 E5KNY5 UPI000019B4D2 NM_133259.3 deleterious(0.04) 21/38 PROSITE_profiles:PS51375,hmmpanther:PTHR24015,hmmpanther:PTHR24015:SF187,Pfam_domain:PF01535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 43946155 43946155 C A 1 0 0 0 0 1 0 0 0 8860 884 31 1 1 LRPPRC 2 43946155 Missense_Mutation SNP C C3L-00913_T 3830699 43946155 198247374 33 6907 ETAA1 0 . GRCh38 2 67403965 67403965 + Nonsense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.1283C>G p.Ser428Ter p.S428* ENST00000272342 5/6 128 118 10 115 115 0 strelka-varscan ETAA1,stop_gained,p.Ser428Ter,ENST00000272342,NM_019002.3;ETAA1,intron_variant,,ENST00000462772,; G ENST00000272342 Transcript stop_gained 1413/3418 1283/2781 428/926 S/* tCa/tGa 1 1 ETAA1 HGNC HGNC:24648 protein_coding YES CCDS1882.1 ENSP00000272342 Q9NY74 UPI00001414BC NM_019002.3 5/6 Pfam_domain:PF15350,hmmpanther:PTHR16434 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.10671 0.9999997 1 1 1 0 G 4 3 21 67403965 67403965 C G 1 0 0 0 0 0 1 0 0 5129 838 29 4 4 ETAA1 2 67403965 Nonsense_Mutation SNP C C3L-00913_T 23457810 67403965 174789564 34 6908 ADD2 0 . GRCh38 2 70696286 70696286 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.433G>A p.Asp145Asn p.D145N ENST00000264436 5/16 364 316 48 278 277 1 strelka-varscan ADD2,missense_variant,p.Asp145Asn,ENST00000264436,NM_001617.3;ADD2,missense_variant,p.Asp145Asn,ENST00000413157,NM_017482.3;ADD2,missense_variant,p.Asp145Asn,ENST00000407644,NM_001185054.1;ADD2,missense_variant,p.Asp145Asn,ENST00000355733,NM_017488.3;ADD2,missense_variant,p.Asp161Asn,ENST00000430656,NM_001185055.1;ADD2,missense_variant,p.Asp145Asn,ENST00000456320,;ADD2,missense_variant,p.Asp145Asn,ENST00000415348,;ADD2,missense_variant,p.Asp145Asn,ENST00000522886,;ADD2,downstream_gene_variant,,ENST00000425976,;AC007395.3,downstream_gene_variant,,ENST00000457851,;ADD2,missense_variant,p.Asp145Asn,ENST00000403045,; T ENST00000264436 Transcript missense_variant 878/9267 433/2181 145/726 D/N Gac/Aac 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 deleterious(0) 5/16 hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6,Pfam_domain:PF00596,Gene3D:3.40.225.10,SMART_domains:SM01007,Superfamily_domains:SSF53639 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 70696286 70696286 C T 1 0 0 0 0 1 0 0 0 349 855 30 3 3 ADD2 2 70696286 Missense_Mutation SNP C C3L-00913_T 3292321 70696286 171497243 35 6909 SFXN5 0 . GRCh38 2 72968459 72968459 + Silent SNP G G A novel C3L-00913_T C3L-00913_N G G c.816C>T p.= p.S272S ENST00000272433 12/14 163 143 20 104 104 0 strelka-varscan SFXN5,missense_variant,p.His224Tyr,ENST00000411783,;SFXN5,synonymous_variant,p.=,ENST00000272433,NM_144579.2;SFXN5,intron_variant,,ENST00000410065,;SFXN5,non_coding_transcript_exon_variant,,ENST00000474528,;SFXN5,non_coding_transcript_exon_variant,,ENST00000461352,;SFXN5,non_coding_transcript_exon_variant,,ENST00000490056,;SFXN5,non_coding_transcript_exon_variant,,ENST00000482289,;SFXN5,non_coding_transcript_exon_variant,,ENST00000495208,;SFXN5,non_coding_transcript_exon_variant,,ENST00000463277,;SFXN5,non_coding_transcript_exon_variant,,ENST00000482542,;SFXN5,downstream_gene_variant,,ENST00000416579,; A ENST00000272433 Transcript synonymous_variant 947/4140 816/1023 272/340 S tcC/tcT 1 -1 SFXN5 HGNC HGNC:16073 protein_coding YES CCDS1922.1 ENSP00000272433 Q8TD22 UPI000006D292 NM_144579.2 12/14 Pfam_domain:PF03820,hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF17,TIGRFAM_domain:TIGR00798,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 72968459 72968459 G A 1 0 0 0 0 0 0 0 1 14458 1335 47 3 3 SFXN5 2 72968459 Silent SNP G C3L-00913_T 2272173 72968459 169225070 36 6910 SLC4A5 0 . GRCh38 2 74252379 74252379 + Silent SNP C C G novel C3L-00913_T C3L-00913_N C C c.1278G>C p.= p.V426V ENST00000346834 13/29 203 184 19 113 113 0 strelka-varscan SLC4A5,synonymous_variant,p.=,ENST00000394019,NM_133478.2;SLC4A5,synonymous_variant,p.=,ENST00000346834,NM_021196.3;SLC4A5,synonymous_variant,p.=,ENST00000423644,;SLC4A5,synonymous_variant,p.=,ENST00000377634,;SLC4A5,synonymous_variant,p.=,ENST00000358683,;SLC4A5,synonymous_variant,p.=,ENST00000377632,;SLC4A5,synonymous_variant,p.=,ENST00000425249,;SLC4A5,non_coding_transcript_exon_variant,,ENST00000483195,;RP11-287D1.3,3_prime_UTR_variant,,ENST00000451608,;SLC4A5,upstream_gene_variant,,ENST00000479776,; G ENST00000346834 Transcript synonymous_variant 1514/6233 1278/3414 426/1137 V gtG/gtC 1 -1 SLC4A5 HGNC HGNC:18168 protein_coding YES CCDS1936.1 ENSP00000251768 Q9BY07 UPI000013C97B NM_021196.3 13/29 Gene3D:1hynR00,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF20,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 74252379 74252379 C G 1 0 0 0 0 0 0 0 1 14934 465 17 4 4 SLC4A5 2 74252379 Silent SNP C C3L-00913_T 1283920 74252379 167941150 37 6911 COX5B 0 . GRCh38 2 97646094 97646094 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.8C>T p.Ser3Leu p.S3L ENST00000258424 1/4 286 259 27 183 183 0 strelka-varscan COX5B,missense_variant,p.Ser3Leu,ENST00000258424,NM_001862.2;COX5B,upstream_gene_variant,,ENST00000464949,;COX5B,upstream_gene_variant,,ENST00000491989,;COX5B,upstream_gene_variant,,ENST00000494306,; T ENST00000258424 Transcript missense_variant 55/712 8/390 3/129 S/L tCa/tTa 1 1 COX5B HGNC HGNC:2269 protein_coding YES CCDS2032.1 ENSP00000258424 P10606 UPI0000128135 NM_001862.2 deleterious(0.03) 1/4 hmmpanther:PTHR10122,hmmpanther:PTHR10122:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 97646094 97646094 C T 1 0 0 0 0 1 0 0 0 3568 838 29 3 3 COX5B 2 97646094 Missense_Mutation SNP C C3L-00913_T 23393715 97646094 144547435 38 6912 SH3RF3 0 . GRCh38 2 109419584 109419584 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1345G>T p.Ala449Ser p.A449S ENST00000309415 5/10 290 272 18 205 204 1 strelka-varscan SH3RF3,missense_variant,p.Ala449Ser,ENST00000309415,NM_001099289.2; T ENST00000309415 Transcript missense_variant 1538/5803 1345/2649 449/882 A/S Gct/Tct 1 1 SH3RF3 HGNC HGNC:24699 protein_coding YES CCDS74557.1 ENSP00000309186 Q8TEJ3 UPI0000DD7AEA NM_001099289.2 tolerated(0.99) 5/10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 109419584 109419584 G T 1 0 0 0 0 1 0 0 0 14519 1203 42 2 2 SH3RF3 2 109419584 Missense_Mutation SNP G C3L-00913_T 11773490 109419584 132773945 39 6913 MCM6 0 . GRCh38 2 135840894 135840894 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.2407G>A p.Glu803Lys p.E803K ENST00000264156 17/17 319 283 36 242 241 1 strelka-varscan-mutect MCM6,missense_variant,p.Glu803Lys,ENST00000264156,NM_005915.5;LCT,upstream_gene_variant,,ENST00000264162,NM_002299.2;MCM6,downstream_gene_variant,,ENST00000492091,; T ENST00000264156 Transcript missense_variant 2468/3736 2407/2466 803/821 E/K Gag/Aag 1 -1 MCM6 HGNC HGNC:6949 protein_coding YES CCDS2179.1 ENSP00000264156 Q14566 UPI0000001611 NM_005915.5 tolerated(0.1) 17/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 135840894 135840894 C T 1 0 0 0 0 1 0 0 0 9323 835 29 3 3 MCM6 2 135840894 Missense_Mutation SNP C C3L-00913_T 26421310 135840894 106352635 40 6914 MCM6 0 . GRCh38 2 135857997 135857997 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.1370G>A p.Cys457Tyr p.C457Y ENST00000264156 10/17 184 174 10 123 123 0 strelka-mutect MCM6,missense_variant,p.Cys457Tyr,ENST00000264156,NM_005915.5;MCM6,intron_variant,,ENST00000492091,; T ENST00000264156 Transcript missense_variant 1431/3736 1370/2466 457/821 C/Y tGt/tAt 1 -1 MCM6 HGNC HGNC:6949 protein_coding YES CCDS2179.1 ENSP00000264156 Q14566 UPI0000001611 NM_005915.5 deleterious(0) 10/17 Gene3D:3.40.50.300,Pfam_domain:PF00493,Prints_domain:PR01657,PROSITE_patterns:PS00847,PROSITE_profiles:PS50051,hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF73,SMART_domains:SM00350,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -17.88103 1 1 1 1 0 T 3 4 21 135857997 135857997 C T 1 0 0 0 0 1 0 0 0 9323 478 17 3 3 MCM6 2 135857997 Missense_Mutation SNP C C3L-00913_T 17103 135857997 106335532 41 6915 LRP1B 0 . GRCh38 2 141049057 141049058 + Frame_Shift_Ins INS - - A novel C3L-00913_T C3L-00913_N - - c.1717_1718insT p.Ala573ValfsTer2 p.A573Vfs*2 ENST00000389484 11/91 351 316 35 271 271 0 sindel-varindel LRP1B,frameshift_variant,p.Ala573ValfsTer2,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript frameshift_variant 2689-2690/16535 1717-1718/13800 573/4599 A/VX gct/gTct 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 11/91 PROSITE_profiles:PS51120,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 21 141049057 141049057 - A 1 0 1 1 0 0 0 0 0 8850 971 34 0 0 LRP1B 2 141049057 Frame_Shift_Ins INS - C3L-00913_T 5191060 141049057 101144472 42 6916 CYTIP 0 . GRCh38 2 157415826 157415826 + Nonsense_Mutation SNP C C A C3L-00913_T C3L-00913_N C C c.931G>T p.Gly311Ter p.G311* ENST00000264192 8/8 438 406 32 295 295 0 strelka-varscan-mutect CYTIP,stop_gained,p.Gly311Ter,ENST00000264192,NM_004288.4;CYTIP,downstream_gene_variant,,ENST00000418920,;CYTIP,downstream_gene_variant,,ENST00000457793,; A ENST00000264192 Transcript stop_gained 1053/2260 931/1080 311/359 G/* Gga/Tga COSM5006322 1 -1 CYTIP HGNC HGNC:9506 protein_coding YES CCDS2204.1 ENSP00000264192 O60759 UPI0000035D67 NM_004288.4 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR15963:SF1,hmmpanther:PTHR15963 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 21 157415826 157415826 C A 1 0 0 0 0 0 1 0 0 4012 661 23 1 1 CYTIP 2 157415826 Nonsense_Mutation SNP C C3L-00913_T 16366769 157415826 84777703 43 6917 BAZ2B 0 . GRCh38 2 159412538 159412538 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.2474A>T p.Gln825Leu p.Q825L ENST00000392783 14/37 325 307 18 249 248 1 strelka-varscan-mutect BAZ2B,missense_variant,p.Gln825Leu,ENST00000392783,NM_013450.3;BAZ2B,missense_variant,p.Gln789Leu,ENST00000392782,NM_001289975.1;BAZ2B,missense_variant,p.Gln531Leu,ENST00000343439,;BAZ2B,missense_variant,p.Gln159Leu,ENST00000441143,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000482501,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000472953,; A ENST00000392783 Transcript missense_variant 2970/8289 2474/6507 825/2168 Q/L cAg/cTg 1 -1 BAZ2B HGNC HGNC:963 protein_coding YES CCDS2209.2 ENSP00000376534 Q9UIF8 UPI0000D74C4A NM_013450.3 deleterious(0) 14/37 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF154,Superfamily_domains:SSF54171 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 159412538 159412538 T A 1 0 0 0 0 1 0 0 0 1477 1580 55 4 4 BAZ2B 2 159412538 Missense_Mutation SNP T C3L-00913_T 1996712 159412538 82780991 44 6918 FIGN 0 . GRCh38 2 163611493 163611493 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.339G>T p.Leu113Phe p.L113F ENST00000333129 3/3 441 398 43 313 313 0 strelka-varscan-mutect FIGN,missense_variant,p.Leu113Phe,ENST00000333129,NM_018086.2;FIGN,intron_variant,,ENST00000409634,;FIGN,non_coding_transcript_exon_variant,,ENST00000482917,; A ENST00000333129 Transcript missense_variant 654/9536 339/2280 113/759 L/F ttG/ttT 1 -1 FIGN HGNC HGNC:13285 protein_coding YES CCDS2221.2 ENSP00000333836 Q5HY92 UPI000022BD13 NM_018086.2 tolerated(0.48) 3/3 hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 163611493 163611493 C A 1 0 0 0 0 1 0 0 0 5755 825 29 2 2 FIGN 2 163611493 Missense_Mutation SNP C C3L-00913_T 4198955 163611493 78582036 45 6919 FSIP2 0 . GRCh38 2 185794033 185794033 + Silent SNP T T C novel C3L-00913_T C3L-00913_N T T c.7164T>C p.= p.F2388F ENST00000343098 16/23 172 150 22 144 144 0 strelka-varscan-mutect FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,; C ENST00000343098 Transcript synonymous_variant 7164/21054 7164/20991 2388/6996 F ttT/ttC 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS rs1442251252 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 21 185794033 185794033 T C 1 0 0 0 0 0 0 0 1 5949 1838 64 5 5 FSIP2 2 185794033 Silent SNP T C3L-00913_T 22182540 185794033 56399496 46 6920 PLCL1 0 . GRCh38 2 198085539 198085539 + Silent SNP G G T rs558973603 C3L-00913_T C3L-00913_N G G c.2022G>T p.= p.P674P ENST00000428675 2/6 236 211 25 178 177 1 strelka-varscan-mutect PLCL1,synonymous_variant,p.=,ENST00000437704,;PLCL1,synonymous_variant,p.=,ENST00000428675,NM_006226.3;PLCL1,synonymous_variant,p.=,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript synonymous_variant 2420/5125 2022/3288 674/1095 P ccG/ccT rs558973603,COSM1530062,COSM1530063 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 2/6 PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF00387,Gene3D:3.20.20.190,SMART_domains:SM00149,Superfamily_domains:SSF51695,Prints_domain:PR00390 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs558973603 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 198085539 198085539 G T 1 0 0 0 0 0 0 0 1 12133 1103 39 1 1 PLCL1 2 198085539 Silent SNP G C3L-00913_T 12291506 198085539 44107990 47 6921 MROH2A 0 . GRCh38 2 233814656 233814656 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.2844G>T p.Lys948Asn p.K948N ENST00000610772 26/42 169 144 25 114 114 0 strelka-varscan-mutect MROH2A,missense_variant,p.Lys945Asn,ENST00000389758,;MROH2A,missense_variant,p.Lys948Asn,ENST00000610772,NM_001287395.1; T ENST00000610772 Transcript missense_variant 2937/5324 2844/5067 948/1688 K/N aaG/aaT 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 deleterious(0.03) 26/42 Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 233814656 233814656 G T 1 0 0 0 0 1 0 0 0 9744 991 35 2 2 MROH2A 2 233814656 Missense_Mutation SNP G C3L-00913_T 35729117 233814656 8378873 48 6922 ITPR1 0 . GRCh38 3 4693539 4693539 + Missense_Mutation SNP C C G C3L-00913_T C3L-00913_N C C c.4034C>G p.Ser1345Cys p.S1345C ENST00000302640 32/61 250 236 14 167 167 0 strelka-varscan-mutect ITPR1,missense_variant,p.Ser1360Cys,ENST00000354582,;ITPR1,missense_variant,p.Ser1345Cys,ENST00000302640,NM_001168272.1;ITPR1,missense_variant,p.Ser1351Cys,ENST00000357086,NM_001099952.2;ITPR1,missense_variant,p.Ser1336Cys,ENST00000456211,NM_002222.5;ITPR1,missense_variant,p.Ser1345Cys,ENST00000443694,;ITPR1,intron_variant,,ENST00000544951,; G ENST00000302640 Transcript missense_variant 4384/10197 4034/8232 1345/2743 S/C tCt/tGt COSM261461 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 deleterious(0) 32/61 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 4693539 4693539 C G 1 0 0 0 0 1 0 0 0 7826 913 32 4 4 ITPR1 3 4693539 Missense_Mutation SNP C C3L-00913_T 4693539 193602020 49 6923 GRIP2 0 . GRCh38 3 14523639 14523639 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.754G>T p.Gly252Cys p.G252C ENST00000619221 6/25 250 222 28 214 214 0 strelka-varscan-mutect GRIP2,missense_variant,p.Gly252Cys,ENST00000619221,;GRIP2,missense_variant,p.Gly155Cys,ENST00000621039,NM_001080423.3;GRIP2,missense_variant,p.Gly160Cys,ENST00000637182,;GRIP2,downstream_gene_variant,,ENST00000637939,;GRIP2,non_coding_transcript_exon_variant,,ENST00000422481,;GRIP2,non_coding_transcript_exon_variant,,ENST00000413414,; A ENST00000619221 Transcript missense_variant 754/7977 754/3423 252/1140 G/C Ggc/Tgc 1 -1 GRIP2 HGNC HGNC:23841 protein_coding YES ENSP00000480660 A0A087WX15 UPI0001DD380B deleterious(0) 6/25 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF42,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 14523639 14523639 C A 1 0 0 0 0 1 0 0 0 6669 623 22 2 2 GRIP2 3 14523639 Missense_Mutation SNP C C3L-00913_T 9830100 14523639 183771920 50 6924 MYL3 0 . GRCh38 3 46859502 46859502 + Missense_Mutation SNP C C G rs199474705 C3L-00913_T C3L-00913_N C C c.454G>C p.Glu152Gln p.E152Q ENST00000395869 4/6 240 218 22 216 216 0 strelka-varscan-mutect MYL3,missense_variant,p.Glu152Gln,ENST00000395869,;MYL3,missense_variant,p.Glu152Gln,ENST00000292327,NM_000258.2;MYL3,downstream_gene_variant,,ENST00000431168,; G ENST00000395869 Transcript missense_variant 506/1012 454/588 152/195 E/Q Gag/Cag rs199474705,CM0910617 1 -1 MYL3 HGNC HGNC:7584 protein_coding YES CCDS2746.1 ENSP00000379210 P08590 A0A024R2Q5 UPI0000000CA2 deleterious(0) 4/6 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR23048,hmmpanther:PTHR23048:SF2,Superfamily_domains:SSF47473 not_provided 20031618 MODERATE 1 SNV 1 1,1 1 PASS rs199474705 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 46859502 46859502 C G 1 0 0 0 0 1 0 0 0 10048 835 29 4 4 MYL3 3 46859502 Missense_Mutation SNP C C3L-00913_T 32335863 46859502 151436057 51 6925 ZNF717 0 . GRCh38 3 75737293 75737293 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.2180A>T p.Gln727Leu p.Q727L ENST00000478296 4/4 381 345 36 342 342 0 varscan-mutect ZNF717,missense_variant,p.Gln727Leu,ENST00000478296,NM_001290209.1;ZNF717,intron_variant,,ENST00000477374,NM_001290210.1;ZNF717,downstream_gene_variant,,ENST00000468296,;ZNF717,downstream_gene_variant,,ENST00000471541,;MIR4273,upstream_gene_variant,,ENST00000582824,;ZNF717,intron_variant,,ENST00000491507,; A ENST00000478296 Transcript missense_variant 2457/3875 2180/2595 727/864 Q/L cAg/cTg 1 -1 ZNF717 HGNC HGNC:29448 protein_coding YES CCDS77773.1 ENSP00000419377 C9JVC3 UPI0001B794C0 NM_001290209.1 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF241,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 75737293 75737293 T A 1 0 0 0 0 1 0 0 0 18695 1580 55 4 4 ZNF717 3 75737293 Missense_Mutation SNP T C3L-00913_T 28877791 75737293 122558266 52 6926 ADGRG7 0 . GRCh38 3 100646104 100646104 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1106C>A p.Pro369Gln p.P369Q ENST00000273352 9/16 289 258 31 185 185 0 strelka-varscan-mutect ADGRG7,missense_variant,p.Pro369Gln,ENST00000273352,NM_032787.2;ADGRG7,missense_variant,p.Pro74Gln,ENST00000475887,NM_001308362.1;SNORA31,upstream_gene_variant,,ENST00000517180,;ADGRG7,downstream_gene_variant,,ENST00000481361,; A ENST00000273352 Transcript missense_variant 1374/3140 1106/2394 369/797 P/Q cCa/cAa 1 1 ADGRG7 HGNC HGNC:19241 protein_coding YES CCDS2938.1 ENSP00000273352 Q96K78 UPI000004B6DF NM_032787.2 deleterious(0.03) 9/16 hmmpanther:PTHR12011:SF305,hmmpanther:PTHR12011 MODERATE 1 SNV 1 1 PASS rs1476513280 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 100646104 100646104 C A 1 0 0 0 0 1 0 0 0 374 608 21 2 2 ADGRG7 3 100646104 Missense_Mutation SNP C C3L-00913_T 24908811 100646104 97649455 53 6927 IMPG2 0 . GRCh38 3 101275727 101275727 + Frame_Shift_Del DEL G G - novel C3L-00913_T C3L-00913_N G G c.602delC p.Pro201HisfsTer30 p.P201Hfs*30 ENST00000193391 6/19 394 362 32 301 301 0 sindel-varindel-pindel IMPG2,frameshift_variant,p.Pro201HisfsTer30,ENST00000193391,NM_016247.3; - ENST00000193391 Transcript frameshift_variant 790/8337 602/3726 201/1241 P/X cCa/ca 1 -1 IMPG2 HGNC HGNC:18362 protein_coding YES CCDS2940.1 ENSP00000193391 Q9BZV3 F1T0J3 UPI000013C605 NM_016247.3 6/19 hmmpanther:PTHR12199,hmmpanther:PTHR12199:SF4 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 101275727 101275727 G - 1 0 1 0 1 0 0 0 0 7631 1348 47 0 0 IMPG2 3 101275727 Frame_Shift_Del DEL G C3L-00913_T 629623 101275727 97019832 54 6928 UPK1B 0 . GRCh38 3 119194378 119194378 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.628C>A p.Pro210Thr p.P210T ENST00000264234 6/8 171 153 18 135 135 0 varscan-mutect UPK1B,missense_variant,p.Pro210Thr,ENST00000264234,NM_006952.3;UPK1B,missense_variant,p.Pro202Thr,ENST00000460625,;UPK1B,missense_variant,p.Pro130Thr,ENST00000497685,;UPK1B,downstream_gene_variant,,ENST00000479520,;UPK1B,downstream_gene_variant,,ENST00000494855,; A ENST00000264234 Transcript missense_variant 777/2118 628/783 210/260 P/T Cct/Act 1 1 UPK1B HGNC HGNC:12578 protein_coding YES CCDS2985.1 ENSP00000264234 O75841 UPI000013D4E8 NM_006952.3 tolerated(0.68) 6/8 hmmpanther:PTHR19282:SF24,hmmpanther:PTHR19282,Pfam_domain:PF00335,Superfamily_domains:0037997 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 119194378 119194378 C A 1 0 0 0 0 1 0 0 0 17534 739 26 2 2 UPK1B 3 119194378 Missense_Mutation SNP C C3L-00913_T 17918651 119194378 79101181 55 6929 STXBP5L 0 . GRCh38 3 121233638 121233638 + Silent SNP C C A rs189961487 C3L-00913_T C3L-00913_N C C c.1134C>A p.= p.V378V ENST00000273666 12/28 244 225 19 173 172 1 strelka-varscan-mutect STXBP5L,synonymous_variant,p.=,ENST00000273666,NM_014980.2;STXBP5L,synonymous_variant,p.=,ENST00000471454,NM_001308330.1;STXBP5L,synonymous_variant,p.=,ENST00000471262,;STXBP5L,synonymous_variant,p.=,ENST00000492541,;STXBP5L,synonymous_variant,p.=,ENST00000472879,;STXBP5L,synonymous_variant,p.=,ENST00000497029,; A ENST00000273666 Transcript synonymous_variant 1405/9496 1134/3561 378/1186 V gtC/gtA rs189961487 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 12/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08366,Prints_domain:PR00962 LOW 1 SNV 1 1 PASS rs189961487 . 0 205 0 2 0 0 0 2 -9.033947 0 0 1 0 0 A 2 1 21 121233638 121233638 C A 1 0 0 0 0 0 0 0 1 15741 871 31 1 1 STXBP5L 3 121233638 Silent SNP C C3L-00913_T 2039260 121233638 77061921 56 6930 IQCB1 0 . GRCh38 3 121795483 121795484 + Frame_Shift_Ins INS - - G novel C3L-00913_T C3L-00913_N - - c.959dupC p.Val321CysfsTer21 p.V321Cfs*21 ENST00000310864 10/15 354 316 38 284 284 0 sindel-varindel-pindel IQCB1,frameshift_variant,p.Val321CysfsTer21,ENST00000310864,NM_001319107.1,NM_001023570.2;IQCB1,frameshift_variant,p.Val137CysfsTer?,ENST00000460108,;IQCB1,intron_variant,,ENST00000349820,NM_001023571.2;IQCB1,downstream_gene_variant,,ENST00000498104,;IQCB1,intron_variant,,ENST00000393650,; G ENST00000310864 Transcript frameshift_variant 1174-1175/2594 959-960/1797 320/598 A/AX gct/gcCt 1 -1 IQCB1 HGNC HGNC:28949 protein_coding YES CCDS33837.1 ENSP00000311505 Q15051 UPI0000139154 NM_001319107.1,NM_001023570.2 10/15 PROSITE_profiles:PS50096,hmmpanther:PTHR15673,Superfamily_domains:SSF52540 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 21 121795483 121795483 - G 1 0 1 1 0 0 0 0 0 7707 175 7 0 0 IQCB1 3 121795483 Frame_Shift_Ins INS - C3L-00913_T 561845 121795483 76500076 57 6931 HEG1 0 . GRCh38 3 125019544 125019544 + Missense_Mutation SNP T T A rs751829674 C3L-00913_T C3L-00913_N T T c.1306A>T p.Met436Leu p.M436L ENST00000311127 5/17 159 140 19 95 95 0 strelka-varscan-mutect HEG1,missense_variant,p.Met436Leu,ENST00000311127,NM_020733.1;HEG1,upstream_gene_variant,,ENST00000477536,; A ENST00000311127 Transcript missense_variant 1374/9156 1306/4146 436/1381 M/L Atg/Ttg rs751829674 1 -1 HEG1 HGNC HGNC:29227 protein_coding YES CCDS46898.1 ENSP00000311502 Q9ULI3 UPI00006C069B NM_020733.1 tolerated(0.31) 5/17 hmmpanther:PTHR24037:SF3,hmmpanther:PTHR24037 MODERATE 1 SNV 5 1 PASS rs751829674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 125019544 125019544 T A 1 0 0 0 0 1 0 0 0 6926 1464 51 4 4 HEG1 3 125019544 Missense_Mutation SNP T C3L-00913_T 3224061 125019544 73276015 58 6932 SI 0 . GRCh38 3 165015130 165015130 + Missense_Mutation SNP C C A rs776755426 C3L-00913_T C3L-00913_N C C c.3992G>T p.Trp1331Leu p.W1331L ENST00000264382 33/48 444 404 40 319 318 1 strelka-varscan SI,missense_variant,p.Trp1331Leu,ENST00000264382,NM_001041.3; A ENST00000264382 Transcript missense_variant 4055/6011 3992/5484 1331/1827 W/L tGg/tTg rs776755426,COSM354351 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.08) 33/48 Pfam_domain:PF01055,Superfamily_domains:SSF51445 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 165015130 165015130 C A 1 0 0 0 0 1 0 0 0 14561 595 21 2 2 SI 3 165015130 Missense_Mutation SNP C C3L-00913_T 39995586 165015130 33280429 59 6933 COX7B2 0 . GRCh38 4 46735136 46735136 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.57G>T p.= p.L19L ENST00000396533 4/4 254 210 44 169 169 0 strelka-varscan-mutect COX7B2,synonymous_variant,p.=,ENST00000396533,;COX7B2,synonymous_variant,p.=,ENST00000543208,;COX7B2,synonymous_variant,p.=,ENST00000355591,NM_130902.2;COX7B2,synonymous_variant,p.=,ENST00000505102,; A ENST00000396533 Transcript synonymous_variant 308/617 57/246 19/81 L ctG/ctT 1 -1 COX7B2 HGNC HGNC:24381 protein_coding YES CCDS3472.2 ENSP00000379784 Q8TF08 UPI000005034B 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR16716:SF1,hmmpanther:PTHR16716,Pfam_domain:PF05392 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 46735136 46735136 C A 1 0 0 0 0 0 0 0 1 3578 697 25 2 2 COX7B2 4 46735136 Silent SNP C C3L-00913_T 46735136 143479419 60 6934 MTTP 0 . GRCh38 4 99582063 99582063 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.301G>A p.Gly101Ser p.G101S ENST00000511045 2/18 373 350 23 279 279 0 strelka-varscan-mutect MTTP,missense_variant,p.Gly74Ser,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Gly74Ser,ENST00000265517,;MTTP,missense_variant,p.Gly101Ser,ENST00000511045,NM_001300785.1;MTTP,missense_variant,p.Gly74Ser,ENST00000422897,;MTTP,missense_variant,p.Gly84Ser,ENST00000506883,;MTTP,3_prime_UTR_variant,,ENST00000515141,;MTTP,3_prime_UTR_variant,,ENST00000513404,;MTTP,3_prime_UTR_variant,,ENST00000505094,;MTTP,downstream_gene_variant,,ENST00000511610,;MTTP,downstream_gene_variant,,ENST00000505142,; A ENST00000511045 Transcript missense_variant 314/3154 301/2766 101/921 G/S Ggt/Agt 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 tolerated(0.23) 2/18 Gene3D:1lshA01,Pfam_domain:PF01347,PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1,SMART_domains:SM00638,Superfamily_domains:SSF56968 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 99582063 99582063 G A 1 0 0 0 0 1 0 0 0 9961 1348 47 3 3 MTTP 4 99582063 Missense_Mutation SNP G C3L-00913_T 52846927 99582063 90632492 61 6935 ANKRD50 0 . GRCh38 4 124670372 124670372 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.2905G>T p.Gly969Cys p.G969C ENST00000504087 4/5 265 248 17 263 262 1 strelka-varscan-mutect ANKRD50,missense_variant,p.Gly969Cys,ENST00000504087,NM_020337.2;ANKRD50,missense_variant,p.Gly790Cys,ENST00000515641,NM_001167882.1; A ENST00000504087 Transcript missense_variant 3943/8794 2905/4290 969/1429 G/C Ggt/Tgt 1 -1 ANKRD50 HGNC HGNC:29223 protein_coding YES CCDS34060.1 ENSP00000425658 Q9ULJ7 UPI00002377E8 NM_020337.2 deleterious(0) 4/5 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24151,hmmpanther:PTHR24151:SF1,Pfam_domain:PF13637,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 124670372 124670372 C A 1 0 0 0 0 1 0 0 0 781 594 21 2 2 ANKRD50 4 124670372 Missense_Mutation SNP C C3L-00913_T 25088309 124670372 65544183 62 6936 TENM3 0 . GRCh38 4 182730933 182730933 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.2761C>A p.Pro921Thr p.P921T ENST00000511685 16/28 277 258 19 197 195 2 strelka-varscan-mutect TENM3,missense_variant,p.Pro921Thr,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,; A ENST00000511685 Transcript missense_variant 2884/10896 2761/8100 921/2699 P/T Cca/Aca 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 deleterious(0) 16/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10,Superfamily_domains:SSF49464 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 182730933 182730933 C A 1 0 0 0 0 1 0 0 0 16173 623 22 2 2 TENM3 4 182730933 Missense_Mutation SNP C C3L-00913_T 58060561 182730933 7483622 63 6937 ADAMTS16 0 . GRCh38 5 5303763 5303763 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.3183C>A p.= p.S1061S ENST00000274181 20/23 251 217 34 160 160 0 strelka-varscan-mutect ADAMTS16,synonymous_variant,p.=,ENST00000274181,NM_139056.2;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript synonymous_variant 3321/4979 3183/3675 1061/1224 S tcC/tcA 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 20/23 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 5303763 5303763 C A 1 0 0 0 0 0 0 0 1 305 637 22 2 2 ADAMTS16 5 5303763 Silent SNP C C3L-00913_T 5303763 176234496 64 6938 ADAMTS12 0 . GRCh38 5 33637746 33637746 + Missense_Mutation SNP C C A C3L-00913_T C3L-00913_N C C c.1719G>T p.Glu573Asp p.E573D ENST00000504830 12/24 168 151 17 117 117 0 strelka-varscan ADAMTS12,missense_variant,p.Glu573Asp,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Glu573Asp,ENST00000352040,;ADAMTS12,splice_region_variant,,ENST00000504582,; A ENST00000504830 Transcript missense_variant,splice_region_variant 2055/8774 1719/4785 573/1594 E/D gaG/gaT COSM3381238 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.22) 12/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 33637746 33637746 C A 1 0 0 0 0 1 0 0 0 301 753 26 2 2 ADAMTS12 5 33637746 Missense_Mutation SNP C C3L-00913_T 28333983 33637746 147900513 65 6939 RICTOR 0 . GRCh38 5 38950188 38950188 + Silent SNP G G A novel C3L-00913_T C3L-00913_N G G c.3660C>T p.= p.F1220F ENST00000296782 31/39 270 255 15 258 258 0 strelka-varscan RICTOR,synonymous_variant,p.=,ENST00000357387,NM_152756.4,NM_001285440.1;RICTOR,synonymous_variant,p.=,ENST00000296782,NM_001285439.1;RICTOR,downstream_gene_variant,,ENST00000503698,;RICTOR,3_prime_UTR_variant,,ENST00000511516,;OSMR,downstream_gene_variant,,ENST00000509237,; A ENST00000296782 Transcript synonymous_variant 3682/7505 3660/5199 1220/1732 F ttC/ttT 1 -1 RICTOR HGNC HGNC:28611 protein_coding YES CCDS68861.1 ENSP00000296782 Q6R327 UPI0000EE67F5 NM_001285439.1 31/39 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 38950188 38950188 G A 1 0 0 0 0 0 0 0 1 13531 1281 45 3 3 RICTOR 5 38950188 Silent SNP G C3L-00913_T 5312442 38950188 142588071 66 6940 POU5F2 0 . GRCh38 5 93740850 93740850 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.714G>T p.Gln238His p.Q238H ENST00000606183 1/1 502 457 45 315 314 1 strelka-varscan POU5F2,missense_variant,p.Gln238His,ENST00000606183,NM_153216.1;FAM172A,intron_variant,,ENST00000395965,NM_032042.5;FAM172A,intron_variant,,ENST00000505869,NM_001163418.1;FAM172A,intron_variant,,ENST00000509163,NM_001163417.1;FAM172A,intron_variant,,ENST00000509739,;RP11-185E12.2,upstream_gene_variant,,ENST00000606528,;FAM172A,intron_variant,,ENST00000502503,; A ENST00000606183 Transcript missense_variant 788/8418 714/987 238/328 Q/H caG/caT 1 -1 POU5F2 HGNC HGNC:26367 protein_coding YES CCDS59489.1 ENSP00000489796 Q8N7G0 UPI0000135E4C NM_153216.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50071,hmmpanther:PTHR11636:SF14,hmmpanther:PTHR11636,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 93740850 93740850 C A 1 0 0 0 0 1 0 0 0 12399 796 28 2 2 POU5F2 5 93740850 Missense_Mutation SNP C C3L-00913_T 54790662 93740850 87797409 67 6941 TTC37 0 . GRCh38 5 95528142 95528142 + Silent SNP G G A rs774106534 C3L-00913_T C3L-00913_N G G c.1005C>T p.= p.I335I ENST00000358746 13/43 569 509 60 332 332 0 strelka-varscan TTC37,synonymous_variant,p.=,ENST00000358746,NM_014639.3;TTC37,synonymous_variant,p.=,ENST00000514952,;TTC37,non_coding_transcript_exon_variant,,ENST00000504421,;TTC37,intron_variant,,ENST00000505578,;TTC37,upstream_gene_variant,,ENST00000513232,;TTC37,downstream_gene_variant,,ENST00000503279,; A ENST00000358746 Transcript synonymous_variant 1304/5706 1005/4695 335/1564 I atC/atT rs774106534,COSM3618827 1 -1 TTC37 HGNC HGNC:23639 protein_coding YES CCDS4072.1 ENSP00000351596 Q6PGP7 UPI00000709BD NM_014639.3 13/43 Gene3D:1.25.40.10,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR15704,hmmpanther:PTHR15704:SF7,SMART_domains:SM00028,Superfamily_domains:SSF48452 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 95528142 95528142 G A 1 0 0 0 0 0 0 0 1 17214 1048 37 1 1 TTC37 5 95528142 Silent SNP G C3L-00913_T 1787292 95528142 86010117 68 6942 SH3PXD2B 0 . GRCh38 5 172353917 172353917 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.756G>C p.Gln252His p.Q252H ENST00000311601 9/13 471 435 36 345 345 0 strelka-varscan SH3PXD2B,missense_variant,p.Gln252His,ENST00000311601,NM_001017995.2;SH3PXD2B,missense_variant,p.Gln266His,ENST00000636523,;SH3PXD2B,missense_variant,p.Gln252His,ENST00000519643,NM_001308175.1;SH3PXD2B,upstream_gene_variant,,ENST00000518522,; G ENST00000311601 Transcript missense_variant 927/7777 756/2736 252/911 Q/H caG/caC 1 -1 SH3PXD2B HGNC HGNC:29242 protein_coding YES CCDS34291.1 ENSP00000309714 A1X283 UPI000020C12E NM_001017995.2 tolerated(0.11) 9/13 Gene3D:2.30.30.40,Pfam_domain:PF00018,PROSITE_profiles:PS50002,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF8,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 172353917 172353917 C G 1 0 0 0 0 1 0 0 0 14516 912 32 4 4 SH3PXD2B 5 172353917 Missense_Mutation SNP C C3L-00913_T 76825775 172353917 9184342 69 6943 BTNL9 0 . GRCh38 5 181056581 181056581 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.999G>T p.Gln333His p.Q333H ENST00000376841 10/11 255 213 42 164 164 0 strelka-varscan BTNL9,missense_variant,p.Gln333His,ENST00000376841,NM_001308245.1;BTNL9,intron_variant,,ENST00000327705,NM_152547.4;BTNL9,downstream_gene_variant,,ENST00000515271,;BTNL9,downstream_gene_variant,,ENST00000511589,;BTNL9,intron_variant,,ENST00000512570,;BTNL9,downstream_gene_variant,,ENST00000491209,;BTNL9,downstream_gene_variant,,ENST00000506782,;BTNL9,downstream_gene_variant,,ENST00000509395,;BTNL9,downstream_gene_variant,,ENST00000511056,; T ENST00000376841 Transcript missense_variant 1230/1626 999/1035 333/344 Q/H caG/caT 1 1 BTNL9 HGNC HGNC:24176 protein_coding CCDS78104.1 ENSP00000366037 Q6UXG8 UPI000021FB76 NM_001308245.1 tolerated_low_confidence(0.46) 10/11 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 181056581 181056581 G T 1 0 0 0 0 1 0 0 0 1744 991 35 2 2 BTNL9 5 181056581 Missense_Mutation SNP G C3L-00913_T 8702664 181056581 481678 70 6944 DSP 0 . GRCh38 6 7580333 7580333 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.4143C>A p.= p.T1381T ENST00000379802 23/24 228 189 39 210 209 1 strelka-varscan-mutect DSP,synonymous_variant,p.=,ENST00000379802,NM_004415.2;DSP,intron_variant,,ENST00000418664,NM_001008844.1; A ENST00000379802 Transcript synonymous_variant 4484/9796 4143/8616 1381/2871 T acC/acA 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 23/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,PD936484 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 7580333 7580333 C A 1 0 0 0 0 0 0 0 1 4602 581 21 2 2 DSP 6 7580333 Silent SNP C C3L-00913_T 7580333 163225646 71 6945 ID4 0 . GRCh38 6 19837845 19837845 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.91C>A p.His31Asn p.H31N ENST00000378700 1/3 29 24 5 23 23 0 strelka-varscan-mutect ID4,missense_variant,p.His31Asn,ENST00000378700,NM_001546.3;RP4-625H18.2,intron_variant,,ENST00000432171,; A ENST00000378700 Transcript missense_variant 460/2344 91/486 31/161 H/N Cac/Aac 1 1 ID4 HGNC HGNC:5363 protein_coding YES CCDS4544.1 ENSP00000367972 P47928 UPI000012D193 NM_001546.3 deleterious(0.03) 1/3 hmmpanther:PTHR11723,hmmpanther:PTHR11723:SF6 MODERATE 1 SNV 1 1 PASS rs1374749619 . 63 146 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 19837845 19837845 C A 1 0 0 0 0 1 0 0 0 7392 710 25 2 2 ID4 6 19837845 Missense_Mutation SNP C C3L-00913_T 12257512 19837845 150968134 72 6946 OR10C1 0 . GRCh38 6 29440280 29440280 + Missense_Mutation SNP C C G rs11755182 C3L-00913_T C3L-00913_N C C c.265C>G p.Arg89Gly p.R89G ENST00000444197 1/1 353 295 58 258 258 0 strelka-varscan OR10C1,missense_variant,p.Arg89Gly,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Arg91Gly,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; G ENST00000444197 Transcript missense_variant 975/1649 265/939 89/312 R/G Cgc/Ggc rs11755182 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 tolerated(0.09) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321 19833159 MODERATE 1 SNV 1 PASS . . 0 201 0 0 0 0 0 8 -2.732922 0 0 1 0 0 G 3 3 21 29440280 29440280 C G 1 0 0 0 0 1 0 0 0 10973 768 27 4 4 OR10C1 6 29440280 Missense_Mutation SNP C C3L-00913_T 9602435 29440280 141365699 73 6947 TREML4 0 . GRCh38 6 41229568 41229568 + Missense_Mutation SNP A A T novel C3L-00913_T C3L-00913_N A A c.442A>T p.Thr148Ser p.T148S ENST00000341495 3/6 354 320 34 244 243 1 strelka-varscan TREML4,missense_variant,p.Thr148Ser,ENST00000341495,NM_198153.2;TREML4,missense_variant,p.Thr148Ser,ENST00000448827,;TREML4,missense_variant,p.Thr47Ser,ENST00000461240,; T ENST00000341495 Transcript missense_variant 546/2070 442/603 148/200 T/S Aca/Tca 1 1 TREML4 HGNC HGNC:30807 protein_coding YES CCDS34446.1 ENSP00000342570 Q6UXN2 UPI00001D696F NM_198153.2 tolerated(0.17) 3/6 hmmpanther:PTHR16423,hmmpanther:PTHR16423:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 41229568 41229568 A T 1 0 0 0 0 1 0 0 0 16963 173 6 4 4 TREML4 6 41229568 Missense_Mutation SNP A C3L-00913_T 11789288 41229568 129576411 74 6948 TCTE1 0 . GRCh38 6 44286252 44286252 + Missense_Mutation SNP A A T novel C3L-00913_T C3L-00913_N A A c.558T>A p.Asn186Lys p.N186K ENST00000371505 3/5 224 192 32 197 196 1 strelka-varscan TCTE1,missense_variant,p.Asn186Lys,ENST00000371505,NM_182539.3;TCTE1,missense_variant,p.Asn33Lys,ENST00000371504,;TMEM151B,intron_variant,,ENST00000438774,;RP11-444E17.6,intron_variant,,ENST00000505802,; T ENST00000371505 Transcript missense_variant 681/3067 558/1506 186/501 N/K aaT/aaA 1 -1 TCTE1 HGNC HGNC:11693 protein_coding YES CCDS4910.1 ENSP00000360560 Q5JU00 UPI0000160BC0 NM_182539.3 tolerated(0.28) 3/5 hmmpanther:PTHR24107:SF2,hmmpanther:PTHR24107 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 44286252 44286252 A T 1 0 0 0 0 1 0 0 0 16125 98 4 4 4 TCTE1 6 44286252 Missense_Mutation SNP A C3L-00913_T 3056684 44286252 126519727 75 6949 PKHD1 0 . GRCh38 6 52053196 52053196 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.2020C>T p.Leu674Phe p.L674F ENST00000371117 21/67 306 266 40 227 227 0 strelka-varscan PKHD1,missense_variant,p.Leu674Phe,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Leu674Phe,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 2296/16282 2020/12225 674/4074 L/F Ctc/Ttc 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.02) 21/67 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 52053196 52053196 G A 1 0 0 0 0 1 0 0 0 12067 942 33 3 3 PKHD1 6 52053196 Missense_Mutation SNP G C3L-00913_T 7766944 52053196 118752783 76 6950 KLHL31 0 . GRCh38 6 53652178 53652178 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1325C>T p.Ser442Phe p.S442F ENST00000370905 3/3 153 132 21 140 139 1 strelka-varscan KLHL31,missense_variant,p.Ser442Phe,ENST00000370905,NM_001003760.4;KLHL31,missense_variant,p.Ser442Phe,ENST00000407079,; A ENST00000370905 Transcript missense_variant 1466/5743 1325/1905 442/634 S/F tCc/tTc 1 -1 KLHL31 HGNC HGNC:21353 protein_coding YES CCDS34478.1 ENSP00000359942 Q9H511 UPI000006D624 NM_001003760.4 deleterious(0.01) 3/3 hmmpanther:PTHR24412:SF247,hmmpanther:PTHR24412,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 53652178 53652178 G A 1 0 0 0 0 1 0 0 0 8250 1174 41 3 3 KLHL31 6 53652178 Missense_Mutation SNP G C3L-00913_T 1598982 53652178 117153801 77 6951 ADGRB3 0 . GRCh38 6 69233315 69233315 + Missense_Mutation SNP A A T novel C3L-00913_T C3L-00913_N A A c.2506A>T p.Thr836Ser p.T836S ENST00000370598 18/32 222 197 25 151 151 0 strelka-varscan ADGRB3,missense_variant,p.Thr836Ser,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Thr836Ser,ENST00000546190,;ADGRB3,missense_variant,p.Thr42Ser,ENST00000238918,;ADGRB3,missense_variant,p.Thr20Ser,ENST00000603207,;ADGRB3,5_prime_UTR_variant,,ENST00000604969,; T ENST00000370598 Transcript missense_variant 3327/6010 2506/4569 836/1522 T/S Acc/Tcc 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 tolerated(0.25) 18/32 PROSITE_profiles:PS50221,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF01825,SMART_domains:SM00303 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 69233315 69233315 A T 1 0 0 0 0 1 0 0 0 357 159 6 4 4 ADGRB3 6 69233315 Missense_Mutation SNP A C3L-00913_T 15581137 69233315 101572664 78 6952 RIMS1 0 . GRCh38 6 72292002 72292002 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.3806G>A p.Arg1269Lys p.R1269K ENST00000521978 26/34 216 203 13 160 159 1 strelka-varscan RIMS1,missense_variant,p.Arg1118Lys,ENST00000264839,;RIMS1,missense_variant,p.Arg1269Lys,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Arg1092Lys,ENST00000491071,;RIMS1,missense_variant,p.Arg1091Lys,ENST00000520567,;RIMS1,missense_variant,p.Arg1061Lys,ENST00000517960,;RIMS1,missense_variant,p.Arg1120Lys,ENST00000518273,;RIMS1,missense_variant,p.Arg1040Lys,ENST00000522291,;RIMS1,missense_variant,p.Arg589Lys,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Arg615Lys,ENST00000517433,;RIMS1,missense_variant,p.Arg566Lys,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Arg575Lys,ENST00000517827,NM_001168410.1;RIMS1,missense_variant,p.Arg509Lys,ENST00000425662,NM_001168409.1;RIMS1,missense_variant,p.Arg434Lys,ENST00000453976,;RIMS1,missense_variant,p.Arg177Lys,ENST00000522211,;RIMS1,missense_variant,p.Arg317Lys,ENST00000370420,;RIMS1,non_coding_transcript_exon_variant,,ENST00000463023,; A ENST00000521978 Transcript missense_variant 3806/5079 3806/5079 1269/1692 R/K aGa/aAa 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious(0) 26/34 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 72292002 72292002 G A 1 0 0 0 0 1 0 0 0 13542 942 33 3 3 RIMS1 6 72292002 Missense_Mutation SNP G C3L-00913_T 3058687 72292002 98513977 79 6953 BCKDHB 0 . GRCh38 6 80129181 80129181 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.295G>T p.Ala99Ser p.A99S ENST00000320393 3/10 313 277 36 228 228 0 strelka-varscan BCKDHB,missense_variant,p.Ala99Ser,ENST00000320393,NM_001318975.1,NM_183050.2;BCKDHB,missense_variant,p.Ala99Ser,ENST00000356489,NM_000056.3;BCKDHB,missense_variant,p.Ala99Ser,ENST00000369760,;BCKDHB,non_coding_transcript_exon_variant,,ENST00000486968,; T ENST00000320393 Transcript missense_variant 342/3692 295/1179 99/392 A/S Gcc/Tcc 1 1 BCKDHB HGNC HGNC:987 protein_coding YES CCDS4994.1 ENSP00000318351 P21953 A0A140VKB3 UPI0000001C97 NM_001318975.1,NM_183050.2 tolerated(0.1) 3/10 Gene3D:3.40.50.970,Pfam_domain:PF02779,hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF21,SMART_domains:SM00861,Superfamily_domains:SSF52518 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 80129181 80129181 G T 1 0 0 0 0 1 0 0 0 1507 1319 46 2 2 BCKDHB 6 80129181 Missense_Mutation SNP G C3L-00913_T 7837179 80129181 90676798 80 6954 ME1 0 . GRCh38 6 83227448 83227448 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.1162G>A p.Glu388Lys p.E388K ENST00000369705 11/14 129 114 15 88 88 0 strelka-varscan ME1,missense_variant,p.Glu388Lys,ENST00000369705,NM_002395.5; T ENST00000369705 Transcript missense_variant 1279/3371 1162/1719 388/572 E/K Gaa/Aaa 1 -1 ME1 HGNC HGNC:6983 protein_coding YES CCDS34492.1 ENSP00000358719 P48163 UPI000000127E NM_002395.5 tolerated(0.65) 11/14 Gene3D:3.40.50.720,Pfam_domain:PF03949,PIRSF_domain:PIRSF000106,hmmpanther:PTHR23406,hmmpanther:PTHR23406:SF17,SMART_domains:SM00919,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999966 1 1 1 0 T 3 4 21 83227448 83227448 C T 1 0 0 0 0 1 0 0 0 9356 922 32 3 3 ME1 6 83227448 Missense_Mutation SNP C C3L-00913_T 3098267 83227448 87578531 81 6955 ORC3 0 . GRCh38 6 87616366 87616366 + Frame_Shift_Del DEL T T - novel C3L-00913_T C3L-00913_N T T c.927delT p.Leu310Ter p.L310* ENST00000257789 9/20 222 202 20 153 153 0 sindel-varindel-pindel ORC3,frameshift_variant,p.Leu310Ter,ENST00000392844,NM_012381.3;ORC3,frameshift_variant,p.Leu310Ter,ENST00000257789,NM_181837.2;ORC3,frameshift_variant,p.Leu167Ter,ENST00000546266,NM_001197259.1; - ENST00000257789 Transcript frameshift_variant 960/2501 926/2139 309/712 V/X gTt/gt 1 1 ORC3 HGNC HGNC:8489 protein_coding YES CCDS5012.1 ENSP00000257789 Q9UBD5 UPI00001B216A NM_181837.2 9/20 Pfam_domain:PF07034,hmmpanther:PTHR12748,hmmpanther:PTHR12748:SF0 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 87616366 87616366 T - 1 0 1 0 1 0 0 0 0 11329 1725 60 0 0 ORC3 6 87616366 Frame_Shift_Del DEL T C3L-00913_T 4388918 87616366 83189613 82 6956 REV3L 0 . GRCh38 6 111365281 111365281 + Missense_Mutation SNP A A C novel C3L-00913_T C3L-00913_N A A c.6737T>G p.Leu2246Arg p.L2246R ENST00000358835 16/33 278 259 19 247 247 0 strelka-varscan-mutect REV3L,missense_variant,p.Leu2168Arg,ENST00000435970,NM_001286431.1,NM_001286432.1;REV3L,missense_variant,p.Leu2246Arg,ENST00000358835,NM_002912.4;REV3L,missense_variant,p.Leu2246Arg,ENST00000368802,;REV3L,missense_variant,p.Leu2246Arg,ENST00000368805,;REV3L-IT1,upstream_gene_variant,,ENST00000411895,;REV3L,missense_variant,p.Leu103Arg,ENST00000413831,;REV3L,3_prime_UTR_variant,,ENST00000422377,;REV3L,3_prime_UTR_variant,,ENST00000434009,; C ENST00000358835 Transcript missense_variant 7195/10815 6737/9393 2246/3130 L/R cTg/cGg 1 -1 REV3L HGNC HGNC:9968 protein_coding YES CCDS5091.2 ENSP00000351697 O60673 UPI0000140023 NM_002912.4 deleterious(0) 16/33 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 111365281 111365281 A C 1 0 0 0 0 1 0 0 0 13411 188 7 5 5 REV3L 6 111365281 Missense_Mutation SNP A C3L-00913_T 23748915 111365281 59440698 83 6957 HIVEP2 0 . GRCh38 6 142760051 142760051 + Frame_Shift_Del DEL C C - novel C3L-00913_T C3L-00913_N C C c.6237delG p.Arg2080GlufsTer6 p.R2080Efs*6 ENST00000367603 9/10 215 193 22 199 199 0 sindel-varindel-pindel HIVEP2,frameshift_variant,p.Arg2080GlufsTer6,ENST00000367603,NM_006734.3;HIVEP2,frameshift_variant,p.Arg2080GlufsTer6,ENST00000367604,;HIVEP2,frameshift_variant,p.Arg2080GlufsTer6,ENST00000012134,; - ENST00000367603 Transcript frameshift_variant 6980/9723 6237/7341 2079/2446 R/X agG/ag 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 9/10 hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 142760051 142760051 C - 1 0 1 0 1 0 0 0 0 7076 854 30 0 0 HIVEP2 6 142760051 Frame_Shift_Del DEL C C3L-00913_T 31394770 142760051 28045928 84 6958 SYNE1 0 . GRCh38 6 152466051 152466051 + Nonsense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1660G>T p.Glu554Ter p.E554* ENST00000367255 17/146 269 239 30 157 157 0 strelka-varscan-mutect SYNE1,stop_gained,p.Glu554Ter,ENST00000367255,NM_182961.3;SYNE1,stop_gained,p.Glu561Ter,ENST00000423061,NM_033071.3;SYNE1,stop_gained,p.Glu544Ter,ENST00000341594,;SYNE1,stop_gained,p.Glu544Ter,ENST00000367248,;SYNE1,stop_gained,p.Glu554Ter,ENST00000367253,;SYNE1,stop_gained,p.Glu554Ter,ENST00000413186,;SYNE1,stop_gained,p.Glu537Ter,ENST00000537750,;SYNE1,stop_gained,p.Glu554Ter,ENST00000466159,;SYNE1,stop_gained,p.Glu121Ter,ENST00000495090,;SYNE1,non_coding_transcript_exon_variant,,ENST00000535896,;SYNE1,non_coding_transcript_exon_variant,,ENST00000481502,;SYNE1,upstream_gene_variant,,ENST00000498751,;SYNE1,3_prime_UTR_variant,,ENST00000474655,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,;SYNE1,non_coding_transcript_exon_variant,,ENST00000468937,; A ENST00000367255 Transcript stop_gained 2262/27748 1660/26394 554/8797 E/* Gaa/Taa 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 17/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 21 152466051 152466051 C A 1 0 0 0 0 0 1 0 0 15837 835 29 2 2 SYNE1 6 152466051 Nonsense_Mutation SNP C C3L-00913_T 9706000 152466051 18339928 85 6959 AGMO 0 . GRCh38 7 15560270 15560270 + Missense_Mutation SNP G G T C3L-00913_T C3L-00913_N G G c.128C>A p.Ala43Glu p.A43E ENST00000342526 2/13 123 111 12 100 99 1 strelka-varscan-mutect AGMO,missense_variant,p.Ala43Glu,ENST00000342526,NM_001004320.1; T ENST00000342526 Transcript missense_variant,splice_region_variant 298/2475 128/1338 43/445 A/E gCa/gAa COSM5612440 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 deleterious(0) 2/13 hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 1 MODERATE 1 SNV 1 1 1 PASS rs1286930315 . 0 207 3 0 0 0 0 0 -19.99992 1 1 1 1 0 T 3 4 21 15560270 15560270 G T 1 0 0 0 0 1 0 0 0 463 1333 46 2 2 AGMO 7 15560270 Missense_Mutation SNP G C3L-00913_T 15560270 143785703 86 6960 DNAH11 0 . GRCh38 7 21681554 21681554 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.5337G>T p.Gln1779His p.Q1779H ENST00000409508 31/82 271 248 23 227 227 0 strelka-varscan-mutect DNAH11,missense_variant,p.Gln1779His,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.Gln1784His,ENST00000328843,;DNAH11,missense_variant,p.Gln1784His,ENST00000620169,; T ENST00000409508 Transcript missense_variant 5368/14167 5337/13551 1779/4516 Q/H caG/caT 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 deleterious(0) 31/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 21681554 21681554 G T 1 0 0 0 0 1 0 0 0 4413 962 34 2 2 DNAH11 7 21681554 Missense_Mutation SNP G C3L-00913_T 6121284 21681554 137664419 87 6961 CREB5 0 . GRCh38 7 28570503 28570503 + Missense_Mutation SNP A A T C3L-00913_T C3L-00913_N A A c.430A>T p.Ile144Phe p.I144F ENST00000357727 5/11 148 127 21 105 105 0 strelka-varscan-mutect CREB5,missense_variant,p.Ile144Phe,ENST00000357727,NM_182898.3;CREB5,missense_variant,p.Ile137Phe,ENST00000396300,NM_004904.3;CREB5,missense_variant,p.Ile111Phe,ENST00000396299,NM_182899.4;CREB5,missense_variant,p.Ile111Phe,ENST00000409603,;CREB5,downstream_gene_variant,,ENST00000424599,;CREB5,non_coding_transcript_exon_variant,,ENST00000461921,; T ENST00000357727 Transcript missense_variant 820/8532 430/1527 144/508 I/F Atc/Ttc COSM131375 1 1 CREB5 HGNC HGNC:16844 protein_coding YES CCDS5417.1 ENSP00000350359 Q02930 UPI0000457534 NM_182898.3 deleterious(0) 5/11 PIRSF_domain:PIRSF003153,hmmpanther:PTHR19304,hmmpanther:PTHR19304:SF8 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 28570503 28570503 A T 1 0 0 0 0 1 0 0 0 3660 217 8 4 4 CREB5 7 28570503 Missense_Mutation SNP A C3L-00913_T 6888949 28570503 130775470 88 6962 AEBP1 0 . GRCh38 7 44106676 44106676 + Silent SNP C C A rs200224104 C3L-00913_T C3L-00913_N C C c.384C>A p.= p.T128T ENST00000223357 2/21 557 515 42 376 376 0 varscan-mutect AEBP1,synonymous_variant,p.=,ENST00000223357,NM_001129.4;AEBP1,synonymous_variant,p.=,ENST00000455443,;AEBP1,synonymous_variant,p.=,ENST00000449162,;AEBP1,upstream_gene_variant,,ENST00000450684,;AEBP1,upstream_gene_variant,,ENST00000582839,;AEBP1,upstream_gene_variant,,ENST00000454218,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,upstream_gene_variant,,ENST00000453052,;AEBP1,upstream_gene_variant,,ENST00000434445,; A ENST00000223357 Transcript synonymous_variant 689/4081 384/3477 128/1158 T acC/acA rs200224104 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 2/21 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs200224104 . 0 207 0 0 0 0 0 3 -17.49729 0 0 1 0 0 A 2 1 21 44106676 44106676 C A 1 0 0 0 0 0 0 0 1 424 581 21 2 2 AEBP1 7 44106676 Silent SNP C C3L-00913_T 15536173 44106676 115239297 89 6963 EGFR 0 . GRCh38 7 55181340 55181340 + Silent SNP G G T novel C3L-00913_T C3L-00913_N G G c.2331G>T p.= p.L777L ENST00000275493 20/28 327 285 42 222 222 0 strelka-varscan-mutect EGFR,synonymous_variant,p.=,ENST00000275493,NM_005228.3;EGFR,synonymous_variant,p.=,ENST00000454757,;EGFR,synonymous_variant,p.=,ENST00000455089,;EGFR-AS1,non_coding_transcript_exon_variant,,ENST00000442411,; T ENST00000275493 Transcript synonymous_variant 2508/9821 2331/3633 777/1210 L ctG/ctT 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 20/28 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs1210093278 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 55181340 55181340 G T 1 0 0 0 0 0 0 0 1 4803 1306 46 2 2 EGFR 7 55181340 Silent SNP G C3L-00913_T 11074664 55181340 104164633 90 6964 CLIP2 0 . GRCh38 7 74356553 74356553 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.947G>T p.Ser316Ile p.S316I ENST00000223398 5/17 625 553 72 409 408 1 strelka-varscan-mutect CLIP2,missense_variant,p.Ser316Ile,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Ser316Ile,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Ser316Ile,ENST00000395060,; T ENST00000223398 Transcript missense_variant 1274/5563 947/3141 316/1046 S/I aGc/aTc 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 deleterious(0) 5/17 hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10,Low_complexity_(Seg):seg,Superfamily_domains:SSF74924 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 74356553 74356553 G T 1 0 0 0 0 1 0 0 0 3302 971 34 2 2 CLIP2 7 74356553 Missense_Mutation SNP G C3L-00913_T 19175213 74356553 84989420 91 6965 PCLO 0 . GRCh38 7 82847148 82847148 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.13754G>T p.Cys4585Phe p.C4585F ENST00000333891 11/25 209 184 25 136 136 0 strelka-varscan-mutect PCLO,missense_variant,p.Cys4585Phe,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Cys4585Phe,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Val18Leu,ENST00000618073,;PCLO,splice_region_variant,,ENST00000426442,;PCLO,3_prime_UTR_variant,,ENST00000413807,;PCLO,3_prime_UTR_variant,,ENST00000456006,; A ENST00000333891 Transcript missense_variant 14092/20329 13754/15429 4585/5142 C/F tGt/tTt 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0) 11/25 PROSITE_profiles:PS50106,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 82847148 82847148 C A 1 0 0 0 0 1 0 0 0 11671 492 17 2 2 PCLO 7 82847148 Missense_Mutation SNP C C3L-00913_T 8490595 82847148 76498825 92 6966 SMURF1 0 . GRCh38 7 99038482 99038482 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.1672G>A p.Glu558Lys p.E558K ENST00000361125 15/19 262 246 16 220 220 0 strelka-varscan-mutect SMURF1,missense_variant,p.Glu558Lys,ENST00000361125,NM_020429.2;SMURF1,missense_variant,p.Glu532Lys,ENST00000361368,NM_001199847.1,NM_181349.2;AC004893.11,intron_variant,,ENST00000468960,;AC004893.11,downstream_gene_variant,,ENST00000360902,; T ENST00000361125 Transcript missense_variant 1992/5737 1672/2274 558/757 E/K Gaa/Aaa 1 -1 SMURF1 HGNC HGNC:16807 protein_coding YES CCDS34690.1 ENSP00000354621 Q9HCE7 UPI00000015C4 NM_020429.2 deleterious(0) 15/19 PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF293,hmmpanther:PTHR11254,Gene3D:1c4zA02,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 99038482 99038482 C T 1 0 0 0 0 1 0 0 0 15140 864 30 3 3 SMURF1 7 99038482 Missense_Mutation SNP C C3L-00913_T 16191334 99038482 60307491 93 6967 MUC17 0 . GRCh38 7 101040523 101040523 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.9107T>A p.Ile3036Lys p.I3036K ENST00000306151 3/13 204 184 20 180 180 0 strelka-varscan-mutect MUC17,missense_variant,p.Ile3036Lys,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ile3036Lys,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; A ENST00000306151 Transcript missense_variant 9171/14247 9107/13482 3036/4493 I/K aTa/aAa 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0.01) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 101040523 101040523 T A 1 0 0 0 0 1 0 0 0 9973 1406 49 4 4 MUC17 7 101040523 Missense_Mutation SNP T C3L-00913_T 2002041 101040523 58305450 94 6968 PPP1R3A 0 . GRCh38 7 113878065 113878065 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.3027G>A p.= p.G1009G ENST00000284601 4/4 619 558 61 440 439 1 strelka-varscan-mutect PPP1R3A,synonymous_variant,p.=,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; T ENST00000284601 Transcript synonymous_variant 3096/4384 3027/3369 1009/1122 G ggG/ggA 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 113878065 113878065 C T 1 0 0 0 0 0 0 0 1 12492 726 26 3 3 PPP1R3A 7 113878065 Silent SNP C C3L-00913_T 12837542 113878065 45467908 95 6969 AGBL3 0 . GRCh38 7 135034345 135034345 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.754C>T p.His252Tyr p.H252Y ENST00000436302 7/17 236 219 17 177 176 1 strelka-varscan-mutect AGBL3,missense_variant,p.His252Tyr,ENST00000436302,NM_178563.3;AGBL3,missense_variant,p.His252Tyr,ENST00000435976,;AGBL3,missense_variant,p.His252Tyr,ENST00000275763,; T ENST00000436302 Transcript missense_variant 1007/3533 754/2763 252/920 H/Y Cat/Tat 1 1 AGBL3 HGNC HGNC:27981 protein_coding YES CCDS47718.1 ENSP00000388275 Q8NEM8 UPI000192952B NM_178563.3 tolerated(0.13) 7/17 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF23 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 135034345 135034345 C T 1 0 0 0 0 1 0 0 0 453 826 29 3 3 AGBL3 7 135034345 Missense_Mutation SNP C C3L-00913_T 21156280 135034345 24311628 96 6970 OR2F2 0 . GRCh38 7 143936012 143936012 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.780C>G p.Ile260Met p.I260M ENST00000408955 1/1 320 275 45 223 223 0 strelka-varscan-mutect OR2F2,missense_variant,p.Ile260Met,ENST00000408955,NM_001004685.1; G ENST00000408955 Transcript missense_variant 847/1114 780/954 260/317 I/M atC/atG 1 1 OR2F2 HGNC HGNC:8247 protein_coding YES CCDS43666.1 ENSP00000386222 O95006 UPI0000041C25 NM_001004685.1 tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF63,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 143936012 143936012 C G 1 0 0 0 0 1 0 0 0 11075 845 30 4 4 OR2F2 7 143936012 Missense_Mutation SNP C C3L-00913_T 8901667 143936012 15409961 97 6971 NOBOX 0 . GRCh38 7 144400233 144400233 + Silent SNP C C A rs780163926 C3L-00913_T C3L-00913_N C C c.924G>T p.= p.T308T ENST00000467773 5/10 397 366 31 246 246 0 strelka-varscan-mutect NOBOX,synonymous_variant,p.=,ENST00000467773,NM_001080413.3;NOBOX,synonymous_variant,p.=,ENST00000483238,; A ENST00000467773 Transcript synonymous_variant 924/2076 924/2076 308/691 T acG/acT rs780163926 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 5/10 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF282,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 5 1 PASS rs780163926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 144400233 144400233 C A 1 0 0 0 0 0 0 0 1 10554 639 23 1 1 NOBOX 7 144400233 Silent SNP C C3L-00913_T 464221 144400233 14945740 98 6972 AOC1 0 . GRCh38 7 150856781 150856781 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.311G>A p.Gly104Asp p.G104D ENST00000416793 2/5 359 320 39 265 265 0 strelka-varscan-mutect AOC1,missense_variant,p.Gly104Asp,ENST00000493429,;AOC1,missense_variant,p.Gly104Asp,ENST00000467291,;AOC1,missense_variant,p.Gly104Asp,ENST00000360937,NM_001091.3;AOC1,missense_variant,p.Gly104Asp,ENST00000416793,NM_001272072.1;AOC1,missense_variant,p.Gly104Asp,ENST00000483043,;AOC1,missense_variant,p.Gly104Asp,ENST00000460213,;AOC1,upstream_gene_variant,,ENST00000480582,; A ENST00000416793 Transcript missense_variant 371/2453 311/2313 104/770 G/D gGt/gAt 1 1 AOC1 HGNC HGNC:80 protein_coding YES CCDS64797.1 ENSP00000411613 P19801 UPI000020F2D0 NM_001272072.1 deleterious(0) 2/5 hmmpanther:PTHR10638,hmmpanther:PTHR10638:SF3,Gene3D:3.10.450.40,Pfam_domain:PF02727,Superfamily_domains:SSF54416,Prints_domain:PR00766 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 150856781 150856781 G A 1 0 0 0 0 1 0 0 0 836 1261 44 3 3 AOC1 7 150856781 Missense_Mutation SNP G C3L-00913_T 6456548 150856781 8489192 99 6973 ASB10 0 . GRCh38 7 151187619 151187619 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.104G>T p.Trp35Leu p.W35L ENST00000377867 1/6 94 88 6 55 55 0 strelka-mutect ASB10,missense_variant,p.Trp35Leu,ENST00000377867,NM_080871.3;IQCA1L,downstream_gene_variant,,ENST00000615129,NM_001304419.1;ASB10,upstream_gene_variant,,ENST00000275838,NM_001142460.1;ASB10,upstream_gene_variant,,ENST00000420175,NM_001142459.1;ASB10,missense_variant,p.Trp35Leu,ENST00000415615,;IQCA1L,downstream_gene_variant,,ENST00000611102,; A ENST00000377867 Transcript missense_variant 214/1738 104/1359 35/452 W/L tGg/tTg 1 -1 ASB10 HGNC HGNC:17185 protein_coding CCDS5921.2 ENSP00000367098 Q8WXI3 UPI0000D61D05 NM_080871.3 tolerated(0.63) 1/6 MODERATE SNV 2 1 PASS rs1406872923 . 0 206 4 0 0 0 0 0 -12.71023 1 1 1 1 0 A 3 1 21 151187619 151187619 C A 1 0 0 0 0 1 0 0 0 1156 595 21 2 2 ASB10 7 151187619 Missense_Mutation SNP C C3L-00913_T 330838 151187619 8158354 100 6974 DLGAP2 0 . GRCh38 8 1678231 1678231 + Missense_Mutation SNP G G A C3L-00913_T C3L-00913_N G G c.2024G>A p.Arg675His p.R675H ENST00000612087 8/11 128 106 22 103 103 0 strelka-varscan-mutect DLGAP2,missense_variant,p.Arg675His,ENST00000612087,NM_001277161.1;DLGAP2,missense_variant,p.Arg692His,ENST00000520901,;DLGAP2,missense_variant,p.Arg769His,ENST00000637795,;DLGAP2,missense_variant,p.Arg768His,ENST00000421627,;DLGAP2,missense_variant,p.Arg689His,ENST00000637152,NM_004745.4;DLGAP2,missense_variant,p.Arg34His,ENST00000522499,;DLGAP2,upstream_gene_variant,,ENST00000518530,;DLGAP2,upstream_gene_variant,,ENST00000524065,; A ENST00000612087 Transcript missense_variant 2158/10088 2024/2886 675/961 R/H cGt/cAt COSM3382174,COSM3382175 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 deleterious(0.04) 8/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3,Pfam_domain:PF03359 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1259369243 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 1678231 1678231 G A 1 0 0 0 0 1 0 0 0 4367 1145 40 1 1 DLGAP2 8 1678231 Missense_Mutation SNP G C3L-00913_T 1678231 143460405 101 6975 SNTG1 0 . GRCh38 8 50658592 50658592 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.967G>T p.Val323Leu p.V323L ENST00000522124 15/19 143 127 16 117 117 0 strelka-varscan-mutect SNTG1,missense_variant,p.Val323Leu,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Val323Leu,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Val323Leu,ENST00000517473,NM_001287814.1;SNTG1,missense_variant,p.Val323Leu,ENST00000520825,;SNTG1,missense_variant,p.Val97Leu,ENST00000524004,; T ENST00000522124 Transcript missense_variant,splice_region_variant 1628/3504 967/1554 323/517 V/L Gtg/Ttg 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 tolerated(0.26) 15/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 50658592 50658592 G T 1 0 0 0 0 1 0 0 0 15194 1275 44 2 2 SNTG1 8 50658592 Missense_Mutation SNP G C3L-00913_T 48980361 50658592 94480044 102 6976 ST18 0 . GRCh38 8 52166982 52166982 + Silent SNP T T C novel C3L-00913_T C3L-00913_N T T c.1074A>G p.= p.S358S ENST00000276480 11/26 81 72 9 61 61 0 strelka-varscan-mutect ST18,synonymous_variant,p.=,ENST00000276480,NM_014682.2;ST18,synonymous_variant,p.=,ENST00000517580,;ST18,3_prime_UTR_variant,,ENST00000522251,;ST18,3_prime_UTR_variant,,ENST00000521582,;ST18,3_prime_UTR_variant,,ENST00000521824,; C ENST00000276480 Transcript synonymous_variant 1758/6187 1074/3144 358/1047 S tcA/tcG 1 -1 ST18 HGNC HGNC:18695 protein_coding YES CCDS6149.1 ENSP00000276480 O60284 UPI0000046C30 NM_014682.2 11/26 hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816 LOW 1 SNV 1 1 PASS rs1426457295 . 0 207 3 0 0 0 0 0 -19.41314 1 1 1 1 0 C 2 2 21 52166982 52166982 T C 1 0 0 0 0 0 0 0 1 15590 1710 59 5 5 ST18 8 52166982 Silent SNP T C3L-00913_T 1508390 52166982 92971654 103 6977 ZFPM2 0 . GRCh38 8 105801376 105801376 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1294G>A p.Ala432Thr p.A432T ENST00000407775 8/8 579 545 34 446 446 0 strelka-varscan-mutect ZFPM2,missense_variant,p.Ala432Thr,ENST00000407775,NM_012082.3;ZFPM2,missense_variant,p.Ala300Thr,ENST00000520492,;ZFPM2,missense_variant,p.Ala300Thr,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; A ENST00000407775 Transcript missense_variant 1544/4700 1294/3456 432/1151 A/T Gcg/Acg 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 tolerated(0.56) 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 105801376 105801376 G A 1 0 0 0 0 1 0 0 0 18236 1319 46 3 3 ZFPM2 8 105801376 Missense_Mutation SNP G C3L-00913_T 53634394 105801376 39337260 104 6978 CSMD3 0 . GRCh38 8 112291528 112291529 + Frame_Shift_Ins INS - - T novel C3L-00913_T C3L-00913_N - - c.8955dupA p.Pro2986ThrfsTer9 p.P2986Tfs*9 ENST00000297405 56/71 347 301 46 274 274 0 sindel-varindel-pindel CSMD3,frameshift_variant,p.Pro2986ThrfsTer9,ENST00000297405,NM_198123.1;CSMD3,frameshift_variant,p.Pro2946ThrfsTer9,ENST00000343508,NM_198124.1;CSMD3,frameshift_variant,p.Pro2817ThrfsTer9,ENST00000455883,NM_052900.2;CSMD3,frameshift_variant,p.Pro2256ThrfsTer9,ENST00000339701,; T ENST00000297405 Transcript frameshift_variant 9200-9201/13212 8955-8956/11124 2985-2986/3707 -/X -/A 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 56/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 21 112291528 112291528 - T 1 0 1 1 0 0 0 0 0 3747 1261 44 0 0 CSMD3 8 112291528 Frame_Shift_Ins INS - C3L-00913_T 6490152 112291528 32847108 105 6979 CSMD3 0 . GRCh38 8 112921720 112921720 + Nonsense_Mutation SNP C C A C3L-00913_T C3L-00913_N C C c.1540G>T p.Glu514Ter p.E514* ENST00000297405 10/71 563 472 91 464 463 1 strelka-varscan-mutect CSMD3,stop_gained,p.Glu514Ter,ENST00000297405,NM_198123.1;CSMD3,stop_gained,p.Glu474Ter,ENST00000343508,NM_198124.1;CSMD3,stop_gained,p.Glu410Ter,ENST00000455883,NM_052900.2; A ENST00000297405 Transcript stop_gained 1785/13212 1540/11124 514/3707 E/* Gaa/Taa COSM3164151,COSM3164152 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 10/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 21 112921720 112921720 C A 1 0 0 0 0 0 1 0 0 3747 835 29 2 2 CSMD3 8 112921720 Nonsense_Mutation SNP C C3L-00913_T 630192 112921720 32216916 106 6980 KIAA2026 0 . GRCh38 9 5922239 5922239 + Missense_Mutation SNP T T C novel C3L-00913_T C3L-00913_N T T c.3757A>G p.Asn1253Asp p.N1253D ENST00000399933 8/8 425 374 51 380 380 0 strelka-varscan-mutect KIAA2026,missense_variant,p.Asn1253Asp,ENST00000399933,NM_001017969.2;KIAA2026,missense_variant,p.Asn1223Asp,ENST00000381461,;KIAA2026,3_prime_UTR_variant,,ENST00000540714,;KIAA2026,upstream_gene_variant,,ENST00000436015,; C ENST00000399933 Transcript missense_variant 3757/6988 3757/6312 1253/2103 N/D Aac/Gac 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 tolerated(0.17) 8/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3 MODERATE 1 SNV 5 1 PASS rs1327661205 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 5922239 5922239 T C 1 0 0 0 0 1 0 0 0 8134 1812 63 5 5 KIAA2026 9 5922239 Missense_Mutation SNP T C3L-00913_T 5922239 132472478 107 6981 SPATA31A6 0 . GRCh38 9 42187767 42187767 + Missense_Mutation SNP G G T rs772274413 C3L-00913_T C3L-00913_N G G c.2065G>T p.Val689Phe p.V689F ENST00000332857 4/4 85 66 19 52 52 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Val689Phe,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; T ENST00000332857 Transcript missense_variant 2094/4209 2065/4032 689/1343 V/F Gtt/Ttt rs772274413 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(0.36) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS rs772274413 . 12 197 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 42187767 42187767 G T 1 0 0 0 0 1 0 0 0 15345 1261 44 2 2 SPATA31A6 9 42187767 Missense_Mutation SNP G C3L-00913_T 36265528 42187767 96206950 108 6982 GRIN3A 0 . GRCh38 9 101670401 101670401 + Missense_Mutation SNP A A T rs755679939 C3L-00913_T C3L-00913_N A A c.2011T>A p.Trp671Arg p.W671R ENST00000361820 3/9 440 390 50 316 316 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Trp671Arg,ENST00000361820,NM_133445.2; T ENST00000361820 Transcript missense_variant 2612/7770 2011/3348 671/1115 W/R Tgg/Agg rs755679939 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 tolerated(0.11) 3/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Gene3D:3.40.190.10,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS rs755679939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 101670401 101670401 A T 1 0 0 0 0 1 0 0 0 6665 159 6 4 4 GRIN3A 9 101670401 Missense_Mutation SNP A C3L-00913_T 59482634 101670401 36724316 109 6983 OR13C4 0 . GRCh38 9 104526716 104526716 + Missense_Mutation SNP C C T rs75737900 C3L-00913_T C3L-00913_N C C c.494G>A p.Arg165Gln p.R165Q ENST00000277216 1/1 182 162 20 185 185 0 strelka-varscan-mutect OR13C4,missense_variant,p.Arg165Gln,ENST00000277216,NM_001001919.1;RP11-317C20.9,intron_variant,,ENST00000635678,; T ENST00000277216 Transcript missense_variant 494/957 494/957 165/318 R/Q cGa/cAa rs75737900,COSM3432723 1 -1 OR13C4 HGNC HGNC:14722 protein_coding YES CCDS35088.1 ENSP00000277216 Q8NGS5 A0A126GVC9 UPI0000041B46 NM_001001919.1 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF14,Superfamily_domains:SSF81321 0,1 MODERATE SNV 0,1 1 PASS rs75737900 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 104526716 104526716 C T 1 0 0 0 0 1 0 0 0 11012 884 31 1 1 OR13C4 9 104526716 Missense_Mutation SNP C C3L-00913_T 2856315 104526716 33868001 110 6984 ASTN2 0 . GRCh38 9 117291393 117291393 + Missense_Mutation SNP G G A C3L-00913_T C3L-00913_N G G c.563C>T p.Ala188Val p.A188V ENST00000361209 2/22 330 276 54 198 198 0 strelka-varscan-mutect ASTN2,missense_variant,p.Ala188Val,ENST00000313400,;ASTN2,missense_variant,p.Ala188Val,ENST00000361209,NM_014010.4;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; A ENST00000361209 Transcript missense_variant 695/4622 563/3867 188/1288 A/V gCc/gTc COSM3903569,COSM3903570 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 tolerated_low_confidence(0.17) 2/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 117291393 117291393 G A 1 0 0 0 0 1 0 0 0 1212 1203 42 3 3 ASTN2 9 117291393 Missense_Mutation SNP G C3L-00913_T 12764677 117291393 21103324 111 6985 OR1L3 0 . GRCh38 9 122675799 122675799 + Missense_Mutation SNP G G A rs200264223 C3L-00913_T C3L-00913_N G G c.670G>A p.Ala224Thr p.A224T ENST00000304820 1/1 319 287 32 276 276 0 strelka-varscan-mutect OR1L3,missense_variant,p.Ala224Thr,ENST00000304820,NM_001005234.1; A ENST00000304820 Transcript missense_variant 670/975 670/975 224/324 A/T Gct/Act rs200264223,COSM4709704 1 1 OR1L3 HGNC HGNC:8215 protein_coding YES CCDS35128.1 ENSP00000302863 Q8NH93 A0A126GVD1 UPI000004618D NM_001005234.1 tolerated(0.48) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF198,SMART_domains:SM01381,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs200264223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 122675799 122675799 G A 1 0 0 0 0 1 0 0 0 11042 1087 38 1 1 OR1L3 9 122675799 Missense_Mutation SNP G C3L-00913_T 5384406 122675799 15718918 112 6986 OR1K1 0 . GRCh38 9 122800245 122800245 + Silent SNP G G A C3L-00913_T C3L-00913_N G G c.123G>A p.= p.L41L ENST00000277309 1/1 348 316 32 207 207 0 strelka-varscan-mutect OR1K1,synonymous_variant,p.=,ENST00000277309,NM_080859.1;PDCL,intron_variant,,ENST00000436632,; A ENST00000277309 Transcript synonymous_variant 123/951 123/951 41/316 L ctG/ctA COSM3675224 1 1 OR1K1 HGNC HGNC:8212 protein_coding YES CCDS35132.1 ENSP00000277309 Q8NGR3 A0A126GVB9 UPI000004B1FE NM_080859.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF331,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 122800245 122800245 G A 1 0 0 0 0 0 0 0 1 11040 1335 47 3 3 OR1K1 9 122800245 Silent SNP G C3L-00913_T 124446 122800245 15594472 113 6987 HMCN2 0 . GRCh38 9 130425781 130425781 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.13676G>T p.Arg4559Leu p.R4559L ENST00000624552 90/98 466 422 44 345 345 0 strelka-varscan-mutect HMCN2,missense_variant,p.Arg4559Leu,ENST00000624552,NM_001291815.1;HMCN2,missense_variant,p.Arg23Leu,ENST00000428715,;HMCN2,upstream_gene_variant,,ENST00000623487,; T ENST00000624552 Transcript missense_variant 13676/15610 13676/15180 4559/5059 R/L cGc/cTc 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.01) 90/98 Gene3D:2.40.155.10,Pfam_domain:PF07474,PROSITE_profiles:PS50993,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00682,Superfamily_domains:SSF54511 MODERATE 1 SNV 5 1 PASS rs926380414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 130425781 130425781 G T 1 0 0 0 0 1 0 0 0 7112 1087 38 1 1 HMCN2 9 130425781 Missense_Mutation SNP G C3L-00913_T 7625536 130425781 7968936 114 6988 GLT6D1 0 . GRCh38 9 135624433 135624433 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.495G>A p.= p.E165E ENST00000371763 5/5 253 228 25 216 216 0 strelka-varscan-mutect GLT6D1,synonymous_variant,p.=,ENST00000371763,NM_182974.2;GLT6D1,synonymous_variant,p.=,ENST00000613244,; T ENST00000371763 Transcript synonymous_variant 749/1526 495/831 165/276 E gaG/gaA 1 -1 GLT6D1 HGNC HGNC:23671 protein_coding YES CCDS43900.1 ENSP00000360829 Q7Z4J2 UPI0000246F68 NM_182974.2 5/5 hmmpanther:PTHR10462:SF27,hmmpanther:PTHR10462,Gene3D:3.90.550.10,Pfam_domain:PF03414,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 135624433 135624433 C T 1 0 0 0 0 0 0 0 1 6345 680 24 3 3 GLT6D1 9 135624433 Silent SNP C C3L-00913_T 5198652 135624433 2770284 115 6989 GLT6D1 0 . GRCh38 9 135624647 135624647 + Missense_Mutation SNP G G T rs753115294 C3L-00913_T C3L-00913_N G G c.281C>A p.Pro94Gln p.P94Q ENST00000371763 5/5 80 71 9 65 65 0 strelka-varscan-mutect GLT6D1,missense_variant,p.Pro94Gln,ENST00000371763,NM_182974.2;GLT6D1,missense_variant,p.Pro94Gln,ENST00000613244,; T ENST00000371763 Transcript missense_variant 535/1526 281/831 94/276 P/Q cCg/cAg rs753115294 1 -1 GLT6D1 HGNC HGNC:23671 protein_coding YES CCDS43900.1 ENSP00000360829 Q7Z4J2 UPI0000246F68 NM_182974.2 tolerated(0.6) 5/5 hmmpanther:PTHR10462:SF27,hmmpanther:PTHR10462,Gene3D:3.90.550.10,Pfam_domain:PF03414,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs753115294 . 0 199 11 0 0 0 0 0 -18.99038 0.9999298 1 1 1 0 T 3 4 21 135624647 135624647 G T 1 0 0 0 0 1 0 0 0 6345 1116 39 1 1 GLT6D1 9 135624647 Missense_Mutation SNP G C3L-00913_T 214 135624647 2770070 116 6990 FAM208B 0 . GRCh38 10 5748303 5748303 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.4882G>A p.Gly1628Ser p.G1628S ENST00000328090 15/21 434 402 32 276 275 1 strelka-varscan-mutect FAM208B,missense_variant,p.Gly1628Ser,ENST00000328090,NM_001321784.1,NM_001321783.1,NM_017782.4;RP11-336A10.2,upstream_gene_variant,,ENST00000411512,; A ENST00000328090 Transcript missense_variant 5507/8626 4882/7293 1628/2430 G/S Ggc/Agc 1 1 FAM208B HGNC HGNC:23484 protein_coding YES CCDS41485.1 ENSP00000328426 Q5VWN6 UPI00004589BB NM_001321784.1,NM_001321783.1,NM_017782.4 tolerated(0.21) 15/21 hmmpanther:PTHR16207,hmmpanther:PTHR16207:SF10 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 5748303 5748303 G A 1 0 0 0 0 1 0 0 0 5390 1000 35 3 3 FAM208B 10 5748303 Missense_Mutation SNP G C3L-00913_T 5748303 128049119 117 6991 MEIG1 0 . GRCh38 10 14972618 14972618 + Missense_Mutation SNP A A G novel C3L-00913_T C3L-00913_N A A c.244A>G p.Lys82Glu p.K82E ENST00000407572 3/3 186 171 15 111 111 0 strelka-varscan-mutect MEIG1,missense_variant,p.Lys82Glu,ENST00000407572,NM_001080836.2;MEIG1,missense_variant,p.Lys82Glu,ENST00000378240,;MEIG1,splice_region_variant,,ENST00000467536,;MEIG1,non_coding_transcript_exon_variant,,ENST00000496225,;MEIG1,non_coding_transcript_exon_variant,,ENST00000477770,; G ENST00000407572 Transcript missense_variant 392/625 244/267 82/88 K/E Aaa/Gaa 1 1 MEIG1 HGNC HGNC:23429 protein_coding YES CCDS31151.1 ENSP00000384334 Q5JSS6 UPI000013EEBE NM_001080836.2 deleterious(0.01) 3/3 PD062760,Pfam_domain:PF15163,hmmpanther:PTHR17008,hmmpanther:PTHR17008:SF1 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 14972618 14972618 A G 1 0 0 0 0 1 0 0 0 9407 131 5 5 5 MEIG1 10 14972618 Missense_Mutation SNP A C3L-00913_T 9224315 14972618 118824804 118 6992 GDF10 0 . GRCh38 10 47310103 47310103 + Silent SNP C C A rs373114581 C3L-00913_T C3L-00913_N C C c.627C>A p.= p.I209I ENST00000580279 2/3 164 149 15 142 141 1 strelka-varscan-mutect GDF10,synonymous_variant,p.=,ENST00000580279,NM_004962.3; A ENST00000580279 Transcript synonymous_variant 893/2458 627/1437 209/478 I atC/atA rs373114581 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 2/3 PIRSF_domain:PIRSF037403,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF145 LOW 1 SNV 1 1 PASS rs373114581 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 47310103 47310103 C A 1 0 0 0 0 0 0 0 1 6184 874 31 1 1 GDF10 10 47310103 Silent SNP C C3L-00913_T 32337485 47310103 86487319 119 6993 GDF10 0 . GRCh38 10 47312715 47312715 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.1360C>T p.Leu454Phe p.L454F ENST00000580279 3/3 129 115 14 78 78 0 strelka-varscan-mutect GDF10,missense_variant,p.Leu454Phe,ENST00000580279,NM_004962.3; T ENST00000580279 Transcript missense_variant 1626/2458 1360/1437 454/478 L/F Ctc/Ttc 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 deleterious(0) 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00019,PIRSF_domain:PIRSF037403,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF145,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 47312715 47312715 C T 1 0 0 0 0 1 0 0 0 6184 681 24 3 3 GDF10 10 47312715 Missense_Mutation SNP C C3L-00913_T 2612 47312715 86484707 120 6994 C10orf71 0 . GRCh38 10 49326481 49326481 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.3936C>A p.= p.I1312I ENST00000374144 3/3 209 188 21 171 171 0 strelka-varscan-mutect C10orf71,synonymous_variant,p.=,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript synonymous_variant 4224/5230 3936/4308 1312/1435 I atC/atA 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR33775,Pfam_domain:PF15232 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 49326481 49326481 C A 1 0 0 0 0 0 0 0 1 1769 845 30 2 2 C10orf71 10 49326481 Silent SNP C C3L-00913_T 2013766 49326481 84470941 121 6995 PCDH15 0 . GRCh38 10 53806885 53806885 + Missense_Mutation SNP G G C C3L-00913_T C3L-00913_N G G c.4740C>G p.Asp1580Glu p.D1580E ENST00000614895 35/35 504 452 52 434 434 0 strelka-varscan-mutect PCDH15,missense_variant,p.Asp1580Glu,ENST00000614895,;PCDH15,missense_variant,p.Asp1576Glu,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Asp1575Glu,ENST00000414778,;PCDH15,missense_variant,p.Asp1574Glu,ENST00000616114,;PCDH15,missense_variant,p.Asp1581Glu,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Asp315Glu,ENST00000495484,;PCDH15,missense_variant,p.Asp359Glu,ENST00000618301,;PCDH15,downstream_gene_variant,,ENST00000617271,NM_001142770.1;PCDH15,downstream_gene_variant,,ENST00000613657,NM_001142769.1;PCDH15,downstream_gene_variant,,ENST00000395445,;PCDH15,downstream_gene_variant,,ENST00000395438,;PCDH15,downstream_gene_variant,,ENST00000612394,;PCDH15,downstream_gene_variant,,ENST00000409834,;PCDH15,downstream_gene_variant,,ENST00000395446,;PCDH15,downstream_gene_variant,,ENST00000395440,;PCDH15,downstream_gene_variant,,ENST00000395442,;PCDH15,downstream_gene_variant,,ENST00000615043,;PCDH15,downstream_gene_variant,,ENST00000414367,;PCDH15,downstream_gene_variant,,ENST00000476074,; C ENST00000614895 Transcript missense_variant 5135/9249 4740/5046 1580/1681 D/E gaC/gaG COSM5667361 1 -1 PCDH15 HGNC HGNC:14674 protein_coding ENSP00000478512 A0A087WUA8 UPI0004E4CB60 tolerated_low_confidence(0.25) 35/35 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 53806885 53806885 G C 1 0 0 0 0 1 0 0 0 11598 1368 48 4 4 PCDH15 10 53806885 Missense_Mutation SNP G C3L-00913_T 4480404 53806885 79990537 122 6996 JMJD1C 0 . GRCh38 10 63217245 63217245 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.640G>C p.Asp214His p.D214H ENST00000399262 5/26 260 237 23 199 199 0 strelka-varscan-mutect JMJD1C,missense_variant,p.Asp214His,ENST00000399262,NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2;JMJD1C,missense_variant,p.Asp32His,ENST00000542921,NM_001318153.1,NM_001282948.1;JMJD1C,non_coding_transcript_exon_variant,,ENST00000402544,;JMJD1C,non_coding_transcript_exon_variant,,ENST00000489372,;JMJD1C,non_coding_transcript_exon_variant,,ENST00000469152,;JMJD1C,downstream_gene_variant,,ENST00000633035,;TATDN1P1,upstream_gene_variant,,ENST00000414123,; G ENST00000399262 Transcript missense_variant 859/8666 640/7623 214/2540 D/H Gat/Cat 1 -1 JMJD1C HGNC HGNC:12313 protein_coding YES CCDS41532.1 ENSP00000382204 Q15652 UPI0000198BEF NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2 deleterious(0) 5/26 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF6 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 63217245 63217245 C G 1 0 0 0 0 1 0 0 0 7864 826 29 4 4 JMJD1C 10 63217245 Missense_Mutation SNP C C3L-00913_T 9410360 63217245 70580177 123 6997 FFAR4 0 . GRCh38 10 93567273 93567273 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.553C>G p.Pro185Ala p.P185A ENST00000371483 1/4 257 228 29 166 166 0 strelka-varscan-mutect FFAR4,missense_variant,p.Pro185Ala,ENST00000371483,NM_181745.3;FFAR4,missense_variant,p.Pro185Ala,ENST00000371481,NM_001195755.1;FFAR4,missense_variant,p.Pro185Ala,ENST00000604414,; G ENST00000371483 Transcript missense_variant 609/3653 553/1134 185/377 P/A Ccc/Gcc 1 1 FFAR4 HGNC HGNC:19061 protein_coding YES CCDS31248.1 ENSP00000360538 Q5NUL3 UPI00001C1EE5 NM_181745.3 tolerated(0.07) 1/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF67,hmmpanther:PTHR24241,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 93567273 93567273 C G 1 0 0 0 0 1 0 0 0 5693 623 22 4 4 FFAR4 10 93567273 Missense_Mutation SNP C C3L-00913_T 30350028 93567273 40230149 124 6998 PYROXD2 0 . GRCh38 10 98390638 98390638 + Nonsense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1252C>T p.Gln418Ter p.Q418* ENST00000370575 12/16 90 82 8 66 66 0 strelka-varscan-mutect PYROXD2,stop_gained,p.Gln418Ter,ENST00000370575,NM_032709.2;PYROXD2,downstream_gene_variant,,ENST00000408492,;PYROXD2,non_coding_transcript_exon_variant,,ENST00000483923,;PYROXD2,upstream_gene_variant,,ENST00000464808,; A ENST00000370575 Transcript stop_gained 1301/2028 1252/1746 418/581 Q/* Cag/Tag 1 -1 PYROXD2 HGNC HGNC:23517 protein_coding YES CCDS7474.1 ENSP00000359607 Q8N2H3 UPI000013CA6A NM_032709.2 12/16 hmmpanther:PTHR10668:SF83,hmmpanther:PTHR10668 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -16.76086 1 1 1 1 0 A 4 1 21 98390638 98390638 G A 1 0 0 0 0 0 1 0 0 13022 1299 45 3 3 PYROXD2 10 98390638 Nonsense_Mutation SNP G C3L-00913_T 4823365 98390638 35406784 125 6999 MGEA5 0 . GRCh38 10 101798913 101798914 + Frame_Shift_Ins INS - - T novel C3L-00913_T C3L-00913_N - - c.1737dupA p.Arg580ThrfsTer10 p.R580Tfs*10 ENST00000361464 9/16 230 210 20 170 170 0 varindel-pindel MGEA5,frameshift_variant,p.Arg580ThrfsTer10,ENST00000361464,NM_012215.3;MGEA5,frameshift_variant,p.Arg527ThrfsTer10,ENST00000439817,NM_001142434.1;MGEA5,frameshift_variant,p.Arg580ThrfsTer10,ENST00000370094,;MGEA5,frameshift_variant,p.Arg527ThrfsTer10,ENST00000357797,;MGEA5,downstream_gene_variant,,ENST00000429860,;MGEA5,non_coding_transcript_exon_variant,,ENST00000482611,;MGEA5,upstream_gene_variant,,ENST00000479811,;MGEA5,upstream_gene_variant,,ENST00000492204,; T ENST00000361464 Transcript frameshift_variant 2133-2134/5155 1737-1738/2751 579-580/916 -/X -/A 1 -1 MGEA5 HGNC HGNC:7056 protein_coding YES CCDS7520.1 ENSP00000354850 O60502 UPI0000073533 NM_012215.3 9/16 hmmpanther:PTHR13170:SF16,hmmpanther:PTHR13170 HIGH 1 insertion 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999795 1 1 1 0 T 7 5 21 101798913 101798913 - T 1 0 1 1 0 0 0 0 0 9511 1144 40 0 0 MGEA5 10 101798913 Frame_Shift_Ins INS - C3L-00913_T 3408275 101798913 31998509 126 7000 NFKB2 0 . GRCh38 10 102399431 102399431 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1261G>T p.Ala421Ser p.A421S ENST00000369966 13/23 84 72 12 89 89 0 strelka-varscan-mutect NFKB2,missense_variant,p.Ala421Ser,ENST00000428099,NM_001288724.1;NFKB2,missense_variant,p.Ala421Ser,ENST00000369966,NM_001077494.3;NFKB2,missense_variant,p.Ala421Ser,ENST00000189444,NM_001322934.1,NM_001261403.2,NM_002502.5;PSD,downstream_gene_variant,,ENST00000020673,NM_002779.4;PSD,downstream_gene_variant,,ENST00000406432,NM_001270965.1;PSD,downstream_gene_variant,,ENST00000611678,NM_001270966.1;NFKB2,downstream_gene_variant,,ENST00000601386,;NFKB2,downstream_gene_variant,,ENST00000471698,;NFKB2,non_coding_transcript_exon_variant,,ENST00000336486,;NFKB2,downstream_gene_variant,,ENST00000593908,;NFKB2,downstream_gene_variant,,ENST00000467116,;NFKB2,upstream_gene_variant,,ENST00000473400,; T ENST00000369966 Transcript missense_variant 1511/3101 1261/2703 421/900 A/S Gcg/Tcg 1 1 NFKB2 HGNC HGNC:7795 protein_coding YES CCDS41564.1 ENSP00000358983 Q00653 UPI000016A5CD NM_001077494.3 tolerated(0.72) 13/23 MODERATE 1 SNV 1 1 PASS rs1211166977 . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 21 102399431 102399431 G T 1 0 0 0 0 1 0 0 0 10413 1087 38 1 1 NFKB2 10 102399431 Missense_Mutation SNP G C3L-00913_T 600518 102399431 31397991 127 7001 SEC23IP 0 . GRCh38 10 119892856 119892856 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.74C>T p.Ser25Phe p.S25F ENST00000369075 1/19 201 184 17 148 148 0 strelka-varscan-mutect SEC23IP,missense_variant,p.Ser25Phe,ENST00000369075,NM_007190.3;SEC23IP,missense_variant,p.Ser25Phe,ENST00000543134,;SEC23IP,non_coding_transcript_exon_variant,,ENST00000470478,;MCMBP,upstream_gene_variant,,ENST00000569515,; T ENST00000369075 Transcript missense_variant 146/7168 74/3003 25/1000 S/F tCc/tTc 1 1 SEC23IP HGNC HGNC:17018 protein_coding YES CCDS7618.1 ENSP00000358071 Q9Y6Y8 UPI000006FCCE NM_007190.3 deleterious(0) 1/19 Low_complexity_(Seg):seg,hmmpanther:PTHR23509,hmmpanther:PTHR23509:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 119892856 119892856 C T 1 0 0 0 0 1 0 0 0 14270 855 30 3 3 SEC23IP 10 119892856 Missense_Mutation SNP C C3L-00913_T 17493425 119892856 13904566 128 7002 SYCE1 0 . GRCh38 10 133555400 133555400 + Missense_Mutation SNP G G C C3L-00913_T C3L-00913_N G G c.869C>G p.Pro290Arg p.P290R ENST00000343131 12/13 351 319 32 253 253 0 strelka-varscan-mutect SYCE1,missense_variant,p.Pro254Arg,ENST00000368517,NM_130784.2;SYCE1,missense_variant,p.Pro290Arg,ENST00000343131,NM_001143764.1;SYCE1,missense_variant,p.Pro290Arg,ENST00000303903,NM_001143763.1;CYP2E1,non_coding_transcript_exon_variant,,ENST00000368520,;SYCE1,non_coding_transcript_exon_variant,,ENST00000479535,; C ENST00000343131 Transcript missense_variant 974/1309 869/1056 290/351 P/R cCt/cGt COSM5678382,COSM5678383 1 -1 SYCE1 HGNC HGNC:28852 protein_coding YES CCDS44501.1 ENSP00000341282 Q8N0S2 UPI000013F901 NM_001143764.1 deleterious(0.02) 12/13 hmmpanther:PTHR21731:SF0,hmmpanther:PTHR21731 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 133555400 133555400 G C 1 0 0 0 0 1 0 0 0 15816 1000 35 4 4 SYCE1 10 133555400 Missense_Mutation SNP G C3L-00913_T 13662544 133555400 242022 129 7003 TRIM21 0 . GRCh38 11 4390354 4390354 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.56G>T p.Cys19Phe p.C19F ENST00000254436 2/7 144 127 17 114 114 0 strelka-varscan-mutect TRIM21,missense_variant,p.Cys19Phe,ENST00000254436,NM_003141.3;TRIM21,upstream_gene_variant,,ENST00000533692,; A ENST00000254436 Transcript missense_variant 169/1924 56/1428 19/475 C/F tGc/tTc 1 -1 TRIM21 HGNC HGNC:11312 protein_coding YES CCDS44525.1 ENSP00000254436 P19474 UPI000013450B NM_003141.3 deleterious(0) 2/7 PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF46,Pfam_domain:PF15227,Gene3D:3.30.40.10,SMART_domains:SM00184,SMART_domains:SM00504,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999896 1 1 1 0 A 3 1 21 4390354 4390354 C A 1 0 0 0 0 1 0 0 0 16984 710 25 2 2 TRIM21 11 4390354 Missense_Mutation SNP C C3L-00913_T 4390354 130696268 130 7004 OR51S1 0 . GRCh38 11 4848854 4848854 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.355G>A p.Glu119Lys p.E119K ENST00000322101 1/1 249 226 23 225 225 0 strelka-varscan-mutect OR51S1,missense_variant,p.Glu119Lys,ENST00000322101,NM_001004758.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322101 Transcript missense_variant 355/972 355/972 119/323 E/K Gag/Aag 1 -1 OR51S1 HGNC HGNC:15204 protein_coding YES CCDS31362.1 ENSP00000322754 Q8NGJ8 A0A126GWN3 UPI0000041C33 NM_001004758.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF73,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 4848854 4848854 C T 1 0 0 0 0 1 0 0 0 11179 864 30 3 3 OR51S1 11 4848854 Missense_Mutation SNP C C3L-00913_T 458500 4848854 130237768 131 7005 OR51B6 0 . GRCh38 11 5351729 5351729 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.222C>A p.= p.T74T ENST00000380219 1/1 160 138 22 152 152 0 strelka-varscan-mutect OR51B6,synonymous_variant,p.=,ENST00000380219,NM_001004750.1;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;AC104389.31,upstream_gene_variant,,ENST00000450768,; A ENST00000380219 Transcript synonymous_variant 222/939 222/939 74/312 T acC/acA 1 1 OR51B6 HGNC HGNC:19600 protein_coding YES CCDS31379.1 ENSP00000369568 Q9H340 UPI000014017D NM_001004750.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF22,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 5351729 5351729 C A 1 0 0 0 0 0 0 0 1 11166 581 21 2 2 OR51B6 11 5351729 Silent SNP C C3L-00913_T 502875 5351729 129734893 132 7006 SOX6 0 . GRCh38 11 16055872 16055872 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1131G>T p.Met377Ile p.M377I ENST00000396356 10/16 420 370 50 322 322 0 strelka-varscan-mutect SOX6,missense_variant,p.Met377Ile,ENST00000396356,NM_033326.3;SOX6,missense_variant,p.Met377Ile,ENST00000316399,;SOX6,missense_variant,p.Met336Ile,ENST00000528252,NM_001145811.1;SOX6,missense_variant,p.Met339Ile,ENST00000527619,NM_017508.2;SOX6,missense_variant,p.Met377Ile,ENST00000528429,NM_001145819.1;SOX6,non_coding_transcript_exon_variant,,ENST00000524650,; A ENST00000396356 Transcript missense_variant 1209/8865 1131/2427 377/808 M/I atG/atT 1 -1 SOX6 HGNC HGNC:16421 protein_coding YES CCDS7821.1 ENSP00000379644 P35712 UPI00001F9DE4 NM_033326.3 deleterious(0.03) 10/16 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF89 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 16055872 16055872 C A 1 0 0 0 0 1 0 0 0 15281 710 25 2 2 SOX6 11 16055872 Missense_Mutation SNP C C3L-00913_T 10704143 16055872 119030750 133 7007 KIAA1549L 0 . GRCh38 11 33667981 33667981 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.5377C>A p.Leu1793Met p.L1793M ENST00000321505 20/20 368 323 45 293 293 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Leu1793Met,ENST00000321505,NM_012194.2;RP4-541C22.5,intron_variant,,ENST00000534431,; A ENST00000321505 Transcript missense_variant 5557/11678 5377/5550 1793/1849 L/M Ctg/Atg 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 deleterious(0) 20/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 33667981 33667981 C A 1 0 0 0 0 1 0 0 0 8121 680 24 2 2 KIAA1549L 11 33667981 Missense_Mutation SNP C C3L-00913_T 17612109 33667981 101418641 134 7008 OR4C13 0 . GRCh38 11 49952677 49952677 + Silent SNP T T C novel C3L-00913_T C3L-00913_N T T c.255T>C p.= p.Y85Y ENST00000555099 1/1 669 625 44 319 319 0 varscan-mutect OR4C13,synonymous_variant,p.=,ENST00000555099,NM_001001955.2; C ENST00000555099 Transcript synonymous_variant 287/1029 255/930 85/309 Y taT/taC 1 1 OR4C13 HGNC HGNC:15169 protein_coding YES CCDS31495.1 ENSP00000452277 Q8NGP0 UPI000013F7D1 NM_001001955.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF60,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 21 49952677 49952677 T C 1 0 0 0 0 0 0 0 1 11124 1471 51 5 5 OR4C13 11 49952677 Silent SNP T C3L-00913_T 16284696 49952677 85133945 135 7009 OR10AG1 0 . GRCh38 11 55968164 55968164 + Silent SNP G G C novel C3L-00913_T C3L-00913_N G G c.300C>G p.= p.G100G ENST00000312345 1/1 217 195 22 160 160 0 strelka-varscan-mutect OR10AG1,synonymous_variant,p.=,ENST00000312345,NM_001005491.1; C ENST00000312345 Transcript synonymous_variant 300/906 300/906 100/301 G ggC/ggG 1 -1 OR10AG1 HGNC HGNC:19607 protein_coding YES CCDS31514.1 ENSP00000311477 Q8NH19 A0A126GVM8 UPI000004B22B NM_001005491.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF159,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 21 55968164 55968164 G C 1 0 0 0 0 0 0 0 1 10972 1306 46 4 4 OR10AG1 11 55968164 Silent SNP G C3L-00913_T 6015487 55968164 79118458 136 7010 MS4A3 0 . GRCh38 11 60069618 60069618 + Missense_Mutation SNP C C G rs778541342 C3L-00913_T C3L-00913_N C C c.558C>G p.Cys186Trp p.C186W ENST00000278865 6/7 276 259 17 190 190 0 strelka-varscan-mutect MS4A3,missense_variant,p.Cys186Trp,ENST00000278865,NM_006138.4;MS4A3,missense_variant,p.Cys140Trp,ENST00000358152,NM_001031809.1;MS4A3,missense_variant,p.Cys63Trp,ENST00000395032,NM_001031666.1;MS4A3,missense_variant,p.Cys140Trp,ENST00000534744,;MS4A3,3_prime_UTR_variant,,ENST00000525686,;MS4A3,non_coding_transcript_exon_variant,,ENST00000528952,; G ENST00000278865 Transcript missense_variant 631/1613 558/645 186/214 C/W tgC/tgG rs778541342,COSM245777 1 1 MS4A3 HGNC HGNC:7317 protein_coding YES CCDS31567.1 ENSP00000278865 Q96HJ5 UPI000006E45E NM_006138.4 deleterious(0) 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF74,hmmpanther:PTHR23320,Pfam_domain:PF04103 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778541342 . 0 207 0 3 0 0 0 0 -19.49893 0.9999594 1 1 1 0 G 3 3 21 60069618 60069618 C G 1 0 0 0 0 1 0 0 0 9839 776 27 4 4 MS4A3 11 60069618 Missense_Mutation SNP C C3L-00913_T 4101454 60069618 75017004 137 7011 CD6 0 . GRCh38 11 61018360 61018360 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1909C>A p.Gln637Lys p.Q637K ENST00000313421 12/13 192 174 18 119 119 0 strelka-varscan-mutect CD6,missense_variant,p.Gln637Lys,ENST00000313421,NM_006725.4;CD6,intron_variant,,ENST00000352009,NM_001254750.1;CD6,intron_variant,,ENST00000452451,NM_001254751.1;CD6,downstream_gene_variant,,ENST00000433107,;CD6,downstream_gene_variant,,ENST00000542157,;CD6,downstream_gene_variant,,ENST00000538611,;CD6,downstream_gene_variant,,ENST00000545105,;CD6,non_coding_transcript_exon_variant,,ENST00000505761,;CD6,intron_variant,,ENST00000344931,;CD6,downstream_gene_variant,,ENST00000419282,; A ENST00000313421 Transcript missense_variant 2095/3252 1909/2007 637/668 Q/K Cag/Aag 1 1 CD6 HGNC HGNC:1691 protein_coding YES CCDS7999.1 ENSP00000323280 P30203 UPI000013F532 NM_006725.4 tolerated(0.09) 12/13 Low_complexity_(Seg):seg,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF331 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99997 0.9999998 1 1 1 0 A 3 1 21 61018360 61018360 C A 1 0 0 0 0 1 0 0 0 2732 595 21 2 2 CD6 11 61018360 Missense_Mutation SNP C C3L-00913_T 948742 61018360 74068262 138 7012 MYRF 0 . GRCh38 11 61784353 61784353 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.3268C>A p.Pro1090Thr p.P1090T ENST00000278836 25/27 291 264 27 178 177 1 strelka-varscan-mutect MYRF,missense_variant,p.Pro1090Thr,ENST00000278836,NM_001127392.2;MYRF,missense_variant,p.Pro1050Thr,ENST00000265460,NM_013279.3;MYRF,missense_variant,p.Pro476Thr,ENST00000389602,;TMEM258,downstream_gene_variant,,ENST00000543510,;TMEM258,downstream_gene_variant,,ENST00000537328,NM_014206.3;TMEM258,intron_variant,,ENST00000535042,;MYRF,non_coding_transcript_exon_variant,,ENST00000539361,;MYRF,downstream_gene_variant,,ENST00000537318,;MYRF,downstream_gene_variant,,ENST00000536352,;MYRF,downstream_gene_variant,,ENST00000546247,;TMEM258,downstream_gene_variant,,ENST00000545210,;TMEM258,downstream_gene_variant,,ENST00000541893,;TMEM258,downstream_gene_variant,,ENST00000257262,;TMEM258,downstream_gene_variant,,ENST00000535297,; A ENST00000278836 Transcript missense_variant 3364/5927 3268/3456 1090/1151 P/T Cca/Aca 1 1 MYRF HGNC HGNC:1181 protein_coding YES CCDS44622.1 ENSP00000278836 Q9Y2G1 UPI0000D45F7B NM_001127392.2 tolerated(0.58) 25/27 Pfam_domain:PF13888,hmmpanther:PTHR13029,hmmpanther:PTHR13029:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 61784353 61784353 C A 1 0 0 0 0 1 0 0 0 10101 855 30 2 2 MYRF 11 61784353 Missense_Mutation SNP C C3L-00913_T 765993 61784353 73302269 139 7013 INCENP 0 . GRCh38 11 62146897 62146897 + Silent SNP C C T rs35595038 C3L-00913_T C3L-00913_N C C c.2199C>T p.= p.A733A ENST00000394818 15/19 303 262 41 227 227 0 strelka-varscan-mutect INCENP,synonymous_variant,p.=,ENST00000394818,NM_001040694.1;INCENP,synonymous_variant,p.=,ENST00000278849,NM_020238.2; T ENST00000394818 Transcript synonymous_variant 2401/3964 2199/2757 733/918 A gcC/gcT rs35595038 1 1 INCENP HGNC HGNC:6058 protein_coding YES CCDS44624.1 ENSP00000378295 Q9NQS7 UPI0000D7D6F3 NM_001040694.1 15/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13142:SF1,hmmpanther:PTHR13142 LOW 1 SNV 1 1 PASS rs35595038 . 0 198 0 0 0 0 0 11 -3.984447 0 0 1 0 0 T 2 4 21 62146897 62146897 C T 1 0 0 0 0 0 0 0 1 7635 666 23 1 1 INCENP 11 62146897 Silent SNP C C3L-00913_T 362544 62146897 72939725 140 7014 CHRM1 0 . GRCh38 11 62910544 62910544 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.557C>A p.Pro186His p.P186H ENST00000306960 2/2 294 258 36 256 255 1 strelka-varscan-mutect CHRM1,missense_variant,p.Pro186His,ENST00000306960,NM_000738.2;CHRM1,missense_variant,p.Pro186His,ENST00000543973,;CHRM1,downstream_gene_variant,,ENST00000536524,;AP000438.2,intron_variant,,ENST00000543624,; T ENST00000306960 Transcript missense_variant 1099/2964 557/1383 186/460 P/H cCc/cAc 1 -1 CHRM1 HGNC HGNC:1950 protein_coding YES CCDS8040.1 ENSP00000306490 P11229 Q53XZ3 UPI00001252AB NM_000738.2 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF283,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00243 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 62910544 62910544 G T 1 0 0 0 0 1 0 0 0 3136 1232 43 2 2 CHRM1 11 62910544 Missense_Mutation SNP G C3L-00913_T 763647 62910544 72176078 141 7015 PCF11 0 . GRCh38 11 83169396 83169396 + Missense_Mutation SNP G G A rs777465037 C3L-00913_T C3L-00913_N G G c.3061G>A p.Glu1021Lys p.E1021K ENST00000298281 8/16 377 320 57 293 293 0 strelka-varscan-mutect PCF11,missense_variant,p.Glu1021Lys,ENST00000298281,NM_015885.3;PCF11,downstream_gene_variant,,ENST00000530660,;PCF11,downstream_gene_variant,,ENST00000530304,;PCF11,upstream_gene_variant,,ENST00000530906,; A ENST00000298281 Transcript missense_variant 3513/7677 3061/4668 1021/1555 E/K Gaa/Aaa rs777465037 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 deleterious(0.04) 8/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 MODERATE 1 SNV 1 1 PASS rs777465037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 83169396 83169396 G A 1 0 0 0 0 1 0 0 0 11661 1291 45 3 3 PCF11 11 83169396 Missense_Mutation SNP G C3L-00913_T 20258852 83169396 51917226 142 7016 PCF11 0 . GRCh38 11 83169441 83169441 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.3106G>T p.Ala1036Ser p.A1036S ENST00000298281 8/16 341 294 47 264 264 0 strelka-varscan-mutect PCF11,missense_variant,p.Ala1036Ser,ENST00000298281,NM_015885.3;PCF11,downstream_gene_variant,,ENST00000530660,;PCF11,downstream_gene_variant,,ENST00000530304,;PCF11,upstream_gene_variant,,ENST00000530906,; T ENST00000298281 Transcript missense_variant 3558/7677 3106/4668 1036/1555 A/S Gct/Tct 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 tolerated(0.77) 8/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 83169441 83169441 G T 1 0 0 0 0 1 0 0 0 11661 1319 46 2 2 PCF11 11 83169441 Missense_Mutation SNP G C3L-00913_T 45 83169441 51917181 143 7017 GRM5 0 . GRCh38 11 88604914 88604914 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1198G>T p.Val400Leu p.V400L ENST00000305447 4/9 424 356 68 276 276 0 strelka-varscan-mutect GRM5,missense_variant,p.Val400Leu,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Val400Leu,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Val400Leu,ENST00000305432,; A ENST00000305447 Transcript missense_variant 1348/4571 1198/3639 400/1212 V/L Gtg/Ttg 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 4/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00593,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs1281123762 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 88604914 88604914 C A 1 0 0 0 0 1 0 0 0 6682 478 17 2 2 GRM5 11 88604914 Missense_Mutation SNP C C3L-00913_T 5435473 88604914 46481708 144 7018 ATM 0 . GRCh38 11 108353764 108353764 + Splice_Site SNP A A G novel C3L-00913_T C3L-00913_N A A c.8672-2A>G p.X2891_splice ENST00000278616 507 429 78 396 396 0 strelka-varscan-mutect ATM,splice_acceptor_variant,,ENST00000278616,NM_000051.3;ATM,splice_acceptor_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000615746,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;ATM,splice_acceptor_variant,,ENST00000525178,;C11orf65,intron_variant,,ENST00000526725,;ATM,splice_acceptor_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000527181,;C11orf65,intron_variant,,ENST00000527531,; G ENST00000278616 Transcript splice_acceptor_variant -/13147 8672/9171 2891/3056 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 59/62 HIGH SNV 5 1 PASS rs779170307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 21 108353764 108353764 A G 1 0 0 0 0 0 0 1 0 1261 434 15 5 5 ATM 11 108353764 Splice_Site SNP A C3L-00913_T 19748850 108353764 26732858 145 7019 OR8B4 0 . GRCh38 11 124424104 124424104 + Missense_Mutation SNP G G C C3L-00913_T C3L-00913_N G G c.768C>G p.Phe256Leu p.F256L ENST00000356130 1/1 346 325 21 259 259 0 strelka-varscan-mutect OR8B4,missense_variant,p.Phe256Leu,ENST00000356130,NM_001005196.1; C ENST00000356130 Transcript missense_variant 790/990 768/930 256/309 F/L ttC/ttG COSM3444781 1 -1 OR8B4 HGNC HGNC:8473 protein_coding YES CCDS31710.1 ENSP00000348449 Q96RC9 UPI00000015B0 NM_001005196.1 tolerated_low_confidence(0.23) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF208,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 124424104 124424104 G C 1 0 0 0 0 1 0 0 0 11299 1281 45 4 4 OR8B4 11 124424104 Missense_Mutation SNP G C3L-00913_T 16070340 124424104 10662518 146 7020 DDX25 0 . GRCh38 11 125905572 125905572 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.150C>T p.= p.I50I ENST00000263576 3/12 236 223 13 169 169 0 strelka-varscan-mutect DDX25,synonymous_variant,p.=,ENST00000263576,NM_013264.4;DDX25,synonymous_variant,p.=,ENST00000530414,;DDX25,synonymous_variant,p.=,ENST00000530129,;DDX25,5_prime_UTR_variant,,ENST00000525943,;HYLS1,downstream_gene_variant,,ENST00000425380,NM_001134793.1;PUS3,upstream_gene_variant,,ENST00000227474,NM_031307.3;HYLS1,downstream_gene_variant,,ENST00000356438,NM_145014.2;HYLS1,downstream_gene_variant,,ENST00000526028,;DDX25,upstream_gene_variant,,ENST00000526875,;PUS3,upstream_gene_variant,,ENST00000613398,NM_001271985.1;PUS3,upstream_gene_variant,,ENST00000534158,;PUS3,upstream_gene_variant,,ENST00000529801,;RP11-680F20.9,intron_variant,,ENST00000533033,;DDX25,5_prime_UTR_variant,,ENST00000637851,; T ENST00000263576 Transcript synonymous_variant 305/7555 150/1452 50/483 I atC/atT 1 1 DDX25 HGNC HGNC:18698 protein_coding YES CCDS44766.1 ENSP00000263576 Q9UHL0 UPI000018CE78 NM_013264.4 3/12 hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF331,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99543 1 1 1 1 0 T 2 4 21 125905572 125905572 C T 1 0 0 0 0 0 0 0 1 4155 816 29 3 3 DDX25 11 125905572 Silent SNP C C3L-00913_T 1481468 125905572 9181050 147 7021 PRMT8 0 . GRCh38 12 3593125 3593125 + Missense_Mutation SNP G G T C3L-00913_T C3L-00913_N G G c.1128G>T p.Leu376Phe p.L376F ENST00000382622 10/10 459 405 54 358 357 1 strelka-varscan-mutect PRMT8,missense_variant,p.Leu376Phe,ENST00000382622,NM_019854.4;PRMT8,missense_variant,p.Leu367Phe,ENST00000452611,NM_001256536.1;PRMT8,non_coding_transcript_exon_variant,,ENST00000261252,;PRMT8,non_coding_transcript_exon_variant,,ENST00000543701,; T ENST00000382622 Transcript missense_variant 1518/2366 1128/1185 376/394 L/F ttG/ttT COSM5375062,COSM5375063 1 1 PRMT8 HGNC HGNC:5188 protein_coding YES CCDS8521.2 ENSP00000372067 Q9NR22 UPI00005B2E00 NM_019854.4 tolerated(0.15) 10/10 Gene3D:2.70.160.11,PROSITE_profiles:PS51678,hmmpanther:PTHR11006,hmmpanther:PTHR11006:SF47,Superfamily_domains:SSF53335 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 3593125 3593125 G T 1 0 0 0 0 1 0 0 0 12673 1339 47 2 2 PRMT8 12 3593125 Missense_Mutation SNP G C3L-00913_T 3593125 129682184 148 7022 CHD4 0 . GRCh38 12 6582267 6582268 + Frame_Shift_Del DEL AG AG - novel C3L-00913_T C3L-00913_N AG AG c.4384_4385delCT p.Leu1462PhefsTer7 p.L1462Ffs*7 ENST00000357008 30/40 42 36 6 23 23 0 sindel-pindel CHD4,frameshift_variant,p.Leu1487PhefsTer7,ENST00000544484,;CHD4,frameshift_variant,p.Leu1455PhefsTer7,ENST00000544040,NM_001297553.1;CHD4,frameshift_variant,p.Leu1462PhefsTer7,ENST00000357008,NM_001273.3;SCARNA11,upstream_gene_variant,,ENST00000516089,;RP5-940J5.6,intron_variant,,ENST00000501075,;CHD4,non_coding_transcript_exon_variant,,ENST00000540960,;CHD4,intron_variant,,ENST00000536301,;CHD4,upstream_gene_variant,,ENST00000542717,; - ENST00000357008 Transcript frameshift_variant 4548-4549/6496 4384-4385/5739 1462/1912 L/X CTt/t 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 30/40 hmmpanther:PTHR10799:SF554,hmmpanther:PTHR10799,Pfam_domain:PF06461,SMART_domains:SM01146 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.22565 1 1 1 1 0 - 7 5 21 6582267 6582267 AG - 1 0 1 0 1 0 0 0 0 3086 72 3 0 0 CHD4 12 6582267 Frame_Shift_Del DEL AG C3L-00913_T 2989142 6582267 126693042 149 7023 KRAS 0 . GRCh38 12 25245348 25245348 + Missense_Mutation SNP C C A rs121913535 C3L-00913_T C3L-00913_N C C c.37G>T p.Gly13Cys p.G13C ENST00000256078 2/6 479 419 60 344 343 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly13Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly13Cys,ENST00000556131,;KRAS,missense_variant,p.Gly13Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly13Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 101/1119 37/570 13/189 G/C Ggc/Tgc rs121913535,COSM1152505,COSM3384258,COSM527,COSM528,COSM529 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.02) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS rs121913535 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 25245348 25245348 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245348 Missense_Mutation SNP C C3L-00913_T 18663081 25245348 108029961 150 7024 TMTC1 0 . GRCh38 12 29751811 29751811 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.793C>A p.Leu265Met p.L265M ENST00000539277 5/18 210 193 17 148 148 0 strelka-mutect TMTC1,missense_variant,p.Leu157Met,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Leu265Met,ENST00000551659,;TMTC1,missense_variant,p.Leu265Met,ENST00000552618,;TMTC1,missense_variant,p.Leu265Met,ENST00000539277,NM_001193451.1;TMTC1,non_coding_transcript_exon_variant,,ENST00000553189,; T ENST00000539277 Transcript missense_variant 852/2758 793/2649 265/882 L/M Ctg/Atg 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 tolerated(0.09) 5/18 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 29751811 29751811 G T 1 0 0 0 0 1 0 0 0 16734 1020 36 2 2 TMTC1 12 29751811 Missense_Mutation SNP G C3L-00913_T 4506463 29751811 103523498 151 7025 CAPRIN2 0 . GRCh38 12 30719209 30719209 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.2060G>T p.Gly687Val p.G687V ENST00000395805 12/17 182 161 21 114 114 0 strelka-varscan-mutect CAPRIN2,missense_variant,p.Gly687Val,ENST00000395805,NM_001206856.2;CAPRIN2,missense_variant,p.Gly722Val,ENST00000417045,NM_032156.4;CAPRIN2,missense_variant,p.Gly468Val,ENST00000433722,;CAPRIN2,missense_variant,p.Gly641Val,ENST00000537108,;CAPRIN2,intron_variant,,ENST00000298892,NM_023925.4,NM_001002259.2;CAPRIN2,non_coding_transcript_exon_variant,,ENST00000620681,;CAPRIN2,3_prime_UTR_variant,,ENST00000537553,;CAPRIN2,3_prime_UTR_variant,,ENST00000454014,NM_001319842.1;CAPRIN2,3_prime_UTR_variant,,ENST00000548676,;CAPRIN2,upstream_gene_variant,,ENST00000614865,; A ENST00000395805 Transcript missense_variant 2608/4156 2060/2718 687/905 G/V gGc/gTc 1 -1 CAPRIN2 HGNC HGNC:21259 protein_coding CCDS55816.1 ENSP00000379150 Q6IMN6 UPI0000DA6CAD NM_001206856.2 tolerated(0.43) 12/17 hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF5 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 30719209 30719209 C A 1 0 0 0 0 1 0 0 0 2331 739 26 2 2 CAPRIN2 12 30719209 Missense_Mutation SNP C C3L-00913_T 967398 30719209 102556100 152 7026 DNM1L 0 . GRCh38 12 32742668 32742698 + Frame_Shift_Del DEL AAATCATCCTTATTGGATGATCTTCTGACAG AAATCATCCTTATTGGATGATCTTCTGACAG - novel C3L-00913_T C3L-00913_N AAATCATCCTTATTGGATGATCTTCTGACAG AAATCATCCTTATTGGATGATCTTCTGACAG c.2115_2145delATCATCCTTATTGGATGATCTTCTGACAGAA p.Lys705AsnfsTer16 p.K705Nfs*16 ENST00000553257 20/21 689 617 72 474 474 0 sindel-pindel DNM1L,frameshift_variant,p.Lys666AsnfsTer16,ENST00000452533,NM_012063.3;DNM1L,frameshift_variant,p.Lys694AsnfsTer16,ENST00000381000,NM_001278465.1;DNM1L,frameshift_variant,p.Lys489AsnfsTer16,ENST00000414834,NM_001278466.1;DNM1L,frameshift_variant,p.Lys668AsnfsTer16,ENST00000358214,;DNM1L,frameshift_variant,p.Lys655AsnfsTer16,ENST00000266481,NM_005690.4;DNM1L,frameshift_variant,p.Lys705AsnfsTer16,ENST00000553257,NM_001278464.1;DNM1L,frameshift_variant,p.Lys692AsnfsTer16,ENST00000549701,NM_012062.4;DNM1L,frameshift_variant,p.Lys681AsnfsTer16,ENST00000547312,NM_001278463.1;YARS2,downstream_gene_variant,,ENST00000324868,NM_001040436.2;YARS2,intron_variant,,ENST00000551673,;DNM1L,3_prime_UTR_variant,,ENST00000546757,;DNM1L,3_prime_UTR_variant,,ENST00000546649,;DNM1L,non_coding_transcript_exon_variant,,ENST00000553031,;DNM1L,non_coding_transcript_exon_variant,,ENST00000547640,;YARS2,downstream_gene_variant,,ENST00000548490,;DNM1L,downstream_gene_variant,,ENST00000552743,;DNM1L,downstream_gene_variant,,ENST00000550093,;DNM1L,downstream_gene_variant,,ENST00000549157,;DNM1L,downstream_gene_variant,,ENST00000547078,; - ENST00000553257 Transcript frameshift_variant 2190-2220/2699 2113-2143/2250 705-715/749 KSSLLDDLLTE/X AAATCATCCTTATTGGATGATCTTCTGACAGaa/aa 1 1 DNM1L HGNC HGNC:2973 protein_coding YES CCDS61095.1 ENSP00000449089 O00429 UPI00017A7CB6 NM_001278464.1 20/21 Low_complexity_(Seg):seg,PROSITE_profiles:PS51388,hmmpanther:PTHR11566:SF39,hmmpanther:PTHR11566,Pfam_domain:PF02212,SMART_domains:SM00302 HIGH deletion 2 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 32742668 32742668 AAATCATCCTTATTGGATGATCTTCTGACAG - 1 0 1 0 1 0 0 0 0 4484 363 13 0 0 DNM1L 12 32742668 Frame_Shift_Del DEL AAATCATCCTTATTGGATGATCTTCTGACAG C3L-00913_T 2023459 32742668 100532641 153 7027 ADAMTS20 0 . GRCh38 12 43492540 43492540 + Missense_Mutation SNP G G C novel C3L-00913_T C3L-00913_N G G c.1041C>G p.His347Gln p.H347Q ENST00000389420 6/39 339 297 42 211 211 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.His347Gln,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.His347Gln,ENST00000395541,;ADAMTS20,missense_variant,p.His347Gln,ENST00000553158,; C ENST00000389420 Transcript missense_variant 1041/6076 1041/5733 347/1910 H/Q caC/caG 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(0.13) 6/39 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 43492540 43492540 G C 1 0 0 0 0 1 0 0 0 310 1252 44 4 4 ADAMTS20 12 43492540 Missense_Mutation SNP G C3L-00913_T 10749872 43492540 89782769 154 7028 DDX23 0 . GRCh38 12 48837636 48837636 + Missense_Mutation SNP C C T rs768510377 C3L-00913_T C3L-00913_N C C c.641G>A p.Arg214His p.R214H ENST00000308025 7/17 276 251 25 175 175 0 strelka-varscan-mutect DDX23,missense_variant,p.Arg214His,ENST00000308025,NM_004818.2;DDX23,missense_variant,p.Arg58His,ENST00000550834,;DDX23,downstream_gene_variant,,ENST00000552512,;DDX23,downstream_gene_variant,,ENST00000551468,;DDX23,intron_variant,,ENST00000553182,;DDX23,downstream_gene_variant,,ENST00000552369,;DDX23,downstream_gene_variant,,ENST00000552555,;DDX23,non_coding_transcript_exon_variant,,ENST00000551098,;DDX23,non_coding_transcript_exon_variant,,ENST00000547165,;DDX23,non_coding_transcript_exon_variant,,ENST00000551189,;DDX23,intron_variant,,ENST00000547135,;DDX23,upstream_gene_variant,,ENST00000552802,;DDX23,upstream_gene_variant,,ENST00000547290,;DDX23,upstream_gene_variant,,ENST00000551331,;DDX23,upstream_gene_variant,,ENST00000552069,;DDX23,upstream_gene_variant,,ENST00000549795,;DDX23,upstream_gene_variant,,ENST00000547842,;DDX23,upstream_gene_variant,,ENST00000553065,; T ENST00000308025 Transcript missense_variant 721/3248 641/2463 214/820 R/H cGt/cAt rs768510377,COSM4676782 1 -1 DDX23 HGNC HGNC:17347 protein_coding YES CCDS8770.1 ENSP00000310723 Q9BUQ8 A0A024R0Z3 UPI0000073875 NM_004818.2 tolerated(0.13) 7/17 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768510377 . 0 207 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 21 48837636 48837636 C T 1 0 0 0 0 1 0 0 0 4153 536 19 1 1 DDX23 12 48837636 Missense_Mutation SNP C C3L-00913_T 5345096 48837636 84437673 155 7029 KMT2D 0 . GRCh38 12 49048041 49048041 + Missense_Mutation SNP C C G C3L-00913_T C3L-00913_N C C c.4160G>C p.Gly1387Ala p.G1387A ENST00000301067 14/54 85 73 12 50 50 0 strelka-varscan-mutect KMT2D,missense_variant,p.Gly1387Ala,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000550356,; G ENST00000301067 Transcript missense_variant 4160/19419 4160/16614 1387/5537 G/A gGc/gCc COSM693665,COSM693666,COSM940073,COSM940074 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 deleterious(0) 14/54 PROSITE_profiles:PS50016,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF380,Gene3D:3.30.40.10,SMART_domains:SM00184,SMART_domains:SM00249,Superfamily_domains:SSF57903 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999978 1 1 1 0 G 3 3 21 49048041 49048041 C G 1 0 0 0 0 1 0 0 0 8298 739 26 4 4 KMT2D 12 49048041 Missense_Mutation SNP C C3L-00913_T 210405 49048041 84227268 156 7030 ARHGAP9 0 . GRCh38 12 57476443 57476443 + Missense_Mutation SNP C C A rs773143456 C3L-00913_T C3L-00913_N C C c.1037G>T p.Gly346Val p.G346V ENST00000393791 8/18 201 183 18 135 135 0 strelka-varscan-mutect ARHGAP9,missense_variant,p.Gly417Val,ENST00000393797,NM_001319850.1;ARHGAP9,missense_variant,p.Gly425Val,ENST00000550288,;ARHGAP9,missense_variant,p.Gly346Val,ENST00000393791,NM_032496.2;ARHGAP9,missense_variant,p.Gly346Val,ENST00000424809,NM_001080157.1;ARHGAP9,missense_variant,p.Gly162Val,ENST00000430041,NM_001080156.1;ARHGAP9,missense_variant,p.Gly162Val,ENST00000548139,;ARHGAP9,missense_variant,p.Gly131Val,ENST00000552604,;GLI1,downstream_gene_variant,,ENST00000228682,NM_005269.2;GLI1,downstream_gene_variant,,ENST00000546141,NM_001167609.1;GLI1,downstream_gene_variant,,ENST00000543426,NM_001160045.1;GLI1,downstream_gene_variant,,ENST00000528467,;ARHGAP9,upstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552066,;ARHGAP9,downstream_gene_variant,,ENST00000552249,;ARHGAP9,downstream_gene_variant,,ENST00000549602,;ARHGAP9,downstream_gene_variant,,ENST00000551452,;ARHGAP9,upstream_gene_variant,,ENST00000550130,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000550454,;MARS,intron_variant,,ENST00000549133,;ARHGAP9,upstream_gene_variant,,ENST00000547200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000546200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000552953,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000548148,;ARHGAP9,downstream_gene_variant,,ENST00000552420,;ARHGAP9,upstream_gene_variant,,ENST00000550440,;ARHGAP9,downstream_gene_variant,,ENST00000547216,;ARHGAP9,upstream_gene_variant,,ENST00000546704,;ARHGAP9,downstream_gene_variant,,ENST00000551000,;ARHGAP9,downstream_gene_variant,,ENST00000551574,; A ENST00000393791 Transcript missense_variant 1176/2597 1037/2196 346/731 G/V gGc/gTc rs773143456 1 -1 ARHGAP9 HGNC HGNC:14130 protein_coding YES CCDS8941.2 ENSP00000377380 Q9BRR9 UPI000007131B NM_032496.2 tolerated(0.14) 8/18 PROSITE_profiles:PS50003,hmmpanther:PTHR23181:SF4,hmmpanther:PTHR23181,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs773143456 . 0 208 0 2 0 0 0 0 -19.99994 0.9999998 1 1 1 0 A 3 1 21 57476443 57476443 C A 1 0 0 0 0 1 0 0 0 1019 739 26 2 2 ARHGAP9 12 57476443 Missense_Mutation SNP C C3L-00913_T 8428402 57476443 75798866 157 7031 KCNC2 0 . GRCh38 12 75051274 75051274 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.731C>A p.Thr244Lys p.T244K ENST00000549446 3/5 70 60 10 74 73 1 strelka-varscan-mutect KCNC2,missense_variant,p.Thr244Lys,ENST00000549446,NM_139137.3;KCNC2,missense_variant,p.Thr244Lys,ENST00000298972,NM_139136.3;KCNC2,missense_variant,p.Thr244Lys,ENST00000350228,NM_153748.2;KCNC2,missense_variant,p.Thr244Lys,ENST00000548513,;KCNC2,missense_variant,p.Thr244Lys,ENST00000550433,NM_001260498.1;KCNC2,missense_variant,p.Thr244Lys,ENST00000393288,NM_001260497.1;KCNC2,missense_variant,p.Thr244Lys,ENST00000540018,NM_001260499.1;KCNC2,non_coding_transcript_exon_variant,,ENST00000546456,;KCNC2,upstream_gene_variant,,ENST00000548243,; T ENST00000549446 Transcript missense_variant 1412/5625 731/1917 244/638 T/K aCa/aAa 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 tolerated(0.05) 3/5 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.9975 1 1 1 1 0 T 3 4 21 75051274 75051274 G T 1 0 0 0 0 1 0 0 0 7931 1377 48 2 2 KCNC2 12 75051274 Missense_Mutation SNP G C3L-00913_T 17574831 75051274 58224035 158 7032 LRRIQ1 0 . GRCh38 12 85153094 85153094 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.4490G>T p.Cys1497Phe p.C1497F ENST00000393217 21/27 264 229 35 193 193 0 strelka-varscan-mutect LRRIQ1,missense_variant,p.Cys1497Phe,ENST00000393217,NM_001079910.1; T ENST00000393217 Transcript missense_variant 4551/5394 4490/5169 1497/1722 C/F tGt/tTt 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 deleterious(0.03) 21/27 MODERATE 1 SNV 5 1 PASS rs1179266189 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 21 85153094 85153094 G T 1 0 0 0 0 1 0 0 0 8935 1377 48 2 2 LRRIQ1 12 85153094 Missense_Mutation SNP G C3L-00913_T 10101820 85153094 48122215 159 7033 UTP20 0 . GRCh38 12 101381191 101381191 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.7636G>A p.Asp2546Asn p.D2546N ENST00000261637 58/62 281 253 28 276 276 0 strelka-varscan-mutect UTP20,missense_variant,p.Asp2546Asn,ENST00000261637,NM_014503.2; A ENST00000261637 Transcript missense_variant 7810/9025 7636/8358 2546/2785 D/N Gat/Aat 1 1 UTP20 HGNC HGNC:17897 protein_coding YES CCDS9081.1 ENSP00000261637 O75691 UPI00001FB38B NM_014503.2 tolerated(0.05) 58/62 hmmpanther:PTHR17695,hmmpanther:PTHR17695:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 101381191 101381191 G A 1 0 0 0 0 1 0 0 0 17642 1174 41 3 3 UTP20 12 101381191 Missense_Mutation SNP G C3L-00913_T 16228097 101381191 31894118 160 7034 ZNF140 0 . GRCh38 12 133093424 133093424 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.245C>T p.Ser82Leu p.S82L ENST00000319849 5/6 210 196 14 160 160 0 strelka-mutect ZNF140,missense_variant,p.Ser82Leu,ENST00000319849,;ZNF140,intron_variant,,ENST00000355557,NM_003440.3;ZNF140,intron_variant,,ENST00000544426,NM_001300776.1,NM_001300778.1,NM_001300777.1;ZNF140,intron_variant,,ENST00000429434,;ZNF140,intron_variant,,ENST00000440550,;ZNF140,intron_variant,,ENST00000356456,;ZNF140,intron_variant,,ENST00000412146,;ZNF140,intron_variant,,ENST00000536790,;ZNF140,intron_variant,,ENST00000392041,; T ENST00000319849 Transcript missense_variant 434/596 245/345 82/114 S/L tCa/tTa 1 1 ZNF140 HGNC HGNC:12925 protein_coding ENSP00000437913 F5H644 UPI000204AC09 deleterious(0) 5/6 MODERATE SNV 5 1 PASS . . 0 194 4 7 5 0 0 0 -4.334593 0.1047085 1 1 0 0 T 3 4 21 133093424 133093424 C T 1 0 0 0 0 1 0 0 0 18310 838 29 3 3 ZNF140 12 133093424 Missense_Mutation SNP C C3L-00913_T 31712233 133093424 181885 161 7035 TRPC4 0 . GRCh38 13 37637365 37637365 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.2487G>T p.= p.V829V ENST00000625583 10/10 241 228 13 236 236 0 strelka-varscan-mutect TRPC4,synonymous_variant,p.=,ENST00000379705,NM_016179.2;TRPC4,synonymous_variant,p.=,ENST00000625583,NM_003306.1;TRPC4,synonymous_variant,p.=,ENST00000338947,NM_001135958.1;TRPC4,synonymous_variant,p.=,ENST00000379679,;TRPC4,intron_variant,,ENST00000358477,NM_001135955.1;TRPC4,intron_variant,,ENST00000355779,NM_001135957.1;TRPC4,intron_variant,,ENST00000379673,NM_001135956.1;TRPC4,intron_variant,,ENST00000426868,;TRPC4,3_prime_UTR_variant,,ENST00000488717,; A ENST00000625583 Transcript synonymous_variant 2487/3009 2487/2949 829/982 V gtG/gtT 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 10/10 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,Prints_domain:PR01645 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 37637365 37637365 C A 1 0 0 0 0 0 0 0 1 17085 581 21 2 2 TRPC4 13 37637365 Silent SNP C C3L-00913_T 37637365 76726963 162 7036 FREM2 0 . GRCh38 13 38690586 38690586 + Missense_Mutation SNP A A G rs762896753 C3L-00913_T C3L-00913_N A A c.3242A>G p.Asp1081Gly p.D1081G ENST00000280481 1/24 668 627 41 520 519 1 strelka-varscan-mutect FREM2,missense_variant,p.Asp1081Gly,ENST00000280481,NM_207361.5; G ENST00000280481 Transcript missense_variant 3458/16070 3242/9510 1081/3169 D/G gAt/gGt rs762896753 1 1 FREM2 HGNC HGNC:25396 protein_coding YES CCDS31960.1 ENSP00000280481 Q5SZK8 UPI000443805C NM_207361.5 tolerated(0.49) 1/24 hmmpanther:PTHR11878:SF32,hmmpanther:PTHR11878,Pfam_domain:PF16184 MODERATE 1 SNV 2 1 PASS rs762896753 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 38690586 38690586 A G 1 0 0 0 0 1 0 0 0 5912 333 12 5 5 FREM2 13 38690586 Missense_Mutation SNP A C3L-00913_T 1053221 38690586 75673742 163 7037 ATP7B 0 . GRCh38 13 51968537 51968537 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1614G>T p.Gln538His p.Q538H ENST00000242839 4/21 510 467 43 414 413 1 strelka-varscan-mutect ATP7B,missense_variant,p.Gln538His,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Gln538His,ENST00000448424,;ATP7B,missense_variant,p.Gln427His,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Gln538His,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Gln538His,ENST00000634844,;ATP7B,missense_variant,p.Gln538His,ENST00000418097,;ATP7B,intron_variant,,ENST00000400370,;ATP7B,non_coding_transcript_exon_variant,,ENST00000483772,;ATP7B,intron_variant,,ENST00000482841,;ATP7B,intron_variant,,ENST00000635406,;ATP7B,missense_variant,p.Gln538His,ENST00000634308,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634620,;ATP7B,upstream_gene_variant,,ENST00000634296,;FABP5P2,downstream_gene_variant,,ENST00000439042,; A ENST00000242839 Transcript missense_variant 1771/6638 1614/4398 538/1465 Q/H caG/caT 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 tolerated(0.07) 4/21 PROSITE_profiles:PS50846,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,Gene3D:3.30.70.100,Pfam_domain:PF00403,TIGRFAM_domain:TIGR00003,Superfamily_domains:SSF55008,Prints_domain:PR00942 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 51968537 51968537 C A 1 0 0 0 0 1 0 0 0 1344 796 28 2 2 ATP7B 13 51968537 Missense_Mutation SNP C C3L-00913_T 13277951 51968537 62395791 164 7038 CCDC168 0 . GRCh38 13 102742105 102742105 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.8592G>C p.Lys2864Asn p.K2864N ENST00000322527 4/4 290 271 19 248 248 0 strelka-varscan-mutect CCDC168,missense_variant,p.Lys2864Asn,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; G ENST00000322527 Transcript missense_variant 8730/21466 8592/21246 2864/7081 K/N aaG/aaC 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.04) 4/4 Pfam_domain:PF15804 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 102742105 102742105 C G 1 0 0 0 0 1 0 0 0 2484 796 28 4 4 CCDC168 13 102742105 Missense_Mutation SNP C C3L-00913_T 50773568 102742105 11622223 165 7039 RALGAPA1 0 . GRCh38 14 35595660 35595660 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.5665G>A p.Asp1889Asn p.D1889N ENST00000307138 36/40 447 420 27 365 364 1 strelka-varscan-mutect RALGAPA1,missense_variant,p.Asp2348Asn,ENST00000637992,;RALGAPA1,missense_variant,p.Asp1889Asn,ENST00000307138,NM_194301.2;RALGAPA1,missense_variant,p.Asp1889Asn,ENST00000389698,NM_014990.1;RALGAPA1,missense_variant,p.Asp1902Asn,ENST00000382366,NM_001283043.1;RALGAPA1,missense_variant,p.Asp1936Asn,ENST00000553892,NM_001283044.1;RALGAPA1,missense_variant,p.Asp527Asn,ENST00000554259,;RALGAPA1,missense_variant,p.Asp172Asn,ENST00000554573,; T ENST00000307138 Transcript missense_variant 6134/7911 5665/6252 1889/2083 D/N Gat/Aat 1 -1 RALGAPA1 HGNC HGNC:17770 protein_coding YES CCDS32064.1 ENSP00000302647 Q6GYQ0 UPI00003B5C51 NM_194301.2 tolerated(0.06) 36/40 PROSITE_profiles:PS50085,hmmpanther:PTHR10063:SF3,hmmpanther:PTHR10063,Pfam_domain:PF02145,Superfamily_domains:0043732 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 35595660 35595660 C T 1 0 0 0 0 1 0 0 0 13172 826 29 3 3 RALGAPA1 14 35595660 Missense_Mutation SNP C C3L-00913_T 35595660 71448058 166 7040 LRFN5 0 . GRCh38 14 41886863 41886863 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.238C>A p.Leu80Met p.L80M ENST00000298119 3/6 185 166 19 158 158 0 strelka-varscan-mutect LRFN5,missense_variant,p.Leu80Met,ENST00000554171,;LRFN5,missense_variant,p.Leu80Met,ENST00000298119,NM_152447.3;LRFN5,missense_variant,p.Leu80Met,ENST00000554120,; A ENST00000298119 Transcript missense_variant 1427/3723 238/2160 80/719 L/M Ctg/Atg 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0.01) 3/6 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,Pfam_domain:PF13306,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 41886863 41886863 C A 1 0 0 0 0 1 0 0 0 8835 680 24 2 2 LRFN5 14 41886863 Missense_Mutation SNP C C3L-00913_T 6291203 41886863 65156855 167 7041 CCDC175 0 . GRCh38 14 59545185 59545185 + Nonsense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1150C>T p.Gln384Ter p.Q384* ENST00000537690 9/20 199 159 40 142 141 1 strelka-varscan-mutect CCDC175,stop_gained,p.Gln384Ter,ENST00000537690,NM_001164399.1;CCDC175,stop_gained,p.Gln384Ter,ENST00000281581,;CCDC175,intron_variant,,ENST00000556936,; A ENST00000537690 Transcript stop_gained 1206/2616 1150/2382 384/793 Q/* Caa/Taa 1 -1 CCDC175 HGNC HGNC:19847 protein_coding YES CCDS53898.1 ENSP00000453940 P0C221 UPI000059D254 NM_001164399.1 9/20 hmmpanther:PTHR35347 HIGH 1 SNV 5 1 PASS . . 0 187 8 15 0 0 0 0 -20 0.7626636 0 1 1 0 A 4 1 21 59545185 59545185 G A 1 0 0 0 0 0 1 0 0 2492 1328 46 3 3 CCDC175 14 59545185 Nonsense_Mutation SNP G C3L-00913_T 17658322 59545185 47498533 168 7042 VIPAS39 0 . GRCh38 14 77453318 77453318 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.177G>T p.Trp59Cys p.W59C ENST00000553888 3/20 657 565 92 464 464 0 strelka-varscan-mutect VIPAS39,missense_variant,p.Trp59Cys,ENST00000553888,NM_022067.3,NM_001193314.1,NM_001193317.1;VIPAS39,missense_variant,p.Trp59Cys,ENST00000343765,;VIPAS39,missense_variant,p.Trp59Cys,ENST00000327028,;VIPAS39,missense_variant,p.Trp59Cys,ENST00000557658,NM_001193315.1;VIPAS39,missense_variant,p.Trp85Cys,ENST00000556412,;VIPAS39,missense_variant,p.Trp59Cys,ENST00000448935,NM_001193316.1;AHSA1,upstream_gene_variant,,ENST00000216479,NM_012111.2;AHSA1,upstream_gene_variant,,ENST00000535854,;AHSA1,upstream_gene_variant,,ENST00000555133,;AHSA1,upstream_gene_variant,,ENST00000555517,;VIPAS39,downstream_gene_variant,,ENST00000557466,;VIPAS39,downstream_gene_variant,,ENST00000556909,;VIPAS39,non_coding_transcript_exon_variant,,ENST00000553691,;AHSA1,upstream_gene_variant,,ENST00000556963,;AHSA1,upstream_gene_variant,,ENST00000554156,; A ENST00000553888 Transcript missense_variant 688/2934 177/1482 59/493 W/C tgG/tgT 1 -1 VIPAS39 HGNC HGNC:20347 protein_coding YES CCDS9862.1 ENSP00000452181 Q9H9C1 Q6IA61 UPI00000735EF NM_022067.3,NM_001193314.1,NM_001193317.1 deleterious(0) 3/20 hmmpanther:PTHR13364,hmmpanther:PTHR13364:SF6 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 77453318 77453318 C A 1 0 0 0 0 1 0 0 0 17715 856 30 2 2 VIPAS39 14 77453318 Missense_Mutation SNP C C3L-00913_T 17908133 77453318 29590400 169 7043 CEP170B 0 . GRCh38 14 104886067 104886067 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1972G>T p.Gly658Cys p.G658C ENST00000414716 11/19 66 54 12 35 35 0 strelka-varscan-mutect CEP170B,missense_variant,p.Gly659Cys,ENST00000453495,;CEP170B,missense_variant,p.Gly658Cys,ENST00000414716,NM_001112726.2;CEP170B,missense_variant,p.Gly588Cys,ENST00000556508,NM_015005.2; T ENST00000414716 Transcript missense_variant 2200/6705 1972/4665 658/1554 G/C Ggt/Tgt 1 1 CEP170B HGNC HGNC:20362 protein_coding YES CCDS45175.1 ENSP00000404151 Q9Y4F5 UPI00001FDCF7 NM_001112726.2 deleterious(0) 11/19 hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18 MODERATE 1 SNV 1 1 PASS rs1316601109 . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 21 104886067 104886067 G T 1 0 0 0 0 1 0 0 0 2965 1232 43 2 2 CEP170B 14 104886067 Missense_Mutation SNP G C3L-00913_T 27432749 104886067 2157651 170 7044 GABRG3 0 . GRCh38 15 26977093 26977093 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.145C>A p.Leu49Ile p.L49I ENST00000615808 2/10 243 226 17 175 175 0 strelka-mutect GABRG3,missense_variant,p.Leu49Ile,ENST00000615808,NM_033223.4;GABRG3,missense_variant,p.Leu49Ile,ENST00000555083,NM_001270873.1;GABRG3,non_coding_transcript_exon_variant,,ENST00000553440,; A ENST00000615808 Transcript missense_variant 399/10768 145/1404 49/467 L/I Ctt/Att 1 1 GABRG3 HGNC HGNC:4088 protein_coding YES CCDS45195.1 ENSP00000479113 Q99928 UPI000012AFCB NM_033223.4 tolerated(0.2) 2/10 Superfamily_domains:0038932,Prints_domain:PR01620,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF195,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 26977093 26977093 C A 1 0 0 0 0 1 0 0 0 6044 913 32 2 2 GABRG3 15 26977093 Missense_Mutation SNP C C3L-00913_T 26977093 75014096 171 7045 PLA2G4D 0 . GRCh38 15 42072351 42072351 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.1359A>T p.Glu453Asp p.E453D ENST00000290472 14/20 183 161 22 137 137 0 strelka-varscan-mutect PLA2G4D,missense_variant,p.Glu453Asp,ENST00000290472,NM_178034.3;PLA2G4D,upstream_gene_variant,,ENST00000560932,; A ENST00000290472 Transcript missense_variant 1454/3584 1359/2457 453/818 E/D gaA/gaT 1 -1 PLA2G4D HGNC HGNC:30038 protein_coding YES CCDS32203.1 ENSP00000290472 Q86XP0 UPI00001FE2F2 NM_178034.3 tolerated(0.44) 14/20 Gene3D:3.40.1090.10,Pfam_domain:PF01735,PROSITE_profiles:PS51210,hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF31,SMART_domains:SM00022,Superfamily_domains:SSF52151 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.99999 1 1 1 0 A 3 1 21 42072351 42072351 T A 1 0 0 0 0 1 0 0 0 12100 1722 60 4 4 PLA2G4D 15 42072351 Missense_Mutation SNP T C3L-00913_T 15095258 42072351 59918838 172 7046 CYP19A1 0 . GRCh38 15 51227788 51227788 + Missense_Mutation SNP A A C novel C3L-00913_T C3L-00913_N A A c.442T>G p.Phe148Val p.F148V ENST00000396402 4/10 460 407 53 287 286 1 strelka-varscan-mutect CYP19A1,missense_variant,p.Phe148Val,ENST00000396402,NM_000103.3;CYP19A1,missense_variant,p.Phe148Val,ENST00000396404,NM_031226.2;CYP19A1,missense_variant,p.Phe148Val,ENST00000559878,;CYP19A1,missense_variant,p.Phe148Val,ENST00000405913,;CYP19A1,missense_variant,p.Phe148Val,ENST00000453807,;CYP19A1,missense_variant,p.Phe148Val,ENST00000558328,;CYP19A1,missense_variant,p.Phe148Val,ENST00000559980,;CYP19A1,missense_variant,p.Phe148Val,ENST00000561075,;CYP19A1,missense_variant,p.Phe148Val,ENST00000557858,;CYP19A1,missense_variant,p.Phe148Val,ENST00000405011,;CYP19A1,missense_variant,p.Phe148Val,ENST00000559646,;RP11-108K3.1,intron_variant,,ENST00000559909,;CYP19A1,missense_variant,p.Phe148Val,ENST00000439712,;CYP19A1,missense_variant,p.Phe148Val,ENST00000557934,; C ENST00000396402 Transcript missense_variant 596/4417 442/1512 148/503 F/V Ttt/Gtt 1 -1 CYP19A1 HGNC HGNC:2594 protein_coding YES CCDS10139.1 ENSP00000379683 P11511 A0A024R5S8 UPI000013D0D7 NM_000103.3 deleterious(0) 4/10 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF43,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 51227788 51227788 A C 1 0 0 0 0 1 0 0 0 3951 72 3 5 5 CYP19A1 15 51227788 Missense_Mutation SNP A C3L-00913_T 9155437 51227788 50763401 173 7047 CEMIP 0 . GRCh38 15 80942015 80942015 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.3574G>A p.Asp1192Asn p.D1192N ENST00000394685 26/30 480 416 64 387 387 0 strelka-varscan-mutect CEMIP,missense_variant,p.Asp1192Asn,ENST00000394685,NM_001293298.1;CEMIP,missense_variant,p.Asp1192Asn,ENST00000356249,NM_001293304.1;CEMIP,missense_variant,p.Asp1192Asn,ENST00000220244,NM_018689.2;CEMIP,intron_variant,,ENST00000611615,;CEMIP,downstream_gene_variant,,ENST00000560027,;RP11-351M8.2,intron_variant,,ENST00000560873,;CEMIP,intron_variant,,ENST00000495041,;MESDC2,downstream_gene_variant,,ENST00000619987,;CEMIP,upstream_gene_variant,,ENST00000559966,; A ENST00000394685 Transcript missense_variant 3993/7357 3574/4086 1192/1361 D/N Gac/Aac 1 1 CEMIP HGNC HGNC:29213 protein_coding YES CCDS10315.1 ENSP00000378177 Q8WUJ3 UPI00001D7799 NM_001293298.1 tolerated(0.51) 26/30 hmmpanther:PTHR15535,hmmpanther:PTHR15535:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 80942015 80942015 G A 1 0 0 0 0 1 0 0 0 2931 942 33 3 3 CEMIP 15 80942015 Missense_Mutation SNP G C3L-00913_T 29714227 80942015 21049174 174 7048 AGBL1 0 . GRCh38 15 86397423 86397423 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.2432G>T p.Ser811Ile p.S811I ENST00000441037 18/25 161 140 21 127 127 0 strelka-varscan-mutect AGBL1,missense_variant,p.Ser31Ile,ENST00000614907,;AGBL1,missense_variant,p.Ser811Ile,ENST00000441037,;AGBL1,missense_variant,p.Ser765Ile,ENST00000635782,NM_152336.2;AGBL1,missense_variant,p.Ser765Ile,ENST00000421325,; T ENST00000441037 Transcript missense_variant 2432/3551 2432/3339 811/1112 S/I aGt/aTt 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 deleterious(0) 18/25 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5,Superfamily_domains:SSF53187 MODERATE 1 SNV 5 1 PASS rs765741949 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 86397423 86397423 G T 1 0 0 0 0 1 0 0 0 451 1029 36 2 2 AGBL1 15 86397423 Missense_Mutation SNP G C3L-00913_T 5455408 86397423 15593766 175 7049 LRRK1 0 . GRCh38 15 101066155 101066155 + Missense_Mutation SNP C C A rs373703455 C3L-00913_T C3L-00913_N C C c.5718C>A p.His1906Gln p.H1906Q ENST00000388948 32/34 150 134 16 118 118 0 strelka-varscan-mutect LRRK1,missense_variant,p.His1906Gln,ENST00000388948,NM_024652.4;RP11-505E24.2,intron_variant,,ENST00000559857,;LRRK1,non_coding_transcript_exon_variant,,ENST00000532145,;LRRK1,downstream_gene_variant,,ENST00000525395,;LRRK1,missense_variant,p.His583Gln,ENST00000526457,;LRRK1,3_prime_UTR_variant,,ENST00000525284,;LRRK1,3_prime_UTR_variant,,ENST00000531270,; A ENST00000388948 Transcript missense_variant 6077/7671 5718/6048 1906/2015 H/Q caC/caA rs373703455 1 1 LRRK1 HGNC HGNC:18608 protein_coding YES CCDS42086.1 ENSP00000373600 Q38SD2 UPI0000D4FE63 NM_024652.4 tolerated_low_confidence(0.07) 32/34 hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF498 MODERATE SNV 5 1 PASS rs373703455 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 101066155 101066155 C A 1 0 0 0 0 1 0 0 0 8938 506 18 2 2 LRRK1 15 101066155 Missense_Mutation SNP C C3L-00913_T 14668732 101066155 925034 176 7050 RAB11FIP3 0 . GRCh38 16 488916 488916 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1181G>T p.Gly394Val p.G394V ENST00000262305 5/14 261 229 32 178 178 0 strelka-varscan-mutect RAB11FIP3,missense_variant,p.Gly394Val,ENST00000262305,NM_014700.3;RAB11FIP3,missense_variant,p.Gly270Val,ENST00000434585,;RAB11FIP3,missense_variant,p.Gly98Val,ENST00000450428,NM_001142272.1;RAB11FIP3,missense_variant,p.Gly84Val,ENST00000452814,;RAB11FIP3,missense_variant,p.Gly98Val,ENST00000449879,;RAB11FIP3,missense_variant,p.Gly49Val,ENST00000412256,;RAB11FIP3,non_coding_transcript_exon_variant,,ENST00000483002,;RAB11FIP3,upstream_gene_variant,,ENST00000495663,; T ENST00000262305 Transcript missense_variant 1569/4831 1181/2271 394/756 G/V gGt/gTt 1 1 RAB11FIP3 HGNC HGNC:17224 protein_coding YES CCDS32351.1 ENSP00000262305 O75154 UPI0000129C9C NM_014700.3 deleterious(0) 5/14 hmmpanther:PTHR15726,hmmpanther:PTHR15726:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 488916 488916 G T 1 0 0 0 0 1 0 0 0 13053 1261 44 2 2 RAB11FIP3 16 488916 Missense_Mutation SNP G C3L-00913_T 488916 89849429 177 7051 MSLN 0 . GRCh38 16 763263 763263 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.116G>T p.Gly39Val p.G39V ENST00000382862 3/17 166 157 9 134 134 0 strelka-varscan-mutect MSLN,missense_variant,p.Gly39Val,ENST00000566549,;MSLN,missense_variant,p.Gly39Val,ENST00000545450,NM_005823.5;MSLN,missense_variant,p.Gly39Val,ENST00000382862,NM_013404.4;MSLN,missense_variant,p.Gly39Val,ENST00000563941,NM_001177355.1;MSLN,missense_variant,p.Gly39Val,ENST00000563651,;MSLN,missense_variant,p.Gly39Val,ENST00000569566,;MSLN,upstream_gene_variant,,ENST00000561896,;MSLN,upstream_gene_variant,,ENST00000566269,; T ENST00000382862 Transcript missense_variant 211/2116 116/1893 39/630 G/V gGa/gTa 1 1 MSLN HGNC HGNC:7371 protein_coding YES CCDS32356.1 ENSP00000372313 Q13421 UPI000004EC9C NM_013404.4 tolerated(0.42) 3/17 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF6,Pfam_domain:PF06060 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -16.53493 1 1 1 1 0 T 3 4 21 763263 763263 G T 1 0 0 0 0 1 0 0 0 9863 1174 41 2 2 MSLN 16 763263 Missense_Mutation SNP G C3L-00913_T 274347 763263 89575082 178 7052 ADCY9 0 . GRCh38 16 3965890 3965890 + Missense_Mutation SNP A A C novel C3L-00913_T C3L-00913_N A A c.3947T>G p.Val1316Gly p.V1316G ENST00000294016 11/11 456 433 23 312 311 1 strelka-varscan ADCY9,missense_variant,p.Val1316Gly,ENST00000294016,NM_001116.3;ADCY9,intron_variant,,ENST00000576936,; C ENST00000294016 Transcript missense_variant 4486/7725 3947/4062 1316/1353 V/G gTc/gGc 1 -1 ADCY9 HGNC HGNC:240 protein_coding YES CCDS32382.1 ENSP00000294016 O60503 UPI000012887F NM_001116.3 tolerated_low_confidence(0.5) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 3965890 3965890 A C 1 0 0 0 0 1 0 0 0 345 275 10 5 5 ADCY9 16 3965890 Missense_Mutation SNP A C3L-00913_T 3202627 3965890 86372455 179 7053 MGRN1 0 . GRCh38 16 4625008 4625008 + Missense_Mutation SNP C C G rs773522921 C3L-00913_T C3L-00913_N C C c.48C>G p.Asp16Glu p.D16E ENST00000262370 1/17 342 323 19 232 232 0 strelka-varscan-mutect MGRN1,missense_variant,p.Asp16Glu,ENST00000399577,NM_001142290.2;MGRN1,missense_variant,p.Asp16Glu,ENST00000415496,NM_001142291.2;MGRN1,missense_variant,p.Asp16Glu,ENST00000262370,NM_015246.3;MGRN1,missense_variant,p.Asp16Glu,ENST00000587747,;MGRN1,missense_variant,p.Asp16Glu,ENST00000586183,;MGRN1,missense_variant,p.Asp16Glu,ENST00000588994,NM_001142289.2;MGRN1,intron_variant,,ENST00000591895,;MGRN1,missense_variant,p.Asp16Glu,ENST00000536343,; G ENST00000262370 Transcript missense_variant 219/3968 48/1731 16/576 D/E gaC/gaG rs773522921 1 1 MGRN1 HGNC HGNC:20254 protein_coding YES CCDS42115.1 ENSP00000262370 O60291 UPI000018CE7F NM_015246.3 tolerated(0.09) 1/17 hmmpanther:PTHR22996,hmmpanther:PTHR22996:SF2 MODERATE 1 SNV 1 1 PASS rs773522921 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 4625008 4625008 C G 1 0 0 0 0 1 0 0 0 9516 477 17 4 4 MGRN1 16 4625008 Missense_Mutation SNP C C3L-00913_T 659118 4625008 85713337 180 7054 ITGAM 0 . GRCh38 16 31277980 31277980 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.1227C>A p.= p.A409A ENST00000544665 12/30 145 129 16 103 103 0 strelka-varscan-mutect ITGAM,synonymous_variant,p.=,ENST00000544665,NM_001145808.1;ITGAM,synonymous_variant,p.=,ENST00000287497,NM_000632.3;ITGAM,intron_variant,,ENST00000567031,;ITGAM,downstream_gene_variant,,ENST00000570242,; A ENST00000544665 Transcript synonymous_variant 1298/4718 1227/3462 409/1153 A gcC/gcA 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 12/30 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,SMART_domains:SM00191,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 31277980 31277980 C A 1 0 0 0 0 0 0 0 1 7794 581 21 2 2 ITGAM 16 31277980 Silent SNP C C3L-00913_T 26652972 31277980 59060365 181 7055 RPGRIP1L 0 . GRCh38 16 53645952 53645952 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.2356G>A p.Asp786Asn p.D786N ENST00000379925 17/27 323 294 29 295 294 1 strelka-varscan-mutect RPGRIP1L,missense_variant,p.Asp786Asn,ENST00000262135,NM_001127897.1;RPGRIP1L,missense_variant,p.Asp786Asn,ENST00000621565,NM_001308334.1;RPGRIP1L,missense_variant,p.Asp786Asn,ENST00000379925,NM_015272.2;RPGRIP1L,missense_variant,p.Asp786Asn,ENST00000563746,;RPGRIP1L,missense_variant,p.Asp786Asn,ENST00000564374,; T ENST00000379925 Transcript missense_variant 2407/5297 2356/3948 786/1315 D/N Gat/Aat 1 -1 RPGRIP1L HGNC HGNC:29168 protein_coding YES CCDS32447.1 ENSP00000369257 Q68CZ1 UPI000047DAF2 NM_015272.2 deleterious(0.02) 17/27 hmmpanther:PTHR14240:SF4,hmmpanther:PTHR14240,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 53645952 53645952 C T 1 0 0 0 0 1 0 0 0 13802 913 32 3 3 RPGRIP1L 16 53645952 Missense_Mutation SNP C C3L-00913_T 22367972 53645952 36692393 182 7056 COQ9 0 . GRCh38 16 57456519 57456519 + Missense_Mutation SNP A A C novel C3L-00913_T C3L-00913_N A A c.394A>C p.Ser132Arg p.S132R ENST00000262507 4/9 648 609 39 450 450 0 strelka-varscan-mutect COQ9,missense_variant,p.Ser132Arg,ENST00000262507,NM_020312.3;COQ9,missense_variant,p.Ser132Arg,ENST00000567072,;COQ9,missense_variant,p.Ser136Arg,ENST00000564655,;COQ9,5_prime_UTR_variant,,ENST00000563391,;COQ9,intron_variant,,ENST00000567933,;COQ9,intron_variant,,ENST00000565964,;COQ9,intron_variant,,ENST00000563166,;COQ9,downstream_gene_variant,,ENST00000567384,;AC009052.12,upstream_gene_variant,,ENST00000567090,;COQ9,missense_variant,p.Ser132Arg,ENST00000564115,;COQ9,non_coding_transcript_exon_variant,,ENST00000562734,;COQ9,non_coding_transcript_exon_variant,,ENST00000568790,;COQ9,non_coding_transcript_exon_variant,,ENST00000562426,;COQ9,non_coding_transcript_exon_variant,,ENST00000567576,;COQ9,non_coding_transcript_exon_variant,,ENST00000567480,;COQ9,downstream_gene_variant,,ENST00000566388,;COQ9,upstream_gene_variant,,ENST00000569980,; C ENST00000262507 Transcript missense_variant 463/1677 394/957 132/318 S/R Agt/Cgt 1 1 COQ9 HGNC HGNC:25302 protein_coding YES CCDS32459.1 ENSP00000262507 O75208 A0A024R6U3 UPI0000070ECA NM_020312.3 tolerated(0.16) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR21427,TIGRFAM_domain:TIGR02396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 57456519 57456519 A C 1 0 0 0 0 1 0 0 0 3545 188 7 5 5 COQ9 16 57456519 Missense_Mutation SNP A C3L-00913_T 3810567 57456519 32881826 183 7057 ADGRG5 0 . GRCh38 16 57575041 57575041 + Missense_Mutation SNP G G T rs570246683 C3L-00913_T C3L-00913_N G G c.1435G>T p.Val479Phe p.V479F ENST00000340339 11/12 178 166 12 154 154 0 strelka-varscan-mutect ADGRG5,missense_variant,p.Val479Phe,ENST00000340339,NM_153837.2;ADGRG5,missense_variant,p.Val479Phe,ENST00000349457,NM_001304376.1;ADGRG5,non_coding_transcript_exon_variant,,ENST00000394361,;ADGRG5,non_coding_transcript_exon_variant,,ENST00000569839,;ADGRG5,non_coding_transcript_exon_variant,,ENST00000564607,; T ENST00000340339 Transcript missense_variant 1958/3767 1435/1587 479/528 V/F Gtc/Ttc rs570246683 1 1 ADGRG5 HGNC HGNC:19010 protein_coding YES CCDS10785.1 ENSP00000342981 Q8IZF4 A0A024R6S3 UPI0000039944 NM_153837.2 deleterious(0) 11/12 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF326,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs570246683 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 57575041 57575041 G T 1 0 0 0 0 1 0 0 0 372 1145 40 1 1 ADGRG5 16 57575041 Missense_Mutation SNP G C3L-00913_T 118522 57575041 32763304 184 7058 TRADD 0 . GRCh38 16 67154746 67154746 + Missense_Mutation SNP G G A C3L-00913_T C3L-00913_N G G c.842C>T p.Thr281Met p.T281M ENST00000345057 5/5 215 195 20 149 149 0 strelka-varscan-mutect TRADD,missense_variant,p.Thr281Met,ENST00000345057,NM_003789.3;TRADD,missense_variant,p.Thr221Met,ENST00000486556,;B3GNT9,upstream_gene_variant,,ENST00000449549,NM_033309.2;TRADD,downstream_gene_variant,,ENST00000566104,;TRADD,downstream_gene_variant,,ENST00000563348,;TRADD,downstream_gene_variant,,ENST00000566247,; A ENST00000345057 Transcript missense_variant 1311/1877 842/939 281/312 T/M aCg/aTg COSM703896 1 -1 TRADD HGNC HGNC:12030 protein_coding YES CCDS10829.1 ENSP00000341268 Q15628 UPI00001372E3 NM_003789.3 deleterious(0) 5/5 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50017,hmmpanther:PTHR14913,Pfam_domain:PF00531,Gene3D:1.10.533.10,SMART_domains:SM00005,Superfamily_domains:SSF47986 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 67154746 67154746 G A 1 0 0 0 0 1 0 0 0 16919 1145 40 1 1 TRADD 16 67154746 Missense_Mutation SNP G C3L-00913_T 9579705 67154746 23183599 185 7059 COG4 0 . GRCh38 16 70496371 70496371 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.1542G>T p.Gln514His p.Q514H ENST00000323786 12/19 564 508 56 364 364 0 strelka-varscan-mutect COG4,missense_variant,p.Gln514His,ENST00000323786,NM_015386.2;COG4,missense_variant,p.Gln514His,ENST00000393612,NM_001195139.1;COG4,3_prime_UTR_variant,,ENST00000564415,;COG4,3_prime_UTR_variant,,ENST00000482252,;COG4,non_coding_transcript_exon_variant,,ENST00000530314,;COG4,non_coding_transcript_exon_variant,,ENST00000526700,;COG4,non_coding_transcript_exon_variant,,ENST00000564315,;COG4,downstream_gene_variant,,ENST00000567244,; A ENST00000323786 Transcript missense_variant 1564/2833 1542/2370 514/789 Q/H caG/caT 1 -1 COG4 HGNC HGNC:18620 protein_coding YES CCDS10892.2 ENSP00000315775 J3KNI1 UPI000059D3B0 NM_015386.2 deleterious(0) 12/19 hmmpanther:PTHR24016:SF0,hmmpanther:PTHR24016 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 70496371 70496371 C A 1 0 0 0 0 1 0 0 0 3448 796 28 2 2 COG4 16 70496371 Missense_Mutation SNP C C3L-00913_T 3341625 70496371 19841974 186 7060 WDR59 0 . GRCh38 16 74887751 74887751 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.2351G>T p.Ser784Ile p.S784I ENST00000262144 23/26 194 178 16 136 136 0 strelka-varscan-mutect WDR59,missense_variant,p.Ser784Ile,ENST00000262144,NM_030581.3;WDR59,missense_variant,p.Ser99Ile,ENST00000563797,;WDR59,downstream_gene_variant,,ENST00000569229,;WDR59,upstream_gene_variant,,ENST00000569183,;WDR59,downstream_gene_variant,,ENST00000569788,;WDR59,downstream_gene_variant,,ENST00000563381,;WDR59,downstream_gene_variant,,ENST00000566924,;WDR59,downstream_gene_variant,,ENST00000567018,;WDR59,upstream_gene_variant,,ENST00000569968,; A ENST00000262144 Transcript missense_variant 2482/5898 2351/2925 784/974 S/I aGc/aTc 1 -1 WDR59 HGNC HGNC:25706 protein_coding YES CCDS32488.1 ENSP00000262144 Q6PJI9 UPI000019839C NM_030581.3 tolerated(0.17) 23/26 hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF116,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 74887751 74887751 C A 1 0 0 0 0 1 0 0 0 17867 811 28 2 2 WDR59 16 74887751 Missense_Mutation SNP C C3L-00913_T 4391380 74887751 15450594 187 7061 CHST5 0 . GRCh38 16 75530366 75530366 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.19G>A p.Val7Ile p.V7I ENST00000336257 3/3 85 77 8 71 71 0 strelka-varscan-mutect CHST5,missense_variant,p.Val7Ile,ENST00000336257,NM_024533.4;CHST5,intron_variant,,ENST00000565039,;RP11-77K12.7,intron_variant,,ENST00000460606,; T ENST00000336257 Transcript missense_variant 1414/3245 19/1236 7/411 V/I Gtc/Atc 1 -1 CHST5 HGNC HGNC:1973 protein_coding YES CCDS10919.1 ENSP00000338783 Q9GZS9 UPI000006EAEA NM_024533.4 deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -17.08711 1 1 1 1 0 T 3 4 21 75530366 75530366 C T 1 0 0 0 0 1 0 0 0 3167 507 18 3 3 CHST5 16 75530366 Missense_Mutation SNP C C3L-00913_T 642615 75530366 14807979 188 7062 ADAD2 0 . GRCh38 16 84194570 84194570 + Missense_Mutation SNP C C G rs763776438 C3L-00913_T C3L-00913_N C C c.763C>G p.Leu255Val p.L255V ENST00000268624 3/11 323 287 36 228 228 0 strelka-varscan-mutect ADAD2,missense_variant,p.Leu255Val,ENST00000268624,NM_139174.3;ADAD2,missense_variant,p.Leu183Val,ENST00000315906,NM_001145400.1;ADAD2,missense_variant,p.Leu108Val,ENST00000567685,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000536986,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000565643,;RP11-486L19.2,non_coding_transcript_exon_variant,,ENST00000561900,;RP11-486L19.2,downstream_gene_variant,,ENST00000569834,;ADAD2,downstream_gene_variant,,ENST00000567413,;ADAD2,non_coding_transcript_exon_variant,,ENST00000564430,;ADAD2,non_coding_transcript_exon_variant,,ENST00000566526,;ADAD2,non_coding_transcript_exon_variant,,ENST00000564169,;ADAD2,non_coding_transcript_exon_variant,,ENST00000569221,;ADAD2,upstream_gene_variant,,ENST00000563849,; G ENST00000268624 Transcript missense_variant 856/2283 763/1998 255/665 L/V Ctg/Gtg rs763776438 1 1 ADAD2 HGNC HGNC:30714 protein_coding YES CCDS10944.1 ENSP00000268624 Q8NCV1 UPI000013D7CA NM_139174.3 tolerated(0.1) 3/11 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF106,Superfamily_domains:SSF54768 MODERATE 1 SNV 2 1 PASS rs763776438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 84194570 84194570 C G 1 0 0 0 0 1 0 0 0 276 796 28 4 4 ADAD2 16 84194570 Missense_Mutation SNP C C3L-00913_T 8664204 84194570 6143775 189 7063 SLC43A2 0 . GRCh38 17 1585927 1585927 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.1215G>C p.Glu405Asp p.E405D ENST00000571650 11/15 357 319 38 314 314 0 strelka-varscan-mutect SLC43A2,missense_variant,p.Glu401Asp,ENST00000301335,NM_001321364.1,NM_001321365.1,NM_152346.2;SLC43A2,missense_variant,p.Glu405Asp,ENST00000571650,NM_001284498.1;SLC43A2,missense_variant,p.Glu264Asp,ENST00000412517,NM_001284499.1;SLC43A2,downstream_gene_variant,,ENST00000574274,;SLC43A2,non_coding_transcript_exon_variant,,ENST00000572135,;SLC43A2,non_coding_transcript_exon_variant,,ENST00000574743,;SLC43A2,downstream_gene_variant,,ENST00000572801,;SLC43A2,upstream_gene_variant,,ENST00000576769,; G ENST00000571650 Transcript missense_variant 1522/3261 1215/1722 405/573 E/D gaG/gaC 1 -1 SLC43A2 HGNC HGNC:23087 protein_coding YES CCDS67108.1 ENSP00000461382 Q8N370 UPI00004EAF8C NM_001284498.1 tolerated(0.58) 11/15 hmmpanther:PTHR20766,hmmpanther:PTHR20766:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 1585927 1585927 C G 1 0 0 0 0 1 0 0 0 14911 912 32 4 4 SLC43A2 17 1585927 Missense_Mutation SNP C C3L-00913_T 1585927 81671514 190 7064 OR3A2 0 . GRCh38 17 3278033 3278033 + Silent SNP G G C novel C3L-00913_T C3L-00913_N G G c.903C>G p.= p.L301L ENST00000408891 1/1 101 94 7 84 84 0 strelka-varscan-mutect OR3A2,synonymous_variant,p.=,ENST00000408891,NM_002551.3;RP11-64J4.2,downstream_gene_variant,,ENST00000573491,;RP11-64J4.2,downstream_gene_variant,,ENST00000576166,; C ENST00000408891 Transcript synonymous_variant 942/1076 903/966 301/321 L ctC/ctG 1 -1 OR3A2 HGNC HGNC:8283 protein_coding YES CCDS42233.1 ENSP00000386180 P47893 A0A126GVQ3 UPI0000050B3C NM_002551.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF449,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 204 6 0 0 0 0 0 -14.23932 0.9999997 1 1 1 0 C 2 2 21 3278033 3278033 G C 1 0 0 0 0 0 0 0 1 11115 1277 45 4 4 OR3A2 17 3278033 Silent SNP G C3L-00913_T 1692106 3278033 79979408 191 7065 OR1E1 0 . GRCh38 17 3397954 3397954 + Missense_Mutation SNP T T C novel C3L-00913_T C3L-00913_N T T c.457A>G p.Thr153Ala p.T153A ENST00000322608 1/1 421 363 58 341 341 0 strelka-varscan-mutect OR1E1,missense_variant,p.Thr153Ala,ENST00000322608,NM_003553.2; C ENST00000322608 Transcript missense_variant 457/1307 457/945 153/314 T/A Acc/Gcc 1 -1 OR1E1 HGNC HGNC:8189 protein_coding YES CCDS11024.1 ENSP00000313384 P30953 UPI0000041BB6 NM_003553.2 tolerated(0.24) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF367,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 3397954 3397954 T C 1 0 0 0 0 1 0 0 0 11032 1696 59 5 5 OR1E1 17 3397954 Missense_Mutation SNP T C3L-00913_T 119921 3397954 79859487 192 7066 TP53 0 . GRCh38 17 7676056 7676056 + Missense_Mutation SNP C C A C3L-00913_T C3L-00913_N C C c.313G>T p.Gly105Cys p.G105C ENST00000269305 4/11 187 155 32 140 140 0 strelka-varscan-mutect TP53,missense_variant,p.Gly105Cys,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly105Cys,ENST00000420246,;TP53,missense_variant,p.Gly66Cys,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly66Cys,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly105Cys,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly66Cys,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly105Cys,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly66Cys,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly105Cys,ENST00000445888,;TP53,missense_variant,p.Gly66Cys,ENST00000619485,;TP53,missense_variant,p.Gly105Cys,ENST00000359597,;TP53,missense_variant,p.Gly105Cys,ENST00000615910,;TP53,missense_variant,p.Gly105Cys,ENST00000413465,;TP53,missense_variant,p.Gly105Cys,ENST00000508793,;TP53,missense_variant,p.Gly105Cys,ENST00000604348,;TP53,missense_variant,p.Gly105Cys,ENST00000503591,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000510385,NM_001126116.1;TP53,upstream_gene_variant,,ENST00000618944,NM_001276698.1;TP53,upstream_gene_variant,,ENST00000504290,NM_001126117.1;TP53,upstream_gene_variant,,ENST00000610623,NM_001276699.1;TP53,upstream_gene_variant,,ENST00000504937,NM_001126115.1;TP53,upstream_gene_variant,,ENST00000619186,NM_001276697.1;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly66Cys,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 503/2579 313/1182 105/393 G/C Ggc/Tgc CM043949,TP53_g.11544G>T,TP53_g.11544G>C,TP53_g.11544del,TP53_g.11544G>A,COSM2155200,COSM2155201,COSM2155202,COSM338570,COSM338571,COSM3403300,COSM44481,COSM45179,COSM45833,COSM5318159,COSM5318160,COSM78687 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 4/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1060501195 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 7676056 7676056 C A 1 0 0 0 0 1 0 0 0 16859 623 22 2 2 TP53 17 7676056 Missense_Mutation SNP C C3L-00913_T 4278102 7676056 75581385 193 7067 CFAP52 0 . GRCh38 17 9635519 9635519 + Missense_Mutation SNP G G A rs766179265 C3L-00913_T C3L-00913_N G G c.1435G>A p.Ala479Thr p.A479T ENST00000352665 11/14 317 284 33 233 232 1 strelka-varscan-mutect CFAP52,missense_variant,p.Ala479Thr,ENST00000352665,NM_145054.4;CFAP52,missense_variant,p.Ala411Thr,ENST00000396219,NM_001080556.1;CFAP52,missense_variant,p.Ala31Thr,ENST00000574097,;RP11-55L4.2,downstream_gene_variant,,ENST00000584676,;CFAP52,non_coding_transcript_exon_variant,,ENST00000576714,;CFAP52,3_prime_UTR_variant,,ENST00000576630,; A ENST00000352665 Transcript missense_variant 1504/2193 1435/1863 479/620 A/T Gcc/Acc rs766179265,COSM180362,COSM5104919 1 1 CFAP52 HGNC HGNC:16053 protein_coding YES CCDS11149.2 ENSP00000339449 Q8N1V2 UPI00001AECC1 NM_145054.4 deleterious(0.02) 11/14 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_patterns:PS00678,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF14,SMART_domains:SM00320,Superfamily_domains:SSF50978 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766179265 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 9635519 9635519 G A 1 0 0 0 0 1 0 0 0 3023 1087 38 1 1 CFAP52 17 9635519 Missense_Mutation SNP G C3L-00913_T 1959463 9635519 73621922 194 7068 KCNJ18 0 . GRCh38 17 21703957 21703957 + Nonsense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1171G>T p.Glu391Ter p.E391* ENST00000567955 3/3 170 144 26 132 132 0 varscan-mutect KCNJ18,stop_gained,p.Glu391Ter,ENST00000567955,NM_001194958.2; T ENST00000567955 Transcript stop_gained 1541/2196 1171/1302 391/433 E/* Gag/Tag 1 1 KCNJ18 HGNC HGNC:39080 protein_coding YES CCDS74015.1 ENSP00000457807 B7U540 UPI0002064ECF NM_001194958.2 3/3 Prints_domain:PR01325,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 21 21703957 21703957 G T 1 0 0 0 0 0 1 0 0 7967 1291 45 2 2 KCNJ18 17 21703957 Nonsense_Mutation SNP G C3L-00913_T 12068438 21703957 61553484 195 7069 SLC9A3R1 0 . GRCh38 17 74749056 74749056 + Missense_Mutation SNP G G T rs747050189 C3L-00913_T C3L-00913_N G G c.210G>T p.Glu70Asp p.E70D ENST00000262613 1/6 285 268 17 237 237 0 strelka-varscan-mutect SLC9A3R1,missense_variant,p.Glu70Asp,ENST00000262613,NM_004252.4;SLC9A3R1,missense_variant,p.Glu70Asp,ENST00000583369,;RAB37,downstream_gene_variant,,ENST00000340415,;RAB37,downstream_gene_variant,,ENST00000392610,;RAB37,downstream_gene_variant,,ENST00000392614,NM_001163989.1;RAB37,downstream_gene_variant,,ENST00000392615,;RAB37,downstream_gene_variant,,ENST00000392613,NM_001006638.2;RAB37,downstream_gene_variant,,ENST00000392612,NM_001163990.1;RAB37,downstream_gene_variant,,ENST00000613645,;RAB37,downstream_gene_variant,,ENST00000402449,NM_175738.4;RAB37,downstream_gene_variant,,ENST00000528438,;SLC9A3R1,downstream_gene_variant,,ENST00000581999,;RP11-452I5.2,upstream_gene_variant,,ENST00000585285,;RAB37,downstream_gene_variant,,ENST00000392617,;RAB37,downstream_gene_variant,,ENST00000488977,;RAB37,downstream_gene_variant,,ENST00000481224,;RAB37,downstream_gene_variant,,ENST00000577548,;RAB37,downstream_gene_variant,,ENST00000533530,;RAB37,downstream_gene_variant,,ENST00000531420,;RAB37,downstream_gene_variant,,ENST00000527040,; T ENST00000262613 Transcript missense_variant 405/1969 210/1077 70/358 E/D gaG/gaT rs747050189 1 1 SLC9A3R1 HGNC HGNC:11075 protein_coding YES CCDS11705.1 ENSP00000262613 O14745 UPI0000072521 NM_004252.4 tolerated(0.09) 1/6 Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF037866,PROSITE_profiles:PS50106,hmmpanther:PTHR14191,hmmpanther:PTHR14191:SF7,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs747050189 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 74749056 74749056 G T 1 0 0 0 0 1 0 0 0 14996 933 33 2 2 SLC9A3R1 17 74749056 Missense_Mutation SNP G C3L-00913_T 53045099 74749056 8508385 196 7070 RECQL5 0 . GRCh38 17 75658323 75658323 + Missense_Mutation SNP A A T novel C3L-00913_T C3L-00913_N A A c.1124T>A p.Ile375Asn p.I375N ENST00000317905 7/20 167 155 12 144 143 1 strelka-varscan-mutect RECQL5,missense_variant,p.Ile375Asn,ENST00000420326,NM_001003716.3;RECQL5,missense_variant,p.Ile375Asn,ENST00000317905,NM_004259.6;RECQL5,missense_variant,p.Ile348Asn,ENST00000423245,;RECQL5,missense_variant,p.Ile375Asn,ENST00000578201,;RECQL5,missense_variant,p.Ile375Asn,ENST00000584999,;RECQL5,missense_variant,p.Ile375Asn,ENST00000340830,NM_001003715.3;RECQL5,3_prime_UTR_variant,,ENST00000580078,;RECQL5,non_coding_transcript_exon_variant,,ENST00000579274,;RECQL5,missense_variant,p.Ile58Asn,ENST00000582464,; T ENST00000317905 Transcript missense_variant 1284/3704 1124/2976 375/991 I/N aTc/aAc 1 -1 RECQL5 HGNC HGNC:9950 protein_coding YES CCDS42380.1 ENSP00000317636 O94762 A0A024R8M9 UPI0000133477 NM_004259.6 deleterious(0) 7/20 Gene3D:1.10.10.10,Pfam_domain:PF16124,PROSITE_profiles:PS51194,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF85,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00614 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 75658323 75658323 A T 1 0 0 0 0 1 0 0 0 13373 333 12 4 4 RECQL5 17 75658323 Missense_Mutation SNP A C3L-00913_T 909267 75658323 7599118 197 7071 RNF213 0 . GRCh38 17 80345403 80345403 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.7068C>T p.= p.L2356L ENST00000582970 29/68 151 140 11 141 141 0 strelka-varscan-mutect RNF213,synonymous_variant,p.=,ENST00000582970,NM_001256071.2;RNF213,synonymous_variant,p.=,ENST00000508628,;CTD-2047H16.3,downstream_gene_variant,,ENST00000622931,; T ENST00000582970 Transcript synonymous_variant 7211/21055 7068/15624 2356/5207 L ctC/ctT 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 29/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 80345403 80345403 C T 1 0 0 0 0 0 0 0 1 13656 842 30 3 3 RNF213 17 80345403 Silent SNP C C3L-00913_T 4687080 80345403 2912038 198 7072 DUS1L 0 . GRCh38 17 82060039 82060039 + Missense_Mutation SNP C C A rs200132619 C3L-00913_T C3L-00913_N C C c.1077G>T p.Glu359Asp p.E359D ENST00000354321 10/13 201 189 12 176 176 0 strelka-varscan-mutect DUS1L,missense_variant,p.Glu359Asp,ENST00000354321,;DUS1L,missense_variant,p.Glu359Asp,ENST00000306796,NM_022156.4;DUS1L,missense_variant,p.Glu227Asp,ENST00000538833,;DUS1L,missense_variant,p.Glu44Asp,ENST00000542088,;DUS1L,missense_variant,p.Glu19Asp,ENST00000577574,;GPS1,downstream_gene_variant,,ENST00000392358,NM_212492.1;GPS1,downstream_gene_variant,,ENST00000320548,NM_001321093.1;GPS1,downstream_gene_variant,,ENST00000623761,;GPS1,downstream_gene_variant,,ENST00000578552,NM_001321092.1;GPS1,downstream_gene_variant,,ENST00000306823,NM_004127.4;GPS1,downstream_gene_variant,,ENST00000623691,;GPS1,downstream_gene_variant,,ENST00000624957,;DUS1L,downstream_gene_variant,,ENST00000582529,;DUS1L,downstream_gene_variant,,ENST00000578907,;DUS1L,downstream_gene_variant,,ENST00000578176,;DUS1L,downstream_gene_variant,,ENST00000577907,;GPS1,downstream_gene_variant,,ENST00000578168,;DUS1L,missense_variant,p.Arg174Met,ENST00000580731,;DUS1L,non_coding_transcript_exon_variant,,ENST00000578846,;DUS1L,non_coding_transcript_exon_variant,,ENST00000578428,;DUS1L,non_coding_transcript_exon_variant,,ENST00000579854,;GPS1,downstream_gene_variant,,ENST00000392357,;GPS1,downstream_gene_variant,,ENST00000584460,;DUS1L,downstream_gene_variant,,ENST00000578264,;GPS1,downstream_gene_variant,,ENST00000580141,;GPS1,downstream_gene_variant,,ENST00000578279,;GPS1,downstream_gene_variant,,ENST00000583486,;DUS1L,downstream_gene_variant,,ENST00000582407,;DUS1L,upstream_gene_variant,,ENST00000584871,; A ENST00000354321 Transcript missense_variant 1563/2151 1077/1422 359/473 E/D gaG/gaT rs200132619 1 -1 DUS1L HGNC HGNC:30086 protein_coding YES CCDS32775.1 ENSP00000346280 Q6P1R4 UPI00002004B5 tolerated(0.25) 10/13 hmmpanther:PTHR11082,hmmpanther:PTHR11082:SF5 MODERATE 1 SNV 1 1 PASS rs200132619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 82060039 82060039 C A 1 0 0 0 0 1 0 0 0 4627 680 24 2 2 DUS1L 17 82060039 Missense_Mutation SNP C C3L-00913_T 1714636 82060039 1197402 199 7073 LAMA3 0 . GRCh38 18 23847578 23847578 + Missense_Mutation SNP C C G novel C3L-00913_T C3L-00913_N C C c.4046C>G p.Pro1349Arg p.P1349R ENST00000313654 32/75 570 526 44 456 456 0 strelka-varscan-mutect LAMA3,missense_variant,p.Pro1349Arg,ENST00000313654,NM_198129.2;LAMA3,missense_variant,p.Pro1349Arg,ENST00000399516,NM_001127717.2; G ENST00000313654 Transcript missense_variant 4287/10661 4046/10002 1349/3333 P/R cCc/cGc 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 deleterious(0) 32/75 Gene3D:2.10.25.10,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285,SMART_domains:SM00180 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 23847578 23847578 C G 1 0 0 0 0 1 0 0 0 8511 623 22 4 4 LAMA3 18 23847578 Missense_Mutation SNP C C3L-00913_T 23847578 56525707 200 7074 MAPRE2 0 . GRCh38 18 35005533 35005533 + Silent SNP G G A rs760492138 C3L-00913_T C3L-00913_N G G c.66G>A p.= p.G22G ENST00000436190 2/8 165 150 15 154 153 1 strelka-varscan-mutect MAPRE2,synonymous_variant,p.=,ENST00000436190,NM_001143827.2;MAPRE2,5_prime_UTR_variant,,ENST00000413393,NM_001143826.2;MAPRE2,5_prime_UTR_variant,,ENST00000591734,;MAPRE2,5_prime_UTR_variant,,ENST00000587359,;MAPRE2,5_prime_UTR_variant,,ENST00000589180,;MAPRE2,5_prime_UTR_variant,,ENST00000588349,; A ENST00000436190 Transcript synonymous_variant 340/4323 66/948 22/315 G ggG/ggA rs760492138 1 1 MAPRE2 HGNC HGNC:6891 protein_coding CCDS45850.1 ENSP00000407723 Q15555 UPI00018AC3AF NM_001143827.2 2/8 LOW 1 SNV 2 1 PASS rs760492138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 35005533 35005533 G A 1 0 0 0 0 0 0 0 1 9218 1161 41 3 3 MAPRE2 18 35005533 Silent SNP G C3L-00913_T 11157955 35005533 45367752 201 7075 SYT4 0 . GRCh38 18 43273970 43273970 + Silent SNP C C T C3L-00913_T C3L-00913_N C C c.459G>A p.= p.K153K ENST00000255224 2/4 323 305 18 311 311 0 strelka-varscan-mutect SYT4,synonymous_variant,p.=,ENST00000255224,NM_020783.3;SYT4,synonymous_variant,p.=,ENST00000590752,;SYT4,intron_variant,,ENST00000596867,;SYT4,intron_variant,,ENST00000593720,;SYT4,intron_variant,,ENST00000586678,;SYT4,intron_variant,,ENST00000585604,;SYT4,upstream_gene_variant,,ENST00000589479,;SYT4,downstream_gene_variant,,ENST00000591820,; T ENST00000255224 Transcript synonymous_variant 828/4110 459/1278 153/425 K aaG/aaA COSM563990,COSM563991 1 -1 SYT4 HGNC HGNC:11512 protein_coding YES CCDS11922.1 ENSP00000255224 Q9H2B2 UPI000013669E NM_020783.3 2/4 Gene3D:2.60.40.150,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114,Low_complexity_(Seg):seg,Superfamily_domains:SSF49562 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 43273970 43273970 C T 1 0 0 0 0 0 0 0 1 15870 796 28 3 3 SYT4 18 43273970 Silent SNP C C3L-00913_T 8268437 43273970 37099315 202 7076 ALPK2 0 . GRCh38 18 58537826 58537826 + Silent SNP G G T novel C3L-00913_T C3L-00913_N G G c.2361C>A p.= p.T787T ENST00000361673 5/13 234 209 25 208 208 0 strelka-varscan-mutect ALPK2,synonymous_variant,p.=,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,upstream_gene_variant,,ENST00000589204,; T ENST00000361673 Transcript synonymous_variant 2575/7303 2361/6513 787/2170 T acC/acA 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 58537826 58537826 G T 1 0 0 0 0 0 0 0 1 645 1219 43 2 2 ALPK2 18 58537826 Silent SNP G C3L-00913_T 15263856 58537826 21835459 203 7077 NFATC1 0 . GRCh38 18 79410458 79410458 + Silent SNP G G C rs776245598 C3L-00913_T C3L-00913_N G G c.183G>C p.= p.A61A ENST00000427363 2/10 143 130 13 153 153 0 strelka-varscan-mutect NFATC1,synonymous_variant,p.=,ENST00000591814,NM_172390.2;NFATC1,synonymous_variant,p.=,ENST00000253506,NM_006162.4;NFATC1,synonymous_variant,p.=,ENST00000329101,NM_172387.2;NFATC1,synonymous_variant,p.=,ENST00000318065,NM_172389.2;NFATC1,synonymous_variant,p.=,ENST00000427363,NM_001278669.1;NFATC1,synonymous_variant,p.=,ENST00000592223,NM_001278675.1;NFATC1,synonymous_variant,p.=,ENST00000587635,;NFATC1,synonymous_variant,p.=,ENST00000542384,NM_001278670.1;NFATC1,synonymous_variant,p.=,ENST00000586434,NM_001278672.1;NFATC1,intron_variant,,ENST00000545796,NM_001278673.1;NFATC1,intron_variant,,ENST00000397790,NM_172388.2;NFATC1,intron_variant,,ENST00000590313,; C ENST00000427363 Transcript synonymous_variant 183/2832 183/2832 61/943 A gcG/gcC rs776245598,COSM4790157,COSM4790158 1 1 NFATC1 HGNC HGNC:7775 protein_coding YES CCDS62467.1 ENSP00000389377 O95644 UPI000012FFB5 NM_001278669.1 2/10 hmmpanther:PTHR12533:SF5,hmmpanther:PTHR12533 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs776245598 . 0 204 3 2 0 0 0 0 -18.49273 0.9999813 1 1 1 0 C 2 2 21 79410458 79410458 G C 1 0 0 0 0 0 0 0 1 10398 1074 38 4 4 NFATC1 18 79410458 Silent SNP G C3L-00913_T 20872632 79410458 962827 204 7078 THOP1 0 . GRCh38 19 2790512 2790512 + Silent SNP C C T C3L-00913_T C3L-00913_N C C c.108C>T p.= p.R36R ENST00000307741 2/13 68 58 10 59 59 0 strelka-varscan-mutect THOP1,synonymous_variant,p.=,ENST00000307741,NM_003249.3;THOP1,synonymous_variant,p.=,ENST00000585338,;THOP1,non_coding_transcript_exon_variant,,ENST00000585673,;THOP1,non_coding_transcript_exon_variant,,ENST00000586780,; T ENST00000307741 Transcript synonymous_variant 311/4804 108/2070 36/689 R cgC/cgT COSM5149797 1 1 THOP1 HGNC HGNC:11793 protein_coding YES CCDS12095.1 ENSP00000304467 P52888 UPI0000000C3E NM_003249.3 2/13 Gene3D:2o36A01,hmmpanther:PTHR11804,hmmpanther:PTHR11804:SF50,Superfamily_domains:SSF55486 1 LOW 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99893 1 1 1 1 0 T 2 4 21 2790512 2790512 C T 1 0 0 0 0 0 0 0 1 16305 697 25 3 3 THOP1 19 2790512 Silent SNP C C3L-00913_T 2790512 55827104 205 7079 ZNF358 0 . GRCh38 19 7520464 7520464 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1222G>T p.Ala408Ser p.A408S ENST00000597229 2/2 132 109 23 146 146 0 strelka-varscan-mutect ZNF358,missense_variant,p.Ala408Ser,ENST00000597229,NM_018083.4;MCOLN1,upstream_gene_variant,,ENST00000264079,NM_020533.2;MCOLN1,upstream_gene_variant,,ENST00000601003,;ZNF358,downstream_gene_variant,,ENST00000596712,;CTD-2207O23.12,downstream_gene_variant,,ENST00000599312,;CTD-2207O23.11,upstream_gene_variant,,ENST00000602083,;MCOLN1,upstream_gene_variant,,ENST00000394321,;MCOLN1,upstream_gene_variant,,ENST00000596390,;CTD-2207O23.12,downstream_gene_variant,,ENST00000597384,; T ENST00000597229 Transcript missense_variant 1392/1954 1222/1707 408/568 A/S Gcc/Tcc 1 1 ZNF358 HGNC HGNC:16838 protein_coding YES CCDS32890.2 ENSP00000472305 Q9NW07 UPI0000201F0C NM_018083.4 deleterious(0.02) 2/2 Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 7520464 7520464 G T 1 0 0 0 0 1 0 0 0 18439 1203 42 2 2 ZNF358 19 7520464 Missense_Mutation SNP G C3L-00913_T 4729952 7520464 51097152 206 7080 ZNF439 0 . GRCh38 19 11867464 11867464 + Missense_Mutation SNP A A G novel C3L-00913_T C3L-00913_N A A c.395A>G p.Asn132Ser p.N132S ENST00000304030 3/3 392 344 48 296 296 0 strelka-varscan-mutect ZNF439,missense_variant,p.Asn132Ser,ENST00000304030,NM_152262.2;ZNF439,5_prime_UTR_variant,,ENST00000455282,;ZNF439,downstream_gene_variant,,ENST00000442091,;ZNF439,intron_variant,,ENST00000592534,; G ENST00000304030 Transcript missense_variant 595/2622 395/1500 132/499 N/S aAc/aGc 1 1 ZNF439 HGNC HGNC:20873 protein_coding YES CCDS12268.1 ENSP00000305077 Q8NDP4 UPI000006F768 NM_152262.2 deleterious(0.02) 3/3 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 11867464 11867464 A G 1 0 0 0 0 1 0 0 0 18482 43 2 5 5 ZNF439 19 11867464 Missense_Mutation SNP A C3L-00913_T 4347000 11867464 46750152 207 7081 ZNF136 0 . GRCh38 19 12187989 12187989 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.1611G>T p.Trp537Cys p.W537C ENST00000343979 4/4 28 20 8 31 31 0 varscan-mutect ZNF136,missense_variant,p.Trp537Cys,ENST00000343979,NM_003437.3;ZNF136,downstream_gene_variant,,ENST00000418338,;ZNF136,downstream_gene_variant,,ENST00000439995,;ZNF136,downstream_gene_variant,,ENST00000425827,;ZNF136,non_coding_transcript_exon_variant,,ENST00000464860,;ZNF136,downstream_gene_variant,,ENST00000476676,; T ENST00000343979 Transcript missense_variant 1751/3643 1611/1623 537/540 W/C tgG/tgT 1 1 ZNF136 HGNC HGNC:12920 protein_coding YES CCDS32916.1 ENSP00000344162 P52737 UPI0000000C7B NM_003437.3 deleterious_low_confidence(0) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 12187989 12187989 G T 1 0 0 0 0 1 0 0 0 18307 1241 43 2 2 ZNF136 19 12187989 Missense_Mutation SNP G C3L-00913_T 320525 12187989 46429627 208 7082 COMP 0 . GRCh38 19 18791218 18791218 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.52G>T p.Ala18Ser p.A18S ENST00000222271 1/19 267 238 29 207 207 0 strelka-varscan-mutect COMP,missense_variant,p.Ala18Ser,ENST00000222271,NM_000095.2;COMP,missense_variant,p.Ala18Ser,ENST00000425807,;COMP,5_prime_UTR_variant,,ENST00000542601,;COMP,upstream_gene_variant,,ENST00000612179,; A ENST00000222271 Transcript missense_variant 97/2461 52/2274 18/757 A/S Gcg/Tcg 1 -1 COMP HGNC HGNC:2227 protein_coding YES CCDS12385.1 ENSP00000222271 P49747 UPI000013C7F6 NM_000095.2 tolerated_low_confidence(0.34) 1/19 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 18791218 18791218 C A 1 0 0 0 0 1 0 0 0 3516 768 27 1 1 COMP 19 18791218 Missense_Mutation SNP C C3L-00913_T 6603229 18791218 39826398 209 7083 ZNF724P 0 . GRCh38 19 23232203 23232203 + Missense_Mutation SNP C C G rs762886653 C3L-00913_T C3L-00913_N C C c.94G>C p.Val32Leu p.V32L ENST00000418100 2/4 277 242 35 260 260 0 strelka-varscan-mutect ZNF724P,missense_variant,p.Val32Leu,ENST00000418100,;RP11-15H20.8,missense_variant,p.Val26Leu,ENST00000611392,;ZNF724P,missense_variant,p.Val32Leu,ENST00000597037,;ZNF724P,missense_variant,p.Val26Leu,ENST00000597537,;BNIP3P38,upstream_gene_variant,,ENST00000601117,; G ENST00000418100 Transcript missense_variant 212/2764 94/1860 32/619 V/L Gtg/Ctg rs762886653 1 -1 ZNF724P HGNC HGNC:32460 protein_coding YES ENSP00000413411 A8MTY0 UPI0000EE61E4 deleterious(0) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF123,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS rs762886653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 23232203 23232203 C G 1 0 0 0 0 1 0 0 0 18699 536 19 4 4 ZNF724P 19 23232203 Missense_Mutation SNP C C3L-00913_T 4440985 23232203 35385413 210 7084 SBSN 0 . GRCh38 19 35528027 35528027 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.255A>T p.Lys85Asn p.K85N ENST00000452271 1/4 393 276 117 285 285 0 strelka-varscan-mutect SBSN,missense_variant,p.Lys85Asn,ENST00000452271,NM_001166034.1;SBSN,missense_variant,p.Lys85Asn,ENST00000518157,NM_198538.3;SBSN,missense_variant,p.Lys65Asn,ENST00000588674,NM_001166035.1; A ENST00000452271 Transcript missense_variant 284/1945 255/1773 85/590 K/N aaA/aaT 1 -1 SBSN HGNC HGNC:24950 protein_coding YES CCDS54253.1 ENSP00000430242 Q6UWP8 UPI000059D6E7 NM_001166034.1 deleterious(0) 1/4 hmmpanther:PTHR23243,hmmpanther:PTHR23243:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 35528027 35528027 T A 1 0 0 0 0 1 0 0 0 14129 1606 56 4 4 SBSN 19 35528027 Missense_Mutation SNP T C3L-00913_T 12295824 35528027 23089589 211 7085 DYRK1B 0 . GRCh38 19 39825844 39825844 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.1761G>T p.= p.P587P ENST00000593685 11/11 151 106 45 116 116 0 strelka-varscan-mutect DYRK1B,synonymous_variant,p.=,ENST00000593685,;DYRK1B,synonymous_variant,p.=,ENST00000323039,NM_004714.2;DYRK1B,synonymous_variant,p.=,ENST00000348817,NM_006484.2;DYRK1B,synonymous_variant,p.=,ENST00000430012,NM_006483.2;DYRK1B,synonymous_variant,p.=,ENST00000597639,;DYRK1B,downstream_gene_variant,,ENST00000601972,;DYRK1B,downstream_gene_variant,,ENST00000600611,;MIR6719,downstream_gene_variant,,ENST00000622428,;DYRK1B,downstream_gene_variant,,ENST00000601696,; A ENST00000593685 Transcript synonymous_variant 2230/2724 1761/1890 587/629 P ccG/ccT 1 -1 DYRK1B HGNC HGNC:3092 protein_coding YES CCDS12543.1 ENSP00000469863 Q9Y463 A0A024R0I0 UPI0000001059 11/11 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF27,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1014387393 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 39825844 39825844 C A 1 0 0 0 0 0 0 0 1 4679 639 23 1 1 DYRK1B 19 39825844 Silent SNP C C3L-00913_T 4297817 39825844 18791772 212 7086 ATP1A3 0 . GRCh38 19 41976502 41976502 + Missense_Mutation SNP C C G rs782439924 C3L-00913_T C3L-00913_N C C c.2047G>C p.Glu683Gln p.E683Q ENST00000545399 15/23 592 429 163 350 350 0 strelka-varscan-mutect ATP1A3,missense_variant,p.Glu683Gln,ENST00000545399,NM_001256214.1;ATP1A3,missense_variant,p.Glu670Gln,ENST00000302102,NM_152296.4;ATP1A3,missense_variant,p.Glu640Gln,ENST00000602133,;ATP1A3,missense_variant,p.Glu681Gln,ENST00000543770,NM_001256213.1;ATP1A3,missense_variant,p.Glu670Gln,ENST00000441343,; G ENST00000545399 Transcript missense_variant 2231/3618 2047/3081 683/1026 E/Q Gag/Cag rs782439924,COSM1712386 1 -1 ATP1A3 HGNC HGNC:801 protein_coding YES CCDS58664.1 ENSP00000444688 P13637 UPI0001914BDE NM_001256214.1 tolerated(0.13) 15/23 Gene3D:1.20.1110.10,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01106 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs782439924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 41976502 41976502 C G 1 0 0 0 0 1 0 0 0 1282 893 31 4 4 ATP1A3 19 41976502 Missense_Mutation SNP C C3L-00913_T 2150658 41976502 16641114 213 7087 PPP5C 0 . GRCh38 19 46376518 46376518 + Nonsense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.577G>T p.Glu193Ter p.E193* ENST00000012443 4/13 266 196 70 173 173 0 strelka-varscan-mutect PPP5C,stop_gained,p.Glu193Ter,ENST00000012443,NM_001204284.1,NM_006247.3;PPP5C,stop_gained,p.Glu87Ter,ENST00000391919,;PPP5C,stop_gained,p.Glu192Ter,ENST00000478046,;PPP5C,non_coding_transcript_exon_variant,,ENST00000527193,;PPP5C,non_coding_transcript_exon_variant,,ENST00000467902,;PPP5C,upstream_gene_variant,,ENST00000487483,; T ENST00000012443 Transcript stop_gained 680/2109 577/1500 193/499 E/* Gag/Tag 1 1 PPP5C HGNC HGNC:9322 protein_coding YES CCDS12684.1 ENSP00000012443 P53041 A0A024R0Q7 UPI0000041859 NM_001204284.1,NM_006247.3 4/13 hmmpanther:PTHR11668:SF21,hmmpanther:PTHR11668,Pfam_domain:PF08321,Gene3D:3.60.21.10,PIRSF_domain:PIRSF033096,Superfamily_domains:SSF56300 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 21 46376518 46376518 G T 1 0 0 0 0 0 1 0 0 12531 1175 41 2 2 PPP5C 19 46376518 Nonsense_Mutation SNP G C3L-00913_T 4400016 46376518 12241098 214 7088 MYH14 0 . GRCh38 19 50286683 50286683 + Missense_Mutation SNP G G T rs680446 C3L-00913_T C3L-00913_N G G c.4741G>T p.Val1581Phe p.V1581F ENST00000601313 34/43 197 184 13 183 183 0 strelka-varscan-mutect MYH14,missense_variant,p.Val1581Phe,ENST00000601313,NM_001145809.1;MYH14,missense_variant,p.Val1548Phe,ENST00000425460,NM_001077186.1;MYH14,missense_variant,p.Val1540Phe,ENST00000376970,NM_024729.3;MYH14,missense_variant,p.Val1548Phe,ENST00000598205,;MYH14,missense_variant,p.Val1540Phe,ENST00000596571,;MYH14,missense_variant,p.Val183Phe,ENST00000440075,;MYH14,3_prime_UTR_variant,,ENST00000262269,;MYH14,non_coding_transcript_exon_variant,,ENST00000595016,; T ENST00000601313 Transcript missense_variant 4771/6896 4741/6111 1581/2036 V/F Gtc/Ttc rs680446 1 1 MYH14 HGNC HGNC:23212 protein_coding YES CCDS54295.1 ENSP00000470298 Q7Z406 UPI0001641C2F NM_001145809.1 tolerated(0.07) 34/43 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF462,Pfam_domain:PF01576,Superfamily_domains:SSF90257 benign MODERATE 1 SNV 1 1 1 PASS rs680446 . 0 208 0 2 0 0 0 0 -16.55653 0.9999996 1 1 1 0 T 3 4 21 50286683 50286683 G T 1 0 0 0 0 1 0 0 0 10033 1145 40 1 1 MYH14 19 50286683 Missense_Mutation SNP G C3L-00913_T 3910165 50286683 8330933 215 7089 C19orf84 0 . GRCh38 19 51389219 51389219 + Nonsense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.326G>A p.Trp109Ter p.W109* ENST00000574814 2/2 120 112 8 124 124 0 strelka-varscan-mutect C19orf84,stop_gained,p.Trp109Ter,ENST00000574814,NM_001193623.1;C19orf84,5_prime_UTR_variant,,ENST00000570516,;LIM2,upstream_gene_variant,,ENST00000221973,NM_030657.3;LIM2,upstream_gene_variant,,ENST00000596399,NM_001161748.1; T ENST00000574814 Transcript stop_gained 388/1318 326/561 109/186 W/* tGg/tAg 1 -1 C19orf84 HGNC HGNC:27112 protein_coding YES CCDS58676.1 ENSP00000458772 I3L1E1 UPI0000161964 NM_001193623.1 2/2 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.01196 1 1 1 1 0 T 4 4 21 51389219 51389219 C T 1 0 0 0 0 0 1 0 0 1927 595 21 3 3 C19orf84 19 51389219 Nonsense_Mutation SNP C C3L-00913_T 1102536 51389219 7228397 216 7090 SIGLEC6 0 . GRCh38 19 51530733 51530733 + Silent SNP C C A C3L-00913_T C3L-00913_N C C c.654G>T p.= p.T218T ENST00000425629 3/8 302 283 19 278 278 0 strelka-varscan-mutect SIGLEC6,synonymous_variant,p.=,ENST00000346477,NM_198845.4;SIGLEC6,synonymous_variant,p.=,ENST00000425629,NM_001245.5;SIGLEC6,synonymous_variant,p.=,ENST00000359982,NM_001177548.1;SIGLEC6,synonymous_variant,p.=,ENST00000343300,NM_198846.4;SIGLEC6,synonymous_variant,p.=,ENST00000436458,NM_001177547.1;SIGLEC6,synonymous_variant,p.=,ENST00000391797,NM_001177549.1;SIGLEC6,upstream_gene_variant,,ENST00000474054,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000496422,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000489837,; A ENST00000425629 Transcript synonymous_variant 809/1852 654/1362 218/453 T acG/acT COSM2926002,COSM2926003 1 -1 SIGLEC6 HGNC HGNC:10875 protein_coding YES CCDS12834.3 ENSP00000401502 O43699 A0A024R4K4 UPI0000223FFD NM_001245.5 3/8 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF52,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 LOW 1 SNV 2 1,1 1 PASS rs1339012854 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 51530733 51530733 C A 1 0 0 0 0 0 0 0 1 14576 523 19 1 1 SIGLEC6 19 51530733 Silent SNP C C3L-00913_T 141514 51530733 7086883 217 7091 SLC27A5 0 . GRCh38 19 58498873 58498873 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.1808C>T p.Pro603Leu p.P603L ENST00000263093 9/10 166 150 16 108 108 0 strelka-varscan-mutect SLC27A5,missense_variant,p.Pro603Leu,ENST00000263093,NM_012254.2;SLC27A5,missense_variant,p.Pro519Leu,ENST00000601355,NM_001321196.1;SLC27A5,missense_variant,p.Pro8Leu,ENST00000594786,;CTD-2619J13.27,upstream_gene_variant,,ENST00000619318,;SLC27A5,intron_variant,,ENST00000599700,;SLC27A5,missense_variant,p.Pro8Leu,ENST00000595851,;SLC27A5,non_coding_transcript_exon_variant,,ENST00000601997,;SLC27A5,downstream_gene_variant,,ENST00000594683,; A ENST00000263093 Transcript missense_variant 1918/2361 1808/2073 603/690 P/L cCc/cTc 1 -1 SLC27A5 HGNC HGNC:10999 protein_coding YES CCDS12983.1 ENSP00000263093 Q9Y2P5 UPI0000072ECE NM_012254.2 deleterious(0.01) 9/10 Gene3D:3.30.300.30,Pfam_domain:PF13193,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF99,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 58498873 58498873 G A 1 0 0 0 0 1 0 0 0 14799 1232 43 3 3 SLC27A5 19 58498873 Missense_Mutation SNP G C3L-00913_T 6968140 58498873 118743 218 7092 SIRPB1 0 . GRCh38 20 1571749 1571749 + Missense_Mutation SNP C C A novel C3L-00913_T C3L-00913_N C C c.722G>T p.Gly241Val p.G241V ENST00000381605 3/6 452 405 47 331 330 1 strelka-varscan-mutect SIRPB1,missense_variant,p.Gly241Val,ENST00000381605,NM_006065.3;SIRPB1,missense_variant,p.Gly55Val,ENST00000565076,;SIRPB1,intron_variant,,ENST00000381603,NM_001083910.2;SIRPB1,intron_variant,,ENST00000262929,;RP4-576H24.4,intron_variant,,ENST00000564763,;SIRPB1,intron_variant,,ENST00000563840,;RP4-576H24.4,intron_variant,,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPB1,intron_variant,,ENST00000569629,; A ENST00000381605 Transcript missense_variant 787/3241 722/1197 241/398 G/V gGg/gTg 1 -1 SIRPB1 HGNC HGNC:15928 protein_coding YES CCDS13019.1 ENSP00000371018 O00241 UPI000036700F NM_006065.3 deleterious(0.01) 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12 MODERATE 1 SNV 1 1 PASS rs895241919 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 1571749 1571749 C A 1 0 0 0 0 1 0 0 0 14596 623 22 2 2 SIRPB1 20 1571749 Missense_Mutation SNP C C3L-00913_T 1571749 62872418 219 7093 PLCB4 0 . GRCh38 20 9337165 9337165 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.124G>A p.Asp42Asn p.D42N ENST00000378501 2/36 248 231 17 197 197 0 strelka-varscan-mutect PLCB4,missense_variant,p.Asp42Asn,ENST00000378501,NM_000933.3;PLCB4,missense_variant,p.Asp42Asn,ENST00000378493,;PLCB4,missense_variant,p.Asp42Asn,ENST00000378473,NM_001172646.1;PLCB4,missense_variant,p.Asp42Asn,ENST00000278655,NM_182797.2;PLCB4,missense_variant,p.Asp42Asn,ENST00000414679,;PLCB4,missense_variant,p.Asp42Asn,ENST00000407043,;PLCB4,missense_variant,p.Asp42Asn,ENST00000416836,;PLCB4,missense_variant,p.Asp42Asn,ENST00000441846,;PLCB4,missense_variant,p.Asp42Asn,ENST00000437503,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,; A ENST00000378501 Transcript missense_variant 139/5833 124/3585 42/1194 D/N Gat/Aat 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 deleterious(0) 2/36 Gene3D:2.30.29.30,PIRSF_domain:PIRSF000956,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS rs897976423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 9337165 9337165 G A 1 0 0 0 0 1 0 0 0 12124 1174 41 3 3 PLCB4 20 9337165 Missense_Mutation SNP G C3L-00913_T 7765416 9337165 55107002 220 7094 KIAA1755 0 . GRCh38 20 38241367 38241367 + Missense_Mutation SNP C C T rs41282824 C3L-00913_T C3L-00913_N C C c.764G>A p.Arg255Gln p.R255Q ENST00000279024 3/14 447 407 40 314 314 0 strelka-varscan-mutect KIAA1755,missense_variant,p.Arg255Gln,ENST00000279024,NM_001029864.1;KIAA1755,missense_variant,p.Arg255Gln,ENST00000496900,;KIAA1755,upstream_gene_variant,,ENST00000611812,; T ENST00000279024 Transcript missense_variant 1036/6429 764/3603 255/1200 R/Q cGg/cAg rs41282824 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 tolerated(0.26) 3/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF125 MODERATE 1 SNV 5 1 PASS rs41282824 . 0 206 0 0 0 0 0 4 -11.64726 0 0 1 0 0 T 3 4 21 38241367 38241367 C T 1 0 0 0 0 1 0 0 0 8128 652 23 1 1 KIAA1755 20 38241367 Missense_Mutation SNP C C3L-00913_T 28904202 38241367 26202800 221 7095 PTPRT 0 . GRCh38 20 42084752 42084752 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.4123G>A p.Val1375Met p.V1375M ENST00000373198 30/32 67 62 5 34 34 0 strelka-mutect PTPRT,missense_variant,p.Val1375Met,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Val1378Met,ENST00000373193,;PTPRT,missense_variant,p.Val1346Met,ENST00000373201,;PTPRT,missense_variant,p.Val1355Met,ENST00000373190,;PTPRT,missense_variant,p.Val1366Met,ENST00000373184,;PTPRT,missense_variant,p.Val1365Met,ENST00000356100,;PTPRT,missense_variant,p.Val1356Met,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Val974Met,ENST00000612229,;PTPRT,missense_variant,p.Val991Met,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript missense_variant 4359/12746 4123/4383 1375/1460 V/M Gtg/Atg 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0.03) 30/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 42084752 42084752 C T 1 0 0 0 0 1 0 0 0 12967 565 20 3 3 PTPRT 20 42084752 Missense_Mutation SNP C C3L-00913_T 3843385 42084752 22359415 222 7096 CTCFL 0 . GRCh38 20 57519330 57519330 + Missense_Mutation SNP T T C novel C3L-00913_T C3L-00913_N T T c.802A>G p.Arg268Gly p.R268G ENST00000423479 4/12 244 218 26 170 169 1 strelka-varscan-mutect CTCFL,missense_variant,p.Arg268Gly,ENST00000608263,NM_001269041.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000429804,NM_001269046.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000609232,NM_080618.3;CTCFL,missense_variant,p.Arg268Gly,ENST00000243914,;CTCFL,missense_variant,p.Arg268Gly,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000422869,NM_001269047.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000432255,NM_001269048.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000608425,NM_001269045.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000608440,NM_001269044.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000423479,NM_001269043.1;CTCFL,missense_variant,p.Arg63Gly,ENST00000539382,NM_001269050.1;CTCFL,missense_variant,p.Arg63Gly,ENST00000433949,NM_001269049.1;CTCFL,missense_variant,p.Arg6Gly,ENST00000608903,NM_001269055.1;CTCFL,missense_variant,p.Arg6Gly,ENST00000502686,NM_001269054.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000608158,NM_001269052.1;CTCFL,missense_variant,p.Arg268Gly,ENST00000481655,NM_001269051.1;CTCFL,non_coding_transcript_exon_variant,,ENST00000608858,;CTCFL,missense_variant,p.Arg268Gly,ENST00000426658,;CTCFL,missense_variant,p.Arg268Gly,ENST00000422109,;CTCFL,missense_variant,p.Arg268Gly,ENST00000608720,;CTCFL,non_coding_transcript_exon_variant,,ENST00000607923,;CTCFL,non_coding_transcript_exon_variant,,ENST00000608108,; C ENST00000423479 Transcript missense_variant 893/2478 802/2103 268/700 R/G Aga/Gga 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 deleterious(0) 4/12 PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF96,hmmpanther:PTHR24375,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 21 57519330 57519330 T C 1 0 0 0 0 1 0 0 0 3808 1530 53 5 5 CTCFL 20 57519330 Missense_Mutation SNP T C3L-00913_T 15434578 57519330 6924837 223 7097 HRH3 0 . GRCh38 20 62218609 62218619 + Frame_Shift_Del DEL CAGCGGCCTGT CAGCGGCCTGT - novel C3L-00913_T C3L-00913_N CAGCGGCCTGT CAGCGGCCTGT c.289_299delACAGGCCGCTG p.Thr97AspfsTer48 p.T97Dfs*48 ENST00000340177 2/3 294 260 34 228 228 0 sindel-varindel-pindel HRH3,frameshift_variant,p.Thr97AspfsTer48,ENST00000340177,NM_007232.2;HRH3,frameshift_variant,p.Thr97AspfsTer48,ENST00000317393,;HRH3,frameshift_variant,p.Thr97AspfsTer48,ENST00000611492,; - ENST00000340177 Transcript frameshift_variant 574-584/2659 289-299/1338 97-100/445 TGRW/X ACAGGCCGCTGg/g 1 -1 HRH3 HGNC HGNC:5184 protein_coding YES CCDS13493.1 ENSP00000342560 Q9Y5N1 UPI000012C6ED NM_007232.2 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF292,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 62218609 62218609 CAGCGGCCTGT - 1 0 1 0 1 0 0 0 0 7252 595 21 0 0 HRH3 20 62218609 Frame_Shift_Del DEL CAGCGGCCTGT C3L-00913_T 4699279 62218609 2225558 224 7098 COL20A1 0 . GRCh38 20 63329617 63329617 + Missense_Mutation SNP C C A rs372046790 C3L-00913_T C3L-00913_N C C c.3814C>A p.Pro1272Thr p.P1272T ENST00000358894 35/36 176 154 22 108 108 0 strelka-mutect COL20A1,missense_variant,p.Pro1285Thr,ENST00000422202,;COL20A1,missense_variant,p.Pro1272Thr,ENST00000358894,NM_020882.2;COL20A1,downstream_gene_variant,,ENST00000415763,;COL20A1,downstream_gene_variant,,ENST00000455906,;COL20A1,non_coding_transcript_exon_variant,,ENST00000496810,;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,;COL20A1,non_coding_transcript_exon_variant,,ENST00000471582,;COL20A1,non_coding_transcript_exon_variant,,ENST00000494913,; A ENST00000358894 Transcript missense_variant 3914/4172 3814/3855 1272/1284 P/T Cct/Act rs372046790 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 tolerated(0.05) 35/36 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF131 MODERATE 1 SNV 1 1 PASS rs372046790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 63329617 63329617 C A 1 0 0 0 0 1 0 0 0 3467 623 22 2 2 COL20A1 20 63329617 Missense_Mutation SNP C C3L-00913_T 1111008 63329617 1114550 225 7099 KRTAP27-1 0 . GRCh38 21 30337423 30337423 + Silent SNP G G A rs139729864 C3L-00913_T C3L-00913_N G G c.246C>T p.= p.P82P ENST00000382835 1/1 385 334 51 286 286 0 strelka-varscan-mutect KRTAP27-1,synonymous_variant,p.=,ENST00000382835,NM_001077711.1; A ENST00000382835 Transcript synonymous_variant 272/682 246/624 82/207 P ccC/ccT rs139729864,COSM2842165,COSM4101102 1 -1 KRTAP27-1 HGNC HGNC:33864 protein_coding YES CCDS33532.1 ENSP00000372286 Q3LI81 UPI00001618F6 NM_001077711.1 1/1 hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF5,Pfam_domain:PF05287 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs139729864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 30337423 30337423 G A 1 0 0 0 0 0 0 0 1 8436 1103 39 1 1 KRTAP27-1 21 30337423 Silent SNP G C3L-00913_T 30337423 16372560 226 7100 KRTAP19-3 0 . GRCh38 21 30491861 30491861 + Missense_Mutation SNP G G T rs529648956 C3L-00913_T C3L-00913_N G G c.97C>A p.Arg33Ser p.R33S ENST00000334063 1/1 452 418 34 330 330 0 varscan-mutect KRTAP19-3,missense_variant,p.Arg33Ser,ENST00000334063,NM_181609.3;KRTAP19-2,upstream_gene_variant,,ENST00000334055,NM_181608.1;KRTAP19-4,downstream_gene_variant,,ENST00000334058,NM_181610.1; T ENST00000334063 Transcript missense_variant 125/522 97/246 33/81 R/S Cgc/Agc rs529648956 1 -1 KRTAP19-3 HGNC HGNC:18938 protein_coding YES CCDS13596.1 ENSP00000386376 Q7Z4W3 UPI00001A9E52 NM_181609.3 tolerated_low_confidence(0.33) 1/1 Pfam_domain:PF11759 MODERATE 1 SNV 1 PASS rs529648956 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 30491861 30491861 G T 1 0 0 0 0 1 0 0 0 8414 1116 39 1 1 KRTAP19-3 21 30491861 Missense_Mutation SNP G C3L-00913_T 154438 30491861 16218122 227 7101 KRTAP20-3 0 . GRCh38 21 30642926 30642926 + Missense_Mutation SNP A A G novel C3L-00913_T C3L-00913_N A A c.38A>G p.Tyr13Cys p.Y13C ENST00000382826 1/1 215 185 30 165 165 0 strelka-varscan-mutect KRTAP20-3,missense_variant,p.Tyr13Cys,ENST00000382826,NM_001128077.1; G ENST00000382826 Transcript missense_variant 63/273 38/135 13/44 Y/C tAt/tGt 1 1 KRTAP20-3 HGNC HGNC:34001 protein_coding YES CCDS46642.1 ENSP00000372276 Q3LI60 UPI00003D4D74 NM_001128077.1 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 21 30642926 30642926 A G 1 0 0 0 0 1 0 0 0 8425 449 16 5 5 KRTAP20-3 21 30642926 Missense_Mutation SNP A C3L-00913_T 151065 30642926 16067057 228 7102 KRTAP10-10 0 . GRCh38 21 44637504 44637504 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.87C>A p.= p.P29P ENST00000380095 1/1 216 172 44 149 149 0 strelka-varscan-mutect KRTAP10-10,synonymous_variant,p.=,ENST00000380095,NM_181688.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; A ENST00000380095 Transcript synonymous_variant 149/1100 87/756 29/251 P ccC/ccA 1 1 KRTAP10-10 HGNC HGNC:22972 protein_coding YES CCDS33585.1 ENSP00000369438 P60014 UPI00001A95B8 NM_181688.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF61 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 44637504 44637504 C A 1 0 0 0 0 0 0 0 1 8389 668 24 2 2 KRTAP10-10 21 44637504 Silent SNP C C3L-00913_T 13994578 44637504 2072479 229 7103 KRTAP10-10 0 . GRCh38 21 44637951 44637951 + Nonsense_Mutation SNP C C A rs782673603 C3L-00913_T C3L-00913_N C C c.534C>A p.Cys178Ter p.C178* ENST00000380095 1/1 593 558 35 427 427 0 varscan-mutect KRTAP10-10,stop_gained,p.Cys178Ter,ENST00000380095,NM_181688.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; A ENST00000380095 Transcript stop_gained 596/1100 534/756 178/251 C/* tgC/tgA rs782673603 1 1 KRTAP10-10 HGNC HGNC:22972 protein_coding YES CCDS33585.1 ENSP00000369438 P60014 UPI00001A95B8 NM_181688.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262:SF61,hmmpanther:PTHR23262 HIGH SNV 1 PASS rs782673603 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 21 44637951 44637951 C A 1 0 0 0 0 0 1 0 0 8389 805 28 2 2 KRTAP10-10 21 44637951 Nonsense_Mutation SNP C C3L-00913_T 447 44637951 2072032 230 7104 SLC25A18 0 . GRCh38 22 17581387 17581387 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.173C>T p.Ala58Val p.A58V ENST00000327451 5/11 194 171 23 129 129 0 strelka-varscan-mutect SLC25A18,missense_variant,p.Ala58Val,ENST00000327451,NM_031481.2;SLC25A18,missense_variant,p.Ala58Val,ENST00000399813,NM_001303484.1;AC004019.13,non_coding_transcript_exon_variant,,ENST00000443935,;AC004019.13,non_coding_transcript_exon_variant,,ENST00000611039,;SLC25A18,non_coding_transcript_exon_variant,,ENST00000497401,;SLC25A18,non_coding_transcript_exon_variant,,ENST00000467228,; T ENST00000327451 Transcript missense_variant 711/2244 173/948 58/315 A/V gCg/gTg 1 1 SLC25A18 HGNC HGNC:10988 protein_coding YES CCDS13744.1 ENSP00000329033 Q9H1K4 A0A024R0W0 UPI00000015FA NM_031481.2 tolerated(0.08) 5/11 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF277,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 21 17581387 17581387 C T 1 0 0 0 0 1 0 0 0 14745 768 27 1 1 SLC25A18 22 17581387 Missense_Mutation SNP C C3L-00913_T 17581387 33237081 231 7105 COMT 0 . GRCh38 22 19963678 19963678 + Silent SNP G G C rs769223 C3L-00913_T C3L-00913_N G G c.402G>C p.= p.A134A ENST00000361682 4/6 437 404 33 349 349 0 strelka-varscan-mutect COMT,synonymous_variant,p.=,ENST00000361682,NM_000754.3,NM_001135161.1;COMT,synonymous_variant,p.=,ENST00000403184,;COMT,synonymous_variant,p.=,ENST00000403710,;COMT,synonymous_variant,p.=,ENST00000407537,;COMT,synonymous_variant,p.=,ENST00000406520,NM_001135162.1;COMT,synonymous_variant,p.=,ENST00000449653,NM_007310.2;COMT,synonymous_variant,p.=,ENST00000412786,;COMT,upstream_gene_variant,,ENST00000428707,;COMT,upstream_gene_variant,,ENST00000585066,;COMT,non_coding_transcript_exon_variant,,ENST00000493893,;COMT,synonymous_variant,p.=,ENST00000207636,;COMT,downstream_gene_variant,,ENST00000467943,; C ENST00000361682 Transcript synonymous_variant 784/2437 402/816 134/271 A gcG/gcC rs769223 1 1 COMT HGNC HGNC:2228 protein_coding YES CCDS13770.1 ENSP00000354511 P21964 A0A140VJG8 UPI0000000CBF NM_000754.3,NM_001135161.1 4/6 Gene3D:3.40.50.150,Pfam_domain:PF01596,PIRSF_domain:PIRSF037177,PROSITE_profiles:PS51682,hmmpanther:PTHR10509,hmmpanther:PTHR10509:SF2,Superfamily_domains:SSF53335 1866336916816940 LOW 1 SNV 1 1 PASS rs769223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 21 19963678 19963678 G C 1 0 0 0 0 0 0 0 1 3517 1045 37 4 4 COMT 22 19963678 Silent SNP G C3L-00913_T 2382291 19963678 30854790 232 7106 SEZ6L 0 . GRCh38 22 26347721 26347721 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.2215G>T p.Val739Leu p.V739L ENST00000248933 11/17 246 209 37 166 166 0 strelka-varscan-mutect SEZ6L,missense_variant,p.Val739Leu,ENST00000529632,NM_001184775.1;SEZ6L,missense_variant,p.Val739Leu,ENST00000360929,NM_001184776.1;SEZ6L,missense_variant,p.Val739Leu,ENST00000404234,NM_001184773.1;SEZ6L,missense_variant,p.Val512Leu,ENST00000402979,;SEZ6L,missense_variant,p.Val739Leu,ENST00000248933,NM_021115.4;SEZ6L,missense_variant,p.Val739Leu,ENST00000629590,NM_001184774.1;SEZ6L,missense_variant,p.Val512Leu,ENST00000403121,;SEZ6L,missense_variant,p.Val739Leu,ENST00000343706,NM_001184777.1;SEZ6L,upstream_gene_variant,,ENST00000483291,; T ENST00000248933 Transcript missense_variant,splice_region_variant 2310/3248 2215/3075 739/1024 V/L Gta/Tta 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 deleterious(0) 11/17 PROSITE_profiles:PS01180,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81,SMART_domains:SM00042 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 26347721 26347721 G T 1 0 0 0 0 1 0 0 0 14422 1275 44 2 2 SEZ6L 22 26347721 Missense_Mutation SNP G C3L-00913_T 6384043 26347721 24470747 233 7107 SLC5A4 0 . GRCh38 22 32235023 32235023 + Missense_Mutation SNP C C A rs781767196 C3L-00913_T C3L-00913_N C C c.735G>T p.Glu245Asp p.E245D ENST00000266086 8/15 300 264 36 245 245 0 strelka-varscan-mutect SLC5A4,missense_variant,p.Glu245Asp,ENST00000266086,NM_014227.2;RP1-90G24.10,intron_variant,,ENST00000434942,; A ENST00000266086 Transcript missense_variant 747/2030 735/1980 245/659 E/D gaG/gaT rs781767196 1 -1 SLC5A4 HGNC HGNC:11039 protein_coding YES CCDS13903.1 ENSP00000266086 Q9NY91 UPI00001359F4 NM_014227.2 tolerated(0.62) 8/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF112,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS rs781767196 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 32235023 32235023 C A 1 0 0 0 0 1 0 0 0 14950 680 24 2 2 SLC5A4 22 32235023 Missense_Mutation SNP C C3L-00913_T 5887302 32235023 18583445 234 7108 APOBEC3A 0 . GRCh38 22 38961596 38961596 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.384C>T p.= p.R128R ENST00000402255 4/6 674 631 43 462 461 1 varscan-mutect APOBEC3A,synonymous_variant,p.=,ENST00000402255,;APOBEC3A,synonymous_variant,p.=,ENST00000249116,NM_001270406.1,NM_145699.3;APOBEC3A,synonymous_variant,p.=,ENST00000618553,;APOBEC3A,downstream_gene_variant,,ENST00000488758,; T ENST00000402255 Transcript synonymous_variant 588/1478 384/600 128/199 R cgC/cgT 1 1 APOBEC3A HGNC HGNC:17343 protein_coding YES CCDS13981.1 ENSP00000384359 P31941 A0A0K0MJ49 UPI00001318F4 4/6 PROSITE_profiles:PS51747,hmmpanther:PTHR13857:SF14,hmmpanther:PTHR13857,Pfam_domain:PF08210,Superfamily_domains:SSF53927 LOW 1 SNV 5 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 38961596 38961596 C T 1 0 0 0 0 0 0 0 1 910 697 25 3 3 APOBEC3A 22 38961596 Silent SNP C C3L-00913_T 6726573 38961596 11856872 235 7109 FAM118A 0 . GRCh38 22 45332661 45332661 + Silent SNP A A G novel C3L-00913_T C3L-00913_N A A c.888A>G p.= p.P296P ENST00000216214 7/10 176 166 10 117 117 0 strelka-varscan-mutect FAM118A,synonymous_variant,p.=,ENST00000216214,NM_001104595.1;FAM118A,synonymous_variant,p.=,ENST00000441876,NM_017911.2;FAM118A,downstream_gene_variant,,ENST00000405673,;FAM118A,downstream_gene_variant,,ENST00000427777,;FAM118A,non_coding_transcript_exon_variant,,ENST00000459849,;FAM118A,downstream_gene_variant,,ENST00000476754,;FAM118A,upstream_gene_variant,,ENST00000483102,;FAM118A,upstream_gene_variant,,ENST00000479180,;FAM118A,downstream_gene_variant,,ENST00000476478,;FAM118A,non_coding_transcript_exon_variant,,ENST00000487732,;FAM118A,downstream_gene_variant,,ENST00000477714,;FAM118A,upstream_gene_variant,,ENST00000462361,; G ENST00000216214 Transcript synonymous_variant 1722/3458 888/1074 296/357 P ccA/ccG 1 1 FAM118A HGNC HGNC:1313 protein_coding YES CCDS14065.1 ENSP00000216214 Q9NWS6 A0A024R4V3 UPI000022B897 NM_001104595.1 7/10 hmmpanther:PTHR28623:SF2,hmmpanther:PTHR28623 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 45332661 45332661 A G 1 0 0 0 0 0 0 0 1 5270 175 7 5 5 FAM118A 22 45332661 Silent SNP A C3L-00913_T 6371065 45332661 5485807 236 7110 TBC1D22A 0 . GRCh38 22 47037179 47037179 + Missense_Mutation SNP G G C rs753037531 C3L-00913_T C3L-00913_N G G c.1310G>C p.Arg437Pro p.R437P ENST00000337137 11/13 261 219 42 174 174 0 strelka-varscan-mutect TBC1D22A,missense_variant,p.Arg407Pro,ENST00000380995,NM_001284304.1;TBC1D22A,missense_variant,p.Arg437Pro,ENST00000337137,NM_014346.3;TBC1D22A,missense_variant,p.Arg390Pro,ENST00000406733,NM_001284305.1;TBC1D22A,missense_variant,p.Arg378Pro,ENST00000407381,;TBC1D22A,missense_variant,p.Arg359Pro,ENST00000355704,NM_001284303.1;TBC1D22A,3_prime_UTR_variant,,ENST00000441162,;TBC1D22A,3_prime_UTR_variant,,ENST00000394449,; C ENST00000337137 Transcript missense_variant 1476/3787 1310/1554 437/517 R/P cGc/cCc rs753037531,COSM1416921 1 1 TBC1D22A HGNC HGNC:1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 UPI0000128722 NM_014346.3 deleterious(0) 11/13 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF255,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753037531 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 21 47037179 47037179 G C 1 0 0 0 0 1 0 0 0 16011 1087 38 4 4 TBC1D22A 22 47037179 Missense_Mutation SNP G C3L-00913_T 1704518 47037179 3781289 237 7111 TUBGCP6 0 . GRCh38 22 50221564 50221564 + Nonsense_Mutation SNP G G C rs775980514 C3L-00913_T C3L-00913_N G G c.2795C>G p.Ser932Ter p.S932* ENST00000248846 16/25 85 78 7 69 69 0 strelka-varscan-mutect TUBGCP6,stop_gained,p.Ser932Ter,ENST00000439308,;TUBGCP6,stop_gained,p.Ser932Ter,ENST00000248846,NM_020461.3;SELO,downstream_gene_variant,,ENST00000380903,NM_031454.1;SELO,downstream_gene_variant,,ENST00000611222,;TUBGCP6,upstream_gene_variant,,ENST00000425018,;TUBGCP6,non_coding_transcript_exon_variant,,ENST00000491449,;TUBGCP6,downstream_gene_variant,,ENST00000473946,;SELO,downstream_gene_variant,,ENST00000492092,;TUBGCP6,downstream_gene_variant,,ENST00000489511,;TUBGCP6,non_coding_transcript_exon_variant,,ENST00000498611,; C ENST00000248846 Transcript stop_gained 2900/5612 2795/5460 932/1819 S/* tCa/tGa rs775980514,COSM4484303 1 -1 TUBGCP6 HGNC HGNC:18127 protein_coding YES CCDS14087.1 ENSP00000248846 Q96RT7 UPI000013CC55 NM_020461.3 16/25 Low_complexity_(Seg):seg,Pfam_domain:PF04130 0,1 HIGH 1 SNV 1 0,1 1 PASS rs775980514 . 0 207 3 0 0 0 0 0 -15.15043 1 1 1 1 0 C 4 2 21 50221564 50221564 G C 1 0 0 0 0 0 1 0 0 17280 1294 45 4 4 TUBGCP6 22 50221564 Nonsense_Mutation SNP G C3L-00913_T 3184385 50221564 596904 238 7112 TLR7 0 . GRCh38 X 12886511 12886511 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.1003T>A p.Phe335Ile p.F335I ENST00000380659 3/3 185 141 44 124 124 0 strelka-varscan-mutect TLR7,missense_variant,p.Phe335Ile,ENST00000380659,NM_016562.3; A ENST00000380659 Transcript missense_variant 1142/5011 1003/3150 335/1049 F/I Ttt/Att 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 deleterious(0) 3/3 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 12886511 12886511 T A 1 0 0 0 0 1 0 0 0 16402 1493 52 4 4 TLR7 23 12886511 Missense_Mutation SNP T C3L-00913_T 12886511 143154384 239 7113 EGFL6 0 . GRCh38 X 13603427 13603427 + Missense_Mutation SNP G G T rs771301705 C3L-00913_T C3L-00913_N G G c.511G>T p.Asp171Tyr p.D171Y ENST00000380602 5/12 78 52 26 56 56 0 strelka-varscan-mutect EGFL6,missense_variant,p.Asp171Tyr,ENST00000361306,NM_015507.3;EGFL6,missense_variant,p.Asp171Tyr,ENST00000380602,NM_001167890.1; T ENST00000380602 Transcript missense_variant 751/2385 511/1665 171/554 D/Y Gac/Tac rs771301705 1 1 EGFL6 HGNC HGNC:3235 protein_coding YES CCDS55370.1 ENSP00000369976 Q8IUX8 UPI0000034CAE NM_001167890.1 deleterious(0) 5/12 Gene3D:2.10.25.10,hmmpanther:PTHR24050,hmmpanther:PTHR24050:SF18,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs771301705 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 13603427 13603427 G T 1 0 0 0 0 1 0 0 0 4799 942 33 2 2 EGFL6 23 13603427 Missense_Mutation SNP G C3L-00913_T 716916 13603427 142437468 240 7114 MAGEB18 0 . GRCh38 X 26139240 26139240 + Silent SNP C C A novel C3L-00913_T C3L-00913_N C C c.255C>A p.= p.A85A ENST00000325250 2/3 222 167 55 158 156 2 strelka-varscan-mutect MAGEB18,synonymous_variant,p.=,ENST00000325250,NM_173699.3; A ENST00000325250 Transcript synonymous_variant 442/1811 255/1032 85/343 A gcC/gcA 1 1 MAGEB18 HGNC HGNC:28515 protein_coding YES CCDS14216.1 ENSP00000314543 Q96M61 UPI00001415E3 NM_173699.3 2/3 hmmpanther:PTHR11736:SF23,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 26139240 26139240 C A 1 0 0 0 0 0 0 0 1 9091 581 21 2 2 MAGEB18 23 26139240 Silent SNP C C3L-00913_T 12535813 26139240 129901655 241 7115 FAM47A 0 . GRCh38 X 34130840 34130840 + Missense_Mutation SNP G G T rs773204999 C3L-00913_T C3L-00913_N G G c.1439C>A p.Pro480Gln p.P480Q ENST00000346193 1/1 37 30 7 43 43 0 strelka-varscan-mutect FAM47A,missense_variant,p.Pro480Gln,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.Pro480Gln,ENST00000613251,; T ENST00000346193 Transcript missense_variant 1472/2556 1439/2376 480/791 P/Q cCg/cAg rs773204999 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 deleterious(0.05) 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS rs773204999 . 0 205 5 0 0 0 0 0 -17.94168 1 1 1 1 0 T 3 4 21 34130840 34130840 G T 1 0 0 0 0 1 0 0 0 5447 1116 39 1 1 FAM47A 23 34130840 Missense_Mutation SNP G C3L-00913_T 7991600 34130840 121910055 242 7116 FAM47B 0 . GRCh38 X 34943395 34943395 + Frame_Shift_Del DEL C C - novel C3L-00913_T C3L-00913_N C C c.566delC p.Pro189ArgfsTer161 p.P189Rfs*161 ENST00000329357 1/1 113 90 23 103 103 0 sindel-varindel-pindel FAM47B,frameshift_variant,p.Pro189ArgfsTer161,ENST00000329357,NM_152631.2; - ENST00000329357 Transcript frameshift_variant 600/2120 564/1938 188/645 C/X tgC/tg 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192 HIGH 1 deletion 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 21 34943395 34943395 C - 1 0 1 0 1 0 0 0 0 5448 747 26 0 0 FAM47B 23 34943395 Frame_Shift_Del DEL C C3L-00913_T 812555 34943395 121097500 243 7117 VSIG4 0 . GRCh38 X 66032592 66032592 + Silent SNP T T G novel C3L-00913_T C3L-00913_N T T c.570A>C p.= p.V190V ENST00000374737 3/8 255 198 57 168 168 0 strelka-varscan-mutect VSIG4,synonymous_variant,p.=,ENST00000455586,NM_001184830.1,NM_001184831.1,NM_001257403.1;VSIG4,synonymous_variant,p.=,ENST00000374737,NM_007268.2;VSIG4,synonymous_variant,p.=,ENST00000427538,;VSIG4,intron_variant,,ENST00000412866,NM_001100431.1; G ENST00000374737 Transcript synonymous_variant 679/1834 570/1200 190/399 V gtA/gtC 1 -1 VSIG4 HGNC HGNC:17032 protein_coding YES CCDS14383.1 ENSP00000363869 Q9Y279 UPI000006F146 NM_007268.2 3/8 PROSITE_profiles:PS50835,hmmpanther:PTHR15466:SF2,hmmpanther:PTHR15466,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1297300550 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 21 66032592 66032592 T G 1 0 0 0 0 0 0 0 1 17776 1509 53 5 5 VSIG4 23 66032592 Silent SNP T C3L-00913_T 31089197 66032592 90008303 244 7118 MAGEE1 0 . GRCh38 X 76428509 76428509 + Missense_Mutation SNP T T A novel C3L-00913_T C3L-00913_N T T c.579T>A p.Asp193Glu p.D193E ENST00000361470 1/1 196 147 49 144 144 0 strelka-varscan-mutect MAGEE1,missense_variant,p.Asp193Glu,ENST00000361470,NM_020932.2; A ENST00000361470 Transcript missense_variant 786/3630 579/2874 193/957 D/E gaT/gaA 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 deleterious_low_confidence(0.05) 1/1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 76428509 76428509 T A 1 0 0 0 0 1 0 0 0 9103 1461 51 4 4 MAGEE1 23 76428509 Missense_Mutation SNP T C3L-00913_T 10395917 76428509 79612386 245 7119 VSIG1 0 . GRCh38 X 108058189 108058189 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.201G>A p.Met67Ile p.M67I ENST00000415430 2/8 64 49 15 49 49 0 strelka-varscan-mutect VSIG1,missense_variant,p.Met67Ile,ENST00000415430,NM_001170553.1;VSIG1,missense_variant,p.Met67Ile,ENST00000217957,NM_182607.4;VSIG1,missense_variant,p.Met67Ile,ENST00000458383,; A ENST00000415430 Transcript missense_variant 362/3236 201/1272 67/423 M/I atG/atA 1 1 VSIG1 HGNC HGNC:28675 protein_coding YES CCDS55474.1 ENSP00000402219 Q86XK7 UPI00017A7E2F NM_001170553.1 tolerated(0.21) 2/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF115,SMART_domains:SM00409,SMART_domains:SM00406,SMART_domains:SM00408 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 21 108058189 108058189 G A 1 0 0 0 0 1 0 0 0 17772 1348 47 3 3 VSIG1 23 108058189 Missense_Mutation SNP G C3L-00913_T 31629680 108058189 47982706 246 7120 HTR2C 0 . GRCh38 X 114906863 114906863 + Missense_Mutation SNP G G T novel C3L-00913_T C3L-00913_N G G c.825G>T p.Glu275Asp p.E275D ENST00000276198 6/6 291 224 67 191 191 0 strelka-varscan-mutect HTR2C,stop_gained,p.Glu244Ter,ENST00000371950,NM_001256761.2;HTR2C,missense_variant,p.Glu275Asp,ENST00000276198,NM_000868.3;HTR2C,missense_variant,p.Glu275Asp,ENST00000371951,NM_001256760.2; T ENST00000276198 Transcript missense_variant 1553/4751 825/1377 275/458 E/D gaG/gaT 1 1 HTR2C HGNC HGNC:5295 protein_coding YES CCDS14564.1 ENSP00000276198 P28335 UPI000014653A NM_000868.3 tolerated(0.67) 6/6 Pfam_domain:PF00001,SMART_domains:SM01381,PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF32,hmmpanther:PTHR24247,Prints_domain:PR00517 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 114906863 114906863 G T 1 0 0 0 0 1 0 0 0 7339 943 33 2 2 HTR2C 23 114906863 Missense_Mutation SNP G C3L-00913_T 6848674 114906863 41134032 247 7121 RP13-347D8.7 0 . GRCh38 X 119073397 119073397 + Missense_Mutation SNP G G A novel C3L-00913_T C3L-00913_N G G c.172G>A p.Glu58Lys p.E58K ENST00000620151 1/3 96 71 25 71 71 0 strelka-varscan-mutect RP13-347D8.7,missense_variant,p.Glu58Lys,ENST00000620151,; A ENST00000620151 Transcript missense_variant 172/1147 172/975 58/324 E/K Gag/Aag 1 1 RP13-347D8.7 Clone_based_vega_gene protein_coding YES ENSP00000488984 A0A0U1RQG5 UPI000719A0D1 tolerated(0.06) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32157,hmmpanther:PTHR32157:SF2,Pfam_domain:PF15623 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 21 119073397 119073397 G A 1 0 0 0 0 1 0 0 0 13772 1175 41 3 3 RP13-347D8.7 23 119073397 Missense_Mutation SNP G C3L-00913_T 4166534 119073397 36967498 248 7122 TENM1 0 . GRCh38 X 124737160 124737160 + Silent SNP T T C novel C3L-00913_T C3L-00913_N T T c.573A>G p.= p.R191R ENST00000422452 4/32 118 108 10 80 80 0 strelka-varscan-mutect TENM1,synonymous_variant,p.=,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,synonymous_variant,p.=,ENST00000371130,NM_014253.3; C ENST00000422452 Transcript synonymous_variant 637/12891 573/8199 191/2732 R agA/agG 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 4/32 PROSITE_profiles:PS51361,hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,Pfam_domain:PF06484 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.62633 1 1 1 1 0 C 2 2 21 124737160 124737160 T C 1 0 0 0 0 0 0 0 1 16171 1664 58 5 5 TENM1 23 124737160 Silent SNP T C3L-00913_T 5663763 124737160 31303735 249 7123 ADGRG4 0 . GRCh38 X 136346244 136346244 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.2538C>T p.= p.S846S ENST00000394143 6/26 136 102 34 88 88 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; T ENST00000394143 Transcript synonymous_variant 2829/9931 2538/9243 846/3080 S tcC/tcT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 136346244 136346244 C T 1 0 0 0 0 0 0 0 1 371 610 22 3 3 ADGRG4 23 136346244 Silent SNP C C3L-00913_T 11609084 136346244 19694651 250 7124 ADGRG4 0 . GRCh38 X 136347099 136347099 + Silent SNP C C A C3L-00913_T C3L-00913_N C C c.3393C>A p.= p.T1131T ENST00000394143 6/26 126 90 36 103 103 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; A ENST00000394143 Transcript synonymous_variant 3684/9931 3393/9243 1131/3080 T acC/acA COSM1331234 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 136347099 136347099 C A 1 0 0 0 0 0 0 0 1 371 668 24 2 2 ADGRG4 23 136347099 Silent SNP C C3L-00913_T 855 136347099 19693796 251 7125 CD40LG 0 . GRCh38 X 136648305 136648305 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.57C>T p.= p.I19I ENST00000370629 1/5 273 209 64 189 189 0 strelka-varscan-mutect CD40LG,synonymous_variant,p.=,ENST00000370629,NM_000074.2;CD40LG,synonymous_variant,p.=,ENST00000370628,; T ENST00000370629 Transcript synonymous_variant 113/1817 57/786 19/261 I atC/atT 1 1 CD40LG HGNC HGNC:11935 protein_coding YES CCDS14659.1 ENSP00000359663 P29965 UPI00000315E7 NM_000074.2 1/5 hmmpanther:PTHR11471:SF5,hmmpanther:PTHR11471,PIRSF_domain:PIRSF016527 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 136648305 136648305 C T 1 0 0 0 0 0 0 0 1 2720 816 29 3 3 CD40LG 23 136648305 Silent SNP C C3L-00913_T 301206 136648305 19392590 252 7126 SLITRK2 0 . GRCh38 X 145824239 145824239 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.1814C>T p.Ser605Phe p.S605F ENST00000370490 1/1 170 150 20 121 121 0 strelka-varscan-mutect SLITRK2,missense_variant,p.Ser605Phe,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,missense_variant,p.Ser605Phe,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript missense_variant 6069/7672 1814/2538 605/845 S/F tCt/tTt 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 tolerated(0.33) 1/1 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 145824239 145824239 C T 1 0 0 0 0 1 0 0 0 15034 913 32 3 3 SLITRK2 23 145824239 Missense_Mutation SNP C C3L-00913_T 9175934 145824239 10216656 253 7127 MAMLD1 0 . GRCh38 X 150470480 150470480 + Missense_Mutation SNP C C T novel C3L-00913_T C3L-00913_N C C c.832C>T p.His278Tyr p.H278Y ENST00000432680 3/5 212 187 25 137 136 1 strelka-varscan-mutect MAMLD1,missense_variant,p.His303Tyr,ENST00000370401,;MAMLD1,missense_variant,p.His303Tyr,ENST00000262858,NM_005491.4;MAMLD1,missense_variant,p.His278Tyr,ENST00000426613,NM_001177466.2;MAMLD1,missense_variant,p.His278Tyr,ENST00000432680,NM_001177465.2;MAMLD1,downstream_gene_variant,,ENST00000358892,;MAMLD1,downstream_gene_variant,,ENST00000468306,; T ENST00000432680 Transcript missense_variant 1007/3224 832/2997 278/998 H/Y Cac/Tac 1 1 MAMLD1 HGNC HGNC:2568 protein_coding YES CCDS55526.1 ENSP00000414517 Q13495 UPI00017A6EBC NM_001177465.2 deleterious(0) 3/5 hmmpanther:PTHR15275,hmmpanther:PTHR15275:SF0 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 150470480 150470480 C T 1 0 0 0 0 1 0 0 0 9129 826 29 3 3 MAMLD1 23 150470480 Missense_Mutation SNP C C3L-00913_T 4646241 150470480 5570415 254 7128 GABRA3 0 . GRCh38 X 152255948 152255948 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.381G>A p.= p.L127L ENST00000370314 5/10 365 335 30 218 217 1 strelka-varscan-mutect GABRA3,synonymous_variant,p.=,ENST00000370314,NM_000808.3;GABRA3,synonymous_variant,p.=,ENST00000535043,;GABRA3,non_coding_transcript_exon_variant,,ENST00000417858,; T ENST00000370314 Transcript synonymous_variant 620/3712 381/1479 127/492 L ctG/ctA 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 5/10 hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 152255948 152255948 C T 1 0 0 0 0 0 0 0 1 6033 813 29 3 3 GABRA3 23 152255948 Silent SNP C C3L-00913_T 1785468 152255948 3784947 255 7129 L1CAM 0 . GRCh38 X 153864885 153864885 + Silent SNP C C T novel C3L-00913_T C3L-00913_N C C c.2982G>A p.= p.Q994Q ENST00000370060 23/29 252 151 101 134 134 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000455590,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000484652,; T ENST00000370060 Transcript synonymous_variant 3172/5113 2982/3774 994/1257 Q caG/caA 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 23/29 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 21 153864885 153864885 C T 1 0 0 0 0 0 0 0 1 8489 680 24 3 3 L1CAM 23 153864885 Silent SNP C C3L-00913_T 1608937 153864885 2176010 256 7130 HCFC1 0 . GRCh38 X 153952820 153952820 + Missense_Mutation SNP C C A rs782151196 C3L-00913_T C3L-00913_N C C c.4636G>T p.Ala1546Ser p.A1546S ENST00000310441 19/26 73 63 10 41 41 0 strelka-varscan-mutect HCFC1,missense_variant,p.Ala1546Ser,ENST00000310441,NM_005334.2;HCFC1,missense_variant,p.Ala1590Ser,ENST00000369984,;HCFC1,missense_variant,p.Ala121Ser,ENST00000444191,; A ENST00000310441 Transcript missense_variant 5603/8869 4636/6108 1546/2035 A/S Gcc/Tcc rs782151196 1 -1 HCFC1 HGNC HGNC:4839 protein_coding YES CCDS44020.1 ENSP00000309555 P51610 UPI0000142F1F NM_005334.2 tolerated_low_confidence(0.23) 19/26 MODERATE 1 SNV 1 1 PASS rs782151196 . 0 205 5 0 0 0 0 0 -19.99594 1 1 1 1 0 A 3 1 21 153952820 153952820 C A 1 0 0 0 0 1 0 0 0 6879 768 27 1 1 HCFC1 23 153952820 Missense_Mutation SNP C C3L-00913_T 87935 153952820 2088075 257 7131 FLNA 0 . GRCh38 X 154366345 154366345 + Silent SNP G G A rs200048692 C3L-00913_T C3L-00913_N G G c.1191C>T p.= p.I397I ENST00000369850 8/48 383 342 41 205 205 0 strelka-varscan-mutect FLNA,synonymous_variant,p.=,ENST00000422373,NM_001456.3;FLNA,synonymous_variant,p.=,ENST00000369850,NM_001110556.1;FLNA,synonymous_variant,p.=,ENST00000360319,;FLNA,synonymous_variant,p.=,ENST00000369856,;FLNA,synonymous_variant,p.=,ENST00000344736,;FLNA,synonymous_variant,p.=,ENST00000610817,;FLNA,synonymous_variant,p.=,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000465144,; A ENST00000369850 Transcript synonymous_variant 1428/8382 1191/7944 397/2647 I atC/atT rs200048692,COSM4684939,COSM4684940 1 -1 FLNA HGNC HGNC:3754 protein_coding YES CCDS48194.1 ENSP00000358866 P21333 UPI000013C596 NM_001110556.1 8/48 PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF173,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296 benign 0,1,1 LOW 1 SNV 1 1,1,1 1 PASS rs200048692 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 21 154366345 154366345 G A 1 0 0 0 0 0 0 0 1 5789 1048 37 1 1 FLNA 23 154366345 Silent SNP G C3L-00913_T 413525 154366345 1674550 258 7132 PLXNA3 0 . GRCh38 X 154466041 154466041 + Missense_Mutation SNP G G T rs782688882 C3L-00913_T C3L-00913_N G G c.2639G>T p.Arg880Leu p.R880L ENST00000369682 14/33 96 55 41 74 74 0 strelka-varscan-mutect PLXNA3,missense_variant,p.Arg880Leu,ENST00000369682,NM_017514.4;PLXNA3,upstream_gene_variant,,ENST00000493546,;PLXNA3,downstream_gene_variant,,ENST00000495040,;PLXNA3,upstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000480645,;PLXNA3,upstream_gene_variant,,ENST00000497802,;PLXNA3,upstream_gene_variant,,ENST00000491066,;PLXNA3,upstream_gene_variant,,ENST00000478236,;PLXNA3,downstream_gene_variant,,ENST00000482598,; T ENST00000369682 Transcript missense_variant 2814/10885 2639/5616 880/1871 R/L cGt/cTt rs782688882 1 1 PLXNA3 HGNC HGNC:9101 protein_coding YES CCDS14752.1 ENSP00000358696 P51805 UPI0002AB801F NM_017514.4 tolerated(0.34) 14/33 hmmpanther:PTHR22625:SF32,hmmpanther:PTHR22625,Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs782688882 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 21 154466041 154466041 G T 1 0 0 0 0 1 0 0 0 12227 1145 40 1 1 PLXNA3 23 154466041 Missense_Mutation SNP G C3L-00913_T 99696 154466041 1574854 259 7133 NBPF10 0 . GRCh38 1 146074374 146074374 + Silent SNP T T C novel C3L-00973_T C3L-00973_N T T c.9975A>G p.= p.S3325S ENST00000583866 80/90 58 38 20 54 54 0 varscan-mutect NBPF10,synonymous_variant,p.=,ENST00000583866,NM_001039703.5,NM_001302371.1;NBPF10,synonymous_variant,p.=,ENST00000617010,;NBPF10,intron_variant,,ENST00000610925,;NBPF10,intron_variant,,ENST00000622244,;NBPF10,intron_variant,,ENST00000613557,;NBPF10,intron_variant,,ENST00000616399,;NBPF10,intron_variant,,ENST00000613224,; C ENST00000583866 Transcript synonymous_variant 10010/13042 9975/11388 3325/3795 S tcA/tcG 1 -1 NBPF10 HGNC HGNC:31992 protein_coding YES CCDS76206.1 ENSP00000463957 A0A075B762 UPI00051EF319 NM_001039703.5,NM_001302371.1 80/90 Pfam_domain:PF06758,PROSITE_profiles:PS51316,SMART_domains:SM01148 LOW 1 SNV 5 1 PASS . . 5 176 19 9 0 0 0 0 -20 0.9290578 0 1 1 0 C 2 2 22 146074374 146074374 T C 1 0 0 0 0 0 0 0 1 10204 1799 63 5 5 NBPF10 1 146074374 Silent SNP T C3L-00973_T 146074374 102882048 1 7134 PGBD2 0 . GRCh38 1 248917258 248917258 + Missense_Mutation SNP T T G novel C3L-00973_T C3L-00973_N T T c.674T>G p.Phe225Cys p.F225C ENST00000329291 3/3 436 368 68 322 322 0 strelka-varscan-mutect PGBD2,missense_variant,p.Phe225Cys,ENST00000329291,NM_170725.2;PGBD2,intron_variant,,ENST00000355360,NM_001017434.1;RNU6-1205P,upstream_gene_variant,,ENST00000363625,;PGBD2,intron_variant,,ENST00000462488,; G ENST00000329291 Transcript missense_variant 821/2136 674/1779 225/592 F/C tTc/tGc 1 1 PGBD2 HGNC HGNC:19399 protein_coding YES CCDS31128.1 ENSP00000331643 Q6P3X8 UPI000016196D NM_170725.2 deleterious(0) 3/3 Pfam_domain:PF13843,hmmpanther:PTHR28576,hmmpanther:PTHR28576:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 22 248917258 248917258 T G 1 0 0 0 0 1 0 0 0 11871 1783 62 5 5 PGBD2 1 248917258 Missense_Mutation SNP T C3L-00973_T 102842884 248917258 39164 2 7135 WNT7A 0 . GRCh38 3 13819261 13819261 + Missense_Mutation SNP G G A novel C3L-00973_T C3L-00973_N G G c.733C>T p.Arg245Cys p.R245C ENST00000285018 4/4 183 168 15 179 179 0 strelka-varscan-mutect WNT7A,missense_variant,p.Arg245Cys,ENST00000285018,NM_004625.3; A ENST00000285018 Transcript missense_variant 1038/4041 733/1050 245/349 R/C Cgc/Tgc 1 -1 WNT7A HGNC HGNC:12786 protein_coding YES CCDS2616.1 ENSP00000285018 O00755 UPI0000033777 NM_004625.3 deleterious(0) 4/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF78,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 22 13819261 13819261 G A 1 0 0 0 0 1 0 0 0 17950 1116 39 1 1 WNT7A 3 13819261 Missense_Mutation SNP G C3L-00973_T 13819261 184476298 3 7136 XRN1 0 . GRCh38 3 142422697 142422697 + Missense_Mutation SNP C C A C3L-00973_T C3L-00973_N C C c.852G>T p.Leu284Phe p.L284F ENST00000264951 8/42 259 223 36 205 204 1 strelka-mutect XRN1,missense_variant,p.Leu284Phe,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Leu284Phe,ENST00000392981,NM_001282857.1;XRN1,missense_variant,p.Leu284Phe,ENST00000463916,NM_001282859.1;XRN1,missense_variant,p.Leu145Phe,ENST00000477237,;RNU1-100P,upstream_gene_variant,,ENST00000365255,;XRN1,3_prime_UTR_variant,,ENST00000486211,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,;XRN1,downstream_gene_variant,,ENST00000470537,; A ENST00000264951 Transcript missense_variant 970/10143 852/5121 284/1706 L/F ttG/ttT COSM3588255,COSM3588256 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 deleterious(0.03) 8/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1455187290 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 22 142422697 142422697 C A 1 0 0 0 0 1 0 0 0 18017 825 29 2 2 XRN1 3 142422697 Missense_Mutation SNP C C3L-00973_T 128603436 142422697 55872862 4 7137 ATP13A3 0 . GRCh38 3 194441456 194441456 + Missense_Mutation SNP A A G novel C3L-00973_T C3L-00973_N A A c.1565T>C p.Leu522Pro p.L522P ENST00000439040 16/33 131 112 19 93 93 0 strelka-varscan-mutect ATP13A3,missense_variant,p.Leu522Pro,ENST00000439040,;ATP13A3,missense_variant,p.Leu522Pro,ENST00000256031,NM_024524.3;ATP13A3,missense_variant,p.Leu245Pro,ENST00000619199,; G ENST00000439040 Transcript missense_variant 2357/7720 1565/3681 522/1226 L/P cTt/cCt 1 -1 ATP13A3 HGNC HGNC:24113 protein_coding YES CCDS43187.1 ENSP00000416508 Q9H7F0 UPI000049DFC3 tolerated(0.21) 16/33 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF249,TIGRFAM_domain:TIGR01657,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF81660 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 22 194441456 194441456 A G 1 0 0 0 0 1 0 0 0 1277 86 3 5 5 ATP13A3 3 194441456 Missense_Mutation SNP A C3L-00973_T 52018759 194441456 3854103 5 7138 PDHA2 0 . GRCh38 4 95840359 95840359 + Missense_Mutation SNP G G A novel C3L-00973_T C3L-00973_N G G c.209G>A p.Arg70His p.R70H ENST00000295266 1/1 211 188 23 183 183 0 strelka-varscan-mutect PDHA2,missense_variant,p.Arg70His,ENST00000295266,NM_005390.4; A ENST00000295266 Transcript missense_variant 341/1456 209/1167 70/388 R/H cGc/cAc 1 1 PDHA2 HGNC HGNC:8807 protein_coding YES CCDS3644.1 ENSP00000295266 P29803 UPI0000130C31 NM_005390.4 deleterious(0) 1/1 hmmpanther:PTHR11516:SF27,hmmpanther:PTHR11516,Pfam_domain:PF00676,TIGRFAM_domain:TIGR03182,Gene3D:3.40.50.970,Superfamily_domains:SSF52518 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 22 95840359 95840359 G A 1 0 0 0 0 1 0 0 0 11753 1087 38 1 1 PDHA2 4 95840359 Missense_Mutation SNP G C3L-00973_T 95840359 94374196 6 7139 BBS7 0 . GRCh38 4 121828221 121828221 + Missense_Mutation SNP G G C novel C3L-00973_T C3L-00973_N G G c.1939C>G p.His647Asp p.H647D ENST00000264499 18/19 336 304 32 241 241 0 strelka-varscan-mutect BBS7,missense_variant,p.His647Asp,ENST00000264499,NM_176824.2;BBS7,missense_variant,p.His647Asp,ENST00000506636,NM_018190.3;BBS7,missense_variant,p.His70Asp,ENST00000507814,;CCNA2,upstream_gene_variant,,ENST00000274026,;CCNA2,upstream_gene_variant,,ENST00000618014,NM_001237.3; C ENST00000264499 Transcript missense_variant 2123/3752 1939/2148 647/715 H/D Cac/Gac 1 -1 BBS7 HGNC HGNC:18758 protein_coding YES CCDS3724.1 ENSP00000264499 Q8IWZ6 UPI00001684D7 NM_176824.2 deleterious(0.01) 18/19 hmmpanther:PTHR16074,hmmpanther:PTHR16074:SF4,PIRSF_domain:PIRSF011091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 22 121828221 121828221 G C 1 0 0 0 0 1 0 0 0 1488 1290 45 4 4 BBS7 4 121828221 Missense_Mutation SNP G C3L-00973_T 25987862 121828221 68386334 7 7140 CCDC110 0 . GRCh38 4 185462647 185462661 + In_Frame_Del DEL CTGACATTCTGCAAA CTGACATTCTGCAAA - novel C3L-00973_T C3L-00973_N CTGACATTCTGCAAA CTGACATTCTGCAAA c.219_233delTTTGCAGAATGTCAG p.Leu74_Ser78del p.L74_S78del ENST00000307588 4/7 222 206 16 178 178 0 sindel-varindel-pindel CCDC110,inframe_deletion,p.Leu74_Ser78del,ENST00000307588,NM_152775.3;CCDC110,inframe_deletion,p.Leu74_Ser78del,ENST00000393540,NM_001145411.1;CCDC110,inframe_deletion,p.Leu74_Ser78del,ENST00000510617,;CCDC110,inframe_deletion,p.Leu74_Ser78del,ENST00000506876,;CCDC110,inframe_deletion,p.Leu4_Ser8del,ENST00000507501,;CCDC110,inframe_deletion,p.Leu4_Ser8del,ENST00000506962,;CCDC110,upstream_gene_variant,,ENST00000508538,;CCDC110,inframe_deletion,p.Phe55_Gln59del,ENST00000510481,;CCDC110,3_prime_UTR_variant,,ENST00000504020,; - ENST00000307588 Transcript inframe_deletion 295-309/2898 219-233/2502 73-78/833 TLQNVS/T acTTTGCAGAATGTCAGc/acc 1 -1 CCDC110 HGNC HGNC:28504 protein_coding YES CCDS3843.1 ENSP00000306776 Q8TBZ0 UPI0000070BFC NM_152775.3 4/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF32 MODERATE 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.73038 0.9999997 1 1 1 0 - 7 5 22 185462647 185462647 CTGACATTCTGCAAA - 1 0 1 0 1 0 0 0 0 2441 811 28 0 0 CCDC110 4 185462647 In_Frame_Del DEL CTGACATTCTGCAAA C3L-00973_T 63634426 185462647 4751908 8 7141 C6orf163 0 . GRCh38 6 87356344 87356344 + Missense_Mutation SNP A A T novel C3L-00973_T C3L-00973_N A A c.395A>T p.Asp132Val p.D132V ENST00000388923 4/5 313 283 30 214 213 1 strelka-varscan-mutect C6orf163,missense_variant,p.Asp2Val,ENST00000608326,;C6orf163,missense_variant,p.Asp132Val,ENST00000388923,NM_001010868.2;SMIM8,intron_variant,,ENST00000369572,;RP1-102H19.7,upstream_gene_variant,,ENST00000623904,;C6orf163,upstream_gene_variant,,ENST00000608891,;C6orf163,non_coding_transcript_exon_variant,,ENST00000369574,;SMIM8,intron_variant,,ENST00000448282,; T ENST00000388923 Transcript missense_variant 646/1308 395/990 132/329 D/V gAt/gTt 1 1 C6orf163 HGNC HGNC:21403 protein_coding YES CCDS55042.1 ENSP00000373575 Q5TEZ5 UPI0000DBEE6F NM_001010868.2 deleterious(0.04) 4/5 hmmpanther:PTHR34645 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 22 87356344 87356344 A T 1 0 0 0 0 1 0 0 0 2121 333 12 4 4 C6orf163 6 87356344 Missense_Mutation SNP A C3L-00973_T 87356344 83449635 9 7142 MACC1 0 . GRCh38 7 20159595 20159595 + Missense_Mutation SNP C C A novel C3L-00973_T C3L-00973_N C C c.766G>T p.Asp256Tyr p.D256Y ENST00000400331 5/7 259 233 26 249 248 1 strelka-varscan-mutect MACC1,missense_variant,p.Asp256Tyr,ENST00000400331,NM_182762.3;MACC1,missense_variant,p.Asp256Tyr,ENST00000332878,;MACC1,missense_variant,p.Asp256Tyr,ENST00000589011,;MACC1,downstream_gene_variant,,ENST00000471019,; A ENST00000400331 Transcript missense_variant 1075/9159 766/2559 256/852 D/Y Gat/Tat 1 -1 MACC1 HGNC HGNC:30215 protein_coding YES CCDS5369.1 ENSP00000383185 Q6ZN28 UPI00001B2F47 NM_182762.3 deleterious(0.02) 5/7 Pfam_domain:PF00791,hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF1 MODERATE 1 SNV 2 1 PASS rs752730820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 22 20159595 20159595 C A 1 0 0 0 0 1 0 0 0 9059 826 29 2 2 MACC1 7 20159595 Missense_Mutation SNP C C3L-00973_T 20159595 139186378 10 7143 SHFM1 0 . GRCh38 7 96486236 96486236 + Missense_Mutation SNP G G T novel C3L-00973_T C3L-00973_N G G c.194C>A p.Ser65Tyr p.S65Y ENST00000615352 2/3 383 333 50 286 286 0 strelka-varscan-mutect SHFM1,missense_variant,p.Ser65Tyr,ENST00000356686,NM_001201450.1;SHFM1,missense_variant,p.Ser65Tyr,ENST00000615352,NM_001201451.1;SHFM1,non_coding_transcript_exon_variant,,ENST00000493858,;SHFM1,non_coding_transcript_exon_variant,,ENST00000611360,;SHFM1,3_prime_UTR_variant,,ENST00000466986,;SHFM1,downstream_gene_variant,,ENST00000613919,;SHFM1,downstream_gene_variant,,ENST00000617133,;SHFM1,downstream_gene_variant,,ENST00000618105,;SHFM1,downstream_gene_variant,,ENST00000619259,; T ENST00000615352 Transcript missense_variant 241/2637 194/357 65/118 S/Y tCc/tAc 1 -1 SHFM1 HGNC HGNC:10845 protein_coding YES CCDS75638.1 ENSP00000481021 B7ZVW6 UPI000189A9A3 NM_001201451.1 deleterious_low_confidence(0) 2/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 22 96486236 96486236 G T 1 0 0 0 0 1 0 0 0 14538 1174 41 2 2 SHFM1 7 96486236 Missense_Mutation SNP G C3L-00973_T 76326641 96486236 62859737 11 7144 PIK3CG 0 . GRCh38 7 106868111 106868111 + Missense_Mutation SNP C C T C3L-00973_T C3L-00973_N C C c.550C>T p.Arg184Cys p.R184C ENST00000359195 2/11 79 71 8 88 88 0 strelka-varscan-mutect PIK3CG,missense_variant,p.Arg184Cys,ENST00000359195,NM_002649.3;PIK3CG,missense_variant,p.Arg184Cys,ENST00000496166,NM_001282426.1;PIK3CG,missense_variant,p.Arg184Cys,ENST00000440650,NM_001282427.1;PIK3CG,intron_variant,,ENST00000473541,; T ENST00000359195 Transcript missense_variant 860/5377 550/3309 184/1102 R/C Cgc/Tgc COSM4992816 1 1 PIK3CG HGNC HGNC:8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 A0A024R720 UPI00000746B8 NM_002649.3 deleterious(0) 2/11 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34,Gene3D:3.10.20.90,Superfamily_domains:SSF54236 1 MODERATE 1 SNV 1 1 1 PASS rs1189118505 . 0 198 11 0 0 0 0 0 -16.9429 0.9999096 1 1 1 0 T 3 4 22 106868111 106868111 C T 1 0 0 0 0 1 0 0 0 12011 768 27 1 1 PIK3CG 7 106868111 Missense_Mutation SNP C C3L-00973_T 10381875 106868111 52477862 12 7145 BMP1 0 . GRCh38 8 22177954 22177954 + Missense_Mutation SNP C C T novel C3L-00973_T C3L-00973_N C C c.833C>T p.Ser278Phe p.S278F ENST00000306385 6/20 68 59 9 44 44 0 strelka-varscan-mutect BMP1,missense_variant,p.Ser278Phe,ENST00000306385,NM_006129.4;BMP1,missense_variant,p.Ser278Phe,ENST00000306349,NM_001199.3;BMP1,3_prime_UTR_variant,,ENST00000354870,;BMP1,downstream_gene_variant,,ENST00000397814,;BMP1,downstream_gene_variant,,ENST00000523849,;BMP1,downstream_gene_variant,,ENST00000521521,;BMP1,missense_variant,p.Ser278Phe,ENST00000520970,;BMP1,missense_variant,p.Ser278Phe,ENST00000471755,;BMP1,missense_variant,p.Ser278Phe,ENST00000521385,;BMP1,3_prime_UTR_variant,,ENST00000520626,;BMP1,3_prime_UTR_variant,,ENST00000520982,;BMP1,3_prime_UTR_variant,,ENST00000518913,;BMP1,3_prime_UTR_variant,,ENST00000483364,;BMP1,downstream_gene_variant,,ENST00000518656,;BMP1,upstream_gene_variant,,ENST00000523457,; T ENST00000306385 Transcript missense_variant 1503/4229 833/2961 278/986 S/F tCc/tTc 1 1 BMP1 HGNC HGNC:1067 protein_coding YES CCDS6026.1 ENSP00000305714 P13497 UPI0000049818 NM_006129.4 deleterious(0) 6/20 hmmpanther:PTHR10127:SF638,hmmpanther:PTHR10127,Pfam_domain:PF01400,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001199,Superfamily_domains:SSF55486,Prints_domain:PR00480 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.83553 1 1 1 1 0 T 3 4 22 22177954 22177954 C T 1 0 0 0 0 1 0 0 0 1611 869 30 3 3 BMP1 8 22177954 Missense_Mutation SNP C C3L-00973_T 22177954 122960682 13 7146 PXDNL 0 . GRCh38 8 51408882 51408882 + Silent SNP C C T rs570625073 C3L-00973_T C3L-00973_N C C c.2742G>A p.= p.S914S ENST00000356297 17/23 84 75 9 96 96 0 strelka-varscan-mutect PXDNL,synonymous_variant,p.=,ENST00000356297,NM_144651.4;PXDNL,synonymous_variant,p.=,ENST00000522933,;PXDNL,synonymous_variant,p.=,ENST00000522628,; T ENST00000356297 Transcript synonymous_variant 2843/4805 2742/4392 914/1463 S tcG/tcA rs570625073,COSM4719570,COSM4719571 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs570625073 . 0 204 6 0 0 0 0 0 -19.02914 0.9999999 1 1 1 0 T 2 4 22 51408882 51408882 C T 1 0 0 0 0 0 0 0 1 13002 639 23 1 1 PXDNL 8 51408882 Silent SNP C C3L-00973_T 29230928 51408882 93729754 14 7147 KIAA1217 0 . GRCh38 10 24543719 24543719 + Frame_Shift_Del DEL G G - novel C3L-00973_T C3L-00973_N G G c.4450delG p.Glu1484LysfsTer9 p.E1484Kfs*9 ENST00000376454 19/21 314 291 23 267 267 0 varindel-pindel KIAA1217,frameshift_variant,p.Glu1167LysfsTer9,ENST00000376451,;KIAA1217,frameshift_variant,p.Glu1484LysfsTer9,ENST00000376454,NM_019590.4;KIAA1217,frameshift_variant,p.Glu367LysfsTer9,ENST00000635163,;KIAA1217,intron_variant,,ENST00000376462,NM_001098500.2;KIAA1217,intron_variant,,ENST00000376452,NM_001282767.1;KIAA1217,intron_variant,,ENST00000458595,NM_001282768.1;KIAA1217,intron_variant,,ENST00000430453,;KIAA1217,intron_variant,,ENST00000396445,;KIAA1217,intron_variant,,ENST00000307544,NM_001282769.1;KIAA1217,intron_variant,,ENST00000396446,NM_001282770.1;KIAA1217,downstream_gene_variant,,ENST00000492009,; - ENST00000376454 Transcript frameshift_variant 4479/7381 4449/5832 1483/1943 E/X gaG/ga 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 19/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 22 24543719 24543719 G - 1 0 1 0 1 0 0 0 0 8109 991 35 0 0 KIAA1217 10 24543719 Frame_Shift_Del DEL G C3L-00973_T 24543719 109253703 15 7148 MRGPRX2 0 . GRCh38 11 19055704 19055704 + Silent SNP G G A novel C3L-00973_T C3L-00973_N G G c.699C>T p.= p.L233L ENST00000329773 2/2 255 229 26 206 206 0 strelka-varscan-mutect MRGPRX2,synonymous_variant,p.=,ENST00000329773,NM_001303615.1,NM_054030.3; A ENST00000329773 Transcript synonymous_variant 787/2036 699/993 233/330 L ctC/ctT 1 -1 MRGPRX2 HGNC HGNC:17983 protein_coding YES CCDS7847.1 ENSP00000333800 Q96LB1 UPI0000038C81 NM_001303615.1,NM_054030.3 2/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,Prints_domain:PR02108,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF35,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 22 19055704 19055704 G A 1 0 0 0 0 0 0 0 1 9734 1161 41 3 3 MRGPRX2 11 19055704 Silent SNP G C3L-00973_T 19055704 116030918 16 7149 RAG1 0 . GRCh38 11 36573919 36573919 + Frame_Shift_Del DEL C C - rs760237407 C3L-00973_T C3L-00973_N C C c.619delC p.His207ThrfsTer57 p.H207Tfs*57 ENST00000299440 2/2 273 236 37 247 247 0 sindel-varindel-pindel RAG1,frameshift_variant,p.His207ThrfsTer57,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,frameshift_variant,p.His207ThrfsTer57,ENST00000534663,; - ENST00000299440 Transcript frameshift_variant 727/6564 615/3132 205/1043 H/X caC/ca rs760237407,COSM4746985 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 2/2 Pfam_domain:PF12560,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 0,1 HIGH 1 deletion 1 4 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 22 36573919 36573919 C - 1 0 1 0 1 0 0 0 0 13164 506 18 0 0 RAG1 11 36573919 Frame_Shift_Del DEL C C3L-00973_T 17518215 36573919 98512703 17 7150 DSCAML1 0 . GRCh38 11 117524890 117524890 + Silent SNP C C T novel C3L-00973_T C3L-00973_N C C c.1032G>A p.= p.L344L ENST00000321322 5/33 302 268 34 211 211 0 strelka-varscan-mutect DSCAML1,synonymous_variant,p.=,ENST00000321322,NM_020693.3;DSCAML1,synonymous_variant,p.=,ENST00000527706,; T ENST00000321322 Transcript synonymous_variant 1034/6899 1032/6342 344/2113 L ttG/ttA 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 5/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 22 117524890 117524890 C T 1 0 0 0 0 0 0 0 1 4590 709 25 3 3 DSCAML1 11 117524890 Silent SNP C C3L-00973_T 80950971 117524890 17561732 18 7151 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3L-00973_T C3L-00973_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 512 374 138 268 268 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 22 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3L-00973_T 25245350 108029959 19 7152 UBE3B 0 . GRCh38 12 109483923 109483923 + Missense_Mutation SNP G G C rs755365552 C3L-00973_T C3L-00973_N G G c.224G>C p.Cys75Ser p.C75S ENST00000342494 4/28 177 160 17 133 133 0 strelka-varscan-mutect UBE3B,missense_variant,p.Cys75Ser,ENST00000342494,NM_130466.3;UBE3B,missense_variant,p.Cys75Ser,ENST00000434735,NM_183415.2;UBE3B,missense_variant,p.Cys75Ser,ENST00000537063,;UBE3B,missense_variant,p.Cys75Ser,ENST00000539599,;UBE3B,missense_variant,p.Cys75Ser,ENST00000540230,;UBE3B,missense_variant,p.Cys75Ser,ENST00000340074,NM_001270449.1;UBE3B,missense_variant,p.Cys75Ser,ENST00000536398,NM_001270450.1,NM_001270451.1;UBE3B,missense_variant,p.Cys75Ser,ENST00000449510,;UBE3B,non_coding_transcript_exon_variant,,ENST00000539843,; C ENST00000342494 Transcript missense_variant 819/5722 224/3207 75/1068 C/S tGt/tCt rs755365552 1 1 UBE3B HGNC HGNC:13478 protein_coding YES CCDS9129.1 ENSP00000340596 Q7Z3V4 A0A024RBI2 UPI000013DC3B NM_130466.3 tolerated(0.76) 4/28 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF352 MODERATE 1 SNV 1 1 PASS rs755365552 . 0 208 0 2 0 0 0 0 -19.99979 0.9999998 1 1 1 0 C 3 2 22 109483923 109483923 G C 1 0 0 0 0 1 0 0 0 17403 1377 48 4 4 UBE3B 12 109483923 Missense_Mutation SNP G C3L-00973_T 84238573 109483923 23791386 20 7153 RB1 0 . GRCh38 13 48453046 48453049 + Frame_Shift_Del DEL TGAT TGAT - novel C3L-00973_T C3L-00973_N TGAT TGAT c.1749_1752delTGAT p.Asp584ThrfsTer26 p.D584Tfs*26 ENST00000267163 18/27 309 282 27 254 254 0 sindel-varindel-pindel RB1,frameshift_variant,p.Asp584ThrfsTer26,ENST00000267163,NM_000321.2;RB1,non_coding_transcript_exon_variant,,ENST00000480491,; - ENST00000267163 Transcript frameshift_variant 1887-1890/4840 1749-1752/2787 583-584/928 TD/X acTGAT/ac 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 18/27 hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 22 48453046 48453046 TGAT - 1 0 1 0 1 0 0 0 0 13259 1567 55 0 0 RB1 13 48453046 Frame_Shift_Del DEL TGAT C3L-00973_T 48453046 65911282 21 7154 NKX2-1 0 . GRCh38 14 36517564 36517571 + Frame_Shift_Del DEL GGCGCGGG GGCGCGGG - novel C3L-00973_T C3L-00973_N GGCGCGGG GGCGCGGG c.913_920delCCCGCGCC p.Pro305GlyfsTer131 p.P305Gfs*131 ENST00000354822 3/3 74 65 9 134 134 0 sindel-varindel-pindel NKX2-1,frameshift_variant,p.Pro275GlyfsTer131,ENST00000518149,;NKX2-1,frameshift_variant,p.Pro275GlyfsTer131,ENST00000498187,NM_003317.3;NKX2-1,frameshift_variant,p.Pro305GlyfsTer131,ENST00000354822,NM_001079668.2;NKX2-1,frameshift_variant,p.Pro275GlyfsTer?,ENST00000522719,;SFTA3,upstream_gene_variant,,ENST00000518529,NM_001101341.1;NKX2-1,downstream_gene_variant,,ENST00000546983,;RP11-964E11.3,intron_variant,,ENST00000634305,;NKX2-1-AS1,upstream_gene_variant,,ENST00000521292,;RP11-896J10.3,intron_variant,,ENST00000521945,;SFTA3,upstream_gene_variant,,ENST00000518987,;SFTA3,upstream_gene_variant,,ENST00000521114,;SFTA3,upstream_gene_variant,,ENST00000418548,;SFTA3,upstream_gene_variant,,ENST00000518446,;SFTA3,upstream_gene_variant,,ENST00000518002,;SFTA3,upstream_gene_variant,,ENST00000524122,; - ENST00000354822 Transcript frameshift_variant 1012-1019/2191 913-920/1206 305-307/401 PAP/X CCCGCGCCg/g 1 -1 NKX2-1 HGNC HGNC:11825 protein_coding YES CCDS41945.1 ENSP00000346879 P43699 UPI000007328C NM_001079668.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF33 HIGH 1 deletion 1 1 PASS . . 0 205 3 2 0 0 0 0 -15.40848 0.9999903 1 1 1 0 - 7 5 22 36517564 36517564 GGCGCGGG - 1 0 1 0 1 0 0 0 0 10485 1116 39 0 0 NKX2-1 14 36517564 Frame_Shift_Del DEL GGCGCGGG C3L-00973_T 36517564 70526154 22 7155 SMCR8 0 . GRCh38 17 18316552 18316552 + Missense_Mutation SNP T T C novel C3L-00973_T C3L-00973_N T T c.763T>C p.Ser255Pro p.S255P ENST00000406438 1/2 216 189 27 237 237 0 strelka-varscan-mutect SMCR8,missense_variant,p.Ser255Pro,ENST00000406438,NM_144775.2;TOP3A,upstream_gene_variant,,ENST00000542570,NM_004618.3;TOP3A,upstream_gene_variant,,ENST00000321105,;TOP3A,upstream_gene_variant,,ENST00000580095,;TOP3A,upstream_gene_variant,,ENST00000582230,;TOP3A,upstream_gene_variant,,ENST00000584669,;TOP3A,upstream_gene_variant,,ENST00000584887,;TOP3A,upstream_gene_variant,,ENST00000584582,;TOP3A,upstream_gene_variant,,ENST00000582981,;TOP3A,upstream_gene_variant,,ENST00000472959,;TOP3A,upstream_gene_variant,,ENST00000461127,;TOP3A,upstream_gene_variant,,ENST00000583328,;TOP3A,upstream_gene_variant,,ENST00000585031,;TOP3A,upstream_gene_variant,,ENST00000580713,;RPL7AP65,downstream_gene_variant,,ENST00000418183,;RPL21P121,downstream_gene_variant,,ENST00000439258,; C ENST00000406438 Transcript missense_variant 1243/8279 763/2814 255/937 S/P Tca/Cca 1 1 SMCR8 HGNC HGNC:17921 protein_coding YES CCDS11195.2 ENSP00000385025 Q8TEV9 UPI0000E0322D NM_144775.2 deleterious(0.01) 1/2 hmmpanther:PTHR31334:SF1,hmmpanther:PTHR31334 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 22 18316552 18316552 T C 1 0 0 0 0 1 0 0 0 15087 1551 54 5 5 SMCR8 17 18316552 Missense_Mutation SNP T C3L-00973_T 18316552 64940889 23 7156 SIRPD 0 . GRCh38 20 1534426 1534426 + Silent SNP T T C novel C3L-00973_T C3L-00973_N T T c.593A>G p.= p.*198* ENST00000381623 4/4 293 266 27 194 194 0 strelka-varscan-mutect SIRPD,stop_retained_variant,p.=,ENST00000381623,NM_178460.2;SIRPD,stop_retained_variant,p.=,ENST00000381621,;SIRPD,stop_retained_variant,p.=,ENST00000429387,;RP4-576H24.2,intron_variant,,ENST00000453770,; C ENST00000381623 Transcript stop_retained_variant 1783/1958 593/594 198/197 * tAa/tGa 1 -1 SIRPD HGNC HGNC:16248 protein_coding YES CCDS13018.1 ENSP00000371036 Q9H106 UPI000013CBD7 NM_178460.2 4/4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 22 1534426 1534426 T C 1 0 0 0 0 0 0 0 1 14598 1761 61 5 5 SIRPD 20 1534426 Silent SNP T C3L-00973_T 1534426 62909741 24 7157 NRK 0 . GRCh38 X 105923148 105923148 + Missense_Mutation SNP T T C novel C3L-00973_T C3L-00973_N T T c.2641T>C p.Ser881Pro p.S881P ENST00000243300 18/29 97 61 36 71 71 0 strelka-varscan-mutect NRK,missense_variant,p.Ser881Pro,ENST00000243300,NM_198465.3;NRK,3_prime_UTR_variant,,ENST00000428173,; C ENST00000243300 Transcript missense_variant 2944/8062 2641/4749 881/1582 S/P Tca/Cca 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 tolerated(0.05) 18/29 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 22 105923148 105923148 T C 1 0 0 0 0 1 0 0 0 10713 1435 50 5 5 NRK 23 105923148 Missense_Mutation SNP T C3L-00973_T 105923148 50117747 25 7158 MEGF6 0 . GRCh38 1 3499159 3499159 + Missense_Mutation SNP T T A novel C3L-01330_T C3L-01330_N T T c.3073A>T p.Met1025Leu p.M1025L ENST00000356575 24/37 327 307 20 256 256 0 strelka-varscan-mutect MEGF6,missense_variant,p.Met1025Leu,ENST00000356575,NM_001409.3;MEGF6,intron_variant,,ENST00000294599,;MEGF6,upstream_gene_variant,,ENST00000491842,;MEGF6,missense_variant,p.Met1032Leu,ENST00000485002,;MEGF6,upstream_gene_variant,,ENST00000475790,;MEGF6,upstream_gene_variant,,ENST00000461795,; A ENST00000356575 Transcript missense_variant 3300/5455 3073/4626 1025/1541 M/L Atg/Ttg 1 -1 MEGF6 HGNC HGNC:3232 protein_coding YES CCDS41237.1 ENSP00000348982 O75095 UPI0000DACACB NM_001409.3 deleterious(0.05) 24/37 PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF106,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00180,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -4.986336 0.9831472 1 1 1 0 A 3 1 23 3499159 3499159 T A 1 0 0 0 0 1 0 0 0 9402 1435 50 4 4 MEGF6 1 3499159 Missense_Mutation SNP T C3L-01330_T 3499159 245457263 1 7159 GRIK3 0 . GRCh38 1 36872252 36872252 + Missense_Mutation SNP C C T rs773388016 C3L-01330_T C3L-01330_N C C c.668G>A p.Arg223Gln p.R223Q ENST00000373091 4/16 144 133 11 91 91 0 strelka-varscan-mutect GRIK3,missense_variant,p.Arg223Gln,ENST00000373091,NM_000831.3;GRIK3,missense_variant,p.Arg223Gln,ENST00000373093,; T ENST00000373091 Transcript missense_variant 685/9101 668/2760 223/919 R/Q cGa/cAa rs773388016 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 tolerated(0.32) 4/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs773388016 . 0 206 4 0 0 0 0 0 -19.92434 1 1 1 1 0 T 3 4 23 36872252 36872252 C T 1 0 0 0 0 1 0 0 0 6657 884 31 1 1 GRIK3 1 36872252 Missense_Mutation SNP C C3L-01330_T 33373093 36872252 212084170 2 7160 JUN 0 . GRCh38 1 58782841 58782842 + Frame_Shift_Ins INS - - C novel C3L-01330_T C3L-01330_N - - c.229dupG p.Glu77GlyfsTer30 p.E77Gfs*30 ENST00000371222 1/1 87 72 15 86 86 0 sindel-varindel-pindel JUN,frameshift_variant,p.Glu77GlyfsTer30,ENST00000371222,NM_002228.3;LINC01135,upstream_gene_variant,,ENST00000419531,; C ENST00000371222 Transcript frameshift_variant 1486-1487/3540 229-230/996 77/331 E/GX gag/gGag 1 -1 JUN HGNC HGNC:6204 protein_coding YES CCDS610.1 ENSP00000360266 P05412 UPI000000D908 NM_002228.3 1/1 Pfam_domain:PF03957,hmmpanther:PTHR11462,hmmpanther:PTHR11462:SF8 HIGH insertion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 23 58782841 58782841 - C 1 0 1 1 0 0 0 0 0 7879 1551 54 0 0 JUN 1 58782841 Frame_Shift_Ins INS - C3L-01330_T 21910589 58782841 190173581 3 7161 OR2T6 0 . GRCh38 1 248388468 248388468 + Missense_Mutation SNP C C G rs867677850 C3L-01330_T C3L-01330_N C C c.860C>G p.Pro287Arg p.P287R ENST00000355728 1/1 28 24 4 37 37 0 strelka-varscan OR2T6,missense_variant,p.Pro287Arg,ENST00000355728,NM_001005471.1; G ENST00000355728 Transcript missense_variant 860/927 860/927 287/308 P/R cCt/cGt rs867677850 1 1 OR2T6 HGNC HGNC:15018 protein_coding YES CCDS31114.1 ENSP00000347965 Q8NHC8 UPI0000199147 NM_001005471.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF57,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -11.65419 1 1 1 1 0 G 3 3 23 248388468 248388468 C G 1 0 0 0 0 1 0 0 0 11106 681 24 4 4 OR2T6 1 248388468 Missense_Mutation SNP C C3L-01330_T 189605627 248388468 567954 4 7162 TANC1 0 . GRCh38 2 159229671 159229671 + Silent SNP G G A novel C3L-01330_T C3L-01330_N G G c.4245G>A p.= p.E1415E ENST00000263635 27/27 272 185 87 299 299 0 strelka-varscan TANC1,synonymous_variant,p.=,ENST00000263635,NM_033394.2,NM_001145909.1;TANC1,intron_variant,,ENST00000454300,;TANC1,non_coding_transcript_exon_variant,,ENST00000496406,;TANC1,non_coding_transcript_exon_variant,,ENST00000470074,; A ENST00000263635 Transcript synonymous_variant 4482/7470 4245/5586 1415/1861 E gaG/gaA 1 1 TANC1 HGNC HGNC:29364 protein_coding YES CCDS42766.1 ENSP00000263635 Q9C0D5 UPI0000421D80 NM_033394.2,NM_001145909.1 27/27 Gene3D:1.25.40.10,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF23,Superfamily_domains:SSF48452 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 23 159229671 159229671 G A 1 0 0 0 0 0 0 0 1 15941 991 35 3 3 TANC1 2 159229671 Silent SNP G C3L-01330_T 159229671 82963858 5 7163 CD302 0 . GRCh38 2 159780116 159780116 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.5281G>A p.Asp1761Asn p.D1761N ENST00000504764 37/39 110 94 16 148 148 0 strelka-varscan LY75-CD302,missense_variant,p.Asp1761Asn,ENST00000504764,NM_001198759.1;LY75-CD302,missense_variant,p.Asp1705Asn,ENST00000505052,NM_001198760.1;CD302,missense_variant,p.Asp83Asn,ENST00000553424,NM_001198764.1;CD302,missense_variant,p.Asp120Asn,ENST00000259053,NM_014880.4;CD302,intron_variant,,ENST00000429078,NM_001198763.1;CD302,non_coding_transcript_exon_variant,,ENST00000480212,; T ENST00000504764 Transcript missense_variant 5309/5650 5281/5622 1761/1873 D/N Gat/Aat 1 -1 LY75-CD302 HGNC HGNC:38828 protein_coding YES CCDS56141.1 ENSP00000423463 UPI00018817E3 NM_001198759.1 tolerated(0.35) 37/39 Low_complexity_(Seg):seg,PROSITE_profiles:PS50041,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 159780116 159780116 C T 1 0 0 0 0 1 0 0 0 2707 826 29 3 3 CD302 2 159780116 Missense_Mutation SNP C C3L-01330_T 550445 159780116 82413413 6 7164 CPS1 0 . GRCh38 2 210608492 210608492 + Missense_Mutation SNP G G A rs766970243 C3L-01330_T C3L-01330_N G G c.2342G>A p.Arg781His p.R781H ENST00000430249 20/39 267 222 45 272 272 0 strelka-varscan-mutect CPS1,missense_variant,p.Arg775His,ENST00000233072,NM_001875.4;CPS1,missense_variant,p.Arg781His,ENST00000430249,NM_001122633.2;CPS1,missense_variant,p.Arg324His,ENST00000451903,NM_001122634.3;CPS1,downstream_gene_variant,,ENST00000467353,; A ENST00000430249 Transcript missense_variant 2397/5698 2342/4521 781/1506 R/H cGc/cAc rs766970243,COSM4090801,COSM4090802 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 deleterious(0) 20/39 hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,TIGRFAM_domain:TIGR01369,Gene3D:3.30.470.20,Superfamily_domains:SSF56059 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766970243 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 210608492 210608492 G A 1 0 0 0 0 1 0 0 0 3619 1087 38 1 1 CPS1 2 210608492 Missense_Mutation SNP G C3L-01330_T 50828376 210608492 31585037 7 7165 OBSL1 0 . GRCh38 2 219552661 219552661 + Missense_Mutation SNP A A C rs769360822 C3L-01330_T C3L-01330_N A A c.5183T>G p.Val1728Gly p.V1728G ENST00000404537 18/21 195 156 39 155 154 1 strelka-varscan-mutect OBSL1,missense_variant,p.Val1728Gly,ENST00000404537,NM_015311.2;OBSL1,missense_variant,p.Val1636Gly,ENST00000373876,;OBSL1,downstream_gene_variant,,ENST00000603926,NM_001173431.1;TMEM198,downstream_gene_variant,,ENST00000344458,NM_001303098.1;TMEM198,downstream_gene_variant,,ENST00000373883,NM_001005209.2;OBSL1,downstream_gene_variant,,ENST00000604031,;OBSL1,downstream_gene_variant,,ENST00000456147,;TMEM198,downstream_gene_variant,,ENST00000421791,;MIR3132,upstream_gene_variant,,ENST00000581997,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,;OBSL1,non_coding_transcript_exon_variant,,ENST00000489804,;OBSL1,upstream_gene_variant,,ENST00000462534,;OBSL1,downstream_gene_variant,,ENST00000472388,;OBSL1,downstream_gene_variant,,ENST00000596474,; C ENST00000404537 Transcript missense_variant 5240/5841 5183/5691 1728/1896 V/G gTg/gGg rs769360822 1 -1 OBSL1 HGNC HGNC:29092 protein_coding YES CCDS46520.1 ENSP00000385636 O75147 UPI0000E07EA0 NM_015311.2 deleterious(0.02) 18/21 hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs769360822 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 219552661 219552661 A C 1 0 0 0 0 1 0 0 0 10890 159 6 5 5 OBSL1 2 219552661 Missense_Mutation SNP A C3L-01330_T 8944169 219552661 22640868 8 7166 CACNA2D2 0 . GRCh38 3 50384214 50384214 + Missense_Mutation SNP T T C novel C3L-01330_T C3L-01330_N T T c.634A>G p.Thr212Ala p.T212A ENST00000479441 6/39 105 99 6 127 127 0 strelka-mutect CACNA2D2,missense_variant,p.Thr212Ala,ENST00000266039,NM_001005505.2;CACNA2D2,missense_variant,p.Thr212Ala,ENST00000423994,;CACNA2D2,missense_variant,p.Thr212Ala,ENST00000429770,;CACNA2D2,missense_variant,p.Thr143Ala,ENST00000360963,NM_001291101.1;CACNA2D2,missense_variant,p.Thr212Ala,ENST00000424201,NM_006030.3;CACNA2D2,missense_variant,p.Thr212Ala,ENST00000479441,NM_001174051.2; C ENST00000479441 Transcript missense_variant 634/3453 634/3453 212/1150 T/A Acg/Gcg 1 -1 CACNA2D2 HGNC HGNC:1400 protein_coding YES CCDS54588.1 ENSP00000418081 Q9NY47 UPI0000E5A6AF NM_001174051.2 deleterious(0.01) 6/39 Pfam_domain:PF08399,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 50384214 50384214 T C 1 0 0 0 0 1 0 0 0 2237 1638 57 5 5 CACNA2D2 3 50384214 Missense_Mutation SNP T C3L-01330_T 50384214 147911345 9 7167 ALCAM 0 . GRCh38 3 105545258 105545258 + Missense_Mutation SNP A A T novel C3L-01330_T C3L-01330_N A A c.1027A>T p.Thr343Ser p.T343S ENST00000306107 9/16 323 284 39 337 337 0 strelka-varscan-mutect ALCAM,missense_variant,p.Thr343Ser,ENST00000306107,NM_001627.3,NM_001243281.1;ALCAM,missense_variant,p.Thr343Ser,ENST00000472644,NM_001243280.1;ALCAM,missense_variant,p.Thr104Ser,ENST00000465413,;ALCAM,missense_variant,p.Thr292Ser,ENST00000486979,;ALCAM,non_coding_transcript_exon_variant,,ENST00000481337,;ALCAM,non_coding_transcript_exon_variant,,ENST00000491388,;ALCAM,upstream_gene_variant,,ENST00000489178,; T ENST00000306107 Transcript missense_variant 1527/4701 1027/1752 343/583 T/S Act/Tct 1 1 ALCAM HGNC HGNC:400 protein_coding YES CCDS33810.1 ENSP00000305988 Q13740 UPI0000209ECA NM_001627.3,NM_001243281.1 deleterious(0.04) 9/16 hmmpanther:PTHR11973,hmmpanther:PTHR11973:SF2,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 105545258 105545258 A T 1 0 0 0 0 1 0 0 0 587 275 10 4 4 ALCAM 3 105545258 Missense_Mutation SNP A C3L-01330_T 55161044 105545258 92750301 10 7168 MAP1B 0 . GRCh38 5 72199901 72199901 + Silent SNP C C T rs77733766 C3L-01330_T C3L-01330_N C C c.6546C>T p.= p.D2182D ENST00000296755 5/7 198 186 12 214 214 0 strelka-mutect MAP1B,synonymous_variant,p.=,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; T ENST00000296755 Transcript synonymous_variant 6844/12036 6546/7407 2182/2468 D gaC/gaT rs77733766,COSM3856179 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 5/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 0,1 LOW 1 SNV 2 0,1 1 PASS rs77733766 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 72199901 72199901 C T 1 0 0 0 0 0 0 0 1 9151 535 19 1 1 MAP1B 5 72199901 Silent SNP C C3L-01330_T 72199901 109338358 11 7169 TMED7 0 . GRCh38 5 115620459 115620459 + Silent SNP C C T novel C3L-01330_T C3L-01330_N C C c.414G>A p.= p.E138E ENST00000456936 2/3 42 38 4 33 33 0 strelka-mutect TMED7,synonymous_variant,p.=,ENST00000456936,NM_181836.5;TMED7-TICAM2,synonymous_variant,p.=,ENST00000282382,NM_001164468.3;TMED7-TICAM2,synonymous_variant,p.=,ENST00000333314,NM_001164469.3;TMED7,downstream_gene_variant,,ENST00000508420,;AC010226.4,non_coding_transcript_exon_variant,,ENST00000515570,;AC010226.4,downstream_gene_variant,,ENST00000508517,;TMED7,non_coding_transcript_exon_variant,,ENST00000503010,;TMED7-TICAM2,upstream_gene_variant,,ENST00000514548,; T ENST00000456936 Transcript synonymous_variant 795/3757 414/675 138/224 E gaG/gaA 1 -1 TMED7 HGNC HGNC:24253 protein_coding YES CCDS4120.1 ENSP00000405926 Q9Y3B3 UPI000007008A NM_181836.5 2/3 hmmpanther:PTHR22811:SF49,hmmpanther:PTHR22811,Pfam_domain:PF01105,SMART_domains:SM01190 LOW 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -11.0515 1 1 1 1 0 T 2 4 23 115620459 115620459 C T 1 0 0 0 0 0 0 0 1 16454 912 32 3 3 TMED7 5 115620459 Silent SNP C C3L-01330_T 43420558 115620459 65917800 12 7170 ETF1 0 . GRCh38 5 138511197 138511197 + Missense_Mutation SNP C C A novel C3L-01330_T C3L-01330_N C C c.866G>T p.Arg289Leu p.R289L ENST00000360541 8/11 92 58 34 82 82 0 strelka-varscan-mutect ETF1,missense_variant,p.Arg256Leu,ENST00000499810,NM_001256302.1,NM_001291975.1,NM_001291974.1;ETF1,missense_variant,p.Arg289Leu,ENST00000360541,NM_004730.3;ETF1,missense_variant,p.Arg275Leu,ENST00000503014,NM_001282185.1;ETF1,downstream_gene_variant,,ENST00000572514,;ETF1,downstream_gene_variant,,ENST00000507939,;ETF1,non_coding_transcript_exon_variant,,ENST00000506345,;ETF1,downstream_gene_variant,,ENST00000512198,;ETF1,downstream_gene_variant,,ENST00000503183,; A ENST00000360541 Transcript missense_variant 1088/3742 866/1314 289/437 R/L cGa/cTa 1 -1 ETF1 HGNC HGNC:3477 protein_coding YES CCDS4207.1 ENSP00000353741 P62495 UPI00001110CB NM_004730.3 deleterious(0.05) 8/11 hmmpanther:PTHR10113,TIGRFAM_domain:TIGR03676,Gene3D:3.30.1330.30,Pfam_domain:PF03465,Superfamily_domains:SSF55315 MODERATE 1 SNV 1 1 PASS rs1435593497 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 138511197 138511197 C A 1 0 0 0 0 1 0 0 0 5130 898 31 1 1 ETF1 5 138511197 Missense_Mutation SNP C C3L-01330_T 22890738 138511197 43027062 13 7171 ZSCAN31 0 . GRCh38 6 28326540 28326540 + Missense_Mutation SNP T T A novel C3L-01330_T C3L-01330_N T T c.847A>T p.Asn283Tyr p.N283Y ENST00000414429 8/8 183 151 32 159 159 0 strelka-varscan-mutect ZSCAN31,missense_variant,p.Asn283Tyr,ENST00000414429,NM_001135215.1;ZSCAN31,missense_variant,p.Asn283Tyr,ENST00000396838,NM_145909.2;ZSCAN31,missense_variant,p.Asn283Tyr,ENST00000439158,NM_001135216.1;ZSCAN31,missense_variant,p.Asn124Tyr,ENST00000611469,NM_001243242.1,NM_001243244.1;ZSCAN31,missense_variant,p.Asn283Tyr,ENST00000344279,NM_030899.4,NM_001243241.1;ZSCAN31,missense_variant,p.Asn124Tyr,ENST00000446474,NM_001243243.1;ZSCAN31,missense_variant,p.Asn124Tyr,ENST00000435857,;ZSCAN31,downstream_gene_variant,,ENST00000453745,;ZSCAN31,downstream_gene_variant,,ENST00000446222,;ZSCAN31,downstream_gene_variant,,ENST00000434036,;ZSCAN31,downstream_gene_variant,,ENST00000439636,;ZSCAN31,downstream_gene_variant,,ENST00000447021,;ZSCAN31,downstream_gene_variant,,ENST00000439628,;ZSCAN31,downstream_gene_variant,,ENST00000426756,;ZSCAN31,downstream_gene_variant,,ENST00000426434,;ZSCAN31,downstream_gene_variant,,ENST00000414431,;ZSCAN31,downstream_gene_variant,,ENST00000444081,;ZSCAN31,non_coding_transcript_exon_variant,,ENST00000481934,; A ENST00000414429 Transcript missense_variant 1751/3551 847/1221 283/406 N/Y Aat/Tat 1 -1 ZSCAN31 HGNC HGNC:14097 protein_coding YES CCDS4649.1 ENSP00000390076 Q96LW9 A0A024RCL4 UPI000013C358 NM_001135215.1 deleterious(0.01) 8/8 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF48,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 28326540 28326540 T A 1 0 0 0 0 1 0 0 0 18834 1783 62 4 4 ZSCAN31 6 28326540 Missense_Mutation SNP T C3L-01330_T 28326540 142479439 14 7172 PRDM1 0 . GRCh38 6 106088291 106088291 + Missense_Mutation SNP G G A rs762587225 C3L-01330_T C3L-01330_N G G c.133G>A p.Asp45Asn p.D45N ENST00000369096 2/7 315 292 23 338 338 0 strelka-varscan PRDM1,missense_variant,p.Asp45Asn,ENST00000369096,NM_001198.3;PRDM1,missense_variant,p.Asp9Asn,ENST00000369091,;PRDM1,missense_variant,p.Asp9Asn,ENST00000424894,;ATG5,intron_variant,,ENST00000636437,;ATG5,intron_variant,,ENST00000636335,;PRDM1,upstream_gene_variant,,ENST00000489365,; A ENST00000369096 Transcript missense_variant 367/5164 133/2478 45/825 D/N Gat/Aat rs762587225 1 1 PRDM1 HGNC HGNC:9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 UPI0000D49069 NM_001198.3 deleterious(0) 2/7 PIRSF_domain:PIRSF013212 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 106088291 106088291 G A 1 0 0 0 0 1 0 0 0 12581 1174 41 3 3 PRDM1 6 106088291 Missense_Mutation SNP G C3L-01330_T 77761751 106088291 64717688 15 7173 ROS1 0 . GRCh38 6 117386964 117386964 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.2050G>A p.Asp684Asn p.D684N ENST00000368508 14/43 91 82 9 102 102 0 strelka-varscan ROS1,missense_variant,p.Asp684Asn,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Asp679Asn,ENST00000368507,;RP1-179P9.3,intron_variant,,ENST00000467125,; T ENST00000368508 Transcript missense_variant 2249/7435 2050/7044 684/2347 D/N Gat/Aat 1 -1 ROS1 HGNC HGNC:10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 tolerated(0.12) 14/43 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 117386964 117386964 C T 1 0 0 0 0 1 0 0 0 13708 913 32 3 3 ROS1 6 117386964 Missense_Mutation SNP C C3L-01330_T 11298673 117386964 53419015 16 7174 RNF216 0 . GRCh38 7 5741798 5741798 + Silent SNP T T C novel C3L-01330_T C3L-01330_N T T c.219A>G p.= p.R73R ENST00000389902 4/17 107 97 10 84 84 0 strelka-varscan-mutect RNF216,synonymous_variant,p.=,ENST00000389902,NM_207111.3;RNF216,intron_variant,,ENST00000425013,NM_207116.2;RNF216,intron_variant,,ENST00000389900,;RNF216,intron_variant,,ENST00000411812,;RNF216,upstream_gene_variant,,ENST00000479541,; C ENST00000389902 Transcript synonymous_variant 487/3293 219/2772 73/923 R agA/agG 1 -1 RNF216 HGNC HGNC:21698 protein_coding YES CCDS34594.1 ENSP00000374552 Q9NWF9 UPI000013F5B3 NM_207111.3 4/17 hmmpanther:PTHR22770,hmmpanther:PTHR22770:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 23 5741798 5741798 T C 1 0 0 0 0 0 0 0 1 13659 1432 50 5 5 RNF216 7 5741798 Silent SNP T C3L-01330_T 5741798 153604175 17 7175 THSD7A 0 . GRCh38 7 11411265 11411265 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.3740G>A p.Arg1247Lys p.R1247K ENST00000423059 19/28 137 125 12 132 132 0 strelka-varscan-mutect THSD7A,missense_variant,p.Arg1247Lys,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Arg1247Lys,ENST00000617773,;AC004538.3,intron_variant,,ENST00000445839,;AC004160.4,intron_variant,,ENST00000425837,; T ENST00000423059 Transcript missense_variant 3992/10663 3740/4974 1247/1657 R/K aGg/aAg 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 deleterious(0) 19/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 11411265 11411265 C T 1 0 0 0 0 1 0 0 0 16313 681 24 3 3 THSD7A 7 11411265 Missense_Mutation SNP C C3L-01330_T 5669467 11411265 147934708 18 7176 MYO1G 0 . GRCh38 7 44965701 44965701 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.2317G>A p.Val773Met p.V773M ENST00000258787 17/22 191 164 27 205 205 0 strelka-varscan MYO1G,missense_variant,p.Val773Met,ENST00000258787,NM_033054.2;RP4-647J21.1,upstream_gene_variant,,ENST00000568457,;MYO1G,3_prime_UTR_variant,,ENST00000495831,;MYO1G,non_coding_transcript_exon_variant,,ENST00000488554,;MYO1G,non_coding_transcript_exon_variant,,ENST00000463516,;MYO1G,non_coding_transcript_exon_variant,,ENST00000483585,;MYO1G,downstream_gene_variant,,ENST00000480503,;MYO1G,downstream_gene_variant,,ENST00000464434,; T ENST00000258787 Transcript missense_variant 2454/3267 2317/3057 773/1018 V/M Gtg/Atg 1 -1 MYO1G HGNC HGNC:13880 protein_coding YES CCDS34629.1 ENSP00000258787 B0I1T2 UPI00001D747C NM_033054.2 tolerated(0.1) 17/22 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 44965701 44965701 C T 1 0 0 0 0 1 0 0 0 10075 478 17 3 3 MYO1G 7 44965701 Missense_Mutation SNP C C3L-01330_T 33554436 44965701 114380272 19 7177 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3L-01330_T C3L-01330_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 496 389 107 396 396 0 strelka-varscan EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 23 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3L-01330_T 10226121 55191822 104154151 20 7178 TPK1 0 . GRCh38 7 144453554 144453554 + Missense_Mutation SNP G G C novel C3L-01330_T C3L-01330_N G G c.723C>G p.Ile241Met p.I241M ENST00000360057 9/9 128 119 9 129 129 0 strelka-varscan-mutect TPK1,missense_variant,p.Ile241Met,ENST00000360057,NM_022445.3;TPK1,missense_variant,p.Ile192Met,ENST00000378099,NM_001042482.1;TPK1,missense_variant,p.Ile187Met,ENST00000538212,;RNU6ATAC40P,downstream_gene_variant,,ENST00000408580,;TPK1,non_coding_transcript_exon_variant,,ENST00000547966,;TPK1,3_prime_UTR_variant,,ENST00000482940,;TPK1,3_prime_UTR_variant,,ENST00000378098,; C ENST00000360057 Transcript missense_variant 826/2439 723/732 241/243 I/M atC/atG 1 -1 TPK1 HGNC HGNC:17358 protein_coding YES CCDS5888.1 ENSP00000353165 Q9H3S4 A0A090N8Y0 UPI000004FD50 NM_022445.3 deleterious(0) 9/9 hmmpanther:PTHR13622,PIRSF_domain:PIRSF031057,Gene3D:2.60.120.320,Superfamily_domains:SSF63862 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.00016 0.9999997 1 1 1 0 C 3 2 23 144453554 144453554 G C 1 0 0 0 0 1 0 0 0 16885 1280 45 4 4 TPK1 7 144453554 Missense_Mutation SNP G C3L-01330_T 89261732 144453554 14892419 21 7179 CSMD3 0 . GRCh38 8 112289410 112289410 + Missense_Mutation SNP A A C novel C3L-01330_T C3L-01330_N A A c.9103T>G p.Cys3035Gly p.C3035G ENST00000297405 57/71 683 625 58 428 427 1 strelka-varscan-mutect CSMD3,missense_variant,p.Cys3035Gly,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Cys2995Gly,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Cys2866Gly,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Cys2305Gly,ENST00000339701,; C ENST00000297405 Transcript missense_variant 9348/13212 9103/11124 3035/3707 C/G Tgc/Ggc 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 57/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 112289410 112289410 A C 1 0 0 0 0 1 0 0 0 3747 188 7 5 5 CSMD3 8 112289410 Missense_Mutation SNP A C3L-01330_T 112289410 32849226 22 7180 SLC45A4 0 . GRCh38 8 141218670 141218670 + Missense_Mutation SNP G G C C3L-01330_T C3L-01330_N G G c.970C>G p.Leu324Val p.L324V ENST00000517878 4/8 194 164 30 155 155 0 strelka-varscan-mutect SLC45A4,missense_variant,p.Leu273Val,ENST00000519067,NM_001286648.1;SLC45A4,missense_variant,p.Leu273Val,ENST00000024061,NM_001080431.2;SLC45A4,missense_variant,p.Leu324Val,ENST00000517878,NM_001286646.1;SLC45A4,downstream_gene_variant,,ENST00000520137,;SLC45A4,downstream_gene_variant,,ENST00000519986,; C ENST00000517878 Transcript missense_variant 970/3470 970/2427 324/808 L/V Ctg/Gtg COSM1623676,COSM4781356 1 -1 SLC45A4 HGNC HGNC:29196 protein_coding YES CCDS75795.1 ENSP00000428137 E7EV90 UPI0001E8F5C7 NM_001286646.1 tolerated(0.15) 4/8 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 141218670 141218670 G C 1 0 0 0 0 1 0 0 0 14920 962 34 4 4 SLC45A4 8 141218670 Missense_Mutation SNP G C3L-01330_T 28929260 141218670 3919966 23 7181 CACNA1B 0 . GRCh38 9 138073553 138073553 + Silent SNP C C T C3L-01330_T C3L-01330_N C C c.4740C>T p.= p.R1580R ENST00000371372 33/47 119 107 12 176 176 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1;CACNA1B,upstream_gene_variant,,ENST00000413253,; T ENST00000371372 Transcript synonymous_variant 4885/9790 4740/7020 1580/2339 R cgC/cgT COSM3906208 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 33/47 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 138073553 138073553 C T 1 0 0 0 0 0 0 0 1 2227 726 26 3 3 CACNA1B 9 138073553 Silent SNP C C3L-01330_T 138073553 321164 24 7182 PLXDC2 0 . GRCh38 10 20211711 20211711 + Silent SNP C C T novel C3L-01330_T C3L-01330_N C C c.1104C>T p.= p.D368D ENST00000377252 10/14 102 78 24 123 123 0 strelka-varscan-mutect PLXDC2,synonymous_variant,p.=,ENST00000377252,NM_032812.8;PLXDC2,synonymous_variant,p.=,ENST00000377242,NM_001282736.1;PLXDC2,non_coding_transcript_exon_variant,,ENST00000377238,; T ENST00000377252 Transcript synonymous_variant 1945/12468 1104/1590 368/529 D gaC/gaT 1 1 PLXDC2 HGNC HGNC:21013 protein_coding YES CCDS7132.1 ENSP00000366460 Q6UX71 UPI0000048F2C NM_032812.8 10/14 hmmpanther:PTHR13055:SF11,hmmpanther:PTHR13055,Pfam_domain:PF01437,SMART_domains:SM00423 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 20211711 20211711 C T 1 0 0 0 0 0 0 0 1 12224 477 17 3 3 PLXDC2 10 20211711 Silent SNP C C3L-01330_T 20211711 113585711 25 7183 SVIL 0 . GRCh38 10 29473969 29473969 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.5398G>A p.Glu1800Lys p.E1800K ENST00000355867 30/38 189 174 15 176 176 0 strelka-varscan-mutect SVIL,missense_variant,p.Glu1768Lys,ENST00000375398,;SVIL,missense_variant,p.Glu1800Lys,ENST00000355867,NM_021738.2;SVIL,missense_variant,p.Glu1374Lys,ENST00000375400,NM_003174.3;SVIL,missense_variant,p.Glu726Lys,ENST00000632315,;SVIL-AS1,intron_variant,,ENST00000414457,;SVIL-AS1,intron_variant,,ENST00000446807,;SVIL-AS1,intron_variant,,ENST00000413405,;SVIL-AS1,intron_variant,,ENST00000423223,;SVIL-AS1,downstream_gene_variant,,ENST00000455774,;SVIL,non_coding_transcript_exon_variant,,ENST00000460007,; T ENST00000355867 Transcript missense_variant 6151/7586 5398/6645 1800/2214 E/K Gag/Aag 1 -1 SVIL HGNC HGNC:11480 protein_coding YES CCDS7164.1 ENSP00000348128 O95425 UPI0000366678 NM_021738.2 deleterious(0) 30/38 hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF45,Gene3D:3.40.20.10,SMART_domains:SM00262,Superfamily_domains:SSF55753 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 29473969 29473969 C T 1 0 0 0 0 1 0 0 0 15806 922 32 3 3 SVIL 10 29473969 Missense_Mutation SNP C C3L-01330_T 9262258 29473969 104323453 26 7184 HECTD2 0 . GRCh38 10 91482989 91482989 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.734C>T p.Ser245Phe p.S245F ENST00000446394 8/22 118 108 10 115 115 0 strelka-varscan-mutect HECTD2,missense_variant,p.Ser245Phe,ENST00000446394,NM_001284274.1;HECTD2,missense_variant,p.Ser245Phe,ENST00000298068,NM_182765.4;HECTD2,upstream_gene_variant,,ENST00000371667,;HECTD2,upstream_gene_variant,,ENST00000498446,; T ENST00000446394 Transcript missense_variant 888/4939 734/2343 245/780 S/F tCt/tTt 1 1 HECTD2 HGNC HGNC:26736 protein_coding YES CCDS60591.1 ENSP00000401023 E7ERR3 UPI0001AE6DAB NM_001284274.1 tolerated(0.08) 8/22 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF301 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 91482989 91482989 C T 1 0 0 0 0 1 0 0 0 6921 913 32 3 3 HECTD2 10 91482989 Missense_Mutation SNP C C3L-01330_T 62009020 91482989 42314433 27 7185 DKK3 0 . GRCh38 11 11964720 11964720 + Missense_Mutation SNP C C A rs770613373 C3L-01330_T C3L-01330_N C C c.839G>T p.Arg280Leu p.R280L ENST00000525493 8/8 115 84 31 126 126 0 strelka-varscan-mutect DKK3,missense_variant,p.Arg280Leu,ENST00000525493,;DKK3,intron_variant,,ENST00000396505,NM_015881.5;DKK3,intron_variant,,ENST00000326932,NM_001018057.1,NM_013253.4;DKK3,downstream_gene_variant,,ENST00000533813,;DKK3,downstream_gene_variant,,ENST00000534511,;DKK3,downstream_gene_variant,,ENST00000529338,;DKK3,intron_variant,,ENST00000527132,;DKK3,intron_variant,,ENST00000528188,;DKK3,downstream_gene_variant,,ENST00000532873,;DKK3,downstream_gene_variant,,ENST00000525927,;DKK3,downstream_gene_variant,,ENST00000532372,; A ENST00000525493 Transcript missense_variant 997/1326 839/1095 280/364 R/L cGt/cTt rs770613373 1 -1 DKK3 HGNC HGNC:2893 protein_coding ENSP00000433112 F6SYF8 UPI0001AE6B78 tolerated_low_confidence(0.11) 8/8 hmmpanther:PTHR12113:SF8,hmmpanther:PTHR12113 MODERATE SNV 2 1 PASS rs770613373 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 11964720 11964720 C A 1 0 0 0 0 1 0 0 0 4352 536 19 1 1 DKK3 11 11964720 Missense_Mutation SNP C C3L-01330_T 11964720 123121902 28 7186 UBE3B 0 . GRCh38 12 109509670 109509670 + Missense_Mutation SNP T T C novel C3L-01330_T C3L-01330_N T T c.1697T>C p.Phe566Ser p.F566S ENST00000342494 16/28 73 61 12 90 90 0 strelka-varscan-mutect UBE3B,missense_variant,p.Phe566Ser,ENST00000342494,NM_130466.3;UBE3B,missense_variant,p.Phe566Ser,ENST00000434735,NM_183415.2;UBE3B,missense_variant,p.Phe566Ser,ENST00000539599,;UBE3B,intron_variant,,ENST00000535900,;UBE3B,missense_variant,p.Phe566Ser,ENST00000449510,;UBE3B,non_coding_transcript_exon_variant,,ENST00000539584,; C ENST00000342494 Transcript missense_variant 2292/5722 1697/3207 566/1068 F/S tTc/tCc 1 1 UBE3B HGNC HGNC:13478 protein_coding YES CCDS9129.1 ENSP00000340596 Q7Z3V4 A0A024RBI2 UPI000013DC3B NM_130466.3 deleterious(0) 16/28 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF352 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 109509670 109509670 T C 1 0 0 0 0 1 0 0 0 17403 1783 62 5 5 UBE3B 12 109509670 Missense_Mutation SNP T C3L-01330_T 109509670 23765639 29 7187 BRCA2 0 . GRCh38 13 32326100 32326100 + Splice_Site SNP G G C novel C3L-01330_T C3L-01330_N G G c.426-1G>C p.X142_splice ENST00000380152 74 67 7 92 92 0 strelka-varscan-mutect BRCA2,splice_acceptor_variant,,ENST00000380152,;BRCA2,splice_acceptor_variant,,ENST00000544455,NM_000059.3;BRCA2,splice_acceptor_variant,,ENST00000614259,;BRCA2,splice_acceptor_variant,,ENST00000530893,; C ENST00000380152 Transcript splice_acceptor_variant -/11986 426/10257 142/3418 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC 4/26 HIGH 1 SNV 5 1 PASS rs1060502485 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 23 32326100 32326100 G C 1 0 0 0 0 0 0 1 0 1669 1043 36 4 4 BRCA2 13 32326100 Splice_Site SNP G C3L-01330_T 32326100 82038228 30 7188 CMTM5 0 . GRCh38 14 23378705 23378705 + Silent SNP C C T novel C3L-01330_T C3L-01330_N C C c.316C>T p.= p.L106L ENST00000339180 3/6 184 165 19 221 221 0 strelka-varscan-mutect CMTM5,synonymous_variant,p.=,ENST00000339180,NM_001288746.1;CMTM5,intron_variant,,ENST00000359320,NM_138460.2;CMTM5,intron_variant,,ENST00000555731,;CMTM5,intron_variant,,ENST00000397227,NM_001288744.1;CMTM5,intron_variant,,ENST00000342473,NM_001288745.1;CMTM5,intron_variant,,ENST00000382809,NM_001037288.1;MYH6,downstream_gene_variant,,ENST00000405093,NM_002471.3;MYH6,downstream_gene_variant,,ENST00000356287,;IL25,downstream_gene_variant,,ENST00000329715,NM_022789.3;IL25,downstream_gene_variant,,ENST00000397242,NM_172314.1;CMTM5,non_coding_transcript_exon_variant,,ENST00000555487,;CMTM5,intron_variant,,ENST00000553750,; T ENST00000339180 Transcript synonymous_variant 532/1173 316/672 106/223 L Cta/Tta 1 1 CMTM5 HGNC HGNC:19176 protein_coding YES CCDS73617.1 ENSP00000344819 Q96DZ9 UPI00001B5BF1 NM_001288746.1 3/6 Pfam_domain:PF01284,PROSITE_profiles:PS51225 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 23378705 23378705 C T 1 0 0 0 0 0 0 0 1 3362 796 28 3 3 CMTM5 14 23378705 Silent SNP C C3L-01330_T 23378705 83665013 31 7189 NUMB 0 . GRCh38 14 73279375 73279375 + Silent SNP A A T novel C3L-01330_T C3L-01330_N A A c.1146T>A p.= p.T382T ENST00000555238 12/13 75 62 13 82 82 0 strelka-varscan-mutect NUMB,synonymous_variant,p.=,ENST00000556772,;NUMB,synonymous_variant,p.=,ENST00000555238,NM_001005743.1;NUMB,synonymous_variant,p.=,ENST00000557597,NM_003744.5;NUMB,synonymous_variant,p.=,ENST00000355058,;NUMB,synonymous_variant,p.=,ENST00000359560,;NUMB,intron_variant,,ENST00000554546,NM_001005745.1;NUMB,intron_variant,,ENST00000356296,NM_001320114.1;NUMB,intron_variant,,ENST00000535282,;NUMB,intron_variant,,ENST00000555394,NM_001005744.1;NUMB,intron_variant,,ENST00000544991,;NUMB,intron_variant,,ENST00000560335,;NUMB,intron_variant,,ENST00000555738,;NUMB,intron_variant,,ENST00000559312,;NUMB,intron_variant,,ENST00000554521,;PAPLN,downstream_gene_variant,,ENST00000340738,NM_173462.3;PAPLN,downstream_gene_variant,,ENST00000559759,;NUMB,downstream_gene_variant,,ENST00000555307,;NUMB,downstream_gene_variant,,ENST00000554394,;NUMB,downstream_gene_variant,,ENST00000555859,;NUMB,downstream_gene_variant,,ENST00000553997,;NUMB,intron_variant,,ENST00000554014,;PAPLN,downstream_gene_variant,,ENST00000555700,;PAPLN,downstream_gene_variant,,ENST00000557061,;NUMB,downstream_gene_variant,,ENST00000557486,; T ENST00000555238 Transcript synonymous_variant 1416/3588 1146/1956 382/651 T acT/acA 1 -1 NUMB HGNC HGNC:8060 protein_coding YES CCDS32116.1 ENSP00000451300 P49757 A0A024R6F4 UPI00001309BF NM_001005743.1 12/13 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF33,PIRSF_domain:PIRSF017607 LOW 1 SNV 1 1 PASS rs1443202767 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 73279375 73279375 A T 1 0 0 0 0 0 0 0 1 10816 175 7 4 4 NUMB 14 73279375 Silent SNP A C3L-01330_T 49900670 73279375 33764343 32 7190 SPINT1 0 . GRCh38 15 40844662 40844662 + Silent SNP G G C novel C3L-01330_T C3L-01330_N G G c.108G>C p.= p.G36G ENST00000344051 2/11 209 173 36 176 176 0 strelka-varscan-mutect SPINT1,synonymous_variant,p.=,ENST00000344051,NM_181642.2;SPINT1,synonymous_variant,p.=,ENST00000562057,NM_003710.3,NM_001032367.1;SPINT1,synonymous_variant,p.=,ENST00000563656,;SPINT1,synonymous_variant,p.=,ENST00000568823,;SPINT1,upstream_gene_variant,,ENST00000568580,;RP11-532F12.5,upstream_gene_variant,,ENST00000564302,;RP11-532F12.5,upstream_gene_variant,,ENST00000565315,;RP11-532F12.5,upstream_gene_variant,,ENST00000568419,;RP11-532F12.5,upstream_gene_variant,,ENST00000568525,;RP11-532F12.5,upstream_gene_variant,,ENST00000563217,; C ENST00000344051 Transcript synonymous_variant 342/3056 108/1590 36/529 G ggG/ggC 1 1 SPINT1 HGNC HGNC:11246 protein_coding YES CCDS10067.1 ENSP00000342098 O43278 UPI00001AE46F NM_181642.2 2/11 Low_complexity_(Seg):seg,hmmpanther:PTHR10083:SF231,hmmpanther:PTHR10083 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 23 40844662 40844662 G C 1 0 0 0 0 0 0 0 1 15420 1190 42 4 4 SPINT1 15 40844662 Silent SNP G C3L-01330_T 40844662 61146527 33 7191 LRRC49 0 . GRCh38 15 70963932 70963934 + Splice_Site DEL GGT GGT - novel C3L-01330_T C3L-01330_N GGT GGT c.936+1_936+3delGTG p.X312_splice ENST00000560369 9/16 61 43 18 51 51 0 sindel-varindel-pindel LRRC49,splice_donor_variant,,ENST00000544974,NM_001284357.1;LRRC49,splice_donor_variant,,ENST00000443425,NM_001199018.2;LRRC49,splice_donor_variant,,ENST00000260382,NM_017691.4;LRRC49,splice_donor_variant,,ENST00000560369,NM_001199017.2;LRRC49,splice_donor_variant,,ENST00000560691,;LRRC49,splice_donor_variant,,ENST00000559806,;LRRC49,splice_donor_variant,,ENST00000558808,;LRRC49,splice_donor_variant,,ENST00000558456,;LRRC49,splice_donor_variant,,ENST00000559069,;LRRC49,intron_variant,,ENST00000560158,;LRRC49,splice_donor_variant,,ENST00000436542,;LRRC49,downstream_gene_variant,,ENST00000558137,;LRRC49,downstream_gene_variant,,ENST00000561285,;LRRC49,splice_donor_variant,,ENST00000561081,;LRRC49,splice_donor_variant,,ENST00000560107,;LRRC49,splice_donor_variant,,ENST00000560980,;LRRC49,splice_donor_variant,,ENST00000559685,;LRRC49,non_coding_transcript_exon_variant,,ENST00000559469,; - ENST00000560369 Transcript splice_donor_variant,coding_sequence_variant 1205-?/2586 936-?/2076 312-?/691 1 1 LRRC49 HGNC HGNC:25965 protein_coding YES CCDS58376.1 ENSP00000453273 Q8IUZ0 UPI0001E92A32 NM_001199017.2 9/16 9/15 HIGH 1 deletion 2 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999953 1 1 1 0 - 8 5 23 70963932 70963932 GGT - 1 0 1 0 1 0 0 1 0 8901 1130 39 0 0 LRRC49 15 70963932 Splice_Site DEL GGT C3L-01330_T 30119270 70963932 31027257 34 7192 RP11-566K11.2 0 . GRCh38 16 89935172 89935172 + Missense_Mutation SNP C C T rs751967547 C3L-01330_T C3L-01330_N C C c.1762C>T p.Arg588Cys p.R588C ENST00000556922 5/5 429 346 83 483 483 0 strelka-varscan-mutect RP11-566K11.2,missense_variant,p.Arg588Cys,ENST00000556922,;TUBB3,missense_variant,p.Arg169Cys,ENST00000554444,NM_001197181.1;TUBB3,missense_variant,p.Arg241Cys,ENST00000315491,NM_006086.3;TUBB3,missense_variant,p.Arg169Cys,ENST00000555810,;TUBB3,intron_variant,,ENST00000555576,;TUBB3,downstream_gene_variant,,ENST00000554336,;TUBB3,downstream_gene_variant,,ENST00000553967,;TUBB3,downstream_gene_variant,,ENST00000625617,;TUBB3,downstream_gene_variant,,ENST00000556565,;TUBB3,downstream_gene_variant,,ENST00000554116,;TUBB3,3_prime_UTR_variant,,ENST00000555609,;TUBB3,downstream_gene_variant,,ENST00000556536,;TUBB3,downstream_gene_variant,,ENST00000557262,;TUBB3,downstream_gene_variant,,ENST00000557490,;TUBB3,downstream_gene_variant,,ENST00000554927,;TUBB3,downstream_gene_variant,,ENST00000553656,; T ENST00000556922 Transcript missense_variant 1856/2776 1762/2394 588/797 R/C Cgc/Tgc rs751967547 1 1 RP11-566K11.2 Clone_based_vega_gene protein_coding YES ENSP00000451560 A0A0B4J269 UPI00000718A4 deleterious_low_confidence(0.02) 5/5 Gene3D:3.40.50.1440,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF43,SMART_domains:SM00864,Superfamily_domains:SSF52490 MODERATE SNV 2 1 PASS rs751967547 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 89935172 89935172 C T 1 0 0 0 0 1 0 0 0 13753 768 27 1 1 RP11-566K11.2 16 89935172 Missense_Mutation SNP C C3L-01330_T 89935172 403173 35 7193 ARHGEF15 0 . GRCh38 17 8315852 8315852 + Missense_Mutation SNP T T C novel C3L-01330_T C3L-01330_N T T c.1519T>C p.Tyr507His p.Y507H ENST00000361926 8/16 128 109 19 152 152 0 strelka-varscan-mutect ARHGEF15,missense_variant,p.Tyr507His,ENST00000361926,NM_173728.3;ARHGEF15,missense_variant,p.Tyr507His,ENST00000421050,NM_025014.1;ARHGEF15,downstream_gene_variant,,ENST00000579439,;ARHGEF15,downstream_gene_variant,,ENST00000583529,;AC135178.7,downstream_gene_variant,,ENST00000458568,;ARHGEF15,upstream_gene_variant,,ENST00000582060,;ARHGEF15,downstream_gene_variant,,ENST00000455564,;ARHGEF15,downstream_gene_variant,,ENST00000581809,;ARHGEF15,downstream_gene_variant,,ENST00000578286,; C ENST00000361926 Transcript missense_variant 1629/4159 1519/2526 507/841 Y/H Tat/Cat 1 1 ARHGEF15 HGNC HGNC:15590 protein_coding YES CCDS11139.1 ENSP00000355026 O94989 A0A0S2Z547 UPI000013D2C0 NM_173728.3 deleterious(0) 8/16 Gene3D:1.20.900.10,Pfam_domain:PF00621,PROSITE_profiles:PS50010,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF7,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 23 8315852 8315852 T C 1 0 0 0 0 1 0 0 0 1028 1638 57 5 5 ARHGEF15 17 8315852 Missense_Mutation SNP T C3L-01330_T 8315852 74941589 36 7194 CNTNAP1 0 . GRCh38 17 42688484 42688492 + In_Frame_Del DEL TTGGCACGA TTGGCACGA - novel C3L-01330_T C3L-01330_N TTGGCACGA TTGGCACGA c.1329_1337delTTGGCACGA p.Phe443_Glu446delinsLeu p.F443_E446delinsL ENST00000264638 9/24 190 157 33 191 191 0 sindel-varindel CNTNAP1,inframe_deletion,p.Phe443_Glu446delinsLeu,ENST00000264638,NM_003632.2;CCR10,upstream_gene_variant,,ENST00000591568,;CTD-3193K9.3,intron_variant,,ENST00000592440,;CNTNAP1,inframe_deletion,p.Phe443_Glu446delinsLeu,ENST00000591662,;CNTNAP1,non_coding_transcript_exon_variant,,ENST00000586801,;CNTNAP1,upstream_gene_variant,,ENST00000585534,; - ENST00000264638 Transcript inframe_deletion 1546-1554/5276 1329-1337/4155 443-446/1384 FWHE/L ttTTGGCACGAg/ttg 1 1 CNTNAP1 HGNC HGNC:8011 protein_coding YES CCDS11436.1 ENSP00000264638 P78357 UPI00001285F6 NM_003632.2 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF4,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 23 42688484 42688484 TTGGCACGA - 1 0 1 0 1 0 0 0 0 3427 1838 64 0 0 CNTNAP1 17 42688484 In_Frame_Del DEL TTGGCACGA C3L-01330_T 34372632 42688484 40568957 37 7195 SLC4A1 0 . GRCh38 17 44258606 44258606 + Silent SNP G G A novel C3L-01330_T C3L-01330_N G G c.894C>T p.= p.A298A ENST00000262418 10/20 288 222 66 201 201 0 strelka-varscan-mutect SLC4A1,synonymous_variant,p.=,ENST00000262418,NM_000342.3;SLC4A1,intron_variant,,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; A ENST00000262418 Transcript synonymous_variant 1050/4965 894/2736 298/911 A gcC/gcT 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 10/20 Gene3D:1hynR00,Pfam_domain:PF07565,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 23 44258606 44258606 G A 1 0 0 0 0 0 0 0 1 14927 987 35 3 3 SLC4A1 17 44258606 Silent SNP G C3L-01330_T 1570122 44258606 38998835 38 7196 GAA 0 . GRCh38 17 80117686 80117686 + Silent SNP G G A rs371528938 C3L-01330_T C3L-01330_N G G c.2418G>A p.= p.T806T ENST00000302262 17/20 279 252 27 264 264 0 strelka-varscan-mutect GAA,synonymous_variant,p.=,ENST00000302262,NM_000152.3;GAA,synonymous_variant,p.=,ENST00000390015,NM_001079803.1,NM_001079804.1;GAA,non_coding_transcript_exon_variant,,ENST00000573556,;GAA,downstream_gene_variant,,ENST00000572080,;GAA,downstream_gene_variant,,ENST00000572803,;GAA,downstream_gene_variant,,ENST00000570716,; A ENST00000302262 Transcript synonymous_variant 2637/3626 2418/2859 806/952 T acG/acA rs371528938,COSM2803174 1 1 GAA HGNC HGNC:4065 protein_coding YES CCDS32760.1 ENSP00000305692 P10253 UPI00000744FF NM_000152.3 17/20 hmmpanther:PTHR22762:SF92,hmmpanther:PTHR22762,Pfam_domain:PF01055,Superfamily_domains:SSF51011 0,1 LOW 1 SNV 1 0,1 1 PASS rs371528938 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 23 80117686 80117686 G A 1 0 0 0 0 0 0 0 1 6018 1074 38 1 1 GAA 17 80117686 Silent SNP G C3L-01330_T 35859080 80117686 3139755 39 7197 LAMA1 0 . GRCh38 18 7049079 7049079 + Missense_Mutation SNP C C T rs748576952 C3L-01330_T C3L-01330_N C C c.767G>A p.Arg256His p.R256H ENST00000389658 5/63 328 288 40 278 278 0 strelka-varscan-mutect LAMA1,missense_variant,p.Arg256His,ENST00000389658,NM_005559.3;LAMA1,splice_region_variant,,ENST00000579014,; T ENST00000389658 Transcript missense_variant,splice_region_variant 861/9657 767/9228 256/3075 R/H cGc/cAc rs748576952,COSM3146046 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 5/63 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00136 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs748576952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 7049079 7049079 C T 1 0 0 0 0 1 0 0 0 8509 782 27 1 1 LAMA1 18 7049079 Missense_Mutation SNP C C3L-01330_T 7049079 73324206 40 7198 ANKRD30B 0 . GRCh38 18 14752980 14752980 + Missense_Mutation SNP T T G novel C3L-01330_T C3L-01330_N T T c.478T>G p.Ser160Ala p.S160A ENST00000358984 3/36 107 97 10 103 103 0 strelka-mutect ANKRD30B,missense_variant,p.Ser160Ala,ENST00000358984,NM_001145029.1;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Ser160Ala,ENST00000580206,; G ENST00000358984 Transcript missense_variant 658/4359 478/4179 160/1392 S/A Tcc/Gcc 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.29) 3/36 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 23 14752980 14752980 T G 1 0 0 0 0 1 0 0 0 762 1667 58 5 5 ANKRD30B 18 14752980 Missense_Mutation SNP T C3L-01330_T 7703901 14752980 65620305 41 7199 ARHGAP45 0 . GRCh38 19 1074383 1074385 + In_Frame_Del DEL CTG CTG - novel C3L-01330_T C3L-01330_N CTG CTG c.1018_1020delTGC p.Cys340del p.C340del ENST00000539243 8/23 33 25 8 45 45 0 sindel-varindel ARHGAP45,inframe_deletion,p.Cys324del,ENST00000313093,NM_012292.4;ARHGAP45,inframe_deletion,p.Cys351del,ENST00000590214,;ARHGAP45,inframe_deletion,p.Cys340del,ENST00000539243,NM_001258328.2;ARHGAP45,inframe_deletion,p.Cys328del,ENST00000586866,;ARHGAP45,inframe_deletion,p.Cys207del,ENST00000543365,NM_001282335.1;ARHGAP45,upstream_gene_variant,,ENST00000590577,NM_001282334.1;ARHGAP45,downstream_gene_variant,,ENST00000587186,;ARHGAP45,downstream_gene_variant,,ENST00000592335,;ARHGAP45,3_prime_UTR_variant,,ENST00000587602,;ARHGAP45,non_coding_transcript_exon_variant,,ENST00000586033,;ARHGAP45,intron_variant,,ENST00000591293,; - ENST00000539243 Transcript inframe_deletion 1120-1122/4184 1017-1019/3459 339-340/1152 NC/N aaCTGc/aac 1 1 ARHGAP45 HGNC HGNC:17102 protein_coding YES CCDS58637.1 ENSP00000439601 Q92619 UPI0001AE63E1 NM_001258328.2 8/23 PROSITE_profiles:PS51741,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF18,SMART_domains:SM00055,Superfamily_domains:SSF103657 MODERATE 1 deletion 2 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.94997 1 1 1 1 0 - 7 5 23 1074383 1074383 CTG - 1 0 1 0 1 0 0 0 0 1015 564 20 0 0 ARHGAP45 19 1074383 In_Frame_Del DEL CTG C3L-01330_T 1074383 57543233 42 7200 PROCR 0 . GRCh38 20 35176261 35176261 + Missense_Mutation SNP C C T novel C3L-01330_T C3L-01330_N C C c.416C>T p.Ser139Phe p.S139F ENST00000216968 3/4 458 401 57 464 464 0 strelka-varscan-mutect PROCR,missense_variant,p.Ser139Phe,ENST00000216968,NM_006404.4;PROCR,missense_variant,p.Ser106Phe,ENST00000635377,;PROCR,upstream_gene_variant,,ENST00000634509,;RP11-42O4.2,upstream_gene_variant,,ENST00000615962,; T ENST00000216968 Transcript missense_variant 498/1348 416/717 139/238 S/F tCc/tTc 1 1 PROCR HGNC HGNC:9452 protein_coding YES CCDS13248.1 ENSP00000216968 Q9UNN8 UPI000012A08E NM_006404.4 deleterious(0) 3/4 hmmpanther:PTHR15349,Gene3D:3.30.500.10,Pfam_domain:PF16497,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 23 35176261 35176261 C T 1 0 0 0 0 1 0 0 0 12681 855 30 3 3 PROCR 20 35176261 Missense_Mutation SNP C C3L-01330_T 35176261 29267906 43 7201 PIN4 0 . GRCh38 X 72262794 72262794 + Nonstop_Mutation SNP T T G novel C3L-01330_T C3L-01330_N T T c.400T>G p.Ter134GluextTer15 p.*134Eext*15 ENST00000423432 4/4 80 54 26 101 101 0 strelka-mutect PIN4,stop_lost,p.Ter134GluextTer15,ENST00000423432,NM_001170747.1;PIN4,stop_lost,p.Ter116GluextTer15,ENST00000496835,;RPS4X,intron_variant,,ENST00000470671,;RPS4X,intron_variant,,ENST00000492695,;PIN4,intron_variant,,ENST00000439980,; G ENST00000423432 Transcript stop_lost 435/1605 400/402 134/133 */E Taa/Gaa 1 1 PIN4 HGNC HGNC:8992 protein_coding CCDS55447.1 ENSP00000409154 Q9Y237 UPI0001C0B3B6 NM_001170747.1 4/4 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 23 72262794 72262794 T G 1 0 0 0 0 0 0 0 0 12026 1767 61 5 5 PIN4 23 72262794 Nonstop_Mutation SNP T C3L-01330_T 72262794 83778101 44 7202 TENM1 0 . GRCh38 X 124420527 124420527 + Missense_Mutation SNP C C A novel C3L-01330_T C3L-01330_N C C c.4766G>T p.Ser1589Ile p.S1589I ENST00000422452 25/32 183 155 28 167 167 0 strelka-varscan-mutect TENM1,missense_variant,p.Ser1589Ile,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Ser1582Ile,ENST00000371130,NM_014253.3;STAG2,intron_variant,,ENST00000469481,; A ENST00000422452 Transcript missense_variant 4830/12891 4766/8199 1589/2732 S/I aGc/aTc 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0.01) 25/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,Gene3D:2.120.10.30,Superfamily_domains:SSF63829 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999939 1 1 1 0 A 3 1 23 124420527 124420527 C A 1 0 0 0 0 1 0 0 0 16171 797 28 2 2 TENM1 23 124420527 Missense_Mutation SNP C C3L-01330_T 52157733 124420527 31620368 45 7203 CXorf66 0 . GRCh38 X 139956389 139956389 + Missense_Mutation SNP C C A novel C3L-01330_T C3L-01330_N C C c.593G>T p.Cys198Phe p.C198F ENST00000370540 3/3 222 188 34 205 205 0 strelka-varscan-mutect CXorf66,missense_variant,p.Cys198Phe,ENST00000370540,NM_001013403.2; A ENST00000370540 Transcript missense_variant 617/1281 593/1086 198/361 C/F tGt/tTt 1 -1 CXorf66 HGNC HGNC:33743 protein_coding YES CCDS35411.1 ENSP00000359571 Q5JRM2 UPI00001D7C1C NM_001013403.2 tolerated(0.7) 3/3 hmmpanther:PTHR37340,hmmpanther:PTHR37340:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 23 139956389 139956389 C A 1 0 0 0 0 1 0 0 0 3920 478 17 2 2 CXorf66 23 139956389 Missense_Mutation SNP C C3L-01330_T 15535862 139956389 16084506 46 7204 SLITRK2 0 . GRCh38 X 145823415 145823415 + Silent SNP C C T C3L-01330_T C3L-01330_N C C c.990C>T p.= p.Y330Y ENST00000370490 1/1 327 287 40 252 252 0 strelka-varscan-mutect SLITRK2,synonymous_variant,p.=,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,synonymous_variant,p.=,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript synonymous_variant 5245/7672 990/2538 330/845 Y taC/taT COSM5320754 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 1/1 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 23 145823415 145823415 C T 1 0 0 0 0 0 0 0 1 15034 518 18 3 3 SLITRK2 23 145823415 Silent SNP C C3L-01330_T 5867026 145823415 10217480 47 7205 CAMTA1 0 . GRCh38 1 7664193 7664193 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1646C>A p.Ser549Tyr p.S549Y ENST00000303635 9/23 394 341 53 509 509 0 strelka-varscan-mutect CAMTA1,missense_variant,p.Ser549Tyr,ENST00000303635,NM_015215.3; A ENST00000303635 Transcript missense_variant 1853/8444 1646/5022 549/1673 S/Y tCc/tAc 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 tolerated_low_confidence(1) 9/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 MODERATE 1 SNV 1 1 PASS rs1230605537 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 7664193 7664193 C A 1 0 0 0 0 1 0 0 0 2306 855 30 2 2 CAMTA1 1 7664193 Missense_Mutation SNP C C3L-01632_T 7664193 241292229 1 7206 NRDC 0 . GRCh38 1 51814063 51814063 + Missense_Mutation SNP T T A novel C3L-01632_T C3L-01632_N T T c.1850A>T p.Glu617Val p.E617V ENST00000354831 16/33 83 72 11 131 131 0 strelka-varscan-mutect NRDC,missense_variant,p.Glu617Val,ENST00000354831,NM_002525.2;NRDC,missense_variant,p.Glu549Val,ENST00000544028,;NRDC,missense_variant,p.Glu549Val,ENST00000352171,NM_001101662.1;NRDC,missense_variant,p.Glu485Val,ENST00000539524,NM_001242361.1;NRDC,missense_variant,p.Glu4Val,ENST00000440943,;NRDC,non_coding_transcript_exon_variant,,ENST00000485608,;NRDC,non_coding_transcript_exon_variant,,ENST00000483007,;NRDC,downstream_gene_variant,,ENST00000473805,; A ENST00000354831 Transcript missense_variant 2040/3895 1850/3660 617/1219 E/V gAg/gTg 1 -1 NRDC HGNC HGNC:7995 protein_coding YES CCDS559.1 ENSP00000346890 B1AKJ5 UPI0000458A53 NM_002525.2 deleterious(0) 16/33 Low_complexity_(Seg):seg,Gene3D:3.30.830.10,Superfamily_domains:SSF63411 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 A 3 1 24 51814063 51814063 T A 1 0 0 0 0 1 0 0 0 10701 1551 54 4 4 NRDC 1 51814063 Missense_Mutation SNP T C3L-01632_T 44149870 51814063 197142359 2 7207 FAM102B 0 . GRCh38 1 108629647 108629647 + Missense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.1030C>T p.Leu344Phe p.L344F ENST00000370035 10/11 172 156 16 248 248 0 strelka-varscan-mutect FAM102B,missense_variant,p.Leu344Phe,ENST00000370035,NM_001010883.2;FAM102B,missense_variant,p.Leu344Phe,ENST00000405454,;FAM102B,non_coding_transcript_exon_variant,,ENST00000483371,; T ENST00000370035 Transcript missense_variant 1370/5600 1030/1083 344/360 L/F Ctt/Ttt 1 1 FAM102B HGNC HGNC:27637 protein_coding YES CCDS30786.2 ENSP00000359052 Q5T8I3 UPI00001D7585 NM_001010883.2 deleterious(0.01) 10/11 hmmpanther:PTHR21456,hmmpanther:PTHR21456:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 108629647 108629647 C T 1 0 0 0 0 1 0 0 0 5251 913 32 3 3 FAM102B 1 108629647 Missense_Mutation SNP C C3L-01632_T 56815584 108629647 140326775 3 7208 TCHHL1 0 . GRCh38 1 152086227 152086227 + Missense_Mutation SNP G G T rs150195731 C3L-01632_T C3L-01632_N G G c.1455C>A p.Asn485Lys p.N485K ENST00000368806 3/3 293 239 54 343 342 1 strelka-varscan-mutect TCHHL1,missense_variant,p.Asn485Lys,ENST00000368806,NM_001008536.1; T ENST00000368806 Transcript missense_variant 1520/3603 1455/2715 485/904 N/K aaC/aaA rs150195731,COSM3399701 1 -1 TCHHL1 HGNC HGNC:31796 protein_coding YES CCDS30857.1 ENSP00000357796 Q5QJ38 UPI0000496834 NM_001008536.1 deleterious(0.01) 3/3 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF65 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs150195731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 152086227 152086227 G T 1 0 0 0 0 1 0 0 0 16108 1136 40 1 1 TCHHL1 1 152086227 Missense_Mutation SNP G C3L-01632_T 43456580 152086227 96870195 4 7209 SPTA1 0 . GRCh38 1 158620257 158620257 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.6330G>T p.Lys2110Asn p.K2110N ENST00000368147 44/52 269 182 87 316 314 2 strelka-varscan-mutect SPTA1,missense_variant,p.Lys2110Asn,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript missense_variant 6511/7999 6330/7260 2110/2419 K/N aaG/aaT 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 44/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 158620257 158620257 C A 1 0 0 0 0 1 0 0 0 15472 680 24 2 2 SPTA1 1 158620257 Missense_Mutation SNP C C3L-01632_T 6534030 158620257 90336165 5 7210 LAMC2 0 . GRCh38 1 183227622 183227622 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1393C>A p.His465Asn p.H465N ENST00000264144 10/23 265 177 88 367 367 0 strelka-varscan-mutect LAMC2,missense_variant,p.His465Asn,ENST00000264144,NM_005562.2;LAMC2,missense_variant,p.His465Asn,ENST00000493293,NM_018891.2; A ENST00000264144 Transcript missense_variant 1458/5147 1393/3582 465/1193 H/N Cat/Aat 1 1 LAMC2 HGNC HGNC:6493 protein_coding YES CCDS1352.1 ENSP00000264144 Q13753 UPI000013D4CA NM_005562.2 tolerated(0.54) 10/23 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF270,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1195000634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 183227622 183227622 C A 1 0 0 0 0 1 0 0 0 8519 826 29 2 2 LAMC2 1 183227622 Missense_Mutation SNP C C3L-01632_T 24607365 183227622 65728800 6 7211 IGFN1 0 . GRCh38 1 201213462 201213462 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.8569C>T p.= p.L2857L ENST00000335211 12/24 333 289 44 486 486 0 strelka-varscan IGFN1,synonymous_variant,p.=,ENST00000335211,NM_001164586.1;IGFN1,synonymous_variant,p.=,ENST00000412892,;IGFN1,intron_variant,,ENST00000295591,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,;IGFN1,intron_variant,,ENST00000437879,; T ENST00000335211 Transcript synonymous_variant 8699/11810 8569/11127 2857/3708 L Ctg/Ttg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 12/24 hmmpanther:PTHR10489:SF630,hmmpanther:PTHR10489 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 201213462 201213462 C T 1 0 0 0 0 0 0 0 1 7497 796 28 3 3 IGFN1 1 201213462 Silent SNP C C3L-01632_T 17985840 201213462 47742960 7 7212 PKP1 0 . GRCh38 1 201319838 201319838 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.1255C>A p.Leu419Ile p.L419I ENST00000263946 7/15 425 369 56 519 519 0 strelka-varscan PKP1,missense_variant,p.Leu419Ile,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Leu419Ile,ENST00000352845,;PKP1,intron_variant,,ENST00000367324,NM_001005337.2;PKP1,non_coding_transcript_exon_variant,,ENST00000475988,; A ENST00000263946 Transcript missense_variant 1506/5447 1255/2244 419/747 L/I Ctt/Att COSM1659264 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 tolerated_low_confidence(0.32) 7/15 Gene3D:1.25.10.10,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 201319838 201319838 C A 1 0 0 0 0 1 0 0 0 12080 797 28 2 2 PKP1 1 201319838 Missense_Mutation SNP C C3L-01632_T 106376 201319838 47636584 8 7213 TATDN3 0 . GRCh38 1 212807757 212807757 + Frame_Shift_Del DEL A A - novel C3L-01632_T C3L-01632_N A A c.509delA p.His170LeufsTer9 p.H170Lfs*9 ENST00000532324 8/10 164 114 50 169 169 0 sindel-varindel TATDN3,frameshift_variant,p.His170LeufsTer9,ENST00000366974,NM_001042552.2;TATDN3,frameshift_variant,p.His170LeufsTer9,ENST00000366973,NM_001042553.2;TATDN3,frameshift_variant,p.His170LeufsTer9,ENST00000532324,NM_001146171.1;TATDN3,frameshift_variant,p.His170LeufsTer9,ENST00000531963,NM_001146169.1;TATDN3,frameshift_variant,p.His149LeufsTer9,ENST00000526641,NM_001146170.1;TATDN3,intron_variant,,ENST00000527693,;TATDN3,intron_variant,,ENST00000526997,;TATDN3,downstream_gene_variant,,ENST00000530399,;TATDN3,downstream_gene_variant,,ENST00000488246,;TATDN3,downstream_gene_variant,,ENST00000530441,;TATDN3,non_coding_transcript_exon_variant,,ENST00000525569,;TATDN3,downstream_gene_variant,,ENST00000530392,;TATDN3,frameshift_variant,p.Met94CysfsTer3,ENST00000533650,;TATDN3,3_prime_UTR_variant,,ENST00000525574,; - ENST00000532324 Transcript frameshift_variant 603/1381 509/846 170/281 H/X cAt/ct 1 1 TATDN3 HGNC HGNC:27010 protein_coding YES CCDS53475.1 ENSP00000431376 Q17R31 UPI0000205E43 NM_001146171.1 8/10 hmmpanther:PTHR10060,hmmpanther:PTHR10060:SF25,Gene3D:3.20.20.140,Pfam_domain:PF01026,PIRSF_domain:PIRSF005902,Superfamily_domains:SSF51556 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 212807757 212807757 A - 1 0 1 0 1 0 0 0 0 15992 217 8 0 0 TATDN3 1 212807757 Frame_Shift_Del DEL A C3L-01632_T 11487919 212807757 36148665 9 7214 USH2A 0 . GRCh38 1 215647598 215647598 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.14715C>A p.Tyr4905Ter p.Y4905* ENST00000307340 67/72 478 414 64 599 599 0 strelka-varscan USH2A,stop_gained,p.Tyr4905Ter,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript stop_gained 15102/18883 14715/15609 4905/5202 Y/* taC/taA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 67/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 215647598 215647598 G T 1 0 0 0 0 0 1 0 0 17570 1372 48 2 2 USH2A 1 215647598 Nonsense_Mutation SNP G C3L-01632_T 2839841 215647598 33308824 10 7215 ACBD3 0 . GRCh38 1 226161638 226161638 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.621G>A p.= p.L207L ENST00000366812 4/8 267 240 27 306 306 0 strelka-varscan ACBD3,synonymous_variant,p.=,ENST00000366812,NM_022735.3;ACBD3,upstream_gene_variant,,ENST00000464927,; T ENST00000366812 Transcript synonymous_variant 676/3573 621/1587 207/528 L ctG/ctA 1 -1 ACBD3 HGNC HGNC:15453 protein_coding YES CCDS1551.1 ENSP00000355777 Q9H3P7 A0A024R3P9 UPI000006F1E1 NM_022735.3 4/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22973,hmmpanther:PTHR22973:SF11,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 226161638 226161638 C T 1 0 0 0 0 0 0 0 1 166 697 25 3 3 ACBD3 1 226161638 Silent SNP C C3L-01632_T 10514040 226161638 22794784 11 7216 OBSCN 0 . GRCh38 1 228318141 228318141 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.16970G>T p.Gly5657Val p.G5657V ENST00000570156 64/116 202 167 35 250 250 0 strelka-varscan OBSCN,missense_variant,p.Gly5657Val,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Gly5657Val,ENST00000366707,;OBSCN,missense_variant,p.Gly4700Val,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Gly4700Val,ENST00000636875,;OBSCN,missense_variant,p.Gly4700Val,ENST00000284548,NM_052843.3;OBSCN,intron_variant,,ENST00000483539,; T ENST00000570156 Transcript missense_variant 17044/26925 16970/26772 5657/8923 G/V gGc/gTc 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0.01) 64/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,SMART_domains:SM00408,SMART_domains:SM00409 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 228318141 228318141 G T 1 0 0 0 0 1 0 0 0 10889 1203 42 2 2 OBSCN 1 228318141 Missense_Mutation SNP G C3L-01632_T 2156503 228318141 20638281 12 7217 DISC1 0 . GRCh38 1 231818361 231818361 + Nonsense_Mutation SNP G G T rs150138912 C3L-01632_T C3L-01632_N G G c.1825G>T p.Glu609Ter p.E609* ENST00000366633 9/10 355 306 49 392 391 1 strelka-varscan DISC1,stop_gained,p.Glu609Ter,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,stop_gained,p.Glu609Ter,ENST00000366637,NM_001012957.1;DISC1,stop_gained,p.Glu487Ter,ENST00000620189,NM_001164540.1;DISC1,stop_gained,p.Glu609Ter,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,stop_gained,p.Glu609Ter,ENST00000366633,NM_001164539.1;DISC1,stop_gained,p.Glu609Ter,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,stop_gained,p.Glu609Ter,ENST00000366636,NM_001012959.1;DISC1,synonymous_variant,p.=,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,3_prime_UTR_variant,,ENST00000622252,;DISC1,3_prime_UTR_variant,,ENST00000537876,;DISC1,3_prime_UTR_variant,,ENST00000602873,NM_001164556.1;DISC1,intron_variant,,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC2,downstream_gene_variant,,ENST00000612827,;DISC1,upstream_gene_variant,,ENST00000427560,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000535944,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,3_prime_UTR_variant,,ENST00000295051,;DISC1,3_prime_UTR_variant,,ENST00000602822,;DISC1,3_prime_UTR_variant,,ENST00000602713,;DISC1,3_prime_UTR_variant,,ENST00000602700,;DISC1,3_prime_UTR_variant,,ENST00000366632,; T ENST00000366633 Transcript stop_gained 1878/2676 1825/2268 609/755 E/* Gag/Tag rs150138912 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 9/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 231818361 231818361 G T 1 0 0 0 0 0 1 0 0 4344 1059 37 1 1 DISC1 1 231818361 Nonsense_Mutation SNP G C3L-01632_T 3500220 231818361 17138061 13 7218 ACTN2 0 . GRCh38 1 236744741 236744741 + Silent SNP C C T rs114008185 C3L-01632_T C3L-01632_N C C c.1371C>T p.= p.R457R ENST00000542672 12/21 275 256 19 397 397 0 strelka-varscan ACTN2,synonymous_variant,p.=,ENST00000546208,NM_001278344.1;ACTN2,synonymous_variant,p.=,ENST00000542672,NM_001278343.1;ACTN2,synonymous_variant,p.=,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000492634,;ACTN2,downstream_gene_variant,,ENST00000494762,;ACTN2,upstream_gene_variant,,ENST00000492101,; T ENST00000542672 Transcript synonymous_variant 1591/4906 1371/2685 457/894 R cgC/cgT rs114008185,COSM1748245 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 12/21 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00150,Superfamily_domains:SSF46966 benign 0,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 236744741 236744741 C T 1 0 0 0 0 0 0 0 1 249 755 27 1 1 ACTN2 1 236744741 Silent SNP C C3L-01632_T 4926380 236744741 12211681 14 7219 RYR2 0 . GRCh38 1 237602091 237602091 + Missense_Mutation SNP T T C novel C3L-01632_T C3L-01632_N T T c.4663T>C p.Phe1555Leu p.F1555L ENST00000366574 35/105 216 188 28 228 228 0 strelka-varscan RYR2,missense_variant,p.Phe1555Leu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Phe1539Leu,ENST00000360064,; C ENST00000366574 Transcript missense_variant 4980/16562 4663/14904 1555/4967 F/L Ttt/Ctt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.05) 35/105 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 237602091 237602091 T C 1 0 0 0 0 1 0 0 0 14029 1725 60 5 5 RYR2 1 237602091 Missense_Mutation SNP T C3L-01632_T 857350 237602091 11354331 15 7220 ADSS 0 . GRCh38 1 244437721 244437721 + Nonsense_Mutation SNP A A T novel C3L-01632_T C3L-01632_N A A c.231T>A p.Tyr77Ter p.Y77* ENST00000366535 2/13 287 246 41 297 297 0 strelka-varscan ADSS,stop_gained,p.Tyr77Ter,ENST00000366535,NM_001126.3; T ENST00000366535 Transcript stop_gained 548/2780 231/1371 77/456 Y/* taT/taA 1 -1 ADSS HGNC HGNC:292 protein_coding YES CCDS1624.1 ENSP00000355493 P30520 A0A024R5Q7 UPI0000132AF5 NM_001126.3 2/13 HAMAP:MF_00011,HAMAP:MF_03127,hmmpanther:PTHR11846:SF1,hmmpanther:PTHR11846,Pfam_domain:PF00709,TIGRFAM_domain:TIGR00184,Gene3D:2v40A01,SMART_domains:SM00788,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 244437721 244437721 A T 1 0 0 0 0 0 1 0 0 421 224 8 4 4 ADSS 1 244437721 Nonsense_Mutation SNP A C3L-01632_T 6835630 244437721 4518701 16 7221 SMYD3 0 . GRCh38 1 246330530 246330530 + Missense_Mutation SNP C C G C3L-01632_T C3L-01632_N C C c.344G>C p.Gly115Ala p.G115A ENST00000490107 4/12 128 114 14 156 156 0 strelka-varscan SMYD3,missense_variant,p.Gly115Ala,ENST00000490107,NM_001167740.1;SMYD3,missense_variant,p.Gly56Ala,ENST00000630181,NM_022743.2;SMYD3,missense_variant,p.Gly115Ala,ENST00000403792,;SMYD3,missense_variant,p.Gly56Ala,ENST00000455277,;SMYD3,missense_variant,p.Gly56Ala,ENST00000453676,;SMYD3,non_coding_transcript_exon_variant,,ENST00000470863,;SMYD3,non_coding_transcript_exon_variant,,ENST00000462422,; G ENST00000490107 Transcript missense_variant 384/1548 344/1287 115/428 G/A gGa/gCa COSM277402 1 -1 SMYD3 HGNC HGNC:15513 protein_coding YES CCDS53486.1 ENSP00000419184 Q9H7B4 UPI000022AFDA NM_001167740.1 tolerated(0.47) 4/12 Pfam_domain:PF00856,PROSITE_profiles:PS50280,PROSITE_profiles:PS51574,hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF163,SMART_domains:SM00317,Superfamily_domains:SSF82199 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 246330530 246330530 C G 1 0 0 0 0 1 0 0 0 15144 855 30 4 4 SMYD3 1 246330530 Missense_Mutation SNP C C3L-01632_T 1892809 246330530 2625892 17 7222 NLRP3 0 . GRCh38 1 247424954 247424954 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1511G>T p.Arg504Met p.R504M ENST00000336119 3/9 268 161 107 413 412 1 strelka-varscan NLRP3,missense_variant,p.Arg504Met,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Arg504Met,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Arg504Met,ENST00000366496,;NLRP3,missense_variant,p.Arg504Met,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Arg504Met,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Arg504Met,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; T ENST00000336119 Transcript missense_variant 2257/4170 1511/3111 504/1036 R/M aGg/aTg 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 deleterious(0) 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 247424954 247424954 G T 1 0 0 0 0 1 0 0 0 10516 1000 35 2 2 NLRP3 1 247424954 Missense_Mutation SNP G C3L-01632_T 1094424 247424954 1531468 18 7223 OR11L1 0 . GRCh38 1 247841880 247841880 + Missense_Mutation SNP G G C C3L-01632_T C3L-01632_N G G c.17C>G p.Thr6Ser p.T6S ENST00000355784 1/1 94 61 33 114 114 0 strelka-varscan OR11L1,missense_variant,p.Thr6Ser,ENST00000355784,NM_001001959.1; C ENST00000355784 Transcript missense_variant 17/969 17/969 6/322 T/S aCc/aGc COSM357935 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 tolerated(0.74) 1/1 hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 247841880 247841880 G C 1 0 0 0 0 1 0 0 0 11007 1261 44 4 4 OR11L1 1 247841880 Missense_Mutation SNP G C3L-01632_T 416926 247841880 1114542 19 7224 OR2L2 0 . GRCh38 1 248039055 248039055 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.788C>A p.Ser263Tyr p.S263Y ENST00000366479 1/1 219 147 72 282 281 1 strelka-varscan OR2L2,missense_variant,p.Ser263Tyr,ENST00000366479,NM_001004686.2; A ENST00000366479 Transcript missense_variant 788/939 788/939 263/312 S/Y tCc/tAc 1 1 OR2L2 HGNC HGNC:8266 protein_coding YES CCDS31103.1 ENSP00000355435 Q8NH16 A0A126GW34 UPI0000061EAA NM_001004686.2 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF189,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 248039055 248039055 C A 1 0 0 0 0 1 0 0 0 11085 855 30 2 2 OR2L2 1 248039055 Missense_Mutation SNP C C3L-01632_T 197175 248039055 917367 20 7225 OR14C36 0 . GRCh38 1 248348883 248348883 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.109C>A p.Leu37Ile p.L37I ENST00000317861 1/1 204 169 35 282 281 1 strelka-varscan OR14C36,missense_variant,p.Leu37Ile,ENST00000317861,NM_001001918.1; A ENST00000317861 Transcript missense_variant 109/939 109/939 37/312 L/I Cta/Ata COSM3487131 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 tolerated(0.06) 1/1 hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 248348883 248348883 C A 1 0 0 0 0 1 0 0 0 11023 912 32 2 2 OR14C36 1 248348883 Missense_Mutation SNP C C3L-01632_T 309828 248348883 607539 21 7226 ZNF692 0 . GRCh38 1 248857278 248857278 + Missense_Mutation SNP C C A rs758599570 C3L-01632_T C3L-01632_N C C c.446G>T p.Arg149Leu p.R149L ENST00000451251 4/12 207 182 25 303 303 0 strelka-varscan ZNF692,missense_variant,p.Arg149Leu,ENST00000451251,NM_001136036.2;ZNF692,missense_variant,p.Arg144Leu,ENST00000306601,NM_017865.3;ZNF692,missense_variant,p.Arg144Leu,ENST00000366471,NM_001193328.1;ZNF692,upstream_gene_variant,,ENST00000476503,;ZNF692,downstream_gene_variant,,ENST00000496231,;AL672294.1,upstream_gene_variant,,ENST00000417047,;ZNF692,non_coding_transcript_exon_variant,,ENST00000468455,;ZNF692,downstream_gene_variant,,ENST00000533614,;ZNF692,downstream_gene_variant,,ENST00000495731,;ZNF692,missense_variant,p.Arg74Leu,ENST00000477070,;ZNF692,3_prime_UTR_variant,,ENST00000463519,;ZNF692,3_prime_UTR_variant,,ENST00000412341,;ZNF692,3_prime_UTR_variant,,ENST00000496411,;ZNF692,3_prime_UTR_variant,,ENST00000483223,;ZNF692,3_prime_UTR_variant,,ENST00000533647,;ZNF692,non_coding_transcript_exon_variant,,ENST00000533927,;ZNF692,non_coding_transcript_exon_variant,,ENST00000470787,;ZNF692,non_coding_transcript_exon_variant,,ENST00000478107,;ZNF692,non_coding_transcript_exon_variant,,ENST00000491971,;ZNF692,downstream_gene_variant,,ENST00000497847,;ZNF692,downstream_gene_variant,,ENST00000530699,;ZNF692,upstream_gene_variant,,ENST00000474351,;ZNF692,upstream_gene_variant,,ENST00000482023,;ZNF692,upstream_gene_variant,,ENST00000462037,;ZNF692,downstream_gene_variant,,ENST00000496053,;ZNF692,downstream_gene_variant,,ENST00000483791,;ZNF692,downstream_gene_variant,,ENST00000530986,;ZNF692,downstream_gene_variant,,ENST00000534456,;ZNF692,downstream_gene_variant,,ENST00000528141,;ZNF692,downstream_gene_variant,,ENST00000534660,;ZNF692,downstream_gene_variant,,ENST00000533976,; A ENST00000451251 Transcript missense_variant 792/2065 446/1575 149/524 R/L cGg/cTg rs758599570,COSM4816971 1 -1 ZNF692 HGNC HGNC:26049 protein_coding YES CCDS44348.1 ENSP00000391200 Q9BU19 UPI00017A804A NM_001136036.2 tolerated(0.25) 4/12 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 248857278 248857278 C A 1 0 0 0 0 1 0 0 0 18670 652 23 1 1 ZNF692 1 248857278 Missense_Mutation SNP C C3L-01632_T 508395 248857278 99144 22 7227 NBAS 0 . GRCh38 2 15558593 15558593 + Silent SNP C C A C3L-01632_T C3L-01632_N C C c.159G>T p.= p.T53T ENST00000281513 2/52 190 164 26 310 310 0 strelka-varscan-mutect NBAS,synonymous_variant,p.=,ENST00000281513,NM_015909.3; A ENST00000281513 Transcript synonymous_variant 185/7281 159/7116 53/2371 T acG/acT COSM235019 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 2/52 hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 15558593 15558593 C A 1 0 0 0 0 0 0 0 1 10197 871 31 1 1 NBAS 2 15558593 Silent SNP C C3L-01632_T 15558593 226634936 23 7228 LTBP1 0 . GRCh38 2 32948922 32948922 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.542C>A p.Pro181His p.P181H ENST00000404816 2/34 250 200 50 360 359 1 strelka-varscan LTBP1,missense_variant,p.Pro181His,ENST00000404816,NM_206943.2;Y_RNA,upstream_gene_variant,,ENST00000384224,; A ENST00000404816 Transcript missense_variant 895/6333 542/5166 181/1721 P/H cCt/cAt 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0) 2/34 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 32948922 32948922 C A 1 0 0 0 0 1 0 0 0 8979 681 24 2 2 LTBP1 2 32948922 Missense_Mutation SNP C C3L-01632_T 17390329 32948922 209244607 24 7229 PLEKHH2 0 . GRCh38 2 43678902 43678902 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.163C>A p.Gln55Lys p.Q55K ENST00000282406 3/30 60 50 10 111 111 0 strelka-varscan-mutect PLEKHH2,missense_variant,p.Gln55Lys,ENST00000282406,NM_172069.3;C1GALT1C1L,upstream_gene_variant,,ENST00000475092,NM_001101330.2;PLEKHH2,missense_variant,p.Gln55Lys,ENST00000491692,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405000,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405223,;AC011242.5,downstream_gene_variant,,ENST00000433596,; A ENST00000282406 Transcript missense_variant 273/6981 163/4482 55/1493 Q/K Caa/Aaa 1 1 PLEKHH2 HGNC HGNC:30506 protein_coding YES CCDS1812.1 ENSP00000282406 Q8IVE3 UPI000016021B NM_172069.3 tolerated(0.06) 3/30 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22903,hmmpanther:PTHR22903:SF3 MODERATE 1 SNV 1 1 PASS . . 0 192 16 2 0 0 0 0 -18.20432 0.9953897 1 1 1 0 A 3 1 24 43678902 43678902 C A 1 0 0 0 0 1 0 0 0 12170 827 29 2 2 PLEKHH2 2 43678902 Missense_Mutation SNP C C3L-01632_T 10729980 43678902 198514627 25 7230 KIAA1841 0 . GRCh38 2 61117369 61117369 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.1849G>A p.Asp617Asn p.D617N ENST00000402291 18/22 277 232 45 405 405 0 strelka-varscan-mutect KIAA1841,missense_variant,p.Asp617Asn,ENST00000402291,NM_001129993.1;KIAA1841,missense_variant,p.Asp617Asn,ENST00000453873,;KIAA1841,missense_variant,p.Asp471Asn,ENST00000612149,;KIAA1841,missense_variant,p.Asp617Asn,ENST00000295031,NM_032506.2;KIAA1841,missense_variant,p.Asp617Asn,ENST00000356719,;RP11-493E12.3,non_coding_transcript_exon_variant,,ENST00000462959,;KIAA1841,non_coding_transcript_exon_variant,,ENST00000488322,;KIAA1841,3_prime_UTR_variant,,ENST00000453186,;KIAA1841,non_coding_transcript_exon_variant,,ENST00000471625,; A ENST00000402291 Transcript missense_variant 2090/4516 1849/2157 617/718 D/N Gat/Aat 1 1 KIAA1841 HGNC HGNC:29387 protein_coding YES CCDS46296.1 ENSP00000385579 Q6NSI8 UPI0000197410 NM_001129993.1 tolerated(0.17) 18/22 hmmpanther:PTHR20946:SF0,hmmpanther:PTHR20946 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 61117369 61117369 G A 1 0 0 0 0 1 0 0 0 8129 942 33 3 3 KIAA1841 2 61117369 Missense_Mutation SNP G C3L-01632_T 17438467 61117369 181076160 26 7231 LRP2 0 . GRCh38 2 169318877 169318877 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.195G>T p.= p.V65V ENST00000263816 3/79 466 386 80 602 600 2 strelka-varscan-mutect LRP2,synonymous_variant,p.=,ENST00000263816,NM_004525.2;LRP2,synonymous_variant,p.=,ENST00000443831,; A ENST00000263816 Transcript synonymous_variant 481/15808 195/13968 65/4655 V gtG/gtT 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 3/79 Gene3D:4.10.400.10,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 169318877 169318877 C A 1 0 0 0 0 0 0 0 1 8851 813 29 2 2 LRP2 2 169318877 Silent SNP C C3L-01632_T 108201508 169318877 72874652 27 7232 FAM171B 0 . GRCh38 2 186762804 186762804 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.2462C>A p.Pro821Gln p.P821Q ENST00000304698 8/8 55 47 8 117 117 0 strelka-varscan-mutect FAM171B,missense_variant,p.Pro821Gln,ENST00000304698,NM_177454.3; A ENST00000304698 Transcript missense_variant 2665/5826 2462/2481 821/826 P/Q cCa/cAa 1 1 FAM171B HGNC HGNC:29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 UPI0000161631 NM_177454.3 deleterious(0) 8/8 hmmpanther:PTHR31626:SF2,hmmpanther:PTHR31626,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -18.73777 1 1 1 1 0 A 3 1 24 186762804 186762804 C A 1 0 0 0 0 1 0 0 0 5339 594 21 2 2 FAM171B 2 186762804 Missense_Mutation SNP C C3L-01632_T 17443927 186762804 55430725 28 7233 IQCA1 0 . GRCh38 2 236419186 236419186 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1118C>A p.Ala373Asp p.A373D ENST00000431676 8/19 146 115 31 239 237 2 strelka-varscan-mutect IQCA1,missense_variant,p.Ala366Asp,ENST00000409907,NM_024726.4;IQCA1,missense_variant,p.Ala373Asp,ENST00000431676,NM_001270585.1;IQCA1,missense_variant,p.Ala385Asp,ENST00000418802,;IQCA1,intron_variant,,ENST00000309507,NM_001270584.1;IQCA1,non_coding_transcript_exon_variant,,ENST00000465621,;IQCA1,missense_variant,p.Ala366Asp,ENST00000254653,; T ENST00000431676 Transcript missense_variant 1153/3069 1118/2493 373/830 A/D gCc/gAc 1 -1 IQCA1 HGNC HGNC:26195 protein_coding YES CCDS74677.1 ENSP00000407213 A0A0A0MSY6 UPI0001AE77A0 NM_001270585.1 tolerated(0.16) 8/19 hmmpanther:PTHR14690,hmmpanther:PTHR14690:SF8,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 174 10 18 7 0 0 0 -19.24598 0.08500824 0 1 0 0 T 3 4 24 236419186 236419186 G T 1 0 0 0 0 1 0 0 0 7705 1203 42 2 2 IQCA1 2 236419186 Missense_Mutation SNP G C3L-01632_T 49656382 236419186 5774343 29 7234 GAL3ST2 0 . GRCh38 2 241803459 241803459 + Missense_Mutation SNP G G T C3L-01632_T C3L-01632_N G G c.490G>T p.Ala164Ser p.A164S ENST00000192314 4/4 214 184 30 376 375 1 strelka-varscan-mutect GAL3ST2,missense_variant,p.Ala164Ser,ENST00000192314,NM_022134.2;AC114730.3,downstream_gene_variant,,ENST00000413820,;AC114730.5,upstream_gene_variant,,ENST00000437438,; T ENST00000192314 Transcript missense_variant 621/1370 490/1197 164/398 A/S Gcc/Tcc COSM1207821 1 1 GAL3ST2 HGNC HGNC:24869 protein_coding YES CCDS33427.1 ENSP00000192314 Q9H3Q3 UPI000049DF44 NM_022134.2 tolerated(0.59) 4/4 hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF55,Pfam_domain:PF06990,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs750473496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 241803459 241803459 G T 1 0 0 0 0 1 0 0 0 6066 1087 38 1 1 GAL3ST2 2 241803459 Missense_Mutation SNP G C3L-01632_T 5384273 241803459 390070 30 7235 FANCD2 0 . GRCh38 3 10094345 10094345 + Missense_Mutation SNP C C G novel C3L-01632_T C3L-01632_N C C c.3945C>G p.Phe1315Leu p.F1315L ENST00000287647 40/43 416 383 33 611 611 0 strelka-varscan-mutect FANCD2,missense_variant,p.Phe1315Leu,ENST00000287647,NM_033084.3;FANCD2,missense_variant,p.Phe1315Leu,ENST00000419585,NM_001319984.1;FANCD2,missense_variant,p.Phe1315Leu,ENST00000383807,NM_001018115.1;FANCD2OS,intron_variant,,ENST00000524279,NM_173472.1;FANCD2,intron_variant,,ENST00000470028,;FANCD2OS,intron_variant,,ENST00000436517,;FANCD2OS,intron_variant,,ENST00000431315,;FANCD2,3_prime_UTR_variant,,ENST00000421731,; G ENST00000287647 Transcript missense_variant 4038/5219 3945/4416 1315/1471 F/L ttC/ttG 1 1 FANCD2 HGNC HGNC:3585 protein_coding YES CCDS2595.1 ENSP00000287647 Q9BXW9 UPI000006F678 NM_033084.3 tolerated(0.22) 40/43 hmmpanther:PTHR32086,Pfam_domain:PF14631 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 10094345 10094345 C G 1 0 0 0 0 1 0 0 0 5524 825 29 4 4 FANCD2 3 10094345 Missense_Mutation SNP C C3L-01632_T 10094345 188201214 31 7236 KCNH8 0 . GRCh38 3 19533557 19533557 + Missense_Mutation SNP T T G novel C3L-01632_T C3L-01632_N T T c.2782T>G p.Trp928Gly p.W928G ENST00000328405 16/16 358 340 18 538 538 0 strelka-varscan-mutect KCNH8,missense_variant,p.Trp928Gly,ENST00000328405,NM_144633.2;KCNH8,3_prime_UTR_variant,,ENST00000452398,; G ENST00000328405 Transcript missense_variant 3048/5137 2782/3324 928/1107 W/G Tgg/Ggg 1 1 KCNH8 HGNC HGNC:18864 protein_coding YES CCDS2632.1 ENSP00000328813 Q96L42 UPI0000167D12 NM_144633.2 tolerated_low_confidence(0.09) 16/16 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 19533557 19533557 T G 1 0 0 0 0 1 0 0 0 7954 1580 55 5 5 KCNH8 3 19533557 Missense_Mutation SNP T C3L-01632_T 9439212 19533557 178762002 32 7237 NEK10 0 . GRCh38 3 27344326 27344326 + Missense_Mutation SNP C C A rs200401044 C3L-01632_T C3L-01632_N C C c.308G>T p.Arg103Leu p.R103L ENST00000341435 6/25 170 146 24 258 258 0 strelka-varscan-mutect NEK10,missense_variant,p.Arg103Leu,ENST00000429845,NM_152534.4;NEK10,missense_variant,p.Arg103Leu,ENST00000341435,NM_199347.3;NEK10,missense_variant,p.Arg103Leu,ENST00000435750,;NEK10,non_coding_transcript_exon_variant,,ENST00000491627,; A ENST00000341435 Transcript missense_variant 582/2638 308/2139 103/712 R/L cGt/cTt rs200401044,COSM1043439,COSM1593597,COSM1593598 1 -1 NEK10 HGNC HGNC:18592 protein_coding YES CCDS46781.1 ENSP00000343847 Q6ZWH5 UPI00001C089B NM_199347.3 tolerated(0.07) 6/25 0,1,1,1 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs200401044 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 27344326 27344326 C A 1 0 0 0 0 1 0 0 0 10350 536 19 1 1 NEK10 3 27344326 Missense_Mutation SNP C C3L-01632_T 7810769 27344326 170951233 33 7238 DOCK3 0 . GRCh38 3 51381545 51381545 + Nonsense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.6079C>T p.Arg2027Ter p.R2027* ENST00000266037 53/53 33 26 7 78 78 0 strelka-varscan-mutect DOCK3,stop_gained,p.Arg2027Ter,ENST00000266037,NM_004947.4;MANF,upstream_gene_variant,,ENST00000528157,NM_006010.5;MANF,upstream_gene_variant,,ENST00000470900,;MANF,upstream_gene_variant,,ENST00000446668,; T ENST00000266037 Transcript stop_gained 6102/8755 6079/6093 2027/2030 R/* Cga/Tga 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 53/53 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 51381545 51381545 C T 1 0 0 0 0 0 1 0 0 4503 644 23 1 1 DOCK3 3 51381545 Nonsense_Mutation SNP C C3L-01632_T 24037219 51381545 146914014 34 7239 ALAS1 0 . GRCh38 3 52202683 52202683 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.376G>A p.Ala126Thr p.A126T ENST00000394965 4/12 186 171 15 326 325 1 strelka-varscan-mutect ALAS1,missense_variant,p.Ala126Thr,ENST00000394965,NM_000688.5,NM_001304444.1;ALAS1,missense_variant,p.Ala126Thr,ENST00000484952,;ALAS1,missense_variant,p.Ala126Thr,ENST00000310271,NM_001304443.1,NM_199166.2;ALAS1,missense_variant,p.Ala126Thr,ENST00000469224,;ALAS1,upstream_gene_variant,,ENST00000493402,; A ENST00000394965 Transcript missense_variant 736/2430 376/1923 126/640 A/T Gcc/Acc 1 1 ALAS1 HGNC HGNC:396 protein_coding YES CCDS2847.1 ENSP00000378416 P13196 Q5JAM2 UPI0000001230 NM_000688.5,NM_001304444.1 deleterious(0.02) 4/12 hmmpanther:PTHR13693,hmmpanther:PTHR13693:SF50,Pfam_domain:PF09029 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 52202683 52202683 G A 1 0 0 0 0 1 0 0 0 584 971 34 3 3 ALAS1 3 52202683 Missense_Mutation SNP G C3L-01632_T 821138 52202683 146092876 35 7240 ASB14 0 . GRCh38 3 57278573 57278573 + Missense_Mutation SNP A A T novel C3L-01632_T C3L-01632_N A A c.1235T>A p.Val412Asp p.V412D ENST00000487349 8/11 129 116 13 232 232 0 strelka-varscan-mutect ASB14,missense_variant,p.Val412Asp,ENST00000487349,NM_001142733.2;ASB14,missense_variant,p.Val412Asp,ENST00000389601,;ASB14,non_coding_transcript_exon_variant,,ENST00000515033,; T ENST00000487349 Transcript missense_variant 1356/3179 1235/1764 412/587 V/D gTc/gAc 1 -1 ASB14 HGNC HGNC:19766 protein_coding YES CCDS46856.2 ENSP00000419199 A6NK59 UPI0000E5A753 NM_001142733.2 deleterious(0) 8/11 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF0,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1384769833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 57278573 57278573 A T 1 0 0 0 0 1 0 0 0 1160 275 10 4 4 ASB14 3 57278573 Missense_Mutation SNP A C3L-01632_T 5075890 57278573 141016986 36 7241 PDZRN3 0 . GRCh38 3 73404330 73404330 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.984G>T p.Lys328Asn p.K328N ENST00000263666 4/10 195 164 31 301 301 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Lys328Asn,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Lys45Asn,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Lys26Asn,ENST00000492909,NM_001303139.1;PDZRN3,5_prime_UTR_variant,,ENST00000462146,NM_001303141.1;PDZRN3,5_prime_UTR_variant,,ENST00000466780,NM_001303140.1;PDZRN3,upstream_gene_variant,,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000308537,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000498048,;PDZRN3,upstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000477434,;PDZRN3,upstream_gene_variant,,ENST00000484487,; A ENST00000263666 Transcript missense_variant 1099/4248 984/3201 328/1066 K/N aaG/aaT 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 4/10 PROSITE_profiles:PS50106,hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 73404330 73404330 C A 1 0 0 0 0 1 0 0 0 11797 680 24 2 2 PDZRN3 3 73404330 Missense_Mutation SNP C C3L-01632_T 16125757 73404330 124891229 37 7242 TP63 0 . GRCh38 3 189868604 189868604 + Frame_Shift_Del DEL C C - novel C3L-01632_T C3L-01632_N C C c.1017delC p.Phe340LeufsTer48 p.F340Lfs*48 ENST00000264731 8/14 301 247 54 533 533 0 sindel-varindel-pindel TP63,frameshift_variant,p.Phe340LeufsTer48,ENST00000264731,NM_003722.4;TP63,frameshift_variant,p.Phe246LeufsTer48,ENST00000354600,NM_001114980.1;TP63,frameshift_variant,p.Phe340LeufsTer48,ENST00000418709,NM_001114979.1;TP63,frameshift_variant,p.Phe246LeufsTer48,ENST00000437221,NM_001114982.1;TP63,frameshift_variant,p.Phe340LeufsTer48,ENST00000320472,;TP63,frameshift_variant,p.Phe340LeufsTer44,ENST00000440651,;TP63,frameshift_variant,p.Phe246LeufsTer44,ENST00000456148,;TP63,frameshift_variant,p.Phe340LeufsTer48,ENST00000392460,NM_001114978.1;TP63,frameshift_variant,p.Phe161LeufsTer48,ENST00000449992,;TP63,frameshift_variant,p.Phe246LeufsTer48,ENST00000392463,NM_001114981.1;TP63,frameshift_variant,p.Phe246LeufsTer48,ENST00000392461,;TP63,downstream_gene_variant,,ENST00000434928,;TP63,non_coding_transcript_exon_variant,,ENST00000460036,; - ENST00000264731 Transcript frameshift_variant 1106/4909 1017/2043 339/680 C/X tgC/tg 1 1 TP63 HGNC HGNC:15979 protein_coding YES CCDS3293.1 ENSP00000264731 Q9H3D4 A0A0S2Z4N5 UPI0000073CF2 NM_003722.4 8/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF8,Pfam_domain:PF00870,Gene3D:2.60.40.720,Superfamily_domains:SSF49417,Prints_domain:PR00386 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 189868604 189868604 C - 1 0 1 0 1 0 0 0 0 16871 805 28 0 0 TP63 3 189868604 Frame_Shift_Del DEL C C3L-01632_T 116464274 189868604 8426955 38 7243 WDR19 0 . GRCh38 4 39232230 39232230 + Silent SNP G G A novel C3L-01632_T C3L-01632_N G G c.2211G>A p.= p.Q737Q ENST00000399820 19/37 97 83 14 128 128 0 strelka-varscan WDR19,synonymous_variant,p.=,ENST00000399820,NM_025132.3;WDR19,non_coding_transcript_exon_variant,,ENST00000515631,;WDR19,non_coding_transcript_exon_variant,,ENST00000511729,;WDR19,upstream_gene_variant,,ENST00000502718,;WDR19,missense_variant,p.Arg121Lys,ENST00000507228,;WDR19,3_prime_UTR_variant,,ENST00000506869,NM_001317924.1;WDR19,non_coding_transcript_exon_variant,,ENST00000512095,; A ENST00000399820 Transcript synonymous_variant 2365/4520 2211/4029 737/1342 Q caG/caA 1 1 WDR19 HGNC HGNC:18340 protein_coding YES CCDS47042.1 ENSP00000382717 Q8NEZ3 UPI000004CC24 NM_025132.3 19/37 hmmpanther:PTHR14920,hmmpanther:PTHR14920:SF0 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 39232230 39232230 G A 1 0 0 0 0 0 0 0 1 17839 991 35 3 3 WDR19 4 39232230 Silent SNP G C3L-01632_T 39232230 150982325 39 7244 RFC1 0 . GRCh38 4 39311457 39311457 + Silent SNP T T C novel C3L-01632_T C3L-01632_N T T c.1476A>G p.= p.A492A ENST00000381897 12/25 175 148 27 225 225 0 strelka-varscan RFC1,synonymous_variant,p.=,ENST00000381897,NM_001204747.1;RFC1,synonymous_variant,p.=,ENST00000349703,NM_002913.4;RFC1,synonymous_variant,p.=,ENST00000504554,;RFC1,non_coding_transcript_exon_variant,,ENST00000502706,;RFC1,downstream_gene_variant,,ENST00000509084,; C ENST00000381897 Transcript synonymous_variant 1610/4886 1476/3447 492/1148 A gcA/gcG 1 -1 RFC1 HGNC HGNC:9969 protein_coding YES CCDS56329.1 ENSP00000371321 P35251 UPI0000167BB4 NM_001204747.1 12/25 hmmpanther:PTHR23389:SF10,hmmpanther:PTHR23389,PIRSF_domain:PIRSF036578 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 24 39311457 39311457 T C 1 0 0 0 0 0 0 0 1 13415 1567 55 5 5 RFC1 4 39311457 Silent SNP T C3L-01632_T 79227 39311457 150903098 40 7245 GABRG1 0 . GRCh38 4 46058336 46058336 + Missense_Mutation SNP A A C novel C3L-01632_T C3L-01632_N A A c.797T>G p.Leu266Arg p.L266R ENST00000295452 7/9 107 92 15 154 153 1 strelka-varscan GABRG1,missense_variant,p.Leu266Arg,ENST00000295452,NM_173536.3; C ENST00000295452 Transcript missense_variant 965/6785 797/1398 266/465 L/R cTg/cGg 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 deleterious(0) 7/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR00252,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 205 2 2 0 0 0 0 -19.99993 0.9999977 1 1 1 0 C 3 2 24 46058336 46058336 A C 1 0 0 0 0 1 0 0 0 6042 188 7 5 5 GABRG1 4 46058336 Missense_Mutation SNP A C3L-01632_T 6746879 46058336 144156219 41 7246 LRRC66 0 . GRCh38 4 51995992 51995992 + Missense_Mutation SNP C C A rs369693787 C3L-01632_T C3L-01632_N C C c.1030G>T p.Gly344Cys p.G344C ENST00000343457 4/4 165 128 37 303 303 0 strelka-varscan LRRC66,missense_variant,p.Gly344Cys,ENST00000343457,NM_001024611.1; A ENST00000343457 Transcript missense_variant 1037/3327 1030/2643 344/880 G/C Ggt/Tgt rs369693787 1 -1 LRRC66 HGNC HGNC:34299 protein_coding YES CCDS43229.1 ENSP00000341944 Q68CR7 UPI0000425C5B NM_001024611.1 deleterious(0.03) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 51995992 51995992 C A 1 0 0 0 0 1 0 0 0 8914 594 21 2 2 LRRC66 4 51995992 Missense_Mutation SNP C C3L-01632_T 5937656 51995992 138218563 42 7247 UGT2B11 0 . GRCh38 4 69208424 69208424 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.929G>T p.Gly310Val p.G310V ENST00000446444 3/6 206 164 42 304 302 2 strelka-varscan-mutect UGT2B11,missense_variant,p.Gly310Val,ENST00000446444,NM_001073.1;RP11-704M14.1,intron_variant,,ENST00000505646,;RP11-704M14.1,intron_variant,,ENST00000504301,;UGT2B11,upstream_gene_variant,,ENST00000513315,; A ENST00000446444 Transcript missense_variant 938/2088 929/1590 310/529 G/V gGg/gTg 1 -1 UGT2B11 HGNC HGNC:12545 protein_coding YES CCDS3527.1 ENSP00000387683 O75310 UPI0000137A97 NM_001073.1 deleterious(0) 3/6 Gene3D:3.40.50.2000,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF365,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 69208424 69208424 C A 1 0 0 0 0 1 0 0 0 17481 623 22 2 2 UGT2B11 4 69208424 Missense_Mutation SNP C C3L-01632_T 17212432 69208424 121006131 43 7248 PTPN13 0 . GRCh38 4 86745069 86745069 + Missense_Mutation SNP A A G novel C3L-01632_T C3L-01632_N A A c.2591A>G p.Gln864Arg p.Q864R ENST00000436978 17/48 106 89 17 195 195 0 strelka-varscan-mutect PTPN13,missense_variant,p.Gln864Arg,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Gln864Arg,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Gln864Arg,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Gln864Arg,ENST00000511467,;PTPN13,missense_variant,p.Gln864Arg,ENST00000316707,NM_080684.2; G ENST00000436978 Transcript missense_variant 3071/8573 2591/7473 864/2490 Q/R cAg/cGg 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0.01) 17/48 PROSITE_profiles:PS50057,hmmpanther:PTHR19134:SF197,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000933,Gene3D:2.30.29.30,Pfam_domain:PF09380,SMART_domains:SM01196,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 86745069 86745069 A G 1 0 0 0 0 1 0 0 0 12935 188 7 5 5 PTPN13 4 86745069 Missense_Mutation SNP A C3L-01632_T 17536645 86745069 103469486 44 7249 ADH7 0 . GRCh38 4 99415497 99415497 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1141C>A p.Leu381Met p.L381M ENST00000476959 8/9 60 56 4 120 120 0 varscan-mutect ADH7,missense_variant,p.Leu361Met,ENST00000437033,;ADH7,missense_variant,p.Leu373Met,ENST00000209665,NM_000673.4;ADH7,missense_variant,p.Leu304Met,ENST00000482593,;ADH7,missense_variant,p.Leu381Met,ENST00000476959,NM_001166504.1;ADH7,non_coding_transcript_exon_variant,,ENST00000485660,; T ENST00000476959 Transcript missense_variant 1171/1325 1141/1185 381/394 L/M Ctg/Atg 1 -1 ADH7 HGNC HGNC:256 protein_coding YES CCDS54781.1 ENSP00000420269 P40394 UPI00017A81B5 NM_001166504.1 deleterious(0.01) 8/9 hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF355,Superfamily_domains:SSF50129 MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -10.09091 1 1 1 1 0 T 3 4 24 99415497 99415497 G T 1 0 0 0 0 1 0 0 0 386 962 34 2 2 ADH7 4 99415497 Missense_Mutation SNP G C3L-01632_T 12670428 99415497 90799058 45 7250 USP38 0 . GRCh38 4 143213779 143213779 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1803G>T p.Leu601Phe p.L601F ENST00000307017 9/10 137 106 31 245 244 1 strelka-varscan-mutect USP38,missense_variant,p.Leu601Phe,ENST00000307017,NM_001290326.1,NM_032557.6;USP38,missense_variant,p.Leu601Phe,ENST00000510377,NM_001290325.1;USP38,3_prime_UTR_variant,,ENST00000511739,; T ENST00000307017 Transcript missense_variant 2309/7009 1803/3129 601/1042 L/F ttG/ttT 1 1 USP38 HGNC HGNC:20067 protein_coding YES CCDS3758.1 ENSP00000303434 Q8NB14 UPI0000047AF9 NM_001290326.1,NM_032557.6 deleterious(0) 9/10 Gene3D:1nbfA02,Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF500,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 143213779 143213779 G T 1 0 0 0 0 1 0 0 0 17611 1281 45 2 2 USP38 4 143213779 Missense_Mutation SNP G C3L-01632_T 43798282 143213779 47000776 46 7251 FSTL5 0 . GRCh38 4 161542623 161542623 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1086C>A p.Cys362Ter p.C362* ENST00000306100 9/16 138 130 8 188 188 0 strelka-varscan-mutect FSTL5,stop_gained,p.Cys362Ter,ENST00000306100,NM_020116.4;FSTL5,stop_gained,p.Cys361Ter,ENST00000379164,NM_001128427.2;FSTL5,stop_gained,p.Cys361Ter,ENST00000427802,NM_001128428.2;FSTL5,non_coding_transcript_exon_variant,,ENST00000511170,; T ENST00000306100 Transcript stop_gained 1523/4831 1086/2544 362/847 C/* tgC/tgA 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 9/16 PROSITE_profiles:PS50835,hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -10.96594 0.9994467 1 1 1 0 T 4 4 24 161542623 161542623 G T 1 0 0 0 0 0 1 0 0 5954 1195 42 2 2 FSTL5 4 161542623 Nonsense_Mutation SNP G C3L-01632_T 18328844 161542623 28671932 47 7252 FSTL5 0 . GRCh38 4 161920516 161920516 + Silent SNP A A T novel C3L-01632_T C3L-01632_N A A c.297T>A p.= p.P99P ENST00000306100 4/16 280 259 21 432 432 0 strelka-varscan-mutect FSTL5,synonymous_variant,p.=,ENST00000306100,NM_020116.4;FSTL5,synonymous_variant,p.=,ENST00000379164,NM_001128427.2;FSTL5,synonymous_variant,p.=,ENST00000427802,NM_001128428.2; T ENST00000306100 Transcript synonymous_variant 734/4831 297/2544 99/847 P ccT/ccA 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 4/16 PROSITE_profiles:PS51465,hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Gene3D:3.30.60.30,Pfam_domain:PF07648,SMART_domains:SM00280,Superfamily_domains:SSF100895 LOW 1 SNV 1 1 PASS rs1231455420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 161920516 161920516 A T 1 0 0 0 0 0 0 0 1 5954 175 7 4 4 FSTL5 4 161920516 Silent SNP A C3L-01632_T 377893 161920516 28294039 48 7253 TENM3 0 . GRCh38 4 182775039 182775039 + Silent SNP G G C rs183374276 C3L-01632_T C3L-01632_N G G c.5190G>C p.= p.T1730T ENST00000511685 24/28 349 256 93 577 577 0 strelka-varscan TENM3,synonymous_variant,p.=,ENST00000511685,NM_001080477.2;RP11-18D7.2,upstream_gene_variant,,ENST00000513255,; C ENST00000511685 Transcript synonymous_variant 5313/10896 5190/8100 1730/2699 T acG/acC rs183374276 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 24/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 24 182775039 182775039 G C 1 0 0 0 0 0 0 0 1 16173 1103 39 4 4 TENM3 4 182775039 Silent SNP G C3L-01632_T 20854523 182775039 7439516 49 7254 DNAH5 0 . GRCh38 5 13701341 13701341 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.13434C>A p.His4478Gln p.H4478Q ENST00000265104 77/79 337 272 65 406 406 0 strelka-varscan-mutect DNAH5,missense_variant,p.His4478Gln,ENST00000265104,NM_001369.2; T ENST00000265104 Transcript missense_variant 13539/15633 13434/13875 4478/4624 H/Q caC/caA 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 tolerated(0.12) 77/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 13701341 13701341 G T 1 0 0 0 0 1 0 0 0 4419 1020 36 2 2 DNAH5 5 13701341 Missense_Mutation SNP G C3L-01632_T 13701341 167836918 50 7255 CDH10 0 . GRCh38 5 24492882 24492882 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1559G>T p.Gly520Val p.G520V ENST00000264463 10/12 140 116 24 199 198 1 strelka-varscan CDH10,missense_variant,p.Gly520Val,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; A ENST00000264463 Transcript missense_variant 2067/3438 1559/2367 520/788 G/V gGt/gTt 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 tolerated(0.37) 10/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 24492882 24492882 C A 1 0 0 0 0 1 0 0 0 2799 507 18 2 2 CDH10 5 24492882 Missense_Mutation SNP C C3L-01632_T 10791541 24492882 157045377 51 7256 NPR3 0 . GRCh38 5 32780741 32780741 + Silent SNP C C T C3L-01632_T C3L-01632_N C C c.1215C>T p.= p.S405S ENST00000265074 5/8 337 275 62 407 407 0 strelka-varscan NPR3,synonymous_variant,p.=,ENST00000265074,NM_001204375.1;NPR3,synonymous_variant,p.=,ENST00000326958,NM_001204376.1;NPR3,synonymous_variant,p.=,ENST00000434067,;NPR3,synonymous_variant,p.=,ENST00000415167,NM_000908.3;NPR3,synonymous_variant,p.=,ENST00000509104,;NPR3,non_coding_transcript_exon_variant,,ENST00000506712,; T ENST00000265074 Transcript synonymous_variant 1558/7344 1215/1626 405/541 S tcC/tcT COSM1067337,COSM5332799,COSM5332800 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 5/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00255 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 32780741 32780741 C T 1 0 0 0 0 0 0 0 1 10652 581 21 3 3 NPR3 5 32780741 Silent SNP C C3L-01632_T 8287859 32780741 148757518 52 7257 C9 0 . GRCh38 5 39342096 39342096 + Missense_Mutation SNP G G T rs372918983 C3L-01632_T C3L-01632_N G G c.178C>A p.Gln60Lys p.Q60K ENST00000263408 2/11 236 194 42 263 263 0 strelka-varscan C9,missense_variant,p.Gln60Lys,ENST00000263408,NM_001737.3;C9,non_coding_transcript_exon_variant,,ENST00000509186,;C9,non_coding_transcript_exon_variant,,ENST00000483232,;C9,non_coding_transcript_exon_variant,,ENST00000467285,; T ENST00000263408 Transcript missense_variant 274/2713 178/1680 60/559 Q/K Caa/Aaa rs372918983 1 -1 C9 HGNC HGNC:1358 protein_coding YES CCDS3929.1 ENSP00000263408 P02748 UPI0000001065 NM_001737.3 tolerated(0.07) 2/11 PROSITE_profiles:PS50092,hmmpanther:PTHR19325:SF362,hmmpanther:PTHR19325,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 39342096 39342096 G T 1 0 0 0 0 1 0 0 0 2169 1391 48 2 2 C9 5 39342096 Missense_Mutation SNP G C3L-01632_T 6561355 39342096 142196163 53 7258 BHMT2 0 . GRCh38 5 79077585 79077585 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.139G>T p.Glu47Ter p.E47* ENST00000255192 2/8 140 109 31 174 174 0 strelka-varscan-mutect BHMT2,stop_gained,p.Glu47Ter,ENST00000255192,NM_017614.4;BHMT2,stop_gained,p.Glu47Ter,ENST00000521567,NM_001178005.1;BHMT2,5_prime_UTR_variant,,ENST00000518666,;DMGDH,intron_variant,,ENST00000520388,;BHMT2,splice_region_variant,,ENST00000519743,;BHMT2,non_coding_transcript_exon_variant,,ENST00000523472,;BHMT2,non_coding_transcript_exon_variant,,ENST00000518758,;BHMT2,upstream_gene_variant,,ENST00000523046,; T ENST00000255192 Transcript stop_gained 205/2050 139/1092 47/363 E/* Gag/Tag 1 1 BHMT2 HGNC HGNC:1048 protein_coding YES CCDS4045.1 ENSP00000255192 Q9H2M3 A0A024RAQ0 UPI00000701B9 NM_017614.4 2/8 PROSITE_profiles:PS50970,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF115,PIRSF_domain:PIRSF037505,Gene3D:3.20.20.330,Pfam_domain:PF02574,Superfamily_domains:SSF82282 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 79077585 79077585 G T 1 0 0 0 0 0 1 0 0 1575 943 33 2 2 BHMT2 5 79077585 Nonsense_Mutation SNP G C3L-01632_T 39735489 79077585 102460674 54 7259 VCAN 0 . GRCh38 5 83538814 83538814 + Missense_Mutation SNP C C G C3L-01632_T C3L-01632_N C C c.5811C>G p.Asp1937Glu p.D1937E ENST00000265077 8/15 358 337 21 553 553 0 strelka-varscan-mutect VCAN,missense_variant,p.Asp1937Glu,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Asp950Glu,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Asp950Glu,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; G ENST00000265077 Transcript missense_variant 6376/12625 5811/10191 1937/3396 D/E gaC/gaG COSM4766736 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.39) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 1 MODERATE 1 SNV 1 1 1 PASS rs1428527779 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 83538814 83538814 C G 1 0 0 0 0 1 0 0 0 17683 564 20 4 4 VCAN 5 83538814 Missense_Mutation SNP C C3L-01632_T 4461229 83538814 97999445 55 7260 FBN2 0 . GRCh38 5 128311314 128311314 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.5060C>A p.Thr1687Asn p.T1687N ENST00000508053 45/71 289 241 48 474 474 0 strelka-varscan-mutect FBN2,missense_variant,p.Thr1687Asn,ENST00000508053,;FBN2,missense_variant,p.Thr1687Asn,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Thr1686Asn,ENST00000619499,; T ENST00000508053 Transcript missense_variant 6035/11132 5060/8739 1687/2912 T/N aCc/aAc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0.04) 45/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 128311314 128311314 G T 1 0 0 0 0 1 0 0 0 5566 1261 44 2 2 FBN2 5 128311314 Missense_Mutation SNP G C3L-01632_T 44772500 128311314 53226945 56 7261 1 6 2 2 12 G 6.909801e-05 FBN2 0 . GRCh38 5 128311325 128311325 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.5049C>A p.= p.L1683L ENST00000508053 45/71 317 256 61 486 486 0 strelka-varscan-mutect FBN2,synonymous_variant,p.=,ENST00000508053,;FBN2,synonymous_variant,p.=,ENST00000262464,NM_001999.3;FBN2,synonymous_variant,p.=,ENST00000619499,; T ENST00000508053 Transcript synonymous_variant 6024/11132 5049/8739 1683/2912 L ctC/ctA 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 45/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 128311325 128311325 G T 1 0 0 0 0 0 0 0 1 5566 1277 45 2 2 FBN2 5 128311325 Silent SNP G C3L-01632_T 11 128311325 53226934 57 7262 1 6 2 2 12 G 6.909801e-05 FNIP1 0 . GRCh38 5 131671508 131671508 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.2936C>T p.Pro979Leu p.P979L ENST00000510461 14/18 57 45 12 122 122 0 strelka-varscan-mutect FNIP1,missense_variant,p.Pro731Leu,ENST00000615660,;FNIP1,missense_variant,p.Pro951Leu,ENST00000307968,NM_001008738.2;FNIP1,missense_variant,p.Pro934Leu,ENST00000307954,;FNIP1,missense_variant,p.Pro979Leu,ENST00000510461,NM_133372.2;CTC-432M15.3,intron_variant,,ENST00000514667,; A ENST00000510461 Transcript missense_variant 3032/3845 2936/3501 979/1166 P/L cCt/cTt 1 -1 FNIP1 HGNC HGNC:29418 protein_coding YES CCDS34227.1 ENSP00000421985 Q8TF40 UPI00001AEE81 NM_133372.2 deleterious(0) 14/18 Pfam_domain:PF14638,hmmpanther:PTHR21634,hmmpanther:PTHR21634:SF12 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 131671508 131671508 G A 1 0 0 0 0 1 0 0 0 5833 1014 35 3 3 FNIP1 5 131671508 Missense_Mutation SNP G C3L-01632_T 3360183 131671508 49866751 58 7263 CSF2 0 . GRCh38 5 132075773 132075773 + Missense_Mutation SNP C C T rs755412035 C3L-01632_T C3L-01632_N C C c.356C>T p.Thr119Ile p.T119I ENST00000296871 4/4 275 230 45 422 420 2 strelka-varscan-mutect CSF2,missense_variant,p.Thr119Ile,ENST00000296871,NM_000758.3;snoZ6,upstream_gene_variant,,ENST00000517258,; T ENST00000296871 Transcript missense_variant 390/787 356/435 119/144 T/I aCc/aTc rs755412035 1 1 CSF2 HGNC HGNC:2434 protein_coding YES CCDS4150.1 ENSP00000296871 P04141 UPI00000358DB NM_000758.3 deleterious(0.03) 4/4 Gene3D:1.20.1250.10,PD007349,Pfam_domain:PF01109,Prints_domain:PR00693,hmmpanther:PTHR10059,hmmpanther:PTHR10059:SF0,SMART_domains:SM00040,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS rs755412035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 132075773 132075773 C T 1 0 0 0 0 1 0 0 0 3734 507 18 3 3 CSF2 5 132075773 Missense_Mutation SNP C C3L-01632_T 404265 132075773 49462486 59 7264 SLIT3 0 . GRCh38 5 168671243 168671243 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.4103G>T p.Gly1368Val p.G1368V ENST00000332966 34/36 119 96 23 203 203 0 strelka-varscan-mutect SLIT3,missense_variant,p.Gly1361Val,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Gly1231Val,ENST00000404867,;SLIT3,missense_variant,p.Gly1368Val,ENST00000332966,NM_001271946.1;CTC-558O2.2,downstream_gene_variant,,ENST00000520041,; A ENST00000332966 Transcript missense_variant 4176/4895 4103/4593 1368/1530 G/V gGc/gTc 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 deleterious(0.02) 34/36 PROSITE_profiles:PS50026,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Pfam_domain:PF12661,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999962 1 1 1 0 A 3 1 24 168671243 168671243 C A 1 0 0 0 0 1 0 0 0 15032 739 26 2 2 SLIT3 5 168671243 Missense_Mutation SNP C C3L-01632_T 36595470 168671243 12867016 60 7265 FAM196B 0 . GRCh38 5 169882654 169882654 + Silent SNP T T G novel C3L-01632_T C3L-01632_N T T c.1245A>C p.= p.R415R ENST00000377365 2/4 222 205 17 306 305 1 strelka-mutect FAM196B,synonymous_variant,p.=,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; G ENST00000377365 Transcript synonymous_variant 2627/2999 1245/1608 415/535 R cgA/cgC 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 24 169882654 169882654 T G 1 0 0 0 0 0 0 0 1 5374 1654 58 5 5 FAM196B 5 169882654 Silent SNP T C3L-01632_T 1211411 169882654 11655605 61 7266 LCP2 0 . GRCh38 5 170270816 170270816 + Missense_Mutation SNP G G C rs561432915 C3L-01632_T C3L-01632_N G G c.426C>G p.Asp142Glu p.D142E ENST00000046794 7/21 147 120 27 182 182 0 strelka-varscan-mutect LCP2,missense_variant,p.Asp142Glu,ENST00000046794,NM_005565.3;LCP2,missense_variant,p.Asp142Glu,ENST00000628092,;LCP2,upstream_gene_variant,,ENST00000521416,;LCP2,upstream_gene_variant,,ENST00000520344,;LCP2,non_coding_transcript_exon_variant,,ENST00000519594,;LCP2,downstream_gene_variant,,ENST00000522760,;LCP2,downstream_gene_variant,,ENST00000522823,; C ENST00000046794 Transcript missense_variant 1042/4678 426/1602 142/533 D/E gaC/gaG rs561432915,COSM4919377,COSM4919378 1 -1 LCP2 HGNC HGNC:6529 protein_coding YES CCDS47339.1 ENSP00000046794 Q13094 UPI000012E2AE NM_005565.3 tolerated(0.11) 7/21 hmmpanther:PTHR14098,hmmpanther:PTHR14098:SF1,Low_complexity_(Seg):seg 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs561432915 . 0 207 0 3 0 0 0 0 -20 0.9999958 1 1 1 0 C 3 2 24 170270816 170270816 G C 1 0 0 0 0 1 0 0 0 8598 1136 40 4 4 LCP2 5 170270816 Missense_Mutation SNP G C3L-01632_T 388162 170270816 11267443 62 7267 ZNF354C 0 . GRCh38 5 179079654 179079654 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1222G>T p.Gly408Ter p.G408* ENST00000315475 5/5 174 130 44 305 305 0 strelka-varscan-mutect ZNF354C,stop_gained,p.Gly408Ter,ENST00000315475,NM_014594.1;RP11-281O15.7,downstream_gene_variant,,ENST00000523735,; T ENST00000315475 Transcript stop_gained 1528/5411 1222/1665 408/554 G/* Gga/Tga 1 1 ZNF354C HGNC HGNC:16736 protein_coding YES CCDS4443.1 ENSP00000324064 Q86Y25 UPI0000161A6A NM_014594.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF140,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 206 0 0 3 0 0 0 -20 0.9868152 1 1 1 0 T 4 4 24 179079654 179079654 G T 1 0 0 0 0 0 1 0 0 18438 1349 47 2 2 ZNF354C 5 179079654 Nonsense_Mutation SNP G C3L-01632_T 8808838 179079654 2458605 63 7268 RREB1 0 . GRCh38 6 7229303 7229303 + Nonsense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.1204C>T p.Gln402Ter p.Q402* ENST00000379938 10/13 146 131 15 318 318 0 strelka-varscan-mutect RREB1,stop_gained,p.Gln402Ter,ENST00000379938,NM_001003699.3;RREB1,stop_gained,p.Gln402Ter,ENST00000349384,NM_001003698.3;RREB1,stop_gained,p.Gln402Ter,ENST00000379933,NM_001168344.1;RREB1,stop_gained,p.Gln402Ter,ENST00000334984,NM_001003700.1;RREB1,stop_gained,p.Gln402Ter,ENST00000483150,;RREB1,upstream_gene_variant,,ENST00000611109,; T ENST00000379938 Transcript stop_gained 1741/8778 1204/5229 402/1742 Q/* Cag/Tag 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 10/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.98818 0.9999999 1 1 1 0 T 4 4 24 7229303 7229303 C T 1 0 0 0 0 0 1 0 0 13933 827 29 3 3 RREB1 6 7229303 Nonsense_Mutation SNP C C3L-01632_T 7229303 163576676 64 7269 ZNF184 0 . GRCh38 6 27452289 27452289 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1270G>T p.Gly424Trp p.G424W ENST00000211936 6/6 126 111 15 245 245 0 strelka-varscan-mutect ZNF184,missense_variant,p.Gly424Trp,ENST00000211936,NM_001318892.1,NM_007149.2;ZNF184,missense_variant,p.Gly424Trp,ENST00000377419,; A ENST00000211936 Transcript missense_variant 1555/3101 1270/2256 424/751 G/W Ggg/Tgg 1 -1 ZNF184 HGNC HGNC:12975 protein_coding YES CCDS4624.1 ENSP00000211936 Q99676 A0A024RCM2 UPI000013C311 NM_001318892.1,NM_007149.2 deleterious(0) 6/6 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF22,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 27452289 27452289 C A 1 0 0 0 0 1 0 0 0 18331 594 21 2 2 ZNF184 6 27452289 Missense_Mutation SNP C C3L-01632_T 20222986 27452289 143353690 65 7270 GRM4 0 . GRCh38 6 34133137 34133137 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.360G>A p.= p.L120L ENST00000538487 2/11 110 87 23 223 222 1 strelka-varscan-mutect GRM4,synonymous_variant,p.=,ENST00000374181,NM_001256811.2;GRM4,synonymous_variant,p.=,ENST00000538487,NM_000841.3;GRM4,intron_variant,,ENST00000374177,NM_001256809.2;GRM4,synonymous_variant,p.=,ENST00000609278,;GRM4,non_coding_transcript_exon_variant,,ENST00000607916,;GRM4,upstream_gene_variant,,ENST00000609973,; T ENST00000538487 Transcript synonymous_variant 804/4153 360/2739 120/912 L ctG/ctA 1 -1 GRM4 HGNC HGNC:4596 protein_coding YES CCDS4787.1 ENSP00000440556 Q14833 A1L4F9 UPI000004A7DE NM_000841.3 2/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF23,Superfamily_domains:SSF53822 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 34133137 34133137 C T 1 0 0 0 0 0 0 0 1 6681 813 29 3 3 GRM4 6 34133137 Silent SNP C C3L-01632_T 6680848 34133137 136672842 66 7271 CUL9 0 . GRCh38 6 43198711 43198711 + Missense_Mutation SNP G G C rs145736095 C3L-01632_T C3L-01632_N G G c.2906G>C p.Arg969Pro p.R969P ENST00000252050 12/41 341 292 49 501 501 0 strelka-varscan-mutect CUL9,missense_variant,p.Arg969Pro,ENST00000252050,NM_015089.3;CUL9,missense_variant,p.Arg969Pro,ENST00000372647,;CUL9,non_coding_transcript_exon_variant,,ENST00000515773,;CUL9,upstream_gene_variant,,ENST00000515344,; C ENST00000252050 Transcript missense_variant 2990/7780 2906/7554 969/2517 R/P cGt/cCt rs145736095,COSM1319088 1 1 CUL9 HGNC HGNC:15982 protein_coding YES CCDS4890.1 ENSP00000252050 Q8IWT3 UPI000006F22F NM_015089.3 deleterious(0) 12/41 hmmpanther:PTHR22771:SF2,hmmpanther:PTHR22771 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs145736095 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 43198711 43198711 G C 1 0 0 0 0 1 0 0 0 3871 1145 40 4 4 CUL9 6 43198711 Missense_Mutation SNP G C3L-01632_T 9065574 43198711 127607268 67 7272 SPATS1 0 . GRCh38 6 44360552 44360552 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.394C>A p.Leu132Met p.L132M ENST00000288390 3/8 140 117 23 199 199 0 strelka-varscan-mutect SPATS1,missense_variant,p.Leu132Met,ENST00000288390,;SPATS1,missense_variant,p.Leu132Met,ENST00000323108,NM_145026.3;SPATS1,downstream_gene_variant,,ENST00000515220,;RP11-444E17.6,3_prime_UTR_variant,,ENST00000505802,;SPATS1,3_prime_UTR_variant,,ENST00000506468,; A ENST00000288390 Transcript missense_variant 741/1354 394/903 132/300 L/M Ctg/Atg 1 1 SPATS1 HGNC HGNC:22957 protein_coding YES CCDS4911.1 ENSP00000424400 Q496A3 UPI0000072310 deleterious(0.02) 3/8 hmmpanther:PTHR35845,Pfam_domain:PF15160 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 44360552 44360552 C A 1 0 0 0 0 1 0 0 0 15364 680 24 2 2 SPATS1 6 44360552 Missense_Mutation SNP C C3L-01632_T 1161841 44360552 126445427 68 7273 CRISP3 0 . GRCh38 6 49735562 49735562 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.288C>A p.= p.A96A ENST00000433368 4/8 162 133 29 245 245 0 strelka-varscan-mutect CRISP3,synonymous_variant,p.=,ENST00000433368,NM_001190986.1;CRISP3,synonymous_variant,p.=,ENST00000263045,NM_006061.2;CRISP3,synonymous_variant,p.=,ENST00000371159,;CRISP3,synonymous_variant,p.=,ENST00000354620,; T ENST00000433368 Transcript synonymous_variant 358/2205 288/807 96/268 A gcC/gcA 1 -1 CRISP3 HGNC HGNC:16904 protein_coding YES CCDS55019.1 ENSP00000389026 P54108 UPI0001DBC27E NM_001190986.1 4/8 Gene3D:3.40.33.10,Pfam_domain:PF00188,Prints_domain:PR00837,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF228,SMART_domains:SM00198,Superfamily_domains:SSF55797 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 49735562 49735562 G T 1 0 0 0 0 0 0 0 1 3682 1219 43 2 2 CRISP3 6 49735562 Silent SNP G C3L-01632_T 5375010 49735562 121070417 69 7274 COL9A1 0 . GRCh38 6 70300331 70300331 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.144G>T p.Arg48Ser p.R48S ENST00000357250 3/38 324 292 32 452 451 1 strelka-varscan-mutect COL9A1,missense_variant,p.Arg48Ser,ENST00000357250,NM_001851.4;COL9A1,missense_variant,p.Arg48Ser,ENST00000370496,; A ENST00000357250 Transcript missense_variant 303/4761 144/2766 48/921 R/S agG/agT 1 -1 COL9A1 HGNC HGNC:2217 protein_coding YES CCDS4971.1 ENSP00000349790 P20849 UPI000020D14B NM_001851.4 3/38 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 70300331 70300331 C A 1 0 0 0 0 1 0 0 0 3496 854 30 2 2 COL9A1 6 70300331 Missense_Mutation SNP C C3L-01632_T 20564769 70300331 100505648 70 7275 COL12A1 0 . GRCh38 6 75151141 75151141 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.4147G>T p.Gly1383Cys p.G1383C ENST00000322507 21/66 63 52 11 118 117 1 strelka-varscan-mutect COL12A1,missense_variant,p.Gly1383Cys,ENST00000322507,NM_004370.5;COL12A1,missense_variant,p.Gly194Cys,ENST00000615798,;COL12A1,missense_variant,p.Gly1383Cys,ENST00000483888,;COL12A1,missense_variant,p.Gly1383Cys,ENST00000416123,;COL12A1,missense_variant,p.Gly219Cys,ENST00000345356,NM_080645.2;COL12A1,missense_variant,p.Gly125Cys,ENST00000419671,;COL12A1,upstream_gene_variant,,ENST00000474564,; A ENST00000322507 Transcript missense_variant,splice_region_variant 4457/11723 4147/9192 1383/3063 G/C Ggt/Tgt 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 deleterious(0) 21/66 hmmpanther:PTHR11132:SF106,hmmpanther:PTHR11132 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 75151141 75151141 C A 1 0 0 0 0 1 0 0 0 3457 695 24 2 2 COL12A1 6 75151141 Missense_Mutation SNP C C3L-01632_T 4850810 75151141 95654838 71 7276 LAMA4 0 . GRCh38 6 112114112 112114112 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.5290G>T p.Asp1764Tyr p.D1764Y ENST00000230538 38/39 252 210 42 361 361 0 strelka-varscan-mutect LAMA4,missense_variant,p.Asp1764Tyr,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Asp1757Tyr,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Asp1757Tyr,ENST00000389463,;LAMA4,missense_variant,p.Asp1757Tyr,ENST00000424408,; A ENST00000230538 Transcript missense_variant 5688/6547 5290/5472 1764/1823 D/Y Gat/Tat 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0.01) 38/39 PROSITE_profiles:PS50025,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 112114112 112114112 C A 1 0 0 0 0 1 0 0 0 8512 826 29 2 2 LAMA4 6 112114112 Missense_Mutation SNP C C3L-01632_T 36962971 112114112 58691867 72 7277 HS3ST5 0 . GRCh38 6 114057692 114057692 + Frame_Shift_Del DEL C C - C3L-01632_T C3L-01632_N C C c.606delG p.Lys203ArgfsTer13 p.K203Rfs*13 ENST00000312719 5/5 157 143 14 289 288 1 varindel-pindel HS3ST5,frameshift_variant,p.Lys203ArgfsTer13,ENST00000312719,;HS3ST5,frameshift_variant,p.Lys203ArgfsTer13,ENST00000411826,NM_153612.3;RP3-399L15.3,intron_variant,,ENST00000519104,;RP3-399L15.3,intron_variant,,ENST00000519270,;RP3-399L15.3,intron_variant,,ENST00000523087,; - ENST00000312719 Transcript frameshift_variant 1795/3901 606/1041 202/346 R/X agG/ag COSM3619635 1 -1 HS3ST5 HGNC HGNC:19419 protein_coding YES CCDS34517.1 ENSP00000427888 Q8IZT8 UPI00000740A8 5/5 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF46,Superfamily_domains:SSF52540 1 HIGH deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 114057692 114057692 C - 1 0 1 0 1 0 0 0 0 7262 854 30 0 0 HS3ST5 6 114057692 Frame_Shift_Del DEL C C3L-01632_T 1943580 114057692 56748287 73 7278 SNX9 0 . GRCh38 6 157940882 157940882 + Splice_Site SNP G G T novel C3L-01632_T C3L-01632_N G G c.1649-1G>T p.X550_splice ENST00000392185 112 86 26 181 181 0 strelka-mutect SNX9,splice_acceptor_variant,,ENST00000392185,NM_016224.4; T ENST00000392185 Transcript splice_acceptor_variant -/4198 1649/1788 550/595 1 1 SNX9 HGNC HGNC:14973 protein_coding YES CCDS5253.1 ENSP00000376024 Q9Y5X1 UPI0000135B47 NM_016224.4 16/17 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 24 157940882 157940882 G T 1 0 0 0 0 0 0 1 0 15230 985 34 2 2 SNX9 6 157940882 Splice_Site SNP G C3L-01632_T 43883190 157940882 12865097 74 7279 DACT2 0 . GRCh38 6 168308236 168308236 + Silent SNP C C A C3L-01632_T C3L-01632_N C C c.1521G>T p.= p.V507V ENST00000366795 4/4 210 197 13 427 427 0 strelka-varscan-mutect DACT2,synonymous_variant,p.=,ENST00000366795,NM_214462.4;DACT2,synonymous_variant,p.=,ENST00000610183,NM_001286350.1;DACT2,synonymous_variant,p.=,ENST00000607983,;DACT2,intron_variant,,ENST00000366796,NM_001286351.1; A ENST00000366795 Transcript synonymous_variant 1610/2942 1521/2325 507/774 V gtG/gtT COSM1076090,COSM1076091 1 -1 DACT2 HGNC HGNC:21231 protein_coding YES CCDS47519.1 ENSP00000355760 Q5SW24 UPI00001D8145 NM_214462.4 4/4 hmmpanther:PTHR15919:SF13,hmmpanther:PTHR15919,Pfam_domain:PF15268 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 168308236 168308236 C A 1 0 0 0 0 0 0 0 1 4024 697 25 2 2 DACT2 6 168308236 Silent SNP C C3L-01632_T 10367354 168308236 2497743 75 7280 THSD7A 0 . GRCh38 7 11636926 11636926 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.226C>T p.Pro76Ser p.P76S ENST00000423059 2/28 106 93 13 202 202 0 strelka-varscan-mutect THSD7A,missense_variant,p.Pro76Ser,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Pro76Ser,ENST00000617773,;THSD7A,non_coding_transcript_exon_variant,,ENST00000480061,; A ENST00000423059 Transcript missense_variant 478/10663 226/4974 76/1657 P/S Ccc/Tcc 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 tolerated(0.29) 2/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 11636926 11636926 G A 1 0 0 0 0 1 0 0 0 16313 1174 41 3 3 THSD7A 7 11636926 Missense_Mutation SNP G C3L-01632_T 11636926 147709047 76 7281 HOXA10 0 . GRCh38 7 27173448 27173448 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.859C>A p.Gln287Lys p.Q287K ENST00000283921 1/2 109 86 23 203 203 0 strelka-varscan-mutect HOXA10,missense_variant,p.Gln287Lys,ENST00000283921,NM_018951.3;HOXA10,missense_variant,p.Ala165Glu,ENST00000613671,;HOXA10,intron_variant,,ENST00000396344,;HOXA10-HOXA9,intron_variant,,ENST00000470747,;HOXA9,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,downstream_gene_variant,,ENST00000519935,;HOXA10-AS,downstream_gene_variant,,ENST00000523790,;HOXA10-AS,downstream_gene_variant,,ENST00000519694,;HOXA9,intron_variant,,ENST00000465941,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA10,upstream_gene_variant,,ENST00000521421,;HOXA10,upstream_gene_variant,,ENST00000524368,;HOXA10,upstream_gene_variant,,ENST00000519593,;HOXA9,upstream_gene_variant,,ENST00000487384,;HOXA9,upstream_gene_variant,,ENST00000489695,; T ENST00000283921 Transcript missense_variant 859/2541 859/1233 287/410 Q/K Cag/Aag 1 -1 HOXA10 HGNC HGNC:5100 protein_coding YES CCDS5410.2 ENSP00000283921 P31260 UPI0000EE42DA NM_018951.3 tolerated(0.77) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 27173448 27173448 G T 1 0 0 0 0 1 0 0 0 7183 1328 46 2 2 HOXA10 7 27173448 Missense_Mutation SNP G C3L-01632_T 15536522 27173448 132172525 77 7282 ZNF804B 0 . GRCh38 7 89327434 89327434 + Nonsense_Mutation SNP C C T C3L-01632_T C3L-01632_N C C c.340C>T p.Arg114Ter p.R114* ENST00000333190 3/4 236 190 46 359 359 0 strelka-varscan-mutect ZNF804B,stop_gained,p.Arg114Ter,ENST00000333190,NM_181646.3;ZNF804B,stop_gained,p.Arg31Ter,ENST00000611114,; T ENST00000333190 Transcript stop_gained 949/4659 340/4050 114/1349 R/* Cga/Tga COSM3785798 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 3/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 1 HIGH 1 SNV 1 1 1 PASS rs950169909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 89327434 89327434 C T 1 0 0 0 0 0 1 0 0 18756 528 19 1 1 ZNF804B 7 89327434 Nonsense_Mutation SNP C C3L-01632_T 62153986 89327434 70018539 78 7283 PDK4 0 . GRCh38 7 95589678 95589678 + Missense_Mutation SNP G G C C3L-01632_T C3L-01632_N G G c.733C>G p.Pro245Ala p.P245A ENST00000005178 7/11 73 69 4 122 122 0 varscan-mutect PDK4,missense_variant,p.Pro245Ala,ENST00000005178,NM_002612.3;PDK4,non_coding_transcript_exon_variant,,ENST00000473796,;PDK4,non_coding_transcript_exon_variant,,ENST00000498190,;PDK4,upstream_gene_variant,,ENST00000468445,; C ENST00000005178 Transcript missense_variant 931/3576 733/1236 245/411 P/A Cct/Gct COSM5536892 1 -1 PDK4 HGNC HGNC:8812 protein_coding YES CCDS5643.1 ENSP00000005178 Q16654 A4D1H4 UPI000000D984 NM_002612.3 deleterious(0) 7/11 PROSITE_profiles:PS50109,hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF22,Gene3D:3.30.565.10,Pfam_domain:PF02518,SMART_domains:SM00387,Superfamily_domains:SSF55874 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 95589678 95589678 G C 1 0 0 0 0 1 0 0 0 11766 1174 41 4 4 PDK4 7 95589678 Missense_Mutation SNP G C3L-01632_T 6262244 95589678 63756295 79 7284 TECPR1 0 . GRCh38 7 98241161 98241161 + Missense_Mutation SNP C C G novel C3L-01632_T C3L-01632_N C C c.741G>C p.Gln247His p.Q247H ENST00000447648 7/26 99 75 24 217 217 0 strelka-varscan-mutect TECPR1,missense_variant,p.Gln247His,ENST00000447648,NM_015395.2;TECPR1,downstream_gene_variant,,ENST00000420697,;TECPR1,downstream_gene_variant,,ENST00000423128,;TECPR1,downstream_gene_variant,,ENST00000415086,;TECPR1,intron_variant,,ENST00000471397,;TECPR1,downstream_gene_variant,,ENST00000472845,;TECPR1,non_coding_transcript_exon_variant,,ENST00000463648,; G ENST00000447648 Transcript missense_variant 1041/6564 741/3498 247/1165 Q/H caG/caC 1 -1 TECPR1 HGNC HGNC:22214 protein_coding YES CCDS47648.1 ENSP00000404923 Q7Z6L1 UPI0000161940 NM_015395.2 deleterious(0) 7/26 Gene3D:2.130.10.30,hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1,SMART_domains:SM00706 MODERATE 1 SNV 1 1 PASS rs1213591165 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 98241161 98241161 C G 1 0 0 0 0 1 0 0 0 16154 912 32 4 4 TECPR1 7 98241161 Missense_Mutation SNP C C3L-01632_T 2651483 98241161 61104812 80 7285 CHRM2 0 . GRCh38 7 137015760 137015760 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.895G>A p.Asp299Asn p.D299N ENST00000445907 3/3 173 153 20 282 282 0 strelka-varscan-mutect CHRM2,missense_variant,p.Asp299Asn,ENST00000445907,NM_001006630.1,NM_001006627.1;CHRM2,missense_variant,p.Asp299Asn,ENST00000401861,NM_000739.2,NM_001006626.1,NM_001006628.1;CHRM2,missense_variant,p.Asp299Asn,ENST00000453373,NM_001006631.1,NM_001006629.1;CHRM2,missense_variant,p.Asp299Asn,ENST00000320658,NM_001006632.1;AC009264.1,intron_variant,,ENST00000439694,;AC009264.1,intron_variant,,ENST00000425981,;AC009264.1,intron_variant,,ENST00000586239,;AC009264.1,intron_variant,,ENST00000597642,;AC009264.1,intron_variant,,ENST00000598184,;AC009264.1,intron_variant,,ENST00000593789,;AC009264.1,intron_variant,,ENST00000592183,; A ENST00000445907 Transcript missense_variant 1423/5918 895/1401 299/466 D/N Gat/Aat 1 1 CHRM2 HGNC HGNC:1951 protein_coding YES CCDS5843.1 ENSP00000399745 P08172 A4D1Q0 UPI0000050410 NM_001006630.1,NM_001006627.1 tolerated(0.37) 3/3 Pfam_domain:PF00001,Prints_domain:PR00539,PROSITE_profiles:PS50262,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 137015760 137015760 G A 1 0 0 0 0 1 0 0 0 3137 1290 45 3 3 CHRM2 7 137015760 Missense_Mutation SNP G C3L-01632_T 38774599 137015760 22330213 81 7286 MGAM 0 . GRCh38 7 142047809 142047809 + Missense_Mutation SNP C C G rs747370287 C3L-01632_T C3L-01632_N C C c.2523C>G p.Ile841Met p.I841M ENST00000549489 22/48 312 250 62 438 438 0 strelka-varscan-mutect MGAM,missense_variant,p.Ile841Met,ENST00000475668,;MGAM,missense_variant,p.Ile841Met,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Ile841Met,ENST00000620571,; G ENST00000549489 Transcript missense_variant 2618/6525 2523/5574 841/1857 I/M atC/atG rs747370287 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 22/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63 MODERATE 1 SNV 1 1 PASS rs747370287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 142047809 142047809 C G 1 0 0 0 0 1 0 0 0 9499 816 29 4 4 MGAM 7 142047809 Missense_Mutation SNP C C3L-01632_T 5032049 142047809 17298164 82 7287 MGAM 0 . GRCh38 7 142066692 142066692 + Silent SNP C C A rs531387144 C3L-01632_T C3L-01632_N C C c.4890C>A p.= p.G1630G ENST00000475668 41/71 165 127 38 254 254 0 strelka-varscan-mutect MGAM,synonymous_variant,p.=,ENST00000475668,;MGAM,intron_variant,,ENST00000549489,NM_004668.2;MGAM,intron_variant,,ENST00000620571,; A ENST00000475668 Transcript synonymous_variant 4944/9172 4890/8262 1630/2753 G ggC/ggA rs531387144,COSM2862417 1 1 MGAM HGNC HGNC:7043 protein_coding ENSP00000417515 E7ER45 UPI0002B832FC 41/71 Pfam_domain:PF01055,Superfamily_domains:SSF51445 0,1 LOW SNV 5 0,1 1 PASS rs531387144 . 10 198 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 142066692 142066692 C A 1 0 0 0 0 0 0 0 1 9499 755 27 1 1 MGAM 7 142066692 Silent SNP C C3L-01632_T 18883 142066692 17279281 83 7288 CNTNAP2 0 . GRCh38 7 146839835 146839835 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.333C>A p.= p.T111T ENST00000361727 3/24 243 218 25 378 378 0 strelka-varscan-mutect CNTNAP2,synonymous_variant,p.=,ENST00000361727,NM_014141.5;CNTNAP2,synonymous_variant,p.=,ENST00000625365,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; A ENST00000361727 Transcript synonymous_variant 851/9896 333/3996 111/1331 T acC/acA 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 3/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,SMART_domains:SM00231,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 146839835 146839835 C A 1 0 0 0 0 0 0 0 1 3428 610 22 2 2 CNTNAP2 7 146839835 Silent SNP C C3L-01632_T 4773143 146839835 12506138 84 7289 CNTNAP2 0 . GRCh38 7 148383816 148383816 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.3643G>T p.Gly1215Trp p.G1215W ENST00000361727 22/24 205 167 38 356 356 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Gly1215Trp,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Gly274Trp,ENST00000628930,;CNTNAP2,5_prime_UTR_variant,,ENST00000463592,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636242,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636399,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,; T ENST00000361727 Transcript missense_variant 4161/9896 3643/3996 1215/1331 G/W Ggg/Tgg 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 22/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644 MODERATE 1 SNV 1 1 PASS rs1212113314 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 148383816 148383816 G T 1 0 0 0 0 1 0 0 0 3428 1116 39 1 1 CNTNAP2 7 148383816 Missense_Mutation SNP G C3L-01632_T 1543981 148383816 10962157 85 7290 AOC1 0 . GRCh38 7 150861010 150861010 + Missense_Mutation SNP C C A rs770606382 C3L-01632_T C3L-01632_N C C c.2114C>A p.Ala705Asp p.A705D ENST00000416793 5/5 128 107 21 225 224 1 strelka-varscan-mutect AOC1,missense_variant,p.Ala686Asp,ENST00000493429,;AOC1,missense_variant,p.Ala686Asp,ENST00000467291,;AOC1,missense_variant,p.Ala686Asp,ENST00000360937,NM_001091.3;AOC1,missense_variant,p.Ala705Asp,ENST00000416793,NM_001272072.1;AOC1,downstream_gene_variant,,ENST00000483043,;AOC1,downstream_gene_variant,,ENST00000460213,;AOC1,non_coding_transcript_exon_variant,,ENST00000480582,; A ENST00000416793 Transcript missense_variant 2174/2453 2114/2313 705/770 A/D gCc/gAc rs770606382 1 1 AOC1 HGNC HGNC:80 protein_coding YES CCDS64797.1 ENSP00000411613 P19801 UPI000020F2D0 NM_001272072.1 deleterious(0) 5/5 hmmpanther:PTHR10638:SF3,hmmpanther:PTHR10638,Pfam_domain:PF01179,Gene3D:2.70.98.20,Superfamily_domains:SSF49998 MODERATE 1 SNV 1 1 PASS rs770606382 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 150861010 150861010 C A 1 0 0 0 0 1 0 0 0 836 739 26 2 2 AOC1 7 150861010 Missense_Mutation SNP C C3L-01632_T 2477194 150861010 8484963 86 7291 ANK1 0 . GRCh38 8 41692856 41692856 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.3773C>T p.Pro1258Leu p.P1258L ENST00000265709 32/43 395 356 39 628 628 0 strelka-varscan-mutect ANK1,missense_variant,p.Pro1217Leu,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Pro1217Leu,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Pro1258Leu,ENST00000265709,NM_001142446.1;ANK1,missense_variant,p.Pro539Leu,ENST00000520299,;ANK1,non_coding_transcript_exon_variant,,ENST00000524227,;ANK1,non_coding_transcript_exon_variant,,ENST00000524069,;ANK1,upstream_gene_variant,,ENST00000518061,; A ENST00000265709 Transcript missense_variant 4055/6379 3773/5694 1258/1897 P/L cCt/cTt 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 tolerated(0.07) 32/43 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 41692856 41692856 G A 1 0 0 0 0 1 0 0 0 720 1000 35 3 3 ANK1 8 41692856 Missense_Mutation SNP G C3L-01632_T 41692856 103445780 87 7292 CSMD3 0 . GRCh38 8 112587142 112587142 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.3809G>T p.Ser1270Ile p.S1270I ENST00000297405 23/71 139 110 29 224 224 0 strelka-mutect CSMD3,missense_variant,p.Ser1270Ile,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser1230Ile,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser1166Ile,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser610Ile,ENST00000339701,; A ENST00000297405 Transcript missense_variant 4054/13212 3809/11124 1270/3707 S/I aGt/aTt COSM1645270,COSM1645271,COSM3951192,COSM3951193 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.03) 23/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 112587142 112587142 C A 1 0 0 0 0 1 0 0 0 3747 565 20 2 2 CSMD3 8 112587142 Missense_Mutation SNP C C3L-01632_T 70894286 112587142 32551494 88 7293 28 3 CSMD3 0 . GRCh38 8 112587143 112587143 + Missense_Mutation SNP T T A rs368012163 C3L-01632_T C3L-01632_N T T c.3808A>T p.Ser1270Cys p.S1270C ENST00000297405 23/71 135 109 26 222 222 0 strelka-mutect CSMD3,missense_variant,p.Ser1270Cys,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser1230Cys,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser1166Cys,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser610Cys,ENST00000339701,; A ENST00000297405 Transcript missense_variant 4053/13212 3808/11124 1270/3707 S/C Agt/Tgt rs368012163 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 23/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs368012163 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 112587143 112587143 T A 1 0 0 0 0 1 0 0 0 3747 1522 53 4 4 CSMD3 8 112587143 Missense_Mutation SNP T C3L-01632_T 1 112587143 32551493 89 7294 28 3 CSMD3 0 . GRCh38 8 112587144 112587144 + Nonsense_Mutation SNP A A T novel C3L-01632_T C3L-01632_N A A c.3807T>A p.Tyr1269Ter p.Y1269* ENST00000297405 23/71 134 108 26 217 216 1 strelka-mutect CSMD3,stop_gained,p.Tyr1269Ter,ENST00000297405,NM_198123.1;CSMD3,stop_gained,p.Tyr1229Ter,ENST00000343508,NM_198124.1;CSMD3,stop_gained,p.Tyr1165Ter,ENST00000455883,NM_052900.2;CSMD3,stop_gained,p.Tyr609Ter,ENST00000339701,; T ENST00000297405 Transcript stop_gained 4052/13212 3807/11124 1269/3707 Y/* taT/taA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 23/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 112587144 112587144 A T 1 0 0 0 0 0 1 0 0 3747 456 16 4 4 CSMD3 8 112587144 Nonsense_Mutation SNP A C3L-01632_T 1 112587144 32551492 90 7295 28 3 ADCY8 0 . GRCh38 8 131039950 131039950 + Silent SNP G G T C3L-01632_T C3L-01632_N G G c.384C>A p.= p.G128G ENST00000286355 1/18 87 68 19 195 195 0 strelka-varscan-mutect ADCY8,synonymous_variant,p.=,ENST00000286355,NM_001115.2;ADCY8,synonymous_variant,p.=,ENST00000377928,; T ENST00000286355 Transcript synonymous_variant 2477/5938 384/3756 128/1251 G ggC/ggA COSM4439238 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 1/18 hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 1 LOW 1 SNV 1 1 1 PASS rs991369629 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 131039950 131039950 G T 1 0 0 0 0 0 0 0 1 344 958 34 2 2 ADCY8 8 131039950 Silent SNP G C3L-01632_T 18452806 131039950 14098686 91 7296 PLEC 0 . GRCh38 8 143929186 143929186 + Silent SNP C C A rs376090972 C3L-01632_T C3L-01632_N C C c.3588G>T p.= p.A1196A ENST00000322810 25/32 174 122 52 241 241 0 strelka-varscan-mutect PLEC,synonymous_variant,p.=,ENST00000322810,NM_201380.3;PLEC,synonymous_variant,p.=,ENST00000345136,NM_201384.2;PLEC,synonymous_variant,p.=,ENST00000436759,NM_000445.4;PLEC,synonymous_variant,p.=,ENST00000354958,NM_201379.2;PLEC,synonymous_variant,p.=,ENST00000354589,NM_201382.3;PLEC,synonymous_variant,p.=,ENST00000357649,NM_201383.2;PLEC,synonymous_variant,p.=,ENST00000356346,NM_201378.3;PLEC,synonymous_variant,p.=,ENST00000398774,NM_201381.2;PLEC,synonymous_variant,p.=,ENST00000527096,;PLEC,downstream_gene_variant,,ENST00000528025,;PLEC,upstream_gene_variant,,ENST00000527303,; A ENST00000322810 Transcript synonymous_variant 3758/15249 3588/14055 1196/4684 A gcG/gcT rs376090972 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 25/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,SMART_domains:SM00150 LOW 1 SNV 1 1 PASS rs376090972 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 143929186 143929186 C A 1 0 0 0 0 0 0 0 1 12145 639 23 1 1 PLEC 8 143929186 Silent SNP C C3L-01632_T 12889236 143929186 1209450 92 7297 UNC13B 0 . GRCh38 9 35231216 35231218 + In_Frame_Del DEL TGT TGT - novel C3L-01632_T C3L-01632_N TGT TGT c.152_152+2delTGT ENST00000378495 3/39 93 78 15 145 145 0 sindel-varindel-pindel UNC13B,inframe_deletion,,ENST00000635942,;UNC13B,inframe_deletion,,ENST00000619578,;UNC13B,inframe_deletion,,ENST00000378495,NM_006377.3;UNC13B,inframe_deletion,,ENST00000396787,;UNC13B,splice_region_variant,,ENST00000617908,;UNC13B,splice_region_variant,,ENST00000378496,;UNC13B,splice_region_variant,,ENST00000485086,;UNC13B,inframe_deletion,,ENST00000634487,; - ENST00000378495 Transcript inframe_deletion,splice_region_variant 371-373/6303 149-151/4776 50-51/1591 MF/I aTGTtt/att 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 3/39 Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR10480,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 deletion 1 3 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 35231216 35231216 TGT - 1 0 1 0 1 0 0 0 0 17509 1478 51 0 0 UNC13B 9 35231216 In_Frame_Del DEL TGT C3L-01632_T 35231216 103163501 93 7298 SPAG8 0 . GRCh38 9 35811651 35811651 + Missense_Mutation SNP C C T rs148749223 C3L-01632_T C3L-01632_N C C c.395G>A p.Ser132Asn p.S132N ENST00000340291 2/8 142 128 14 340 340 0 strelka-varscan-mutect SPAG8,missense_variant,p.Ser132Asn,ENST00000340291,NM_172312.1;SPAG8,missense_variant,p.Ser130Asn,ENST00000484764,;SPAG8,missense_variant,p.Ser132Asn,ENST00000396638,NM_001039592.1;SPAG8,missense_variant,p.Ser130Asn,ENST00000497810,;NPR2,downstream_gene_variant,,ENST00000342694,NM_003995.3;TMEM8B,upstream_gene_variant,,ENST00000377996,;NPR2,downstream_gene_variant,,ENST00000421267,;HINT2,downstream_gene_variant,,ENST00000259667,NM_032593.2;NPR2,downstream_gene_variant,,ENST00000447210,;SPAG8,intron_variant,,ENST00000463889,;HINT2,downstream_gene_variant,,ENST00000474908,;SPAG8,upstream_gene_variant,,ENST00000479751,;HINT2,downstream_gene_variant,,ENST00000474848,;HINT2,downstream_gene_variant,,ENST00000461169,;HINT2,downstream_gene_variant,,ENST00000490578,;SPAG8,upstream_gene_variant,,ENST00000489063,;HINT2,downstream_gene_variant,,ENST00000472085,;HINT2,downstream_gene_variant,,ENST00000471774,;SPAG8,missense_variant,p.Ser132Asn,ENST00000475644,;SPAG8,intron_variant,,ENST00000472605,;SPAG8,intron_variant,,ENST00000495667,;SPAG8,intron_variant,,ENST00000471631,;FAM221B,downstream_gene_variant,,ENST00000388950,;NPR2,downstream_gene_variant,,ENST00000464810,;NPR2,downstream_gene_variant,,ENST00000448821,;SPAG8,upstream_gene_variant,,ENST00000460836,;NPR2,downstream_gene_variant,,ENST00000469249,; T ENST00000340291 Transcript missense_variant 520/1759 395/1506 132/501 S/N aGt/aAt rs148749223 1 -1 SPAG8 HGNC HGNC:14105 protein_coding YES CCDS6592.1 ENSP00000340982 Q99932 UPI000013E78B NM_172312.1 tolerated_low_confidence(0.1) 2/8 Low_complexity_(Seg):seg,hmmpanther:PTHR15510 MODERATE 1 SNV 1 1 PASS rs148749223 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 35811651 35811651 C T 1 0 0 0 0 1 0 0 0 15315 565 20 3 3 SPAG8 9 35811651 Missense_Mutation SNP C C3L-01632_T 580435 35811651 102583066 94 7299 RECK 0 . GRCh38 9 36109996 36109996 + Missense_Mutation SNP C C G rs749734137 C3L-01632_T C3L-01632_N C C c.1805C>G p.Ser602Cys p.S602C ENST00000377966 15/21 77 68 9 136 136 0 strelka-varscan-mutect RECK,missense_variant,p.Ser602Cys,ENST00000377966,NM_021111.2; G ENST00000377966 Transcript missense_variant 2371/4888 1805/2916 602/971 S/C tCt/tGt rs749734137 1 1 RECK HGNC HGNC:11345 protein_coding YES CCDS6597.1 ENSP00000367202 O95980 UPI0000133587 NM_021111.2 deleterious(0.01) 15/21 hmmpanther:PTHR13487 MODERATE 1 SNV 1 1 PASS rs749734137 . 0 204 5 0 0 0 0 0 -19.41835 1 1 1 1 0 G 3 3 24 36109996 36109996 C G 1 0 0 0 0 1 0 0 0 13370 913 32 4 4 RECK 9 36109996 Missense_Mutation SNP C C3L-01632_T 298345 36109996 102284721 95 7300 ZBTB5 0 . GRCh38 9 37441863 37441863 + Missense_Mutation SNP T T G novel C3L-01632_T C3L-01632_N T T c.689A>C p.Glu230Ala p.E230A ENST00000307750 2/2 198 180 18 448 446 2 strelka-varscan-mutect ZBTB5,missense_variant,p.Glu230Ala,ENST00000307750,NM_014872.2;GRHPR,downstream_gene_variant,,ENST00000318158,NM_012203.1;GRHPR,downstream_gene_variant,,ENST00000497693,;GRHPR,downstream_gene_variant,,ENST00000480596,;GRHPR,downstream_gene_variant,,ENST00000494290,; G ENST00000307750 Transcript missense_variant 878/4627 689/2034 230/677 E/A gAg/gCg 1 -1 ZBTB5 HGNC HGNC:23836 protein_coding YES CCDS6610.1 ENSP00000307604 O15062 Q5T942 UPI000006FAE2 NM_014872.2 tolerated(0.12) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 37441863 37441863 T G 1 0 0 0 0 1 0 0 0 18121 1551 54 5 5 ZBTB5 9 37441863 Missense_Mutation SNP T C3L-01632_T 1331867 37441863 100952854 96 7301 TLE1 0 . GRCh38 9 81600098 81600098 + Silent SNP T T A novel C3L-01632_T C3L-01632_N T T c.375A>T p.= p.P125P ENST00000376484 4/4 126 102 24 193 193 0 strelka-varscan-mutect TLE1,synonymous_variant,p.=,ENST00000376484,;TLE1,intron_variant,,ENST00000376499,NM_005077.4,NM_001303104.1,NM_001303103.1; A ENST00000376484 Transcript synonymous_variant 433/666 375/384 125/127 P ccA/ccT 1 -1 TLE1 HGNC HGNC:11837 protein_coding ENSP00000365667 F6T2C8 UPI000046FE90 4/4 LOW SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 81600098 81600098 T A 1 0 0 0 0 0 0 0 1 16384 1567 55 4 4 TLE1 9 81600098 Silent SNP T C3L-01632_T 44158235 81600098 56794619 97 7302 SPTLC1 0 . GRCh38 9 92038284 92038284 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1218G>T p.Glu406Asp p.E406D ENST00000262554 13/15 310 249 61 450 450 0 strelka-varscan-mutect SPTLC1,missense_variant,p.Glu406Asp,ENST00000262554,NM_006415.3,NM_001281303.1;SPTLC1,non_coding_transcript_exon_variant,,ENST00000469778,; A ENST00000262554 Transcript missense_variant 1224/1894 1218/1422 406/473 E/D gaG/gaT 1 -1 SPTLC1 HGNC HGNC:11277 protein_coding YES CCDS6692.1 ENSP00000262554 O15269 A0A024R277 UPI000012E27B NM_006415.3,NM_001281303.1 tolerated(0.43) 13/15 hmmpanther:PTHR13693:SF2,hmmpanther:PTHR13693,Pfam_domain:PF00155,Gene3D:3.90.1150.10,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 92038284 92038284 C A 1 0 0 0 0 1 0 0 0 15479 796 28 2 2 SPTLC1 9 92038284 Missense_Mutation SNP C C3L-01632_T 10438186 92038284 46356433 98 7303 TUBAL3 0 . GRCh38 10 5393865 5393865 + Silent SNP G G C novel C3L-01632_T C3L-01632_N G G c.993C>G p.= p.V331V ENST00000380419 4/4 201 158 43 273 273 0 strelka-varscan-mutect TUBAL3,synonymous_variant,p.=,ENST00000380419,NM_024803.2;TUBAL3,synonymous_variant,p.=,ENST00000479328,NM_001171864.1; C ENST00000380419 Transcript synonymous_variant 1031/1798 993/1341 331/446 V gtC/gtG 1 -1 TUBAL3 HGNC HGNC:23534 protein_coding YES CCDS7066.2 ENSP00000369784 A6NHL2 UPI00000497AE NM_024803.2 4/4 hmmpanther:PTHR11588:SF130,hmmpanther:PTHR11588,Gene3D:3.30.1330.20,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307,Prints_domain:PR01162 LOW 1 SNV 1 1 PASS rs947999143 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 24 5393865 5393865 G C 1 0 0 0 0 0 0 0 1 17262 1161 41 4 4 TUBAL3 10 5393865 Silent SNP G C3L-01632_T 5393865 128403557 99 7304 PFKFB3 0 . GRCh38 10 6232922 6232922 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.1585G>A p.Asp529Asn p.D529N ENST00000536985 15/15 131 119 12 205 205 0 strelka-varscan-mutect PFKFB3,missense_variant,p.Asp515Asn,ENST00000379775,NM_001323016.1,NM_004566.3;PFKFB3,missense_variant,p.Asp529Asn,ENST00000536985,NM_001282630.1;PFKFB3,missense_variant,p.Asp495Asn,ENST00000379789,NM_001145443.1;PFKFB3,missense_variant,p.Asp138Asn,ENST00000450232,;PFKFB3,missense_variant,p.Asp26Asn,ENST00000441697,;PFKFB3,3_prime_UTR_variant,,ENST00000379785,;PFKFB3,3_prime_UTR_variant,,ENST00000360521,;PFKFB3,3_prime_UTR_variant,,ENST00000414237,;PFKFB3,downstream_gene_variant,,ENST00000317350,;PFKFB3,downstream_gene_variant,,ENST00000626882,;PFKFB3,3_prime_UTR_variant,,ENST00000467491,;PFKFB3,3_prime_UTR_variant,,ENST00000490474,;PFKFB3,3_prime_UTR_variant,,ENST00000477914,;PFKFB3,3_prime_UTR_variant,,ENST00000475881,;PFKFB3,downstream_gene_variant,,ENST00000461744,; A ENST00000536985 Transcript missense_variant 1648/4271 1585/1605 529/534 D/N Gac/Aac 1 1 PFKFB3 HGNC HGNC:8874 protein_coding YES CCDS60479.1 ENSP00000443319 Q16875 UPI0001915356 NM_001282630.1 15/15 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 6232922 6232922 G A 1 0 0 0 0 1 0 0 0 11852 1290 45 3 3 PFKFB3 10 6232922 Missense_Mutation SNP G C3L-01632_T 839057 6232922 127564500 100 7305 ARMC3 0 . GRCh38 10 22981652 22981652 + Missense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.1127C>T p.Ala376Val p.A376V ENST00000298032 10/19 183 162 21 218 218 0 strelka-varscan-mutect ARMC3,missense_variant,p.Ala113Val,ENST00000376528,NM_001282747.1;ARMC3,missense_variant,p.Ala376Val,ENST00000298032,NM_173081.4;ARMC3,missense_variant,p.Ala376Val,ENST00000409983,NM_001282745.1;ARMC3,missense_variant,p.Ala376Val,ENST00000409049,NM_001282746.1;ARMC3,downstream_gene_variant,,ENST00000484642,;ARMC3,downstream_gene_variant,,ENST00000496741,; T ENST00000298032 Transcript missense_variant 1211/2811 1127/2619 376/872 A/V gCa/gTa 1 1 ARMC3 HGNC HGNC:30964 protein_coding YES CCDS7142.1 ENSP00000298032 Q5W041 UPI0000161785 NM_173081.4 deleterious(0.04) 10/19 Low_complexity_(Seg):seg,PROSITE_profiles:PS50176,hmmpanther:PTHR23315:SF78,hmmpanther:PTHR23315,Gene3D:1.25.10.10,Pfam_domain:PF13646,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 22981652 22981652 C T 1 0 0 0 0 1 0 0 0 1093 710 25 3 3 ARMC3 10 22981652 Missense_Mutation SNP C C3L-01632_T 16748730 22981652 110815770 101 7306 KIAA1217 0 . GRCh38 10 24543519 24543519 + Missense_Mutation SNP G G A rs200657746 C3L-01632_T C3L-01632_N G G c.4249G>A p.Asp1417Asn p.D1417N ENST00000376454 19/21 256 223 33 357 356 1 strelka-varscan-mutect KIAA1217,missense_variant,p.Asp1100Asn,ENST00000376451,;KIAA1217,missense_variant,p.Asp1417Asn,ENST00000376454,NM_019590.4;KIAA1217,missense_variant,p.Asp300Asn,ENST00000635163,;KIAA1217,intron_variant,,ENST00000376462,NM_001098500.2;KIAA1217,intron_variant,,ENST00000376452,NM_001282767.1;KIAA1217,intron_variant,,ENST00000458595,NM_001282768.1;KIAA1217,intron_variant,,ENST00000430453,;KIAA1217,intron_variant,,ENST00000396445,;KIAA1217,intron_variant,,ENST00000307544,NM_001282769.1;KIAA1217,intron_variant,,ENST00000396446,NM_001282770.1;KIAA1217,non_coding_transcript_exon_variant,,ENST00000492009,; A ENST00000376454 Transcript missense_variant 4279/7381 4249/5832 1417/1943 D/N Gat/Aat rs200657746,COSM917126 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 tolerated(0.06) 19/21 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200657746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 24543519 24543519 G A 1 0 0 0 0 1 0 0 0 8109 1058 37 1 1 KIAA1217 10 24543519 Missense_Mutation SNP G C3L-01632_T 1561867 24543519 109253903 102 7307 ARHGAP21 0 . GRCh38 10 24584567 24584567 + Missense_Mutation SNP T T A novel C3L-01632_T C3L-01632_N T T c.5722A>T p.Arg1908Trp p.R1908W ENST00000396432 26/26 213 194 19 270 269 1 varscan-mutect ARHGAP21,missense_variant,p.Arg1908Trp,ENST00000396432,NM_020824.3;ARHGAP21,missense_variant,p.Arg1356Trp,ENST00000612832,;ARHGAP21,missense_variant,p.Arg1357Trp,ENST00000320481,;ARHGAP21,downstream_gene_variant,,ENST00000636789,;ARHGAP21,downstream_gene_variant,,ENST00000418033,;ARHGAP21,3_prime_UTR_variant,,ENST00000638156,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,;ARHGAP21,downstream_gene_variant,,ENST00000477190,; A ENST00000396432 Transcript missense_variant 6209/7167 5722/5877 1908/1958 R/W Agg/Tgg 1 -1 ARHGAP21 HGNC HGNC:23725 protein_coding YES CCDS7144.2 ENSP00000379709 Q5T5U3 UPI0001639C78 NM_020824.3 deleterious_low_confidence(0.01) 26/26 hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 24584567 24584567 T A 1 0 0 0 0 1 0 0 0 995 1579 55 4 4 ARHGAP21 10 24584567 Missense_Mutation SNP T C3L-01632_T 41048 24584567 109212855 103 7308 MTPAP 0 . GRCh38 10 30349262 30349262 + Missense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.14G>A p.Gly5Asp p.G5D ENST00000263063 1/9 242 206 36 376 376 0 strelka-varscan-mutect MTPAP,missense_variant,p.Gly5Asp,ENST00000263063,NM_018109.3;MTPAP,upstream_gene_variant,,ENST00000417581,;MTPAP,upstream_gene_variant,,ENST00000421701,;MTPAP,intron_variant,,ENST00000488290,;DNM1P17,upstream_gene_variant,,ENST00000512082,; T ENST00000263063 Transcript missense_variant 58/5601 14/1749 5/582 G/D gGc/gAc 1 -1 MTPAP HGNC HGNC:25532 protein_coding YES CCDS7165.1 ENSP00000263063 Q9NVV4 UPI0000070081 NM_018109.3 deleterious_low_confidence(0.01) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 30349262 30349262 C T 1 0 0 0 0 1 0 0 0 9942 739 26 3 3 MTPAP 10 30349262 Missense_Mutation SNP C C3L-01632_T 5764695 30349262 103448160 104 7309 GDF2 0 . GRCh38 10 47324972 47324972 + Missense_Mutation SNP G G T rs144705412 C3L-01632_T C3L-01632_N G G c.478G>T p.Val160Leu p.V160L ENST00000581492 2/2 328 280 48 500 499 1 strelka-varscan-mutect GDF2,missense_variant,p.Val160Leu,ENST00000581492,NM_016204.2; T ENST00000581492 Transcript missense_variant 657/1955 478/1290 160/429 V/L Gtg/Ttg rs144705412 1 1 GDF2 HGNC HGNC:4217 protein_coding YES CCDS73118.1 ENSP00000463051 Q9UK05 UPI000012B394 NM_016204.2 tolerated(0.36) 2/2 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF157,Pfam_domain:PF00688 MODERATE 1 SNV 1 1 PASS rs144705412 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 47324972 47324972 G T 1 0 0 0 0 1 0 0 0 6186 1145 40 1 1 GDF2 10 47324972 Missense_Mutation SNP G C3L-01632_T 16975710 47324972 86472450 105 7310 TSPAN14 0 . GRCh38 10 80509361 80509361 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.340C>T p.= p.L114L ENST00000429989 5/9 269 195 74 346 346 0 strelka-varscan-mutect TSPAN14,synonymous_variant,p.=,ENST00000429989,NM_030927.2;TSPAN14,synonymous_variant,p.=,ENST00000372164,;TSPAN14,synonymous_variant,p.=,ENST00000616406,;TSPAN14,synonymous_variant,p.=,ENST00000372156,;TSPAN14,synonymous_variant,p.=,ENST00000372158,;TSPAN14,synonymous_variant,p.=,ENST00000372157,;TSPAN14,intron_variant,,ENST00000341863,;TSPAN14,intron_variant,,ENST00000481124,NM_001128309.1;TSPAN14,non_coding_transcript_exon_variant,,ENST00000469149,; T ENST00000429989 Transcript synonymous_variant 563/16183 340/813 114/270 L Ctg/Ttg 1 1 TSPAN14 HGNC HGNC:23303 protein_coding YES CCDS7369.1 ENSP00000396270 Q8NG11 UPI000004ACAE NM_030927.2 5/9 Superfamily_domains:0037997,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF256,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 80509361 80509361 C T 1 0 0 0 0 0 0 0 1 17143 680 24 3 3 TSPAN14 10 80509361 Silent SNP C C3L-01632_T 33184389 80509361 53288061 106 7311 NUTM2A 0 . GRCh38 10 87234555 87234555 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.2484C>A p.= p.S828S ENST00000381707 7/7 176 143 33 203 203 0 strelka-varscan-mutect NUTM2A,synonymous_variant,p.=,ENST00000381707,NM_001099338.1;NUTM2A,intron_variant,,ENST00000381689,;NUTM2A-AS1,intron_variant,,ENST00000451940,;NUTM2A-AS1,downstream_gene_variant,,ENST00000433920,;NUTM2A-AS1,downstream_gene_variant,,ENST00000447424,;NUTM2A-AS1,downstream_gene_variant,,ENST00000456104,;NUTM2A-AS1,downstream_gene_variant,,ENST00000433530,; A ENST00000381707 Transcript synonymous_variant 2867/3290 2484/2637 828/878 S tcC/tcA 1 1 NUTM2A HGNC HGNC:23438 protein_coding YES CCDS44452.1 ENSP00000371126 Q8IVF1 UPI00001B6532 NM_001099338.1 7/7 Pfam_domain:PF12881,hmmpanther:PTHR22879 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 87234555 87234555 C A 1 0 0 0 0 0 0 0 1 10847 610 22 2 2 NUTM2A 10 87234555 Silent SNP C C3L-01632_T 6725194 87234555 46562867 107 7312 LGI1 0 . GRCh38 10 93758211 93758211 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.67C>A p.Leu23Ile p.L23I ENST00000371418 1/8 521 387 134 645 643 2 strelka-varscan-mutect LGI1,missense_variant,p.Leu23Ile,ENST00000630184,;LGI1,missense_variant,p.Leu23Ile,ENST00000371418,NM_005097.2;LGI1,missense_variant,p.Leu23Ile,ENST00000629035,;LGI1,missense_variant,p.Leu23Ile,ENST00000630047,;LGI1,missense_variant,p.Leu23Ile,ENST00000636155,;LGI1,missense_variant,p.Leu23Ile,ENST00000371413,NM_001308275.1;LGI1,missense_variant,p.Leu23Ile,ENST00000627699,;LGI1,missense_variant,p.Leu23Ile,ENST00000478763,;LGI1,intron_variant,,ENST00000637689,;RP11-437J2.3,upstream_gene_variant,,ENST00000630034,;LGI1,upstream_gene_variant,,ENST00000637347,;LGI1,upstream_gene_variant,,ENST00000636683,;LGI1,upstream_gene_variant,,ENST00000636140,;LGI1,missense_variant,p.Leu23Ile,ENST00000637037,;LGI1,missense_variant,p.Leu23Ile,ENST00000635953,;LGI1,missense_variant,p.Leu23Ile,ENST00000627420,;LGI1,missense_variant,p.Leu23Ile,ENST00000637611,;LGI1,missense_variant,p.Leu23Ile,ENST00000636754,;LGI1,missense_variant,p.Leu23Ile,ENST00000636232,;LGI1,missense_variant,p.Leu23Ile,ENST00000637925,;LGI1,missense_variant,p.Leu23Ile,ENST00000638049,;LGI1,missense_variant,p.Leu23Ile,ENST00000636946,;LGI1,missense_variant,p.Leu23Ile,ENST00000630487,; A ENST00000371418 Transcript missense_variant 403/2381 67/1674 23/557 L/I Cta/Ata COSM921623 1 1 LGI1 HGNC HGNC:6572 protein_coding YES CCDS7431.1 ENSP00000360472 O95970 A0A0S2Z4S7 UPI0000048F03 NM_005097.2 tolerated(0.32) 1/8 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF17,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 93758211 93758211 C A 1 0 0 0 0 1 0 0 0 8661 680 24 2 2 LGI1 10 93758211 Missense_Mutation SNP C C3L-01632_T 6523656 93758211 40039211 108 7313 OR51F2 0 . GRCh38 11 4821888 4821888 + Missense_Mutation SNP C C A rs752518921 C3L-01632_T C3L-01632_N C C c.503C>A p.Ala168Asp p.A168D ENST00000322110 1/1 126 103 23 247 247 0 strelka-varscan-mutect OR51F2,missense_variant,p.Ala168Asp,ENST00000322110,NM_001004753.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; A ENST00000322110 Transcript missense_variant 503/1029 503/1029 168/342 A/D gCc/gAc rs752518921 1 1 OR51F2 HGNC HGNC:15197 protein_coding YES CCDS31361.1 ENSP00000323952 Q8NH61 UPI000004B219 NM_001004753.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF87,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs752518921 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 4821888 4821888 C A 1 0 0 0 0 1 0 0 0 11170 739 26 2 2 OR51F2 11 4821888 Missense_Mutation SNP C C3L-01632_T 4821888 130264734 109 7314 CCDC73 0 . GRCh38 11 32642064 32642064 + Frame_Shift_Del DEL C C - novel C3L-01632_T C3L-01632_N C C c.958delG p.Glu320SerfsTer7 p.E320Sfs*7 ENST00000335185 13/18 82 66 16 158 158 0 sindel-varindel-pindel CCDC73,frameshift_variant,p.Glu320SerfsTer7,ENST00000335185,NM_001008391.3;CCDC73,non_coding_transcript_exon_variant,,ENST00000534415,; - ENST00000335185 Transcript frameshift_variant 1002/3849 958/3240 320/1079 E/X Gag/ag 1 -1 CCDC73 HGNC HGNC:23261 protein_coding YES CCDS41630.1 ENSP00000335325 Q6ZRK6 UPI000066725E NM_001008391.3 13/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15818,hmmpanther:PTHR28660,hmmpanther:PTHR28660:SF1 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 32642064 32642064 C - 1 0 1 0 1 0 0 0 0 2546 835 29 0 0 CCDC73 11 32642064 Frame_Shift_Del DEL C C3L-01632_T 27820176 32642064 102444558 110 7315 ALX4 0 . GRCh38 11 44264955 44264955 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1135G>T p.Gly379Cys p.G379C ENST00000329255 4/4 225 192 33 376 373 3 strelka-varscan-mutect ALX4,missense_variant,p.Gly379Cys,ENST00000329255,NM_021926.3; A ENST00000329255 Transcript missense_variant 1239/5750 1135/1236 379/411 G/C Ggc/Tgc 1 -1 ALX4 HGNC HGNC:450 protein_coding YES CCDS31468.1 ENSP00000332744 Q9H161 UPI000016A402 NM_021926.3 deleterious(0) 4/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF322 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 44264955 44264955 C A 1 0 0 0 0 1 0 0 0 656 594 21 2 2 ALX4 11 44264955 Missense_Mutation SNP C C3L-01632_T 11622891 44264955 90821667 111 7316 TRIM49B 0 . GRCh38 11 49031749 49031749 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.150C>A p.= p.V50V ENST00000622138 3/8 376 293 83 664 663 1 strelka-varscan-mutect TRIM49B,synonymous_variant,p.=,ENST00000622138,;TRIM49B,synonymous_variant,p.=,ENST00000332682,NM_001206626.1; A ENST00000622138 Transcript synonymous_variant 479/2162 150/1359 50/452 V gtC/gtA 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 3/8 PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Pfam_domain:PF15227,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 49031749 49031749 C A 1 0 0 0 0 0 0 0 1 17015 842 30 2 2 TRIM49B 11 49031749 Silent SNP C C3L-01632_T 4766794 49031749 86054873 112 7317 TRIM49B 0 . GRCh38 11 49032365 49032365 + Nonsense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.501C>A p.Cys167Ter p.C167* ENST00000622138 4/8 131 101 30 216 216 0 strelka-varscan-mutect TRIM49B,stop_gained,p.Cys167Ter,ENST00000622138,;TRIM49B,stop_gained,p.Cys167Ter,ENST00000332682,NM_001206626.1; A ENST00000622138 Transcript stop_gained 830/2162 501/1359 167/452 C/* tgC/tgA 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 4/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 24 49032365 49032365 C A 1 0 0 0 0 0 1 0 0 17015 805 28 2 2 TRIM49B 11 49032365 Nonsense_Mutation SNP C C3L-01632_T 616 49032365 86054257 113 7318 OR5L2 0 . GRCh38 11 55827357 55827357 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.139G>T p.Ala47Ser p.A47S ENST00000378397 1/1 202 165 37 324 324 0 strelka-varscan-mutect OR5L2,missense_variant,p.Ala47Ser,ENST00000378397,NM_001004739.1; T ENST00000378397 Transcript missense_variant 139/936 139/936 47/311 A/S Gca/Tca 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 deleterious(0.04) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 55827357 55827357 G T 1 0 0 0 0 1 0 0 0 11240 1319 46 2 2 OR5L2 11 55827357 Missense_Mutation SNP G C3L-01632_T 6794992 55827357 79259265 114 7319 OR5F1 0 . GRCh38 11 55993936 55993936 + Silent SNP C C G rs144082157 C3L-01632_T C3L-01632_N C C c.690G>C p.= p.S230S ENST00000278409 1/1 145 125 20 212 212 0 strelka-varscan-mutect OR5F1,synonymous_variant,p.=,ENST00000278409,NM_003697.1; G ENST00000278409 Transcript synonymous_variant 690/945 690/945 230/314 S tcG/tcC rs144082157,COSM543307 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 0,1 1 PASS rs144082157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 24 55993936 55993936 C G 1 0 0 0 0 0 0 0 1 11228 639 23 4 4 OR5F1 11 55993936 Silent SNP C C3L-01632_T 166579 55993936 79092686 115 7320 OR5J2 0 . GRCh38 11 56176693 56176693 + Missense_Mutation SNP G G C C3L-01632_T C3L-01632_N G G c.76G>C p.Val26Leu p.V26L ENST00000312298 1/1 119 103 16 178 178 0 strelka-varscan-mutect OR5J2,missense_variant,p.Val26Leu,ENST00000312298,NM_001005492.1; C ENST00000312298 Transcript missense_variant 76/939 76/939 26/312 V/L Gtg/Ctg COSM4962884 1 1 OR5J2 HGNC HGNC:19612 protein_coding YES CCDS31522.1 ENSP00000310788 Q8NH18 A0A126GVP0 UPI000004B232 NM_001005492.1 tolerated(0.66) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26452:SF343,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs1463945328 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 56176693 56176693 G C 1 0 0 0 0 1 0 0 0 11235 1377 48 4 4 OR5J2 11 56176693 Missense_Mutation SNP G C3L-01632_T 182757 56176693 78909929 116 7321 TCN1 0 . GRCh38 11 59861592 59861592 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.491C>A p.Ala164Asp p.A164D ENST00000257264 4/9 395 344 51 570 569 1 strelka-varscan-mutect TCN1,missense_variant,p.Ala164Asp,ENST00000257264,NM_001062.3;TCN1,non_coding_transcript_exon_variant,,ENST00000532419,;TCN1,non_coding_transcript_exon_variant,,ENST00000534531,;TCN1,non_coding_transcript_exon_variant,,ENST00000533734,; T ENST00000257264 Transcript missense_variant 596/1582 491/1302 164/433 A/D gCc/gAc 1 -1 TCN1 HGNC HGNC:11652 protein_coding YES CCDS7978.1 ENSP00000257264 P20061 UPI000013CF55 NM_001062.3 deleterious(0.01) 4/9 Pfam_domain:PF01122,hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 59861592 59861592 G T 1 0 0 0 0 1 0 0 0 16113 1203 42 2 2 TCN1 11 59861592 Missense_Mutation SNP G C3L-01632_T 3684899 59861592 75225030 117 7322 TMEM135 0 . GRCh38 11 87038067 87038067 + Missense_Mutation SNP A A G novel C3L-01632_T C3L-01632_N A A c.22A>G p.Ile8Val p.I8V ENST00000305494 1/15 414 322 92 665 665 0 strelka-varscan-mutect TMEM135,missense_variant,p.Ile8Val,ENST00000340353,NM_001168724.1;TMEM135,missense_variant,p.Ile8Val,ENST00000305494,NM_022918.3;TMEM135,missense_variant,p.Ile8Val,ENST00000525018,;TMEM135,missense_variant,p.Ile8Val,ENST00000526733,;TMEM135,5_prime_UTR_variant,,ENST00000532959,;TMEM135,non_coding_transcript_exon_variant,,ENST00000529023,; G ENST00000305494 Transcript missense_variant 61/2433 22/1377 8/458 I/V Atc/Gtc 1 1 TMEM135 HGNC HGNC:26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 UPI00001FB0C7 NM_022918.3 tolerated(0.11) 1/15 hmmpanther:PTHR12459,hmmpanther:PTHR12459:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 87038067 87038067 A G 1 0 0 0 0 1 0 0 0 16496 217 8 5 5 TMEM135 11 87038067 Missense_Mutation SNP A C3L-01632_T 27176475 87038067 48048555 118 7323 FAT3 0 . GRCh38 11 92810048 92810048 + Silent SNP C C A rs779982599 C3L-01632_T C3L-01632_N C C c.9003C>A p.= p.T3001T ENST00000525166 12/27 117 99 18 195 195 0 strelka-varscan-mutect FAT3,synonymous_variant,p.=,ENST00000409404,NM_001008781.2;FAT3,synonymous_variant,p.=,ENST00000525166,; A ENST00000525166 Transcript synonymous_variant 9025/18699 9003/13320 3001/4439 T acC/acA rs779982599 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 12/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS rs779982599 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 92810048 92810048 C A 1 0 0 0 0 0 0 0 1 5551 581 21 2 2 FAT3 11 92810048 Silent SNP C C3L-01632_T 5771981 92810048 42276574 119 7324 CNTN5 0 . GRCh38 11 99916058 99916058 + Frame_Shift_Del DEL G G - novel C3L-01632_T C3L-01632_N G G c.584delG p.Gly195GlufsTer13 p.G195Efs*13 ENST00000524871 7/25 74 63 11 140 140 0 sindel-varindel-pindel CNTN5,frameshift_variant,p.Gly195GlufsTer13,ENST00000524871,NM_014361.3;CNTN5,frameshift_variant,p.Gly179GlufsTer13,ENST00000279463,;CNTN5,frameshift_variant,p.Gly117GlufsTer13,ENST00000619298,;CNTN5,frameshift_variant,p.Gly195GlufsTer13,ENST00000527185,NM_001243271.1;CNTN5,frameshift_variant,p.Gly195GlufsTer13,ENST00000528682,NM_001243270.1;CNTN5,frameshift_variant,p.Gly121GlufsTer13,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; - ENST00000524871 Transcript frameshift_variant 872/6258 582/3303 194/1100 L/X ctG/ct 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 7/25 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51 HIGH 1 deletion 1 2 1 PASS . . 0 204 4 2 0 0 0 0 -18.91708 0.9999826 1 1 1 0 - 7 5 24 99916058 99916058 G - 1 0 1 0 1 0 0 0 0 3425 1362 47 0 0 CNTN5 11 99916058 Frame_Shift_Del DEL G C3L-01632_T 7106010 99916058 35170564 120 7325 DLAT 0 . GRCh38 11 112045204 112045204 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.1264G>A p.Asp422Asn p.D422N ENST00000280346 9/14 353 331 22 455 455 0 strelka-varscan-mutect DLAT,missense_variant,p.Asp422Asn,ENST00000280346,NM_001931.4;DLAT,missense_variant,p.Asp317Asn,ENST00000393051,;DLAT,missense_variant,p.Asp254Asn,ENST00000531306,;DLAT,3_prime_UTR_variant,,ENST00000533297,; A ENST00000280346 Transcript missense_variant 1923/4458 1264/1944 422/647 D/N Gat/Aat 1 1 DLAT HGNC HGNC:2896 protein_coding YES CCDS8354.1 ENSP00000280346 P10515 Q86YI5 UPI000000D963 NM_001931.4 deleterious(0) 9/14 Gene3D:3.30.559.10,Pfam_domain:PF00198,hmmpanther:PTHR23151,hmmpanther:PTHR23151:SF9,Superfamily_domains:SSF52777,TIGRFAM_domain:TIGR01349 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 112045204 112045204 G A 1 0 0 0 0 1 0 0 0 4355 942 33 3 3 DLAT 11 112045204 Missense_Mutation SNP G C3L-01632_T 12129146 112045204 23041418 121 7326 CEP164 0 . GRCh38 11 117410873 117410873 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.4142G>T p.Arg1381Met p.R1381M ENST00000278935 31/33 97 78 19 166 165 1 strelka-varscan-mutect CEP164,missense_variant,p.Arg1381Met,ENST00000278935,NM_001271933.1,NM_014956.4;CEP164,non_coding_transcript_exon_variant,,ENST00000533706,;CEP164,non_coding_transcript_exon_variant,,ENST00000533675,;CEP164,non_coding_transcript_exon_variant,,ENST00000528706,;CEP164,non_coding_transcript_exon_variant,,ENST00000532187,;CEP164,downstream_gene_variant,,ENST00000533223,;CEP164,upstream_gene_variant,,ENST00000533433,; T ENST00000278935 Transcript missense_variant 4289/5630 4142/4383 1381/1460 R/M aGg/aTg 1 1 CEP164 HGNC HGNC:29182 protein_coding YES CCDS31683.1 ENSP00000278935 Q9UPV0 UPI00001FA422 NM_001271933.1,NM_014956.4 deleterious(0.04) 31/33 hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 117410873 117410873 G T 1 0 0 0 0 1 0 0 0 2963 1000 35 2 2 CEP164 11 117410873 Missense_Mutation SNP G C3L-01632_T 5365669 117410873 17675749 122 7327 TMPRSS13 0 . GRCh38 11 117918478 117918478 + Missense_Mutation SNP C C A rs752289870 C3L-01632_T C3L-01632_N C C c.382G>T p.Gly128Trp p.G128W ENST00000524993 2/13 239 172 67 433 431 2 strelka-varscan-mutect TMPRSS13,missense_variant,p.Gly128Trp,ENST00000528626,NM_001206789.1;TMPRSS13,missense_variant,p.Gly128Trp,ENST00000526090,NM_001206790.1;TMPRSS13,missense_variant,p.Gly128Trp,ENST00000445164,;TMPRSS13,missense_variant,p.Gly128Trp,ENST00000430170,NM_001244995.1;TMPRSS13,missense_variant,p.Gly128Trp,ENST00000524993,NM_001077263.2;TMPRSS13,non_coding_transcript_exon_variant,,ENST00000525794,;TMPRSS13,intron_variant,,ENST00000528135,; A ENST00000524993 Transcript missense_variant 440/1950 382/1704 128/567 G/W Ggg/Tgg rs752289870 1 -1 TMPRSS13 HGNC HGNC:29808 protein_coding YES CCDS41721.1 ENSP00000434279 E9PRA0 UPI0000E5923F NM_001077263.2 deleterious(0.01) 2/13 PIRSF_domain:PIRSF037935 MODERATE 1 SNV 1 1 PASS rs752289870 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 117918478 117918478 C A 1 0 0 0 0 1 0 0 0 16721 623 22 2 2 TMPRSS13 11 117918478 Missense_Mutation SNP C C3L-01632_T 507605 117918478 17168144 123 7328 IL10RA 0 . GRCh38 11 117999236 117999236 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.1332G>C p.Gln444His p.Q444H ENST00000227752 7/7 186 150 36 332 332 0 strelka-varscan-mutect IL10RA,missense_variant,p.Gln444His,ENST00000227752,NM_001558.3;TMPRSS4-AS1,downstream_gene_variant,,ENST00000636151,;IL10RA,non_coding_transcript_exon_variant,,ENST00000533700,;IL10RA,3_prime_UTR_variant,,ENST00000534574,;IL10RA,3_prime_UTR_variant,,ENST00000526544,;IL10RA,non_coding_transcript_exon_variant,,ENST00000529924,;IL10RA,non_coding_transcript_exon_variant,,ENST00000530761,;IL10RA,non_coding_transcript_exon_variant,,ENST00000525467,;IL10RA,downstream_gene_variant,,ENST00000530178,; C ENST00000227752 Transcript missense_variant 1452/3695 1332/1737 444/578 Q/H caG/caC 1 1 IL10RA HGNC HGNC:5964 protein_coding YES CCDS8388.1 ENSP00000227752 Q13651 UPI000013C8BF NM_001558.3 deleterious(0) 7/7 hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF43 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 117999236 117999236 G C 1 0 0 0 0 1 0 0 0 7528 991 35 4 4 IL10RA 11 117999236 Missense_Mutation SNP G C3L-01632_T 80758 117999236 17087386 124 7329 TRIM29 0 . GRCh38 11 120137321 120137321 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.711G>A p.= p.Q237Q ENST00000341846 1/9 324 298 26 506 505 1 strelka-varscan-mutect TRIM29,synonymous_variant,p.=,ENST00000341846,NM_012101.3;TRIM29,downstream_gene_variant,,ENST00000532833,;TRIM29,downstream_gene_variant,,ENST00000529495,;TRIM29,downstream_gene_variant,,ENST00000529040,;TRIM29,downstream_gene_variant,,ENST00000529011,;TRIM29,downstream_gene_variant,,ENST00000627238,;TRIM29,3_prime_UTR_variant,,ENST00000475051,; T ENST00000341846 Transcript synonymous_variant 1133/3328 711/1767 237/588 Q caG/caA 1 -1 TRIM29 HGNC HGNC:17274 protein_coding YES CCDS8428.1 ENSP00000343129 Q14134 A0A024R3J1 UPI0000073FDE NM_012101.3 1/9 Gene3D:1freA00,Pfam_domain:PF00643,PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF412,SMART_domains:SM00336,Superfamily_domains:SSF57845 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 120137321 120137321 C T 1 0 0 0 0 0 0 0 1 16992 912 32 3 3 TRIM29 11 120137321 Silent SNP C C3L-01632_T 2138085 120137321 14949301 125 7330 ACSM4 0 . GRCh38 12 7328309 7328309 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.1679C>A p.Pro560Gln p.P560Q ENST00000399422 13/13 168 132 36 213 213 0 strelka-varscan-mutect ACSM4,missense_variant,p.Pro560Gln,ENST00000399422,NM_001080454.1; A ENST00000399422 Transcript missense_variant 1727/2142 1679/1743 560/580 P/Q cCa/cAa 1 1 ACSM4 HGNC HGNC:32016 protein_coding YES CCDS44825.1 ENSP00000382349 P0C7M7 UPI0000DD812A NM_001080454.1 deleterious(0) 13/13 hmmpanther:PTHR24095:SF127,hmmpanther:PTHR24095,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 7328309 7328309 C A 1 0 0 0 0 1 0 0 0 228 594 21 2 2 ACSM4 12 7328309 Missense_Mutation SNP C C3L-01632_T 7328309 125947000 126 7331 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3L-01632_T C3L-01632_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 277 220 57 369 369 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3L-01632_T 17917042 25245351 108029958 127 7332 AGAP2 0 . GRCh38 12 57734668 57734668 + Silent SNP G G C rs536899006 C3L-01632_T C3L-01632_N G G c.1239C>G p.= p.G413G ENST00000547588 3/19 160 137 23 282 282 0 strelka-varscan-mutect AGAP2,synonymous_variant,p.=,ENST00000257897,NM_014770.3;AGAP2,synonymous_variant,p.=,ENST00000328568,;AGAP2,synonymous_variant,p.=,ENST00000547588,NM_001122772.2;AGAP2,upstream_gene_variant,,ENST00000549129,;TSPAN31,upstream_gene_variant,,ENST00000553221,; C ENST00000547588 Transcript synonymous_variant 1239/3579 1239/3579 413/1192 G ggC/ggG rs536899006 1 -1 AGAP2 HGNC HGNC:16921 protein_coding YES CCDS44932.1 ENSP00000449241 F8VVT9 UPI00001AF80C NM_001122772.2 3/19 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51419,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs536899006 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 24 57734668 57734668 G C 1 0 0 0 0 0 0 0 1 445 1074 38 4 4 AGAP2 12 57734668 Silent SNP G C3L-01632_T 32489317 57734668 75540641 128 7333 METTL1 0 . GRCh38 12 57772068 57772068 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.16C>A p.= p.R6R ENST00000324871 1/6 66 52 14 147 147 0 strelka-mutect METTL1,synonymous_variant,p.=,ENST00000324871,NM_005371.5;METTL1,synonymous_variant,p.=,ENST00000257848,NM_023033.3;METTL21B,intron_variant,,ENST00000548256,;METTL21B,upstream_gene_variant,,ENST00000333012,NM_206914.1;METTL21B,upstream_gene_variant,,ENST00000300209,NM_015433.2;CYP27B1,upstream_gene_variant,,ENST00000228606,NM_000785.3;METTL21B,upstream_gene_variant,,ENST00000551420,;METTL1,upstream_gene_variant,,ENST00000547653,;CYP27B1,upstream_gene_variant,,ENST00000546609,;RP11-571M6.15,upstream_gene_variant,,ENST00000546504,;METTL1,upstream_gene_variant,,ENST00000548504,;METTL1,non_coding_transcript_exon_variant,,ENST00000548681,;METTL21B,upstream_gene_variant,,ENST00000552307,;RP11-571M6.15,upstream_gene_variant,,ENST00000553083,;METTL1,synonymous_variant,p.=,ENST00000553125,;METTL1,synonymous_variant,p.=,ENST00000551117,;METTL1,non_coding_transcript_exon_variant,,ENST00000549773,;CYP27B1,upstream_gene_variant,,ENST00000547344,;RP11-571M6.15,upstream_gene_variant,,ENST00000471530,; T ENST00000324871 Transcript synonymous_variant 726/2066 16/831 6/276 R Cgg/Agg 1 -1 METTL1 HGNC HGNC:7030 protein_coding YES CCDS8955.3 ENSP00000314441 Q9UBP6 UPI0000072720 NM_005371.5 1/6 hmmpanther:PTHR23417:SF16,hmmpanther:PTHR23417 LOW 1 SNV 1 1 PASS rs1293312643 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 57772068 57772068 G T 1 0 0 0 0 0 0 0 1 9436 1057 37 1 1 METTL1 12 57772068 Silent SNP G C3L-01632_T 37400 57772068 75503241 129 7334 NAV3 0 . GRCh38 12 78006473 78006473 + Missense_Mutation SNP C C G C3L-01632_T C3L-01632_N C C c.935C>G p.Pro312Arg p.P312R ENST00000397909 8/40 131 108 23 236 236 0 varscan-mutect NAV3,missense_variant,p.Pro312Arg,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Pro312Arg,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Pro312Arg,ENST00000549464,;NAV3,missense_variant,p.Pro255Arg,ENST00000550042,;NAV3,missense_variant,p.Pro136Arg,ENST00000550503,;NAV3,splice_region_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,; G ENST00000397909 Transcript missense_variant 1108/9821 935/7158 312/2385 P/R cCc/cGc COSM5331521,COSM5331522 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0.01) 8/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1260108374 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 78006473 78006473 C G 1 0 0 0 0 1 0 0 0 10194 623 22 4 4 NAV3 12 78006473 Missense_Mutation SNP C C3L-01632_T 20234405 78006473 55268836 130 7335 TUBA3C 0 . GRCh38 13 19179476 19179476 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.91C>G p.Gln31Glu p.Q31E ENST00000400113 2/5 235 185 50 367 367 0 strelka-varscan-mutect TUBA3C,missense_variant,p.Gln31Glu,ENST00000400113,NM_006001.2;TUBA3C,missense_variant,p.Gln31Glu,ENST00000618094,; C ENST00000400113 Transcript missense_variant 196/1551 91/1353 31/450 Q/E Cag/Gag 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 deleterious_low_confidence(0.05) 2/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.40.50.1440,Pfam_domain:PF00091,Superfamily_domains:SSF52490,Prints_domain:PR01162 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 19179476 19179476 G C 1 0 0 0 0 1 0 0 0 17256 1299 45 4 4 TUBA3C 13 19179476 Missense_Mutation SNP G C3L-01632_T 19179476 95184852 131 7336 MTUS2 0 . GRCh38 13 29492708 29492708 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.3598C>A p.Leu1200Met p.L1200M ENST00000612955 12/16 127 110 17 187 187 0 strelka-varscan-mutect MTUS2,missense_variant,p.Leu1200Met,ENST00000612955,NM_001033602.2;MTUS2,missense_variant,p.Leu169Met,ENST00000380808,NM_015233.5;MTUS2,missense_variant,p.Leu79Met,ENST00000542829,;MTUS2-AS1,upstream_gene_variant,,ENST00000323380,;MTUS2,upstream_gene_variant,,ENST00000400542,;MTUS2,upstream_gene_variant,,ENST00000467990,; A ENST00000612955 Transcript missense_variant 4147/7430 3598/4140 1200/1379 L/M Ctg/Atg COSM3688666,COSM3688667 1 1 MTUS2 HGNC HGNC:20595 protein_coding YES CCDS45022.1 ENSP00000483729 J3KQA9 UPI0000F734AC NM_001033602.2 deleterious(0) 12/16 hmmpanther:PTHR24200:SF8,hmmpanther:PTHR24200,Coiled-coils_(Ncoils):Coil 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 29492708 29492708 C A 1 0 0 0 0 1 0 0 0 9964 796 28 2 2 MTUS2 13 29492708 Missense_Mutation SNP C C3L-01632_T 10313232 29492708 84871620 132 7337 PCDH17 0 . GRCh38 13 57632761 57632761 + Missense_Mutation SNP C C G C3L-01632_T C3L-01632_N C C c.215C>G p.Pro72Arg p.P72R ENST00000377918 1/4 354 295 59 626 626 0 strelka-varscan-mutect PCDH17,missense_variant,p.Pro72Arg,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,non_coding_transcript_exon_variant,,ENST00000610846,;PCDH17,missense_variant,p.Pro72Arg,ENST00000484979,; G ENST00000377918 Transcript missense_variant 950/8232 215/3480 72/1159 P/R cCg/cGg COSM3885437 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.16) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS rs1254284380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 57632761 57632761 C G 1 0 0 0 0 1 0 0 0 11599 652 23 4 4 PCDH17 13 57632761 Missense_Mutation SNP C C3L-01632_T 28140053 57632761 56731567 133 7338 ABCC4 0 . GRCh38 13 95163648 95163648 + Splice_Site SNP C C A novel C3L-01632_T C3L-01632_N C C c.2176-1G>T p.X726_splice ENST00000376887 170 147 23 251 251 0 strelka-varscan-mutect ABCC4,splice_acceptor_variant,,ENST00000376887,NM_005845.4,NM_001301829.1;ABCC4,splice_acceptor_variant,,ENST00000629385,NM_001105515.2;ABCC4,splice_acceptor_variant,,ENST00000536256,NM_001301830.1; A ENST00000376887 Transcript splice_acceptor_variant -/5839 2176/3978 726/1325 1 -1 ABCC4 HGNC HGNC:55 protein_coding YES CCDS9474.1 ENSP00000366084 O15439 UPI00001A36E6 NM_005845.4,NM_001301829.1 16/30 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 5 1 24 95163648 95163648 C A 1 0 0 0 0 0 0 1 0 59 695 24 2 2 ABCC4 13 95163648 Splice_Site SNP C C3L-01632_T 37530887 95163648 19200680 134 7339 MYO16 0 . GRCh38 13 109127403 109127403 + Missense_Mutation SNP G G T rs772784357 C3L-01632_T C3L-01632_N G G c.3904G>T p.Val1302Leu p.V1302L ENST00000457511 31/35 212 172 40 319 319 0 strelka-varscan-mutect MYO16,missense_variant,p.Val1302Leu,ENST00000457511,NM_001198950.1;MYO16,missense_variant,p.Val1280Leu,ENST00000356711,NM_015011.1;MYO16,missense_variant,p.Val1280Leu,ENST00000357550,; T ENST00000457511 Transcript missense_variant 4526/7436 3904/5643 1302/1880 V/L Gtg/Ttg rs772784357 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 deleterious(0.01) 31/35 Pfam_domain:PF15439 MODERATE 1 SNV 1 1 PASS rs772784357 . 0 207 0 3 0 0 0 0 -20 0.999996 1 1 1 0 T 3 4 24 109127403 109127403 G T 1 0 0 0 0 1 0 0 0 10065 1261 44 2 2 MYO16 13 109127403 Missense_Mutation SNP G C3L-01632_T 13963755 109127403 5236925 135 7340 DIO2 0 . GRCh38 14 80202994 80202994 + Missense_Mutation SNP G G T rs760217727 C3L-01632_T C3L-01632_N G G c.625C>A p.Pro209Thr p.P209T ENST00000555750 3/3 165 137 28 291 290 1 strelka-varscan-mutect DIO2,stop_gained,p.Tyr47Ter,ENST00000557125,;DIO2,missense_variant,p.Pro173Thr,ENST00000557010,NM_001324462.1,NM_000793.5;DIO2,missense_variant,p.Pro173Thr,ENST00000438257,NM_013989.4;DIO2,missense_variant,p.Pro209Thr,ENST00000555750,NM_001007023.3;DIO2,3_prime_UTR_variant,,ENST00000422005,NM_001242503.2,NM_001242502.1;DIO2,3_prime_UTR_variant,,ENST00000556811,;DIO2,3_prime_UTR_variant,,ENST00000555844,; T ENST00000555750 Transcript missense_variant 653/1049 625/930 209/309 P/T Ccg/Acg rs760217727 1 -1 DIO2 HGNC HGNC:2884 protein_coding YES CCDS55934.1 ENSP00000450980 A0A0A0MTQ2 UPI000046D384 NM_001007023.3 tolerated(0.17) 3/3 Gene3D:3.40.30.10,Pfam_domain:PF00837,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF3,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS rs760217727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 80202994 80202994 G T 1 0 0 0 0 1 0 0 0 4330 1265 44 2 2 DIO2 14 80202994 Missense_Mutation SNP G C3L-01632_T 80202994 26840724 136 7341 C14orf159 0 . GRCh38 14 91189040 91189040 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.1065G>C p.Glu355Asp p.E355D ENST00000518868 12/17 389 292 97 623 623 0 strelka-varscan-mutect C14orf159,missense_variant,p.Glu355Asp,ENST00000518868,NM_001286470.1;C14orf159,missense_variant,p.Glu350Asp,ENST00000523771,NM_001286471.1;C14orf159,missense_variant,p.Glu355Asp,ENST00000256324,NM_001102368.2;C14orf159,missense_variant,p.Glu350Asp,ENST00000522322,NM_001102367.2;C14orf159,missense_variant,p.Glu350Asp,ENST00000523816,NM_001102366.2;C14orf159,missense_variant,p.Glu355Asp,ENST00000521077,NM_001286472.1;C14orf159,missense_variant,p.Glu338Asp,ENST00000520328,NM_001102369.2;C14orf159,missense_variant,p.Glu355Asp,ENST00000412671,;C14orf159,missense_variant,p.Glu350Asp,ENST00000428926,NM_024952.7;C14orf159,missense_variant,p.Glu355Asp,ENST00000525393,;C14orf159,missense_variant,p.Glu355Asp,ENST00000517518,;C14orf159,upstream_gene_variant,,ENST00000557303,;C14orf159,missense_variant,p.Glu340Asp,ENST00000523461,;C14orf159,missense_variant,p.Glu231Asp,ENST00000517306,;C14orf159,3_prime_UTR_variant,,ENST00000523837,;C14orf159,downstream_gene_variant,,ENST00000519994,; C ENST00000518868 Transcript missense_variant 1755/3075 1065/1866 355/621 E/D gaG/gaC 1 1 C14orf159 HGNC HGNC:20498 protein_coding YES CCDS41979.1 ENSP00000428263 Q7Z3D6 UPI000000CC60 NM_001286470.1 deleterious(0) 12/17 hmmpanther:PTHR32022,Pfam_domain:PF14336,PIRSF_domain:PIRSF037204 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 91189040 91189040 G C 1 0 0 0 0 1 0 0 0 1830 933 33 4 4 C14orf159 14 91189040 Missense_Mutation SNP G C3L-01632_T 10986046 91189040 15854678 137 7342 SERPINA11 0 . GRCh38 14 94448418 94448418 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.357C>A p.Phe119Leu p.F119L ENST00000334708 2/5 227 166 61 425 425 0 strelka-varscan-mutect SERPINA11,missense_variant,p.Phe119Leu,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; T ENST00000334708 Transcript missense_variant 422/1476 357/1269 119/422 F/L ttC/ttA 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 deleterious(0) 2/5 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 94448418 94448418 G T 1 0 0 0 0 1 0 0 0 14364 1165 41 2 2 SERPINA11 14 94448418 Missense_Mutation SNP G C3L-01632_T 3259378 94448418 12595300 138 7343 RYR3 0 . GRCh38 15 33662556 33662556 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.5026G>C p.Gly1676Arg p.G1676R ENST00000634891 35/104 196 163 33 305 305 0 strelka-varscan-mutect RYR3,missense_variant,p.Gly1676Arg,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Gly1676Arg,ENST00000622037,;RYR3,missense_variant,p.Gly1676Arg,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Gly1676Arg,ENST00000389232,;RYR3,missense_variant,p.Gly1676Arg,ENST00000634418,; C ENST00000634891 Transcript missense_variant 5127/15591 5026/14613 1676/4870 G/R Ggt/Cgt 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.5) 35/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 33662556 33662556 G C 1 0 0 0 0 1 0 0 0 14030 1348 47 4 4 RYR3 15 33662556 Missense_Mutation SNP G C3L-01632_T 33662556 68328633 139 7344 RPAP1 0 . GRCh38 15 41520429 41520429 + Missense_Mutation SNP C C T rs143725774 C3L-01632_T C3L-01632_N C C c.3757G>A p.Val1253Met p.V1253M ENST00000304330 22/25 115 109 6 198 198 0 strelka-varscan RPAP1,missense_variant,p.Val1253Met,ENST00000304330,NM_015540.3;RPAP1,intron_variant,,ENST00000561603,;RPAP1,downstream_gene_variant,,ENST00000565035,;RPAP1,missense_variant,p.Val1253Met,ENST00000562303,;RPAP1,non_coding_transcript_exon_variant,,ENST00000565167,;RPAP1,downstream_gene_variant,,ENST00000564934,;RPAP1,downstream_gene_variant,,ENST00000561631,; T ENST00000304330 Transcript missense_variant 3874/4665 3757/4182 1253/1393 V/M Gtg/Atg rs143725774,COSM4054516 1 -1 RPAP1 HGNC HGNC:24567 protein_coding YES CCDS10079.1 ENSP00000306123 Q9BWH6 UPI000013D465 NM_015540.3 tolerated(0.07) 22/25 hmmpanther:PTHR21483,hmmpanther:PTHR21483:SF18 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 41520429 41520429 C T 1 0 0 0 0 1 0 0 0 13793 536 19 1 1 RPAP1 15 41520429 Missense_Mutation SNP C C3L-01632_T 7857873 41520429 60470760 140 7345 UNC13C 0 . GRCh38 15 54567908 54567908 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.6067G>T p.Ala2023Ser p.A2023S ENST00000260323 29/32 101 94 7 163 163 0 strelka-varscan-mutect UNC13C,missense_variant,p.Ala2023Ser,ENST00000260323,NM_001080534.1; T ENST00000260323 Transcript missense_variant 6067/12946 6067/6645 2023/2214 A/S Gcc/Tcc 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 tolerated_low_confidence(0.13) 29/32 Pfam_domain:PF10540,PROSITE_profiles:PS51259,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 54567908 54567908 G T 1 0 0 0 0 1 0 0 0 17510 1319 46 2 2 UNC13C 15 54567908 Missense_Mutation SNP G C3L-01632_T 13047479 54567908 47423281 141 7346 ITGA11 0 . GRCh38 15 68358528 68358528 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.530C>T p.Pro177Leu p.P177L ENST00000315757 6/30 163 145 18 242 242 0 strelka-mutect ITGA11,missense_variant,p.Pro177Leu,ENST00000423218,;ITGA11,missense_variant,p.Pro177Leu,ENST00000315757,NM_001004439.1;ITGA11,non_coding_transcript_exon_variant,,ENST00000562826,;ITGA11,non_coding_transcript_exon_variant,,ENST00000568677,;ITGA11,non_coding_transcript_exon_variant,,ENST00000565868,; A ENST00000315757 Transcript missense_variant 626/3955 530/3567 177/1188 P/L cCc/cTc 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 deleterious(0) 6/30 PROSITE_profiles:PS50234,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300,Prints_domain:PR00453 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 68358528 68358528 G A 1 0 0 0 0 1 0 0 0 7781 1232 43 3 3 ITGA11 15 68358528 Missense_Mutation SNP G C3L-01632_T 13790620 68358528 33632661 142 7347 CORO2B 0 . GRCh38 15 68719452 68719452 + Missense_Mutation SNP C C T novel C3L-01632_T C3L-01632_N C C c.1211C>T p.Ser404Phe p.S404F ENST00000566799 11/12 123 114 9 206 206 0 strelka-mutect CORO2B,missense_variant,p.Ser399Phe,ENST00000543950,NM_001190457.1;CORO2B,missense_variant,p.Ser399Phe,ENST00000261861,NM_001324015.1,NM_001324014.1;CORO2B,missense_variant,p.Ser404Phe,ENST00000566799,NM_006091.4;CORO2B,missense_variant,p.Ser399Phe,ENST00000540068,NM_001190456.1; T ENST00000566799 Transcript missense_variant 1505/3566 1211/1443 404/480 S/F tCc/tTc 1 1 CORO2B HGNC HGNC:2256 protein_coding YES CCDS10229.2 ENSP00000454783 Q9UQ03 UPI0000E59C95 NM_006091.4 tolerated(0.1) 11/12 hmmpanther:PTHR10856:SF17,hmmpanther:PTHR10856 MODERATE 1 SNV 1 1 PASS rs1400602853 . 0 203 0 4 2 0 0 0 -4.384992 0.8536433 1 1 1 0 T 3 4 24 68719452 68719452 C T 1 0 0 0 0 1 0 0 0 3551 855 30 3 3 CORO2B 15 68719452 Missense_Mutation SNP C C3L-01632_T 360924 68719452 33271737 143 7348 AGBL1 0 . GRCh38 15 86295409 86295409 + Splice_Site SNP G G T rs760446554 C3L-01632_T C3L-01632_N G G c.2374+1G>T p.X792_splice ENST00000441037 46 35 11 98 97 1 strelka-varscan-mutect AGBL1,splice_donor_variant,,ENST00000614907,;AGBL1,splice_donor_variant,,ENST00000441037,;AGBL1,splice_donor_variant,,ENST00000635782,NM_152336.2;AGBL1,splice_donor_variant,,ENST00000421325,;AGBL1-AS1,downstream_gene_variant,,ENST00000564487,;AGBL1-AS1,downstream_gene_variant,,ENST00000566878,;AGBL1,non_coding_transcript_exon_variant,,ENST00000567715,;AGBL1,non_coding_transcript_exon_variant,,ENST00000568785,; T ENST00000441037 Transcript splice_donor_variant -/3551 2374/3339 792/1112 rs760446554,COSM3944304,COSM4422286,COSM966099 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 17/24 0,1,1,1 HIGH SNV 5 0,1,1,1 1 PASS rs760446554 . 0 199 11 0 0 0 0 0 -20 0.9999842 1 1 1 0 T 5 4 24 86295409 86295409 G T 1 0 0 0 0 0 0 1 0 451 1159 40 1 1 AGBL1 15 86295409 Splice_Site SNP G C3L-01632_T 17575957 86295409 15695780 144 7349 NTRK3 0 . GRCh38 15 87933079 87933079 + Missense_Mutation SNP C C A rs760692815 C3L-01632_T C3L-01632_N C C c.1822G>T p.Gly608Cys p.G608C ENST00000360948 16/20 323 284 39 475 475 0 strelka-varscan-mutect NTRK3,missense_variant,p.Gly608Cys,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Gly600Cys,ENST00000558676,;NTRK3,missense_variant,p.Gly608Cys,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Gly600Cys,ENST00000357724,;NTRK3,missense_variant,p.Gly600Cys,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Gly608Cys,ENST00000626019,;NTRK3,missense_variant,p.Gly608Cys,ENST00000629765,;NTRK3,missense_variant,p.Gly600Cys,ENST00000557856,;NTRK3,missense_variant,p.Gly510Cys,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Gly5Cys,ENST00000558576,;NTRK3,non_coding_transcript_exon_variant,,ENST00000559680,; A ENST00000360948 Transcript missense_variant 2128/3004 1822/2520 608/839 G/C Ggc/Tgc rs760692815,COSM1517967,COSM1517968,COSM4708559,COSM88799 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0.01) 16/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs760692815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 87933079 87933079 C A 1 0 0 0 0 1 0 0 0 10774 652 23 1 1 NTRK3 15 87933079 Missense_Mutation SNP C C3L-01632_T 1637670 87933079 14058110 145 7350 MSLN 0 . GRCh38 16 764063 764063 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.220G>A p.Val74Met p.V74M ENST00000382862 5/17 168 154 14 296 296 0 strelka-varscan-mutect MSLN,missense_variant,p.Val74Met,ENST00000566549,;MSLN,missense_variant,p.Val74Met,ENST00000545450,NM_005823.5;MSLN,missense_variant,p.Val74Met,ENST00000382862,NM_013404.4;MSLN,missense_variant,p.Val74Met,ENST00000563941,NM_001177355.1;MSLN,missense_variant,p.Val74Met,ENST00000563651,;MSLN,missense_variant,p.Val74Met,ENST00000569566,;MSLN,upstream_gene_variant,,ENST00000561896,;MSLN,upstream_gene_variant,,ENST00000566269,; A ENST00000382862 Transcript missense_variant 315/2116 220/1893 74/630 V/M Gtg/Atg 1 1 MSLN HGNC HGNC:7371 protein_coding YES CCDS32356.1 ENSP00000372313 Q13421 UPI000004EC9C NM_013404.4 deleterious(0.02) 5/17 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF6,Pfam_domain:PF06060 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 764063 764063 G A 1 0 0 0 0 1 0 0 0 9863 1261 44 3 3 MSLN 16 764063 Missense_Mutation SNP G C3L-01632_T 764063 89574282 146 7351 ABCA3 0 . GRCh38 16 2297913 2297913 + Silent SNP G G A novel C3L-01632_T C3L-01632_N G G c.1905C>T p.= p.G635G ENST00000301732 16/33 194 165 29 313 313 0 strelka-varscan-mutect ABCA3,synonymous_variant,p.=,ENST00000301732,NM_001089.2;ABCA3,synonymous_variant,p.=,ENST00000382381,;ABCA3,non_coding_transcript_exon_variant,,ENST00000563623,; A ENST00000301732 Transcript synonymous_variant 2606/6609 1905/5115 635/1704 G ggC/ggT 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 16/33 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 2297913 2297913 G A 1 0 0 0 0 0 0 0 1 37 1190 42 3 3 ABCA3 16 2297913 Silent SNP G C3L-01632_T 1533850 2297913 88040432 147 7352 DNAH3 0 . GRCh38 16 20933285 20933285 + Missense_Mutation SNP C C G novel C3L-01632_T C3L-01632_N C C c.12220G>C p.Ala4074Pro p.A4074P ENST00000261383 62/62 261 236 25 320 320 0 strelka-varscan-mutect DNAH3,missense_variant,p.Ala4074Pro,ENST00000261383,NM_017539.2; G ENST00000261383 Transcript missense_variant 12220/12394 12220/12351 4074/4116 A/P Gcc/Ccc 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0.03) 62/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 20933285 20933285 C G 1 0 0 0 0 1 0 0 0 4418 710 25 4 4 DNAH3 16 20933285 Missense_Mutation SNP C C3L-01632_T 18635372 20933285 69405060 148 7353 RP11-457D20.2 0 . GRCh38 16 60358762 60358762 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.719C>A p.Pro240His p.P240H ENST00000614215 1/1 155 141 14 301 301 0 varscan-mutect RP11-457D20.2,missense_variant,p.Pro240His,ENST00000614215,NM_001282301.1;RP11-354I13.2,upstream_gene_variant,,ENST00000565506,;RP11-354I13.2,upstream_gene_variant,,ENST00000565133,;RP11-457D20.1,downstream_gene_variant,,ENST00000563482,; T ENST00000614215 Transcript missense_variant 719/1026 719/1026 240/341 P/H cCc/cAc 1 -1 RP11-457D20.2 Clone_based_vega_gene protein_coding YES ENSP00000482925 A8MU76 UPI00017616FE NM_001282301.1 deleterious(0) 1/1 Pfam_domain:PF15229,hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF76 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 60358762 60358762 G T 1 0 0 0 0 1 0 0 0 13744 1232 43 2 2 RP11-457D20.2 16 60358762 Missense_Mutation SNP G C3L-01632_T 39425477 60358762 29979583 149 7354 TSNAXIP1 0 . GRCh38 16 67827481 67827481 + Frame_Shift_Del DEL G G - novel C3L-01632_T C3L-01632_N G G c.1802delG p.Gly601AlafsTer25 p.G601Afs*25 ENST00000561639 15/16 139 126 13 275 275 0 varindel-pindel TSNAXIP1,frameshift_variant,p.Gly547AlafsTer25,ENST00000388833,NM_018430.3;TSNAXIP1,frameshift_variant,p.Gly532AlafsTer25,ENST00000415766,NM_001288993.1,NM_001288992.1,NM_001288991.1;TSNAXIP1,frameshift_variant,p.Gly601AlafsTer25,ENST00000561639,NM_001288990.1;TSNAXIP1,frameshift_variant,p.Gly418AlafsTer?,ENST00000431934,;CENPT,downstream_gene_variant,,ENST00000562787,NM_025082.3;CENPT,downstream_gene_variant,,ENST00000440851,;CENPT,downstream_gene_variant,,ENST00000626059,;CENPT,downstream_gene_variant,,ENST00000564817,;CENPT,downstream_gene_variant,,ENST00000566758,;TSNAXIP1,downstream_gene_variant,,ENST00000567852,;CENPT,downstream_gene_variant,,ENST00000561593,;TSNAXIP1,downstream_gene_variant,,ENST00000565148,;TSNAXIP1,downstream_gene_variant,,ENST00000561654,;CENPT,downstream_gene_variant,,ENST00000562947,;CENPT,downstream_gene_variant,,ENST00000564538,;TSNAXIP1,downstream_gene_variant,,ENST00000562321,;TSNAXIP1,3_prime_UTR_variant,,ENST00000568990,;TSNAXIP1,3_prime_UTR_variant,,ENST00000466164,;TSNAXIP1,non_coding_transcript_exon_variant,,ENST00000487120,;TSNAXIP1,non_coding_transcript_exon_variant,,ENST00000569504,;TSNAXIP1,non_coding_transcript_exon_variant,,ENST00000565339,;CENPT,downstream_gene_variant,,ENST00000569862,;CENPT,downstream_gene_variant,,ENST00000564128,;CENPT,downstream_gene_variant,,ENST00000565157,;CENPT,downstream_gene_variant,,ENST00000436104,;CENPT,downstream_gene_variant,,ENST00000563885,;CENPT,downstream_gene_variant,,ENST00000562513,;CENPT,downstream_gene_variant,,ENST00000568495,;CENPT,downstream_gene_variant,,ENST00000562462,;CENPT,downstream_gene_variant,,ENST00000574569,;CENPT,downstream_gene_variant,,ENST00000565713,;TSNAXIP1,upstream_gene_variant,,ENST00000565558,;CENPT,downstream_gene_variant,,ENST00000562483,;CENPT,downstream_gene_variant,,ENST00000566067,;TSNAXIP1,downstream_gene_variant,,ENST00000563363,;CENPT,downstream_gene_variant,,ENST00000562338,;CENPT,downstream_gene_variant,,ENST00000568564,;CENPT,downstream_gene_variant,,ENST00000568069,; - ENST00000561639 Transcript frameshift_variant 1845/2258 1800/2139 600/712 E/X gaG/ga 1 1 TSNAXIP1 HGNC HGNC:18586 protein_coding YES CCDS73903.1 ENSP00000457241 B4DXD0 UPI00017A80C1 NM_001288990.1 15/16 hmmpanther:PTHR16306,hmmpanther:PTHR16306:SF0 HIGH 1 deletion 2 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 24 67827481 67827481 G - 1 0 1 0 1 0 0 0 0 17137 991 35 0 0 TSNAXIP1 16 67827481 Frame_Shift_Del DEL G C3L-01632_T 7468719 67827481 22510864 150 7355 OR3A2 0 . GRCh38 17 3278389 3278389 + Missense_Mutation SNP C C A rs772174674 C3L-01632_T C3L-01632_N C C c.547G>T p.Val183Phe p.V183F ENST00000408891 1/1 241 223 18 399 398 1 varscan-mutect OR3A2,missense_variant,p.Val183Phe,ENST00000408891,NM_002551.3;RP11-64J4.2,downstream_gene_variant,,ENST00000573491,;RP11-64J4.2,downstream_gene_variant,,ENST00000576166,; A ENST00000408891 Transcript missense_variant 586/1076 547/966 183/321 V/F Gtc/Ttc rs772174674,COSM3516051 1 -1 OR3A2 HGNC HGNC:8283 protein_coding YES CCDS42233.1 ENSP00000386180 P47893 A0A126GVQ3 UPI0000050B3C NM_002551.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF449,Superfamily_domains:SSF81321 0,1 MODERATE SNV 0,1 1 PASS rs772174674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 3278389 3278389 C A 1 0 0 0 0 1 0 0 0 11115 507 18 2 2 OR3A2 17 3278389 Missense_Mutation SNP C C3L-01632_T 3278389 79979052 151 7356 OR3A3 0 . GRCh38 17 3421173 3421173 + Silent SNP A A G novel C3L-01632_T C3L-01632_N A A c.606A>G p.= p.Q202Q ENST00000291231 1/1 324 256 68 554 553 1 strelka-varscan-mutect OR3A3,synonymous_variant,p.=,ENST00000291231,NM_012373.2; G ENST00000291231 Transcript synonymous_variant 606/966 606/966 202/321 Q caA/caG 1 1 OR3A3 HGNC HGNC:8284 protein_coding YES CCDS11025.1 ENSP00000291231 P47888 UPI000013E033 NM_012373.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF7,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 24 3421173 3421173 A G 1 0 0 0 0 0 0 0 1 11116 40 2 5 5 OR3A3 17 3421173 Silent SNP A C3L-01632_T 142784 3421173 79836268 152 7357 P2RX1 0 . GRCh38 17 3916096 3916096 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.130G>T p.Val44Phe p.V44F ENST00000225538 1/12 155 135 20 232 232 0 strelka-varscan-mutect P2RX1,missense_variant,p.Val44Phe,ENST00000225538,NM_002558.3;P2RX1,missense_variant,p.Val44Phe,ENST00000571637,;P2RX1,non_coding_transcript_exon_variant,,ENST00000572418,; A ENST00000225538 Transcript missense_variant 405/2697 130/1200 44/399 V/F Gtc/Ttc 1 -1 P2RX1 HGNC HGNC:8533 protein_coding YES CCDS11040.1 ENSP00000225538 P51575 UPI000000DAAB NM_002558.3 deleterious(0.02) 1/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR10125:SF9,hmmpanther:PTHR10125,TIGRFAM_domain:TIGR00863,PIRSF_domain:PIRSF005713,Pfam_domain:PF00864 MODERATE 1 SNV 1 1 PASS rs1454866122 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 3916096 3916096 C A 1 0 0 0 0 1 0 0 0 11412 536 19 1 1 P2RX1 17 3916096 Missense_Mutation SNP C C3L-01632_T 494923 3916096 79341345 153 7358 ARHGEF15 0 . GRCh38 17 8312370 8312370 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.331G>T p.Glu111Ter p.E111* ENST00000361926 2/16 40 31 9 109 108 1 strelka-mutect ARHGEF15,stop_gained,p.Glu111Ter,ENST00000361926,NM_173728.3;ARHGEF15,stop_gained,p.Glu111Ter,ENST00000421050,NM_025014.1;ARHGEF15,stop_gained,p.Glu111Ter,ENST00000579439,;ARHGEF15,stop_gained,p.Glu111Ter,ENST00000583529,;ARHGEF15,non_coding_transcript_exon_variant,,ENST00000455564,;ARHGEF15,upstream_gene_variant,,ENST00000581809,;ARHGEF15,upstream_gene_variant,,ENST00000578286,; T ENST00000361926 Transcript stop_gained 441/4159 331/2526 111/841 E/* Gaa/Taa 1 1 ARHGEF15 HGNC HGNC:15590 protein_coding YES CCDS11139.1 ENSP00000355026 O94989 A0A0S2Z547 UPI000013D2C0 NM_173728.3 2/16 hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF7,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 8312370 8312370 G T 1 0 0 0 0 0 1 0 0 1028 943 33 2 2 ARHGEF15 17 8312370 Nonsense_Mutation SNP G C3L-01632_T 4396274 8312370 74945071 154 7359 MYH8 0 . GRCh38 17 10394252 10394252 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.5163C>A p.= p.T1721T ENST00000403437 35/40 390 313 77 606 606 0 strelka-varscan-mutect MYH8,synonymous_variant,p.=,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript synonymous_variant 5258/6041 5163/5814 1721/1937 T acC/acA 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 35/40 hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 10394252 10394252 G T 1 0 0 0 0 0 0 0 1 10041 1246 43 2 2 MYH8 17 10394252 Silent SNP G C3L-01632_T 2081882 10394252 72863189 155 7360 SPECC1 0 . GRCh38 17 20247317 20247317 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.2596C>A p.Gln866Lys p.Q866K ENST00000261503 9/15 172 163 9 156 156 0 strelka-varscan-mutect SPECC1,missense_variant,p.Gln785Lys,ENST00000395530,NM_001033555.2;SPECC1,missense_variant,p.Gln866Lys,ENST00000261503,NM_001033553.2;SPECC1,missense_variant,p.Gln866Lys,ENST00000395527,NM_001243439.1;SPECC1,missense_variant,p.Gln371Lys,ENST00000581399,;AC004702.2,intron_variant,,ENST00000580225,; A ENST00000261503 Transcript missense_variant,splice_region_variant 2647/3948 2596/3207 866/1068 Q/K Cag/Aag 1 1 SPECC1 HGNC HGNC:30615 protein_coding YES CCDS32590.1 ENSP00000261503 Q5M775 A0A024QYY9 UPI000020187D NM_001033553.2 deleterious(0.03) 9/15 hmmpanther:PTHR23167,hmmpanther:PTHR23167:SF3 MODERATE 1 SNV 1 1 PASS . . 0 205 0 3 0 0 0 0 -11.56125 0.9999369 1 1 1 0 A 3 1 24 20247317 20247317 C A 1 0 0 0 0 1 0 0 0 15383 724 25 2 2 SPECC1 17 20247317 Missense_Mutation SNP C C3L-01632_T 9853065 20247317 63010124 156 7361 TNFAIP1 0 . GRCh38 17 28344519 28344519 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.870C>T p.= p.D290D ENST00000226225 7/7 342 299 43 542 542 0 strelka-varscan-mutect TNFAIP1,synonymous_variant,p.=,ENST00000226225,NM_021137.4;TNFAIP1,synonymous_variant,p.=,ENST00000544907,;POLDIP2,downstream_gene_variant,,ENST00000540200,NM_015584.4;POLDIP2,downstream_gene_variant,,ENST00000618887,NM_001290145.1;TNFAIP1,downstream_gene_variant,,ENST00000582302,;TNFAIP1,downstream_gene_variant,,ENST00000578158,;TNFAIP1,downstream_gene_variant,,ENST00000577535,;TNFAIP1,downstream_gene_variant,,ENST00000583213,; T ENST00000226225 Transcript synonymous_variant 1137/3627 870/951 290/316 D gaC/gaT 1 1 TNFAIP1 HGNC HGNC:11894 protein_coding YES CCDS11227.1 ENSP00000226225 Q13829 UPI00001370D5 NM_021137.4 7/7 hmmpanther:PTHR11145,hmmpanther:PTHR11145:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 28344519 28344519 C T 1 0 0 0 0 0 0 0 1 16746 506 18 3 3 TNFAIP1 17 28344519 Silent SNP C C3L-01632_T 8097202 28344519 54912922 157 7362 CNTNAP1 0 . GRCh38 17 42698708 42698708 + Missense_Mutation SNP A A G novel C3L-01632_T C3L-01632_N A A c.3953A>G p.Asn1318Ser p.N1318S ENST00000264638 24/24 152 124 28 236 236 0 strelka-varscan-mutect CNTNAP1,missense_variant,p.Asn1318Ser,ENST00000264638,NM_003632.2;EZH1,downstream_gene_variant,,ENST00000428826,NM_001321079.1,NM_001991.3;EZH1,downstream_gene_variant,,ENST00000415827,NM_001321081.1;EZH1,downstream_gene_variant,,ENST00000592743,;EZH1,downstream_gene_variant,,ENST00000585893,;EZH1,downstream_gene_variant,,ENST00000590078,;CTD-3193K9.3,intron_variant,,ENST00000592440,;CNTNAP1,3_prime_UTR_variant,,ENST00000591662,;EZH1,downstream_gene_variant,,ENST00000586103,;EZH1,downstream_gene_variant,,ENST00000591330,;EZH1,downstream_gene_variant,,ENST00000585912,;EZH1,downstream_gene_variant,,ENST00000588897,;EZH1,downstream_gene_variant,,ENST00000585550,;EZH1,downstream_gene_variant,,ENST00000586714,; G ENST00000264638 Transcript missense_variant 4170/5276 3953/4155 1318/1384 N/S aAt/aGt 1 1 CNTNAP1 HGNC HGNC:8011 protein_coding YES CCDS11436.1 ENSP00000264638 P78357 UPI00001285F6 NM_003632.2 deleterious(0.04) 24/24 SMART_domains:SM00294 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 42698708 42698708 A G 1 0 0 0 0 1 0 0 0 3427 101 4 5 5 CNTNAP1 17 42698708 Missense_Mutation SNP A C3L-01632_T 14354189 42698708 40558733 158 7363 KANSL1 0 . GRCh38 17 46034271 46034271 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.2556G>T p.Arg852Ser p.R852S ENST00000262419 11/15 300 277 23 460 458 2 strelka-varscan-mutect KANSL1,missense_variant,p.Arg852Ser,ENST00000262419,NM_001193466.1;KANSL1,missense_variant,p.Arg852Ser,ENST00000574590,;KANSL1,missense_variant,p.Arg851Ser,ENST00000432791,NM_001193465.1;KANSL1,missense_variant,p.Arg852Ser,ENST00000572904,NM_015443.3;KANSL1,missense_variant,p.Arg788Ser,ENST00000575318,;RP11-669E14.6,upstream_gene_variant,,ENST00000570454,;KANSL1,non_coding_transcript_exon_variant,,ENST00000572218,;KANSL1,non_coding_transcript_exon_variant,,ENST00000576870,;KANSL1,non_coding_transcript_exon_variant,,ENST00000576137,;KANSL1,upstream_gene_variant,,ENST00000574963,;KANSL1,downstream_gene_variant,,ENST00000573286,;KANSL1,downstream_gene_variant,,ENST00000572679,;KANSL1,upstream_gene_variant,,ENST00000573682,; A ENST00000262419 Transcript missense_variant 3027/5309 2556/3318 852/1105 R/S agG/agT 1 -1 KANSL1 HGNC HGNC:24565 protein_coding YES CCDS11503.2 ENSP00000262419 Q7Z3B3 A0A024R9Y2 UPI000013D2AE NM_001193466.1 deleterious(0.02) 11/15 hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 46034271 46034271 C A 1 0 0 0 0 1 0 0 0 7889 854 30 2 2 KANSL1 17 46034271 Missense_Mutation SNP C C3L-01632_T 3335563 46034271 37223170 159 7364 TTLL6 0 . GRCh38 17 48770059 48770059 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.2079C>A p.= p.T693T ENST00000393382 14/16 67 59 8 181 178 3 strelka-varscan-mutect TTLL6,synonymous_variant,p.=,ENST00000393382,NM_001130918.1;TTLL6,synonymous_variant,p.=,ENST00000433608,NM_173623.3;RN7SL125P,upstream_gene_variant,,ENST00000480790,;TTLL6,non_coding_transcript_exon_variant,,ENST00000490027,;TTLL6,intron_variant,,ENST00000376681,;TTLL6,intron_variant,,ENST00000416950,; T ENST00000393382 Transcript synonymous_variant 2221/3551 2079/2676 693/891 T acC/acA 1 -1 TTLL6 HGNC HGNC:26664 protein_coding YES CCDS45724.1 ENSP00000377043 Q8N841 UPI00017BCE80 NM_001130918.1 14/16 LOW 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -18.0457 1 1 1 1 0 T 2 4 24 48770059 48770059 G T 1 0 0 0 0 0 0 0 1 17242 1219 43 2 2 TTLL6 17 48770059 Silent SNP G C3L-01632_T 2735788 48770059 34487382 160 7365 DLX3 0 . GRCh38 17 49994913 49994913 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.86C>T p.Ser29Leu p.S29L ENST00000434704 1/3 200 189 11 347 347 0 strelka-varscan-mutect DLX3,missense_variant,p.Ser29Leu,ENST00000434704,NM_005220.2;DLX3,upstream_gene_variant,,ENST00000512495,;RP11-1094H24.3,upstream_gene_variant,,ENST00000511867,; A ENST00000434704 Transcript missense_variant 312/2602 86/864 29/287 S/L tCg/tTg 1 -1 DLX3 HGNC HGNC:2916 protein_coding YES CCDS11556.1 ENSP00000389870 O60479 UPI00001294B0 NM_005220.2 deleterious(0.03) 1/3 Pfam_domain:PF12413,hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 49994913 49994913 G A 1 0 0 0 0 1 0 0 0 4379 1059 37 1 1 DLX3 17 49994913 Missense_Mutation SNP G C3L-01632_T 1224854 49994913 33262528 161 7366 CACNA1G 0 . GRCh38 17 50626682 50626682 + Silent SNP G G T C3L-01632_T C3L-01632_N G G c.7065G>T p.= p.S2355S ENST00000359106 38/38 132 106 26 236 236 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CTB-22K21.2,downstream_gene_variant,,ENST00000502435,;CACNA1G,3_prime_UTR_variant,,ENST00000506406,;CACNA1G,3_prime_UTR_variant,,ENST00000504076,;CACNA1G,3_prime_UTR_variant,,ENST00000511765,;CACNA1G,3_prime_UTR_variant,,ENST00000503436,;CACNA1G,3_prime_UTR_variant,,ENST00000511768,;CACNA1G,3_prime_UTR_variant,,ENST00000503607,; T ENST00000359106 Transcript synonymous_variant 7065/7648 7065/7134 2355/2377 S tcG/tcT COSM3192739,COSM3192740,COSM3192741 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 38/38 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS rs1033768096 . 0 205 3 2 0 0 0 0 -20 0.9999964 1 1 1 0 T 2 4 24 50626682 50626682 G T 1 0 0 0 0 0 0 0 1 2232 1074 38 1 1 CACNA1G 17 50626682 Silent SNP G C3L-01632_T 631769 50626682 32630759 162 7367 KIF2B 0 . GRCh38 17 53823526 53823526 + Missense_Mutation SNP C C T rs374635000 C3L-01632_T C3L-01632_N C C c.493C>T p.Arg165Trp p.R165W ENST00000268919 1/1 162 151 11 335 335 0 strelka-varscan-mutect KIF2B,missense_variant,p.Arg165Trp,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 626/2313 493/2022 165/673 R/W Cgg/Tgg rs374635000,COSM4755188 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 tolerated(0.19) 1/1 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil 0,1 MODERATE 1 SNV 0,1 1 PASS rs374635000 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 53823526 53823526 C T 1 0 0 0 0 1 0 0 0 8163 759 27 1 1 KIF2B 17 53823526 Missense_Mutation SNP C C3L-01632_T 3196844 53823526 29433915 163 7368 ANKRD62 0 . GRCh38 18 12125941 12125941 + Missense_Mutation SNP C C G novel C3L-01632_T C3L-01632_N C C c.2120C>G p.Ser707Cys p.S707C ENST00000587848 13/14 148 121 27 183 183 0 strelka-varscan-mutect ANKRD62,missense_variant,p.Ser707Cys,ENST00000587848,NM_001277333.1;ANKRD62,non_coding_transcript_exon_variant,,ENST00000418274,; G ENST00000587848 Transcript missense_variant 2285/2919 2120/2754 707/917 S/C tCt/tGt 1 1 ANKRD62 HGNC HGNC:35241 protein_coding YES CCDS67439.1 ENSP00000467740 A6NC57 UPI0000DD848C NM_001277333.1 deleterious(0.01) 13/14 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF29,Pfam_domain:PF14915,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS rs1221984172 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 12125941 12125941 C G 1 0 0 0 0 1 0 0 0 789 913 32 4 4 ANKRD62 18 12125941 Missense_Mutation SNP C C3L-01632_T 12125941 68247344 164 7369 KEAP1 0 . GRCh38 19 10499694 10499694 + Missense_Mutation SNP C C A C3L-01632_T C3L-01632_N C C c.340G>T p.Gly114Trp p.G114W ENST00000171111 2/6 136 105 31 309 309 0 strelka-varscan-mutect KEAP1,missense_variant,p.Gly114Trp,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Gly114Trp,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Gly114Trp,ENST00000591419,;KEAP1,missense_variant,p.Gly114Trp,ENST00000592055,;KEAP1,missense_variant,p.Gly114Trp,ENST00000591039,;KEAP1,upstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; A ENST00000171111 Transcript missense_variant 888/2955 340/1875 114/624 G/W Ggg/Tgg COSM1725916 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 2/6 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 10499694 10499694 C A 1 0 0 0 0 1 0 0 0 8061 652 23 1 1 KEAP1 19 10499694 Missense_Mutation SNP C C3L-01632_T 10499694 48117922 165 7370 SMARCA4 0 . GRCh38 19 11030826 11030826 + Missense_Mutation SNP G G A C3L-01632_T C3L-01632_N G G c.3479G>A p.Gly1160Glu p.G1160E ENST00000429416 26/36 184 174 10 369 369 0 strelka-varscan-mutect SMARCA4,missense_variant,p.Gly1160Glu,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Gly1224Glu,ENST00000413806,;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.Gly1160Glu,ENST00000444061,NM_001128848.1;SMARCA4,missense_variant,p.Gly5Glu,ENST00000592158,;uc_338,upstream_gene_variant,,ENST00000620113,;SMARCA4,upstream_gene_variant,,ENST00000538456,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,upstream_gene_variant,,ENST00000586892,; A ENST00000429416 Transcript missense_variant 3760/5691 3479/4944 1160/1647 G/E gGg/gAg COSM4915594,COSM4915595 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 deleterious(0) 26/36 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 11030826 11030826 G A 1 0 0 0 0 1 0 0 0 15063 1232 43 3 3 SMARCA4 19 11030826 Missense_Mutation SNP G C3L-01632_T 531132 11030826 47586790 166 7371 ZNF493 0 . GRCh38 19 21423363 21423363 + Missense_Mutation SNP A A G novel C3L-01632_T C3L-01632_N A A c.704A>G p.Glu235Gly p.E235G ENST00000392288 4/4 124 105 19 268 268 0 strelka-varscan-mutect ZNF493,missense_variant,p.Glu235Gly,ENST00000392288,NM_001076678.2;ZNF493,missense_variant,p.Glu107Gly,ENST00000355504,NM_175910.6;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,; G ENST00000392288 Transcript missense_variant 813/5023 704/2325 235/774 E/G gAg/gGg 1 1 ZNF493 HGNC HGNC:23708 protein_coding YES CCDS42536.1 ENSP00000376110 Q6ZR52 UPI000022ABBF NM_001076678.2 deleterious(0.02) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF247,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 24 21423363 21423363 A G 1 0 0 0 0 1 0 0 0 18517 304 11 5 5 ZNF493 19 21423363 Missense_Mutation SNP A C3L-01632_T 10392537 21423363 37194253 167 7372 ZNF792 0 . GRCh38 19 34960237 34960237 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.281C>G p.Ser94Cys p.S94C ENST00000404801 3/4 65 50 15 106 106 0 strelka-varscan-mutect ZNF792,missense_variant,p.Ser94Cys,ENST00000404801,NM_175872.4;ZNF792,missense_variant,p.Ser27Cys,ENST00000605484,; C ENST00000404801 Transcript missense_variant,splice_region_variant 668/3888 281/1899 94/632 S/C tCt/tGt 1 -1 ZNF792 HGNC HGNC:24751 protein_coding YES CCDS12440.2 ENSP00000385099 Q3KQV3 UPI0000202090 NM_175872.4 deleterious(0.01) 3/4 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF187 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 24 34960237 34960237 G C 1 0 0 0 0 1 0 0 0 18749 956 33 4 4 ZNF792 19 34960237 Missense_Mutation SNP G C3L-01632_T 13536874 34960237 23657379 168 7373 NPHS1 0 . GRCh38 19 35849310 35849310 + Missense_Mutation SNP G G A rs386833960 C3L-01632_T C3L-01632_N G G c.766C>T p.Arg256Trp p.R256W ENST00000378910 7/29 125 93 32 283 283 0 strelka-varscan-mutect NPHS1,missense_variant,p.Arg256Trp,ENST00000378910,NM_004646.3;NPHS1,missense_variant,p.Arg256Trp,ENST00000353632,;NPHS1,downstream_gene_variant,,ENST00000591817,;NPHS1,upstream_gene_variant,,ENST00000585400,;NPHS1,upstream_gene_variant,,ENST00000592132,; A ENST00000378910 Transcript missense_variant 766/4276 766/3726 256/1241 R/W Cgg/Tgg rs386833960,CM081720 1 -1 NPHS1 HGNC HGNC:7908 protein_coding YES CCDS32996.1 ENSP00000368190 O60500 UPI000004EF61 NM_004646.3 deleterious(0) 7/29 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF31,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 likely_pathogenic 18503012 MODERATE 1 SNV 1 1,1 1 PASS rs386833960 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 35849310 35849310 G A 1 0 0 0 0 1 0 0 0 10630 1086 38 1 1 NPHS1 19 35849310 Missense_Mutation SNP G C3L-01632_T 889073 35849310 22768306 169 7374 ACTN4 0 . GRCh38 19 38724472 38724472 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1917G>T p.Glu639Asp p.E639D ENST00000252699 16/21 515 441 74 902 902 0 strelka-varscan-mutect ACTN4,missense_variant,p.Glu639Asp,ENST00000252699,NM_004924.4;ACTN4,missense_variant,p.Glu75Asp,ENST00000440400,;ACTN4,missense_variant,p.Glu420Asp,ENST00000390009,;ACTN4,missense_variant,p.Glu249Asp,ENST00000424234,;ACTN4,intron_variant,,ENST00000589528,;ACTN4,downstream_gene_variant,,ENST00000588618,;ACTN4,upstream_gene_variant,,ENST00000497637,;ACTN4,upstream_gene_variant,,ENST00000477174,; T ENST00000252699 Transcript missense_variant 1993/4963 1917/2736 639/911 E/D gaG/gaT 1 1 ACTN4 HGNC HGNC:166 protein_coding YES CCDS12518.1 ENSP00000252699 O43707 A0A0S2Z3G9 UPI0000125093 NM_004924.4 tolerated(0.23) 16/21 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF271,Gene3D:1.20.58.60,Pfam_domain:PF00435,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs1314840744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 38724472 38724472 G T 1 0 0 0 0 1 0 0 0 251 991 35 2 2 ACTN4 19 38724472 Missense_Mutation SNP G C3L-01632_T 2875162 38724472 19893144 170 7375 CCDC155 0 . GRCh38 19 49407618 49407618 + Missense_Mutation SNP C C A rs145761002 C3L-01632_T C3L-01632_N C C c.940C>A p.Arg314Ser p.R314S ENST00000447857 12/20 219 173 46 368 368 0 strelka-varscan-mutect CCDC155,missense_variant,p.Arg314Ser,ENST00000447857,NM_144688.4;CCDC155,missense_variant,p.Arg278Ser,ENST00000600570,;CCDC155,non_coding_transcript_exon_variant,,ENST00000596130,;CCDC155,upstream_gene_variant,,ENST00000593362,;CCDC155,upstream_gene_variant,,ENST00000596419,; A ENST00000447857 Transcript missense_variant 1145/2378 940/1689 314/562 R/S Cgc/Agc rs145761002 1 1 CCDC155 HGNC HGNC:26520 protein_coding YES CCDS46140.1 ENSP00000404220 Q8N6L0 UPI000006F690 NM_144688.4 tolerated(0.45) 12/20 Pfam_domain:PF14662,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF341 MODERATE 1 SNV 1 1 PASS rs145761002 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 49407618 49407618 C A 1 0 0 0 0 1 0 0 0 2476 884 31 1 1 CCDC155 19 49407618 Missense_Mutation SNP C C3L-01632_T 10683146 49407618 9209998 171 7376 LILRB3 0 . GRCh38 19 54221215 54221216 + Frame_Shift_Ins INS - - A novel C3L-01632_T C3L-01632_N - - c.822dupT p.Gly275TrpfsTer37 p.G275Wfs*37 ENST00000245620 5/13 59 43 16 92 92 0 sindel-varindel-pindel LILRB3,frameshift_variant,p.Gly275TrpfsTer37,ENST00000391750,NM_006864.3;LILRB3,frameshift_variant,p.Gly275TrpfsTer37,ENST00000346401,;LILRB3,frameshift_variant,p.Gly275TrpfsTer37,ENST00000245620,NM_001081450.2;LILRB3,downstream_gene_variant,,ENST00000445347,;CTB-83J4.1,upstream_gene_variant,,ENST00000601161,;LILRB3,upstream_gene_variant,,ENST00000469273,;LILRB3,3_prime_UTR_variant,,ENST00000414379,;RPS9,intron_variant,,ENST00000448962,;LILRB3,downstream_gene_variant,,ENST00000468668,;LILRB3,upstream_gene_variant,,ENST00000460208,;LILRB3,upstream_gene_variant,,ENST00000436504,; A ENST00000245620 Transcript frameshift_variant 824-825/2066 822-823/1899 274-275/632 -/X -/T 1 -1 LILRB3 HGNC HGNC:6607 protein_coding YES CCDS46175.1 ENSP00000245620 O75022 UPI00034F2393 NM_001081450.2 5/13 hmmpanther:PTHR11738:SF116,hmmpanther:PTHR11738,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 HIGH 1 insertion 1 1 PASS . . 7 201 2 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 24 54221215 54221215 - A 1 0 1 1 0 0 0 0 0 8700 594 21 0 0 LILRB3 19 54221215 Frame_Shift_Ins INS - C3L-01632_T 4813597 54221215 4396401 172 7377 VSTM2L 0 . GRCh38 20 37931714 37931714 + Missense_Mutation SNP C C A rs773073130 C3L-01632_T C3L-01632_N C C c.201C>A p.Ser67Arg p.S67R ENST00000373461 2/4 215 185 30 285 285 0 strelka-varscan-mutect VSTM2L,missense_variant,p.Ser67Arg,ENST00000373461,NM_080607.2;VSTM2L,missense_variant,p.Ser67Arg,ENST00000448944,;VSTM2L,intron_variant,,ENST00000373459,; A ENST00000373461 Transcript missense_variant 448/1959 201/615 67/204 S/R agC/agA rs773073130 1 1 VSTM2L HGNC HGNC:16096 protein_coding YES CCDS13299.1 ENSP00000362560 Q96N03 UPI0000128674 NM_080607.2 deleterious(0) 2/4 PROSITE_profiles:PS50835,hmmpanther:PTHR10075,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs773073130 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 37931714 37931714 C A 1 0 0 0 0 1 0 0 0 17782 767 27 1 1 VSTM2L 20 37931714 Missense_Mutation SNP C C3L-01632_T 37931714 26512453 173 7378 RBM38 0 . GRCh38 20 57391808 57391808 + Missense_Mutation SNP G G T C3L-01632_T C3L-01632_N G G c.227G>T p.Gly76Val p.G76V ENST00000356208 1/4 118 95 23 198 198 0 strelka-varscan-mutect RBM38,missense_variant,p.Gly76Val,ENST00000356208,NM_017495.5;RBM38,missense_variant,p.Gly76Val,ENST00000440234,NM_183425.2;RBM38,upstream_gene_variant,,ENST00000371219,;RP4-800J21.3,intron_variant,,ENST00000417346,;RBM38,missense_variant,p.Gly53Val,ENST00000344785,;RBM38,intron_variant,,ENST00000342690,; T ENST00000356208 Transcript missense_variant 402/2382 227/720 76/239 G/V gGc/gTc COSM5653747 1 1 RBM38 HGNC HGNC:15818 protein_coding YES CCDS46617.1 ENSP00000348538 Q9H0Z9 UPI00001C1571 NM_017495.5 deleterious(0) 1/4 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 57391808 57391808 G T 1 0 0 0 0 1 0 0 0 13298 1203 42 2 2 RBM38 20 57391808 Missense_Mutation SNP G C3L-01632_T 19460094 57391808 7052359 174 7379 ADAMTS5 0 . GRCh38 21 26934611 26934611 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.1544C>A p.Ala515Asp p.A515D ENST00000284987 4/8 413 347 66 577 577 0 strelka-varscan-mutect ADAMTS5,missense_variant,p.Ala515Asp,ENST00000284987,NM_007038.3;AP001601.2,intron_variant,,ENST00000426771,; T ENST00000284987 Transcript missense_variant 1666/9056 1544/2793 515/930 A/D gCt/gAt 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 deleterious(0.01) 4/8 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 26934611 26934611 G T 1 0 0 0 0 1 0 0 0 313 971 34 2 2 ADAMTS5 21 26934611 Missense_Mutation SNP G C3L-01632_T 26934611 19775372 175 7380 CCT8L2 0 . GRCh38 22 16592511 16592511 + Silent SNP G G T rs553618420 C3L-01632_T C3L-01632_N G G c.40C>A p.= p.R14R ENST00000359963 1/1 102 75 27 151 151 0 strelka-varscan-mutect CCT8L2,synonymous_variant,p.=,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; T ENST00000359963 Transcript synonymous_variant 300/2060 40/1674 14/557 R Cgg/Agg rs553618420,COSM3673210 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 1/1 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100 0,1 LOW 1 SNV 0,1 1 PASS rs553618420 . 0 204 4 2 0 0 0 0 -20 0.9999945 1 1 1 0 T 2 4 24 16592511 16592511 G T 1 0 0 0 0 0 0 0 1 2662 1086 38 1 1 CCT8L2 22 16592511 Silent SNP G C3L-01632_T 16592511 34225957 176 7381 MICAL3 0 . GRCh38 22 17841929 17841929 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.2694G>T p.= p.L898L ENST00000441493 20/32 206 170 36 296 296 0 strelka-varscan-mutect MICAL3,synonymous_variant,p.=,ENST00000441493,NM_015241.2;MICAL3,synonymous_variant,p.=,ENST00000414725,;MICAL3,synonymous_variant,p.=,ENST00000400561,NM_001122731.2;MICAL3,synonymous_variant,p.=,ENST00000383094,;MICAL3,3_prime_UTR_variant,,ENST00000495076,;MICAL3,non_coding_transcript_exon_variant,,ENST00000578905,; A ENST00000441493 Transcript synonymous_variant 3047/9445 2694/6009 898/2002 L ctG/ctT 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 20/32 LOW 1 SNV 5 1 PASS rs1325327112 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 17841929 17841929 C A 1 0 0 0 0 0 0 0 1 9528 465 17 2 2 MICAL3 22 17841929 Silent SNP C C3L-01632_T 1249418 17841929 32976539 177 7382 BCR 0 . GRCh38 22 23181185 23181185 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.225G>T p.Trp75Cys p.W75C ENST00000305877 1/23 55 45 10 81 81 0 strelka-varscan-mutect BCR,missense_variant,p.Trp75Cys,ENST00000305877,NM_004327.3;BCR,missense_variant,p.Trp75Cys,ENST00000398512,;BCR,missense_variant,p.Trp75Cys,ENST00000359540,NM_021574.2;BCR,intron_variant,,ENST00000479188,;BCRP8,upstream_gene_variant,,ENST00000412037,; T ENST00000305877 Transcript missense_variant 976/7082 225/3816 75/1271 W/C tgG/tgT 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 deleterious_low_confidence(0) 1/23 hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3,Pfam_domain:PF09036 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99988 1 1 1 1 0 T 3 4 24 23181185 23181185 G T 1 0 0 0 0 1 0 0 0 1535 1241 43 2 2 BCR 22 23181185 Missense_Mutation SNP G C3L-01632_T 5339256 23181185 27637283 178 7383 GAS2L1 0 . GRCh38 22 29308405 29308405 + Frame_Shift_Del DEL C C - novel C3L-01632_T C3L-01632_N C C c.300delC p.Asp101ThrfsTer100 p.D101Tfs*100 ENST00000618518 1/5 66 51 15 171 171 0 sindel-varindel GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000618518,;GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000616432,;GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000621062,NM_006478.4;GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000611648,NM_152236.2;GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000610653,;GAS2L1,frameshift_variant,p.Asp101ThrfsTer100,ENST00000406549,NM_001278730.1;GAS2L1,frameshift_variant,p.Asp101ThrfsTer?,ENST00000416823,;GAS2L1,frameshift_variant,p.Asp101ThrfsTer?,ENST00000428622,;RASL10A,downstream_gene_variant,,ENST00000401450,;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.4;GAS2L1,upstream_gene_variant,,ENST00000491016,;GAS2L1,downstream_gene_variant,,ENST00000487341,; - ENST00000618518 Transcript frameshift_variant 1348/3382 300/2046 100/681 R/X cgC/cg 1 1 GAS2L1 HGNC HGNC:16955 protein_coding YES CCDS74840.1 ENSP00000481012 A0A5E8 UPI0000073BD7 1/5 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF296,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH deletion 2 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999971 1 1 1 0 - 7 5 24 29308405 29308405 C - 1 0 1 0 1 0 0 0 0 6116 755 27 0 0 GAS2L1 22 29308405 Frame_Shift_Del DEL C C3L-01632_T 6127220 29308405 21510063 179 7384 FAM9C 0 . GRCh38 X 13039807 13039807 + Splice_Site SNP C C A novel C3L-01632_T C3L-01632_N C C c.438+1G>T p.X146_splice ENST00000333995 72 64 8 103 103 0 strelka-varscan-mutect FAM9C,splice_donor_variant,,ENST00000542843,;FAM9C,splice_donor_variant,,ENST00000333995,;FAM9C,splice_donor_variant,,ENST00000380625,NM_174901.5;FAM9C,splice_donor_variant,,ENST00000438997,;FAM9C,splice_donor_variant,,ENST00000468287,; A ENST00000333995 Transcript splice_donor_variant -/3361 438/501 146/166 1 -1 FAM9C HGNC HGNC:18405 protein_coding YES CCDS35203.1 ENSP00000334430 Q8IZT9 A0A024RBW5 UPI000012A41A 6/6 HIGH 1 SNV 1 1 PASS . . 1 200 9 0 0 0 0 0 -17.40475 0.9999877 1 1 1 0 A 5 1 24 13039807 13039807 C A 1 0 0 0 0 0 0 1 0 5519 492 17 2 2 FAM9C 23 13039807 Splice_Site SNP C C3L-01632_T 13039807 143001088 180 7385 SCML2 0 . GRCh38 X 18256893 18256893 + Missense_Mutation SNP T T A novel C3L-01632_T C3L-01632_N T T c.1411A>T p.Arg471Trp p.R471W ENST00000251900 11/15 103 80 23 160 160 0 strelka-varscan-mutect SCML2,missense_variant,p.Arg471Trp,ENST00000251900,NM_006089.2; A ENST00000251900 Transcript missense_variant 1571/4200 1411/2103 471/700 R/W Agg/Tgg 1 -1 SCML2 HGNC HGNC:10581 protein_coding YES CCDS14185.1 ENSP00000251900 Q9UQR0 UPI0000071E54 NM_006089.2 tolerated(0.09) 11/15 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF84 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 18256893 18256893 T A 1 0 0 0 0 1 0 0 0 14179 1579 55 4 4 SCML2 23 18256893 Missense_Mutation SNP T C3L-01632_T 5217086 18256893 137784002 181 7386 PPEF1 0 . GRCh38 X 18789244 18789244 + Missense_Mutation SNP G G C novel C3L-01632_T C3L-01632_N G G c.1036G>C p.Glu346Gln p.E346Q ENST00000361511 13/19 152 120 32 188 188 0 strelka-varscan-mutect PPEF1,missense_variant,p.Glu346Gln,ENST00000361511,NM_006240.2,NM_152224.1;PPEF1,missense_variant,p.Glu346Gln,ENST00000349874,NM_152226.1;PPEF1,downstream_gene_variant,,ENST00000496075,;PPEF1,non_coding_transcript_exon_variant,,ENST00000379962,; C ENST00000361511 Transcript missense_variant 1530/2890 1036/1962 346/653 E/Q Gaa/Caa 1 1 PPEF1 HGNC HGNC:9243 protein_coding YES CCDS14188.1 ENSP00000354871 O14829 A0A024RBZ9 UPI0000001C4F NM_006240.2,NM_152224.1 tolerated(0.17) 13/19 Pfam_domain:PF00149,PIRSF_domain:PIRSF000912,SMART_domains:SM00156,Prints_domain:PR00114 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 3 2 24 18789244 18789244 G C 1 0 0 0 0 1 0 0 0 12416 1291 45 4 4 PPEF1 23 18789244 Missense_Mutation SNP G C3L-01632_T 532351 18789244 137251651 182 7387 HDAC6 0 . GRCh38 X 48808138 48808138 + Splice_Site SNP G G T novel C3L-01632_T C3L-01632_N G G c.737+1G>T p.X246_splice ENST00000334136 186 162 24 364 363 1 strelka-varscan-mutect HDAC6,splice_donor_variant,,ENST00000334136,NM_001321227.1,NM_001321229.1;HDAC6,splice_donor_variant,,ENST00000376619,NM_001321225.1,NM_001321228.1,NM_006044.2;HDAC6,splice_donor_variant,,ENST00000426196,;HDAC6,downstream_gene_variant,,ENST00000376643,;HDAC6,downstream_gene_variant,,ENST00000376610,;HDAC6,downstream_gene_variant,,ENST00000440653,;HDAC6,downstream_gene_variant,,ENST00000441703,;HDAC6,downstream_gene_variant,,ENST00000423941,;HDAC6,downstream_gene_variant,,ENST00000443563,;HDAC6,splice_donor_variant,,ENST00000477561,;HDAC6,downstream_gene_variant,,ENST00000469223,;HDAC6,downstream_gene_variant,,ENST00000483656,;HDAC6,splice_donor_variant,,ENST00000477528,;HDAC6,downstream_gene_variant,,ENST00000462730,;HDAC6,downstream_gene_variant,,ENST00000465269,;HDAC6,downstream_gene_variant,,ENST00000476625,;HDAC6,downstream_gene_variant,,ENST00000481929,;HDAC6,downstream_gene_variant,,ENST00000489352,;HDAC6,downstream_gene_variant,,ENST00000468949,;HDAC6,downstream_gene_variant,,ENST00000493923,;HDAC6,downstream_gene_variant,,ENST00000461608,; T ENST00000334136 Transcript splice_donor_variant -/4190 737/3648 246/1215 1 1 HDAC6 HGNC HGNC:14064 protein_coding YES CCDS14306.1 ENSP00000334061 Q9UBN7 A0A024QZ26 UPI0000073E04 NM_001321227.1,NM_001321229.1 9/28 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 24 48808138 48808138 G T 1 0 0 0 0 0 0 1 0 6898 1275 44 2 2 HDAC6 23 48808138 Splice_Site SNP G C3L-01632_T 30018894 48808138 107232757 183 7388 WNK3 0 . GRCh38 X 54250110 54250110 + Missense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.2597C>A p.Ser866Tyr p.S866Y ENST00000354646 16/24 178 145 33 237 236 1 strelka-varscan-mutect WNK3,missense_variant,p.Ser866Tyr,ENST00000354646,NM_020922.4;WNK3,missense_variant,p.Ser866Tyr,ENST00000375169,NM_001002838.3;WNK3,missense_variant,p.Ser866Tyr,ENST00000375159,;WNK3,missense_variant,p.Ser866Tyr,ENST00000620763,; T ENST00000354646 Transcript missense_variant 3036/11341 2597/5403 866/1800 S/Y tCc/tAc 1 -1 WNK3 HGNC HGNC:14543 protein_coding YES CCDS14357.1 ENSP00000346667 Q9BYP7 UPI00001AF003 NM_020922.4 deleterious(0) 16/24 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF47 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 54250110 54250110 G T 1 0 0 0 0 1 0 0 0 17935 1174 41 2 2 WNK3 23 54250110 Missense_Mutation SNP G C3L-01632_T 5441972 54250110 101790785 184 7389 RRAGB 0 . GRCh38 X 55722258 55722258 + Nonsense_Mutation SNP A A T novel C3L-01632_T C3L-01632_N A A c.199A>T p.Arg67Ter p.R67* ENST00000262850 3/11 85 75 10 115 114 1 strelka-varscan-mutect RRAGB,stop_gained,p.Arg67Ter,ENST00000374941,NM_006064.4;RRAGB,stop_gained,p.Arg67Ter,ENST00000262850,NM_016656.3;RRAGB,stop_gained,p.Arg29Ter,ENST00000414239,;RRAGB,non_coding_transcript_exon_variant,,ENST00000498762,; T ENST00000262850 Transcript stop_gained 642/1573 199/1125 67/374 R/* Aga/Tga 1 1 RRAGB HGNC HGNC:19901 protein_coding YES CCDS14372.1 ENSP00000262850 Q5VZM2 UPI00001AE856 NM_016656.3 3/11 Gene3D:3.40.50.300,Pfam_domain:PF04670,hmmpanther:PTHR11259,hmmpanther:PTHR11259:SF4,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99065 1 1 1 1 0 T 4 4 24 55722258 55722258 A T 1 0 0 0 0 0 1 0 0 13927 180 7 4 4 RRAGB 23 55722258 Nonsense_Mutation SNP A C3L-01632_T 1472148 55722258 100318637 185 7390 CHIC1 0 . GRCh38 X 73563530 73563530 + Silent SNP G G C novel C3L-01632_T C3L-01632_N G G c.246G>C p.= p.R82R ENST00000373502 1/6 29 25 4 49 49 0 strelka-varscan-mutect CHIC1,synonymous_variant,p.=,ENST00000373504,NM_001300884.1;CHIC1,synonymous_variant,p.=,ENST00000373502,NM_001039840.2;MAP2K4P1,upstream_gene_variant,,ENST00000602584,;CHIC1,synonymous_variant,p.=,ENST00000498318,;CHIC1,synonymous_variant,p.=,ENST00000498407,; C ENST00000373502 Transcript synonymous_variant 323/4158 246/675 82/224 R cgG/cgC 1 1 CHIC1 HGNC HGNC:1934 protein_coding YES CCDS35335.2 ENSP00000362601 Q5VXU3 UPI0000160F74 NM_001039840.2 1/6 hmmpanther:PTHR13005,hmmpanther:PTHR13005:SF2 LOW 1 SNV 1 1 PASS rs1171093632 . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 24 73563530 73563530 G C 1 0 0 0 0 0 0 0 1 3102 1161 41 4 4 CHIC1 23 73563530 Silent SNP G C3L-01632_T 17841272 73563530 82477365 186 7391 DRP2 0 . GRCh38 X 101256169 101256169 + Missense_Mutation SNP G G T rs775130803 C3L-01632_T C3L-01632_N G G c.2298G>T p.Glu766Asp p.E766D ENST00000395209 21/24 96 75 21 119 119 0 strelka-varscan-mutect DRP2,missense_variant,p.Glu766Asp,ENST00000395209,NM_001939.2;DRP2,missense_variant,p.Glu766Asp,ENST00000402866,;DRP2,missense_variant,p.Glu766Asp,ENST00000538510,;DRP2,missense_variant,p.Glu688Asp,ENST00000541709,NM_001171184.1;DRP2,downstream_gene_variant,,ENST00000372916,; T ENST00000395209 Transcript missense_variant 2825/7277 2298/2874 766/957 E/D gaG/gaT rs775130803 1 1 DRP2 HGNC HGNC:3032 protein_coding YES CCDS14480.2 ENSP00000378635 Q13474 A0A024RCH3 UPI000013D388 NM_001939.2 tolerated(0.39) 21/24 hmmpanther:PTHR11915,PIRSF_domain:PIRSF038205 MODERATE 1 SNV 1 1 PASS rs775130803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 24 101256169 101256169 G T 1 0 0 0 0 1 0 0 0 4585 962 34 2 2 DRP2 23 101256169 Missense_Mutation SNP G C3L-01632_T 27692639 101256169 54784726 187 7392 MORC4 0 . GRCh38 X 106958380 106958380 + Missense_Mutation SNP T T A novel C3L-01632_T C3L-01632_N T T c.1341A>T p.Leu447Phe p.L447F ENST00000355610 11/17 125 110 15 205 205 0 strelka-varscan-mutect MORC4,missense_variant,p.Leu447Phe,ENST00000355610,NM_024657.4;MORC4,missense_variant,p.Leu447Phe,ENST00000255495,NM_001085354.2;MORC4,intron_variant,,ENST00000604604,; A ENST00000355610 Transcript missense_variant 1616/3834 1341/2814 447/937 L/F ttA/ttT 1 -1 MORC4 HGNC HGNC:23485 protein_coding YES CCDS14525.2 ENSP00000347821 Q8TE76 UPI00003E75D3 NM_024657.4 tolerated(0.06) 11/17 PROSITE_profiles:PS51050,hmmpanther:PTHR23336,hmmpanther:PTHR23336:SF22,Pfam_domain:PF07496 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 106958380 106958380 T A 1 0 0 0 0 1 0 0 0 9668 1635 57 4 4 MORC4 23 106958380 Missense_Mutation SNP T C3L-01632_T 5702211 106958380 49082515 188 7393 PRPS1 0 . GRCh38 X 107639422 107639422 + Silent SNP C C A novel C3L-01632_T C3L-01632_N C C c.250C>A p.= p.R84R ENST00000372435 2/7 379 310 69 595 594 1 strelka-varscan-mutect PRPS1,synonymous_variant,p.=,ENST00000372435,NM_002764.3;PRPS1,synonymous_variant,p.=,ENST00000372418,;PRPS1,synonymous_variant,p.=,ENST00000372419,;PRPS1,intron_variant,,ENST00000372428,NM_001204402.1; A ENST00000372435 Transcript synonymous_variant 372/2073 250/957 84/318 R Cgg/Agg 1 1 PRPS1 HGNC HGNC:9462 protein_coding YES CCDS14529.1 ENSP00000361512 P60891 UPI00000000A5 NM_002764.3 2/7 Gene3D:3.40.50.2020,HAMAP:MF_00583_B,Pfam_domain:PF13793,hmmpanther:PTHR10210,hmmpanther:PTHR10210:SF60,SMART_domains:SM01400,Superfamily_domains:SSF53271,TIGRFAM_domain:TIGR01251 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 24 107639422 107639422 C A 1 0 0 0 0 0 0 0 1 12714 643 23 1 1 PRPS1 23 107639422 Silent SNP C C3L-01632_T 681042 107639422 48401473 189 7394 IGSF1 0 . GRCh38 X 131283228 131283228 + Missense_Mutation SNP C C A novel C3L-01632_T C3L-01632_N C C c.704G>T p.Gly235Val p.G235V ENST00000370903 6/20 98 85 13 187 187 0 strelka-varscan-mutect IGSF1,missense_variant,p.Gly226Val,ENST00000370904,;IGSF1,missense_variant,p.Gly235Val,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Gly226Val,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Gly235Val,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000370901,NM_205833.3;IGSF1,downstream_gene_variant,,ENST00000370900,NM_001170963.1;IGSF1,upstream_gene_variant,,ENST00000469836,; A ENST00000370903 Transcript missense_variant 987/4594 704/4026 235/1341 G/V gGg/gTg 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 deleterious(0.01) 6/20 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 131283228 131283228 C A 1 0 0 0 0 1 0 0 0 7503 623 22 2 2 IGSF1 23 131283228 Missense_Mutation SNP C C3L-01632_T 23643806 131283228 24757667 190 7395 PHF6 0 . GRCh38 X 134393910 134393910 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.376G>A p.Val126Ile p.V126I ENST00000332070 5/10 220 195 25 366 364 2 strelka-varscan-mutect PHF6,missense_variant,p.Val126Ile,ENST00000332070,NM_032458.2,NM_001015877.1;PHF6,missense_variant,p.Val126Ile,ENST00000370803,;PHF6,missense_variant,p.Val126Ile,ENST00000625464,;PHF6,missense_variant,p.Val126Ile,ENST00000370799,;PHF6,missense_variant,p.Val126Ile,ENST00000370800,NM_032335.3; A ENST00000332070 Transcript missense_variant,splice_region_variant 578/4759 376/1098 126/365 V/I Gtc/Atc 1 1 PHF6 HGNC HGNC:18145 protein_coding YES CCDS14639.1 ENSP00000329097 Q8IWS0 UPI0000074487 NM_032458.2,NM_001015877.1 tolerated(0.77) 5/10 hmmpanther:PTHR12420:SF15,hmmpanther:PTHR12420,Pfam_domain:PF13771,Gene3D:3.30.40.10,SMART_domains:SM00249 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999888 1 1 1 0 A 3 1 24 134393910 134393910 G A 1 0 0 0 0 1 0 0 0 11925 1275 44 3 3 PHF6 23 134393910 Missense_Mutation SNP G C3L-01632_T 3110682 134393910 21646985 191 7396 SMIM10 0 . GRCh38 X 134991203 134991203 + Silent SNP C C T novel C3L-01632_T C3L-01632_N C C c.108C>T p.= p.R36R ENST00000330288 1/1 182 145 37 278 277 1 strelka-varscan-mutect SMIM10,synonymous_variant,p.=,ENST00000330288,NM_001163438.1; T ENST00000330288 Transcript synonymous_variant 266/1536 108/252 36/83 R cgC/cgT 1 1 SMIM10 HGNC HGNC:41913 protein_coding YES CCDS55502.1 ENSP00000328335 Q96HG1,P0DMW3 UPI00003FCD5A NM_001163438.1 1/1 Pfam_domain:PF15118,hmmpanther:PTHR34446,hmmpanther:PTHR34446:SF4 LOW 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 24 134991203 134991203 C T 1 0 0 0 0 0 0 0 1 15096 755 27 1 1 SMIM10 23 134991203 Silent SNP C C3L-01632_T 597293 134991203 21049692 192 7397 MCF2 0 . GRCh38 X 139617522 139617522 + Silent SNP G G T novel C3L-01632_T C3L-01632_N G G c.1170C>A p.= p.L390L ENST00000519895 11/29 46 38 8 97 97 0 strelka-varscan-mutect MCF2,synonymous_variant,p.=,ENST00000520602,;MCF2,synonymous_variant,p.=,ENST00000414978,NM_001099855.1;MCF2,synonymous_variant,p.=,ENST00000370576,NM_005369.4;MCF2,synonymous_variant,p.=,ENST00000536274,NM_001171877.1;MCF2,synonymous_variant,p.=,ENST00000519895,NM_001171876.1;MCF2,synonymous_variant,p.=,ENST00000338585,NM_001171879.1;MCF2,synonymous_variant,p.=,ENST00000370573,NM_001171878.1;MCF2,upstream_gene_variant,,ENST00000446225,;MCF2,upstream_gene_variant,,ENST00000483690,; T ENST00000519895 Transcript synonymous_variant 1336/3346 1170/3006 390/1001 L ctC/ctA 1 -1 MCF2 HGNC HGNC:6940 protein_coding YES CCDS55517.1 ENSP00000430276 P10911 UPI0001C33995 NM_001171876.1 11/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF138 LOW 1 SNV 2 1 PASS . . 1 205 4 0 0 0 0 0 -19.45491 1 1 1 1 0 T 2 4 24 139617522 139617522 G T 1 0 0 0 0 0 0 0 1 9309 1161 41 2 2 MCF2 23 139617522 Silent SNP G C3L-01632_T 4626319 139617522 16423373 193 7398 SLITRK2 0 . GRCh38 X 145822540 145822540 + Nonsense_Mutation SNP G G T novel C3L-01632_T C3L-01632_N G G c.115G>T p.Glu39Ter p.E39* ENST00000370490 1/1 232 193 39 373 372 1 strelka-varscan-mutect SLITRK2,stop_gained,p.Glu39Ter,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,stop_gained,p.Glu39Ter,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript stop_gained 4370/7672 115/2538 39/845 E/* Gaa/Taa 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 1/1 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36,SMART_domains:SM00013,Superfamily_domains:SSF52058 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 24 145822540 145822540 G T 1 0 0 0 0 0 1 0 0 15034 1175 41 2 2 SLITRK2 23 145822540 Nonsense_Mutation SNP G C3L-01632_T 6205018 145822540 10218355 194 7399 AFF2 0 . GRCh38 X 148980782 148980783 + Frame_Shift_Ins INS - - A novel C3L-01632_T C3L-01632_N - - c.3617dupA p.Asn1206LysfsTer24 p.N1206Kfs*24 ENST00000370460 19/21 90 77 13 144 144 0 sindel-varindel-pindel AFF2,frameshift_variant,p.Asn1206LysfsTer24,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,frameshift_variant,p.Asn847LysfsTer24,ENST00000286437,NM_001170628.1;AFF2,frameshift_variant,p.Asn1171LysfsTer24,ENST00000342251,NM_001169122.1;AFF2,frameshift_variant,p.Asn1171LysfsTer24,ENST00000370457,NM_001169124.1,NM_001169125.1; A ENST00000370460 Transcript frameshift_variant 4094-4095/13746 3615-3616/3936 1205-1206/1311 -/X -/A 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 19/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 HIGH 1 insertion 5 2 1 PASS . . 0 199 8 3 0 0 0 0 -19.97518 0.9988411 1 1 1 0 A 7 5 24 148980782 148980782 - A 1 0 1 1 0 0 0 0 0 434 709 25 0 0 AFF2 23 148980782 Frame_Shift_Ins INS - C3L-01632_T 3158242 148980782 7060113 195 7400 FLNA 0 . GRCh38 X 154361412 154361412 + Missense_Mutation SNP G G A novel C3L-01632_T C3L-01632_N G G c.3103C>T p.Pro1035Ser p.P1035S ENST00000369850 21/48 360 340 20 563 561 2 strelka-varscan FLNA,missense_variant,p.Pro1035Ser,ENST00000422373,NM_001456.3;FLNA,missense_variant,p.Pro1035Ser,ENST00000369850,NM_001110556.1;FLNA,missense_variant,p.Pro1035Ser,ENST00000360319,;FLNA,missense_variant,p.Pro1008Ser,ENST00000369856,;FLNA,missense_variant,p.Pro1035Ser,ENST00000344736,;FLNA,missense_variant,p.Pro1008Ser,ENST00000610817,;FLNA,upstream_gene_variant,,ENST00000466319,;FLNA,3_prime_UTR_variant,,ENST00000420627,;FLNA,upstream_gene_variant,,ENST00000490936,;FLNA,downstream_gene_variant,,ENST00000465144,; A ENST00000369850 Transcript missense_variant 3340/8382 3103/7944 1035/2647 P/S Ccc/Tcc 1 -1 FLNA HGNC HGNC:3754 protein_coding YES CCDS48194.1 ENSP00000358866 P21333 UPI000013C596 NM_001110556.1 deleterious(0) 21/48 PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF173,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 24 154361412 154361412 G A 1 0 0 0 0 1 0 0 0 5789 1203 42 3 3 FLNA 23 154361412 Missense_Mutation SNP G C3L-01632_T 5380630 154361412 1679483 196 7401 PLK3 0 . GRCh38 1 44800643 44800643 + Silent SNP C C A novel C3L-01682_T C3L-01682_N C C c.180C>A p.= p.R60R ENST00000372201 1/15 221 196 25 215 215 0 strelka-varscan-mutect PLK3,synonymous_variant,p.=,ENST00000372201,NM_004073.2;PLK3,non_coding_transcript_exon_variant,,ENST00000465443,;PLK3,upstream_gene_variant,,ENST00000492398,;PLK3,upstream_gene_variant,,ENST00000493100,;PLK3,upstream_gene_variant,,ENST00000461358,;PLK3,upstream_gene_variant,,ENST00000476731,;PLK3,upstream_gene_variant,,ENST00000461769,; A ENST00000372201 Transcript synonymous_variant 419/2492 180/1941 60/646 R cgC/cgA 1 1 PLK3 HGNC HGNC:2154 protein_coding YES CCDS515.1 ENSP00000361275 Q9H4B4 UPI000013ED1D NM_004073.2 1/15 hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF42,Gene3D:3.30.200.20 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 25 44800643 44800643 C A 1 0 0 0 0 0 0 0 1 12192 697 25 2 2 PLK3 1 44800643 Silent SNP C C3L-01682_T 44800643 204155779 1 7402 PLPPR4 0 . GRCh38 1 99306995 99306995 + Silent SNP G G T novel C3L-01682_T C3L-01682_N G G c.2277G>T p.= p.R759R ENST00000370185 7/7 75 65 10 82 81 1 strelka-varscan-mutect PLPPR4,synonymous_variant,p.=,ENST00000370185,NM_014839.4;PLPPR4,synonymous_variant,p.=,ENST00000457765,NM_001166252.1;PLPPR4,synonymous_variant,p.=,ENST00000370184,; T ENST00000370185 Transcript synonymous_variant 2774/5369 2277/2292 759/763 R cgG/cgT 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 7/7 LOW 1 SNV 1 1 PASS rs1320737744 . 0 195 14 0 0 0 0 0 -19.98465 0.9996469 1 1 1 0 T 2 4 25 99306995 99306995 G T 1 0 0 0 0 0 0 0 1 12212 1219 43 2 2 PLPPR4 1 99306995 Silent SNP G C3L-01682_T 54506352 99306995 149649427 2 7403 SLC6A17 0 . GRCh38 1 110198394 110198394 + Missense_Mutation SNP C C A rs142470334 C3L-01682_T C3L-01682_N C C c.2134C>A p.Arg712Ser p.R712S ENST00000331565 12/12 172 150 22 151 151 0 varscan-mutect SLC6A17,missense_variant,p.Arg712Ser,ENST00000331565,NM_001010898.2;SLC6A17,downstream_gene_variant,,ENST00000465159,; A ENST00000331565 Transcript missense_variant 2619/6427 2134/2184 712/727 R/S Cgc/Agc rs142470334 1 1 SLC6A17 HGNC HGNC:31399 protein_coding YES CCDS30799.1 ENSP00000330199 Q9H1V8 UPI0000470B3D NM_001010898.2 tolerated_low_confidence(0.13) 12/12 hmmpanther:PTHR11616:SF102,hmmpanther:PTHR11616 MODERATE 1 SNV 2 1 PASS rs142470334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 110198394 110198394 C A 1 0 0 0 0 1 0 0 0 14963 536 19 1 1 SLC6A17 1 110198394 Missense_Mutation SNP C C3L-01682_T 10891399 110198394 138758028 3 7404 RNF115 0 . GRCh38 1 145823773 145823773 + Missense_Mutation SNP G G A novel C3L-01682_T C3L-01682_N G G c.101C>T p.Pro34Leu p.P34L ENST00000582693 1/9 122 105 17 109 109 0 strelka-varscan-mutect RNF115,missense_variant,p.Pro34Leu,ENST00000582693,NM_014455.3;POLR3C,upstream_gene_variant,,ENST00000334163,NM_006468.7,NM_001303456.1;POLR3C,upstream_gene_variant,,ENST00000369294,;POLR3C,upstream_gene_variant,,ENST00000471254,;POLR3C,upstream_gene_variant,,ENST00000466003,; A ENST00000582693 Transcript missense_variant,splice_region_variant 305/9117 101/915 34/304 P/L cCg/cTg 1 -1 RNF115 HGNC HGNC:18154 protein_coding YES CCDS72863.1 ENSP00000463650 Q9Y4L5 UPI00001B061B NM_014455.3 deleterious(0) 1/9 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF3 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999923 1 1 1 0 A 3 1 25 145823773 145823773 G A 1 0 0 0 0 1 0 0 0 13608 1130 39 1 1 RNF115 1 145823773 Missense_Mutation SNP G C3L-01682_T 35625379 145823773 103132649 4 7405 LMNA 0 . GRCh38 1 156134458 156134458 + Missense_Mutation SNP G G T rs267607571 C3L-01682_T C3L-01682_N G G c.569G>T p.Arg190Leu p.R190L ENST00000368300 3/12 590 525 65 623 621 2 strelka-varscan LMNA,missense_variant,p.Arg190Leu,ENST00000368300,NM_170707.3;LMNA,missense_variant,p.Arg190Leu,ENST00000347559,NM_170708.3;LMNA,missense_variant,p.Arg190Leu,ENST00000368301,NM_001282625.1,NM_005572.3;LMNA,missense_variant,p.Arg190Leu,ENST00000368299,NM_001282626.1;LMNA,missense_variant,p.Arg91Leu,ENST00000473598,;LMNA,missense_variant,p.Arg78Leu,ENST00000448611,NM_001257374.2;LMNA,missense_variant,p.Arg190Leu,ENST00000361308,;LMNA,missense_variant,p.Arg109Leu,ENST00000368297,NM_001282624.1;LMNA,missense_variant,p.Arg107Leu,ENST00000504687,;LMNA,upstream_gene_variant,,ENST00000508500,;LMNA,non_coding_transcript_exon_variant,,ENST00000502751,;LMNA,non_coding_transcript_exon_variant,,ENST00000470199,;LMNA,non_coding_transcript_exon_variant,,ENST00000502357,;LMNA,upstream_gene_variant,,ENST00000496738,;LMNA,upstream_gene_variant,,ENST00000459904,;LMNA,downstream_gene_variant,,ENST00000469565,;LMNA,3_prime_UTR_variant,,ENST00000515459,;LMNA,upstream_gene_variant,,ENST00000368298,;LMNA,upstream_gene_variant,,ENST00000498722,;LMNA,upstream_gene_variant,,ENST00000506981,;LMNA,upstream_gene_variant,,ENST00000515824,; T ENST00000368300 Transcript missense_variant 781/3190 569/1995 190/664 R/L cGg/cTg rs267607571,CM050658,HIFD_LMNA:c.569G>A,COSM1472743,COSM5229102 1 1 LMNA HGNC HGNC:6636 protein_coding YES CCDS1129.1 ENSP00000357283 P02545 UPI000012E20D NM_170707.3 deleterious(0) 3/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF158,Pfam_domain:PF00038,SMART_domains:SM01391 pathogenic 0,0,0,1,1 MODERATE 1 SNV 1 1,1,0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 156134458 156134458 G T 1 0 0 0 0 1 0 0 0 8772 1116 39 1 1 LMNA 1 156134458 Missense_Mutation SNP G C3L-01682_T 10310685 156134458 92821964 5 7406 FCRL5 0 . GRCh38 1 157521230 157521230 + Missense_Mutation SNP G G T rs780580169 C3L-01682_T C3L-01682_N G G c.2302C>A p.Leu768Met p.L768M ENST00000361835 11/17 211 189 22 177 177 0 strelka-varscan FCRL5,missense_variant,p.Leu768Met,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,downstream_gene_variant,,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000461387,;FCRL5,non_coding_transcript_exon_variant,,ENST00000497286,;FCRL5,upstream_gene_variant,,ENST00000483875,; T ENST00000361835 Transcript missense_variant 2460/5390 2302/2934 768/977 L/M Ctg/Atg rs780580169 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(0.36) 11/17 PROSITE_profiles:PS50835,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 157521230 157521230 G T 1 0 0 0 0 1 0 0 0 5660 991 35 2 2 FCRL5 1 157521230 Missense_Mutation SNP G C3L-01682_T 1386772 157521230 91435192 6 7407 OLFML2B 0 . GRCh38 1 161983695 161983695 + Missense_Mutation SNP G G T C3L-01682_T C3L-01682_N G G c.2236C>A p.His746Asn p.H746N ENST00000367940 8/8 105 88 17 80 80 0 strelka-varscan OLFML2B,missense_variant,p.His745Asn,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.His746Asn,ENST00000367940,NM_001297713.1;OLFML2B,missense_variant,p.His228Asn,ENST00000367938,;OLFML2B,missense_variant,p.His83Asn,ENST00000525589,;OLFML2B,missense_variant,p.His85Asn,ENST00000533556,; T ENST00000367940 Transcript missense_variant 2446/2685 2236/2256 746/751 H/N Cat/Aat COSM4429085 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 tolerated(0.54) 8/8 PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF37,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284 1 MODERATE 1 SNV 2 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 161983695 161983695 G T 1 0 0 0 0 1 0 0 0 10933 1348 47 2 2 OLFML2B 1 161983695 Missense_Mutation SNP G C3L-01682_T 4462465 161983695 86972727 7 7408 DTL 0 . GRCh38 1 212100660 212100660 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.1670C>T p.Ser557Leu p.S557L ENST00000366991 14/15 390 364 26 353 353 0 strelka-varscan DTL,missense_variant,p.Ser557Leu,ENST00000366991,NM_016448.3;DTL,missense_variant,p.Ser515Leu,ENST00000542077,NM_001286229.1,NM_001286230.1;RN7SKP98,upstream_gene_variant,,ENST00000517070,;DTL,non_coding_transcript_exon_variant,,ENST00000475419,;DTL,non_coding_transcript_exon_variant,,ENST00000489149,;DTL,non_coding_transcript_exon_variant,,ENST00000496442,;DTL,downstream_gene_variant,,ENST00000463791,; T ENST00000366991 Transcript missense_variant 1984/4573 1670/2193 557/730 S/L tCa/tTa 1 1 DTL HGNC HGNC:30288 protein_coding YES CCDS1502.1 ENSP00000355958 Q9NZJ0 UPI000013E1C1 NM_016448.3 deleterious(0.03) 14/15 hmmpanther:PTHR22852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 212100660 212100660 C T 1 0 0 0 0 1 0 0 0 4610 838 29 3 3 DTL 1 212100660 Missense_Mutation SNP C C3L-01682_T 50116965 212100660 36855762 8 7409 HEATR1 0 . GRCh38 1 236576943 236576943 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.2762C>A p.Thr921Lys p.T921K ENST00000366582 21/45 95 90 5 80 80 0 strelka-varscan HEATR1,missense_variant,p.Thr921Lys,ENST00000366582,NM_018072.5;HEATR1,missense_variant,p.Thr921Lys,ENST00000366581,;HEATR1,upstream_gene_variant,,ENST00000490339,; T ENST00000366582 Transcript missense_variant 2877/8447 2762/6435 921/2144 T/K aCa/aAa 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 tolerated(0.07) 21/45 Gene3D:1.25.10.10,hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -10.78655 1 1 1 1 0 T 3 4 25 236576943 236576943 G T 1 0 0 0 0 1 0 0 0 6910 1377 48 2 2 HEATR1 1 236576943 Missense_Mutation SNP G C3L-01682_T 24476283 236576943 12379479 9 7410 OR14A16 0 . GRCh38 1 247815020 247815020 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.710C>A p.Ser237Tyr p.S237Y ENST00000357627 1/1 192 178 14 212 212 0 strelka-varscan OR14A16,missense_variant,p.Ser237Tyr,ENST00000357627,NM_001001966.1; T ENST00000357627 Transcript missense_variant 710/930 710/930 237/309 S/Y tCt/tAt 1 -1 OR14A16 HGNC HGNC:15022 protein_coding YES CCDS31097.1 ENSP00000350248 Q8NHC5 UPI0000041CE2 NM_001001966.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF352,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 247815020 247815020 G T 1 0 0 0 0 1 0 0 0 11021 942 33 2 2 OR14A16 1 247815020 Missense_Mutation SNP G C3L-01682_T 11238077 247815020 1141402 10 7411 29 2 OR14A16 0 . GRCh38 1 247815022 247815022 + Nonsense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.708C>A p.Tyr236Ter p.Y236* ENST00000357627 1/1 202 184 18 212 211 1 strelka-varscan OR14A16,stop_gained,p.Tyr236Ter,ENST00000357627,NM_001001966.1; T ENST00000357627 Transcript stop_gained 708/930 708/930 236/309 Y/* taC/taA 1 -1 OR14A16 HGNC HGNC:15022 protein_coding YES CCDS31097.1 ENSP00000350248 Q8NHC5 UPI0000041CE2 NM_001001966.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF352,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 25 247815022 247815022 G T 1 0 0 0 0 0 1 0 0 11021 1024 36 2 2 OR14A16 1 247815022 Nonsense_Mutation SNP G C3L-01682_T 2 247815022 1141400 11 7412 29 2 DRC1 0 . GRCh38 2 26453373 26453373 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.1743C>A p.Ser581Arg p.S581R ENST00000288710 14/17 415 366 49 412 412 0 strelka-varscan DRC1,missense_variant,p.Ser581Arg,ENST00000288710,NM_145038.3;OTOF,downstream_gene_variant,,ENST00000272371,NM_194248.2;OTOF,downstream_gene_variant,,ENST00000403946,NM_001287489.1;OTOF,downstream_gene_variant,,ENST00000402415,NM_194322.2;OTOF,downstream_gene_variant,,ENST00000338581,NM_004802.3;OTOF,downstream_gene_variant,,ENST00000339598,NM_194323.2;DRC1,non_coding_transcript_exon_variant,,ENST00000439066,; A ENST00000288710 Transcript missense_variant 1817/2491 1743/2223 581/740 S/R agC/agA 1 1 DRC1 HGNC HGNC:24245 protein_coding YES CCDS1723.1 ENSP00000288710 Q96MC2 UPI000013DF36 NM_145038.3 tolerated(0.25) 14/17 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 26453373 26453373 C A 1 0 0 0 0 1 0 0 0 4572 709 25 2 2 DRC1 2 26453373 Missense_Mutation SNP C C3L-01682_T 26453373 215740156 12 7413 ABCG8 0 . GRCh38 2 43844527 43844527 + Silent SNP C C T novel C3L-01682_T C3L-01682_N C C c.84C>T p.= p.F28F ENST00000272286 2/13 461 417 44 414 413 1 strelka-varscan-mutect ABCG8,synonymous_variant,p.=,ENST00000272286,NM_022437.2; T ENST00000272286 Transcript synonymous_variant 174/2665 84/2022 28/673 F ttC/ttT 1 1 ABCG8 HGNC HGNC:13887 protein_coding YES CCDS1815.1 ENSP00000272286 Q9H221 UPI000004C4CD NM_022437.2 2/13 hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF239 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 43844527 43844527 C T 1 0 0 0 0 0 0 0 1 76 912 32 3 3 ABCG8 2 43844527 Silent SNP C C3L-01682_T 17391154 43844527 198349002 13 7414 LHCGR 0 . GRCh38 2 48687737 48687737 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.2060G>T p.Gly687Val p.G687V ENST00000294954 11/11 281 251 30 266 266 0 strelka-varscan-mutect LHCGR,missense_variant,p.Gly687Val,ENST00000294954,NM_000233.3;LHCGR,missense_variant,p.Gly660Val,ENST00000405626,;LHCGR,3_prime_UTR_variant,,ENST00000403273,;LHCGR,3_prime_UTR_variant,,ENST00000401907,;STON1-GTF2A1L,intron_variant,,ENST00000402114,NM_001198593.1;GTF2A1L,intron_variant,,ENST00000508440,;RP11-310N16.1,intron_variant,,ENST00000602369,; A ENST00000294954 Transcript missense_variant 2082/3044 2060/2100 687/699 G/V gGt/gTt 1 -1 LHCGR HGNC HGNC:6585 protein_coding YES CCDS1842.1 ENSP00000294954 P22888 UPI000013E1E1 NM_000233.3 tolerated(0.52) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 48687737 48687737 C A 1 0 0 0 0 1 0 0 0 8671 507 18 2 2 LHCGR 2 48687737 Missense_Mutation SNP C C3L-01682_T 4843210 48687737 193505792 14 7415 INO80B 0 . GRCh38 2 74455596 74455596 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.249G>T p.Lys83Asn p.K83N ENST00000233331 2/5 111 99 12 98 98 0 strelka-varscan-mutect INO80B,missense_variant,p.Lys83Asn,ENST00000233331,NM_031288.3;INO80B,missense_variant,p.Lys83Asn,ENST00000409917,;INO80B,missense_variant,p.Lys88Asn,ENST00000409493,;INO80B,missense_variant,p.Lys83Asn,ENST00000431187,;WBP1,upstream_gene_variant,,ENST00000393972,;WBP1,upstream_gene_variant,,ENST00000233615,NM_012477.3;WBP1,upstream_gene_variant,,ENST00000409737,;WBP1,upstream_gene_variant,,ENST00000428943,;INO80B,splice_region_variant,,ENST00000494986,;INO80B,intron_variant,,ENST00000469849,;WBP1,upstream_gene_variant,,ENST00000494741,;WBP1,upstream_gene_variant,,ENST00000470536,;WBP1,upstream_gene_variant,,ENST00000466835,;WBP1,upstream_gene_variant,,ENST00000464774,;WBP1,upstream_gene_variant,,ENST00000474185,;INO80B-WBP1,missense_variant,p.Lys83Asn,ENST00000452361,;INO80B-WBP1,missense_variant,p.Lys83Asn,ENST00000441673,;INO80B,missense_variant,p.Lys35Asn,ENST00000455562,;INO80B,splice_region_variant,,ENST00000471577,;INO80B,splice_region_variant,,ENST00000473618,;WBP1,upstream_gene_variant,,ENST00000484744,;WBP1,upstream_gene_variant,,ENST00000490120,;WBP1,upstream_gene_variant,,ENST00000473467,;WBP1,upstream_gene_variant,,ENST00000466303,;WBP1,upstream_gene_variant,,ENST00000492047,; T ENST00000233331 Transcript missense_variant,splice_region_variant 343/1261 249/1071 83/356 K/N aaG/aaT 1 1 INO80B HGNC HGNC:13324 protein_coding YES CCDS1942.2 ENSP00000233331 Q9C086 UPI0000456DE1 NM_031288.3 deleterious(0) 2/5 hmmpanther:PTHR21561 MODERATE 1 SNV 1 1 PASS rs1236415024 . 0 205 5 0 0 0 0 0 -19.99997 1 1 1 1 0 T 3 4 25 74455596 74455596 G T 1 0 0 0 0 1 0 0 0 7650 956 33 2 2 INO80B 2 74455596 Missense_Mutation SNP G C3L-01682_T 25767859 74455596 167737933 15 7416 DNAH6 0 . GRCh38 2 84544446 84544446 + Missense_Mutation SNP G G C novel C3L-01682_T C3L-01682_N G G c.876G>C p.Lys292Asn p.K292N ENST00000389394 5/77 173 158 15 159 159 0 strelka-varscan-mutect DNAH6,missense_variant,p.Lys292Asn,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Lys292Asn,ENST00000237449,;DNAH6,downstream_gene_variant,,ENST00000468661,;DNAH6,intron_variant,,ENST00000476689,;DNAH6,intron_variant,,ENST00000494025,; C ENST00000389394 Transcript missense_variant 1013/12795 876/12477 292/4158 K/N aaG/aaC 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated(0.2) 5/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 84544446 84544446 G C 1 0 0 0 0 1 0 0 0 4420 933 33 4 4 DNAH6 2 84544446 Missense_Mutation SNP G C3L-01682_T 10088850 84544446 157649083 16 7417 LRP1B 0 . GRCh38 2 140536593 140536593 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.7630C>A p.Leu2544Met p.L2544M ENST00000389484 46/91 357 328 29 331 331 0 strelka-varscan-mutect LRP1B,missense_variant,p.Leu2544Met,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript missense_variant 8602/16535 7630/13800 2544/4599 L/M Ctg/Atg 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.22) 46/91 PROSITE_profiles:PS50068,PROSITE_patterns:PS01209,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 140536593 140536593 G T 1 0 0 0 0 1 0 0 0 8850 1020 36 2 2 LRP1B 2 140536593 Missense_Mutation SNP G C3L-01682_T 55992147 140536593 101656936 17 7418 LRP1B 0 . GRCh38 2 141005435 141005435 + Missense_Mutation SNP A A T rs749949683 C3L-01682_T C3L-01682_N A A c.2403T>A p.Asn801Lys p.N801K ENST00000389484 15/91 271 255 16 230 229 1 strelka-varscan-mutect LRP1B,missense_variant,p.Asn801Lys,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; T ENST00000389484 Transcript missense_variant 3375/16535 2403/13800 801/4599 N/K aaT/aaA rs749949683 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.05) 15/91 Pfam_domain:PF14670,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs749949683 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 141005435 141005435 A T 1 0 0 0 0 1 0 0 0 8850 446 16 4 4 LRP1B 2 141005435 Missense_Mutation SNP A C3L-01682_T 468842 141005435 101188094 18 7419 WDSUB1 0 . GRCh38 2 159256249 159256249 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.1079G>A p.Gly360Glu p.G360E ENST00000409990 9/11 176 162 14 192 192 0 strelka-varscan-mutect WDSUB1,missense_variant,p.Gly360Glu,ENST00000409990,NM_001128213.1;WDSUB1,missense_variant,p.Gly360Glu,ENST00000359774,NM_001128212.1;WDSUB1,missense_variant,p.Gly360Glu,ENST00000392796,NM_152528.2;WDSUB1,missense_variant,p.Gly360Glu,ENST00000409124,;WDSUB1,missense_variant,p.Gly268Glu,ENST00000358147,NM_001307994.1; T ENST00000409990 Transcript missense_variant 1336/1920 1079/1431 360/476 G/E gGa/gAa 1 -1 WDSUB1 HGNC HGNC:26697 protein_coding YES CCDS2208.1 ENSP00000387078 Q8N9V3 D3DPA6 UPI000058E905 NM_001128213.1 deleterious(0) 9/11 PROSITE_profiles:PS50105,hmmpanther:PTHR22849,hmmpanther:PTHR22849:SF0,Pfam_domain:PF07647,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 159256249 159256249 C T 1 0 0 0 0 1 0 0 0 17898 855 30 3 3 WDSUB1 2 159256249 Missense_Mutation SNP C C3L-01682_T 18250814 159256249 82937280 19 7420 TTN 0 . GRCh38 2 178804579 178804579 + Missense_Mutation SNP T T A C3L-01682_T C3L-01682_N T T c.64A>T p.Thr22Ser p.T22S ENST00000589042 2/363 504 473 31 433 433 0 strelka-varscan-mutect TTN,missense_variant,p.Thr22Ser,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Thr22Ser,ENST00000591111,;TTN,missense_variant,p.Thr22Ser,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Thr22Ser,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Thr22Ser,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Thr22Ser,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Thr22Ser,ENST00000359218,NM_133432.3;TTN,missense_variant,p.Thr22Ser,ENST00000360870,NM_133379.4;TTN,missense_variant,p.Thr22Ser,ENST00000412264,;TTN,non_coding_transcript_exon_variant,,ENST00000470257,; A ENST00000589042 Transcript missense_variant 289/109224 64/107976 22/35991 T/S Acc/Tcc COSM5354841,COSM5354842,COSM5354843,COSM5354844,COSM5354846 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 2/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs1305775594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 178804579 178804579 T A 1 0 0 0 0 1 0 0 0 17245 1638 57 4 4 TTN 2 178804579 Missense_Mutation SNP T C3L-01682_T 19548330 178804579 63388950 20 7421 GULP1 0 . GRCh38 2 188584272 188584272 + Missense_Mutation SNP G G T rs777660706 C3L-01682_T C3L-01682_N G G c.617G>T p.Ser206Ile p.S206I ENST00000409580 11/13 150 137 13 137 137 0 varscan-mutect GULP1,missense_variant,p.Ser31Ile,ENST00000451191,;GULP1,missense_variant,p.Ser206Ile,ENST00000409580,;GULP1,missense_variant,p.Ser206Ile,ENST00000359135,;GULP1,missense_variant,p.Ser206Ile,ENST00000409843,NM_001252668.1;GULP1,missense_variant,p.Ser206Ile,ENST00000409609,;GULP1,missense_variant,p.Ser206Ile,ENST00000409830,NM_016315.3;GULP1,missense_variant,p.Ser103Ile,ENST00000409805,NM_001252669.1;GULP1,missense_variant,p.Ser91Ile,ENST00000433052,;GULP1,non_coding_transcript_exon_variant,,ENST00000478306,;GULP1,non_coding_transcript_exon_variant,,ENST00000495745,;GULP1,non_coding_transcript_exon_variant,,ENST00000467422,;GULP1,non_coding_transcript_exon_variant,,ENST00000476422,; T ENST00000409580 Transcript missense_variant 1331/3544 617/915 206/304 S/I aGt/aTt rs777660706 1 1 GULP1 HGNC HGNC:18649 protein_coding YES CCDS2295.1 ENSP00000386289 Q9UBP9 UPI0000031CE3 tolerated(0.21) 11/13 hmmpanther:PTHR11232:SF48,hmmpanther:PTHR11232 MODERATE 1 SNV 2 1 PASS rs777660706 . 0 204 5 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 25 188584272 188584272 G T 1 0 0 0 0 1 0 0 0 6783 1029 36 2 2 GULP1 2 188584272 Missense_Mutation SNP G C3L-01682_T 9779693 188584272 53609257 21 7422 MAP2 0 . GRCh38 2 209730248 209730248 + Missense_Mutation SNP A A T novel C3L-01682_T C3L-01682_N A A c.5335A>T p.Ile1779Phe p.I1779F ENST00000360351 15/15 405 362 43 344 344 0 strelka-varscan-mutect MAP2,missense_variant,p.Ile1779Phe,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Ile1775Phe,ENST00000447185,;MAP2,missense_variant,p.Ile423Phe,ENST00000392194,NM_031845.2;MAP2,missense_variant,p.Ile511Phe,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,missense_variant,p.Ile423Phe,ENST00000361559,;MAP2,downstream_gene_variant,,ENST00000475600,; T ENST00000360351 Transcript missense_variant 5841/9711 5335/5484 1779/1827 I/F Att/Ttt 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious(0) 15/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 209730248 209730248 A T 1 0 0 0 0 1 0 0 0 9157 217 8 4 4 MAP2 2 209730248 Missense_Mutation SNP A C3L-01682_T 21145976 209730248 32463281 22 7423 GRIP2 0 . GRCh38 3 14524423 14524423 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.664C>A p.Leu222Met p.L222M ENST00000619221 5/25 199 178 21 224 224 0 strelka-varscan-mutect GRIP2,missense_variant,p.Leu222Met,ENST00000619221,;GRIP2,missense_variant,p.Leu125Met,ENST00000621039,NM_001080423.3;GRIP2,missense_variant,p.Leu130Met,ENST00000637182,;GRIP2,missense_variant,p.Leu132Met,ENST00000637939,;GRIP2,non_coding_transcript_exon_variant,,ENST00000422481,;GRIP2,non_coding_transcript_exon_variant,,ENST00000413414,; T ENST00000619221 Transcript missense_variant 664/7977 664/3423 222/1140 L/M Ctg/Atg 1 -1 GRIP2 HGNC HGNC:23841 protein_coding YES ENSP00000480660 A0A087WX15 UPI0001DD380B deleterious(0) 5/25 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF42,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 25 14524423 14524423 G T 1 0 0 0 0 1 0 0 0 6669 962 34 2 2 GRIP2 3 14524423 Missense_Mutation SNP G C3L-01682_T 14524423 183771136 23 7424 PLXNB1 0 . GRCh38 3 48415705 48415705 + Silent SNP C C A rs756546017 C3L-01682_T C3L-01682_N C C c.3672G>T p.= p.T1224T ENST00000358536 19/38 164 145 19 157 157 0 strelka-varscan-mutect PLXNB1,synonymous_variant,p.=,ENST00000358536,NM_002673.5;PLXNB1,synonymous_variant,p.=,ENST00000296440,NM_001130082.2;PLXNB1,synonymous_variant,p.=,ENST00000456774,;PLXNB1,upstream_gene_variant,,ENST00000465117,;PLXNB1,downstream_gene_variant,,ENST00000466353,;PLXNB1,downstream_gene_variant,,ENST00000484485,;PLXNB1,3_prime_UTR_variant,,ENST00000449094,;PLXNB1,non_coding_transcript_exon_variant,,ENST00000464294,;PLXNB1,upstream_gene_variant,,ENST00000485535,;PLXNB1,upstream_gene_variant,,ENST00000473996,;PLXNB1,upstream_gene_variant,,ENST00000461261,;PLXNB1,upstream_gene_variant,,ENST00000470525,;PLXNB1,upstream_gene_variant,,ENST00000467913,;PLXNB1,downstream_gene_variant,,ENST00000462738,; A ENST00000358536 Transcript synonymous_variant 3942/7308 3672/6408 1224/2135 T acG/acT rs756546017 1 -1 PLXNB1 HGNC HGNC:9103 protein_coding YES CCDS2765.1 ENSP00000351338 O43157 UPI0000038131 NM_002673.5 19/38 Gene3D:2.60.40.10,Pfam_domain:PF01833,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF36,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS rs756546017 . 0 206 0 3 0 0 0 0 -20 0.9999887 1 1 1 0 A 2 1 25 48415705 48415705 C A 1 0 0 0 0 0 0 0 1 12229 755 27 1 1 PLXNB1 3 48415705 Silent SNP C C3L-01682_T 33891282 48415705 149879854 24 7425 GPR62 0 . GRCh38 3 51956679 51956679 + Missense_Mutation SNP G G A C3L-01682_T C3L-01682_N G G c.1027G>A p.Glu343Lys p.E343K ENST00000322241 1/1 233 219 14 229 229 0 strelka-varscan-mutect GPR62,missense_variant,p.Glu343Lys,ENST00000322241,NM_080865.3;PCBP4,downstream_gene_variant,,ENST00000461554,NM_001174100.1;PCBP4,downstream_gene_variant,,ENST00000355852,NM_033008.2;PCBP4,downstream_gene_variant,,ENST00000484633,NM_020418.3;PCBP4,downstream_gene_variant,,ENST00000322099,NM_033010.2;PCBP4,downstream_gene_variant,,ENST00000428823,;PCBP4,downstream_gene_variant,,ENST00000471622,;PCBP4,downstream_gene_variant,,ENST00000395014,;PCBP4,downstream_gene_variant,,ENST00000466412,;PCBP4,downstream_gene_variant,,ENST00000468324,;PCBP4,downstream_gene_variant,,ENST00000483411,;PCBP4,downstream_gene_variant,,ENST00000461544,;PCBP4,downstream_gene_variant,,ENST00000497653,;PCBP4,downstream_gene_variant,,ENST00000489595,;PCBP4,downstream_gene_variant,,ENST00000490063,;RP11-155D18.13,upstream_gene_variant,,ENST00000624646,;RP11-155D18.12,downstream_gene_variant,,ENST00000488257,;PCBP4,downstream_gene_variant,,ENST00000492809,;PCBP4,downstream_gene_variant,,ENST00000498822,;PCBP4,downstream_gene_variant,,ENST00000497390,;PCBP4,downstream_gene_variant,,ENST00000471308,;PCBP4,downstream_gene_variant,,ENST00000471358,; A ENST00000322241 Transcript missense_variant 1366/2191 1027/1107 343/368 E/K Gag/Aag COSM3775211 1 1 GPR62 HGNC HGNC:13301 protein_coding YES CCDS2838.1 ENSP00000319250 Q9BZJ7 UPI0000457117 NM_080865.3 tolerated(0.58) 1/1 hmmpanther:PTHR22752:SF6,hmmpanther:PTHR22752 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 51956679 51956679 G A 1 0 0 0 0 1 0 0 0 6587 1291 45 3 3 GPR62 3 51956679 Missense_Mutation SNP G C3L-01682_T 3540974 51956679 146338880 25 7426 SLC34A2 0 . GRCh38 4 25676472 25676485 + Frame_Shift_Del DEL CGCTGAAGCCCTGG CGCTGAAGCCCTGG - novel C3L-01682_T C3L-01682_N CGCTGAAGCCCTGG CGCTGAAGCCCTGG c.1796_1809delCGCTGAAGCCCTGG p.Ser599Ter p.S599* ENST00000382051 13/13 87 79 8 76 76 0 sindel-pindel SLC34A2,frameshift_variant,p.Ser599Ter,ENST00000382051,NM_006424.2;SLC34A2,frameshift_variant,p.Ser598Ter,ENST00000503434,NM_001177999.1;SLC34A2,frameshift_variant,p.Ser598Ter,ENST00000504570,NM_001177998.1;RP11-302F12.1,upstream_gene_variant,,ENST00000496507,; - ENST00000382051 Transcript frameshift_variant 1846-1859/4122 1796-1809/2073 599-603/690 SLKPW/X tCGCTGAAGCCCTGG/t 1 1 SLC34A2 HGNC HGNC:11020 protein_coding YES CCDS3435.1 ENSP00000371483 O95436 UPI000013DF24 NM_006424.2 13/13 hmmpanther:PTHR10010,hmmpanther:PTHR10010:SF23,TIGRFAM_domain:TIGR01013 HIGH 1 deletion 1 1 PASS . . 0 204 6 0 0 0 0 0 -16.81776 0.9999998 1 1 1 0 - 7 5 25 25676472 25676472 CGCTGAAGCCCTGG - 1 0 1 0 1 0 0 0 0 14838 893 31 0 0 SLC34A2 4 25676472 Frame_Shift_Del DEL CGCTGAAGCCCTGG C3L-01682_T 25676472 164538083 26 7427 KLB 0 . GRCh38 4 39434291 39434291 + Missense_Mutation SNP C C G novel C3L-01682_T C3L-01682_N C C c.907C>G p.His303Asp p.H303D ENST00000257408 2/5 191 178 13 220 219 1 strelka-varscan KLB,missense_variant,p.His303Asp,ENST00000257408,NM_175737.3; G ENST00000257408 Transcript missense_variant 1004/6082 907/3135 303/1044 H/D Cat/Gat 1 1 KLB HGNC HGNC:15527 protein_coding YES CCDS3451.1 ENSP00000257408 Q86Z14 UPI000000D726 NM_175737.3 tolerated(0.05) 2/5 Gene3D:3.20.20.80,Pfam_domain:PF00232,hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF68,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 25 39434291 39434291 C G 1 0 0 0 0 1 0 0 0 8197 826 29 4 4 KLB 4 39434291 Missense_Mutation SNP C C3L-01682_T 13757819 39434291 150780264 27 7428 ATP10D 0 . GRCh38 4 47568871 47568871 + Missense_Mutation SNP A A T novel C3L-01682_T C3L-01682_N A A c.2888A>T p.Lys963Ile p.K963I ENST00000273859 16/23 143 135 8 132 132 0 strelka-varscan ATP10D,missense_variant,p.Lys963Ile,ENST00000273859,NM_020453.3;ATP10D,3_prime_UTR_variant,,ENST00000503288,; T ENST00000273859 Transcript missense_variant 3157/6655 2888/4281 963/1426 K/I aAa/aTa 1 1 ATP10D HGNC HGNC:13549 protein_coding YES CCDS3476.1 ENSP00000273859 Q9P241 UPI00001AE9B7 NM_020453.3 tolerated(0.05) 16/23 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF84,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 47568871 47568871 A T 1 0 0 0 0 1 0 0 0 1270 14 1 4 4 ATP10D 4 47568871 Missense_Mutation SNP A C3L-01682_T 8134580 47568871 142645684 28 7429 IBSP 0 . GRCh38 4 87811587 87811587 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.631G>T p.Ala211Ser p.A211S ENST00000226284 7/7 224 211 13 206 206 0 strelka-varscan-mutect IBSP,missense_variant,p.Ala211Ser,ENST00000226284,NM_004967.3; T ENST00000226284 Transcript missense_variant 698/1546 631/954 211/317 A/S Gca/Tca 1 1 IBSP HGNC HGNC:5341 protein_coding YES CCDS3624.1 ENSP00000226284 P21815 UPI000013C899 NM_004967.3 tolerated(0.38) 7/7 hmmpanther:PTHR10345:SF0,hmmpanther:PTHR10345,Pfam_domain:PF05432 MODERATE 1 SNV 1 1 PASS rs1349058180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 87811587 87811587 G T 1 0 0 0 0 1 0 0 0 7375 1319 46 2 2 IBSP 4 87811587 Missense_Mutation SNP G C3L-01682_T 40242716 87811587 102402968 29 7430 RAB33B 0 . GRCh38 4 139454407 139454407 + Missense_Mutation SNP G G A novel C3L-01682_T C3L-01682_N G G c.212G>A p.Arg71Gln p.R71Q ENST00000305626 1/2 241 228 13 190 190 0 strelka-varscan-mutect RAB33B,missense_variant,p.Arg71Gln,ENST00000305626,NM_031296.1;RP11-83A24.2,upstream_gene_variant,,ENST00000610159,;RP11-83A24.2,upstream_gene_variant,,ENST00000608661,;RP11-83A24.2,upstream_gene_variant,,ENST00000609359,;RP11-83A24.2,upstream_gene_variant,,ENST00000608663,;RAB33B,downstream_gene_variant,,ENST00000507271,; A ENST00000305626 Transcript missense_variant 601/4562 212/690 71/229 R/Q cGa/cAa 1 1 RAB33B HGNC HGNC:16075 protein_coding YES CCDS3747.1 ENSP00000306496 Q9H082 UPI000000123D NM_031296.1 deleterious(0.04) 1/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF378,hmmpanther:PTHR24073,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 139454407 139454407 G A 1 0 0 0 0 1 0 0 0 13082 1058 37 1 1 RAB33B 4 139454407 Missense_Mutation SNP G C3L-01682_T 51642820 139454407 50760148 30 7431 DDX60 0 . GRCh38 4 168283602 168283602 + Missense_Mutation SNP T T A novel C3L-01682_T C3L-01682_N T T c.1566A>T p.Lys522Asn p.K522N ENST00000393743 13/38 134 113 21 131 131 0 strelka-varscan DDX60,missense_variant,p.Lys522Asn,ENST00000393743,NM_017631.5; A ENST00000393743 Transcript missense_variant 1858/6071 1566/5139 522/1712 K/N aaA/aaT 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 tolerated(0.15) 13/38 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 168283602 168283602 T A 1 0 0 0 0 1 0 0 0 4181 1507 52 4 4 DDX60 4 168283602 Missense_Mutation SNP T C3L-01682_T 28829195 168283602 21930953 31 7432 FAT1 0 . GRCh38 4 186599933 186599933 + Missense_Mutation SNP T T A novel C3L-01682_T C3L-01682_N T T c.12068A>T p.Gln4023Leu p.Q4023L ENST00000441802 22/27 155 130 25 150 150 0 strelka-varscan-mutect FAT1,missense_variant,p.Gln4023Leu,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Gln4025Leu,ENST00000614102,;FAT1,upstream_gene_variant,,ENST00000512772,;FAT1,upstream_gene_variant,,ENST00000507105,;FAT1,upstream_gene_variant,,ENST00000509927,;FAT1,upstream_gene_variant,,ENST00000512347,;FAT1,upstream_gene_variant,,ENST00000507662,;FAT1,upstream_gene_variant,,ENST00000500085,;FAT1,upstream_gene_variant,,ENST00000509537,;FAT1,downstream_gene_variant,,ENST00000503253,; A ENST00000441802 Transcript missense_variant 12278/14786 12068/13767 4023/4588 Q/L cAg/cTg 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 tolerated(1) 22/27 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_profiles:PS50026,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 186599933 186599933 T A 1 0 0 0 0 1 0 0 0 5549 1580 55 4 4 FAT1 4 186599933 Missense_Mutation SNP T C3L-01682_T 18316331 186599933 3614622 32 7433 TARS 0 . GRCh38 5 33462191 33462198 + Frame_Shift_Del DEL ATGGGGGC ATGGGGGC - novel C3L-01682_T C3L-01682_N ATGGGGGC ATGGGGGC c.1923_1930delTGGGGGCA p.Tyr641Ter p.Y641* ENST00000455217 17/20 220 194 26 263 263 0 sindel-varindel-pindel TARS,frameshift_variant,p.Tyr608Ter,ENST00000265112,NM_152295.4;TARS,frameshift_variant,p.Tyr608Ter,ENST00000502553,NM_001258437.1;TARS,frameshift_variant,p.Tyr641Ter,ENST00000455217,NM_001258438.1;TARS,non_coding_transcript_exon_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,upstream_gene_variant,,ENST00000503422,;TARS,downstream_gene_variant,,ENST00000504698,; - ENST00000455217 Transcript frameshift_variant 2044-2051/2523 1922-1929/2271 641-643/756 YGG/X tATGGGGGC/t 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 17/20 PROSITE_profiles:PS50862,HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF36,TIGRFAM_domain:TIGR00418,Gene3D:3.30.930.10,Gene3D:3.40.50.800,Pfam_domain:PF00587,Superfamily_domains:SSF52954 HIGH 1 deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 25 33462191 33462191 ATGGGGGC - 1 0 1 0 1 0 0 0 0 15958 449 16 0 0 TARS 5 33462191 Frame_Shift_Del DEL ATGGGGGC C3L-01682_T 33462191 148076068 33 7434 CARTPT 0 . GRCh38 5 71720593 71720593 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.329C>A p.Ser110Tyr p.S110Y ENST00000296777 3/3 474 427 47 472 470 2 strelka-varscan-mutect CARTPT,missense_variant,p.Ser110Tyr,ENST00000296777,NM_004291.3;CARTPT,non_coding_transcript_exon_variant,,ENST00000513096,; A ENST00000296777 Transcript missense_variant 460/915 329/351 110/116 S/Y tCc/tAc 1 1 CARTPT HGNC HGNC:24323 protein_coding YES CCDS4011.1 ENSP00000296777 Q16568 UPI00000015E9 NM_004291.3 tolerated(0.44) 3/3 hmmpanther:PTHR16655,Pfam_domain:PF06373,Gene3D:1hy9A00,Superfamily_domains:0047261 MODERATE 1 SNV 1 1 PASS rs1302611855 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 71720593 71720593 C A 1 0 0 0 0 1 0 0 0 2358 855 30 2 2 CARTPT 5 71720593 Missense_Mutation SNP C C3L-01682_T 38258402 71720593 109817666 34 7435 KDM3B 0 . GRCh38 5 138429893 138429893 + Silent SNP A A G novel C3L-01682_T C3L-01682_N A A c.4821A>G p.= p.K1607K ENST00000314358 21/24 381 344 37 343 343 0 strelka-varscan-mutect KDM3B,synonymous_variant,p.=,ENST00000314358,NM_016604.3;KDM3B,synonymous_variant,p.=,ENST00000542866,;KDM3B,3_prime_UTR_variant,,ENST00000510866,;KDM3B,3_prime_UTR_variant,,ENST00000507996,;KDM3B,downstream_gene_variant,,ENST00000505756,;KDM3B,downstream_gene_variant,,ENST00000509468,; G ENST00000314358 Transcript synonymous_variant 5021/6813 4821/5286 1607/1761 K aaA/aaG 1 1 KDM3B HGNC HGNC:1337 protein_coding YES CCDS34242.1 ENSP00000326563 Q7LBC6 UPI000020C6A8 NM_016604.3 21/24 Pfam_domain:PF02373,PROSITE_profiles:PS51184,hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF8,SMART_domains:SM00558 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 25 138429893 138429893 A G 1 0 0 0 0 0 0 0 1 8045 69 3 5 5 KDM3B 5 138429893 Silent SNP A C3L-01682_T 66709300 138429893 43108366 35 7436 ADAM19 0 . GRCh38 5 157481853 157481853 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.2641C>A p.Pro881Thr p.P881T ENST00000257527 22/23 297 268 29 284 284 0 strelka-varscan-mutect ADAM19,missense_variant,p.Pro881Thr,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Pro881Thr,ENST00000517905,;ADAM19,missense_variant,p.Pro452Thr,ENST00000517374,;ADAM19,intron_variant,,ENST00000517951,; T ENST00000257527 Transcript missense_variant 2720/6481 2641/2757 881/918 P/T Cca/Aca 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 tolerated(0.76) 22/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 157481853 157481853 G T 1 0 0 0 0 1 0 0 0 284 1232 43 2 2 ADAM19 5 157481853 Missense_Mutation SNP G C3L-01682_T 19051960 157481853 24056406 36 7437 ADAM19 0 . GRCh38 5 157491685 157491686 + Frame_Shift_Ins INS - - C novel C3L-01682_T C3L-01682_N - - c.2024dupG p.Trp676LeufsTer23 p.W676Lfs*23 ENST00000257527 18/23 36 31 5 54 54 0 sindel-pindel ADAM19,frameshift_variant,p.Trp676LeufsTer23,ENST00000257527,NM_033274.4;ADAM19,frameshift_variant,p.Trp676LeufsTer23,ENST00000517905,;ADAM19,frameshift_variant,p.Trp247LeufsTer23,ENST00000517374,;ADAM19,3_prime_UTR_variant,,ENST00000517951,; C ENST00000257527 Transcript frameshift_variant 2103-2104/6481 2024-2025/2757 675/918 G/GX ggc/ggGc 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 18/23 PROSITE_profiles:PS50026,hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905,PROSITE_patterns:PS01186 HIGH 1 insertion 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.26841 1 1 1 1 0 C 7 5 25 157491685 157491685 - C 1 0 1 1 0 0 0 0 0 284 958 34 0 0 ADAM19 5 157491685 Frame_Shift_Ins INS - C3L-01682_T 9832 157491685 24046574 37 7438 LRFN2 0 . GRCh38 6 40431975 40431975 + Frame_Shift_Del DEL G G - novel C3L-01682_T C3L-01682_N G G c.1139delC p.Pro380HisfsTer52 p.P380Hfs*52 ENST00000338305 2/3 223 204 19 236 236 0 sindel-varindel-pindel LRFN2,frameshift_variant,p.Pro380HisfsTer52,ENST00000338305,NM_020737.2; - ENST00000338305 Transcript frameshift_variant 1682/3270 1139/2370 380/789 P/X cCa/ca 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 2/3 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99999 0.9999998 1 1 1 0 - 7 5 25 40431975 40431975 G - 1 0 1 0 1 0 0 0 0 8832 1348 47 0 0 LRFN2 6 40431975 Frame_Shift_Del DEL G C3L-01682_T 40431975 130374004 38 7439 TREML4 0 . GRCh38 6 41230109 41230109 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.493G>T p.Gly165Cys p.G165C ENST00000341495 4/6 186 169 17 152 152 0 strelka-varscan-mutect TREML4,missense_variant,p.Gly165Cys,ENST00000341495,NM_198153.2;TREML4,missense_variant,p.Gly165Cys,ENST00000448827,;TREML4,missense_variant,p.Gly64Cys,ENST00000461240,; T ENST00000341495 Transcript missense_variant 597/2070 493/603 165/200 G/C Ggc/Tgc 1 1 TREML4 HGNC HGNC:30807 protein_coding YES CCDS34446.1 ENSP00000342570 Q6UXN2 UPI00001D696F NM_198153.2 deleterious(0) 4/6 hmmpanther:PTHR16423,hmmpanther:PTHR16423:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 41230109 41230109 G T 1 0 0 0 0 1 0 0 0 16963 1348 47 2 2 TREML4 6 41230109 Missense_Mutation SNP G C3L-01682_T 798134 41230109 129575870 39 7440 OOEP 0 . GRCh38 6 73369279 73369279 + Silent SNP C C A novel C3L-01682_T C3L-01682_N C C c.297G>T p.= p.R99R ENST00000370359 2/3 215 202 13 192 192 0 strelka-mutect OOEP,synonymous_variant,p.=,ENST00000370363,;OOEP,synonymous_variant,p.=,ENST00000441145,;OOEP,synonymous_variant,p.=,ENST00000370359,NM_001080507.2;OOEP-AS1,upstream_gene_variant,,ENST00000445350,;RPL39P3,downstream_gene_variant,,ENST00000424573,; A ENST00000370359 Transcript synonymous_variant 297/478 297/450 99/149 R cgG/cgT 1 -1 OOEP HGNC HGNC:21382 protein_coding YES CCDS47451.1 ENSP00000359384 A6NGQ2 UPI00001D8132 NM_001080507.2 2/3 hmmpanther:PTHR19447:SF14,hmmpanther:PTHR19447,Pfam_domain:PF16005 LOW 1 SNV 1 1 PASS rs1255565067 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 25 73369279 73369279 C A 1 0 0 0 0 0 0 0 1 10946 726 26 2 2 OOEP 6 73369279 Silent SNP C C3L-01682_T 32139170 73369279 97436700 40 7441 SNX14 0 . GRCh38 6 85533755 85533755 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.1654G>T p.Ala552Ser p.A552S ENST00000314673 18/29 349 315 34 332 331 1 strelka-varscan-mutect SNX14,missense_variant,p.Ala552Ser,ENST00000314673,NM_153816.5;SNX14,missense_variant,p.Ala499Ser,ENST00000346348,NM_020468.5;SNX14,missense_variant,p.Ala470Ser,ENST00000515216,;SNX14,missense_variant,p.Ala500Ser,ENST00000505648,NM_001304479.1;SNX14,missense_variant,p.Ala543Ser,ENST00000369627,NM_001297614.2;SNX14,intron_variant,,ENST00000513865,;SNX14,non_coding_transcript_exon_variant,,ENST00000508980,;SNX14,3_prime_UTR_variant,,ENST00000369635,;SNX14,non_coding_transcript_exon_variant,,ENST00000503491,;SNX14,non_coding_transcript_exon_variant,,ENST00000506182,;SNX14,non_coding_transcript_exon_variant,,ENST00000514801,;SNX14,upstream_gene_variant,,ENST00000503608,; A ENST00000314673 Transcript missense_variant 1831/3486 1654/2841 552/946 A/S Gct/Tct 1 -1 SNX14 HGNC HGNC:14977 protein_coding YES CCDS5004.1 ENSP00000313121 Q9Y5W7 UPI000013F8C8 NM_153816.5 tolerated(0.72) 18/29 hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 85533755 85533755 C A 1 0 0 0 0 1 0 0 0 15206 739 26 2 2 SNX14 6 85533755 Missense_Mutation SNP C C3L-01682_T 12164476 85533755 85272224 41 7442 REV3L 0 . GRCh38 6 111373453 111373453 + Silent SNP T T G novel C3L-01682_T C3L-01682_N T T c.4902A>C p.= p.S1634S ENST00000358835 14/33 216 203 13 201 201 0 strelka-varscan-mutect REV3L,synonymous_variant,p.=,ENST00000435970,NM_001286431.1,NM_001286432.1;REV3L,synonymous_variant,p.=,ENST00000358835,NM_002912.4;REV3L,synonymous_variant,p.=,ENST00000368802,;REV3L,synonymous_variant,p.=,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000422377,;REV3L,3_prime_UTR_variant,,ENST00000434009,; G ENST00000358835 Transcript synonymous_variant 5360/10815 4902/9393 1634/3130 S tcA/tcC 1 -1 REV3L HGNC HGNC:9968 protein_coding YES CCDS5091.2 ENSP00000351697 O60673 UPI0000140023 NM_002912.4 14/33 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 25 111373453 111373453 T G 1 0 0 0 0 0 0 0 1 13411 1683 59 5 5 REV3L 6 111373453 Silent SNP T C3L-01682_T 25839698 111373453 59432526 42 7443 FAM26D 0 . GRCh38 6 116557864 116557864 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.169G>T p.Ala57Ser p.A57S ENST00000405399 4/4 173 155 18 148 148 0 strelka-varscan-mutect FAM26D,missense_variant,p.Ala200Ser,ENST00000368596,;FAM26D,missense_variant,p.Ala14Ser,ENST00000368597,NM_001256889.1,NM_153036.3;FAM26D,missense_variant,p.Ala57Ser,ENST00000405399,NM_001256887.1;FAM26D,missense_variant,p.Ala56Ser,ENST00000628083,NM_001256888.1;FAM26D,missense_variant,p.Ala14Ser,ENST00000452373,; T ENST00000405399 Transcript missense_variant 454/1165 169/516 57/171 A/S Gcc/Tcc 1 1 FAM26D HGNC HGNC:21094 protein_coding YES CCDS59032.1 ENSP00000385836 Q5JW98 UPI000056D4A2 NM_001256887.1 deleterious(0) 4/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR32261,hmmpanther:PTHR32261:SF5,Pfam_domain:PF14798 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 116557864 116557864 G T 1 0 0 0 0 1 0 0 0 5431 1319 46 2 2 FAM26D 6 116557864 Missense_Mutation SNP G C3L-01682_T 5184411 116557864 54248115 43 7444 TTLL2 0 . GRCh38 6 167341073 167341073 + Silent SNP A A T novel C3L-01682_T C3L-01682_N A A c.1173A>T p.= p.P391P ENST00000239587 3/3 359 327 32 333 333 0 strelka-varscan-mutect TTLL2,synonymous_variant,p.=,ENST00000239587,NM_031949.4;TTLL2,synonymous_variant,p.=,ENST00000515138,;TTLL2,downstream_gene_variant,,ENST00000512917,; T ENST00000239587 Transcript synonymous_variant 1261/2075 1173/1779 391/592 P ccA/ccT 1 1 TTLL2 HGNC HGNC:21211 protein_coding YES CCDS5301.1 ENSP00000239587 Q9BWV7 UPI00001A3A8B NM_031949.4 3/3 Pfam_domain:PF03133,PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF11,Superfamily_domains:SSF56059 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 167341073 167341073 A T 1 0 0 0 0 0 0 0 1 17238 175 7 4 4 TTLL2 6 167341073 Silent SNP A C3L-01682_T 50783209 167341073 3464906 44 7445 TRIM50 0 . GRCh38 7 73313199 73313199 + Nonsense_Mutation SNP C C A rs370311701 C3L-01682_T C3L-01682_N C C c.1186G>T p.Glu396Ter p.E396* ENST00000333149 7/7 178 168 10 186 186 0 strelka-varscan-mutect TRIM50,stop_gained,p.Glu396Ter,ENST00000333149,NM_178125.3,NM_001281450.1;TRIM50,stop_gained,p.Glu396Ter,ENST00000453152,NM_001281451.1;NSUN5,upstream_gene_variant,,ENST00000428206,NM_001168348.2;NSUN5,upstream_gene_variant,,ENST00000252594,NM_018044.4;NSUN5,upstream_gene_variant,,ENST00000438747,NM_148956.3;NSUN5,upstream_gene_variant,,ENST00000310326,NM_001168347.2;NSUN5,upstream_gene_variant,,ENST00000471461,;TRIM50,downstream_gene_variant,,ENST00000488217,;NSUN5,upstream_gene_variant,,ENST00000455763,;RP11-483G21.3,upstream_gene_variant,,ENST00000417100,; A ENST00000333149 Transcript stop_gained 1387/2047 1186/1464 396/487 E/* Gaa/Taa rs370311701 1 -1 TRIM50 HGNC HGNC:19017 protein_coding YES CCDS34654.1 ENSP00000327994 Q86XT4 Q2M204 UPI0000684286 NM_178125.3,NM_001281450.1 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF399,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS rs370311701 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 25 73313199 73313199 C A 1 0 0 0 0 0 1 0 0 17018 893 31 1 1 TRIM50 7 73313199 Nonsense_Mutation SNP C C3L-01682_T 73313199 86032774 45 7446 MAGI2 0 . GRCh38 7 78135022 78135022 + Missense_Mutation SNP C C G novel C3L-01682_T C3L-01682_N C C c.3030G>C p.Glu1010Asp p.E1010D ENST00000354212 17/22 116 108 8 119 119 0 strelka-varscan-mutect MAGI2,missense_variant,p.Glu1010Asp,ENST00000354212,NM_012301.3;MAGI2,missense_variant,p.Glu996Asp,ENST00000419488,NM_001301128.1;MAGI2,missense_variant,p.Glu833Asp,ENST00000629359,;MAGI2,missense_variant,p.Glu872Asp,ENST00000628980,;MAGI2,missense_variant,p.Glu858Asp,ENST00000535697,;MAGI2,missense_variant,p.Glu1010Asp,ENST00000522391,;MAGI2,missense_variant,p.Glu847Asp,ENST00000626691,;MAGI2,missense_variant,p.Glu603Asp,ENST00000519748,;MAGI2,missense_variant,p.Glu603Asp,ENST00000637282,;MAGI2,missense_variant,p.Glu700Asp,ENST00000636178,;MAGI2,intron_variant,,ENST00000637441,;RP4-587D13.1,downstream_gene_variant,,ENST00000627965,;MAGI2,splice_region_variant,,ENST00000637486,; G ENST00000354212 Transcript missense_variant,splice_region_variant 3284/6880 3030/4368 1010/1455 E/D gaG/gaC 1 -1 MAGI2 HGNC HGNC:18957 protein_coding YES CCDS5594.1 ENSP00000346151 Q86UL8 UPI00001615D2 NM_012301.3 tolerated(0.75) 17/22 PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF27,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -16.14642 1 1 1 1 0 G 3 3 25 78135022 78135022 C G 1 0 0 0 0 1 0 0 0 9109 695 24 4 4 MAGI2 7 78135022 Missense_Mutation SNP C C3L-01682_T 4821823 78135022 81210951 46 7447 SEMA3A 0 . GRCh38 7 83961670 83961670 + Missense_Mutation SNP A A C rs750951156 C3L-01682_T C3L-01682_N A A c.2017T>G p.Leu673Val p.L673V ENST00000265362 17/17 149 138 11 152 152 0 strelka-varscan-mutect SEMA3A,missense_variant,p.Leu673Val,ENST00000265362,NM_006080.2;SEMA3A,missense_variant,p.Leu673Val,ENST00000436949,; C ENST00000265362 Transcript missense_variant 2332/8225 2017/2316 673/771 L/V Ttg/Gtg rs750951156 1 -1 SEMA3A HGNC HGNC:10723 protein_coding YES CCDS5599.1 ENSP00000265362 Q14563 UPI0000135A60 NM_006080.2 tolerated(0.87) 17/17 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF23 MODERATE 1 SNV 1 1 PASS rs750951156 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 83961670 83961670 A C 1 0 0 0 0 1 0 0 0 14300 11 1 5 5 SEMA3A 7 83961670 Missense_Mutation SNP A C3L-01682_T 5826648 83961670 75384303 47 7448 FBXL13 0 . GRCh38 7 102963631 102963631 + Missense_Mutation SNP T T A novel C3L-01682_T C3L-01682_N T T c.626A>T p.Asp209Val p.D209V ENST00000313221 8/20 254 228 26 269 269 0 strelka-varscan-mutect FBXL13,missense_variant,p.Asp209Val,ENST00000313221,NM_145032.3;FBXL13,missense_variant,p.Asp299Val,ENST00000379308,;FBXL13,missense_variant,p.Asp209Val,ENST00000436908,;FBXL13,missense_variant,p.Asp209Val,ENST00000379305,NM_001287150.1;FBXL13,missense_variant,p.Asp209Val,ENST00000455112,NM_001111038.1;FBXL13,missense_variant,p.Asp209Val,ENST00000456695,;FBXL13,non_coding_transcript_exon_variant,,ENST00000471074,;FBXL13,non_coding_transcript_exon_variant,,ENST00000477915,;FBXL13,missense_variant,p.Asp299Val,ENST00000448002,; A ENST00000313221 Transcript missense_variant 1053/2744 626/2208 209/735 D/V gAt/gTt 1 -1 FBXL13 HGNC HGNC:21658 protein_coding YES CCDS5726.1 ENSP00000321927 Q8NEE6 UPI000020F830 NM_145032.3 deleterious(0) 8/20 Gene3D:3.80.10.10,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF485,Superfamily_domains:SSF52047 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 102963631 102963631 T A 1 0 0 0 0 1 0 0 0 5573 1435 50 4 4 FBXL13 7 102963631 Missense_Mutation SNP T C3L-01682_T 19001961 102963631 56382342 48 7449 TRIM35 0 . GRCh38 8 27287616 27287616 + Silent SNP G G A rs117847001 C3L-01682_T C3L-01682_N G G c.1416C>T p.= p.A472A ENST00000305364 6/6 163 140 23 192 191 1 strelka-mutect TRIM35,synonymous_variant,p.=,ENST00000305364,NM_171982.4;TRIM35,intron_variant,,ENST00000521283,;TRIM35,downstream_gene_variant,,ENST00000521253,NM_001304495.1; A ENST00000305364 Transcript synonymous_variant 1500/4229 1416/1482 472/493 A gcC/gcT rs117847001 1 -1 TRIM35 HGNC HGNC:16285 protein_coding YES CCDS6056.2 ENSP00000301924 Q9UPQ4 UPI00001649FB NM_171982.4 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF404,hmmpanther:PTHR24103,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs117847001 . 0 206 0 0 0 0 0 4 -3.231229 0 0 1 0 0 A 2 1 25 27287616 27287616 G A 1 0 0 0 0 0 0 0 1 16998 1103 39 1 1 TRIM35 8 27287616 Silent SNP G C3L-01682_T 27287616 117851020 49 7450 KIAA1429 0 . GRCh38 8 94529261 94529261 + Missense_Mutation SNP T T C novel C3L-01682_T C3L-01682_N T T c.689A>G p.Gln230Arg p.Q230R ENST00000297591 7/24 270 254 16 303 303 0 strelka-varscan-mutect KIAA1429,missense_variant,p.Gln230Arg,ENST00000297591,NM_015496.4;KIAA1429,missense_variant,p.Gln230Arg,ENST00000421249,NM_183009.2;RP11-267M23.3,upstream_gene_variant,,ENST00000521010,;KIAA1429,non_coding_transcript_exon_variant,,ENST00000519001,;KIAA1429,upstream_gene_variant,,ENST00000522263,; C ENST00000297591 Transcript missense_variant 765/6528 689/5439 230/1812 Q/R cAg/cGg 1 -1 KIAA1429 HGNC HGNC:24500 protein_coding YES CCDS34923.1 ENSP00000297591 Q69YN4 UPI00001BBB23 NM_015496.4 tolerated(0.27) 7/24 Pfam_domain:PF15912,hmmpanther:PTHR23185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 94529261 94529261 T C 1 0 0 0 0 1 0 0 0 8114 1580 55 5 5 KIAA1429 8 94529261 Missense_Mutation SNP T C3L-01682_T 67241645 94529261 50609375 50 7451 DCSTAMP 0 . GRCh38 8 104349018 104349018 + Missense_Mutation SNP A A G novel C3L-01682_T C3L-01682_N A A c.466A>G p.Thr156Ala p.T156A ENST00000297581 2/4 283 268 15 317 316 1 strelka-varscan DCSTAMP,missense_variant,p.Thr156Ala,ENST00000297581,NM_030788.3;DCSTAMP,missense_variant,p.Thr156Ala,ENST00000622554,NM_001257317.1;DCSTAMP,missense_variant,p.Thr156Ala,ENST00000517991,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,downstream_gene_variant,,ENST00000518023,;DCSTAMP,upstream_gene_variant,,ENST00000518051,;DCSTAMP,downstream_gene_variant,,ENST00000517364,;DCSTAMP,downstream_gene_variant,,ENST00000519562,; G ENST00000297581 Transcript missense_variant 515/1953 466/1413 156/470 T/A Act/Gct 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 tolerated(0.25) 2/4 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 25 104349018 104349018 A G 1 0 0 0 0 1 0 0 0 4106 159 6 5 5 DCSTAMP 8 104349018 Missense_Mutation SNP A C3L-01682_T 9819757 104349018 40789618 51 7452 TMEM74 0 . GRCh38 8 108784356 108784356 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.743G>A p.Cys248Tyr p.C248Y ENST00000297459 2/2 217 191 26 210 210 0 strelka-varscan-mutect TMEM74,missense_variant,p.Cys248Tyr,ENST00000297459,NM_153015.1;TMEM74,intron_variant,,ENST00000518838,; T ENST00000297459 Transcript missense_variant 922/1741 743/918 248/305 C/Y tGc/tAc 1 -1 TMEM74 HGNC HGNC:26409 protein_coding YES CCDS6310.1 ENSP00000297459 Q96NL1 A0A024R9D4 UPI000006E80B NM_153015.1 deleterious(0.01) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR16125,hmmpanther:PTHR16125:SF3,Pfam_domain:PF14927 MODERATE 1 SNV 1 1 PASS . . 0 204 0 4 2 0 0 0 -11.19189 0.9360899 1 1 1 0 T 3 4 25 108784356 108784356 C T 1 0 0 0 0 1 0 0 0 16677 710 25 3 3 TMEM74 8 108784356 Missense_Mutation SNP C C3L-01682_T 4435338 108784356 36354280 52 7453 SAXO1 0 . GRCh38 9 18928698 18928698 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.779G>T p.Arg260Met p.R260M ENST00000380534 4/4 339 316 23 385 384 1 strelka-varscan-mutect SAXO1,missense_variant,p.Arg260Met,ENST00000380534,NM_153707.3;SAXO1,missense_variant,p.Arg195Met,ENST00000542071,NM_001287049.1;SAXO1,3_prime_UTR_variant,,ENST00000380530,NM_001287050.1; A ENST00000380534 Transcript missense_variant 1059/2099 779/1425 260/474 R/M aGg/aTg 1 -1 SAXO1 HGNC HGNC:28566 protein_coding YES CCDS6487.1 ENSP00000369907 Q8IYX7 UPI0000367609 NM_153707.3 tolerated(0.07) 4/4 hmmpanther:PTHR31516,hmmpanther:PTHR31516:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 18928698 18928698 C A 1 0 0 0 0 1 0 0 0 14118 681 24 2 2 SAXO1 9 18928698 Missense_Mutation SNP C C3L-01682_T 18928698 119466019 53 7454 PRRC2B 0 . GRCh38 9 131477833 131477833 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.4496C>T p.Ala1499Val p.A1499V ENST00000357304 16/31 214 203 11 244 244 0 strelka-varscan-mutect PRRC2B,missense_variant,p.Ala1499Val,ENST00000357304,NM_013318.3;PRRC2B,missense_variant,p.Ala805Val,ENST00000405995,;PRRC2B,missense_variant,p.Ala233Val,ENST00000451855,;PRRC2B,downstream_gene_variant,,ENST00000456307,; T ENST00000357304 Transcript missense_variant 4551/11042 4496/6690 1499/2229 A/V gCc/gTc 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 tolerated(0.28) 16/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 131477833 131477833 C T 1 0 0 0 0 1 0 0 0 12749 739 26 3 3 PRRC2B 9 131477833 Missense_Mutation SNP C C3L-01682_T 112549135 131477833 6916884 54 7455 COL5A1 0 . GRCh38 9 134730282 134730282 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.971G>T p.Ser324Ile p.S324I ENST00000371817 7/66 564 524 40 564 564 0 strelka-varscan-mutect COL5A1,missense_variant,p.Ser324Ile,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Ser324Ile,ENST00000618395,NM_001278074.1;COL5A1,upstream_gene_variant,,ENST00000469093,; T ENST00000371817 Transcript missense_variant 1385/8471 971/5517 324/1838 S/I aGt/aTt 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 tolerated(0.19) 7/66 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 134730282 134730282 G T 1 0 0 0 0 1 0 0 0 3485 1029 36 2 2 COL5A1 9 134730282 Missense_Mutation SNP G C3L-01682_T 3252449 134730282 3664435 55 7456 COL5A1 0 . GRCh38 9 134812668 134812668 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.3808G>T p.Gly1270Cys p.G1270C ENST00000371817 48/66 478 446 32 495 494 1 strelka-varscan-mutect COL5A1,missense_variant,p.Gly1270Cys,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly1270Cys,ENST00000618395,NM_001278074.1;COL5A1,downstream_gene_variant,,ENST00000463925,; T ENST00000371817 Transcript missense_variant 4222/8471 3808/5517 1270/1838 G/C Ggt/Tgt 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0) 48/66 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF387,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 134812668 134812668 G T 1 0 0 0 0 1 0 0 0 3485 1000 35 2 2 COL5A1 9 134812668 Missense_Mutation SNP G C3L-01682_T 82386 134812668 3582049 56 7457 LRRC18 0 . GRCh38 10 48913750 48913750 + Missense_Mutation SNP C C T rs138127999 C3L-01682_T C3L-01682_N C C c.406G>A p.Val136Met p.V136M ENST00000374160 1/2 126 101 25 127 127 0 strelka-varscan-mutect LRRC18,missense_variant,p.Val136Met,ENST00000374160,NM_001006939.3;WDFY4,intron_variant,,ENST00000325239,NM_020945.1;WDFY4,intron_variant,,ENST00000265453,;RP11-523O18.7,intron_variant,,ENST00000430438,; T ENST00000374160 Transcript missense_variant 483/1617 406/786 136/261 V/M Gtg/Atg rs138127999,COSM2144922 1 -1 LRRC18 HGNC HGNC:23199 protein_coding YES CCDS31197.1 ENSP00000363275 Q8N456 UPI00001F98A9 NM_001006939.3 deleterious(0.01) 1/2 PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF593,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs138127999 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 48913750 48913750 C T 1 0 0 0 0 1 0 0 0 8869 536 19 1 1 LRRC18 10 48913750 Missense_Mutation SNP C C3L-01682_T 48913750 84883672 57 7458 SLC18A3 0 . GRCh38 10 49611148 49611148 + Silent SNP G G T novel C3L-01682_T C3L-01682_N G G c.408G>T p.= p.L136L ENST00000374115 1/1 435 380 55 499 499 0 strelka-varscan-mutect SLC18A3,synonymous_variant,p.=,ENST00000374115,NM_003055.2;CHAT,intron_variant,,ENST00000339797,NM_020984.3;CHAT,upstream_gene_variant,,ENST00000395562,NM_001142933.1;CHAT,upstream_gene_variant,,ENST00000337653,NM_020549.4;CHAT,upstream_gene_variant,,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,upstream_gene_variant,,ENST00000395559,NM_020986.3;CHAT,upstream_gene_variant,,ENST00000460699,;CHAT,upstream_gene_variant,,ENST00000490270,;CHAT,upstream_gene_variant,,ENST00000481336,;CHAT,upstream_gene_variant,,ENST00000466590,; T ENST00000374115 Transcript synonymous_variant 848/2420 408/1599 136/532 L ctG/ctT 1 1 SLC18A3 HGNC HGNC:10936 protein_coding YES CCDS7231.1 ENSP00000363229 Q16572 UPI00001F98C1 NM_003055.2 1/1 PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF13,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW SNV 1 PASS rs1311479958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 49611148 49611148 G T 1 0 0 0 0 0 0 0 1 14692 1306 46 2 2 SLC18A3 10 49611148 Silent SNP G C3L-01682_T 697398 49611148 84186274 58 7459 ANK3 0 . GRCh38 10 60075103 60075103 + Silent SNP C C T rs771306574 C3L-01682_T C3L-01682_N C C c.5778G>A p.= p.E1926E ENST00000280772 37/44 371 327 44 403 403 0 strelka-varscan-mutect ANK3,synonymous_variant,p.=,ENST00000280772,NM_020987.3;ANK3,synonymous_variant,p.=,ENST00000610321,;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000616444,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000511043,;ANK3,upstream_gene_variant,,ENST00000610901,;ANK3,upstream_gene_variant,,ENST00000613207,;ANK3,upstream_gene_variant,,ENST00000621739,; T ENST00000280772 Transcript synonymous_variant 5970/16874 5778/13134 1926/4377 E gaG/gaA rs771306574 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 37/44 hmmpanther:PTHR24123:SF22,hmmpanther:PTHR24123 LOW 1 SNV 1 1 PASS rs771306574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 60075103 60075103 C T 1 0 0 0 0 0 0 0 1 722 912 32 3 3 ANK3 10 60075103 Silent SNP C C3L-01682_T 10463955 60075103 73722319 59 7460 NOC3L 0 . GRCh38 10 94346465 94346465 + Frame_Shift_Del DEL A A - novel C3L-01682_T C3L-01682_N A A c.1349delT p.Phe450SerfsTer22 p.F450Sfs*22 ENST00000371361 11/21 122 110 12 152 151 1 varindel-pindel NOC3L,frameshift_variant,p.Phe450SerfsTer22,ENST00000371361,NM_022451.10;NOC3L,downstream_gene_variant,,ENST00000463649,; - ENST00000371361 Transcript frameshift_variant 1450/3455 1349/2403 450/800 F/X tTc/tc 1 -1 NOC3L HGNC HGNC:24034 protein_coding YES CCDS7433.1 ENSP00000360412 Q8WTT2 UPI000006DE09 NM_022451.10 11/21 hmmpanther:PTHR14428,hmmpanther:PTHR14428:SF5,PIRSF_domain:PIRSF028977 HIGH 1 deletion 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99995 1 1 1 1 0 - 7 5 25 94346465 94346465 A - 1 0 1 0 1 0 0 0 0 10556 246 9 0 0 NOC3L 10 94346465 Frame_Shift_Del DEL A C3L-01682_T 34271362 94346465 39450957 60 7461 XPNPEP1 0 . GRCh38 10 109877857 109877857 + Missense_Mutation SNP C C A C3L-01682_T C3L-01682_N C C c.1252G>T p.Asp418Tyr p.D418Y ENST00000502935 14/21 445 394 51 417 415 2 strelka-varscan-mutect XPNPEP1,missense_variant,p.Asp418Tyr,ENST00000502935,NM_001324132.1,NM_020383.3;XPNPEP1,missense_variant,p.Asp418Tyr,ENST00000322238,NM_001167604.1;XPNPEP1,missense_variant,p.Asp304Tyr,ENST00000369683,NM_001324128.1;XPNPEP1,downstream_gene_variant,,ENST00000403138,;XPNPEP1,downstream_gene_variant,,ENST00000423625,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000494564,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000510988,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000460055,;XPNPEP1,downstream_gene_variant,,ENST00000430337,;XPNPEP1,downstream_gene_variant,,ENST00000460523,;XPNPEP1,downstream_gene_variant,,ENST00000443078,;XPNPEP1,downstream_gene_variant,,ENST00000507328,;XPNPEP1,downstream_gene_variant,,ENST00000508059,;XPNPEP1,downstream_gene_variant,,ENST00000509646,;XPNPEP1,downstream_gene_variant,,ENST00000512582,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000488118,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000513817,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000472336,;XPNPEP1,non_coding_transcript_exon_variant,,ENST00000508525,;XPNPEP1,upstream_gene_variant,,ENST00000369658,; A ENST00000502935 Transcript missense_variant 1372/2539 1252/2001 418/666 D/Y Gac/Tac COSM348181 1 -1 XPNPEP1 HGNC HGNC:12822 protein_coding YES CCDS7560.2 ENSP00000421566 Q9NQW7 UPI00003D2EAD NM_001324132.1,NM_020383.3 tolerated(0.56) 14/21 hmmpanther:PTHR10804:SF87,hmmpanther:PTHR10804,Pfam_domain:PF00557,Gene3D:3.90.230.10,Superfamily_domains:SSF55920 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 109877857 109877857 C A 1 0 0 0 0 1 0 0 0 18001 913 32 2 2 XPNPEP1 10 109877857 Missense_Mutation SNP C C3L-01682_T 15531392 109877857 23919565 61 7462 EPS8L2 0 . GRCh38 11 721988 721988 + Silent SNP G G A novel C3L-01682_T C3L-01682_N G G c.981G>A p.= p.L327L ENST00000533256 12/22 113 104 9 160 160 0 strelka-varscan-mutect EPS8L2,synonymous_variant,p.=,ENST00000533256,;EPS8L2,synonymous_variant,p.=,ENST00000614442,;EPS8L2,synonymous_variant,p.=,ENST00000318562,NM_022772.3;EPS8L2,synonymous_variant,p.=,ENST00000530636,;EPS8L2,synonymous_variant,p.=,ENST00000526198,;EPS8L2,5_prime_UTR_variant,,ENST00000610855,;EPS8L2,downstream_gene_variant,,ENST00000533500,;EPS8L2,downstream_gene_variant,,ENST00000531348,;EPS8L2,downstream_gene_variant,,ENST00000524763,;EPS8L2,downstream_gene_variant,,ENST00000534755,;AP006621.9,intron_variant,,ENST00000527021,;EPS8L2,upstream_gene_variant,,ENST00000534449,;EPS8L2,upstream_gene_variant,,ENST00000524973,;EPS8L2,3_prime_UTR_variant,,ENST00000526909,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000531393,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000529346,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000524474,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000526651,;EPS8L2,non_coding_transcript_exon_variant,,ENST00000533816,;EPS8L2,intron_variant,,ENST00000528770,;EPS8L2,intron_variant,,ENST00000530452,;EPS8L2,upstream_gene_variant,,ENST00000527832,;EPS8L2,downstream_gene_variant,,ENST00000527807,;EPS8L2,upstream_gene_variant,,ENST00000534679,;EPS8L2,downstream_gene_variant,,ENST00000530118,;EPS8L2,downstream_gene_variant,,ENST00000531471,;EPS8L2,downstream_gene_variant,,ENST00000532545,;EPS8L2,upstream_gene_variant,,ENST00000534027,; A ENST00000533256 Transcript synonymous_variant 1356/3266 981/2148 327/715 L ttG/ttA 1 1 EPS8L2 HGNC HGNC:21296 protein_coding YES CCDS31328.1 ENSP00000435585 Q9H6S3 UPI000006226C 12/22 Low_complexity_(Seg):seg,hmmpanther:PTHR12287:SF20,hmmpanther:PTHR12287 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -18.22207 1 1 1 1 0 A 2 1 25 721988 721988 G A 1 0 0 0 0 0 0 0 1 5044 1333 46 3 3 EPS8L2 11 721988 Silent SNP G C3L-01682_T 721988 134364634 62 7463 SLC5A12 0 . GRCh38 11 26686523 26686523 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.1175G>A p.Cys392Tyr p.C392Y ENST00000396005 10/15 220 208 12 226 222 4 varscan-mutect SLC5A12,missense_variant,p.Cys392Tyr,ENST00000396005,NM_178498.3;SLC5A12,synonymous_variant,p.=,ENST00000527405,; T ENST00000396005 Transcript missense_variant 1485/6250 1175/1857 392/618 C/Y tGt/tAt 1 -1 SLC5A12 HGNC HGNC:28750 protein_coding YES CCDS7860.2 ENSP00000379326 Q1EHB4 UPI000003ED2C NM_178498.3 deleterious(0) 10/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF152,Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 26686523 26686523 C T 1 0 0 0 0 1 0 0 0 14947 478 17 3 3 SLC5A12 11 26686523 Missense_Mutation SNP C C3L-01682_T 25964535 26686523 108400099 63 7464 RAG1 0 . GRCh38 11 36573835 36573835 + Silent SNP T T C novel C3L-01682_T C3L-01682_N T T c.531T>C p.= p.H177H ENST00000299440 2/2 526 495 31 516 516 0 strelka-varscan-mutect RAG1,synonymous_variant,p.=,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,synonymous_variant,p.=,ENST00000534663,; C ENST00000299440 Transcript synonymous_variant 643/6564 531/3132 177/1043 H caT/caC 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 2/2 Pfam_domain:PF12560,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 25 36573835 36573835 T C 1 0 0 0 0 0 0 0 1 13164 1403 49 5 5 RAG1 11 36573835 Silent SNP T C3L-01682_T 9887312 36573835 98512787 64 7465 DDB1 0 . GRCh38 11 61304030 61304030 + Silent SNP C C A novel C3L-01682_T C3L-01682_N C C c.2667G>T p.= p.R889R ENST00000301764 22/27 155 147 8 175 175 0 strelka-varscan-mutect DDB1,synonymous_variant,p.=,ENST00000301764,NM_001923.4;DDB1,synonymous_variant,p.=,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000539332,;DDB1,upstream_gene_variant,,ENST00000545894,;DDB1,upstream_gene_variant,,ENST00000451943,;DDB1,upstream_gene_variant,,ENST00000538470,; A ENST00000301764 Transcript synonymous_variant 3065/4506 2667/3423 889/1140 R cgG/cgT 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 22/27 hmmpanther:PTHR10644,Pfam_domain:PF03178,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs1159285940 . 0 208 2 0 0 0 0 0 -15.00236 1 1 1 1 0 A 2 1 25 61304030 61304030 C A 1 0 0 0 0 0 0 0 1 4126 753 26 2 2 DDB1 11 61304030 Silent SNP C C3L-01682_T 24730195 61304030 73782592 65 7466 CAPN5 0 . GRCh38 11 77116262 77116262 + Silent SNP G G T novel C3L-01682_T C3L-01682_N G G c.930G>T p.= p.R310R ENST00000278559 7/13 365 335 30 347 347 0 strelka-varscan-mutect CAPN5,synonymous_variant,p.=,ENST00000278559,NM_004055.4;CAPN5,synonymous_variant,p.=,ENST00000456580,;CAPN5,synonymous_variant,p.=,ENST00000529629,;CAPN5,intron_variant,,ENST00000531028,;CAPN5,upstream_gene_variant,,ENST00000527129,;CAPN5,downstream_gene_variant,,ENST00000533889,; T ENST00000278559 Transcript synonymous_variant 1119/4397 930/1923 310/640 R cgG/cgT 1 1 CAPN5 HGNC HGNC:1482 protein_coding YES CCDS8248.1 ENSP00000278559 O15484 A0A140VKH4 UPI0000126E9F NM_004055.4 7/13 PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF138,Pfam_domain:PF00648,SMART_domains:SM00230,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 77116262 77116262 G T 1 0 0 0 0 0 0 0 1 2323 1219 43 2 2 CAPN5 11 77116262 Silent SNP G C3L-01682_T 15812232 77116262 57970360 66 7467 GRM5 0 . GRCh38 11 88567624 88567624 + Missense_Mutation SNP A A T novel C3L-01682_T C3L-01682_N A A c.2059T>A p.Phe687Ile p.F687I ENST00000305447 7/9 369 339 30 349 349 0 strelka-varscan-mutect GRM5,missense_variant,p.Phe687Ile,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Phe687Ile,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Phe687Ile,ENST00000305432,; T ENST00000305447 Transcript missense_variant 2209/4571 2059/3639 687/1212 F/I Ttc/Atc 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 7/9 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 88567624 88567624 A T 1 0 0 0 0 1 0 0 0 6682 101 4 4 4 GRM5 11 88567624 Missense_Mutation SNP A C3L-01682_T 11451362 88567624 46518998 67 7468 DDI1 0 . GRCh38 11 104037908 104037908 + Silent SNP T T G novel C3L-01682_T C3L-01682_N T T c.1086T>G p.= p.P362P ENST00000302259 1/1 251 216 35 283 282 1 strelka-varscan-mutect DDI1,synonymous_variant,p.=,ENST00000302259,NM_001001711.2;PDGFD,intron_variant,,ENST00000302251,NM_033135.3;PDGFD,intron_variant,,ENST00000393158,NM_025208.4;PDGFD,upstream_gene_variant,,ENST00000529268,; G ENST00000302259 Transcript synonymous_variant 1329/2609 1086/1191 362/396 P ccT/ccG 1 1 DDI1 HGNC HGNC:18961 protein_coding YES CCDS31660.1 ENSP00000302805 Q8WTU0 UPI0000047AEA NM_001001711.2 1/1 hmmpanther:PTHR12917,hmmpanther:PTHR12917:SF15 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 25 104037908 104037908 T G 1 0 0 0 0 0 0 0 1 4131 1567 55 5 5 DDI1 11 104037908 Silent SNP T C3L-01682_T 15470284 104037908 31048714 68 7469 KRT75 0 . GRCh38 12 52433076 52433076 + Silent SNP C C T novel C3L-01682_T C3L-01682_N C C c.675G>A p.= p.L225L ENST00000252245 2/9 727 679 48 716 715 1 strelka-varscan-mutect KRT75,synonymous_variant,p.=,ENST00000252245,NM_004693.2;RP11-1020M18.10,downstream_gene_variant,,ENST00000548135,; T ENST00000252245 Transcript synonymous_variant 896/2324 675/1656 225/551 L ctG/ctA 1 -1 KRT75 HGNC HGNC:24431 protein_coding YES CCDS8827.1 ENSP00000252245 O95678 UPI000013CD4E NM_004693.2 2/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01276,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF200,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 25 52433076 52433076 C T 1 0 0 0 0 0 0 0 1 8370 813 29 3 3 KRT75 12 52433076 Silent SNP C C3L-01682_T 52433076 80842233 69 7470 EFNB2 0 . GRCh38 13 106512708 106512708 + Missense_Mutation SNP T T C novel C3L-01682_T C3L-01682_N T T c.227A>G p.Tyr76Cys p.Y76C ENST00000245323 2/5 265 249 16 257 257 0 strelka-varscan-mutect EFNB2,missense_variant,p.Tyr76Cys,ENST00000245323,NM_004093.3; C ENST00000245323 Transcript missense_variant 377/4461 227/1002 76/333 Y/C tAt/tGt 1 -1 EFNB2 HGNC HGNC:3227 protein_coding YES CCDS9507.1 ENSP00000245323 P52799 UPI0000129C9B NM_004093.3 deleterious(0) 2/5 PROSITE_profiles:PS51551,hmmpanther:PTHR11304:SF18,hmmpanther:PTHR11304,Gene3D:2.60.40.420,Pfam_domain:PF00812,Superfamily_domains:SSF49503,Prints_domain:PR01347,PD002533 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 106512708 106512708 T C 1 0 0 0 0 1 0 0 0 4792 1406 49 5 5 EFNB2 13 106512708 Missense_Mutation SNP T C3L-01682_T 106512708 7851620 70 7471 SLC8A3 0 . GRCh38 14 70167218 70167218 + Missense_Mutation SNP G G A novel C3L-01682_T C3L-01682_N G G c.1205C>T p.Pro402Leu p.P402L ENST00000381269 2/8 295 250 45 321 320 1 strelka-varscan-mutect SLC8A3,missense_variant,p.Pro402Leu,ENST00000381269,NM_183002.2;SLC8A3,missense_variant,p.Pro402Leu,ENST00000357887,NM_033262.4;SLC8A3,missense_variant,p.Pro402Leu,ENST00000356921,NM_182932.2;SLC8A3,missense_variant,p.Pro402Leu,ENST00000528359,;SLC8A3,missense_variant,p.Pro402Leu,ENST00000534137,NM_058240.3;SLC8A3,missense_variant,p.Pro402Leu,ENST00000494208,; A ENST00000381269 Transcript missense_variant 1959/5268 1205/2784 402/927 P/L cCa/cTa 1 -1 SLC8A3 HGNC HGNC:11070 protein_coding YES CCDS35498.1 ENSP00000370669 P57103 UPI0000073C9A NM_183002.2 deleterious(0) 2/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF7,Pfam_domain:PF03160,TIGRFAM_domain:TIGR00845,SMART_domains:SM00237,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 70167218 70167218 G A 1 0 0 0 0 1 0 0 0 14991 1348 47 3 3 SLC8A3 14 70167218 Missense_Mutation SNP G C3L-01682_T 70167218 36876500 71 7472 GABRA5 0 . GRCh38 15 26937289 26937289 + Missense_Mutation SNP G G A novel C3L-01682_T C3L-01682_N G G c.685G>A p.Gly229Arg p.G229R ENST00000335625 8/11 124 117 7 160 160 0 strelka-varscan-mutect GABRA5,missense_variant,p.Gly229Arg,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Gly229Arg,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Gly229Arg,ENST00000355395,;GABRB3,intron_variant,,ENST00000541819,;GABRA5,downstream_gene_variant,,ENST00000555182,; A ENST00000335625 Transcript missense_variant 1573/3251 685/1389 229/462 G/R Ggg/Agg 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0.01) 8/11 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 26937289 26937289 G A 1 0 0 0 0 1 0 0 0 6035 1232 43 3 3 GABRA5 15 26937289 Missense_Mutation SNP G C3L-01682_T 26937289 75053900 72 7473 PLCB2 0 . GRCh38 15 40299177 40299178 + Frame_Shift_Del DEL GG GG - novel C3L-01682_T C3L-01682_N GG GG c.633_634delCC p.Leu212HisfsTer11 p.L212Hfs*11 ENST00000260402 8/32 150 142 8 176 176 0 varindel-pindel PLCB2,frameshift_variant,p.Leu212HisfsTer11,ENST00000260402,NM_004573.2;PLCB2,frameshift_variant,p.Leu212HisfsTer11,ENST00000557821,NM_001284297.1;PLCB2,frameshift_variant,p.Leu212HisfsTer11,ENST00000456256,NM_001284298.1;PLCB2,downstream_gene_variant,,ENST00000543785,NM_001284299.1;PLCB2-AS1,upstream_gene_variant,,ENST00000559520,;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588,;PLCB2,non_coding_transcript_exon_variant,,ENST00000560093,;PLCB2,downstream_gene_variant,,ENST00000559634,;PLCB2,upstream_gene_variant,,ENST00000558409,; - ENST00000260402 Transcript frameshift_variant 883-884/4616 633-634/3558 211-212/1185 FL/FX ttCCtc/tttc 1 -1 PLCB2 HGNC HGNC:9055 protein_coding YES CCDS42020.1 ENSP00000260402 Q00722 UPI0000D79B75 NM_004573.2 8/32 hmmpanther:PTHR10336:SF10,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000956,Superfamily_domains:SSF47473 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 25 40299177 40299177 GG - 1 0 1 0 1 0 0 0 0 12122 1000 35 0 0 PLCB2 15 40299177 Frame_Shift_Del DEL GG C3L-01682_T 13361888 40299177 61692012 73 7474 MEFV 0 . GRCh38 16 3243682 3243682 + Missense_Mutation SNP A A G novel C3L-01682_T C3L-01682_N A A c.1805T>C p.Leu602Pro p.L602P ENST00000219596 10/10 122 115 7 112 112 0 strelka-varscan-mutect MEFV,missense_variant,p.Leu602Pro,ENST00000219596,NM_000243.2;MEFV,missense_variant,p.Leu422Pro,ENST00000339854,;MEFV,missense_variant,p.Leu391Pro,ENST00000536379,;MEFV,3_prime_UTR_variant,,ENST00000541159,NM_001198536.1;MEFV,3_prime_UTR_variant,,ENST00000542898,;MEFV,3_prime_UTR_variant,,ENST00000537682,;MEFV,3_prime_UTR_variant,,ENST00000538326,;MEFV,3_prime_UTR_variant,,ENST00000536980,;MEFV,3_prime_UTR_variant,,ENST00000570511,;MEFV,3_prime_UTR_variant,,ENST00000539145,;MEFV,3_prime_UTR_variant,,ENST00000576315,;MEFV,3_prime_UTR_variant,,ENST00000574583,;MEFV,3_prime_UTR_variant,,ENST00000572244,;MEFV,downstream_gene_variant,,ENST00000539154,; G ENST00000219596 Transcript missense_variant 1845/3499 1805/2346 602/781 L/P cTg/cCg 1 -1 MEFV HGNC HGNC:6998 protein_coding YES CCDS10498.1 ENSP00000219596 O15553 UPI000004C0CA NM_000243.2 deleterious(0) 10/10 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -13.8767 1 1 1 1 0 G 3 3 25 3243682 3243682 A G 1 0 0 0 0 1 0 0 0 9399 188 7 5 5 MEFV 16 3243682 Missense_Mutation SNP A C3L-01682_T 3243682 87094663 74 7475 KIAA0430 0 . GRCh38 16 15608438 15608438 + Silent SNP T T C novel C3L-01682_T C3L-01682_N T T c.4035A>G p.= p.K1345K ENST00000396368 21/27 516 489 27 441 441 0 strelka-varscan-mutect KIAA0430,synonymous_variant,p.=,ENST00000396368,NM_014647.3;KIAA0430,synonymous_variant,p.=,ENST00000540441,;KIAA0430,synonymous_variant,p.=,ENST00000551742,NM_001184998.1;KIAA0430,synonymous_variant,p.=,ENST00000548025,NM_001184999.1;C16orf45,intron_variant,,ENST00000565857,;KIAA0430,downstream_gene_variant,,ENST00000614811,;CTB-193M12.1,upstream_gene_variant,,ENST00000549756,;KIAA0430,upstream_gene_variant,,ENST00000547936,;KIAA0430,3_prime_UTR_variant,,ENST00000552553,;KIAA0430,downstream_gene_variant,,ENST00000552535,; C ENST00000396368 Transcript synonymous_variant 4242/7743 4035/5229 1345/1742 K aaA/aaG 1 -1 KIAA0430 HGNC HGNC:29562 protein_coding YES CCDS10562.2 ENSP00000379654 Q9Y4F3 UPI00006881BC NM_014647.3 21/27 Pfam_domain:PF12872,PROSITE_profiles:PS51644,hmmpanther:PTHR14379,hmmpanther:PTHR14379:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 25 15608438 15608438 T C 1 0 0 0 0 0 0 0 1 8086 1722 60 5 5 KIAA0430 16 15608438 Silent SNP T C3L-01682_T 12364756 15608438 74729907 75 7476 CBLN1 0 . GRCh38 16 49279532 49279532 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.454G>A p.Ala152Thr p.A152T ENST00000219197 3/3 511 476 35 398 398 0 strelka-varscan-mutect CBLN1,missense_variant,p.Ala152Thr,ENST00000219197,NM_004352.3;CBLN1,missense_variant,p.Ala152Thr,ENST00000536749,;CBLN1,3_prime_UTR_variant,,ENST00000564786,; T ENST00000219197 Transcript missense_variant 820/2435 454/582 152/193 A/T Gcc/Acc 1 -1 CBLN1 HGNC HGNC:1543 protein_coding YES CCDS10736.1 ENSP00000219197 P23435 UPI0000127506 NM_004352.3 tolerated(0.37) 3/3 PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842,Prints_domain:PR00007 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 49279532 49279532 C T 1 0 0 0 0 1 0 0 0 2405 739 26 3 3 CBLN1 16 49279532 Missense_Mutation SNP C C3L-01682_T 33671094 49279532 41058813 76 7477 PELP1 0 . GRCh38 17 4672773 4672773 + Missense_Mutation SNP G G C C3L-01682_T C3L-01682_N G G c.2368C>G p.Leu790Val p.L790V ENST00000572293 16/17 157 137 20 188 188 0 strelka-varscan-mutect PELP1,missense_variant,p.Leu790Val,ENST00000572293,;PELP1,missense_variant,p.Leu790Val,ENST00000301396,NM_014389.2;PELP1,missense_variant,p.Leu593Val,ENST00000436683,NM_001278241.1;PELP1,missense_variant,p.Leu740Val,ENST00000574876,;PELP1,downstream_gene_variant,,ENST00000570571,;PELP1,downstream_gene_variant,,ENST00000570387,;PELP1,downstream_gene_variant,,ENST00000575101,;AC091153.4,upstream_gene_variant,,ENST00000441700,;AC091153.4,upstream_gene_variant,,ENST00000631268,;PELP1,3_prime_UTR_variant,,ENST00000575329,;PELP1,non_coding_transcript_exon_variant,,ENST00000573523,;PELP1,downstream_gene_variant,,ENST00000575534,;PELP1,downstream_gene_variant,,ENST00000573242,;PELP1,downstream_gene_variant,,ENST00000573506,; C ENST00000572293 Transcript missense_variant 2432/5272 2368/3543 790/1180 L/V Ctt/Gtt COSM4579797,COSM4579798 1 -1 PELP1 HGNC HGNC:30134 protein_coding YES CCDS58503.2 ENSP00000460300 C9JFV4 UPI0001AE6688 deleterious_low_confidence(0.01) 16/17 Prints_domain:PR01217 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1456100311 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 4672773 4672773 G C 1 0 0 0 0 1 0 0 0 11813 1000 35 4 4 PELP1 17 4672773 Missense_Mutation SNP G C3L-01682_T 4672773 78584668 77 7478 TP53 0 . GRCh38 17 7675095 7675095 + Missense_Mutation SNP C C A C3L-01682_T C3L-01682_N C C c.517G>T p.Val173Leu p.V173L ENST00000269305 5/11 424 357 67 417 417 0 strelka-varscan-mutect TP53,missense_variant,p.Val173Leu,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Val173Leu,ENST00000420246,;TP53,missense_variant,p.Val134Leu,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Val134Leu,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Val173Leu,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Val134Leu,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Val173Leu,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Val134Leu,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Val173Leu,ENST00000445888,;TP53,missense_variant,p.Val134Leu,ENST00000619485,;TP53,missense_variant,p.Val41Leu,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Val14Leu,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Val41Leu,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Val14Leu,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Val41Leu,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Val14Leu,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Val173Leu,ENST00000359597,;TP53,missense_variant,p.Val162Leu,ENST00000615910,;TP53,missense_variant,p.Val173Leu,ENST00000413465,;TP53,missense_variant,p.Val41Leu,ENST00000509690,;TP53,missense_variant,p.Val80Leu,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.Val134Leu,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 707/2579 517/1182 173/393 V/L Gtg/Ttg CM070299,TP53_g.12505G>T,TP53_g.12505G>C,TP53_g.12505del,TP53_g.12505G>A,COSM11084,COSM121041,COSM121042,COSM121043,COSM121044,COSM121045,COSM1741210,COSM2744864,COSM3388205,COSM3723936,COSM3723937,COSM3970358,COSM43559,COSM43732,COSM44057,COSM98964,COSM98965,COSM98966,COSM99638,COSM99639,COSM99640,COSM99641 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs876660754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 7675095 7675095 C A 1 0 0 0 0 1 0 0 0 16859 478 17 2 2 TP53 17 7675095 Missense_Mutation SNP C C3L-01682_T 3002322 7675095 75582346 78 7479 TRPV2 0 . GRCh38 17 16426115 16426115 + Missense_Mutation SNP T T A novel C3L-01682_T C3L-01682_N T T c.941T>A p.Leu314Gln p.L314Q ENST00000338560 6/15 105 91 14 132 132 0 strelka-varscan-mutect TRPV2,missense_variant,p.Leu314Gln,ENST00000338560,NM_016113.4;TRPV2,downstream_gene_variant,,ENST00000455666,;TRPV2,upstream_gene_variant,,ENST00000577277,;TRPV2,upstream_gene_variant,,ENST00000583241,;AC093484.4,upstream_gene_variant,,ENST00000441875,; A ENST00000338560 Transcript missense_variant 1340/2808 941/2295 314/764 L/Q cTg/cAg 1 1 TRPV2 HGNC HGNC:18082 protein_coding YES CCDS32576.1 ENSP00000342222 Q9Y5S1 UPI0000032F4E NM_016113.4 deleterious(0) 6/15 PROSITE_profiles:PS50297,hmmpanther:PTHR10582:SF5,hmmpanther:PTHR10582,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 16426115 16426115 T A 1 0 0 0 0 1 0 0 0 17102 1580 55 4 4 TRPV2 17 16426115 Missense_Mutation SNP T C3L-01682_T 8751020 16426115 66831326 79 7480 GSDMA 0 . GRCh38 17 39976879 39976879 + Nonsense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.1159G>T p.Glu387Ter p.E387* ENST00000301659 12/12 476 434 42 457 457 0 strelka-varscan-mutect GSDMA,stop_gained,p.Glu387Ter,ENST00000301659,NM_178171.4;GSDMA,stop_gained,p.Glu387Ter,ENST00000635792,;PSMD3,upstream_gene_variant,,ENST00000264639,NM_002809.3;PSMD3,upstream_gene_variant,,ENST00000415039,; T ENST00000301659 Transcript stop_gained 1277/2164 1159/1338 387/445 E/* Gag/Tag 1 1 GSDMA HGNC HGNC:13311 protein_coding YES CCDS45669.1 ENSP00000301659 Q96QA5 UPI0000140D2A NM_178171.4 12/12 hmmpanther:PTHR16399:SF18,hmmpanther:PTHR16399,Pfam_domain:PF04598 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 25 39976879 39976879 G T 1 0 0 0 0 0 1 0 0 6698 1291 45 2 2 GSDMA 17 39976879 Nonsense_Mutation SNP G C3L-01682_T 23550764 39976879 43280562 80 7481 KRTAP1-4 0 . GRCh38 17 41029984 41029984 + Missense_Mutation SNP G G T rs748894240 C3L-01682_T C3L-01682_N G G c.95C>A p.Thr32Asn p.T32N ENST00000377747 1/1 562 485 77 446 446 0 strelka-varscan-mutect KRTAP1-4,missense_variant,p.Thr32Asn,ENST00000377747,NM_001257305.1;KRTAP1-5,upstream_gene_variant,,ENST00000361883,NM_031957.1;KRTAP1-3,downstream_gene_variant,,ENST00000344363,NM_030966.1; T ENST00000377747 Transcript missense_variant 121/408 95/366 32/121 T/N aCc/aAc rs748894240,COSM4938892,COSM4938893 1 -1 KRTAP1-4 HGNC HGNC:18904 protein_coding YES CCDS58548.1 ENSP00000366976 P0C5Y4 UPI0000198A7D NM_001257305.1 tolerated(0.12) 1/1 Pfam_domain:PF01500,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF58,Low_complexity_(Seg):seg 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs748894240 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 41029984 41029984 G T 1 0 0 0 0 1 0 0 0 8386 1261 44 2 2 KRTAP1-4 17 41029984 Missense_Mutation SNP G C3L-01682_T 1053105 41029984 42227457 81 7482 KAT2A 0 . GRCh38 17 42119331 42119331 + Silent SNP G G A novel C3L-01682_T C3L-01682_N G G c.987C>T p.= p.T329T ENST00000225916 6/18 237 221 16 221 221 0 strelka-mutect KAT2A,synonymous_variant,p.=,ENST00000225916,NM_021078.2;HSPB9,upstream_gene_variant,,ENST00000565659,NM_033194.2;CTD-2132N18.3,downstream_gene_variant,,ENST00000592574,;KAT2A,synonymous_variant,p.=,ENST00000465682,;KAT2A,upstream_gene_variant,,ENST00000586972,;CTD-2132N18.3,downstream_gene_variant,,ENST00000592248,;CTD-2132N18.3,downstream_gene_variant,,ENST00000585562,;KAT2A,upstream_gene_variant,,ENST00000592310,;KAT2A,upstream_gene_variant,,ENST00000588759,; A ENST00000225916 Transcript synonymous_variant 1041/3109 987/2514 329/837 T acC/acT 1 -1 KAT2A HGNC HGNC:4201 protein_coding YES CCDS11417.1 ENSP00000225916 Q92830 UPI000000D978 NM_021078.2 6/18 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF124,PIRSF_domain:PIRSF003048,Pfam_domain:PF06466 LOW 1 SNV 1 1 PASS rs1245480291 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 25 42119331 42119331 G A 1 0 0 0 0 0 0 0 1 7895 1219 43 3 3 KAT2A 17 42119331 Silent SNP G C3L-01682_T 1089347 42119331 41138110 82 7483 HOXB1 0 . GRCh38 17 48530473 48530473 + Silent SNP A A G novel C3L-01682_T C3L-01682_N A A c.432T>C p.= p.Y144Y ENST00000239174 1/2 246 220 26 225 225 0 strelka-varscan-mutect HOXB1,synonymous_variant,p.=,ENST00000239174,NM_002144.3;HOXB1,synonymous_variant,p.=,ENST00000577092,; G ENST00000239174 Transcript synonymous_variant 525/2020 432/906 144/301 Y taT/taC 1 -1 HOXB1 HGNC HGNC:5111 protein_coding YES CCDS32675.1 ENSP00000355140 P14653 UPI0000163BFF NM_002144.3 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF167,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 25 48530473 48530473 A G 1 0 0 0 0 0 0 0 1 7193 224 8 5 5 HOXB1 17 48530473 Silent SNP A C3L-01682_T 6411142 48530473 34726968 83 7484 KCNH6 0 . GRCh38 17 63534205 63534205 + Missense_Mutation SNP G G A rs759222952 C3L-01682_T C3L-01682_N G G c.995G>A p.Ser332Asn p.S332N ENST00000583023 5/14 383 336 47 327 327 0 strelka-varscan-mutect KCNH6,missense_variant,p.Ser332Asn,ENST00000583023,NM_030779.3;KCNH6,missense_variant,p.Ser332Asn,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,missense_variant,p.Ser332Asn,ENST00000581784,NM_173092.2;KCNH6,missense_variant,p.Ser332Asn,ENST00000456941,;KCNH6,missense_variant,p.Ser332Asn,ENST00000580652,;KCNH6,3_prime_UTR_variant,,ENST00000583465,; A ENST00000583023 Transcript missense_variant 1006/3821 995/2985 332/994 S/N aGc/aAc rs759222952 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 deleterious(0) 5/14 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs759222952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 63534205 63534205 G A 1 0 0 0 0 1 0 0 0 7952 971 34 3 3 KCNH6 17 63534205 Missense_Mutation SNP G C3L-01682_T 15003732 63534205 19723236 84 7485 FASN 0 . GRCh38 17 82082647 82082647 + Missense_Mutation SNP C C A rs779145049 C3L-01682_T C3L-01682_N C C c.5799G>T p.Arg1933Ser p.R1933S ENST00000306749 34/43 363 337 26 307 307 0 strelka-varscan-mutect FASN,missense_variant,p.Arg1933Ser,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Arg1931Ser,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000636628,;FASN,upstream_gene_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,upstream_gene_variant,,ENST00000580382,;FASN,downstream_gene_variant,,ENST00000579410,; A ENST00000306749 Transcript missense_variant 6018/8565 5799/7536 1933/2511 R/S agG/agT rs779145049 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 deleterious(0) 34/43 Gene3D:3.40.50.720,Pfam_domain:PF08659,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,Low_complexity_(Seg):seg,SMART_domains:SM00822,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs779145049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 82082647 82082647 C A 1 0 0 0 0 1 0 0 0 5543 738 26 2 2 FASN 17 82082647 Missense_Mutation SNP C C3L-01682_T 18548442 82082647 1174794 85 7486 SERPINB10 0 . GRCh38 18 63935112 63935112 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.1064G>T p.Ser355Ile p.S355I ENST00000238508 8/8 177 167 10 218 218 0 strelka-varscan-mutect SERPINB10,missense_variant,p.Ser355Ile,ENST00000238508,;SERPINB10,missense_variant,p.Ser355Ile,ENST00000619595,NM_005024.1; T ENST00000238508 Transcript missense_variant 1123/2122 1064/1194 355/397 S/I aGt/aTt 1 1 SERPINB10 HGNC HGNC:8942 protein_coding YES CCDS11990.1 ENSP00000238508 P48595 UPI000013558E deleterious(0.02) 8/8 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF175,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 63935112 63935112 G T 1 0 0 0 0 1 0 0 0 14373 1029 36 2 2 SERPINB10 18 63935112 Missense_Mutation SNP G C3L-01682_T 63935112 16438173 86 7487 SALL3 0 . GRCh38 18 78994999 78994999 + Missense_Mutation SNP G G T C3L-01682_T C3L-01682_N G G c.3008G>T p.Arg1003Leu p.R1003L ENST00000537592 2/3 282 261 21 288 288 0 strelka-varscan-mutect SALL3,missense_variant,p.Arg1003Leu,ENST00000537592,NM_171999.3;SALL3,intron_variant,,ENST00000536229,;SALL3,intron_variant,,ENST00000575389,;SALL3,intron_variant,,ENST00000616649,;SALL3,intron_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript missense_variant 3008/6555 3008/3903 1003/1300 R/L cGg/cTg COSM1750593 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 deleterious(0.02) 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 5 1 1 PASS rs1413367730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 78994999 78994999 G T 1 0 0 0 0 1 0 0 0 14071 1116 39 1 1 SALL3 18 78994999 Missense_Mutation SNP G C3L-01682_T 15059887 78994999 1378286 87 7488 KDM4B 0 . GRCh38 19 5131319 5131319 + Missense_Mutation SNP C C G novel C3L-01682_T C3L-01682_N C C c.1559C>G p.Ala520Gly p.A520G ENST00000159111 12/23 245 220 25 271 271 0 strelka-varscan-mutect KDM4B,missense_variant,p.Ala554Gly,ENST00000611640,;KDM4B,missense_variant,p.Ala520Gly,ENST00000159111,NM_015015.2;KDM4B,missense_variant,p.Ala554Gly,ENST00000536461,;KDM4B,missense_variant,p.Ala266Gly,ENST00000588361,;KDM4B,upstream_gene_variant,,ENST00000588166,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,; G ENST00000159111 Transcript missense_variant 1777/5593 1559/3291 520/1096 A/G gCc/gGc 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 tolerated(0.35) 12/23 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 25 5131319 5131319 C G 1 0 0 0 0 1 0 0 0 8047 739 26 4 4 KDM4B 19 5131319 Missense_Mutation SNP C C3L-01682_T 5131319 53486297 88 7489 FBN3 0 . GRCh38 19 8096516 8096516 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.5467G>A p.Asp1823Asn p.D1823N ENST00000600128 44/64 162 152 10 167 167 0 strelka-varscan-mutect FBN3,missense_variant,p.Asp1823Asn,ENST00000600128,;FBN3,missense_variant,p.Asp1823Asn,ENST00000270509,NM_032447.3;FBN3,missense_variant,p.Asp1823Asn,ENST00000601739,NM_001321431.1;FBN3,missense_variant,p.Asp84Asn,ENST00000602121,; T ENST00000600128 Transcript missense_variant 5882/9362 5467/8430 1823/2809 D/N Gac/Aac 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F tolerated(0.45) 44/64 PROSITE_profiles:PS50026,hmmpanther:PTHR24039:SF0,hmmpanther:PTHR24039,PROSITE_patterns:PS00010,PIRSF_domain:PIRSF036312,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.37126 0.9999995 1 1 1 0 T 3 4 25 8096516 8096516 C T 1 0 0 0 0 1 0 0 0 5567 855 30 3 3 FBN3 19 8096516 Missense_Mutation SNP C C3L-01682_T 2965197 8096516 50521100 89 7490 CACNA1A 0 . GRCh38 19 13303780 13303780 + Silent SNP C C A rs16016 C3L-01682_T C3L-01682_N C C c.2091G>T p.= p.T697T ENST00000360228 16/47 266 245 21 250 250 0 strelka-varscan-mutect CACNA1A,synonymous_variant,p.=,ENST00000638009,NM_001127221.1;CACNA1A,synonymous_variant,p.=,ENST00000635895,;CACNA1A,synonymous_variant,p.=,ENST00000637769,;CACNA1A,synonymous_variant,p.=,ENST00000360228,NM_001127222.1;CACNA1A,synonymous_variant,p.=,ENST00000614285,;CACNA1A,synonymous_variant,p.=,ENST00000637736,;CACNA1A,synonymous_variant,p.=,ENST00000636389,;CACNA1A,synonymous_variant,p.=,ENST00000638029,NM_023035.2;CACNA1A,synonymous_variant,p.=,ENST00000637432,NM_000068.3;CACNA1A,synonymous_variant,p.=,ENST00000573710,;CACNA1A,synonymous_variant,p.=,ENST00000635727,;CACNA1A,synonymous_variant,p.=,ENST00000636012,;CACNA1A,synonymous_variant,p.=,ENST00000637276,;CACNA1A,synonymous_variant,p.=,ENST00000637927,;CACNA1A,synonymous_variant,p.=,ENST00000636549,NM_001174080.1;CACNA1A,downstream_gene_variant,,ENST00000637966,;CACNA1A,downstream_gene_variant,,ENST00000636974,;CACNA1A,downstream_gene_variant,,ENST00000637117,; A ENST00000360228 Transcript synonymous_variant 2326/8627 2091/7521 697/2506 T acG/acT rs16016 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 16/47 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Superfamily_domains:SSF81324 likely_benign LOW 1 SNV 1 1 1 PASS rs16016 . 0 112 0 0 0 0 0 98 -7.776463 0 0 1 0 0 A 2 1 25 13303780 13303780 C A 1 0 0 0 0 0 0 0 1 2226 755 27 1 1 CACNA1A 19 13303780 Silent SNP C C3L-01682_T 5207264 13303780 45313836 90 7491 SLC1A6 0 . GRCh38 19 14956645 14956645 + Missense_Mutation SNP C C A rs751282250 C3L-01682_T C3L-01682_N C C c.1000G>T p.Val334Phe p.V334F ENST00000221742 6/9 166 146 20 165 165 0 strelka-varscan-mutect SLC1A6,missense_variant,p.Val270Phe,ENST00000430939,;SLC1A6,missense_variant,p.Val334Phe,ENST00000221742,NM_005071.2;SLC1A6,intron_variant,,ENST00000600144,;SLC1A6,downstream_gene_variant,,ENST00000598504,NM_001272087.1;SLC1A6,downstream_gene_variant,,ENST00000544886,NM_001272088.1; A ENST00000221742 Transcript missense_variant 1008/1719 1000/1695 334/564 V/F Gtc/Ttc rs751282250,COSM349515,COSM84500 1 -1 SLC1A6 HGNC HGNC:10944 protein_coding YES CCDS12321.1 ENSP00000221742 P48664 UPI0000129B1A NM_005071.2 deleterious(0.02) 6/9 hmmpanther:PTHR11958:SF67,hmmpanther:PTHR11958,Pfam_domain:PF00375,Gene3D:2nwlC00,Superfamily_domains:0053221 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs751282250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 14956645 14956645 C A 1 0 0 0 0 1 0 0 0 14702 536 19 1 1 SLC1A6 19 14956645 Missense_Mutation SNP C C3L-01682_T 1652865 14956645 43660971 91 7492 RASAL3 0 . GRCh38 19 15458638 15458638 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.680G>T p.Gly227Val p.G227V ENST00000343625 7/18 197 175 22 239 239 0 strelka-mutect RASAL3,missense_variant,p.Gly227Val,ENST00000343625,NM_022904.1;RASAL3,upstream_gene_variant,,ENST00000609274,;RASAL3,upstream_gene_variant,,ENST00000599694,;RASAL3,upstream_gene_variant,,ENST00000608577,;RASAL3,upstream_gene_variant,,ENST00000595098,;RASAL3,non_coding_transcript_exon_variant,,ENST00000602101,;RASAL3,upstream_gene_variant,,ENST00000597025,; A ENST00000343625 Transcript missense_variant 766/3293 680/3036 227/1011 G/V gGc/gTc 1 -1 RASAL3 HGNC HGNC:26129 protein_coding YES CCDS46006.1 ENSP00000341905 Q86YV0 UPI0000197831 NM_022904.1 deleterious(0) 7/18 hmmpanther:PTHR10194:SF96,hmmpanther:PTHR10194 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 15458638 15458638 C A 1 0 0 0 0 1 0 0 0 13226 739 26 2 2 RASAL3 19 15458638 Missense_Mutation SNP C C3L-01682_T 501993 15458638 43158978 92 7493 POP4 0 . GRCh38 19 29610595 29610595 + Missense_Mutation SNP G G C novel C3L-01682_T C3L-01682_N G G c.247G>C p.Glu83Gln p.E83Q ENST00000585603 3/7 265 251 14 308 308 0 strelka-varscan-mutect POP4,missense_variant,p.Glu83Gln,ENST00000585603,NM_006627.2;POP4,missense_variant,p.Glu83Gln,ENST00000586420,;POP4,missense_variant,p.Glu112Gln,ENST00000590688,;POP4,intron_variant,,ENST00000221770,;POP4,non_coding_transcript_exon_variant,,ENST00000591824,;POP4,non_coding_transcript_exon_variant,,ENST00000586136,;POP4,non_coding_transcript_exon_variant,,ENST00000592759,;POP4,3_prime_UTR_variant,,ENST00000586823,;POP4,non_coding_transcript_exon_variant,,ENST00000588551,;POP4,intron_variant,,ENST00000591061,;POP4,downstream_gene_variant,,ENST00000586173,;POP4,upstream_gene_variant,,ENST00000587232,;POP4,upstream_gene_variant,,ENST00000592749,; C ENST00000585603 Transcript missense_variant 2549/3385 247/663 83/220 E/Q Gag/Cag 1 1 POP4 HGNC HGNC:30081 protein_coding YES CCDS12416.1 ENSP00000465213 O95707 UPI0000034DFA NM_006627.2 tolerated(0.2) 3/7 hmmpanther:PTHR13348,PIRSF_domain:PIRSF027081 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 29610595 29610595 G C 1 0 0 0 0 1 0 0 0 12366 1175 41 4 4 POP4 19 29610595 Missense_Mutation SNP G C3L-01682_T 14151957 29610595 29007021 93 7494 ZNF780A 0 . GRCh38 19 40075509 40075509 + Frame_Shift_Del DEL C C - novel C3L-01682_T C3L-01682_N C C c.936delG p.Met313TrpfsTer34 p.M313Wfs*34 ENST00000455521 6/6 397 370 27 382 381 1 varindel-pindel ZNF780A,frameshift_variant,p.Met278TrpfsTer34,ENST00000450241,;ZNF780A,frameshift_variant,p.Met312TrpfsTer34,ENST00000340963,NM_001010880.2,NM_001142578.1;ZNF780A,frameshift_variant,p.Met313TrpfsTer34,ENST00000455521,NM_001142577.1;ZNF780A,frameshift_variant,p.Met312TrpfsTer34,ENST00000595687,;ZNF780A,frameshift_variant,p.Met313TrpfsTer34,ENST00000594395,;ZNF780A,intron_variant,,ENST00000414720,NM_001142579.1;ZNF780A,downstream_gene_variant,,ENST00000595773,;ZNF780A,downstream_gene_variant,,ENST00000599972,;AC005614.5,intron_variant,,ENST00000595508,;ZNF780A,downstream_gene_variant,,ENST00000599368,;ZNF780A,downstream_gene_variant,,ENST00000601688,;ZNF780A,downstream_gene_variant,,ENST00000601715,; - ENST00000455521 Transcript frameshift_variant 1084/3600 936/1929 312/642 G/X ggG/gg 1 -1 ZNF780A HGNC HGNC:27603 protein_coding YES CCDS46079.1 ENSP00000400997 O75290 UPI0001881B53 NM_001142577.1 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF313,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 25 40075509 40075509 C - 1 0 1 0 1 0 0 0 0 18735 842 30 0 0 ZNF780A 19 40075509 Frame_Shift_Del DEL C C3L-01682_T 10464914 40075509 18542107 94 7495 MCM8 0 . GRCh38 20 5983030 5983030 + Missense_Mutation SNP C C T novel C3L-01682_T C3L-01682_N C C c.1718C>T p.Ala573Val p.A573V ENST00000378886 14/19 346 307 39 404 404 0 strelka-varscan-mutect MCM8,missense_variant,p.Ala533Val,ENST00000610722,;MCM8,missense_variant,p.Ala573Val,ENST00000378886,NM_001281521.1;MCM8,missense_variant,p.Ala533Val,ENST00000378896,NM_001281520.1,NM_032485.5;MCM8,missense_variant,p.Ala486Val,ENST00000378883,NM_001281522.1;MCM8,missense_variant,p.Ala517Val,ENST00000265187,NM_182802.2; T ENST00000378886 Transcript missense_variant 2095/3835 1718/2643 573/880 A/V gCc/gTc 1 1 MCM8 HGNC HGNC:16147 protein_coding YES CCDS63227.1 ENSP00000368164 Q9UJA3 UPI0000D61029 NM_001281521.1 deleterious(0.03) 14/19 PROSITE_profiles:PS50051,hmmpanther:PTHR11630:SF47,hmmpanther:PTHR11630,Pfam_domain:PF00493,Gene3D:3.40.50.300,SMART_domains:SM00382,SMART_domains:SM00350,Superfamily_domains:SSF52540,Prints_domain:PR01657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 5983030 5983030 C T 1 0 0 0 0 1 0 0 0 9325 739 26 3 3 MCM8 20 5983030 Missense_Mutation SNP C C3L-01682_T 5983030 58461137 95 7496 LAMA5 0 . GRCh38 20 62309786 62309786 + Missense_Mutation SNP G G C novel C3L-01682_T C3L-01682_N G G c.10878C>G p.Asn3626Lys p.N3626K ENST00000252999 79/80 209 194 15 226 226 0 strelka-varscan-mutect LAMA5,missense_variant,p.Asn3626Lys,ENST00000252999,NM_005560.4;ADRM1,downstream_gene_variant,,ENST00000491935,;ADRM1,downstream_gene_variant,,ENST00000253003,NM_007002.3,NM_175573.2;ADRM1,downstream_gene_variant,,ENST00000620230,NM_001281437.1,NM_001281438.1;ADRM1,downstream_gene_variant,,ENST00000462554,;RP11-157P1.4,upstream_gene_variant,,ENST00000414042,;LAMA5,upstream_gene_variant,,ENST00000492698,;ADRM1,downstream_gene_variant,,ENST00000465805,;LAMA5,non_coding_transcript_exon_variant,,ENST00000370691,;LAMA5,non_coding_transcript_exon_variant,,ENST00000495695,;LAMA5,downstream_gene_variant,,ENST00000491036,;LAMA5,downstream_gene_variant,,ENST00000462415,;LAMA5,downstream_gene_variant,,ENST00000468786,; C ENST00000252999 Transcript missense_variant 10945/11426 10878/11088 3626/3695 N/K aaC/aaG 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 deleterious(0.01) 79/80 PROSITE_profiles:PS50025,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.9992 0.9999997 1 1 1 0 C 3 2 25 62309786 62309786 G C 1 0 0 0 0 1 0 0 0 8513 1252 44 4 4 LAMA5 20 62309786 Missense_Mutation SNP G C3L-01682_T 56326756 62309786 2134381 96 7497 TNFRSF6B 0 . GRCh38 20 63697330 63697330 + Missense_Mutation SNP A A T novel C3L-01682_T C3L-01682_N A A c.427A>T p.Thr143Ser p.T143S ENST00000369996 2/3 208 176 32 237 237 0 strelka-varscan-mutect TNFRSF6B,missense_variant,p.Thr143Ser,ENST00000369996,NM_003823.3;RTEL1,downstream_gene_variant,,ENST00000370018,NM_016434.3;RTEL1,downstream_gene_variant,,ENST00000318100,NM_001283010.1;RTEL1,downstream_gene_variant,,ENST00000360203,NM_001283009.1;RTEL1,downstream_gene_variant,,ENST00000508582,NM_032957.4;ARFRP1,downstream_gene_variant,,ENST00000612256,;ARFRP1,downstream_gene_variant,,ENST00000622789,NM_001267547.2,NM_003224.5;ARFRP1,downstream_gene_variant,,ENST00000614942,NM_001267545.2;ARFRP1,downstream_gene_variant,,ENST00000619493,NM_001267548.2;RTEL1,downstream_gene_variant,,ENST00000370003,;ARFRP1,downstream_gene_variant,,ENST00000612157,NM_001267549.2,NM_001134758.3,NM_001267544.2;ARFRP1,downstream_gene_variant,,ENST00000618838,;ARFRP1,downstream_gene_variant,,ENST00000607873,NM_001267546.2;ARFRP1,downstream_gene_variant,,ENST00000612772,;ARFRP1,downstream_gene_variant,,ENST00000610414,;ARFRP1,downstream_gene_variant,,ENST00000609188,;RTEL1-TNFRSF6B,splice_region_variant,,ENST00000480273,;RTEL1-TNFRSF6B,splice_region_variant,,ENST00000496281,;RTEL1-TNFRSF6B,splice_region_variant,,ENST00000482936,;RTEL1-TNFRSF6B,splice_region_variant,,ENST00000492259,;ARFRP1,downstream_gene_variant,,ENST00000610774,;RTEL1,downstream_gene_variant,,ENST00000496816,;ARFRP1,downstream_gene_variant,,ENST00000618568,;ARFRP1,downstream_gene_variant,,ENST00000609537,; T ENST00000369996 Transcript missense_variant,splice_region_variant 527/1124 427/903 143/300 T/S Acc/Tcc 1 1 TNFRSF6B HGNC HGNC:11921 protein_coding YES CCDS13532.1 ENSP00000359013 O95407 UPI0000032CAD NM_003823.3 tolerated(0.06) 2/3 Gene3D:2.10.50.10,Pfam_domain:PF00020,hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF116,SMART_domains:SM00208,Superfamily_domains:SSF57586 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 63697330 63697330 A T 1 0 0 0 0 1 0 0 0 16772 173 6 4 4 TNFRSF6B 20 63697330 Missense_Mutation SNP A C3L-01682_T 1387544 63697330 746837 97 7498 SHROOM2 0 . GRCh38 X 9895238 9895238 + Missense_Mutation SNP G G T novel C3L-01682_T C3L-01682_N G G c.1330G>T p.Gly444Trp p.G444W ENST00000380913 4/10 85 71 14 94 93 1 strelka-varscan-mutect SHROOM2,missense_variant,p.Gly444Trp,ENST00000380913,NM_001649.2;SHROOM2,upstream_gene_variant,,ENST00000493668,; T ENST00000380913 Transcript missense_variant 1420/7447 1330/4851 444/1616 G/W Ggg/Tgg 1 1 SHROOM2 HGNC HGNC:630 protein_coding YES CCDS14135.1 ENSP00000370299 Q13796 UPI0000125D05 NM_001649.2 tolerated(0.07) 4/10 hmmpanther:PTHR15012:SF8,hmmpanther:PTHR15012 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 25 9895238 9895238 G T 1 0 0 0 0 1 0 0 0 14557 1348 47 2 2 SHROOM2 23 9895238 Missense_Mutation SNP G C3L-01682_T 9895238 146145657 98 7499 BMX 0 . GRCh38 X 15534223 15534223 + Missense_Mutation SNP G G C rs756542747 C3L-01682_T C3L-01682_N G G c.1031G>C p.Gly344Ala p.G344A ENST00000357607 12/19 153 145 8 142 142 0 strelka-varscan-mutect BMX,missense_variant,p.Gly344Ala,ENST00000357607,;BMX,missense_variant,p.Gly344Ala,ENST00000348343,NM_001320866.1,NM_203281.2;BMX,missense_variant,p.Gly344Ala,ENST00000342014,NM_001721.6;BMX,intron_variant,,ENST00000489983,; C ENST00000357607 Transcript missense_variant 1219/2598 1031/2028 344/675 G/A gGa/gCa rs756542747 1 1 BMX HGNC HGNC:1079 protein_coding YES CCDS14168.1 ENSP00000350224 P51813 UPI0000000DFF tolerated(0.11) 12/19 Gene3D:3.30.505.10,Pfam_domain:PF00017,PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF91,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 2 1 PASS rs756542747 . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 25 15534223 15534223 G C 1 0 0 0 0 1 0 0 0 1629 1174 41 4 4 BMX 23 15534223 Missense_Mutation SNP G C3L-01682_T 5638985 15534223 140506672 99 7500 RPGR 0 . GRCh38 X 38310614 38310614 + Splice_Site SNP C C A C3L-01682_T C3L-01682_N C C c.778+1G>T p.X260_splice ENST00000378505 437 405 32 485 484 1 strelka-varscan-mutect RPGR,splice_donor_variant,,ENST00000378505,NM_001034853.1;RPGR,splice_donor_variant,,ENST00000339363,;RPGR,splice_donor_variant,,ENST00000318842,NM_000328.2;RP5-972B16.2,intron_variant,,ENST00000465127,;SNORA31,upstream_gene_variant,,ENST00000516241,;RPGR,splice_donor_variant,,ENST00000482855,;RPGR,splice_donor_variant,,ENST00000474584,; A ENST00000378505 Transcript splice_donor_variant -/4767 778/3459 260/1152 CS067115,RPGR_00318 1 -1 RPGR HGNC HGNC:10295 protein_coding YES CCDS35229.1 ENSP00000367766 Q92834 UPI00005D3C95 NM_001034853.1 7/14 HIGH 1 SNV 5 1,0 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 25 38310614 38310614 C A 1 0 0 0 0 0 0 1 0 13800 521 18 2 2 RPGR 23 38310614 Splice_Site SNP C C3L-01682_T 22776391 38310614 117730281 100 7501 FAM155B 0 . GRCh38 X 69505459 69505459 + Silent SNP C C T novel C3L-01682_T C3L-01682_N C C c.177C>T p.= p.D59D ENST00000252338 1/3 99 87 12 83 83 0 strelka-varscan-mutect FAM155B,synonymous_variant,p.=,ENST00000252338,NM_015686.2; T ENST00000252338 Transcript synonymous_variant 219/4013 177/1419 59/472 D gaC/gaT 1 1 FAM155B HGNC HGNC:30701 protein_coding YES CCDS35317.1 ENSP00000252338 O75949 UPI0000070EAA NM_015686.2 1/3 hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF8 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99999 1 1 1 1 0 T 2 4 25 69505459 69505459 C T 1 0 0 0 0 0 0 0 1 5314 506 18 3 3 FAM155B 23 69505459 Silent SNP C C3L-01682_T 31194845 69505459 86535436 101 7502 ZCCHC13 0 . GRCh38 X 74304557 74304557 + Silent SNP A A G novel C3L-01682_T C3L-01682_N A A c.291A>G p.= p.L97L ENST00000339534 1/1 319 286 33 317 317 0 strelka-varscan-mutect ZCCHC13,synonymous_variant,p.=,ENST00000339534,NM_203303.2; G ENST00000339534 Transcript synonymous_variant 368/842 291/501 97/166 L ctA/ctG 1 1 ZCCHC13 HGNC HGNC:31749 protein_coding YES CCDS14425.1 ENSP00000345633 Q8WW36 UPI0000070721 NM_203303.2 1/1 Gene3D:4.10.60.10,Pfam_domain:PF00098,PROSITE_profiles:PS50158,hmmpanther:PTHR23002,hmmpanther:PTHR23002:SF53,SMART_domains:SM00343,Superfamily_domains:SSF57756 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 25 74304557 74304557 A G 1 0 0 0 0 0 0 0 1 18157 407 15 5 5 ZCCHC13 23 74304557 Silent SNP A C3L-01682_T 4799098 74304557 81736338 102 7503 GPR174 0 . GRCh38 X 79171266 79171266 + Missense_Mutation SNP G G A C3L-01682_T C3L-01682_N G G c.259G>A p.Gly87Arg p.G87R ENST00000276077 1/1 241 224 17 239 239 0 strelka-varscan-mutect GPR174,missense_variant,p.Gly87Arg,ENST00000276077,NM_032553.1; A ENST00000276077 Transcript missense_variant 295/1258 259/1002 87/333 G/R Ggg/Agg COSM5320570 1 1 GPR174 HGNC HGNC:30245 protein_coding YES CCDS14443.1 ENSP00000276077 Q9BXC1 UPI0000050477 NM_032553.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF4,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 79171266 79171266 G A 1 0 0 0 0 1 0 0 0 6556 1348 47 3 3 GPR174 23 79171266 Missense_Mutation SNP G C3L-01682_T 4866709 79171266 76869629 103 7504 RPL36A-HNRNPH2 0 . GRCh38 X 101411935 101411935 + Splice_Site SNP G G T novel C3L-01682_T C3L-01682_N G G c.-53-1G>T ENST00000316594 49 42 7 35 35 0 varscan-mutect HNRNPH2,splice_acceptor_variant,,ENST00000316594,NM_001032393.2,NM_019597.4;RPL36A-HNRNPH2,splice_acceptor_variant,,ENST00000409338,;RPL36A-HNRNPH2,splice_acceptor_variant,,ENST00000409170,NM_001199973.1;GLA,upstream_gene_variant,,ENST00000218516,NM_000169.2;GLA,upstream_gene_variant,,ENST00000479445,;GLA,upstream_gene_variant,,ENST00000486121,;GLA,upstream_gene_variant,,ENST00000480513,;GLA,upstream_gene_variant,,ENST00000493905,; T ENST00000316594 Transcript splice_acceptor_variant -/2223 -/1350 -/449 1 1 HNRNPH2 HGNC HGNC:5042 protein_coding YES CCDS14485.1 ENSP00000361927 P55795 UPI0000134537 NM_001032393.2,NM_019597.4 1/1 HIGH 1 SNV 1 1 PASS . . 2 143 49 14 0 0 0 0 -12.67774 0.1582593 0 1 0 0 T 5 4 25 101411935 101411935 G T 1 0 0 0 0 0 0 1 0 13840 985 34 2 2 RPL36A-HNRNPH2 23 101411935 Splice_Site SNP G C3L-01682_T 22240669 101411935 54628960 104 7505 MID2 0 . GRCh38 X 107854632 107854632 + Silent SNP C C A novel C3L-01682_T C3L-01682_N C C c.744C>A p.= p.T248T ENST00000262843 3/10 318 300 18 277 276 1 strelka-varscan-mutect MID2,synonymous_variant,p.=,ENST00000262843,NM_012216.3;MID2,synonymous_variant,p.=,ENST00000443968,NM_052817.2; A ENST00000262843 Transcript synonymous_variant 1292/2876 744/2208 248/735 T acC/acA 1 1 MID2 HGNC HGNC:7096 protein_coding YES CCDS14532.2 ENSP00000262843 Q9UJV3 UPI0000D4F411 NM_012216.3 3/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF283,SMART_domains:SM00502,Superfamily_domains:SSF57845 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 25 107854632 107854632 C A 1 0 0 0 0 0 0 0 1 9538 581 21 2 2 MID2 23 107854632 Silent SNP C C3L-01682_T 6442697 107854632 48186263 105 7506 TENM1 0 . GRCh38 X 124385872 124385872 + Missense_Mutation SNP C C A C3L-01682_T C3L-01682_N C C c.5881G>T p.Gly1961Cys p.G1961C ENST00000422452 29/32 238 191 47 212 212 0 strelka-varscan-mutect TENM1,missense_variant,p.Gly1961Cys,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Gly1954Cys,ENST00000371130,NM_014253.3;STAG2,intron_variant,,ENST00000469481,; A ENST00000422452 Transcript missense_variant 5945/12891 5881/8199 1961/2732 G/C Ggc/Tgc COSM5271025,COSM610617 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 29/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 124385872 124385872 C A 1 0 0 0 0 1 0 0 0 16171 594 21 2 2 TENM1 23 124385872 Missense_Mutation SNP C C3L-01682_T 16531240 124385872 31655023 106 7507 ATP2B3 0 . GRCh38 X 153564979 153564979 + Missense_Mutation SNP C C A novel C3L-01682_T C3L-01682_N C C c.3218C>A p.Pro1073His p.P1073H ENST00000263519 19/20 200 189 11 196 195 1 strelka-mutect ATP2B3,missense_variant,p.Pro1059His,ENST00000370186,;ATP2B3,missense_variant,p.Pro1073His,ENST00000263519,NM_001001344.2;ATP2B3,missense_variant,p.Pro1073His,ENST00000349466,;ATP2B3,missense_variant,p.Pro1073His,ENST00000359149,NM_021949.3;ATP2B3,missense_variant,p.Pro1059His,ENST00000393842,;ATP2B3,downstream_gene_variant,,ENST00000460549,;ATP2B3,upstream_gene_variant,,ENST00000496610,; A ENST00000263519 Transcript missense_variant 3344/6420 3218/3663 1073/1220 P/H cCc/cAc 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 tolerated(0.14) 19/20 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.05582 1 1 1 1 0 A 3 1 25 153564979 153564979 C A 1 0 0 0 0 1 0 0 0 1294 623 22 2 2 ATP2B3 23 153564979 Missense_Mutation SNP C C3L-01682_T 29179107 153564979 2475916 107 7508 HCFC1 0 . GRCh38 X 153954312 153954312 + Missense_Mutation SNP T T A novel C3L-01682_T C3L-01682_N T T c.4087A>T p.Thr1363Ser p.T1363S ENST00000310441 17/26 114 87 27 83 82 1 strelka-varscan-mutect HCFC1,missense_variant,p.Thr1363Ser,ENST00000310441,NM_005334.2;HCFC1,missense_variant,p.Thr1363Ser,ENST00000369984,;HCFC1,upstream_gene_variant,,ENST00000444191,; A ENST00000310441 Transcript missense_variant 5054/8869 4087/6108 1363/2035 T/S Act/Tct 1 -1 HCFC1 HGNC HGNC:4839 protein_coding YES CCDS44020.1 ENSP00000309555 P51610 UPI0000142F1F NM_005334.2 tolerated_low_confidence(0.68) 17/26 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 25 153954312 153954312 T A 1 0 0 0 0 1 0 0 0 6879 1696 59 4 4 HCFC1 23 153954312 Missense_Mutation SNP T C3L-01682_T 389333 153954312 2086583 108 7509 TMEM61 0 . GRCh38 1 54986310 54986310 + Missense_Mutation SNP G G T novel C3L-01683_T C3L-01683_N G G c.229G>T p.Gly77Cys p.G77C ENST00000371268 2/3 170 158 12 208 208 0 strelka-varscan-mutect TMEM61,missense_variant,p.Gly77Cys,ENST00000371268,NM_182532.2;RP11-12C17.2,intron_variant,,ENST00000436960,; T ENST00000371268 Transcript missense_variant 503/1097 229/633 77/210 G/C Ggt/Tgt 1 1 TMEM61 HGNC HGNC:27296 protein_coding YES CCDS601.1 ENSP00000360315 Q8N0U2 UPI00000361F8 NM_182532.2 deleterious(0) 2/3 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR37151,hmmpanther:PTHR37151:SF1,Pfam_domain:PF15105 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 26 54986310 54986310 G T 1 0 0 0 0 1 0 0 0 16664 1000 35 2 2 TMEM61 1 54986310 Missense_Mutation SNP G C3L-01683_T 54986310 193970112 1 7510 LRRC7 0 . GRCh38 1 70038177 70038177 + Missense_Mutation SNP C C A novel C3L-01683_T C3L-01683_N C C c.2239C>A p.Pro747Thr p.P747T ENST00000035383 19/25 123 116 7 155 155 0 varscan-mutect LRRC7,missense_variant,p.Pro752Thr,ENST00000310961,;LRRC7,missense_variant,p.Pro747Thr,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Pro31Thr,ENST00000415775,; A ENST00000035383 Transcript missense_variant 2269/5000 2239/4614 747/1537 P/T Ccc/Acc 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious_low_confidence(0) 19/25 MODERATE 1 SNV 1 1 PASS rs1355662935 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 26 70038177 70038177 C A 1 0 0 0 0 1 0 0 0 8916 855 30 2 2 LRRC7 1 70038177 Missense_Mutation SNP C C3L-01683_T 15051867 70038177 178918245 2 7511 ADIPOR1 0 . GRCh38 1 202943926 202943926 + Missense_Mutation SNP C C A novel C3L-01683_T C3L-01683_N C C c.637G>T p.Ala213Ser p.A213S ENST00000340990 6/8 95 88 7 139 139 0 strelka-varscan-mutect ADIPOR1,missense_variant,p.Ala213Ser,ENST00000340990,NM_015999.5,NM_001290553.1,NM_001290557.1,NM_001290629.1;ADIPOR1,missense_variant,p.Ala213Ser,ENST00000417068,;ADIPOR1,intron_variant,,ENST00000367254,;ADIPOR1,downstream_gene_variant,,ENST00000426229,;ADIPOR1,non_coding_transcript_exon_variant,,ENST00000495562,; A ENST00000340990 Transcript missense_variant 936/2177 637/1128 213/375 A/S Gct/Tct 1 -1 ADIPOR1 HGNC HGNC:24040 protein_coding YES CCDS1430.1 ENSP00000341785 Q96A54 UPI000003779A NM_015999.5,NM_001290553.1,NM_001290557.1,NM_001290629.1 tolerated(0.18) 6/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR20855,hmmpanther:PTHR20855:SF40,Pfam_domain:PF03006 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -14.63158 1 1 1 1 0 A 3 1 26 202943926 202943926 C A 1 0 0 0 0 1 0 0 0 391 710 25 2 2 ADIPOR1 1 202943926 Missense_Mutation SNP C C3L-01683_T 132905749 202943926 46012496 3 7512 EPHA5 0 . GRCh38 4 65336095 65336095 + Silent SNP G G A C3L-01683_T C3L-01683_N G G c.2692C>T p.= p.L898L ENST00000622150 16/18 113 107 6 111 111 0 strelka-mutect EPHA5,synonymous_variant,p.=,ENST00000622150,NM_001281765.1;EPHA5,synonymous_variant,p.=,ENST00000613740,NM_001281766.1;EPHA5,synonymous_variant,p.=,ENST00000273854,NM_004439.6;EPHA5,synonymous_variant,p.=,ENST00000511294,NM_001281767.1;EPHA5,synonymous_variant,p.=,ENST00000432638,;EPHA5,synonymous_variant,p.=,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript synonymous_variant 3445/8421 2692/3117 898/1038 L Ctg/Ttg COSM4848483 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 16/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 1 LOW 1 SNV 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -9.188872 0.9999825 1 1 1 0 A 2 1 26 65336095 65336095 G A 1 0 0 0 0 0 0 0 1 5017 933 33 3 3 EPHA5 4 65336095 Silent SNP G C3L-01683_T 65336095 124878460 4 7513 PCDHGA1 0 . GRCh38 5 141332211 141332211 + Silent SNP C C A rs761988261 C3L-01683_T C3L-01683_N C C c.1527C>A p.= p.S509S ENST00000517417 1/4 207 196 11 276 276 0 strelka-varscan-mutect PCDHGA1,synonymous_variant,p.=,ENST00000517417,NM_018912.2;PCDHGA1,synonymous_variant,p.=,ENST00000378105,NM_031993.1;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,; A ENST00000517417 Transcript synonymous_variant 1527/4604 1527/2796 509/931 S tcC/tcA rs761988261,COSM1434347,COSM1434348 1 1 PCDHGA1 HGNC HGNC:8696 protein_coding YES CCDS54922.1 ENSP00000431083 Q9Y5H4 UPI0000070596 NM_018912.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF108,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs761988261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 26 141332211 141332211 C A 1 0 0 0 0 0 0 0 1 11637 639 23 1 1 PCDHGA1 5 141332211 Silent SNP C C3L-01683_T 141332211 40206048 5 7514 MICAL1 0 . GRCh38 6 109449472 109449472 + Missense_Mutation SNP G G T novel C3L-01683_T C3L-01683_N G G c.1501C>A p.Leu501Met p.L501M ENST00000630715 11/25 314 293 21 343 343 0 strelka-varscan-mutect MICAL1,missense_variant,p.Leu501Met,ENST00000630715,NM_001286613.1;MICAL1,missense_variant,p.Leu482Met,ENST00000358807,NM_022765.3;MICAL1,missense_variant,p.Leu396Met,ENST00000358577,NM_001159291.1;MICAL1,missense_variant,p.Leu47Met,ENST00000433205,;MICAL1,downstream_gene_variant,,ENST00000431946,;MICAL1,downstream_gene_variant,,ENST00000483856,;MICAL1,non_coding_transcript_exon_variant,,ENST00000465904,;MICAL1,non_coding_transcript_exon_variant,,ENST00000456101,; T ENST00000630715 Transcript missense_variant 1792/3678 1501/3261 501/1086 L/M Ctg/Atg 1 -1 MICAL1 HGNC HGNC:20619 protein_coding YES CCDS69170.1 ENSP00000486901 Q8TDZ2 UPI0002064DFD NM_001286613.1 deleterious(0.01) 11/25 hmmpanther:PTHR11915,Superfamily_domains:SSF47576 MODERATE 1 SNV 2 1 PASS rs1036164647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 26 109449472 109449472 G T 1 0 0 0 0 1 0 0 0 9526 991 35 2 2 MICAL1 6 109449472 Missense_Mutation SNP G C3L-01683_T 109449472 61356507 6 7515 POM121L12 0 . GRCh38 7 53036406 53036406 + Silent SNP C C G C3L-01683_T C3L-01683_N C C c.735C>G p.= p.L245L ENST00000408890 1/1 153 145 8 197 197 0 strelka-varscan-mutect POM121L12,synonymous_variant,p.=,ENST00000408890,NM_182595.3; G ENST00000408890 Transcript synonymous_variant 765/1283 735/891 245/296 L ctC/ctG COSM1313175 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 1 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.87256 0.9999993 1 1 1 0 G 2 3 26 53036406 53036406 C G 1 0 0 0 0 0 0 0 1 12352 813 29 4 4 POM121L12 7 53036406 Silent SNP C C3L-01683_T 53036406 106309567 7 7516 FAT3 0 . GRCh38 11 92801216 92801216 + Missense_Mutation SNP A A T rs752304576 C3L-01683_T C3L-01683_N A A c.7753A>T p.Ser2585Cys p.S2585C ENST00000525166 9/27 153 145 8 187 187 0 strelka-varscan-mutect FAT3,missense_variant,p.Ser2735Cys,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ser2585Cys,ENST00000525166,; T ENST00000525166 Transcript missense_variant 7775/18699 7753/13320 2585/4439 S/C Agt/Tgt rs752304576 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.04) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs752304576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 26 92801216 92801216 A T 1 0 0 0 0 1 0 0 0 5551 188 7 4 4 FAT3 11 92801216 Missense_Mutation SNP A C3L-01683_T 92801216 42285406 8 7517 GGT7 0 . GRCh38 20 34863436 34863436 + Silent SNP G G T novel C3L-01683_T C3L-01683_N G G c.282C>A p.= p.S94S ENST00000336431 2/15 272 257 15 270 270 0 strelka-mutect GGT7,synonymous_variant,p.=,ENST00000336431,NM_178026.2;GGT7,synonymous_variant,p.=,ENST00000427420,; T ENST00000336431 Transcript synonymous_variant 327/2642 282/1989 94/662 S tcC/tcA 1 -1 GGT7 HGNC HGNC:4259 protein_coding YES CCDS13242.2 ENSP00000338964 Q9UJ14 UPI000004C2AB NM_178026.2 2/15 hmmpanther:PTHR11686:SF20,hmmpanther:PTHR11686 LOW 1 SNV 1 1 PASS rs972812335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 26 34863436 34863436 G T 1 0 0 0 0 0 0 0 1 6241 1103 39 1 1 GGT7 20 34863436 Silent SNP G C3L-01683_T 34863436 29580731 9 7518 DMD 0 . GRCh38 X 31169575 31169575 + Missense_Mutation SNP T T G novel C3L-01683_T C3L-01683_N T T c.10421A>C p.His3474Pro p.H3474P ENST00000357033 74/79 113 105 8 149 148 1 strelka-varscan-mutect DMD,missense_variant,p.His3474Pro,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.His3470Pro,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.His3473Pro,ENST00000620040,;DMD,missense_variant,p.His3469Pro,ENST00000619831,;DMD,missense_variant,p.His1014Pro,ENST00000378707,NM_004013.2;DMD,missense_variant,p.His1001Pro,ENST00000359836,NM_004022.2;DMD,missense_variant,p.His1157Pro,ENST00000358062,;DMD,missense_variant,p.His745Pro,ENST00000343523,NM_004014.2;DMD,missense_variant,p.His1014Pro,ENST00000474231,NM_004021.2;DMD,missense_variant,p.His406Pro,ENST00000378723,NM_004016.2;DMD,missense_variant,p.His406Pro,ENST00000378702,NM_004015.2,NM_004017.2;DMD,missense_variant,p.His393Pro,ENST00000361471,NM_004018.2;DMD,intron_variant,,ENST00000541735,NM_004020.3,NM_004023.2;DMD,intron_variant,,ENST00000378680,;DMD,downstream_gene_variant,,ENST00000378705,;DMD,upstream_gene_variant,,ENST00000481143,; G ENST00000357033 Transcript missense_variant 10628/13956 10421/11058 3474/3685 H/P cAt/cCt 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0.01) 74/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 26 31169575 31169575 T G 1 0 0 0 0 1 0 0 0 4387 1464 51 5 5 DMD 23 31169575 Missense_Mutation SNP T C3L-01683_T 31169575 124871320 10 7519 SYTL5 0 . GRCh38 X 38089521 38089521 + Silent SNP T T C novel C3L-01683_T C3L-01683_N T T c.765T>C p.= p.G255G ENST00000456733 6/17 117 110 7 126 126 0 strelka-varscan-mutect SYTL5,synonymous_variant,p.=,ENST00000297875,NM_138780.2,NM_001163335.1;SYTL5,synonymous_variant,p.=,ENST00000456733,NM_001163334.1;RP5-972B16.2,intron_variant,,ENST00000465127,; C ENST00000456733 Transcript synonymous_variant 1121/4704 765/2259 255/752 G ggT/ggC 1 1 SYTL5 HGNC HGNC:15589 protein_coding YES CCDS55399.1 ENSP00000395220 Q8TDW5 UPI0000F0599F NM_001163334.1 6/17 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 26 38089521 38089521 T C 1 0 0 0 0 0 0 0 1 15880 1683 59 5 5 SYTL5 23 38089521 Silent SNP T C3L-01683_T 6919946 38089521 117951374 11 7520 MAGEA8 0 . GRCh38 X 149884989 149884989 + Missense_Mutation SNP C C A novel C3L-01683_T C3L-01683_N C C c.717C>A p.His239Gln p.H239Q ENST00000535454 4/4 53 48 5 57 57 0 strelka-varscan-mutect MAGEA8,missense_variant,p.His239Gln,ENST00000535454,NM_001166400.1;MAGEA8,missense_variant,p.His239Gln,ENST00000542674,NM_001166401.1;MAGEA8,missense_variant,p.His239Gln,ENST00000286482,NM_005364.4;MAGEA8-AS1,upstream_gene_variant,,ENST00000427671,;MAGEA8,downstream_gene_variant,,ENST00000493910,;MAGEA8,downstream_gene_variant,,ENST00000345830,; A ENST00000535454 Transcript missense_variant 1266/2112 717/957 239/318 H/Q caC/caA 1 1 MAGEA8 HGNC HGNC:6806 protein_coding YES CCDS14692.1 ENSP00000438293 P43361 UPI0000071C79 NM_001166400.1 deleterious(0.04) 4/4 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF65,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 3 1 PASS . . 0 205 5 0 0 0 0 0 -12.22904 1 1 1 1 0 A 3 1 26 149884989 149884989 C A 1 0 0 0 0 1 0 0 0 9086 477 17 2 2 MAGEA8 23 149884989 Missense_Mutation SNP C C3L-01683_T 111795468 149884989 6155906 12 7521 PANK4 0 . GRCh38 1 2520387 2520387 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.658G>T p.Val220Phe p.V220F ENST00000378466 5/19 201 168 33 176 176 0 strelka-varscan-mutect PANK4,missense_variant,p.Val220Phe,ENST00000378466,NM_018216.2;PANK4,missense_variant,p.Val176Phe,ENST00000435556,;PANK4,downstream_gene_variant,,ENST00000491212,;PANK4,missense_variant,p.Val70Phe,ENST00000505228,;PANK4,3_prime_UTR_variant,,ENST00000486396,;PANK4,downstream_gene_variant,,ENST00000502770,;PANK4,upstream_gene_variant,,ENST00000468002,;PANK4,downstream_gene_variant,,ENST00000514922,;PANK4,upstream_gene_variant,,ENST00000515423,; A ENST00000378466 Transcript missense_variant 675/2677 658/2346 220/781 V/F Gtc/Ttc 1 -1 PANK4 HGNC HGNC:19366 protein_coding YES ENSP00000367727 Q9NVE7 UPI0001AE783E NM_018216.2 deleterious(0) 5/19 hmmpanther:PTHR12280,Pfam_domain:PF03630,TIGRFAM_domain:TIGR00555,PIRSF_domain:PIRSF036939,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 2520387 2520387 C A 1 0 0 0 0 1 0 0 0 11500 507 18 2 2 PANK4 1 2520387 Missense_Mutation SNP C C3L-01862_T 2520387 246436035 1 7522 SPEN 0 . GRCh38 1 15933146 15933146 + Frame_Shift_Del DEL A A - novel C3L-01862_T C3L-01862_N A A c.6906delA p.Gly2303GlufsTer50 p.G2303Efs*50 ENST00000375759 11/15 181 153 28 276 276 0 sindel-varindel-pindel SPEN,frameshift_variant,p.Gly2303GlufsTer50,ENST00000375759,NM_015001.2; - ENST00000375759 Transcript frameshift_variant 7110/12232 6906/10995 2302/3664 R/X agA/ag 1 1 SPEN HGNC HGNC:17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 11/15 hmmpanther:PTHR23189:SF48,hmmpanther:PTHR23189 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 27 15933146 15933146 A - 1 0 1 0 1 0 0 0 0 15389 301 11 0 0 SPEN 1 15933146 Frame_Shift_Del DEL A C3L-01862_T 13412759 15933146 233023276 2 7523 ARHGEF19 0 . GRCh38 1 16207102 16207102 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.983C>T p.Pro328Leu p.P328L ENST00000270747 6/16 105 90 15 97 97 0 strelka-varscan-mutect ARHGEF19,missense_variant,p.Pro328Leu,ENST00000270747,NM_153213.3;ARHGEF19,upstream_gene_variant,,ENST00000449495,;ARHGEF19,upstream_gene_variant,,ENST00000441785,;ARHGEF19,upstream_gene_variant,,ENST00000478117,;ARHGEF19,upstream_gene_variant,,ENST00000478210,;ARHGEF19,upstream_gene_variant,,ENST00000471928,; A ENST00000270747 Transcript missense_variant 1120/3029 983/2409 328/802 P/L cCg/cTg 1 -1 ARHGEF19 HGNC HGNC:26604 protein_coding YES CCDS170.1 ENSP00000270747 Q8IW93 UPI0000074533 NM_153213.3 tolerated(0.11) 6/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF6 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 16207102 16207102 G A 1 0 0 0 0 1 0 0 0 1032 1116 39 1 1 ARHGEF19 1 16207102 Missense_Mutation SNP G C3L-01862_T 273956 16207102 232749320 3 7524 GRIK3 0 . GRCh38 1 36872199 36872199 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.721A>G p.Ile241Val p.I241V ENST00000373091 4/16 41 28 13 37 37 0 strelka-varscan-mutect GRIK3,missense_variant,p.Ile241Val,ENST00000373091,NM_000831.3;GRIK3,missense_variant,p.Ile241Val,ENST00000373093,; C ENST00000373091 Transcript missense_variant 738/9101 721/2760 241/919 I/V Atc/Gtc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 tolerated(0.55) 4/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 36872199 36872199 T C 1 0 0 0 0 1 0 0 0 6657 1435 50 5 5 GRIK3 1 36872199 Missense_Mutation SNP T C3L-01862_T 20665097 36872199 212084223 4 7525 ZNF684 0 . GRCh38 1 40546965 40546965 + Silent SNP C C G novel C3L-01862_T C3L-01862_N C C c.642C>G p.= p.P214P ENST00000372699 5/5 133 112 21 186 186 0 strelka-varscan-mutect ZNF684,synonymous_variant,p.=,ENST00000372699,NM_152373.3;ZNF684,downstream_gene_variant,,ENST00000372697,;ZNF684,downstream_gene_variant,,ENST00000372696,;ZNF684,non_coding_transcript_exon_variant,,ENST00000493756,;ZNF684,downstream_gene_variant,,ENST00000465152,;ZNF684,downstream_gene_variant,,ENST00000472043,; G ENST00000372699 Transcript synonymous_variant 893/2097 642/1137 214/378 P ccC/ccG 1 1 ZNF684 HGNC HGNC:28418 protein_coding YES CCDS454.1 ENSP00000361784 Q5T5D7 UPI00000437E3 NM_152373.3 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF0,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 27 40546965 40546965 C G 1 0 0 0 0 0 0 0 1 18664 668 24 4 4 ZNF684 1 40546965 Silent SNP C C3L-01862_T 3674766 40546965 208409457 5 7526 DMRTA2 0 . GRCh38 1 50421504 50421504 + Silent SNP G G T novel C3L-01862_T C3L-01862_N G G c.33C>A p.= p.P11P ENST00000404795 2/3 37 30 7 56 56 0 strelka-mutect DMRTA2,synonymous_variant,p.=,ENST00000404795,NM_032110.2;DMRTA2,synonymous_variant,p.=,ENST00000418121,; T ENST00000404795 Transcript synonymous_variant 426/3137 33/1629 11/542 P ccC/ccA 1 -1 DMRTA2 HGNC HGNC:13908 protein_coding YES CCDS44141.1 ENSP00000383909 Q96SC8 UPI00003D7962 NM_032110.2 2/3 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -18.161 1 1 1 1 0 T 2 4 27 50421504 50421504 G T 1 0 0 0 0 0 0 0 1 4396 1103 39 1 1 DMRTA2 1 50421504 Silent SNP G C3L-01862_T 9874539 50421504 198534918 6 7527 MROH7 0 . GRCh38 1 54665167 54665167 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1232G>T p.Gly411Val p.G411V ENST00000421030 4/24 145 129 16 117 117 0 strelka-varscan-mutect MROH7,missense_variant,p.Gly411Val,ENST00000421030,NM_001039464.3;MROH7,missense_variant,p.Gly411Val,ENST00000339553,;MROH7,missense_variant,p.Gly411Val,ENST00000395690,;MROH7,splice_region_variant,,ENST00000409996,NM_001291332.1;MROH7,splice_region_variant,,ENST00000478097,;MROH7,downstream_gene_variant,,ENST00000472987,;MROH7-TTC4,missense_variant,p.Gly436Val,ENST00000425300,;MROH7-TTC4,missense_variant,p.Gly411Val,ENST00000414150,;MROH7-TTC4,missense_variant,p.Gly411Val,ENST00000606515,;MROH7,missense_variant,p.Gly411Val,ENST00000413188,;MROH7,missense_variant,p.Gly411Val,ENST00000422659,;MROH7,missense_variant,p.Gly411Val,ENST00000440047,;MROH7,missense_variant,p.Gly411Val,ENST00000438846,;MROH7,splice_region_variant,,ENST00000440217,; T ENST00000421030 Transcript missense_variant,splice_region_variant 1517/4329 1232/3972 411/1323 G/V gGa/gTa 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 deleterious_low_confidence(0) 4/24 MODERATE 1 SNV 2 1 PASS rs1161473803 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 54665167 54665167 G T 1 0 0 0 0 1 0 0 0 9747 1188 41 2 2 MROH7 1 54665167 Missense_Mutation SNP G C3L-01862_T 4243663 54665167 194291255 7 7528 MROH7 0 . GRCh38 1 54674145 54674145 + Nonsense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.1930C>T p.Gln644Ter p.Q644* ENST00000421030 10/24 107 88 19 88 88 0 strelka-varscan-mutect MROH7,stop_gained,p.Gln644Ter,ENST00000421030,NM_001039464.3;MROH7,stop_gained,p.Gln644Ter,ENST00000339553,;MROH7,stop_gained,p.Gln644Ter,ENST00000395690,;MROH7,stop_gained,p.Gln212Ter,ENST00000409996,NM_001291332.1;MROH7,downstream_gene_variant,,ENST00000478097,;MROH7-TTC4,stop_gained,p.Gln644Ter,ENST00000414150,;MROH7,stop_gained,p.Gln644Ter,ENST00000440047,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000606515,;MROH7,3_prime_UTR_variant,,ENST00000413188,;MROH7,3_prime_UTR_variant,,ENST00000422659,;MROH7,3_prime_UTR_variant,,ENST00000438846,;MROH7,3_prime_UTR_variant,,ENST00000440217,; T ENST00000421030 Transcript stop_gained 2215/4329 1930/3972 644/1323 Q/* Caa/Taa 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 10/24 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF17,Superfamily_domains:SSF48371 HIGH 1 SNV 2 1 PASS rs1446614517 . 0 200 9 0 0 0 0 0 -20 0.9999953 1 1 1 0 T 4 4 27 54674145 54674145 C T 1 0 0 0 0 0 1 0 0 9747 595 21 3 3 MROH7 1 54674145 Nonsense_Mutation SNP C C3L-01862_T 8978 54674145 194282277 8 7529 USP33 0 . GRCh38 1 77717989 77717989 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1889G>T p.Ser630Ile p.S630I ENST00000370793 18/25 156 143 13 167 167 0 strelka-varscan-mutect USP33,missense_variant,p.Ser630Ile,ENST00000370793,NM_015017.4;USP33,missense_variant,p.Ser599Ile,ENST00000370794,NM_201624.2;USP33,missense_variant,p.Ser630Ile,ENST00000357428,;USP33,missense_variant,p.Ser622Ile,ENST00000370792,NM_201626.2;USP33,missense_variant,p.Ser235Ile,ENST00000481579,;USP33,missense_variant,p.Ser47Ile,ENST00000527390,;USP33,non_coding_transcript_exon_variant,,ENST00000461986,;USP33,non_coding_transcript_exon_variant,,ENST00000498328,;USP33,non_coding_transcript_exon_variant,,ENST00000531637,;USP33,upstream_gene_variant,,ENST00000477949,;USP33,downstream_gene_variant,,ENST00000462192,;USP33,upstream_gene_variant,,ENST00000472462,; A ENST00000370793 Transcript missense_variant 2236/4502 1889/2829 630/942 S/I aGt/aTt 1 -1 USP33 HGNC HGNC:20059 protein_coding YES CCDS678.1 ENSP00000359829 Q8TEY7 UPI000022ABDA NM_015017.4 deleterious(0.02) 18/25 PROSITE_profiles:PS50235,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 77717989 77717989 C A 1 0 0 0 0 1 0 0 0 17606 565 20 2 2 USP33 1 77717989 Missense_Mutation SNP C C3L-01862_T 23043844 77717989 171238433 9 7530 COL11A1 0 . GRCh38 1 102935112 102935112 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.3440G>T p.Gly1147Val p.G1147V ENST00000370096 45/67 277 235 42 272 272 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly1159Val,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly1147Val,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly1108Val,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly1031Val,ENST00000512756,NM_080630.3;COL11A1,splice_region_variant,,ENST00000635193,; A ENST00000370096 Transcript missense_variant,splice_region_variant 3753/7286 3440/5421 1147/1806 G/V gGc/gTc 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.03) 45/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 102935112 102935112 C A 1 0 0 0 0 1 0 0 0 3455 753 26 2 2 COL11A1 1 102935112 Missense_Mutation SNP C C3L-01862_T 25217123 102935112 146021310 10 7531 SEMA6C 0 . GRCh38 1 151135603 151135603 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.1421A>G p.Tyr474Cys p.Y474C ENST00000368913 14/20 131 82 49 104 104 0 strelka-varscan-mutect SEMA6C,missense_variant,p.Tyr474Cys,ENST00000341697,;SEMA6C,missense_variant,p.Tyr474Cys,ENST00000368914,NM_030913.4;SEMA6C,missense_variant,p.Tyr474Cys,ENST00000368913,NM_001178061.1;SEMA6C,missense_variant,p.Tyr434Cys,ENST00000368912,NM_001178062.1;SEMA6C,splice_region_variant,,ENST00000613223,;SEMA6C,intron_variant,,ENST00000621728,;RP11-68I18.10,upstream_gene_variant,,ENST00000563624,;SEMA6C,upstream_gene_variant,,ENST00000479820,;SEMA6C,upstream_gene_variant,,ENST00000464018,;SEMA6C,upstream_gene_variant,,ENST00000489944,;SEMA6C,downstream_gene_variant,,ENST00000485745,; C ENST00000368913 Transcript missense_variant 1550/3817 1421/2889 474/962 Y/C tAc/tGc 1 -1 SEMA6C HGNC HGNC:10740 protein_coding YES CCDS53364.1 ENSP00000357909 Q9H3T2 UPI00001414D0 NM_001178061.1 deleterious(0) 14/20 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF11,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 27 151135603 151135603 T C 1 0 0 0 0 1 0 0 0 14317 1652 57 5 5 SEMA6C 1 151135603 Missense_Mutation SNP T C3L-01862_T 48200491 151135603 97820819 11 7532 OLFML2B 0 . GRCh38 1 162000308 162000308 + Missense_Mutation SNP C C T rs750492409 C3L-01862_T C3L-01862_N C C c.757G>A p.Val253Met p.V253M ENST00000367940 5/8 214 178 36 138 138 0 strelka-varscan-mutect OLFML2B,missense_variant,p.Val252Met,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Val253Met,ENST00000367940,NM_001297713.1; T ENST00000367940 Transcript missense_variant 967/2685 757/2256 253/751 V/M Gtg/Atg rs750492409,COSM898637 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 tolerated(0.11) 5/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs750492409 . 0 207 0 3 0 0 0 0 -20 0.999995 1 1 1 0 T 3 4 27 162000308 162000308 C T 1 0 0 0 0 1 0 0 0 10933 536 19 1 1 OLFML2B 1 162000308 Missense_Mutation SNP C C3L-01862_T 10864705 162000308 86956114 12 7533 CREG1 0 . GRCh38 1 167553444 167553444 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.298A>T p.Ser100Cys p.S100C ENST00000370509 1/4 123 109 14 84 84 0 strelka-varscan-mutect CREG1,missense_variant,p.Ser100Cys,ENST00000370509,NM_003851.2; A ENST00000370509 Transcript missense_variant 324/1974 298/663 100/220 S/C Agc/Tgc 1 -1 CREG1 HGNC HGNC:2351 protein_coding YES CCDS1262.1 ENSP00000359540 O75629 UPI0000047822 NM_003851.2 deleterious(0) 1/4 hmmpanther:PTHR13343:SF12,hmmpanther:PTHR13343,Gene3D:2.30.110.10,PIRSF_domain:PIRSF036911,Pfam_domain:PF13883,Superfamily_domains:SSF50475 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 167553444 167553444 T A 1 0 0 0 0 1 0 0 0 3665 1580 55 4 4 CREG1 1 167553444 Missense_Mutation SNP T C3L-01862_T 5553136 167553444 81402978 13 7534 OPTC 0 . GRCh38 1 203496231 203496231 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.226C>T p.Pro76Ser p.P76S ENST00000367222 2/8 671 581 90 489 489 0 strelka-varscan-mutect OPTC,missense_variant,p.Pro76Ser,ENST00000367222,NM_014359.3;OPTC,missense_variant,p.Pro76Ser,ENST00000448911,;PRELP,downstream_gene_variant,,ENST00000343110,NM_002725.3,NM_201348.1; T ENST00000367222 Transcript missense_variant 342/1359 226/999 76/332 P/S Ccc/Tcc 1 1 OPTC HGNC HGNC:8158 protein_coding YES CCDS1439.1 ENSP00000356191 Q9UBM4 UPI00000015D9 NM_014359.3 tolerated(0.16) 2/8 hmmpanther:PTHR24370 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 203496231 203496231 C T 1 0 0 0 0 1 0 0 0 10964 637 22 3 3 OPTC 1 203496231 Missense_Mutation SNP C C3L-01862_T 35942787 203496231 45460191 14 7535 LYPLAL1 0 . GRCh38 1 219173958 219173958 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.68C>A p.Ser23Tyr p.S23Y ENST00000366928 1/5 309 196 113 218 218 0 strelka-varscan-mutect LYPLAL1,missense_variant,p.Ser23Tyr,ENST00000366928,NM_001300772.1,NM_001300771.1,NM_138794.4;LYPLAL1,missense_variant,p.Ser23Tyr,ENST00000366927,NM_001300770.1;LYPLAL1-AS1,non_coding_transcript_exon_variant,,ENST00000441331,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000483635,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000463964,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000477938,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000460522,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000474379,;LYPLAL1,non_coding_transcript_exon_variant,,ENST00000496776,;LYPLAL1,upstream_gene_variant,,ENST00000469590,;LYPLAL1,upstream_gene_variant,,ENST00000478794,; A ENST00000366928 Transcript missense_variant 115/1898 68/714 23/237 S/Y tCt/tAt 1 1 LYPLAL1 HGNC HGNC:20440 protein_coding YES CCDS1522.1 ENSP00000355895 Q5VWZ2 UPI000013D8ED NM_001300772.1,NM_001300771.1,NM_138794.4 deleterious(0) 1/5 Gene3D:3.40.50.1820,Pfam_domain:PF02230,hmmpanther:PTHR10655,hmmpanther:PTHR10655:SF27,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 219173958 219173958 C A 1 0 0 0 0 1 0 0 0 9030 913 32 2 2 LYPLAL1 1 219173958 Missense_Mutation SNP C C3L-01862_T 15677727 219173958 29782464 15 7536 LEFTY1 0 . GRCh38 1 225888986 225888986 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.81C>T p.= p.L27L ENST00000272134 1/4 73 68 5 71 71 0 strelka-varscan-mutect LEFTY1,synonymous_variant,p.=,ENST00000272134,NM_020997.3;RP4-559A3.7,intron_variant,,ENST00000432920,;LEFTY1,intron_variant,,ENST00000492457,; A ENST00000272134 Transcript synonymous_variant 161/1626 81/1101 27/366 L ctC/ctT 1 -1 LEFTY1 HGNC HGNC:6552 protein_coding YES CCDS1548.1 ENSP00000272134 O75610 UPI000003721B NM_020997.3 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11848:SF167,hmmpanther:PTHR11848,PIRSF_domain:PIRSF037402,Prints_domain:PR01427 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.3808 1 1 1 1 0 A 2 1 27 225888986 225888986 G A 1 0 0 0 0 0 0 0 1 8623 1161 41 3 3 LEFTY1 1 225888986 Silent SNP G C3L-01862_T 6715028 225888986 23067436 16 7537 PGBD5 0 . GRCh38 1 230337154 230337154 + Silent SNP C C A novel C3L-01862_T C3L-01862_N C C c.1029G>T p.= p.G343G ENST00000391860 4/7 248 150 98 163 163 0 strelka-varscan-mutect PGBD5,synonymous_variant,p.=,ENST00000391860,NM_001258311.1;PGBD5,synonymous_variant,p.=,ENST00000525115,;PGBD5,upstream_gene_variant,,ENST00000530424,; A ENST00000391860 Transcript synonymous_variant 1472/10961 1029/1575 343/524 G ggG/ggT 1 -1 PGBD5 HGNC HGNC:19405 protein_coding YES ENSP00000375733 A0A0A0MS21 UPI000004EBDA NM_001258311.1 4/7 hmmpanther:PTHR28576,hmmpanther:PTHR28576:SF2,Pfam_domain:PF13843 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999991 1 1 1 0 A 2 1 27 230337154 230337154 C A 1 0 0 0 0 0 0 0 1 11874 726 26 2 2 PGBD5 1 230337154 Silent SNP C C3L-01862_T 4448168 230337154 18619268 17 7538 RYR2 0 . GRCh38 1 237614556 237614556 + Missense_Mutation SNP G G T rs754364233 C3L-01862_T C3L-01862_N G G c.5428G>T p.Val1810Phe p.V1810F ENST00000366574 37/105 440 378 62 425 424 1 strelka-varscan-mutect RYR2,missense_variant,p.Val1810Phe,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Val1794Phe,ENST00000360064,; T ENST00000366574 Transcript missense_variant 5745/16562 5428/14904 1810/4967 V/F Gtt/Ttt rs754364233,CM122155 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 37/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 0,1 1 PASS rs754364233 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 237614556 237614556 G T 1 0 0 0 0 1 0 0 0 14029 1029 36 2 2 RYR2 1 237614556 Missense_Mutation SNP G C3L-01862_T 7277402 237614556 11341866 18 7539 RYR2 0 . GRCh38 1 237732107 237732107 + Missense_Mutation SNP A A T novel C3L-01862_T C3L-01862_N A A c.10997A>T p.Gln3666Leu p.Q3666L ENST00000366574 78/105 174 146 28 153 153 0 strelka-varscan-mutect RYR2,missense_variant,p.Gln3666Leu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gln3650Leu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,;RYR2,downstream_gene_variant,,ENST00000609253,; T ENST00000366574 Transcript missense_variant 11314/16562 10997/14904 3666/4967 Q/L cAg/cTg 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.01) 78/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 237732107 237732107 A T 1 0 0 0 0 1 0 0 0 14029 188 7 4 4 RYR2 1 237732107 Missense_Mutation SNP A C3L-01862_T 117551 237732107 11224315 19 7540 FMN2 0 . GRCh38 1 240092380 240092380 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.271G>T p.Gly91Cys p.G91C ENST00000319653 1/18 146 78 68 143 143 0 strelka-varscan-mutect FMN2,missense_variant,p.Gly91Cys,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,intron_variant,,ENST00000447095,; T ENST00000319653 Transcript missense_variant 501/6434 271/5169 91/1722 G/C Ggc/Tgc 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 tolerated_low_confidence(0.14) 1/18 MODERATE 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999993 1 1 1 0 T 3 4 27 240092380 240092380 G T 1 0 0 0 0 1 0 0 0 5806 1116 39 1 1 FMN2 1 240092380 Missense_Mutation SNP G C3L-01862_T 2360273 240092380 8864042 20 7541 OR14C36 0 . GRCh38 1 248349037 248349037 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.263C>A p.Thr88Asn p.T88N ENST00000317861 1/1 272 168 104 263 263 0 strelka-varscan-mutect OR14C36,missense_variant,p.Thr88Asn,ENST00000317861,NM_001001918.1; A ENST00000317861 Transcript missense_variant 263/939 263/939 88/312 T/N aCc/aAc 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 tolerated(0.06) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 248349037 248349037 C A 1 0 0 0 0 1 0 0 0 11023 507 18 2 2 OR14C36 1 248349037 Missense_Mutation SNP C C3L-01862_T 8256657 248349037 607385 21 7542 CAD 0 . GRCh38 2 27235271 27235271 + Missense_Mutation SNP G G T C3L-01862_T C3L-01862_N G G c.3813G>T p.Leu1271Phe p.L1271F ENST00000264705 24/44 97 75 22 95 95 0 strelka-varscan-mutect CAD,missense_variant,p.Leu1271Phe,ENST00000264705,NM_004341.3;CAD,missense_variant,p.Leu1208Phe,ENST00000403525,NM_001306079.1;CAD,upstream_gene_variant,,ENST00000456311,;CAD,upstream_gene_variant,,ENST00000458503,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,upstream_gene_variant,,ENST00000491461,;CAD,non_coding_transcript_exon_variant,,ENST00000479002,;CAD,upstream_gene_variant,,ENST00000487239,;CAD,downstream_gene_variant,,ENST00000475695,;CAD,downstream_gene_variant,,ENST00000491891,; T ENST00000264705 Transcript missense_variant 3975/7265 3813/6678 1271/2225 L/F ttG/ttT COSM290431 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 deleterious(0) 24/44 Gene3D:3.30.470.20,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF5,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01369 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 27235271 27235271 G T 1 0 0 0 0 1 0 0 0 2255 1339 47 2 2 CAD 2 27235271 Missense_Mutation SNP G C3L-01862_T 27235271 214958258 22 7543 EML6 0 . GRCh38 2 54894922 54894922 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.2750T>C p.Val917Ala p.V917A ENST00000356458 19/41 154 116 38 163 163 0 strelka-varscan-mutect EML6,missense_variant,p.Val917Ala,ENST00000356458,NM_001039753.2; C ENST00000356458 Transcript missense_variant 3270/8320 2750/5877 917/1958 V/A gTa/gCa 1 1 EML6 HGNC HGNC:35412 protein_coding YES CCDS46286.1 ENSP00000348842 Q6ZMW3 UPI00006C0432 NM_001039753.2 tolerated(0.06) 19/41 PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF8,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 54894922 54894922 T C 1 0 0 0 0 1 0 0 0 4944 1638 57 5 5 EML6 2 54894922 Missense_Mutation SNP T C3L-01862_T 27659651 54894922 187298607 23 7544 CCDC85A 0 . GRCh38 2 56375830 56375830 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1467G>T p.Leu489Phe p.L489F ENST00000407595 5/6 217 186 31 264 263 1 strelka-varscan-mutect CCDC85A,missense_variant,p.Leu489Phe,ENST00000407595,NM_001080433.1;RP11-482H16.1,intron_variant,,ENST00000607540,; T ENST00000407595 Transcript missense_variant 1969/3982 1467/1662 489/553 L/F ttG/ttT 1 1 CCDC85A HGNC HGNC:29400 protein_coding YES CCDS46290.1 ENSP00000384040 Q96PX6 UPI00001C1DC1 NM_001080433.1 tolerated_low_confidence(0.09) 5/6 MODERATE 1 SNV 1 1 PASS rs1310275422 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 56375830 56375830 G T 1 0 0 0 0 1 0 0 0 2557 1368 48 2 2 CCDC85A 2 56375830 Missense_Mutation SNP G C3L-01862_T 1480908 56375830 185817699 24 7545 KIF5C 0 . GRCh38 2 149010330 149010330 + Missense_Mutation SNP A A T novel C3L-01862_T C3L-01862_N A A c.2746A>T p.Arg916Trp p.R916W ENST00000435030 24/26 82 67 15 96 95 1 strelka-varscan-mutect KIF5C,missense_variant,p.Arg916Trp,ENST00000435030,NM_004522.2;KIF5C,non_coding_transcript_exon_variant,,ENST00000464066,;KIF5C,non_coding_transcript_exon_variant,,ENST00000482151,; T ENST00000435030 Transcript missense_variant 3114/6931 2746/2874 916/957 R/W Agg/Tgg 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 deleterious(0) 24/26 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 149010330 149010330 A T 1 0 0 0 0 1 0 0 0 8172 63 3 4 4 KIF5C 2 149010330 Missense_Mutation SNP A C3L-01862_T 92634500 149010330 93183199 25 7546 SCN9A 0 . GRCh38 2 166199071 166199071 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.5535G>A p.Met1845Ile p.M1845I ENST00000409672 27/27 296 249 47 411 410 1 strelka-varscan-mutect SCN9A,missense_variant,p.Met1856Ile,ENST00000303354,;SCN9A,missense_variant,p.Met1845Ile,ENST00000409672,NM_002977.3;SCN9A,missense_variant,p.Met1856Ile,ENST00000409435,;AC010127.3,intron_variant,,ENST00000447809,; T ENST00000409672 Transcript missense_variant 5882/9768 5535/5934 1845/1977 M/I atG/atA 1 -1 SCN9A HGNC HGNC:10597 protein_coding YES CCDS46441.1 ENSP00000386306 Q15858 UPI0000140AC7 NM_002977.3 deleterious(0) 27/27 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF221 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 166199071 166199071 C T 1 0 0 0 0 1 0 0 0 14194 594 21 3 3 SCN9A 2 166199071 Missense_Mutation SNP C C3L-01862_T 17188741 166199071 75994458 26 7547 DYNC1I2 0 . GRCh38 2 171728391 171728391 + Nonsense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.1230G>A p.Trp410Ter p.W410* ENST00000397119 13/18 93 81 12 117 116 1 varscan-mutect DYNC1I2,stop_gained,p.Trp410Ter,ENST00000397119,NM_001378.2;DYNC1I2,stop_gained,p.Trp384Ter,ENST00000340296,NM_001271788.1;DYNC1I2,stop_gained,p.Trp410Ter,ENST00000409773,NM_001271785.1;DYNC1I2,stop_gained,p.Trp384Ter,ENST00000409197,NM_001271789.1;DYNC1I2,stop_gained,p.Trp410Ter,ENST00000409453,;DYNC1I2,stop_gained,p.Trp384Ter,ENST00000508530,NM_001271790.1;DYNC1I2,stop_gained,p.Trp404Ter,ENST00000409317,;DYNC1I2,stop_gained,p.Trp402Ter,ENST00000410079,NM_001271786.1,NM_001271787.1;DYNC1I2,downstream_gene_variant,,ENST00000435234,;DYNC1I2,downstream_gene_variant,,ENST00000452242,;DYNC1I2,downstream_gene_variant,,ENST00000438879,;DYNC1I2,downstream_gene_variant,,ENST00000456808,;DYNC1I2,downstream_gene_variant,,ENST00000425485,;DYNC1I2,downstream_gene_variant,,ENST00000423910,;DYNC1I2,downstream_gene_variant,,ENST00000422646,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000482454,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000479806,;DYNC1I2,downstream_gene_variant,,ENST00000470286,;DYNC1I2,downstream_gene_variant,,ENST00000445378,; A ENST00000397119 Transcript stop_gained 1397/2604 1230/1917 410/638 W/* tgG/tgA 1 1 DYNC1I2 HGNC HGNC:2964 protein_coding YES CCDS46450.1 ENSP00000380308 Q13409 A0A140VKE9 UPI0000129A05 NM_001378.2 13/18 PROSITE_profiles:PS50294,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF36,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 27 171728391 171728391 G A 1 0 0 0 0 0 1 0 0 4667 1183 41 3 3 DYNC1I2 2 171728391 Nonsense_Mutation SNP G C3L-01862_T 5529320 171728391 70465138 27 7548 GPR155 0 . GRCh38 2 174453766 174453766 + Missense_Mutation SNP C C G novel C3L-01862_T C3L-01862_N C C c.1847G>C p.Ser616Thr p.S616T ENST00000392552 11/16 162 129 33 170 170 0 strelka-varscan-mutect GPR155,missense_variant,p.Ser588Thr,ENST00000614352,NM_001267051.1;GPR155,missense_variant,p.Ser616Thr,ENST00000392552,NM_152529.6;GPR155,missense_variant,p.Ser616Thr,ENST00000392551,NM_001267050.1;GPR155,missense_variant,p.Ser616Thr,ENST00000295500,NM_001033045.3; G ENST00000392552 Transcript missense_variant 2086/6730 1847/2613 616/870 S/T aGt/aCt 1 -1 GPR155 HGNC HGNC:22951 protein_coding YES CCDS2259.1 ENSP00000376335 Q7Z3F1 UPI000013E262 NM_152529.6 tolerated(0.66) 11/16 hmmpanther:PTHR22829 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 174453766 174453766 C G 1 0 0 0 0 1 0 0 0 6546 565 20 4 4 GPR155 2 174453766 Missense_Mutation SNP C C3L-01862_T 2725375 174453766 67739763 28 7549 TTN 0 . GRCh38 2 178557443 178557443 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.87819C>T p.= p.H29273H ENST00000589042 329/363 637 534 103 667 667 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,non_coding_transcript_exon_variant,,ENST00000624360,; A ENST00000589042 Transcript synonymous_variant 88044/109224 87819/107976 29273/35991 H caC/caT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 329/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 178557443 178557443 G A 1 0 0 0 0 0 0 0 1 17245 1252 44 3 3 TTN 2 178557443 Silent SNP G C3L-01862_T 4103677 178557443 63636086 29 7550 COL3A1 0 . GRCh38 2 188998276 188998276 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1934G>T p.Gly645Val p.G645V ENST00000304636 28/51 285 245 40 302 302 0 strelka-varscan-mutect COL3A1,missense_variant,p.Gly645Val,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Gly645Val,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000450867,;COL3A1,downstream_gene_variant,,ENST00000637672,; T ENST00000304636 Transcript missense_variant 2104/5543 1934/4401 645/1466 G/V gGt/gTt 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0) 28/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 188998276 188998276 G T 1 0 0 0 0 1 0 0 0 3477 1261 44 2 2 COL3A1 2 188998276 Missense_Mutation SNP G C3L-01862_T 10440833 188998276 53195253 30 7551 SLC11A1 0 . GRCh38 2 218382373 218382373 + Frame_Shift_Del DEL C C - rs551043157 C3L-01862_T C3L-01862_N C C c.5delC p.Thr2LysfsTer9 p.T2Kfs*9 ENST00000233202 1/15 109 95 14 95 95 0 sindel-varindel-pindel SLC11A1,frameshift_variant,p.Thr2LysfsTer9,ENST00000233202,NM_000578.3;SLC11A1,frameshift_variant,p.Thr2LysfsTer9,ENST00000354352,;SLC11A1,frameshift_variant,p.Thr2LysfsTer378,ENST00000539932,;SLC11A1,frameshift_variant,p.Thr2LysfsTer9,ENST00000473367,;SLC11A1,frameshift_variant,p.Thr2LysfsTer?,ENST00000481524,;SLC11A1,splice_region_variant,,ENST00000468221,;SLC11A1,splice_region_variant,,ENST00000465984,;SLC11A1,splice_region_variant,,ENST00000494322,;SLC11A1,splice_region_variant,,ENST00000475225,;SLC11A1,splice_region_variant,,ENST00000492413,;SLC11A1,splice_region_variant,,ENST00000469799,;SLC11A1,splice_region_variant,,ENST00000471875,;SLC11A1,upstream_gene_variant,,ENST00000469449,;SLC11A1,upstream_gene_variant,,ENST00000483487,;SLC11A1,upstream_gene_variant,,ENST00000460592,; - ENST00000233202 Transcript frameshift_variant,splice_region_variant 345/3852 5/1653 2/550 T/X aCa/aa rs551043157 1 1 SLC11A1 HGNC HGNC:10907 protein_coding YES CCDS2415.1 ENSP00000233202 P49279 A0A024R474 UPI0000130520 NM_000578.3 1/15 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 27 218382373 218382373 C - 1 0 1 0 1 0 0 0 0 14645 492 17 0 0 SLC11A1 2 218382373 Frame_Shift_Del DEL C C3L-01862_T 29384097 218382373 23811156 31 7552 RBMS3 0 . GRCh38 3 29739865 29739865 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.545T>A p.Val182Asp p.V182D ENST00000383767 5/15 77 64 13 80 79 1 varscan-mutect RBMS3,missense_variant,p.Val181Asp,ENST00000434693,;RBMS3,missense_variant,p.Val181Asp,ENST00000383766,NM_001003792.2;RBMS3,missense_variant,p.Val182Asp,ENST00000383767,NM_001003793.2;RBMS3,missense_variant,p.Val248Asp,ENST00000636680,;RBMS3,missense_variant,p.Val182Asp,ENST00000273139,NM_014483.3;RBMS3,missense_variant,p.Val182Asp,ENST00000452462,NM_001177711.1;RBMS3,missense_variant,p.Val182Asp,ENST00000456853,NM_001177712.1;RBMS3,missense_variant,p.Val182Asp,ENST00000445033,;RBMS3,downstream_gene_variant,,ENST00000478716,;RP11-9J18.1,3_prime_UTR_variant,,ENST00000635992,;RBMS3,3_prime_UTR_variant,,ENST00000637842,;RBMS3,non_coding_transcript_exon_variant,,ENST00000497205,; A ENST00000383767 Transcript missense_variant 881/1864 545/1314 182/437 V/D gTt/gAt 1 1 RBMS3 HGNC HGNC:13427 protein_coding YES CCDS33724.1 ENSP00000373277 Q6XE24 UPI000023FE75 NM_001003793.2 deleterious(0.03) 5/15 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF473,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 29739865 29739865 T A 1 0 0 0 0 1 0 0 0 13316 1725 60 4 4 RBMS3 3 29739865 Missense_Mutation SNP T C3L-01862_T 29739865 168555694 32 7553 BSN 0 . GRCh38 3 49663333 49663333 + Silent SNP C C A novel C3L-01862_T C3L-01862_N C C c.11175C>A p.= p.S3725S ENST00000296452 7/12 365 310 55 348 348 0 strelka-varscan-mutect BSN,synonymous_variant,p.=,ENST00000296452,NM_003458.3; A ENST00000296452 Transcript synonymous_variant 11289/15955 11175/11781 3725/3926 S tcC/tcA 1 1 BSN HGNC HGNC:1117 protein_coding YES CCDS2800.1 ENSP00000296452 Q9UPA5 UPI000013E33C NM_003458.3 7/12 hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 49663333 49663333 C A 1 0 0 0 0 0 0 0 1 1704 610 22 2 2 BSN 3 49663333 Silent SNP C C3L-01862_T 19923468 49663333 148632226 33 7554 IQCF3 0 . GRCh38 3 51830539 51830539 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.203G>A p.Arg68Lys p.R68K ENST00000456080 8/8 136 116 20 143 143 0 strelka-varscan-mutect IQCF3,missense_variant,p.Arg68Lys,ENST00000456080,;IQCF3,missense_variant,p.Arg68Lys,ENST00000437810,NM_001085479.2;IQCF3,missense_variant,p.Arg68Lys,ENST00000446775,NM_001207023.1;IQCF3,missense_variant,p.Arg68Lys,ENST00000440739,;IQCF3,synonymous_variant,p.=,ENST00000444293,;IQCF3,non_coding_transcript_exon_variant,,ENST00000462079,;IQCF3,downstream_gene_variant,,ENST00000472485,;IQCF3,downstream_gene_variant,,ENST00000474242,;IQCF3,downstream_gene_variant,,ENST00000465028,; A ENST00000456080 Transcript missense_variant 1368/1685 203/465 68/154 R/K aGg/aAg 1 1 IQCF3 HGNC HGNC:31816 protein_coding YES CCDS46837.1 ENSP00000415609 P0C7M6 UPI000015EE9E tolerated(0.07) 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR21633:SF5,hmmpanther:PTHR21633 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 51830539 51830539 G A 1 0 0 0 0 1 0 0 0 7713 1000 35 3 3 IQCF3 3 51830539 Missense_Mutation SNP G C3L-01862_T 2167206 51830539 146465020 34 7555 CPB1 0 . GRCh38 3 148841839 148841840 + Frame_Shift_Del DEL AA AA - novel C3L-01862_T C3L-01862_N AA AA c.493_494delAA p.Asn165Ter p.N165* ENST00000491148 7/12 80 65 15 133 133 0 sindel-varindel-pindel CPB1,frameshift_variant,p.Asn165Ter,ENST00000491148,;CPB1,frameshift_variant,p.Asn165Ter,ENST00000282957,NM_001871.2;CPB1,frameshift_variant,p.Asn131Ter,ENST00000468341,;CPB1,downstream_gene_variant,,ENST00000462345,;CPB1,non_coding_transcript_exon_variant,,ENST00000484877,;CPB1,downstream_gene_variant,,ENST00000465718,; - ENST00000491148 Transcript frameshift_variant 825-826/1773 491-492/1254 164/417 Q/X cAA/c 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD 7/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 HIGH 1 deletion 5 2 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 27 148841839 148841839 AA - 1 0 1 0 1 0 0 0 0 3590 130 5 0 0 CPB1 3 148841839 Frame_Shift_Del DEL AA C3L-01862_T 97011300 148841839 49453720 35 7556 SLITRK3 0 . GRCh38 3 165188931 165188931 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1900G>T p.Gly634Trp p.G634W ENST00000475390 2/2 243 213 30 279 278 1 strelka-varscan-mutect SLITRK3,missense_variant,p.Gly634Trp,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Gly634Trp,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; A ENST00000475390 Transcript missense_variant 2344/4555 1900/2934 634/977 G/W Ggg/Tgg 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 deleterious(0.01) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 165188931 165188931 C A 1 0 0 0 0 1 0 0 0 15035 594 21 2 2 SLITRK3 3 165188931 Missense_Mutation SNP C C3L-01862_T 16347092 165188931 33106628 36 7557 SPATA18 0 . GRCh38 4 52079844 52079844 + Missense_Mutation SNP C C T rs766949831 C3L-01862_T C3L-01862_N C C c.1280C>T p.Ala427Val p.A427V ENST00000295213 9/13 288 247 41 285 285 0 strelka-varscan-mutect SPATA18,missense_variant,p.Ala427Val,ENST00000295213,NM_145263.3;SPATA18,missense_variant,p.Ala395Val,ENST00000419395,NM_001297608.1;SPATA18,downstream_gene_variant,,ENST00000514670,;SPATA18,missense_variant,p.Ala427Val,ENST00000505320,;SPATA18,non_coding_transcript_exon_variant,,ENST00000511028,;SPATA18,non_coding_transcript_exon_variant,,ENST00000510549,; T ENST00000295213 Transcript missense_variant 1654/4396 1280/1617 427/538 A/V gCc/gTc rs766949831 1 1 SPATA18 HGNC HGNC:29579 protein_coding YES CCDS3489.1 ENSP00000295213 Q8TC71 A0A140VKF4 UPI000006FB0D NM_145263.3 deleterious(0) 9/13 Pfam_domain:PF16026,hmmpanther:PTHR21771,hmmpanther:PTHR21771:SF0 MODERATE 1 SNV 1 1 PASS rs766949831 . 0 207 0 0 0 0 0 2 -4.202445 0 0 1 0 0 T 3 4 27 52079844 52079844 C T 1 0 0 0 0 1 0 0 0 15333 739 26 3 3 SPATA18 4 52079844 Missense_Mutation SNP C C3L-01862_T 52079844 138134711 37 7558 SRD5A3 0 . GRCh38 4 55369964 55369964 + Missense_Mutation SNP G G C novel C3L-01862_T C3L-01862_N G G c.830G>C p.Trp277Ser p.W277S ENST00000264228 5/5 285 241 44 351 351 0 strelka-varscan-mutect SRD5A3,missense_variant,p.Trp277Ser,ENST00000264228,NM_024592.4;SRD5A3,missense_variant,p.Trp141Ser,ENST00000505210,;SRD5A3-AS1,intron_variant,,ENST00000433175,;SRD5A3-AS1,intron_variant,,ENST00000510637,;SRD5A3-AS1,intron_variant,,ENST00000595734,;SRD5A3-AS1,intron_variant,,ENST00000596289,;SRD5A3-AS1,intron_variant,,ENST00000609573,;SRD5A3-AS1,intron_variant,,ENST00000609051,;SRD5A3-AS1,intron_variant,,ENST00000596312,;SRD5A3-AS1,intron_variant,,ENST00000598906,;SRD5A3-AS1,intron_variant,,ENST00000608086,;SRD5A3-AS1,intron_variant,,ENST00000608265,;SRD5A3-AS1,intron_variant,,ENST00000609580,;SRD5A3-AS1,intron_variant,,ENST00000609487,;SRD5A3-AS1,intron_variant,,ENST00000608558,;SRD5A3-AS1,intron_variant,,ENST00000595103,;SRD5A3-AS1,intron_variant,,ENST00000619912,;SRD5A3-AS1,intron_variant,,ENST00000609700,;SRD5A3-AS1,intron_variant,,ENST00000609500,;SRD5A3-AS1,intron_variant,,ENST00000613794,;SRD5A3-AS1,downstream_gene_variant,,ENST00000592823,;SRD5A3,non_coding_transcript_exon_variant,,ENST00000514398,;SRD5A3-AS1,intron_variant,,ENST00000610396,;SRD5A3-AS1,intron_variant,,ENST00000619685,;SRD5A3-AS1,downstream_gene_variant,,ENST00000619203,; C ENST00000264228 Transcript missense_variant 1058/4190 830/957 277/318 W/S tGg/tCg 1 1 SRD5A3 HGNC HGNC:25812 protein_coding YES CCDS3498.1 ENSP00000264228 Q9H8P0 UPI0000043F70 NM_024592.4 deleterious(0) 5/5 Pfam_domain:PF02544,PROSITE_profiles:PS50244,hmmpanther:PTHR14624,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 55369964 55369964 G C 1 0 0 0 0 1 0 0 0 15497 1357 47 4 4 SRD5A3 4 55369964 Missense_Mutation SNP G C3L-01862_T 3290120 55369964 134844591 38 7559 AASDH 0 . GRCh38 4 56378449 56378449 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.367C>T p.His123Tyr p.H123Y ENST00000205214 4/15 85 74 11 133 133 0 strelka-varscan-mutect AASDH,missense_variant,p.His123Tyr,ENST00000205214,NM_181806.3;AASDH,missense_variant,p.His23Tyr,ENST00000513376,NM_001286668.1;AASDH,missense_variant,p.His123Tyr,ENST00000451613,NM_001286671.1;AASDH,missense_variant,p.His123Tyr,ENST00000502617,NM_001286672.1;AASDH,5_prime_UTR_variant,,ENST00000602986,NM_001286669.1;AASDH,non_coding_transcript_exon_variant,,ENST00000510762,;AASDH,synonymous_variant,p.=,ENST00000503808,;AASDH,intron_variant,,ENST00000514745,NM_001286670.1;AASDH,downstream_gene_variant,,ENST00000510012,;AASDH,downstream_gene_variant,,ENST00000514796,; A ENST00000205214 Transcript missense_variant 548/3590 367/3297 123/1098 H/Y Cat/Tat 1 -1 AASDH HGNC HGNC:23993 protein_coding YES CCDS3504.1 ENSP00000205214 Q4L235 UPI000020B8EF NM_181806.3 tolerated(0.54) 4/15 hmmpanther:PTHR24095:SF185,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 56378449 56378449 G A 1 0 0 0 0 1 0 0 0 26 1290 45 3 3 AASDH 4 56378449 Missense_Mutation SNP G C3L-01862_T 1008485 56378449 133836106 39 7560 EPHA5 0 . GRCh38 4 65365080 65365080 + Missense_Mutation SNP C C T C3L-01862_T C3L-01862_N C C c.2176G>A p.Ala726Thr p.A726T ENST00000622150 12/18 221 192 29 282 282 0 strelka-varscan-mutect EPHA5,missense_variant,p.Ala726Thr,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Ala704Thr,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Ala725Thr,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Ala726Thr,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Ala562Thr,ENST00000432638,;EPHA5,missense_variant,p.Ala703Thr,ENST00000354839,NM_182472.3; T ENST00000622150 Transcript missense_variant 2929/8421 2176/3117 726/1038 A/T Gca/Aca COSM4125548,COSM4681295 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 12/18 Gene3D:3.30.200.20,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 65365080 65365080 C T 1 0 0 0 0 1 0 0 0 5017 797 28 3 3 EPHA5 4 65365080 Missense_Mutation SNP C C3L-01862_T 8986631 65365080 124849475 40 7561 EPHA5 0 . GRCh38 4 65490701 65490701 + Missense_Mutation SNP C C G novel C3L-01862_T C3L-01862_N C C c.1078G>C p.Ala360Pro p.A360P ENST00000622150 5/18 117 93 24 145 145 0 strelka-varscan-mutect EPHA5,missense_variant,p.Ala360Pro,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Ala360Pro,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Ala360Pro,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Ala360Pro,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Ala360Pro,ENST00000354839,NM_182472.3;EPHA5,intron_variant,,ENST00000432638,; G ENST00000622150 Transcript missense_variant 1831/8421 1078/3117 360/1038 A/P Gct/Cct 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.12) 5/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 65490701 65490701 C G 1 0 0 0 0 1 0 0 0 5017 710 25 4 4 EPHA5 4 65490701 Missense_Mutation SNP C C3L-01862_T 125621 65490701 124723854 41 7562 ADH7 0 . GRCh38 4 99427816 99427816 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.581G>T p.Cys194Phe p.C194F ENST00000476959 5/9 66 54 12 73 73 0 strelka-varscan-mutect ADH7,missense_variant,p.Cys174Phe,ENST00000437033,;ADH7,missense_variant,p.Cys186Phe,ENST00000209665,NM_000673.4;ADH7,missense_variant,p.Cys117Phe,ENST00000482593,;ADH7,missense_variant,p.Cys194Phe,ENST00000476959,NM_001166504.1;ADH7,downstream_gene_variant,,ENST00000474027,; A ENST00000476959 Transcript missense_variant 611/1325 581/1185 194/394 C/F tGt/tTt 1 -1 ADH7 HGNC HGNC:256 protein_coding YES CCDS54781.1 ENSP00000420269 P40394 UPI00017A81B5 NM_001166504.1 deleterious(0) 5/9 hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF355,Gene3D:3.90.180.10,Superfamily_domains:SSF50129,Superfamily_domains:SSF51735 MODERATE 1 SNV 2 1 PASS rs1323092909 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 99427816 99427816 C A 1 0 0 0 0 1 0 0 0 386 478 17 2 2 ADH7 4 99427816 Missense_Mutation SNP C C3L-01862_T 33937115 99427816 90786739 42 7563 NIPBL 0 . GRCh38 5 36984682 36984682 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.1502C>T p.Pro501Leu p.P501L ENST00000282516 10/47 95 81 14 161 161 0 strelka-varscan-mutect NIPBL,missense_variant,p.Pro501Leu,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Pro501Leu,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,; T ENST00000282516 Transcript missense_variant 2001/10435 1502/8415 501/2804 P/L cCt/cTt 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 deleterious_low_confidence(0) 10/47 MODERATE 1 SNV 1 1 PASS . . 0 197 9 4 0 0 0 0 -19.99877 0.9956495 1 1 1 0 T 3 4 27 36984682 36984682 C T 1 0 0 0 0 1 0 0 0 10463 681 24 3 3 NIPBL 5 36984682 Missense_Mutation SNP C C3L-01862_T 36984682 144553577 43 7564 CWC27 0 . GRCh38 5 64801301 64801301 + Splice_Site SNP G G T novel C3L-01862_T C3L-01862_N G G c.750-1G>T p.X250_splice ENST00000381070 84 68 16 149 149 0 strelka-varscan-mutect CWC27,splice_acceptor_variant,,ENST00000508024,NM_001297645.1;CWC27,splice_acceptor_variant,,ENST00000381070,NM_001297644.1,NM_005869.3;CWC27,splice_acceptor_variant,,ENST00000506168,; T ENST00000381070 Transcript splice_acceptor_variant -/2078 750/1419 250/472 1 1 CWC27 HGNC HGNC:10664 protein_coding YES CCDS3982.2 ENSP00000370460 Q6UX04 UPI0000048ECC NM_001297644.1,NM_005869.3 8/13 HIGH 1 SNV 1 1 PASS . . 4 196 10 0 0 0 0 0 -20 0.9999874 1 1 1 0 T 5 4 27 64801301 64801301 G T 1 0 0 0 0 0 0 1 0 3880 1043 36 2 2 CWC27 5 64801301 Splice_Site SNP G C3L-01862_T 27816619 64801301 116736958 44 7565 VCAN 0 . GRCh38 5 83537810 83537810 + Missense_Mutation SNP C C G novel C3L-01862_T C3L-01862_N C C c.4807C>G p.Leu1603Val p.L1603V ENST00000265077 8/15 332 287 45 442 442 0 strelka-varscan-mutect VCAN,missense_variant,p.Leu1603Val,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Leu616Val,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Leu616Val,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; G ENST00000265077 Transcript missense_variant 5372/12625 4807/10191 1603/3396 L/V Cta/Gta 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.23) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 83537810 83537810 C G 1 0 0 0 0 1 0 0 0 17683 680 24 4 4 VCAN 5 83537810 Missense_Mutation SNP C C3L-01862_T 18736509 83537810 98000449 45 7566 ADGRV1 0 . GRCh38 5 90756474 90756474 + Missense_Mutation SNP G G C novel C3L-01862_T C3L-01862_N G G c.11601G>C p.Glu3867Asp p.E3867D ENST00000405460 56/90 60 52 8 120 120 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Glu3867Asp,ENST00000405460,NM_032119.3;ADGRV1,missense_variant,p.Glu1433Asp,ENST00000509621,; C ENST00000405460 Transcript missense_variant 11697/19338 11601/18921 3867/6306 E/D gaG/gaC 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 tolerated(0.27) 56/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -18.3936 1 1 1 1 0 C 3 2 27 90756474 90756474 G C 1 0 0 0 0 1 0 0 0 379 991 35 4 4 ADGRV1 5 90756474 Missense_Mutation SNP G C3L-01862_T 7218664 90756474 90781785 46 7567 MCTP1 0 . GRCh38 5 94894778 94894778 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1710G>T p.Gln570His p.Q570H ENST00000515393 11/23 82 75 7 54 54 0 strelka-varscan-mutect MCTP1,missense_variant,p.Gln570His,ENST00000515393,NM_024717.5;MCTP1,missense_variant,p.Gln303His,ENST00000429576,NM_001297777.1;MCTP1,missense_variant,p.Gln86His,ENST00000505078,;MCTP1,missense_variant,p.Gln171His,ENST00000506568,;MCTP1,missense_variant,p.Gln349His,ENST00000312216,NM_001002796.3;MCTP1,missense_variant,p.Gln290His,ENST00000508509,;MCTP1,missense_variant,p.Gln349His,ENST00000505208,;MCTP1,missense_variant,p.Gln231His,ENST00000512425,; A ENST00000515393 Transcript missense_variant 1710/5396 1710/3000 570/999 Q/H caG/caT 1 -1 MCTP1 HGNC HGNC:26183 protein_coding YES CCDS34203.1 ENSP00000424126 Q6DN14 UPI0000D6165C NM_024717.5 tolerated(0.11) 11/23 Low_complexity_(Seg):seg,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF56,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -11.69508 0.9999797 1 1 1 0 A 3 1 27 94894778 94894778 C A 1 0 0 0 0 1 0 0 0 9336 796 28 2 2 MCTP1 5 94894778 Missense_Mutation SNP C C3L-01862_T 4138304 94894778 86643481 47 7568 SPOCK1 0 . GRCh38 5 137067742 137067742 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.562C>A p.Pro188Thr p.P188T ENST00000394945 6/11 180 142 38 166 166 0 strelka-varscan-mutect SPOCK1,missense_variant,p.Pro188Thr,ENST00000394945,NM_004598.3;SPOCK1,missense_variant,p.Pro126Thr,ENST00000282223,;SPOCK1,missense_variant,p.Pro43Thr,ENST00000510689,;SPOCK1,non_coding_transcript_exon_variant,,ENST00000635347,; T ENST00000394945 Transcript missense_variant 732/4846 562/1320 188/439 P/T Cca/Aca 1 -1 SPOCK1 HGNC HGNC:11251 protein_coding YES CCDS4191.1 ENSP00000378401 Q08629 UPI0000136F50 NM_004598.3 tolerated(1) 6/11 hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 137067742 137067742 G T 1 0 0 0 0 1 0 0 0 15432 1203 42 2 2 SPOCK1 5 137067742 Missense_Mutation SNP G C3L-01862_T 42172964 137067742 44470517 48 7569 PCDHA13 0 . GRCh38 5 140883002 140883002 + Missense_Mutation SNP C C G novel C3L-01862_T C3L-01862_N C C c.734C>G p.Ser245Cys p.S245C ENST00000289272 1/4 175 148 27 240 240 0 strelka-varscan-mutect PCDHA13,missense_variant,p.Ser245Cys,ENST00000289272,NM_018904.2;PCDHA13,missense_variant,p.Ser245Cys,ENST00000409494,;PCDHA13,missense_variant,p.Ser245Cys,ENST00000617769,NM_031865.1;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;AC005609.17,upstream_gene_variant,,ENST00000625195,; G ENST00000289272 Transcript missense_variant 734/5260 734/2853 245/950 S/C tCc/tGc 1 1 PCDHA13 HGNC HGNC:8667 protein_coding YES CCDS4240.1 ENSP00000289272 Q9Y5I0 UPI00001273D6 NM_018904.2 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 140883002 140883002 C G 1 0 0 0 0 1 0 0 0 11610 855 30 4 4 PCDHA13 5 140883002 Missense_Mutation SNP C C3L-01862_T 3815260 140883002 40655257 49 7570 PCDHGA4 0 . GRCh38 5 141355593 141355593 + Silent SNP C C A rs770322971 C3L-01862_T C3L-01862_N C C c.486C>A p.= p.P162P ENST00000571252 1/4 140 115 25 199 197 2 strelka-varscan-mutect PCDHGA4,synonymous_variant,p.=,ENST00000571252,NM_018917.3;PCDHGA4,synonymous_variant,p.=,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;AC005618.8,upstream_gene_variant,,ENST00000625053,;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000571252 Transcript synonymous_variant 569/4778 486/2889 162/962 P ccC/ccA rs770322971 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs770322971 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 141355593 141355593 C A 1 0 0 0 0 0 0 0 1 11643 581 21 2 2 PCDHGA4 5 141355593 Silent SNP C C3L-01862_T 472591 141355593 40182666 50 7571 CSF1R 0 . GRCh38 5 150080803 150080803 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.271C>A p.Leu91Met p.L91M ENST00000286301 3/22 239 198 41 239 239 0 strelka-varscan-mutect CSF1R,missense_variant,p.Leu91Met,ENST00000286301,NM_001288705.1,NM_005211.3;CSF1R,missense_variant,p.Leu91Met,ENST00000543093,;CSF1R,5_prime_UTR_variant,,ENST00000511344,;CSF1R,missense_variant,p.Leu91Met,ENST00000504875,;CSF1R,non_coding_transcript_exon_variant,,ENST00000502660,; T ENST00000286301 Transcript missense_variant 563/3989 271/2919 91/972 L/M Ctg/Atg 1 -1 CSF1R HGNC HGNC:2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 UPI000004984A NM_001288705.1,NM_005211.3 tolerated(0.14) 3/22 hmmpanther:PTHR24416:SF47,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000615,Gene3D:2.60.40.10,PIRSF_domain:PIRSF500947,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 150080803 150080803 G T 1 0 0 0 0 1 0 0 0 3733 991 35 2 2 CSF1R 5 150080803 Missense_Mutation SNP G C3L-01862_T 8725210 150080803 31457456 51 7572 ARSI 0 . GRCh38 5 150297925 150297925 + Silent SNP C C A novel C3L-01862_T C3L-01862_N C C c.999G>T p.= p.L333L ENST00000328668 2/2 98 85 13 113 113 0 strelka-varscan-mutect ARSI,synonymous_variant,p.=,ENST00000328668,NM_001012301.2;ARSI,synonymous_variant,p.=,ENST00000515301,;ARSI,downstream_gene_variant,,ENST00000509146,; A ENST00000328668 Transcript synonymous_variant 1579/3161 999/1710 333/569 L ctG/ctT 1 -1 ARSI HGNC HGNC:32521 protein_coding YES CCDS34275.1 ENSP00000333395 Q5FYB1 UPI000003FD83 NM_001012301.2 2/2 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF68,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS rs1170814129 . 0 201 8 0 0 0 0 0 -20 0.9999974 1 1 1 0 A 2 1 27 150297925 150297925 C A 1 0 0 0 0 0 0 0 1 1137 697 25 2 2 ARSI 5 150297925 Silent SNP C C3L-01862_T 217122 150297925 31240334 52 7573 FAM71B 0 . GRCh38 5 157163188 157163188 + Silent SNP C C T rs369213663 C3L-01862_T C3L-01862_N C C c.1077G>A p.= p.S359S ENST00000302938 2/2 145 128 17 220 220 0 strelka-varscan-mutect FAM71B,synonymous_variant,p.=,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; T ENST00000302938 Transcript synonymous_variant 1173/2515 1077/1818 359/605 S tcG/tcA rs369213663,COSM260817 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 0,1 LOW 1 SNV 1 0,1 1 PASS rs369213663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 157163188 157163188 C T 1 0 0 0 0 0 0 0 1 5472 871 31 1 1 FAM71B 5 157163188 Silent SNP C C3L-01862_T 6865263 157163188 24375071 53 7574 TRIM7 0 . GRCh38 5 181195364 181195364 + Silent SNP G G C novel C3L-01862_T C3L-01862_N G G c.1338C>G p.= p.T446T ENST00000274773 7/7 116 102 14 116 115 1 strelka-varscan-mutect TRIM7,synonymous_variant,p.=,ENST00000393315,NM_203294.1,NM_203296.1;TRIM7,synonymous_variant,p.=,ENST00000274773,NM_203293.2;TRIM7,synonymous_variant,p.=,ENST00000393319,NM_203297.1;TRIM7,synonymous_variant,p.=,ENST00000422067,NM_203295.1;CTC-338M12.2,upstream_gene_variant,,ENST00000513771,;CTC-338M12.6,upstream_gene_variant,,ENST00000511517,;CTC-338M12.6,upstream_gene_variant,,ENST00000509080,;CTC-338M12.6,upstream_gene_variant,,ENST00000502812,;CTC-338M12.6,upstream_gene_variant,,ENST00000512508,;CTC-338M12.5,downstream_gene_variant,,ENST00000508877,;CTC-338M12.6,upstream_gene_variant,,ENST00000419707,;CTC-338M12.5,downstream_gene_variant,,ENST00000514487,;TRIM7,non_coding_transcript_exon_variant,,ENST00000504241,; C ENST00000274773 Transcript synonymous_variant 1400/2840 1338/1536 446/511 T acC/acG 1 -1 TRIM7 HGNC HGNC:16278 protein_coding YES CCDS4462.1 ENSP00000274773 Q9C029 UPI000006D24A NM_203293.2 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF361,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 197 11 2 0 0 0 0 -19.98616 0.9983714 1 1 1 0 C 2 2 27 181195364 181195364 G C 1 0 0 0 0 0 0 0 1 17039 1335 47 4 4 TRIM7 5 181195364 Silent SNP G C3L-01862_T 24032176 181195364 342895 54 7575 OR10C1 0 . GRCh38 6 29440174 29440175 + Frame_Shift_Ins INS - - T novel C3L-01862_T C3L-01862_N - - c.159_160insT p.Leu54SerfsTer67 p.L54Sfs*67 ENST00000444197 1/1 238 192 46 281 281 0 sindel-varindel OR10C1,frameshift_variant,p.Leu54SerfsTer67,ENST00000444197,NM_013941.3;OR10C1,frameshift_variant,p.Leu56SerfsTer67,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript frameshift_variant 869-870/1649 159-160/939 53-54/312 -/X -/T 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321 HIGH 1 insertion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 27 29440174 29440174 - T 1 0 1 1 0 0 0 0 0 10973 610 22 0 0 OR10C1 6 29440174 Frame_Shift_Ins INS - C3L-01862_T 29440174 141365805 55 7576 ZFP57 0 . GRCh38 6 29673172 29673172 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.939G>T p.Arg313Ser p.R313S ENST00000488757 4/4 206 168 38 304 303 1 strelka-varscan-mutect ZFP57,missense_variant,p.Arg293Ser,ENST00000376883,;ZFP57,missense_variant,p.Arg313Ser,ENST00000488757,NM_001109809.2;ZFP57,missense_variant,p.Arg229Ser,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.3;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.3;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.5;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.4;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.3;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.3;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.2;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.2;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.1;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,; A ENST00000488757 Transcript missense_variant 1090/1870 939/1611 313/536 R/S agG/agT 1 -1 ZFP57 HGNC HGNC:18791 protein_coding YES CCDS43436.2 ENSP00000418259 Q9NU63 UPI0001951170 NM_001109809.2 tolerated(0.46) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 29673172 29673172 C A 1 0 0 0 0 1 0 0 0 18226 506 18 2 2 ZFP57 6 29673172 Missense_Mutation SNP C C3L-01862_T 232998 29673172 141132807 56 7577 PTCHD4 0 . GRCh38 6 47879225 47879225 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1619G>T p.Arg540Ile p.R540I ENST00000339488 3/3 134 107 27 207 207 0 strelka-varscan-mutect PTCHD4,missense_variant,p.Arg540Ile,ENST00000339488,NM_001013732.3; A ENST00000339488 Transcript missense_variant 1653/2850 1619/2541 540/846 R/I aGa/aTa 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 tolerated(0.06) 3/3 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 47879225 47879225 C A 1 0 0 0 0 1 0 0 0 12887 913 32 2 2 PTCHD4 6 47879225 Missense_Mutation SNP C C3L-01862_T 18206053 47879225 122926754 57 7578 LAMA4 0 . GRCh38 6 112119195 112119195 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.4782G>T p.Leu1594Phe p.L1594F ENST00000230538 34/39 454 386 68 423 423 0 strelka-varscan-mutect LAMA4,missense_variant,p.Leu1594Phe,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Leu1587Phe,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Leu1587Phe,ENST00000389463,;LAMA4,missense_variant,p.Leu1587Phe,ENST00000424408,;LAMA4,downstream_gene_variant,,ENST00000604740,;LAMA4,downstream_gene_variant,,ENST00000521693,; A ENST00000230538 Transcript missense_variant 5180/6547 4782/5472 1594/1823 L/F ttG/ttT 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0) 34/39 PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 112119195 112119195 C A 1 0 0 0 0 1 0 0 0 8512 593 21 2 2 LAMA4 6 112119195 Missense_Mutation SNP C C3L-01862_T 64239970 112119195 58686784 58 7579 SMOC2 0 . GRCh38 6 168509952 168509952 + Missense_Mutation SNP G G T rs746350725 C3L-01862_T C3L-01862_N G G c.122G>T p.Ser41Ile p.S41I ENST00000354536 2/13 150 122 28 150 150 0 strelka-varscan-mutect SMOC2,missense_variant,p.Ser41Ile,ENST00000354536,NM_022138.2;SMOC2,missense_variant,p.Ser41Ile,ENST00000356284,NM_001166412.1; T ENST00000354536 Transcript missense_variant 342/3150 122/1374 41/457 S/I aGc/aTc rs746350725 1 1 SMOC2 HGNC HGNC:20323 protein_coding YES CCDS5307.1 ENSP00000346537 Q9H3U7 UPI0000072A56 NM_022138.2 tolerated(0.06) 2/13 PROSITE_profiles:PS51465,hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF14,SMART_domains:SM00280,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS rs746350725 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 168509952 168509952 G T 1 0 0 0 0 1 0 0 0 15123 971 34 2 2 SMOC2 6 168509952 Missense_Mutation SNP G C3L-01862_T 56390757 168509952 2296027 59 7580 TNRC18 0 . GRCh38 7 5361697 5361697 + Missense_Mutation SNP T T G novel C3L-01862_T C3L-01862_N T T c.4558A>C p.Ser1520Arg p.S1520R ENST00000430969 14/30 173 151 22 163 163 0 strelka-varscan-mutect TNRC18,missense_variant,p.Ser1520Arg,ENST00000399537,;TNRC18,missense_variant,p.Ser1520Arg,ENST00000430969,NM_001080495.2;TNRC18,intron_variant,,ENST00000440081,; G ENST00000430969 Transcript missense_variant 4907/10562 4558/8907 1520/2968 S/R Agc/Cgc 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious(0.01) 14/30 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF21 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 5361697 5361697 T G 1 0 0 0 0 1 0 0 0 16812 1609 56 5 5 TNRC18 7 5361697 Missense_Mutation SNP T C3L-01862_T 5361697 153984276 60 7581 CDK13 0 . GRCh38 7 40001947 40001947 + Missense_Mutation SNP C C T rs549473641 C3L-01862_T C3L-01862_N C C c.2269C>T p.Arg757Trp p.R757W ENST00000181839 5/14 253 223 30 288 288 0 strelka-varscan-mutect CDK13,missense_variant,p.Arg757Trp,ENST00000181839,NM_003718.4;CDK13,missense_variant,p.Arg757Trp,ENST00000340829,NM_031267.3;CDK13,missense_variant,p.Arg143Trp,ENST00000613626,;CDK13,missense_variant,p.Arg143Trp,ENST00000611390,;CDK13,non_coding_transcript_exon_variant,,ENST00000484589,; T ENST00000181839 Transcript missense_variant 2874/7298 2269/4539 757/1512 R/W Cgg/Tgg rs549473641,COSM5635517 1 1 CDK13 HGNC HGNC:1733 protein_coding YES CCDS5461.1 ENSP00000181839 Q14004 A0A024RA85 UPI000013C5E3 NM_003718.4 deleterious(0) 5/14 PROSITE_profiles:PS50011,hmmpanther:PTHR24056:SF125,hmmpanther:PTHR24056,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs549473641 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 40001947 40001947 C T 1 0 0 0 0 1 0 0 0 2833 643 23 1 1 CDK13 7 40001947 Missense_Mutation SNP C C3L-01862_T 34640250 40001947 119344026 61 7582 ZNF716 0 . GRCh38 7 57469653 57469653 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1192C>A p.His398Asn p.H398N ENST00000420713 4/4 253 217 36 392 390 2 strelka-varscan-mutect ZNF716,missense_variant,p.His398Asn,ENST00000420713,NM_001159279.1; A ENST00000420713 Transcript missense_variant 1304/5197 1192/1488 398/495 H/N Cac/Aac 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 57469653 57469653 C A 1 0 0 0 0 1 0 0 0 18694 594 21 2 2 ZNF716 7 57469653 Missense_Mutation SNP C C3L-01862_T 17467706 57469653 101876320 62 7583 GATAD1 0 . GRCh38 7 92456487 92456487 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.735G>A p.= p.E245E ENST00000287957 5/5 208 180 28 201 201 0 strelka-varscan-mutect GATAD1,synonymous_variant,p.=,ENST00000287957,NM_021167.4;AC007566.10,upstream_gene_variant,,ENST00000427458,;GATAD1,non_coding_transcript_exon_variant,,ENST00000493878,;GATAD1,non_coding_transcript_exon_variant,,ENST00000465247,; A ENST00000287957 Transcript synonymous_variant 1012/3361 735/810 245/269 E gaG/gaA 1 1 GATAD1 HGNC HGNC:29941 protein_coding YES CCDS5625.1 ENSP00000287957 Q8WUU5 UPI000006FF00 NM_021167.4 5/5 hmmpanther:PTHR13340 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 92456487 92456487 G A 1 0 0 0 0 0 0 0 1 6129 933 33 3 3 GATAD1 7 92456487 Silent SNP G C3L-01862_T 34986834 92456487 66889486 63 7584 ZAN 0 . GRCh38 7 100736824 100736824 + Missense_Mutation SNP A A T rs763870641 C3L-01862_T C3L-01862_N A A c.269A>T p.His90Leu p.H90L ENST00000613979 5/48 131 114 17 218 218 0 strelka-varscan-mutect ZAN,missense_variant,p.His90Leu,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.His90Leu,ENST00000618565,;ZAN,missense_variant,p.His90Leu,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.His90Leu,ENST00000546292,;ZAN,missense_variant,p.His90Leu,ENST00000542585,;ZAN,missense_variant,p.His90Leu,ENST00000538115,;ZAN,missense_variant,p.His90Leu,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; T ENST00000613979 Transcript missense_variant 434/8669 269/8439 90/2812 H/L cAt/cTt rs763870641 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 tolerated(0.18) 5/48 Pfam_domain:PF00629,PROSITE_profiles:PS50060,SMART_domains:SM00137,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs763870641 . 8 201 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 100736824 100736824 A T 1 0 0 0 0 1 0 0 0 18074 217 8 4 4 ZAN 7 100736824 Missense_Mutation SNP A C3L-01862_T 8280337 100736824 58609149 64 7585 WNT16 0 . GRCh38 7 121331741 121331741 + Missense_Mutation SNP G G C novel C3L-01862_T C3L-01862_N G G c.410G>C p.Arg137Thr p.R137T ENST00000222462 3/4 252 205 47 283 283 0 strelka-varscan-mutect WNT16,missense_variant,p.Arg137Thr,ENST00000222462,NM_057168.1;WNT16,missense_variant,p.Arg127Thr,ENST00000361301,NM_016087.2; C ENST00000222462 Transcript missense_variant 700/3147 410/1098 137/365 R/T aGg/aCg 1 1 WNT16 HGNC HGNC:16267 protein_coding YES CCDS5781.1 ENSP00000222462 Q9UBV4 UPI000005104C NM_057168.1 tolerated(0.12) 3/4 Pfam_domain:PF00110,Prints_domain:PR01349,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF70,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 121331741 121331741 G C 1 0 0 0 0 1 0 0 0 17941 1000 35 4 4 WNT16 7 121331741 Missense_Mutation SNP G C3L-01862_T 20594917 121331741 38014232 65 7586 CNTNAP2 0 . GRCh38 7 147043988 147043988 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.484G>T p.Val162Leu p.V162L ENST00000361727 4/24 485 401 84 469 468 1 strelka-varscan-mutect CNTNAP2,missense_variant,p.Val162Leu,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,;CNTNAP2,upstream_gene_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637555,; T ENST00000361727 Transcript missense_variant 1002/9896 484/3996 162/1331 V/L Gtg/Ttg 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(0.7) 4/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00231,Superfamily_domains:SSF49785,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 147043988 147043988 G T 1 0 0 0 0 1 0 0 0 3428 1029 36 2 2 CNTNAP2 7 147043988 Missense_Mutation SNP G C3L-01862_T 25712247 147043988 12301985 66 7587 PTPRN2 0 . GRCh38 7 158133691 158133691 + Silent SNP G G A rs201964824 C3L-01862_T C3L-01862_N G G c.1542C>T p.= p.I514I ENST00000389418 9/23 28 21 7 50 49 1 strelka-varscan-mutect PTPRN2,synonymous_variant,p.=,ENST00000389413,NM_130843.2;PTPRN2,synonymous_variant,p.=,ENST00000409483,NM_001308267.1;PTPRN2,synonymous_variant,p.=,ENST00000389418,NM_001308268.1,NM_002847.3;PTPRN2,synonymous_variant,p.=,ENST00000389416,NM_130842.2;PTPRN2,synonymous_variant,p.=,ENST00000404321,; A ENST00000389418 Transcript synonymous_variant 1552/4706 1542/3048 514/1015 I atC/atT rs201964824,COSM289758,COSM3636794 1 -1 PTPRN2 HGNC HGNC:9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 UPI000002E7C7 NM_001308268.1,NM_002847.3 9/23 Pfam_domain:PF11548,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF266 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs201964824 . 0 207 3 0 0 0 0 0 -19.15377 1 1 1 1 0 A 2 1 27 158133691 158133691 G A 1 0 0 0 0 0 0 0 1 12962 1048 37 1 1 PTPRN2 7 158133691 Silent SNP G C3L-01862_T 11089703 158133691 1212282 67 7588 VPS37A 0 . GRCh38 8 17274927 17274927 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.611T>C p.Leu204Ser p.L204S ENST00000324849 5/12 123 101 22 185 185 0 strelka-varscan-mutect VPS37A,missense_variant,p.Leu204Ser,ENST00000324849,NM_152415.2;VPS37A,missense_variant,p.Leu179Ser,ENST00000521829,NM_001145152.1;VPS37A,upstream_gene_variant,,ENST00000521976,;VPS37A,missense_variant,p.Leu204Ser,ENST00000520140,;VPS37A,3_prime_UTR_variant,,ENST00000425020,; C ENST00000324849 Transcript missense_variant 1285/4906 611/1194 204/397 L/S tTa/tCa 1 1 VPS37A HGNC HGNC:24928 protein_coding YES CCDS6001.1 ENSP00000318629 Q8NEZ2 UPI0000039EC3 NM_152415.2 tolerated(0.27) 5/12 hmmpanther:PTHR13678,hmmpanther:PTHR13678:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 17274927 17274927 T C 1 0 0 0 0 1 0 0 0 17751 1764 61 5 5 VPS37A 8 17274927 Missense_Mutation SNP T C3L-01862_T 17274927 127863709 68 7589 CCAR2 0 . GRCh38 8 22614997 22614997 + Nonsense_Mutation SNP A A T novel C3L-01862_T C3L-01862_N A A c.1201A>T p.Lys401Ter p.K401* ENST00000308511 11/21 64 53 11 80 79 1 strelka-varscan-mutect CCAR2,stop_gained,p.Lys401Ter,ENST00000308511,;CCAR2,stop_gained,p.Lys401Ter,ENST00000389279,NM_021174.5;CCAR2,stop_gained,p.Lys76Ter,ENST00000520861,;CCAR2,stop_gained,p.Lys93Ter,ENST00000520738,;CCAR2,stop_gained,p.Lys219Ter,ENST00000522599,;CCAR2,upstream_gene_variant,,ENST00000613179,;RP11-582J16.5,non_coding_transcript_exon_variant,,ENST00000521025,;CCAR2,upstream_gene_variant,,ENST00000520536,;CCAR2,upstream_gene_variant,,ENST00000521436,;CCAR2,downstream_gene_variant,,ENST00000521020,; T ENST00000308511 Transcript stop_gained 1450/4853 1201/2772 401/923 K/* Aag/Tag 1 1 CCAR2 HGNC HGNC:23360 protein_coding YES CCDS34863.1 ENSP00000310670 Q8N163 UPI0000070A46 11/21 Pfam_domain:PF14443,hmmpanther:PTHR14304,hmmpanther:PTHR14304:SF12,SMART_domains:SM01122 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 27 22614997 22614997 A T 1 0 0 0 0 0 1 0 0 2432 144 5 4 4 CCAR2 8 22614997 Nonsense_Mutation SNP A C3L-01862_T 5340070 22614997 122523639 69 7590 EYA1 0 . GRCh38 8 71271878 71271878 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.846C>A p.Ser282Arg p.S282R ENST00000340726 10/18 501 412 89 581 577 4 strelka-varscan-mutect EYA1,missense_variant,p.Ser282Arg,ENST00000340726,NM_000503.5;EYA1,missense_variant,p.Ser276Arg,ENST00000303824,NM_001288575.1,NM_001288574.1;EYA1,missense_variant,p.Ser282Arg,ENST00000388742,NM_172058.3;EYA1,missense_variant,p.Ser249Arg,ENST00000388740,NM_172060.3;EYA1,missense_variant,p.Ser248Arg,ENST00000388741,;EYA1,missense_variant,p.Ser281Arg,ENST00000388743,;EYA1,missense_variant,p.Ser277Arg,ENST00000419131,NM_172059.3;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,5_prime_UTR_variant,,ENST00000493349,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,; T ENST00000340726 Transcript missense_variant 1486/4326 846/1779 282/592 S/R agC/agA 1 -1 EYA1 HGNC HGNC:3519 protein_coding YES CCDS34906.1 ENSP00000342626 Q99502 A0A024R813 UPI000012A3B3 NM_000503.5 tolerated(0.07) 10/18 hmmpanther:PTHR10190,hmmpanther:PTHR10190:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 71271878 71271878 G T 1 0 0 0 0 1 0 0 0 5196 1194 42 2 2 EYA1 8 71271878 Missense_Mutation SNP G C3L-01862_T 48656881 71271878 73866758 70 7591 MMP16 0 . GRCh38 8 88041695 88041695 + Missense_Mutation SNP C C A C3L-01862_T C3L-01862_N C C c.1590G>T p.Met530Ile p.M530I ENST00000286614 10/10 209 168 41 287 287 0 strelka-varscan-mutect MMP16,missense_variant,p.Met530Ile,ENST00000286614,NM_005941.4; A ENST00000286614 Transcript missense_variant 1872/11558 1590/1824 530/607 M/I atG/atT COSM2790060,COSM5294083 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 deleterious(0) 10/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00045,SMART_domains:SM00120,Superfamily_domains:SSF50923 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 88041695 88041695 C A 1 0 0 0 0 1 0 0 0 9618 594 21 2 2 MMP16 8 88041695 Missense_Mutation SNP C C3L-01862_T 16769817 88041695 57096941 71 7592 MMP16 0 . GRCh38 8 88056160 88056160 + Missense_Mutation SNP G G C rs200751407 C3L-01862_T C3L-01862_N G G c.1341C>G p.Asp447Glu p.D447E ENST00000286614 8/10 98 81 17 125 125 0 strelka-varscan-mutect MMP16,missense_variant,p.Asp447Glu,ENST00000286614,NM_005941.4; C ENST00000286614 Transcript missense_variant 1623/11558 1341/1824 447/607 D/E gaC/gaG rs200751407,COSM2790078 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 tolerated(0.08) 8/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00045,SMART_domains:SM00120,Superfamily_domains:SSF50923 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200751407 . 0 204 4 2 0 0 0 0 -20 0.9999873 1 1 1 0 C 3 2 27 88056160 88056160 G C 1 0 0 0 0 1 0 0 0 9618 1136 40 4 4 MMP16 8 88056160 Missense_Mutation SNP G C3L-01862_T 14465 88056160 57082476 72 7593 RUNX1T1 0 . GRCh38 8 91986315 91986315 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1265G>T p.Cys422Phe p.C422F ENST00000436581 9/12 214 182 32 243 243 0 strelka-varscan-mutect RUNX1T1,missense_variant,p.Cys363Phe,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.Cys363Phe,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.Cys363Phe,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.Cys363Phe,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.Cys422Phe,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.Cys336Phe,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.Cys343Phe,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.Cys363Phe,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.Cys336Phe,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.Cys336Phe,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.Cys326Phe,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.Cys326Phe,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.Cys374Phe,ENST00000520724,NM_001198634.1;RUNX1T1,missense_variant,p.Cys63Phe,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,downstream_gene_variant,,ENST00000518361,; A ENST00000436581 Transcript missense_variant 1452/7454 1265/1992 422/663 C/F tGc/tTc 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 deleterious(0) 9/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,Pfam_domain:PF08788 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 91986315 91986315 C A 1 0 0 0 0 1 0 0 0 14008 710 25 2 2 RUNX1T1 8 91986315 Missense_Mutation SNP C C3L-01862_T 3930155 91986315 53152321 73 7594 VPS13B 0 . GRCh38 8 99818864 99818864 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.8672T>A p.Val2891Glu p.V2891E ENST00000358544 47/62 350 297 53 401 401 0 strelka-varscan-mutect VPS13B,missense_variant,p.Val2891Glu,ENST00000358544,NM_017890.4;VPS13B,missense_variant,p.Val2866Glu,ENST00000357162,NM_152564.4; A ENST00000358544 Transcript missense_variant 8783/14094 8672/12069 2891/4022 V/E gTa/gAa 1 1 VPS13B HGNC HGNC:2183 protein_coding YES CCDS6280.1 ENSP00000351346 Q7Z7G8 UPI00001D2D35 NM_017890.4 deleterious(0.01) 47/62 hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 99818864 99818864 T A 1 0 0 0 0 1 0 0 0 17737 1638 57 4 4 VPS13B 8 99818864 Missense_Mutation SNP T C3L-01862_T 7832549 99818864 45319772 74 7595 CSMD3 0 . GRCh38 8 112859195 112859195 + Missense_Mutation SNP C C T C3L-01862_T C3L-01862_N C C c.1705G>A p.Asp569Asn p.D569N ENST00000297405 11/71 299 266 33 339 339 0 strelka-varscan-mutect CSMD3,missense_variant,p.Asp569Asn,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Asp529Asn,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Asp465Asn,ENST00000455883,NM_052900.2; T ENST00000297405 Transcript missense_variant 1950/13212 1705/11124 569/3707 D/N Gac/Aac COSM5313257,COSM5313258,COSM5328062,COSM5328063 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.03) 11/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 112859195 112859195 C T 1 0 0 0 0 1 0 0 0 3747 826 29 3 3 CSMD3 8 112859195 Missense_Mutation SNP C C3L-01862_T 13040331 112859195 32279441 75 7596 EFR3A 0 . GRCh38 8 131968399 131968399 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.960G>T p.Glu320Asp p.E320D ENST00000254624 9/23 193 171 22 198 198 0 strelka-varscan-mutect EFR3A,missense_variant,p.Glu320Asp,ENST00000254624,NM_001323553.1,NM_001323557.1,NM_015137.4;EFR3A,missense_variant,p.Glu284Asp,ENST00000519656,NM_001323553.1,NM_001323556.1,NM_001323557.1;EFR3A,missense_variant,p.Glu347Asp,ENST00000637848,; T ENST00000254624 Transcript missense_variant 1185/5438 960/2466 320/821 E/D gaG/gaT 1 1 EFR3A HGNC HGNC:28970 protein_coding YES CCDS34942.2 ENSP00000254624 Q14156 UPI00001C1E8F NM_001323553.1,NM_001323557.1,NM_015137.4 tolerated(0.06) 9/23 Gene3D:1.25.10.10,hmmpanther:PTHR12444,hmmpanther:PTHR12444:SF1,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 131968399 131968399 G T 1 0 0 0 0 1 0 0 0 4794 991 35 2 2 EFR3A 8 131968399 Missense_Mutation SNP G C3L-01862_T 19109204 131968399 13170237 76 7597 ADGRB1 0 . GRCh38 8 142477486 142477486 + Frame_Shift_Del DEL G G - C3L-01862_T C3L-01862_N G G c.1328delG p.Gly443AlafsTer147 p.G443Afs*147 ENST00000517894 6/31 171 145 26 163 163 0 sindel-varindel-pindel ADGRB1,frameshift_variant,p.Gly443AlafsTer147,ENST00000517894,;ADGRB1,frameshift_variant,p.Gly443AlafsTer147,ENST00000323289,NM_001702.2;ADGRB1,frameshift_variant,p.Gly443AlafsTer147,ENST00000521208,;ADGRB1,upstream_gene_variant,,ENST00000518820,; - ENST00000517894 Transcript frameshift_variant 2218/6241 1324/4755 442/1584 G/X Ggg/gg COSM4613744 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 6/31 PROSITE_profiles:PS50092,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF39,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 HIGH 1 deletion 5 4 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 27 142477486 142477486 G - 1 0 1 0 1 0 0 0 0 355 1348 47 0 0 ADGRB1 8 142477486 Frame_Shift_Del DEL G C3L-01862_T 10509087 142477486 2661150 77 7598 BNC2 0 . GRCh38 9 16436039 16436039 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.2155G>A p.Glu719Lys p.E719K ENST00000380672 6/7 273 249 24 408 408 0 strelka-varscan-mutect BNC2,missense_variant,p.Glu719Lys,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Glu545Lys,ENST00000545497,;BNC2,missense_variant,p.Glu676Lys,ENST00000418777,;BNC2,missense_variant,p.Glu652Lys,ENST00000380667,;BNC2,missense_variant,p.Glu112Lys,ENST00000411752,;BNC2,downstream_gene_variant,,ENST00000380666,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,missense_variant,p.Glu719Lys,ENST00000484726,; T ENST00000380672 Transcript missense_variant 2213/12844 2155/3300 719/1099 E/K Gag/Aag 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 tolerated(0.14) 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 16436039 16436039 C T 1 0 0 0 0 1 0 0 0 1631 835 29 3 3 BNC2 9 16436039 Missense_Mutation SNP C C3L-01862_T 16436039 121958678 78 7599 SLC24A2 0 . GRCh38 9 19786341 19786341 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.526G>A p.Gly176Arg p.G176R ENST00000341998 1/10 443 378 65 516 516 0 strelka-varscan-mutect SLC24A2,missense_variant,p.Gly176Arg,ENST00000341998,NM_020344.3;SLC24A2,missense_variant,p.Gly176Arg,ENST00000286344,NM_001193288.2; T ENST00000341998 Transcript missense_variant 588/10749 526/1986 176/661 G/R Gga/Aga 1 -1 SLC24A2 HGNC HGNC:10976 protein_coding YES CCDS6493.1 ENSP00000344801 Q9UI40 UPI000004FA46 NM_020344.3 deleterious(0) 1/10 hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF41,Pfam_domain:PF01699,TIGRFAM_domain:TIGR00367 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 19786341 19786341 C T 1 0 0 0 0 1 0 0 0 14732 603 21 3 3 SLC24A2 9 19786341 Missense_Mutation SNP C C3L-01862_T 3350302 19786341 118608376 79 7600 IFNA8 0 . GRCh38 9 21409210 21409210 + Missense_Mutation SNP G G C novel C3L-01862_T C3L-01862_N G G c.34G>C p.Val12Leu p.V12L ENST00000380205 1/1 211 174 37 262 262 0 strelka-varscan-mutect IFNA8,missense_variant,p.Val12Leu,ENST00000380205,NM_002170.3;IFNA1,missense_variant,p.Val12Leu,ENST00000613815,; C ENST00000380205 Transcript missense_variant 64/1039 34/570 12/189 V/L Gtg/Ctg 1 1 IFNA8 HGNC HGNC:5429 protein_coding YES CCDS6507.1 ENSP00000369553 P32881 UPI000002C35B NM_002170.3 tolerated(0.12) 1/1 hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF28,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 21409210 21409210 G C 1 0 0 0 0 1 0 0 0 7443 1029 36 4 4 IFNA8 9 21409210 Missense_Mutation SNP G C3L-01862_T 1622869 21409210 116985507 80 7601 PHF24 0 . GRCh38 9 34976634 34976634 + Missense_Mutation SNP C C A rs751086037 C3L-01862_T C3L-01862_N C C c.743C>A p.Ala248Glu p.A248E ENST00000242315 5/8 217 189 28 182 182 0 strelka-varscan-mutect PHF24,missense_variant,p.Ala248Glu,ENST00000242315,NM_001304333.1,NM_015297.2;PHF24,non_coding_transcript_exon_variant,,ENST00000476115,;PHF24,upstream_gene_variant,,ENST00000440503,; A ENST00000242315 Transcript missense_variant 825/5718 743/1203 248/400 A/E gCg/gAg rs751086037,COSM1108532 1 1 PHF24 HGNC HGNC:29180 protein_coding YES CCDS43796.1 ENSP00000242315 Q9UPV7 UPI00001C1EB1 NM_001304333.1,NM_015297.2 tolerated(0.29) 5/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10891:SF579,hmmpanther:PTHR10891,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751086037 . 0 206 0 2 2 0 0 0 -12.56948 0.9808404 1 1 1 0 A 3 1 27 34976634 34976634 C A 1 0 0 0 0 1 0 0 0 11922 768 27 1 1 PHF24 9 34976634 Missense_Mutation SNP C C3L-01862_T 13567424 34976634 103418083 81 7602 SPATA31D1 0 . GRCh38 9 81993979 81993979 + Nonsense_Mutation SNP C C A rs758789167 C3L-01862_T C3L-01862_N C C c.3509C>A p.Ser1170Ter p.S1170* ENST00000344803 4/4 197 172 25 252 252 0 strelka-varscan-mutect SPATA31D1,stop_gained,p.Ser1170Ter,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; A ENST00000344803 Transcript stop_gained 3556/4833 3509/4731 1170/1576 S/* tCa/tAa rs758789167 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 4/4 hmmpanther:PTHR21859:SF12,hmmpanther:PTHR21859 HIGH 1 SNV 2 1 PASS rs758789167 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 27 81993979 81993979 C A 1 0 0 0 0 0 1 0 0 15347 838 29 2 2 SPATA31D1 9 81993979 Nonsense_Mutation SNP C C3L-01862_T 47017345 81993979 56400738 82 7603 SECISBP2 0 . GRCh38 9 89358159 89358159 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.2429C>T p.Pro810Leu p.P810L ENST00000375807 16/17 369 301 68 380 380 0 strelka-varscan-mutect SECISBP2,missense_variant,p.Pro742Leu,ENST00000534113,NM_001282690.1;SECISBP2,missense_variant,p.Pro810Leu,ENST00000375807,NM_001282688.1,NM_024077.4;SECISBP2,missense_variant,p.Pro737Leu,ENST00000339901,NM_001282689.1;SEMA4D,downstream_gene_variant,,ENST00000420987,NM_001142287.1;SEMA4D,downstream_gene_variant,,ENST00000339861,;SEMA4D,downstream_gene_variant,,ENST00000455551,;SEMA4D,downstream_gene_variant,,ENST00000420101,;SEMA4D,downstream_gene_variant,,ENST00000469653,;SEMA4D,downstream_gene_variant,,ENST00000475255,;SECISBP2,downstream_gene_variant,,ENST00000496597,;SECISBP2,downstream_gene_variant,,ENST00000498819,;SEMA4D,downstream_gene_variant,,ENST00000429836,;SEMA4D,downstream_gene_variant,,ENST00000537934,;SEMA4D,downstream_gene_variant,,ENST00000492386,; T ENST00000375807 Transcript missense_variant 2500/3462 2429/2565 810/854 P/L cCa/cTa 1 1 SECISBP2 HGNC HGNC:30972 protein_coding YES CCDS6683.1 ENSP00000364965 Q96T21 UPI00001AEA0A NM_001282688.1,NM_024077.4 tolerated(0.55) 16/17 hmmpanther:PTHR13284,hmmpanther:PTHR13284:SF9 MODERATE 1 SNV 1 1 PASS rs1248757496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 89358159 89358159 C T 1 0 0 0 0 1 0 0 0 14283 594 21 3 3 SECISBP2 9 89358159 Missense_Mutation SNP C C3L-01862_T 7364180 89358159 49036558 83 7604 ABCA1 0 . GRCh38 9 104832573 104832573 + Splice_Site SNP C C A novel C3L-01862_T C3L-01862_N C C c.1509+1G>T p.X503_splice ENST00000374736 399 321 78 464 464 0 strelka-varscan-mutect ABCA1,splice_donor_variant,,ENST00000374736,NM_005502.3;ABCA1,upstream_gene_variant,,ENST00000494467,; A ENST00000374736 Transcript splice_donor_variant -/10494 1509/6786 503/2261 1 -1 ABCA1 HGNC HGNC:29 protein_coding YES CCDS6762.1 ENSP00000363868 O95477 UPI000013E441 NM_005502.3 12/49 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 27 104832573 104832573 C A 1 0 0 0 0 0 0 1 0 32 521 18 2 2 ABCA1 9 104832573 Splice_Site SNP C C3L-01862_T 15474414 104832573 33562144 84 7605 UGCG 0 . GRCh38 9 111914686 111914686 + Missense_Mutation SNP A A C novel C3L-01862_T C3L-01862_N A A c.180A>C p.Lys60Asn p.K60N ENST00000374279 2/9 242 209 33 268 268 0 strelka-varscan-mutect UGCG,missense_variant,p.Lys60Asn,ENST00000374279,NM_003358.2;UGCG,non_coding_transcript_exon_variant,,ENST00000495085,;UGCG,non_coding_transcript_exon_variant,,ENST00000490110,;UGCG,non_coding_transcript_exon_variant,,ENST00000489355,; C ENST00000374279 Transcript missense_variant 630/4007 180/1185 60/394 K/N aaA/aaC 1 1 UGCG HGNC HGNC:12524 protein_coding YES CCDS6782.1 ENSP00000363397 Q16739 A0A024R157 UPI0000052740 NM_003358.2 deleterious(0.03) 2/9 Gene3D:3.90.550.10,hmmpanther:PTHR12726,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 111914686 111914686 A C 1 0 0 0 0 1 0 0 0 17464 69 3 5 5 UGCG 9 111914686 Missense_Mutation SNP A C3L-01862_T 7082113 111914686 26480031 85 7606 GAPVD1 0 . GRCh38 9 125350335 125350335 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.3421G>T p.Asp1141Tyr p.D1141Y ENST00000394105 21/27 182 154 28 185 185 0 strelka-varscan-mutect GAPVD1,missense_variant,p.Asp1087Tyr,ENST00000470056,;GAPVD1,missense_variant,p.Asp1132Tyr,ENST00000394104,;GAPVD1,missense_variant,p.Asp1114Tyr,ENST00000297933,NM_001282680.1;GAPVD1,missense_variant,p.Asp1132Tyr,ENST00000495955,NM_001282679.1;GAPVD1,missense_variant,p.Asp1141Tyr,ENST00000394105,NM_015635.3;GAPVD1,missense_variant,p.Asp1066Tyr,ENST00000394083,;GAPVD1,missense_variant,p.Asp1093Tyr,ENST00000312123,NM_001282681.1;GAPVD1,non_coding_transcript_exon_variant,,ENST00000474637,;GAPVD1,upstream_gene_variant,,ENST00000467707,; T ENST00000394105 Transcript missense_variant 3581/5207 3421/4464 1141/1487 D/Y Gac/Tac 1 1 GAPVD1 HGNC HGNC:23375 protein_coding YES CCDS35138.1 ENSP00000377665 Q14C86 A0A024R8A2 UPI00001D76F1 NM_015635.3 deleterious(0) 21/27 hmmpanther:PTHR23101:SF68,hmmpanther:PTHR23101 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 125350335 125350335 G T 1 0 0 0 0 1 0 0 0 6107 1174 41 2 2 GAPVD1 9 125350335 Missense_Mutation SNP G C3L-01862_T 13435649 125350335 13044382 86 7607 KYAT1 0 . GRCh38 9 128838105 128838105 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.666C>T p.= p.Y222Y ENST00000436267 7/15 260 208 52 270 269 1 strelka-varscan-mutect KYAT1,synonymous_variant,p.=,ENST00000436267,NM_001287390.1;KYAT1,synonymous_variant,p.=,ENST00000302586,NM_001122671.1,NM_004059.4;KYAT1,synonymous_variant,p.=,ENST00000320665,NM_001122672.1;KYAT1,synonymous_variant,p.=,ENST00000451800,;KYAT1,synonymous_variant,p.=,ENST00000416084,;KYAT1,downstream_gene_variant,,ENST00000427720,;KYAT1,non_coding_transcript_exon_variant,,ENST00000483599,;KYAT1,non_coding_transcript_exon_variant,,ENST00000462722,;KYAT1,non_coding_transcript_exon_variant,,ENST00000474824,;KYAT1,upstream_gene_variant,,ENST00000466418,; A ENST00000436267 Transcript synonymous_variant 960/2487 666/1551 222/516 Y taC/taT 1 -1 KYAT1 HGNC HGNC:1564 protein_coding YES CCDS75915.1 ENSP00000399415 B7Z4W5 UPI0000EE5683 NM_001287390.1 7/15 hmmpanther:PTHR11751:SF349,hmmpanther:PTHR11751,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383 LOW 1 SNV 2 1 PASS rs1047703673 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 128838105 128838105 G A 1 0 0 0 0 0 0 0 1 8486 1140 40 1 1 KYAT1 9 128838105 Silent SNP G C3L-01862_T 3487770 128838105 9556612 87 7608 ABCA2 0 . GRCh38 9 137011957 137011957 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.5422G>T p.Ala1808Ser p.A1808S ENST00000341511 35/49 226 198 28 235 234 1 strelka-varscan-mutect ABCA2,missense_variant,p.Ala1808Ser,ENST00000265662,;ABCA2,missense_variant,p.Ala1807Ser,ENST00000371605,;ABCA2,missense_variant,p.Ala1838Ser,ENST00000614293,;ABCA2,missense_variant,p.Ala1808Ser,ENST00000341511,NM_001606.4,NM_212533.2;ABCA2,upstream_gene_variant,,ENST00000490486,;ABCA2,upstream_gene_variant,,ENST00000437791,;ABCA2,upstream_gene_variant,,ENST00000464157,;ABCA2,missense_variant,p.Ala1158Ser,ENST00000479446,;ABCA2,3_prime_UTR_variant,,ENST00000487109,;ABCA2,non_coding_transcript_exon_variant,,ENST00000459850,;ABCA2,non_coding_transcript_exon_variant,,ENST00000431584,;ABCA2,downstream_gene_variant,,ENST00000488535,;ABCA2,upstream_gene_variant,,ENST00000464520,;ABCA2,upstream_gene_variant,,ENST00000463603,; A ENST00000341511 Transcript missense_variant 5472/8063 5422/7311 1808/2436 A/S Gcc/Tcc 1 -1 ABCA2 HGNC HGNC:32 protein_coding YES CCDS43909.1 ENSP00000344155 Q9BZC7 UPI0000049F97 NM_001606.4,NM_212533.2 deleterious(0) 35/49 Transmembrane_helices:TMhelix,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF116,Pfam_domain:PF12698 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 137011957 137011957 C A 1 0 0 0 0 1 0 0 0 36 739 26 2 2 ABCA2 9 137011957 Missense_Mutation SNP C C3L-01862_T 8173852 137011957 1382760 88 7609 ALOX5 0 . GRCh38 10 45443798 45443798 + Silent SNP C C T novel C3L-01862_T C3L-01862_N C C c.1644C>T p.= p.S548S ENST00000374391 12/14 220 185 35 187 187 0 strelka-varscan-mutect ALOX5,synonymous_variant,p.=,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,synonymous_variant,p.=,ENST00000542434,NM_001256154.1;ALOX5,3_prime_UTR_variant,,ENST00000612635,;RP11-67C2.2,downstream_gene_variant,,ENST00000435635,;ALOX5,non_coding_transcript_exon_variant,,ENST00000498461,;ALOX5,non_coding_transcript_exon_variant,,ENST00000481117,;ALOX5,downstream_gene_variant,,ENST00000493336,;ALOX5,downstream_gene_variant,,ENST00000475300,; T ENST00000374391 Transcript synonymous_variant 1697/2506 1644/2025 548/674 S tcC/tcT 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 12/14 PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Gene3D:1.20.245.10,Pfam_domain:PF00305,Superfamily_domains:SSF48484 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 45443798 45443798 C T 1 0 0 0 0 0 0 0 1 640 639 23 1 1 ALOX5 10 45443798 Silent SNP C C3L-01862_T 45443798 88353624 89 7610 MYPN 0 . GRCh38 10 68121502 68121502 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.64G>A p.Ala22Thr p.A22T ENST00000358913 2/20 115 95 20 185 184 1 strelka-varscan-mutect MYPN,missense_variant,p.Ala22Thr,ENST00000358913,NM_032578.3;MYPN,missense_variant,p.Ala22Thr,ENST00000540630,NM_001256267.1;MYPN,missense_variant,p.Ala22Thr,ENST00000373675,;MYPN,5_prime_UTR_variant,,ENST00000613327,NM_001256268.1;MYPN,intron_variant,,ENST00000354393,; A ENST00000358913 Transcript missense_variant 552/6013 64/3963 22/1320 A/T Gct/Act 1 1 MYPN HGNC HGNC:23246 protein_coding YES CCDS7275.1 ENSP00000351790 Q86TC9 UPI00002288CF NM_032578.3 deleterious(0) 2/20 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 68121502 68121502 G A 1 0 0 0 0 1 0 0 0 10099 971 34 3 3 MYPN 10 68121502 Missense_Mutation SNP G C3L-01862_T 22677704 68121502 65675920 90 7611 CDH23 0 . GRCh38 10 71732355 71732355 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.4099T>A p.Phe1367Ile p.F1367I ENST00000224721 32/70 203 167 36 228 228 0 strelka-varscan-mutect CDH23,missense_variant,p.Phe1367Ile,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Phe1362Ile,ENST00000622827,;CDH23,missense_variant,p.Phe1362Ile,ENST00000616684,NM_001171930.1;CDH23,missense_variant,p.Phe1361Ile,ENST00000398809,;C10orf105,intron_variant,,ENST00000398786,NM_001168390.1;CDH23,non_coding_transcript_exon_variant,,ENST00000398792,; A ENST00000224721 Transcript missense_variant 4489/11139 4099/10080 1367/3359 F/I Ttc/Atc 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 deleterious(0) 32/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 71732355 71732355 T A 1 0 0 0 0 1 0 0 0 2811 1609 56 4 4 CDH23 10 71732355 Missense_Mutation SNP T C3L-01862_T 3610853 71732355 62065067 91 7612 C10orf54 0 . GRCh38 10 71751291 71751291 + Splice_Site SNP C C A novel C3L-01862_T C3L-01862_N C C c.899-1G>T p.X300_splice ENST00000394957 142 118 24 153 153 0 strelka-varscan-mutect C10orf54,splice_acceptor_variant,,ENST00000394957,NM_022153.1;C10orf54,splice_acceptor_variant,,ENST00000470317,;CDH23,intron_variant,,ENST00000224721,NM_022124.5;CDH23,intron_variant,,ENST00000622827,; A ENST00000394957 Transcript splice_acceptor_variant -/4689 899/936 300/311 1 -1 C10orf54 HGNC HGNC:30085 protein_coding YES CCDS31218.1 ENSP00000378409 Q9H7M9 UPI000004781D NM_022153.1 6/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 27 71751291 71751291 C A 1 0 0 0 0 0 0 1 0 1765 927 32 2 2 C10orf54 10 71751291 Splice_Site SNP C C3L-01862_T 18936 71751291 62046131 92 7613 RGR 0 . GRCh38 10 84258638 84258638 + Nonstop_Mutation SNP G G C rs776462561 C3L-01862_T C3L-01862_N G G c.887G>C p.Ter296SerextTer98 p.*296Sext*98 ENST00000359452 7/7 385 326 59 391 391 0 strelka-varscan-mutect RGR,stop_lost,p.Ter296SerextTer98,ENST00000359452,NM_002921.3,NM_001012720.1;RGR,stop_lost,p.Ter254SerextTer98,ENST00000358110,NM_001012722.1;RGR,non_coding_transcript_exon_variant,,ENST00000479725,;RGR,downstream_gene_variant,,ENST00000478727,;RGR,downstream_gene_variant,,ENST00000483660,;RGR,downstream_gene_variant,,ENST00000497161,;RGR,downstream_gene_variant,,ENST00000483744,;RGR,non_coding_transcript_exon_variant,,ENST00000483771,; C ENST00000359452 Transcript stop_lost 925/2247 887/888 296/295 */S tGa/tCa rs776462561 1 1 RGR HGNC HGNC:9990 protein_coding YES CCDS7374.1 ENSP00000352427 P47804 A0A0S2Z498 UPI0000072293 NM_002921.3,NM_001012720.1 7/7 HIGH 1 SNV 1 1 PASS rs776462561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 27 84258638 84258638 G C 1 0 0 0 0 0 0 0 0 13462 1285 45 4 4 RGR 10 84258638 Nonstop_Mutation SNP G C3L-01862_T 12507347 84258638 49538784 93 7614 TBC1D12 0 . GRCh38 10 94402850 94402850 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.237G>A p.= p.E79E ENST00000225235 1/13 118 93 25 155 155 0 strelka-varscan-mutect TBC1D12,synonymous_variant,p.=,ENST00000225235,NM_015188.1; A ENST00000225235 Transcript synonymous_variant 347/5272 237/2328 79/775 E gaG/gaA 1 1 TBC1D12 HGNC HGNC:29082 protein_coding YES CCDS41553.1 ENSP00000225235 O60347 UPI00001C1ED6 NM_015188.1 1/13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 94402850 94402850 G A 1 0 0 0 0 0 0 0 1 16001 962 34 3 3 TBC1D12 10 94402850 Silent SNP G C3L-01862_T 10144212 94402850 39394572 94 7615 TLL2 0 . GRCh38 10 96373724 96373724 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.2534C>A p.Pro845His p.P845H ENST00000357947 19/21 352 293 59 307 306 1 strelka-varscan-mutect TLL2,missense_variant,p.Pro845His,ENST00000357947,NM_012465.3;TLL2,non_coding_transcript_exon_variant,,ENST00000506028,; T ENST00000357947 Transcript missense_variant 2760/6756 2534/3048 845/1015 P/H cCc/cAc 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 tolerated(0.15) 19/21 PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF638,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 96373724 96373724 G T 1 0 0 0 0 1 0 0 0 16392 1232 43 2 2 TLL2 10 96373724 Missense_Mutation SNP G C3L-01862_T 1970874 96373724 37423698 95 7616 TEAD1 0 . GRCh38 11 12862259 12862259 + Missense_Mutation SNP A A C novel C3L-01862_T C3L-01862_N A A c.212A>C p.Glu71Ala p.E71A ENST00000527636 4/13 314 271 43 352 352 0 strelka-varscan-mutect TEAD1,missense_variant,p.Glu56Ala,ENST00000334310,;TEAD1,missense_variant,p.Glu71Ala,ENST00000527575,;TEAD1,missense_variant,p.Glu71Ala,ENST00000527636,NM_021961.5;TEAD1,non_coding_transcript_exon_variant,,ENST00000525312,; C ENST00000527636 Transcript missense_variant 663/2544 212/1281 71/426 E/A gAa/gCa 1 1 TEAD1 HGNC HGNC:11714 protein_coding YES CCDS7810.2 ENSP00000435233 H0YE88 UPI000013D412 NM_021961.5 deleterious(0.03) 4/13 PROSITE_profiles:PS51088,hmmpanther:PTHR11834,PROSITE_patterns:PS00554,Pfam_domain:PF01285,PIRSF_domain:PIRSF002603,SMART_domains:SM00426,Prints_domain:PR00065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 12862259 12862259 A C 1 0 0 0 0 1 0 0 0 16149 246 9 5 5 TEAD1 11 12862259 Missense_Mutation SNP A C3L-01862_T 12862259 122224363 96 7617 INSC 0 . GRCh38 11 15112561 15112561 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.92G>T p.Cys31Phe p.C31F ENST00000379554 1/13 68 51 17 63 63 0 strelka-varscan-mutect INSC,missense_variant,p.Cys31Phe,ENST00000379554,NM_001031853.4;INSC,upstream_gene_variant,,ENST00000379556,NM_001042536.2; T ENST00000379554 Transcript missense_variant 138/2954 92/1740 31/579 C/F tGt/tTt 1 1 INSC HGNC HGNC:33116 protein_coding YES CCDS41621.1 ENSP00000368872 Q1MX18 UPI0000D63F1D NM_001031853.4 deleterious_low_confidence(0) 1/13 hmmpanther:PTHR21386:SF0,hmmpanther:PTHR21386 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 15112561 15112561 G T 1 0 0 0 0 1 0 0 0 7666 1391 48 2 2 INSC 11 15112561 Missense_Mutation SNP G C3L-01862_T 2250302 15112561 119974061 97 7618 NAV2 0 . GRCh38 11 19713889 19713889 + Missense_Mutation SNP G G C novel C3L-01862_T C3L-01862_N G G c.194G>C p.Gly65Ala p.G65A ENST00000396087 1/41 242 204 38 188 187 1 strelka-varscan-mutect NAV2,missense_variant,p.Gly65Ala,ENST00000527559,;NAV2,missense_variant,p.Gly65Ala,ENST00000540292,;NAV2,missense_variant,p.Gly65Ala,ENST00000396085,NM_182964.5;NAV2,missense_variant,p.Gly65Ala,ENST00000349880,NM_145117.4;NAV2,missense_variant,p.Gly65Ala,ENST00000396087,NM_001244963.1;NAV2,intron_variant,,ENST00000360655,NM_001111018.1;RP11-359E10.1,upstream_gene_variant,,ENST00000603468,; C ENST00000396087 Transcript missense_variant 293/7882 194/7467 65/2488 G/A gGg/gCg 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 tolerated_low_confidence(0.09) 1/41 Superfamily_domains:SSF47576 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 19713889 19713889 G C 1 0 0 0 0 1 0 0 0 10193 1232 43 4 4 NAV2 11 19713889 Missense_Mutation SNP G C3L-01862_T 4601328 19713889 115372733 98 7619 NELL1 0 . GRCh38 11 21573235 21573235 + Missense_Mutation SNP G G T C3L-01862_T C3L-01862_N G G c.2292G>T p.Glu764Asp p.E764D ENST00000298925 20/21 175 155 20 229 229 0 strelka-varscan-mutect NELL1,missense_variant,p.Glu764Asp,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Glu679Asp,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Glu736Asp,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Glu689Asp,ENST00000532434,NM_201551.2;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,; T ENST00000298925 Transcript missense_variant 2445/3329 2292/2517 764/838 E/D gaG/gaT COSM5046249 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 tolerated(0.33) 20/21 Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 21573235 21573235 G T 1 0 0 0 0 1 0 0 0 10364 1020 36 2 2 NELL1 11 21573235 Missense_Mutation SNP G C3L-01862_T 1859346 21573235 113513387 99 7620 TRIM49B 0 . GRCh38 11 49032344 49032344 + Silent SNP G G T novel C3L-01862_T C3L-01862_N G G c.480G>T p.= p.V160V ENST00000622138 4/8 181 151 30 245 245 0 strelka-varscan-mutect TRIM49B,synonymous_variant,p.=,ENST00000622138,;TRIM49B,synonymous_variant,p.=,ENST00000332682,NM_001206626.1; T ENST00000622138 Transcript synonymous_variant 809/2162 480/1359 160/452 V gtG/gtT 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 4/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 49032344 49032344 G T 1 0 0 0 0 0 0 0 1 17015 1335 47 2 2 TRIM49B 11 49032344 Silent SNP G C3L-01862_T 27459109 49032344 86054278 100 7621 FOLH1 0 . GRCh38 11 49173453 49173453 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.1129C>T p.His377Tyr p.H377Y ENST00000256999 10/19 104 81 23 127 127 0 strelka-varscan-mutect FOLH1,missense_variant,p.His362Tyr,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.His377Tyr,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.His377Tyr,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.His69Tyr,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.His362Tyr,ENST00000533034,NM_001193472.1;FOLH1,non_coding_transcript_exon_variant,,ENST00000525629,;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,; A ENST00000256999 Transcript missense_variant 1390/2635 1129/2253 377/750 H/Y Cac/Tac 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 10/19 Gene3D:3.40.630.10,Pfam_domain:PF04389,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 49173453 49173453 G A 1 0 0 0 0 1 0 0 0 5840 1290 45 3 3 FOLH1 11 49173453 Missense_Mutation SNP G C3L-01862_T 141109 49173453 85913169 101 7622 OR5T1 0 . GRCh38 11 56276552 56276552 + Missense_Mutation SNP G G A rs143790336 C3L-01862_T C3L-01862_N G G c.914G>A p.Arg305Gln p.R305Q ENST00000313033 1/1 109 92 17 174 173 1 strelka-varscan-mutect OR5T1,missense_variant,p.Arg305Gln,ENST00000313033,NM_001004745.1; A ENST00000313033 Transcript missense_variant 914/981 914/981 305/326 R/Q cGg/cAg rs143790336,COSM4033856 1 1 OR5T1 HGNC HGNC:14821 protein_coding YES CCDS31525.1 ENSP00000323612 Q8NG75 A0A126GVL6 UPI000004B22E NM_001004745.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF33,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245 0,1 MODERATE 1 SNV 0,1 1 PASS rs143790336 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 56276552 56276552 G A 1 0 0 0 0 1 0 0 0 11249 1116 39 1 1 OR5T1 11 56276552 Missense_Mutation SNP G C3L-01862_T 7103099 56276552 78810070 102 7623 GLYATL2 0 . GRCh38 11 58834506 58834506 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.808G>T p.Ala270Ser p.A270S ENST00000287275 6/6 106 83 23 135 133 2 strelka-varscan-mutect GLYATL2,missense_variant,p.Ala270Ser,ENST00000287275,NM_145016.3;GLYATL2,missense_variant,p.Ala270Ser,ENST00000532258,;GLYATL2,downstream_gene_variant,,ENST00000533636,; A ENST00000287275 Transcript missense_variant 1199/1640 808/885 270/294 A/S Gca/Tca 1 -1 GLYATL2 HGNC HGNC:24178 protein_coding YES CCDS41649.1 ENSP00000287275 Q8WU03 A0A024R4Z5 UPI000003FFB7 NM_145016.3 tolerated(0.55) 6/6 hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF4,Gene3D:3.40.630.30,Pfam_domain:PF08444,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 58834506 58834506 C A 1 0 0 0 0 1 0 0 0 6359 739 26 2 2 GLYATL2 11 58834506 Missense_Mutation SNP C C3L-01862_T 2557954 58834506 76252116 103 7624 TSGA10IP 0 . GRCh38 11 65947255 65947255 + Missense_Mutation SNP C C A rs776914318 C3L-01862_T C3L-01862_N C C c.430C>A p.Arg144Ser p.R144S ENST00000532620 3/8 269 229 40 242 242 0 strelka-varscan-mutect TSGA10IP,missense_variant,p.Arg144Ser,ENST00000532620,NM_152762.2;TSGA10IP,missense_variant,p.Arg144Ser,ENST00000608857,;TSGA10IP,3_prime_UTR_variant,,ENST00000528291,;TSGA10IP,non_coding_transcript_exon_variant,,ENST00000531518,;TSGA10IP,intron_variant,,ENST00000534740,; A ENST00000532620 Transcript missense_variant 661/1925 430/1671 144/556 R/S Cgt/Agt rs776914318 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 tolerated(0.4) 3/8 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs776914318 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 65947255 65947255 C A 1 0 0 0 0 1 0 0 0 17124 768 27 1 1 TSGA10IP 11 65947255 Missense_Mutation SNP C C3L-01862_T 7112749 65947255 69139367 104 7625 PC 0 . GRCh38 11 66866234 66866234 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.1138A>G p.Thr380Ala p.T380A ENST00000393960 11/23 114 92 22 100 100 0 strelka-varscan-mutect PC,missense_variant,p.Thr380Ala,ENST00000393960,NM_001040716.1;PC,missense_variant,p.Thr380Ala,ENST00000393958,NM_000920.3;PC,missense_variant,p.Thr380Ala,ENST00000393955,NM_022172.2;PC,missense_variant,p.Thr340Ala,ENST00000524491,;PC,missense_variant,p.Thr340Ala,ENST00000628663,; C ENST00000393960 Transcript missense_variant 1420/4192 1138/3537 380/1178 T/A Acc/Gcc 1 -1 PC HGNC HGNC:8636 protein_coding YES CCDS8152.1 ENSP00000377532 P11498 A0A024R5C5 UPI0000132BC4 NM_001040716.1 deleterious(0.01) 11/23 PROSITE_profiles:PS50979,hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF110,Gene3D:3.30.470.20,TIGRFAM_domain:TIGR01235,Pfam_domain:PF02785,PIRSF_domain:PIRSF001594,SMART_domains:SM00878,Superfamily_domains:SSF51246,Superfamily_domains:SSF56059 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 66866234 66866234 T C 1 0 0 0 0 1 0 0 0 11584 1696 59 5 5 PC 11 66866234 Missense_Mutation SNP T C3L-01862_T 918979 66866234 68220388 105 7626 FAT3 0 . GRCh38 11 92883266 92883266 + Silent SNP G G A rs768838868 C3L-01862_T C3L-01862_N G G c.12360G>A p.= p.S4120S ENST00000525166 23/27 257 220 37 232 231 1 strelka-varscan-mutect FAT3,synonymous_variant,p.=,ENST00000409404,NM_001008781.2;FAT3,synonymous_variant,p.=,ENST00000525166,;FAT3,synonymous_variant,p.=,ENST00000533797,;FAT3,upstream_gene_variant,,ENST00000489716,;FAT3,upstream_gene_variant,,ENST00000469900,; A ENST00000525166 Transcript synonymous_variant 12382/18699 12360/13320 4120/4439 S tcG/tcA rs768838868 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 23/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 LOW 1 SNV 5 1 PASS rs768838868 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 92883266 92883266 G A 1 0 0 0 0 0 0 0 1 5551 1074 38 1 1 FAT3 11 92883266 Silent SNP G C3L-01862_T 26017032 92883266 42203356 106 7627 NFRKB 0 . GRCh38 11 129882112 129882112 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1240C>A p.Leu414Met p.L414M ENST00000524794 9/25 89 76 13 125 125 0 strelka-varscan-mutect NFRKB,missense_variant,p.Leu389Met,ENST00000446488,NM_001143835.1;NFRKB,missense_variant,p.Leu414Met,ENST00000524794,NM_006165.3;NFRKB,missense_variant,p.Leu389Met,ENST00000524746,;NFRKB,missense_variant,p.Leu401Met,ENST00000531755,;NFRKB,downstream_gene_variant,,ENST00000532225,;NFRKB,downstream_gene_variant,,ENST00000529319,;NFRKB,downstream_gene_variant,,ENST00000530278,; T ENST00000524794 Transcript missense_variant 1361/4351 1240/3975 414/1324 L/M Ctg/Atg 1 -1 NFRKB HGNC HGNC:7802 protein_coding YES CCDS8483.1 ENSP00000436926 Q6P4R8 UPI000006E542 NM_006165.3 tolerated(0.19) 9/25 Low_complexity_(Seg):seg,hmmpanther:PTHR13052:SF0,hmmpanther:PTHR13052,Pfam_domain:PF14465 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.97885 0.999993 1 1 1 0 T 3 4 27 129882112 129882112 G T 1 0 0 0 0 1 0 0 0 10420 962 34 2 2 NFRKB 11 129882112 Missense_Mutation SNP G C3L-01862_T 36998846 129882112 5204510 107 7628 WNK1 0 . GRCh38 12 861160 861160 + Missense_Mutation SNP A A G novel C3L-01862_T C3L-01862_N A A c.1768A>G p.Lys590Glu p.K590E ENST00000340908 7/28 214 170 44 295 294 1 strelka-varscan-mutect WNK1,missense_variant,p.Lys590Glu,ENST00000530271,;WNK1,missense_variant,p.Lys590Glu,ENST00000537687,NM_001184985.1;WNK1,missense_variant,p.Lys590Glu,ENST00000340908,NM_213655.4;WNK1,missense_variant,p.Lys590Glu,ENST00000315939,NM_018979.3;WNK1,missense_variant,p.Lys590Glu,ENST00000535572,NM_014823.2;WNK1,upstream_gene_variant,,ENST00000535698,;WNK1,upstream_gene_variant,,ENST00000544965,;WNK1,upstream_gene_variant,,ENST00000545285,;WNK1,downstream_gene_variant,,ENST00000540360,;WNK1,downstream_gene_variant,,ENST00000538787,; G ENST00000340908 Transcript missense_variant 2411/11208 1768/7905 590/2634 K/E Aaa/Gaa 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 tolerated(0.21) 7/28 Gene3D:1.10.510.10,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 204 0 0 5 0 0 0 -20 0.809113 1 1 1 0 G 3 3 27 861160 861160 A G 1 0 0 0 0 1 0 0 0 17933 131 5 5 5 WNK1 12 861160 Missense_Mutation SNP A C3L-01862_T 861160 132414149 108 7629 KRAS 0 . GRCh38 12 25227341 25227341 + Missense_Mutation SNP T T G rs17851045 C3L-01862_T C3L-01862_N T T c.183A>C p.Gln61His p.Q61H ENST00000256078 3/6 151 117 34 201 201 0 strelka-varscan-mutect KRAS,missense_variant,p.Gln61His,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gln61His,ENST00000256078,NM_033360.3;KRAS,intron_variant,,ENST00000557334,;RP11-295I5.4,downstream_gene_variant,,ENST00000620933,; G ENST00000256078 Transcript missense_variant 247/1119 183/570 61/189 Q/H caA/caC rs17851045,COSM1135364,COSM1146992,COSM554,COSM555 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 3/6 PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs17851045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 25227341 25227341 T G 1 0 0 0 0 1 0 0 0 8318 1606 56 5 5 KRAS 12 25227341 Missense_Mutation SNP T C3L-01862_T 24366181 25227341 108047968 109 7630 KRT6B 0 . GRCh38 12 52452033 52452033 + Silent SNP G G T rs768946287 C3L-01862_T C3L-01862_N G G c.46C>A p.= p.R16R ENST00000252252 1/9 317 274 43 238 238 0 varscan-mutect KRT6B,synonymous_variant,p.=,ENST00000252252,NM_005555.3; T ENST00000252252 Transcript synonymous_variant 94/2282 46/1695 16/564 R Cgg/Agg rs768946287 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 1/9 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs768946287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 52452033 52452033 G T 1 0 0 0 0 0 0 0 1 8363 1115 39 1 1 KRT6B 12 52452033 Silent SNP G C3L-01862_T 27224692 52452033 80823276 110 7631 SDR9C7 0 . GRCh38 12 56934058 56934058 + Missense_Mutation SNP A A C novel C3L-01862_T C3L-01862_N A A c.204T>G p.Asp68Glu p.D68E ENST00000293502 1/4 202 172 30 213 213 0 strelka-varscan-mutect SDR9C7,missense_variant,p.Asp68Glu,ENST00000293502,NM_148897.2; C ENST00000293502 Transcript missense_variant 348/1765 204/942 68/313 D/E gaT/gaG 1 -1 SDR9C7 HGNC HGNC:29958 protein_coding YES CCDS8926.1 ENSP00000293502 Q8NEX9 UPI0000046169 NM_148897.2 tolerated(1) 1/4 hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF646,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 56934058 56934058 A C 1 0 0 0 0 1 0 0 0 14250 446 16 5 5 SDR9C7 12 56934058 Missense_Mutation SNP A C3L-01862_T 4482025 56934058 76341251 111 7632 SDR9C7 0 . GRCh38 12 56934120 56934120 + Silent SNP G G T rs760003577 C3L-01862_T C3L-01862_N G G c.142C>A p.= p.R48R ENST00000293502 1/4 322 268 54 311 311 0 strelka-varscan-mutect SDR9C7,synonymous_variant,p.=,ENST00000293502,NM_148897.2; T ENST00000293502 Transcript synonymous_variant 286/1765 142/942 48/313 R Cgg/Agg rs760003577 1 -1 SDR9C7 HGNC HGNC:29958 protein_coding YES CCDS8926.1 ENSP00000293502 Q8NEX9 UPI0000046169 NM_148897.2 1/4 hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF646,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS rs760003577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 56934120 56934120 G T 1 0 0 0 0 0 0 0 1 14250 1057 37 1 1 SDR9C7 12 56934120 Silent SNP G C3L-01862_T 62 56934120 76341189 112 7633 DPY19L2 0 . GRCh38 12 63644420 63644420 + Missense_Mutation SNP C C A rs768747258 C3L-01862_T C3L-01862_N C C c.786G>T p.Met262Ile p.M262I ENST00000324472 6/22 109 94 15 136 136 0 varscan-mutect DPY19L2,missense_variant,p.Met262Ile,ENST00000324472,NM_173812.4;RP11-415I12.3,intron_variant,,ENST00000509615,;DPY19L2,3_prime_UTR_variant,,ENST00000306389,; A ENST00000324472 Transcript missense_variant 970/4060 786/2277 262/758 M/I atG/atT rs768747258 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 tolerated(1) 6/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs768747258 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 63644420 63644420 C A 1 0 0 0 0 1 0 0 0 4556 478 17 2 2 DPY19L2 12 63644420 Missense_Mutation SNP C C3L-01862_T 6710300 63644420 69630889 113 7634 SNRPF 0 . GRCh38 12 95866062 95866062 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.252G>A p.Met84Ile p.M84I ENST00000266735 4/4 190 149 41 252 252 0 strelka-varscan-mutect SNRPF,missense_variant,p.Met84Ile,ENST00000266735,NM_003095.2;SNRPF,intron_variant,,ENST00000552085,;SNRPF,intron_variant,,ENST00000553192,;CCDC38,downstream_gene_variant,,ENST00000344280,NM_182496.2;SNRPF,non_coding_transcript_exon_variant,,ENST00000549580,;SNRPF,downstream_gene_variant,,ENST00000551316,;CCDC38,downstream_gene_variant,,ENST00000549876,;CCDC38,downstream_gene_variant,,ENST00000546816,; A ENST00000266735 Transcript missense_variant 398/1389 252/261 84/86 M/I atG/atA 1 1 SNRPF HGNC HGNC:11162 protein_coding YES CCDS9055.1 ENSP00000266735 P62306 UPI0000027DBC NM_003095.2 tolerated(0.09) 4/4 hmmpanther:PTHR11021,hmmpanther:PTHR11021:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 95866062 95866062 G A 1 0 0 0 0 1 0 0 0 15188 1290 45 3 3 SNRPF 12 95866062 Missense_Mutation SNP G C3L-01862_T 32221642 95866062 37409247 114 7635 PTPN11 0 . GRCh38 12 112489160 112489160 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1584G>T p.Arg528Ser p.R528S ENST00000351677 13/16 494 409 85 507 507 0 strelka-varscan-mutect PTPN11,missense_variant,p.Arg528Ser,ENST00000351677,NM_002834.3;PTPN11,missense_variant,p.Arg532Ser,ENST00000635625,;PTPN11,downstream_gene_variant,,ENST00000392597,NM_080601.1;PTPN11,downstream_gene_variant,,ENST00000635652,; T ENST00000351677 Transcript missense_variant 1782/6101 1584/1782 528/593 R/S agG/agT 1 1 PTPN11 HGNC HGNC:9644 protein_coding YES CCDS9163.1 ENSP00000340944 Q06124 UPI000013296E NM_002834.3 deleterious(0) 13/16 PIRSF_domain:PIRSF000929,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 112489160 112489160 G T 1 0 0 0 0 1 0 0 0 12933 1165 41 2 2 PTPN11 12 112489160 Missense_Mutation SNP G C3L-01862_T 16623098 112489160 20786149 115 7636 TPCN1 0 . GRCh38 12 113292971 113292971 + Missense_Mutation SNP A A C novel C3L-01862_T C3L-01862_N A A c.2367A>C p.Lys789Asn p.K789N ENST00000550785 27/29 116 98 18 130 129 1 strelka-varscan-mutect TPCN1,missense_variant,p.Lys789Asn,ENST00000550785,NM_001143819.2;TPCN1,missense_variant,p.Lys717Asn,ENST00000335509,NM_017901.5;TPCN1,missense_variant,p.Lys789Asn,ENST00000541517,;TPCN1,missense_variant,p.Lys649Asn,ENST00000392569,NM_001301214.1;MIR6762,downstream_gene_variant,,ENST00000613340,;TPCN1,upstream_gene_variant,,ENST00000546787,;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077,;TPCN1,non_coding_transcript_exon_variant,,ENST00000551127,;TPCN1,downstream_gene_variant,,ENST00000428632,;TPCN1,downstream_gene_variant,,ENST00000547955,;TPCN1,downstream_gene_variant,,ENST00000546907,; C ENST00000550785 Transcript missense_variant 2536/5345 2367/2667 789/888 K/N aaA/aaC 1 1 TPCN1 HGNC HGNC:18182 protein_coding YES CCDS44985.1 ENSP00000448083 Q9ULQ1 UPI00004066FB NM_001143819.2 tolerated(0.44) 27/29 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 113292971 113292971 A C 1 0 0 0 0 1 0 0 0 16874 69 3 5 5 TPCN1 12 113292971 Missense_Mutation SNP A C3L-01862_T 803811 113292971 19982338 116 7637 ULK1 0 . GRCh38 12 131913759 131913759 + Silent SNP G G T novel C3L-01862_T C3L-01862_N G G c.1170G>T p.= p.V390V ENST00000321867 15/28 35 29 6 27 27 0 strelka-varscan-mutect ULK1,synonymous_variant,p.=,ENST00000321867,NM_003565.2;ULK1,upstream_gene_variant,,ENST00000541761,;ULK1,upstream_gene_variant,,ENST00000540647,;ULK1,downstream_gene_variant,,ENST00000537421,;ULK1,downstream_gene_variant,,ENST00000542313,; T ENST00000321867 Transcript synonymous_variant 1521/5310 1170/3153 390/1050 V gtG/gtT 1 1 ULK1 HGNC HGNC:12558 protein_coding YES CCDS9274.1 ENSP00000324560 O75385 UPI00001FB0D9 NM_003565.2 15/28 PIRSF_domain:PIRSF000580,hmmpanther:PTHR24348,hmmpanther:PTHR24348:SF19 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.80959 1 1 1 1 0 T 2 4 27 131913759 131913759 G T 1 0 0 0 0 0 0 0 1 17499 1335 47 2 2 ULK1 12 131913759 Silent SNP G C3L-01862_T 18620788 131913759 1361550 117 7638 RNF17 0 . GRCh38 13 24799578 24799578 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.1583T>A p.Val528Asp p.V528D ENST00000255324 12/36 75 62 13 124 124 0 strelka-varscan-mutect RNF17,missense_variant,p.Val528Asp,ENST00000255324,NM_031277.2,NM_001184993.1;RNF17,missense_variant,p.Val528Asp,ENST00000255325,;RNF17,upstream_gene_variant,,ENST00000418120,;RNF17,downstream_gene_variant,,ENST00000255326,; A ENST00000255324 Transcript missense_variant 1635/5119 1583/4872 528/1623 V/D gTc/gAc 1 1 RNF17 HGNC HGNC:10060 protein_coding YES CCDS9308.2 ENSP00000255324 Q9BXT8 UPI00001FC8BA NM_031277.2,NM_001184993.1 deleterious(0.02) 12/36 hmmpanther:PTHR16442 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 24799578 24799578 T A 1 0 0 0 0 1 0 0 0 13638 1667 58 4 4 RNF17 13 24799578 Missense_Mutation SNP T C3L-01862_T 24799578 89564750 118 7639 TRPC4 0 . GRCh38 13 37637567 37637567 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.2285G>T p.Ser762Ile p.S762I ENST00000625583 10/10 88 71 17 114 114 0 strelka-varscan-mutect TRPC4,missense_variant,p.Ser757Ile,ENST00000379705,NM_016179.2;TRPC4,missense_variant,p.Ser762Ile,ENST00000625583,NM_003306.1;TRPC4,missense_variant,p.Ser757Ile,ENST00000358477,NM_001135955.1;TRPC4,missense_variant,p.Ser584Ile,ENST00000338947,NM_001135958.1;TRPC4,missense_variant,p.Ser692Ile,ENST00000379673,NM_001135956.1;TRPC4,missense_variant,p.Ser584Ile,ENST00000379679,;TRPC4,3_prime_UTR_variant,,ENST00000426868,;TRPC4,intron_variant,,ENST00000355779,NM_001135957.1;TRPC4,3_prime_UTR_variant,,ENST00000488717,; A ENST00000625583 Transcript missense_variant 2285/3009 2285/2949 762/982 S/I aGc/aTc 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 deleterious(0.02) 10/10 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,Prints_domain:PR01645 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 37637567 37637567 C A 1 0 0 0 0 1 0 0 0 17085 797 28 2 2 TRPC4 13 37637567 Missense_Mutation SNP C C3L-01862_T 12837989 37637567 76726761 119 7640 KLHL1 0 . GRCh38 13 70107573 70107573 + Missense_Mutation SNP T T A novel C3L-01862_T C3L-01862_N T T c.127A>T p.Ser43Cys p.S43C ENST00000377844 1/11 44 35 9 101 101 0 strelka-varscan-mutect KLHL1,missense_variant,p.Ser43Cys,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Ser43Cys,ENST00000545028,NM_001286725.1;ATXN8OS,non_coding_transcript_exon_variant,,ENST00000414504,;ATXN8OS,upstream_gene_variant,,ENST00000424524,; A ENST00000377844 Transcript missense_variant 887/4115 127/2247 43/748 S/C Agt/Tgt 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 tolerated_low_confidence(0.25) 1/11 MODERATE 1 SNV 1 1 PASS rs1016613270 . 0 202 8 0 0 0 0 0 -19.99492 0.999999 1 1 1 0 A 3 1 27 70107573 70107573 T A 1 0 0 0 0 1 0 0 0 8229 1580 55 4 4 KLHL1 13 70107573 Missense_Mutation SNP T C3L-01862_T 32470006 70107573 44256755 120 7641 OR6J1 0 . GRCh38 14 22633891 22633891 + Silent SNP A A C novel C3L-01862_T C3L-01862_N A A c.921T>G p.= p.V307V ENST00000540461 1/1 202 177 25 223 223 0 strelka-varscan-mutect OR6J1,synonymous_variant,p.=,ENST00000540461,;AC243945.1,downstream_gene_variant,,ENST00000623775,; C ENST00000540461 Transcript synonymous_variant 921/1044 921/1044 307/347 V gtT/gtG 1 -1 OR6J1 HGNC HGNC:14707 protein_coding YES ENSP00000437629 Q8NGC5 UPI000462094B 1/1 hmmpanther:PTHR26454:SF53,hmmpanther:PTHR26454,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 27 22633891 22633891 A C 1 0 0 0 0 0 0 0 1 11270 233 9 5 5 OR6J1 14 22633891 Silent SNP A C3L-01862_T 22633891 84409827 121 7642 RP11-244E17.1 0 . GRCh38 14 23101708 23101708 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.1437G>A p.Met479Ile p.M479I ENST00000637218 12/16 270 239 31 289 289 0 strelka-varscan-mutect RP11-244E17.1,missense_variant,p.Met479Ile,ENST00000637218,;C14orf119,downstream_gene_variant,,ENST00000319074,NM_017924.3;C14orf119,downstream_gene_variant,,ENST00000554203,; T ENST00000637218 Transcript missense_variant 1509/2656 1437/2367 479/788 M/I atG/atA 1 -1 RP11-244E17.1 Clone_based_vega_gene protein_coding YES ENSP00000489869 12/16 hmmpanther:PTHR10942,hmmpanther:PTHR10942:SF6,Pfam_domain:PF01457,Superfamily_domains:SSF55486 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 23101708 23101708 C T 1 0 0 0 0 1 0 0 0 13723 710 25 3 3 RP11-244E17.1 14 23101708 Missense_Mutation SNP C C3L-01862_T 467817 23101708 83942010 122 7643 FITM1 0 . GRCh38 14 24132559 24132559 + Silent SNP C C A rs746849731 C3L-01862_T C3L-01862_N C C c.615C>A p.= p.A205A ENST00000267426 2/2 256 225 31 308 308 0 strelka-varscan-mutect FITM1,synonymous_variant,p.=,ENST00000267426,NM_203402.2;FITM1,synonymous_variant,p.=,ENST00000559294,;PSME1,upstream_gene_variant,,ENST00000382708,NM_176783.2;PSME1,upstream_gene_variant,,ENST00000559123,;PSME1,upstream_gene_variant,,ENST00000206451,NM_001281529.1,NM_006263.3;PSME1,upstream_gene_variant,,ENST00000561435,NM_001281528.1;RP11-468E2.6,downstream_gene_variant,,ENST00000558325,;PSME1,upstream_gene_variant,,ENST00000470718,;PSME1,upstream_gene_variant,,ENST00000561059,;PSME1,upstream_gene_variant,,ENST00000560420,;PSME1,upstream_gene_variant,,ENST00000561142,;PSME1,upstream_gene_variant,,ENST00000559741,;PSME1,upstream_gene_variant,,ENST00000558112,; A ENST00000267426 Transcript synonymous_variant 904/1194 615/879 205/292 A gcC/gcA rs746849731 1 1 FITM1 HGNC HGNC:33714 protein_coding YES CCDS9611.1 ENSP00000267426 A5D6W6 UPI000016146D NM_203402.2 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR23129,hmmpanther:PTHR23129:SF3 LOW 1 SNV 1 1 PASS rs746849731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 24132559 24132559 C A 1 0 0 0 0 0 0 0 1 5761 581 21 2 2 FITM1 14 24132559 Silent SNP C C3L-01862_T 1030851 24132559 82911159 123 7644 TRIM9 0 . GRCh38 14 51094340 51094340 + Silent SNP G G T C3L-01862_T C3L-01862_N G G c.600C>A p.= p.P200P ENST00000298355 1/10 239 205 34 207 206 1 strelka-varscan-mutect TRIM9,synonymous_variant,p.=,ENST00000298355,NM_015163.5;TRIM9,synonymous_variant,p.=,ENST00000360392,NM_052978.4;TRIM9,synonymous_variant,p.=,ENST00000338969,;RP11-1140I5.1,downstream_gene_variant,,ENST00000554475,; T ENST00000298355 Transcript synonymous_variant 1722/5284 600/2133 200/710 P ccC/ccA COSM4246274,COSM4246275,COSM4246276 1 -1 TRIM9 HGNC HGNC:16288 protein_coding YES CCDS9703.1 ENSP00000298355 Q9C026 UPI000006D630 NM_015163.5 1/10 PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF400,SMART_domains:SM00336 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 51094340 51094340 G T 1 0 0 0 0 0 0 0 1 17046 1219 43 2 2 TRIM9 14 51094340 Silent SNP G C3L-01862_T 26961781 51094340 55949378 124 7645 SYNE2 0 . GRCh38 14 64130097 64130097 + Missense_Mutation SNP T T G novel C3L-01862_T C3L-01862_N T T c.14189T>G p.Leu4730Arg p.L4730R ENST00000358025 76/116 421 349 72 471 471 0 strelka-varscan-mutect SYNE2,missense_variant,p.Leu4730Arg,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Leu4730Arg,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Leu4647Arg,ENST00000357395,;SYNE2,missense_variant,p.Leu4647Arg,ENST00000554584,;SYNE2,missense_variant,p.Leu1364Arg,ENST00000555002,;SYNE2,missense_variant,p.Leu1115Arg,ENST00000394768,;ESR2,intron_variant,,ENST00000556275,; G ENST00000358025 Transcript missense_variant 14401/21842 14189/20724 4730/6907 L/R cTc/cGc 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0) 76/116 hmmpanther:PTHR11915:SF317,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 64130097 64130097 T G 1 0 0 0 0 1 0 0 0 15838 1551 54 5 5 SYNE2 14 64130097 Missense_Mutation SNP T C3L-01862_T 13035757 64130097 42913621 125 7646 TTLL5 0 . GRCh38 14 75793032 75793032 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.3103C>T p.Arg1035Trp p.R1035W ENST00000298832 27/32 126 104 22 135 135 0 strelka-varscan-mutect TTLL5,missense_variant,p.Arg1035Trp,ENST00000298832,NM_015072.4;TTLL5,missense_variant,p.Arg1050Trp,ENST00000557636,;TTLL5,missense_variant,p.Arg586Trp,ENST00000556893,;TTLL5,missense_variant,p.Arg544Trp,ENST00000554510,;TTLL5,upstream_gene_variant,,ENST00000555018,; T ENST00000298832 Transcript missense_variant 3308/4683 3103/3846 1035/1281 R/W Cgg/Tgg 1 1 TTLL5 HGNC HGNC:19963 protein_coding YES CCDS32124.1 ENSP00000298832 Q6EMB2 UPI00003FF22B NM_015072.4 deleterious(0) 27/32 MODERATE 1 SNV 1 1 PASS rs1348688599 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 75793032 75793032 C T 1 0 0 0 0 1 0 0 0 17241 759 27 1 1 TTLL5 14 75793032 Missense_Mutation SNP C C3L-01862_T 11662935 75793032 31250686 126 7647 TUBGCP5 0 . GRCh38 15 23008774 23008774 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.2252C>T p.Thr751Ile p.T751I ENST00000615383 16/23 183 155 28 221 221 0 strelka-varscan-mutect TUBGCP5,missense_variant,p.Thr751Ile,ENST00000615383,NM_052903.4;TUBGCP5,missense_variant,p.Thr751Ile,ENST00000620435,NM_001102610.1;TUBGCP5,missense_variant,p.Thr37Ile,ENST00000610294,;TUBGCP5,downstream_gene_variant,,ENST00000615455,;TUBGCP5,missense_variant,p.Thr751Ile,ENST00000614508,;TUBGCP5,non_coding_transcript_exon_variant,,ENST00000613552,;TUBGCP5,upstream_gene_variant,,ENST00000620238,; A ENST00000615383 Transcript missense_variant 2382/3849 2252/3075 751/1024 T/I aCa/aTa 1 -1 TUBGCP5 HGNC HGNC:18600 protein_coding YES CCDS73698.1 ENSP00000480316 Q96RT8 UPI000012B2EE NM_052903.4 tolerated(0.35) 16/23 hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF33,Pfam_domain:PF04130 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 23008774 23008774 G A 1 0 0 0 0 1 0 0 0 17279 1377 48 3 3 TUBGCP5 15 23008774 Missense_Mutation SNP G C3L-01862_T 23008774 78982415 127 7648 STARD9 0 . GRCh38 15 42686773 42686773 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.5195G>T p.Trp1732Leu p.W1732L ENST00000290607 23/33 169 133 36 221 221 0 strelka-varscan-mutect STARD9,missense_variant,p.Trp1732Leu,ENST00000290607,NM_020759.2;STARD9,upstream_gene_variant,,ENST00000562619,;STARD9,downstream_gene_variant,,ENST00000562139,; T ENST00000290607 Transcript missense_variant 5252/15567 5195/14103 1732/4700 W/L tGg/tTg 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 deleterious(0.01) 23/33 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 42686773 42686773 G T 1 0 0 0 0 1 0 0 0 15639 1357 47 2 2 STARD9 15 42686773 Missense_Mutation SNP G C3L-01862_T 19677999 42686773 59304416 128 7649 ALPK3 0 . GRCh38 15 84859846 84859846 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.4642T>C p.Cys1548Arg p.C1548R ENST00000258888 8/14 228 191 37 222 222 0 strelka-varscan-mutect ALPK3,missense_variant,p.Cys1548Arg,ENST00000258888,NM_020778.4;ALPK3,upstream_gene_variant,,ENST00000558077,; C ENST00000258888 Transcript missense_variant 4809/10917 4642/5724 1548/1907 C/R Tgc/Cgc 1 1 ALPK3 HGNC HGNC:17574 protein_coding YES CCDS10333.1 ENSP00000258888 Q96L96 UPI000013D013 NM_020778.4 deleterious(0) 8/14 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF667,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 84859846 84859846 T C 1 0 0 0 0 1 0 0 0 646 1696 59 5 5 ALPK3 15 84859846 Missense_Mutation SNP T C3L-01862_T 42173073 84859846 17131343 129 7650 RBBP6 0 . GRCh38 16 24540750 24540750 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.124G>T p.Ala42Ser p.A42S ENST00000319715 1/18 117 102 15 111 110 1 strelka-varscan-mutect RBBP6,missense_variant,p.Ala42Ser,ENST00000319715,NM_006910.4;RBBP6,missense_variant,p.Ala42Ser,ENST00000348022,NM_018703.3;RBBP6,missense_variant,p.Ala42Ser,ENST00000381039,;RBBP6,missense_variant,p.Ala42Ser,ENST00000567686,;RBBP6,missense_variant,p.Ala42Ser,ENST00000452655,NM_032626.5;RBBP6,missense_variant,p.Ala42Ser,ENST00000568015,;RBBP6,intron_variant,,ENST00000564314,;RBBP6,downstream_gene_variant,,ENST00000568316,; T ENST00000319715 Transcript missense_variant 556/6229 124/5379 42/1792 A/S Gcc/Tcc 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 tolerated_low_confidence(0.06) 1/18 PROSITE_profiles:PS51282,hmmpanther:PTHR15439,hmmpanther:PTHR15439:SF3,Pfam_domain:PF08783,SMART_domains:SM01180 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99969 0.9999999 1 1 1 0 T 3 4 27 24540750 24540750 G T 1 0 0 0 0 1 0 0 0 13264 1319 46 2 2 RBBP6 16 24540750 Missense_Mutation SNP G C3L-01862_T 24540750 65797595 130 7651 ITGAM 0 . GRCh38 16 31297524 31297524 + Missense_Mutation SNP A A G novel C3L-01862_T C3L-01862_N A A c.1367A>G p.Tyr456Cys p.Y456C ENST00000544665 13/30 420 361 59 359 359 0 strelka-varscan-mutect ITGAM,missense_variant,p.Tyr456Cys,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Tyr456Cys,ENST00000287497,NM_000632.3;ITGAM,synonymous_variant,p.=,ENST00000567031,; G ENST00000544665 Transcript missense_variant 1438/4718 1367/3462 456/1153 Y/C tAc/tGc 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0) 13/30 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 27 31297524 31297524 A G 1 0 0 0 0 1 0 0 0 7794 391 14 5 5 ITGAM 16 31297524 Missense_Mutation SNP A C3L-01862_T 6756774 31297524 59040821 131 7652 CDH8 0 . GRCh38 16 61817564 61817564 + Missense_Mutation SNP G G A novel C3L-01862_T C3L-01862_N G G c.1192C>T p.Leu398Phe p.L398F ENST00000577390 7/12 248 203 45 236 236 0 strelka-varscan-mutect CDH8,missense_variant,p.Leu398Phe,ENST00000577390,NM_001796.4;CDH8,missense_variant,p.Leu398Phe,ENST00000577730,;CDH8,missense_variant,p.Leu398Phe,ENST00000584337,;CDH8,missense_variant,p.Leu398Phe,ENST00000299345,;CDH8,missense_variant,p.Leu398Phe,ENST00000583382,;CDH8,missense_variant,p.Leu398Phe,ENST00000585315,;CDH8,non_coding_transcript_exon_variant,,ENST00000582242,; A ENST00000577390 Transcript missense_variant 2147/9721 1192/2400 398/799 L/F Ctt/Ttt 1 -1 CDH8 HGNC HGNC:1767 protein_coding YES CCDS10802.1 ENSP00000462701 P55286 UPI0000126D9F NM_001796.4 tolerated(0.24) 7/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF273,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 61817564 61817564 G A 1 0 0 0 0 1 0 0 0 2819 1029 36 3 3 CDH8 16 61817564 Missense_Mutation SNP G C3L-01862_T 30520040 61817564 28520781 132 7653 PIEZO1 0 . GRCh38 16 88736333 88736333 + Missense_Mutation SNP T T C novel C3L-01862_T C3L-01862_N T T c.1372A>G p.Ser458Gly p.S458G ENST00000301015 12/51 238 190 48 183 182 1 strelka-varscan-mutect PIEZO1,missense_variant,p.Ser458Gly,ENST00000301015,NM_001142864.2;RP5-1142A6.2,intron_variant,,ENST00000440406,;RP5-1142A6.2,upstream_gene_variant,,ENST00000567968,;PIEZO1,upstream_gene_variant,,ENST00000490756,; C ENST00000301015 Transcript missense_variant 1619/8072 1372/7566 458/2521 S/G Agc/Ggc 1 -1 PIEZO1 HGNC HGNC:28993 protein_coding YES CCDS54058.1 ENSP00000301015 Q92508 UPI0001B300F3 NM_001142864.2 deleterious(0.03) 12/51 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF40 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 88736333 88736333 T C 1 0 0 0 0 1 0 0 0 11974 1580 55 5 5 PIEZO1 16 88736333 Missense_Mutation SNP T C3L-01862_T 26918769 88736333 1602012 133 7654 PDK2 0 . GRCh38 17 50108331 50108331 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.775G>T p.Ala259Ser p.A259S ENST00000503176 8/11 209 167 42 237 237 0 strelka-varscan-mutect PDK2,missense_variant,p.Ala259Ser,ENST00000503176,NM_002611.4;PDK2,missense_variant,p.Ala195Ser,ENST00000614357,NM_001199899.1;PDK2,missense_variant,p.Ala195Ser,ENST00000007708,NM_001199898.1;PDK2,missense_variant,p.Ala195Ser,ENST00000503614,;SAMD14,downstream_gene_variant,,ENST00000330175,NM_001257359.1;SAMD14,downstream_gene_variant,,ENST00000285206,;SAMD14,downstream_gene_variant,,ENST00000503131,NM_174920.3;PDK2,downstream_gene_variant,,ENST00000505440,;PDK2,downstream_gene_variant,,ENST00000512238,;PDK2,downstream_gene_variant,,ENST00000508030,;PDK2,downstream_gene_variant,,ENST00000510219,;PDK2,non_coding_transcript_exon_variant,,ENST00000512204,;PDK2,non_coding_transcript_exon_variant,,ENST00000506647,;SAMD14,downstream_gene_variant,,ENST00000508892,;SAMD14,downstream_gene_variant,,ENST00000573376,;PDK2,downstream_gene_variant,,ENST00000505897,;PDK2,downstream_gene_variant,,ENST00000515040,;PDK2,downstream_gene_variant,,ENST00000503076,;PDK2,downstream_gene_variant,,ENST00000506242,; T ENST00000503176 Transcript missense_variant 936/3440 775/1224 259/407 A/S Gcg/Tcg 1 1 PDK2 HGNC HGNC:8810 protein_coding YES CCDS11559.1 ENSP00000420927 Q15119 UPI000000D98D NM_002611.4 deleterious(0) 8/11 Gene3D:3.30.565.10,Pfam_domain:PF02518,PROSITE_profiles:PS50109,hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF15,SMART_domains:SM00387,Superfamily_domains:SSF55874 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 50108331 50108331 G T 1 0 0 0 0 1 0 0 0 11764 1203 42 2 2 PDK2 17 50108331 Missense_Mutation SNP G C3L-01862_T 50108331 33149110 134 7655 RBFOX3 0 . GRCh38 17 79101631 79101631 + Missense_Mutation SNP G G A C3L-01862_T C3L-01862_N G G c.521C>T p.Thr174Met p.T174M ENST00000580155 9/15 393 333 60 323 323 0 strelka-varscan-mutect RBFOX3,missense_variant,p.Thr173Met,ENST00000583458,;RBFOX3,missense_variant,p.Thr174Met,ENST00000584778,;RBFOX3,missense_variant,p.Thr174Met,ENST00000580155,NM_001082575.2;RBFOX3,missense_variant,p.Thr143Met,ENST00000582043,;RBFOX3,upstream_gene_variant,,ENST00000582880,;RBFOX3,upstream_gene_variant,,ENST00000582894,;RBFOX3,upstream_gene_variant,,ENST00000578998,;RBFOX3,upstream_gene_variant,,ENST00000581393,; A ENST00000580155 Transcript missense_variant 1034/1519 521/939 174/312 T/M aCg/aTg COSM2802458,COSM2802459 1 -1 RBFOX3 HGNC HGNC:27097 protein_coding YES CCDS45805.1 ENSP00000463653 A6NFN3 UPI000020041C NM_001082575.2 deleterious(0) 9/15 PROSITE_profiles:PS50102,hmmpanther:PTHR15597,Gene3D:3.30.70.330,PIRSF_domain:PIRSF037932,Superfamily_domains:SSF54928 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1207425560 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 79101631 79101631 G A 1 0 0 0 0 1 0 0 0 13273 1145 40 1 1 RBFOX3 17 79101631 Missense_Mutation SNP G C3L-01862_T 28993300 79101631 4155810 135 7656 LAMA1 0 . GRCh38 18 6974924 6974924 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.6602G>T p.Trp2201Leu p.W2201L ENST00000389658 46/63 357 295 62 344 344 0 strelka-varscan-mutect LAMA1,missense_variant,p.Trp2201Leu,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,upstream_gene_variant,,ENST00000484335,; A ENST00000389658 Transcript missense_variant 6696/9657 6602/9228 2201/3075 W/L tGg/tTg 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 46/63 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 6974924 6974924 C A 1 0 0 0 0 1 0 0 0 8509 595 21 2 2 LAMA1 18 6974924 Missense_Mutation SNP C C3L-01862_T 6974924 73398361 136 7657 MOCOS 0 . GRCh38 18 36220074 36220074 + Missense_Mutation SNP G G C rs571933510 C3L-01862_T C3L-01862_N G G c.1817G>C p.Gly606Ala p.G606A ENST00000261326 9/15 478 396 82 484 484 0 strelka-varscan-mutect MOCOS,missense_variant,p.Gly606Ala,ENST00000261326,NM_017947.2; C ENST00000261326 Transcript missense_variant 1838/6160 1817/2667 606/888 G/A gGa/gCa rs571933510 1 1 MOCOS HGNC HGNC:18234 protein_coding YES CCDS11919.1 ENSP00000261326 Q96EN8 UPI000013D165 NM_017947.2 deleterious(0.01) 9/15 Superfamily_domains:0052540,HAMAP:MF_03050,Pfam_domain:PF03476 MODERATE 1 SNV 1 1 PASS rs571933510 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 36220074 36220074 G C 1 0 0 0 0 1 0 0 0 9652 1174 41 4 4 MOCOS 18 36220074 Missense_Mutation SNP G C3L-01862_T 29245150 36220074 44153211 137 7658 STK11 0 . GRCh38 19 1207093 1207093 + Nonsense_Mutation SNP C C A rs778376925 C3L-01862_T C3L-01862_N C C c.180C>A p.Tyr60Ter p.Y60* ENST00000326873 1/10 284 230 54 290 290 0 strelka-varscan-mutect STK11,stop_gained,p.Tyr60Ter,ENST00000586243,;STK11,stop_gained,p.Tyr60Ter,ENST00000326873,NM_000455.4;STK11,stop_gained,p.Tyr60Ter,ENST00000585851,;STK11,intron_variant,,ENST00000585748,;STK11,stop_gained,p.Tyr60Ter,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;HMGB2P1,downstream_gene_variant,,ENST00000591146,; A ENST00000326873 Transcript stop_gained 630/2611 180/1302 60/433 Y/* taC/taA rs778376925,CD064644,CM981863,CM991149,KinMutBase_STK11_DNA:g.1180C>G,COSM20874,COSM27322,COSM48900,COSM5328246,COSM5490514 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 1/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,0,0,0,0,1,1,1,1,1 HIGH 1 SNV 1 0,1,1,1,0,1,1,1,1,1 1 PASS rs778376925 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 27 1207093 1207093 C A 1 0 0 0 0 0 1 0 0 15664 547 19 1 1 STK11 19 1207093 Nonsense_Mutation SNP C C3L-01862_T 1207093 57410523 138 7659 CLEC4G 0 . GRCh38 19 7731704 7731704 + Frame_Shift_Del DEL G G - rs759251117 C3L-01862_T C3L-01862_N G G c.123delC p.Thr42GlnfsTer6 p.T42Qfs*6 ENST00000328853 2/9 163 130 33 196 196 0 sindel-varindel-pindel CLEC4G,frameshift_variant,p.Thr42GlnfsTer6,ENST00000328853,NM_198492.3,NM_001244856.1;CLEC4G,frameshift_variant,p.Thr84GlnfsTer6,ENST00000599020,;CLEC4G,non_coding_transcript_exon_variant,,ENST00000598081,; - ENST00000328853 Transcript frameshift_variant 192/1360 123/882 41/293 T/X acC/ac rs759251117 1 -1 CLEC4G HGNC HGNC:24591 protein_coding YES CCDS12185.1 ENSP00000327599 Q6UXB4 Q08G24 UPI000004C65D NM_198492.3,NM_001244856.1 2/9 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF245 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 27 7731704 7731704 G - 1 0 1 0 1 0 0 0 0 3285 1335 47 0 0 CLEC4G 19 7731704 Frame_Shift_Del DEL G C3L-01862_T 6524611 7731704 50885912 139 7660 MYO1F 0 . GRCh38 19 8550291 8550291 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.970C>A p.Arg324Ser p.R324S ENST00000338257 10/28 176 135 41 190 189 1 strelka-varscan-mutect MYO1F,missense_variant,p.Arg324Ser,ENST00000338257,NM_012335.3;MYO1F,missense_variant,p.Arg324Ser,ENST00000613525,;MYO1F,downstream_gene_variant,,ENST00000596675,;AC092316.1,downstream_gene_variant,,ENST00000598703,;MYO1F,non_coding_transcript_exon_variant,,ENST00000594977,;MYO1F,non_coding_transcript_exon_variant,,ENST00000595191,;MYO1F,non_coding_transcript_exon_variant,,ENST00000600825,;MYO1F,non_coding_transcript_exon_variant,,ENST00000596937,;MYO1F,downstream_gene_variant,,ENST00000595325,;MYO1F,downstream_gene_variant,,ENST00000594774,;MYO1F,downstream_gene_variant,,ENST00000598529,;MYO1F,upstream_gene_variant,,ENST00000602136,;MYO1F,downstream_gene_variant,,ENST00000598321,;MYO1F,downstream_gene_variant,,ENST00000599123,;MYO1F,upstream_gene_variant,,ENST00000601502,; T ENST00000338257 Transcript missense_variant 1238/4303 970/3297 324/1098 R/S Cgc/Agc 1 -1 MYO1F HGNC HGNC:7600 protein_coding YES CCDS42494.1 ENSP00000344871 O00160 UPI00001678F0 NM_012335.3 deleterious(0) 10/28 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF288,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 8550291 8550291 G T 1 0 0 0 0 1 0 0 0 10074 1116 39 1 1 MYO1F 19 8550291 Missense_Mutation SNP G C3L-01862_T 818587 8550291 50067325 140 7661 ZNF317 0 . GRCh38 19 9160897 9160897 + Missense_Mutation SNP G G T rs781139661 C3L-01862_T C3L-01862_N G G c.1252G>T p.Val418Leu p.V418L ENST00000247956 7/7 196 159 37 271 271 0 strelka-varscan-mutect ZNF317,missense_variant,p.Val418Leu,ENST00000247956,NM_020933.4;ZNF317,missense_variant,p.Val386Leu,ENST00000360385,NM_001190791.1;ZNF317,intron_variant,,ENST00000591508,;ZNF317,3_prime_UTR_variant,,ENST00000591278,;ZNF317,non_coding_transcript_exon_variant,,ENST00000590152,;ZNF317,downstream_gene_variant,,ENST00000419608,; T ENST00000247956 Transcript missense_variant 1557/4073 1252/1788 418/595 V/L Gtg/Ttg rs781139661,COSM2701801 1 1 ZNF317 HGNC HGNC:13507 protein_coding YES CCDS12210.1 ENSP00000247956 Q96PQ6 A0A024R7B1 UPI0000366D00 NM_020933.4 deleterious(0.02) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF22,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781139661 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 9160897 9160897 G T 1 0 0 0 0 1 0 0 0 18410 1145 40 1 1 ZNF317 19 9160897 Missense_Mutation SNP G C3L-01862_T 610606 9160897 49456719 141 7662 KEAP1 0 . GRCh38 19 10489271 10489274 + Frame_Shift_Del DEL CGTC CGTC - novel C3L-01862_T C3L-01862_N CGTC CGTC c.1626_1629delGACG p.Glu542AspfsTer5 p.E542Dfs*5 ENST00000171111 5/6 141 118 23 141 141 0 sindel-varindel-pindel KEAP1,frameshift_variant,p.Glu542AspfsTer5,ENST00000171111,NM_203500.1;KEAP1,frameshift_variant,p.Glu542AspfsTer5,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000590593,;KEAP1,non_coding_transcript_exon_variant,,ENST00000590237,;KEAP1,downstream_gene_variant,,ENST00000585845,; - ENST00000171111 Transcript frameshift_variant 2174-2177/2955 1626-1629/1875 542-543/624 ET/X gaGACG/ga 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 5/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 HIGH 1 deletion 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999944 1 1 1 0 - 7 5 27 10489271 10489271 CGTC - 1 0 1 0 1 0 0 0 0 8061 523 19 0 0 KEAP1 19 10489271 Frame_Shift_Del DEL CGTC C3L-01862_T 1328374 10489271 48128345 142 7663 SMARCA4 0 . GRCh38 19 10984360 10984361 + Frame_Shift_Ins INS - - C novel C3L-01862_T C3L-01862_N - - c.211dupC p.Gln71ProfsTer11 p.Q71Pfs*11 ENST00000429416 3/36 199 157 42 297 297 0 sindel-varindel-pindel SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000429416,NM_001128844.1;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000413806,;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000450717,NM_001128849.1;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000344626,NM_003072.3;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000590574,NM_001128847.1;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000589677,NM_001128846.1;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000541122,NM_001128845.1;SMARCA4,frameshift_variant,p.Gln71ProfsTer11,ENST00000444061,NM_001128848.1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,; C ENST00000429416 Transcript frameshift_variant 490-491/5691 209-210/4944 70/1647 H/HX cac/caCc 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 3/36 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76 HIGH 1 insertion 2 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 27 10984360 10984360 - C 1 0 1 1 0 0 0 0 0 15063 159 6 0 0 SMARCA4 19 10984360 Frame_Shift_Ins INS - C3L-01862_T 495089 10984360 47633256 143 7664 SLC1A6 0 . GRCh38 19 14954170 14954170 + Missense_Mutation SNP G G T rs779747638 C3L-01862_T C3L-01862_N G G c.1329C>A p.Asn443Lys p.N443K ENST00000221742 7/9 58 42 16 122 122 0 strelka-varscan-mutect SLC1A6,missense_variant,p.Asn379Lys,ENST00000430939,;SLC1A6,missense_variant,p.Asn365Lys,ENST00000600144,;SLC1A6,missense_variant,p.Asn443Lys,ENST00000221742,NM_005071.2; T ENST00000221742 Transcript missense_variant 1337/1719 1329/1695 443/564 N/K aaC/aaA rs779747638 1 -1 SLC1A6 HGNC HGNC:10944 protein_coding YES CCDS12321.1 ENSP00000221742 P48664 UPI0000129B1A NM_005071.2 deleterious(0.01) 7/9 hmmpanther:PTHR11958:SF67,hmmpanther:PTHR11958,Pfam_domain:PF00375,Gene3D:2nwlC00,Superfamily_domains:0053221 MODERATE 1 SNV 1 1 PASS rs779747638 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 14954170 14954170 G T 1 0 0 0 0 1 0 0 0 14702 1020 36 2 2 SLC1A6 19 14954170 Missense_Mutation SNP G C3L-01862_T 3969810 14954170 43663446 144 7665 CCDC105 0 . GRCh38 19 15010940 15010940 + Frame_Shift_Del DEL T T - novel C3L-01862_T C3L-01862_N T T c.115delT p.Cys39AlafsTer6 p.C39Afs*6 ENST00000292574 1/7 205 166 39 231 231 0 sindel-varindel CCDC105,frameshift_variant,p.Cys39AlafsTer6,ENST00000292574,NM_173482.2;SLC1A6,intron_variant,,ENST00000595863,;SLC1A6,upstream_gene_variant,,ENST00000430939,;SLC1A6,upstream_gene_variant,,ENST00000599636,; - ENST00000292574 Transcript frameshift_variant 197/1732 115/1500 39/499 C/X Tgc/gc 1 1 CCDC105 HGNC HGNC:26866 protein_coding YES CCDS12322.1 ENSP00000292574 Q8IYK2 UPI0000073091 NM_173482.2 1/7 hmmpanther:PTHR35081 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 27 15010940 15010940 T - 1 0 1 0 1 0 0 0 0 2437 1580 55 0 0 CCDC105 19 15010940 Frame_Shift_Del DEL T C3L-01862_T 56770 15010940 43606676 145 7666 OR10H3 0 . GRCh38 19 15741396 15741396 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.4C>T p.Pro2Ser p.P2S ENST00000305892 1/1 44 33 11 109 109 0 strelka-varscan-mutect OR10H3,missense_variant,p.Pro2Ser,ENST00000305892,NM_013938.1; T ENST00000305892 Transcript missense_variant 4/951 4/951 2/316 P/S Cct/Tct 1 1 OR10H3 HGNC HGNC:8174 protein_coding YES CCDS12334.1 ENSP00000307130 O60404 A0A126GW93 UPI0000041DB5 NM_013938.1 tolerated(0.61) 1/1 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF78,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1356616155 . 0 201 9 0 0 0 0 0 -20 0.9999977 1 1 1 0 T 3 4 27 15741396 15741396 C T 1 0 0 0 0 1 0 0 0 10984 753 26 3 3 OR10H3 19 15741396 Missense_Mutation SNP C C3L-01862_T 730456 15741396 42876220 146 7667 ZNF568 0 . GRCh38 19 36950493 36950493 + Missense_Mutation SNP A A T novel C3L-01862_T C3L-01862_N A A c.1340A>T p.Glu447Val p.E447V ENST00000619231 5/5 175 143 32 235 235 0 strelka-varscan-mutect ZNF568,missense_variant,p.Glu447Val,ENST00000619231,;ZNF568,missense_variant,p.Glu383Val,ENST00000415168,NM_001204837.1,NM_001204836.1;ZNF568,missense_variant,p.Glu447Val,ENST00000333987,NM_001204835.1,NM_198539.3;ZNF568,missense_variant,p.Glu383Val,ENST00000587857,;ZNF568,3_prime_UTR_variant,,ENST00000616085,;ZNF568,intron_variant,,ENST00000617745,NM_001204838.1;ZNF568,intron_variant,,ENST00000455427,NM_001204839.1;ZNF568,intron_variant,,ENST00000444991,;ZNF568,intron_variant,,ENST00000427117,; T ENST00000619231 Transcript missense_variant 1549/3797 1340/1935 447/644 E/V gAa/gTa 1 1 ZNF568 HGNC HGNC:25392 protein_coding YES CCDS42558.1 ENSP00000481819 Q3ZCX4 UPI000059D700 deleterious(0.03) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF372,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 36950493 36950493 A T 1 0 0 0 0 1 0 0 0 18573 246 9 4 4 ZNF568 19 36950493 Missense_Mutation SNP A C3L-01862_T 21209097 36950493 21667123 147 7668 IL4I1 0 . GRCh38 19 49894463 49894463 + Silent SNP G G T rs754928014 C3L-01862_T C3L-01862_N G G c.438C>A p.= p.L146L ENST00000595948 7/10 195 147 48 211 211 0 strelka-varscan-mutect IL4I1,synonymous_variant,p.=,ENST00000595948,NM_001258018.1;IL4I1,synonymous_variant,p.=,ENST00000341114,NM_172374.2,NM_001258017.1;IL4I1,synonymous_variant,p.=,ENST00000391826,NM_152899.1;IL4I1,synonymous_variant,p.=,ENST00000593956,;IL4I1,downstream_gene_variant,,ENST00000596022,;IL4I1,downstream_gene_variant,,ENST00000596011,;IL4I1,downstream_gene_variant,,ENST00000597295,;IL4I1,3_prime_UTR_variant,,ENST00000601717,; T ENST00000595948 Transcript synonymous_variant 1059/2407 438/1770 146/589 L ctC/ctA rs754928014,COSM5583630 1 -1 IL4I1 HGNC HGNC:19094 protein_coding YES CCDS12786.1 ENSP00000472474 Q96RQ9 UPI00001678CE NM_001258018.1 7/10 hmmpanther:PTHR10742,hmmpanther:PTHR10742:SF21,Pfam_domain:PF01593,Gene3D:3.90.660.10,Superfamily_domains:SSF51905 0,1 LOW 1 SNV 1 0,1 1 PASS rs754928014 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 49894463 49894463 G T 1 0 0 0 0 0 0 0 1 7601 1161 41 2 2 IL4I1 19 49894463 Silent SNP G C3L-01862_T 12943970 49894463 8723153 148 7669 AC018755.18 0 . GRCh38 19 51629490 51629490 + Missense_Mutation SNP G G C rs772339797 C3L-01862_T C3L-01862_N G G c.568C>G p.Pro190Ala p.P190A ENST00000534261 4/10 122 107 15 156 156 0 varscan-mutect SIGLEC5,missense_variant,p.Pro190Ala,ENST00000534261,NM_003830.3;AC018755.18,missense_variant,p.Pro190Ala,ENST00000429354,;AC018755.18,missense_variant,p.Pro190Ala,ENST00000599649,; C ENST00000534261 Transcript missense_variant 968/2360 568/1656 190/551 P/A Ccc/Gcc rs772339797 1 -1 SIGLEC5 HGNC HGNC:10874 protein_coding YES CCDS33088.1 ENSP00000473238 O15389 UPI000011B40C NM_003830.3 deleterious(0.03) 4/10 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF67,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs772339797 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 27 51629490 51629490 G C 1 0 0 0 0 1 0 0 0 125 1232 43 4 4 AC018755.18 19 51629490 Missense_Mutation SNP G C3L-01862_T 1735027 51629490 6988126 149 7670 ZNF805 0 . GRCh38 19 57248610 57248610 + Missense_Mutation SNP C C T novel C3L-01862_T C3L-01862_N C C c.163C>T p.Pro55Ser p.P55S ENST00000414468 3/4 262 226 36 296 296 0 strelka-varscan-mutect ZNF805,missense_variant,p.Pro55Ser,ENST00000414468,NM_001023563.3;ZNF805,5_prime_UTR_variant,,ENST00000354309,NM_001145078.1; T ENST00000414468 Transcript missense_variant 163/1884 163/1884 55/627 P/S Cct/Tct 1 1 ZNF805 HGNC HGNC:23272 protein_coding YES CCDS46207.1 ENSP00000412999 Q5CZA5 UPI000041AAAF NM_001023563.3 tolerated(0.08) 3/4 Superfamily_domains:0044637,PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF192,SMART_domains:SM00349 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 57248610 57248610 C T 1 0 0 0 0 1 0 0 0 18757 869 30 3 3 ZNF805 19 57248610 Missense_Mutation SNP C C3L-01862_T 5619120 57248610 1369006 150 7671 ZNF416 0 . GRCh38 19 57572186 57572186 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.1718C>A p.Thr573Asn p.T573N ENST00000196489 4/4 106 87 19 134 134 0 strelka-varscan-mutect ZNF416,missense_variant,p.Thr573Asn,ENST00000196489,NM_017879.1; T ENST00000196489 Transcript missense_variant 1941/2561 1718/1785 573/594 T/N aCt/aAt 1 -1 ZNF416 HGNC HGNC:20645 protein_coding YES CCDS12954.1 ENSP00000196489 Q9BWM5 UPI000007314D NM_017879.1 deleterious(0.01) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF160,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1491111421 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 57572186 57572186 G T 1 0 0 0 0 1 0 0 0 18465 1029 36 2 2 ZNF416 19 57572186 Missense_Mutation SNP G C3L-01862_T 323576 57572186 1045430 151 7672 TTLL9 0 . GRCh38 20 31937486 31937486 + Silent SNP G G A novel C3L-01862_T C3L-01862_N G G c.1095G>A p.= p.L365L ENST00000535842 12/14 203 179 24 184 184 0 strelka-varscan-mutect TTLL9,synonymous_variant,p.=,ENST00000535842,;TTLL9,synonymous_variant,p.=,ENST00000620043,;TTLL9,synonymous_variant,p.=,ENST00000375938,NM_001008409.2;TTLL9,synonymous_variant,p.=,ENST00000612972,;TTLL9,non_coding_transcript_exon_variant,,ENST00000375922,;TTLL9,3_prime_UTR_variant,,ENST00000375921,;TTLL9,3_prime_UTR_variant,,ENST00000619753,;TTLL9,3_prime_UTR_variant,,ENST00000616761,;TTLL9,3_prime_UTR_variant,,ENST00000611624,;TTLL9,3_prime_UTR_variant,,ENST00000310998,;TTLL9,3_prime_UTR_variant,,ENST00000375934,; A ENST00000535842 Transcript synonymous_variant 1095/3261 1095/1320 365/439 L ctG/ctA 1 1 TTLL9 HGNC HGNC:16118 protein_coding YES CCDS42863.1 ENSP00000442515 Q3SXZ7 UPI00001998D0 12/14 PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF39,Pfam_domain:PF03133 LOW 1 SNV 5 1 PASS rs1287052164 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 31937486 31937486 G A 1 0 0 0 0 0 0 0 1 17244 1306 46 3 3 TTLL9 20 31937486 Silent SNP G C3L-01862_T 31937486 32506681 152 7673 KCNB1 0 . GRCh38 20 49374097 49374097 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.1463G>T p.Trp488Leu p.W488L ENST00000371741 2/2 183 149 34 235 234 1 strelka-varscan-mutect KCNB1,missense_variant,p.Trp488Leu,ENST00000371741,NM_004975.2;KCNB1,missense_variant,p.Trp488Leu,ENST00000635465,;KCNB1,intron_variant,,ENST00000635878,;RP4-791K14.2,intron_variant,,ENST00000637341,;KCNB1,upstream_gene_variant,,ENST00000636838,;RP4-791K14.2,downstream_gene_variant,,ENST00000637091,;RP4-791K14.2,downstream_gene_variant,,ENST00000637575,;KCNB1,downstream_gene_variant,,ENST00000635210,;KCNB1,upstream_gene_variant,,ENST00000637131,; A ENST00000371741 Transcript missense_variant 1659/11879 1463/2577 488/858 W/L tGg/tTg 1 -1 KCNB1 HGNC HGNC:6231 protein_coding YES CCDS13418.1 ENSP00000360806 Q14721 UPI000012DC80 NM_004975.2 tolerated_low_confidence(0.05) 2/2 hmmpanther:PTHR11537:SF134,hmmpanther:PTHR11537,Pfam_domain:PF03521 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 49374097 49374097 C A 1 0 0 0 0 1 0 0 0 7928 595 21 2 2 KCNB1 20 49374097 Missense_Mutation SNP C C3L-01862_T 17436611 49374097 15070070 153 7674 KRTAP25-1 0 . GRCh38 21 30289365 30289365 + Silent SNP G G T novel C3L-01862_T C3L-01862_N G G c.126C>A p.= p.T42T ENST00000416044 1/1 261 226 35 275 272 3 strelka-varscan-mutect KRTAP25-1,synonymous_variant,p.=,ENST00000416044,NM_001128598.1; T ENST00000416044 Transcript synonymous_variant 150/370 126/309 42/102 T acC/acA 1 -1 KRTAP25-1 HGNC HGNC:34003 protein_coding YES CCDS46640.1 ENSP00000398619 Q3LHN0 UPI00005C50FC NM_001128598.1 1/1 hmmpanther:PTHR19051:SF19,hmmpanther:PTHR19051,Pfam_domain:PF05287 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 30289365 30289365 G T 1 0 0 0 0 0 0 0 1 8434 987 35 2 2 KRTAP25-1 21 30289365 Silent SNP G C3L-01862_T 30289365 16420618 154 7675 DHRSX 0 . GRCh38 X 2243039 2243039 + Missense_Mutation SNP C C A novel C3L-01862_T C3L-01862_N C C c.788G>T p.Gly263Val p.G263V ENST00000334651 6/7 86 70 16 108 108 0 varscan-mutect DHRSX,missense_variant,p.Gly263Val,ENST00000334651,NM_145177.2;DHRSX,downstream_gene_variant,,ENST00000412516,; A ENST00000334651 Transcript missense_variant 841/2571 788/993 263/330 G/V gGc/gTc 1 -1 DHRSX HGNC HGNC:18399 protein_coding YES CCDS35195.1 ENSP00000334113 Q8N5I4 UPI0000D61D1C NM_145177.2 deleterious(0.01) 6/7 hmmpanther:PTHR24319,hmmpanther:PTHR24319:SF33,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 27 2243039 2243039 C A 1 0 0 0 0 1 0 0 0 4303 739 26 2 2 DHRSX 23 2243039 Missense_Mutation SNP C C3L-01862_T 2243039 153797856 155 7676 MAGEB17 0 . GRCh38 X 16170981 16170981 + Missense_Mutation SNP G G T novel C3L-01862_T C3L-01862_N G G c.599G>T p.Gly200Val p.G200V ENST00000400004 2/2 40 28 12 70 69 1 strelka-varscan-mutect MAGEB17,missense_variant,p.Gly200Val,ENST00000400004,NM_001277307.1;MAGEB17,missense_variant,p.Gly200Val,ENST00000400003,;RP11-431J24.2,upstream_gene_variant,,ENST00000435789,; T ENST00000400004 Transcript missense_variant 951/1434 599/1011 200/336 G/V gGg/gTg 1 1 MAGEB17 HGNC HGNC:17418 protein_coding YES CCDS59524.1 ENSP00000382884 A8MXT2 UPI00001602F1 NM_001277307.1 deleterious(0) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF67,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 27 16170981 16170981 G T 1 0 0 0 0 1 0 0 0 9090 1232 43 2 2 MAGEB17 23 16170981 Missense_Mutation SNP G C3L-01862_T 13927942 16170981 139869914 156 7677 MAP3K15 0 . GRCh38 X 19371441 19371441 + Silent SNP C C T novel C3L-01862_T C3L-01862_N C C c.3198G>A p.= p.V1066V ENST00000338883 23/29 73 65 8 63 63 0 strelka-varscan-mutect MAP3K15,synonymous_variant,p.=,ENST00000338883,NM_001001671.3;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;MAP3K15,3_prime_UTR_variant,,ENST00000359173,;MAP3K15,non_coding_transcript_exon_variant,,ENST00000470101,; T ENST00000338883 Transcript synonymous_variant 3198/4012 3198/3942 1066/1313 V gtG/gtA 1 -1 MAP3K15 HGNC HGNC:31689 protein_coding YES CCDS35212.2 ENSP00000345629 Q6ZN16 UPI0000E444D0 NM_001001671.3 23/29 hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 27 19371441 19371441 C T 1 0 0 0 0 0 0 0 1 9171 813 29 3 3 MAP3K15 23 19371441 Silent SNP C C3L-01862_T 3200460 19371441 136669454 157 7678 GPR50 0 . GRCh38 X 151180216 151180216 + Silent SNP C C A C3L-01862_T C3L-01862_N C C c.633C>A p.= p.I211I ENST00000218316 2/2 70 50 20 75 75 0 strelka-varscan-mutect GPR50,synonymous_variant,p.=,ENST00000218316,NM_004224.3;AF003625.3,upstream_gene_variant,,ENST00000602313,;GPR50-AS1,upstream_gene_variant,,ENST00000454196,; A ENST00000218316 Transcript synonymous_variant 702/1951 633/1854 211/617 I atC/atA COSM1253560,COSM1253561 1 1 GPR50 HGNC HGNC:4506 protein_coding YES CCDS44012.1 ENSP00000218316 Q13585 UPI000013C755 NM_004224.3 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF51,hmmpanther:PTHR24242,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 27 151180216 151180216 C A 1 0 0 0 0 0 0 0 1 6582 903 32 2 2 GPR50 23 151180216 Silent SNP C C3L-01862_T 131808775 151180216 4860679 158 7679 PRAMEF1 0 . GRCh38 1 12795678 12795678 + Silent SNP C C A novel C3L-01889_T C3L-01889_N C C c.1107C>A p.= p.I369I ENST00000332296 4/4 268 201 67 320 319 1 strelka-varscan-mutect PRAMEF1,synonymous_variant,p.=,ENST00000332296,NM_001291380.1,NM_023013.4;PRAMEF1,non_coding_transcript_exon_variant,,ENST00000400814,; A ENST00000332296 Transcript synonymous_variant 1210/2160 1107/1425 369/474 I atC/atA 1 1 PRAMEF1 HGNC HGNC:28840 protein_coding YES CCDS148.1 ENSP00000332134 O95521 UPI0004620BB8 NM_001291380.1,NM_023013.4 4/4 Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF2,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 12795678 12795678 C A 1 0 0 0 0 0 0 0 1 12554 845 30 2 2 PRAMEF1 1 12795678 Silent SNP C C3L-01889_T 12795678 236160744 1 7680 ADGRB2 0 . GRCh38 1 31756317 31756317 + Missense_Mutation SNP C C A rs200554940 C3L-01889_T C3L-01889_N C C c.520G>T p.Ala174Ser p.A174S ENST00000373655 4/33 355 259 96 299 298 1 strelka-varscan-mutect ADGRB2,missense_variant,p.Ala174Ser,ENST00000373658,;ADGRB2,missense_variant,p.Ala174Ser,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Ala162Ser,ENST00000398542,;ADGRB2,missense_variant,p.Ala174Ser,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Ala177Ser,ENST00000398556,;ADGRB2,missense_variant,p.Ala162Ser,ENST00000398547,;ADGRB2,missense_variant,p.Ala162Ser,ENST00000398538,;ADGRB2,missense_variant,p.Ala167Ser,ENST00000420125,;ADGRB2,missense_variant,p.Ala208Ser,ENST00000533175,;ADGRB2,downstream_gene_variant,,ENST00000436464,;MIR4254,downstream_gene_variant,,ENST00000581063,;ADGRB2,upstream_gene_variant,,ENST00000530134,; A ENST00000373655 Transcript missense_variant 862/5400 520/4755 174/1584 A/S Gcg/Tcg rs200554940 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 tolerated(0.57) 4/33 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs200554940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 31756317 31756317 C A 1 0 0 0 0 1 0 0 0 356 739 26 2 2 ADGRB2 1 31756317 Missense_Mutation SNP C C3L-01889_T 18960639 31756317 217200105 2 7681 CSMD2 0 . GRCh38 1 33523413 33523413 + Missense_Mutation SNP T T A rs555430648 C3L-01889_T C3L-01889_N T T c.10403A>T p.Tyr3468Phe p.Y3468F ENST00000373381 67/71 131 94 37 157 157 0 strelka-varscan-mutect CSMD2,missense_variant,p.Tyr3468Phe,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Tyr3428Phe,ENST00000619121,;CSMD2,missense_variant,p.Tyr3324Phe,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Tyr3324Phe,ENST00000241312,; A ENST00000373381 Transcript missense_variant 10580/13698 10403/10896 3468/3631 Y/F tAc/tTc rs555430648 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 deleterious(0.03) 67/71 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF371 MODERATE 1 SNV 1 1 PASS rs555430648 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 33523413 33523413 T A 1 0 0 0 0 1 0 0 0 3746 1638 57 4 4 CSMD2 1 33523413 Missense_Mutation SNP T C3L-01889_T 1767096 33523413 215433009 3 7682 GRIK3 0 . GRCh38 1 37034058 37034058 + Frame_Shift_Del DEL G G - novel C3L-01889_T C3L-01889_N G G c.51delC p.Leu19SerfsTer35 p.L19Sfs*35 ENST00000373091 1/16 145 118 27 157 157 0 sindel-varindel-pindel GRIK3,frameshift_variant,p.Leu19SerfsTer35,ENST00000373091,NM_000831.3;GRIK3,frameshift_variant,p.Leu19SerfsTer35,ENST00000373093,; - ENST00000373091 Transcript frameshift_variant 68/9101 51/2760 17/919 A/X gcC/gc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 1/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,Cleavage_site_(Signalp):SignalP-noTM HIGH 1 deletion 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999957 1 1 1 0 - 7 5 28 37034058 37034058 G - 1 0 1 0 1 0 0 0 0 6657 1103 39 0 0 GRIK3 1 37034058 Frame_Shift_Del DEL G C3L-01889_T 3510645 37034058 211922364 4 7683 PTCH2 0 . GRCh38 1 44830946 44830946 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.715G>A p.Asp239Asn p.D239N ENST00000372192 6/22 44 31 13 56 56 0 strelka-varscan-mutect PTCH2,missense_variant,p.Asp239Asn,ENST00000447098,NM_001166292.1;PTCH2,missense_variant,p.Asp239Asn,ENST00000372192,NM_003738.4; T ENST00000372192 Transcript missense_variant 846/4225 715/3612 239/1203 D/N Gac/Aac 1 -1 PTCH2 HGNC HGNC:9586 protein_coding YES CCDS516.1 ENSP00000361266 Q9Y6C5 UPI00001328B8 NM_003738.4 tolerated(0.47) 6/22 hmmpanther:PTHR10796:SF62,hmmpanther:PTHR10796,TIGRFAM_domain:TIGR00918 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 44830946 44830946 C T 1 0 0 0 0 1 0 0 0 12884 913 32 3 3 PTCH2 1 44830946 Missense_Mutation SNP C C3L-01889_T 7796888 44830946 204125476 5 7684 DMRTA2 0 . GRCh38 1 50418760 50418760 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1534C>A p.Arg512Ser p.R512S ENST00000404795 3/3 79 67 12 90 90 0 strelka-varscan-mutect DMRTA2,missense_variant,p.Arg512Ser,ENST00000404795,NM_032110.2;DMRTA2,missense_variant,p.Arg512Ser,ENST00000418121,; T ENST00000404795 Transcript missense_variant 1927/3137 1534/1629 512/542 R/S Cgc/Agc 1 -1 DMRTA2 HGNC HGNC:13908 protein_coding YES CCDS44141.1 ENSP00000383909 Q96SC8 UPI00003D7962 NM_032110.2 tolerated(0.57) 3/3 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF76 MODERATE 1 SNV 5 1 PASS . . 0 202 5 3 0 0 0 0 -19.79712 0.9997351 1 1 1 0 T 3 4 28 50418760 50418760 G T 1 0 0 0 0 1 0 0 0 4396 1116 39 1 1 DMRTA2 1 50418760 Missense_Mutation SNP G C3L-01889_T 5587814 50418760 198537662 6 7685 PARS2 0 . GRCh38 1 54759106 54759106 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.56G>T p.Arg19Leu p.R19L ENST00000371279 2/2 65 53 12 53 53 0 strelka-varscan-mutect PARS2,missense_variant,p.Arg19Leu,ENST00000371279,NM_152268.3; A ENST00000371279 Transcript missense_variant 139/2347 56/1428 19/475 R/L cGc/cTc 1 -1 PARS2 HGNC HGNC:30563 protein_coding YES CCDS597.1 ENSP00000360327 Q7L3T8 UPI00000492D2 NM_152268.3 tolerated_low_confidence(0.42) 2/2 MODERATE 1 SNV 1 1 PASS rs1369337533 . 0 193 15 2 0 0 0 0 -19.98852 0.9971176 1 1 1 0 A 3 1 28 54759106 54759106 C A 1 0 0 0 0 1 0 0 0 11548 768 27 1 1 PARS2 1 54759106 Missense_Mutation SNP C C3L-01889_T 4340346 54759106 194197316 7 7686 ST6GALNAC5 0 . GRCh38 1 77044493 77044493 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.551A>T p.Gln184Leu p.Q184L ENST00000477717 3/5 90 69 21 76 76 0 strelka-varscan-mutect ST6GALNAC5,missense_variant,p.Gln184Leu,ENST00000477717,NM_030965.1;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000488940,;ST6GALNAC5,missense_variant,p.Gln184Leu,ENST00000318803,; T ENST00000477717 Transcript missense_variant 786/3751 551/1011 184/336 Q/L cAg/cTg 1 1 ST6GALNAC5 HGNC HGNC:19342 protein_coding YES CCDS673.1 ENSP00000417583 Q9BVH7 UPI0000001C9F NM_030965.1 3/5 Pfam_domain:PF00777,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF33 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 77044493 77044493 A T 1 0 0 0 0 1 0 0 0 15605 188 7 4 4 ST6GALNAC5 1 77044493 Missense_Mutation SNP A C3L-01889_T 22285387 77044493 171911929 8 7687 COL11A1 0 . GRCh38 1 102962742 102962742 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.2935G>T p.Gly979Cys p.G979C ENST00000370096 39/67 255 186 69 222 222 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly991Cys,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly979Cys,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly940Cys,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly863Cys,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,;COL11A1,upstream_gene_variant,,ENST00000465209,; A ENST00000370096 Transcript missense_variant 3248/7286 2935/5421 979/1806 G/C Ggt/Tgt 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 39/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 102962742 102962742 C A 1 0 0 0 0 1 0 0 0 3455 594 21 2 2 COL11A1 1 102962742 Missense_Mutation SNP C C3L-01889_T 25918249 102962742 145993680 9 7688 TCHH 0 . GRCh38 1 152112615 152112615 + Frame_Shift_Del DEL G G - rs756454573 C3L-01889_T C3L-01889_N G G c.602delC p.Thr201MetfsTer18 p.T201Mfs*18 ENST00000614923 3/3 271 209 62 227 227 0 sindel-varindel TCHH,frameshift_variant,p.Thr201MetfsTer18,ENST00000614923,NM_007113.3;TCHH,frameshift_variant,p.Thr201MetfsTer18,ENST00000368804,; - ENST00000614923 Transcript frameshift_variant 697/6995 602/5832 201/1943 T/X aCt/at rs756454573 1 -1 TCHH HGNC HGNC:11791 protein_coding YES CCDS41396.1 ENSP00000480484 Q07283 UPI0000458A5E NM_007113.3 3/3 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 152112615 152112615 G - 1 0 1 0 1 0 0 0 0 16107 1029 36 0 0 TCHH 1 152112615 Frame_Shift_Del DEL G C3L-01889_T 49149873 152112615 96843807 10 7689 NFASC 0 . GRCh38 1 204952034 204952034 + Nonsense_Mutation SNP A A T rs138945016 C3L-01889_T C3L-01889_N A A c.133A>T p.Lys45Ter p.K45* ENST00000339876 5/30 238 140 98 183 183 0 strelka-varscan-mutect NFASC,stop_gained,p.Lys45Ter,ENST00000339876,NM_001005388.2;NFASC,stop_gained,p.Lys45Ter,ENST00000401399,;NFASC,stop_gained,p.Lys39Ter,ENST00000539706,NM_001160332.1;NFASC,stop_gained,p.Lys39Ter,ENST00000360049,NM_015090.3;NFASC,stop_gained,p.Lys39Ter,ENST00000404076,;NFASC,stop_gained,p.Lys39Ter,ENST00000404907,;NFASC,stop_gained,p.Lys15Ter,ENST00000430393,NM_001160331.1;NFASC,stop_gained,p.Lys15Ter,ENST00000367173,;NFASC,stop_gained,p.Lys39Ter,ENST00000513543,;NFASC,stop_gained,p.Lys45Ter,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,stop_gained,p.Lys45Ter,ENST00000505079,;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,stop_gained,p.Lys45Ter,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000514644,;RP11-494K3.2,downstream_gene_variant,,ENST00000452580,; T ENST00000339876 Transcript stop_gained 461/10333 133/3723 45/1240 K/* Aag/Tag rs138945016 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 5/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Pfam_domain:PF13927,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS rs138945016 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 28 204952034 204952034 A T 1 0 0 0 0 0 1 0 0 10396 131 5 4 4 NFASC 1 204952034 Nonsense_Mutation SNP A C3L-01889_T 52839419 204952034 44004388 11 7690 CNTN2 0 . GRCh38 1 205072021 205072021 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.2619C>T p.= p.A873A ENST00000331830 20/23 206 165 41 132 132 0 strelka-varscan-mutect CNTN2,synonymous_variant,p.=,ENST00000331830,NM_005076.3;CNTN2,downstream_gene_variant,,ENST00000636641,;CNTN2,3_prime_UTR_variant,,ENST00000638050,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,;CNTN2,upstream_gene_variant,,ENST00000525433,;CNTN2,upstream_gene_variant,,ENST00000636312,; T ENST00000331830 Transcript synonymous_variant 2976/8214 2619/3123 873/1040 A gcC/gcT 1 1 CNTN2 HGNC HGNC:2172 protein_coding YES CCDS1449.1 ENSP00000330633 Q02246 A0A024R9B4 UPI00001266A5 NM_005076.3 20/23 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 205072021 205072021 C T 1 0 0 0 0 0 0 0 1 3422 610 22 3 3 CNTN2 1 205072021 Silent SNP C C3L-01889_T 119987 205072021 43884401 12 7691 HSD11B1 0 . GRCh38 1 209705916 209705916 + Missense_Mutation SNP C C A rs374234875 C3L-01889_T C3L-01889_N C C c.194C>A p.Ala65Glu p.A65E ENST00000367028 3/7 319 260 59 289 288 1 strelka-varscan-mutect HSD11B1,missense_variant,p.Ala65Glu,ENST00000367028,NM_181755.2,NM_001206741.1;HSD11B1,missense_variant,p.Ala65Glu,ENST00000367027,NM_005525.3;HSD11B1,missense_variant,p.Ala65Glu,ENST00000261465,;HSD11B1,missense_variant,p.Ala65Glu,ENST00000615289,;RP1-28O10.1,intron_variant,,ENST00000441672,; A ENST00000367028 Transcript missense_variant 348/1461 194/879 65/292 A/E gCg/gAg rs374234875 1 1 HSD11B1 HGNC HGNC:5208 protein_coding YES CCDS1489.1 ENSP00000355995 P28845 X5D2L1 UPI000004C796 NM_181755.2,NM_001206741.1 deleterious(0) 3/7 Gene3D:3.40.50.720,Pfam_domain:PF00106,hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF249,Superfamily_domains:SSF51735 MODERATE SNV 5 1 PASS rs374234875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 209705916 209705916 C A 1 0 0 0 0 1 0 0 0 7270 768 27 1 1 HSD11B1 1 209705916 Missense_Mutation SNP C C3L-01889_T 4633895 209705916 39250506 13 7692 RYR2 0 . GRCh38 1 237702036 237702036 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.9426C>T p.= p.T3142T ENST00000366574 66/105 285 243 42 196 196 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 9743/16562 9426/14904 3142/4967 T acC/acT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 66/105 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 237702036 237702036 C T 1 0 0 0 0 0 0 0 1 14029 581 21 3 3 RYR2 1 237702036 Silent SNP C C3L-01889_T 27996120 237702036 11254386 14 7693 AKT3 0 . GRCh38 1 243695604 243695604 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.159C>G p.Asn53Lys p.N53K ENST00000263826 2/13 210 110 100 145 145 0 strelka-varscan-mutect AKT3,missense_variant,p.Asn53Lys,ENST00000263826,NM_005465.4;AKT3,missense_variant,p.Asn53Lys,ENST00000366539,;AKT3,missense_variant,p.Asn53Lys,ENST00000336199,NM_181690.2;AKT3,missense_variant,p.Asn53Lys,ENST00000366540,NM_001206729.1;AKT3,missense_variant,p.Asn53Lys,ENST00000552631,;AKT3,non_coding_transcript_exon_variant,,ENST00000490018,;AKT3,non_coding_transcript_exon_variant,,ENST00000491219,;AKT3,non_coding_transcript_exon_variant,,ENST00000463991,; C ENST00000263826 Transcript missense_variant 271/7081 159/1440 53/479 N/K aaC/aaG 1 -1 AKT3 HGNC HGNC:393 protein_coding YES CCDS31077.1 ENSP00000263826 Q9Y243 UPI00000335E8 NM_005465.4 tolerated(0.07) 2/13 PROSITE_profiles:PS50003,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF190,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1415162628 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 243695604 243695604 G C 1 0 0 0 0 1 0 0 0 564 1020 36 4 4 AKT3 1 243695604 Missense_Mutation SNP G C3L-01889_T 5993568 243695604 5260818 15 7694 NBAS 0 . GRCh38 2 15558613 15558613 + Missense_Mutation SNP C C G novel C3L-01889_T C3L-01889_N C C c.139G>C p.Gly47Arg p.G47R ENST00000281513 2/52 273 215 58 278 278 0 strelka-varscan-mutect NBAS,missense_variant,p.Gly47Arg,ENST00000281513,NM_015909.3; G ENST00000281513 Transcript missense_variant 165/7281 139/7116 47/2371 G/R Ggt/Cgt 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 deleterious(0.01) 2/52 hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 15558613 15558613 C G 1 0 0 0 0 1 0 0 0 10197 594 21 4 4 NBAS 2 15558613 Missense_Mutation SNP C C3L-01889_T 15558613 226634916 16 7695 NT5C1B 0 . GRCh38 2 18587127 18587127 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.167T>A p.Phe56Tyr p.F56Y ENST00000359846 3/10 167 143 24 121 121 0 strelka-varscan-mutect NT5C1B,missense_variant,p.Phe56Tyr,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Phe56Tyr,ENST00000532967,NM_001199104.1;NT5C1B,missense_variant,p.Phe56Tyr,ENST00000416783,;NT5C1B,intron_variant,,ENST00000304081,NM_033253.3;NT5C1B-RDH14,intron_variant,,ENST00000444297,NM_001199103.1;NT5C1B,upstream_gene_variant,,ENST00000418427,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,intron_variant,,ENST00000460052,;NT5C1B,intron_variant,,ENST00000406971,;NT5C1B,upstream_gene_variant,,ENST00000490687,; T ENST00000359846 Transcript missense_variant 245/2475 167/1833 56/610 F/Y tTc/tAc 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 deleterious_low_confidence(0) 3/10 hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 18587127 18587127 A T 1 0 0 0 0 1 0 0 0 10749 246 9 4 4 NT5C1B 2 18587127 Missense_Mutation SNP A C3L-01889_T 3028514 18587127 223606402 17 7696 NRXN1 0 . GRCh38 2 51027856 51027856 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.418G>T p.Val140Phe p.V140F ENST00000404971 2/24 406 296 110 369 369 0 strelka-varscan NRXN1,missense_variant,p.Val140Phe,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Val140Phe,ENST00000625672,;NRXN1,missense_variant,p.Val140Phe,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Val140Phe,ENST00000401669,;NRXN1,missense_variant,p.Val140Phe,ENST00000405472,;NRXN1,missense_variant,p.Val140Phe,ENST00000405581,;NRXN1,missense_variant,p.Val140Phe,ENST00000630543,;NRXN1,missense_variant,p.Val140Phe,ENST00000637511,;NRXN1,missense_variant,p.Val140Phe,ENST00000628515,;NRXN1,missense_variant,p.Val140Phe,ENST00000626899,;NRXN1,upstream_gene_variant,,ENST00000636066,;NRXN1,upstream_gene_variant,,ENST00000627198,;NRXN1,upstream_gene_variant,,ENST00000496792,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000635126,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,upstream_gene_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; A ENST00000404971 Transcript missense_variant 1758/7578 418/4644 140/1547 V/F Gtc/Ttc 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.04) 2/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 51027856 51027856 C A 1 0 0 0 0 1 0 0 0 10724 507 18 2 2 NRXN1 2 51027856 Missense_Mutation SNP C C3L-01889_T 32440729 51027856 191165673 18 7697 CNGA3 0 . GRCh38 2 98395917 98395917 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.747C>A p.Phe249Leu p.F249L ENST00000393504 8/8 183 128 55 197 197 0 strelka-varscan CNGA3,missense_variant,p.Phe249Leu,ENST00000393504,NM_001298.2;CNGA3,missense_variant,p.Phe249Leu,ENST00000272602,;CNGA3,missense_variant,p.Phe253Leu,ENST00000409937,;CNGA3,missense_variant,p.Phe231Leu,ENST00000436404,NM_001079878.1; A ENST00000393504 Transcript missense_variant 1164/3841 747/2085 249/694 F/L ttC/ttA 1 1 CNGA3 HGNC HGNC:2150 protein_coding YES CCDS2034.1 ENSP00000377140 Q16281 UPI000004717B NM_001298.2 deleterious(0) 8/8 hmmpanther:PTHR10217:SF390,hmmpanther:PTHR10217,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 98395917 98395917 C A 1 0 0 0 0 1 0 0 0 3378 825 29 2 2 CNGA3 2 98395917 Missense_Mutation SNP C C3L-01889_T 47368061 98395917 143797612 19 7698 CCDC74B 0 . GRCh38 2 130140259 130140259 + Missense_Mutation SNP G G T rs745983669 C3L-01889_T C3L-01889_N G G c.796C>A p.Leu266Met p.L266M ENST00000310463 5/8 127 95 32 131 131 0 strelka-varscan CCDC74B,missense_variant,p.Leu266Met,ENST00000310463,NM_207310.2;CCDC74B,missense_variant,p.Leu200Met,ENST00000409943,NM_001258307.1;CCDC74B,intron_variant,,ENST00000392984,;CCDC74B,downstream_gene_variant,,ENST00000409234,;CCDC74B,downstream_gene_variant,,ENST00000409128,;CCDC74B,downstream_gene_variant,,ENST00000457413,;CCDC74B,downstream_gene_variant,,ENST00000441670,;MED15P9,downstream_gene_variant,,ENST00000427638,;CCDC74B,non_coding_transcript_exon_variant,,ENST00000496704,;CCDC74B,downstream_gene_variant,,ENST00000423263,;CCDC74B,downstream_gene_variant,,ENST00000434929,;CCDC74B,upstream_gene_variant,,ENST00000498526,;MED15P9,downstream_gene_variant,,ENST00000424716,; T ENST00000310463 Transcript missense_variant 934/1549 796/1143 266/380 L/M Ctg/Atg rs745983669 1 -1 CCDC74B HGNC HGNC:25267 protein_coding YES CCDS2155.1 ENSP00000308873 Q96LY2 UPI000006D822 NM_207310.2 tolerated(0.16) 5/8 Low_complexity_(Seg):seg,hmmpanther:PTHR14882,hmmpanther:PTHR14882:SF5,Pfam_domain:PF14917 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 130140259 130140259 G T 1 0 0 0 0 1 0 0 0 2548 991 35 2 2 CCDC74B 2 130140259 Missense_Mutation SNP G C3L-01889_T 31744342 130140259 112053270 20 7699 LRP1B 0 . GRCh38 2 140335815 140335815 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.11916G>T p.Arg3972Ser p.R3972S ENST00000389484 78/91 175 126 49 224 224 0 strelka-varscan LRP1B,missense_variant,p.Arg3972Ser,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Arg204Ser,ENST00000437977,; A ENST00000389484 Transcript missense_variant 12888/16535 11916/13800 3972/4599 R/S agG/agT 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.06) 78/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 140335815 140335815 C A 1 0 0 0 0 1 0 0 0 8850 622 22 2 2 LRP1B 2 140335815 Missense_Mutation SNP C C3L-01889_T 10195556 140335815 101857714 21 7700 BAZ2B 0 . GRCh38 2 159453625 159453625 + Missense_Mutation SNP C C A rs749608430 C3L-01889_T C3L-01889_N C C c.322G>T p.Ala108Ser p.A108S ENST00000392783 4/37 92 65 27 111 111 0 strelka-varscan BAZ2B,missense_variant,p.Ala108Ser,ENST00000392783,NM_013450.3;BAZ2B,missense_variant,p.Ala108Ser,ENST00000392782,NM_001289975.1;BAZ2B,missense_variant,p.Ala108Ser,ENST00000437839,;BAZ2B,5_prime_UTR_variant,,ENST00000343439,;BAZ2B,intron_variant,,ENST00000541068,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000482503,;BAZ2B,downstream_gene_variant,,ENST00000483316,;BAZ2B,intron_variant,,ENST00000467184,; A ENST00000392783 Transcript missense_variant 818/8289 322/6507 108/2168 A/S Gca/Tca rs749608430 1 -1 BAZ2B HGNC HGNC:963 protein_coding YES CCDS2209.2 ENSP00000376534 Q9UIF8 UPI0000D74C4A NM_013450.3 tolerated_low_confidence(0.12) 4/37 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 159453625 159453625 C A 1 0 0 0 0 1 0 0 0 1477 797 28 2 2 BAZ2B 2 159453625 Missense_Mutation SNP C C3L-01889_T 19117810 159453625 82739904 22 7701 LRP2 0 . GRCh38 2 169207098 169207098 + Missense_Mutation SNP C C G novel C3L-01889_T C3L-01889_N C C c.6622G>C p.Asp2208His p.D2208H ENST00000263816 39/79 84 66 18 125 125 0 strelka-varscan LRP2,missense_variant,p.Asp2208His,ENST00000263816,NM_004525.2; G ENST00000263816 Transcript missense_variant 6908/15808 6622/13968 2208/4655 D/H Gac/Cac 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 deleterious(0) 39/79 Gene3D:2.120.10.30,Pfam_domain:PF00058,PROSITE_profiles:PS51120,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 169207098 169207098 C G 1 0 0 0 0 1 0 0 0 8851 826 29 4 4 LRP2 2 169207098 Missense_Mutation SNP C C3L-01889_T 9753473 169207098 72986431 23 7702 ORC2 0 . GRCh38 2 200935810 200935810 + Silent SNP T T C novel C3L-01889_T C3L-01889_N T T c.597A>G p.= p.E199E ENST00000234296 9/18 237 176 61 247 247 0 strelka-varscan ORC2,synonymous_variant,p.=,ENST00000234296,NM_006190.4;ORC2,non_coding_transcript_exon_variant,,ENST00000474877,; C ENST00000234296 Transcript synonymous_variant 847/4312 597/1734 199/577 E gaA/gaG 1 -1 ORC2 HGNC HGNC:8488 protein_coding YES CCDS2334.1 ENSP00000234296 Q13416 A0A024R411 UPI0000130E5A NM_006190.4 9/18 hmmpanther:PTHR14052,hmmpanther:PTHR14052:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 28 200935810 200935810 T C 1 0 0 0 0 0 0 0 1 11328 1606 56 5 5 ORC2 2 200935810 Silent SNP T C3L-01889_T 31728712 200935810 41257719 24 7703 NYAP2 0 . GRCh38 2 225582924 225582924 + Missense_Mutation SNP C C T rs752903462 C3L-01889_T C3L-01889_N C C c.1507C>T p.Arg503Trp p.R503W ENST00000636099 5/7 289 229 60 237 237 0 strelka-varscan NYAP2,missense_variant,p.Arg503Trp,ENST00000636099,;NYAP2,missense_variant,p.Arg503Trp,ENST00000272907,NM_020864.1; T ENST00000636099 Transcript missense_variant 2553/5461 1507/1962 503/653 R/W Cgg/Tgg rs752903462,COSM3798691 1 1 NYAP2 HGNC HGNC:29291 protein_coding YES CCDS46529.1 ENSP00000490942 UPI00001C1DB6 deleterious(0.01) 5/7 hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF1,Pfam_domain:PF15452 0,1 MODERATE 1 SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 225582924 225582924 C T 1 0 0 0 0 1 0 0 0 10873 643 23 1 1 NYAP2 2 225582924 Missense_Mutation SNP C C3L-01889_T 24647114 225582924 16610605 25 7704 SLC16A14 0 . GRCh38 2 230059168 230059168 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.185T>A p.Leu62Gln p.L62Q ENST00000295190 2/5 144 112 32 131 131 0 strelka-varscan-mutect SLC16A14,missense_variant,p.Leu62Gln,ENST00000295190,NM_152527.4;SLC16A14,missense_variant,p.Leu62Gln,ENST00000457406,;SLC16A14,missense_variant,p.Leu62Gln,ENST00000412034,;SLC16A14,downstream_gene_variant,,ENST00000436869,;SLC16A14,downstream_gene_variant,,ENST00000425822,;RNY4P19,upstream_gene_variant,,ENST00000362530,; T ENST00000295190 Transcript missense_variant 644/4398 185/1533 62/510 L/Q cTg/cAg 1 -1 SLC16A14 HGNC HGNC:26417 protein_coding YES CCDS2473.1 ENSP00000295190 Q7RTX9 UPI000004EE99 NM_152527.4 deleterious(0) 2/5 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF121,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 230059168 230059168 A T 1 0 0 0 0 1 0 0 0 14673 188 7 4 4 SLC16A14 2 230059168 Missense_Mutation SNP A C3L-01889_T 4476244 230059168 12134361 26 7705 EFHB 0 . GRCh38 3 19933280 19933280 + Silent SNP T T G novel C3L-01889_T C3L-01889_N T T c.739A>C p.= p.R247R ENST00000295824 1/13 144 108 36 172 172 0 varscan-mutect EFHB,synonymous_variant,p.=,ENST00000295824,NM_144715.3;EFHB,synonymous_variant,p.=,ENST00000344838,;EFHB,synonymous_variant,p.=,ENST00000440022,;EFHB,non_coding_transcript_exon_variant,,ENST00000498089,;EFHB,synonymous_variant,p.=,ENST00000389256,; G ENST00000295824 Transcript synonymous_variant 901/2823 739/2502 247/833 R Aga/Cga 1 -1 EFHB HGNC HGNC:26330 protein_coding YES CCDS33715.2 ENSP00000295824 Q8N7U6 UPI0000209A4C NM_144715.3 1/13 hmmpanther:PTHR12086:SF12,hmmpanther:PTHR12086 LOW 1 SNV 1 1 PASS rs1339742005 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 19933280 19933280 T G 1 0 0 0 0 0 0 0 1 4780 1588 55 5 5 EFHB 3 19933280 Silent SNP T C3L-01889_T 19933280 178362279 27 7706 SCN11A 0 . GRCh38 3 38919952 38919952 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.942C>A p.= p.G314G ENST00000302328 7/26 230 174 56 214 214 0 strelka-varscan-mutect SCN11A,synonymous_variant,p.=,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,synonymous_variant,p.=,ENST00000444237,;SCN11A,synonymous_variant,p.=,ENST00000456224,; T ENST00000302328 Transcript synonymous_variant 1141/6500 942/5376 314/1791 G ggC/ggA 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 7/26 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 38919952 38919952 G T 1 0 0 0 0 0 0 0 1 14182 1306 46 2 2 SCN11A 3 38919952 Silent SNP G C3L-01889_T 18986672 38919952 159375607 28 7707 CCR1 0 . GRCh38 3 46203512 46203512 + Frame_Shift_Del DEL G G - novel C3L-01889_T C3L-01889_N G G c.802delC p.Leu268CysfsTer18 p.L268Cfs*18 ENST00000296140 2/2 131 100 31 218 218 0 sindel-varindel-pindel CCR1,frameshift_variant,p.Leu268CysfsTer18,ENST00000296140,NM_001295.2;CCR3,intron_variant,,ENST00000357422,; - ENST00000296140 Transcript frameshift_variant 928/2731 802/1068 268/355 L/X Ctg/tg 1 -1 CCR1 HGNC HGNC:1602 protein_coding YES CCDS2737.1 ENSP00000296140 P32246 Q5U003 UPI0000043584 NM_001295.2 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR10489:SF711,hmmpanther:PTHR10489,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01106 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 46203512 46203512 G - 1 0 1 0 1 0 0 0 0 2639 991 35 0 0 CCR1 3 46203512 Frame_Shift_Del DEL G C3L-01889_T 7283560 46203512 152092047 29 7708 SYNPR 0 . GRCh38 3 63278544 63278544 + Missense_Mutation SNP T T A C3L-01889_T C3L-01889_N T T c.11T>A p.Val4Glu p.V4E ENST00000478300 1/6 92 74 18 78 78 0 strelka-varscan-mutect SYNPR,missense_variant,p.Val4Glu,ENST00000478300,NM_001130003.1;SYNPR,missense_variant,p.Val4Glu,ENST00000450542,;SYNPR,intron_variant,,ENST00000478456,;SYNPR,upstream_gene_variant,,ENST00000496889,;SYNPR,upstream_gene_variant,,ENST00000460142,;SYNPR,missense_variant,p.Val4Glu,ENST00000468110,; A ENST00000478300 Transcript missense_variant 422/2709 11/858 4/285 V/E gTg/gAg COSM1047994 1 1 SYNPR HGNC HGNC:16507 protein_coding YES CCDS46859.1 ENSP00000418994 Q8TBG9 UPI00005796D8 NM_001130003.1 deleterious(0) 1/6 hmmpanther:PTHR10306,hmmpanther:PTHR10306:SF16 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 63278544 63278544 T A 1 0 0 0 0 1 0 0 0 15853 1696 59 4 4 SYNPR 3 63278544 Missense_Mutation SNP T C3L-01889_T 17075032 63278544 135017015 30 7709 SHQ1 0 . GRCh38 3 72792945 72792945 + Silent SNP T T C novel C3L-01889_T C3L-01889_N T T c.1152A>G p.= p.S384S ENST00000325599 10/11 245 183 62 246 245 1 strelka-varscan-mutect SHQ1,synonymous_variant,p.=,ENST00000325599,NM_018130.2;SHQ1,synonymous_variant,p.=,ENST00000463369,;SHQ1,non_coding_transcript_exon_variant,,ENST00000468371,;SHQ1,3_prime_UTR_variant,,ENST00000444040,; C ENST00000325599 Transcript synonymous_variant 1292/2879 1152/1734 384/577 S tcA/tcG 1 -1 SHQ1 HGNC HGNC:25543 protein_coding YES CCDS33788.1 ENSP00000315182 Q6PI26 UPI00001416C5 NM_018130.2 10/11 Pfam_domain:PF04925,hmmpanther:PTHR12967,hmmpanther:PTHR12967:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 28 72792945 72792945 T C 1 0 0 0 0 0 0 0 1 14555 1567 55 5 5 SHQ1 3 72792945 Silent SNP T C3L-01889_T 9514401 72792945 125502614 31 7710 EPHA6 0 . GRCh38 3 96866836 96866836 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.397G>C p.Asp133His p.D133H ENST00000389672 2/18 183 145 38 191 191 0 strelka-varscan-mutect EPHA6,missense_variant,p.Asp133His,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Asp133His,ENST00000470610,;EPHA6,missense_variant,p.Asp78His,ENST00000506569,NM_001278301.1; C ENST00000389672 Transcript missense_variant 435/3971 397/3393 133/1130 D/H Gat/Cat 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 2/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 96866836 96866836 G C 1 0 0 0 0 1 0 0 0 5018 1290 45 4 4 EPHA6 3 96866836 Missense_Mutation SNP G C3L-01889_T 24073891 96866836 101428723 32 7711 OR5H15 0 . GRCh38 3 98168777 98168777 + Silent SNP C C A rs188567114 C3L-01889_T C3L-01889_N C C c.78C>A p.= p.P26P ENST00000356526 1/1 270 203 67 255 254 1 strelka-varscan-mutect OR5H15,synonymous_variant,p.=,ENST00000356526,NM_001005515.1;OR5H15,synonymous_variant,p.=,ENST00000615035,; A ENST00000356526 Transcript synonymous_variant 78/942 78/942 26/313 P ccC/ccA rs188567114,COSM5260318 1 1 OR5H15 HGNC HGNC:31287 protein_coding YES CCDS33799.1 ENSP00000373195 A6NDH6 UPI00001606CE NM_001005515.1 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF325,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 0,1 1 PASS rs188567114 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 98168777 98168777 C A 1 0 0 0 0 0 0 0 1 11231 610 22 2 2 OR5H15 3 98168777 Silent SNP C C3L-01889_T 1301941 98168777 100126782 33 7712 ESYT3 0 . GRCh38 3 138434814 138434814 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.16C>T p.Pro6Ser p.P6S ENST00000389567 1/23 75 61 14 81 81 0 strelka-varscan-mutect ESYT3,missense_variant,p.Pro6Ser,ENST00000389567,NM_031913.3;ESYT3,missense_variant,p.Pro6Ser,ENST00000289135,;ESYT3,missense_variant,p.Pro6Ser,ENST00000490835,;ESYT3,non_coding_transcript_exon_variant,,ENST00000486831,; T ENST00000389567 Transcript missense_variant 202/4407 16/2661 6/886 P/S Ccc/Tcc 1 1 ESYT3 HGNC HGNC:24295 protein_coding YES CCDS3101.2 ENSP00000374218 A0FGR9 UPI0000251E45 NM_031913.3 tolerated(0.07) 1/23 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 138434814 138434814 C T 1 0 0 0 0 1 0 0 0 5128 739 26 3 3 ESYT3 3 138434814 Missense_Mutation SNP C C3L-01889_T 40266037 138434814 59860745 34 7713 RNF13 0 . GRCh38 3 149872115 149872115 + Silent SNP C C A rs142620410 C3L-01889_T C3L-01889_N C C c.282C>A p.= p.I94I ENST00000344229 5/11 130 100 30 150 150 0 strelka-varscan-mutect RNF13,synonymous_variant,p.=,ENST00000344229,NM_007282.4;RNF13,synonymous_variant,p.=,ENST00000392894,NM_183381.2;RNF13,synonymous_variant,p.=,ENST00000459632,;RNF13,synonymous_variant,p.=,ENST00000466795,;RNF13,synonymous_variant,p.=,ENST00000490631,;RNF13,synonymous_variant,p.=,ENST00000468648,;RNF13,5_prime_UTR_variant,,ENST00000361785,;RNF13,5_prime_UTR_variant,,ENST00000491086,;RNF13,5_prime_UTR_variant,,ENST00000467977,;RNF13,downstream_gene_variant,,ENST00000470151,;RNF13,downstream_gene_variant,,ENST00000466478,;ANKUB1,intron_variant,,ENST00000481585,;RNF13,synonymous_variant,p.=,ENST00000474348,;RNF13,5_prime_UTR_variant,,ENST00000467996,; A ENST00000344229 Transcript synonymous_variant 984/2866 282/1146 94/381 I atC/atA rs142620410 1 1 RNF13 HGNC HGNC:10057 protein_coding YES CCDS3146.1 ENSP00000341361 O43567 UPI0000134318 NM_007282.4 5/11 Gene3D:3.50.30.30,Pfam_domain:PF02225,hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF34,Superfamily_domains:SSF52025 LOW 1 SNV 1 1 PASS rs142620410 . 0 206 0 3 0 0 0 0 -20 0.9999972 1 1 1 0 A 2 1 28 149872115 149872115 C A 1 0 0 0 0 0 0 0 1 13615 874 31 1 1 RNF13 3 149872115 Silent SNP C C3L-01889_T 11437301 149872115 48423444 35 7714 SAMD7 0 . GRCh38 3 169927117 169927117 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.855G>A p.= p.Q285Q ENST00000428432 6/9 48 37 11 57 57 0 strelka-varscan-mutect SAMD7,synonymous_variant,p.=,ENST00000428432,NM_182610.3;SAMD7,synonymous_variant,p.=,ENST00000335556,NM_001304366.1;SAMD7,3_prime_UTR_variant,,ENST00000487910,;RP11-379K17.2,upstream_gene_variant,,ENST00000493762,; A ENST00000428432 Transcript synonymous_variant 1244/2399 855/1341 285/446 Q caG/caA 1 1 SAMD7 HGNC HGNC:25394 protein_coding YES CCDS3209.1 ENSP00000391299 Q7Z3H4 UPI00001A9D13 NM_182610.3 6/9 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF89 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 169927117 169927117 G A 1 0 0 0 0 0 0 0 1 14084 933 33 3 3 SAMD7 3 169927117 Silent SNP G C3L-01889_T 20055002 169927117 28368442 36 7715 CPN2 0 . GRCh38 3 194341344 194341344 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.1359C>A p.= p.G453G ENST00000323830 2/2 190 131 59 165 165 0 strelka-varscan-mutect CPN2,synonymous_variant,p.=,ENST00000323830,NM_001291988.1,NM_001080513.3;CPN2,synonymous_variant,p.=,ENST00000429275,; T ENST00000323830 Transcript synonymous_variant 1449/3028 1359/1638 453/545 G ggC/ggA 1 -1 CPN2 HGNC HGNC:2313 protein_coding YES CCDS33920.1 ENSP00000319464 P22792 UPI0001AE76B7 NM_001291988.1,NM_001080513.3 2/2 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF278 LOW 1 SNV 1 1 PASS rs973433962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 194341344 194341344 G T 1 0 0 0 0 0 0 0 1 3605 958 34 2 2 CPN2 3 194341344 Silent SNP G C3L-01889_T 24414227 194341344 3954215 37 7716 FAM43A 0 . GRCh38 3 194687275 194687275 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.449C>T p.Pro150Leu p.P150L ENST00000329759 1/1 159 126 33 163 163 0 strelka-varscan-mutect FAM43A,missense_variant,p.Pro150Leu,ENST00000329759,NM_153690.4; T ENST00000329759 Transcript missense_variant 732/2494 449/1272 150/423 P/L cCc/cTc 1 1 FAM43A HGNC HGNC:26888 protein_coding YES CCDS33923.1 ENSP00000371397 Q8N2R8 UPI0000074368 NM_153690.4 deleterious(0) 1/1 hmmpanther:PTHR11232:SF36,hmmpanther:PTHR11232,Pfam_domain:PF14719,Gene3D:2.30.29.30,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 194687275 194687275 C T 1 0 0 0 0 1 0 0 0 5440 623 22 3 3 FAM43A 3 194687275 Missense_Mutation SNP C C3L-01889_T 345931 194687275 3608284 38 7717 GABRG1 0 . GRCh38 4 46041245 46041245 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.1141G>T p.Gly381Cys p.G381C ENST00000295452 9/9 133 112 21 165 164 1 strelka-varscan-mutect GABRG1,missense_variant,p.Gly381Cys,ENST00000295452,NM_173536.3; A ENST00000295452 Transcript missense_variant 1309/6785 1141/1398 381/465 G/C Ggt/Tgt 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 deleterious(0.04) 9/9 Prints_domain:PR01621,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 46041245 46041245 C A 1 0 0 0 0 1 0 0 0 6042 594 21 2 2 GABRG1 4 46041245 Missense_Mutation SNP C C3L-01889_T 46041245 144173310 39 7718 ADGRL3 0 . GRCh38 4 62031441 62031441 + Splice_Site SNP G G T novel C3L-01889_T C3L-01889_N G G c.3219-1G>T p.X1073_splice ENST00000514591 118 84 34 107 107 0 strelka-varscan-mutect ADGRL3,splice_acceptor_variant,,ENST00000512091,NM_001322246.1;ADGRL3,splice_acceptor_variant,,ENST00000514591,NM_015236.4;ADGRL3,splice_acceptor_variant,,ENST00000509896,;ADGRL3,splice_acceptor_variant,,ENST00000511324,;ADGRL3,splice_acceptor_variant,,ENST00000508693,;ADGRL3,splice_acceptor_variant,,ENST00000507164,;ADGRL3,splice_acceptor_variant,,ENST00000506720,;ADGRL3,splice_acceptor_variant,,ENST00000506746,;ADGRL3,splice_acceptor_variant,,ENST00000507625,;ADGRL3,splice_acceptor_variant,,ENST00000506700,;ADGRL3,splice_acceptor_variant,,ENST00000504896,;ADGRL3,splice_acceptor_variant,,ENST00000514157,;ADGRL3,splice_acceptor_variant,,ENST00000508946,;ADGRL3,splice_acceptor_variant,,ENST00000514996,;ADGRL3,splice_acceptor_variant,,ENST00000502815,; T ENST00000514591 Transcript splice_acceptor_variant -/6297 3219/4410 1073/1469 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 21/24 HIGH 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 28 62031441 62031441 G T 1 0 0 0 0 0 0 1 0 377 1014 35 2 2 ADGRL3 4 62031441 Splice_Site SNP G C3L-01889_T 15990196 62031441 128183114 40 7719 PDHA2 0 . GRCh38 4 95840535 95840535 + Missense_Mutation SNP G G A novel C3L-01889_T C3L-01889_N G G c.385G>A p.Val129Ile p.V129I ENST00000295266 1/1 187 141 46 191 191 0 strelka-varscan-mutect PDHA2,missense_variant,p.Val129Ile,ENST00000295266,NM_005390.4; A ENST00000295266 Transcript missense_variant 517/1456 385/1167 129/388 V/I Gtc/Atc 1 1 PDHA2 HGNC HGNC:8807 protein_coding YES CCDS3644.1 ENSP00000295266 P29803 UPI0000130C31 NM_005390.4 tolerated(0.22) 1/1 hmmpanther:PTHR11516:SF27,hmmpanther:PTHR11516,Pfam_domain:PF00676,TIGRFAM_domain:TIGR03182,Gene3D:3.40.50.970,Superfamily_domains:SSF52518 MODERATE 1 SNV 1 PASS rs1401316578 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 95840535 95840535 G A 1 0 0 0 0 1 0 0 0 11753 1377 48 3 3 PDHA2 4 95840535 Missense_Mutation SNP G C3L-01889_T 33809094 95840535 94374020 41 7720 JADE1 0 . GRCh38 4 128861854 128861854 + Missense_Mutation SNP C C G novel C3L-01889_T C3L-01889_N C C c.1132C>G p.Leu378Val p.L378V ENST00000226319 9/11 288 216 72 267 267 0 strelka-varscan-mutect JADE1,missense_variant,p.Leu378Val,ENST00000226319,NM_199320.3;JADE1,missense_variant,p.Leu378Val,ENST00000611140,NM_001287443.1;JADE1,missense_variant,p.Leu378Val,ENST00000610919,NM_001287442.1;JADE1,missense_variant,p.Leu366Val,ENST00000452328,NM_001287437.1;JADE1,missense_variant,p.Leu378Val,ENST00000413543,NM_001287441.1;JADE1,missense_variant,p.Leu378Val,ENST00000511647,NM_024900.4;JADE1,missense_variant,p.Leu378Val,ENST00000512960,NM_001287439.1,NM_001287440.1;SCLT1,downstream_gene_variant,,ENST00000503565,; G ENST00000226319 Transcript missense_variant 1413/5772 1132/2529 378/842 L/V Ctt/Gtt 1 1 JADE1 HGNC HGNC:30027 protein_coding YES CCDS34062.1 ENSP00000226319 Q6IE81 UPI000020B45B NM_199320.3 tolerated(0.41) 9/11 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF79 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 128861854 128861854 C G 1 0 0 0 0 1 0 0 0 7844 913 32 4 4 JADE1 4 128861854 Missense_Mutation SNP C C3L-01889_T 33021319 128861854 61352701 42 7721 IL15 0 . GRCh38 4 141720549 141720558 + Frame_Shift_Del DEL TCATGTCTTC TCATGTCTTC - novel C3L-01889_T C3L-01889_N TCATGTCTTC TCATGTCTTC c.93_102delTCATGTCTTC p.His32PhefsTer17 p.H32Ffs*17 ENST00000296545 4/8 352 274 78 386 386 0 sindel-varindel-pindel IL15,frameshift_variant,p.His32PhefsTer17,ENST00000296545,;IL15,frameshift_variant,p.His32PhefsTer17,ENST00000320650,NM_000585.4;IL15,frameshift_variant,p.His32PhefsTer17,ENST00000529613,;IL15,5_prime_UTR_variant,,ENST00000477265,;IL15,5_prime_UTR_variant,,ENST00000514653,NM_172175.2;IL15,upstream_gene_variant,,ENST00000394159,;IL15,non_coding_transcript_exon_variant,,ENST00000505351,;IL15,upstream_gene_variant,,ENST00000509249,; - ENST00000296545 Transcript frameshift_variant 937-946/2472 93-102/489 31-34/162 IHVF/X atTCATGTCTTC/at 1 1 IL15 HGNC HGNC:5977 protein_coding YES CCDS3755.1 ENSP00000296545 P40933 UPI0000031AC7 4/8 Pfam_domain:PF02372,Prints_domain:PR01947,hmmpanther:PTHR11323,hmmpanther:PTHR11323:SF0 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 141720549 141720549 TCATGTCTTC - 1 0 1 0 1 0 0 0 0 7539 1771 62 0 0 IL15 4 141720549 Frame_Shift_Del DEL TCATGTCTTC C3L-01889_T 12858695 141720549 48494006 43 7722 LPCAT1 0 . GRCh38 5 1494865 1494865 + Missense_Mutation SNP C C A rs369052835 C3L-01889_T C3L-01889_N C C c.328G>T p.Gly110Cys p.G110C ENST00000283415 3/14 213 165 48 166 166 0 strelka-varscan-mutect LPCAT1,missense_variant,p.Gly110Cys,ENST00000283415,NM_024830.3;LPCAT1,non_coding_transcript_exon_variant,,ENST00000514484,;LPCAT1,missense_variant,p.Gly110Cys,ENST00000475622,;LPCAT1,non_coding_transcript_exon_variant,,ENST00000507282,;LPCAT1,upstream_gene_variant,,ENST00000513757,; A ENST00000283415 Transcript missense_variant 461/3966 328/1605 110/534 G/C Ggc/Tgc rs369052835 1 -1 LPCAT1 HGNC HGNC:25718 protein_coding YES CCDS3864.1 ENSP00000283415 Q8NF37 UPI000004771C NM_024830.3 tolerated(0.07) 3/14 hmmpanther:PTHR23063:SF11,hmmpanther:PTHR23063,Superfamily_domains:0039877 MODERATE 1 SNV 1 1 PASS rs369052835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 1494865 1494865 C A 1 0 0 0 0 1 0 0 0 8813 652 23 1 1 LPCAT1 5 1494865 Missense_Mutation SNP C C3L-01889_T 1494865 180043394 44 7723 PRDM9 0 . GRCh38 5 23526850 23526850 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1762G>T p.Gly588Cys p.G588C ENST00000296682 11/11 140 104 36 96 96 0 strelka-varscan-mutect PRDM9,missense_variant,p.Gly588Cys,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; T ENST00000296682 Transcript missense_variant 1944/3691 1762/2685 588/894 G/C Ggc/Tgc 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 23526850 23526850 G T 1 0 0 0 0 1 0 0 0 12595 1232 43 2 2 PRDM9 5 23526850 Missense_Mutation SNP G C3L-01889_T 22031985 23526850 158011409 45 7724 CWC27 0 . GRCh38 5 64971782 64971782 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.1122G>A p.= p.Q374Q ENST00000381070 12/14 134 107 27 152 152 0 strelka-varscan-mutect CWC27,synonymous_variant,p.=,ENST00000381070,NM_001297644.1,NM_005869.3;CWC27,non_coding_transcript_exon_variant,,ENST00000545000,; A ENST00000381070 Transcript synonymous_variant 1339/2078 1122/1419 374/472 Q caG/caA 1 1 CWC27 HGNC HGNC:10664 protein_coding YES CCDS3982.2 ENSP00000370460 Q6UX04 UPI0000048ECC NM_001297644.1,NM_005869.3 12/14 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs1325597558 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 64971782 64971782 G A 1 0 0 0 0 0 0 0 1 3880 1020 36 3 3 CWC27 5 64971782 Silent SNP G C3L-01889_T 41444932 64971782 116566477 46 7725 MAP1B 0 . GRCh38 5 72107598 72107598 + Missense_Mutation SNP T T G novel C3L-01889_T C3L-01889_N T T c.67T>G p.Ser23Ala p.S23A ENST00000296755 1/7 214 172 42 166 165 1 strelka-varscan-mutect MAP1B,missense_variant,p.Ser23Ala,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,missense_variant,p.Ser23Ala,ENST00000511641,;MAP1B,missense_variant,p.Ser23Ala,ENST00000512974,;MAP1B,non_coding_transcript_exon_variant,,ENST00000504183,;MAP1B,missense_variant,p.Ser23Ala,ENST00000513526,; G ENST00000296755 Transcript missense_variant 365/12036 67/7407 23/2468 S/A Tcc/Gcc 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 tolerated_low_confidence(0.37) 1/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 72107598 72107598 T G 1 0 0 0 0 1 0 0 0 9151 1667 58 5 5 MAP1B 5 72107598 Missense_Mutation SNP T C3L-01889_T 7135816 72107598 109430661 47 7726 VCAN 0 . GRCh38 5 83541022 83541022 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.8019G>T p.= p.G2673G ENST00000265077 8/15 250 172 78 271 270 1 strelka-varscan-mutect VCAN,synonymous_variant,p.=,ENST00000265077,NM_004385.4;VCAN,synonymous_variant,p.=,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; T ENST00000265077 Transcript synonymous_variant 8584/12625 8019/10191 2673/3396 G ggG/ggT 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 83541022 83541022 G T 1 0 0 0 0 0 0 0 1 17683 1161 41 2 2 VCAN 5 83541022 Silent SNP G C3L-01889_T 11433424 83541022 97997237 48 7727 PCSK1 0 . GRCh38 5 96394971 96394971 + Missense_Mutation SNP C C A C3L-01889_T C3L-01889_N C C c.1777G>T p.Gly593Trp p.G593W ENST00000311106 13/14 407 301 106 373 373 0 strelka-varscan-mutect PCSK1,missense_variant,p.Gly593Trp,ENST00000311106,NM_000439.4;PCSK1,missense_variant,p.Gly546Trp,ENST00000508626,NM_001177875.1;CTD-2337A12.1,intron_variant,,ENST00000502645,;PCSK1,non_coding_transcript_exon_variant,,ENST00000513085,; A ENST00000311106 Transcript missense_variant 2015/5086 1777/2262 593/753 G/W Ggg/Tgg CM971141 1 -1 PCSK1 HGNC HGNC:8743 protein_coding YES CCDS4081.1 ENSP00000308024 P29120 UPI000013F0F5 NM_000439.4 deleterious(0) 13/14 hmmpanther:PTHR10795:SF407,hmmpanther:PTHR10795,Gene3D:2.60.120.260,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 96394971 96394971 C A 1 0 0 0 0 1 0 0 0 11688 652 23 1 1 PCSK1 5 96394971 Missense_Mutation SNP C C3L-01889_T 12853949 96394971 85143288 49 7728 HNRNPA0 0 . GRCh38 5 137753737 137753737 + Silent SNP A A T novel C3L-01889_T C3L-01889_N A A c.330T>A p.= p.A110A ENST00000314940 1/1 228 170 58 237 237 0 strelka-varscan-mutect HNRNPA0,synonymous_variant,p.=,ENST00000314940,NM_006805.3; T ENST00000314940 Transcript synonymous_variant 640/8726 330/918 110/305 A gcT/gcA 1 -1 HNRNPA0 HGNC HGNC:5030 protein_coding YES CCDS4193.1 ENSP00000316042 Q13151 UPI0000000C1D NM_006805.3 1/1 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF492,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 PASS rs899506386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 137753737 137753737 A T 1 0 0 0 0 0 0 0 1 7147 175 7 4 4 HNRNPA0 5 137753737 Silent SNP A C3L-01889_T 41358766 137753737 43784522 50 7729 PCDHB9 0 . GRCh38 5 141188797 141188797 + Silent SNP C C A novel C3L-01889_T C3L-01889_N C C c.1479C>A p.= p.P493P ENST00000316105 1/1 493 336 157 438 438 0 strelka-varscan-mutect PCDHB9,synonymous_variant,p.=,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,non_coding_transcript_exon_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; A ENST00000316105 Transcript synonymous_variant 1671/4415 1479/2394 493/797 P ccC/ccA 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW SNV 1 PASS rs1259803022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 141188797 141188797 C A 1 0 0 0 0 0 0 0 1 11636 610 22 2 2 PCDHB9 5 141188797 Silent SNP C C3L-01889_T 3435060 141188797 40349462 51 7730 DOCK2 0 . GRCh38 5 169803146 169803146 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.2643G>C p.Glu881Asp p.E881D ENST00000256935 26/52 155 109 46 184 184 0 strelka-varscan-mutect DOCK2,missense_variant,p.Glu881Asp,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Glu373Asp,ENST00000520908,;DOCK2,missense_variant,p.Glu261Asp,ENST00000540750,;DOCK2,missense_variant,p.Glu85Asp,ENST00000519628,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520181,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520836,;DOCK2,missense_variant,p.Glu881Asp,ENST00000524185,; C ENST00000256935 Transcript missense_variant 2723/6097 2643/5493 881/1830 E/D gaG/gaC 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 tolerated(0.51) 26/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 169803146 169803146 G C 1 0 0 0 0 1 0 0 0 4502 933 33 4 4 DOCK2 5 169803146 Missense_Mutation SNP G C3L-01889_T 28614349 169803146 11735113 52 7731 NEURL1B 0 . GRCh38 5 172683931 172683931 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1090G>T p.Asp364Tyr p.D364Y ENST00000369800 3/5 77 61 16 80 80 0 strelka-varscan-mutect NEURL1B,missense_variant,p.Asp364Tyr,ENST00000369800,NM_001142651.1;NEURL1B,missense_variant,p.Asp182Tyr,ENST00000522853,;NEURL1B,intron_variant,,ENST00000520919,NM_001308178.1; T ENST00000369800 Transcript missense_variant 1231/6424 1090/1668 364/555 D/Y Gac/Tac 1 1 NEURL1B HGNC HGNC:35422 protein_coding YES CCDS47342.1 ENSP00000358815 A8MQ27 UPI0000D6E5EA NM_001142651.1 deleterious(0) 3/5 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS rs1429888653 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 172683931 172683931 G T 1 0 0 0 0 1 0 0 0 10381 1058 37 1 1 NEURL1B 5 172683931 Missense_Mutation SNP G C3L-01889_T 2880785 172683931 8854328 53 7732 BNIP1 0 . GRCh38 5 173158792 173158792 + Missense_Mutation SNP C C G rs142359158 C3L-01889_T C3L-01889_N C C c.447C>G p.Ile149Met p.I149M ENST00000231668 5/7 189 154 35 188 188 0 strelka-varscan-mutect BNIP1,missense_variant,p.Ile149Met,ENST00000231668,NM_013979.2;BNIP1,missense_variant,p.Ile106Met,ENST00000351486,NM_001205.2;BNIP1,intron_variant,,ENST00000352523,NM_013980.2;BNIP1,intron_variant,,ENST00000393770,NM_013978.2;BNIP1,upstream_gene_variant,,ENST00000519459,; G ENST00000231668 Transcript missense_variant 551/1339 447/816 149/271 I/M atC/atG rs142359158 1 1 BNIP1 HGNC HGNC:1082 protein_coding YES CCDS4385.1 ENSP00000231668 Q12981 UPI000000D92A NM_013979.2 tolerated(0.11) 5/7 hmmpanther:PTHR12825:SF1,hmmpanther:PTHR12825 MODERATE 1 SNV 1 1 PASS rs142359158 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 173158792 173158792 C G 1 0 0 0 0 1 0 0 0 1632 874 31 4 4 BNIP1 5 173158792 Missense_Mutation SNP C C3L-01889_T 474861 173158792 8379467 54 7733 UNC5A 0 . GRCh38 5 176874029 176874029 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.948G>T p.= p.L316L ENST00000329542 7/15 143 108 35 108 108 0 strelka-varscan-mutect UNC5A,synonymous_variant,p.=,ENST00000329542,NM_133369.2;UNC5A,synonymous_variant,p.=,ENST00000509580,;UNC5A,3_prime_UTR_variant,,ENST00000513890,; T ENST00000329542 Transcript synonymous_variant 1222/3812 948/2529 316/842 L ctG/ctT 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 7/15 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582 LOW 1 SNV 1 1 PASS rs1193491972 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 176874029 176874029 G T 1 0 0 0 0 0 0 0 1 17515 1335 47 2 2 UNC5A 5 176874029 Silent SNP G C3L-01889_T 3715237 176874029 4664230 55 7734 TAP2 0 . GRCh38 6 32835202 32835202 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.897C>G p.His299Gln p.H299Q ENST00000374897 5/12 263 194 69 176 176 0 strelka-varscan TAP2,missense_variant,p.His299Gln,ENST00000374897,NM_001290043.1;TAP2,missense_variant,p.His299Gln,ENST00000620123,NM_000544.3;XXbac-BPG246D15.9,missense_variant,p.His299Gln,ENST00000452392,;TAP2,missense_variant,p.His299Gln,ENST00000374899,NM_018833.2;TAP2,upstream_gene_variant,,ENST00000485701,;TAP2,upstream_gene_variant,,ENST00000464100,; C ENST00000374897 Transcript missense_variant 1029/5684 897/2061 299/686 H/Q caC/caG 1 -1 TAP2 HGNC HGNC:44 protein_coding YES CCDS78129.1 ENSP00000364032 Q03519 Q5JNW1 UPI000011D578 NM_001290043.1 deleterious(0.02) 5/12 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF237,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,PIRSF_domain:PIRSF002773,TIGRFAM_domain:TIGR00958,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 32835202 32835202 G C 1 0 0 0 0 1 0 0 0 15950 1368 48 4 4 TAP2 6 32835202 Missense_Mutation SNP G C3L-01889_T 32835202 137970777 56 7735 MAPK14 0 . GRCh38 6 36075962 36075962 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.610G>T p.Val204Phe p.V204F ENST00000229795 7/12 216 149 67 214 213 1 strelka-varscan MAPK14,missense_variant,p.Val204Phe,ENST00000229795,NM_001315.2;MAPK14,missense_variant,p.Val204Phe,ENST00000229794,NM_139012.2;MAPK14,missense_variant,p.Val127Phe,ENST00000468133,;MAPK14,missense_variant,p.Val204Phe,ENST00000310795,NM_139014.2;MAPK14,missense_variant,p.Val127Phe,ENST00000472333,;MAPK14,downstream_gene_variant,,ENST00000622903,;MAPK14,splice_region_variant,,ENST00000491957,;MAPK14,splice_region_variant,,ENST00000496250,;MAPK14,splice_region_variant,,ENST00000474429,;MAPK14,splice_region_variant,,ENST00000490379,; T ENST00000229795 Transcript missense_variant,splice_region_variant 1057/4319 610/1083 204/360 V/F Gtt/Ttt 1 1 MAPK14 HGNC HGNC:6876 protein_coding YES CCDS4815.1 ENSP00000229795 Q16539 L7RSM2 UPI000002AE13 NM_001315.2 deleterious(0) 7/12 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF110,hmmpanther:PTHR24055,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 36075962 36075962 G T 1 0 0 0 0 1 0 0 0 9200 1014 35 2 2 MAPK14 6 36075962 Missense_Mutation SNP G C3L-01889_T 3240760 36075962 134730017 57 7736 CPNE5 0 . GRCh38 6 36746500 36746500 + Missense_Mutation SNP C C A rs150078502 C3L-01889_T C3L-01889_N C C c.1096G>T p.Val366Phe p.V366F ENST00000244751 16/21 202 144 58 189 189 0 strelka-varscan CPNE5,missense_variant,p.Val366Phe,ENST00000244751,NM_020939.1;CPNE5,missense_variant,p.Val74Phe,ENST00000393189,NM_001314018.1,NM_001314020.1;CPNE5,non_coding_transcript_exon_variant,,ENST00000459703,;CPNE5,non_coding_transcript_exon_variant,,ENST00000633929,;CPNE5,non_coding_transcript_exon_variant,,ENST00000493411,; A ENST00000244751 Transcript missense_variant 1721/3897 1096/1782 366/593 V/F Gtc/Ttc rs150078502 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 deleterious(0) 16/21 PROSITE_profiles:PS50234,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF51,Pfam_domain:PF07002,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 36746500 36746500 C A 1 0 0 0 0 1 0 0 0 3610 536 19 1 1 CPNE5 6 36746500 Missense_Mutation SNP C C3L-01889_T 670538 36746500 134059479 58 7737 RUNX2 0 . GRCh38 6 45512308 45512308 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.922A>T p.Ser308Cys p.S308C ENST00000371438 6/8 303 228 75 276 276 0 strelka-varscan RUNX2,missense_variant,p.Ser308Cys,ENST00000371438,NM_001024630.3;RUNX2,missense_variant,p.Ser308Cys,ENST00000371432,NM_001015051.3;RUNX2,missense_variant,p.Ser294Cys,ENST00000359524,;RUNX2,missense_variant,p.Ser308Cys,ENST00000576263,;RUNX2,missense_variant,p.Ser308Cys,ENST00000465038,;RUNX2,missense_variant,p.Ser308Cys,ENST00000371436,;RUNX2,missense_variant,p.Ser294Cys,ENST00000625924,NM_001278478.1;RUNX2,missense_variant,p.Ser236Cys,ENST00000478660,;RUNX2,3_prime_UTR_variant,,ENST00000483377,; T ENST00000371438 Transcript missense_variant 1280/5698 922/1566 308/521 S/C Agc/Tgc 1 1 RUNX2 HGNC HGNC:10472 protein_coding YES CCDS43467.2 ENSP00000360493 Q13950 UPI000013532F NM_001024630.3 deleterious(0.02) 6/8 hmmpanther:PTHR11950:SF7,hmmpanther:PTHR11950,PIRSF_domain:PIRSF009374 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 45512308 45512308 A T 1 0 0 0 0 1 0 0 0 14009 304 11 4 4 RUNX2 6 45512308 Missense_Mutation SNP A C3L-01889_T 8765808 45512308 125293671 59 7738 ADGRB3 0 . GRCh38 6 69239206 69239206 + Missense_Mutation SNP C C G novel C3L-01889_T C3L-01889_N C C c.2794C>G p.Gln932Glu p.Q932E ENST00000370598 20/32 137 119 18 138 138 0 strelka-varscan ADGRB3,missense_variant,p.Gln932Glu,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Gln932Glu,ENST00000546190,;ADGRB3,missense_variant,p.Gln138Glu,ENST00000238918,;ADGRB3,missense_variant,p.Gln62Glu,ENST00000604969,;ADGRB3,missense_variant,p.Gln116Glu,ENST00000603207,; G ENST00000370598 Transcript missense_variant 3615/6010 2794/4569 932/1522 Q/E Cag/Gag 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 deleterious(0.02) 20/32 PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF00002 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999917 1 1 1 0 G 3 3 28 69239206 69239206 C G 1 0 0 0 0 1 0 0 0 357 479 17 4 4 ADGRB3 6 69239206 Missense_Mutation SNP C C3L-01889_T 23726898 69239206 101566773 60 7739 GRIK2 0 . GRCh38 6 101928580 101928580 + Missense_Mutation SNP C C A rs763591971 C3L-01889_T C3L-01889_N C C c.2033C>A p.Thr678Asn p.T678N ENST00000421544 13/16 241 188 53 286 286 0 strelka-varscan GRIK2,missense_variant,p.Thr678Asn,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Thr678Asn,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Thr678Asn,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Thr640Asn,ENST00000318991,;GRIK2,missense_variant,p.Thr640Asn,ENST00000369137,;GRIK2,missense_variant,p.Thr640Asn,ENST00000369134,;GRIK2,non_coding_transcript_exon_variant,,ENST00000487395,;GRIK2,non_coding_transcript_exon_variant,,ENST00000487161,; A ENST00000421544 Transcript missense_variant 2523/4789 2033/2727 678/908 T/N aCc/aAc rs763591971 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 deleterious(0.02) 13/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 101928580 101928580 C A 1 0 0 0 0 1 0 0 0 6656 507 18 2 2 GRIK2 6 101928580 Missense_Mutation SNP C C3L-01889_T 32689374 101928580 68877399 61 7740 DDO 0 . GRCh38 6 110392864 110392864 + Missense_Mutation SNP C C A C3L-01889_T C3L-01889_N C C c.1021G>T p.Val341Leu p.V341L ENST00000368924 5/5 102 71 31 82 82 0 strelka-varscan DDO,missense_variant,p.Val341Leu,ENST00000368924,NM_003649.2;DDO,missense_variant,p.Val282Leu,ENST00000368923,NM_004032.2;DDO,3_prime_UTR_variant,,ENST00000479373,; A ENST00000368924 Transcript missense_variant 1037/2130 1021/1110 341/369 V/L Gtg/Ttg COSM2155895 1 -1 DDO HGNC HGNC:2727 protein_coding YES CCDS5082.1 ENSP00000357920 Q99489 UPI000006D9AB NM_003649.2 tolerated(0.33) 5/5 hmmpanther:PTHR11530:SF12,hmmpanther:PTHR11530,PROSITE_patterns:PS00677,Gene3D:3.50.50.60,PIRSF_domain:PIRSF000189,Pfam_domain:PF01266,Superfamily_domains:SSF51971 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 110392864 110392864 C A 1 0 0 0 0 1 0 0 0 4138 565 20 2 2 DDO 6 110392864 Missense_Mutation SNP C C3L-01889_T 8464284 110392864 60413115 62 7741 LAMA2 0 . GRCh38 6 129438697 129438697 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.6020C>A p.Ala2007Asp p.A2007D ENST00000421865 42/65 277 212 65 304 304 0 strelka-varscan LAMA2,missense_variant,p.Ala2007Asp,ENST00000618192,;LAMA2,missense_variant,p.Ala2007Asp,ENST00000617695,;LAMA2,missense_variant,p.Ala2007Asp,ENST00000421865,NM_001079823.1,NM_000426.3;RNU6-861P,upstream_gene_variant,,ENST00000516745,; A ENST00000421865 Transcript missense_variant 6069/9640 6020/9369 2007/3122 A/D gCt/gAt 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.45) 42/65 Coiled-coils_(Ncoils):Coil,PD936484,Superfamily_domains:SSF58104 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 129438697 129438697 C A 1 0 0 0 0 1 0 0 0 8510 797 28 2 2 LAMA2 6 129438697 Missense_Mutation SNP C C3L-01889_T 19045833 129438697 41367282 63 7742 STX11 0 . GRCh38 6 144187256 144187256 + Missense_Mutation SNP G G A novel C3L-01889_T C3L-01889_N G G c.629G>A p.Arg210His p.R210H ENST00000367568 2/2 207 184 23 210 210 0 strelka-varscan STX11,missense_variant,p.Arg210His,ENST00000367568,NM_003764.3; A ENST00000367568 Transcript missense_variant 812/1926 629/864 210/287 R/H cGc/cAc 1 1 STX11 HGNC HGNC:11429 protein_coding YES CCDS5205.1 ENSP00000356540 O75558 UPI0000001C25 NM_003764.3 deleterious(0) 2/2 Gene3D:1.20.58.70,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00804,PROSITE_patterns:PS00914,PROSITE_profiles:PS50192,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF30,Low_complexity_(Seg):seg,SMART_domains:SM00397,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 144187256 144187256 G A 1 0 0 0 0 1 0 0 0 15721 1087 38 1 1 STX11 6 144187256 Missense_Mutation SNP G C3L-01889_T 14748559 144187256 26618723 64 7743 ADGB 0 . GRCh38 6 146788488 146788488 + Frame_Shift_Del DEL G G - novel C3L-01889_T C3L-01889_N G G c.4416delG p.Trp1472Ter p.W1472* ENST00000397944 33/36 324 241 83 389 389 0 sindel-varindel-pindel ADGB,frameshift_variant,p.Trp1472Ter,ENST00000397944,NM_024694.3;ADGB,frameshift_variant,p.Trp430Ter,ENST00000367490,;ADGB,frameshift_variant,p.Trp195Ter,ENST00000326916,;ADGB,frameshift_variant,p.Trp136Ter,ENST00000470716,;ADGB,downstream_gene_variant,,ENST00000523560,;ADGB,3_prime_UTR_variant,,ENST00000493950,;ADGB,3_prime_UTR_variant,,ENST00000480328,; - ENST00000397944 Transcript frameshift_variant 4491/5325 4415/5004 1472/1667 W/X tGg/tg 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 33/36 HIGH 1 deletion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 146788488 146788488 G - 1 0 1 0 1 0 0 0 0 351 1357 47 0 0 ADGB 6 146788488 Frame_Shift_Del DEL G C3L-01889_T 2601232 146788488 24017491 65 7744 MAD1L1 0 . GRCh38 7 2230027 2230027 + Missense_Mutation SNP G G A rs776910007 C3L-01889_T C3L-01889_N G G c.107C>T p.Ser36Leu p.S36L ENST00000406869 3/19 175 139 36 152 152 0 strelka-varscan-mutect MAD1L1,missense_variant,p.Ser36Leu,ENST00000406869,;MAD1L1,missense_variant,p.Ser36Leu,ENST00000399654,NM_001013836.1,NM_003550.2,NM_001013837.1,NM_001304523.1;MAD1L1,missense_variant,p.Ser36Leu,ENST00000265854,;MAD1L1,missense_variant,p.Ser36Leu,ENST00000455998,;MAD1L1,missense_variant,p.Ser36Leu,ENST00000429779,;MAD1L1,intron_variant,,ENST00000402746,NM_001304524.1;MRM2,downstream_gene_variant,,ENST00000242257,NM_013393.1;MRM2,downstream_gene_variant,,ENST00000440306,;MAD1L1,upstream_gene_variant,,ENST00000429625,;MRM2,downstream_gene_variant,,ENST00000486040,;MRM2,downstream_gene_variant,,ENST00000467199,; A ENST00000406869 Transcript missense_variant 665/2991 107/2157 36/718 S/L tCg/tTg rs776910007,COSM1450018 1 -1 MAD1L1 HGNC HGNC:6762 protein_coding YES CCDS43539.1 ENSP00000385334 Q9Y6D9 UPI0000072C4D deleterious(0.03) 3/19 hmmpanther:PTHR23168:SF0,hmmpanther:PTHR23168 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776910007 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 2230027 2230027 G A 1 0 0 0 0 1 0 0 0 9063 1059 37 1 1 MAD1L1 7 2230027 Missense_Mutation SNP G C3L-01889_T 2230027 157115946 66 7745 CCDC129 0 . GRCh38 7 31651937 31651937 + Splice_Site SNP A A T novel C3L-01889_T C3L-01889_N A A c.2790-2A>T p.X930_splice ENST00000451887 135 94 41 121 121 0 strelka-varscan-mutect CCDC129,splice_acceptor_variant,,ENST00000319386,;CCDC129,splice_acceptor_variant,,ENST00000615280,NM_001257967.1;CCDC129,splice_acceptor_variant,,ENST00000409210,;CCDC129,splice_acceptor_variant,,ENST00000451887,NM_001257968.1;CCDC129,splice_acceptor_variant,,ENST00000407970,NM_194300.3;CCDC129,upstream_gene_variant,,ENST00000463693,; T ENST00000451887 Transcript splice_acceptor_variant -/3611 2790/3189 930/1062 1 1 CCDC129 HGNC HGNC:27363 protein_coding YES CCDS59050.1 ENSP00000395835 Q6ZRS4 UPI00020655D9 NM_001257968.1 12/14 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 28 31651937 31651937 A T 1 0 0 0 0 0 0 1 0 2456 202 7 4 4 CCDC129 7 31651937 Splice_Site SNP A C3L-01889_T 29421910 31651937 127694036 67 7746 NPC1L1 0 . GRCh38 7 44539200 44539200 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.1197G>A p.= p.Q399Q ENST00000289547 2/20 454 417 37 394 394 0 strelka-varscan-mutect NPC1L1,synonymous_variant,p.=,ENST00000289547,NM_013389.2;NPC1L1,synonymous_variant,p.=,ENST00000546276,;NPC1L1,synonymous_variant,p.=,ENST00000381160,NM_001101648.1;NPC1L1,synonymous_variant,p.=,ENST00000423141,NM_001300967.1; T ENST00000289547 Transcript synonymous_variant 1253/5048 1197/4080 399/1359 Q caG/caA 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 2/20 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 44539200 44539200 C T 1 0 0 0 0 0 0 0 1 10619 796 28 3 3 NPC1L1 7 44539200 Silent SNP C C3L-01889_T 12887263 44539200 114806773 68 7747 NPC1L1 0 . GRCh38 7 44541239 44541239 + Missense_Mutation SNP C C A rs751337767 C3L-01889_T C3L-01889_N C C c.21G>T p.Arg7Ser p.R7S ENST00000289547 1/20 121 91 30 99 99 0 strelka-varscan-mutect NPC1L1,missense_variant,p.Arg7Ser,ENST00000289547,NM_013389.2;NPC1L1,missense_variant,p.Arg7Ser,ENST00000546276,;NPC1L1,missense_variant,p.Arg7Ser,ENST00000381160,NM_001101648.1;NPC1L1,missense_variant,p.Arg7Ser,ENST00000423141,NM_001300967.1; A ENST00000289547 Transcript missense_variant 77/5048 21/4080 7/1359 R/S agG/agT rs751337767 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 deleterious_low_confidence(0.01) 1/20 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89 MODERATE 1 SNV 1 1 PASS rs751337767 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 44541239 44541239 C A 1 0 0 0 0 1 0 0 0 10619 622 22 2 2 NPC1L1 7 44541239 Missense_Mutation SNP C C3L-01889_T 2039 44541239 114804734 69 7748 ZNF679 0 . GRCh38 7 64266285 64266285 + Frame_Shift_Del DEL G G - rs779462779 C3L-01889_T C3L-01889_N G G c.653delG p.Gly218AlafsTer127 p.G218Afs*127 ENST00000421025 5/5 122 87 35 146 146 0 sindel-varindel-pindel ZNF679,frameshift_variant,p.Gly218AlafsTer127,ENST00000421025,NM_153363.2;ZNF679,frameshift_variant,p.Gly218AlafsTer127,ENST00000255746,; - ENST00000421025 Transcript frameshift_variant 921/1567 652/1236 218/411 G/X Ggc/gc rs779462779 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF91,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 1 PASS . . 0 201 2 6 0 0 0 0 -20 0.9990137 1 1 1 0 - 7 5 28 64266285 64266285 G - 1 0 1 0 1 0 0 0 0 18659 1116 39 0 0 ZNF679 7 64266285 Frame_Shift_Del DEL G C3L-01889_T 19725046 64266285 95079688 70 7749 FZD1 0 . GRCh38 7 91265684 91265684 + Silent SNP G G A rs780354235 C3L-01889_T C3L-01889_N G G c.804G>A p.= p.A268A ENST00000287934 1/1 63 47 16 69 69 0 strelka-varscan-mutect FZD1,synonymous_variant,p.=,ENST00000287934,NM_003505.1; A ENST00000287934 Transcript synonymous_variant 1321/6963 804/1944 268/647 A gcG/gcA rs780354235 1 1 FZD1 HGNC HGNC:4038 protein_coding YES CCDS5620.1 ENSP00000287934 Q9UP38 UPI000005104D NM_003505.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF81 LOW 1 SNV 1 PASS rs780354235 . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 2 1 28 91265684 91265684 G A 1 0 0 0 0 0 0 0 1 5999 1132 40 1 1 FZD1 7 91265684 Silent SNP G C3L-01889_T 26999399 91265684 68080289 71 7750 ZSCAN21 0 . GRCh38 7 100057379 100057379 + Missense_Mutation SNP C C T rs373816425 C3L-01889_T C3L-01889_N C C c.373C>T p.Arg125Trp p.R125W ENST00000292450 2/4 45 31 14 51 51 0 strelka-varscan-mutect ZSCAN21,missense_variant,p.Arg125Trp,ENST00000292450,NM_145914.2;ZSCAN21,missense_variant,p.Arg125Trp,ENST00000456748,;ZSCAN21,missense_variant,p.Arg125Trp,ENST00000438937,;ZSCAN21,intron_variant,,ENST00000543588,;ZSCAN21,non_coding_transcript_exon_variant,,ENST00000477297,; T ENST00000292450 Transcript missense_variant 537/2005 373/1422 125/473 R/W Cgg/Tgg rs373816425,COSM73507 1 1 ZSCAN21 HGNC HGNC:13104 protein_coding YES CCDS5681.1 ENSP00000292450 Q9Y5A6 UPI000000DBCC NM_145914.2 deleterious(0) 2/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50804,hmmpanther:PTHR23226:SF10,hmmpanther:PTHR23226,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373816425 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 100057379 100057379 C T 1 0 0 0 0 1 0 0 0 18827 759 27 1 1 ZSCAN21 7 100057379 Missense_Mutation SNP C C3L-01889_T 8791695 100057379 59288594 72 7751 MUC17 0 . GRCh38 7 101037205 101037205 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.5789G>T p.Ser1930Ile p.S1930I ENST00000306151 3/13 63 44 19 91 91 0 strelka-varscan-mutect MUC17,missense_variant,p.Ser1930Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ser1930Ile,ENST00000379439,; T ENST00000306151 Transcript missense_variant 5853/14247 5789/13482 1930/4493 S/I aGt/aTt 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.06) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS rs1252236878 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 101037205 101037205 G T 1 0 0 0 0 1 0 0 0 9973 1029 36 2 2 MUC17 7 101037205 Missense_Mutation SNP G C3L-01889_T 979826 101037205 58308768 73 7752 KMT2E 0 . GRCh38 7 105105451 105105451 + Nonsense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.2209G>T p.Glu737Ter p.E737* ENST00000311117 18/27 86 63 23 111 111 0 strelka-varscan-mutect KMT2E,stop_gained,p.Glu737Ter,ENST00000311117,NM_182931.2;KMT2E,stop_gained,p.Glu737Ter,ENST00000257745,NM_018682.3;KMT2E,downstream_gene_variant,,ENST00000622386,;KMT2E,downstream_gene_variant,,ENST00000479838,;KMT2E,upstream_gene_variant,,ENST00000473063,;CTB-152G17.6,non_coding_transcript_exon_variant,,ENST00000607968,;KMT2E,stop_gained,p.Glu737Ter,ENST00000334884,;KMT2E,upstream_gene_variant,,ENST00000478079,; T ENST00000311117 Transcript stop_gained 2754/6874 2209/5577 737/1858 E/* Gaa/Taa 1 1 KMT2E HGNC HGNC:18541 protein_coding YES CCDS34723.1 ENSP00000312379 Q8IZD2 UPI0000074133 NM_182931.2 18/27 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 28 105105451 105105451 G T 1 0 0 0 0 0 1 0 0 8299 1291 45 2 2 KMT2E 7 105105451 Nonsense_Mutation SNP G C3L-01889_T 4068246 105105451 54240522 74 7753 GRM8 0 . GRCh38 7 126533130 126533130 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.2252G>T p.Cys751Phe p.C751F ENST00000339582 9/11 124 89 35 137 137 0 strelka-varscan GRM8,missense_variant,p.Cys751Phe,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Cys751Phe,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Cys259Phe,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Cys751Phe,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; A ENST00000339582 Transcript missense_variant 3061/4057 2252/2727 751/908 C/F tGt/tTt 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.35) 9/11 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 126533130 126533130 C A 1 0 0 0 0 1 0 0 0 6685 478 17 2 2 GRM8 7 126533130 Missense_Mutation SNP C C3L-01889_T 21427679 126533130 32812843 75 7754 LRGUK 0 . GRCh38 7 134249038 134249038 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.2160C>A p.Asp720Glu p.D720E ENST00000285928 18/20 42 27 15 51 51 0 strelka-varscan-mutect LRGUK,missense_variant,p.Asp720Glu,ENST00000285928,NM_144648.1; A ENST00000285928 Transcript missense_variant 2229/3163 2160/2478 720/825 D/E gaC/gaA 1 1 LRGUK HGNC HGNC:21964 protein_coding YES CCDS5830.1 ENSP00000285928 Q96M69 UPI0000072C76 NM_144648.1 tolerated(0.16) 18/20 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 134249038 134249038 C A 1 0 0 0 0 1 0 0 0 8837 564 20 2 2 LRGUK 7 134249038 Missense_Mutation SNP C C3L-01889_T 7715908 134249038 25096935 76 7755 CHRM2 0 . GRCh38 7 137015374 137015374 + Missense_Mutation SNP C C G C3L-01889_T C3L-01889_N C C c.509C>G p.Thr170Ser p.T170S ENST00000445907 3/3 286 208 78 338 338 0 strelka-varscan-mutect CHRM2,missense_variant,p.Thr170Ser,ENST00000445907,NM_001006630.1,NM_001006627.1;CHRM2,missense_variant,p.Thr170Ser,ENST00000401861,NM_000739.2,NM_001006626.1,NM_001006628.1;CHRM2,missense_variant,p.Thr170Ser,ENST00000453373,NM_001006631.1,NM_001006629.1;CHRM2,missense_variant,p.Thr170Ser,ENST00000320658,NM_001006632.1;AC009264.1,intron_variant,,ENST00000439694,;AC009264.1,intron_variant,,ENST00000425981,;AC009264.1,intron_variant,,ENST00000586239,;AC009264.1,intron_variant,,ENST00000597642,;AC009264.1,intron_variant,,ENST00000598184,;AC009264.1,intron_variant,,ENST00000593789,;AC009264.1,intron_variant,,ENST00000592183,; G ENST00000445907 Transcript missense_variant 1037/5918 509/1401 170/466 T/S aCt/aGt COSM4497973 1 1 CHRM2 HGNC HGNC:1951 protein_coding YES CCDS5843.1 ENSP00000399745 P08172 A4D1Q0 UPI0000050410 NM_001006630.1,NM_001006627.1 deleterious(0) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00243,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 137015374 137015374 C G 1 0 0 0 0 1 0 0 0 3137 565 20 4 4 CHRM2 7 137015374 Missense_Mutation SNP C C3L-01889_T 2766336 137015374 22330599 77 7756 BRAF 0 . GRCh38 7 140753393 140753393 + Missense_Mutation SNP T T C rs121913370 C3L-01889_T C3L-01889_N T T c.1742A>G p.Asn581Ser p.N581S ENST00000288602 15/18 274 182 92 287 287 0 strelka-varscan-mutect BRAF,missense_variant,p.Asn189Ser,ENST00000496384,;BRAF,missense_variant,p.Asn581Ser,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Asn9Ser,ENST00000479537,;BRAF,splice_region_variant,,ENST00000497784,; C ENST00000288602 Transcript missense_variant,splice_region_variant 1803/2480 1742/2301 581/766 N/S aAt/aGt rs121913370,COSM1699452,COSM26460,COSM462 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious(0.04) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_patterns:PS00108,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF43,SMART_domains:SM00220,Superfamily_domains:SSF56112 likely_pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913370 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 140753393 140753393 T C 1 0 0 0 0 1 0 0 0 1665 1449 50 5 5 BRAF 7 140753393 Missense_Mutation SNP T C3L-01889_T 3738019 140753393 18592580 78 7757 KEL 0 . GRCh38 7 142942488 142942488 + Silent SNP G G T rs769151837 C3L-01889_T C3L-01889_N G G c.1983C>A p.= p.V661V ENST00000355265 18/19 311 235 76 282 281 1 strelka-varscan-mutect KEL,synonymous_variant,p.=,ENST00000355265,NM_000420.2;C7orf34,downstream_gene_variant,,ENST00000409607,NM_178829.4;C7orf34,downstream_gene_variant,,ENST00000458732,;KEL,downstream_gene_variant,,ENST00000479768,;KEL,non_coding_transcript_exon_variant,,ENST00000470850,;KEL,non_coding_transcript_exon_variant,,ENST00000478969,;KEL,downstream_gene_variant,,ENST00000465697,; T ENST00000355265 Transcript synonymous_variant 2458/2812 1983/2199 661/732 V gtC/gtA rs769151837 1 -1 KEL HGNC HGNC:6308 protein_coding YES CCDS34766.1 ENSP00000347409 P23276 A0A077QP03 UPI000000D923 NM_000420.2 18/19 hmmpanther:PTHR11733:SF128,hmmpanther:PTHR11733,Pfam_domain:PF01431,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS rs769151837 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 142942488 142942488 G T 1 0 0 0 0 0 0 0 1 8062 1161 41 2 2 KEL 7 142942488 Silent SNP G C3L-01889_T 2189095 142942488 16403485 79 7758 OR6V1 0 . GRCh38 7 143053182 143053182 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.842C>A p.Pro281His p.P281H ENST00000418316 1/1 237 184 53 213 213 0 strelka-varscan-mutect OR6V1,missense_variant,p.Pro281His,ENST00000418316,NM_001001667.1; A ENST00000418316 Transcript missense_variant 863/1028 842/942 281/313 P/H cCc/cAc 1 1 OR6V1 HGNC HGNC:15090 protein_coding YES CCDS47728.1 ENSP00000396085 Q8N148 A0A126GWQ4 UPI0000041C19 NM_001001667.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 143053182 143053182 C A 1 0 0 0 0 1 0 0 0 11281 623 22 2 2 OR6V1 7 143053182 Missense_Mutation SNP C C3L-01889_T 110694 143053182 16292791 80 7759 OR2F2 0 . GRCh38 7 143935687 143935687 + Missense_Mutation SNP G G T rs759869818 C3L-01889_T C3L-01889_N G G c.455G>T p.Gly152Val p.G152V ENST00000408955 1/1 175 134 41 212 212 0 strelka-varscan-mutect OR2F2,missense_variant,p.Gly152Val,ENST00000408955,NM_001004685.1; T ENST00000408955 Transcript missense_variant 522/1114 455/954 152/317 G/V gGc/gTc rs759869818 1 1 OR2F2 HGNC HGNC:8247 protein_coding YES CCDS43666.1 ENSP00000386222 O95006 UPI0000041C25 NM_001004685.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF63,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs759869818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 143935687 143935687 G T 1 0 0 0 0 1 0 0 0 11075 1203 42 2 2 OR2F2 7 143935687 Missense_Mutation SNP G C3L-01889_T 882505 143935687 15410286 81 7760 CNTNAP2 0 . GRCh38 7 147903695 147903695 + Nonsense_Mutation SNP T T A novel C3L-01889_T C3L-01889_N T T c.2229T>A p.Cys743Ter p.C743* ENST00000361727 14/24 396 283 113 387 387 0 strelka-varscan-mutect CNTNAP2,stop_gained,p.Cys743Ter,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,downstream_gene_variant,,ENST00000636755,;CNTNAP2,downstream_gene_variant,,ENST00000637654,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000455301,; A ENST00000361727 Transcript stop_gained 2747/9896 2229/3996 743/1331 C/* tgT/tgA 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 14/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644 HIGH 1 SNV 1 1 PASS rs929257551 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 28 147903695 147903695 T A 1 0 0 0 0 0 1 0 0 3428 1644 57 4 4 CNTNAP2 7 147903695 Nonsense_Mutation SNP T C3L-01889_T 3968008 147903695 11442278 82 7761 MYOM2 0 . GRCh38 8 2116068 2116068 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.3289G>T p.Ala1097Ser p.A1097S ENST00000262113 26/37 164 135 29 156 153 3 strelka-varscan-mutect MYOM2,missense_variant,p.Ala1097Ser,ENST00000262113,NM_003970.3;MYOM2,missense_variant,p.Ala522Ser,ENST00000523438,;MYOM2,upstream_gene_variant,,ENST00000520072,;MYOM2,upstream_gene_variant,,ENST00000519631,;MYOM2,non_coding_transcript_exon_variant,,ENST00000523443,; T ENST00000262113 Transcript missense_variant 3430/5014 3289/4398 1097/1465 A/S Gcc/Tcc 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 deleterious(0) 26/37 MODERATE 1 SNV 1 1 PASS rs1411394617 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 2116068 2116068 G T 1 0 0 0 0 1 0 0 0 10093 971 34 2 2 MYOM2 8 2116068 Missense_Mutation SNP G C3L-01889_T 2116068 143022568 83 7762 PXDNL 0 . GRCh38 8 51409187 51409187 + Missense_Mutation SNP C C A rs866469976 C3L-01889_T C3L-01889_N C C c.2437G>T p.Asp813Tyr p.D813Y ENST00000356297 17/23 124 88 36 122 122 0 strelka-varscan-mutect PXDNL,missense_variant,p.Asp813Tyr,ENST00000356297,NM_144651.4;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,missense_variant,p.Asp79Tyr,ENST00000522628,; A ENST00000356297 Transcript missense_variant 2538/4805 2437/4392 813/1463 D/Y Gac/Tac rs866469976 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS rs866469976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 51409187 51409187 C A 1 0 0 0 0 1 0 0 0 13002 884 31 1 1 PXDNL 8 51409187 Missense_Mutation SNP C C3L-01889_T 49293119 51409187 93729449 84 7763 ZFHX4 0 . GRCh38 8 76705137 76705137 + Missense_Mutation SNP C C T rs370676988 C3L-01889_T C3L-01889_N C C c.1049C>T p.Thr350Ile p.T350I ENST00000521891 2/11 155 112 43 177 177 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Thr350Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Thr350Ile,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; T ENST00000521891 Transcript missense_variant 1497/14019 1049/10851 350/3616 T/I aCt/aTt rs370676988 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS rs370676988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 76705137 76705137 C T 1 0 0 0 0 1 0 0 0 18213 565 20 3 3 ZFHX4 8 76705137 Missense_Mutation SNP C C3L-01889_T 25295950 76705137 68433499 85 7764 ZFHX4 0 . GRCh38 8 76851910 76851910 + Silent SNP C C G novel C3L-01889_T C3L-01889_N C C c.4989C>G p.= p.T1663T ENST00000521891 10/11 192 150 42 245 245 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; G ENST00000521891 Transcript synonymous_variant 5437/14019 4989/10851 1663/3616 T acC/acG 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 76851910 76851910 C G 1 0 0 0 0 0 0 0 1 18213 610 22 4 4 ZFHX4 8 76851910 Silent SNP C C3L-01889_T 146773 76851910 68286726 86 7765 PUF60 0 . GRCh38 8 143818049 143818049 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.630G>T p.Gln210His p.Q210H ENST00000526683 8/12 322 234 88 246 246 0 strelka-varscan-mutect PUF60,missense_variant,p.Gln210His,ENST00000526683,NM_001271098.1,NM_078480.2;PUF60,missense_variant,p.Gln167His,ENST00000453551,NM_001136033.2;PUF60,missense_variant,p.Gln193His,ENST00000349157,NM_014281.4,NM_001271096.1;PUF60,missense_variant,p.Gln150His,ENST00000313352,NM_001271100.1;PUF60,missense_variant,p.Gln181His,ENST00000456095,NM_001271099.1;PUF60,missense_variant,p.Gln164His,ENST00000527197,NM_001271097.1;PUF60,missense_variant,p.Gln208His,ENST00000527744,;PUF60,missense_variant,p.Gln192His,ENST00000526459,;PUF60,missense_variant,p.Gln230His,ENST00000529999,;PUF60,missense_variant,p.Gln230His,ENST00000531897,;PUF60,intron_variant,,ENST00000532884,;SCRIB,upstream_gene_variant,,ENST00000356994,NM_182706.4;SCRIB,upstream_gene_variant,,ENST00000320476,NM_015356.4;SCRIB,upstream_gene_variant,,ENST00000377533,;PUF60,downstream_gene_variant,,ENST00000533162,;PUF60,non_coding_transcript_exon_variant,,ENST00000524570,;PUF60,non_coding_transcript_exon_variant,,ENST00000531951,;PUF60,non_coding_transcript_exon_variant,,ENST00000528999,;PUF60,downstream_gene_variant,,ENST00000533362,;PUF60,non_coding_transcript_exon_variant,,ENST00000528320,;PUF60,downstream_gene_variant,,ENST00000529693,;PUF60,downstream_gene_variant,,ENST00000531995,;PUF60,downstream_gene_variant,,ENST00000532127,;PUF60,downstream_gene_variant,,ENST00000526151,;PUF60,downstream_gene_variant,,ENST00000527584,; A ENST00000526683 Transcript missense_variant 1186/2412 630/1680 210/559 Q/H caG/caT 1 -1 PUF60 HGNC HGNC:17042 protein_coding YES CCDS47934.1 ENSP00000434359 Q9UHX1 UPI00000713CF NM_001271098.1,NM_078480.2 deleterious(0) 8/12 Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01645 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 143818049 143818049 C A 1 0 0 0 0 1 0 0 0 12981 680 24 2 2 PUF60 8 143818049 Missense_Mutation SNP C C3L-01889_T 66966139 143818049 1320587 87 7766 ADAMTSL1 0 . GRCh38 9 18639378 18639378 + Missense_Mutation SNP G G A novel C3L-01889_T C3L-01889_N G G c.801G>A p.Met267Ile p.M267I ENST00000380548 7/29 135 127 8 160 160 0 strelka-varscan-mutect ADAMTSL1,missense_variant,p.Met267Ile,ENST00000380548,NM_001040272.5;ADAMTSL1,missense_variant,p.Met267Ile,ENST00000276935,;ADAMTSL1,missense_variant,p.Met267Ile,ENST00000380566,;ADAMTSL1,missense_variant,p.Met267Ile,ENST00000327883,NM_052866.4; A ENST00000380548 Transcript missense_variant 1140/8030 801/5289 267/1762 M/I atG/atA 1 1 ADAMTSL1 HGNC HGNC:14632 protein_coding YES CCDS47954.1 ENSP00000369921 Q8N6G6 UPI000004FD83 NM_001040272.5 tolerated(1) 7/29 hmmpanther:PTHR13723:SF157,hmmpanther:PTHR13723 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 18639378 18639378 G A 1 0 0 0 0 1 0 0 0 318 1348 47 3 3 ADAMTSL1 9 18639378 Missense_Mutation SNP G C3L-01889_T 18639378 119755339 88 7767 LINC00961 0 . GRCh38 9 35910529 35910529 + Silent SNP C C A rs41312816 C3L-01889_T C3L-01889_N C C c.66C>A p.= p.V22V ENST00000443779 2/2 326 244 82 264 263 1 strelka-varscan-mutect LINC00961,synonymous_variant,p.=,ENST00000443779,;LINC00961,synonymous_variant,p.=,ENST00000636776,;HRCT1,downstream_gene_variant,,ENST00000354323,NM_001039792.1;LINC00961,synonymous_variant,p.=,ENST00000638062,; A ENST00000443779 Transcript synonymous_variant 455/1612 66/228 22/75 V gtC/gtA rs41312816 1 1 LINC00961 HGNC HGNC:27244 protein_coding YES ENSP00000490187 UPI00002113C6 2/2 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS rs41312816 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 35910529 35910529 C A 1 0 0 0 0 0 0 0 1 8731 842 30 2 2 LINC00961 9 35910529 Silent SNP C C3L-01889_T 17271151 35910529 102484188 89 7768 SHC3 0 . GRCh38 9 89038047 89038047 + Silent SNP C C A rs575391468 C3L-01889_T C3L-01889_N C C c.1602G>T p.= p.T534T ENST00000375835 11/12 164 110 54 179 179 0 strelka-varscan-mutect SHC3,synonymous_variant,p.=,ENST00000375835,NM_016848.5;SHC3,synonymous_variant,p.=,ENST00000375831,; A ENST00000375835 Transcript synonymous_variant 1909/9768 1602/1785 534/594 T acG/acT rs575391468 1 -1 SHC3 HGNC HGNC:18181 protein_coding YES CCDS6681.1 ENSP00000364995 Q92529 UPI0000073E1F NM_016848.5 11/12 PROSITE_profiles:PS50001,hmmpanther:PTHR10337:SF4,hmmpanther:PTHR10337,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550 LOW 1 SNV 1 1 PASS rs575391468 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 89038047 89038047 C A 1 0 0 0 0 0 0 0 1 14531 639 23 1 1 SHC3 9 89038047 Silent SNP C C3L-01889_T 53127518 89038047 49356670 90 7769 OR13C3 0 . GRCh38 9 104536777 104536777 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.37G>T p.Ala13Ser p.A13S ENST00000374781 1/1 113 79 34 114 114 0 strelka-varscan-mutect OR13C3,missense_variant,p.Ala13Ser,ENST00000374781,NM_001001961.1;RP11-317C20.9,non_coding_transcript_exon_variant,,ENST00000635678,; A ENST00000374781 Transcript missense_variant 80/1108 37/1044 13/347 A/S Gca/Tca 1 -1 OR13C3 HGNC HGNC:14704 protein_coding YES CCDS35089.1 ENSP00000363913 Q8NGS6 A0A126GVY9 UPI000015F232 NM_001001961.1 tolerated_low_confidence(0.72) 1/1 Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 104536777 104536777 C A 1 0 0 0 0 1 0 0 0 11011 739 26 2 2 OR13C3 9 104536777 Missense_Mutation SNP C C3L-01889_T 15498730 104536777 33857940 91 7770 AMBP 0 . GRCh38 9 114061053 114061053 + Missense_Mutation SNP A A G novel C3L-01889_T C3L-01889_N A A c.899T>C p.Ile300Thr p.I300T ENST00000265132 9/10 207 161 46 164 164 0 strelka-varscan-mutect AMBP,missense_variant,p.Ile300Thr,ENST00000265132,NM_001633.3;AMBP,missense_variant,p.Ile173Thr,ENST00000466610,;ZNF618,downstream_gene_variant,,ENST00000615615,NM_001318040.1,NM_001318042.1,NM_001318041.1;ZNF618,downstream_gene_variant,,ENST00000288466,NM_133374.2;AMBP,non_coding_transcript_exon_variant,,ENST00000540645,;AMBP,downstream_gene_variant,,ENST00000603230,; G ENST00000265132 Transcript missense_variant 1162/1434 899/1059 300/352 I/T aTc/aCc 1 -1 AMBP HGNC HGNC:453 protein_coding YES CCDS6800.1 ENSP00000265132 P02760 UPI000000D9AF NM_001633.3 tolerated(0.39) 9/10 PROSITE_profiles:PS50279,hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF18,Gene3D:4.10.410.10,Pfam_domain:PF00014,SMART_domains:SM00131,Superfamily_domains:SSF57362 MODERATE 1 SNV 1 1 PASS rs1388694890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 114061053 114061053 A G 1 0 0 0 0 1 0 0 0 660 333 12 5 5 AMBP 9 114061053 Missense_Mutation SNP A C3L-01889_T 9524276 114061053 24333664 92 7771 GARNL3 0 . GRCh38 9 127355342 127355342 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1805G>T p.Arg602Met p.R602M ENST00000373387 20/28 169 130 39 187 187 0 strelka-varscan-mutect GARNL3,missense_variant,p.Arg602Met,ENST00000373387,NM_032293.4;GARNL3,missense_variant,p.Arg580Met,ENST00000435213,NM_001286779.1;GARNL3,non_coding_transcript_exon_variant,,ENST00000478696,;GARNL3,upstream_gene_variant,,ENST00000496711,;GARNL3,missense_variant,p.Arg584Met,ENST00000373386,;GARNL3,3_prime_UTR_variant,,ENST00000460176,;GARNL3,non_coding_transcript_exon_variant,,ENST00000481875,; T ENST00000373387 Transcript missense_variant 2157/3800 1805/3042 602/1013 R/M aGg/aTg 1 1 GARNL3 HGNC HGNC:25425 protein_coding YES CCDS6869.2 ENSP00000362485 Q5VVW2 UPI0000EE56F2 NM_032293.4 deleterious(0) 20/28 PROSITE_profiles:PS50219,hmmpanther:PTHR15711:SF24,hmmpanther:PTHR15711,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 127355342 127355342 G T 1 0 0 0 0 1 0 0 0 6111 1000 35 2 2 GARNL3 9 127355342 Missense_Mutation SNP G C3L-01889_T 13294289 127355342 11039375 93 7772 ITGA8 0 . GRCh38 10 15684065 15684065 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.507C>A p.= p.G169G ENST00000378076 4/30 235 182 53 233 233 0 strelka-varscan-mutect ITGA8,synonymous_variant,p.=,ENST00000378076,NM_003638.2,NM_001291494.1; T ENST00000378076 Transcript synonymous_variant 861/6755 507/3192 169/1063 G ggC/ggA 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 4/30 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 15684065 15684065 G T 1 0 0 0 0 0 0 0 1 7789 1306 46 2 2 ITGA8 10 15684065 Silent SNP G C3L-01889_T 15684065 118113357 94 7773 LRRTM3 0 . GRCh38 10 66927985 66927985 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.1069A>T p.Asn357Tyr p.N357Y ENST00000361320 2/3 282 211 71 320 320 0 strelka-varscan-mutect LRRTM3,missense_variant,p.Asn357Tyr,ENST00000361320,NM_178011.4;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2,NM_013266.3;CTNNA3,intron_variant,,ENST00000494580,; T ENST00000361320 Transcript missense_variant 1647/4358 1069/1746 357/581 N/Y Aac/Tac 1 1 LRRTM3 HGNC HGNC:19410 protein_coding YES CCDS7270.1 ENSP00000355187 Q86VH5 UPI0000088C0F NM_178011.4 tolerated(0.76) 2/3 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 66927985 66927985 A T 1 0 0 0 0 1 0 0 0 8947 246 9 4 4 LRRTM3 10 66927985 Missense_Mutation SNP A C3L-01889_T 51243920 66927985 66869437 95 7774 ANKRD22 0 . GRCh38 10 88831846 88831846 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.202C>A p.Leu68Ile p.L68I ENST00000371930 2/6 60 56 4 69 69 0 varscan-mutect ANKRD22,missense_variant,p.Leu68Ile,ENST00000371930,NM_144590.2; T ENST00000371930 Transcript missense_variant 413/1596 202/576 68/191 L/I Ctc/Atc 1 -1 ANKRD22 HGNC HGNC:28321 protein_coding YES CCDS7390.1 ENSP00000360998 Q5VYY1 UPI000013DCF6 NM_144590.2 tolerated(0.58) 2/6 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24139,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1437457952 . 0 196 12 2 0 0 0 0 -7.912184 0.9925765 1 1 1 0 T 3 4 28 88831846 88831846 G T 1 0 0 0 0 1 0 0 0 754 1000 35 2 2 ANKRD22 10 88831846 Missense_Mutation SNP G C3L-01889_T 21903861 88831846 44965576 96 7775 ZNF518A 0 . GRCh38 10 96158386 96158386 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.2064G>A p.= p.Q688Q ENST00000624776 6/6 207 155 52 206 206 0 strelka-varscan-mutect ZNF518A,synonymous_variant,p.=,ENST00000624776,NM_001278525.1;ZNF518A,synonymous_variant,p.=,ENST00000614149,;ZNF518A,synonymous_variant,p.=,ENST00000316045,NM_001278524.1,NM_014803.3;ZNF518A,downstream_gene_variant,,ENST00000478086,;ZNF518A,intron_variant,,ENST00000563195,;ZNF518A,intron_variant,,ENST00000442635,;ZNF518A,downstream_gene_variant,,ENST00000488700,;ZNF518A,non_coding_transcript_exon_variant,,ENST00000534948,; A ENST00000624776 Transcript synonymous_variant 2628/7994 2064/4452 688/1483 Q caG/caA 1 1 ZNF518A HGNC HGNC:29009 protein_coding YES CCDS73170.1 ENSP00000485614 Q6AHZ1 UPI00003FEC7C NM_001278525.1 6/6 hmmpanther:PTHR10032:SF198,hmmpanther:PTHR10032 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 96158386 96158386 G A 1 0 0 0 0 0 0 0 1 18534 991 35 3 3 ZNF518A 10 96158386 Silent SNP G C3L-01889_T 7326540 96158386 37639036 97 7776 GFRA1 0 . GRCh38 10 116125472 116125472 + Silent SNP C C G rs768119844 C3L-01889_T C3L-01889_N C C c.519G>C p.= p.A173A ENST00000355422 6/11 167 122 45 186 186 0 strelka-varscan-mutect GFRA1,synonymous_variant,p.=,ENST00000439649,NM_001145453.1;GFRA1,synonymous_variant,p.=,ENST00000369236,NM_145793.3;GFRA1,synonymous_variant,p.=,ENST00000355422,NM_005264.4;GFRA1,synonymous_variant,p.=,ENST00000369234,; G ENST00000355422 Transcript synonymous_variant 1070/2583 519/1398 173/465 A gcG/gcC rs768119844 1 -1 GFRA1 HGNC HGNC:4243 protein_coding YES CCDS44481.1 ENSP00000347591 P56159 UPI000012B3A8 NM_005264.4 6/11 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF3,Pfam_domain:PF02351,PIRSF_domain:PIRSF038071,SMART_domains:SM00907 LOW 1 SNV 5 1 PASS rs768119844 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 116125472 116125472 C G 1 0 0 0 0 0 0 0 1 6221 523 19 4 4 GFRA1 10 116125472 Silent SNP C C3L-01889_T 19967086 116125472 17671950 98 7777 PNLIPRP1 0 . GRCh38 10 116594810 116594810 + Silent SNP C C A C3L-01889_T C3L-01889_N C C c.411C>A p.= p.A137A ENST00000528052 5/13 276 211 65 226 226 0 strelka-varscan-mutect PNLIPRP1,synonymous_variant,p.=,ENST00000528052,NM_001303135.1;PNLIPRP1,synonymous_variant,p.=,ENST00000358834,NM_006229.3;PNLIPRP1,synonymous_variant,p.=,ENST00000534537,;PNLIPRP1,synonymous_variant,p.=,ENST00000531984,;PNLIPRP1,intron_variant,,ENST00000530319,;PNLIPRP1,intron_variant,,ENST00000527980,;PNLIPRP1,downstream_gene_variant,,ENST00000471549,;PNLIPRP1,downstream_gene_variant,,ENST00000480870,;PNLIPRP1,downstream_gene_variant,,ENST00000525157,;PNLIPRP1,downstream_gene_variant,,ENST00000510125,;PNLIPRP1,synonymous_variant,p.=,ENST00000482833,;PNLIPRP1,3_prime_UTR_variant,,ENST00000497792,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000484402,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000529584,;PNLIPRP1,downstream_gene_variant,,ENST00000482159,;PNLIPRP1,downstream_gene_variant,,ENST00000530626,;PNLIPRP1,upstream_gene_variant,,ENST00000534513,;PNLIPRP1,downstream_gene_variant,,ENST00000470678,; A ENST00000528052 Transcript synonymous_variant 482/1533 411/1404 137/467 A gcC/gcA COSM2153960 1 1 PNLIPRP1 HGNC HGNC:9156 protein_coding YES CCDS7595.1 ENSP00000433933 P54315 UPI000012E6AA NM_001303135.1 5/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Prints_domain:PR00823,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF108,Superfamily_domains:SSF53474 1 LOW 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 116594810 116594810 C A 1 0 0 0 0 0 0 0 1 12258 581 21 2 2 PNLIPRP1 10 116594810 Silent SNP C C3L-01889_T 469338 116594810 17202612 99 7778 DEAF1 0 . GRCh38 11 688391 688391 + Missense_Mutation SNP T T A rs772491770 C3L-01889_T C3L-01889_N T T c.457A>T p.Thr153Ser p.T153S ENST00000382409 3/12 247 180 67 204 204 0 strelka-varscan-mutect DEAF1,missense_variant,p.Thr153Ser,ENST00000382409,NM_021008.3;DEAF1,non_coding_transcript_exon_variant,,ENST00000525626,;DEAF1,non_coding_transcript_exon_variant,,ENST00000528864,;DEAF1,non_coding_transcript_exon_variant,,ENST00000524786,;DEAF1,upstream_gene_variant,,ENST00000530813,;DEAF1,downstream_gene_variant,,ENST00000529727,;DEAF1,3_prime_UTR_variant,,ENST00000529717,;DEAF1,upstream_gene_variant,,ENST00000527170,; A ENST00000382409 Transcript missense_variant 942/2500 457/1698 153/565 T/S Aca/Tca rs772491770 1 -1 DEAF1 HGNC HGNC:14677 protein_coding YES CCDS31327.1 ENSP00000371846 O75398 UPI00001290E6 NM_021008.3 tolerated(0.08) 3/12 hmmpanther:PTHR10237 MODERATE 1 SNV 1 1 PASS rs772491770 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 688391 688391 T A 1 0 0 0 0 1 0 0 0 4183 1696 59 4 4 DEAF1 11 688391 Missense_Mutation SNP T C3L-01889_T 688391 134398231 100 7779 DNHD1 0 . GRCh38 11 6498689 6498689 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.474C>T p.= p.H158H ENST00000254579 3/43 165 127 38 157 157 0 strelka-varscan-mutect DNHD1,synonymous_variant,p.=,ENST00000254579,NM_144666.2;DNHD1,synonymous_variant,p.=,ENST00000527990,;DNHD1,synonymous_variant,p.=,ENST00000354685,NM_173589.3;DNHD1,downstream_gene_variant,,ENST00000496802,;DNHD1,non_coding_transcript_exon_variant,,ENST00000477562,;DNHD1,intron_variant,,ENST00000473019,; T ENST00000254579 Transcript synonymous_variant 1038/14862 474/14262 158/4753 H caC/caT 1 1 DNHD1 HGNC HGNC:26532 protein_coding YES CCDS44532.1 ENSP00000254579 Q96M86 UPI0001929529 NM_144666.2 3/43 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF244 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 6498689 6498689 C T 1 0 0 0 0 0 0 0 1 4481 477 17 3 3 DNHD1 11 6498689 Silent SNP C C3L-01889_T 5810298 6498689 128587933 101 7780 OTOG 0 . GRCh38 11 17586572 17586572 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.2894G>T p.Cys965Phe p.C965F ENST00000399391 23/55 17 12 5 25 25 0 strelka-varscan-mutect OTOG,missense_variant,p.Cys953Phe,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Cys965Phe,ENST00000399391,NM_001277269.1;OTOG,missense_variant,p.Leu26Phe,ENST00000342528,; T ENST00000399391 Transcript missense_variant 2894/8778 2894/8778 965/2925 C/F tGc/tTc 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0.01) 23/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 17586572 17586572 G T 1 0 0 0 0 1 0 0 0 11370 1319 46 2 2 OTOG 11 17586572 Missense_Mutation SNP G C3L-01889_T 11087883 17586572 117500050 102 7781 BBOX1 0 . GRCh38 11 27125773 27125773 + Missense_Mutation SNP A A G novel C3L-01889_T C3L-01889_N A A c.956A>G p.Asp319Gly p.D319G ENST00000263182 8/9 174 134 40 194 194 0 strelka-varscan-mutect BBOX1,missense_variant,p.Asp319Gly,ENST00000263182,NM_003986.2;BBOX1,missense_variant,p.Asp319Gly,ENST00000529202,;BBOX1,missense_variant,p.Asp319Gly,ENST00000528583,;BBOX1,missense_variant,p.Asp319Gly,ENST00000525090,;BBOX1-AS1,intron_variant,,ENST00000530430,;BBOX1-AS1,intron_variant,,ENST00000525302,;BBOX1-AS1,intron_variant,,ENST00000526061,; G ENST00000263182 Transcript missense_variant 1324/1886 956/1164 319/387 D/G gAc/gGc 1 1 BBOX1 HGNC HGNC:964 protein_coding YES CCDS7862.1 ENSP00000263182 O75936 UPI0000126A4C NM_003986.2 deleterious(0.04) 8/9 hmmpanther:PTHR10696:SF33,hmmpanther:PTHR10696,TIGRFAM_domain:TIGR02409,Gene3D:3.60.130.10,Pfam_domain:PF02668,Superfamily_domains:SSF51197 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 28 27125773 27125773 A G 1 0 0 0 0 1 0 0 0 1481 275 10 5 5 BBOX1 11 27125773 Missense_Mutation SNP A C3L-01889_T 9539201 27125773 107960849 103 7782 HSD17B12 0 . GRCh38 11 43815502 43815503 + Splice_Site INS - - T novel C3L-01889_T C3L-01889_N - - c.456+2dupT p.X152_splice ENST00000278353 52 39 13 54 54 0 sindel-varindel-pindel HSD17B12,splice_donor_variant,,ENST00000278353,NM_016142.2;HSD17B12,splice_donor_variant,,ENST00000637401,;HSD17B12,splice_donor_variant,,ENST00000531185,;HSD17B12,splice_donor_variant,,ENST00000638034,;RP11-472I20.4,splice_donor_variant,,ENST00000532864,;RP11-472I20.4,splice_donor_variant,,ENST00000529261,;HSD17B12,splice_donor_variant,,ENST00000527213,;HSD17B12,splice_donor_variant,,ENST00000527433,;HSD17B12,intron_variant,,ENST00000636007,; T ENST00000278353 Transcript splice_donor_variant -/2571 456/939 152/312 1 1 HSD17B12 HGNC HGNC:18646 protein_coding YES CCDS7905.1 ENSP00000278353 Q53GQ0 UPI000004C79B NM_016142.2 5/10 HIGH 1 insertion 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 8 5 28 43815502 43815502 - T 1 0 1 1 0 0 0 1 0 7276 1391 48 0 0 HSD17B12 11 43815502 Splice_Site INS - C3L-01889_T 16689729 43815502 91271120 104 7783 OR5T3 0 . GRCh38 11 56252576 56252576 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.377G>C p.Gly126Ala p.G126A ENST00000303059 1/1 270 193 77 304 304 0 strelka-varscan-mutect OR5T3,missense_variant,p.Gly126Ala,ENST00000303059,NM_001004747.1; C ENST00000303059 Transcript missense_variant 377/1023 377/1023 126/340 G/A gGa/gCa 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 tolerated(0.19) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 56252576 56252576 G C 1 0 0 0 0 1 0 0 0 11251 1174 41 4 4 OR5T3 11 56252576 Missense_Mutation SNP G C3L-01889_T 12437074 56252576 78834046 105 7784 MPEG1 0 . GRCh38 11 59211440 59211440 + Missense_Mutation SNP C C T rs753784064 C3L-01889_T C3L-01889_N C C c.1426G>A p.Gly476Arg p.G476R ENST00000361050 1/1 135 121 14 168 168 0 strelka-varscan-mutect MPEG1,missense_variant,p.Gly476Arg,ENST00000361050,NM_001039396.1;DTX4,downstream_gene_variant,,ENST00000227451,NM_015177.1;RN7SL42P,downstream_gene_variant,,ENST00000579786,; T ENST00000361050 Transcript missense_variant 1512/4442 1426/2151 476/716 G/R Gga/Aga rs753784064 1 -1 MPEG1 HGNC HGNC:29619 protein_coding YES CCDS41650.1 ENSP00000354335 Q2M385 UPI0000049D9F NM_001039396.1 deleterious(0) 1/1 hmmpanther:PTHR31463,hmmpanther:PTHR31463:SF4 MODERATE SNV 1 PASS rs753784064 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 59211440 59211440 C T 1 0 0 0 0 1 0 0 0 9688 690 24 3 3 MPEG1 11 59211440 Missense_Mutation SNP C C3L-01889_T 2958864 59211440 75875182 106 7785 ALDH3B2 0 . GRCh38 11 67666593 67666593 + Silent SNP C C A novel C3L-01889_T C3L-01889_N C C c.132G>T p.= p.L44L ENST00000349015 4/10 183 128 55 161 161 0 strelka-varscan-mutect ALDH3B2,synonymous_variant,p.=,ENST00000349015,NM_000695.3;ALDH3B2,synonymous_variant,p.=,ENST00000530069,NM_001031615.1;ALDH3B2,synonymous_variant,p.=,ENST00000525827,;ALDH3B2,synonymous_variant,p.=,ENST00000528756,;ALDH3B2,upstream_gene_variant,,ENST00000531248,;ALDH3B2,non_coding_transcript_exon_variant,,ENST00000531881,;ALDH3B2,downstream_gene_variant,,ENST00000533962,;ALDH3B2,non_coding_transcript_exon_variant,,ENST00000534425,; A ENST00000349015 Transcript synonymous_variant 571/2649 132/1158 44/385 L ctG/ctT 1 -1 ALDH3B2 HGNC HGNC:411 protein_coding YES CCDS31622.1 ENSP00000255084 P48448 UPI000013CE83 NM_000695.3 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF179,Pfam_domain:PF00171,Gene3D:3.40.605.10,Superfamily_domains:SSF53720 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 67666593 67666593 C A 1 0 0 0 0 0 0 0 1 600 581 21 2 2 ALDH3B2 11 67666593 Silent SNP C C3L-01889_T 8455153 67666593 67420029 107 7786 CEP57 0 . GRCh38 11 95818825 95818825 + Splice_Site SNP A A G novel C3L-01889_T C3L-01889_N A A c.622-2A>G p.X208_splice ENST00000325542 273 198 75 285 285 0 strelka-varscan-mutect CEP57,splice_acceptor_variant,,ENST00000325542,NM_014679.4;CEP57,splice_acceptor_variant,,ENST00000325486,NM_001243777.1;CEP57,splice_acceptor_variant,,ENST00000541150,NM_001243776.1;CEP57,splice_acceptor_variant,,ENST00000538658,;CEP57,splice_acceptor_variant,,ENST00000537677,;CEP57,splice_acceptor_variant,,ENST00000541365,;CEP57,splice_acceptor_variant,,ENST00000535224,;CEP57,splice_acceptor_variant,,ENST00000537093,;CEP57,downstream_gene_variant,,ENST00000544522,;CEP57,downstream_gene_variant,,ENST00000536587,;CEP57,splice_acceptor_variant,,ENST00000540830,;CEP57,splice_acceptor_variant,,ENST00000539855,;CEP57,downstream_gene_variant,,ENST00000541768,; G ENST00000325542 Transcript splice_acceptor_variant -/3178 622/1503 208/500 1 1 CEP57 HGNC HGNC:30794 protein_coding YES CCDS8304.1 ENSP00000317902 Q86XR8 UPI0000070D0B NM_014679.4 5/10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 28 95818825 95818825 A G 1 0 0 0 0 0 0 1 0 2976 434 15 5 5 CEP57 11 95818825 Splice_Site SNP A C3L-01889_T 28152232 95818825 39267797 108 7787 ARHGAP42 0 . GRCh38 11 100973304 100973304 + Silent SNP G G T C3L-01889_T C3L-01889_N G G c.1680G>T p.= p.V560V ENST00000298815 18/24 200 135 65 210 210 0 strelka-varscan-mutect ARHGAP42,synonymous_variant,p.=,ENST00000524892,;ARHGAP42,synonymous_variant,p.=,ENST00000298815,NM_152432.2;ARHGAP42,synonymous_variant,p.=,ENST00000529535,; T ENST00000298815 Transcript synonymous_variant 1683/4752 1680/2625 560/874 V gtG/gtT COSM3383133,COSM3383134 1 1 ARHGAP42 HGNC HGNC:26545 protein_coding YES ENSP00000298815 A6NI28 UPI00005778C9 NM_152432.2 18/24 PROSITE_profiles:PS50238,hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF3,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 1,1 LOW 1 SNV 5 1,1 1 PASS rs1362276486 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 100973304 100973304 G T 1 0 0 0 0 0 0 0 1 1013 1335 47 2 2 ARHGAP42 11 100973304 Silent SNP G C3L-01889_T 5154479 100973304 34113318 109 7788 NXPE1 0 . GRCh38 11 114530277 114530277 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.305G>T p.Cys102Phe p.C102F ENST00000251921 3/6 194 152 42 213 212 1 strelka-mutect NXPE1,missense_variant,p.Cys244Phe,ENST00000536312,;NXPE1,missense_variant,p.Cys244Phe,ENST00000424269,;NXPE1,missense_variant,p.Cys102Phe,ENST00000251921,NM_152315.3;NXPE1,upstream_gene_variant,,ENST00000536271,;NXPE1,downstream_gene_variant,,ENST00000539878,;NXPE1,downstream_gene_variant,,ENST00000534921,;snoU13,downstream_gene_variant,,ENST00000459372,; A ENST00000251921 Transcript missense_variant 722/1888 305/1218 102/405 C/F tGt/tTt 1 -1 NXPE1 HGNC HGNC:28527 protein_coding YES CCDS8372.1 ENSP00000251921 Q8N323 UPI000013CD22 NM_152315.3 deleterious(0) 3/6 Pfam_domain:PF06312,hmmpanther:PTHR16165,hmmpanther:PTHR16165:SF4 MODERATE 1 SNV 1 1 PASS rs1326349872 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 114530277 114530277 C A 1 0 0 0 0 1 0 0 0 10862 478 17 2 2 NXPE1 11 114530277 Missense_Mutation SNP C C3L-01889_T 13556973 114530277 20556345 110 7789 OR4D5 0 . GRCh38 11 123940426 123940426 + Silent SNP C C T C3L-01889_T C3L-01889_N C C c.810C>T p.= p.A270A ENST00000307033 1/1 198 152 46 200 200 0 strelka-varscan-mutect OR4D5,synonymous_variant,p.=,ENST00000307033,NM_001001965.1;OR6T1,downstream_gene_variant,,ENST00000321252,NM_001005187.1; T ENST00000307033 Transcript synonymous_variant 884/1095 810/957 270/318 A gcC/gcT COSM3687142 1 1 OR4D5 HGNC HGNC:14852 protein_coding YES CCDS31699.1 ENSP00000305970 Q8NGN0 A0A126GVD9 UPI000003F227 NM_001001965.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF73,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS rs1244893409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 123940426 123940426 C T 1 0 0 0 0 0 0 0 1 11134 639 23 1 1 OR4D5 11 123940426 Silent SNP C C3L-01889_T 9410149 123940426 11146196 111 7790 KDM5A 0 . GRCh38 12 285519 285519 + Silent SNP T T G novel C3L-01889_T C3L-01889_N T T c.5010A>C p.= p.A1670A ENST00000399788 28/28 269 194 75 310 310 0 strelka-varscan-mutect KDM5A,synonymous_variant,p.=,ENST00000399788,NM_001042603.2;KDM5A,non_coding_transcript_exon_variant,,ENST00000540838,; G ENST00000399788 Transcript synonymous_variant 5373/10763 5010/5073 1670/1690 A gcA/gcC 1 -1 KDM5A HGNC HGNC:9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.2 28/28 Low_complexity_(Seg):seg,hmmpanther:PTHR10694:SF17,hmmpanther:PTHR10694 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 285519 285519 T G 1 0 0 0 0 0 0 0 1 8051 1683 59 5 5 KDM5A 12 285519 Silent SNP T C3L-01889_T 285519 132989790 112 7791 GRIN2B 0 . GRCh38 12 13563516 13563516 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.3722G>T p.Arg1241Leu p.R1241L ENST00000609686 13/13 245 193 52 234 234 0 strelka-varscan-mutect GRIN2B,missense_variant,p.Arg1241Leu,ENST00000609686,NM_000834.3;GRIN2B,intron_variant,,ENST00000637214,;GRIN2B,non_coding_transcript_exon_variant,,ENST00000628166,;GRIN2B,upstream_gene_variant,,ENST00000636207,; A ENST00000609686 Transcript missense_variant 4176/30355 3722/4455 1241/1484 R/L cGg/cTg 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 deleterious(0) 13/13 Pfam_domain:PF10565 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 13563516 13563516 C A 1 0 0 0 0 1 0 0 0 6662 652 23 1 1 GRIN2B 12 13563516 Missense_Mutation SNP C C3L-01889_T 13277997 13563516 119711793 113 7792 KRT77 0 . GRCh38 12 52697783 52697783 + Silent SNP G G A rs760106782 C3L-01889_T C3L-01889_N G G c.657C>T p.= p.I219I ENST00000341809 2/9 357 274 83 340 340 0 strelka-varscan-mutect KRT77,synonymous_variant,p.=,ENST00000341809,NM_175078.2;RP11-641A6.3,downstream_gene_variant,,ENST00000547533,;KRT77,missense_variant,p.Arg248Trp,ENST00000553168,;KRT77,upstream_gene_variant,,ENST00000550823,; A ENST00000341809 Transcript synonymous_variant 686/3305 657/1737 219/578 I atC/atT rs760106782,COSM4042918 1 -1 KRT77 HGNC HGNC:20411 protein_coding YES CCDS8837.1 ENSP00000342710 Q7Z794 UPI00001D797A NM_175078.2 2/9 hmmpanther:PTHR23239:SF87,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391 0,1 LOW 1 SNV 1 0,1 1 PASS rs760106782 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 52697783 52697783 G A 1 0 0 0 0 0 0 0 1 8372 1048 37 1 1 KRT77 12 52697783 Silent SNP G C3L-01889_T 39134267 52697783 80577526 114 7793 PPP1CC 0 . GRCh38 12 110731801 110731801 + Silent SNP T T A novel C3L-01889_T C3L-01889_N T T c.156A>T p.= p.L52L ENST00000340766 2/8 85 53 32 84 84 0 strelka-varscan-mutect PPP1CC,synonymous_variant,p.=,ENST00000335007,NM_002710.3;PPP1CC,synonymous_variant,p.=,ENST00000546933,;PPP1CC,synonymous_variant,p.=,ENST00000550991,;PPP1CC,synonymous_variant,p.=,ENST00000551676,;PPP1CC,synonymous_variant,p.=,ENST00000340766,NM_001244974.1;PPP1CC,downstream_gene_variant,,ENST00000551690,;PPP1CC,synonymous_variant,p.=,ENST00000620030,;PPP1CC,upstream_gene_variant,,ENST00000550261,; A ENST00000340766 Transcript synonymous_variant 388/1472 156/1014 52/337 L ctA/ctT 1 -1 PPP1CC HGNC HGNC:9283 protein_coding YES CCDS58279.1 ENSP00000341779 P36873 UPI000002B16F NM_001244974.1 2/8 hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF255,Pfam_domain:PF16891,Gene3D:3.60.21.10,SMART_domains:SM00156,Superfamily_domains:SSF56300 LOW 1 SNV 2 1 PASS rs1164020939 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 110731801 110731801 T A 1 0 0 0 0 0 0 0 1 12461 1625 57 4 4 PPP1CC 12 110731801 Silent SNP T C3L-01889_T 58034018 110731801 22543508 115 7794 ORAI1 0 . GRCh38 12 121641281 121641281 + Missense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.355A>T p.Ile119Phe p.I119F ENST00000617316 2/2 322 208 114 362 362 0 strelka-varscan-mutect ORAI1,missense_variant,p.Ile119Phe,ENST00000617316,NM_032790.3;ORAI1,3_prime_UTR_variant,,ENST00000611718,; T ENST00000617316 Transcript missense_variant 742/2138 355/717 119/238 I/F Atc/Ttc 1 1 ORAI1 HGNC HGNC:25896 protein_coding YES ENSP00000482568 A0A0B4J2E8 UPI0000036A44 NM_032790.3 tolerated(0.13) 2/2 Pfam_domain:PF07856,hmmpanther:PTHR31501,hmmpanther:PTHR31501:SF3,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1266070960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 121641281 121641281 A T 1 0 0 0 0 1 0 0 0 11323 217 8 4 4 ORAI1 12 121641281 Missense_Mutation SNP A C3L-01889_T 10909480 121641281 11634028 116 7795 PIWIL1 0 . GRCh38 12 130347064 130347064 + Splice_Site SNP T T A novel C3L-01889_T C3L-01889_N T T c.653+2T>A p.X218_splice ENST00000245255 195 162 33 122 122 0 strelka-varscan-mutect PIWIL1,splice_donor_variant,,ENST00000245255,NM_004764.4,NM_001190971.1;PIWIL1,downstream_gene_variant,,ENST00000542723,;PIWIL1,downstream_gene_variant,,ENST00000546060,;PIWIL1,downstream_gene_variant,,ENST00000535956,;PIWIL1,downstream_gene_variant,,ENST00000539995,;PIWIL1,downstream_gene_variant,,ENST00000539400,;RP11-200K12.3,downstream_gene_variant,,ENST00000624997,;PIWIL1,splice_donor_variant,,ENST00000540672,; A ENST00000245255 Transcript splice_donor_variant -/3897 653/2586 218/861 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 6/20 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 28 130347064 130347064 T A 1 0 0 0 0 0 0 1 0 12053 1652 57 4 4 PIWIL1 12 130347064 Splice_Site SNP T C3L-01889_T 8705783 130347064 2928245 117 7796 LATS2 0 . GRCh38 13 21045908 21045908 + Missense_Mutation SNP C C A C3L-01889_T C3L-01889_N C C c.119G>T p.Gly40Val p.G40V ENST00000382592 2/8 335 248 87 316 312 4 strelka-varscan-mutect LATS2,missense_variant,p.Gly40Val,ENST00000382592,NM_014572.2; A ENST00000382592 Transcript missense_variant 525/5511 119/3267 40/1088 G/V gGa/gTa COSM12866 1 -1 LATS2 HGNC HGNC:6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 A0A024RDM3 UPI000013DBF5 NM_014572.2 deleterious_low_confidence(0.01) 2/8 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 21045908 21045908 C A 1 0 0 0 0 1 0 0 0 8552 855 30 2 2 LATS2 13 21045908 Missense_Mutation SNP C C3L-01889_T 21045908 93318420 118 7797 ATP12A 0 . GRCh38 13 24690392 24690392 + Missense_Mutation SNP G G A novel C3L-01889_T C3L-01889_N G G c.601G>A p.Val201Met p.V201M ENST00000218548 6/23 132 103 29 105 104 1 strelka-varscan-mutect ATP12A,missense_variant,p.Val201Met,ENST00000381946,NM_001676.5;ATP12A,missense_variant,p.Val201Met,ENST00000218548,NM_001185085.1; A ENST00000218548 Transcript missense_variant 934/3732 601/3138 201/1045 V/M Gtg/Atg 1 1 ATP12A HGNC HGNC:13816 protein_coding YES CCDS53858.1 ENSP00000218548 P54707 UPI000006D1DE NM_001185085.1 deleterious(0) 6/23 hmmpanther:PTHR24093:SF282,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,Gene3D:2.70.150.10,TIGRFAM_domain:TIGR01106,Superfamily_domains:0049471 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 24690392 24690392 G A 1 0 0 0 0 1 0 0 0 1274 1261 44 3 3 ATP12A 13 24690392 Missense_Mutation SNP G C3L-01889_T 3644484 24690392 89673936 119 7798 AKAP11 0 . GRCh38 13 42301278 42301278 + Silent SNP A A T novel C3L-01889_T C3L-01889_N A A c.2532A>T p.= p.P844P ENST00000025301 8/13 138 88 50 160 159 1 strelka-varscan-mutect AKAP11,synonymous_variant,p.=,ENST00000025301,NM_016248.3; T ENST00000025301 Transcript synonymous_variant 2707/9920 2532/5706 844/1901 P ccA/ccT 1 1 AKAP11 HGNC HGNC:369 protein_coding YES CCDS9383.1 ENSP00000025301 Q9UKA4 UPI0000125747 NM_016248.3 8/13 hmmpanther:PTHR10226:SF3,hmmpanther:PTHR10226 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 42301278 42301278 A T 1 0 0 0 0 0 0 0 1 530 175 7 4 4 AKAP11 13 42301278 Silent SNP A C3L-01889_T 17610886 42301278 72063050 120 7799 KLHL1 0 . GRCh38 13 69839103 69839103 + Silent SNP C C A novel C3L-01889_T C3L-01889_N C C c.1287G>T p.= p.L429L ENST00000377844 6/11 111 85 26 129 129 0 strelka-varscan-mutect KLHL1,synonymous_variant,p.=,ENST00000377844,NM_020866.2;KLHL1,synonymous_variant,p.=,ENST00000545028,NM_001286725.1; A ENST00000377844 Transcript synonymous_variant 2047/4115 1287/2247 429/748 L ctG/ctT 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 6/11 hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412 LOW 1 SNV 1 1 PASS rs1205461810 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 69839103 69839103 C A 1 0 0 0 0 0 0 0 1 8229 813 29 2 2 KLHL1 13 69839103 Silent SNP C C3L-01889_T 27537825 69839103 44525225 121 7800 UGGT2 0 . GRCh38 13 95854351 95854351 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.4133G>T p.Trp1378Leu p.W1378L ENST00000376747 35/39 113 83 30 125 125 0 strelka-varscan-mutect UGGT2,missense_variant,p.Trp1378Leu,ENST00000376747,NM_020121.3;UGGT2,3_prime_UTR_variant,,ENST00000621375,;UGGT2,downstream_gene_variant,,ENST00000462472,; A ENST00000376747 Transcript missense_variant 4204/4832 4133/4551 1378/1516 W/L tGg/tTg 1 -1 UGGT2 HGNC HGNC:15664 protein_coding YES CCDS9480.1 ENSP00000365938 Q9NYU1 UPI00001FC9AA NM_020121.3 deleterious(0) 35/39 Gene3D:3.90.550.10,Pfam_domain:PF01501,hmmpanther:PTHR11226,hmmpanther:PTHR11226:SF1,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 95854351 95854351 C A 1 0 0 0 0 1 0 0 0 17467 595 21 2 2 UGGT2 13 95854351 Missense_Mutation SNP C C3L-01889_T 26015248 95854351 18509977 122 7801 HS6ST3 0 . GRCh38 13 96091425 96091425 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.563G>T p.Arg188Leu p.R188L ENST00000376705 1/2 195 132 63 170 170 0 strelka-varscan-mutect HS6ST3,missense_variant,p.Arg188Leu,ENST00000376705,NM_153456.3; T ENST00000376705 Transcript missense_variant 587/7804 563/1416 188/471 R/L cGg/cTg 1 1 HS6ST3 HGNC HGNC:19134 protein_coding YES CCDS9481.1 ENSP00000365895 Q8IZP7 UPI00001AF933 NM_153456.3 deleterious(0.02) 1/2 hmmpanther:PTHR12812,hmmpanther:PTHR12812:SF3,Pfam_domain:PF03567,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 96091425 96091425 G T 1 0 0 0 0 1 0 0 0 7266 1116 39 1 1 HS6ST3 13 96091425 Missense_Mutation SNP G C3L-01889_T 237074 96091425 18272903 123 7802 OR4K5 0 . GRCh38 14 19921028 19921028 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.422G>T p.Cys141Phe p.C141F ENST00000315915 1/1 275 260 15 287 287 0 strelka-mutect OR4K5,missense_variant,p.Cys141Phe,ENST00000315915,NM_001005483.1; T ENST00000315915 Transcript missense_variant 447/1078 422/972 141/323 C/F tGc/tTc 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 19921028 19921028 G T 1 0 0 0 0 1 0 0 0 11150 1319 46 2 2 OR4K5 14 19921028 Missense_Mutation SNP G C3L-01889_T 19921028 87122690 124 7803 PPP2R3C 0 . GRCh38 14 35116631 35116631 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.165C>T p.= p.T55T ENST00000261475 2/13 113 87 26 99 99 0 strelka-varscan-mutect PPP2R3C,synonymous_variant,p.=,ENST00000261475,NM_017917.2;PPP2R3C,synonymous_variant,p.=,ENST00000555644,;PPP2R3C,synonymous_variant,p.=,ENST00000557278,;PPP2R3C,synonymous_variant,p.=,ENST00000554361,;PPP2R3C,synonymous_variant,p.=,ENST00000555630,;PPP2R3C,synonymous_variant,p.=,ENST00000554563,;PPP2R3C,3_prime_UTR_variant,,ENST00000553282,;PPP2R3C,non_coding_transcript_exon_variant,,ENST00000557773,;PPP2R3C,non_coding_transcript_exon_variant,,ENST00000556254,;PPP2R3C,intron_variant,,ENST00000557217,NM_001305155.1;PPP2R3C,intron_variant,,ENST00000554222,NM_001305156.1;PPP2R3C,intron_variant,,ENST00000553273,;PPP2R3C,intron_variant,,ENST00000554265,;PPP2R3C,intron_variant,,ENST00000554899,;PPP2R3C,intron_variant,,ENST00000554488,;PPP2R3C,intron_variant,,ENST00000555726,;PPP2R3C,intron_variant,,ENST00000557288,;FAM177A1,downstream_gene_variant,,ENST00000555260,; A ENST00000261475 Transcript synonymous_variant 519/1839 165/1362 55/453 T acC/acT 1 -1 PPP2R3C HGNC HGNC:17485 protein_coding YES CCDS9654.1 ENSP00000261475 Q969Q6 UPI000006E6EC NM_017917.2 2/13 hmmpanther:PTHR12085 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 28 35116631 35116631 G A 1 0 0 0 0 0 0 0 1 12513 1335 47 3 3 PPP2R3C 14 35116631 Silent SNP G C3L-01889_T 15195603 35116631 71927087 125 7804 GPR135 0 . GRCh38 14 59463842 59463842 + Missense_Mutation SNP C C G rs201849909 C3L-01889_T C3L-01889_N C C c.1385G>C p.Arg462Pro p.R462P ENST00000395116 1/1 159 123 36 153 153 0 strelka-varscan-mutect GPR135,missense_variant,p.Arg462Pro,ENST00000395116,NM_022571.5;L3HYPDH,intron_variant,,ENST00000466522,;GPR135,missense_variant,p.Arg462Pro,ENST00000481661,; G ENST00000395116 Transcript missense_variant 1501/4578 1385/1485 462/494 R/P cGc/cCc rs201849909,COSM311561 1 -1 GPR135 HGNC HGNC:19991 protein_coding YES CCDS9738.1 ENSP00000378548 Q8IZ08 UPI0000046D5B NM_022571.5 tolerated(0.25) 1/1 hmmpanther:PTHR22752,hmmpanther:PTHR22752:SF3 0,1 MODERATE 1 SNV 0,1 1 PASS rs201849909 . 0 201 0 7 2 0 0 0 -19.99986 0.9278972 1 1 1 0 G 3 3 28 59463842 59463842 C G 1 0 0 0 0 1 0 0 0 6530 768 27 4 4 GPR135 14 59463842 Missense_Mutation SNP C C3L-01889_T 24347211 59463842 47579876 126 7805 FUT8 0 . GRCh38 14 65733328 65733328 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1357G>T p.Asp453Tyr p.D453Y ENST00000360689 10/11 103 93 10 86 86 0 strelka-varscan-mutect FUT8,missense_variant,p.Asp453Tyr,ENST00000360689,NM_178155.2;FUT8,missense_variant,p.Asp453Tyr,ENST00000394586,NM_178156.2;FUT8,missense_variant,p.Asp324Tyr,ENST00000358307,;FUT8,missense_variant,p.Asp290Tyr,ENST00000557164,NM_004480.4;FUT8,3_prime_UTR_variant,,ENST00000342677,; T ENST00000360689 Transcript missense_variant 3084/5166 1357/1728 453/575 D/Y Gat/Tat 1 1 FUT8 HGNC HGNC:4019 protein_coding YES CCDS9775.1 ENSP00000353910 Q9BYC5 Q546E0 UPI000000DCC9 NM_178155.2 deleterious(0) 10/11 PROSITE_profiles:PS51659,hmmpanther:PTHR13132,hmmpanther:PTHR13132:SF29,PIRSF_domain:PIRSF000472 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -15.53558 0.9999998 1 1 1 0 T 3 4 28 65733328 65733328 G T 1 0 0 0 0 1 0 0 0 5982 1174 41 2 2 FUT8 14 65733328 Missense_Mutation SNP G C3L-01889_T 6269486 65733328 41310390 127 7806 ASB2 0 . GRCh38 14 93939423 93939423 + Silent SNP G G A C3L-01889_T C3L-01889_N G G c.1302C>T p.= p.G434G ENST00000555019 8/10 215 202 13 191 191 0 strelka-varscan-mutect ASB2,synonymous_variant,p.=,ENST00000555019,NM_001202429.1;ASB2,synonymous_variant,p.=,ENST00000315988,NM_016150.4;ASB2,synonymous_variant,p.=,ENST00000555507,;RP11-131H24.4,upstream_gene_variant,,ENST00000557646,;ASB2,non_coding_transcript_exon_variant,,ENST00000556337,;ASB2,non_coding_transcript_exon_variant,,ENST00000553883,; A ENST00000555019 Transcript synonymous_variant 1733/2842 1302/1908 434/635 G ggC/ggT COSM4933412 1 -1 ASB2 HGNC HGNC:16012 protein_coding YES CCDS55940.1 ENSP00000451575 Q96Q27 A0A024R6E7 UPI000013D23C NM_001202429.1 8/10 Gene3D:1.25.40.20,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF33,SMART_domains:SM00248,Superfamily_domains:SSF48403 1 LOW 1 SNV 1 1 1 PASS rs1185256349 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 93939423 93939423 G A 1 0 0 0 0 0 0 0 1 1165 1074 38 1 1 ASB2 14 93939423 Silent SNP G C3L-01889_T 28206095 93939423 13104295 128 7807 TNFAIP2 0 . GRCh38 14 103130362 103130362 + Frame_Shift_Del DEL G G - novel C3L-01889_T C3L-01889_N G G c.1148delG p.Gly383AlafsTer4 p.G383Afs*4 ENST00000560869 6/12 146 114 32 113 113 0 sindel-varindel TNFAIP2,frameshift_variant,p.Gly383AlafsTer4,ENST00000560869,;TNFAIP2,frameshift_variant,p.Gly383AlafsTer4,ENST00000333007,NM_006291.2;TNFAIP2,frameshift_variant,p.Gly76AlafsTer4,ENST00000560670,;TNFAIP2,upstream_gene_variant,,ENST00000559255,;TNFAIP2,downstream_gene_variant,,ENST00000558056,;TNFAIP2,downstream_gene_variant,,ENST00000559195,;TNFAIP2,3_prime_UTR_variant,,ENST00000559406,;TNFAIP2,3_prime_UTR_variant,,ENST00000560562,;TNFAIP2,non_coding_transcript_exon_variant,,ENST00000560428,;TNFAIP2,upstream_gene_variant,,ENST00000561156,; - ENST00000560869 Transcript frameshift_variant 1785/4683 1146/1965 382/654 L/X ttG/tt 1 1 TNFAIP2 HGNC HGNC:11895 protein_coding YES CCDS9979.1 ENSP00000452634 Q03169 UPI0000164A41 6/12 hmmpanther:PTHR21292:SF4,hmmpanther:PTHR21292,Pfam_domain:PF06046 HIGH 1 deletion 5 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 103130362 103130362 G - 1 0 1 0 1 0 0 0 0 16747 1339 47 0 0 TNFAIP2 14 103130362 Frame_Shift_Del DEL G C3L-01889_T 9190939 103130362 3913356 129 7808 KIF26A 0 . GRCh38 14 104173224 104173224 + Silent SNP C C A rs376308267 C3L-01889_T C3L-01889_N C C c.1668C>A p.= p.P556P ENST00000423312 8/15 79 57 22 71 71 0 strelka-varscan-mutect KIF26A,synonymous_variant,p.=,ENST00000315264,;KIF26A,synonymous_variant,p.=,ENST00000423312,NM_015656.1; A ENST00000423312 Transcript synonymous_variant 1668/5649 1668/5649 556/1882 P ccC/ccA rs376308267 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 8/15 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF407,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs376308267 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 104173224 104173224 C A 1 0 0 0 0 0 0 0 1 8159 639 23 1 1 KIF26A 14 104173224 Silent SNP C C3L-01889_T 1042862 104173224 2870494 130 7809 POTEB3 0 . GRCh38 15 21439880 21439880 + Silent SNP G G T novel C3L-01889_T C3L-01889_N G G c.132C>A p.= p.G44G ENST00000611217 1/11 466 408 58 430 430 0 varscan-mutect POTEB3,synonymous_variant,p.=,ENST00000611217,NM_207355.3;POTEB3,synonymous_variant,p.=,ENST00000624267,;POTEB3,synonymous_variant,p.=,ENST00000612601,; T ENST00000611217 Transcript synonymous_variant 180/1813 132/1746 44/581 G ggC/ggA 1 -1 POTEB3 HGNC HGNC:51240 protein_coding YES CCDS73690.1 ENSP00000483103 A0JP26,Q6S5H4 UPI0000197FCA NM_207355.3 1/11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 21439880 21439880 G T 1 0 0 0 0 0 0 0 1 12375 1306 46 2 2 POTEB3 15 21439880 Silent SNP G C3L-01889_T 21439880 80551309 131 7810 FAM189A1 0 . GRCh38 15 29123389 29123389 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.1570C>G p.Arg524Gly p.R524G ENST00000261275 11/11 64 46 18 73 73 0 strelka-varscan-mutect FAM189A1,missense_variant,p.Arg524Gly,ENST00000261275,NM_015307.1;FAM189A1,non_coding_transcript_exon_variant,,ENST00000560021,; C ENST00000261275 Transcript missense_variant 1570/4705 1570/1620 524/539 R/G Cgc/Ggc 1 -1 FAM189A1 HGNC HGNC:29075 protein_coding YES CCDS45198.1 ENSP00000261275 O60320 UPI0001641C10 NM_015307.1 tolerated(0.12) 11/11 hmmpanther:PTHR17615,hmmpanther:PTHR17615:SF6 MODERATE 1 SNV 5 1 PASS rs1314160163 . 0 200 9 0 0 0 0 0 -20 0.9999981 1 1 1 0 C 3 2 28 29123389 29123389 G C 1 0 0 0 0 1 0 0 0 5367 1087 38 4 4 FAM189A1 15 29123389 Missense_Mutation SNP G C3L-01889_T 7683509 29123389 72867800 132 7811 TRIP4 0 . GRCh38 15 64387877 64387877 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.14G>C p.Gly5Ala p.G5A ENST00000261884 1/13 77 59 18 64 64 0 strelka-varscan-mutect TRIP4,missense_variant,p.Gly5Ala,ENST00000261884,NM_016213.4;TRIP4,non_coding_transcript_exon_variant,,ENST00000557834,;TRIP4,non_coding_transcript_exon_variant,,ENST00000558442,;TRIP4,intron_variant,,ENST00000559565,;TRIP4,intron_variant,,ENST00000559833,;KIAA0101,upstream_gene_variant,,ENST00000558250,;KIAA0101,upstream_gene_variant,,ENST00000560234,;TRIP4,missense_variant,p.Gly5Ala,ENST00000560567,;TRIP4,missense_variant,p.Gly5Ala,ENST00000558820,;TRIP4,missense_variant,p.Gly5Ala,ENST00000560920,; C ENST00000261884 Transcript missense_variant 74/2045 14/1746 5/581 G/A gGg/gCg 1 1 TRIP4 HGNC HGNC:12310 protein_coding YES CCDS10194.1 ENSP00000261884 Q15650 UPI0000035D96 NM_016213.4 tolerated_low_confidence(0.07) 1/13 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 64387877 64387877 G C 1 0 0 0 0 1 0 0 0 17055 1232 43 4 4 TRIP4 15 64387877 Missense_Mutation SNP G C3L-01889_T 35264488 64387877 37603312 133 7812 IGDCC3 0 . GRCh38 15 65329840 65329840 + Missense_Mutation SNP C C A rs776056063 C3L-01889_T C3L-01889_N C C c.1883G>T p.Arg628Leu p.R628L ENST00000327987 12/14 201 136 65 192 192 0 strelka-varscan-mutect IGDCC3,missense_variant,p.Arg628Leu,ENST00000327987,NM_004884.3;IGDCC3,missense_variant,p.Arg491Leu,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559058,;IGDCC3,downstream_gene_variant,,ENST00000559231,; A ENST00000327987 Transcript missense_variant 2135/4479 1883/2445 628/814 R/L cGg/cTg rs776056063,COSM1749270 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 tolerated(0.25) 12/14 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776056063 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 65329840 65329840 C A 1 0 0 0 0 1 0 0 0 7474 652 23 1 1 IGDCC3 15 65329840 Missense_Mutation SNP C C3L-01889_T 941963 65329840 36661349 134 7813 STRA6 0 . GRCh38 15 74181334 74181334 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.1762C>A p.Leu588Ile p.L588I ENST00000563965 17/19 181 145 36 191 191 0 strelka-varscan-mutect STRA6,missense_variant,p.Leu549Ile,ENST00000323940,NM_001142617.1;STRA6,missense_variant,p.Leu549Ile,ENST00000616000,NM_001142618.1;STRA6,missense_variant,p.Leu549Ile,ENST00000395105,NM_022369.3;STRA6,missense_variant,p.Leu540Ile,ENST00000423167,NM_001142619.1;STRA6,missense_variant,p.Leu541Ile,ENST00000416286,;STRA6,missense_variant,p.Leu549Ile,ENST00000449139,;STRA6,missense_variant,p.Leu586Ile,ENST00000535552,NM_001199040.1;STRA6,missense_variant,p.Leu588Ile,ENST00000563965,NM_001199042.1;STRA6,missense_variant,p.Leu564Ile,ENST00000574278,NM_001199041.1;STRA6,missense_variant,p.Leu168Ile,ENST00000572785,;ISLR,downstream_gene_variant,,ENST00000249842,NM_005545.3;ISLR,downstream_gene_variant,,ENST00000395118,NM_201526.1;RP11-665J16.1,upstream_gene_variant,,ENST00000561647,;STRA6,non_coding_transcript_exon_variant,,ENST00000574439,;STRA6,non_coding_transcript_exon_variant,,ENST00000545137,;STRA6,downstream_gene_variant,,ENST00000569936,;STRA6,downstream_gene_variant,,ENST00000575272,; T ENST00000563965 Transcript missense_variant 2101/2565 1762/2121 588/706 L/I Ctc/Atc 1 -1 STRA6 HGNC HGNC:30650 protein_coding YES CCDS55973.1 ENSP00000456609 Q9BX79 UPI00015F460B NM_001199042.1 tolerated(0.85) 17/19 hmmpanther:PTHR21444:SF16,hmmpanther:PTHR21444,Pfam_domain:PF14752 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 74181334 74181334 G T 1 0 0 0 0 1 0 0 0 15703 1000 35 2 2 STRA6 15 74181334 Missense_Mutation SNP G C3L-01889_T 8851494 74181334 27809855 135 7814 COG7 0 . GRCh38 16 23418755 23418755 + Missense_Mutation SNP T T C novel C3L-01889_T C3L-01889_N T T c.1082A>G p.Lys361Arg p.K361R ENST00000307149 8/17 395 289 106 370 370 0 strelka-varscan-mutect COG7,missense_variant,p.Lys361Arg,ENST00000307149,NM_153603.3;RN7SKP23,downstream_gene_variant,,ENST00000625159,;COG7,upstream_gene_variant,,ENST00000567821,; C ENST00000307149 Transcript missense_variant 1268/2926 1082/2313 361/770 K/R aAg/aGg 1 -1 COG7 HGNC HGNC:18622 protein_coding YES CCDS10610.1 ENSP00000305442 P83436 A0A0S2Z652 UPI0000127E42 NM_153603.3 tolerated(0.36) 8/17 hmmpanther:PTHR21443,Pfam_domain:PF10191 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 23418755 23418755 T C 1 0 0 0 0 1 0 0 0 3451 1609 56 5 5 COG7 16 23418755 Missense_Mutation SNP T C3L-01889_T 23418755 66919590 136 7815 NIP7 0 . GRCh38 16 69341197 69341197 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.300G>A p.= p.K100K ENST00000254940 4/5 132 90 42 139 139 0 strelka-varscan-mutect NIP7,synonymous_variant,p.=,ENST00000254940,NM_016101.4;NIP7,synonymous_variant,p.=,ENST00000562523,;NIP7,synonymous_variant,p.=,ENST00000567202,;NIP7,intron_variant,,ENST00000254941,NM_001199434.1;RP11-343C2.9,intron_variant,,ENST00000563634,;COG8,upstream_gene_variant,,ENST00000306875,NM_032382.4;COG8,upstream_gene_variant,,ENST00000562595,;COG8,upstream_gene_variant,,ENST00000562081,;NIP7,downstream_gene_variant,,ENST00000569637,;TMED6,downstream_gene_variant,,ENST00000288025,NM_144676.3;COG8,upstream_gene_variant,,ENST00000567493,;COG8,upstream_gene_variant,,ENST00000615447,;NIP7,non_coding_transcript_exon_variant,,ENST00000565034,;NIP7,non_coding_transcript_exon_variant,,ENST00000563364,;RP11-343C2.7,intron_variant,,ENST00000564737,;RP11-343C2.7,intron_variant,,ENST00000570293,;TMED6,downstream_gene_variant,,ENST00000568748,;NIP7,downstream_gene_variant,,ENST00000562131,; A ENST00000254940 Transcript synonymous_variant 700/2402 300/543 100/180 K aaG/aaA 1 1 NIP7 HGNC HGNC:24328 protein_coding YES CCDS10877.1 ENSP00000254940 Q9Y221 UPI000006FFF0 NM_016101.4 4/5 PROSITE_profiles:PS50890,hmmpanther:PTHR23415,hmmpanther:PTHR23415:SF4,Pfam_domain:PF03657,Gene3D:2.30.130.10,PIRSF_domain:PIRSF017190,SMART_domains:SM00359,Superfamily_domains:SSF88697 LOW 1 SNV 1 1 PASS rs914626529 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 69341197 69341197 G A 1 0 0 0 0 0 0 0 1 10456 962 34 3 3 NIP7 16 69341197 Silent SNP G C3L-01889_T 45922442 69341197 20997148 137 7816 CNTNAP4 0 . GRCh38 16 76553310 76553310 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.3470C>A p.Ala1157Glu p.A1157E ENST00000611870 22/24 87 58 29 104 104 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Ala1157Glu,ENST00000307431,;CNTNAP4,missense_variant,p.Ala1157Glu,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Ala1109Glu,ENST00000377504,;CNTNAP4,missense_variant,p.Ala1160Glu,ENST00000476707,;CNTNAP4,missense_variant,p.Ala1109Glu,ENST00000622250,;CNTNAP4,missense_variant,p.Ala1084Glu,ENST00000478060,NM_138994.3;CNTNAP4,upstream_gene_variant,,ENST00000619533,;RP11-58C22.1,upstream_gene_variant,,ENST00000563764,; A ENST00000611870 Transcript missense_variant 3855/4867 3470/3927 1157/1308 A/E gCa/gAa 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 tolerated(0.23) 22/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 76553310 76553310 C A 1 0 0 0 0 1 0 0 0 3431 710 25 2 2 CNTNAP4 16 76553310 Missense_Mutation SNP C C3L-01889_T 7212113 76553310 13785035 138 7817 30 2 CNTNAP4 0 . GRCh38 16 76553312 76553312 + Missense_Mutation SNP C C A rs368462428 C3L-01889_T C3L-01889_N C C c.3472C>A p.Leu1158Met p.L1158M ENST00000611870 22/24 88 61 27 110 110 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Leu1158Met,ENST00000307431,;CNTNAP4,missense_variant,p.Leu1158Met,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Leu1110Met,ENST00000377504,;CNTNAP4,missense_variant,p.Leu1161Met,ENST00000476707,;CNTNAP4,missense_variant,p.Leu1110Met,ENST00000622250,;CNTNAP4,missense_variant,p.Leu1085Met,ENST00000478060,NM_138994.3;CNTNAP4,upstream_gene_variant,,ENST00000619533,;RP11-58C22.1,upstream_gene_variant,,ENST00000563764,; A ENST00000611870 Transcript missense_variant 3857/4867 3472/3927 1158/1308 L/M Ctg/Atg rs368462428 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0.04) 22/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs368462428 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 76553312 76553312 C A 1 0 0 0 0 1 0 0 0 3431 564 20 2 2 CNTNAP4 16 76553312 Missense_Mutation SNP C C3L-01889_T 2 76553312 13785033 139 7818 30 2 TRPV1 0 . GRCh38 17 3573863 3573891 + Frame_Shift_Del DEL CGGGGGGCCTGCAGGCAGGCCCCCGCCAC CGGGGGGCCTGCAGGCAGGCCCCCGCCAC - novel C3L-01889_T C3L-01889_N CGGGGGGCCTGCAGGCAGGCCCCCGCCAC CGGGGGGCCTGCAGGCAGGCCCCCGCCAC c.1845_1873delGTGGCGGGGGCCTGCCTGCAGGCCCCCCG p.Trp616Ter p.W616* ENST00000572705 14/17 267 204 63 296 296 0 sindel-pindel TRPV1,frameshift_variant,p.Trp616Ter,ENST00000572705,NM_080704.3;TRPV1,frameshift_variant,p.Trp616Ter,ENST00000571088,NM_018727.5;TRPV1,frameshift_variant,p.Trp616Ter,ENST00000399759,NM_080705.3;TRPV1,frameshift_variant,p.Trp616Ter,ENST00000399756,NM_080706.3;TRPV1,frameshift_variant,p.Trp627Ter,ENST00000425167,;TRPV1,frameshift_variant,p.Trp606Ter,ENST00000576351,;TRPV1,frameshift_variant,p.Trp556Ter,ENST00000310522,;RP11-235E17.3,downstream_gene_variant,,ENST00000573568,;TRPV1,non_coding_transcript_exon_variant,,ENST00000574085,;TRPV1,non_coding_transcript_exon_variant,,ENST00000570742,; - ENST00000572705 Transcript frameshift_variant 2120-2148/4166 1845-1873/2520 615-625/839 RWRGPACRPPD/RX agGTGGCGGGGGCCTGCCTGCAGGCCCCCCGat/agat 1 -1 TRPV1 HGNC HGNC:12716 protein_coding YES CCDS45576.1 ENSP00000459962 Q8NER1 UPI00005B2E0C NM_080704.3 14/17 Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 3573863 3573863 CGGGGGGCCTGCAGGCAGGCCCCCGCCAC - 1 0 1 0 1 0 0 0 0 17101 884 31 0 0 TRPV1 17 3573863 Frame_Shift_Del DEL CGGGGGGCCTGCAGGCAGGCCCCCGCCAC C3L-01889_T 3573863 79683578 140 7819 DNAH9 0 . GRCh38 17 11807731 11807731 + Splice_Site SNP G G T rs760328778 C3L-01889_T C3L-01889_N G G c.8421-1G>T p.X2807_splice ENST00000262442 47 29 18 47 47 0 strelka-varscan-mutect DNAH9,splice_acceptor_variant,,ENST00000262442,NM_001372.3;DNAH9,splice_acceptor_variant,,ENST00000454412,; T ENST00000262442 Transcript splice_acceptor_variant -/13750 8421/13461 2807/4486 rs760328778 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 43/68 HIGH 1 SNV 1 1 PASS rs760328778 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 28 11807731 11807731 G T 1 0 0 0 0 0 0 1 0 4423 985 34 2 2 DNAH9 17 11807731 Splice_Site SNP G C3L-01889_T 8233868 11807731 71449710 141 7820 CWC25 0 . GRCh38 17 38821008 38821008 + Missense_Mutation SNP C C A rs754703083 C3L-01889_T C3L-01889_N C C c.84G>T p.Gln28His p.Q28H ENST00000614790 2/10 107 67 40 158 158 0 strelka-varscan-mutect CWC25,missense_variant,p.Gln28His,ENST00000614790,NM_017748.4;MIR4727,upstream_gene_variant,,ENST00000622232,;CWC25,non_coding_transcript_exon_variant,,ENST00000619818,;CWC25,missense_variant,p.Gln28His,ENST00000619299,;CWC25,missense_variant,p.Gln28His,ENST00000622665,; A ENST00000614790 Transcript missense_variant 382/3234 84/1278 28/425 Q/H caG/caT rs754703083 1 -1 CWC25 HGNC HGNC:25989 protein_coding YES CCDS45663.1 ENSP00000478070 Q9NXE8 UPI000007081D NM_017748.4 deleterious(0) 2/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16196,Pfam_domain:PF10197,SMART_domains:SM01083 MODERATE 1 SNV 1 1 PASS rs754703083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 38821008 38821008 C A 1 0 0 0 0 1 0 0 0 3879 912 32 2 2 CWC25 17 38821008 Missense_Mutation SNP C C3L-01889_T 27013277 38821008 44436433 142 7821 SLC4A1 0 . GRCh38 17 44258412 44258412 + Splice_Site SNP C C T novel C3L-01889_T C3L-01889_N C C c.1087+1G>A p.X363_splice ENST00000262418 117 72 45 130 130 0 strelka-varscan-mutect SLC4A1,splice_donor_variant,,ENST00000262418,NM_000342.3;SLC4A1,intron_variant,,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,splice_donor_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; T ENST00000262418 Transcript splice_donor_variant -/4965 1087/2736 363/911 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 10/19 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 28 44258412 44258412 C T 1 0 0 0 0 0 0 1 0 14927 521 18 3 3 SLC4A1 17 44258412 Splice_Site SNP C C3L-01889_T 5437404 44258412 38999029 143 7822 KIF18B 0 . GRCh38 17 44935283 44935283 + Missense_Mutation SNP G G T rs200332226 C3L-01889_T C3L-01889_N G G c.447C>A p.Phe149Leu p.F149L ENST00000593135 3/16 63 59 4 62 62 0 strelka-mutect KIF18B,missense_variant,p.Phe149Leu,ENST00000587309,NM_001264573.1;KIF18B,missense_variant,p.Phe149Leu,ENST00000593135,NM_001265577.1;KIF18B,missense_variant,p.Phe158Leu,ENST00000590129,;MIR6783,upstream_gene_variant,,ENST00000619908,;KIF18B,upstream_gene_variant,,ENST00000585687,; T ENST00000593135 Transcript missense_variant 545/2745 447/2559 149/852 F/L ttC/ttA rs200332226,COSM4267808,COSM980079 1 -1 KIF18B HGNC HGNC:27102 protein_coding YES CCDS45709.2 ENSP00000465992 A0A0C4DGP5 UPI000192C418 NM_001265577.1 tolerated(0.1) 3/16 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF414,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs200332226 . 0 207 2 0 0 0 0 0 -10.16032 1 1 1 1 0 T 3 4 28 44935283 44935283 G T 1 0 0 0 0 1 0 0 0 8145 1049 37 1 1 KIF18B 17 44935283 Missense_Mutation SNP G C3L-01889_T 676871 44935283 38322158 144 7823 MRPL27 0 . GRCh38 17 50373135 50373135 + Silent SNP T T A novel C3L-01889_T C3L-01889_N T T c.36A>T p.= p.T12T ENST00000225969 1/4 534 472 62 220 220 0 strelka-varscan-mutect MRPL27,synonymous_variant,p.=,ENST00000442592,;MRPL27,synonymous_variant,p.=,ENST00000503633,;MRPL27,synonymous_variant,p.=,ENST00000225969,NM_016504.2;EME1,upstream_gene_variant,,ENST00000393271,NM_001166131.1;EME1,upstream_gene_variant,,ENST00000338165,NM_152463.2;EME1,upstream_gene_variant,,ENST00000511648,;EME1,upstream_gene_variant,,ENST00000510246,;MRPL27,upstream_gene_variant,,ENST00000511860,;MRPL27,upstream_gene_variant,,ENST00000507088,;MRPL27,upstream_gene_variant,,ENST00000508200,;EME1,upstream_gene_variant,,ENST00000511519,;LRRC59,downstream_gene_variant,,ENST00000503118,;MRPL27,non_coding_transcript_exon_variant,,ENST00000514928,;EME1,upstream_gene_variant,,ENST00000510007,;EME1,upstream_gene_variant,,ENST00000511711,;EME1,upstream_gene_variant,,ENST00000513077,; A ENST00000225969 Transcript synonymous_variant 80/716 36/447 12/148 T acA/acT 1 -1 MRPL27 HGNC HGNC:14483 protein_coding YES CCDS11564.1 ENSP00000225969 Q9P0M9 UPI00001342E1 NM_016504.2 1/4 hmmpanther:PTHR15893 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 50373135 50373135 T A 1 0 0 0 0 0 0 0 1 9766 1594 55 4 4 MRPL27 17 50373135 Silent SNP T C3L-01889_T 5437852 50373135 32884306 145 7824 WFIKKN2 0 . GRCh38 17 50840165 50840165 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.877G>T p.Ala293Ser p.A293S ENST00000311378 2/2 415 389 26 244 243 1 strelka-varscan-mutect WFIKKN2,missense_variant,p.Ala293Ser,ENST00000311378,NM_175575.5;WFIKKN2,missense_variant,p.Ala200Ser,ENST00000426127,;RP11-506D12.5,non_coding_transcript_exon_variant,,ENST00000572491,; T ENST00000311378 Transcript missense_variant 1405/3588 877/1731 293/576 A/S Gct/Tct 1 1 WFIKKN2 HGNC HGNC:30916 protein_coding YES CCDS11575.1 ENSP00000311184 Q8TEU8 UPI000004139B NM_175575.5 tolerated(0.17) 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR10083:SF87,hmmpanther:PTHR10083,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 50840165 50840165 G T 1 0 0 0 0 1 0 0 0 17916 1203 42 2 2 WFIKKN2 17 50840165 Missense_Mutation SNP G C3L-01889_T 467030 50840165 32417276 146 7825 HELZ 0 . GRCh38 17 67194004 67194004 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.520G>A p.Gly174Arg p.G174R ENST00000358691 9/33 397 164 233 214 213 1 strelka-varscan-mutect HELZ,missense_variant,p.Gly174Arg,ENST00000358691,NM_014877.3;HELZ,missense_variant,p.Gly174Arg,ENST00000580168,;HELZ,intron_variant,,ENST00000580662,;HELZ,missense_variant,p.Gly174Arg,ENST00000579953,;HELZ,missense_variant,p.Gly174Arg,ENST00000417253,;HELZ,upstream_gene_variant,,ENST00000582864,; T ENST00000358691 Transcript missense_variant 687/13810 520/5829 174/1942 G/R Gga/Aga 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 deleterious(0) 9/33 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 67194004 67194004 C T 1 0 0 0 0 1 0 0 0 6931 632 22 3 3 HELZ 17 67194004 Missense_Mutation SNP C C3L-01889_T 16353839 67194004 16063437 147 7826 TMEM94 0 . GRCh38 17 75498967 75498967 + Missense_Mutation SNP G G A novel C3L-01889_T C3L-01889_N G G c.3883G>A p.Asp1295Asn p.D1295N ENST00000314256 31/32 76 36 40 40 40 0 strelka-varscan-mutect TMEM94,missense_variant,p.Asp1295Asn,ENST00000314256,NM_001321149.1,NM_014738.4;TMEM94,missense_variant,p.Asp1305Asn,ENST00000375248,;TMEM94,missense_variant,p.Asp946Asn,ENST00000579208,;TMEM94,missense_variant,p.Asp234Asn,ENST00000577247,;TMEM94,missense_variant,p.Asp142Asn,ENST00000584694,;CASKIN2,downstream_gene_variant,,ENST00000321617,NM_020753.4;CASKIN2,downstream_gene_variant,,ENST00000433559,NM_001142643.2;TMEM94,downstream_gene_variant,,ENST00000577245,;TMEM94,downstream_gene_variant,,ENST00000618984,;TMEM94,non_coding_transcript_exon_variant,,ENST00000585105,;TMEM94,non_coding_transcript_exon_variant,,ENST00000581085,;TMEM94,non_coding_transcript_exon_variant,,ENST00000579898,;TMEM94,downstream_gene_variant,,ENST00000581453,;TMEM94,downstream_gene_variant,,ENST00000581867,;CASKIN2,downstream_gene_variant,,ENST00000580021,;TMEM94,downstream_gene_variant,,ENST00000581723,;TMEM94,downstream_gene_variant,,ENST00000577194,; A ENST00000314256 Transcript missense_variant 4277/5213 3883/4071 1295/1356 D/N Gac/Aac 1 1 TMEM94 HGNC HGNC:28983 protein_coding YES CCDS32732.1 ENSP00000313885 Q12767 A0A024R8S6 UPI0000139439 NM_001321149.1,NM_014738.4 tolerated(0.42) 31/32 hmmpanther:PTHR13219,hmmpanther:PTHR13219:SF6,Pfam_domain:PF00689,Gene3D:1.20.1110.10,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 75498967 75498967 G A 1 0 0 0 0 1 0 0 0 16697 1174 41 3 3 TMEM94 17 75498967 Missense_Mutation SNP G C3L-01889_T 8304963 75498967 7758474 148 7827 TRIM47 0 . GRCh38 17 75876344 75876344 + Missense_Mutation SNP T T A novel C3L-01889_T C3L-01889_N T T c.920A>T p.Gln307Leu p.Q307L ENST00000254816 3/6 246 102 144 127 127 0 strelka-varscan-mutect TRIM47,missense_variant,p.Gln307Leu,ENST00000254816,NM_033452.2;TRIM65,downstream_gene_variant,,ENST00000591668,;TRIM47,downstream_gene_variant,,ENST00000586495,;TRIM47,upstream_gene_variant,,ENST00000585333,;TRIM65,downstream_gene_variant,,ENST00000592642,;RP11-552F3.9,upstream_gene_variant,,ENST00000586076,;TRIM47,3_prime_UTR_variant,,ENST00000587339,;TRIM47,non_coding_transcript_exon_variant,,ENST00000593089,;TRIM47,upstream_gene_variant,,ENST00000592942,;TRIM47,downstream_gene_variant,,ENST00000587774,; A ENST00000254816 Transcript missense_variant 947/2266 920/1917 307/638 Q/L cAg/cTg 1 -1 TRIM47 HGNC HGNC:19020 protein_coding YES CCDS32737.1 ENSP00000254816 Q96LD4 UPI000013CE62 NM_033452.2 tolerated(0.31) 3/6 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103:SF328,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 75876344 75876344 T A 1 0 0 0 0 1 0 0 0 17012 1580 55 4 4 TRIM47 17 75876344 Missense_Mutation SNP T C3L-01889_T 377377 75876344 7381097 149 7828 WDR45B 0 . GRCh38 17 82627257 82627257 + Silent SNP A A C novel C3L-01889_T C3L-01889_N A A c.279T>G p.= p.V93V ENST00000392325 4/10 311 204 107 349 348 1 strelka-varscan-mutect WDR45B,synonymous_variant,p.=,ENST00000392325,NM_019613.3;WDR45B,non_coding_transcript_exon_variant,,ENST00000571835,;WDR45B,non_coding_transcript_exon_variant,,ENST00000574828,;FOXK2,intron_variant,,ENST00000574694,;WDR45B,upstream_gene_variant,,ENST00000571767,;WDR45B,synonymous_variant,p.=,ENST00000572583,;WDR45B,synonymous_variant,p.=,ENST00000573616,;WDR45B,3_prime_UTR_variant,,ENST00000571817,;WDR45B,upstream_gene_variant,,ENST00000573656,; C ENST00000392325 Transcript synonymous_variant 474/2587 279/1035 93/344 V gtT/gtG 1 -1 WDR45B HGNC HGNC:25072 protein_coding YES CCDS11815.2 ENSP00000376139 Q5MNZ6 A0A024R8U4 UPI000020051D NM_019613.3 4/10 hmmpanther:PTHR11227,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs1476732300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 28 82627257 82627257 A C 1 0 0 0 0 0 0 0 1 17858 349 13 5 5 WDR45B 17 82627257 Silent SNP A C3L-01889_T 6750913 82627257 630184 150 7829 ANKRD30B 0 . GRCh38 18 14840632 14840632 + Frame_Shift_Del DEL G G - novel C3L-01889_T C3L-01889_N G G c.2677delG p.Ala893LeufsTer7 p.A893Lfs*7 ENST00000358984 31/36 148 113 35 150 150 0 sindel-varindel-pindel ANKRD30B,frameshift_variant,p.Ala893LeufsTer7,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; - ENST00000358984 Transcript frameshift_variant 2856/4359 2676/4179 892/1392 E/X gaG/ga 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 31/36 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 HIGH 1 deletion 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 28 14840632 14840632 G - 1 0 1 0 1 0 0 0 0 762 991 35 0 0 ANKRD30B 18 14840632 Frame_Shift_Del DEL G C3L-01889_T 14840632 65532653 151 7830 BOD1L2 0 . GRCh38 18 57147383 57147383 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.71G>T p.Gly24Val p.G24V ENST00000585477 1/1 59 34 25 74 74 0 strelka-varscan-mutect BOD1L2,missense_variant,p.Gly24Val,ENST00000585477,NM_001257964.1;CTD-2526M8.3,upstream_gene_variant,,ENST00000590942,; T ENST00000585477 Transcript missense_variant 322/3239 71/519 24/172 G/V gGc/gTc 1 1 BOD1L2 HGNC HGNC:28505 protein_coding YES CCDS59322.1 ENSP00000467843 Q8IYS8 UPI000006F702 NM_001257964.1 tolerated_low_confidence(0.07) 1/1 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF5,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs1291210995 . 0 201 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 28 57147383 57147383 G T 1 0 0 0 0 1 0 0 0 1640 1203 42 2 2 BOD1L2 18 57147383 Missense_Mutation SNP G C3L-01889_T 42306751 57147383 23225902 152 7831 CD226 0 . GRCh38 18 69873203 69873203 + Silent SNP T T A novel C3L-01889_T C3L-01889_N T T c.771A>T p.= p.T257T ENST00000280200 5/7 276 206 70 283 283 0 strelka-varscan-mutect CD226,synonymous_variant,p.=,ENST00000280200,NM_006566.3;CD226,synonymous_variant,p.=,ENST00000581982,NM_001303619.1;CD226,synonymous_variant,p.=,ENST00000582621,NM_001303618.1;CD226,synonymous_variant,p.=,ENST00000579496,;CD226,synonymous_variant,p.=,ENST00000577287,;CD226,intron_variant,,ENST00000578928,; A ENST00000280200 Transcript synonymous_variant 1040/12319 771/1011 257/336 T acA/acT 1 -1 CD226 HGNC HGNC:16961 protein_coding YES CCDS11997.1 ENSP00000280200 Q15762 UPI000013DC05 NM_006566.3 5/7 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF58 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 69873203 69873203 T A 1 0 0 0 0 0 0 0 1 2689 1567 55 4 4 CD226 18 69873203 Silent SNP T C3L-01889_T 12725820 69873203 10500082 153 7832 NETO1 0 . GRCh38 18 72794195 72794195 + Silent SNP T T C novel C3L-01889_T C3L-01889_N T T c.561A>G p.= p.Q187Q ENST00000327305 6/11 305 226 79 315 315 0 strelka-varscan-mutect NETO1,synonymous_variant,p.=,ENST00000327305,NM_138966.3;NETO1,synonymous_variant,p.=,ENST00000583169,NM_001201465.1;NETO1,intron_variant,,ENST00000579730,; C ENST00000327305 Transcript synonymous_variant 1219/3058 561/1602 187/533 Q caA/caG 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 6/11 Gene3D:2.60.120.290,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 28 72794195 72794195 T C 1 0 0 0 0 0 0 0 1 10374 1838 64 5 5 NETO1 18 72794195 Silent SNP T C3L-01889_T 2920992 72794195 7579090 154 7833 STK11 0 . GRCh38 19 1218493 1218493 + Nonsense_Mutation SNP C C T C3L-01889_T C3L-01889_N C C c.367C>T p.Gln123Ter p.Q123* ENST00000326873 2/10 124 98 26 199 199 0 strelka-varscan-mutect STK11,stop_gained,p.Gln123Ter,ENST00000586243,;STK11,stop_gained,p.Gln123Ter,ENST00000326873,NM_000455.4;STK11,5_prime_UTR_variant,,ENST00000585748,;STK11,intron_variant,,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,3_prime_UTR_variant,,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,upstream_gene_variant,,ENST00000591133,; T ENST00000326873 Transcript stop_gained 817/2611 367/1302 123/433 Q/* Cag/Tag CM041078,COSM380443,COSM5224269 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 2/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 HIGH 1 SNV 1 1,1,1 1 PASS rs1131690925 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 28 1218493 1218493 C T 1 0 0 0 0 0 1 0 0 15664 711 25 3 3 STK11 19 1218493 Nonsense_Mutation SNP C C3L-01889_T 1218493 57399123 155 7834 ATCAY 0 . GRCh38 19 3913813 3913813 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.922C>T p.Leu308Phe p.L308F ENST00000450849 9/13 178 125 53 210 208 2 strelka-varscan-mutect ATCAY,missense_variant,p.Leu308Phe,ENST00000450849,NM_033064.4;ATCAY,missense_variant,p.Leu308Phe,ENST00000600960,;ATCAY,3_prime_UTR_variant,,ENST00000597739,; T ENST00000450849 Transcript missense_variant 1389/5070 922/1116 308/371 L/F Ctc/Ttc 1 1 ATCAY HGNC HGNC:779 protein_coding YES CCDS45923.1 ENSP00000390941 Q86WG3 A0A0S2Z5T8 UPI000006DE3B NM_033064.4 tolerated(0.14) 9/13 Gene3D:3.40.525.10,Pfam_domain:PF13716,PROSITE_profiles:PS50191,hmmpanther:PTHR12112,hmmpanther:PTHR12112:SF9,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 3913813 3913813 C T 1 0 0 0 0 1 0 0 0 1226 565 20 3 3 ATCAY 19 3913813 Missense_Mutation SNP C C3L-01889_T 2695320 3913813 54703803 156 7835 C19orf45 0 . GRCh38 19 7506152 7506152 + Silent SNP G G A rs776584000 C3L-01889_T C3L-01889_N G G c.1194G>A p.= p.P398P ENST00000361664 7/9 61 40 21 85 85 0 strelka-varscan-mutect C19orf45,synonymous_variant,p.=,ENST00000361664,NM_198534.2;C19orf45,downstream_gene_variant,,ENST00000601176,;C19orf45,downstream_gene_variant,,ENST00000596132,;C19orf45,downstream_gene_variant,,ENST00000597207,;CTD-2207O23.12,upstream_gene_variant,,ENST00000599312,;C19orf45,non_coding_transcript_exon_variant,,ENST00000600112,;CTD-2207O23.12,upstream_gene_variant,,ENST00000597384,;C19orf45,upstream_gene_variant,,ENST00000601292,;C19orf45,downstream_gene_variant,,ENST00000596524,; A ENST00000361664 Transcript synonymous_variant 1335/1679 1194/1518 398/505 P ccG/ccA rs776584000,COSM4581575,COSM4881822 1 1 C19orf45 HGNC HGNC:24745 protein_coding YES CCDS12179.2 ENSP00000355241 Q8NA69 UPI00001D83AB NM_198534.2 7/9 Pfam_domain:PF15373,hmmpanther:PTHR34828 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs776584000 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 7506152 7506152 G A 1 0 0 0 0 0 0 0 1 1912 1074 38 1 1 C19orf45 19 7506152 Silent SNP G C3L-01889_T 3592339 7506152 51111464 157 7836 KEAP1 0 . GRCh38 19 10492130 10492130 + Nonsense_Mutation SNP C C A rs374324474 C3L-01889_T C3L-01889_N C C c.772G>T p.Glu258Ter p.E258* ENST00000171111 3/6 225 138 87 268 268 0 strelka-varscan-mutect KEAP1,stop_gained,p.Glu258Ter,ENST00000171111,NM_203500.1;KEAP1,stop_gained,p.Glu258Ter,ENST00000393623,NM_012289.3;KEAP1,stop_gained,p.Glu258Ter,ENST00000592055,;KEAP1,upstream_gene_variant,,ENST00000592478,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590593,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENST00000171111 Transcript stop_gained 1320/2955 772/1875 258/624 E/* Gaa/Taa rs374324474 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,SMART_domains:SM00875 HIGH 1 SNV 1 1 PASS rs374324474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 28 10492130 10492130 C A 1 0 0 0 0 0 1 0 0 8061 893 31 1 1 KEAP1 19 10492130 Nonsense_Mutation SNP C C3L-01889_T 2985978 10492130 48125486 158 7837 PLVAP 0 . GRCh38 19 17365507 17365507 + Nonsense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.958G>T p.Glu320Ter p.E320* ENST00000252590 3/6 117 80 37 154 154 0 strelka-varscan-mutect PLVAP,stop_gained,p.Glu320Ter,ENST00000252590,NM_031310.2;PLVAP,intron_variant,,ENST00000599426,;PLVAP,intron_variant,,ENST00000595816,;CTD-2278I10.1,downstream_gene_variant,,ENST00000597592,; A ENST00000252590 Transcript stop_gained 1020/2305 958/1329 320/442 E/* Gag/Tag 1 -1 PLVAP HGNC HGNC:13635 protein_coding YES CCDS32952.1 ENSP00000252590 Q9BX97 UPI000003ED36 NM_031310.2 3/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21687:SF5,hmmpanther:PTHR21687,Pfam_domain:PF06637 HIGH 1 SNV 1 1 PASS rs1228702428 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 28 17365507 17365507 C A 1 0 0 0 0 0 1 0 0 12222 864 30 2 2 PLVAP 19 17365507 Nonsense_Mutation SNP C C3L-01889_T 6873377 17365507 41252109 159 7838 ZNF615 0 . GRCh38 19 51993975 51993975 + Silent SNP A A T novel C3L-01889_T C3L-01889_N A A c.1134T>A p.= p.T378T ENST00000594083 6/6 116 82 34 203 203 0 strelka-varscan-mutect ZNF615,synonymous_variant,p.=,ENST00000602063,NM_001321320.1,NM_001321317.1;ZNF615,synonymous_variant,p.=,ENST00000376716,NM_198480.3;ZNF615,synonymous_variant,p.=,ENST00000594083,NM_001321322.1,NM_001321321.1,NM_001321323.1,NM_001321319.1,NM_001321318.1;ZNF615,synonymous_variant,p.=,ENST00000391795,;ZNF615,synonymous_variant,p.=,ENST00000598071,NM_001199324.1;ZNF615,synonymous_variant,p.=,ENST00000618049,;ZNF615,synonymous_variant,p.=,ENST00000618487,;ZNF615,downstream_gene_variant,,ENST00000593650,;ZNF615,downstream_gene_variant,,ENST00000601178,;ZNF615,3_prime_UTR_variant,,ENST00000599177,;ZNF615,downstream_gene_variant,,ENST00000599115,; T ENST00000594083 Transcript synonymous_variant 1379/4020 1134/2229 378/742 T acT/acA 1 -1 ZNF615 HGNC HGNC:24740 protein_coding YES CCDS59418.1 ENSP00000471549 Q8N8J6 UPI000022A99B NM_001321322.1,NM_001321321.1,NM_001321323.1,NM_001321319.1,NM_001321318.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF167,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 51993975 51993975 A T 1 0 0 0 0 0 0 0 1 18615 175 7 4 4 ZNF615 19 51993975 Silent SNP A C3L-01889_T 34628468 51993975 6623641 160 7839 KIR2DL1 0 . GRCh38 19 54775459 54775459 + Splice_Site SNP G G T novel C3L-01889_T C3L-01889_N G G c.664+1G>T p.X222_splice ENST00000336077 102 60 42 132 132 0 strelka-varscan-mutect KIR2DL1,splice_donor_variant,,ENST00000336077,NM_014218.2;KIR2DL1,splice_donor_variant,,ENST00000291633,;CTB-61M7.1,intron_variant,,ENST00000400864,; T ENST00000336077 Transcript splice_donor_variant -/1596 664/1047 222/348 1 1 KIR2DL1 HGNC HGNC:6329 protein_coding YES CCDS12904.1 ENSP00000336769 Q6H2H3 UPI00001195F7 NM_014218.2 4/7 HIGH 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 28 54775459 54775459 G T 1 0 0 0 0 0 0 1 0 8181 1275 44 2 2 KIR2DL1 19 54775459 Splice_Site SNP G C3L-01889_T 2781484 54775459 3842157 161 7840 PDYN 0 . GRCh38 20 1980393 1980393 + Missense_Mutation SNP C C A rs774175877 C3L-01889_T C3L-01889_N C C c.695G>T p.Arg232Leu p.R232L ENST00000539905 3/3 187 122 65 212 212 0 strelka-varscan-mutect PDYN,missense_variant,p.Arg232Leu,ENST00000539905,NM_001190899.2;PDYN,missense_variant,p.Arg232Leu,ENST00000217305,NM_024411.4,NM_001190898.2;PDYN,missense_variant,p.Arg232Leu,ENST00000540134,NM_001190892.1,NM_001190900.1;RP4-684O24.5,intron_variant,,ENST00000446562,; A ENST00000539905 Transcript missense_variant 1089/2725 695/765 232/254 R/L cGc/cTc rs774175877,COSM98097 1 -1 PDYN HGNC HGNC:8820 protein_coding YES CCDS13023.1 ENSP00000440185 P01213 UPI000012FE6A NM_001190899.2 deleterious(0) 3/3 hmmpanther:PTHR11438,hmmpanther:PTHR11438:SF4 0,1 MODERATE SNV 4 0,1 1 PASS rs774175877 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 1980393 1980393 C A 1 0 0 0 0 1 0 0 0 11787 768 27 1 1 PDYN 20 1980393 Missense_Mutation SNP C C3L-01889_T 1980393 62463774 162 7841 GPCPD1 0 . GRCh38 20 5559991 5559991 + Missense_Mutation SNP G G A rs777683264 C3L-01889_T C3L-01889_N G G c.1481C>T p.Ser494Phe p.S494F ENST00000379019 17/20 88 74 14 74 74 0 strelka-varscan-mutect GPCPD1,missense_variant,p.Ser494Phe,ENST00000379019,NM_019593.3;GPCPD1,intron_variant,,ENST00000418646,;GPCPD1,3_prime_UTR_variant,,ENST00000633552,;GPCPD1,non_coding_transcript_exon_variant,,ENST00000481038,; A ENST00000379019 Transcript missense_variant 1694/5489 1481/2019 494/672 S/F tCt/tTt rs777683264 1 -1 GPCPD1 HGNC HGNC:26957 protein_coding YES CCDS13090.1 ENSP00000368305 Q9NPB8 UPI0000062241 NM_019593.3 deleterious(0) 17/20 PROSITE_profiles:PS51704,hmmpanther:PTHR22958,Gene3D:3.20.20.190,Pfam_domain:PF03009,Superfamily_domains:SSF51695 MODERATE 1 SNV 1 1 PASS rs777683264 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 5559991 5559991 G A 1 0 0 0 0 1 0 0 0 6505 942 33 3 3 GPCPD1 20 5559991 Missense_Mutation SNP G C3L-01889_T 3579598 5559991 58884176 163 7842 ANKEF1 0 . GRCh38 20 10050079 10050079 + Missense_Mutation SNP G G T C3L-01889_T C3L-01889_N G G c.1510G>T p.Asp504Tyr p.D504Y ENST00000378380 6/10 292 220 72 277 277 0 strelka-varscan-mutect ANKEF1,missense_variant,p.Asp504Tyr,ENST00000378380,NM_198798.2,NM_001303472.1;ANKEF1,missense_variant,p.Asp504Tyr,ENST00000378392,NM_022096.5;SNAP25-AS1,intron_variant,,ENST00000603542,;SNAP25-AS1,intron_variant,,ENST00000421143,;ANKEF1,non_coding_transcript_exon_variant,,ENST00000488991,; T ENST00000378380 Transcript missense_variant 1839/5303 1510/2331 504/776 D/Y Gat/Tat COSM5391549 1 1 ANKEF1 HGNC HGNC:15803 protein_coding YES CCDS13108.1 ENSP00000367631 Q9NU02 UPI0000125B51 NM_198798.2,NM_001303472.1 deleterious(0) 6/10 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR24127,hmmpanther:PTHR24127:SF1,Superfamily_domains:SSF48403 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 10050079 10050079 G T 1 0 0 0 0 1 0 0 0 726 1174 41 2 2 ANKEF1 20 10050079 Missense_Mutation SNP G C3L-01889_T 4490088 10050079 54394088 164 7843 ARHGAP40 0 . GRCh38 20 38641733 38641733 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.1128C>T p.= p.P376P ENST00000373345 10/15 205 145 60 171 171 0 strelka-varscan-mutect ARHGAP40,synonymous_variant,p.=,ENST00000373345,NM_001164431.1;ARHGAP40,synonymous_variant,p.=,ENST00000243967,;ARHGAP40,upstream_gene_variant,,ENST00000373346,; T ENST00000373345 Transcript synonymous_variant 1296/2841 1128/1869 376/622 P ccC/ccT 1 1 ARHGAP40 HGNC HGNC:16226 protein_coding YES ENSP00000362442 Q5TG30 UPI0000DD8570 NM_001164431.1 10/15 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF4,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 38641733 38641733 C T 1 0 0 0 0 0 0 0 1 1012 581 21 3 3 ARHGAP40 20 38641733 Silent SNP C C3L-01889_T 28591654 38641733 25802434 165 7844 OCSTAMP 0 . GRCh38 20 46541568 46541568 + Silent SNP G G C novel C3L-01889_T C3L-01889_N G G c.1407C>G p.= p.V469V ENST00000279028 3/3 281 203 78 264 264 0 strelka-varscan-mutect OCSTAMP,synonymous_variant,p.=,ENST00000279028,NM_080721.2; C ENST00000279028 Transcript synonymous_variant 1421/2043 1407/1701 469/566 V gtC/gtG 1 -1 OCSTAMP HGNC HGNC:16116 protein_coding YES CCDS54468.1 ENSP00000279028 Q9BR26 UPI00006C1A90 NM_080721.2 3/3 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF3 LOW 1 SNV 5 1 PASS rs1259257985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 28 46541568 46541568 G C 1 0 0 0 0 0 0 0 1 10901 1161 41 4 4 OCSTAMP 20 46541568 Silent SNP G C3L-01889_T 7899835 46541568 17902599 166 7845 TPTE 0 . GRCh38 21 10559494 10559494 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.234C>A p.Asp78Glu p.D78E ENST00000618007 9/24 248 212 36 249 248 1 strelka-varscan-mutect TPTE,missense_variant,p.Asp60Glu,ENST00000622113,NM_199259.3;TPTE,missense_variant,p.Asp78Glu,ENST00000618007,NM_199261.3;TPTE,missense_variant,p.Ser40Arg,ENST00000427445,NM_199260.3;TPTE,missense_variant,p.Asp60Glu,ENST00000612957,;TPTE,splice_region_variant,,ENST00000612746,NM_001290224.1;AL078471.5,splice_region_variant,,ENST00000612267,; A ENST00000618007 Transcript missense_variant,splice_region_variant 564/2150 234/1656 78/551 D/E gaC/gaA 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 tolerated(0.27) 9/24 MODERATE 1 SNV 1 1 PASS rs1244920047 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 10559494 10559494 C A 1 0 0 0 0 1 0 0 0 16911 724 25 2 2 TPTE 21 10559494 Missense_Mutation SNP C C3L-01889_T 10559494 36150489 167 7846 PAXBP1 0 . GRCh38 21 32771661 32771661 + Missense_Mutation SNP C C T novel C3L-01889_T C3L-01889_N C C c.8G>A p.Arg3Gln p.R3Q ENST00000331923 1/18 54 39 15 62 62 0 strelka-mutect PAXBP1,missense_variant,p.Arg3Gln,ENST00000331923,NM_016631.3;PAXBP1,missense_variant,p.Arg3Gln,ENST00000290178,NM_013329.3;C21orf62-AS1,upstream_gene_variant,,ENST00000382375,;C21orf62-AS1,upstream_gene_variant,,ENST00000612326,;C21orf62-AS1,upstream_gene_variant,,ENST00000382377,;C21orf62-AS1,upstream_gene_variant,,ENST00000491756,;C21orf62-AS1,upstream_gene_variant,,ENST00000382378,;C21orf62-AS1,upstream_gene_variant,,ENST00000454365,;C21orf62-AS1,upstream_gene_variant,,ENST00000477513,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000472588,;PAXBP1,missense_variant,p.Arg3Gln,ENST00000443785,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000464256,; T ENST00000331923 Transcript missense_variant 198/3995 8/2754 3/917 R/Q cGa/cAa 1 -1 PAXBP1 HGNC HGNC:13579 protein_coding YES CCDS13619.1 ENSP00000328992 Q9Y5B6 UPI000012B294 NM_016631.3 tolerated_low_confidence(0.06) 1/18 Low_complexity_(Seg):seg,hmmpanther:PTHR12214:SF2,hmmpanther:PTHR12214 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 28 32771661 32771661 C T 1 0 0 0 0 1 0 0 0 11572 884 31 1 1 PAXBP1 21 32771661 Missense_Mutation SNP C C3L-01889_T 22212167 32771661 13938322 168 7847 BRWD1 0 . GRCh38 21 39210906 39210906 + Silent SNP G G A novel C3L-01889_T C3L-01889_N G G c.3924C>T p.= p.I1308I ENST00000333229 35/42 240 145 95 181 181 0 strelka-varscan-mutect BRWD1,synonymous_variant,p.=,ENST00000342449,NM_033656.3;BRWD1,synonymous_variant,p.=,ENST00000333229,NM_018963.4;BRWD1,synonymous_variant,p.=,ENST00000380800,;BRWD1,intron_variant,,ENST00000424441,;BRWD1,3_prime_UTR_variant,,ENST00000446924,;BRWD1,non_coding_transcript_exon_variant,,ENST00000473813,; A ENST00000333229 Transcript synonymous_variant 4252/10141 3924/6963 1308/2320 I atC/atT 1 -1 BRWD1 HGNC HGNC:12760 protein_coding YES CCDS13662.1 ENSP00000330753 Q9NSI6 UPI0000163C12 NM_018963.4 35/42 hmmpanther:PTHR16266:SF26,hmmpanther:PTHR16266 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 39210906 39210906 G A 1 0 0 0 0 0 0 0 1 1699 1280 45 3 3 BRWD1 21 39210906 Silent SNP G C3L-01889_T 6439245 39210906 7499077 169 7848 DIP2A 0 . GRCh38 21 46556020 46556020 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.3427C>A p.Pro1143Thr p.P1143T ENST00000417564 29/38 355 212 143 284 283 1 strelka-varscan-mutect DIP2A,missense_variant,p.Pro1139Thr,ENST00000400274,NM_001146116.1;DIP2A,missense_variant,p.Pro1143Thr,ENST00000417564,NM_015151.3;DIP2A,non_coding_transcript_exon_variant,,ENST00000481883,;DIP2A,non_coding_transcript_exon_variant,,ENST00000472364,; A ENST00000417564 Transcript missense_variant 3448/6967 3427/4716 1143/1571 P/T Ccc/Acc 1 1 DIP2A HGNC HGNC:17217 protein_coding YES CCDS46655.1 ENSP00000392066 Q14689 UPI00001B2E47 NM_015151.3 tolerated(0.05) 29/38 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF24,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 46556020 46556020 C A 1 0 0 0 0 1 0 0 0 4332 739 26 2 2 DIP2A 21 46556020 Missense_Mutation SNP C C3L-01889_T 7345114 46556020 153963 170 7849 MICAL3 0 . GRCh38 22 17901939 17901939 + Silent SNP A A G novel C3L-01889_T C3L-01889_N A A c.630T>C p.= p.P210P ENST00000441493 5/32 128 99 29 88 88 0 strelka-varscan-mutect MICAL3,synonymous_variant,p.=,ENST00000441493,NM_015241.2;MICAL3,synonymous_variant,p.=,ENST00000414725,;MICAL3,synonymous_variant,p.=,ENST00000585038,NM_001136004.3;MICAL3,synonymous_variant,p.=,ENST00000400561,NM_001122731.2;MICAL3,synonymous_variant,p.=,ENST00000383094,;MICAL3,downstream_gene_variant,,ENST00000424046,;MICAL3,synonymous_variant,p.=,ENST00000495076,; G ENST00000441493 Transcript synonymous_variant 983/9445 630/6009 210/2002 P ccT/ccC 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 5/32 hmmpanther:PTHR11915:SF239,hmmpanther:PTHR11915,Gene3D:3.50.50.60,Superfamily_domains:SSF51905 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 17901939 17901939 A G 1 0 0 0 0 0 0 0 1 9528 175 7 5 5 MICAL3 22 17901939 Silent SNP A C3L-01889_T 17901939 32916529 171 7850 CCDC117 0 . GRCh38 22 28773777 28773782 + Splice_Site DEL GAGTAA GAGTAA - novel C3L-01889_T C3L-01889_N GAGTAA GAGTAA c.239_239+5delAGTAAG p.X80_splice ENST00000249064 2/5 143 113 30 161 161 0 sindel-varindel-pindel CCDC117,splice_donor_variant,,ENST00000249064,NM_001284265.1,NM_173510.3;CCDC117,splice_donor_variant,,ENST00000421503,NM_001284264.1;CCDC117,splice_donor_variant,,ENST00000432510,;CCDC117,intron_variant,,ENST00000448492,NM_001284263.1;CCDC117,intron_variant,,ENST00000444523,;CCDC117,splice_donor_variant,,ENST00000453543,; - ENST00000249064 Transcript splice_donor_variant,coding_sequence_variant,intron_variant 414-?/3985 238-?/840 80-?/279 1 1 CCDC117 HGNC HGNC:26599 protein_coding YES CCDS13846.1 ENSP00000249064 Q8IWD4 A0A024R1C5 UPI000007450B NM_001284265.1,NM_173510.3 2/5 2/4 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 28 28773777 28773777 GAGTAA - 1 0 1 0 1 0 0 1 0 2447 1304 45 0 0 CCDC117 22 28773777 Splice_Site DEL GAGTAA C3L-01889_T 10871838 28773777 22044691 172 7851 CELSR1 0 . GRCh38 22 46535036 46535036 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.2135G>T p.Arg712Leu p.R712L ENST00000262738 1/35 173 125 48 118 118 0 strelka-varscan-mutect CELSR1,missense_variant,p.Arg712Leu,ENST00000262738,NM_014246.1;CELSR1,missense_variant,p.Arg87Leu,ENST00000454637,;CELSR1,upstream_gene_variant,,ENST00000497509,; A ENST00000262738 Transcript missense_variant 2135/11389 2135/9045 712/3014 R/L cGc/cTc 1 -1 CELSR1 HGNC HGNC:1850 protein_coding YES CCDS14076.1 ENSP00000262738 Q9NYQ6 UPI0000040648 NM_014246.1 tolerated(0.14) 1/35 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF36,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 46535036 46535036 C A 1 0 0 0 0 1 0 0 0 2928 768 27 1 1 CELSR1 22 46535036 Missense_Mutation SNP C C3L-01889_T 17761259 46535036 4283432 173 7852 PDK3 0 . GRCh38 X 24533979 24533979 + Silent SNP A A T rs746656692 C3L-01889_T C3L-01889_N A A c.1128A>T p.= p.A376A ENST00000441463 11/12 131 96 35 104 104 0 strelka-varscan-mutect PDK3,synonymous_variant,p.=,ENST00000441463,NM_001142386.2;PDK3,synonymous_variant,p.=,ENST00000379162,NM_005391.4; T ENST00000441463 Transcript synonymous_variant 1128/1921 1128/1248 376/415 A gcA/gcT rs746656692 1 1 PDK3 HGNC HGNC:8811 protein_coding YES CCDS48088.1 ENSP00000387536 Q15120 UPI00002124D4 NM_001142386.2 11/12 hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF21 LOW 1 SNV 2 1 PASS rs746656692 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 24533979 24533979 A T 1 0 0 0 0 0 0 0 1 11765 204 8 4 4 PDK3 23 24533979 Silent SNP A C3L-01889_T 24533979 131506916 174 7853 DMD 0 . GRCh38 X 32644284 32644284 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.1179G>T p.Gln393His p.Q393H ENST00000357033 11/79 304 236 68 286 286 0 strelka-varscan-mutect DMD,missense_variant,p.Gln393His,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Gln389His,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Gln393His,ENST00000620040,;DMD,missense_variant,p.Gln389His,ENST00000619831,;DMD,missense_variant,p.Gln385His,ENST00000288447,;DMD,intron_variant,,ENST00000447523,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;MIR548F5,upstream_gene_variant,,ENST00000408421,;DMD,intron_variant,,ENST00000488902,;DMD,intron_variant,,ENST00000480751,; A ENST00000357033 Transcript missense_variant 1386/13956 1179/11058 393/3685 Q/H caG/caT 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0) 11/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002341,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 32644284 32644284 C A 1 0 0 0 0 1 0 0 0 4387 680 24 2 2 DMD 23 32644284 Missense_Mutation SNP C C3L-01889_T 8110305 32644284 123396611 175 7854 MAOB 0 . GRCh38 X 43795872 43795872 + Missense_Mutation SNP C C A rs780719254 C3L-01889_T C3L-01889_N C C c.635G>T p.Gly212Val p.G212V ENST00000378069 7/15 90 65 25 82 82 0 strelka-varscan-mutect MAOB,missense_variant,p.Gly212Val,ENST00000378069,NM_000898.4;MAOB,downstream_gene_variant,,ENST00000487544,; A ENST00000378069 Transcript missense_variant 783/2566 635/1563 212/520 G/V gGc/gTc rs780719254 1 -1 MAOB HGNC HGNC:6834 protein_coding YES CCDS14261.1 ENSP00000367309 P27338 UPI0000049071 NM_000898.4 deleterious(0) 7/15 Pfam_domain:PF01593,Prints_domain:PR00757,hmmpanther:PTHR10742,hmmpanther:PTHR10742:SF267,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS rs780719254 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 43795872 43795872 C A 1 0 0 0 0 1 0 0 0 9148 739 26 2 2 MAOB 23 43795872 Missense_Mutation SNP C C3L-01889_T 11151588 43795872 112245023 176 7855 ZNF630 0 . GRCh38 X 48059951 48059951 + Missense_Mutation SNP C C A rs782800953 C3L-01889_T C3L-01889_N C C c.491G>T p.Arg164Leu p.R164L ENST00000442455 5/5 285 204 81 345 344 1 strelka-varscan-mutect ZNF630,missense_variant,p.Arg164Leu,ENST00000442455,NM_001190255.2,NM_001282201.1;ZNF630,missense_variant,p.Arg40Leu,ENST00000276054,NM_001282202.1;ZNF630,missense_variant,p.Arg164Leu,ENST00000409324,NM_001037735.3;ZNF630,missense_variant,p.Arg150Leu,ENST00000616492,;ZNF630,missense_variant,p.Arg164Leu,ENST00000428686,;ZNF630,missense_variant,p.Arg150Leu,ENST00000627643,;ZNF630,missense_variant,p.Arg40Leu,ENST00000421903,;ZNF630-AS1,intron_variant,,ENST00000614448,;ZNF630,intron_variant,,ENST00000428463,; A ENST00000442455 Transcript missense_variant 1058/2829 491/1974 164/657 R/L cGg/cTg rs782800953 1 -1 ZNF630 HGNC HGNC:28855 protein_coding YES CCDS35237.2 ENSP00000393163 Q2M218 UPI0000160BE4 NM_001190255.2,NM_001282201.1 tolerated(0.3) 5/5 MODERATE SNV 4 1 PASS rs782800953 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 48059951 48059951 C A 1 0 0 0 0 1 0 0 0 18629 652 23 1 1 ZNF630 23 48059951 Missense_Mutation SNP C C3L-01889_T 4264079 48059951 107980944 177 7856 SMC1A 0 . GRCh38 X 53403796 53403796 + Nonsense_Mutation SNP A A T novel C3L-01889_T C3L-01889_N A A c.2294T>A p.Leu765Ter p.L765* ENST00000322213 14/25 479 347 132 518 518 0 strelka-varscan-mutect SMC1A,stop_gained,p.Leu743Ter,ENST00000375340,NM_001281463.1;SMC1A,stop_gained,p.Leu765Ter,ENST00000322213,NM_006306.3;MIR6857,downstream_gene_variant,,ENST00000613267,; T ENST00000322213 Transcript stop_gained 2422/9784 2294/3702 765/1233 L/* tTg/tAg 1 -1 SMC1A HGNC HGNC:11111 protein_coding YES CCDS14352.1 ENSP00000323421 Q14683 UPI0000135A4D NM_006306.3 14/25 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF170 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 28 53403796 53403796 A T 1 0 0 0 0 0 1 0 0 15074 131 5 4 4 SMC1A 23 53403796 Nonsense_Mutation SNP A C3L-01889_T 5343845 53403796 102637099 178 7857 RP11-402P6.15 0 . GRCh38 X 71667836 71667836 + Missense_Mutation SNP G G T novel C3L-01889_T C3L-01889_N G G c.33G>T p.Arg11Ser p.R11S ENST00000636096 1/5 19 13 6 22 22 0 strelka-varscan-mutect RP11-402P6.15,missense_variant,p.Arg11Ser,ENST00000636096,;RP11-402P6.15,intron_variant,,ENST00000636797,;RP11-402P6.9,upstream_gene_variant,,ENST00000422194,;RP11-402P6.9,upstream_gene_variant,,ENST00000433410,;RP11-402P6.9,upstream_gene_variant,,ENST00000637198,; T ENST00000636096 Transcript missense_variant 33/1732 33/1590 11/529 R/S agG/agT 1 1 RP11-402P6.15 Clone_based_vega_gene protein_coding YES ENSP00000490941 tolerated(0.05) 1/5 hmmpanther:PTHR31866,hmmpanther:PTHR31866:SF1 MODERATE 1 SNV 1 PASS . . 15 195 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 28 71667836 71667836 G T 1 0 0 0 0 1 0 0 0 13738 1223 43 2 2 RP11-402P6.15 23 71667836 Missense_Mutation SNP G C3L-01889_T 18264040 71667836 84373059 179 7858 CDX4 0 . GRCh38 X 73453596 73453596 + Silent SNP C C T novel C3L-01889_T C3L-01889_N C C c.582C>T p.= p.C194C ENST00000373514 2/3 285 207 78 244 244 0 strelka-varscan-mutect CDX4,synonymous_variant,p.=,ENST00000373514,NM_005193.1; T ENST00000373514 Transcript synonymous_variant 582/1515 582/855 194/284 C tgC/tgT 1 1 CDX4 HGNC HGNC:1808 protein_coding YES CCDS14424.1 ENSP00000362613 O14627 UPI0000127473 NM_005193.1 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24332:SF15,hmmpanther:PTHR24332,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 28 73453596 73453596 C T 1 0 0 0 0 0 0 0 1 2890 718 25 3 3 CDX4 23 73453596 Silent SNP C C3L-01889_T 1785760 73453596 82587299 180 7859 CHIC1 0 . GRCh38 X 73679708 73679708 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.619G>C p.Glu207Gln p.E207Q ENST00000373502 5/6 79 75 4 94 94 0 varscan-mutect CHIC1,missense_variant,p.Glu207Gln,ENST00000373502,NM_001039840.2;CHIC1,intron_variant,,ENST00000373504,NM_001300884.1;CHIC1,missense_variant,p.Glu200Gln,ENST00000498407,;CHIC1,3_prime_UTR_variant,,ENST00000498318,; C ENST00000373502 Transcript missense_variant 696/4158 619/675 207/224 E/Q Gag/Cag 1 1 CHIC1 HGNC HGNC:1934 protein_coding YES CCDS35335.2 ENSP00000362601 Q5VXU3 UPI0000160F74 NM_001039840.2 deleterious(0) 5/6 hmmpanther:PTHR13005,hmmpanther:PTHR13005:SF2 MODERATE 1 SNV 1 1 PASS . . 4 203 3 0 0 0 0 0 -9.491294 1 1 1 1 0 C 3 2 28 73679708 73679708 G C 1 0 0 0 0 1 0 0 0 3102 1188 41 4 4 CHIC1 23 73679708 Missense_Mutation SNP G C3L-01889_T 226112 73679708 82361187 181 7860 TEX13A 0 . GRCh38 X 105219416 105219416 + Missense_Mutation SNP A A C novel C3L-01889_T C3L-01889_N A A c.778T>G p.Trp260Gly p.W260G ENST00000600991 3/3 349 267 82 375 375 0 strelka-varscan-mutect TEX13A,missense_variant,p.Trp260Gly,ENST00000600991,NM_031274.4;TEX13A,missense_variant,p.Trp260Gly,ENST00000609007,NM_001291277.1;IL1RAPL2,intron_variant,,ENST00000372582,NM_017416.1; C ENST00000600991 Transcript missense_variant 890/1377 778/1230 260/409 W/G Tgg/Ggg 1 -1 TEX13A HGNC HGNC:11735 protein_coding YES CCDS76005.1 ENSP00000471604 Q9BXU3 UPI0000042200 NM_031274.4 tolerated(1) 3/3 hmmpanther:PTHR23111:SF25,hmmpanther:PTHR23111 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 105219416 105219416 A C 1 0 0 0 0 1 0 0 0 16197 130 5 5 5 TEX13A 23 105219416 Missense_Mutation SNP A C3L-01889_T 31539708 105219416 50821479 182 7861 PAK3 0 . GRCh38 X 111196615 111196615 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.1490C>A p.Pro497His p.P497H ENST00000360648 14/16 319 243 76 350 350 0 strelka-varscan-mutect PAK3,missense_variant,p.Pro461His,ENST00000372007,NM_001324327.1,NM_001324326.1,NM_001324331.1,NM_001324333.1,NM_001324332.1,NM_001324334.1,NM_001324328.1,NM_001324330.1,NM_001324325.1,NM_002578.3;PAK3,missense_variant,p.Pro482His,ENST00000519681,;PAK3,missense_variant,p.Pro476His,ENST00000372010,;PAK3,missense_variant,p.Pro461His,ENST00000446737,NM_001128166.1;PAK3,missense_variant,p.Pro461His,ENST00000425146,NM_001128167.1;PAK3,missense_variant,p.Pro497His,ENST00000360648,NM_001128168.1;PAK3,missense_variant,p.Pro482His,ENST00000417227,NM_001128172.1;PAK3,missense_variant,p.Pro476His,ENST00000262836,NM_001128173.1;PAK3,missense_variant,p.Pro460His,ENST00000620137,;PAK3,missense_variant,p.Pro497His,ENST00000518291,; A ENST00000360648 Transcript missense_variant 1517/2241 1490/1743 497/580 P/H cCt/cAt 1 1 PAK3 HGNC HGNC:8592 protein_coding YES CCDS48151.1 ENSP00000353864 O75914 UPI0000D61DBC NM_001128168.1 deleterious(0.02) 14/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF250,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 111196615 111196615 C A 1 0 0 0 0 1 0 0 0 11482 681 24 2 2 PAK3 23 111196615 Missense_Mutation SNP C C3L-01889_T 5977199 111196615 44844280 183 7862 ALG13 0 . GRCh38 X 111708072 111708072 + Silent SNP T T A novel C3L-01889_T C3L-01889_N T T c.429T>A p.= p.P143P ENST00000394780 4/27 104 76 28 104 104 0 strelka-varscan-mutect ALG13,synonymous_variant,p.=,ENST00000610588,NM_001257231.1;ALG13,synonymous_variant,p.=,ENST00000394780,NM_001099922.2;ALG13,synonymous_variant,p.=,ENST00000251943,NM_001324292.1,NM_001257237.1;ALG13,synonymous_variant,p.=,ENST00000621367,NM_001257230.1,NM_001257234.1;ALG13,synonymous_variant,p.=,ENST00000436609,;ALG13-AS1,intron_variant,,ENST00000430794,;ALG13,missense_variant,p.Trp124Arg,ENST00000624881,;ALG13,synonymous_variant,p.=,ENST00000636363,;ALG13,3_prime_UTR_variant,,ENST00000624161,;ALG13,3_prime_UTR_variant,,ENST00000623144,;ALG13,3_prime_UTR_variant,,ENST00000623148,;ALG13,3_prime_UTR_variant,,ENST00000495283,;ALG13,3_prime_UTR_variant,,ENST00000486353,;ALG13,3_prime_UTR_variant,,ENST00000471924,;ALG13,intron_variant,,ENST00000470971,;ALG13,intron_variant,,ENST00000487141,;ALG13,intron_variant,,ENST00000622997,;ALG13,intron_variant,,ENST00000470704,; A ENST00000394780 Transcript synonymous_variant 498/4133 429/3414 143/1137 P ccT/ccA 1 1 ALG13 HGNC HGNC:30881 protein_coding YES CCDS55477.1 ENSP00000378260 Q9NP73 UPI0000E5AFF9 NM_001099922.2 4/27 hmmpanther:PTHR12867:SF5,hmmpanther:PTHR12867 LOW 1 SNV 2 1 PASS rs1173829709 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 28 111708072 111708072 T A 1 0 0 0 0 0 0 0 1 615 1567 55 4 4 ALG13 23 111708072 Silent SNP T C3L-01889_T 511457 111708072 44332823 184 7863 DCAF12L2 0 . GRCh38 X 126165356 126165356 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.569G>T p.Arg190Leu p.R190L ENST00000360028 1/1 294 245 49 271 271 0 strelka-mutect DCAF12L2,missense_variant,p.Arg190Leu,ENST00000360028,NM_001013628.2; A ENST00000360028 Transcript missense_variant 742/2599 569/1392 190/463 R/L cGc/cTc 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 tolerated(0.25) 1/1 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 PASS . . 2 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 126165356 126165356 C A 1 0 0 0 0 1 0 0 0 4066 768 27 1 1 DCAF12L2 23 126165356 Missense_Mutation SNP C C3L-01889_T 14457284 126165356 29875539 185 7864 31 3 DCAF12L2 0 . GRCh38 X 126165361 126165361 + Silent SNP G G A C3L-01889_T C3L-01889_N G G c.564C>T p.= p.G188G ENST00000360028 1/1 281 235 46 263 263 0 strelka-mutect DCAF12L2,synonymous_variant,p.=,ENST00000360028,NM_001013628.2; A ENST00000360028 Transcript synonymous_variant 737/2599 564/1392 188/463 G ggC/ggT COSM4790853,COSM4790854 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 1/1 hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 1,1 LOW 1 SNV 1,1 1 PASS rs1224019540 . 2 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 28 126165361 126165361 G A 1 0 0 0 0 0 0 0 1 4066 1074 38 1 1 DCAF12L2 23 126165361 Silent SNP G C3L-01889_T 5 126165361 29875534 186 7865 31 3 DCAF12L2 0 . GRCh38 X 126165363 126165363 + Missense_Mutation SNP C C A novel C3L-01889_T C3L-01889_N C C c.562G>T p.Gly188Cys p.G188C ENST00000360028 1/1 279 233 46 254 254 0 strelka-mutect DCAF12L2,missense_variant,p.Gly188Cys,ENST00000360028,NM_001013628.2; A ENST00000360028 Transcript missense_variant 735/2599 562/1392 188/463 G/C Ggc/Tgc 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 deleterious(0) 1/1 hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 PASS . . 2 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 126165363 126165363 C A 1 0 0 0 0 1 0 0 0 4066 623 22 2 2 DCAF12L2 23 126165363 Missense_Mutation SNP C C3L-01889_T 2 126165363 29875532 187 7866 31 3 BCORL1 0 . GRCh38 X 130015939 130015939 + Missense_Mutation SNP G G C novel C3L-01889_T C3L-01889_N G G c.3167G>C p.Gly1056Ala p.G1056A ENST00000540052 3/12 287 214 73 305 305 0 strelka-varscan-mutect BCORL1,missense_variant,p.Gly1056Ala,ENST00000540052,NM_021946.4;BCORL1,missense_variant,p.Gly1056Ala,ENST00000218147,;BCORL1,missense_variant,p.Gly656Ala,ENST00000456822,;BCORL1,missense_variant,p.Gly492Ala,ENST00000441294,;BCORL1,downstream_gene_variant,,ENST00000488135,; C ENST00000540052 Transcript missense_variant 3211/7127 3167/5136 1056/1711 G/A gGt/gCt 1 1 BCORL1 HGNC HGNC:25657 protein_coding YES CCDS14616.1 ENSP00000437775 Q5H9F3 UPI0001D3414A NM_021946.4 3/12 hmmpanther:PTHR24117,hmmpanther:PTHR24117:SF6 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 28 130015939 130015939 G C 1 0 0 0 0 1 0 0 0 1534 1261 44 4 4 BCORL1 23 130015939 Missense_Mutation SNP G C3L-01889_T 3850576 130015939 26024956 188 7867 MAGEC3 0 . GRCh38 X 141895353 141895353 + Nonsense_Mutation SNP G G T C3L-01889_T C3L-01889_N G G c.994G>T p.Glu332Ter p.E332* ENST00000298296 5/8 189 132 57 195 194 1 strelka-varscan-mutect MAGEC3,stop_gained,p.Glu332Ter,ENST00000298296,NM_138702.1;MAGEC3,5_prime_UTR_variant,,ENST00000544766,NM_177456.2;MAGEC3,intron_variant,,ENST00000443323,;MAGEC3,upstream_gene_variant,,ENST00000409007,;MAGEC3,non_coding_transcript_exon_variant,,ENST00000483584,; T ENST00000298296 Transcript stop_gained 994/1932 994/1932 332/643 E/* Gag/Tag COSM1214232 1 1 MAGEC3 HGNC HGNC:23798 protein_coding YES CCDS14676.1 ENSP00000298296 Q8TD91 UPI000006E09B NM_138702.1 5/8 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF86,SMART_domains:SM01373 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 28 141895353 141895353 G T 1 0 0 0 0 0 1 0 0 9100 1175 41 2 2 MAGEC3 23 141895353 Nonsense_Mutation SNP G C3L-01889_T 11879414 141895353 14145542 189 7868 SLITRK4 0 . GRCh38 X 143629294 143629294 + Silent SNP A A G novel C3L-01889_T C3L-01889_N A A c.1815T>C p.= p.G605G ENST00000596188 2/2 205 154 51 220 220 0 strelka-varscan-mutect SLITRK4,synonymous_variant,p.=,ENST00000596188,NM_001184750.2;SLITRK4,synonymous_variant,p.=,ENST00000338017,NM_173078.4;SLITRK4,synonymous_variant,p.=,ENST00000356928,NM_001184749.2; G ENST00000596188 Transcript synonymous_variant 2041/8545 1815/2514 605/837 G ggT/ggC 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 28 143629294 143629294 A G 1 0 0 0 0 0 0 0 1 15036 262 10 5 5 SLITRK4 23 143629294 Silent SNP A C3L-01889_T 1733941 143629294 12411601 190 7869 AFF2 0 . GRCh38 X 148956175 148956175 + Missense_Mutation SNP C C A C3L-01889_T C3L-01889_N C C c.2130C>A p.Phe710Leu p.F710L ENST00000370460 11/21 346 257 89 364 363 1 strelka-varscan-mutect AFF2,missense_variant,p.Phe710Leu,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Phe351Leu,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Phe677Leu,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Phe675Leu,ENST00000370457,NM_001169124.1,NM_001169125.1; A ENST00000370460 Transcript missense_variant 2609/13746 2130/3936 710/1311 F/L ttC/ttA COSM4477189,COSM4477190,COSM4477191 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 deleterious(0) 11/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 28 148956175 148956175 C A 1 0 0 0 0 1 0 0 0 434 825 29 2 2 AFF2 23 148956175 Missense_Mutation SNP C C3L-01889_T 5326881 148956175 7084720 191 7870 MMEL1 0 . GRCh38 1 2629479 2629479 + Silent SNP C C A rs562014966 C3L-01924_T C3L-01924_N C C c.6G>T p.= p.G2G ENST00000378412 2/24 68 49 19 50 50 0 strelka-varscan-mutect MMEL1,synonymous_variant,p.=,ENST00000378412,NM_033467.3;MMEL1,synonymous_variant,p.=,ENST00000502556,;RP13-436F16.1,upstream_gene_variant,,ENST00000427302,;MMEL1,downstream_gene_variant,,ENST00000511099,;MMEL1,synonymous_variant,p.=,ENST00000504800,; A ENST00000378412 Transcript synonymous_variant 168/2849 6/2340 2/779 G ggG/ggT rs562014966 1 -1 MMEL1 HGNC HGNC:14668 protein_coding YES CCDS30569.2 ENSP00000367668 Q495T6 UPI0000047596 NM_033467.3 2/24 LOW 1 SNV 2 1 PASS rs562014966 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 2629479 2629479 C A 1 0 0 0 0 0 0 0 1 9609 842 30 2 2 MMEL1 1 2629479 Silent SNP C C3L-01924_T 2629479 246326943 1 7871 ACTRT2 0 . GRCh38 1 3022272 3022272 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.586C>A p.Leu196Met p.L196M ENST00000378404 1/1 118 77 41 162 162 0 strelka-varscan-mutect ACTRT2,missense_variant,p.Leu196Met,ENST00000378404,NM_080431.4; A ENST00000378404 Transcript missense_variant 790/1421 586/1134 196/377 L/M Ctg/Atg 1 1 ACTRT2 HGNC HGNC:24026 protein_coding YES CCDS45.1 ENSP00000367658 Q8TDY3 UPI0000070494 NM_080431.4 deleterious(0.02) 1/1 Gene3D:3.90.640.10,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF38,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 3022272 3022272 C A 1 0 0 0 0 1 0 0 0 262 796 28 2 2 ACTRT2 1 3022272 Missense_Mutation SNP C C3L-01924_T 392793 3022272 245934150 2 7872 ACTRT2 0 . GRCh38 1 3022752 3022752 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1066C>A p.Gln356Lys p.Q356K ENST00000378404 1/1 153 143 10 179 179 0 strelka-mutect ACTRT2,missense_variant,p.Gln356Lys,ENST00000378404,NM_080431.4; A ENST00000378404 Transcript missense_variant 1270/1421 1066/1134 356/377 Q/K Cag/Aag 1 1 ACTRT2 HGNC HGNC:24026 protein_coding YES CCDS45.1 ENSP00000367658 Q8TDY3 UPI0000070494 NM_080431.4 tolerated(0.11) 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF38,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS . . 0 207 0 3 0 0 0 0 -13.46473 0.9999642 1 1 1 0 A 3 1 29 3022752 3022752 C A 1 0 0 0 0 1 0 0 0 262 711 25 2 2 ACTRT2 1 3022752 Missense_Mutation SNP C C3L-01924_T 480 3022752 245933670 3 7873 CHD5 0 . GRCh38 1 6131694 6131694 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.3199T>A p.Tyr1067Asn p.Y1067N ENST00000262450 21/42 110 98 12 115 115 0 strelka-varscan-mutect CHD5,missense_variant,p.Tyr1067Asn,ENST00000262450,NM_015557.2;CHD5,missense_variant,p.Tyr1067Asn,ENST00000496404,;CHD5,missense_variant,p.Tyr450Asn,ENST00000462991,;CHD5,missense_variant,p.Tyr16Asn,ENST00000377999,;CHD5,upstream_gene_variant,,ENST00000491020,; T ENST00000262450 Transcript missense_variant 3299/9646 3199/5865 1067/1954 Y/N Tat/Aat 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 deleterious(0) 21/42 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 29 6131694 6131694 A T 1 0 0 0 0 1 0 0 0 3087 391 14 4 4 CHD5 1 6131694 Missense_Mutation SNP A C3L-01924_T 3108942 6131694 242824728 4 7874 GPR153 0 . GRCh38 1 6253913 6253913 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.591G>T p.Gln197His p.Q197H ENST00000377893 3/6 147 116 31 141 141 0 strelka-varscan-mutect GPR153,missense_variant,p.Gln197His,ENST00000377893,NM_207370.2; A ENST00000377893 Transcript missense_variant 851/4082 591/1830 197/609 Q/H caG/caT 1 -1 GPR153 HGNC HGNC:23618 protein_coding YES CCDS64.1 ENSP00000367125 Q6NV75 A0A0I9QQ03 UPI000040E9D7 NM_207370.2 tolerated(0.1) 3/6 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01992,PROSITE_profiles:PS50262,hmmpanther:PTHR16518,hmmpanther:PTHR16518:SF5,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs1218269797 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 6253913 6253913 C A 1 0 0 0 0 1 0 0 0 6545 912 32 2 2 GPR153 1 6253913 Missense_Mutation SNP C C3L-01924_T 122219 6253913 242702509 5 7875 PIK3CD 0 . GRCh38 1 9722020 9722020 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2101C>A p.Leu701Met p.L701M ENST00000377346 17/24 494 383 111 493 493 0 strelka-varscan-mutect PIK3CD,missense_variant,p.Leu725Met,ENST00000536656,;PIK3CD,missense_variant,p.Leu725Met,ENST00000628140,;PIK3CD,missense_variant,p.Leu701Met,ENST00000377346,NM_005026.3;PIK3CD,missense_variant,p.Leu725Met,ENST00000361110,;PIK3CD,missense_variant,p.Leu725Met,ENST00000543390,;PIK3CD,downstream_gene_variant,,ENST00000479223,; A ENST00000377346 Transcript missense_variant 2296/5203 2101/3135 701/1044 L/M Ctg/Atg 1 1 PIK3CD HGNC HGNC:8977 protein_coding YES CCDS104.1 ENSP00000366563 O00329 UPI000013E807 NM_005026.3 tolerated(0.1) 17/24 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF35,Gene3D:3.30.1010.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 9722020 9722020 C A 1 0 0 0 0 1 0 0 0 12010 796 28 2 2 PIK3CD 1 9722020 Missense_Mutation SNP C C3L-01924_T 3468107 9722020 239234402 6 7876 AADACL4 0 . GRCh38 1 12661839 12661839 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.434T>A p.Val145Glu p.V145E ENST00000376221 3/4 255 229 26 269 269 0 strelka-mutect AADACL4,missense_variant,p.Val145Glu,ENST00000376221,NM_001013630.1; A ENST00000376221 Transcript missense_variant 434/1575 434/1224 145/407 V/E gTa/gAa 1 1 AADACL4 HGNC HGNC:32038 protein_coding YES CCDS30590.1 ENSP00000365395 Q5VUY2 UPI0000160609 NM_001013630.1 deleterious(0) 3/4 hmmpanther:PTHR23024:SF197,hmmpanther:PTHR23024,PIRSF_domain:PIRSF037251,Gene3D:3.40.50.1820,Pfam_domain:PF07859,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 12661839 12661839 T A 1 0 0 0 0 1 0 0 0 13 1638 57 4 4 AADACL4 1 12661839 Missense_Mutation SNP T C3L-01924_T 2939819 12661839 236294583 7 7877 PRAMEF6 0 . GRCh38 1 12938784 12938784 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1322G>T p.Arg441Ile p.R441I ENST00000376189 4/4 937 831 106 933 933 0 varscan-mutect PRAMEF6,missense_variant,p.Arg441Ile,ENST00000376189,NM_001010889.2;PRAMEF6,missense_variant,p.Arg441Ile,ENST00000415464,; A ENST00000376189 Transcript missense_variant 1408/1720 1322/1431 441/476 R/I aGa/aTa 1 -1 PRAMEF6 HGNC HGNC:30583 protein_coding YES CCDS30594.1 ENSP00000365360 Q5VXH4 UPI0000418E57 NM_001010889.2 tolerated(1) 4/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 12938784 12938784 C A 1 0 0 0 0 1 0 0 0 12568 913 32 2 2 PRAMEF6 1 12938784 Missense_Mutation SNP C C3L-01924_T 276945 12938784 236017638 8 7878 PRAMEF15 0 . GRCh38 1 13322198 13322198 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.1371T>A p.= p.T457T ENST00000376152 4/4 215 192 23 267 267 0 varscan-mutect PRAMEF15,synonymous_variant,p.=,ENST00000376152,NM_001098376.2;PRAMEF15,synonymous_variant,p.=,ENST00000613530,;RP11-219C24.10,upstream_gene_variant,,ENST00000432559,; A ENST00000376152 Transcript synonymous_variant 1465/1865 1371/1437 457/478 T acT/acA 1 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES CCDS44059.1 ENSP00000365322 Q5VWM5 UPI0000199BA7 NM_001098376.2 4/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 13322198 13322198 T A 1 0 0 0 0 0 0 0 1 12559 1567 55 4 4 PRAMEF15 1 13322198 Silent SNP T C3L-01924_T 383414 13322198 235634224 9 7879 ATP13A2 0 . GRCh38 1 16988339 16988339 + Silent SNP G G A rs372361807 C3L-01924_T C3L-01924_N G G c.2745C>T p.= p.C915C ENST00000326735 24/29 651 618 33 627 626 1 strelka-varscan-mutect ATP13A2,synonymous_variant,p.=,ENST00000452699,NM_001141973.2;ATP13A2,synonymous_variant,p.=,ENST00000326735,NM_022089.3;ATP13A2,synonymous_variant,p.=,ENST00000341676,NM_001141974.2;ATP13A2,synonymous_variant,p.=,ENST00000502418,;ATP13A2,downstream_gene_variant,,ENST00000503552,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000466561,; A ENST00000326735 Transcript synonymous_variant 2779/3840 2745/3543 915/1180 C tgC/tgT rs372361807,COSM1560446,COSM4225870 1 -1 ATP13A2 HGNC HGNC:30213 protein_coding YES CCDS175.1 ENSP00000327214 Q9NQ11 UPI0000049724 NM_022089.3 24/29 Gene3D:3.40.50.1000,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01657 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs372361807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 16988339 16988339 G A 1 0 0 0 0 0 0 0 1 1276 1079 38 1 1 ATP13A2 1 16988339 Silent SNP G C3L-01924_T 3666141 16988339 231968083 10 7880 SH2D5 0 . GRCh38 1 20724563 20724563 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.463delG p.Ala155HisfsTer15 p.A155Hfs*15 ENST00000444387 6/10 126 102 24 100 100 0 sindel-varindel SH2D5,frameshift_variant,p.Ala71HisfsTer15,ENST00000375031,NM_001103160.1;SH2D5,frameshift_variant,p.Ala155HisfsTer15,ENST00000444387,NM_001103161.1;SH2D5,downstream_gene_variant,,ENST00000517430,;SH2D5,downstream_gene_variant,,ENST00000447746,;SH2D5,downstream_gene_variant,,ENST00000519434,;SH2D5,downstream_gene_variant,,ENST00000518294,;SH2D5,non_coding_transcript_exon_variant,,ENST00000460804,; - ENST00000444387 Transcript frameshift_variant 861/1934 463/1272 155/423 A/X Gca/ca 1 -1 SH2D5 HGNC HGNC:28819 protein_coding YES CCDS44080.1 ENSP00000406026 Q6ZV89 UPI0000EE70C3 NM_001103161.1 6/10 SMART_domains:SM00462 HIGH 1 deletion 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 20724563 20724563 C - 1 0 1 0 1 0 0 0 0 14495 739 26 0 0 SH2D5 1 20724563 Frame_Shift_Del DEL C C3L-01924_T 3736224 20724563 228231859 11 7881 GPR3 0 . GRCh38 1 27393973 27393973 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.175G>T p.Ala59Ser p.A59S ENST00000374024 2/2 92 84 8 120 120 0 strelka-varscan-mutect GPR3,missense_variant,p.Ala59Ser,ENST00000374024,NM_005281.3;RP1-144C9.2,downstream_gene_variant,,ENST00000443746,; T ENST00000374024 Transcript missense_variant 274/2115 175/993 59/330 A/S Gcg/Tcg 1 1 GPR3 HGNC HGNC:4484 protein_coding YES CCDS303.1 ENSP00000363136 P46089 F1DAM5 UPI0000001624 NM_005281.3 tolerated(0.08) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF39,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 27393973 27393973 G T 1 0 0 0 0 1 0 0 0 6570 1319 46 2 2 GPR3 1 27393973 Missense_Mutation SNP G C3L-01924_T 6669410 27393973 221562449 12 7882 CLSPN 0 . GRCh38 1 35746850 35746850 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.2770G>A p.Glu924Lys p.E924K ENST00000318121 15/25 366 279 87 409 409 0 strelka-varscan-mutect CLSPN,missense_variant,p.Glu924Lys,ENST00000251195,;CLSPN,missense_variant,p.Glu924Lys,ENST00000318121,NM_022111.3;CLSPN,missense_variant,p.Glu871Lys,ENST00000520551,;CLSPN,missense_variant,p.Glu860Lys,ENST00000373220,NM_001190481.1;RP11-435D7.3,downstream_gene_variant,,ENST00000373226,;CLSPN,downstream_gene_variant,,ENST00000517467,; T ENST00000318121 Transcript missense_variant 2828/4169 2770/4020 924/1339 E/K Gaa/Aaa 1 -1 CLSPN HGNC HGNC:19715 protein_coding YES CCDS396.1 ENSP00000312995 Q9HAW4 UPI0000161087 NM_022111.3 tolerated(0.15) 15/25 hmmpanther:PTHR14396:SF10,hmmpanther:PTHR14396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 35746850 35746850 C T 1 0 0 0 0 1 0 0 0 3332 835 29 3 3 CLSPN 1 35746850 Missense_Mutation SNP C C3L-01924_T 8352877 35746850 213209572 13 7883 HIVEP3 0 . GRCh38 1 41584133 41584133 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.665G>T p.Cys222Phe p.C222F ENST00000372583 4/9 226 198 28 221 221 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Cys222Phe,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Cys222Phe,ENST00000372583,NM_024503.4;HIVEP3,upstream_gene_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 1551/12193 665/7221 222/2406 C/F tGc/tTc 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious(0) 4/9 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 41584133 41584133 C A 1 0 0 0 0 1 0 0 0 7077 710 25 2 2 HIVEP3 1 41584133 Missense_Mutation SNP C C3L-01924_T 5837283 41584133 207372289 14 7884 CDC20 0 . GRCh38 1 43363040 43363040 + Missense_Mutation SNP C C T rs761756771 C3L-01924_T C3L-01924_N C C c.1411C>T p.Arg471Cys p.R471C ENST00000372462 10/10 129 114 15 138 138 0 strelka-varscan-mutect CDC20,missense_variant,p.Arg471Cys,ENST00000372462,;CDC20,missense_variant,p.Arg471Cys,ENST00000310955,NM_001255.2;ELOVL1,downstream_gene_variant,,ENST00000621943,NM_001256399.1;ELOVL1,downstream_gene_variant,,ENST00000372458,NM_001256402.1,NM_022821.3;ELOVL1,downstream_gene_variant,,ENST00000413844,NM_001256401.1;ELOVL1,downstream_gene_variant,,ENST00000621166,;RP1-92O14.3,upstream_gene_variant,,ENST00000424948,;CDC20,non_coding_transcript_exon_variant,,ENST00000482046,;ELOVL1,downstream_gene_variant,,ENST00000470769,;ELOVL1,downstream_gene_variant,,ENST00000464204,;ELOVL1,downstream_gene_variant,,ENST00000482302,;ELOVL1,downstream_gene_variant,,ENST00000497050,;ELOVL1,downstream_gene_variant,,ENST00000470968,;ELOVL1,downstream_gene_variant,,ENST00000497569,;ELOVL1,downstream_gene_variant,,ENST00000487209,;ELOVL1,downstream_gene_variant,,ENST00000468865,;ELOVL1,downstream_gene_variant,,ENST00000496932,;CDC20,downstream_gene_variant,,ENST00000478882,;ELOVL1,downstream_gene_variant,,ENST00000465321,;ELOVL1,downstream_gene_variant,,ENST00000479439,;ELOVL1,downstream_gene_variant,,ENST00000478481,;ELOVL1,downstream_gene_variant,,ENST00000479686,; T ENST00000372462 Transcript missense_variant 1614/1777 1411/1500 471/499 R/C Cgc/Tgc rs761756771,COSM1736946 1 1 CDC20 HGNC HGNC:1723 protein_coding YES CCDS484.1 ENSP00000361540 Q12834 UPI0000072C04 deleterious(0) 10/10 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF3,SMART_domains:SM00320,Superfamily_domains:SSF50978 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761756771 . 0 208 0 2 0 0 0 0 -19.99844 0.9999999 1 1 1 0 T 3 4 29 43363040 43363040 C T 1 0 0 0 0 1 0 0 0 2762 768 27 1 1 CDC20 1 43363040 Missense_Mutation SNP C C3L-01924_T 1778907 43363040 205593382 15 7885 CYP4A22 0 . GRCh38 1 47145920 47145920 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1277C>A p.Pro426His p.P426H ENST00000371891 10/12 159 132 27 184 183 1 strelka-varscan-mutect CYP4A22,missense_variant,p.Pro426His,ENST00000371891,NM_001010969.2;CYP4A22,missense_variant,p.Pro328His,ENST00000619754,NM_001308102.1;CYP4A22,missense_variant,p.Pro328His,ENST00000371890,;CYP4A22,missense_variant,p.Pro427His,ENST00000620131,;CYP4A22,missense_variant,p.Pro426His,ENST00000294337,;CYP4A22-AS1,intron_variant,,ENST00000444042,;CYP4A22,non_coding_transcript_exon_variant,,ENST00000485117,;CYP4A22,non_coding_transcript_exon_variant,,ENST00000490948,; A ENST00000371891 Transcript missense_variant 1308/2535 1277/1560 426/519 P/H cCc/cAc 1 1 CYP4A22 HGNC HGNC:20575 protein_coding YES CCDS30707.1 ENSP00000360958 Q5TCH4 UPI00002371F0 NM_001010969.2 deleterious(0.01) 10/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF39,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 47145920 47145920 C A 1 0 0 0 0 1 0 0 0 3987 623 22 2 2 CYP4A22 1 47145920 Missense_Mutation SNP C C3L-01924_T 3782880 47145920 201810502 16 7886 ZYG11A 0 . GRCh38 1 52857404 52857404 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.663T>C p.= p.S221S ENST00000371528 3/14 126 118 8 157 157 0 strelka-varscan-mutect ZYG11A,synonymous_variant,p.=,ENST00000371528,NM_001004339.2;ZYG11A,intron_variant,,ENST00000371532,;ZYG11A,intron_variant,,ENST00000612017,; C ENST00000371528 Transcript synonymous_variant 811/4469 663/2280 221/759 S tcT/tcC 1 1 ZYG11A HGNC HGNC:32058 protein_coding YES CCDS44148.1 ENSP00000360583 Q6WRX3 UPI000066D8BB NM_001004339.2 3/14 Gene3D:3.80.10.10,hmmpanther:PTHR12904,hmmpanther:PTHR12904:SF20,Superfamily_domains:SSF52047 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 52857404 52857404 T C 1 0 0 0 0 0 0 0 1 18856 1567 55 5 5 ZYG11A 1 52857404 Silent SNP T C3L-01924_T 5711484 52857404 196099018 17 7887 MROH7 0 . GRCh38 1 54701190 54701190 + Silent SNP G G A rs776782420 C3L-01924_T C3L-01924_N G G c.3153G>A p.= p.K1051K ENST00000421030 19/24 126 116 10 122 122 0 strelka-varscan-mutect MROH7,synonymous_variant,p.=,ENST00000421030,NM_001039464.3;MROH7,synonymous_variant,p.=,ENST00000409996,NM_001291332.1;MROH7,downstream_gene_variant,,ENST00000339553,;MROH7,downstream_gene_variant,,ENST00000395690,;MROH7-TTC4,synonymous_variant,p.=,ENST00000414150,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000606515,;MROH7,3_prime_UTR_variant,,ENST00000413188,;MROH7,3_prime_UTR_variant,,ENST00000422659,;MROH7,3_prime_UTR_variant,,ENST00000440047,;MROH7,3_prime_UTR_variant,,ENST00000440217,;MROH7,non_coding_transcript_exon_variant,,ENST00000371287,;MROH7-TTC4,non_coding_transcript_exon_variant,,ENST00000460155,;MROH7,downstream_gene_variant,,ENST00000438846,; A ENST00000421030 Transcript synonymous_variant 3438/4329 3153/3972 1051/1323 K aaG/aaA rs776782420 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 19/24 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF17,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 2 1 PASS rs776782420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 54701190 54701190 G A 1 0 0 0 0 0 0 0 1 9747 933 33 3 3 MROH7 1 54701190 Silent SNP G C3L-01924_T 1843786 54701190 194255232 18 7888 C8A 0 . GRCh38 1 56883652 56883652 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.826T>G p.Leu276Val p.L276V ENST00000361249 6/11 184 168 16 249 248 1 strelka-varscan-mutect C8A,missense_variant,p.Leu276Val,ENST00000361249,NM_000562.2; G ENST00000361249 Transcript missense_variant 922/2356 826/1755 276/584 L/V Ttg/Gtg 1 1 C8A HGNC HGNC:1352 protein_coding YES CCDS606.1 ENSP00000354458 P07357 UPI0000127C5A NM_000562.2 tolerated(0.08) 6/11 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325,Pfam_domain:PF01823 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 56883652 56883652 T G 1 0 0 0 0 1 0 0 0 2150 1606 56 5 5 C8A 1 56883652 Missense_Mutation SNP T C3L-01924_T 2182462 56883652 192072770 19 7889 DAB1 0 . GRCh38 1 57010774 57010774 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.1589C>T p.Ala530Val p.A530V ENST00000371236 14/15 32 26 6 38 38 0 strelka-varscan-mutect DAB1,missense_variant,p.Ala530Val,ENST00000371236,;DAB1,missense_variant,p.Ala530Val,ENST00000414851,NM_021080.3;DAB1,missense_variant,p.Ala528Val,ENST00000420954,;DAB1,missense_variant,p.Ala563Val,ENST00000371231,;DAB1,downstream_gene_variant,,ENST00000371232,;DAB1,non_coding_transcript_exon_variant,,ENST00000485760,; A ENST00000371236 Transcript missense_variant 1853/5298 1589/1668 530/555 A/V gCc/gTc 1 -1 DAB1 HGNC HGNC:2661 protein_coding YES CCDS607.1 ENSP00000360280 O75553 UPI000013EE33 tolerated(0.05) 14/15 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF40 MODERATE 1 SNV 5 1 PASS rs1187002473 . 0 207 3 0 0 0 0 0 -16.22427 1 1 1 1 0 A 3 1 29 57010774 57010774 G A 1 0 0 0 0 1 0 0 0 4018 1203 42 3 3 DAB1 1 57010774 Missense_Mutation SNP G C3L-01924_T 127122 57010774 191945648 20 7890 DOCK7 0 . GRCh38 1 62474045 62474045 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.6116G>T p.Ser2039Ile p.S2039I ENST00000454575 47/49 140 126 14 173 172 1 strelka-varscan-mutect DOCK7,missense_variant,p.Ser2041Ile,ENST00000251157,;DOCK7,missense_variant,p.Ser2039Ile,ENST00000454575,NM_001271999.1;DOCK7,missense_variant,p.Ser2019Ile,ENST00000340370,NM_033407.3;DOCK7,missense_variant,p.Ser2050Ile,ENST00000635253,;DOCK7,missense_variant,p.Ser2010Ile,ENST00000634264,NM_001272000.1;DOCK7,missense_variant,p.Ser2008Ile,ENST00000635123,NM_001272001.1;DOCK7,missense_variant,p.Ser1139Ile,ENST00000637255,;DOCK7,non_coding_transcript_exon_variant,,ENST00000634495,;DOCK7,downstream_gene_variant,,ENST00000637839,;DOCK7,downstream_gene_variant,,ENST00000637487,;DOCK7,downstream_gene_variant,,ENST00000636370,;DOCK7,upstream_gene_variant,,ENST00000637306,;DOCK7,downstream_gene_variant,,ENST00000638042,;DOCK7,non_coding_transcript_exon_variant,,ENST00000635983,;DOCK7,non_coding_transcript_exon_variant,,ENST00000489185,;DOCK7,downstream_gene_variant,,ENST00000467758,;DOCK7,downstream_gene_variant,,ENST00000635088,; A ENST00000454575 Transcript missense_variant 6127/6985 6116/6390 2039/2129 S/I aGt/aTt 1 -1 DOCK7 HGNC HGNC:19190 protein_coding YES CCDS60156.1 ENSP00000413583 Q96N67 H0Y7L2 UPI0000E45660 NM_001271999.1 tolerated(0.1) 47/49 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF78,hmmpanther:PTHR23317,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 62474045 62474045 C A 1 0 0 0 0 1 0 0 0 4507 565 20 2 2 DOCK7 1 62474045 Missense_Mutation SNP C C3L-01924_T 5463271 62474045 186482377 21 7891 LRRC7 0 . GRCh38 1 70039701 70039701 + Missense_Mutation SNP A A T rs770654648 C3L-01924_T C3L-01924_N A A c.3763A>T p.Thr1255Ser p.T1255S ENST00000035383 19/25 139 107 32 221 220 1 strelka-varscan-mutect LRRC7,missense_variant,p.Thr1260Ser,ENST00000310961,;LRRC7,missense_variant,p.Thr1255Ser,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Thr539Ser,ENST00000415775,; T ENST00000035383 Transcript missense_variant 3793/5000 3763/4614 1255/1537 T/S Act/Tct rs770654648 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated(0.33) 19/25 MODERATE 1 SNV 1 1 PASS rs770654648 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 70039701 70039701 A T 1 0 0 0 0 1 0 0 0 8916 391 14 4 4 LRRC7 1 70039701 Missense_Mutation SNP A C3L-01924_T 7565656 70039701 178916721 22 7892 LRRIQ3 0 . GRCh38 1 74182603 74182603 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.508C>T p.Leu170Phe p.L170F ENST00000354431 3/8 134 102 32 165 165 0 strelka-varscan-mutect LRRIQ3,missense_variant,p.Leu170Phe,ENST00000354431,NM_001105659.1;LRRIQ3,missense_variant,p.Leu170Phe,ENST00000395089,;LRRIQ3,missense_variant,p.Leu170Phe,ENST00000370911,;LRRIQ3,intron_variant,,ENST00000370909,;LRRIQ3,intron_variant,,ENST00000444984,;LRRIQ3,non_coding_transcript_exon_variant,,ENST00000495179,;LRRIQ3,missense_variant,p.Leu170Phe,ENST00000415760,;LRRIQ3,non_coding_transcript_exon_variant,,ENST00000463724,; A ENST00000354431 Transcript missense_variant 700/2849 508/1875 170/624 L/F Ctt/Ttt 1 -1 LRRIQ3 HGNC HGNC:28318 protein_coding YES CCDS41350.1 ENSP00000346414 A6PVS8 UPI000155D493 NM_001105659.1 deleterious(0) 3/8 hmmpanther:PTHR24365 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 74182603 74182603 G A 1 0 0 0 0 1 0 0 0 8936 942 33 3 3 LRRIQ3 1 74182603 Missense_Mutation SNP G C3L-01924_T 4142902 74182603 174773819 23 7893 LRRC53 0 . GRCh38 1 74475677 74475677 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1038A>T p.Arg346Ser p.R346S ENST00000294635 4/5 69 65 4 86 86 0 varscan-mutect LRRC53,missense_variant,p.Arg346Ser,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2; A ENST00000294635 Transcript missense_variant 1153/3859 1038/3744 346/1247 R/S agA/agT 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE deleterious(0) 4/5 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -9.660782 1 1 1 1 0 A 3 1 29 74475677 74475677 T A 1 0 0 0 0 1 0 0 0 8905 1780 62 4 4 LRRC53 1 74475677 Missense_Mutation SNP T C3L-01924_T 293074 74475677 174480745 24 7894 ERICH3 0 . GRCh38 1 74641347 74641347 + Missense_Mutation SNP G G T rs755253909 C3L-01924_T C3L-01924_N G G c.428C>A p.Ser143Tyr p.S143Y ENST00000326665 5/15 219 202 17 267 266 1 strelka-varscan-mutect ERICH3,missense_variant,p.Ser143Tyr,ENST00000326665,NM_001002912.4; T ENST00000326665 Transcript missense_variant 647/7159 428/4593 143/1530 S/Y tCc/tAc rs755253909 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0) 5/15 hmmpanther:PTHR23034 MODERATE 1 SNV 5 1 PASS rs755253909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 74641347 74641347 G T 1 0 0 0 0 1 0 0 0 5083 1174 41 2 2 ERICH3 1 74641347 Missense_Mutation SNP G C3L-01924_T 165670 74641347 174315075 25 7895 GBP4 0 . GRCh38 1 89195374 89195374 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.286T>A p.Trp96Arg p.W96R ENST00000355754 3/11 218 192 26 231 231 0 strelka-varscan-mutect GBP4,missense_variant,p.Trp96Arg,ENST00000355754,NM_052941.4; T ENST00000355754 Transcript missense_variant 384/6127 286/1923 96/640 W/R Tgg/Agg 1 -1 GBP4 HGNC HGNC:20480 protein_coding YES CCDS721.1 ENSP00000359490 Q96PP9 UPI000013E1A4 NM_052941.4 deleterious(0.02) 3/11 Gene3D:3.40.50.300,Pfam_domain:PF02263,PROSITE_profiles:PS51715,hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF17,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 89195374 89195374 A T 1 0 0 0 0 1 0 0 0 6146 159 6 4 4 GBP4 1 89195374 Missense_Mutation SNP A C3L-01924_T 14554027 89195374 159761048 26 7896 ABCA4 0 . GRCh38 1 94098970 94098970 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.592C>A p.Leu198Met p.L198M ENST00000370225 6/50 288 247 41 304 304 0 strelka-varscan-mutect ABCA4,missense_variant,p.Leu198Met,ENST00000370225,NM_000350.2; T ENST00000370225 Transcript missense_variant 679/7309 592/6822 198/2273 L/M Ctg/Atg 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 tolerated(0.12) 6/50 TIGRFAM_domain:TIGR01257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 94098970 94098970 G T 1 0 0 0 0 1 0 0 0 38 991 35 2 2 ABCA4 1 94098970 Missense_Mutation SNP G C3L-01924_T 4903596 94098970 154857452 27 7897 AMPD2 0 . GRCh38 1 109621186 109621186 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.173A>G p.Tyr58Cys p.Y58C ENST00000256578 1/18 130 123 7 122 121 1 strelka-varscan-mutect AMPD2,missense_variant,p.Tyr58Cys,ENST00000256578,NM_004037.7;AMPD2,missense_variant,p.Tyr58Cys,ENST00000528667,NM_001257360.1;AMPD2,missense_variant,p.Tyr29Cys,ENST00000369840,;AMPD2,missense_variant,p.Ile27Val,ENST00000358729,NM_001308170.1;AMPD2,intron_variant,,ENST00000342115,NM_139156.3;AMPD2,intron_variant,,ENST00000474459,;AMPD2,intron_variant,,ENST00000531203,;AMPD2,intron_variant,,ENST00000531734,;GNAI3,downstream_gene_variant,,ENST00000369851,NM_006496.3;AMPD2,upstream_gene_variant,,ENST00000393688,NM_203404.1;AMPD2,upstream_gene_variant,,ENST00000528454,NM_001257361.1;AMPD2,upstream_gene_variant,,ENST00000527846,;AMPD2,downstream_gene_variant,,ENST00000469039,;GNAT2,upstream_gene_variant,,ENST00000622865,;AMPD2,intron_variant,,ENST00000526301,;AMPD2,upstream_gene_variant,,ENST00000459643,;AMPD2,missense_variant,p.Tyr12Cys,ENST00000528270,;AMPD2,non_coding_transcript_exon_variant,,ENST00000486282,;AMPD2,upstream_gene_variant,,ENST00000534144,; G ENST00000256578 Transcript missense_variant 533/3899 173/2640 58/879 Y/C tAt/tGt 1 1 AMPD2 HGNC HGNC:469 protein_coding YES CCDS805.1 ENSP00000256578 Q01433 A0A024R098 UPI0000125956 NM_004037.7 deleterious_low_confidence(0.05) 1/18 PIRSF_domain:PIRSF001251,hmmpanther:PTHR11359,hmmpanther:PTHR11359:SF3,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 109621186 109621186 A G 1 0 0 0 0 1 0 0 0 684 449 16 5 5 AMPD2 1 109621186 Missense_Mutation SNP A C3L-01924_T 15522216 109621186 139335236 28 7898 RSBN1 0 . GRCh38 1 113766399 113766399 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.1990C>T p.Arg664Cys p.R664C ENST00000261441 7/7 98 81 17 141 141 0 strelka-varscan-mutect RSBN1,missense_variant,p.Arg664Cys,ENST00000261441,NM_018364.4;RSBN1,missense_variant,p.Arg664Cys,ENST00000612242,;RSBN1,missense_variant,p.Arg547Cys,ENST00000616024,;RSBN1,missense_variant,p.Arg616Cys,ENST00000615321,;RSBN1,non_coding_transcript_exon_variant,,ENST00000369581,;RSBN1,3_prime_UTR_variant,,ENST00000476412,; A ENST00000261441 Transcript missense_variant 2054/6621 1990/2409 664/802 R/C Cgt/Tgt 1 -1 RSBN1 HGNC HGNC:25642 protein_coding YES CCDS862.1 ENSP00000261441 Q5VWQ0 UPI00002263B4 NM_018364.4 deleterious(0) 7/7 hmmpanther:PTHR13354,hmmpanther:PTHR13354:SF8 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 113766399 113766399 G A 1 0 0 0 0 1 0 0 0 13952 1058 37 1 1 RSBN1 1 113766399 Missense_Mutation SNP G C3L-01924_T 4145213 113766399 135190023 29 7899 TRIM33 0 . GRCh38 1 114405733 114405733 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.2445A>G p.= p.T815T ENST00000358465 15/20 107 94 13 143 142 1 strelka-varscan-mutect TRIM33,synonymous_variant,p.=,ENST00000358465,NM_015906.3;TRIM33,synonymous_variant,p.=,ENST00000369543,NM_033020.2;TRIM33,synonymous_variant,p.=,ENST00000448034,;TRIM33,non_coding_transcript_exon_variant,,ENST00000476908,; C ENST00000358465 Transcript synonymous_variant 2529/8339 2445/3384 815/1127 T acA/acG 1 -1 TRIM33 HGNC HGNC:16290 protein_coding YES CCDS872.1 ENSP00000351250 Q9UPN9 UPI000013D8CD NM_015906.3 15/20 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 114405733 114405733 T C 1 0 0 0 0 0 0 0 1 16996 1683 59 5 5 TRIM33 1 114405733 Silent SNP T C3L-01924_T 639334 114405733 134550689 30 7900 PPIAL4D 0 . GRCh38 1 145241858 145241858 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.267C>A p.= p.I89I ENST00000544708 1/1 182 145 37 181 181 0 strelka-varscan-mutect PPIAL4D,synonymous_variant,p.=,ENST00000544708,NM_001164261.1; T ENST00000544708 Transcript synonymous_variant 267/495 267/495 89/164 I atC/atA 1 -1 PPIAL4D HGNC HGNC:33998 protein_coding YES CCDS59199.1 ENSP00000439444 F5H284 UPI000016003C NM_001164261.1 1/1 PROSITE_profiles:PS50072,hmmpanther:PTHR11071,hmmpanther:PTHR11071:SF281,Gene3D:2.40.100.10,PIRSF_domain:PIRSF001467,Pfam_domain:PF00160,Superfamily_domains:SSF50891 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 145241858 145241858 G T 1 0 0 0 0 0 0 0 1 12428 1164 41 2 2 PPIAL4D 1 145241858 Silent SNP G C3L-01924_T 30836125 145241858 103714564 31 7901 SF3B4 0 . GRCh38 1 149925924 149925924 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.825C>T p.= p.P275P ENST00000271628 4/6 51 27 24 46 46 0 strelka-varscan-mutect SF3B4,synonymous_variant,p.=,ENST00000271628,NM_005850.4;MTMR11,downstream_gene_variant,,ENST00000439741,NM_001145862.1;MTMR11,downstream_gene_variant,,ENST00000369140,NM_181873.3;SF3B4,downstream_gene_variant,,ENST00000457312,;MTMR11,downstream_gene_variant,,ENST00000492824,;MTMR11,downstream_gene_variant,,ENST00000482025,;MTMR11,downstream_gene_variant,,ENST00000466496,;MTMR11,downstream_gene_variant,,ENST00000490310,;MTMR11,downstream_gene_variant,,ENST00000495054,;MTMR11,downstream_gene_variant,,ENST00000482343,; A ENST00000271628 Transcript synonymous_variant 1410/2085 825/1275 275/424 P ccC/ccT 1 -1 SF3B4 HGNC HGNC:10771 protein_coding YES CCDS72900.1 ENSP00000271628 Q15427 UPI0000135472 NM_005850.4 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF449 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 149925924 149925924 G A 1 0 0 0 0 0 0 0 1 14431 1219 43 3 3 SF3B4 1 149925924 Silent SNP G C3L-01924_T 4684066 149925924 99030498 32 7902 VPS72 0 . GRCh38 1 151185579 151185579 + Silent SNP C C A rs752210930 C3L-01924_T C3L-01924_N C C c.312G>T p.= p.P104P ENST00000354473 3/6 386 297 89 301 298 3 strelka-varscan-mutect VPS72,synonymous_variant,p.=,ENST00000368892,NM_001271088.1,NM_005997.2;VPS72,synonymous_variant,p.=,ENST00000354473,NM_001271087.1;VPS72,non_coding_transcript_exon_variant,,ENST00000496809,;VPS72,non_coding_transcript_exon_variant,,ENST00000463470,;VPS72,non_coding_transcript_exon_variant,,ENST00000491094,;VPS72,non_coding_transcript_exon_variant,,ENST00000471423,; A ENST00000354473 Transcript synonymous_variant 349/1347 312/1128 104/375 P ccG/ccT rs752210930,COSM3965797,COSM4740589 1 -1 VPS72 HGNC HGNC:11644 protein_coding YES CCDS59201.1 ENSP00000346464 Q15906 UPI0000204210 NM_001271087.1 3/6 hmmpanther:PTHR13275,Pfam_domain:PF05764 0,1,1 LOW 1 SNV 3 0,1,1 1 PASS rs752210930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 151185579 151185579 C A 1 0 0 0 0 0 0 0 1 17765 639 23 1 1 VPS72 1 151185579 Silent SNP C C3L-01924_T 1259655 151185579 97770843 33 7903 FLG 0 . GRCh38 1 152304568 152304569 + Frame_Shift_Ins INS - - C novel C3L-01924_T C3L-01924_N - - c.10317dupG p.Ser3440ValfsTer17 p.S3440Vfs*17 ENST00000368799 3/3 549 425 124 474 473 1 sindel-varindel-pindel FLG,frameshift_variant,p.Ser3440ValfsTer17,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENST00000368799 Transcript frameshift_variant 10353-10354/12747 10317-10318/12186 3439-3440/4061 -/X -/G 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 HIGH 1 insertion 1 1 PASS . . 0 202 0 0 0 8 0 0 -2.621455 0.01555754 1 1 0 0 C 7 5 29 152304568 152304568 - C 1 0 1 1 0 0 0 0 0 5784 275 10 0 0 FLG 1 152304568 Frame_Shift_Ins INS - C3L-01924_T 1118989 152304568 96651854 34 7904 SNAPIN 0 . GRCh38 1 153659531 153659531 + Missense_Mutation SNP G G C rs376802072 C3L-01924_T C3L-01924_N G G c.274G>C p.Val92Leu p.V92L ENST00000368685 3/4 319 220 99 248 248 0 strelka-varscan-mutect SNAPIN,missense_variant,p.Val92Leu,ENST00000368685,NM_012437.5;ILF2,downstream_gene_variant,,ENST00000615950,NM_001267809.1;ILF2,downstream_gene_variant,,ENST00000361891,NM_004515.3;SNAPIN,non_coding_transcript_exon_variant,,ENST00000478558,;SNAPIN,non_coding_transcript_exon_variant,,ENST00000462880,;SNAPIN,non_coding_transcript_exon_variant,,ENST00000474959,;ILF2,downstream_gene_variant,,ENST00000480213,; C ENST00000368685 Transcript missense_variant 364/1030 274/411 92/136 V/L Gtt/Ctt rs376802072,COSM4444223 1 1 SNAPIN HGNC HGNC:17145 protein_coding YES CCDS1049.1 ENSP00000357674 O95295 UPI000003E7DC NM_012437.5 deleterious(0.04) 3/4 hmmpanther:PTHR31305,PIRSF_domain:PIRSF037631,Pfam_domain:PF14712,Coiled-coils_(Ncoils):Coil 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs376802072 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 153659531 153659531 G C 1 0 0 0 0 1 0 0 0 15160 1145 40 4 4 SNAPIN 1 153659531 Missense_Mutation SNP G C3L-01924_T 1354963 153659531 95296891 35 7905 KIRREL 0 . GRCh38 1 158091553 158091553 + Silent SNP C C A C3L-01924_T C3L-01924_N C C c.1468C>A p.= p.R490R ENST00000359209 11/15 201 143 58 172 172 0 strelka-varscan-mutect KIRREL,synonymous_variant,p.=,ENST00000368173,NM_001286349.1;KIRREL,synonymous_variant,p.=,ENST00000368172,;KIRREL,synonymous_variant,p.=,ENST00000360089,;KIRREL,synonymous_variant,p.=,ENST00000359209,NM_018240.6; A ENST00000359209 Transcript synonymous_variant 1535/2874 1468/2274 490/757 R Cga/Aga COSM1212529,COSM1212530,COSM1212531 1 1 KIRREL HGNC HGNC:15734 protein_coding YES CCDS1172.2 ENSP00000352138 Q96J84 UPI0000443FBD NM_018240.6 11/15 Gene3D:2.60.40.10,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF14,SMART_domains:SM00409 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 158091553 158091553 C A 1 0 0 0 0 0 0 0 1 8188 782 27 1 1 KIRREL 1 158091553 Silent SNP C C3L-01924_T 4432022 158091553 90864869 36 7906 CD1C 0 . GRCh38 1 158292660 158292660 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.675T>C p.= p.C225C ENST00000368170 4/6 224 167 57 208 208 0 strelka-varscan-mutect CD1C,synonymous_variant,p.=,ENST00000368170,NM_001765.2;CD1C,synonymous_variant,p.=,ENST00000443761,; C ENST00000368170 Transcript synonymous_variant 954/1435 675/1002 225/333 C tgT/tgC 1 1 CD1C HGNC HGNC:1636 protein_coding YES CCDS1175.1 ENSP00000357152 P29017 UPI000013DF78 NM_001765.2 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 158292660 158292660 T C 1 0 0 0 0 0 0 0 1 2679 1673 58 5 5 CD1C 1 158292660 Silent SNP T C3L-01924_T 201107 158292660 90663762 37 7907 OR10Z1 0 . GRCh38 1 158606763 158606763 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.325T>A p.Cys109Ser p.C109S ENST00000361284 1/1 332 270 62 348 348 0 strelka-varscan-mutect OR10Z1,missense_variant,p.Cys109Ser,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000485680,; A ENST00000361284 Transcript missense_variant 325/942 325/942 109/313 C/S Tgt/Agt 1 1 OR10Z1 HGNC HGNC:14996 protein_coding YES CCDS30901.1 ENSP00000354707 Q8NGY1 A0A126GV63 UPI000004CA23 NM_001004478.1 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs1159672050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 158606763 158606763 T A 1 0 0 0 0 1 0 0 0 10999 1580 55 4 4 OR10Z1 1 158606763 Missense_Mutation SNP T C3L-01924_T 314103 158606763 90349659 38 7908 SPTA1 0 . GRCh38 1 158626858 158626858 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.5814T>G p.Asp1938Glu p.D1938E ENST00000368147 41/52 471 354 117 421 419 2 strelka-varscan-mutect SPTA1,missense_variant,p.Asp1938Glu,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,; C ENST00000368147 Transcript missense_variant 5995/7999 5814/7260 1938/2419 D/E gaT/gaG 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.05) 41/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 158626858 158626858 A C 1 0 0 0 0 1 0 0 0 15472 214 8 5 5 SPTA1 1 158626858 Missense_Mutation SNP A C3L-01924_T 20095 158626858 90329564 39 7909 PEX19 0 . GRCh38 1 160279576 160279576 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.875G>C p.Ser292Thr p.S292T ENST00000368072 8/8 475 355 120 379 379 0 strelka-varscan-mutect PEX19,missense_variant,p.Ser292Thr,ENST00000368072,NM_002857.3,NM_001193644.1;PEX19,3_prime_UTR_variant,,ENST00000495624,;RP11-574F21.3,intron_variant,,ENST00000556710,;RP11-574F21.3,intron_variant,,ENST00000485079,;PEX19,downstream_gene_variant,,ENST00000392220,;PEX19,non_coding_transcript_exon_variant,,ENST00000532508,;PEX19,intron_variant,,ENST00000467711,;PEX19,downstream_gene_variant,,ENST00000533699,;PEX19,downstream_gene_variant,,ENST00000533104,;PEX19,3_prime_UTR_variant,,ENST00000472750,;PEX19,3_prime_UTR_variant,,ENST00000462644,;PEX19,3_prime_UTR_variant,,ENST00000532643,;PEX19,downstream_gene_variant,,ENST00000532516,;PEX19,downstream_gene_variant,,ENST00000524939,; G ENST00000368072 Transcript missense_variant 897/3661 875/900 292/299 S/T aGt/aCt 1 -1 PEX19 HGNC HGNC:9713 protein_coding YES CCDS1201.1 ENSP00000357051 P40855 A0A0S2Z497 UPI0000132BAD NM_002857.3,NM_001193644.1 tolerated(0.19) 8/8 hmmpanther:PTHR12774,Pfam_domain:PF04614 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 160279576 160279576 C G 1 0 0 0 0 1 0 0 0 11834 565 20 4 4 PEX19 1 160279576 Missense_Mutation SNP C C3L-01924_T 1652718 160279576 88676846 40 7910 COPA 0 . GRCh38 1 160290631 160290631 + Missense_Mutation SNP T T C rs757736121 C3L-01924_T C3L-01924_N T T c.3503A>G p.Asn1168Ser p.N1168S ENST00000368069 32/33 251 186 65 218 218 0 strelka-varscan-mutect COPA,missense_variant,p.Asn1159Ser,ENST00000241704,NM_004371.3;COPA,missense_variant,p.Asn1168Ser,ENST00000368069,NM_001098398.1;PEX19,upstream_gene_variant,,ENST00000533699,;COPA,downstream_gene_variant,,ENST00000545284,; C ENST00000368069 Transcript missense_variant 3581/4664 3503/3702 1168/1233 N/S aAt/aGt rs757736121 1 -1 COPA HGNC HGNC:2230 protein_coding YES CCDS41424.1 ENSP00000357048 P53621 UPI0000074301 NM_001098398.1 tolerated(0.37) 32/33 hmmpanther:PTHR19876,PIRSF_domain:PIRSF003354,Pfam_domain:PF06957 MODERATE 1 SNV 1 1 PASS rs757736121 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 160290631 160290631 T C 1 0 0 0 0 1 0 0 0 3519 1493 52 5 5 COPA 1 160290631 Missense_Mutation SNP T C3L-01924_T 11055 160290631 88665791 41 7911 ITLN2 0 . GRCh38 1 160947977 160947977 + Silent SNP G G T rs750602994 C3L-01924_T C3L-01924_N G G c.777C>A p.= p.A259A ENST00000368029 7/8 267 216 51 252 251 1 strelka-varscan-mutect ITLN2,synonymous_variant,p.=,ENST00000368029,NM_080878.2;RP11-544M22.1,intron_variant,,ENST00000356006,;ITLN2,non_coding_transcript_exon_variant,,ENST00000494442,;ITLN2,downstream_gene_variant,,ENST00000490489,; T ENST00000368029 Transcript synonymous_variant 835/1151 777/978 259/325 A gcC/gcA rs750602994 1 -1 ITLN2 HGNC HGNC:20599 protein_coding YES CCDS1212.1 ENSP00000357008 Q8WWU7 UPI0000048F3E NM_080878.2 7/8 hmmpanther:PTHR16146:SF21,hmmpanther:PTHR16146 LOW 1 SNV 1 1 PASS rs750602994 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 160947977 160947977 G T 1 0 0 0 0 0 0 0 1 7817 1335 47 2 2 ITLN2 1 160947977 Silent SNP G C3L-01924_T 657346 160947977 88008445 42 7912 LMX1A 0 . GRCh38 1 165249447 165249447 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.457G>T p.Glu153Ter p.E153* ENST00000342310 4/9 247 194 53 224 224 0 strelka-varscan-mutect LMX1A,stop_gained,p.Glu153Ter,ENST00000342310,NM_177398.3;LMX1A,stop_gained,p.Glu153Ter,ENST00000294816,NM_001174069.1;LMX1A,stop_gained,p.Glu153Ter,ENST00000367893,; A ENST00000342310 Transcript stop_gained 840/3545 457/1149 153/382 E/* Gag/Tag 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 4/9 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 165249447 165249447 C A 1 0 0 0 0 0 1 0 0 8788 864 30 2 2 LMX1A 1 165249447 Nonsense_Mutation SNP C C3L-01924_T 4301470 165249447 83706975 43 7913 DUSP27 0 . GRCh38 1 167126717 167126717 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1586C>A p.Ser529Tyr p.S529Y ENST00000361200 6/6 280 259 21 258 258 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ser529Tyr,ENST00000361200,;DUSP27,missense_variant,p.Ser529Tyr,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ser529Tyr,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; A ENST00000361200 Transcript missense_variant 1752/4164 1586/3477 529/1158 S/Y tCc/tAc COSM5530261 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 6/6 1 MODERATE 1 SNV 5 1 1 PASS rs1021409386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 167126717 167126717 C A 1 0 0 0 0 1 0 0 0 4646 855 30 2 2 DUSP27 1 167126717 Missense_Mutation SNP C C3L-01924_T 1877270 167126717 81829705 44 7914 RGS18 0 . GRCh38 1 192160385 192160385 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.229C>A p.Pro77Thr p.P77T ENST00000367460 3/5 161 124 37 164 163 1 strelka-varscan-mutect RGS18,missense_variant,p.Pro77Thr,ENST00000367460,NM_130782.2;RGS18,non_coding_transcript_exon_variant,,ENST00000481707,;RGS18,non_coding_transcript_exon_variant,,ENST00000492967,;RGS18,non_coding_transcript_exon_variant,,ENST00000491030,; A ENST00000367460 Transcript missense_variant 410/2150 229/708 77/235 P/T Cct/Act 1 1 RGS18 HGNC HGNC:14261 protein_coding YES CCDS1374.1 ENSP00000356430 Q9NS28 UPI0000044571 NM_130782.2 tolerated(0.12) 3/5 hmmpanther:PTHR10845:SF155,hmmpanther:PTHR10845,Gene3D:1.10.196.10,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 192160385 192160385 C A 1 0 0 0 0 1 0 0 0 13471 623 22 2 2 RGS18 1 192160385 Missense_Mutation SNP C C3L-01924_T 25033668 192160385 56796037 45 7915 KCNT2 0 . GRCh38 1 196489899 196489899 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.214C>T p.= p.L72L ENST00000294725 3/28 159 142 17 168 168 0 strelka-varscan-mutect KCNT2,synonymous_variant,p.=,ENST00000367433,NM_001287819.1;KCNT2,synonymous_variant,p.=,ENST00000294725,NM_198503.3;KCNT2,synonymous_variant,p.=,ENST00000609185,NM_001287820.1;KCNT2,5_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; A ENST00000294725 Transcript synonymous_variant 1130/4409 214/3408 72/1135 L Cta/Tta 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 3/28 Gene3D:1.10.287.70,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 196489899 196489899 G A 1 0 0 0 0 0 0 0 1 8008 1020 36 3 3 KCNT2 1 196489899 Silent SNP G C3L-01924_T 4329514 196489899 52466523 46 7916 CFH 0 . GRCh38 1 196728393 196728393 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2284G>A p.Glu762Lys p.E762K ENST00000367429 15/22 170 134 36 164 164 0 strelka-varscan-mutect CFH,missense_variant,p.Glu762Lys,ENST00000367429,NM_000186.3;CFH,non_coding_transcript_exon_variant,,ENST00000466229,; A ENST00000367429 Transcript missense_variant 2524/4127 2284/3696 762/1231 E/K Gag/Aag 1 1 CFH HGNC HGNC:4883 protein_coding YES CCDS1385.1 ENSP00000356399 P08603 A0A024R962 UPI000013C4D1 NM_000186.3 tolerated(0.11) 15/22 PROSITE_profiles:PS50923,SMART_domains:SM00032 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 196728393 196728393 G A 1 0 0 0 0 1 0 0 0 3041 1291 45 3 3 CFH 1 196728393 Missense_Mutation SNP G C3L-01924_T 238494 196728393 52228029 47 7917 ASPM 0 . GRCh38 1 197105040 197105040 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.4211G>T p.Trp1404Leu p.W1404L ENST00000367409 18/28 64 43 21 58 58 0 strelka-varscan-mutect ASPM,missense_variant,p.Trp1404Leu,ENST00000367409,NM_018136.4;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000612785,;ASPM,intron_variant,,ENST00000367408,; A ENST00000367409 Transcript missense_variant 4468/10887 4211/10434 1404/3477 W/L tGg/tTg 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.58) 18/28 Pfam_domain:PF00612,PROSITE_profiles:PS50096,SMART_domains:SM00015 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 29 197105040 197105040 C A 1 0 0 0 0 1 0 0 0 1203 595 21 2 2 ASPM 1 197105040 Missense_Mutation SNP C C3L-01924_T 376647 197105040 51851382 48 7918 IGFN1 0 . GRCh38 1 201208726 201208726 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.3833G>A p.Gly1278Glu p.G1278E ENST00000335211 12/24 192 181 11 186 185 1 strelka-varscan-mutect IGFN1,missense_variant,p.Gly1278Glu,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,;IGFN1,downstream_gene_variant,,ENST00000444705,; A ENST00000335211 Transcript missense_variant 3963/11810 3833/11127 1278/3708 G/E gGg/gAg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 tolerated(0.05) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 201208726 201208726 G A 1 0 0 0 0 1 0 0 0 7497 1232 43 3 3 IGFN1 1 201208726 Missense_Mutation SNP G C3L-01924_T 4103686 201208726 47747696 49 7919 LAD1 0 . GRCh38 1 201386523 201386523 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.838G>T p.Ala280Ser p.A280S ENST00000391967 3/10 56 40 16 84 84 0 strelka-varscan-mutect LAD1,missense_variant,p.Ala280Ser,ENST00000391967,NM_005558.3;LAD1,missense_variant,p.Ala294Ser,ENST00000367313,;LAD1,downstream_gene_variant,,ENST00000633953,;LAD1,upstream_gene_variant,,ENST00000503578,;LAD1,downstream_gene_variant,,ENST00000632743,;LAD1,downstream_gene_variant,,ENST00000631576,;LAD1,upstream_gene_variant,,ENST00000488842,;LAD1,upstream_gene_variant,,ENST00000475136,; A ENST00000391967 Transcript missense_variant 1140/2906 838/1554 280/517 A/S Gcc/Tcc COSM1290086 1 -1 LAD1 HGNC HGNC:6472 protein_coding YES CCDS1410.1 ENSP00000375829 O00515 UPI000006CD59 NM_005558.3 tolerated(0.15) 3/10 hmmpanther:PTHR12392,PIRSF_domain:PIRSF038144 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999952 1 1 1 0 A 3 1 29 201386523 201386523 C A 1 0 0 0 0 1 0 0 0 8503 739 26 2 2 LAD1 1 201386523 Missense_Mutation SNP C C3L-01924_T 177797 201386523 47569899 50 7920 ELK4 0 . GRCh38 1 205620168 205620168 + Missense_Mutation SNP G G A rs191743893 C3L-01924_T C3L-01924_N G G c.878C>T p.Pro293Leu p.P293L ENST00000357992 3/5 362 272 90 339 338 1 strelka-varscan-mutect ELK4,missense_variant,p.Pro293Leu,ENST00000357992,NM_001973.3;ELK4,missense_variant,p.Pro293Leu,ENST00000289703,NM_021795.2;ELK4,downstream_gene_variant,,ENST00000468523,;ELK4,missense_variant,p.Pro293Leu,ENST00000616704,; A ENST00000357992 Transcript missense_variant 1218/10239 878/1296 293/431 P/L cCa/cTa rs191743893 1 -1 ELK4 HGNC HGNC:3326 protein_coding YES CCDS1456.1 ENSP00000350681 P28324 A0A024R9C2 UPI0000129E67 NM_001973.3 deleterious(0.02) 3/5 MODERATE 1 SNV 1 1 PASS rs191743893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 205620168 205620168 G A 1 0 0 0 0 1 0 0 0 4895 1348 47 3 3 ELK4 1 205620168 Missense_Mutation SNP G C3L-01924_T 4233645 205620168 43336254 51 7921 DIEXF 0 . GRCh38 1 209838972 209838972 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1126C>A p.Leu376Ile p.L376I ENST00000491415 7/12 370 350 20 326 326 0 strelka-varscan-mutect DIEXF,missense_variant,p.Leu376Ile,ENST00000491415,NM_014388.6;DIEXF,missense_variant,p.Leu57Ile,ENST00000457820,; A ENST00000491415 Transcript missense_variant 1183/8446 1126/2271 376/756 L/I Ctc/Atc 1 1 DIEXF HGNC HGNC:28440 protein_coding YES CCDS1493.1 ENSP00000419005 Q68CQ4 UPI000006D987 NM_014388.6 deleterious(0.03) 7/12 Gene3D:3.40.50.300,Pfam_domain:PF06862,hmmpanther:PTHR12933,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 209838972 209838972 C A 1 0 0 0 0 1 0 0 0 4327 681 24 2 2 DIEXF 1 209838972 Missense_Mutation SNP C C3L-01924_T 4218804 209838972 39117450 52 7922 USH2A 0 . GRCh38 1 215782866 215782866 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.10457T>A p.Leu3486His p.L3486H ENST00000307340 53/72 223 198 25 243 243 0 strelka-varscan-mutect USH2A,missense_variant,p.Leu3486His,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 10844/18883 10457/15609 3486/5202 L/H cTc/cAc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.18) 53/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 215782866 215782866 A T 1 0 0 0 0 1 0 0 0 17570 304 11 4 4 USH2A 1 215782866 Missense_Mutation SNP A C3L-01924_T 5943894 215782866 33173556 53 7923 GPATCH2 0 . GRCh38 1 217449252 217449252 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1363G>T p.Ala455Ser p.A455S ENST00000366935 9/10 250 185 65 218 217 1 strelka-varscan-mutect GPATCH2,missense_variant,p.Ala455Ser,ENST00000366935,NM_018040.3; A ENST00000366935 Transcript missense_variant 1474/5851 1363/1587 455/528 A/S Gca/Tca 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 tolerated(0.47) 9/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4 MODERATE 1 SNV 2 1 PASS rs771425837 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 217449252 217449252 C A 1 0 0 0 0 1 0 0 0 6491 724 25 2 2 GPATCH2 1 217449252 Missense_Mutation SNP C C3L-01924_T 1666386 217449252 31507170 54 7924 RRP15 0 . GRCh38 1 218330983 218330983 + Silent SNP G G T rs763400227 C3L-01924_T C3L-01924_N G G c.741G>T p.= p.T247T ENST00000366932 5/5 240 206 34 200 200 0 strelka-varscan-mutect RRP15,synonymous_variant,p.=,ENST00000366932,NM_016052.3; T ENST00000366932 Transcript synonymous_variant 771/7771 741/849 247/282 T acG/acT rs763400227,COSM267364 1 1 RRP15 HGNC HGNC:24255 protein_coding YES CCDS1520.2 ENSP00000355899 Q9Y3B9 UPI0000205BC1 NM_016052.3 5/5 hmmpanther:PTHR13245 0,1 LOW 1 SNV 1 0,1 1 PASS rs763400227 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 218330983 218330983 G T 1 0 0 0 0 0 0 0 1 13942 1045 37 1 1 RRP15 1 218330983 Silent SNP G C3L-01924_T 881731 218330983 30625439 55 7925 ZC3H11B 0 . GRCh38 1 219611899 219611899 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.164T>A p.Met55Lys p.M55K ENST00000636126 2/2 184 168 16 169 169 0 varscan-mutect ZC3H11B,missense_variant,p.Met55Lys,ENST00000636126,;ZC3H11B,missense_variant,p.Met55Lys,ENST00000367211,; T ENST00000636126 Transcript missense_variant 880/4432 164/2418 55/805 M/K aTg/aAg 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C deleterious(0) 2/2 Pfam_domain:PF15663,PROSITE_profiles:PS50103,hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2,SMART_domains:SM00356 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 219611899 219611899 A T 1 0 0 0 0 1 0 0 0 18135 217 8 4 4 ZC3H11B 1 219611899 Missense_Mutation SNP A C3L-01924_T 1280916 219611899 29344523 56 7926 SLC30A10 0 . GRCh38 1 219915512 219915512 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1395C>G p.Asp465Glu p.D465E ENST00000366926 4/4 212 194 18 222 222 0 strelka-varscan-mutect SLC30A10,missense_variant,p.Asp465Glu,ENST00000366926,NM_018713.2;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484079,;SLC30A10,intron_variant,,ENST00000484239,;SLC30A10,3_prime_UTR_variant,,ENST00000356609,; C ENST00000366926 Transcript missense_variant 1557/1915 1395/1458 465/485 D/E gaC/gaG 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 tolerated(0.3) 4/4 MODERATE 1 SNV 1 1 PASS rs1358458562 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 219915512 219915512 G C 1 0 0 0 0 1 0 0 0 14824 1252 44 4 4 SLC30A10 1 219915512 Missense_Mutation SNP G C3L-01924_T 303613 219915512 29040910 57 7927 MARK1 0 . GRCh38 1 220635879 220635879 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1323G>T p.Gln441His p.Q441H ENST00000611084 13/18 187 135 52 138 138 0 strelka-varscan-mutect MARK1,missense_variant,p.Gln441His,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Gln441His,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Gln419His,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Gln441His,ENST00000366917,NM_018650.4; T ENST00000611084 Transcript missense_variant 1963/5321 1323/2391 441/796 Q/H caG/caT 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 tolerated(0.14) 13/18 hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 220635879 220635879 G T 1 0 0 0 0 1 0 0 0 9237 991 35 2 2 MARK1 1 220635879 Missense_Mutation SNP G C3L-01924_T 720367 220635879 28320543 58 7928 TLR5 0 . GRCh38 1 223111849 223111849 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1183G>A p.Ala395Thr p.A395T ENST00000540964 4/4 206 190 16 272 272 0 strelka-varscan-mutect TLR5,missense_variant,p.Ala395Thr,ENST00000540964,;TLR5,missense_variant,p.Ala395Thr,ENST00000366881,NM_003268.5;TLR5,downstream_gene_variant,,ENST00000407096,; T ENST00000540964 Transcript missense_variant 1645/4088 1183/2577 395/858 A/T Gct/Act 1 -1 TLR5 HGNC HGNC:11851 protein_coding YES CCDS31033.1 ENSP00000440643 O60602 UPI000013E1D3 deleterious(0) 4/4 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF311,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 223111849 223111849 C T 1 0 0 0 0 1 0 0 0 16400 710 25 3 3 TLR5 1 223111849 Missense_Mutation SNP C C3L-01924_T 2475970 223111849 25844573 59 7929 LIN9 0 . GRCh38 1 226233143 226233143 + Silent SNP T T G novel C3L-01924_T C3L-01924_N T T c.1524A>C p.= p.T508T ENST00000328205 14/15 184 162 22 161 161 0 strelka-varscan-mutect LIN9,synonymous_variant,p.=,ENST00000328205,NM_173083.3;LIN9,synonymous_variant,p.=,ENST00000366808,NM_001270410.1;LIN9,synonymous_variant,p.=,ENST00000460719,NM_001270409.1;LIN9,synonymous_variant,p.=,ENST00000481685,; G ENST00000328205 Transcript synonymous_variant 2070/3567 1524/1677 508/558 T acA/acC 1 -1 LIN9 HGNC HGNC:30830 protein_coding YES CCDS1553.1 ENSP00000329102 Q5TKA1 UPI00001B2F3C NM_173083.3 14/15 hmmpanther:PTHR21689 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 226233143 226233143 T G 1 0 0 0 0 0 0 0 1 8721 1567 55 5 5 LIN9 1 226233143 Silent SNP T C3L-01924_T 3121294 226233143 22723279 60 7930 RYR2 0 . GRCh38 1 237511695 237511695 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.2726A>G p.Asp909Gly p.D909G ENST00000366574 24/105 151 140 11 129 129 0 strelka-varscan-mutect RYR2,missense_variant,p.Asp909Gly,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp893Gly,ENST00000360064,; G ENST00000366574 Transcript missense_variant 3043/16562 2726/14904 909/4967 D/G gAt/gGt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 24/105 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 237511695 237511695 A G 1 0 0 0 0 1 0 0 0 14029 333 12 5 5 RYR2 1 237511695 Missense_Mutation SNP A C3L-01924_T 11278552 237511695 11444727 61 7931 WDR64 0 . GRCh38 1 241796308 241796308 + Nonsense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.3100C>T p.Gln1034Ter p.Q1034* ENST00000366552 26/27 194 175 19 196 196 0 strelka-varscan-mutect WDR64,stop_gained,p.Gln1034Ter,ENST00000366552,NM_144625.4;WDR64,stop_gained,p.Gln587Ter,ENST00000437684,;WDR64,stop_gained,p.Gln638Ter,ENST00000414635,;WDR64,stop_gained,p.Gln513Ter,ENST00000425826,;WDR64,downstream_gene_variant,,ENST00000472717,; T ENST00000366552 Transcript stop_gained 3307/4371 3100/3246 1034/1081 Q/* Caa/Taa 1 1 WDR64 HGNC HGNC:26570 protein_coding YES ENSP00000355510 B1ANS9 UPI0000519142 NM_144625.4 26/27 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 241796308 241796308 C T 1 0 0 0 0 0 1 0 0 17874 595 21 3 3 WDR64 1 241796308 Nonsense_Mutation SNP C C3L-01924_T 4284613 241796308 7160114 62 7932 EXO1 0 . GRCh38 1 241853399 241853399 + Missense_Mutation SNP G G C rs147687027 C3L-01924_T C3L-01924_N G G c.323G>C p.Arg108Pro p.R108P ENST00000366548 6/16 360 285 75 341 341 0 strelka-varscan-mutect EXO1,missense_variant,p.Arg108Pro,ENST00000366548,NM_130398.3;EXO1,missense_variant,p.Arg108Pro,ENST00000348581,NM_001319224.1,NM_006027.4;EXO1,missense_variant,p.Arg108Pro,ENST00000518483,NM_003686.4;EXO1,missense_variant,p.Arg68Pro,ENST00000423131,;EXO1,missense_variant,p.Arg68Pro,ENST00000523590,;EXO1,missense_variant,p.Arg108Pro,ENST00000450748,;EXO1,missense_variant,p.Arg68Pro,ENST00000437497,;EXO1,downstream_gene_variant,,ENST00000519225,;EXO1,non_coding_transcript_exon_variant,,ENST00000493702,;EXO1,intron_variant,,ENST00000469419,; C ENST00000366548 Transcript missense_variant 916/3473 323/2541 108/846 R/P cGt/cCt rs147687027 1 1 EXO1 HGNC HGNC:3511 protein_coding YES CCDS1620.1 ENSP00000355506 Q9UQ84 UPI000013DDA8 NM_130398.3 deleterious(0) 6/16 hmmpanther:PTHR11081:SF8,hmmpanther:PTHR11081,Gene3D:3.40.50.1010,Superfamily_domains:SSF88723 MODERATE 1 SNV 1 1 PASS rs147687027 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 241853399 241853399 G C 1 0 0 0 0 1 0 0 0 5167 1145 40 4 4 EXO1 1 241853399 Missense_Mutation SNP G C3L-01924_T 57091 241853399 7103023 63 7933 OR2AK2 0 . GRCh38 1 247965794 247965794 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.463A>T p.Ile155Phe p.I155F ENST00000366480 1/1 60 47 13 88 88 0 strelka-varscan-mutect OR2AK2,missense_variant,p.Ile155Phe,ENST00000366480,NM_001004491.1; T ENST00000366480 Transcript missense_variant 562/1107 463/1008 155/335 I/F Atc/Ttc 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 247965794 247965794 A T 1 0 0 0 0 1 0 0 0 11064 333 12 4 4 OR2AK2 1 247965794 Missense_Mutation SNP A C3L-01924_T 6112395 247965794 990628 64 7934 OR2L2 0 . GRCh38 1 248038418 248038418 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.151G>T p.Asp51Tyr p.D51Y ENST00000366479 1/1 321 274 47 327 326 1 strelka-varscan-mutect OR2L2,missense_variant,p.Asp51Tyr,ENST00000366479,NM_001004686.2; T ENST00000366479 Transcript missense_variant 151/939 151/939 51/312 D/Y Gac/Tac COSM534322 1 1 OR2L2 HGNC HGNC:8266 protein_coding YES CCDS31103.1 ENSP00000355435 Q8NH16 A0A126GW34 UPI0000061EAA NM_001004686.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF189,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 205 0 2 2 0 0 0 -19.95684 0.9842929 1 1 1 0 T 3 4 29 248038418 248038418 G T 1 0 0 0 0 1 0 0 0 11085 1174 41 2 2 OR2L2 1 248038418 Missense_Mutation SNP G C3L-01924_T 72624 248038418 918004 65 7935 OR2M5 0 . GRCh38 1 248145879 248145879 + Missense_Mutation SNP C C A rs760262593 C3L-01924_T C3L-01924_N C C c.732C>A p.His244Gln p.H244Q ENST00000366476 1/1 318 293 25 366 366 0 varscan-mutect OR2M5,missense_variant,p.His244Gln,ENST00000366476,NM_001004690.1; A ENST00000366476 Transcript missense_variant 732/939 732/939 244/312 H/Q caC/caA rs760262593,COSM1502265 1 1 OR2M5 HGNC HGNC:19576 protein_coding YES CCDS31105.1 ENSP00000355432 A3KFT3 UPI00001612E2 NM_001004690.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs1320736496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 248145879 248145879 C A 1 0 0 0 0 1 0 0 0 11091 506 18 2 2 OR2M5 1 248145879 Missense_Mutation SNP C C3L-01924_T 107461 248145879 810543 66 7936 OR2T33 0 . GRCh38 1 248273274 248273274 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.541G>T p.Val181Leu p.V181L ENST00000318021 1/1 257 243 14 299 299 0 varscan-mutect OR2T33,missense_variant,p.Val181Leu,ENST00000318021,NM_001004695.1; A ENST00000318021 Transcript missense_variant 541/963 541/963 181/320 V/L Gtg/Ttg 1 -1 OR2T33 HGNC HGNC:31255 protein_coding YES CCDS31109.1 ENSP00000324687 Q8NG76 UPI000004B237 NM_001004695.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs919264329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 248273274 248273274 C A 1 0 0 0 0 1 0 0 0 11101 536 19 1 1 OR2T33 1 248273274 Missense_Mutation SNP C C3L-01924_T 127395 248273274 683148 67 7937 ALLC 0 . GRCh38 2 3702429 3702429 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1042G>T p.Ala348Ser p.A348S ENST00000252505 12/12 183 131 52 192 191 1 strelka-varscan-mutect ALLC,missense_variant,p.Ala348Ser,ENST00000252505,NM_018436.3;DCDC2C,upstream_gene_variant,,ENST00000399143,NM_001287444.1;DCDC2C,upstream_gene_variant,,ENST00000423741,;AC010907.5,downstream_gene_variant,,ENST00000441632,;ALLC,non_coding_transcript_exon_variant,,ENST00000471711,;ALLC,non_coding_transcript_exon_variant,,ENST00000476389,; T ENST00000252505 Transcript missense_variant 1204/1446 1042/1176 348/391 A/S Gcc/Tcc 1 1 ALLC HGNC HGNC:17377 protein_coding YES CCDS46223.1 ENSP00000252505 B4DY77 UPI000050BBEF NM_018436.3 deleterious(0) 12/12 hmmpanther:PTHR12045,TIGRFAM_domain:TIGR02961,PIRSF_domain:PIRSF016516,Pfam_domain:PF03561,Gene3D:2.60.120.260,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999982 1 1 1 0 T 3 4 29 3702429 3702429 G T 1 0 0 0 0 1 0 0 0 634 1087 38 1 1 ALLC 2 3702429 Missense_Mutation SNP G C3L-01924_T 3702429 238491100 68 7938 NOL10 0 . GRCh38 2 10682063 10682063 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.119G>T p.Arg40Leu p.R40L ENST00000381685 3/21 63 56 7 69 68 1 strelka-varscan-mutect NOL10,missense_variant,p.Arg40Leu,ENST00000538384,NM_001261392.1;NOL10,missense_variant,p.Arg40Leu,ENST00000345985,NM_001261394.1;NOL10,missense_variant,p.Arg40Leu,ENST00000381685,NM_024894.3;NOL10,non_coding_transcript_exon_variant,,ENST00000473087,; A ENST00000381685 Transcript missense_variant 225/2589 119/2067 40/688 R/L cGt/cTt 1 -1 NOL10 HGNC HGNC:25862 protein_coding YES CCDS1673.2 ENSP00000371101 Q9BSC4 UPI000006F6E2 NM_024894.3 deleterious(0.01) 3/21 hmmpanther:PTHR14927,hmmpanther:PTHR14927:SF0 MODERATE 1 SNV 1 1 PASS rs1356857139 . 0 202 8 0 0 0 0 0 -15.7947 0.9999964 1 1 1 0 A 3 1 29 10682063 10682063 C A 1 0 0 0 0 1 0 0 0 10563 536 19 1 1 NOL10 2 10682063 Missense_Mutation SNP C C3L-01924_T 6979634 10682063 231511466 69 7939 MYCN 0 . GRCh38 2 15945648 15945648 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.946A>G p.Ser316Gly p.S316G ENST00000281043 3/3 223 168 55 220 220 0 strelka-varscan-mutect MYCN,missense_variant,p.Ser316Gly,ENST00000281043,NM_001293233.1,NM_001293228.1,NM_005378.5;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000448719,; G ENST00000281043 Transcript missense_variant 1243/2602 946/1395 316/464 S/G Agc/Ggc 1 1 MYCN HGNC HGNC:7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 UPI000012FAF8 NM_001293233.1,NM_001293228.1,NM_005378.5 tolerated(0.48) 3/3 Pfam_domain:PF01056,PIRSF_domain:PIRSF001705,hmmpanther:PTHR11514,hmmpanther:PTHR11514:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 15945648 15945648 A G 1 0 0 0 0 1 0 0 0 10021 188 7 5 5 MYCN 2 15945648 Missense_Mutation SNP A C3L-01924_T 5263585 15945648 226247881 70 7940 GAREM2 0 . GRCh38 2 26182494 26182494 + Splice_Site SNP G G T novel C3L-01924_T C3L-01924_N G G c.22+1G>T p.X8_splice ENST00000407684 137 99 38 134 133 1 strelka-varscan-mutect GAREM2,splice_donor_variant,,ENST00000407684,NM_001191033.1;GAREM2,intron_variant,,ENST00000401533,NM_001168241.1;GAREM2,upstream_gene_variant,,ENST00000496070,; T ENST00000407684 Transcript splice_donor_variant -/5138 22/1995 8/664 1 1 GAREM2 HGNC HGNC:27172 protein_coding CCDS54337.1 ENSP00000384581 Q75VX8 UPI00001C1DD0 NM_001191033.1 1/5 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 29 26182494 26182494 G T 1 0 0 0 0 0 0 1 0 6110 1275 44 2 2 GAREM2 2 26182494 Splice_Site SNP G C3L-01924_T 10236846 26182494 216011035 71 7941 MAP4K3 0 . GRCh38 2 39343442 39343442 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.256C>T p.Leu86Phe p.L86F ENST00000263881 4/34 194 171 23 206 206 0 strelka-varscan-mutect MAP4K3,missense_variant,p.Leu86Phe,ENST00000263881,NM_003618.3;MAP4K3,missense_variant,p.Leu86Phe,ENST00000341681,NM_001270425.1;MAP4K3,missense_variant,p.Leu23Phe,ENST00000437545,;MAP4K3,missense_variant,p.Leu86Phe,ENST00000429397,;MAP4K3,3_prime_UTR_variant,,ENST00000437968,; A ENST00000263881 Transcript missense_variant 581/4362 256/2685 86/894 L/F Ctt/Ttt 1 -1 MAP4K3 HGNC HGNC:6865 protein_coding YES CCDS1803.1 ENSP00000263881 Q8IVH8 UPI00000747E6 NM_003618.3 deleterious(0) 4/34 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF205,PIRSF_domain:PIRSF038172,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 39343442 39343442 G A 1 0 0 0 0 1 0 0 0 9185 971 34 3 3 MAP4K3 2 39343442 Missense_Mutation SNP G C3L-01924_T 13160948 39343442 202850087 72 7942 SLC8A1 0 . GRCh38 2 40429154 40429154 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.1127delG p.Gly376AlafsTer4 p.G376Afs*4 ENST00000403092 2/11 80 60 20 124 124 0 sindel-varindel-pindel SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000406785,;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000403092,;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000405901,NM_001112800.1;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000402441,NM_001112802.1;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000405269,;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000332839,NM_021097.2;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,frameshift_variant,p.Gly376AlafsTer4,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,frameshift_variant,p.Gly373AlafsTer4,ENST00000407929,; - ENST00000403092 Transcript frameshift_variant 1161/3178 1127/2922 376/973 G/X gGc/gc 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 2/11 Pfam_domain:PF16494,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 40429154 40429154 C - 1 0 1 0 1 0 0 0 0 14989 739 26 0 0 SLC8A1 2 40429154 Frame_Shift_Del DEL C C3L-01924_T 1085712 40429154 201764375 73 7943 SIX3 0 . GRCh38 2 44942208 44942208 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.104G>A p.Gly35Glu p.G35E ENST00000260653 1/2 111 89 22 97 97 0 strelka-varscan-mutect SIX3,missense_variant,p.Gly35Glu,ENST00000260653,NM_005413.3;RP11-89K21.1,upstream_gene_variant,,ENST00000437916,;SIX3-AS1,upstream_gene_variant,,ENST00000419364,;RP11-89K21.1,upstream_gene_variant,,ENST00000444871,;SIX3-AS1,upstream_gene_variant,,ENST00000456467,;Six3os1_5,downstream_gene_variant,,ENST00000611000,;Six3os1_7,downstream_gene_variant,,ENST00000621512,;Six3os1_6,downstream_gene_variant,,ENST00000620790,; A ENST00000260653 Transcript missense_variant 311/2523 104/999 35/332 G/E gGg/gAg 1 1 SIX3 HGNC HGNC:10889 protein_coding YES CCDS1821.1 ENSP00000260653 O95343 UPI00001359C4 NM_005413.3 tolerated_low_confidence(0.53) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10390:SF31,hmmpanther:PTHR10390 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 44942208 44942208 G A 1 0 0 0 0 1 0 0 0 14611 1232 43 3 3 SIX3 2 44942208 Missense_Mutation SNP G C3L-01924_T 4513054 44942208 197251321 74 7944 BCL11A 0 . GRCh38 2 60462014 60462014 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.898G>T p.Val300Leu p.V300L ENST00000335712 4/4 81 62 19 111 111 0 strelka-varscan-mutect BCL11A,missense_variant,p.Val300Leu,ENST00000335712,NM_022893.3;BCL11A,missense_variant,p.Val300Leu,ENST00000356842,NM_018014.3;BCL11A,missense_variant,p.Val266Leu,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,intron_variant,,ENST00000631857,; A ENST00000335712 Transcript missense_variant 1126/5942 898/2508 300/835 V/L Gtg/Ttg 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 tolerated(0.07) 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 60462014 60462014 C A 1 0 0 0 0 1 0 0 0 1510 507 18 2 2 BCL11A 2 60462014 Missense_Mutation SNP C C3L-01924_T 15519806 60462014 181731515 75 7945 LRRTM4 0 . GRCh38 2 77518918 77518918 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.951G>T p.= p.R317R ENST00000409093 3/4 144 136 8 196 195 1 strelka-varscan-mutect LRRTM4,synonymous_variant,p.=,ENST00000409088,NM_024993.4;LRRTM4,synonymous_variant,p.=,ENST00000409911,;LRRTM4,synonymous_variant,p.=,ENST00000409282,NM_001282928.1;LRRTM4,synonymous_variant,p.=,ENST00000409093,NM_001282924.1;LRRTM4,synonymous_variant,p.=,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; A ENST00000409093 Transcript synonymous_variant 1288/2247 951/1773 317/590 R cgG/cgT 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 77518918 77518918 C A 1 0 0 0 0 0 0 0 1 8948 842 30 2 2 LRRTM4 2 77518918 Silent SNP C C3L-01924_T 17056904 77518918 164674611 76 7946 REG3A 0 . GRCh38 2 79158759 79158759 + Silent SNP G G T C3L-01924_T C3L-01924_N G G c.87C>A p.= p.P29P ENST00000393878 2/5 118 81 37 154 154 0 strelka-varscan-mutect REG3A,synonymous_variant,p.=,ENST00000393878,NM_138938.2;REG3A,synonymous_variant,p.=,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,synonymous_variant,p.=,ENST00000305165,;AC011754.1,intron_variant,,ENST00000415201,;REG3A,non_coding_transcript_exon_variant,,ENST00000490901,;REG3A,downstream_gene_variant,,ENST00000464746,; T ENST00000393878 Transcript synonymous_variant 435/1095 87/528 29/175 P ccC/ccA COSM1752681 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 2/5 hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 79158759 79158759 G T 1 0 0 0 0 0 0 0 1 13382 1219 43 2 2 REG3A 2 79158759 Silent SNP G C3L-01924_T 1639841 79158759 163034770 77 7947 RGPD1 0 . GRCh38 2 86986896 86986896 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.3973T>A p.Leu1325Ile p.L1325I ENST00000559485 20/23 141 106 35 146 146 0 strelka-varscan-mutect RGPD1,missense_variant,p.Leu1325Ile,ENST00000559485,NM_001024457.3;RGPD1,missense_variant,p.Leu1325Ile,ENST00000409776,;RGPD1,missense_variant,p.Leu1333Ile,ENST00000398193,;RGPD1,3_prime_UTR_variant,,ENST00000428128,; A ENST00000559485 Transcript missense_variant 3989/6697 3973/5247 1325/1748 L/I Tta/Ata 1 1 RGPD1 HGNC HGNC:32414 protein_coding YES CCDS46358.2 ENSP00000453170 P0DJD0 UPI00018815D1 NM_001024457.3 deleterious(0) 20/23 Low_complexity_(Seg):seg,PROSITE_profiles:PS50196,hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138,SMART_domains:SM00160,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 86986896 86986896 T A 1 0 0 0 0 1 0 0 0 13457 1838 64 4 4 RGPD1 2 86986896 Missense_Mutation SNP T C3L-01924_T 7828137 86986896 155206633 78 7948 ASTL 0 . GRCh38 2 96123890 96123890 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1256G>A p.Cys419Tyr p.C419Y ENST00000342380 9/9 138 111 27 163 163 0 strelka-varscan-mutect ASTL,missense_variant,p.Cys419Tyr,ENST00000342380,NM_001002036.3; T ENST00000342380 Transcript missense_variant 1256/1296 1256/1296 419/431 C/Y tGt/tAt 1 -1 ASTL HGNC HGNC:31704 protein_coding YES CCDS33249.1 ENSP00000343674 Q6HA08 UPI0000161978 NM_001002036.3 tolerated_low_confidence(1) 9/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 96123890 96123890 C T 1 0 0 0 0 1 0 0 0 1210 478 17 3 3 ASTL 2 96123890 Missense_Mutation SNP C C3L-01924_T 9136994 96123890 146069639 79 7949 IL1R1 0 . GRCh38 2 102168662 102168662 + Missense_Mutation SNP G G T rs758499965 C3L-01924_T C3L-01924_N G G c.720G>T p.Leu240Phe p.L240F ENST00000410023 7/12 139 124 15 132 132 0 varscan-mutect IL1R1,missense_variant,p.Leu240Phe,ENST00000410023,NM_001320978.1,NM_001320980.1,NM_001320981.1,NM_001320982.1,NM_001320983.1,NM_000877.3;IL1R1,missense_variant,p.Leu240Phe,ENST00000424272,;IL1R1,missense_variant,p.Leu240Phe,ENST00000409329,;IL1R1,missense_variant,p.Leu240Phe,ENST00000409929,NM_001288706.1;IL1R1,missense_variant,p.Leu240Phe,ENST00000409288,;IL1R1,missense_variant,p.Leu96Phe,ENST00000428279,;IL1R1,intron_variant,,ENST00000409589,;IL1R1,downstream_gene_variant,,ENST00000430171,;IL1R1,downstream_gene_variant,,ENST00000452403,;IL1R1,downstream_gene_variant,,ENST00000442590,;IL1R1,downstream_gene_variant,,ENST00000450319,;AC007271.3,downstream_gene_variant,,ENST00000428188,;IL1R1,splice_region_variant,,ENST00000413623,;IL1R1,splice_region_variant,,ENST00000422532,; T ENST00000410023 Transcript missense_variant,splice_region_variant 1038/5143 720/1710 240/569 L/F ttG/ttT rs758499965 1 1 IL1R1 HGNC HGNC:5993 protein_coding YES CCDS2055.1 ENSP00000386380 P14778 UPI0000034759 NM_001320978.1,NM_001320980.1,NM_001320981.1,NM_001320982.1,NM_001320983.1,NM_000877.3 deleterious(0.04) 7/12 Gene3D:2.60.40.10,Prints_domain:PR01536,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF26,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs758499965 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 102168662 102168662 G T 1 0 0 0 0 1 0 0 0 7561 1362 47 2 2 IL1R1 2 102168662 Missense_Mutation SNP G C3L-01924_T 6044772 102168662 140024867 80 7950 ST6GAL2 0 . GRCh38 2 106843327 106843327 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.651G>T p.= p.L217L ENST00000409382 2/6 207 164 43 214 214 0 strelka-varscan-mutect ST6GAL2,synonymous_variant,p.=,ENST00000409382,NM_001142351.1;ST6GAL2,synonymous_variant,p.=,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,synonymous_variant,p.=,ENST00000409087,NM_001142352.1;ST6GAL2,downstream_gene_variant,,ENST00000419159,;AC016994.2,downstream_gene_variant,,ENST00000425419,; A ENST00000409382 Transcript synonymous_variant 1262/7275 651/1590 217/529 L ctG/ctT 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 2/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713 LOW 1 SNV 1 1 PASS rs998584220 . 0 208 0 0 2 0 0 0 -20 0.9982862 1 1 1 0 A 2 1 29 106843327 106843327 C A 1 0 0 0 0 0 0 0 1 15600 813 29 2 2 ST6GAL2 2 106843327 Silent SNP C C3L-01924_T 4674665 106843327 135350202 81 7951 ANAPC1 0 . GRCh38 2 111821443 111821443 + Nonsense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.3002C>G p.Ser1001Ter p.S1001* ENST00000341068 26/48 164 152 12 206 206 0 varscan-mutect ANAPC1,stop_gained,p.Ser1001Ter,ENST00000341068,NM_022662.3;ANAPC1,stop_gained,p.Ser536Ter,ENST00000427997,;ANAPC1,non_coding_transcript_exon_variant,,ENST00000485325,; C ENST00000341068 Transcript stop_gained 3775/8262 3002/5835 1001/1944 S/* tCa/tGa 1 -1 ANAPC1 HGNC HGNC:19988 protein_coding YES CCDS2093.1 ENSP00000339109 Q9H1A4 UPI000006EC6E NM_022662.3 26/48 hmmpanther:PTHR12827 HIGH 1 SNV 1 1 PASS rs1267218406 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 29 111821443 111821443 G C 1 0 0 0 0 0 1 0 0 695 1294 45 4 4 ANAPC1 2 111821443 Nonsense_Mutation SNP G C3L-01924_T 4978116 111821443 130372086 82 7952 UGGT1 0 . GRCh38 2 128182178 128182178 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.4132G>C p.Ala1378Pro p.A1378P ENST00000259253 37/41 153 118 35 201 201 0 strelka-varscan-mutect UGGT1,missense_variant,p.Ala1378Pro,ENST00000259253,NM_020120.3;UGGT1,intron_variant,,ENST00000418197,;UGGT1,3_prime_UTR_variant,,ENST00000376723,; C ENST00000259253 Transcript missense_variant 4179/10650 4132/4668 1378/1555 A/P Gct/Cct 1 1 UGGT1 HGNC HGNC:15663 protein_coding YES CCDS2154.1 ENSP00000259253 Q9NYU2 UPI00000707D8 NM_020120.3 deleterious(0) 37/41 Gene3D:3.90.550.10,hmmpanther:PTHR11226,hmmpanther:PTHR11226:SF3,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 128182178 128182178 G C 1 0 0 0 0 1 0 0 0 17466 1319 46 4 4 UGGT1 2 128182178 Missense_Mutation SNP G C3L-01924_T 16360735 128182178 114011351 83 7953 AMER3 0 . GRCh38 2 130764570 130764570 + Missense_Mutation SNP G G T rs752266201 C3L-01924_T C3L-01924_N G G c.2498G>T p.Arg833Leu p.R833L ENST00000423981 2/2 166 144 22 203 203 0 strelka-varscan-mutect AMER3,missense_variant,p.Arg833Leu,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Arg833Leu,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; T ENST00000423981 Transcript missense_variant 2608/6172 2498/2586 833/861 R/L cGc/cTc rs752266201 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 tolerated(0.6) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 MODERATE 1 SNV 4 1 PASS rs752266201 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 29 130764570 130764570 G T 1 0 0 0 0 1 0 0 0 669 1087 38 1 1 AMER3 2 130764570 Missense_Mutation SNP G C3L-01924_T 2582392 130764570 111428959 84 7954 POTEE 0 . GRCh38 2 131263729 131263729 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.2274C>A p.= p.A758A ENST00000356920 15/15 182 143 39 241 240 1 strelka-varscan-mutect POTEE,synonymous_variant,p.=,ENST00000356920,NM_001083538.1;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000613282,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; A ENST00000356920 Transcript synonymous_variant 2610/4159 2274/3228 758/1075 A gcC/gcA 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 15/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 131263729 131263729 C A 1 0 0 0 0 0 0 0 1 12378 610 22 2 2 POTEE 2 131263729 Silent SNP C C3L-01924_T 499159 131263729 110929800 85 7955 THSD7B 0 . GRCh38 2 137656875 137656875 + Silent SNP G G T rs755829942 C3L-01924_T C3L-01924_N G G c.4191G>T p.= p.V1397V ENST00000272643 22/27 182 130 52 186 186 0 strelka-varscan-mutect THSD7B,synonymous_variant,p.=,ENST00000409968,NM_001316349.1;THSD7B,synonymous_variant,p.=,ENST00000272643,;THSD7B,synonymous_variant,p.=,ENST00000413152,NM_001080427.1;THSD7B,downstream_gene_variant,,ENST00000480352,; T ENST00000272643 Transcript synonymous_variant 4191/5939 4191/4827 1397/1608 V gtG/gtT rs755829942 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A 22/27 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 5 1 PASS rs755829942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 137656875 137656875 G T 1 0 0 0 0 0 0 0 1 16314 1335 47 2 2 THSD7B 2 137656875 Silent SNP G C3L-01924_T 6393146 137656875 104536654 86 7956 LRP1B 0 . GRCh38 2 140334537 140334537 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.12139G>T p.Gly4047Trp p.G4047W ENST00000389484 79/91 82 60 22 115 115 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gly4047Trp,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Gly279Trp,ENST00000437977,; A ENST00000389484 Transcript missense_variant 13111/16535 12139/13800 4047/4599 G/W Ggg/Tgg 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 79/91 PROSITE_profiles:PS51120,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 140334537 140334537 C A 1 0 0 0 0 1 0 0 0 8850 594 21 2 2 LRP1B 2 140334537 Missense_Mutation SNP C C3L-01924_T 2677662 140334537 101858992 87 7957 KCNH7 0 . GRCh38 2 162446240 162446240 + Nonsense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.1332T>A p.Cys444Ter p.C444* ENST00000332142 7/16 281 208 73 363 363 0 strelka-varscan-mutect KCNH7,stop_gained,p.Cys444Ter,ENST00000332142,NM_033272.3;KCNH7,stop_gained,p.Cys344Ter,ENST00000618399,;KCNH7,stop_gained,p.Cys437Ter,ENST00000328032,NM_173162.2;KCNH7,stop_gained,p.Cys335Ter,ENST00000621889,; T ENST00000332142 Transcript stop_gained 1432/4113 1332/3591 444/1196 C/* tgT/tgA 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 7/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 HIGH 1 SNV 1 1 PASS rs1469001235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 162446240 162446240 A T 1 0 0 0 0 0 1 0 0 7953 157 6 4 4 KCNH7 2 162446240 Nonsense_Mutation SNP A C3L-01924_T 22111703 162446240 79747289 88 7958 SCN3A 0 . GRCh38 2 165131348 165131348 + Missense_Mutation SNP G G T rs367827161 C3L-01924_T C3L-01924_N G G c.2461C>A p.Gln821Lys p.Q821K ENST00000283254 16/28 295 280 15 331 331 0 strelka-varscan-mutect SCN3A,missense_variant,p.Gln821Lys,ENST00000360093,;SCN3A,missense_variant,p.Gln821Lys,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Gln772Lys,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Gln772Lys,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000628085,;SCN3A,upstream_gene_variant,,ENST00000484898,; T ENST00000283254 Transcript missense_variant 2929/9091 2461/6003 821/2000 Q/K Caa/Aaa rs367827161 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 16/28 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs367827161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 165131348 165131348 G T 1 0 0 0 0 1 0 0 0 14187 1357 47 2 2 SCN3A 2 165131348 Missense_Mutation SNP G C3L-01924_T 2685108 165131348 77062181 89 7959 CSRNP3 0 . GRCh38 2 165679189 165679189 + Silent SNP C C G novel C3L-01924_T C3L-01924_N C C c.1194C>G p.= p.G398G ENST00000314499 7/7 160 145 15 242 242 0 strelka-varscan-mutect CSRNP3,synonymous_variant,p.=,ENST00000314499,NM_001172173.1;CSRNP3,synonymous_variant,p.=,ENST00000342316,NM_024969.3;CSRNP3,synonymous_variant,p.=,ENST00000409420,;CSRNP3,synonymous_variant,p.=,ENST00000421875,;CSRNP3,downstream_gene_variant,,ENST00000409664,; G ENST00000314499 Transcript synonymous_variant 1570/11788 1194/1758 398/585 G ggC/ggG 1 1 CSRNP3 HGNC HGNC:30729 protein_coding YES CCDS2225.1 ENSP00000318258 Q8WYN3 UPI0000136882 NM_001172173.1 7/7 hmmpanther:PTHR13580,hmmpanther:PTHR13580:SF13 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 165679189 165679189 C G 1 0 0 0 0 0 0 0 1 3766 697 25 4 4 CSRNP3 2 165679189 Silent SNP C C3L-01924_T 547841 165679189 76514340 90 7960 SCN7A 0 . GRCh38 2 166465882 166465882 + Missense_Mutation SNP C C A rs560243693 C3L-01924_T C3L-01924_N C C c.770G>T p.Gly257Val p.G257V ENST00000409855 7/25 278 206 72 330 329 1 strelka-varscan-mutect SCN7A,missense_variant,p.Gly257Val,ENST00000619410,;SCN7A,missense_variant,p.Gly257Val,ENST00000621965,;SCN7A,missense_variant,p.Gly257Val,ENST00000409855,NM_002976.3;SCN7A,missense_variant,p.Gly257Val,ENST00000419992,;SCN7A,missense_variant,p.Gly257Val,ENST00000441411,;SCN7A,missense_variant,p.Gly257Val,ENST00000424326,;SCN7A,upstream_gene_variant,,ENST00000497562,; A ENST00000409855 Transcript missense_variant 897/7183 770/5049 257/1682 G/V gGg/gTg rs560243693 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0) 7/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs560243693 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 166465882 166465882 C A 1 0 0 0 0 1 0 0 0 14192 623 22 2 2 SCN7A 2 166465882 Missense_Mutation SNP C C3L-01924_T 786693 166465882 75727647 91 7961 XIRP2 0 . GRCh38 2 167246534 167246534 + Silent SNP A A G novel C3L-01924_T C3L-01924_N A A c.5142A>G p.= p.K1714K ENST00000409195 9/11 135 116 19 193 193 0 strelka-varscan-mutect XIRP2,synonymous_variant,p.=,ENST00000409195,NM_152381.5;XIRP2,synonymous_variant,p.=,ENST00000409273,NM_001199144.1;XIRP2,synonymous_variant,p.=,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; G ENST00000409195 Transcript synonymous_variant 5231/12675 5142/10650 1714/3549 K aaA/aaG 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 167246534 167246534 A G 1 0 0 0 0 0 0 0 1 17989 40 2 5 5 XIRP2 2 167246534 Silent SNP A C3L-01924_T 780652 167246534 74946995 92 7962 DYNC1I2 0 . GRCh38 2 171725638 171725638 + Missense_Mutation SNP G G T rs372723362 C3L-01924_T C3L-01924_N G G c.532G>T p.Val178Leu p.V178L ENST00000397119 8/18 97 74 23 135 135 0 strelka-varscan-mutect DYNC1I2,missense_variant,p.Val178Leu,ENST00000397119,NM_001378.2;DYNC1I2,missense_variant,p.Val152Leu,ENST00000340296,NM_001271788.1;DYNC1I2,missense_variant,p.Val178Leu,ENST00000409773,NM_001271785.1;DYNC1I2,missense_variant,p.Val152Leu,ENST00000409197,NM_001271789.1;DYNC1I2,missense_variant,p.Val178Leu,ENST00000409453,;DYNC1I2,missense_variant,p.Val152Leu,ENST00000508530,NM_001271790.1;DYNC1I2,missense_variant,p.Val172Leu,ENST00000409317,;DYNC1I2,missense_variant,p.Val170Leu,ENST00000410079,NM_001271786.1,NM_001271787.1;DYNC1I2,missense_variant,p.Val152Leu,ENST00000435234,;DYNC1I2,missense_variant,p.Val172Leu,ENST00000452242,;DYNC1I2,missense_variant,p.Val190Leu,ENST00000438879,;DYNC1I2,missense_variant,p.Val170Leu,ENST00000456808,;DYNC1I2,missense_variant,p.Val152Leu,ENST00000425485,;DYNC1I2,missense_variant,p.Val170Leu,ENST00000423910,;DYNC1I2,missense_variant,p.Val172Leu,ENST00000422646,;DYNC1I2,missense_variant,p.Met121Ile,ENST00000445378,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000482454,;DYNC1I2,non_coding_transcript_exon_variant,,ENST00000470286,;DYNC1I2,upstream_gene_variant,,ENST00000479806,; T ENST00000397119 Transcript missense_variant 699/2604 532/1917 178/638 V/L Gta/Tta rs372723362 1 1 DYNC1I2 HGNC HGNC:2964 protein_coding YES CCDS46450.1 ENSP00000380308 Q13409 A0A140VKE9 UPI0000129A05 NM_001378.2 tolerated(0.73) 8/18 hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF36 MODERATE 1 SNV 2 1 PASS rs372723362 . 0 201 7 2 0 0 0 0 -20 0.999936 1 1 1 0 T 3 4 29 171725638 171725638 G T 1 0 0 0 0 1 0 0 0 4667 1377 48 2 2 DYNC1I2 2 171725638 Missense_Mutation SNP G C3L-01924_T 4479104 171725638 70467891 93 7963 TTC30A 0 . GRCh38 2 177618156 177618156 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.546G>T p.Gln182His p.Q182H ENST00000355689 1/1 328 240 88 339 339 0 strelka-varscan-mutect TTC30A,missense_variant,p.Gln182His,ENST00000355689,NM_152275.3;AC073834.3,intron_variant,,ENST00000357045,; A ENST00000355689 Transcript missense_variant 811/5975 546/1998 182/665 Q/H caG/caT 1 -1 TTC30A HGNC HGNC:25853 protein_coding YES CCDS2276.1 ENSP00000347915 Q86WT1 UPI0000209161 NM_152275.3 tolerated(0.12) 1/1 PROSITE_profiles:PS50293,hmmpanther:PTHR20931:SF3,hmmpanther:PTHR20931,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452,Superfamily_domains:SSF48452 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 177618156 177618156 C A 1 0 0 0 0 1 0 0 0 17207 680 24 2 2 TTC30A 2 177618156 Missense_Mutation SNP C C3L-01924_T 5892518 177618156 64575373 94 7964 TTN 0 . GRCh38 2 178615706 178615706 + Missense_Mutation SNP C C G rs397517593 C3L-01924_T C3L-01924_N C C c.48395G>C p.Arg16132Pro p.R16132P ENST00000589042 258/363 229 215 14 304 304 0 strelka-varscan-mutect TTN,missense_variant,p.Arg16132Pro,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Arg14491Pro,ENST00000591111,;TTN,missense_variant,p.Arg14491Pro,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Arg13564Pro,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Arg7067Pro,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Arg7259Pro,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Arg7192Pro,ENST00000359218,NM_133432.3;RP11-171I2.4,upstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000627527,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,upstream_gene_variant,,ENST00000604956,;TTN-AS1,downstream_gene_variant,,ENST00000589234,;TTN-AS1,downstream_gene_variant,,ENST00000610290,; G ENST00000589042 Transcript missense_variant 48620/109224 48395/107976 16132/35991 R/P cGt/cCt rs397517593,COSM1402937,COSM1402938,COSM1402939,COSM1402940,COSM5287272,COSM5287273,COSM5287274,COSM5287275 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 258/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 uncertain_significance 0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1,1,1,1,1 1 PASS rs397517593 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 178615706 178615706 C G 1 0 0 0 0 1 0 0 0 17245 536 19 4 4 TTN 2 178615706 Missense_Mutation SNP C C3L-01924_T 997550 178615706 63577823 95 7965 ZNF804A 0 . GRCh38 2 184937423 184937423 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2027C>A p.Thr676Lys p.T676K ENST00000302277 4/4 105 88 17 164 164 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Thr676Lys,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Thr591Lys,ENST00000613975,; A ENST00000302277 Transcript missense_variant 2621/4690 2027/3630 676/1209 T/K aCa/aAa 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.09) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 1 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 184937423 184937423 C A 1 0 0 0 0 1 0 0 0 18755 478 17 2 2 ZNF804A 2 184937423 Missense_Mutation SNP C C3L-01924_T 6321717 184937423 57256106 96 7966 ZNF804A 0 . GRCh38 2 184937718 184937718 + Missense_Mutation SNP A A T rs751143229 C3L-01924_T C3L-01924_N A A c.2322A>T p.Gln774His p.Q774H ENST00000302277 4/4 170 156 14 225 225 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Gln774His,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Gln689His,ENST00000613975,; T ENST00000302277 Transcript missense_variant 2916/4690 2322/3630 774/1209 Q/H caA/caT rs751143229 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 deleterious(0.04) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS rs751143229 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 184937718 184937718 A T 1 0 0 0 0 1 0 0 0 18755 40 2 4 4 ZNF804A 2 184937718 Missense_Mutation SNP A C3L-01924_T 295 184937718 57255811 97 7967 ZNF804A 0 . GRCh38 2 184938430 184938430 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.3034G>A p.Val1012Ile p.V1012I ENST00000302277 4/4 185 139 46 243 243 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Val1012Ile,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Val927Ile,ENST00000613975,; A ENST00000302277 Transcript missense_variant 3628/4690 3034/3630 1012/1209 V/I Gtc/Atc 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.28) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS rs1487864350 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 184938430 184938430 G A 1 0 0 0 0 1 0 0 0 18755 1377 48 3 3 ZNF804A 2 184938430 Missense_Mutation SNP G C3L-01924_T 712 184938430 57255099 98 7968 FSIP2 0 . GRCh38 2 185796312 185796312 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.9443A>C p.Asn3148Thr p.N3148T ENST00000343098 16/23 145 123 22 193 193 0 strelka-varscan-mutect FSIP2,missense_variant,p.Asn3148Thr,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Asn3059Thr,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,missense_variant,p.Asn566Thr,ENST00000415915,; C ENST00000343098 Transcript missense_variant 9443/21054 9443/20991 3148/6996 N/T aAt/aCt 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 tolerated(0.06) 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 185796312 185796312 A C 1 0 0 0 0 1 0 0 0 5949 101 4 5 5 FSIP2 2 185796312 Missense_Mutation SNP A C3L-01924_T 857882 185796312 56397217 99 7969 CALCRL 0 . GRCh38 2 187360679 187360679 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.700G>T p.Gly234Cys p.G234C ENST00000409998 11/16 160 142 18 170 170 0 strelka-varscan-mutect CALCRL,missense_variant,p.Gly234Cys,ENST00000409998,;CALCRL,missense_variant,p.Gly234Cys,ENST00000392370,NM_005795.5;CALCRL,missense_variant,p.Gly234Cys,ENST00000410068,NM_001271751.1;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; A ENST00000409998 Transcript missense_variant 1482/5223 700/1386 234/461 G/C Ggc/Tgc 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF deleterious(0) 11/16 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF67,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 187360679 187360679 C A 1 0 0 0 0 1 0 0 0 2270 681 24 2 2 CALCRL 2 187360679 Missense_Mutation SNP C C3L-01924_T 1564367 187360679 54832850 100 7970 COL3A1 0 . GRCh38 2 188997385 188997385 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1865C>A p.Pro622His p.P622H ENST00000304636 26/51 291 263 28 374 371 3 strelka-mutect COL3A1,missense_variant,p.Pro622His,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Pro622His,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000450867,;COL3A1,downstream_gene_variant,,ENST00000637672,; A ENST00000304636 Transcript missense_variant 2035/5543 1865/4401 622/1466 P/H cCt/cAt COSM4473659,COSM4473660 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0) 26/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 188997385 188997385 C A 1 0 0 0 0 1 0 0 0 3477 695 24 2 2 COL3A1 2 188997385 Missense_Mutation SNP C C3L-01924_T 1636706 188997385 53196144 101 7971 SGO2 0 . GRCh38 2 200573899 200573899 + Nonsense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.3553C>T p.Gln1185Ter p.Q1185* ENST00000357799 7/9 85 77 8 124 124 0 strelka-mutect SGO2,stop_gained,p.Gln1185Ter,ENST00000357799,NM_001160046.1,NM_001160033.1,NM_152524.5;SGO2,downstream_gene_variant,,ENST00000409203,; T ENST00000357799 Transcript stop_gained 3651/4214 3553/3798 1185/1265 Q/* Caa/Taa 1 1 SGO2 HGNC HGNC:30812 protein_coding YES CCDS42796.1 ENSP00000350447 Q562F6 UPI00001AEBF5 NM_001160046.1,NM_001160033.1,NM_152524.5 7/9 hmmpanther:PTHR21577,hmmpanther:PTHR21577:SF5 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -17.08711 1 1 1 1 0 T 4 4 29 200573899 200573899 C T 1 0 0 0 0 0 1 0 0 14475 827 29 3 3 SGO2 2 200573899 Nonsense_Mutation SNP C C3L-01924_T 11576514 200573899 41619630 102 7972 MAP2 0 . GRCh38 2 209693260 209693260 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1090G>C p.Asp364His p.D364H ENST00000360351 7/15 171 134 37 193 193 0 strelka-varscan-mutect MAP2,missense_variant,p.Asp364His,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Asp360His,ENST00000447185,;MAP2,missense_variant,p.Asp446His,ENST00000445941,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; C ENST00000360351 Transcript missense_variant 1596/9711 1090/5484 364/1827 D/H Gat/Cat 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 209693260 209693260 G C 1 0 0 0 0 1 0 0 0 9157 942 33 4 4 MAP2 2 209693260 Missense_Mutation SNP G C3L-01924_T 9119361 209693260 32500269 103 7973 UNC80 0 . GRCh38 2 209995362 209995362 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.9544G>C p.Glu3182Gln p.E3182Q ENST00000439458 64/64 183 160 23 246 246 0 strelka-varscan-mutect UNC80,missense_variant,p.Glu3182Gln,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Glu3158Gln,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,; C ENST00000439458 Transcript missense_variant 9624/13562 9544/9777 3182/3258 E/Q Gag/Cag 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 tolerated_low_confidence(0.15) 64/64 Low_complexity_(Seg):seg,hmmpanther:PTHR31781:SF1,hmmpanther:PTHR31781 MODERATE 1 SNV 5 1 PASS rs1400301227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 209995362 209995362 G C 1 0 0 0 0 1 0 0 0 17521 1175 41 4 4 UNC80 2 209995362 Missense_Mutation SNP G C3L-01924_T 302102 209995362 32198167 104 7974 TNS1 0 . GRCh38 2 217818606 217818606 + Silent SNP C C A rs367925904 C3L-01924_T C3L-01924_N C C c.3414G>T p.= p.P1138P ENST00000171887 24/33 266 242 24 280 279 1 strelka-varscan-mutect TNS1,synonymous_variant,p.=,ENST00000171887,NM_022648.4;TNS1,synonymous_variant,p.=,ENST00000611415,;TNS1,synonymous_variant,p.=,ENST00000615025,;TNS1,synonymous_variant,p.=,ENST00000419504,;TNS1,synonymous_variant,p.=,ENST00000430930,NM_001308023.1;TNS1,synonymous_variant,p.=,ENST00000446688,;TNS1,upstream_gene_variant,,ENST00000490566,;TNS1,upstream_gene_variant,,ENST00000495556,; A ENST00000171887 Transcript synonymous_variant 3867/10331 3414/5208 1138/1735 P ccG/ccT rs367925904 1 -1 TNS1 HGNC HGNC:11973 protein_coding YES CCDS2407.1 ENSP00000171887 Q9HBL0 UPI0000456EEB NM_022648.4 24/33 LOW 1 SNV 1 1 PASS rs367925904 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 217818606 217818606 C A 1 0 0 0 0 0 0 0 1 16816 871 31 1 1 TNS1 2 217818606 Silent SNP C C3L-01924_T 7823244 217818606 24374923 105 7975 CATIP 0 . GRCh38 2 218367887 218367887 + Missense_Mutation SNP G G T rs142470785 C3L-01924_T C3L-01924_N G G c.1087G>T p.Ala363Ser p.A363S ENST00000289388 10/10 264 173 91 311 311 0 strelka-varscan-mutect CATIP,missense_variant,p.Ala363Ser,ENST00000289388,NM_198559.1;CATIP-AS1,upstream_gene_variant,,ENST00000441749,;CATIP,non_coding_transcript_exon_variant,,ENST00000481940,;CATIP,non_coding_transcript_exon_variant,,ENST00000494447,;CATIP-AS1,upstream_gene_variant,,ENST00000425481,; T ENST00000289388 Transcript missense_variant 1116/1323 1087/1164 363/387 A/S Gcc/Tcc rs142470785 1 1 CATIP HGNC HGNC:25062 protein_coding YES CCDS2414.1 ENSP00000289388 Q7Z7H3 UPI000019B2D3 NM_198559.1 tolerated(0.7) 10/10 hmmpanther:PTHR15505,hmmpanther:PTHR15505:SF3 MODERATE 1 SNV 1 1 PASS rs142470785 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 218367887 218367887 G T 1 0 0 0 0 1 0 0 0 2386 1203 42 2 2 CATIP 2 218367887 Missense_Mutation SNP G C3L-01924_T 549281 218367887 23825642 106 7976 TMEM198 0 . GRCh38 2 219549847 219549847 + Missense_Mutation SNP G G T rs374243531 C3L-01924_T C3L-01924_N G G c.1076G>T p.Arg359Leu p.R359L ENST00000344458 6/6 94 78 16 92 92 0 strelka-varscan-mutect TMEM198,missense_variant,p.Arg359Leu,ENST00000344458,NM_001303098.1;TMEM198,missense_variant,p.Arg359Leu,ENST00000373883,NM_001005209.2;OBSL1,downstream_gene_variant,,ENST00000404537,NM_015311.2;OBSL1,downstream_gene_variant,,ENST00000373876,;TMEM198,downstream_gene_variant,,ENST00000421791,;TMEM198,downstream_gene_variant,,ENST00000451952,;MIR3132,upstream_gene_variant,,ENST00000581997,;RP11-256I23.1,upstream_gene_variant,,ENST00000596829,;OBSL1,downstream_gene_variant,,ENST00000465149,;OBSL1,downstream_gene_variant,,ENST00000489804,;OBSL1,downstream_gene_variant,,ENST00000462534,;OBSL1,downstream_gene_variant,,ENST00000596474,; T ENST00000344458 Transcript missense_variant 1661/2393 1076/1083 359/360 R/L cGg/cTg rs374243531 1 1 TMEM198 HGNC HGNC:33704 protein_coding YES CCDS33385.1 ENSP00000343507 Q66K66 A0A024R483 UPI0000160257 NM_001303098.1 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR31247,hmmpanther:PTHR31247:SF7 MODERATE 1 SNV 1 1 PASS rs374243531 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 219549847 219549847 G T 1 0 0 0 0 1 0 0 0 16559 1116 39 1 1 TMEM198 2 219549847 Missense_Mutation SNP G C3L-01924_T 1181960 219549847 22643682 107 7977 SPHKAP 0 . GRCh38 2 228019777 228019777 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1077G>T p.= p.V359V ENST00000392056 7/12 142 125 17 200 200 0 strelka-varscan-mutect SPHKAP,synonymous_variant,p.=,ENST00000392056,NM_001142644.1;SPHKAP,synonymous_variant,p.=,ENST00000344657,NM_030623.3; A ENST00000392056 Transcript synonymous_variant 1124/6917 1077/5103 359/1700 V gtG/gtT 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 LOW 1 SNV 1 1 PASS rs1198639071 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 228019777 228019777 C A 1 0 0 0 0 0 0 0 1 15399 581 21 2 2 SPHKAP 2 228019777 Silent SNP C C3L-01924_T 8469930 228019777 14173752 108 7978 COL6A3 0 . GRCh38 2 237366794 237366794 + Missense_Mutation SNP C C A rs371441617 C3L-01924_T C3L-01924_N C C c.5393G>T p.Arg1798Leu p.R1798L ENST00000295550 11/44 307 280 27 390 389 1 strelka-varscan-mutect COL6A3,missense_variant,p.Arg1798Leu,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Arg1592Leu,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Arg1592Leu,ENST00000409809,;COL6A3,missense_variant,p.Arg1191Leu,ENST00000472056,NM_057166.4;COL6A3,missense_variant,p.Arg1191Leu,ENST00000347401,;COL6A3,downstream_gene_variant,,ENST00000392004,NM_057165.4;COL6A3,downstream_gene_variant,,ENST00000392003,NM_057164.4; A ENST00000295550 Transcript missense_variant 5846/10749 5393/9534 1798/3177 R/L cGc/cTc rs371441617,COSM210539 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 deleterious(0.03) 11/44 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371441617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 237366794 237366794 C A 1 0 0 0 0 1 0 0 0 3490 768 27 1 1 COL6A3 2 237366794 Missense_Mutation SNP C C3L-01924_T 9347017 237366794 4826735 109 7979 COL6A3 0 . GRCh38 2 237374530 237374530 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.3561C>T p.= p.A1187A ENST00000295550 8/44 357 309 48 434 434 0 strelka-varscan-mutect COL6A3,synonymous_variant,p.=,ENST00000295550,NM_004369.3;COL6A3,synonymous_variant,p.=,ENST00000353578,NM_057167.3;COL6A3,synonymous_variant,p.=,ENST00000409809,;COL6A3,synonymous_variant,p.=,ENST00000472056,NM_057166.4;COL6A3,synonymous_variant,p.=,ENST00000347401,;COL6A3,synonymous_variant,p.=,ENST00000392004,NM_057165.4;COL6A3,synonymous_variant,p.=,ENST00000392003,NM_057164.4;COL6A3,downstream_gene_variant,,ENST00000433762,; A ENST00000295550 Transcript synonymous_variant 4014/10749 3561/9534 1187/3177 A gcC/gcT 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 8/44 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 237374530 237374530 G A 1 0 0 0 0 0 0 0 1 3490 1335 47 3 3 COL6A3 2 237374530 Silent SNP G C3L-01924_T 7736 237374530 4818999 110 7980 UBE2F 0 . GRCh38 2 238030597 238030597 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.395C>T p.Pro132Leu p.P132L ENST00000612130 7/10 197 184 13 239 239 0 strelka-varscan-mutect UBE2F,missense_variant,p.Pro132Leu,ENST00000612130,NM_001278305.1;UBE2F,missense_variant,p.Pro100Leu,ENST00000414443,NM_001278307.1;UBE2F,missense_variant,p.Pro132Leu,ENST00000272930,NM_080678.2;UBE2F,missense_variant,p.Pro110Leu,ENST00000409332,;UBE2F,missense_variant,p.Pro108Leu,ENST00000409953,NM_001278306.1;UBE2F,missense_variant,p.Pro132Leu,ENST00000409633,NM_001278308.1;UBE2F,missense_variant,p.Pro132Leu,ENST00000434655,;UBE2F,missense_variant,p.Pro100Leu,ENST00000416292,;UBE2F,missense_variant,p.Pro122Leu,ENST00000434137,;UBE2F,downstream_gene_variant,,ENST00000448502,;RNU6-1333P,upstream_gene_variant,,ENST00000516162,;UBE2F-SCLY,3_prime_UTR_variant,,ENST00000449891,;UBE2F,3_prime_UTR_variant,,ENST00000454786,;UBE2F,3_prime_UTR_variant,,ENST00000441728,;UBE2F,3_prime_UTR_variant,,ENST00000417231,;UBE2F,3_prime_UTR_variant,,ENST00000439338,;UBE2F,3_prime_UTR_variant,,ENST00000445676,;UBE2F,3_prime_UTR_variant,,ENST00000440223,;UBE2F,3_prime_UTR_variant,,ENST00000455999,;UBE2F,non_coding_transcript_exon_variant,,ENST00000480828,;UBE2F,non_coding_transcript_exon_variant,,ENST00000482096,;UBE2F-SCLY,intron_variant,,ENST00000449191,;UBE2F,intron_variant,,ENST00000433241,;UBE2F,intron_variant,,ENST00000439780,;UBE2F,upstream_gene_variant,,ENST00000472479,; T ENST00000612130 Transcript missense_variant 528/2135 395/558 132/185 P/L cCc/cTc 1 1 UBE2F HGNC HGNC:12480 protein_coding YES CCDS2523.1 ENSP00000478474 Q969M7 UPI000007332C NM_001278305.1 deleterious(0) 7/10 PROSITE_profiles:PS50127,hmmpanther:PTHR24067:SF152,hmmpanther:PTHR24067,Gene3D:3.10.110.10,Pfam_domain:PF00179,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 238030597 238030597 C T 1 0 0 0 0 1 0 0 0 17376 623 22 3 3 UBE2F 2 238030597 Missense_Mutation SNP C C3L-01924_T 656067 238030597 4162932 111 7981 KIF1A 0 . GRCh38 2 240757379 240757379 + Missense_Mutation SNP G G T rs760841799 C3L-01924_T C3L-01924_N G G c.2798C>A p.Ala933Glu p.A933E ENST00000498729 27/49 194 137 57 194 194 0 strelka-varscan-mutect KIF1A,missense_variant,p.Ala933Glu,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Ala933Glu,ENST00000404283,;KIF1A,intron_variant,,ENST00000320389,NM_004321.6; T ENST00000498729 Transcript missense_variant 3045/9223 2798/5376 933/1791 A/E gCg/gAg rs760841799 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 tolerated(0.69) 27/49 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361 MODERATE 1 SNV 1 1 PASS rs760841799 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 240757379 240757379 G T 1 0 0 0 0 1 0 0 0 8147 1087 38 1 1 KIF1A 2 240757379 Missense_Mutation SNP G C3L-01924_T 2726782 240757379 1436150 112 7982 CROCC2 0 . GRCh38 2 240932821 240932821 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1164C>A p.= p.S388S ENST00000443866 9/32 63 53 10 87 87 0 strelka-varscan-mutect CROCC2,synonymous_variant,p.=,ENST00000443866,;CROCC2,non_coding_transcript_exon_variant,,ENST00000477311,; A ENST00000443866 Transcript synonymous_variant 1348/5382 1164/4968 388/1655 S tcC/tcA 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A 9/32 hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -19.99927 1 1 1 1 0 A 2 1 29 240932821 240932821 C A 1 0 0 0 0 0 0 0 1 3695 610 22 2 2 CROCC2 2 240932821 Silent SNP C C3L-01924_T 175442 240932821 1260708 113 7983 GRM7 0 . GRCh38 3 7298797 7298797 + Missense_Mutation SNP G G C rs772917243 C3L-01924_T C3L-01924_N G G c.850G>C p.Val284Leu p.V284L ENST00000357716 3/10 310 283 27 363 363 0 strelka-varscan-mutect GRM7,missense_variant,p.Val284Leu,ENST00000486284,NM_181874.2;GRM7,missense_variant,p.Val284Leu,ENST00000357716,NM_000844.3;GRM7,missense_variant,p.Val284Leu,ENST00000389336,;GRM7,missense_variant,p.Val39Leu,ENST00000402647,;GRM7,missense_variant,p.Val76Leu,ENST00000448328,;GRM7,missense_variant,p.Val284Leu,ENST00000467425,;GRM7,missense_variant,p.Val284Leu,ENST00000440923,;GRM7,missense_variant,p.Val284Leu,ENST00000389335,;GRM7,3_prime_UTR_variant,,ENST00000435689,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,;GRM7,non_coding_transcript_exon_variant,,ENST00000461677,; C ENST00000357716 Transcript missense_variant 1124/4127 850/2748 284/915 V/L Gtg/Ctg rs772917243,COSM4326991,COSM4326992,COSM4326993 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 deleterious(0.02) 3/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs772917243 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 7298797 7298797 G C 1 0 0 0 0 1 0 0 0 6684 1145 40 4 4 GRM7 3 7298797 Missense_Mutation SNP G C3L-01924_T 7298797 190996762 114 7984 HRH1 0 . GRCh38 3 11259762 11259762 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.725A>G p.Glu242Gly p.E242G ENST00000397056 3/3 200 150 50 271 270 1 strelka-varscan-mutect HRH1,missense_variant,p.Glu242Gly,ENST00000397056,NM_000861.3;HRH1,missense_variant,p.Glu242Gly,ENST00000431010,NM_001098212.1,NM_001098211.1;HRH1,missense_variant,p.Glu242Gly,ENST00000438284,NM_001098213.1;HRH1,downstream_gene_variant,,ENST00000413416,; G ENST00000397056 Transcript missense_variant 916/4711 725/1464 242/487 E/G gAg/gGg 1 1 HRH1 HGNC HGNC:5182 protein_coding YES CCDS2604.1 ENSP00000380247 P35367 UPI0000050401 NM_000861.3 tolerated(0.12) 3/3 Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF239,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 11259762 11259762 A G 1 0 0 0 0 1 0 0 0 7250 304 11 5 5 HRH1 3 11259762 Missense_Mutation SNP A C3L-01924_T 3960965 11259762 187035797 115 7985 EFHB 0 . GRCh38 3 19896740 19896740 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1672G>T p.Val558Phe p.V558F ENST00000295824 9/13 296 266 30 405 405 0 strelka-varscan-mutect EFHB,missense_variant,p.Val558Phe,ENST00000295824,NM_144715.3;EFHB,missense_variant,p.Val428Phe,ENST00000344838,;EFHB,downstream_gene_variant,,ENST00000440022,;EFHB,non_coding_transcript_exon_variant,,ENST00000498089,;EFHB,non_coding_transcript_exon_variant,,ENST00000467602,;EFHB,missense_variant,p.Val558Phe,ENST00000389256,; A ENST00000295824 Transcript missense_variant 1834/2823 1672/2502 558/833 V/F Gtt/Ttt 1 -1 EFHB HGNC HGNC:26330 protein_coding YES CCDS33715.2 ENSP00000295824 Q8N7U6 UPI0000209A4C NM_144715.3 tolerated(0.64) 9/13 hmmpanther:PTHR12086:SF12,hmmpanther:PTHR12086,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 19896740 19896740 C A 1 0 0 0 0 1 0 0 0 4780 565 20 2 2 EFHB 3 19896740 Missense_Mutation SNP C C3L-01924_T 8636978 19896740 178398819 116 7986 KAT2B 0 . GRCh38 3 20114985 20114985 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.1147A>G p.Thr383Ala p.T383A ENST00000263754 7/18 116 98 18 139 139 0 strelka-varscan-mutect KAT2B,missense_variant,p.Thr383Ala,ENST00000263754,NM_003884.4;KAT2B,non_coding_transcript_exon_variant,,ENST00000469085,; G ENST00000263754 Transcript missense_variant 1602/4833 1147/2499 383/832 T/A Aca/Gca 1 1 KAT2B HGNC HGNC:8638 protein_coding YES CCDS2634.1 ENSP00000263754 Q92831 UPI00002132DE NM_003884.4 tolerated(0.66) 7/18 PIRSF_domain:PIRSF003048,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF116 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 20114985 20114985 A G 1 0 0 0 0 1 0 0 0 7896 57 2 5 5 KAT2B 3 20114985 Missense_Mutation SNP A C3L-01924_T 218245 20114985 178180574 117 7987 CLEC3B 0 . GRCh38 3 45035861 45035861 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.546C>T p.= p.G182G ENST00000296130 3/3 111 105 6 147 147 0 strelka-mutect CLEC3B,synonymous_variant,p.=,ENST00000296130,NM_003278.2;CLEC3B,synonymous_variant,p.=,ENST00000428034,NM_001308394.1;RNU5B-3P,upstream_gene_variant,,ENST00000516601,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000481405,;CLEC3B,non_coding_transcript_exon_variant,,ENST00000490386,; T ENST00000296130 Transcript synonymous_variant 726/936 546/609 182/202 G ggC/ggT 1 1 CLEC3B HGNC HGNC:11891 protein_coding YES CCDS2726.1 ENSP00000296130 P05452 A0A024R2Q7 UPI000013E305 NM_003278.2 3/3 PROSITE_profiles:PS50041,hmmpanther:PTHR22799,PROSITE_patterns:PS00615,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 45035861 45035861 C T 1 0 0 0 0 0 0 0 1 3279 697 25 3 3 CLEC3B 3 45035861 Silent SNP C C3L-01924_T 24920876 45035861 153259698 118 7988 LAMB2 0 . GRCh38 3 49131390 49131390 + Nonsense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.701C>G p.Ser234Ter p.S234* ENST00000418109 7/33 254 226 28 332 332 0 strelka-varscan-mutect LAMB2,stop_gained,p.Ser234Ter,ENST00000418109,NM_002292.3;LAMB2,stop_gained,p.Ser234Ter,ENST00000305544,;LAMB2,stop_gained,p.Ser85Ter,ENST00000494831,;LAMB2,upstream_gene_variant,,ENST00000486298,;LAMB2,upstream_gene_variant,,ENST00000493571,;LAMB2,upstream_gene_variant,,ENST00000483321,;LAMB2,upstream_gene_variant,,ENST00000488638,; C ENST00000418109 Transcript stop_gained 866/5674 701/5397 234/1798 S/* tCa/tGa 1 -1 LAMB2 HGNC HGNC:6487 protein_coding YES CCDS2789.1 ENSP00000388325 P55268 A0A024R319 UPI000013EA62 NM_002292.3 7/33 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF36,SMART_domains:SM00136 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 29 49131390 49131390 G C 1 0 0 0 0 0 1 0 0 8515 1294 45 4 4 LAMB2 3 49131390 Nonsense_Mutation SNP G C3L-01924_T 4095529 49131390 149164169 119 7989 AMIGO3 0 . GRCh38 3 49718518 49718518 + Missense_Mutation SNP C C G C3L-01924_T C3L-01924_N C C c.948G>C p.Gln316His p.Q316H ENST00000320431 1/1 426 357 69 406 406 0 strelka-varscan-mutect AMIGO3,missense_variant,p.Gln316His,ENST00000320431,NM_198722.2;GMPPB,3_prime_UTR_variant,,ENST00000480687,;RNF123,intron_variant,,ENST00000327697,NM_022064.3;RNF123,intron_variant,,ENST00000433785,;GMPPB,downstream_gene_variant,,ENST00000308375,NM_013334.3;GMPPB,downstream_gene_variant,,ENST00000308388,NM_021971.2;RNF123,non_coding_transcript_exon_variant,,ENST00000497099,;RNF123,intron_variant,,ENST00000487805,;RNF123,intron_variant,,ENST00000486102,;RNF123,intron_variant,,ENST00000457726,;GMPPB,downstream_gene_variant,,ENST00000481959,;RNF123,downstream_gene_variant,,ENST00000469978,;RNF123,upstream_gene_variant,,ENST00000498376,;GMPPB,downstream_gene_variant,,ENST00000495627,;RNF123,downstream_gene_variant,,ENST00000444689,; G ENST00000320431 Transcript missense_variant 1178/2862 948/1515 316/504 Q/H caG/caC COSM1182678 1 -1 AMIGO3 HGNC HGNC:24075 protein_coding YES CCDS33759.1 ENSP00000323096 Q86WK7 UPI00000622D6 NM_198722.2 tolerated(1) 1/1 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR24368,hmmpanther:PTHR24368:SF62,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 49718518 49718518 C G 1 0 0 0 0 1 0 0 0 675 680 24 4 4 AMIGO3 3 49718518 Missense_Mutation SNP C C3L-01924_T 587128 49718518 148577041 120 7990 CAMKV 0 . GRCh38 3 49861450 49861450 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.430A>T p.Arg144Trp p.R144W ENST00000477224 5/11 131 113 18 173 173 0 strelka-varscan-mutect CAMKV,splice_acceptor_variant,,ENST00000466940,;CAMKV,missense_variant,p.Arg144Trp,ENST00000477224,NM_024046.3;CAMKV,missense_variant,p.Arg144Trp,ENST00000296471,;CAMKV,missense_variant,p.Arg144Trp,ENST00000488336,;CAMKV,missense_variant,p.Arg144Trp,ENST00000463537,;CAMKV,missense_variant,p.Arg69Trp,ENST00000467248,;CAMKV,missense_variant,p.Arg144Trp,ENST00000620470,;CAMKV,missense_variant,p.Arg57Trp,ENST00000480398,;TRAIP,upstream_gene_variant,,ENST00000331456,NM_005879.2;TRAIP,upstream_gene_variant,,ENST00000469027,;TRAIP,upstream_gene_variant,,ENST00000482582,;TRAIP,upstream_gene_variant,,ENST00000482243,;RN7SL217P,downstream_gene_variant,,ENST00000584520,;CAMKV,downstream_gene_variant,,ENST00000498324,;TRAIP,upstream_gene_variant,,ENST00000473863,;CAMKV,synonymous_variant,p.=,ENST00000466535,;CAMKV,3_prime_UTR_variant,,ENST00000487726,;CAMKV,non_coding_transcript_exon_variant,,ENST00000475665,;CAMKV,non_coding_transcript_exon_variant,,ENST00000483811,;CAMKV,non_coding_transcript_exon_variant,,ENST00000472895,;CAMKV,non_coding_transcript_exon_variant,,ENST00000479704,;TRAIP,upstream_gene_variant,,ENST00000477546,;TRAIP,upstream_gene_variant,,ENST00000473195,;CAMKV,upstream_gene_variant,,ENST00000478149,;CAMKV,downstream_gene_variant,,ENST00000476105,;TRAIP,upstream_gene_variant,,ENST00000489948,; A ENST00000477224 Transcript missense_variant 909/3314 430/1506 144/501 R/W Agg/Tgg 1 -1 CAMKV HGNC HGNC:28788 protein_coding YES CCDS33762.1 ENSP00000419195 Q8NCB2 A0A140VKD5 UPI000004184F NM_024046.3 deleterious(0) 5/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF18,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 49861450 49861450 T A 1 0 0 0 0 1 0 0 0 2300 1594 55 4 4 CAMKV 3 49861450 Missense_Mutation SNP T C3L-01924_T 142932 49861450 148434109 121 7991 FAM107A 0 . GRCh38 3 58567279 58567279 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.349G>T p.Glu117Ter p.E117* ENST00000474531 4/5 337 287 50 351 350 1 strelka-varscan-mutect FAM107A,stop_gained,p.Glu86Ter,ENST00000394481,NM_007177.3;FAM107A,stop_gained,p.Glu86Ter,ENST00000360997,NM_001076778.2;FAM107A,stop_gained,p.Glu117Ter,ENST00000474531,NM_001282714.1;FAM107A,stop_gained,p.Glu86Ter,ENST00000464064,;FAM107A,stop_gained,p.Glu114Ter,ENST00000447756,NM_001282713.1;FAM107A,stop_gained,p.Glu86Ter,ENST00000465970,; A ENST00000474531 Transcript stop_gained 965/2271 349/528 117/175 E/* Gag/Tag 1 -1 FAM107A HGNC HGNC:30827 protein_coding YES CCDS63673.1 ENSP00000419124 O95990 A0A024R327 UPI000020AE2A NM_001282714.1 4/5 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06625,hmmpanther:PTHR16768,hmmpanther:PTHR16768:SF3,Low_complexity_(Seg):seg HIGH 1 SNV 2 1 PASS rs1176317305 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 58567279 58567279 C A 1 0 0 0 0 0 1 0 0 5257 864 30 2 2 FAM107A 3 58567279 Nonsense_Mutation SNP C C3L-01924_T 8705829 58567279 139728280 122 7992 EOGT 0 . GRCh38 3 68978415 68978415 + Missense_Mutation SNP C C T rs193201126 C3L-01924_T C3L-01924_N C C c.1355G>A p.Arg452His p.R452H ENST00000383701 17/18 115 95 20 168 168 0 strelka-varscan-mutect EOGT,missense_variant,p.Arg452His,ENST00000383701,NM_001278689.1;EOGT,missense_variant,p.Arg368His,ENST00000295571,NM_173654.2;EOGT,missense_variant,p.Arg452His,ENST00000540764,;EOGT,missense_variant,p.Arg368His,ENST00000540955,;EOGT,upstream_gene_variant,,ENST00000615922,;EOGT,3_prime_UTR_variant,,ENST00000403140,;EOGT,non_coding_transcript_exon_variant,,ENST00000496647,;EOGT,downstream_gene_variant,,ENST00000480846,; T ENST00000383701 Transcript missense_variant 2098/4731 1355/1584 452/527 R/H cGc/cAc rs193201126,COSM4119963,COSM4119964 1 -1 EOGT HGNC HGNC:28526 protein_coding YES CCDS63684.1 ENSP00000373206 Q5NDL2 UPI00004982AF NM_001278689.1 tolerated(0.24) 17/18 Pfam_domain:PF04577,hmmpanther:PTHR20961,hmmpanther:PTHR20961:SF0 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs193201126 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 68978415 68978415 C T 1 0 0 0 0 1 0 0 0 4992 768 27 1 1 EOGT 3 68978415 Missense_Mutation SNP C C3L-01924_T 10411136 68978415 129317144 123 7993 EPHA3 0 . GRCh38 3 89210264 89210264 + Silent SNP T T G novel C3L-01924_T C3L-01924_N T T c.558T>G p.= p.V186V ENST00000336596 3/17 186 169 17 231 231 0 strelka-varscan-mutect EPHA3,synonymous_variant,p.=,ENST00000336596,NM_005233.5;EPHA3,synonymous_variant,p.=,ENST00000494014,;EPHA3,synonymous_variant,p.=,ENST00000452448,NM_182644.2; G ENST00000336596 Transcript synonymous_variant 783/5809 558/2952 186/983 V gtT/gtG 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PROSITE_patterns:PS00790,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 89210264 89210264 T G 1 0 0 0 0 0 0 0 1 5015 1799 63 5 5 EPHA3 3 89210264 Silent SNP T C3L-01924_T 20231849 89210264 109085295 124 7994 ZPLD1 0 . GRCh38 3 102462342 102462342 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.692T>A p.Val231Glu p.V231E ENST00000306176 6/11 136 121 15 146 146 0 strelka-varscan-mutect ZPLD1,missense_variant,p.Val231Glu,ENST00000306176,NM_175056.1;ZPLD1,missense_variant,p.Val215Glu,ENST00000491959,;ZPLD1,missense_variant,p.Val215Glu,ENST00000466937,; A ENST00000306176 Transcript missense_variant 792/3619 692/1296 231/431 V/E gTa/gAa 1 1 ZPLD1 HGNC HGNC:27022 protein_coding YES CCDS2947.1 ENSP00000307801 Q8TCW7 UPI000006EC89 NM_175056.1 deleterious(0) 6/11 PROSITE_profiles:PS51034,hmmpanther:PTHR24044:SF333,hmmpanther:PTHR24044,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 102462342 102462342 T A 1 0 0 0 0 1 0 0 0 18813 1638 57 4 4 ZPLD1 3 102462342 Missense_Mutation SNP T C3L-01924_T 13252078 102462342 95833217 125 7995 SLC15A2 0 . GRCh38 3 121931645 121931645 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.1671T>C p.= p.P557P ENST00000489711 19/22 141 129 12 169 169 0 strelka-varscan-mutect SLC15A2,synonymous_variant,p.=,ENST00000489711,NM_021082.3;SLC15A2,synonymous_variant,p.=,ENST00000295605,NM_001145998.1;SLC15A2,downstream_gene_variant,,ENST00000465060,;SLC15A2,downstream_gene_variant,,ENST00000489957,; C ENST00000489711 Transcript synonymous_variant 2059/5673 1671/2190 557/729 P ccT/ccC 1 1 SLC15A2 HGNC HGNC:10921 protein_coding YES CCDS3007.1 ENSP00000417085 Q16348 UPI000013E27D NM_021082.3 19/22 TIGRFAM_domain:TIGR00926 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 121931645 121931645 T C 1 0 0 0 0 0 0 0 1 14664 1567 55 5 5 SLC15A2 3 121931645 Silent SNP T C3L-01924_T 19469303 121931645 76363914 126 7996 CASR 0 . GRCh38 3 122261648 122261648 + Missense_Mutation SNP C C T rs775751453 C3L-01924_T C3L-01924_N C C c.613C>T p.Arg205Cys p.R205C ENST00000498619 4/7 328 283 45 415 415 0 strelka-varscan-mutect CASR,missense_variant,p.Arg205Cys,ENST00000498619,NM_001178065.1;CASR,missense_variant,p.Arg205Cys,ENST00000490131,NM_000388.3; T ENST00000498619 Transcript missense_variant 1051/5011 613/3267 205/1088 R/C Cgc/Tgc rs775751453,CM123746,COSM1037084 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 deleterious(0) 4/7 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF358,Superfamily_domains:SSF53822 0,0,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs775751453 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 122261648 122261648 C T 1 0 0 0 0 1 0 0 0 2381 652 23 1 1 CASR 3 122261648 Missense_Mutation SNP C C3L-01924_T 330003 122261648 76033911 127 7997 MYLK 0 . GRCh38 3 123707958 123707958 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2186C>A p.Ser729Ter p.S729* ENST00000360304 15/33 303 261 42 335 334 1 strelka-varscan-mutect MYLK,stop_gained,p.Ser729Ter,ENST00000360772,;MYLK,stop_gained,p.Ser729Ter,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,stop_gained,p.Ser729Ter,ENST00000359169,NM_053027.3;MYLK,stop_gained,p.Ser660Ter,ENST00000354792,;MYLK,stop_gained,p.Ser660Ter,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,stop_gained,p.Ser729Ter,ENST00000475616,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,downstream_gene_variant,,ENST00000514623,; T ENST00000360304 Transcript stop_gained 2372/7738 2186/5745 729/1914 S/* tCa/tAa 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 15/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 123707958 123707958 G T 1 0 0 0 0 0 1 0 0 10056 1294 45 2 2 MYLK 3 123707958 Nonsense_Mutation SNP G C3L-01924_T 1446310 123707958 74587601 128 7998 EEFSEC 0 . GRCh38 3 128153790 128153790 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.283G>T p.Gly95Trp p.G95W ENST00000254730 1/7 226 195 31 233 233 0 strelka-varscan-mutect EEFSEC,missense_variant,p.Gly95Trp,ENST00000254730,NM_021937.4;EEFSEC,missense_variant,p.Gly95Trp,ENST00000483457,;RUVBL1,5_prime_UTR_variant,,ENST00000464873,NM_001319086.1;EEFSEC,non_coding_transcript_exon_variant,,ENST00000484438,; T ENST00000254730 Transcript missense_variant 337/2232 283/1791 95/596 G/W Ggg/Tgg 1 1 EEFSEC HGNC HGNC:24614 protein_coding YES CCDS33849.1 ENSP00000254730 P57772 UPI000013CE58 NM_021937.4 deleterious(0) 1/7 Gene3D:3.40.50.300,Pfam_domain:PF00009,Prints_domain:PR00315,PROSITE_profiles:PS51722,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF91,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 128153790 128153790 G T 1 0 0 0 0 1 0 0 0 4762 1116 39 1 1 EEFSEC 3 128153790 Missense_Mutation SNP G C3L-01924_T 4445832 128153790 70141769 129 7999 COL6A6 0 . GRCh38 3 130649256 130649256 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.5427C>A p.= p.A1809A ENST00000358511 32/36 145 123 22 174 174 0 strelka-varscan-mutect COL6A6,synonymous_variant,p.=,ENST00000358511,NM_001102608.1;COL6A6,intron_variant,,ENST00000506143,; A ENST00000358511 Transcript synonymous_variant 5458/9581 5427/6792 1809/2263 A gcC/gcA 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 32/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 130649256 130649256 C A 1 0 0 0 0 0 0 0 1 3492 581 21 2 2 COL6A6 3 130649256 Silent SNP C C3L-01924_T 2495466 130649256 67646303 130 8000 CLSTN2 0 . GRCh38 3 140448553 140448553 + Silent SNP C C G rs143908906 C3L-01924_T C3L-01924_N C C c.822C>G p.= p.S274S ENST00000458420 6/17 106 91 15 151 151 0 strelka-varscan-mutect CLSTN2,synonymous_variant,p.=,ENST00000458420,NM_022131.2;RP11-68L1.2,downstream_gene_variant,,ENST00000509191,;RP11-68L1.2,downstream_gene_variant,,ENST00000502712,;RP11-68L1.2,downstream_gene_variant,,ENST00000503357,;CLSTN2,non_coding_transcript_exon_variant,,ENST00000511524,; G ENST00000458420 Transcript synonymous_variant 1012/14202 822/2868 274/955 S tcC/tcG rs143908906 1 1 CLSTN2 HGNC HGNC:17448 protein_coding YES CCDS3112.1 ENSP00000402460 Q9H4D0 UPI00001B0051 NM_022131.2 6/17 PROSITE_profiles:PS50268,hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF3 LOW 1 SNV 1 1 PASS rs143908906 . 0 207 0 2 0 0 0 0 -19.99994 0.9999999 1 1 1 0 G 2 3 29 140448553 140448553 C G 1 0 0 0 0 0 0 0 1 3334 639 23 4 4 CLSTN2 3 140448553 Silent SNP C C3L-01924_T 9799297 140448553 57847006 131 8001 XRN1 0 . GRCh38 3 142370606 142370606 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.3083A>T p.Gln1028Leu p.Q1028L ENST00000264951 27/42 102 87 15 138 138 0 strelka-varscan-mutect XRN1,missense_variant,p.Gln1028Leu,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Gln494Leu,ENST00000498077,;XRN1,missense_variant,p.Gln1028Leu,ENST00000392981,NM_001282857.1;XRN1,non_coding_transcript_exon_variant,,ENST00000472625,;XRN1,upstream_gene_variant,,ENST00000467077,; A ENST00000264951 Transcript missense_variant 3201/10143 3083/5121 1028/1706 Q/L cAa/cTa 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 tolerated(0.14) 27/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 142370606 142370606 T A 1 0 0 0 0 1 0 0 0 18017 1812 63 4 4 XRN1 3 142370606 Missense_Mutation SNP T C3L-01924_T 1922053 142370606 55924953 132 8002 P2RY13 0 . GRCh38 3 151328525 151328525 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.531A>T p.= p.P177P ENST00000325602 2/2 316 289 27 413 412 1 strelka-varscan-mutect P2RY13,synonymous_variant,p.=,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; A ENST00000325602 Transcript synonymous_variant 551/2764 531/1065 177/354 P ccA/ccT 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 151328525 151328525 T A 1 0 0 0 0 0 0 0 1 11423 1799 63 4 4 P2RY13 3 151328525 Silent SNP T C3L-01924_T 8957919 151328525 46967034 133 8003 SLITRK3 0 . GRCh38 3 165188355 165188355 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.2476C>A p.Gln826Lys p.Q826K ENST00000475390 2/2 204 170 34 251 251 0 strelka-varscan-mutect SLITRK3,missense_variant,p.Gln826Lys,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Gln826Lys,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; T ENST00000475390 Transcript missense_variant 2920/4555 2476/2934 826/977 Q/K Cag/Aag COSM3589617 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 tolerated(1) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 165188355 165188355 G T 1 0 0 0 0 1 0 0 0 15035 1357 47 2 2 SLITRK3 3 165188355 Missense_Mutation SNP G C3L-01924_T 13859830 165188355 33107204 134 8004 ZBBX 0 . GRCh38 3 167333828 167333828 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.686A>T p.Glu229Val p.E229V ENST00000455345 9/21 58 45 13 83 83 0 strelka-varscan-mutect ZBBX,missense_variant,p.Glu229Val,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Glu229Val,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Glu229Val,ENST00000307529,;ZBBX,missense_variant,p.Glu200Val,ENST00000392767,;ZBBX,missense_variant,p.Glu200Val,ENST00000392764,NM_001199202.1;ZBBX,intron_variant,,ENST00000469220,; A ENST00000455345 Transcript missense_variant,splice_region_variant 970/3185 686/2520 229/839 E/V gAg/gTg 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 deleterious(0.01) 9/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 167333828 167333828 T A 1 0 0 0 0 1 0 0 0 18078 1565 54 4 4 ZBBX 3 167333828 Missense_Mutation SNP T C3L-01924_T 2145473 167333828 30961731 135 8005 LRRC31 0 . GRCh38 3 169860730 169860730 + Splice_Site SNP T T A novel C3L-01924_T C3L-01924_N T T c.320-2A>T p.X107_splice ENST00000316428 111 102 9 184 184 0 strelka-varscan-mutect LRRC31,splice_acceptor_variant,,ENST00000316428,NM_024727.3;LRRC31,splice_acceptor_variant,,ENST00000523069,NM_001277127.1;LRRC31,intron_variant,,ENST00000264676,NM_001277128.1;LRRC31,splice_acceptor_variant,,ENST00000397805,; A ENST00000316428 Transcript splice_acceptor_variant -/2520 320/1659 107/552 1 -1 LRRC31 HGNC HGNC:26261 protein_coding YES CCDS43167.1 ENSP00000325978 Q6UY01 UPI00001D690F NM_024727.3 2/8 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 29 169860730 169860730 T A 1 0 0 0 0 0 0 1 0 8881 1536 53 4 4 LRRC31 3 169860730 Splice_Site SNP T C3L-01924_T 2526902 169860730 28434829 136 8006 ECT2 0 . GRCh38 3 172807831 172807831 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.2307C>T p.= p.L769L ENST00000392692 22/25 131 121 10 170 170 0 strelka-mutect ECT2,synonymous_variant,p.=,ENST00000540509,NM_001258316.1;ECT2,synonymous_variant,p.=,ENST00000417960,;ECT2,synonymous_variant,p.=,ENST00000392692,NM_001258315.1;ECT2,synonymous_variant,p.=,ENST00000232458,NM_018098.5;ECT2,synonymous_variant,p.=,ENST00000441497,;ECT2,synonymous_variant,p.=,ENST00000437296,;ECT2,non_coding_transcript_exon_variant,,ENST00000486027,;ECT2,downstream_gene_variant,,ENST00000460860,; T ENST00000392692 Transcript synonymous_variant 2483/4158 2307/2745 769/914 L ctC/ctT 1 1 ECT2 HGNC HGNC:3155 protein_coding YES CCDS58860.1 ENSP00000376457 Q9H8V3 UPI00003DFD0A NM_001258315.1 22/25 Gene3D:2.30.29.30,hmmpanther:PTHR16777,hmmpanther:PTHR16777:SF2,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS rs1363886717 . 0 208 0 2 0 0 0 0 -14.37819 0.9999997 1 1 1 0 T 2 4 29 172807831 172807831 C T 1 0 0 0 0 0 0 0 1 4729 813 29 3 3 ECT2 3 172807831 Silent SNP C C3L-01924_T 2947101 172807831 25487728 137 8007 USP13 0 . GRCh38 3 179708874 179708874 + Missense_Mutation SNP G G T rs773037853 C3L-01924_T C3L-01924_N G G c.722G>T p.Gly241Val p.G241V ENST00000263966 6/21 189 175 14 200 200 0 strelka-varscan-mutect USP13,missense_variant,p.Gly241Val,ENST00000263966,NM_003940.2;USP13,missense_variant,p.Gly176Val,ENST00000496897,;USP13,non_coding_transcript_exon_variant,,ENST00000482333,;USP13,downstream_gene_variant,,ENST00000497380,; T ENST00000263966 Transcript missense_variant 1193/8323 722/2592 241/863 G/V gGc/gTc rs773037853 1 1 USP13 HGNC HGNC:12611 protein_coding YES CCDS3235.1 ENSP00000263966 Q92995 A0A0A6YZ17 UPI000006DC10 NM_003940.2 deleterious(0) 6/21 PROSITE_profiles:PS50271,Gene3D:3.30.40.10,PIRSF_domain:PIRSF016308,Pfam_domain:PF02148,SMART_domains:SM00290,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs773037853 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 179708874 179708874 G T 1 0 0 0 0 1 0 0 0 17578 1203 42 2 2 USP13 3 179708874 Missense_Mutation SNP G C3L-01924_T 6901043 179708874 18586685 138 8008 EIF4G1 0 . GRCh38 3 184322706 184322706 + Nonsense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.1792G>T p.Glu598Ter p.E598* ENST00000424196 11/32 526 461 65 616 615 1 strelka-varscan-mutect EIF4G1,stop_gained,p.Glu591Ter,ENST00000342981,NM_182917.4;EIF4G1,stop_gained,p.Glu598Ter,ENST00000424196,;EIF4G1,stop_gained,p.Glu551Ter,ENST00000414031,NM_001291157.1;EIF4G1,stop_gained,p.Glu591Ter,ENST00000346169,NM_198241.2;EIF4G1,stop_gained,p.Glu598Ter,ENST00000352767,NM_001194947.1;EIF4G1,stop_gained,p.Glu504Ter,ENST00000392537,NM_198244.2;EIF4G1,stop_gained,p.Glu598Ter,ENST00000382330,NM_001194946.1;EIF4G1,stop_gained,p.Glu504Ter,ENST00000427845,;EIF4G1,stop_gained,p.Glu395Ter,ENST00000434061,NM_004953.4;EIF4G1,stop_gained,p.Glu427Ter,ENST00000350481,NM_198242.2;EIF4G1,stop_gained,p.Glu551Ter,ENST00000411531,;EIF4G1,stop_gained,p.Glu395Ter,ENST00000435046,;EIF4G1,stop_gained,p.Glu427Ter,ENST00000441154,;EIF4G1,stop_gained,p.Glu532Ter,ENST00000426123,;EIF4G1,stop_gained,p.Glu598Ter,ENST00000421110,;EIF4G1,stop_gained,p.Glu591Ter,ENST00000450424,;EIF4G1,stop_gained,p.Glu427Ter,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000457456,;EIF4G1,downstream_gene_variant,,ENST00000427141,;EIF4G1,downstream_gene_variant,,ENST00000456033,;EIF4G1,upstream_gene_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000440448,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000455679,;EIF4G1,downstream_gene_variant,,ENST00000428387,;SNORD66,upstream_gene_variant,,ENST00000390856,;EIF4G1,3_prime_UTR_variant,,ENST00000442406,;EIF4G1,3_prime_UTR_variant,,ENST00000413967,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,upstream_gene_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000493299,;EIF4G1,upstream_gene_variant,,ENST00000482303,; T ENST00000424196 Transcript stop_gained 2181/5653 1792/4821 598/1606 E/* Gaa/Taa COSM3331176 1 1 EIF4G1 HGNC HGNC:3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 11/32 hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF10 1 HIGH 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 184322706 184322706 G T 1 0 0 0 0 0 1 0 0 4870 1175 41 2 2 EIF4G1 3 184322706 Nonsense_Mutation SNP G C3L-01924_T 4613832 184322706 13972853 139 8009 GAK 0 . GRCh38 4 851771 851771 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.3487G>C p.Gly1163Arg p.G1163R ENST00000314167 25/28 118 100 18 115 114 1 strelka-varscan-mutect GAK,missense_variant,p.Gly1163Arg,ENST00000314167,NM_005255.2;GAK,missense_variant,p.Gly1084Arg,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,missense_variant,p.Gly319Arg,ENST00000511980,;GAK,missense_variant,p.Gly268Arg,ENST00000618573,;GAK,downstream_gene_variant,,ENST00000510799,;GAK,non_coding_transcript_exon_variant,,ENST00000509566,;GAK,missense_variant,p.Gly51Arg,ENST00000504668,;GAK,non_coding_transcript_exon_variant,,ENST00000515868,;GAK,non_coding_transcript_exon_variant,,ENST00000511345,;GAK,upstream_gene_variant,,ENST00000502799,; G ENST00000314167 Transcript missense_variant 3598/4442 3487/3936 1163/1311 G/R Ggg/Cgg 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 deleterious(0) 25/28 hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172,Superfamily_domains:SSF46565 MODERATE 1 SNV 1 1 PASS rs1455189049 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 851771 851771 C G 1 0 0 0 0 1 0 0 0 6063 623 22 4 4 GAK 4 851771 Missense_Mutation SNP C C3L-01924_T 851771 189362784 140 8010 CTBP1 0 . GRCh38 4 1237899 1237899 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.446A>G p.Gln149Arg p.Q149R ENST00000510568 2/2 128 114 14 157 157 0 strelka-varscan-mutect CTBP1,missense_variant,p.Gln149Arg,ENST00000510568,;CTBP1,intron_variant,,ENST00000382952,NM_001012614.1;CTBP1,intron_variant,,ENST00000290921,NM_001328.2;CTBP1,intron_variant,,ENST00000515399,;CTBP1,intron_variant,,ENST00000514210,;CTBP1,intron_variant,,ENST00000506180,;CTBP1,intron_variant,,ENST00000513420,;CTBP1,upstream_gene_variant,,ENST00000629223,;CTBP1,intron_variant,,ENST00000515690,;CTBP1,intron_variant,,ENST00000514495,;CTBP1,upstream_gene_variant,,ENST00000514669,; C ENST00000510568 Transcript missense_variant 1038/4250 446/507 149/168 Q/R cAg/cGg 1 -1 CTBP1 HGNC HGNC:2494 protein_coding ENSP00000423872 E7EUB3 UPI0000070FA2 2/2 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 1237899 1237899 T C 1 0 0 0 0 1 0 0 0 3803 1580 55 5 5 CTBP1 4 1237899 Missense_Mutation SNP T C3L-01924_T 386128 1237899 188976656 141 8011 CFAP99 0 . GRCh38 4 2436926 2436926 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.164T>C p.Leu55Pro p.L55P ENST00000616117 2/15 241 218 23 255 255 0 strelka-varscan-mutect CFAP99,missense_variant,p.Leu55Pro,ENST00000635017,;CFAP99,missense_variant,p.Leu55Pro,ENST00000616117,NM_001193282.2;CFAP99,non_coding_transcript_exon_variant,,ENST00000511731,; C ENST00000616117 Transcript missense_variant 164/1941 164/1941 55/646 L/P cTc/cCc 1 1 CFAP99 HGNC HGNC:51180 protein_coding YES CCDS75092.1 ENSP00000480601 A0A087WWY8 UPI00043788D2 NM_001193282.2 deleterious(0) 2/15 hmmpanther:PTHR34649,hmmpanther:PTHR34649:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 2436926 2436926 T C 1 0 0 0 0 1 0 0 0 3036 1551 54 5 5 CFAP99 4 2436926 Missense_Mutation SNP T C3L-01924_T 1199027 2436926 187777629 142 8012 PROM1 0 . GRCh38 4 15980449 15980449 + Missense_Mutation SNP C C T rs370736469 C3L-01924_T C3L-01924_N C C c.2462G>A p.Arg821Gln p.R821Q ENST00000510224 24/28 184 171 13 249 249 0 strelka-varscan-mutect PROM1,missense_variant,p.Arg812Gln,ENST00000505450,NM_001145848.1;PROM1,missense_variant,p.Arg812Gln,ENST00000508167,NM_001145847.1;PROM1,missense_variant,p.Arg821Gln,ENST00000510224,;PROM1,missense_variant,p.Arg821Gln,ENST00000447510,NM_006017.2;PROM1,missense_variant,p.Arg821Gln,ENST00000540805,NM_001145849.1,NM_001145851.1;PROM1,missense_variant,p.Arg821Gln,ENST00000539194,NM_001145850.1,NM_001145852.1;PROM1,missense_variant,p.Arg72Gln,ENST00000513946,;PROM1,missense_variant,p.Arg44Gln,ENST00000503884,; T ENST00000510224 Transcript missense_variant 2711/4006 2462/2598 821/865 R/Q cGa/cAa rs370736469 1 -1 PROM1 HGNC HGNC:9454 protein_coding YES CCDS47029.1 ENSP00000426809 O43490 UPI000004ECD6 deleterious(0.03) 24/28 hmmpanther:PTHR22730,hmmpanther:PTHR22730:SF3 MODERATE 1 SNV 5 1 PASS rs370736469 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 15980449 15980449 C T 1 0 0 0 0 1 0 0 0 12687 884 31 1 1 PROM1 4 15980449 Missense_Mutation SNP C C3L-01924_T 13543523 15980449 174234106 143 8013 DHX15 0 . GRCh38 4 24554750 24554750 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.1055T>A p.Leu352His p.L352H ENST00000336812 5/14 162 131 31 219 219 0 strelka-varscan-mutect DHX15,missense_variant,p.Leu352His,ENST00000336812,NM_001358.2; T ENST00000336812 Transcript missense_variant 1212/2994 1055/2388 352/795 L/H cTt/cAt 1 -1 DHX15 HGNC HGNC:2738 protein_coding YES CCDS33966.1 ENSP00000336741 O43143 UPI000012907A NM_001358.2 deleterious(0) 5/14 PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF95,Pfam_domain:PF00271,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 24554750 24554750 A T 1 0 0 0 0 1 0 0 0 4305 72 3 4 4 DHX15 4 24554750 Missense_Mutation SNP A C3L-01924_T 8574301 24554750 165659805 144 8014 CNGA1 0 . GRCh38 4 47937033 47937033 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1668G>T p.= p.L556L ENST00000402813 10/10 251 234 17 323 322 1 strelka-varscan-mutect CNGA1,synonymous_variant,p.=,ENST00000402813,NM_001142564.1;CNGA1,synonymous_variant,p.=,ENST00000514170,;CNGA1,synonymous_variant,p.=,ENST00000420489,NM_000087.3;CNGA1,synonymous_variant,p.=,ENST00000544810,;CNGA1,synonymous_variant,p.=,ENST00000358519,;NIPAL1,intron_variant,,ENST00000513724,;NIPAL1,intron_variant,,ENST00000500571,; A ENST00000402813 Transcript synonymous_variant 1811/2867 1668/2280 556/759 L ctG/ctT 1 -1 CNGA1 HGNC HGNC:2148 protein_coding YES CCDS47050.1 ENSP00000384264 P29973 UPI0001881B54 NM_001142564.1 10/10 Gene3D:2.60.120.10,PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF387,SMART_domains:SM00100,Superfamily_domains:SSF51206 LOW 1 SNV 1 1 PASS rs1188728815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 47937033 47937033 C A 1 0 0 0 0 0 0 0 1 3376 465 17 2 2 CNGA1 4 47937033 Silent SNP C C3L-01924_T 23382283 47937033 142277522 145 8015 KDR 0 . GRCh38 4 55115397 55115397 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.373T>A p.Phe125Ile p.F125I ENST00000263923 4/30 210 177 33 267 267 0 strelka-varscan-mutect KDR,missense_variant,p.Phe125Ile,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; T ENST00000263923 Transcript missense_variant 669/5831 373/4071 125/1356 F/I Ttt/Att 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0) 4/30 Gene3D:2.60.40.10,Prints_domain:PR01832,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 55115397 55115397 A T 1 0 0 0 0 1 0 0 0 8059 101 4 4 4 KDR 4 55115397 Missense_Mutation SNP A C3L-01924_T 7178364 55115397 135099158 146 8016 HTN3 0 . GRCh38 4 70031991 70031991 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.64C>A p.His22Asn p.H22N ENST00000530128 3/6 169 143 26 254 254 0 strelka-varscan-mutect HTN3,missense_variant,p.His22Asn,ENST00000530128,;HTN3,missense_variant,p.His22Asn,ENST00000526767,NM_000200.2;HTN3,missense_variant,p.His22Asn,ENST00000381057,;HTN3,non_coding_transcript_exon_variant,,ENST00000529625,;HTN3,non_coding_transcript_exon_variant,,ENST00000533547,;HTN3,downstream_gene_variant,,ENST00000528003,; A ENST00000530128 Transcript missense_variant 139/775 64/156 22/51 H/N Cat/Aat 1 1 HTN3 HGNC HGNC:5284 protein_coding YES CCDS33999.1 ENSP00000432561 P15516 UPI000012C7A2 tolerated_low_confidence(0.31) 3/6 hmmpanther:PTHR15057:SF1,hmmpanther:PTHR15057 MODERATE 1 SNV 2 1 PASS rs1370726708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 70031991 70031991 C A 1 0 0 0 0 1 0 0 0 7331 478 17 2 2 HTN3 4 70031991 Missense_Mutation SNP C C3L-01924_T 14916594 70031991 120182564 147 8017 GK2 0 . GRCh38 4 79407112 79407112 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.1089C>A p.= p.A363A ENST00000358842 1/1 224 184 40 292 292 0 strelka-varscan-mutect GK2,synonymous_variant,p.=,ENST00000358842,NM_033214.2; T ENST00000358842 Transcript synonymous_variant 1182/1942 1089/1662 363/553 A gcC/gcA 1 -1 GK2 HGNC HGNC:4291 protein_coding YES CCDS3585.1 ENSP00000351706 Q14410 A0A140VKG0 UPI000011E629 NM_033214.2 1/1 hmmpanther:PTHR10196:SF46,hmmpanther:PTHR10196,TIGRFAM_domain:TIGR01311,PIRSF_domain:PIRSF000538,Gene3D:3.30.420.40,Pfam_domain:PF02782,Superfamily_domains:SSF53067 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 79407112 79407112 G T 1 0 0 0 0 0 0 0 1 6299 987 35 2 2 GK2 4 79407112 Silent SNP G C3L-01924_T 9375121 79407112 110807443 148 8018 GPAT3 0 . GRCh38 4 83604757 83604757 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1295C>T p.Ser432Phe p.S432F ENST00000611707 13/13 114 97 17 148 148 0 strelka-varscan-mutect GPAT3,missense_variant,p.Ser432Phe,ENST00000611707,NM_001256422.1;GPAT3,missense_variant,p.Ser432Phe,ENST00000395226,NM_001256421.1;GPAT3,missense_variant,p.Ser432Phe,ENST00000264409,NM_032717.4;GPAT3,non_coding_transcript_exon_variant,,ENST00000509044,; T ENST00000611707 Transcript missense_variant 1518/2633 1295/1305 432/434 S/F tCt/tTt 1 1 GPAT3 HGNC HGNC:28157 protein_coding YES CCDS3606.1 ENSP00000482571 Q53EU6 A0A024RDG5 UPI000004B62F NM_001256422.1 deleterious(0) 13/13 hmmpanther:PTHR23063:SF10,hmmpanther:PTHR23063 MODERATE 1 SNV 5 1 PASS rs763892708 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 83604757 83604757 C T 1 0 0 0 0 1 0 0 0 6487 913 32 3 3 GPAT3 4 83604757 Missense_Mutation SNP C C3L-01924_T 4197645 83604757 106609798 149 8019 UNC5C 0 . GRCh38 4 95219148 95219148 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1466C>A p.Thr489Asn p.T489N ENST00000453304 9/16 231 218 13 319 319 0 strelka-varscan-mutect UNC5C,missense_variant,p.Thr489Asn,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Thr448Asn,ENST00000610318,;UNC5C,missense_variant,p.Thr508Asn,ENST00000513796,;UNC5C,missense_variant,p.Thr508Asn,ENST00000506749,; T ENST00000453304 Transcript missense_variant 1815/9875 1466/2796 489/931 T/N aCc/aAc 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 tolerated(0.57) 9/16 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7 MODERATE 1 SNV 1 1 PASS rs1169277663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 95219148 95219148 G T 1 0 0 0 0 1 0 0 0 17517 1261 44 2 2 UNC5C 4 95219148 Missense_Mutation SNP G C3L-01924_T 11614391 95219148 94995407 150 8020 ARHGEF38 0 . GRCh38 4 105659139 105659139 + Missense_Mutation SNP G G T rs187252943 C3L-01924_T C3L-01924_N G G c.1319G>T p.Arg440Leu p.R440L ENST00000420470 10/14 211 177 34 231 231 0 strelka-varscan-mutect ARHGEF38,missense_variant,p.Arg440Leu,ENST00000420470,NM_001242729.1;ARHGEF38,non_coding_transcript_exon_variant,,ENST00000508036,; T ENST00000420470 Transcript missense_variant 1463/5454 1319/2334 440/777 R/L cGc/cTc rs187252943 1 1 ARHGEF38 HGNC HGNC:25968 protein_coding YES CCDS56338.1 ENSP00000416125 Q9NXL2 UPI0001D3B6A5 NM_001242729.1 deleterious(0) 10/14 PROSITE_profiles:PS51021,hmmpanther:PTHR22834,hmmpanther:PTHR22834:SF17,Gene3D:1.20.1270.60,SMART_domains:SM00721,Superfamily_domains:SSF103657 MODERATE 1 SNV 5 1 PASS rs187252943 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 105659139 105659139 G T 1 0 0 0 0 1 0 0 0 1041 1087 38 1 1 ARHGEF38 4 105659139 Missense_Mutation SNP G C3L-01924_T 10439991 105659139 84555416 151 8021 EGF 0 . GRCh38 4 109943970 109943970 + Missense_Mutation SNP G G A rs373552129 C3L-01924_T C3L-01924_N G G c.638G>A p.Arg213Gln p.R213Q ENST00000265171 4/24 374 338 36 542 542 0 strelka-varscan-mutect EGF,missense_variant,p.Arg213Gln,ENST00000265171,NM_001963.4;EGF,missense_variant,p.Arg213Gln,ENST00000509793,NM_001178131.1;EGF,missense_variant,p.Arg213Gln,ENST00000503392,NM_001178130.1;EGF,non_coding_transcript_exon_variant,,ENST00000502723,; A ENST00000265171 Transcript missense_variant 1083/4880 638/3624 213/1207 R/Q cGg/cAg rs373552129,COSM4121342 1 1 EGF HGNC HGNC:3229 protein_coding YES CCDS3689.1 ENSP00000265171 P01133 UPI000013D5C8 NM_001963.4 deleterious(0.01) 4/24 Gene3D:2.120.10.30,PIRSF_domain:PIRSF001778,PROSITE_profiles:PS51120,SMART_domains:SM00135,Superfamily_domains:SSF63825 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373552129 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 109943970 109943970 G A 1 0 0 0 0 1 0 0 0 4798 1116 39 1 1 EGF 4 109943970 Missense_Mutation SNP G C3L-01924_T 4284831 109943970 80270585 152 8022 ENPEP 0 . GRCh38 4 110509670 110509670 + Missense_Mutation SNP G G T rs772717391 C3L-01924_T C3L-01924_N G G c.1057G>T p.Asp353Tyr p.D353Y ENST00000265162 5/20 121 105 16 166 166 0 strelka-varscan-mutect ENPEP,missense_variant,p.Asp353Tyr,ENST00000265162,NM_001977.3;RP11-380D23.1,downstream_gene_variant,,ENST00000503998,;ENPEP,downstream_gene_variant,,ENST00000510961,;ENPEP,upstream_gene_variant,,ENST00000509344,; T ENST00000265162 Transcript missense_variant 1399/6943 1057/2874 353/957 D/Y Gat/Tat rs772717391 1 1 ENPEP HGNC HGNC:3355 protein_coding YES CCDS3691.1 ENSP00000265162 Q07075 UPI000013D5C6 NM_001977.3 deleterious(0) 5/20 Pfam_domain:PF01433,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF188,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs772717391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 110509670 110509670 G T 1 0 0 0 0 1 0 0 0 4973 942 33 2 2 ENPEP 4 110509670 Missense_Mutation SNP G C3L-01924_T 565700 110509670 79704885 153 8023 ANK2 0 . GRCh38 4 113356689 113356689 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.8071C>A p.Pro2691Thr p.P2691T ENST00000357077 38/46 327 269 58 456 456 0 strelka-varscan-mutect ANK2,missense_variant,p.Pro2691Thr,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Pro2658Thr,ENST00000264366,;ANK2,5_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript missense_variant 8124/14196 8071/11874 2691/3957 P/T Cct/Act 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0) 38/46 Low_complexity_(Seg):seg,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 113356689 113356689 C A 1 0 0 0 0 1 0 0 0 721 507 18 2 2 ANK2 4 113356689 Missense_Mutation SNP C C3L-01924_T 2847019 113356689 76857866 154 8024 ANK2 0 . GRCh38 4 113359148 113359148 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.10530C>A p.= p.A3510A ENST00000357077 38/46 95 75 20 149 148 1 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript synonymous_variant 10583/14196 10530/11874 3510/3957 A gcC/gcA 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 113359148 113359148 C A 1 0 0 0 0 0 0 0 1 721 610 22 2 2 ANK2 4 113359148 Silent SNP C C3L-01924_T 2459 113359148 76855407 155 8025 TRAM1L1 0 . GRCh38 4 117084617 117084617 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.777G>C p.Leu259Phe p.L259F ENST00000310754 1/1 231 210 21 303 303 0 strelka-varscan-mutect TRAM1L1,missense_variant,p.Leu259Phe,ENST00000310754,NM_152402.2; G ENST00000310754 Transcript missense_variant 960/2023 777/1110 259/369 L/F ttG/ttC 1 -1 TRAM1L1 HGNC HGNC:28371 protein_coding YES CCDS3707.1 ENSP00000309402 Q8N609 UPI000013F075 NM_152402.2 tolerated(0.19) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50922,hmmpanther:PTHR12371,hmmpanther:PTHR12371:SF9,PIRSF_domain:PIRSF005449,Pfam_domain:PF03798,SMART_domains:SM00724 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 117084617 117084617 C G 1 0 0 0 0 1 0 0 0 16935 593 21 4 4 TRAM1L1 4 117084617 Missense_Mutation SNP C C3L-01924_T 3725469 117084617 73129938 156 8026 MFSD8 0 . GRCh38 4 127921672 127921673 + Frame_Shift_Ins INS - - A novel C3L-01924_T C3L-01924_N - - c.1201dupT p.Cys401LeufsTer4 p.C401Lfs*4 ENST00000296468 12/13 378 320 58 482 481 1 sindel-varindel-pindel MFSD8,frameshift_variant,p.Cys401LeufsTer4,ENST00000296468,NM_152778.2;MFSD8,frameshift_variant,p.Cys356LeufsTer4,ENST00000513559,;MFSD8,non_coding_transcript_exon_variant,,ENST00000515130,;MFSD8,downstream_gene_variant,,ENST00000505284,;MFSD8,upstream_gene_variant,,ENST00000503928,;MFSD8,non_coding_transcript_exon_variant,,ENST00000504126,;MFSD8,downstream_gene_variant,,ENST00000509826,; A ENST00000296468 Transcript frameshift_variant 1329-1330/4510 1201-1202/1557 401/518 C/LX tgc/tTgc 1 -1 MFSD8 HGNC HGNC:28486 protein_coding YES CCDS3736.1 ENSP00000296468 Q8NHS3 UPI000004DAF1 NM_152778.2 12/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23510:SF3,hmmpanther:PTHR23510 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 29 127921672 127921672 - A 1 0 1 1 0 0 0 0 0 9496 710 25 0 0 MFSD8 4 127921672 Frame_Shift_Ins INS - C3L-01924_T 10837055 127921672 62292883 157 8027 ABHD18 0 . GRCh38 4 128030582 128030582 + Missense_Mutation SNP G G T rs771220150 C3L-01924_T C3L-01924_N G G c.1151G>T p.Arg384Leu p.R384L ENST00000398965 11/11 128 119 9 118 118 0 strelka-varscan-mutect ABHD18,missense_variant,p.Arg336Leu,ENST00000388795,NM_001319305.1,NM_001319306.1;ABHD18,missense_variant,p.Arg384Leu,ENST00000398965,NM_001039717.1;ABHD18,missense_variant,p.Arg384Leu,ENST00000444616,;ABHD18,missense_variant,p.Arg291Leu,ENST00000611882,;ABHD18,3_prime_UTR_variant,,ENST00000473040,; T ENST00000398965 Transcript missense_variant 1469/2177 1151/1245 384/414 R/L cGa/cTa rs771220150 1 1 ABHD18 HGNC HGNC:26111 protein_coding YES CCDS47131.1 ENSP00000381937 Q0P651 UPI00006C511D NM_001039717.1 tolerated(0.36) 11/11 hmmpanther:PTHR13617,Gene3D:3.40.50.1820,Pfam_domain:PF09752,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs771220150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 128030582 128030582 G T 1 0 0 0 0 1 0 0 0 91 1058 37 1 1 ABHD18 4 128030582 Missense_Mutation SNP G C3L-01924_T 108910 128030582 62183973 158 8028 PCDH10 0 . GRCh38 4 133152527 133152527 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2387C>A p.Pro796His p.P796H ENST00000264360 1/5 243 214 29 314 314 0 strelka-varscan-mutect PCDH10,missense_variant,p.Pro796His,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Pro796His,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; A ENST00000264360 Transcript missense_variant 3213/8489 2387/3123 796/1040 P/H cCc/cAc 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 deleterious(0.05) 1/5 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 133152527 133152527 C A 1 0 0 0 0 1 0 0 0 11594 623 22 2 2 PCDH10 4 133152527 Missense_Mutation SNP C C3L-01924_T 5121945 133152527 57062028 159 8029 SMARCA5 0 . GRCh38 4 143528692 143528692 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1067C>T p.Pro356Leu p.P356L ENST00000283131 8/24 120 102 18 205 202 3 strelka-varscan-mutect SMARCA5,missense_variant,p.Pro356Leu,ENST00000283131,NM_003601.3; T ENST00000283131 Transcript missense_variant 1529/7923 1067/3159 356/1052 P/L cCa/cTa 1 1 SMARCA5 HGNC HGNC:11101 protein_coding YES CCDS3761.1 ENSP00000283131 O60264 UPI000006E693 NM_003601.3 deleterious(0) 8/24 PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF691,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 29 143528692 143528692 C T 1 0 0 0 0 1 0 0 0 15064 594 21 3 3 SMARCA5 4 143528692 Missense_Mutation SNP C C3L-01924_T 10376165 143528692 46685863 160 8030 DCHS2 0 . GRCh38 4 154489317 154489317 + Missense_Mutation SNP T T A rs750128177 C3L-01924_T C3L-01924_N T T c.2039A>T p.His680Leu p.H680L ENST00000339452 1/8 28 24 4 56 56 0 strelka-varscan-mutect DCHS2,missense_variant,p.His680Leu,ENST00000339452,NM_001142552.1;DCHS2,non_coding_transcript_exon_variant,,ENST00000456341,; A ENST00000339452 Transcript missense_variant 2400/5064 2039/4110 680/1369 H/L cAc/cTc rs750128177 1 -1 DCHS2 HGNC HGNC:23111 protein_coding CCDS47150.1 ENSP00000345062 A0A0A0MRC0 UPI00002372F1 NM_001142552.1 tolerated(0.19) 1/8 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.55728 1 1 1 1 0 A 3 1 29 154489317 154489317 T A 1 0 0 0 0 1 0 0 0 4091 1696 59 4 4 DCHS2 4 154489317 Missense_Mutation SNP T C3L-01924_T 10960625 154489317 35725238 161 8031 NAF1 0 . GRCh38 4 163166458 163166458 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.270G>T p.= p.P90P ENST00000274054 1/8 74 70 4 93 93 0 strelka-varscan-mutect NAF1,synonymous_variant,p.=,ENST00000274054,NM_138386.2;NAF1,synonymous_variant,p.=,ENST00000422287,NM_001128931.1;NAF1,non_coding_transcript_exon_variant,,ENST00000509232,;NAF1,non_coding_transcript_exon_variant,,ENST00000502973,; A ENST00000274054 Transcript synonymous_variant 464/1907 270/1485 90/494 P ccG/ccT 1 -1 NAF1 HGNC HGNC:25126 protein_coding YES CCDS3803.1 ENSP00000274054 Q96HR8 UPI000013D9EB NM_138386.2 1/8 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 163166458 163166458 C A 1 0 0 0 0 0 0 0 1 10147 639 23 1 1 NAF1 4 163166458 Silent SNP C C3L-01924_T 8677141 163166458 27048097 162 8032 TKTL2 0 . GRCh38 4 163472194 163472194 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.1541T>G p.Val514Gly p.V514G ENST00000280605 1/1 178 156 22 234 233 1 strelka-varscan-mutect TKTL2,missense_variant,p.Val514Gly,ENST00000280605,NM_032136.4; C ENST00000280605 Transcript missense_variant 1553/2654 1541/1881 514/626 V/G gTt/gGt 1 -1 TKTL2 HGNC HGNC:25313 protein_coding YES CCDS3805.1 ENSP00000280605 Q9H0I9 A0A140VKC2 UPI0000037C67 NM_032136.4 deleterious(0) 1/1 hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF49,Pfam_domain:PF02780,Gene3D:3.40.50.920,Superfamily_domains:SSF52922 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 163472194 163472194 A C 1 0 0 0 0 1 0 0 0 16379 43 2 5 5 TKTL2 4 163472194 Missense_Mutation SNP A C3L-01924_T 305736 163472194 26742361 163 8033 RP11-668G10.2 0 . GRCh38 4 165279377 165279377 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.269T>A p.Val90Asp p.V90D ENST00000505354 1/1 382 314 68 571 571 0 strelka-varscan-mutect RP11-668G10.2,missense_variant,p.Val90Asp,ENST00000505354,;KLHL2,intron_variant,,ENST00000226725,NM_007246.3;KLHL2,intron_variant,,ENST00000538127,NM_001161522.1;KLHL2,intron_variant,,ENST00000421009,;KLHL2,intron_variant,,ENST00000514860,NM_001161521.1;KLHL2,intron_variant,,ENST00000506761,;KLHL2,intron_variant,,ENST00000509028,;KLHL2,intron_variant,,ENST00000506541,;KLHL2,intron_variant,,ENST00000506824,; T ENST00000505354 Transcript missense_variant 303/1868 269/1662 90/553 V/D gTc/gAc 1 -1 RP11-668G10.2 Clone_based_vega_gene protein_coding YES ENSP00000489687 Q14409 UPI000013EB4C 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00370,PIRSF_domain:PIRSF000538,hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF63,Superfamily_domains:SSF53067,TIGRFAM_domain:TIGR01311 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 165279377 165279377 A T 1 0 0 0 0 1 0 0 0 13756 275 10 4 4 RP11-668G10.2 4 165279377 Missense_Mutation SNP A C3L-01924_T 1807183 165279377 24935178 164 8034 TLL1 0 . GRCh38 4 166055109 166055109 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1558C>A p.Leu520Met p.L520M ENST00000061240 13/21 127 110 17 141 141 0 strelka-varscan-mutect TLL1,missense_variant,p.Leu520Met,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Leu543Met,ENST00000507499,;RNA5SP170,upstream_gene_variant,,ENST00000517150,;TLL1,3_prime_UTR_variant,,ENST00000509505,; A ENST00000061240 Transcript missense_variant 2205/6708 1558/3042 520/1013 L/M Ctg/Atg 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 deleterious(0) 13/21 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 203 4 3 0 0 0 0 -20 0.9998074 1 1 1 0 A 3 1 29 166055109 166055109 C A 1 0 0 0 0 1 0 0 0 16391 680 24 2 2 TLL1 4 166055109 Missense_Mutation SNP C C3L-01924_T 775732 166055109 24159446 165 8035 HAND2 0 . GRCh38 4 173529075 173529075 + Missense_Mutation SNP G G T rs758127022 C3L-01924_T C3L-01924_N G G c.215C>A p.Ala72Asp p.A72D ENST00000359562 1/2 63 58 5 90 90 0 strelka-varscan-mutect HAND2,missense_variant,p.Ala72Asp,ENST00000359562,NM_021973.2;HAND2,splice_region_variant,,ENST00000621866,;HAND2-AS1,intron_variant,,ENST00000512099,;HAND2-AS1,intron_variant,,ENST00000515310,;HAND2-AS1,upstream_gene_variant,,ENST00000502896,;HAND2-AS1,upstream_gene_variant,,ENST00000507062,;HAND2-AS1,upstream_gene_variant,,ENST00000510339,;HAND2-AS1,upstream_gene_variant,,ENST00000515350,;HAND2-AS1,upstream_gene_variant,,ENST00000507571,;HAND2-AS1,upstream_gene_variant,,ENST00000508534,;HAND2-AS1,upstream_gene_variant,,ENST00000503198,;HAND2-AS1,upstream_gene_variant,,ENST00000616485,;HAND2-AS1,upstream_gene_variant,,ENST00000503474,;HAND2-AS1,upstream_gene_variant,,ENST00000502334,;HAND2-AS1,upstream_gene_variant,,ENST00000514673,;HAND2-AS1,upstream_gene_variant,,ENST00000508887,;HAND2-AS1,upstream_gene_variant,,ENST00000515376,;HAND2-AS1,upstream_gene_variant,,ENST00000514431,;HAND2-AS1,upstream_gene_variant,,ENST00000512246,;HAND2-AS1,upstream_gene_variant,,ENST00000505621,;HAND2-AS1,upstream_gene_variant,,ENST00000507322,;HAND2-AS1,upstream_gene_variant,,ENST00000504740,;HAND2-AS1,upstream_gene_variant,,ENST00000515741,;HAND2-AS1,upstream_gene_variant,,ENST00000515345,;HAND2-AS1,upstream_gene_variant,,ENST00000504429,;HAND2-AS1,upstream_gene_variant,,ENST00000509640,;HAND2-AS1,upstream_gene_variant,,ENST00000509866,;HAND2-AS1,upstream_gene_variant,,ENST00000510268,;HAND2-AS1,upstream_gene_variant,,ENST00000511728,;HAND2-AS1,upstream_gene_variant,,ENST00000512929,;HAND2-AS1,upstream_gene_variant,,ENST00000507636,;HAND2-AS1,upstream_gene_variant,,ENST00000510221,;HAND2-AS1,upstream_gene_variant,,ENST00000511196,;HAND2-AS1,upstream_gene_variant,,ENST00000512209,;HAND2-AS1,upstream_gene_variant,,ENST00000512943,;HAND2-AS1,upstream_gene_variant,,ENST00000505032,;HAND2-AS1,upstream_gene_variant,,ENST00000503309,;HAND2-AS1,upstream_gene_variant,,ENST00000505817,;HAND2-AS1,upstream_gene_variant,,ENST00000502941,;HAND2,non_coding_transcript_exon_variant,,ENST00000505300,;HAND2,upstream_gene_variant,,ENST00000503024,; T ENST00000359562 Transcript missense_variant 1155/2780 215/654 72/217 A/D gCc/gAc rs758127022 1 -1 HAND2 HGNC HGNC:4808 protein_coding YES CCDS3819.1 ENSP00000352565 P61296 UPI0000003FE8 NM_021973.2 tolerated(0.14) 1/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF41 MODERATE 1 SNV 1 1 PASS rs758127022 . 0 208 2 0 0 0 0 0 -12.16787 1 1 1 1 0 T 3 4 29 173529075 173529075 G T 1 0 0 0 0 1 0 0 0 6836 1217 42 2 2 HAND2 4 173529075 Missense_Mutation SNP G C3L-01924_T 7473966 173529075 16685480 166 8036 ASB5 0 . GRCh38 4 176216948 176216948 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.732C>A p.= p.S244S ENST00000296525 6/7 152 117 35 192 192 0 strelka-varscan-mutect ASB5,synonymous_variant,p.=,ENST00000296525,NM_080874.3;ASB5,synonymous_variant,p.=,ENST00000512254,;ASB5,downstream_gene_variant,,ENST00000511879,; T ENST00000296525 Transcript synonymous_variant 846/3031 732/990 244/329 S tcC/tcA 1 -1 ASB5 HGNC HGNC:17180 protein_coding YES CCDS3827.1 ENSP00000296525 Q8WWX0 Q5HYF3 UPI00000015CF NM_080874.3 6/7 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24136,hmmpanther:PTHR24136:SF18,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 176216948 176216948 G T 1 0 0 0 0 0 0 0 1 1168 1335 47 2 2 ASB5 4 176216948 Silent SNP G C3L-01924_T 2687873 176216948 13997607 167 8037 MTNR1A 0 . GRCh38 4 186533856 186533856 + Missense_Mutation SNP C C T C3L-01924_T C3L-01924_N C C c.886G>A p.Gly296Arg p.G296R ENST00000307161 2/2 439 384 55 481 481 0 strelka-varscan-mutect MTNR1A,missense_variant,p.Gly296Arg,ENST00000307161,NM_005958.3;RP11-215A19.2,intron_variant,,ENST00000509111,; T ENST00000307161 Transcript missense_variant 1088/1289 886/1053 296/350 G/R Ggg/Agg COSM3602629 1 -1 MTNR1A HGNC HGNC:7463 protein_coding YES CCDS3848.1 ENSP00000302811 P48039 UPI0000050407 NM_005958.3 deleterious(0.03) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF52,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 1 PASS rs1483013458 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 186533856 186533856 C T 1 0 0 0 0 1 0 0 0 9938 652 23 1 1 MTNR1A 4 186533856 Missense_Mutation SNP C C3L-01924_T 10316908 186533856 3680699 168 8038 ICE1 0 . GRCh38 5 5464880 5464880 + Missense_Mutation SNP G G T rs757017386 C3L-01924_T C3L-01924_N G G c.5546G>T p.Arg1849Leu p.R1849L ENST00000296564 13/19 333 304 29 313 313 0 strelka-varscan-mutect ICE1,missense_variant,p.Arg1849Leu,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 5768/7927 5546/6801 1849/2266 R/L cGc/cTc rs757017386 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0) 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS rs757017386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 5464880 5464880 G T 1 0 0 0 0 1 0 0 0 7384 1087 38 1 1 ICE1 5 5464880 Missense_Mutation SNP G C3L-01924_T 5464880 176073379 169 8039 ADCY2 0 . GRCh38 5 7707768 7707768 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.1331G>T p.Gly444Val p.G444V ENST00000338316 9/25 295 251 44 268 267 1 strelka-varscan-mutect ADCY2,missense_variant,p.Gly444Val,ENST00000338316,NM_020546.2;RP11-711G10.1,downstream_gene_variant,,ENST00000514105,; T ENST00000338316 Transcript missense_variant 1420/6575 1331/3276 444/1091 G/V gGa/gTa COSM365829,COSM4956689,COSM4956690 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0.04) 9/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,Superfamily_domains:SSF55073 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 7707768 7707768 G T 1 0 0 0 0 1 0 0 0 338 1174 41 2 2 ADCY2 5 7707768 Missense_Mutation SNP G C3L-01924_T 2242888 7707768 173830491 170 8040 DNAH5 0 . GRCh38 5 13753288 13753288 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.10817C>T p.Pro3606Leu p.P3606L ENST00000265104 63/79 366 222 144 335 334 1 strelka-varscan-mutect DNAH5,missense_variant,p.Pro3606Leu,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript missense_variant 10922/15633 10817/13875 3606/4624 P/L cCa/cTa 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 63/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF12781 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 13753288 13753288 G A 1 0 0 0 0 1 0 0 0 4419 1348 47 3 3 DNAH5 5 13753288 Missense_Mutation SNP G C3L-01924_T 6045520 13753288 167784971 171 8041 CDH12 0 . GRCh38 5 21751916 21751916 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2206C>A p.Leu736Met p.L736M ENST00000382254 15/15 511 478 33 386 386 0 strelka-varscan-mutect CDH12,missense_variant,p.Leu736Met,ENST00000382254,NM_004061.3;CDH12,missense_variant,p.Leu736Met,ENST00000504376,;CDH12,missense_variant,p.Leu696Met,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript missense_variant 3293/4164 2206/2385 736/794 L/M Ctg/Atg 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 deleterious(0) 15/15 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 21751916 21751916 G T 1 0 0 0 0 1 0 0 0 2801 1020 36 2 2 CDH12 5 21751916 Missense_Mutation SNP G C3L-01924_T 7998628 21751916 159786343 172 8042 CDH10 0 . GRCh38 5 24491618 24491618 + Missense_Mutation SNP C C A rs369284486 C3L-01924_T C3L-01924_N C C c.1834G>T p.Gly612Trp p.G612W ENST00000264463 11/12 262 216 46 219 219 0 strelka-varscan-mutect CDH10,missense_variant,p.Gly612Trp,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; A ENST00000264463 Transcript missense_variant 2342/3438 1834/2367 612/788 G/W Ggg/Tgg rs369284486,COSM5351188 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 deleterious(0) 11/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369284486 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 24491618 24491618 C A 1 0 0 0 0 1 0 0 0 2799 594 21 2 2 CDH10 5 24491618 Missense_Mutation SNP C C3L-01924_T 2739702 24491618 157046641 173 8043 RAI14 0 . GRCh38 5 34824161 34824161 + Silent SNP A A G novel C3L-01924_T C3L-01924_N A A c.2328A>G p.= p.L776L ENST00000515799 17/20 194 166 28 203 203 0 strelka-varscan-mutect RAI14,synonymous_variant,p.=,ENST00000265109,NM_015577.2;RAI14,synonymous_variant,p.=,ENST00000428746,NM_001145520.1;RAI14,synonymous_variant,p.=,ENST00000515799,NM_001145525.1;RAI14,synonymous_variant,p.=,ENST00000503673,NM_001145521.1;RAI14,synonymous_variant,p.=,ENST00000506376,NM_001145523.1;RAI14,synonymous_variant,p.=,ENST00000512629,NM_001145522.1;RAI14,downstream_gene_variant,,ENST00000508777,;RAI14,upstream_gene_variant,,ENST00000507883,;RAI14,upstream_gene_variant,,ENST00000513772,; G ENST00000515799 Transcript synonymous_variant 2820/3486 2328/2952 776/983 L ttA/ttG 1 1 RAI14 HGNC HGNC:14873 protein_coding YES CCDS54839.1 ENSP00000427123 Q9P0K7 UPI00001B296B NM_001145525.1 17/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24129 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 34824161 34824161 A G 1 0 0 0 0 0 0 0 1 13167 417 15 5 5 RAI14 5 34824161 Silent SNP A C3L-01924_T 10332543 34824161 146714098 174 8044 CARD6 0 . GRCh38 5 40853141 40853141 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1809G>T p.Lys603Asn p.K603N ENST00000254691 3/3 349 291 58 274 274 0 strelka-varscan-mutect CARD6,missense_variant,p.Lys603Asn,ENST00000254691,NM_032587.3;CARD6,intron_variant,,ENST00000381677,; T ENST00000254691 Transcript missense_variant 2008/4221 1809/3114 603/1037 K/N aaG/aaT 1 1 CARD6 HGNC HGNC:16394 protein_coding YES CCDS3935.1 ENSP00000254691 Q9BX69 UPI000013CE50 NM_032587.3 tolerated(0.12) 3/3 hmmpanther:PTHR22797,hmmpanther:PTHR22797:SF36 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 40853141 40853141 G T 1 0 0 0 0 1 0 0 0 2346 962 34 2 2 CARD6 5 40853141 Missense_Mutation SNP G C3L-01924_T 6028980 40853141 140685118 175 8045 MROH2B 0 . GRCh38 5 41038866 41038866 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2084G>T p.Ser695Ile p.S695I ENST00000399564 21/42 94 76 18 85 85 0 strelka-varscan-mutect MROH2B,missense_variant,p.Ser695Ile,ENST00000399564,NM_173489.4;MROH2B,missense_variant,p.Ser250Ile,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,; A ENST00000399564 Transcript missense_variant 2535/5239 2084/4758 695/1585 S/I aGc/aTc 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 tolerated(0.07) 21/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 41038866 41038866 C A 1 0 0 0 0 1 0 0 0 9745 797 28 2 2 MROH2B 5 41038866 Missense_Mutation SNP C C3L-01924_T 185725 41038866 140499393 176 8046 CDC20B 0 . GRCh38 5 55146649 55146649 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.334G>A p.Glu112Lys p.E112K ENST00000381375 3/12 245 208 37 237 237 0 strelka-varscan-mutect CDC20B,missense_variant,p.Glu112Lys,ENST00000296733,NM_152623.2;CDC20B,missense_variant,p.Glu112Lys,ENST00000381375,NM_001170402.1;CDC20B,missense_variant,p.Glu112Lys,ENST00000322374,NM_001145734.2;CDC20B,missense_variant,p.Glu91Lys,ENST00000507931,;CDC20B,missense_variant,p.Glu112Lys,ENST00000513180,; T ENST00000381375 Transcript missense_variant 480/2591 334/1560 112/519 E/K Gag/Aag 1 -1 CDC20B HGNC HGNC:24222 protein_coding YES CCDS54852.1 ENSP00000370781 Q86Y33 UPI0000D61625 NM_001170402.1 tolerated(0.33) 3/12 hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 55146649 55146649 C T 1 0 0 0 0 1 0 0 0 2763 835 29 3 3 CDC20B 5 55146649 Missense_Mutation SNP C C3L-01924_T 14107783 55146649 126391610 177 8047 MAP1B 0 . GRCh38 5 72194811 72194811 + Nonsense_Mutation SNP C C T rs868169901 C3L-01924_T C3L-01924_N C C c.1456C>T p.Arg486Ter p.R486* ENST00000296755 5/7 214 157 57 224 224 0 strelka-varscan-mutect MAP1B,stop_gained,p.Arg486Ter,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,stop_gained,p.Arg360Ter,ENST00000504492,;MAP1B,stop_gained,p.Arg503Ter,ENST00000511641,;MAP1B,3_prime_UTR_variant,,ENST00000513526,; T ENST00000296755 Transcript stop_gained 1754/12036 1456/7407 486/2468 R/* Cga/Tga rs868169901,COSM1695858 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 5/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 0,1 HIGH 1 SNV 2 0,1 1 PASS rs868169901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 72194811 72194811 C T 1 0 0 0 0 0 1 0 0 9151 644 23 1 1 MAP1B 5 72194811 Nonsense_Mutation SNP C C3L-01924_T 17048162 72194811 109343448 178 8048 HAPLN1 0 . GRCh38 5 83673488 83673488 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.36C>A p.= p.I12I ENST00000274341 2/5 197 148 49 229 229 0 strelka-varscan-mutect HAPLN1,synonymous_variant,p.=,ENST00000274341,NM_001884.3;HAPLN1,synonymous_variant,p.=,ENST00000514416,;HAPLN1,synonymous_variant,p.=,ENST00000510978,;HAPLN1,synonymous_variant,p.=,ENST00000504713,;HAPLN1,synonymous_variant,p.=,ENST00000508307,;HAPLN1,synonymous_variant,p.=,ENST00000503117,;HAPLN1,synonymous_variant,p.=,ENST00000515590,; T ENST00000274341 Transcript synonymous_variant 887/5607 36/1065 12/354 I atC/atA 1 -1 HAPLN1 HGNC HGNC:2380 protein_coding YES CCDS4061.1 ENSP00000274341 P10915 A0A024RAK9 UPI0000131BFF NM_001884.3 2/5 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22804:SF10,hmmpanther:PTHR22804 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 83673488 83673488 G T 1 0 0 0 0 0 0 0 1 6840 932 33 2 2 HAPLN1 5 83673488 Silent SNP G C3L-01924_T 11478677 83673488 97864771 179 8049 PCSK1 0 . GRCh38 5 96393216 96393216 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2047C>A p.Gln683Lys p.Q683K ENST00000311106 14/14 161 138 23 226 226 0 strelka-varscan-mutect PCSK1,missense_variant,p.Gln683Lys,ENST00000311106,NM_000439.4;PCSK1,missense_variant,p.Gln636Lys,ENST00000508626,NM_001177875.1;CTD-2337A12.1,intron_variant,,ENST00000502645,;PCSK1,non_coding_transcript_exon_variant,,ENST00000513085,; T ENST00000311106 Transcript missense_variant 2285/5086 2047/2262 683/753 Q/K Caa/Aaa 1 -1 PCSK1 HGNC HGNC:8743 protein_coding YES CCDS4081.1 ENSP00000308024 P29120 UPI000013F0F5 NM_000439.4 tolerated_low_confidence(0.23) 14/14 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 96393216 96393216 G T 1 0 0 0 0 1 0 0 0 11688 1328 46 2 2 PCSK1 5 96393216 Missense_Mutation SNP G C3L-01924_T 12719728 96393216 85145043 180 8050 TSLP 0 . GRCh38 5 111071952 111071952 + Missense_Mutation SNP A A T rs144616951 C3L-01924_T C3L-01924_N A A c.62A>T p.Gln21Leu p.Q21L ENST00000344895 1/4 133 106 27 182 182 0 strelka-varscan-mutect TSLP,missense_variant,p.Gln21Leu,ENST00000420978,;TSLP,missense_variant,p.Gln21Leu,ENST00000344895,NM_033035.4;TSLP,upstream_gene_variant,,ENST00000379706,NM_138551.4;CTC-551A13.2,downstream_gene_variant,,ENST00000507269,; T ENST00000344895 Transcript missense_variant 261/736 62/480 21/159 Q/L cAa/cTa rs144616951 1 1 TSLP HGNC HGNC:30743 protein_coding YES CCDS4101.1 ENSP00000339804 Q969D9 UPI000006DB21 NM_033035.4 deleterious(0) 1/4 hmmpanther:PTHR38003 MODERATE 1 SNV 1 1 PASS rs144616951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 111071952 111071952 A T 1 0 0 0 0 1 0 0 0 17133 130 5 4 4 TSLP 5 111071952 Missense_Mutation SNP A C3L-01924_T 14678736 111071952 70466307 181 8051 CDO1 0 . GRCh38 5 115811305 115811305 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.259G>T p.Asp87Tyr p.D87Y ENST00000250535 3/5 108 93 15 147 147 0 strelka-varscan-mutect CDO1,missense_variant,p.Asp87Tyr,ENST00000250535,NM_001801.2;CDO1,non_coding_transcript_exon_variant,,ENST00000502631,;CDO1,downstream_gene_variant,,ENST00000504613,;CDO1,downstream_gene_variant,,ENST00000504877,; A ENST00000250535 Transcript missense_variant 816/1860 259/603 87/200 D/Y Gat/Tat 1 -1 CDO1 HGNC HGNC:1795 protein_coding YES CCDS4121.1 ENSP00000250535 Q16878 UPI000016A7B9 NM_001801.2 deleterious(0) 3/5 Gene3D:2.60.120.10,Pfam_domain:PF05995,hmmpanther:PTHR12918,Superfamily_domains:SSF51182 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 115811305 115811305 C A 1 0 0 0 0 1 0 0 0 2873 826 29 2 2 CDO1 5 115811305 Missense_Mutation SNP C C3L-01924_T 4739353 115811305 65726954 182 8052 FBN2 0 . GRCh38 5 128376766 128376766 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1937G>T p.Gly646Val p.G646V ENST00000508053 20/71 458 387 71 571 570 1 strelka-varscan-mutect FBN2,missense_variant,p.Gly646Val,ENST00000508053,;FBN2,missense_variant,p.Gly646Val,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Gly645Val,ENST00000619499,;FBN2,missense_variant,p.Gly613Val,ENST00000508989,;FBN2,non_coding_transcript_exon_variant,,ENST00000511489,; A ENST00000508053 Transcript missense_variant 2912/11132 1937/8739 646/2912 G/V gGa/gTa COSM4891127,COSM4891128 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 20/71 Gene3D:2.10.25.10,Pfam_domain:PF12662,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 128376766 128376766 C A 1 0 0 0 0 1 0 0 0 5566 855 30 2 2 FBN2 5 128376766 Missense_Mutation SNP C C3L-01924_T 12565461 128376766 53161493 183 8053 FBN2 0 . GRCh38 5 128527958 128527958 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.446G>T p.Cys149Phe p.C149F ENST00000508053 10/71 285 258 27 371 371 0 strelka-varscan-mutect FBN2,missense_variant,p.Cys149Phe,ENST00000508053,;FBN2,missense_variant,p.Cys149Phe,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Cys149Phe,ENST00000619499,;FBN2,missense_variant,p.Cys116Phe,ENST00000508989,;FBN2,missense_variant,p.Cys149Phe,ENST00000502468,;FBN2,non_coding_transcript_exon_variant,,ENST00000514742,; A ENST00000508053 Transcript missense_variant 1421/11132 446/8739 149/2912 C/F tGc/tTc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 10/71 PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00181 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 128527958 128527958 C A 1 0 0 0 0 1 0 0 0 5566 710 25 2 2 FBN2 5 128527958 Missense_Mutation SNP C C3L-01924_T 151192 128527958 53010301 184 8054 SPOCK1 0 . GRCh38 5 136979393 136979393 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1068G>T p.Trp356Cys p.W356C ENST00000394945 10/11 227 172 55 224 224 0 strelka-varscan-mutect SPOCK1,missense_variant,p.Trp356Cys,ENST00000394945,NM_004598.3;SPOCK1,missense_variant,p.Trp294Cys,ENST00000282223,;SPOCK1,non_coding_transcript_exon_variant,,ENST00000509978,;SPOCK1,non_coding_transcript_exon_variant,,ENST00000515091,; A ENST00000394945 Transcript missense_variant 1238/4846 1068/1320 356/439 W/C tgG/tgT 1 -1 SPOCK1 HGNC HGNC:11251 protein_coding YES CCDS4191.1 ENSP00000378401 Q08629 UPI0000136F50 NM_004598.3 deleterious(0) 10/11 Gene3D:4.10.800.10,Pfam_domain:PF00086,PROSITE_patterns:PS00484,PROSITE_profiles:PS51162,hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF9,SMART_domains:SM00211,Superfamily_domains:SSF57610 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 136979393 136979393 C A 1 0 0 0 0 1 0 0 0 15432 508 18 2 2 SPOCK1 5 136979393 Missense_Mutation SNP C C3L-01924_T 8451435 136979393 44558866 185 8055 PCDHA1 0 . GRCh38 5 140788330 140788330 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.2040G>T p.= p.S680S ENST00000504120 1/4 249 186 63 301 301 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; T ENST00000504120 Transcript synonymous_variant 2040/5263 2040/2853 680/950 S tcG/tcT 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 140788330 140788330 G T 1 0 0 0 0 0 0 0 1 11606 1074 38 1 1 PCDHA1 5 140788330 Silent SNP G C3L-01924_T 3808937 140788330 40749929 186 8056 PCDHA1 0 . GRCh38 5 140788696 140788696 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.2406T>A p.= p.T802T ENST00000378133 1/1 39 29 10 55 55 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,non_coding_transcript_exon_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000378133 Transcript synonymous_variant 2561/2726 2406/2424 802/807 T acT/acA 1 1 PCDHA1 HGNC HGNC:8663 protein_coding ENSP00000367373 Q9Y5I3 UPI000002A611 NM_031410.2 1/1 LOW SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 140788696 140788696 T A 1 0 0 0 0 0 0 0 1 11606 1596 56 4 4 PCDHA1 5 140788696 Silent SNP T C3L-01924_T 366 140788696 40749563 187 8057 PCDHA11 0 . GRCh38 5 140870720 140870720 + Silent SNP G G T rs544150374 C3L-01924_T C3L-01924_N G G c.1617G>T p.= p.A539A ENST00000398640 1/4 660 495 165 703 702 1 strelka-varscan-mutect PCDHA11,synonymous_variant,p.=,ENST00000398640,NM_018902.4;PCDHA11,synonymous_variant,p.=,ENST00000616325,NM_031861.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA10,downstream_gene_variant,,ENST00000562220,NM_031859.2;PCDHA12,upstream_gene_variant,,ENST00000398631,NM_018903.3;PCDHA12,upstream_gene_variant,,ENST00000613593,NM_031864.2;PCDHA11,upstream_gene_variant,,ENST00000617408,;AC005609.18,downstream_gene_variant,,ENST00000624566,;AC005609.20,upstream_gene_variant,,ENST00000625071,; T ENST00000398640 Transcript synonymous_variant 2475/6115 1617/2850 539/949 A gcG/gcT rs544150374 1 1 PCDHA11 HGNC HGNC:8665 protein_coding YES CCDS47284.1 ENSP00000381636 Q9Y5I1 UPI00001273D4 NM_018902.4 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF68,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs544150374 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 140870720 140870720 G T 1 0 0 0 0 0 0 0 1 11608 1103 39 1 1 PCDHA11 5 140870720 Silent SNP G C3L-01924_T 82024 140870720 40667539 188 8058 PCDHB7 0 . GRCh38 5 141175012 141175012 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2177C>A p.Pro726His p.P726H ENST00000231137 1/1 220 158 62 263 262 1 strelka-varscan-mutect PCDHB7,missense_variant,p.Pro726His,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; A ENST00000231137 Transcript missense_variant 2394/3765 2177/2382 726/793 P/H cCt/cAt 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 deleterious_low_confidence(0) 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 141175012 141175012 C A 1 0 0 0 0 1 0 0 0 11634 681 24 2 2 PCDHB7 5 141175012 Missense_Mutation SNP C C3L-01924_T 304292 141175012 40363247 189 8059 PCDHB8 0 . GRCh38 5 141179826 141179826 + Missense_Mutation SNP G G T rs782362169 C3L-01924_T C3L-01924_N G G c.1792G>T p.Gly598Cys p.G598C ENST00000239444 1/1 308 251 57 311 310 1 strelka-varscan-mutect PCDHB8,missense_variant,p.Gly598Cys,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; T ENST00000239444 Transcript missense_variant 2037/2740 1792/2406 598/801 G/C Ggc/Tgc rs782362169 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS rs782362169 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 141179826 141179826 G T 1 0 0 0 0 1 0 0 0 11635 1232 43 2 2 PCDHB8 5 141179826 Missense_Mutation SNP G C3L-01924_T 4814 141179826 40358433 190 8060 PCDHB10 0 . GRCh38 5 141194796 141194796 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.2244C>A p.= p.S748S ENST00000239446 1/1 213 186 27 236 235 1 strelka-varscan-mutect PCDHB10,synonymous_variant,p.=,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB11,upstream_gene_variant,,ENST00000354757,NM_018931.2;PCDHB11,upstream_gene_variant,,ENST00000624887,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,upstream_gene_variant,,ENST00000625144,; A ENST00000239446 Transcript synonymous_variant 2444/3290 2244/2403 748/800 S tcC/tcA 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 1/1 hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Pfam_domain:PF16492 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 141194796 141194796 C A 1 0 0 0 0 0 0 0 1 11622 610 22 2 2 PCDHB10 5 141194796 Silent SNP C C3L-01924_T 14970 141194796 40343463 191 8061 PCDHB14 0 . GRCh38 5 141223530 141223530 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.25C>A p.Leu9Met p.L9M ENST00000239449 1/1 66 60 6 104 103 1 strelka-varscan-mutect PCDHB14,missense_variant,p.Leu9Met,ENST00000239449,NM_018934.3;CH17-140K24.8,missense_variant,p.Leu9Met,ENST00000624396,;PCDHB14,5_prime_UTR_variant,,ENST00000624896,;PCDHB13,downstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239449 Transcript missense_variant 599/4828 25/2397 9/798 L/M Ctg/Atg 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 tolerated_low_confidence(0.22) 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 PASS rs1301560778 . 0 203 7 0 0 0 0 0 -13.56058 0.9999987 1 1 1 0 A 3 1 29 141223530 141223530 C A 1 0 0 0 0 1 0 0 0 11626 912 32 2 2 PCDHB14 5 141223530 Missense_Mutation SNP C C3L-01924_T 28734 141223530 40314729 192 8062 PCDHGB1 0 . GRCh38 5 141350773 141350773 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.513C>T p.= p.P171P ENST00000523390 1/4 250 186 64 307 307 0 strelka-varscan-mutect PCDHGB1,synonymous_variant,p.=,ENST00000523390,NM_018922.2;PCDHGB1,synonymous_variant,p.=,ENST00000611598,NM_032095.1;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA4,upstream_gene_variant,,ENST00000571252,NM_018917.3;PCDHGA3,downstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA4,upstream_gene_variant,,ENST00000612927,NM_032053.2;AC005618.8,upstream_gene_variant,,ENST00000625053,;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000523390 Transcript synonymous_variant 513/4590 513/2784 171/927 P ccC/ccT 1 1 PCDHGB1 HGNC HGNC:8708 protein_coding YES CCDS54923.1 ENSP00000429273 Q9Y5G3 UPI0000073588 NM_018922.2 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 141350773 141350773 C T 1 0 0 0 0 0 0 0 1 11649 581 21 3 3 PCDHGB1 5 141350773 Silent SNP C C3L-01924_T 127243 141350773 40187486 193 8063 PCDHGB2 0 . GRCh38 5 141362089 141362089 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1954C>A p.Pro652Thr p.P652T ENST00000522605 1/4 319 242 77 376 376 0 strelka-varscan-mutect PCDHGB2,missense_variant,p.Pro652Thr,ENST00000522605,NM_018923.2;PCDHGB2,missense_variant,p.Pro652Thr,ENST00000622527,NM_032096.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA5,upstream_gene_variant,,ENST00000518069,NM_018918.2;PCDHGA5,upstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA4,downstream_gene_variant,,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000522605 Transcript missense_variant 1954/4602 1954/2796 652/931 P/T Ccg/Acg COSM1434431,COSM5093035 1 1 PCDHGB2 HGNC HGNC:8709 protein_coding YES CCDS54924.1 ENSP00000429018 Q9Y5G2 UPI000006EE67 NM_018923.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF73,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 141362089 141362089 C A 1 0 0 0 0 1 0 0 0 11650 739 26 2 2 PCDHGB2 5 141362089 Missense_Mutation SNP C C3L-01924_T 11316 141362089 40176170 194 8064 PCDHGA7 0 . GRCh38 5 141384141 141384141 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.1242A>T p.= p.T414T ENST00000518325 1/4 218 193 25 233 232 1 strelka-varscan-mutect PCDHGA7,synonymous_variant,p.=,ENST00000518325,NM_018920.3;PCDHGA7,synonymous_variant,p.=,ENST00000617050,NM_032087.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,downstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGB4,upstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB4,upstream_gene_variant,,ENST00000519479,NM_003736.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000518325 Transcript synonymous_variant 1242/4605 1242/2799 414/932 T acA/acT 1 1 PCDHGA7 HGNC HGNC:8705 protein_coding YES CCDS54927.1 ENSP00000430024 Q9Y5G6 UPI000007146F NM_018920.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs765902130 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 141384141 141384141 A T 1 0 0 0 0 0 0 0 1 11646 146 6 4 4 PCDHGA7 5 141384141 Silent SNP A C3L-01924_T 22052 141384141 40154118 195 8065 PCDHGB6 0 . GRCh38 5 141408409 141408409 + Missense_Mutation SNP C C A rs780778580 C3L-01924_T C3L-01924_N C C c.207C>A p.Ser69Arg p.S69R ENST00000520790 1/4 212 163 49 325 325 0 strelka-varscan-mutect PCDHGB6,missense_variant,p.Ser69Arg,ENST00000616430,NM_032100.1;PCDHGB6,missense_variant,p.Ser69Arg,ENST00000520790,NM_018926.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA10,upstream_gene_variant,,ENST00000398610,NM_018913.2;PCDHGA10,upstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA9,downstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000520790 Transcript missense_variant 207/4599 207/2793 69/930 S/R agC/agA rs780778580 1 1 PCDHGB6 HGNC HGNC:8713 protein_coding YES CCDS54929.1 ENSP00000428603 Q9Y5F9 UPI000006EB47 NM_018926.2 tolerated(0.23) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF66,Pfam_domain:PF08266,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs780778580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 141408409 141408409 C A 1 0 0 0 0 1 0 0 0 11654 767 27 1 1 PCDHGB6 5 141408409 Missense_Mutation SNP C C3L-01924_T 24268 141408409 40129850 196 8066 PCDHGA1 0 . GRCh38 5 141511028 141511028 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.2744T>A p.Leu915Gln p.L915Q ENST00000571252 4/4 442 385 57 436 436 0 strelka-varscan-mutect PCDHGA4,missense_variant,p.Leu915Gln,ENST00000571252,NM_018917.3;PCDHGA6,missense_variant,p.Leu885Gln,ENST00000517434,NM_018919.2;PCDHGA3,missense_variant,p.Leu885Gln,ENST00000253812,NM_018916.3;PCDHGB7,missense_variant,p.Leu882Gln,ENST00000398594,NM_018927.3;PCDHGC5,missense_variant,p.Leu897Gln,ENST00000252087,NM_018929.2;PCDHGA12,missense_variant,p.Leu885Gln,ENST00000252085,NM_003735.2;PCDHGB3,missense_variant,p.Leu882Gln,ENST00000576222,NM_018924.4;PCDHGC3,missense_variant,p.Leu887Gln,ENST00000308177,NM_002588.3;PCDHGA11,missense_variant,p.Leu888Gln,ENST00000398587,NM_018914.2;PCDHGC4,missense_variant,p.Leu891Gln,ENST00000306593,NM_018928.2;PCDHGA10,missense_variant,p.Leu889Gln,ENST00000398610,NM_018913.2;PCDHGA2,missense_variant,p.Leu885Gln,ENST00000394576,NM_018915.3;PCDHGA8,missense_variant,p.Leu885Gln,ENST00000398604,NM_032088.1;PCDHGA7,missense_variant,p.Leu885Gln,ENST00000518325,NM_018920.3;PCDHGA9,missense_variant,p.Leu885Gln,ENST00000573521,NM_018921.2;PCDHGA1,missense_variant,p.Leu884Gln,ENST00000517417,NM_018912.2;PCDHGA5,missense_variant,p.Leu884Gln,ENST00000518069,NM_018918.2;PCDHGB2,missense_variant,p.Leu884Gln,ENST00000522605,NM_018923.2;PCDHGB6,missense_variant,p.Leu883Gln,ENST00000520790,NM_018926.2;PCDHGB1,missense_variant,p.Leu880Gln,ENST00000523390,NM_018922.2;PCDHGB4,missense_variant,p.Leu876Gln,ENST00000519479,NM_003736.2;PCDHGB5,missense_variant,p.Leu876Gln,ENST00000617380,NM_018925.2;PCDHGC3,missense_variant,p.Leu87Gln,ENST00000617641,NM_032403.2;PCDHGA11,missense_variant,p.Leu703Gln,ENST00000518882,NM_032092.1;PCDHGC4,missense_variant,p.Leu81Gln,ENST00000618371,;PCDHGC3,missense_variant,p.Leu138Gln,ENST00000617222,;DIAPH1,downstream_gene_variant,,ENST00000389054,NM_005219.4;DIAPH1,downstream_gene_variant,,ENST00000253811,;DIAPH1,downstream_gene_variant,,ENST00000398557,;DIAPH1,downstream_gene_variant,,ENST00000389057,;DIAPH1,downstream_gene_variant,,ENST00000518047,NM_001079812.2;DIAPH1,downstream_gene_variant,,ENST00000448451,;PCDHGC3,non_coding_transcript_exon_variant,,ENST00000622836,;PCDHGC3,downstream_gene_variant,,ENST00000622656,;PCDHGA3,3_prime_UTR_variant,,ENST00000612467,;DIAPH1,downstream_gene_variant,,ENST00000476339,; A ENST00000571252 Transcript missense_variant 2827/4778 2744/2889 915/962 L/Q cTg/cAg 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0) 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Pfam_domain:PF15974 MODERATE 1 SNV 1 1 PASS rs1279056657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 141511028 141511028 T A 1 0 0 0 0 1 0 0 0 11637 1580 55 4 4 PCDHGA1 5 141511028 Missense_Mutation SNP T C3L-01924_T 102619 141511028 40027231 197 8067 FAM71B 0 . GRCh38 5 157165752 157165752 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.417G>T p.Gln139His p.Q139H ENST00000302938 1/2 202 150 52 237 236 1 strelka-varscan-mutect FAM71B,missense_variant,p.Gln139His,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,; A ENST00000302938 Transcript missense_variant 513/2515 417/1818 139/605 Q/H caG/caT 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 deleterious(0.01) 1/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2,Pfam_domain:PF12480 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 157165752 157165752 C A 1 0 0 0 0 1 0 0 0 5472 796 28 2 2 FAM71B 5 157165752 Missense_Mutation SNP C C3L-01924_T 15654724 157165752 24372507 198 8068 ATP10B 0 . GRCh38 5 160612866 160612866 + Missense_Mutation SNP G G A rs760610785 C3L-01924_T C3L-01924_N G G c.2713C>T p.Arg905Trp p.R905W ENST00000327245 18/26 154 113 41 179 179 0 strelka-varscan-mutect ATP10B,missense_variant,p.Arg905Trp,ENST00000327245,NM_025153.2;ATP10B,missense_variant,p.Arg513Trp,ENST00000520108,;CTC-348L5.1,upstream_gene_variant,,ENST00000523598,;ATP10B,non_coding_transcript_exon_variant,,ENST00000522169,; A ENST00000327245 Transcript missense_variant 3560/7566 2713/4386 905/1461 R/W Cgg/Tgg rs760610785 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0) 18/26 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF79,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS rs760610785 . 0 206 0 4 0 0 0 0 -20 0.9999731 1 1 1 0 A 3 1 29 160612866 160612866 G A 1 0 0 0 0 1 0 0 0 1269 1086 38 1 1 ATP10B 5 160612866 Missense_Mutation SNP G C3L-01924_T 3447114 160612866 20925393 199 8069 F12 0 . GRCh38 5 177405178 177405178 + Silent SNP G G A C3L-01924_T C3L-01924_N G G c.405C>T p.= p.C135C ENST00000253496 6/14 447 329 118 537 537 0 strelka-varscan-mutect F12,synonymous_variant,p.=,ENST00000253496,NM_000505.3;GRK6,intron_variant,,ENST00000506296,;GRK6,intron_variant,,ENST00000502598,;PFN3,upstream_gene_variant,,ENST00000358571,NM_001029886.2;F12,upstream_gene_variant,,ENST00000514943,;F12,upstream_gene_variant,,ENST00000510358,;F12,upstream_gene_variant,,ENST00000502854,;F12,upstream_gene_variant,,ENST00000504406,;F12,upstream_gene_variant,,ENST00000503736,; A ENST00000253496 Transcript synonymous_variant 454/2049 405/1848 135/615 C tgC/tgT CM102609 1 -1 F12 HGNC HGNC:3530 protein_coding YES CCDS34302.1 ENSP00000253496 P00748 UPI000048055F NM_000505.3 6/14 Gene3D:2.10.25.10,Pfam_domain:PF00039,PIRSF_domain:PIRSF001146,PROSITE_patterns:PS01253,PROSITE_profiles:PS51091,SMART_domains:SM00058 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 177405178 177405178 G A 1 0 0 0 0 0 0 0 1 5207 963 34 3 3 F12 5 177405178 Silent SNP G C3L-01924_T 16792312 177405178 4133081 200 8070 ADAMTS2 0 . GRCh38 5 179154817 179154817 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1235A>T p.His412Leu p.H412L ENST00000251582 7/22 133 125 8 142 142 0 strelka-mutect ADAMTS2,missense_variant,p.His412Leu,ENST00000251582,NM_014244.4;ADAMTS2,missense_variant,p.His412Leu,ENST00000274609,NM_021599.2; A ENST00000251582 Transcript missense_variant 1337/6754 1235/3636 412/1211 H/L cAc/cTc 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 deleterious(0) 7/22 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 179154817 179154817 T A 1 0 0 0 0 1 0 0 0 309 1710 59 4 4 ADAMTS2 5 179154817 Missense_Mutation SNP T C3L-01924_T 1749639 179154817 2383442 201 8071 HIST1H3D 0 . GRCh38 6 26196901 26196901 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.350G>A p.Arg117Gln p.R117Q ENST00000356476 1/1 316 300 16 352 352 0 strelka-varscan-mutect HIST1H3D,missense_variant,p.Arg117Gln,ENST00000356476,NM_003530.4;RP1-34B20.21,3_prime_UTR_variant,,ENST00000635200,;HIST1H2BF,upstream_gene_variant,,ENST00000356530,NM_003522.3;HIST1H2AD,downstream_gene_variant,,ENST00000341023,NM_021065.3;RP1-34B20.21,3_prime_UTR_variant,,ENST00000635641,;HIST1H1PS1,downstream_gene_variant,,ENST00000404269,; T ENST00000356476 Transcript missense_variant 350/411 350/411 117/136 R/Q cGa/cAa 1 -1 HIST1H3D HGNC HGNC:4767 protein_coding YES CCDS4590.1 ENSP00000366999 P68431 UPI00000003C7 NM_003530.4 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 26196901 26196901 C T 1 0 0 0 0 1 0 0 0 7046 884 31 1 1 HIST1H3D 6 26196901 Missense_Mutation SNP C C3L-01924_T 26196901 144609078 202 8072 BTN3A2 0 . GRCh38 6 26368799 26368799 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.320G>T p.Gly107Val p.G107V ENST00000356386 4/11 208 169 39 219 219 0 varscan-mutect BTN3A2,missense_variant,p.Gly65Val,ENST00000508906,NM_001197249.2;BTN3A2,missense_variant,p.Gly84Val,ENST00000396934,NM_001197248.2;BTN3A2,missense_variant,p.Gly107Val,ENST00000356386,NM_007047.4,NM_001197247.2,NM_001197246.2;BTN3A2,missense_variant,p.Gly107Val,ENST00000377708,;BTN3A2,missense_variant,p.Gly107Val,ENST00000396948,;BTN3A2,missense_variant,p.Gly107Val,ENST00000527422,;BTN3A2,missense_variant,p.Gly65Val,ENST00000532865,;BTN3A2,missense_variant,p.Gly107Val,ENST00000527417,;BTN3A2,missense_variant,p.Gly65Val,ENST00000530653,;BTN3A2,upstream_gene_variant,,ENST00000527639,;BTN3A2,non_coding_transcript_exon_variant,,ENST00000532994,;BTN3A2,non_coding_transcript_exon_variant,,ENST00000524682,;BTN3A2,non_coding_transcript_exon_variant,,ENST00000532627,;BTN3A2,3_prime_UTR_variant,,ENST00000524459,;BTN3A2,upstream_gene_variant,,ENST00000604202,;BTN3A2,downstream_gene_variant,,ENST00000528222,;BTN3A2,upstream_gene_variant,,ENST00000531055,;BTN3A2,downstream_gene_variant,,ENST00000528541,;BTN3A2,upstream_gene_variant,,ENST00000532294,; T ENST00000356386 Transcript missense_variant 508/3017 320/1005 107/334 G/V gGg/gTg 1 1 BTN3A2 HGNC HGNC:1139 protein_coding YES CCDS4605.1 ENSP00000348751 P78410 UPI000006E484 NM_007047.4,NM_001197247.2,NM_001197246.2 deleterious(0) 4/11 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF70,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 26368799 26368799 G T 1 0 0 0 0 1 0 0 0 1739 1232 43 2 2 BTN3A2 6 26368799 Missense_Mutation SNP G C3L-01924_T 171898 26368799 144437180 203 8073 PRRC2A 0 . GRCh38 6 31625835 31625835 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.803A>T p.Gln268Leu p.Q268L ENST00000376033 8/31 160 139 21 193 193 0 strelka-varscan-mutect PRRC2A,missense_variant,p.Gln268Leu,ENST00000376033,NM_004638.3;PRRC2A,missense_variant,p.Gln268Leu,ENST00000376007,NM_080686.2;SNORA38,downstream_gene_variant,,ENST00000363946,;PRRC2A,non_coding_transcript_exon_variant,,ENST00000469577,;PRRC2A,non_coding_transcript_exon_variant,,ENST00000464890,;PRRC2A,upstream_gene_variant,,ENST00000483470,;PRRC2A,downstream_gene_variant,,ENST00000464079,; T ENST00000376033 Transcript missense_variant 1037/6893 803/6474 268/2157 Q/L cAg/cTg 1 1 PRRC2A HGNC HGNC:13918 protein_coding YES CCDS4708.1 ENSP00000365201 P48634 UPI000020E56F NM_004638.3 deleterious(0.01) 8/31 Low_complexity_(Seg):seg,hmmpanther:PTHR14038:SF5,hmmpanther:PTHR14038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 31625835 31625835 A T 1 0 0 0 0 1 0 0 0 12748 188 7 4 4 PRRC2A 6 31625835 Missense_Mutation SNP A C3L-01924_T 5257036 31625835 139180144 204 8074 C2 0 . GRCh38 6 31928147 31928147 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.239delC p.Ser80LeufsTer111 p.S80Lfs*111 ENST00000456570 2/30 307 272 35 357 357 0 sindel-varindel-pindel XXbac-BPG116M5.17,frameshift_variant,p.Ser80LeufsTer111,ENST00000456570,;XXbac-BPG116M5.17,frameshift_variant,p.Ser80LeufsTer34,ENST00000477310,;C2,frameshift_variant,p.Ser80LeufsTer34,ENST00000299367,NM_001282458.1,NM_000063.5;C2,frameshift_variant,p.Ser80LeufsTer34,ENST00000418949,NM_001282459.1;C2,frameshift_variant,p.Ser80LeufsTer112,ENST00000447952,;C2,frameshift_variant,p.Ser80LeufsTer34,ENST00000413154,;C2,intron_variant,,ENST00000442278,NM_001145903.2;C2,intron_variant,,ENST00000452323,NM_001178063.2;C2,intron_variant,,ENST00000469372,NM_001282457.1;C2,intron_variant,,ENST00000383177,;C2,intron_variant,,ENST00000497706,;C2,intron_variant,,ENST00000452202,;C2,upstream_gene_variant,,ENST00000494905,;C2,frameshift_variant,p.Ser80LeufsTer683,ENST00000482060,;C2,intron_variant,,ENST00000411571,;C2,intron_variant,,ENST00000484636,; - ENST00000456570 Transcript frameshift_variant 294/3874 239/3801 80/1266 S/X tCt/tt 1 1 XXbac-BPG116M5.17 Clone_based_vega_gene protein_coding YES ENSP00000410815 B4E1Z4 UPI00017A8869 2/30 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF394,Gene3D:2.10.70.10 HIGH deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 31928147 31928147 C - 1 0 1 0 1 0 0 0 0 2001 913 32 0 0 C2 6 31928147 Frame_Shift_Del DEL C C3L-01924_T 302312 31928147 138877832 205 8075 TMEM217 0 . GRCh38 6 37218923 37218923 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.108C>T p.= p.H36H ENST00000336655 2/4 276 204 72 289 289 0 strelka-varscan-mutect TMEM217,synonymous_variant,p.=,ENST00000336655,NM_145316.3;TMEM217,synonymous_variant,p.=,ENST00000356757,NM_001286401.1;TMEM217,intron_variant,,ENST00000497775,;TMEM217,intron_variant,,ENST00000478262,;TMEM217,upstream_gene_variant,,ENST00000482580,;TMEM217,non_coding_transcript_exon_variant,,ENST00000357219,; A ENST00000336655 Transcript synonymous_variant 148/1546 108/690 36/229 H caC/caT 1 -1 TMEM217 HGNC HGNC:21238 protein_coding YES CCDS4831.1 ENSP00000338164 Q8N7C4 UPI0000071695 NM_145316.3 2/4 Pfam_domain:PF15049,hmmpanther:PTHR34928,hmmpanther:PTHR34928:SF2 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 37218923 37218923 G A 1 0 0 0 0 0 0 0 1 16581 1252 44 3 3 TMEM217 6 37218923 Silent SNP G C3L-01924_T 5290776 37218923 133587056 206 8076 CMTR1 0 . GRCh38 6 37459664 37459664 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1075C>T p.His359Tyr p.H359Y ENST00000373451 10/24 236 224 12 272 272 0 strelka-mutect CMTR1,missense_variant,p.His359Tyr,ENST00000373451,NM_015050.2;CMTR1,missense_variant,p.His303Tyr,ENST00000455891,;CMTR1,non_coding_transcript_exon_variant,,ENST00000493656,; T ENST00000373451 Transcript missense_variant 1239/4033 1075/2508 359/835 H/Y Cat/Tat 1 1 CMTR1 HGNC HGNC:21077 protein_coding YES CCDS4835.1 ENSP00000362550 Q8N1G2 UPI00000700C2 NM_015050.2 deleterious(0.03) 10/24 PROSITE_profiles:PS51613,hmmpanther:PTHR16121:SF0,hmmpanther:PTHR16121,Gene3D:3.40.50.150,Pfam_domain:PF01728,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 37459664 37459664 C T 1 0 0 0 0 1 0 0 0 3366 594 21 3 3 CMTR1 6 37459664 Missense_Mutation SNP C C3L-01924_T 240741 37459664 133346315 207 8077 DNAH8 0 . GRCh38 6 38850282 38850282 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.5231C>G p.Ser1744Cys p.S1744C ENST00000327475 38/93 154 105 49 176 176 0 strelka-varscan-mutect DNAH8,missense_variant,p.Ser1744Cys,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Ser1527Cys,ENST00000359357,;DNAH8,missense_variant,p.Ser1744Cys,ENST00000449981,; G ENST00000327475 Transcript missense_variant 5340/14360 5231/14124 1744/4707 S/C tCt/tGt 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 38/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF08393 MODERATE 1 SNV 5 1 PASS rs1023281989 . 0 206 0 4 0 0 0 0 -20 0.9999809 1 1 1 0 G 3 3 29 38850282 38850282 C G 1 0 0 0 0 1 0 0 0 4422 913 32 4 4 DNAH8 6 38850282 Missense_Mutation SNP C C3L-01924_T 1390618 38850282 131955697 208 8078 KIF6 0 . GRCh38 6 39540114 39540114 + Missense_Mutation SNP G G T rs757976747 C3L-01924_T C3L-01924_N G G c.1534C>A p.Arg512Ser p.R512S ENST00000287152 13/23 224 191 33 246 245 1 strelka-varscan-mutect KIF6,missense_variant,p.Arg512Ser,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,missense_variant,p.Arg404Ser,ENST00000458470,;KIF6,intron_variant,,ENST00000538893,; T ENST00000287152 Transcript missense_variant 1629/9082 1534/2445 512/814 R/S Cgc/Agc rs757976747,COSM1487731,COSM1487732 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 tolerated(0.82) 13/23 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs757976747 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 39540114 39540114 G T 1 0 0 0 0 1 0 0 0 8173 1116 39 1 1 KIF6 6 39540114 Missense_Mutation SNP G C3L-01924_T 689832 39540114 131265865 209 8079 MOCS1 0 . GRCh38 6 39906980 39906981 + Frame_Shift_Ins INS - - T novel C3L-01924_T C3L-01924_N - - c.978_979insA p.Pro327ThrfsTer34 p.P327Tfs*34 ENST00000373195 9/9 62 40 22 66 66 0 sindel-pindel MOCS1,frameshift_variant,p.Pro327ThrfsTer34,ENST00000373195,;MOCS1,frameshift_variant,p.Pro430ThrfsTer34,ENST00000340692,;MOCS1,frameshift_variant,p.Pro430ThrfsTer34,ENST00000425303,;MOCS1,3_prime_UTR_variant,,ENST00000373186,NM_005943.5;MOCS1,3_prime_UTR_variant,,ENST00000373188,NM_001075098.3;DAAM2,downstream_gene_variant,,ENST00000538976,NM_015345.3;DAAM2,downstream_gene_variant,,ENST00000398904,;DAAM2,downstream_gene_variant,,ENST00000274867,NM_001201427.1;DAAM2,downstream_gene_variant,,ENST00000633794,;MOCS1,downstream_gene_variant,,ENST00000432280,;MOCS1,intron_variant,,ENST00000373181,;DAAM2,downstream_gene_variant,,ENST00000631498,; T ENST00000373195 Transcript frameshift_variant 1192-1193/2852 978-979/1602 326-327/533 -/X -/A 1 -1 MOCS1 HGNC HGNC:7190 protein_coding ENSP00000362291 Q9NZB8 UPI0000415071 9/9 HIGH insertion 2 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 29 39906980 39906980 - T 1 0 1 1 0 0 0 0 0 9653 1232 43 0 0 MOCS1 6 39906980 Frame_Shift_Ins INS - C3L-01924_T 366866 39906980 130898999 210 8080 ZNF318 0 . GRCh38 6 43357207 43357207 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1107G>T p.= p.R369R ENST00000361428 3/10 182 160 22 214 212 2 strelka-varscan-mutect ZNF318,synonymous_variant,p.=,ENST00000361428,NM_014345.2;ZNF318,synonymous_variant,p.=,ENST00000605935,; A ENST00000361428 Transcript synonymous_variant 1185/8006 1107/6840 369/2279 R cgG/cgT 1 -1 ZNF318 HGNC HGNC:13578 protein_coding YES CCDS4895.2 ENSP00000354964 Q5VUA4 UPI000049E044 NM_014345.2 3/10 hmmpanther:PTHR15577:SF2,hmmpanther:PTHR15577 LOW 1 SNV 1 1 PASS rs1382386281 . 0 205 0 3 2 0 0 0 -10.06771 0.961522 1 1 1 0 A 2 1 29 43357207 43357207 C A 1 0 0 0 0 0 0 0 1 18411 726 26 2 2 ZNF318 6 43357207 Silent SNP C C3L-01924_T 3450227 43357207 127448772 211 8081 PHF3 0 . GRCh38 6 63712532 63712532 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.4944G>A p.= p.L1648L ENST00000262043 16/16 254 229 25 317 317 0 strelka-varscan-mutect PHF3,synonymous_variant,p.=,ENST00000262043,NM_001290259.1;PHF3,synonymous_variant,p.=,ENST00000393387,NM_015153.3;PHF3,intron_variant,,ENST00000505138,;PHF3,downstream_gene_variant,,ENST00000506783,;PHF3,downstream_gene_variant,,ENST00000515594,;PHF3,3_prime_UTR_variant,,ENST00000509876,; A ENST00000262043 Transcript synonymous_variant 5284/8233 4944/6120 1648/2039 L ctG/ctA 1 1 PHF3 HGNC HGNC:8921 protein_coding YES CCDS4966.1 ENSP00000262043 Q92576 UPI000007154D NM_001290259.1 16/16 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 63712532 63712532 G A 1 0 0 0 0 0 0 0 1 11923 1277 45 3 3 PHF3 6 63712532 Silent SNP G C3L-01924_T 20355325 63712532 107093447 212 8082 EYS 0 . GRCh38 6 64590884 64590884 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.4983G>T p.Leu1661Phe p.L1661F ENST00000370621 26/44 179 153 26 243 243 0 strelka-varscan-mutect EYS,missense_variant,p.Leu1661Phe,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Leu1661Phe,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; A ENST00000370621 Transcript missense_variant 5510/10485 4983/9498 1661/3165 L/F ttG/ttT 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious_low_confidence(0.02) 26/44 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 64590884 64590884 C A 1 0 0 0 0 1 0 0 0 5200 593 21 2 2 EYS 6 64590884 Missense_Mutation SNP C C3L-01924_T 878352 64590884 106215095 213 8083 EYS 0 . GRCh38 6 64813380 64813380 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.3441C>A p.Cys1147Ter p.C1147* ENST00000370621 22/44 205 193 12 216 216 0 strelka-varscan-mutect EYS,stop_gained,p.Cys1147Ter,ENST00000503581,NM_001142800.1;EYS,stop_gained,p.Cys1147Ter,ENST00000370621,NM_001292009.1; T ENST00000370621 Transcript stop_gained,splice_region_variant 3968/10485 3441/9498 1147/3165 C/* tgC/tgA 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 22/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 64813380 64813380 G T 1 0 0 0 0 0 1 0 0 5200 1333 46 2 2 EYS 6 64813380 Nonsense_Mutation SNP G C3L-01924_T 222496 64813380 105992599 214 8084 EYS 0 . GRCh38 6 65332390 65332390 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1794C>A p.His598Gln p.H598Q ENST00000393380 12/12 217 171 46 278 276 2 strelka-varscan-mutect EYS,missense_variant,p.His598Gln,ENST00000393380,NM_001142801.1;EYS,intron_variant,,ENST00000503581,NM_001142800.1;EYS,intron_variant,,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000342421,NM_198283.1; T ENST00000393380 Transcript missense_variant 2332/5450 1794/1860 598/619 H/Q caC/caA 1 -1 EYS HGNC HGNC:21555 protein_coding CCDS47446.1 ENSP00000377042 Q5T1H1 UPI00001D812F NM_001142801.1 tolerated_low_confidence(0.65) 12/12 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 65332390 65332390 G T 1 0 0 0 0 1 0 0 0 5200 1252 44 2 2 EYS 6 65332390 Missense_Mutation SNP G C3L-01924_T 519010 65332390 105473589 215 8085 EYS 0 . GRCh38 6 65405262 65405262 + Missense_Mutation SNP C C A rs752456937 C3L-01924_T C3L-01924_N C C c.968G>T p.Gly323Val p.G323V ENST00000370621 6/44 317 285 32 332 331 1 strelka-varscan-mutect EYS,missense_variant,p.Gly323Val,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Gly323Val,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Gly323Val,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Gly323Val,ENST00000342421,NM_198283.1; A ENST00000370621 Transcript missense_variant 1495/10485 968/9498 323/3165 G/V gGa/gTa rs752456937,COSM4563317,COSM4563318 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0) 6/44 hmmpanther:PTHR24033,SMART_domains:SM00181 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs1411803360 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 65405262 65405262 C A 1 0 0 0 0 1 0 0 0 5200 855 30 2 2 EYS 6 65405262 Missense_Mutation SNP C C3L-01924_T 72872 65405262 105400717 216 8086 COL19A1 0 . GRCh38 6 69929610 69929610 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.576T>C p.= p.I192I ENST00000620364 6/51 223 182 41 303 303 0 strelka-mutect COL19A1,synonymous_variant,p.=,ENST00000620364,NM_001858.5; C ENST00000620364 Transcript synonymous_variant 678/6233 576/3429 192/1142 I atT/atC 1 1 COL19A1 HGNC HGNC:2196 protein_coding YES CCDS4970.1 ENSP00000480474 Q14993 UPI000004F1E3 NM_001858.5 6/51 Gene3D:2.60.120.200,SMART_domains:SM00210,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 69929610 69929610 T C 1 0 0 0 0 0 0 0 1 3464 1800 63 5 5 COL19A1 6 69929610 Silent SNP T C3L-01924_T 4524348 69929610 100876369 217 8087 MYO6 0 . GRCh38 6 75914879 75914879 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.3725C>T p.Ala1242Val p.A1242V ENST00000369977 35/35 315 261 54 365 365 0 strelka-varscan-mutect MYO6,missense_variant,p.Ala1252Val,ENST00000369981,;MYO6,missense_variant,p.Ala1219Val,ENST00000369985,NM_001300899.1;MYO6,missense_variant,p.Ala1242Val,ENST00000369977,NM_004999.3;MYO6,missense_variant,p.Ala1210Val,ENST00000369975,;MYO6,missense_variant,p.Ala1251Val,ENST00000627432,;MYO6,missense_variant,p.Ala1219Val,ENST00000615563,; T ENST00000369977 Transcript missense_variant 3864/5597 3725/3858 1242/1285 A/V gCt/gTt 1 1 MYO6 HGNC HGNC:7605 protein_coding YES CCDS34487.1 ENSP00000358994 Q9UM54 UPI00000727CF NM_004999.3 deleterious(0) 35/35 Pfam_domain:PF16521 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 75914879 75914879 C T 1 0 0 0 0 1 0 0 0 10082 797 28 3 3 MYO6 6 75914879 Missense_Mutation SNP C C3L-01924_T 5985269 75914879 94891100 218 8088 SIM1 0 . GRCh38 6 100448615 100448615 + Missense_Mutation SNP C C A rs755172740 C3L-01924_T C3L-01924_N C C c.607G>T p.Gly203Cys p.G203C ENST00000369208 7/12 138 116 22 168 168 0 strelka-mutect SIM1,missense_variant,p.Gly203Cys,ENST00000369208,;SIM1,missense_variant,p.Gly203Cys,ENST00000262901,NM_005068.2; A ENST00000369208 Transcript missense_variant 1390/8430 607/2301 203/766 G/C Ggc/Tgc rs755172740,COSM1071586 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 deleterious(0.04) 7/12 hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755172740 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 100448615 100448615 C A 1 0 0 0 0 1 0 0 0 14586 652 23 1 1 SIM1 6 100448615 Missense_Mutation SNP C C3L-01924_T 24533736 100448615 70357364 219 8089 SLC22A16 0 . GRCh38 6 110456864 110456864 + Missense_Mutation SNP C C A rs374020837 C3L-01924_T C3L-01924_N C C c.207G>T p.Trp69Cys p.W69C ENST00000368919 2/8 103 90 13 167 167 0 strelka-varscan-mutect SLC22A16,missense_variant,p.Trp69Cys,ENST00000368919,NM_033125.3;SLC22A16,missense_variant,p.Trp26Cys,ENST00000437378,;SLC22A16,missense_variant,p.Trp26Cys,ENST00000424139,;SLC22A16,intron_variant,,ENST00000330550,;SLC22A16,intron_variant,,ENST00000434949,;SLC22A16,upstream_gene_variant,,ENST00000451557,;SLC22A16,non_coding_transcript_exon_variant,,ENST00000461487,; A ENST00000368919 Transcript missense_variant 274/1987 207/1734 69/577 W/C tgG/tgT rs374020837,COSM227276 1 -1 SLC22A16 HGNC HGNC:20302 protein_coding YES CCDS5084.1 ENSP00000357915 Q86VW1 A0A0K0K1K9 UPI000000DC13 NM_033125.3 tolerated(0.07) 2/8 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF186 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374020837 . 0 208 0 2 0 0 0 0 -19.89229 0.9999999 1 1 1 0 A 3 1 29 110456864 110456864 C A 1 0 0 0 0 1 0 0 0 14713 856 30 2 2 SLC22A16 6 110456864 Missense_Mutation SNP C C3L-01924_T 10008249 110456864 60349115 220 8090 MARCKS 0 . GRCh38 6 113860151 113860151 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.571G>C p.Gly191Arg p.G191R ENST00000612661 2/2 76 63 13 64 64 0 strelka-varscan-mutect MARCKS,missense_variant,p.Gly191Arg,ENST00000612661,NM_002356.6; C ENST00000612661 Transcript missense_variant 955/4275 571/999 191/332 G/R Ggc/Cgc 1 1 MARCKS HGNC HGNC:6759 protein_coding YES CCDS5101.1 ENSP00000478061 P29966 UPI000013DDF0 NM_002356.6 deleterious_low_confidence(0.01) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR14353,hmmpanther:PTHR14353:SF9,Pfam_domain:PF02063 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 113860151 113860151 G C 1 0 0 0 0 1 0 0 0 9234 1000 35 4 4 MARCKS 6 113860151 Missense_Mutation SNP G C3L-01924_T 3403287 113860151 56945828 221 8091 RFX6 0 . GRCh38 6 116919138 116919138 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.1024T>G p.Leu342Val p.L342V ENST00000332958 11/19 175 160 15 261 260 1 strelka-varscan-mutect RFX6,missense_variant,p.Leu342Val,ENST00000332958,NM_173560.3;RFX6,downstream_gene_variant,,ENST00000471966,;RFX6,splice_region_variant,,ENST00000487683,; G ENST00000332958 Transcript missense_variant,splice_region_variant 1040/3460 1024/2787 342/928 L/V Tta/Gta 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 deleterious(0) 11/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 116919138 116919138 T G 1 0 0 0 0 1 0 0 0 13441 1623 56 5 5 RFX6 6 116919138 Missense_Mutation SNP T C3L-01924_T 3058987 116919138 53886841 222 8092 C6orf58 0 . GRCh38 6 127578735 127578735 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.351A>T p.= p.G117G ENST00000329722 2/6 143 123 20 173 172 1 strelka-varscan-mutect C6orf58,synonymous_variant,p.=,ENST00000329722,NM_001010905.2;C6orf58,downstream_gene_variant,,ENST00000498112,; T ENST00000329722 Transcript synonymous_variant 363/1200 351/993 117/330 G ggA/ggT 1 1 C6orf58 HGNC HGNC:20960 protein_coding YES CCDS34533.1 ENSP00000328069 Q6P5S2 UPI00001D80C9 NM_001010905.2 2/6 Pfam_domain:PF05612,hmmpanther:PTHR18820,hmmpanther:PTHR18820:SF4 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 29 127578735 127578735 A T 1 0 0 0 0 0 0 0 1 2131 291 11 4 4 C6orf58 6 127578735 Silent SNP A C3L-01924_T 10659597 127578735 43227244 223 8093 ENPP3 0 . GRCh38 6 131740286 131740286 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.2363A>C p.Lys788Thr p.K788T ENST00000414305 25/26 140 127 13 186 186 0 strelka-varscan-mutect ENPP3,missense_variant,p.Lys788Thr,ENST00000414305,;ENPP3,missense_variant,p.Lys788Thr,ENST00000357639,NM_005021.3;ENPP3,3_prime_UTR_variant,,ENST00000358229,; C ENST00000414305 Transcript missense_variant 2691/3418 2363/2628 788/875 K/T aAa/aCa 1 1 ENPP3 HGNC HGNC:3358 protein_coding YES CCDS5148.1 ENSP00000406261 O14638 UPI000013DD9F tolerated(0.08) 25/26 hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF64,Pfam_domain:PF01223,Gene3D:1g8tA00,SMART_domains:SM00892,SMART_domains:SM00477,Superfamily_domains:SSF54060 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 131740286 131740286 A C 1 0 0 0 0 1 0 0 0 4976 14 1 5 5 ENPP3 6 131740286 Missense_Mutation SNP A C3L-01924_T 4161551 131740286 39065693 224 8094 TAAR9 0 . GRCh38 6 132539186 132539186 + Nonsense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.897T>A p.Cys299Ter p.C299* ENST00000434551 1/1 89 75 14 109 109 0 strelka-varscan-mutect TAAR9,stop_gained,p.Cys299Ter,ENST00000434551,NM_175057.3; A ENST00000434551 Transcript stop_gained 897/1047 897/1047 299/348 C/* tgT/tgA 1 1 TAAR9 HGNC HGNC:20977 protein_coding YES CCDS75520.1 ENSP00000424607 Q96RI9 UPI000000D880 NM_175057.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF79,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 132539186 132539186 T A 1 0 0 0 0 0 1 0 0 15890 1702 59 4 4 TAAR9 6 132539186 Nonsense_Mutation SNP T C3L-01924_T 798900 132539186 38266793 225 8095 SLC35D3 0 . GRCh38 6 136924390 136924390 + Missense_Mutation SNP G G T rs755575098 C3L-01924_T C3L-01924_N G G c.945G>T p.Glu315Asp p.E315D ENST00000331858 2/2 288 254 34 372 369 3 strelka-varscan-mutect SLC35D3,missense_variant,p.Glu315Asp,ENST00000331858,NM_001008783.2; T ENST00000331858 Transcript missense_variant 1110/2359 945/1251 315/416 E/D gaG/gaT rs755575098 1 1 SLC35D3 HGNC HGNC:15621 protein_coding YES CCDS34544.1 ENSP00000333591 Q5M8T2 UPI00003673E9 NM_001008783.2 deleterious(0.04) 2/2 MODERATE 1 SNV 1 1 PASS rs755575098 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 136924390 136924390 G T 1 0 0 0 0 1 0 0 0 14853 991 35 2 2 SLC35D3 6 136924390 Missense_Mutation SNP G C3L-01924_T 4385204 136924390 33881589 226 8096 ADGRG6 0 . GRCh38 6 142417332 142417332 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2998G>T p.Gly1000Ter p.G1000* ENST00000367609 21/25 233 198 35 279 278 1 strelka-varscan-mutect ADGRG6,stop_gained,p.Gly1000Ter,ENST00000230173,NM_020455.5;ADGRG6,stop_gained,p.Gly1000Ter,ENST00000367609,NM_198569.2;ADGRG6,stop_gained,p.Gly972Ter,ENST00000367608,NM_001032395.2;ADGRG6,stop_gained,p.Gly972Ter,ENST00000296932,NM_001032394.2;ADGRG6,non_coding_transcript_exon_variant,,ENST00000472054,; T ENST00000367609 Transcript stop_gained 3399/6887 2998/3753 1000/1250 G/* Gga/Tga 1 1 ADGRG6 HGNC HGNC:13841 protein_coding YES CCDS47489.1 ENSP00000356581 Q86SQ4 UPI000022CCE4 NM_198569.2 21/25 Gene3D:1.20.1070.10,Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF290,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 142417332 142417332 G T 1 0 0 0 0 0 1 0 0 373 1349 47 2 2 ADGRG6 6 142417332 Nonsense_Mutation SNP G C3L-01924_T 5492942 142417332 28388647 227 8097 SHPRH 0 . GRCh38 6 145913478 145913478 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.4326G>T p.Gln1442His p.Q1442H ENST00000367505 24/30 176 167 9 206 206 0 strelka-mutect SHPRH,missense_variant,p.Gln1446His,ENST00000629427,;SHPRH,missense_variant,p.Gln1442His,ENST00000367505,;SHPRH,missense_variant,p.Gln1446His,ENST00000438092,NM_173082.3;SHPRH,missense_variant,p.Gln1442His,ENST00000275233,NM_001042683.2;SHPRH,downstream_gene_variant,,ENST00000367503,;SHPRH,splice_region_variant,,ENST00000433355,;SHPRH,downstream_gene_variant,,ENST00000519632,;SHPRH,downstream_gene_variant,,ENST00000523276,; A ENST00000367505 Transcript missense_variant,splice_region_variant 4591/7201 4326/5052 1442/1683 Q/H caG/caT 1 -1 SHPRH HGNC HGNC:19336 protein_coding YES CCDS43513.2 ENSP00000356475 Q149N8 UPI0000458A24 tolerated(0.1) 24/30 PROSITE_profiles:PS50089,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -11.64015 0.9999993 1 1 1 0 A 3 1 29 145913478 145913478 C A 1 0 0 0 0 1 0 0 0 14554 695 24 2 2 SHPRH 6 145913478 Missense_Mutation SNP C C3L-01924_T 3496146 145913478 24892501 228 8098 ADGB 0 . GRCh38 6 146672244 146672244 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.864G>T p.Trp288Cys p.W288C ENST00000397944 8/36 97 91 6 138 136 2 strelka-varscan-mutect ADGB,missense_variant,p.Trp288Cys,ENST00000397944,NM_024694.3;ADGB,stop_gained,p.Gly213Ter,ENST00000493950,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,; T ENST00000397944 Transcript missense_variant 940/5325 864/5004 288/1667 W/C tgG/tgT 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 deleterious(0) 8/36 PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF304,Pfam_domain:PF00648,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 146672244 146672244 G T 1 0 0 0 0 1 0 0 0 351 1241 43 2 2 ADGB 6 146672244 Missense_Mutation SNP G C3L-01924_T 758766 146672244 24133735 229 8099 FBXO5 0 . GRCh38 6 152973104 152973104 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.851T>A p.Ile284Asn p.I284N ENST00000229758 3/5 212 201 11 211 211 0 strelka-varscan-mutect FBXO5,missense_variant,p.Ile238Asn,ENST00000367241,NM_001142522.1;FBXO5,missense_variant,p.Ile284Asn,ENST00000229758,NM_012177.3;FBXO5,non_coding_transcript_exon_variant,,ENST00000477822,; T ENST00000229758 Transcript missense_variant 910/2037 851/1344 284/447 I/N aTc/aAc 1 -1 FBXO5 HGNC HGNC:13584 protein_coding YES CCDS5242.1 ENSP00000229758 Q9UKT4 UPI000012A585 NM_012177.3 deleterious(0) 3/5 Gene3D:1.20.1280.50,Pfam_domain:PF00646,hmmpanther:PTHR15493,hmmpanther:PTHR15493:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 152973104 152973104 A T 1 0 0 0 0 1 0 0 0 5621 333 12 4 4 FBXO5 6 152973104 Missense_Mutation SNP A C3L-01924_T 6300860 152973104 17832875 230 8100 CLDN20 0 . GRCh38 6 155275979 155275979 + Missense_Mutation SNP C C A rs201661997 C3L-01924_T C3L-01924_N C C c.260C>A p.Ala87Glu p.A87E ENST00000367165 2/2 243 196 47 335 335 0 strelka-varscan-mutect CLDN20,missense_variant,p.Ala87Glu,ENST00000367165,NM_001001346.3;TFB1M,intron_variant,,ENST00000367166,NM_016020.3;TFB1M,intron_variant,,ENST00000468889,;TFB1M,intron_variant,,ENST00000489874,;TFB1M,intron_variant,,ENST00000495806,;TFB1M,intron_variant,,ENST00000470239,; A ENST00000367165 Transcript missense_variant 640/1209 260/660 87/219 A/E gCg/gAg rs201661997,COSM3859952 1 1 CLDN20 HGNC HGNC:2042 protein_coding YES CCDS5249.1 ENSP00000356133 P56880 A0A140VKA2 UPI0000001069 NM_001001346.3 deleterious(0.01) 2/2 Pfam_domain:PF00822,Prints_domain:PR01077,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF17,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201661997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 155275979 155275979 C A 1 0 0 0 0 1 0 0 0 3246 768 27 1 1 CLDN20 6 155275979 Missense_Mutation SNP C C3L-01924_T 2302875 155275979 15530000 231 8101 TULP4 0 . GRCh38 6 158502034 158502034 + Nonsense_Mutation SNP G G T rs537043044 C3L-01924_T C3L-01924_N G G c.2371G>T p.Gly791Ter p.G791* ENST00000367097 13/14 87 76 11 130 130 0 strelka-varscan-mutect TULP4,stop_gained,p.Gly791Ter,ENST00000367097,NM_020245.4;TULP4,intron_variant,,ENST00000367094,NM_001007466.2;TULP4,downstream_gene_variant,,ENST00000613390,; T ENST00000367097 Transcript stop_gained 3900/11295 2371/4632 791/1543 G/* Gga/Tga rs537043044 1 1 TULP4 HGNC HGNC:15530 protein_coding YES CCDS34561.1 ENSP00000356064 Q9NRJ4 UPI000013CD76 NM_020245.4 13/14 hmmpanther:PTHR16517:SF33,hmmpanther:PTHR16517 HIGH 1 SNV 1 1 PASS rs537043044 . 0 203 7 0 0 0 0 0 -19.99972 0.9999994 1 1 1 0 T 4 4 29 158502034 158502034 G T 1 0 0 0 0 0 1 0 0 17286 1349 47 2 2 TULP4 6 158502034 Nonsense_Mutation SNP G C3L-01924_T 3226055 158502034 12303945 232 8102 TCP1 0 . GRCh38 6 159788096 159788096 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.112C>T p.Pro38Ser p.P38S ENST00000321394 2/12 237 218 19 302 302 0 strelka-varscan-mutect TCP1,missense_variant,p.Pro38Ser,ENST00000321394,NM_030752.2;TCP1,missense_variant,p.Pro38Ser,ENST00000420894,;TCP1,missense_variant,p.Pro16Ser,ENST00000539948,;TCP1,missense_variant,p.Pro16Ser,ENST00000537390,;TCP1,missense_variant,p.Pro16Ser,ENST00000536394,;TCP1,intron_variant,,ENST00000392168,NM_001008897.1;TCP1,intron_variant,,ENST00000544255,;TCP1,intron_variant,,ENST00000539756,;TCP1,intron_variant,,ENST00000538128,;MRPL18,upstream_gene_variant,,ENST00000367034,NM_014161.3;SNORA29,upstream_gene_variant,,ENST00000384183,;TCP1,non_coding_transcript_exon_variant,,ENST00000543532,;TCP1,downstream_gene_variant,,ENST00000546023,;MRPL18,upstream_gene_variant,,ENST00000480842,;MRPL18,upstream_gene_variant,,ENST00000476826,;MRPL18,upstream_gene_variant,,ENST00000479638,;TCP1,missense_variant,p.Pro38Ser,ENST00000538530,;TCP1,missense_variant,p.Pro38Ser,ENST00000543517,;TCP1,non_coding_transcript_exon_variant,,ENST00000545764,;TCP1,non_coding_transcript_exon_variant,,ENST00000536607,;TCP1,upstream_gene_variant,,ENST00000536807,;TCP1,upstream_gene_variant,,ENST00000467544,; A ENST00000321394 Transcript missense_variant 393/2499 112/1671 38/556 P/S Cca/Tca 1 -1 TCP1 HGNC HGNC:11655 protein_coding YES CCDS5269.1 ENSP00000317334 P17987 UPI0000136AEA NM_030752.2 deleterious(0) 2/12 hmmpanther:PTHR11353,PROSITE_patterns:PS00750,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02340,Gene3D:1.10.560.10,Superfamily_domains:SSF48592,Prints_domain:PR00304 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 159788096 159788096 G A 1 0 0 0 0 1 0 0 0 16116 1174 41 3 3 TCP1 6 159788096 Missense_Mutation SNP G C3L-01924_T 1286062 159788096 11017883 233 8103 KDELR2 0 . GRCh38 7 6469742 6469742 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.205G>T p.Ala69Ser p.A69S ENST00000258739 3/5 107 74 33 110 110 0 strelka-varscan-mutect KDELR2,missense_variant,p.Ala69Ser,ENST00000258739,NM_006854.3;KDELR2,missense_variant,p.Ala69Ser,ENST00000490996,NM_001100603.1;DAGLB,intron_variant,,ENST00000436575,;KDELR2,intron_variant,,ENST00000463747,;KDELR2,3_prime_UTR_variant,,ENST00000382267,;KDELR2,non_coding_transcript_exon_variant,,ENST00000454368,;KDELR2,downstream_gene_variant,,ENST00000462052,; A ENST00000258739 Transcript missense_variant 390/2884 205/639 69/212 A/S Gcc/Tcc 1 -1 KDELR2 HGNC HGNC:6305 protein_coding YES CCDS5351.1 ENSP00000258739 P33947 A0A024QZT7 UPI000012A0CC NM_006854.3 tolerated(0.42) 3/5 Pfam_domain:PF00810,hmmpanther:PTHR10585,hmmpanther:PTHR10585:SF37,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1328710222 . 0 203 5 2 0 0 0 0 -20 0.9999903 1 1 1 0 A 3 1 29 6469742 6469742 C A 1 0 0 0 0 1 0 0 0 8037 710 25 2 2 KDELR2 7 6469742 Missense_Mutation SNP C C3L-01924_T 6469742 152876231 234 8104 DGKB 0 . GRCh38 7 14149198 14149198 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.2348G>A p.Gly783Asp p.G783D ENST00000403951 26/26 236 221 15 259 259 0 strelka-varscan-mutect DGKB,missense_variant,p.Gly783Asp,ENST00000403951,;DGKB,missense_variant,p.Gly783Asp,ENST00000399322,NM_004080.2;DGKB,missense_variant,p.Gly782Asp,ENST00000402815,;DGKB,missense_variant,p.Gly775Asp,ENST00000407950,;DGKB,non_coding_transcript_exon_variant,,ENST00000493142,; T ENST00000403951 Transcript missense_variant 2768/6917 2348/2415 783/804 G/D gGc/gAc 1 -1 DGKB HGNC HGNC:2850 protein_coding YES CCDS47547.1 ENSP00000385780 Q9Y6T7 UPI0000033B9B deleterious(0) 26/26 hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255 MODERATE 1 SNV 5 1 PASS rs1260652993 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 14149198 14149198 C T 1 0 0 0 0 1 0 0 0 4272 739 26 3 3 DGKB 7 14149198 Missense_Mutation SNP C C3L-01924_T 7679456 14149198 145196775 235 8105 AGMO 0 . GRCh38 7 15544899 15544899 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.282G>T p.= p.L94L ENST00000342526 3/13 100 78 22 122 121 1 strelka-varscan-mutect AGMO,synonymous_variant,p.=,ENST00000342526,NM_001004320.1; A ENST00000342526 Transcript synonymous_variant 452/2475 282/1338 94/445 L ctG/ctT 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 3/13 hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 LOW 1 SNV 1 1 PASS rs1248944917 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 29 15544899 15544899 C A 1 0 0 0 0 0 0 0 1 463 813 29 2 2 AGMO 7 15544899 Silent SNP C C3L-01924_T 1395701 15544899 143801074 236 8106 HDAC9 0 . GRCh38 7 18590420 18590420 + Missense_Mutation SNP G G A rs867599481 C3L-01924_T C3L-01924_N G G c.349G>A p.Glu117Lys p.E117K ENST00000441542 3/25 249 222 27 269 269 0 strelka-varscan-mutect HDAC9,missense_variant,p.Glu114Lys,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Glu117Lys,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,missense_variant,p.Glu114Lys,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Glu145Lys,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,missense_variant,p.Glu117Lys,ENST00000401921,;HDAC9,missense_variant,p.Glu117Lys,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Glu114Lys,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Glu156Lys,ENST00000417496,NM_001204144.1;HDAC9,missense_variant,p.Glu114Lys,ENST00000428307,NM_001204145.1;HDAC9,missense_variant,p.Glu86Lys,ENST00000456174,NM_001204148.1;HDAC9,missense_variant,p.Glu83Lys,ENST00000524023,NM_001204147.1;HDAC9,missense_variant,p.Glu117Lys,ENST00000413380,;HDAC9,missense_variant,p.Glu83Lys,ENST00000441986,;HDAC9,missense_variant,p.Glu117Lys,ENST00000413509,;HDAC9,downstream_gene_variant,,ENST00000430454,;HDAC9,downstream_gene_variant,,ENST00000476135,;HDAC9,3_prime_UTR_variant,,ENST00000446646,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; A ENST00000441542 Transcript missense_variant 349/3210 349/3210 117/1069 E/K Gaa/Aaa rs867599481,COSM4549183,COSM4549184,COSM4549185,COSM4549186 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0) 3/25 Low_complexity_(Seg):seg,Pfam_domain:PF12203,PIRSF_domain:PIRSF037911,Coiled-coils_(Ncoils):Coil 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs867599481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 18590420 18590420 G A 1 0 0 0 0 1 0 0 0 6901 1175 41 3 3 HDAC9 7 18590420 Missense_Mutation SNP G C3L-01924_T 3045521 18590420 140755553 237 8107 HOXA6 0 . GRCh38 7 27145703 27145703 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.657C>A p.= p.S219S ENST00000222728 2/2 139 106 33 130 130 0 strelka-varscan-mutect HOXA6,synonymous_variant,p.=,ENST00000222728,NM_024014.3;HOXA5,upstream_gene_variant,,ENST00000222726,NM_019102.3;HOXA-AS3,intron_variant,,ENST00000521197,;HOXA-AS3,intron_variant,,ENST00000518848,;HOXA-AS3,upstream_gene_variant,,ENST00000518947,;HOXA-AS3,upstream_gene_variant,,ENST00000524304,;HOXA-AS3,upstream_gene_variant,,ENST00000521231,;HOXA6,non_coding_transcript_exon_variant,,ENST00000521478,;RP1-170O19.22,intron_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000518451,;RP1-170O19.23,downstream_gene_variant,,ENST00000498652,;HOXA5,upstream_gene_variant,,ENST00000520854,; T ENST00000222728 Transcript synonymous_variant 682/989 657/702 219/233 S tcC/tcA 1 -1 HOXA6 HGNC HGNC:5107 protein_coding YES CCDS5407.1 ENSP00000222728 P31267 UPI000012CF32 NM_024014.3 2/2 hmmpanther:PTHR24326:SF223,hmmpanther:PTHR24326 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 27145703 27145703 G T 1 0 0 0 0 0 0 0 1 7190 1335 47 2 2 HOXA6 7 27145703 Silent SNP G C3L-01924_T 8555283 27145703 132200270 238 8108 NEUROD6 0 . GRCh38 7 31338906 31338906 + Silent SNP G G C rs188459254 C3L-01924_T C3L-01924_N G G c.363C>G p.= p.V121V ENST00000297142 2/2 326 294 32 426 426 0 strelka-varscan-mutect NEUROD6,synonymous_variant,p.=,ENST00000297142,NM_022728.3; C ENST00000297142 Transcript synonymous_variant 686/2131 363/1014 121/337 V gtC/gtG rs188459254 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 2/2 PROSITE_profiles:PS50888,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS rs188459254 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 31338906 31338906 G C 1 0 0 0 0 0 0 0 1 10388 1161 41 4 4 NEUROD6 7 31338906 Silent SNP G C3L-01924_T 4193203 31338906 128007067 239 8109 POLD2 0 . GRCh38 7 44117625 44117625 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.565G>A p.Val189Ile p.V189I ENST00000610533 4/11 180 145 35 160 159 1 strelka-varscan-mutect POLD2,missense_variant,p.Val154Ile,ENST00000406581,NM_001256879.1;POLD2,missense_variant,p.Val154Ile,ENST00000452185,NM_001127218.2;POLD2,missense_variant,p.Val189Ile,ENST00000610533,NM_006230.3;POLD2,missense_variant,p.Val154Ile,ENST00000223361,;POLD2,missense_variant,p.Val154Ile,ENST00000433715,;POLD2,missense_variant,p.Val154Ile,ENST00000456038,;POLD2,intron_variant,,ENST00000436844,;AEBP1,downstream_gene_variant,,ENST00000223357,NM_001129.4;AEBP1,downstream_gene_variant,,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000418438,;POLD2,upstream_gene_variant,,ENST00000436400,;POLD2,downstream_gene_variant,,ENST00000481763,;POLD2,non_coding_transcript_exon_variant,,ENST00000463464,;POLD2,non_coding_transcript_exon_variant,,ENST00000470867,;POLD2,non_coding_transcript_exon_variant,,ENST00000464871,;POLD2,non_coding_transcript_exon_variant,,ENST00000467469,;POLD2,non_coding_transcript_exon_variant,,ENST00000461116,;AEBP1,downstream_gene_variant,,ENST00000413907,;POLD2,downstream_gene_variant,,ENST00000496539,;POLD2,upstream_gene_variant,,ENST00000481104,;POLD2,upstream_gene_variant,,ENST00000489883,; T ENST00000610533 Transcript missense_variant 565/1619 565/1515 189/504 V/I Gtt/Att 1 -1 POLD2 HGNC HGNC:9176 protein_coding YES CCDS75586.1 ENSP00000480186 A0A087WWF6 UPI0002528875 NM_006230.3 tolerated(0.14) 4/11 hmmpanther:PTHR10416,hmmpanther:PTHR10416:SF0 MODERATE 1 SNV 1 1 PASS rs1248600158 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 44117625 44117625 C T 1 0 0 0 0 1 0 0 0 12301 507 18 3 3 POLD2 7 44117625 Missense_Mutation SNP C C3L-01924_T 12778719 44117625 115228348 240 8110 CAMK2B 0 . GRCh38 7 44228925 44228925 + Splice_Site SNP C C A rs745379322 C3L-01924_T C3L-01924_N C C c.1340-1G>T p.X447_splice ENST00000395749 88 76 12 109 109 0 strelka-varscan-mutect CAMK2B,splice_acceptor_variant,,ENST00000395749,NM_001220.4;CAMK2B,intron_variant,,ENST00000457475,NM_172079.2;CAMK2B,intron_variant,,ENST00000350811,NM_001293170.1;CAMK2B,intron_variant,,ENST00000440254,NM_172078.2;CAMK2B,intron_variant,,ENST00000358707,NM_172081.2;CAMK2B,intron_variant,,ENST00000258682,NM_172080.2;CAMK2B,intron_variant,,ENST00000353625,NM_172083.2;CAMK2B,intron_variant,,ENST00000347193,NM_172082.2;CAMK2B,intron_variant,,ENST00000395747,;CAMK2B,intron_variant,,ENST00000346990,NM_172084.2;CAMK2B,intron_variant,,ENST00000433930,;CAMK2B,upstream_gene_variant,,ENST00000425809,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000489429,;CAMK2B,intron_variant,,ENST00000497584,;CAMK2B,intron_variant,,ENST00000523845,;CAMK2B,intron_variant,,ENST00000353185,; A ENST00000395749 Transcript splice_acceptor_variant -/4447 1340/2001 447/666 rs745379322 1 -1 CAMK2B HGNC HGNC:1461 protein_coding YES CCDS5483.1 ENSP00000379098 Q13554 A4D2J9 UPI0000164A3E NM_001220.4 18/23 HIGH 1 SNV 1 1 PASS rs745379322 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 29 44228925 44228925 C A 1 0 0 0 0 0 0 1 0 2291 811 28 2 2 CAMK2B 7 44228925 Splice_Site SNP C C3L-01924_T 111300 44228925 115117048 241 8111 OGDH 0 . GRCh38 7 44674515 44674515 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.893G>T p.Ser298Ile p.S298I ENST00000222673 7/23 207 168 39 193 193 0 strelka-varscan-mutect OGDH,missense_variant,p.Ser298Ile,ENST00000222673,NM_002541.3;OGDH,missense_variant,p.Ser298Ile,ENST00000631326,;OGDH,missense_variant,p.Ser294Ile,ENST00000449767,NM_001165036.1;OGDH,missense_variant,p.Ser309Ile,ENST00000447398,;OGDH,missense_variant,p.Ser313Ile,ENST00000444676,;OGDH,missense_variant,p.Ser148Ile,ENST00000439616,;OGDH,missense_variant,p.Ser298Ile,ENST00000443864,NM_001003941.2;OGDH,non_coding_transcript_exon_variant,,ENST00000459672,;OGDH,non_coding_transcript_exon_variant,,ENST00000497326,; T ENST00000222673 Transcript missense_variant 935/4181 893/3072 298/1023 S/I aGt/aTt 1 1 OGDH HGNC HGNC:8124 protein_coding YES CCDS34627.1 ENSP00000222673 Q02218 UPI000006D5FE NM_002541.3 tolerated(0.31) 7/23 Gene3D:3.40.50.970,Pfam_domain:PF00676,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF7,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 44674515 44674515 G T 1 0 0 0 0 1 0 0 0 10913 1029 36 2 2 OGDH 7 44674515 Missense_Mutation SNP G C3L-01924_T 445590 44674515 114671458 242 8112 MYO1G 0 . GRCh38 7 44965650 44965650 + Missense_Mutation SNP C C A rs755972612 C3L-01924_T C3L-01924_N C C c.2368G>T p.Ala790Ser p.A790S ENST00000258787 17/22 121 91 30 144 144 0 strelka-varscan-mutect MYO1G,missense_variant,p.Ala790Ser,ENST00000258787,NM_033054.2;RP4-647J21.1,upstream_gene_variant,,ENST00000568457,;MYO1G,3_prime_UTR_variant,,ENST00000495831,;MYO1G,non_coding_transcript_exon_variant,,ENST00000488554,;MYO1G,non_coding_transcript_exon_variant,,ENST00000463516,;MYO1G,non_coding_transcript_exon_variant,,ENST00000483585,;MYO1G,downstream_gene_variant,,ENST00000480503,;MYO1G,downstream_gene_variant,,ENST00000464434,; A ENST00000258787 Transcript missense_variant 2505/3267 2368/3057 790/1018 A/S Gca/Tca rs755972612,COSM4704938 1 -1 MYO1G HGNC HGNC:13880 protein_coding YES CCDS34629.1 ENSP00000258787 B0I1T2 UPI00001D747C NM_033054.2 tolerated(0.76) 17/22 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF381 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755972612 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 44965650 44965650 C A 1 0 0 0 0 1 0 0 0 10075 768 27 1 1 MYO1G 7 44965650 Missense_Mutation SNP C C3L-01924_T 291135 44965650 114380323 243 8113 CCT6A 0 . GRCh38 7 56058051 56058051 + Missense_Mutation SNP G G A rs146242535 C3L-01924_T C3L-01924_N G G c.673G>A p.Val225Met p.V225M ENST00000275603 6/14 175 142 33 169 169 0 strelka-varscan-mutect CCT6A,missense_variant,p.Val225Met,ENST00000275603,NM_001762.3;CCT6A,missense_variant,p.Val180Met,ENST00000335503,NM_001009186.1;SNORA22,downstream_gene_variant,,ENST00000383876,;SNORA15,upstream_gene_variant,,ENST00000384439,;CCT6A,upstream_gene_variant,,ENST00000462133,;CCT6A,non_coding_transcript_exon_variant,,ENST00000482776,;CCT6A,upstream_gene_variant,,ENST00000466479,;CCT6A,upstream_gene_variant,,ENST00000492618,;CCT6A,upstream_gene_variant,,ENST00000466572,;CCT6A,upstream_gene_variant,,ENST00000494736,;CCT6A,downstream_gene_variant,,ENST00000493855,; A ENST00000275603 Transcript missense_variant 892/2719 673/1596 225/531 V/M Gtg/Atg rs146242535 1 1 CCT6A HGNC HGNC:1620 protein_coding YES CCDS5523.1 ENSP00000275603 P40227 A0A024RDL1 UPI0000136B11 NM_001762.3 deleterious(0.05) 6/14 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF58,Pfam_domain:PF00118,Gene3D:3.50.7.10,TIGRFAM_domain:TIGR02347,Superfamily_domains:SSF52029 MODERATE 1 SNV 1 1 PASS rs146242535 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 56058051 56058051 G A 1 0 0 0 0 1 0 0 0 2658 1261 44 3 3 CCT6A 7 56058051 Missense_Mutation SNP G C3L-01924_T 11092401 56058051 103287922 244 8114 ZNF736 0 . GRCh38 7 64348620 64348620 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.757G>T p.Gly253Ter p.G253* ENST00000423484 4/4 170 137 33 199 198 1 strelka-varscan-mutect ZNF736,stop_gained,p.Gly253Ter,ENST00000423484,NM_001170905.2;ZNF736,stop_gained,p.Gly253Ter,ENST00000355095,; T ENST00000423484 Transcript stop_gained 879/7119 757/1284 253/427 G/* Gga/Tga 1 1 ZNF736 HGNC HGNC:32467 protein_coding YES CCDS55114.1 ENSP00000400852 B4DX44 UPI0001662442 NM_001170905.2 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF98,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 64348620 64348620 G T 1 0 0 0 0 0 1 0 0 18707 1349 47 2 2 ZNF736 7 64348620 Nonsense_Mutation SNP G C3L-01924_T 8290569 64348620 94997353 245 8115 HGF 0 . GRCh38 7 81705658 81705658 + Frame_Shift_Del DEL C C - rs771594786 C3L-01924_T C3L-01924_N C C c.1853delG p.Gly618AlafsTer5 p.G618Afs*5 ENST00000222390 16/18 390 317 73 417 416 1 sindel-varindel-pindel HGF,frameshift_variant,p.Gly618AlafsTer5,ENST00000222390,NM_000601.4;HGF,frameshift_variant,p.Gly613AlafsTer5,ENST00000457544,NM_001010932.1; - ENST00000222390 Transcript frameshift_variant 2080/5989 1853/2187 618/728 G/X gGc/gc rs771594786 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 16/18 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 81705658 81705658 C - 1 0 1 0 1 0 0 0 0 6969 739 26 0 0 HGF 7 81705658 Frame_Shift_Del DEL C C3L-01924_T 17357038 81705658 77640315 246 8116 HGF 0 . GRCh38 7 81769936 81769936 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.36G>A p.= p.L12L ENST00000222390 1/18 362 317 45 342 341 1 strelka-varscan-mutect HGF,synonymous_variant,p.=,ENST00000222390,NM_000601.4;HGF,synonymous_variant,p.=,ENST00000457544,NM_001010932.1;HGF,synonymous_variant,p.=,ENST00000423064,NM_001010934.1;HGF,synonymous_variant,p.=,ENST00000354224,;HGF,synonymous_variant,p.=,ENST00000444829,NM_001010931.1;HGF,synonymous_variant,p.=,ENST00000453411,NM_001010933.1;HGF,synonymous_variant,p.=,ENST00000412881,;HGF,synonymous_variant,p.=,ENST00000421558,;HGF,non_coding_transcript_exon_variant,,ENST00000465234,; T ENST00000222390 Transcript synonymous_variant 263/5989 36/2187 12/728 L ctG/ctA 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 1/18 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 81769936 81769936 C T 1 0 0 0 0 0 0 0 1 6969 697 25 3 3 HGF 7 81769936 Silent SNP C C3L-01924_T 64278 81769936 77576037 247 8117 PCLO 0 . GRCh38 7 82955057 82955057 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.5896A>T p.Asn1966Tyr p.N1966Y ENST00000333891 5/25 251 185 66 316 316 0 strelka-varscan-mutect PCLO,missense_variant,p.Asn1966Tyr,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Asn1966Tyr,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript missense_variant 6234/20329 5896/15429 1966/5142 N/Y Aat/Tat 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.03) 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 82955057 82955057 T A 1 0 0 0 0 1 0 0 0 11671 1812 63 4 4 PCLO 7 82955057 Missense_Mutation SNP T C3L-01924_T 1185121 82955057 76390916 248 8118 ZNF804B 0 . GRCh38 7 89333707 89333707 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.725C>G p.Thr242Arg p.T242R ENST00000333190 4/4 180 171 9 231 231 0 strelka-varscan-mutect ZNF804B,missense_variant,p.Thr242Arg,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Thr159Arg,ENST00000611114,; G ENST00000333190 Transcript missense_variant 1334/4659 725/4050 242/1349 T/R aCa/aGa 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 deleterious(0) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 89333707 89333707 C G 1 0 0 0 0 1 0 0 0 18756 478 17 4 4 ZNF804B 7 89333707 Missense_Mutation SNP C C3L-01924_T 6378650 89333707 70012266 249 8119 FZD1 0 . GRCh38 7 91266042 91266042 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1162G>T p.Asp388Tyr p.D388Y ENST00000287934 1/1 238 181 57 232 232 0 strelka-varscan-mutect FZD1,missense_variant,p.Asp388Tyr,ENST00000287934,NM_003505.1; T ENST00000287934 Transcript missense_variant 1679/6963 1162/1944 388/647 D/Y Gac/Tac 1 1 FZD1 HGNC HGNC:4038 protein_coding YES CCDS5620.1 ENSP00000287934 Q9UP38 UPI000005104D NM_003505.1 tolerated(0.05) 1/1 PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF81,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 91266042 91266042 G T 1 0 0 0 0 1 0 0 0 5999 1174 41 2 2 FZD1 7 91266042 Missense_Mutation SNP G C3L-01924_T 1932335 91266042 68079931 250 8120 DYNC1I1 0 . GRCh38 7 96035698 96035698 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.1361A>C p.Asn454Thr p.N454T ENST00000324972 13/17 208 196 12 215 215 0 strelka-mutect DYNC1I1,missense_variant,p.Asn454Thr,ENST00000324972,NM_004411.4;DYNC1I1,missense_variant,p.Asn437Thr,ENST00000447467,NM_001135556.1;DYNC1I1,missense_variant,p.Asn434Thr,ENST00000437599,NM_001278421.1;DYNC1I1,missense_variant,p.Asn417Thr,ENST00000359388,NM_001135557.1;DYNC1I1,missense_variant,p.Asn437Thr,ENST00000457059,;DYNC1I1,missense_variant,p.Asn417Thr,ENST00000630942,NM_001278422.1;DYNC1I1,missense_variant,p.Asn359Thr,ENST00000537881,;DYNC1I1,non_coding_transcript_exon_variant,,ENST00000497626,; C ENST00000324972 Transcript missense_variant 1554/2950 1361/1938 454/645 N/T aAc/aCc 1 1 DYNC1I1 HGNC HGNC:2963 protein_coding YES CCDS5644.1 ENSP00000320130 O14576 A4D1I7 UPI0000129A01 NM_004411.4 deleterious(0) 13/17 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 96035698 96035698 A C 1 0 0 0 0 1 0 0 0 4666 43 2 5 5 DYNC1I1 7 96035698 Missense_Mutation SNP A C3L-01924_T 4769656 96035698 63310275 251 8121 MUC12 0 . GRCh38 7 100991998 100991998 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1435G>T p.Ala479Ser p.A479S ENST00000536621 2/12 502 426 76 501 498 3 strelka-varscan-mutect MUC12,missense_variant,p.Ala622Ser,ENST00000379442,;MUC12,missense_variant,p.Ala479Ser,ENST00000536621,NM_001164462.1; T ENST00000536621 Transcript missense_variant 1435/16321 1435/16008 479/5335 A/S Gcg/Tcg 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 tolerated(0.1) 2/12 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 100991998 100991998 G T 1 0 0 0 0 1 0 0 0 9969 971 34 2 2 MUC12 7 100991998 Missense_Mutation SNP G C3L-01924_T 4956300 100991998 58353975 252 8122 MUC17 0 . GRCh38 7 101035100 101035100 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.3684C>A p.His1228Gln p.H1228Q ENST00000306151 3/13 140 113 27 202 201 1 strelka-varscan-mutect MUC17,missense_variant,p.His1228Gln,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.His1228Gln,ENST00000379439,; A ENST00000306151 Transcript missense_variant 3748/14247 3684/13482 1228/4493 H/Q caC/caA 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0.02) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 101035100 101035100 C A 1 0 0 0 0 1 0 0 0 9973 477 17 2 2 MUC17 7 101035100 Missense_Mutation SNP C C3L-01924_T 43102 101035100 58310873 253 8123 MUC17 0 . GRCh38 7 101048008 101048008 + Missense_Mutation SNP C C A rs375341069 C3L-01924_T C3L-01924_N C C c.12428C>A p.Thr4143Lys p.T4143K ENST00000306151 4/13 83 72 11 80 80 0 strelka-varscan-mutect MUC17,missense_variant,p.Thr4143Lys,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Thr4143Lys,ENST00000379439,;MUC17,non_coding_transcript_exon_variant,,ENST00000470303,;MUC17,upstream_gene_variant,,ENST00000497859,; A ENST00000306151 Transcript missense_variant 12492/14247 12428/13482 4143/4493 T/K aCg/aAg rs375341069 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.18) 4/13 PROSITE_profiles:PS50026,hmmpanther:PTHR37999:SF1,hmmpanther:PTHR37999,Gene3D:2.10.25.10 MODERATE 1 SNV 1 1 PASS rs375341069 . 0 187 22 0 0 0 0 0 -19.99952 0.9927949 0 1 1 0 A 3 1 29 101048008 101048008 C A 1 0 0 0 0 1 0 0 0 9973 536 19 1 1 MUC17 7 101048008 Missense_Mutation SNP C C3L-01924_T 12908 101048008 58297965 254 8124 PSMC2 0 . GRCh38 7 103367412 103367412 + Splice_Site SNP G G T novel C3L-01924_T C3L-01924_N G G c.845-1G>T p.X282_splice ENST00000435765 186 170 16 186 186 0 strelka-varscan-mutect PSMC2,splice_acceptor_variant,,ENST00000435765,;PSMC2,splice_acceptor_variant,,ENST00000292644,NM_002803.3;SLC26A5,intron_variant,,ENST00000339444,NM_206883.2;SLC26A5,intron_variant,,ENST00000393735,NM_206884.2;SLC26A5,intron_variant,,ENST00000356767,NM_206885.2;PSMC2,downstream_gene_variant,,ENST00000460021,; T ENST00000435765 Transcript splice_acceptor_variant -/3054 845/1302 282/433 1 1 PSMC2 HGNC HGNC:9548 protein_coding YES CCDS5731.1 ENSP00000391211 P35998 A0A140VK70 UPI000013237A 10/12 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 29 103367412 103367412 G T 1 0 0 0 0 0 0 1 0 12837 1014 35 2 2 PSMC2 7 103367412 Splice_Site SNP G C3L-01924_T 2319404 103367412 55978561 255 8125 PIK3CG 0 . GRCh38 7 106874795 106874795 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2383G>A p.Ala795Thr p.A795T ENST00000359195 5/11 128 92 36 102 102 0 strelka-varscan-mutect PIK3CG,missense_variant,p.Ala795Thr,ENST00000359195,NM_002649.3;PIK3CG,missense_variant,p.Ala795Thr,ENST00000496166,NM_001282426.1;PIK3CG,missense_variant,p.Ala795Thr,ENST00000440650,NM_001282427.1;PIK3CG,missense_variant,p.Ala68Thr,ENST00000473541,; A ENST00000359195 Transcript missense_variant 2693/5377 2383/3309 795/1102 A/T Gcg/Acg 1 1 PIK3CG HGNC HGNC:8978 protein_coding YES CCDS5739.1 ENSP00000352121 P48736 A0A024R720 UPI00000746B8 NM_002649.3 tolerated(0.69) 5/11 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF34,Gene3D:3.30.1010.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs945222564 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 106874795 106874795 G A 1 0 0 0 0 1 0 0 0 12011 971 34 3 3 PIK3CG 7 106874795 Missense_Mutation SNP G C3L-01924_T 3507383 106874795 52471178 256 8126 PPP1R3A 0 . GRCh38 7 113882300 113882300 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.803C>A p.Thr268Lys p.T268K ENST00000284601 2/4 230 180 50 255 255 0 strelka-varscan-mutect PPP1R3A,missense_variant,p.Thr268Lys,ENST00000284601,NM_002711.3;PPP1R3A,5_prime_UTR_variant,,ENST00000449795,;PPP1R3A,3_prime_UTR_variant,,ENST00000284602,; T ENST00000284601 Transcript missense_variant 872/4384 803/3369 268/1122 T/K aCa/aAa 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 deleterious(0) 2/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 113882300 113882300 G T 1 0 0 0 0 1 0 0 0 12492 1377 48 2 2 PPP1R3A 7 113882300 Missense_Mutation SNP G C3L-01924_T 7007505 113882300 45463673 257 8127 WNT2 0 . GRCh38 7 117297774 117297774 + Missense_Mutation SNP C C A rs750454001 C3L-01924_T C3L-01924_N C C c.691G>T p.Gly231Cys p.G231C ENST00000265441 4/5 171 155 16 166 166 0 strelka-varscan-mutect WNT2,missense_variant,p.Gly231Cys,ENST00000265441,NM_003391.2;WNT2,missense_variant,p.Gly138Val,ENST00000491214,;AC002465.2,upstream_gene_variant,,ENST00000436097,;WNT2,3_prime_UTR_variant,,ENST00000449446,; A ENST00000265441 Transcript missense_variant 991/2907 691/1083 231/360 G/C Ggc/Tgc rs750454001 1 -1 WNT2 HGNC HGNC:12780 protein_coding YES CCDS5771.1 ENSP00000265441 P09544 UPI0000051044 NM_003391.2 deleterious(0) 4/5 hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF86,Pfam_domain:PF00110,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS rs750454001 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 117297774 117297774 C A 1 0 0 0 0 1 0 0 0 17942 623 22 2 2 WNT2 7 117297774 Missense_Mutation SNP C C3L-01924_T 3415474 117297774 42048199 258 8128 PTPRZ1 0 . GRCh38 7 122011909 122011909 + Missense_Mutation SNP G G T rs763354591 C3L-01924_T C3L-01924_N G G c.2863G>T p.Gly955Cys p.G955C ENST00000393386 12/30 284 209 75 381 380 1 strelka-varscan-mutect PTPRZ1,missense_variant,p.Gly955Cys,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; T ENST00000393386 Transcript missense_variant 3274/8175 2863/6948 955/2315 G/C Ggt/Tgt rs763354591,COSM1222725,COSM1222726 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious_low_confidence(0.01) 12/30 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs763354591 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 122011909 122011909 G T 1 0 0 0 0 1 0 0 0 12969 1232 43 2 2 PTPRZ1 7 122011909 Missense_Mutation SNP G C3L-01924_T 4714135 122011909 37334064 259 8129 FEZF1 0 . GRCh38 7 122304345 122304345 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.93C>A p.Phe31Leu p.F31L ENST00000442488 1/4 41 31 10 43 43 0 strelka-varscan-mutect FEZF1,missense_variant,p.Phe31Leu,ENST00000442488,NM_001024613.3;FEZF1,missense_variant,p.Phe31Leu,ENST00000427185,NM_001160264.2;FEZF1,missense_variant,p.Phe31Leu,ENST00000418046,;FEZF1-AS1,intron_variant,,ENST00000428449,;FEZF1-AS1,upstream_gene_variant,,ENST00000437317,;FEZF1-AS1,upstream_gene_variant,,ENST00000424404,; T ENST00000442488 Transcript missense_variant 161/2099 93/1428 31/475 F/L ttC/ttA 1 -1 FEZF1 HGNC HGNC:22788 protein_coding YES CCDS34741.2 ENSP00000411145 A0PJY2 UPI00004193D6 NM_001024613.3 deleterious(0) 1/4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 122304345 122304345 G T 1 0 0 0 0 1 0 0 0 5688 933 33 2 2 FEZF1 7 122304345 Missense_Mutation SNP G C3L-01924_T 292436 122304345 37041628 260 8130 TMEM140 0 . GRCh38 7 135164529 135164529 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.88T>C p.Tyr30His p.Y30H ENST00000275767 2/2 105 96 9 131 131 0 strelka-varscan-mutect TMEM140,missense_variant,p.Tyr30His,ENST00000275767,NM_018295.4;C7orf49,downstream_gene_variant,,ENST00000424142,;C7orf49,downstream_gene_variant,,ENST00000617987,NM_001243751.1,NM_001243753.1,NM_001243749.1,NM_001243752.1;C7orf49,downstream_gene_variant,,ENST00000430372,;C7orf49,downstream_gene_variant,,ENST00000393114,NM_024033.3;C7orf49,downstream_gene_variant,,ENST00000620897,NM_001243755.1;C7orf49,downstream_gene_variant,,ENST00000483029,NM_001243754.1;RP11-134L10.1,upstream_gene_variant,,ENST00000608819,;C7orf49,intron_variant,,ENST00000459937,;C7orf49,downstream_gene_variant,,ENST00000472428,;C7orf49,downstream_gene_variant,,ENST00000477820,;C7orf49,downstream_gene_variant,,ENST00000488161,;C7orf49,downstream_gene_variant,,ENST00000481410,;C7orf49,downstream_gene_variant,,ENST00000487774,;C7orf49,downstream_gene_variant,,ENST00000486115,; C ENST00000275767 Transcript missense_variant 311/1997 88/558 30/185 Y/H Tac/Cac 1 1 TMEM140 HGNC HGNC:21870 protein_coding YES CCDS5837.1 ENSP00000275767 Q9NV12 UPI000045760C NM_018295.4 deleterious(0.03) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR16103:SF0,hmmpanther:PTHR16103,Pfam_domain:PF14985 MODERATE 1 SNV 1 1 PASS rs1489262160 . 0 208 2 0 0 0 0 0 -18.54059 1 1 1 1 0 C 3 2 29 135164529 135164529 T C 1 0 0 0 0 1 0 0 0 16500 1754 61 5 5 TMEM140 7 135164529 Missense_Mutation SNP T C3L-01924_T 12860184 135164529 24181444 261 8131 CLCN1 0 . GRCh38 7 143345609 143345609 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.2019A>T p.= p.A673A ENST00000343257 17/23 166 141 25 141 141 0 strelka-varscan-mutect CLCN1,synonymous_variant,p.=,ENST00000343257,NM_000083.2; T ENST00000343257 Transcript synonymous_variant 2106/3172 2019/2967 673/988 A gcA/gcT 1 1 CLCN1 HGNC HGNC:2019 protein_coding YES CCDS5881.1 ENSP00000339867 P35523 UPI000020F1EC NM_000083.2 17/23 hmmpanther:PTHR11689:SF29,hmmpanther:PTHR11689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 143345609 143345609 A T 1 0 0 0 0 0 0 0 1 3226 175 7 4 4 CLCN1 7 143345609 Silent SNP A C3L-01924_T 8181080 143345609 16000364 262 8132 OR6B1 0 . GRCh38 7 144004614 144004614 + Silent SNP C C A C3L-01924_T C3L-01924_N C C c.618C>A p.= p.I206I ENST00000408922 1/1 373 281 92 418 417 1 strelka-varscan-mutect OR6B1,synonymous_variant,p.=,ENST00000408922,NM_001005281.1; A ENST00000408922 Transcript synonymous_variant 686/1055 618/936 206/311 I atC/atA COSM745117 1 1 OR6B1 HGNC HGNC:8354 protein_coding YES CCDS43667.1 ENSP00000386151 O95007 UPI0000041B18 NM_001005281.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF284,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 144004614 144004614 C A 1 0 0 0 0 0 0 0 1 11255 903 32 2 2 OR6B1 7 144004614 Silent SNP C C3L-01924_T 659005 144004614 15341359 263 8133 CNTNAP2 0 . GRCh38 7 147108301 147108301 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.705C>A p.Tyr235Ter p.Y235* ENST00000361727 5/24 194 176 18 173 173 0 strelka-varscan-mutect CNTNAP2,stop_gained,p.Tyr235Ter,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637555,; A ENST00000361727 Transcript stop_gained 1223/9896 705/3996 235/1331 Y/* taC/taA 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 5/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 147108301 147108301 C A 1 0 0 0 0 0 1 0 0 3428 489 17 2 2 CNTNAP2 7 147108301 Nonsense_Mutation SNP C C3L-01924_T 3103687 147108301 12237672 264 8134 CNTNAP2 0 . GRCh38 7 148172452 148172452 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2984C>A p.Ala995Glu p.A995E ENST00000361727 18/24 376 281 95 398 398 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Ala995Glu,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Ala54Glu,ENST00000628930,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636988,;CNTNAP2,downstream_gene_variant,,ENST00000631199,; A ENST00000361727 Transcript missense_variant 3502/9896 2984/3996 995/1331 A/E gCa/gAa 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 18/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 148172452 148172452 C A 1 0 0 0 0 1 0 0 0 3428 710 25 2 2 CNTNAP2 7 148172452 Missense_Mutation SNP C C3L-01924_T 1064151 148172452 11173521 265 8135 SSPO 0 . GRCh38 7 149803504 149803504 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.7996C>T p.His2666Tyr p.H2666Y ENST00000378016 53/107 77 70 7 59 59 0 strelka-varscan-mutect SSPO,missense_variant,p.His2666Tyr,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000475488,; T ENST00000378016 Transcript missense_variant 7996/15589 7996/15453 2666/5150 H/Y Cat/Tat 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 tolerated(0.16) 53/107 Pfam_domain:PF01826,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS rs1300279600 . 0 205 4 0 0 0 0 0 -15.37709 1 1 1 1 0 T 3 4 29 149803504 149803504 C T 1 0 0 0 0 1 0 0 0 15566 710 25 3 3 SSPO 7 149803504 Missense_Mutation SNP C C3L-01924_T 1631052 149803504 9542469 266 8136 SSPO 0 . GRCh38 7 149815269 149815269 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.10680T>C p.= p.S3560S ENST00000378016 74/107 89 70 19 59 59 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000481772,; C ENST00000378016 Transcript synonymous_variant 10680/15589 10680/15453 3560/5150 S tcT/tcC 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 74/107 Pfam_domain:PF01826,Gene3D:2.10.25.10,hmmpanther:PTHR11339:SF294,hmmpanther:PTHR11339 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 149815269 149815269 T C 1 0 0 0 0 0 0 0 1 15566 1567 55 5 5 SSPO 7 149815269 Silent SNP T C3L-01924_T 11765 149815269 9530704 267 8137 GIMAP8 0 . GRCh38 7 150477734 150477734 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1952C>A p.Ser651Tyr p.S651Y ENST00000307271 5/5 188 167 21 197 196 1 strelka-varscan-mutect GIMAP8,missense_variant,p.Ser651Tyr,ENST00000307271,NM_175571.3; A ENST00000307271 Transcript missense_variant 2526/4184 1952/1998 651/665 S/Y tCc/tAc COSM3832274 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 tolerated(0.12) 5/5 hmmpanther:PTHR10903:SF73,hmmpanther:PTHR10903,Pfam_domain:PF04548 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 150477734 150477734 C A 1 0 0 0 0 1 0 0 0 6265 855 30 2 2 GIMAP8 7 150477734 Missense_Mutation SNP C C3L-01924_T 662465 150477734 8868239 268 8138 KMT2C 0 . GRCh38 7 152273779 152273779 + Missense_Mutation SNP C C G rs771643713 C3L-01924_T C3L-01924_N C C c.938G>C p.Gly313Ala p.G313A ENST00000262189 7/59 472 443 29 441 441 0 varscan-mutect KMT2C,missense_variant,p.Gly313Ala,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Gly313Ala,ENST00000355193,;KMT2C,missense_variant,p.Gly313Ala,ENST00000558084,; G ENST00000262189 Transcript missense_variant 1157/16862 938/14736 313/4911 G/A gGa/gCa rs771643713 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 tolerated(0.88) 7/59 Pfam_domain:PF13771,SMART_domains:SM00249 MODERATE 1 SNV 1 1 PASS rs771643713 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 152273779 152273779 C G 1 0 0 0 0 1 0 0 0 8297 855 30 4 4 KMT2C 7 152273779 Missense_Mutation SNP C C3L-01924_T 1796045 152273779 7072194 269 8139 UBE3C 0 . GRCh38 7 157256991 157256991 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.3028A>G p.Lys1010Glu p.K1010E ENST00000348165 22/23 246 173 73 244 244 0 strelka-varscan-mutect UBE3C,missense_variant,p.Lys1010Glu,ENST00000348165,NM_014671.2;UBE3C,non_coding_transcript_exon_variant,,ENST00000470408,;UBE3C,non_coding_transcript_exon_variant,,ENST00000474153,; G ENST00000348165 Transcript missense_variant 3388/5229 3028/3252 1010/1083 K/E Aaa/Gaa 1 1 UBE3C HGNC HGNC:16803 protein_coding YES CCDS34789.1 ENSP00000309198 Q15386 UPI000020E72A NM_014671.2 deleterious(0.03) 22/23 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF336,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 157256991 157256991 A G 1 0 0 0 0 1 0 0 0 17404 131 5 5 5 UBE3C 7 157256991 Missense_Mutation SNP A C3L-01924_T 4983212 157256991 2088982 270 8140 CSMD1 0 . GRCh38 8 4032036 4032036 + Missense_Mutation SNP C C A rs866901808 C3L-01924_T C3L-01924_N C C c.479G>T p.Arg160Ile p.R160I ENST00000520002 4/71 170 149 21 225 225 0 strelka-varscan-mutect CSMD1,missense_variant,p.Arg22Ile,ENST00000537824,;CSMD1,missense_variant,p.Arg160Ile,ENST00000520002,;CSMD1,missense_variant,p.Arg160Ile,ENST00000602557,;CSMD1,missense_variant,p.Arg160Ile,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Arg160Ile,ENST00000400186,;CSMD1,missense_variant,p.Arg160Ile,ENST00000602723,; A ENST00000520002 Transcript missense_variant 1035/11740 479/10698 160/3565 R/I aGa/aTa rs866901808 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.05) 4/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs866901808 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 4032036 4032036 C A 1 0 0 0 0 1 0 0 0 3745 913 32 2 2 CSMD1 8 4032036 Missense_Mutation SNP C C3L-01924_T 4032036 141106600 271 8141 STMN4 0 . GRCh38 8 27241111 27241111 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.342A>G p.= p.R114R ENST00000350889 5/7 85 76 9 160 160 0 strelka-varscan-mutect STMN4,synonymous_variant,p.=,ENST00000350889,NM_030795.3;STMN4,synonymous_variant,p.=,ENST00000519997,NM_001283055.1;STMN4,synonymous_variant,p.=,ENST00000519614,;STMN4,synonymous_variant,p.=,ENST00000265770,NM_001283054.1;STMN4,synonymous_variant,p.=,ENST00000523048,NM_001283053.1;STMN4,synonymous_variant,p.=,ENST00000522908,;STMN4,downstream_gene_variant,,ENST00000522750,; C ENST00000350889 Transcript synonymous_variant 456/2288 342/651 114/216 R cgA/cgG 1 -1 STMN4 HGNC HGNC:16078 protein_coding YES CCDS6055.1 ENSP00000342538 Q9H169 UPI000002B451 NM_030795.3 5/7 Superfamily_domains:0043535,Pfam_domain:PF00836,PIRSF_domain:PIRSF002285,Prints_domain:PR00345,PROSITE_patterns:PS00563,PROSITE_profiles:PS51663,hmmpanther:PTHR10104,hmmpanther:PTHR10104:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 27241111 27241111 T C 1 0 0 0 0 0 0 0 1 15689 1538 54 5 5 STMN4 8 27241111 Silent SNP T C3L-01924_T 23209075 27241111 117897525 272 8142 KCNU1 0 . GRCh38 8 36840543 36840543 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1599C>A p.Asp533Glu p.D533E ENST00000399881 15/27 121 110 11 174 173 1 strelka-varscan-mutect KCNU1,missense_variant,p.Asp533Glu,ENST00000399881,NM_001031836.2;KCNU1,missense_variant,p.Asp533Glu,ENST00000522372,; A ENST00000399881 Transcript missense_variant 1636/3695 1599/3450 533/1149 D/E gaC/gaA 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 deleterious(0.01) 15/27 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF23,Pfam_domain:PF03493 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 36840543 36840543 C A 1 0 0 0 0 1 0 0 0 8009 564 20 2 2 KCNU1 8 36840543 Missense_Mutation SNP C C3L-01924_T 9599432 36840543 108298093 273 8143 SPIDR 0 . GRCh38 8 47700403 47700403 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1686G>C p.Arg562Ser p.R562S ENST00000297423 12/20 225 212 13 272 272 0 strelka-mutect SPIDR,missense_variant,p.Arg562Ser,ENST00000297423,NM_001080394.3;SPIDR,missense_variant,p.Arg492Ser,ENST00000541342,NM_001282916.1;SPIDR,missense_variant,p.Arg502Ser,ENST00000518074,NM_001282919.1;SPIDR,missense_variant,p.Arg244Ser,ENST00000519401,;SPIDR,missense_variant,p.Arg37Ser,ENST00000517693,;SPIDR,splice_region_variant,,ENST00000521214,;SPIDR,splice_region_variant,,ENST00000521550,;SPIDR,splice_region_variant,,ENST00000519141,;SPIDR,splice_region_variant,,ENST00000522321,;SPIDR,splice_region_variant,,ENST00000518692,;SPIDR,splice_region_variant,,ENST00000524141,;SPIDR,splice_region_variant,,ENST00000522117,;SPIDR,splice_region_variant,,ENST00000524126,;SPIDR,splice_region_variant,,ENST00000519362,; C ENST00000297423 Transcript missense_variant,splice_region_variant 2070/3988 1686/2748 562/915 R/S agG/agC 1 1 SPIDR HGNC HGNC:28971 protein_coding YES CCDS43737.1 ENSP00000297423 Q14159 UPI0000253B92 NM_001080394.3 deleterious(0) 12/20 Pfam_domain:PF14951,hmmpanther:PTHR34347,hmmpanther:PTHR34347:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 47700403 47700403 G C 1 0 0 0 0 1 0 0 0 15404 1188 41 4 4 SPIDR 8 47700403 Missense_Mutation SNP G C3L-01924_T 10859860 47700403 97438233 274 8144 SOX17 0 . GRCh38 8 54459747 54459747 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.997C>T p.Pro333Ser p.P333S ENST00000297316 2/2 284 243 41 298 298 0 strelka-varscan-mutect SOX17,missense_variant,p.Pro333Ser,ENST00000297316,NM_022454.3; T ENST00000297316 Transcript missense_variant 1201/2342 997/1245 333/414 P/S Ccg/Tcg 1 1 SOX17 HGNC HGNC:18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 UPI00001362B7 NM_022454.3 tolerated(0.13) 2/2 PROSITE_profiles:PS51516,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF216,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 54459747 54459747 C T 1 0 0 0 0 1 0 0 0 15273 739 26 3 3 SOX17 8 54459747 Missense_Mutation SNP C C3L-01924_T 6759344 54459747 90678889 275 8145 SULF1 0 . GRCh38 8 69627805 69627805 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.1981A>G p.Arg661Gly p.R661G ENST00000260128 17/23 116 94 22 150 150 0 strelka-varscan-mutect SULF1,missense_variant,p.Arg661Gly,ENST00000260128,NM_015170.2;SULF1,missense_variant,p.Arg661Gly,ENST00000458141,NM_001128204.1;SULF1,missense_variant,p.Arg661Gly,ENST00000402687,NM_001128205.1;SULF1,missense_variant,p.Arg661Gly,ENST00000419716,NM_001128206.1;SULF1,missense_variant,p.Arg445Gly,ENST00000616868,;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,;SULF1,non_coding_transcript_exon_variant,,ENST00000524731,;SULF1,missense_variant,p.Arg2Gly,ENST00000531512,; G ENST00000260128 Transcript missense_variant 2698/5710 1981/2616 661/871 R/G Aga/Gga 1 1 SULF1 HGNC HGNC:20391 protein_coding YES CCDS6204.1 ENSP00000260128 Q8IWU6 A0A024R809 UPI000003FD82 NM_015170.2 deleterious(0) 17/23 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF036665,Pfam_domain:PF12548 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 69627805 69627805 A G 1 0 0 0 0 1 0 0 0 15758 64 3 5 5 SULF1 8 69627805 Missense_Mutation SNP A C3L-01924_T 15168058 69627805 75510831 276 8146 JPH1 0 . GRCh38 8 74244643 74244643 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1791A>T p.Lys597Asn p.K597N ENST00000342232 4/6 206 177 29 234 234 0 strelka-varscan-mutect JPH1,missense_variant,p.Lys597Asn,ENST00000342232,NM_020647.2;JPH1,non_coding_transcript_exon_variant,,ENST00000518195,;JPH1,3_prime_UTR_variant,,ENST00000519947,; A ENST00000342232 Transcript missense_variant 1832/4378 1791/1986 597/661 K/N aaA/aaT 1 -1 JPH1 HGNC HGNC:14201 protein_coding YES CCDS6217.1 ENSP00000344488 Q9HDC5 UPI000012DAC0 NM_020647.2 deleterious(0.05) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF6,PIRSF_domain:PIRSF037387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 74244643 74244643 T A 1 0 0 0 0 1 0 0 0 7872 1722 60 4 4 JPH1 8 74244643 Missense_Mutation SNP T C3L-01924_T 4616838 74244643 70893993 277 8147 HNF4G 0 . GRCh38 8 75543939 75543939 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.217T>G p.Phe73Val p.F73V ENST00000396423 2/10 101 94 7 79 79 0 strelka-mutect HNF4G,missense_variant,p.Phe73Val,ENST00000396423,NM_004133.4;HNF4G,missense_variant,p.Phe36Val,ENST00000354370,;HNF4G,intron_variant,,ENST00000396419,; G ENST00000396423 Transcript missense_variant 341/4209 217/1338 73/445 F/V Ttc/Gtc 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 deleterious(0.02) 2/10 PROSITE_profiles:PS51030,hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -14.54035 1 1 1 1 0 G 3 3 29 75543939 75543939 T G 1 0 0 0 0 1 0 0 0 7145 1609 56 5 5 HNF4G 8 75543939 Missense_Mutation SNP T C3L-01924_T 1299296 75543939 69594697 278 8148 HNF4G 0 . GRCh38 8 75558625 75558625 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.811G>T p.Asp271Tyr p.D271Y ENST00000396423 7/10 259 235 24 188 188 0 strelka-varscan-mutect HNF4G,missense_variant,p.Asp271Tyr,ENST00000396423,NM_004133.4;HNF4G,missense_variant,p.Asp234Tyr,ENST00000354370,; T ENST00000396423 Transcript missense_variant 935/4209 811/1338 271/445 D/Y Gac/Tac 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 deleterious(0) 7/10 hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 75558625 75558625 G T 1 0 0 0 0 1 0 0 0 7145 1290 45 2 2 HNF4G 8 75558625 Missense_Mutation SNP G C3L-01924_T 14686 75558625 69580011 279 8149 ZFHX4 0 . GRCh38 8 76854290 76854290 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.7369C>A p.Gln2457Lys p.Q2457K ENST00000521891 10/11 411 348 63 309 308 1 strelka-varscan-mutect ZFHX4,missense_variant,p.Gln2457Lys,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Gln2431Lys,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript missense_variant 7817/14019 7369/10851 2457/3616 Q/K Caa/Aaa 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(0.19) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 76854290 76854290 C A 1 0 0 0 0 1 0 0 0 18213 595 21 2 2 ZFHX4 8 76854290 Missense_Mutation SNP C C3L-01924_T 1295665 76854290 68284346 280 8150 TPD52 0 . GRCh38 8 80038225 80038225 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.635G>T p.Gly212Val p.G212V ENST00000520527 8/8 121 89 32 121 120 1 strelka-varscan-mutect TPD52,missense_variant,p.Gly203Val,ENST00000448733,NM_001287142.1;TPD52,missense_variant,p.Gly149Val,ENST00000379096,NM_001287144.1,NM_005079.3;TPD52,missense_variant,p.Gly172Val,ENST00000518937,NM_001025253.2;TPD52,missense_variant,p.Gly212Val,ENST00000520527,NM_001287140.1;TPD52,missense_variant,p.Gly198Val,ENST00000517427,NM_001287143.1;TPD52,missense_variant,p.Gly189Val,ENST00000379097,NM_001025252.2;TPD52,missense_variant,p.Gly25Val,ENST00000519303,;RP11-92K15.3,upstream_gene_variant,,ENST00000607017,;TPD52,non_coding_transcript_exon_variant,,ENST00000523395,;TPD52,non_coding_transcript_exon_variant,,ENST00000520877,;TPD52,3_prime_UTR_variant,,ENST00000517462,;TPD52,3_prime_UTR_variant,,ENST00000521354,;TPD52,3_prime_UTR_variant,,ENST00000521241,;TPD52,3_prime_UTR_variant,,ENST00000518517,;TPD52,non_coding_transcript_exon_variant,,ENST00000523193,;TPD52,non_coding_transcript_exon_variant,,ENST00000523319,;TPD52,non_coding_transcript_exon_variant,,ENST00000521618,;TPD52,non_coding_transcript_exon_variant,,ENST00000524194,;RP11-26J3.4,intron_variant,,ENST00000522938,;TPD52,downstream_gene_variant,,ENST00000517445,; A ENST00000520527 Transcript missense_variant 998/2638 635/744 212/247 G/V gGg/gTg 1 -1 TPD52 HGNC HGNC:12005 protein_coding YES CCDS75759.1 ENSP00000429309 P55327 UPI0001BB3A09 NM_001287140.1 tolerated(0.5) 8/8 hmmpanther:PTHR19307,hmmpanther:PTHR19307:SF12,Pfam_domain:PF04201 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 80038225 80038225 C A 1 0 0 0 0 1 0 0 0 16876 623 22 2 2 TPD52 8 80038225 Missense_Mutation SNP C C3L-01924_T 3183935 80038225 65100411 281 8151 CA2 0 . GRCh38 8 85477151 85477151 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.539C>A p.Pro180His p.P180H ENST00000285379 6/7 462 432 30 353 351 2 strelka-varscan-mutect CA2,missense_variant,p.Pro180His,ENST00000285379,NM_001293675.1,NM_000067.2;CA2,3_prime_UTR_variant,,ENST00000520127,;CA2,3_prime_UTR_variant,,ENST00000522742,;CA2,downstream_gene_variant,,ENST00000520996,;CA2,downstream_gene_variant,,ENST00000518231,; A ENST00000285379 Transcript missense_variant 769/1717 539/783 180/260 P/H cCt/cAt COSM1755812 1 1 CA2 HGNC HGNC:1373 protein_coding YES CCDS6239.1 ENSP00000285379 P00918 V9HW21 UPI0000110BA2 NM_001293675.1,NM_000067.2 deleterious(0) 6/7 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF120,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069 1 MODERATE 1 SNV 1 1 1 PASS rs886063150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 85477151 85477151 C A 1 0 0 0 0 1 0 0 0 2202 681 24 2 2 CA2 8 85477151 Missense_Mutation SNP C C3L-01924_T 5438926 85477151 59661485 282 8152 CA2 0 . GRCh38 8 85477236 85477236 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.624G>T p.Trp208Cys p.W208C ENST00000285379 6/7 496 446 50 329 328 1 strelka-varscan-mutect CA2,missense_variant,p.Trp208Cys,ENST00000285379,NM_001293675.1,NM_000067.2;CA2,3_prime_UTR_variant,,ENST00000520127,;CA2,downstream_gene_variant,,ENST00000522742,;CA2,downstream_gene_variant,,ENST00000520996,;CA2,downstream_gene_variant,,ENST00000518231,; T ENST00000285379 Transcript missense_variant 854/1717 624/783 208/260 W/C tgG/tgT COSM5252048 1 1 CA2 HGNC HGNC:1373 protein_coding YES CCDS6239.1 ENSP00000285379 P00918 V9HW21 UPI0000110BA2 NM_001293675.1,NM_000067.2 deleterious(0) 6/7 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF120,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 85477236 85477236 G T 1 0 0 0 0 1 0 0 0 2202 1183 41 2 2 CA2 8 85477236 Missense_Mutation SNP G C3L-01924_T 85 85477236 59661400 283 8153 SLC7A13 0 . GRCh38 8 86217540 86217540 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1109G>C p.Trp370Ser p.W370S ENST00000297524 3/4 141 93 48 125 125 0 strelka-varscan-mutect SLC7A13,missense_variant,p.Trp370Ser,ENST00000297524,NM_138817.2;SLC7A13,missense_variant,p.Trp361Ser,ENST00000419776,;SLC7A13,downstream_gene_variant,,ENST00000520624,; G ENST00000297524 Transcript missense_variant 1213/1878 1109/1413 370/470 W/S tGg/tCg 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 tolerated(0.15) 3/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS rs1161580204 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 86217540 86217540 C G 1 0 0 0 0 1 0 0 0 14978 595 21 4 4 SLC7A13 8 86217540 Missense_Mutation SNP C C3L-01924_T 740304 86217540 58921096 284 8154 SLC7A13 0 . GRCh38 8 86229683 86229683 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.595G>T p.Ala199Ser p.A199S ENST00000297524 1/4 317 216 101 320 319 1 strelka-varscan-mutect SLC7A13,missense_variant,p.Ala199Ser,ENST00000297524,NM_138817.2;SLC7A13,missense_variant,p.Ala199Ser,ENST00000419776,;SLC7A13,intron_variant,,ENST00000520624,; A ENST00000297524 Transcript missense_variant 699/1878 595/1413 199/470 A/S Gct/Tct 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 tolerated(0.14) 1/4 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 86229683 86229683 C A 1 0 0 0 0 1 0 0 0 14978 710 25 2 2 SLC7A13 8 86229683 Missense_Mutation SNP C C3L-01924_T 12143 86229683 58908953 285 8155 MMP16 0 . GRCh38 8 88074659 88074659 + Missense_Mutation SNP G G T rs774237231 C3L-01924_T C3L-01924_N G G c.1168C>A p.Pro390Thr p.P390T ENST00000286614 7/10 223 133 90 226 226 0 strelka-varscan-mutect MMP16,missense_variant,p.Pro390Thr,ENST00000286614,NM_005941.4;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; T ENST00000286614 Transcript missense_variant 1450/11558 1168/1824 390/607 P/T Cct/Act rs774237231,COSM5599944 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 tolerated(0.54) 7/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,PROSITE_patterns:PS00024,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00045,SMART_domains:SM00120,Superfamily_domains:SSF50923 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774237231 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 88074659 88074659 G T 1 0 0 0 0 1 0 0 0 9618 1174 41 2 2 MMP16 8 88074659 Missense_Mutation SNP G C3L-01924_T 1844976 88074659 57063977 286 8156 MMP16 0 . GRCh38 8 88074735 88074735 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1092G>C p.Trp364Cys p.W364C ENST00000286614 7/10 154 134 20 142 142 0 strelka-varscan-mutect MMP16,missense_variant,p.Trp364Cys,ENST00000286614,NM_005941.4;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; G ENST00000286614 Transcript missense_variant 1374/11558 1092/1824 364/607 W/C tgG/tgC 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 deleterious(0) 7/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00045,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 88074735 88074735 C G 1 0 0 0 0 1 0 0 0 9618 508 18 4 4 MMP16 8 88074735 Missense_Mutation SNP C C3L-01924_T 76 88074735 57063901 287 8157 RUNX1T1 0 . GRCh38 8 91986907 91986907 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1234G>T p.Glu412Ter p.E412* ENST00000436581 8/12 308 255 53 251 250 1 strelka-varscan-mutect RUNX1T1,stop_gained,p.Glu353Ter,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,stop_gained,p.Glu353Ter,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,stop_gained,p.Glu353Ter,ENST00000523629,NM_175634.2;RUNX1T1,stop_gained,p.Glu353Ter,ENST00000614812,NM_001198631.1;RUNX1T1,stop_gained,p.Glu412Ter,ENST00000436581,NM_001198679.1;RUNX1T1,stop_gained,p.Glu326Ter,ENST00000613886,NM_001198632.1;RUNX1T1,stop_gained,p.Glu333Ter,ENST00000615601,NM_001198633.1;RUNX1T1,stop_gained,p.Glu353Ter,ENST00000265814,NM_001198628.1;RUNX1T1,stop_gained,p.Glu326Ter,ENST00000396218,NM_004349.3;RUNX1T1,stop_gained,p.Glu326Ter,ENST00000518844,NM_001198625.1;RUNX1T1,stop_gained,p.Glu316Ter,ENST00000422361,NM_175636.2;RUNX1T1,stop_gained,p.Glu316Ter,ENST00000360348,NM_175635.2;RUNX1T1,stop_gained,p.Glu364Ter,ENST00000520724,NM_001198634.1;RUNX1T1,stop_gained,p.Glu53Ter,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,downstream_gene_variant,,ENST00000520047,;RUNX1T1,downstream_gene_variant,,ENST00000518361,; A ENST00000436581 Transcript stop_gained 1421/7454 1234/1992 412/663 E/* Gag/Tag 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 8/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,Pfam_domain:PF08788 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 91986907 91986907 C A 1 0 0 0 0 0 1 0 0 14008 922 32 2 2 RUNX1T1 8 91986907 Nonsense_Mutation SNP C C3L-01924_T 3912172 91986907 53151729 288 8158 POP1 0 . GRCh38 8 98130112 98130112 + Missense_Mutation SNP G G C rs749388629 C3L-01924_T C3L-01924_N G G c.621G>C p.Trp207Cys p.W207C ENST00000401707 5/16 477 318 159 394 394 0 strelka-varscan-mutect POP1,missense_variant,p.Trp207Cys,ENST00000401707,NM_001145860.1,NM_001145861.1;POP1,missense_variant,p.Trp207Cys,ENST00000349693,NM_015029.2;POP1,downstream_gene_variant,,ENST00000522319,; C ENST00000401707 Transcript missense_variant 702/4719 621/3075 207/1024 W/C tgG/tgC rs749388629 1 1 POP1 HGNC HGNC:30129 protein_coding YES CCDS6277.1 ENSP00000385787 Q99575 UPI0000131F33 NM_001145860.1,NM_001145861.1 deleterious(0) 5/16 hmmpanther:PTHR22731,hmmpanther:PTHR22731:SF3,Pfam_domain:PF06978 MODERATE 1 SNV 2 1 PASS rs749388629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 98130112 98130112 G C 1 0 0 0 0 1 0 0 0 12365 1212 42 4 4 POP1 8 98130112 Missense_Mutation SNP G C3L-01924_T 6143205 98130112 47008524 289 8159 KCNS2 0 . GRCh38 8 98428369 98428369 + Silent SNP C C A rs764750909 C3L-01924_T C3L-01924_N C C c.390C>A p.= p.P130P ENST00000287042 2/2 510 415 95 396 396 0 strelka-varscan-mutect KCNS2,synonymous_variant,p.=,ENST00000287042,NM_020697.2;KCNS2,synonymous_variant,p.=,ENST00000521839,;STK3,intron_variant,,ENST00000517832,; A ENST00000287042 Transcript synonymous_variant 740/5219 390/1434 130/477 P ccC/ccA rs764750909 1 1 KCNS2 HGNC HGNC:6301 protein_coding YES CCDS6279.1 ENSP00000287042 Q9ULS6 UPI0000001653 NM_020697.2 2/2 Gene3D:3.30.710.10,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF60 LOW 1 SNV 1 1 PASS rs764750909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 98428369 98428369 C A 1 0 0 0 0 0 0 0 1 8005 639 23 1 1 KCNS2 8 98428369 Silent SNP C C3L-01924_T 298257 98428369 46710267 290 8160 RIMS2 0 . GRCh38 8 103501006 103501006 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.120C>A p.= p.I40I ENST00000504942 1/24 188 170 18 151 151 0 strelka-varscan-mutect RIMS2,synonymous_variant,p.=,ENST00000504942,NM_001100117.2;RIMS2,synonymous_variant,p.=,ENST00000632716,;RP11-1C8.4,intron_variant,,ENST00000523422,;RP11-1C8.4,upstream_gene_variant,,ENST00000517376,; A ENST00000504942 Transcript synonymous_variant 259/4228 120/4050 40/1349 I atC/atA 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 1/24 Gene3D:3.30.40.10,Pfam_domain:PF02318,PROSITE_profiles:PS50916,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Superfamily_domains:SSF57903 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 103501006 103501006 C A 1 0 0 0 0 0 0 0 1 13543 845 30 2 2 RIMS2 8 103501006 Silent SNP C C3L-01924_T 5072637 103501006 41637630 291 8161 DCSTAMP 0 . GRCh38 8 104348820 104348820 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.268G>T p.Gly90Cys p.G90C ENST00000297581 2/4 466 427 39 404 403 1 strelka-varscan-mutect DCSTAMP,missense_variant,p.Gly90Cys,ENST00000297581,NM_030788.3;DCSTAMP,missense_variant,p.Gly90Cys,ENST00000622554,NM_001257317.1;DCSTAMP,missense_variant,p.Gly90Cys,ENST00000517991,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000518023,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,upstream_gene_variant,,ENST00000518051,;DCSTAMP,downstream_gene_variant,,ENST00000517364,;DCSTAMP,downstream_gene_variant,,ENST00000519562,; T ENST00000297581 Transcript missense_variant 317/1953 268/1413 90/470 G/C Ggc/Tgc 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 deleterious(0) 2/4 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 104348820 104348820 G T 1 0 0 0 0 1 0 0 0 4106 1348 47 2 2 DCSTAMP 8 104348820 Missense_Mutation SNP G C3L-01924_T 847814 104348820 40789816 292 8162 DPYS 0 . GRCh38 8 104392960 104392960 + Missense_Mutation SNP C C A rs776933209 C3L-01924_T C3L-01924_N C C c.1267G>T p.Val423Phe p.V423F ENST00000351513 8/10 404 262 142 359 359 0 strelka-varscan-mutect DPYS,missense_variant,p.Val423Phe,ENST00000351513,NM_001385.2;DPYS,upstream_gene_variant,,ENST00000533874,;DPYS,non_coding_transcript_exon_variant,,ENST00000521372,;DPYS,intron_variant,,ENST00000521601,;DPYS,non_coding_transcript_exon_variant,,ENST00000520483,; A ENST00000351513 Transcript missense_variant 1400/2127 1267/1560 423/519 V/F Gtt/Ttt rs776933209 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 deleterious(0.03) 8/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,TIGRFAM_domain:TIGR02033,Gene3D:2.30.40.10,Pfam_domain:PF01979,Superfamily_domains:SSF51338 MODERATE 1 SNV 1 1 PASS rs776933209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 104392960 104392960 C A 1 0 0 0 0 1 0 0 0 4561 478 17 2 2 DPYS 8 104392960 Missense_Mutation SNP C C3L-01924_T 44140 104392960 40745676 293 8163 DPYS 0 . GRCh38 8 104466903 104466903 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.18G>T p.= p.R6R ENST00000351513 1/10 133 122 11 90 90 0 strelka-varscan-mutect DPYS,synonymous_variant,p.=,ENST00000351513,NM_001385.2;DPYS,synonymous_variant,p.=,ENST00000521573,; A ENST00000351513 Transcript synonymous_variant 151/2127 18/1560 6/519 R cgG/cgT 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 1/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,Gene3D:2.30.40.10,Superfamily_domains:SSF51338 LOW 1 SNV 1 1 PASS rs1020926040 . 0 204 6 0 0 0 0 0 -19.95563 0.9999998 1 1 1 0 A 2 1 29 104466903 104466903 C A 1 0 0 0 0 0 0 0 1 4561 726 26 2 2 DPYS 8 104466903 Silent SNP C C3L-01924_T 73943 104466903 40671733 294 8164 CSMD3 0 . GRCh38 8 112947849 112947849 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.1449C>A p.= p.S483S ENST00000297405 9/71 381 331 50 325 324 1 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2; T ENST00000297405 Transcript synonymous_variant 1694/13212 1449/11124 483/3707 S tcC/tcA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 9/71 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 112947849 112947849 G T 1 0 0 0 0 0 0 0 1 3747 1335 47 2 2 CSMD3 8 112947849 Silent SNP G C3L-01924_T 8480946 112947849 32190787 295 8165 TRPS1 0 . GRCh38 8 115414235 115414235 + Missense_Mutation SNP C C G C3L-01924_T C3L-01924_N C C c.3673G>C p.Glu1225Gln p.E1225Q ENST00000395715 7/7 567 523 44 489 489 0 strelka-varscan-mutect TRPS1,missense_variant,p.Glu1225Gln,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Glu1212Gln,ENST00000220888,;TRPS1,missense_variant,p.Glu1216Gln,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Glu966Gln,ENST00000519076,;TRPS1,downstream_gene_variant,,ENST00000518018,; G ENST00000395715 Transcript missense_variant 4251/9990 3673/3885 1225/1294 E/Q Gaa/Caa COSM5317923,COSM5317924 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 deleterious_low_confidence(0.03) 7/7 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 115414235 115414235 C G 1 0 0 0 0 1 0 0 0 17099 835 29 4 4 TRPS1 8 115414235 Missense_Mutation SNP C C3L-01924_T 2466386 115414235 29724401 296 8166 COL14A1 0 . GRCh38 8 120270058 120270058 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.3097C>A p.Leu1033Met p.L1033M ENST00000297848 26/48 220 175 45 157 156 1 strelka-varscan-mutect COL14A1,missense_variant,p.Leu1033Met,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Leu1033Met,ENST00000309791,;COL14A1,5_prime_UTR_variant,,ENST00000247781,;COL14A1,downstream_gene_variant,,ENST00000434620,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,; A ENST00000297848 Transcript missense_variant 3367/6466 3097/5391 1033/1796 L/M Ctg/Atg 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 deleterious(0.01) 26/48 PROSITE_profiles:PS50234,hmmpanther:PTHR11132:SF53,hmmpanther:PTHR11132,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300,Prints_domain:PR00453 MODERATE 1 SNV 5 1 PASS rs1273671029 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 120270058 120270058 C A 1 0 0 0 0 1 0 0 0 3459 680 24 2 2 COL14A1 8 120270058 Missense_Mutation SNP C C3L-01924_T 4855823 120270058 24868578 297 8167 COL22A1 0 . GRCh38 8 138663714 138663714 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.3177A>G p.= p.K1059K ENST00000303045 42/65 223 206 17 137 137 0 strelka-varscan-mutect COL22A1,synonymous_variant,p.=,ENST00000303045,NM_152888.2;COL22A1,synonymous_variant,p.=,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; C ENST00000303045 Transcript synonymous_variant 3624/6346 3177/4881 1059/1626 K aaA/aaG 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 42/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 138663714 138663714 T C 1 0 0 0 0 0 0 0 1 3469 1606 56 5 5 COL22A1 8 138663714 Silent SNP T C3L-01924_T 18393656 138663714 6474922 298 8168 EEF1D 0 . GRCh38 8 143580568 143580568 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1648G>C p.Glu550Gln p.E550Q ENST00000423316 7/9 241 193 48 168 168 0 strelka-varscan-mutect EEF1D,missense_variant,p.Glu600Gln,ENST00000532741,;EEF1D,missense_variant,p.Glu550Gln,ENST00000423316,NM_001130053.2;EEF1D,missense_variant,p.Glu550Gln,ENST00000618139,;EEF1D,missense_variant,p.Glu550Gln,ENST00000442189,NM_032378.4;EEF1D,missense_variant,p.Glu184Gln,ENST00000317198,NM_001130057.2;EEF1D,missense_variant,p.Glu184Gln,ENST00000419152,NM_001130055.2;EEF1D,missense_variant,p.Glu184Gln,ENST00000529272,;EEF1D,missense_variant,p.Glu184Gln,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,missense_variant,p.Glu160Gln,ENST00000524624,;EEF1D,missense_variant,p.Glu184Gln,ENST00000534380,;EEF1D,missense_variant,p.Glu165Gln,ENST00000526838,NM_001195203.1;EEF1D,missense_variant,p.Glu160Gln,ENST00000528610,NM_001130056.2;EEF1D,missense_variant,p.Glu184Gln,ENST00000530191,;EEF1D,missense_variant,p.Glu184Gln,ENST00000533204,;EEF1D,missense_variant,p.Glu141Gln,ENST00000531621,;EEF1D,missense_variant,p.Glu184Gln,ENST00000531218,;EEF1D,missense_variant,p.Glu160Gln,ENST00000534377,;EEF1D,missense_variant,p.Glu59Gln,ENST00000530109,;EEF1D,missense_variant,p.Glu24Gln,ENST00000529576,;EEF1D,3_prime_UTR_variant,,ENST00000530616,;EEF1D,5_prime_UTR_variant,,ENST00000528382,;EEF1D,intron_variant,,ENST00000532400,;NAPRT,upstream_gene_variant,,ENST00000449291,NM_145201.5;NAPRT,upstream_gene_variant,,ENST00000435154,;NAPRT,upstream_gene_variant,,ENST00000426292,NM_001286829.1;EEF1D,downstream_gene_variant,,ENST00000530445,;EEF1D,downstream_gene_variant,,ENST00000533494,;EEF1D,downstream_gene_variant,,ENST00000533749,;EEF1D,downstream_gene_variant,,ENST00000529516,;RP11-661A12.7,non_coding_transcript_exon_variant,,ENST00000529247,;RP11-661A12.9,downstream_gene_variant,,ENST00000531730,;RP11-661A12.8,non_coding_transcript_exon_variant,,ENST00000623257,;EEF1D,3_prime_UTR_variant,,ENST00000524397,;EEF1D,3_prime_UTR_variant,,ENST00000529007,;EEF1D,3_prime_UTR_variant,,ENST00000533833,;EEF1D,non_coding_transcript_exon_variant,,ENST00000527741,;EEF1D,non_coding_transcript_exon_variant,,ENST00000526786,;EEF1D,non_coding_transcript_exon_variant,,ENST00000530848,;NAPRT,upstream_gene_variant,,ENST00000340490,;NAPRT,upstream_gene_variant,,ENST00000464332,;NAPRT,upstream_gene_variant,,ENST00000480946,;NAPRT,upstream_gene_variant,,ENST00000525583,;NAPRT,upstream_gene_variant,,ENST00000488096,;NAPRT,upstream_gene_variant,,ENST00000532645,;EEF1D,downstream_gene_variant,,ENST00000534232,;NAPRT,upstream_gene_variant,,ENST00000462059,;NAPRT,upstream_gene_variant,,ENST00000460623,;NAPRT,upstream_gene_variant,,ENST00000491904,; G ENST00000423316 Transcript missense_variant 1987/2378 1648/1944 550/647 E/Q Gag/Cag 1 -1 EEF1D HGNC HGNC:3211 protein_coding YES CCDS6404.1 ENSP00000410059 P29692 UPI000013C7A6 NM_001130053.2 deleterious(0.04) 7/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11595:SF26,hmmpanther:PTHR11595,Pfam_domain:PF10587,SMART_domains:SM01182 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 143580568 143580568 C G 1 0 0 0 0 1 0 0 0 4756 864 30 4 4 EEF1D 8 143580568 Missense_Mutation SNP C C3L-01924_T 4916854 143580568 1558068 299 8169 EPPK1 0 . GRCh38 8 143859709 143859709 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.13545C>G p.Ser4515Arg p.S4515R ENST00000615648 2/2 118 110 8 129 129 0 varscan-mutect EPPK1,missense_variant,p.Ser4515Arg,ENST00000615648,NM_031308.3;EPPK1,missense_variant,p.Ser4490Arg,ENST00000568225,; C ENST00000615648 Transcript missense_variant 13617/16002 13545/15267 4515/5088 S/R agC/agG 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 deleterious(0.02) 2/2 Gene3D:3.90.1290.10,SMART_domains:SM00250,Superfamily_domains:SSF75399 MODERATE 1 SNV 5 1 PASS rs1321322855 . 71 137 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 143859709 143859709 G C 1 0 0 0 0 1 0 0 0 5038 1078 38 4 4 EPPK1 8 143859709 Missense_Mutation SNP G C3L-01924_T 279141 143859709 1278927 300 8170 MROH1 0 . GRCh38 8 144248898 144248898 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.3142C>T p.Pro1048Ser p.P1048S ENST00000528919 31/43 695 440 255 492 492 0 strelka-varscan-mutect MROH1,missense_variant,p.Pro1048Ser,ENST00000528919,NM_032450.2;MROH1,missense_variant,p.Pro1048Ser,ENST00000326134,;MROH1,missense_variant,p.Pro1039Ser,ENST00000534366,NM_001288814.1;MROH1,missense_variant,p.Pro10Ser,ENST00000544576,;MROH1,non_coding_transcript_exon_variant,,ENST00000527552,;MROH1,non_coding_transcript_exon_variant,,ENST00000532255,; T ENST00000528919 Transcript missense_variant 3263/5234 3142/4926 1048/1641 P/S Cca/Tca 1 1 MROH1 HGNC HGNC:26958 protein_coding YES CCDS47938.1 ENSP00000435565 Q8NDA8 UPI0001AE6FA6 NM_032450.2 tolerated(0.19) 31/43 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1485751985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 144248898 144248898 C T 1 0 0 0 0 1 0 0 0 9743 623 22 3 3 MROH1 8 144248898 Missense_Mutation SNP C C3L-01924_T 389189 144248898 889738 301 8171 KIAA2026 0 . GRCh38 9 5919900 5919911 + In_Frame_Del DEL ACTTGGCAGTGG ACTTGGCAGTGG - novel C3L-01924_T C3L-01924_N ACTTGGCAGTGG ACTTGGCAGTGG c.6085_6096delCCACTGCCAAGT p.Pro2029_Ser2032del p.P2029_S2032del ENST00000399933 8/8 156 144 12 267 267 0 sindel-varindel-pindel KIAA2026,inframe_deletion,p.Pro2029_Ser2032del,ENST00000399933,NM_001017969.2;KIAA2026,inframe_deletion,p.Pro1999_Ser2002del,ENST00000381461,;KIAA2026,3_prime_UTR_variant,,ENST00000540714,;KIAA2026,intron_variant,,ENST00000436015,; - ENST00000399933 Transcript inframe_deletion 6085-6096/6988 6085-6096/6312 2029-2032/2103 PLPS/- CCACTGCCAAGT/- 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 8/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3 MODERATE 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 5919900 5919900 ACTTGGCAGTGG - 1 0 1 0 1 0 0 0 0 8134 388 14 0 0 KIAA2026 9 5919900 In_Frame_Del DEL ACTTGGCAGTGG C3L-01924_T 5919900 132474817 302 8172 GLDC 0 . GRCh38 9 6605191 6605191 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.801A>G p.= p.P267P ENST00000321612 6/25 397 351 46 469 468 1 strelka-varscan-mutect GLDC,synonymous_variant,p.=,ENST00000321612,NM_000170.2;GLDC,non_coding_transcript_exon_variant,,ENST00000463305,; C ENST00000321612 Transcript synonymous_variant 952/3767 801/3063 267/1020 P ccA/ccG 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 6/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Gene3D:3.40.640.10,Pfam_domain:PF02347,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 6605191 6605191 T C 1 0 0 0 0 0 0 0 1 6311 1567 55 5 5 GLDC 9 6605191 Silent SNP T C3L-01924_T 685291 6605191 131789526 303 8173 EQTN 0 . GRCh38 9 27292400 27292400 + Splice_Site SNP C C T novel C3L-01924_T C3L-01924_N C C c.376+1G>A p.X126_splice ENST00000380032 94 67 27 102 102 0 strelka-varscan-mutect EQTN,splice_donor_variant,,ENST00000380032,NM_020641.2;EQTN,missense_variant,p.Ser126Asn,ENST00000380031,;EQTN,intron_variant,,ENST00000537675,NM_001161585.1;EQTN,downstream_gene_variant,,ENST00000484994,; T ENST00000380032 Transcript splice_donor_variant -/1033 376/885 126/294 1 -1 EQTN HGNC HGNC:1359 protein_coding YES CCDS35001.1 ENSP00000369371 Q9NQ60 UPI000013CA7C NM_020641.2 4/7 HIGH 1 SNV 1 1 PASS . . 1 205 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 29 27292400 27292400 C T 1 0 0 0 0 0 0 1 0 5050 579 20 3 3 EQTN 9 27292400 Splice_Site SNP C C3L-01924_T 20687209 27292400 111102317 304 8174 TAF1L 0 . GRCh38 9 32630393 32630394 + In_Frame_Ins INS - - TCC novel C3L-01924_T C3L-01924_N - - c.5184_5186dupGGA p.Glu1728dup p.E1728dup ENST00000242310 1/1 270 232 38 421 421 0 sindel-varindel TAF1L,inframe_insertion,p.Glu1728dup,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; TCC ENST00000242310 Transcript inframe_insertion 5276-5277/6216 5186-5187/5481 1729/1826 D/ED gat/gaGGAt 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 1/1 PIRSF_domain:PIRSF003047,Low_complexity_(Seg):seg MODERATE insertion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 TCC 7 5 29 32630393 32630393 - TCC 1 0 1 1 0 0 0 0 0 15919 214 8 0 0 TAF1L 9 32630393 In_Frame_Ins INS - C3L-01924_T 5337993 32630393 105764324 305 8175 TAF1L 0 . GRCh38 9 32631220 32631220 + Missense_Mutation SNP G G T rs545988745 C3L-01924_T C3L-01924_N G G c.4360C>A p.Arg1454Ser p.R1454S ENST00000242310 1/1 382 336 46 516 516 0 strelka-varscan-mutect TAF1L,missense_variant,p.Arg1454Ser,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; T ENST00000242310 Transcript missense_variant 4450/6216 4360/5481 1454/1826 R/S Cgt/Agt rs545988745,COSM1267362 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 tolerated(0.12) 1/1 Gene3D:1.20.920.10,Pfam_domain:PF00439,PIRSF_domain:PIRSF003047,PROSITE_patterns:PS00633,PROSITE_profiles:PS50014,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0,SMART_domains:SM00297,Superfamily_domains:SSF47370 0,1 MODERATE SNV 0,1 1 PASS rs545988745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 32631220 32631220 G T 1 0 0 0 0 1 0 0 0 15919 1087 38 1 1 TAF1L 9 32631220 Missense_Mutation SNP G C3L-01924_T 827 32631220 105763497 306 8176 CNTNAP3B 0 . GRCh38 9 41938397 41938397 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2084G>T p.Gly695Val p.G695V ENST00000377561 14/24 105 94 11 135 134 1 varscan-mutect CNTNAP3B,missense_variant,p.Gly694Val,ENST00000612828,;CNTNAP3B,missense_variant,p.Gly695Val,ENST00000377561,NM_001201380.2;CNTNAP3B,missense_variant,p.Gly694Val,ENST00000341990,;CNTNAP3B,missense_variant,p.Gly601Val,ENST00000617422,;CNTNAP3B,intron_variant,,ENST00000489789,;CNTNAP3B,missense_variant,p.Gly601Val,ENST00000619138,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,;CNTNAP3B,intron_variant,,ENST00000479351,; A ENST00000377561 Transcript missense_variant 2477/5379 2084/3867 695/1288 G/V gGa/gTa 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 deleterious(0) 14/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 41938397 41938397 C A 1 0 0 0 0 1 0 0 0 3430 869 30 2 2 CNTNAP3B 9 41938397 Missense_Mutation SNP C C3L-01924_T 9307177 41938397 96456320 307 8177 GDA 0 . GRCh38 9 72223127 72223127 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.614G>T p.Arg205Ile p.R205I ENST00000238018 7/16 123 105 18 142 142 0 strelka-varscan-mutect GDA,missense_variant,p.Arg131Ile,ENST00000545168,NM_001242507.2,NM_001242506.2;GDA,missense_variant,p.Arg205Ile,ENST00000358399,NM_004293.4;GDA,missense_variant,p.Arg205Ile,ENST00000238018,NM_001242505.2;GDA,missense_variant,p.Arg71Ile,ENST00000414671,;GDA,intron_variant,,ENST00000376986,;GDA,upstream_gene_variant,,ENST00000436438,;GDA,non_coding_transcript_exon_variant,,ENST00000477618,;GDA,missense_variant,p.Arg205Ile,ENST00000475764,;GDA,upstream_gene_variant,,ENST00000489618,; T ENST00000238018 Transcript missense_variant 823/2074 614/1416 205/471 R/I aGa/aTa 1 1 GDA HGNC HGNC:4212 protein_coding YES CCDS56576.1 ENSP00000238018 Q9Y2T3 UPI000015828B NM_001242505.2 tolerated(0.06) 7/16 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11271,hmmpanther:PTHR11271:SF6,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02967 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 72223127 72223127 G T 1 0 0 0 0 1 0 0 0 6178 942 33 2 2 GDA 9 72223127 Missense_Mutation SNP G C3L-01924_T 30284730 72223127 66171590 308 8178 ZFAND5 0 . GRCh38 9 72356089 72356089 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.506G>T p.Arg169Leu p.R169L ENST00000237937 6/6 135 106 29 183 183 0 strelka-varscan-mutect ZFAND5,missense_variant,p.Arg169Leu,ENST00000237937,NM_001278245.1,NM_001278244.1,NM_001278243.1;ZFAND5,missense_variant,p.Arg169Leu,ENST00000376962,NM_001102420.2;ZFAND5,missense_variant,p.Arg169Leu,ENST00000376960,NM_006007.3,NM_001102421.2;ZFAND5,missense_variant,p.Arg169Leu,ENST00000343431,;ZFAND5,downstream_gene_variant,,ENST00000376956,;ZFAND5,non_coding_transcript_exon_variant,,ENST00000488164,;ZFAND5,non_coding_transcript_exon_variant,,ENST00000471197,;ZFAND5,downstream_gene_variant,,ENST00000487330,; A ENST00000237937 Transcript missense_variant 646/5310 506/642 169/213 R/L cGa/cTa 1 -1 ZFAND5 HGNC HGNC:13008 protein_coding YES CCDS6642.1 ENSP00000237937 O76080 A0A024R219 UPI000013C322 NM_001278245.1,NM_001278244.1,NM_001278243.1 deleterious(0.01) 6/6 Gene3D:4.10.1110.10,Pfam_domain:PF01428,PROSITE_profiles:PS51039,hmmpanther:PTHR10634,hmmpanther:PTHR10634:SF26,SMART_domains:SM00154,Superfamily_domains:SSF118310 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 72356089 72356089 C A 1 0 0 0 0 1 0 0 0 18207 884 31 1 1 ZFAND5 9 72356089 Missense_Mutation SNP C C3L-01924_T 132962 72356089 66038628 309 8179 RMI1 0 . GRCh38 9 84002150 84002150 + Silent SNP A A G novel C3L-01924_T C3L-01924_N A A c.1164A>G p.= p.S388S ENST00000325875 3/3 234 202 32 296 295 1 strelka-varscan-mutect RMI1,synonymous_variant,p.=,ENST00000325875,NM_024945.2;RMI1,synonymous_variant,p.=,ENST00000445877,; G ENST00000325875 Transcript synonymous_variant 1496/3420 1164/1878 388/625 S tcA/tcG 1 1 RMI1 HGNC HGNC:25764 protein_coding YES CCDS6669.1 ENSP00000317039 Q9H9A7 UPI000014178F NM_024945.2 3/3 hmmpanther:PTHR14790,hmmpanther:PTHR14790:SF15 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 84002150 84002150 A G 1 0 0 0 0 0 0 0 1 13573 204 8 5 5 RMI1 9 84002150 Silent SNP A C3L-01924_T 11646061 84002150 54392567 310 8180 COL15A1 0 . GRCh38 9 99049755 99049755 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.2859A>T p.Lys953Asn p.K953N ENST00000375001 29/42 203 179 24 257 257 0 strelka-varscan-mutect COL15A1,missense_variant,p.Lys953Asn,ENST00000375001,NM_001855.4;COL15A1,missense_variant,p.Lys939Asn,ENST00000610452,; T ENST00000375001 Transcript missense_variant 3282/5496 2859/4167 953/1388 K/N aaA/aaT 1 1 COL15A1 HGNC HGNC:2192 protein_coding YES CCDS35081.1 ENSP00000364140 P39059 UPI0000211506 NM_001855.4 tolerated(0.17) 29/42 Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 99049755 99049755 A T 1 0 0 0 0 1 0 0 0 3460 86 3 4 4 COL15A1 9 99049755 Missense_Mutation SNP A C3L-01924_T 15047605 99049755 39344962 311 8181 RGS3 0 . GRCh38 9 113462193 113462193 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.407A>T p.Gln136Leu p.Q136L ENST00000374140 4/26 107 91 16 138 138 0 strelka-varscan-mutect RGS3,missense_variant,p.Gln136Leu,ENST00000374140,NM_144488.5;RGS3,missense_variant,p.Gln136Leu,ENST00000350696,NM_001282923.1;RGS3,upstream_gene_variant,,ENST00000317613,NM_017790.4;RGS3,upstream_gene_variant,,ENST00000478599,; T ENST00000374140 Transcript missense_variant 616/4591 407/3597 136/1198 Q/L cAg/cTg 1 1 RGS3 HGNC HGNC:9999 protein_coding YES CCDS43869.1 ENSP00000363255 P49796 UPI00001C0F58 NM_144488.5 tolerated(0.18) 4/26 Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 113462193 113462193 A T 1 0 0 0 0 1 0 0 0 13477 188 7 4 4 RGS3 9 113462193 Missense_Mutation SNP A C3L-01924_T 14412438 113462193 24932524 312 8182 AMBP 0 . GRCh38 9 114074089 114074089 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.401T>A p.Leu134Gln p.L134Q ENST00000265132 4/10 276 241 35 267 267 0 strelka-varscan-mutect AMBP,missense_variant,p.Leu134Gln,ENST00000265132,NM_001633.3;AMBP,missense_variant,p.Leu25Gln,ENST00000466610,;AMBP,missense_variant,p.Leu134Gln,ENST00000603230,;AMBP,non_coding_transcript_exon_variant,,ENST00000540645,; T ENST00000265132 Transcript missense_variant 664/1434 401/1059 134/352 L/Q cTg/cAg 1 -1 AMBP HGNC HGNC:453 protein_coding YES CCDS6800.1 ENSP00000265132 P02760 UPI000000D9AF NM_001633.3 deleterious(0.02) 4/10 hmmpanther:PTHR10083,hmmpanther:PTHR10083:SF18,Gene3D:2.40.128.20,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR00179 MODERATE 1 SNV 1 1 PASS rs1286445690 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 114074089 114074089 A T 1 0 0 0 0 1 0 0 0 660 188 7 4 4 AMBP 9 114074089 Missense_Mutation SNP A C3L-01924_T 611896 114074089 24320628 313 8183 PDCL 0 . GRCh38 9 122820102 122820102 + Missense_Mutation SNP C C A rs747053060 C3L-01924_T C3L-01924_N C C c.889G>T p.Asp297Tyr p.D297Y ENST00000259467 4/4 73 65 8 77 77 0 strelka-mutect PDCL,missense_variant,p.Asp297Tyr,ENST00000259467,NM_005388.4;PDCL,intron_variant,,ENST00000436632,;PDCL,downstream_gene_variant,,ENST00000394285,; A ENST00000259467 Transcript missense_variant 1055/2813 889/906 297/301 D/Y Gac/Tac rs747053060 1 -1 PDCL HGNC HGNC:8770 protein_coding YES CCDS6845.1 ENSP00000259467 Q13371 UPI0000131988 NM_005388.4 deleterious(0) 4/4 Pfam_domain:PF02114,hmmpanther:PTHR21148,hmmpanther:PTHR21148:SF21 MODERATE 1 SNV 1 1 PASS rs747053060 . 0 200 10 0 0 0 0 0 -17.3033 0.9999678 1 1 1 0 A 3 1 29 122820102 122820102 C A 1 0 0 0 0 1 0 0 0 11714 884 31 1 1 PDCL 9 122820102 Missense_Mutation SNP C C3L-01924_T 8746013 122820102 15574615 314 8184 RC3H2 0 . GRCh38 9 122865376 122865376 + Missense_Mutation SNP C C A rs764672649 C3L-01924_T C3L-01924_N C C c.1607G>T p.Gly536Val p.G536V ENST00000373670 9/20 107 87 20 154 152 2 strelka-varscan-mutect RC3H2,missense_variant,p.Gly536Val,ENST00000373670,;RC3H2,missense_variant,p.Gly536Val,ENST00000357244,NM_001100588.1;RC3H2,missense_variant,p.Gly536Val,ENST00000423239,NM_018835.2;RC3H2,3_prime_UTR_variant,,ENST00000498479,; A ENST00000373670 Transcript missense_variant 2208/9248 1607/3576 536/1191 G/V gGg/gTg rs764672649 1 -1 RC3H2 HGNC HGNC:21461 protein_coding YES CCDS43874.1 ENSP00000362774 Q9HBD1 A0A024R899 UPI0000048D91 deleterious(0.01) 9/20 hmmpanther:PTHR13139,hmmpanther:PTHR13139:SF2 MODERATE 1 SNV 5 1 PASS rs764672649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 122865376 122865376 C A 1 0 0 0 0 1 0 0 0 13336 623 22 2 2 RC3H2 9 122865376 Missense_Mutation SNP C C3L-01924_T 45274 122865376 15529341 315 8185 CRB2 0 . GRCh38 9 123373200 123373200 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2669G>T p.Gly890Val p.G890V ENST00000373631 10/13 167 141 26 176 175 1 strelka-varscan-mutect CRB2,missense_variant,p.Gly890Val,ENST00000373631,NM_173689.6;CRB2,missense_variant,p.Gly890Val,ENST00000359999,;CRB2,missense_variant,p.Gly558Val,ENST00000460253,; T ENST00000373631 Transcript missense_variant 2670/5550 2669/3858 890/1285 G/V gGg/gTg 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 tolerated(0.21) 10/13 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1,Low_complexity_(Seg):seg,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 123373200 123373200 G T 1 0 0 0 0 1 0 0 0 3649 1232 43 2 2 CRB2 9 123373200 Missense_Mutation SNP G C3L-01924_T 507824 123373200 15021517 316 8186 PKN3 0 . GRCh38 9 128713076 128713076 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.860G>T p.Gly287Val p.G287V ENST00000291906 7/22 62 50 12 71 71 0 strelka-varscan-mutect PKN3,missense_variant,p.Gly287Val,ENST00000291906,NM_013355.3;RN7SL560P,downstream_gene_variant,,ENST00000577943,;PKN3,upstream_gene_variant,,ENST00000485301,;PKN3,upstream_gene_variant,,ENST00000483521,; T ENST00000291906 Transcript missense_variant 1253/3375 860/2670 287/889 G/V gGc/gTc 1 1 PKN3 HGNC HGNC:17999 protein_coding YES CCDS6908.1 ENSP00000291906 Q6P5Z2 A0A024R8D6 UPI000013E087 NM_013355.3 deleterious(0) 7/22 Gene3D:2.60.40.150,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF166,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 128713076 128713076 G T 1 0 0 0 0 1 0 0 0 12077 1203 42 2 2 PKN3 9 128713076 Missense_Mutation SNP G C3L-01924_T 5339876 128713076 9681641 317 8187 LAMC3 0 . GRCh38 9 131079271 131079271 + Silent SNP G G C rs145960571 C3L-01924_T C3L-01924_N G G c.3900G>C p.= p.T1300T ENST00000361069 23/28 216 190 26 242 242 0 strelka-varscan-mutect LAMC3,synonymous_variant,p.=,ENST00000361069,NM_006059.3;LAMC3,synonymous_variant,p.=,ENST00000355452,;LAMC3,intron_variant,,ENST00000480883,; C ENST00000361069 Transcript synonymous_variant 4033/6133 3900/4728 1300/1575 T acG/acC rs145960571,COSM1460587 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 23/28 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240,Low_complexity_(Seg):seg 0,1 LOW 1 SNV 2 0,1 1 PASS rs145960571 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 131079271 131079271 G C 1 0 0 0 0 0 0 0 1 8520 1074 38 4 4 LAMC3 9 131079271 Silent SNP G C3L-01924_T 2366195 131079271 7315446 318 8188 PRRC2B 0 . GRCh38 9 131475929 131475929 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.3800G>T p.Gly1267Val p.G1267V ENST00000357304 15/31 95 68 27 88 88 0 strelka-varscan-mutect PRRC2B,missense_variant,p.Gly1267Val,ENST00000357304,NM_013318.3;PRRC2B,intron_variant,,ENST00000405995,;PRRC2B,upstream_gene_variant,,ENST00000451855,;PRRC2B,downstream_gene_variant,,ENST00000456307,; T ENST00000357304 Transcript missense_variant 3855/11042 3800/6690 1267/2229 G/V gGt/gTt 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 tolerated(0.15) 15/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 131475929 131475929 G T 1 0 0 0 0 1 0 0 0 12749 1261 44 2 2 PRRC2B 9 131475929 Missense_Mutation SNP G C3L-01924_T 396658 131475929 6918788 319 8189 DDX31 0 . GRCh38 9 132648459 132648459 + Missense_Mutation SNP C C A rs200289752 C3L-01924_T C3L-01924_N C C c.1148G>T p.Arg383Leu p.R383L ENST00000372159 10/20 135 113 22 169 169 0 strelka-varscan-mutect DDX31,missense_variant,p.Arg383Leu,ENST00000372159,;DDX31,missense_variant,p.Arg383Leu,ENST00000372153,NM_022779.7;DDX31,missense_variant,p.Arg278Leu,ENST00000438527,;DDX31,missense_variant,p.Arg383Leu,ENST00000310532,NM_138620.1; A ENST00000372159 Transcript missense_variant 1300/4577 1148/2556 383/851 R/L cGg/cTg rs200289752 1 -1 DDX31 HGNC HGNC:16715 protein_coding YES CCDS6951.1 ENSP00000361232 Q9H8H2 UPI00000736CA deleterious(0.04) 10/20 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF89,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs200289752 . 0 207 0 3 0 0 0 0 -20 0.9999947 1 1 1 0 A 3 1 29 132648459 132648459 C A 1 0 0 0 0 1 0 0 0 4158 652 23 1 1 DDX31 9 132648459 Missense_Mutation SNP C C3L-01924_T 1172530 132648459 5746258 320 8190 SARDH 0 . GRCh38 9 133696226 133696226 + Missense_Mutation SNP G G A C3L-01924_T C3L-01924_N G G c.1804C>T p.Pro602Ser p.P602S ENST00000371872 14/21 106 94 12 141 141 0 varscan-mutect SARDH,missense_variant,p.Pro602Ser,ENST00000371872,NM_007101.3;SARDH,missense_variant,p.Pro602Ser,ENST00000439388,NM_001134707.1;SARDH,missense_variant,p.Pro322Ser,ENST00000422262,;SARDH,missense_variant,p.Pro30Ser,ENST00000371868,;SARDH,missense_variant,p.Pro602Ser,ENST00000427237,; A ENST00000371872 Transcript missense_variant 2062/3344 1804/2757 602/918 P/S Cca/Tca COSM4655446,COSM4655447 1 -1 SARDH HGNC HGNC:10536 protein_coding YES CCDS6978.1 ENSP00000360938 Q9UL12 UPI000006F076 NM_007101.3 tolerated(0.23) 14/21 Gene3D:3.30.70.1400,Pfam_domain:PF01571,Superfamily_domains:SSF103025 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 133696226 133696226 G A 1 0 0 0 0 1 0 0 0 14102 1246 43 3 3 SARDH 9 133696226 Missense_Mutation SNP G C3L-01924_T 1047767 133696226 4698491 321 8191 SLC39A12 0 . GRCh38 10 17981400 17981400 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1013C>G p.Pro338Arg p.P338R ENST00000377369 6/13 66 56 10 125 125 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Pro338Arg,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Pro338Arg,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Pro338Arg,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Pro204Arg,ENST00000539911,NM_001282734.1; G ENST00000377369 Transcript missense_variant 1286/2808 1013/2076 338/691 P/R cCa/cGa 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 deleterious(0) 6/13 hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 17981400 17981400 C G 1 0 0 0 0 1 0 0 0 14893 594 21 4 4 SLC39A12 10 17981400 Missense_Mutation SNP C C3L-01924_T 17981400 115816022 322 8192 CCDC7 0 . GRCh38 10 32472527 32472527 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.724G>T p.Ala242Ser p.A242S ENST00000362006 8/18 169 145 24 195 195 0 strelka-varscan-mutect CCDC7,missense_variant,p.Ala242Ser,ENST00000362006,NM_145023.5,NM_001026383.2;CCDC7,missense_variant,p.Ala242Ser,ENST00000277657,;CCDC7,3_prime_UTR_variant,,ENST00000545067,;CCDC7,3_prime_UTR_variant,,ENST00000535327,;CCDC7,intron_variant,,ENST00000537047,;CCDC7,intron_variant,,ENST00000539197,; T ENST00000362006 Transcript missense_variant 1231/2093 724/1461 242/486 A/S Gca/Tca 1 1 CCDC7 HGNC HGNC:26533 protein_coding YES CCDS7173.1 ENSP00000355078 Q96M83 UPI00000745EB NM_145023.5,NM_001026383.2 tolerated(0.18) 8/18 hmmpanther:PTHR22035:SF4,hmmpanther:PTHR22035 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 32472527 32472527 G T 1 0 0 0 0 1 0 0 0 2542 1203 42 2 2 CCDC7 10 32472527 Missense_Mutation SNP G C3L-01924_T 14491127 32472527 101324895 323 8193 BMS1 0 . GRCh38 10 42823183 42823183 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.3198G>T p.= p.G1066G ENST00000374518 20/23 74 56 18 76 76 0 strelka-varscan-mutect BMS1,synonymous_variant,p.=,ENST00000374518,NM_014753.3; T ENST00000374518 Transcript synonymous_variant 3261/7753 3198/3849 1066/1282 G ggG/ggT 1 1 BMS1 HGNC HGNC:23505 protein_coding YES CCDS7199.1 ENSP00000363642 Q14692 UPI0000126A3E NM_014753.3 20/23 hmmpanther:PTHR12858:SF2,hmmpanther:PTHR12858,Pfam_domain:PF04950,SMART_domains:SM01362 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 42823183 42823183 G T 1 0 0 0 0 0 0 0 1 1627 1161 41 2 2 BMS1 10 42823183 Silent SNP G C3L-01924_T 10350656 42823183 90974239 324 8194 ALOX5 0 . GRCh38 10 45424039 45424039 + Splice_Site SNP A A G novel C3L-01924_T C3L-01924_N A A c.555-2A>G p.X185_splice ENST00000374391 122 104 18 111 111 0 strelka-varscan-mutect ALOX5,splice_acceptor_variant,,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,splice_acceptor_variant,,ENST00000542434,NM_001256154.1;ALOX5,splice_acceptor_variant,,ENST00000612635,;ALOX5,upstream_gene_variant,,ENST00000483623,; G ENST00000374391 Transcript splice_acceptor_variant -/2506 555/2025 185/674 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 4/13 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 29 45424039 45424039 A G 1 0 0 0 0 0 0 1 0 640 202 7 5 5 ALOX5 10 45424039 Splice_Site SNP A C3L-01924_T 2600856 45424039 88373383 325 8195 MBL2 0 . GRCh38 10 52768191 52768191 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.693G>T p.Trp231Cys p.W231C ENST00000373968 4/4 108 89 19 109 108 1 strelka-varscan-mutect MBL2,missense_variant,p.Trp231Cys,ENST00000373968,NM_000242.2; A ENST00000373968 Transcript missense_variant 758/3569 693/747 231/248 W/C tgG/tgT 1 -1 MBL2 HGNC HGNC:6922 protein_coding YES CCDS7247.1 ENSP00000363079 P11226 UPI0000035011 NM_000242.2 deleterious(0) 4/4 PROSITE_profiles:PS50041,hmmpanther:PTHR24020,PROSITE_patterns:PS00615,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 52768191 52768191 C A 1 0 0 0 0 1 0 0 0 9282 856 30 2 2 MBL2 10 52768191 Missense_Mutation SNP C C3L-01924_T 7344152 52768191 81029231 326 8196 ANK3 0 . GRCh38 10 60070784 60070784 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.10097G>A p.Gly3366Glu p.G3366E ENST00000280772 37/44 343 308 35 330 330 0 strelka-varscan-mutect ANK3,missense_variant,p.Gly3366Glu,ENST00000280772,NM_020987.3;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000610321,;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000616444,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000511043,;ANK3,upstream_gene_variant,,ENST00000610901,;ANK3,upstream_gene_variant,,ENST00000613207,;ANK3,missense_variant,p.Gly596Glu,ENST00000621739,; T ENST00000280772 Transcript missense_variant 10289/16874 10097/13134 3366/4377 G/E gGa/gAa 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 tolerated_low_confidence(0.15) 37/44 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 60070784 60070784 C T 1 0 0 0 0 1 0 0 0 722 855 30 3 3 ANK3 10 60070784 Missense_Mutation SNP C C3L-01924_T 7302593 60070784 73726638 327 8197 CDH23 0 . GRCh38 10 71810475 71810475 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.2263C>G p.His755Asp p.H755D ENST00000398788 15/23 255 207 48 242 242 0 strelka-varscan-mutect CDH23,missense_variant,p.His3000Asp,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.His2995Asp,ENST00000622827,;CDH23,missense_variant,p.His755Asp,ENST00000398788,NM_001171933.1;CDH23,missense_variant,p.His755Asp,ENST00000619887,NM_001171934.1;CDH23,non_coding_transcript_exon_variant,,ENST00000475158,; G ENST00000398788 Transcript missense_variant 2580/4329 2263/3345 755/1114 H/D Cat/Gat 1 1 CDH23 HGNC HGNC:13733 protein_coding YES CCDS53540.1 ENSP00000381768 Q9H251 UPI0000496839 NM_001171933.1 deleterious(0) 15/23 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 71810475 71810475 C G 1 0 0 0 0 1 0 0 0 2811 608 21 4 4 CDH23 10 71810475 Missense_Mutation SNP C C3L-01924_T 11739691 71810475 61986947 328 8198 P4HA1 0 . GRCh38 10 73074827 73074827 + Silent SNP T T G novel C3L-01924_T C3L-01924_N T T c.57A>C p.= p.P19P ENST00000263556 2/15 327 272 55 343 343 0 strelka-varscan-mutect P4HA1,synonymous_variant,p.=,ENST00000263556,NM_000917.3;P4HA1,synonymous_variant,p.=,ENST00000394890,NM_001017962.2,NM_001142595.1;P4HA1,synonymous_variant,p.=,ENST00000440381,NM_001142596.1;P4HA1,synonymous_variant,p.=,ENST00000307116,;P4HA1,synonymous_variant,p.=,ENST00000373008,;RP11-344N10.2,downstream_gene_variant,,ENST00000431293,; G ENST00000263556 Transcript synonymous_variant 298/2844 57/1605 19/534 P ccA/ccC 1 -1 P4HA1 HGNC HGNC:8546 protein_coding YES CCDS7320.1 ENSP00000263556 P13674 Q5VSQ6 UPI000002B050 NM_000917.3 2/15 hmmpanther:PTHR10869,hmmpanther:PTHR10869:SF76 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 73074827 73074827 T G 1 0 0 0 0 0 0 0 1 11433 1567 55 5 5 P4HA1 10 73074827 Silent SNP T C3L-01924_T 1264352 73074827 60722595 329 8199 GRID1 0 . GRCh38 10 85724599 85724599 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1611G>T p.Met537Ile p.M537I ENST00000327946 11/16 188 164 24 219 219 0 varscan-mutect GRID1,missense_variant,p.Met537Ile,ENST00000327946,NM_017551.2;GRID1,missense_variant,p.Met537Ile,ENST00000464741,; A ENST00000327946 Transcript missense_variant 1697/5834 1611/3030 537/1009 M/I atG/atT COSM4529446 1 -1 GRID1 HGNC HGNC:4575 protein_coding YES CCDS31236.1 ENSP00000330148 Q9ULK0 UPI00001D8051 NM_017551.2 deleterious(0.01) 11/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,SMART_domains:SM00079,Superfamily_domains:SSF53850 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 85724599 85724599 C A 1 0 0 0 0 1 0 0 0 6651 594 21 2 2 GRID1 10 85724599 Missense_Mutation SNP C C3L-01924_T 12649772 85724599 48072823 330 8200 WAPL 0 . GRCh38 10 86471052 86471052 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.2082G>A p.= p.L694L ENST00000298767 8/19 251 238 13 253 253 0 strelka-varscan WAPL,synonymous_variant,p.=,ENST00000298767,NM_001318328.1,NM_015045.2;WAPL,synonymous_variant,p.=,ENST00000618527,;WAPL,5_prime_UTR_variant,,ENST00000263070,;WAPL,upstream_gene_variant,,ENST00000372075,;WAPL,non_coding_transcript_exon_variant,,ENST00000489996,; T ENST00000298767 Transcript synonymous_variant 2555/6333 2082/3573 694/1190 L ctG/ctA 1 -1 WAPL HGNC HGNC:23293 protein_coding YES CCDS7375.1 ENSP00000298767 Q7Z5K2 UPI00001AE41A NM_001318328.1,NM_015045.2 8/19 PROSITE_profiles:PS51271,hmmpanther:PTHR22100:SF13,hmmpanther:PTHR22100,Pfam_domain:PF07814,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 86471052 86471052 C T 1 0 0 0 0 0 0 0 1 17808 813 29 3 3 WAPL 10 86471052 Silent SNP C C3L-01924_T 746453 86471052 47326370 331 8201 MINPP1 0 . GRCh38 10 87505112 87505112 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.197C>T p.Ala66Val p.A66V ENST00000371996 1/5 465 361 104 373 373 0 strelka-varscan-mutect MINPP1,missense_variant,p.Ala66Val,ENST00000371996,NM_004897.4;MINPP1,missense_variant,p.Ala66Val,ENST00000371994,NM_001178117.1;MINPP1,upstream_gene_variant,,ENST00000536010,NM_001178118.1;MIR4678,downstream_gene_variant,,ENST00000636979,; T ENST00000371996 Transcript missense_variant 238/2415 197/1464 66/487 A/V gCt/gTt 1 1 MINPP1 HGNC HGNC:7102 protein_coding YES CCDS7384.1 ENSP00000361064 Q9UNW1 UPI0000035984 NM_004897.4 tolerated(0.14) 1/5 hmmpanther:PTHR20963,hmmpanther:PTHR20963:SF8,PIRSF_domain:PIRSF000894,Superfamily_domains:SSF53254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 87505112 87505112 C T 1 0 0 0 0 1 0 0 0 9553 797 28 3 3 MINPP1 10 87505112 Missense_Mutation SNP C C3L-01924_T 1034060 87505112 46292310 332 8202 CYP26C1 0 . GRCh38 10 93062850 93062850 + Missense_Mutation SNP C C G rs558795251 C3L-01924_T C3L-01924_N C C c.560C>G p.Ala187Gly p.A187G ENST00000285949 3/6 201 163 38 178 178 0 strelka-varscan-mutect CYP26C1,missense_variant,p.Ala187Gly,ENST00000285949,NM_183374.2;EXOC6,downstream_gene_variant,,ENST00000260762,NM_001319195.1,NM_019053.4;EXOC6,downstream_gene_variant,,ENST00000371552,NM_001319194.1,NM_001013848.2;EXOC6,downstream_gene_variant,,ENST00000443748,NM_001319200.1;RP11-348J12.2,upstream_gene_variant,,ENST00000444965,;CYP26C1,missense_variant,p.Ala187Gly,ENST00000624358,;EXOC6,downstream_gene_variant,,ENST00000495132,; G ENST00000285949 Transcript missense_variant 560/1569 560/1569 187/522 A/G gCg/gGg rs558795251 1 1 CYP26C1 HGNC HGNC:20577 protein_coding YES CCDS7425.1 ENSP00000285949 Q6V0L0 UPI00002289F0 NM_183374.2 tolerated(0.1) 3/6 hmmpanther:PTHR24286,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs558795251 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 93062850 93062850 C G 1 0 0 0 0 1 0 0 0 3960 768 27 4 4 CYP26C1 10 93062850 Missense_Mutation SNP C C3L-01924_T 5557738 93062850 40734572 333 8203 ALDH18A1 0 . GRCh38 10 95621245 95621245 + Missense_Mutation SNP A A C rs201069261 C3L-01924_T C3L-01924_N A A c.1253T>G p.Leu418Arg p.L418R ENST00000371224 12/18 315 299 16 347 347 0 strelka-varscan-mutect ALDH18A1,missense_variant,p.Leu418Arg,ENST00000371224,NM_001323414.1,NM_002860.3;ALDH18A1,missense_variant,p.Leu416Arg,ENST00000371221,NM_001017423.1;ALDH18A1,upstream_gene_variant,,ENST00000485428,;ALDH18A1,downstream_gene_variant,,ENST00000489386,; C ENST00000371224 Transcript missense_variant 1391/3359 1253/2388 418/795 L/R cTt/cGt rs201069261 1 -1 ALDH18A1 HGNC HGNC:9722 protein_coding YES CCDS7443.1 ENSP00000360268 P54886 UPI0000131056 NM_001323414.1,NM_002860.3 deleterious(0.01) 12/18 HAMAP:MF_00412,hmmpanther:PTHR11063:SF8,hmmpanther:PTHR11063,TIGRFAM_domain:TIGR01092,Gene3D:3.40.605.10,TIGRFAM_domain:TIGR00407,Pfam_domain:PF00171,PIRSF_domain:PIRSF036429,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS rs201069261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 95621245 95621245 A C 1 0 0 0 0 1 0 0 0 589 72 3 5 5 ALDH18A1 10 95621245 Missense_Mutation SNP A C3L-01924_T 2558395 95621245 38176177 334 8204 PIK3AP1 0 . GRCh38 10 96626897 96626897 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.1480A>G p.Met494Val p.M494V ENST00000339364 10/17 205 191 14 219 219 0 strelka-varscan-mutect PIK3AP1,missense_variant,p.Met494Val,ENST00000339364,NM_152309.2;PIK3AP1,missense_variant,p.Met316Val,ENST00000371110,;PIK3AP1,missense_variant,p.Met93Val,ENST00000371109,;PIK3AP1,downstream_gene_variant,,ENST00000468783,; C ENST00000339364 Transcript missense_variant 1600/4803 1480/2418 494/805 M/V Atg/Gtg 1 -1 PIK3AP1 HGNC HGNC:30034 protein_coding YES CCDS31259.1 ENSP00000339826 Q6ZUJ8 UPI00001F947F NM_152309.2 tolerated(0.52) 10/17 hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 96626897 96626897 T C 1 0 0 0 0 1 0 0 0 12003 1464 51 5 5 PIK3AP1 10 96626897 Missense_Mutation SNP T C3L-01924_T 1005652 96626897 37170525 335 8205 MFSD13A 0 . GRCh38 10 102473934 102473934 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1213G>T p.Gly405Cys p.G405C ENST00000238936 9/10 72 49 23 81 81 0 strelka-varscan-mutect MFSD13A,missense_variant,p.Gly405Cys,ENST00000238936,NM_024789.3;MFSD13A,downstream_gene_variant,,ENST00000369931,;MFSD13A,downstream_gene_variant,,ENST00000450947,;MFSD13A,downstream_gene_variant,,ENST00000469294,;ACTR1A,intron_variant,,ENST00000636707,; T ENST00000238936 Transcript missense_variant 1450/2852 1213/1554 405/517 G/C Ggc/Tgc 1 1 MFSD13A HGNC HGNC:26196 protein_coding YES CCDS7535.1 ENSP00000238936 Q14CX5 UPI00002374ED NM_024789.3 deleterious(0) 9/10 hmmpanther:PTHR28658:SF3,hmmpanther:PTHR28658,Pfam_domain:PF13347,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 102473934 102473934 G T 1 0 0 0 0 1 0 0 0 9483 1348 47 2 2 MFSD13A 10 102473934 Missense_Mutation SNP G C3L-01924_T 5847037 102473934 31323488 336 8206 CFAP43 0 . GRCh38 10 104172416 104172416 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.2580G>T p.= p.V860V ENST00000357060 20/38 276 226 50 302 300 2 strelka-varscan-mutect CFAP43,synonymous_variant,p.=,ENST00000357060,NM_025145.5;CFAP43,synonymous_variant,p.=,ENST00000434629,;CFAP43,synonymous_variant,p.=,ENST00000278064,; A ENST00000357060 Transcript synonymous_variant 2696/5365 2580/4998 860/1665 V gtG/gtT 1 -1 CFAP43 HGNC HGNC:26684 protein_coding YES CCDS31281.1 ENSP00000349568 Q8NDM7 UPI0000D60FC7 NM_025145.5 20/38 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14885,hmmpanther:PTHR14885:SF1 LOW 1 SNV 1 1 PASS rs1305781688 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 104172416 104172416 C A 1 0 0 0 0 0 0 0 1 3018 581 21 2 2 CFAP43 10 104172416 Silent SNP C C3L-01924_T 1698482 104172416 29625006 337 8207 SORCS3 0 . GRCh38 10 105201223 105201223 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.2231C>G p.Pro744Arg p.P744R ENST00000369701 16/27 139 108 31 177 177 0 strelka-varscan-mutect SORCS3,missense_variant,p.Pro744Arg,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Pro744Arg,ENST00000369699,;SORCS3,intron_variant,,ENST00000393176,; G ENST00000369701 Transcript missense_variant 2458/5757 2231/3669 744/1222 P/R cCc/cGc 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0.01) 16/27 Pfam_domain:PF15901,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,SMART_domains:SM00602 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 105201223 105201223 C G 1 0 0 0 0 1 0 0 0 15254 623 22 4 4 SORCS3 10 105201223 Missense_Mutation SNP C C3L-01924_T 1028807 105201223 28596199 338 8208 RBM20 0 . GRCh38 10 110781130 110781130 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.521C>A p.Pro174His p.P174H ENST00000369519 2/14 468 362 106 443 443 0 strelka-varscan-mutect RBM20,missense_variant,p.Pro174His,ENST00000369519,NM_001134363.2; A ENST00000369519 Transcript missense_variant 579/7233 521/3684 174/1227 P/H cCc/cAc 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 tolerated(0.09) 2/14 MODERATE 1 SNV 1 1 PASS rs971703468 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 110781130 110781130 C A 1 0 0 0 0 1 0 0 0 13287 623 22 2 2 RBM20 10 110781130 Missense_Mutation SNP C C3L-01924_T 5579907 110781130 23016292 339 8209 RBM20 0 . GRCh38 10 110812520 110812520 + Missense_Mutation SNP C C A rs762685493 C3L-01924_T C3L-01924_N C C c.2123C>A p.Ala708Glu p.A708E ENST00000369519 9/14 340 256 84 358 358 0 strelka-varscan-mutect RBM20,missense_variant,p.Ala708Glu,ENST00000369519,NM_001134363.2; A ENST00000369519 Transcript missense_variant 2181/7233 2123/3684 708/1227 A/E gCa/gAa rs762685493 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 tolerated(0.74) 9/14 MODERATE 1 SNV 1 1 PASS rs762685493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 110812520 110812520 C A 1 0 0 0 0 1 0 0 0 13287 710 25 2 2 RBM20 10 110812520 Missense_Mutation SNP C C3L-01924_T 31390 110812520 22984902 340 8210 BCCIP 0 . GRCh38 10 125853172 125853172 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.898C>A p.Leu300Ile p.L300I ENST00000368759 8/8 120 110 10 146 146 0 strelka-varscan-mutect BCCIP,missense_variant,p.Leu300Ile,ENST00000368759,NM_016567.3;DHX32,intron_variant,,ENST00000284690,NM_018180.2;DHX32,intron_variant,,ENST00000368721,; A ENST00000368759 Transcript missense_variant 910/1433 898/969 300/322 L/I Cta/Ata 1 1 BCCIP HGNC HGNC:978 protein_coding YES CCDS7649.1 ENSP00000357748 Q9P287 UPI0000073C44 NM_016567.3 tolerated_low_confidence(0.33) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 204 0 5 0 0 0 0 -14.40023 0.9985443 1 1 1 0 A 3 1 29 125853172 125853172 C A 1 0 0 0 0 1 0 0 0 1503 564 20 2 2 BCCIP 10 125853172 Missense_Mutation SNP C C3L-01924_T 15040652 125853172 7944250 341 8211 JAKMIP3 0 . GRCh38 10 132135155 132135155 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.964G>T p.Glu322Ter p.E322* ENST00000298622 4/24 60 51 9 89 89 0 strelka-varscan-mutect JAKMIP3,stop_gained,p.Glu322Ter,ENST00000298622,NM_001105521.2; T ENST00000298622 Transcript stop_gained 1102/6626 964/2535 322/844 E/* Gag/Tag 1 1 JAKMIP3 HGNC HGNC:23523 protein_coding YES CCDS44494.1 ENSP00000298622 Q5VZ66 UPI000157482F NM_001105521.2 4/24 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF9 HIGH 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.96578 1 1 1 1 0 T 4 4 29 132135155 132135155 G T 1 0 0 0 0 0 1 0 0 7855 1304 45 2 2 JAKMIP3 10 132135155 Nonsense_Mutation SNP G C3L-01924_T 6281983 132135155 1662267 342 8212 IGF2 0 . GRCh38 11 2135476 2135476 + Silent SNP C C T C3L-01924_T C3L-01924_N C C c.216G>A p.= p.L72L ENST00000434045 3/5 143 119 24 118 118 0 strelka-varscan-mutect IGF2,synonymous_variant,p.=,ENST00000416167,NM_000612.5;IGF2,synonymous_variant,p.=,ENST00000381406,;IGF2,synonymous_variant,p.=,ENST00000381395,NM_001007139.5,NM_001291861.2;IGF2,synonymous_variant,p.=,ENST00000434045,NM_001127598.2;IGF2,synonymous_variant,p.=,ENST00000381389,NM_001291862.2;IGF2,synonymous_variant,p.=,ENST00000381392,;IGF2,synonymous_variant,p.=,ENST00000418738,;MIR483,upstream_gene_variant,,ENST00000385070,;INS-IGF2,3_prime_UTR_variant,,ENST00000356578,; T ENST00000434045 Transcript synonymous_variant 601/1583 216/711 72/236 L ttG/ttA COSM5372267,COSM5372268 1 -1 IGF2 HGNC HGNC:5466 protein_coding YES CCDS44517.1 ENSP00000391826 P01344 UPI0001751501 NM_001127598.2 3/5 Gene3D:1.10.100.10,hmmpanther:PTHR11454,hmmpanther:PTHR11454:SF10,Superfamily_domains:SSF56994 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 2135476 2135476 C T 1 0 0 0 0 0 0 0 1 7478 593 21 3 3 IGF2 11 2135476 Silent SNP C C3L-01924_T 2135476 132951146 343 8213 NLRP14 0 . GRCh38 11 7057677 7057677 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2292G>T p.Arg764Ser p.R764S ENST00000299481 7/12 334 253 81 439 439 0 strelka-varscan-mutect NLRP14,missense_variant,p.Arg764Ser,ENST00000299481,NM_176822.3; T ENST00000299481 Transcript missense_variant,splice_region_variant 2638/3628 2292/3282 764/1093 R/S agG/agT 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 tolerated(0.44) 7/12 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF154,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 7057677 7057677 G T 1 0 0 0 0 1 0 0 0 10513 1217 42 2 2 NLRP14 11 7057677 Missense_Mutation SNP G C3L-01924_T 4922201 7057677 128028945 344 8214 OR10A3 0 . GRCh38 11 7938753 7938753 + Silent SNP A A G rs138525938 C3L-01924_T C3L-01924_N A A c.768T>C p.= p.N256N ENST00000360759 1/1 169 149 20 245 245 0 strelka-varscan-mutect OR10A3,synonymous_variant,p.=,ENST00000360759,NM_001003745.1; G ENST00000360759 Transcript synonymous_variant 842/1061 768/945 256/314 N aaT/aaC rs138525938 1 -1 OR10A3 HGNC HGNC:8162 protein_coding YES CCDS31421.1 ENSP00000353988 P58181 A0A126GVZ2 UPI00000015AD NM_001003745.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF30,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs138525938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 7938753 7938753 A G 1 0 0 0 0 0 0 0 1 10967 446 16 5 5 OR10A3 11 7938753 Silent SNP A C3L-01924_T 881076 7938753 127147869 345 8215 DENND5A 0 . GRCh38 11 9178367 9178367 + Splice_Site SNP C C A novel C3L-01924_T C3L-01924_N C C c.1672-1G>T p.X558_splice ENST00000328194 121 107 14 180 180 0 strelka-varscan-mutect DENND5A,splice_acceptor_variant,,ENST00000328194,NM_015213.3;DENND5A,splice_acceptor_variant,,ENST00000530044,NM_001243254.1;DENND5A,upstream_gene_variant,,ENST00000526523,;DENND5A,splice_acceptor_variant,,ENST00000526707,;DENND5A,splice_acceptor_variant,,ENST00000527896,;DENND5A,splice_acceptor_variant,,ENST00000530867,; A ENST00000328194 Transcript splice_acceptor_variant -/5031 1672/3864 558/1287 1 -1 DENND5A HGNC HGNC:19344 protein_coding YES CCDS31423.1 ENSP00000328524 Q6IQ26 UPI00001C1F29 NM_015213.3 7/22 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 29 9178367 9178367 C A 1 0 0 0 0 0 0 1 0 4240 695 24 2 2 DENND5A 11 9178367 Splice_Site SNP C C3L-01924_T 1239614 9178367 125908255 346 8216 PDE3B 0 . GRCh38 11 14830732 14830732 + Silent SNP C C T rs540418989 C3L-01924_T C3L-01924_N C C c.1842C>T p.= p.F614F ENST00000282096 8/16 75 65 10 76 76 0 strelka-varscan-mutect PDE3B,synonymous_variant,p.=,ENST00000282096,NM_000922.3;PDE3B,synonymous_variant,p.=,ENST00000455098,; T ENST00000282096 Transcript synonymous_variant 2195/6076 1842/3339 614/1112 F ttC/ttT rs540418989 1 1 PDE3B HGNC HGNC:8779 protein_coding YES CCDS7817.1 ENSP00000282096 Q13370 UPI000013DCB7 NM_000922.3 8/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF29 LOW 1 SNV 1 1 PASS rs540418989 . 0 200 9 0 0 0 0 0 -19.99007 0.9999916 1 1 1 0 T 2 4 29 14830732 14830732 C T 1 0 0 0 0 0 0 0 1 11726 825 29 3 3 PDE3B 11 14830732 Silent SNP C C3L-01924_T 5652365 14830732 120255890 347 8217 OTOG 0 . GRCh38 11 17576599 17576599 + Missense_Mutation SNP G G A rs867715728 C3L-01924_T C3L-01924_N G G c.2566G>A p.Gly856Arg p.G856R ENST00000399391 20/55 186 169 17 178 177 1 strelka-varscan-mutect OTOG,missense_variant,p.Gly844Arg,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Gly856Arg,ENST00000399391,NM_001277269.1;OTOG,upstream_gene_variant,,ENST00000342528,; A ENST00000399391 Transcript missense_variant 2566/8778 2566/8778 856/2925 G/R Gga/Aga rs867715728,COSM3383370 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 20/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Gene3D:2.10.25.10 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs867715728 . 0 208 0 2 0 0 0 0 -19.99948 0.9999998 1 1 1 0 A 3 1 29 17576599 17576599 G A 1 0 0 0 0 1 0 0 0 11370 1117 39 1 1 OTOG 11 17576599 Missense_Mutation SNP G C3L-01924_T 2745867 17576599 117510023 348 8218 KCNC1 0 . GRCh38 11 17772559 17772559 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1465C>T p.Pro489Ser p.P489S ENST00000265969 2/4 161 139 22 178 178 0 strelka-varscan-mutect KCNC1,missense_variant,p.Pro489Ser,ENST00000379472,NM_004976.4;KCNC1,missense_variant,p.Pro489Ser,ENST00000265969,NM_001112741.1;KCNC1,upstream_gene_variant,,ENST00000525802,; T ENST00000265969 Transcript missense_variant 2656/3887 1465/1758 489/585 P/S Ccg/Tcg 1 1 KCNC1 HGNC HGNC:6233 protein_coding YES CCDS44547.1 ENSP00000265969 P48547 UPI0000E2291F NM_001112741.1 tolerated(0.11) 2/4 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,Prints_domain:PR01581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 17772559 17772559 C T 1 0 0 0 0 1 0 0 0 7930 855 30 3 3 KCNC1 11 17772559 Missense_Mutation SNP C C3L-01924_T 195960 17772559 117314063 349 8219 PTPN5 0 . GRCh38 11 18743363 18743363 + Missense_Mutation SNP C C G rs202083124 C3L-01924_T C3L-01924_N C C c.358G>C p.Val120Leu p.V120L ENST00000358540 5/15 252 222 30 315 315 0 strelka-varscan-mutect PTPN5,missense_variant,p.Val120Leu,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,missense_variant,p.Val96Leu,ENST00000396168,NM_001278238.1,NM_001278239.1;PTPN5,5_prime_UTR_variant,,ENST00000477854,;PTPN5,intron_variant,,ENST00000396170,NM_001039970.1,NM_001278236.1;RP11-1081L13.4,downstream_gene_variant,,ENST00000527285,;PTPN5,non_coding_transcript_exon_variant,,ENST00000496201,; G ENST00000358540 Transcript missense_variant 789/3135 358/1698 120/565 V/L Gtc/Ctc rs202083124,COSM3770046,COSM3770047 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 tolerated_low_confidence(1) 5/15 Low_complexity_(Seg):seg,hmmpanther:PTHR19134:SF40,hmmpanther:PTHR19134,PIRSF_domain:PIRSF001997 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs202083124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 18743363 18743363 C G 1 0 0 0 0 1 0 0 0 12945 536 19 4 4 PTPN5 11 18743363 Missense_Mutation SNP C C3L-01924_T 970804 18743363 116343259 350 8220 PTPN5 0 . GRCh38 11 18744113 18744113 + Missense_Mutation SNP G G T rs780842182 C3L-01924_T C3L-01924_N G G c.184C>A p.Pro62Thr p.P62T ENST00000358540 4/15 92 75 17 79 79 0 strelka-varscan-mutect PTPN5,missense_variant,p.Pro62Thr,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,missense_variant,p.Pro62Thr,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,missense_variant,p.Pro38Thr,ENST00000396168,NM_001278238.1,NM_001278239.1;PTPN5,upstream_gene_variant,,ENST00000477854,;RP11-1081L13.4,downstream_gene_variant,,ENST00000527285,;PTPN5,non_coding_transcript_exon_variant,,ENST00000496201,; T ENST00000358540 Transcript missense_variant 615/3135 184/1698 62/565 P/T Ccc/Acc rs780842182,COSM4473445,COSM4473446 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 tolerated_low_confidence(0.12) 4/15 Low_complexity_(Seg):seg,hmmpanther:PTHR19134:SF40,hmmpanther:PTHR19134,PIRSF_domain:PIRSF001997 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs780842182 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 18744113 18744113 G T 1 0 0 0 0 1 0 0 0 12945 1174 41 2 2 PTPN5 11 18744113 Missense_Mutation SNP G C3L-01924_T 750 18744113 116342509 351 8221 MUC15 0 . GRCh38 11 26563137 26563137 + Missense_Mutation SNP A A T rs777978468 C3L-01924_T C3L-01924_N A A c.904T>A p.Tyr302Asn p.Y302N ENST00000436318 3/4 112 103 9 155 155 0 strelka-varscan-mutect MUC15,missense_variant,p.Tyr275Asn,ENST00000455601,NM_145650.3;MUC15,missense_variant,p.Tyr302Asn,ENST00000436318,;MUC15,missense_variant,p.Tyr302Asn,ENST00000529533,NM_001135091.1;ANO3,intron_variant,,ENST00000256737,NM_031418.2;ANO3,intron_variant,,ENST00000525139,;ANO3,intron_variant,,ENST00000531568,;MUC15,intron_variant,,ENST00000281268,;MUC15,intron_variant,,ENST00000527569,NM_001135092.1;ANO3,non_coding_transcript_exon_variant,,ENST00000529242,; T ENST00000436318 Transcript missense_variant 904/3118 904/1086 302/361 Y/N Tat/Aat rs777978468 1 -1 MUC15 HGNC HGNC:14956 protein_coding YES CCDS44557.1 ENSP00000416753 A0A0A0MT67 UPI0000D4B9CF deleterious(0) 3/4 hmmpanther:PTHR12231,Pfam_domain:PF15672 MODERATE SNV 5 1 PASS rs777978468 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 26563137 26563137 A T 1 0 0 0 0 1 0 0 0 9971 362 13 4 4 MUC15 11 26563137 Missense_Mutation SNP A C3L-01924_T 7819024 26563137 108523485 352 8222 RAG2 0 . GRCh38 11 36592731 36592731 + Nonsense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1438G>T p.Glu480Ter p.E480* ENST00000618712 3/3 389 342 47 479 477 2 strelka-varscan-mutect RAG2,stop_gained,p.Glu480Ter,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,stop_gained,p.Glu480Ter,ENST00000311485,NM_000536.3;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000529083,;RAG2,downstream_gene_variant,,ENST00000527033,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,intron_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; A ENST00000618712 Transcript stop_gained 2032/2818 1438/1584 480/527 E/* Gag/Tag CM114604,COSM687405 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 3/3 Pfam_domain:PF13341,hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0,Superfamily_domains:SSF57903 0,1 HIGH 1 SNV 4 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 36592731 36592731 C A 1 0 0 0 0 0 1 0 0 13165 835 29 2 2 RAG2 11 36592731 Nonsense_Mutation SNP C C3L-01924_T 10029594 36592731 98493891 353 8223 LRRC4C 0 . GRCh38 11 40115515 40115515 + Silent SNP G G T rs765406670 C3L-01924_T C3L-01924_N G G c.778C>A p.= p.R260R ENST00000278198 2/2 233 166 67 310 310 0 strelka-varscan-mutect LRRC4C,synonymous_variant,p.=,ENST00000278198,;LRRC4C,synonymous_variant,p.=,ENST00000527150,;LRRC4C,synonymous_variant,p.=,ENST00000530763,NM_020929.2;LRRC4C,synonymous_variant,p.=,ENST00000528697,NM_001258419.1;LRRC4C,synonymous_variant,p.=,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript synonymous_variant 2742/4054 778/1923 260/640 R Cgg/Agg rs765406670,COSM3764301,COSM5263339 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs765406670 . 0 207 0 0 2 0 0 0 -20 0.9990178 1 1 1 0 T 2 4 29 40115515 40115515 G T 1 0 0 0 0 0 0 0 1 8903 1144 40 1 1 LRRC4C 11 40115515 Silent SNP G C3L-01924_T 3522784 40115515 94971107 354 8224 CHRM4 0 . GRCh38 11 46386076 46386076 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.482T>A p.Phe161Tyr p.F161Y ENST00000433765 1/1 269 231 38 336 336 0 strelka-varscan-mutect CHRM4,missense_variant,p.Phe161Tyr,ENST00000433765,NM_000741.3;MDK,downstream_gene_variant,,ENST00000405308,NM_001270550.1;MDK,downstream_gene_variant,,ENST00000407067,NM_001270551.1;MDK,downstream_gene_variant,,ENST00000359803,NM_001012334.2;MDK,downstream_gene_variant,,ENST00000395565,NM_001012333.2;MDK,downstream_gene_variant,,ENST00000395566,NM_002391.4;MDK,downstream_gene_variant,,ENST00000395569,NM_001270552.1;MDK,downstream_gene_variant,,ENST00000617138,;MDK,downstream_gene_variant,,ENST00000441869,;MDK,downstream_gene_variant,,ENST00000533952,;MDK,downstream_gene_variant,,ENST00000533283,;MDK,downstream_gene_variant,,ENST00000489525,;MDK,downstream_gene_variant,,ENST00000481047,;MDK,downstream_gene_variant,,ENST00000490240,; T ENST00000433765 Transcript missense_variant 533/1511 482/1440 161/479 F/Y tTc/tAc 1 -1 CHRM4 HGNC HGNC:1953 protein_coding YES CCDS44581.1 ENSP00000409378 P08173 UPI00001252BB NM_000741.3 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF60,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 46386076 46386076 A T 1 0 0 0 0 1 0 0 0 3139 246 9 4 4 CHRM4 11 46386076 Missense_Mutation SNP A C3L-01924_T 6270561 46386076 88700546 355 8225 CKAP5 0 . GRCh38 11 46753457 46753457 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.4910G>T p.Gly1637Val p.G1637V ENST00000529230 37/44 138 128 10 124 124 0 strelka-varscan-mutect CKAP5,missense_variant,p.Gly1637Val,ENST00000529230,NM_001008938.3;CKAP5,missense_variant,p.Gly1577Val,ENST00000312055,NM_014756.3;CKAP5,missense_variant,p.Gly1577Val,ENST00000354558,;CKAP5,missense_variant,p.Gly166Val,ENST00000527333,;CKAP5,upstream_gene_variant,,ENST00000525896,;CKAP5,downstream_gene_variant,,ENST00000526876,;MIR5582,upstream_gene_variant,,ENST00000579697,;CKAP5,non_coding_transcript_exon_variant,,ENST00000533413,; A ENST00000529230 Transcript missense_variant 4957/7121 4910/6099 1637/2032 G/V gGa/gTa 1 -1 CKAP5 HGNC HGNC:28959 protein_coding YES CCDS31477.1 ENSP00000432768 Q14008 UPI000013F21E NM_001008938.3 tolerated(0.18) 37/44 hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -14.13008 0.9999997 1 1 1 0 A 3 1 29 46753457 46753457 C A 1 0 0 0 0 1 0 0 0 3208 855 30 2 2 CKAP5 11 46753457 Missense_Mutation SNP C C3L-01924_T 367381 46753457 88333165 356 8226 AGBL2 0 . GRCh38 11 47686017 47686017 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1664G>T p.Cys555Phe p.C555F ENST00000525123 11/19 247 189 58 265 265 0 strelka-varscan-mutect AGBL2,missense_variant,p.Cys555Phe,ENST00000525123,NM_024783.3;AGBL2,missense_variant,p.Cys555Phe,ENST00000357610,;AGBL2,missense_variant,p.Cys517Phe,ENST00000528244,;AGBL2,downstream_gene_variant,,ENST00000532595,;AGBL2,non_coding_transcript_exon_variant,,ENST00000529712,;AGBL2,intron_variant,,ENST00000528609,; A ENST00000525123 Transcript missense_variant 1950/3577 1664/2709 555/902 C/F tGt/tTt 1 -1 AGBL2 HGNC HGNC:26296 protein_coding YES CCDS7944.1 ENSP00000435582 Q5U5Z8 A0A140VKH9 UPI00001A95E3 NM_024783.3 deleterious(0) 11/19 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF19,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs1296611340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 47686017 47686017 C A 1 0 0 0 0 1 0 0 0 452 478 17 2 2 AGBL2 11 47686017 Missense_Mutation SNP C C3L-01924_T 932560 47686017 87400605 357 8227 OR4B1 0 . GRCh38 11 48216868 48216868 + Missense_Mutation SNP C C A rs758861637 C3L-01924_T C3L-01924_N C C c.59C>A p.Ala20Asp p.A20D ENST00000309562 1/1 151 120 31 215 215 0 strelka-varscan-mutect OR4B1,missense_variant,p.Ala20Asp,ENST00000309562,NM_001005470.1; A ENST00000309562 Transcript missense_variant 77/971 59/930 20/309 A/D gCt/gAt rs758861637,COSM1508129,COSM4033330 1 1 OR4B1 HGNC HGNC:8290 protein_coding YES CCDS31485.1 ENSP00000311605 Q8NGF8 A0A126GVH6 UPI0000041BD9 NM_001005470.1 tolerated(0.24) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF377,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs758861637 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 48216868 48216868 C A 1 0 0 0 0 1 0 0 0 11121 797 28 2 2 OR4B1 11 48216868 Missense_Mutation SNP C C3L-01924_T 530851 48216868 86869754 358 8228 TRIM49B 0 . GRCh38 11 49031814 49031814 + Missense_Mutation SNP A A C rs746889281 C3L-01924_T C3L-01924_N A A c.215A>C p.Lys72Thr p.K72T ENST00000622138 3/8 312 295 17 464 464 0 varscan-mutect TRIM49B,missense_variant,p.Lys72Thr,ENST00000622138,;TRIM49B,missense_variant,p.Lys72Thr,ENST00000332682,NM_001206626.1; C ENST00000622138 Transcript missense_variant 544/2162 215/1359 72/452 K/T aAg/aCg rs746889281 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 tolerated(0.29) 3/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Gene3D:3.30.40.10,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS rs746889281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 49031814 49031814 A C 1 0 0 0 0 1 0 0 0 17015 72 3 5 5 TRIM49B 11 49031814 Missense_Mutation SNP A C3L-01924_T 814946 49031814 86054808 359 8229 OR5D16 0 . GRCh38 11 55839062 55839062 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.311T>C p.Phe104Ser p.F104S ENST00000378396 1/1 306 284 22 369 369 0 strelka-varscan-mutect OR5D16,missense_variant,p.Phe104Ser,ENST00000378396,NM_001005496.1; C ENST00000378396 Transcript missense_variant 311/987 311/987 104/328 F/S tTt/tCt 1 1 OR5D16 HGNC HGNC:15283 protein_coding YES CCDS31512.1 ENSP00000367649 Q8NGK9 UPI0000046198 NM_001005496.1 tolerated(0.1) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 55839062 55839062 T C 1 0 0 0 0 1 0 0 0 11226 1841 64 5 5 OR5D16 11 55839062 Missense_Mutation SNP T C3L-01924_T 6807248 55839062 79247560 360 8230 OR8I2 0 . GRCh38 11 56093963 56093963 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.656T>G p.Ile219Ser p.I219S ENST00000302124 1/1 184 165 19 227 226 1 strelka-varscan-mutect OR8I2,missense_variant,p.Ile219Ser,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; G ENST00000302124 Transcript missense_variant 656/933 656/933 219/310 I/S aTc/aGc 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 tolerated(0.86) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 56093963 56093963 T G 1 0 0 0 0 1 0 0 0 11308 1435 50 5 5 OR8I2 11 56093963 Missense_Mutation SNP T C3L-01924_T 254901 56093963 78992659 361 8231 OR8K5 0 . GRCh38 11 56160298 56160298 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.20C>T p.Thr7Ile p.T7I ENST00000313447 1/1 82 66 16 106 106 0 strelka-varscan-mutect OR8K5,missense_variant,p.Thr7Ile,ENST00000313447,NM_001004058.2; A ENST00000313447 Transcript missense_variant 20/924 20/924 7/307 T/I aCa/aTa 1 -1 OR8K5 HGNC HGNC:15315 protein_coding YES CCDS31521.1 ENSP00000323853 Q8NH50 UPI000004B231 NM_001004058.2 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 56160298 56160298 G A 1 0 0 0 0 1 0 0 0 11312 1377 48 3 3 OR8K5 11 56160298 Missense_Mutation SNP G C3L-01924_T 66335 56160298 78926324 362 8232 OR5T3 0 . GRCh38 11 56252980 56252980 + Missense_Mutation SNP G G A C3L-01924_T C3L-01924_N G G c.781G>A p.Ala261Thr p.A261T ENST00000303059 1/1 204 160 44 237 237 0 strelka-varscan-mutect OR5T3,missense_variant,p.Ala261Thr,ENST00000303059,NM_001004747.1; A ENST00000303059 Transcript missense_variant 781/1023 781/1023 261/340 A/T Gct/Act COSM5250430,COSM543194 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 tolerated(0.1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 56252980 56252980 G A 1 0 0 0 0 1 0 0 0 11251 1319 46 3 3 OR5T3 11 56252980 Missense_Mutation SNP G C3L-01924_T 92682 56252980 78833642 363 8233 OR5M8 0 . GRCh38 11 56491342 56491342 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.29A>C p.Glu10Ala p.E10A ENST00000327216 1/1 61 55 6 60 60 0 strelka-varscan-mutect OR5M8,missense_variant,p.Glu10Ala,ENST00000327216,NM_001005282.1;CTD-3051L14.13,upstream_gene_variant,,ENST00000525853,; G ENST00000327216 Transcript missense_variant 29/936 29/936 10/311 E/A gAg/gCg 1 -1 OR5M8 HGNC HGNC:14846 protein_coding YES CCDS31533.1 ENSP00000323354 Q8NGP6 A0A126GWD6 UPI00000405CC NM_001005282.1 deleterious(0) 1/1 hmmpanther:PTHR26452:SF146,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -14.3503 1 1 1 1 0 G 3 3 29 56491342 56491342 T G 1 0 0 0 0 1 0 0 0 11245 1551 54 5 5 OR5M8 11 56491342 Missense_Mutation SNP T C3L-01924_T 238362 56491342 78595280 364 8234 OR5AP2 0 . GRCh38 11 56642178 56642178 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.262C>A p.Leu88Met p.L88M ENST00000302981 1/1 308 238 70 397 397 0 strelka-varscan-mutect OR5AP2,missense_variant,p.Leu89Met,ENST00000544374,;OR5AP2,missense_variant,p.Leu88Met,ENST00000302981,NM_001002925.1; T ENST00000302981 Transcript missense_variant 262/951 262/951 88/316 L/M Ctg/Atg 1 -1 OR5AP2 HGNC HGNC:15258 protein_coding YES CCDS31534.1 ENSP00000303111 Q8NGF4 UPI0000061EE6 NM_001002925.1 tolerated(0.07) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF151,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 56642178 56642178 G T 1 0 0 0 0 1 0 0 0 11216 962 34 2 2 OR5AP2 11 56642178 Missense_Mutation SNP G C3L-01924_T 150836 56642178 78444444 365 8235 OR10Q1 0 . GRCh38 11 58228478 58228478 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.398C>A p.Pro133Gln p.P133Q ENST00000316770 1/1 179 157 22 242 242 0 strelka-varscan-mutect OR10Q1,missense_variant,p.Pro133Gln,ENST00000316770,NM_001004471.2; T ENST00000316770 Transcript missense_variant 441/1037 398/960 133/319 P/Q cCg/cAg COSM1676039 1 -1 OR10Q1 HGNC HGNC:15134 protein_coding YES CCDS31547.1 ENSP00000314324 Q8NGQ4 UPI0000041C4C NM_001004471.2 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF253,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs775674520 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 58228478 58228478 G T 1 0 0 0 0 1 0 0 0 10993 1116 39 1 1 OR10Q1 11 58228478 Missense_Mutation SNP G C3L-01924_T 1586300 58228478 76858144 366 8236 OR5AN1 0 . GRCh38 11 59365158 59365158 + Frame_Shift_Del DEL G G - novel C3L-01924_T C3L-01924_N G G c.701delG p.Gly234AlafsTer13 p.G234Afs*13 ENST00000313940 1/1 103 81 22 170 170 0 sindel-varindel-pindel OR5AN1,frameshift_variant,p.Gly234AlafsTer13,ENST00000313940,NM_001004729.1; - ENST00000313940 Transcript frameshift_variant 747/1037 700/936 234/311 G/X Ggc/gc 1 1 OR5AN1 HGNC HGNC:15255 protein_coding YES CCDS31559.1 ENSP00000320302 Q8NGI8 A0A126GVP9 UPI000004B1FD NM_001004729.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF262,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 59365158 59365158 G - 1 0 1 0 1 0 0 0 0 11215 1000 35 0 0 OR5AN1 11 59365158 Frame_Shift_Del DEL G C3L-01924_T 1136680 59365158 75721464 367 8237 VWCE 0 . GRCh38 11 61281109 61281109 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.914G>A p.Gly305Glu p.G305E ENST00000335613 8/20 112 81 31 136 136 0 strelka-varscan-mutect VWCE,missense_variant,p.Gly305Glu,ENST00000335613,NM_152718.2;VWCE,missense_variant,p.Gly22Glu,ENST00000613271,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,downstream_gene_variant,,ENST00000535599,; T ENST00000335613 Transcript missense_variant 1301/3640 914/2868 305/955 G/E gGg/gAg 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 deleterious(0.03) 8/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 61281109 61281109 C T 1 0 0 0 0 1 0 0 0 17804 623 22 3 3 VWCE 11 61281109 Missense_Mutation SNP C C3L-01924_T 1915951 61281109 73805513 368 8238 CARNS1 0 . GRCh38 11 67424314 67424314 + Missense_Mutation SNP C C T rs754430149 C3L-01924_T C3L-01924_N C C c.2566C>T p.Arg856Cys p.R856C ENST00000445895 9/9 224 192 32 273 272 1 strelka-varscan-mutect CARNS1,missense_variant,p.Arg856Cys,ENST00000445895,NM_001166222.1;CARNS1,missense_variant,p.Arg733Cys,ENST00000307823,NM_020811.1;CARNS1,missense_variant,p.Arg830Cys,ENST00000531040,;RPS6KB2,upstream_gene_variant,,ENST00000312629,NM_003952.2;PPP1CA,upstream_gene_variant,,ENST00000542876,;PPP1CA,upstream_gene_variant,,ENST00000546202,;RPS6KB2,upstream_gene_variant,,ENST00000524934,;RPS6KB2,upstream_gene_variant,,ENST00000420069,;RPS6KB2,upstream_gene_variant,,ENST00000524814,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;CARNS1,intron_variant,,ENST00000531958,;RPS6KB2,upstream_gene_variant,,ENST00000525088,;RPS6KB2,upstream_gene_variant,,ENST00000528964,;RPS6KB2,upstream_gene_variant,,ENST00000556575,;RPS6KB2,upstream_gene_variant,,ENST00000530623,; T ENST00000445895 Transcript missense_variant 2680/3971 2566/2853 856/950 R/C Cgt/Tgt rs754430149,COSM2041827,COSM2041828 1 1 CARNS1 HGNC HGNC:29268 protein_coding YES CCDS53667.1 ENSP00000389009 A5YM72 UPI0001B99E02 NM_001166222.1 deleterious(0) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR10578,hmmpanther:PTHR10578:SF57,Gene3D:3.30.470.20 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs754430149 . 0 208 0 0 0 0 0 2 -3.821841 0 0 1 0 0 T 3 4 29 67424314 67424314 C T 1 0 0 0 0 1 0 0 0 2355 884 31 1 1 CARNS1 11 67424314 Missense_Mutation SNP C C3L-01924_T 6143205 67424314 67662308 369 8239 C11orf24 0 . GRCh38 11 68261769 68261769 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1226G>T p.Gly409Val p.G409V ENST00000304271 4/4 238 184 54 281 281 0 strelka-varscan-mutect C11orf24,missense_variant,p.Gly409Val,ENST00000304271,NM_022338.3;C11orf24,intron_variant,,ENST00000533310,NM_001300913.1;C11orf24,downstream_gene_variant,,ENST00000527280,;C11orf24,non_coding_transcript_exon_variant,,ENST00000531745,;C11orf24,downstream_gene_variant,,ENST00000530166,; A ENST00000304271 Transcript missense_variant 1629/2063 1226/1350 409/449 G/V gGg/gTg 1 -1 C11orf24 HGNC HGNC:1174 protein_coding YES CCDS8180.1 ENSP00000307264 Q96F05 A0A024R5K9 UPI000006E42A NM_022338.3 deleterious(0) 4/4 hmmpanther:PTHR16021,hmmpanther:PTHR16021:SF9,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 68261769 68261769 C A 1 0 0 0 0 1 0 0 0 1779 623 22 2 2 C11orf24 11 68261769 Missense_Mutation SNP C C3L-01924_T 837455 68261769 66824853 370 8240 TESMIN 0 . GRCh38 11 68715842 68715842 + Missense_Mutation SNP T T C rs763444744 C3L-01924_T C3L-01924_N T T c.1015A>G p.Ile339Val p.I339V ENST00000255087 7/10 110 103 7 169 169 0 strelka-varscan-mutect TESMIN,missense_variant,p.Ile339Val,ENST00000255087,NM_004923.3;TESMIN,missense_variant,p.Ile32Val,ENST00000543240,; C ENST00000255087 Transcript missense_variant 1199/2579 1015/1527 339/508 I/V Att/Gtt rs763444744 1 -1 TESMIN HGNC HGNC:7446 protein_coding YES CCDS8184.1 ENSP00000255087 Q9Y4I5 UPI00001FAE07 NM_004923.3 tolerated(0.09) 7/10 PROSITE_profiles:PS51634,hmmpanther:PTHR12446:SF22,hmmpanther:PTHR12446 MODERATE 1 SNV 1 1 PASS rs763444744 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 68715842 68715842 T C 1 0 0 0 0 1 0 0 0 16188 1478 51 5 5 TESMIN 11 68715842 Missense_Mutation SNP T C3L-01924_T 454073 68715842 66370780 371 8241 PRCP 0 . GRCh38 11 82850417 82850417 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.563G>C p.Gly188Ala p.G188A ENST00000393399 5/10 132 119 13 123 123 0 strelka-varscan-mutect PRCP,missense_variant,p.Gly167Ala,ENST00000313010,NM_005040.2;PRCP,missense_variant,p.Gly188Ala,ENST00000393399,NM_199418.2;PRCP,missense_variant,p.Gly62Ala,ENST00000531801,;PRCP,missense_variant,p.Gly62Ala,ENST00000527444,;PRCP,missense_variant,p.Gly62Ala,ENST00000534631,;PRCP,missense_variant,p.Gly62Ala,ENST00000534396,;PRCP,missense_variant,p.Gly126Ala,ENST00000529671,;PRCP,missense_variant,p.Gly62Ala,ENST00000531128,;PRCP,missense_variant,p.Gly113Ala,ENST00000532809,;PRCP,missense_variant,p.Gly62Ala,ENST00000528082,;PRCP,downstream_gene_variant,,ENST00000534264,;PRCP,downstream_gene_variant,,ENST00000533126,;PRCP,upstream_gene_variant,,ENST00000525772,;PRCP,upstream_gene_variant,,ENST00000532476,;PRCP,upstream_gene_variant,,ENST00000531283,;PRCP,upstream_gene_variant,,ENST00000526918,;PRCP,upstream_gene_variant,,ENST00000524642,; G ENST00000393399 Transcript missense_variant 591/2120 563/1554 188/517 G/A gGa/gCa 1 -1 PRCP HGNC HGNC:9344 protein_coding YES CCDS41695.1 ENSP00000377055 P42785 UPI00001FB052 NM_199418.2 tolerated(0.05) 5/10 hmmpanther:PTHR11010,hmmpanther:PTHR11010:SF38,Pfam_domain:PF05577,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 82850417 82850417 C G 1 0 0 0 0 1 0 0 0 12580 855 30 4 4 PRCP 11 82850417 Missense_Mutation SNP C C3L-01924_T 14134575 82850417 52236205 372 8242 NOX4 0 . GRCh38 11 89342136 89342136 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.1275C>T p.= p.V425V ENST00000263317 14/18 131 122 9 145 145 0 varscan-mutect NOX4,synonymous_variant,p.=,ENST00000424319,NM_001291926.1;NOX4,synonymous_variant,p.=,ENST00000343727,NM_001291927.1;NOX4,synonymous_variant,p.=,ENST00000263317,NM_016931.4;NOX4,synonymous_variant,p.=,ENST00000527956,NM_001143837.1;NOX4,synonymous_variant,p.=,ENST00000528341,NM_001291929.1;NOX4,synonymous_variant,p.=,ENST00000527626,;NOX4,synonymous_variant,p.=,ENST00000375979,;NOX4,intron_variant,,ENST00000534731,NM_001143836.2;NOX4,intron_variant,,ENST00000532825,NM_001300995.1;NOX4,intron_variant,,ENST00000525196,;NOX4,intron_variant,,ENST00000531342,;NOX4,3_prime_UTR_variant,,ENST00000529343,; A ENST00000263317 Transcript synonymous_variant 1514/2388 1275/1737 425/578 V gtC/gtT 1 -1 NOX4 HGNC HGNC:7891 protein_coding YES CCDS8285.1 ENSP00000263317 Q9NPH5 UPI000045655B NM_016931.4 14/18 Pfam_domain:PF08030,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF78,Superfamily_domains:SSF52343 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 89342136 89342136 G A 1 0 0 0 0 0 0 0 1 10604 1277 45 3 3 NOX4 11 89342136 Silent SNP G C3L-01924_T 6491719 89342136 45744486 373 8243 ENDOD1 0 . GRCh38 11 95128579 95128579 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.503A>T p.Gln168Leu p.Q168L ENST00000278505 2/2 177 124 53 185 185 0 strelka-varscan-mutect ENDOD1,missense_variant,p.Gln168Leu,ENST00000278505,NM_015036.2; T ENST00000278505 Transcript missense_variant 621/4687 503/1503 168/500 Q/L cAg/cTg 1 1 ENDOD1 HGNC HGNC:29129 protein_coding YES CCDS41699.1 ENSP00000278505 O94919 UPI0000071599 NM_015036.2 tolerated(0.08) 2/2 hmmpanther:PTHR21472,hmmpanther:PTHR21472:SF8,Gene3D:1g8tA00,Pfam_domain:PF01223,SMART_domains:SM00477,SMART_domains:SM00892,Superfamily_domains:SSF54060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 95128579 95128579 A T 1 0 0 0 0 1 0 0 0 4956 188 7 4 4 ENDOD1 11 95128579 Missense_Mutation SNP A C3L-01924_T 5786443 95128579 39958043 374 8244 PGR 0 . GRCh38 11 101039152 101039152 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.2766A>T p.= p.A922A ENST00000325455 8/8 296 245 51 312 312 0 strelka-varscan-mutect PGR,synonymous_variant,p.=,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,synonymous_variant,p.=,ENST00000263463,NM_001271161.2;PGR,synonymous_variant,p.=,ENST00000534013,NM_001271162.1;PGR,3_prime_UTR_variant,,ENST00000534780,;PGR,3_prime_UTR_variant,,ENST00000528960,;PGR,3_prime_UTR_variant,,ENST00000526300,;PGR,non_coding_transcript_exon_variant,,ENST00000533207,;PGR,downstream_gene_variant,,ENST00000530764,; A ENST00000325455 Transcript synonymous_variant 4220/13748 2766/2802 922/933 A gcA/gcT 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 8/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 101039152 101039152 T A 1 0 0 0 0 0 0 0 1 11894 1567 55 4 4 PGR 11 101039152 Silent SNP T C3L-01924_T 5910573 101039152 34047470 375 8245 GRIA4 0 . GRCh38 11 105979580 105979580 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.2550C>A p.= p.T850T ENST00000282499 17/17 114 95 19 112 111 1 strelka-varscan-mutect GRIA4,synonymous_variant,p.=,ENST00000282499,NM_000829.3;GRIA4,synonymous_variant,p.=,ENST00000530497,;GRIA4,3_prime_UTR_variant,,ENST00000393127,NM_001077243.2;GRIA4,3_prime_UTR_variant,,ENST00000525187,;RNU6-277P,upstream_gene_variant,,ENST00000516272,;GRIA4,non_coding_transcript_exon_variant,,ENST00000533094,; A ENST00000282499 Transcript synonymous_variant 2996/5508 2550/2709 850/902 T acC/acA 1 1 GRIA4 HGNC HGNC:4574 protein_coding YES CCDS8333.1 ENSP00000282499 P48058 UPI000013DCE6 NM_000829.3 17/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF100 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 105979580 105979580 C A 1 0 0 0 0 0 0 0 1 6650 695 24 2 2 GRIA4 11 105979580 Silent SNP C C3L-01924_T 4940428 105979580 29107042 376 8246 CWF19L2 0 . GRCh38 11 107353688 107353688 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1921G>T p.Val641Phe p.V641F ENST00000282251 13/18 261 211 50 349 348 1 strelka-varscan-mutect CWF19L2,missense_variant,p.Val641Phe,ENST00000282251,NM_152434.2;CWF19L2,missense_variant,p.Val522Phe,ENST00000431778,;CWF19L2,non_coding_transcript_exon_variant,,ENST00000462890,;CWF19L2,intron_variant,,ENST00000532251,; A ENST00000282251 Transcript missense_variant 1949/3278 1921/2685 641/894 V/F Gtc/Ttc 1 -1 CWF19L2 HGNC HGNC:26508 protein_coding YES CCDS8336.2 ENSP00000282251 Q2TBE0 UPI00005A81B4 NM_152434.2 deleterious(0) 13/18 hmmpanther:PTHR12072,hmmpanther:PTHR12072:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 107353688 107353688 C A 1 0 0 0 0 1 0 0 0 3882 478 17 2 2 CWF19L2 11 107353688 Missense_Mutation SNP C C3L-01924_T 1374108 107353688 27732934 377 8247 PPP2R1B 0 . GRCh38 11 111760881 111760881 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.477A>T p.= p.A159A ENST00000311129 4/16 362 280 82 366 366 0 strelka-varscan-mutect PPP2R1B,synonymous_variant,p.=,ENST00000527614,NM_002716.4;PPP2R1B,synonymous_variant,p.=,ENST00000311129,NM_181699.2;PPP2R1B,synonymous_variant,p.=,ENST00000341980,NM_001177562.1;PPP2R1B,synonymous_variant,p.=,ENST00000426998,NM_181700.1;PPP2R1B,intron_variant,,ENST00000393055,NM_001177563.1;PPP2R1B,downstream_gene_variant,,ENST00000531373,;PPP2R1B,3_prime_UTR_variant,,ENST00000534500,;PPP2R1B,intron_variant,,ENST00000534521,; A ENST00000311129 Transcript synonymous_variant 498/2082 477/2004 159/667 A gcA/gcT 1 -1 PPP2R1B HGNC HGNC:9303 protein_coding YES CCDS8348.1 ENSP00000311344 P30154 UPI000006CEE0 NM_181699.2 4/16 Gene3D:1.25.10.10,hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs868994631 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 111760881 111760881 T A 1 0 0 0 0 0 0 0 1 12506 1451 51 4 4 PPP2R1B 11 111760881 Silent SNP T C3L-01924_T 4407193 111760881 23325741 378 8248 RNF214 0 . GRCh38 11 117238958 117238958 + Silent SNP A A G novel C3L-01924_T C3L-01924_N A A c.465A>G p.= p.P155P ENST00000300650 3/15 298 228 70 296 296 0 strelka-varscan-mutect RNF214,synonymous_variant,p.=,ENST00000300650,NM_207343.3;RNF214,synonymous_variant,p.=,ENST00000531452,NM_001077239.1;RNF214,intron_variant,,ENST00000530849,;RNF214,intron_variant,,ENST00000531287,NM_001278249.1;RNF214,downstream_gene_variant,,ENST00000534428,;RNF214,non_coding_transcript_exon_variant,,ENST00000529869,; G ENST00000300650 Transcript synonymous_variant 573/2755 465/2112 155/703 P ccA/ccG 1 1 RNF214 HGNC HGNC:25335 protein_coding YES CCDS41720.1 ENSP00000300650 Q8ND24 A0A024R3D4 UPI00001D7749 NM_207343.3 3/15 hmmpanther:PTHR15727 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 117238958 117238958 A G 1 0 0 0 0 0 0 0 1 13657 146 6 5 5 RNF214 11 117238958 Silent SNP A C3L-01924_T 5478077 117238958 17847664 379 8249 OR10G8 0 . GRCh38 11 124030550 124030550 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.928A>T p.Ser310Cys p.S310C ENST00000431524 1/1 58 44 14 65 65 0 strelka-varscan-mutect OR10G8,missense_variant,p.Ser310Cys,ENST00000431524,NM_001004464.1; T ENST00000431524 Transcript missense_variant 961/1045 928/936 310/311 S/C Agc/Tgc 1 1 OR10G8 HGNC HGNC:14845 protein_coding YES CCDS31704.1 ENSP00000389072 Q8NGN5 A0A126GVX3 UPI0000040A8F NM_001004464.1 tolerated(0.06) 1/1 MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 124030550 124030550 A T 1 0 0 0 0 1 0 0 0 10980 304 11 4 4 OR10G8 11 124030550 Missense_Mutation SNP A C3L-01924_T 6791592 124030550 11056072 380 8250 ROBO4 0 . GRCh38 11 124894228 124894228 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1291C>A p.Pro431Thr p.P431T ENST00000306534 8/18 81 69 12 104 104 0 strelka-mutect ROBO4,missense_variant,p.Pro431Thr,ENST00000306534,NM_019055.5;ROBO4,missense_variant,p.Pro286Thr,ENST00000533054,NM_001301088.1;RP11-664I21.6,downstream_gene_variant,,ENST00000524433,;ROBO4,downstream_gene_variant,,ENST00000526899,;ROBO4,downstream_gene_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000529941,;ROBO4,non_coding_transcript_exon_variant,,ENST00000525182,;ROBO4,upstream_gene_variant,,ENST00000534407,;ROBO4,upstream_gene_variant,,ENST00000532216,;ROBO4,downstream_gene_variant,,ENST00000533337,;ROBO4,downstream_gene_variant,,ENST00000532300,; T ENST00000306534 Transcript missense_variant 1777/4710 1291/3024 431/1007 P/T Ccc/Acc 1 -1 ROBO4 HGNC HGNC:17985 protein_coding YES CCDS8455.1 ENSP00000304945 Q8WZ75 UPI000004A023 NM_019055.5 deleterious(0.02) 8/18 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999935 1 1 1 0 T 3 4 29 124894228 124894228 G T 1 0 0 0 0 1 0 0 0 13694 1203 42 2 2 ROBO4 11 124894228 Missense_Mutation SNP G C3L-01924_T 863678 124894228 10192394 381 8251 HEPN1 0 . GRCh38 11 124919958 124919958 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.208T>A p.Trp70Arg p.W70R ENST00000408930 1/1 219 178 41 252 252 0 strelka-varscan-mutect HEPN1,missense_variant,p.Trp70Arg,ENST00000408930,NM_001037558.2;HEPACAM,3_prime_UTR_variant,,ENST00000298251,NM_152722.4;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; A ENST00000408930 Transcript missense_variant 715/1434 208/267 70/88 W/R Tgg/Agg 1 1 HEPN1 HGNC HGNC:34400 protein_coding YES CCDS41729.1 ENSP00000386143 Q6WQI6 UPI0000D6269C NM_001037558.2 tolerated_low_confidence(0.36) 1/1 MODERATE SNV 1 PASS rs996510629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 124919958 124919958 T A 1 0 0 0 0 1 0 0 0 6940 1696 59 4 4 HEPN1 11 124919958 Missense_Mutation SNP T C3L-01924_T 25730 124919958 10166664 382 8252 FEZ1 0 . GRCh38 11 125460555 125460555 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.610C>A p.Leu204Ile p.L204I ENST00000278919 5/10 169 133 36 200 200 0 strelka-varscan-mutect FEZ1,missense_variant,p.Leu204Ile,ENST00000278919,NM_005103.4;FEZ1,missense_variant,p.Leu137Ile,ENST00000577924,;FEZ1,intron_variant,,ENST00000527350,;FEZ1,non_coding_transcript_exon_variant,,ENST00000392709,;FEZ1,non_coding_transcript_exon_variant,,ENST00000533294,;FEZ1,non_coding_transcript_exon_variant,,ENST00000534022,;FEZ1,upstream_gene_variant,,ENST00000524427,;FEZ1,downstream_gene_variant,,ENST00000532981,; T ENST00000278919 Transcript missense_variant 845/1748 610/1179 204/392 L/I Ctc/Atc 1 -1 FEZ1 HGNC HGNC:3659 protein_coding YES CCDS31716.1 ENSP00000278919 Q99689 UPI000012A6FE NM_005103.4 deleterious(0.05) 5/10 hmmpanther:PTHR12394:SF4,hmmpanther:PTHR12394,Pfam_domain:PF07763 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 125460555 125460555 G T 1 0 0 0 0 1 0 0 0 5686 1000 35 2 2 FEZ1 11 125460555 Missense_Mutation SNP G C3L-01924_T 540597 125460555 9626067 383 8253 SLC6A13 0 . GRCh38 12 237249 237249 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.605G>T p.Gly202Val p.G202V ENST00000343164 6/15 175 131 44 168 167 1 strelka-varscan-mutect SLC6A13,missense_variant,p.Gly202Val,ENST00000343164,NM_016615.4;SLC6A13,missense_variant,p.Gly110Val,ENST00000445055,NM_001190997.2;SLC6A13,missense_variant,p.Gly110Val,ENST00000546319,;SLC6A13,upstream_gene_variant,,ENST00000542379,;SLC6A13,non_coding_transcript_exon_variant,,ENST00000536842,;SLC6A13,non_coding_transcript_exon_variant,,ENST00000534887,;SLC6A13,downstream_gene_variant,,ENST00000539260,;SLC6A13,downstream_gene_variant,,ENST00000542272,; A ENST00000343164 Transcript missense_variant 658/2185 605/1809 202/602 G/V gGg/gTg 1 -1 SLC6A13 HGNC HGNC:11046 protein_coding YES CCDS8502.1 ENSP00000339260 Q9NSD5 UPI0000046060 NM_016615.4 deleterious(0.01) 6/15 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF111,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 237249 237249 C A 1 0 0 0 0 1 0 0 0 14959 623 22 2 2 SLC6A13 12 237249 Missense_Mutation SNP C C3L-01924_T 237249 133038060 384 8254 STRAP 0 . GRCh38 12 15890619 15890619 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.353G>T p.Gly118Val p.G118V ENST00000419869 4/10 173 134 39 238 238 0 strelka-varscan-mutect STRAP,missense_variant,p.Gly118Val,ENST00000419869,NM_007178.3;STRAP,missense_variant,p.Gly131Val,ENST00000025399,;STRAP,3_prime_UTR_variant,,ENST00000541731,;STRAP,upstream_gene_variant,,ENST00000536737,; T ENST00000419869 Transcript missense_variant 666/1866 353/1053 118/350 G/V gGg/gTg 1 1 STRAP HGNC HGNC:30796 protein_coding YES CCDS8676.1 ENSP00000392270 Q9Y3F4 UPI0000137C97 NM_007178.3 deleterious(0) 4/10 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19877,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 15890619 15890619 G T 1 0 0 0 0 1 0 0 0 15707 1232 43 2 2 STRAP 12 15890619 Missense_Mutation SNP G C3L-01924_T 15653370 15890619 117384690 385 8255 ETNK1 0 . GRCh38 12 22673654 22673654 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1206T>A p.Phe402Leu p.F402L ENST00000266517 6/8 83 72 11 81 81 0 strelka-varscan-mutect ETNK1,missense_variant,p.Phe402Leu,ENST00000266517,NM_018638.4;ETNK1,missense_variant,p.Phe393Leu,ENST00000538218,;ETNK1,non_coding_transcript_exon_variant,,ENST00000544191,; A ENST00000266517 Transcript missense_variant 1295/7159 1206/1359 402/452 F/L ttT/ttA 1 1 ETNK1 HGNC HGNC:24649 protein_coding YES CCDS8698.1 ENSP00000266517 Q9HBU6 UPI0000129E2F NM_018638.4 deleterious(0.05) 6/8 hmmpanther:PTHR22603,hmmpanther:PTHR22603:SF22,Gene3D:3.90.1200.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 A 3 1 29 22673654 22673654 T A 1 0 0 0 0 1 0 0 0 5136 1809 63 4 4 ETNK1 12 22673654 Missense_Mutation SNP T C3L-01924_T 6783035 22673654 110601655 386 8256 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3L-01924_T C3L-01924_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 271 201 70 368 368 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3L-01924_T 2571697 25245351 108029958 387 8257 OVOS2 0 . GRCh38 12 31148085 31148085 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.1241G>A p.Ser414Asn p.S414N ENST00000632817 11/34 242 175 67 253 253 0 strelka-varscan-mutect OVOS2,missense_variant,p.Ser414Asn,ENST00000398963,;OVOS2,missense_variant,p.Ser414Asn,ENST00000632817,; T ENST00000632817 Transcript missense_variant 1241/4299 1241/4299 414/1432 S/N aGc/aAc 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 tolerated(0.21) 11/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 31148085 31148085 C T 1 0 0 0 0 1 0 0 0 11399 797 28 3 3 OVOS2 12 31148085 Missense_Mutation SNP C C3L-01924_T 5902734 31148085 102127224 388 8258 YAF2 0 . GRCh38 12 42161693 42161693 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.297G>A p.= p.K99K ENST00000327791 4/5 196 169 27 264 261 3 strelka-varscan YAF2,synonymous_variant,p.=,ENST00000327791,NM_001190979.1;YAF2,synonymous_variant,p.=,ENST00000534854,NM_005748.4;YAF2,synonymous_variant,p.=,ENST00000380790,NM_001190977.1;YAF2,downstream_gene_variant,,ENST00000548917,;YAF2,non_coding_transcript_exon_variant,,ENST00000547622,;YAF2,non_coding_transcript_exon_variant,,ENST00000547724,;YAF2,3_prime_UTR_variant,,ENST00000552109,;YAF2,3_prime_UTR_variant,,ENST00000547351,;YAF2,3_prime_UTR_variant,,ENST00000551268,;YAF2,3_prime_UTR_variant,,ENST00000546726,;YAF2,3_prime_UTR_variant,,ENST00000552928,;YAF2,3_prime_UTR_variant,,ENST00000548661,;YAF2,non_coding_transcript_exon_variant,,ENST00000551528,;YAF2,non_coding_transcript_exon_variant,,ENST00000546972,;YAF2,upstream_gene_variant,,ENST00000550315,;YAF2,downstream_gene_variant,,ENST00000547254,; T ENST00000327791 Transcript synonymous_variant 353/4156 297/615 99/204 K aaG/aaA 1 -1 YAF2 HGNC HGNC:17363 protein_coding YES CCDS53779.1 ENSP00000328004 Q8IY57 UPI00000742C8 NM_001190979.1 4/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12920,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 137 0 5 68 0 0 0 -11.39451 0 0 1 0 0 T 2 4 29 42161693 42161693 C T 1 0 0 0 0 0 0 0 1 18025 912 32 3 3 YAF2 12 42161693 Silent SNP C C3L-01924_T 11013608 42161693 91113616 389 8259 PUS7L 0 . GRCh38 12 43754980 43754980 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.266A>G p.His89Arg p.H89R ENST00000344862 2/9 104 95 9 173 173 0 strelka-varscan-mutect PUS7L,missense_variant,p.His89Arg,ENST00000344862,NM_031292.4;PUS7L,missense_variant,p.His89Arg,ENST00000416848,NM_001098615.1;PUS7L,missense_variant,p.His89Arg,ENST00000551923,NM_001098614.2;PUS7L,missense_variant,p.His89Arg,ENST00000549868,;PUS7L,intron_variant,,ENST00000431332,NM_001271826.1;PUS7L,intron_variant,,ENST00000550784,;PUS7L,intron_variant,,ENST00000547156,;IRAK4,upstream_gene_variant,,ENST00000613694,NM_016123.3;IRAK4,upstream_gene_variant,,ENST00000431837,NM_001145257.1,NM_001145256.1;IRAK4,upstream_gene_variant,,ENST00000551736,NM_001114182.2;IRAK4,upstream_gene_variant,,ENST00000440781,NM_001145258.1;IRAK4,upstream_gene_variant,,ENST00000550616,;PUS7L,missense_variant,p.His89Arg,ENST00000553166,;IRAK4,upstream_gene_variant,,ENST00000547521,;IRAK4,upstream_gene_variant,,ENST00000550386,;IRAK4,upstream_gene_variant,,ENST00000547101,;IRAK4,upstream_gene_variant,,ENST00000550615,;IRAK4,upstream_gene_variant,,ENST00000552309,;IRAK4,upstream_gene_variant,,ENST00000550361,;IRAK4,upstream_gene_variant,,ENST00000546780,; C ENST00000344862 Transcript missense_variant 370/13593 266/2106 89/701 H/R cAt/cGt 1 -1 PUS7L HGNC HGNC:25276 protein_coding YES CCDS8743.1 ENSP00000343081 Q9H0K6 UPI0000037C53 NM_031292.4 tolerated(0.62) 2/9 PIRSF_domain:PIRSF037016,hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 43754980 43754980 T C 1 0 0 0 0 1 0 0 0 12992 1464 51 5 5 PUS7L 12 43754980 Missense_Mutation SNP T C3L-01924_T 1593287 43754980 89520329 390 8260 NELL2 0 . GRCh38 12 44779855 44779855 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.653G>T p.Cys218Phe p.C218F ENST00000437801 5/21 136 118 18 171 171 0 strelka-varscan-mutect NELL2,missense_variant,p.Cys168Phe,ENST00000429094,NM_001145108.1;NELL2,missense_variant,p.Cys218Phe,ENST00000437801,NM_001145107.1;NELL2,missense_variant,p.Cys167Phe,ENST00000395487,NM_001145109.1;NELL2,missense_variant,p.Cys168Phe,ENST00000452445,NM_006159.2;NELL2,missense_variant,p.Cys167Phe,ENST00000551601,;NELL2,missense_variant,p.Cys167Phe,ENST00000549027,;NELL2,missense_variant,p.Cys191Phe,ENST00000333837,NM_001145110.1;NELL2,missense_variant,p.Cys168Phe,ENST00000552993,;NELL2,missense_variant,p.Cys165Phe,ENST00000553120,;NELL2,upstream_gene_variant,,ENST00000550313,;NELL2,upstream_gene_variant,,ENST00000550462,;NELL2,non_coding_transcript_exon_variant,,ENST00000547172,;NELL2,non_coding_transcript_exon_variant,,ENST00000547751,; A ENST00000437801 Transcript missense_variant 1025/3279 653/2601 218/866 C/F tGc/tTc 1 -1 NELL2 HGNC HGNC:7751 protein_coding YES CCDS44863.1 ENSP00000416341 Q99435 UPI000191537D NM_001145107.1 deleterious(0) 5/21 hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF0,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,SMART_domains:SM00210,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 44779855 44779855 C A 1 0 0 0 0 1 0 0 0 10365 710 25 2 2 NELL2 12 44779855 Missense_Mutation SNP C C3L-01924_T 1024875 44779855 88495454 391 8261 SLC4A8 0 . GRCh38 12 51480074 51480074 + Nonsense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2096G>A p.Trp699Ter p.W699* ENST00000514353 17/17 33 28 5 60 60 0 strelka-varscan-mutect SLC4A8,stop_gained,p.Trp699Ter,ENST00000514353,NM_001258403.1;SLC4A8,intron_variant,,ENST00000453097,NM_001039960.2;SLC4A8,intron_variant,,ENST00000358657,NM_001258401.2;SLC4A8,intron_variant,,ENST00000551071,;SLC4A8,intron_variant,,ENST00000604314,;SLC4A8,intron_variant,,ENST00000319957,; A ENST00000514353 Transcript stop_gained 2505/3041 2096/2244 699/747 W/* tGg/tAg 1 1 SLC4A8 HGNC HGNC:11034 protein_coding CCDS58232.1 ENSP00000442561 Q2Y0W8 UPI0000E59655 NM_001258403.1 17/17 HIGH SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -13.20395 0.9999833 1 1 1 0 A 4 1 29 51480074 51480074 G A 1 0 0 0 0 0 1 0 0 14936 1357 47 3 3 SLC4A8 12 51480074 Nonsense_Mutation SNP G C3L-01924_T 6700219 51480074 81795235 392 8262 SOAT2 0 . GRCh38 12 53119157 53119157 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.943C>A p.Leu315Met p.L315M ENST00000301466 10/15 165 131 34 177 177 0 strelka-varscan-mutect SOAT2,missense_variant,p.Leu315Met,ENST00000301466,NM_003578.3;SOAT2,downstream_gene_variant,,ENST00000551896,;SOAT2,synonymous_variant,p.=,ENST00000542365,; A ENST00000301466 Transcript missense_variant 1003/2044 943/1569 315/522 L/M Ctg/Atg 1 1 SOAT2 HGNC HGNC:11178 protein_coding YES CCDS8847.1 ENSP00000301466 O75908 UPI0000135B61 NM_003578.3 deleterious(0.02) 10/15 Pfam_domain:PF03062,PIRSF_domain:PIRSF000439,PIRSF_domain:PIRSF500230,hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1180278542 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 53119157 53119157 C A 1 0 0 0 0 1 0 0 0 15232 680 24 2 2 SOAT2 12 53119157 Missense_Mutation SNP C C3L-01924_T 1639083 53119157 80156152 393 8263 SP7 0 . GRCh38 12 53328922 53328922 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.520C>A p.Gln174Lys p.Q174K ENST00000536324 3/3 122 102 20 114 114 0 strelka-varscan-mutect SP7,missense_variant,p.Gln174Lys,ENST00000536324,NM_001173467.2;SP7,missense_variant,p.Gln174Lys,ENST00000303846,NM_152860.1;SP7,missense_variant,p.Gln156Lys,ENST00000537210,NM_001300837.1;SP7,missense_variant,p.Gln156Lys,ENST00000547755,;AAAS,upstream_gene_variant,,ENST00000550286,;AAAS,upstream_gene_variant,,ENST00000551724,;AAAS,upstream_gene_variant,,ENST00000548258,; T ENST00000536324 Transcript missense_variant 804/3151 520/1296 174/431 Q/K Cag/Aag 1 -1 SP7 HGNC HGNC:17321 protein_coding YES CCDS44897.1 ENSP00000443827 Q8TDD2 UPI000000D7AE NM_001173467.2 tolerated(0.51) 3/3 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 53328922 53328922 G T 1 0 0 0 0 1 0 0 0 15295 1357 47 2 2 SP7 12 53328922 Missense_Mutation SNP G C3L-01924_T 209765 53328922 79946387 394 8264 PAN2 0 . GRCh38 12 56333025 56333025 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.70G>C p.Val24Leu p.V24L ENST00000425394 2/26 215 154 61 256 256 0 strelka-varscan-mutect PAN2,missense_variant,p.Val24Leu,ENST00000425394,NM_001127460.2;PAN2,missense_variant,p.Val24Leu,ENST00000610546,;PAN2,missense_variant,p.Val24Leu,ENST00000548043,;PAN2,missense_variant,p.Val24Leu,ENST00000440411,NM_014871.4;PAN2,missense_variant,p.Val24Leu,ENST00000257931,NM_001166279.1;PAN2,intron_variant,,ENST00000547572,;IL23A,upstream_gene_variant,,ENST00000619177,;IL23A,upstream_gene_variant,,ENST00000622119,;PAN2,non_coding_transcript_exon_variant,,ENST00000551359,;PAN2,non_coding_transcript_exon_variant,,ENST00000547994,;PAN2,non_coding_transcript_exon_variant,,ENST00000549964,;PAN2,upstream_gene_variant,,ENST00000547518,; G ENST00000425394 Transcript missense_variant 447/5372 70/3609 24/1202 V/L Gtc/Ctc 1 -1 PAN2 HGNC HGNC:20074 protein_coding YES CCDS44922.1 ENSP00000401721 Q504Q3 UPI0000577D0A NM_001127460.2 tolerated_low_confidence(0.11) 2/26 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 56333025 56333025 C G 1 0 0 0 0 1 0 0 0 11495 478 17 4 4 PAN2 12 56333025 Missense_Mutation SNP C C3L-01924_T 3004103 56333025 76942284 395 8265 STAT2 0 . GRCh38 12 56346166 56346166 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.2082G>A p.= p.R694R ENST00000314128 22/24 169 140 29 217 217 0 strelka-varscan-mutect STAT2,synonymous_variant,p.=,ENST00000314128,NM_005419.3;STAT2,synonymous_variant,p.=,ENST00000557235,NM_198332.1;STAT2,downstream_gene_variant,,ENST00000418572,;STAT2,non_coding_transcript_exon_variant,,ENST00000556539,;STAT2,downstream_gene_variant,,ENST00000557252,;STAT2,non_coding_transcript_exon_variant,,ENST00000555488,;STAT2,downstream_gene_variant,,ENST00000557199,;STAT2,downstream_gene_variant,,ENST00000555519,; T ENST00000314128 Transcript synonymous_variant 2106/3259 2082/2556 694/851 R agG/agA 1 -1 STAT2 HGNC HGNC:11363 protein_coding YES CCDS8917.1 ENSP00000315768 P52630 R9QE65 UPI00000473FC NM_005419.3 22/24 Gene3D:3.30.505.10,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF41 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 56346166 56346166 C T 1 0 0 0 0 0 0 0 1 15641 738 26 3 3 STAT2 12 56346166 Silent SNP C C3L-01924_T 13141 56346166 76929143 396 8266 NXPH4 0 . GRCh38 12 57225196 57225196 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.376G>T p.Gly126Cys p.G126C ENST00000349394 2/2 42 35 7 50 50 0 strelka-varscan-mutect NXPH4,missense_variant,p.Gly126Cys,ENST00000349394,NM_007224.3;SHMT2,upstream_gene_variant,,ENST00000328923,NM_005412.5;SHMT2,upstream_gene_variant,,ENST00000414700,NM_001166358.1;SHMT2,upstream_gene_variant,,ENST00000557487,NM_001166356.1;SHMT2,upstream_gene_variant,,ENST00000555634,;SHMT2,upstream_gene_variant,,ENST00000556689,;SHMT2,upstream_gene_variant,,ENST00000554310,;SHMT2,upstream_gene_variant,,ENST00000553529,;SHMT2,upstream_gene_variant,,ENST00000557703,;RP11-123K3.9,downstream_gene_variant,,ENST00000617433,;NXPH4,non_coding_transcript_exon_variant,,ENST00000555154,;SHMT2,upstream_gene_variant,,ENST00000554600,;SHMT2,upstream_gene_variant,,ENST00000557740,;NXPH4,3_prime_UTR_variant,,ENST00000556415,;SHMT2,upstream_gene_variant,,ENST00000554467,;SHMT2,upstream_gene_variant,,ENST00000556825,;SHMT2,upstream_gene_variant,,ENST00000557433,;SHMT2,upstream_gene_variant,,ENST00000557348,;SHMT2,upstream_gene_variant,,ENST00000555563,;SHMT2,upstream_gene_variant,,ENST00000553950,;SHMT2,upstream_gene_variant,,ENST00000557269,;SHMT2,upstream_gene_variant,,ENST00000553324,;SHMT2,upstream_gene_variant,,ENST00000557302,; T ENST00000349394 Transcript missense_variant 551/1804 376/927 126/308 G/C Ggc/Tgc 1 1 NXPH4 HGNC HGNC:8078 protein_coding YES CCDS8933.1 ENSP00000333593 O95158 UPI000004C619 NM_007224.3 deleterious(0) 2/2 Pfam_domain:PF06312,hmmpanther:PTHR17103,hmmpanther:PTHR17103:SF10 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -17.27044 0.9999985 1 1 1 0 T 3 4 29 57225196 57225196 G T 1 0 0 0 0 1 0 0 0 10869 1116 39 1 1 NXPH4 12 57225196 Missense_Mutation SNP G C3L-01924_T 879030 57225196 76050113 397 8267 DYRK2 0 . GRCh38 12 67658064 67658064 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1157G>C p.Arg386Pro p.R386P ENST00000344096 3/3 340 322 18 417 417 0 strelka-varscan-mutect DYRK2,missense_variant,p.Arg386Pro,ENST00000344096,NM_006482.2;DYRK2,missense_variant,p.Arg313Pro,ENST00000393555,NM_003583.3;DYRK2,downstream_gene_variant,,ENST00000543747,;DYRK2,downstream_gene_variant,,ENST00000319833,;DYRK2,downstream_gene_variant,,ENST00000542503,;RP11-335O4.3,downstream_gene_variant,,ENST00000425371,; C ENST00000344096 Transcript missense_variant 1570/8912 1157/1806 386/601 R/P cGt/cCt 1 1 DYRK2 HGNC HGNC:3093 protein_coding YES CCDS8978.1 ENSP00000342105 Q92630 UPI000006E92B NM_006482.2 deleterious(0) 3/3 PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF51,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 67658064 67658064 G C 1 0 0 0 0 1 0 0 0 4680 1145 40 4 4 DYRK2 12 67658064 Missense_Mutation SNP G C3L-01924_T 10432868 67658064 65617245 398 8268 TRHDE 0 . GRCh38 12 72656991 72656991 + Nonsense_Mutation SNP G G T rs750417544 C3L-01924_T C3L-01924_N G G c.2914G>T p.Glu972Ter p.E972* ENST00000261180 18/19 163 151 12 242 242 0 strelka-varscan-mutect TRHDE,stop_gained,p.Glu972Ter,ENST00000261180,NM_013381.2; T ENST00000261180 Transcript stop_gained 3010/10733 2914/3075 972/1024 E/* Gaa/Taa rs750417544 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 18/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 HIGH 1 SNV 1 1 PASS rs750417544 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 72656991 72656991 G T 1 0 0 0 0 0 1 0 0 16968 1291 45 2 2 TRHDE 12 72656991 Nonsense_Mutation SNP G C3L-01924_T 4998927 72656991 60618318 399 8269 NAV3 0 . GRCh38 12 78006720 78006720 + Silent SNP G G T C3L-01924_T C3L-01924_N G G c.1182G>T p.= p.R394R ENST00000397909 8/40 267 185 82 313 312 1 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,synonymous_variant,p.=,ENST00000550042,;NAV3,synonymous_variant,p.=,ENST00000550503,;NAV3,downstream_gene_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,; T ENST00000397909 Transcript synonymous_variant 1355/9821 1182/7158 394/2385 R cgG/cgT COSM4522836,COSM4522837 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 8/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 78006720 78006720 G T 1 0 0 0 0 0 0 0 1 10194 1161 41 2 2 NAV3 12 78006720 Silent SNP G C3L-01924_T 5349729 78006720 55268589 400 8270 OTOGL 0 . GRCh38 12 80251745 80251745 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1078T>A p.Cys360Ser p.C360S ENST00000458043 11/58 237 201 36 282 281 1 strelka-varscan-mutect OTOGL,missense_variant,p.Cys360Ser,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Cys360Ser,ENST00000547103,; A ENST00000458043 Transcript missense_variant 1084/8083 1078/7035 360/2344 C/S Tgc/Agc 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 11/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Pfam_domain:PF08742,SMART_domains:SM00832 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 80251745 80251745 T A 1 0 0 0 0 1 0 0 0 11371 1580 55 4 4 OTOGL 12 80251745 Missense_Mutation SNP T C3L-01924_T 2245025 80251745 53023564 401 8271 BTBD11 0 . GRCh38 12 107610288 107610288 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1742G>C p.Arg581Pro p.R581P ENST00000280758 5/17 211 174 37 257 257 0 strelka-varscan-mutect BTBD11,missense_variant,p.Arg581Pro,ENST00000280758,NM_001018072.1;BTBD11,missense_variant,p.Arg581Pro,ENST00000490090,;BTBD11,missense_variant,p.Arg118Pro,ENST00000357167,NM_001017523.1;BTBD11,missense_variant,p.Arg581Pro,ENST00000420571,;BTBD11,missense_variant,p.Arg215Pro,ENST00000415943,;BTBD11,missense_variant,p.Arg212Pro,ENST00000550706,;RP11-128P10.1,non_coding_transcript_exon_variant,,ENST00000548473,; C ENST00000280758 Transcript missense_variant 2270/5767 1742/3315 581/1104 R/P cGa/cCa 1 1 BTBD11 HGNC HGNC:23844 protein_coding YES CCDS31893.1 ENSP00000280758 A6QL63 UPI000051901E NM_001018072.1 deleterious(0) 5/17 Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE SNV 5 1 PASS rs1485751402 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 107610288 107610288 G C 1 0 0 0 0 1 0 0 0 1714 1058 37 4 4 BTBD11 12 107610288 Missense_Mutation SNP G C3L-01924_T 27358543 107610288 25665021 402 8272 ACACB 0 . GRCh38 12 109188080 109188080 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2062G>T p.Ala688Ser p.A688S ENST00000338432 13/53 111 103 8 105 105 0 strelka-varscan-mutect ACACB,missense_variant,p.Ala688Ser,ENST00000338432,;ACACB,missense_variant,p.Ala688Ser,ENST00000377848,NM_001093.3;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,upstream_gene_variant,,ENST00000544651,; T ENST00000338432 Transcript missense_variant 2181/9360 2062/7377 688/2458 A/S Gct/Tct 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB tolerated(0.3) 13/53 PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF02785,Gene3D:3.30.470.20,SMART_domains:SM00878,Superfamily_domains:SSF51246 MODERATE 1 SNV 1 1 PASS rs1247806490 . 0 205 3 2 0 0 0 0 -12.10792 0.9999709 1 1 1 0 T 3 4 29 109188080 109188080 G T 1 0 0 0 0 1 0 0 0 150 1087 38 1 1 ACACB 12 109188080 Missense_Mutation SNP G C3L-01924_T 1577792 109188080 24087229 403 8273 MMAB 0 . GRCh38 12 109561045 109561045 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.579G>C p.Glu193Asp p.E193D ENST00000545712 7/9 420 396 24 412 412 0 strelka-varscan-mutect MMAB,missense_variant,p.Glu193Asp,ENST00000545712,NM_052845.3;MMAB,missense_variant,p.Glu141Asp,ENST00000540016,;MMAB,3_prime_UTR_variant,,ENST00000541763,;MMAB,3_prime_UTR_variant,,ENST00000537496,;MMAB,3_prime_UTR_variant,,ENST00000544051,;MMAB,downstream_gene_variant,,ENST00000536760,;MMAB,downstream_gene_variant,,ENST00000420167,;MMAB,downstream_gene_variant,,ENST00000503497,;MMAB,downstream_gene_variant,,ENST00000542390,; G ENST00000545712 Transcript missense_variant 973/4438 579/753 193/250 E/D gaG/gaC 1 -1 MMAB HGNC HGNC:19331 protein_coding YES CCDS9131.1 ENSP00000445920 Q96EY8 UPI0000073CBF NM_052845.3 deleterious(0) 7/9 Low_complexity_(Seg):seg,hmmpanther:PTHR12213:SF0,hmmpanther:PTHR12213,TIGRFAM_domain:TIGR00636,Gene3D:1.20.1200.10,Pfam_domain:PF01923,Superfamily_domains:SSF89028,PD007457 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 109561045 109561045 C G 1 0 0 0 0 1 0 0 0 9603 927 32 4 4 MMAB 12 109561045 Missense_Mutation SNP C C3L-01924_T 372965 109561045 23714264 404 8274 OAS3 0 . GRCh38 12 112965946 112965946 + Missense_Mutation SNP G G T rs16942374 C3L-01924_T C3L-01924_N G G c.2606G>T p.Arg869Leu p.R869L ENST00000228928 12/16 292 259 33 322 321 1 strelka-varscan-mutect OAS3,missense_variant,p.Arg869Leu,ENST00000228928,NM_006187.3;OAS3,missense_variant,p.Arg41Leu,ENST00000546973,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS3,upstream_gene_variant,,ENST00000549918,;OAS3,downstream_gene_variant,,ENST00000546800,; T ENST00000228928 Transcript missense_variant 2785/6719 2606/3264 869/1087 R/L cGc/cTc rs16942374 1 1 OAS3 HGNC HGNC:8088 protein_coding YES CCDS44981.1 ENSP00000228928 Q9Y6K5 UPI000034ECD3 NM_006187.3 deleterious(0.01) 12/16 hmmpanther:PTHR11258:SF4,hmmpanther:PTHR11258,Gene3D:3.30.460.10,Pfam_domain:PF01909,Superfamily_domains:SSF81301 MODERATE 1 SNV 1 1 PASS rs16942374 . 0 208 0 0 0 0 0 2 -6.336529 0 0 1 0 0 T 3 4 29 112965946 112965946 G T 1 0 0 0 0 1 0 0 0 10880 1087 38 1 1 OAS3 12 112965946 Missense_Mutation SNP G C3L-01924_T 3404901 112965946 20309363 405 8275 GCN1 0 . GRCh38 12 120144666 120144666 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.5325G>T p.= p.V1775V ENST00000300648 41/58 117 86 31 163 163 0 strelka-varscan-mutect GCN1,synonymous_variant,p.=,ENST00000300648,NM_006836.1; A ENST00000300648 Transcript synonymous_variant 5338/8675 5325/8016 1775/2671 V gtG/gtT 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 41/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 120144666 120144666 C A 1 0 0 0 0 0 0 0 1 6169 581 21 2 2 GCN1 12 120144666 Silent SNP C C3L-01924_T 7178720 120144666 13130643 406 8276 TMEM132D 0 . GRCh38 12 129209552 129209552 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1411G>T p.Glu471Ter p.E471* ENST00000422113 5/9 176 125 51 192 192 0 strelka-varscan-mutect TMEM132D,stop_gained,p.Glu471Ter,ENST00000422113,NM_133448.2;RP11-669N7.3,splice_region_variant,,ENST00000542578,; A ENST00000422113 Transcript stop_gained 1738/5776 1411/3300 471/1099 E/* Gag/Tag 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 5/9 Pfam_domain:PF16070,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 129209552 129209552 C A 1 0 0 0 0 0 1 0 0 16492 864 30 2 2 TMEM132D 12 129209552 Nonsense_Mutation SNP C C3L-01924_T 9064886 129209552 4065757 407 8277 RIMBP2 0 . GRCh38 12 130437138 130437138 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.1759delG p.Val587CysfsTer16 p.V587Cfs*16 ENST00000261655 10/19 47 43 4 71 71 0 sindel-pindel RIMBP2,frameshift_variant,p.Val587CysfsTer16,ENST00000261655,NM_015347.4;RIMBP2,frameshift_variant,p.Val495CysfsTer16,ENST00000535703,; - ENST00000261655 Transcript frameshift_variant 1923/6321 1759/3159 587/1052 V/X Gtg/tg 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 10/19 PROSITE_profiles:PS50853,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18,Low_complexity_(Seg):seg,Superfamily_domains:SSF49265 HIGH 1 deletion 1 1 PASS . . 0 199 9 0 0 0 0 0 -10.14996 0.9999776 1 1 1 0 - 7 5 29 130437138 130437138 C - 1 0 1 0 1 0 0 0 0 13538 507 18 0 0 RIMBP2 12 130437138 Frame_Shift_Del DEL C C3L-01924_T 1227586 130437138 2838171 408 8278 KL 0 . GRCh38 13 33060726 33060726 + Missense_Mutation SNP G G T rs143984655 C3L-01924_T C3L-01924_N G G c.1647G>T p.Trp549Cys p.W549C ENST00000380099 4/5 205 174 31 306 305 1 strelka-varscan-mutect KL,missense_variant,p.Trp549Cys,ENST00000380099,NM_004795.3;KL,non_coding_transcript_exon_variant,,ENST00000487852,; T ENST00000380099 Transcript missense_variant 1655/5006 1647/3039 549/1012 W/C tgG/tgT rs143984655,COSM109105 1 1 KL HGNC HGNC:6344 protein_coding YES CCDS9347.1 ENSP00000369442 Q9UEF7 UPI000013CEBA NM_004795.3 deleterious(0) 4/5 hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF10,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs143984655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 33060726 33060726 G T 1 0 0 0 0 1 0 0 0 8196 1241 43 2 2 KL 13 33060726 Missense_Mutation SNP G C3L-01924_T 33060726 81303602 409 8279 DCLK1 0 . GRCh38 13 35871252 35871252 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.912T>A p.= p.R304R ENST00000255448 5/18 142 121 21 222 221 1 strelka-varscan-mutect DCLK1,synonymous_variant,p.=,ENST00000360631,;DCLK1,synonymous_variant,p.=,ENST00000255448,NM_004734.4;DCLK1,synonymous_variant,p.=,ENST00000379892,; T ENST00000255448 Transcript synonymous_variant 1124/5703 912/2190 304/729 R cgT/cgA 1 -1 DCLK1 HGNC HGNC:2700 protein_coding YES CCDS9354.1 ENSP00000255448 O15075 UPI000002A7C2 NM_004734.4 5/18 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF122,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 35871252 35871252 A T 1 0 0 0 0 0 0 0 1 4093 378 14 4 4 DCLK1 13 35871252 Silent SNP A C3L-01924_T 2810526 35871252 78493076 410 8280 LCP1 0 . GRCh38 13 46158576 46158576 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.304G>T p.Ala102Ser p.A102S ENST00000398576 7/19 189 169 20 286 286 0 strelka-varscan-mutect LCP1,missense_variant,p.Ala102Ser,ENST00000398576,;LCP1,missense_variant,p.Ala102Ser,ENST00000323076,NM_002298.4;LCP1,missense_variant,p.Ala102Ser,ENST00000416500,;LCP1,downstream_gene_variant,,ENST00000442275,;LCP1,downstream_gene_variant,,ENST00000460190,; A ENST00000398576 Transcript missense_variant 693/3944 304/1884 102/627 A/S Gca/Tca 1 -1 LCP1 HGNC HGNC:6528 protein_coding YES CCDS9403.1 ENSP00000381581 P13796 A0A024RDT4 UPI0000070B5C tolerated(0.54) 7/19 hmmpanther:PTHR19961,hmmpanther:PTHR19961:SF35 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 46158576 46158576 C A 1 0 0 0 0 1 0 0 0 8597 710 25 2 2 LCP1 13 46158576 Missense_Mutation SNP C C3L-01924_T 10287324 46158576 68205752 411 8281 PCDH8 0 . GRCh38 13 52846809 52846809 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1628G>T p.Arg543Leu p.R543L ENST00000377942 1/3 102 84 18 150 150 0 strelka-varscan-mutect PCDH8,missense_variant,p.Arg543Leu,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Arg543Leu,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; A ENST00000377942 Transcript missense_variant 1832/5088 1628/3213 543/1070 R/L cGc/cTc 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 tolerated(0.49) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 52846809 52846809 C A 1 0 0 0 0 1 0 0 0 11604 768 27 1 1 PCDH8 13 52846809 Missense_Mutation SNP C C3L-01924_T 6688233 52846809 61517519 412 8282 PCDH17 0 . GRCh38 13 57634754 57634754 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.2208G>T p.Glu736Asp p.E736D ENST00000377918 1/4 289 255 34 334 334 0 strelka-varscan-mutect PCDH17,missense_variant,p.Glu736Asp,ENST00000377918,NM_001040429.2;PCDH17,missense_variant,p.Glu124Asp,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,upstream_gene_variant,,ENST00000610846,;PCDH17,missense_variant,p.Glu736Asp,ENST00000484979,; T ENST00000377918 Transcript missense_variant 2943/8232 2208/3480 736/1159 E/D gaG/gaT COSM416332 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.06) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 57634754 57634754 G T 1 0 0 0 0 1 0 0 0 11599 933 33 2 2 PCDH17 13 57634754 Missense_Mutation SNP G C3L-01924_T 4787945 57634754 56729574 413 8283 PCDH17 0 . GRCh38 13 57724864 57724864 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.3050C>A p.Pro1017His p.P1017H ENST00000377918 4/4 224 197 27 309 309 0 strelka-varscan-mutect PCDH17,missense_variant,p.Pro1017His,ENST00000377918,NM_001040429.2;PCDH17,missense_variant,p.Pro404His,ENST00000612954,;PCDH17,downstream_gene_variant,,ENST00000615375,;PCDH17,3_prime_UTR_variant,,ENST00000484979,; A ENST00000377918 Transcript missense_variant 3785/8232 3050/3480 1017/1159 P/H cCt/cAt COSM3469399 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 deleterious(0.01) 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 57724864 57724864 C A 1 0 0 0 0 1 0 0 0 11599 681 24 2 2 PCDH17 13 57724864 Missense_Mutation SNP C C3L-01924_T 90110 57724864 56639464 414 8284 SLITRK5 0 . GRCh38 13 87677774 87677774 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.2386C>G p.Gln796Glu p.Q796E ENST00000325089 2/2 137 121 16 201 200 1 strelka-varscan-mutect SLITRK5,missense_variant,p.Gln796Glu,ENST00000325089,NM_015567.1; G ENST00000325089 Transcript missense_variant 2605/21103 2386/2877 796/958 Q/E Cag/Gag 1 1 SLITRK5 HGNC HGNC:20295 protein_coding YES CCDS9465.1 ENSP00000366283 O94991 UPI000015F6F7 NM_015567.1 tolerated(1) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 87677774 87677774 C G 1 0 0 0 0 1 0 0 0 15037 711 25 4 4 SLITRK5 13 87677774 Missense_Mutation SNP C C3L-01924_T 29952910 87677774 26686554 415 8285 RNF113B 0 . GRCh38 13 98177142 98177142 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.95G>A p.Gly32Asp p.G32D ENST00000267291 1/2 67 62 5 107 107 0 strelka-varscan-mutect RNF113B,missense_variant,p.Gly32Asp,ENST00000267291,NM_178861.4;FARP1,intron_variant,,ENST00000596580,;FARP1,intron_variant,,ENST00000319562,NM_005766.3;FARP1,intron_variant,,ENST00000627049,;FARP1,intron_variant,,ENST00000595437,NM_001286839.1;FARP1,intron_variant,,ENST00000376581,NM_001001715.3;FARP1,upstream_gene_variant,,ENST00000598389,;FARP1,intron_variant,,ENST00000600648,; T ENST00000267291 Transcript missense_variant 124/1376 95/969 32/322 G/D gGc/gAc 1 -1 RNF113B HGNC HGNC:17267 protein_coding YES CCDS9486.1 ENSP00000267291 Q8IZP6 UPI000006F203 NM_178861.4 tolerated(0.1) 1/2 hmmpanther:PTHR12930,hmmpanther:PTHR12930:SF1 MODERATE 1 SNV 1 1 PASS rs1368939643 . 0 208 2 0 0 0 0 0 -12.00504 1 1 1 1 0 T 3 4 29 98177142 98177142 C T 1 0 0 0 0 1 0 0 0 13606 739 26 3 3 RNF113B 13 98177142 Missense_Mutation SNP C C3L-01924_T 10499368 98177142 16187186 416 8286 CCDC168 0 . GRCh38 13 102740477 102740477 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.10220C>G p.Ser3407Cys p.S3407C ENST00000322527 4/4 133 118 15 217 217 0 strelka-varscan-mutect CCDC168,missense_variant,p.Ser3407Cys,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; C ENST00000322527 Transcript missense_variant 10358/21466 10220/21246 3407/7081 S/C tCt/tGt 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.13) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 102740477 102740477 G C 1 0 0 0 0 1 0 0 0 2484 942 33 4 4 CCDC168 13 102740477 Missense_Mutation SNP G C3L-01924_T 4563335 102740477 11623851 417 8287 DAOA 0 . GRCh38 13 105489947 105489947 + Missense_Mutation SNP A A C C3L-01924_T C3L-01924_N A A c.328A>C p.Asn110His p.N110H ENST00000618629 4/4 218 200 18 279 279 0 strelka-varscan-mutect DAOA,missense_variant,p.Asn39His,ENST00000329625,NM_001161814.1;DAOA,missense_variant,p.Asn110His,ENST00000618629,;DAOA,missense_variant,p.Asn110His,ENST00000375936,NM_172370.4,NM_001161812.1;DAOA-AS1,non_coding_transcript_exon_variant,,ENST00000448407,;DAOA,missense_variant,p.Asn39His,ENST00000559369,;DAOA,missense_variant,p.Asn39His,ENST00000600388,;DAOA,missense_variant,p.Asn82His,ENST00000595812,;DAOA,3_prime_UTR_variant,,ENST00000473269,;DAOA,3_prime_UTR_variant,,ENST00000471432,;DAOA,3_prime_UTR_variant,,ENST00000488534,;DAOA,3_prime_UTR_variant,,ENST00000601240,;DAOA,3_prime_UTR_variant,,ENST00000489237,; C ENST00000618629 Transcript missense_variant 328/1368 328/462 110/153 N/H Aac/Cac COSM945222 1 1 DAOA HGNC HGNC:21191 protein_coding YES CCDS41905.1 ENSP00000483757 P59103 UPI00001B01AA deleterious_low_confidence(0.02) 4/4 Pfam_domain:PF15199 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 105489947 105489947 A C 1 0 0 0 0 1 0 0 0 4033 14 1 5 5 DAOA 13 105489947 Missense_Mutation SNP A C3L-01924_T 2749470 105489947 8874381 418 8288 GRK1 0 . GRCh38 13 113731309 113731309 + Missense_Mutation SNP C C T rs766150912 C3L-01924_T C3L-01924_N C C c.1160C>T p.Ala387Val p.A387V ENST00000335678 5/7 176 153 23 212 212 0 strelka-varscan-mutect GRK1,missense_variant,p.Ala387Val,ENST00000335678,;GRK1,non_coding_transcript_exon_variant,,ENST00000545304,;GRK1,upstream_gene_variant,,ENST00000606140,; T ENST00000335678 Transcript missense_variant 1392/4296 1160/1692 387/563 A/V gCg/gTg rs766150912,COSM945649 1 1 GRK1 HGNC HGNC:10013 protein_coding YES ENSP00000334876 Q15835 UPI0000133B08 deleterious(0.03) 5/7 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF11,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs766150912 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 29 113731309 113731309 C T 1 0 0 0 0 1 0 0 0 6671 768 27 1 1 GRK1 13 113731309 Missense_Mutation SNP C C3L-01924_T 8241362 113731309 633019 419 8289 OR11H2 0 . GRCh38 14 19713263 19713263 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.654C>A p.Ser218Arg p.S218R ENST00000556246 1/1 228 203 25 295 294 1 varscan-mutect OR11H2,missense_variant,p.Ser218Arg,ENST00000556246,NM_001197287.1; T ENST00000556246 Transcript missense_variant 658/985 654/981 218/326 S/R agC/agA 1 -1 OR11H2 HGNC HGNC:14716 protein_coding YES CCDS76655.1 ENSP00000485150 Q8NH07 UPI0000061EAC NM_001197287.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF201,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 19713263 19713263 G T 1 0 0 0 0 1 0 0 0 11004 962 34 2 2 OR11H2 14 19713263 Missense_Mutation SNP G C3L-01924_T 19713263 87330455 420 8290 OR4M1 0 . GRCh38 14 19780383 19780383 + Silent SNP C C A rs748644352 C3L-01924_T C3L-01924_N C C c.61C>A p.= p.R21R ENST00000315957 1/1 130 120 10 156 156 0 varscan-mutect OR4M1,synonymous_variant,p.=,ENST00000315957,NM_001005500.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000315957 Transcript synonymous_variant 142/1116 61/942 21/313 R Cgg/Agg rs748644352 1 1 OR4M1 HGNC HGNC:14735 protein_coding YES CCDS32021.1 ENSP00000319654 Q8NGD0 A0A126GWC3 UPI0000061F0F NM_001005500.1 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF53,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs748644352 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 19780383 19780383 C A 1 0 0 0 0 0 0 0 1 11152 875 31 1 1 OR4M1 14 19780383 Silent SNP C C3L-01924_T 67120 19780383 87263335 421 8291 RNASE3 0 . GRCh38 14 20891923 20891923 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.237T>C p.= p.V79V ENST00000304639 2/2 480 313 167 520 520 0 strelka-varscan-mutect RNASE3,synonymous_variant,p.=,ENST00000304639,NM_002935.2; C ENST00000304639 Transcript synonymous_variant 295/720 237/483 79/160 V gtT/gtC 1 1 RNASE3 HGNC HGNC:10046 protein_coding YES CCDS9560.1 ENSP00000302324 P12724 UPI000013E9AE NM_002935.2 2/2 hmmpanther:PTHR11437:SF26,hmmpanther:PTHR11437,Gene3D:3.10.130.10,Pfam_domain:PF00074,SMART_domains:SM00092,Superfamily_domains:SSF54076,Prints_domain:PR00794,PD000535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 20891923 20891923 T C 1 0 0 0 0 0 0 0 1 13584 1741 61 5 5 RNASE3 14 20891923 Silent SNP T C3L-01924_T 1111540 20891923 86151795 422 8292 DAD1 0 . GRCh38 14 22589146 22589146 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.12G>T p.= p.S4S ENST00000250498 1/3 212 198 14 203 202 1 strelka-varscan-mutect DAD1,synonymous_variant,p.=,ENST00000250498,NM_001344.3;DAD1,synonymous_variant,p.=,ENST00000543337,;DAD1,synonymous_variant,p.=,ENST00000538631,;DAD1,synonymous_variant,p.=,ENST00000535847,; A ENST00000250498 Transcript synonymous_variant 124/731 12/342 4/113 S tcG/tcT 1 -1 DAD1 HGNC HGNC:2664 protein_coding YES CCDS9571.1 ENSP00000250498 P61803 UPI00000040DF NM_001344.3 1/3 PIRSF_domain:PIRSF005588,hmmpanther:PTHR10705 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 22589146 22589146 C A 1 0 0 0 0 0 0 0 1 4026 639 23 1 1 DAD1 14 22589146 Silent SNP C C3L-01924_T 1697223 22589146 84454572 423 8293 NPAS3 0 . GRCh38 14 33800610 33800610 + Missense_Mutation SNP G G T rs773780585 C3L-01924_T C3L-01924_N G G c.2303G>T p.Gly768Val p.G768V ENST00000356141 12/12 92 63 29 87 87 0 strelka-varscan-mutect NPAS3,missense_variant,p.Gly736Val,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Gly738Val,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Gly773Val,ENST00000551492,;NPAS3,missense_variant,p.Gly768Val,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Gly755Val,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Gly742Val,ENST00000551634,; T ENST00000356141 Transcript missense_variant 2303/2802 2303/2802 768/933 G/V gGc/gTc rs773780585 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious_low_confidence(0.01) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS rs773780585 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 33800610 33800610 G T 1 0 0 0 0 1 0 0 0 10612 1203 42 2 2 NPAS3 14 33800610 Missense_Mutation SNP G C3L-01924_T 11211464 33800610 73243108 424 8294 RALGAPA1 0 . GRCh38 14 35760888 35760888 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.488C>G p.Ser163Cys p.S163C ENST00000307138 6/40 118 97 21 144 144 0 strelka-varscan-mutect RALGAPA1,missense_variant,p.Ser163Cys,ENST00000637992,;RALGAPA1,missense_variant,p.Ser163Cys,ENST00000307138,NM_194301.2;RALGAPA1,missense_variant,p.Ser163Cys,ENST00000389698,NM_014990.1;RALGAPA1,missense_variant,p.Ser163Cys,ENST00000382366,NM_001283043.1;RALGAPA1,missense_variant,p.Ser163Cys,ENST00000553892,NM_001283044.1;SNORA31,downstream_gene_variant,,ENST00000517250,;RALGAPA1,upstream_gene_variant,,ENST00000554704,;RALGAPA1,upstream_gene_variant,,ENST00000555828,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554652,;QRSL1P3,upstream_gene_variant,,ENST00000552666,; C ENST00000307138 Transcript missense_variant 957/7911 488/6252 163/2083 S/C tCt/tGt 1 -1 RALGAPA1 HGNC HGNC:17770 protein_coding YES CCDS32064.1 ENSP00000302647 Q6GYQ0 UPI00003B5C51 NM_194301.2 deleterious(0.04) 6/40 hmmpanther:PTHR10063:SF3,hmmpanther:PTHR10063 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 35760888 35760888 G C 1 0 0 0 0 1 0 0 0 13172 942 33 4 4 RALGAPA1 14 35760888 Missense_Mutation SNP G C3L-01924_T 1960278 35760888 71282830 425 8295 C14orf37 0 . GRCh38 14 58138568 58138568 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.791A>T p.Asn264Ile p.N264I ENST00000267485 2/8 152 138 14 198 197 1 strelka-varscan-mutect C14orf37,missense_variant,p.Asn264Ile,ENST00000267485,NM_001001872.2;C14orf37,non_coding_transcript_exon_variant,,ENST00000334342,;C14orf37,non_coding_transcript_exon_variant,,ENST00000557175,;C14orf37,downstream_gene_variant,,ENST00000554218,;UBA52P3,upstream_gene_variant,,ENST00000491303,; A ENST00000267485 Transcript missense_variant 986/6495 791/2325 264/774 N/I aAc/aTc 1 -1 C14orf37 HGNC HGNC:19846 protein_coding YES CCDS32089.1 ENSP00000267485 Q86TY3 UPI000000CC37 NM_001001872.2 tolerated(0.09) 2/8 hmmpanther:PTHR21585,hmmpanther:PTHR21585:SF0,Pfam_domain:PF15767 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 58138568 58138568 T A 1 0 0 0 0 1 0 0 0 1838 1725 60 4 4 C14orf37 14 58138568 Missense_Mutation SNP T C3L-01924_T 22377680 58138568 48905150 426 8296 SIX4 0 . GRCh38 14 60714188 60714188 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1565G>T p.Ser522Ile p.S522I ENST00000216513 3/3 87 54 33 107 107 0 strelka-varscan-mutect SIX4,missense_variant,p.Ser522Ile,ENST00000216513,NM_017420.4;SIX4,non_coding_transcript_exon_variant,,ENST00000554079,; A ENST00000216513 Transcript missense_variant 1625/6285 1565/2346 522/781 S/I aGc/aTc 1 -1 SIX4 HGNC HGNC:10890 protein_coding YES CCDS9749.2 ENSP00000216513 Q9UIU6 UPI000066D924 NM_017420.4 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF36 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 60714188 60714188 C A 1 0 0 0 0 1 0 0 0 14612 797 28 2 2 SIX4 14 60714188 Missense_Mutation SNP C C3L-01924_T 2575620 60714188 46329530 427 8297 PSEN1 0 . GRCh38 14 73192665 73192665 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.570C>T p.= p.N190N ENST00000324501 7/12 238 156 82 346 346 0 strelka-varscan-mutect PSEN1,synonymous_variant,p.=,ENST00000324501,NM_000021.3;PSEN1,synonymous_variant,p.=,ENST00000406768,;PSEN1,synonymous_variant,p.=,ENST00000394164,;PSEN1,synonymous_variant,p.=,ENST00000357710,NM_007318.2;PSEN1,synonymous_variant,p.=,ENST00000557511,;PSEN1,synonymous_variant,p.=,ENST00000555386,;PSEN1,synonymous_variant,p.=,ENST00000553855,;RP4-687K1.2,downstream_gene_variant,,ENST00000554078,; T ENST00000324501 Transcript synonymous_variant 842/6078 570/1404 190/467 N aaC/aaT 1 1 PSEN1 HGNC HGNC:9508 protein_coding YES CCDS9812.1 ENSP00000326366 P49768 A0A024R6A3 UPI000003F05F NM_000021.3 7/12 Pfam_domain:PF01080,hmmpanther:PTHR10202,hmmpanther:PTHR10202:SF18,SMART_domains:SM00730 LOW 1 SNV 1 1 PASS rs1260743710 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 73192665 73192665 C T 1 0 0 0 0 0 0 0 1 12801 535 19 1 1 PSEN1 14 73192665 Silent SNP C C3L-01924_T 12478477 73192665 33851053 428 8298 NEK9 0 . GRCh38 14 75109751 75109751 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1116G>T p.= p.R372R ENST00000238616 10/22 238 165 73 299 299 0 strelka-varscan-mutect NEK9,synonymous_variant,p.=,ENST00000238616,NM_033116.4;NEK9,non_coding_transcript_exon_variant,,ENST00000557026,;NEK9,non_coding_transcript_exon_variant,,ENST00000556170,; A ENST00000238616 Transcript synonymous_variant 1275/8310 1116/2940 372/979 R cgG/cgT 1 -1 NEK9 HGNC HGNC:18591 protein_coding YES CCDS9839.1 ENSP00000238616 Q8TD19 UPI00001FD89B NM_033116.4 10/22 Gene3D:2.130.10.30,hmmpanther:PTHR24362,hmmpanther:PTHR24362:SF256,Superfamily_domains:SSF50985 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 75109751 75109751 C A 1 0 0 0 0 0 0 0 1 10359 726 26 2 2 NEK9 14 75109751 Silent SNP C C3L-01924_T 1917086 75109751 31933967 429 8299 NEK9 0 . GRCh38 14 75117271 75117271 + Missense_Mutation SNP T T C C3L-01924_T C3L-01924_N T T c.686A>G p.Asn229Ser p.N229S ENST00000238616 6/22 173 140 33 242 242 0 strelka-varscan-mutect NEK9,missense_variant,p.Asn229Ser,ENST00000238616,NM_033116.4;NEK9,missense_variant,p.Asn111Ser,ENST00000557673,;NEK9,downstream_gene_variant,,ENST00000553823,;NEK9,3_prime_UTR_variant,,ENST00000554258,;NEK9,non_coding_transcript_exon_variant,,ENST00000556170,;NEK9,upstream_gene_variant,,ENST00000557026,;NEK9,downstream_gene_variant,,ENST00000553945,;NEK9,downstream_gene_variant,,ENST00000555961,;HIF1AP1,upstream_gene_variant,,ENST00000553642,; C ENST00000238616 Transcript missense_variant 845/8310 686/2940 229/979 N/S aAt/aGt COSM470261 1 -1 NEK9 HGNC HGNC:18591 protein_coding YES CCDS9839.1 ENSP00000238616 Q8TD19 UPI00001FD89B NM_033116.4 tolerated(0.07) 6/22 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24362,hmmpanther:PTHR24362:SF256,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS rs954321670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 75117271 75117271 T C 1 0 0 0 0 1 0 0 0 10359 1493 52 5 5 NEK9 14 75117271 Missense_Mutation SNP T C3L-01924_T 7520 75117271 31926447 430 8300 ZC3H14 0 . GRCh38 14 88568037 88568037 + Splice_Site SNP A A T novel C3L-01924_T C3L-01924_N A A c.80-2A>T p.X27_splice ENST00000251038 290 178 112 331 331 0 strelka-varscan-mutect ZC3H14,splice_acceptor_variant,,ENST00000251038,NM_001160103.1,NM_024824.4;ZC3H14,splice_acceptor_variant,,ENST00000302216,NM_207660.3;ZC3H14,splice_acceptor_variant,,ENST00000555755,NM_001160104.1;ZC3H14,splice_acceptor_variant,,ENST00000393514,;ZC3H14,splice_acceptor_variant,,ENST00000556945,;ZC3H14,splice_acceptor_variant,,ENST00000336693,NM_207661.2;ZC3H14,splice_acceptor_variant,,ENST00000556158,;ZC3H14,splice_acceptor_variant,,ENST00000555799,;ZC3H14,splice_acceptor_variant,,ENST00000557693,;ZC3H14,5_prime_UTR_variant,,ENST00000554602,;ZC3H14,5_prime_UTR_variant,,ENST00000555120,;ZC3H14,intron_variant,,ENST00000557607,;ZC3H14,upstream_gene_variant,,ENST00000556000,;ZC3H14,splice_acceptor_variant,,ENST00000553495,; T ENST00000251038 Transcript splice_acceptor_variant -/18281 80/2211 27/736 1 1 ZC3H14 HGNC HGNC:20509 protein_coding YES CCDS32133.1 ENSP00000251038 Q6PJT7 UPI00001BDB9B NM_001160103.1,NM_024824.4 2/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 29 88568037 88568037 A T 1 0 0 0 0 0 0 1 0 18141 434 15 4 4 ZC3H14 14 88568037 Splice_Site SNP A C3L-01924_T 13450766 88568037 18475681 431 8301 BTBD7 0 . GRCh38 14 93242548 93242548 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.3124delG p.Ala1042GlnfsTer19 p.A1042Qfs*19 ENST00000334746 11/11 301 180 121 393 393 0 sindel-varindel-pindel BTBD7,frameshift_variant,p.Ala1042GlnfsTer19,ENST00000334746,NM_001002860.3;BTBD7,frameshift_variant,p.Ala691GlnfsTer19,ENST00000554565,NM_001289133.1;BTBD7,frameshift_variant,p.Ala657GlnfsTer19,ENST00000553975,;BTBD7,3_prime_UTR_variant,,ENST00000355125,;RP11-85G20.2,upstream_gene_variant,,ENST00000492041,; - ENST00000334746 Transcript frameshift_variant 3432/8430 3124/3399 1042/1132 A/X Gca/ca 1 -1 BTBD7 HGNC HGNC:18269 protein_coding YES CCDS32146.1 ENSP00000335615 Q9P203 UPI00001FDA78 NM_001002860.3 11/11 hmmpanther:PTHR16064 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 93242548 93242548 C - 1 0 1 0 1 0 0 0 0 1722 739 26 0 0 BTBD7 14 93242548 Frame_Shift_Del DEL C C3L-01924_T 4674511 93242548 13801170 432 8302 GSC 0 . GRCh38 14 94769990 94769990 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.26A>T p.Asp9Val p.D9V ENST00000238558 1/3 125 110 15 136 136 0 strelka-varscan-mutect GSC,missense_variant,p.Asp9Val,ENST00000238558,NM_173849.2; A ENST00000238558 Transcript missense_variant 241/1264 26/774 9/257 D/V gAc/gTc 1 -1 GSC HGNC HGNC:4612 protein_coding YES CCDS9930.1 ENSP00000238558 P56915 UPI000000D86A NM_173849.2 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR24329:SF275,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 94769990 94769990 T A 1 0 0 0 0 1 0 0 0 6696 1667 58 4 4 GSC 14 94769990 Missense_Mutation SNP T C3L-01924_T 1527442 94769990 12273728 433 8303 RTL1 0 . GRCh38 14 100882119 100882119 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.2670G>T p.= p.L890L ENST00000534062 1/1 130 105 25 187 186 1 strelka-varscan-mutect RTL1,synonymous_variant,p.=,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; A ENST00000534062 Transcript synonymous_variant 2729/4193 2670/4077 890/1358 L ctG/ctT 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 1/1 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF9,Superfamily_domains:SSF56672 LOW 1 SNV 1 PASS rs1299749614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 100882119 100882119 C A 1 0 0 0 0 0 0 0 1 13984 813 29 2 2 RTL1 14 100882119 Silent SNP C C3L-01924_T 6112129 100882119 6161599 434 8304 RCOR1 0 . GRCh38 14 102722274 102722274 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.1277A>G p.Asn426Ser p.N426S ENST00000262241 11/12 252 164 88 292 292 0 strelka-varscan-mutect RCOR1,missense_variant,p.Asn426Ser,ENST00000262241,NM_015156.3;RCOR1,3_prime_UTR_variant,,ENST00000560472,;RCOR1,downstream_gene_variant,,ENST00000559597,; G ENST00000262241 Transcript missense_variant 1503/5754 1277/1458 426/485 N/S aAt/aGt 1 1 RCOR1 HGNC HGNC:17441 protein_coding YES CCDS9974.2 ENSP00000262241 J3KN32 UPI0000D6A053 NM_015156.3 tolerated(0.2) 11/12 Gene3D:1.10.10.60,Pfam_domain:PF00249,PROSITE_profiles:PS51293,hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF11,SMART_domains:SM00717,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 3 0 0 0 -20 0.992584 1 1 1 0 G 3 3 29 102722274 102722274 A G 1 0 0 0 0 1 0 0 0 13352 101 4 5 5 RCOR1 14 102722274 Missense_Mutation SNP A C3L-01924_T 1840155 102722274 4321444 435 8305 AHNAK2 0 . GRCh38 14 104943923 104943923 + Missense_Mutation SNP T T G novel C3L-01924_T C3L-01924_N T T c.11528A>C p.Gln3843Pro p.Q3843P ENST00000333244 7/7 360 324 36 393 392 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Gln3843Pro,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; G ENST00000333244 Transcript missense_variant 11648/18254 11528/17388 3843/5795 Q/P cAg/cCg 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.21) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 104943923 104943923 T G 1 0 0 0 0 1 0 0 0 492 1580 55 5 5 AHNAK2 14 104943923 Missense_Mutation SNP T C3L-01924_T 2221649 104943923 2099795 436 8306 32 2 AHNAK2 0 . GRCh38 14 104943925 104943925 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.11526G>T p.Met3842Ile p.M3842I ENST00000333244 7/7 358 322 36 393 392 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Met3842Ile,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript missense_variant 11646/18254 11526/17388 3842/5795 M/I atG/atT 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.59) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 104943925 104943925 C A 1 0 0 0 0 1 0 0 0 492 710 25 2 2 AHNAK2 14 104943925 Missense_Mutation SNP C C3L-01924_T 2 104943925 2099793 437 8307 32 2 GOLGA6L6 0 . GRCh38 15 20535111 20535111 + Silent SNP C C G novel C3L-01924_T C3L-01924_N C C c.1323G>C p.= p.R441R ENST00000619213 8/9 112 105 7 169 169 0 varscan-mutect GOLGA6L6,synonymous_variant,p.=,ENST00000619213,NM_001145004.2; G ENST00000619213 Transcript synonymous_variant 1414/4013 1323/2175 441/724 R cgG/cgC 1 -1 GOLGA6L6 HGNC HGNC:37225 protein_coding YES CCDS45184.1 ENSP00000480376 A8MZA4 A0A087WWN6 UPI000442CF04 NM_001145004.2 8/9 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 20535111 20535111 C G 1 0 0 0 0 0 0 0 1 6442 610 22 4 4 GOLGA6L6 15 20535111 Silent SNP C C3L-01924_T 20535111 81456078 438 8308 NPAP1 0 . GRCh38 15 24677569 24677569 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1702C>A p.Gln568Lys p.Q568K ENST00000329468 1/1 230 165 65 305 305 0 strelka-varscan-mutect NPAP1,missense_variant,p.Gln568Lys,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1702/7526 1702/3471 568/1156 Q/K Cag/Aag 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.35) 1/1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 24677569 24677569 C A 1 0 0 0 0 1 0 0 0 10609 479 17 2 2 NPAP1 15 24677569 Missense_Mutation SNP C C3L-01924_T 4142458 24677569 77313620 439 8309 GABRA5 0 . GRCh38 15 26937213 26937213 + Nonsense_Mutation SNP C C G rs751197696 C3L-01924_T C3L-01924_N C C c.609C>G p.Tyr203Ter p.Y203* ENST00000335625 8/11 226 180 46 259 259 0 strelka-varscan-mutect GABRA5,stop_gained,p.Tyr203Ter,ENST00000335625,NM_000810.3;GABRA5,stop_gained,p.Tyr203Ter,ENST00000400081,NM_001165037.1;GABRA5,stop_gained,p.Tyr203Ter,ENST00000355395,;GABRB3,intron_variant,,ENST00000541819,;GABRA5,downstream_gene_variant,,ENST00000555182,; G ENST00000335625 Transcript stop_gained 1497/3251 609/1389 203/462 Y/* taC/taG rs751197696,COSM2083013 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 8/11 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,TIGRFAM_domain:TIGR00860 0,1 HIGH 1 SNV 1 0,1 1 PASS rs751197696 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 29 26937213 26937213 C G 1 0 0 0 0 0 1 0 0 6035 547 19 4 4 GABRA5 15 26937213 Nonsense_Mutation SNP C C3L-01924_T 2259644 26937213 75053976 440 8310 CHRNA7 0 . GRCh38 15 32157645 32157645 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.555G>T p.Trp185Cys p.W185C ENST00000454250 6/10 139 106 33 165 165 0 strelka-varscan-mutect CHRNA7,missense_variant,p.Trp156Cys,ENST00000306901,NM_000746.5;CHRNA7,missense_variant,p.Trp94Cys,ENST00000637033,;CHRNA7,missense_variant,p.Trp77Cys,ENST00000637183,;CHRNA7,missense_variant,p.Trp185Cys,ENST00000454250,NM_001190455.2;CHRNA7,missense_variant,p.Trp94Cys,ENST00000636603,;CHRNA7,missense_variant,p.Trp94Cys,ENST00000635884,;CHRNA7,missense_variant,p.Trp156Cys,ENST00000637552,;CHRNA7,missense_variant,p.Trp77Cys,ENST00000635978,;CHRNA7,missense_variant,p.Trp163Cys,ENST00000636440,;CHRNA7,missense_variant,p.Trp12Cys,ENST00000638081,;CHRNA7,5_prime_UTR_variant,,ENST00000638106,;CHRNA7,upstream_gene_variant,,ENST00000637348,;CHRNA7,upstream_gene_variant,,ENST00000635883,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636245,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636957,;CHRNA7,missense_variant,p.Gly171Val,ENST00000637350,;CHRNA7,missense_variant,p.Trp104Cys,ENST00000636271,;CHRNA7,missense_variant,p.Gly93Val,ENST00000437966,;CHRNA7,missense_variant,p.Val130Phe,ENST00000636044,;CHRNA7,3_prime_UTR_variant,,ENST00000637519,;CHRNA7,3_prime_UTR_variant,,ENST00000637971,;CHRNA7,3_prime_UTR_variant,,ENST00000638031,;CHRNA7,3_prime_UTR_variant,,ENST00000635722,;CHRNA7,3_prime_UTR_variant,,ENST00000636850,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636709,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000637189,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636292,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636898,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636647,;CHRNA7,non_coding_transcript_exon_variant,,ENST00000636521,;CHRNA7,upstream_gene_variant,,ENST00000637649,; T ENST00000454250 Transcript missense_variant 662/2093 555/1596 185/531 W/C tgG/tgT 1 1 CHRNA7 HGNC HGNC:1960 protein_coding YES CCDS53924.1 ENSP00000407546 P36544 UPI0000E23BA6 NM_001190455.2 deleterious(0) 6/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF572,PROSITE_patterns:PS00236,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 2 1 PASS . . 25 185 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 32157645 32157645 G T 1 0 0 0 0 1 0 0 0 3148 1270 44 2 2 CHRNA7 15 32157645 Missense_Mutation SNP G C3L-01924_T 5220432 32157645 69833544 441 8311 ACTC1 0 . GRCh38 15 34794746 34794746 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.63C>A p.= p.A21A ENST00000290378 2/7 133 115 18 122 122 0 strelka-varscan-mutect ACTC1,synonymous_variant,p.=,ENST00000290378,NM_005159.4;RP11-814P5.1,intron_variant,,ENST00000503496,;RP11-814P5.1,downstream_gene_variant,,ENST00000558707,;ACTC1,upstream_gene_variant,,ENST00000557860,;ACTC1,upstream_gene_variant,,ENST00000560563,; T ENST00000290378 Transcript synonymous_variant 719/4106 63/1134 21/377 A gcC/gcA 1 -1 ACTC1 HGNC HGNC:143 protein_coding YES CCDS10041.1 ENSP00000290378 P68032 UPI0000003F15 NM_005159.4 2/7 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF238,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 34794746 34794746 G T 1 0 0 0 0 0 0 0 1 238 1103 39 1 1 ACTC1 15 34794746 Silent SNP G C3L-01924_T 2637101 34794746 67196443 442 8312 EIF2AK4 0 . GRCh38 15 39998780 39998780 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.2918A>T p.Lys973Met p.K973M ENST00000263791 20/39 209 165 44 228 228 0 strelka-varscan-mutect EIF2AK4,missense_variant,p.Lys973Met,ENST00000263791,NM_001013703.3;EIF2AK4,missense_variant,p.Lys751Met,ENST00000560855,;EIF2AK4,upstream_gene_variant,,ENST00000559311,;EIF2AK4,non_coding_transcript_exon_variant,,ENST00000558629,;EIF2AK4,upstream_gene_variant,,ENST00000558557,; T ENST00000263791 Transcript missense_variant 2961/5499 2918/4950 973/1649 K/M aAg/aTg 1 1 EIF2AK4 HGNC HGNC:19687 protein_coding YES CCDS42016.1 ENSP00000263791 Q9P2K8 UPI0000160791 NM_001013703.3 deleterious(0.03) 20/39 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF90,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 39998780 39998780 A T 1 0 0 0 0 1 0 0 0 4835 86 3 4 4 EIF2AK4 15 39998780 Missense_Mutation SNP A C3L-01924_T 5204034 39998780 61992409 443 8313 SPINT1 0 . GRCh38 15 40844738 40844738 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.184G>T p.Val62Leu p.V62L ENST00000344051 2/11 125 86 39 157 157 0 strelka-varscan-mutect SPINT1,missense_variant,p.Val62Leu,ENST00000344051,NM_181642.2;SPINT1,missense_variant,p.Val62Leu,ENST00000562057,NM_003710.3,NM_001032367.1;SPINT1,missense_variant,p.Val22Leu,ENST00000568580,;SPINT1,missense_variant,p.Val62Leu,ENST00000563656,;SPINT1,missense_variant,p.Val124Leu,ENST00000568823,;RP11-532F12.5,upstream_gene_variant,,ENST00000564302,;RP11-532F12.5,upstream_gene_variant,,ENST00000565315,;RP11-532F12.5,upstream_gene_variant,,ENST00000568419,;RP11-532F12.5,upstream_gene_variant,,ENST00000568525,;RP11-532F12.5,upstream_gene_variant,,ENST00000563217,; T ENST00000344051 Transcript missense_variant 418/3056 184/1590 62/529 V/L Gtg/Ttg 1 1 SPINT1 HGNC HGNC:11246 protein_coding YES CCDS10067.1 ENSP00000342098 O43278 UPI00001AE46F NM_181642.2 deleterious(0) 2/11 PROSITE_profiles:PS50986,hmmpanther:PTHR10083:SF231,hmmpanther:PTHR10083,Pfam_domain:PF07502,SMART_domains:SM00765 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 40844738 40844738 G T 1 0 0 0 0 1 0 0 0 15420 1145 40 1 1 SPINT1 15 40844738 Missense_Mutation SNP G C3L-01924_T 845958 40844738 61146451 444 8314 ZNF106 0 . GRCh38 15 42450315 42450315 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1888C>G p.Arg630Gly p.R630G ENST00000263805 2/19 171 158 13 208 208 0 strelka-varscan-mutect ZNF106,missense_variant,p.Arg630Gly,ENST00000263805,NM_022473.2;ZNF106,missense_variant,p.Arg413Gly,ENST00000565948,;ZNF106,intron_variant,,ENST00000565380,NM_001284307.1;ZNF106,intron_variant,,ENST00000565611,NM_001284306.1;ZNF106,upstream_gene_variant,,ENST00000565500,;ZNF106,downstream_gene_variant,,ENST00000564754,;ZNF106,upstream_gene_variant,,ENST00000567772,;ZNF106,downstream_gene_variant,,ENST00000567041,; C ENST00000263805 Transcript missense_variant 2215/10460 1888/5652 630/1883 R/G Cgc/Ggc 1 -1 ZNF106 HGNC HGNC:12886 protein_coding YES CCDS32208.1 ENSP00000263805 Q9H2Y7 UPI000006D6CC NM_022473.2 tolerated(0.14) 2/19 hmmpanther:PTHR14435 MODERATE 1 SNV 1 1 PASS rs1186725179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 42450315 42450315 G C 1 0 0 0 0 1 0 0 0 18294 1116 39 4 4 ZNF106 15 42450315 Missense_Mutation SNP G C3L-01924_T 1605577 42450315 59540874 445 8315 RORA 0 . GRCh38 15 60511239 60511239 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.906C>T p.= p.S302S ENST00000261523 6/12 73 65 8 105 105 0 strelka-varscan-mutect RORA,synonymous_variant,p.=,ENST00000335670,NM_134261.2;RORA,synonymous_variant,p.=,ENST00000261523,NM_134260.2;RORA,synonymous_variant,p.=,ENST00000309157,NM_002943.3;RORA,synonymous_variant,p.=,ENST00000449337,NM_134262.2;RORA,downstream_gene_variant,,ENST00000559343,;RORA-AS1,intron_variant,,ENST00000558140,;RORA-AS1,intron_variant,,ENST00000501579,;RORA-AS1,intron_variant,,ENST00000559824,;RORA-AS1,intron_variant,,ENST00000559902,;RORA-AS1,intron_variant,,ENST00000558235,;RORA,non_coding_transcript_exon_variant,,ENST00000559587,;RORA,downstream_gene_variant,,ENST00000560004,;RORA,downstream_gene_variant,,ENST00000551975,; A ENST00000261523 Transcript synonymous_variant 995/1951 906/1671 302/556 S tcC/tcT 1 -1 RORA HGNC HGNC:10258 protein_coding YES CCDS10179.1 ENSP00000261523 P35398 UPI0000134548 NM_134260.2 6/12 Prints_domain:PR01293,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF318 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -17.82414 1 1 1 1 0 A 2 1 29 60511239 60511239 G A 1 0 0 0 0 0 0 0 1 13705 1335 47 3 3 RORA 15 60511239 Silent SNP G C3L-01924_T 18060924 60511239 41479950 446 8316 SNX22 0 . GRCh38 15 64153678 64153678 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.386A>G p.Asp129Gly p.D129G ENST00000325881 5/7 224 190 34 264 264 0 strelka-varscan-mutect SNX22,missense_variant,p.Asp129Gly,ENST00000325881,NM_024798.2;PPIB,downstream_gene_variant,,ENST00000300026,NM_000942.4;PPIB,downstream_gene_variant,,ENST00000558492,;SNX22,3_prime_UTR_variant,,ENST00000558466,;SNX22,non_coding_transcript_exon_variant,,ENST00000557789,;SNX22,non_coding_transcript_exon_variant,,ENST00000560997,;SNX22,non_coding_transcript_exon_variant,,ENST00000561334,;SNX22,non_coding_transcript_exon_variant,,ENST00000560945,;SNX22,non_coding_transcript_exon_variant,,ENST00000560607,; G ENST00000325881 Transcript missense_variant 445/3614 386/582 129/193 D/G gAc/gGc 1 1 SNX22 HGNC HGNC:16315 protein_coding YES CCDS10190.1 ENSP00000323435 Q96L94 A0A024R5Y5 UPI0000135B52 NM_024798.2 tolerated(0.06) 5/7 hmmpanther:PTHR15813:SF8,hmmpanther:PTHR15813 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 64153678 64153678 A G 1 0 0 0 0 1 0 0 0 15215 275 10 5 5 SNX22 15 64153678 Missense_Mutation SNP A C3L-01924_T 3642439 64153678 37837511 447 8317 KBTBD13 0 . GRCh38 15 65077507 65077507 + Missense_Mutation SNP A A T rs746972923 C3L-01924_T C3L-01924_N A A c.692A>T p.Tyr231Phe p.Y231F ENST00000432196 1/1 46 41 5 51 51 0 strelka-varscan-mutect KBTBD13,missense_variant,p.Tyr231Phe,ENST00000432196,NM_001101362.2;RASL12,upstream_gene_variant,,ENST00000434605,; T ENST00000432196 Transcript missense_variant 692/1377 692/1377 231/458 Y/F tAc/tTc rs746972923 1 1 KBTBD13 HGNC HGNC:37227 protein_coding YES CCDS45281.1 ENSP00000388723 C9JR72 UPI0000161560 NM_001101362.2 deleterious(0.03) 1/1 hmmpanther:PTHR24412:SF57,hmmpanther:PTHR24412,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 PASS rs746972923 . 0 208 2 0 0 0 0 0 -13.00555 1 1 1 1 0 T 3 4 29 65077507 65077507 A T 1 0 0 0 0 1 0 0 0 7909 391 14 4 4 KBTBD13 15 65077507 Missense_Mutation SNP A C3L-01924_T 923829 65077507 36913682 448 8318 ITGA11 0 . GRCh38 15 68320337 68320337 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.2464C>G p.Leu822Val p.L822V ENST00000315757 20/30 179 154 25 209 209 0 strelka-varscan-mutect ITGA11,missense_variant,p.Leu822Val,ENST00000423218,;ITGA11,missense_variant,p.Leu822Val,ENST00000315757,NM_001004439.1; C ENST00000315757 Transcript missense_variant 2560/3955 2464/3567 822/1188 L/V Ctg/Gtg 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 tolerated(0.42) 20/30 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF21,Gene3D:2.60.40.1510,Pfam_domain:PF08441 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 68320337 68320337 G C 1 0 0 0 0 1 0 0 0 7781 962 34 4 4 ITGA11 15 68320337 Missense_Mutation SNP G C3L-01924_T 3242830 68320337 33670852 449 8319 LOXL1 0 . GRCh38 15 73946494 73946494 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1289G>T p.Gly430Val p.G430V ENST00000261921 3/7 170 144 26 203 203 0 strelka-varscan-mutect LOXL1,missense_variant,p.Gly430Val,ENST00000261921,NM_005576.2;LOXL1,upstream_gene_variant,,ENST00000567675,;LOXL1,3_prime_UTR_variant,,ENST00000566011,;LOXL1,non_coding_transcript_exon_variant,,ENST00000566530,;LOXL1,upstream_gene_variant,,ENST00000562548,; T ENST00000261921 Transcript missense_variant 1615/2351 1289/1725 430/574 G/V gGc/gTc 1 1 LOXL1 HGNC HGNC:6665 protein_coding YES CCDS10253.1 ENSP00000261921 Q08397 UPI000013D224 NM_005576.2 deleterious(0) 3/7 hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF4,Pfam_domain:PF01186,Prints_domain:PR00074 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 73946494 73946494 G T 1 0 0 0 0 1 0 0 0 8802 1203 42 2 2 LOXL1 15 73946494 Missense_Mutation SNP G C3L-01924_T 5626157 73946494 28044695 450 8320 GOLGA6A 0 . GRCh38 15 74074926 74074926 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.923G>T p.Arg308Met p.R308M ENST00000290438 11/18 129 122 7 164 164 0 varscan-mutect GOLGA6A,missense_variant,p.Arg308Met,ENST00000290438,NM_001038640.2;RN7SL429P,upstream_gene_variant,,ENST00000479090,;GOLGA6A,upstream_gene_variant,,ENST00000562157,;GOLGA6A,downstream_gene_variant,,ENST00000568723,;GOLGA6A,upstream_gene_variant,,ENST00000569486,; A ENST00000290438 Transcript missense_variant 964/3176 923/2082 308/693 R/M aGg/aTg 1 -1 GOLGA6A HGNC HGNC:13567 protein_coding YES CCDS32290.1 ENSP00000290438 Q9NYA3 UPI00001AEB5B NM_001038640.2 deleterious(0) 11/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF47 MODERATE 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 74074926 74074926 C A 1 0 0 0 0 1 0 0 0 6435 681 24 2 2 GOLGA6A 15 74074926 Missense_Mutation SNP C C3L-01924_T 128432 74074926 27916263 451 8321 HYKK 0 . GRCh38 15 78513397 78513397 + Silent SNP A A G novel C3L-01924_T C3L-01924_N A A c.309A>G p.= p.G103G ENST00000569878 1/4 118 110 8 170 170 0 strelka-varscan-mutect HYKK,synonymous_variant,p.=,ENST00000569878,;HYKK,synonymous_variant,p.=,ENST00000566332,;HYKK,synonymous_variant,p.=,ENST00000388988,NM_001013619.2;HYKK,synonymous_variant,p.=,ENST00000408962,NM_001083612.1;HYKK,synonymous_variant,p.=,ENST00000563233,;HYKK,synonymous_variant,p.=,ENST00000566289,; G ENST00000569878 Transcript synonymous_variant 309/4097 309/1122 103/373 G ggA/ggG 1 1 HYKK HGNC HGNC:34403 protein_coding YES CCDS42063.1 ENSP00000455459 A2RU49 UPI0000366A7F 1/4 Pfam_domain:PF01636,hmmpanther:PTHR21064,hmmpanther:PTHR21064:SF1,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 78513397 78513397 A G 1 0 0 0 0 0 0 0 1 7365 291 11 5 5 HYKK 15 78513397 Silent SNP A C3L-01924_T 4438471 78513397 23477792 452 8322 CHRNA3 0 . GRCh38 15 78602124 78602124 + Missense_Mutation SNP C C G rs555968931 C3L-01924_T C3L-01924_N C C c.518G>C p.Cys173Ser p.C173S ENST00000326828 5/6 190 165 25 230 230 0 strelka-varscan-mutect CHRNA3,missense_variant,p.Cys173Ser,ENST00000326828,NM_000743.4;CHRNA3,missense_variant,p.Cys173Ser,ENST00000348639,NM_001166694.1;CHRNA3,non_coding_transcript_exon_variant,,ENST00000558903,;RP11-335K5.3,upstream_gene_variant,,ENST00000624172,;CHRNA3,missense_variant,p.Cys173Ser,ENST00000559658,; G ENST00000326828 Transcript missense_variant 903/3202 518/1518 173/505 C/S tGt/tCt rs555968931 1 -1 CHRNA3 HGNC HGNC:1957 protein_coding YES CCDS10305.1 ENSP00000315602 P32297 UPI000013D783 NM_000743.4 deleterious(0) 5/6 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF445,PROSITE_patterns:PS00236,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS rs555968931 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 78602124 78602124 C G 1 0 0 0 0 1 0 0 0 3144 478 17 4 4 CHRNA3 15 78602124 Missense_Mutation SNP C C3L-01924_T 88727 78602124 23389065 453 8323 SAXO2 0 . GRCh38 15 82271802 82271802 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.253G>T p.Asp85Tyr p.D85Y ENST00000339465 2/3 120 101 19 170 170 0 varscan-mutect SAXO2,missense_variant,p.Asp85Tyr,ENST00000339465,NM_001008226.1;SAXO2,missense_variant,p.Gly98Cys,ENST00000565432,;SAXO2,splice_region_variant,,ENST00000565501,; T ENST00000339465 Transcript missense_variant,splice_region_variant 322/3134 253/1197 85/398 D/Y Gac/Tac 1 1 SAXO2 HGNC HGNC:33727 protein_coding YES CCDS32310.1 ENSP00000340445 Q658L1 UPI00001D779A NM_001008226.1 deleterious(0) 2/3 hmmpanther:PTHR31516:SF6,hmmpanther:PTHR31516 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 82271802 82271802 G T 1 0 0 0 0 1 0 0 0 14119 1014 35 2 2 SAXO2 15 82271802 Missense_Mutation SNP G C3L-01924_T 3669678 82271802 19719387 454 8324 ADAMTSL3 0 . GRCh38 15 83892713 83892713 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1292C>G p.Ser431Cys p.S431C ENST00000286744 13/30 218 171 47 340 340 0 strelka-varscan-mutect ADAMTSL3,missense_variant,p.Ser431Cys,ENST00000286744,NM_207517.2;ADAMTSL3,missense_variant,p.Ser431Cys,ENST00000567476,NM_001301110.1;ADAMTSL3,downstream_gene_variant,,ENST00000567663,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,; G ENST00000286744 Transcript missense_variant 1516/7336 1292/5076 431/1691 S/C tCc/tGc 1 1 ADAMTSL3 HGNC HGNC:14633 protein_coding YES CCDS10326.1 ENSP00000286744 P82987 UPI00001615A5 NM_207517.2 deleterious(0) 13/30 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF169,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 83892713 83892713 C G 1 0 0 0 0 1 0 0 0 320 855 30 4 4 ADAMTSL3 15 83892713 Missense_Mutation SNP C C3L-01924_T 1620911 83892713 18098476 455 8325 ACAN 0 . GRCh38 15 88856853 88856853 + Missense_Mutation SNP C C A rs759176877 C3L-01924_T C3L-01924_N C C c.4268C>A p.Ala1423Asp p.A1423D ENST00000439576 12/18 376 309 67 497 497 0 strelka-varscan-mutect ACAN,missense_variant,p.Ala1423Asp,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Ala1404Asp,ENST00000617301,;ACAN,missense_variant,p.Ala1423Asp,ENST00000559004,;ACAN,missense_variant,p.Ala1423Asp,ENST00000561243,;ACAN,missense_variant,p.Ala1423Asp,ENST00000352105,NM_001135.3;ACAN,upstream_gene_variant,,ENST00000560601,; A ENST00000439576 Transcript missense_variant 4642/8840 4268/7593 1423/2530 A/D gCc/gAc rs759176877 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 tolerated(0.21) 12/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 MODERATE 1 SNV 5 1 PASS rs759176877 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 88856853 88856853 C A 1 0 0 0 0 1 0 0 0 160 739 26 2 2 ACAN 15 88856853 Missense_Mutation SNP C C3L-01924_T 4964140 88856853 13134336 456 8326 PIGQ 0 . GRCh38 16 574625 574625 + Missense_Mutation SNP G G T rs755768099 C3L-01924_T C3L-01924_N G G c.551G>T p.Gly184Val p.G184V ENST00000026218 2/10 149 138 11 128 128 0 strelka-varscan-mutect PIGQ,missense_variant,p.Gly184Val,ENST00000321878,NM_004204.3;PIGQ,missense_variant,p.Gly184Val,ENST00000026218,NM_148920.2;PIGQ,missense_variant,p.Gly184Val,ENST00000470411,;PIGQ,missense_variant,p.Gly184Val,ENST00000422307,;PIGQ,missense_variant,p.Gly184Val,ENST00000409527,;PIGQ,upstream_gene_variant,,ENST00000540241,;PIGQ,downstream_gene_variant,,ENST00000293874,;PIGQ,downstream_gene_variant,,ENST00000439574,;LA16c-407A10.3,non_coding_transcript_exon_variant,,ENST00000635107,;LA16c-407A10.3,non_coding_transcript_exon_variant,,ENST00000409439,;PIGQ,upstream_gene_variant,,ENST00000635935,;PIGQ,upstream_gene_variant,,ENST00000544860,;PIGQ,downstream_gene_variant,,ENST00000637701,;PIGQ,missense_variant,p.Gly198Val,ENST00000443147,;PIGQ,3_prime_UTR_variant,,ENST00000636657,;PIGQ,intron_variant,,ENST00000635909,;PIGQ,upstream_gene_variant,,ENST00000480424,;PIGQ,upstream_gene_variant,,ENST00000636005,;PIGQ,upstream_gene_variant,,ENST00000635205,;PIGQ,upstream_gene_variant,,ENST00000420990,;PIGQ,upstream_gene_variant,,ENST00000637468,;PIGQ,upstream_gene_variant,,ENST00000638143,;PIGQ,upstream_gene_variant,,ENST00000537901,; T ENST00000026218 Transcript missense_variant 639/2846 551/2283 184/760 G/V gGc/gTc rs755768099 1 1 PIGQ HGNC HGNC:14135 protein_coding YES CCDS10411.1 ENSP00000026218 Q9BRB3 UPI000006CC88 NM_148920.2 deleterious_low_confidence(0.03) 2/10 hmmpanther:PTHR21329,hmmpanther:PTHR21329:SF3 MODERATE 1 SNV 1 1 PASS rs755768099 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 574625 574625 G T 1 0 0 0 0 1 0 0 0 11990 1203 42 2 2 PIGQ 16 574625 Missense_Mutation SNP G C3L-01924_T 574625 89763720 457 8327 SOX8 0 . GRCh38 16 983873 983873 + Missense_Mutation SNP G G A C3L-01924_T C3L-01924_N G G c.568G>A p.Ala190Thr p.A190T ENST00000293894 2/3 106 99 7 89 89 0 strelka-varscan-mutect SOX8,missense_variant,p.Ala190Thr,ENST00000293894,NM_014587.4;LMF1,upstream_gene_variant,,ENST00000570014,;RP11-161M6.2,upstream_gene_variant,,ENST00000565467,;RP11-161M6.2,upstream_gene_variant,,ENST00000568394,;RP11-161M6.2,upstream_gene_variant,,ENST00000562570,;RP11-161M6.2,upstream_gene_variant,,ENST00000563863,;RP11-161M6.2,upstream_gene_variant,,ENST00000565069,;RP11-161M6.2,upstream_gene_variant,,ENST00000563837,;SOX8,non_coding_transcript_exon_variant,,ENST00000566034,;LMF1,upstream_gene_variant,,ENST00000545827,; A ENST00000293894 Transcript missense_variant 683/3049 568/1341 190/446 A/T Gcg/Acg COSM1380647 1 1 SOX8 HGNC HGNC:11203 protein_coding YES CCDS10428.1 ENSP00000293894 P57073 UPI00000015FB NM_014587.4 tolerated(0.4) 2/3 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF20 1 MODERATE 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -14.00218 0.9999975 1 1 1 0 A 3 1 29 983873 983873 G A 1 0 0 0 0 1 0 0 0 15283 1087 38 1 1 SOX8 16 983873 Missense_Mutation SNP G C3L-01924_T 409248 983873 89354472 458 8328 CASKIN1 0 . GRCh38 16 2189319 2189319 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.405A>T p.= p.L135L ENST00000343516 5/20 297 265 32 298 297 1 strelka-varscan-mutect CASKIN1,synonymous_variant,p.=,ENST00000343516,NM_020764.3;CASKIN1,upstream_gene_variant,,ENST00000564289,;CASKIN1,non_coding_transcript_exon_variant,,ENST00000562055,; A ENST00000343516 Transcript synonymous_variant 498/5759 405/4296 135/1431 L ctA/ctT 1 -1 CASKIN1 HGNC HGNC:20879 protein_coding YES CCDS42103.1 ENSP00000345436 Q8WXD9 UPI0000073A3B NM_020764.3 5/20 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24177:SF12,hmmpanther:PTHR24177,Gene3D:1.25.40.20,Pfam_domain:PF13637,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 2189319 2189319 T A 1 0 0 0 0 0 0 0 1 2366 1625 57 4 4 CASKIN1 16 2189319 Silent SNP T C3L-01924_T 1205446 2189319 88149026 459 8329 PPL 0 . GRCh38 16 4883545 4883545 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.5110A>G p.Asn1704Asp p.N1704D ENST00000345988 22/22 173 132 41 163 163 0 strelka-varscan-mutect PPL,missense_variant,p.Asn1704Asp,ENST00000345988,NM_002705.4;PPL,missense_variant,p.Asn1702Asp,ENST00000590782,;UBN1,downstream_gene_variant,,ENST00000396658,;UBN1,downstream_gene_variant,,ENST00000262376,NM_001079514.2;PPL,downstream_gene_variant,,ENST00000592772,;UBN1,downstream_gene_variant,,ENST00000590769,NM_001288656.1;UBN1,downstream_gene_variant,,ENST00000589191,; C ENST00000345988 Transcript missense_variant 5200/6238 5110/5271 1704/1756 N/D Aat/Gat 1 -1 PPL HGNC HGNC:9273 protein_coding YES CCDS10526.1 ENSP00000340510 O60437 UPI00001AE832 NM_002705.4 tolerated(0.19) 22/22 hmmpanther:PTHR23169,SMART_domains:SM00250,Superfamily_domains:SSF75399 MODERATE 1 SNV 1 1 PASS rs1346444200 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 4883545 4883545 T C 1 0 0 0 0 1 0 0 0 12444 1812 63 5 5 PPL 16 4883545 Missense_Mutation SNP T C3L-01924_T 2694226 4883545 85454800 460 8330 TXNDC11 0 . GRCh38 16 11692044 11692044 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.1227G>T p.= p.G409G ENST00000356957 9/13 28 23 5 40 40 0 strelka-varscan-mutect TXNDC11,synonymous_variant,p.=,ENST00000356957,NM_001303447.1;TXNDC11,synonymous_variant,p.=,ENST00000283033,NM_015914.6;TXNDC11,synonymous_variant,p.=,ENST00000575591,;TXNDC11,upstream_gene_variant,,ENST00000570917,;TXNDC11,3_prime_UTR_variant,,ENST00000576969,;TXNDC11,non_coding_transcript_exon_variant,,ENST00000572732,;TXNDC11,downstream_gene_variant,,ENST00000571882,;TXNDC11,upstream_gene_variant,,ENST00000575349,; A ENST00000356957 Transcript synonymous_variant 1335/3178 1227/2958 409/985 G ggG/ggT 1 -1 TXNDC11 HGNC HGNC:28030 protein_coding YES CCDS76822.1 ENSP00000349439 Q6PKC3 UPI000041D75B NM_001303447.1 9/13 LOW 1 SNV 1 1 PASS rs1470590332 . 1 207 2 0 0 0 0 0 -14.35304 1 1 1 1 0 A 2 1 29 11692044 11692044 C A 1 0 0 0 0 0 0 0 1 17308 610 22 2 2 TXNDC11 16 11692044 Silent SNP C C3L-01924_T 6808499 11692044 78646301 461 8331 KNOP1 0 . GRCh38 16 19714144 19714144 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.892G>T p.Gly298Trp p.G298W ENST00000219837 2/5 134 119 15 146 144 2 strelka-varscan-mutect KNOP1,missense_variant,p.Gly298Trp,ENST00000219837,NM_001012991.2;KNOP1,missense_variant,p.Gly146Trp,ENST00000567367,;IQCK,upstream_gene_variant,,ENST00000320394,NM_153208.1;KNOP1,upstream_gene_variant,,ENST00000568230,;KNOP1,downstream_gene_variant,,ENST00000564480,;IQCK,upstream_gene_variant,,ENST00000564186,;AC002550.5,intron_variant,,ENST00000565916,;KNOP1,non_coding_transcript_exon_variant,,ENST00000565844,;IQCK,upstream_gene_variant,,ENST00000308214,;IQCK,upstream_gene_variant,,ENST00000568300,;IQCK,upstream_gene_variant,,ENST00000568126,;IQCK,upstream_gene_variant,,ENST00000561839,;IQCK,upstream_gene_variant,,ENST00000564955,;IQCK,upstream_gene_variant,,ENST00000561935,;IQCK,upstream_gene_variant,,ENST00000564515,;IQCK,upstream_gene_variant,,ENST00000566312,; A ENST00000219837 Transcript missense_variant 971/6432 892/1377 298/458 G/W Ggg/Tgg 1 -1 KNOP1 HGNC HGNC:34404 protein_coding YES CCDS42127.1 ENSP00000219837 Q1ED39 UPI00001982F5 NM_001012991.2 deleterious(0.02) 2/5 hmmpanther:PTHR22426 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 19714144 19714144 C A 1 0 0 0 0 1 0 0 0 8306 594 21 2 2 KNOP1 16 19714144 Missense_Mutation SNP C C3L-01924_T 8022100 19714144 70624201 462 8332 ZP2 0 . GRCh38 16 21201744 21201744 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1466A>T p.Lys489Met p.K489M ENST00000574002 14/20 216 167 49 223 222 1 strelka-varscan-mutect ZP2,missense_variant,p.Lys489Met,ENST00000574002,NM_003460.2;ZP2,missense_variant,p.Lys480Met,ENST00000574091,NM_001290104.1;AF001550.7,intron_variant,,ENST00000572747,;ZP2,downstream_gene_variant,,ENST00000576162,;ZP2,downstream_gene_variant,,ENST00000572752,;ZP2,downstream_gene_variant,,ENST00000573114,; A ENST00000574002 Transcript missense_variant 1949/2749 1466/2238 489/745 K/M aAg/aTg 1 -1 ZP2 HGNC HGNC:13188 protein_coding YES CCDS10596.1 ENSP00000460971 Q05996 UPI000013C45C NM_003460.2 deleterious(0) 14/20 PROSITE_profiles:PS51034,hmmpanther:PTHR23343:SF4,hmmpanther:PTHR23343,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 1 1 PASS rs1488853858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 21201744 21201744 T A 1 0 0 0 0 1 0 0 0 18808 1609 56 4 4 ZP2 16 21201744 Missense_Mutation SNP T C3L-01924_T 1487600 21201744 69136601 463 8333 EEF2K 0 . GRCh38 16 22257652 22257652 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.911G>T p.Gly304Val p.G304V ENST00000263026 9/18 115 96 19 135 135 0 strelka-varscan-mutect EEF2K,missense_variant,p.Gly304Val,ENST00000263026,NM_013302.3;EEF2K,missense_variant,p.Gly304Val,ENST00000568269,;EEF2K,non_coding_transcript_exon_variant,,ENST00000563555,; T ENST00000263026 Transcript missense_variant 1385/7388 911/2178 304/725 G/V gGg/gTg 1 1 EEF2K HGNC HGNC:24615 protein_coding YES CCDS10604.1 ENSP00000263026 O00418 UPI000013D387 NM_013302.3 deleterious(0) 9/18 PROSITE_profiles:PS51158,hmmpanther:PTHR14187,Pfam_domain:PF02816,PIRSF_domain:PIRSF038139,SMART_domains:SM00811,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 22257652 22257652 G T 1 0 0 0 0 1 0 0 0 4760 1232 43 2 2 EEF2K 16 22257652 Missense_Mutation SNP G C3L-01924_T 1055908 22257652 68080693 464 8334 IL21R 0 . GRCh38 16 27437626 27437626 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.291C>A p.Asn97Lys p.N97K ENST00000337929 4/9 416 382 34 414 414 0 strelka-varscan-mutect IL21R,missense_variant,p.Asn97Lys,ENST00000337929,NM_181078.2;IL21R,missense_variant,p.Asn97Lys,ENST00000564089,NM_181079.4;IL21R,missense_variant,p.Asn97Lys,ENST00000395754,NM_021798.3; A ENST00000337929 Transcript missense_variant 764/4849 291/1617 97/538 N/K aaC/aaA 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 deleterious(0.01) 4/9 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 27437626 27437626 C A 1 0 0 0 0 1 0 0 0 7574 477 17 2 2 IL21R 16 27437626 Missense_Mutation SNP C C3L-01924_T 5179974 27437626 62900719 465 8335 GTF3C1 0 . GRCh38 16 27489629 27489629 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.3266G>T p.Arg1089Leu p.R1089L ENST00000356183 20/37 173 147 26 168 168 0 strelka-varscan-mutect GTF3C1,missense_variant,p.Arg1089Leu,ENST00000356183,NM_001520.3;GTF3C1,missense_variant,p.Arg1089Leu,ENST00000561623,NM_001286242.1;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,upstream_gene_variant,,ENST00000568569,;GTF3C1,upstream_gene_variant,,ENST00000570129,;GTF3C1,upstream_gene_variant,,ENST00000564664,; A ENST00000356183 Transcript missense_variant 3282/7018 3266/6330 1089/2109 R/L cGc/cTc COSM1377027 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 deleterious(0.02) 20/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 1 MODERATE 1 SNV 1 1 1 PASS rs1167472934 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 27489629 27489629 C A 1 0 0 0 0 1 0 0 0 6753 768 27 1 1 GTF3C1 16 27489629 Missense_Mutation SNP C C3L-01924_T 52003 27489629 62848716 466 8336 SEZ6L2 0 . GRCh38 16 29880025 29880025 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1412A>T p.His471Leu p.H471L ENST00000617533 9/18 182 167 15 186 186 0 strelka-varscan-mutect SEZ6L2,missense_variant,p.His471Leu,ENST00000308713,NM_201575.3,NM_001114099.2;SEZ6L2,missense_variant,p.His471Leu,ENST00000617533,NM_001243332.1;SEZ6L2,missense_variant,p.His427Leu,ENST00000537485,NM_001243333.1;SEZ6L2,missense_variant,p.His401Leu,ENST00000350527,NM_012410.3;SEZ6L2,missense_variant,p.His357Leu,ENST00000346932,NM_001114100.2;SEZ6L2,intron_variant,,ENST00000563118,;SEZ6L2,non_coding_transcript_exon_variant,,ENST00000568407,; A ENST00000617533 Transcript missense_variant 1657/3555 1412/2772 471/923 H/L cAt/cTt 1 -1 SEZ6L2 HGNC HGNC:30844 protein_coding YES CCDS73865.1 ENSP00000481917 A0A087WYL5 UPI00001FFE46 NM_001243332.1 tolerated(0.07) 9/18 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF92,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 29880025 29880025 T A 1 0 0 0 0 1 0 0 0 14423 1464 51 4 4 SEZ6L2 16 29880025 Missense_Mutation SNP T C3L-01924_T 2390396 29880025 60458320 467 8337 SRCAP 0 . GRCh38 16 30722597 30722597 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.3741G>T p.Gln1247His p.Q1247H ENST00000262518 23/34 182 143 39 126 126 0 strelka-varscan-mutect SRCAP,missense_variant,p.Gln1247His,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Gln947His,ENST00000483083,;SRCAP,intron_variant,,ENST00000395059,;RP11-2C24.9,intron_variant,,ENST00000380361,; T ENST00000262518 Transcript missense_variant 4126/11754 3741/9693 1247/3230 Q/H caG/caT 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 deleterious(0) 23/34 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 30722597 30722597 G T 1 0 0 0 0 1 0 0 0 15493 962 34 2 2 SRCAP 16 30722597 Missense_Mutation SNP G C3L-01924_T 842572 30722597 59615748 468 8338 FBXL19 0 . GRCh38 16 30927316 30927316 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.246C>T p.= p.L82L ENST00000380310 3/11 90 80 10 99 99 0 strelka-varscan-mutect FBXL19,synonymous_variant,p.=,ENST00000338343,;FBXL19,synonymous_variant,p.=,ENST00000380310,NM_001099784.2;FBXL19,synonymous_variant,p.=,ENST00000427128,;FBXL19,synonymous_variant,p.=,ENST00000565690,;FBXL19,synonymous_variant,p.=,ENST00000562319,;FBXL19,5_prime_UTR_variant,,ENST00000471231,NM_001282351.1;FBXL19,downstream_gene_variant,,ENST00000562798,;FBXL19-AS1,upstream_gene_variant,,ENST00000563777,; T ENST00000380310 Transcript synonymous_variant 404/3796 246/2085 82/694 L ctC/ctT 1 1 FBXL19 HGNC HGNC:25300 protein_coding YES CCDS45465.1 ENSP00000369666 Q6PCT2 UPI00015C725E NM_001099784.2 3/11 Pfam_domain:PF16866,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF10,Superfamily_domains:SSF57903 LOW 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -19.98218 1 1 1 1 0 T 2 4 29 30927316 30927316 C T 1 0 0 0 0 0 0 0 1 5579 842 30 3 3 FBXL19 16 30927316 Silent SNP C C3L-01924_T 204719 30927316 59411029 469 8339 PRSS8 0 . GRCh38 16 31135172 31135172 + Splice_Site SNP C C A novel C3L-01924_T C3L-01924_N C C c.86-1G>T p.X29_splice ENST00000317508 199 174 25 181 180 1 strelka-varscan-mutect PRSS8,splice_acceptor_variant,,ENST00000317508,NM_002773.3;PRSS8,splice_acceptor_variant,,ENST00000568261,;PRSS8,splice_acceptor_variant,,ENST00000567531,;PRSS8,intron_variant,,ENST00000567797,;PRSS36,downstream_gene_variant,,ENST00000268281,NM_173502.4;PRSS36,downstream_gene_variant,,ENST00000569305,NM_001258290.1;PRSS36,downstream_gene_variant,,ENST00000418068,NM_001258291.1;KAT8,downstream_gene_variant,,ENST00000543774,;KAT8,downstream_gene_variant,,ENST00000448516,NM_182958.2;KAT8,downstream_gene_variant,,ENST00000219797,NM_032188.2;KAT8,downstream_gene_variant,,ENST00000537402,;RP11-388M20.2,downstream_gene_variant,,ENST00000563605,;PRSS8,splice_acceptor_variant,,ENST00000567833,;PRSS8,splice_acceptor_variant,,ENST00000564025,;PRSS36,downstream_gene_variant,,ENST00000562368,;KAT8,downstream_gene_variant,,ENST00000538768,;KAT8,downstream_gene_variant,,ENST00000573144,;PRSS36,downstream_gene_variant,,ENST00000571878,; A ENST00000317508 Transcript splice_acceptor_variant -/1872 86/1032 29/343 1 -1 PRSS8 HGNC HGNC:9491 protein_coding YES CCDS45469.1 ENSP00000319730 Q16651 UPI0000046DCB NM_002773.3 1/5 HIGH 1 SNV 1 1 PASS rs1355144035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 29 31135172 31135172 C A 1 0 0 0 0 0 0 1 0 12786 695 24 2 2 PRSS8 16 31135172 Splice_Site SNP C C3L-01924_T 207856 31135172 59203173 470 8340 TRIM72 0 . GRCh38 16 31220916 31220916 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.738C>A p.Ser246Arg p.S246R ENST00000322122 5/7 258 233 25 253 252 1 strelka-varscan-mutect TRIM72,missense_variant,p.Ser246Arg,ENST00000322122,NM_001008274.3;TRIM72,missense_variant,p.Ser246Arg,ENST00000613872,;PYDC1,upstream_gene_variant,,ENST00000302964,NM_152901.3;PYDC1,upstream_gene_variant,,ENST00000568383,; A ENST00000322122 Transcript missense_variant,splice_region_variant 1022/8500 738/1434 246/477 S/R agC/agA 1 1 TRIM72 HGNC HGNC:32671 protein_coding YES CCDS32437.1 ENSP00000312675 Q6ZMU5 UPI00001FFF74 NM_001008274.3 deleterious(0) 5/7 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF11 MODERATE SNV 2 1 PASS . . 0 208 0 0 2 0 0 0 -8.989156 0.9929719 1 1 1 0 A 3 1 29 31220916 31220916 C A 1 0 0 0 0 1 0 0 0 17041 724 25 2 2 TRIM72 16 31220916 Missense_Mutation SNP C C3L-01924_T 85744 31220916 59117429 471 8341 PHKB 0 . GRCh38 16 47661794 47661794 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.2272A>G p.Lys758Glu p.K758E ENST00000323584 23/31 332 298 34 427 427 0 strelka-varscan-mutect PHKB,missense_variant,p.Lys758Glu,ENST00000299167,;PHKB,missense_variant,p.Lys758Glu,ENST00000323584,NM_000293.2;PHKB,missense_variant,p.Lys751Glu,ENST00000566044,NM_001031835.2;PHKB,missense_variant,p.Lys65Glu,ENST00000566275,;PHKB,non_coding_transcript_exon_variant,,ENST00000568171,;PHKB,upstream_gene_variant,,ENST00000566319,; G ENST00000323584 Transcript missense_variant 2296/4283 2272/3282 758/1093 K/E Aag/Gag 1 1 PHKB HGNC HGNC:8927 protein_coding YES CCDS10729.1 ENSP00000313504 Q93100 UPI0000141140 NM_000293.2 tolerated(0.66) 23/31 Pfam_domain:PF00723,hmmpanther:PTHR10749 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 47661794 47661794 A G 1 0 0 0 0 1 0 0 0 11933 15 1 5 5 PHKB 16 47661794 Missense_Mutation SNP A C3L-01924_T 16440878 47661794 42676551 472 8342 SALL1 0 . GRCh38 16 51139767 51139767 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2455G>T p.Asp819Tyr p.D819Y ENST00000251020 2/3 382 346 36 466 466 0 strelka-varscan-mutect SALL1,missense_variant,p.Asp722Tyr,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Asp819Tyr,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Asp722Tyr,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 2489/5146 2455/3975 819/1324 D/Y Gat/Tat 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 51139767 51139767 C A 1 0 0 0 0 1 0 0 0 14069 826 29 2 2 SALL1 16 51139767 Missense_Mutation SNP C C3L-01924_T 3477973 51139767 39198578 473 8343 CDH8 0 . GRCh38 16 61727050 61727050 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.1580A>G p.Asn527Ser p.N527S ENST00000584337 9/9 94 86 8 99 99 0 varscan-mutect CDH8,missense_variant,p.Asn527Ser,ENST00000584337,;CDH8,intron_variant,,ENST00000577390,NM_001796.4;CDH8,intron_variant,,ENST00000577730,;CDH8,intron_variant,,ENST00000299345,;CDH8,intron_variant,,ENST00000585315,; C ENST00000584337 Transcript missense_variant 2102/3986 1580/1599 527/532 N/S aAc/aGc 1 -1 CDH8 HGNC HGNC:1767 protein_coding ENSP00000463511 J3QLE6 UPI00001FF328 tolerated_low_confidence(1) 9/9 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -16.98435 1 1 1 1 0 C 3 2 29 61727050 61727050 T C 1 0 0 0 0 1 0 0 0 2819 1725 60 5 5 CDH8 16 61727050 Missense_Mutation SNP T C3L-01924_T 10587283 61727050 28611295 474 8344 WWP2 0 . GRCh38 16 69799184 69799184 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.229G>T p.Ala77Ser p.A77S ENST00000359154 4/24 63 44 19 87 87 0 strelka-varscan-mutect WWP2,missense_variant,p.Ala77Ser,ENST00000359154,NM_007014.4,NM_001270454.1;WWP2,missense_variant,p.Ala77Ser,ENST00000569174,NM_001270455.1;WWP2,missense_variant,p.Ala77Ser,ENST00000561780,;WWP2,downstream_gene_variant,,ENST00000563659,;WWP2,non_coding_transcript_exon_variant,,ENST00000544162,;WWP2,missense_variant,p.Ala77Ser,ENST00000569620,;WWP2,non_coding_transcript_exon_variant,,ENST00000569658,;WWP2,non_coding_transcript_exon_variant,,ENST00000567986,; T ENST00000359154 Transcript missense_variant 330/4515 229/2613 77/870 A/S Gca/Tca 1 1 WWP2 HGNC HGNC:16804 protein_coding YES CCDS10885.1 ENSP00000352069 O00308 A0A024R711 UPI000006CD16 NM_007014.4,NM_001270454.1 deleterious(0.03) 4/24 hmmpanther:PTHR11254:SF287,hmmpanther:PTHR11254,Gene3D:2.60.40.150,PIRSF_domain:PIRSF001569,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999895 1 1 1 0 T 3 4 29 69799184 69799184 G T 1 0 0 0 0 1 0 0 0 17974 1203 42 2 2 WWP2 16 69799184 Missense_Mutation SNP G C3L-01924_T 8072134 69799184 20539161 475 8345 CNTNAP4 0 . GRCh38 16 76452615 76452615 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.1179T>A p.= p.S393S ENST00000611870 8/24 153 101 52 184 184 0 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; A ENST00000611870 Transcript synonymous_variant 1564/4867 1179/3927 393/1308 S tcT/tcA 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 8/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1320439694 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 76452615 76452615 T A 1 0 0 0 0 0 0 0 1 3431 1567 55 4 4 CNTNAP4 16 76452615 Silent SNP T C3L-01924_T 6653431 76452615 13885730 476 8346 RTN4RL1 0 . GRCh38 17 1937465 1937465 + Missense_Mutation SNP C C A rs760986954 C3L-01924_T C3L-01924_N C C c.357G>T p.Glu119Asp p.E119D ENST00000331238 2/2 171 148 23 197 197 0 strelka-varscan-mutect RTN4RL1,missense_variant,p.Glu119Asp,ENST00000331238,NM_178568.3; A ENST00000331238 Transcript missense_variant 837/3625 357/1326 119/441 E/D gaG/gaT rs760986954 1 -1 RTN4RL1 HGNC HGNC:21329 protein_coding YES CCDS45569.1 ENSP00000330631 Q86UN2 UPI000018CD23 NM_178568.3 tolerated(1) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF11,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs760986954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 1937465 1937465 C A 1 0 0 0 0 1 0 0 0 13991 912 32 2 2 RTN4RL1 17 1937465 Missense_Mutation SNP C C3L-01924_T 1937465 81319976 477 8347 TRPV1 0 . GRCh38 17 3590059 3590059 + Silent SNP G G A rs753718104 C3L-01924_T C3L-01924_N G G c.792C>T p.= p.I264I ENST00000572705 7/17 85 76 9 117 117 0 strelka-varscan-mutect TRPV1,synonymous_variant,p.=,ENST00000572705,NM_080704.3;TRPV1,synonymous_variant,p.=,ENST00000571088,NM_018727.5;TRPV1,synonymous_variant,p.=,ENST00000399759,NM_080705.3;TRPV1,synonymous_variant,p.=,ENST00000399756,NM_080706.3;TRPV1,synonymous_variant,p.=,ENST00000425167,;TRPV1,synonymous_variant,p.=,ENST00000576351,;TRPV1,synonymous_variant,p.=,ENST00000310522,;RP11-235E17.2,3_prime_UTR_variant,,ENST00000572919,;TRPV1,non_coding_transcript_exon_variant,,ENST00000574085,; A ENST00000572705 Transcript synonymous_variant 1067/4166 792/2520 264/839 I atC/atT rs753718104,COSM3516430,COSM3516431,COSM3516432 1 -1 TRPV1 HGNC HGNC:12716 protein_coding YES CCDS45576.1 ENSP00000459962 Q8NER1 UPI00005B2E0C NM_080704.3 7/17 PROSITE_profiles:PS50297,hmmpanther:PTHR10582:SF17,hmmpanther:PTHR10582,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01768 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs753718104 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 3590059 3590059 G A 1 0 0 0 0 0 0 0 1 17101 1048 37 1 1 TRPV1 17 3590059 Silent SNP G C3L-01924_T 1652594 3590059 79667382 478 8348 TP53 0 . GRCh38 17 7673772 7673772 + Missense_Mutation SNP C C G rs371409680 C3L-01924_T C3L-01924_N C C c.848G>C p.Arg283Pro p.R283P ENST00000269305 8/11 453 320 133 558 558 0 strelka-varscan-mutect TP53,missense_variant,p.Arg283Pro,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg283Pro,ENST00000420246,;TP53,missense_variant,p.Arg244Pro,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg244Pro,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg283Pro,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg244Pro,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg283Pro,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg244Pro,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg283Pro,ENST00000445888,;TP53,missense_variant,p.Arg244Pro,ENST00000619485,;TP53,missense_variant,p.Arg151Pro,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg124Pro,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg151Pro,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg124Pro,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg151Pro,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg124Pro,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg283Pro,ENST00000359597,;TP53,missense_variant,p.Arg272Pro,ENST00000615910,;TP53,missense_variant,p.Arg151Pro,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg244Pro,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 1038/2579 848/1182 283/393 R/P cGc/cCc rs371409680,CM021154,TP53_g.13828G>A,TP53_g.13828G>T,TP53_g.13828G>C,COSM10743,COSM11483,COSM1646817,COSM4271752,COSM44463,COSM99941 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.01) 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_benign,likely_pathogenic 0,0,0,0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1 1 PASS rs371409680 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 7673772 7673772 C G 1 0 0 0 0 1 0 0 0 16859 768 27 4 4 TP53 17 7673772 Missense_Mutation SNP C C3L-01924_T 4083713 7673772 75583669 479 8349 WRAP53 0 . GRCh38 17 7689605 7689605 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.546C>T p.= p.S182S ENST00000316024 3/10 286 257 29 413 412 1 strelka-varscan-mutect WRAP53,synonymous_variant,p.=,ENST00000316024,;WRAP53,synonymous_variant,p.=,ENST00000396463,NM_018081.2,NM_001143992.1;WRAP53,synonymous_variant,p.=,ENST00000457584,NM_001143991.1;WRAP53,synonymous_variant,p.=,ENST00000431639,NM_001143990.1;WRAP53,synonymous_variant,p.=,ENST00000534050,;TP53,upstream_gene_variant,,ENST00000617185,NM_001126114.2;TP53,upstream_gene_variant,,ENST00000420246,;TP53,upstream_gene_variant,,ENST00000622645,NM_001276696.1;TP53,upstream_gene_variant,,ENST00000610292,NM_001126118.1;TP53,upstream_gene_variant,,ENST00000455263,NM_001126113.2;TP53,upstream_gene_variant,,ENST00000610538,NM_001276695.1;TP53,upstream_gene_variant,,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,upstream_gene_variant,,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,upstream_gene_variant,,ENST00000445888,;TP53,upstream_gene_variant,,ENST00000619485,;TP53,upstream_gene_variant,,ENST00000509690,;TP53,upstream_gene_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000514944,;RP11-199F11.2,upstream_gene_variant,,ENST00000571370,;WRAP53,synonymous_variant,p.=,ENST00000498311,;WRAP53,non_coding_transcript_exon_variant,,ENST00000467699,;TP53,upstream_gene_variant,,ENST00000635293,;TP53,upstream_gene_variant,,ENST00000505014,; T ENST00000316024 Transcript synonymous_variant 2894/4011 546/1647 182/548 S tcC/tcT 1 1 WRAP53 HGNC HGNC:25522 protein_coding YES CCDS11119.1 ENSP00000324203 Q9BUR4 UPI000007261E 3/10 Gene3D:2.130.10.10,hmmpanther:PTHR13211,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 7689605 7689605 C T 1 0 0 0 0 0 0 0 1 17956 668 24 3 3 WRAP53 17 7689605 Silent SNP C C3L-01924_T 15833 7689605 75567836 480 8350 MYH13 0 . GRCh38 17 10311197 10311197 + Missense_Mutation SNP G G A rs777192178 C3L-01924_T C3L-01924_N G G c.4562C>T p.Ala1521Val p.A1521V ENST00000418404 32/41 183 139 44 230 230 0 strelka-varscan-mutect MYH13,missense_variant,p.Ala1521Val,ENST00000418404,;MYH13,missense_variant,p.Ala1521Val,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Ala1521Val,ENST00000621918,;RP11-401O9.4,intron_variant,,ENST00000609088,; A ENST00000418404 Transcript missense_variant 4726/6296 4562/5817 1521/1938 A/V gCa/gTa rs777192178 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0.03) 32/41 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS rs777192178 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 10311197 10311197 G A 1 0 0 0 0 1 0 0 0 10032 1319 46 3 3 MYH13 17 10311197 Missense_Mutation SNP G C3L-01924_T 2621592 10311197 72946244 481 8351 MYH4 0 . GRCh38 17 10453681 10453681 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.2896G>T p.Ala966Ser p.A966S ENST00000255381 23/40 279 215 64 361 361 0 strelka-varscan-mutect MYH4,missense_variant,p.Ala966Ser,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript missense_variant 3007/6016 2896/5820 966/1939 A/S Gcc/Tcc COSM3988757 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0.03) 23/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,Superfamily_domains:SSF90257,Superfamily_domains:SSF90257 1 MODERATE 1 SNV 1 1 1 PASS rs1462271152 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 10453681 10453681 C A 1 0 0 0 0 1 0 0 0 10037 739 26 2 2 MYH4 17 10453681 Missense_Mutation SNP C C3L-01924_T 142484 10453681 72803760 482 8352 MYH4 0 . GRCh38 17 10455653 10455653 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2135G>T p.Gly712Val p.G712V ENST00000255381 19/40 148 122 26 172 172 0 strelka-varscan-mutect MYH4,missense_variant,p.Gly712Val,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript missense_variant 2246/6016 2135/5820 712/1939 G/V gGc/gTc 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0.01) 19/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1014306463 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 10455653 10455653 C A 1 0 0 0 0 1 0 0 0 10037 739 26 2 2 MYH4 17 10455653 Missense_Mutation SNP C C3L-01924_T 1972 10455653 72801788 483 8353 MYH4 0 . GRCh38 17 10455717 10455717 + Nonsense_Mutation SNP C C A rs745388693 C3L-01924_T C3L-01924_N C C c.2071G>T p.Glu691Ter p.E691* ENST00000255381 19/40 156 119 37 183 183 0 strelka-varscan-mutect MYH4,stop_gained,p.Glu691Ter,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript stop_gained 2182/6016 2071/5820 691/1939 E/* Gag/Tag rs745388693,COSM5331814 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 19/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1 HIGH 1 SNV 1 0,1 1 PASS rs745388693 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 10455717 10455717 C A 1 0 0 0 0 0 1 0 0 10037 835 29 2 2 MYH4 17 10455717 Nonsense_Mutation SNP C C3L-01924_T 64 10455717 72801724 484 8354 TRPV2 0 . GRCh38 17 16423527 16423527 + Silent SNP C C A rs757975900 C3L-01924_T C3L-01924_N C C c.684C>A p.= p.L228L ENST00000338560 5/15 104 92 12 97 96 1 strelka-varscan-mutect TRPV2,synonymous_variant,p.=,ENST00000338560,NM_016113.4;TRPV2,synonymous_variant,p.=,ENST00000455666,;TRPV2,upstream_gene_variant,,ENST00000577277,;TRPV2,upstream_gene_variant,,ENST00000583241,;AC093484.4,upstream_gene_variant,,ENST00000441875,; A ENST00000338560 Transcript synonymous_variant 1083/2808 684/2295 228/764 L ctC/ctA rs757975900 1 1 TRPV2 HGNC HGNC:18082 protein_coding YES CCDS32576.1 ENSP00000342222 Q9Y5S1 UPI0000032F4E NM_016113.4 5/15 PROSITE_profiles:PS50297,hmmpanther:PTHR10582:SF5,hmmpanther:PTHR10582,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01768 LOW 1 SNV 1 1 PASS rs757975900 . 0 202 7 0 0 0 0 0 -19.99998 0.9999992 1 1 1 0 A 2 1 29 16423527 16423527 C A 1 0 0 0 0 0 0 0 1 17102 842 30 2 2 TRPV2 17 16423527 Silent SNP C C3L-01924_T 5967810 16423527 66833914 485 8355 MAP2K3 0 . GRCh38 17 21300906 21300906 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.312G>T p.Gln104His p.Q104H ENST00000342679 5/12 305 268 37 340 340 0 strelka-varscan MAP2K3,missense_variant,p.Gln104His,ENST00000342679,NM_145109.2;MAP2K3,missense_variant,p.Gln75His,ENST00000361818,NM_002756.4;MAP2K3,missense_variant,p.Gln75His,ENST00000613338,;MAP2K3,missense_variant,p.Gln75His,ENST00000316920,;MAP2K3,missense_variant,p.Gln75His,ENST00000526076,;MAP2K3,downstream_gene_variant,,ENST00000529517,;MAP2K3,missense_variant,p.Gln104His,ENST00000496046,;MAP2K3,3_prime_UTR_variant,,ENST00000395491,NM_001316332.1;MAP2K3,non_coding_transcript_exon_variant,,ENST00000583508,;MAP2K3,downstream_gene_variant,,ENST00000479129,;MAP2K3,downstream_gene_variant,,ENST00000483928,; T ENST00000342679 Transcript missense_variant 561/2303 312/1044 104/347 Q/H caG/caT 1 1 MAP2K3 HGNC HGNC:6843 protein_coding YES CCDS11217.1 ENSP00000345083 P46734 Q6FI23 UPI000012F48C NM_145109.2 deleterious(0) 5/12 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF191,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 21300906 21300906 G T 1 0 0 0 0 1 0 0 0 9160 933 33 2 2 MAP2K3 17 21300906 Missense_Mutation SNP G C3L-01924_T 4877379 21300906 61956535 486 8356 POLDIP2 0 . GRCh38 17 28353779 28353779 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.354T>A p.= p.P118P ENST00000540200 4/11 173 151 22 146 146 0 strelka-varscan-mutect POLDIP2,synonymous_variant,p.=,ENST00000540200,NM_015584.4;POLDIP2,synonymous_variant,p.=,ENST00000618887,NM_001290145.1;TMEM199,upstream_gene_variant,,ENST00000292114,NM_152464.2;TMEM199,upstream_gene_variant,,ENST00000395404,;CTB-96E2.3,upstream_gene_variant,,ENST00000591482,;TMEM199,upstream_gene_variant,,ENST00000581386,;TMEM199,upstream_gene_variant,,ENST00000579762,;TMEM199,upstream_gene_variant,,ENST00000483505,;TMEM199,upstream_gene_variant,,ENST00000555264,;TMEM199,upstream_gene_variant,,ENST00000580868,; T ENST00000540200 Transcript synonymous_variant 428/2121 354/1107 118/368 P ccT/ccA 1 -1 POLDIP2 HGNC HGNC:23781 protein_coding YES CCDS74018.1 ENSP00000475924 Q9Y2S7 UPI00000722ED NM_015584.4 4/11 hmmpanther:PTHR14289:SF20,hmmpanther:PTHR14289,Pfam_domain:PF08755,SMART_domains:SM00992,Superfamily_domains:0050131 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 28353779 28353779 A T 1 0 0 0 0 0 0 0 1 12304 175 7 4 4 POLDIP2 17 28353779 Silent SNP A C3L-01924_T 7052873 28353779 54903662 487 8357 SEBOX 0 . GRCh38 17 28364827 28364827 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.160T>A p.Trp54Arg p.W54R ENST00000536498 2/3 160 131 29 234 233 1 strelka-varscan-mutect SEBOX,missense_variant,p.Trp54Arg,ENST00000536498,NM_001080837.3;CTB-96E2.2,3_prime_UTR_variant,,ENST00000555059,;TMEM199,downstream_gene_variant,,ENST00000292114,NM_152464.2;VTN,downstream_gene_variant,,ENST00000226218,NM_000638.3;TMEM199,downstream_gene_variant,,ENST00000395404,;VTN,downstream_gene_variant,,ENST00000542029,;TMEM199,downstream_gene_variant,,ENST00000585070,;CTB-96E2.7,upstream_gene_variant,,ENST00000577850,;SARM1,intron_variant,,ENST00000379061,;CTB-96E2.3,intron_variant,,ENST00000591482,;TMEM199,downstream_gene_variant,,ENST00000483505,;TMEM199,downstream_gene_variant,,ENST00000555264,;TMEM199,downstream_gene_variant,,ENST00000509083,;VTN,downstream_gene_variant,,ENST00000539746,;TMEM199,downstream_gene_variant,,ENST00000585027,;TMEM199,downstream_gene_variant,,ENST00000580868,; T ENST00000536498 Transcript missense_variant 253/666 160/573 54/190 W/R Tgg/Agg 1 -1 SEBOX HGNC HGNC:32942 protein_coding YES CCDS45634.2 ENSP00000444503 F6T8T6 UPI000443806B NM_001080837.3 tolerated(1) 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF44,hmmpanther:PTHR24329,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 28364827 28364827 A T 1 0 0 0 0 1 0 0 0 14253 188 7 4 4 SEBOX 17 28364827 Missense_Mutation SNP A C3L-01924_T 11048 28364827 54892614 488 8358 NF1 0 . GRCh38 17 31226603 31226603 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2170G>A p.Asp724Asn p.D724N ENST00000358273 18/58 360 318 42 461 461 0 strelka-varscan-mutect NF1,missense_variant,p.Asp724Asn,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Asp724Asn,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Asp390Asn,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000431387,NM_001128147.2;NF1,missense_variant,p.Asp758Asn,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,; A ENST00000358273 Transcript missense_variant 2553/12425 2170/8520 724/2839 D/N Gat/Aat 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 tolerated(0.08) 18/58 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 31226603 31226603 G A 1 0 0 0 0 1 0 0 0 10393 1174 41 3 3 NF1 17 31226603 Missense_Mutation SNP G C3L-01924_T 2861776 31226603 52030838 489 8359 TADA2A 0 . GRCh38 17 37442616 37442616 + Frame_Shift_Del DEL G G - novel C3L-01924_T C3L-01924_N G G c.496delG p.Ala166ProfsTer22 p.A166Pfs*22 ENST00000615182 7/16 227 176 51 230 230 0 sindel-varindel-pindel TADA2A,frameshift_variant,p.Ala166ProfsTer22,ENST00000615182,NM_001166105.2;TADA2A,frameshift_variant,p.Ala166ProfsTer22,ENST00000612272,NM_001488.4;TADA2A,frameshift_variant,p.Ala166ProfsTer22,ENST00000620367,NM_001291918.1,NM_133439.3;TADA2A,frameshift_variant,p.Ala86ProfsTer22,ENST00000615328,;TADA2A,frameshift_variant,,ENST00000614112,;TADA2A,downstream_gene_variant,,ENST00000621780,;TADA2A,non_coding_transcript_exon_variant,,ENST00000620086,;TADA2A,frameshift_variant,p.Ala166ProfsTer22,ENST00000620628,;TADA2A,3_prime_UTR_variant,,ENST00000614122,;TADA2A,intron_variant,,ENST00000619777,;TADA2A,downstream_gene_variant,,ENST00000610834,;TADA2A,downstream_gene_variant,,ENST00000620838,; - ENST00000615182 Transcript frameshift_variant 668/4253 495/1332 165/443 M/X atG/at 1 1 TADA2A HGNC HGNC:11531 protein_coding YES CCDS11319.1 ENSP00000481091 A0A024R0Y4 UPI00001254E3 NM_001166105.2 7/16 PIRSF_domain:PIRSF025024,hmmpanther:PTHR12374 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999972 1 1 1 0 - 7 5 29 37442616 37442616 G - 1 0 1 0 1 0 0 0 0 15906 1348 47 0 0 TADA2A 17 37442616 Frame_Shift_Del DEL G C3L-01924_T 6216013 37442616 45814825 490 8360 FBXO47 0 . GRCh38 17 38945129 38945129 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.624C>A p.= p.A208A ENST00000378079 7/11 100 78 22 107 107 0 strelka-varscan-mutect FBXO47,synonymous_variant,p.=,ENST00000378079,NM_001008777.2; T ENST00000378079 Transcript synonymous_variant 824/2302 624/1359 208/452 A gcC/gcA 1 -1 FBXO47 HGNC HGNC:31969 protein_coding YES CCDS32639.1 ENSP00000367319 Q5MNV8 UPI00004DDAF1 NM_001008777.2 7/11 hmmpanther:PTHR34098:SF1,hmmpanther:PTHR34098 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 38945129 38945129 G T 1 0 0 0 0 0 0 0 1 5619 1219 43 2 2 FBXO47 17 38945129 Silent SNP G C3L-01924_T 1502513 38945129 44312312 491 8361 AARSD1 0 . GRCh38 17 42956448 42956448 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1024G>T p.Val342Leu p.V342L ENST00000421990 10/17 163 120 43 136 136 0 strelka-varscan-mutect PTGES3L-AARSD1,missense_variant,p.Val342Leu,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,missense_variant,p.Val342Leu,ENST00000409399,;PTGES3L-AARSD1,missense_variant,p.Val281Leu,ENST00000360221,NM_025267.3;PTGES3L-AARSD1,missense_variant,p.Val251Leu,ENST00000409103,;AARSD1,missense_variant,p.Val168Leu,ENST00000427569,NM_001261434.1;AARSD1,missense_variant,p.Val63Leu,ENST00000430739,;PTGES3L-AARSD1,downstream_gene_variant,,ENST00000452752,;AARSD1,non_coding_transcript_exon_variant,,ENST00000416949,;AARSD1,missense_variant,p.Val63Leu,ENST00000450475,;AARSD1,3_prime_UTR_variant,,ENST00000591910,;AARSD1,3_prime_UTR_variant,,ENST00000436545,;PTGES3L-AARSD1,3_prime_UTR_variant,,ENST00000423601,;AARSD1,non_coding_transcript_exon_variant,,ENST00000441280,;AARSD1,non_coding_transcript_exon_variant,,ENST00000483774,;AARSD1,non_coding_transcript_exon_variant,,ENST00000491665,;AARSD1,non_coding_transcript_exon_variant,,ENST00000486664,;AARSD1,non_coding_transcript_exon_variant,,ENST00000478040,;AARSD1,upstream_gene_variant,,ENST00000593123,;AARSD1,upstream_gene_variant,,ENST00000474578,;AARSD1,downstream_gene_variant,,ENST00000492036,;AARSD1,upstream_gene_variant,,ENST00000591096,;AARSD1,upstream_gene_variant,,ENST00000587023,;AARSD1,upstream_gene_variant,,ENST00000592136,;AARSD1,upstream_gene_variant,,ENST00000483535,;AARSD1,upstream_gene_variant,,ENST00000486493,; A ENST00000421990 Transcript missense_variant 1370/2150 1024/1761 342/586 V/L Gtg/Ttg 1 -1 PTGES3L-AARSD1 HGNC HGNC:43946 protein_coding YES CCDS45691.1 ENSP00000409924 Q9BTE6 UPI0000D4E5DF NM_001136042.2 deleterious(0.02) 10/17 PROSITE_profiles:PS50860,hmmpanther:PTHR11777,Superfamily_domains:SSF55186 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 42956448 42956448 C A 1 0 0 0 0 1 0 0 0 25 478 17 2 2 AARSD1 17 42956448 Missense_Mutation SNP C C3L-01924_T 4011319 42956448 40300993 492 8362 USP32 0 . GRCh38 17 60205596 60205596 + Nonsense_Mutation SNP G G A C3L-01924_T C3L-01924_N G G c.3100C>T p.Arg1034Ter p.R1034* ENST00000300896 26/34 246 182 64 306 306 0 strelka-varscan-mutect USP32,stop_gained,p.Arg1034Ter,ENST00000300896,NM_032582.3;USP32,stop_gained,p.Arg704Ter,ENST00000592339,;USP32,downstream_gene_variant,,ENST00000590133,;USP32,downstream_gene_variant,,ENST00000585720,; A ENST00000300896 Transcript stop_gained 3295/5171 3100/4815 1034/1604 R/* Cga/Tga COSM5364401 1 -1 USP32 HGNC HGNC:19143 protein_coding YES CCDS32697.1 ENSP00000300896 Q8NFA0 UPI0000047AF8 NM_032582.3 26/34 PROSITE_profiles:PS50235,Pfam_domain:PF00443 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 60205596 60205596 G A 1 0 0 0 0 0 1 0 0 17605 1124 39 1 1 USP32 17 60205596 Nonsense_Mutation SNP G C3L-01924_T 17249148 60205596 23051845 493 8363 ABCA8 0 . GRCh38 17 68881875 68881875 + Missense_Mutation SNP A A G C3L-01924_T C3L-01924_N A A c.3934T>C p.Cys1312Arg p.C1312R ENST00000586539 31/40 213 200 13 207 207 0 strelka-varscan-mutect ABCA8,missense_variant,p.Cys1307Arg,ENST00000430352,NM_001288986.1;ABCA8,missense_variant,p.Cys1272Arg,ENST00000269080,NM_007168.3;ABCA8,missense_variant,p.Cys1312Arg,ENST00000586539,NM_001288985.1;ABCA8,non_coding_transcript_exon_variant,,ENST00000586292,;ABCA8,non_coding_transcript_exon_variant,,ENST00000589980,;ABCA8,downstream_gene_variant,,ENST00000541225,;ABCA8,upstream_gene_variant,,ENST00000591459,;ABCA8,upstream_gene_variant,,ENST00000588458,; G ENST00000586539 Transcript missense_variant 4123/5088 3934/4866 1312/1621 C/R Tgt/Cgt COSM301603 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 deleterious(0.01) 31/40 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 68881875 68881875 A G 1 0 0 0 0 1 0 0 0 42 188 7 5 5 ABCA8 17 68881875 Missense_Mutation SNP A C3L-01924_T 8676279 68881875 14375566 494 8364 ABCA8 0 . GRCh38 17 68940923 68940923 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.136A>G p.Ile46Val p.I46V ENST00000586539 4/40 209 149 60 217 217 0 strelka-varscan-mutect ABCA8,missense_variant,p.Ile46Val,ENST00000430352,NM_001288986.1;ABCA8,missense_variant,p.Ile46Val,ENST00000269080,NM_007168.3;ABCA8,missense_variant,p.Ile46Val,ENST00000586539,NM_001288985.1;ABCA8,missense_variant,p.Ile46Val,ENST00000585531,;ABCA8,5_prime_UTR_variant,,ENST00000615593,;ABCA9-AS1,upstream_gene_variant,,ENST00000630625,;ABCA8,non_coding_transcript_exon_variant,,ENST00000541225,;ABCA8,non_coding_transcript_exon_variant,,ENST00000428549,;ABCA8,non_coding_transcript_exon_variant,,ENST00000585850,; C ENST00000586539 Transcript missense_variant 325/5088 136/4866 46/1621 I/V Ata/Gta 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 tolerated(0.11) 4/40 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 68940923 68940923 T C 1 0 0 0 0 1 0 0 0 42 1406 49 5 5 ABCA8 17 68940923 Missense_Mutation SNP T C3L-01924_T 59048 68940923 14316518 495 8365 NUP85 0 . GRCh38 17 75231577 75231577 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1183G>T p.Gly395Cys p.G395C ENST00000245544 13/19 285 232 53 239 239 0 strelka-varscan-mutect NUP85,missense_variant,p.Gly395Cys,ENST00000245544,NM_024844.4;NUP85,missense_variant,p.Gly283Cys,ENST00000579324,NM_001303276.1;NUP85,missense_variant,p.Gly350Cys,ENST00000579298,;NUP85,missense_variant,p.Gly91Cys,ENST00000583070,;NUP85,missense_variant,p.Gly168Cys,ENST00000579557,;NUP85,5_prime_UTR_variant,,ENST00000540768,;NUP85,upstream_gene_variant,,ENST00000579900,;NUP85,upstream_gene_variant,,ENST00000579838,;NUP85,downstream_gene_variant,,ENST00000449421,;NUP85,downstream_gene_variant,,ENST00000581335,;NUP85,3_prime_UTR_variant,,ENST00000581104,;NUP85,3_prime_UTR_variant,,ENST00000578830,;NUP85,3_prime_UTR_variant,,ENST00000580879,;NUP85,non_coding_transcript_exon_variant,,ENST00000577645,;NUP85,non_coding_transcript_exon_variant,,ENST00000582681,;NUP85,upstream_gene_variant,,ENST00000578987,;NUP85,upstream_gene_variant,,ENST00000578294,;NUP85,upstream_gene_variant,,ENST00000584155,; T ENST00000245544 Transcript missense_variant 1254/2121 1183/1971 395/656 G/C Ggt/Tgt 1 1 NUP85 HGNC HGNC:8734 protein_coding YES CCDS32730.1 ENSP00000245544 Q9BW27 UPI00000735DC NM_024844.4 deleterious(0.01) 13/19 Pfam_domain:PF07575,hmmpanther:PTHR13373,hmmpanther:PTHR13373:SF21 MODERATE 1 SNV 1 1 PASS rs1294115930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 75231577 75231577 G T 1 0 0 0 0 1 0 0 0 10836 1130 39 1 1 NUP85 17 75231577 Missense_Mutation SNP G C3L-01924_T 6290654 75231577 8025864 496 8366 MYO15B 0 . GRCh38 17 75594905 75594905 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.3041G>T p.Arg1014Leu p.R1014L ENST00000610510 10/63 219 196 23 237 237 0 strelka-varscan-mutect MYO15B,missense_variant,p.Arg1014Leu,ENST00000610510,;MYO15B,upstream_gene_variant,,ENST00000633867,;MYO15B,upstream_gene_variant,,ENST00000584762,;MYO15B,downstream_gene_variant,,ENST00000582561,;MYO15B,downstream_gene_variant,,ENST00000578564,;MYO15B,missense_variant,p.Arg1014Leu,ENST00000621743,;MYO15B,3_prime_UTR_variant,,ENST00000619501,;MYO15B,3_prime_UTR_variant,,ENST00000584516,;MYO15B,non_coding_transcript_exon_variant,,ENST00000580701,;MYO15B,downstream_gene_variant,,ENST00000581612,;MYO15B,downstream_gene_variant,,ENST00000581866,; T ENST00000610510 Transcript missense_variant 3041/9195 3041/9195 1014/3064 R/L cGg/cTg 1 1 MYO15B HGNC HGNC:14083 protein_coding YES ENSP00000488624 A0A0J9YY01 UPI00064546F0 tolerated(0.18) 10/63 PROSITE_profiles:PS51456,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs991290816 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 75594905 75594905 G T 1 0 0 0 0 1 0 0 0 10064 1116 39 1 1 MYO15B 17 75594905 Missense_Mutation SNP G C3L-01924_T 363328 75594905 7662536 497 8367 AKAIN1 0 . GRCh38 18 5145616 5145616 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.156G>T p.= p.R52R ENST00000434239 2/2 134 124 10 152 152 0 strelka-varscan-mutect AKAIN1,synonymous_variant,p.=,ENST00000434239,NM_001145194.1;AKAIN1,synonymous_variant,p.=,ENST00000580650,; A ENST00000434239 Transcript synonymous_variant 328/575 156/210 52/69 R cgG/cgT 1 -1 AKAIN1 HGNC HGNC:28285 protein_coding YES CCDS54179.1 ENSP00000399075 P0CW23 UPI0000201977 NM_001145194.1 2/2 hmmpanther:PTHR15934 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 5145616 5145616 C A 1 0 0 0 0 0 0 0 1 527 610 22 2 2 AKAIN1 18 5145616 Silent SNP C C3L-01924_T 5145616 75227669 498 8368 LAMA1 0 . GRCh38 18 7012120 7012120 + Nonsense_Mutation SNP G G A C3L-01924_T C3L-01924_N G G c.3382C>T p.Gln1128Ter p.Q1128* ENST00000389658 24/63 329 307 22 350 350 0 strelka-varscan-mutect LAMA1,stop_gained,p.Gln1128Ter,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript stop_gained 3476/9657 3382/9228 1128/3075 Q/* Cag/Tag COSM4950734 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 24/63 Gene3D:2.10.25.10,Pfam_domain:PF00053,Prints_domain:PR00011,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,SMART_domains:SM00180 1 HIGH 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 7012120 7012120 G A 1 0 0 0 0 0 1 0 0 8509 1299 45 3 3 LAMA1 18 7012120 Nonsense_Mutation SNP G C3L-01924_T 1866504 7012120 73361165 499 8369 PIEZO2 0 . GRCh38 18 10800351 10800351 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1364C>A p.Ser455Tyr p.S455Y ENST00000503781 11/52 215 166 49 247 246 1 strelka-varscan-mutect PIEZO2,missense_variant,p.Ser404Tyr,ENST00000383408,;PIEZO2,missense_variant,p.Ser455Tyr,ENST00000302079,;PIEZO2,missense_variant,p.Ser455Tyr,ENST00000580640,;PIEZO2,missense_variant,p.Ser455Tyr,ENST00000503781,NM_022068.3;PIEZO2,missense_variant,p.Ser165Tyr,ENST00000579112,;PIEZO2,missense_variant,p.Ser455Tyr,ENST00000582913,; T ENST00000503781 Transcript missense_variant 1364/8259 1364/8259 455/2752 S/Y tCt/tAt 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 11/52 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 10800351 10800351 G T 1 0 0 0 0 1 0 0 0 11975 942 33 2 2 PIEZO2 18 10800351 Missense_Mutation SNP G C3L-01924_T 3788231 10800351 69572934 500 8370 ANKRD30B 0 . GRCh38 18 14797810 14797810 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1985C>A p.Pro662Gln p.P662Q ENST00000358984 20/36 153 102 51 208 206 2 strelka-varscan-mutect ANKRD30B,missense_variant,p.Pro662Gln,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000579292,;ANKRD30B,3_prime_UTR_variant,,ENST00000580206,; A ENST00000358984 Transcript missense_variant 2165/4359 1985/4179 662/1392 P/Q cCa/cAa 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.47) 20/36 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 14797810 14797810 C A 1 0 0 0 0 1 0 0 0 762 594 21 2 2 ANKRD30B 18 14797810 Missense_Mutation SNP C C3L-01924_T 3997459 14797810 65575475 501 8371 ZNF521 0 . GRCh38 18 25225235 25225235 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.2683T>A p.Tyr895Asn p.Y895N ENST00000361524 4/8 241 165 76 317 317 0 strelka-varscan-mutect ZNF521,missense_variant,p.Tyr895Asn,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Tyr675Asn,ENST00000584787,NM_001308225.1;ZNF521,missense_variant,p.Tyr895Asn,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,missense_variant,p.Tyr895Asn,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; T ENST00000361524 Transcript missense_variant 2832/4871 2683/3936 895/1311 Y/N Tac/Aac 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 deleterious(0.01) 4/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 25225235 25225235 A T 1 0 0 0 0 1 0 0 0 18537 420 15 4 4 ZNF521 18 25225235 Missense_Mutation SNP A C3L-01924_T 10427425 25225235 55148050 502 8372 DSG1 0 . GRCh38 18 31339795 31339795 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.1457T>C p.Phe486Ser p.F486S ENST00000257192 11/15 135 98 37 199 199 0 strelka-varscan-mutect DSG1,missense_variant,p.Phe486Ser,ENST00000257192,NM_001942.3;DSG1,upstream_gene_variant,,ENST00000462981,;DSG1-AS1,downstream_gene_variant,,ENST00000581856,;DSG1-AS1,downstream_gene_variant,,ENST00000578119,; C ENST00000257192 Transcript missense_variant 1669/5045 1457/3150 486/1049 F/S tTt/tCt 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 tolerated(0.55) 11/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 31339795 31339795 T C 1 0 0 0 0 1 0 0 0 4597 1841 64 5 5 DSG1 18 31339795 Missense_Mutation SNP T C3L-01924_T 6114560 31339795 49033490 503 8373 GAREM1 0 . GRCh38 18 32268559 32268559 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1943G>C p.Arg648Thr p.R648T ENST00000269209 6/6 237 161 76 368 368 0 strelka-varscan-mutect GAREM1,missense_variant,p.Arg647Thr,ENST00000399218,NM_022751.2;GAREM1,missense_variant,p.Arg648Thr,ENST00000269209,NM_001242409.1;GAREM1,intron_variant,,ENST00000583696,; G ENST00000269209 Transcript missense_variant 1947/3006 1943/2631 648/876 R/T aGg/aCg 1 -1 GAREM1 HGNC HGNC:26136 protein_coding YES CCDS56057.1 ENSP00000269209 Q9H706 UPI00005A72DA NM_001242409.1 tolerated(0.08) 6/6 hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 32268559 32268559 C G 1 0 0 0 0 1 0 0 0 6109 681 24 4 4 GAREM1 18 32268559 Missense_Mutation SNP C C3L-01924_T 928764 32268559 48104726 504 8374 KIAA1328 0 . GRCh38 18 37160293 37160293 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.1326G>A p.= p.K442K ENST00000280020 8/10 178 125 53 257 256 1 strelka-varscan-mutect KIAA1328,synonymous_variant,p.=,ENST00000591619,;KIAA1328,synonymous_variant,p.=,ENST00000280020,NM_020776.1;KIAA1328,synonymous_variant,p.=,ENST00000587139,;KIAA1328,synonymous_variant,p.=,ENST00000586135,;KIAA1328,3_prime_UTR_variant,,ENST00000590617,;KIAA1328,3_prime_UTR_variant,,ENST00000592611,; A ENST00000280020 Transcript synonymous_variant 1348/4853 1326/1734 442/577 K aaG/aaA 1 1 KIAA1328 HGNC HGNC:29248 protein_coding YES CCDS45855.1 ENSP00000280020 Q86T90 UPI00001C1FF0 NM_020776.1 8/10 hmmpanther:PTHR28375,hmmpanther:PTHR28375:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 37160293 37160293 G A 1 0 0 0 0 0 0 0 1 8113 991 35 3 3 KIAA1328 18 37160293 Silent SNP G C3L-01924_T 4891734 37160293 43212992 505 8375 MYO5B 0 . GRCh38 18 49902666 49902666 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.2739A>G p.= p.A913A ENST00000285039 21/40 428 297 131 464 464 0 strelka-varscan-mutect MYO5B,synonymous_variant,p.=,ENST00000285039,NM_001080467.2;MYO5B,synonymous_variant,p.=,ENST00000324581,; C ENST00000285039 Transcript synonymous_variant 3039/9505 2739/5547 913/1848 A gcA/gcG 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 21/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 49902666 49902666 T C 1 0 0 0 0 0 0 0 1 10080 1567 55 5 5 MYO5B 18 49902666 Silent SNP T C3L-01924_T 12742373 49902666 30470619 506 8376 ST8SIA3 0 . GRCh38 18 57357443 57357443 + Missense_Mutation SNP C C A rs145313732 C3L-01924_T C3L-01924_N C C c.833C>A p.Pro278Gln p.P278Q ENST00000324000 3/4 95 89 6 135 135 0 strelka-varscan-mutect ST8SIA3,missense_variant,p.Pro278Gln,ENST00000324000,NM_015879.2;ST8SIA3,missense_variant,p.Pro98Gln,ENST00000586360,; A ENST00000324000 Transcript missense_variant 2867/11833 833/1143 278/380 P/Q cCg/cAg rs145313732 1 1 ST8SIA3 HGNC HGNC:14269 protein_coding YES CCDS32834.1 ENSP00000320431 O43173 UPI000014126D NM_015879.2 3/4 hmmpanther:PTHR11987:SF36,hmmpanther:PTHR11987,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557 MODERATE 1 SNV 1 1 PASS rs35655447 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 57357443 57357443 C A 1 0 0 0 0 1 0 0 0 15611 652 23 1 1 ST8SIA3 18 57357443 Missense_Mutation SNP C C3L-01924_T 7454777 57357443 23015842 507 8377 SERPINB13 0 . GRCh38 18 63595179 63595179 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.793G>T p.Glu265Ter p.E265* ENST00000269489 7/8 73 51 22 83 83 0 strelka-varscan-mutect SERPINB13,stop_gained,p.Glu265Ter,ENST00000269489,NM_001307923.1;SERPINB13,stop_gained,p.Glu256Ter,ENST00000344731,NM_012397.3;SERPINB13,stop_gained,p.Glu105Ter,ENST00000415733,;SERPINB13,downstream_gene_variant,,ENST00000431153,;SERPINB13,3_prime_UTR_variant,,ENST00000438844,; T ENST00000269489 Transcript stop_gained 961/3206 793/1203 265/400 E/* Gag/Tag 1 1 SERPINB13 HGNC HGNC:8944 protein_coding YES CCDS77195.1 ENSP00000269489 A0A0A0MQW3 UPI000004EE0A NM_001307923.1 7/8 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF161,SMART_domains:SM00093,Superfamily_domains:SSF56574 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 63595179 63595179 G T 1 0 0 0 0 0 1 0 0 14376 1188 41 2 2 SERPINB13 18 63595179 Nonsense_Mutation SNP G C3L-01924_T 6237736 63595179 16778106 508 8378 SERPINB13 0 . GRCh38 18 63597241 63597241 + Missense_Mutation SNP G G T rs369861529 C3L-01924_T C3L-01924_N G G c.1081G>T p.Gly361Cys p.G361C ENST00000269489 8/8 167 131 36 212 211 1 strelka-varscan-mutect SERPINB13,missense_variant,p.Gly361Cys,ENST00000269489,NM_001307923.1;SERPINB13,missense_variant,p.Gly352Cys,ENST00000344731,NM_012397.3;SERPINB13,intron_variant,,ENST00000415733,;SERPINB13,downstream_gene_variant,,ENST00000431153,;SERPINB13,3_prime_UTR_variant,,ENST00000438844,; T ENST00000269489 Transcript missense_variant 1249/3206 1081/1203 361/400 G/C Ggc/Tgc rs369861529,COSM564073 1 1 SERPINB13 HGNC HGNC:8944 protein_coding YES CCDS77195.1 ENSP00000269489 A0A0A0MQW3 UPI000004EE0A NM_001307923.1 tolerated(0.05) 8/8 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF161,SMART_domains:SM00093,Superfamily_domains:SSF56574 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369861529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 63597241 63597241 G T 1 0 0 0 0 1 0 0 0 14376 1000 35 2 2 SERPINB13 18 63597241 Missense_Mutation SNP G C3L-01924_T 2062 63597241 16776044 509 8379 GZMM 0 . GRCh38 19 549136 549136 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.563C>A p.Pro188His p.P188H ENST00000264553 4/5 120 88 32 90 90 0 strelka-varscan-mutect GZMM,missense_variant,p.Pro149His,ENST00000592501,NM_001258351.1;GZMM,missense_variant,p.Pro188His,ENST00000264553,NM_005317.3; A ENST00000264553 Transcript missense_variant 600/940 563/774 188/257 P/H cCc/cAc 1 1 GZMM HGNC HGNC:4712 protein_coding YES CCDS12031.1 ENSP00000264553 P51124 UPI000013D531 NM_005317.3 tolerated(0.05) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF132,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs1306542422 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 549136 549136 C A 1 0 0 0 0 1 0 0 0 6801 623 22 2 2 GZMM 19 549136 Missense_Mutation SNP C C3L-01924_T 549136 58068480 510 8380 PTBP1 0 . GRCh38 19 804565 804565 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.469G>C p.Val157Leu p.V157L ENST00000356948 6/15 85 69 16 98 98 0 strelka-varscan-mutect PTBP1,missense_variant,p.Val188Leu,ENST00000635647,;PTBP1,missense_variant,p.Val157Leu,ENST00000356948,NM_002819.4;PTBP1,missense_variant,p.Val157Leu,ENST00000394601,NM_031990.3;PTBP1,missense_variant,p.Val157Leu,ENST00000349038,NM_031991.3;PTBP1,missense_variant,p.Val127Leu,ENST00000350092,;PTBP1,missense_variant,p.Val154Leu,ENST00000589575,;PTBP1,missense_variant,p.Val127Leu,ENST00000586481,;PTBP1,intron_variant,,ENST00000627714,;PTBP1,intron_variant,,ENST00000587191,;PTBP1,intron_variant,,ENST00000585535,;PTBP1,upstream_gene_variant,,ENST00000585956,;PTBP1,downstream_gene_variant,,ENST00000587094,;PTBP1,upstream_gene_variant,,ENST00000577608,;PTBP1,missense_variant,p.Val29Leu,ENST00000621737,;PTBP1,non_coding_transcript_exon_variant,,ENST00000586944,;PTBP1,non_coding_transcript_exon_variant,,ENST00000592113,;PTBP1,non_coding_transcript_exon_variant,,ENST00000590887,;PTBP1,upstream_gene_variant,,ENST00000585856,;PTBP1,upstream_gene_variant,,ENST00000585932,;PTBP1,upstream_gene_variant,,ENST00000592804,;PTBP1,upstream_gene_variant,,ENST00000589883,;PTBP1,upstream_gene_variant,,ENST00000587136,; C ENST00000356948 Transcript missense_variant 892/3598 469/1674 157/557 V/L Gtc/Ctc 1 1 PTBP1 HGNC HGNC:9583 protein_coding YES CCDS42456.1 ENSP00000349428 P26599 UPI00000720B7 NM_002819.4 tolerated(0.12) 6/15 TIGRFAM_domain:TIGR01649 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 804565 804565 G C 1 0 0 0 0 1 0 0 0 12877 1261 44 4 4 PTBP1 19 804565 Missense_Mutation SNP G C3L-01924_T 255429 804565 57813051 511 8381 TLE2 0 . GRCh38 19 3009639 3009639 + Missense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.1079G>T p.Ser360Ile p.S360I ENST00000590536 13/20 199 181 18 185 185 0 strelka-varscan-mutect TLE2,missense_variant,p.Ser359Ile,ENST00000262953,NM_003260.4;TLE2,missense_variant,p.Ser373Ile,ENST00000591529,NM_001144761.1;TLE2,missense_variant,p.Ser373Ile,ENST00000426948,;TLE2,missense_variant,p.Ser360Ile,ENST00000590536,NM_001300846.1;TLE2,missense_variant,p.Ser237Ile,ENST00000455444,;TLE2,missense_variant,p.Ser237Ile,ENST00000443826,NM_001144762.1;TLE2,intron_variant,,ENST00000589364,;TLE2,intron_variant,,ENST00000586422,;TLE2,downstream_gene_variant,,ENST00000587137,;TLE2,downstream_gene_variant,,ENST00000591457,;TLE2,downstream_gene_variant,,ENST00000587217,;TLE2,downstream_gene_variant,,ENST00000589205,;TLE2,downstream_gene_variant,,ENST00000590183,;TLE2,upstream_gene_variant,,ENST00000586492,;TLE2,non_coding_transcript_exon_variant,,ENST00000587672,;TLE2,downstream_gene_variant,,ENST00000590101,; A ENST00000590536 Transcript missense_variant 1188/2344 1079/2235 360/744 S/I aGc/aTc COSM2750011 1 -1 TLE2 HGNC HGNC:11838 protein_coding YES CCDS74255.1 ENSP00000466542 K7EMK7 UPI0000203012 NM_001300846.1 deleterious(0.04) 13/20 hmmpanther:PTHR10814,hmmpanther:PTHR10814:SF4 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99995 0.9999998 1 1 1 0 A 3 1 29 3009639 3009639 C A 1 0 0 0 0 1 0 0 0 16385 797 28 2 2 TLE2 19 3009639 Missense_Mutation SNP C C3L-01924_T 2205074 3009639 55607977 512 8382 TBXA2R 0 . GRCh38 19 3599898 3599898 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.737A>T p.Gln246Leu p.Q246L ENST00000411851 2/4 229 161 68 242 241 1 strelka-varscan-mutect TBXA2R,missense_variant,p.Gln246Leu,ENST00000375190,NM_001060.5;TBXA2R,missense_variant,p.Gln246Leu,ENST00000411851,NM_201636.2;TBXA2R,intron_variant,,ENST00000589966,;TBXA2R,non_coding_transcript_exon_variant,,ENST00000587717,; A ENST00000411851 Transcript missense_variant 951/1494 737/1224 246/407 Q/L cAg/cTg 1 -1 TBXA2R HGNC HGNC:11608 protein_coding YES CCDS54198.1 ENSP00000393333 P21731 UPI00000711C4 NM_201636.2 deleterious(0) 2/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR01788,PROSITE_profiles:PS50262,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF5,Superfamily_domains:SSF81321 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 3599898 3599898 T A 1 0 0 0 0 1 0 0 0 16067 1580 55 4 4 TBXA2R 19 3599898 Missense_Mutation SNP T C3L-01924_T 590259 3599898 55017718 513 8383 TICAM1 0 . GRCh38 19 4816985 4816985 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.1393A>T p.Ser465Cys p.S465C ENST00000248244 2/2 293 232 61 304 304 0 strelka-varscan-mutect TICAM1,missense_variant,p.Ser465Cys,ENST00000248244,NM_182919.3;TICAM1,missense_variant,p.Ser326Cys,ENST00000621756,; A ENST00000248244 Transcript missense_variant 1623/2676 1393/2139 465/712 S/C Agc/Tgc 1 -1 TICAM1 HGNC HGNC:18348 protein_coding YES CCDS12136.1 ENSP00000248244 Q8IUC6 UPI000000D72E NM_182919.3 tolerated(0.13) 2/2 PIRSF_domain:PIRSF037744 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 4816985 4816985 T A 1 0 0 0 0 1 0 0 0 16326 1551 54 4 4 TICAM1 19 4816985 Missense_Mutation SNP T C3L-01924_T 1217087 4816985 53800631 514 8384 CATSPERD 0 . GRCh38 19 5778544 5778544 + Silent SNP C C A rs562529395 C3L-01924_T C3L-01924_N C C c.2265C>A p.= p.I755I ENST00000381624 22/22 323 251 72 330 330 0 strelka-varscan-mutect CATSPERD,synonymous_variant,p.=,ENST00000381624,NM_152784.3;PRR22,downstream_gene_variant,,ENST00000390672,;PRR22,downstream_gene_variant,,ENST00000419421,NM_001134316.1;CATSPERD,non_coding_transcript_exon_variant,,ENST00000309164,;CATSPERD,downstream_gene_variant,,ENST00000448307,; A ENST00000381624 Transcript synonymous_variant 2326/2516 2265/2397 755/798 I atC/atA rs562529395 1 1 CATSPERD HGNC HGNC:28598 protein_coding YES CCDS12149.2 ENSP00000371037 Q86XM0 UPI000059D641 NM_152784.3 22/22 Pfam_domain:PF15020,hmmpanther:PTHR33722,hmmpanther:PTHR33722:SF1 LOW 1 SNV 1 1 PASS rs562529395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 5778544 5778544 C A 1 0 0 0 0 0 0 0 1 2392 816 29 2 2 CATSPERD 19 5778544 Silent SNP C C3L-01924_T 961559 5778544 52839072 515 8385 VAV1 0 . GRCh38 19 6828101 6828101 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.953G>T p.Gly318Val p.G318V ENST00000602142 10/27 159 127 32 155 155 0 strelka-varscan-mutect VAV1,missense_variant,p.Gly318Val,ENST00000304076,NM_001258206.1;VAV1,missense_variant,p.Gly286Val,ENST00000596764,NM_001258207.1;VAV1,missense_variant,p.Gly263Val,ENST00000599806,;VAV1,missense_variant,p.Gly262Val,ENST00000539284,;VAV1,missense_variant,p.Gly318Val,ENST00000602142,NM_005428.3;VAV1,upstream_gene_variant,,ENST00000601452,;VAV1,downstream_gene_variant,,ENST00000594082,;VAV1,upstream_gene_variant,,ENST00000600396,;VAV1,upstream_gene_variant,,ENST00000597967,; T ENST00000602142 Transcript missense_variant 1035/2620 953/2538 318/845 G/V gGg/gTg COSM5541528,COSM5541529 1 1 VAV1 HGNC HGNC:12657 protein_coding YES CCDS12174.1 ENSP00000472929 P15498 UPI0000138213 NM_005428.3 deleterious(0.01) 10/27 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 6828101 6828101 G T 1 0 0 0 0 1 0 0 0 17676 1232 43 2 2 VAV1 19 6828101 Missense_Mutation SNP G C3L-01924_T 1049557 6828101 51789515 516 8386 MUC16 0 . GRCh38 19 8917702 8917702 + Silent SNP T T G novel C3L-01924_T C3L-01924_N T T c.36414A>C p.= p.S12138S ENST00000397910 11/84 178 162 16 171 171 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; G ENST00000397910 Transcript synonymous_variant 36618/43816 36414/43524 12138/14507 S tcA/tcC 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 11/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,SMART_domains:SM00200,Superfamily_domains:0047452 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 8917702 8917702 T G 1 0 0 0 0 0 0 0 1 9972 1567 55 5 5 MUC16 19 8917702 Silent SNP T C3L-01924_T 2089601 8917702 49699914 517 8387 MUC16 0 . GRCh38 19 8972910 8972910 + Silent SNP C C T C3L-01924_T C3L-01924_N C C c.8229G>A p.= p.S2743S ENST00000397910 1/84 141 128 13 196 195 1 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 8433/43816 8229/43524 2743/14507 S tcG/tcA COSM3543436,COSM3543437 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 1,1 LOW 1 SNV 5 1,1 1 PASS rs1364992085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 8972910 8972910 C T 1 0 0 0 0 0 0 0 1 9972 871 31 1 1 MUC16 19 8972910 Silent SNP C C3L-01924_T 55208 8972910 49644706 518 8388 MUC16 0 . GRCh38 19 8976891 8976891 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.4248T>A p.= p.P1416P ENST00000397910 1/84 228 183 45 291 291 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 4452/43816 4248/43524 1416/14507 P ccT/ccA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 8976891 8976891 A T 1 0 0 0 0 0 0 0 1 9972 175 7 4 4 MUC16 19 8976891 Silent SNP A C3L-01924_T 3981 8976891 49640725 519 8389 MUC16 0 . GRCh38 19 8980353 8980353 + Silent SNP T T C rs773941579 C3L-01924_T C3L-01924_N T T c.786A>G p.= p.G262G ENST00000397910 1/84 163 151 12 215 215 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript synonymous_variant 990/43816 786/43524 262/14507 G ggA/ggG rs773941579,COSM3363129,COSM3363130 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs773941579 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 8980353 8980353 T C 1 0 0 0 0 0 0 0 1 9972 1422 50 5 5 MUC16 19 8980353 Silent SNP T C3L-01924_T 3462 8980353 49637263 520 8390 ZNF562 0 . GRCh38 19 9659425 9659425 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.68C>A p.Thr23Lys p.T23K ENST00000453372 3/6 107 94 13 150 150 0 strelka-varscan-mutect ZNF562,missense_variant,p.Thr23Lys,ENST00000453372,NM_001130032.1,NM_001130031.1;ZNF562,missense_variant,p.Thr23Lys,ENST00000590155,NM_001300885.1;ZNF562,missense_variant,p.Thr23Lys,ENST00000587392,;ZNF562,missense_variant,p.Thr23Lys,ENST00000589542,;ZNF562,intron_variant,,ENST00000293648,NM_017656.3;ZNF562,intron_variant,,ENST00000588653,;ZNF562,downstream_gene_variant,,ENST00000585350,;ZNF562,missense_variant,p.Thr23Lys,ENST00000585688,; T ENST00000453372 Transcript missense_variant 228/2111 68/1281 23/426 T/K aCa/aAa 1 -1 ZNF562 HGNC HGNC:25950 protein_coding YES CCDS45956.1 ENSP00000410734 Q6V9R5 A0A024R7A3 UPI000067CA26 NM_001130032.1,NM_001130031.1 tolerated(0.08) 3/6 MODERATE 1 SNV 3 1 PASS rs1186523581 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 9659425 9659425 G T 1 0 0 0 0 1 0 0 0 18567 1377 48 2 2 ZNF562 19 9659425 Missense_Mutation SNP G C3L-01924_T 679072 9659425 48958191 521 8391 C19orf38 0 . GRCh38 19 10850553 10850553 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.326A>T p.Asn109Ile p.N109I ENST00000397820 2/7 294 249 45 255 254 1 strelka-varscan-mutect C19orf38,missense_variant,p.Asn109Ile,ENST00000397820,NM_001136482.1;C19orf38,missense_variant,p.Asn109Ile,ENST00000592854,;C19orf38,non_coding_transcript_exon_variant,,ENST00000587494,; T ENST00000397820 Transcript missense_variant 433/1223 326/693 109/230 N/I aAc/aTc 1 1 C19orf38 HGNC HGNC:34073 protein_coding YES CCDS45970.1 ENSP00000380920 A8MVS5 UPI0000160991 NM_001136482.1 tolerated(0.18) 2/7 hmmpanther:PTHR36859,Gene3D:2.60.40.10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 10850553 10850553 A T 1 0 0 0 0 1 0 0 0 1909 43 2 4 4 C19orf38 19 10850553 Missense_Mutation SNP A C3L-01924_T 1191128 10850553 47767063 522 8392 ECSIT 0 . GRCh38 19 11514120 11514120 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.198C>A p.= p.T66T ENST00000270517 3/8 124 99 25 142 141 1 strelka-varscan-mutect ECSIT,synonymous_variant,p.=,ENST00000270517,NM_016581.4;ECSIT,synonymous_variant,p.=,ENST00000252440,NM_001142464.2;ECSIT,synonymous_variant,p.=,ENST00000591104,NM_001243204.1;ECSIT,synonymous_variant,p.=,ENST00000590480,;ECSIT,5_prime_UTR_variant,,ENST00000592312,;ECSIT,5_prime_UTR_variant,,ENST00000585318,;ECSIT,5_prime_UTR_variant,,ENST00000592665,;ECSIT,intron_variant,,ENST00000417981,NM_001142465.2;ECSIT,intron_variant,,ENST00000588998,;ECSIT,downstream_gene_variant,,ENST00000586149,;RN7SL833P,downstream_gene_variant,,ENST00000498758,;ECSIT,upstream_gene_variant,,ENST00000591352,;ECSIT,upstream_gene_variant,,ENST00000592571,;ECSIT,upstream_gene_variant,,ENST00000593231,; T ENST00000270517 Transcript synonymous_variant 334/1700 198/1296 66/431 T acC/acA 1 -1 ECSIT HGNC HGNC:29548 protein_coding YES CCDS12262.1 ENSP00000270517 Q9BQ95 UPI0000072F31 NM_016581.4 3/8 hmmpanther:PTHR13113,Pfam_domain:PF06239 LOW 1 SNV 1 1 PASS rs1402053357 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 11514120 11514120 G T 1 0 0 0 0 0 0 0 1 4728 1335 47 2 2 ECSIT 19 11514120 Silent SNP G C3L-01924_T 663567 11514120 47103496 523 8393 ZNF20 0 . GRCh38 19 12135779 12135779 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.129G>T p.= p.L43L ENST00000334213 2/4 235 210 25 266 266 0 strelka-varscan-mutect ZNF20,synonymous_variant,p.=,ENST00000334213,NM_001203250.1,NM_021143.3;ZNF20,synonymous_variant,p.=,ENST00000418866,;ZNF20,synonymous_variant,p.=,ENST00000600335,;ZNF20,non_coding_transcript_exon_variant,,ENST00000485451,;ZNF788,non_coding_transcript_exon_variant,,ENST00000601686,;ZNF20,non_coding_transcript_exon_variant,,ENST00000480770,;ZNF20,downstream_gene_variant,,ENST00000480477,;ZNF625-ZNF20,3_prime_UTR_variant,,ENST00000430024,;ZNF20,3_prime_UTR_variant,,ENST00000454949,;ZNF20,non_coding_transcript_exon_variant,,ENST00000478942,;ZNF625-ZNF20,downstream_gene_variant,,ENST00000434822,; A ENST00000334213 Transcript synonymous_variant 354/3061 129/1599 43/532 L ctG/ctT 1 -1 ZNF20 HGNC HGNC:12992 protein_coding YES CCDS45986.1 ENSP00000335437 P17024 UPI000013C404 NM_001203250.1,NM_021143.3 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF162,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 LOW 1 SNV 1 1 PASS rs1350474487 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 12135779 12135779 C A 1 0 0 0 0 0 0 0 1 18338 813 29 2 2 ZNF20 19 12135779 Silent SNP C C3L-01924_T 621659 12135779 46481837 524 8394 PRDX2 0 . GRCh38 19 12800269 12800269 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.288G>T p.Leu96Phe p.L96F ENST00000301522 4/6 95 75 20 90 90 0 strelka-varscan-mutect PRDX2,missense_variant,p.Leu96Phe,ENST00000301522,NM_005809.5;PRDX2,missense_variant,p.Leu96Phe,ENST00000334482,;CTD-2659N19.10,intron_variant,,ENST00000585496,;HOOK2,intron_variant,,ENST00000589765,;PRDX2,non_coding_transcript_exon_variant,,ENST00000466174,;PRDX2,non_coding_transcript_exon_variant,,ENST00000477555,;PRDX2,non_coding_transcript_exon_variant,,ENST00000478908,;PRDX2,upstream_gene_variant,,ENST00000498785,; A ENST00000301522 Transcript missense_variant 417/987 288/597 96/198 L/F ttG/ttT 1 -1 PRDX2 HGNC HGNC:9353 protein_coding YES CCDS12281.1 ENSP00000301522 P32119 V9HW12 UPI0000001C80 NM_005809.5 deleterious(0.03) 4/6 PROSITE_profiles:PS51352,hmmpanther:PTHR10681:SF124,hmmpanther:PTHR10681,Gene3D:3.40.30.10,PIRSF_domain:PIRSF000239,Pfam_domain:PF00578,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 12800269 12800269 C A 1 0 0 0 0 1 0 0 0 12597 593 21 2 2 PRDX2 19 12800269 Missense_Mutation SNP C C3L-01924_T 664490 12800269 45817347 525 8395 CACNA1A 0 . GRCh38 19 13261595 13261595 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.4105G>C p.Val1369Leu p.V1369L ENST00000360228 26/47 170 143 27 203 203 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Val1370Leu,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Val1370Leu,ENST00000635895,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000637769,;CACNA1A,missense_variant,p.Val1369Leu,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Val1373Leu,ENST00000614285,;CACNA1A,missense_variant,p.Val1323Leu,ENST00000637736,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000636389,;CACNA1A,missense_variant,p.Val1373Leu,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Val1373Leu,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Val1371Leu,ENST00000573710,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000635727,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000636012,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000637276,;CACNA1A,missense_variant,p.Val1371Leu,ENST00000637927,;CACNA1A,missense_variant,p.Val1370Leu,ENST00000636549,NM_001174080.1;CACNA1A,upstream_gene_variant,,ENST00000587525,;CACNA1A,upstream_gene_variant,,ENST00000637297,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000590205,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637004,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636816,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635742,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635917,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637692,;CACNA1A,upstream_gene_variant,,ENST00000637168,;CACNA1A,upstream_gene_variant,,ENST00000636984,; G ENST00000360228 Transcript missense_variant 4340/8627 4105/7521 1369/2506 V/L Gtg/Ctg 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0.02) 26/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 29 13261595 13261595 C G 1 0 0 0 0 1 0 0 0 2226 478 17 4 4 CACNA1A 19 13261595 Missense_Mutation SNP C C3L-01924_T 461326 13261595 45356021 526 8396 CACNA1A 0 . GRCh38 19 13275908 13275908 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.3931C>A p.Leu1311Ile p.L1311I ENST00000360228 24/47 218 201 17 199 199 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Leu1312Ile,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000635895,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000637769,;CACNA1A,missense_variant,p.Leu1311Ile,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Leu1315Ile,ENST00000614285,;CACNA1A,missense_variant,p.Leu1265Ile,ENST00000637736,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000636389,;CACNA1A,missense_variant,p.Leu1315Ile,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Leu1315Ile,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Leu1313Ile,ENST00000573710,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000635727,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000636012,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000637276,;CACNA1A,missense_variant,p.Leu1313Ile,ENST00000637927,;CACNA1A,missense_variant,p.Leu1312Ile,ENST00000636549,NM_001174080.1;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637485,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637774,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635786,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637004,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635917,; T ENST00000360228 Transcript missense_variant 4166/8627 3931/7521 1311/2506 L/I Ctc/Atc 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0.01) 24/47 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 13275908 13275908 G T 1 0 0 0 0 1 0 0 0 2226 1000 35 2 2 CACNA1A 19 13275908 Missense_Mutation SNP G C3L-01924_T 14313 13275908 45341708 527 8397 PKN1 0 . GRCh38 19 14458342 14458342 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.1404G>T p.= p.L468L ENST00000342216 9/22 141 123 18 178 178 0 strelka-varscan-mutect PKN1,synonymous_variant,p.=,ENST00000242783,NM_002741.3;PKN1,synonymous_variant,p.=,ENST00000342216,NM_213560.1;PKN1,downstream_gene_variant,,ENST00000586557,;CTC-548K16.6,upstream_gene_variant,,ENST00000589702,;PKN1,non_coding_transcript_exon_variant,,ENST00000585839,;PKN1,downstream_gene_variant,,ENST00000588200,; T ENST00000342216 Transcript synonymous_variant 1435/2960 1404/2847 468/948 L ctG/ctT 1 1 PKN1 HGNC HGNC:9405 protein_coding YES CCDS42514.1 ENSP00000343325 Q16512 UPI0000366D4D NM_213560.1 9/22 Gene3D:2.60.40.150,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF158,Superfamily_domains:SSF49562 LOW 1 SNV 2 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9998834 1 1 1 0 T 2 4 29 14458342 14458342 G T 1 0 0 0 0 0 0 0 1 12075 1335 47 2 2 PKN1 19 14458342 Silent SNP G C3L-01924_T 1182434 14458342 44159274 528 8398 FCHO1 0 . GRCh38 19 17786581 17786581 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2434G>A p.Glu812Lys p.E812K ENST00000594202 27/29 137 109 28 97 97 0 strelka-varscan-mutect FCHO1,missense_variant,p.Glu812Lys,ENST00000594202,NM_001161357.1;FCHO1,missense_variant,p.Glu812Lys,ENST00000596536,NM_015122.2;FCHO1,missense_variant,p.Glu812Lys,ENST00000252771,;FCHO1,missense_variant,p.Glu812Lys,ENST00000600676,NM_001161358.1;FCHO1,missense_variant,p.Glu812Lys,ENST00000596951,;FCHO1,missense_variant,p.Glu819Lys,ENST00000597512,;FCHO1,missense_variant,p.Glu762Lys,ENST00000595033,NM_001161359.1;FCHO1,downstream_gene_variant,,ENST00000600058,;FCHO1,downstream_gene_variant,,ENST00000595594,;FCHO1,downstream_gene_variant,,ENST00000602111,;FCHO1,downstream_gene_variant,,ENST00000599766,; A ENST00000594202 Transcript missense_variant 2713/3214 2434/2676 812/891 E/K Gag/Aag 1 1 FCHO1 HGNC HGNC:29002 protein_coding YES CCDS59365.1 ENSP00000473001 A0A0C3SFZ9 UPI000059D6B0 NM_001161357.1 deleterious(0.01) 27/29 Pfam_domain:PF10291,PROSITE_profiles:PS51072,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF6 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 17786581 17786581 G A 1 0 0 0 0 1 0 0 0 5649 1175 41 3 3 FCHO1 19 17786581 Missense_Mutation SNP G C3L-01924_T 3328239 17786581 40831035 529 8399 ZNF738 0 . GRCh38 19 21361765 21361765 + Splice_Site SNP G G C novel C3L-01924_T C3L-01924_N G G c.4-1G>C p.X2_splice ENST00000311015 282 240 42 326 326 0 strelka-varscan-mutect ZNF738,splice_acceptor_variant,,ENST00000311015,;ZNF738,splice_acceptor_variant,,ENST00000380870,;ZNF738,splice_acceptor_variant,,ENST00000594245,;ZNF738,splice_acceptor_variant,,ENST00000597810,;ZNF738,splice_acceptor_variant,,ENST00000597492,; C ENST00000311015 Transcript splice_acceptor_variant -/2442 4/414 2/137 1 1 ZNF738 HGNC HGNC:32469 protein_coding YES ENSP00000311957 Q8NE65 UPI000006D73F 1/4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 29 21361765 21361765 G C 1 0 0 0 0 0 0 1 0 18709 1014 35 4 4 ZNF738 19 21361765 Splice_Site SNP G C3L-01924_T 3575184 21361765 37255851 530 8400 ZNF208 0 . GRCh38 19 21987227 21987227 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.215A>T p.Glu72Val p.E72V ENST00000397126 3/4 118 100 18 143 143 0 strelka-varscan-mutect ZNF208,missense_variant,p.Glu72Val,ENST00000397126,NM_007153.3;ZNF208,missense_variant,p.Glu72Val,ENST00000609966,;ZNF208,missense_variant,p.Glu72Val,ENST00000601773,;ZNF208,missense_variant,p.Glu40Val,ENST00000597040,;ZNF208,missense_variant,p.Glu72Val,ENST00000599916,;ZNF208,missense_variant,p.Glu71Val,ENST00000599723,;ZNF208,downstream_gene_variant,,ENST00000601993,; A ENST00000397126 Transcript missense_variant 364/3992 215/3843 72/1280 E/V gAa/gTa 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 tolerated(0.27) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103 MODERATE 1 SNV 3 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 21987227 21987227 T A 1 0 0 0 0 1 0 0 0 18343 1783 62 4 4 ZNF208 19 21987227 Missense_Mutation SNP T C3L-01924_T 625462 21987227 36630389 531 8401 ZNF676 0 . GRCh38 19 22180583 22180583 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.1134A>T p.= p.S378S ENST00000397121 3/3 309 280 29 381 381 0 varscan-mutect ZNF676,synonymous_variant,p.=,ENST00000397121,NM_001001411.2; A ENST00000397121 Transcript synonymous_variant 1452/2944 1134/1767 378/588 S tcA/tcT 1 -1 ZNF676 HGNC HGNC:20429 protein_coding YES CCDS42539.1 ENSP00000380310 Q8N7Q3 UPI00002376EC NM_001001411.2 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 22180583 22180583 T A 1 0 0 0 0 0 0 0 1 18656 1799 63 4 4 ZNF676 19 22180583 Silent SNP T C3L-01924_T 193356 22180583 36437033 532 8402 ZNF729 0 . GRCh38 19 22316016 22316016 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.2599C>G p.Leu867Val p.L867V ENST00000601693 4/4 320 254 66 430 430 0 strelka-varscan-mutect ZNF729,missense_variant,p.Leu867Val,ENST00000601693,NM_001242680.1; G ENST00000601693 Transcript missense_variant 2717/3877 2599/3759 867/1252 L/V Ctt/Gtt 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0.02) 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 22316016 22316016 C G 1 0 0 0 0 1 0 0 0 18703 681 24 4 4 ZNF729 19 22316016 Missense_Mutation SNP C C3L-01924_T 135433 22316016 36301600 533 8403 ZNF492 0 . GRCh38 19 22664666 22664666 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.997G>C p.Gly333Arg p.G333R ENST00000456783 4/4 189 171 18 225 225 0 varscan-mutect ZNF492,missense_variant,p.Gly333Arg,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; C ENST00000456783 Transcript missense_variant 1241/4245 997/1596 333/531 G/R Gga/Cga 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 22664666 22664666 G C 1 0 0 0 0 1 0 0 0 18516 1349 47 4 4 ZNF492 19 22664666 Missense_Mutation SNP G C3L-01924_T 348650 22664666 35952950 534 8404 UQCRFS1 0 . GRCh38 19 29207766 29207766 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.607G>C p.Asp203His p.D203H ENST00000304863 2/2 251 201 50 296 296 0 strelka-varscan-mutect UQCRFS1,missense_variant,p.Asp203His,ENST00000304863,NM_006003.2; G ENST00000304863 Transcript missense_variant 1030/3475 607/825 203/274 D/H Gat/Cat 1 -1 UQCRFS1 HGNC HGNC:12587 protein_coding YES CCDS12415.1 ENSP00000306397 P47985 UPI000013E9D6 NM_006003.2 deleterious(0) 2/2 PROSITE_profiles:PS51296,hmmpanther:PTHR10134,hmmpanther:PTHR10134:SF9,TIGRFAM_domain:TIGR01416,Gene3D:2.102.10.10,Pfam_domain:PF00355,Superfamily_domains:SSF50022 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 29207766 29207766 C G 1 0 0 0 0 1 0 0 0 17549 913 32 4 4 UQCRFS1 19 29207766 Missense_Mutation SNP C C3L-01924_T 6543100 29207766 29409850 535 8405 URI1 0 . GRCh38 19 30012516 30012516 + Silent SNP A A G C3L-01924_T C3L-01924_N A A c.1410A>G p.= p.L470L ENST00000392271 10/11 123 109 14 192 192 0 strelka-varscan-mutect URI1,synonymous_variant,p.=,ENST00000392271,NM_003796.3;URI1,synonymous_variant,p.=,ENST00000360605,NM_001252641.1;URI1,synonymous_variant,p.=,ENST00000575242,;URI1,synonymous_variant,p.=,ENST00000573052,;URI1,downstream_gene_variant,,ENST00000576442,;URI1,downstream_gene_variant,,ENST00000574176,;URI1,downstream_gene_variant,,ENST00000570704,;URI1,3_prime_UTR_variant,,ENST00000574110,; G ENST00000392271 Transcript synonymous_variant 1707/3444 1410/1608 470/535 L ttA/ttG COSM4999332 1 1 URI1 HGNC HGNC:13236 protein_coding YES CCDS12420.1 ENSP00000376097 O94763 UPI00001604C8 NM_003796.3 10/11 hmmpanther:PTHR15111,hmmpanther:PTHR15111:SF0 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 29 30012516 30012516 A G 1 0 0 0 0 0 0 0 1 17558 446 16 5 5 URI1 19 30012516 Silent SNP A C3L-01924_T 804750 30012516 28605100 536 8406 RGS9BP 0 . GRCh38 19 32676795 32676795 + Missense_Mutation SNP C C T rs749442416 C3L-01924_T C3L-01924_N C C c.532C>T p.Arg178Trp p.R178W ENST00000334176 1/1 263 211 52 303 303 0 strelka-varscan-mutect RGS9BP,missense_variant,p.Arg178Trp,ENST00000334176,NM_207391.2;ANKRD27,upstream_gene_variant,,ENST00000306065,NM_032139.2;ANKRD27,upstream_gene_variant,,ENST00000587352,;ANKRD27,upstream_gene_variant,,ENST00000590519,;ANKRD27,upstream_gene_variant,,ENST00000586463,;ANKRD27,upstream_gene_variant,,ENST00000586693,;CTC-379B2.4,downstream_gene_variant,,ENST00000589127,;ANKRD27,upstream_gene_variant,,ENST00000588700,; T ENST00000334176 Transcript missense_variant 1389/2894 532/708 178/235 R/W Cgg/Tgg rs749442416,COSM5564771 1 1 RGS9BP HGNC HGNC:30304 protein_coding YES CCDS12424.1 ENSP00000334134 Q6ZS82 UPI0000198BA8 NM_207391.2 deleterious(0) 1/1 hmmpanther:PTHR21029,hmmpanther:PTHR21029:SF1 0,1 MODERATE SNV 0,1 1 PASS rs749442416 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 32676795 32676795 C T 1 0 0 0 0 1 0 0 0 13485 643 23 1 1 RGS9BP 19 32676795 Missense_Mutation SNP C C3L-01924_T 2664279 32676795 25940821 537 8407 CHST8 0 . GRCh38 19 33772485 33772485 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.697C>T p.Leu233Phe p.L233F ENST00000262622 4/4 188 174 14 147 147 0 strelka-varscan-mutect CHST8,missense_variant,p.Leu233Phe,ENST00000262622,NM_022467.3;CHST8,missense_variant,p.Leu233Phe,ENST00000434302,NM_001127895.1;CHST8,missense_variant,p.Leu233Phe,ENST00000438847,NM_001127896.1;CHST8,downstream_gene_variant,,ENST00000591231,; T ENST00000262622 Transcript missense_variant 1455/2479 697/1275 233/424 L/F Ctc/Ttc 1 1 CHST8 HGNC HGNC:15993 protein_coding YES CCDS12433.1 ENSP00000262622 Q9H2A9 UPI000006F966 NM_022467.3 deleterious(0) 4/4 Pfam_domain:PF03567,hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 33772485 33772485 C T 1 0 0 0 0 1 0 0 0 3170 913 32 3 3 CHST8 19 33772485 Missense_Mutation SNP C C3L-01924_T 1095690 33772485 24845131 538 8408 ZNF599 0 . GRCh38 19 34760377 34760377 + Frame_Shift_Del DEL G G - rs375923674 C3L-01924_T C3L-01924_N G G c.424delC p.His142ThrfsTer9 p.H142Tfs*9 ENST00000329285 4/4 221 177 44 312 312 0 sindel-varindel-pindel ZNF599,frameshift_variant,p.His142ThrfsTer9,ENST00000329285,NM_001007248.2;ZNF599,downstream_gene_variant,,ENST00000587354,; - ENST00000329285 Transcript frameshift_variant 798/3099 424/1767 142/588 H/X Cac/ac rs375923674 1 -1 ZNF599 HGNC HGNC:26408 protein_coding YES CCDS32991.1 ENSP00000333802 Q96NL3 UPI0000071186 NM_001007248.2 4/4 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF20 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 34760377 34760377 G - 1 0 1 0 1 0 0 0 0 18604 1348 47 0 0 ZNF599 19 34760377 Frame_Shift_Del DEL G C3L-01924_T 987892 34760377 23857239 539 8409 KMT2B 0 . GRCh38 19 35730748 35730748 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.5318G>A p.Arg1773His p.R1773H ENST00000420124 26/37 198 185 13 211 209 2 strelka-varscan-mutect KMT2B,missense_variant,p.Arg1773His,ENST00000420124,NM_014727.2;KMT2B,upstream_gene_variant,,ENST00000585476,;KMT2B,upstream_gene_variant,,ENST00000592092,; A ENST00000420124 Transcript missense_variant 5318/8469 5318/8148 1773/2715 R/H cGc/cAc 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 deleterious(0) 26/37 Pfam_domain:PF05964,PROSITE_profiles:PS51542,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF341,SMART_domains:SM00541 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 35730748 35730748 G A 1 0 0 0 0 1 0 0 0 8296 1087 38 1 1 KMT2B 19 35730748 Missense_Mutation SNP G C3L-01924_T 970371 35730748 22886868 540 8410 U2AF1L4 0 . GRCh38 19 35744534 35744534 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.206T>G p.Val69Gly p.V69G ENST00000412391 4/8 143 110 33 218 216 2 strelka-varscan-mutect U2AF1L4,missense_variant,p.Val69Gly,ENST00000412391,;U2AF1L4,intron_variant,,ENST00000378975,NM_001040425.2;U2AF1L4,intron_variant,,ENST00000292879,NM_144987.3;U2AF1L4,intron_variant,,ENST00000587886,;PSENEN,upstream_gene_variant,,ENST00000587708,;IGFLR1,upstream_gene_variant,,ENST00000246532,;IGFLR1,upstream_gene_variant,,ENST00000592537,NM_024660.2;LIN37,upstream_gene_variant,,ENST00000301159,NM_019104.2;PSENEN,upstream_gene_variant,,ENST00000591949,;IGFLR1,upstream_gene_variant,,ENST00000592889,;IGFLR1,upstream_gene_variant,,ENST00000588992,;PSENEN,upstream_gene_variant,,ENST00000222266,NM_001281532.1,NM_172341.2;IGFLR1,upstream_gene_variant,,ENST00000591277,;IGFLR1,upstream_gene_variant,,ENST00000591748,;LIN37,upstream_gene_variant,,ENST00000587751,;IGFLR1,upstream_gene_variant,,ENST00000586140,;AC002398.11,downstream_gene_variant,,ENST00000591091,;AC002398.11,downstream_gene_variant,,ENST00000585365,;IGFLR1,upstream_gene_variant,,ENST00000587101,;U2AF1L4,downstream_gene_variant,,ENST00000588100,;LIN37,upstream_gene_variant,,ENST00000591076,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000588892,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000588980,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000586476,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000585554,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000591855,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000585771,;AD000671.6,intron_variant,,ENST00000589807,;U2AF1L4,intron_variant,,ENST00000590135,;U2AF1L4,intron_variant,,ENST00000587987,;U2AF1L4,intron_variant,,ENST00000592913,;U2AF1L4,intron_variant,,ENST00000591084,;U2AF1L4,intron_variant,,ENST00000594792,;U2AF1L4,intron_variant,,ENST00000591057,;U2AF1L4,intron_variant,,ENST00000589429,;U2AF1L4,intron_variant,,ENST00000600296,;U2AF1L4,intron_variant,,ENST00000601236,;LIN37,upstream_gene_variant,,ENST00000595455,;LIN37,upstream_gene_variant,,ENST00000587108,;LIN37,upstream_gene_variant,,ENST00000590706,;IGFLR1,upstream_gene_variant,,ENST00000588018,;AC002398.9,upstream_gene_variant,,ENST00000591613,;IGFLR1,upstream_gene_variant,,ENST00000592693,;LIN37,upstream_gene_variant,,ENST00000592871,;IGFLR1,upstream_gene_variant,,ENST00000589175,;U2AF1L4,downstream_gene_variant,,ENST00000590650,; C ENST00000412391 Transcript missense_variant 257/904 206/663 69/220 V/G gTg/gGg 1 -1 U2AF1L4 HGNC HGNC:23020 protein_coding ENSP00000397645 Q8WU68 UPI00015E0FE8 deleterious(0.04) 4/8 PROSITE_profiles:PS50102,hmmpanther:PTHR12620:SF3,hmmpanther:PTHR12620,Gene3D:3.30.70.330,SMART_domains:SM00361,Superfamily_domains:SSF54928 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 35744534 35744534 A C 1 0 0 0 0 1 0 0 0 17338 159 6 5 5 U2AF1L4 19 35744534 Missense_Mutation SNP A C3L-01924_T 13786 35744534 22873082 541 8411 ZNF382 0 . GRCh38 19 36627237 36627237 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.1340A>G p.Gln447Arg p.Q447R ENST00000292928 5/5 187 166 21 214 214 0 strelka-varscan-mutect ZNF382,missense_variant,p.Gln447Arg,ENST00000292928,NM_032825.4;ZNF382,missense_variant,p.Gln446Arg,ENST00000435416,;ZNF382,missense_variant,p.Gln446Arg,ENST00000439428,NM_001256838.1;ZNF382,missense_variant,p.Gln398Arg,ENST00000423582,;ZNF382,downstream_gene_variant,,ENST00000590785,;ZNF382,upstream_gene_variant,,ENST00000585467,; G ENST00000292928 Transcript missense_variant 1453/8329 1340/1653 447/550 Q/R cAa/cGa 1 1 ZNF382 HGNC HGNC:17409 protein_coding YES CCDS33004.1 ENSP00000292928 Q96SR6 UPI000013E0E2 NM_032825.4 tolerated(0.44) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF22,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 36627237 36627237 A G 1 0 0 0 0 1 0 0 0 18445 130 5 5 5 ZNF382 19 36627237 Missense_Mutation SNP A C3L-01924_T 882703 36627237 21990379 542 8412 ZNF527 0 . GRCh38 19 37389811 37389811 + Missense_Mutation SNP G G T rs552214606 C3L-01924_T C3L-01924_N G G c.1762G>T p.Gly588Trp p.G588W ENST00000436120 5/5 126 111 15 122 122 0 strelka-varscan-mutect ZNF527,missense_variant,p.Gly588Trp,ENST00000436120,NM_032453.1;ZNF527,intron_variant,,ENST00000587349,;ZNF527,downstream_gene_variant,,ENST00000483919,;ZNF527,downstream_gene_variant,,ENST00000588911,;ZNF527,3_prime_UTR_variant,,ENST00000356178,;ZNF527,downstream_gene_variant,,ENST00000588512,; T ENST00000436120 Transcript missense_variant 1869/2828 1762/1830 588/609 G/W Ggg/Tgg rs552214606 1 1 ZNF527 HGNC HGNC:29385 protein_coding YES CCDS42559.1 ENSP00000390179 Q8NB42 UPI00002021F5 NM_032453.1 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF71,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS rs552214606 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 37389811 37389811 G T 1 0 0 0 0 1 0 0 0 18541 1348 47 2 2 ZNF527 19 37389811 Missense_Mutation SNP G C3L-01924_T 762574 37389811 21227805 543 8413 WDR87 0 . GRCh38 19 37887395 37887395 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.6276C>A p.= p.A2092A ENST00000447313 6/6 274 247 27 316 316 0 strelka-varscan-mutect WDR87,synonymous_variant,p.=,ENST00000447313,NM_001291088.1;WDR87,synonymous_variant,p.=,ENST00000303868,NM_031951.4; T ENST00000447313 Transcript synonymous_variant 6437/9009 6276/8739 2092/2912 A gcC/gcA 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 6/6 PD936484 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 37887395 37887395 G T 1 0 0 0 0 0 0 0 1 17890 1335 47 2 2 WDR87 19 37887395 Silent SNP G C3L-01924_T 497584 37887395 20730221 544 8414 SIPA1L3 0 . GRCh38 19 38082453 38082453 + Silent SNP G G T rs768508924 C3L-01924_T C3L-01924_N G G c.888G>T p.= p.T296T ENST00000222345 3/22 74 55 19 63 63 0 strelka-varscan-mutect SIPA1L3,synonymous_variant,p.=,ENST00000222345,NM_015073.2;SIPA1L3,downstream_gene_variant,,ENST00000476317,; T ENST00000222345 Transcript synonymous_variant 1397/7987 888/5346 296/1781 T acG/acT rs768508924 1 1 SIPA1L3 HGNC HGNC:23801 protein_coding YES CCDS33007.1 ENSP00000222345 O60292 UPI00001D8160 NM_015073.2 3/22 hmmpanther:PTHR15711:SF15,hmmpanther:PTHR15711 LOW 1 SNV 1 1 PASS rs768508924 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 38082453 38082453 G T 1 0 0 0 0 0 0 0 1 14594 1103 39 1 1 SIPA1L3 19 38082453 Silent SNP G C3L-01924_T 195058 38082453 20535163 545 8415 LGALS16 0 . GRCh38 19 39658524 39658524 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.157C>A p.His53Asn p.H53N ENST00000392051 3/4 298 231 67 325 324 1 strelka-varscan-mutect LGALS16,missense_variant,p.His53Asn,ENST00000392051,NM_001190441.2;LGALS16,3_prime_UTR_variant,,ENST00000594480,; A ENST00000392051 Transcript missense_variant 225/624 157/429 53/142 H/N Cat/Aat 1 1 LGALS16 HGNC HGNC:40039 protein_coding YES CCDS54267.1 ENSP00000375904 A8MUM7 UPI00006C1A40 NM_001190441.2 deleterious(0.01) 3/4 PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF77,Pfam_domain:PF00337,Gene3D:2.60.120.200,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1478129963 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 39658524 39658524 C A 1 0 0 0 0 1 0 0 0 8649 594 21 2 2 LGALS16 19 39658524 Missense_Mutation SNP C C3L-01924_T 1576071 39658524 18959092 546 8416 AKT2 0 . GRCh38 19 40234895 40234895 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1330G>T p.Val444Phe p.V444F ENST00000579047 12/12 55 39 16 94 94 0 strelka-varscan-mutect AKT2,missense_variant,p.Val444Phe,ENST00000579047,NM_001243027.2,NM_001243028.2;AKT2,intron_variant,,ENST00000392038,NM_001626.5;AKT2,intron_variant,,ENST00000424901,;AKT2,intron_variant,,ENST00000311278,;AKT2,intron_variant,,ENST00000476247,;AKT2,intron_variant,,ENST00000497948,;AKT2,downstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000391845,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,intron_variant,,ENST00000483166,;AKT2,intron_variant,,ENST00000476266,;AKT2,intron_variant,,ENST00000391844,;AKT2,intron_variant,,ENST00000584288,;AKT2,intron_variant,,ENST00000496089,;AKT2,intron_variant,,ENST00000489375,;AKT2,downstream_gene_variant,,ENST00000537834,;AKT2,downstream_gene_variant,,ENST00000492463,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000578282,; A ENST00000579047 Transcript missense_variant 1632/2029 1330/1353 444/450 V/F Gtt/Ttt 1 -1 AKT2 HGNC HGNC:392 protein_coding ENSP00000471369 M0R0P9 UPI00024D0DDF NM_001243027.2,NM_001243028.2 deleterious_low_confidence(0.01) 12/12 PROSITE_profiles:PS51285 MODERATE SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 40234895 40234895 C A 1 0 0 0 0 1 0 0 0 563 478 17 2 2 AKT2 19 40234895 Missense_Mutation SNP C C3L-01924_T 576371 40234895 18382721 547 8417 DMRTC2 0 . GRCh38 19 41850527 41850527 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.818C>A p.Ala273Asp p.A273D ENST00000269945 8/9 69 62 7 77 77 0 strelka-varscan-mutect DMRTC2,missense_variant,p.Ala273Asp,ENST00000269945,NM_001040283.2;DMRTC2,missense_variant,p.Ala324Asp,ENST00000596827,;DMRTC2,downstream_gene_variant,,ENST00000596660,;DMRTC2,downstream_gene_variant,,ENST00000600017,;DMRTC2,downstream_gene_variant,,ENST00000596258,;DMRTC2,downstream_gene_variant,,ENST00000602098,;DMRTC2,3_prime_UTR_variant,,ENST00000601660,;DMRTC2,non_coding_transcript_exon_variant,,ENST00000599022,; A ENST00000269945 Transcript missense_variant,splice_region_variant 869/1792 818/1104 273/367 A/D gCc/gAc 1 1 DMRTC2 HGNC HGNC:13911 protein_coding YES CCDS33034.1 ENSP00000269945 Q8IXT2 UPI0000071B2A NM_001040283.2 deleterious(0.02) 8/9 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF15,Pfam_domain:PF15791 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -15.46807 0.9999954 1 1 1 0 A 3 1 29 41850527 41850527 C A 1 0 0 0 0 1 0 0 0 4399 753 26 2 2 DMRTC2 19 41850527 Missense_Mutation SNP C C3L-01924_T 1615632 41850527 16767089 548 8418 PSG11 0 . GRCh38 19 43010038 43010038 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.968C>T p.Pro323Leu p.P323L ENST00000320078 5/6 179 153 26 164 164 0 strelka-varscan-mutect PSG11,missense_variant,p.Pro323Leu,ENST00000320078,NM_002785.2;PSG11,missense_variant,p.Pro201Leu,ENST00000403486,NM_203287.1,NM_001113410.1;PSG11,missense_variant,p.Pro201Leu,ENST00000306322,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG11,downstream_gene_variant,,ENST00000599976,;PSG11,3_prime_UTR_variant,,ENST00000593983,;PSG11,non_coding_transcript_exon_variant,,ENST00000593994,;PSG11,downstream_gene_variant,,ENST00000595138,;PSG11,downstream_gene_variant,,ENST00000594655,; A ENST00000320078 Transcript missense_variant 1108/1575 968/1008 323/335 P/L cCt/cTt 1 -1 PSG11 HGNC HGNC:9516 protein_coding YES CCDS12614.2 ENSP00000319140 Q9UQ72 UPI000004EE8C NM_002785.2 deleterious(0.05) 5/6 Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS rs1481421509 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 43010038 43010038 G A 1 0 0 0 0 1 0 0 0 12805 1014 35 3 3 PSG11 19 43010038 Missense_Mutation SNP G C3L-01924_T 1159511 43010038 15607578 549 8419 RSPH6A 0 . GRCh38 19 45804670 45804670 + Missense_Mutation SNP G G T rs200271765 C3L-01924_T C3L-01924_N G G c.1235C>A p.Pro412His p.P412H ENST00000221538 3/6 269 219 50 289 289 0 strelka-varscan-mutect RSPH6A,missense_variant,p.Pro412His,ENST00000221538,NM_030785.3;RSPH6A,missense_variant,p.Pro412His,ENST00000597055,;RSPH6A,missense_variant,p.Pro148His,ENST00000600188,; T ENST00000221538 Transcript missense_variant 1378/2456 1235/2154 412/717 P/H cCc/cAc rs200271765 1 -1 RSPH6A HGNC HGNC:14241 protein_coding YES CCDS12675.1 ENSP00000221538 Q9H0K4 UPI0000037C58 NM_030785.3 deleterious(0) 3/6 Pfam_domain:PF04712,hmmpanther:PTHR13159,hmmpanther:PTHR13159:SF1 MODERATE 1 SNV 1 1 PASS rs200271765 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 45804670 45804670 G T 1 0 0 0 0 1 0 0 0 13965 1232 43 2 2 RSPH6A 19 45804670 Missense_Mutation SNP G C3L-01924_T 2794632 45804670 12812946 550 8420 PPFIA3 0 . GRCh38 19 49139694 49139694 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.2103A>T p.= p.G701G ENST00000334186 17/30 49 39 10 56 55 1 strelka-varscan-mutect PPFIA3,synonymous_variant,p.=,ENST00000334186,NM_003660.3;PPFIA3,synonymous_variant,p.=,ENST00000602351,;PPFIA3,upstream_gene_variant,,ENST00000602848,;PPFIA3,missense_variant,p.Glu627Val,ENST00000602655,;PPFIA3,non_coding_transcript_exon_variant,,ENST00000421230,;PPFIA3,downstream_gene_variant,,ENST00000602716,; T ENST00000334186 Transcript synonymous_variant 2452/4733 2103/3585 701/1194 G ggA/ggT 1 1 PPFIA3 HGNC HGNC:9247 protein_coding YES CCDS12758.1 ENSP00000335614 O75145 UPI00001AE464 NM_003660.3 17/30 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF4 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.99995 0.9999998 1 1 1 0 T 2 4 29 49139694 49139694 A T 1 0 0 0 0 0 0 0 1 12420 291 11 4 4 PPFIA3 19 49139694 Silent SNP A C3L-01924_T 3335024 49139694 9477922 551 8421 PRR12 0 . GRCh38 19 49595722 49595722 + Frame_Shift_Del DEL G G - rs770385100 C3L-01924_T C3L-01924_N G G c.1392delG p.Gln465ArgfsTer5 p.Q465Rfs*5 ENST00000418929 4/14 50 40 10 98 98 0 sindel-varindel-pindel PRR12,frameshift_variant,p.Gln465ArgfsTer5,ENST00000418929,NM_020719.1;PRR12,intron_variant,,ENST00000615927,;PRRG2,downstream_gene_variant,,ENST00000246794,NM_000951.2;PRRG2,downstream_gene_variant,,ENST00000543867,;PRRG2,downstream_gene_variant,,ENST00000597121,NM_001316335.1; - ENST00000418929 Transcript frameshift_variant 1399/6955 1387/6111 463/2036 G/X Ggg/gg rs770385100,COSM1395271 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1,Low_complexity_(Seg):seg 0,1 HIGH deletion 5 5 0,1 1 PASS . . 0 190 19 0 0 0 0 0 -19.99982 0.9986366 1 1 1 0 - 7 5 29 49595722 49595722 G - 1 0 1 0 1 0 0 0 0 12719 1000 35 0 0 PRR12 19 49595722 Frame_Shift_Del DEL G C3L-01924_T 456028 49595722 9021894 552 8422 BCL2L12 0 . GRCh38 19 49666733 49666733 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.293T>C p.Leu98Pro p.L98P ENST00000616144 2/7 93 86 7 116 116 0 varscan-mutect BCL2L12,missense_variant,p.Leu98Pro,ENST00000616144,NM_138639.1;BCL2L12,missense_variant,p.Leu98Pro,ENST00000619007,NM_001282520.1,NM_001282516.1,NM_001282519.1;BCL2L12,missense_variant,p.Leu98Pro,ENST00000246785,;BCL2L12,missense_variant,p.Leu98Pro,ENST00000614495,NM_001282521.1;BCL2L12,missense_variant,p.Leu98Pro,ENST00000441864,NM_001040668.1;BCL2L12,missense_variant,p.Leu98Pro,ENST00000611631,;BCL2L12,missense_variant,p.Leu14Pro,ENST00000246784,;BCL2L12,missense_variant,p.Leu14Pro,ENST00000600947,;BCL2L12,missense_variant,p.Leu14Pro,ENST00000594157,NM_001282517.1;BCL2L12,missense_variant,p.Leu14Pro,ENST00000598306,;IRF3,upstream_gene_variant,,ENST00000597198,;IRF3,upstream_gene_variant,,ENST00000309877,;IRF3,upstream_gene_variant,,ENST00000600911,;IRF3,upstream_gene_variant,,ENST00000377139,NM_001571.5;IRF3,upstream_gene_variant,,ENST00000601291,NM_001197122.1;IRF3,upstream_gene_variant,,ENST00000593922,NM_001197123.1;IRF3,upstream_gene_variant,,ENST00000598808,;IRF3,upstream_gene_variant,,ENST00000377135,NM_001197125.1;IRF3,upstream_gene_variant,,ENST00000598108,;IRF3,upstream_gene_variant,,ENST00000599144,NM_001197126.1;IRF3,upstream_gene_variant,,ENST00000599223,NM_001197124.1;IRF3,upstream_gene_variant,,ENST00000596756,;IRF3,upstream_gene_variant,,ENST00000593818,;IRF3,upstream_gene_variant,,ENST00000600022,NM_001197127.1;IRF3,upstream_gene_variant,,ENST00000596822,;IRF3,upstream_gene_variant,,ENST00000601809,;IRF3,upstream_gene_variant,,ENST00000595034,;IRF3,upstream_gene_variant,,ENST00000596765,NM_001197128.1;IRF3,upstream_gene_variant,,ENST00000600453,;IRF3,upstream_gene_variant,,ENST00000601373,;IRF3,upstream_gene_variant,,ENST00000593337,;IRF3,upstream_gene_variant,,ENST00000442265,;IRF3,upstream_gene_variant,,ENST00000602190,;IRF3,upstream_gene_variant,,ENST00000597180,;BCL2L12,missense_variant,p.Leu14Pro,ENST00000598979,;BCL2L12,non_coding_transcript_exon_variant,,ENST00000601168,;IRF3,upstream_gene_variant,,ENST00000597636,;IRF3,upstream_gene_variant,,ENST00000594387,;IRF3,upstream_gene_variant,,ENST00000595240,;IRF3,upstream_gene_variant,,ENST00000597369,;IRF3,upstream_gene_variant,,ENST00000596788,; C ENST00000616144 Transcript missense_variant 975/1854 293/1005 98/334 L/P cTg/cCg 1 1 BCL2L12 HGNC HGNC:13787 protein_coding YES CCDS12776.1 ENSP00000482218 Q9HB09 UPI00001267BC NM_138639.1 deleterious_low_confidence(0) 2/7 hmmpanther:PTHR14965 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 49666733 49666733 T C 1 0 0 0 0 1 0 0 0 1517 1580 55 5 5 BCL2L12 19 49666733 Missense_Mutation SNP T C3L-01924_T 71011 49666733 8950883 553 8423 KLK4 0 . GRCh38 19 50908691 50908691 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.363G>T p.Lys121Asn p.K121N ENST00000324041 3/5 434 325 109 511 509 2 strelka-varscan-mutect KLK4,missense_variant,p.Lys121Asn,ENST00000324041,NM_004917.4,NM_001302961.1;KLK4,missense_variant,p.Lys72Asn,ENST00000431178,;KLK4,upstream_gene_variant,,ENST00000597441,;KLK4,missense_variant,p.Lys26Asn,ENST00000598305,;KLK4,missense_variant,p.Lys26Asn,ENST00000593885,;KLK4,3_prime_UTR_variant,,ENST00000602148,;KLK4,non_coding_transcript_exon_variant,,ENST00000596876,;KLK4,non_coding_transcript_exon_variant,,ENST00000599865,; A ENST00000324041 Transcript missense_variant 363/1347 363/765 121/254 K/N aaG/aaT 1 -1 KLK4 HGNC HGNC:6365 protein_coding YES CCDS12809.1 ENSP00000326159 A0A0C4DFQ5 UPI0000000896 NM_004917.4,NM_001302961.1 deleterious(0) 3/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF164,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 50908691 50908691 C A 1 0 0 0 0 1 0 0 0 8275 564 20 2 2 KLK4 19 50908691 Missense_Mutation SNP C C3L-01924_T 1241958 50908691 7708925 554 8424 TARM1 0 . GRCh38 19 54075043 54075043 + Nonsense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.142C>T p.Arg48Ter p.R48* ENST00000432826 3/5 223 196 27 244 244 0 strelka-varscan-mutect TARM1,stop_gained,p.Arg56Ter,ENST00000616041,;TARM1,stop_gained,p.Arg48Ter,ENST00000432826,NM_001135686.2; A ENST00000432826 Transcript stop_gained 167/897 142/816 48/271 R/* Cga/Tga 1 -1 TARM1 HGNC HGNC:37250 protein_coding YES CCDS46173.1 ENSP00000439454 B6A8C7 UPI00034F23B2 NM_001135686.2 3/5 Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF84,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS rs1335591843 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 54075043 54075043 G A 1 0 0 0 0 0 1 0 0 15957 1095 38 1 1 TARM1 19 54075043 Nonsense_Mutation SNP G C3L-01924_T 3166352 54075043 4542573 555 8425 LENG8 0 . GRCh38 19 54454969 54454969 + Missense_Mutation SNP G G C rs200747306 C3L-01924_T C3L-01924_N G G c.698G>C p.Gly233Ala p.G233A ENST00000326764 7/16 136 99 37 179 178 1 strelka-varscan-mutect LENG8,missense_variant,p.Gly233Ala,ENST00000610347,;LENG8,missense_variant,p.Gly196Ala,ENST00000376514,;LENG8,missense_variant,p.Gly233Ala,ENST00000326764,NM_052925.3;LENG8,missense_variant,p.Gly196Ala,ENST00000616932,;LENG8,missense_variant,p.Gly233Ala,ENST00000439657,;LENG8,upstream_gene_variant,,ENST00000421200,;LENG8,downstream_gene_variant,,ENST00000443957,;LENG8,downstream_gene_variant,,ENST00000436479,;LENG8,downstream_gene_variant,,ENST00000462541,; C ENST00000326764 Transcript missense_variant 1177/3991 698/2403 233/800 G/A gGt/gCt rs200747306 1 1 LENG8 HGNC HGNC:15500 protein_coding YES CCDS12894.1 ENSP00000318374 Q96PV6 A0A024R4R9 UPI0000074196 NM_052925.3 tolerated(0.21) 7/16 hmmpanther:PTHR12436:SF4,hmmpanther:PTHR12436 MODERATE 1 SNV 1 1 PASS rs200747306 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 54454969 54454969 G C 1 0 0 0 0 1 0 0 0 8632 1261 44 4 4 LENG8 19 54454969 Missense_Mutation SNP G C3L-01924_T 379926 54454969 4162647 556 8426 TNNT1 0 . GRCh38 19 55138043 55138043 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.419C>A p.Ala140Asp p.A140D ENST00000588981 10/14 434 335 99 582 581 1 strelka-varscan-mutect TNNT1,missense_variant,p.Ala140Asp,ENST00000588981,NM_003283.5;TNNT1,missense_variant,p.Ala70Asp,ENST00000587465,;TNNT1,missense_variant,p.Ala129Asp,ENST00000587758,NM_001291774.1;TNNT1,missense_variant,p.Ala70Asp,ENST00000585321,;TNNT1,missense_variant,p.Ala140Asp,ENST00000291901,NM_001126132.2;TNNT1,missense_variant,p.Ala129Asp,ENST00000356783,NM_001126133.2;TNNT1,missense_variant,p.Ala70Asp,ENST00000536926,;TNNT1,missense_variant,p.Ala140Asp,ENST00000593046,;TNNT1,missense_variant,p.Ala88Asp,ENST00000593194,;TNNT1,missense_variant,p.Ala37Asp,ENST00000588426,;TNNT1,missense_variant,p.Ala129Asp,ENST00000589226,;TNNT1,missense_variant,p.Ala25Asp,ENST00000589745,;TNNT1,missense_variant,p.Ala136Asp,ENST00000588147,;TNNT1,upstream_gene_variant,,ENST00000586649,;TNNT1,non_coding_transcript_exon_variant,,ENST00000592920,;TNNT1,3_prime_UTR_variant,,ENST00000587089,; T ENST00000588981 Transcript missense_variant 624/1163 419/837 140/278 A/D gCc/gAc COSM1526397 1 -1 TNNT1 HGNC HGNC:11948 protein_coding YES CCDS12917.1 ENSP00000467176 P13805 UPI000016A37B NM_003283.5 deleterious(0.02) 10/14 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11521,hmmpanther:PTHR11521:SF6,Pfam_domain:PF00992 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 55138043 55138043 G T 1 0 0 0 0 1 0 0 0 16803 1203 42 2 2 TNNT1 19 55138043 Missense_Mutation SNP G C3L-01924_T 683074 55138043 3479573 557 8427 NLRP13 0 . GRCh38 19 55932175 55932175 + Nonsense_Mutation SNP G G T rs373438857 C3L-01924_T C3L-01924_N G G c.137C>A p.Ser46Ter p.S46* ENST00000342929 1/11 175 152 23 274 274 0 strelka-varscan-mutect NLRP13,stop_gained,p.Ser46Ter,ENST00000588751,NM_001321057.1;NLRP13,stop_gained,p.Ser46Ter,ENST00000342929,NM_176810.2; T ENST00000342929 Transcript stop_gained 137/3132 137/3132 46/1043 S/* tCg/tAg rs373438857 1 -1 NLRP13 HGNC HGNC:22937 protein_coding YES CCDS33119.1 ENSP00000343891 Q86W25 UPI00001AEEC8 NM_176810.2 1/11 Gene3D:1.10.533.10,Pfam_domain:PF02758,PROSITE_profiles:PS50824,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,SMART_domains:SM01289,Superfamily_domains:SSF47986 HIGH 1 SNV 1 1 PASS rs373438857 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 55932175 55932175 G T 1 0 0 0 0 0 1 0 0 10512 1059 37 1 1 NLRP13 19 55932175 Nonsense_Mutation SNP G C3L-01924_T 794132 55932175 2685441 558 8428 PEG3 0 . GRCh38 19 56816799 56816799 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1643C>G p.Pro548Arg p.P548R ENST00000326441 10/10 152 106 46 233 233 0 strelka-varscan-mutect PEG3,missense_variant,p.Pro548Arg,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Pro424Arg,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Pro548Arg,ENST00000599534,;PEG3,missense_variant,p.Pro548Arg,ENST00000599577,;PEG3,missense_variant,p.Pro422Arg,ENST00000593695,NM_001146185.1;PEG3,missense_variant,p.Pro393Arg,ENST00000600833,;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; C ENST00000326441 Transcript missense_variant 2007/8723 1643/4767 548/1588 P/R cCc/cGc 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0) 10/10 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1200148515 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 56816799 56816799 G C 1 0 0 0 0 1 0 0 0 11808 1232 43 4 4 PEG3 19 56816799 Missense_Mutation SNP G C3L-01924_T 884624 56816799 1800817 559 8429 ZSCAN4 0 . GRCh38 19 57678691 57678691 + Missense_Mutation SNP C C G novel C3L-01924_T C3L-01924_N C C c.1088C>G p.Thr363Arg p.T363R ENST00000318203 5/5 153 124 29 183 183 0 strelka-varscan-mutect ZSCAN4,missense_variant,p.Thr363Arg,ENST00000318203,NM_152677.2;ZSCAN4,missense_variant,p.Thr363Arg,ENST00000612521,;ZNF551,upstream_gene_variant,,ENST00000282296,NM_138347.4;ZNF551,upstream_gene_variant,,ENST00000601064,NM_001270938.1;AC003006.7,upstream_gene_variant,,ENST00000594684,;ZNF551,upstream_gene_variant,,ENST00000596085,;ZNF551,upstream_gene_variant,,ENST00000599402,;AC003006.7,upstream_gene_variant,,ENST00000599221,; G ENST00000318203 Transcript missense_variant 1785/2246 1088/1302 363/433 T/R aCa/aGa 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 tolerated(0.51) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 57678691 57678691 C G 1 0 0 0 0 1 0 0 0 18836 478 17 4 4 ZSCAN4 19 57678691 Missense_Mutation SNP C C3L-01924_T 861892 57678691 938925 560 8430 ZNF135 0 . GRCh38 19 58066824 58066824 + Missense_Mutation SNP G G A rs746813877 C3L-01924_T C3L-01924_N G G c.412G>A p.Glu138Lys p.E138K ENST00000401053 4/4 202 154 48 314 314 0 strelka-varscan-mutect ZNF135,missense_variant,p.Glu72Lys,ENST00000506786,NM_001289402.1;ZNF135,missense_variant,p.Glu138Lys,ENST00000401053,NM_001164529.1,NM_007134.1;ZNF135,missense_variant,p.Glu114Lys,ENST00000313434,NM_001289401.1;ZNF135,missense_variant,p.Glu126Lys,ENST00000511556,NM_003436.3;ZNF135,missense_variant,p.Glu126Lys,ENST00000359978,NM_001164530.1;RN7SL526P,upstream_gene_variant,,ENST00000469492,;ZNF135,intron_variant,,ENST00000515535,; A ENST00000401053 Transcript missense_variant 415/3346 412/2049 138/682 E/K Gaa/Aaa rs746813877 1 1 ZNF135 HGNC HGNC:12919 protein_coding YES CCDS54329.1 ENSP00000441410 P52742 UPI0001B3CB2A NM_001164529.1,NM_007134.1 tolerated(0.17) 4/4 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF250 MODERATE 1 SNV 1 1 PASS rs746813877 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 58066824 58066824 G A 1 0 0 0 0 1 0 0 0 18306 943 33 3 3 ZNF135 19 58066824 Missense_Mutation SNP G C3L-01924_T 388133 58066824 550792 561 8431 SIRPA 0 . GRCh38 20 1915350 1915350 + Missense_Mutation SNP A A G novel C3L-01924_T C3L-01924_N A A c.331A>G p.Ile111Val p.I111V ENST00000400068 3/9 265 200 65 228 228 0 strelka-varscan-mutect SIRPA,missense_variant,p.Ile111Val,ENST00000622179,;SIRPA,missense_variant,p.Ile111Val,ENST00000400068,NM_001040022.1;SIRPA,missense_variant,p.Ile111Val,ENST00000358771,NM_001040023.1;SIRPA,missense_variant,p.Ile111Val,ENST00000356025,NM_080792.2; G ENST00000400068 Transcript missense_variant 691/4201 331/1515 111/504 I/V Atc/Gtc 1 1 SIRPA HGNC HGNC:9662 protein_coding YES CCDS13022.1 ENSP00000382941 P78324 UPI0000073ADE NM_001040022.1 tolerated(0.85) 3/9 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 29 1915350 1915350 A G 1 0 0 0 0 1 0 0 0 14595 217 8 5 5 SIRPA 20 1915350 Missense_Mutation SNP A C3L-01924_T 1915350 62528817 562 8432 LAMP5 0 . GRCh38 20 9529665 9529665 + Silent SNP C C A rs368961716 C3L-01924_T C3L-01924_N C C c.688C>A p.= p.R230R ENST00000246070 6/6 74 70 4 107 107 0 varscan-mutect LAMP5,synonymous_variant,p.=,ENST00000246070,NM_012261.3;LAMP5,synonymous_variant,p.=,ENST00000427562,NM_001199897.1; A ENST00000246070 Transcript synonymous_variant 1180/2039 688/843 230/280 R Cgg/Agg rs368961716 1 1 LAMP5 HGNC HGNC:16097 protein_coding YES CCDS13106.1 ENSP00000246070 Q9UJQ1 UPI0000128675 NM_012261.3 6/6 hmmpanther:PTHR11506,Pfam_domain:PF01299 LOW 1 SNV 1 1 PASS rs368961716 . 0 203 6 0 0 0 0 0 -9.332366 0.9999994 1 1 1 0 A 2 1 29 9529665 9529665 C A 1 0 0 0 0 0 0 0 1 8524 759 27 1 1 LAMP5 20 9529665 Silent SNP C C3L-01924_T 7614315 9529665 54914502 563 8433 FOXA2 0 . GRCh38 20 22582349 22582349 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.893G>T p.Gly298Val p.G298V ENST00000419308 2/2 29 23 6 52 52 0 strelka-mutect FOXA2,missense_variant,p.Gly298Val,ENST00000419308,NM_021784.4;FOXA2,missense_variant,p.Gly292Val,ENST00000377115,NM_153675.2;LINC00261,upstream_gene_variant,,ENST00000564492,; A ENST00000419308 Transcript missense_variant 1078/2422 893/1392 298/463 G/V gGg/gTg 1 -1 FOXA2 HGNC HGNC:5022 protein_coding YES CCDS46585.1 ENSP00000400341 Q9Y261 B0ZTD4 UPI000040F9A0 NM_021784.4 deleterious(0.03) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF167 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.42005 1 1 1 1 0 A 3 1 29 22582349 22582349 C A 1 0 0 0 0 1 0 0 0 5850 623 22 2 2 FOXA2 20 22582349 Missense_Mutation SNP C C3L-01924_T 13052684 22582349 41861818 564 8434 CST8 0 . GRCh38 20 23492957 23492957 + Splice_Site SNP G G C novel C3L-01924_T C3L-01924_N G G c.232-1G>C p.X78_splice ENST00000246012 115 78 37 180 179 1 strelka-varscan-mutect CST8,splice_acceptor_variant,,ENST00000246012,NM_001281730.1,NM_005492.3;CST8,splice_acceptor_variant,,ENST00000449810,;RP3-333B15.4,intron_variant,,ENST00000619495,;RP3-333B15.6,upstream_gene_variant,,ENST00000615088,; C ENST00000246012 Transcript splice_acceptor_variant -/890 232/429 78/142 1 1 CST8 HGNC HGNC:2480 protein_coding YES CCDS13156.1 ENSP00000246012 O60676 UPI00001285BB NM_001281730.1,NM_005492.3 2/3 HIGH 1 SNV 1 1 PASS rs1346114504 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 29 23492957 23492957 G C 1 0 0 0 0 0 0 1 0 3778 1014 35 4 4 CST8 20 23492957 Splice_Site SNP G C3L-01924_T 910608 23492957 40951210 565 8435 BPIFB2 0 . GRCh38 20 33013844 33013844 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.343G>C p.Glu115Gln p.E115Q ENST00000170150 5/16 119 105 14 126 125 1 strelka-varscan-mutect BPIFB2,missense_variant,p.Glu115Gln,ENST00000170150,NM_025227.2; C ENST00000170150 Transcript missense_variant 538/1898 343/1377 115/458 E/Q Gaa/Caa 1 1 BPIFB2 HGNC HGNC:16177 protein_coding YES CCDS13210.1 ENSP00000170150 Q8N4F0 UPI00000377B0 NM_025227.2 tolerated(0.56) 5/16 Low_complexity_(Seg):seg,hmmpanther:PTHR10504:SF92,hmmpanther:PTHR10504,Pfam_domain:PF01273,PIRSF_domain:PIRSF002417,Superfamily_domains:SSF55394 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 33013844 33013844 G C 1 0 0 0 0 1 0 0 0 1658 1175 41 4 4 BPIFB2 20 33013844 Missense_Mutation SNP G C3L-01924_T 9520887 33013844 31430323 566 8436 CDK5RAP1 0 . GRCh38 20 33387501 33387501 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.577C>T p.Leu193Phe p.L193F ENST00000346416 6/14 219 161 58 238 238 0 strelka-varscan-mutect CDK5RAP1,missense_variant,p.Leu193Phe,ENST00000357886,;CDK5RAP1,missense_variant,p.Leu193Phe,ENST00000346416,NM_016082.4,NM_001278167.1,NM_016408.3;CDK5RAP1,missense_variant,p.Leu103Phe,ENST00000473997,NM_001278169.1;CDK5RAP1,missense_variant,p.Leu193Phe,ENST00000339269,NM_001278168.1;CDK5RAP1,missense_variant,p.Leu12Phe,ENST00000427097,;CDK5RAP1,non_coding_transcript_exon_variant,,ENST00000477105,;CDK5RAP1,non_coding_transcript_exon_variant,,ENST00000498525,;CDK5RAP1,non_coding_transcript_exon_variant,,ENST00000461356,;CDK5RAP1,non_coding_transcript_exon_variant,,ENST00000488723,;CDK5RAP1,intron_variant,,ENST00000481964,;CDK5RAP1,intron_variant,,ENST00000496381,;CDK5RAP1,intron_variant,,ENST00000482967,;CDK5RAP1,intron_variant,,ENST00000471264,;CDK5RAP1,intron_variant,,ENST00000460043,; A ENST00000346416 Transcript missense_variant 731/2122 577/1764 193/587 L/F Ctc/Ttc 1 -1 CDK5RAP1 HGNC HGNC:15880 protein_coding YES CCDS13219.1 ENSP00000217372 Q96SZ6 A0A0S2Z5J9 UPI000004495E NM_016082.4,NM_001278167.1,NM_016408.3 deleterious(0.01) 6/14 PROSITE_profiles:PS51449,HAMAP:MF_01864,hmmpanther:PTHR11918,hmmpanther:PTHR11918:SF43,TIGRFAM_domain:TIGR01574,TIGRFAM_domain:TIGR00089,Pfam_domain:PF00919 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 33387501 33387501 G A 1 0 0 0 0 1 0 0 0 2849 942 33 3 3 CDK5RAP1 20 33387501 Missense_Mutation SNP G C3L-01924_T 373657 33387501 31056666 567 8437 RALY 0 . GRCh38 20 34072280 34072280 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.206G>T p.Arg69Leu p.R69L ENST00000246194 3/10 202 172 30 196 195 1 strelka-varscan-mutect RALY,missense_variant,p.Arg69Leu,ENST00000375114,NM_007367.3;RALY,missense_variant,p.Arg69Leu,ENST00000246194,NM_016732.2;RALY,missense_variant,p.Arg69Leu,ENST00000448364,;RALY,missense_variant,p.Arg69Leu,ENST00000442805,;RALY,missense_variant,p.Arg69Leu,ENST00000413297,;RALY,intron_variant,,ENST00000333552,;RALY,intron_variant,,ENST00000493399,;RALY,upstream_gene_variant,,ENST00000488227,;RALY,upstream_gene_variant,,ENST00000489384,;RALY,upstream_gene_variant,,ENST00000481580,; T ENST00000246194 Transcript missense_variant 708/1789 206/921 69/306 R/L cGg/cTg 1 1 RALY HGNC HGNC:15921 protein_coding YES CCDS13230.1 ENSP00000246194 Q9UKM9 UPI00000467E6 NM_016732.2 deleterious(0.04) 3/10 Gene3D:3.30.70.330,Pfam_domain:PF00076,PIRSF_domain:PIRSF037992,PROSITE_profiles:PS50102,hmmpanther:PTHR13968,hmmpanther:PTHR13968:SF6,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs1417682106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 34072280 34072280 G T 1 0 0 0 0 1 0 0 0 13178 1116 39 1 1 RALY 20 34072280 Missense_Mutation SNP G C3L-01924_T 684779 34072280 30371887 568 8438 LPIN3 0 . GRCh38 20 41354865 41354865 + Splice_Site SNP T T A novel C3L-01924_T C3L-01924_N T T c.1664+2T>A p.X555_splice ENST00000373257 75 68 7 89 88 1 strelka-varscan-mutect LPIN3,splice_donor_variant,,ENST00000373257,;LPIN3,splice_donor_variant,,ENST00000632009,NM_001301860.1;LPIN3,splice_donor_variant,,ENST00000445975,;LPIN3,upstream_gene_variant,,ENST00000491528,;LPIN3,upstream_gene_variant,,ENST00000496565,; A ENST00000373257 Transcript splice_donor_variant -/4363 1664/2556 555/851 1 1 LPIN3 HGNC HGNC:14451 protein_coding YES ENSP00000362354 Q9BQK8 UPI0000470AE3 13/19 HIGH 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -15.22792 0.9999988 1 1 1 0 A 5 1 29 41354865 41354865 T A 1 0 0 0 0 0 0 1 0 8820 1710 59 4 4 LPIN3 20 41354865 Splice_Site SNP T C3L-01924_T 7282585 41354865 23089302 569 8439 PTPRT 0 . GRCh38 20 42448324 42448324 + Missense_Mutation SNP C C T C3L-01924_T C3L-01924_N C C c.1456G>A p.Gly486Arg p.G486R ENST00000373198 9/32 206 179 27 219 219 0 strelka-mutect PTPRT,missense_variant,p.Gly486Arg,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Gly486Arg,ENST00000373193,;PTPRT,missense_variant,p.Gly486Arg,ENST00000373201,;PTPRT,missense_variant,p.Gly486Arg,ENST00000373190,;PTPRT,missense_variant,p.Gly486Arg,ENST00000373184,;PTPRT,missense_variant,p.Gly486Arg,ENST00000356100,;PTPRT,missense_variant,p.Gly486Arg,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Gly104Arg,ENST00000612229,;PTPRT,missense_variant,p.Gly102Arg,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript missense_variant 1692/12746 1456/4383 486/1460 G/R Gga/Aga COSM3291959,COSM4292159 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 9/32 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 42448324 42448324 C T 1 0 0 0 0 1 0 0 0 12967 695 24 3 3 PTPRT 20 42448324 Missense_Mutation SNP C C3L-01924_T 1093459 42448324 21995843 570 8440 SGK2 0 . GRCh38 20 43567098 43567098 + Missense_Mutation SNP G G T C3L-01924_T C3L-01924_N G G c.247G>T p.Gly83Trp p.G83W ENST00000341458 2/12 213 146 67 214 214 0 strelka-varscan-mutect SGK2,missense_variant,p.Gly83Trp,ENST00000341458,NM_016276.3;SGK2,missense_variant,p.Gly23Trp,ENST00000373100,;SGK2,missense_variant,p.Gly23Trp,ENST00000423407,NM_001199264.1;SGK2,missense_variant,p.Gly23Trp,ENST00000373092,NM_170693.2;SGK2,missense_variant,p.Gly49Trp,ENST00000426287,;SGK2,missense_variant,p.Gly23Trp,ENST00000412111,;SGK2,downstream_gene_variant,,ENST00000617268,;SGK2,upstream_gene_variant,,ENST00000485914,;SGK2,missense_variant,p.Gly23Trp,ENST00000496343,;SGK2,missense_variant,p.Gly23Trp,ENST00000373077,;RP1-138B7.6,3_prime_UTR_variant,,ENST00000621802,;SGK2,non_coding_transcript_exon_variant,,ENST00000617358,; T ENST00000341458 Transcript missense_variant 800/2498 247/1284 83/427 G/W Ggg/Tgg COSM4913390,COSM723611 1 1 SGK2 HGNC HGNC:13900 protein_coding YES CCDS13320.1 ENSP00000340608 Q9HBY8 UPI0000033528 NM_016276.3 deleterious(0) 2/12 hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF197 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 43567098 43567098 G T 1 0 0 0 0 1 0 0 0 14468 1232 43 2 2 SGK2 20 43567098 Missense_Mutation SNP G C3L-01924_T 1118774 43567098 20877069 571 8441 TOX2 0 . GRCh38 20 44066802 44066802 + Missense_Mutation SNP A A C novel C3L-01924_T C3L-01924_N A A c.1429A>C p.Ser477Arg p.S477R ENST00000341197 8/9 178 151 27 166 166 0 strelka-varscan-mutect TOX2,missense_variant,p.Ser459Arg,ENST00000358131,NM_001098798.1;TOX2,missense_variant,p.Ser435Arg,ENST00000372999,NM_032883.2;TOX2,missense_variant,p.Ser477Arg,ENST00000341197,NM_001098797.1;TOX2,missense_variant,p.Ser435Arg,ENST00000423191,NM_001098796.1;TOX2,synonymous_variant,p.=,ENST00000413823,;TOX2,non_coding_transcript_exon_variant,,ENST00000435864,; C ENST00000341197 Transcript missense_variant 1457/1880 1429/1521 477/506 S/R Agc/Cgc 1 1 TOX2 HGNC HGNC:16095 protein_coding YES CCDS46603.1 ENSP00000344724 Q96NM4 UPI000040F535 NM_001098797.1 deleterious(0.01) 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF220 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 44066802 44066802 A C 1 0 0 0 0 1 0 0 0 16856 188 7 5 5 TOX2 20 44066802 Missense_Mutation SNP A C3L-01924_T 499704 44066802 20377365 572 8442 CASS4 0 . GRCh38 20 56451918 56451918 + Missense_Mutation SNP G G T rs764535764 C3L-01924_T C3L-01924_N G G c.742G>T p.Val248Leu p.V248L ENST00000360314 6/7 200 171 29 255 255 0 strelka-varscan-mutect CASS4,missense_variant,p.Val248Leu,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,intron_variant,,ENST00000434344,NM_001164115.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; T ENST00000360314 Transcript missense_variant 967/2619 742/2361 248/786 V/L Gtg/Ttg rs764535764 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0.04) 6/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654 MODERATE 1 SNV 1 1 PASS rs764535764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 56451918 56451918 G T 1 0 0 0 0 1 0 0 0 2382 1029 36 2 2 CASS4 20 56451918 Missense_Mutation SNP G C3L-01924_T 12385116 56451918 7992249 573 8443 PCMTD2 0 . GRCh38 20 64265291 64265291 + Silent SNP G G A novel C3L-01924_T C3L-01924_N G G c.444G>A p.= p.G148G ENST00000308824 4/6 90 65 25 93 93 0 strelka-varscan-mutect PCMTD2,synonymous_variant,p.=,ENST00000308824,NM_018257.2;PCMTD2,synonymous_variant,p.=,ENST00000369758,NM_001104925.1;PCMTD2,synonymous_variant,p.=,ENST00000299468,;PCMTD2,intron_variant,,ENST00000609372,;PCMTD2,downstream_gene_variant,,ENST00000609764,;PCMTD2,upstream_gene_variant,,ENST00000609818,;PCMTD2,downstream_gene_variant,,ENST00000610074,;PCMTD2,downstream_gene_variant,,ENST00000608844,; A ENST00000308824 Transcript synonymous_variant 571/3843 444/1086 148/361 G ggG/ggA 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 4/6 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2,Superfamily_domains:SSF53335 LOW 1 SNV 2 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999752 1 1 1 0 A 2 1 29 64265291 64265291 G A 1 0 0 0 0 0 0 0 1 11675 1161 41 3 3 PCMTD2 20 64265291 Silent SNP G C3L-01924_T 7813373 64265291 178876 574 8444 APP 0 . GRCh38 21 25911840 25911840 + Missense_Mutation SNP C C A rs199887707 C3L-01924_T C3L-01924_N C C c.1810G>T p.Val604Leu p.V604L ENST00000346798 14/18 546 416 130 569 569 0 strelka-varscan-mutect APP,missense_variant,p.Val585Leu,ENST00000357903,NM_201413.2,NM_001204302.1;APP,missense_variant,p.Val604Leu,ENST00000346798,NM_000484.3;APP,missense_variant,p.Val529Leu,ENST00000348990,NM_201414.2,NM_001204303.1;APP,missense_variant,p.Val494Leu,ENST00000359726,NM_001136131.2;APP,missense_variant,p.Val473Leu,ENST00000354192,NM_001136129.2;APP,missense_variant,p.Val580Leu,ENST00000440126,NM_001136016.3;APP,missense_variant,p.Val548Leu,ENST00000439274,NM_001136130.2;APP,missense_variant,p.Val604Leu,ENST00000358918,NM_001204301.1; A ENST00000346798 Transcript missense_variant 1844/3467 1810/2313 604/770 V/L Gtg/Ttg rs199887707,COSM1580523 1 -1 APP HGNC HGNC:620 protein_coding YES CCDS13576.1 ENSP00000284981 P05067 A0A140VJC8 UPI000002DB1C NM_000484.3 tolerated(0.54) 14/18 hmmpanther:PTHR23103,hmmpanther:PTHR23103:SF7 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199887707 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 25911840 25911840 C A 1 0 0 0 0 1 0 0 0 938 536 19 1 1 APP 21 25911840 Missense_Mutation SNP C C3L-01924_T 25911840 20798143 575 8445 ADAMTS1 0 . GRCh38 21 26838279 26838279 + Splice_Site SNP C C A rs111919920 C3L-01924_T C3L-01924_N C C c.2205-1G>T p.X735_splice ENST00000284984 60 45 15 74 74 0 strelka-varscan-mutect ADAMTS1,splice_acceptor_variant,,ENST00000284984,NM_006988.4;ADAMTS1,downstream_gene_variant,,ENST00000451462,;ADAMTS1,downstream_gene_variant,,ENST00000517777,;ADAMTS1,downstream_gene_variant,,ENST00000517452,;ADAMTS1,splice_acceptor_variant,,ENST00000464589,;ADAMTS1,splice_acceptor_variant,,ENST00000492656,; A ENST00000284984 Transcript splice_acceptor_variant -/5191 2205/2904 735/967 rs111919920 1 -1 ADAMTS1 HGNC HGNC:217 protein_coding YES CCDS33524.1 ENSP00000284984 Q9UHI8 UPI000013DDC6 NM_006988.4 8/8 HIGH 1 SNV 1 1 PASS rs111919920 . 0 199 11 0 0 0 0 0 -20 0.9999855 1 1 1 0 A 5 1 29 26838279 26838279 C A 1 0 0 0 0 0 0 1 0 299 927 32 2 2 ADAMTS1 21 26838279 Splice_Site SNP C C3L-01924_T 926439 26838279 19871704 576 8446 KRTAP23-1 0 . GRCh38 21 30348493 30348493 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.114C>A p.Ser38Arg p.S38R ENST00000334160 1/1 368 297 71 362 361 1 strelka-varscan-mutect KRTAP23-1,missense_variant,p.Ser38Arg,ENST00000334160,NM_181624.1; T ENST00000334160 Transcript missense_variant 117/211 114/198 38/65 S/R agC/agA 1 -1 KRTAP23-1 HGNC HGNC:18928 protein_coding YES CCDS33533.1 ENSP00000346536 A1A580 UPI00001A9E49 NM_181624.1 tolerated_low_confidence(0.09) 1/1 hmmpanther:PTHR19051:SF7,hmmpanther:PTHR19051,Pfam_domain:PF05287 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 30348493 30348493 G T 1 0 0 0 0 1 0 0 0 8432 1310 46 2 2 KRTAP23-1 21 30348493 Missense_Mutation SNP G C3L-01924_T 3510214 30348493 16361490 577 8447 KRTAP19-2 0 . GRCh38 21 30487196 30487196 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.153C>G p.Phe51Leu p.F51L ENST00000334055 1/1 178 143 35 185 185 0 strelka-varscan-mutect KRTAP19-2,missense_variant,p.Phe51Leu,ENST00000334055,NM_181608.1;KRTAP19-3,downstream_gene_variant,,ENST00000334063,NM_181609.3; C ENST00000334055 Transcript missense_variant 241/380 153/159 51/52 F/L ttC/ttG 1 -1 KRTAP19-2 HGNC HGNC:18937 protein_coding YES CCDS13595.1 ENSP00000335660 Q3LHN2 UPI00001A9E55 NM_181608.1 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 30487196 30487196 G C 1 0 0 0 0 1 0 0 0 8413 933 33 4 4 KRTAP19-2 21 30487196 Missense_Mutation SNP G C3L-01924_T 138703 30487196 16222787 578 8448 KRTAP19-5 0 . GRCh38 21 30502000 30502000 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.91A>G p.Ser31Gly p.S31G ENST00000334151 1/1 436 390 46 413 412 1 strelka-varscan-mutect KRTAP19-5,missense_variant,p.Ser31Gly,ENST00000334151,NM_181611.1;KRTAP19-4,upstream_gene_variant,,ENST00000334058,NM_181610.1; C ENST00000334151 Transcript missense_variant 118/461 91/219 31/72 S/G Agc/Ggc 1 -1 KRTAP19-5 HGNC HGNC:18940 protein_coding YES CCDS13597.1 ENSP00000334985 Q3LI72 UPI00001A9E50 NM_181611.1 tolerated_low_confidence(0.17) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR38140:SF4,hmmpanther:PTHR38140,Pfam_domain:PF11759 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 30502000 30502000 T C 1 0 0 0 0 1 0 0 0 8416 1580 55 5 5 KRTAP19-5 21 30502000 Missense_Mutation SNP T C3L-01924_T 14804 30502000 16207983 579 8449 URB1 0 . GRCh38 21 32361909 32361909 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1622G>T p.Cys541Phe p.C541F ENST00000382751 12/39 163 122 41 139 139 0 strelka-varscan-mutect URB1,missense_variant,p.Cys541Phe,ENST00000382751,NM_014825.2; A ENST00000382751 Transcript missense_variant 1738/10832 1622/6816 541/2271 C/F tGc/tTc 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 tolerated(0.07) 12/39 hmmpanther:PTHR13500 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 32361909 32361909 C A 1 0 0 0 0 1 0 0 0 17554 710 25 2 2 URB1 21 32361909 Missense_Mutation SNP C C3L-01924_T 1859909 32361909 14348074 580 8450 RCAN1 0 . GRCh38 21 34518210 34518210 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.708G>T p.= p.V236V ENST00000381135 4/4 206 155 51 168 168 0 strelka-varscan-mutect RCAN1,synonymous_variant,p.=,ENST00000481448,;RCAN1,synonymous_variant,p.=,ENST00000482533,;RCAN1,synonymous_variant,p.=,ENST00000381135,NM_001285391.2;RCAN1,synonymous_variant,p.=,ENST00000487990,;RCAN1,synonymous_variant,p.=,ENST00000313806,NM_004414.6;RCAN1,synonymous_variant,p.=,ENST00000381132,NM_203418.2;RCAN1,synonymous_variant,p.=,ENST00000443408,NM_203417.2;RCAN1,synonymous_variant,p.=,ENST00000620920,NM_001285392.2,NM_001285393.2;RCAN1,synonymous_variant,p.=,ENST00000399272,NM_001285389.2;RCAN1,downstream_gene_variant,,ENST00000492600,;RCAN1,non_coding_transcript_exon_variant,,ENST00000489903,;RCAN1,intron_variant,,ENST00000487434,;RCAN1,downstream_gene_variant,,ENST00000609325,; A ENST00000381135 Transcript synonymous_variant 761/2526 708/834 236/277 V gtG/gtT 1 -1 RCAN1 HGNC HGNC:3040 protein_coding YES CCDS74788.1 ENSP00000370527 E9PDJ2 UPI0003C35586 NM_001285391.2 4/4 Pfam_domain:PF04847,hmmpanther:PTHR10300,hmmpanther:PTHR10300:SF4 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 34518210 34518210 C A 1 0 0 0 0 0 0 0 1 13337 581 21 2 2 RCAN1 21 34518210 Silent SNP C C3L-01924_T 2156301 34518210 12191773 581 8451 RUNX1 0 . GRCh38 21 34792539 34792539 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.1039A>G p.Met347Val p.M347V ENST00000300305 8/8 149 114 35 174 174 0 strelka-varscan-mutect RUNX1,missense_variant,p.Met320Val,ENST00000344691,NM_001001890.2;RUNX1,missense_variant,p.Met347Val,ENST00000300305,;RUNX1,missense_variant,p.Met347Val,ENST00000437180,NM_001754.4;RUNX1,missense_variant,p.Met256Val,ENST00000399240,;RUNX1,3_prime_UTR_variant,,ENST00000482318,; C ENST00000300305 Transcript missense_variant 1484/6222 1039/1443 347/480 M/V Atg/Gtg 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A tolerated(0.11) 8/8 Gene3D:1b8xA03,PIRSF_domain:PIRSF009374,hmmpanther:PTHR11950 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 34792539 34792539 T C 1 0 0 0 0 1 0 0 0 14007 1464 51 5 5 RUNX1 21 34792539 Missense_Mutation SNP T C3L-01924_T 274329 34792539 11917444 582 8452 TMPRSS2 0 . GRCh38 21 41480507 41480507 + Missense_Mutation SNP C C T rs781089181 C3L-01924_T C3L-01924_N C C c.652G>A p.Gly218Arg p.G218R ENST00000398585 6/14 268 216 52 252 252 0 strelka-varscan-mutect TMPRSS2,missense_variant,p.Gly218Arg,ENST00000398585,NM_001135099.1;TMPRSS2,missense_variant,p.Gly181Arg,ENST00000332149,NM_005656.3;TMPRSS2,missense_variant,p.Gly181Arg,ENST00000454499,;TMPRSS2,missense_variant,p.Gly181Arg,ENST00000458356,;TMPRSS2,missense_variant,p.Gly141Arg,ENST00000424093,; T ENST00000398585 Transcript missense_variant 713/3240 652/1590 218/529 G/R Ggg/Agg rs781089181 1 -1 TMPRSS2 HGNC HGNC:11876 protein_coding YES CCDS54486.1 ENSP00000381588 O15393 UPI00019D3EE0 NM_001135099.1 deleterious(0) 6/14 PROSITE_profiles:PS50287,hmmpanther:PTHR24256:SF94,hmmpanther:PTHR24256,Gene3D:3.10.250.10,Pfam_domain:PF15494,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 2 1 PASS rs781089181 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 41480507 41480507 C T 1 0 0 0 0 1 0 0 0 16723 652 23 1 1 TMPRSS2 21 41480507 Missense_Mutation SNP C C3L-01924_T 6687968 41480507 5229476 583 8453 TRPM2 0 . GRCh38 21 44423733 44423733 + Splice_Site SNP G G A novel C3L-01924_T C3L-01924_N G G c.3549+1G>A p.X1183_splice ENST00000397928 175 164 11 163 163 0 strelka-varscan-mutect TRPM2,splice_donor_variant,,ENST00000397928,NM_003307.3;TRPM2,splice_donor_variant,,ENST00000300482,;TRPM2,splice_donor_variant,,ENST00000300481,;TRPM2,splice_donor_variant,,ENST00000397932,;TRPM2,upstream_gene_variant,,ENST00000621064,;TRPM2-AS,intron_variant,,ENST00000423310,;TRPM2,splice_donor_variant,,ENST00000498430,;TRPM2,upstream_gene_variant,,ENST00000490982,; A ENST00000397928 Transcript splice_donor_variant -/6221 3549/4512 1183/1503 1 1 TRPM2 HGNC HGNC:12339 protein_coding YES CCDS13710.1 ENSP00000381023 O94759 UPI0000169D60 NM_003307.3 23/31 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 29 44423733 44423733 G A 1 0 0 0 0 0 0 1 0 17092 1275 44 3 3 TRPM2 21 44423733 Splice_Site SNP G C3L-01924_T 2943226 44423733 2286250 584 8454 SLC19A1 0 . GRCh38 21 45531886 45531886 + Missense_Mutation SNP C C A rs754075330 C3L-01924_T C3L-01924_N C C c.452G>T p.Arg151Leu p.R151L ENST00000311124 3/6 178 129 49 194 194 0 strelka-varscan-mutect SLC19A1,missense_variant,p.Arg151Leu,ENST00000311124,NM_194255.2;SLC19A1,missense_variant,p.Arg151Leu,ENST00000567670,;SLC19A1,missense_variant,p.Arg111Leu,ENST00000485649,NM_001205207.1;SLC19A1,missense_variant,p.Arg151Leu,ENST00000380010,NM_001205206.1;SLC19A1,missense_variant,p.Arg151Leu,ENST00000443742,;SLC19A1,missense_variant,p.Arg151Leu,ENST00000427839,;SLC19A1,upstream_gene_variant,,ENST00000417954,;SLC19A1,downstream_gene_variant,,ENST00000486303,; A ENST00000311124 Transcript missense_variant 605/3811 452/1776 151/591 R/L cGt/cTt rs754075330 1 -1 SLC19A1 HGNC HGNC:10937 protein_coding YES CCDS13725.1 ENSP00000308895 P41440 UPI000012AA0F NM_194255.2 deleterious(0) 3/6 Gene3D:1.20.1250.20,Pfam_domain:PF01770,PIRSF_domain:PIRSF028739,PIRSF_domain:PIRSF500793,hmmpanther:PTHR10686,hmmpanther:PTHR10686:SF12,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00806 MODERATE 1 SNV 1 1 PASS rs754075330 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 45531886 45531886 C A 1 0 0 0 0 1 0 0 0 14694 536 19 1 1 SLC19A1 21 45531886 Missense_Mutation SNP C C3L-01924_T 1108153 45531886 1178097 585 8455 COL6A1 0 . GRCh38 21 45990256 45990256 + Splice_Site SNP A A T novel C3L-01924_T C3L-01924_N A A c.931-2A>T p.X311_splice ENST00000361866 339 263 76 287 287 0 strelka-varscan-mutect COL6A1,splice_acceptor_variant,,ENST00000361866,NM_001848.2;COL6A1,splice_acceptor_variant,,ENST00000612273,;COL6A1,downstream_gene_variant,,ENST00000492851,; T ENST00000361866 Transcript splice_acceptor_variant -/4238 931/3087 311/1028 1 1 COL6A1 HGNC HGNC:2211 protein_coding YES CCDS13727.1 ENSP00000355180 P12109 UPI000019B179 NM_001848.2 11/34 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 29 45990256 45990256 A T 1 0 0 0 0 0 0 1 0 3488 202 7 4 4 COL6A1 21 45990256 Splice_Site SNP A C3L-01924_T 458370 45990256 719727 586 8456 COL6A2 0 . GRCh38 21 46132039 46132039 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2547C>A p.Phe849Leu p.F849L ENST00000300527 28/28 418 318 100 405 403 2 strelka-varscan-mutect COL6A2,missense_variant,p.Phe849Leu,ENST00000300527,NM_001849.3;COL6A2,downstream_gene_variant,,ENST00000310645,NM_058175.2;COL6A2,downstream_gene_variant,,ENST00000409416,;COL6A2,downstream_gene_variant,,ENST00000397763,NM_058174.2;FTCD,downstream_gene_variant,,ENST00000397748,NM_001320412.1;FTCD,downstream_gene_variant,,ENST00000291670,NM_006657.2;FTCD,downstream_gene_variant,,ENST00000397746,NM_206965.1;FTCD,downstream_gene_variant,,ENST00000397743,;FTCD,downstream_gene_variant,,ENST00000446405,;FTCD,downstream_gene_variant,,ENST00000498355,;FTCD,downstream_gene_variant,,ENST00000460011,;FTCD,downstream_gene_variant,,ENST00000483568,; A ENST00000300527 Transcript missense_variant 2651/3461 2547/3060 849/1019 F/L ttC/ttA 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 tolerated(0.06) 28/28 PROSITE_profiles:PS50234,hmmpanther:PTHR24023:SF119,hmmpanther:PTHR24023,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs1169525618 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 46132039 46132039 C A 1 0 0 0 0 1 0 0 0 3489 854 30 2 2 COL6A2 21 46132039 Missense_Mutation SNP C C3L-01924_T 141783 46132039 577944 587 8457 S100B 0 . GRCh38 21 46599396 46599396 + Silent SNP A A T novel C3L-01924_T C3L-01924_N A A c.246T>A p.= p.T82T ENST00000291700 3/3 268 183 85 263 263 0 strelka-varscan-mutect S100B,synonymous_variant,p.=,ENST00000291700,NM_006272.2;S100B,synonymous_variant,p.=,ENST00000397648,;S100B,3_prime_UTR_variant,,ENST00000367071,; T ENST00000291700 Transcript synonymous_variant 443/877 246/279 82/92 T acT/acA 1 -1 S100B HGNC HGNC:10500 protein_coding YES CCDS13736.1 ENSP00000291700 P04271 A0A0S2Z4C5 UPI0000000D5F NM_006272.2 3/3 PROSITE_profiles:PS50222,hmmpanther:PTHR11639:SF17,hmmpanther:PTHR11639,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 46599396 46599396 A T 1 0 0 0 0 0 0 0 1 14047 407 15 4 4 S100B 21 46599396 Silent SNP A C3L-01924_T 467357 46599396 110587 588 8458 SLC25A1 0 . GRCh38 22 19177777 19177777 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.391G>T p.Ala131Ser p.A131S ENST00000215882 4/9 488 438 50 311 311 0 strelka-varscan-mutect SLC25A1,missense_variant,p.Ala131Ser,ENST00000215882,NM_001256534.1,NM_005984.4;SLC25A1,missense_variant,p.Ala28Ser,ENST00000451283,NM_001287387.1;CLTCL1,downstream_gene_variant,,ENST00000427926,NM_007098.3;CLTCL1,downstream_gene_variant,,ENST00000621271,NM_001835.3;CLTCL1,downstream_gene_variant,,ENST00000622493,;CLTCL1,downstream_gene_variant,,ENST00000617926,;LINC01311,downstream_gene_variant,,ENST00000565162,;SLC25A1,non_coding_transcript_exon_variant,,ENST00000461267,;SLC25A1,downstream_gene_variant,,ENST00000468824,;SLC25A1,non_coding_transcript_exon_variant,,ENST00000470922,;CLTCL1,downstream_gene_variant,,ENST00000615606,;CLTCL1,downstream_gene_variant,,ENST00000617103,;CLTCL1,downstream_gene_variant,,ENST00000412649,; A ENST00000215882 Transcript missense_variant 548/1648 391/936 131/311 A/S Gct/Tct 1 -1 SLC25A1 HGNC HGNC:10979 protein_coding YES CCDS13758.1 ENSP00000215882 P53007 UPI0000137851 NM_001256534.1,NM_005984.4 deleterious(0.02) 4/9 Low_complexity_(Seg):seg,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF379,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 19177777 19177777 C A 1 0 0 0 0 1 0 0 0 14736 768 27 1 1 SLC25A1 22 19177777 Missense_Mutation SNP C C3L-01924_T 19177777 31640691 589 8459 CDC45 0 . GRCh38 22 19516560 19516560 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1570G>T p.Val524Leu p.V524L ENST00000437685 17/20 284 248 36 180 180 0 strelka-varscan-mutect CDC45,missense_variant,p.Val492Leu,ENST00000407835,;CDC45,missense_variant,p.Val524Leu,ENST00000437685,NM_001178010.2;CDC45,missense_variant,p.Val492Leu,ENST00000263201,NM_003504.4;CDC45,missense_variant,p.Val446Leu,ENST00000404724,NM_001178011.2;CDC45,non_coding_transcript_exon_variant,,ENST00000493724,;CDC45,downstream_gene_variant,,ENST00000471470,; T ENST00000437685 Transcript missense_variant 1713/2072 1570/1797 524/598 V/L Gtg/Ttg 1 1 CDC45 HGNC HGNC:1739 protein_coding YES CCDS54499.1 ENSP00000405726 O75419 UPI000042153E NM_001178010.2 tolerated(0.08) 17/20 Pfam_domain:PF02724,hmmpanther:PTHR10507,hmmpanther:PTHR10507:SF0 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 19516560 19516560 G T 1 0 0 0 0 1 0 0 0 2784 1261 44 2 2 CDC45 22 19516560 Missense_Mutation SNP G C3L-01924_T 338783 19516560 31301908 590 8460 MORC2 0 . GRCh38 22 30941503 30941503 + Missense_Mutation SNP G G A rs864309503 C3L-01924_T C3L-01924_N G G c.754C>T p.Arg252Trp p.R252W ENST00000397641 9/26 139 131 8 140 140 0 strelka-varscan-mutect MORC2,missense_variant,p.Arg252Trp,ENST00000397641,NM_001303257.1,NM_001303256.1;MORC2,missense_variant,p.Arg190Trp,ENST00000215862,NM_014941.2;MORC2,non_coding_transcript_exon_variant,,ENST00000469915,;MORC2,downstream_gene_variant,,ENST00000476152,; A ENST00000397641 Transcript missense_variant 1163/5181 754/3099 252/1032 R/W Cgg/Tgg rs864309503,COSM5511209,COSM5511210 1 -1 MORC2 HGNC HGNC:23573 protein_coding YES CCDS77668.1 ENSP00000380763 Q9Y6X9 UPI000041AB7E NM_001303257.1,NM_001303256.1 tolerated(0.1) 9/26 hmmpanther:PTHR23337:SF7,hmmpanther:PTHR23337,Superfamily_domains:SSF55874 pathogenic 0,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs864309503 . 0 208 0 2 0 0 0 0 -11.23928 0.9999995 1 1 1 0 A 3 1 29 30941503 30941503 G A 1 0 0 0 0 1 0 0 0 9666 1115 39 1 1 MORC2 22 30941503 Missense_Mutation SNP G C3L-01924_T 11424943 30941503 19876965 591 8461 INPP5J 0 . GRCh38 22 31128497 31128497 + Missense_Mutation SNP C C T novel C3L-01924_T C3L-01924_N C C c.2036C>T p.Thr679Ile p.T679I ENST00000331075 9/13 240 217 23 250 250 0 strelka-varscan-mutect INPP5J,missense_variant,p.Thr612Ile,ENST00000412277,NM_001284286.1;INPP5J,missense_variant,p.Thr679Ile,ENST00000331075,NM_001284285.1;INPP5J,missense_variant,p.Thr312Ile,ENST00000405300,NM_001284289.1;INPP5J,missense_variant,p.Thr312Ile,ENST00000400294,NM_001284288.1;INPP5J,missense_variant,p.Thr244Ile,ENST00000620191,NM_001284287.1;INPP5J,missense_variant,p.Thr311Ile,ENST00000404390,NM_001002837.2;INPP5J,missense_variant,p.Thr44Ile,ENST00000401755,;INPP5J,missense_variant,p.Thr44Ile,ENST00000404453,;INPP5J,missense_variant,p.Thr44Ile,ENST00000402238,;INPP5J,downstream_gene_variant,,ENST00000412985,;INPP5J,downstream_gene_variant,,ENST00000420017,;INPP5J,downstream_gene_variant,,ENST00000463528,;INPP5J,non_coding_transcript_exon_variant,,ENST00000461241,; T ENST00000331075 Transcript missense_variant 2085/3347 2036/3021 679/1006 T/I aCa/aTa 1 1 INPP5J HGNC HGNC:8956 protein_coding YES CCDS63453.1 ENSP00000333262 Q15735 UPI000004CB11 NM_001284285.1 deleterious(0) 9/13 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF127,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 31128497 31128497 C T 1 0 0 0 0 1 0 0 0 7662 478 17 3 3 INPP5J 22 31128497 Missense_Mutation SNP C C3L-01924_T 186994 31128497 19689971 592 8462 SSTR3 0 . GRCh38 22 37206722 37206722 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1082G>T p.Ser361Ile p.S361I ENST00000610913 2/2 151 136 15 177 177 0 strelka-varscan-mutect SSTR3,missense_variant,p.Ser361Ile,ENST00000610913,NM_001051.4;SSTR3,missense_variant,p.Ser361Ile,ENST00000617123,NM_001278687.2; A ENST00000610913 Transcript missense_variant 1616/4100 1082/1257 361/418 S/I aGc/aTc 1 -1 SSTR3 HGNC HGNC:11332 protein_coding YES CCDS13944.1 ENSP00000480971 P32745 UPI0000050435 NM_001051.4 tolerated(0.17) 2/2 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 37206722 37206722 C A 1 0 0 0 0 1 0 0 0 15576 797 28 2 2 SSTR3 22 37206722 Missense_Mutation SNP C C3L-01924_T 6078225 37206722 13611746 593 8463 SGSM3 0 . GRCh38 22 40407282 40407282 + Missense_Mutation SNP G G T rs371516999 C3L-01924_T C3L-01924_N G G c.1322G>T p.Arg441Leu p.R441L ENST00000248929 12/22 213 192 21 223 222 1 strelka-varscan-mutect SGSM3,missense_variant,p.Arg441Leu,ENST00000248929,NM_015705.5,NM_001301849.1;MKL1,downstream_gene_variant,,ENST00000396617,NM_001282662.1;MKL1,downstream_gene_variant,,ENST00000355630,NM_020831.4;MKL1,downstream_gene_variant,,ENST00000402042,NM_001282661.1;MKL1,downstream_gene_variant,,ENST00000618196,NM_001318139.1;MKL1,downstream_gene_variant,,ENST00000407029,NM_001282660.1;MKL1,downstream_gene_variant,,ENST00000614754,;MKL1,downstream_gene_variant,,ENST00000620651,;MKL1,downstream_gene_variant,,ENST00000618417,;SGSM3,downstream_gene_variant,,ENST00000457767,;SGSM3,upstream_gene_variant,,ENST00000427834,;SGSM3,upstream_gene_variant,,ENST00000417424,;SGSM3,non_coding_transcript_exon_variant,,ENST00000478085,;SGSM3,non_coding_transcript_exon_variant,,ENST00000485962,;SGSM3,non_coding_transcript_exon_variant,,ENST00000480830,;SGSM3,non_coding_transcript_exon_variant,,ENST00000481408,;SGSM3,non_coding_transcript_exon_variant,,ENST00000470518,;SGSM3,non_coding_transcript_exon_variant,,ENST00000481028,;SGSM3,upstream_gene_variant,,ENST00000469719,;SGSM3,upstream_gene_variant,,ENST00000462457,;SGSM3,upstream_gene_variant,,ENST00000467915,;MKL1,downstream_gene_variant,,ENST00000477468,; T ENST00000248929 Transcript missense_variant 1511/2969 1322/2250 441/749 R/L cGc/cTc rs371516999,COSM1632617 1 1 SGSM3 HGNC HGNC:25228 protein_coding YES CCDS14002.1 ENSP00000248929 Q96HU1 B9A6J5 UPI0000035D8C NM_015705.5,NM_001301849.1 tolerated(0.31) 12/22 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF296 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371516999 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 40407282 40407282 G T 1 0 0 0 0 1 0 0 0 14482 1087 38 1 1 SGSM3 22 40407282 Missense_Mutation SNP G C3L-01924_T 3200560 40407282 10411186 594 8464 RANGAP1 0 . GRCh38 22 41254409 41254409 + Nonsense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1159G>T p.Glu387Ter p.E387* ENST00000455915 10/15 147 132 15 192 192 0 strelka-varscan-mutect RANGAP1,stop_gained,p.Glu387Ter,ENST00000455915,;RANGAP1,stop_gained,p.Glu387Ter,ENST00000405486,NM_001278651.1;RANGAP1,stop_gained,p.Glu387Ter,ENST00000356244,NM_002883.3;RANGAP1,downstream_gene_variant,,ENST00000446258,;MIR6889,upstream_gene_variant,,ENST00000613185,; A ENST00000455915 Transcript stop_gained 2629/4222 1159/1764 387/587 E/* Gag/Tag 1 -1 RANGAP1 HGNC HGNC:9854 protein_coding YES CCDS14012.1 ENSP00000401470 P46060 A0A024R1U0 UPI0000000DD9 10/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24113,hmmpanther:PTHR24113:SF5,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs1441490195 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 41254409 41254409 C A 1 0 0 0 0 0 1 0 0 13192 864 30 2 2 RANGAP1 22 41254409 Nonsense_Mutation SNP C C3L-01924_T 847127 41254409 9564059 595 8465 ASMTL 0 . GRCh38 X 1435053 1435053 + Silent SNP T T A novel C3L-01924_T C3L-01924_N T T c.369A>T p.= p.T123T ENST00000381317 5/13 262 191 71 336 336 0 strelka-varscan-mutect ASMTL,synonymous_variant,p.=,ENST00000534940,NM_001173473.1;ASMTL,synonymous_variant,p.=,ENST00000381333,NM_001173474.1;ASMTL,synonymous_variant,p.=,ENST00000381317,NM_004192.3;ASMTL,non_coding_transcript_exon_variant,,ENST00000463763,;ASMTL,non_coding_transcript_exon_variant,,ENST00000462195,; A ENST00000381317 Transcript synonymous_variant 402/2027 369/1866 123/621 T acA/acT 1 -1 ASMTL HGNC HGNC:751 protein_coding YES CCDS43917.1 ENSP00000370718 O95671 UPI0000141AF9 NM_004192.3 5/13 Gene3D:3.90.950.10,HAMAP:MF_00528,Pfam_domain:PF02545,Superfamily_domains:SSF52972,TIGRFAM_domain:TIGR00172 LOW 1 SNV 1 1 PASS rs1387308138 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 1435053 1435053 T A 1 0 0 0 0 0 0 0 1 1193 1567 55 4 4 ASMTL 23 1435053 Silent SNP T C3L-01924_T 1435053 154605842 596 8466 MXRA5 0 . GRCh38 X 3317554 3317554 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.6127G>T p.Ala2043Ser p.A2043S ENST00000217939 6/7 152 111 41 194 194 0 strelka-varscan-mutect MXRA5,missense_variant,p.Ala2043Ser,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 6282/9793 6127/8487 2043/2828 A/S Gcg/Tcg 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0.03) 6/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 3317554 3317554 C A 1 0 0 0 0 1 0 0 0 10002 739 26 2 2 MXRA5 23 3317554 Missense_Mutation SNP C C3L-01924_T 1882501 3317554 152723341 597 8467 MXRA5 0 . GRCh38 X 3330364 3330364 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.363G>T p.Gln121His p.Q121H ENST00000217939 4/7 101 94 7 171 171 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gln121His,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 518/9793 363/8487 121/2828 Q/H caG/caT 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.12) 4/7 Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 3330364 3330364 C A 1 0 0 0 0 1 0 0 0 10002 912 32 2 2 MXRA5 23 3330364 Missense_Mutation SNP C C3L-01924_T 12810 3330364 152710531 598 8468 NLGN4X 0 . GRCh38 X 5903265 5903265 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.1413C>A p.= p.A471A ENST00000381095 5/6 396 375 21 518 518 0 varscan-mutect NLGN4X,synonymous_variant,p.=,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,synonymous_variant,p.=,ENST00000381093,NM_001282146.1;NLGN4X,synonymous_variant,p.=,ENST00000275857,NM_020742.3;NLGN4X,synonymous_variant,p.=,ENST00000381092,;NLGN4X,synonymous_variant,p.=,ENST00000538097,;NLGN4X,non_coding_transcript_exon_variant,,ENST00000477079,; T ENST00000381095 Transcript synonymous_variant 2041/5870 1413/2451 471/816 A gcC/gcA 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 5903265 5903265 G T 1 0 0 0 0 0 0 0 1 10501 987 35 2 2 NLGN4X 23 5903265 Silent SNP G C3L-01924_T 2572901 5903265 150137630 599 8469 CLDN34 0 . GRCh38 X 9967540 9967540 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.183G>T p.= p.R61R ENST00000445307 1/1 219 206 13 273 272 1 strelka-mutect CLDN34,synonymous_variant,p.=,ENST00000445307,NM_001195081.1; T ENST00000445307 Transcript synonymous_variant 183/995 183/645 61/214 R cgG/cgT 1 1 CLDN34 HGNC HGNC:51259 protein_coding YES CCDS75951.1 ENSP00000403980 H7C241 UPI0001A5E8EC NM_001195081.1 1/1 hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF4 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 9967540 9967540 G T 1 0 0 0 0 0 0 0 1 3252 1190 42 2 2 CLDN34 23 9967540 Silent SNP G C3L-01924_T 4064275 9967540 146073355 600 8470 CLCN4 0 . GRCh38 X 10208309 10208309 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1108G>T p.Val370Leu p.V370L ENST00000380833 9/13 135 102 33 210 210 0 strelka-varscan-mutect CLCN4,missense_variant,p.Val370Leu,ENST00000380833,NM_001830.3;CLCN4,missense_variant,p.Val276Leu,ENST00000421085,NM_001256944.1;CLCN4,missense_variant,p.Val339Leu,ENST00000380829,;CLCN4,downstream_gene_variant,,ENST00000454850,; T ENST00000380833 Transcript missense_variant 1499/6750 1108/2283 370/760 V/L Gtg/Ttg 1 1 CLCN4 HGNC HGNC:2022 protein_coding YES CCDS14137.1 ENSP00000370213 P51793 UPI0000127A99 NM_001830.3 deleterious(0.04) 9/13 Gene3D:1otsB00,Pfam_domain:PF00654,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF18,Superfamily_domains:SSF81340,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 10208309 10208309 G T 1 0 0 0 0 1 0 0 0 3229 1261 44 2 2 CLCN4 23 10208309 Missense_Mutation SNP G C3L-01924_T 240769 10208309 145832586 601 8471 TLR7 0 . GRCh38 X 12886457 12886457 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.949C>A p.Gln317Lys p.Q317K ENST00000380659 3/3 188 136 52 281 281 0 strelka-varscan-mutect TLR7,missense_variant,p.Gln317Lys,ENST00000380659,NM_016562.3; A ENST00000380659 Transcript missense_variant 1088/5011 949/3150 317/1049 Q/K Cag/Aag 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(1) 3/3 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 12886457 12886457 C A 1 0 0 0 0 1 0 0 0 16402 595 21 2 2 TLR7 23 12886457 Missense_Mutation SNP C C3L-01924_T 2678148 12886457 143154438 602 8472 TLR7 0 . GRCh38 X 12887757 12887757 + Missense_Mutation SNP G G C rs765513485 C3L-01924_T C3L-01924_N G G c.2249G>C p.Arg750Pro p.R750P ENST00000380659 3/3 130 116 14 180 180 0 strelka-varscan-mutect TLR7,missense_variant,p.Arg750Pro,ENST00000380659,NM_016562.3; C ENST00000380659 Transcript missense_variant 2388/5011 2249/3150 750/1049 R/P cGa/cCa rs765513485 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(0.18) 3/3 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs765513485 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 12887757 12887757 G C 1 0 0 0 0 1 0 0 0 16402 1058 37 4 4 TLR7 23 12887757 Missense_Mutation SNP G C3L-01924_T 1300 12887757 143153138 603 8473 RAI2 0 . GRCh38 X 17801645 17801645 + Silent SNP C C A rs537190832 C3L-01924_T C3L-01924_N C C c.366G>T p.= p.L122L ENST00000545871 3/3 156 147 9 187 186 1 strelka-mutect RAI2,synonymous_variant,p.=,ENST00000545871,NM_001172739.1,NM_001172743.1;RAI2,synonymous_variant,p.=,ENST00000360011,;RAI2,synonymous_variant,p.=,ENST00000331511,;RAI2,synonymous_variant,p.=,ENST00000451717,NM_021785.4;RAI2,synonymous_variant,p.=,ENST00000415486,NM_001172732.1;RAI2,downstream_gene_variant,,ENST00000509491,; A ENST00000545871 Transcript synonymous_variant 827/2421 366/1593 122/530 L ctG/ctT rs537190832 1 -1 RAI2 HGNC HGNC:9835 protein_coding YES CCDS14183.1 ENSP00000444210 Q9Y5P3 UPI000013CE19 NM_001172739.1,NM_001172743.1 3/3 hmmpanther:PTHR23186:SF3,hmmpanther:PTHR23186,Pfam_domain:PF15279 LOW 1 SNV 4 1 PASS rs537190832 . 0 202 6 2 0 0 0 0 -12.15185 0.9994412 1 1 1 0 A 2 1 29 17801645 17801645 C A 1 0 0 0 0 0 0 0 1 13168 697 25 2 2 RAI2 23 17801645 Silent SNP C C3L-01924_T 4913888 17801645 138239250 604 8474 MAGEB6P1 0 . GRCh38 X 26161014 26161014 + Silent SNP C C A novel C3L-01924_T C3L-01924_N C C c.414C>A p.= p.T138T ENST00000416929 1/1 268 240 28 316 315 1 strelka-varscan-mutect MAGEB6P1,synonymous_variant,p.=,ENST00000416929,; A ENST00000416929 Transcript synonymous_variant 414/1224 414/1224 138/407 T acC/acA 1 1 MAGEB6P1 HGNC HGNC:28824 protein_coding YES ENSP00000488257 A0A0J9YX57 UPI0000237759 1/1 Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 26161014 26161014 C A 1 0 0 0 0 0 0 0 1 9097 668 24 2 2 MAGEB6P1 23 26161014 Silent SNP C C3L-01924_T 8359369 26161014 129879881 605 8475 DMD 0 . GRCh38 X 32472217 32472217 + Nonsense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.2896C>T p.Gln966Ter p.Q966* ENST00000357033 22/79 396 372 24 406 406 0 strelka-varscan-mutect DMD,stop_gained,p.Gln966Ter,ENST00000357033,NM_000109.3,NM_004006.2;DMD,stop_gained,p.Gln962Ter,ENST00000378677,NM_004010.3,NM_004009.3;DMD,stop_gained,p.Gln966Ter,ENST00000620040,;DMD,stop_gained,p.Gln962Ter,ENST00000619831,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000488902,; A ENST00000357033 Transcript stop_gained 3103/13956 2896/11058 966/3685 Q/* Caa/Taa 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 22/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,Pfam_domain:PF00435,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150 HIGH 1 SNV 1 1 PASS rs1424174974 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 29 32472217 32472217 G A 1 0 0 0 0 0 1 0 0 4387 1299 45 3 3 DMD 23 32472217 Nonsense_Mutation SNP G C3L-01924_T 6311203 32472217 123568678 606 8476 FAM47C 0 . GRCh38 X 37009105 37009105 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.695C>A p.Ser232Tyr p.S232Y ENST00000358047 1/1 342 317 25 413 413 0 varscan-mutect FAM47C,missense_variant,p.Ser232Tyr,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript missense_variant 709/3270 695/3108 232/1035 S/Y tCc/tAc 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0) 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 37009105 37009105 C A 1 0 0 0 0 1 0 0 0 5449 855 30 2 2 FAM47C 23 37009105 Missense_Mutation SNP C C3L-01924_T 4536888 37009105 119031790 607 8477 OTC 0 . GRCh38 X 38409000 38409000 + Missense_Mutation SNP T T C C3L-01924_T C3L-01924_N T T c.842T>C p.Phe281Ser p.F281S ENST00000039007 8/10 395 284 111 547 547 0 strelka-varscan-mutect OTC,missense_variant,p.Phe281Ser,ENST00000039007,NM_000531.5;RP5-972B16.2,intron_variant,,ENST00000465127,; C ENST00000039007 Transcript missense_variant 994/1585 842/1065 281/354 F/S tTc/tCc CM065363 1 1 OTC HGNC HGNC:8512 protein_coding YES CCDS14247.1 ENSP00000039007 P00480 UPI000013C550 NM_000531.5 deleterious(0) 8/10 Gene3D:3.40.50.1370,Pfam_domain:PF00185,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF1,Superfamily_domains:SSF53671,TIGRFAM_domain:TIGR00658 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 38409000 38409000 T C 1 0 0 0 0 1 0 0 0 11367 1783 62 5 5 OTC 23 38409000 Missense_Mutation SNP T C3L-01924_T 1399895 38409000 117631895 608 8478 CHST7 0 . GRCh38 X 46574384 46574384 + Silent SNP C C A C3L-01924_T C3L-01924_N C C c.453C>A p.= p.G151G ENST00000276055 1/2 263 247 16 264 264 0 strelka-varscan-mutect CHST7,synonymous_variant,p.=,ENST00000276055,NM_019886.3; A ENST00000276055 Transcript synonymous_variant 601/2289 453/1461 151/486 G ggC/ggA COSM4109582 1 1 CHST7 HGNC HGNC:13817 protein_coding YES CCDS14268.1 ENSP00000276055 Q9NS84 UPI000000DADD NM_019886.3 1/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF5 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 29 46574384 46574384 C A 1 0 0 0 0 0 0 0 1 3169 755 27 1 1 CHST7 23 46574384 Silent SNP C C3L-01924_T 8165384 46574384 109466511 609 8479 SYP 0 . GRCh38 X 49193280 49193280 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.607A>T p.Thr203Ser p.T203S ENST00000263233 5/7 328 309 19 368 367 1 strelka-varscan-mutect SYP,missense_variant,p.Thr203Ser,ENST00000263233,NM_003179.2;SYP,missense_variant,p.Thr203Ser,ENST00000479808,;SYP,missense_variant,p.Thr93Ser,ENST00000472598,;SYP,3_prime_UTR_variant,,ENST00000376303,;SYP,downstream_gene_variant,,ENST00000494396,;SYP,downstream_gene_variant,,ENST00000469389,;SYP,downstream_gene_variant,,ENST00000472737,;SYP,downstream_gene_variant,,ENST00000466635,; A ENST00000263233 Transcript missense_variant 680/2498 607/942 203/313 T/S Acc/Tcc 1 -1 SYP HGNC HGNC:11506 protein_coding YES CCDS14321.1 ENSP00000263233 P08247 UPI0000117AEC NM_003179.2 tolerated(0.13) 5/7 Pfam_domain:PF01284,PROSITE_profiles:PS51225,hmmpanther:PTHR10306,hmmpanther:PTHR10306:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 49193280 49193280 T A 1 0 0 0 0 1 0 0 0 15855 1696 59 4 4 SYP 23 49193280 Missense_Mutation SNP T C3L-01924_T 2618896 49193280 106847615 610 8480 PPP1R3F 0 . GRCh38 X 49286781 49286781 + Silent SNP C C T novel C3L-01924_T C3L-01924_N C C c.2091C>T p.= p.V697V ENST00000055335 4/4 62 57 5 97 96 1 strelka-varscan-mutect PPP1R3F,synonymous_variant,p.=,ENST00000055335,NM_033215.4;PPP1R3F,synonymous_variant,p.=,ENST00000376188,;PPP1R3F,synonymous_variant,p.=,ENST00000466508,;PPP1R3F,synonymous_variant,p.=,ENST00000495799,NM_001184745.1;PPP1R3F,intron_variant,,ENST00000471261,; T ENST00000055335 Transcript synonymous_variant 2107/3421 2091/2400 697/799 V gtC/gtT 1 1 PPP1R3F HGNC HGNC:14944 protein_coding YES CCDS35254.1 ENSP00000055335 Q6ZSY5 UPI00001D7BA8 NM_033215.4 4/4 hmmpanther:PTHR12307:SF5,hmmpanther:PTHR12307 LOW 1 SNV 2 1 PASS rs782168549 . 0 206 4 0 0 0 0 0 -11.90922 1 1 1 1 0 T 2 4 29 49286781 49286781 C T 1 0 0 0 0 0 0 0 1 12496 842 30 3 3 PPP1R3F 23 49286781 Silent SNP C C3L-01924_T 93501 49286781 106754114 611 8481 MAGED1 0 . GRCh38 X 51896614 51896614 + Missense_Mutation SNP G G T rs373153783 C3L-01924_T C3L-01924_N G G c.1127G>T p.Arg376Leu p.R376L ENST00000375695 5/14 221 188 33 259 259 0 strelka-varscan-mutect MAGED1,missense_variant,p.Arg376Leu,ENST00000375695,NM_001005333.1;MAGED1,missense_variant,p.Arg320Leu,ENST00000375722,;MAGED1,missense_variant,p.Arg320Leu,ENST00000326587,NM_006986.3;MAGED1,missense_variant,p.Arg320Leu,ENST00000375772,NM_001005332.1;MAGED1,non_coding_transcript_exon_variant,,ENST00000494718,;MAGED1,non_coding_transcript_exon_variant,,ENST00000485420,;MAGED1,upstream_gene_variant,,ENST00000473931,;MAGED1,downstream_gene_variant,,ENST00000470461,;MAGED1,downstream_gene_variant,,ENST00000482188,;MAGED1,downstream_gene_variant,,ENST00000482599,; T ENST00000375695 Transcript missense_variant 1280/2875 1127/2505 376/834 R/L cGt/cTt rs373153783,COSM1122846 1 1 MAGED1 HGNC HGNC:6813 protein_coding YES CCDS35279.1 ENSP00000364847 Q9Y5V3 UPI0000074161 NM_001005333.1 deleterious_low_confidence(0) 5/14 hmmpanther:PTHR11736:SF28,hmmpanther:PTHR11736 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373153783 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 51896614 51896614 G T 1 0 0 0 0 1 0 0 0 9101 1145 40 1 1 MAGED1 23 51896614 Missense_Mutation SNP G C3L-01924_T 2609833 51896614 104144281 612 8482 PFKFB1 0 . GRCh38 X 54952085 54952085 + Missense_Mutation SNP G G T rs766396112 C3L-01924_T C3L-01924_N G G c.666C>A p.Asp222Glu p.D222E ENST00000375006 8/14 161 150 11 189 189 0 strelka-mutect PFKFB1,missense_variant,p.Asp222Glu,ENST00000375006,NM_001271804.1,NM_002625.3;PFKFB1,missense_variant,p.Asp157Glu,ENST00000545676,NM_001271805.1;PFKFB1,5_prime_UTR_variant,,ENST00000614686,;PFKFB1,intron_variant,,ENST00000374992,; T ENST00000375006 Transcript missense_variant 737/1929 666/1416 222/471 D/E gaC/gaA rs766396112,COSM1558584,COSM3965386 1 -1 PFKFB1 HGNC HGNC:8872 protein_coding YES CCDS14364.1 ENSP00000364145 P16118 UPI000012A3ED NM_001271804.1,NM_002625.3 8/14 Gene3D:3.40.50.300,Pfam_domain:PF01591,PIRSF_domain:PIRSF000709,hmmpanther:PTHR10606,hmmpanther:PTHR10606:SF15,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766396112 . 0 206 4 0 0 0 0 0 -19.75816 1 1 1 1 0 T 3 4 29 54952085 54952085 G T 1 0 0 0 0 1 0 0 0 11850 1136 40 1 1 PFKFB1 23 54952085 Missense_Mutation SNP G C3L-01924_T 3055471 54952085 101088810 613 8483 LAS1L 0 . GRCh38 X 65534573 65534573 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.143G>T p.Arg48Met p.R48M ENST00000374811 1/14 312 288 24 268 267 1 strelka-varscan-mutect LAS1L,missense_variant,p.Arg48Met,ENST00000374811,NM_031206.4;LAS1L,missense_variant,p.Arg48Met,ENST00000374807,NM_001170649.1;LAS1L,missense_variant,p.Arg48Met,ENST00000374804,NM_001170650.1;LAS1L,missense_variant,p.Arg48Met,ENST00000484069,; A ENST00000374811 Transcript missense_variant 184/2439 143/2205 48/734 R/M aGg/aTg 1 -1 LAS1L HGNC HGNC:25726 protein_coding YES CCDS14381.1 ENSP00000363944 Q9Y4W2 UPI0000073CB7 NM_031206.4 deleterious(0) 1/14 Pfam_domain:PF04031,hmmpanther:PTHR15002 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 65534573 65534573 C A 1 0 0 0 0 1 0 0 0 8547 681 24 2 2 LAS1L 23 65534573 Missense_Mutation SNP C C3L-01924_T 10582488 65534573 90506322 614 8484 HEPH 0 . GRCh38 X 66256291 66256291 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.3019C>A p.Leu1007Ile p.L1007I ENST00000519389 17/21 159 143 16 215 215 0 strelka-varscan-mutect HEPH,missense_variant,p.Leu1007Ile,ENST00000519389,NM_138737.4;HEPH,missense_variant,p.Leu953Ile,ENST00000343002,;HEPH,missense_variant,p.Leu956Ile,ENST00000441993,NM_001130860.3;HEPH,missense_variant,p.Leu686Ile,ENST00000336279,NM_014799.3;HEPH,missense_variant,p.Leu764Ile,ENST00000419594,NM_001282141.1; A ENST00000519389 Transcript missense_variant 3198/6013 3019/3639 1007/1212 L/I Cta/Ata 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 tolerated(0.38) 17/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 66256291 66256291 C A 1 0 0 0 0 1 0 0 0 6938 680 24 2 2 HEPH 23 66256291 Missense_Mutation SNP C C3L-01924_T 721718 66256291 89784604 615 8485 PJA1 0 . GRCh38 X 69161972 69161972 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1267G>T p.Ala423Ser p.A423S ENST00000361478 2/2 240 220 20 249 249 0 strelka-varscan-mutect PJA1,missense_variant,p.Ala423Ser,ENST00000361478,NM_145119.3;PJA1,missense_variant,p.Ala423Ser,ENST00000374583,;PJA1,missense_variant,p.Ala368Ser,ENST00000374571,NM_001032396.2;PJA1,missense_variant,p.Ala235Ser,ENST00000374584,NM_022368.4;PJA1,intron_variant,,ENST00000471141,;PJA1,downstream_gene_variant,,ENST00000590146,;PJA1,downstream_gene_variant,,ENST00000477231,; A ENST00000361478 Transcript missense_variant 1645/2755 1267/1932 423/643 A/S Gcc/Tcc 1 -1 PJA1 HGNC HGNC:16648 protein_coding YES CCDS14393.1 ENSP00000355014 Q8NG27 UPI000006D00A NM_145119.3 tolerated(0.58) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 69161972 69161972 C A 1 0 0 0 0 1 0 0 0 12057 710 25 2 2 PJA1 23 69161972 Missense_Mutation SNP C C3L-01924_T 2905681 69161972 86878923 616 8486 P2RY4 0 . GRCh38 X 70259564 70259564 + Missense_Mutation SNP T T C novel C3L-01924_T C3L-01924_N T T c.61A>G p.Ser21Gly p.S21G ENST00000374519 1/1 126 119 7 182 181 1 strelka-varscan-mutect P2RY4,missense_variant,p.Ser21Gly,ENST00000374519,NM_002565.3; C ENST00000374519 Transcript missense_variant 201/1595 61/1098 21/365 S/G Agt/Ggt 1 -1 P2RY4 HGNC HGNC:8542 protein_coding YES CCDS14398.1 ENSP00000363643 P51582 UPI000002E776 NM_002565.3 tolerated(0.38) 1/1 hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF21,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 70259564 70259564 T C 1 0 0 0 0 1 0 0 0 11426 1580 55 5 5 P2RY4 23 70259564 Missense_Mutation SNP T C3L-01924_T 1097592 70259564 85781331 617 8487 MAGEE1 0 . GRCh38 X 76429053 76429053 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1123G>T p.Gly375Ter p.G375* ENST00000361470 1/1 260 161 99 271 271 0 strelka-varscan-mutect MAGEE1,stop_gained,p.Gly375Ter,ENST00000361470,NM_020932.2; T ENST00000361470 Transcript stop_gained 1330/3630 1123/2874 375/957 G/* Gga/Tga 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 1/1 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF9 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 76429053 76429053 G T 1 0 0 0 0 0 1 0 0 9103 1349 47 2 2 MAGEE1 23 76429053 Nonsense_Mutation SNP G C3L-01924_T 6169489 76429053 79611842 618 8488 LPAR4 0 . GRCh38 X 78755968 78755968 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.1099G>T p.Glu367Ter p.E367* ENST00000435339 2/2 69 63 6 129 127 2 strelka-varscan-mutect LPAR4,stop_gained,p.Glu367Ter,ENST00000435339,NM_005296.2;LPAR4,stop_gained,p.Glu367Ter,ENST00000614823,NM_001278000.1;LPAR4,downstream_gene_variant,,ENST00000514744,;LPAR4,downstream_gene_variant,,ENST00000610214,;LPAR4,downstream_gene_variant,,ENST00000607964,; T ENST00000435339 Transcript stop_gained 1485/2611 1099/1113 367/370 E/* Gaa/Taa 1 1 LPAR4 HGNC HGNC:4478 protein_coding YES CCDS14441.1 ENSP00000408205 Q99677 UPI000005041D NM_005296.2 2/2 hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF41 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.66536 1 1 1 1 0 T 4 4 29 78755968 78755968 G T 1 0 0 0 0 0 1 0 0 8810 943 33 2 2 LPAR4 23 78755968 Nonsense_Mutation SNP G C3L-01924_T 2326915 78755968 77284927 619 8489 BRWD3 0 . GRCh38 X 80676683 80676683 + Missense_Mutation SNP T T A novel C3L-01924_T C3L-01924_N T T c.5335A>T p.Thr1779Ser p.T1779S ENST00000373275 41/41 165 147 18 219 219 0 strelka-varscan-mutect BRWD3,missense_variant,p.Thr1779Ser,ENST00000373275,NM_153252.4;BRWD3,downstream_gene_variant,,ENST00000473691,; A ENST00000373275 Transcript missense_variant 5552/11381 5335/5409 1779/1802 T/S Aca/Tca 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 deleterious_low_confidence(0.02) 41/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 80676683 80676683 T A 1 0 0 0 0 1 0 0 0 1700 1638 57 4 4 BRWD3 23 80676683 Missense_Mutation SNP T C3L-01924_T 1920715 80676683 75364212 620 8490 TAF7L 0 . GRCh38 X 101292889 101292889 + Frame_Shift_Del DEL C C - novel C3L-01924_T C3L-01924_N C C c.157delG p.Glu53LysfsTer35 p.E53Kfs*35 ENST00000372907 1/13 310 293 17 377 376 1 varindel-pindel TAF7L,frameshift_variant,p.Glu53LysfsTer35,ENST00000372907,NM_024885.3;TAF7L,upstream_gene_variant,,ENST00000356784,NM_001168474.1; - ENST00000372907 Transcript frameshift_variant 169/2341 157/1389 53/462 E/X Gaa/aa 1 -1 TAF7L HGNC HGNC:11548 protein_coding YES CCDS35347.1 ENSP00000361998 Q5H9L4 UPI0000212176 NM_024885.3 1/13 hmmpanther:PTHR12228:SF8,hmmpanther:PTHR12228 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 29 101292889 101292889 C - 1 0 1 0 1 0 0 0 0 15929 893 31 0 0 TAF7L 23 101292889 Frame_Shift_Del DEL C C3L-01924_T 20616206 101292889 54748006 621 8491 RAB40A 0 . GRCh38 X 103500386 103500386 + Missense_Mutation SNP A A T novel C3L-01924_T C3L-01924_N A A c.371T>A p.Val124Glu p.V124E ENST00000372633 1/1 200 184 16 301 301 0 varscan-mutect RAB40A,missense_variant,p.Val124Glu,ENST00000372633,;RAB40A,missense_variant,p.Val124Glu,ENST00000304236,NM_080879.2;LL0XNC01-250H12.3,downstream_gene_variant,,ENST00000445990,; T ENST00000372633 Transcript missense_variant 2490/3126 371/834 124/277 V/E gTg/gAg 1 -1 RAB40A HGNC HGNC:18283 protein_coding YES CCDS35357.1 ENSP00000361716 Q8WXH6 UPI000013E953 deleterious(0) 1/1 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF442,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE SNV 1 PASS rs1427761871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 103500386 103500386 A T 1 0 0 0 0 1 0 0 0 13098 159 6 4 4 RAB40A 23 103500386 Missense_Mutation SNP A C3L-01924_T 2207497 103500386 52540509 622 8492 MUM1L1 0 . GRCh38 X 106207346 106207346 + Missense_Mutation SNP A A C rs749708056 C3L-01924_T C3L-01924_N A A c.1914A>C p.Glu638Asp p.E638D ENST00000337685 5/5 148 139 9 208 207 1 strelka-varscan-mutect MUM1L1,missense_variant,p.Glu638Asp,ENST00000337685,NM_152423.4;MUM1L1,missense_variant,p.Glu638Asp,ENST00000357175,NM_001171020.1;MUM1L1,missense_variant,p.Glu638Asp,ENST00000372552,; C ENST00000337685 Transcript missense_variant 2699/4308 1914/2091 638/696 E/D gaA/gaC rs749708056,COSM5432931,COSM5432932 1 1 MUM1L1 HGNC HGNC:26583 protein_coding YES CCDS55469.1 ENSP00000338641 Q5H9M0 UPI0000212206 NM_152423.4 deleterious(0.04) 5/5 hmmpanther:PTHR31333,hmmpanther:PTHR31333:SF3 0,1,1 MODERATE 1 SNV 3 0,1,1 1 PASS rs749708056 . 0 207 2 0 0 0 0 0 -17.03753 1 1 1 1 0 C 3 2 29 106207346 106207346 A C 1 0 0 0 0 1 0 0 0 9984 69 3 5 5 MUM1L1 23 106207346 Missense_Mutation SNP A C3L-01924_T 2706960 106207346 49833549 623 8493 COL4A6 0 . GRCh38 X 108180962 108180962 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.2009C>A p.Thr670Asn p.T670N ENST00000394872 25/46 185 170 15 198 198 0 strelka-varscan-mutect COL4A6,missense_variant,p.Thr670Asn,ENST00000394872,NM_001287758.1;COL4A6,missense_variant,p.Thr653Asn,ENST00000334504,NM_033641.3;COL4A6,missense_variant,p.Thr653Asn,ENST00000621266,NM_001287759.1;COL4A6,missense_variant,p.Thr654Asn,ENST00000372216,NM_001847.3;COL4A6,missense_variant,p.Thr653Asn,ENST00000538570,NM_001287760.1;COL4A6,missense_variant,p.Thr653Asn,ENST00000545689,; T ENST00000394872 Transcript missense_variant 2243/6750 2009/5124 670/1707 T/N aCc/aAc 1 -1 COL4A6 HGNC HGNC:2208 protein_coding YES CCDS76010.1 ENSP00000378340 A8MXH5 UPI000387C996 NM_001287758.1 tolerated(0.09) 25/46 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 108180962 108180962 G T 1 0 0 0 0 1 0 0 0 3484 1261 44 2 2 COL4A6 23 108180962 Missense_Mutation SNP G C3L-01924_T 1973616 108180962 47859933 624 8494 SEPT6 0 . GRCh38 X 119650084 119650084 + Silent SNP G G T novel C3L-01924_T C3L-01924_N G G c.543C>A p.= p.P181P ENST00000343984 5/10 120 114 6 135 135 0 strelka-mutect SEPT6,synonymous_variant,p.=,ENST00000394610,NM_145799.3;SEPT6,synonymous_variant,p.=,ENST00000354416,;SEPT6,synonymous_variant,p.=,ENST00000343984,NM_015129.5;SEPT6,synonymous_variant,p.=,ENST00000360156,NM_145800.3;SEPT6,synonymous_variant,p.=,ENST00000489216,;SEPT6,synonymous_variant,p.=,ENST00000354228,NM_145802.3;MIR766,upstream_gene_variant,,ENST00000390223,;SEPT6,synonymous_variant,p.=,ENST00000460411,; T ENST00000343984 Transcript synonymous_variant 808/2693 543/1305 181/434 P ccC/ccA 1 -1 SEPT6 HGNC HGNC:15848 protein_coding YES CCDS14584.1 ENSP00000341524 Q14141 UPI0000001C54 NM_015129.5 5/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF55,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -11.52383 0.9996119 1 1 1 0 T 2 4 29 119650084 119650084 G T 1 0 0 0 0 0 0 0 1 14344 1335 47 2 2 SEPT6 23 119650084 Silent SNP G C3L-01924_T 11469122 119650084 36390811 625 8495 ATP1B4 0 . GRCh38 X 120371207 120371207 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.559C>A p.Gln187Lys p.Q187K ENST00000218008 4/8 177 137 40 150 150 0 strelka-varscan-mutect ATP1B4,missense_variant,p.Gln144Lys,ENST00000539306,;ATP1B4,missense_variant,p.Gln187Lys,ENST00000218008,NM_001142447.2;ATP1B4,missense_variant,p.Gln183Lys,ENST00000361319,NM_012069.4; A ENST00000218008 Transcript missense_variant 616/3868 559/1074 187/357 Q/K Cag/Aag 1 1 ATP1B4 HGNC HGNC:808 protein_coding YES CCDS48158.1 ENSP00000218008 Q9UN42 UPI00001262A4 NM_001142447.2 tolerated(0.35) 4/8 Gene3D:2zxeB02,Pfam_domain:PF00287,hmmpanther:PTHR11523,hmmpanther:PTHR11523:SF12,TIGRFAM_domain:TIGR01107 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 120371207 120371207 C A 1 0 0 0 0 1 0 0 0 1287 608 21 2 2 ATP1B4 23 120371207 Missense_Mutation SNP C C3L-01924_T 721123 120371207 35669688 626 8496 CT47B1 0 . GRCh38 X 120875469 120875469 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.202C>A p.Gln68Lys p.Q68K ENST00000371311 1/3 541 503 38 611 611 0 varscan-mutect CT47B1,missense_variant,p.Gln68Lys,ENST00000371311,NM_001145718.1;RP1-321E8.5,downstream_gene_variant,,ENST00000613352,;RP1-321E8.4,upstream_gene_variant,,ENST00000604718,; T ENST00000371311 Transcript missense_variant 461/1328 202/900 68/299 Q/K Cag/Aag 1 -1 CT47B1 HGNC HGNC:33293 protein_coding YES CCDS48161.1 ENSP00000360360 P0C2W7 UPI000036776D NM_001145718.1 tolerated(0.54) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32157:SF4,hmmpanther:PTHR32157,Pfam_domain:PF15623 MODERATE SNV 5 1 PASS rs1323365017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 120875469 120875469 G T 1 0 0 0 0 1 0 0 0 3791 1328 46 2 2 CT47B1 23 120875469 Missense_Mutation SNP G C3L-01924_T 504262 120875469 35165426 627 8497 TENM1 0 . GRCh38 X 124565414 124565414 + Nonsense_Mutation SNP C C A C3L-01924_T C3L-01924_N C C c.2224G>T p.Glu742Ter p.E742* ENST00000422452 12/32 125 114 11 146 146 0 strelka-varscan-mutect TENM1,stop_gained,p.Glu742Ter,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,stop_gained,p.Glu742Ter,ENST00000371130,NM_014253.3; A ENST00000422452 Transcript stop_gained 2288/12891 2224/8199 742/2732 E/* Gag/Tag COSM4823737,COSM4823738 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 12/32 PROSITE_profiles:PS50026,hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Pfam_domain:PF12661,Gene3D:2.10.25.10,SMART_domains:SM00181 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -19.98225 1 1 1 1 0 A 4 1 29 124565414 124565414 C A 1 0 0 0 0 0 1 0 0 16171 835 29 2 2 TENM1 23 124565414 Nonsense_Mutation SNP C C3L-01924_T 3689945 124565414 31475481 628 8498 GPR119 0 . GRCh38 X 130385371 130385371 + Missense_Mutation SNP G G A novel C3L-01924_T C3L-01924_N G G c.77C>T p.Ala26Val p.A26V ENST00000276218 1/1 162 103 59 202 202 0 strelka-varscan-mutect GPR119,missense_variant,p.Ala26Val,ENST00000276218,NM_178471.2; A ENST00000276218 Transcript missense_variant 77/1008 77/1008 26/335 A/V gCt/gTt 1 -1 GPR119 HGNC HGNC:19060 protein_coding YES CCDS14625.1 ENSP00000276218 Q8TDV5 UPI000003AFD2 NM_178471.2 tolerated(0.22) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF7,hmmpanther:PTHR22750,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 29 130385371 130385371 G A 1 0 0 0 0 1 0 0 0 6527 971 34 3 3 GPR119 23 130385371 Missense_Mutation SNP G C3L-01924_T 5819957 130385371 25655524 629 8499 OR13H1 0 . GRCh38 X 131544541 131544541 + Silent SNP T T C novel C3L-01924_T C3L-01924_N T T c.468T>C p.= p.T156T ENST00000338616 1/1 238 196 42 284 284 0 strelka-varscan-mutect OR13H1,synonymous_variant,p.=,ENST00000338616,NM_001004486.1;IGSF1,intron_variant,,ENST00000370904,; C ENST00000338616 Transcript synonymous_variant 468/927 468/927 156/308 T acT/acC 1 1 OR13H1 HGNC HGNC:14755 protein_coding YES CCDS35396.1 ENSP00000340748 Q8NG92 A0A126GW70 UPI000003CAC9 NM_001004486.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF76,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 29 131544541 131544541 T C 1 0 0 0 0 0 0 0 1 11019 1567 55 5 5 OR13H1 23 131544541 Silent SNP T C3L-01924_T 1159170 131544541 24496354 630 8500 USP26 0 . GRCh38 X 133026552 133026552 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.1669C>G p.Pro557Ala p.P557A ENST00000511190 6/6 163 149 14 205 205 0 strelka-varscan-mutect USP26,missense_variant,p.Pro557Ala,ENST00000511190,;USP26,missense_variant,p.Pro557Ala,ENST00000370832,NM_031907.1; C ENST00000511190 Transcript missense_variant 2139/3665 1669/2742 557/913 P/A Cca/Gca 1 -1 USP26 HGNC HGNC:13485 protein_coding YES CCDS14635.1 ENSP00000423390 Q9BXU7 UPI00000421FD deleterious(0.04) 6/6 PROSITE_profiles:PS50235,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 2 1 PASS rs1174150387 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 133026552 133026552 G C 1 0 0 0 0 1 0 0 0 17598 1261 44 4 4 USP26 23 133026552 Missense_Mutation SNP G C3L-01924_T 1482011 133026552 23014343 631 8501 GPC3 0 . GRCh38 X 133536160 133536160 + Silent SNP G G T rs769273303 C3L-01924_T C3L-01924_N G G c.1776C>A p.= p.A592A ENST00000394299 9/9 211 195 16 300 299 1 strelka-varscan-mutect GPC3,synonymous_variant,p.=,ENST00000370818,NM_004484.3,NM_001164618.1;GPC3,synonymous_variant,p.=,ENST00000394299,NM_001164617.1;GPC3,synonymous_variant,p.=,ENST00000631057,NM_001164619.1;RNU6-203P,upstream_gene_variant,,ENST00000384038,; T ENST00000394299 Transcript synonymous_variant 1973/2379 1776/1812 592/603 A gcC/gcA rs769273303 1 -1 GPC3 HGNC HGNC:4451 protein_coding YES CCDS55496.1 ENSP00000377836 P51654 UPI00015E044A NM_001164617.1 9/9 Pfam_domain:PF01153,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF4 LOW 1 SNV 1 1 PASS rs769273303 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 29 133536160 133536160 G T 1 0 0 0 0 0 0 0 1 6501 1335 47 2 2 GPC3 23 133536160 Silent SNP G C3L-01924_T 509608 133536160 22504735 632 8502 ADGRG4 0 . GRCh38 X 136349050 136349050 + Missense_Mutation SNP A A C rs776278812 C3L-01924_T C3L-01924_N A A c.5344A>C p.Lys1782Gln p.K1782Q ENST00000394143 6/26 118 110 8 195 195 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Lys1782Gln,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Lys1782Gln,ENST00000370652,;ADGRG4,missense_variant,p.Lys1577Gln,ENST00000394141,; C ENST00000394143 Transcript missense_variant 5635/9931 5344/9243 1782/3080 K/Q Aaa/Caa rs776278812 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0.03) 6/26 MODERATE 1 SNV 1 1 PASS rs776278812 . 0 208 2 0 0 0 0 0 -16.0786 1 1 1 1 0 C 3 2 29 136349050 136349050 A C 1 0 0 0 0 1 0 0 0 371 15 1 5 5 ADGRG4 23 136349050 Missense_Mutation SNP A C3L-01924_T 2812890 136349050 19691845 633 8503 ADGRG4 0 . GRCh38 X 136414236 136414236 + Missense_Mutation SNP G G C novel C3L-01924_T C3L-01924_N G G c.9114G>C p.Leu3038Phe p.L3038F ENST00000394143 25/26 189 175 14 203 203 0 strelka-mutect ADGRG4,missense_variant,p.Leu3038Phe,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Leu3038Phe,ENST00000370652,;ADGRG4,missense_variant,p.Leu2833Phe,ENST00000394141,; C ENST00000394143 Transcript missense_variant 9405/9931 9114/9243 3038/3080 L/F ttG/ttC 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 25/26 hmmpanther:PTHR12011:SF277,hmmpanther:PTHR12011 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 136414236 136414236 G C 1 0 0 0 0 1 0 0 0 371 1281 45 4 4 ADGRG4 23 136414236 Missense_Mutation SNP G C3L-01924_T 65186 136414236 19626659 634 8504 F9 0 . GRCh38 X 139541100 139541100 + Missense_Mutation SNP C C T C3L-01924_T C3L-01924_N C C c.302C>T p.Pro101Leu p.P101L ENST00000218099 4/8 288 248 40 377 377 0 strelka-varscan-mutect F9,missense_variant,p.Pro101Leu,ENST00000218099,NM_000133.3;F9,intron_variant,,ENST00000394090,;F9,non_coding_transcript_exon_variant,,ENST00000479617,; T ENST00000218099 Transcript missense_variant 309/2780 302/1386 101/461 P/L cCa/cTa CM940456,CM940457,CM990569 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 deleterious(0.02) 4/8 Gene3D:2.10.25.10,Pfam_domain:PF00008,PIRSF_domain:PIRSF001143,Prints_domain:PR00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF135,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57630 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 29 139541100 139541100 C T 1 0 0 0 0 1 0 0 0 5220 594 21 3 3 F9 23 139541100 Missense_Mutation SNP C C3L-01924_T 3126864 139541100 16499795 635 8505 MAGEC1 0 . GRCh38 X 141906890 141906890 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.1486C>A p.Gln496Lys p.Q496K ENST00000285879 4/4 322 288 34 429 427 2 strelka-varscan-mutect MAGEC1,missense_variant,p.Gln496Lys,ENST00000285879,NM_005462.4;MAGEC1,intron_variant,,ENST00000406005,; A ENST00000285879 Transcript missense_variant 1772/4270 1486/3429 496/1142 Q/K Cag/Aag 1 1 MAGEC1 HGNC HGNC:6812 protein_coding YES CCDS35417.1 ENSP00000285879 O60732 UPI000006F2FD NM_005462.4 deleterious_low_confidence(0.01) 4/4 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs918312137 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 141906890 141906890 C A 1 0 0 0 0 1 0 0 0 9098 595 21 2 2 MAGEC1 23 141906890 Missense_Mutation SNP C C3L-01924_T 2365790 141906890 14134005 636 8506 GABRA3 0 . GRCh38 X 152255853 152255853 + Nonsense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.476C>A p.Ser159Ter p.S159* ENST00000370314 5/10 387 364 23 468 468 0 strelka-varscan-mutect GABRA3,stop_gained,p.Ser159Ter,ENST00000370314,NM_000808.3;GABRA3,stop_gained,p.Ser159Ter,ENST00000535043,;GABRA3,non_coding_transcript_exon_variant,,ENST00000417858,; T ENST00000370314 Transcript stop_gained 715/3712 476/1479 159/492 S/* tCa/tAa 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 5/10 hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 HIGH 1 SNV 1 1 PASS rs1162760458 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 29 152255853 152255853 G T 1 0 0 0 0 0 1 0 0 6033 1294 45 2 2 GABRA3 23 152255853 Nonsense_Mutation SNP G C3L-01924_T 10348963 152255853 3785042 637 8507 GABRA3 0 . GRCh38 X 152255967 152255967 + Missense_Mutation SNP G G T novel C3L-01924_T C3L-01924_N G G c.362C>A p.Thr121Lys p.T121K ENST00000370314 5/10 278 259 19 372 371 1 strelka-varscan-mutect GABRA3,missense_variant,p.Thr121Lys,ENST00000370314,NM_000808.3;GABRA3,missense_variant,p.Thr121Lys,ENST00000535043,;GABRA3,non_coding_transcript_exon_variant,,ENST00000417858,; T ENST00000370314 Transcript missense_variant 601/3712 362/1479 121/492 T/K aCa/aAa 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 tolerated(0.14) 5/10 hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS . . 0 201 0 8 0 0 0 0 -19.99543 0.9600257 1 1 1 0 T 3 4 29 152255967 152255967 G T 1 0 0 0 0 1 0 0 0 6033 1377 48 2 2 GABRA3 23 152255967 Missense_Mutation SNP G C3L-01924_T 114 152255967 3784928 638 8508 MAGEA6 0 . GRCh38 X 152766717 152766717 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.934G>T p.Gly312Trp p.G312W ENST00000616035 3/3 108 100 8 128 128 0 varscan-mutect MAGEA6,missense_variant,p.Gly312Trp,ENST00000616035,NM_175868.1;MAGEA6,missense_variant,p.Gly312Trp,ENST00000329342,NM_005363.2;MAGEA6,downstream_gene_variant,,ENST00000457643,;MAGEA6,downstream_gene_variant,,ENST00000412733,; A ENST00000616035 Transcript missense_variant 1192/1762 934/945 312/314 G/W Ggg/Tgg 1 -1 MAGEA6 HGNC HGNC:6804 protein_coding YES CCDS76050.1 ENSP00000480637 P43360 UPI000000D9B0 NM_175868.1 deleterious(0) 3/3 hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736 MODERATE 1 SNV 5 1 PASS rs1285705665 . 0 205 4 0 0 0 0 0 -16.12943 1 1 1 1 0 A 3 1 29 152766717 152766717 C A 1 0 0 0 0 1 0 0 0 9085 623 22 2 2 MAGEA6 23 152766717 Missense_Mutation SNP C C3L-01924_T 510750 152766717 3274178 639 8509 PDZD4 0 . GRCh38 X 153803603 153803603 + Missense_Mutation SNP C C A novel C3L-01924_T C3L-01924_N C C c.2078G>T p.Arg693Leu p.R693L ENST00000393758 8/8 145 90 55 192 192 0 strelka-varscan-mutect PDZD4,missense_variant,p.Arg693Leu,ENST00000393758,NM_001303515.1,NM_001303513.1,NM_001303512.1;PDZD4,missense_variant,p.Arg687Leu,ENST00000164640,NM_001303516.1,NM_032512.3;PDZD4,missense_variant,p.Arg578Leu,ENST00000544474,NM_001303514.1;PDZD4,downstream_gene_variant,,ENST00000475140,;PDZD4,downstream_gene_variant,,ENST00000483693,;PDZD4,downstream_gene_variant,,ENST00000484792,;PDZD4,downstream_gene_variant,,ENST00000468491,;PDZD4,downstream_gene_variant,,ENST00000480418,;PDZD4,downstream_gene_variant,,ENST00000480650,; A ENST00000393758 Transcript missense_variant 2328/3763 2078/2328 693/775 R/L cGg/cTg 1 -1 PDZD4 HGNC HGNC:21167 protein_coding YES CCDS78518.1 ENSP00000377355 Q17RL8 UPI0000211CB2 NM_001303515.1,NM_001303513.1,NM_001303512.1 deleterious(0) 8/8 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF4 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 29 153803603 153803603 C A 1 0 0 0 0 1 0 0 0 11791 652 23 1 1 PDZD4 23 153803603 Missense_Mutation SNP C C3L-01924_T 1036886 153803603 2237292 640 8510 RENBP 0 . GRCh38 X 153935514 153935514 + Silent SNP G G C novel C3L-01924_T C3L-01924_N G G c.1140C>G p.= p.L380L ENST00000393700 10/11 165 156 9 170 170 0 strelka-varscan-mutect RENBP,synonymous_variant,p.=,ENST00000393700,NM_002910.5;RENBP,synonymous_variant,p.=,ENST00000369997,;RENBP,synonymous_variant,p.=,ENST00000451114,;NAA10,upstream_gene_variant,,ENST00000464845,NM_003491.3,NM_001256120.1;NAA10,upstream_gene_variant,,ENST00000370015,;NAA10,upstream_gene_variant,,ENST00000393712,;NAA10,upstream_gene_variant,,ENST00000370009,NM_001256119.1;NAA10,upstream_gene_variant,,ENST00000432089,;NAA10,upstream_gene_variant,,ENST00000370011,;NAA10,upstream_gene_variant,,ENST00000393710,;RENBP,3_prime_UTR_variant,,ENST00000423624,;RENBP,3_prime_UTR_variant,,ENST00000457282,;ARHGAP4,upstream_gene_variant,,ENST00000494813,;NAA10,upstream_gene_variant,,ENST00000466877,;NAA10,upstream_gene_variant,,ENST00000482485,;NAA10,upstream_gene_variant,,ENST00000477750,;NAA10,upstream_gene_variant,,ENST00000460996,;NAA10,upstream_gene_variant,,ENST00000484950,;RENBP,downstream_gene_variant,,ENST00000442361,;NAA10,upstream_gene_variant,,ENST00000477882,;NAA10,upstream_gene_variant,,ENST00000467451,;NAA10,upstream_gene_variant,,ENST00000478177,;NAA10,upstream_gene_variant,,ENST00000488481,; C ENST00000393700 Transcript synonymous_variant 1221/1388 1140/1284 380/427 L ctC/ctG 1 -1 RENBP HGNC HGNC:9959 protein_coding YES CCDS14738.2 ENSP00000377303 P51606 UPI0000E5B00C NM_002910.5 10/11 Gene3D:1.50.10.10,Pfam_domain:PF07221,hmmpanther:PTHR15108,Superfamily_domains:SSF48208 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.56134 1 1 1 1 0 C 2 2 29 153935514 153935514 G C 1 0 0 0 0 0 0 0 1 13395 929 33 4 4 RENBP 23 153935514 Silent SNP G C3L-01924_T 131911 153935514 2105381 641 8511 PLXNA3 0 . GRCh38 X 154465145 154465145 + Missense_Mutation SNP G G C rs367770095 C3L-01924_T C3L-01924_N G G c.2171G>C p.Arg724Pro p.R724P ENST00000369682 11/33 273 253 20 241 241 0 strelka-varscan-mutect PLXNA3,missense_variant,p.Arg724Pro,ENST00000369682,NM_017514.4;PLXNA3,upstream_gene_variant,,ENST00000493546,;PLXNA3,downstream_gene_variant,,ENST00000495040,;PLXNA3,upstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000480645,;PLXNA3,upstream_gene_variant,,ENST00000491066,;PLXNA3,upstream_gene_variant,,ENST00000478236,;PLXNA3,downstream_gene_variant,,ENST00000482598,; C ENST00000369682 Transcript missense_variant 2346/10885 2171/5616 724/1871 R/P cGg/cCg rs367770095 1 1 PLXNA3 HGNC HGNC:9101 protein_coding YES CCDS14752.1 ENSP00000358696 P51805 UPI0002AB801F NM_017514.4 deleterious(0.03) 11/33 Low_complexity_(Seg):seg,hmmpanther:PTHR22625:SF32,hmmpanther:PTHR22625 MODERATE 1 SNV 1 1 PASS rs367770095 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 29 154465145 154465145 G C 1 0 0 0 0 1 0 0 0 12227 1116 39 4 4 PLXNA3 23 154465145 Missense_Mutation SNP G C3L-01924_T 529631 154465145 1575750 642 8512 PKN2 0 . GRCh38 1 88784716 88784716 + Missense_Mutation SNP G G T rs745647473 C3L-02219_T C3L-02219_N G G c.1063G>T p.Ala355Ser p.A355S ENST00000370521 7/22 177 161 16 172 172 0 strelka-varscan-mutect PKN2,missense_variant,p.Ala355Ser,ENST00000370521,NM_006256.2;PKN2,missense_variant,p.Ala355Ser,ENST00000370513,;PKN2,missense_variant,p.Ala355Ser,ENST00000316005,;PKN2,intron_variant,,ENST00000436111,; T ENST00000370521 Transcript missense_variant 1422/6121 1063/2955 355/984 A/S Gca/Tca rs745647473 1 1 PKN2 HGNC HGNC:9406 protein_coding YES CCDS714.1 ENSP00000359552 Q16513 UPI000004D291 NM_006256.2 tolerated(0.96) 7/22 hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF175,SMART_domains:SM00239 MODERATE 1 SNV 1 1 PASS rs745647473 . 0 208 0 2 0 0 0 0 -19.99225 0.9999998 1 1 1 0 T 3 4 30 88784716 88784716 G T 1 0 0 0 0 1 0 0 0 12076 1319 46 2 2 PKN2 1 88784716 Missense_Mutation SNP G C3L-02219_T 88784716 160171706 1 8513 RHBG 0 . GRCh38 1 156384844 156384844 + Nonstop_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.1376A>T p.Ter459LeuextTer6 p.*459Lext*6 ENST00000537040 10/10 93 85 8 111 111 0 strelka-varscan-mutect RHBG,stop_lost,p.Ter459LeuextTer6,ENST00000537040,NM_001256395.1,NM_020407.4,NM_001256396.1;RP11-139I14.2,upstream_gene_variant,,ENST00000451362,;RHBG,non_coding_transcript_exon_variant,,ENST00000494874,;RHBG,3_prime_UTR_variant,,ENST00000620376,;RHBG,3_prime_UTR_variant,,ENST00000451864,;RHBG,3_prime_UTR_variant,,ENST00000613460,;RHBG,3_prime_UTR_variant,,ENST00000612897,;RHBG,non_coding_transcript_exon_variant,,ENST00000618120,;RHBG,downstream_gene_variant,,ENST00000622297,; T ENST00000537040 Transcript stop_lost 1414/1789 1376/1377 459/458 */L tAa/tTa 1 1 RHBG HGNC HGNC:14572 protein_coding YES ENSP00000441197 Q9H310 UPI000004F267 NM_001256395.1,NM_020407.4,NM_001256396.1 10/10 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -17.02714 1 1 1 1 0 T 4 4 30 156384844 156384844 A T 1 0 0 0 0 0 0 0 0 13496 369 13 4 4 RHBG 1 156384844 Nonstop_Mutation SNP A C3L-02219_T 67600128 156384844 92571578 2 8514 RFWD2 0 . GRCh38 1 176175987 176175987 + Missense_Mutation SNP C C T novel C3L-02219_T C3L-02219_N C C c.488G>A p.Ser163Asn p.S163N ENST00000367669 3/20 145 132 13 160 159 1 strelka-varscan-mutect RFWD2,missense_variant,p.Ser163Asn,ENST00000367669,NM_022457.6,NM_001286644.1;RFWD2,missense_variant,p.Ser163Asn,ENST00000308769,NM_001001740.3;RFWD2,missense_variant,p.Ser18Asn,ENST00000367666,;RFWD2,missense_variant,p.Ser22Asn,ENST00000498306,;RFWD2,missense_variant,p.Ser68Asn,ENST00000367667,;RFWD2,missense_variant,p.Ser22Asn,ENST00000491600,;RFWD2,intron_variant,,ENST00000474194,; T ENST00000367669 Transcript missense_variant 1003/3033 488/2196 163/731 S/N aGt/aAt 1 -1 RFWD2 HGNC HGNC:17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 UPI0000061E51 NM_022457.6,NM_001286644.1 tolerated(0.15) 3/20 PROSITE_profiles:PS50089,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF451,Pfam_domain:PF13923,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 176175987 176175987 C T 1 0 0 0 0 1 0 0 0 13434 565 20 3 3 RFWD2 1 176175987 Missense_Mutation SNP C C3L-02219_T 19791143 176175987 72780435 3 8515 SLC26A9 0 . GRCh38 1 205932751 205932753 + In_Frame_Del DEL GAA GAA - novel C3L-02219_T C3L-02219_N GAA GAA c.325_327delTTC p.Phe109del p.F109del ENST00000367134 4/22 44 38 6 58 58 0 sindel-varindel-pindel SLC26A9,inframe_deletion,p.Phe109del,ENST00000367135,NM_052934.3;SLC26A9,inframe_deletion,p.Phe109del,ENST00000367134,NM_134325.2;SLC26A9,inframe_deletion,p.Phe109del,ENST00000340781,;RP4-681L3.2,upstream_gene_variant,,ENST00000421166,;SLC26A9,upstream_gene_variant,,ENST00000491127,;SLC26A9,upstream_gene_variant,,ENST00000469392,; - ENST00000367134 Transcript inframe_deletion 439-441/4616 325-327/2664 109/887 F/- TTC/- 1 -1 SLC26A9 HGNC HGNC:14469 protein_coding YES CCDS30989.1 ENSP00000356102 Q7LBE3 UPI000013DF98 NM_134325.2 4/22 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF17,TIGRFAM_domain:TIGR00815,Transmembrane_helices:TMhelix MODERATE 1 deletion 5 1 PASS . . 0 195 15 0 0 0 0 0 -14.50371 0.9994596 1 1 1 0 - 7 5 30 205932751 205932751 GAA - 1 0 1 0 1 0 0 0 0 14794 1165 41 0 0 SLC26A9 1 205932751 In_Frame_Del DEL GAA C3L-02219_T 29756764 205932751 43023671 4 8516 DIEXF 0 . GRCh38 1 209840922 209840922 + Missense_Mutation SNP C C T rs773562424 C3L-02219_T C3L-02219_N C C c.1352C>T p.Ser451Phe p.S451F ENST00000491415 8/12 463 419 44 514 513 1 strelka-varscan-mutect DIEXF,missense_variant,p.Ser451Phe,ENST00000491415,NM_014388.6;DIEXF,missense_variant,p.Ser132Phe,ENST00000457820,; T ENST00000491415 Transcript missense_variant 1409/8446 1352/2271 451/756 S/F tCc/tTc rs773562424,COSM1240921,COSM3482940 1 1 DIEXF HGNC HGNC:28440 protein_coding YES CCDS1493.1 ENSP00000419005 Q68CQ4 UPI000006D987 NM_014388.6 deleterious(0) 8/12 Gene3D:3.40.50.300,Pfam_domain:PF06862,hmmpanther:PTHR12933,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 209840922 209840922 C T 1 0 0 0 0 1 0 0 0 4327 855 30 3 3 DIEXF 1 209840922 Missense_Mutation SNP C C3L-02219_T 3908171 209840922 39115500 5 8517 KCNH1 0 . GRCh38 1 210919714 210919714 + Missense_Mutation SNP C C T C3L-02219_T C3L-02219_N C C c.1388G>A p.Ser463Asn p.S463N ENST00000271751 7/11 185 168 17 280 280 0 strelka-varscan-mutect KCNH1,missense_variant,p.Ser463Asn,ENST00000271751,NM_172362.2;KCNH1,missense_variant,p.Ser436Asn,ENST00000367007,NM_002238.3; T ENST00000271751 Transcript missense_variant 1416/7964 1388/2970 463/989 S/N aGt/aAt COSM4694313 1 -1 KCNH1 HGNC HGNC:6250 protein_coding YES CCDS1496.1 ENSP00000271751 O95259 UPI000003230D NM_172362.2 deleterious(0) 7/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR01463 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 210919714 210919714 C T 1 0 0 0 0 1 0 0 0 7947 565 20 3 3 KCNH1 1 210919714 Missense_Mutation SNP C C3L-02219_T 1078792 210919714 38036708 6 8518 CEP170 0 . GRCh38 1 243191260 243191260 + Missense_Mutation SNP G G A novel C3L-02219_T C3L-02219_N G G c.866C>T p.Pro289Leu p.P289L ENST00000366542 8/20 197 178 19 208 207 1 varscan-mutect CEP170,missense_variant,p.Pro289Leu,ENST00000366542,NM_014812.2;CEP170,missense_variant,p.Pro289Leu,ENST00000366544,NM_001042404.1;CEP170,missense_variant,p.Pro289Leu,ENST00000366543,NM_001042405.1;CEP170,missense_variant,p.Pro191Leu,ENST00000336415,;CEP170,upstream_gene_variant,,ENST00000522895,;CEP170,upstream_gene_variant,,ENST00000461671,;CEP170,upstream_gene_variant,,ENST00000521911,; A ENST00000366542 Transcript missense_variant 918/6828 866/4755 289/1584 P/L cCa/cTa 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 deleterious(0) 8/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 243191260 243191260 G A 1 0 0 0 0 1 0 0 0 2964 1348 47 3 3 CEP170 1 243191260 Missense_Mutation SNP G C3L-02219_T 32271546 243191260 5765162 7 8519 OR2C3 0 . GRCh38 1 247531762 247531762 + Silent SNP A A G novel C3L-02219_T C3L-02219_N A A c.750T>C p.= p.S250S ENST00000366487 2/2 443 402 41 490 488 2 strelka-varscan-mutect OR2C3,synonymous_variant,p.=,ENST00000366487,NM_198074.4;OR2C3,synonymous_variant,p.=,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; G ENST00000366487 Transcript synonymous_variant 1112/2742 750/963 250/320 S tcT/tcC 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 30 247531762 247531762 A G 1 0 0 0 0 0 0 0 1 11072 291 11 5 5 OR2C3 1 247531762 Silent SNP A C3L-02219_T 4340502 247531762 1424660 8 8520 DCDC2C 0 . GRCh38 2 3752898 3752898 + Missense_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.681A>T p.Gln227His p.Q227H ENST00000399143 5/11 122 108 14 154 154 0 strelka-varscan-mutect DCDC2C,missense_variant,p.Gln227His,ENST00000399143,NM_001287444.1;DCDC2C,missense_variant,p.Gln190His,ENST00000423741,;DCDC2C,intron_variant,,ENST00000537457,; T ENST00000399143 Transcript missense_variant,splice_region_variant 841/1480 681/1095 227/364 Q/H caA/caT 1 1 DCDC2C HGNC HGNC:32696 protein_coding YES CCDS74481.1 ENSP00000382097 A8MYV0 UPI0002742D44 NM_001287444.1 deleterious(0.03) 5/11 hmmpanther:PTHR23004:SF9,hmmpanther:PTHR23004,Superfamily_domains:SSF89837 MODERATE 1 SNV 5 1 PASS rs1004536359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 3752898 3752898 A T 1 0 0 0 0 1 0 0 0 4089 57 2 4 4 DCDC2C 2 3752898 Missense_Mutation SNP A C3L-02219_T 3752898 238440631 9 8521 ROCK2 0 . GRCh38 2 11197265 11197265 + Silent SNP T T A novel C3L-02219_T C3L-02219_N T T c.3363A>T p.= p.S1121S ENST00000315872 27/33 233 210 23 276 276 0 strelka-varscan-mutect ROCK2,synonymous_variant,p.=,ENST00000315872,NM_001321643.1,NM_004850.3;ROCK2,synonymous_variant,p.=,ENST00000616279,;ROCK2,synonymous_variant,p.=,ENST00000401753,;ROCK2,upstream_gene_variant,,ENST00000460262,;ROCK2,upstream_gene_variant,,ENST00000493096,; A ENST00000315872 Transcript synonymous_variant 3812/8292 3363/4167 1121/1388 S tcA/tcT 1 -1 ROCK2 HGNC HGNC:10252 protein_coding YES CCDS42654.1 ENSP00000317985 O75116 UPI000034ECB0 NM_001321643.1,NM_004850.3 27/33 hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,PIRSF_domain:PIRSF037568 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 11197265 11197265 T A 1 0 0 0 0 0 0 0 1 13696 1683 59 4 4 ROCK2 2 11197265 Silent SNP T C3L-02219_T 7444367 11197265 230996264 10 8522 ST6GAL2 0 . GRCh38 2 106806852 106806852 + Silent SNP G G A C3L-02219_T C3L-02219_N G G c.1416C>T p.= p.Y472Y ENST00000409382 6/6 243 225 18 324 323 1 strelka-varscan ST6GAL2,synonymous_variant,p.=,ENST00000409382,NM_001142351.1;ST6GAL2,synonymous_variant,p.=,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,synonymous_variant,p.=,ENST00000361803,; A ENST00000409382 Transcript synonymous_variant 2027/7275 1416/1590 472/529 Y taC/taT COSM1669194 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 6/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713,Pfam_domain:PF00777 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 106806852 106806852 G A 1 0 0 0 0 0 0 0 1 15600 1024 36 3 3 ST6GAL2 2 106806852 Silent SNP G C3L-02219_T 95609587 106806852 135386677 11 8523 GLI2 0 . GRCh38 2 120988820 120988820 + Missense_Mutation SNP C C A novel C3L-02219_T C3L-02219_N C C c.2906C>A p.Ala969Asp p.A969D ENST00000452319 14/14 72 64 8 80 80 0 strelka-varscan GLI2,missense_variant,p.Ala969Asp,ENST00000452319,;GLI2,missense_variant,p.Ala969Asp,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,downstream_gene_variant,,ENST00000437950,; A ENST00000452319 Transcript missense_variant 2966/6799 2906/4761 969/1586 A/D gCc/gAc 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 deleterious(0) 14/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -17.87967 1 1 1 1 0 A 3 1 30 120988820 120988820 C A 1 0 0 0 0 1 0 0 0 6316 739 26 2 2 GLI2 2 120988820 Missense_Mutation SNP C C3L-02219_T 14181968 120988820 121204709 12 8524 FARP2 0 . GRCh38 2 241403843 241403843 + Nonsense_Mutation SNP C C T novel C3L-02219_T C3L-02219_N C C c.199C>T p.Gln67Ter p.Q67* ENST00000264042 3/27 151 111 40 238 238 0 strelka-varscan-mutect FARP2,stop_gained,p.Gln67Ter,ENST00000264042,NM_014808.3;FARP2,stop_gained,p.Gln67Ter,ENST00000373287,NM_001282983.1;FARP2,stop_gained,p.Gln67Ter,ENST00000627550,NM_001282984.1;FARP2,stop_gained,p.Gln67Ter,ENST00000445489,;FARP2,stop_gained,p.Gln67Ter,ENST00000418082,;FARP2,non_coding_transcript_exon_variant,,ENST00000478489,;FARP2,non_coding_transcript_exon_variant,,ENST00000467260,;FARP2,non_coding_transcript_exon_variant,,ENST00000464142,;FARP2,non_coding_transcript_exon_variant,,ENST00000473082,; T ENST00000264042 Transcript stop_gained 369/4051 199/3165 67/1054 Q/* Cag/Tag 1 1 FARP2 HGNC HGNC:16460 protein_coding YES CCDS33424.1 ENSP00000264042 O94887 UPI0000073D5B NM_014808.3 3/27 Gene3D:3.10.20.90,Pfam_domain:PF09379,Prints_domain:PR00661,PROSITE_profiles:PS50057,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF58,SMART_domains:SM00295,Superfamily_domains:SSF54236 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 30 241403843 241403843 C T 1 0 0 0 0 0 1 0 0 5537 595 21 3 3 FARP2 2 241403843 Nonsense_Mutation SNP C C3L-02219_T 120415023 241403843 789686 13 8525 MAATS1 0 . GRCh38 3 119707443 119707443 + Missense_Mutation SNP A A G novel C3L-02219_T C3L-02219_N A A c.241A>G p.Ile81Val p.I81V ENST00000273390 3/18 66 60 6 77 77 0 strelka-varscan-mutect MAATS1,missense_variant,p.Ile81Val,ENST00000273390,NM_001320318.1,NM_001320316.1,NM_033364.3;MAATS1,missense_variant,p.Ile81Val,ENST00000463700,;MAATS1,3_prime_UTR_variant,,ENST00000482573,NM_001320318.1,NM_001320317.1;MAATS1,3_prime_UTR_variant,,ENST00000482927,;MAATS1,non_coding_transcript_exon_variant,,ENST00000483134,;MAATS1,non_coding_transcript_exon_variant,,ENST00000468630,;MAATS1,non_coding_transcript_exon_variant,,ENST00000469659,;MAATS1,intron_variant,,ENST00000475093,;MAATS1,upstream_gene_variant,,ENST00000498167,;MAATS1,downstream_gene_variant,,ENST00000488533,; G ENST00000273390 Transcript missense_variant 318/4433 241/2304 81/767 I/V Atc/Gtc 1 1 MAATS1 HGNC HGNC:24010 protein_coding YES CCDS2994.1 ENSP00000273390 Q7Z4T9 UPI00001C1DFE NM_001320318.1,NM_001320316.1,NM_033364.3 tolerated(0.57) 3/18 hmmpanther:PTHR22455,hmmpanther:PTHR22455:SF10 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -13.70671 1 1 1 1 0 G 3 3 30 119707443 119707443 A G 1 0 0 0 0 1 0 0 0 9055 333 12 5 5 MAATS1 3 119707443 Missense_Mutation SNP A C3L-02219_T 119707443 78588116 14 8526 KIAA1211 0 . GRCh38 4 56314271 56314271 + Nonsense_Mutation SNP G G T rs772735246 C3L-02219_T C3L-02219_N G G c.769G>T p.Glu257Ter p.E257* ENST00000504228 6/9 275 245 30 357 356 1 strelka-varscan-mutect KIAA1211,stop_gained,p.Glu257Ter,ENST00000504228,;KIAA1211,stop_gained,p.Glu250Ter,ENST00000541073,;KIAA1211,stop_gained,p.Glu257Ter,ENST00000264229,NM_020722.1;KIAA1211,stop_gained,p.Glu257Ter,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; T ENST00000504228 Transcript stop_gained 874/4628 769/3702 257/1233 E/* Gag/Tag rs772735246 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil HIGH 1 SNV 5 1 PASS rs772735246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 30 56314271 56314271 G T 1 0 0 0 0 0 1 0 0 8107 1175 41 2 2 KIAA1211 4 56314271 Nonsense_Mutation SNP G C3L-02219_T 56314271 133900284 15 8527 FBXW7 0 . GRCh38 4 152346953 152346955 + In_Frame_Del DEL GGA GGA - novel C3L-02219_T C3L-02219_N GGA GGA c.701_703delTCC p.Leu234del p.L234del ENST00000281708 4/12 130 115 15 167 167 0 sindel-varindel-pindel FBXW7,inframe_deletion,p.Leu234del,ENST00000281708,NM_033632.3;FBXW7,inframe_deletion,p.Leu154del,ENST00000263981,NM_018315.4;FBXW7,inframe_deletion,p.Leu116del,ENST00000296555,NM_001013415.1;FBXW7,inframe_deletion,p.Leu234del,ENST00000603548,;FBXW7,inframe_deletion,p.Leu234del,ENST00000603841,;FBXW7,inframe_deletion,p.Leu58del,ENST00000393956,;FBXW7,non_coding_transcript_exon_variant,,ENST00000604822,; - ENST00000281708 Transcript inframe_deletion 1931-1933/4976 701-703/2124 234-235/707 LQ/Q cTCCag/cag 1 -1 FBXW7 HGNC HGNC:16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 UPI000007007E NM_033632.3 4/12 hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF217 MODERATE 1 deletion 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.99734 0.9999891 1 1 1 0 - 7 5 30 152346953 152346953 GGA - 1 0 1 0 1 0 0 0 0 5632 1357 47 0 0 FBXW7 4 152346953 In_Frame_Del DEL GGA C3L-02219_T 96032682 152346953 37867602 16 8528 NPR3 0 . GRCh38 5 32711837 32711837 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.61G>T p.Ala21Ser p.A21S ENST00000265074 1/8 48 43 5 39 39 0 strelka-mutect NPR3,missense_variant,p.Ala21Ser,ENST00000265074,NM_001204375.1;NPR3,missense_variant,p.Ala21Ser,ENST00000415167,NM_000908.3;NPR3,intron_variant,,ENST00000326958,NM_001204376.1;NPR3,intron_variant,,ENST00000434067,;NPR3,intron_variant,,ENST00000509104,;NPR3,upstream_gene_variant,,ENST00000507141,;NPR3,intron_variant,,ENST00000506712,; T ENST00000265074 Transcript missense_variant 404/7344 61/1626 21/541 A/S Gcc/Tcc 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 tolerated_low_confidence(0.08) 1/8 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.89157 1 1 1 1 0 T 3 4 30 32711837 32711837 G T 1 0 0 0 0 1 0 0 0 10652 1203 42 2 2 NPR3 5 32711837 Missense_Mutation SNP G C3L-02219_T 32711837 148826422 17 8529 ANKHD1 0 . GRCh38 5 140526260 140526260 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.4757G>T p.Gly1586Val p.G1586V ENST00000532219 26/36 364 298 66 418 418 0 strelka-varscan-mutect ANKHD1-EIF4EBP3,missense_variant,p.Gly1586Val,ENST00000532219,NM_020690.5;ANKHD1,missense_variant,p.Gly1586Val,ENST00000360839,NM_017747.2;ANKHD1,missense_variant,p.Gly242Val,ENST00000431508,;ANKHD1,missense_variant,p.Gly108Val,ENST00000433049,;ANKHD1,missense_variant,p.Gly77Val,ENST00000435794,;ANKHD1,missense_variant,p.Gly37Val,ENST00000432301,;ANKHD1,5_prime_UTR_variant,,ENST00000297183,;ANKHD1,downstream_gene_variant,,ENST00000421134,;ANKHD1-EIF4EBP3,upstream_gene_variant,,ENST00000437495,;ANKHD1,downstream_gene_variant,,ENST00000246149,;ANKHD1,downstream_gene_variant,,ENST00000412116,;SNORD45,downstream_gene_variant,,ENST00000363181,;ANKHD1-EIF4EBP3,upstream_gene_variant,,ENST00000474060,;ANKHD1,upstream_gene_variant,,ENST00000475148,; T ENST00000532219 Transcript missense_variant 4817/8246 4757/7854 1586/2617 G/V gGt/gTt 1 1 ANKHD1-EIF4EBP3 HGNC HGNC:33530 protein_coding YES CCDS4224.1 ENSP00000432016 UPI0000074448 NM_020690.5 tolerated_low_confidence(0.27) 26/36 Low_complexity_(Seg):seg,hmmpanther:PTHR23206:SF5,hmmpanther:PTHR23206 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 140526260 140526260 G T 1 0 0 0 0 1 0 0 0 730 1261 44 2 2 ANKHD1 5 140526260 Missense_Mutation SNP G C3L-02219_T 107814423 140526260 41011999 18 8530 PCDHA6 0 . GRCh38 5 140828854 140828854 + Missense_Mutation SNP G G A novel C3L-02219_T C3L-02219_N G G c.763G>A p.Ala255Thr p.A255T ENST00000529310 1/4 303 273 30 399 399 0 strelka-varscan-mutect PCDHA6,missense_variant,p.Ala255Thr,ENST00000529310,NM_018909.3;PCDHA6,missense_variant,p.Ala255Thr,ENST00000378126,NM_031848.2;PCDHA6,missense_variant,p.Ala255Thr,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA5,downstream_gene_variant,,ENST00000614258,NM_031501.1; A ENST00000529310 Transcript missense_variant 877/5374 763/2853 255/950 A/T Gca/Aca 1 1 PCDHA6 HGNC HGNC:8672 protein_coding YES CCDS47281.1 ENSP00000433378 Q9UN73 UPI00001273CE NM_018909.3 tolerated_low_confidence(0.47) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF131,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 140828854 140828854 G A 1 0 0 0 0 1 0 0 0 11615 1319 46 3 3 PCDHA6 5 140828854 Missense_Mutation SNP G C3L-02219_T 302594 140828854 40709405 19 8531 ID4 0 . GRCh38 6 19837955 19837955 + Silent SNP T T C novel C3L-02219_T C3L-02219_N T T c.201T>C p.= p.D67D ENST00000378700 1/3 195 160 35 213 213 0 strelka-varscan-mutect ID4,synonymous_variant,p.=,ENST00000378700,NM_001546.3;RP4-625H18.2,intron_variant,,ENST00000432171,; C ENST00000378700 Transcript synonymous_variant 570/2344 201/486 67/161 D gaT/gaC 1 1 ID4 HGNC HGNC:5363 protein_coding YES CCDS4544.1 ENSP00000367972 P47928 UPI000012D193 NM_001546.3 1/3 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR11723,hmmpanther:PTHR11723:SF6,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS rs1162203947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 30 19837955 19837955 T C 1 0 0 0 0 0 0 0 1 7392 1403 49 5 5 ID4 6 19837955 Silent SNP T C3L-02219_T 19837955 150968024 20 8532 UHRF1BP1 0 . GRCh38 6 34858352 34858352 + Missense_Mutation SNP T T A novel C3L-02219_T C3L-02219_N T T c.1996T>A p.Leu666Met p.L666M ENST00000192788 14/21 366 308 58 457 457 0 strelka-varscan-mutect UHRF1BP1,missense_variant,p.Leu666Met,ENST00000192788,NM_017754.3;UHRF1BP1,missense_variant,p.Leu666Met,ENST00000452449,; A ENST00000192788 Transcript missense_variant 2167/9570 1996/4323 666/1440 L/M Ttg/Atg 1 1 UHRF1BP1 HGNC HGNC:21216 protein_coding YES CCDS43455.1 ENSP00000192788 Q6BDS2 UPI00001B654C NM_017754.3 tolerated(0.07) 14/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 34858352 34858352 T A 1 0 0 0 0 1 0 0 0 17492 1838 64 4 4 UHRF1BP1 6 34858352 Missense_Mutation SNP T C3L-02219_T 15020397 34858352 135947627 21 8533 IMPG1 0 . GRCh38 6 75950590 75950590 + Missense_Mutation SNP C C T rs368049446 C3L-02219_T C3L-02219_N C C c.1796G>A p.Arg599Gln p.R599Q ENST00000369950 13/17 117 106 11 126 126 0 strelka-varscan IMPG1,missense_variant,p.Arg599Gln,ENST00000369950,NM_001563.3;IMPG1,missense_variant,p.Arg521Gln,ENST00000611179,NM_001282368.1; T ENST00000369950 Transcript missense_variant 1986/3558 1796/2394 599/797 R/Q cGa/cAa rs368049446 1 -1 IMPG1 HGNC HGNC:6055 protein_coding YES CCDS4985.1 ENSP00000358966 Q17R60 UPI0000073F12 NM_001563.3 tolerated(1) 13/17 Superfamily_domains:0047452,Gene3D:1ivzA00,Pfam_domain:PF01390,PROSITE_profiles:PS50024,hmmpanther:PTHR12199,SMART_domains:SM00200 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99207 1 1 1 1 0 T 3 4 30 75950590 75950590 C T 1 0 0 0 0 1 0 0 0 7630 884 31 1 1 IMPG1 6 75950590 Missense_Mutation SNP C C3L-02219_T 41092238 75950590 94855389 22 8534 ELOVL4 0 . GRCh38 6 79921651 79921651 + Missense_Mutation SNP C C G C3L-02219_T C3L-02219_N C C c.515G>C p.Gly172Ala p.G172A ENST00000369816 4/6 426 400 26 447 447 0 strelka-varscan ELOVL4,missense_variant,p.Gly172Ala,ENST00000369816,NM_022726.3; G ENST00000369816 Transcript missense_variant 816/3042 515/945 172/314 G/A gGa/gCa COSM5061960 1 -1 ELOVL4 HGNC HGNC:14415 protein_coding YES CCDS4992.1 ENSP00000358831 Q9GZR5 UPI0000049DA1 NM_022726.3 deleterious(0) 4/6 Pfam_domain:PF01151,hmmpanther:PTHR11157,hmmpanther:PTHR11157:SF45,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 79921651 79921651 C G 1 0 0 0 0 1 0 0 0 4911 855 30 4 4 ELOVL4 6 79921651 Missense_Mutation SNP C C3L-02219_T 3971061 79921651 90884328 23 8535 CNR1 0 . GRCh38 6 88143945 88143945 + Missense_Mutation SNP T T A rs750464422 C3L-02219_T C3L-02219_N T T c.1330A>T p.Arg444Trp p.R444W ENST00000369501 2/2 266 228 38 290 290 0 strelka-varscan-mutect CNR1,missense_variant,p.Arg444Trp,ENST00000369501,NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1;CNR1,missense_variant,p.Arg444Trp,ENST00000369499,;CNR1,missense_variant,p.Arg444Trp,ENST00000549890,;CNR1,missense_variant,p.Arg444Trp,ENST00000428600,;CNR1,missense_variant,p.Arg411Trp,ENST00000468898,NM_033181.3;CNR1,3_prime_UTR_variant,,ENST00000362094,;CNR1,downstream_gene_variant,,ENST00000551417,; A ENST00000369501 Transcript missense_variant 1950/6031 1330/1419 444/472 R/W Agg/Tgg rs750464422 1 -1 CNR1 HGNC HGNC:2159 protein_coding YES CCDS5015.1 ENSP00000358513 P21554 S5TLS4 UPI00000008AA NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1 deleterious(0) 2/2 hmmpanther:PTHR22750:SF47,hmmpanther:PTHR22750,PIRSF_domain:PIRSF037995,Prints_domain:PR00522 MODERATE 1 SNV 1 1 PASS rs750464422 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 88143945 88143945 T A 1 0 0 0 0 1 0 0 0 3413 1579 55 4 4 CNR1 6 88143945 Missense_Mutation SNP T C3L-02219_T 8222294 88143945 82662034 24 8536 HEY2 0 . GRCh38 6 125759572 125759572 + Missense_Mutation SNP G G C novel C3L-02219_T C3L-02219_N G G c.784G>C p.Ala262Pro p.A262P ENST00000368364 5/5 149 137 12 168 168 0 strelka-varscan-mutect HEY2,missense_variant,p.Ala262Pro,ENST00000368364,NM_012259.2;HEY2,missense_variant,p.Ala216Pro,ENST00000368365,; C ENST00000368364 Transcript missense_variant 981/2678 784/1014 262/337 A/P Gcc/Ccc 1 1 HEY2 HGNC HGNC:4881 protein_coding YES CCDS5131.1 ENSP00000357348 Q9UBP5 UPI0000037AFE NM_012259.2 tolerated(0.37) 5/5 hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF88,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 125759572 125759572 G C 1 0 0 0 0 1 0 0 0 6963 1319 46 4 4 HEY2 6 125759572 Missense_Mutation SNP G C3L-02219_T 37615627 125759572 45046407 25 8537 ARID1B 0 . GRCh38 6 157148624 157148624 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.2552G>T p.Gly851Val p.G851V ENST00000346085 9/20 47 42 5 63 63 0 varscan-mutect ARID1B,missense_variant,p.Gly851Val,ENST00000346085,NM_020732.3;ARID1B,missense_variant,p.Gly838Val,ENST00000636930,;ARID1B,missense_variant,p.Gly838Val,ENST00000350026,NM_017519.2;ARID1B,missense_variant,p.Gly307Val,ENST00000414678,;ARID1B,missense_variant,p.Gly88Val,ENST00000637904,;ARID1B,missense_variant,p.Gly28Val,ENST00000635849,;ARID1B,missense_variant,p.Gly88Val,ENST00000637810,;ARID1B,missense_variant,p.Gly259Val,ENST00000319584,;ARID1B,coding_sequence_variant,p.=,ENST00000637015,;ARID1B,upstream_gene_variant,,ENST00000635957,;ARID1B,upstream_gene_variant,,ENST00000400790,;ARID1B,splice_region_variant,,ENST00000452544,;ARID1B,upstream_gene_variant,,ENST00000637568,;ARID1B,upstream_gene_variant,,ENST00000636426,; T ENST00000346085 Transcript missense_variant,splice_region_variant 3108/10194 2552/6750 851/2249 G/V gGt/gTt 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 deleterious_low_confidence(0.04) 9/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 MODERATE 1 SNV 1 1 PASS . . 0 161 40 8 0 0 0 0 -9.511862 0.3253579 0 1 0 0 T 3 4 30 157148624 157148624 G T 1 0 0 0 0 1 0 0 0 1050 1275 44 2 2 ARID1B 6 157148624 Missense_Mutation SNP G C3L-02219_T 31389052 157148624 13657355 26 8538 IGF2R 0 . GRCh38 6 160048380 160048380 + Missense_Mutation SNP C C T novel C3L-02219_T C3L-02219_N C C c.2351C>T p.Ala784Val p.A784V ENST00000356956 18/48 438 374 64 532 532 0 strelka-varscan-mutect IGF2R,missense_variant,p.Ala784Val,ENST00000356956,NM_000876.2; T ENST00000356956 Transcript missense_variant 2499/14044 2351/7476 784/2491 A/V gCa/gTa 1 1 IGF2R HGNC HGNC:5467 protein_coding YES CCDS5273.1 ENSP00000349437 P11717 UPI0000072478 NM_000876.2 tolerated(0.14) 18/48 Gene3D:2.70.130.10,Pfam_domain:PF00878,hmmpanther:PTHR15071,hmmpanther:PTHR15071:SF5,SMART_domains:SM01404,Superfamily_domains:SSF50911 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 160048380 160048380 C T 1 0 0 0 0 1 0 0 0 7482 724 25 3 3 IGF2R 6 160048380 Missense_Mutation SNP C C3L-02219_T 2899756 160048380 10757599 27 8539 DLL1 0 . GRCh38 6 170285610 170285610 + Missense_Mutation SNP C C T novel C3L-02219_T C3L-02219_N C C c.821G>A p.Cys274Tyr p.C274Y ENST00000366756 6/11 360 336 24 404 404 0 strelka-varscan-mutect DLL1,missense_variant,p.Cys274Tyr,ENST00000366756,NM_005618.3;DLL1,downstream_gene_variant,,ENST00000630500,; T ENST00000366756 Transcript missense_variant 1155/3174 821/2172 274/723 C/Y tGc/tAc 1 -1 DLL1 HGNC HGNC:2908 protein_coding YES CCDS5313.1 ENSP00000355718 O00548 UPI000004C656 NM_005618.3 deleterious(0) 6/11 Gene3D:2gy5A03,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF283,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 170285610 170285610 C T 1 0 0 0 0 1 0 0 0 4373 710 25 3 3 DLL1 6 170285610 Missense_Mutation SNP C C3L-02219_T 10237230 170285610 520369 28 8540 FERD3L 0 . GRCh38 7 19144934 19144934 + Silent SNP G G A novel C3L-02219_T C3L-02219_N G G c.429C>T p.= p.L143L ENST00000275461 1/1 253 178 75 259 259 0 strelka-varscan-mutect FERD3L,synonymous_variant,p.=,ENST00000275461,NM_152898.2;AC003986.5,non_coding_transcript_exon_variant,,ENST00000452700,; A ENST00000275461 Transcript synonymous_variant 488/640 429/501 143/166 L ctC/ctT 1 -1 FERD3L HGNC HGNC:16660 protein_coding YES CCDS5368.1 ENSP00000275461 Q96RJ6 UPI0000073BBA NM_152898.2 1/1 PROSITE_profiles:PS50888,hmmpanther:PTHR23349:SF63,hmmpanther:PTHR23349,Pfam_domain:PF00010,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 19144934 19144934 G A 1 0 0 0 0 0 0 0 1 5679 1161 41 3 3 FERD3L 7 19144934 Silent SNP G C3L-02219_T 19144934 140201039 29 8541 MUC17 0 . GRCh38 7 101038603 101038603 + Missense_Mutation SNP G G T rs767302410 C3L-02219_T C3L-02219_N G G c.7187G>T p.Ser2396Ile p.S2396I ENST00000306151 3/13 145 129 16 278 278 0 strelka-varscan-mutect MUC17,missense_variant,p.Ser2396Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ser2396Ile,ENST00000379439,; T ENST00000306151 Transcript missense_variant 7251/14247 7187/13482 2396/4493 S/I aGc/aTc rs767302410 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS rs767302410 . 0 206 0 3 0 0 0 0 -19.99963 0.9999875 1 1 1 0 T 3 4 30 101038603 101038603 G T 1 0 0 0 0 1 0 0 0 9973 971 34 2 2 MUC17 7 101038603 Missense_Mutation SNP G C3L-02219_T 81893669 101038603 58307370 30 8542 PRSS2 0 . GRCh38 7 142772179 142772179 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.171G>T p.Trp57Cys p.W57C ENST00000633969 2/6 223 188 35 340 340 0 strelka-varscan-mutect PRSS2,missense_variant,p.Trp57Cys,ENST00000633969,NM_001303414.1;PRSS2,missense_variant,p.Trp57Cys,ENST00000632998,;PRSS2,missense_variant,p.Trp57Cys,ENST00000632805,;PRSS2,missense_variant,p.Trp57Cys,ENST00000539842,NM_002770.3;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS2,non_coding_transcript_exon_variant,,ENST00000618750,;PRSS2,non_coding_transcript_exon_variant,,ENST00000610835,; T ENST00000633969 Transcript missense_variant 187/852 171/786 57/261 W/C tgG/tgT 1 1 PRSS2 HGNC HGNC:9483 protein_coding YES ENSP00000488437 A6XMV9 UPI0001578AE2 NM_001303414.1 deleterious(0.02) 2/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF21,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 MODERATE 1 SNV 1 1 PASS rs1388816308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 142772179 142772179 G T 1 0 0 0 0 1 0 0 0 12764 1241 43 2 2 PRSS2 7 142772179 Missense_Mutation SNP G C3L-02219_T 41733576 142772179 16573794 31 8543 PLAT 0 . GRCh38 8 42182827 42182827 + Nonsense_Mutation SNP G G T rs758349613 C3L-02219_T C3L-02219_N G G c.695C>A p.Ser232Ter p.S232* ENST00000220809 8/14 171 152 19 205 205 0 strelka-varscan-mutect PLAT,stop_gained,p.Ser232Ter,ENST00000220809,NM_000930.3;PLAT,stop_gained,p.Ser232Ter,ENST00000429089,;PLAT,stop_gained,p.Ser186Ter,ENST00000352041,NM_033011.2;PLAT,stop_gained,p.Ser169Ter,ENST00000519510,;PLAT,stop_gained,p.Ser106Ter,ENST00000429710,;PLAT,stop_gained,p.Ser143Ter,ENST00000524009,;PLAT,downstream_gene_variant,,ENST00000520523,;PLAT,downstream_gene_variant,,ENST00000521694,;PLAT,non_coding_transcript_exon_variant,,ENST00000524261,;PLAT,intron_variant,,ENST00000521042,;PLAT,downstream_gene_variant,,ENST00000521647,;PLAT,upstream_gene_variant,,ENST00000522812,; T ENST00000220809 Transcript stop_gained 952/2706 695/1689 232/562 S/* tCg/tAg rs758349613 1 -1 PLAT HGNC HGNC:9051 protein_coding YES CCDS6126.1 ENSP00000220809 P00750 UPI0000000DD4 NM_000930.3 8/14 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001145,Prints_domain:PR00018,PROSITE_profiles:PS50070,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF142,SMART_domains:SM00130,Superfamily_domains:SSF57440 HIGH 1 SNV 1 1 PASS rs758349613 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 30 42182827 42182827 G T 1 0 0 0 0 0 1 0 0 12115 1059 37 1 1 PLAT 8 42182827 Nonsense_Mutation SNP G C3L-02219_T 42182827 102955809 32 8544 SNTG1 0 . GRCh38 8 50792788 50792788 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.1513G>T p.Ala505Ser p.A505S ENST00000522124 19/19 147 136 11 186 186 0 strelka-varscan-mutect SNTG1,missense_variant,p.Ala505Ser,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Ala505Ser,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Ala468Ser,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,; T ENST00000522124 Transcript missense_variant 2174/3504 1513/1554 505/517 A/S Gcc/Tcc 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 tolerated_low_confidence(0.7) 19/19 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -15.29542 0.9999997 1 1 1 0 T 3 4 30 50792788 50792788 G T 1 0 0 0 0 1 0 0 0 15194 1319 46 2 2 SNTG1 8 50792788 Missense_Mutation SNP G C3L-02219_T 8609961 50792788 94345848 33 8545 PXDNL 0 . GRCh38 8 51339722 51339722 + Missense_Mutation SNP C C A novel C3L-02219_T C3L-02219_N C C c.4048G>T p.Ala1350Ser p.A1350S ENST00000356297 21/23 184 156 28 245 245 0 strelka-varscan-mutect PXDNL,missense_variant,p.Ala1350Ser,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.Ala424Ser,ENST00000522933,;PXDNL,non_coding_transcript_exon_variant,,ENST00000519183,;PXDNL,intron_variant,,ENST00000522628,; A ENST00000356297 Transcript missense_variant 4149/4805 4048/4392 1350/1463 A/S Gct/Tct 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 tolerated(0.8) 21/23 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 30 51339722 51339722 C A 1 0 0 0 0 1 0 0 0 13002 710 25 2 2 PXDNL 8 51339722 Missense_Mutation SNP C C3L-02219_T 546934 51339722 93798914 34 8546 FAM91A1 0 . GRCh38 8 123812575 123812575 + Silent SNP A A G novel C3L-02219_T C3L-02219_N A A c.2388A>G p.= p.S796S ENST00000334705 24/24 110 89 21 120 120 0 strelka-varscan-mutect FAM91A1,synonymous_variant,p.=,ENST00000334705,NM_001317917.1,NM_144963.2;FAM91A1,downstream_gene_variant,,ENST00000521166,NM_001317918.1;FAM91A1,3_prime_UTR_variant,,ENST00000519721,;FAM91A1,3_prime_UTR_variant,,ENST00000518976,;FAM91A1,non_coding_transcript_exon_variant,,ENST00000518333,;FAM91A1,downstream_gene_variant,,ENST00000520246,; G ENST00000334705 Transcript synonymous_variant 2634/5511 2388/2517 796/838 S tcA/tcG 1 1 FAM91A1 HGNC HGNC:26306 protein_coding YES CCDS6346.2 ENSP00000335082 Q658Y4 UPI0000E5AF4E NM_001317917.1,NM_144963.2 24/24 Pfam_domain:PF14648,hmmpanther:PTHR28441,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 30 123812575 123812575 A G 1 0 0 0 0 0 0 0 1 5509 146 6 5 5 FAM91A1 8 123812575 Silent SNP A C3L-02219_T 72472853 123812575 21326061 35 8547 SQLE 0 . GRCh38 8 125018631 125018631 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.1348G>T p.Ala450Ser p.A450S ENST00000265896 9/11 128 120 8 149 149 0 varscan-mutect SQLE,missense_variant,p.Ala450Ser,ENST00000265896,NM_003129.3;SQLE,missense_variant,p.Ala355Ser,ENST00000523430,;SQLE,missense_variant,p.Ala102Ser,ENST00000518931,;SQLE,splice_region_variant,,ENST00000518604,;SQLE,downstream_gene_variant,,ENST00000520493,; T ENST00000265896 Transcript missense_variant,splice_region_variant 2246/2961 1348/1725 450/574 A/S Gcc/Tcc 1 1 SQLE HGNC HGNC:11279 protein_coding YES CCDS47918.1 ENSP00000265896 Q14534 Q9UNR6 UPI0000073EEE NM_003129.3 deleterious(0) 9/11 hmmpanther:PTHR10835,Pfam_domain:PF08491,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 192 8 10 0 0 0 0 -10.85721 0.6572908 1 1 1 0 T 3 4 30 125018631 125018631 G T 1 0 0 0 0 1 0 0 0 15487 1217 42 2 2 SQLE 8 125018631 Missense_Mutation SNP G C3L-02219_T 1206056 125018631 20120005 36 8548 ASAP1 0 . GRCh38 8 130112108 130112108 + Missense_Mutation SNP C C T novel C3L-02219_T C3L-02219_N C C c.2387G>A p.Arg796Lys p.R796K ENST00000518721 24/30 166 157 9 198 198 0 strelka-varscan-mutect ASAP1,missense_variant,p.Arg789Lys,ENST00000357668,NM_001247996.1;ASAP1,missense_variant,p.Arg796Lys,ENST00000518721,NM_018482.3;ASAP1,missense_variant,p.Arg617Lys,ENST00000524124,;ASAP1,missense_variant,p.Arg210Lys,ENST00000519483,;ASAP1,3_prime_UTR_variant,,ENST00000521075,;ASAP1,non_coding_transcript_exon_variant,,ENST00000520189,;ASAP1,downstream_gene_variant,,ENST00000521057,; T ENST00000518721 Transcript missense_variant 2615/5507 2387/3390 796/1129 R/K aGg/aAg 1 -1 ASAP1 HGNC HGNC:2720 protein_coding YES CCDS6362.1 ENSP00000429900 Q9ULH1 UPI0000351D6E NM_018482.3 tolerated(0.15) 24/30 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF192 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 130112108 130112108 C T 1 0 0 0 0 1 0 0 0 1152 681 24 3 3 ASAP1 8 130112108 Missense_Mutation SNP C C3L-02219_T 5093477 130112108 15026528 37 8549 SCX 0 . GRCh38 8 144266665 144266665 + Missense_Mutation SNP G G A novel C3L-02219_T C3L-02219_N G G c.52G>A p.Glu18Lys p.E18K ENST00000567180 1/2 140 128 12 91 91 0 strelka-varscan-mutect SCX,missense_variant,p.Glu18Lys,ENST00000567180,NM_001080514.2;BOP1,intron_variant,,ENST00000569669,NM_015201.4;BOP1,intron_variant,,ENST00000569403,;MROH1,downstream_gene_variant,,ENST00000528919,NM_032450.2;MROH1,downstream_gene_variant,,ENST00000326134,;MROH1,downstream_gene_variant,,ENST00000534366,NM_001288814.1;MROH1,downstream_gene_variant,,ENST00000544576,;BOP1,upstream_gene_variant,,ENST00000616126,;BOP1,upstream_gene_variant,,ENST00000563210,;BOP1,upstream_gene_variant,,ENST00000568812,;BOP1,upstream_gene_variant,,ENST00000569160,; A ENST00000567180 Transcript missense_variant 106/999 52/606 18/201 E/K Gag/Aag 1 1 SCX HGNC HGNC:32322 protein_coding YES CCDS43779.1 ENSP00000476384 Q7RTU7 UPI00001D965C NM_001080514.2 deleterious(0.01) 1/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 144266665 144266665 G A 1 0 0 0 0 1 0 0 0 14218 1059 37 1 1 SCX 8 144266665 Missense_Mutation SNP G C3L-02219_T 14154557 144266665 871971 38 8550 TYRP1 0 . GRCh38 9 12702411 12702414 + Frame_Shift_Del DEL ACAA ACAA - rs752724988 C3L-02219_T C3L-02219_N ACAA ACAA c.1057_1060delAACA p.Asn353ValfsTer31 p.N353Vfs*31 ENST00000388918 5/8 319 289 30 454 454 0 sindel-varindel-pindel TYRP1,frameshift_variant,p.Asn353ValfsTer31,ENST00000388918,NM_000550.2;TYRP1,frameshift_variant,p.Asn63ValfsTer31,ENST00000381136,;LURAP1L-AS1,intron_variant,,ENST00000417638,;TYRP1,non_coding_transcript_exon_variant,,ENST00000381142,;TYRP1,non_coding_transcript_exon_variant,,ENST00000470909,; - ENST00000388918 Transcript frameshift_variant 1183-1186/2851 1054-1057/1614 352-353/537 TN/X ACAAac/ac rs752724988,COSM166262 1 1 TYRP1 HGNC HGNC:12450 protein_coding YES CCDS34990.1 ENSP00000373570 P17643 UPI0000039DCA NM_000550.2 5/8 Gene3D:1.10.1280.10,Pfam_domain:PF00264,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF3,Superfamily_domains:SSF48056 0,1 HIGH 1 deletion 1 3 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 30 12702411 12702411 ACAA - 1 0 1 0 1 0 0 0 0 17331 391 14 0 0 TYRP1 9 12702411 Frame_Shift_Del DEL ACAA C3L-02219_T 12702411 125692306 39 8551 ABCA1 0 . GRCh38 9 104824557 104824557 + Missense_Mutation SNP G G C novel C3L-02219_T C3L-02219_N G G c.2564C>G p.Pro855Arg p.P855R ENST00000374736 18/50 348 312 36 489 489 0 strelka-varscan-mutect ABCA1,missense_variant,p.Pro855Arg,ENST00000374736,NM_005502.3;ABCA1,downstream_gene_variant,,ENST00000494467,; C ENST00000374736 Transcript missense_variant 2959/10494 2564/6786 855/2261 P/R cCc/cGc 1 -1 ABCA1 HGNC HGNC:29 protein_coding YES CCDS6762.1 ENSP00000363868 O95477 UPI000013E441 NM_005502.3 deleterious(0) 18/50 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF34 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 104824557 104824557 G C 1 0 0 0 0 1 0 0 0 32 1232 43 4 4 ABCA1 9 104824557 Missense_Mutation SNP G C3L-02219_T 92122146 104824557 33570160 40 8552 GOLGA2 0 . GRCh38 9 128261224 128261224 + Missense_Mutation SNP C C G novel C3L-02219_T C3L-02219_N C C c.1287G>C p.Met429Ile p.M429I ENST00000421699 16/26 146 138 8 190 190 0 strelka-varscan-mutect GOLGA2,missense_variant,p.Met429Ile,ENST00000421699,NM_004486.4;GOLGA2,missense_variant,p.Met429Ile,ENST00000611957,;GOLGA2,missense_variant,p.Met417Ile,ENST00000609374,;GOLGA2,missense_variant,p.Met456Ile,ENST00000450617,;GOLGA2,intron_variant,,ENST00000610329,;GOLGA2,downstream_gene_variant,,ENST00000458730,;GOLGA2,non_coding_transcript_exon_variant,,ENST00000490257,;GOLGA2,non_coding_transcript_exon_variant,,ENST00000470630,;GOLGA2,upstream_gene_variant,,ENST00000462089,;GOLGA2,upstream_gene_variant,,ENST00000486411,;GOLGA2,downstream_gene_variant,,ENST00000468488,;GOLGA2,upstream_gene_variant,,ENST00000461031,;GOLGA2,upstream_gene_variant,,ENST00000496221,; G ENST00000421699 Transcript missense_variant 1300/4260 1287/3009 429/1002 M/I atG/atC 1 -1 GOLGA2 HGNC HGNC:4425 protein_coding YES CCDS6896.2 ENSP00000416097 Q08379 UPI0000D4C11A NM_004486.4 tolerated(0.64) 16/26 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF45 MODERATE 1 SNV 1 1 PASS rs1211215333 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 128261224 128261224 C G 1 0 0 0 0 1 0 0 0 6431 826 29 4 4 GOLGA2 9 128261224 Missense_Mutation SNP C C3L-02219_T 23436667 128261224 10133493 41 8553 PRDM12 0 . GRCh38 9 130666626 130666626 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.242G>T p.Ser81Ile p.S81I ENST00000253008 2/5 127 106 21 164 164 0 strelka-varscan-mutect PRDM12,missense_variant,p.Ser81Ile,ENST00000253008,NM_021619.2; T ENST00000253008 Transcript missense_variant 302/2476 242/1104 81/367 S/I aGc/aTc 1 1 PRDM12 HGNC HGNC:13997 protein_coding YES CCDS6934.1 ENSP00000253008 Q9H4Q4 UPI0000132184 NM_021619.2 deleterious(0) 2/5 Gene3D:2.170.270.10,PIRSF_domain:PIRSF037163 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 130666626 130666626 G T 1 0 0 0 0 1 0 0 0 12584 971 34 2 2 PRDM12 9 130666626 Missense_Mutation SNP G C3L-02219_T 2405402 130666626 7728091 42 8554 ATP5C1 0 . GRCh38 10 7802825 7802825 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.861G>T p.Leu287Phe p.L287F ENST00000356708 8/10 170 149 21 266 265 1 strelka-varscan-mutect ATP5C1,missense_variant,p.Leu287Phe,ENST00000356708,NM_001001973.1;ATP5C1,missense_variant,p.Leu287Phe,ENST00000335698,NM_005174.2;ATP5C1,non_coding_transcript_exon_variant,,ENST00000493053,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000473809,;ATP5C1,non_coding_transcript_exon_variant,,ENST00000480528,;ATP5C1,intron_variant,,ENST00000465936,;ATP5C1,downstream_gene_variant,,ENST00000460820,;ATP5C1,downstream_gene_variant,,ENST00000472202,; T ENST00000356708 Transcript missense_variant 940/1163 861/897 287/298 L/F ttG/ttT 1 1 ATP5C1 HGNC HGNC:833 protein_coding YES CCDS31142.1 ENSP00000349142 P36542 UPI0000126574 NM_001001973.1 deleterious(0) 8/10 hmmpanther:PTHR11693,PROSITE_patterns:PS00153,TIGRFAM_domain:TIGR01146,PIRSF_domain:PIRSF039089,Gene3D:1.10.287.80,Pfam_domain:PF00231,Superfamily_domains:SSF52943,Prints_domain:PR00126 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 7802825 7802825 G T 1 0 0 0 0 1 0 0 0 1302 1281 45 2 2 ATP5C1 10 7802825 Missense_Mutation SNP G C3L-02219_T 7802825 125994597 43 8555 SVIL 0 . GRCh38 10 29550908 29550908 + Silent SNP C C A novel C3L-02219_T C3L-02219_N C C c.516G>T p.= p.T172T ENST00000355867 6/38 240 210 30 325 325 0 strelka-varscan-mutect SVIL,synonymous_variant,p.=,ENST00000375398,;SVIL,synonymous_variant,p.=,ENST00000355867,NM_021738.2;SVIL,synonymous_variant,p.=,ENST00000375400,NM_003174.3;SVIL,downstream_gene_variant,,ENST00000483758,; A ENST00000355867 Transcript synonymous_variant 1269/7586 516/6645 172/2214 T acG/acT 1 -1 SVIL HGNC HGNC:11480 protein_coding YES CCDS7164.1 ENSP00000348128 O95425 UPI0000366678 NM_021738.2 6/38 hmmpanther:PTHR11977:SF45,hmmpanther:PTHR11977 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 29550908 29550908 C A 1 0 0 0 0 0 0 0 1 15806 871 31 1 1 SVIL 10 29550908 Silent SNP C C3L-02219_T 21748083 29550908 104246514 44 8556 NRP1 0 . GRCh38 10 33185670 33185670 + Missense_Mutation SNP C C T rs757346128 C3L-02219_T C3L-02219_N C C c.2389G>A p.Asp797Asn p.D797N ENST00000265371 16/18 237 217 20 262 262 0 strelka-varscan-mutect NRP1,missense_variant,p.Asp797Asn,ENST00000265371,;NRP1,missense_variant,p.Asp797Asn,ENST00000374867,NM_003873.5,NM_001244973.1,NM_001244972.1;NRP1,missense_variant,p.Asp797Asn,ENST00000395995,;NRP1,missense_variant,p.Asp609Asn,ENST00000374875,;NRP1,upstream_gene_variant,,ENST00000413802,; T ENST00000265371 Transcript missense_variant 2915/5882 2389/2772 797/923 D/N Gac/Aac rs757346128 1 -1 NRP1 HGNC HGNC:8004 protein_coding YES CCDS7177.1 ENSP00000265371 O14786 UPI000013D60A tolerated(0.66) 16/18 Pfam_domain:PF00629,PIRSF_domain:PIRSF036960,Prints_domain:PR00020,PROSITE_profiles:PS50060,SMART_domains:SM00137,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS rs757346128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 33185670 33185670 C T 1 0 0 0 0 1 0 0 0 10718 826 29 3 3 NRP1 10 33185670 Missense_Mutation SNP C C3L-02219_T 3634762 33185670 100611752 45 8557 CCNJ 0 . GRCh38 10 96058210 96058210 + Missense_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.1121A>T p.Tyr374Phe p.Y374F ENST00000465148 6/6 89 75 14 112 112 0 strelka-varscan-mutect CCNJ,missense_variant,p.Tyr363Phe,ENST00000265992,NM_019084.4;CCNJ,missense_variant,p.Tyr362Phe,ENST00000403870,NM_001134376.1;CCNJ,missense_variant,p.Tyr374Phe,ENST00000465148,NM_001134375.1;ENTPD1-AS1,intron_variant,,ENST00000416301,;ENTPD1-AS1,intron_variant,,ENST00000458228,;ENTPD1-AS1,intron_variant,,ENST00000454638,;ENTPD1-AS1,intron_variant,,ENST00000452728,;ENTPD1-AS1,intron_variant,,ENST00000427846,;ENTPD1-AS1,intron_variant,,ENST00000451364,; T ENST00000465148 Transcript missense_variant 1299/2677 1121/1152 374/383 Y/F tAc/tTc 1 1 CCNJ HGNC HGNC:23434 protein_coding YES CCDS44462.1 ENSP00000435373 Q5T5M9 UPI00001F9448 NM_001134375.1 tolerated(0.92) 6/6 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 96058210 96058210 A T 1 0 0 0 0 1 0 0 0 2627 391 14 4 4 CCNJ 10 96058210 Missense_Mutation SNP A C3L-02219_T 62872540 96058210 37739212 46 8558 BTRC 0 . GRCh38 10 101462013 101462013 + Silent SNP C C T rs759103744 C3L-02219_T C3L-02219_N C C c.189C>T p.= p.G63G ENST00000370187 3/15 161 151 10 197 197 0 strelka-varscan-mutect BTRC,synonymous_variant,p.=,ENST00000370187,NM_033637.3;BTRC,synonymous_variant,p.=,ENST00000408038,NM_003939.4;BTRC,synonymous_variant,p.=,ENST00000370183,;BTRC,intron_variant,,ENST00000393441,NM_001256856.1;BTRC,non_coding_transcript_exon_variant,,ENST00000465182,;BTRC,non_coding_transcript_exon_variant,,ENST00000475200,; T ENST00000370187 Transcript synonymous_variant 307/6134 189/1818 63/605 G ggC/ggT rs759103744,COSM4011121 1 1 BTRC HGNC HGNC:1144 protein_coding YES CCDS7512.1 ENSP00000359206 Q9Y297 A0A0S2Z4P6 UPI00000012B5 NM_033637.3 3/15 0,1 LOW 1 SNV 1 0,1 1 PASS rs759103744 . 0 204 0 6 0 0 0 0 -12.92329 0.9914787 1 1 1 0 T 2 4 30 101462013 101462013 C T 1 0 0 0 0 0 0 0 1 1745 755 27 1 1 BTRC 10 101462013 Silent SNP C C3L-02219_T 5403803 101462013 32335409 47 8559 EMX2 0 . GRCh38 10 117545698 117545698 + Missense_Mutation SNP G G A C3L-02219_T C3L-02219_N G G c.473G>A p.Arg158Gln p.R158Q ENST00000553456 2/3 128 117 11 127 126 1 strelka-varscan-mutect EMX2,missense_variant,p.Arg158Gln,ENST00000553456,NM_004098.3;EMX2,intron_variant,,ENST00000442245,NM_001165924.1;EMX2,intron_variant,,ENST00000616794,;EMX2OS,upstream_gene_variant,,ENST00000551288,;EMX2OS,upstream_gene_variant,,ENST00000440007,;EMX2OS,upstream_gene_variant,,ENST00000450314,;EMX2,non_coding_transcript_exon_variant,,ENST00000546446,; A ENST00000553456 Transcript missense_variant 1297/2897 473/759 158/252 R/Q cGa/cAa COSM280793 1 1 EMX2 HGNC HGNC:3341 protein_coding YES CCDS7601.1 ENSP00000450962 Q04743 UPI000004CC07 NM_004098.3 deleterious(0) 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF25,SMART_domains:SM00389,Superfamily_domains:SSF46689 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 117545698 117545698 G A 1 0 0 0 0 1 0 0 0 4950 1058 37 1 1 EMX2 10 117545698 Missense_Mutation SNP G C3L-02219_T 16083685 117545698 16251724 48 8560 FADS3 0 . GRCh38 11 61876169 61876169 + Missense_Mutation SNP C C G rs202232198 C3L-02219_T C3L-02219_N C C c.1102G>C p.Glu368Gln p.E368Q ENST00000278829 10/12 222 206 16 191 191 0 strelka-varscan-mutect FADS3,missense_variant,p.Glu368Gln,ENST00000278829,NM_021727.4;FADS3,missense_variant,p.Glu244Gln,ENST00000527697,;FADS3,missense_variant,p.Glu340Gln,ENST00000525588,;FADS3,missense_variant,p.Glu143Gln,ENST00000527379,;FADS3,missense_variant,p.Glu39Gln,ENST00000525094,;FADS3,downstream_gene_variant,,ENST00000531956,;FADS3,downstream_gene_variant,,ENST00000534223,;MIR6746,downstream_gene_variant,,ENST00000620971,;FADS3,non_coding_transcript_exon_variant,,ENST00000533676,;FADS3,non_coding_transcript_exon_variant,,ENST00000529404,;FADS3,downstream_gene_variant,,ENST00000414624,;FADS3,downstream_gene_variant,,ENST00000534426,;FADS3,downstream_gene_variant,,ENST00000526294,; G ENST00000278829 Transcript missense_variant 1255/1779 1102/1338 368/445 E/Q Gag/Cag rs202232198 1 -1 FADS3 HGNC HGNC:3576 protein_coding YES CCDS8013.1 ENSP00000278829 Q9Y5Q0 A0A024R564 UPI000003405F NM_021727.4 tolerated(0.06) 10/12 Pfam_domain:PF00487,PIRSF_domain:PIRSF015921,hmmpanther:PTHR19353,hmmpanther:PTHR19353:SF11 MODERATE 1 SNV 1 1 PASS rs202232198 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 61876169 61876169 C G 1 0 0 0 0 1 0 0 0 5239 864 30 4 4 FADS3 11 61876169 Missense_Mutation SNP C C3L-02219_T 61876169 73210453 49 8561 ATM 0 . GRCh38 11 108329125 108329125 + Nonsense_Mutation SNP C C A novel C3L-02219_T C3L-02219_N C C c.7194C>A p.Tyr2398Ter p.Y2398* ENST00000278616 49/63 289 212 77 407 407 0 strelka-varscan-mutect ATM,stop_gained,p.Tyr2398Ter,ENST00000278616,NM_000051.3;ATM,stop_gained,p.Tyr2398Ter,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,downstream_gene_variant,,ENST00000615746,;C11orf65,downstream_gene_variant,,ENST00000524755,;ATM,upstream_gene_variant,,ENST00000533979,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,non_coding_transcript_exon_variant,,ENST00000525537,;ATM,non_coding_transcript_exon_variant,,ENST00000527389,;C11orf65,downstream_gene_variant,,ENST00000527531,;ATM,upstream_gene_variant,,ENST00000525056,; A ENST00000278616 Transcript stop_gained 7579/13147 7194/9171 2398/3056 Y/* taC/taA 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 49/63 PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF72,hmmpanther:PTHR11139,Pfam_domain:PF02259,Superfamily_domains:SSF48371 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 30 108329125 108329125 C A 1 0 0 0 0 0 1 0 0 1261 518 18 2 2 ATM 11 108329125 Nonsense_Mutation SNP C C3L-02219_T 46452956 108329125 26757497 50 8562 OR6X1 0 . GRCh38 11 123754366 123754366 + Silent SNP G G A novel C3L-02219_T C3L-02219_N G G c.153C>T p.= p.P51P ENST00000327930 1/1 120 99 21 178 178 0 strelka-varscan-mutect OR6X1,synonymous_variant,p.=,ENST00000327930,NM_001005188.1; A ENST00000327930 Transcript synonymous_variant 180/1058 153/939 51/312 P ccC/ccT 1 -1 OR6X1 HGNC HGNC:14737 protein_coding YES CCDS31695.1 ENSP00000333724 Q8NH79 A0A126GVM0 UPI000004B1D5 NM_001005188.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF30,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 123754366 123754366 G A 1 0 0 0 0 0 0 0 1 11282 1335 47 3 3 OR6X1 11 123754366 Silent SNP G C3L-02219_T 15425241 123754366 11332256 51 8563 ANKS1B 0 . GRCh38 12 99246677 99246677 + Missense_Mutation SNP G G C novel C3L-02219_T C3L-02219_N G G c.1944C>G p.Phe648Leu p.F648L ENST00000547776 13/26 152 126 26 221 221 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Phe648Leu,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Phe228Leu,ENST00000547010,;ANKS1B,downstream_gene_variant,,ENST00000549866,;ANKS1B,upstream_gene_variant,,ENST00000550778,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000550833,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000546631,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000550157,; C ENST00000547776 Transcript missense_variant 1944/3885 1944/3747 648/1248 F/L ttC/ttG 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 tolerated(0.7) 13/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 99246677 99246677 G C 1 0 0 0 0 1 0 0 0 795 1281 45 4 4 ANKS1B 12 99246677 Missense_Mutation SNP G C3L-02219_T 99246677 34028632 52 8564 PCDH9 0 . GRCh38 13 67227665 67227665 + Missense_Mutation SNP A A G novel C3L-02219_T C3L-02219_N A A c.776T>C p.Val259Ala p.V259A ENST00000377865 2/5 124 108 16 168 168 0 strelka-varscan-mutect PCDH9,missense_variant,p.Val259Ala,ENST00000377861,;PCDH9,missense_variant,p.Val259Ala,ENST00000544246,NM_020403.4;PCDH9,missense_variant,p.Val259Ala,ENST00000377865,NM_203487.2;PCDH9,missense_variant,p.Val259Ala,ENST00000456367,; G ENST00000377865 Transcript missense_variant 950/5709 776/3714 259/1237 V/A gTg/gCg 1 -1 PCDH9 HGNC HGNC:8661 protein_coding YES CCDS9444.1 ENSP00000367096 Q9HC56 X5D7N0 UPI00001FCE90 NM_203487.2 tolerated(1) 2/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 67227665 67227665 A G 1 0 0 0 0 1 0 0 0 11605 159 6 5 5 PCDH9 13 67227665 Missense_Mutation SNP A C3L-02219_T 67227665 47136663 53 8565 HAUS4 0 . GRCh38 14 22947221 22947221 + Silent SNP A A T novel C3L-02219_T C3L-02219_N A A c.858T>A p.= p.I286I ENST00000206474 9/10 191 151 40 233 233 0 strelka-varscan-mutect HAUS4,synonymous_variant,p.=,ENST00000206474,;HAUS4,synonymous_variant,p.=,ENST00000541587,NM_001166269.1,NM_017815.2;HAUS4,synonymous_variant,p.=,ENST00000555986,;HAUS4,synonymous_variant,p.=,ENST00000342454,NM_001166270.1;HAUS4,synonymous_variant,p.=,ENST00000555367,;HAUS4,synonymous_variant,p.=,ENST00000490506,;HAUS4,synonymous_variant,p.=,ENST00000347758,;RP11-298I3.5,synonymous_variant,p.=,ENST00000555074,;HAUS4,downstream_gene_variant,,ENST00000555040,;HAUS4,downstream_gene_variant,,ENST00000554516,;HAUS4,downstream_gene_variant,,ENST00000554406,;HAUS4,downstream_gene_variant,,ENST00000557591,;HAUS4,downstream_gene_variant,,ENST00000556915,;HAUS4,downstream_gene_variant,,ENST00000553420,;RP11-298I3.1,intron_variant,,ENST00000548322,;RP11-298I3.1,intron_variant,,ENST00000548819,;HAUS4,non_coding_transcript_exon_variant,,ENST00000554446,;HAUS4,downstream_gene_variant,,ENST00000554373,;HAUS4,downstream_gene_variant,,ENST00000554651,;HAUS4,downstream_gene_variant,,ENST00000554349,;HAUS4,downstream_gene_variant,,ENST00000553794,;HAUS4,3_prime_UTR_variant,,ENST00000553859,;HAUS4,non_coding_transcript_exon_variant,,ENST00000556421,;HAUS4,downstream_gene_variant,,ENST00000554063,; T ENST00000206474 Transcript synonymous_variant 1111/1642 858/1092 286/363 I atT/atA 1 -1 HAUS4 HGNC HGNC:20163 protein_coding YES CCDS9580.1 ENSP00000206474 Q9H6D7 UPI000006F422 9/10 hmmpanther:PTHR16219,hmmpanther:PTHR16219:SF1,Pfam_domain:PF14735,PD360721 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 30 22947221 22947221 A T 1 0 0 0 0 0 0 0 1 6854 10 1 4 4 HAUS4 14 22947221 Silent SNP A C3L-02219_T 22947221 84096497 54 8566 SERPINA12 0 . GRCh38 14 94497791 94497791 + Missense_Mutation SNP G G C novel C3L-02219_T C3L-02219_N G G c.607C>G p.Leu203Val p.L203V ENST00000341228 3/6 105 74 31 162 162 0 strelka-varscan-mutect SERPINA12,missense_variant,p.Leu203Val,ENST00000341228,NM_173850.3;SERPINA12,missense_variant,p.Leu203Val,ENST00000556881,NM_001304461.1; C ENST00000341228 Transcript missense_variant 1403/2061 607/1245 203/414 L/V Ctt/Gtt 1 -1 SERPINA12 HGNC HGNC:18359 protein_coding YES CCDS9926.1 ENSP00000342109 Q8IW75 UPI000000D86C NM_173850.3 tolerated(0.6) 3/6 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF157,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 94497791 94497791 G C 1 0 0 0 0 1 0 0 0 14365 971 34 4 4 SERPINA12 14 94497791 Missense_Mutation SNP G C3L-02219_T 71550570 94497791 12545927 55 8567 CCNK 0 . GRCh38 14 99510597 99510597 + Missense_Mutation SNP C C G novel C3L-02219_T C3L-02219_N C C c.1558C>G p.Pro520Ala p.P520A ENST00000389879 11/11 19 12 7 23 23 0 strelka-varscan-mutect CCNK,missense_variant,p.Pro520Ala,ENST00000389879,NM_001099402.1;CCDC85C,3_prime_UTR_variant,,ENST00000380243,NM_001144995.1;CCNK,intron_variant,,ENST00000555049,;CCDC85C,downstream_gene_variant,,ENST00000557769,;CCDC85C,downstream_gene_variant,,ENST00000555822,;CCDC85C,downstream_gene_variant,,ENST00000557576,;CCDC85C,downstream_gene_variant,,ENST00000554996,;CCDC85C,downstream_gene_variant,,ENST00000554877,;RP11-688G15.3,upstream_gene_variant,,ENST00000557733,;CCNK,non_coding_transcript_exon_variant,,ENST00000553865,; G ENST00000389879 Transcript missense_variant 1681/3524 1558/1743 520/580 P/A Cca/Gca 1 1 CCNK HGNC HGNC:1596 protein_coding YES CCDS45160.1 ENSP00000374529 O75909 A0A024R6K1 UPI00001FDB50 NM_001099402.1 deleterious_low_confidence(0.02) 11/11 Low_complexity_(Seg):seg,hmmpanther:PTHR10026:SF71,hmmpanther:PTHR10026 MODERATE 1 SNV 5 1 PASS . . 2 205 3 0 0 0 0 0 -19.92884 1 1 1 1 0 G 3 3 30 99510597 99510597 C G 1 0 0 0 0 1 0 0 0 2629 623 22 4 4 CCNK 14 99510597 Missense_Mutation SNP C C3L-02219_T 5012806 99510597 7533121 56 8568 GOLGA6L2 0 . GRCh38 15 23443855 23443855 + Missense_Mutation SNP C C A novel C3L-02219_T C3L-02219_N C C c.513G>T p.Leu171Phe p.L171F ENST00000567107 5/8 187 150 37 284 284 0 strelka-varscan-mutect GOLGA6L2,missense_variant,p.Leu171Phe,ENST00000567107,NM_001304388.1;GOLGA6L2,missense_variant,p.Leu159Phe,ENST00000312015,;GOLGA6L2,5_prime_UTR_variant,,ENST00000345070,;GOLGA6L2,missense_variant,p.Leu161Phe,ENST00000566571,; A ENST00000567107 Transcript missense_variant 566/3030 513/2730 171/909 L/F ttG/ttT 1 -1 GOLGA6L2 HGNC HGNC:26695 protein_coding YES CCDS76728.1 ENSP00000454407 H3BMJ4 UPI00024672CE NM_001304388.1 deleterious_low_confidence(0) 5/8 hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF11 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 23443855 23443855 C A 1 0 0 0 0 1 0 0 0 6440 709 25 2 2 GOLGA6L2 15 23443855 Missense_Mutation SNP C C3L-02219_T 23443855 78547334 57 8569 HERC2 0 . GRCh38 15 28192080 28192080 + Silent SNP G G A novel C3L-02219_T C3L-02219_N G G c.8332C>T p.= p.L2778L ENST00000261609 53/93 145 131 14 180 180 0 strelka-varscan-mutect HERC2,synonymous_variant,p.=,ENST00000261609,NM_004667.5;HERC2,non_coding_transcript_exon_variant,,ENST00000567869,; A ENST00000261609 Transcript synonymous_variant 8441/15337 8332/14505 2778/4834 L Ctg/Ttg 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 53/93 Gene3D:2.60.120.260,PROSITE_profiles:PS51284,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 30 28192080 28192080 G A 1 0 0 0 0 0 0 0 1 6942 962 34 3 3 HERC2 15 28192080 Silent SNP G C3L-02219_T 4748225 28192080 73799109 58 8570 AP4E1 0 . GRCh38 15 50929080 50929080 + Missense_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.614A>T p.His205Leu p.H205L ENST00000261842 6/21 313 281 32 467 466 1 strelka-varscan-mutect AP4E1,missense_variant,p.His205Leu,ENST00000261842,NM_007347.4;AP4E1,missense_variant,p.His130Leu,ENST00000560508,NM_001252127.1;AP4E1,missense_variant,p.His205Leu,ENST00000558439,;AP4E1,missense_variant,p.His130Leu,ENST00000561393,;AP4E1,missense_variant,p.His205Leu,ENST00000561441,; T ENST00000261842 Transcript missense_variant 720/6758 614/3414 205/1137 H/L cAt/cTt 1 1 AP4E1 HGNC HGNC:573 protein_coding YES CCDS32240.1 ENSP00000261842 Q9UPM8 UPI00001D89D8 NM_007347.4 deleterious(0) 6/21 hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF13,Pfam_domain:PF01602,PIRSF_domain:PIRSF037097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 50929080 50929080 A T 1 0 0 0 0 1 0 0 0 868 217 8 4 4 AP4E1 15 50929080 Missense_Mutation SNP A C3L-02219_T 22737000 50929080 51062109 59 8571 KIF23 0 . GRCh38 15 69446287 69446287 + Silent SNP C C A rs778267317 C3L-02219_T C3L-02219_N C C c.2719C>A p.= p.R907R ENST00000260363 21/23 292 243 49 435 431 4 strelka-varscan-mutect KIF23,splice_region_variant,p.=,ENST00000395392,;KIF23,synonymous_variant,p.=,ENST00000260363,NM_138555.3,NM_001281301.1;KIF23,synonymous_variant,p.=,ENST00000559279,NM_004856.6;KIF23,synonymous_variant,p.=,ENST00000352331,;KIF23,synonymous_variant,p.=,ENST00000558585,;KIF23,3_prime_UTR_variant,,ENST00000561089,;KIF23,non_coding_transcript_exon_variant,,ENST00000558303,;KIF23,non_coding_transcript_exon_variant,,ENST00000560125,;KIF23,upstream_gene_variant,,ENST00000559944,; A ENST00000260363 Transcript synonymous_variant 2939/3713 2719/2883 907/960 R Cga/Aga rs778267317,COSM4655234,COSM4655235 1 1 KIF23 HGNC HGNC:6392 protein_coding YES CCDS32278.1 ENSP00000260363 Q02241 UPI0000072141 NM_138555.3,NM_001281301.1 21/23 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs778267317 . 0 208 0 0 2 0 0 0 -19.99998 0.9974686 1 1 1 0 A 2 1 30 69446287 69446287 C A 1 0 0 0 0 0 0 0 1 8156 898 31 1 1 KIF23 15 69446287 Silent SNP C C3L-02219_T 18517207 69446287 32544902 60 8572 FAHD1 0 . GRCh38 16 1827657 1827657 + Missense_Mutation SNP C C G C3L-02219_T C3L-02219_N C C c.428C>G p.Pro143Arg p.P143R ENST00000382666 1/3 401 367 34 324 324 0 strelka-varscan-mutect FAHD1,missense_variant,p.Pro143Arg,ENST00000427358,NM_031208.3;FAHD1,missense_variant,p.Pro143Arg,ENST00000382666,NM_001018104.2;FAHD1,missense_variant,p.Pro143Arg,ENST00000382668,NM_001142398.1;FAHD1,missense_variant,p.Pro143Arg,ENST00000615972,;HAGH,upstream_gene_variant,,ENST00000397356,NM_005326.4;HAGH,upstream_gene_variant,,ENST00000566709,;HAGH,upstream_gene_variant,,ENST00000455446,NM_001286249.1;HAGH,upstream_gene_variant,,ENST00000397353,NM_001040427.1;HAGH,upstream_gene_variant,,ENST00000564445,;HAGH,upstream_gene_variant,,ENST00000569339,;HAGH,upstream_gene_variant,,ENST00000569700,;HAGH,upstream_gene_variant,,ENST00000565097,;HAGH,upstream_gene_variant,,ENST00000564518,;HAGH,upstream_gene_variant,,ENST00000567190,; G ENST00000382666 Transcript missense_variant 691/1964 428/747 143/248 P/R cCt/cGt COSM967690 1 1 FAHD1 HGNC HGNC:14169 protein_coding YES CCDS32367.1 ENSP00000372112 Q6P587 UPI000051946E NM_001018104.2 deleterious(0) 1/3 hmmpanther:PTHR11820:SF7,hmmpanther:PTHR11820,Pfam_domain:PF01557,Gene3D:3.90.850.10,Superfamily_domains:SSF56529 1 MODERATE SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 1827657 1827657 C G 1 0 0 0 0 1 0 0 0 5244 681 24 4 4 FAHD1 16 1827657 Missense_Mutation SNP C C3L-02219_T 1827657 88510688 61 8573 DOC2A 0 . GRCh38 16 30009489 30009489 + Missense_Mutation SNP G G C novel C3L-02219_T C3L-02219_N G G c.331C>G p.Leu111Val p.L111V ENST00000350119 3/11 427 391 36 416 416 0 strelka-varscan-mutect DOC2A,missense_variant,p.Leu111Val,ENST00000350119,NM_003586.2,NM_001282062.1;DOC2A,missense_variant,p.Leu111Val,ENST00000616445,NM_001282063.1;DOC2A,missense_variant,p.Leu111Val,ENST00000564944,;DOC2A,missense_variant,p.Leu111Val,ENST00000564979,NM_001282068.1;DOC2A,missense_variant,p.Leu111Val,ENST00000565273,;DOC2A,missense_variant,p.Leu111Val,ENST00000563378,;DOC2A,5_prime_UTR_variant,,ENST00000563125,;DOC2A,5_prime_UTR_variant,,ENST00000567332,;DOC2A,5_prime_UTR_variant,,ENST00000574405,;INO80E,downstream_gene_variant,,ENST00000563197,NM_173618.2;INO80E,downstream_gene_variant,,ENST00000304516,NM_001304562.1;INO80E,downstream_gene_variant,,ENST00000567705,;INO80E,downstream_gene_variant,,ENST00000562291,;DOC2A,downstream_gene_variant,,ENST00000567824,;DOC2A,downstream_gene_variant,,ENST00000570194,;DOC2A,5_prime_UTR_variant,,ENST00000566310,;DOC2A,5_prime_UTR_variant,,ENST00000561671,;DOC2A,non_coding_transcript_exon_variant,,ENST00000564233,;DOC2A,non_coding_transcript_exon_variant,,ENST00000566456,;INO80E,downstream_gene_variant,,ENST00000569957,;INO80E,downstream_gene_variant,,ENST00000540562,;INO80E,downstream_gene_variant,,ENST00000567987,;INO80E,downstream_gene_variant,,ENST00000562441,;DOC2A,upstream_gene_variant,,ENST00000564357,;INO80E,downstream_gene_variant,,ENST00000567065,; C ENST00000350119 Transcript missense_variant 522/2071 331/1203 111/400 L/V Ctc/Gtc 1 -1 DOC2A HGNC HGNC:2985 protein_coding YES CCDS10666.1 ENSP00000340017 Q14183 UPI000013DBC8 NM_003586.2,NM_001282062.1 tolerated(0.53) 3/11 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF233,PIRSF_domain:PIRSF036931,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs1470378618 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 30009489 30009489 G C 1 0 0 0 0 1 0 0 0 4497 1000 35 4 4 DOC2A 16 30009489 Missense_Mutation SNP G C3L-02219_T 28181832 30009489 60328856 62 8574 ALDOA 0 . GRCh38 16 30069373 30069373 + Missense_Mutation SNP A A G novel C3L-02219_T C3L-02219_N A A c.770A>G p.Gln257Arg p.Q257R ENST00000395248 13/16 670 602 68 643 643 0 strelka-varscan-mutect ALDOA,missense_variant,p.Gln203Arg,ENST00000566897,;ALDOA,missense_variant,p.Gln257Arg,ENST00000395248,;ALDOA,missense_variant,p.Gln207Arg,ENST00000627059,;ALDOA,missense_variant,p.Gln203Arg,ENST00000338110,NM_000034.3;ALDOA,missense_variant,p.Gln203Arg,ENST00000564546,NM_184041.2;ALDOA,missense_variant,p.Gln257Arg,ENST00000564595,NM_001243177.1;ALDOA,missense_variant,p.Gln203Arg,ENST00000412304,NM_001127617.2;ALDOA,missense_variant,p.Gln203Arg,ENST00000563060,NM_184043.2;ALDOA,missense_variant,p.Gln203Arg,ENST00000569798,;ALDOA,missense_variant,p.Gln207Arg,ENST00000395240,;ALDOA,missense_variant,p.Gln203Arg,ENST00000569545,;ALDOA,missense_variant,p.Gln257Arg,ENST00000562679,;ALDOA,intron_variant,,ENST00000564688,;ALDOA,downstream_gene_variant,,ENST00000568435,;ALDOA,downstream_gene_variant,,ENST00000562168,;ALDOA,downstream_gene_variant,,ENST00000563987,;ALDOA,upstream_gene_variant,,ENST00000565355,;ALDOA,downstream_gene_variant,,ENST00000566846,;CTD-2515O10.5,upstream_gene_variant,,ENST00000617969,;ALDOA,downstream_gene_variant,,ENST00000566012,;ALDOA,non_coding_transcript_exon_variant,,ENST00000564521,;ALDOA,non_coding_transcript_exon_variant,,ENST00000566130,;ALDOA,non_coding_transcript_exon_variant,,ENST00000566146,;ALDOA,downstream_gene_variant,,ENST00000567555,;ALDOA,downstream_gene_variant,,ENST00000562302,; G ENST00000395248 Transcript missense_variant 1752/2447 770/1257 257/418 Q/R cAg/cGg 1 1 ALDOA HGNC HGNC:414 protein_coding YES CCDS58450.1 ENSP00000378669 P04075 UPI0000E59D76 deleterious(0.01) 13/16 hmmpanther:PTHR11627,Gene3D:3.20.20.70,Pfam_domain:PF00274,Superfamily_domains:SSF51569 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 30069373 30069373 A G 1 0 0 0 0 1 0 0 0 607 188 7 5 5 ALDOA 16 30069373 Missense_Mutation SNP A C3L-02219_T 59884 30069373 60268972 63 8575 FBXO31 0 . GRCh38 16 87334078 87334078 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.1205C>A p.Pro402Gln p.P402Q ENST00000311635 8/9 97 71 26 109 109 0 strelka-varscan-mutect FBXO31,missense_variant,p.Pro402Gln,ENST00000311635,NM_024735.4;FBXO31,missense_variant,p.Pro230Gln,ENST00000618298,NM_001282683.1;RP11-178L8.4,missense_variant,p.Pro66Gln,ENST00000568879,;FBXO31,downstream_gene_variant,,ENST00000563113,;FBXO31,missense_variant,p.Gln111Lys,ENST00000565593,; T ENST00000311635 Transcript missense_variant 1218/5934 1205/1620 402/539 P/Q cCa/cAa 1 -1 FBXO31 HGNC HGNC:16510 protein_coding YES CCDS32501.1 ENSP00000310841 Q5XUX0 UPI000021D235 NM_024735.4 tolerated(0.4) 8/9 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 87334078 87334078 G T 1 0 0 0 0 1 0 0 0 5604 1348 47 2 2 FBXO31 16 87334078 Missense_Mutation SNP G C3L-02219_T 57264705 87334078 3004267 64 8576 KRTAP9-4 0 . GRCh38 17 41250023 41250023 + Silent SNP C C T novel C3L-02219_T C3L-02219_N C C c.303C>T p.= p.C101C ENST00000334109 1/1 535 472 63 714 714 0 strelka-varscan-mutect KRTAP9-4,synonymous_variant,p.=,ENST00000334109,NM_033191.2; T ENST00000334109 Transcript synonymous_variant 337/967 303/465 101/154 C tgC/tgT 1 1 KRTAP9-4 HGNC HGNC:18902 protein_coding YES CCDS11386.1 ENSP00000334922 Q9BYQ2 UPI000013F6DA NM_033191.2 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF65,Pfam_domain:PF13885 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 30 41250023 41250023 C T 1 0 0 0 0 0 0 0 1 8472 718 25 3 3 KRTAP9-4 17 41250023 Silent SNP C C3L-02219_T 41250023 42007418 65 8577 MYCBPAP 0 . GRCh38 17 50517309 50517309 + Missense_Mutation SNP T T C novel C3L-02219_T C3L-02219_N T T c.350T>C p.Leu117Pro p.L117P ENST00000323776 3/19 261 202 59 303 303 0 strelka-varscan-mutect MYCBPAP,missense_variant,p.Leu117Pro,ENST00000323776,NM_032133.4;MYCBPAP,missense_variant,p.Leu80Pro,ENST00000436259,;MYCBPAP,missense_variant,p.Leu117Pro,ENST00000452039,;MYCBPAP,downstream_gene_variant,,ENST00000576179,;MYCBPAP,upstream_gene_variant,,ENST00000468821,;MYCBPAP,missense_variant,p.Leu92Pro,ENST00000437498,;MYCBPAP,3_prime_UTR_variant,,ENST00000458692,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,;MYCBPAP,upstream_gene_variant,,ENST00000459754,; C ENST00000323776 Transcript missense_variant 512/3186 350/2955 117/984 L/P cTt/cCt 1 1 MYCBPAP HGNC HGNC:19677 protein_coding YES CCDS32680.2 ENSP00000323184 Q8TBZ2 A0A140VK87 UPI0000E5A00B NM_032133.4 tolerated(0.28) 3/19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 50517309 50517309 T C 1 0 0 0 0 1 0 0 0 10019 1609 56 5 5 MYCBPAP 17 50517309 Missense_Mutation SNP T C3L-02219_T 9267286 50517309 32740132 66 8578 SHD 0 . GRCh38 19 4282886 4282886 + Missense_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.314A>T p.Glu105Val p.E105V ENST00000543264 2/6 153 139 14 171 171 0 strelka-varscan-mutect SHD,missense_variant,p.Glu105Val,ENST00000543264,NM_020209.3;SHD,missense_variant,p.Glu105Val,ENST00000599689,;SHD,upstream_gene_variant,,ENST00000600475,;SHD,upstream_gene_variant,,ENST00000593383,; T ENST00000543264 Transcript missense_variant 1777/2577 314/1023 105/340 E/V gAg/gTg 1 1 SHD HGNC HGNC:30633 protein_coding YES CCDS12125.1 ENSP00000446058 Q96IW2 UPI000007030D NM_020209.3 deleterious(0.01) 2/6 hmmpanther:PTHR15127,hmmpanther:PTHR15127:SF33 MODERATE 1 SNV 1 1 PASS . . 0 202 3 5 0 0 0 0 -19.17541 0.9959717 1 1 1 0 T 3 4 30 4282886 4282886 A T 1 0 0 0 0 1 0 0 0 14535 304 11 4 4 SHD 19 4282886 Missense_Mutation SNP A C3L-02219_T 4282886 54334730 67 8579 MUC16 0 . GRCh38 19 8972740 8972740 + Missense_Mutation SNP C C T C3L-02219_T C3L-02219_N C C c.8399G>A p.Gly2800Glu p.G2800E ENST00000397910 1/84 170 154 16 239 239 0 strelka-varscan-mutect MUC16,missense_variant,p.Gly2800Glu,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 8603/43816 8399/43524 2800/14507 G/E gGa/gAa COSM3543424,COSM3543425 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1199809085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 8972740 8972740 C T 1 0 0 0 0 1 0 0 0 9972 855 30 3 3 MUC16 19 8972740 Missense_Mutation SNP C C3L-02219_T 4689854 8972740 49644876 68 8580 OR10H5 0 . GRCh38 19 15794343 15794343 + Missense_Mutation SNP A A G novel C3L-02219_T C3L-02219_N A A c.295A>G p.Ser99Gly p.S99G ENST00000308940 1/1 182 162 20 215 215 0 varscan-mutect OR10H5,missense_variant,p.Ser99Gly,ENST00000308940,NM_001004466.1; G ENST00000308940 Transcript missense_variant 393/1132 295/948 99/315 S/G Agt/Ggt 1 1 OR10H5 HGNC HGNC:15389 protein_coding YES CCDS32940.1 ENSP00000310704 Q8NGA6 A0A126GWE9 UPI0000041C8F NM_001004466.1 tolerated(0.06) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF122,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 15794343 15794343 A G 1 0 0 0 0 1 0 0 0 10986 188 7 5 5 OR10H5 19 15794343 Missense_Mutation SNP A C3L-02219_T 6821603 15794343 42823273 69 8581 ZNF729 0 . GRCh38 19 22315774 22315774 + Missense_Mutation SNP A A T novel C3L-02219_T C3L-02219_N A A c.2357A>T p.His786Leu p.H786L ENST00000601693 4/4 264 240 24 378 378 0 strelka-varscan-mutect ZNF729,missense_variant,p.His786Leu,ENST00000601693,NM_001242680.1; T ENST00000601693 Transcript missense_variant 2475/3877 2357/3759 786/1252 H/L cAt/cTt 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 22315774 22315774 A T 1 0 0 0 0 1 0 0 0 18703 217 8 4 4 ZNF729 19 22315774 Missense_Mutation SNP A C3L-02219_T 6521431 22315774 36301842 70 8582 C19orf47 0 . GRCh38 19 40333880 40333881 + Frame_Shift_Ins INS - - G novel C3L-02219_T C3L-02219_N - - c.382dupC p.Leu128ProfsTer23 p.L128Pfs*23 ENST00000582783 5/9 131 117 14 141 140 1 sindel-varindel-pindel C19orf47,frameshift_variant,p.Leu128ProfsTer23,ENST00000582783,NM_001256441.1,NM_001256440.1;C19orf47,frameshift_variant,p.Leu61ProfsTer23,ENST00000392035,;C19orf47,frameshift_variant,p.Leu91ProfsTer23,ENST00000580606,;C19orf47,frameshift_variant,p.Leu61ProfsTer23,ENST00000582006,;C19orf47,frameshift_variant,p.Leu101ProfsTer11,ENST00000357884,;C19orf47,3_prime_UTR_variant,,ENST00000580977,; G ENST00000582783 Transcript frameshift_variant 395-396/3628 382-383/1269 128/422 L/PX ctt/cCtt 1 -1 C19orf47 HGNC HGNC:26723 protein_coding YES CCDS58662.1 ENSP00000463159 Q8N9M1 UPI000006FE9B NM_001256441.1,NM_001256440.1 5/9 hmmpanther:PTHR21359,hmmpanther:PTHR21359:SF1 HIGH 1 insertion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 30 40333880 40333880 - G 1 0 1 1 0 0 0 0 0 1913 72 3 0 0 C19orf47 19 40333880 Frame_Shift_Ins INS - C3L-02219_T 18018106 40333880 18283736 71 8583 SHANK1 0 . GRCh38 19 50662008 50662008 + Missense_Mutation SNP C C A C3L-02219_T C3L-02219_N C C c.6443G>T p.Arg2148Leu p.R2148L ENST00000293441 23/23 237 205 32 263 262 1 strelka-varscan-mutect SHANK1,missense_variant,p.Arg2148Leu,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Arg2156Leu,ENST00000391814,;SHANK1,missense_variant,p.Arg2139Leu,ENST00000359082,;SHANK1,missense_variant,p.Arg1535Leu,ENST00000391813,;C19orf81,downstream_gene_variant,,ENST00000425202,NM_001195076.1;C19orf81,downstream_gene_variant,,ENST00000458538,;C19orf81,downstream_gene_variant,,ENST00000490451,;SHANK1,downstream_gene_variant,,ENST00000483981,;SHANK1,downstream_gene_variant,,ENST00000468654,; A ENST00000293441 Transcript missense_variant 6462/6643 6443/6486 2148/2161 R/L cGc/cTc COSM4725726,COSM4725727 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 deleterious(0) 23/23 PROSITE_profiles:PS50105,hmmpanther:PTHR24135:SF3,hmmpanther:PTHR24135,Pfam_domain:PF00536,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1259178592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 50662008 50662008 C A 1 0 0 0 0 1 0 0 0 14523 768 27 1 1 SHANK1 19 50662008 Missense_Mutation SNP C C3L-02219_T 10328128 50662008 7955608 72 8584 NLRP11 0 . GRCh38 19 55809640 55809640 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.970C>A p.Gln324Lys p.Q324K ENST00000589093 3/10 208 181 27 251 251 0 strelka-varscan-mutect NLRP11,missense_variant,p.Gln324Lys,ENST00000589093,NM_145007.3;NLRP11,missense_variant,p.Gln324Lys,ENST00000589824,;NLRP11,missense_variant,p.Gln225Lys,ENST00000592953,NM_001297743.1;NLRP11,downstream_gene_variant,,ENST00000593208,;NLRP11,missense_variant,p.Gln225Lys,ENST00000590409,;NLRP11,missense_variant,p.Gln324Lys,ENST00000593244,; T ENST00000589093 Transcript missense_variant 1064/3417 970/3102 324/1033 Q/K Cag/Aag 1 -1 NLRP11 HGNC HGNC:22945 protein_coding YES CCDS12935.1 ENSP00000466285 P59045 UPI000013ED9D NM_145007.3 tolerated(1) 3/10 hmmpanther:PTHR24106:SF62,hmmpanther:PTHR24106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 55809640 55809640 G T 1 0 0 0 0 1 0 0 0 10510 1357 47 2 2 NLRP11 19 55809640 Missense_Mutation SNP G C3L-02219_T 5147632 55809640 2807976 73 8585 NLRP5 0 . GRCh38 19 56028433 56028433 + Missense_Mutation SNP C C T rs771396943 C3L-02219_T C3L-02219_N C C c.2200C>T p.Arg734Trp p.R734W ENST00000390649 7/15 191 162 29 241 241 0 strelka-varscan-mutect NLRP5,missense_variant,p.Arg734Trp,ENST00000390649,NM_153447.4;NLRP5,missense_variant,p.Arg734Trp,ENST00000621651,; T ENST00000390649 Transcript missense_variant 2200/3888 2200/3603 734/1200 R/W Cgg/Tgg rs771396943,COSM2150536 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 deleterious(0.05) 7/15 Gene3D:3.80.10.10 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771396943 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 56028433 56028433 C T 1 0 0 0 0 1 0 0 0 10518 759 27 1 1 NLRP5 19 56028433 Missense_Mutation SNP C C3L-02219_T 218793 56028433 2589183 74 8586 ZNF814 0 . GRCh38 19 57874749 57874749 + Missense_Mutation SNP T T C novel C3L-02219_T C3L-02219_N T T c.641A>G p.Tyr214Cys p.Y214C ENST00000435989 3/3 347 306 41 449 449 0 strelka-varscan-mutect ZNF814,missense_variant,p.Tyr214Cys,ENST00000435989,NM_001144989.1;ZNF814,missense_variant,p.Tyr214Cys,ENST00000614383,;ZNF814,intron_variant,,ENST00000597832,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000600634,;ZNF814,intron_variant,,ENST00000595048,;ZNF814,downstream_gene_variant,,ENST00000597807,;ZNF814,intron_variant,,ENST00000594629,;ZNF814,intron_variant,,ENST00000597348,;ZNF814,intron_variant,,ENST00000595894,;ZNF814,upstream_gene_variant,,ENST00000594159,;CTD-2583A14.9,downstream_gene_variant,,ENST00000602124,; C ENST00000435989 Transcript missense_variant 876/3146 641/2568 214/855 Y/C tAc/tGc 1 -1 ZNF814 HGNC HGNC:33258 protein_coding YES CCDS46212.1 ENSP00000410545 B7Z6K7 UPI0001662BAD NM_001144989.1 tolerated(0.13) 3/3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 30 57874749 57874749 T C 1 0 0 0 0 1 0 0 0 18762 1638 57 5 5 ZNF814 19 57874749 Missense_Mutation SNP T C3L-02219_T 1846316 57874749 742867 75 8587 TMC2 0 . GRCh38 20 2624320 2624320 + Missense_Mutation SNP T T A novel C3L-02219_T C3L-02219_N T T c.2230T>A p.Phe744Ile p.F744I ENST00000358864 17/20 118 86 32 183 182 1 strelka-varscan-mutect TMC2,missense_variant,p.Phe744Ile,ENST00000358864,NM_080751.2; A ENST00000358864 Transcript missense_variant 2245/3169 2230/2721 744/906 F/I Ttc/Atc 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 tolerated(0.06) 17/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 2624320 2624320 T A 1 0 0 0 0 1 0 0 0 16431 1841 64 4 4 TMC2 20 2624320 Missense_Mutation SNP T C3L-02219_T 2624320 61819847 76 8588 MACROD2 0 . GRCh38 20 15862807 15862807 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.708G>T p.Met236Ile p.M236I ENST00000217246 9/17 97 90 7 143 142 1 strelka-varscan-mutect MACROD2,start_lost,p.Met1?,ENST00000402914,NM_001033087.1;MACROD2,start_lost,p.Met1?,ENST00000378058,;MACROD2,missense_variant,p.Met236Ile,ENST00000217246,NM_080676.5; T ENST00000217246 Transcript missense_variant 1103/4994 708/1278 236/425 M/I atG/atT 1 1 MACROD2 HGNC HGNC:16126 protein_coding YES CCDS13120.2 ENSP00000217246 A1Z1Q3 UPI00005B2E12 NM_080676.5 tolerated(0.13) 9/17 Gene3D:3.40.220.10,PROSITE_profiles:PS51154,hmmpanther:PTHR11106,hmmpanther:PTHR11106:SF67,Superfamily_domains:SSF52949 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 15862807 15862807 G T 1 0 0 0 0 1 0 0 0 9062 1290 45 2 2 MACROD2 20 15862807 Missense_Mutation SNP G C3L-02219_T 13238487 15862807 48581360 77 8589 KIAA1755 0 . GRCh38 20 38223558 38223558 + Missense_Mutation SNP C C A rs768672282 C3L-02219_T C3L-02219_N C C c.2248G>T p.Asp750Tyr p.D750Y ENST00000279024 9/14 86 74 12 131 130 1 strelka-varscan-mutect KIAA1755,missense_variant,p.Asp750Tyr,ENST00000279024,NM_001029864.1;KIAA1755,missense_variant,p.Asp49Tyr,ENST00000435901,;KIAA1755,downstream_gene_variant,,ENST00000496900,;KIAA1755,upstream_gene_variant,,ENST00000484362,; A ENST00000279024 Transcript missense_variant 2520/6429 2248/3603 750/1200 D/Y Gac/Tac rs768672282,COSM1212298 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 deleterious(0) 9/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF125 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs768672282 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 30 38223558 38223558 C A 1 0 0 0 0 1 0 0 0 8128 884 31 1 1 KIAA1755 20 38223558 Missense_Mutation SNP C C3L-02219_T 22360751 38223558 26220609 78 8590 SLC2A10 0 . GRCh38 20 46725350 46725350 + Missense_Mutation SNP G G T rs753280877 C3L-02219_T C3L-02219_N G G c.314G>T p.Arg105Leu p.R105L ENST00000359271 2/5 337 287 50 437 437 0 strelka-varscan-mutect SLC2A10,missense_variant,p.Arg105Leu,ENST00000359271,NM_030777.3;SLC2A10,non_coding_transcript_exon_variant,,ENST00000611837,; T ENST00000359271 Transcript missense_variant 564/4389 314/1626 105/541 R/L cGc/cTc rs753280877 1 1 SLC2A10 HGNC HGNC:13444 protein_coding YES CCDS13402.1 ENSP00000352216 O95528 UPI000012BC8D NM_030777.3 deleterious(0) 2/5 PROSITE_profiles:PS50850,hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF81,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Prints_domain:PR00171 likely_pathogenic MODERATE 1 SNV 1 1 1 PASS rs753280877 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 30 46725350 46725350 G T 1 0 0 0 0 1 0 0 0 14809 1087 38 1 1 SLC2A10 20 46725350 Missense_Mutation SNP G C3L-02219_T 8501792 46725350 17718817 79 8591 BACH1 0 . GRCh38 21 29342410 29342410 + Silent SNP G G A novel C3L-02219_T C3L-02219_N G G c.1788G>A p.= p.K596K ENST00000399921 5/5 93 84 9 118 117 1 strelka-varscan-mutect BACH1,synonymous_variant,p.=,ENST00000399921,NM_206866.2;BACH1,synonymous_variant,p.=,ENST00000286800,NM_001186.3;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; A ENST00000399921 Transcript synonymous_variant 2031/5769 1788/2211 596/736 K aaG/aaA 1 1 BACH1 HGNC HGNC:935 protein_coding YES CCDS13585.1 ENSP00000382805 O14867 UPI000012673F NM_206866.2 5/5 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50217,Pfam_domain:PF03131,Gene3D:1.20.5.370,SMART_domains:SM00338,Superfamily_domains:SSF57959 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -18.60323 0.9999998 1 1 1 0 A 2 1 30 29342410 29342410 G A 1 0 0 0 0 0 0 0 1 1441 991 35 3 3 BACH1 21 29342410 Silent SNP G C3L-02219_T 29342410 17367573 80 8592 LZTR1 0 . GRCh38 22 20989624 20989624 + Splice_Site SNP G G T novel C3L-02219_T C3L-02219_N G G c.594-1G>T p.X198_splice ENST00000215739 186 176 10 251 250 1 strelka-varscan-mutect LZTR1,splice_acceptor_variant,,ENST00000215739,NM_006767.3;LZTR1,splice_acceptor_variant,,ENST00000479606,;LZTR1,splice_acceptor_variant,,ENST00000480895,;LZTR1,upstream_gene_variant,,ENST00000497716,;LZTR1,splice_acceptor_variant,,ENST00000414985,;LZTR1,splice_acceptor_variant,,ENST00000443265,;LZTR1,upstream_gene_variant,,ENST00000495142,;LZTR1,upstream_gene_variant,,ENST00000492480,;LZTR1,upstream_gene_variant,,ENST00000415354,;LZTR1,upstream_gene_variant,,ENST00000491432,;LZTR1,upstream_gene_variant,,ENST00000461510,;LZTR1,downstream_gene_variant,,ENST00000493460,; T ENST00000215739 Transcript splice_acceptor_variant -/4572 594/2523 198/840 1 1 LZTR1 HGNC HGNC:6742 protein_coding YES CCDS33606.1 ENSP00000215739 Q8N653 UPI000013C695 NM_006767.3 6/20 HIGH 1 SNV 1 1 PASS rs1401166273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 30 20989624 20989624 G T 1 0 0 0 0 0 0 1 0 9050 1014 35 2 2 LZTR1 22 20989624 Splice_Site SNP G C3L-02219_T 20989624 29828844 81 8593 MAPK8IP2 0 . GRCh38 22 50604766 50604766 + Silent SNP C C T novel C3L-02219_T C3L-02219_N C C c.1467C>T p.= p.P489P ENST00000329492 5/12 135 122 13 173 173 0 strelka-mutect MAPK8IP2,synonymous_variant,p.=,ENST00000329492,NM_012324.4;CHKB,upstream_gene_variant,,ENST00000463053,;MAPK8IP2,non_coding_transcript_exon_variant,,ENST00000008876,; T ENST00000329492 Transcript synonymous_variant 1601/3381 1467/2475 489/824 P ccC/ccT 1 1 MAPK8IP2 HGNC HGNC:6883 protein_coding YES CCDS74886.1 ENSP00000330572 Q13387 UPI000012DAB7 NM_012324.4 5/12 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -6.204224 0.9928888 1 1 1 0 T 2 4 30 50604766 50604766 C T 1 0 0 0 0 0 0 0 1 9209 639 23 1 1 MAPK8IP2 22 50604766 Silent SNP C C3L-02219_T 29615142 50604766 213702 82 8594 RBM10 0 . GRCh38 X 47179318 47179318 + Splice_Site SNP G G T novel C3L-02219_T C3L-02219_N G G c.920-1G>T p.X307_splice ENST00000329236 239 97 142 179 179 0 strelka-varscan-mutect RBM10,splice_acceptor_variant,,ENST00000377604,NM_005676.4,NM_001204467.1;RBM10,splice_acceptor_variant,,ENST00000329236,NM_001204468.1;RBM10,splice_acceptor_variant,,ENST00000345781,NM_001204466.1;RBM10,splice_acceptor_variant,,ENST00000628161,NM_152856.2;RBM10,non_coding_transcript_exon_variant,,ENST00000478410,;RBM10,intron_variant,,ENST00000496012,; T ENST00000329236 Transcript splice_acceptor_variant -/3201 920/2988 307/995 1 1 RBM10 HGNC HGNC:9896 protein_coding YES CCDS75969.1 ENSP00000328848 A0A0A0MR66 UPI0000211F0E NM_001204468.1 8/23 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 30 47179318 47179318 G T 1 0 0 0 0 0 0 1 0 13277 956 33 2 2 RBM10 23 47179318 Splice_Site SNP G C3L-02219_T 47179318 108861577 83 8595 WAS 0 . GRCh38 X 48688893 48688893 + Missense_Mutation SNP G G T novel C3L-02219_T C3L-02219_N G G c.1165G>T p.Gly389Cys p.G389C ENST00000376701 10/12 54 47 7 45 45 0 strelka-varscan-mutect WAS,missense_variant,p.Gly389Cys,ENST00000376701,NM_000377.2;WAS,downstream_gene_variant,,ENST00000450772,;WAS,non_coding_transcript_exon_variant,,ENST00000474174,;WAS,downstream_gene_variant,,ENST00000483750,;WAS,downstream_gene_variant,,ENST00000465982,;WAS,upstream_gene_variant,,ENST00000470107,;WAS,downstream_gene_variant,,ENST00000490627,; T ENST00000376701 Transcript missense_variant 1240/1849 1165/1509 389/502 G/C Ggt/Tgt 1 1 WAS HGNC HGNC:12731 protein_coding YES CCDS14303.1 ENSP00000365891 P42768 A0A024QYX8 UPI000003CA0A NM_000377.2 deleterious(0.01) 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23202,hmmpanther:PTHR23202:SF35 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.77749 1 1 1 1 0 T 3 4 30 48688893 48688893 G T 1 0 0 0 0 1 0 0 0 17811 1348 47 2 2 WAS 23 48688893 Missense_Mutation SNP G C3L-02219_T 1509575 48688893 107352002 84 8596 CLCN5 0 . GRCh38 X 50088754 50088754 + Silent SNP T T C novel C3L-02219_T C3L-02219_N T T c.1614T>C p.= p.L538L ENST00000376088 12/15 253 205 48 247 247 0 strelka-varscan-mutect CLCN5,synonymous_variant,p.=,ENST00000376088,NM_001127899.3,NM_001127898.3;CLCN5,synonymous_variant,p.=,ENST00000307367,NM_001282163.1;CLCN5,synonymous_variant,p.=,ENST00000376091,;CLCN5,synonymous_variant,p.=,ENST00000376108,NM_000084.4; C ENST00000376088 Transcript synonymous_variant 2255/10108 1614/2451 538/816 L ctT/ctC 1 1 CLCN5 HGNC HGNC:2023 protein_coding YES CCDS48115.1 ENSP00000365256 P51795 UPI0000212052 NM_001127899.3,NM_001127898.3 12/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR11689:SF63,hmmpanther:PTHR11689,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340,Prints_domain:PR00762 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 30 50088754 50088754 T C 1 0 0 0 0 0 0 0 1 3230 1770 62 5 5 CLCN5 23 50088754 Silent SNP T C3L-02219_T 1399861 50088754 105952141 85 8597 EDA 0 . GRCh38 X 69957044 69957044 + Missense_Mutation SNP C C G novel C3L-02219_T C3L-02219_N C C c.414C>G p.Phe138Leu p.F138L ENST00000374552 2/8 184 156 28 202 202 0 strelka-varscan-mutect EDA,missense_variant,p.Phe138Leu,ENST00000374552,NM_001399.4;EDA,missense_variant,p.Phe138Leu,ENST00000374553,NM_001005609.1;EDA,missense_variant,p.Phe6Leu,ENST00000616899,;EDA,missense_variant,p.Phe138Leu,ENST00000524573,NM_001005612.2;EDA,missense_variant,p.Phe6Leu,ENST00000503592,;EDA,non_coding_transcript_exon_variant,,ENST00000502251,;EDA,non_coding_transcript_exon_variant,,ENST00000533317,;EDA,non_coding_transcript_exon_variant,,ENST00000374548,; G ENST00000374552 Transcript missense_variant 656/5278 414/1176 138/391 F/L ttC/ttG 1 1 EDA HGNC HGNC:3157 protein_coding YES CCDS14394.1 ENSP00000363680 Q92838 UPI0000052244 NM_001399.4 tolerated_low_confidence(0.11) 2/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 30 69957044 69957044 C G 1 0 0 0 0 1 0 0 0 4731 912 32 4 4 EDA 23 69957044 Missense_Mutation SNP C C3L-02219_T 19868290 69957044 86083851 86 8598 H6PD 0 . GRCh38 1 9264557 9264557 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.2097G>T p.= p.L699L ENST00000602477 5/5 111 101 10 167 167 0 strelka-varscan-mutect H6PD,synonymous_variant,p.=,ENST00000377403,NM_004285.3;H6PD,synonymous_variant,p.=,ENST00000602477,NM_001282587.1;H6PD,upstream_gene_variant,,ENST00000495451,; T ENST00000602477 Transcript synonymous_variant 2249/5590 2097/2409 699/802 L ctG/ctT 1 1 H6PD HGNC HGNC:4795 protein_coding YES CCDS72697.1 ENSP00000473348 R4GMU1 UPI0000D61E40 NM_001282587.1 5/5 Gene3D:3.40.50.1360,Pfam_domain:PF01182,TIGRFAM_domain:TIGR01198,Superfamily_domains:SSF100950 LOW 1 SNV 1 1 PASS rs1255181873 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 9264557 9264557 G T 1 0 0 0 0 0 0 0 1 6818 1335 47 2 2 H6PD 1 9264557 Silent SNP G C3L-02345_T 9264557 239691865 1 8599 UBE4B 0 . GRCh38 1 10179493 10179493 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.3778C>T p.Arg1260Trp p.R1260W ENST00000343090 27/28 198 162 36 283 283 0 strelka-varscan-mutect UBE4B,missense_variant,p.Arg1260Trp,ENST00000343090,NM_001105562.2;UBE4B,missense_variant,p.Arg1131Trp,ENST00000253251,NM_006048.4;UBE4B,non_coding_transcript_exon_variant,,ENST00000465408,;UBE4B,non_coding_transcript_exon_variant,,ENST00000487244,; T ENST00000343090 Transcript missense_variant 3853/5267 3778/3909 1260/1302 R/W Cgg/Tgg 1 1 UBE4B HGNC HGNC:12500 protein_coding YES CCDS41245.1 ENSP00000343001 O95155 UPI0000137944 NM_001105562.2 deleterious(0) 27/28 PROSITE_profiles:PS51698,hmmpanther:PTHR13931,hmmpanther:PTHR13931:SF14,Pfam_domain:PF04564,Gene3D:3.30.40.10,SMART_domains:SM00504,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 10179493 10179493 C T 1 0 0 0 0 1 0 0 0 17407 759 27 1 1 UBE4B 1 10179493 Missense_Mutation SNP C C3L-02345_T 914936 10179493 238776929 2 8600 C1orf167 0 . GRCh38 1 11775555 11775555 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.2181C>A p.= p.L727L ENST00000433342 9/21 145 125 20 168 168 0 strelka-varscan-mutect C1orf167,synonymous_variant,p.=,ENST00000433342,NM_001010881.1;C1orf167,synonymous_variant,p.=,ENST00000312793,;C1orf167,upstream_gene_variant,,ENST00000444493,;C1orf167,upstream_gene_variant,,ENST00000449278,;RP11-56N19.5,downstream_gene_variant,,ENST00000376620,;C1orf167,non_coding_transcript_exon_variant,,ENST00000484153,; A ENST00000433342 Transcript synonymous_variant 2181/4545 2181/4407 727/1468 L ctC/ctA 1 1 C1orf167 HGNC HGNC:25262 protein_coding YES ENSP00000414909 Q5SNV9 UPI0000DD7886 NM_001010881.1 9/21 hmmpanther:PTHR38493,hmmpanther:PTHR38493:SF1 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 11775555 11775555 C A 1 0 0 0 0 0 0 0 1 1972 842 30 2 2 C1orf167 1 11775555 Silent SNP C C3L-02345_T 1596062 11775555 237180867 3 8601 RAP1GAP 0 . GRCh38 1 21617353 21617353 + Nonsense_Mutation SNP C C A rs771983527 C3L-02345_T C3L-02345_N C C c.436G>T p.Glu146Ter p.E146* ENST00000495204 7/25 172 141 31 234 233 1 strelka-varscan-mutect RAP1GAP,stop_gained,p.Glu82Ter,ENST00000290101,;RAP1GAP,stop_gained,p.Glu82Ter,ENST00000542643,NM_001145657.1;RAP1GAP,stop_gained,p.Glu82Ter,ENST00000374763,;RAP1GAP,stop_gained,p.Glu113Ter,ENST00000374761,;RAP1GAP,stop_gained,p.Glu82Ter,ENST00000374765,NM_002885.2;RAP1GAP,stop_gained,p.Glu146Ter,ENST00000495204,NM_001145658.1;RAP1GAP,stop_gained,p.Glu82Ter,ENST00000317967,;RAP1GAP,downstream_gene_variant,,ENST00000447293,;RAP1GAP,non_coding_transcript_exon_variant,,ENST00000374757,;RAP1GAP,downstream_gene_variant,,ENST00000482984,;RAP1GAP,stop_gained,p.Glu82Ter,ENST00000471600,;RAP1GAP,non_coding_transcript_exon_variant,,ENST00000611549,; A ENST00000495204 Transcript stop_gained 450/2489 436/2184 146/727 E/* Gag/Tag rs771983527 1 -1 RAP1GAP HGNC HGNC:9858 protein_coding YES CCDS53277.1 ENSP00000434033 P47736 UPI0000EE7109 NM_001145658.1 7/25 hmmpanther:PTHR15711,Superfamily_domains:0043732 HIGH 1 SNV 1 1 PASS rs771983527 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 21617353 21617353 C A 1 0 0 0 0 0 1 0 0 13196 893 31 1 1 RAP1GAP 1 21617353 Nonsense_Mutation SNP C C3L-02345_T 9841798 21617353 227339069 4 8602 AIM1L 0 . GRCh38 1 26345706 26345706 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.952G>T p.Gly318Cys p.G318C ENST00000308182 2/20 94 78 16 132 132 0 strelka-varscan-mutect AIM1L,missense_variant,p.Gly318Cys,ENST00000308182,NM_001039775.3;AIM1L,missense_variant,p.Gly318Cys,ENST00000475866,;AIM1L,upstream_gene_variant,,ENST00000527815,;AIM1L,intron_variant,,ENST00000374207,; A ENST00000308182 Transcript missense_variant 1102/5245 952/4986 318/1661 G/C Ggc/Tgc 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 deleterious_low_confidence(0.02) 2/20 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 26345706 26345706 C A 1 0 0 0 0 1 0 0 0 508 623 22 2 2 AIM1L 1 26345706 Missense_Mutation SNP C C3L-02345_T 4728353 26345706 222610716 5 8603 ZMYM4 0 . GRCh38 1 35419598 35419598 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.4568G>A p.Arg1523His p.R1523H ENST00000314607 30/30 321 287 34 352 352 0 strelka-varscan-mutect ZMYM4,missense_variant,p.Arg1523His,ENST00000314607,NM_005095.2;ZMYM4,missense_variant,p.Arg1182His,ENST00000457946,; A ENST00000314607 Transcript missense_variant 4648/6994 4568/4647 1523/1548 R/H cGt/cAt 1 1 ZMYM4 HGNC HGNC:13055 protein_coding YES CCDS389.1 ENSP00000322915 Q5VZL5 UPI0000203EE6 NM_005095.2 deleterious(0) 30/30 Pfam_domain:PF12012,hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF10 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 35419598 35419598 G A 1 0 0 0 0 1 0 0 0 18282 1145 40 1 1 ZMYM4 1 35419598 Missense_Mutation SNP G C3L-02345_T 9073892 35419598 213536824 6 8604 COL8A2 0 . GRCh38 1 36098912 36098912 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.769C>T p.Pro257Ser p.P257S ENST00000397799 4/4 132 109 23 134 134 0 strelka-varscan-mutect COL8A2,missense_variant,p.Pro257Ser,ENST00000397799,NM_005202.3;COL8A2,missense_variant,p.Pro257Ser,ENST00000303143,;COL8A2,missense_variant,p.Pro192Ser,ENST00000481785,NM_001294347.1;COL8A2,missense_variant,p.Pro257Ser,ENST00000615990,;ADPRHL2,downstream_gene_variant,,ENST00000373178,NM_017825.2; A ENST00000397799 Transcript missense_variant 994/4670 769/2112 257/703 P/S Cct/Tct 1 -1 COL8A2 HGNC HGNC:2216 protein_coding YES CCDS403.1 ENSP00000380901 P25067 UPI00001B2F2D NM_005202.3 deleterious(0.05) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF584 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 36098912 36098912 G A 1 0 0 0 0 1 0 0 0 3495 1188 41 3 3 COL8A2 1 36098912 Missense_Mutation SNP G C3L-02345_T 679314 36098912 212857510 7 8605 LRRC8B 0 . GRCh38 1 89583852 89583852 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.1202T>A p.Leu401His p.L401H ENST00000330947 5/6 133 125 8 208 208 0 varscan-mutect LRRC8B,missense_variant,p.Leu401His,ENST00000330947,NM_001134476.1;LRRC8B,missense_variant,p.Leu401His,ENST00000439853,NM_015350.2;LRRC8B,3_prime_UTR_variant,,ENST00000358200,;LRRC8B,downstream_gene_variant,,ENST00000449440,;FLJ27354,intron_variant,,ENST00000443562,; A ENST00000330947 Transcript missense_variant 1562/7593 1202/2412 401/803 L/H cTc/cAc 1 1 LRRC8B HGNC HGNC:30692 protein_coding YES CCDS724.1 ENSP00000332674 Q6P9F7 UPI00000739FF NM_001134476.1 deleterious(0) 5/6 hmmpanther:PTHR23155:SF465,hmmpanther:PTHR23155 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 89583852 89583852 T A 1 0 0 0 0 1 0 0 0 8926 1551 54 4 4 LRRC8B 1 89583852 Missense_Mutation SNP T C3L-02345_T 53484940 89583852 159372570 8 8606 BRDT 0 . GRCh38 1 92014211 92014211 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.2793G>T p.= p.V931V ENST00000399546 19/19 159 130 29 234 233 1 strelka-varscan-mutect BRDT,synonymous_variant,p.=,ENST00000370389,NM_001242810.2;BRDT,synonymous_variant,p.=,ENST00000362005,NM_001242805.2,NM_207189.3;BRDT,synonymous_variant,p.=,ENST00000399546,NM_001242806.2;BRDT,synonymous_variant,p.=,ENST00000394530,NM_001242808.2,NM_001242807.2;BRDT,synonymous_variant,p.=,ENST00000402388,NM_001726.4; T ENST00000399546 Transcript synonymous_variant 3142/3357 2793/2856 931/951 V gtG/gtT 1 1 BRDT HGNC HGNC:1105 protein_coding YES CCDS72820.1 ENSP00000387822 Q58F21 UPI000292A27D NM_001242806.2 19/19 Pfam_domain:PF17105 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 92014211 92014211 G T 1 0 0 0 0 0 0 0 1 1678 1362 47 2 2 BRDT 1 92014211 Silent SNP G C3L-02345_T 2430359 92014211 156942211 9 8607 COL11A1 0 . GRCh38 1 102995989 102995989 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.2295G>T p.Lys765Asn p.K765N ENST00000370096 27/67 262 234 28 322 322 0 strelka-varscan-mutect COL11A1,missense_variant,p.Lys777Asn,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Lys765Asn,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Lys726Asn,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Lys649Asn,ENST00000512756,NM_080630.3;COL11A1,missense_variant,p.Lys538Asn,ENST00000635193,; A ENST00000370096 Transcript missense_variant,splice_region_variant 2608/7286 2295/5421 765/1806 K/N aaG/aaT COSM4930870,COSM4930871,COSM674598,COSM674599 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 27/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 102995989 102995989 C A 1 0 0 0 0 1 0 0 0 3455 695 24 2 2 COL11A1 1 102995989 Missense_Mutation SNP C C3L-02345_T 10981778 102995989 145960433 10 8608 VAV3 0 . GRCh38 1 107772843 107772843 + Missense_Mutation SNP A A C rs769973929 C3L-02345_T C3L-02345_N A A c.447T>G p.Asp149Glu p.D149E ENST00000370056 5/27 119 105 14 142 142 0 strelka-varscan-mutect VAV3,missense_variant,p.Asp149Glu,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Asp149Glu,ENST00000527011,;VAV3,missense_variant,p.Asp144Glu,ENST00000490388,;VAV3,splice_region_variant,,ENST00000343258,;VAV3,splice_region_variant,,ENST00000469325,;VAV3,splice_region_variant,,ENST00000530671,;VAV3,splice_region_variant,,ENST00000524574,; C ENST00000370056 Transcript missense_variant,splice_region_variant 722/4990 447/2544 149/847 D/E gaT/gaG rs769973929 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 deleterious(0.03) 5/27 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs769973929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 107772843 107772843 A C 1 0 0 0 0 1 0 0 0 17678 173 6 5 5 VAV3 1 107772843 Missense_Mutation SNP A C3L-02345_T 4776854 107772843 141183579 11 8609 KCND3 0 . GRCh38 1 111982290 111982290 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.437G>A p.Arg146Gln p.R146Q ENST00000315987 2/8 272 237 35 288 288 0 strelka-varscan-mutect KCND3,missense_variant,p.Arg146Gln,ENST00000369697,;KCND3,missense_variant,p.Arg146Gln,ENST00000315987,NM_004980.4;KCND3,missense_variant,p.Arg146Gln,ENST00000302127,NM_172198.2; T ENST00000315987 Transcript missense_variant 917/2716 437/1968 146/655 R/Q cGg/cAg 1 -1 KCND3 HGNC HGNC:6239 protein_coding YES CCDS843.1 ENSP00000319591 Q9UK17 UPI000003050A NM_004980.4 deleterious(0.03) 2/8 Gene3D:3.30.710.10,Coiled-coils_(Ncoils):Coil,Prints_domain:PR01497,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF149 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 111982290 111982290 C T 1 0 0 0 0 1 0 0 0 7936 652 23 1 1 KCND3 1 111982290 Missense_Mutation SNP C C3L-02345_T 4209447 111982290 136974132 12 8610 BOLA1 0 . GRCh38 1 149900203 149900203 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.144G>T p.= p.V48V ENST00000369153 3/3 162 128 34 142 142 0 strelka-varscan-mutect BOLA1,synonymous_variant,p.=,ENST00000369153,;BOLA1,synonymous_variant,p.=,ENST00000369152,NM_016074.3;BOLA1,synonymous_variant,p.=,ENST00000369150,;SV2A,downstream_gene_variant,,ENST00000369146,NM_014849.4;BOLA1,non_coding_transcript_exon_variant,,ENST00000476344,; T ENST00000369153 Transcript synonymous_variant 808/1096 144/414 48/137 V gtG/gtT 1 1 BOLA1 HGNC HGNC:24263 protein_coding YES CCDS939.1 ENSP00000358149 Q9Y3E2 UPI000013A5F7 3/3 hmmpanther:PTHR12735:SF20,hmmpanther:PTHR12735,Gene3D:1ny8A00,Pfam_domain:PF01722,Superfamily_domains:SSF82657 LOW SNV 3 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 149900203 149900203 G T 1 0 0 0 0 0 0 0 1 1642 1306 46 2 2 BOLA1 1 149900203 Silent SNP G C3L-02345_T 37917913 149900203 99056219 13 8611 ANP32E 0 . GRCh38 1 150231781 150231781 + Missense_Mutation SNP C C T rs782603651 C3L-02345_T C3L-02345_N C C c.200G>A p.Arg67Gln p.R67Q ENST00000583931 2/7 114 108 6 122 122 0 strelka-varscan-mutect ANP32E,missense_variant,p.Arg67Gln,ENST00000583931,NM_001280559.1,NM_030920.4;ANP32E,missense_variant,p.Arg19Gln,ENST00000616917,NM_001136479.2;ANP32E,missense_variant,p.Arg67Gln,ENST00000436748,NM_001136478.3;ANP32E,missense_variant,p.Arg67Gln,ENST00000369114,;ANP32E,missense_variant,p.Arg67Gln,ENST00000533654,NM_001280560.1;ANP32E,intron_variant,,ENST00000629042,;ANP32E,intron_variant,,ENST00000369115,;ANP32E,intron_variant,,ENST00000532744,;ANP32E,intron_variant,,ENST00000534220,; T ENST00000583931 Transcript missense_variant 570/3451 200/807 67/268 R/Q cGa/cAa rs782603651,COSM895468 1 -1 ANP32E HGNC HGNC:16673 protein_coding YES CCDS946.1 ENSP00000463154 Q9BTT0 UPI0000071679 NM_001280559.1,NM_030920.4 tolerated(0.09) 2/7 PROSITE_profiles:PS51450,hmmpanther:PTHR11375:SF5,hmmpanther:PTHR11375,Gene3D:3.80.10.10,Pfam_domain:PF14580,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs782603651 . 0 201 9 0 0 0 0 0 -11.76739 0.9999431 1 1 1 0 T 3 4 31 150231781 150231781 C T 1 0 0 0 0 1 0 0 0 816 898 31 1 1 ANP32E 1 150231781 Missense_Mutation SNP C C3L-02345_T 331578 150231781 98724641 14 8612 VHLL 0 . GRCh38 1 156298999 156298999 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.191G>T p.Arg64Leu p.R64L ENST00000339922 1/1 333 226 107 284 284 0 strelka-varscan-mutect VHLL,missense_variant,p.Arg64Leu,ENST00000339922,NM_001004319.2;GLMP,upstream_gene_variant,,ENST00000614643,NM_001256609.1;GLMP,upstream_gene_variant,,ENST00000362007,NM_144580.2,NM_001256604.1;GLMP,upstream_gene_variant,,ENST00000612353,NM_001256608.1;GLMP,upstream_gene_variant,,ENST00000622703,NM_001256605.1;GLMP,upstream_gene_variant,,ENST00000481050,;GLMP,upstream_gene_variant,,ENST00000472870,;GLMP,upstream_gene_variant,,ENST00000497955,;GLMP,upstream_gene_variant,,ENST00000484214,;GLMP,upstream_gene_variant,,ENST00000479084,;GLMP,upstream_gene_variant,,ENST00000368264,;GLMP,upstream_gene_variant,,ENST00000476177,; A ENST00000339922 Transcript missense_variant 301/676 191/420 64/139 R/L cGa/cTa 1 -1 VHLL HGNC HGNC:30666 protein_coding YES ENSP00000464258 Q6RSH7 UPI0000253B18 NM_001004319.2 deleterious(0.01) 1/1 Superfamily_domains:0040561,Gene3D:1lm8V02,PD035809,Pfam_domain:PF01847,hmmpanther:PTHR15160,hmmpanther:PTHR15160:SF5 MODERATE SNV 1 PASS rs1052325769 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 156298999 156298999 C A 1 0 0 0 0 1 0 0 0 17709 884 31 1 1 VHLL 1 156298999 Missense_Mutation SNP C C3L-02345_T 6067218 156298999 92657423 15 8613 LRRC71 0 . GRCh38 1 156929406 156929406 + Missense_Mutation SNP G G T rs746690317 C3L-02345_T C3L-02345_N G G c.1123G>T p.Gly375Cys p.G375C ENST00000337428 10/15 219 118 101 206 204 2 strelka-varscan-mutect LRRC71,missense_variant,p.Gly375Cys,ENST00000337428,NM_144702.2;LRRC71,non_coding_transcript_exon_variant,,ENST00000490146,;LRRC71,intron_variant,,ENST00000476550,;LRRC71,upstream_gene_variant,,ENST00000472465,; T ENST00000337428 Transcript missense_variant 1277/1959 1123/1680 375/559 G/C Ggc/Tgc rs746690317 1 1 LRRC71 HGNC HGNC:26556 protein_coding YES CCDS44249.1 ENSP00000336661 Q8N4P6 UPI00000719B9 NM_144702.2 deleterious(0.02) 10/15 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs746690317 . 0 202 0 4 3 0 0 0 -20 0.9733674 1 1 1 0 T 3 4 31 156929406 156929406 G T 1 0 0 0 0 1 0 0 0 8918 1232 43 2 2 LRRC71 1 156929406 Missense_Mutation SNP G C3L-02345_T 630407 156929406 92027016 16 8614 TEX35 0 . GRCh38 1 178520863 178520863 + Missense_Mutation SNP G G T rs778823356 C3L-02345_T C3L-02345_N G G c.532G>T p.Gly178Trp p.G178W ENST00000319416 7/9 342 291 51 344 344 0 strelka-varscan-mutect TEX35,missense_variant,p.Gly178Trp,ENST00000367641,;TEX35,missense_variant,p.Gly178Trp,ENST00000319416,NM_032126.4;TEX35,missense_variant,p.Gly178Trp,ENST00000367643,NM_001170723.1;TEX35,missense_variant,p.Gly186Trp,ENST00000367639,NM_001170722.1,NM_001170724.1;TEX35,missense_variant,p.Trp12Leu,ENST00000442872,;TEX35,3_prime_UTR_variant,,ENST00000367642,;TEX35,3_prime_UTR_variant,,ENST00000419909,; T ENST00000319416 Transcript missense_variant 644/1023 532/702 178/233 G/W Ggg/Tgg rs778823356 1 1 TEX35 HGNC HGNC:25366 protein_coding YES CCDS1323.1 ENSP00000323795 Q5T0J7 UPI00001405CF NM_032126.4 deleterious_low_confidence(0.02) 7/9 Pfam_domain:PF15079,hmmpanther:PTHR36860 MODERATE 1 SNV 1 1 PASS rs778823356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 178520863 178520863 G T 1 0 0 0 0 1 0 0 0 16211 1348 47 2 2 TEX35 1 178520863 Missense_Mutation SNP G C3L-02345_T 21591457 178520863 70435559 17 8615 LHX4 0 . GRCh38 1 180248402 180248402 + Missense_Mutation SNP C C T rs752455651 C3L-02345_T C3L-02345_N C C c.194C>T p.Ala65Val p.A65V ENST00000263726 2/6 323 295 28 336 336 0 strelka-varscan-mutect LHX4,missense_variant,p.Ala65Val,ENST00000263726,NM_033343.3;LHX4,synonymous_variant,p.=,ENST00000561113,;LHX4,non_coding_transcript_exon_variant,,ENST00000558139,; T ENST00000263726 Transcript missense_variant 438/5820 194/1173 65/390 A/V gCg/gTg rs752455651,COSM3849336 1 1 LHX4 HGNC HGNC:21734 protein_coding YES CCDS1338.1 ENSP00000263726 Q969G2 A0A0S2Z5S4 UPI000007340D NM_033343.3 deleterious(0.04) 2/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF116,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752455651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 180248402 180248402 C T 1 0 0 0 0 1 0 0 0 8682 768 27 1 1 LHX4 1 180248402 Missense_Mutation SNP C C3L-02345_T 1727539 180248402 68708020 18 8616 KIF21B 0 . GRCh38 1 200984940 200984940 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.3722C>A p.Ser1241Tyr p.S1241Y ENST00000422435 27/35 139 105 34 109 109 0 strelka-varscan-mutect KIF21B,missense_variant,p.Ser1241Tyr,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Ser1241Tyr,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Ser1241Tyr,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Ser1241Tyr,ENST00000360529,NM_001252103.1; T ENST00000422435 Transcript missense_variant 4039/5519 3722/4914 1241/1637 S/Y tCc/tAc 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0) 27/35 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 200984940 200984940 G T 1 0 0 0 0 1 0 0 0 8154 1174 41 2 2 KIF21B 1 200984940 Missense_Mutation SNP G C3L-02345_T 20736538 200984940 47971482 19 8617 CR2 0 . GRCh38 1 207466626 207466626 + Silent SNP T T C novel C3L-02345_T C3L-02345_N T T c.159T>C p.= p.G53G ENST00000367057 2/20 447 422 25 418 418 0 strelka-varscan-mutect CR2,synonymous_variant,p.=,ENST00000367057,NM_001006658.2;CR2,synonymous_variant,p.=,ENST00000367058,NM_001877.4;CR2,synonymous_variant,p.=,ENST00000367059,;CR2,non_coding_transcript_exon_variant,,ENST00000479186,;CR2,upstream_gene_variant,,ENST00000485707,;CR2,upstream_gene_variant,,ENST00000475194,; C ENST00000367057 Transcript synonymous_variant 348/4240 159/3279 53/1092 G ggT/ggC 1 1 CR2 HGNC HGNC:2336 protein_coding YES CCDS31007.1 ENSP00000356024 P20023 UPI0000366600 NM_001006658.2 2/20 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF391,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 207466626 207466626 T C 1 0 0 0 0 0 0 0 1 3640 1625 57 5 5 CR2 1 207466626 Silent SNP T C3L-02345_T 6481686 207466626 41489796 20 8618 KCNH1 0 . GRCh38 1 211107337 211107337 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.120G>T p.Trp40Cys p.W40C ENST00000271751 2/11 197 176 21 212 212 0 strelka-varscan-mutect KCNH1,missense_variant,p.Trp40Cys,ENST00000271751,NM_172362.2;KCNH1,missense_variant,p.Trp40Cys,ENST00000367007,NM_002238.3; A ENST00000271751 Transcript missense_variant 148/7964 120/2970 40/989 W/C tgG/tgT 1 -1 KCNH1 HGNC HGNC:6250 protein_coding YES CCDS1496.1 ENSP00000271751 O95259 UPI000003230D NM_172362.2 tolerated(0.32) 2/11 PROSITE_profiles:PS50112,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Gene3D:3.30.450.20,TIGRFAM_domain:TIGR00229,Superfamily_domains:SSF55785 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 211107337 211107337 C A 1 0 0 0 0 1 0 0 0 7947 740 26 2 2 KCNH1 1 211107337 Missense_Mutation SNP C C3L-02345_T 3640711 211107337 37849085 21 8619 ACTN2 0 . GRCh38 1 236739505 236739505 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.1080C>A p.Phe360Leu p.F360L ENST00000542672 10/21 460 414 46 476 476 0 strelka-varscan-mutect ACTN2,missense_variant,p.Phe152Leu,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Phe360Leu,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Phe360Leu,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000492634,;ACTN2,non_coding_transcript_exon_variant,,ENST00000494762,; A ENST00000542672 Transcript missense_variant 1300/4906 1080/2685 360/894 F/L ttC/ttA COSM4458297,COSM4458298 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0) 10/21 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 236739505 236739505 C A 1 0 0 0 0 1 0 0 0 249 825 29 2 2 ACTN2 1 236739505 Missense_Mutation SNP C C3L-02345_T 25632168 236739505 12216917 22 8620 RYR2 0 . GRCh38 1 237788030 237788030 + Frame_Shift_Del DEL G G - rs769311004 C3L-02345_T C3L-02345_N G G c.13373delG p.Gly4458AlafsTer5 p.G4458Afs*5 ENST00000366574 92/105 230 212 18 236 236 0 varindel-pindel RYR2,frameshift_variant,p.Gly4458AlafsTer5,ENST00000366574,NM_001035.2;RYR2,frameshift_variant,p.Gly4441AlafsTer5,ENST00000360064,;RYR2,downstream_gene_variant,,ENST00000609119,;RYR2,upstream_gene_variant,,ENST00000608590,; - ENST00000366574 Transcript frameshift_variant 13688/16562 13371/14904 4457/4967 K/X aaG/aa rs769311004 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 92/105 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg HIGH 1 deletion 1 2 1 PASS . . 0 207 0 0 2 0 0 0 -6.099487 0.9891621 1 1 1 0 - 7 5 31 237788030 237788030 G - 1 0 1 0 1 0 0 0 0 14029 991 35 0 0 RYR2 1 237788030 Frame_Shift_Del DEL G C3L-02345_T 1048525 237788030 11168392 23 8621 CEP170 0 . GRCh38 1 243164961 243164961 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.2999G>T p.Gly1000Val p.G1000V ENST00000366542 13/20 368 346 22 416 416 0 varscan-mutect CEP170,missense_variant,p.Gly1000Val,ENST00000366542,NM_014812.2;CEP170,missense_variant,p.Gly902Val,ENST00000366544,NM_001042404.1;CEP170,missense_variant,p.Gly902Val,ENST00000366543,NM_001042405.1;CEP170,missense_variant,p.Gly964Val,ENST00000336415,;CEP170,upstream_gene_variant,,ENST00000490813,;CEP170,upstream_gene_variant,,ENST00000413359,;CEP170,upstream_gene_variant,,ENST00000464936,;CEP170,downstream_gene_variant,,ENST00000522895,;CEP170,upstream_gene_variant,,ENST00000492145,;RP11-261C10.4,intron_variant,,ENST00000437499,;RP11-261C10.4,intron_variant,,ENST00000422938,;CEP170,non_coding_transcript_exon_variant,,ENST00000451408,;CEP170,downstream_gene_variant,,ENST00000518289,;CEP170,downstream_gene_variant,,ENST00000461671,; A ENST00000366542 Transcript missense_variant 3051/6828 2999/4755 1000/1584 G/V gGt/gTt COSM4577085,COSM4577086 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 deleterious(0.02) 13/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715,Pfam_domain:PF15308 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 243164961 243164961 C A 1 0 0 0 0 1 0 0 0 2964 507 18 2 2 CEP170 1 243164961 Missense_Mutation SNP C C3L-02345_T 5376931 243164961 5791461 24 8622 ZNF669 0 . GRCh38 1 247100540 247100540 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.1229G>C p.Arg410Thr p.R410T ENST00000343381 4/4 195 165 30 212 212 0 strelka-varscan-mutect ZNF669,missense_variant,p.Arg410Thr,ENST00000343381,NM_024804.2;ZNF669,missense_variant,p.Arg324Thr,ENST00000448299,NM_001142572.1;ZNF669,downstream_gene_variant,,ENST00000366501,;ZNF669,downstream_gene_variant,,ENST00000476158,;ZNF669,downstream_gene_variant,,ENST00000366500,; G ENST00000343381 Transcript missense_variant 1402/1951 1229/1395 410/464 R/T aGa/aCa 1 -1 ZNF669 HGNC HGNC:25736 protein_coding YES CCDS31088.1 ENSP00000342818 Q96BR6 A0A024R5S3 UPI000013E1E0 NM_024804.2 deleterious(0.01) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF127,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 247100540 247100540 C G 1 0 0 0 0 1 0 0 0 18650 913 32 4 4 ZNF669 1 247100540 Missense_Mutation SNP C C3L-02345_T 3935579 247100540 1855882 25 8623 OR2B11 0 . GRCh38 1 247451215 247451215 + Nonsense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.768C>G p.Tyr256Ter p.Y256* ENST00000318749 1/1 55 42 13 68 68 0 strelka-varscan-mutect OR2B11,stop_gained,p.Tyr256Ter,ENST00000318749,NM_001004492.1;NLRP3,downstream_gene_variant,,ENST00000366497,NM_001127461.2;NLRP3,downstream_gene_variant,,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,downstream_gene_variant,,ENST00000366496,;NLRP3,downstream_gene_variant,,ENST00000391828,NM_001079821.2;NLRP3,downstream_gene_variant,,ENST00000348069,NM_183395.2;NLRP3,downstream_gene_variant,,ENST00000391827,NM_001127462.2;NLRP3,downstream_gene_variant,,ENST00000532083,; C ENST00000318749 Transcript stop_gained 768/954 768/954 256/317 Y/* taC/taG 1 -1 OR2B11 HGNC HGNC:31249 protein_coding YES CCDS31090.1 ENSP00000325682 Q5JQS5 A0A126GVY5 UPI0000418F50 NM_001004492.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF112,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 31 247451215 247451215 G C 1 0 0 0 0 0 1 0 0 11067 1256 44 4 4 OR2B11 1 247451215 Nonsense_Mutation SNP G C3L-02345_T 350675 247451215 1505207 26 8624 OR2M5 0 . GRCh38 1 248145168 248145168 + Silent SNP C C A rs751103552 C3L-02345_T C3L-02345_N C C c.21C>A p.= p.T7T ENST00000366476 1/1 85 74 11 102 102 0 strelka-varscan-mutect OR2M5,synonymous_variant,p.=,ENST00000366476,NM_001004690.1; A ENST00000366476 Transcript synonymous_variant 21/939 21/939 7/312 T acC/acA rs751103552,COSM3785228 1 1 OR2M5 HGNC HGNC:19576 protein_coding YES CCDS31105.1 ENSP00000355432 A3KFT3 UPI00001612E2 NM_001004690.1 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 0,1 1 PASS rs751103552 . 0 202 7 0 0 0 0 0 -19.99979 0.9999994 1 1 1 0 A 2 1 31 248145168 248145168 C A 1 0 0 0 0 0 0 0 1 11091 668 24 2 2 OR2M5 1 248145168 Silent SNP C C3L-02345_T 693953 248145168 811254 27 8625 OR2G6 0 . GRCh38 1 248521787 248521787 + Frame_Shift_Del DEL A A - rs148863520 C3L-02345_T C3L-02345_N A A c.141delA p.Val48TyrfsTer38 p.V48Yfs*38 ENST00000343414 1/1 316 288 28 350 350 0 varindel-pindel OR2G6,frameshift_variant,p.Val48TyrfsTer38,ENST00000343414,NM_001013355.1; - ENST00000343414 Transcript frameshift_variant 141/951 141/951 47/316 L/X ctA/ct rs148863520 1 1 OR2G6 HGNC HGNC:27019 protein_coding YES CCDS31119.1 ENSP00000341291 Q5TZ20 A0A126GW53 UPI0000237253 NM_001013355.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF110,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 248521787 248521787 A - 1 0 1 0 1 0 0 0 0 11078 407 15 0 0 OR2G6 1 248521787 Frame_Shift_Del DEL A C3L-02345_T 376619 248521787 434635 28 8626 MYT1L 0 . GRCh38 2 1922842 1922842 + Silent SNP T T A novel C3L-02345_T C3L-02345_N T T c.927A>T p.= p.G309G ENST00000399161 10/25 240 207 33 284 284 0 strelka-varscan-mutect MYT1L,synonymous_variant,p.=,ENST00000399161,NM_001303052.1;MYT1L,synonymous_variant,p.=,ENST00000428368,NM_015025.3;MYT1L,upstream_gene_variant,,ENST00000602387,; A ENST00000399161 Transcript synonymous_variant 1675/7063 927/3561 309/1186 G ggA/ggT 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 10/25 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 1922842 1922842 T A 1 0 0 0 0 0 0 0 1 10106 1654 58 4 4 MYT1L 2 1922842 Silent SNP T C3L-02345_T 1922842 240270687 29 8627 APOB 0 . GRCh38 2 21004332 21004332 + Silent SNP G G C rs145269223 C3L-02345_T C3L-02345_N G G c.12024C>G p.= p.T4008T ENST00000233242 28/29 280 213 67 359 359 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; C ENST00000233242 Transcript synonymous_variant 12152/14121 12024/13692 4008/4563 T acC/acG rs145269223 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 28/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS rs145269223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 21004332 21004332 G C 1 0 0 0 0 0 0 0 1 907 1103 39 4 4 APOB 2 21004332 Silent SNP G C3L-02345_T 19081490 21004332 221189197 30 8628 C2orf16 0 . GRCh38 2 27578156 27578156 + Silent SNP G G A C3L-02345_T C3L-02345_N G G c.1584G>A p.= p.T528T ENST00000408964 1/1 302 271 31 316 315 1 strelka-varscan C2orf16,synonymous_variant,p.=,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,; A ENST00000408964 Transcript synonymous_variant 1635/6199 1584/5955 528/1984 T acG/acA COSM3580690,COSM3580691 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 1/1 hmmpanther:PTHR33888 1,1 LOW SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 27578156 27578156 G A 1 0 0 0 0 0 0 0 1 2032 1045 37 1 1 C2orf16 2 27578156 Silent SNP G C3L-02345_T 6573824 27578156 214615373 31 8629 USP34 0 . GRCh38 2 61301374 61301374 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.3898C>T p.Leu1300Phe p.L1300F ENST00000398571 28/80 161 121 40 168 167 1 strelka-varscan USP34,missense_variant,p.Leu1300Phe,ENST00000398571,NM_014709.3;USP34,upstream_gene_variant,,ENST00000472706,; A ENST00000398571 Transcript missense_variant 3975/11357 3898/10641 1300/3546 L/F Ctt/Ttt 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 deleterious(0.01) 28/80 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 61301374 61301374 G A 1 0 0 0 0 1 0 0 0 17607 971 34 3 3 USP34 2 61301374 Missense_Mutation SNP G C3L-02345_T 33723218 61301374 180892155 32 8630 WDR92 0 . GRCh38 2 68138837 68138837 + Nonsense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.538G>T p.Glu180Ter p.E180* ENST00000295121 5/8 162 116 46 180 180 0 strelka-varscan WDR92,stop_gained,p.Glu180Ter,ENST00000295121,NM_138458.3;WDR92,stop_gained,p.Glu180Ter,ENST00000409164,NM_001256476.1;WDR92,stop_gained,p.Glu79Ter,ENST00000406245,;WDR92,upstream_gene_variant,,ENST00000457114,;WDR92,non_coding_transcript_exon_variant,,ENST00000492039,;RP11-474G23.1,3_prime_UTR_variant,,ENST00000406334,; A ENST00000295121 Transcript stop_gained 655/2626 538/1074 180/357 E/* Gaa/Taa 1 -1 WDR92 HGNC HGNC:25176 protein_coding YES CCDS1884.1 ENSP00000295121 Q96MX6 A0A140VK67 UPI000006F50D NM_138458.3 5/8 Gene3D:2.130.10.10,hmmpanther:PTHR10971,hmmpanther:PTHR10971:SF2,Superfamily_domains:SSF50978 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 68138837 68138837 C A 1 0 0 0 0 0 1 0 0 17895 922 32 2 2 WDR92 2 68138837 Nonsense_Mutation SNP C C3L-02345_T 6837463 68138837 174054692 33 8631 ZNF638 0 . GRCh38 2 71393408 71393408 + Frame_Shift_Del DEL C C - novel C3L-02345_T C3L-02345_N C C c.2494delC p.Gln832SerfsTer12 p.Q832Sfs*12 ENST00000410075 12/13 109 93 16 156 156 0 sindel-varindel-pindel ZNF638,frameshift_variant,p.Gln832SerfsTer12,ENST00000410075,;ZNF638,intron_variant,,ENST00000409544,NM_001252612.1;ZNF638,intron_variant,,ENST00000264447,NM_014497.4,NM_001014972.2,NM_001252613.1;ZNF638,intron_variant,,ENST00000491843,;ZNF638,upstream_gene_variant,,ENST00000487638,; - ENST00000410075 Transcript frameshift_variant 2857/3518 2493/2757 831/918 F/X ttC/tt 1 1 ZNF638 HGNC HGNC:17894 protein_coding ENSP00000485608 A0A096LPH6 UPI000188166D 12/13 HIGH deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 71393408 71393408 C - 1 0 1 0 1 0 0 0 0 18630 854 30 0 0 ZNF638 2 71393408 Frame_Shift_Del DEL C C3L-02345_T 3254571 71393408 170800121 34 8632 DYSF 0 . GRCh38 2 71517034 71517034 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.997T>A p.Phe333Ile p.F333I ENST00000410020 10/56 407 346 61 441 440 1 strelka-varscan DYSF,missense_variant,p.Phe301Ile,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Phe332Ile,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Phe332Ile,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Phe301Ile,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Phe332Ile,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Phe333Ile,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Phe333Ile,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Phe302Ile,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Phe333Ile,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Phe302Ile,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Phe302Ile,ENST00000394120,NM_001130455.1; A ENST00000410020 Transcript missense_variant 1138/6657 997/6360 333/2119 F/I Ttc/Atc 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0) 10/56 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 71517034 71517034 T A 1 0 0 0 0 1 0 0 0 4683 1739 60 4 4 DYSF 2 71517034 Missense_Mutation SNP T C3L-02345_T 123626 71517034 170676495 35 8633 DQX1 0 . GRCh38 2 74525160 74525160 + Nonsense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.280C>T p.Gln94Ter p.Q94* ENST00000404568 3/12 82 60 22 94 94 0 strelka-varscan DQX1,stop_gained,p.Gln94Ter,ENST00000404568,NM_133637.2;DQX1,stop_gained,p.Gln94Ter,ENST00000393951,;DQX1,5_prime_UTR_variant,,ENST00000451518,;HTRA2,upstream_gene_variant,,ENST00000258080,NM_013247.4;AUP1,downstream_gene_variant,,ENST00000377526,NM_181575.4;HTRA2,upstream_gene_variant,,ENST00000437202,;HTRA2,upstream_gene_variant,,ENST00000352222,NM_145074.2;DQX1,intron_variant,,ENST00000498552,;HTRA2,upstream_gene_variant,,ENST00000467961,;HTRA2,upstream_gene_variant,,ENST00000462909,;HTRA2,upstream_gene_variant,,ENST00000484881,;DQX1,upstream_gene_variant,,ENST00000495597,;DQX1,non_coding_transcript_exon_variant,,ENST00000473508,;DQX1,upstream_gene_variant,,ENST00000418139,;AUP1,downstream_gene_variant,,ENST00000466894,;AUP1,downstream_gene_variant,,ENST00000463900,;AUP1,downstream_gene_variant,,ENST00000425118,;AUP1,downstream_gene_variant,,ENST00000486234,;AUP1,downstream_gene_variant,,ENST00000464887,;DQX1,upstream_gene_variant,,ENST00000483555,;AUP1,downstream_gene_variant,,ENST00000472800,;AUP1,downstream_gene_variant,,ENST00000462297,; A ENST00000404568 Transcript stop_gained 500/2689 280/2154 94/717 Q/* Cag/Tag 1 -1 DQX1 HGNC HGNC:20410 protein_coding YES CCDS1949.2 ENSP00000384621 Q8TE96 UPI0000208758 NM_133637.2 3/12 PROSITE_profiles:PS51192,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF108,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 HIGH SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999946 1 1 1 0 A 4 1 31 74525160 74525160 G A 1 0 0 0 0 0 1 0 0 4566 1357 47 3 3 DQX1 2 74525160 Nonsense_Mutation SNP G C3L-02345_T 3008126 74525160 167668369 36 8634 ST3GAL5 0 . GRCh38 2 85846456 85846456 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.770C>T p.Ser257Phe p.S257F ENST00000377332 5/7 327 247 80 306 306 0 strelka-varscan ST3GAL5,missense_variant,p.Ser257Phe,ENST00000377332,NM_003896.3;ST3GAL5,missense_variant,p.Ser229Phe,ENST00000393805,;ST3GAL5,missense_variant,p.Ser234Phe,ENST00000393808,NM_001042437.1;ST3GAL5,downstream_gene_variant,,ENST00000455892,;ST3GAL5,downstream_gene_variant,,ENST00000487896,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000461206,;ST3GAL5,downstream_gene_variant,,ENST00000306262,;ST3GAL5,downstream_gene_variant,,ENST00000433665,; A ENST00000377332 Transcript missense_variant 879/2366 770/1257 257/418 S/F tCc/tTc 1 -1 ST3GAL5 HGNC HGNC:10872 protein_coding YES CCDS1986.2 ENSP00000366549 Q9UNP4 UPI000015F319 NM_003896.3 deleterious(0) 5/7 hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF60,PIRSF_domain:PIRSF005557,Pfam_domain:PF00777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 85846456 85846456 G A 1 0 0 0 0 1 0 0 0 15596 1174 41 3 3 ST3GAL5 2 85846456 Missense_Mutation SNP G C3L-02345_T 11321296 85846456 156347073 37 8635 RGPD4 0 . GRCh38 2 107882730 107882730 + Missense_Mutation SNP C C A rs774575902 C3L-02345_T C3L-02345_N C C c.5123C>A p.Ala1708Asp p.A1708D ENST00000408999 22/23 454 380 74 472 472 0 strelka-varscan RGPD4,missense_variant,p.Ala1708Asp,ENST00000408999,NM_182588.2; A ENST00000408999 Transcript missense_variant 5200/5464 5123/5277 1708/1758 A/D gCt/gAt rs774575902 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 deleterious_low_confidence(0) 22/23 PROSITE_profiles:PS50913,Gene3D:1uptF00,Pfam_domain:PF01465,SMART_domains:SM00755 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 107882730 107882730 C A 1 0 0 0 0 1 0 0 0 13460 797 28 2 2 RGPD4 2 107882730 Missense_Mutation SNP C C3L-02345_T 22036274 107882730 134310799 38 8636 MARCO 0 . GRCh38 2 118993172 118993172 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1301G>T p.Arg434Leu p.R434L ENST00000327097 16/17 215 174 41 267 267 0 strelka-varscan MARCO,missense_variant,p.Arg434Leu,ENST00000327097,NM_006770.3;MARCO,non_coding_transcript_exon_variant,,ENST00000494979,; T ENST00000327097 Transcript missense_variant 1436/1838 1301/1563 434/520 R/L cGg/cTg 1 1 MARCO HGNC HGNC:6895 protein_coding YES CCDS2124.1 ENSP00000318916 Q9UEW3 Q4ZG40 UPI0000000DF8 NM_006770.3 deleterious(0) 16/17 PROSITE_profiles:PS50287,hmmpanther:PTHR24023:SF525,hmmpanther:PTHR24023,PROSITE_patterns:PS00420,Gene3D:3.10.250.10,Pfam_domain:PF00530,SMART_domains:SM00202,Superfamily_domains:SSF56487,Prints_domain:PR00258 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 118993172 118993172 G T 1 0 0 0 0 1 0 0 0 9236 1116 39 1 1 MARCO 2 118993172 Missense_Mutation SNP G C3L-02345_T 11110442 118993172 123200357 39 8637 CNTNAP5 0 . GRCh38 2 124764044 124764044 + Frame_Shift_Del DEL G G - rs746143355 C3L-02345_T C3L-02345_N G G c.2428delG p.Glu810AsnfsTer20 p.E810Nfs*20 ENST00000431078 16/24 153 140 13 206 205 1 varindel-pindel CNTNAP5,frameshift_variant,p.Glu810AsnfsTer20,ENST00000431078,NM_130773.3; - ENST00000431078 Transcript frameshift_variant 2791/5284 2427/3921 809/1306 A/X gcG/gc rs746143355,COSM715967 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 16/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Gene3D:2.60.120.200,Superfamily_domains:SSF49899 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 124764044 124764044 G - 1 0 1 0 1 0 0 0 0 3432 1103 39 0 0 CNTNAP5 2 124764044 Frame_Shift_Del DEL G C3L-02345_T 5770872 124764044 117429485 40 8638 LRP1B 0 . GRCh38 2 140495642 140495642 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.8957A>T p.Tyr2986Phe p.Y2986F ENST00000389484 56/91 106 86 20 136 136 0 strelka-varscan LRP1B,missense_variant,p.Tyr2986Phe,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 9929/16535 8957/13800 2986/4599 Y/F tAc/tTc 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.13) 56/91 PROSITE_profiles:PS50026,PROSITE_patterns:PS01187,PROSITE_patterns:PS00010,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 140495642 140495642 T A 1 0 0 0 0 1 0 0 0 8850 1638 57 4 4 LRP1B 2 140495642 Missense_Mutation SNP T C3L-02345_T 15731598 140495642 101697887 41 8639 FSIP2 0 . GRCh38 2 185805275 185805275 + Missense_Mutation SNP T T G novel C3L-02345_T C3L-02345_N T T c.16236T>G p.Phe5412Leu p.F5412L ENST00000343098 17/23 84 68 16 115 115 0 strelka-varscan-mutect FSIP2,missense_variant,p.Phe5412Leu,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Phe5323Leu,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2,intron_variant,,ENST00000415915,; G ENST00000343098 Transcript missense_variant 16236/21054 16236/20991 5412/6996 F/L ttT/ttG 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 185805275 185805275 T G 1 0 0 0 0 1 0 0 0 5949 1751 61 5 5 FSIP2 2 185805275 Missense_Mutation SNP T C3L-02345_T 45309633 185805275 56388254 42 8640 COL3A1 0 . GRCh38 2 189007895 189007895 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.3374G>T p.Gly1125Val p.G1125V ENST00000304636 46/51 455 357 98 478 476 2 strelka-varscan-mutect COL3A1,missense_variant,p.Gly1125Val,ENST00000304636,NM_000090.3;COL3A1,intron_variant,,ENST00000317840,;COL3A1,upstream_gene_variant,,ENST00000487010,;COL3A1,downstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript missense_variant 3544/5543 3374/4401 1125/1466 G/V gGt/gTt 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0) 46/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 189007895 189007895 G T 1 0 0 0 0 1 0 0 0 3477 1261 44 2 2 COL3A1 2 189007895 Missense_Mutation SNP G C3L-02345_T 3202620 189007895 53185634 43 8641 NBEAL1 0 . GRCh38 2 203135921 203135921 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.3971T>C p.Val1324Ala p.V1324A ENST00000449802 27/55 200 170 30 235 235 0 strelka-varscan-mutect NBEAL1,missense_variant,p.Val1324Ala,ENST00000449802,NM_001114132.1; C ENST00000449802 Transcript missense_variant 4304/10938 3971/8085 1324/2694 V/A gTg/gCg 1 1 NBEAL1 HGNC HGNC:20681 protein_coding YES CCDS46495.1 ENSP00000399903 Q6ZS30 UPI000194EC27 NM_001114132.1 tolerated(1) 27/55 hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 203135921 203135921 T C 1 0 0 0 0 1 0 0 0 10199 1696 59 5 5 NBEAL1 2 203135921 Missense_Mutation SNP T C3L-02345_T 14128026 203135921 39057608 44 8642 SLC4A3 0 . GRCh38 2 219632346 219632346 + Nonsense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1126G>T p.Glu376Ter p.E376* ENST00000273063 8/23 150 116 34 185 185 0 strelka-varscan-mutect SLC4A3,stop_gained,p.Glu349Ter,ENST00000358055,NM_005070.3;SLC4A3,stop_gained,p.Glu376Ter,ENST00000273063,NM_001326559.1,NM_201574.2;SLC4A3,stop_gained,p.Glu349Ter,ENST00000373760,;SLC4A3,stop_gained,p.Glu349Ter,ENST00000317151,;SLC4A3,stop_gained,p.Glu151Ter,ENST00000413743,;SLC4A3,non_coding_transcript_exon_variant,,ENST00000497589,;SLC4A3,stop_gained,p.Glu349Ter,ENST00000425141,;SLC4A3,stop_gained,p.Glu49Ter,ENST00000416910,;SLC4A3,upstream_gene_variant,,ENST00000444906,; T ENST00000273063 Transcript stop_gained 1340/4246 1126/3780 376/1259 E/* Gag/Tag 1 1 SLC4A3 HGNC HGNC:11029 protein_coding YES CCDS2446.1 ENSP00000273063 P48751 UPI000022BE50 NM_001326559.1,NM_201574.2 8/23 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF15,Gene3D:1hynR00,TIGRFAM_domain:TIGR00834,Superfamily_domains:SSF55804 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 T 4 4 31 219632346 219632346 G T 1 0 0 0 0 0 1 0 0 14932 1175 41 2 2 SLC4A3 2 219632346 Nonsense_Mutation SNP G C3L-02345_T 16496425 219632346 22561183 45 8643 GPR55 0 . GRCh38 2 230910883 230910883 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.80A>G p.His27Arg p.H27R ENST00000392040 2/2 88 78 10 162 161 1 strelka-varscan-mutect GPR55,missense_variant,p.His27Arg,ENST00000392040,NM_005683.3;GPR55,missense_variant,p.His27Arg,ENST00000622008,;GPR55,missense_variant,p.His27Arg,ENST00000392039,;GPR55,missense_variant,p.His27Arg,ENST00000438398,;AC012507.4,downstream_gene_variant,,ENST00000454890,;GPR55,missense_variant,p.His27Arg,ENST00000444078,; C ENST00000392040 Transcript missense_variant 273/3828 80/960 27/319 H/R cAc/cGc 1 -1 GPR55 HGNC HGNC:4511 protein_coding YES CCDS2480.1 ENSP00000375894 Q9Y2T6 A8K858 UPI000006D64F NM_005683.3 tolerated(0.08) 2/2 Gene3D:1.20.1070.10,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF56,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS rs1194338874 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 230910883 230910883 T C 1 0 0 0 0 1 0 0 0 6584 1696 59 5 5 GPR55 2 230910883 Missense_Mutation SNP T C3L-02345_T 11278537 230910883 11282646 46 8644 TIGD1 0 . GRCh38 2 232548445 232548445 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1438G>T p.Asp480Tyr p.D480Y ENST00000408957 1/1 76 67 9 77 77 0 strelka-varscan-mutect TIGD1,missense_variant,p.Asp480Tyr,ENST00000408957,NM_145702.2;EIF4E2,upstream_gene_variant,,ENST00000409514,NM_001282958.1;EIF4E2,upstream_gene_variant,,ENST00000409098,NM_001276336.1;CHRNG,downstream_gene_variant,,ENST00000389494,NM_005199.4;EIF4E2,upstream_gene_variant,,ENST00000258416,NM_004846.3;CHRNG,downstream_gene_variant,,ENST00000389492,;EIF4E2,upstream_gene_variant,,ENST00000409167,;EIF4E2,upstream_gene_variant,,ENST00000454501,;EIF4E2,upstream_gene_variant,,ENST00000409495,;EIF4E2,upstream_gene_variant,,ENST00000409322,;EIF4E2,upstream_gene_variant,,ENST00000409394,NM_001276337.1;TIGD1,downstream_gene_variant,,ENST00000580185,;EIF4E2,upstream_gene_variant,,ENST00000479834,;EIF4E2,upstream_gene_variant,,ENST00000498242,;EIF4E2,upstream_gene_variant,,ENST00000463074,; A ENST00000408957 Transcript missense_variant 2148/2625 1438/1776 480/591 D/Y Gat/Tat 1 -1 TIGD1 HGNC HGNC:14523 protein_coding YES CCDS2495.1 ENSP00000386186 Q96MW7 UPI000006D1F3 NM_145702.2 deleterious(0.03) 1/1 hmmpanther:PTHR19303:SF253,hmmpanther:PTHR19303 MODERATE SNV 1 PASS . . 1 205 4 0 0 0 0 0 -19.52783 1 1 1 1 0 A 3 1 31 232548445 232548445 C A 1 0 0 0 0 1 0 0 0 16333 913 32 2 2 TIGD1 2 232548445 Missense_Mutation SNP C C3L-02345_T 1637562 232548445 9645084 47 8645 UGT1A1 0 . GRCh38 2 233760913 233760913 + Missense_Mutation SNP G G T rs747662045 C3L-02345_T C3L-02345_N G G c.626G>T p.Arg209Leu p.R209L ENST00000305208 1/5 74 57 17 71 71 0 strelka-varscan-mutect UGT1A1,missense_variant,p.Arg209Leu,ENST00000360418,;UGT1A1,missense_variant,p.Arg209Leu,ENST00000305208,NM_000463.2;UGT1A6,intron_variant,,ENST00000305139,NM_001072.3;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A4,intron_variant,,ENST00000373409,NM_007120.2;UGT1A3,intron_variant,,ENST00000482026,NM_019093.2;UGT1A5,intron_variant,,ENST00000373414,NM_019078.1;UGT1A7,intron_variant,,ENST00000373426,NM_019077.2;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,NM_205862.1;UGT1A6,intron_variant,,ENST00000406651,;UGT1A6,downstream_gene_variant,,ENST00000480628,;UGT1A4,intron_variant,,ENST00000450233,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,; T ENST00000305208 Transcript missense_variant 666/2382 626/1602 209/533 R/L cGg/cTg rs747662045,COSM5611129,COSM574371 1 1 UGT1A1 HGNC HGNC:12530 protein_coding YES CCDS2510.1 ENSP00000304845 P22309 Q5DT03 UPI00000000C2 NM_000463.2 deleterious(0) 1/5 hmmpanther:PTHR11926:SF393,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747662045 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 31 233760913 233760913 G T 1 0 0 0 0 1 0 0 0 17469 1116 39 1 1 UGT1A1 2 233760913 Missense_Mutation SNP G C3L-02345_T 1212468 233760913 8432616 48 8646 MROH2A 0 . GRCh38 2 233794380 233794380 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.840C>G p.Ile280Met p.I280M ENST00000610772 8/42 188 149 39 185 185 0 strelka-varscan-mutect MROH2A,missense_variant,p.Ile280Met,ENST00000389758,;MROH2A,missense_variant,p.Ile280Met,ENST00000610772,NM_001287395.1;MROH2A,downstream_gene_variant,,ENST00000480634,;MROH2A,upstream_gene_variant,,ENST00000477506,; G ENST00000610772 Transcript missense_variant 933/5324 840/5067 280/1688 I/M atC/atG 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 deleterious(0) 8/42 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14 MODERATE 1 SNV 5 1 PASS rs1439068456 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 233794380 233794380 C G 1 0 0 0 0 1 0 0 0 9744 816 29 4 4 MROH2A 2 233794380 Missense_Mutation SNP C C3L-02345_T 33467 233794380 8399149 49 8647 NDUFA10 0 . GRCh38 2 239982214 239982214 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.1005G>T p.= p.G335G ENST00000404554 10/11 232 194 38 241 241 0 strelka-varscan-mutect NDUFA10,synonymous_variant,p.=,ENST00000404554,;NDUFA10,intron_variant,,ENST00000252711,NM_004544.3;NDUFA10,intron_variant,,ENST00000620965,;NDUFA10,intron_variant,,ENST00000443626,;NDUFA10,intron_variant,,ENST00000419408,;NDUFA10,intron_variant,,ENST00000444548,;NDUFA10,intron_variant,,ENST00000448880,;NDUFA10,downstream_gene_variant,,ENST00000307300,;NDUFA10,intron_variant,,ENST00000485344,;NDUFA10,intron_variant,,ENST00000476216,; A ENST00000404554 Transcript synonymous_variant 1010/1557 1005/1173 335/390 G ggG/ggT 1 -1 NDUFA10 HGNC HGNC:7684 protein_coding ENSP00000385697 E7ESZ7 UPI000173A5F9 10/11 PIRSF_domain:PIRSF000543,hmmpanther:PTHR10513,hmmpanther:PTHR10513:SF15 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 239982214 239982214 C A 1 0 0 0 0 0 0 0 1 10281 869 30 2 2 NDUFA10 2 239982214 Silent SNP C C3L-02345_T 6187834 239982214 2211315 50 8648 DCAF1 0 . GRCh38 3 51418681 51418681 + Silent SNP G G C novel C3L-02345_T C3L-02345_N G G c.3432C>G p.= p.S1144S ENST00000423656 15/25 68 63 5 110 110 0 strelka-varscan-mutect DCAF1,synonymous_variant,p.=,ENST00000504652,NM_001171904.1;DCAF1,synonymous_variant,p.=,ENST00000423656,NM_014703.2;DCAF1,synonymous_variant,p.=,ENST00000335891,; C ENST00000423656 Transcript synonymous_variant 3562/5946 3432/4524 1144/1507 S tcC/tcG 1 -1 DCAF1 HGNC HGNC:30911 protein_coding YES CCDS74943.1 ENSP00000393183 Q9Y4B6 UPI00000716AC NM_014703.2 15/25 hmmpanther:PTHR13129,hmmpanther:PTHR13129:SF4,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -11.42183 0.999998 1 1 1 0 C 2 2 31 51418681 51418681 G C 1 0 0 0 0 0 0 0 1 4061 1362 47 4 4 DCAF1 3 51418681 Silent SNP G C3L-02345_T 51418681 146876878 51 8649 P2RY13 0 . GRCh38 3 151328905 151328905 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.151T>C p.Tyr51His p.Y51H ENST00000325602 2/2 254 220 34 246 246 0 strelka-varscan-mutect P2RY13,missense_variant,p.Tyr51His,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; G ENST00000325602 Transcript missense_variant 171/2764 151/1065 51/354 Y/H Tac/Cac 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 deleterious(0) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 151328905 151328905 A G 1 0 0 0 0 1 0 0 0 11423 420 15 5 5 P2RY13 3 151328905 Missense_Mutation SNP A C3L-02345_T 99910224 151328905 46966654 52 8650 OTOL1 0 . GRCh38 3 161503296 161503296 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.788G>T p.Gly263Val p.G263V ENST00000327928 4/4 25 15 10 41 41 0 strelka-varscan-mutect OTOL1,missense_variant,p.Gly263Val,ENST00000327928,NM_001080440.1; T ENST00000327928 Transcript missense_variant 788/1434 788/1434 263/477 G/V gGg/gTg 1 1 OTOL1 HGNC HGNC:34071 protein_coding YES CCDS46948.1 ENSP00000330808 A6NHN0 UPI0000D61BA3 NM_001080440.1 deleterious(0) 4/4 Pfam_domain:PF01391,hmmpanther:PTHR24023,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 161503296 161503296 G T 1 0 0 0 0 1 0 0 0 11372 1232 43 2 2 OTOL1 3 161503296 Missense_Mutation SNP G C3L-02345_T 10174391 161503296 36792263 53 8651 AASDH 0 . GRCh38 4 56351373 56351373 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.1661A>G p.Asp554Gly p.D554G ENST00000205214 10/15 194 166 28 232 232 0 strelka-varscan-mutect AASDH,missense_variant,p.Asp554Gly,ENST00000205214,NM_181806.3;AASDH,missense_variant,p.Asp401Gly,ENST00000602986,NM_001286669.1;AASDH,missense_variant,p.Asp454Gly,ENST00000513376,NM_001286668.1;AASDH,missense_variant,p.Asp554Gly,ENST00000451613,NM_001286671.1;AASDH,missense_variant,p.Asp554Gly,ENST00000502617,NM_001286672.1;AASDH,downstream_gene_variant,,ENST00000510762,;AASDH,3_prime_UTR_variant,,ENST00000514745,NM_001286670.1;AASDH,3_prime_UTR_variant,,ENST00000503808,;RPL7AP31,upstream_gene_variant,,ENST00000470544,; C ENST00000205214 Transcript missense_variant 1842/3590 1661/3297 554/1098 D/G gAc/gGc 1 -1 AASDH HGNC HGNC:23993 protein_coding YES CCDS3504.1 ENSP00000205214 Q4L235 UPI000020B8EF NM_181806.3 deleterious(0.01) 10/15 hmmpanther:PTHR24095:SF185,hmmpanther:PTHR24095,Gene3D:1.10.1200.10,Superfamily_domains:SSF47336 MODERATE 1 SNV 1 1 PASS rs747906678 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 56351373 56351373 T C 1 0 0 0 0 1 0 0 0 26 1667 58 5 5 AASDH 4 56351373 Missense_Mutation SNP T C3L-02345_T 56351373 133863182 54 8652 EPHA5 0 . GRCh38 4 65367387 65367387 + Missense_Mutation SNP C C T C3L-02345_T C3L-02345_N C C c.1897G>A p.Glu633Lys p.E633K ENST00000622150 10/18 238 201 37 277 277 0 strelka-varscan-mutect EPHA5,missense_variant,p.Glu633Lys,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Glu611Lys,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Glu632Lys,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Glu633Lys,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Glu469Lys,ENST00000432638,;EPHA5,missense_variant,p.Glu610Lys,ENST00000354839,NM_182472.3; T ENST00000622150 Transcript missense_variant 2650/8421 1897/3117 633/1038 E/K Gag/Aag COSM733897 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.08) 10/18 Pfam_domain:PF14575,PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17 1 MODERATE 1 SNV 1 1 1 PASS rs1198864954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 65367387 65367387 C T 1 0 0 0 0 1 0 0 0 5017 922 32 3 3 EPHA5 4 65367387 Missense_Mutation SNP C C3L-02345_T 9016014 65367387 124847168 55 8653 RUFY3 0 . GRCh38 4 70722617 70722617 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.44C>T p.Thr15Ile p.T15I ENST00000381006 1/18 118 97 21 130 129 1 strelka-varscan-mutect RUFY3,missense_variant,p.Thr15Ile,ENST00000226328,NM_001291994.1,NM_014961.4;RUFY3,missense_variant,p.Thr15Ile,ENST00000381006,NM_001037442.3;RUFY3,intron_variant,,ENST00000417478,NM_001130709.1;RUFY3,intron_variant,,ENST00000503876,; T ENST00000381006 Transcript missense_variant 623/3098 44/1863 15/620 T/I aCt/aTt 1 1 RUFY3 HGNC HGNC:30285 protein_coding YES CCDS34001.1 ENSP00000370394 Q7L099 UPI00005FB126 NM_001037442.3 deleterious(0.01) 1/18 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 70722617 70722617 C T 1 0 0 0 0 1 0 0 0 14002 565 20 3 3 RUFY3 4 70722617 Missense_Mutation SNP C C3L-02345_T 5355230 70722617 119491938 56 8654 NPFFR2 0 . GRCh38 4 72147405 72147405 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.1162T>C p.Ser388Pro p.S388P ENST00000308744 4/4 339 268 71 418 417 1 strelka-varscan-mutect NPFFR2,missense_variant,p.Ser388Pro,ENST00000308744,NM_004885.2;NPFFR2,missense_variant,p.Ser289Pro,ENST00000395999,NM_001144756.1;NPFFR2,missense_variant,p.Ser286Pro,ENST00000358749,NM_053036.2;NPFFR2,3_prime_UTR_variant,,ENST00000344413,;NPFFR2,non_coding_transcript_exon_variant,,ENST00000506359,; C ENST00000308744 Transcript missense_variant 1260/1922 1162/1569 388/522 S/P Tca/Cca 1 1 NPFFR2 HGNC HGNC:4525 protein_coding YES CCDS3551.1 ENSP00000307822 Q9Y5X5 UPI000012FFBD NM_004885.2 deleterious(0) 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF3,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 72147405 72147405 T C 1 0 0 0 0 1 0 0 0 10626 1551 54 5 5 NPFFR2 4 72147405 Missense_Mutation SNP T C3L-02345_T 1424788 72147405 118067150 57 8655 GRID2 0 . GRCh38 4 93422891 93422891 + Missense_Mutation SNP G G T rs10034345 C3L-02345_T C3L-02345_N G G c.1468G>T p.Val490Leu p.V490L ENST00000282020 10/16 329 281 48 369 369 0 strelka-varscan-mutect GRID2,missense_variant,p.Val490Leu,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Val409Leu,ENST00000611049,;GRID2,missense_variant,p.Val395Leu,ENST00000510992,NM_001286838.1; T ENST00000282020 Transcript missense_variant 2503/6117 1468/3024 490/1007 V/L Gta/Tta rs10034345 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 tolerated(0.14) 10/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Pfam_domain:PF10613,Gene3D:3.40.190.10,SMART_domains:SM00079,SMART_domains:SM00918,Superfamily_domains:SSF53850,Prints_domain:PR00177 MODERATE 1 SNV 1 1 PASS rs10034345 . 0 191 0 0 0 0 0 18 -3.255636 0 0 1 0 0 T 3 4 31 93422891 93422891 G T 1 0 0 0 0 1 0 0 0 6652 1145 40 1 1 GRID2 4 93422891 Missense_Mutation SNP G C3L-02345_T 21275486 93422891 96791664 58 8656 POU4F2 0 . GRCh38 4 146639369 146639369 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.229G>T p.Gly77Cys p.G77C ENST00000281321 1/2 97 76 21 71 71 0 strelka-varscan-mutect POU4F2,missense_variant,p.Gly77Cys,ENST00000281321,NM_004575.2; T ENST00000281321 Transcript missense_variant 477/3144 229/1230 77/409 G/C Ggc/Tgc 1 1 POU4F2 HGNC HGNC:9219 protein_coding YES CCDS34074.1 ENSP00000281321 Q12837 UPI000013DC6C NM_004575.2 tolerated_low_confidence(0.1) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11636:SF41,hmmpanther:PTHR11636 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 146639369 146639369 G T 1 0 0 0 0 1 0 0 0 12395 1348 47 2 2 POU4F2 4 146639369 Missense_Mutation SNP G C3L-02345_T 53216478 146639369 43575186 59 8657 GRIA2 0 . GRCh38 4 157334110 157334110 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1256C>A p.Thr419Asn p.T419N ENST00000296526 9/16 185 136 49 146 146 0 strelka-varscan-mutect GRIA2,missense_variant,p.Thr419Asn,ENST00000296526,NM_000826.3;GRIA2,missense_variant,p.Thr372Asn,ENST00000393815,NM_001083620.1;GRIA2,missense_variant,p.Thr419Asn,ENST00000264426,NM_001083619.1;GRIA2,missense_variant,p.Thr372Asn,ENST00000507898,;GRIA2,missense_variant,p.Thr372Asn,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; A ENST00000296526 Transcript missense_variant 1581/5621 1256/2652 419/883 T/N aCc/aAc 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 deleterious(0) 9/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 157334110 157334110 C A 1 0 0 0 0 1 0 0 0 6648 507 18 2 2 GRIA2 4 157334110 Missense_Mutation SNP C C3L-02345_T 10694741 157334110 32880445 60 8658 CTNND2 0 . GRCh38 5 11412061 11412061 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.296A>G p.Glu99Gly p.E99G ENST00000304623 4/22 188 167 21 228 228 0 strelka-varscan-mutect CTNND2,missense_variant,p.Glu99Gly,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Glu8Gly,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Glu8Gly,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Glu85Gly,ENST00000508761,;CTNND2,missense_variant,p.Glu8Gly,ENST00000513598,;CTNND2,missense_variant,p.Glu85Gly,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000511278,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,missense_variant,p.Glu99Gly,ENST00000513588,;CTNND2,missense_variant,p.Glu99Gly,ENST00000504499,; C ENST00000304623 Transcript missense_variant 486/5481 296/3678 99/1225 E/G gAa/gGa 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0.04) 4/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 11412061 11412061 T C 1 0 0 0 0 1 0 0 0 3829 1783 62 5 5 CTNND2 5 11412061 Missense_Mutation SNP T C3L-02345_T 11412061 170126198 61 8659 DNAH5 0 . GRCh38 5 13810198 13810198 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.7470G>T p.Trp2490Cys p.W2490C ENST00000265104 45/79 123 94 29 166 166 0 strelka-varscan-mutect DNAH5,missense_variant,p.Trp2490Cys,ENST00000265104,NM_001369.2;DNAH5,non_coding_transcript_exon_variant,,ENST00000512443,; A ENST00000265104 Transcript missense_variant 7575/15633 7470/13875 2490/4624 W/C tgG/tgT 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 45/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 13810198 13810198 C A 1 0 0 0 0 1 0 0 0 4419 856 30 2 2 DNAH5 5 13810198 Missense_Mutation SNP C C3L-02345_T 2398137 13810198 167728061 62 8660 PDZD2 0 . GRCh38 5 32091127 32091127 + Missense_Mutation SNP C C T rs768394344 C3L-02345_T C3L-02345_N C C c.7679C>T p.Thr2560Met p.T2560M ENST00000438447 20/25 43 34 9 48 48 0 strelka-varscan-mutect PDZD2,missense_variant,p.Thr2560Met,ENST00000438447,NM_178140.2; T ENST00000438447 Transcript missense_variant 8067/11704 7679/8520 2560/2839 T/M aCg/aTg rs768394344,COSM257704 1 1 PDZD2 HGNC HGNC:18486 protein_coding YES CCDS34137.1 ENSP00000402033 O15018 A0A024RE15 UPI000069648B NM_178140.2 tolerated(0.16) 20/25 hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF16 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768394344 . 0 205 5 0 0 0 0 0 -19.99752 1 1 1 1 0 T 3 4 31 32091127 32091127 C T 1 0 0 0 0 1 0 0 0 11789 536 19 1 1 PDZD2 5 32091127 Missense_Mutation SNP C C3L-02345_T 18280929 32091127 149447132 63 8661 C6 0 . GRCh38 5 41160326 41160326 + Silent SNP T T A rs369321987 C3L-02345_T C3L-02345_N T T c.1500A>T p.= p.A500A ENST00000263413 11/18 320 267 53 380 380 0 strelka-varscan-mutect C6,synonymous_variant,p.=,ENST00000263413,NM_001115131.2;C6,synonymous_variant,p.=,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000475349,;C6,non_coding_transcript_exon_variant,,ENST00000473450,;C6,non_coding_transcript_exon_variant,,ENST00000511470,; A ENST00000263413 Transcript synonymous_variant 1765/3661 1500/2805 500/934 A gcA/gcT rs369321987,COSM3697359 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 11/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Pfam_domain:PF01823,SMART_domains:SM00457,Prints_domain:PR00764 0,1 LOW 1 SNV 1 0,1 1 PASS rs369321987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 41160326 41160326 T A 1 0 0 0 0 0 0 0 1 2111 1567 55 4 4 C6 5 41160326 Silent SNP T C3L-02345_T 9069199 41160326 140377933 64 8662 IGIP 0 . GRCh38 5 140128607 140128607 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.131G>T p.Ser44Ile p.S44I ENST00000333305 1/1 298 241 57 319 319 0 strelka-varscan-mutect IGIP,missense_variant,p.Ser44Ile,ENST00000333305,NM_001007189.1;PURA,downstream_gene_variant,,ENST00000331327,NM_005859.4; T ENST00000333305 Transcript missense_variant 2673/3458 131/162 44/53 S/I aGc/aTc 1 1 IGIP HGNC HGNC:33847 protein_coding YES CCDS34244.1 ENSP00000327344 A6NJ69 A0A158RFU4 UPI000046D390 NM_001007189.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR39224 MODERATE 1 SNV 1 PASS rs1197009380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 140128607 140128607 G T 1 0 0 0 0 1 0 0 0 7499 971 34 2 2 IGIP 5 140128607 Missense_Mutation SNP G C3L-02345_T 98968281 140128607 41409652 65 8663 PCDHB5 0 . GRCh38 5 141136362 141136362 + Missense_Mutation SNP G G T C3L-02345_T C3L-02345_N G G c.928G>T p.Ala310Ser p.A310S ENST00000231134 1/1 112 89 23 146 145 1 strelka-varscan-mutect PCDHB5,missense_variant,p.Ala310Ser,ENST00000231134,NM_015669.4;PCDHB5,intron_variant,,ENST00000623915,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;CH17-140K24.2,downstream_gene_variant,,ENST00000624192,; T ENST00000231134 Transcript missense_variant 1145/3408 928/2388 310/795 A/S Gca/Tca COSM5615467 1 1 PCDHB5 HGNC HGNC:8690 protein_coding YES CCDS4247.1 ENSP00000231134 Q9Y5E4 UPI0000169DEA NM_015669.4 tolerated_low_confidence(0.44) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 PASS rs975207995 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 141136362 141136362 G T 1 0 0 0 0 1 0 0 0 11632 1203 42 2 2 PCDHB5 5 141136362 Missense_Mutation SNP G C3L-02345_T 1007755 141136362 40401897 66 8664 PCDHB7 0 . GRCh38 5 141174944 141174944 + Silent SNP G G T rs150314773 C3L-02345_T C3L-02345_N G G c.2109G>T p.= p.V703V ENST00000231137 1/1 374 302 72 454 453 1 strelka-varscan-mutect PCDHB7,synonymous_variant,p.=,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; T ENST00000231137 Transcript synonymous_variant 2326/3765 2109/2382 703/793 V gtG/gtT rs150314773 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 1 PASS rs150314773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 141174944 141174944 G T 1 0 0 0 0 0 0 0 1 11634 1306 46 2 2 PCDHB7 5 141174944 Silent SNP G C3L-02345_T 38582 141174944 40363315 67 8665 PCDHB12 0 . GRCh38 5 141210617 141210617 + Silent SNP G G A rs782059381 C3L-02345_T C3L-02345_N G G c.1710G>A p.= p.A570A ENST00000239450 1/1 756 671 85 839 839 0 varscan-mutect PCDHB12,synonymous_variant,p.=,ENST00000239450,NM_018932.3;PCDHB12,synonymous_variant,p.=,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239450 Transcript synonymous_variant 1899/3853 1710/2388 570/795 A gcG/gcA rs782059381,COSM5284619 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 1/1 hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 0,1 LOW 1 SNV 0,1 1 PASS rs782059381 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 141210617 141210617 G A 1 0 0 0 0 0 0 0 1 11624 1074 38 1 1 PCDHB12 5 141210617 Silent SNP G C3L-02345_T 35673 141210617 40327642 68 8666 PCDHGA6 0 . GRCh38 5 141375515 141375515 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.1432G>C p.Asp478His p.D478H ENST00000517434 1/4 352 289 63 499 499 0 strelka-varscan-mutect PCDHGA6,missense_variant,p.Asp478His,ENST00000610583,NM_032086.1;PCDHGA6,missense_variant,p.Asp478His,ENST00000517434,NM_018919.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; C ENST00000517434 Transcript missense_variant 1602/4775 1432/2799 478/932 D/H Gac/Cac 1 1 PCDHGA6 HGNC HGNC:8704 protein_coding YES CCDS54926.1 ENSP00000429601 Q9Y5G7 UPI00000715C8 NM_018919.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF107,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 141375515 141375515 G C 1 0 0 0 0 1 0 0 0 11645 1174 41 4 4 PCDHGA6 5 141375515 Missense_Mutation SNP G C3L-02345_T 164898 141375515 40162744 69 8667 PCDHGB7 0 . GRCh38 5 141419245 141419245 + Silent SNP A A G novel C3L-02345_T C3L-02345_N A A c.1386A>G p.= p.P462P ENST00000398594 1/4 241 183 58 282 282 0 strelka-varscan-mutect PCDHGB7,synonymous_variant,p.=,ENST00000398594,NM_018927.3;PCDHGB7,synonymous_variant,p.=,ENST00000612073,NM_032101.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,upstream_gene_variant,,ENST00000398587,NM_018914.2;PCDHGA10,downstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA11,upstream_gene_variant,,ENST00000622044,NM_032091.1;PCDHGA11,upstream_gene_variant,,ENST00000518882,NM_032092.1;PCDHGA3,intron_variant,,ENST00000612467,; G ENST00000398594 Transcript synonymous_variant 1555/4765 1386/2790 462/929 P ccA/ccG 1 1 PCDHGB7 HGNC HGNC:8714 protein_coding YES CCDS47293.1 ENSP00000381594 Q9Y5F8 UPI000007141F NM_018927.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF113,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 31 141419245 141419245 A G 1 0 0 0 0 0 0 0 1 11655 175 7 5 5 PCDHGB7 5 141419245 Silent SNP A C3L-02345_T 43730 141419245 40119014 70 8668 SGCD 0 . GRCh38 5 156589311 156589311 + Silent SNP T T A novel C3L-02345_T C3L-02345_N T T c.375T>A p.= p.L125L ENST00000337851 5/9 95 84 11 135 135 0 strelka-varscan-mutect SGCD,synonymous_variant,p.=,ENST00000435422,NM_001128209.1;SGCD,synonymous_variant,p.=,ENST00000337851,NM_000337.5;SGCD,synonymous_variant,p.=,ENST00000517913,NM_172244.2;SGCD,downstream_gene_variant,,ENST00000524347,; A ENST00000337851 Transcript synonymous_variant 894/1606 375/873 125/290 L ctT/ctA 1 1 SGCD HGNC HGNC:10807 protein_coding YES CCDS47325.1 ENSP00000338343 Q92629 UPI00001678CF NM_000337.5 5/9 hmmpanther:PTHR12939:SF6,hmmpanther:PTHR12939,Pfam_domain:PF04790 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99976 1 1 1 1 0 A 2 1 31 156589311 156589311 T A 1 0 0 0 0 0 0 0 1 14461 1741 61 4 4 SGCD 5 156589311 Silent SNP T C3L-02345_T 15170066 156589311 24948948 71 8669 LCP2 0 . GRCh38 5 170258084 170258084 + Frame_Shift_Del DEL G G - novel C3L-02345_T C3L-02345_N G G c.1053delC p.Met352Ter p.M352* ENST00000046794 16/21 233 179 54 248 248 0 sindel-varindel-pindel LCP2,frameshift_variant,p.Met352Ter,ENST00000046794,NM_005565.3;LCP2,frameshift_variant,p.Met352Ter,ENST00000628092,;LCP2,frameshift_variant,p.Met147Ter,ENST00000521416,;LCP2,frameshift_variant,p.Met119Ter,ENST00000520344,;LCP2,non_coding_transcript_exon_variant,,ENST00000523369,; - ENST00000046794 Transcript frameshift_variant 1669/4678 1053/1602 351/533 P/X ccC/cc 1 -1 LCP2 HGNC HGNC:6529 protein_coding YES CCDS47339.1 ENSP00000046794 Q13094 UPI000012E2AE NM_005565.3 16/21 hmmpanther:PTHR14098,hmmpanther:PTHR14098:SF1 HIGH 1 deletion 1 1 PASS . . 0 207 0 0 2 0 0 0 -20 0.9985516 1 1 1 0 - 7 5 31 170258084 170258084 G - 1 0 1 0 1 0 0 0 0 8598 1335 47 0 0 LCP2 5 170258084 Frame_Shift_Del DEL G C3L-02345_T 13668773 170258084 11280175 72 8670 TSPAN17 0 . GRCh38 5 176651783 176651783 + Silent SNP A A T novel C3L-02345_T C3L-02345_N A A c.168A>T p.= p.T56T ENST00000310032 3/9 186 146 40 243 243 0 strelka-varscan-mutect TSPAN17,synonymous_variant,p.=,ENST00000310032,NM_012171.2;TSPAN17,synonymous_variant,p.=,ENST00000508164,NM_130465.4;TSPAN17,synonymous_variant,p.=,ENST00000515708,NM_001006616.2;TSPAN17,synonymous_variant,p.=,ENST00000503045,;TSPAN17,synonymous_variant,p.=,ENST00000504168,;TSPAN17,intron_variant,,ENST00000298564,;TSPAN17,intron_variant,,ENST00000507471,;TSPAN17,3_prime_UTR_variant,,ENST00000503030,;TSPAN17,non_coding_transcript_exon_variant,,ENST00000514705,; T ENST00000310032 Transcript synonymous_variant 397/2550 168/999 56/332 T acA/acT 1 1 TSPAN17 HGNC HGNC:13594 protein_coding YES CCDS34298.1 ENSP00000309036 J3KNG2 UPI00004542F1 NM_012171.2 3/9 hmmpanther:PTHR19282:SF64,hmmpanther:PTHR19282,Pfam_domain:PF00335 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 176651783 176651783 A T 1 0 0 0 0 0 0 0 1 17146 175 7 4 4 TSPAN17 5 176651783 Silent SNP A C3L-02345_T 6393699 176651783 4886476 73 8671 TUBB2B 0 . GRCh38 6 3226254 3226254 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.182C>T p.Pro61Leu p.P61L ENST00000259818 3/4 325 251 74 408 408 0 strelka-varscan-mutect TUBB2B,missense_variant,p.Pro61Leu,ENST00000259818,NM_178012.4;TUBB2B,non_coding_transcript_exon_variant,,ENST00000473006,; A ENST00000259818 Transcript missense_variant 374/2020 182/1338 61/445 P/L cCt/cTt 1 -1 TUBB2B HGNC HGNC:30829 protein_coding YES CCDS4485.1 ENSP00000259818 Q9BVA1 UPI0000024E6E NM_178012.4 deleterious_low_confidence(0.01) 3/4 Gene3D:3.40.50.1440,Pfam_domain:PF00091,Prints_domain:PR01161,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF138,SMART_domains:SM00864,Superfamily_domains:SSF52490 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 3226254 3226254 G A 1 0 0 0 0 1 0 0 0 17266 1000 35 3 3 TUBB2B 6 3226254 Missense_Mutation SNP G C3L-02345_T 3226254 167579725 74 8672 ZSCAN9 0 . GRCh38 6 28232683 28232683 + Silent SNP A A T novel C3L-02345_T C3L-02345_N A A c.843A>T p.= p.S281S ENST00000425468 5/5 315 263 52 350 350 0 strelka-varscan ZSCAN9,synonymous_variant,p.=,ENST00000425468,NM_001199479.1;ZSCAN9,synonymous_variant,p.=,ENST00000252207,NM_006299.4;ZSCAN9,synonymous_variant,p.=,ENST00000531979,NM_001199480.1;ZSCAN9,synonymous_variant,p.=,ENST00000527844,;ZSCAN9,downstream_gene_variant,,ENST00000527436,;ZSCAN9,downstream_gene_variant,,ENST00000531981,;ZSCAN9,downstream_gene_variant,,ENST00000526391,; T ENST00000425468 Transcript synonymous_variant 1008/1791 843/1338 281/445 S tcA/tcT 1 1 ZSCAN9 HGNC HGNC:12984 protein_coding YES CCDS56407.1 ENSP00000404074 O15535 UPI0000E09E19 NM_001199479.1 5/5 hmmpanther:PTHR23226:SF15,hmmpanther:PTHR23226 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 28232683 28232683 A T 1 0 0 0 0 0 0 0 1 18840 146 6 4 4 ZSCAN9 6 28232683 Silent SNP A C3L-02345_T 25006429 28232683 142573296 75 8673 OR10C1 0 . GRCh38 6 29440032 29440032 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.17C>T p.Ser6Phe p.S6F ENST00000444197 1/1 89 68 21 104 104 0 strelka-varscan OR10C1,missense_variant,p.Ser6Phe,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Ser8Phe,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript missense_variant 727/1649 17/939 6/312 S/F tCc/tTc 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 29440032 29440032 C T 1 0 0 0 0 1 0 0 0 10973 855 30 3 3 OR10C1 6 29440032 Missense_Mutation SNP C C3L-02345_T 1207349 29440032 141365947 76 8674 OR2H2 0 . GRCh38 6 29588330 29588330 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.386A>T p.His129Leu p.H129L ENST00000383640 1/1 134 100 34 129 128 1 strelka-varscan OR2H2,missense_variant,p.His129Leu,ENST00000383640,NM_007160.3;GABBR1,intron_variant,,ENST00000355973,; T ENST00000383640 Transcript missense_variant 876/1584 386/939 129/312 H/L cAc/cTc 1 1 OR2H2 HGNC HGNC:8253 protein_coding YES CCDS34365.1 ENSP00000373136 O95918 UPI00001404DC NM_007160.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF199,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 29588330 29588330 A T 1 0 0 0 0 1 0 0 0 11080 159 6 4 4 OR2H2 6 29588330 Missense_Mutation SNP A C3L-02345_T 148298 29588330 141217649 77 8675 SKIV2L 0 . GRCh38 6 31960527 31960527 + Silent SNP T T A novel C3L-02345_T C3L-02345_N T T c.450T>A p.= p.T150T ENST00000375394 5/28 221 181 40 242 241 1 strelka-varscan SKIV2L,synonymous_variant,p.=,ENST00000375394,NM_006929.4;SKIV2L,intron_variant,,ENST00000628157,;NELFE,upstream_gene_variant,,ENST00000375429,NM_002904.5;NELFE,upstream_gene_variant,,ENST00000375425,;NELFE,upstream_gene_variant,,ENST00000444811,;NELFE,upstream_gene_variant,,ENST00000441998,;NELFE,upstream_gene_variant,,ENST00000454913,;NELFE,upstream_gene_variant,,ENST00000436289,;NELFE,upstream_gene_variant,,ENST00000426722,;NELFE,upstream_gene_variant,,ENST00000625905,;NELFE,upstream_gene_variant,,ENST00000408340,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000488648,;SKIV2L,synonymous_variant,p.=,ENST00000461073,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000465703,;SKIV2L,intron_variant,,ENST00000474839,;NELFE,upstream_gene_variant,,ENST00000488426,;NELFE,upstream_gene_variant,,ENST00000492185,;NELFE,upstream_gene_variant,,ENST00000481121,;SKIV2L,downstream_gene_variant,,ENST00000492900,;SKIV2L,upstream_gene_variant,,ENST00000466290,;NELFE,upstream_gene_variant,,ENST00000492539,;NELFE,upstream_gene_variant,,ENST00000491139,;NELFE,upstream_gene_variant,,ENST00000494956,; A ENST00000375394 Transcript synonymous_variant 563/3894 450/3741 150/1246 T acT/acA 1 1 SKIV2L HGNC HGNC:10898 protein_coding YES CCDS4731.1 ENSP00000364543 Q15477 UPI000045740B NM_006929.4 5/28 PIRSF_domain:PIRSF005198 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 31960527 31960527 T A 1 0 0 0 0 0 0 0 1 14622 1538 54 4 4 SKIV2L 6 31960527 Silent SNP T C3L-02345_T 2372197 31960527 138845452 78 8676 IP6K3 0 . GRCh38 6 33735314 33735314 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.163C>A p.Pro55Thr p.P55T ENST00000293756 2/6 147 106 41 116 116 0 strelka-varscan IP6K3,missense_variant,p.Pro55Thr,ENST00000293756,NM_054111.4;IP6K3,missense_variant,p.Pro55Thr,ENST00000451316,NM_001142883.1;IP6K3,missense_variant,p.Pro55Thr,ENST00000634274,; T ENST00000293756 Transcript missense_variant 490/2610 163/1233 55/410 P/T Ccg/Acg 1 -1 IP6K3 HGNC HGNC:17269 protein_coding YES CCDS34435.1 ENSP00000293756 Q96PC2 Q5TAQ4 UPI000013E117 NM_054111.4 deleterious(0) 2/6 hmmpanther:PTHR12400:SF40,hmmpanther:PTHR12400,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 33735314 33735314 G T 1 0 0 0 0 1 0 0 0 7693 1203 42 2 2 IP6K3 6 33735314 Missense_Mutation SNP G C3L-02345_T 1774787 33735314 137070665 79 8677 TULP1 0 . GRCh38 6 35506158 35506158 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.844C>A p.Pro282Thr p.P282T ENST00000229771 10/15 140 114 26 177 177 0 strelka-varscan TULP1,missense_variant,p.Pro282Thr,ENST00000229771,NM_003322.4;TULP1,missense_variant,p.Pro280Thr,ENST00000614066,;TULP1,missense_variant,p.Pro229Thr,ENST00000322263,NM_001289395.1;TULP1,downstream_gene_variant,,ENST00000428978,;TULP1,non_coding_transcript_exon_variant,,ENST00000373892,;TULP1,upstream_gene_variant,,ENST00000495781,;TULP1,downstream_gene_variant,,ENST00000448446,;TULP1,upstream_gene_variant,,ENST00000496434,; T ENST00000229771 Transcript missense_variant 924/2162 844/1629 282/542 P/T Ccg/Acg 1 -1 TULP1 HGNC HGNC:12423 protein_coding YES CCDS4807.1 ENSP00000229771 O00294 UPI000045742A NM_003322.4 tolerated(0.1) 10/15 hmmpanther:PTHR16517,hmmpanther:PTHR16517:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 35506158 35506158 G T 1 0 0 0 0 1 0 0 0 17283 1232 43 2 2 TULP1 6 35506158 Missense_Mutation SNP G C3L-02345_T 1770844 35506158 135299821 80 8678 PTCRA 0 . GRCh38 6 42923112 42923112 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.144G>T p.= p.L48L ENST00000616441 2/4 411 336 75 402 402 0 strelka-varscan PTCRA,synonymous_variant,p.=,ENST00000616441,NM_001243168.1;PTCRA,synonymous_variant,p.=,ENST00000304672,NM_138296.2;PTCRA,intron_variant,,ENST00000441198,NM_001243169.1;PTCRA,intron_variant,,ENST00000446507,NM_001243170.1; T ENST00000616441 Transcript synonymous_variant 225/1125 144/891 48/296 L ctG/ctT 1 1 PTCRA HGNC HGNC:21290 protein_coding YES CCDS75457.1 ENSP00000477815 A0A087WTE9 UPI000016A2C4 NM_001243168.1 2/4 hmmpanther:PTHR37866,hmmpanther:PTHR37866:SF1,Gene3D:2.60.40.10,Pfam_domain:PF15028,Superfamily_domains:SSF48726 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 42923112 42923112 G T 1 0 0 0 0 0 0 0 1 12888 1335 47 2 2 PTCRA 6 42923112 Silent SNP G C3L-02345_T 7416954 42923112 127882867 81 8679 TINAG 0 . GRCh38 6 54349720 54349720 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.904G>A p.Val302Ile p.V302I ENST00000259782 7/11 77 55 22 113 113 0 strelka-varscan TINAG,missense_variant,p.Val302Ile,ENST00000259782,NM_014464.3; A ENST00000259782 Transcript missense_variant 1000/1754 904/1431 302/476 V/I Gta/Ata 1 1 TINAG HGNC HGNC:14599 protein_coding YES CCDS4955.1 ENSP00000259782 Q9UJW2 UPI000013D078 NM_014464.3 deleterious(0) 7/11 Gene3D:3.90.70.10,Pfam_domain:PF00112,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF274,SMART_domains:SM00645,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 54349720 54349720 G A 1 0 0 0 0 1 0 0 0 16362 1275 44 3 3 TINAG 6 54349720 Missense_Mutation SNP G C3L-02345_T 11426608 54349720 116456259 82 8680 DST 0 . GRCh38 6 56642464 56642464 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1305G>T p.Arg435Ser p.R435S ENST00000312431 13/95 386 296 90 408 406 2 strelka-varscan DST,missense_variant,p.Arg395Ser,ENST00000361203,;DST,missense_variant,p.Arg395Ser,ENST00000421834,NM_183380.3;DST,missense_variant,p.Arg435Ser,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Arg395Ser,ENST00000370788,;DST,missense_variant,p.Arg69Ser,ENST00000244364,NM_015548.4;DST,missense_variant,p.Arg69Ser,ENST00000439203,;DST,missense_variant,p.Arg69Ser,ENST00000370765,NM_001723.5;DST,missense_variant,p.Arg435Ser,ENST00000520645,;DST,missense_variant,p.Arg69Ser,ENST00000518935,;DST,missense_variant,p.Arg573Ser,ENST00000449297,;DST,non_coding_transcript_exon_variant,,ENST00000521104,;DST,non_coding_transcript_exon_variant,,ENST00000523967,;DST,non_coding_transcript_exon_variant,,ENST00000518828,; A ENST00000312431 Transcript missense_variant 1431/17756 1305/16614 435/5537 R/S agG/agT 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.1) 13/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 56642464 56642464 C A 1 0 0 0 0 1 0 0 0 4604 622 22 2 2 DST 6 56642464 Missense_Mutation SNP C C3L-02345_T 2292744 56642464 114163515 83 8681 SNAP91 0 . GRCh38 6 83594432 83594432 + Silent SNP G G A rs764376228 C3L-02345_T C3L-02345_N G G c.1374C>T p.= p.A458A ENST00000439399 17/30 103 92 11 141 141 0 strelka-varscan-mutect SNAP91,synonymous_variant,p.=,ENST00000521485,;SNAP91,synonymous_variant,p.=,ENST00000439399,NM_014841.2;SNAP91,synonymous_variant,p.=,ENST00000369694,NM_001242792.1;SNAP91,synonymous_variant,p.=,ENST00000195649,NM_001256718.1;SNAP91,synonymous_variant,p.=,ENST00000521743,;SNAP91,synonymous_variant,p.=,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,intron_variant,,ENST00000520213,NM_001242794.1;SNAP91,intron_variant,,ENST00000521931,;SNAP91,intron_variant,,ENST00000369691,;SNAP91,upstream_gene_variant,,ENST00000523448,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,;SNAP91,non_coding_transcript_exon_variant,,ENST00000523780,; A ENST00000439399 Transcript synonymous_variant 1691/4452 1374/2724 458/907 A gcC/gcT rs764376228,COSM5100598,COSM5100599 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 17/30 Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs764376228 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 83594432 83594432 G A 1 0 0 0 0 0 0 0 1 15154 1103 39 1 1 SNAP91 6 83594432 Silent SNP G C3L-02345_T 26951968 83594432 87211547 84 8682 TRDN 0 . GRCh38 6 123464933 123464933 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.904C>A p.Pro302Thr p.P302T ENST00000334268 10/41 215 185 30 214 213 1 strelka-varscan TRDN,missense_variant,p.Pro302Thr,ENST00000334268,NM_006073.3;TRDN,missense_variant,p.Pro282Thr,ENST00000628709,NM_001256020.1;RP11-532N4.2,intron_variant,,ENST00000587106,;RP11-532N4.2,intron_variant,,ENST00000625262,;RP11-532N4.2,intron_variant,,ENST00000629087,;RP11-532N4.2,intron_variant,,ENST00000418467,;RP11-532N4.2,intron_variant,,ENST00000589182,;RP11-532N4.2,intron_variant,,ENST00000628939,;RP11-532N4.2,intron_variant,,ENST00000434768,;RP11-532N4.2,intron_variant,,ENST00000625415,;RP11-532N4.2,intron_variant,,ENST00000427828,;RP11-532N4.2,downstream_gene_variant,,ENST00000587049,; T ENST00000334268 Transcript missense_variant 1222/4770 904/2190 302/729 P/T Ccc/Acc 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 deleterious_low_confidence(0.01) 10/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 123464933 123464933 G T 1 0 0 0 0 1 0 0 0 16957 1261 44 2 2 TRDN 6 123464933 Missense_Mutation SNP G C3L-02345_T 39870501 123464933 47341046 85 8683 ESR1 0 . GRCh38 6 151944219 151944219 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.807C>A p.= p.R269R ENST00000440973 6/10 184 125 59 281 279 2 strelka-varscan ESR1,synonymous_variant,p.=,ENST00000440973,NM_001122742.1;ESR1,synonymous_variant,p.=,ENST00000206249,NM_001291230.1,NM_001122741.1,NM_001291241.1,NM_000125.3;ESR1,synonymous_variant,p.=,ENST00000443427,NM_001122740.1;ESR1,synonymous_variant,p.=,ENST00000427531,NM_001328100.1;ESR1,synonymous_variant,p.=,ENST00000338799,;ESR1,intron_variant,,ENST00000456483,;ESR1,intron_variant,,ENST00000406599,;ESR1,intron_variant,,ENST00000415488,;ESR1,non_coding_transcript_exon_variant,,ENST00000482101,; A ENST00000440973 Transcript synonymous_variant 1177/6466 807/1788 269/595 R cgC/cgA 1 1 ESR1 HGNC HGNC:3467 protein_coding YES CCDS5234.1 ENSP00000405330 P03372 G4XH65 UPI000004A328 NM_001122742.1 6/10 hmmpanther:PTHR24084,PIRSF_domain:PIRSF500101,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 151944219 151944219 C A 1 0 0 0 0 0 0 0 1 5118 726 26 2 2 ESR1 6 151944219 Silent SNP C C3L-02345_T 28479286 151944219 18861760 86 8684 GPER1 0 . GRCh38 7 1092601 1092601 + Silent SNP C C A rs374017708 C3L-02345_T C3L-02345_N C C c.873C>A p.= p.A291A ENST00000397092 3/3 139 107 32 139 139 0 strelka-varscan-mutect GPER1,synonymous_variant,p.=,ENST00000397092,NM_001039966.1;GPER1,synonymous_variant,p.=,ENST00000297469,NM_001505.2;GPER1,synonymous_variant,p.=,ENST00000397088,NM_001098201.1;GPER1,synonymous_variant,p.=,ENST00000617001,;GPER1,synonymous_variant,p.=,ENST00000401670,;C7orf50,intron_variant,,ENST00000397098,NM_001318252.1;C7orf50,intron_variant,,ENST00000357429,NM_001134395.1,NM_032350.5;C7orf50,intron_variant,,ENST00000397100,NM_001134396.1;C7orf50,intron_variant,,ENST00000491163,;GPER1,downstream_gene_variant,,ENST00000413368,;GPER1,upstream_gene_variant,,ENST00000619052,;C7orf50,intron_variant,,ENST00000488073,; A ENST00000397092 Transcript synonymous_variant 1757/2971 873/1128 291/375 A gcC/gcA rs374017708 1 1 GPER1 HGNC HGNC:4485 protein_coding YES CCDS5322.1 ENSP00000380281 Q99527 A0A024R849 UPI00000503F2 NM_001039966.1 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24226:SF2,hmmpanther:PTHR24226,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW SNV 2 1 PASS rs374017708 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 1092601 1092601 C A 1 0 0 0 0 0 0 0 1 6509 639 23 1 1 GPER1 7 1092601 Silent SNP C C3L-02345_T 1092601 158253372 87 8685 GRID2IP 0 . GRCh38 7 6551167 6551167 + Silent SNP G G A novel C3L-02345_T C3L-02345_N G G c.270C>T p.= p.G90G ENST00000457091 1/22 71 56 15 65 65 0 strelka-varscan-mutect GRID2IP,synonymous_variant,p.=,ENST00000457091,NM_001145118.1; A ENST00000457091 Transcript synonymous_variant 270/3636 270/3636 90/1211 G ggC/ggT 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 1/22 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 6551167 6551167 G A 1 0 0 0 0 0 0 0 1 6653 1190 42 3 3 GRID2IP 7 6551167 Silent SNP G C3L-02345_T 5458566 6551167 152794806 88 8686 MEOX2 0 . GRCh38 7 15686184 15686184 + Silent SNP G G A novel C3L-02345_T C3L-02345_N G G c.219C>T p.= p.H73H ENST00000262041 1/3 141 107 34 164 164 0 strelka-varscan-mutect MEOX2,synonymous_variant,p.=,ENST00000262041,NM_005924.4;MEOX2-AS1,upstream_gene_variant,,ENST00000442176,;AC005550.5,downstream_gene_variant,,ENST00000438923,;AC005550.3,downstream_gene_variant,,ENST00000451240,; A ENST00000262041 Transcript synonymous_variant 629/2500 219/915 73/304 H caC/caT 1 -1 MEOX2 HGNC HGNC:7014 protein_coding YES CCDS34605.1 ENSP00000262041 P50222 UPI000013D247 NM_005924.4 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24328,hmmpanther:PTHR24328:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 15686184 15686184 G A 1 0 0 0 0 0 0 0 1 9419 1252 44 3 3 MEOX2 7 15686184 Silent SNP G C3L-02345_T 9135017 15686184 143659789 89 8687 TMEM196 0 . GRCh38 7 19772657 19772657 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.40C>G p.Leu14Val p.L14V ENST00000405764 1/4 89 72 17 91 91 0 strelka-varscan-mutect TMEM196,missense_variant,p.Leu14Val,ENST00000405844,;TMEM196,missense_variant,p.Leu14Val,ENST00000405764,NM_152774.3;TMEM196,intron_variant,,ENST00000422233,;TMEM196,intron_variant,,ENST00000433641,;TMEM196,intron_variant,,ENST00000493519,; C ENST00000405764 Transcript missense_variant 737/3975 40/519 14/172 L/V Ctc/Gtc 1 -1 TMEM196 HGNC HGNC:22431 protein_coding YES CCDS34607.2 ENSP00000384234 Q5HYL7 UPI00005A9078 NM_152774.3 deleterious_low_confidence(0.03) 1/4 hmmpanther:PTHR28681,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1382694040 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 19772657 19772657 G C 1 0 0 0 0 1 0 0 0 16558 971 34 4 4 TMEM196 7 19772657 Missense_Mutation SNP G C3L-02345_T 4086473 19772657 139573316 90 8688 SCRN1 0 . GRCh38 7 29936609 29936609 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.912G>T p.Gln304His p.Q304H ENST00000434476 6/8 57 51 6 55 55 0 strelka-varscan SCRN1,missense_variant,p.Gln284His,ENST00000426154,NM_001145513.1;SCRN1,missense_variant,p.Gln284His,ENST00000242059,NM_014766.4;SCRN1,missense_variant,p.Gln284His,ENST00000409497,;SCRN1,missense_variant,p.Gln216His,ENST00000425819,NM_001145515.1;SCRN1,missense_variant,p.Gln304His,ENST00000434476,NM_001145514.1;SCRN1,downstream_gene_variant,,ENST00000421434,; A ENST00000434476 Transcript missense_variant 961/1454 912/1305 304/434 Q/H caG/caT COSM1089035,COSM1596974 1 -1 SCRN1 HGNC HGNC:22192 protein_coding YES CCDS47567.1 ENSP00000388942 Q12765 UPI000194EC2F NM_001145514.1 deleterious(0.03) 6/8 hmmpanther:PTHR12994:SF7,hmmpanther:PTHR12994 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -14.38638 1 1 1 1 0 A 3 1 31 29936609 29936609 C A 1 0 0 0 0 1 0 0 0 14208 912 32 2 2 SCRN1 7 29936609 Missense_Mutation SNP C C3L-02345_T 10163952 29936609 129409364 91 8689 DPY19L1 0 . GRCh38 7 35011372 35011372 + Frame_Shift_Del DEL C C - rs189464206 C3L-02345_T C3L-02345_N C C c.409delG p.Val137LeufsTer26 p.V137Lfs*26 ENST00000310974 5/22 267 206 61 275 275 0 sindel-varindel-pindel DPY19L1,frameshift_variant,p.Val210LeufsTer26,ENST00000638088,;DPY19L1,frameshift_variant,p.Val137LeufsTer26,ENST00000310974,NM_015283.1;DPY19L1,non_coding_transcript_exon_variant,,ENST00000481923,; - ENST00000310974 Transcript frameshift_variant 554/4870 409/2028 137/675 V/X Gtt/tt rs189464206 1 -1 DPY19L1 HGNC HGNC:22205 protein_coding YES CCDS43567.1 ENSP00000308695 Q2PZI1 UPI000067CB92 NM_015283.1 5/22 hmmpanther:PTHR31488:SF5,hmmpanther:PTHR31488,Pfam_domain:PF10034 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 35011372 35011372 C - 1 0 1 0 1 0 0 0 0 4555 507 18 0 0 DPY19L1 7 35011372 Frame_Shift_Del DEL C C3L-02345_T 5074763 35011372 124334601 92 8690 PKD1L1 0 . GRCh38 7 47931999 47931999 + Silent SNP C C T rs759739549 C3L-02345_T C3L-02345_N C C c.456G>A p.= p.R152R ENST00000289672 5/57 148 128 20 170 169 1 strelka-varscan PKD1L1,synonymous_variant,p.=,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; T ENST00000289672 Transcript synonymous_variant 507/9092 456/8550 152/2849 R agG/agA rs759739549 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 5/57 hmmpanther:PTHR10877:SF145,hmmpanther:PTHR10877 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 31 47931999 47931999 C T 1 0 0 0 0 0 0 0 1 12060 506 18 3 3 PKD1L1 7 47931999 Silent SNP C C3L-02345_T 12920627 47931999 111413974 93 8691 ABCA13 0 . GRCh38 7 48313099 48313099 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.9549C>A p.= p.L3183L ENST00000435803 25/62 68 49 19 105 105 0 strelka-varscan ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,non_coding_transcript_exon_variant,,ENST00000484268,; A ENST00000435803 Transcript synonymous_variant 9573/17184 9549/15177 3183/5058 L ctC/ctA 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 25/62 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 48313099 48313099 C A 1 0 0 0 0 0 0 0 1 35 813 29 2 2 ABCA13 7 48313099 Silent SNP C C3L-02345_T 381100 48313099 111032874 94 8692 ABCA13 0 . GRCh38 7 48516776 48516776 + Silent SNP G G T rs371594909 C3L-02345_T C3L-02345_N G G c.13692G>T p.= p.S4564S ENST00000435803 52/62 189 155 34 178 178 0 strelka-varscan ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000544596,;ABCA13,synonymous_variant,p.=,ENST00000411975,;ABCA13,synonymous_variant,p.=,ENST00000435451,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,synonymous_variant,p.=,ENST00000453246,; T ENST00000435803 Transcript synonymous_variant 13716/17184 13692/15177 4564/5058 S tcG/tcT rs371594909,COSM3639400,COSM3639401 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 52/62 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Pfam_domain:PF12698 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 48516776 48516776 G T 1 0 0 0 0 0 0 0 1 35 1103 39 1 1 ABCA13 7 48516776 Silent SNP G C3L-02345_T 203677 48516776 110829197 95 8693 PCLO 0 . GRCh38 7 82955497 82955497 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.5456G>A p.Arg1819Lys p.R1819K ENST00000333891 5/25 140 110 30 160 160 0 strelka-varscan PCLO,missense_variant,p.Arg1819Lys,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Arg1819Lys,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; T ENST00000333891 Transcript missense_variant 5794/20329 5456/15429 1819/5142 R/K aGa/aAa 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0.03) 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 82955497 82955497 C T 1 0 0 0 0 1 0 0 0 11671 913 32 3 3 PCLO 7 82955497 Missense_Mutation SNP C C3L-02345_T 34438721 82955497 76390476 96 8694 PEG10 0 . GRCh38 7 94664510 94664510 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.1182G>T p.= p.A394A ENST00000488574 2/2 161 126 35 200 198 2 strelka-varscan PEG10,missense_variant,p.Gly352Trp,ENST00000612941,;PEG10,missense_variant,p.Gly318Trp,ENST00000617526,;PEG10,missense_variant,p.Gly394Trp,ENST00000612748,;PEG10,synonymous_variant,p.=,ENST00000482108,NM_015068.3,NM_001184961.1,NM_001172437.2,NM_001040152.1;PEG10,synonymous_variant,p.=,ENST00000615790,NM_001184962.1;PEG10,synonymous_variant,p.=,ENST00000488574,NM_001172438.2;PEG10,downstream_gene_variant,,ENST00000613043,;PEG10,intron_variant,,ENST00000493935,;PEG10,upstream_gene_variant,,ENST00000465184,; T ENST00000488574 Transcript synonymous_variant 1399/2587 1182/1206 394/401 A gcG/gcT 1 1 PEG10 HGNC HGNC:14005 protein_coding YES CCDS75636.1 ENSP00000418944 B4DSP0 UPI0000037665 NM_001172438.2 2/2 hmmpanther:PTHR15503:SF10,hmmpanther:PTHR15503 LOW 1 SNV 2 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999588 1 1 1 0 T 2 4 31 94664510 94664510 G T 1 0 0 0 0 0 0 0 1 11807 1130 39 1 1 PEG10 7 94664510 Silent SNP G C3L-02345_T 11709013 94664510 64681463 97 8695 SLC12A9 0 . GRCh38 7 100860225 100860225 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.1211T>A p.Leu404Gln p.L404Q ENST00000354161 9/14 131 117 14 161 161 0 varscan-mutect SLC12A9,missense_variant,p.Leu404Gln,ENST00000354161,NM_020246.3;SLC12A9,missense_variant,p.Leu404Gln,ENST00000540482,NM_001267812.1;SLC12A9,missense_variant,p.Leu315Gln,ENST00000415287,NM_001267814.1;SLC12A9,missense_variant,p.Leu140Gln,ENST00000418037,;SLC12A9,missense_variant,p.Leu212Gln,ENST00000416675,;SLC12A9,downstream_gene_variant,,ENST00000434158,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475623,;SLC12A9,upstream_gene_variant,,ENST00000482184,;SLC12A9,downstream_gene_variant,,ENST00000461016,;SLC12A9,3_prime_UTR_variant,,ENST00000448342,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000487651,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000467972,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000475687,;SLC12A9,non_coding_transcript_exon_variant,,ENST00000497958,;SLC12A9,downstream_gene_variant,,ENST00000462106,; A ENST00000354161 Transcript missense_variant 1336/3273 1211/2745 404/914 L/Q cTg/cAg 1 1 SLC12A9 HGNC HGNC:17435 protein_coding YES CCDS5707.1 ENSP00000275730 Q9BXP2 UPI000006CD28 NM_020246.3 deleterious(0) 9/14 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF52,Pfam_domain:PF00324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 100860225 100860225 T A 1 0 0 0 0 1 0 0 0 14655 1580 55 4 4 SLC12A9 7 100860225 Missense_Mutation SNP T C3L-02345_T 6195715 100860225 58485748 98 8696 MUC17 0 . GRCh38 7 101036549 101036549 + Silent SNP A A T novel C3L-02345_T C3L-02345_N A A c.5133A>T p.= p.S1711S ENST00000306151 3/13 86 64 22 103 103 0 strelka-varscan-mutect MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; T ENST00000306151 Transcript synonymous_variant 5197/14247 5133/13482 1711/4493 S tcA/tcT 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 203 4 2 0 0 0 0 -20 0.9999938 1 1 1 0 T 2 4 31 101036549 101036549 A T 1 0 0 0 0 0 0 0 1 9973 117 5 4 4 MUC17 7 101036549 Silent SNP A C3L-02345_T 176324 101036549 58309424 99 8697 CCDC136 0 . GRCh38 7 128814758 128814758 + Nonsense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.2884G>T p.Glu962Ter p.E962* ENST00000297788 15/18 178 130 48 199 199 0 strelka-varscan-mutect CCDC136,stop_gained,p.Glu962Ter,ENST00000297788,NM_022742.4;CCDC136,stop_gained,p.Glu839Ter,ENST00000494552,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000464672,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000378685,NM_001201372.1;CCDC136,non_coding_transcript_exon_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000460941,; T ENST00000297788 Transcript stop_gained 3251/4169 2884/3465 962/1154 E/* Gag/Tag 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 15/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26,Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 128814758 128814758 G T 1 0 0 0 0 0 1 0 0 2459 1175 41 2 2 CCDC136 7 128814758 Nonsense_Mutation SNP G C3L-02345_T 27778209 128814758 30531215 100 8698 TSGA13 0 . GRCh38 7 130671693 130671693 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.626C>A p.Ala209Asp p.A209D ENST00000456951 8/9 158 150 8 167 167 0 strelka-mutect TSGA13,missense_variant,p.Ala209Asp,ENST00000456951,NM_001304968.1;TSGA13,missense_variant,p.Ala209Asp,ENST00000356588,NM_052933.3;COPG2,upstream_gene_variant,,ENST00000425248,NM_012133.5;COPG2,upstream_gene_variant,,ENST00000330992,NM_001290033.1; T ENST00000456951 Transcript missense_variant 1478/2046 626/828 209/275 A/D gCt/gAt 1 -1 TSGA13 HGNC HGNC:12369 protein_coding YES CCDS5824.1 ENSP00000406047 Q96PP4 A0A024R769 UPI0000073CFB NM_001304968.1 deleterious(0.04) 8/9 Pfam_domain:PF14994,hmmpanther:PTHR37352 MODERATE SNV 2 1 PASS . . 0 206 0 3 0 0 0 0 -10.57412 0.9999353 1 1 1 0 T 3 4 31 130671693 130671693 G T 1 0 0 0 0 1 0 0 0 17125 971 34 2 2 TSGA13 7 130671693 Missense_Mutation SNP G C3L-02345_T 1856935 130671693 28674280 101 8699 MRPS33 0 . GRCh38 7 141010523 141010523 + Silent SNP A A G rs761120401 C3L-02345_T C3L-02345_N A A c.111T>C p.= p.F37F ENST00000324787 2/3 457 354 103 499 499 0 strelka-varscan-mutect MRPS33,synonymous_variant,p.=,ENST00000324787,NM_053035.2;MRPS33,synonymous_variant,p.=,ENST00000393008,NM_016071.3;MRPS33,synonymous_variant,p.=,ENST00000469351,;MRPS33,synonymous_variant,p.=,ENST00000496958,;MRPS33,synonymous_variant,p.=,ENST00000467334,;MRPS33,intron_variant,,ENST00000484502,;MRPS33,upstream_gene_variant,,ENST00000472343,;MRPS33,non_coding_transcript_exon_variant,,ENST00000496641,;MRPS33,non_coding_transcript_exon_variant,,ENST00000485202,; G ENST00000324787 Transcript synonymous_variant 211/4241 111/321 37/106 F ttT/ttC rs761120401 1 -1 MRPS33 HGNC HGNC:16634 protein_coding YES CCDS5864.1 ENSP00000320567 Q9Y291 A4D1T3 UPI00001352B2 NM_053035.2 2/3 Pfam_domain:PF08293,hmmpanther:PTHR13362,hmmpanther:PTHR13362:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 31 141010523 141010523 A G 1 0 0 0 0 0 0 0 1 9819 359 13 5 5 MRPS33 7 141010523 Silent SNP A C3L-02345_T 10338830 141010523 18335450 102 8700 GIMAP2 0 . GRCh38 7 150693260 150693260 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.974G>T p.Arg325Ile p.R325I ENST00000223293 3/3 76 58 18 82 82 0 strelka-varscan-mutect GIMAP2,missense_variant,p.Arg325Ile,ENST00000223293,NM_015660.2;GIMAP2,downstream_gene_variant,,ENST00000474605,; T ENST00000223293 Transcript missense_variant 1068/1449 974/1014 325/337 R/I aGa/aTa 1 1 GIMAP2 HGNC HGNC:21789 protein_coding YES CCDS5905.1 ENSP00000223293 Q9UG22 A0A090N8H4 UPI000006D114 NM_015660.2 deleterious_low_confidence(0) 3/3 hmmpanther:PTHR10903:SF7,hmmpanther:PTHR10903 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 150693260 150693260 G T 1 0 0 0 0 1 0 0 0 6260 942 33 2 2 GIMAP2 7 150693260 Missense_Mutation SNP G C3L-02345_T 9682737 150693260 8652713 103 8701 HTR5A 0 . GRCh38 7 155071146 155071146 + Missense_Mutation SNP G G T rs759496883 C3L-02345_T C3L-02345_N G G c.247G>T p.Ala83Ser p.A83S ENST00000287907 1/2 120 84 36 128 127 1 strelka-varscan-mutect HTR5A,missense_variant,p.Ala83Ser,ENST00000287907,NM_024012.3;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000395731,;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000493904,;RP11-5C23.4,upstream_gene_variant,,ENST00000637588,; T ENST00000287907 Transcript missense_variant 823/2912 247/1074 83/357 A/S Gcc/Tcc rs759496883 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 deleterious(0) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs759496883 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 155071146 155071146 G T 1 0 0 0 0 1 0 0 0 7346 1203 42 2 2 HTR5A 7 155071146 Missense_Mutation SNP G C3L-02345_T 4377886 155071146 4274827 104 8702 EN2 0 . GRCh38 7 155462516 155462516 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.831G>T p.= p.L277L ENST00000297375 2/2 335 261 74 333 333 0 strelka-varscan-mutect EN2,synonymous_variant,p.=,ENST00000297375,NM_001427.3; T ENST00000297375 Transcript synonymous_variant 1080/3395 831/1002 277/333 L ctG/ctT 1 1 EN2 HGNC HGNC:3343 protein_coding YES CCDS5940.1 ENSP00000297375 P19622 UPI000012CA05 NM_001427.3 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24341:SF5,hmmpanther:PTHR24341,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 155462516 155462516 G T 1 0 0 0 0 0 0 0 1 4952 1335 47 2 2 EN2 7 155462516 Silent SNP G C3L-02345_T 391370 155462516 3883457 105 8703 USP17L4 0 . GRCh38 8 7338293 7338293 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.1179C>A p.= p.A393A ENST00000526929 1/1 101 58 43 119 119 0 strelka-varscan-mutect USP17L4,synonymous_variant,p.=,ENST00000526929,NM_001256874.1;USP17L1,downstream_gene_variant,,ENST00000529559,NM_001256873.1;FAM66B,intron_variant,,ENST00000606573,;FAM66B,intron_variant,,ENST00000529456,;AC130360.8,upstream_gene_variant,,ENST00000425489,; A ENST00000526929 Transcript synonymous_variant 1179/1593 1179/1593 393/530 A gcC/gcA 1 1 USP17L4 HGNC HGNC:37176 protein_coding YES CCDS78299.1 ENSP00000485243 A6NCW7 UPI0000251F84 NM_001256874.1 1/1 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511 LOW SNV 1 PASS . . 6 204 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 7338293 7338293 C A 1 0 0 0 0 0 0 0 1 17588 610 22 2 2 USP17L4 8 7338293 Silent SNP C C3L-02345_T 7338293 137800343 106 8704 SPIDR 0 . GRCh38 8 47293917 47293917 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.412A>G p.Ser138Gly p.S138G ENST00000297423 5/20 195 144 51 219 219 0 strelka-varscan-mutect SPIDR,missense_variant,p.Ser138Gly,ENST00000297423,NM_001080394.3;SPIDR,missense_variant,p.Ser68Gly,ENST00000541342,NM_001282916.1;SPIDR,missense_variant,p.Ser78Gly,ENST00000518074,NM_001282919.1;SPIDR,intron_variant,,ENST00000524006,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521214,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521550,;SPIDR,non_coding_transcript_exon_variant,,ENST00000522900,;SPIDR,missense_variant,p.Ser138Gly,ENST00000524126,;SPIDR,missense_variant,p.Ser138Gly,ENST00000519661,;SPIDR,missense_variant,p.Ser138Gly,ENST00000524033,;SPIDR,3_prime_UTR_variant,,ENST00000522117,;SPIDR,non_coding_transcript_exon_variant,,ENST00000524141,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521798,;SPIDR,intron_variant,,ENST00000517824,;SPIDR,intron_variant,,ENST00000523814,;SPIDR,intron_variant,,ENST00000522222,; G ENST00000297423 Transcript missense_variant 796/3988 412/2748 138/915 S/G Agt/Ggt 1 1 SPIDR HGNC HGNC:28971 protein_coding YES CCDS43737.1 ENSP00000297423 Q14159 UPI0000253B92 NM_001080394.3 tolerated(0.59) 5/20 Pfam_domain:PF14950,hmmpanther:PTHR34347,hmmpanther:PTHR34347:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 47293917 47293917 A G 1 0 0 0 0 1 0 0 0 15404 420 15 5 5 SPIDR 8 47293917 Missense_Mutation SNP A C3L-02345_T 39955624 47293917 97844719 107 8705 VCPIP1 0 . GRCh38 8 66665460 66665460 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1499G>T p.Gly500Val p.G500V ENST00000310421 1/3 138 107 31 168 168 0 strelka-varscan-mutect VCPIP1,missense_variant,p.Gly500Val,ENST00000310421,NM_025054.4;C8orf44-SGK3,upstream_gene_variant,,ENST00000519289,NM_001204173.1;C8orf44,upstream_gene_variant,,ENST00000519561,NM_019607.2;C8orf44,upstream_gene_variant,,ENST00000521889,;C8orf44-SGK3,upstream_gene_variant,,ENST00000520044,;C8orf44,upstream_gene_variant,,ENST00000521113,; A ENST00000310421 Transcript missense_variant 1758/9942 1499/3669 500/1222 G/V gGa/gTa 1 -1 VCPIP1 HGNC HGNC:30897 protein_coding YES CCDS6192.1 ENSP00000309031 Q96JH7 UPI00001D3EF3 NM_025054.4 deleterious(0.05) 1/3 hmmpanther:PTHR14843,hmmpanther:PTHR14843:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 66665460 66665460 C A 1 0 0 0 0 1 0 0 0 17686 855 30 2 2 VCPIP1 8 66665460 Missense_Mutation SNP C C3L-02345_T 19371543 66665460 78473176 108 8706 RALYL 0 . GRCh38 8 84529368 84529368 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.86C>A p.Pro29His p.P29H ENST00000517638 2/9 300 223 77 347 346 1 strelka-varscan-mutect RALYL,missense_variant,p.Pro16His,ENST00000521268,NM_173848.5;RALYL,missense_variant,p.Pro16His,ENST00000518566,NM_001287243.1;RALYL,missense_variant,p.Pro16His,ENST00000522455,NM_001100392.1;RALYL,missense_variant,p.Pro29His,ENST00000517638,NM_001100391.1;RALYL,missense_variant,p.Pro16His,ENST00000521695,NM_001100393.1;RALYL,missense_variant,p.Pro16His,ENST00000522613,;RALYL,missense_variant,p.Pro16His,ENST00000517988,;RALYL,missense_variant,p.Pro16His,ENST00000522647,; A ENST00000517638 Transcript missense_variant 210/1972 86/915 29/304 P/H cCc/cAc 1 1 RALYL HGNC HGNC:27036 protein_coding YES CCDS55252.1 ENSP00000430128 Q86SE5 UPI00002108E6 NM_001100391.1 deleterious(0.01) 2/9 hmmpanther:PTHR13968:SF21,hmmpanther:PTHR13968,Gene3D:3.30.70.330,PIRSF_domain:PIRSF037992,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 84529368 84529368 C A 1 0 0 0 0 1 0 0 0 13179 623 22 2 2 RALYL 8 84529368 Missense_Mutation SNP C C3L-02345_T 17863908 84529368 60609268 109 8707 VPS13B 0 . GRCh38 8 99121433 99121433 + Silent SNP G G T C3L-02345_T C3L-02345_N G G c.1194G>T p.= p.T398T ENST00000358544 8/62 125 98 27 127 127 0 strelka-varscan-mutect VPS13B,synonymous_variant,p.=,ENST00000358544,NM_017890.4;VPS13B,synonymous_variant,p.=,ENST00000357162,NM_152564.4;VPS13B,synonymous_variant,p.=,ENST00000355155,NM_015243.2;VPS13B,synonymous_variant,p.=,ENST00000441350,NM_181661.2;CTD-2340D6.1,downstream_gene_variant,,ENST00000523226,;VPS13B,downstream_gene_variant,,ENST00000524330,;VPS13B,synonymous_variant,p.=,ENST00000496144,; T ENST00000358544 Transcript synonymous_variant 1305/14094 1194/12069 398/4022 T acG/acT COSM5004317,COSM5004318,COSM5004319,COSM5004320 1 1 VPS13B HGNC HGNC:2183 protein_coding YES CCDS6280.1 ENSP00000351346 Q7Z7G8 UPI00001D2D35 NM_017890.4 8/62 hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 99121433 99121433 G T 1 0 0 0 0 0 0 0 1 17737 1103 39 1 1 VPS13B 8 99121433 Silent SNP G C3L-02345_T 14592065 99121433 46017203 110 8708 CSMD3 0 . GRCh38 8 112921636 112921636 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.1624G>T p.Val542Leu p.V542L ENST00000297405 10/71 358 292 66 379 379 0 strelka-varscan-mutect CSMD3,missense_variant,p.Val542Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Val502Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Val438Leu,ENST00000455883,NM_052900.2; A ENST00000297405 Transcript missense_variant 1869/13212 1624/11124 542/3707 V/L Gtg/Ttg COSM5666177,COSM5666178 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.16) 10/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1407449531 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 112921636 112921636 C A 1 0 0 0 0 1 0 0 0 3747 478 17 2 2 CSMD3 8 112921636 Missense_Mutation SNP C C3L-02345_T 13800203 112921636 32217000 111 8709 KHDRBS3 0 . GRCh38 8 135557552 135557552 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.576G>T p.Leu192Phe p.L192F ENST00000355849 5/9 232 176 56 249 249 0 strelka-varscan-mutect KHDRBS3,missense_variant,p.Leu192Phe,ENST00000355849,NM_006558.2;KHDRBS3,missense_variant,p.Leu164Phe,ENST00000524199,;KHDRBS3,missense_variant,p.Leu107Phe,ENST00000524282,;KHDRBS3,intron_variant,,ENST00000520981,;KHDRBS3,downstream_gene_variant,,ENST00000517394,;KHDRBS3,non_coding_transcript_exon_variant,,ENST00000522079,;KHDRBS3,missense_variant,p.Leu117Phe,ENST00000517859,; T ENST00000355849 Transcript missense_variant 986/1977 576/1041 192/346 L/F ttG/ttT 1 1 KHDRBS3 HGNC HGNC:18117 protein_coding YES CCDS6374.1 ENSP00000348108 O75525 UPI0000073E6F NM_006558.2 tolerated(0.7) 5/9 hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF29 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 135557552 135557552 G T 1 0 0 0 0 1 0 0 0 8069 1310 46 2 2 KHDRBS3 8 135557552 Missense_Mutation SNP G C3L-02345_T 22635916 135557552 9581084 112 8710 SCRIB 0 . GRCh38 8 143812875 143812875 + Silent SNP C C G novel C3L-02345_T C3L-02345_N C C c.729G>C p.= p.V243V ENST00000356994 8/37 154 125 29 150 150 0 strelka-varscan-mutect SCRIB,synonymous_variant,p.=,ENST00000356994,NM_182706.4;SCRIB,synonymous_variant,p.=,ENST00000320476,NM_015356.4;SCRIB,synonymous_variant,p.=,ENST00000377533,;PUF60,downstream_gene_variant,,ENST00000526683,NM_001271098.1,NM_078480.2;PUF60,downstream_gene_variant,,ENST00000453551,NM_001136033.2;PUF60,downstream_gene_variant,,ENST00000349157,NM_014281.4,NM_001271096.1;PUF60,downstream_gene_variant,,ENST00000313352,NM_001271100.1;PUF60,downstream_gene_variant,,ENST00000456095,NM_001271099.1;PUF60,downstream_gene_variant,,ENST00000527197,NM_001271097.1;PUF60,downstream_gene_variant,,ENST00000527744,;PUF60,downstream_gene_variant,,ENST00000526459,;PUF60,downstream_gene_variant,,ENST00000532884,;SCRIB,upstream_gene_variant,,ENST00000531942,;SCRIB,downstream_gene_variant,,ENST00000401271,;PUF60,downstream_gene_variant,,ENST00000524570,;PUF60,downstream_gene_variant,,ENST00000531951,; G ENST00000356994 Transcript synonymous_variant 736/5218 729/4968 243/1655 V gtG/gtC 1 -1 SCRIB HGNC HGNC:30377 protein_coding YES CCDS6412.1 ENSP00000349486 Q14160 UPI000232E1C0 NM_182706.4 8/37 Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 LOW SNV 2 1 PASS rs1245907254 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 31 143812875 143812875 C G 1 0 0 0 0 0 0 0 1 14207 697 25 4 4 SCRIB 8 143812875 Silent SNP C C3L-02345_T 8255323 143812875 1325761 113 8711 DMRTA1 0 . GRCh38 9 22451676 22451676 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1280G>A p.Gly427Asp p.G427D ENST00000325870 2/2 251 223 28 361 361 0 strelka-varscan-mutect DMRTA1,missense_variant,p.Gly427Asp,ENST00000325870,NM_022160.2; A ENST00000325870 Transcript missense_variant 1505/5569 1280/1515 427/504 G/D gGc/gAc 1 1 DMRTA1 HGNC HGNC:13826 protein_coding YES CCDS6514.1 ENSP00000319651 Q5VZB9 UPI000014178A NM_022160.2 tolerated(0.24) 2/2 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF71 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 22451676 22451676 G A 1 0 0 0 0 1 0 0 0 4395 1203 42 3 3 DMRTA1 9 22451676 Missense_Mutation SNP G C3L-02345_T 22451676 115943041 114 8712 SPATA31A1 0 . GRCh38 9 39359058 39359058 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.1335C>A p.= p.A445A ENST00000377647 4/4 139 115 24 229 227 2 strelka-varscan-mutect SPATA31A1,synonymous_variant,p.=,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript synonymous_variant 1355/4256 1335/4086 445/1361 A gcC/gcA 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF14650 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 39359058 39359058 C A 1 0 0 0 0 0 0 0 1 15343 668 24 2 2 SPATA31A1 9 39359058 Silent SNP C C3L-02345_T 16907382 39359058 99035659 115 8713 TRPM6 0 . GRCh38 9 74752295 74752295 + Nonsense_Mutation SNP G G T rs750345449 C3L-02345_T C3L-02345_N G G c.4980C>A p.Tyr1660Ter p.Y1660* ENST00000360774 29/39 176 165 11 225 225 0 strelka-varscan-mutect TRPM6,stop_gained,p.Tyr1660Ter,ENST00000360774,NM_017662.4;TRPM6,stop_gained,p.Tyr1655Ter,ENST00000361255,NM_001177311.1;TRPM6,stop_gained,p.Tyr1655Ter,ENST00000449912,NM_001177310.1; T ENST00000360774 Transcript stop_gained 5218/8425 4980/6069 1660/2022 Y/* taC/taA rs750345449 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 29/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 HIGH 1 SNV 1 1 PASS rs750345449 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 74752295 74752295 G T 1 0 0 0 0 0 1 0 0 17096 1256 44 2 2 TRPM6 9 74752295 Nonsense_Mutation SNP G C3L-02345_T 35393237 74752295 63642422 116 8714 TRPM6 0 . GRCh38 9 74775938 74775938 + Silent SNP G G A novel C3L-02345_T C3L-02345_N G G c.3348C>T p.= p.R1116R ENST00000360774 24/39 210 197 13 306 306 0 strelka-varscan-mutect TRPM6,synonymous_variant,p.=,ENST00000360774,NM_017662.4;TRPM6,synonymous_variant,p.=,ENST00000361255,NM_001177311.1;TRPM6,synonymous_variant,p.=,ENST00000449912,NM_001177310.1; A ENST00000360774 Transcript synonymous_variant 3586/8425 3348/6069 1116/2022 R cgC/cgT 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 24/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 74775938 74775938 G A 1 0 0 0 0 0 0 0 1 17096 1190 42 3 3 TRPM6 9 74775938 Silent SNP G C3L-02345_T 23643 74775938 63618779 117 8715 AGTPBP1 0 . GRCh38 9 85657491 85657491 + Nonsense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1009G>T p.Gly337Ter p.G337* ENST00000337006 9/25 193 181 12 309 307 2 strelka-mutect AGTPBP1,stop_gained,p.Gly337Ter,ENST00000337006,NM_001286715.1;AGTPBP1,stop_gained,p.Gly285Ter,ENST00000357081,;AGTPBP1,stop_gained,p.Gly337Ter,ENST00000628899,NM_001286717.1;AGTPBP1,stop_gained,p.Gly285Ter,ENST00000376083,NM_015239.2;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000491784,;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000376080,;AGTPBP1,intron_variant,,ENST00000376081,; A ENST00000337006 Transcript stop_gained 1076/4473 1009/3837 337/1278 G/* Gga/Tga 1 -1 AGTPBP1 HGNC HGNC:17258 protein_coding YES CCDS75854.1 ENSP00000338512 J3KNS1 UPI000387D56E NM_001286715.1 9/25 hmmpanther:PTHR12756:SF24,hmmpanther:PTHR12756,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 85657491 85657491 C A 1 0 0 0 0 0 1 0 0 479 632 22 2 2 AGTPBP1 9 85657491 Nonsense_Mutation SNP C C3L-02345_T 10881553 85657491 52737226 118 8716 WNK2 0 . GRCh38 9 93261891 93261891 + Silent SNP G G T rs756092305 C3L-02345_T C3L-02345_N G G c.3144G>T p.= p.A1048A ENST00000297954 12/30 127 99 28 171 171 0 strelka-varscan-mutect WNK2,synonymous_variant,p.=,ENST00000432730,;WNK2,synonymous_variant,p.=,ENST00000297954,NM_001282394.1;WNK2,synonymous_variant,p.=,ENST00000395477,NM_006648.3;WNK2,synonymous_variant,p.=,ENST00000411624,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000448251,;WNK2,downstream_gene_variant,,ENST00000448039,;WNK2,downstream_gene_variant,,ENST00000464625,;WNK2,upstream_gene_variant,,ENST00000478583,; T ENST00000297954 Transcript synonymous_variant 3144/7138 3144/6894 1048/2297 A gcG/gcT rs756092305 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 12/30 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs756092305 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 93261891 93261891 G T 1 0 0 0 0 0 0 0 1 17934 1103 39 1 1 WNK2 9 93261891 Silent SNP G C3L-02345_T 7604400 93261891 45132826 119 8717 PTCH1 0 . GRCh38 9 95476034 95476034 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1728G>T p.Gln576His p.Q576H ENST00000331920 12/24 367 339 28 488 488 0 strelka-varscan-mutect PTCH1,missense_variant,p.Gln510His,ENST00000430669,;PTCH1,missense_variant,p.Gln576His,ENST00000331920,NM_000264.3;PTCH1,missense_variant,p.Gln510His,ENST00000437951,NM_001083602.1;PTCH1,missense_variant,p.Gln425His,ENST00000418258,NM_001083607.1;PTCH1,missense_variant,p.Gln425His,ENST00000421141,NM_001083604.1,NM_001083605.1;PTCH1,missense_variant,p.Gln425His,ENST00000429896,NM_001083606.1;PTCH1,missense_variant,p.Gln575His,ENST00000375274,NM_001083603.1;PTCH1,missense_variant,p.Gln241His,ENST00000375271,;PTCH1,downstream_gene_variant,,ENST00000553011,;PTCH1,downstream_gene_variant,,ENST00000547672,;PTCH1,downstream_gene_variant,,ENST00000546820,;PTCH1,downstream_gene_variant,,ENST00000551845,;PTCH1,downstream_gene_variant,,ENST00000548420,;PTCH1,downstream_gene_variant,,ENST00000548379,;PTCH1,downstream_gene_variant,,ENST00000553256,;PTCH1,downstream_gene_variant,,ENST00000548945,;PTCH1,missense_variant,p.Gln455His,ENST00000375290,;PTCH1,downstream_gene_variant,,ENST00000550914,;PTCH1,downstream_gene_variant,,ENST00000488809,; A ENST00000331920 Transcript missense_variant,splice_region_variant 2028/8057 1728/4344 576/1447 Q/H caG/caT 1 -1 PTCH1 HGNC HGNC:9585 protein_coding YES CCDS6714.1 ENSP00000332353 Q13635 UPI00001AFF9C NM_000264.3 deleterious(0.01) 12/24 Gene3D:2j8sB01,Pfam_domain:PF02460,PROSITE_profiles:PS50156,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF61,Superfamily_domains:SSF82866,TIGRFAM_domain:TIGR00918,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 95476034 95476034 C A 1 0 0 0 0 1 0 0 0 12883 695 24 2 2 PTCH1 9 95476034 Missense_Mutation SNP C C3L-02345_T 2214143 95476034 42918683 120 8718 CYLC2 0 . GRCh38 9 103005349 103005349 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.718G>A p.Asp240Asn p.D240N ENST00000374798 5/8 200 186 14 273 273 0 strelka-varscan-mutect CYLC2,missense_variant,p.Asp240Asn,ENST00000374798,NM_001340.4;CYLC2,missense_variant,p.Asp240Asn,ENST00000487798,;CYLC2,missense_variant,p.Asp240Asn,ENST00000612124,; A ENST00000374798 Transcript missense_variant 788/2171 718/1047 240/348 D/N Gat/Aat 1 1 CYLC2 HGNC HGNC:2583 protein_coding YES CCDS35085.1 ENSP00000420256 Q14093 A0A024R146 UPI0000128C36 NM_001340.4 tolerated(0.18) 5/8 hmmpanther:PTHR16742,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 103005349 103005349 G A 1 0 0 0 0 1 0 0 0 3945 942 33 3 3 CYLC2 9 103005349 Missense_Mutation SNP G C3L-02345_T 7529315 103005349 35389368 121 8719 SMC2 0 . GRCh38 9 104096239 104096239 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.260A>T p.Asp87Val p.D87V ENST00000286398 3/25 135 128 7 179 178 1 strelka-varscan-mutect SMC2,missense_variant,p.Asp87Val,ENST00000286398,NM_001042551.1,NM_006444.2,NM_001265602.1;SMC2,missense_variant,p.Asp87Val,ENST00000374793,;SMC2,missense_variant,p.Asp87Val,ENST00000374787,NM_001042550.1;SMC2,intron_variant,,ENST00000440179,;SMC2-AS1,upstream_gene_variant,,ENST00000603487,;SMC2-AS1,upstream_gene_variant,,ENST00000603949,; T ENST00000286398 Transcript missense_variant 564/5992 260/3594 87/1197 D/V gAc/gTc 1 1 SMC2 HGNC HGNC:14011 protein_coding YES CCDS35086.1 ENSP00000286398 O95347 A0A024R158 UPI000013DE44 NM_001042551.1,NM_006444.2,NM_001265602.1 deleterious(0) 3/25 Gene3D:3.40.50.300,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF9,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1202967392 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 104096239 104096239 A T 1 0 0 0 0 1 0 0 0 15076 275 10 4 4 SMC2 9 104096239 Missense_Mutation SNP A C3L-02345_T 1090890 104096239 34298478 122 8720 OR1L6 0 . GRCh38 9 122750599 122750599 + Frame_Shift_Del DEL T T - novel C3L-02345_T C3L-02345_N T T c.755delT p.Phe252SerfsTer23 p.F252Sfs*23 ENST00000304720 1/1 123 97 26 167 167 0 sindel-varindel-pindel OR1L6,frameshift_variant,p.Phe288SerfsTer23,ENST00000373684,;OR1L6,frameshift_variant,p.Phe252SerfsTer23,ENST00000304720,NM_001004453.2; - ENST00000304720 Transcript frameshift_variant 752/936 752/936 251/311 L/X cTt/ct 1 1 OR1L6 HGNC HGNC:8218 protein_coding YES CCDS35130.2 ENSP00000304235 A0A0C4DFP2 UPI000003CAAE NM_001004453.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF342,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 deletion 3 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 122750599 122750599 T - 1 0 1 0 1 0 0 0 0 11044 1609 56 0 0 OR1L6 9 122750599 Frame_Shift_Del DEL T C3L-02345_T 18654360 122750599 15644118 123 8721 CRB2 0 . GRCh38 9 123366091 123366091 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.593C>G p.Thr198Arg p.T198R ENST00000373631 3/13 47 43 4 69 69 0 strelka-varscan-mutect CRB2,missense_variant,p.Thr198Arg,ENST00000373631,NM_173689.6;CRB2,missense_variant,p.Thr198Arg,ENST00000359999,;CRB2,upstream_gene_variant,,ENST00000460253,; G ENST00000373631 Transcript missense_variant 594/5550 593/3858 198/1285 T/R aCg/aGg 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 tolerated(0.3) 3/13 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1168773901 . 0 199 9 2 0 0 0 0 -8.442008 0.9986497 1 1 1 0 G 3 3 31 123366091 123366091 C G 1 0 0 0 0 1 0 0 0 3649 536 19 4 4 CRB2 9 123366091 Missense_Mutation SNP C C3L-02345_T 615492 123366091 15028626 124 8722 ENTPD8 0 . GRCh38 9 137438064 137438064 + Silent SNP C C A rs531135716 C3L-02345_T C3L-02345_N C C c.147G>T p.= p.A49A ENST00000371506 3/10 103 80 23 110 110 0 strelka-varscan-mutect ENTPD8,synonymous_variant,p.=,ENST00000371506,NM_001033113.1;ENTPD8,synonymous_variant,p.=,ENST00000344119,NM_198585.2;ENTPD8,synonymous_variant,p.=,ENST00000472938,;ENTPD8,synonymous_variant,p.=,ENST00000493135,;NOXA1,downstream_gene_variant,,ENST00000341349,NM_001256067.1,NM_006647.1;NOXA1,downstream_gene_variant,,ENST00000392815,NM_001256068.1;ENTPD8,non_coding_transcript_exon_variant,,ENST00000461823,; A ENST00000371506 Transcript synonymous_variant 331/2222 147/1488 49/495 A gcG/gcT rs531135716,COSM3375186,COSM3375187,COSM3656026,COSM3656027 1 -1 ENTPD8 HGNC HGNC:24860 protein_coding YES CCDS43913.1 ENSP00000360561 Q5MY95 UPI0000D6195D NM_001033113.1 3/10 Pfam_domain:PF01150,hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF31 0,1,1,1,1 LOW SNV 5 0,1,1,1,1 1 PASS rs531135716 . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 31 137438064 137438064 C A 1 0 0 0 0 0 0 0 1 4990 639 23 1 1 ENTPD8 9 137438064 Silent SNP C C3L-02345_T 14071973 137438064 956653 125 8723 MRC1 0 . GRCh38 10 17881162 17881162 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.2961A>G p.Ile987Met p.I987M ENST00000569591 21/30 322 263 59 333 333 0 strelka-mutect MRC1,missense_variant,p.Ile987Met,ENST00000569591,NM_002438.3; G ENST00000569591 Transcript missense_variant 3083/5198 2961/4371 987/1456 I/M atA/atG 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 deleterious(0) 21/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 17881162 17881162 A G 1 0 0 0 0 1 0 0 0 9722 381 14 5 5 MRC1 10 17881162 Missense_Mutation SNP A C3L-02345_T 17881162 115916260 126 8724 ZNF33B 0 . GRCh38 10 42593333 42593333 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.1617C>G p.Asp539Glu p.D539E ENST00000359467 5/5 200 155 45 278 278 0 strelka-varscan-mutect ZNF33B,missense_variant,p.Asp539Glu,ENST00000359467,NM_001305036.1,NM_001305033.1,NM_006955.1;ZNF33B,missense_variant,p.Asp539Glu,ENST00000613419,;ZNF33B,intron_variant,,ENST00000465206,;ZNF33B,intron_variant,,ENST00000462075,;ZNF33B,intron_variant,,ENST00000486187,; C ENST00000359467 Transcript missense_variant 1732/5958 1617/2337 539/778 D/E gaC/gaG 1 -1 ZNF33B HGNC HGNC:13097 protein_coding YES CCDS7198.1 ENSP00000352444 Q06732 UPI000007257B NM_001305036.1,NM_001305033.1,NM_006955.1 tolerated(0.28) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF204,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 42593333 42593333 G C 1 0 0 0 0 1 0 0 0 18427 1252 44 4 4 ZNF33B 10 42593333 Missense_Mutation SNP G C3L-02345_T 24712171 42593333 91204089 127 8725 FRMPD2 0 . GRCh38 10 48236546 48236546 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.929G>T p.Arg310Met p.R310M ENST00000374201 9/29 176 152 24 224 223 1 strelka-varscan-mutect FRMPD2,missense_variant,p.Arg310Met,ENST00000374201,NM_001018071.3;FRMPD2,missense_variant,p.Arg286Met,ENST00000305531,NM_001318191.1;FRMPD2,missense_variant,p.Arg310Met,ENST00000636244,;FRMPD2,3_prime_UTR_variant,,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,; A ENST00000374201 Transcript missense_variant 1232/4997 929/3930 310/1309 R/M aGg/aTg 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 tolerated(0.06) 9/29 hmmpanther:PTHR19964:SF42,hmmpanther:PTHR19964 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 31 48236546 48236546 C A 1 0 0 0 0 1 0 0 0 5928 681 24 2 2 FRMPD2 10 48236546 Missense_Mutation SNP C C3L-02345_T 5643213 48236546 85560876 128 8726 DNA2 0 . GRCh38 10 68470121 68470121 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.117G>T p.= p.L39L ENST00000358410 2/21 209 162 47 180 179 1 strelka-varscan-mutect DNA2,synonymous_variant,p.=,ENST00000358410,NM_001080449.2;DNA2,synonymous_variant,p.=,ENST00000551118,;DNA2,synonymous_variant,p.=,ENST00000399180,;DNA2,synonymous_variant,p.=,ENST00000399179,;DNA2,3_prime_UTR_variant,,ENST00000550357,; A ENST00000358410 Transcript synonymous_variant 168/4208 117/3183 39/1060 L ctG/ctT 1 -1 DNA2 HGNC HGNC:2939 protein_coding YES CCDS44415.2 ENSP00000351185 P51530 UPI00001C1EDB NM_001080449.2 2/21 hmmpanther:PTHR10887:SF14,hmmpanther:PTHR10887 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 68470121 68470121 C A 1 0 0 0 0 0 0 0 1 4405 813 29 2 2 DNA2 10 68470121 Silent SNP C C3L-02345_T 20233575 68470121 65327301 129 8727 RGR 0 . GRCh38 10 84253003 84253003 + Missense_Mutation SNP G G A C3L-02345_T C3L-02345_N G G c.517G>A p.Gly173Arg p.G173R ENST00000359452 4/7 155 129 26 181 181 0 strelka-varscan-mutect RGR,missense_variant,p.Gly173Arg,ENST00000359452,NM_002921.3,NM_001012720.1;RGR,missense_variant,p.Gly169Arg,ENST00000358110,NM_001012722.1;RGR,downstream_gene_variant,,ENST00000372092,;RGR,non_coding_transcript_exon_variant,,ENST00000478727,;RGR,non_coding_transcript_exon_variant,,ENST00000483660,;RGR,non_coding_transcript_exon_variant,,ENST00000497161,;RGR,non_coding_transcript_exon_variant,,ENST00000483744,;RGR,upstream_gene_variant,,ENST00000479725,;RGR,non_coding_transcript_exon_variant,,ENST00000483771,; A ENST00000359452 Transcript missense_variant 555/2247 517/888 173/295 G/R Ggg/Agg COSM3441123 1 1 RGR HGNC HGNC:9990 protein_coding YES CCDS7374.1 ENSP00000352427 P47804 A0A0S2Z498 UPI0000072293 NM_002921.3,NM_001012720.1 tolerated(0.05) 4/7 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00667,PROSITE_profiles:PS50262,hmmpanther:PTHR24240,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 1 PASS rs1173272937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 84253003 84253003 G A 1 0 0 0 0 1 0 0 0 13462 1232 43 3 3 RGR 10 84253003 Missense_Mutation SNP G C3L-02345_T 15782882 84253003 49544419 130 8728 NUTM2A 0 . GRCh38 10 87228638 87228638 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.758C>G p.Pro253Arg p.P253R ENST00000381707 2/7 62 55 7 101 101 0 varscan-mutect NUTM2A,missense_variant,p.Pro253Arg,ENST00000381689,;NUTM2A,missense_variant,p.Pro253Arg,ENST00000381707,NM_001099338.1;NUTM2A-AS1,intron_variant,,ENST00000451940,; G ENST00000381707 Transcript missense_variant 1141/3290 758/2637 253/878 P/R cCt/cGt 1 1 NUTM2A HGNC HGNC:23438 protein_coding YES CCDS44452.1 ENSP00000371126 Q8IVF1 UPI00001B6532 NM_001099338.1 tolerated(0.21) 2/7 Pfam_domain:PF12881,hmmpanther:PTHR22879,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.27822 1 1 1 1 0 G 3 3 31 87228638 87228638 C G 1 0 0 0 0 1 0 0 0 10847 681 24 4 4 NUTM2A 10 87228638 Missense_Mutation SNP C C3L-02345_T 2975635 87228638 46568784 131 8729 PNLIP 0 . GRCh38 10 116546106 116546106 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.14G>C p.Trp5Ser p.W5S ENST00000369221 2/13 185 157 28 214 214 0 strelka-varscan-mutect PNLIP,missense_variant,p.Trp5Ser,ENST00000369221,NM_000936.2;PNLIP,non_coding_transcript_exon_variant,,ENST00000470562,; C ENST00000369221 Transcript missense_variant 42/1483 14/1398 5/465 W/S tGg/tCg 1 1 PNLIP HGNC HGNC:9155 protein_coding YES CCDS7594.1 ENSP00000358223 P16233 UPI000004F1A0 NM_000936.2 deleterious(0) 2/13 PIRSF_domain:PIRSF000865,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 116546106 116546106 G C 1 0 0 0 0 1 0 0 0 12257 1357 47 4 4 PNLIP 10 116546106 Missense_Mutation SNP G C3L-02345_T 29317468 116546106 17251316 132 8730 CPXM2 0 . GRCh38 10 123862655 123862655 + Missense_Mutation SNP G G T rs761486980 C3L-02345_T C3L-02345_N G G c.472C>A p.Arg158Ser p.R158S ENST00000241305 3/14 336 290 46 351 351 0 strelka-varscan-mutect CPXM2,missense_variant,p.Arg158Ser,ENST00000241305,NM_198148.2;CPXM2,5_prime_UTR_variant,,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; T ENST00000241305 Transcript missense_variant 627/3554 472/2271 158/756 R/S Cgc/Agc rs761486980 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 tolerated(0.17) 3/14 PROSITE_profiles:PS50022,hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS rs761486980 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 123862655 123862655 G T 1 0 0 0 0 1 0 0 0 3636 1087 38 1 1 CPXM2 10 123862655 Missense_Mutation SNP G C3L-02345_T 7316549 123862655 9934767 133 8731 OR52N4 0 . GRCh38 11 5754881 5754881 + Silent SNP C C T novel C3L-02345_T C3L-02345_N C C c.141C>T p.= p.L47L ENST00000317254 1/1 317 252 65 345 345 0 strelka-varscan-mutect OR52N4,synonymous_variant,p.=,ENST00000317254,NM_001005175.3;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000317254 Transcript synonymous_variant 189/1037 141/966 47/321 L ctC/ctT 1 1 OR52N4 HGNC HGNC:15230 protein_coding YES CCDS44528.1 ENSP00000323224 Q8NGI2 UPI00001AF18B NM_001005175.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF74,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 5754881 5754881 C T 1 0 0 0 0 0 0 0 1 11202 842 30 3 3 OR52N4 11 5754881 Silent SNP C C3L-02345_T 5754881 129331741 134 8732 ARNTL 0 . GRCh38 11 13374126 13374126 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1099G>A p.Glu367Lys p.E367K ENST00000403290 14/20 225 184 41 241 240 1 strelka-varscan-mutect ARNTL,missense_variant,p.Glu324Lys,ENST00000401424,NM_001297724.1;ARNTL,missense_variant,p.Glu366Lys,ENST00000389707,NM_001030272.2,NM_001178.5;ARNTL,missense_variant,p.Glu367Lys,ENST00000403290,NM_001297722.1,NM_001297719.1;ARNTL,missense_variant,p.Glu323Lys,ENST00000403510,NM_001030273.2;ARNTL,missense_variant,p.Glu365Lys,ENST00000403482,;ARNTL,downstream_gene_variant,,ENST00000497429,;ARNTL,missense_variant,p.Glu12Lys,ENST00000524392,;ARNTL,non_coding_transcript_exon_variant,,ENST00000529390,;ARNTL,upstream_gene_variant,,ENST00000472842,;ARNTL,downstream_gene_variant,,ENST00000534102,; A ENST00000403290 Transcript missense_variant 1454/2746 1099/1881 367/626 E/K Gaa/Aaa 1 1 ARNTL HGNC HGNC:701 protein_coding YES CCDS73259.1 ENSP00000384517 O00327 UPI000002A4E9 NM_001297722.1,NM_001297719.1 deleterious(0) 14/20 Gene3D:3.30.450.20,Pfam_domain:PF14598,PROSITE_profiles:PS50112,hmmpanther:PTHR23042,hmmpanther:PTHR23042:SF52,SMART_domains:SM00091,Superfamily_domains:SSF55785,TIGRFAM_domain:TIGR00229 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 13374126 13374126 G A 1 0 0 0 0 1 0 0 0 1109 943 33 3 3 ARNTL 11 13374126 Missense_Mutation SNP G C3L-02345_T 7619245 13374126 121712496 135 8733 C1QTNF4 0 . GRCh38 11 47590479 47590479 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.332G>T p.Arg111Leu p.R111L ENST00000302514 2/2 78 57 21 79 79 0 strelka-varscan-mutect C1QTNF4,missense_variant,p.Arg111Leu,ENST00000302514,NM_031909.2;C1QTNF4,intron_variant,,ENST00000530097,;FAM180B,downstream_gene_variant,,ENST00000538490,NM_001164379.1; A ENST00000302514 Transcript missense_variant 849/1664 332/990 111/329 R/L cGg/cTg 1 -1 C1QTNF4 HGNC HGNC:14346 protein_coding YES CCDS7942.1 ENSP00000302274 Q9BXJ3 UPI00000746B6 NM_031909.2 deleterious(0.02) 2/2 Gene3D:2.60.120.40,Pfam_domain:PF00386,PROSITE_profiles:PS50871,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF551,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 47590479 47590479 C A 1 0 0 0 0 1 0 0 0 1943 652 23 1 1 C1QTNF4 11 47590479 Missense_Mutation SNP C C3L-02345_T 34216353 47590479 87496143 136 8734 OR4P4 0 . GRCh38 11 55638837 55638837 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.480C>A p.= p.L160L ENST00000314612 1/1 89 49 40 118 118 0 strelka-varscan-mutect OR4P4,synonymous_variant,p.=,ENST00000314612,NM_001004124.2; A ENST00000314612 Transcript synonymous_variant 480/939 480/939 160/312 L ctC/ctA 1 1 OR4P4 HGNC HGNC:15180 protein_coding YES CCDS31504.1 ENSP00000324831 Q8NGL7 UPI0000061E8A NM_001004124.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF386,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 23 184 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 55638837 55638837 C A 1 0 0 0 0 0 0 0 1 11156 813 29 2 2 OR4P4 11 55638837 Silent SNP C C3L-02345_T 8048358 55638837 79447785 137 8735 OR8H3 0 . GRCh38 11 56123309 56123309 + Nonstop_Mutation SNP T T A rs773933096 C3L-02345_T C3L-02345_N T T c.937T>A p.Ter313LysextTer? p.*313Kext*? ENST00000313472 1/1 47 38 9 61 61 0 strelka-varscan-mutect OR8H3,stop_lost,p.Ter313LysextTer?,ENST00000313472,NM_001005201.1; A ENST00000313472 Transcript stop_lost 937/939 937/939 313/312 */K Tag/Aag rs773933096 1 1 OR8H3 HGNC HGNC:15309 protein_coding YES CCDS31519.1 ENSP00000323928 Q8N146 UPI0000041D25 NM_001005201.1 1/1 HIGH 1 SNV 1 PASS rs773933096 . 1 207 2 0 0 0 0 0 -19.99739 1 1 1 1 0 A 4 1 31 56123309 56123309 T A 1 0 0 0 0 0 0 0 0 11307 1652 57 4 4 OR8H3 11 56123309 Nonstop_Mutation SNP T C3L-02345_T 484472 56123309 78963313 138 8736 OR5B3 0 . GRCh38 11 58403349 58403349 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.61C>A p.Leu21Met p.L21M ENST00000309403 1/1 56 47 9 70 70 0 strelka-varscan-mutect OR5B3,missense_variant,p.Leu21Met,ENST00000309403,NM_001005469.1; T ENST00000309403 Transcript missense_variant 61/946 61/945 21/314 L/M Ctg/Atg 1 -1 OR5B3 HGNC HGNC:8324 protein_coding YES CCDS31549.1 ENSP00000308270 Q8NH48 A0A126GVH3 UPI0000041DD0 NM_001005469.1 deleterious_low_confidence(0.02) 1/1 hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF336,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -19.95147 0.9999999 1 1 1 0 T 3 4 31 58403349 58403349 G T 1 0 0 0 0 1 0 0 0 11223 1020 36 2 2 OR5B3 11 58403349 Missense_Mutation SNP G C3L-02345_T 2280040 58403349 76683273 139 8737 TMEM132A 0 . GRCh38 11 60927741 60927741 + Missense_Mutation SNP C C A C3L-02345_T C3L-02345_N C C c.416C>A p.Ala139Asp p.A139D ENST00000005286 3/11 278 217 61 276 276 0 strelka-varscan-mutect TMEM132A,missense_variant,p.Ala139Asp,ENST00000005286,NM_017870.3;TMEM132A,missense_variant,p.Ala139Asp,ENST00000453848,NM_178031.2;TMEM132A,5_prime_UTR_variant,,ENST00000544065,;TMEM109,downstream_gene_variant,,ENST00000227525,NM_024092.2;TMEM109,downstream_gene_variant,,ENST00000536171,;TMEM132A,upstream_gene_variant,,ENST00000536409,;RP11-881M11.4,upstream_gene_variant,,ENST00000543907,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000540276,;TMEM132A,downstream_gene_variant,,ENST00000543732,;TMEM109,downstream_gene_variant,,ENST00000540280,;TMEM132A,downstream_gene_variant,,ENST00000537110,;TMEM132A,downstream_gene_variant,,ENST00000537065,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000544098,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000534983,; A ENST00000005286 Transcript missense_variant 569/3480 416/3075 139/1024 A/D gCc/gAc COSM4734248,COSM4734249 1 1 TMEM132A HGNC HGNC:31092 protein_coding YES CCDS7997.1 ENSP00000005286 Q24JP5 UPI0000190977 NM_017870.3 deleterious(0.01) 3/11 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF9,Pfam_domain:PF15705 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 60927741 60927741 C A 1 0 0 0 0 1 0 0 0 16489 739 26 2 2 TMEM132A 11 60927741 Missense_Mutation SNP C C3L-02345_T 2524392 60927741 74158881 140 8738 B3GNT6 0 . GRCh38 11 77040109 77040109 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.558G>T p.= p.L186L ENST00000622824 2/2 201 159 42 201 200 1 strelka-varscan-mutect B3GNT6,synonymous_variant,p.=,ENST00000622824,NM_138706.4;B3GNT6,downstream_gene_variant,,ENST00000528622,; T ENST00000622824 Transcript synonymous_variant 639/2503 558/1155 186/384 L ctG/ctT 1 1 B3GNT6 HGNC HGNC:24141 protein_coding YES CCDS53681.1 ENSP00000484640 Q6ZMB0 A8K9Q8 UPI000006D55A NM_138706.4 2/2 Pfam_domain:PF01762,hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF24 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 77040109 77040109 G T 1 0 0 0 0 0 0 0 1 1417 1306 46 2 2 B3GNT6 11 77040109 Silent SNP G C3L-02345_T 16112368 77040109 58046513 141 8739 PRCP 0 . GRCh38 11 82850475 82850475 + Nonsense_Mutation SNP C C A rs774570476 C3L-02345_T C3L-02345_N C C c.505G>T p.Glu169Ter p.E169* ENST00000393399 5/10 53 40 13 79 79 0 strelka-varscan-mutect PRCP,stop_gained,p.Glu148Ter,ENST00000313010,NM_005040.2;PRCP,stop_gained,p.Glu169Ter,ENST00000393399,NM_199418.2;PRCP,stop_gained,p.Glu43Ter,ENST00000531801,;PRCP,stop_gained,p.Glu43Ter,ENST00000527444,;PRCP,stop_gained,p.Glu43Ter,ENST00000534631,;PRCP,stop_gained,p.Glu43Ter,ENST00000534396,;PRCP,stop_gained,p.Glu107Ter,ENST00000529671,;PRCP,stop_gained,p.Glu43Ter,ENST00000531128,;PRCP,stop_gained,p.Glu94Ter,ENST00000532809,;PRCP,stop_gained,p.Glu43Ter,ENST00000528082,;PRCP,stop_gained,p.Glu43Ter,ENST00000533126,;PRCP,downstream_gene_variant,,ENST00000534264,;PRCP,upstream_gene_variant,,ENST00000525772,;PRCP,upstream_gene_variant,,ENST00000532476,;PRCP,upstream_gene_variant,,ENST00000531283,;PRCP,upstream_gene_variant,,ENST00000526918,;PRCP,upstream_gene_variant,,ENST00000524642,; A ENST00000393399 Transcript stop_gained 533/2120 505/1554 169/517 E/* Gaa/Taa rs774570476 1 -1 PRCP HGNC HGNC:9344 protein_coding YES CCDS41695.1 ENSP00000377055 P42785 UPI00001FB052 NM_199418.2 5/10 hmmpanther:PTHR11010,hmmpanther:PTHR11010:SF38,Pfam_domain:PF05577,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 HIGH 1 SNV 2 1 PASS rs774570476 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 82850475 82850475 C A 1 0 0 0 0 0 1 0 0 12580 922 32 2 2 PRCP 11 82850475 Nonsense_Mutation SNP C C3L-02345_T 5810366 82850475 52236147 142 8740 TYR 0 . GRCh38 11 89295279 89295279 + Silent SNP T T A novel C3L-02345_T C3L-02345_N T T c.1503T>A p.= p.R501R ENST00000263321 5/5 243 187 56 307 307 0 strelka-varscan-mutect TYR,synonymous_variant,p.=,ENST00000263321,NM_000372.4;TYR,non_coding_transcript_exon_variant,,ENST00000528243,;RP11-796A5.3,upstream_gene_variant,,ENST00000625091,;CBX3P7,upstream_gene_variant,,ENST00000532876,; A ENST00000263321 Transcript synonymous_variant 2005/2485 1503/1590 501/529 R cgT/cgA 1 1 TYR HGNC HGNC:12442 protein_coding YES CCDS8284.1 ENSP00000263321 P14679 L8B082 UPI000004441A NM_000372.4 5/5 hmmpanther:PTHR11474:SF16,hmmpanther:PTHR11474 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 89295279 89295279 T A 1 0 0 0 0 0 0 0 1 17328 1654 58 4 4 TYR 11 89295279 Silent SNP T C3L-02345_T 6444804 89295279 45791343 143 8741 NOX4 0 . GRCh38 11 89402507 89402507 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.665A>T p.His222Leu p.H222L ENST00000263317 9/18 142 106 36 171 171 0 strelka-varscan-mutect NOX4,missense_variant,p.His198Leu,ENST00000424319,NM_001291926.1;NOX4,missense_variant,p.His198Leu,ENST00000343727,NM_001291927.1;NOX4,missense_variant,p.His222Leu,ENST00000263317,NM_016931.4;NOX4,missense_variant,p.His198Leu,ENST00000527956,NM_001143837.1;NOX4,missense_variant,p.His222Leu,ENST00000534731,NM_001143836.2;NOX4,missense_variant,p.His198Leu,ENST00000532825,NM_001300995.1;NOX4,missense_variant,p.His197Leu,ENST00000528341,NM_001291929.1;NOX4,missense_variant,p.His56Leu,ENST00000527626,;NOX4,intron_variant,,ENST00000525196,;NOX4,intron_variant,,ENST00000375979,;NOX4,intron_variant,,ENST00000531342,;NOX4,intron_variant,,ENST00000529343,; A ENST00000263317 Transcript missense_variant 904/2388 665/1737 222/578 H/L cAc/cTc 1 -1 NOX4 HGNC HGNC:7891 protein_coding YES CCDS8285.1 ENSP00000263317 Q9NPH5 UPI000045655B NM_016931.4 deleterious(0) 9/18 MODERATE 1 SNV 1 1 PASS rs752858739 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 89402507 89402507 T A 1 0 0 0 0 1 0 0 0 10604 1696 59 4 4 NOX4 11 89402507 Missense_Mutation SNP T C3L-02345_T 107228 89402507 45684115 144 8742 CBL 0 . GRCh38 11 119278166 119278166 + Nonsense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1096G>T p.Glu366Ter p.E366* ENST00000264033 8/16 159 126 33 240 239 1 strelka-varscan-mutect CBL,stop_gained,p.Glu366Ter,ENST00000264033,NM_005188.3;CBL,stop_gained,p.Glu366Ter,ENST00000634840,;CBL,stop_gained,p.Glu366Ter,ENST00000634586,;CBL,stop_gained,p.Glu364Ter,ENST00000637974,; T ENST00000264033 Transcript stop_gained,splice_region_variant 1238/11231 1096/2721 366/906 E/* Gaa/Taa 1 1 CBL HGNC HGNC:1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 8/16 Gene3D:3.30.40.10,hmmpanther:PTHR23007,hmmpanther:PTHR23007:SF5,Superfamily_domains:SSF57850 HIGH 1 SNV 1 1 PASS rs1245863855 . 0 198 0 9 3 0 0 0 -19.85744 0.7112886 1 1 1 0 T 4 4 31 119278166 119278166 G T 1 0 0 0 0 0 1 0 0 2401 1188 41 2 2 CBL 11 119278166 Nonsense_Mutation SNP G C3L-02345_T 29875659 119278166 15808456 145 8743 KCNA5 0 . GRCh38 12 5045616 5045616 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1469C>A p.Thr490Asn p.T490N ENST00000252321 1/1 196 110 86 258 258 0 strelka-varscan-mutect KCNA5,missense_variant,p.Thr490Asn,ENST00000252321,NM_002234.3; A ENST00000252321 Transcript missense_variant 1628/2800 1469/1842 490/613 T/N aCt/aAt 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 deleterious(0) 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 5045616 5045616 C A 1 0 0 0 0 1 0 0 0 7922 565 20 2 2 KCNA5 12 5045616 Missense_Mutation SNP C C3L-02345_T 5045616 128229693 146 8744 ABCC9 0 . GRCh38 12 21894110 21894110 + Missense_Mutation SNP A A T C3L-02345_T C3L-02345_N A A c.1724T>A p.Leu575Gln p.L575Q ENST00000261200 12/38 356 225 131 400 399 1 strelka-varscan-mutect ABCC9,missense_variant,p.Leu575Gln,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Leu575Gln,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Leu238Gln,ENST00000544039,; T ENST00000261200 Transcript missense_variant 1724/8293 1724/4650 575/1549 L/Q cTg/cAg COSM3871292,COSM3871293 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 deleterious(0) 12/38 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 21894110 21894110 A T 1 0 0 0 0 1 0 0 0 63 188 7 4 4 ABCC9 12 21894110 Missense_Mutation SNP A C3L-02345_T 16848494 21894110 111381199 147 8745 KRAS 0 . GRCh38 12 25245348 25245348 + Missense_Mutation SNP C C A rs121913535 C3L-02345_T C3L-02345_N C C c.37G>T p.Gly13Cys p.G13C ENST00000256078 2/6 341 222 119 387 387 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly13Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly13Cys,ENST00000556131,;KRAS,missense_variant,p.Gly13Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly13Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 101/1119 37/570 13/189 G/C Ggc/Tgc rs121913535,COSM1152505,COSM3384258,COSM527,COSM528,COSM529 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.02) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS rs121913535 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 25245348 25245348 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245348 Missense_Mutation SNP C C3L-02345_T 3351238 25245348 108029961 148 8746 DTX3 0 . GRCh38 12 57608580 57608580 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.820G>T p.Asp274Tyr p.D274Y ENST00000551632 5/6 100 54 46 83 83 0 strelka-varscan-mutect DTX3,missense_variant,p.Asp271Tyr,ENST00000548198,;DTX3,missense_variant,p.Asp271Tyr,ENST00000548804,NM_001286246.1;DTX3,missense_variant,p.Asp271Tyr,ENST00000337737,NM_178502.3;DTX3,missense_variant,p.Asp274Tyr,ENST00000551632,NM_001286245.1;DTX3,missense_variant,p.Asp59Tyr,ENST00000550300,;ARHGEF25,upstream_gene_variant,,ENST00000286494,NM_182947.3;DTX3,downstream_gene_variant,,ENST00000548478,;ARHGEF25,upstream_gene_variant,,ENST00000333972,NM_001111270.2;ARHGEF25,upstream_gene_variant,,ENST00000616622,;DTX3,downstream_gene_variant,,ENST00000549583,;DTX3,downstream_gene_variant,,ENST00000550596,;DTX3,downstream_gene_variant,,ENST00000551835,;AC025165.8,downstream_gene_variant,,ENST00000356672,;AC025165.8,downstream_gene_variant,,ENST00000444467,; T ENST00000551632 Transcript missense_variant 955/1840 820/1053 274/350 D/Y Gac/Tac 1 1 DTX3 HGNC HGNC:24457 protein_coding YES CCDS66410.1 ENSP00000448696 Q8N9I9 UPI000006EA20 NM_001286245.1 deleterious(0) 5/6 hmmpanther:PTHR12622,hmmpanther:PTHR12622:SF24 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 57608580 57608580 G T 1 0 0 0 0 1 0 0 0 4618 1174 41 2 2 DTX3 12 57608580 Missense_Mutation SNP G C3L-02345_T 32363232 57608580 75666729 149 8747 TBC1D30 0 . GRCh38 12 64843425 64843425 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.978G>T p.Met326Ile p.M326I ENST00000539867 8/12 180 124 56 169 169 0 strelka-varscan-mutect TBC1D30,missense_variant,p.Met212Ile,ENST00000542120,;TBC1D30,missense_variant,p.Met326Ile,ENST00000539867,NM_015279.1; T ENST00000539867 Transcript missense_variant 1286/2594 978/2286 326/761 M/I atG/atT 1 1 TBC1D30 HGNC HGNC:29164 protein_coding YES CCDS53813.1 ENSP00000440207 Q9Y2I9 UPI000013F308 NM_015279.1 deleterious(0) 8/12 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF291,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS rs1483626358 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 64843425 64843425 G T 1 0 0 0 0 1 0 0 0 16020 1348 47 2 2 TBC1D30 12 64843425 Missense_Mutation SNP G C3L-02345_T 7234845 64843425 68431884 150 8748 ENOX1 0 . GRCh38 13 43213999 43213999 + Silent SNP T T C novel C3L-02345_T C3L-02345_N T T c.1923A>G p.= p.K641K ENST00000261488 17/17 86 65 21 94 94 0 strelka-varscan-mutect ENOX1,synonymous_variant,p.=,ENST00000261488,NM_001242863.1,NM_017993.3,NM_001127615.1; C ENST00000261488 Transcript synonymous_variant 2501/2982 1923/1932 641/643 K aaA/aaG 1 -1 ENOX1 HGNC HGNC:25474 protein_coding YES CCDS9389.1 ENSP00000261488 Q8TC92 A0A024RDT8 UPI0000071D6F NM_001242863.1,NM_017993.3,NM_001127615.1 17/17 hmmpanther:PTHR16001,hmmpanther:PTHR16001:SF6 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 43213999 43213999 T C 1 0 0 0 0 0 0 0 1 4971 1838 64 5 5 ENOX1 13 43213999 Silent SNP T C3L-02345_T 43213999 71150329 151 8749 UGGT2 0 . GRCh38 13 95902888 95902888 + Missense_Mutation SNP T T G novel C3L-02345_T C3L-02345_N T T c.2468A>C p.Tyr823Ser p.Y823S ENST00000376747 21/39 215 173 42 270 270 0 strelka-varscan-mutect UGGT2,missense_variant,p.Tyr823Ser,ENST00000376747,NM_020121.3;UGGT2,intron_variant,,ENST00000621375,; G ENST00000376747 Transcript missense_variant 2539/4832 2468/4551 823/1516 Y/S tAc/tCc 1 -1 UGGT2 HGNC HGNC:15664 protein_coding YES CCDS9480.1 ENSP00000365938 Q9NYU1 UPI00001FC9AA NM_020121.3 tolerated(0.5) 21/39 Pfam_domain:PF06427,hmmpanther:PTHR11226,hmmpanther:PTHR11226:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 95902888 95902888 T G 1 0 0 0 0 1 0 0 0 17467 1638 57 5 5 UGGT2 13 95902888 Missense_Mutation SNP T C3L-02345_T 52688889 95902888 18461440 152 8750 ZIC5 0 . GRCh38 13 99970914 99970914 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.762C>A p.Ser254Arg p.S254R ENST00000267294 1/2 80 64 16 52 52 0 strelka-varscan-mutect ZIC5,missense_variant,p.Ser254Arg,ENST00000267294,NM_033132.3; T ENST00000267294 Transcript missense_variant 996/4639 762/1992 254/663 S/R agC/agA 1 -1 ZIC5 HGNC HGNC:20322 protein_coding YES CCDS9494.2 ENSP00000267294 Q96T25 UPI0000458928 NM_033132.3 deleterious(0.03) 1/2 hmmpanther:PTHR19818 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 99970914 99970914 G T 1 0 0 0 0 1 0 0 0 18260 1078 38 1 1 ZIC5 13 99970914 Missense_Mutation SNP G C3L-02345_T 4068026 99970914 14393414 153 8751 CCDC168 0 . GRCh38 13 102749316 102749316 + Missense_Mutation SNP C C T rs865995674 C3L-02345_T C3L-02345_N C C c.1381G>A p.Val461Ile p.V461I ENST00000322527 4/4 226 195 31 289 289 0 strelka-varscan-mutect CCDC168,missense_variant,p.Val461Ile,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; T ENST00000322527 Transcript missense_variant 1519/21466 1381/21246 461/7081 V/I Gta/Ata rs865995674 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.3) 4/4 MODERATE 1 SNV 3 1 PASS rs865995674 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 102749316 102749316 C T 1 0 0 0 0 1 0 0 0 2484 478 17 3 3 CCDC168 13 102749316 Missense_Mutation SNP C C3L-02345_T 2778402 102749316 11615012 154 8752 MYO16 0 . GRCh38 13 109052337 109052337 + Silent SNP G G A rs144060419 C3L-02345_T C3L-02345_N G G c.2910G>A p.= p.S970S ENST00000457511 25/35 312 264 48 364 364 0 strelka-varscan-mutect MYO16,synonymous_variant,p.=,ENST00000457511,NM_001198950.1;MYO16,synonymous_variant,p.=,ENST00000356711,NM_015011.1;MYO16,synonymous_variant,p.=,ENST00000357550,;MYO16,downstream_gene_variant,,ENST00000251041,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,; A ENST00000457511 Transcript synonymous_variant 3532/7436 2910/5643 970/1880 S tcG/tcA rs144060419,COSM3467072,COSM945298 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 25/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs144060419 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 109052337 109052337 G A 1 0 0 0 0 0 0 0 1 10065 1045 37 1 1 MYO16 13 109052337 Silent SNP G C3L-02345_T 6303021 109052337 5311991 155 8753 RIPK3 0 . GRCh38 14 24336285 24336287 + In_Frame_Del DEL CCG CCG - novel C3L-02345_T C3L-02345_N CCG CCG c.1445_1447delCGG p.Ser482_Gly483delinsCys p.S482_G483delinsC ENST00000216274 10/10 198 165 33 235 235 0 sindel-varindel-pindel RIPK3,inframe_deletion,p.Ser482_Gly483delinsCys,ENST00000216274,NM_006871.3;RP11-934B9.3,intron_variant,,ENST00000555591,;ADCY4,upstream_gene_variant,,ENST00000310677,NM_139247.3,NM_001198568.1,NM_001198592.1;ADCY4,upstream_gene_variant,,ENST00000554068,;ADCY4,upstream_gene_variant,,ENST00000418030,;RIPK3,downstream_gene_variant,,ENST00000554569,;ADCY4,upstream_gene_variant,,ENST00000559167,;ADCY4,upstream_gene_variant,,ENST00000561138,;ADCY4,upstream_gene_variant,,ENST00000558563,;RIPK3,downstream_gene_variant,,ENST00000554338,;ADCY4,upstream_gene_variant,,ENST00000558125,;RIPK3,3_prime_UTR_variant,,ENST00000554756,;ADCY4,upstream_gene_variant,,ENST00000554577,;ADCY4,upstream_gene_variant,,ENST00000557056,;ADCY4,upstream_gene_variant,,ENST00000554781,;RIPK3,downstream_gene_variant,,ENST00000557624,;ADCY4,upstream_gene_variant,,ENST00000557099,;ADCY4,upstream_gene_variant,,ENST00000554674,;RIPK3,downstream_gene_variant,,ENST00000557253,;RIPK3,downstream_gene_variant,,ENST00000557662,; - ENST00000216274 Transcript inframe_deletion 1664-1666/1930 1445-1447/1557 482-483/518 SG/C tCGGgc/tgc 1 -1 RIPK3 HGNC HGNC:10021 protein_coding YES CCDS9628.1 ENSP00000216274 Q9Y572 UPI00000369E2 NM_006871.3 10/10 hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF496 MODERATE 1 deletion 1 1 PASS . . 0 207 0 0 0 0 0 2 -2.903963 0 0 1 0 0 - 7 5 31 24336285 24336285 CCG - 1 0 1 0 1 0 0 0 0 13556 623 22 0 0 RIPK3 14 24336285 In_Frame_Del DEL CCG C3L-02345_T 24336285 82707433 156 8754 AKAP6 0 . GRCh38 14 32822984 32822984 + Missense_Mutation SNP G G A rs748631841 C3L-02345_T C3L-02345_N G G c.5171G>A p.Arg1724His p.R1724H ENST00000280979 13/14 243 213 30 354 352 2 strelka-varscan-mutect AKAP6,missense_variant,p.Arg1724His,ENST00000280979,NM_004274.4;AKAP6,intron_variant,,ENST00000557272,; A ENST00000280979 Transcript missense_variant 5341/15006 5171/6960 1724/2319 R/H cGt/cAt rs748631841,COSM368592 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 tolerated(0.26) 13/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748631841 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 32822984 32822984 G A 1 0 0 0 0 1 0 0 0 539 1145 40 1 1 AKAP6 14 32822984 Missense_Mutation SNP G C3L-02345_T 8486699 32822984 74220734 157 8755 FBXO34 0 . GRCh38 14 55352419 55352419 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.2029G>T p.Gly677Cys p.G677C ENST00000313833 2/2 162 130 32 205 205 0 strelka-varscan-mutect FBXO34,missense_variant,p.Gly677Cys,ENST00000313833,NM_017943.3;FBXO34,missense_variant,p.Gly677Cys,ENST00000440021,NM_152231.1;FBXO34,intron_variant,,ENST00000557647,;FBXO34,downstream_gene_variant,,ENST00000555087,;FBXO34,downstream_gene_variant,,ENST00000554940,;FBXO34,missense_variant,p.Gly543Cys,ENST00000555280,; T ENST00000313833 Transcript missense_variant 2274/3464 2029/2136 677/711 G/C Ggc/Tgc 1 1 FBXO34 HGNC HGNC:20201 protein_coding YES CCDS32086.1 ENSP00000313159 Q9NWN3 A0A024R653 UPI00001FD5AD NM_017943.3 deleterious(0) 2/2 hmmpanther:PTHR16271,hmmpanther:PTHR16271:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 55352419 55352419 G T 1 0 0 0 0 1 0 0 0 5607 1348 47 2 2 FBXO34 14 55352419 Missense_Mutation SNP G C3L-02345_T 22529435 55352419 51691299 158 8756 GPHB5 0 . GRCh38 14 63312958 63312958 + Frame_Shift_Del DEL G G - novel C3L-02345_T C3L-02345_N G G c.363delC p.Thr122LeufsTer? p.T122Lfs*? ENST00000621500 3/3 109 92 17 123 123 0 sindel-varindel-pindel GPHB5,frameshift_variant,p.Thr122LeufsTer?,ENST00000621500,NM_145171.3;GPHB5,frameshift_variant,p.Thr122LeufsTer?,ENST00000314140,; - ENST00000621500 Transcript frameshift_variant 420/543 363/393 121/130 S/X tcC/tc 1 -1 GPHB5 HGNC HGNC:18055 protein_coding YES CCDS73643.1 ENSP00000478993 Q86YW7 A0A0F7RPU1 UPI000000D7AF NM_145171.3 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00007,hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF14,SMART_domains:SM00068,Superfamily_domains:SSF57501 HIGH 1 deletion 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 63312958 63312958 G - 1 0 1 0 1 0 0 0 0 6511 1335 47 0 0 GPHB5 14 63312958 Frame_Shift_Del DEL G C3L-02345_T 7960539 63312958 43730760 159 8757 SPTB 0 . GRCh38 14 64774401 64774401 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.4969G>A p.Glu1657Lys p.E1657K ENST00000556626 24/36 133 126 7 157 157 0 strelka-mutect SPTB,missense_variant,p.Glu1657Lys,ENST00000556626,;SPTB,missense_variant,p.Glu1657Lys,ENST00000389722,NM_001024858.2;SPTB,missense_variant,p.Glu1657Lys,ENST00000389721,NM_000347.5;SPTB,missense_variant,p.Glu1657Lys,ENST00000389720,;SPTB,missense_variant,p.Glu322Lys,ENST00000553938,; T ENST00000556626 Transcript missense_variant 5112/10153 4969/6987 1657/2328 E/K Gag/Aag 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D tolerated(0.07) 24/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.03128 0.9999994 1 1 1 0 T 3 4 31 64774401 64774401 C T 1 0 0 0 0 1 0 0 0 15474 840 29 3 3 SPTB 14 64774401 Missense_Mutation SNP C C3L-02345_T 1461443 64774401 42269317 160 8758 ASB2 0 . GRCh38 14 93953431 93953431 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.555G>T p.= p.L185L ENST00000555019 5/10 87 73 14 86 86 0 strelka-varscan-mutect ASB2,synonymous_variant,p.=,ENST00000555019,NM_001202429.1;ASB2,synonymous_variant,p.=,ENST00000315988,NM_016150.4;ASB2,synonymous_variant,p.=,ENST00000555507,;ASB2,synonymous_variant,p.=,ENST00000555287,;ASB2,intron_variant,,ENST00000556062,;ASB2,downstream_gene_variant,,ENST00000557613,;ASB2,intron_variant,,ENST00000556337,;ASB2,downstream_gene_variant,,ENST00000556793,; A ENST00000555019 Transcript synonymous_variant 986/2842 555/1908 185/635 L ctG/ctT 1 -1 ASB2 HGNC HGNC:16012 protein_coding YES CCDS55940.1 ENSP00000451575 Q96Q27 A0A024R6E7 UPI000013D23C NM_001202429.1 5/10 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF33,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 93953431 93953431 C A 1 0 0 0 0 0 0 0 1 1165 581 21 2 2 ASB2 14 93953431 Silent SNP C C3L-02345_T 29179030 93953431 13090287 161 8759 BCL11B 0 . GRCh38 14 99257741 99257741 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.157C>A p.Pro53Thr p.P53T ENST00000357195 2/4 41 33 8 58 57 1 strelka-varscan-mutect BCL11B,missense_variant,p.Pro53Thr,ENST00000345514,NM_001282238.1,NM_022898.2;BCL11B,missense_variant,p.Pro53Thr,ENST00000357195,NM_001282237.1,NM_138576.3;BCL11B,intron_variant,,ENST00000443726,; T ENST00000357195 Transcript missense_variant 167/7559 157/2685 53/894 P/T Cct/Act 1 -1 BCL11B HGNC HGNC:13222 protein_coding YES CCDS9950.1 ENSP00000349723 Q9C0K0 L8B7P7 UPI000006E083 NM_001282237.1,NM_138576.3 tolerated(0.21) 2/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF45 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.8501 1 1 1 1 0 T 3 4 31 99257741 99257741 G T 1 0 0 0 0 1 0 0 0 1511 1232 43 2 2 BCL11B 14 99257741 Missense_Mutation SNP G C3L-02345_T 5304310 99257741 7785977 162 8760 NPAP1 0 . GRCh38 15 24676814 24676814 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.947C>A p.Ala316Asp p.A316D ENST00000329468 1/1 102 89 13 134 134 0 strelka-varscan-mutect NPAP1,missense_variant,p.Ala316Asp,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 947/7526 947/3471 316/1156 A/D gCt/gAt 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.11) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 24676814 24676814 C A 1 0 0 0 0 1 0 0 0 10609 797 28 2 2 NPAP1 15 24676814 Missense_Mutation SNP C C3L-02345_T 24676814 77314375 163 8761 HERC2 0 . GRCh38 15 28256282 28256282 + Silent SNP T T C novel C3L-02345_T C3L-02345_N T T c.2553A>G p.= p.E851E ENST00000261609 18/93 159 127 32 200 200 0 strelka-varscan-mutect HERC2,synonymous_variant,p.=,ENST00000261609,NM_004667.5;HERC2,3_prime_UTR_variant,,ENST00000564734,; C ENST00000261609 Transcript synonymous_variant 2662/15337 2553/14505 851/4834 E gaA/gaG 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 18/93 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF325 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 28256282 28256282 T C 1 0 0 0 0 0 0 0 1 6942 1490 52 5 5 HERC2 15 28256282 Silent SNP T C3L-02345_T 3579468 28256282 73734907 164 8762 GOLGA8F 0 . GRCh38 15 28385290 28385290 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.1079A>T p.Glu360Val p.E360V ENST00000532622 12/19 173 159 14 172 172 0 varscan-mutect GOLGA8F,missense_variant,p.Glu142Val,ENST00000526619,;GOLGA8F,missense_variant,p.Glu360Val,ENST00000532622,;RN7SL238P,upstream_gene_variant,,ENST00000613832,;GOLGA8F,downstream_gene_variant,,ENST00000568250,;GOLGA8F,downstream_gene_variant,,ENST00000568913,;GOLGA8F,downstream_gene_variant,,ENST00000565126,;GOLGA8F,downstream_gene_variant,,ENST00000564114,; T ENST00000532622 Transcript missense_variant 1141/2009 1079/1947 360/648 E/V gAg/gTg 1 1 GOLGA8F HGNC HGNC:32378 protein_coding YES ENSP00000454322 H3BMC3 UPI00024672FE deleterious(0) 12/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 28385290 28385290 A T 1 0 0 0 0 1 0 0 0 6449 304 11 4 4 GOLGA8F 15 28385290 Missense_Mutation SNP A C3L-02345_T 129008 28385290 73605899 165 8763 RYR3 0 . GRCh38 15 33750018 33750018 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.8239T>A p.Trp2747Arg p.W2747R ENST00000634891 56/104 216 187 29 282 282 0 strelka-varscan-mutect RYR3,missense_variant,p.Trp2747Arg,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Trp2747Arg,ENST00000622037,;RYR3,missense_variant,p.Trp2747Arg,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Trp2746Arg,ENST00000389232,;RYR3,missense_variant,p.Trp2746Arg,ENST00000634418,;RYR3,missense_variant,p.Trp452Arg,ENST00000635790,; A ENST00000634891 Transcript missense_variant 8340/15591 8239/14613 2747/4870 W/R Tgg/Agg 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 56/104 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 33750018 33750018 T A 1 0 0 0 0 1 0 0 0 14030 1580 55 4 4 RYR3 15 33750018 Missense_Mutation SNP T C3L-02345_T 5364728 33750018 68241171 166 8764 MEIS2 0 . GRCh38 15 36895200 36895200 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1098G>T p.Met366Ile p.M366I ENST00000561208 11/12 193 143 50 234 234 0 strelka-varscan-mutect MEIS2,missense_variant,p.Met359Ile,ENST00000338564,NM_001220482.1,NM_170676.4;MEIS2,missense_variant,p.Met366Ile,ENST00000561208,NM_170675.4;MEIS2,missense_variant,p.Met346Ile,ENST00000340545,NM_002399.3;MEIS2,missense_variant,p.Met366Ile,ENST00000424352,NM_170677.4;MEIS2,missense_variant,p.Met271Ile,ENST00000397624,;MEIS2,missense_variant,p.Met346Ile,ENST00000557796,;MEIS2,missense_variant,p.Met353Ile,ENST00000559085,NM_172315.2;MEIS2,missense_variant,p.Met271Ile,ENST00000397620,NM_172316.2;MEIS2,missense_variant,p.Met359Ile,ENST00000559561,NM_170674.4;MEIS2,missense_variant,p.Met218Ile,ENST00000607277,;MEIS2,non_coding_transcript_exon_variant,,ENST00000559408,;MEIS2,3_prime_UTR_variant,,ENST00000314177,;MEIS2,3_prime_UTR_variant,,ENST00000560570,;MEIS2,non_coding_transcript_exon_variant,,ENST00000560702,;MEIS2,non_coding_transcript_exon_variant,,ENST00000558643,;MEIS2,non_coding_transcript_exon_variant,,ENST00000559371,;MEIS2,non_coding_transcript_exon_variant,,ENST00000561284,;MEIS2,non_coding_transcript_exon_variant,,ENST00000561264,;MEIS2,non_coding_transcript_exon_variant,,ENST00000557992,;MEIS2,non_coding_transcript_exon_variant,,ENST00000559972,; A ENST00000561208 Transcript missense_variant 1517/4822 1098/1434 366/477 M/I atG/atT 1 -1 MEIS2 HGNC HGNC:7001 protein_coding YES CCDS10044.1 ENSP00000453793 O14770 UPI000012EEBC NM_170675.4 tolerated(0.11) 11/12 hmmpanther:PTHR11850:SF47,hmmpanther:PTHR11850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 36895200 36895200 C A 1 0 0 0 0 1 0 0 0 9412 594 21 2 2 MEIS2 15 36895200 Missense_Mutation SNP C C3L-02345_T 3145182 36895200 65095989 167 8765 TP53BP1 0 . GRCh38 15 43456567 43456567 + Nonsense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.2041G>T p.Gly681Ter p.G681* ENST00000382044 12/28 79 57 22 135 134 1 varscan-mutect TP53BP1,stop_gained,p.Gly681Ter,ENST00000382044,NM_001141980.1;TP53BP1,stop_gained,p.Gly676Ter,ENST00000263801,NM_005657.2;TP53BP1,stop_gained,p.Gly681Ter,ENST00000450115,NM_001141979.1;TP53BP1,stop_gained,p.Gly681Ter,ENST00000382039,;TP53BP1,stop_gained,p.Gly681Ter,ENST00000413546,;TP53BP1,upstream_gene_variant,,ENST00000605155,;TP53BP1,upstream_gene_variant,,ENST00000414758,;TP53BP1,non_coding_transcript_exon_variant,,ENST00000572085,;TP53BP1,upstream_gene_variant,,ENST00000411772,;TP53BP1,upstream_gene_variant,,ENST00000480860,; A ENST00000382044 Transcript stop_gained 2169/10384 2041/5934 681/1977 G/* Gga/Tga 1 -1 TP53BP1 HGNC HGNC:11999 protein_coding YES CCDS45250.1 ENSP00000371475 Q12888 UPI0000D720ED NM_001141980.1 12/28 hmmpanther:PTHR15321,hmmpanther:PTHR15321:SF3 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 43456567 43456567 C A 1 0 0 0 0 0 1 0 0 16861 690 24 2 2 TP53BP1 15 43456567 Nonsense_Mutation SNP C C3L-02345_T 6561367 43456567 58534622 168 8766 ATP8B4 0 . GRCh38 15 49862344 49862344 + Silent SNP G G A novel C3L-02345_T C3L-02345_N G G c.3198C>T p.= p.C1066C ENST00000284509 27/28 145 110 35 194 194 0 strelka-varscan-mutect ATP8B4,synonymous_variant,p.=,ENST00000284509,NM_024837.3;ATP8B4,synonymous_variant,p.=,ENST00000559829,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000558498,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000560479,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,3_prime_UTR_variant,,ENST00000558906,;ATP8B4,3_prime_UTR_variant,,ENST00000557955,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000558203,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000560354,; A ENST00000284509 Transcript synonymous_variant 3340/5676 3198/3579 1066/1192 C tgC/tgT 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 27/28 Transmembrane_helices:TMhelix,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF80,Pfam_domain:PF16212,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 49862344 49862344 G A 1 0 0 0 0 0 0 0 1 1350 1311 46 3 3 ATP8B4 15 49862344 Silent SNP G C3L-02345_T 6405777 49862344 52128845 169 8767 GOLGA6B 0 . GRCh38 15 72661546 72661546 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.739A>G p.Met247Val p.M247V ENST00000421285 9/18 31 23 8 73 73 0 varscan-mutect GOLGA6B,missense_variant,p.Met247Val,ENST00000421285,NM_018652.4;RN7SL853P,upstream_gene_variant,,ENST00000617250,;GOLGA6B,downstream_gene_variant,,ENST00000568532,; G ENST00000421285 Transcript missense_variant 739/2134 739/2082 247/693 M/V Atg/Gtg 1 1 GOLGA6B HGNC HGNC:32205 protein_coding YES CCDS10245.2 ENSP00000408132 A6NDN3 UPI0000D74C4D NM_018652.4 deleterious(0.02) 9/18 Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF47 MODERATE 1 SNV 1 1 PASS rs1386609036 . 0 204 6 0 0 0 0 0 -19.96718 1 1 1 1 0 G 3 3 31 72661546 72661546 A G 1 0 0 0 0 1 0 0 0 6436 333 12 5 5 GOLGA6B 15 72661546 Missense_Mutation SNP A C3L-02345_T 22799202 72661546 29329643 170 8768 ACAN 0 . GRCh38 15 88843611 88843611 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.1014C>A p.= p.P338P ENST00000439576 6/18 51 37 14 63 63 0 strelka-varscan-mutect ACAN,synonymous_variant,p.=,ENST00000439576,NM_013227.3;ACAN,synonymous_variant,p.=,ENST00000617301,;ACAN,synonymous_variant,p.=,ENST00000559004,;ACAN,synonymous_variant,p.=,ENST00000561243,;ACAN,synonymous_variant,p.=,ENST00000352105,NM_001135.3;ACAN,synonymous_variant,p.=,ENST00000558207,; A ENST00000439576 Transcript synonymous_variant 1388/8840 1014/7593 338/2530 P ccC/ccA 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 6/18 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436 LOW 1 SNV 5 1 PASS rs1236933263 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 88843611 88843611 C A 1 0 0 0 0 0 0 0 1 160 639 23 1 1 ACAN 15 88843611 Silent SNP C C3L-02345_T 16182065 88843611 13147578 171 8769 ACAN 0 . GRCh38 15 88859063 88859063 + Nonsense_Mutation SNP G G T rs373460432 C3L-02345_T C3L-02345_N G G c.6478G>T p.Glu2160Ter p.E2160* ENST00000439576 12/18 255 203 52 258 258 0 strelka-varscan-mutect ACAN,stop_gained,p.Glu2160Ter,ENST00000439576,NM_013227.3;ACAN,stop_gained,p.Glu2141Ter,ENST00000617301,;ACAN,stop_gained,p.Glu2160Ter,ENST00000559004,;ACAN,stop_gained,p.Glu2160Ter,ENST00000561243,;ACAN,stop_gained,p.Glu2160Ter,ENST00000352105,NM_001135.3;ACAN,upstream_gene_variant,,ENST00000560601,; T ENST00000439576 Transcript stop_gained 6852/8840 6478/7593 2160/2530 E/* Gag/Tag rs373460432 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 12/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 HIGH 1 SNV 5 1 PASS rs373460432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 88859063 88859063 G T 1 0 0 0 0 0 1 0 0 160 1059 37 1 1 ACAN 15 88859063 Nonsense_Mutation SNP G C3L-02345_T 15452 88859063 13132126 172 8770 GP2 0 . GRCh38 16 20323994 20323994 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.357G>T p.Met119Ile p.M119I ENST00000381362 3/12 195 160 35 253 253 0 strelka-varscan-mutect GP2,missense_variant,p.Met119Ile,ENST00000302555,NM_001502.3;GP2,missense_variant,p.Met119Ile,ENST00000381362,NM_001007240.2;GP2,missense_variant,p.Met31Ile,ENST00000572347,;GP2,missense_variant,p.Met119Ile,ENST00000575449,;GP2,missense_variant,p.Met54Ile,ENST00000572478,;GP2,intron_variant,,ENST00000381360,NM_001007241.2;GP2,intron_variant,,ENST00000341642,NM_001007242.2;GP2,intron_variant,,ENST00000575582,;GP2,upstream_gene_variant,,ENST00000573897,;GP2,downstream_gene_variant,,ENST00000575730,;GP2,intron_variant,,ENST00000574982,; A ENST00000381362 Transcript missense_variant 434/2425 357/1614 119/537 M/I atG/atT 1 -1 GP2 HGNC HGNC:4441 protein_coding YES CCDS42128.1 ENSP00000370767 P55259 UPI000059D333 NM_001007240.2 deleterious(0.01) 3/12 hmmpanther:PTHR24044:SF284,hmmpanther:PTHR24044 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 20323994 20323994 C A 1 0 0 0 0 1 0 0 0 6477 478 17 2 2 GP2 16 20323994 Missense_Mutation SNP C C3L-02345_T 20323994 70014351 173 8771 OTOA 0 . GRCh38 16 21716953 21716953 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1535G>A p.Gly512Glu p.G512E ENST00000388958 14/28 315 253 62 395 394 1 strelka-varscan-mutect OTOA,missense_variant,p.Gly512Glu,ENST00000388958,NM_144672.3;OTOA,missense_variant,p.Gly526Glu,ENST00000286149,;OTOA,missense_variant,p.Gly433Glu,ENST00000388956,NM_001161683.1;OTOA,missense_variant,p.Gly188Glu,ENST00000388957,NM_170664.2;OTOA,non_coding_transcript_exon_variant,,ENST00000563871,; A ENST00000388958 Transcript missense_variant 1536/3610 1535/3420 512/1139 G/E gGg/gAg 1 1 OTOA HGNC HGNC:16378 protein_coding YES CCDS10600.2 ENSP00000373610 Q7RTW8 UPI00005C8607 NM_144672.3 tolerated(0.08) 14/28 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF18 MODERATE 1 SNV 1 1 PASS rs1418508879 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 21716953 21716953 G A 1 0 0 0 0 1 0 0 0 11368 1232 43 3 3 OTOA 16 21716953 Missense_Mutation SNP G C3L-02345_T 1392959 21716953 68621392 174 8772 VWA3A 0 . GRCh38 16 22152561 22152561 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.3332A>T p.Tyr1111Phe p.Y1111F ENST00000389398 31/34 327 266 61 316 316 0 strelka-varscan-mutect VWA3A,missense_variant,p.Tyr1111Phe,ENST00000389398,NM_173615.4;VWA3A,missense_variant,p.Tyr213Phe,ENST00000563755,;VWA3A,3_prime_UTR_variant,,ENST00000299840,; T ENST00000389398 Transcript missense_variant 3428/4600 3332/3555 1111/1184 Y/F tAt/tTt 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 tolerated(0.23) 31/34 PROSITE_profiles:PS50234,Pfam_domain:PF13768,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 22152561 22152561 A T 1 0 0 0 0 1 0 0 0 17794 449 16 4 4 VWA3A 16 22152561 Missense_Mutation SNP A C3L-02345_T 435608 22152561 68185784 175 8773 C16orf82 0 . GRCh38 16 27067269 27067269 + Missense_Mutation SNP G G T rs765348127 C3L-02345_T C3L-02345_N G G c.463G>T p.Ala155Ser p.A155S ENST00000505035 1/1 253 200 53 303 303 0 strelka-varscan-mutect C16orf82,missense_variant,p.Ala155Ser,ENST00000505035,;C16orf82,missense_variant,p.Ala92Ser,ENST00000418886,NM_001145545.1;RP11-673P17.2,intron_variant,,ENST00000565783,; T ENST00000505035 Transcript missense_variant 563/2459 463/654 155/217 A/S Gca/Tca rs765348127 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 tolerated(0.21) 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 MODERATE SNV 1 PASS rs765348127 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 27067269 27067269 G T 1 0 0 0 0 1 0 0 0 1867 1087 38 1 1 C16orf82 16 27067269 Missense_Mutation SNP G C3L-02345_T 4914708 27067269 63271076 176 8774 GTF3C1 0 . GRCh38 16 27537872 27537872 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.664A>T p.Ile222Phe p.I222F ENST00000356183 4/37 206 160 46 221 221 0 strelka-varscan-mutect GTF3C1,missense_variant,p.Ile222Phe,ENST00000356183,NM_001520.3;GTF3C1,missense_variant,p.Ile222Phe,ENST00000561623,NM_001286242.1; A ENST00000356183 Transcript missense_variant 680/7018 664/6330 222/2109 I/F Att/Ttt 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 deleterious(0) 4/37 Pfam_domain:PF04182,hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 27537872 27537872 T A 1 0 0 0 0 1 0 0 0 6753 1435 50 4 4 GTF3C1 16 27537872 Missense_Mutation SNP T C3L-02345_T 470603 27537872 62800473 177 8775 FUS 0 . GRCh38 16 31188333 31188333 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.808G>T p.Asp270Tyr p.D270Y ENST00000254108 8/15 247 196 51 246 245 1 strelka-varscan-mutect FUS,missense_variant,p.Asp270Tyr,ENST00000254108,NM_004960.3,NM_001170937.1;FUS,missense_variant,p.Asp269Tyr,ENST00000380244,NM_001170634.1;FUS,missense_variant,p.Asp270Tyr,ENST00000568685,;FUS,non_coding_transcript_exon_variant,,ENST00000474990,;FUS,missense_variant,p.Gly258Val,ENST00000566605,;FUS,non_coding_transcript_exon_variant,,ENST00000487509,;FUS,non_coding_transcript_exon_variant,,ENST00000568901,;FUS,downstream_gene_variant,,ENST00000487045,;FUS,upstream_gene_variant,,ENST00000564766,;FUS,upstream_gene_variant,,ENST00000483853,;FUS,downstream_gene_variant,,ENST00000487974,;FUS,upstream_gene_variant,,ENST00000569760,;FUS,downstream_gene_variant,,ENST00000570090,; T ENST00000254108 Transcript missense_variant 913/5119 808/1581 270/526 D/Y Gac/Tac 1 1 FUS HGNC HGNC:4010 protein_coding YES CCDS10707.1 ENSP00000254108 P35637 Q6IBQ5 UPI000012AD9A NM_004960.3,NM_001170937.1 deleterious(0) 8/15 Gene3D:3.30.70.330,hmmpanther:PTHR23238,hmmpanther:PTHR23238:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 31188333 31188333 G T 1 0 0 0 0 1 0 0 0 5972 1174 41 2 2 FUS 16 31188333 Missense_Mutation SNP G C3L-02345_T 3650461 31188333 59150012 178 8776 CYLD 0 . GRCh38 16 50751662 50751662 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.563A>T p.Gln188Leu p.Q188L ENST00000427738 3/18 210 150 60 228 227 1 strelka-varscan-mutect CYLD,missense_variant,p.Gln188Leu,ENST00000427738,;CYLD,missense_variant,p.Gln188Leu,ENST00000311559,NM_015247.2;CYLD,missense_variant,p.Gln188Leu,ENST00000398568,NM_001042412.1;CYLD,missense_variant,p.Gln188Leu,ENST00000569418,NM_001042355.1;CYLD,missense_variant,p.Gln188Leu,ENST00000568704,;CYLD,missense_variant,p.Gln188Leu,ENST00000564326,;CYLD,missense_variant,p.Gln188Leu,ENST00000566206,;CYLD,missense_variant,p.Gln188Leu,ENST00000566679,;CYLD,downstream_gene_variant,,ENST00000569681,;CYLD,downstream_gene_variant,,ENST00000564634,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,; T ENST00000427738 Transcript missense_variant 768/8503 563/2871 188/956 Q/L cAg/cTg 1 1 CYLD HGNC HGNC:2584 protein_coding YES CCDS45482.1 ENSP00000392025 Q9NQC7 UPI0000073A15 tolerated(0.12) 3/18 PROSITE_profiles:PS50245,hmmpanther:PTHR11830:SF3,hmmpanther:PTHR11830,Pfam_domain:PF01302,Gene3D:2.30.30.190,SMART_domains:SM01052,Superfamily_domains:SSF74924 MODERATE 1 SNV 5 1 PASS . . 0 205 0 0 4 0 0 0 -20 0.9545231 1 1 1 0 T 3 4 31 50751662 50751662 A T 1 0 0 0 0 1 0 0 0 3946 188 7 4 4 CYLD 16 50751662 Missense_Mutation SNP A C3L-02345_T 19563329 50751662 39586683 179 8777 ZFHX3 0 . GRCh38 16 72950750 72950750 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.2935G>T p.Val979Leu p.V979L ENST00000268489 3/10 205 158 47 245 245 0 strelka-varscan-mutect ZFHX3,missense_variant,p.Val979Leu,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Val65Leu,ENST00000397992,NM_001164766.1; A ENST00000268489 Transcript missense_variant 3608/16064 2935/11112 979/3703 V/L Gtg/Ttg 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 tolerated(0.18) 3/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 72950750 72950750 C A 1 0 0 0 0 1 0 0 0 18212 507 18 2 2 ZFHX3 16 72950750 Missense_Mutation SNP C C3L-02345_T 22199088 72950750 17387595 180 8778 TCF25 0 . GRCh38 16 89887709 89887709 + Silent SNP G G C novel C3L-02345_T C3L-02345_N G G c.606G>C p.= p.G202G ENST00000263346 5/18 68 62 6 80 80 0 strelka-varscan-mutect TCF25,synonymous_variant,p.=,ENST00000263346,NM_014972.2;TCF25,synonymous_variant,p.=,ENST00000614813,;TCF25,synonymous_variant,p.=,ENST00000562256,;TCF25,synonymous_variant,p.=,ENST00000568409,;TCF25,5_prime_UTR_variant,,ENST00000263347,;TCF25,intron_variant,,ENST00000568412,;TCF25,intron_variant,,ENST00000561958,;TCF25,intron_variant,,ENST00000565196,;TCF25,downstream_gene_variant,,ENST00000565404,;TCF25,non_coding_transcript_exon_variant,,ENST00000566751,;TCF25,downstream_gene_variant,,ENST00000563406,;TCF25,3_prime_UTR_variant,,ENST00000564652,;TCF25,downstream_gene_variant,,ENST00000561585,;TCF25,upstream_gene_variant,,ENST00000568870,; C ENST00000263346 Transcript synonymous_variant 662/2233 606/2031 202/676 G ggG/ggC 1 1 TCF25 HGNC HGNC:29181 protein_coding YES CCDS10987.1 ENSP00000263346 Q9BQ70 UPI000012A80B NM_014972.2 5/18 hmmpanther:PTHR22684,hmmpanther:PTHR22684:SF0 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -13.83568 1 1 1 1 0 C 2 2 31 89887709 89887709 G C 1 0 0 0 0 0 0 0 1 16100 1219 43 4 4 TCF25 16 89887709 Silent SNP G C3L-02345_T 16936959 89887709 450636 181 8779 OR1E2 0 . GRCh38 17 3433720 3433720 + Missense_Mutation SNP C C T C3L-02345_T C3L-02345_N C C c.122G>A p.Gly41Glu p.G41E ENST00000248384 1/1 249 198 51 291 291 0 strelka-varscan-mutect OR1E2,missense_variant,p.Gly41Glu,ENST00000248384,NM_003554.2; T ENST00000248384 Transcript missense_variant 122/972 122/972 41/323 G/E gGg/gAg COSM1743972 1 -1 OR1E2 HGNC HGNC:8190 protein_coding YES CCDS11026.1 ENSP00000248384 P47887 A0A126GW81 UPI0000041BBF NM_003554.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF367,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 3433720 3433720 C T 1 0 0 0 0 1 0 0 0 11033 623 22 3 3 OR1E2 17 3433720 Missense_Mutation SNP C C3L-02345_T 3433720 79823721 182 8780 CAMTA2 0 . GRCh38 17 4972950 4972950 + Silent SNP G G C novel C3L-02345_T C3L-02345_N G G c.2391C>G p.= p.L797L ENST00000414043 15/23 243 201 42 251 251 0 strelka-varscan-mutect CAMTA2,synonymous_variant,p.=,ENST00000361571,NM_001171168.1;CAMTA2,synonymous_variant,p.=,ENST00000414043,NM_001171167.1;CAMTA2,synonymous_variant,p.=,ENST00000572543,;CAMTA2,synonymous_variant,p.=,ENST00000348066,NM_015099.3;CAMTA2,synonymous_variant,p.=,ENST00000381311,NM_001171166.1;MIR6864,upstream_gene_variant,,ENST00000617935,;MIR6865,upstream_gene_variant,,ENST00000614295,;RP5-1050D4.2,non_coding_transcript_exon_variant,,ENST00000430920,;RP5-1050D4.3,downstream_gene_variant,,ENST00000576752,;CAMTA2,downstream_gene_variant,,ENST00000572326,;CAMTA2,downstream_gene_variant,,ENST00000575365,;CAMTA2,3_prime_UTR_variant,,ENST00000574951,;CAMTA2,upstream_gene_variant,,ENST00000576872,;CAMTA2,upstream_gene_variant,,ENST00000572192,;CAMTA2,upstream_gene_variant,,ENST00000574442,;CAMTA2,downstream_gene_variant,,ENST00000575192,; C ENST00000414043 Transcript synonymous_variant 2545/4589 2391/3726 797/1241 L ctC/ctG 1 -1 CAMTA2 HGNC HGNC:18807 protein_coding YES CCDS54072.1 ENSP00000412886 O94983 UPI0001892BAE NM_001171167.1 15/23 PROSITE_profiles:PS50297,hmmpanther:PTHR23335,hmmpanther:PTHR23335:SF9,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 4972950 4972950 G C 1 0 0 0 0 0 0 0 1 2307 1161 41 4 4 CAMTA2 17 4972950 Silent SNP G C3L-02345_T 1539230 4972950 78284491 183 8781 DNAH9 0 . GRCh38 17 11883592 11883592 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.10813C>T p.Leu3605Phe p.L3605F ENST00000262442 56/69 90 72 18 114 114 0 strelka-varscan-mutect DNAH9,missense_variant,p.Leu3605Phe,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Leu3605Phe,ENST00000454412,;DNAH9,5_prime_UTR_variant,,ENST00000608377,NM_004662.2;DNAH9,downstream_gene_variant,,ENST00000579703,;DNAH9,non_coding_transcript_exon_variant,,ENST00000396001,;DNAH9,upstream_gene_variant,,ENST00000581682,;DNAH9,downstream_gene_variant,,ENST00000580255,; T ENST00000262442 Transcript missense_variant 10881/13750 10813/13461 3605/4486 L/F Ctc/Ttc 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0) 56/69 Pfam_domain:PF12781,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 11883592 11883592 C T 1 0 0 0 0 1 0 0 0 4423 913 32 3 3 DNAH9 17 11883592 Missense_Mutation SNP C C3L-02345_T 6910642 11883592 71373849 184 8782 NF1 0 . GRCh38 17 31201079 31201079 + Nonsense_Mutation SNP C C T C3L-02345_T C3L-02345_N C C c.1105C>T p.Gln369Ter p.Q369* ENST00000358273 10/58 389 308 81 368 368 0 strelka-varscan-mutect NF1,stop_gained,p.Gln369Ter,ENST00000358273,NM_001042492.2;NF1,stop_gained,p.Gln369Ter,ENST00000356175,NM_000267.3;NF1,stop_gained,p.Gln35Ter,ENST00000456735,;NF1,stop_gained,p.Gln369Ter,ENST00000431387,NM_001128147.2;NF1,stop_gained,p.Gln403Ter,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,; T ENST00000358273 Transcript stop_gained 1488/12425 1105/8520 369/2839 Q/* Cag/Tag COSM24452 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 10/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 31201079 31201079 C T 1 0 0 0 0 0 1 0 0 10393 827 29 3 3 NF1 17 31201079 Nonsense_Mutation SNP C C3L-02345_T 19317487 31201079 52056362 185 8783 CSF3 0 . GRCh38 17 40016236 40016236 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.208G>C p.Ala70Pro p.A70P ENST00000225474 3/5 61 45 16 61 61 0 strelka-varscan-mutect CSF3,missense_variant,p.Ala63Pro,ENST00000331769,;CSF3,missense_variant,p.Ala67Pro,ENST00000394149,NM_172219.2;CSF3,missense_variant,p.Ala70Pro,ENST00000225474,NM_000759.3;CSF3,intron_variant,,ENST00000577675,;CSF3,intron_variant,,ENST00000394148,NM_172220.2,NM_001178147.1;CSF3,intron_variant,,ENST00000583218,;MED24,downstream_gene_variant,,ENST00000394126,;MED24,downstream_gene_variant,,ENST00000394128,NM_014815.3;MED24,downstream_gene_variant,,ENST00000394127,NM_001079518.1;MED24,downstream_gene_variant,,ENST00000356271,NM_001267797.1;MED24,downstream_gene_variant,,ENST00000501516,;MED24,downstream_gene_variant,,ENST00000422942,;MED24,downstream_gene_variant,,ENST00000614384,;RP11-387H17.6,upstream_gene_variant,,ENST00000583462,;RP11-387H17.6,upstream_gene_variant,,ENST00000584649,;MED24,downstream_gene_variant,,ENST00000470126,;CSF3,missense_variant,p.Cys15Ser,ENST00000579852,;CSF3,non_coding_transcript_exon_variant,,ENST00000479880,;MED24,downstream_gene_variant,,ENST00000535508,;MED24,downstream_gene_variant,,ENST00000491466,;MED24,downstream_gene_variant,,ENST00000579364,;CSF3,downstream_gene_variant,,ENST00000582798,; C ENST00000225474 Transcript missense_variant 239/1509 208/624 70/207 A/P Gcc/Ccc 1 1 CSF3 HGNC HGNC:2438 protein_coding YES CCDS11357.1 ENSP00000225474 P09919 UPI0000128525 NM_000759.3 tolerated(0.09) 3/5 Gene3D:1.20.1250.10,Pfam_domain:PF16647,PIRSF_domain:PIRSF001935,Prints_domain:PR00433,hmmpanther:PTHR10511,SMART_domains:SM00126,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 40016236 40016236 G C 1 0 0 0 0 1 0 0 0 3737 1333 46 4 4 CSF3 17 40016236 Missense_Mutation SNP G C3L-02345_T 8815157 40016236 43241205 186 8784 KRT222 0 . GRCh38 17 40657694 40657694 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.503T>C p.Val168Ala p.V168A ENST00000394052 4/6 184 156 28 205 205 0 strelka-varscan-mutect KRT222,missense_variant,p.Val168Ala,ENST00000394052,NM_152349.2;RP5-1028K7.3,missense_variant,p.Val168Ala,ENST00000476049,;KRT222,3_prime_UTR_variant,,ENST00000394049,;KRT222,3_prime_UTR_variant,,ENST00000581564,;KRT222,downstream_gene_variant,,ENST00000580719,; G ENST00000394052 Transcript missense_variant 545/1712 503/888 168/295 V/A gTt/gCt 1 -1 KRT222 HGNC HGNC:28695 protein_coding YES CCDS11371.1 ENSP00000377616 Q8N1A0 UPI0000072F8A NM_152349.2 tolerated(0.15) 4/6 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF217 MODERATE 1 SNV 1 1 PASS rs759752785 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 40657694 40657694 A G 1 0 0 0 0 1 0 0 0 8341 43 2 5 5 KRT222 17 40657694 Missense_Mutation SNP A C3L-02345_T 641458 40657694 42599747 187 8785 BRCA1 0 . GRCh38 17 43045694 43045694 + Missense_Mutation SNP G G A rs80357322 C3L-02345_T C3L-02345_N G G c.5639C>T p.Pro1880Leu p.P1880L ENST00000471181 24/24 97 70 27 155 155 0 strelka-varscan-mutect BRCA1,missense_variant,p.Pro1859Leu,ENST00000357654,NM_007294.3;BRCA1,missense_variant,p.Pro1880Leu,ENST00000471181,NM_007300.3;BRCA1,missense_variant,p.Pro1812Leu,ENST00000493795,NM_007297.3;BRCA1,missense_variant,p.Pro717Leu,ENST00000352993,;BRCA1,missense_variant,p.Pro755Leu,ENST00000491747,NM_007298.3;BRCA1,missense_variant,p.Pro350Leu,ENST00000591534,;BRCA1,missense_variant,p.Pro169Leu,ENST00000586385,;BRCA1,missense_variant,p.Pro92Leu,ENST00000591849,;BRCA1,3_prime_UTR_variant,,ENST00000468300,NM_007299.3;BRCA1,3_prime_UTR_variant,,ENST00000461221,; A ENST00000471181 Transcript missense_variant 5871/5936 5639/5655 1880/1884 P/L cCc/cTc rs80357322 1 -1 BRCA1 HGNC HGNC:1100 protein_coding YES CCDS11456.2 ENSP00000418960 P38398 UPI0000E0360B NM_007300.3 deleterious_low_confidence(0) 24/24 hmmpanther:PTHR13763:SF0,hmmpanther:PTHR13763 uncertain_significance,benign,likely_benign MODERATE 1 SNV 1 1 1 PASS rs80357322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 43045694 43045694 G A 1 0 0 0 0 1 0 0 0 1668 1232 43 3 3 BRCA1 17 43045694 Missense_Mutation SNP G C3L-02345_T 2388000 43045694 40211747 188 8786 HOXB6 0 . GRCh38 17 48597926 48597926 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.225G>T p.= p.G75G ENST00000484302 2/3 137 112 25 156 156 0 strelka-varscan-mutect HOXB6,synonymous_variant,p.=,ENST00000484302,;HOXB6,synonymous_variant,p.=,ENST00000225648,NM_018952.4;HOXB5,upstream_gene_variant,,ENST00000239151,NM_002147.3;HOXB-AS3,intron_variant,,ENST00000477144,;HOXB-AS3,intron_variant,,ENST00000474040,;HOXB-AS3,intron_variant,,ENST00000460041,;HOXB-AS3,intron_variant,,ENST00000476204,;HOXB-AS3,intron_variant,,ENST00000481995,;HOXB-AS3,intron_variant,,ENST00000466037,;HOXB-AS3,intron_variant,,ENST00000467155,;HOXB-AS3,intron_variant,,ENST00000480872,;HOXB-AS3,intron_variant,,ENST00000429755,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS3,intron_variant,,ENST00000487849,;HOXB-AS3,intron_variant,,ENST00000474324,;HOXB-AS3,intron_variant,,ENST00000492897,;HOXB-AS3,upstream_gene_variant,,ENST00000491264,;HOXB-AS3,upstream_gene_variant,,ENST00000494420,;HOXB3,intron_variant,,ENST00000552000,;HOXB6,downstream_gene_variant,,ENST00000490419,;HOXB6,upstream_gene_variant,,ENST00000470193,; A ENST00000484302 Transcript synonymous_variant 848/1960 225/675 75/224 G ggG/ggT 1 -1 HOXB6 HGNC HGNC:5117 protein_coding YES CCDS11531.1 ENSP00000420009 P17509 UPI000013C877 2/3 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF253 LOW SNV 2 1 PASS rs1282860525 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 48597926 48597926 C A 1 0 0 0 0 0 0 0 1 7199 726 26 2 2 HOXB6 17 48597926 Silent SNP C C3L-02345_T 5552232 48597926 34659515 189 8787 ANKFN1 0 . GRCh38 17 56457959 56457959 + Missense_Mutation SNP G G T rs766900651 C3L-02345_T C3L-02345_N G G c.1546G>T p.Ala516Ser p.A516S ENST00000318698 13/17 175 136 39 161 161 0 strelka-varscan-mutect ANKFN1,missense_variant,p.Ala516Ser,ENST00000566473,;ANKFN1,missense_variant,p.Ala516Ser,ENST00000318698,NM_153228.2;ANKFN1,non_coding_transcript_exon_variant,,ENST00000572321,; T ENST00000318698 Transcript missense_variant 1581/2426 1546/2292 516/763 A/S Gca/Tca rs766900651,COSM3194396 1 1 ANKFN1 HGNC HGNC:26766 protein_coding YES CCDS32686.1 ENSP00000321627 Q8N957 UPI000049DE57 NM_153228.2 tolerated(0.88) 13/17 hmmpanther:PTHR21437,hmmpanther:PTHR21437:SF3 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs766900651 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 56457959 56457959 G T 1 0 0 0 0 1 0 0 0 727 1087 38 1 1 ANKFN1 17 56457959 Missense_Mutation SNP G C3L-02345_T 7860033 56457959 26799482 190 8788 TLK2 0 . GRCh38 17 62606143 62606143 + Nonsense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1939G>T p.Glu647Ter p.E647* ENST00000326270 21/23 54 45 9 51 51 0 varscan-mutect TLK2,stop_gained,p.Glu476Ter,ENST00000582809,;TLK2,stop_gained,p.Glu647Ter,ENST00000326270,NM_001284333.1;TLK2,stop_gained,p.Glu625Ter,ENST00000346027,NM_006852.3;TLK2,stop_gained,p.Glu593Ter,ENST00000343388,NM_001284363.1;TLK2,stop_gained,p.Glu561Ter,ENST00000581041,;TLK2,non_coding_transcript_exon_variant,,ENST00000578931,;TLK2,non_coding_transcript_exon_variant,,ENST00000583310,; T ENST00000326270 Transcript stop_gained 2207/3512 1939/2319 647/772 E/* Gag/Tag 1 1 TLK2 HGNC HGNC:11842 protein_coding YES CCDS62283.1 ENSP00000316512 Q86UE8 UPI00001B6B0E NM_001284333.1 21/23 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF20,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS rs1187350981 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 62606143 62606143 G T 1 0 0 0 0 0 1 0 0 16390 943 33 2 2 TLK2 17 62606143 Nonsense_Mutation SNP G C3L-02345_T 6148184 62606143 20651298 191 8789 TANC2 0 . GRCh38 17 63389537 63389537 + Missense_Mutation SNP G G T rs371161191 C3L-02345_T C3L-02345_N G G c.2822G>T p.Arg941Leu p.R941L ENST00000424789 15/25 389 315 74 420 419 1 strelka-varscan-mutect TANC2,missense_variant,p.Arg941Leu,ENST00000424789,NM_025185.3;TANC2,missense_variant,p.Arg870Leu,ENST00000583356,;TANC2,missense_variant,p.Arg941Leu,ENST00000389520,;TANC2,missense_variant,p.Arg42Leu,ENST00000613171,;AC015923.1,intron_variant,,ENST00000431604,;RP11-269G24.3,downstream_gene_variant,,ENST00000583552,;TANC2,non_coding_transcript_exon_variant,,ENST00000583545,;TANC2,non_coding_transcript_exon_variant,,ENST00000581143,;RP11-269G24.7,upstream_gene_variant,,ENST00000606610,; T ENST00000424789 Transcript missense_variant 2826/11721 2822/5973 941/1990 R/L cGg/cTg rs371161191 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 deleterious(0.01) 15/25 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs371161191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 63389537 63389537 G T 1 0 0 0 0 1 0 0 0 15942 1116 39 1 1 TANC2 17 63389537 Missense_Mutation SNP G C3L-02345_T 783394 63389537 19867904 192 8790 BPTF 0 . GRCh38 17 67826175 67826201 + In_Frame_Del DEL GACGCCGAGGAGACCCAGGATTCTGAG GACGCCGAGGAGACCCAGGATTCTGAG - novel C3L-02345_T C3L-02345_N GACGCCGAGGAGACCCAGGATTCTGAG GACGCCGAGGAGACCCAGGATTCTGAG c.455_481delCCGAGGAGACCCAGGATTCTGAGGACG p.Ala152_Asp160del p.A152_D160del ENST00000306378 1/28 225 188 37 283 283 0 sindel-pindel BPTF,inframe_deletion,p.Ala152_Asp160del,ENST00000321892,NM_004459.6;BPTF,inframe_deletion,p.Ala152_Asp160del,ENST00000306378,NM_182641.3;BPTF,inframe_deletion,p.Ala13_Asp21del,ENST00000424123,;BPTF,inframe_deletion,p.Ala152_Asp160del,ENST00000544778,;BPTF,inframe_deletion,p.Ala13_Asp21del,ENST00000335221,; - ENST00000306378 Transcript inframe_deletion 511-537/9688 451-477/8763 151-159/2920 DAEETQDSE/- GACGCCGAGGAGACCCAGGATTCTGAG/- 1 1 BPTF HGNC HGNC:3581 protein_coding YES CCDS11673.1 ENSP00000307208 Q12830 UPI00002263BF NM_182641.3 1/28 Low_complexity_(Seg):seg MODERATE 1 deletion 1 4 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 31 67826175 67826175 GACGCCGAGGAGACCCAGGATTCTGAG - 1 0 1 0 1 0 0 0 0 1664 1058 37 0 0 BPTF 17 67826175 In_Frame_Del DEL GACGCCGAGGAGACCCAGGATTCTGAG C3L-02345_T 4436638 67826175 15431266 193 8791 SSTR2 0 . GRCh38 17 73169779 73169779 + Missense_Mutation SNP A A T C3L-02345_T C3L-02345_N A A c.460A>T p.Arg154Trp p.R154W ENST00000357585 2/2 233 212 21 218 218 0 strelka-varscan-mutect SSTR2,missense_variant,p.Arg154Trp,ENST00000357585,NM_001050.2;RP11-143K11.5,intron_variant,,ENST00000580671,;SSTR2,downstream_gene_variant,,ENST00000579323,; T ENST00000357585 Transcript missense_variant 829/7683 460/1110 154/369 R/W Agg/Tgg COSM437266,COSM5207106 1 1 SSTR2 HGNC HGNC:11331 protein_coding YES CCDS11691.1 ENSP00000350198 P30874 UPI0000000808 NM_001050.2 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF6,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 73169779 73169779 A T 1 0 0 0 0 1 0 0 0 15575 295 11 4 4 SSTR2 17 73169779 Missense_Mutation SNP A C3L-02345_T 5343604 73169779 10087662 194 8792 TMC8 0 . GRCh38 17 78138160 78138160 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.1505T>A p.Phe502Tyr p.F502Y ENST00000318430 12/16 403 322 81 400 400 0 strelka-varscan-mutect TMC8,missense_variant,p.Phe502Tyr,ENST00000318430,NM_152468.4;TMC8,missense_variant,p.Phe279Tyr,ENST00000589691,;TMC8,non_coding_transcript_exon_variant,,ENST00000591003,;TMC8,upstream_gene_variant,,ENST00000591144,;TMC8,downstream_gene_variant,,ENST00000592399,;TMC8,downstream_gene_variant,,ENST00000590184,;TMC8,downstream_gene_variant,,ENST00000591983,; A ENST00000318430 Transcript missense_variant 1879/4411 1505/2181 502/726 F/Y tTc/tAc 1 1 TMC8 HGNC HGNC:20474 protein_coding YES CCDS32749.1 ENSP00000325561 Q8IU68 A0A024R8N8 UPI00000747D3 NM_152468.4 tolerated(0.08) 12/16 Pfam_domain:PF07810,hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF39,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 78138160 78138160 T A 1 0 0 0 0 1 0 0 0 16437 1783 62 4 4 TMC8 17 78138160 Missense_Mutation SNP T C3L-02345_T 4968381 78138160 5119281 195 8793 TXNDC2 0 . GRCh38 18 9887270 9887270 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.791C>A p.Pro264His p.P264H ENST00000306084 2/2 222 184 38 262 262 0 strelka-varscan-mutect TXNDC2,missense_variant,p.Pro197His,ENST00000357775,NM_032243.5;TXNDC2,missense_variant,p.Pro264His,ENST00000611534,;TXNDC2,missense_variant,p.Pro264His,ENST00000306084,NM_001098529.1;TXNDC2,intron_variant,,ENST00000536353,;TXNDC2,downstream_gene_variant,,ENST00000584255,;TXNDC2,downstream_gene_variant,,ENST00000426718,; A ENST00000306084 Transcript missense_variant 990/1873 791/1662 264/553 P/H cCc/cAc 1 1 TXNDC2 HGNC HGNC:16470 protein_coding YES CCDS42414.1 ENSP00000304908 Q86VQ3 A0A140VJY8 UPI000013EAE7 NM_001098529.1 deleterious(0.01) 2/2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 9887270 9887270 C A 1 0 0 0 0 1 0 0 0 17313 623 22 2 2 TXNDC2 18 9887270 Missense_Mutation SNP C C3L-02345_T 9887270 70486015 196 8794 DSG4 0 . GRCh38 18 31409503 31409503 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1985G>A p.Gly662Asp p.G662D ENST00000359747 13/15 550 474 76 577 577 0 strelka-varscan-mutect DSG4,missense_variant,p.Gly662Asp,ENST00000359747,NM_001134453.1;DSG4,missense_variant,p.Gly662Asp,ENST00000308128,NM_177986.3;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578477,; A ENST00000359747 Transcript missense_variant 2014/4526 1985/3180 662/1059 G/D gGc/gAc 1 1 DSG4 HGNC HGNC:21307 protein_coding YES CCDS45845.1 ENSP00000352785 Q86SJ6 UPI000035DB4E NM_001134453.1 deleterious(0.02) 13/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 31409503 31409503 G A 1 0 0 0 0 1 0 0 0 4600 1203 42 3 3 DSG4 18 31409503 Missense_Mutation SNP G C3L-02345_T 21522233 31409503 48963782 197 8795 PRSS57 0 . GRCh38 19 687161 687161 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.409G>C p.Ala137Pro p.A137P ENST00000613411 4/5 38 29 9 50 50 0 strelka-varscan-mutect PRSS57,missense_variant,p.Ala137Pro,ENST00000613411,NM_214710.3;PRSS57,missense_variant,p.Ala136Pro,ENST00000329267,NM_001308209.1;FSTL3,downstream_gene_variant,,ENST00000166139,NM_005860.2;FSTL3,downstream_gene_variant,,ENST00000592947,;RPS2P52,upstream_gene_variant,,ENST00000469610,; G ENST00000613411 Transcript missense_variant 477/1090 409/852 137/283 A/P Gca/Cca 1 -1 PRSS57 HGNC HGNC:31397 protein_coding YES CCDS12041.1 ENSP00000482358 Q6UWY2 UPI000022AA4D NM_214710.3 tolerated(0.19) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF159,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.99936 1 1 1 1 0 G 3 3 31 687161 687161 C G 1 0 0 0 0 1 0 0 0 12784 710 25 4 4 PRSS57 19 687161 Missense_Mutation SNP C C3L-02345_T 687161 57930455 198 8796 ABCA7 0 . GRCh38 19 1046996 1046996 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1817G>T p.Ser606Ile p.S606I ENST00000263094 14/47 114 88 26 176 176 0 strelka-varscan-mutect ABCA7,missense_variant,p.Ser606Ile,ENST00000263094,NM_019112.3;ABCA7,missense_variant,p.Ser606Ile,ENST00000433129,;ABCA7,missense_variant,p.Ser468Ile,ENST00000435683,;ABCA7,downstream_gene_variant,,ENST00000524850,;ABCA7,downstream_gene_variant,,ENST00000531467,;ABCA7,intron_variant,,ENST00000533574,;ABCA7,downstream_gene_variant,,ENST00000525238,;ABCA7,downstream_gene_variant,,ENST00000526885,;ABCA7,downstream_gene_variant,,ENST00000527496,; T ENST00000263094 Transcript missense_variant 2048/6816 1817/6441 606/2146 S/I aGc/aTc 1 1 ABCA7 HGNC HGNC:37 protein_coding YES CCDS12055.1 ENSP00000263094 Q8IZY2 UPI000013D3A4 NM_019112.3 deleterious(0) 14/47 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF49,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 1046996 1046996 G T 1 0 0 0 0 1 0 0 0 41 971 34 2 2 ABCA7 19 1046996 Missense_Mutation SNP G C3L-02345_T 359835 1046996 57570620 199 8797 STK11 0 . GRCh38 19 1207077 1207078 + Frame_Shift_Ins INS - - G novel C3L-02345_T C3L-02345_N - - c.169dupG p.Glu57GlyfsTer106 p.E57Gfs*106 ENST00000326873 1/10 236 183 53 310 309 1 sindel-varindel-pindel STK11,frameshift_variant,p.Glu57GlyfsTer106,ENST00000586243,;STK11,frameshift_variant,p.Glu57GlyfsTer106,ENST00000326873,NM_000455.4;STK11,frameshift_variant,p.Glu57GlyfsTer48,ENST00000585851,;STK11,intron_variant,,ENST00000585748,;STK11,frameshift_variant,p.Glu57GlyfsTer?,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,upstream_gene_variant,,ENST00000586358,;HMGB2P1,downstream_gene_variant,,ENST00000591146,; G ENST00000326873 Transcript frameshift_variant 614-615/2611 164-165/1302 55/433 L/LX ctg/ctGg 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 1/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 insertion 1 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 31 1207077 1207077 - G 1 0 1 1 0 0 0 0 0 15664 1580 55 0 0 STK11 19 1207077 Frame_Shift_Ins INS - C3L-02345_T 160081 1207077 57410539 200 8798 SMARCA4 0 . GRCh38 19 11059834 11059834 + Nonsense_Mutation SNP G G T rs775433905 C3L-02345_T C3L-02345_N G G c.4717G>T p.Glu1573Ter p.E1573* ENST00000429416 34/36 293 218 75 355 354 1 strelka-varscan-mutect SMARCA4,stop_gained,p.Glu1573Ter,ENST00000429416,NM_001128844.1;SMARCA4,stop_gained,p.Glu1607Ter,ENST00000413806,;SMARCA4,stop_gained,p.Glu1605Ter,ENST00000450717,NM_001128849.1;SMARCA4,stop_gained,p.Glu1573Ter,ENST00000344626,NM_003072.3;SMARCA4,stop_gained,p.Glu1540Ter,ENST00000590574,NM_001128847.1;SMARCA4,stop_gained,p.Glu1542Ter,ENST00000589677,NM_001128846.1;SMARCA4,stop_gained,p.Glu1543Ter,ENST00000541122,NM_001128845.1;SMARCA4,stop_gained,p.Glu1539Ter,ENST00000444061,NM_001128848.1;SMARCA4,stop_gained,p.Glu47Ter,ENST00000586985,;SMARCA4,upstream_gene_variant,,ENST00000586921,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,; T ENST00000429416 Transcript stop_gained 4998/5691 4717/4944 1573/1647 E/* Gag/Tag rs775433905 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 34/36 Low_complexity_(Seg):seg HIGH 1 SNV 2 1 PASS rs775433905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 11059834 11059834 G T 1 0 0 0 0 0 1 0 0 15063 1059 37 1 1 SMARCA4 19 11059834 Nonsense_Mutation SNP G C3L-02345_T 9852757 11059834 47557782 201 8799 MAST1 0 . GRCh38 19 12858680 12858680 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1307G>T p.Gly436Val p.G436V ENST00000251472 12/26 386 295 91 460 460 0 strelka-varscan-mutect MAST1,missense_variant,p.Gly436Val,ENST00000251472,NM_014975.2;MAST1,missense_variant,p.Gly432Val,ENST00000591495,;MAST1,missense_variant,p.Gly390Val,ENST00000588379,;HOOK2,intron_variant,,ENST00000589765,;MAST1,non_coding_transcript_exon_variant,,ENST00000589040,; T ENST00000251472 Transcript missense_variant 1346/4833 1307/4713 436/1570 G/V gGc/gTc 1 1 MAST1 HGNC HGNC:19034 protein_coding YES CCDS32921.1 ENSP00000251472 Q9Y2H9 UPI000004A042 NM_014975.2 deleterious(0) 12/26 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF150,hmmpanther:PTHR24356,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 12858680 12858680 G T 1 0 0 0 0 1 0 0 0 9250 1203 42 2 2 MAST1 19 12858680 Missense_Mutation SNP G C3L-02345_T 1798846 12858680 45758936 202 8800 SUGP2 0 . GRCh38 19 19004375 19004375 + Missense_Mutation SNP C C A rs202004163 C3L-02345_T C3L-02345_N C C c.2722G>T p.Ala908Ser p.A908S ENST00000452918 7/11 83 58 25 141 140 1 strelka-varscan-mutect SUGP2,missense_variant,p.Ala908Ser,ENST00000452918,NM_001321699.1,NM_001017392.3;SUGP2,missense_variant,p.Ala908Ser,ENST00000601879,;SUGP2,missense_variant,p.Ala922Ser,ENST00000600377,;SUGP2,missense_variant,p.Ala908Ser,ENST00000337018,NM_001321697.1,NM_001321698.1,NM_014884.3;SUGP2,3_prime_UTR_variant,,ENST00000600239,;SUGP2,3_prime_UTR_variant,,ENST00000598240,;SUGP2,intron_variant,,ENST00000594773,;SUGP2,intron_variant,,ENST00000330854,;SUGP2,upstream_gene_variant,,ENST00000597280,;SUGP2,upstream_gene_variant,,ENST00000593795,; A ENST00000452918 Transcript missense_variant 2796/6176 2722/3249 908/1082 A/S Gct/Tct rs202004163 1 -1 SUGP2 HGNC HGNC:18641 protein_coding YES CCDS12392.1 ENSP00000389380 Q8IX01 UPI000019825D NM_001321699.1,NM_001017392.3 tolerated(0.86) 7/11 Low_complexity_(Seg):seg,hmmpanther:PTHR23340,hmmpanther:PTHR23340:SF2 MODERATE 1 SNV 1 1 PASS rs202004163 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 19004375 19004375 C A 1 0 0 0 0 1 0 0 0 15756 768 27 1 1 SUGP2 19 19004375 Missense_Mutation SNP C C3L-02345_T 6145695 19004375 39613241 203 8801 ARMC6 0 . GRCh38 19 19055389 19055389 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1148G>T p.Ser383Ile p.S383I ENST00000535612 7/9 61 41 20 68 68 0 strelka-mutect ARMC6,missense_variant,p.Ser383Ile,ENST00000535612,NM_001199196.1;ARMC6,missense_variant,p.Ser358Ile,ENST00000269932,;ARMC6,missense_variant,p.Ser358Ile,ENST00000392335,NM_033415.3;ARMC6,missense_variant,p.Ser383Ile,ENST00000392336,;ARMC6,missense_variant,p.Ser290Ile,ENST00000546344,;ARMC6,missense_variant,p.Ser47Ile,ENST00000535795,;ARMC6,missense_variant,p.Ser73Ile,ENST00000535478,;ARMC6,upstream_gene_variant,,ENST00000540634,;ARMC6,downstream_gene_variant,,ENST00000537263,;ARMC6,downstream_gene_variant,,ENST00000541898,;ARMC6,downstream_gene_variant,,ENST00000540792,;ARMC6,downstream_gene_variant,,ENST00000535288,;ARMC6,downstream_gene_variant,,ENST00000536098,;ARMC6,downstream_gene_variant,,ENST00000541725,;ARMC6,downstream_gene_variant,,ENST00000538663,;ARMC6,downstream_gene_variant,,ENST00000539985,;ARMC6,downstream_gene_variant,,ENST00000545091,;ARMC6,downstream_gene_variant,,ENST00000535758,; T ENST00000535612 Transcript missense_variant 1580/2488 1148/1506 383/501 S/I aGc/aTc 1 1 ARMC6 HGNC HGNC:25049 protein_coding YES CCDS56089.1 ENSP00000444156 Q6NXE6 UPI0000D4C04D NM_001199196.1 deleterious(0.02) 7/9 Gene3D:1.25.10.10,hmmpanther:PTHR22895,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 19055389 19055389 G T 1 0 0 0 0 1 0 0 0 1096 971 34 2 2 ARMC6 19 19055389 Missense_Mutation SNP G C3L-02345_T 51014 19055389 39562227 204 8802 UPK1A 0 . GRCh38 19 35668625 35668625 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.256C>A p.Leu86Ile p.L86I ENST00000616789 3/9 154 118 36 183 183 0 strelka-varscan-mutect UPK1A,missense_variant,p.Leu86Ile,ENST00000616789,NM_001281443.1;UPK1A,missense_variant,p.Leu86Ile,ENST00000617999,NM_007000.3;UPK1A,missense_variant,p.Leu86Ile,ENST00000222275,;UPK1A,missense_variant,p.Leu86Ile,ENST00000379013,;UPK1A-AS1,non_coding_transcript_exon_variant,,ENST00000443196,; A ENST00000616789 Transcript missense_variant 283/1366 256/822 86/273 L/I Ctc/Atc 1 1 UPK1A HGNC HGNC:12577 protein_coding YES CCDS62640.1 ENSP00000478942 O00322 UPI00005C40C1 NM_001281443.1 tolerated(0.35) 3/9 Pfam_domain:PF00335,Prints_domain:PR00259,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF25 MODERATE SNV 5 1 PASS rs981011094 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 35668625 35668625 C A 1 0 0 0 0 1 0 0 0 17533 565 20 2 2 UPK1A 19 35668625 Missense_Mutation SNP C C3L-02345_T 16613236 35668625 22948991 205 8803 ZNF345 0 . GRCh38 19 36877356 36877356 + Missense_Mutation SNP T T A novel C3L-02345_T C3L-02345_N T T c.526T>A p.Cys176Ser p.C176S ENST00000529555 2/2 216 180 36 234 233 1 strelka-varscan-mutect ZNF345,missense_variant,p.Cys176Ser,ENST00000529555,;ZNF345,missense_variant,p.Cys176Ser,ENST00000589046,NM_003419.4;ZNF345,missense_variant,p.Cys176Ser,ENST00000614069,NM_001242474.1;ZNF345,missense_variant,p.Cys176Ser,ENST00000612719,NM_001242476.1,NM_001242475.1;ZNF345,missense_variant,p.Cys176Ser,ENST00000420450,NM_001242472.1;ZNF345,missense_variant,p.Cys176Ser,ENST00000585396,;ZNF345,intron_variant,,ENST00000586933,;ZNF345,intron_variant,,ENST00000526123,;ZNF345,downstream_gene_variant,,ENST00000532141,;ZNF345,downstream_gene_variant,,ENST00000586646,;ZNF345,downstream_gene_variant,,ENST00000331800,;ZNF345,intron_variant,,ENST00000432005,;ZNF345,intron_variant,,ENST00000529989,;ZNF345,intron_variant,,ENST00000525851,;ZNF345,intron_variant,,ENST00000534729,; A ENST00000529555 Transcript missense_variant 1314/3527 526/1467 176/488 C/S Tgt/Agt 1 1 ZNF345 HGNC HGNC:16367 protein_coding YES CCDS12497.1 ENSP00000431202 Q14585 UPI000013C364 deleterious(0) 2/2 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 36877356 36877356 T A 1 0 0 0 0 1 0 0 0 18431 1696 59 4 4 ZNF345 19 36877356 Missense_Mutation SNP T C3L-02345_T 1208731 36877356 21740260 206 8804 ZNF420 0 . GRCh38 19 37127787 37127787 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.796C>G p.Leu266Val p.L266V ENST00000337995 5/5 205 170 35 240 240 0 strelka-varscan-mutect ZNF420,missense_variant,p.Leu266Val,ENST00000337995,NM_144689.3;ZNF420,missense_variant,p.Leu266Val,ENST00000304239,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,downstream_gene_variant,,ENST00000589245,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000590332,;ZNF420,upstream_gene_variant,,ENST00000585862,;CTC-454I21.4,downstream_gene_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,upstream_gene_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,; G ENST00000337995 Transcript missense_variant 1011/3535 796/2067 266/688 L/V Ctt/Gtt 1 1 ZNF420 HGNC HGNC:20649 protein_coding YES CCDS12498.1 ENSP00000338770 Q8TAQ5 UPI000007049F NM_144689.3 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF290,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 37127787 37127787 C G 1 0 0 0 0 1 0 0 0 18469 565 20 4 4 ZNF420 19 37127787 Missense_Mutation SNP C C3L-02345_T 250431 37127787 21489829 207 8805 LTBP4 0 . GRCh38 19 40605456 40605456 + Missense_Mutation SNP T T G novel C3L-02345_T C3L-02345_N T T c.695T>G p.Val232Gly p.V232G ENST00000308370 6/33 323 254 69 330 330 0 strelka-varscan-mutect LTBP4,missense_variant,p.Val195Gly,ENST00000204005,NM_003573.2;LTBP4,missense_variant,p.Val232Gly,ENST00000308370,NM_001042544.1;LTBP4,missense_variant,p.Val165Gly,ENST00000396819,NM_001042545.1;LTBP4,upstream_gene_variant,,ENST00000243562,;LTBP4,3_prime_UTR_variant,,ENST00000599016,;LTBP4,3_prime_UTR_variant,,ENST00000594537,;LTBP4,intron_variant,,ENST00000598717,;LTBP4,upstream_gene_variant,,ENST00000546155,;LTBP4,upstream_gene_variant,,ENST00000595529,;LTBP4,upstream_gene_variant,,ENST00000598256,;LTBP4,downstream_gene_variant,,ENST00000600026,;LTBP4,downstream_gene_variant,,ENST00000593738,; G ENST00000308370 Transcript missense_variant 695/4948 695/4875 232/1624 V/G gTg/gGg 1 1 LTBP4 HGNC HGNC:6717 protein_coding YES CCDS74369.1 ENSP00000311905 Q8N2S1 UPI0000DACAC4 NM_001042544.1 deleterious(0) 6/33 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF43 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 40605456 40605456 T G 1 0 0 0 0 1 0 0 0 8982 1696 59 5 5 LTBP4 19 40605456 Missense_Mutation SNP T C3L-02345_T 3477669 40605456 18012160 208 8806 SHANK1 0 . GRCh38 19 50668308 50668308 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.3652G>T p.Ala1218Ser p.A1218S ENST00000293441 22/23 32 22 10 20 20 0 strelka-varscan-mutect SHANK1,missense_variant,p.Ala1218Ser,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Ala1226Ser,ENST00000391814,;SHANK1,missense_variant,p.Ala1209Ser,ENST00000359082,;SHANK1,missense_variant,p.Ala605Ser,ENST00000391813,;SHANK1,upstream_gene_variant,,ENST00000468654,; A ENST00000293441 Transcript missense_variant 3671/6643 3652/6486 1218/2161 A/S Gcc/Tcc 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 tolerated_low_confidence(0.91) 22/23 Low_complexity_(Seg):seg,hmmpanther:PTHR24135:SF3,hmmpanther:PTHR24135 MODERATE 1 SNV 1 1 PASS . . 1 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 31 50668308 50668308 C A 1 0 0 0 0 1 0 0 0 14523 768 27 1 1 SHANK1 19 50668308 Missense_Mutation SNP C C3L-02345_T 10062852 50668308 7949308 209 8807 ZNF611 0 . GRCh38 19 52705371 52705371 + Nonsense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1684G>T p.Gly562Ter p.G562* ENST00000543227 6/6 208 159 49 216 216 0 strelka-varscan-mutect ZNF611,stop_gained,p.Gly562Ter,ENST00000543227,NM_001161499.1;ZNF611,stop_gained,p.Gly562Ter,ENST00000540744,NM_001161500.1;ZNF611,stop_gained,p.Gly493Ter,ENST00000453741,NM_001161501.1;ZNF611,stop_gained,p.Gly493Ter,ENST00000602162,;ZNF611,stop_gained,p.Gly562Ter,ENST00000319783,NM_030972.3;ZNF611,stop_gained,p.Gly493Ter,ENST00000595798,;ZNF611,downstream_gene_variant,,ENST00000600943,;ZNF611,downstream_gene_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000601643,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,3_prime_UTR_variant,,ENST00000601249,;ZNF611,downstream_gene_variant,,ENST00000597343,;ZNF611,downstream_gene_variant,,ENST00000598639,;ZNF611,downstream_gene_variant,,ENST00000598723,; A ENST00000543227 Transcript stop_gained 1959/4517 1684/2118 562/705 G/* Gga/Tga 1 -1 ZNF611 HGNC HGNC:28766 protein_coding YES CCDS12855.1 ENSP00000437616 Q8N823 UPI00001406C1 NM_001161499.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF375,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 31 52705371 52705371 C A 1 0 0 0 0 0 1 0 0 18612 603 21 2 2 ZNF611 19 52705371 Nonsense_Mutation SNP C C3L-02345_T 2037063 52705371 5912245 210 8808 LAIR2 0 . GRCh38 19 54507995 54507995 + Missense_Mutation SNP C C T rs763891376 C3L-02345_T C3L-02345_N C C c.175C>T p.Arg59Cys p.R59C ENST00000301202 3/5 305 245 60 280 280 0 strelka-varscan-mutect LAIR2,missense_variant,p.Arg59Cys,ENST00000301202,NM_002288.5;LAIR2,missense_variant,p.Arg53Cys,ENST00000412608,;LAIR2,missense_variant,p.Arg41Cys,ENST00000610651,;LAIR2,missense_variant,p.Arg59Cys,ENST00000351841,NM_021270.4; T ENST00000301202 Transcript missense_variant 297/699 175/459 59/152 R/C Cgc/Tgc rs763891376 1 1 LAIR2 HGNC HGNC:6478 protein_coding YES CCDS12897.1 ENSP00000301202 Q6ISS4 UPI000013E6E5 NM_002288.5 deleterious(0) 3/5 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF122,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs763891376 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 54507995 54507995 C T 1 0 0 0 0 1 0 0 0 8507 652 23 1 1 LAIR2 19 54507995 Missense_Mutation SNP C C3L-02345_T 1802624 54507995 4109621 211 8809 LILRB1 0 . GRCh38 19 54636821 54636821 + Silent SNP C C A C3L-02345_T C3L-02345_N C C c.1902C>A p.= p.S634S ENST00000324602 15/15 238 199 39 287 287 0 strelka-varscan-mutect LILRB1,synonymous_variant,p.=,ENST00000396331,NM_006669.6;LILRB1,synonymous_variant,p.=,ENST00000396327,NM_001081638.3;LILRB1,synonymous_variant,p.=,ENST00000396332,NM_001081639.3;LILRB1,synonymous_variant,p.=,ENST00000324602,NM_001081637.2;LILRB1,synonymous_variant,p.=,ENST00000427581,;LILRB1,synonymous_variant,p.=,ENST00000396315,;LILRB1,synonymous_variant,p.=,ENST00000396317,NM_001278398.2;AC009892.10,intron_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,3_prime_UTR_variant,,ENST00000421584,;LILRB1,downstream_gene_variant,,ENST00000480375,;LILRB1,downstream_gene_variant,,ENST00000487425,; A ENST00000324602 Transcript synonymous_variant 2067/2774 1902/1959 634/652 S tcC/tcA COSM1612799 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 15/15 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117 1 LOW SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 54636821 54636821 C A 1 0 0 0 0 0 0 0 1 8698 610 22 2 2 LILRB1 19 54636821 Silent SNP C C3L-02345_T 128826 54636821 3980795 212 8810 PEG3 0 . GRCh38 19 56815104 56815104 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.3338G>T p.Gly1113Val p.G1113V ENST00000326441 10/10 79 58 21 102 102 0 strelka-varscan-mutect PEG3,missense_variant,p.Gly1113Val,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Gly989Val,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Gly1113Val,ENST00000599534,;PEG3,missense_variant,p.Gly1113Val,ENST00000599577,;PEG3,missense_variant,p.Gly987Val,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 3702/8723 3338/4767 1113/1588 G/V gGc/gTc 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 deleterious(0) 10/10 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 56815104 56815104 C A 1 0 0 0 0 1 0 0 0 11808 739 26 2 2 PEG3 19 56815104 Missense_Mutation SNP C C3L-02345_T 2178283 56815104 1802512 213 8811 ZNF329 0 . GRCh38 19 58128283 58128283 + Silent SNP A A G novel C3L-02345_T C3L-02345_N A A c.1221T>C p.= p.T407T ENST00000597186 5/5 57 53 4 65 65 0 varscan-mutect ZNF329,synonymous_variant,p.=,ENST00000597186,;ZNF329,synonymous_variant,p.=,ENST00000598312,NM_024620.3;ZNF329,synonymous_variant,p.=,ENST00000358067,;ZNF329,downstream_gene_variant,,ENST00000601887,;ZNF329,synonymous_variant,p.=,ENST00000500161,; G ENST00000597186 Transcript synonymous_variant 1899/3930 1221/1626 407/541 T acT/acC 1 -1 ZNF329 HGNC HGNC:14209 protein_coding YES CCDS12972.1 ENSP00000470323 Q86UD4 A0A024R4Q4 UPI0000246E79 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF118,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -9.835233 0.9999978 1 1 1 0 G 2 3 31 58128283 58128283 A G 1 0 0 0 0 0 0 0 1 18419 59 3 5 5 ZNF329 19 58128283 Silent SNP A C3L-02345_T 1313179 58128283 489333 214 8812 TMC2 0 . GRCh38 20 2558520 2558520 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.147G>T p.Arg49Ser p.R49S ENST00000358864 3/20 402 307 95 370 369 1 strelka-varscan-mutect TMC2,missense_variant,p.Arg49Ser,ENST00000358864,NM_080751.2; T ENST00000358864 Transcript missense_variant 162/3169 147/2721 49/906 R/S agG/agT 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 deleterious_low_confidence(0.01) 3/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 MODERATE 1 SNV 1 1 PASS rs1331512839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 2558520 2558520 G T 1 0 0 0 0 1 0 0 0 16431 1194 42 2 2 TMC2 20 2558520 Missense_Mutation SNP G C3L-02345_T 2558520 61885647 215 8813 PROKR2 0 . GRCh38 20 5313987 5313987 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.383G>T p.Cys128Phe p.C128F ENST00000217270 1/2 168 120 48 174 173 1 strelka-varscan-mutect PROKR2,missense_variant,p.Cys128Phe,ENST00000217270,NM_144773.2; A ENST00000217270 Transcript missense_variant 383/1155 383/1155 128/384 C/F tGt/tTt 1 -1 PROKR2 HGNC HGNC:15836 protein_coding YES CCDS13089.1 ENSP00000217270 Q8NFJ6 UPI000003BCC6 NM_144773.2 deleterious(0) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF234,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 5313987 5313987 C A 1 0 0 0 0 1 0 0 0 12686 478 17 2 2 PROKR2 20 5313987 Missense_Mutation SNP C C3L-02345_T 2755467 5313987 59130180 216 8814 NINL 0 . GRCh38 20 25491468 25491468 + Silent SNP C C A rs774422757 C3L-02345_T C3L-02345_N C C c.1368G>T p.= p.A456A ENST00000278886 11/24 178 147 31 187 187 0 strelka-varscan-mutect NINL,synonymous_variant,p.=,ENST00000278886,NM_025176.4;NINL,synonymous_variant,p.=,ENST00000422516,NM_001318226.1;NINL,non_coding_transcript_exon_variant,,ENST00000489780,;NINL,intron_variant,,ENST00000461642,; A ENST00000278886 Transcript synonymous_variant 1442/4969 1368/4149 456/1382 A gcG/gcT rs774422757 1 -1 NINL HGNC HGNC:29163 protein_coding YES CCDS33452.1 ENSP00000278886 Q9Y2I6 UPI0000206B64 NM_025176.4 11/24 hmmpanther:PTHR18905:SF12,hmmpanther:PTHR18905 LOW 1 SNV 1 1 PASS rs774422757 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 25491468 25491468 C A 1 0 0 0 0 0 0 0 1 10455 639 23 1 1 NINL 20 25491468 Silent SNP C C3L-02345_T 20177481 25491468 38952699 217 8815 DEFB115 0 . GRCh38 20 31259511 31259511 + Frame_Shift_Del DEL G G - rs115431286 C3L-02345_T C3L-02345_N G G c.146delG p.Cys49SerfsTer? p.C49Sfs*? ENST00000400552 2/2 116 88 28 148 148 0 sindel-pindel DEFB115,frameshift_variant,p.Cys49SerfsTer?,ENST00000400552,NM_001037730.1; - ENST00000400552 Transcript frameshift_variant 146/267 146/267 49/88 C/X tGc/tc rs115431286 1 1 DEFB115 HGNC HGNC:18096 protein_coding YES CCDS42859.1 ENSP00000383398 Q30KQ5 UPI00005E4A74 NM_001037730.1 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF20 HIGH 1 deletion 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999845 1 1 1 0 - 7 5 31 31259511 31259511 G - 1 0 1 0 1 0 0 0 0 4207 1319 46 0 0 DEFB115 20 31259511 Frame_Shift_Del DEL G C3L-02345_T 5768043 31259511 33184656 218 8816 REM1 0 . GRCh38 20 31476711 31476711 + Missense_Mutation SNP C C G novel C3L-02345_T C3L-02345_N C C c.266C>G p.Pro89Arg p.P89R ENST00000201979 2/5 176 136 40 172 172 0 strelka-varscan-mutect REM1,missense_variant,p.Pro89Arg,ENST00000201979,NM_014012.5;DEFB124,upstream_gene_variant,,ENST00000317676,NM_001037500.1;DEFB124,non_coding_transcript_exon_variant,,ENST00000481595,; G ENST00000201979 Transcript missense_variant 559/1665 266/897 89/298 P/R cCt/cGt 1 1 REM1 HGNC HGNC:15922 protein_coding YES CCDS13181.1 ENSP00000201979 O75628 UPI0000073CEB NM_014012.5 tolerated(0.2) 2/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,PIRSF_domain:PIRSF038017,Prints_domain:PR00449,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF260,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 31476711 31476711 C G 1 0 0 0 0 1 0 0 0 13392 681 24 4 4 REM1 20 31476711 Missense_Mutation SNP C C3L-02345_T 217200 31476711 32967456 219 8817 DLGAP4 0 . GRCh38 20 36432288 36432288 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.571G>T p.Gly191Trp p.G191W ENST00000373913 3/13 274 218 56 323 322 1 strelka-varscan-mutect DLGAP4,missense_variant,p.Gly191Trp,ENST00000373913,NM_014902.5;DLGAP4,missense_variant,p.Gly191Trp,ENST00000339266,;DLGAP4,missense_variant,p.Gly191Trp,ENST00000401952,;DLGAP4,missense_variant,p.Gly191Trp,ENST00000373907,; T ENST00000373913 Transcript missense_variant 1051/5056 571/2970 191/989 G/W Ggg/Tgg 1 1 DLGAP4 HGNC HGNC:24476 protein_coding YES CCDS13274.1 ENSP00000363023 Q9Y2H0 UPI000013D34B NM_014902.5 deleterious(0.01) 3/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 36432288 36432288 G T 1 0 0 0 0 1 0 0 0 4369 1348 47 2 2 DLGAP4 20 36432288 Missense_Mutation SNP G C3L-02345_T 4955577 36432288 28011879 220 8818 SLC12A5 0 . GRCh38 20 46043169 46043169 + Silent SNP C C A C3L-02345_T C3L-02345_N C C c.1152C>A p.= p.S384S ENST00000454036 9/26 128 97 31 118 118 0 strelka-varscan-mutect SLC12A5,synonymous_variant,p.=,ENST00000243964,NM_020708.4;SLC12A5,synonymous_variant,p.=,ENST00000454036,NM_001134771.1;SLC12A5,synonymous_variant,p.=,ENST00000616201,;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,intron_variant,,ENST00000539566,;SLC12A5,downstream_gene_variant,,ENST00000629054,;SLC12A5,downstream_gene_variant,,ENST00000625683,;SLC12A5,downstream_gene_variant,,ENST00000372315,;SLC12A5,downstream_gene_variant,,ENST00000622711,;SLC12A5,upstream_gene_variant,,ENST00000626144,;SLC12A5,upstream_gene_variant,,ENST00000608594,; A ENST00000454036 Transcript synonymous_variant 1228/3593 1152/3420 384/1139 S tcC/tcA COSM5568164,COSM5568165 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 9/26 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF54,TIGRFAM_domain:TIGR00930 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 46043169 46043169 C A 1 0 0 0 0 0 0 0 1 14651 668 24 2 2 SLC12A5 20 46043169 Silent SNP C C3L-02345_T 9610881 46043169 18400998 221 8819 OCSTAMP 0 . GRCh38 20 46541593 46541593 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.1382T>A p.Leu461Gln p.L461Q ENST00000279028 3/3 323 252 71 308 307 1 strelka-varscan-mutect OCSTAMP,missense_variant,p.Leu461Gln,ENST00000279028,NM_080721.2; T ENST00000279028 Transcript missense_variant 1396/2043 1382/1701 461/566 L/Q cTg/cAg 1 -1 OCSTAMP HGNC HGNC:16116 protein_coding YES CCDS54468.1 ENSP00000279028 Q9BR26 UPI00006C1A90 NM_080721.2 deleterious(0.03) 3/3 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 46541593 46541593 A T 1 0 0 0 0 1 0 0 0 10901 188 7 4 4 OCSTAMP 20 46541593 Missense_Mutation SNP A C3L-02345_T 498424 46541593 17902574 222 8820 MOCS3 0 . GRCh38 20 50960009 50960009 + Silent SNP A A G novel C3L-02345_T C3L-02345_N A A c.1167A>G p.= p.L389L ENST00000244051 1/1 259 205 54 275 275 0 strelka-varscan-mutect MOCS3,synonymous_variant,p.=,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; G ENST00000244051 Transcript synonymous_variant 1184/5106 1167/1383 389/460 L ttA/ttG 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 1/1 Gene3D:3.40.250.10,HAMAP:MF_03049,Pfam_domain:PF00581,PROSITE_profiles:PS50206,hmmpanther:PTHR10953,SMART_domains:SM00450,Superfamily_domains:SSF69572 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 31 50960009 50960009 A G 1 0 0 0 0 0 0 0 1 9655 359 13 5 5 MOCS3 20 50960009 Silent SNP A C3L-02345_T 4418416 50960009 13484158 223 8821 ZBP1 0 . GRCh38 20 57611889 57611889 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.712G>T p.Asp238Tyr p.D238Y ENST00000371173 6/8 223 186 37 219 219 0 strelka-varscan-mutect ZBP1,missense_variant,p.Asp238Tyr,ENST00000371173,NM_001160417.1,NM_030776.2;ZBP1,missense_variant,p.Asp163Tyr,ENST00000395822,NM_001160418.1;ZBP1,downstream_gene_variant,,ENST00000541799,NM_001160419.2;ZBP1,upstream_gene_variant,,ENST00000453793,;ZBP1,downstream_gene_variant,,ENST00000538947,;ZBP1,downstream_gene_variant,,ENST00000432548,;ZBP1,downstream_gene_variant,,ENST00000546110,;ZBP1,non_coding_transcript_exon_variant,,ENST00000461547,;ZBP1,downstream_gene_variant,,ENST00000480037,; A ENST00000371173 Transcript missense_variant 890/2195 712/1290 238/429 D/Y Gat/Tat 1 -1 ZBP1 HGNC HGNC:16176 protein_coding YES CCDS13461.1 ENSP00000360215 Q9H171 UPI000013CB5B NM_001160417.1,NM_030776.2 deleterious(0.01) 6/8 hmmpanther:PTHR14966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 57611889 57611889 C A 1 0 0 0 0 1 0 0 0 18087 826 29 2 2 ZBP1 20 57611889 Missense_Mutation SNP C C3L-02345_T 6651880 57611889 6832278 224 8822 IFNAR1 0 . GRCh38 21 33345275 33345275 + Missense_Mutation SNP A A T C3L-02345_T C3L-02345_N A A c.703A>T p.Ile235Leu p.I235L ENST00000270139 6/11 157 112 45 229 229 0 strelka-varscan-mutect IFNAR1,missense_variant,p.Ile235Leu,ENST00000270139,NM_000629.2;IFNAR1,missense_variant,p.Ile136Leu,ENST00000442071,; T ENST00000270139 Transcript missense_variant 855/6139 703/1674 235/557 I/L Ata/Tta COSM3708025,COSM5629585 1 1 IFNAR1 HGNC HGNC:5432 protein_coding YES CCDS13624.1 ENSP00000270139 P17181 UPI000006FE3C NM_000629.2 tolerated(0.52) 6/11 PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF54,Gene3D:2.60.40.10,PIRSF_domain:PIRSF016567,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 33345275 33345275 A T 1 0 0 0 0 1 0 0 0 7444 449 16 4 4 IFNAR1 21 33345275 Missense_Mutation SNP A C3L-02345_T 33345275 13364708 225 8823 CRYBB1 0 . GRCh38 22 26601947 26601947 + Silent SNP G G A rs549883505 C3L-02345_T C3L-02345_N G G c.507C>T p.= p.D169D ENST00000215939 5/6 521 427 94 559 559 0 strelka-varscan-mutect CRYBB1,synonymous_variant,p.=,ENST00000215939,NM_001887.3; A ENST00000215939 Transcript synonymous_variant 638/1102 507/759 169/252 D gaC/gaT rs549883505,COSM183939 1 -1 CRYBB1 HGNC HGNC:2397 protein_coding YES CCDS13840.1 ENSP00000215939 P53674 UPI000000165D NM_001887.3 5/6 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF12,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695,Prints_domain:PR01367 0,1 LOW 1 SNV 1 0,1 1 PASS rs549883505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 26601947 26601947 G A 1 0 0 0 0 0 0 0 1 3712 1136 40 1 1 CRYBB1 22 26601947 Silent SNP G C3L-02345_T 26601947 24216521 226 8824 SEC14L2 0 . GRCh38 22 30410642 30410642 + Silent SNP G G C rs749351257 C3L-02345_T C3L-02345_N G G c.627G>C p.= p.L209L ENST00000615189 8/12 180 150 30 179 179 0 strelka-varscan-mutect SEC14L2,synonymous_variant,p.=,ENST00000615189,NM_012429.4;SEC14L2,synonymous_variant,p.=,ENST00000617837,NM_001291932.1;SEC14L2,synonymous_variant,p.=,ENST00000405717,NM_033382.2;RP4-539M6.19,synonymous_variant,p.=,ENST00000439838,;SEC14L2,synonymous_variant,p.=,ENST00000402592,NM_001204204.2;SEC14L2,synonymous_variant,p.=,ENST00000428195,;RP4-539M6.19,synonymous_variant,p.=,ENST00000439023,;RNF215,intron_variant,,ENST00000431544,;SEC14L2,downstream_gene_variant,,ENST00000429917,;SEC14L2,downstream_gene_variant,,ENST00000415072,;SEC14L2,downstream_gene_variant,,ENST00000459728,;SEC14L2,downstream_gene_variant,,ENST00000416523,;RP4-539M6.19,synonymous_variant,p.=,ENST00000454552,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000619483,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000620251,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000464335,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000483116,;SEC14L2,downstream_gene_variant,,ENST00000452649,;SEC14L2,downstream_gene_variant,,ENST00000437022,; C ENST00000615189 Transcript synonymous_variant 887/4382 627/1212 209/403 L ctG/ctC rs749351257 1 1 SEC14L2 HGNC HGNC:10699 protein_coding YES CCDS13876.1 ENSP00000478755 O76054 A0A024R1I5 UPI0000135433 NM_012429.4 8/12 Gene3D:3.40.525.10,Pfam_domain:PF00650,Prints_domain:PR00180,PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF64,SMART_domains:SM00516,Superfamily_domains:SSF52087 LOW 1 SNV 1 1 PASS rs749351257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 31 30410642 30410642 G C 1 0 0 0 0 0 0 0 1 14258 1277 45 4 4 SEC14L2 22 30410642 Silent SNP G C3L-02345_T 3808695 30410642 20407826 227 8825 PHF21B 0 . GRCh38 22 44914031 44914031 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.622C>A p.Pro208Thr p.P208T ENST00000313237 5/13 54 37 17 57 57 0 strelka-varscan-mutect PHF21B,missense_variant,p.Pro208Thr,ENST00000313237,NM_138415.4;PHF21B,intron_variant,,ENST00000403565,NM_001284296.1;PHF21B,intron_variant,,ENST00000396103,NM_001242450.1;PHF21B,intron_variant,,ENST00000629843,NM_001135862.2;PHF21B,intron_variant,,ENST00000420689,;PHF21B,intron_variant,,ENST00000414269,;PHF21B,downstream_gene_variant,,ENST00000490679,;PHF21B,downstream_gene_variant,,ENST00000460507,;PHF21B,downstream_gene_variant,,ENST00000474327,; T ENST00000313237 Transcript missense_variant 773/3671 622/1596 208/531 P/T Ccc/Acc 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 tolerated_low_confidence(0.46) 5/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1211467722 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 44914031 44914031 G T 1 0 0 0 0 1 0 0 0 11920 1232 43 2 2 PHF21B 22 44914031 Missense_Mutation SNP G C3L-02345_T 14503389 44914031 5904437 228 8826 SHOX 0 . GRCh38 X 644446 644446 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.689C>A p.Pro230Gln p.P230Q ENST00000381578 6/6 408 269 139 275 275 0 strelka-varscan-mutect SHOX,missense_variant,p.Pro230Gln,ENST00000381578,NM_000451.3;SHOX,missense_variant,p.Pro230Gln,ENST00000554971,;SHOX,intron_variant,,ENST00000334060,NM_006883.2;SHOX,intron_variant,,ENST00000381575,; A ENST00000381578 Transcript missense_variant 1380/3757 689/879 230/292 P/Q cCg/cAg 1 1 SHOX HGNC HGNC:10853 protein_coding YES CCDS14107.1 ENSP00000370990 O15266 A0A024R385 UPI0000053471 NM_000451.3 deleterious(0.02) 6/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 644446 644446 C A 1 0 0 0 0 1 0 0 0 14551 652 23 1 1 SHOX 23 644446 Missense_Mutation SNP C C3L-02345_T 644446 155396449 229 8827 MXRA5 0 . GRCh38 X 3311517 3311517 + Missense_Mutation SNP T T C novel C3L-02345_T C3L-02345_N T T c.6686A>G p.Asp2229Gly p.D2229G ENST00000217939 7/7 475 407 68 396 396 0 strelka-varscan-mutect MXRA5,missense_variant,p.Asp2229Gly,ENST00000217939,NM_015419.3; C ENST00000217939 Transcript missense_variant 6841/9793 6686/8487 2229/2828 D/G gAt/gGt 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 3311517 3311517 T C 1 0 0 0 0 1 0 0 0 10002 1435 50 5 5 MXRA5 23 3311517 Missense_Mutation SNP T C3L-02345_T 2667071 3311517 152729378 230 8828 NLGN4X 0 . GRCh38 X 5893661 5893661 + Frame_Shift_Del DEL G G - novel C3L-02345_T C3L-02345_N G G c.1607delC p.Pro536GlnfsTer39 p.P536Qfs*39 ENST00000381095 6/6 257 171 86 312 312 0 sindel-varindel-pindel NLGN4X,frameshift_variant,p.Pro536GlnfsTer39,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,frameshift_variant,p.Pro536GlnfsTer39,ENST00000381093,NM_001282146.1;NLGN4X,frameshift_variant,p.Pro536GlnfsTer39,ENST00000275857,NM_020742.3;NLGN4X,frameshift_variant,p.Pro536GlnfsTer39,ENST00000381092,;NLGN4X,frameshift_variant,p.Pro537GlnfsTer39,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,; - ENST00000381095 Transcript frameshift_variant 2235/5870 1607/2451 536/816 P/X cCa/ca 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 6/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 HIGH 1 deletion 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 - 7 5 31 5893661 5893661 G - 1 0 1 0 1 0 0 0 0 10501 1362 47 0 0 NLGN4X 23 5893661 Frame_Shift_Del DEL G C3L-02345_T 2582144 5893661 150147234 231 8829 ARHGAP6 0 . GRCh38 X 11169577 11169577 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.1737C>A p.= p.A579A ENST00000337414 9/13 156 105 51 144 144 0 strelka-varscan-mutect ARHGAP6,synonymous_variant,p.=,ENST00000337414,NM_013427.2;ARHGAP6,synonymous_variant,p.=,ENST00000303025,NM_013423.2;ARHGAP6,synonymous_variant,p.=,ENST00000380736,NM_001287242.1;ARHGAP6,synonymous_variant,p.=,ENST00000380718,NM_006125.2;ARHGAP6,synonymous_variant,p.=,ENST00000380717,;ARHGAP6,non_coding_transcript_exon_variant,,ENST00000491514,;ARHGAP6,synonymous_variant,p.=,ENST00000495242,;ARHGAP6,non_coding_transcript_exon_variant,,ENST00000489330,; T ENST00000337414 Transcript synonymous_variant 2610/5117 1737/2925 579/974 A gcC/gcA 1 -1 ARHGAP6 HGNC HGNC:676 protein_coding YES CCDS14140.1 ENSP00000338967 O43182 UPI00001AED54 NM_013427.2 9/13 Gene3D:1.10.555.10,PROSITE_profiles:PS50238,hmmpanther:PTHR12635,hmmpanther:PTHR12635:SF6,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 11169577 11169577 G T 1 0 0 0 0 0 0 0 1 1017 1219 43 2 2 ARHGAP6 23 11169577 Silent SNP G C3L-02345_T 5275916 11169577 144871318 232 8830 AMELX 0 . GRCh38 X 11298886 11298886 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.525G>A p.Met175Ile p.M175I ENST00000380712 6/7 218 179 39 175 175 0 strelka-varscan-mutect AMELX,missense_variant,p.Met175Ile,ENST00000380712,NM_182680.1;AMELX,missense_variant,p.Met161Ile,ENST00000380714,NM_001142.2;AMELX,missense_variant,p.Met145Ile,ENST00000348912,NM_182681.1;ARHGAP6,intron_variant,,ENST00000337414,NM_013427.2;ARHGAP6,intron_variant,,ENST00000380736,NM_001287242.1;ARHGAP6,intron_variant,,ENST00000380718,NM_006125.2;ARHGAP6,intron_variant,,ENST00000489330,;ARHGAP6,intron_variant,,ENST00000495242,; A ENST00000380712 Transcript missense_variant 593/835 525/618 175/205 M/I atG/atA 1 1 AMELX HGNC HGNC:461 protein_coding YES CCDS14145.1 ENSP00000370088 Q99217 UPI000002A3B7 NM_182680.1 tolerated(1) 6/7 Low_complexity_(Seg):seg,hmmpanther:PTHR10039,hmmpanther:PTHR10039:SF7,Pfam_domain:PF02948,SMART_domains:SM00818 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 11298886 11298886 G A 1 0 0 0 0 1 0 0 0 665 1377 48 3 3 AMELX 23 11298886 Missense_Mutation SNP G C3L-02345_T 129309 11298886 144742009 233 8831 MAGEB17 0 . GRCh38 X 16171102 16171102 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.720G>T p.= p.G240G ENST00000400004 2/2 168 113 55 175 175 0 strelka-varscan-mutect MAGEB17,synonymous_variant,p.=,ENST00000400004,NM_001277307.1;MAGEB17,synonymous_variant,p.=,ENST00000400003,;RP11-431J24.2,upstream_gene_variant,,ENST00000435789,; T ENST00000400004 Transcript synonymous_variant 1072/1434 720/1011 240/336 G ggG/ggT 1 1 MAGEB17 HGNC HGNC:17418 protein_coding YES CCDS59524.1 ENSP00000382884 A8MXT2 UPI00001602F1 NM_001277307.1 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF67,Pfam_domain:PF01454,SMART_domains:SM01373 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 16171102 16171102 G T 1 0 0 0 0 0 0 0 1 9090 1219 43 2 2 MAGEB17 23 16171102 Silent SNP G C3L-02345_T 4872216 16171102 139869793 234 8832 KLHL34 0 . GRCh38 X 21655977 21655977 + Missense_Mutation SNP G G T rs761704504 C3L-02345_T C3L-02345_N G G c.1812C>A p.Asp604Glu p.D604E ENST00000379499 1/1 210 181 29 143 143 0 strelka-varscan-mutect KLHL34,missense_variant,p.Asp604Glu,ENST00000379499,NM_153270.2;CNKSR2,downstream_gene_variant,,ENST00000425654,NM_001168647.1;CNKSR2,downstream_gene_variant,,ENST00000379510,NM_014927.3; T ENST00000379499 Transcript missense_variant 2354/3641 1812/1935 604/644 D/E gaC/gaA rs761704504 1 -1 KLHL34 HGNC HGNC:26634 protein_coding YES CCDS14199.1 ENSP00000368813 Q8N239 UPI0000072CC4 NM_153270.2 tolerated(1) 1/1 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF199 MODERATE SNV 1 PASS rs761704504 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 21655977 21655977 G T 1 0 0 0 0 1 0 0 0 8253 1368 48 2 2 KLHL34 23 21655977 Missense_Mutation SNP G C3L-02345_T 5484875 21655977 134384918 235 8833 MAGEB5 0 . GRCh38 X 26217480 26217480 + Missense_Mutation SNP G G T rs754656027 C3L-02345_T C3L-02345_N G G c.179G>T p.Arg60Leu p.R60L ENST00000602297 2/2 176 122 54 211 210 1 strelka-varscan-mutect MAGEB5,missense_variant,p.Arg60Leu,ENST00000602297,NM_001271752.1; T ENST00000602297 Transcript missense_variant 426/1216 179/828 60/275 R/L cGt/cTt rs754656027 1 1 MAGEB5 HGNC HGNC:23795 protein_coding YES CCDS65233.1 ENSP00000473493 Q9BZ81 UPI0000237754 NM_001271752.1 tolerated(0.08) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF35,SMART_domains:SM01373 MODERATE 1 SNV 3 1 PASS rs754656027 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 26217480 26217480 G T 1 0 0 0 0 1 0 0 0 9095 1145 40 1 1 MAGEB5 23 26217480 Missense_Mutation SNP G C3L-02345_T 4561503 26217480 129823415 236 8834 FAM47A 0 . GRCh38 X 34130560 34130560 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.1719C>A p.= p.P573P ENST00000346193 1/1 298 251 47 259 259 0 strelka-varscan-mutect FAM47A,synonymous_variant,p.=,ENST00000346193,NM_203408.3;FAM47A,synonymous_variant,p.=,ENST00000613251,; T ENST00000346193 Transcript synonymous_variant 1752/2556 1719/2376 573/791 P ccC/ccA 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 31 34130560 34130560 G T 1 0 0 0 0 0 0 0 1 5447 1335 47 2 2 FAM47A 23 34130560 Silent SNP G C3L-02345_T 7913080 34130560 121910335 237 8835 XK 0 . GRCh38 X 37727900 37727900 + Missense_Mutation SNP G G T rs137995644 C3L-02345_T C3L-02345_N G G c.773G>T p.Cys258Phe p.C258F ENST00000378616 3/3 384 271 113 389 388 1 strelka-varscan-mutect XK,missense_variant,p.Cys258Phe,ENST00000378616,NM_021083.2;RP5-972B16.2,intron_variant,,ENST00000465127,; T ENST00000378616 Transcript missense_variant 976/5206 773/1335 258/444 C/F tGc/tTc rs137995644 1 1 XK HGNC HGNC:12811 protein_coding YES CCDS14241.1 ENSP00000367879 P51811 UPI0000139000 NM_021083.2 tolerated(0.7) 3/3 Pfam_domain:PF09815,hmmpanther:PTHR14297,hmmpanther:PTHR14297:SF8 MODERATE 1 SNV 1 1 PASS rs137995644 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 37727900 37727900 G T 1 0 0 0 0 1 0 0 0 17990 1319 46 2 2 XK 23 37727900 Missense_Mutation SNP G C3L-02345_T 3597340 37727900 118312995 238 8836 SYN1 0 . GRCh38 X 47575151 47575151 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1282C>T p.Pro428Ser p.P428S ENST00000295987 10/13 197 164 33 164 164 0 strelka-varscan-mutect SYN1,missense_variant,p.Pro428Ser,ENST00000295987,NM_006950.3;SYN1,missense_variant,p.Pro428Ser,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,NM_001256196.1;ARAF,downstream_gene_variant,,ENST00000377045,NM_001654.4;ARAF,downstream_gene_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; A ENST00000295987 Transcript missense_variant 1407/3209 1282/2118 428/705 P/S Cct/Tct 1 -1 SYN1 HGNC HGNC:11494 protein_coding YES CCDS14280.1 ENSP00000295987 P17600 UPI0000167B47 NM_006950.3 tolerated(0.16) 10/13 hmmpanther:PTHR10841:SF22,hmmpanther:PTHR10841 MODERATE SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 47575151 47575151 G A 1 0 0 0 0 1 0 0 0 15830 1232 43 3 3 SYN1 23 47575151 Missense_Mutation SNP G C3L-02345_T 9847251 47575151 108465744 239 8837 ZNF81 0 . GRCh38 X 47915217 47915217 + Missense_Mutation SNP A A C novel C3L-02345_T C3L-02345_N A A c.571A>C p.Lys191Gln p.K191Q ENST00000376954 6/6 116 86 30 155 155 0 strelka-varscan-mutect ZNF81,missense_variant,p.Lys191Gln,ENST00000376954,;ZNF81,missense_variant,p.Lys191Gln,ENST00000338637,NM_007137.3;ZNF81,intron_variant,,ENST00000376950,; C ENST00000376954 Transcript missense_variant 939/7933 571/1986 191/661 K/Q Aaa/Caa 1 1 ZNF81 HGNC HGNC:13156 protein_coding YES CCDS43933.1 ENSP00000366153 P51508 UPI000023FCDA tolerated(0.19) 6/6 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 47915217 47915217 A C 1 0 0 0 0 1 0 0 0 18759 363 13 5 5 ZNF81 23 47915217 Missense_Mutation SNP A C3L-02345_T 340066 47915217 108125678 240 8838 ZNF630 0 . GRCh38 X 48059134 48059134 + Nonsense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.1308T>A p.Cys436Ter p.C436* ENST00000442455 5/5 291 204 87 285 285 0 strelka-varscan-mutect ZNF630,stop_gained,p.Cys436Ter,ENST00000442455,NM_001190255.2,NM_001282201.1;ZNF630,stop_gained,p.Cys312Ter,ENST00000276054,NM_001282202.1;ZNF630,stop_gained,p.Cys436Ter,ENST00000409324,NM_001037735.3;ZNF630,stop_gained,p.Cys422Ter,ENST00000616492,;ZNF630,downstream_gene_variant,,ENST00000428686,;ZNF630,downstream_gene_variant,,ENST00000627643,;ZNF630,downstream_gene_variant,,ENST00000421903,;ZNF630-AS1,intron_variant,,ENST00000614448,;ZNF630,intron_variant,,ENST00000428463,; T ENST00000442455 Transcript stop_gained 1875/2829 1308/1974 436/657 C/* tgT/tgA 1 -1 ZNF630 HGNC HGNC:28855 protein_coding YES CCDS35237.2 ENSP00000393163 Q2M218 UPI0000160BE4 NM_001190255.2,NM_001282201.1 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF216,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH SNV 4 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 31 48059134 48059134 A T 1 0 0 0 0 0 1 0 0 18629 157 6 4 4 ZNF630 23 48059134 Nonsense_Mutation SNP A C3L-02345_T 143917 48059134 107981761 241 8839 MAGED1 0 . GRCh38 X 51894636 51894636 + Missense_Mutation SNP G G A rs781866143 C3L-02345_T C3L-02345_N G G c.55G>A p.Ala19Thr p.A19T ENST00000375695 3/14 125 104 21 103 103 0 strelka-varscan-mutect MAGED1,missense_variant,p.Ala19Thr,ENST00000375695,NM_001005333.1;MAGED1,intron_variant,,ENST00000375722,;MAGED1,intron_variant,,ENST00000326587,NM_006986.3;MAGED1,intron_variant,,ENST00000375772,NM_001005332.1;MAGED1,intron_variant,,ENST00000494718,;MAGED1,intron_variant,,ENST00000485420,;MAGED1,intron_variant,,ENST00000470461,;MAGED1,intron_variant,,ENST00000482188,;MAGED1,upstream_gene_variant,,ENST00000473931,;MAGED1,upstream_gene_variant,,ENST00000482599,; A ENST00000375695 Transcript missense_variant 208/2875 55/2505 19/834 A/T Gct/Act rs781866143 1 1 MAGED1 HGNC HGNC:6813 protein_coding YES CCDS35279.1 ENSP00000364847 Q9Y5V3 UPI0000074161 NM_001005333.1 tolerated_low_confidence(0.14) 3/14 MODERATE 1 SNV 1 1 PASS rs781866143 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 51894636 51894636 G A 1 0 0 0 0 1 0 0 0 9101 1087 38 1 1 MAGED1 23 51894636 Missense_Mutation SNP G C3L-02345_T 3835502 51894636 104146259 242 8840 HUWE1 0 . GRCh38 X 53593504 53593504 + Missense_Mutation SNP C C T rs782060360 C3L-02345_T C3L-02345_N C C c.3601G>A p.Ala1201Thr p.A1201T ENST00000342160 31/83 362 314 48 341 341 0 strelka-varscan-mutect HUWE1,missense_variant,p.Ala1201Thr,ENST00000342160,;HUWE1,missense_variant,p.Ala1201Thr,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Ala1192Thr,ENST00000612484,;HUWE1,non_coding_transcript_exon_variant,,ENST00000218328,; T ENST00000342160 Transcript missense_variant 4059/14796 3601/13125 1201/4374 A/T Gcc/Acc rs782060360 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC deleterious(0) 31/83 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF291 MODERATE 1 SNV 5 1 PASS rs782060360 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 53593504 53593504 C T 1 0 0 0 0 1 0 0 0 7357 710 25 3 3 HUWE1 23 53593504 Missense_Mutation SNP C C3L-02345_T 1698868 53593504 102447391 243 8841 HUWE1 0 . GRCh38 X 53595215 53595215 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.3352C>G p.Pro1118Ala p.P1118A ENST00000342160 29/83 263 190 73 279 279 0 strelka-varscan-mutect HUWE1,missense_variant,p.Pro1118Ala,ENST00000342160,;HUWE1,missense_variant,p.Pro1118Ala,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Pro1109Ala,ENST00000612484,;HUWE1,non_coding_transcript_exon_variant,,ENST00000218328,; C ENST00000342160 Transcript missense_variant 3810/14796 3352/13125 1118/4374 P/A Cca/Gca 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC tolerated(0.18) 29/83 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF291 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 53595215 53595215 G C 1 0 0 0 0 1 0 0 0 7357 1232 43 4 4 HUWE1 23 53595215 Missense_Mutation SNP G C3L-02345_T 1711 53595215 102445680 244 8842 SPIN4 0 . GRCh38 X 63350771 63350771 + Missense_Mutation SNP A A G novel C3L-02345_T C3L-02345_N A A c.49T>C p.Tyr17His p.Y17H ENST00000374884 1/1 81 68 13 112 112 0 strelka-varscan-mutect SPIN4,missense_variant,p.Tyr17His,ENST00000374884,NM_001012968.2;LINC01278,intron_variant,,ENST00000610234,;LINC01278,intron_variant,,ENST00000610088,;SPIN4-AS1,intron_variant,,ENST00000451979,; G ENST00000374884 Transcript missense_variant 574/4117 49/750 17/249 Y/H Tac/Cac 1 -1 SPIN4 HGNC HGNC:27040 protein_coding YES CCDS43964.1 ENSP00000364018 Q56A73 X6R8Y7 UPI000013FD3C NM_001012968.2 tolerated(0.32) 1/1 hmmpanther:PTHR10405,hmmpanther:PTHR10405:SF9 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 31 63350771 63350771 A G 1 0 0 0 0 1 0 0 0 15409 449 16 5 5 SPIN4 23 63350771 Missense_Mutation SNP A C3L-02345_T 9755556 63350771 92690124 245 8843 AMER1 0 . GRCh38 X 64190769 64190769 + Missense_Mutation SNP C C A rs773987432 C3L-02345_T C3L-02345_N C C c.2518G>T p.Ala840Ser p.A840S ENST00000330258 2/2 420 339 81 467 466 1 strelka-varscan-mutect AMER1,missense_variant,p.Ala840Ser,ENST00000330258,NM_152424.3;AMER1,intron_variant,,ENST00000374869,; A ENST00000330258 Transcript missense_variant 2791/8443 2518/3408 840/1135 A/S Gcc/Tcc rs773987432 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 deleterious(0.01) 2/2 hmmpanther:PTHR22237:SF0,hmmpanther:PTHR22237 MODERATE 1 SNV 1 1 PASS rs773987432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 64190769 64190769 C A 1 0 0 0 0 1 0 0 0 667 797 28 2 2 AMER1 23 64190769 Missense_Mutation SNP C C3L-02345_T 839998 64190769 91850126 246 8844 HEPH 0 . GRCh38 X 66197852 66197852 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.1833G>T p.= p.L611L ENST00000519389 10/21 328 272 56 330 330 0 strelka-varscan-mutect HEPH,synonymous_variant,p.=,ENST00000519389,NM_138737.4;HEPH,synonymous_variant,p.=,ENST00000343002,;HEPH,synonymous_variant,p.=,ENST00000441993,NM_001130860.3;HEPH,synonymous_variant,p.=,ENST00000336279,NM_014799.3;HEPH,synonymous_variant,p.=,ENST00000425114,;HEPH,intron_variant,,ENST00000419594,NM_001282141.1;HEPH,upstream_gene_variant,,ENST00000471121,; T ENST00000519389 Transcript synonymous_variant 2012/6013 1833/3639 611/1212 L ctG/ctT 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 10/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Pfam_domain:PF07732,Superfamily_domains:SSF49503 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 66197852 66197852 G T 1 0 0 0 0 0 0 0 1 6938 1306 46 2 2 HEPH 23 66197852 Silent SNP G C3L-02345_T 2007083 66197852 89843043 247 8845 MED12 0 . GRCh38 X 71130108 71130108 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.3941G>T p.Ser1314Ile p.S1314I ENST00000374080 28/45 199 163 36 246 246 0 strelka-varscan-mutect MED12,missense_variant,p.Ser1161Ile,ENST00000333646,;MED12,missense_variant,p.Ser1314Ile,ENST00000374102,;MED12,missense_variant,p.Ser1314Ile,ENST00000374080,NM_005120.2;MED12,downstream_gene_variant,,ENST00000462984,;MED12,downstream_gene_variant,,ENST00000471663,;MED12,downstream_gene_variant,,ENST00000489199,;MED12,downstream_gene_variant,,ENST00000460771,; T ENST00000374080 Transcript missense_variant 3973/6795 3941/6534 1314/2177 S/I aGt/aTt 1 1 MED12 HGNC HGNC:11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 UPI00004257E2 NM_005120.2 tolerated(0.15) 28/45 hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 71130108 71130108 G T 1 0 0 0 0 1 0 0 0 9367 1029 36 2 2 MED12 23 71130108 Missense_Mutation SNP G C3L-02345_T 4932256 71130108 84910787 248 8846 OGT 0 . GRCh38 X 71562942 71562942 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.2073G>T p.Gln691His p.Q691H ENST00000373719 16/22 114 87 27 122 122 0 strelka-varscan-mutect OGT,missense_variant,p.Gln691His,ENST00000373719,NM_181672.2;OGT,missense_variant,p.Gln681His,ENST00000373701,NM_181673.2;OGT,non_coding_transcript_exon_variant,,ENST00000488174,;OGT,upstream_gene_variant,,ENST00000474633,; T ENST00000373719 Transcript missense_variant 2290/5461 2073/3141 691/1046 Q/H caG/caT 1 1 OGT HGNC HGNC:8127 protein_coding YES CCDS14414.1 ENSP00000362824 O15294 UPI0000073C9F NM_181672.2 tolerated(0.56) 16/22 Pfam_domain:PF13844,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs1488273153 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 71562942 71562942 G T 1 0 0 0 0 1 0 0 0 10922 1020 36 2 2 OGT 23 71562942 Missense_Mutation SNP G C3L-02345_T 432834 71562942 84477953 249 8847 ABCB7 0 . GRCh38 X 75076612 75076612 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.499G>T p.Asp167Tyr p.D167Y ENST00000253577 5/16 439 352 87 515 515 0 strelka-varscan-mutect ABCB7,missense_variant,p.Asp127Tyr,ENST00000620875,NM_001271699.1;ABCB7,missense_variant,p.Asp167Tyr,ENST00000253577,NM_004299.4;ABCB7,missense_variant,p.Asp166Tyr,ENST00000373394,NM_001271696.1;ABCB7,missense_variant,p.Asp126Tyr,ENST00000339447,NM_001271697.1;ABCB7,missense_variant,p.Asp140Tyr,ENST00000529949,NM_001271698.1;ABCB7,missense_variant,p.Asp111Tyr,ENST00000534524,;ABCB7,downstream_gene_variant,,ENST00000526404,;ABCB7,upstream_gene_variant,,ENST00000534570,; A ENST00000253577 Transcript missense_variant 524/2377 499/2262 167/753 D/Y Gac/Tac 1 -1 ABCB7 HGNC HGNC:48 protein_coding YES CCDS14428.1 ENSP00000253577 O75027 A0A0S2Z2Z3 UPI0000169E78 NM_004299.4 deleterious(0) 5/16 PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF187,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 75076612 75076612 C A 1 0 0 0 0 1 0 0 0 50 913 32 2 2 ABCB7 23 75076612 Missense_Mutation SNP C C3L-02345_T 3513670 75076612 80964283 250 8848 PGAM4 0 . GRCh38 X 77969119 77969119 + Frame_Shift_Del DEL G G - novel C3L-02345_T C3L-02345_N G G c.520delC p.Gln174ArgfsTer9 p.Q174Rfs*9 ENST00000458128 1/1 246 199 47 296 295 1 sindel-varindel-pindel PGAM4,frameshift_variant,p.Gln174ArgfsTer9,ENST00000458128,NM_001029891.2;ATP7A,intron_variant,,ENST00000341514,NM_000052.6;ATP7A,intron_variant,,ENST00000343533,NM_001282224.1;RP5-1000K24.2,downstream_gene_variant,,ENST00000602791,; - ENST00000458128 Transcript frameshift_variant 520/765 520/765 174/254 Q/X Cag/ag 1 -1 PGAM4 HGNC HGNC:21731 protein_coding YES CCDS35338.1 ENSP00000412189 Q8N0Y7 UPI0000131CD2 NM_001029891.2 1/1 HAMAP:MF_01039,hmmpanther:PTHR11931:SF14,hmmpanther:PTHR11931,Gene3D:3.40.50.1240,Pfam_domain:PF00300,TIGRFAM_domain:TIGR01258,SMART_domains:SM00855,Superfamily_domains:SSF53254 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 31 77969119 77969119 G - 1 0 1 0 1 0 0 0 0 11865 1357 47 0 0 PGAM4 23 77969119 Frame_Shift_Del DEL G C3L-02345_T 2892507 77969119 78071776 251 8849 KLHL4 0 . GRCh38 X 87632254 87632254 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1369C>A p.Leu457Ile p.L457I ENST00000373114 7/11 146 125 21 153 153 0 varscan-mutect KLHL4,missense_variant,p.Leu457Ile,ENST00000373119,NM_019117.4;KLHL4,missense_variant,p.Leu457Ile,ENST00000373114,NM_057162.2; A ENST00000373114 Transcript missense_variant 1449/2445 1369/2163 457/720 L/I Cta/Ata 1 1 KLHL4 HGNC HGNC:6355 protein_coding YES CCDS14456.1 ENSP00000362206 Q9C0H6 UPI000002ACC4 NM_057162.2 tolerated(0.6) 7/11 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF74,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS rs1273051674 . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 31 87632254 87632254 C A 1 0 0 0 0 1 0 0 0 8257 796 28 2 2 KLHL4 23 87632254 Missense_Mutation SNP C C3L-02345_T 9663135 87632254 68408641 252 8850 PCDH19 0 . GRCh38 X 100407078 100407078 + Missense_Mutation SNP G G A novel C3L-02345_T C3L-02345_N G G c.1520C>T p.Ser507Phe p.S507F ENST00000373034 1/6 395 303 92 477 477 0 strelka-varscan-mutect PCDH19,missense_variant,p.Ser507Phe,ENST00000373034,NM_001184880.1;PCDH19,missense_variant,p.Ser507Phe,ENST00000255531,NM_001105243.1;PCDH19,missense_variant,p.Ser507Phe,ENST00000420881,NM_020766.2;PCDH19,upstream_gene_variant,,ENST00000636150,; A ENST00000373034 Transcript missense_variant 3196/9756 1520/3447 507/1148 S/F tCc/tTc 1 -1 PCDH19 HGNC HGNC:14270 protein_coding YES CCDS55462.1 ENSP00000362125 Q8TAB3 UPI00001D7BCD NM_001184880.1 deleterious(0) 1/6 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF40,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 100407078 100407078 G A 1 0 0 0 0 1 0 0 0 11601 1174 41 3 3 PCDH19 23 100407078 Missense_Mutation SNP G C3L-02345_T 12774824 100407078 55633817 253 8851 SRPX2 0 . GRCh38 X 100664927 100664927 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.509G>T p.Ser170Ile p.S170I ENST00000373004 5/11 401 328 73 459 458 1 strelka-varscan-mutect SRPX2,missense_variant,p.Ser170Ile,ENST00000373004,NM_014467.2; T ENST00000373004 Transcript missense_variant 937/2138 509/1398 170/465 S/I aGt/aTt 1 1 SRPX2 HGNC HGNC:30668 protein_coding YES CCDS14471.1 ENSP00000362095 O60687 UPI000006CCC6 NM_014467.2 deleterious(0) 5/11 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF93,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs763276086 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 100664927 100664927 G T 1 0 0 0 0 1 0 0 0 15526 1029 36 2 2 SRPX2 23 100664927 Missense_Mutation SNP G C3L-02345_T 257849 100664927 55375968 254 8852 SYTL4 0 . GRCh38 X 100689856 100689856 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.912G>T p.Met304Ile p.M304I ENST00000372989 11/19 118 92 26 146 146 0 strelka-varscan-mutect SYTL4,missense_variant,p.Met304Ile,ENST00000372981,;SYTL4,missense_variant,p.Met304Ile,ENST00000372989,NM_080737.2;SYTL4,missense_variant,p.Met304Ile,ENST00000276141,NM_001174068.1;SYTL4,missense_variant,p.Met304Ile,ENST00000263033,NM_001129896.2; A ENST00000372989 Transcript missense_variant,splice_region_variant 1244/3885 912/2016 304/671 M/I atG/atT 1 -1 SYTL4 HGNC HGNC:15588 protein_coding YES CCDS14472.1 ENSP00000362080 Q96C24 A0A024RCF8 UPI00001AE9F2 NM_080737.2 tolerated(0.39) 11/19 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF9 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 100689856 100689856 C A 1 0 0 0 0 1 0 0 0 15879 608 21 2 2 SYTL4 23 100689856 Missense_Mutation SNP C C3L-02345_T 24929 100689856 55351039 255 8853 ARL13A 0 . GRCh38 X 100985896 100985896 + Silent SNP G G T novel C3L-02345_T C3L-02345_N G G c.360G>T p.= p.V120V ENST00000450049 4/8 92 66 26 134 134 0 strelka-varscan-mutect ARL13A,synonymous_variant,p.=,ENST00000450049,NM_001162491.1;ARL13A,upstream_gene_variant,,ENST00000372953,;ARL13A,synonymous_variant,p.=,ENST00000450457,;ARL13A,upstream_gene_variant,,ENST00000494863,; T ENST00000450049 Transcript synonymous_variant 473/1102 360/771 120/256 V gtG/gtT 1 1 ARL13A HGNC HGNC:31709 protein_coding YES CCDS55463.1 ENSP00000398637 Q5H913 UPI0001747A4A NM_001162491.1 4/8 Gene3D:3.40.50.300,Pfam_domain:PF00025,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF111,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 2 4 31 100985896 100985896 G T 1 0 0 0 0 0 0 0 1 1065 1335 47 2 2 ARL13A 23 100985896 Silent SNP G C3L-02345_T 296040 100985896 55054999 256 8854 COL4A6 0 . GRCh38 X 108187101 108187101 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1946C>A p.Ser649Tyr p.S649Y ENST00000394872 23/46 31 23 8 33 33 0 strelka-varscan-mutect COL4A6,missense_variant,p.Ser649Tyr,ENST00000394872,NM_001287758.1;COL4A6,missense_variant,p.Ser649Tyr,ENST00000334504,NM_033641.3;COL4A6,missense_variant,p.Ser649Tyr,ENST00000621266,NM_001287759.1;COL4A6,missense_variant,p.Ser650Tyr,ENST00000372216,NM_001847.3;COL4A6,missense_variant,p.Ser649Tyr,ENST00000538570,NM_001287760.1;COL4A6,missense_variant,p.Ser649Tyr,ENST00000545689,; T ENST00000394872 Transcript missense_variant 2180/6750 1946/5124 649/1707 S/Y tCt/tAt 1 -1 COL4A6 HGNC HGNC:2208 protein_coding YES CCDS76010.1 ENSP00000378340 A8MXH5 UPI000387C996 NM_001287758.1 tolerated(0.26) 23/46 Pfam_domain:PF01391,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 2 206 2 0 0 0 0 0 -19.98878 1 1 1 1 0 T 3 4 31 108187101 108187101 G T 1 0 0 0 0 1 0 0 0 3484 956 33 2 2 COL4A6 23 108187101 Missense_Mutation SNP G C3L-02345_T 7201205 108187101 47853794 257 8855 TEX13C 0 . GRCh38 X 125321845 125321845 + Missense_Mutation SNP C C A novel C3L-02345_T C3L-02345_N C C c.1726C>A p.Gln576Lys p.Q576K ENST00000632600 1/1 434 347 87 517 517 0 strelka-varscan-mutect TEX13C,missense_variant,p.Gln576Lys,ENST00000632600,NM_001195272.1; A ENST00000632600 Transcript missense_variant 1726/5095 1726/2982 576/993 Q/K Cag/Aag 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 tolerated(0.14) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 31 125321845 125321845 C A 1 0 0 0 0 1 0 0 0 16199 595 21 2 2 TEX13C 23 125321845 Missense_Mutation SNP C C3L-02345_T 17134744 125321845 30719050 258 8856 DCAF12L1 0 . GRCh38 X 126552476 126552476 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.133C>A p.Pro45Thr p.P45T ENST00000371126 1/2 234 185 49 230 230 0 strelka-varscan-mutect DCAF12L1,missense_variant,p.Pro45Thr,ENST00000371126,NM_178470.4; T ENST00000371126 Transcript missense_variant 376/3382 133/1392 45/463 P/T Ccg/Acg 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 tolerated(0.21) 1/2 hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 126552476 126552476 G T 1 0 0 0 0 1 0 0 0 4065 1203 42 2 2 DCAF12L1 23 126552476 Missense_Mutation SNP G C3L-02345_T 1230631 126552476 29488419 259 8857 AIFM1 0 . GRCh38 X 130136695 130136695 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.1112C>G p.Ser371Cys p.S371C ENST00000287295 11/16 442 358 84 445 444 1 strelka-varscan-mutect AIFM1,missense_variant,p.Ser371Cys,ENST00000287295,NM_004208.3;AIFM1,missense_variant,p.Ser367Cys,ENST00000319908,NM_145812.2;AIFM1,missense_variant,p.Ser32Cys,ENST00000460436,NM_001130846.2;AIFM1,missense_variant,p.Ser84Cys,ENST00000346424,NM_145813.2;AIFM1,3_prime_UTR_variant,,ENST00000535724,NM_001130847.3;AIFM1,3_prime_UTR_variant,,ENST00000416073,;AIFM1,3_prime_UTR_variant,,ENST00000527892,;AIFM1,non_coding_transcript_exon_variant,,ENST00000533719,; C ENST00000287295 Transcript missense_variant 1343/2260 1112/1842 371/613 S/C tCc/tGc 1 -1 AIFM1 HGNC HGNC:8768 protein_coding YES CCDS14618.1 ENSP00000287295 O95831 UPI00001313DB NM_004208.3 deleterious(0.03) 11/16 Gene3D:3.50.50.60,Pfam_domain:PF07992,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF150,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 130136695 130136695 G C 1 0 0 0 0 1 0 0 0 503 1174 41 4 4 AIFM1 23 130136695 Missense_Mutation SNP G C3L-02345_T 3584219 130136695 25904200 260 8858 SAGE1 0 . GRCh38 X 135909673 135909673 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.1617G>C p.Arg539Ser p.R539S ENST00000324447 14/20 82 68 14 85 85 0 strelka-varscan-mutect SAGE1,missense_variant,p.Arg539Ser,ENST00000324447,;SAGE1,missense_variant,p.Arg539Ser,ENST00000370709,NM_018666.2;SAGE1,missense_variant,p.Arg163Ser,ENST00000537770,; C ENST00000324447 Transcript missense_variant 1691/2952 1617/2715 539/904 R/S agG/agC 1 1 SAGE1 HGNC HGNC:30369 protein_coding YES CCDS14652.1 ENSP00000323191 Q9NXZ1 UPI00001413AB deleterious(0) 14/20 hmmpanther:PTHR12957:SF25,hmmpanther:PTHR12957 MODERATE 1 SNV 1 1 PASS rs1452292692 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 135909673 135909673 G C 1 0 0 0 0 1 0 0 0 14068 1165 41 4 4 SAGE1 23 135909673 Missense_Mutation SNP G C3L-02345_T 5772978 135909673 20131222 261 8859 VGLL1 0 . GRCh38 X 136536125 136536125 + Silent SNP G G T rs867662759 C3L-02345_T C3L-02345_N G G c.105G>T p.= p.G35G ENST00000370634 2/5 302 238 64 336 336 0 strelka-varscan-mutect VGLL1,synonymous_variant,p.=,ENST00000370634,NM_016267.3;VGLL1,upstream_gene_variant,,ENST00000440515,;VGLL1,upstream_gene_variant,,ENST00000456412,; T ENST00000370634 Transcript synonymous_variant 275/1215 105/777 35/258 G ggG/ggT rs867662759 1 1 VGLL1 HGNC HGNC:20985 protein_coding YES CCDS14658.1 ENSP00000359668 Q99990 UPI0000071D9A NM_016267.3 2/5 Pfam_domain:PF07545,hmmpanther:PTHR15950,hmmpanther:PTHR15950:SF20 LOW 1 SNV 1 1 PASS rs867662759 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 31 136536125 136536125 G T 1 0 0 0 0 0 0 0 1 17704 1219 43 2 2 VGLL1 23 136536125 Silent SNP G C3L-02345_T 626452 136536125 19504770 262 8860 SPANXN1 0 . GRCh38 X 145255698 145255698 + Missense_Mutation SNP G G T rs782409226 C3L-02345_T C3L-02345_N G G c.103G>T p.Ala35Ser p.A35S ENST00000370493 2/2 266 201 65 286 286 0 strelka-varscan-mutect SPANXN1,missense_variant,p.Ala35Ser,ENST00000370493,NM_001009614.2; T ENST00000370493 Transcript missense_variant 862/1276 103/219 35/72 A/S Gcc/Tcc rs782409226 1 1 SPANXN1 HGNC HGNC:33174 protein_coding YES CCDS35421.1 ENSP00000359524 Q5VSR9 UPI0000458AF7 NM_001009614.2 tolerated(0.21) 2/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF7 MODERATE 1 SNV 1 1 PASS rs782409226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 145255698 145255698 G T 1 0 0 0 0 1 0 0 0 15321 971 34 2 2 SPANXN1 23 145255698 Missense_Mutation SNP G C3L-02345_T 8719573 145255698 10785197 263 8861 AFF2 0 . GRCh38 X 148955661 148955661 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.1616C>T p.Ser539Phe p.S539F ENST00000370460 11/21 137 113 24 157 157 0 strelka-varscan-mutect AFF2,missense_variant,p.Ser539Phe,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Ser180Phe,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Ser506Phe,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Ser504Phe,ENST00000370457,NM_001169124.1,NM_001169125.1; T ENST00000370460 Transcript missense_variant 2095/13746 1616/3936 539/1311 S/F tCc/tTc 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 deleterious(0) 11/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 148955661 148955661 C T 1 0 0 0 0 1 0 0 0 434 855 30 3 3 AFF2 23 148955661 Missense_Mutation SNP C C3L-02345_T 3699963 148955661 7085234 264 8862 AFF2 0 . GRCh38 X 148955752 148955752 + Missense_Mutation SNP G G C novel C3L-02345_T C3L-02345_N G G c.1707G>C p.Gln569His p.Q569H ENST00000370460 11/21 278 222 56 291 291 0 strelka-varscan-mutect AFF2,missense_variant,p.Gln569His,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Gln210His,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Gln536His,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Gln534His,ENST00000370457,NM_001169124.1,NM_001169125.1; C ENST00000370460 Transcript missense_variant 2186/13746 1707/3936 569/1311 Q/H caG/caC 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 tolerated(0.16) 11/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 31 148955752 148955752 G C 1 0 0 0 0 1 0 0 0 434 933 33 4 4 AFF2 23 148955752 Missense_Mutation SNP G C3L-02345_T 91 148955752 7085143 265 8863 MAGEA11 0 . GRCh38 X 149716628 149716628 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.1142G>T p.Cys381Phe p.C381F ENST00000355220 5/5 189 165 24 243 241 2 strelka-varscan-mutect MAGEA11,missense_variant,p.Cys381Phe,ENST00000355220,NM_005366.4;MAGEA11,missense_variant,p.Cys352Phe,ENST00000333104,NM_001011544.1;MAGEA11,downstream_gene_variant,,ENST00000412632,;MAGEA11,non_coding_transcript_exon_variant,,ENST00000518694,; T ENST00000355220 Transcript missense_variant 1244/1864 1142/1290 381/429 C/F tGc/tTc 1 1 MAGEA11 HGNC HGNC:6798 protein_coding YES CCDS48180.1 ENSP00000347358 P43364 UPI0000211BB0 NM_005366.4 deleterious(0.05) 5/5 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF71,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 149716628 149716628 G T 1 0 0 0 0 1 0 0 0 9081 1319 46 2 2 MAGEA11 23 149716628 Missense_Mutation SNP G C3L-02345_T 760876 149716628 6324267 266 8864 PASD1 0 . GRCh38 X 151671074 151671074 + Missense_Mutation SNP A A T novel C3L-02345_T C3L-02345_N A A c.1108A>T p.Ile370Phe p.I370F ENST00000370357 12/16 141 113 28 207 207 0 strelka-varscan-mutect PASD1,missense_variant,p.Ile370Phe,ENST00000370357,NM_173493.2;PASD1,non_coding_transcript_exon_variant,,ENST00000464219,;RP11-45D17.1,non_coding_transcript_exon_variant,,ENST00000413236,; T ENST00000370357 Transcript missense_variant 1353/3163 1108/2322 370/773 I/F Att/Ttt 1 1 PASD1 HGNC HGNC:20686 protein_coding YES CCDS35431.1 ENSP00000359382 Q8IV76 UPI0000074686 NM_173493.2 tolerated(0.09) 12/16 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 151671074 151671074 A T 1 0 0 0 0 1 0 0 0 11552 217 8 4 4 PASD1 23 151671074 Missense_Mutation SNP A C3L-02345_T 1954446 151671074 4369821 267 8865 MAGEA6 0 . GRCh38 X 152767011 152767011 + Missense_Mutation SNP C C T novel C3L-02345_T C3L-02345_N C C c.640G>A p.Asp214Asn p.D214N ENST00000616035 3/3 424 349 75 470 469 1 strelka-varscan-mutect MAGEA6,missense_variant,p.Asp214Asn,ENST00000616035,NM_175868.1;MAGEA6,missense_variant,p.Asp214Asn,ENST00000329342,NM_005363.2;MAGEA6,missense_variant,p.Asp214Asn,ENST00000457643,;MAGEA6,downstream_gene_variant,,ENST00000412733,; T ENST00000616035 Transcript missense_variant 898/1762 640/945 214/314 D/N Gac/Aac 1 -1 MAGEA6 HGNC HGNC:6804 protein_coding YES CCDS76050.1 ENSP00000480637 P43360 UPI000000D9B0 NM_175868.1 tolerated(1) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 31 152767011 152767011 C T 1 0 0 0 0 1 0 0 0 9085 884 31 1 1 MAGEA6 23 152767011 Missense_Mutation SNP C C3L-02345_T 1095937 152767011 3273884 268 8866 HAUS7 0 . GRCh38 X 153456314 153456314 + Missense_Mutation SNP G G T novel C3L-02345_T C3L-02345_N G G c.686C>A p.Ala229Asp p.A229D ENST00000370211 7/10 206 154 52 225 225 0 strelka-varscan-mutect HAUS7,missense_variant,p.Ala229Asp,ENST00000370211,NM_017518.7;HAUS7,missense_variant,p.Ala13Asp,ENST00000435662,;TREX2,5_prime_UTR_variant,,ENST00000330912,;TREX2,5_prime_UTR_variant,,ENST00000338525,;TREX2,5_prime_UTR_variant,,ENST00000334497,;TREX2,5_prime_UTR_variant,,ENST00000370232,;HAUS7,non_coding_transcript_exon_variant,,ENST00000484394,;HAUS7,non_coding_transcript_exon_variant,,ENST00000491286,;HAUS7,non_coding_transcript_exon_variant,,ENST00000490165,;HAUS7,downstream_gene_variant,,ENST00000464993,;HAUS7,downstream_gene_variant,,ENST00000490453,;HAUS7,upstream_gene_variant,,ENST00000437046,;HAUS7,upstream_gene_variant,,ENST00000460898,; T ENST00000370211 Transcript missense_variant 730/1363 686/1107 229/368 A/D gCc/gAc 1 -1 HAUS7 HGNC HGNC:32979 protein_coding YES CCDS35438.1 ENSP00000359230 Q99871 UPI00000731E0 NM_017518.7 deleterious(0.04) 7/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14352,hmmpanther:PTHR14352:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999978 1 1 1 0 T 3 4 31 153456314 153456314 G T 1 0 0 0 0 1 0 0 0 6857 1203 42 2 2 HAUS7 23 153456314 Missense_Mutation SNP G C3L-02345_T 689303 153456314 2584581 269 8867 SLC10A3 0 . GRCh38 X 154488137 154488137 + Silent SNP C C A novel C3L-02345_T C3L-02345_N C C c.804G>T p.= p.G268G ENST00000263512 2/2 281 230 51 353 353 0 strelka-varscan-mutect SLC10A3,synonymous_variant,p.=,ENST00000263512,NM_019848.4;SLC10A3,synonymous_variant,p.=,ENST00000393586,;SLC10A3,synonymous_variant,p.=,ENST00000393587,NM_001142392.2;SLC10A3,synonymous_variant,p.=,ENST00000369649,NM_001142391.2;UBL4A,upstream_gene_variant,,ENST00000369660,NM_014235.4;SLC10A3,downstream_gene_variant,,ENST00000453912,;UBL4A,upstream_gene_variant,,ENST00000369653,;UBL4A,upstream_gene_variant,,ENST00000630530,;UBL4A,upstream_gene_variant,,ENST00000477777,;UBL4A,upstream_gene_variant,,ENST00000421431,;UBL4A,upstream_gene_variant,,ENST00000417913,;UBL4A,upstream_gene_variant,,ENST00000481237,; A ENST00000263512 Transcript synonymous_variant 1330/2161 804/1434 268/477 G ggG/ggT 1 -1 SLC10A3 HGNC HGNC:22979 protein_coding YES CCDS14755.1 ENSP00000263512 P09131 UPI0000131021 NM_019848.4 2/2 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF3,TIGRFAM_domain:TIGR00841,Pfam_domain:PF01758 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 31 154488137 154488137 C A 1 0 0 0 0 0 0 0 1 14640 610 22 2 2 SLC10A3 23 154488137 Silent SNP C C3L-02345_T 1031823 154488137 1552758 270 8868 FAM110D 0 . GRCh38 1 26161791 26161791 + Missense_Mutation SNP A A C rs745461816 C3L-02348_T C3L-02348_N A A c.500A>C p.Asn167Thr p.N167T ENST00000374268 2/2 118 101 17 136 136 0 strelka-varscan-mutect FAM110D,missense_variant,p.Asn167Thr,ENST00000374268,NM_024869.2;RP11-96L14.8,downstream_gene_variant,,ENST00000634842,;RP11-96L14.8,downstream_gene_variant,,ENST00000635463,; C ENST00000374268 Transcript missense_variant 687/2858 500/816 167/271 N/T aAc/aCc rs745461816 1 1 FAM110D HGNC HGNC:25860 protein_coding YES CCDS41285.1 ENSP00000363386 Q8TAY7 UPI000006DD1D NM_024869.2 deleterious(0) 2/2 hmmpanther:PTHR14758,Pfam_domain:PF14160 MODERATE 1 SNV 1 1 PASS rs745461816 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 32 26161791 26161791 A C 1 0 0 0 0 1 0 0 0 5263 43 2 5 5 FAM110D 1 26161791 Missense_Mutation SNP A C3L-02348_T 26161791 222794631 1 8869 COL9A2 0 . GRCh38 1 40303539 40303539 + Missense_Mutation SNP C C G novel C3L-02348_T C3L-02348_N C C c.1539G>C p.Gln513His p.Q513H ENST00000372748 28/32 340 271 69 339 338 1 strelka-varscan-mutect COL9A2,missense_variant,p.Gln513His,ENST00000372748,NM_001852.3;COL9A2,missense_variant,p.Arg117Thr,ENST00000427563,;COL9A2,non_coding_transcript_exon_variant,,ENST00000466267,;COL9A2,non_coding_transcript_exon_variant,,ENST00000482722,;COL9A2,downstream_gene_variant,,ENST00000488463,; G ENST00000372748 Transcript missense_variant 1636/2862 1539/2070 513/689 Q/H caG/caC 1 -1 COL9A2 HGNC HGNC:2218 protein_coding YES CCDS450.1 ENSP00000361834 Q14055 UPI0000126D47 NM_001852.3 deleterious(0.03) 28/32 Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 40303539 40303539 C G 1 0 0 0 0 1 0 0 0 3497 680 24 4 4 COL9A2 1 40303539 Missense_Mutation SNP C C3L-02348_T 14141748 40303539 208652883 2 8870 HYI 0 . GRCh38 1 43451527 43451527 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.643C>A p.Gln215Lys p.Q215K ENST00000372425 7/8 126 99 27 154 154 0 strelka-varscan-mutect HYI,missense_variant,p.Gln240Lys,ENST00000583037,NM_001243526.1;HYI,missense_variant,p.Gln215Lys,ENST00000372425,NM_001190880.2;HYI,missense_variant,p.Gln215Lys,ENST00000372432,NM_031207.5;HYI,missense_variant,p.Gln240Lys,ENST00000372434,;HYI,missense_variant,p.Gln215Lys,ENST00000486909,;HYI,missense_variant,p.Gln176Lys,ENST00000372430,;HYI,missense_variant,p.Gln181Lys,ENST00000372433,;HYI,missense_variant,p.Gln124Lys,ENST00000470662,;HYI,missense_variant,p.Gln129Lys,ENST00000487366,;SZT2,3_prime_UTR_variant,,ENST00000562955,NM_015284.3;SZT2,downstream_gene_variant,,ENST00000634258,;MIR6735,downstream_gene_variant,,ENST00000615179,;SZT2-AS1,upstream_gene_variant,,ENST00000396885,;HYI-AS1,upstream_gene_variant,,ENST00000444386,;SZT2,non_coding_transcript_exon_variant,,ENST00000460536,;HYI,non_coding_transcript_exon_variant,,ENST00000372427,;HYI,non_coding_transcript_exon_variant,,ENST00000483618,;HYI,downstream_gene_variant,,ENST00000469587,;HYI,downstream_gene_variant,,ENST00000496142,; T ENST00000372425 Transcript missense_variant 839/1265 643/834 215/277 Q/K Cag/Aag 1 -1 HYI HGNC HGNC:26948 protein_coding YES CCDS53309.1 ENSP00000361502 Q5T013 UPI0000EE302B NM_001190880.2 deleterious(0.04) 7/8 hmmpanther:PTHR12110,hmmpanther:PTHR12110:SF22,PIRSF_domain:PIRSF006241,Gene3D:3.20.20.150,Pfam_domain:PF01261,Superfamily_domains:SSF51658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 43451527 43451527 G T 1 0 0 0 0 1 0 0 0 7364 1386 48 2 2 HYI 1 43451527 Missense_Mutation SNP G C3L-02348_T 3147988 43451527 205504895 3 8871 ZNF281 0 . GRCh38 1 200409511 200409511 + Frame_Shift_Del DEL C C - novel C3L-02348_T C3L-02348_N C C c.195delG p.Pro66ArgfsTer33 p.P66Rfs*33 ENST00000294740 2/2 131 88 43 176 176 0 sindel-varindel-pindel ZNF281,frameshift_variant,p.Pro66ArgfsTer33,ENST00000294740,NM_012482.4,NM_001281293.1;ZNF281,frameshift_variant,p.Pro66ArgfsTer33,ENST00000367353,;ZNF281,intron_variant,,ENST00000367352,NM_001281294.1;RP11-469A15.2,intron_variant,,ENST00000637430,;RP11-469A15.2,upstream_gene_variant,,ENST00000634596,;RP11-469A15.2,upstream_gene_variant,,ENST00000635220,; - ENST00000294740 Transcript frameshift_variant 320/4891 195/2688 65/895 R/X cgG/cg 1 -1 ZNF281 HGNC HGNC:13075 protein_coding YES CCDS1402.1 ENSP00000294740 Q9Y2X9 UPI000013C345 NM_012482.4,NM_001281293.1 2/2 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 32 200409511 200409511 C - 1 0 1 0 1 0 0 0 0 18394 726 26 0 0 ZNF281 1 200409511 Frame_Shift_Del DEL C C3L-02348_T 156957984 200409511 48546911 4 8872 CNTNAP5 0 . GRCh38 2 124865345 124865345 + Missense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.3254C>A p.Thr1085Asn p.T1085N ENST00000431078 20/24 206 158 48 226 224 2 strelka-varscan-mutect CNTNAP5,missense_variant,p.Thr1085Asn,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 3618/5284 3254/3921 1085/1306 T/N aCc/aAc 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 tolerated(0.08) 20/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 124865345 124865345 C A 1 0 0 0 0 1 0 0 0 3432 507 18 2 2 CNTNAP5 2 124865345 Missense_Mutation SNP C C3L-02348_T 124865345 117328184 5 8873 SLC4A10 0 . GRCh38 2 161855005 161855005 + Missense_Mutation SNP G G A novel C3L-02348_T C3L-02348_N G G c.452G>A p.Gly151Glu p.G151E ENST00000446997 5/27 150 123 27 186 186 0 strelka-varscan-mutect SLC4A10,missense_variant,p.Gly162Glu,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Gly151Glu,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Gly151Glu,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Gly151Glu,ENST00000272716,;SLC4A10,missense_variant,p.Gly151Glu,ENST00000421911,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000493021,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000461456,;SLC4A10,missense_variant,p.Gly151Glu,ENST00000446228,; A ENST00000446997 Transcript missense_variant 545/5551 452/3357 151/1118 G/E gGa/gAa 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 deleterious(0) 5/27 hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Gene3D:1hynR00,TIGRFAM_domain:TIGR00834,Pfam_domain:PF07565,Superfamily_domains:SSF55804,Prints_domain:PR01232 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 161855005 161855005 G A 1 0 0 0 0 1 0 0 0 14928 1174 41 3 3 SLC4A10 2 161855005 Missense_Mutation SNP G C3L-02348_T 36989660 161855005 80338524 6 8874 TTN 0 . GRCh38 2 178770415 178770415 + Missense_Mutation SNP C C T novel C3L-02348_T C3L-02348_N C C c.8377G>A p.Glu2793Lys p.E2793K ENST00000589042 35/363 438 358 80 408 408 0 strelka-varscan-mutect TTN,missense_variant,p.Glu2793Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Glu2793Lys,ENST00000591111,;TTN,missense_variant,p.Glu2793Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Glu2793Lys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Glu2747Lys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Glu2747Lys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Glu2747Lys,ENST00000359218,NM_133432.3;TTN,missense_variant,p.Glu2793Lys,ENST00000360870,NM_133379.4;TTN,upstream_gene_variant,,ENST00000634225,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000610005,;TTN-AS1,upstream_gene_variant,,ENST00000584485,;TTN-AS1,upstream_gene_variant,,ENST00000629094,; T ENST00000589042 Transcript missense_variant 8602/109224 8377/107976 2793/35991 E/K Gag/Aag 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 35/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,SMART_domains:SM00409 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 178770415 178770415 C T 1 0 0 0 0 1 0 0 0 17245 869 30 3 3 TTN 2 178770415 Missense_Mutation SNP C C3L-02348_T 16915410 178770415 63423114 7 8875 FGD5 0 . GRCh38 3 14819220 14819220 + Missense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.149C>A p.Pro50His p.P50H ENST00000285046 1/20 108 85 23 105 105 0 strelka-varscan-mutect FGD5,missense_variant,p.Pro50His,ENST00000285046,NM_152536.3;FGD5,5_prime_UTR_variant,,ENST00000543601,NM_001320276.1;FGD5,upstream_gene_variant,,ENST00000457774,; A ENST00000285046 Transcript missense_variant 259/5720 149/4389 50/1462 P/H cCc/cAc 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 tolerated_low_confidence(0.66) 1/20 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 14819220 14819220 C A 1 0 0 0 0 1 0 0 0 5700 623 22 2 2 FGD5 3 14819220 Missense_Mutation SNP C C3L-02348_T 14819220 183476339 8 8876 CCDC50 0 . GRCh38 3 191389556 191389556 + Silent SNP G G A novel C3L-02348_T C3L-02348_N G G c.1383G>A p.= p.Q461Q ENST00000392456 11/12 399 372 27 429 429 0 strelka-varscan-mutect CCDC50,synonymous_variant,p.=,ENST00000392455,NM_174908.3;CCDC50,synonymous_variant,p.=,ENST00000392456,NM_178335.2; A ENST00000392456 Transcript synonymous_variant 1973/2454 1383/1449 461/482 Q caG/caA 1 1 CCDC50 HGNC HGNC:18111 protein_coding YES CCDS33912.1 ENSP00000376250 Q8IVM0 UPI000018F5EF NM_178335.2 11/12 hmmpanther:PTHR22115,hmmpanther:PTHR22115:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 32 191389556 191389556 G A 1 0 0 0 0 0 0 0 1 2525 962 34 3 3 CCDC50 3 191389556 Silent SNP G C3L-02348_T 176570336 191389556 6906003 9 8877 LAP3 0 . GRCh38 4 17582358 17582358 + Missense_Mutation SNP A A G novel C3L-02348_T C3L-02348_N A A c.344A>G p.His115Arg p.H115R ENST00000226299 4/13 252 203 49 259 259 0 strelka-varscan-mutect LAP3,missense_variant,p.His115Arg,ENST00000226299,;LAP3,missense_variant,p.His115Arg,ENST00000618908,NM_015907.2;LAP3,missense_variant,p.His84Arg,ENST00000606142,;LAP3,upstream_gene_variant,,ENST00000513105,;LAP3,upstream_gene_variant,,ENST00000503467,;LAP3,upstream_gene_variant,,ENST00000504614,;LAP3,upstream_gene_variant,,ENST00000507960,;LAP3,non_coding_transcript_exon_variant,,ENST00000512397,;LAP3,intron_variant,,ENST00000509583,;LAP3,downstream_gene_variant,,ENST00000508497,;LAP3,upstream_gene_variant,,ENST00000508014,; G ENST00000226299 Transcript missense_variant 618/2213 344/1560 115/519 H/R cAt/cGt 1 1 LAP3 HGNC HGNC:18449 protein_coding YES CCDS3422.1 ENSP00000226299 P28838 UPI000014F97D tolerated(0.07) 4/13 Gene3D:3.40.220.10,HAMAP:MF_00181,Pfam_domain:PF02789,hmmpanther:PTHR11963,hmmpanther:PTHR11963:SF19,Superfamily_domains:SSF52949 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 17582358 17582358 A G 1 0 0 0 0 1 0 0 0 8533 217 8 5 5 LAP3 4 17582358 Missense_Mutation SNP A C3L-02348_T 17582358 172632197 10 8878 PRR16 0 . GRCh38 5 120686482 120686482 + Nonsense_Mutation SNP G G T C3L-02348_T C3L-02348_N G G c.688G>T p.Glu230Ter p.E230* ENST00000407149 2/2 205 177 28 281 281 0 strelka-varscan-mutect PRR16,stop_gained,p.Glu207Ter,ENST00000379551,NM_016644.2;PRR16,stop_gained,p.Glu230Ter,ENST00000407149,NM_001300783.1;PRR16,stop_gained,p.Glu160Ter,ENST00000505123,NM_001308087.1;PRR16,stop_gained,p.Glu177Ter,ENST00000446965,;PRR16,downstream_gene_variant,,ENST00000509923,; T ENST00000407149 Transcript stop_gained 897/1747 688/915 230/304 E/* Gag/Tag COSM481789 1 1 PRR16 HGNC HGNC:29654 protein_coding YES CCDS75290.1 ENSP00000385118 Q569H4 UPI00004F9C36 NM_001300783.1 2/2 Pfam_domain:PF15252,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0 1 HIGH 1 SNV 1 1 1 PASS rs1186244854 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 32 120686482 120686482 G T 1 0 0 0 0 0 1 0 0 12725 1175 41 2 2 PRR16 5 120686482 Nonsense_Mutation SNP G C3L-02348_T 120686482 60851777 11 8879 ZSCAN31 0 . GRCh38 6 28326492 28326492 + Nonsense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.895G>T p.Glu299Ter p.E299* ENST00000414429 8/8 215 175 40 228 228 0 strelka-varscan-mutect ZSCAN31,stop_gained,p.Glu299Ter,ENST00000414429,NM_001135215.1;ZSCAN31,stop_gained,p.Glu299Ter,ENST00000396838,NM_145909.2;ZSCAN31,stop_gained,p.Glu299Ter,ENST00000439158,NM_001135216.1;ZSCAN31,stop_gained,p.Glu140Ter,ENST00000611469,NM_001243242.1,NM_001243244.1;ZSCAN31,stop_gained,p.Glu299Ter,ENST00000344279,NM_030899.4,NM_001243241.1;ZSCAN31,stop_gained,p.Glu140Ter,ENST00000446474,NM_001243243.1;ZSCAN31,stop_gained,p.Glu140Ter,ENST00000435857,;ZSCAN31,downstream_gene_variant,,ENST00000453745,;ZSCAN31,downstream_gene_variant,,ENST00000446222,;ZSCAN31,downstream_gene_variant,,ENST00000434036,;ZSCAN31,downstream_gene_variant,,ENST00000439636,;ZSCAN31,downstream_gene_variant,,ENST00000447021,;ZSCAN31,downstream_gene_variant,,ENST00000439628,;ZSCAN31,downstream_gene_variant,,ENST00000426756,;ZSCAN31,downstream_gene_variant,,ENST00000426434,;ZSCAN31,downstream_gene_variant,,ENST00000414431,;ZSCAN31,downstream_gene_variant,,ENST00000444081,;ZSCAN31,non_coding_transcript_exon_variant,,ENST00000481934,; A ENST00000414429 Transcript stop_gained 1799/3551 895/1221 299/406 E/* Gag/Tag 1 -1 ZSCAN31 HGNC HGNC:14097 protein_coding YES CCDS4649.1 ENSP00000390076 Q96LW9 A0A024RCL4 UPI000013C358 NM_001135215.1 8/8 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF48,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS rs971227763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 32 28326492 28326492 C A 1 0 0 0 0 0 1 0 0 18834 864 30 2 2 ZSCAN31 6 28326492 Nonsense_Mutation SNP C C3L-02348_T 28326492 142479487 12 8880 EYS 0 . GRCh38 6 65402549 65402549 + Missense_Mutation SNP T T A rs780396364 C3L-02348_T C3L-02348_N T T c.1113A>T p.Gln371His p.Q371H ENST00000370621 7/44 155 129 26 224 224 0 strelka-varscan-mutect EYS,missense_variant,p.Gln371His,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Gln371His,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Gln371His,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Gln371His,ENST00000342421,NM_198283.1; A ENST00000370621 Transcript missense_variant 1640/10485 1113/9498 371/3165 Q/H caA/caT rs780396364 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.57) 7/44 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24033 MODERATE 1 SNV 1 1 PASS rs780396364 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 65402549 65402549 T A 1 0 0 0 0 1 0 0 0 5200 1838 64 4 4 EYS 6 65402549 Missense_Mutation SNP T C3L-02348_T 37076057 65402549 105403430 13 8881 PEG10 0 . GRCh38 7 94663544 94663544 + Silent SNP G G A novel C3L-02348_T C3L-02348_N G G c.216G>A p.= p.A72A ENST00000488574 2/2 107 83 24 114 114 0 strelka-varscan-mutect PEG10,synonymous_variant,p.=,ENST00000615790,NM_001184962.1;PEG10,synonymous_variant,p.=,ENST00000612941,;PEG10,synonymous_variant,p.=,ENST00000488574,NM_001172438.2;PEG10,synonymous_variant,p.=,ENST00000612748,;PEG10,5_prime_UTR_variant,,ENST00000482108,NM_015068.3,NM_001184961.1,NM_001172437.2,NM_001040152.1;PEG10,5_prime_UTR_variant,,ENST00000617526,;PEG10,5_prime_UTR_variant,,ENST00000613043,;PEG10,intron_variant,,ENST00000493935,;PEG10,upstream_gene_variant,,ENST00000465184,; A ENST00000488574 Transcript synonymous_variant 433/2587 216/1206 72/401 A gcG/gcA 1 1 PEG10 HGNC HGNC:14005 protein_coding YES CCDS75636.1 ENSP00000418944 B4DSP0 UPI0000037665 NM_001172438.2 2/2 hmmpanther:PTHR15503:SF10,hmmpanther:PTHR15503 LOW 1 SNV 2 1 PASS rs1359839744 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 32 94663544 94663544 G A 1 0 0 0 0 0 0 0 1 11807 1132 40 1 1 PEG10 7 94663544 Silent SNP G C3L-02348_T 94663544 64682429 14 8882 EPHB4 0 . GRCh38 7 100807369 100807369 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.2330C>A p.Ser777Tyr p.S777Y ENST00000358173 13/17 120 110 10 141 141 0 strelka-varscan-mutect EPHB4,missense_variant,p.Ser777Tyr,ENST00000358173,NM_004444.4;EPHB4,missense_variant,p.Ser777Tyr,ENST00000360620,;EPHB4,3_prime_UTR_variant,,ENST00000616502,;EPHB4,non_coding_transcript_exon_variant,,ENST00000487222,;EPHB4,non_coding_transcript_exon_variant,,ENST00000478459,;EPHB4,non_coding_transcript_exon_variant,,ENST00000492403,;EPHB4,non_coding_transcript_exon_variant,,ENST00000467515,; T ENST00000358173 Transcript missense_variant 2799/4329 2330/2964 777/987 S/Y tCc/tAc 1 -1 EPHB4 HGNC HGNC:3395 protein_coding YES CCDS5706.1 ENSP00000350896 P54760 Q541P7 UPI0000000DBB NM_004444.4 deleterious(0.01) 13/17 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF296,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 100807369 100807369 G T 1 0 0 0 0 1 0 0 0 5024 1188 41 2 2 EPHB4 7 100807369 Missense_Mutation SNP G C3L-02348_T 6143825 100807369 58538604 15 8883 RECQL4 0 . GRCh38 8 144513216 144513216 + Splice_Site SNP A A G novel C3L-02348_T C3L-02348_N A A c.2463+2T>C p.X821_splice ENST00000617875 83 71 12 88 88 0 strelka-varscan-mutect RECQL4,splice_donor_variant,,ENST00000621189,;RECQL4,splice_donor_variant,,ENST00000617875,NM_004260.3;RECQL4,intron_variant,,ENST00000534626,;LRRC14,upstream_gene_variant,,ENST00000292524,NM_014665.3;LRRC14,upstream_gene_variant,,ENST00000529022,NM_001272036.1;MFSD3,downstream_gene_variant,,ENST00000301327,NM_138431.2;RECQL4,downstream_gene_variant,,ENST00000532846,;RECQL4,upstream_gene_variant,,ENST00000531875,;LRRC14,upstream_gene_variant,,ENST00000527730,;RECQL4,downstream_gene_variant,,ENST00000524998,;CTD-2517M22.17,intron_variant,,ENST00000580385,;RECQL4,upstream_gene_variant,,ENST00000529424,;MFSD3,downstream_gene_variant,,ENST00000528047,;MFSD3,downstream_gene_variant,,ENST00000526749,;MFSD3,downstream_gene_variant,,ENST00000534427,;RECQL4,upstream_gene_variant,,ENST00000301323,;RECQL4,downstream_gene_variant,,ENST00000534538,;RECQL4,downstream_gene_variant,,ENST00000534270,; G ENST00000617875 Transcript splice_donor_variant -/3809 2463/3627 821/1208 1 -1 RECQL4 HGNC HGNC:9949 protein_coding YES CCDS75804.1 ENSP00000482313 A0A087WZ30 UPI0000E5E124 NM_004260.3 14/20 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999979 1 1 1 0 G 5 3 32 144513216 144513216 A G 1 0 0 0 0 0 0 1 0 13372 57 2 5 5 RECQL4 8 144513216 Splice_Site SNP A C3L-02348_T 144513216 625420 16 8884 HMCN2 0 . GRCh38 9 130299116 130299116 + Silent SNP C C A novel C3L-02348_T C3L-02348_N C C c.1101C>A p.= p.P367P ENST00000624552 8/98 267 219 48 234 234 0 strelka-varscan-mutect HMCN2,synonymous_variant,p.=,ENST00000624552,NM_001291815.1; A ENST00000624552 Transcript synonymous_variant 1101/15610 1101/15180 367/5059 P ccC/ccA 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 8/98 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 32 130299116 130299116 C A 1 0 0 0 0 0 0 0 1 7112 610 22 2 2 HMCN2 9 130299116 Silent SNP C C3L-02348_T 130299116 8095601 17 8885 FAM149B1 0 . GRCh38 10 73235199 73235199 + Missense_Mutation SNP C C T novel C3L-02348_T C3L-02348_N C C c.1483C>T p.His495Tyr p.H495Y ENST00000242505 12/14 185 139 46 189 189 0 strelka-varscan-mutect FAM149B1,missense_variant,p.His495Tyr,ENST00000242505,NM_173348.1;FAM149B1,missense_variant,p.His428Tyr,ENST00000372955,;FAM149B1,intron_variant,,ENST00000445951,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000470798,;DNAJC9,intron_variant,,ENST00000469143,;FAM149B1,downstream_gene_variant,,ENST00000607940,;DNAJC9,downstream_gene_variant,,ENST00000453189,;FAM149B1,3_prime_UTR_variant,,ENST00000475829,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000468462,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000466261,; T ENST00000242505 Transcript missense_variant 1657/5408 1483/1749 495/582 H/Y Cat/Tat 1 1 FAM149B1 HGNC HGNC:29162 protein_coding YES CCDS44435.1 ENSP00000242505 Q96BN6 UPI00001617A8 NM_173348.1 deleterious(0.01) 12/14 hmmpanther:PTHR31997,hmmpanther:PTHR31997:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 73235199 73235199 C T 1 0 0 0 0 1 0 0 0 5305 594 21 3 3 FAM149B1 10 73235199 Missense_Mutation SNP C C3L-02348_T 73235199 60562223 18 8886 FOXI2 0 . GRCh38 10 127737521 127737521 + Missense_Mutation SNP G G C novel C3L-02348_T C3L-02348_N G G c.248G>C p.Gly83Ala p.G83A ENST00000388920 1/2 41 31 10 57 57 0 strelka-varscan-mutect FOXI2,missense_variant,p.Gly83Ala,ENST00000388920,NM_207426.2;RP11-288A5.2,upstream_gene_variant,,ENST00000623953,; C ENST00000388920 Transcript missense_variant 287/3217 248/957 83/318 G/A gGc/gCc 1 1 FOXI2 HGNC HGNC:32448 protein_coding YES CCDS7655.2 ENSP00000373572 Q6ZQN5 UPI0000253B9D NM_207426.2 tolerated(0.13) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF192,hmmpanther:PTHR11829 MODERATE 1 SNV 1 1 PASS rs1177608982 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 32 127737521 127737521 G C 1 0 0 0 0 1 0 0 0 5872 1203 42 4 4 FOXI2 10 127737521 Missense_Mutation SNP G C3L-02348_T 54502322 127737521 6059901 19 8887 DEAF1 0 . GRCh38 11 686892 686892 + Missense_Mutation SNP C C T C3L-02348_T C3L-02348_N C C c.770G>A p.Arg257His p.R257H ENST00000382409 5/12 384 361 23 420 420 0 strelka-varscan-mutect DEAF1,missense_variant,p.Arg257His,ENST00000382409,NM_021008.3;DEAF1,upstream_gene_variant,,ENST00000530813,;DEAF1,downstream_gene_variant,,ENST00000525626,;DEAF1,downstream_gene_variant,,ENST00000528864,;DEAF1,downstream_gene_variant,,ENST00000524786,;DEAF1,downstream_gene_variant,,ENST00000529727,;DEAF1,missense_variant,p.Arg45His,ENST00000527170,;DEAF1,downstream_gene_variant,,ENST00000529717,; T ENST00000382409 Transcript missense_variant 1255/2500 770/1698 257/565 R/H cGc/cAc COSM4676924 1 -1 DEAF1 HGNC HGNC:14677 protein_coding YES CCDS31327.1 ENSP00000371846 O75398 UPI00001290E6 NM_021008.3 deleterious(0.01) 5/12 Gene3D:3.10.390.10,Pfam_domain:PF01342,PROSITE_profiles:PS50864,hmmpanther:PTHR10237,SMART_domains:SM00258,Superfamily_domains:SSF63763 1 MODERATE 1 SNV 1 1 1 PASS rs1373112573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 686892 686892 C T 1 0 0 0 0 1 0 0 0 4183 768 27 1 1 DEAF1 11 686892 Missense_Mutation SNP C C3L-02348_T 686892 134399730 20 8888 OVCH2 0 . GRCh38 11 7700326 7700326 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.871C>A p.Leu291Ile p.L291I ENST00000533663 7/16 103 96 7 148 148 0 strelka-varscan-mutect OVCH2,missense_variant,p.Leu291Ile,ENST00000533663,;OVCH2,missense_variant,p.Leu291Ile,ENST00000612000,NM_198185.4;RP11-35J10.5,downstream_gene_variant,,ENST00000527565,;RP11-35J10.4,upstream_gene_variant,,ENST00000527443,;RP11-35J10.6,upstream_gene_variant,,ENST00000612456,;RP11-35J10.7,upstream_gene_variant,,ENST00000611809,;OVCH2,upstream_gene_variant,,ENST00000534817,; T ENST00000533663 Transcript missense_variant 898/1921 871/1698 291/565 L/I Ctt/Att 1 -1 OVCH2 HGNC HGNC:29970 protein_coding YES CCDS73251.1 ENSP00000484497 A0A087X1V8 UPI00024A9A3D deleterious(0.01) 7/16 PROSITE_profiles:PS50240,hmmpanther:PTHR24251:SF16,hmmpanther:PTHR24251,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 7700326 7700326 G T 1 0 0 0 0 1 0 0 0 11394 971 34 2 2 OVCH2 11 7700326 Missense_Mutation SNP G C3L-02348_T 7013434 7700326 127386296 21 8889 RBM14 0 . GRCh38 11 66616856 66616856 + Frame_Shift_Del DEL G G - novel C3L-02348_T C3L-02348_N G G c.136delG p.Ala46ArgfsTer66 p.A46Rfs*66 ENST00000310137 1/3 153 122 31 160 160 0 sindel-varindel-pindel RBM14,frameshift_variant,p.Ala46ArgfsTer66,ENST00000310137,NM_006328.3;RBM14-RBM4,frameshift_variant,p.Ala46ArgfsTer66,ENST00000412278,NM_001198845.1;RBM14,frameshift_variant,p.Ala46ArgfsTer66,ENST00000393979,NM_001198836.1;RBM14,frameshift_variant,p.Ala46ArgfsTer66,ENST00000409372,;RBM14-RBM4,frameshift_variant,p.Ala46ArgfsTer66,ENST00000500635,NM_001198846.1;RBM14,frameshift_variant,p.Ala46ArgfsTer66,ENST00000443702,;RBM14,frameshift_variant,p.Ala46ArgfsTer66,ENST00000409738,NM_001198837.1;RNU4-39P,upstream_gene_variant,,ENST00000362455,;RBM14,non_coding_transcript_exon_variant,,ENST00000512283,;RBM14-RBM4,non_coding_transcript_exon_variant,,ENST00000511114,;RBM14,upstream_gene_variant,,ENST00000461478,;RBM14,upstream_gene_variant,,ENST00000496694,;RBM14,upstream_gene_variant,,ENST00000460762,;RBM14-RBM4,frameshift_variant,p.Ala46ArgfsTer66,ENST00000421355,; - ENST00000310137 Transcript frameshift_variant 275/2828 136/2010 46/669 A/X Gcg/cg 1 1 RBM14 HGNC HGNC:14219 protein_coding YES CCDS8147.1 ENSP00000311747 Q96PK6 A0A0S2Z4Z0 UPI0000073D46 NM_006328.3 1/3 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF413,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 HIGH 1 deletion 1 1 PASS . . 0 206 0 2 2 0 0 0 -19.16997 0.991392 1 1 1 0 - 7 5 32 66616856 66616856 G - 1 0 1 0 1 0 0 0 0 13281 1087 38 0 0 RBM14 11 66616856 Frame_Shift_Del DEL G C3L-02348_T 58916530 66616856 68469766 22 8890 ANO1 0 . GRCh38 11 70149761 70149761 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.1310G>T p.Arg437Leu p.R437L ENST00000355303 12/26 238 196 42 285 284 1 strelka-varscan-mutect ANO1,missense_variant,p.Arg437Leu,ENST00000355303,NM_018043.5;ANO1,missense_variant,p.Arg172Leu,ENST00000531349,;ANO1,missense_variant,p.Arg321Leu,ENST00000530676,;ANO1,missense_variant,p.Arg409Leu,ENST00000316296,;ANO1,missense_variant,p.Arg14Leu,ENST00000531300,;RP11-805J14.3,downstream_gene_variant,,ENST00000530525,; T ENST00000355303 Transcript missense_variant 1615/4790 1310/2961 437/986 R/L cGc/cTc 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 tolerated(0.76) 12/26 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 MODERATE 1 SNV 1 1 PASS rs1459928181 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 70149761 70149761 G T 1 0 0 0 0 1 0 0 0 802 1087 38 1 1 ANO1 11 70149761 Missense_Mutation SNP G C3L-02348_T 3532905 70149761 64936861 23 8891 CEP295 0 . GRCh38 11 93698196 93698196 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.3284G>T p.Gly1095Val p.G1095V ENST00000325212 15/30 203 153 50 254 253 1 strelka-varscan-mutect CEP295,missense_variant,p.Gly1095Val,ENST00000325212,NM_033395.1;CEP295,intron_variant,,ENST00000531700,;CEP295,upstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000531877,;CEP295,downstream_gene_variant,,ENST00000531622,; T ENST00000325212 Transcript missense_variant 3446/8057 3284/7806 1095/2601 G/V gGg/gTg 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 tolerated(0.18) 15/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 93698196 93698196 G T 1 0 0 0 0 1 0 0 0 2970 1232 43 2 2 CEP295 11 93698196 Missense_Mutation SNP G C3L-02348_T 23548435 93698196 41388426 24 8892 NCAPD3 0 . GRCh38 11 134210312 134210312 + Missense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.525G>T p.Arg175Ser p.R175S ENST00000534548 4/35 105 78 27 149 149 0 strelka-varscan-mutect NCAPD3,missense_variant,p.Arg175Ser,ENST00000534548,NM_015261.2;NCAPD3,missense_variant,p.Arg175Ser,ENST00000534532,;NCAPD3,missense_variant,p.Arg175Ser,ENST00000525964,;NCAPD3,3_prime_UTR_variant,,ENST00000533155,;NCAPD3,upstream_gene_variant,,ENST00000528065,; A ENST00000534548 Transcript missense_variant 590/5061 525/4497 175/1498 R/S agG/agT 1 -1 NCAPD3 HGNC HGNC:28952 protein_coding YES CCDS31723.1 ENSP00000433681 P42695 UPI00001C1EFE NM_015261.2 tolerated(0.21) 4/35 Low_complexity_(Seg):seg,hmmpanther:PTHR14222:SF1,hmmpanther:PTHR14222,PIRSF_domain:PIRSF036508 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 134210312 134210312 C A 1 0 0 0 0 1 0 0 0 10222 738 26 2 2 NCAPD3 11 134210312 Missense_Mutation SNP C C3L-02348_T 40512116 134210312 876310 25 8893 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3L-02348_T C3L-02348_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 231 175 56 383 383 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3L-02348_T 25245351 108029958 26 8894 KIAA1551 0 . GRCh38 12 31981598 31981598 + Missense_Mutation SNP C C T novel C3L-02348_T C3L-02348_N C C c.643C>T p.Pro215Ser p.P215S ENST00000312561 4/6 401 331 70 390 389 1 strelka-varscan-mutect KIAA1551,missense_variant,p.Pro215Ser,ENST00000312561,NM_018169.3;KIAA1551,missense_variant,p.Pro215Ser,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,; T ENST00000312561 Transcript missense_variant 1057/6230 643/5244 215/1747 P/S Cca/Tca 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 tolerated(0.07) 4/6 hmmpanther:PTHR21604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 31981598 31981598 C T 1 0 0 0 0 1 0 0 0 8122 855 30 3 3 KIAA1551 12 31981598 Missense_Mutation SNP C C3L-02348_T 6736247 31981598 101293711 27 8895 KRT76 0 . GRCh38 12 52768989 52768991 + In_Frame_Del DEL ACT ACT - rs370657661 C3L-02348_T C3L-02348_N ACT ACT c.1639_1641delAGT p.Ser547del p.S547del ENST00000332411 9/9 152 144 8 138 137 1 varindel-pindel KRT76,inframe_deletion,p.Ser547del,ENST00000332411,NM_015848.4; - ENST00000332411 Transcript inframe_deletion 1693-1695/2529 1639-1641/1917 547/638 S/- AGT/- rs370657661,COSM1362583 1 -1 KRT76 HGNC HGNC:24430 protein_coding YES CCDS8838.1 ENSP00000330101 Q01546 UPI000019B3C1 NM_015848.4 9/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF199,Low_complexity_(Seg):seg 0,1 MODERATE 1 deletion 1 0,1 1 PASS . . 0 0 0 0 0 0 0 210 -6.749149 0 0 1 0 0 - 7 5 32 52768989 52768989 ACT - 1 0 1 0 1 0 0 0 0 8371 156 6 0 0 KRT76 12 52768989 In_Frame_Del DEL ACT C3L-02348_T 20787391 52768989 80506320 28 8896 DPY19L2 0 . GRCh38 12 63570801 63570801 + Missense_Mutation SNP G G A C3L-02348_T C3L-02348_N G G c.1957C>T p.His653Tyr p.H653Y ENST00000324472 20/22 229 192 37 243 243 0 strelka-varscan-mutect DPY19L2,missense_variant,p.His653Tyr,ENST00000324472,NM_173812.4;DPY19L2,3_prime_UTR_variant,,ENST00000439061,;DPY19L2,non_coding_transcript_exon_variant,,ENST00000413230,;DPY19L2,upstream_gene_variant,,ENST00000541911,; A ENST00000324472 Transcript missense_variant 2141/4060 1957/2277 653/758 H/Y Cat/Tat COSM4474990 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 deleterious(0) 20/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 63570801 63570801 G A 1 0 0 0 0 1 0 0 0 4556 1290 45 3 3 DPY19L2 12 63570801 Missense_Mutation SNP G C3L-02348_T 10801812 63570801 69704508 29 8897 LIN7A 0 . GRCh38 12 80889253 80889253 + Missense_Mutation SNP C C T novel C3L-02348_T C3L-02348_N C C c.199G>A p.Glu67Lys p.E67K ENST00000552864 2/6 309 241 68 332 332 0 strelka-varscan-mutect LIN7A,missense_variant,p.Glu67Lys,ENST00000552864,NM_001324423.1,NM_004664.2;LIN7A,missense_variant,p.Glu61Lys,ENST00000549417,;LIN7A,missense_variant,p.Glu33Lys,ENST00000552093,;LIN7A,missense_variant,p.Glu67Lys,ENST00000261203,; T ENST00000552864 Transcript missense_variant,splice_region_variant 402/6112 199/702 67/233 E/K Gag/Aag 1 -1 LIN7A HGNC HGNC:17787 protein_coding YES CCDS9021.1 ENSP00000447488 O14910 UPI0000073ECD NM_001324423.1,NM_004664.2 deleterious(0) 2/6 Pfam_domain:PF02828,PROSITE_profiles:PS51022,hmmpanther:PTHR14063,hmmpanther:PTHR14063:SF4,SMART_domains:SM00569,Superfamily_domains:SSF101288 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 80889253 80889253 C T 1 0 0 0 0 1 0 0 0 8718 927 32 3 3 LIN7A 12 80889253 Missense_Mutation SNP C C3L-02348_T 17318452 80889253 52386056 30 8898 CCDC59 0 . GRCh38 12 82358228 82358228 + Missense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.149G>T p.Arg50Leu p.R50L ENST00000256151 1/4 148 116 32 167 167 0 strelka-varscan-mutect CCDC59,missense_variant,p.Arg50Leu,ENST00000256151,NM_014167.4;CCDC59,missense_variant,p.Arg50Leu,ENST00000552377,;METTL25,upstream_gene_variant,,ENST00000248306,NM_032230.2;METTL25,upstream_gene_variant,,ENST00000548200,;METTL25,upstream_gene_variant,,ENST00000550058,;CCDC59,non_coding_transcript_exon_variant,,ENST00000552412,;CCDC59,intron_variant,,ENST00000548126,;METTL25,upstream_gene_variant,,ENST00000547357,;METTL25,upstream_gene_variant,,ENST00000548569,;METTL25,upstream_gene_variant,,ENST00000547985,;CCDC59,non_coding_transcript_exon_variant,,ENST00000552606,;CCDC59,intron_variant,,ENST00000547758,;CCDC59,upstream_gene_variant,,ENST00000550589,; A ENST00000256151 Transcript missense_variant 561/1983 149/726 50/241 R/L cGc/cTc 1 -1 CCDC59 HGNC HGNC:25005 protein_coding YES CCDS9023.1 ENSP00000256151 Q9P031 UPI0000034DFE NM_014167.4 tolerated(0.08) 1/4 hmmpanther:PTHR15657:SF1,hmmpanther:PTHR15657,Prints_domain:PR01854 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 82358228 82358228 C A 1 0 0 0 0 1 0 0 0 2531 782 27 1 1 CCDC59 12 82358228 Missense_Mutation SNP C C3L-02348_T 1468975 82358228 50917081 31 8899 FAM124A 0 . GRCh38 13 51252158 51252158 + Missense_Mutation SNP G G A rs374624217 C3L-02348_T C3L-02348_N G G c.899G>A p.Arg300His p.R300H ENST00000280057 4/5 142 111 31 151 151 0 strelka-mutect FAM124A,missense_variant,p.Arg264His,ENST00000322475,NM_001242312.1;FAM124A,missense_variant,p.Arg264His,ENST00000615498,;FAM124A,missense_variant,p.Arg300His,ENST00000280057,NM_145019.3; A ENST00000280057 Transcript missense_variant 1030/2104 899/1749 300/582 R/H cGc/cAc rs374624217,COSM4048004 1 1 FAM124A HGNC HGNC:26413 protein_coding YES CCDS9427.1 ENSP00000280057 Q86V42 UPI0000140E33 NM_145019.3 deleterious(0) 4/5 Pfam_domain:PF15067,hmmpanther:PTHR14715,hmmpanther:PTHR14715:SF4 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs374624217 . 0 202 2 6 0 0 0 0 -20 0.9984341 1 1 1 0 A 3 1 32 51252158 51252158 G A 1 0 0 0 0 1 0 0 0 5279 1087 38 1 1 FAM124A 13 51252158 Missense_Mutation SNP G C3L-02348_T 51252158 63112170 32 8900 PPP4R3A 0 . GRCh38 14 91481706 91481706 + Missense_Mutation SNP T T G novel C3L-02348_T C3L-02348_N T T c.785A>C p.His262Pro p.H262P ENST00000554684 4/15 197 165 32 209 209 0 strelka-varscan-mutect PPP4R3A,missense_variant,p.His262Pro,ENST00000554684,NM_001284280.1;PPP4R3A,missense_variant,p.His262Pro,ENST00000554943,;PPP4R3A,missense_variant,p.His57Pro,ENST00000555470,;PPP4R3A,intron_variant,,ENST00000555462,NM_001284281.1;PPP4R3A,intron_variant,,ENST00000555029,;PPP4R3A,downstream_gene_variant,,ENST00000554511,;PPP4R3A,downstream_gene_variant,,ENST00000557018,;PPP4R3A,missense_variant,p.His262Pro,ENST00000554390,;PPP4R3A,missense_variant,p.His265Pro,ENST00000554308,;PPP4R3A,non_coding_transcript_exon_variant,,ENST00000554574,; G ENST00000554684 Transcript missense_variant 1282/4108 785/2463 262/820 H/P cAt/cCt 1 -1 PPP4R3A HGNC HGNC:20219 protein_coding YES CCDS9895.1 ENSP00000450864 Q6IN85 A0A024R6M2 UPI00001A95E2 NM_001284280.1 deleterious(0) 4/15 hmmpanther:PTHR23318:SF3,hmmpanther:PTHR23318,Pfam_domain:PF04802,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 91481706 91481706 T G 1 0 0 0 0 1 0 0 0 12527 1464 51 5 5 PPP4R3A 14 91481706 Missense_Mutation SNP T C3L-02348_T 91481706 15562012 33 8901 DDX24 0 . GRCh38 14 94062547 94062547 + Missense_Mutation SNP G G A novel C3L-02348_T C3L-02348_N G G c.793C>T p.Pro265Ser p.P265S ENST00000621632 3/9 167 143 24 157 157 0 strelka-varscan-mutect DDX24,missense_variant,p.Pro265Ser,ENST00000621632,NM_020414.3;DDX24,missense_variant,p.Pro222Ser,ENST00000555054,;DDX24,missense_variant,p.Pro210Ser,ENST00000330836,;DDX24,missense_variant,p.Pro15Ser,ENST00000544005,;DDX24,upstream_gene_variant,,ENST00000622786,;DDX24,non_coding_transcript_exon_variant,,ENST00000555762,; A ENST00000621632 Transcript missense_variant 925/5612 793/2580 265/859 P/S Cct/Tct 1 -1 DDX24 HGNC HGNC:13266 protein_coding YES CCDS9918.1 ENSP00000481495 Q9GZR7 UPI0000129082 NM_020414.3 tolerated(0.31) 3/9 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF91,hmmpanther:PTHR24031,Pfam_domain:PF00270,SMART_domains:SM00487 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 94062547 94062547 G A 1 0 0 0 0 1 0 0 0 4154 1232 43 3 3 DDX24 14 94062547 Missense_Mutation SNP G C3L-02348_T 2580841 94062547 12981171 34 8902 EML1 0 . GRCh38 14 99850917 99850917 + Missense_Mutation SNP A A T novel C3L-02348_T C3L-02348_N A A c.132A>T p.Arg44Ser p.R44S ENST00000334192 2/23 162 152 10 176 176 0 strelka-varscan-mutect EML1,missense_variant,p.Arg44Ser,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Arg44Ser,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Arg13Ser,ENST00000327921,;EML1,missense_variant,p.Arg31Ser,ENST00000554479,;EML1,missense_variant,p.Arg13Ser,ENST00000556714,;EML1,missense_variant,p.Arg13Ser,ENST00000556199,;EML1,missense_variant,p.Arg13Ser,ENST00000556835,;EML1,missense_variant,p.Arg31Ser,ENST00000555145,;EML1,missense_variant,p.Arg50Ser,ENST00000556947,;EML1,missense_variant,p.Arg25Ser,ENST00000553720,;EML1,non_coding_transcript_exon_variant,,ENST00000556758,;EML1,missense_variant,p.Arg44Ser,ENST00000555096,; T ENST00000334192 Transcript missense_variant 266/4064 132/2505 44/834 R/S agA/agT 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 deleterious(0) 2/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 99850917 99850917 A T 1 0 0 0 0 1 0 0 0 4939 301 11 4 4 EML1 14 99850917 Missense_Mutation SNP A C3L-02348_T 5788370 99850917 7192801 35 8903 AKAP13 0 . GRCh38 15 85722055 85722055 + Missense_Mutation SNP A A T novel C3L-02348_T C3L-02348_N A A c.6329A>T p.Gln2110Leu p.Q2110L ENST00000361243 24/37 250 201 49 308 308 0 strelka-varscan-mutect AKAP13,missense_variant,p.Gln2106Leu,ENST00000394518,NM_007200.4;AKAP13,missense_variant,p.Gln2110Leu,ENST00000361243,NM_006738.5;AKAP13,missense_variant,p.Gln727Leu,ENST00000394510,NM_001270546.1;AKAP13,missense_variant,p.Gln722Leu,ENST00000560579,;AKAP13,missense_variant,p.Gln727Leu,ENST00000560676,;RP11-158M2.2,downstream_gene_variant,,ENST00000561417,;AKAP13,downstream_gene_variant,,ENST00000559820,;AKAP13,non_coding_transcript_exon_variant,,ENST00000558644,;AKAP13,non_coding_transcript_exon_variant,,ENST00000558009,;AKAP13,downstream_gene_variant,,ENST00000560482,;AKAP13,downstream_gene_variant,,ENST00000559278,; T ENST00000361243 Transcript missense_variant 6410/9468 6329/8454 2110/2817 Q/L cAg/cTg 1 1 AKAP13 HGNC HGNC:371 protein_coding YES CCDS32320.1 ENSP00000354718 Q12802 UPI00001A8BEB NM_006738.5 deleterious(0) 24/37 PROSITE_profiles:PS50010,hmmpanther:PTHR13944,hmmpanther:PTHR13944:SF12,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 85722055 85722055 A T 1 0 0 0 0 1 0 0 0 532 188 7 4 4 AKAP13 15 85722055 Missense_Mutation SNP A C3L-02348_T 85722055 16269134 36 8904 ISG20 0 . GRCh38 15 88639402 88639402 + Missense_Mutation SNP C C G rs773881244 C3L-02348_T C3L-02348_N C C c.36C>G p.Cys12Trp p.C12W ENST00000306072 2/4 125 111 14 157 157 0 strelka-varscan-mutect ISG20,missense_variant,p.Cys12Trp,ENST00000306072,NM_001303233.1,NM_002201.5;ISG20,missense_variant,p.Cys12Trp,ENST00000560741,NM_001303234.1;ISG20,missense_variant,p.Cys12Trp,ENST00000559876,NM_001303237.1;ISG20,missense_variant,p.Cys12Trp,ENST00000379224,;ISG20,downstream_gene_variant,,ENST00000558992,;ISG20,non_coding_transcript_exon_variant,,ENST00000560573,;ISG20,non_coding_transcript_exon_variant,,ENST00000558942,; G ENST00000306072 Transcript missense_variant 394/1856 36/546 12/181 C/W tgC/tgG rs773881244 1 1 ISG20 HGNC HGNC:6130 protein_coding YES CCDS10345.1 ENSP00000306565 Q96AZ6 UPI000006FE4D NM_001303233.1,NM_002201.5 deleterious(0) 2/4 Gene3D:3.30.420.10,Pfam_domain:PF00929,hmmpanther:PTHR12801,hmmpanther:PTHR12801:SF74,SMART_domains:SM00479,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS rs773881244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 88639402 88639402 C G 1 0 0 0 0 1 0 0 0 7761 776 27 4 4 ISG20 15 88639402 Missense_Mutation SNP C C3L-02348_T 2917347 88639402 13351787 37 8905 SLC9A3R2 0 . GRCh38 16 2036384 2036384 + Nonsense_Mutation SNP C C T novel C3L-02348_T C3L-02348_N C C c.475C>T p.Gln159Ter p.Q159* ENST00000424542 3/7 162 143 19 168 168 0 strelka-varscan-mutect SLC9A3R2,stop_gained,p.Gln159Ter,ENST00000424542,NM_001130012.2;SLC9A3R2,stop_gained,p.Gln159Ter,ENST00000432365,NM_004785.5;SLC9A3R2,stop_gained,p.Gln48Ter,ENST00000566198,NM_001252073.1,NM_001252076.1;SLC9A3R2,stop_gained,p.Gln53Ter,ENST00000563587,;SLC9A3R2,stop_gained,p.Gln46Ter,ENST00000565855,NM_001252075.1;SLC9A3R2,stop_gained,p.Gln31Ter,ENST00000561844,;SLC9A3R2,stop_gained,p.Gln150Ter,ENST00000567504,;NTHL1,downstream_gene_variant,,ENST00000219066,NM_002528.5;NTHL1,downstream_gene_variant,,ENST00000566380,;SLC9A3R2,non_coding_transcript_exon_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;SLC9A3R2,non_coding_transcript_exon_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000565406,;NTHL1,downstream_gene_variant,,ENST00000567727,;NTHL1,downstream_gene_variant,,ENST00000561862,; T ENST00000424542 Transcript stop_gained 613/2194 475/1014 159/337 Q/* Cag/Tag 1 1 SLC9A3R2 HGNC HGNC:11076 protein_coding YES CCDS45382.1 ENSP00000408005 Q15599 UPI0000070578 NM_001130012.2 3/7 PROSITE_profiles:PS50106,hmmpanther:PTHR14191:SF4,hmmpanther:PTHR14191,Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF037866,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 32 2036384 2036384 C T 1 0 0 0 0 0 1 0 0 14997 827 29 3 3 SLC9A3R2 16 2036384 Nonsense_Mutation SNP C C3L-02348_T 2036384 88301961 38 8906 CREBBP 0 . GRCh38 16 3850807 3850807 + Missense_Mutation SNP C C G rs370300481 C3L-02348_T C3L-02348_N C C c.288G>C p.Gln96His p.Q96H ENST00000262367 2/31 266 203 63 304 304 0 strelka-varscan-mutect CREBBP,missense_variant,p.Gln96His,ENST00000262367,NM_004380.2;CREBBP,missense_variant,p.Gln96His,ENST00000382070,NM_001079846.1;CREBBP,upstream_gene_variant,,ENST00000636895,; G ENST00000262367 Transcript missense_variant 1098/10803 288/7329 96/2442 Q/H caG/caC rs370300481 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 tolerated_low_confidence(0.11) 2/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 MODERATE 1 SNV 1 1 PASS rs370300481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 3850807 3850807 C G 1 0 0 0 0 1 0 0 0 3661 796 28 4 4 CREBBP 16 3850807 Missense_Mutation SNP C C3L-02348_T 1814423 3850807 86487538 39 8907 ACSM2A 0 . GRCh38 16 20475771 20475771 + Missense_Mutation SNP A A G novel C3L-02348_T C3L-02348_N A A c.1096A>G p.Thr366Ala p.T366A ENST00000573854 8/14 139 113 26 123 121 2 strelka-varscan-mutect ACSM2A,missense_variant,p.Thr366Ala,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,missense_variant,p.Thr366Ala,ENST00000396104,;ACSM2A,missense_variant,p.Thr366Ala,ENST00000575690,;ACSM2A,missense_variant,p.Thr366Ala,ENST00000219054,;ACSM2A,missense_variant,p.Thr287Ala,ENST00000417235,NM_001308169.1;ACSM2A,splice_region_variant,,ENST00000575558,;ACSM2A,downstream_gene_variant,,ENST00000572921,;ACSM2A,splice_region_variant,,ENST00000570698,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000572843,;ACSM2A,upstream_gene_variant,,ENST00000576101,;ACSM2A,downstream_gene_variant,,ENST00000574692,; G ENST00000573854 Transcript missense_variant,splice_region_variant 1210/2837 1096/1734 366/577 T/A Acg/Gcg 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 deleterious(0.02) 8/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 20475771 20475771 A G 1 0 0 0 0 1 0 0 0 225 57 2 5 5 ACSM2A 16 20475771 Missense_Mutation SNP A C3L-02348_T 16624964 20475771 69862574 40 8908 ZNF768 0 . GRCh38 16 30524997 30524997 + Nonsense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.1143C>A p.Cys381Ter p.C381* ENST00000380412 2/2 320 274 46 280 278 2 strelka-varscan-mutect ZNF768,stop_gained,p.Cys381Ter,ENST00000380412,NM_024671.3;ZNF768,stop_gained,p.Cys350Ter,ENST00000562803,;ITGAL,downstream_gene_variant,,ENST00000356798,NM_002209.2;ITGAL,downstream_gene_variant,,ENST00000358164,NM_001114380.1;ITGAL,downstream_gene_variant,,ENST00000433423,;AC002310.14,upstream_gene_variant,,ENST00000624451,;AC002310.11,downstream_gene_variant,,ENST00000569360,;ITGAL,downstream_gene_variant,,ENST00000564632,; T ENST00000380412 Transcript stop_gained 1319/2315 1143/1623 381/540 C/* tgC/tgA 1 -1 ZNF768 HGNC HGNC:26273 protein_coding YES CCDS10681.2 ENSP00000369777 Q9H5H4 A0A024QZC8 UPI00001FFEED NM_024671.3 2/2 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF208,SMART_domains:SM00355 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 32 30524997 30524997 G T 1 0 0 0 0 0 1 0 0 18724 963 34 2 2 ZNF768 16 30524997 Nonsense_Mutation SNP G C3L-02348_T 10049226 30524997 59813348 41 8909 ACLY 0 . GRCh38 17 41910221 41910221 + Splice_Site SNP C C T novel C3L-02348_T C3L-02348_N C C c.345+1G>A p.X115_splice ENST00000352035 131 121 10 127 127 0 strelka-varscan-mutect ACLY,splice_donor_variant,,ENST00000352035,NM_001303274.1,NM_001096.2;ACLY,splice_donor_variant,,ENST00000353196,NM_001303275.1,NM_198830.1;ACLY,splice_donor_variant,,ENST00000590151,;ACLY,splice_donor_variant,,ENST00000393896,;ACLY,intron_variant,,ENST00000537919,;ACLY,intron_variant,,ENST00000590770,;ACLY,downstream_gene_variant,,ENST00000592970,;ACLY,splice_donor_variant,,ENST00000590735,;ACLY,upstream_gene_variant,,ENST00000588547,; T ENST00000352035 Transcript splice_donor_variant -/4339 345/3306 115/1101 1 -1 ACLY HGNC HGNC:115 protein_coding YES CCDS11412.1 ENSP00000253792 P53396 A0A024R1T9 UPI000013CDF3 NM_001303274.1,NM_001096.2 4/28 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 32 41910221 41910221 C T 1 0 0 0 0 0 0 1 0 185 521 18 3 3 ACLY 17 41910221 Splice_Site SNP C C3L-02348_T 41910221 41347220 42 8910 HRH4 0 . GRCh38 18 24468822 24468822 + Silent SNP G G T rs758519592 C3L-02348_T C3L-02348_N G G c.228G>T p.= p.T76T ENST00000256906 2/3 159 141 18 178 178 0 strelka-varscan-mutect HRH4,synonymous_variant,p.=,ENST00000256906,NM_021624.3;HRH4,intron_variant,,ENST00000426880,NM_001143828.1; T ENST00000256906 Transcript synonymous_variant 328/3668 228/1173 76/390 T acG/acT rs758519592,COSM4071584 1 1 HRH4 HGNC HGNC:17383 protein_coding YES CCDS11887.1 ENSP00000256906 Q9H3N8 UPI0000039A92 NM_021624.3 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF290,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 1 0,1 1 PASS rs758519592 . 0 205 3 2 0 0 0 0 -20 0.9999887 1 1 1 0 T 2 4 32 24468822 24468822 G T 1 0 0 0 0 0 0 0 1 7253 1074 38 1 1 HRH4 18 24468822 Silent SNP G C3L-02348_T 24468822 55904463 43 8911 RNF125 0 . GRCh38 18 32065916 32065916 + Silent SNP C C T novel C3L-02348_T C3L-02348_N C C c.519C>T p.= p.C173C ENST00000217740 5/6 125 102 23 167 167 0 strelka-varscan-mutect RNF125,synonymous_variant,p.=,ENST00000217740,NM_017831.3;RNF125,non_coding_transcript_exon_variant,,ENST00000583384,;RP11-53I6.2,intron_variant,,ENST00000583184,;RNF125,3_prime_UTR_variant,,ENST00000580209,;RNF125,non_coding_transcript_exon_variant,,ENST00000580863,;RNF125,intron_variant,,ENST00000583814,; T ENST00000217740 Transcript synonymous_variant 1011/6020 519/699 173/232 C tgC/tgT 1 1 RNF125 HGNC HGNC:21150 protein_coding YES CCDS11902.1 ENSP00000217740 Q96EQ8 UPI000013C731 NM_017831.3 5/6 hmmpanther:PTHR23327,hmmpanther:PTHR23327:SF17,Pfam_domain:PF05605 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 32 32065916 32065916 C T 1 0 0 0 0 0 0 0 1 13612 747 26 3 3 RNF125 18 32065916 Silent SNP C C3L-02348_T 7597094 32065916 48307369 44 8912 KIAA1468 0 . GRCh38 18 62287397 62287397 + Silent SNP G G A C3L-02348_T C3L-02348_N G G c.3300G>A p.= p.Q1100Q ENST00000398130 26/29 250 231 19 296 296 0 strelka-varscan-mutect KIAA1468,synonymous_variant,p.=,ENST00000398130,NM_020854.3;KIAA1468,synonymous_variant,p.=,ENST00000256858,;KIAA1468,non_coding_transcript_exon_variant,,ENST00000587764,;KIAA1468,downstream_gene_variant,,ENST00000593217,;KIAA1468,downstream_gene_variant,,ENST00000587714,;KIAA1468,non_coding_transcript_exon_variant,,ENST00000587198,; A ENST00000398130 Transcript synonymous_variant 3532/6178 3300/3651 1100/1216 Q caG/caA COSM1303804 1 1 KIAA1468 HGNC HGNC:29289 protein_coding YES CCDS11979.2 ENSP00000381198 Q9P260 UPI0000DA5AF7 NM_020854.3 26/29 hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0,Superfamily_domains:SSF48371 1 LOW 1 SNV 1 1 1 PASS rs1414082475 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 32 62287397 62287397 G A 1 0 0 0 0 0 0 0 1 8117 933 33 3 3 KIAA1468 18 62287397 Silent SNP G C3L-02348_T 30221481 62287397 18085888 45 8913 GPR108 0 . GRCh38 19 6735645 6735645 + Silent SNP G G A novel C3L-02348_T C3L-02348_N G G c.351C>T p.= p.F117F ENST00000264080 4/18 183 159 24 211 211 0 strelka-varscan-mutect GPR108,synonymous_variant,p.=,ENST00000264080,NM_001080452.1;GPR108,synonymous_variant,p.=,ENST00000601716,;GPR108,5_prime_UTR_variant,,ENST00000430424,;GPR108,5_prime_UTR_variant,,ENST00000597298,;TRIP10,upstream_gene_variant,,ENST00000600428,;TRIP10,upstream_gene_variant,,ENST00000313244,NM_001288962.1;TRIP10,upstream_gene_variant,,ENST00000313285,NM_004240.3;TRIP10,upstream_gene_variant,,ENST00000596758,NM_001288963.1;GPR108,upstream_gene_variant,,ENST00000594034,;GPR108,upstream_gene_variant,,ENST00000598955,;GPR108,upstream_gene_variant,,ENST00000594500,;GPR108,downstream_gene_variant,,ENST00000621745,;GPR108,upstream_gene_variant,,ENST00000537722,;GPR108,upstream_gene_variant,,ENST00000598626,;TRIP10,upstream_gene_variant,,ENST00000596543,;GPR108,synonymous_variant,p.=,ENST00000597706,;GPR108,synonymous_variant,p.=,ENST00000595908,;GPR108,non_coding_transcript_exon_variant,,ENST00000595108,;GPR108,non_coding_transcript_exon_variant,,ENST00000601402,;GPR108,non_coding_transcript_exon_variant,,ENST00000595620,;GPR108,intron_variant,,ENST00000598052,;TRIP10,upstream_gene_variant,,ENST00000595305,;TRIP10,upstream_gene_variant,,ENST00000600677,;GPR108,upstream_gene_variant,,ENST00000600773,;GPR108,downstream_gene_variant,,ENST00000597043,; A ENST00000264080 Transcript synonymous_variant 378/2057 351/1632 117/543 F ttC/ttT 1 -1 GPR108 HGNC HGNC:17829 protein_coding YES CCDS42479.1 ENSP00000264080 Q9NPR9 UPI00001D8222 NM_001080452.1 4/18 hmmpanther:PTHR21229,hmmpanther:PTHR21229:SF11 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 32 6735645 6735645 G A 1 0 0 0 0 0 0 0 1 6526 1165 41 3 3 GPR108 19 6735645 Silent SNP G C3L-02348_T 6735645 51881971 46 8914 SLC1A6 0 . GRCh38 19 14968301 14968301 + Splice_Site SNP A A G novel C3L-02348_T C3L-02348_N A A c.548+2T>C p.X183_splice ENST00000221742 127 115 12 120 120 0 strelka-varscan-mutect SLC1A6,splice_donor_variant,,ENST00000598504,NM_001272087.1;SLC1A6,splice_donor_variant,,ENST00000544886,NM_001272088.1;SLC1A6,splice_donor_variant,,ENST00000600144,;SLC1A6,splice_donor_variant,,ENST00000221742,NM_005071.2;SLC1A6,intron_variant,,ENST00000430939,;SLC1A6,downstream_gene_variant,,ENST00000597262,;SLC1A6,downstream_gene_variant,,ENST00000599636,;SLC1A6,downstream_gene_variant,,ENST00000601761,;SLC1A6,downstream_gene_variant,,ENST00000594383,;SLC1A6,downstream_gene_variant,,ENST00000595863,;SLC1A6,splice_donor_variant,,ENST00000596697,; G ENST00000221742 Transcript splice_donor_variant -/1719 548/1695 183/564 1 -1 SLC1A6 HGNC HGNC:10944 protein_coding YES CCDS12321.1 ENSP00000221742 P48664 UPI0000129B1A NM_005071.2 3/8 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99984 1 1 1 1 0 G 5 3 32 14968301 14968301 A G 1 0 0 0 0 0 0 1 0 14702 173 6 5 5 SLC1A6 19 14968301 Splice_Site SNP A C3L-02348_T 8232656 14968301 43649315 47 8915 TMEM221 0 . GRCh38 19 17448325 17448325 + Silent SNP G G T novel C3L-02348_T C3L-02348_N G G c.138C>A p.= p.A46A ENST00000341130 1/3 47 34 13 13 13 0 varscan-mutect TMEM221,synonymous_variant,p.=,ENST00000341130,NM_001190844.1;CTD-2521M24.10,intron_variant,,ENST00000594663,;CTD-2521M24.11,downstream_gene_variant,,ENST00000598950,;TMEM221,upstream_gene_variant,,ENST00000593461,; T ENST00000341130 Transcript synonymous_variant 243/1930 138/876 46/291 A gcC/gcA 1 -1 TMEM221 HGNC HGNC:21943 protein_coding YES CCDS54230.1 ENSP00000342162 A6NGB7 UPI00002036E7 NM_001190844.1 1/3 Pfam_domain:PF15038,hmmpanther:PTHR36132,hmmpanther:PTHR36132:SF1 LOW 1 SNV 2 1 PASS rs954832303 . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 2 4 32 17448325 17448325 G T 1 0 0 0 0 0 0 0 1 16585 1103 39 1 1 TMEM221 19 17448325 Silent SNP G C3L-02348_T 2480024 17448325 41169291 48 8916 LSR 0 . GRCh38 19 35266950 35266957 + Frame_Shift_Del DEL GTGGCCGT GTGGCCGT - novel C3L-02348_T C3L-02348_N GTGGCCGT GTGGCCGT c.1275_1282delCCGTGTGG p.Arg426AlafsTer5 p.R426Afs*5 ENST00000621372 8/10 89 81 8 117 117 0 sindel-varindel-pindel LSR,frameshift_variant,p.Arg406AlafsTer5,ENST00000602122,NM_001260489.1;LSR,frameshift_variant,p.Arg426AlafsTer5,ENST00000621372,NM_205834.3;LSR,frameshift_variant,p.Arg426AlafsTer5,ENST00000361790,;LSR,frameshift_variant,p.Arg407AlafsTer5,ENST00000354900,NM_015925.6;LSR,frameshift_variant,p.Arg358AlafsTer5,ENST00000360798,NM_205835.3;LSR,frameshift_variant,p.Arg378AlafsTer5,ENST00000605618,;LSR,frameshift_variant,p.Arg368AlafsTer5,ENST00000347609,;LSR,frameshift_variant,p.Arg270AlafsTer5,ENST00000427250,NM_001260490.1;USF2,upstream_gene_variant,,ENST00000222305,NM_003367.2;USF2,upstream_gene_variant,,ENST00000595068,;USF2,upstream_gene_variant,,ENST00000343550,NM_207291.1;USF2,upstream_gene_variant,,ENST00000594064,;USF2,upstream_gene_variant,,ENST00000599471,;USF2,upstream_gene_variant,,ENST00000379134,;USF2,upstream_gene_variant,,ENST00000596380,;LSR,downstream_gene_variant,,ENST00000601623,;USF2,upstream_gene_variant,,ENST00000598058,;USF2,upstream_gene_variant,,ENST00000599625,;LSR,downstream_gene_variant,,ENST00000599658,;AD000684.2,downstream_gene_variant,,ENST00000602262,;USF2,upstream_gene_variant,,ENST00000600341,;LSR,downstream_gene_variant,,ENST00000597933,;LSR,non_coding_transcript_exon_variant,,ENST00000597446,;USF2,upstream_gene_variant,,ENST00000607959,;USF2,upstream_gene_variant,,ENST00000602164,;USF2,upstream_gene_variant,,ENST00000593708,;USF2,upstream_gene_variant,,ENST00000597671,; - ENST00000621372 Transcript frameshift_variant 1494-1501/2274 1271-1278/1950 424-426/649 SGR/X aGTGGCCGT/a 1 1 LSR HGNC HGNC:29572 protein_coding YES CCDS12450.1 ENSP00000480821 Q86X29 UPI000003117A NM_205834.3 8/10 hmmpanther:PTHR15923:SF1,hmmpanther:PTHR15923 HIGH 1 deletion 1 4 1 PASS . . 0 203 6 0 0 0 0 0 -16.72654 0.9999998 1 1 1 0 - 7 5 32 35266950 35266950 GTGGCCGT - 1 0 1 0 1 0 0 0 0 8971 1029 36 0 0 LSR 19 35266950 Frame_Shift_Del DEL GTGGCCGT C3L-02348_T 17818625 35266950 23350666 49 8917 FCGBP 0 . GRCh38 19 39875705 39875705 + Missense_Mutation SNP T T G novel C3L-02348_T C3L-02348_N T T c.10286A>C p.Lys3429Thr p.K3429T ENST00000616721 22/28 652 554 98 662 662 0 strelka-varscan-mutect FCGBP,missense_variant,p.Lys3429Thr,ENST00000616721,NM_003890.2; G ENST00000616721 Transcript missense_variant 10294/12787 10286/12615 3429/4204 K/T aAg/aCg 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 tolerated(0.33) 22/28 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF244 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 39875705 39875705 T G 1 0 0 0 0 1 0 0 0 5641 1609 56 5 5 FCGBP 19 39875705 Missense_Mutation SNP T C3L-02348_T 4608755 39875705 18741911 50 8918 LILRA6 0 . GRCh38 19 54240941 54240941 + Missense_Mutation SNP G G T novel C3L-02348_T C3L-02348_N G G c.845C>A p.Thr282Asn p.T282N ENST00000396365 5/8 576 531 45 626 625 1 varscan-mutect LILRA6,missense_variant,p.Thr282Asn,ENST00000396365,NM_024318.3;LILRA6,missense_variant,p.Thr282Asn,ENST00000245621,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000270464,; T ENST00000396365 Transcript missense_variant 885/1890 845/1446 282/481 T/N aCc/aAc 1 -1 LILRA6 HGNC HGNC:15495 protein_coding YES CCDS42610.1 ENSP00000379651 Q6PI73 U5XH19 UPI000292EF7A NM_024318.3 deleterious(0.03) 5/8 Gene3D:2.60.40.10,PIRSF_domain:PIRSF001979,PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF116,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1241984592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 54240941 54240941 G T 1 0 0 0 0 1 0 0 0 8697 1261 44 2 2 LILRA6 19 54240941 Missense_Mutation SNP G C3L-02348_T 14365236 54240941 4376675 51 8919 GNAS 0 . GRCh38 20 58909541 58909541 + Missense_Mutation SNP A A T rs121913494 C3L-02348_T C3L-02348_N A A c.2609A>T p.Gln870Leu p.Q870L ENST00000371100 9/13 734 587 147 751 750 1 strelka-varscan-mutect GNAS,missense_variant,p.Gln870Leu,ENST00000371100,NM_080425.2;GNAS,missense_variant,p.Gln856Leu,ENST00000371102,;GNAS,missense_variant,p.Gln228Leu,ENST00000354359,NM_001077488.2;GNAS,missense_variant,p.Gln227Leu,ENST00000371085,NM_000516.4;GNAS,missense_variant,p.Gln213Leu,ENST00000371095,NM_080426.2;GNAS,missense_variant,p.Gln212Leu,ENST00000265620,NM_001077489.2;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000306090,;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000604005,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000488652,;GNAS,non_coding_transcript_exon_variant,,ENST00000470512,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000480232,;GNAS,non_coding_transcript_exon_variant,,ENST00000476935,;GNAS,non_coding_transcript_exon_variant,,ENST00000492907,;GNAS,non_coding_transcript_exon_variant,,ENST00000481039,;GNAS,non_coding_transcript_exon_variant,,ENST00000467321,;GNAS,non_coding_transcript_exon_variant,,ENST00000468895,;GNAS,non_coding_transcript_exon_variant,,ENST00000493958,;GNAS,intron_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000472183,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000482112,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000464788,;GNAS,downstream_gene_variant,,ENST00000467227,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000487981,;GNAS,non_coding_transcript_exon_variant,,ENST00000479025,;GNAS,upstream_gene_variant,,ENST00000475610,; T ENST00000371100 Transcript missense_variant 3161/4029 2609/3114 870/1037 Q/L cAg/cTg rs121913494,COSM1566191,COSM1731065,COSM27888,COSM27896 1 1 GNAS HGNC HGNC:4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 UPI0000E444AE NM_080425.2 deleterious(0.04) 9/13 Gene3D:3.40.50.300,Pfam_domain:PF00503,Prints_domain:PR00318,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF36,SMART_domains:SM00275,Superfamily_domains:SSF52540 pathogenic 0,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs121913494 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 32 58909541 58909541 A T 1 0 0 0 0 1 0 0 0 6390 188 7 4 4 GNAS 20 58909541 Missense_Mutation SNP A C3L-02348_T 58909541 5534626 52 8920 SYCP2 0 . GRCh38 20 59901664 59901664 + Missense_Mutation SNP T T A novel C3L-02348_T C3L-02348_N T T c.1180A>T p.Arg394Trp p.R394W ENST00000357552 16/45 61 49 12 92 92 0 strelka-varscan-mutect SYCP2,missense_variant,p.Arg394Trp,ENST00000357552,;SYCP2,missense_variant,p.Arg394Trp,ENST00000371001,NM_014258.2;SYCP2,missense_variant,p.Arg394Trp,ENST00000446834,;SYCP2,splice_region_variant,,ENST00000461538,; A ENST00000357552 Transcript missense_variant,splice_region_variant 1406/5567 1180/4593 394/1530 R/W Agg/Tgg 1 -1 SYCP2 HGNC HGNC:11490 protein_coding YES CCDS13482.1 ENSP00000350162 Q9BX26 UPI0000135683 deleterious(0.03) 16/45 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12 MODERATE 1 SNV 1 1 PASS . . 2 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 59901664 59901664 T A 1 0 0 0 0 1 0 0 0 15822 1536 53 4 4 SYCP2 20 59901664 Missense_Mutation SNP T C3L-02348_T 992123 59901664 4542503 53 8921 LZTR1 0 . GRCh38 22 20982565 20982565 + Missense_Mutation SNP G G C novel C3L-02348_T C3L-02348_N G G c.194G>C p.Gly65Ala p.G65A ENST00000215739 1/21 193 153 40 171 171 0 strelka-varscan-mutect LZTR1,missense_variant,p.Gly65Ala,ENST00000215739,NM_006767.3;AIFM3,downstream_gene_variant,,ENST00000399167,NM_144704.2;AIFM3,downstream_gene_variant,,ENST00000440238,;AIFM3,downstream_gene_variant,,ENST00000405089,NM_001146288.1;AIFM3,downstream_gene_variant,,ENST00000399163,NM_001018060.2;XXbac-B135H6.18,upstream_gene_variant,,ENST00000610278,;LZTR1,intron_variant,,ENST00000479606,;AIFM3,downstream_gene_variant,,ENST00000465606,;AIFM3,downstream_gene_variant,,ENST00000483107,;LZTR1,upstream_gene_variant,,ENST00000480895,;LZTR1,missense_variant,p.Gly65Ala,ENST00000414985,;LZTR1,missense_variant,p.Gly65Ala,ENST00000443265,;LZTR1,non_coding_transcript_exon_variant,,ENST00000493460,;AIFM3,downstream_gene_variant,,ENST00000486003,; C ENST00000215739 Transcript missense_variant 553/4572 194/2523 65/840 G/A gGt/gCt 1 1 LZTR1 HGNC HGNC:6742 protein_coding YES CCDS33606.1 ENSP00000215739 Q8N653 UPI000013C695 NM_006767.3 tolerated(0.15) 1/21 hmmpanther:PTHR23244:SF285,hmmpanther:PTHR23244,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 32 20982565 20982565 G C 1 0 0 0 0 1 0 0 0 9050 1261 44 4 4 LZTR1 22 20982565 Missense_Mutation SNP G C3L-02348_T 20982565 29835903 54 8922 ZFX 0 . GRCh38 X 24208935 24208935 + Missense_Mutation SNP A A G novel C3L-02348_T C3L-02348_N A A c.1129A>G p.Thr377Ala p.T377A ENST00000379177 10/11 316 242 74 342 342 0 strelka-varscan-mutect ZFX,missense_variant,p.Thr377Ala,ENST00000379177,NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3;ZFX,missense_variant,p.Thr416Ala,ENST00000379188,;ZFX,missense_variant,p.Thr148Ala,ENST00000539115,NM_001178086.1;ZFX,missense_variant,p.Thr377Ala,ENST00000304543,;ZFX,missense_variant,p.Thr327Ala,ENST00000338565,;ZFX,non_coding_transcript_exon_variant,,ENST00000459724,; G ENST00000379177 Transcript missense_variant 1556/7558 1129/2418 377/805 T/A Act/Gct 1 1 ZFX HGNC HGNC:12869 protein_coding YES CCDS14211.1 ENSP00000368475 P17010 A0A024RC04 UPI000013C504 NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3 tolerated(0.82) 10/11 hmmpanther:PTHR24387:SF222,hmmpanther:PTHR24387,Pfam_domain:PF04704 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 32 24208935 24208935 A G 1 0 0 0 0 1 0 0 0 18239 159 6 5 5 ZFX 23 24208935 Missense_Mutation SNP A C3L-02348_T 24208935 131831960 55 8923 FAM47B 0 . GRCh38 X 34942886 34942886 + Missense_Mutation SNP C C A C3L-02348_T C3L-02348_N C C c.55C>A p.Pro19Thr p.P19T ENST00000329357 1/1 102 86 16 138 138 0 strelka-varscan-mutect FAM47B,missense_variant,p.Pro19Thr,ENST00000329357,NM_152631.2; A ENST00000329357 Transcript missense_variant 91/2120 55/1938 19/645 P/T Ccc/Acc COSM1467740,COSM5469082 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 deleterious(0) 1/1 Pfam_domain:PF14642 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 32 34942886 34942886 C A 1 0 0 0 0 1 0 0 0 5448 739 26 2 2 FAM47B 23 34942886 Missense_Mutation SNP C C3L-02348_T 10733951 34942886 121098009 56 8924 APOOL 0 . GRCh38 X 85074083 85074083 + Nonsense_Mutation SNP C C A novel C3L-02348_T C3L-02348_N C C c.572C>A p.Ser191Ter p.S191* ENST00000373173 7/9 170 150 20 234 234 0 strelka-varscan-mutect APOOL,stop_gained,p.Ser191Ter,ENST00000613473,;APOOL,stop_gained,p.Ser191Ter,ENST00000373173,NM_198450.5;APOOL,missense_variant,p.His186Asn,ENST00000622540,; A ENST00000373173 Transcript stop_gained 659/1279 572/807 191/268 S/* tCa/tAa 1 1 APOOL HGNC HGNC:24009 protein_coding YES CCDS48138.1 ENSP00000362268 Q6UXV4 UPI00001D6936 NM_198450.5 7/9 hmmpanther:PTHR14564,hmmpanther:PTHR14564:SF3,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 32 85074083 85074083 C A 1 0 0 0 0 0 1 0 0 936 838 29 2 2 APOOL 23 85074083 Nonsense_Mutation SNP C C3L-02348_T 50131197 85074083 70966812 57 8925 LCE2D 0 . GRCh38 1 152664373 152664373 + Missense_Mutation SNP G G A rs753899892 C3L-02350_T C3L-02350_N G G c.268G>A p.Asp90Asn p.D90N ENST00000368784 2/2 146 123 23 142 142 0 strelka-varscan-mutect LCE2D,missense_variant,p.Asp90Asn,ENST00000368784,NM_178430.3; A ENST00000368784 Transcript missense_variant 323/609 268/333 90/110 D/N Gat/Aat rs753899892,COSM4953408 1 1 LCE2D HGNC HGNC:16518 protein_coding YES CCDS1018.1 ENSP00000357773 Q5TA82 UPI00001927D4 NM_178430.3 tolerated_low_confidence(0.62) 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF51 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753899892 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 33 152664373 152664373 G A 1 0 0 0 0 1 0 0 0 8573 1058 37 1 1 LCE2D 1 152664373 Missense_Mutation SNP G C3L-02350_T 152664373 96292049 1 8926 OR2B11 0 . GRCh38 1 247451337 247451337 + Missense_Mutation SNP C C T novel C3L-02350_T C3L-02350_N C C c.646G>A p.Ala216Thr p.A216T ENST00000318749 1/1 237 214 23 215 215 0 strelka-varscan-mutect OR2B11,missense_variant,p.Ala216Thr,ENST00000318749,NM_001004492.1;NLRP3,downstream_gene_variant,,ENST00000366497,NM_001127461.2;NLRP3,downstream_gene_variant,,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,downstream_gene_variant,,ENST00000366496,;NLRP3,downstream_gene_variant,,ENST00000391828,NM_001079821.2;NLRP3,downstream_gene_variant,,ENST00000348069,NM_183395.2;NLRP3,downstream_gene_variant,,ENST00000391827,NM_001127462.2;NLRP3,downstream_gene_variant,,ENST00000532083,; T ENST00000318749 Transcript missense_variant 646/954 646/954 216/317 A/T Gct/Act 1 -1 OR2B11 HGNC HGNC:31249 protein_coding YES CCDS31090.1 ENSP00000325682 Q5JQS5 A0A126GVY5 UPI0000418F50 NM_001004492.1 tolerated(0.58) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF112,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 33 247451337 247451337 C T 1 0 0 0 0 1 0 0 0 11067 739 26 3 3 OR2B11 1 247451337 Missense_Mutation SNP C C3L-02350_T 94786964 247451337 1505085 2 8927 SOS1 0 . GRCh38 2 39067726 39067726 + Nonsense_Mutation SNP C C A rs375934353 C3L-02350_T C3L-02350_N C C c.115G>T p.Glu39Ter p.E39* ENST00000426016 3/24 325 277 48 359 359 0 strelka-varscan-mutect SOS1,stop_gained,p.Glu39Ter,ENST00000426016,;SOS1,stop_gained,p.Glu39Ter,ENST00000402219,NM_005633.3;SOS1,stop_gained,p.Glu39Ter,ENST00000395038,;SOS1,5_prime_UTR_variant,,ENST00000451331,; A ENST00000426016 Transcript stop_gained 202/8517 115/4002 39/1333 E/* Gag/Tag rs375934353 1 -1 SOS1 HGNC HGNC:11187 protein_coding YES CCDS1802.1 ENSP00000387784 Q07889 UPI0000135CF0 3/24 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF168,Gene3D:1.10.20.10,Superfamily_domains:SSF47113 HIGH 1 SNV 2 1 PASS rs375934353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 33 39067726 39067726 C A 1 0 0 0 0 0 1 0 0 15258 893 31 1 1 SOS1 2 39067726 Nonsense_Mutation SNP C C3L-02350_T 39067726 203125803 3 8928 POLR1A 0 . GRCh38 2 86027458 86027458 + Frame_Shift_Del DEL T T - novel C3L-02350_T C3L-02350_N T T c.5128delA p.Thr1710GlnfsTer10 p.T1710Qfs*10 ENST00000263857 34/34 293 269 24 258 258 0 sindel-varindel-pindel POLR1A,frameshift_variant,p.Thr1710GlnfsTer10,ENST00000263857,NM_015425.3;POLR1A,frameshift_variant,p.Thr1649GlnfsTer10,ENST00000409681,;POLR1A,downstream_gene_variant,,ENST00000492034,;POLR1A,downstream_gene_variant,,ENST00000496892,;POLR1A,downstream_gene_variant,,ENST00000471427,; - ENST00000263857 Transcript frameshift_variant 5507/12749 5128/5163 1710/1720 T/X Aca/ca 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 34/34 hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF11,Superfamily_domains:SSF64484 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 33 86027458 86027458 T - 1 0 1 0 1 0 0 0 0 12319 1667 58 0 0 POLR1A 2 86027458 Frame_Shift_Del DEL T C3L-02350_T 46959732 86027458 156166071 4 8929 SNRNP200 0 . GRCh38 2 96275336 96275336 + Missense_Mutation SNP C C A novel C3L-02350_T C3L-02350_N C C c.6188G>T p.Gly2063Val p.G2063V ENST00000323853 44/45 538 489 49 446 446 0 strelka-varscan-mutect SNRNP200,missense_variant,p.Gly2063Val,ENST00000323853,NM_014014.4;CIAO1,downstream_gene_variant,,ENST00000488633,NM_004804.2;SNRNP200,3_prime_UTR_variant,,ENST00000429650,;SNRNP200,non_coding_transcript_exon_variant,,ENST00000497539,;CIAO1,downstream_gene_variant,,ENST00000272402,;SNRNP200,downstream_gene_variant,,ENST00000493271,;SNRNP200,downstream_gene_variant,,ENST00000484372,;SNRNP200,downstream_gene_variant,,ENST00000480835,; A ENST00000323853 Transcript missense_variant 6266/7165 6188/6411 2063/2136 G/V gGc/gTc 1 -1 SNRNP200 HGNC HGNC:30859 protein_coding YES CCDS2020.1 ENSP00000317123 O75643 UPI0000207C53 NM_014014.4 deleterious(0.02) 44/45 hmmpanther:PTHR24075,Gene3D:2.60.40.150,PIRSF_domain:PIRSF039073,Pfam_domain:PF02889,SMART_domains:SM00973,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 96275336 96275336 C A 1 0 0 0 0 1 0 0 0 15172 739 26 2 2 SNRNP200 2 96275336 Missense_Mutation SNP C C3L-02350_T 10247878 96275336 145918193 5 8930 IL36G 0 . GRCh38 2 112985026 112985026 + Missense_Mutation SNP T T C novel C3L-02350_T C3L-02350_N T T c.487T>C p.Phe163Leu p.F163L ENST00000259205 5/5 154 129 25 169 169 0 strelka-varscan-mutect IL36G,missense_variant,p.Phe163Leu,ENST00000259205,NM_019618.3;IL36G,missense_variant,p.Phe128Leu,ENST00000376489,NM_001278568.1;HMGN2P23,upstream_gene_variant,,ENST00000456759,; C ENST00000259205 Transcript missense_variant 556/1195 487/510 163/169 F/L Ttt/Ctt 1 1 IL36G HGNC HGNC:15741 protein_coding YES CCDS2108.1 ENSP00000259205 Q9NZH8 UPI0000038BF0 NM_019618.3 deleterious(0) 5/5 hmmpanther:PTHR10078:SF27,hmmpanther:PTHR10078,Gene3D:2.80.10.50,SMART_domains:SM00125,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 33 112985026 112985026 T C 1 0 0 0 0 1 0 0 0 7596 1609 56 5 5 IL36G 2 112985026 Missense_Mutation SNP T C3L-02350_T 16709690 112985026 129208503 6 8931 LRP1B 0 . GRCh38 2 140364783 140364783 + Missense_Mutation SNP C C A novel C3L-02350_T C3L-02350_N C C c.11009G>T p.Gly3670Val p.G3670V ENST00000389484 72/91 110 96 14 125 125 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gly3670Val,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant,splice_region_variant 11981/16535 11009/13800 3670/4599 G/V gGa/gTa 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.22) 72/91 MODERATE 1 SNV 1 1 PASS rs1290040715 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 140364783 140364783 C A 1 0 0 0 0 1 0 0 0 8850 869 30 2 2 LRP1B 2 140364783 Missense_Mutation SNP C C3L-02350_T 27379757 140364783 101828746 7 8932 DYTN 0 . GRCh38 2 206663373 206663373 + Missense_Mutation SNP G G A novel C3L-02350_T C3L-02350_N G G c.1163C>T p.Pro388Leu p.P388L ENST00000452335 11/12 91 86 5 106 106 0 strelka-mutect DYTN,missense_variant,p.Pro388Leu,ENST00000452335,NM_001093730.1; A ENST00000452335 Transcript missense_variant 1280/2051 1163/1737 388/578 P/L cCt/cTt 1 -1 DYTN HGNC HGNC:23279 protein_coding YES CCDS46502.1 ENSP00000396593 A2CJ06 UPI0000EE0AB9 NM_001093730.1 deleterious(0.01) 11/12 hmmpanther:PTHR11915:SF282,hmmpanther:PTHR11915 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -11.02397 1 1 1 1 0 A 3 1 33 206663373 206663373 G A 1 0 0 0 0 1 0 0 0 4684 1000 35 3 3 DYTN 2 206663373 Missense_Mutation SNP G C3L-02350_T 66298590 206663373 35530156 8 8933 GRM7 0 . GRCh38 3 7461708 7461709 + Frame_Shift_Del DEL GA GA - novel C3L-02350_T C3L-02350_N GA GA c.1501_1502delGA p.Glu501ThrfsTer12 p.E501Tfs*12 ENST00000357716 7/10 165 139 26 152 152 0 sindel-varindel-pindel GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000486284,NM_181874.2;GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000357716,NM_000844.3;GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000389336,;GRM7,frameshift_variant,p.Glu256ThrfsTer12,ENST00000402647,;GRM7,frameshift_variant,p.Glu158ThrfsTer12,ENST00000445087,;GRM7,non_coding_transcript_exon_variant,,ENST00000458641,;GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000467425,;GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000440923,;GRM7,frameshift_variant,p.Glu501ThrfsTer12,ENST00000389335,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,; - ENST00000357716 Transcript frameshift_variant 1775-1776/4127 1501-1502/2748 501/915 E/X GAa/a 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 7/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Superfamily_domains:SSF53822 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 33 7461708 7461708 GA - 1 0 1 0 1 0 0 0 0 6684 1059 37 0 0 GRM7 3 7461708 Frame_Shift_Del DEL GA C3L-02350_T 7461708 190833851 9 8934 VWA5B2 0 . GRCh38 3 184234668 184234668 + Missense_Mutation SNP C C A novel C3L-02350_T C3L-02350_N C C c.858C>A p.Ser286Arg p.S286R ENST00000426955 6/19 224 204 20 180 179 1 strelka-varscan-mutect VWA5B2,missense_variant,p.Ser286Arg,ENST00000426955,NM_138345.1;VWA5B2,missense_variant,p.Ser67Arg,ENST00000273794,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000461141,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000497229,;VWA5B2,upstream_gene_variant,,ENST00000474580,; A ENST00000426955 Transcript missense_variant 958/4120 858/3729 286/1242 S/R agC/agA 1 1 VWA5B2 HGNC HGNC:25144 protein_coding YES CCDS54686.1 ENSP00000398688 Q8N398 UPI0000412DE9 NM_138345.1 tolerated(0.55) 6/19 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF107 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 184234668 184234668 C A 1 0 0 0 0 1 0 0 0 17798 738 26 2 2 VWA5B2 3 184234668 Missense_Mutation SNP C C3L-02350_T 176772960 184234668 14060891 10 8935 FAM200B 0 . GRCh38 4 15688587 15688587 + Missense_Mutation SNP T T C novel C3L-02350_T C3L-02350_N T T c.1610T>C p.Val537Ala p.V537A ENST00000622362 2/2 122 110 12 185 185 0 varscan-mutect FAM200B,missense_variant,p.Val537Ala,ENST00000622362,NM_001145191.1;FAM200B,missense_variant,p.Val537Ala,ENST00000422728,;FAM200B,downstream_gene_variant,,ENST00000503617,;FAM200B,non_coding_transcript_exon_variant,,ENST00000504137,;FAM200B,non_coding_transcript_exon_variant,,ENST00000505260,;FAM200B,non_coding_transcript_exon_variant,,ENST00000502856,;FAM200B,non_coding_transcript_exon_variant,,ENST00000506610,;FAM200B,non_coding_transcript_exon_variant,,ENST00000504823,;FAM200B,non_coding_transcript_exon_variant,,ENST00000515697,;FAM200B,non_coding_transcript_exon_variant,,ENST00000503600,;FAM200B,intron_variant,,ENST00000504598,;FAM200B,downstream_gene_variant,,ENST00000507305,;FAM200B,downstream_gene_variant,,ENST00000515430,;FAM200B,downstream_gene_variant,,ENST00000513053,;FAM200B,downstream_gene_variant,,ENST00000510920,;FAM200B,downstream_gene_variant,,ENST00000512855,;FAM200B,downstream_gene_variant,,ENST00000510032,;FAM200B,downstream_gene_variant,,ENST00000502502,;FAM200B,downstream_gene_variant,,ENST00000508567,;FAM200B,downstream_gene_variant,,ENST00000514803,;FAM200B,downstream_gene_variant,,ENST00000509022,;FAM200B,downstream_gene_variant,,ENST00000507992,;FAM200B,downstream_gene_variant,,ENST00000510186,; C ENST00000622362 Transcript missense_variant 2525/4377 1610/1974 537/657 V/A gTa/gCa 1 1 FAM200B HGNC HGNC:27740 protein_coding YES CCDS47028.1 ENSP00000483930 P0CF97 UPI0000160C4C NM_001145191.1 deleterious(0) 2/2 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF93,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 33 15688587 15688587 T C 1 0 0 0 0 1 0 0 0 5384 1638 57 5 5 FAM200B 4 15688587 Missense_Mutation SNP T C3L-02350_T 15688587 174525968 11 8936 PPBP 0 . GRCh38 4 73988092 73988092 + Missense_Mutation SNP T T A novel C3L-02350_T C3L-02350_N T T c.12A>T p.Arg4Ser p.R4S ENST00000296028 1/3 190 156 34 231 231 0 strelka-varscan-mutect PPBP,missense_variant,p.Arg4Ser,ENST00000296028,NM_002704.3; A ENST00000296028 Transcript missense_variant 106/715 12/387 4/128 R/S agA/agT 1 -1 PPBP HGNC HGNC:9240 protein_coding YES CCDS3563.1 ENSP00000296028 P02775 UPI00000012C5 NM_002704.3 deleterious(0) 1/3 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 73988092 73988092 T A 1 0 0 0 0 1 0 0 0 12412 1664 58 4 4 PPBP 4 73988092 Missense_Mutation SNP T C3L-02350_T 58299505 73988092 116226463 12 8937 KCNN2 0 . GRCh38 5 114496094 114496094 + Missense_Mutation SNP T T C novel C3L-02350_T C3L-02350_N T T c.1652T>C p.Val551Ala p.V551A ENST00000512097 9/9 407 353 54 324 324 0 strelka-varscan-mutect KCNN2,missense_variant,p.Val551Ala,ENST00000512097,;KCNN2,missense_variant,p.Val551Ala,ENST00000264773,NM_021614.3;KCNN2,missense_variant,p.Val554Ala,ENST00000631899,;KCNN2,missense_variant,p.Val203Ala,ENST00000610748,NM_001278204.1;KCNN2,missense_variant,p.Val203Ala,ENST00000503706,NM_170775.2;RP11-492A10.1,splice_region_variant,,ENST00000514115,;KCNN2,downstream_gene_variant,,ENST00000507750,;KCNN2,downstream_gene_variant,,ENST00000505491,;KCNN2,downstream_gene_variant,,ENST00000506812,;KCNN2,downstream_gene_variant,,ENST00000632892,; C ENST00000512097 Transcript missense_variant 2670/3076 1652/1740 551/579 V/A gTc/gCc 1 1 KCNN2 HGNC HGNC:6291 protein_coding YES CCDS4114.1 ENSP00000427120 Q9H2S1 UPI000013D56A tolerated_low_confidence(0.55) 9/9 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF43 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 33 114496094 114496094 T C 1 0 0 0 0 1 0 0 0 7995 1667 58 5 5 KCNN2 5 114496094 Missense_Mutation SNP T C3L-02350_T 114496094 67042165 13 8938 RFX6 0 . GRCh38 6 116927252 116927252 + Missense_Mutation SNP A A G novel C3L-02350_T C3L-02350_N A A c.2111A>G p.Gln704Arg p.Q704R ENST00000332958 17/19 362 325 37 349 349 0 strelka-varscan-mutect RFX6,missense_variant,p.Gln704Arg,ENST00000332958,NM_173560.3;RFX6,downstream_gene_variant,,ENST00000487683,; G ENST00000332958 Transcript missense_variant 2127/3460 2111/2787 704/928 Q/R cAg/cGg 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 deleterious_low_confidence(0.01) 17/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 116927252 116927252 A G 1 0 0 0 0 1 0 0 0 13441 188 7 5 5 RFX6 6 116927252 Missense_Mutation SNP A C3L-02350_T 116927252 53878727 14 8939 HDAC9 0 . GRCh38 7 18644681 18644681 + Nonsense_Mutation SNP C C A novel C3L-02350_T C3L-02350_N C C c.923C>A p.Ser308Ter p.S308* ENST00000441542 8/25 123 108 15 159 159 0 strelka-varscan-mutect HDAC9,stop_gained,p.Ser305Ter,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,stop_gained,p.Ser264Ter,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,stop_gained,p.Ser305Ter,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,stop_gained,p.Ser292Ter,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,stop_gained,p.Ser264Ter,ENST00000401921,;HDAC9,stop_gained,p.Ser308Ter,ENST00000441542,NM_178425.2;HDAC9,stop_gained,p.Ser305Ter,ENST00000432645,NM_058176.2;HDAC9,stop_gained,p.Ser303Ter,ENST00000417496,NM_001204144.1;HDAC9,stop_gained,p.Ser261Ter,ENST00000428307,NM_001204145.1;HDAC9,stop_gained,p.Ser277Ter,ENST00000456174,NM_001204148.1;HDAC9,stop_gained,p.Ser228Ter,ENST00000524023,NM_001204147.1;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; A ENST00000441542 Transcript stop_gained 923/3210 923/3210 308/1069 S/* tCa/tAa 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 8/25 PIRSF_domain:PIRSF037911 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 33 18644681 18644681 C A 1 0 0 0 0 0 1 0 0 6901 838 29 2 2 HDAC9 7 18644681 Nonsense_Mutation SNP C C3L-02350_T 18644681 140701292 15 8940 ABCB4 0 . GRCh38 7 87439683 87439683 + Missense_Mutation SNP T T G novel C3L-02350_T C3L-02350_N T T c.1715A>C p.Gln572Pro p.Q572P ENST00000265723 14/28 434 373 61 397 397 0 strelka-varscan-mutect ABCB4,missense_variant,p.Gln572Pro,ENST00000265723,NM_018849.2;ABCB4,missense_variant,p.Gln572Pro,ENST00000359206,NM_000443.3;ABCB4,missense_variant,p.Gln572Pro,ENST00000358400,NM_018850.2;ABCB4,missense_variant,p.Gln572Pro,ENST00000453593,; G ENST00000265723 Transcript missense_variant 1827/4020 1715/3861 572/1286 Q/P cAg/cCg 1 -1 ABCB4 HGNC HGNC:45 protein_coding YES CCDS5606.1 ENSP00000265723 P21439 UPI000013D66B NM_018849.2 deleterious(0) 14/28 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 87439683 87439683 T G 1 0 0 0 0 1 0 0 0 47 1580 55 5 5 ABCB4 7 87439683 Missense_Mutation SNP T C3L-02350_T 68795002 87439683 71906290 16 8941 GLDC 0 . GRCh38 9 6558659 6558659 + Missense_Mutation SNP T T G rs386833536 C3L-02350_T C3L-02350_N T T c.1952A>C p.His651Pro p.H651P ENST00000321612 17/25 524 463 61 487 486 1 strelka-varscan-mutect GLDC,missense_variant,p.His651Pro,ENST00000321612,NM_000170.2;GLDC,non_coding_transcript_exon_variant,,ENST00000460457,;GLDC,upstream_gene_variant,,ENST00000467946,; G ENST00000321612 Transcript missense_variant 2103/3767 1952/3063 651/1020 H/P cAt/cCt rs386833536,CM061025 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0) 17/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Gene3D:3.40.640.10,Pfam_domain:PF01212,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 likely_pathogenic 16601880 MODERATE 1 SNV 1 1,1 1 PASS rs386833536 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 6558659 6558659 T G 1 0 0 0 0 1 0 0 0 6311 1464 51 5 5 GLDC 9 6558659 Missense_Mutation SNP T C3L-02350_T 6558659 131836058 17 8942 SPATA31A7 0 . GRCh38 9 61193058 61193058 + Silent SNP C C G novel C3L-02350_T C3L-02350_N C C c.972C>G p.= p.G324G ENST00000619167 4/4 112 98 14 111 111 0 varscan-mutect SPATA31A7,synonymous_variant,p.=,ENST00000619167,NM_015667.2;RP11-101E5.6,downstream_gene_variant,,ENST00000611332,;SPATA31A7,intron_variant,,ENST00000621711,;SPATA31A7,downstream_gene_variant,,ENST00000618860,;SPATA31A7,downstream_gene_variant,,ENST00000619140,;SPATA31A7,downstream_gene_variant,,ENST00000622899,;SPATA31A7,downstream_gene_variant,,ENST00000622751,;SPATA31A7,downstream_gene_variant,,ENST00000376458,;SPATA31A7,downstream_gene_variant,,ENST00000614013,;SPATA31A7,downstream_gene_variant,,ENST00000611017,; G ENST00000619167 Transcript synonymous_variant 1034/4256 972/4044 324/1347 G ggC/ggG 1 1 SPATA31A7 HGNC HGNC:32007 protein_coding YES CCDS75838.1 ENSP00000484807 Q8IWB4 UPI0000457748 NM_015667.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF22 LOW 1 SNV 1 1 PASS . . 28 174 7 0 0 0 0 0 -20 0.9999967 1 1 1 0 G 2 3 33 61193058 61193058 C G 1 0 0 0 0 0 0 0 1 15346 726 26 4 4 SPATA31A7 9 61193058 Silent SNP C C3L-02350_T 54634399 61193058 77201659 18 8943 RNF20 0 . GRCh38 9 101562247 101562248 + Frame_Shift_Ins INS - - A novel C3L-02350_T C3L-02350_N - - c.2754dupA p.Arg919ThrfsTer8 p.R919Tfs*8 ENST00000389120 20/20 50 43 7 68 68 0 sindel-varindel-pindel RNF20,frameshift_variant,p.Arg919ThrfsTer8,ENST00000389120,NM_019592.6;RNF20,downstream_gene_variant,,ENST00000478072,; A ENST00000389120 Transcript frameshift_variant,splice_region_variant 2843-2844/3940 2753-2754/2928 918/975 A/AX gca/gcAa 1 1 RNF20 HGNC HGNC:10062 protein_coding YES CCDS35084.1 ENSP00000373772 Q5VTR2 UPI00001CE3B5 NM_019592.6 20/20 Gene3D:3.30.40.10,hmmpanther:PTHR23163,hmmpanther:PTHR23163:SF2,Superfamily_domains:SSF57850 HIGH 1 insertion 1 1 1 PASS . . 0 180 25 5 0 0 0 0 -13.05185 0.8638971 0 1 1 0 A 7 5 33 101562247 101562247 - A 1 0 1 1 0 0 0 0 0 13651 724 25 0 0 RNF20 9 101562247 Frame_Shift_Ins INS - C3L-02350_T 40369189 101562247 36832470 19 8944 PCDH15 0 . GRCh38 10 54195816 54195816 + Missense_Mutation SNP T T A rs758680936 C3L-02350_T C3L-02350_N T T c.1187A>T p.Gln396Leu p.Q396L ENST00000373957 12/35 492 416 76 503 503 0 strelka-varscan-mutect PCDH15,missense_variant,p.Gln396Leu,ENST00000614895,;PCDH15,missense_variant,p.Gln391Leu,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000414778,;PCDH15,missense_variant,p.Gln396Leu,ENST00000617051,;PCDH15,missense_variant,p.Gln396Leu,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Gln369Leu,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Gln354Leu,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Gln391Leu,ENST00000622048,;PCDH15,missense_variant,p.Gln391Leu,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Gln396Leu,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000395445,;PCDH15,missense_variant,p.Gln391Leu,ENST00000616114,;PCDH15,missense_variant,p.Gln391Leu,ENST00000395438,;PCDH15,missense_variant,p.Gln396Leu,ENST00000612394,;PCDH15,missense_variant,p.Gln396Leu,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Gln391Leu,ENST00000373955,;PCDH15,missense_variant,p.Gln391Leu,ENST00000395446,;PCDH15,missense_variant,p.Gln391Leu,ENST00000395440,;PCDH15,5_prime_UTR_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Gln391Leu,ENST00000448885,;PCDH15,missense_variant,p.Gln391Leu,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript missense_variant 1582/7032 1187/5889 396/1962 Q/L cAa/cTa rs758680936 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.05) 12/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs758680936 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 54195816 54195816 T A 1 0 0 0 0 1 0 0 0 11598 1812 63 4 4 PCDH15 10 54195816 Missense_Mutation SNP T C3L-02350_T 54195816 79601606 20 8945 SFTPD 0 . GRCh38 10 79942010 79942010 + Missense_Mutation SNP T T A novel C3L-02350_T C3L-02350_N T T c.494A>T p.Lys165Met p.K165M ENST00000372292 5/8 230 205 25 177 177 0 strelka-varscan-mutect SFTPD,missense_variant,p.Lys165Met,ENST00000372292,NM_003019.4;SFTPD,missense_variant,p.Lys178Met,ENST00000444384,;MBL1P,intron_variant,,ENST00000421889,; A ENST00000372292 Transcript missense_variant 535/1281 494/1128 165/375 K/M aAg/aTg 1 -1 SFTPD HGNC HGNC:10803 protein_coding YES CCDS7362.1 ENSP00000361366 P35247 UPI000013CEE7 NM_003019.4 deleterious(0) 5/8 hmmpanther:PTHR24024:SF15,hmmpanther:PTHR24024,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 33 79942010 79942010 T A 1 0 0 0 0 1 0 0 0 14453 1609 56 4 4 SFTPD 10 79942010 Missense_Mutation SNP T C3L-02350_T 25746194 79942010 53855412 21 8946 TLL2 0 . GRCh38 10 96370311 96370311 + Silent SNP G G A novel C3L-02350_T C3L-02350_N G G c.2667C>T p.= p.C889C ENST00000357947 20/21 35 30 5 41 41 0 strelka-varscan-mutect TLL2,synonymous_variant,p.=,ENST00000357947,NM_012465.3;TLL2,downstream_gene_variant,,ENST00000506028,; A ENST00000357947 Transcript synonymous_variant 2893/6756 2667/3048 889/1015 C tgC/tgT 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 20/21 PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF638,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,SMART_domains:SM00042 LOW 1 SNV 1 1 PASS . . 0 194 16 0 0 0 0 0 -12.83973 0.9992194 1 1 1 0 A 2 1 33 96370311 96370311 G A 1 0 0 0 0 0 0 0 1 16392 1101 38 1 1 TLL2 10 96370311 Silent SNP G C3L-02350_T 16428301 96370311 37427111 22 8947 PHC1 0 . GRCh38 12 8936907 8936907 + Missense_Mutation SNP C C T novel C3L-02350_T C3L-02350_N C C c.2420C>T p.Ala807Val p.A807V ENST00000543824 13/16 261 246 15 226 226 0 varscan-mutect PHC1,missense_variant,p.Ala762Val,ENST00000433083,;PHC1,missense_variant,p.Ala807Val,ENST00000543824,;PHC1,missense_variant,p.Ala807Val,ENST00000544916,NM_004426.2;PHC1,intron_variant,,ENST00000542346,;M6PR,downstream_gene_variant,,ENST00000000412,NM_002355.3;M6PR,downstream_gene_variant,,ENST00000536844,NM_001207024.1;M6PR,downstream_gene_variant,,ENST00000539143,;M6PR,downstream_gene_variant,,ENST00000543704,;PHC1,downstream_gene_variant,,ENST00000537610,;M6PR,downstream_gene_variant,,ENST00000544193,;PHC1,downstream_gene_variant,,ENST00000433847,;PHC1,downstream_gene_variant,,ENST00000539928,;PHC1,3_prime_UTR_variant,,ENST00000540574,;PHC1,3_prime_UTR_variant,,ENST00000535510,;M6PR,downstream_gene_variant,,ENST00000541507,;PHC1,downstream_gene_variant,,ENST00000540809,; T ENST00000543824 Transcript missense_variant 2752/4292 2420/3015 807/1004 A/V gCc/gTc 1 1 PHC1 HGNC HGNC:3182 protein_coding YES CCDS8597.1 ENSP00000440674 P78364 UPI000013CD12 tolerated(0.07) 13/16 PROSITE_profiles:PS51024,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 33 8936907 8936907 C T 1 0 0 0 0 1 0 0 0 11905 739 26 3 3 PHC1 12 8936907 Missense_Mutation SNP C C3L-02350_T 8936907 124338402 23 8948 TESPA1 0 . GRCh38 12 54962714 54962714 + Missense_Mutation SNP A A G novel C3L-02350_T C3L-02350_N A A c.1184T>C p.Leu395Pro p.L395P ENST00000449076 9/11 228 206 22 249 249 0 strelka-varscan-mutect TESPA1,missense_variant,p.Leu257Pro,ENST00000524622,NM_001261844.1,NM_014796.2;TESPA1,missense_variant,p.Leu395Pro,ENST00000449076,NM_001136030.2;TESPA1,missense_variant,p.Leu257Pro,ENST00000532804,;TESPA1,missense_variant,p.Leu395Pro,ENST00000316577,NM_001098815.2;TESPA1,missense_variant,p.Leu257Pro,ENST00000531122,;TESPA1,intron_variant,,ENST00000532757,;TESPA1,downstream_gene_variant,,ENST00000526532,;TESPA1,upstream_gene_variant,,ENST00000528240,;TESPA1,downstream_gene_variant,,ENST00000533446,;TESPA1,downstream_gene_variant,,ENST00000524959,;TESPA1,3_prime_UTR_variant,,ENST00000524923,;TESPA1,downstream_gene_variant,,ENST00000525978,; G ENST00000449076 Transcript missense_variant 1317/2010 1184/1566 395/521 L/P cTg/cCg 1 -1 TESPA1 HGNC HGNC:29109 protein_coding YES CCDS44913.1 ENSP00000400892 A2RU30 A0A024RB73 UPI00001FC438 NM_001136030.2 deleterious_low_confidence(0) 9/11 hmmpanther:PTHR17469 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 54962714 54962714 A G 1 0 0 0 0 1 0 0 0 16189 188 7 5 5 TESPA1 12 54962714 Missense_Mutation SNP A C3L-02350_T 46025807 54962714 78312595 24 8949 METTL25 0 . GRCh38 12 82434705 82434705 + Missense_Mutation SNP G G C rs867620589 C3L-02350_T C3L-02350_N G G c.1385G>C p.Arg462Pro p.R462P ENST00000248306 7/12 234 212 22 258 257 1 strelka-varscan-mutect METTL25,missense_variant,p.Arg462Pro,ENST00000248306,NM_032230.2;METTL25,missense_variant,p.Arg97Pro,ENST00000550298,;METTL25,non_coding_transcript_exon_variant,,ENST00000547357,;METTL25,upstream_gene_variant,,ENST00000548432,; C ENST00000248306 Transcript missense_variant 1454/2093 1385/1812 462/603 R/P cGg/cCg rs867620589,COSM4389323 1 1 METTL25 HGNC HGNC:26228 protein_coding YES CCDS9024.1 ENSP00000248306 Q8N6Q8 UPI000013CC3E NM_032230.2 deleterious(0) 7/12 hmmpanther:PTHR12496,hmmpanther:PTHR12496:SF0 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs867620589 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 33 82434705 82434705 G C 1 0 0 0 0 1 0 0 0 9451 1116 39 4 4 METTL25 12 82434705 Missense_Mutation SNP G C3L-02350_T 27471991 82434705 50840604 25 8950 ATP2A2 0 . GRCh38 12 110282761 110282761 + Missense_Mutation SNP T T G novel C3L-02350_T C3L-02350_N T T c.185T>G p.Val62Gly p.V62G ENST00000539276 3/20 424 400 24 516 516 0 strelka-varscan-mutect ATP2A2,missense_variant,p.Val62Gly,ENST00000308664,NM_001681.3;ATP2A2,missense_variant,p.Val62Gly,ENST00000539276,NM_170665.3;ATP2A2,5_prime_UTR_variant,,ENST00000552636,;ATP2A2,3_prime_UTR_variant,,ENST00000377685,; G ENST00000539276 Transcript missense_variant 294/4094 185/3129 62/1042 V/G gTt/gGt 1 1 ATP2A2 HGNC HGNC:812 protein_coding YES CCDS9144.1 ENSP00000440045 P16615 A0A0S2Z3L2 UPI0000001C3A NM_170665.3 deleterious(0) 3/20 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00690,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF234,SMART_domains:SM00831,TIGRFAM_domain:TIGR01116,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 110282761 110282761 T G 1 0 0 0 0 1 0 0 0 1290 1725 60 5 5 ATP2A2 12 110282761 Missense_Mutation SNP T C3L-02350_T 27848056 110282761 22992548 26 8951 SPERT 0 . GRCh38 13 45714336 45714336 + Silent SNP C C A novel C3L-02350_T C3L-02350_N C C c.1311C>A p.= p.A437A ENST00000310521 3/3 69 58 11 74 74 0 strelka-varscan-mutect SPERT,synonymous_variant,p.=,ENST00000378966,;SPERT,synonymous_variant,p.=,ENST00000310521,NM_152719.2;SPERT,synonymous_variant,p.=,ENST00000610924,NM_001286342.1;SPERT,downstream_gene_variant,,ENST00000533564,; A ENST00000310521 Transcript synonymous_variant 1391/1613 1311/1347 437/448 A gcC/gcA 1 1 SPERT HGNC HGNC:30720 protein_coding YES CCDS9399.1 ENSP00000309189 Q8NA61 A0A140VJV5 UPI0000070F5F NM_152719.2 3/3 hmmpanther:PTHR21533,hmmpanther:PTHR21533:SF13 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 33 45714336 45714336 C A 1 0 0 0 0 0 0 0 1 15390 581 21 2 2 SPERT 13 45714336 Silent SNP C C3L-02350_T 45714336 68649992 27 8952 CDH1 0 . GRCh38 16 68829655 68829655 + Frame_Shift_Del DEL A A - novel C3L-02350_T C3L-02350_N A A c.2297delA p.Asp766AlafsTer4 p.D766Afs*4 ENST00000261769 15/16 318 289 29 288 286 2 varindel-pindel CDH1,frameshift_variant,p.Asp766AlafsTer4,ENST00000261769,NM_004360.3;CDH1,frameshift_variant,p.Asp787AlafsTer4,ENST00000611625,NM_001317185.1;CDH1,frameshift_variant,p.Asp705AlafsTer4,ENST00000422392,;CDH1,intron_variant,,ENST00000621016,;CDH1,intron_variant,,ENST00000612417,;CDH1,splice_region_variant,,ENST00000562836,;CDH1,splice_region_variant,,ENST00000566612,;CDH1,splice_region_variant,,ENST00000566510,;CDH1,splice_region_variant,,ENST00000562118,; - ENST00000261769 Transcript frameshift_variant,splice_region_variant 2488/4889 2297/2649 766/882 D/X gAc/gc 1 1 CDH1 HGNC HGNC:1748 protein_coding YES CCDS10869.1 ENSP00000261769 P12830 A0A0U2ZQU7 UPI00000341EF NM_004360.3 15/16 Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF267,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 201 0 0 9 0 0 0 -8.653218 0.09101405 1 1 0 0 - 7 5 33 68829655 68829655 A - 1 0 1 0 1 0 0 0 0 2798 289 10 0 0 CDH1 16 68829655 Frame_Shift_Del DEL A C3L-02350_T 68829655 21508690 28 8953 SLC46A1 0 . GRCh38 17 28405016 28405016 + Silent SNP A A C novel C3L-02350_T C3L-02350_N A A c.681T>G p.= p.A227A ENST00000612814 2/5 317 280 37 289 289 0 strelka-varscan-mutect SLC46A1,synonymous_variant,p.=,ENST00000612814,NM_080669.5;SLC46A1,synonymous_variant,p.=,ENST00000618626,NM_001242366.2;SLC46A1,synonymous_variant,p.=,ENST00000584995,;SARM1,downstream_gene_variant,,ENST00000585482,NM_015077.3;SLC46A1,downstream_gene_variant,,ENST00000581516,;SLC46A1,upstream_gene_variant,,ENST00000582735,;SLC46A1,downstream_gene_variant,,ENST00000584426,;CTD-2350C19.2,upstream_gene_variant,,ENST00000580714,;SLC46A1,intron_variant,,ENST00000578217,;SLC46A1,non_coding_transcript_exon_variant,,ENST00000582590,;SLC46A1,upstream_gene_variant,,ENST00000619923,; C ENST00000612814 Transcript synonymous_variant 777/6376 681/1380 227/459 A gcT/gcG 1 -1 SLC46A1 HGNC HGNC:30521 protein_coding YES CCDS74020.1 ENSP00000480703 Q96NT5 A0A024QZ15 UPI0000050394 NM_080669.5 2/5 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23507,hmmpanther:PTHR23507:SF2,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 33 28405016 28405016 A C 1 0 0 0 0 0 0 0 1 14921 59 3 5 5 SLC46A1 17 28405016 Silent SNP A C3L-02350_T 28405016 54852425 29 8954 ERBB2 0 . GRCh38 17 39724728 39724729 + In_Frame_Ins INS - - GCATACGTGATG novel C3L-02350_T C3L-02350_N - - c.2313_2324dupATACGTGATGGC p.Tyr772_Ala775dup p.Y772_A775dup ENST00000269571 20/27 86 66 20 80 80 0 sindel-varindel ERBB2,inframe_insertion,p.Tyr742_Ala745dup,ENST00000584601,NM_001005862.2;ERBB2,inframe_insertion,p.Tyr742_Ala745dup,ENST00000406381,;ERBB2,inframe_insertion,p.Tyr772_Ala775dup,ENST00000269571,NM_004448.3;ERBB2,inframe_insertion,p.Tyr757_Ala760dup,ENST00000541774,NM_001289936.1;ERBB2,inframe_insertion,p.Tyr772_Ala775dup,ENST00000584450,NM_001289937.1;ERBB2,inframe_insertion,p.Tyr496_Ala499dup,ENST00000445658,;ERBB2,inframe_insertion,p.Tyr141_Ala144dup,ENST00000580074,;MIEN1,downstream_gene_variant,,ENST00000394231,NM_032339.3;MIEN1,downstream_gene_variant,,ENST00000577810,;ERBB2,downstream_gene_variant,,ENST00000582818,;MIR4728,upstream_gene_variant,,ENST00000580969,;MIEN1,downstream_gene_variant,,ENST00000474210,;ERBB2,upstream_gene_variant,,ENST00000584888,;ERBB2,3_prime_UTR_variant,,ENST00000578373,;ERBB2,non_coding_transcript_exon_variant,,ENST00000583038,;MIEN1,downstream_gene_variant,,ENST00000582963,;MIEN1,downstream_gene_variant,,ENST00000498164,;ERBB2,downstream_gene_variant,,ENST00000578630,;MIEN1,downstream_gene_variant,,ENST00000469568,;ERBB2,downstream_gene_variant,,ENST00000584684,; GCATACGTGATG ENST00000269571 Transcript inframe_insertion 2469-2470/4545 2310-2311/3768 770-771/1255 -/AYVM -/GCATACGTGATG 1 1 ERBB2 HGNC HGNC:3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 X5DNK3 UPI000003F55F NM_004448.3 20/27 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF137,hmmpanther:PTHR24416,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 insertion 1 14 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999974 1 1 1 0 GCATACGTGATG 7 5 33 39724728 39724728 - GCATACGTGATG 1 0 1 1 0 0 0 0 0 5055 86 3 0 0 ERBB2 17 39724728 In_Frame_Ins INS - C3L-02350_T 11319712 39724728 43532713 30 8955 PLCD3 0 . GRCh38 17 45121335 45121335 + Silent SNP C C T novel C3L-02350_T C3L-02350_N C C c.201G>A p.= p.R67R ENST00000619929 2/15 90 76 14 84 84 0 strelka-mutect PLCD3,synonymous_variant,p.=,ENST00000619929,NM_133373.4;PLCD3,synonymous_variant,p.=,ENST00000590644,;PLCD3,synonymous_variant,p.=,ENST00000538093,;PLCD3,non_coding_transcript_exon_variant,,ENST00000544446,;PLCD3,upstream_gene_variant,,ENST00000611986,;PLCD3,upstream_gene_variant,,ENST00000538988,;PLCD3,upstream_gene_variant,,ENST00000546350,;PLCD3,upstream_gene_variant,,ENST00000542173,; T ENST00000619929 Transcript synonymous_variant 289/6107 201/2370 67/789 R cgG/cgA 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 2/15 Gene3D:2.30.29.30,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS rs957805236 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 33 45121335 45121335 C T 1 0 0 0 0 0 0 0 1 12126 610 22 3 3 PLCD3 17 45121335 Silent SNP C C3L-02350_T 5396607 45121335 38136106 31 8956 PPM1E 0 . GRCh38 17 58980798 58980798 + Missense_Mutation SNP C C T rs764019992 C3L-02350_T C3L-02350_N C C c.2035C>T p.His679Tyr p.H679Y ENST00000308249 7/7 194 168 26 214 214 0 strelka-varscan-mutect PPM1E,missense_variant,p.His679Tyr,ENST00000308249,NM_014906.4;TRIM37,downstream_gene_variant,,ENST00000393066,NM_001005207.2;TRIM37,downstream_gene_variant,,ENST00000585287,;TRIM37,downstream_gene_variant,,ENST00000583945,; T ENST00000308249 Transcript missense_variant 2164/6542 2035/2268 679/755 H/Y Cac/Tac rs764019992,COSM3196121 1 1 PPM1E HGNC HGNC:19322 protein_coding YES CCDS11613.1 ENSP00000312411 Q8WY54 UPI000013ECF6 NM_014906.4 deleterious_low_confidence(0.01) 7/7 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764019992 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 33 58980798 58980798 C T 1 0 0 0 0 1 0 0 0 12448 710 25 3 3 PPM1E 17 58980798 Missense_Mutation SNP C C3L-02350_T 13859463 58980798 24276643 32 8957 FASN 0 . GRCh38 17 82091566 82091566 + Missense_Mutation SNP A A G novel C3L-02350_T C3L-02350_N A A c.1148T>C p.Val383Ala p.V383A ENST00000306749 9/43 460 417 43 327 326 1 strelka-varscan-mutect FASN,missense_variant,p.Val383Ala,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Val383Ala,ENST00000634990,;FASN,downstream_gene_variant,,ENST00000635197,;FASN,downstream_gene_variant,,ENST00000636968,;FASN,downstream_gene_variant,,ENST00000637026,;FASN,downstream_gene_variant,,ENST00000637525,;FASN,downstream_gene_variant,,ENST00000635733,; G ENST00000306749 Transcript missense_variant 1367/8565 1148/7536 383/2511 V/A gTc/gCc 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 tolerated(0.07) 9/43 Gene3D:3.40.47.10,Pfam_domain:PF16197,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,SMART_domains:SM00825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 82091566 82091566 A G 1 0 0 0 0 1 0 0 0 5543 275 10 5 5 FASN 17 82091566 Missense_Mutation SNP A C3L-02350_T 23110768 82091566 1165875 33 8958 MBD1 0 . GRCh38 18 50275715 50275715 + Missense_Mutation SNP C C G novel C3L-02350_T C3L-02350_N C C c.677G>C p.Gly226Ala p.G226A ENST00000590208 8/16 188 161 27 251 251 0 strelka-varscan-mutect MBD1,missense_variant,p.Gly226Ala,ENST00000591416,;MBD1,missense_variant,p.Gly226Ala,ENST00000269468,NM_015846.3;MBD1,missense_variant,p.Gly226Ala,ENST00000347968,NM_015844.2;MBD1,missense_variant,p.Gly226Ala,ENST00000269471,NM_015845.3;MBD1,missense_variant,p.Gly226Ala,ENST00000339998,NM_001204142.1;MBD1,missense_variant,p.Gly226Ala,ENST00000590208,NM_001204136.1;MBD1,missense_variant,p.Gly177Ala,ENST00000353909,NM_015847.3;MBD1,missense_variant,p.Gly177Ala,ENST00000585672,NM_001204141.1;MBD1,missense_variant,p.Gly226Ala,ENST00000457839,NM_001204137.1,NM_001204138.1;MBD1,missense_variant,p.Gly226Ala,ENST00000382948,NM_001204139.1;MBD1,missense_variant,p.Gly226Ala,ENST00000585595,;MBD1,missense_variant,p.Gly226Ala,ENST00000398495,NM_001204140.1;MBD1,missense_variant,p.Gly102Ala,ENST00000592060,;MBD1,missense_variant,p.Gly226Ala,ENST00000587605,NM_001204143.1;MBD1,missense_variant,p.Gly226Ala,ENST00000398493,;MBD1,missense_variant,p.Gly226Ala,ENST00000588937,;MBD1,missense_variant,p.Gly226Ala,ENST00000591535,NM_001204151.1;MBD1,missense_variant,p.Gly226Ala,ENST00000398488,NM_002384.2;MBD1,missense_variant,p.Gly94Ala,ENST00000589733,;MBD1,upstream_gene_variant,,ENST00000589541,;MBD1,non_coding_transcript_exon_variant,,ENST00000586118,;MBD1,non_coding_transcript_exon_variant,,ENST00000586679,;MBD1,non_coding_transcript_exon_variant,,ENST00000591661,;MBD1,downstream_gene_variant,,ENST00000590215,;MBD1,downstream_gene_variant,,ENST00000589867,;MBD1,upstream_gene_variant,,ENST00000586884,;MBD1,downstream_gene_variant,,ENST00000589758,; G ENST00000590208 Transcript missense_variant 1024/2913 677/1968 226/655 G/A gGa/gCa 1 -1 MBD1 HGNC HGNC:6916 protein_coding YES CCDS59320.1 ENSP00000468785 Q9UIS9 UPI0001F995B6 NM_001204136.1 deleterious(0) 8/16 Pfam_domain:PF02008,PROSITE_profiles:PS51058,hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 50275715 50275715 C G 1 0 0 0 0 1 0 0 0 9271 855 30 4 4 MBD1 18 50275715 Missense_Mutation SNP C C3L-02350_T 50275715 30097570 34 8959 RYR1 0 . GRCh38 19 38561401 38561401 + Missense_Mutation SNP C C A C3L-02350_T C3L-02350_N C C c.12571C>A p.Arg4191Ser p.R4191S ENST00000359596 90/106 175 166 9 161 161 0 strelka-varscan-mutect RYR1,missense_variant,p.Arg4186Ser,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Arg4191Ser,ENST00000359596,NM_000540.2;RYR1,3_prime_UTR_variant,,ENST00000594335,; A ENST00000359596 Transcript missense_variant 12571/15117 12571/15117 4191/5038 R/S Cgc/Agc COSM5519658 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0) 90/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 38561401 38561401 C A 1 0 0 0 0 1 0 0 0 14028 768 27 1 1 RYR1 19 38561401 Missense_Mutation SNP C C3L-02350_T 38561401 20056215 35 8960 RSPH6A 0 . GRCh38 19 45815053 45815053 + Nonsense_Mutation SNP C C A rs779379990 C3L-02350_T C3L-02350_N C C c.124G>T p.Glu42Ter p.E42* ENST00000221538 1/6 467 407 60 392 392 0 strelka-varscan-mutect RSPH6A,stop_gained,p.Glu42Ter,ENST00000221538,NM_030785.3;RSPH6A,stop_gained,p.Glu42Ter,ENST00000597055,;SYMPK,downstream_gene_variant,,ENST00000599814,;SYMPK,downstream_gene_variant,,ENST00000599460,;SYMPK,downstream_gene_variant,,ENST00000245934,NM_004819.2;RSPH6A,upstream_gene_variant,,ENST00000600188,;SYMPK,downstream_gene_variant,,ENST00000598155,;SYMPK,downstream_gene_variant,,ENST00000600237,;SYMPK,downstream_gene_variant,,ENST00000593504,;SYMPK,downstream_gene_variant,,ENST00000598329,;SYMPK,downstream_gene_variant,,ENST00000598364,;SYMPK,downstream_gene_variant,,ENST00000596824,; A ENST00000221538 Transcript stop_gained 267/2456 124/2154 42/717 E/* Gag/Tag rs779379990 1 -1 RSPH6A HGNC HGNC:14241 protein_coding YES CCDS12675.1 ENSP00000221538 Q9H0K4 UPI0000037C58 NM_030785.3 1/6 HIGH 1 SNV 1 1 PASS rs779379990 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 33 45815053 45815053 C A 1 0 0 0 0 0 1 0 0 13965 864 30 2 2 RSPH6A 19 45815053 Nonsense_Mutation SNP C C3L-02350_T 7253652 45815053 12802563 36 8961 ZNF784 0 . GRCh38 19 55624521 55624525 + Frame_Shift_Del DEL GGTGA GGTGA - novel C3L-02350_T C3L-02350_N GGTGA GGTGA c.37_41delTCACC p.Ser13AspfsTer17 p.S13Dfs*17 ENST00000325351 1/2 128 119 9 112 112 0 sindel-varindel-pindel ZNF784,frameshift_variant,p.Ser13AspfsTer17,ENST00000325351,NM_203374.1;ZNF784,frameshift_variant,p.Ser13AspfsTer47,ENST00000591479,; - ENST00000325351 Transcript frameshift_variant 77-81/2021 37-41/972 13-14/323 SP/X TCACCg/g 1 -1 ZNF784 HGNC HGNC:33111 protein_coding YES CCDS12930.1 ENSP00000320096 Q8NCA9 UPI000006D6D0 NM_203374.1 1/2 HIGH 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.00016 0.9999996 1 1 1 0 - 7 5 33 55624521 55624521 GGTGA - 1 0 1 0 1 0 0 0 0 18740 1116 39 0 0 ZNF784 19 55624521 Frame_Shift_Del DEL GGTGA C3L-02350_T 9809468 55624521 2993095 37 8962 ZNF543 0 . GRCh38 19 57323768 57323768 + Silent SNP G G A novel C3L-02350_T C3L-02350_N G G c.105G>A p.= p.Q35Q ENST00000321545 2/4 192 169 23 155 155 0 strelka-varscan-mutect ZNF543,synonymous_variant,p.=,ENST00000321545,NM_213598.3; A ENST00000321545 Transcript synonymous_variant 450/3659 105/1803 35/600 Q caG/caA 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,SMART_domains:SM00349 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 33 57323768 57323768 G A 1 0 0 0 0 0 0 0 1 18550 991 35 3 3 ZNF543 19 57323768 Silent SNP G C3L-02350_T 1699247 57323768 1293848 38 8963 EMILIN3 0 . GRCh38 20 41362339 41362339 + Silent SNP C C T C3L-02350_T C3L-02350_N C C c.1230G>A p.= p.R410R ENST00000332312 4/4 117 102 15 125 125 0 strelka-varscan-mutect EMILIN3,synonymous_variant,p.=,ENST00000332312,NM_052846.1;LPIN3,downstream_gene_variant,,ENST00000373257,;LPIN3,downstream_gene_variant,,ENST00000632009,NM_001301860.1;LPIN3,downstream_gene_variant,,ENST00000445975,;LPIN3,downstream_gene_variant,,ENST00000491528,;LPIN3,downstream_gene_variant,,ENST00000496565,; T ENST00000332312 Transcript synonymous_variant 1423/3796 1230/2301 410/766 R agG/agA COSM5071757 1 -1 EMILIN3 HGNC HGNC:16123 protein_coding YES CCDS13316.1 ENSP00000332806 Q9NT22 UPI00001D82E8 NM_052846.1 4/4 hmmpanther:PTHR15427:SF2,hmmpanther:PTHR15427 1 LOW 1 SNV 1 1 1 PASS rs1442820571 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 33 41362339 41362339 C T 1 0 0 0 0 0 0 0 1 4938 622 22 3 3 EMILIN3 20 41362339 Silent SNP C C3L-02350_T 41362339 23081828 39 8964 ZNF335 0 . GRCh38 20 45957586 45957586 + Missense_Mutation SNP C C G novel C3L-02350_T C3L-02350_N C C c.2442G>C p.Gln814His p.Q814H ENST00000322927 17/28 271 172 99 186 186 0 strelka-varscan-mutect ZNF335,missense_variant,p.Gln814His,ENST00000322927,NM_022095.3;ZNF335,downstream_gene_variant,,ENST00000475002,; G ENST00000322927 Transcript missense_variant,splice_region_variant 2543/4430 2442/4029 814/1342 Q/H caG/caC 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 deleterious(0) 17/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 45957586 45957586 C G 1 0 0 0 0 1 0 0 0 18424 695 24 4 4 ZNF335 20 45957586 Missense_Mutation SNP C C3L-02350_T 4595247 45957586 18486581 40 8965 1 7 2 2 55 C 8.217862e-05 ZNF335 0 . GRCh38 20 45957640 45957640 + Missense_Mutation SNP C C G novel C3L-02350_T C3L-02350_N C C c.2388G>C p.Leu796Phe p.L796F ENST00000322927 17/28 383 234 149 286 286 0 strelka-varscan-mutect ZNF335,missense_variant,p.Leu796Phe,ENST00000322927,NM_022095.3;ZNF335,downstream_gene_variant,,ENST00000475002,; G ENST00000322927 Transcript missense_variant 2489/4430 2388/4029 796/1342 L/F ttG/ttC 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 deleterious(0.01) 17/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 33 45957640 45957640 C G 1 0 0 0 0 1 0 0 0 18424 593 21 4 4 ZNF335 20 45957640 Missense_Mutation SNP C C3L-02350_T 54 45957640 18486527 41 8966 1 7 2 2 55 C 8.217862e-05 SS18L1 0 . GRCh38 20 62161460 62161460 + Missense_Mutation SNP G G A novel C3L-02350_T C3L-02350_N G G c.256G>A p.Gly86Ser p.G86S ENST00000331758 4/11 407 330 77 289 288 1 strelka-varscan-mutect SS18L1,missense_variant,p.Gly86Ser,ENST00000331758,NM_198935.2;SS18L1,missense_variant,p.Gly4Ser,ENST00000370848,NM_001301778.1;SS18L1,missense_variant,p.Gly89Ser,ENST00000450482,;SS18L1,upstream_gene_variant,,ENST00000491916,;SS18L1,upstream_gene_variant,,ENST00000492466,; A ENST00000331758 Transcript missense_variant 282/4493 256/1191 86/396 G/S Ggc/Agc 1 1 SS18L1 HGNC HGNC:15592 protein_coding YES CCDS13491.1 ENSP00000333012 O75177 UPI000013543D NM_198935.2 deleterious_low_confidence(0.03) 4/11 hmmpanther:PTHR23107,hmmpanther:PTHR23107:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 33 62161460 62161460 G A 1 0 0 0 0 1 0 0 0 15550 1232 43 3 3 SS18L1 20 62161460 Missense_Mutation SNP G C3L-02350_T 16203820 62161460 2282707 42 8967 ALG13 0 . GRCh38 X 111718190 111718190 + Missense_Mutation SNP G G T novel C3L-02350_T C3L-02350_N G G c.1166G>T p.Arg389Leu p.R389L ENST00000394780 10/27 110 86 24 131 130 1 strelka-varscan-mutect ALG13,missense_variant,p.Arg311Leu,ENST00000610588,NM_001257231.1;ALG13,missense_variant,p.Arg389Leu,ENST00000394780,NM_001099922.2;ALG13,missense_variant,p.Arg285Leu,ENST00000251943,NM_001324292.1,NM_001257237.1;ALG13,missense_variant,p.Arg285Leu,ENST00000621367,NM_001257230.1,NM_001257234.1;ALG13,missense_variant,p.Arg285Leu,ENST00000436609,;ALG13,missense_variant,p.Arg43Leu,ENST00000623622,;ALG13,upstream_gene_variant,,ENST00000490774,;ALG13,downstream_gene_variant,,ENST00000635768,;ALG13,3_prime_UTR_variant,,ENST00000624161,;ALG13,3_prime_UTR_variant,,ENST00000623144,;ALG13,3_prime_UTR_variant,,ENST00000623148,;ALG13,3_prime_UTR_variant,,ENST00000636363,;ALG13,3_prime_UTR_variant,,ENST00000495283,;ALG13,intron_variant,,ENST00000470971,;ALG13,downstream_gene_variant,,ENST00000487141,;ALG13,downstream_gene_variant,,ENST00000622997,; T ENST00000394780 Transcript missense_variant 1235/4133 1166/3414 389/1137 R/L cGa/cTa 1 1 ALG13 HGNC HGNC:30881 protein_coding YES CCDS55477.1 ENSP00000378260 Q9NP73 UPI0000E5AFF9 NM_001099922.2 deleterious(0.01) 10/27 hmmpanther:PTHR12867,hmmpanther:PTHR12867:SF5 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 33 111718190 111718190 G T 1 0 0 0 0 1 0 0 0 615 1058 37 1 1 ALG13 23 111718190 Missense_Mutation SNP G C3L-02350_T 111718190 44322705 43 8968 PLS3 0 . GRCh38 X 115646454 115646454 + Frame_Shift_Del DEL C C - novel C3L-02350_T C3L-02350_N C C c.1432delC p.Leu478TrpfsTer9 p.L478Wfs*9 ENST00000355899 13/16 87 64 23 90 90 0 sindel-varindel-pindel PLS3,frameshift_variant,p.Leu478TrpfsTer9,ENST00000355899,NM_005032.6;PLS3,frameshift_variant,p.Leu465TrpfsTer9,ENST00000420625,;PLS3,frameshift_variant,p.Leu478TrpfsTer9,ENST00000539310,NM_001172335.2,NM_001136025.4,NM_001282338.1;PLS3,frameshift_variant,p.Leu465TrpfsTer9,ENST00000289290,NM_001282337.1;PLS3,downstream_gene_variant,,ENST00000497870,;PLS3,3_prime_UTR_variant,,ENST00000481823,;PLS3,downstream_gene_variant,,ENST00000466150,; - ENST00000355899 Transcript frameshift_variant 1517/3280 1430/1893 477/630 S/X tCc/tc 1 1 PLS3 HGNC HGNC:9091 protein_coding YES CCDS14568.1 ENSP00000348163 P13797 UPI000000D962 NM_005032.6 13/16 PROSITE_profiles:PS50021,hmmpanther:PTHR19961,hmmpanther:PTHR19961:SF32,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH 1 deletion 1 2 1 PASS . . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 33 115646454 115646454 C - 1 0 1 0 1 0 0 0 0 12216 855 30 0 0 PLS3 23 115646454 Frame_Shift_Del DEL C C3L-02350_T 3928264 115646454 40394441 44 8969 STAG2 0 . GRCh38 X 124062974 124062974 + Missense_Mutation SNP C C G novel C3L-02350_T C3L-02350_N C C c.1711C>G p.Leu571Val p.L571V ENST00000218089 18/35 99 78 21 131 131 0 strelka-varscan-mutect STAG2,missense_variant,p.Leu571Val,ENST00000371160,NM_001282418.1;STAG2,missense_variant,p.Leu571Val,ENST00000371157,NM_006603.4;STAG2,missense_variant,p.Leu571Val,ENST00000218089,NM_001042749.2;STAG2,missense_variant,p.Leu571Val,ENST00000371145,NM_001042750.1;STAG2,missense_variant,p.Leu571Val,ENST00000371144,NM_001042751.1;STAG2,downstream_gene_variant,,ENST00000455404,;STAG2,non_coding_transcript_exon_variant,,ENST00000466748,;STAG2,non_coding_transcript_exon_variant,,ENST00000483575,;STAG2,non_coding_transcript_exon_variant,,ENST00000471107,;STAG2,intron_variant,,ENST00000469481,; G ENST00000218089 Transcript missense_variant 2221/5218 1711/3807 571/1268 L/V Ctt/Gtt 1 1 STAG2 HGNC HGNC:11355 protein_coding YES CCDS43990.1 ENSP00000218089 Q8N3U4 UPI00004A3A8A NM_001042749.2 deleterious(0) 18/35 hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF3 MODERATE 1 SNV 1 1 PASS . . 0 199 8 2 0 0 0 0 -20 0.9998548 1 1 1 0 G 3 3 33 124062974 124062974 C G 1 0 0 0 0 1 0 0 0 15621 681 24 4 4 STAG2 23 124062974 Missense_Mutation SNP C C3L-02350_T 8416520 124062974 31977921 45 8970 USP26 0 . GRCh38 X 133027674 133027674 + Missense_Mutation SNP T T C novel C3L-02350_T C3L-02350_N T T c.547A>G p.Met183Val p.M183V ENST00000511190 6/6 52 37 15 74 74 0 strelka-varscan-mutect USP26,missense_variant,p.Met183Val,ENST00000511190,;USP26,missense_variant,p.Met183Val,ENST00000370832,NM_031907.1; C ENST00000511190 Transcript missense_variant 1017/3665 547/2742 183/913 M/V Atg/Gtg 1 -1 USP26 HGNC HGNC:13485 protein_coding YES CCDS14635.1 ENSP00000423390 Q9BXU7 UPI00000421FD tolerated(0.27) 6/6 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 33 133027674 133027674 T C 1 0 0 0 0 1 0 0 0 17598 1493 52 5 5 USP26 23 133027674 Missense_Mutation SNP T C3L-02350_T 8964700 133027674 23013221 46 8971 FLNA 0 . GRCh38 X 154370884 154370885 + Frame_Shift_Ins INS - - G novel C3L-02350_T C3L-02350_N - - c.361dupC p.Leu121ProfsTer41 p.L121Pfs*41 ENST00000369850 2/48 76 60 16 83 83 0 sindel-varindel-pindel FLNA,frameshift_variant,p.Leu121ProfsTer41,ENST00000422373,NM_001456.3;FLNA,frameshift_variant,p.Leu121ProfsTer41,ENST00000369850,NM_001110556.1;FLNA,frameshift_variant,p.Leu121ProfsTer41,ENST00000360319,;FLNA,frameshift_variant,p.Leu94ProfsTer41,ENST00000369856,;FLNA,frameshift_variant,p.Leu121ProfsTer41,ENST00000344736,;FLNA,frameshift_variant,p.Leu94ProfsTer41,ENST00000610817,;FLNA,frameshift_variant,p.Leu107ProfsTer41,ENST00000420627,; G ENST00000369850 Transcript frameshift_variant 598-599/8382 361-362/7944 121/2647 L/PX ctg/cCtg 1 -1 FLNA HGNC HGNC:3754 protein_coding YES CCDS48194.1 ENSP00000358866 P21333 UPI000013C596 NM_001110556.1 2/48 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF173,PROSITE_patterns:PS00020,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH 1 insertion 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 G 7 5 33 154370884 154370884 - G 1 0 1 1 0 0 0 0 0 5789 188 7 0 0 FLNA 23 154370884 Frame_Shift_Ins INS - C3L-02350_T 21343210 154370884 1670011 47 8972 CDK11B 0 . GRCh38 1 1645239 1645239 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.518G>T p.Arg173Met p.R173M ENST00000407249 6/20 570 516 54 418 417 1 varscan-mutect CDK11B,missense_variant,p.Arg173Met,ENST00000341832,NM_033487.2,NM_033486.2,NM_033490.2,NM_001291345.1;CDK11B,missense_variant,p.Arg173Met,ENST00000407249,NM_001787.2;CDK11B,missense_variant,p.Arg139Met,ENST00000340677,NM_033489.2;CDK11B,missense_variant,p.Arg176Met,ENST00000629312,;CDK11B,missense_variant,p.Arg174Met,ENST00000629289,;CDK11B,missense_variant,p.Arg163Met,ENST00000626918,;CDK11B,intron_variant,,ENST00000341028,;CDK11B,intron_variant,,ENST00000611150,;CDK11B,intron_variant,,ENST00000615951,; A ENST00000407249 Transcript missense_variant 630/2677 518/2388 173/795 R/M aGg/aTg 1 -1 CDK11B HGNC HGNC:1729 protein_coding YES CCDS72683.1 ENSP00000464036 J3QR44 UPI0003EAF5FB NM_001787.2 deleterious_low_confidence(0) 6/20 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 1645239 1645239 C A 1 0 0 0 0 1 0 0 0 2831 681 24 2 2 CDK11B 1 1645239 Missense_Mutation SNP C C3L-02365_T 1645239 247311183 1 8973 NPHP4 0 . GRCh38 1 5905341 5905341 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.1906G>A p.Asp636Asn p.D636N ENST00000378156 15/30 154 105 49 150 150 0 strelka-varscan-mutect NPHP4,missense_variant,p.Asp636Asn,ENST00000378156,NM_001291594.1,NM_001291593.1,NM_015102.4;NPHP4,missense_variant,p.Asp635Asn,ENST00000622020,;NPHP4,non_coding_transcript_exon_variant,,ENST00000478423,;NPHP4,missense_variant,p.Asp635Asn,ENST00000489180,;NPHP4,3_prime_UTR_variant,,ENST00000378169,;NPHP4,upstream_gene_variant,,ENST00000466897,; T ENST00000378156 Transcript missense_variant 2172/4994 1906/4281 636/1426 D/N Gat/Aat 1 -1 NPHP4 HGNC HGNC:19104 protein_coding YES CCDS44052.1 ENSP00000367398 O75161 UPI00001303E5 NM_001291594.1,NM_001291593.1,NM_015102.4 deleterious(0) 15/30 hmmpanther:PTHR31043,hmmpanther:PTHR31043:SF3 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 5905341 5905341 C T 1 0 0 0 0 1 0 0 0 10629 913 32 3 3 NPHP4 1 5905341 Missense_Mutation SNP C C3L-02365_T 4260102 5905341 243051081 2 8974 SPEN 0 . GRCh38 1 15932086 15932086 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.5846G>T p.Arg1949Leu p.R1949L ENST00000375759 11/15 279 249 30 199 198 1 strelka-varscan-mutect SPEN,missense_variant,p.Arg1949Leu,ENST00000375759,NM_015001.2; T ENST00000375759 Transcript missense_variant 6050/12232 5846/10995 1949/3664 R/L cGg/cTg 1 1 SPEN HGNC HGNC:17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 deleterious(0) 11/15 Low_complexity_(Seg):seg,hmmpanther:PTHR23189:SF48,hmmpanther:PTHR23189 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 15932086 15932086 G T 1 0 0 0 0 1 0 0 0 15389 1116 39 1 1 SPEN 1 15932086 Missense_Mutation SNP G C3L-02365_T 10026745 15932086 233024336 3 8975 33 2 SPEN 0 . GRCh38 1 15932090 15932090 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.5850G>T p.Arg1950Ser p.R1950S ENST00000375759 11/15 265 236 29 194 194 0 strelka-varscan-mutect SPEN,missense_variant,p.Arg1950Ser,ENST00000375759,NM_015001.2; T ENST00000375759 Transcript missense_variant 6054/12232 5850/10995 1950/3664 R/S agG/agT 1 1 SPEN HGNC HGNC:17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 deleterious(0) 11/15 Low_complexity_(Seg):seg,hmmpanther:PTHR23189:SF48,hmmpanther:PTHR23189 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 15932090 15932090 G T 1 0 0 0 0 1 0 0 0 15389 1223 43 2 2 SPEN 1 15932090 Missense_Mutation SNP G C3L-02365_T 4 15932090 233024332 4 8976 33 2 FBXO42 0 . GRCh38 1 16315205 16315205 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.214G>T p.Ala72Ser p.A72S ENST00000375592 2/10 194 165 29 160 159 1 strelka-varscan-mutect FBXO42,missense_variant,p.Ala72Ser,ENST00000375592,NM_018994.2;FBXO42,non_coding_transcript_exon_variant,,ENST00000478089,; A ENST00000375592 Transcript missense_variant 431/6202 214/2154 72/717 A/S Gcc/Tcc 1 -1 FBXO42 HGNC HGNC:29249 protein_coding YES CCDS30613.1 ENSP00000364742 Q6P3S6 A0A024QZB0 UPI0000161A51 NM_018994.2 tolerated(0.16) 2/10 Gene3D:1.20.1280.50,Pfam_domain:PF12937,PROSITE_profiles:PS50181,SMART_domains:SM00256,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS rs1363567705 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 16315205 16315205 C A 1 0 0 0 0 1 0 0 0 5614 739 26 2 2 FBXO42 1 16315205 Missense_Mutation SNP C C3L-02365_T 383115 16315205 232641217 5 8977 IGSF21 0 . GRCh38 1 18376956 18376956 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1258G>T p.Gly420Cys p.G420C ENST00000251296 8/10 65 54 11 42 42 0 strelka-mutect IGSF21,missense_variant,p.Gly420Cys,ENST00000251296,NM_032880.4;IGSF21,downstream_gene_variant,,ENST00000412684,;IGSF21,downstream_gene_variant,,ENST00000473951,;IGSF21,non_coding_transcript_exon_variant,,ENST00000497331,; T ENST00000251296 Transcript missense_variant 1641/1943 1258/1404 420/467 G/C Ggc/Tgc 1 1 IGSF21 HGNC HGNC:28246 protein_coding YES CCDS184.1 ENSP00000251296 Q96ID5 UPI000006FCF2 NM_032880.4 deleterious(0) 8/10 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF442,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -19.99999 0.9999999 1 1 1 0 T 3 4 34 18376956 18376956 G T 1 0 0 0 0 1 0 0 0 7506 1232 43 2 2 IGSF21 1 18376956 Missense_Mutation SNP G C3L-02365_T 2061751 18376956 230579466 6 8978 EMC1 0 . GRCh38 1 19222723 19222723 + Missense_Mutation SNP G G C rs370065062 C3L-02365_T C3L-02365_N G G c.2488C>G p.Leu830Val p.L830V ENST00000477853 20/23 202 115 87 156 156 0 strelka-varscan-mutect EMC1,missense_variant,p.Leu830Val,ENST00000477853,NM_001271428.1,NM_015047.2;EMC1,missense_variant,p.Leu829Val,ENST00000375199,NM_001271427.1;EMC1,missense_variant,p.Leu808Val,ENST00000375208,NM_001271429.1;EMC1,missense_variant,p.Leu75Val,ENST00000486405,;RP1-43E13.2,intron_variant,,ENST00000437898,;EMC1,non_coding_transcript_exon_variant,,ENST00000494770,;EMC1,upstream_gene_variant,,ENST00000480380,;EMC1,upstream_gene_variant,,ENST00000461353,;EMC1,upstream_gene_variant,,ENST00000496654,;EMC1,missense_variant,p.Leu14Val,ENST00000486238,;EMC1,non_coding_transcript_exon_variant,,ENST00000462505,; C ENST00000477853 Transcript missense_variant 2531/6664 2488/2982 830/993 L/V Ctg/Gtg rs370065062 1 -1 EMC1 HGNC HGNC:28957 protein_coding YES CCDS190.1 ENSP00000420608 Q8N766 UPI0000070A23 NM_001271428.1,NM_015047.2 tolerated(0.73) 20/23 hmmpanther:PTHR21573:SF0,hmmpanther:PTHR21573,Pfam_domain:PF07774 MODERATE 1 SNV 1 1 PASS rs370065062 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 19222723 19222723 G C 1 0 0 0 0 1 0 0 0 4921 962 34 4 4 EMC1 1 19222723 Missense_Mutation SNP G C3L-02365_T 845767 19222723 229733699 7 8979 MYOM3 0 . GRCh38 1 24074245 24074245 + Silent SNP G G T C3L-02365_T C3L-02365_N G G c.2883C>A p.= p.P961P ENST00000374434 23/37 216 183 33 120 120 0 strelka-varscan-mutect MYOM3,synonymous_variant,p.=,ENST00000374434,NM_152372.3;RP11-293P20.4,intron_variant,,ENST00000429191,;RP11-293P20.2,intron_variant,,ENST00000439239,;MYOM3,intron_variant,,ENST00000448831,; T ENST00000374434 Transcript synonymous_variant 3046/5804 2883/4314 961/1437 P ccC/ccA COSM4485015,COSM4485016 1 -1 MYOM3 HGNC HGNC:26679 protein_coding YES CCDS41281.1 ENSP00000363557 Q5VTT5 UPI0000203A5D NM_152372.3 23/37 Gene3D:2.60.40.10,SMART_domains:SM00409 1,1 LOW 1 SNV 1 1,1 1 PASS rs1273323576 . 0 206 0 4 0 0 0 0 -20 0.9999212 1 1 1 0 T 2 4 34 24074245 24074245 G T 1 0 0 0 0 0 0 0 1 10094 1103 39 1 1 MYOM3 1 24074245 Silent SNP G C3L-02365_T 4851522 24074245 224882177 8 8980 ZNF683 0 . GRCh38 1 26367773 26367773 + Missense_Mutation SNP G G C C3L-02365_T C3L-02365_N G G c.139C>G p.Pro47Ala p.P47A ENST00000436292 3/7 89 43 46 67 67 0 strelka-varscan-mutect ZNF683,missense_variant,p.Pro47Ala,ENST00000436292,NM_001307925.1;ZNF683,missense_variant,p.Pro47Ala,ENST00000403843,;ZNF683,missense_variant,p.Pro47Ala,ENST00000349618,NM_001114759.1,NM_173574.2;ZNF683,missense_variant,p.Pro55Ala,ENST00000455900,;ZNF683,missense_variant,p.Pro47Ala,ENST00000451801,;ZNF683,missense_variant,p.Pro47Ala,ENST00000416125,;ZNF683,missense_variant,p.Pro55Ala,ENST00000423508,;ZNF683,intron_variant,,ENST00000453132,;ZNF683,intron_variant,,ENST00000454975,; C ENST00000436292 Transcript missense_variant 260/1712 139/1575 47/524 P/A Cca/Gca COSM1243780,COSM1243781 1 -1 ZNF683 HGNC HGNC:28495 protein_coding YES CCDS76126.1 ENSP00000388792 Q8IZ20 UPI0000EE2F2D NM_001307925.1 tolerated(0.08) 3/7 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 3 2 34 26367773 26367773 G C 1 0 0 0 0 1 0 0 0 18663 1174 41 4 4 ZNF683 1 26367773 Missense_Mutation SNP G C3L-02365_T 2293528 26367773 222588649 9 8981 CSMD2 0 . GRCh38 1 33623398 33623398 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.5694C>G p.Asn1898Lys p.N1898K ENST00000373381 36/71 301 246 55 248 248 0 strelka-varscan-mutect CSMD2,missense_variant,p.Asn1898Lys,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Asn1858Lys,ENST00000619121,;CSMD2,missense_variant,p.Asn1858Lys,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Asn771Lys,ENST00000373380,;CSMD2,5_prime_UTR_variant,,ENST00000373377,;CSMD2,missense_variant,p.Asn1858Lys,ENST00000241312,; C ENST00000373381 Transcript missense_variant 5871/13698 5694/10896 1898/3631 N/K aaC/aaG 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 tolerated(0.19) 36/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 33623398 33623398 G C 1 0 0 0 0 1 0 0 0 3746 1368 48 4 4 CSMD2 1 33623398 Missense_Mutation SNP G C3L-02365_T 7255625 33623398 215333024 10 8982 GJB4 0 . GRCh38 1 34761471 34761471 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.217C>T p.His73Tyr p.H73Y ENST00000339480 2/2 543 394 149 402 402 0 strelka-varscan-mutect GJB4,missense_variant,p.His73Tyr,ENST00000339480,NM_153212.2;GJB5,downstream_gene_variant,,ENST00000338513,NM_005268.3;RP1-34M23.5,non_coding_transcript_exon_variant,,ENST00000542839,;SMIM12,intron_variant,,ENST00000426886,; T ENST00000339480 Transcript missense_variant 587/2840 217/801 73/266 H/Y Cac/Tac 1 1 GJB4 HGNC HGNC:4286 protein_coding YES CCDS383.1 ENSP00000345868 Q9NTQ9 UPI0000051E4B NM_153212.2 deleterious(0.02) 2/2 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF30,SMART_domains:SM00037 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 34761471 34761471 C T 1 0 0 0 0 1 0 0 0 6287 594 21 3 3 GJB4 1 34761471 Missense_Mutation SNP C C3L-02365_T 1138073 34761471 214194951 11 8983 MACF1 0 . GRCh38 1 39459244 39459244 + Nonsense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.15178G>T p.Glu5060Ter p.E5060* ENST00000361689 86/93 115 60 55 107 107 0 strelka-varscan-mutect MACF1,stop_gained,p.Glu7119Ter,ENST00000564288,;MACF1,stop_gained,p.Glu7156Ter,ENST00000567887,;MACF1,stop_gained,p.Glu7018Ter,ENST00000372915,;MACF1,stop_gained,p.Glu5562Ter,ENST00000289893,;MACF1,stop_gained,p.Glu5060Ter,ENST00000361689,NM_012090.5;MACF1,stop_gained,p.Glu4064Ter,ENST00000372925,;MACF1,stop_gained,p.Glu162Ter,ENST00000360115,;MACF1,stop_gained,p.Glu42Ter,ENST00000446276,;MACF1,upstream_gene_variant,,ENST00000442046,;MACF1,upstream_gene_variant,,ENST00000422234,;MACF1,non_coding_transcript_exon_variant,,ENST00000497964,;MACF1,upstream_gene_variant,,ENST00000462496,; T ENST00000361689 Transcript stop_gained 15230/17538 15178/16293 5060/5430 E/* Gag/Tag 1 1 MACF1 HGNC HGNC:13664 protein_coding YES CCDS435.1 ENSP00000354573 Q9UPN3 UPI00001B3DC6 NM_012090.5 86/93 Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF37 HIGH 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 39459244 39459244 G T 1 0 0 0 0 0 1 0 0 9060 1188 41 2 2 MACF1 1 39459244 Nonsense_Mutation SNP G C3L-02365_T 4697773 39459244 209497178 12 8984 CACHD1 0 . GRCh38 1 64653779 64653779 + Missense_Mutation SNP C C G rs765925747 C3L-02365_T C3L-02365_N C C c.1409C>G p.Ser470Cys p.S470C ENST00000290039 11/27 199 170 29 180 180 0 strelka-varscan-mutect CACHD1,missense_variant,p.Ser470Cys,ENST00000290039,NM_020925.2,NM_001293274.1;CACHD1,non_coding_transcript_exon_variant,,ENST00000495994,;CACHD1,non_coding_transcript_exon_variant,,ENST00000470527,; G ENST00000290039 Transcript missense_variant 1515/5275 1409/3672 470/1223 S/C tCt/tGt rs765925747 1 1 CACHD1 HGNC HGNC:29314 protein_coding YES CCDS628.2 ENSP00000290039 A0A0A0MQY7 UPI0000458A70 NM_020925.2,NM_001293274.1 deleterious(0) 11/27 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF40 MODERATE 1 SNV 5 1 PASS rs765925747 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 64653779 64653779 C G 1 0 0 0 0 1 0 0 0 2225 913 32 4 4 CACHD1 1 64653779 Missense_Mutation SNP C C3L-02365_T 25194535 64653779 184302643 13 8985 LRRC53 0 . GRCh38 1 74480430 74480430 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.627G>A p.= p.L209L ENST00000294635 3/5 339 292 47 324 324 0 strelka-varscan-mutect LRRC53,synonymous_variant,p.=,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2; T ENST00000294635 Transcript synonymous_variant 742/3859 627/3744 209/1247 L ctG/ctA 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE 3/5 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF379,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 74480430 74480430 C T 1 0 0 0 0 0 0 0 1 8905 813 29 3 3 LRRC53 1 74480430 Silent SNP C C3L-02365_T 9826651 74480430 174475992 14 8986 ACADM 0 . GRCh38 1 75761369 75761369 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.1292A>T p.Gln431Leu p.Q431L ENST00000370834 12/13 330 278 52 365 365 0 strelka-varscan-mutect ACADM,missense_variant,p.Gln398Leu,ENST00000370841,NM_000016.5;ACADM,missense_variant,p.Gln362Leu,ENST00000541113,NM_001286042.1;ACADM,missense_variant,p.Gln431Leu,ENST00000370834,NM_001286043.1;ACADM,missense_variant,p.Gln402Leu,ENST00000420607,NM_001127328.2;ACADM,splice_region_variant,,ENST00000481374,;ACADM,splice_region_variant,,ENST00000526196,;ACADM,splice_region_variant,,ENST00000525808,;ACADM,splice_region_variant,,ENST00000529059,;ACADM,3_prime_UTR_variant,,ENST00000526129,;ACADM,intron_variant,,ENST00000528016,;ACADM,downstream_gene_variant,,ENST00000534334,;ACADM,downstream_gene_variant,,ENST00000532207,; T ENST00000370834 Transcript missense_variant,splice_region_variant 1371/2172 1292/1365 431/454 Q/L cAg/cTg 1 1 ACADM HGNC HGNC:89 protein_coding YES CCDS72807.1 ENSP00000359871 Q5T4U5 UPI0000470C0B NM_001286043.1 deleterious(0) 12/13 Gene3D:1.20.140.10,Pfam_domain:PF00441,hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF240,Superfamily_domains:SSF47203 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 75761369 75761369 A T 1 0 0 0 0 1 0 0 0 156 202 7 4 4 ACADM 1 75761369 Missense_Mutation SNP A C3L-02365_T 1280939 75761369 173195053 15 8987 NEXN 0 . GRCh38 1 77942097 77942097 + Silent SNP A A G novel C3L-02365_T C3L-02365_N A A c.1548A>G p.= p.R516R ENST00000334785 12/13 399 280 119 411 411 0 strelka-varscan-mutect NEXN,synonymous_variant,p.=,ENST00000330010,NM_001172309.1;NEXN,synonymous_variant,p.=,ENST00000342754,;NEXN,synonymous_variant,p.=,ENST00000334785,NM_144573.3;NEXN,non_coding_transcript_exon_variant,,ENST00000480732,;FUBP1,downstream_gene_variant,,ENST00000489495,;FUBP1,downstream_gene_variant,,ENST00000492405,;FUBP1,downstream_gene_variant,,ENST00000474632,;FUBP1,downstream_gene_variant,,ENST00000488814,;FUBP1,downstream_gene_variant,,ENST00000483894,;FUBP1,downstream_gene_variant,,ENST00000492724,;FUBP1,downstream_gene_variant,,ENST00000480673,;NEXN,non_coding_transcript_exon_variant,,ENST00000470735,;FUBP1,downstream_gene_variant,,ENST00000294623,; G ENST00000334785 Transcript synonymous_variant 1732/2607 1548/2028 516/675 R agA/agG 1 1 NEXN HGNC HGNC:29557 protein_coding YES CCDS41351.1 ENSP00000333938 Q0ZGT2 UPI000022ABDC NM_144573.3 12/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10489:SF677,hmmpanther:PTHR10489 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 77942097 77942097 A G 1 0 0 0 0 0 0 0 1 10392 330 12 5 5 NEXN 1 77942097 Silent SNP A C3L-02365_T 2180728 77942097 171014325 16 8988 CLCA2 0 . GRCh38 1 86443967 86443967 + Missense_Mutation SNP C C G rs774054137 C3L-02365_T C3L-02365_N C C c.1669C>G p.Leu557Val p.L557V ENST00000370565 10/14 274 201 73 215 215 0 strelka-varscan-mutect CLCA2,missense_variant,p.Leu557Val,ENST00000370565,NM_006536.5;CLCA2,non_coding_transcript_exon_variant,,ENST00000490884,;CLCA2,upstream_gene_variant,,ENST00000498802,; G ENST00000370565 Transcript missense_variant 1831/4025 1669/2832 557/943 L/V Cta/Gta rs774054137 1 1 CLCA2 HGNC HGNC:2016 protein_coding YES CCDS708.1 ENSP00000359596 Q9UQC9 UPI0000035838 NM_006536.5 tolerated(0.19) 10/14 Pfam_domain:PF08434,hmmpanther:PTHR10579,hmmpanther:PTHR10579:SF66,TIGRFAM_domain:TIGR00868 MODERATE 1 SNV 1 1 PASS rs774054137 . 0 208 0 0 2 0 0 0 -20 0.9989074 1 1 1 0 G 3 3 34 86443967 86443967 C G 1 0 0 0 0 1 0 0 0 3222 912 32 4 4 CLCA2 1 86443967 Missense_Mutation SNP C C3L-02365_T 8501870 86443967 162512455 17 8989 CLCA4 0 . GRCh38 1 86575492 86575492 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1844C>A p.Ala615Glu p.A615E ENST00000370563 11/14 460 427 33 340 339 1 strelka-varscan-mutect CLCA4,missense_variant,p.Ala615Glu,ENST00000370563,NM_012128.3;RP4-651E10.4,intron_variant,,ENST00000456587,;CLCA4,downstream_gene_variant,,ENST00000496322,; A ENST00000370563 Transcript missense_variant 1886/3211 1844/2760 615/919 A/E gCa/gAa 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 deleterious(0) 11/14 hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 86575492 86575492 C A 1 0 0 0 0 1 0 0 0 3223 710 25 2 2 CLCA4 1 86575492 Missense_Mutation SNP C C3L-02365_T 131525 86575492 162380930 18 8990 FAM102B 0 . GRCh38 1 108628805 108628805 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.970+1G>T p.X324_splice ENST00000370035 104 92 12 93 93 0 strelka-varscan-mutect FAM102B,splice_donor_variant,,ENST00000370035,NM_001010883.2;FAM102B,splice_donor_variant,,ENST00000405454,;FAM102B,splice_donor_variant,,ENST00000483371,; T ENST00000370035 Transcript splice_donor_variant -/5600 970/1083 324/360 1 1 FAM102B HGNC HGNC:27637 protein_coding YES CCDS30786.2 ENSP00000359052 Q5T8I3 UPI00001D7585 NM_001010883.2 9/10 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99998 0.9999999 1 1 1 0 T 5 4 34 108628805 108628805 G T 1 0 0 0 0 0 0 1 0 5251 1275 44 2 2 FAM102B 1 108628805 Splice_Site SNP G C3L-02365_T 22053313 108628805 140327617 19 8991 WDR47 0 . GRCh38 1 109011507 109011510 + Frame_Shift_Del DEL CTAT CTAT - novel C3L-02365_T C3L-02365_N CTAT CTAT c.557_560delATAG p.Asp186GlyfsTer3 p.D186Gfs*3 ENST00000400794 5/15 280 143 137 226 226 0 sindel-varindel-pindel WDR47,frameshift_variant,p.Asp179GlyfsTer3,ENST00000369965,NM_014969.5;WDR47,frameshift_variant,p.Asp179GlyfsTer3,ENST00000369962,NM_001142551.1;WDR47,frameshift_variant,p.Asp151GlyfsTer3,ENST00000357672,;WDR47,frameshift_variant,p.Asp186GlyfsTer3,ENST00000400794,NM_001142550.1;WDR47,frameshift_variant,p.Asp151GlyfsTer3,ENST00000361054,;WDR47,downstream_gene_variant,,ENST00000529074,;WDR47,downstream_gene_variant,,ENST00000528747,;WDR47,downstream_gene_variant,,ENST00000530772,;WDR47,downstream_gene_variant,,ENST00000531337,; - ENST00000400794 Transcript frameshift_variant 691-694/4134 557-560/2784 186-187/927 DR/X gATAGg/gg 1 -1 WDR47 HGNC HGNC:29141 protein_coding YES CCDS44186.1 ENSP00000383599 O94967 UPI0001639B05 NM_001142550.1 5/15 hmmpanther:PTHR19863 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 109011507 109011507 CTAT - 1 0 1 0 1 0 0 0 0 17860 681 24 0 0 WDR47 1 109011507 Frame_Shift_Del DEL CTAT C3L-02365_T 382702 109011507 139944915 20 8992 CELSR2 0 . GRCh38 1 109258598 109258598 + Silent SNP G G A rs768656316 C3L-02365_T C3L-02365_N G G c.3477G>A p.= p.T1159T ENST00000271332 2/34 238 118 120 142 142 0 strelka-varscan-mutect CELSR2,synonymous_variant,p.=,ENST00000271332,NM_001408.2; A ENST00000271332 Transcript synonymous_variant 3538/10534 3477/8772 1159/2923 T acG/acA rs768656316 1 1 CELSR2 HGNC HGNC:3231 protein_coding YES CCDS796.1 ENSP00000271332 Q9HCU4 UPI00000015B6 NM_001408.2 2/34 hmmpanther:PTHR24026:SF32,hmmpanther:PTHR24026 LOW 1 SNV 1 1 PASS rs768656316 . 0 203 3 3 0 0 0 0 -20 0.9999916 1 1 1 0 A 2 1 34 109258598 109258598 G A 1 0 0 0 0 0 0 0 1 2929 1074 38 1 1 CELSR2 1 109258598 Silent SNP G C3L-02365_T 247091 109258598 139697824 21 8993 FAM212B 0 . GRCh38 1 111727249 111727249 + Missense_Mutation SNP C C G rs764694872 C3L-02365_T C3L-02365_N C C c.613G>C p.Ala205Pro p.A205P ENST00000357260 2/2 331 287 44 229 229 0 strelka-varscan-mutect FAM212B,missense_variant,p.Ala205Pro,ENST00000357260,NM_019099.4;FAM212B,missense_variant,p.Ala190Pro,ENST00000444059,NM_198926.2;FAM212B,intron_variant,,ENST00000534365,;FAM212B,downstream_gene_variant,,ENST00000527621,;FAM212B,intron_variant,,ENST00000527570,; G ENST00000357260 Transcript missense_variant 795/5980 613/894 205/297 A/P Gcc/Ccc rs764694872 1 -1 FAM212B HGNC HGNC:28045 protein_coding YES CCDS841.1 ENSP00000349805 Q9NTI7 UPI0000072CD1 NM_019099.4 deleterious(0) 2/2 hmmpanther:PTHR28615,hmmpanther:PTHR28615:SF2 MODERATE 1 SNV 1 1 PASS rs764694872 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 111727249 111727249 C G 1 0 0 0 0 1 0 0 0 5399 768 27 4 4 FAM212B 1 111727249 Missense_Mutation SNP C C3L-02365_T 2468651 111727249 137229173 22 8994 PHTF1 0 . GRCh38 1 113705953 113705953 + Silent SNP T T C novel C3L-02365_T C3L-02365_N T T c.1608A>G p.= p.E536E ENST00000369604 13/19 254 173 81 240 239 1 strelka-varscan-mutect PHTF1,synonymous_variant,p.=,ENST00000369604,NM_001323043.1;PHTF1,synonymous_variant,p.=,ENST00000393357,NM_006608.2;PHTF1,synonymous_variant,p.=,ENST00000369600,;PHTF1,synonymous_variant,p.=,ENST00000369598,;PHTF1,synonymous_variant,p.=,ENST00000357783,NM_001323047.1;PHTF1,synonymous_variant,p.=,ENST00000412670,;PHTF1,non_coding_transcript_exon_variant,,ENST00000474926,;PHTF1,non_coding_transcript_exon_variant,,ENST00000481652,; C ENST00000369604 Transcript synonymous_variant 2092/3273 1608/2289 536/762 E gaA/gaG 1 -1 PHTF1 HGNC HGNC:8939 protein_coding YES CCDS861.1 ENSP00000358617 Q9UMS5 UPI000013C9D0 NM_001323043.1 13/19 hmmpanther:PTHR12680,hmmpanther:PTHR12680:SF8 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 34 113705953 113705953 T C 1 0 0 0 0 0 0 0 1 11950 1838 64 5 5 PHTF1 1 113705953 Silent SNP T C3L-02365_T 1978704 113705953 135250469 23 8995 NOTCH2 0 . GRCh38 1 119929064 119929064 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.3804C>T p.= p.C1268C ENST00000256646 23/34 702 610 92 486 486 0 strelka-varscan-mutect NOTCH2,synonymous_variant,p.=,ENST00000256646,NM_024408.3; A ENST00000256646 Transcript synonymous_variant 4024/11389 3804/7416 1268/2471 C tgC/tgT 1 -1 NOTCH2 HGNC HGNC:7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 UPI000013CF1D NM_024408.3 23/34 Gene3D:2gy5A03,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF66,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 119929064 119929064 G A 1 0 0 0 0 0 0 0 1 10593 1195 42 3 3 NOTCH2 1 119929064 Silent SNP G C3L-02365_T 6223111 119929064 129027358 24 8996 PDZK1 0 . GRCh38 1 145673670 145673670 + Nonsense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.1202C>G p.Ser401Ter p.S401* ENST00000417171 7/9 179 167 12 87 87 0 varscan-mutect PDZK1,stop_gained,p.Ser401Ter,ENST00000417171,NM_002614.4,NM_001201325.1;PDZK1,stop_gained,p.Ser401Ter,ENST00000344770,;PDZK1,stop_gained,p.Ser290Ter,ENST00000451928,NM_001201326.1;GPR89A,downstream_gene_variant,,ENST00000313835,NM_001097612.1;GPR89A,downstream_gene_variant,,ENST00000534502,NM_001097613.2;GPR89A,downstream_gene_variant,,ENST00000462900,;PDZK1,non_coding_transcript_exon_variant,,ENST00000465595,;PDZK1,non_coding_transcript_exon_variant,,ENST00000429537,;PDZK1,upstream_gene_variant,,ENST00000466386,;GPR89A,downstream_gene_variant,,ENST00000493684,;GPR89A,downstream_gene_variant,,ENST00000460277,;GPR89A,downstream_gene_variant,,ENST00000465185,; C ENST00000417171 Transcript stop_gained 1288/2230 1202/1560 401/519 S/* tCa/tGa 1 -1 PDZK1 HGNC HGNC:8821 protein_coding YES CCDS72860.1 ENSP00000394485 Q5T2W1 UPI000006D202 NM_002614.4,NM_001201325.1 7/9 PROSITE_profiles:PS50106,hmmpanther:PTHR14191:SF6,hmmpanther:PTHR14191,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 34 145673670 145673670 G C 1 0 0 0 0 0 1 0 0 11795 1294 45 4 4 PDZK1 1 145673670 Nonsense_Mutation SNP G C3L-02365_T 25744606 145673670 103282752 25 8997 GJA8 0 . GRCh38 1 147908622 147908622 + Nonsense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.667G>T p.Glu223Ter p.E223* ENST00000369235 1/1 402 356 46 317 317 0 strelka-varscan-mutect GJA8,stop_gained,p.Glu223Ter,ENST00000369235,NM_005267.4; T ENST00000369235 Transcript stop_gained 667/1302 667/1302 223/433 E/* Gag/Tag 1 1 GJA8 HGNC HGNC:4281 protein_coding YES CCDS30834.1 ENSP00000358238 P48165 X5D7G1 UPI0000049BA0 NM_005267.4 1/1 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF19,SMART_domains:SM01089,Transmembrane_helices:TMhelix HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 147908622 147908622 G T 1 0 0 0 0 0 1 0 0 6284 1175 41 2 2 GJA8 1 147908622 Nonsense_Mutation SNP G C3L-02365_T 2234952 147908622 101047800 26 8998 HIST2H2AC 0 . GRCh38 1 149887143 149887143 + Missense_Mutation SNP G G C C3L-02365_T C3L-02365_N G G c.169G>C p.Glu57Gln p.E57Q ENST00000331380 1/1 795 520 275 508 508 0 strelka-varscan-mutect HIST2H2AC,missense_variant,p.Glu57Gln,ENST00000331380,NM_003517.2;HIST2H2BE,upstream_gene_variant,,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2; C ENST00000331380 Transcript missense_variant 169/390 169/390 57/129 E/Q Gag/Cag COSM383719 1 1 HIST2H2AC HGNC HGNC:4738 protein_coding YES CCDS937.1 ENSP00000332194 Q16777 UPI000007478F NM_003517.2 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00620,hmmpanther:PTHR23430,SMART_domains:SM00414,Superfamily_domains:SSF47113 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 149887143 149887143 G C 1 0 0 0 0 1 0 0 0 7066 1059 37 4 4 HIST2H2AC 1 149887143 Missense_Mutation SNP G C3L-02365_T 1978521 149887143 99069279 27 8999 IQGAP3 0 . GRCh38 1 156530113 156530113 + Missense_Mutation SNP G G T rs200332849 C3L-02365_T C3L-02365_N G G c.4396C>A p.Leu1466Met p.L1466M ENST00000361170 34/38 258 128 130 158 158 0 strelka-varscan-mutect IQGAP3,missense_variant,p.Leu1466Met,ENST00000361170,NM_178229.4;IQGAP3,missense_variant,p.Leu1423Met,ENST00000491900,; T ENST00000361170 Transcript missense_variant 4407/5988 4396/4896 1466/1631 L/M Ctg/Atg rs200332849 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 deleterious(0.04) 34/38 hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149,Pfam_domain:PF03836 MODERATE 1 SNV 1 1 PASS rs200332849 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 156530113 156530113 G T 1 0 0 0 0 1 0 0 0 7722 962 34 2 2 IQGAP3 1 156530113 Missense_Mutation SNP G C3L-02365_T 6642970 156530113 92426309 28 9000 OR10R2 0 . GRCh38 1 158480016 158480016 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.139C>A p.Leu47Ile p.L47I ENST00000368152 1/1 338 204 134 298 297 1 strelka-varscan-mutect OR10R2,missense_variant,p.Leu47Ile,ENST00000368152,NM_001004472.1;RP11-144L1.4,non_coding_transcript_exon_variant,,ENST00000419738,;RP11-144L1.4,intron_variant,,ENST00000426251,; A ENST00000368152 Transcript missense_variant 139/1008 139/1008 47/335 L/I Ctc/Atc 1 1 OR10R2 HGNC HGNC:14820 protein_coding YES CCDS30898.1 ENSP00000357134 Q8NGX6 UPI000004CA1C NM_001004472.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF42,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 158480016 158480016 C A 1 0 0 0 0 1 0 0 0 10994 681 24 2 2 OR10R2 1 158480016 Missense_Mutation SNP C C3L-02365_T 1949903 158480016 90476406 29 9001 ATP1A2 0 . GRCh38 1 160127617 160127617 + Missense_Mutation SNP G G T rs369898494 C3L-02365_T C3L-02365_N G G c.814G>T p.Ala272Ser p.A272S ENST00000361216 8/23 370 316 54 215 215 0 strelka-varscan-mutect ATP1A2,missense_variant,p.Ala272Ser,ENST00000361216,NM_000702.3;ATP1A2,missense_variant,p.Ala272Ser,ENST00000392233,;ATP1A2,upstream_gene_variant,,ENST00000447527,;ATP1A2,non_coding_transcript_exon_variant,,ENST00000472488,;ATP1A2,downstream_gene_variant,,ENST00000468587,; T ENST00000361216 Transcript missense_variant 903/5421 814/3063 272/1020 A/S Gcc/Tcc rs369898494,COSM4995301 1 1 ATP1A2 HGNC HGNC:800 protein_coding YES CCDS1196.1 ENSP00000354490 P50993 A0A0S2Z3W6 UPI0000124FC1 NM_000702.3 deleterious(0.05) 8/23 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01106,Pfam_domain:PF00122 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369898494 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 160127617 160127617 G T 1 0 0 0 0 1 0 0 0 1281 1087 38 1 1 ATP1A2 1 160127617 Missense_Mutation SNP G C3L-02365_T 1647601 160127617 88828805 30 9002 NIT1 0 . GRCh38 1 161118869 161118869 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.86G>C p.Cys29Ser p.C29S ENST00000368009 2/7 431 372 59 266 266 0 strelka-varscan-mutect NIT1,missense_variant,p.Cys29Ser,ENST00000368008,NM_001185092.1;NIT1,missense_variant,p.Cys29Ser,ENST00000368009,NM_005600.2;NIT1,5_prime_UTR_variant,,ENST00000392190,NM_001185094.1;NIT1,intron_variant,,ENST00000368007,NM_001185093.1;DEDD,downstream_gene_variant,,ENST00000368006,NM_032998.2;DEDD,downstream_gene_variant,,ENST00000545495,NM_001039711.1;DEDD,downstream_gene_variant,,ENST00000458050,NM_001039712.1;DEDD,downstream_gene_variant,,ENST00000490843,;DEDD,downstream_gene_variant,,ENST00000368005,;DEDD,downstream_gene_variant,,ENST00000464113,;PFDN2,upstream_gene_variant,,ENST00000368010,NM_012394.3;NIT1,non_coding_transcript_exon_variant,,ENST00000496861,;NIT1,non_coding_transcript_exon_variant,,ENST00000491497,;NIT1,non_coding_transcript_exon_variant,,ENST00000485594,;NIT1,non_coding_transcript_exon_variant,,ENST00000492411,;NIT1,non_coding_transcript_exon_variant,,ENST00000496768,;NIT1,non_coding_transcript_exon_variant,,ENST00000486962,;NIT1,non_coding_transcript_exon_variant,,ENST00000478277,;NIT1,intron_variant,,ENST00000479266,;NIT1,intron_variant,,ENST00000477684,;NIT1,intron_variant,,ENST00000473918,;DEDD,downstream_gene_variant,,ENST00000489249,;DEDD,downstream_gene_variant,,ENST00000486041,;DEDD,downstream_gene_variant,,ENST00000463227,;DEDD,downstream_gene_variant,,ENST00000496632,;DEDD,downstream_gene_variant,,ENST00000473679,;NIT1,upstream_gene_variant,,ENST00000461376,;NIT1,upstream_gene_variant,,ENST00000479728,;PFDN2,upstream_gene_variant,,ENST00000468311,;DEDD,downstream_gene_variant,,ENST00000472996,; C ENST00000368009 Transcript missense_variant 162/1362 86/984 29/327 C/S tGt/tCt 1 1 NIT1 HGNC HGNC:7828 protein_coding YES CCDS1218.1 ENSP00000356988 Q86X76 UPI00000715F9 NM_005600.2 tolerated_low_confidence(0.84) 2/7 MODERATE 1 SNV 1 1 PASS rs1441353426 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 161118869 161118869 G C 1 0 0 0 0 1 0 0 0 10468 1377 48 4 4 NIT1 1 161118869 Missense_Mutation SNP G C3L-02365_T 991252 161118869 87837553 31 9003 ALDH9A1 0 . GRCh38 1 165695335 165695335 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.244G>T p.Ala82Ser p.A82S ENST00000354775 2/11 261 224 37 241 241 0 strelka-varscan-mutect ALDH9A1,missense_variant,p.Ala82Ser,ENST00000354775,NM_000696.3;ALDH9A1,non_coding_transcript_exon_variant,,ENST00000461664,;RP11-466F5.6,upstream_gene_variant,,ENST00000400982,;ALDH9A1,non_coding_transcript_exon_variant,,ENST00000471457,; A ENST00000354775 Transcript missense_variant 549/2696 244/1557 82/518 A/S Gca/Tca 1 -1 ALDH9A1 HGNC HGNC:412 protein_coding YES CCDS1250.2 ENSP00000346827 P49189 B9EKV4 UPI00003E07DD NM_000696.3 tolerated(0.07) 2/11 hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF208,Pfam_domain:PF00171,Gene3D:3.40.605.10,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 165695335 165695335 C A 1 0 0 0 0 1 0 0 0 606 710 25 2 2 ALDH9A1 1 165695335 Missense_Mutation SNP C C3L-02365_T 4576466 165695335 83261087 32 9004 F5 0 . GRCh38 1 169524869 169524869 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.5756C>G p.Ser1919Cys p.S1919C ENST00000367797 19/25 524 468 56 415 415 0 strelka-varscan-mutect F5,missense_variant,p.Ser1924Cys,ENST00000367796,;F5,missense_variant,p.Ser1919Cys,ENST00000367797,NM_000130.4; C ENST00000367797 Transcript missense_variant 5958/7024 5756/6675 1919/2224 S/C tCt/tGt 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 deleterious(0.05) 19/25 PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.120.260,PIRSF_domain:PIRSF000354,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 169524869 169524869 G C 1 0 0 0 0 1 0 0 0 5216 942 33 4 4 F5 1 169524869 Missense_Mutation SNP G C3L-02365_T 3829534 169524869 79431553 33 9005 F5 0 . GRCh38 1 169550670 169550670 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.1366G>A p.Glu456Lys p.E456K ENST00000367797 9/25 557 508 49 457 457 0 strelka-varscan-mutect F5,missense_variant,p.Glu456Lys,ENST00000367796,;F5,missense_variant,p.Glu456Lys,ENST00000367797,NM_000130.4; T ENST00000367797 Transcript missense_variant 1568/7024 1366/6675 456/2224 E/K Gaa/Aaa 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 deleterious(0.02) 9/25 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,PIRSF_domain:PIRSF000354,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 169550670 169550670 C T 1 0 0 0 0 1 0 0 0 5216 835 29 3 3 F5 1 169550670 Missense_Mutation SNP C C3L-02365_T 25801 169550670 79405752 34 9006 SERPINC1 0 . GRCh38 1 173909652 173909652 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.1053C>T p.= p.H351H ENST00000367698 5/7 191 166 25 122 122 0 strelka-varscan-mutect SERPINC1,synonymous_variant,p.=,ENST00000367698,NM_000488.3;SERPINC1,intron_variant,,ENST00000617423,;SERPINC1,downstream_gene_variant,,ENST00000494024,;SERPINC1,downstream_gene_variant,,ENST00000487183,; A ENST00000367698 Transcript synonymous_variant 1172/1594 1053/1395 351/464 H caC/caT 1 -1 SERPINC1 HGNC HGNC:775 protein_coding YES CCDS1313.1 ENSP00000356671 P01008 A0A024R944 UPI000002C0C1 NM_000488.3 5/7 hmmpanther:PTHR11461:SF53,hmmpanther:PTHR11461,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 173909652 173909652 G A 1 0 0 0 0 0 0 0 1 14385 1368 48 3 3 SERPINC1 1 173909652 Silent SNP G C3L-02365_T 4358982 173909652 75046770 35 9007 PAPPA2 0 . GRCh38 1 176769633 176769633 + Silent SNP T T A novel C3L-02365_T C3L-02365_N T T c.4350T>A p.= p.S1450S ENST00000367662 16/23 262 219 43 221 221 0 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2; A ENST00000367662 Transcript synonymous_variant 5514/9691 4350/5376 1450/1791 S tcT/tcA 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 16/23 hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325,SMART_domains:SM00032 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 176769633 176769633 T A 1 0 0 0 0 0 0 0 1 11513 1567 55 4 4 PAPPA2 1 176769633 Silent SNP T C3L-02365_T 2859981 176769633 72186789 36 9008 CACNA1E 0 . GRCh38 1 181733534 181733534 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.3046G>C p.Gly1016Arg p.G1016R ENST00000367573 21/48 94 76 18 63 63 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Gly997Arg,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Gly1016Arg,ENST00000621551,;CACNA1E,missense_variant,p.Gly1016Arg,ENST00000367567,;CACNA1E,missense_variant,p.Gly997Arg,ENST00000358338,;CACNA1E,missense_variant,p.Gly1016Arg,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Gly1016Arg,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Gly1015Arg,ENST00000357570,;CACNA1E,missense_variant,p.Gly997Arg,ENST00000360108,; C ENST00000367573 Transcript missense_variant 3046/7067 3046/6942 1016/2313 G/R Ggg/Cgg 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 tolerated(0.36) 21/48 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 C 3 2 34 181733534 181733534 G C 1 0 0 0 0 1 0 0 0 2230 1232 43 4 4 CACNA1E 1 181733534 Missense_Mutation SNP G C3L-02365_T 4963901 181733534 67222888 37 9009 TNNI1 0 . GRCh38 1 201411457 201411457 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.356C>T p.Ser119Leu p.S119L ENST00000361379 7/9 289 270 19 175 175 0 strelka-varscan-mutect TNNI1,missense_variant,p.Ser119Leu,ENST00000622580,;TNNI1,missense_variant,p.Ser119Leu,ENST00000361379,NM_003281.3;TNNI1,missense_variant,p.Ser119Leu,ENST00000336092,;TNNI1,missense_variant,p.Ser119Leu,ENST00000367312,;TNNI1,missense_variant,p.Ser119Leu,ENST00000556362,;TNNI1,missense_variant,p.Ser98Leu,ENST00000555340,;TNNI1,intron_variant,,ENST00000555948,; A ENST00000361379 Transcript missense_variant 449/5413 356/564 119/187 S/L tCg/tTg 1 -1 TNNI1 HGNC HGNC:11945 protein_coding YES CCDS1411.1 ENSP00000354488 P19237 UPI0000000CCA NM_003281.3 deleterious(0) 7/9 hmmpanther:PTHR13738:SF9,hmmpanther:PTHR13738,Pfam_domain:PF00992,Gene3D:1.20.5.350,Superfamily_domains:SSF90250 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 201411457 201411457 G A 1 0 0 0 0 1 0 0 0 16799 1059 37 1 1 TNNI1 1 201411457 Missense_Mutation SNP G C3L-02365_T 19677923 201411457 47544965 38 9010 ELF3 0 . GRCh38 1 202015290 202015290 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.1083G>T p.Trp361Cys p.W361C ENST00000359651 8/8 312 192 120 228 228 0 strelka-varscan-mutect ELF3,missense_variant,p.Trp361Cys,ENST00000359651,;ELF3,missense_variant,p.Trp361Cys,ENST00000367284,NM_001114309.1,NM_004433.4;ELF3,missense_variant,p.Trp361Cys,ENST00000367283,;ELF3,downstream_gene_variant,,ENST00000446188,;RP11-510N19.5,non_coding_transcript_exon_variant,,ENST00000504773,;RP11-465N4.4,upstream_gene_variant,,ENST00000419190,;ELF3,non_coding_transcript_exon_variant,,ENST00000475698,;ELF3,downstream_gene_variant,,ENST00000495848,;ELF3,downstream_gene_variant,,ENST00000490203,;ELF3,downstream_gene_variant,,ENST00000498017,;ELF3,downstream_gene_variant,,ENST00000470384,;ELF3,downstream_gene_variant,,ENST00000479874,; T ENST00000359651 Transcript missense_variant 4275/4994 1083/1116 361/371 W/C tgG/tgT COSM4841865,COSM4841866 1 1 ELF3 HGNC HGNC:3318 protein_coding YES CCDS1419.1 ENSP00000352673 P78545 A0A024R974 UPI0000034E32 deleterious(0) 8/8 hmmpanther:PTHR11849:SF13,hmmpanther:PTHR11849,Gene3D:1.10.10.10,Superfamily_domains:SSF46785 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 202015290 202015290 G T 1 0 0 0 0 1 0 0 0 4888 1183 41 2 2 ELF3 1 202015290 Missense_Mutation SNP G C3L-02365_T 603833 202015290 46941132 39 9011 MYOG 0 . GRCh38 1 203083945 203083945 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.640T>A p.Ser214Thr p.S214T ENST00000241651 3/3 275 187 88 227 227 0 strelka-varscan-mutect MYOG,missense_variant,p.Ser214Thr,ENST00000241651,NM_002479.5; T ENST00000241651 Transcript missense_variant 715/1528 640/675 214/224 S/T Tct/Act 1 -1 MYOG HGNC HGNC:7612 protein_coding YES CCDS1433.1 ENSP00000241651 P15173 UPI000012FBA4 NM_002479.5 tolerated(0.37) 3/3 hmmpanther:PTHR11534:SF5,hmmpanther:PTHR11534 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 203083945 203083945 A T 1 0 0 0 0 1 0 0 0 10091 275 10 4 4 MYOG 1 203083945 Missense_Mutation SNP A C3L-02365_T 1068655 203083945 45872477 40 9012 INTS7 0 . GRCh38 1 212021201 212021201 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.106G>T p.Gly36Cys p.G36C ENST00000366994 2/20 157 97 60 139 139 0 strelka-varscan-mutect INTS7,missense_variant,p.Gly36Cys,ENST00000366994,NM_015434.3;INTS7,missense_variant,p.Gly36Cys,ENST00000366993,NM_001199811.1;INTS7,missense_variant,p.Gly36Cys,ENST00000366992,NM_001199812.1;INTS7,missense_variant,p.Gly36Cys,ENST00000440600,NM_001199809.1;SNORA26,upstream_gene_variant,,ENST00000390885,;INTS7,missense_variant,p.Gly36Cys,ENST00000469606,;INTS7,3_prime_UTR_variant,,ENST00000619805,; A ENST00000366994 Transcript missense_variant 211/4417 106/2889 36/962 G/C Ggc/Tgc 1 -1 INTS7 HGNC HGNC:24484 protein_coding YES CCDS1501.1 ENSP00000355961 Q9NVH2 UPI000006FE2E NM_015434.3 tolerated(0.08) 2/20 hmmpanther:PTHR13322,hmmpanther:PTHR13322:SF2,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 212021201 212021201 C A 1 0 0 0 0 1 0 0 0 7686 594 21 2 2 INTS7 1 212021201 Missense_Mutation SNP C C3L-02365_T 8937256 212021201 36935221 41 9013 USH2A 0 . GRCh38 1 216247046 216247046 + Missense_Mutation SNP T T G C3L-02365_T C3L-02365_N T T c.2348A>C p.Asn783Thr p.N783T ENST00000307340 13/72 269 254 15 283 283 0 strelka-varscan-mutect USH2A,missense_variant,p.Asn783Thr,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Asn783Thr,ENST00000366942,NM_007123.5; G ENST00000307340 Transcript missense_variant 2735/18883 2348/15609 783/5202 N/T aAc/aCc COSM4028216,COSM4028217,COSM4028218,COSM5036935,COSM5036936,COSM5036937 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.03) 13/72 Gene3D:2.10.25.10,Pfam_domain:PF00053,Prints_domain:PR00011,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00180,Superfamily_domains:SSF57196 1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS rs1224180395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 216247046 216247046 T G 1 0 0 0 0 1 0 0 0 17570 1725 60 5 5 USH2A 1 216247046 Missense_Mutation SNP T C3L-02365_T 4225845 216247046 32709376 42 9014 SPATA17 0 . GRCh38 1 217801783 217801783 + Missense_Mutation SNP A A C novel C3L-02365_T C3L-02365_N A A c.938A>C p.Lys313Thr p.K313T ENST00000366933 9/11 232 220 12 216 216 0 strelka-varscan-mutect SPATA17,missense_variant,p.Lys313Thr,ENST00000366933,NM_138796.3;SPATA17,non_coding_transcript_exon_variant,,ENST00000471021,;SPATA17,downstream_gene_variant,,ENST00000492747,; C ENST00000366933 Transcript missense_variant 993/5818 938/1086 313/361 K/T aAg/aCg 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 deleterious(0.02) 9/11 hmmpanther:PTHR22706 MODERATE 1 SNV 1 1 PASS rs1184733319 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 217801783 217801783 A C 1 0 0 0 0 1 0 0 0 15332 72 3 5 5 SPATA17 1 217801783 Missense_Mutation SNP A C3L-02365_T 1554737 217801783 31154639 43 9015 MIA3 0 . GRCh38 1 222629457 222629457 + Missense_Mutation SNP A A T rs767277066 C3L-02365_T C3L-02365_N A A c.2237A>T p.Asn746Ile p.N746I ENST00000344922 4/28 310 162 148 277 277 0 strelka-varscan-mutect MIA3,missense_variant,p.Asn746Ile,ENST00000344922,NM_001324064.1,NM_198551.3;MIA3,missense_variant,p.Asn329Ile,ENST00000354906,;MIA3,intron_variant,,ENST00000344507,;MIA3,non_coding_transcript_exon_variant,,ENST00000470521,; T ENST00000344922 Transcript missense_variant 2262/8142 2237/5724 746/1907 N/I aAc/aTc rs767277066 1 1 MIA3 HGNC HGNC:24008 protein_coding YES CCDS41470.1 ENSP00000340900 Q5JRA6 UPI00001D75B3 NM_001324064.1,NM_198551.3 tolerated(0.42) 4/28 hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF37 MODERATE 1 SNV 5 1 PASS rs767277066 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 222629457 222629457 A T 1 0 0 0 0 1 0 0 0 9522 43 2 4 4 MIA3 1 222629457 Missense_Mutation SNP A C3L-02365_T 4827674 222629457 26326965 44 9016 ITPKB 0 . GRCh38 1 226736143 226736143 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.1316T>C p.Leu439Pro p.L439P ENST00000429204 2/8 58 34 24 46 46 0 strelka-varscan-mutect ITPKB,missense_variant,p.Leu439Pro,ENST00000429204,NM_002221.3;ITPKB,missense_variant,p.Leu439Pro,ENST00000272117,;ITPKB,missense_variant,p.Leu439Pro,ENST00000366784,; G ENST00000429204 Transcript missense_variant 1656/6162 1316/2841 439/946 L/P cTc/cCc 1 -1 ITPKB HGNC HGNC:6179 protein_coding YES CCDS1555.1 ENSP00000411152 P27987 UPI000013D92B NM_002221.3 tolerated_low_confidence(0.29) 2/8 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 226736143 226736143 A G 1 0 0 0 0 1 0 0 0 7824 304 11 5 5 ITPKB 1 226736143 Missense_Mutation SNP A C3L-02365_T 4106686 226736143 22220279 45 9017 OBSCN 0 . GRCh38 1 228337943 228337943 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.19672-1G>T p.X6558_splice ENST00000570156 175 116 59 107 107 0 strelka-varscan-mutect OBSCN,splice_acceptor_variant,,ENST00000570156,NM_001271223.2;OBSCN,splice_acceptor_variant,,ENST00000366707,;OBSCN,splice_acceptor_variant,,ENST00000422127,NM_001098623.2;OBSCN,splice_acceptor_variant,,ENST00000636875,;OBSCN,splice_acceptor_variant,,ENST00000284548,NM_052843.3;OBSCN,splice_acceptor_variant,,ENST00000636476,;OBSCN,intron_variant,,ENST00000483539,; T ENST00000570156 Transcript splice_acceptor_variant -/26925 19672/26772 6558/8923 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 77/115 HIGH 1 SNV 5 1 PASS rs1379549414 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 228337943 228337943 G T 1 0 0 0 0 0 0 1 0 10889 956 33 2 2 OBSCN 1 228337943 Splice_Site SNP G C3L-02365_T 1601800 228337943 20618479 46 9018 FMN2 0 . GRCh38 1 240207252 240207252 + Missense_Mutation SNP C C A rs757908642 C3L-02365_T C3L-02365_N C C c.2440C>A p.Pro814Thr p.P814T ENST00000319653 5/18 337 202 135 261 261 0 strelka-varscan-mutect FMN2,missense_variant,p.Pro814Thr,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; A ENST00000319653 Transcript missense_variant 2670/6434 2440/5169 814/1722 P/T Cca/Aca rs757908642,COSM1473669,COSM334276 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 tolerated_low_confidence(0.31) 5/18 Low_complexity_(Seg):seg,SMART_domains:SM00498 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs757908642 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 240207252 240207252 C A 1 0 0 0 0 1 0 0 0 5806 855 30 2 2 FMN2 1 240207252 Missense_Mutation SNP C C3L-02365_T 11869309 240207252 8749170 47 9019 FMN2 0 . GRCh38 1 240207609 240207609 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2797C>A p.Pro933Thr p.P933T ENST00000319653 5/18 248 219 29 172 172 0 strelka-varscan-mutect FMN2,missense_variant,p.Pro933Thr,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; A ENST00000319653 Transcript missense_variant 3027/6434 2797/5169 933/1722 P/T Cct/Act 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious_low_confidence(0.01) 5/18 Pfam_domain:PF06346,Low_complexity_(Seg):seg,SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 240207609 240207609 C A 1 0 0 0 0 1 0 0 0 5806 623 22 2 2 FMN2 1 240207609 Missense_Mutation SNP C C3L-02365_T 357 240207609 8748813 48 9020 NLRP3 0 . GRCh38 1 247425190 247425190 + Missense_Mutation SNP C C G rs756111783 C3L-02365_T C3L-02365_N C C c.1747C>G p.Leu583Val p.L583V ENST00000336119 3/9 1544 1392 152 802 801 1 strelka-varscan-mutect NLRP3,missense_variant,p.Leu583Val,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Leu583Val,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Leu583Val,ENST00000366496,;NLRP3,missense_variant,p.Leu583Val,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Leu583Val,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Leu583Val,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; G ENST00000336119 Transcript missense_variant 2493/4170 1747/3111 583/1036 L/V Ctg/Gtg rs756111783 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 deleterious(0) 3/9 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4 MODERATE 1 SNV 1 1 PASS rs756111783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 247425190 247425190 C G 1 0 0 0 0 1 0 0 0 10516 680 24 4 4 NLRP3 1 247425190 Missense_Mutation SNP C C3L-02365_T 7217581 247425190 1531232 49 9021 OR2M2 0 . GRCh38 1 248180613 248180613 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.628C>A p.Pro210Thr p.P210T ENST00000359682 1/1 858 351 507 542 541 1 strelka-varscan-mutect OR2M2,missense_variant,p.Pro210Thr,ENST00000359682,NM_001004688.1; A ENST00000359682 Transcript missense_variant 628/1044 628/1044 210/347 P/T Cct/Act COSM3487017 1 1 OR2M2 HGNC HGNC:8268 protein_coding YES CCDS31106.1 ENSP00000352710 Q96R28 A0A126GWI7 UPI00001612E4 NM_001004688.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 248180613 248180613 C A 1 0 0 0 0 1 0 0 0 11088 623 22 2 2 OR2M2 1 248180613 Missense_Mutation SNP C C3L-02365_T 755423 248180613 775809 50 9022 OR2T1 0 . GRCh38 1 248406360 248406360 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.366G>A p.Met122Ile p.M122I ENST00000366474 1/1 379 326 53 271 271 0 strelka-varscan-mutect OR2T1,missense_variant,p.Met122Ile,ENST00000366474,NM_030904.1; A ENST00000366474 Transcript missense_variant 366/1110 366/1110 122/369 M/I atG/atA 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 tolerated(0.06) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 248406360 248406360 G A 1 0 0 0 0 1 0 0 0 11094 1377 48 3 3 OR2T1 1 248406360 Missense_Mutation SNP G C3L-02365_T 225747 248406360 550062 51 9023 OR2T2 0 . GRCh38 1 248453121 248453121 + Silent SNP G G T C3L-02365_T C3L-02365_N G G c.324G>T p.= p.L108L ENST00000342927 1/1 1778 1687 91 976 976 0 varscan-mutect OR2T2,synonymous_variant,p.=,ENST00000342927,NM_001004136.1; T ENST00000342927 Transcript synonymous_variant 324/975 324/975 108/324 L ctG/ctT COSM401013 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 248453121 248453121 G T 1 0 0 0 0 0 0 0 1 11097 1277 45 2 2 OR2T2 1 248453121 Silent SNP G C3L-02365_T 46761 248453121 503301 52 9024 OR2T10 0 . GRCh38 1 248593490 248593490 + Silent SNP C C A rs61743160 C3L-02365_T C3L-02365_N C C c.279G>T p.= p.S93S ENST00000330500 1/1 560 403 157 342 342 0 strelka-varscan-mutect OR2T10,synonymous_variant,p.=,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; A ENST00000330500 Transcript synonymous_variant 279/939 279/939 93/312 S tcG/tcT rs61743160,COSM1341187,COSM5335900 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs61743160 . 4 205 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 248593490 248593490 C A 1 0 0 0 0 0 0 0 1 11095 639 23 1 1 OR2T10 1 248593490 Silent SNP C C3L-02365_T 140369 248593490 362932 53 9025 XDH 0 . GRCh38 2 31348928 31348928 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.3022A>T p.Ile1008Leu p.I1008L ENST00000379416 27/36 372 203 169 397 397 0 strelka-varscan-mutect XDH,missense_variant,p.Ile1008Leu,ENST00000379416,NM_000379.3; A ENST00000379416 Transcript missense_variant 3071/5688 3022/4002 1008/1333 I/L Ata/Tta 1 -1 XDH HGNC HGNC:12805 protein_coding YES CCDS1775.1 ENSP00000368727 P47989 UPI0000036BC9 NM_000379.3 deleterious(0) 27/36 hmmpanther:PTHR11908,hmmpanther:PTHR11908:SF78,Gene3D:3.30.365.10,PIRSF_domain:PIRSF000127,Pfam_domain:PF02738,Superfamily_domains:SSF56003 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 31348928 31348928 T A 1 0 0 0 0 1 0 0 0 17985 1493 52 4 4 XDH 2 31348928 Missense_Mutation SNP T C3L-02365_T 31348928 210844601 54 9026 CRIM1 0 . GRCh38 2 36544375 36544375 + Splice_Site SNP G G C novel C3L-02365_T C3L-02365_N G G c.2624-1G>C p.X875_splice ENST00000280527 27 16 11 19 19 0 strelka-varscan-mutect CRIM1,splice_acceptor_variant,,ENST00000280527,NM_016441.2;FEZ2,intron_variant,,ENST00000406220,; C ENST00000280527 Transcript splice_acceptor_variant -/5912 2624/3111 875/1036 1 1 CRIM1 HGNC HGNC:2359 protein_coding YES CCDS1783.1 ENSP00000280527 Q9NZV1 UPI000004C628 NM_016441.2 14/16 HIGH 1 SNV 1 1 PASS . . 5 204 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 34 36544375 36544375 G C 1 0 0 0 0 0 0 1 0 3674 956 33 4 4 CRIM1 2 36544375 Splice_Site SNP G C3L-02365_T 5195447 36544375 205649154 55 9027 SPRED2 0 . GRCh38 2 65313868 65313868 + Nonsense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.890C>A p.Ser297Ter p.S297* ENST00000356388 6/6 192 77 115 154 153 1 strelka-varscan-mutect SPRED2,stop_gained,p.Ser297Ter,ENST00000356388,NM_181784.2;SPRED2,stop_gained,p.Ser294Ter,ENST00000443619,NM_001128210.1;SPRED2,stop_gained,p.Ser312Ter,ENST00000452315,;SPRED2,stop_gained,p.Ser179Ter,ENST00000421087,;SPRED2,downstream_gene_variant,,ENST00000474228,; T ENST00000356388 Transcript stop_gained 1080/4097 890/1257 297/418 S/* tCg/tAg COSM263852 1 -1 SPRED2 HGNC HGNC:17722 protein_coding YES CCDS33211.1 ENSP00000348753 Q7Z698 UPI000013E7B4 NM_181784.2 6/6 hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF11 1 HIGH 1 SNV 1 1 1 PASS rs1308584438 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 65313868 65313868 G T 1 0 0 0 0 0 1 0 0 15447 1059 37 1 1 SPRED2 2 65313868 Nonsense_Mutation SNP G C3L-02365_T 28769493 65313868 176879661 56 9028 RAB11FIP5 0 . GRCh38 2 73088954 73088954 + Missense_Mutation SNP A A C rs775637400 C3L-02365_T C3L-02365_N A A c.793T>G p.Leu265Val p.L265V ENST00000258098 2/5 159 139 20 109 109 0 strelka-varscan-mutect RAB11FIP5,missense_variant,p.Leu265Val,ENST00000486777,;RAB11FIP5,missense_variant,p.Leu265Val,ENST00000258098,NM_015470.2;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000475951,;RAB11FIP5,upstream_gene_variant,,ENST00000482554,;RAB11FIP5,upstream_gene_variant,,ENST00000479196,; C ENST00000258098 Transcript missense_variant 1034/4342 793/1962 265/653 L/V Ttg/Gtg rs775637400 1 -1 RAB11FIP5 HGNC HGNC:24845 protein_coding YES CCDS1923.1 ENSP00000258098 Q9BXF6 UPI000007079C NM_015470.2 tolerated(0.47) 2/5 Low_complexity_(Seg):seg,hmmpanther:PTHR15746:SF14,hmmpanther:PTHR15746 MODERATE 1 SNV 1 1 PASS rs775637400 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 73088954 73088954 A C 1 0 0 0 0 1 0 0 0 13055 69 3 5 5 RAB11FIP5 2 73088954 Missense_Mutation SNP A C3L-02365_T 7775086 73088954 169104575 57 9029 LRRTM1 0 . GRCh38 2 80302635 80302635 + Silent SNP C C A C3L-02365_T C3L-02365_N C C c.1185G>T p.= p.A395A ENST00000295057 2/2 167 87 80 146 146 0 strelka-varscan-mutect LRRTM1,synonymous_variant,p.=,ENST00000295057,;LRRTM1,synonymous_variant,p.=,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.=,ENST00000433224,;LRRTM1,synonymous_variant,p.=,ENST00000417012,; A ENST00000295057 Transcript synonymous_variant 1842/2599 1185/1569 395/522 A gcG/gcT COSM3840104,COSM3840105 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3 1,1 LOW 1 SNV 1 1,1 1 PASS rs1191816698 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 80302635 80302635 C A 1 0 0 0 0 0 0 0 1 8945 639 23 1 1 LRRTM1 2 80302635 Silent SNP C C3L-02365_T 7213681 80302635 161890894 58 9030 DNAH6 0 . GRCh38 2 84640562 84640562 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.4954G>C p.Val1652Leu p.V1652L ENST00000389394 32/77 117 71 46 126 126 0 strelka-mutect DNAH6,missense_variant,p.Val1652Leu,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Val1652Leu,ENST00000237449,; C ENST00000389394 Transcript missense_variant 5091/12795 4954/12477 1652/4158 V/L Gtc/Ctc 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 deleterious(0) 32/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF12774,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 84640562 84640562 G C 1 0 0 0 0 1 0 0 0 4420 1377 48 4 4 DNAH6 2 84640562 Missense_Mutation SNP G C3L-02365_T 4337927 84640562 157552967 59 9031 DNAH6 0 . GRCh38 2 84745165 84745165 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.10428G>C p.Lys3476Asn p.K3476N ENST00000389394 63/77 231 166 65 212 212 0 strelka-varscan-mutect DNAH6,missense_variant,p.Lys3476Asn,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Lys3476Asn,ENST00000237449,; C ENST00000389394 Transcript missense_variant 10565/12795 10428/12477 3476/4158 K/N aaG/aaC 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated(0.36) 63/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF03028 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 84745165 84745165 G C 1 0 0 0 0 1 0 0 0 4420 991 35 4 4 DNAH6 2 84745165 Missense_Mutation SNP G C3L-02365_T 104603 84745165 157448364 60 9032 ST6GAL2 0 . GRCh38 2 106806709 106806709 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.1559C>T p.Pro520Leu p.P520L ENST00000409382 6/6 233 203 30 161 161 0 strelka-varscan-mutect ST6GAL2,missense_variant,p.Pro520Leu,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Pro520Leu,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Pro86Leu,ENST00000361803,; A ENST00000409382 Transcript missense_variant 2170/7275 1559/1590 520/529 P/L cCt/cTt 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 6/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 106806709 106806709 G A 1 0 0 0 0 1 0 0 0 15600 1000 35 3 3 ST6GAL2 2 106806709 Missense_Mutation SNP G C3L-02365_T 22061544 106806709 135386820 61 9033 DPP10 0 . GRCh38 2 115836156 115836156 + Splice_Site SNP G G T C3L-02365_T C3L-02365_N G G c.1963-1G>T p.X655_splice ENST00000393147 83 37 46 95 95 0 strelka-varscan-mutect DPP10,splice_acceptor_variant,,ENST00000410059,NM_001321910.1,NM_001321911.1,NM_001321914.1,NM_001321905.1,NM_001321906.1,NM_020868.3;DPP10,splice_acceptor_variant,,ENST00000409163,NM_001178036.1,NM_001178037.1;DPP10,splice_acceptor_variant,,ENST00000310323,NM_001004360.3;DPP10,splice_acceptor_variant,,ENST00000393147,NM_001178034.1;DPP10,splice_acceptor_variant,,ENST00000473362,; T ENST00000393147 Transcript splice_acceptor_variant -/2758 1963/2403 655/800 COSM4923872,COSM4923873 1 1 DPP10 HGNC HGNC:20823 protein_coding YES CCDS54388.1 ENSP00000376855 Q8N608 UPI00015E0A22 NM_001178034.1 21/25 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 204 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 115836156 115836156 G T 1 0 0 0 0 0 0 1 0 4542 1014 35 2 2 DPP10 2 115836156 Splice_Site SNP G C3L-02365_T 9029447 115836156 126357373 62 9034 PTPN4 0 . GRCh38 2 119957064 119957064 + Missense_Mutation SNP C C T rs779332065 C3L-02365_T C3L-02365_N C C c.2120C>T p.Ala707Val p.A707V ENST00000263708 22/27 176 90 86 177 177 0 strelka-varscan-mutect PTPN4,missense_variant,p.Ala707Val,ENST00000263708,NM_002830.3;PTPN4,upstream_gene_variant,,ENST00000441089,;PTPN4,3_prime_UTR_variant,,ENST00000430976,;PTPN4,upstream_gene_variant,,ENST00000469511,; T ENST00000263708 Transcript missense_variant 2891/10300 2120/2781 707/926 A/V gCg/gTg rs779332065,COSM202471 1 1 PTPN4 HGNC HGNC:9656 protein_coding YES CCDS2129.1 ENSP00000263708 P29074 A0A024RAE8 UPI0000000CA9 NM_002830.3 deleterious(0) 22/27 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF321,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000927,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779332065 . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 119957064 119957064 C T 1 0 0 0 0 1 0 0 0 12944 768 27 1 1 PTPN4 2 119957064 Missense_Mutation SNP C C3L-02365_T 4120908 119957064 122236465 63 9035 TUBA3E 0 . GRCh38 2 130196318 130196318 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.57C>A p.= p.A19A ENST00000312988 2/5 225 98 127 188 188 0 strelka-varscan-mutect TUBA3E,synonymous_variant,p.=,ENST00000312988,NM_207312.2; T ENST00000312988 Transcript synonymous_variant 158/1542 57/1353 19/450 A gcC/gcA 1 -1 TUBA3E HGNC HGNC:20765 protein_coding YES CCDS2158.1 ENSP00000318197 Q6PEY2 UPI00001BE8EB NM_207312.2 2/5 Gene3D:3.40.50.1440,Pfam_domain:PF00091,Prints_domain:PR01161,Prints_domain:PR01162,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF94,Superfamily_domains:SSF52490 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 130196318 130196318 G T 1 0 0 0 0 0 0 0 1 17258 987 35 2 2 TUBA3E 2 130196318 Silent SNP G C3L-02365_T 10239254 130196318 111997211 64 9036 LRP1B 0 . GRCh38 2 141188554 141188554 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.880A>T p.Thr294Ser p.T294S ENST00000389484 7/91 196 85 111 172 172 0 strelka-varscan-mutect LRP1B,missense_variant,p.Thr294Ser,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 1852/16535 880/13800 294/4599 T/S Act/Tct 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.26) 7/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 141188554 141188554 T A 1 0 0 0 0 1 0 0 0 8850 1696 59 4 4 LRP1B 2 141188554 Missense_Mutation SNP T C3L-02365_T 10992236 141188554 101004975 65 9037 NEB 0 . GRCh38 2 151553908 151553908 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.19546C>A p.Leu6516Met p.L6516M ENST00000618972 126/183 192 174 18 154 154 0 strelka-varscan-mutect NEB,missense_variant,p.Leu6516Met,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Leu6516Met,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Leu6516Met,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Leu6516Met,ENST00000603639,;NEB,missense_variant,p.Leu6516Met,ENST00000604864,;NEB,missense_variant,p.Leu4815Met,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Leu4815Met,ENST00000172853,;NEB,missense_variant,p.Leu1246Met,ENST00000413693,; T ENST00000618972 Transcript missense_variant 19749/26307 19546/25683 6516/8560 L/M Ctg/Atg 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.13) 126/183 hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 151553908 151553908 G T 1 0 0 0 0 1 0 0 0 10326 991 35 2 2 NEB 2 151553908 Missense_Mutation SNP G C3L-02365_T 10365354 151553908 90639621 66 9038 MYO3B 0 . GRCh38 2 170200221 170200221 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.258G>C p.Lys86Asn p.K86N ENST00000408978 3/35 249 123 126 195 195 0 strelka-varscan-mutect MYO3B,missense_variant,p.Lys86Asn,ENST00000408978,NM_138995.4;MYO3B,missense_variant,p.Lys86Asn,ENST00000409044,NM_001083615.3;MYO3B,missense_variant,p.Lys95Asn,ENST00000484338,;MYO3B,missense_variant,p.Lys86Asn,ENST00000442690,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,missense_variant,p.Lys86Asn,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; C ENST00000408978 Transcript missense_variant 401/5529 258/4026 86/1341 K/N aaG/aaC 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 tolerated(0.07) 3/35 PROSITE_profiles:PS50011,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 170200221 170200221 G C 1 0 0 0 0 1 0 0 0 10078 1020 36 4 4 MYO3B 2 170200221 Missense_Mutation SNP G C3L-02365_T 18646313 170200221 71993308 67 9039 ITGAV 0 . GRCh38 2 186638457 186638457 + Missense_Mutation SNP G G T rs199654707 C3L-02365_T C3L-02365_N G G c.895G>T p.Gly299Cys p.G299C ENST00000261023 10/30 244 118 126 230 230 0 strelka-varscan-mutect ITGAV,missense_variant,p.Gly299Cys,ENST00000261023,NM_002210.4;ITGAV,missense_variant,p.Gly263Cys,ENST00000374907,NM_001145000.2;ITGAV,missense_variant,p.Gly253Cys,ENST00000433736,NM_001144999.2;AC017101.10,downstream_gene_variant,,ENST00000453665,; T ENST00000261023 Transcript missense_variant 1169/7030 895/3147 299/1048 G/C Ggc/Tgc rs199654707 1 1 ITGAV HGNC HGNC:6150 protein_coding YES CCDS2292.1 ENSP00000261023 P06756 L7RXH0 UPI000013D12E NM_002210.4 deleterious(0) 10/30 PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF4,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318,Prints_domain:PR01185 MODERATE 1 SNV 1 1 PASS rs199654707 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 186638457 186638457 G T 1 0 0 0 0 1 0 0 0 7795 1348 47 2 2 ITGAV 2 186638457 Missense_Mutation SNP G C3L-02365_T 16438236 186638457 55555072 68 9040 COL5A2 0 . GRCh38 2 189053479 189053479 + Splice_Site SNP T T A novel C3L-02365_T C3L-02365_N T T c.2500-2A>T p.X834_splice ENST00000374866 463 183 280 387 386 1 strelka-varscan-mutect COL5A2,splice_acceptor_variant,,ENST00000374866,NM_000393.3;COL5A2,splice_acceptor_variant,,ENST00000618828,;COL5A2,downstream_gene_variant,,ENST00000470524,; A ENST00000374866 Transcript splice_acceptor_variant -/6949 2500/4500 834/1499 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 37/53 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 34 189053479 189053479 T A 1 0 0 0 0 0 0 1 0 3486 1536 53 4 4 COL5A2 2 189053479 Splice_Site SNP T C3L-02365_T 2415022 189053479 53140050 69 9041 PLCL1 0 . GRCh38 2 198103852 198103852 + Silent SNP T T C novel C3L-02365_T C3L-02365_N T T c.3021T>C p.= p.H1007H ENST00000428675 5/6 171 74 97 150 150 0 strelka-varscan-mutect PLCL1,synonymous_variant,p.=,ENST00000437704,;PLCL1,synonymous_variant,p.=,ENST00000428675,NM_006226.3;PLCL1,synonymous_variant,p.=,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; C ENST00000428675 Transcript synonymous_variant 3419/5125 3021/3288 1007/1095 H caT/caC 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 5/6 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 34 198103852 198103852 T C 1 0 0 0 0 0 0 0 1 12133 1403 49 5 5 PLCL1 2 198103852 Silent SNP T C3L-02365_T 9050373 198103852 44089677 70 9042 MAP2 0 . GRCh38 2 209692903 209692903 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.733C>G p.Leu245Val p.L245V ENST00000360351 7/15 294 228 66 196 196 0 strelka-varscan-mutect MAP2,missense_variant,p.Leu245Val,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Leu241Val,ENST00000447185,;MAP2,missense_variant,p.Leu327Val,ENST00000445941,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,non_coding_transcript_exon_variant,,ENST00000461253,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000481649,; G ENST00000360351 Transcript missense_variant 1239/9711 733/5484 245/1827 L/V Ctt/Gtt 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 tolerated_low_confidence(0.06) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 209692903 209692903 C G 1 0 0 0 0 1 0 0 0 9157 681 24 4 4 MAP2 2 209692903 Missense_Mutation SNP C C3L-02365_T 11589051 209692903 32500626 71 9043 MOGAT1 0 . GRCh38 2 222694429 222694429 + Silent SNP T T A novel C3L-02365_T C3L-02365_N T T c.546T>A p.= p.S182S ENST00000446656 4/6 269 111 158 257 257 0 strelka-varscan-mutect MOGAT1,synonymous_variant,p.=,ENST00000446656,NM_058165.2;AC016712.1,downstream_gene_variant,,ENST00000444764,; A ENST00000446656 Transcript synonymous_variant 546/1048 546/1008 182/335 S tcT/tcA 1 1 MOGAT1 HGNC HGNC:18210 protein_coding YES CCDS46524.1 ENSP00000406674 Q96PD6 UPI000013D50F NM_058165.2 4/6 hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF26,Pfam_domain:PF03982 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 222694429 222694429 T A 1 0 0 0 0 0 0 0 1 9657 1567 55 4 4 MOGAT1 2 222694429 Silent SNP T C3L-02365_T 13001526 222694429 19499100 72 9044 IQCA1 0 . GRCh38 2 236344578 236344579 + Frame_Shift_Del DEL TT TT - novel C3L-02365_T C3L-02365_N TT TT c.1958_1959delAA p.Lys653SerfsTer9 p.K653Sfs*9 ENST00000431676 16/19 240 180 60 197 197 0 sindel-varindel-pindel IQCA1,frameshift_variant,p.Lys645SerfsTer9,ENST00000409907,NM_024726.4;IQCA1,frameshift_variant,p.Lys604SerfsTer9,ENST00000309507,NM_001270584.1;IQCA1,frameshift_variant,p.Lys653SerfsTer9,ENST00000431676,NM_001270585.1;IQCA1,non_coding_transcript_exon_variant,,ENST00000409100,;IQCA1,frameshift_variant,p.Lys646SerfsTer28,ENST00000254653,; - ENST00000431676 Transcript frameshift_variant 1993-1994/3069 1958-1959/2493 653/830 K/X aAA/a 1 -1 IQCA1 HGNC HGNC:26195 protein_coding YES CCDS74677.1 ENSP00000407213 A0A0A0MSY6 UPI0001AE77A0 NM_001270585.1 16/19 Gene3D:3.40.50.300,Pfam_domain:PF00004,hmmpanther:PTHR14690,hmmpanther:PTHR14690:SF8,Superfamily_domains:SSF52540 HIGH 1 deletion 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 236344578 236344578 TT - 1 0 1 0 1 0 0 0 0 7705 1606 56 0 0 IQCA1 2 236344578 Frame_Shift_Del DEL TT C3L-02365_T 13650149 236344578 5848951 73 9045 ESPNL 0 . GRCh38 2 238131007 238131007 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.2293A>G p.Thr765Ala p.T765A ENST00000343063 9/9 237 91 146 132 132 0 strelka-varscan-mutect ESPNL,missense_variant,p.Thr765Ala,ENST00000343063,NM_194312.2;ESPNL,missense_variant,p.Thr721Ala,ENST00000409169,;ESPNL,missense_variant,p.Thr397Ala,ENST00000409506,NM_001308370.1;ESPNL,5_prime_UTR_variant,,ENST00000612395,;ESPNL,downstream_gene_variant,,ENST00000423032,;ESPNL,non_coding_transcript_exon_variant,,ENST00000477241,; G ENST00000343063 Transcript missense_variant 2556/4836 2293/3018 765/1005 T/A Acc/Gcc 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 tolerated(0.07) 9/9 hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153 MODERATE 1 SNV 2 1 PASS . . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 238131007 238131007 A G 1 0 0 0 0 1 0 0 0 5117 275 10 5 5 ESPNL 2 238131007 Missense_Mutation SNP A C3L-02365_T 1786429 238131007 4062522 74 9046 CNTN4 0 . GRCh38 3 3040253 3040253 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.2380G>C p.Val794Leu p.V794L ENST00000397461 19/24 278 164 114 278 278 0 strelka-varscan-mutect CNTN4,missense_variant,p.Val794Leu,ENST00000397461,NM_001206955.1;CNTN4,missense_variant,p.Val794Leu,ENST00000418658,NM_175607.2;CNTN4,missense_variant,p.Val794Leu,ENST00000427331,;CNTN4,missense_variant,p.Val466Leu,ENST00000397459,NM_001206956.1,NM_175613.2;CNTN4-AS1,non_coding_transcript_exon_variant,,ENST00000442749,;CNTN4-AS1,downstream_gene_variant,,ENST00000629672,;CNTN4,3_prime_UTR_variant,,ENST00000427741,;CNTN4,non_coding_transcript_exon_variant,,ENST00000484686,;CNTN4,downstream_gene_variant,,ENST00000430505,; C ENST00000397461 Transcript missense_variant 2764/5198 2380/3081 794/1026 V/L Gtg/Ctg 1 1 CNTN4 HGNC HGNC:2174 protein_coding YES CCDS43041.1 ENSP00000380602 Q8IWV2 A0A024R2E5 UPI000007446C NM_001206955.1 deleterious(0.02) 19/24 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF568,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 3040253 3040253 G C 1 0 0 0 0 1 0 0 0 3424 1261 44 4 4 CNTN4 3 3040253 Missense_Mutation SNP G C3L-02365_T 3040253 195255306 75 9047 SLC6A1 0 . GRCh38 3 11034647 11034647 + Silent SNP C C T rs200481115 C3L-02365_T C3L-02365_N C C c.1644C>T p.= p.I548I ENST00000287766 15/16 161 135 26 148 148 0 strelka-varscan-mutect SLC6A1,synonymous_variant,p.=,ENST00000287766,NM_003042.3;SLC6A1,non_coding_transcript_exon_variant,,ENST00000495636,; T ENST00000287766 Transcript synonymous_variant 2065/4502 1644/1800 548/599 I atC/atT rs200481115,COSM5539261 1 1 SLC6A1 HGNC HGNC:11042 protein_coding YES CCDS2603.1 ENSP00000287766 P30531 A0A024R2G0 UPI000013DECF NM_003042.3 15/16 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF138,Pfam_domain:PF00209,Superfamily_domains:0053687 0,1 LOW 1 SNV 1 0,1 1 PASS rs200481115 . 0 206 0 3 0 0 0 0 -20 0.9999943 1 1 1 0 T 2 4 34 11034647 11034647 C T 1 0 0 0 0 0 0 0 1 14956 845 30 3 3 SLC6A1 3 11034647 Silent SNP C C3L-02365_T 7994394 11034647 187260912 76 9048 ZNF860 0 . GRCh38 3 31990845 31990845 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.1766T>A p.Met589Lys p.M589K ENST00000360311 2/2 250 209 41 330 330 0 strelka-varscan-mutect ZNF860,missense_variant,p.Met589Lys,ENST00000360311,NM_001137674.2;OSBPL10,intron_variant,,ENST00000479173,;ZNF860,downstream_gene_variant,,ENST00000489408,; A ENST00000360311 Transcript missense_variant 2315/3098 1766/1899 589/632 M/K aTg/aAg 1 1 ZNF860 HGNC HGNC:34513 protein_coding YES CCDS46784.1 ENSP00000373274 A6NHJ4 UPI0000D61AE9 NM_001137674.2 deleterious(0.01) 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF301,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 31990845 31990845 T A 1 0 0 0 0 1 0 0 0 18785 1464 51 4 4 ZNF860 3 31990845 Missense_Mutation SNP T C3L-02365_T 20956198 31990845 166304714 77 9049 TDGF1 0 . GRCh38 3 46581188 46581188 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.505T>A p.Ser169Thr p.S169T ENST00000296145 6/6 427 251 176 574 574 0 strelka-varscan-mutect TDGF1,missense_variant,p.Ser169Thr,ENST00000296145,NM_003212.3;TDGF1,missense_variant,p.Ser153Thr,ENST00000542931,NM_001174136.1;LRRC2,upstream_gene_variant,,ENST00000296144,;AC104304.4,missense_variant,p.Ser14Thr,ENST00000505797,;TDGF1,downstream_gene_variant,,ENST00000471721,;TDGF1,downstream_gene_variant,,ENST00000493282,;TDGF1,downstream_gene_variant,,ENST00000459867,; A ENST00000296145 Transcript missense_variant 1238/2513 505/567 169/188 S/T Tct/Act 1 1 TDGF1 HGNC HGNC:11701 protein_coding YES CCDS2742.1 ENSP00000296145 P13385 UPI000004966D NM_003212.3 tolerated(0.09) 6/6 hmmpanther:PTHR14949,hmmpanther:PTHR14949:SF26,PIRSF_domain:PIRSF036301 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 46581188 46581188 T A 1 0 0 0 0 1 0 0 0 16134 1667 58 4 4 TDGF1 3 46581188 Missense_Mutation SNP T C3L-02365_T 14590343 46581188 151714371 78 9050 PDHB 0 . GRCh38 3 58429776 58429776 + Frame_Shift_Del DEL G G - novel C3L-02365_T C3L-02365_N G G c.724delC p.His242IlefsTer9 p.H242Ifs*9 ENST00000302746 8/10 316 262 54 410 409 1 sindel-varindel-pindel PDHB,frameshift_variant,p.His242IlefsTer9,ENST00000302746,NM_000925.3;PDHB,frameshift_variant,p.His224IlefsTer9,ENST00000474765,;PDHB,frameshift_variant,p.His224IlefsTer9,ENST00000383714,NM_001315536.1;PDHB,frameshift_variant,p.His224IlefsTer9,ENST00000485460,NM_001173468.1;PXK,downstream_gene_variant,,ENST00000383716,NM_001289098.1;PXK,downstream_gene_variant,,ENST00000463280,NM_001289101.1,NM_001289100.1;PXK,downstream_gene_variant,,ENST00000479241,NM_001289095.1;PXK,downstream_gene_variant,,ENST00000356151,NM_001289099.1,NM_001289096.1,NM_017771.4;PXK,downstream_gene_variant,,ENST00000302779,;PXK,downstream_gene_variant,,ENST00000479134,;PXK,downstream_gene_variant,,ENST00000493474,;RP11-802O23.3,downstream_gene_variant,,ENST00000607214,;PDHB,3_prime_UTR_variant,,ENST00000469364,;PDHB,non_coding_transcript_exon_variant,,ENST00000479945,;PDHB,non_coding_transcript_exon_variant,,ENST00000461692,;PXK,downstream_gene_variant,,ENST00000468776,;PXK,downstream_gene_variant,,ENST00000477308,;PDHB,downstream_gene_variant,,ENST00000480626,;PDHB,downstream_gene_variant,,ENST00000469827,;PDHB,downstream_gene_variant,,ENST00000482894,; - ENST00000302746 Transcript frameshift_variant 767/1527 724/1080 242/359 H/X Cat/at 1 -1 PDHB HGNC HGNC:8808 protein_coding YES CCDS2890.1 ENSP00000307241 P11177 UPI000013E81D NM_000925.3 8/10 Gene3D:3.40.50.920,Pfam_domain:PF02780,hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF56,Superfamily_domains:SSF52922 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 58429776 58429776 G - 1 0 1 0 1 0 0 0 0 11754 1348 47 0 0 PDHB 3 58429776 Frame_Shift_Del DEL G C3L-02365_T 11848588 58429776 139865783 79 9051 ROBO1 0 . GRCh38 3 78670123 78670123 + Silent SNP A A G novel C3L-02365_T C3L-02365_N A A c.1521T>C p.= p.N507N ENST00000464233 11/31 113 106 7 129 129 0 strelka-varscan-mutect ROBO1,synonymous_variant,p.=,ENST00000436010,;ROBO1,synonymous_variant,p.=,ENST00000618833,;ROBO1,synonymous_variant,p.=,ENST00000618846,;ROBO1,synonymous_variant,p.=,ENST00000464233,NM_002941.3;ROBO1,synonymous_variant,p.=,ENST00000495273,NM_133631.3;ROBO1,synonymous_variant,p.=,ENST00000467549,NM_001145845.1;ROBO1,synonymous_variant,p.=,ENST00000495961,;ROBO1,non_coding_transcript_exon_variant,,ENST00000498428,;ROBO1,non_coding_transcript_exon_variant,,ENST00000484514,; G ENST00000464233 Transcript synonymous_variant 1635/6742 1521/4956 507/1651 N aaT/aaC 1 -1 ROBO1 HGNC HGNC:10249 protein_coding YES CCDS54611.1 ENSP00000420321 Q9Y6N7 UPI00000713D9 NM_002941.3 11/31 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF107,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 78670123 78670123 A G 1 0 0 0 0 0 0 0 1 13691 214 8 5 5 ROBO1 3 78670123 Silent SNP A C3L-02365_T 20240347 78670123 119625436 80 9052 USF3 0 . GRCh38 3 113659769 113659769 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1913C>A p.Pro638Gln p.P638Q ENST00000316407 7/7 190 136 54 250 249 1 strelka-varscan-mutect USF3,missense_variant,p.Pro638Gln,ENST00000316407,NM_001009899.3;USF3,missense_variant,p.Pro638Gln,ENST00000478658,;USF3,intron_variant,,ENST00000491165,;USF3,non_coding_transcript_exon_variant,,ENST00000496826,; T ENST00000316407 Transcript missense_variant 2324/13708 1913/6738 638/2245 P/Q cCa/cAa 1 -1 USF3 HGNC HGNC:30494 protein_coding YES CCDS43133.1 ENSP00000320794 Q68DE3 UPI0004438052 NM_001009899.3 deleterious(0) 7/7 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 113659769 113659769 G T 1 0 0 0 0 1 0 0 0 17567 1348 47 2 2 USF3 3 113659769 Missense_Mutation SNP G C3L-02365_T 34989646 113659769 84635790 81 9053 EPHB1 0 . GRCh38 3 134951831 134951831 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.584A>T p.Lys195Met p.K195M ENST00000398015 3/16 159 86 73 155 155 0 strelka-varscan-mutect EPHB1,missense_variant,p.Lys195Met,ENST00000398015,NM_004441.4;EPHB1,downstream_gene_variant,,ENST00000460895,;EPHB1,downstream_gene_variant,,ENST00000474732,;EPHB1,downstream_gene_variant,,ENST00000473867,;EPHB1,downstream_gene_variant,,ENST00000497173,;EPHB1,intron_variant,,ENST00000488154,;EPHB1,missense_variant,p.Lys195Met,ENST00000482618,; T ENST00000398015 Transcript missense_variant 954/4672 584/2955 195/984 K/M aAg/aTg 1 1 EPHB1 HGNC HGNC:3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 UPI000012A07E NM_004441.4 deleterious(0.01) 3/16 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_patterns:PS00790,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,SMART_domains:SM00615 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 134951831 134951831 A T 1 0 0 0 0 1 0 0 0 5021 72 3 4 4 EPHB1 3 134951831 Missense_Mutation SNP A C3L-02365_T 21292062 134951831 63343728 82 9054 SOX14 0 . GRCh38 3 137765316 137765316 + Frame_Shift_Del DEL G G - rs780965428 C3L-02365_T C3L-02365_N G G c.533delG p.Gly178AlafsTer47 p.G178Afs*47 ENST00000306087 1/1 159 120 39 165 165 0 sindel-varindel-pindel SOX14,frameshift_variant,p.Gly178AlafsTer47,ENST00000306087,NM_004189.3; - ENST00000306087 Transcript frameshift_variant 1033/2055 532/723 178/240 G/X Ggc/gc rs780965428 1 1 SOX14 HGNC HGNC:11193 protein_coding YES CCDS3094.1 ENSP00000305343 O95416 UPI0000000B2D NM_004189.3 1/1 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF107,Pfam_domain:PF12336 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 137765316 137765316 G - 1 0 1 0 1 0 0 0 0 15271 1116 39 0 0 SOX14 3 137765316 Frame_Shift_Del DEL G C3L-02365_T 2813485 137765316 60530243 83 9055 SAMD7 0 . GRCh38 3 169927053 169927053 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.791G>T p.Gly264Val p.G264V ENST00000428432 6/9 106 58 48 119 118 1 strelka-varscan-mutect SAMD7,missense_variant,p.Gly264Val,ENST00000428432,NM_182610.3;SAMD7,missense_variant,p.Gly264Val,ENST00000335556,NM_001304366.1;SAMD7,3_prime_UTR_variant,,ENST00000487910,;RP11-379K17.2,upstream_gene_variant,,ENST00000493762,; T ENST00000428432 Transcript missense_variant 1180/2399 791/1341 264/446 G/V gGg/gTg 1 1 SAMD7 HGNC HGNC:25394 protein_coding YES CCDS3209.1 ENSP00000391299 Q7Z3H4 UPI00001A9D13 NM_182610.3 tolerated(0.14) 6/9 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF89 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 169927053 169927053 G T 1 0 0 0 0 1 0 0 0 14084 1232 43 2 2 SAMD7 3 169927053 Missense_Mutation SNP G C3L-02365_T 32161737 169927053 28368506 84 9056 SPATA16 0 . GRCh38 3 173117498 173117498 + Missense_Mutation SNP C C G rs779138808 C3L-02365_T C3L-02365_N C C c.234G>C p.Glu78Asp p.E78D ENST00000351008 2/11 413 391 22 505 505 0 strelka-varscan-mutect SPATA16,missense_variant,p.Glu78Asp,ENST00000351008,NM_031955.5; G ENST00000351008 Transcript missense_variant 418/2106 234/1710 78/569 E/D gaG/gaC rs779138808,COSM729034 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 tolerated(1) 2/11 Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779138808 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 173117498 173117498 C G 1 0 0 0 0 1 0 0 0 15331 912 32 4 4 SPATA16 3 173117498 Missense_Mutation SNP C C3L-02365_T 3190445 173117498 25178061 85 9057 HTR3D 0 . GRCh38 3 184038836 184038836 + Missense_Mutation SNP G G T rs775646831 C3L-02365_T C3L-02365_N G G c.1226G>T p.Arg409Leu p.R409L ENST00000382489 8/8 114 93 21 103 103 0 strelka-varscan-mutect HTR3D,missense_variant,p.Arg409Leu,ENST00000382489,NM_001163646.1;HTR3D,missense_variant,p.Arg234Leu,ENST00000334128,NM_182537.2;HTR3D,missense_variant,p.Arg359Leu,ENST00000428798,NM_001145143.1;HTR3D,missense_variant,p.Arg188Leu,ENST00000453435,; T ENST00000382489 Transcript missense_variant 1226/1674 1226/1365 409/454 R/L cGg/cTg rs775646831,COSM5509980,COSM5509981,COSM5509982 1 1 HTR3D HGNC HGNC:24004 protein_coding YES CCDS54685.1 ENSP00000371929 Q70Z44 UPI000024209D NM_001163646.1 tolerated(0.36) 8/8 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF409,Superfamily_domains:SSF90112 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs775646831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 184038836 184038836 G T 1 0 0 0 0 1 0 0 0 7343 1116 39 1 1 HTR3D 3 184038836 Missense_Mutation SNP G C3L-02365_T 10921338 184038836 14256723 86 9058 EIF4A2 0 . GRCh38 3 186785981 186785981 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.447G>T p.Gln149His p.Q149H ENST00000323963 5/11 87 50 37 110 110 0 strelka-varscan-mutect EIF4A2,missense_variant,p.Gln149His,ENST00000323963,NM_001967.3;EIF4A2,missense_variant,p.Gln150His,ENST00000440191,;RFC4,downstream_gene_variant,,ENST00000392481,NM_181573.2;RFC4,downstream_gene_variant,,ENST00000296273,NM_002916.3;RFC4,downstream_gene_variant,,ENST00000433496,;EIF4A2,downstream_gene_variant,,ENST00000445596,;EIF4A2,downstream_gene_variant,,ENST00000498746,;EIF4A2,downstream_gene_variant,,ENST00000441007,;RFC4,downstream_gene_variant,,ENST00000417876,;SNORA81,upstream_gene_variant,,ENST00000408493,;SNORA4,upstream_gene_variant,,ENST00000584302,;SNORA63,upstream_gene_variant,,ENST00000363450,;SNORA63,upstream_gene_variant,,ENST00000363548,;EIF4A2,upstream_gene_variant,,ENST00000629190,;SNORD2,downstream_gene_variant,,ENST00000459163,;RP11-573D15.9,upstream_gene_variant,,ENST00000577781,;EIF4A2,missense_variant,p.Gln149His,ENST00000425053,;EIF4A2,3_prime_UTR_variant,,ENST00000426808,;EIF4A2,3_prime_UTR_variant,,ENST00000443963,;EIF4A2,3_prime_UTR_variant,,ENST00000429589,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000485101,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000468362,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000475653,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000495049,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000467585,;EIF4A2,non_coding_transcript_exon_variant,,ENST00000466362,;EIF4A2,downstream_gene_variant,,ENST00000465267,;RFC4,downstream_gene_variant,,ENST00000479307,;EIF4A2,upstream_gene_variant,,ENST00000492144,;EIF4A2,upstream_gene_variant,,ENST00000497177,;EIF4A2,upstream_gene_variant,,ENST00000475409,;EIF4A2,upstream_gene_variant,,ENST00000465792,;EIF4A2,downstream_gene_variant,,ENST00000465222,;EIF4A2,upstream_gene_variant,,ENST00000494445,;EIF4A2,downstream_gene_variant,,ENST00000486805,;EIF4A2,downstream_gene_variant,,ENST00000491473,;EIF4A2,downstream_gene_variant,,ENST00000465032,;EIF4A2,upstream_gene_variant,,ENST00000461021,;EIF4A2,upstream_gene_variant,,ENST00000496382,; T ENST00000323963 Transcript missense_variant 511/1919 447/1224 149/407 Q/H caG/caT COSM3992933 1 1 EIF4A2 HGNC HGNC:3284 protein_coding YES CCDS3282.1 ENSP00000326381 Q14240 UPI0000000DD2 NM_001967.3 deleterious(0.03) 5/11 PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF226,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 186785981 186785981 G T 1 0 0 0 0 1 0 0 0 4859 991 35 2 2 EIF4A2 3 186785981 Missense_Mutation SNP G C3L-02365_T 2747145 186785981 11509578 87 9059 ZNF518B 0 . GRCh38 4 10443358 10443358 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.2971C>A p.Arg991Ser p.R991S ENST00000326756 3/3 182 131 51 174 174 0 strelka-varscan-mutect ZNF518B,missense_variant,p.Arg991Ser,ENST00000326756,NM_053042.2;ZNF518B,downstream_gene_variant,,ENST00000507515,; T ENST00000326756 Transcript missense_variant 3410/6894 2971/3225 991/1074 R/S Cgc/Agc COSM5318267 1 -1 ZNF518B HGNC HGNC:29365 protein_coding YES CCDS33960.1 ENSP00000317614 Q9C0D4 UPI0000160B97 NM_053042.2 deleterious(0) 3/3 hmmpanther:PTHR10032:SF188,hmmpanther:PTHR10032 1 MODERATE 1 SNV 3 1 1 PASS rs1380410394 . 0 206 0 3 0 0 0 0 -20 0.9999981 1 1 1 0 T 3 4 34 10443358 10443358 G T 1 0 0 0 0 1 0 0 0 18535 1145 40 1 1 ZNF518B 4 10443358 Missense_Mutation SNP G C3L-02365_T 10443358 179771197 88 9060 CORIN 0 . GRCh38 4 47623680 47623680 + Nonsense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2431G>T p.Gly811Ter p.G811* ENST00000273857 19/22 320 265 55 254 254 0 strelka-varscan-mutect CORIN,stop_gained,p.Gly811Ter,ENST00000273857,NM_006587.3;CORIN,stop_gained,p.Gly707Ter,ENST00000610355,NM_001278585.1;CORIN,stop_gained,p.Gly672Ter,ENST00000508498,;CORIN,stop_gained,p.Gly744Ter,ENST00000502252,;CORIN,stop_gained,p.Gly774Ter,ENST00000505909,;CORIN,non_coding_transcript_exon_variant,,ENST00000515827,; A ENST00000273857 Transcript stop_gained 2431/4852 2431/3129 811/1042 G/* Gga/Tga 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 19/22 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF036376,PROSITE_profiles:PS50240,hmmpanther:PTHR24270,SMART_domains:SM00020,Superfamily_domains:SSF50494 HIGH 1 SNV 1 1 PASS rs1234182844 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 47623680 47623680 C A 1 0 0 0 0 0 1 0 0 3546 603 21 2 2 CORIN 4 47623680 Nonsense_Mutation SNP C C3L-02365_T 37180322 47623680 142590875 89 9061 EPHA5 0 . GRCh38 4 65366010 65366010 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.1975G>T p.Asp659Tyr p.D659Y ENST00000622150 11/18 166 132 34 127 127 0 strelka-varscan-mutect EPHA5,missense_variant,p.Asp659Tyr,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Asp637Tyr,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Asp658Tyr,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Asp659Tyr,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Asp495Tyr,ENST00000432638,;EPHA5,missense_variant,p.Asp636Tyr,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 2728/8421 1975/3117 659/1038 D/Y Gat/Tat COSM1671043 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 11/18 Gene3D:3.30.200.20,Pfam_domain:PF14575,PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 65366010 65366010 C A 1 0 0 0 0 1 0 0 0 5017 855 30 2 2 EPHA5 4 65366010 Missense_Mutation SNP C C3L-02365_T 17742330 65366010 124848545 90 9062 RP11-766F14.2 0 . GRCh38 4 99652668 99652668 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.1981T>A p.Trp661Arg p.W661R ENST00000511828 1/2 177 132 45 148 148 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Trp661Arg,ENST00000511828,; T ENST00000511828 Transcript missense_variant 1981/10086 1981/5382 661/1793 W/R Tgg/Agg 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE deleterious(0) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 99652668 99652668 A T 1 0 0 0 0 1 0 0 0 13762 188 7 4 4 RP11-766F14.2 4 99652668 Missense_Mutation SNP A C3L-02365_T 34286658 99652668 90561887 91 9063 NDST4 0 . GRCh38 4 115076350 115076350 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.687C>A p.= p.T229T ENST00000264363 2/14 235 182 53 254 254 0 strelka-varscan-mutect NDST4,synonymous_variant,p.=,ENST00000264363,NM_022569.1;NDST4,5_prime_UTR_variant,,ENST00000613194,;NDST4,intron_variant,,ENST00000504854,;NDST4,intron_variant,,ENST00000514570,; T ENST00000264363 Transcript synonymous_variant 1366/3351 687/2619 229/872 T acC/acA 1 -1 NDST4 HGNC HGNC:20779 protein_coding YES CCDS3706.1 ENSP00000264363 Q9H3R1 UPI000006CED7 NM_022569.1 2/14 Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF45 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 115076350 115076350 G T 1 0 0 0 0 0 0 0 1 10279 987 35 2 2 NDST4 4 115076350 Silent SNP G C3L-02365_T 15423682 115076350 75138205 92 9064 FAT4 0 . GRCh38 4 125490338 125490338 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.13516C>A p.Pro4506Thr p.P4506T ENST00000394329 17/17 430 347 83 411 409 2 strelka-varscan-mutect FAT4,missense_variant,p.Pro4506Thr,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Pro2747Thr,ENST00000335110,; A ENST00000394329 Transcript missense_variant 13529/16123 13516/14946 4506/4981 P/T Cct/Act 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious_low_confidence(0.05) 17/17 Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs1278065148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 125490338 125490338 C A 1 0 0 0 0 1 0 0 0 5552 739 26 2 2 FAT4 4 125490338 Missense_Mutation SNP C C3L-02365_T 10413988 125490338 64724217 93 9065 GRIA2 0 . GRCh38 4 157332925 157332925 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.989G>T p.Cys330Phe p.C330F ENST00000296526 7/16 124 68 56 114 114 0 strelka-varscan-mutect GRIA2,missense_variant,p.Cys330Phe,ENST00000296526,NM_000826.3;GRIA2,missense_variant,p.Cys283Phe,ENST00000393815,NM_001083620.1;GRIA2,missense_variant,p.Cys330Phe,ENST00000264426,NM_001083619.1;GRIA2,missense_variant,p.Cys283Phe,ENST00000507898,;GRIA2,missense_variant,p.Cys283Phe,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; T ENST00000296526 Transcript missense_variant 1314/5621 989/2652 330/883 C/F tGt/tTt 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 deleterious(0.01) 7/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 157332925 157332925 G T 1 0 0 0 0 1 0 0 0 6648 1377 48 2 2 GRIA2 4 157332925 Missense_Mutation SNP G C3L-02365_T 31842587 157332925 32881630 94 9066 TRAPPC11 0 . GRCh38 4 183663929 183663929 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.62C>G p.Thr21Ser p.T21S ENST00000334690 2/30 336 294 42 278 278 0 strelka-varscan-mutect TRAPPC11,missense_variant,p.Thr21Ser,ENST00000334690,NM_021942.5;TRAPPC11,missense_variant,p.Thr21Ser,ENST00000357207,NM_199053.2;RWDD4,upstream_gene_variant,,ENST00000326397,NM_152682.2;RWDD4,upstream_gene_variant,,ENST00000327570,;RWDD4,upstream_gene_variant,,ENST00000510968,;RWDD4,upstream_gene_variant,,ENST00000512740,NM_001307922.1;TRAPPC11,non_coding_transcript_exon_variant,,ENST00000504526,;TRAPPC11,upstream_gene_variant,,ENST00000511409,;TRAPPC11,missense_variant,p.Thr21Ser,ENST00000505676,;RWDD4,upstream_gene_variant,,ENST00000510702,;RWDD4,upstream_gene_variant,,ENST00000514322,;TRAPPC11,upstream_gene_variant,,ENST00000509857,;TRAPPC11,upstream_gene_variant,,ENST00000513600,; G ENST00000334690 Transcript missense_variant 264/4552 62/3402 21/1133 T/S aCt/aGt 1 1 TRAPPC11 HGNC HGNC:25751 protein_coding YES CCDS34112.1 ENSP00000335371 Q7Z392 UPI000020B774 NM_021942.5 tolerated(0.05) 2/30 hmmpanther:PTHR14374 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 183663929 183663929 C G 1 0 0 0 0 1 0 0 0 16941 565 20 4 4 TRAPPC11 4 183663929 Missense_Mutation SNP C C3L-02365_T 26331004 183663929 6550626 95 9067 FBXL7 0 . GRCh38 5 15928082 15928082 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.320C>A p.Pro107His p.P107H ENST00000504595 3/4 259 217 42 95 95 0 strelka-varscan-mutect FBXL7,missense_variant,p.Pro107His,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Pro65His,ENST00000329673,;FBXL7,missense_variant,p.Pro60His,ENST00000510662,NM_001278317.1; A ENST00000504595 Transcript missense_variant 801/4562 320/1476 107/491 P/H cCc/cAc 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.57) 3/4 hmmpanther:PTHR24006,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 15928082 15928082 C A 1 0 0 0 0 1 0 0 0 5587 623 22 2 2 FBXL7 5 15928082 Missense_Mutation SNP C C3L-02365_T 15928082 165610177 96 9068 C1QTNF3 0 . GRCh38 5 34020667 34020667 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.876G>C p.Trp292Cys p.W292C ENST00000382065 6/6 486 409 77 225 225 0 strelka-varscan-mutect C1QTNF3,missense_variant,p.Trp292Cys,ENST00000382065,NM_181435.5;C1QTNF3,missense_variant,p.Trp219Cys,ENST00000231338,NM_030945.3;C1QTNF3,downstream_gene_variant,,ENST00000513065,;C1QTNF3-AMACR,missense_variant,p.Trp203Cys,ENST00000382079,;C1QTNF3,non_coding_transcript_exon_variant,,ENST00000508398,;C1QTNF3,non_coding_transcript_exon_variant,,ENST00000513471,; G ENST00000382065 Transcript missense_variant 1583/2802 876/960 292/319 W/C tgG/tgC 1 -1 C1QTNF3 HGNC HGNC:14326 protein_coding YES CCDS34141.1 ENSP00000371497 Q9BXJ4 UPI0000052243 NM_181435.5 deleterious(0) 6/6 PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF54,hmmpanther:PTHR22923,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842,Prints_domain:PR00007 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 34 34020667 34020667 C G 1 0 0 0 0 1 0 0 0 1942 740 26 4 4 C1QTNF3 5 34020667 Missense_Mutation SNP C C3L-02365_T 18092585 34020667 147517592 97 9069 NIPBL 0 . GRCh38 5 37000847 37000847 + Missense_Mutation SNP A A T rs772932503 C3L-02365_T C3L-02365_N A A c.3533A>T p.Gln1178Leu p.Q1178L ENST00000282516 13/47 570 475 95 283 283 0 strelka-varscan-mutect NIPBL,missense_variant,p.Gln1178Leu,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Gln1178Leu,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,downstream_gene_variant,,ENST00000504430,;NIPBL,downstream_gene_variant,,ENST00000503274,;NIPBL,downstream_gene_variant,,ENST00000509429,; T ENST00000282516 Transcript missense_variant 4032/10435 3533/8415 1178/2804 Q/L cAg/cTg rs772932503 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated(0.11) 13/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs772932503 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 37000847 37000847 A T 1 0 0 0 0 1 0 0 0 10463 188 7 4 4 NIPBL 5 37000847 Missense_Mutation SNP A C3L-02365_T 2980180 37000847 144537412 98 9070 NIPBL 0 . GRCh38 5 37058945 37058945 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.7465G>C p.Glu2489Gln p.E2489Q ENST00000282516 44/47 388 351 37 228 228 0 strelka-varscan-mutect NIPBL,missense_variant,p.Glu2489Gln,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Glu2489Gln,ENST00000448238,NM_015384.4;NIPBL,missense_variant,p.Glu15Gln,ENST00000513819,;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000514335,; C ENST00000282516 Transcript missense_variant 7964/10435 7465/8415 2489/2804 E/Q Gag/Cag 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated(0.5) 44/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 37058945 37058945 G C 1 0 0 0 0 1 0 0 0 10463 1291 45 4 4 NIPBL 5 37058945 Missense_Mutation SNP G C3L-02365_T 58098 37058945 144479314 99 9071 ANXA2R 0 . GRCh38 5 43039490 43039490 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.557G>C p.Arg186Pro p.R186P ENST00000314890 2/2 90 39 51 32 32 0 strelka-varscan-mutect ANXA2R,missense_variant,p.Arg186Pro,ENST00000314890,;ANXA2R,missense_variant,p.Arg186Pro,ENST00000616064,NM_001014279.2;CTD-2035E11.4,downstream_gene_variant,,ENST00000607830,;CTD-2201E18.3,intron_variant,,ENST00000503152,;AC025171.1,upstream_gene_variant,,ENST00000451894,;AC025171.1,upstream_gene_variant,,ENST00000505541,;AC025171.1,upstream_gene_variant,,ENST00000399543,;AC025171.1,upstream_gene_variant,,ENST00000508913,;AC025171.1,upstream_gene_variant,,ENST00000515108,; G ENST00000314890 Transcript missense_variant 1977/2234 557/582 186/193 R/P cGg/cCg 1 -1 ANXA2R HGNC HGNC:33463 protein_coding YES CCDS34153.1 ENSP00000315915 Q3ZCQ2 UPI0000072CD4 tolerated(0.34) 2/2 Pfam_domain:PF15721,hmmpanther:PTHR38820 MODERATE SNV 3 1 PASS rs1252874440 . 0 200 9 0 0 0 0 0 -20 0.9999995 1 1 1 0 G 3 3 34 43039490 43039490 C G 1 0 0 0 0 1 0 0 0 826 652 23 4 4 ANXA2R 5 43039490 Missense_Mutation SNP C C3L-02365_T 5980545 43039490 138498769 100 9072 HCN1 0 . GRCh38 5 45262468 45262468 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.2126A>T p.Gln709Leu p.Q709L ENST00000303230 8/8 318 292 26 147 147 0 strelka-varscan-mutect HCN1,missense_variant,p.Gln709Leu,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; A ENST00000303230 Transcript missense_variant 2367/9885 2126/2673 709/890 Q/L cAg/cTg 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 deleterious_low_confidence(0.01) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 34 45262468 45262468 T A 1 0 0 0 0 1 0 0 0 6883 1580 55 4 4 HCN1 5 45262468 Missense_Mutation SNP T C3L-02365_T 2222978 45262468 136275791 101 9073 SV2C 0 . GRCh38 5 76291836 76291836 + Silent SNP T T A novel C3L-02365_T C3L-02365_N T T c.1317T>A p.= p.V439V ENST00000502798 8/13 105 93 12 170 170 0 strelka-varscan-mutect SV2C,synonymous_variant,p.=,ENST00000502798,NM_014979.3;SV2C,synonymous_variant,p.=,ENST00000322285,NM_001297716.1;RP11-466P24.6,intron_variant,,ENST00000502589,;SV2C,non_coding_transcript_exon_variant,,ENST00000506257,; A ENST00000502798 Transcript synonymous_variant 1759/11035 1317/2184 439/727 V gtT/gtA 1 1 SV2C HGNC HGNC:30670 protein_coding YES CCDS43331.1 ENSP00000423541 Q496J9 UPI000011DDBB NM_014979.3 8/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23511:SF6,hmmpanther:PTHR23511,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR01299,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 76291836 76291836 T A 1 0 0 0 0 0 0 0 1 15803 1828 64 4 4 SV2C 5 76291836 Silent SNP T C3L-02365_T 31029368 76291836 105246423 102 9074 ACOT12 0 . GRCh38 5 81345967 81345967 + Missense_Mutation SNP C C G C3L-02365_T C3L-02365_N C C c.691G>C p.Asp231His p.D231H ENST00000307624 7/15 257 225 32 327 327 0 strelka-varscan-mutect ACOT12,missense_variant,p.Asp231His,ENST00000307624,NM_130767.2;ACOT12,upstream_gene_variant,,ENST00000508234,; G ENST00000307624 Transcript missense_variant 720/2086 691/1668 231/555 D/H Gat/Cat COSM1671735 1 -1 ACOT12 HGNC HGNC:24436 protein_coding YES CCDS4055.1 ENSP00000303246 Q8WYK0 UPI0000126D7B NM_130767.2 deleterious(0) 7/15 Gene3D:3.10.129.10,Pfam_domain:PF03061,PROSITE_profiles:PS51770,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF3,Superfamily_domains:SSF54637 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 81345967 81345967 C G 1 0 0 0 0 1 0 0 0 192 913 32 4 4 ACOT12 5 81345967 Missense_Mutation SNP C C3L-02365_T 5054131 81345967 100192292 103 9075 34 2 ACOT12 0 . GRCh38 5 81345969 81345969 + Missense_Mutation SNP A A T rs746428835 C3L-02365_T C3L-02365_N A A c.689T>A p.Val230Glu p.V230E ENST00000307624 7/15 254 222 32 321 320 1 strelka-varscan-mutect ACOT12,missense_variant,p.Val230Glu,ENST00000307624,NM_130767.2;ACOT12,upstream_gene_variant,,ENST00000508234,; T ENST00000307624 Transcript missense_variant 718/2086 689/1668 230/555 V/E gTa/gAa rs746428835 1 -1 ACOT12 HGNC HGNC:24436 protein_coding YES CCDS4055.1 ENSP00000303246 Q8WYK0 UPI0000126D7B NM_130767.2 deleterious(0) 7/15 Gene3D:3.10.129.10,Pfam_domain:PF03061,PROSITE_profiles:PS51770,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF3,Superfamily_domains:SSF54637 MODERATE 1 SNV 1 1 PASS rs746428835 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 81345969 81345969 A T 1 0 0 0 0 1 0 0 0 192 391 14 4 4 ACOT12 5 81345969 Missense_Mutation SNP A C3L-02365_T 2 81345969 100192290 104 9076 34 2 VCAN 0 . GRCh38 5 83537024 83537024 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.4021A>G p.Ser1341Gly p.S1341G ENST00000265077 8/15 51 29 22 72 72 0 strelka-varscan-mutect VCAN,missense_variant,p.Ser1341Gly,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Ser354Gly,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Ser354Gly,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,non_coding_transcript_exon_variant,,ENST00000515397,; G ENST00000265077 Transcript missense_variant 4586/12625 4021/10191 1341/3396 S/G Agt/Ggt 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.09) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 83537024 83537024 A G 1 0 0 0 0 1 0 0 0 17683 304 11 5 5 VCAN 5 83537024 Missense_Mutation SNP A C3L-02365_T 2191055 83537024 98001235 105 9077 VCAN 0 . GRCh38 5 83537934 83537934 + Frame_Shift_Del DEL A A - novel C3L-02365_T C3L-02365_N A A c.4932delA p.Ala1645GlnfsTer12 p.A1645Qfs*12 ENST00000265077 8/15 209 138 71 336 336 0 sindel-varindel VCAN,frameshift_variant,p.Ala1645GlnfsTer12,ENST00000265077,NM_004385.4;VCAN,frameshift_variant,p.Ala658GlnfsTer12,ENST00000343200,NM_001164097.1;VCAN,frameshift_variant,p.Ala658GlnfsTer12,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; - ENST00000265077 Transcript frameshift_variant 5496/12625 4931/10191 1644/3396 E/X gAa/ga 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 83537934 83537934 A - 1 0 1 0 1 0 0 0 0 17683 246 9 0 0 VCAN 5 83537934 Frame_Shift_Del DEL A C3L-02365_T 910 83537934 98000325 106 9078 EDIL3 0 . GRCh38 5 83943424 83943424 + Nonsense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.1438G>T p.Glu480Ter p.E480* ENST00000296591 11/11 357 307 50 462 460 2 strelka-varscan-mutect EDIL3,stop_gained,p.Glu480Ter,ENST00000296591,NM_005711.4;EDIL3,stop_gained,p.Glu470Ter,ENST00000380138,NM_001278642.1; A ENST00000296591 Transcript stop_gained 1857/4727 1438/1443 480/480 E/* Gaa/Taa COSM1721861 1 -1 EDIL3 HGNC HGNC:3173 protein_coding YES CCDS4062.1 ENSP00000296591 O43854 UPI000004D126 NM_005711.4 11/11 hmmpanther:PTHR10127:SF29,hmmpanther:PTHR10127 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 83943424 83943424 C A 1 0 0 0 0 0 1 0 0 4743 864 30 2 2 EDIL3 5 83943424 Nonsense_Mutation SNP C C3L-02365_T 405490 83943424 97594835 107 9079 EDIL3 0 . GRCh38 5 84064735 84064735 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.917C>T p.Thr306Ile p.T306I ENST00000296591 8/11 105 69 36 124 124 0 strelka-varscan-mutect EDIL3,missense_variant,p.Thr306Ile,ENST00000296591,NM_005711.4;EDIL3,missense_variant,p.Thr296Ile,ENST00000380138,NM_001278642.1;EDIL3,non_coding_transcript_exon_variant,,ENST00000510271,; A ENST00000296591 Transcript missense_variant 1336/4727 917/1443 306/480 T/I aCt/aTt 1 -1 EDIL3 HGNC HGNC:3173 protein_coding YES CCDS4062.1 ENSP00000296591 O43854 UPI000004D126 NM_005711.4 deleterious(0) 8/11 PROSITE_profiles:PS50022,hmmpanther:PTHR10127:SF29,hmmpanther:PTHR10127,PROSITE_patterns:PS01286,Pfam_domain:PF00754,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 84064735 84064735 G A 1 0 0 0 0 1 0 0 0 4743 1029 36 3 3 EDIL3 5 84064735 Missense_Mutation SNP G C3L-02365_T 121311 84064735 97473524 108 9080 COX7C 0 . GRCh38 5 86620672 86620672 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.170G>A p.= p.*57* ENST00000515763 3/3 62 53 9 108 108 0 strelka-varscan-mutect COX7C,stop_retained_variant,p.=,ENST00000515763,;COX7C,3_prime_UTR_variant,,ENST00000509578,;COX7C,3_prime_UTR_variant,,ENST00000247655,NM_001867.2;COX7C,downstream_gene_variant,,ENST00000637229,;COX7C,non_coding_transcript_exon_variant,,ENST00000513124,;COX7C,non_coding_transcript_exon_variant,,ENST00000510447,;COX7C,non_coding_transcript_exon_variant,,ENST00000505430,;COX7C,non_coding_transcript_exon_variant,,ENST00000511472,; A ENST00000515763 Transcript stop_retained_variant 253/347 170/171 57/56 * tGa/tAa 1 1 COX7C HGNC HGNC:2292 protein_coding ENSP00000422012 D6R9Z7 UPI0000E1FF53 3/3 LOW SNV 4 1 PASS . . 0 204 4 2 0 0 0 0 -16.20617 0.9999818 1 1 1 0 A 2 1 34 86620672 86620672 G A 1 0 0 0 0 0 0 0 1 3579 1304 45 3 3 COX7C 5 86620672 Silent SNP G C3L-02365_T 2555937 86620672 94917587 109 9081 NR2F1 0 . GRCh38 5 93585034 93585034 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.11T>G p.Val4Gly p.V4G ENST00000327111 1/3 23 9 14 19 19 0 strelka-mutect NR2F1,missense_variant,p.Val4Gly,ENST00000327111,NM_005654.5;NR2F1,missense_variant,p.Val4Gly,ENST00000615873,;NR2F1-AS1,intron_variant,,ENST00000513055,;NR2F1-AS1,upstream_gene_variant,,ENST00000504474,;NR2F1-AS1,upstream_gene_variant,,ENST00000606696,;NR2F1-AS1,upstream_gene_variant,,ENST00000606233,;NR2F1-AS1,upstream_gene_variant,,ENST00000503134,;NR2F1-AS1,upstream_gene_variant,,ENST00000507963,;NR2F1-AS1,upstream_gene_variant,,ENST00000510254,;NR2F1,upstream_gene_variant,,ENST00000502982,;NR2F1,upstream_gene_variant,,ENST00000512697,; G ENST00000327111 Transcript missense_variant 1698/3732 11/1272 4/423 V/G gTa/gGa 1 1 NR2F1 HGNC HGNC:7975 protein_coding YES CCDS4068.1 ENSP00000325819 P10589 UPI0000000C58 NM_005654.5 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF46 MODERATE 1 SNV 1 1 PASS . . 7 201 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 93585034 93585034 T G 1 0 0 0 0 1 0 0 0 10683 1638 57 5 5 NR2F1 5 93585034 Missense_Mutation SNP T C3L-02365_T 6964362 93585034 87953225 110 9082 KCNN2 0 . GRCh38 5 114496095 114496095 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.1653C>T p.= p.V551V ENST00000512097 9/9 299 258 41 361 361 0 strelka-varscan-mutect KCNN2,synonymous_variant,p.=,ENST00000512097,;KCNN2,synonymous_variant,p.=,ENST00000264773,NM_021614.3;KCNN2,synonymous_variant,p.=,ENST00000631899,;KCNN2,synonymous_variant,p.=,ENST00000610748,NM_001278204.1;KCNN2,synonymous_variant,p.=,ENST00000503706,NM_170775.2;RP11-492A10.1,splice_region_variant,,ENST00000514115,;KCNN2,downstream_gene_variant,,ENST00000507750,;KCNN2,downstream_gene_variant,,ENST00000505491,;KCNN2,downstream_gene_variant,,ENST00000506812,;KCNN2,downstream_gene_variant,,ENST00000632892,; T ENST00000512097 Transcript synonymous_variant 2671/3076 1653/1740 551/579 V gtC/gtT 1 1 KCNN2 HGNC HGNC:6291 protein_coding YES CCDS4114.1 ENSP00000427120 Q9H2S1 UPI000013D56A 9/9 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF43 LOW 1 SNV 5 1 PASS rs1455162701 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 114496095 114496095 C T 1 0 0 0 0 0 0 0 1 7995 813 29 3 3 KCNN2 5 114496095 Silent SNP C C3L-02365_T 20911061 114496095 67042164 111 9083 SLC4A9 0 . GRCh38 5 140371131 140371131 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.2536T>C p.Tyr846His p.Y846H ENST00000507527 18/22 171 99 72 192 192 0 strelka-varscan-mutect SLC4A9,missense_variant,p.Tyr822His,ENST00000506757,NM_031467.2;SLC4A9,missense_variant,p.Tyr846His,ENST00000507527,NM_001258428.1;SLC4A9,missense_variant,p.Tyr808His,ENST00000432095,NM_001258426.1;SLC4A9,missense_variant,p.Tyr759His,ENST00000506545,NM_001258427.1;CTC-329D1.2,non_coding_transcript_exon_variant,,ENST00000507521,;SLC4A9,upstream_gene_variant,,ENST00000504742,;SLC4A9,downstream_gene_variant,,ENST00000514849,; C ENST00000507527 Transcript missense_variant 2558/3258 2536/2952 846/983 Y/H Tat/Cat 1 1 SLC4A9 HGNC HGNC:11035 protein_coding YES CCDS58973.1 ENSP00000427661 Q96Q91 UPI000018336F NM_001258428.1 tolerated(0.11) 18/22 Transmembrane_helices:TMhelix,hmmpanther:PTHR11453:SF52,hmmpanther:PTHR11453,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 140371131 140371131 T C 1 0 0 0 0 1 0 0 0 14937 1638 57 5 5 SLC4A9 5 140371131 Missense_Mutation SNP T C3L-02365_T 25875036 140371131 41167128 112 9084 PCDHA2 0 . GRCh38 5 140795947 140795947 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.983C>T p.Pro328Leu p.P328L ENST00000526136 1/4 223 173 50 255 255 0 strelka-varscan-mutect PCDHA2,missense_variant,p.Pro328Leu,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Pro328Leu,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Pro328Leu,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; T ENST00000526136 Transcript missense_variant 983/5254 983/2847 328/948 P/L cCt/cTt 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 tolerated_low_confidence(0.28) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 140795947 140795947 C T 1 0 0 0 0 1 0 0 0 11611 681 24 3 3 PCDHA2 5 140795947 Missense_Mutation SNP C C3L-02365_T 424816 140795947 40742312 113 9085 PCDHA5 0 . GRCh38 5 140822827 140822827 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.1052T>A p.Ile351Lys p.I351K ENST00000529859 1/4 168 99 69 215 215 0 strelka-varscan-mutect PCDHA5,missense_variant,p.Ile351Lys,ENST00000529859,NM_018908.2;PCDHA5,missense_variant,p.Ile351Lys,ENST00000614258,NM_031501.1;PCDHA5,missense_variant,p.Ile351Lys,ENST00000529619,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA4,intron_variant,,ENST00000512229,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,upstream_gene_variant,,ENST00000624712,; A ENST00000529859 Transcript missense_variant 1052/5218 1052/2811 351/936 I/K aTa/aAa 1 1 PCDHA5 HGNC HGNC:8671 protein_coding YES CCDS54917.1 ENSP00000436557 Q9Y5H7 UPI00001273CD NM_018908.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 140822827 140822827 T A 1 0 0 0 0 1 0 0 0 11614 1406 49 4 4 PCDHA5 5 140822827 Missense_Mutation SNP T C3L-02365_T 26880 140822827 40715432 114 9086 PCDHGA3 0 . GRCh38 5 141344286 141344286 + Missense_Mutation SNP G G T rs776109013 C3L-02365_T C3L-02365_N G G c.253G>T p.Val85Phe p.V85F ENST00000253812 1/4 186 161 25 205 205 0 strelka-varscan-mutect PCDHGA3,missense_variant,p.Val85Phe,ENST00000253812,NM_018916.3;PCDHGA3,missense_variant,p.Val85Phe,ENST00000619750,NM_032011.1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA2,downstream_gene_variant,,ENST00000528330,NM_032009.2;PCDHGA3,missense_variant,p.Val85Phe,ENST00000612467,; T ENST00000253812 Transcript missense_variant 419/4771 253/2799 85/932 V/F Gtc/Ttc rs776109013 1 1 PCDHGA3 HGNC HGNC:8701 protein_coding YES CCDS47290.1 ENSP00000253812 Q9Y5H0 UPI0000161C1A NM_018916.3 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs776109013 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 141344286 141344286 G T 1 0 0 0 0 1 0 0 0 11642 1261 44 2 2 PCDHGA3 5 141344286 Missense_Mutation SNP G C3L-02365_T 521459 141344286 40193973 115 9087 PCDHGA5 0 . GRCh38 5 141366419 141366419 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.2089G>T p.Val697Leu p.V697L ENST00000518069 1/4 215 128 87 276 276 0 strelka-varscan-mutect PCDHGA5,missense_variant,p.Val697Leu,ENST00000518069,NM_018918.2;PCDHGA5,missense_variant,p.Val697Leu,ENST00000611914,NM_032054.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,upstream_gene_variant,,ENST00000576222,NM_018924.4;PCDHGB2,downstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGB3,upstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000518069 Transcript missense_variant 2089/4602 2089/2796 697/931 V/L Gtg/Ttg 1 1 PCDHGA5 HGNC HGNC:8703 protein_coding YES CCDS54925.1 ENSP00000429834 Q9Y5G8 UPI000006CD9F NM_018918.2 deleterious_low_confidence(0.02) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF105,Pfam_domain:PF16492,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 141366419 141366419 G T 1 0 0 0 0 1 0 0 0 11644 1029 36 2 2 PCDHGA5 5 141366419 Missense_Mutation SNP G C3L-02365_T 22133 141366419 40171840 116 9088 SLIT3 0 . GRCh38 5 168762541 168762541 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1608C>A p.Asp536Glu p.D536E ENST00000332966 15/36 97 76 21 103 103 0 strelka-varscan-mutect SLIT3,missense_variant,p.Asp536Glu,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Asp399Glu,ENST00000404867,;SLIT3,missense_variant,p.Asp536Glu,ENST00000332966,NM_001271946.1;SLIT3,splice_region_variant,,ENST00000519486,; T ENST00000332966 Transcript missense_variant,splice_region_variant 1681/4895 1608/4593 536/1530 D/E gaC/gaA 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 tolerated(1) 15/36 SMART_domains:SM00013,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 168762541 168762541 G T 1 0 0 0 0 1 0 0 0 15032 1275 44 2 2 SLIT3 5 168762541 Missense_Mutation SNP G C3L-02365_T 27396122 168762541 12775718 117 9089 NSD1 0 . GRCh38 5 177238452 177238452 + Silent SNP G G T rs770482812 C3L-02365_T C3L-02365_N G G c.4137G>T p.= p.P1379P ENST00000439151 7/23 166 106 60 224 224 0 strelka-varscan-mutect NSD1,synonymous_variant,p.=,ENST00000439151,NM_022455.4;NSD1,synonymous_variant,p.=,ENST00000354179,NM_172349.2;NSD1,synonymous_variant,p.=,ENST00000347982,;NSD1,intron_variant,,ENST00000375350,; T ENST00000439151 Transcript synonymous_variant 4182/12892 4137/8091 1379/2696 P ccG/ccT rs770482812 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 7/23 LOW 1 SNV 1 1 PASS rs770482812 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 177238452 177238452 G T 1 0 0 0 0 0 0 0 1 10728 1103 39 1 1 NSD1 5 177238452 Silent SNP G C3L-02365_T 8475911 177238452 4299807 118 9090 JARID2 0 . GRCh38 6 15374224 15374224 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.153C>T p.= p.G51G ENST00000341776 2/18 218 205 13 214 214 0 strelka-varscan-mutect JARID2,synonymous_variant,p.=,ENST00000341776,NM_004973.3;JARID2,5_prime_UTR_variant,,ENST00000397311,NM_001267040.1; T ENST00000341776 Transcript synonymous_variant 397/5755 153/3741 51/1246 G ggC/ggT 1 1 JARID2 HGNC HGNC:6196 protein_coding YES CCDS4533.1 ENSP00000341280 Q92833 UPI0000161C67 NM_004973.3 2/18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 15374224 15374224 C T 1 0 0 0 0 0 0 0 1 7859 697 25 3 3 JARID2 6 15374224 Silent SNP C C3L-02365_T 15374224 155431755 119 9091 TRIM15 0 . GRCh38 6 30172185 30172185 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1234C>A p.Pro412Thr p.P412T ENST00000376694 7/7 255 122 133 177 177 0 strelka-varscan-mutect TRIM15,missense_variant,p.Pro343Thr,ENST00000619857,;TRIM15,missense_variant,p.Pro412Thr,ENST00000376694,NM_033229.2;TRIM15,intron_variant,,ENST00000376688,;TRIM15,downstream_gene_variant,,ENST00000433744,;TRIM15,downstream_gene_variant,,ENST00000477944,; A ENST00000376694 Transcript missense_variant 1703/2214 1234/1398 412/465 P/T Ccg/Acg 1 1 TRIM15 HGNC HGNC:16284 protein_coding YES CCDS4677.1 ENSP00000365884 Q9C019 Q5SRL0 UPI0000137066 NM_033229.2 deleterious(0) 7/7 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF259,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 30172185 30172185 C A 1 0 0 0 0 1 0 0 0 16979 623 22 2 2 TRIM15 6 30172185 Missense_Mutation SNP C C3L-02365_T 14797961 30172185 140633794 120 9092 DHX16 0 . GRCh38 6 30656709 30656709 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.2199G>A p.= p.K733K ENST00000376442 14/20 258 208 50 254 254 0 strelka-varscan-mutect DHX16,synonymous_variant,p.=,ENST00000376442,NM_003587.4,NM_001164239.1;DHX16,synonymous_variant,p.=,ENST00000376437,;C6orf136,downstream_gene_variant,,ENST00000293604,NM_001161376.1;C6orf136,downstream_gene_variant,,ENST00000446773,;C6orf136,downstream_gene_variant,,ENST00000376473,NM_001109938.2;C6orf136,downstream_gene_variant,,ENST00000465699,;C6orf136,downstream_gene_variant,,ENST00000376471,NM_145029.3;C6orf136,downstream_gene_variant,,ENST00000467801,;C6orf136,downstream_gene_variant,,ENST00000468785,;DHX16,downstream_gene_variant,,ENST00000480966,;C6orf136,downstream_gene_variant,,ENST00000488383,;C6orf136,downstream_gene_variant,,ENST00000487873,;C6orf136,downstream_gene_variant,,ENST00000463794,;C6orf136,downstream_gene_variant,,ENST00000460172,; T ENST00000376442 Transcript synonymous_variant 2395/3445 2199/3126 733/1041 K aaG/aaA 1 -1 DHX16 HGNC HGNC:2739 protein_coding YES CCDS4685.1 ENSP00000365625 O60231 Q5SQH4 UPI000000D73D NM_003587.4,NM_001164239.1 14/20 PROSITE_profiles:PS51194,hmmpanther:PTHR18934:SF83,hmmpanther:PTHR18934,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 30656709 30656709 C T 1 0 0 0 0 0 0 0 1 4306 564 20 3 3 DHX16 6 30656709 Silent SNP C C3L-02365_T 484524 30656709 140149270 121 9093 TNF 0 . GRCh38 6 31577294 31577294 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.459C>A p.= p.T153T ENST00000449264 4/4 412 213 199 299 299 0 strelka-varscan-mutect TNF,synonymous_variant,p.=,ENST00000449264,NM_000594.3;LTA,downstream_gene_variant,,ENST00000454783,NM_001159740.2;LTA,downstream_gene_variant,,ENST00000418386,NM_000595.3;LTB,downstream_gene_variant,,ENST00000429299,NM_002341.1;LTB,downstream_gene_variant,,ENST00000446745,NM_009588.1;LTB,downstream_gene_variant,,ENST00000483972,;LTA,downstream_gene_variant,,ENST00000471842,;LTB,downstream_gene_variant,,ENST00000482429,;LTA,downstream_gene_variant,,ENST00000489638,; A ENST00000449264 Transcript synonymous_variant 634/1676 459/702 153/233 T acC/acA 1 1 TNF HGNC HGNC:11892 protein_coding YES CCDS4702.1 ENSP00000398698 P01375 Q5STB3 UPI000000D745 NM_000594.3 4/4 PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF23,Gene3D:2.60.120.40,Pfam_domain:PF00229,SMART_domains:SM00207,Superfamily_domains:SSF49842,Prints_domain:PR01234 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 31577294 31577294 C A 1 0 0 0 0 0 0 0 1 16745 610 22 2 2 TNF 6 31577294 Silent SNP C C3L-02365_T 920585 31577294 139228685 122 9094 VPS52 0 . GRCh38 6 33271639 33271639 + Nonsense_Mutation SNP C C A rs753567778 C3L-02365_T C3L-02365_N C C c.37G>T p.Glu13Ter p.E13* ENST00000445902 1/20 156 78 78 136 135 1 strelka-varscan-mutect VPS52,stop_gained,p.Glu13Ter,ENST00000482399,;VPS52,stop_gained,p.Glu13Ter,ENST00000445902,NM_001289175.1,NM_001289174.1,NM_022553.5;RPS18,upstream_gene_variant,,ENST00000439602,NM_022551.2;RPS18,upstream_gene_variant,,ENST00000474973,;VPS52,intron_variant,,ENST00000478934,;VPS52,intron_variant,,ENST00000464425,;VPS52,intron_variant,,ENST00000463486,;RPS18,upstream_gene_variant,,ENST00000476222,;RPS18,upstream_gene_variant,,ENST00000472218,;RPS18,upstream_gene_variant,,ENST00000490191,;VPS52,upstream_gene_variant,,ENST00000493379,;RPS18,upstream_gene_variant,,ENST00000496813,;RPS18,upstream_gene_variant,,ENST00000474626,;VPS52,upstream_gene_variant,,ENST00000495755,;RPS18,upstream_gene_variant,,ENST00000479802,; A ENST00000445902 Transcript stop_gained 256/2960 37/2172 13/723 E/* Gaa/Taa rs753567778 1 -1 VPS52 HGNC HGNC:10518 protein_coding YES CCDS4770.2 ENSP00000409952 Q8N1B4 Q4VXZ2 UPI000006E468 NM_001289175.1,NM_001289174.1,NM_022553.5 1/20 hmmpanther:PTHR14190 HIGH 1 SNV 1 1 PASS rs753567778 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 33271639 33271639 C A 1 0 0 0 0 0 1 0 0 17762 864 30 2 2 VPS52 6 33271639 Nonsense_Mutation SNP C C3L-02365_T 1694345 33271639 137534340 123 9095 PKHD1 0 . GRCh38 6 52025199 52025200 + Frame_Shift_Ins INS - - A novel C3L-02365_T C3L-02365_N - - c.4610dupT p.Cys1538ValfsTer27 p.C1538Vfs*27 ENST00000371117 32/67 433 227 206 469 469 0 sindel-varindel-pindel PKHD1,frameshift_variant,p.Cys1538ValfsTer27,ENST00000371117,NM_138694.3;PKHD1,frameshift_variant,p.Cys1538ValfsTer27,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript frameshift_variant 4886-4887/16282 4610-4611/12225 1537/4074 V/VX gtg/gtTg 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 32/67 Gene3D:2.60.40.10,Pfam_domain:PF01833 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 34 52025199 52025199 - A 1 0 1 1 0 0 0 0 0 12067 465 17 0 0 PKHD1 6 52025199 Frame_Shift_Ins INS - C3L-02365_T 18753560 52025199 118780780 124 9096 DDX43 0 . GRCh38 6 73395092 73395092 + Missense_Mutation SNP G G A C3L-02365_T C3L-02365_N G G c.187G>A p.Ala63Thr p.A63T ENST00000370336 1/17 359 301 58 307 307 0 strelka-varscan-mutect DDX43,missense_variant,p.Ala63Thr,ENST00000370336,NM_018665.2;OOEP,5_prime_UTR_variant,,ENST00000370363,;OOEP,5_prime_UTR_variant,,ENST00000441145,;DDX43,non_coding_transcript_exon_variant,,ENST00000464221,;RPS6P8,upstream_gene_variant,,ENST00000421830,; A ENST00000370336 Transcript missense_variant 345/2513 187/1947 63/648 A/T Gct/Act COSM5550299 1 1 DDX43 HGNC HGNC:18677 protein_coding YES CCDS4977.1 ENSP00000359361 Q9NXZ2 UPI000013CA60 NM_018665.2 tolerated(0.28) 1/17 1 MODERATE 1 SNV 1 1 1 PASS rs1293536394 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 73395092 73395092 G A 1 0 0 0 0 1 0 0 0 4166 1101 38 1 1 DDX43 6 73395092 Missense_Mutation SNP G C3L-02365_T 21369893 73395092 97410887 125 9097 KLHL32 0 . GRCh38 6 97113976 97113976 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.821A>T p.Gln274Leu p.Q274L ENST00000369261 7/11 251 205 46 283 283 0 strelka-varscan-mutect KLHL32,missense_variant,p.Gln238Leu,ENST00000536676,NM_001286250.1;KLHL32,missense_variant,p.Gln274Leu,ENST00000369261,NM_001323260.1,NM_052904.3;KLHL32,missense_variant,p.Gln205Leu,ENST00000539200,NM_001286251.1;KLHL32,3_prime_UTR_variant,,ENST00000447886,;KLHL32,intron_variant,,ENST00000544166,;KLHL32,intron_variant,,ENST00000620278,NM_001286254.1;KLHL32,intron_variant,,ENST00000369254,; T ENST00000369261 Transcript missense_variant 1184/3698 821/1863 274/620 Q/L cAg/cTg 1 1 KLHL32 HGNC HGNC:21221 protein_coding YES CCDS5038.1 ENSP00000358265 Q96NJ5 UPI000020DFAB NM_001323260.1,NM_052904.3 deleterious(0) 7/11 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF65 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 97113976 97113976 A T 1 0 0 0 0 1 0 0 0 8251 188 7 4 4 KLHL32 6 97113976 Missense_Mutation SNP A C3L-02365_T 23718884 97113976 73692003 126 9098 BEND3 0 . GRCh38 6 107069628 107069628 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.1563G>T p.= p.R521R ENST00000429433 5/5 286 202 84 269 269 0 strelka-varscan-mutect BEND3,synonymous_variant,p.=,ENST00000429433,NM_001080450.2;BEND3,synonymous_variant,p.=,ENST00000369042,; A ENST00000429433 Transcript synonymous_variant 2213/6654 1563/2487 521/828 R cgG/cgT 1 -1 BEND3 HGNC HGNC:23040 protein_coding YES CCDS34507.1 ENSP00000411268 Q5T5X7 UPI00001D80D7 NM_001080450.2 5/5 hmmpanther:PTHR28665 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 107069628 107069628 C A 1 0 0 0 0 0 0 0 1 1547 726 26 2 2 BEND3 6 107069628 Silent SNP C C3L-02365_T 9955652 107069628 63736351 127 9099 SOBP 0 . GRCh38 6 107634041 107634041 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1197G>T p.Met399Ile p.M399I ENST00000317357 6/7 77 42 35 98 98 0 strelka-varscan-mutect SOBP,missense_variant,p.Met399Ile,ENST00000317357,NM_018013.3;SOBP,upstream_gene_variant,,ENST00000494935,; T ENST00000317357 Transcript missense_variant 1856/5245 1197/2622 399/873 M/I atG/atT 1 1 SOBP HGNC HGNC:29256 protein_coding YES CCDS43488.1 ENSP00000318900 A7XYQ1 UPI0000E6A8ED NM_018013.3 deleterious(0.01) 6/7 hmmpanther:PTHR23186:SF2,hmmpanther:PTHR23186,Pfam_domain:PF15279 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 107634041 107634041 G T 1 0 0 0 0 1 0 0 0 15233 1348 47 2 2 SOBP 6 107634041 Missense_Mutation SNP G C3L-02365_T 564413 107634041 63171938 128 9100 SNX3 0 . GRCh38 6 108214583 108214583 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.298C>A p.Gln100Lys p.Q100K ENST00000230085 3/4 185 144 41 228 228 0 strelka-varscan-mutect SNX3,missense_variant,p.Gln100Lys,ENST00000230085,NM_003795.5;SNX3,missense_variant,p.Gln68Lys,ENST00000426155,NM_152827.3;SNX3,missense_variant,p.Gln78Lys,ENST00000349379,NM_001300929.1;SNX3,3_prime_UTR_variant,,ENST00000368979,; T ENST00000230085 Transcript missense_variant 637/1755 298/489 100/162 Q/K Cag/Aag 1 -1 SNX3 HGNC HGNC:11174 protein_coding YES CCDS5064.1 ENSP00000230085 O60493 UPI00000013A7 NM_003795.5 tolerated(0.37) 3/4 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF145,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 108214583 108214583 G T 1 0 0 0 0 1 0 0 0 15220 1299 45 2 2 SNX3 6 108214583 Missense_Mutation SNP G C3L-02365_T 580542 108214583 62591396 129 9101 KPNA5 0 . GRCh38 6 116692154 116692154 + Nonsense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.238G>T p.Glu80Ter p.E80* ENST00000368564 3/14 151 126 25 202 201 1 strelka-varscan-mutect KPNA5,stop_gained,p.Glu80Ter,ENST00000368564,;KPNA5,stop_gained,p.Glu80Ter,ENST00000356348,NM_002269.2;KPNA5,stop_gained,p.Glu77Ter,ENST00000413340,; T ENST00000368564 Transcript stop_gained,splice_region_variant 386/11311 238/1620 80/539 E/* Gag/Tag 1 1 KPNA5 HGNC HGNC:6398 protein_coding YES CCDS5111.1 ENSP00000357552 O15131 UPI000000DBE6 3/14 Gene3D:1.25.10.10,Pfam_domain:PF01749,PIRSF_domain:PIRSF005673,hmmpanther:PTHR23316,hmmpanther:PTHR23316:SF10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 34 116692154 116692154 G T 1 0 0 0 0 0 1 0 0 8313 956 33 2 2 KPNA5 6 116692154 Nonsense_Mutation SNP G C3L-02365_T 8477571 116692154 54113825 130 9102 GJA1 0 . GRCh38 6 121447240 121447240 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.393G>C p.Glu131Asp p.E131D ENST00000282561 2/2 621 519 102 637 637 0 strelka-varscan-mutect GJA1,missense_variant,p.Glu131Asp,ENST00000282561,NM_000165.4; C ENST00000282561 Transcript missense_variant 550/3037 393/1149 131/382 E/D gaG/gaC 1 1 GJA1 HGNC HGNC:4274 protein_coding YES CCDS5123.1 ENSP00000282561 P17302 UPI000013DCEC NM_000165.4 tolerated(0.43) 2/2 hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF33,Pfam_domain:PF00029,Gene3D:2zw3A00 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 121447240 121447240 G C 1 0 0 0 0 1 0 0 0 6280 933 33 4 4 GJA1 6 121447240 Missense_Mutation SNP G C3L-02365_T 4755086 121447240 49358739 131 9103 CTAGE9 0 . GRCh38 6 131710242 131710242 + Missense_Mutation SNP A A C novel C3L-02365_T C3L-02365_N A A c.776T>G p.Leu259Arg p.L259R ENST00000314099 1/1 206 172 34 264 263 1 strelka-varscan-mutect CTAGE9,missense_variant,p.Leu259Arg,ENST00000314099,NM_001145659.1;ENPP3,intron_variant,,ENST00000414305,;ENPP3,intron_variant,,ENST00000357639,NM_005021.3;ENPP3,intron_variant,,ENST00000358229,; C ENST00000314099 Transcript missense_variant 776/2334 776/2334 259/777 L/R cTg/cGg 1 -1 CTAGE9 HGNC HGNC:37275 protein_coding YES CCDS47475.1 ENSP00000395587 A4FU28 UPI0000073347 NM_001145659.1 deleterious(0) 1/1 hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 131710242 131710242 A C 1 0 0 0 0 1 0 0 0 3802 188 7 5 5 CTAGE9 6 131710242 Missense_Mutation SNP A C3L-02365_T 10263002 131710242 39095737 132 9104 ARFGEF3 0 . GRCh38 6 138311413 138311417 + Frame_Shift_Del DEL TGGAC TGGAC - novel C3L-02365_T C3L-02365_N TGGAC TGGAC c.4105_4109delGACTG p.Asp1369Ter p.D1369* ENST00000251691 25/34 159 118 41 149 149 0 sindel-varindel-pindel ARFGEF3,frameshift_variant,p.Asp1369Ter,ENST00000251691,NM_020340.4; - ENST00000251691 Transcript frameshift_variant 4269-4273/14877 4103-4107/6534 1368-1369/2177 VD/X gTGGAC/g 1 1 ARFGEF3 HGNC HGNC:21213 protein_coding YES CCDS5189.2 ENSP00000251691 Q5TH69 UPI000150AF4A NM_020340.4 25/34 HIGH 1 deletion 1 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 138311413 138311413 TGGAC - 1 0 1 0 1 0 0 0 0 977 1696 59 0 0 ARFGEF3 6 138311413 Frame_Shift_Del DEL TGGAC C3L-02365_T 6601171 138311413 32494566 133 9105 ESR1 0 . GRCh38 6 151944333 151944334 + Frame_Shift_Ins INS - - T novel C3L-02365_T C3L-02365_N - - c.923dupT p.Leu308PhefsTer16 p.L308Ffs*16 ENST00000440973 6/10 387 215 172 370 370 0 sindel-varindel-pindel ESR1,frameshift_variant,p.Leu308PhefsTer16,ENST00000440973,NM_001122742.1;ESR1,frameshift_variant,p.Leu308PhefsTer16,ENST00000206249,NM_001291230.1,NM_001122741.1,NM_001291241.1,NM_000125.3;ESR1,frameshift_variant,p.Leu308PhefsTer16,ENST00000443427,NM_001122740.1;ESR1,frameshift_variant,p.Leu135PhefsTer16,ENST00000427531,NM_001328100.1;ESR1,frameshift_variant,p.Leu308PhefsTer16,ENST00000338799,;ESR1,intron_variant,,ENST00000456483,;ESR1,intron_variant,,ENST00000406599,;ESR1,intron_variant,,ENST00000415488,;ESR1,non_coding_transcript_exon_variant,,ENST00000482101,; T ENST00000440973 Transcript frameshift_variant 1291-1292/6466 921-922/1788 307-308/595 -/X -/T 1 1 ESR1 HGNC HGNC:3467 protein_coding YES CCDS5234.1 ENSP00000405330 P03372 G4XH65 UPI000004A328 NM_001122742.1 6/10 hmmpanther:PTHR24084,PIRSF_domain:PIRSF500101,PIRSF_domain:PIRSF002527 HIGH 1 insertion 5 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 34 151944333 151944333 - T 1 0 1 1 0 0 0 0 0 5118 668 24 0 0 ESR1 6 151944333 Frame_Shift_Ins INS - C3L-02365_T 13632920 151944333 18861646 134 9106 SCAF8 0 . GRCh38 6 154787982 154787982 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.515G>A p.Ser172Asn p.S172N ENST00000417268 5/21 96 88 8 110 110 0 strelka-mutect SCAF8,missense_variant,p.Ser94Asn,ENST00000367178,NM_001286199.1,NM_014892.4;SCAF8,missense_variant,p.Ser172Asn,ENST00000417268,NM_001286188.1,NM_001286194.1;SCAF8,missense_variant,p.Ser160Asn,ENST00000367186,NM_001286189.1;SCAF8,non_coding_transcript_exon_variant,,ENST00000461219,;SCAF8,non_coding_transcript_exon_variant,,ENST00000464628,; A ENST00000417268 Transcript missense_variant 560/4944 515/4050 172/1349 S/N aGc/aAc 1 1 SCAF8 HGNC HGNC:20959 protein_coding YES CCDS75541.1 ENSP00000413098 A0A0A0MT33 UPI0003BD245C NM_001286188.1,NM_001286194.1 tolerated(0.43) 5/21 Gene3D:1.25.40.90,Pfam_domain:PF04818,PROSITE_profiles:PS51391,SMART_domains:SM00582,Superfamily_domains:SSF48464 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 154787982 154787982 G A 1 0 0 0 0 1 0 0 0 14135 971 34 3 3 SCAF8 6 154787982 Missense_Mutation SNP G C3L-02365_T 2843649 154787982 16017997 135 9107 FNDC1 0 . GRCh38 6 159266149 159266149 + Silent SNP C C A rs180849332 C3L-02365_T C3L-02365_N C C c.5350C>A p.= p.R1784R ENST00000297267 21/23 226 147 79 263 263 0 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,synonymous_variant,p.=,ENST00000329629,; A ENST00000297267 Transcript synonymous_variant 5550/6552 5350/5685 1784/1894 R Cgg/Agg rs180849332 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 21/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 LOW 1 SNV 1 1 PASS rs180849332 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 159266149 159266149 C A 1 0 0 0 0 0 0 0 1 5824 527 19 1 1 FNDC1 6 159266149 Silent SNP C C3L-02365_T 4478167 159266149 11539830 136 9108 DLL1 0 . GRCh38 6 170285289 170285289 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.997G>T p.Asp333Tyr p.D333Y ENST00000366756 7/11 330 308 22 331 330 1 strelka-varscan-mutect DLL1,missense_variant,p.Asp333Tyr,ENST00000366756,NM_005618.3;DLL1,downstream_gene_variant,,ENST00000630500,; A ENST00000366756 Transcript missense_variant 1331/3174 997/2172 333/723 D/Y Gac/Tac 1 -1 DLL1 HGNC HGNC:2908 protein_coding YES CCDS5313.1 ENSP00000355718 O00548 UPI000004C656 NM_005618.3 deleterious(0) 7/11 Gene3D:2.10.25.10,PD936484,Pfam_domain:PF00008,Prints_domain:PR00010,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF283,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 170285289 170285289 C A 1 0 0 0 0 1 0 0 0 4373 826 29 2 2 DLL1 6 170285289 Missense_Mutation SNP C C3L-02365_T 11019140 170285289 520690 137 9109 ZNF853 0 . GRCh38 7 6622668 6622668 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.1677C>A p.His559Gln p.H559Q ENST00000457543 3/3 314 275 39 155 155 0 strelka-varscan-mutect ZNF853,missense_variant,p.His559Gln,ENST00000457543,NM_017560.1; A ENST00000457543 Transcript missense_variant 2235/3857 1677/1980 559/659 H/Q caC/caA COSM1451874,COSM1451875 1 1 ZNF853 HGNC HGNC:21767 protein_coding YES CCDS59048.1 ENSP00000455585 P0CG23 UPI00018E24EF NM_017560.1 deleterious_low_confidence(0) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 3 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 34 6622668 6622668 C A 1 0 0 0 0 1 0 0 0 18784 506 18 2 2 ZNF853 7 6622668 Missense_Mutation SNP C C3L-02365_T 6622668 152723305 138 9110 PHF14 0 . GRCh38 7 10990711 10990711 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.909G>A p.= p.L303L ENST00000403050 4/17 196 180 16 156 156 0 strelka-varscan-mutect PHF14,synonymous_variant,p.=,ENST00000403050,NM_014660.3;PHF14,synonymous_variant,p.=,ENST00000634607,;PHF14,non_coding_transcript_exon_variant,,ENST00000476009,;PHF14,missense_variant,p.Asp41Asn,ENST00000423760,;PHF14,missense_variant,p.Asp41Asn,ENST00000521747,;PHF14,non_coding_transcript_exon_variant,,ENST00000490957,; A ENST00000403050 Transcript synonymous_variant 1361/4276 909/2667 303/888 L ctG/ctA 1 1 PHF14 HGNC HGNC:22203 protein_coding YES CCDS47542.1 ENSP00000385795 O94880 UPI000020EB41 NM_014660.3 4/17 hmmpanther:PTHR13793 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 10990711 10990711 G A 1 0 0 0 0 0 0 0 1 11914 1277 45 3 3 PHF14 7 10990711 Silent SNP G C3L-02365_T 4368043 10990711 148355262 139 9111 HOXA10 0 . GRCh38 7 27173535 27173535 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.772T>A p.Ser258Thr p.S258T ENST00000283921 1/2 173 70 103 154 154 0 strelka-varscan-mutect HOXA10,missense_variant,p.Ser258Thr,ENST00000283921,NM_018951.3;HOXA10,missense_variant,p.Leu136His,ENST00000613671,;HOXA10,intron_variant,,ENST00000396344,;HOXA10-HOXA9,intron_variant,,ENST00000470747,;HOXA9,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,downstream_gene_variant,,ENST00000519935,;HOXA10-AS,downstream_gene_variant,,ENST00000523790,;HOXA10-AS,downstream_gene_variant,,ENST00000519694,;HOXA9,intron_variant,,ENST00000465941,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA10,upstream_gene_variant,,ENST00000521421,;HOXA10,upstream_gene_variant,,ENST00000524368,;HOXA10,upstream_gene_variant,,ENST00000519593,;HOXA9,upstream_gene_variant,,ENST00000487384,;HOXA9,upstream_gene_variant,,ENST00000489695,; T ENST00000283921 Transcript missense_variant 772/2541 772/1233 258/410 S/T Tcc/Acc 1 -1 HOXA10 HGNC HGNC:5100 protein_coding YES CCDS5410.2 ENSP00000283921 P31260 UPI0000EE42DA NM_018951.3 tolerated(0.19) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF52 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 27173535 27173535 A T 1 0 0 0 0 1 0 0 0 7183 304 11 4 4 HOXA10 7 27173535 Missense_Mutation SNP A C3L-02365_T 16182824 27173535 132172438 140 9112 CAMK2B 0 . GRCh38 7 44284156 44284156 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.135C>G p.Ile45Met p.I45M ENST00000395749 2/24 799 745 54 279 279 0 strelka-varscan-mutect CAMK2B,missense_variant,p.Ile45Met,ENST00000395749,NM_001220.4;CAMK2B,missense_variant,p.Ile45Met,ENST00000457475,NM_172079.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000350811,NM_001293170.1;CAMK2B,missense_variant,p.Ile45Met,ENST00000440254,NM_172078.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000358707,NM_172081.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000258682,NM_172080.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000353625,NM_172083.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000347193,NM_172082.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000395747,;CAMK2B,missense_variant,p.Ile45Met,ENST00000346990,NM_172084.2;CAMK2B,missense_variant,p.Ile45Met,ENST00000421607,;CAMK2B,missense_variant,p.Ile61Met,ENST00000415369,;CAMK2B,missense_variant,p.Ile45Met,ENST00000424197,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000497584,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000495819,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000470984,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000427209,;CAMK2B,missense_variant,p.Ile45Met,ENST00000523845,;CAMK2B,missense_variant,p.Ile45Met,ENST00000353185,; C ENST00000395749 Transcript missense_variant 212/4447 135/2001 45/666 I/M atC/atG 1 -1 CAMK2B HGNC HGNC:1461 protein_coding YES CCDS5483.1 ENSP00000379098 Q13554 A4D2J9 UPI0000164A3E NM_001220.4 deleterious_low_confidence(0.01) 2/24 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 44284156 44284156 G C 1 0 0 0 0 1 0 0 0 2291 1280 45 4 4 CAMK2B 7 44284156 Missense_Mutation SNP G C3L-02365_T 17110621 44284156 115061817 141 9113 ZNF716 0 . GRCh38 7 57450325 57450325 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.37A>T p.Met13Leu p.M13L ENST00000420713 1/4 378 356 22 324 324 0 varscan-mutect ZNF716,missense_variant,p.Met13Leu,ENST00000420713,NM_001159279.1; T ENST00000420713 Transcript missense_variant,splice_region_variant 149/5197 37/1488 13/495 M/L Atg/Ttg 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 deleterious(0.04) 1/4 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 57450325 57450325 A T 1 0 0 0 0 1 0 0 0 18694 115 4 4 4 ZNF716 7 57450325 Missense_Mutation SNP A C3L-02365_T 13166169 57450325 101895648 142 9114 ZNF735 0 . GRCh38 7 64219619 64219619 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.568T>C p.Tyr190His p.Y190H ENST00000429565 4/4 262 115 147 239 239 0 strelka-varscan-mutect ZNF735,missense_variant,p.Tyr190His,ENST00000429565,NM_001159524.1; C ENST00000429565 Transcript missense_variant 681/1570 568/1239 190/412 Y/H Tat/Cat 1 1 ZNF735 HGNC HGNC:32466 protein_coding YES CCDS78236.1 ENSP00000485547 P0CB33 UPI0001662441 NM_001159524.1 deleterious(0.02) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,Low_complexity_(Seg):seg,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 64219619 64219619 T C 1 0 0 0 0 1 0 0 0 18706 1406 49 5 5 ZNF735 7 64219619 Missense_Mutation SNP T C3L-02365_T 6769294 64219619 95126354 143 9115 CCDC146 0 . GRCh38 7 77260014 77260014 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.764T>C p.Met255Thr p.M255T ENST00000285871 8/19 165 143 22 92 92 0 strelka-varscan-mutect CCDC146,missense_variant,p.Met255Thr,ENST00000285871,NM_020879.2;AC073635.5,upstream_gene_variant,,ENST00000476561,;CCDC146,non_coding_transcript_exon_variant,,ENST00000415740,;CCDC146,downstream_gene_variant,,ENST00000461882,; C ENST00000285871 Transcript missense_variant 891/3333 764/2868 255/955 M/T aTg/aCg 1 1 CCDC146 HGNC HGNC:29296 protein_coding YES CCDS34671.1 ENSP00000285871 Q8IYE0 UPI000020F44F NM_020879.2 tolerated(0.37) 8/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF27 MODERATE 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.999948 1 1 1 0 C 3 2 34 77260014 77260014 T C 1 0 0 0 0 1 0 0 0 2467 1478 51 5 5 CCDC146 7 77260014 Missense_Mutation SNP T C3L-02365_T 13040395 77260014 82085959 144 9116 PTPN12 0 . GRCh38 7 77618506 77618506 + Silent SNP C C T rs770057677 C3L-02365_T C3L-02365_N C C c.966C>T p.= p.V322V ENST00000248594 12/18 310 274 36 221 220 1 strelka-varscan-mutect PTPN12,synonymous_variant,p.=,ENST00000248594,NM_002835.3;PTPN12,synonymous_variant,p.=,ENST00000435495,NM_001131009.1;PTPN12,synonymous_variant,p.=,ENST00000415482,NM_001131008.1; T ENST00000248594 Transcript synonymous_variant 1238/3406 966/2343 322/780 V gtC/gtT rs770057677 1 1 PTPN12 HGNC HGNC:9645 protein_coding YES CCDS5592.1 ENSP00000248594 Q05209 UPI000013CC4C NM_002835.3 12/18 PIRSF_domain:PIRSF000932 LOW 1 SNV 1 1 PASS rs770057677 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 77618506 77618506 C T 1 0 0 0 0 0 0 0 1 12934 813 29 3 3 PTPN12 7 77618506 Silent SNP C C3L-02365_T 358492 77618506 81727467 145 9117 ABCB1 0 . GRCh38 7 87515353 87515353 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.3160C>A p.Gln1054Lys p.Q1054K ENST00000622132 25/28 517 259 258 308 308 0 strelka-varscan-mutect ABCB1,missense_variant,p.Gln1054Lys,ENST00000622132,;ABCB1,missense_variant,p.Gln1054Lys,ENST00000265724,NM_000927.4;ABCB1,missense_variant,p.Gln990Lys,ENST00000543898,;ABCB1,non_coding_transcript_exon_variant,,ENST00000488737,;ABCB1,non_coding_transcript_exon_variant,,ENST00000496821,;ABCB1,non_coding_transcript_exon_variant,,ENST00000475929,;ABCB1,downstream_gene_variant,,ENST00000483831,; T ENST00000622132 Transcript missense_variant 3485/4778 3160/3843 1054/1280 Q/K Cag/Aag 1 -1 ABCB1 HGNC HGNC:40 protein_coding YES CCDS5608.1 ENSP00000478255 P08183 A4D1D2 UPI000013D66C tolerated(0.33) 25/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 87515353 87515353 G T 1 0 0 0 0 1 0 0 0 44 1299 45 2 2 ABCB1 7 87515353 Missense_Mutation SNP G C3L-02365_T 9896847 87515353 71830620 146 9118 AKAP9 0 . GRCh38 7 92002883 92002883 + Missense_Mutation SNP A A C novel C3L-02365_T C3L-02365_N A A c.2966A>C p.Gln989Pro p.Q989P ENST00000356239 8/50 210 95 115 174 174 0 strelka-varscan-mutect AKAP9,missense_variant,p.Gln989Pro,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Gln1000Pro,ENST00000359028,;AKAP9,missense_variant,p.Gln989Pro,ENST00000358100,;AKAP9,missense_variant,p.Gln997Pro,ENST00000619023,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; C ENST00000356239 Transcript missense_variant 3199/12471 2966/11724 989/3907 Q/P cAa/cCa 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 deleterious(0) 8/50 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 92002883 92002883 A C 1 0 0 0 0 1 0 0 0 543 130 5 5 5 AKAP9 7 92002883 Missense_Mutation SNP A C3L-02365_T 4487530 92002883 67343090 147 9119 COL1A2 0 . GRCh38 7 94409607 94409607 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.935C>A p.Ala312Asp p.A312D ENST00000297268 18/52 947 831 116 604 601 3 strelka-varscan-mutect COL1A2,missense_variant,p.Ala312Asp,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Ala310Asp,ENST00000620463,;COL1A2,upstream_gene_variant,,ENST00000473573,;COL1A2,upstream_gene_variant,,ENST00000488298,; A ENST00000297268 Transcript missense_variant,splice_region_variant 1406/5411 935/4101 312/1366 A/D gCt/gAt 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 tolerated(0.34) 18/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 94409607 94409607 C A 1 0 0 0 0 1 0 0 0 3466 811 28 2 2 COL1A2 7 94409607 Missense_Mutation SNP C C3L-02365_T 2406724 94409607 64936366 148 9120 LMTK2 0 . GRCh38 7 98194444 98194444 + Nonsense_Mutation SNP G G T rs200968988 C3L-02365_T C3L-02365_N G G c.3979G>T p.Gly1327Ter p.G1327* ENST00000297293 11/14 609 525 84 364 364 0 strelka-varscan-mutect LMTK2,stop_gained,p.Gly1327Ter,ENST00000297293,NM_014916.3; T ENST00000297293 Transcript stop_gained 4272/8946 3979/4512 1327/1503 G/* Gga/Tga rs200968988,COSM4698279,COSM4698280 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 11/14 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs200968988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 98194444 98194444 G T 1 0 0 0 0 0 1 0 0 8786 1117 39 1 1 LMTK2 7 98194444 Nonsense_Mutation SNP G C3L-02365_T 3784837 98194444 61151529 149 9121 TRIP6 0 . GRCh38 7 100873200 100873200 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1328G>T p.Gly443Val p.G443V ENST00000200457 9/9 251 219 32 120 120 0 strelka-varscan-mutect TRIP6,missense_variant,p.Gly443Val,ENST00000200457,NM_003302.2;TRIP6,3_prime_UTR_variant,,ENST00000619988,;SRRT,upstream_gene_variant,,ENST00000614484,NM_001128852.1;SRRT,upstream_gene_variant,,ENST00000618262,NM_001128853.1;SRRT,upstream_gene_variant,,ENST00000611405,NM_015908.5;SRRT,upstream_gene_variant,,ENST00000618411,NM_001128854.1;TRIP6,downstream_gene_variant,,ENST00000629911,;TRIP6,downstream_gene_variant,,ENST00000429658,;SRRT,upstream_gene_variant,,ENST00000431645,;TRIP6,non_coding_transcript_exon_variant,,ENST00000476870,;TRIP6,downstream_gene_variant,,ENST00000417475,;TRIP6,downstream_gene_variant,,ENST00000437505,;TRIP6,downstream_gene_variant,,ENST00000463125,;TRIP6,downstream_gene_variant,,ENST00000488670,;SRRT,upstream_gene_variant,,ENST00000620394,;SRRT,upstream_gene_variant,,ENST00000614370,; T ENST00000200457 Transcript missense_variant 1688/1942 1328/1431 443/476 G/V gGc/gTc 1 1 TRIP6 HGNC HGNC:12311 protein_coding YES CCDS5708.1 ENSP00000200457 Q15654 UPI00000012CD NM_003302.2 deleterious(0) 9/9 Low_complexity_(Seg):seg,PROSITE_profiles:PS50023,hmmpanther:PTHR24212:SF7,hmmpanther:PTHR24212,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 100873200 100873200 G T 1 0 0 0 0 1 0 0 0 17056 1203 42 2 2 TRIP6 7 100873200 Missense_Mutation SNP G C3L-02365_T 2678756 100873200 58472773 150 9122 RELN 0 . GRCh38 7 103753198 103753198 + Silent SNP A A G novel C3L-02365_T C3L-02365_N A A c.561T>C p.= p.T187T ENST00000428762 5/65 497 444 53 341 341 0 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; G ENST00000428762 Transcript synonymous_variant 721/11571 561/10383 187/3460 T acT/acC 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 5/65 PROSITE_profiles:PS51019,hmmpanther:PTHR11841 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 103753198 103753198 A G 1 0 0 0 0 0 0 0 1 13390 175 7 5 5 RELN 7 103753198 Silent SNP A C3L-02365_T 2879998 103753198 55592775 151 9123 KMT2E 0 . GRCh38 7 105107366 105107366 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.2909A>T p.Tyr970Phe p.Y970F ENST00000311117 22/27 81 71 10 57 56 1 strelka-varscan-mutect KMT2E,missense_variant,p.Tyr970Phe,ENST00000311117,NM_182931.2;KMT2E,missense_variant,p.Tyr970Phe,ENST00000257745,NM_018682.3;KMT2E,downstream_gene_variant,,ENST00000479838,;KMT2E,upstream_gene_variant,,ENST00000473063,;CTB-152G17.6,upstream_gene_variant,,ENST00000607968,;SRPK2,downstream_gene_variant,,ENST00000493638,;KMT2E,3_prime_UTR_variant,,ENST00000334884,;KMT2E,upstream_gene_variant,,ENST00000478079,; T ENST00000311117 Transcript missense_variant 3454/6874 2909/5577 970/1858 Y/F tAt/tTt 1 1 KMT2E HGNC HGNC:18541 protein_coding YES CCDS34723.1 ENSP00000312379 Q8IZD2 UPI0000074133 NM_182931.2 tolerated_low_confidence(0.16) 22/27 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99194 1 1 1 1 0 T 3 4 34 105107366 105107366 A T 1 0 0 0 0 1 0 0 0 8299 463 16 4 4 KMT2E 7 105107366 Missense_Mutation SNP A C3L-02365_T 1354168 105107366 54238607 152 9124 CPED1 0 . GRCh38 7 120989731 120989731 + Missense_Mutation SNP G G T rs771443560 C3L-02365_T C3L-02365_N G G c.110G>T p.Gly37Val p.G37V ENST00000310396 2/23 719 615 104 482 481 1 strelka-varscan-mutect CPED1,missense_variant,p.Gly37Val,ENST00000310396,NM_024913.4;CPED1,missense_variant,p.Gly37Val,ENST00000450913,NM_001105533.1;CPED1,missense_variant,p.Gly37Val,ENST00000428526,;CPED1,missense_variant,p.Gly37Val,ENST00000340646,;CPED1,non_coding_transcript_exon_variant,,ENST00000495036,;CPED1,upstream_gene_variant,,ENST00000520801,; T ENST00000310396 Transcript missense_variant 577/5340 110/3081 37/1026 G/V gGg/gTg rs771443560,COSM4521397,COSM4521398,COSM4521399 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 tolerated(0.06) 2/23 hmmpanther:PTHR14776 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs771443560 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 120989731 120989731 G T 1 0 0 0 0 1 0 0 0 3598 1232 43 2 2 CPED1 7 120989731 Missense_Mutation SNP G C3L-02365_T 15882365 120989731 38356242 153 9125 CADPS2 0 . GRCh38 7 122615241 122615241 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.1163G>C p.Cys388Ser p.C388S ENST00000449022 6/30 169 149 20 141 141 0 strelka-varscan-mutect CADPS2,missense_variant,p.Cys388Ser,ENST00000615869,;CADPS2,missense_variant,p.Cys282Ser,ENST00000313070,NM_001167940.1;CADPS2,missense_variant,p.Cys388Ser,ENST00000334010,;CADPS2,missense_variant,p.Cys388Ser,ENST00000412584,NM_001009571.3;CADPS2,missense_variant,p.Cys388Ser,ENST00000449022,NM_017954.10;CADPS2,missense_variant,p.Cys37Ser,ENST00000397721,; G ENST00000449022 Transcript missense_variant 1183/4073 1163/3891 388/1296 C/S tGt/tCt 1 -1 CADPS2 HGNC HGNC:16018 protein_coding YES CCDS55158.1 ENSP00000398481 Q86UW7 UPI0000668808 NM_017954.10 deleterious(0.01) 6/30 hmmpanther:PTHR12166,hmmpanther:PTHR12166:SF7,Superfamily_domains:SSF49562 MODERATE 1 SNV 5 1 PASS rs1274435030 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 34 122615241 122615241 C G 1 0 0 0 0 1 0 0 0 2261 478 17 4 4 CADPS2 7 122615241 Missense_Mutation SNP C C3L-02365_T 1625510 122615241 36730732 154 9126 RP11-286H14.4 0 . GRCh38 7 129126925 129126925 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.408C>G p.Phe136Leu p.F136L ENST00000467614 1/2 849 431 418 494 494 0 strelka-varscan-mutect RP11-286H14.4,missense_variant,p.Phe136Leu,ENST00000467614,; G ENST00000467614 Transcript missense_variant 408/1263 408/1218 136/405 F/L ttC/ttG 1 1 RP11-286H14.4 Clone_based_vega_gene protein_coding YES ENSP00000490163 deleterious(0) 1/2 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF314,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 129126925 129126925 C G 1 0 0 0 0 1 0 0 0 13725 912 32 4 4 RP11-286H14.4 7 129126925 Missense_Mutation SNP C C3L-02365_T 6511684 129126925 30219048 155 9127 EZH2 0 . GRCh38 7 148807663 148807663 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.2239G>C p.Glu747Gln p.E747Q ENST00000320356 20/20 296 252 44 195 195 0 strelka-varscan-mutect EZH2,missense_variant,p.Glu747Gln,ENST00000320356,NM_004456.4;EZH2,missense_variant,p.Glu742Gln,ENST00000460911,NM_001203247.1;EZH2,missense_variant,p.Glu691Gln,ENST00000476773,NM_001203249.1;EZH2,missense_variant,p.Glu691Gln,ENST00000478654,;EZH2,missense_variant,p.Glu703Gln,ENST00000350995,NM_152998.2;EZH2,missense_variant,p.Glu733Gln,ENST00000483967,NM_001203248.1;EZH2,3_prime_UTR_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000469631,; G ENST00000320356 Transcript missense_variant 2361/2639 2239/2256 747/751 E/Q Gaa/Caa 1 -1 EZH2 HGNC HGNC:3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 A0A090N8E9 UPI000006D77C NM_004456.4 deleterious(0.02) 20/20 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 148807663 148807663 C G 1 0 0 0 0 1 0 0 0 5202 922 32 4 4 EZH2 7 148807663 Missense_Mutation SNP C C3L-02365_T 19680738 148807663 10538310 156 9128 ATP6V0E2 0 . GRCh38 7 149873936 149873936 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.18G>T p.= p.P6P ENST00000421974 1/3 122 98 24 89 89 0 strelka-varscan-mutect ATP6V0E2,synonymous_variant,p.=,ENST00000615196,NM_145230.3;ATP6V0E2,synonymous_variant,p.=,ENST00000456496,;ATP6V0E2,synonymous_variant,p.=,ENST00000421974,NM_001100592.2;ATP6V0E2,synonymous_variant,p.=,ENST00000611515,;ATP6V0E2,upstream_gene_variant,,ENST00000479613,NM_001289990.1;ATP6V0E2,upstream_gene_variant,,ENST00000425642,;ATP6V0E2,upstream_gene_variant,,ENST00000606024,;ATP6V0E2,upstream_gene_variant,,ENST00000464662,;ATP6V0E2-AS1,intron_variant,,ENST00000464939,;ATP6V0E2-AS1,upstream_gene_variant,,ENST00000461019,;ATP6V0E2-AS1,upstream_gene_variant,,ENST00000488315,;ATP6V0E2,upstream_gene_variant,,ENST00000495408,;ATP6V0E2,upstream_gene_variant,,ENST00000490092,;ATP6V0E2,upstream_gene_variant,,ENST00000483478,;ATP6V0E2,upstream_gene_variant,,ENST00000471877,;ATP6V0E2,upstream_gene_variant,,ENST00000464683,; T ENST00000421974 Transcript synonymous_variant 969/2605 18/642 6/213 P ccG/ccT 1 1 ATP6V0E2 HGNC HGNC:21723 protein_coding YES CCDS47742.1 ENSP00000411672 E9PAS2 UPI00001A844C NM_001100592.2 1/3 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 149873936 149873936 G T 1 0 0 0 0 0 0 0 1 1329 1103 39 1 1 ATP6V0E2 7 149873936 Silent SNP G C3L-02365_T 1066273 149873936 9472037 157 9129 GIMAP6 0 . GRCh38 7 150628448 150628448 + Frame_Shift_Del DEL C C - novel C3L-02365_T C3L-02365_N C C c.360delG p.Ser121ValfsTer25 p.S121Vfs*25 ENST00000618759 3/3 306 182 124 263 263 0 sindel-varindel-pindel GIMAP6,frameshift_variant,p.Ser121ValfsTer25,ENST00000618759,NM_001244072.1;GIMAP6,frameshift_variant,p.Ser51ValfsTer25,ENST00000328902,NM_024711.5;GIMAP6,intron_variant,,ENST00000493969,NM_001244071.1; - ENST00000618759 Transcript frameshift_variant 840/3910 360/1089 120/362 G/X ggG/gg 1 -1 GIMAP6 HGNC HGNC:21918 protein_coding YES CCDS75676.1 ENSP00000479580 B4DH95 UPI00017A6DF2 NM_001244072.1 3/3 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF51,hmmpanther:PTHR10903,Pfam_domain:PF04548,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 150628448 150628448 C - 1 0 1 0 1 0 0 0 0 6263 842 30 0 0 GIMAP6 7 150628448 Frame_Shift_Del DEL C C3L-02365_T 754512 150628448 8717525 158 9130 PTPRN2 0 . GRCh38 7 157604025 157604025 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2395G>T p.Asp799Tyr p.D799Y ENST00000389418 16/23 347 203 144 213 213 0 strelka-varscan-mutect PTPRN2,missense_variant,p.Asp770Tyr,ENST00000389413,NM_130843.2;PTPRN2,missense_variant,p.Asp761Tyr,ENST00000409483,NM_001308267.1;PTPRN2,missense_variant,p.Asp799Tyr,ENST00000389418,NM_001308268.1,NM_002847.3;PTPRN2,missense_variant,p.Asp782Tyr,ENST00000389416,NM_130842.2; A ENST00000389418 Transcript missense_variant 2405/4706 2395/3048 799/1015 D/Y Gac/Tac 1 -1 PTPRN2 HGNC HGNC:9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 UPI000002E7C7 NM_001308268.1,NM_002847.3 deleterious(0) 16/23 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF266,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 157604025 157604025 C A 1 0 0 0 0 1 0 0 0 12962 913 32 2 2 PTPRN2 7 157604025 Missense_Mutation SNP C C3L-02365_T 6975577 157604025 1741948 159 9131 RNF122 0 . GRCh38 8 33551381 33551381 + Missense_Mutation SNP C C A rs760602508 C3L-02365_T C3L-02365_N C C c.191G>T p.Arg64Leu p.R64L ENST00000256257 3/6 255 187 68 410 410 0 strelka-varscan-mutect RNF122,missense_variant,p.Arg64Leu,ENST00000256257,NM_024787.3; A ENST00000256257 Transcript missense_variant 593/1868 191/468 64/155 R/L cGg/cTg rs760602508 1 -1 RNF122 HGNC HGNC:21147 protein_coding YES CCDS6091.1 ENSP00000256257 Q9H9V4 UPI000013CEFB NM_024787.3 deleterious(0) 3/6 hmmpanther:PTHR22763:SF14,hmmpanther:PTHR22763 MODERATE 1 SNV 1 1 PASS rs760602508 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 33551381 33551381 C A 1 0 0 0 0 1 0 0 0 13610 652 23 1 1 RNF122 8 33551381 Missense_Mutation SNP C C3L-02365_T 33551381 111587255 160 9132 FGFR1 0 . GRCh38 8 38421814 38421814 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1157G>T p.Trp386Leu p.W386L ENST00000425967 9/19 196 139 57 243 242 1 strelka-varscan-mutect FGFR1,missense_variant,p.Trp355Leu,ENST00000447712,NM_023110.2;FGFR1,missense_variant,p.Trp353Leu,ENST00000397091,NM_015850.3;FGFR1,missense_variant,p.Trp355Leu,ENST00000532791,NM_001174063.1;FGFR1,missense_variant,p.Trp386Leu,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Trp347Leu,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Trp266Leu,ENST00000356207,NM_023105.2,NM_001174066.1;FGFR1,missense_variant,p.Trp264Leu,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Trp353Leu,ENST00000397113,NM_001174065.1;FGFR1,missense_variant,p.Trp353Leu,ENST00000397108,;FGFR1,3_prime_UTR_variant,,ENST00000341462,;FGFR1,intron_variant,,ENST00000619564,;FGFR1,intron_variant,,ENST00000397103,;FGFR1,downstream_gene_variant,,ENST00000525001,;FGFR1,downstream_gene_variant,,ENST00000529552,;FGFR1,downstream_gene_variant,,ENST00000526742,;FGFR1,downstream_gene_variant,,ENST00000533668,;RP11-350N15.4,upstream_gene_variant,,ENST00000528407,;FGFR1,downstream_gene_variant,,ENST00000527203,;FGFR1,downstream_gene_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000466021,;FGFR1,non_coding_transcript_exon_variant,,ENST00000475621,;FGFR1,downstream_gene_variant,,ENST00000470826,;FGFR1,downstream_gene_variant,,ENST00000496296,;FGFR1,upstream_gene_variant,,ENST00000527114,;FGFR1,downstream_gene_variant,,ENST00000484370,;FGFR1,upstream_gene_variant,,ENST00000527745,;FGFR1,downstream_gene_variant,,ENST00000474970,;FGFR1,downstream_gene_variant,,ENST00000532386,;FGFR1,downstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000533619,;FGFR1,upstream_gene_variant,,ENST00000524528,; A ENST00000425967 Transcript missense_variant 1480/5375 1157/2562 386/853 W/L tGg/tTg 1 -1 FGFR1 HGNC HGNC:3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 UPI0001CE06A3 NM_001174067.1 deleterious(0) 9/19 Gene3D:2.60.40.10,Pfam_domain:PF07679,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 38421814 38421814 C A 1 0 0 0 0 1 0 0 0 5727 595 21 2 2 FGFR1 8 38421814 Missense_Mutation SNP C C3L-02365_T 4870433 38421814 106716822 161 9133 PXDNL 0 . GRCh38 8 51408289 51408289 + Missense_Mutation SNP C C A rs753757543 C3L-02365_T C3L-02365_N C C c.3335G>T p.Arg1112Leu p.R1112L ENST00000356297 17/23 321 291 30 195 195 0 strelka-varscan-mutect PXDNL,missense_variant,p.Arg1112Leu,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.Arg231Leu,ENST00000522933,;PXDNL,missense_variant,p.Arg378Leu,ENST00000522628,; A ENST00000356297 Transcript missense_variant 3436/4805 3335/4392 1112/1463 R/L cGg/cTg rs753757543,COSM2718383,COSM2718384 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs753757543 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 51408289 51408289 C A 1 0 0 0 0 1 0 0 0 13002 652 23 1 1 PXDNL 8 51408289 Missense_Mutation SNP C C3L-02365_T 12986475 51408289 93730347 162 9134 PXDNL 0 . GRCh38 8 51409473 51409473 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.2151C>A p.Asn717Lys p.N717K ENST00000356297 17/23 327 308 19 146 146 0 strelka-varscan-mutect PXDNL,missense_variant,p.Asn717Lys,ENST00000356297,NM_144651.4;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,upstream_gene_variant,,ENST00000522628,; T ENST00000356297 Transcript missense_variant 2252/4805 2151/4392 717/1463 N/K aaC/aaA 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0.03) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10 MODERATE 1 SNV 1 1 PASS rs1427045243 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 51409473 51409473 G T 1 0 0 0 0 1 0 0 0 13002 1020 36 2 2 PXDNL 8 51409473 Missense_Mutation SNP G C3L-02365_T 1184 51409473 93729163 163 9135 GGH 0 . GRCh38 8 63024148 63024148 + Missense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.538G>A p.Glu180Lys p.E180K ENST00000260118 6/9 324 301 23 258 257 1 strelka-varscan-mutect GGH,missense_variant,p.Glu180Lys,ENST00000260118,NM_003878.2;RP11-659E9.4,upstream_gene_variant,,ENST00000521556,;GGH,non_coding_transcript_exon_variant,,ENST00000518113,;GGH,non_coding_transcript_exon_variant,,ENST00000518466,;GGH,downstream_gene_variant,,ENST00000523479,;GGH,non_coding_transcript_exon_variant,,ENST00000520609,;GGH,downstream_gene_variant,,ENST00000518966,; T ENST00000260118 Transcript missense_variant 941/1607 538/957 180/318 E/K Gag/Aag COSM5630200 1 -1 GGH HGNC HGNC:4248 protein_coding YES CCDS6177.1 ENSP00000260118 Q92820 UPI000000127C NM_003878.2 deleterious(0.05) 6/9 Gene3D:3.40.50.880,Pfam_domain:PF07722,PROSITE_profiles:PS51275,hmmpanther:PTHR11315,hmmpanther:PTHR11315:SF2,Superfamily_domains:SSF52317 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 63024148 63024148 C T 1 0 0 0 0 1 0 0 0 6233 835 29 3 3 GGH 8 63024148 Missense_Mutation SNP C C3L-02365_T 11614675 63024148 82114488 164 9136 ZFHX4 0 . GRCh38 8 76864373 76864373 + Silent SNP G G T rs762288220 C3L-02365_T C3L-02365_N G G c.10659G>T p.= p.T3553T ENST00000521891 11/11 318 299 19 257 257 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,; T ENST00000521891 Transcript synonymous_variant 11107/14019 10659/10851 3553/3616 T acG/acT rs762288220 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 11/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs762288220 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 76864373 76864373 G T 1 0 0 0 0 0 0 0 1 18213 1103 39 1 1 ZFHX4 8 76864373 Silent SNP G C3L-02365_T 13840225 76864373 68274263 165 9137 DCAF13 0 . GRCh38 8 103420312 103420312 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.575A>T p.Glu192Val p.E192V ENST00000297579 2/11 401 372 29 273 273 0 strelka-varscan-mutect DCAF13,missense_variant,p.Glu192Val,ENST00000297579,NM_015420.6;DCAF13,missense_variant,p.Glu192Val,ENST00000616836,;DCAF13,missense_variant,p.Glu40Val,ENST00000521971,;DCAF13,missense_variant,p.Glu40Val,ENST00000618975,;DCAF13,missense_variant,p.Glu40Val,ENST00000612750,;DCAF13,missense_variant,p.Glu40Val,ENST00000519682,;DCAF13,intron_variant,,ENST00000521999,;DCAF13,non_coding_transcript_exon_variant,,ENST00000518554,;DCAF13,non_coding_transcript_exon_variant,,ENST00000521716,; T ENST00000297579 Transcript missense_variant 852/2642 575/1794 192/597 E/V gAa/gTa 1 1 DCAF13 HGNC HGNC:24535 protein_coding YES CCDS34934.1 ENSP00000297579 A0A087WT20 UPI0000DBEF2A NM_015420.6 deleterious(0) 2/11 hmmpanther:PTHR22851,hmmpanther:PTHR22851:SF0,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 103420312 103420312 A T 1 0 0 0 0 1 0 0 0 4067 246 9 4 4 DCAF13 8 103420312 Missense_Mutation SNP A C3L-02365_T 26555939 103420312 41718324 166 9138 RIMS2 0 . GRCh38 8 103885599 103885599 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.1000C>G p.Arg334Gly p.R334G ENST00000504942 4/24 525 237 288 314 314 0 strelka-varscan-mutect RIMS2,missense_variant,p.Arg142Gly,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Arg112Gly,ENST00000436393,;RIMS2,missense_variant,p.Arg334Gly,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Arg276Gly,ENST00000626043,;RIMS2,missense_variant,p.Arg142Gly,ENST00000408894,;RIMS2,missense_variant,p.Arg142Gly,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Arg338Gly,ENST00000632716,;RIMS2,missense_variant,p.Arg142Gly,ENST00000515551,; G ENST00000504942 Transcript missense_variant 1139/4228 1000/4050 334/1349 R/G Cga/Gga 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 103885599 103885599 C G 1 0 0 0 0 1 0 0 0 13543 644 23 4 4 RIMS2 8 103885599 Missense_Mutation SNP C C3L-02365_T 465287 103885599 41253037 167 9139 RIMS2 0 . GRCh38 8 103975367 103975367 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.2788C>A p.= p.R930R ENST00000504942 16/24 247 231 16 176 174 2 strelka-varscan-mutect RIMS2,synonymous_variant,p.=,ENST00000507740,NM_014677.4;RIMS2,synonymous_variant,p.=,ENST00000436393,;RIMS2,synonymous_variant,p.=,ENST00000504942,NM_001100117.2;RIMS2,synonymous_variant,p.=,ENST00000626043,;RIMS2,synonymous_variant,p.=,ENST00000408894,;RIMS2,synonymous_variant,p.=,ENST00000262231,NM_001282881.1;RIMS2,synonymous_variant,p.=,ENST00000632716,;RIMS2,synonymous_variant,p.=,ENST00000507677,; A ENST00000504942 Transcript synonymous_variant 2927/4228 2788/4050 930/1349 R Cga/Aga 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 16/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 LOW 1 SNV 2 1 PASS rs1198632500 . 0 208 0 2 0 0 0 0 -19.20719 0.9999996 1 1 1 0 A 2 1 34 103975367 103975367 C A 1 0 0 0 0 0 0 0 1 13543 876 31 1 1 RIMS2 8 103975367 Silent SNP C C3L-02365_T 89768 103975367 41163269 168 9140 PKHD1L1 0 . GRCh38 8 109412385 109412385 + Nonsense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.2206G>T p.Gly736Ter p.G736* ENST00000378402 20/78 215 193 22 149 149 0 strelka-varscan-mutect PKHD1L1,stop_gained,p.Gly736Ter,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript stop_gained 2310/13076 2206/12732 736/4243 G/* Gga/Tga COSM3643962 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 20/78 1 HIGH 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 109412385 109412385 G T 1 0 0 0 0 0 1 0 0 12068 1349 47 2 2 PKHD1L1 8 109412385 Nonsense_Mutation SNP G C3L-02365_T 5437018 109412385 35726251 169 9141 PKHD1L1 0 . GRCh38 8 109465040 109465040 + Missense_Mutation SNP G G C rs78508697 C3L-02365_T C3L-02365_N G G c.8208G>C p.Leu2736Phe p.L2736F ENST00000378402 49/78 421 395 26 276 276 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Leu2736Phe,ENST00000378402,NM_177531.4; C ENST00000378402 Transcript missense_variant 8312/13076 8208/12732 2736/4243 L/F ttG/ttC rs78508697 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 tolerated(0.13) 49/78 SMART_domains:SM00710 MODERATE 1 SNV 1 1 PASS rs78508697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 109465040 109465040 G C 1 0 0 0 0 1 0 0 0 12068 1281 45 4 4 PKHD1L1 8 109465040 Missense_Mutation SNP G C3L-02365_T 52655 109465040 35673596 170 9142 CSMD3 0 . GRCh38 8 112287185 112287185 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.9210C>A p.Ser3070Arg p.S3070R ENST00000297405 58/71 794 579 215 554 553 1 strelka-varscan-mutect CSMD3,missense_variant,p.Ser3070Arg,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser3030Arg,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser2901Arg,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser2340Arg,ENST00000339701,; T ENST00000297405 Transcript missense_variant 9455/13212 9210/11124 3070/3707 S/R agC/agA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.04) 58/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 112287185 112287185 G T 1 0 0 0 0 1 0 0 0 3747 1310 46 2 2 CSMD3 8 112287185 Missense_Mutation SNP G C3L-02365_T 2822145 112287185 32851451 171 9143 CSMD3 0 . GRCh38 8 112301960 112301960 + Missense_Mutation SNP G G C rs759145168 C3L-02365_T C3L-02365_N G G c.8273C>G p.Ser2758Cys p.S2758C ENST00000297405 53/71 403 370 33 285 285 0 strelka-varscan-mutect CSMD3,missense_variant,p.Ser2758Cys,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser2718Cys,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser2589Cys,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser2028Cys,ENST00000339701,; C ENST00000297405 Transcript missense_variant 8518/13212 8273/11124 2758/3707 S/C tCc/tGc rs759145168 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 53/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs759145168 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 112301960 112301960 G C 1 0 0 0 0 1 0 0 0 3747 1174 41 4 4 CSMD3 8 112301960 Missense_Mutation SNP G C3L-02365_T 14775 112301960 32836676 172 9144 TBC1D31 0 . GRCh38 8 123097339 123097339 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.729G>T p.Leu243Phe p.L243F ENST00000287380 6/22 387 367 20 249 249 0 strelka-varscan-mutect TBC1D31,missense_variant,p.Leu243Phe,ENST00000287380,NM_145647.3;TBC1D31,missense_variant,p.Leu138Phe,ENST00000521676,;TBC1D31,missense_variant,p.Leu138Phe,ENST00000522420,;TBC1D31,missense_variant,p.Leu243Phe,ENST00000327098,NM_001145088.1;TBC1D31,missense_variant,p.Leu47Phe,ENST00000521914,;TBC1D31,missense_variant,p.Leu233Phe,ENST00000522276,;TBC1D31,intron_variant,,ENST00000519418,;TBC1D31,upstream_gene_variant,,ENST00000518805,;TBC1D31,downstream_gene_variant,,ENST00000518684,;TBC1D31,3_prime_UTR_variant,,ENST00000524307,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000521980,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000518099,; T ENST00000287380 Transcript missense_variant 819/3502 729/3201 243/1066 L/F ttG/ttT 1 1 TBC1D31 HGNC HGNC:30888 protein_coding YES CCDS6338.1 ENSP00000287380 Q96DN5 UPI000013DEAB NM_145647.3 deleterious(0) 6/22 PROSITE_profiles:PS50294,hmmpanther:PTHR19853:SF1,hmmpanther:PTHR19853,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 123097339 123097339 G T 1 0 0 0 0 1 0 0 0 16021 1339 47 2 2 TBC1D31 8 123097339 Missense_Mutation SNP G C3L-02365_T 10795379 123097339 22041297 173 9145 ADCY8 0 . GRCh38 8 131039623 131039623 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.711C>A p.= p.T237T ENST00000286355 1/18 562 410 152 273 272 1 strelka-varscan-mutect ADCY8,synonymous_variant,p.=,ENST00000286355,NM_001115.2;ADCY8,synonymous_variant,p.=,ENST00000377928,; T ENST00000286355 Transcript synonymous_variant 2804/5938 711/3756 237/1251 T acC/acA 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 1/18 hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,Pfam_domain:PF16214 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 131039623 131039623 G T 1 0 0 0 0 0 0 0 1 344 987 35 2 2 ADCY8 8 131039623 Silent SNP G C3L-02365_T 7942284 131039623 14099013 174 9146 ZNF16 0 . GRCh38 8 144931470 144931470 + Frame_Shift_Del DEL C C - novel C3L-02365_T C3L-02365_N C C c.1317delG p.Ala441HisfsTer130 p.A441Hfs*130 ENST00000276816 4/4 310 288 22 203 202 1 varindel-pindel ZNF16,frameshift_variant,p.Ala441HisfsTer130,ENST00000276816,NM_001029976.2;ZNF16,frameshift_variant,p.Ala441HisfsTer130,ENST00000611477,NM_006958.2;ZNF16,frameshift_variant,p.Ala441HisfsTer130,ENST00000394909,;ZNF16,downstream_gene_variant,,ENST00000532351,;ZNF16,downstream_gene_variant,,ENST00000527811,;ZNF16,downstream_gene_variant,,ENST00000532811,;ZNF16,downstream_gene_variant,,ENST00000527512,; - ENST00000276816 Transcript frameshift_variant 1504/2616 1317/2049 439/682 G/X ggG/gg 1 -1 ZNF16 HGNC HGNC:12947 protein_coding YES CCDS6437.1 ENSP00000276816 P17020 UPI00001E058F NM_001029976.2 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF269,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 144931470 144931470 C - 1 0 1 0 1 0 0 0 0 18319 842 30 0 0 ZNF16 8 144931470 Frame_Shift_Del DEL C C3L-02365_T 13891847 144931470 207166 175 9147 ERMP1 0 . GRCh38 9 5813036 5813036 + Splice_Site SNP C C A novel C3L-02365_T C3L-02365_N C C c.875-1G>T p.X292_splice ENST00000339450 177 126 51 206 205 1 varscan-mutect ERMP1,splice_acceptor_variant,,ENST00000339450,NM_024896.2;ERMP1,splice_acceptor_variant,,ENST00000214893,;ERMP1,splice_acceptor_variant,,ENST00000462592,;ERMP1,splice_acceptor_variant,,ENST00000489219,;ERMP1,splice_acceptor_variant,,ENST00000487088,;ERMP1,splice_acceptor_variant,,ENST00000475005,; A ENST00000339450 Transcript splice_acceptor_variant -/5376 875/2715 292/904 1 -1 ERMP1 HGNC HGNC:23703 protein_coding YES CCDS34983.1 ENSP00000340427 Q7Z2K6 UPI00001D7694 NM_024896.2 4/14 HIGH 1 SNV 1 1 PASS rs1158386742 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 34 5813036 5813036 C A 1 0 0 0 0 0 0 1 0 5094 695 24 2 2 ERMP1 9 5813036 Splice_Site SNP C C3L-02365_T 5813036 132581681 176 9148 FRMPD1 0 . GRCh38 9 37746217 37746217 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.4185G>A p.= p.R1395R ENST00000539465 16/16 219 149 70 220 220 0 strelka-varscan-mutect FRMPD1,synonymous_variant,p.=,ENST00000539465,;FRMPD1,synonymous_variant,p.=,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; A ENST00000539465 Transcript synonymous_variant 4778/5465 4185/4737 1395/1578 R agG/agA 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC 16/16 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 37746217 37746217 G A 1 0 0 0 0 0 0 0 1 5927 1165 41 3 3 FRMPD1 9 37746217 Silent SNP G C3L-02365_T 31933181 37746217 100648500 177 9149 TMC1 0 . GRCh38 9 72821027 72821027 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1949C>A p.Pro650His p.P650H ENST00000297784 20/24 672 562 110 620 620 0 strelka-varscan-mutect TMC1,missense_variant,p.Pro650His,ENST00000297784,NM_138691.2;TMC1,missense_variant,p.Pro650His,ENST00000340019,;TMC1,non_coding_transcript_exon_variant,,ENST00000486417,;TMC1,non_coding_transcript_exon_variant,,ENST00000469455,; A ENST00000297784 Transcript missense_variant 2489/3201 1949/2283 650/760 P/H cCt/cAt 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 deleterious(0) 20/24 hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 72821027 72821027 C A 1 0 0 0 0 1 0 0 0 16430 681 24 2 2 TMC1 9 72821027 Missense_Mutation SNP C C3L-02365_T 35074810 72821027 65573690 178 9150 ZCCHC6 0 . GRCh38 9 86322383 86322383 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.2970G>T p.= p.L990L ENST00000375963 14/27 229 199 30 269 269 0 strelka-varscan-mutect ZCCHC6,synonymous_variant,p.=,ENST00000277141,;ZCCHC6,synonymous_variant,p.=,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,intron_variant,,ENST00000375960,NM_001185074.1;ZCCHC6,upstream_gene_variant,,ENST00000375957,;ZCCHC6,downstream_gene_variant,,ENST00000469004,; A ENST00000375963 Transcript synonymous_variant 3143/5379 2970/4488 990/1495 L ctG/ctT 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 14/27 hmmpanther:PTHR12271:SF34,hmmpanther:PTHR12271,Gene3D:4.10.60.10 LOW 1 SNV 5 1 PASS . . 0 207 0 0 2 0 0 0 -13.39202 0.9958804 1 1 1 0 A 2 1 34 86322383 86322383 C A 1 0 0 0 0 0 0 0 1 18167 697 25 2 2 ZCCHC6 9 86322383 Silent SNP C C3L-02365_T 13501356 86322383 52072334 179 9151 SUSD3 0 . GRCh38 9 93077994 93077994 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.425+1G>T p.X142_splice ENST00000375472 187 151 36 167 167 0 strelka-varscan-mutect SUSD3,splice_donor_variant,,ENST00000375472,NM_145006.3;SUSD3,splice_donor_variant,,ENST00000375469,NM_001287005.1;SUSD3,splice_donor_variant,,ENST00000617293,NM_001287006.1;SUSD3,splice_donor_variant,,ENST00000471462,;SUSD3,splice_donor_variant,,ENST00000465709,NM_001287008.1; T ENST00000375472 Transcript splice_donor_variant -/1195 425/768 142/255 1 1 SUSD3 HGNC HGNC:28391 protein_coding YES CCDS6701.1 ENSP00000364621 Q96L08 UPI0000070B4A NM_145006.3 3/4 HIGH 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999498 1 1 1 0 T 5 4 34 93077994 93077994 G T 1 0 0 0 0 0 0 1 0 15794 1275 44 2 2 SUSD3 9 93077994 Splice_Site SNP G C3L-02365_T 6755611 93077994 45316723 180 9152 OR1N2 0 . GRCh38 9 122553575 122553575 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.406G>T p.Ala136Ser p.A136S ENST00000373688 1/1 213 166 47 235 234 1 strelka-varscan-mutect OR1N2,missense_variant,p.Ala136Ser,ENST00000373688,NM_001004457.1;OR1N2,missense_variant,p.Ala118Ser,ENST00000616791,; T ENST00000373688 Transcript missense_variant 464/1103 406/993 136/330 A/S Gca/Tca 1 1 OR1N2 HGNC HGNC:15111 protein_coding YES CCDS35123.1 ENSP00000362792 Q8NGR9 UPI000004618C NM_001004457.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF156,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.999997 1 1 1 0 T 3 4 34 122553575 122553575 G T 1 0 0 0 0 1 0 0 0 11048 1203 42 2 2 OR1N2 9 122553575 Missense_Mutation SNP G C3L-02365_T 29475581 122553575 15841142 181 9153 STXBP1 0 . GRCh38 9 127684406 127684406 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.1741G>C p.Asp581His p.D581H ENST00000373302 19/20 373 308 65 330 330 0 strelka-varscan-mutect STXBP1,missense_variant,p.Asp581His,ENST00000373302,NM_003165.3;STXBP1,missense_variant,p.Asp567His,ENST00000637521,;STXBP1,missense_variant,p.Asp97His,ENST00000494254,;STXBP1,intron_variant,,ENST00000637173,;STXBP1,intron_variant,,ENST00000637953,;STXBP1,intron_variant,,ENST00000626539,;STXBP1,intron_variant,,ENST00000373299,NM_001032221.3;STXBP1,intron_variant,,ENST00000636962,;STXBP1,intron_variant,,ENST00000626416,;STXBP1,intron_variant,,ENST00000628638,;STXBP1,intron_variant,,ENST00000637464,;STXBP1,intron_variant,,ENST00000636509,;STXBP1,intron_variant,,ENST00000637060,;STXBP1,intron_variant,,ENST00000635950,; C ENST00000373302 Transcript missense_variant 1938/3967 1741/1812 581/603 D/H Gac/Cac 1 1 STXBP1 HGNC HGNC:11444 protein_coding YES CCDS6874.1 ENSP00000362399 P61764 UPI0000006C0B NM_003165.3 deleterious(0.01) 19/20 hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF35,PIRSF_domain:PIRSF005715,Gene3D:3.40.50.1910,Superfamily_domains:SSF56815 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 127684406 127684406 G C 1 0 0 0 0 1 0 0 0 15736 1174 41 4 4 STXBP1 9 127684406 Missense_Mutation SNP G C3L-02365_T 5130831 127684406 10710311 182 9154 PRRC2B 0 . GRCh38 9 131436619 131436619 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.294-1G>T p.X98_splice ENST00000357304 107 89 18 89 89 0 strelka-varscan-mutect PRRC2B,splice_acceptor_variant,,ENST00000357304,NM_013318.3;PRRC2B,splice_acceptor_variant,,ENST00000405995,; T ENST00000357304 Transcript splice_acceptor_variant -/11042 294/6690 98/2229 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 2/30 HIGH 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 131436619 131436619 G T 1 0 0 0 0 0 0 1 0 12749 1043 36 2 2 PRRC2B 9 131436619 Splice_Site SNP G C3L-02365_T 3752213 131436619 6958098 183 9155 QSOX2 0 . GRCh38 9 136208770 136208770 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2055G>T p.Arg685Ser p.R685S ENST00000358701 12/12 120 102 18 85 85 0 strelka-varscan-mutect QSOX2,missense_variant,p.Arg685Ser,ENST00000358701,NM_181701.3;LHX3,upstream_gene_variant,,ENST00000371748,NM_178138.4;QSOX2,downstream_gene_variant,,ENST00000455222,; A ENST00000358701 Transcript missense_variant 2093/4530 2055/2097 685/698 R/S agG/agT 1 -1 QSOX2 HGNC HGNC:30249 protein_coding YES CCDS35178.1 ENSP00000351536 Q6ZRP7 UPI00004A7AC1 NM_181701.3 deleterious(0) 12/12 hmmpanther:PTHR22897,hmmpanther:PTHR22897:SF7 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 34 136208770 136208770 C A 1 0 0 0 0 1 0 0 0 13039 506 18 2 2 QSOX2 9 136208770 Missense_Mutation SNP C C3L-02365_T 4772151 136208770 2185947 184 9156 CCDC183 0 . GRCh38 9 136807621 136807621 + Silent SNP C C T rs769002537 C3L-02365_T C3L-02365_N C C c.1536C>T p.= p.A512A ENST00000338005 14/14 264 218 46 182 182 0 strelka-varscan-mutect CCDC183,synonymous_variant,p.=,ENST00000338005,NM_001039374.4;RABL6,upstream_gene_variant,,ENST00000311502,NM_024718.4;RABL6,upstream_gene_variant,,ENST00000371663,;RABL6,upstream_gene_variant,,ENST00000425121,NM_001173988.1;RABL6,upstream_gene_variant,,ENST00000357466,;RABL6,upstream_gene_variant,,ENST00000371671,NM_001173989.2;CCDC183-AS1,intron_variant,,ENST00000414656,;CCDC183,non_coding_transcript_exon_variant,,ENST00000496839,;CCDC183,non_coding_transcript_exon_variant,,ENST00000484858,;CCDC183,downstream_gene_variant,,ENST00000371682,;CCDC183,3_prime_UTR_variant,,ENST00000479371,;CCDC183,non_coding_transcript_exon_variant,,ENST00000430612,;CCDC183,non_coding_transcript_exon_variant,,ENST00000481601,;RP11-216L13.19,intron_variant,,ENST00000415992,;RP11-216L13.19,intron_variant,,ENST00000459985,;RP11-216L13.18,intron_variant,,ENST00000471502,;RABL6,upstream_gene_variant,,ENST00000484471,; T ENST00000338005 Transcript synonymous_variant 1571/1671 1536/1605 512/534 A gcC/gcT rs769002537 1 1 CCDC183 HGNC HGNC:28236 protein_coding YES CCDS43906.1 ENSP00000338013 Q5T5S1 UPI00015E02CD NM_001039374.4 14/14 hmmpanther:PTHR21694,hmmpanther:PTHR21694:SF16 LOW 1 SNV 1 1 PASS rs769002537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 136807621 136807621 C T 1 0 0 0 0 0 0 0 1 2499 639 23 1 1 CCDC183 9 136807621 Silent SNP C C3L-02365_T 598851 136807621 1587096 185 9157 CACNA1B 0 . GRCh38 9 137986464 137986464 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1821G>T p.Lys607Asn p.K607N ENST00000371372 14/47 228 160 68 237 236 1 strelka-varscan-mutect CACNA1B,missense_variant,p.Lys607Asn,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Lys607Asn,ENST00000371363,;CACNA1B,missense_variant,p.Lys608Asn,ENST00000371355,;CACNA1B,missense_variant,p.Lys608Asn,ENST00000371357,;CACNA1B,missense_variant,p.Lys607Asn,ENST00000277549,;CACNA1B,missense_variant,p.Lys607Asn,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 1966/9790 1821/7020 607/2339 K/N aaG/aaT 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 deleterious(0) 14/47 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 137986464 137986464 G T 1 0 0 0 0 1 0 0 0 2227 1020 36 2 2 CACNA1B 9 137986464 Missense_Mutation SNP G C3L-02365_T 1178843 137986464 408253 186 9158 ITIH2 0 . GRCh38 10 7713281 7713281 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.463G>T p.Val155Leu p.V155L ENST00000358415 5/21 269 218 51 187 187 0 strelka-varscan-mutect ITIH2,missense_variant,p.Val155Leu,ENST00000358415,NM_002216.2;ITIH2,missense_variant,p.Val144Leu,ENST00000379587,;ITIH2,missense_variant,p.Val130Leu,ENST00000429820,;ITIH2,non_coding_transcript_exon_variant,,ENST00000480387,;ITIH2,non_coding_transcript_exon_variant,,ENST00000473227,; T ENST00000358415 Transcript missense_variant 629/3193 463/2841 155/946 V/L Gtg/Ttg COSM4970421 1 1 ITIH2 HGNC HGNC:6167 protein_coding YES CCDS31141.1 ENSP00000351190 P19823 UPI000036665E NM_002216.2 deleterious(0.04) 5/21 PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF14,Pfam_domain:PF08487,SMART_domains:SM00609 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 7713281 7713281 G T 1 0 0 0 0 1 0 0 0 7810 1275 44 2 2 ITIH2 10 7713281 Missense_Mutation SNP G C3L-02365_T 7713281 126084141 187 9159 MRC1 0 . GRCh38 10 17870315 17870315 + Nonsense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.2053G>T p.Gly685Ter p.G685* ENST00000569591 13/30 413 234 179 289 289 0 strelka-varscan-mutect MRC1,stop_gained,p.Gly685Ter,ENST00000569591,NM_002438.3;RP11-457D2.3,upstream_gene_variant,,ENST00000442231,; T ENST00000569591 Transcript stop_gained 2175/5198 2053/4371 685/1456 G/* Gga/Tga 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 13/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 17870315 17870315 G T 1 0 0 0 0 0 1 0 0 9722 1349 47 2 2 MRC1 10 17870315 Nonsense_Mutation SNP G C3L-02365_T 10157034 17870315 115927107 188 9160 PDSS1 0 . GRCh38 10 26705285 26705285 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.228-1G>T p.X76_splice ENST00000376215 370 246 124 342 340 2 strelka-varscan-mutect PDSS1,splice_acceptor_variant,,ENST00000376215,NM_014317.3;PDSS1,upstream_gene_variant,,ENST00000473224,; T ENST00000376215 Transcript splice_acceptor_variant -/1626 228/1248 76/415 1 1 PDSS1 HGNC HGNC:17759 protein_coding YES CCDS31168.1 ENSP00000365388 Q5T2R2 UPI000013DB22 NM_014317.3 3/11 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 26705285 26705285 G T 1 0 0 0 0 0 0 1 0 11781 1014 35 2 2 PDSS1 10 26705285 Splice_Site SNP G C3L-02365_T 8834970 26705285 107092137 189 9161 FAM13C 0 . GRCh38 10 59247644 59247644 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.1728C>A p.= p.I576I ENST00000618804 14/14 269 202 67 336 335 1 strelka-varscan-mutect FAM13C,synonymous_variant,p.=,ENST00000618427,NM_001166698.1;FAM13C,synonymous_variant,p.=,ENST00000621119,;FAM13C,synonymous_variant,p.=,ENST00000614220,;FAM13C,synonymous_variant,p.=,ENST00000618804,NM_198215.3;FAM13C,synonymous_variant,p.=,ENST00000611933,NM_001001971.2;FAM13C,synonymous_variant,p.=,ENST00000468840,NM_001143773.1;PHYHIPL,3_prime_UTR_variant,,ENST00000373880,NM_032439.3;PHYHIPL,3_prime_UTR_variant,,ENST00000373878,NM_001143774.1;FAM13C,downstream_gene_variant,,ENST00000435852,;FAM13C,3_prime_UTR_variant,,ENST00000622363,;PHYHIPL,downstream_gene_variant,,ENST00000486074,;FAM13C,downstream_gene_variant,,ENST00000489341,; T ENST00000618804 Transcript synonymous_variant 1818/3333 1728/1758 576/585 I atC/atA 1 -1 FAM13C HGNC HGNC:19371 protein_coding YES CCDS7255.1 ENSP00000481854 Q8NE31 UPI00001AEA18 NM_198215.3 14/14 hmmpanther:PTHR15904:SF19,hmmpanther:PTHR15904 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 59247644 59247644 G T 1 0 0 0 0 0 0 0 1 5303 1280 45 2 2 FAM13C 10 59247644 Silent SNP G C3L-02365_T 32542359 59247644 74549778 190 9162 HERC4 0 . GRCh38 10 68014167 68014167 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.928G>T p.Val310Phe p.V310F ENST00000395198 9/26 89 68 21 98 98 0 strelka-mutect HERC4,missense_variant,p.Val310Phe,ENST00000395198,NM_022079.2;HERC4,missense_variant,p.Val200Phe,ENST00000277817,;HERC4,missense_variant,p.Val310Phe,ENST00000412272,NM_001278185.1;HERC4,missense_variant,p.Val310Phe,ENST00000373700,NM_015601.3,NM_001278186.1;HERC4,missense_variant,p.Val307Phe,ENST00000427635,;HERC4,3_prime_UTR_variant,,ENST00000473533,;POU5F1P5,upstream_gene_variant,,ENST00000445059,; A ENST00000395198 Transcript missense_variant 1176/4445 928/3174 310/1057 V/F Gtt/Ttt 1 -1 HERC4 HGNC HGNC:24521 protein_coding YES CCDS41533.1 ENSP00000378624 Q5GLZ8 UPI00004C6F56 NM_022079.2 deleterious(0) 9/26 PROSITE_profiles:PS50012,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF285,Gene3D:2.130.10.30,Superfamily_domains:SSF50985,Prints_domain:PR00633 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 68014167 68014167 C A 1 0 0 0 0 1 0 0 0 6944 478 17 2 2 HERC4 10 68014167 Missense_Mutation SNP C C3L-02365_T 8766523 68014167 65783255 191 9163 CDH23 0 . GRCh38 10 71679419 71679419 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1800G>T p.Gln600His p.Q600H ENST00000224721 17/70 320 253 67 296 296 0 strelka-varscan-mutect CDH23,missense_variant,p.Gln600His,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Gln595His,ENST00000622827,;CDH23,missense_variant,p.Gln187His,ENST00000442677,;CDH23,missense_variant,p.Gln595His,ENST00000616684,NM_001171930.1;CDH23,missense_variant,p.Gln595His,ENST00000398809,;CDH23,missense_variant,p.Gln406His,ENST00000466757,;CDH23,missense_variant,p.Gln595His,ENST00000299366,NM_001171931.1; T ENST00000224721 Transcript missense_variant 2190/11139 1800/10080 600/3359 Q/H caG/caT 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 tolerated(0.56) 17/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 71679419 71679419 G T 1 0 0 0 0 1 0 0 0 2811 933 33 2 2 CDH23 10 71679419 Missense_Mutation SNP G C3L-02365_T 3665252 71679419 62118003 192 9164 LIPM 0 . GRCh38 10 88817871 88817871 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.977C>T p.Thr326Ile p.T326I ENST00000404743 8/9 134 107 27 190 190 0 strelka-varscan-mutect LIPM,missense_variant,p.Thr326Ile,ENST00000404743,NM_001128215.1;LIPM,missense_variant,p.Thr286Ile,ENST00000539337,;ANKRD22,downstream_gene_variant,,ENST00000371930,NM_144590.2;ANKRD22,downstream_gene_variant,,ENST00000476963,; T ENST00000404743 Transcript missense_variant 1144/1439 977/1272 326/423 T/I aCc/aTc 1 1 LIPM HGNC HGNC:23455 protein_coding YES CCDS44457.1 ENSP00000383901 Q5VYY2 UPI00004B21B5 NM_001128215.1 tolerated(0.39) 8/9 Gene3D:3.40.50.1820,Pfam_domain:PF00561,PIRSF_domain:PIRSF000862,hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF12,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999541 1 1 1 0 T 3 4 34 88817871 88817871 C T 1 0 0 0 0 1 0 0 0 8749 507 18 3 3 LIPM 10 88817871 Missense_Mutation SNP C C3L-02365_T 17138452 88817871 44979551 193 9165 GOT1 0 . GRCh38 10 99406812 99406812 + Missense_Mutation SNP A A C novel C3L-02365_T C3L-02365_N A A c.338T>G p.Leu113Arg p.L113R ENST00000370508 3/9 139 106 33 121 121 0 strelka-varscan-mutect GOT1,missense_variant,p.Leu113Arg,ENST00000370508,NM_002079.2;GOT1,upstream_gene_variant,,ENST00000489349,; C ENST00000370508 Transcript missense_variant 366/1947 338/1242 113/413 L/R cTt/cGt 1 -1 GOT1 HGNC HGNC:4432 protein_coding YES CCDS7479.1 ENSP00000359539 P17174 A0A140VK69 UPI000013CA75 NM_002079.2 deleterious(0) 3/9 hmmpanther:PTHR11879:SF3,hmmpanther:PTHR11879,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 99406812 99406812 A C 1 0 0 0 0 1 0 0 0 6473 72 3 5 5 GOT1 10 99406812 Missense_Mutation SNP A C3L-02365_T 10588941 99406812 34390610 194 9166 PPRC1 0 . GRCh38 10 102147263 102147263 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.4271G>T p.Gly1424Val p.G1424V ENST00000278070 9/14 365 296 69 330 329 1 strelka-varscan-mutect PPRC1,missense_variant,p.Gly1424Val,ENST00000278070,NM_001288728.1,NM_015062.4;PPRC1,missense_variant,p.Gly391Val,ENST00000370012,;PPRC1,intron_variant,,ENST00000413464,NM_001288727.1;NOLC1,upstream_gene_variant,,ENST00000405356,NM_001284388.1;NOLC1,upstream_gene_variant,,ENST00000605788,NM_004741.4;PPRC1,intron_variant,,ENST00000489648,;PPRC1,downstream_gene_variant,,ENST00000462933,;PPRC1,upstream_gene_variant,,ENST00000495914,; T ENST00000278070 Transcript missense_variant 4310/5330 4271/4995 1424/1664 G/V gGc/gTc 1 1 PPRC1 HGNC HGNC:30025 protein_coding YES CCDS7529.1 ENSP00000278070 Q5VV67 UPI000013DB5C NM_001288728.1,NM_015062.4 deleterious_low_confidence(0.01) 9/14 hmmpanther:PTHR15528,hmmpanther:PTHR15528:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 102147263 102147263 G T 1 0 0 0 0 1 0 0 0 12537 1203 42 2 2 PPRC1 10 102147263 Missense_Mutation SNP G C3L-02365_T 2740451 102147263 31650159 195 9167 SUFU 0 . GRCh38 10 102617530 102617530 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.1398G>T p.= p.G466G ENST00000423559 10/10 54 47 7 88 88 0 strelka-varscan-mutect SUFU,synonymous_variant,p.=,ENST00000423559,;SUFU,intron_variant,,ENST00000369902,NM_016169.3;SUFU,intron_variant,,ENST00000369899,NM_001178133.1; T ENST00000423559 Transcript synonymous_variant 1472/2601 1398/1446 466/481 G ggG/ggT 1 1 SUFU HGNC HGNC:16466 protein_coding ENSP00000411597 Q9UMX1 UPI000006D11C 10/10 LOW SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.77749 1 1 1 1 0 T 2 4 34 102617530 102617530 G T 1 0 0 0 0 0 0 0 1 15753 1219 43 2 2 SUFU 10 102617530 Silent SNP G C3L-02365_T 470267 102617530 31179892 196 9168 TCF7L2 0 . GRCh38 10 113089470 113089470 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.239G>T p.Ser80Ile p.S80I ENST00000542695 5/15 216 174 42 250 249 1 strelka-varscan-mutect TCF7L2,missense_variant,p.Ser80Ile,ENST00000542695,;TCF7L2,missense_variant,p.Ser185Ile,ENST00000355717,NM_001146286.1,NM_001146283.1;TCF7L2,missense_variant,p.Ser155Ile,ENST00000346198,;TCF7L2,intron_variant,,ENST00000355995,;TCF7L2,intron_variant,,ENST00000543371,;TCF7L2,intron_variant,,ENST00000538897,NM_001198529.1,NM_001146284.1,NM_001198531.1;TCF7L2,intron_variant,,ENST00000536810,NM_001146285.1;TCF7L2,intron_variant,,ENST00000369397,NM_030756.4;TCF7L2,intron_variant,,ENST00000534894,NM_001198530.1;TCF7L2,intron_variant,,ENST00000627217,NM_001146274.1;TCF7L2,intron_variant,,ENST00000545257,NM_001198525.1;TCF7L2,intron_variant,,ENST00000629706,NM_001198526.1;TCF7L2,intron_variant,,ENST00000352065,NM_001198528.1;TCF7L2,intron_variant,,ENST00000369395,NM_001198527.1; T ENST00000542695 Transcript missense_variant 1064/4136 239/1605 80/534 S/I aGc/aTc COSM4552290 1 1 TCF7L2 HGNC HGNC:11641 protein_coding ENSP00000443883 C6ZRJ6 UPI0001AF9FEB tolerated_low_confidence(0.06) 5/15 Pfam_domain:PF08347 1 MODERATE SNV 5 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999963 1 1 1 0 T 3 4 34 113089470 113089470 G T 1 0 0 0 0 1 0 0 0 16105 971 34 2 2 TCF7L2 10 113089470 Missense_Mutation SNP G C3L-02365_T 10471940 113089470 20707952 197 9169 CCDC186 0 . GRCh38 10 114151218 114151218 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.762A>T p.Leu254Phe p.L254F ENST00000369287 4/16 110 77 33 103 103 0 strelka-varscan-mutect CCDC186,missense_variant,p.Leu254Phe,ENST00000369287,NM_001321829.1,NM_018017.2; A ENST00000369287 Transcript missense_variant,splice_region_variant 1029/7245 762/2697 254/898 L/F ttA/ttT 1 -1 CCDC186 HGNC HGNC:24349 protein_coding YES CCDS7587.1 ENSP00000358293 Q7Z3E2 UPI00001D3EF5 NM_001321829.1,NM_018017.2 deleterious(0.02) 4/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18911 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 114151218 114151218 T A 1 0 0 0 0 1 0 0 0 2502 1536 53 4 4 CCDC186 10 114151218 Missense_Mutation SNP T C3L-02365_T 1061748 114151218 19646204 198 9170 PTPRE 0 . GRCh38 10 128076603 128076603 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1600G>T p.Asp534Tyr p.D534Y ENST00000254667 18/21 111 93 18 127 127 0 strelka-varscan-mutect PTPRE,missense_variant,p.Asp534Tyr,ENST00000254667,NM_001323355.1,NM_001316676.1,NM_001323356.1,NM_006504.4;PTPRE,missense_variant,p.Asp476Tyr,ENST00000306042,NM_001323357.1,NM_130435.3;PTPRE,splice_region_variant,,ENST00000479896,;PTPRE,downstream_gene_variant,,ENST00000463727,; T ENST00000254667 Transcript missense_variant,splice_region_variant 1879/5331 1600/2103 534/700 D/Y Gat/Tat 1 1 PTPRE HGNC HGNC:9669 protein_coding YES CCDS7657.1 ENSP00000254667 P23469 UPI0000132991 NM_001323355.1,NM_001316676.1,NM_001323356.1,NM_006504.4 deleterious(0.01) 18/21 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF002006,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 128076603 128076603 G T 1 0 0 0 0 1 0 0 0 12954 1188 41 2 2 PTPRE 10 128076603 Missense_Mutation SNP G C3L-02365_T 13925385 128076603 5720819 199 9171 STK32C 0 . GRCh38 10 132222736 132222736 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.1156G>C p.Glu386Gln p.E386Q ENST00000298630 10/12 256 206 50 254 254 0 strelka-varscan-mutect STK32C,missense_variant,p.Glu386Gln,ENST00000298630,NM_173575.2;STK32C,missense_variant,p.Glu269Gln,ENST00000368622,NM_001318879.1;STK32C,downstream_gene_variant,,ENST00000368620,;STK32C,non_coding_transcript_exon_variant,,ENST00000462160,; G ENST00000298630 Transcript missense_variant 1263/2086 1156/1461 386/486 E/Q Gag/Cag 1 -1 STK32C HGNC HGNC:21332 protein_coding YES CCDS7666.1 ENSP00000298630 Q86UX6 A0A140VJW0 UPI0000192113 NM_173575.2 deleterious(0) 10/12 hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF153,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 132222736 132222736 C G 1 0 0 0 0 1 0 0 0 15676 864 30 4 4 STK32C 10 132222736 Missense_Mutation SNP C C3L-02365_T 4146133 132222736 1574686 200 9172 OR51S1 0 . GRCh38 11 4849045 4849045 + Nonsense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.164G>A p.Trp55Ter p.W55* ENST00000322101 1/1 257 243 14 245 244 1 strelka-varscan-mutect OR51S1,stop_gained,p.Trp55Ter,ENST00000322101,NM_001004758.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322101 Transcript stop_gained 164/972 164/972 55/323 W/* tGg/tAg 1 -1 OR51S1 HGNC HGNC:15204 protein_coding YES CCDS31362.1 ENSP00000322754 Q8NGJ8 A0A126GWN3 UPI0000041C33 NM_001004758.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF73,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 4849045 4849045 C T 1 0 0 0 0 0 1 0 0 11179 595 21 3 3 OR51S1 11 4849045 Nonsense_Mutation SNP C C3L-02365_T 4849045 130237577 201 9173 OR52A5 0 . GRCh38 11 5132505 5132505 + Silent SNP T T A novel C3L-02365_T C3L-02365_N T T c.138A>T p.= p.L46L ENST00000307388 1/1 173 129 44 184 184 0 strelka-varscan-mutect OR52A5,synonymous_variant,p.=,ENST00000307388,NM_001005160.2; A ENST00000307388 Transcript synonymous_variant 138/951 138/951 46/316 L ctA/ctT 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 5132505 5132505 T A 1 0 0 0 0 0 0 0 1 11183 1741 61 4 4 OR52A5 11 5132505 Silent SNP T C3L-02365_T 283460 5132505 129954117 202 9174 OR52N2 0 . GRCh38 11 5820396 5820396 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.61G>T p.Gly21Trp p.G21W ENST00000317037 1/1 234 197 37 208 207 1 strelka-varscan-mutect OR52N2,missense_variant,p.Gly21Trp,ENST00000317037,NM_001005174.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000317037 Transcript missense_variant 83/1035 61/966 21/321 G/W Ggg/Tgg 1 1 OR52N2 HGNC HGNC:15228 protein_coding YES CCDS31399.1 ENSP00000322801 Q8NGI0 UPI0000041BEB NM_001005174.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF185,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 5820396 5820396 G T 1 0 0 0 0 1 0 0 0 11201 1348 47 2 2 OR52N2 11 5820396 Missense_Mutation SNP G C3L-02365_T 687891 5820396 129266226 203 9175 GAS2 0 . GRCh38 11 22726300 22726300 + Silent SNP G G A rs371383777 C3L-02365_T C3L-02365_N G G c.276G>A p.= p.P92P ENST00000454584 4/8 155 125 30 146 146 0 strelka-varscan-mutect GAS2,synonymous_variant,p.=,ENST00000454584,NM_001143830.1;GAS2,synonymous_variant,p.=,ENST00000278187,NM_177553.2,NM_005256.3;GAS2,synonymous_variant,p.=,ENST00000528582,;GAS2,synonymous_variant,p.=,ENST00000532398,;GAS2,synonymous_variant,p.=,ENST00000630668,;GAS2,synonymous_variant,p.=,ENST00000534801,;GAS2,synonymous_variant,p.=,ENST00000533363,;GAS2,synonymous_variant,p.=,ENST00000524701,; A ENST00000454584 Transcript synonymous_variant 581/2286 276/942 92/313 P ccG/ccA rs371383777,COSM2112696 1 1 GAS2 HGNC HGNC:4167 protein_coding YES CCDS7858.1 ENSP00000401145 O43903 UPI000000D98C NM_001143830.1 4/8 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF298,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576 0,1 LOW 1 SNV 1 0,1 1 PASS rs371383777 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 22726300 22726300 G A 1 0 0 0 0 0 0 0 1 6115 1132 40 1 1 GAS2 11 22726300 Silent SNP G C3L-02365_T 16905904 22726300 112360322 204 9176 HIPK3 0 . GRCh38 11 33339520 33339520 + Silent SNP C C T C3L-02365_T C3L-02365_N C C c.1599C>T p.= p.F533F ENST00000303296 6/17 77 72 5 88 88 0 strelka-varscan-mutect HIPK3,synonymous_variant,p.=,ENST00000303296,NM_005734.4;HIPK3,synonymous_variant,p.=,ENST00000456517,NM_001278162.1;HIPK3,synonymous_variant,p.=,ENST00000379016,NM_001048200.2;HIPK3,synonymous_variant,p.=,ENST00000525975,NM_001278163.1;HIPK3,downstream_gene_variant,,ENST00000534262,; T ENST00000303296 Transcript synonymous_variant 1904/7408 1599/3648 533/1215 F ttC/ttT COSM3446853 1 1 HIPK3 HGNC HGNC:4915 protein_coding YES CCDS7884.1 ENSP00000304226 Q9H422 UPI000006D7F8 NM_005734.4 6/17 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF45,Superfamily_domains:SSF56112 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 33339520 33339520 C T 1 0 0 0 0 0 0 0 1 7006 854 30 3 3 HIPK3 11 33339520 Silent SNP C C3L-02365_T 10613220 33339520 101747102 205 9177 CKAP5 0 . GRCh38 11 46759419 46759419 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.4418A>T p.His1473Leu p.H1473L ENST00000529230 34/44 154 110 44 145 145 0 strelka-varscan-mutect CKAP5,missense_variant,p.His1473Leu,ENST00000529230,NM_001008938.3;CKAP5,missense_variant,p.His1473Leu,ENST00000312055,NM_014756.3;CKAP5,missense_variant,p.His1473Leu,ENST00000354558,;CKAP5,missense_variant,p.His37Leu,ENST00000526876,;CKAP5,missense_variant,p.His30Leu,ENST00000527333,;SNORD67,downstream_gene_variant,,ENST00000390833,;SNORD67,upstream_gene_variant,,ENST00000516618,;CKAP5,non_coding_transcript_exon_variant,,ENST00000533413,;CKAP5,downstream_gene_variant,,ENST00000526943,; A ENST00000529230 Transcript missense_variant 4465/7121 4418/6099 1473/2032 H/L cAt/cTt 1 -1 CKAP5 HGNC HGNC:28959 protein_coding YES CCDS31477.1 ENSP00000432768 Q14008 UPI000013F21E NM_001008938.3 tolerated(0.29) 34/44 hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609 MODERATE 1 SNV 5 1 PASS rs1182184453 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 46759419 46759419 T A 1 0 0 0 0 1 0 0 0 3208 1464 51 4 4 CKAP5 11 46759419 Missense_Mutation SNP T C3L-02365_T 13419899 46759419 88327203 206 9178 OR4C6 0 . GRCh38 11 55665457 55665457 + Silent SNP C C A rs77687368 C3L-02365_T C3L-02365_N C C c.291C>A p.= p.T97T ENST00000314259 1/1 368 306 62 393 393 0 strelka-varscan-mutect OR4C6,synonymous_variant,p.=,ENST00000314259,NM_001004704.1; A ENST00000314259 Transcript synonymous_variant 291/930 291/930 97/309 T acC/acA rs77687368,COSM543456 1 1 OR4C6 HGNC HGNC:14743 protein_coding YES CCDS31506.1 ENSP00000324769 Q8NH72 A0A126GVN0 UPI0000041868 NM_001004704.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF80,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 0,1 1 PASS rs77687368 . 0 207 0 0 0 0 0 2 -3.185765 0 0 1 0 0 A 2 1 34 55665457 55665457 C A 1 0 0 0 0 0 0 0 1 11129 610 22 2 2 OR4C6 11 55665457 Silent SNP C C3L-02365_T 8906038 55665457 79421165 207 9179 OR5F1 0 . GRCh38 11 55994447 55994447 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.179A>G p.Tyr60Cys p.Y60C ENST00000278409 1/1 132 110 22 107 107 0 strelka-varscan-mutect OR5F1,missense_variant,p.Tyr60Cys,ENST00000278409,NM_003697.1; C ENST00000278409 Transcript missense_variant 179/945 179/945 60/314 Y/C tAt/tGt 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 55994447 55994447 T C 1 0 0 0 0 1 0 0 0 11228 1406 49 5 5 OR5F1 11 55994447 Missense_Mutation SNP T C3L-02365_T 328990 55994447 79092175 208 9180 OR8I2 0 . GRCh38 11 56093499 56093499 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.192C>A p.Ser64Arg p.S64R ENST00000302124 1/1 124 103 21 134 134 0 strelka-varscan-mutect OR8I2,missense_variant,p.Ser64Arg,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; A ENST00000302124 Transcript missense_variant 192/933 192/933 64/310 S/R agC/agA COSM1171806 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 deleterious(0.04) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 181 21 8 0 0 0 0 -20 0.8348266 0 1 1 0 A 3 1 34 56093499 56093499 C A 1 0 0 0 0 1 0 0 0 11308 709 25 2 2 OR8I2 11 56093499 Missense_Mutation SNP C C3L-02365_T 99052 56093499 78993123 209 9181 OR8J3 0 . GRCh38 11 56137320 56137320 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.399G>A p.Met133Ile p.M133I ENST00000301529 1/1 193 132 61 197 197 0 strelka-varscan-mutect OR8J3,missense_variant,p.Met133Ile,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; T ENST00000301529 Transcript missense_variant 399/948 399/948 133/315 M/I atG/atA 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 tolerated(0.2) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 56137320 56137320 C T 1 0 0 0 0 1 0 0 0 11310 594 21 3 3 OR8J3 11 56137320 Missense_Mutation SNP C C3L-02365_T 43821 56137320 78949302 210 9182 OR5T3 0 . GRCh38 11 56252203 56252203 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.4G>T p.Asp2Tyr p.D2Y ENST00000303059 1/1 60 52 8 93 93 0 strelka-varscan-mutect OR5T3,missense_variant,p.Asp2Tyr,ENST00000303059,NM_001004747.1; T ENST00000303059 Transcript missense_variant 4/1023 4/1023 2/340 D/Y Gac/Tac 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87 MODERATE 1 SNV 1 PASS . . 1 203 5 0 0 0 0 0 -18.3936 1 1 1 1 0 T 3 4 34 56252203 56252203 G T 1 0 0 0 0 1 0 0 0 11251 1188 41 2 2 OR5T3 11 56252203 Missense_Mutation SNP G C3L-02365_T 114883 56252203 78834419 211 9183 SSRP1 0 . GRCh38 11 57333524 57333524 + Missense_Mutation SNP G G C C3L-02365_T C3L-02365_N G G c.257C>G p.Ser86Cys p.S86C ENST00000278412 4/17 247 197 50 247 247 0 strelka-varscan-mutect SSRP1,missense_variant,p.Ser86Cys,ENST00000278412,NM_003146.2;SSRP1,5_prime_UTR_variant,,ENST00000526696,;SSRP1,5_prime_UTR_variant,,ENST00000529002,;P2RX3,upstream_gene_variant,,ENST00000263314,NM_002559.3;P2RX3,upstream_gene_variant,,ENST00000616487,;SSRP1,upstream_gene_variant,,ENST00000635721,;P2RX3,upstream_gene_variant,,ENST00000533436,;SSRP1,non_coding_transcript_exon_variant,,ENST00000293880,; C ENST00000278412 Transcript missense_variant 524/2819 257/2130 86/709 S/C tCt/tGt COSM928579 1 -1 SSRP1 HGNC HGNC:11327 protein_coding YES CCDS7952.1 ENSP00000278412 Q08945 A0A024R4Z6 UPI000013601D NM_003146.2 tolerated(0.06) 4/17 Pfam_domain:PF03531,Gene3D:2.30.29.30 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 57333524 57333524 G C 1 0 0 0 0 1 0 0 0 15571 942 33 4 4 SSRP1 11 57333524 Missense_Mutation SNP G C3L-02365_T 1081321 57333524 77753098 212 9184 OR5B21 0 . GRCh38 11 58507830 58507830 + Nonsense_Mutation SNP G G T rs146345059 C3L-02365_T C3L-02365_N G G c.276C>A p.Tyr92Ter p.Y92* ENST00000360374 1/1 259 174 85 238 238 0 strelka-varscan-mutect OR5B21,stop_gained,p.Tyr92Ter,ENST00000360374,NM_001005218.1;RP11-655C2.3,upstream_gene_variant,,ENST00000531715,;RP11-655C2.3,upstream_gene_variant,,ENST00000528978,;RP11-655C2.3,upstream_gene_variant,,ENST00000527054,; T ENST00000360374 Transcript stop_gained 276/931 276/930 92/309 Y/* taC/taA rs146345059,COSM1561330 1 -1 OR5B21 HGNC HGNC:19616 protein_coding YES CCDS31552.1 ENSP00000353537 A6NL26 UPI000015FCAA NM_001005218.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF329,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 HIGH SNV 0,1 1 PASS rs146345059 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 58507830 58507830 G T 1 0 0 0 0 0 1 0 0 11222 1140 40 1 1 OR5B21 11 58507830 Nonsense_Mutation SNP G C3L-02365_T 1174306 58507830 76578792 213 9185 KRTAP5-11 0 . GRCh38 11 71582805 71582805 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.33C>T p.= p.G11G ENST00000398530 1/1 313 262 51 245 245 0 strelka-varscan-mutect KRTAP5-11,synonymous_variant,p.=,ENST00000398530,NM_001005405.2;KRTAP5-11,synonymous_variant,p.=,ENST00000617152,;KRTAP5-11,synonymous_variant,p.=,ENST00000616086,;KRTAP5-11,intron_variant,,ENST00000526239,;KRTAP5-14P,upstream_gene_variant,,ENST00000502328,; A ENST00000398530 Transcript synonymous_variant 71/1021 33/471 11/156 G ggC/ggT 1 -1 KRTAP5-11 HGNC HGNC:23606 protein_coding YES CCDS41685.1 ENSP00000381541 Q6L8G4 UPI0000376063 NM_001005405.2 1/1 Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 71582805 71582805 G A 1 0 0 0 0 0 0 0 1 8455 958 34 3 3 KRTAP5-11 11 71582805 Silent SNP G C3L-02365_T 13074975 71582805 63503817 214 9186 FOLR1 0 . GRCh38 11 72196037 72196037 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.634A>T p.Met212Leu p.M212L ENST00000393679 5/5 597 508 89 467 466 1 strelka-varscan-mutect FOLR1,missense_variant,p.Met212Leu,ENST00000393679,;FOLR1,missense_variant,p.Met212Leu,ENST00000312293,NM_016725.2;FOLR1,missense_variant,p.Met212Leu,ENST00000393681,NM_016724.2;FOLR1,missense_variant,p.Met212Leu,ENST00000393676,NM_000802.3,NM_016729.2;RP11-807H22.7,intron_variant,,ENST00000378140,; T ENST00000393679 Transcript missense_variant 1070/1331 634/774 212/257 M/L Atg/Ttg 1 1 FOLR1 HGNC HGNC:3791 protein_coding YES CCDS8211.1 ENSP00000377284 P15328 A0A024R5H1 UPI0000000C4C tolerated(0.24) 5/5 hmmpanther:PTHR10517:SF15,hmmpanther:PTHR10517 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 72196037 72196037 A T 1 0 0 0 0 1 0 0 0 5841 333 12 4 4 FOLR1 11 72196037 Missense_Mutation SNP A C3L-02365_T 613232 72196037 62890585 215 9187 INPPL1 0 . GRCh38 11 72237227 72237227 + Nonsense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.2983C>T p.Gln995Ter p.Q995* ENST00000298229 26/28 256 174 82 186 186 0 strelka-varscan-mutect INPPL1,stop_gained,p.Gln995Ter,ENST00000298229,NM_001567.3;INPPL1,stop_gained,p.Gln753Ter,ENST00000538751,;INPPL1,stop_gained,p.Gln929Ter,ENST00000541756,;INPPL1,stop_gained,p.Gln8Ter,ENST00000541752,;PHOX2A,downstream_gene_variant,,ENST00000298231,NM_005169.3;PHOX2A,downstream_gene_variant,,ENST00000546310,;INPPL1,upstream_gene_variant,,ENST00000320683,;PHOX2A,downstream_gene_variant,,ENST00000544057,;INPPL1,intron_variant,,ENST00000535985,;INPPL1,downstream_gene_variant,,ENST00000541303,;INPPL1,downstream_gene_variant,,ENST00000545355,;INPPL1,downstream_gene_variant,,ENST00000544806,;INPPL1,downstream_gene_variant,,ENST00000537755,; T ENST00000298229 Transcript stop_gained 3187/4733 2983/3777 995/1258 Q/* Cag/Tag COSM4937040 1 1 INPPL1 HGNC HGNC:6080 protein_coding YES CCDS8213.1 ENSP00000298229 O15357 UPI000013E4AF NM_001567.3 26/28 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF15 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 72237227 72237227 C T 1 0 0 0 0 0 1 0 0 7664 595 21 3 3 INPPL1 11 72237227 Nonsense_Mutation SNP C C3L-02365_T 41190 72237227 62849395 216 9188 TENM4 0 . GRCh38 11 78890004 78890004 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.865C>A p.Pro289Thr p.P289T ENST00000278550 9/34 70 49 21 56 56 0 strelka-varscan-mutect TENM4,missense_variant,p.Pro289Thr,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Pro134Thr,ENST00000533074,;TENM4,non_coding_transcript_exon_variant,,ENST00000533013,; T ENST00000278550 Transcript missense_variant 1328/14000 865/8310 289/2769 P/T Cct/Act 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 tolerated_low_confidence(1) 9/34 Pfam_domain:PF06484,PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 78890004 78890004 G T 1 0 0 0 0 1 0 0 0 16174 1203 42 2 2 TENM4 11 78890004 Missense_Mutation SNP G C3L-02365_T 6652777 78890004 56196618 217 9189 PRSS23 0 . GRCh38 11 86808558 86808558 + Silent SNP C C G rs748802260 C3L-02365_T C3L-02365_N C C c.915C>G p.= p.L305L ENST00000280258 2/2 397 318 79 324 324 0 strelka-varscan-mutect PRSS23,synonymous_variant,p.=,ENST00000280258,NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1;PRSS23,intron_variant,,ENST00000533902,;PRSS23,downstream_gene_variant,,ENST00000527521,;PRSS23,intron_variant,,ENST00000531475,;PRSS23,intron_variant,,ENST00000533880,;PRSS23,intron_variant,,ENST00000532234,; G ENST00000280258 Transcript synonymous_variant 1340/4015 915/1152 305/383 L ctC/ctG rs748802260 1 1 PRSS23 HGNC HGNC:14370 protein_coding YES CCDS8278.1 ENSP00000280258 O95084 UPI0000048EBC NM_001293180.1,NM_001293178.1,NM_007173.5,NM_001293179.1 2/2 Gene3D:2.40.10.10,hmmpanther:PTHR15462,hmmpanther:PTHR15462:SF10,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS rs748802260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 86808558 86808558 C G 1 0 0 0 0 0 0 0 1 12767 900 32 4 4 PRSS23 11 86808558 Silent SNP C C3L-02365_T 7918554 86808558 48278064 218 9190 FAT3 0 . GRCh38 11 92800126 92800126 + Missense_Mutation SNP C C A rs760836405 C3L-02365_T C3L-02365_N C C c.6663C>A p.Phe2221Leu p.F2221L ENST00000525166 9/27 155 100 55 150 150 0 strelka-varscan-mutect FAT3,missense_variant,p.Phe2371Leu,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Phe2221Leu,ENST00000525166,; A ENST00000525166 Transcript missense_variant 6685/18699 6663/13320 2221/4439 F/L ttC/ttA rs760836405 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.66) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs760836405 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 92800126 92800126 C A 1 0 0 0 0 1 0 0 0 5551 854 30 2 2 FAT3 11 92800126 Missense_Mutation SNP C C3L-02365_T 5991568 92800126 42286496 219 9191 MTNR1B 0 . GRCh38 11 92969836 92969836 + Silent SNP C C A rs779893016 C3L-02365_T C3L-02365_N C C c.111C>A p.= p.P37P ENST00000257068 1/2 135 88 47 82 82 0 strelka-varscan-mutect MTNR1B,missense_variant,p.Leu19Met,ENST00000528076,;MTNR1B,synonymous_variant,p.=,ENST00000257068,NM_005959.3;RP11-676F20.1,downstream_gene_variant,,ENST00000532770,;MTNR1B,synonymous_variant,p.=,ENST00000532482,; A ENST00000257068 Transcript synonymous_variant 117/1565 111/1089 37/362 P ccC/ccA rs779893016 1 1 MTNR1B HGNC HGNC:7464 protein_coding YES CCDS8290.1 ENSP00000257068 P49286 UPI0000050408 NM_005959.3 1/2 hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF262,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01149 LOW 1 SNV 1 1 PASS rs779893016 . 0 202 6 2 0 0 0 0 -20 0.9999839 1 1 1 0 A 2 1 34 92969836 92969836 C A 1 0 0 0 0 0 0 0 1 9939 668 24 2 2 MTNR1B 11 92969836 Silent SNP C C3L-02365_T 169710 92969836 42116786 220 9192 HEPHL1 0 . GRCh38 11 94064373 94064373 + Missense_Mutation SNP G G C rs73551201 C3L-02365_T C3L-02365_N G G c.671G>C p.Arg224Pro p.R224P ENST00000315765 4/20 137 114 23 130 130 0 strelka-varscan-mutect HEPHL1,missense_variant,p.Arg224Pro,ENST00000315765,NM_001098672.1; C ENST00000315765 Transcript missense_variant 679/5345 671/3480 224/1159 R/P cGa/cCa rs73551201 1 1 HEPHL1 HGNC HGNC:30477 protein_coding YES CCDS44710.1 ENSP00000313699 Q6MZM0 UPI0000237563 NM_001098672.1 tolerated(0.11) 4/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF655,Superfamily_domains:SSF49503 MODERATE 1 SNV 5 1 PASS rs73551201 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 94064373 94064373 G C 1 0 0 0 0 1 0 0 0 6939 1058 37 4 4 HEPHL1 11 94064373 Missense_Mutation SNP G C3L-02365_T 1094537 94064373 41022249 221 9193 CNTN5 0 . GRCh38 11 99819725 99819725 + Silent SNP C C A rs753301950 C3L-02365_T C3L-02365_N C C c.237C>A p.= p.P79P ENST00000524871 4/25 436 343 93 439 439 0 strelka-varscan-mutect CNTN5,synonymous_variant,p.=,ENST00000524871,NM_014361.3;CNTN5,synonymous_variant,p.=,ENST00000279463,;CNTN5,synonymous_variant,p.=,ENST00000527185,NM_001243271.1;CNTN5,synonymous_variant,p.=,ENST00000528682,NM_001243270.1;CNTN5,intron_variant,,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; A ENST00000524871 Transcript synonymous_variant 527/6258 237/3303 79/1100 P ccC/ccA rs753301950 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 4/25 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51 LOW 1 SNV 1 1 PASS rs753301950 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 99819725 99819725 C A 1 0 0 0 0 0 0 0 1 3425 581 21 2 2 CNTN5 11 99819725 Silent SNP C C3L-02365_T 5755352 99819725 35266897 222 9194 MMP8 0 . GRCh38 11 102721643 102721643 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.467C>A p.Ala156Glu p.A156E ENST00000236826 3/10 212 129 83 170 169 1 strelka-varscan-mutect MMP8,missense_variant,p.Ala156Glu,ENST00000236826,NM_002424.2,NM_001304441.1,NM_001304442.1;MMP8,missense_variant,p.Ala132Glu,ENST00000438475,;MMP8,3_prime_UTR_variant,,ENST00000528662,;MMP8,3_prime_UTR_variant,,ENST00000533258,;MMP8,downstream_gene_variant,,ENST00000532799,;MMP8,downstream_gene_variant,,ENST00000531168,; T ENST00000236826 Transcript missense_variant 566/3056 467/1404 156/467 A/E gCa/gAa 1 -1 MMP8 HGNC HGNC:7175 protein_coding YES CCDS8320.1 ENSP00000236826 P22894 UPI00000422BB NM_002424.2,NM_001304441.1,NM_001304442.1 deleterious(0) 3/10 Gene3D:3.40.390.10,Pfam_domain:PF00413,PIRSF_domain:PIRSF001191,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF137,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 102721643 102721643 G T 1 0 0 0 0 1 0 0 0 9631 1319 46 2 2 MMP8 11 102721643 Missense_Mutation SNP G C3L-02365_T 2901918 102721643 32364979 223 9195 DDI1 0 . GRCh38 11 104037883 104037883 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1061C>A p.Thr354Asn p.T354N ENST00000302259 1/1 271 235 36 249 249 0 strelka-varscan-mutect DDI1,missense_variant,p.Thr354Asn,ENST00000302259,NM_001001711.2;PDGFD,intron_variant,,ENST00000302251,NM_033135.3;PDGFD,intron_variant,,ENST00000393158,NM_025208.4;PDGFD,upstream_gene_variant,,ENST00000529268,; A ENST00000302259 Transcript missense_variant 1304/2609 1061/1191 354/396 T/N aCt/aAt 1 1 DDI1 HGNC HGNC:18961 protein_coding YES CCDS31660.1 ENSP00000302805 Q8WTU0 UPI0000047AEA NM_001001711.2 deleterious(0.03) 1/1 hmmpanther:PTHR12917,hmmpanther:PTHR12917:SF15 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 104037883 104037883 C A 1 0 0 0 0 1 0 0 0 4131 565 20 2 2 DDI1 11 104037883 Missense_Mutation SNP C C3L-02365_T 1316240 104037883 31048739 224 9196 ELMOD1 0 . GRCh38 11 107656066 107656066 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.832T>A p.Cys278Ser p.C278S ENST00000265840 11/12 179 140 39 162 162 0 strelka-varscan-mutect ELMOD1,missense_variant,p.Cys278Ser,ENST00000265840,NM_018712.3;ELMOD1,missense_variant,p.Cys270Ser,ENST00000443271,NM_001130037.1;ELMOD1,missense_variant,p.Cys272Ser,ENST00000531234,NM_001308018.1;ELMOD1,downstream_gene_variant,,ENST00000534236,; A ENST00000265840 Transcript missense_variant,splice_region_variant 1097/2852 832/1005 278/334 C/S Tgc/Agc 1 1 ELMOD1 HGNC HGNC:25334 protein_coding YES CCDS44723.1 ENSP00000265840 Q8N336 UPI000006DF30 NM_018712.3 tolerated(0.1) 11/12 PROSITE_profiles:PS51335,hmmpanther:PTHR12771:SF18,hmmpanther:PTHR12771,Pfam_domain:PF04727 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 107656066 107656066 T A 1 0 0 0 0 1 0 0 0 4902 1594 55 4 4 ELMOD1 11 107656066 Missense_Mutation SNP T C3L-02365_T 3618183 107656066 27430556 225 9197 SCN4B 0 . GRCh38 11 118145068 118145068 + Missense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.223G>A p.Ala75Thr p.A75T ENST00000324727 2/5 410 360 50 352 352 0 strelka-varscan-mutect SCN4B,missense_variant,p.Ala75Thr,ENST00000324727,NM_001142349.1,NM_174934.3;SCN4B,intron_variant,,ENST00000529878,NM_001142348.1;SCN4B,upstream_gene_variant,,ENST00000423160,;SCN4B,non_coding_transcript_exon_variant,,ENST00000415030,;SCN4B,non_coding_transcript_exon_variant,,ENST00000532138,;SCN4B,upstream_gene_variant,,ENST00000531550,; T ENST00000324727 Transcript missense_variant 370/4484 223/687 75/228 A/T Gca/Aca COSM2105071 1 -1 SCN4B HGNC HGNC:10592 protein_coding YES CCDS8389.1 ENSP00000322460 Q8IWT1 B0YJ93 UPI00000532AE NM_001142349.1,NM_174934.3 tolerated(1) 2/5 PROSITE_profiles:PS50835,hmmpanther:PTHR13869:SF14,hmmpanther:PTHR13869,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS rs1265062815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 118145068 118145068 C T 1 0 0 0 0 1 0 0 0 14190 768 27 1 1 SCN4B 11 118145068 Missense_Mutation SNP C C3L-02365_T 10489002 118145068 16941554 226 9198 CCDC84 0 . GRCh38 11 119010786 119010786 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.406G>A p.Gly136Ser p.G136S ENST00000334418 4/11 220 193 27 199 199 0 strelka-varscan-mutect CCDC84,missense_variant,p.Gly136Ser,ENST00000334418,NM_198489.2;RPS25,downstream_gene_variant,,ENST00000527673,NM_001028.2;CCDC84,non_coding_transcript_exon_variant,,ENST00000580556,;CCDC84,missense_variant,p.Gly136Ser,ENST00000532132,;CCDC84,3_prime_UTR_variant,,ENST00000526463,;CCDC84,non_coding_transcript_exon_variant,,ENST00000528088,;CCDC84,non_coding_transcript_exon_variant,,ENST00000524670,;CCDC84,upstream_gene_variant,,ENST00000527356,;RPS25,downstream_gene_variant,,ENST00000527853,;CCDC84,upstream_gene_variant,,ENST00000533787,;RPS25,downstream_gene_variant,,ENST00000527791,;CCDC84,upstream_gene_variant,,ENST00000583842,;RPS25,downstream_gene_variant,,ENST00000532567,;RP11-110I1.5,upstream_gene_variant,,ENST00000527269,; A ENST00000334418 Transcript missense_variant 462/1202 406/999 136/332 G/S Ggt/Agt 1 1 CCDC84 HGNC HGNC:30460 protein_coding YES CCDS8405.1 ENSP00000334767 Q86UT8 UPI0000192104 NM_198489.2 tolerated(0.19) 4/11 hmmpanther:PTHR31198,Pfam_domain:PF14968 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 119010786 119010786 G A 1 0 0 0 0 1 0 0 0 2556 1000 35 3 3 CCDC84 11 119010786 Missense_Mutation SNP G C3L-02365_T 865718 119010786 16075836 227 9199 TMEM218 0 . GRCh38 11 125102176 125102176 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.66G>T p.= p.V22V ENST00000531909 3/5 146 119 27 89 88 1 strelka-varscan-mutect TMEM218,synonymous_variant,p.=,ENST00000531909,NM_001080546.2,NM_001258238.1,NM_001258246.1,NM_001258242.1,NM_001258244.1,NM_001258247.1;TMEM218,synonymous_variant,p.=,ENST00000528724,;TMEM218,synonymous_variant,p.=,ENST00000532407,;TMEM218,synonymous_variant,p.=,ENST00000279968,;TMEM218,synonymous_variant,p.=,ENST00000526175,NM_001258240.1;TMEM218,synonymous_variant,p.=,ENST00000532156,;TMEM218,synonymous_variant,p.=,ENST00000524373,;TMEM218,synonymous_variant,p.=,ENST00000533273,;TMEM218,synonymous_variant,p.=,ENST00000529583,NM_001258245.1;TMEM218,synonymous_variant,p.=,ENST00000527766,;TMEM218,synonymous_variant,p.=,ENST00000529609,;TMEM218,synonymous_variant,p.=,ENST00000527271,NM_001258241.1;TMEM218,synonymous_variant,p.=,ENST00000529530,;TMEM218,intron_variant,,ENST00000531262,;TMEM218,non_coding_transcript_exon_variant,,ENST00000527257,;TMEM218,intron_variant,,ENST00000531851,;TMEM218,downstream_gene_variant,,ENST00000532717,; A ENST00000531909 Transcript synonymous_variant 485/1828 66/348 22/115 V gtG/gtT 1 -1 TMEM218 HGNC HGNC:27344 protein_coding YES CCDS31715.1 ENSP00000436596 A2RU14 UPI00001617A4 NM_001080546.2,NM_001258238.1,NM_001258246.1,NM_001258242.1,NM_001258244.1,NM_001258247.1 3/5 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR31622 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 125102176 125102176 C A 1 0 0 0 0 0 0 0 1 16582 697 25 2 2 TMEM218 11 125102176 Silent SNP C C3L-02365_T 6091390 125102176 9984446 228 9200 CDON 0 . GRCh38 11 125961028 125961028 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.3778G>T p.Gly1260Cys p.G1260C ENST00000392693 20/20 443 362 81 377 377 0 strelka-varscan-mutect CDON,missense_variant,p.Gly1260Cys,ENST00000392693,NM_001243597.1;CDON,missense_variant,p.Gly614Cys,ENST00000531738,;CDON,missense_variant,p.Gly1237Cys,ENST00000263577,NM_016952.4; A ENST00000392693 Transcript missense_variant 3906/9138 3778/3864 1260/1287 G/C Ggc/Tgc 1 -1 CDON HGNC HGNC:17104 protein_coding YES CCDS58192.1 ENSP00000376458 Q4KMG0 UPI0000E0013A NM_001243597.1 deleterious(0) 20/20 hmmpanther:PTHR10489:SF12,hmmpanther:PTHR10489 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 125961028 125961028 C A 1 0 0 0 0 1 0 0 0 2874 623 22 2 2 CDON 11 125961028 Missense_Mutation SNP C C3L-02365_T 858852 125961028 9125594 229 9201 CCDC77 0 . GRCh38 12 430711 430711 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.558G>T p.Gln186His p.Q186H ENST00000239830 7/13 233 184 49 267 267 0 strelka-varscan-mutect CCDC77,missense_variant,p.Gln186His,ENST00000239830,NM_032358.3;CCDC77,missense_variant,p.Gln154His,ENST00000422000,NM_001130147.1;CCDC77,missense_variant,p.Gln154His,ENST00000412006,NM_001130146.1;CCDC77,missense_variant,p.Gln154His,ENST00000540180,NM_001130148.1;CCDC77,missense_variant,p.Gln154His,ENST00000543504,;CCDC77,non_coding_transcript_exon_variant,,ENST00000540344,;CCDC77,upstream_gene_variant,,ENST00000540118,; T ENST00000239830 Transcript missense_variant 737/2371 558/1467 186/488 Q/H caG/caT 1 1 CCDC77 HGNC HGNC:28203 protein_coding YES CCDS8503.1 ENSP00000239830 Q9BR77 UPI0000070D97 NM_032358.3 tolerated(0.07) 7/13 hmmpanther:PTHR22091:SF1,hmmpanther:PTHR22091 MODERATE 1 SNV 2 1 PASS rs1308875906 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 430711 430711 G T 1 0 0 0 0 1 0 0 0 2549 933 33 2 2 CCDC77 12 430711 Missense_Mutation SNP G C3L-02365_T 430711 132844598 230 9202 FGF23 0 . GRCh38 12 4370389 4370389 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.710G>C p.Gly237Ala p.G237A ENST00000237837 3/3 147 119 28 88 88 0 strelka-varscan-mutect FGF23,missense_variant,p.Gly237Ala,ENST00000237837,NM_020638.2; G ENST00000237837 Transcript missense_variant 856/3018 710/756 237/251 G/A gGg/gCg 1 -1 FGF23 HGNC HGNC:3680 protein_coding YES CCDS8526.1 ENSP00000237837 Q9GZV9 UPI000003ED58 NM_020638.2 tolerated_low_confidence(0.21) 3/3 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF69 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 4370389 4370389 C G 1 0 0 0 0 1 0 0 0 5716 623 22 4 4 FGF23 12 4370389 Missense_Mutation SNP C C3L-02365_T 3939678 4370389 128904920 231 9203 GSG1 0 . GRCh38 12 13087241 13087241 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.588C>A p.His196Gln p.H196Q ENST00000432710 5/6 146 125 21 157 157 0 strelka-varscan-mutect GSG1,missense_variant,p.His183Gln,ENST00000337630,NM_153823.3;GSG1,missense_variant,p.His225Asn,ENST00000396302,NM_031289.3;GSG1,missense_variant,p.His261Asn,ENST00000351606,NM_001080554.2;GSG1,missense_variant,p.His196Gln,ENST00000432710,NM_001206842.1,NM_001080555.2;GSG1,missense_variant,p.His132Gln,ENST00000457134,NM_001206845.1;GSG1,missense_variant,p.His155Gln,ENST00000537302,NM_001206843.1;FAM234B,intron_variant,,ENST00000537625,;FAM234B,downstream_gene_variant,,ENST00000197268,NM_020853.1;GSG1,downstream_gene_variant,,ENST00000545401,;GSG1,downstream_gene_variant,,ENST00000542415,;GSG1,downstream_gene_variant,,ENST00000545699,;FAM234B,downstream_gene_variant,,ENST00000416494,; T ENST00000432710 Transcript missense_variant 721/1231 588/1020 196/339 H/Q caC/caA 1 -1 GSG1 HGNC HGNC:19716 protein_coding YES CCDS55808.1 ENSP00000405032 Q2KHT4 UPI00001413B2 NM_001206842.1,NM_001080555.2 deleterious(0) 5/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR10671:SF43,hmmpanther:PTHR10671 MODERATE 1 SNV 1 1 PASS rs1220259865 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 13087241 13087241 G T 1 0 0 0 0 1 0 0 0 6703 1377 48 2 2 GSG1 12 13087241 Missense_Mutation SNP G C3L-02365_T 8716852 13087241 120188068 232 9204 PPFIBP1 0 . GRCh38 12 27691765 27691765 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.2720T>G p.Phe907Cys p.F907C ENST00000318304 27/29 103 77 26 112 112 0 strelka-varscan-mutect PPFIBP1,missense_variant,p.Phe907Cys,ENST00000318304,NM_177444.2;PPFIBP1,missense_variant,p.Phe901Cys,ENST00000228425,NM_003622.3;PPFIBP1,missense_variant,p.Phe754Cys,ENST00000537927,NM_001198915.1;PPFIBP1,missense_variant,p.Phe876Cys,ENST00000542629,NM_001198916.1;PPFIBP1,missense_variant,p.Phe738Cys,ENST00000540114,;PPFIBP1,missense_variant,p.Phe138Cys,ENST00000539326,;REP15,upstream_gene_variant,,ENST00000310791,NM_001029874.1;RP11-1060J15.4,downstream_gene_variant,,ENST00000536317,;RP11-1060J15.4,downstream_gene_variant,,ENST00000536922,;PPFIBP1,downstream_gene_variant,,ENST00000540256,; G ENST00000318304 Transcript missense_variant 3003/6001 2720/3036 907/1011 F/C tTt/tGt 1 1 PPFIBP1 HGNC HGNC:9249 protein_coding YES CCDS55812.1 ENSP00000314724 Q86W92 UPI00004565E6 NM_177444.2 deleterious(0) 27/29 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF16 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 27691765 27691765 T G 1 0 0 0 0 1 0 0 0 12422 1841 64 5 5 PPFIBP1 12 27691765 Missense_Mutation SNP T C3L-02365_T 14604524 27691765 105583544 233 9205 SYT10 0 . GRCh38 12 33426446 33426446 + Silent SNP G G T rs767357670 C3L-02365_T C3L-02365_N G G c.201C>A p.= p.A67A ENST00000228567 2/7 122 98 24 129 127 2 strelka-varscan-mutect SYT10,synonymous_variant,p.=,ENST00000228567,NM_198992.3;SYT10,upstream_gene_variant,,ENST00000567656,;SYT10,synonymous_variant,p.=,ENST00000539102,; T ENST00000228567 Transcript synonymous_variant 498/4461 201/1572 67/523 A gcC/gcA rs767357670 1 -1 SYT10 HGNC HGNC:19266 protein_coding YES CCDS8732.1 ENSP00000228567 Q6XYQ8 UPI0000052B30 NM_198992.3 2/7 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs767357670 . 0 204 0 5 0 0 0 0 -20 0.9997213 1 1 1 0 T 2 4 34 33426446 33426446 G T 1 0 0 0 0 0 0 0 1 15860 987 35 2 2 SYT10 12 33426446 Silent SNP G C3L-02365_T 5734681 33426446 99848863 234 9206 ALG10 0 . GRCh38 12 34026345 34026346 + Frame_Shift_Ins INS - - T novel C3L-02365_T C3L-02365_N - - c.853dupT p.Cys285LeufsTer26 p.C285Lfs*26 ENST00000266483 3/3 239 180 59 351 351 0 sindel-varindel ALG10,frameshift_variant,p.Cys285LeufsTer26,ENST00000266483,NM_032834.3;ALG10,intron_variant,,ENST00000538927,;RP11-847H18.2,intron_variant,,ENST00000501954,;ALG10,3_prime_UTR_variant,,ENST00000541875,;ALG10,downstream_gene_variant,,ENST00000541178,; T ENST00000266483 Transcript frameshift_variant 1171-1172/3128 852-853/1422 284-285/473 -/X -/T 1 1 ALG10 HGNC HGNC:23162 protein_coding YES CCDS41769.1 ENSP00000266483 Q5BKT4 UPI000004E870 NM_032834.3 3/3 hmmpanther:PTHR12989,Pfam_domain:PF04922,PIRSF_domain:PIRSF028810 HIGH 1 insertion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 34 34026345 34026345 - T 1 0 1 1 0 0 0 0 0 611 668 24 0 0 ALG10 12 34026345 Frame_Shift_Ins INS - C3L-02365_T 599899 34026345 99248964 235 9207 LRRK2 0 . GRCh38 12 40363435 40363435 + Missense_Mutation SNP C C G rs768811495 C3L-02365_T C3L-02365_N C C c.7062C>G p.Ile2354Met p.I2354M ENST00000298910 48/51 214 172 42 271 271 0 strelka-varscan-mutect LRRK2,missense_variant,p.Ile2354Met,ENST00000298910,NM_198578.3;LRRK2,missense_variant,p.Ile287Met,ENST00000636518,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; G ENST00000298910 Transcript missense_variant 7120/9158 7062/7584 2354/2527 I/M atC/atG rs768811495 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 deleterious(0) 48/51 hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF486,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs768811495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 40363435 40363435 C G 1 0 0 0 0 1 0 0 0 8939 816 29 4 4 LRRK2 12 40363435 Missense_Mutation SNP C C3L-02365_T 6337090 40363435 92911874 236 9208 TMEM117 0 . GRCh38 12 43944273 43944273 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.341G>T p.Ser114Ile p.S114I ENST00000266534 3/8 199 164 35 230 230 0 strelka-varscan-mutect TMEM117,missense_variant,p.Ser114Ile,ENST00000266534,NM_032256.2;TMEM117,missense_variant,p.Ser114Ile,ENST00000551577,NM_001286211.1;TMEM117,intron_variant,,ENST00000550495,NM_001286213.1;TMEM117,missense_variant,p.Ser114Ile,ENST00000546868,; T ENST00000266534 Transcript missense_variant 468/2758 341/1545 114/514 S/I aGc/aTc 1 1 TMEM117 HGNC HGNC:25308 protein_coding YES CCDS8745.1 ENSP00000266534 Q9H0C3 UPI0000037D18 NM_032256.2 tolerated(0.49) 3/8 Pfam_domain:PF15113,hmmpanther:PTHR31226,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 43944273 43944273 G T 1 0 0 0 0 1 0 0 0 16475 971 34 2 2 TMEM117 12 43944273 Missense_Mutation SNP G C3L-02365_T 3580838 43944273 89331036 237 9209 NCKAP5L 0 . GRCh38 12 49796030 49796030 + Silent SNP T T C novel C3L-02365_T C3L-02365_N T T c.1830A>G p.= p.P610P ENST00000335999 8/13 75 59 16 49 49 0 strelka-varscan-mutect NCKAP5L,synonymous_variant,p.=,ENST00000335999,NM_001037806.3;NCKAP5L,synonymous_variant,p.=,ENST00000433948,; C ENST00000335999 Transcript synonymous_variant 2032/4900 1830/4005 610/1334 P ccA/ccG 1 -1 NCKAP5L HGNC HGNC:29321 protein_coding YES CCDS41781.2 ENSP00000337998 Q9HCH0 UPI00006C1298 NM_001037806.3 8/13 hmmpanther:PTHR21740 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 34 49796030 49796030 T C 1 0 0 0 0 0 0 0 1 10242 1567 55 5 5 NCKAP5L 12 49796030 Silent SNP T C3L-02365_T 5851757 49796030 83479279 238 9210 SLC4A8 0 . GRCh38 12 51493728 51493728 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.2725G>A p.Gly909Arg p.G909R ENST00000453097 20/25 150 116 34 139 139 0 strelka-varscan-mutect SLC4A8,missense_variant,p.Gly909Arg,ENST00000453097,NM_001039960.2;SLC4A8,missense_variant,p.Gly856Arg,ENST00000358657,NM_001258401.2;SLC4A8,non_coding_transcript_exon_variant,,ENST00000551071,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000604314,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000319957,;SLC4A8,upstream_gene_variant,,ENST00000548616,;SLC4A8,upstream_gene_variant,,ENST00000546872,; A ENST00000453097 Transcript missense_variant 2942/11824 2725/3282 909/1093 G/R Gga/Aga 1 1 SLC4A8 HGNC HGNC:11034 protein_coding YES CCDS44890.1 ENSP00000405812 Q2Y0W8 UPI00005E6FB4 NM_001039960.2 deleterious(0) 20/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF37,TIGRFAM_domain:TIGR00834,Pfam_domain:PF00955 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -19.99835 0.9985372 1 1 1 0 A 3 1 34 51493728 51493728 G A 1 0 0 0 0 1 0 0 0 14936 1117 39 1 1 SLC4A8 12 51493728 Missense_Mutation SNP G C3L-02365_T 1697698 51493728 81781581 239 9211 KRT79 0 . GRCh38 12 52834121 52834121 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.140G>T p.Gly47Val p.G47V ENST00000330553 1/9 218 169 49 229 228 1 strelka-varscan-mutect KRT79,missense_variant,p.Gly47Val,ENST00000330553,NM_175834.2;KRT78,downstream_gene_variant,,ENST00000359499,NM_001300814.1;KRT78,downstream_gene_variant,,ENST00000304620,NM_173352.3;KRT78,downstream_gene_variant,,ENST00000547920,;KRT79,upstream_gene_variant,,ENST00000546453,;RP11-153F5.3,upstream_gene_variant,,ENST00000550463,; A ENST00000330553 Transcript missense_variant 175/2068 140/1608 47/535 G/V gGg/gTg 1 -1 KRT79 HGNC HGNC:28930 protein_coding YES CCDS8839.1 ENSP00000328358 Q5XKE5 UPI0000198204 NM_175834.2 deleterious(0.03) 1/9 Pfam_domain:PF16208,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF138,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 52834121 52834121 C A 1 0 0 0 0 1 0 0 0 8374 623 22 2 2 KRT79 12 52834121 Missense_Mutation SNP C C3L-02365_T 1340393 52834121 80441188 240 9212 OS9 0 . GRCh38 12 57715930 57715930 + Silent SNP A A G novel C3L-02365_T C3L-02365_N A A c.750A>G p.= p.L250L ENST00000315970 6/15 92 74 18 85 85 0 strelka-varscan-mutect OS9,synonymous_variant,p.=,ENST00000315970,NM_006812.3;OS9,synonymous_variant,p.=,ENST00000257966,NM_001261420.1;OS9,synonymous_variant,p.=,ENST00000389142,NM_001017957.2;OS9,synonymous_variant,p.=,ENST00000435406,NM_001261422.1;OS9,synonymous_variant,p.=,ENST00000551035,NM_001261421.1;OS9,synonymous_variant,p.=,ENST00000552285,NM_001017956.2;OS9,synonymous_variant,p.=,ENST00000389146,NM_001017958.2;OS9,synonymous_variant,p.=,ENST00000439210,NM_001261423.1;OS9,intron_variant,,ENST00000413095,;OS9,intron_variant,,ENST00000547079,;OS9,downstream_gene_variant,,ENST00000550372,;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,3_prime_UTR_variant,,ENST00000552787,;OS9,non_coding_transcript_exon_variant,,ENST00000549307,;OS9,non_coding_transcript_exon_variant,,ENST00000553208,;OS9,non_coding_transcript_exon_variant,,ENST00000550438,;OS9,upstream_gene_variant,,ENST00000546916,;OS9,upstream_gene_variant,,ENST00000550202,;OS9,upstream_gene_variant,,ENST00000550699,; G ENST00000315970 Transcript synonymous_variant 791/2691 750/2004 250/667 L ctA/ctG 1 1 OS9 HGNC HGNC:16994 protein_coding YES CCDS31843.1 ENSP00000318165 Q13438 UPI0000130EAC NM_006812.3 6/15 hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF0 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 57715930 57715930 A G 1 0 0 0 0 0 0 0 1 11338 378 14 5 5 OS9 12 57715930 Silent SNP A C3L-02365_T 4881809 57715930 75559379 241 9213 LRIG3 0 . GRCh38 12 58874450 58874450 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.2819C>T p.Pro940Leu p.P940L ENST00000320743 17/19 181 145 36 164 164 0 strelka-varscan-mutect LRIG3,missense_variant,p.Pro940Leu,ENST00000320743,NM_153377.4;LRIG3,missense_variant,p.Pro880Leu,ENST00000379141,NM_001136051.2;LRIG3,missense_variant,p.Pro42Leu,ENST00000550825,;LRIG3,3_prime_UTR_variant,,ENST00000433272,;LRIG3,non_coding_transcript_exon_variant,,ENST00000552646,; A ENST00000320743 Transcript missense_variant 3106/4070 2819/3360 940/1119 P/L cCt/cTt 1 -1 LRIG3 HGNC HGNC:30991 protein_coding YES CCDS8960.1 ENSP00000326759 Q6UXM1 UPI0000035BB5 NM_153377.4 tolerated_low_confidence(0.15) 17/19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 58874450 58874450 G A 1 0 0 0 0 1 0 0 0 8841 1000 35 3 3 LRIG3 12 58874450 Missense_Mutation SNP G C3L-02365_T 1158520 58874450 74400859 242 9214 DPY19L2 0 . GRCh38 12 63580706 63580706 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.1856C>T p.Pro619Leu p.P619L ENST00000324472 19/22 107 71 36 155 155 0 strelka-varscan-mutect DPY19L2,missense_variant,p.Pro619Leu,ENST00000324472,NM_173812.4;DPY19L2,non_coding_transcript_exon_variant,,ENST00000413230,;DPY19L2,intron_variant,,ENST00000439061,; A ENST00000324472 Transcript missense_variant 2040/4060 1856/2277 619/758 P/L cCt/cTt 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 deleterious(0) 19/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 63580706 63580706 G A 1 0 0 0 0 1 0 0 0 4556 1000 35 3 3 DPY19L2 12 63580706 Missense_Mutation SNP G C3L-02365_T 4706256 63580706 69694603 243 9215 ZFC3H1 0 . GRCh38 12 71633349 71633349 + Missense_Mutation SNP T T A C3L-02365_T C3L-02365_N T T c.2600A>T p.Lys867Met p.K867M ENST00000378743 13/35 118 93 25 160 160 0 strelka-varscan-mutect ZFC3H1,missense_variant,p.Lys867Met,ENST00000378743,NM_144982.4;ZFC3H1,missense_variant,p.Lys867Met,ENST00000552994,;ZFC3H1,upstream_gene_variant,,ENST00000546606,; A ENST00000378743 Transcript missense_variant 2959/7285 2600/5970 867/1989 K/M aAg/aTg COSM549851 1 -1 ZFC3H1 HGNC HGNC:28328 protein_coding YES CCDS41813.1 ENSP00000368017 O60293 UPI00003668E9 NM_144982.4 deleterious(0) 13/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21563 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 71633349 71633349 T A 1 0 0 0 0 1 0 0 0 18210 1609 56 4 4 ZFC3H1 12 71633349 Missense_Mutation SNP T C3L-02365_T 8052643 71633349 61641960 244 9216 PTPRQ 0 . GRCh38 12 80444781 80444781 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.95T>A p.Ile32Lys p.I32K ENST00000614701 2/45 255 200 55 334 333 1 strelka-varscan-mutect PTPRQ,missense_variant,p.Ile32Lys,ENST00000614701,NM_001145026.1;PTPRQ,missense_variant,p.Ile74Lys,ENST00000616559,;PTPRQ,missense_variant,p.Ile234Lys,ENST00000551042,;PTPRQ,missense_variant,p.Ile320Lys,ENST00000547376,;PTPRQ,missense_variant,p.Ile250Lys,ENST00000551573,; A ENST00000614701 Transcript missense_variant 273/8289 95/6900 32/2299 I/K aTa/aAa 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 deleterious(0) 2/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF414,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1032530333 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 80444781 80444781 T A 1 0 0 0 0 1 0 0 0 12964 1406 49 4 4 PTPRQ 12 80444781 Missense_Mutation SNP T C3L-02365_T 8811432 80444781 52830528 245 9217 MYF5 0 . GRCh38 12 80717229 80717229 + Missense_Mutation SNP C C G rs755386072 C3L-02365_T C3L-02365_N C C c.166C>G p.Arg56Gly p.R56G ENST00000228644 1/3 235 193 42 246 246 0 strelka-varscan-mutect MYF5,missense_variant,p.Arg56Gly,ENST00000228644,NM_005593.2; G ENST00000228644 Transcript missense_variant 318/1542 166/768 56/255 R/G Cga/Gga rs755386072,COSM5298404 1 1 MYF5 HGNC HGNC:7565 protein_coding YES CCDS9020.1 ENSP00000228644 P13349 UPI000013C8D9 NM_005593.2 deleterious(0.01) 1/3 hmmpanther:PTHR11534:SF3,hmmpanther:PTHR11534,Pfam_domain:PF01586,SMART_domains:SM00520 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755386072 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 80717229 80717229 C G 1 0 0 0 0 1 0 0 0 10027 760 27 4 4 MYF5 12 80717229 Missense_Mutation SNP C C3L-02365_T 272448 80717229 52558080 246 9218 SLC6A15 0 . GRCh38 12 84885919 84885919 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.439A>T p.Ser147Cys p.S147C ENST00000266682 3/12 102 79 23 120 120 0 strelka-varscan-mutect SLC6A15,missense_variant,p.Ser147Cys,ENST00000266682,NM_182767.5;SLC6A15,missense_variant,p.Ser147Cys,ENST00000450363,NM_018057.6;SLC6A15,missense_variant,p.Ser40Cys,ENST00000552192,NM_001146335.2;SLC6A15,intron_variant,,ENST00000551612,;SLC6A15,non_coding_transcript_exon_variant,,ENST00000547240,;SLC6A15,intron_variant,,ENST00000551388,; A ENST00000266682 Transcript missense_variant 981/4879 439/2193 147/730 S/C Agt/Tgt 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 deleterious(0) 3/12 Superfamily_domains:0053687,Pfam_domain:PF00209,Prints_domain:PR00176,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 84885919 84885919 T A 1 0 0 0 0 1 0 0 0 14961 1609 56 4 4 SLC6A15 12 84885919 Missense_Mutation SNP T C3L-02365_T 4168690 84885919 48389390 247 9219 DCN 0 . GRCh38 12 91151736 91151736 + Missense_Mutation SNP G G T rs3138268 C3L-02365_T C3L-02365_N G G c.803C>A p.Thr268Lys p.T268K ENST00000052754 7/8 353 299 54 390 390 0 strelka-varscan-mutect DCN,missense_variant,p.Thr268Lys,ENST00000052754,NM_001920.3;DCN,missense_variant,p.Thr268Lys,ENST00000393155,NM_133503.2;DCN,missense_variant,p.Thr268Lys,ENST00000552962,;DCN,missense_variant,p.Thr121Lys,ENST00000425043,NM_133505.2;DCN,missense_variant,p.Thr38Lys,ENST00000550758,;DCN,missense_variant,p.Thr121Lys,ENST00000547568,;DCN,missense_variant,p.Thr159Lys,ENST00000420120,NM_133504.2;DCN,missense_variant,p.Thr121Lys,ENST00000546391,;DCN,intron_variant,,ENST00000441303,NM_133506.2;DCN,intron_variant,,ENST00000456569,NM_133507.2; T ENST00000052754 Transcript missense_variant 1305/7156 803/1080 268/359 T/K aCg/aAg rs3138268 1 -1 DCN HGNC HGNC:2705 protein_coding YES CCDS9039.1 ENSP00000052754 P07585 Q6FH10 UPI000013187E NM_001920.3 deleterious(0.01) 7/8 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF5,PIRSF_domain:PIRSF002490,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 1903615621637745 MODERATE 1 SNV 1 1 PASS rs3138268 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 91151736 91151736 G T 1 0 0 0 0 1 0 0 0 4099 1145 40 1 1 DCN 12 91151736 Missense_Mutation SNP G C3L-02365_T 6265817 91151736 42123573 248 9220 BTBD11 0 . GRCh38 12 107319878 107319878 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.938G>C p.Cys313Ser p.C313S ENST00000280758 1/17 69 54 15 85 85 0 strelka-mutect BTBD11,missense_variant,p.Cys313Ser,ENST00000280758,NM_001018072.1;BTBD11,missense_variant,p.Cys313Ser,ENST00000490090,;BTBD11,missense_variant,p.Cys313Ser,ENST00000420571,;BTBD11,upstream_gene_variant,,ENST00000415943,;BTBD11,upstream_gene_variant,,ENST00000550706,; C ENST00000280758 Transcript missense_variant 1466/5767 938/3315 313/1104 C/S tGt/tCt 1 1 BTBD11 HGNC HGNC:23844 protein_coding YES CCDS31893.1 ENSP00000280758 A6QL63 UPI000051901E NM_001018072.1 tolerated_low_confidence(0.73) 1/17 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 107319878 107319878 G C 1 0 0 0 0 1 0 0 0 1714 1377 48 4 4 BTBD11 12 107319878 Missense_Mutation SNP G C3L-02365_T 16168142 107319878 25955431 249 9221 OAS3 0 . GRCh38 12 112944684 112944684 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.669G>T p.Met223Ile p.M223I ENST00000548514 3/3 194 151 43 194 194 0 varscan-mutect OAS3,missense_variant,p.Met223Ile,ENST00000548514,;OAS3,intron_variant,,ENST00000228928,NM_006187.3;OAS3,downstream_gene_variant,,ENST00000551007,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS3,intron_variant,,ENST00000546638,; T ENST00000548514 Transcript missense_variant 740/1392 669/672 223/223 M/I atG/atT 1 1 OAS3 HGNC HGNC:8088 protein_coding ENSP00000448388 F8VS35 UPI0001EE47DB 3/3 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 112944684 112944684 G T 1 0 0 0 0 1 0 0 0 10880 1377 48 2 2 OAS3 12 112944684 Missense_Mutation SNP G C3L-02365_T 5624806 112944684 20330625 250 9222 TESC 0 . GRCh38 12 117049047 117049047 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.321G>T p.= p.V107V ENST00000335209 4/8 214 171 43 226 226 0 strelka-varscan-mutect TESC,synonymous_variant,p.=,ENST00000335209,NM_017899.3;TESC,synonymous_variant,p.=,ENST00000541210,NM_001168325.1;TESC,upstream_gene_variant,,ENST00000549210,;TESC,non_coding_transcript_exon_variant,,ENST00000535198,;TESC,synonymous_variant,p.=,ENST00000470612,;TESC,synonymous_variant,p.=,ENST00000462502,;TESC,non_coding_transcript_exon_variant,,ENST00000482176,; A ENST00000335209 Transcript synonymous_variant 508/1041 321/645 107/214 V gtG/gtT 1 -1 TESC HGNC HGNC:26065 protein_coding YES CCDS9183.3 ENSP00000334785 Q96BS2 UPI0000136BF7 NM_017899.3 4/8 Gene3D:1.10.238.10,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF2,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 117049047 117049047 C A 1 0 0 0 0 0 0 0 1 16185 581 21 2 2 TESC 12 117049047 Silent SNP C C3L-02365_T 4104363 117049047 16226262 251 9223 KSR2 0 . GRCh38 12 117539860 117539860 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.1459G>C p.Asp487His p.D487H ENST00000425217 10/20 236 181 55 221 221 0 strelka-varscan-mutect KSR2,missense_variant,p.Asp516His,ENST00000339824,;KSR2,missense_variant,p.Asp487His,ENST00000425217,NM_173598.4;KSR2,non_coding_transcript_exon_variant,,ENST00000545002,;KSR2,non_coding_transcript_exon_variant,,ENST00000543793,; G ENST00000425217 Transcript missense_variant 1514/17008 1459/2766 487/921 D/H Gac/Cac 1 -1 KSR2 HGNC HGNC:18610 protein_coding YES CCDS61250.1 ENSP00000389715 E9PB13 UPI000164FA1C NM_173598.4 deleterious(0) 10/20 hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF376 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 117539860 117539860 C G 1 0 0 0 0 1 0 0 0 8481 913 32 4 4 KSR2 12 117539860 Missense_Mutation SNP C C3L-02365_T 490813 117539860 15735449 252 9224 FLT3 0 . GRCh38 13 28034350 28034350 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.1655T>C p.Leu552Pro p.L552P ENST00000241453 13/24 222 189 33 258 256 2 strelka-varscan-mutect FLT3,missense_variant,p.Leu552Pro,ENST00000241453,NM_004119.2;FLT3,missense_variant,p.Leu552Pro,ENST00000380987,; G ENST00000241453 Transcript missense_variant 1737/3842 1655/2982 552/993 L/P cTc/cCc 1 -1 FLT3 HGNC HGNC:3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 deleterious(0.04) 13/24 Transmembrane_helices:TMhelix,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF356 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 34 28034350 28034350 A G 1 0 0 0 0 1 0 0 0 5798 304 11 5 5 FLT3 13 28034350 Missense_Mutation SNP A C3L-02365_T 28034350 86329978 253 9225 LRRC63 0 . GRCh38 13 46227938 46227938 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.512T>G p.Leu171Arg p.L171R ENST00000595396 2/9 233 188 45 243 243 0 strelka-varscan-mutect LRRC63,missense_variant,p.Leu171Arg,ENST00000595396,;LRRC63,missense_variant,p.Leu171Arg,ENST00000446175,NM_001282460.1;LRRC63,missense_variant,p.Leu171Arg,ENST00000378805,; G ENST00000595396 Transcript missense_variant 512/2327 512/1764 171/587 L/R cTt/cGt 1 1 LRRC63 HGNC HGNC:34296 protein_coding YES CCDS61325.1 ENSP00000469337 J3KQU2 UPI0002742DC2 tolerated(0.37) 2/9 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 46227938 46227938 T G 1 0 0 0 0 1 0 0 0 8913 1609 56 5 5 LRRC63 13 46227938 Missense_Mutation SNP T C3L-02365_T 18193588 46227938 68136390 254 9226 TPP2 0 . GRCh38 13 102674455 102674455 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.3505G>A p.Glu1169Lys p.E1169K ENST00000376065 27/29 251 222 29 283 283 0 strelka-varscan-mutect TPP2,missense_variant,p.Glu1182Lys,ENST00000376052,;TPP2,missense_variant,p.Glu1169Lys,ENST00000376065,NM_003291.2;TPP2,non_coding_transcript_exon_variant,,ENST00000466153,;TPP2,downstream_gene_variant,,ENST00000482393,; A ENST00000376065 Transcript missense_variant 3541/3931 3505/3750 1169/1249 E/K Gaa/Aaa 1 1 TPP2 HGNC HGNC:12016 protein_coding YES CCDS9502.1 ENSP00000365233 P29144 UPI0000001C91 NM_003291.2 deleterious(0.04) 27/29 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 102674455 102674455 G A 1 0 0 0 0 1 0 0 0 16893 1175 41 3 3 TPP2 13 102674455 Missense_Mutation SNP G C3L-02365_T 56446517 102674455 11689873 255 9227 BIVM 0 . GRCh38 13 102816474 102816474 + Frame_Shift_Del DEL G G - novel C3L-02365_T C3L-02365_N G G c.441delG p.Gly148GlufsTer22 p.G148Efs*22 ENST00000602836 2/21 119 66 53 157 157 0 sindel-varindel-pindel BIVM-ERCC5,frameshift_variant,p.Gly148GlufsTer22,ENST00000602836,NM_001204425.1;BIVM,frameshift_variant,p.Gly176GlufsTer22,ENST00000257336,NM_017693.3;BIVM,5_prime_UTR_variant,,ENST00000448849,NM_001159596.1;BIVM,non_coding_transcript_exon_variant,,ENST00000474443,;BIVM,upstream_gene_variant,,ENST00000490317,; - ENST00000602836 Transcript frameshift_variant 439/4155 441/4157 147/1385 K/X aaG/aa 1 1 BIVM-ERCC5 HGNC HGNC:43690 protein_coding YES ENSP00000473384 R4GMW8 UPI0002B83330 NM_001204425.1 2/21 hmmpanther:PTHR16171:SF5,hmmpanther:PTHR16171 HIGH deletion 5 2 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 102816474 102816474 G - 1 0 1 0 1 0 0 0 0 1592 991 35 0 0 BIVM 13 102816474 Frame_Shift_Del DEL G C3L-02365_T 142019 102816474 11547854 256 9228 COL4A2 0 . GRCh38 13 110424957 110424957 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.320C>A p.Ala107Glu p.A107E ENST00000360467 6/48 202 150 52 230 230 0 strelka-varscan-mutect COL4A2,missense_variant,p.Ala107Glu,ENST00000360467,NM_001846.2;COL4A2,downstream_gene_variant,,ENST00000400163,;RP11-291I6.2,upstream_gene_variant,,ENST00000619688,; A ENST00000360467 Transcript missense_variant 626/6281 320/5139 107/1712 A/E gCa/gAa 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 tolerated(0.59) 6/48 hmmpanther:PTHR24023:SF588,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 5 1 PASS rs932645606 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 110424957 110424957 C A 1 0 0 0 0 1 0 0 0 3479 724 25 2 2 COL4A2 13 110424957 Missense_Mutation SNP C C3L-02365_T 7608483 110424957 3939371 257 9229 OR4M1 0 . GRCh38 14 19780557 19780557 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.235C>A p.Pro79Thr p.P79T ENST00000315957 1/1 469 417 52 442 442 0 strelka-varscan-mutect OR4M1,missense_variant,p.Pro79Thr,ENST00000315957,NM_001005500.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000315957 Transcript missense_variant 316/1116 235/942 79/313 P/T Cct/Act COSM1649083 1 1 OR4M1 HGNC HGNC:14735 protein_coding YES CCDS32021.1 ENSP00000319654 Q8NGD0 A0A126GWC3 UPI0000061F0F NM_001005500.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF53,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS rs1280030056 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 19780557 19780557 C A 1 0 0 0 0 1 0 0 0 11152 623 22 2 2 OR4M1 14 19780557 Missense_Mutation SNP C C3L-02365_T 19780557 87263161 258 9230 OXA1L 0 . GRCh38 14 22766678 22766678 + Nonsense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.157A>T p.Lys53Ter p.K53* ENST00000612549 1/10 507 437 70 427 427 0 strelka-varscan-mutect OXA1L,stop_gained,p.Lys53Ter,ENST00000612549,;OXA1L,stop_gained,p.Lys53Ter,ENST00000285848,NM_005015.3;OXA1L,upstream_gene_variant,,ENST00000358043,;OXA1L,upstream_gene_variant,,ENST00000604262,;OXA1L,upstream_gene_variant,,ENST00000412791,;OXA1L,upstream_gene_variant,,ENST00000431881,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554857,;CTD-2555K7.2,upstream_gene_variant,,ENST00000553792,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554730,;OXA1L,non_coding_transcript_exon_variant,,ENST00000483939,;OXA1L,upstream_gene_variant,,ENST00000495424,;OXA1L,upstream_gene_variant,,ENST00000481218,;OXA1L,upstream_gene_variant,,ENST00000473744,;OXA1L,upstream_gene_variant,,ENST00000442110,;OXA1L,upstream_gene_variant,,ENST00000556473,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554194,;OXA1L,upstream_gene_variant,,ENST00000557299,; T ENST00000612549 Transcript stop_gained 157/2971 157/1488 53/495 K/* Aaa/Taa 1 1 OXA1L HGNC HGNC:8526 protein_coding YES CCDS9573.1 ENSP00000483491 J3KNA0 UPI000013DE11 1/10 hmmpanther:PTHR12428:SF14,hmmpanther:PTHR12428 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 22766678 22766678 A T 1 0 0 0 0 0 1 0 0 11400 15 1 4 4 OXA1L 14 22766678 Nonsense_Mutation SNP A C3L-02365_T 2986121 22766678 84277040 259 9231 ACIN1 0 . GRCh38 14 23093518 23093518 + Silent SNP T T C novel C3L-02365_T C3L-02365_N T T c.339A>G p.= p.K113K ENST00000262710 2/19 349 281 68 313 313 0 strelka-varscan-mutect ACIN1,synonymous_variant,p.=,ENST00000262710,NM_014977.3;ACIN1,synonymous_variant,p.=,ENST00000457657,NM_001164815.1;ACIN1,synonymous_variant,p.=,ENST00000605057,;ACIN1,synonymous_variant,p.=,ENST00000555053,NM_001164814.1;C14orf119,upstream_gene_variant,,ENST00000319074,NM_017924.3;C14orf119,upstream_gene_variant,,ENST00000554203,; C ENST00000262710 Transcript synonymous_variant 667/4935 339/4026 113/1341 K aaA/aaG 1 -1 ACIN1 HGNC HGNC:17066 protein_coding YES CCDS9587.1 ENSP00000262710 Q9UKV3 UPI000013D308 NM_014977.3 2/19 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 34 23093518 23093518 T C 1 0 0 0 0 0 0 0 1 180 1722 60 5 5 ACIN1 14 23093518 Silent SNP T C3L-02365_T 326840 23093518 83950200 260 9232 NYNRIN 0 . GRCh38 14 24408478 24408478 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.808C>A p.Leu270Met p.L270M ENST00000382554 3/9 102 81 21 70 70 0 strelka-varscan-mutect NYNRIN,missense_variant,p.Leu270Met,ENST00000382554,NM_025081.2;NYNRIN,upstream_gene_variant,,ENST00000554505,; A ENST00000382554 Transcript missense_variant 1126/7857 808/5697 270/1898 L/M Ctg/Atg 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 deleterious_low_confidence(0.01) 3/9 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 24408478 24408478 C A 1 0 0 0 0 1 0 0 0 10874 680 24 2 2 NYNRIN 14 24408478 Missense_Mutation SNP C C3L-02365_T 1314960 24408478 82635240 261 9233 PRKD1 0 . GRCh38 14 29725653 29725653 + Nonsense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.286G>T p.Gly96Ter p.G96* ENST00000331968 2/18 182 141 41 164 164 0 strelka-varscan-mutect PRKD1,stop_gained,p.Gly96Ter,ENST00000331968,NM_002742.2;PRKD1,stop_gained,p.Gly96Ter,ENST00000616995,;PRKD1,stop_gained,p.Gly96Ter,ENST00000415220,;PRKD1,stop_gained,p.Gly19Ter,ENST00000549503,; A ENST00000331968 Transcript stop_gained 516/3726 286/2739 96/912 G/* Gga/Tga COSM5046592,COSM5046593 1 -1 PRKD1 HGNC HGNC:9407 protein_coding YES CCDS9637.1 ENSP00000333568 Q15139 UPI0000456761 NM_002742.2 2/18 PIRSF_domain:PIRSF000552,hmmpanther:PTHR22968 1,1 HIGH 1 SNV 1 1,1 1 PASS rs1186546402 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 29725653 29725653 C A 1 0 0 0 0 0 1 0 0 12651 661 23 1 1 PRKD1 14 29725653 Nonsense_Mutation SNP C C3L-02365_T 5317175 29725653 77318065 262 9234 HECTD1 0 . GRCh38 14 31173175 31173175 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.1137A>G p.Ile379Met p.I379M ENST00000399332 6/43 169 138 31 147 146 1 strelka-varscan-mutect HECTD1,missense_variant,p.Ile379Met,ENST00000399332,NM_015382.3;HECTD1,missense_variant,p.Ile379Met,ENST00000553700,;HECTD1,missense_variant,p.Ile379Met,ENST00000611816,;HECTD1,missense_variant,p.Ile379Met,ENST00000556224,;HECTD1,missense_variant,p.Ile200Met,ENST00000554471,;HECTD1,upstream_gene_variant,,ENST00000553957,;HECTD1,downstream_gene_variant,,ENST00000553616,; C ENST00000399332 Transcript missense_variant 1626/9134 1137/7833 379/2610 I/M atA/atG 1 -1 HECTD1 HGNC HGNC:20157 protein_coding YES CCDS41939.1 ENSP00000382269 Q9ULT8 UPI0000D9BBA1 NM_015382.3 tolerated(0.06) 6/43 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF322,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS rs1173440772 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 31173175 31173175 T C 1 0 0 0 0 1 0 0 0 6920 1512 53 5 5 HECTD1 14 31173175 Missense_Mutation SNP T C3L-02365_T 1447522 31173175 75870543 263 9235 NUBPL 0 . GRCh38 14 31673385 31673385 + Missense_Mutation SNP G G T rs201412882 C3L-02365_T C3L-02365_N G G c.413G>T p.Gly138Val p.G138V ENST00000281081 5/11 312 205 107 333 333 0 strelka-varscan-mutect NUBPL,missense_variant,p.Gly138Val,ENST00000281081,NM_025152.2;NUBPL,missense_variant,p.Gly86Val,ENST00000551314,;NUBPL,intron_variant,,ENST00000550649,;NUBPL,non_coding_transcript_exon_variant,,ENST00000550355,;NUBPL,non_coding_transcript_exon_variant,,ENST00000548937,;NUBPL,missense_variant,p.Gly138Val,ENST00000547839,;NUBPL,3_prime_UTR_variant,,ENST00000549838,;NUBPL,3_prime_UTR_variant,,ENST00000552489,; T ENST00000281081 Transcript missense_variant 458/3049 413/960 138/319 G/V gGt/gTt rs201412882 1 1 NUBPL HGNC HGNC:20278 protein_coding YES CCDS41940.1 ENSP00000281081 Q8TB37 X5D2R5 UPI00003669AB NM_025152.2 deleterious(0) 5/11 HAMAP:MF_02040,hmmpanther:PTHR23264:SF31,hmmpanther:PTHR23264,Pfam_domain:PF10609,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 likely_pathogenic MODERATE 1 SNV 1 1 1 PASS rs201412882 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 31673385 31673385 G T 1 0 0 0 0 1 0 0 0 10783 1261 44 2 2 NUBPL 14 31673385 Missense_Mutation SNP G C3L-02365_T 500210 31673385 75370333 264 9236 NPAS3 0 . GRCh38 14 33799873 33799873 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1566C>A p.Asn522Lys p.N522K ENST00000356141 12/12 625 537 88 439 439 0 strelka-varscan-mutect NPAS3,missense_variant,p.Asn490Lys,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Asn492Lys,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Asn527Lys,ENST00000551492,;NPAS3,missense_variant,p.Asn522Lys,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Asn509Lys,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Asn496Lys,ENST00000551634,; A ENST00000356141 Transcript missense_variant 1566/2802 1566/2802 522/933 N/K aaC/aaA 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious(0.03) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 33799873 33799873 C A 1 0 0 0 0 1 0 0 0 10612 506 18 2 2 NPAS3 14 33799873 Missense_Mutation SNP C C3L-02365_T 2126488 33799873 73243845 265 9237 SEC23A 0 . GRCh38 14 39040870 39040870 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.2004G>A p.= p.R668R ENST00000307712 18/20 296 218 78 264 264 0 strelka-varscan-mutect SEC23A,synonymous_variant,p.=,ENST00000537403,;SEC23A,synonymous_variant,p.=,ENST00000307712,NM_006364.2;SEC23A,synonymous_variant,p.=,ENST00000545328,;SEC23A,non_coding_transcript_exon_variant,,ENST00000554615,;SEC23A,non_coding_transcript_exon_variant,,ENST00000555363,; T ENST00000307712 Transcript synonymous_variant 2522/4135 2004/2298 668/765 R cgG/cgA 1 -1 SEC23A HGNC HGNC:10701 protein_coding YES CCDS9668.1 ENSP00000306881 Q15436 UPI000013EC46 NM_006364.2 18/20 Gene3D:3.40.20.10,Pfam_domain:PF00626,hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF7,Superfamily_domains:SSF82754 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 39040870 39040870 C T 1 0 0 0 0 0 0 0 1 14268 842 30 3 3 SEC23A 14 39040870 Silent SNP C C3L-02365_T 5240997 39040870 68002848 266 9238 GNG2 0 . GRCh38 14 51827762 51827762 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.19C>A p.Pro7Thr p.P7T ENST00000553432 2/4 187 101 86 182 182 0 strelka-varscan-mutect GNG2,missense_variant,p.Pro7Thr,ENST00000553432,;GNG2,5_prime_UTR_variant,,ENST00000557376,;RP11-280K24.4,downstream_gene_variant,,ENST00000553312,;GNG2,missense_variant,p.Pro7Thr,ENST00000556522,; A ENST00000553432 Transcript missense_variant 131/577 19/309 7/102 P/T Cct/Act 1 1 GNG2 HGNC HGNC:4404 protein_coding ENSP00000451279 G3V3J9 UPI0000E238D4 tolerated_low_confidence(0.37) 2/4 MODERATE SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 51827762 51827762 C A 1 0 0 0 0 1 0 0 0 6406 507 18 2 2 GNG2 14 51827762 Missense_Mutation SNP C C3L-02365_T 12786892 51827762 55215956 267 9239 ATG14 0 . GRCh38 14 55382117 55382117 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.722G>T p.Arg241Leu p.R241L ENST00000247178 6/10 484 330 154 460 460 0 strelka-varscan-mutect ATG14,missense_variant,p.Arg241Leu,ENST00000247178,NM_014924.4;ATG14,non_coding_transcript_exon_variant,,ENST00000558189,; A ENST00000247178 Transcript missense_variant 758/4742 722/1479 241/492 R/L cGg/cTg 1 -1 ATG14 HGNC HGNC:19962 protein_coding YES CCDS32087.1 ENSP00000247178 Q6ZNE5 UPI00001FD5B2 NM_014924.4 deleterious(0.01) 6/10 Pfam_domain:PF10186,hmmpanther:PTHR13664,hmmpanther:PTHR13664:SF0 MODERATE 1 SNV 1 1 PASS rs1395803520 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 55382117 55382117 C A 1 0 0 0 0 1 0 0 0 1242 652 23 1 1 ATG14 14 55382117 Missense_Mutation SNP C C3L-02365_T 3554355 55382117 51661601 268 9240 C14orf37 0 . GRCh38 14 58138303 58138303 + Silent SNP A A G rs781115260 C3L-02365_T C3L-02365_N A A c.1056T>C p.= p.G352G ENST00000267485 2/8 209 178 31 211 211 0 strelka-varscan-mutect C14orf37,synonymous_variant,p.=,ENST00000267485,NM_001001872.2;C14orf37,non_coding_transcript_exon_variant,,ENST00000334342,;C14orf37,intron_variant,,ENST00000557175,;C14orf37,downstream_gene_variant,,ENST00000554218,;UBA52P3,upstream_gene_variant,,ENST00000491303,; G ENST00000267485 Transcript synonymous_variant 1251/6495 1056/2325 352/774 G ggT/ggC rs781115260 1 -1 C14orf37 HGNC HGNC:19846 protein_coding YES CCDS32089.1 ENSP00000267485 Q86TY3 UPI000000CC37 NM_001001872.2 2/8 hmmpanther:PTHR21585,hmmpanther:PTHR21585:SF0,Pfam_domain:PF15767 LOW 1 SNV 1 1 PASS rs781115260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 58138303 58138303 A G 1 0 0 0 0 0 0 0 1 1838 378 14 5 5 C14orf37 14 58138303 Silent SNP A C3L-02365_T 2756186 58138303 48905415 269 9241 SIX1 0 . GRCh38 14 60646567 60646567 + Missense_Mutation SNP C C T rs771994916 C3L-02365_T C3L-02365_N C C c.571G>A p.Glu191Lys p.E191K ENST00000247182 2/2 251 237 14 211 211 0 strelka-mutect SIX1,missense_variant,p.Glu191Lys,ENST00000247182,NM_005982.3;SIX1,missense_variant,p.Glu18Lys,ENST00000554986,;SALRNA1,downstream_gene_variant,,ENST00000555871,;SIX1,non_coding_transcript_exon_variant,,ENST00000553535,;SIX1,non_coding_transcript_exon_variant,,ENST00000555955,; T ENST00000247182 Transcript missense_variant 844/3996 571/855 191/284 E/K Gaa/Aaa rs771994916 1 -1 SIX1 HGNC HGNC:10887 protein_coding YES CCDS9748.1 ENSP00000247182 Q15475 UPI00001359BA NM_005982.3 tolerated(0.37) 2/2 Gene3D:1.10.10.60,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF13,Low_complexity_(Seg):seg,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs771994916 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 60646567 60646567 C T 1 0 0 0 0 1 0 0 0 14609 893 31 1 1 SIX1 14 60646567 Missense_Mutation SNP C C3L-02365_T 2508264 60646567 46397151 270 9242 SIX1 0 . GRCh38 14 60649013 60649013 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.177C>A p.His59Gln p.H59Q ENST00000247182 1/2 212 131 81 166 166 0 strelka-varscan-mutect SIX1,missense_variant,p.His59Gln,ENST00000247182,NM_005982.3;SIX1,intron_variant,,ENST00000554986,;SIX1,intron_variant,,ENST00000553535,;SIX1,intron_variant,,ENST00000555955,;SIX1,downstream_gene_variant,,ENST00000555627,; T ENST00000247182 Transcript missense_variant 450/3996 177/855 59/284 H/Q caC/caA 1 -1 SIX1 HGNC HGNC:10887 protein_coding YES CCDS9748.1 ENSP00000247182 Q15475 UPI00001359BA NM_005982.3 deleterious(0.02) 1/2 Pfam_domain:PF16878,hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF13 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 60649013 60649013 G T 1 0 0 0 0 1 0 0 0 14609 1252 44 2 2 SIX1 14 60649013 Missense_Mutation SNP G C3L-02365_T 2446 60649013 46394705 271 9243 KCNH5 0 . GRCh38 14 62987151 62987151 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.470C>G p.Thr157Arg p.T157R ENST00000322893 5/11 248 169 79 288 288 0 strelka-varscan-mutect KCNH5,missense_variant,p.Thr157Arg,ENST00000322893,NM_139318.4;KCNH5,missense_variant,p.Thr157Arg,ENST00000420622,NM_172375.2;KCNH5,missense_variant,p.Thr99Arg,ENST00000394968,;KCNH5,non_coding_transcript_exon_variant,,ENST00000394964,; C ENST00000322893 Transcript missense_variant 739/11290 470/2967 157/988 T/R aCa/aGa 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 deleterious(0.01) 5/11 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Prints_domain:PR01464 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 62987151 62987151 G C 1 0 0 0 0 1 0 0 0 7951 1377 48 4 4 KCNH5 14 62987151 Missense_Mutation SNP G C3L-02365_T 2338138 62987151 44056567 272 9244 GPHN 0 . GRCh38 14 67111870 67111870 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.1423G>A p.Glu475Lys p.E475K ENST00000478722 15/23 502 449 53 463 463 0 strelka-varscan-mutect GPHN,missense_variant,p.Glu475Lys,ENST00000478722,NM_020806.4;GPHN,missense_variant,p.Glu442Lys,ENST00000315266,NM_001024218.1;GPHN,missense_variant,p.Glu488Lys,ENST00000543237,;GPHN,upstream_gene_variant,,ENST00000555503,;GPHN,non_coding_transcript_exon_variant,,ENST00000544752,;GPHN,upstream_gene_variant,,ENST00000555527,;GPHN,downstream_gene_variant,,ENST00000556501,; A ENST00000478722 Transcript missense_variant 2544/4297 1423/2310 475/769 E/K Gaa/Aaa 1 1 GPHN HGNC HGNC:15465 protein_coding YES CCDS9777.1 ENSP00000417901 Q9NQX3 UPI0000072592 NM_020806.4 deleterious(0) 15/23 Gene3D:2.170.190.11,Pfam_domain:PF03453,hmmpanther:PTHR10192,Superfamily_domains:SSF63882 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 67111870 67111870 G A 1 0 0 0 0 1 0 0 0 6512 943 33 3 3 GPHN 14 67111870 Missense_Mutation SNP G C3L-02365_T 4124719 67111870 39931848 273 9245 STON2 0 . GRCh38 14 81396154 81396154 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.113G>C p.Gly38Ala p.G38A ENST00000555447 4/8 138 94 44 115 115 0 strelka-varscan-mutect STON2,missense_variant,p.Gly38Ala,ENST00000555447,NM_001256430.1;STON2,missense_variant,p.Gly38Ala,ENST00000267540,NM_033104.3;STON2,missense_variant,p.Gly38Ala,ENST00000614646,;STON2,missense_variant,p.Gly38Ala,ENST00000557055,;STON2,downstream_gene_variant,,ENST00000554710,;STON2,non_coding_transcript_exon_variant,,ENST00000555226,; G ENST00000555447 Transcript missense_variant 526/4302 113/2763 38/920 G/A gGa/gCa 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 tolerated_low_confidence(0.28) 4/8 PIRSF_domain:PIRSF037099,Pfam_domain:PF12016 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 81396154 81396154 C G 1 0 0 0 0 1 0 0 0 15696 855 30 4 4 STON2 14 81396154 Missense_Mutation SNP C C3L-02365_T 14284284 81396154 25647564 274 9246 AHNAK2 0 . GRCh38 14 104944665 104944665 + Missense_Mutation SNP C C A rs371361988 C3L-02365_T C3L-02365_N C C c.10786G>T p.Asp3596Tyr p.D3596Y ENST00000333244 7/7 464 297 167 408 407 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Asp3596Tyr,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript missense_variant 10906/18254 10786/17388 3596/5795 D/Y Gat/Tat rs371361988 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS rs371361988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 104944665 104944665 C A 1 0 0 0 0 1 0 0 0 492 884 31 1 1 AHNAK2 14 104944665 Missense_Mutation SNP C C3L-02365_T 23548511 104944665 2099053 275 9247 JAG2 0 . GRCh38 14 105148842 105148842 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.1923G>T p.= p.L641L ENST00000331782 15/26 783 511 272 474 474 0 strelka-varscan-mutect JAG2,synonymous_variant,p.=,ENST00000331782,NM_002226.4;JAG2,synonymous_variant,p.=,ENST00000347004,NM_145159.2;MIR6765,downstream_gene_variant,,ENST00000614092,;RP11-44N21.4,downstream_gene_variant,,ENST00000548203,;JAG2,upstream_gene_variant,,ENST00000546616,;JAG2,upstream_gene_variant,,ENST00000553244,;JAG2,downstream_gene_variant,,ENST00000553051,; A ENST00000331782 Transcript synonymous_variant 2327/5835 1923/3717 641/1238 L ctG/ctT 1 -1 JAG2 HGNC HGNC:6189 protein_coding YES CCDS9998.1 ENSP00000328169 Q9Y219 UPI0000167BD5 NM_002226.4 15/26 Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF316,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 105148842 105148842 C A 1 0 0 0 0 0 0 0 1 7848 581 21 2 2 JAG2 14 105148842 Silent SNP C C3L-02365_T 204177 105148842 1894876 276 9248 B2M 0 . GRCh38 15 44715686 44715686 + Nonsense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.331A>T p.Lys111Ter p.K111* ENST00000558401 2/4 260 171 89 289 288 1 strelka-varscan-mutect B2M,stop_gained,p.Lys111Ter,ENST00000558401,NM_004048.2;B2M,stop_gained,p.Lys111Ter,ENST00000559916,;B2M,stop_gained,p.Lys93Ter,ENST00000544417,;B2M,non_coding_transcript_exon_variant,,ENST00000559907,;B2M,intron_variant,,ENST00000559220,;PATL2,upstream_gene_variant,,ENST00000558573,;B2M,upstream_gene_variant,,ENST00000560556,;B2M,stop_gained,p.Lys63Ter,ENST00000561139,;B2M,stop_gained,p.Lys111Ter,ENST00000561424,;B2M,3_prime_UTR_variant,,ENST00000349264,;B2M,3_prime_UTR_variant,,ENST00000557901,;B2M,non_coding_transcript_exon_variant,,ENST00000559720,;B2M,non_coding_transcript_exon_variant,,ENST00000560681,;B2M,downstream_gene_variant,,ENST00000632133,;B2M,upstream_gene_variant,,ENST00000623550,; T ENST00000558401 Transcript stop_gained 401/1715 331/360 111/119 K/* Aag/Tag 1 1 B2M HGNC HGNC:914 protein_coding YES CCDS10113.1 ENSP00000452780 P61769 UPI000000D892 NM_004048.2 2/4 PROSITE_profiles:PS50835,hmmpanther:PTHR19944:SF62,hmmpanther:PTHR19944,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 44715686 44715686 A T 1 0 0 0 0 0 1 0 0 1401 131 5 4 4 B2M 15 44715686 Nonsense_Mutation SNP A C3L-02365_T 44715686 57275503 277 9249 UNC13C 0 . GRCh38 15 54014110 54014110 + Nonsense_Mutation SNP G G T rs144045439 C3L-02365_T C3L-02365_N G G c.1207G>T p.Gly403Ter p.G403* ENST00000260323 1/32 171 97 74 185 184 1 strelka-varscan-mutect UNC13C,stop_gained,p.Gly403Ter,ENST00000260323,NM_001080534.1; T ENST00000260323 Transcript stop_gained 1207/12946 1207/6645 403/2214 G/* Gga/Tga rs144045439 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 HIGH 1 SNV 5 1 PASS rs144045439 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 54014110 54014110 G T 1 0 0 0 0 0 1 0 0 17510 1349 47 2 2 UNC13C 15 54014110 Nonsense_Mutation SNP G C3L-02365_T 9298424 54014110 47977079 278 9250 UNC13C 0 . GRCh38 15 54235109 54235109 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.3150+1G>T p.X1050_splice ENST00000260323 208 122 86 209 209 0 strelka-varscan-mutect UNC13C,splice_donor_variant,,ENST00000260323,NM_001080534.1; T ENST00000260323 Transcript splice_donor_variant -/12946 3150/6645 1050/2214 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 4/31 HIGH 1 SNV 5 1 PASS rs778962561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 54235109 54235109 G T 1 0 0 0 0 0 0 1 0 17510 1275 44 2 2 UNC13C 15 54235109 Splice_Site SNP G C3L-02365_T 220999 54235109 47756080 279 9251 ADAMTS7 0 . GRCh38 15 78771603 78771603 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2358G>T p.Lys786Asn p.K786N ENST00000388820 15/24 412 291 121 347 347 0 strelka-varscan-mutect ADAMTS7,missense_variant,p.Lys786Asn,ENST00000388820,NM_014272.3;ADAMTS7,intron_variant,,ENST00000566303,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000565793,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000568712,; A ENST00000388820 Transcript missense_variant 2569/5490 2358/5061 786/1686 K/N aaG/aaT 1 -1 ADAMTS7 HGNC HGNC:223 protein_coding YES CCDS32303.1 ENSP00000373472 Q9UKP4 UPI00002263B3 NM_014272.3 tolerated(0.51) 15/24 Pfam_domain:PF05986,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF142 MODERATE 1 SNV 1 1 PASS rs927716529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 78771603 78771603 C A 1 0 0 0 0 1 0 0 0 315 680 24 2 2 ADAMTS7 15 78771603 Missense_Mutation SNP C C3L-02365_T 24536494 78771603 23219586 280 9252 ADAMTSL3 0 . GRCh38 15 83885171 83885171 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1031G>T p.Arg344Ile p.R344I ENST00000286744 10/30 392 189 203 369 369 0 strelka-varscan-mutect ADAMTSL3,missense_variant,p.Arg344Ile,ENST00000286744,NM_207517.2;ADAMTSL3,missense_variant,p.Arg344Ile,ENST00000567476,NM_001301110.1;ADAMTSL3,intron_variant,,ENST00000567663,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,; T ENST00000286744 Transcript missense_variant 1255/7336 1031/5076 344/1691 R/I aGa/aTa 1 1 ADAMTSL3 HGNC HGNC:14633 protein_coding YES CCDS10326.1 ENSP00000286744 P82987 UPI00001615A5 NM_207517.2 deleterious(0) 10/30 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF169,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 83885171 83885171 G T 1 0 0 0 0 1 0 0 0 320 942 33 2 2 ADAMTSL3 15 83885171 Missense_Mutation SNP G C3L-02365_T 5113568 83885171 18106018 281 9253 ZNF500 0 . GRCh38 16 4760515 4760515 + Missense_Mutation SNP C C G rs561166954 C3L-02365_T C3L-02365_N C C c.737G>C p.Arg246Pro p.R246P ENST00000219478 5/6 211 197 14 153 153 0 strelka-varscan-mutect ZNF500,missense_variant,p.Arg246Pro,ENST00000219478,NM_021646.2;ZNF500,missense_variant,p.Arg246Pro,ENST00000545009,NM_001303450.1;ZNF500,upstream_gene_variant,,ENST00000592425,;Metazoa_SRP,downstream_gene_variant,,ENST00000622471,;ZNF500,3_prime_UTR_variant,,ENST00000589422,; G ENST00000219478 Transcript missense_variant 1037/5880 737/1443 246/480 R/P cGg/cCg rs561166954 1 -1 ZNF500 HGNC HGNC:23716 protein_coding YES CCDS32383.1 ENSP00000219478 O60304 UPI00001C1FB0 NM_021646.2 deleterious(0.01) 5/6 Superfamily_domains:0044637,Pfam_domain:PF01352,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF74 MODERATE 1 SNV 2 1 PASS rs561166954 . 0 208 0 2 0 0 0 0 -17.54518 0.9999996 1 1 1 0 G 3 3 34 4760515 4760515 C G 1 0 0 0 0 1 0 0 0 18520 652 23 4 4 ZNF500 16 4760515 Missense_Mutation SNP C C3L-02365_T 4760515 85577830 282 9254 PDXDC1 0 . GRCh38 16 15030032 15030032 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.1375T>G p.Phe459Val p.F459V ENST00000396410 16/23 276 259 17 226 226 0 varscan-mutect PDXDC1,missense_variant,p.Phe459Val,ENST00000396410,NM_001324019.1,NM_015027.3;PDXDC1,missense_variant,p.Phe368Val,ENST00000450288,NM_001285448.1;PDXDC1,missense_variant,p.Phe432Val,ENST00000569715,NM_001285444.1;PDXDC1,missense_variant,p.Phe477Val,ENST00000563679,NM_001285447.1;PDXDC1,missense_variant,p.Phe431Val,ENST00000627450,NM_001285445.1;PDXDC1,missense_variant,p.Phe459Val,ENST00000535621,NM_001324020.1,NM_001285449.1;PDXDC1,downstream_gene_variant,,ENST00000455313,NM_001285450.1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,;PDXDC1,non_coding_transcript_exon_variant,,ENST00000566633,;PDXDC1,intron_variant,,ENST00000562119,;PDXDC1,upstream_gene_variant,,ENST00000565986,; G ENST00000396410 Transcript missense_variant 1472/4521 1375/2367 459/788 F/V Ttc/Gtc 1 1 PDXDC1 HGNC HGNC:28995 protein_coding YES CCDS32393.1 ENSP00000379691 Q6P996 UPI000004A864 NM_001324019.1,NM_015027.3 deleterious(0.01) 16/23 hmmpanther:PTHR11999:SF108,hmmpanther:PTHR11999,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 15030032 15030032 T G 1 0 0 0 0 1 0 0 0 11784 1725 60 5 5 PDXDC1 16 15030032 Missense_Mutation SNP T C3L-02365_T 10269517 15030032 75308313 283 9255 35 2 PDXDC1 0 . GRCh38 16 15030035 15030035 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.1378A>G p.Ser460Gly p.S460G ENST00000396410 16/23 271 254 17 218 218 0 varscan-mutect PDXDC1,missense_variant,p.Ser460Gly,ENST00000396410,NM_001324019.1,NM_015027.3;PDXDC1,missense_variant,p.Ser369Gly,ENST00000450288,NM_001285448.1;PDXDC1,missense_variant,p.Ser433Gly,ENST00000569715,NM_001285444.1;PDXDC1,missense_variant,p.Ser478Gly,ENST00000563679,NM_001285447.1;PDXDC1,missense_variant,p.Ser432Gly,ENST00000627450,NM_001285445.1;PDXDC1,missense_variant,p.Ser460Gly,ENST00000535621,NM_001324020.1,NM_001285449.1;PDXDC1,downstream_gene_variant,,ENST00000455313,NM_001285450.1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,;PDXDC1,non_coding_transcript_exon_variant,,ENST00000566633,;PDXDC1,intron_variant,,ENST00000562119,;PDXDC1,upstream_gene_variant,,ENST00000565986,; G ENST00000396410 Transcript missense_variant 1475/4521 1378/2367 460/788 S/G Agc/Ggc 1 1 PDXDC1 HGNC HGNC:28995 protein_coding YES CCDS32393.1 ENSP00000379691 Q6P996 UPI000004A864 NM_001324019.1,NM_015027.3 deleterious(0.05) 16/23 hmmpanther:PTHR11999:SF108,hmmpanther:PTHR11999,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 15030035 15030035 A G 1 0 0 0 0 1 0 0 0 11784 188 7 5 5 PDXDC1 16 15030035 Missense_Mutation SNP A C3L-02365_T 3 15030035 75308310 284 9256 35 2 NPIPA5 0 . GRCh38 16 15365344 15365350 + Frame_Shift_Del DEL GAGCACA GAGCACA - novel C3L-02365_T C3L-02365_N GAGCACA GAGCACA c.778_784delTGTGCTC p.Cys260LysfsTer43 p.C260Kfs*43 ENST00000534094 7/7 108 96 12 104 104 0 sindel-varindel NPIPA5,frameshift_variant,p.Cys260LysfsTer43,ENST00000534094,;NPIPA5,intron_variant,,ENST00000360151,NM_001277325.1;NPIPA5,intron_variant,,ENST00000543801,;RP11-72I8.2,downstream_gene_variant,,ENST00000611162,; - ENST00000534094 Transcript frameshift_variant 778-784/954 778-784/954 260-262/317 CAQ/X TGTGCTCaa/aa 1 -1 NPIPA5 HGNC HGNC:41980 protein_coding ENSP00000435611 E9PJ88 UPI0001A5E893 7/7 hmmpanther:PTHR15438 HIGH deletion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 15365344 15365344 GAGCACA - 1 0 1 0 1 0 0 0 0 10634 1299 45 0 0 NPIPA5 16 15365344 Frame_Shift_Del DEL GAGCACA C3L-02365_T 335309 15365344 74973001 285 9257 DNAH3 0 . GRCh38 16 20982851 20982851 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.7729C>A p.Leu2577Met p.L2577M ENST00000261383 49/62 228 179 49 210 210 0 strelka-varscan-mutect DNAH3,missense_variant,p.Leu2577Met,ENST00000261383,NM_017539.2; T ENST00000261383 Transcript missense_variant 7729/12394 7729/12351 2577/4116 L/M Ctg/Atg 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0) 49/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12780,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 20982851 20982851 G T 1 0 0 0 0 1 0 0 0 4418 991 35 2 2 DNAH3 16 20982851 Missense_Mutation SNP G C3L-02365_T 5617507 20982851 69355494 286 9258 XPO6 0 . GRCh38 16 28111988 28111988 + Nonsense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.2170C>T p.Arg724Ter p.R724* ENST00000304658 17/24 139 126 13 110 110 0 strelka-varscan-mutect XPO6,stop_gained,p.Arg724Ter,ENST00000304658,NM_015171.3;XPO6,stop_gained,p.Arg710Ter,ENST00000565698,NM_001270940.1;XPO6,upstream_gene_variant,,ENST00000573275,;XPO6,intron_variant,,ENST00000569216,;XPO6,3_prime_UTR_variant,,ENST00000564905,;TPRKBP2,upstream_gene_variant,,ENST00000565969,; A ENST00000304658 Transcript stop_gained 2671/4422 2170/3378 724/1125 R/* Cga/Tga 1 -1 XPO6 HGNC HGNC:19733 protein_coding YES CCDS42135.1 ENSP00000302790 Q96QU8 UPI000006F228 NM_015171.3 17/24 hmmpanther:PTHR21452,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 28111988 28111988 G A 1 0 0 0 0 0 1 0 0 18007 1124 39 1 1 XPO6 16 28111988 Nonsense_Mutation SNP G C3L-02365_T 7129137 28111988 62226357 287 9259 SPNS1 0 . GRCh38 16 28984257 28984257 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.1545G>T p.= p.R515R ENST00000311008 12/12 122 94 28 116 116 0 strelka-varscan-mutect SPNS1,missense_variant,p.Gly452Val,ENST00000566059,;SPNS1,synonymous_variant,p.=,ENST00000311008,NM_001142448.1,NM_032038.2;SPNS1,synonymous_variant,p.=,ENST00000323081,NM_001142450.1;SPNS1,synonymous_variant,p.=,ENST00000334536,NM_001142451.1;SPNS1,synonymous_variant,p.=,ENST00000565975,;SPNS1,synonymous_variant,p.=,ENST00000352260,NM_001142449.1;SPNS1,synonymous_variant,p.=,ENST00000568829,;LAT,upstream_gene_variant,,ENST00000395456,NM_001014987.1;LAT,upstream_gene_variant,,ENST00000360872,NM_014387.3;LAT,upstream_gene_variant,,ENST00000395461,NM_001014989.1;LAT,upstream_gene_variant,,ENST00000454369,NM_001014988.1;LAT,upstream_gene_variant,,ENST00000564277,;SPNS1,downstream_gene_variant,,ENST00000564476,;LAT,upstream_gene_variant,,ENST00000566177,;SPNS1,downstream_gene_variant,,ENST00000568388,;LAT,upstream_gene_variant,,ENST00000570232,;LAT,upstream_gene_variant,,ENST00000630764,;RP11-264B17.5,downstream_gene_variant,,ENST00000561471,;RP11-264B17.3,upstream_gene_variant,,ENST00000354453,;LAT,upstream_gene_variant,,ENST00000563964,;SPNS1,downstream_gene_variant,,ENST00000561868,;RP11-264B17.3,non_coding_transcript_exon_variant,,ENST00000569969,;LAT,upstream_gene_variant,,ENST00000564447,;SPNS1,downstream_gene_variant,,ENST00000568900,;LAT,upstream_gene_variant,,ENST00000566270,;LAT,upstream_gene_variant,,ENST00000562701,;LAT,upstream_gene_variant,,ENST00000568899,;LAT,upstream_gene_variant,,ENST00000562472,;LAT,upstream_gene_variant,,ENST00000568440,; T ENST00000311008 Transcript synonymous_variant 1922/2208 1545/1587 515/528 R cgG/cgT 1 1 SPNS1 HGNC HGNC:30621 protein_coding YES CCDS10646.1 ENSP00000309945 Q9H2V7 UPI000004DB99 NM_001142448.1,NM_032038.2 12/12 hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF13 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 28984257 28984257 G T 1 0 0 0 0 0 0 0 1 15427 1219 43 2 2 SPNS1 16 28984257 Silent SNP G C3L-02365_T 872269 28984257 61354088 288 9260 ZNF785 0 . GRCh38 16 30583011 30583011 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.767A>T p.Tyr256Phe p.Y256F ENST00000395216 3/3 516 400 116 442 442 0 strelka-varscan-mutect ZNF785,missense_variant,p.Tyr256Phe,ENST00000395216,NM_152458.6;ZNF785,missense_variant,p.Tyr241Phe,ENST00000470110,;ZNF785,downstream_gene_variant,,ENST00000567773,;AC002310.7,non_coding_transcript_exon_variant,,ENST00000492040,;AC002310.7,downstream_gene_variant,,ENST00000486926,;RP11-146F11.5,upstream_gene_variant,,ENST00000563540,;ZNF785,upstream_gene_variant,,ENST00000562128,;AC002310.17,downstream_gene_variant,,ENST00000564755,; A ENST00000395216 Transcript missense_variant 927/3282 767/1218 256/405 Y/F tAc/tTc 1 -1 ZNF785 HGNC HGNC:26496 protein_coding YES CCDS10685.1 ENSP00000378642 A8K8V0 A0A024QZC7 UPI0000074535 NM_152458.6 tolerated(0.05) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF130,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1177694960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 30583011 30583011 T A 1 0 0 0 0 1 0 0 0 18741 1638 57 4 4 ZNF785 16 30583011 Missense_Mutation SNP T C3L-02365_T 1598754 30583011 59755334 289 9261 ITGAM 0 . GRCh38 16 31261699 31261699 + Silent SNP C C A rs769239433 C3L-02365_T C3L-02365_N C C c.36C>A p.= p.T12T ENST00000544665 2/30 165 131 34 162 162 0 strelka-varscan-mutect ITGAM,synonymous_variant,p.=,ENST00000544665,NM_001145808.1;ITGAM,synonymous_variant,p.=,ENST00000287497,NM_000632.3; A ENST00000544665 Transcript synonymous_variant 107/4718 36/3462 12/1153 T acC/acA rs769239433 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 2/30 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs769239433 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 31261699 31261699 C A 1 0 0 0 0 0 0 0 1 7794 668 24 2 2 ITGAM 16 31261699 Silent SNP C C3L-02365_T 678688 31261699 59076646 290 9262 SALL1 0 . GRCh38 16 51140647 51140647 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.1575C>T p.= p.G525G ENST00000251020 2/3 193 152 41 180 180 0 strelka-varscan-mutect SALL1,synonymous_variant,p.=,ENST00000440970,NM_001127892.1;SALL1,synonymous_variant,p.=,ENST00000251020,NM_002968.2;SALL1,synonymous_variant,p.=,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript synonymous_variant 1609/5146 1575/3975 525/1324 G ggC/ggT 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 51140647 51140647 G A 1 0 0 0 0 0 0 0 1 14069 1306 46 3 3 SALL1 16 51140647 Silent SNP G C3L-02365_T 19878948 51140647 39197698 291 9263 IRX3 0 . GRCh38 16 54284974 54284974 + Missense_Mutation SNP G G A rs759825805 C3L-02365_T C3L-02365_N G G c.907C>T p.Arg303Trp p.R303W ENST00000329734 2/4 150 121 29 159 159 0 strelka-varscan-mutect IRX3,missense_variant,p.Arg303Trp,ENST00000329734,NM_024336.2;IRX3,intron_variant,,ENST00000558054,;RP11-434E6.5,upstream_gene_variant,,ENST00000637770,;IRX3,non_coding_transcript_exon_variant,,ENST00000558180,; A ENST00000329734 Transcript missense_variant 1620/2601 907/1506 303/501 R/W Cgg/Tgg rs759825805 1 -1 IRX3 HGNC HGNC:14360 protein_coding YES CCDS10750.1 ENSP00000331608 P78415 UPI000019745F NM_024336.2 deleterious(0) 2/4 hmmpanther:PTHR11211:SF14,hmmpanther:PTHR11211 MODERATE 1 SNV 1 1 PASS rs759825805 . 0 204 0 4 0 0 0 0 -20 0.9999462 1 1 1 0 A 3 1 34 54284974 54284974 G A 1 0 0 0 0 1 0 0 0 7753 1115 39 1 1 IRX3 16 54284974 Missense_Mutation SNP G C3L-02365_T 3144327 54284974 36053371 292 9264 EXOC3L1 0 . GRCh38 16 67187360 67187360 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.905A>G p.Tyr302Cys p.Y302C ENST00000314586 5/14 277 183 94 213 213 0 strelka-varscan-mutect EXOC3L1,missense_variant,p.Tyr302Cys,ENST00000314586,NM_178516.3;EXOC3L1,missense_variant,p.Tyr241Cys,ENST00000545725,;EXOC3L1,missense_variant,p.Tyr246Cys,ENST00000563889,;KIAA0895L,upstream_gene_variant,,ENST00000290881,;KIAA0895L,upstream_gene_variant,,ENST00000561621,;KIAA0895L,upstream_gene_variant,,ENST00000563902,NM_001040715.1;E2F4,upstream_gene_variant,,ENST00000379378,NM_001950.3;EXOC3L1,downstream_gene_variant,,ENST00000564418,;EXOC3L1,intron_variant,,ENST00000562887,;KIAA0895L,upstream_gene_variant,,ENST00000563831,;KIAA0895L,upstream_gene_variant,,ENST00000564423,;EXOC3L1,intron_variant,,ENST00000564324,;E2F4,upstream_gene_variant,,ENST00000567007,;E2F4,upstream_gene_variant,,ENST00000568839,;E2F4,upstream_gene_variant,,ENST00000561904,;E2F4,upstream_gene_variant,,ENST00000569573,;EXOC3L1,upstream_gene_variant,,ENST00000563536,;E2F4,upstream_gene_variant,,ENST00000563238,;E2F4,upstream_gene_variant,,ENST00000568485,;E2F4,upstream_gene_variant,,ENST00000565849,; C ENST00000314586 Transcript missense_variant 1146/2510 905/2241 302/746 Y/C tAc/tGc 1 -1 EXOC3L1 HGNC HGNC:27540 protein_coding YES CCDS10832.1 ENSP00000325674 Q86VI1 A0A024R6U6 UPI000013F886 NM_178516.3 deleterious(0) 5/14 hmmpanther:PTHR21292:SF12,hmmpanther:PTHR21292,Pfam_domain:PF06046 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 67187360 67187360 T C 1 0 0 0 0 1 0 0 0 5171 1638 57 5 5 EXOC3L1 16 67187360 Missense_Mutation SNP T C3L-02365_T 12902386 67187360 23150985 293 9265 CHST5 0 . GRCh38 16 75529945 75529945 + Missense_Mutation SNP G G A rs535515522 C3L-02365_T C3L-02365_N G G c.440C>T p.Thr147Met p.T147M ENST00000336257 3/3 356 190 166 322 322 0 strelka-varscan-mutect CHST5,missense_variant,p.Thr147Met,ENST00000336257,NM_024533.4;CHST5,downstream_gene_variant,,ENST00000565039,;RP11-77K12.7,3_prime_UTR_variant,,ENST00000460606,; A ENST00000336257 Transcript missense_variant 1835/3245 440/1236 147/411 T/M aCg/aTg rs535515522 1 -1 CHST5 HGNC HGNC:1973 protein_coding YES CCDS10919.1 ENSP00000338783 Q9GZS9 UPI000006EAEA NM_024533.4 tolerated(0.13) 3/3 Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF13 MODERATE 1 SNV 1 1 PASS rs535515522 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 75529945 75529945 G A 1 0 0 0 0 1 0 0 0 3167 1145 40 1 1 CHST5 16 75529945 Missense_Mutation SNP G C3L-02365_T 8342585 75529945 14808400 294 9266 CPNE7 0 . GRCh38 16 89583464 89583464 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.518C>G p.Pro173Arg p.P173R ENST00000268720 4/17 331 177 154 281 281 0 strelka-varscan-mutect CPNE7,missense_variant,p.Pro173Arg,ENST00000268720,NM_014427.4;CPNE7,intron_variant,,ENST00000319518,NM_153636.2;CPNE7,upstream_gene_variant,,ENST00000529800,;CPNE7,3_prime_UTR_variant,,ENST00000525982,;CPNE7,upstream_gene_variant,,ENST00000532500,; G ENST00000268720 Transcript missense_variant 648/2657 518/1902 173/633 P/R cCc/cGc 1 1 CPNE7 HGNC HGNC:2320 protein_coding YES CCDS10980.1 ENSP00000268720 Q9UBL6 UPI0000127C17 NM_014427.4 tolerated_low_confidence(0.32) 4/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 89583464 89583464 C G 1 0 0 0 0 1 0 0 0 3612 623 22 4 4 CPNE7 16 89583464 Missense_Mutation SNP C C3L-02365_T 14053519 89583464 754881 295 9267 RPA1 0 . GRCh38 17 1879641 1879641 + Missense_Mutation SNP A A G rs759379338 C3L-02365_T C3L-02365_N A A c.1034A>G p.Asn345Ser p.N345S ENST00000254719 11/17 254 239 15 251 251 0 strelka-varscan-mutect RPA1,missense_variant,p.Asn345Ser,ENST00000254719,NM_002945.3;RPA1,missense_variant,p.Asn101Ser,ENST00000574049,;RPA1,downstream_gene_variant,,ENST00000570451,;RPA1,downstream_gene_variant,,ENST00000573924,; G ENST00000254719 Transcript missense_variant 1144/4340 1034/1851 345/616 N/S aAt/aGt rs759379338 1 1 RPA1 HGNC HGNC:10289 protein_coding YES CCDS11014.1 ENSP00000254719 P27694 UPI000013379A NM_002945.3 tolerated(0.22) 11/17 hmmpanther:PTHR23273,hmmpanther:PTHR23273:SF6,Gene3D:2.40.50.140,TIGRFAM_domain:TIGR00617,Pfam_domain:PF16900,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS rs759379338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 1879641 1879641 A G 1 0 0 0 0 1 0 0 0 13788 101 4 5 5 RPA1 17 1879641 Missense_Mutation SNP A C3L-02365_T 1879641 81377800 296 9268 ZNF594 0 . GRCh38 17 5183462 5183462 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.795A>C p.Lys265Asn p.K265N ENST00000399604 1/1 187 167 20 218 218 0 strelka-varscan-mutect ZNF594,missense_variant,p.Lys265Asn,ENST00000399604,;ZNF594,missense_variant,p.Lys265Asn,ENST00000575779,NM_032530.1;ZNF594,downstream_gene_variant,,ENST00000576772,; G ENST00000399604 Transcript missense_variant 936/4862 795/2424 265/807 K/N aaA/aaC 1 -1 ZNF594 HGNC HGNC:29392 protein_coding YES CCDS42241.1 ENSP00000382513 Q96JF6 UPI00001C1FDF deleterious(0) 1/1 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF155,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 5183462 5183462 T G 1 0 0 0 0 1 0 0 0 18599 1722 60 5 5 ZNF594 17 5183462 Missense_Mutation SNP T C3L-02365_T 3303821 5183462 78073979 297 9269 TP53 0 . GRCh38 17 7674887 7674887 + Missense_Mutation SNP C C A rs587782177 C3L-02365_T C3L-02365_N C C c.644G>T p.Ser215Ile p.S215I ENST00000269305 6/11 502 274 228 459 458 1 strelka-varscan-mutect TP53,missense_variant,p.Ser215Ile,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Ser215Ile,ENST00000420246,;TP53,missense_variant,p.Ser176Ile,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Ser176Ile,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Ser215Ile,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Ser176Ile,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Ser215Ile,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Ser176Ile,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Ser215Ile,ENST00000445888,;TP53,missense_variant,p.Ser176Ile,ENST00000619485,;TP53,missense_variant,p.Ser83Ile,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Ser56Ile,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Ser83Ile,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Ser56Ile,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Ser83Ile,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Ser56Ile,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Ser215Ile,ENST00000359597,;TP53,missense_variant,p.Ser204Ile,ENST00000615910,;TP53,missense_variant,p.Ser215Ile,ENST00000413465,;TP53,missense_variant,p.Ser83Ile,ENST00000509690,;TP53,missense_variant,p.Ser122Ile,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Ser176Ile,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 834/2579 644/1182 215/393 S/I aGt/aTt rs587782177,TP53_g.12713G>A,TP53_g.12713G>T,TP53_g.12713del,TP53_g.12713G>C,COSM11450,COSM2744738,COSM2744739,COSM308327,COSM308328,COSM308329,COSM308330,COSM326719,COSM326720,COSM326721,COSM326722,COSM4271853,COSM4271854,COSM44093,COSM44175,COSM44887 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs587782177 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 7674887 7674887 C A 1 0 0 0 0 1 0 0 0 16859 565 20 2 2 TP53 17 7674887 Missense_Mutation SNP C C3L-02365_T 2491425 7674887 75582554 298 9270 MYH4 0 . GRCh38 17 10457440 10457440 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1877G>T p.Gly626Val p.G626V ENST00000255381 16/40 74 54 20 87 87 0 strelka-varscan-mutect MYH4,missense_variant,p.Gly626Val,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript missense_variant 1988/6016 1877/5820 626/1939 G/V gGg/gTg 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 tolerated(0.06) 16/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 34 10457440 10457440 C A 1 0 0 0 0 1 0 0 0 10037 623 22 2 2 MYH4 17 10457440 Missense_Mutation SNP C C3L-02365_T 2782553 10457440 72800001 299 9271 DNAH9 0 . GRCh38 17 11742174 11742174 + Splice_Site SNP G G T novel C3L-02365_T C3L-02365_N G G c.5973-1G>T p.X1991_splice ENST00000262442 129 106 23 109 109 0 strelka-varscan-mutect DNAH9,splice_acceptor_variant,,ENST00000262442,NM_001372.3;DNAH9,splice_acceptor_variant,,ENST00000454412,; T ENST00000262442 Transcript splice_acceptor_variant -/13750 5973/13461 1991/4486 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 29/68 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 11742174 11742174 G T 1 0 0 0 0 0 0 1 0 4423 1014 35 2 2 DNAH9 17 11742174 Splice_Site SNP G C3L-02365_T 1284734 11742174 71515267 300 9272 DNAH9 0 . GRCh38 17 11807733 11807733 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.8422T>A p.Cys2808Ser p.C2808S ENST00000262442 44/69 83 70 13 57 57 0 strelka-varscan-mutect DNAH9,missense_variant,p.Cys2808Ser,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Cys2808Ser,ENST00000454412,; A ENST00000262442 Transcript missense_variant,splice_region_variant 8490/13750 8422/13461 2808/4486 C/S Tgc/Agc 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0.01) 44/69 Gene3D:3.40.50.300,Pfam_domain:PF12780,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 11807733 11807733 T A 1 0 0 0 0 1 0 0 0 4423 1594 55 4 4 DNAH9 17 11807733 Missense_Mutation SNP T C3L-02365_T 65559 11807733 71449708 301 9273 HS3ST3A1 0 . GRCh38 17 13600692 13600692 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.438C>T p.= p.D146D ENST00000284110 1/2 220 175 45 172 172 0 strelka-varscan-mutect HS3ST3A1,synonymous_variant,p.=,ENST00000284110,NM_006042.2; A ENST00000284110 Transcript synonymous_variant 1236/2527 438/1221 146/406 D gaC/gaT 1 -1 HS3ST3A1 HGNC HGNC:5196 protein_coding YES CCDS11165.1 ENSP00000284110 Q9Y663 UPI000000DAA6 NM_006042.2 1/2 Gene3D:3.40.50.300,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF47,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 13600692 13600692 G A 1 0 0 0 0 0 0 0 1 7259 1136 40 1 1 HS3ST3A1 17 13600692 Silent SNP G C3L-02365_T 1792959 13600692 69656749 302 9274 PIPOX 0 . GRCh38 17 29054595 29054595 + Silent SNP T T C novel C3L-02365_T C3L-02365_N T T c.711T>C p.= p.Y237Y ENST00000323372 5/8 282 232 50 207 207 0 strelka-varscan-mutect PIPOX,synonymous_variant,p.=,ENST00000323372,NM_016518.2;PIPOX,synonymous_variant,p.=,ENST00000469082,;PIPOX,downstream_gene_variant,,ENST00000466889,;PIPOX,non_coding_transcript_exon_variant,,ENST00000583215,;PIPOX,non_coding_transcript_exon_variant,,ENST00000580241,;PIPOX,non_coding_transcript_exon_variant,,ENST00000484308,;PIPOX,downstream_gene_variant,,ENST00000577182,;PIPOX,downstream_gene_variant,,ENST00000580383,;PIPOX,downstream_gene_variant,,ENST00000419875,; C ENST00000323372 Transcript synonymous_variant 1037/2414 711/1173 237/390 Y taT/taC 1 1 PIPOX HGNC HGNC:17804 protein_coding YES CCDS11248.1 ENSP00000317721 Q9P0Z9 UPI00001410B0 NM_016518.2 5/8 hmmpanther:PTHR10961,hmmpanther:PTHR10961:SF7,Gene3D:3.30.9.10,TIGRFAM_domain:TIGR01377,Pfam_domain:PF01266,Superfamily_domains:SSF54373 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 34 29054595 29054595 T C 1 0 0 0 0 0 0 0 1 12038 1471 51 5 5 PIPOX 17 29054595 Silent SNP T C3L-02365_T 15453903 29054595 54202846 303 9275 NSRP1 0 . GRCh38 17 30184769 30184769 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.772G>T p.Asp258Tyr p.D258Y ENST00000247026 7/7 161 140 21 199 199 0 strelka-varscan-mutect NSRP1,missense_variant,p.Asp258Tyr,ENST00000247026,NM_032141.3;NSRP1,missense_variant,p.Asp204Tyr,ENST00000612959,NM_001261467.1;NSRP1,downstream_gene_variant,,ENST00000580103,;NSRP1,non_coding_transcript_exon_variant,,ENST00000540900,;NSRP1,downstream_gene_variant,,ENST00000577289,;NSRP1,3_prime_UTR_variant,,ENST00000394826,;NSRP1,3_prime_UTR_variant,,ENST00000475652,; T ENST00000247026 Transcript missense_variant 835/2541 772/1677 258/558 D/Y Gat/Tat 1 1 NSRP1 HGNC HGNC:25305 protein_coding YES CCDS11255.1 ENSP00000247026 Q9H0G5 UPI000006E653 NM_032141.3 deleterious(0) 7/7 hmmpanther:PTHR31938,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 30184769 30184769 G T 1 0 0 0 0 1 0 0 0 10740 1290 45 2 2 NSRP1 17 30184769 Missense_Mutation SNP G C3L-02365_T 1130174 30184769 53072672 304 9276 KRT24 0 . GRCh38 17 40703578 40703578 + Nonsense_Mutation SNP G G T rs141408122,rs745930893 C3L-02365_T C3L-02365_N G G c.116C>A p.Ser39Ter p.S39* ENST00000264651 1/8 169 142 27 129 129 0 strelka-varscan-mutect KRT24,stop_gained,p.Ser39Ter,ENST00000264651,NM_019016.2; T ENST00000264651 Transcript stop_gained 173/1881 116/1578 39/525 S/* tCg/tAg rs141408122,rs745930893 1 -1 KRT24 HGNC HGNC:18527 protein_coding YES CCDS11372.1 ENSP00000264651 Q2M2I5 UPI000013D54D NM_019016.2 1/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF207,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs141408122 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 40703578 40703578 G T 1 0 0 0 0 0 1 0 0 8343 1059 37 1 1 KRT24 17 40703578 Nonsense_Mutation SNP G C3L-02365_T 10518809 40703578 42553863 305 9277 KRT33B 0 . GRCh38 17 41364846 41364846 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1030G>T p.Asp344Tyr p.D344Y ENST00000251646 6/7 497 410 87 353 353 0 strelka-varscan-mutect KRT33B,missense_variant,p.Asp344Tyr,ENST00000251646,NM_002279.4; A ENST00000251646 Transcript missense_variant 1080/1607 1030/1215 344/404 D/Y Gac/Tac 1 -1 KRT33B HGNC HGNC:6451 protein_coding YES CCDS11389.1 ENSP00000251646 Q14525 UPI000012DAFE NM_002279.4 deleterious(0) 6/7 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF99,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs928718022 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 41364846 41364846 C A 1 0 0 0 0 1 0 0 0 8352 855 30 2 2 KRT33B 17 41364846 Missense_Mutation SNP C C3L-02365_T 661268 41364846 41892595 306 9278 MTMR4 0 . GRCh38 17 58492912 58492912 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.3251T>C p.Phe1084Ser p.F1084S ENST00000323456 17/19 195 149 46 186 186 0 strelka-varscan-mutect MTMR4,missense_variant,p.Phe1084Ser,ENST00000323456,NM_004687.4;MTMR4,missense_variant,p.Phe1027Ser,ENST00000579925,;HSF5,upstream_gene_variant,,ENST00000323777,NM_001080439.2;HSF5,upstream_gene_variant,,ENST00000617946,;MTMR4,upstream_gene_variant,,ENST00000578259,; G ENST00000323456 Transcript missense_variant 3376/5839 3251/3588 1084/1195 F/S tTt/tCt 1 -1 MTMR4 HGNC HGNC:7452 protein_coding YES CCDS11608.1 ENSP00000325285 Q9NYA4 UPI00002010DE NM_004687.4 tolerated(0.37) 17/19 hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF64 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 58492912 58492912 A G 1 0 0 0 0 1 0 0 0 9933 14 1 5 5 MTMR4 17 58492912 Missense_Mutation SNP A C3L-02365_T 17128066 58492912 24764529 307 9279 KCNH6 0 . GRCh38 17 63535729 63535729 + Missense_Mutation SNP C C T rs144043788 C3L-02365_T C3L-02365_N C C c.1162C>T p.Arg388Trp p.R388W ENST00000583023 6/14 141 132 9 113 113 0 strelka-varscan-mutect KCNH6,missense_variant,p.Arg388Trp,ENST00000583023,NM_030779.3;KCNH6,missense_variant,p.Arg388Trp,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,missense_variant,p.Arg388Trp,ENST00000581784,NM_173092.2;KCNH6,missense_variant,p.Arg388Trp,ENST00000456941,;KCNH6,missense_variant,p.Arg388Trp,ENST00000580652,;KCNH6,3_prime_UTR_variant,,ENST00000583465,; T ENST00000583023 Transcript missense_variant 1173/3821 1162/2985 388/994 R/W Cgg/Tgg rs144043788 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 deleterious(0) 6/14 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs144043788 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 63535729 63535729 C T 1 0 0 0 0 1 0 0 0 7952 527 19 1 1 KCNH6 17 63535729 Missense_Mutation SNP C C3L-02365_T 5042817 63535729 19721712 308 9280 ABCA8 0 . GRCh38 17 68917449 68917449 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.2050A>T p.Arg684Trp p.R684W ENST00000586539 17/40 115 108 7 104 104 0 strelka-mutect ABCA8,missense_variant,p.Arg684Trp,ENST00000430352,NM_001288986.1;ABCA8,missense_variant,p.Arg644Trp,ENST00000269080,NM_007168.3;ABCA8,missense_variant,p.Arg684Trp,ENST00000586539,NM_001288985.1;ABCA8,splice_region_variant,,ENST00000615593,;ABCA8,missense_variant,p.Arg332Trp,ENST00000589533,;ABCA8,splice_region_variant,,ENST00000541225,;ABCA8,downstream_gene_variant,,ENST00000587206,; A ENST00000586539 Transcript missense_variant,splice_region_variant 2239/5088 2050/4866 684/1621 R/W Agg/Tgg 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 deleterious(0) 17/40 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -13.51953 0.999753 1 1 1 0 A 3 1 34 68917449 68917449 T A 1 0 0 0 0 1 0 0 0 42 1594 55 4 4 ABCA8 17 68917449 Missense_Mutation SNP T C3L-02365_T 5381720 68917449 14339992 309 9281 ABCA10 0 . GRCh38 17 69149089 69149089 + Splice_Site SNP C C A rs867434771 C3L-02365_T C3L-02365_N C C c.4478-1G>T p.X1493_splice ENST00000269081 208 158 50 178 178 0 strelka-varscan-mutect ABCA10,splice_acceptor_variant,,ENST00000269081,NM_080282.3;ABCA10,splice_acceptor_variant,,ENST00000521538,;ABCA10,splice_acceptor_variant,,ENST00000522787,;ABCA10,splice_acceptor_variant,,ENST00000519732,;ABCA10,splice_acceptor_variant,,ENST00000522406,;ABCA10,splice_acceptor_variant,,ENST00000518929,;ABCA10,splice_acceptor_variant,,ENST00000523419,;ABCA10,splice_acceptor_variant,,ENST00000524231,;ABCA10,non_coding_transcript_exon_variant,,ENST00000588514,; A ENST00000269081 Transcript splice_acceptor_variant -/6362 4478/4632 1493/1543 rs867434771 1 -1 ABCA10 HGNC HGNC:30 protein_coding YES CCDS11684.1 ENSP00000269081 Q8WWZ4 UPI000013D7F6 NM_080282.3 38/39 HIGH 1 SNV 1 1 PASS rs867434771 . 0 207 0 3 0 0 0 0 -20 0.9999976 1 1 1 0 A 5 1 34 69149089 69149089 C A 1 0 0 0 0 0 0 1 0 33 579 20 2 2 ABCA10 17 69149089 Splice_Site SNP C C3L-02365_T 231640 69149089 14108352 310 9282 FADS6 0 . GRCh38 17 74893493 74893493 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.103C>G p.Arg35Gly p.R35G ENST00000612771 1/6 196 166 30 165 165 0 strelka-varscan-mutect FADS6,missense_variant,p.Arg35Gly,ENST00000612771,NM_178128.5;FADS6,missense_variant,p.Arg17Gly,ENST00000614223,;FADS6,missense_variant,p.Arg35Gly,ENST00000621859,; C ENST00000612771 Transcript missense_variant 118/2154 103/1107 35/368 R/G Cgg/Ggg 1 -1 FADS6 HGNC HGNC:30459 protein_coding YES CCDS54163.2 ENSP00000481684 A0A087WYB9 UPI0001639CD9 NM_178128.5 tolerated(0.41) 1/6 hmmpanther:PTHR19353,hmmpanther:PTHR19353:SF13 MODERATE 1 SNV 1 1 PASS rs1244933354 . 0 204 0 4 0 0 0 0 -20 0.9999152 1 1 1 0 C 3 2 34 74893493 74893493 G C 1 0 0 0 0 1 0 0 0 5240 1086 38 4 4 FADS6 17 74893493 Missense_Mutation SNP G C3L-02365_T 5744404 74893493 8363948 311 9283 LAMA1 0 . GRCh38 18 6955450 6955450 + Missense_Mutation SNP C C G rs776782542 C3L-02365_T C3L-02365_N C C c.8110G>C p.Asp2704His p.D2704H ENST00000389658 57/63 466 373 93 373 373 0 strelka-varscan-mutect LAMA1,missense_variant,p.Asp2704His,ENST00000389658,NM_005559.3;RP11-781P6.1,non_coding_transcript_exon_variant,,ENST00000584722,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488089,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488064,;LAMA1,non_coding_transcript_exon_variant,,ENST00000492048,; G ENST00000389658 Transcript missense_variant 8204/9657 8110/9228 2704/3075 D/H Gat/Cat rs776782542 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0.02) 57/63 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299 MODERATE SNV 2 1 PASS rs776782542 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 6955450 6955450 C G 1 0 0 0 0 1 0 0 0 8509 855 30 4 4 LAMA1 18 6955450 Missense_Mutation SNP C C3L-02365_T 6955450 73417835 312 9284 SETBP1 0 . GRCh38 18 45063368 45063368 + Frame_Shift_Del DEL G G - novel C3L-02365_T C3L-02365_N G G c.4461delG p.Lys1488SerfsTer4 p.K1488Sfs*4 ENST00000282030 6/6 55 48 7 93 93 0 sindel-pindel SETBP1,frameshift_variant,p.Lys1488SerfsTer4,ENST00000282030,NM_015559.2; - ENST00000282030 Transcript frameshift_variant 4757/9899 4461/4791 1487/1596 Q/X caG/ca 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 6/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 HIGH 1 deletion 1 1 PASS . . 0 200 9 0 0 0 0 0 -16.234 0.9999907 1 1 1 0 - 7 5 34 45063368 45063368 G - 1 0 1 0 1 0 0 0 0 14406 933 33 0 0 SETBP1 18 45063368 Frame_Shift_Del DEL G C3L-02365_T 38107918 45063368 35309917 313 9285 LIPG 0 . GRCh38 18 49569504 49569504 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.527G>T p.Gly176Val p.G176V ENST00000261292 4/10 416 294 122 459 459 0 strelka-varscan-mutect LIPG,missense_variant,p.Gly176Val,ENST00000261292,NM_006033.2;LIPG,missense_variant,p.Gly212Val,ENST00000577628,;LIPG,missense_variant,p.Gly176Val,ENST00000427224,NM_001308006.1;LIPG,missense_variant,p.Gly176Val,ENST00000580036,;LIPG,downstream_gene_variant,,ENST00000583083,;LIPG,downstream_gene_variant,,ENST00000579750,; T ENST00000261292 Transcript missense_variant 805/10441 527/1503 176/500 G/V gGg/gTg 1 1 LIPG HGNC HGNC:6623 protein_coding YES CCDS11938.1 ENSP00000261292 Q9Y5X9 A0A024R2B5 UPI000012E706 NM_006033.2 deleterious(0.01) 4/10 hmmpanther:PTHR11610:SF13,hmmpanther:PTHR11610,Pfam_domain:PF00151,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474,Prints_domain:PR00821,Prints_domain:PR00822 MODERATE 1 SNV 1 1 PASS rs1387264680 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 49569504 49569504 G T 1 0 0 0 0 1 0 0 0 8744 1232 43 2 2 LIPG 18 49569504 Missense_Mutation SNP G C3L-02365_T 4506136 49569504 30803781 314 9286 FECH 0 . GRCh38 18 57571392 57571392 + Missense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.481G>A p.Ala161Thr p.A161T ENST00000382873 4/11 231 166 65 318 318 0 strelka-varscan-mutect FECH,missense_variant,p.Ala155Thr,ENST00000262093,NM_000140.3;FECH,missense_variant,p.Ala161Thr,ENST00000382873,NM_001012515.2;FECH,missense_variant,p.Ala155Thr,ENST00000592699,;FECH,missense_variant,p.Ala83Thr,ENST00000591215,;FECH,missense_variant,p.Val155Ile,ENST00000585747,;FECH,splice_region_variant,,ENST00000585699,;FECH,splice_region_variant,,ENST00000585494,;FECH,downstream_gene_variant,,ENST00000585878,;FECH,downstream_gene_variant,,ENST00000592111,; T ENST00000382873 Transcript missense_variant,splice_region_variant 515/2526 481/1290 161/429 A/T Gcc/Acc CS961589 1 -1 FECH HGNC HGNC:3647 protein_coding YES CCDS32836.1 ENSP00000372326 P22830 UPI00004E55EB NM_001012515.2 deleterious(0) 4/11 Gene3D:3.40.50.1400,HAMAP:MF_00323,Pfam_domain:PF00762,hmmpanther:PTHR11108,hmmpanther:PTHR11108:SF1,Superfamily_domains:SSF53800,TIGRFAM_domain:TIGR00109 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 57571392 57571392 C T 1 0 0 0 0 1 0 0 0 5671 695 24 3 3 FECH 18 57571392 Missense_Mutation SNP C C3L-02365_T 8001888 57571392 22801893 315 9287 PHLPP1 0 . GRCh38 18 62715983 62715983 + Silent SNP G G A novel C3L-02365_T C3L-02365_N G G c.300G>A p.= p.Q100Q ENST00000262719 1/17 17 13 4 20 20 0 strelka-varscan-mutect PHLPP1,synonymous_variant,p.=,ENST00000262719,NM_194449.3; A ENST00000262719 Transcript synonymous_variant 534/6390 300/5154 100/1717 Q caG/caA 1 1 PHLPP1 HGNC HGNC:20610 protein_coding YES CCDS45881.2 ENSP00000262719 O60346 UPI000051AE2E NM_194449.3 1/17 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 5 203 2 0 0 0 0 0 -13.09302 1 1 1 1 0 A 2 1 34 62715983 62715983 G A 1 0 0 0 0 0 0 0 1 11942 962 34 3 3 PHLPP1 18 62715983 Silent SNP G C3L-02365_T 5144591 62715983 17657302 316 9288 CDH7 0 . GRCh38 18 65857947 65857947 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.1367A>G p.Glu456Gly p.E456G ENST00000397968 8/12 93 84 9 154 154 0 strelka-varscan-mutect CDH7,missense_variant,p.Glu456Gly,ENST00000397968,NM_004361.2;CDH7,missense_variant,p.Glu456Gly,ENST00000536984,NM_001317214.1;CDH7,missense_variant,p.Glu456Gly,ENST00000323011,NM_033646.1; G ENST00000397968 Transcript missense_variant 1793/12231 1367/2358 456/785 E/G gAg/gGg 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 deleterious(0) 8/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 65857947 65857947 A G 1 0 0 0 0 1 0 0 0 2818 318 11 5 5 CDH7 18 65857947 Missense_Mutation SNP A C3L-02365_T 3141964 65857947 14515338 317 9289 NETO1 0 . GRCh38 18 72794363 72794363 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.511G>T p.Ala171Ser p.A171S ENST00000327305 5/11 100 72 28 168 167 1 strelka-varscan-mutect NETO1,missense_variant,p.Ala171Ser,ENST00000327305,NM_138966.3;NETO1,missense_variant,p.Ala171Ser,ENST00000583169,NM_001201465.1;NETO1,intron_variant,,ENST00000579730,; A ENST00000327305 Transcript missense_variant,splice_region_variant 1169/3058 511/1602 171/533 A/S Gcg/Tcg 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 tolerated(0.75) 5/11 Gene3D:2.60.120.290,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 72794363 72794363 C A 1 0 0 0 0 1 0 0 0 10374 695 24 2 2 NETO1 18 72794363 Missense_Mutation SNP C C3L-02365_T 6936416 72794363 7578922 318 9290 TLE6 0 . GRCh38 19 2988097 2988097 + Missense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.709C>T p.Pro237Ser p.P237S ENST00000246112 11/17 203 116 87 197 197 0 strelka-varscan-mutect TLE6,missense_variant,p.Pro237Ser,ENST00000246112,NM_001143986.1;TLE6,missense_variant,p.Pro114Ser,ENST00000452088,NM_024760.2;TLE6,downstream_gene_variant,,ENST00000453329,;TLE6,non_coding_transcript_exon_variant,,ENST00000478073,;TLE6,downstream_gene_variant,,ENST00000468176,;TLE6,downstream_gene_variant,,ENST00000591953,;TLE6,non_coding_transcript_exon_variant,,ENST00000497878,;TLE6,downstream_gene_variant,,ENST00000474207,;TLE6,upstream_gene_variant,,ENST00000469572,; T ENST00000246112 Transcript missense_variant 910/2100 709/1719 237/572 P/S Cct/Tct COSM4816943,COSM4816944 1 1 TLE6 HGNC HGNC:30788 protein_coding YES CCDS45910.1 ENSP00000246112 Q9H808 UPI000059D62B NM_001143986.1 tolerated(0.58) 11/17 hmmpanther:PTHR10814,hmmpanther:PTHR10814:SF2 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 2988097 2988097 C T 1 0 0 0 0 1 0 0 0 16388 855 30 3 3 TLE6 19 2988097 Missense_Mutation SNP C C3L-02365_T 2988097 55629519 319 9291 ADGRE1 0 . GRCh38 19 6937316 6937316 + Nonsense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.2455G>T p.Gly819Ter p.G819* ENST00000312053 19/21 148 97 51 131 131 0 strelka-varscan-mutect ADGRE1,stop_gained,p.Gly819Ter,ENST00000312053,NM_001974.4;ADGRE1,stop_gained,p.Gly800Ter,ENST00000381404,NM_001256252.1;ADGRE1,stop_gained,p.Gly754Ter,ENST00000250572,NM_001256253.1;ADGRE1,stop_gained,p.Gly678Ter,ENST00000381407,NM_001256254.1;ADGRE1,stop_gained,p.Gly642Ter,ENST00000450315,NM_001256255.1; T ENST00000312053 Transcript stop_gained 2492/3128 2455/2661 819/886 G/* Gga/Tga 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 19/21 PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303,Pfam_domain:PF00002,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 34 6937316 6937316 G T 1 0 0 0 0 0 1 0 0 359 1349 47 2 2 ADGRE1 19 6937316 Nonsense_Mutation SNP G C3L-02365_T 3949219 6937316 51680300 320 9292 MUC16 0 . GRCh38 19 8882730 8882730 + Missense_Mutation SNP A A G novel C3L-02365_T C3L-02365_N A A c.41683T>C p.Tyr13895His p.Y13895H ENST00000397910 66/84 178 130 48 190 190 0 strelka-varscan-mutect MUC16,missense_variant,p.Tyr13895His,ENST00000397910,NM_024690.2;MUC16,missense_variant,p.Tyr735His,ENST00000599436,;MUC16,missense_variant,p.Tyr713His,ENST00000601404,;MUC16,missense_variant,p.Tyr515His,ENST00000596768,; G ENST00000397910 Transcript missense_variant 41887/43816 41683/43524 13895/14507 Y/H Tac/Cac 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 66/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,Superfamily_domains:0047452 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 8882730 8882730 A G 1 0 0 0 0 1 0 0 0 9972 420 15 5 5 MUC16 19 8882730 Missense_Mutation SNP A C3L-02365_T 1945414 8882730 49734886 321 9293 KEAP1 0 . GRCh38 19 10491799 10491799 + Missense_Mutation SNP C C A C3L-02365_T C3L-02365_N C C c.1103G>T p.Cys368Phe p.C368F ENST00000171111 3/6 104 48 56 110 110 0 strelka-varscan-mutect KEAP1,missense_variant,p.Cys368Phe,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Cys368Phe,ENST00000393623,NM_012289.3;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,missense_variant,p.Cys28Phe,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENST00000171111 Transcript missense_variant 1651/2955 1103/1875 368/624 C/F tGc/tTc COSM3701407 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 1 MODERATE 1 SNV 1 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 34 10491799 10491799 C A 1 0 0 0 0 1 0 0 0 8061 710 25 2 2 KEAP1 19 10491799 Missense_Mutation SNP C C3L-02365_T 1609069 10491799 48125817 322 9294 BEST2 0 . GRCh38 19 12757933 12757933 + Silent SNP C C G novel C3L-02365_T C3L-02365_N C C c.1386C>G p.= p.A462A ENST00000549706 10/10 528 394 134 444 444 0 strelka-varscan-mutect BEST2,synonymous_variant,p.=,ENST00000549706,;BEST2,synonymous_variant,p.=,ENST00000553030,;BEST2,synonymous_variant,p.=,ENST00000042931,NM_017682.2;BEST2,downstream_gene_variant,,ENST00000552539,; G ENST00000549706 Transcript synonymous_variant 1710/2183 1386/1530 462/509 A gcC/gcG 1 1 BEST2 HGNC HGNC:17107 protein_coding YES CCDS42506.1 ENSP00000448310 Q8NFU1 UPI000007395A 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR10736,hmmpanther:PTHR10736:SF1 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 12757933 12757933 C G 1 0 0 0 0 0 0 0 1 1553 610 22 4 4 BEST2 19 12757933 Silent SNP C C3L-02365_T 2266134 12757933 45859683 323 9295 MAP1S 0 . GRCh38 19 17726094 17726094 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.710G>T p.Arg237Met p.R237M ENST00000324096 5/7 357 188 169 369 369 0 strelka-varscan-mutect MAP1S,missense_variant,p.Arg237Met,ENST00000324096,NM_018174.4;MAP1S,missense_variant,p.Arg211Met,ENST00000544059,NM_001308363.1;MAP1S,intron_variant,,ENST00000597735,;MAP1S,downstream_gene_variant,,ENST00000600186,;MAP1S,downstream_gene_variant,,ENST00000594625,;MAP1S,upstream_gene_variant,,ENST00000597000,;CTD-3149D2.4,downstream_gene_variant,,ENST00000595363,;MAP1S,intron_variant,,ENST00000597681,;MAP1S,downstream_gene_variant,,ENST00000601544,;MAP1S,downstream_gene_variant,,ENST00000599494,;MAP1S,upstream_gene_variant,,ENST00000598756,;MAP1S,downstream_gene_variant,,ENST00000594340,;MAP1S,downstream_gene_variant,,ENST00000595338,;MAP1S,downstream_gene_variant,,ENST00000598916,;MAP1S,downstream_gene_variant,,ENST00000597067,;MAP1S,3_prime_UTR_variant,,ENST00000594212,;MAP1S,downstream_gene_variant,,ENST00000594365,;MAP1S,downstream_gene_variant,,ENST00000598769,;MAP1S,downstream_gene_variant,,ENST00000596637,;MAP1S,downstream_gene_variant,,ENST00000593593,;MAP1S,downstream_gene_variant,,ENST00000600608,; T ENST00000324096 Transcript missense_variant 861/3419 710/3180 237/1059 R/M aGg/aTg 1 1 MAP1S HGNC HGNC:15715 protein_coding YES CCDS32954.1 ENSP00000325313 Q66K74 UPI00002036F9 NM_018174.4 deleterious(0) 5/7 hmmpanther:PTHR13843 MODERATE 1 SNV 1 1 PASS rs1234418364 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 17726094 17726094 G T 1 0 0 0 0 1 0 0 0 9156 1000 35 2 2 MAP1S 19 17726094 Missense_Mutation SNP G C3L-02365_T 4968161 17726094 40891522 324 9296 TSHZ3 0 . GRCh38 19 31276759 31276759 + Missense_Mutation SNP C C T rs376270774 C3L-02365_T C3L-02365_N C C c.3034G>A p.Glu1012Lys p.E1012K ENST00000240587 2/2 126 119 7 110 109 1 varscan-mutect TSHZ3,missense_variant,p.Glu1012Lys,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; T ENST00000240587 Transcript missense_variant 3362/5176 3034/3246 1012/1081 E/K Gaa/Aaa rs376270774,COSM1392497,COSM1392498 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 tolerated(0.23) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs376270774 . 0 198 11 0 0 0 0 0 -13.19954 0.9996889 1 1 1 0 T 3 4 34 31276759 31276759 C T 1 0 0 0 0 1 0 0 0 17130 893 31 1 1 TSHZ3 19 31276759 Missense_Mutation SNP C C3L-02365_T 13550665 31276759 27340857 325 9297 FBXO17 0 . GRCh38 19 38944971 38944971 + Nonsense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.691C>T p.Gln231Ter p.Q231* ENST00000292852 5/6 136 73 63 139 137 2 strelka-varscan-mutect FBXO17,stop_gained,p.Gln231Ter,ENST00000292852,NM_024907.6;CTC-360G5.8,stop_gained,p.Gln136Ter,ENST00000599996,;FBXO17,stop_gained,p.Gln231Ter,ENST00000595329,NM_148169.2;FBXO17,stop_gained,p.Gln90Ter,ENST00000599598,;FBXO17,splice_region_variant,,ENST00000599418,;FBXO17,splice_region_variant,,ENST00000596025,;FBXO17,splice_region_variant,,ENST00000597696,;FBXO17,downstream_gene_variant,,ENST00000601394,; A ENST00000292852 Transcript stop_gained,splice_region_variant 1033/2386 691/837 231/278 Q/* Cag/Tag 1 -1 FBXO17 HGNC HGNC:18754 protein_coding YES CCDS12526.1 ENSP00000292852 Q96EF6 UPI000012ADC1 NM_024907.6 5/6 PROSITE_profiles:PS51114,hmmpanther:PTHR12125,hmmpanther:PTHR12125:SF7,Gene3D:2.60.120.260,Pfam_domain:PF04300,SMART_domains:SM01198,Superfamily_domains:SSF49785 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 38944971 38944971 G A 1 0 0 0 0 0 1 0 0 5593 1391 48 3 3 FBXO17 19 38944971 Nonsense_Mutation SNP G C3L-02365_T 7668212 38944971 19672645 326 9298 SPTBN4 0 . GRCh38 19 40504011 40504011 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.1544G>A p.Arg515His p.R515H ENST00000352632 12/36 207 131 76 177 177 0 strelka-varscan-mutect SPTBN4,missense_variant,p.Arg515His,ENST00000338932,;SPTBN4,missense_variant,p.Arg515His,ENST00000352632,;SPTBN4,missense_variant,p.Arg515His,ENST00000392025,;SPTBN4,missense_variant,p.Arg515His,ENST00000598249,NM_020971.2;SPTBN4,missense_variant,p.Arg515His,ENST00000595535,;SPTBN4,downstream_gene_variant,,ENST00000598775,; A ENST00000352632 Transcript missense_variant 1630/8676 1544/7695 515/2564 R/H cGc/cAc 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB deleterious(0.01) 12/36 Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS rs956153403 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 40504011 40504011 G A 1 0 0 0 0 1 0 0 0 15477 1087 38 1 1 SPTBN4 19 40504011 Missense_Mutation SNP G C3L-02365_T 1559040 40504011 18113605 327 9299 GLTSCR1 0 . GRCh38 19 47701593 47701593 + Frame_Shift_Del DEL C C - novel C3L-02365_T C3L-02365_N C C c.3864delC p.Met1289CysfsTer71 p.M1289Cfs*71 ENST00000396720 15/15 480 366 114 412 412 0 sindel-varindel-pindel GLTSCR1,frameshift_variant,p.Met1289CysfsTer71,ENST00000396720,NM_015711.3;GLTSCR1,frameshift_variant,p.Met1237CysfsTer71,ENST00000614245,;CTD-2571L23.8,intron_variant,,ENST00000599924,;GLTSCR1,non_coding_transcript_exon_variant,,ENST00000602258,; - ENST00000396720 Transcript frameshift_variant 4055/5739 3861/4683 1287/1560 G/X ggC/gg 1 1 GLTSCR1 HGNC HGNC:4332 protein_coding YES CCDS46134.1 ENSP00000379946 Q9NZM4 UPI00016278EE NM_015711.3 15/15 hmmpanther:PTHR15572:SF1,hmmpanther:PTHR15572 HIGH 1 deletion 5 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 34 47701593 47701593 C - 1 0 1 0 1 0 0 0 0 6350 726 26 0 0 GLTSCR1 19 47701593 Frame_Shift_Del DEL C C3L-02365_T 7197582 47701593 10916023 328 9300 CTU1 0 . GRCh38 19 51104413 51104413 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.157G>T p.Val53Leu p.V53L ENST00000421832 2/3 55 30 25 80 80 0 strelka-varscan-mutect CTU1,missense_variant,p.Val53Leu,ENST00000421832,NM_145232.3; A ENST00000421832 Transcript missense_variant 202/2087 157/1047 53/348 V/L Gtg/Ttg 1 -1 CTU1 HGNC HGNC:29590 protein_coding YES CCDS12824.1 ENSP00000390011 Q7Z7A3 UPI000013D897 NM_145232.3 tolerated(0.09) 2/3 Low_complexity_(Seg):seg,HAMAP:MF_03053,hmmpanther:PTHR11807,hmmpanther:PTHR11807:SF12,PIRSF_domain:PIRSF004976,Superfamily_domains:SSF52402 MODERATE 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 51104413 51104413 C A 1 0 0 0 0 1 0 0 0 3856 507 18 2 2 CTU1 19 51104413 Missense_Mutation SNP C C3L-02365_T 3402820 51104413 7513203 329 9301 ZNF264 0 . GRCh38 19 57193873 57193873 + Splice_Site SNP A A T novel C3L-02365_T C3L-02365_N A A c.34-2A>T p.X12_splice ENST00000263095 124 56 68 128 128 0 strelka-varscan-mutect ZNF264,splice_acceptor_variant,,ENST00000263095,NM_003417.4;ZNF264,splice_acceptor_variant,,ENST00000536056,;ZNF264,splice_acceptor_variant,,ENST00000600531,;ZNF264,splice_acceptor_variant,,ENST00000599653,;ZNF264,splice_acceptor_variant,,ENST00000597447,;ZNF264,splice_acceptor_variant,,ENST00000594126,; T ENST00000263095 Transcript splice_acceptor_variant -/12163 34/1884 12/627 1 1 ZNF264 HGNC HGNC:13057 protein_coding YES CCDS33127.1 ENSP00000263095 O43296 UPI000013C33B NM_003417.4 1/3 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 34 57193873 57193873 A T 1 0 0 0 0 0 0 1 0 18380 202 7 4 4 ZNF264 19 57193873 Splice_Site SNP A C3L-02365_T 6089460 57193873 1423743 330 9302 ZNF460 0 . GRCh38 19 57290854 57290854 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.313T>C p.Tyr105His p.Y105H ENST00000360338 3/3 216 192 24 221 221 0 strelka-varscan-mutect ZNF460,missense_variant,p.Tyr105His,ENST00000360338,NM_006635.3;ZNF460,missense_variant,p.Tyr64His,ENST00000537645,;ZNF460,missense_variant,p.Tyr64His,ENST00000599602,;CTC-444N24.7,downstream_gene_variant,,ENST00000623072,; C ENST00000360338 Transcript missense_variant 635/3350 313/1689 105/562 Y/H Tac/Cac 1 1 ZNF460 HGNC HGNC:21628 protein_coding YES CCDS12949.1 ENSP00000353491 Q14592 UPI0000202D11 NM_006635.3 tolerated(0.12) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 57290854 57290854 T C 1 0 0 0 0 1 0 0 0 18495 1406 49 5 5 ZNF460 19 57290854 Missense_Mutation SNP T C3L-02365_T 96981 57290854 1326762 331 9303 ZNF543 0 . GRCh38 19 57327839 57327839 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.377G>T p.Gly126Val p.G126V ENST00000321545 4/4 211 135 76 210 210 0 strelka-varscan-mutect ZNF543,missense_variant,p.Gly126Val,ENST00000321545,NM_213598.3; T ENST00000321545 Transcript missense_variant 722/3659 377/1803 126/600 G/V gGg/gTg 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 tolerated(0.16) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 57327839 57327839 G T 1 0 0 0 0 1 0 0 0 18550 1232 43 2 2 ZNF543 19 57327839 Missense_Mutation SNP G C3L-02365_T 36985 57327839 1289777 332 9304 C19orf18 0 . GRCh38 19 57961488 57961488 + Silent SNP C C G rs199764366 C3L-02365_T C3L-02365_N C C c.435G>C p.= p.P145P ENST00000314391 5/6 168 123 45 198 198 0 strelka-varscan-mutect C19orf18,synonymous_variant,p.=,ENST00000314391,NM_152474.4; G ENST00000314391 Transcript synonymous_variant 537/915 435/648 145/215 P ccG/ccC rs199764366 1 -1 C19orf18 HGNC HGNC:28642 protein_coding YES CCDS12967.1 ENSP00000321519 Q8NEA5 UPI000006D09E NM_152474.4 5/6 hmmpanther:PTHR38000 LOW 1 SNV 1 1 PASS rs199764366 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 57961488 57961488 C G 1 0 0 0 0 0 0 0 1 1904 523 19 4 4 C19orf18 19 57961488 Silent SNP C C3L-02365_T 633649 57961488 656128 333 9305 C20orf194 0 . GRCh38 20 3298145 3298145 + Missense_Mutation SNP T T C novel C3L-02365_T C3L-02365_N T T c.1813A>G p.Ile605Val p.I605V ENST00000252032 22/37 189 91 98 157 157 0 strelka-varscan-mutect C20orf194,missense_variant,p.Ile605Val,ENST00000252032,NM_001009984.2;C20orf194,non_coding_transcript_exon_variant,,ENST00000619760,; C ENST00000252032 Transcript missense_variant 1881/6869 1813/3534 605/1177 I/V Ata/Gta 1 -1 C20orf194 HGNC HGNC:17721 protein_coding YES CCDS42851.1 ENSP00000252032 Q5TEA3 UPI0000470A8D NM_001009984.2 tolerated(0.69) 22/37 hmmpanther:PTHR33664,hmmpanther:PTHR33664:SF1 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 3298145 3298145 T C 1 0 0 0 0 1 0 0 0 2005 1464 51 5 5 C20orf194 20 3298145 Missense_Mutation SNP T C3L-02365_T 3298145 61146022 334 9306 SNAP25 0 . GRCh38 20 10297003 10297003 + Silent SNP A A G novel C3L-02365_T C3L-02365_N A A c.360A>G p.= p.V120V ENST00000254976 6/8 78 70 8 88 88 0 strelka-varscan-mutect SNAP25,synonymous_variant,p.=,ENST00000254976,NM_130811.2;SNAP25,synonymous_variant,p.=,ENST00000304886,NM_003081.3;SNAP25,downstream_gene_variant,,ENST00000430336,;SNAP25-AS1,intron_variant,,ENST00000421143,;SNAP25-AS1,intron_variant,,ENST00000453544,;SNAP25,non_coding_transcript_exon_variant,,ENST00000495883,; G ENST00000254976 Transcript synonymous_variant 571/2053 360/621 120/206 V gtA/gtG 1 1 SNAP25 HGNC HGNC:11132 protein_coding YES CCDS13110.1 ENSP00000254976 P60880 UPI0000001103 NM_130811.2 6/8 hmmpanther:PTHR19305,hmmpanther:PTHR19305:SF5,Pfam_domain:PF00835 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 34 10297003 10297003 A G 1 0 0 0 0 0 0 0 1 15151 407 15 5 5 SNAP25 20 10297003 Silent SNP A C3L-02365_T 6998858 10297003 54147164 335 9307 SSTR4 0 . GRCh38 20 23035930 23035930 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.447G>T p.= p.V149V ENST00000255008 1/1 124 66 58 120 120 0 strelka-varscan-mutect SSTR4,synonymous_variant,p.=,ENST00000255008,NM_001052.2;RP4-753D10.3,intron_variant,,ENST00000440921,;RP4-753D10.3,upstream_gene_variant,,ENST00000419734,; T ENST00000255008 Transcript synonymous_variant 545/1427 447/1167 149/388 V gtG/gtT 1 1 SSTR4 HGNC HGNC:11333 protein_coding YES CCDS42856.1 ENSP00000255008 P31391 UPI000013CE7A NM_001052.2 1/1 Transmembrane_helices:TMhelix,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF0 LOW SNV 1 PASS . . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 23035930 23035930 G T 1 0 0 0 0 0 0 0 1 15577 1306 46 2 2 SSTR4 20 23035930 Silent SNP G C3L-02365_T 12738927 23035930 41408237 336 9308 GSS 0 . GRCh38 20 34941750 34941750 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.571G>A p.Gly191Arg p.G191R ENST00000216951 6/13 515 422 93 390 390 0 strelka-varscan-mutect GSS,missense_variant,p.Gly191Arg,ENST00000216951,NM_001322494.1,NM_000178.2;GSS,intron_variant,,ENST00000451957,; T ENST00000216951 Transcript missense_variant 670/1922 571/1425 191/474 G/R Gga/Aga 1 -1 GSS HGNC HGNC:4624 protein_coding YES CCDS13245.1 ENSP00000216951 P48637 V9HWJ1 UPI0000111B5F NM_001322494.1,NM_000178.2 deleterious(0) 6/13 Gene3D:1m0wB04,Pfam_domain:PF03917,PIRSF_domain:PIRSF001558,hmmpanther:PTHR11130,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01986 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 34941750 34941750 C T 1 0 0 0 0 1 0 0 0 6713 632 22 3 3 GSS 20 34941750 Missense_Mutation SNP C C3L-02365_T 11905820 34941750 29502417 337 9309 GTSF1L 0 . GRCh38 20 43726304 43726304 + Missense_Mutation SNP T T A rs369247239 C3L-02365_T C3L-02365_N T T c.391A>T p.Thr131Ser p.T131S ENST00000373003 1/1 169 135 34 129 129 0 strelka-varscan-mutect GTSF1L,missense_variant,p.Thr131Ser,ENST00000373003,NM_176791.3;GTSF1L,missense_variant,p.Thr106Ser,ENST00000373005,NM_001008901.1; A ENST00000373003 Transcript missense_variant 695/835 391/447 131/148 T/S Acg/Tcg rs369247239 1 -1 GTSF1L HGNC HGNC:16198 protein_coding YES CCDS13323.1 ENSP00000362094 Q9H1H1 UPI00001285E6 NM_176791.3 tolerated(1) 1/1 hmmpanther:PTHR21402:SF3,hmmpanther:PTHR21402 MODERATE 1 SNV 1 PASS rs369247239 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 43726304 43726304 T A 1 0 0 0 0 1 0 0 0 6768 1696 59 4 4 GTSF1L 20 43726304 Missense_Mutation SNP T C3L-02365_T 8784554 43726304 20717863 338 9310 CSTF1 0 . GRCh38 20 56403605 56403605 + Silent SNP C C T novel C3L-02365_T C3L-02365_N C C c.1174C>T p.= p.L392L ENST00000217109 6/6 502 427 75 307 306 1 strelka-varscan-mutect CSTF1,synonymous_variant,p.=,ENST00000217109,NM_001033521.1,NM_001324.2,NM_001033522.1;CSTF1,downstream_gene_variant,,ENST00000415828,;CSTF1,downstream_gene_variant,,ENST00000452950,;CSTF1,3_prime_UTR_variant,,ENST00000493039,;CSTF1,downstream_gene_variant,,ENST00000490539,; T ENST00000217109 Transcript synonymous_variant 1526/4290 1174/1296 392/431 L Ctg/Ttg 1 1 CSTF1 HGNC HGNC:2483 protein_coding YES CCDS13452.1 ENSP00000217109 Q05048 UPI0000000C1E NM_001033521.1,NM_001324.2,NM_001033522.1 6/6 PROSITE_profiles:PS50294,hmmpanther:PTHR22840,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 56403605 56403605 C T 1 0 0 0 0 0 0 0 1 3783 796 28 3 3 CSTF1 20 56403605 Silent SNP C C3L-02365_T 12677301 56403605 8040562 339 9311 CTCFL 0 . GRCh38 20 57523720 57523720 + Silent SNP C C A novel C3L-02365_T C3L-02365_N C C c.486G>T p.= p.V162V ENST00000423479 2/12 279 147 132 198 197 1 strelka-varscan-mutect CTCFL,synonymous_variant,p.=,ENST00000608263,NM_001269041.1;CTCFL,synonymous_variant,p.=,ENST00000429804,NM_001269046.1;CTCFL,synonymous_variant,p.=,ENST00000609232,NM_080618.3;CTCFL,synonymous_variant,p.=,ENST00000243914,;CTCFL,synonymous_variant,p.=,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,synonymous_variant,p.=,ENST00000422869,NM_001269047.1;CTCFL,synonymous_variant,p.=,ENST00000432255,NM_001269048.1;CTCFL,synonymous_variant,p.=,ENST00000608425,NM_001269045.1;CTCFL,synonymous_variant,p.=,ENST00000608440,NM_001269044.1;CTCFL,synonymous_variant,p.=,ENST00000423479,NM_001269043.1;CTCFL,synonymous_variant,p.=,ENST00000608158,NM_001269052.1;CTCFL,synonymous_variant,p.=,ENST00000481655,NM_001269051.1;CTCFL,intron_variant,,ENST00000539382,NM_001269050.1;CTCFL,intron_variant,,ENST00000433949,NM_001269049.1;CTCFL,intron_variant,,ENST00000608903,NM_001269055.1;CTCFL,intron_variant,,ENST00000502686,NM_001269054.1;CTCFL,intron_variant,,ENST00000608858,;CTCFL,synonymous_variant,p.=,ENST00000426658,;CTCFL,synonymous_variant,p.=,ENST00000422109,;CTCFL,synonymous_variant,p.=,ENST00000608720,;CTCFL,non_coding_transcript_exon_variant,,ENST00000607923,;CTCFL,intron_variant,,ENST00000608108,; A ENST00000423479 Transcript synonymous_variant 577/2478 486/2103 162/700 V gtG/gtT 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 2/12 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 34 57523720 57523720 C A 1 0 0 0 0 0 0 0 1 3808 581 21 2 2 CTCFL 20 57523720 Silent SNP C C3L-02365_T 1120115 57523720 6920447 340 9312 RGS19 0 . GRCh38 20 64076871 64076871 + Nonsense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.16G>T p.Glu6Ter p.E6* ENST00000395042 2/6 79 69 10 52 52 0 strelka-varscan-mutect RGS19,stop_gained,p.Glu6Ter,ENST00000395042,NM_005873.2;RGS19,stop_gained,p.Glu6Ter,ENST00000332298,NM_001039467.1;OPRL1,upstream_gene_variant,,ENST00000336866,NM_001318853.1,NM_182647.2;OPRL1,upstream_gene_variant,,ENST00000355631,NM_001318854.1,NM_000913.4;TCEA2,downstream_gene_variant,,ENST00000395053,;TCEA2,downstream_gene_variant,,ENST00000361317,NM_198723.1;TCEA2,downstream_gene_variant,,ENST00000343484,NM_003195.4;TCEA2,downstream_gene_variant,,ENST00000458442,;MIR6813,downstream_gene_variant,,ENST00000621638,;RGS19,non_coding_transcript_exon_variant,,ENST00000493165,;RGS19,intron_variant,,ENST00000479996,;TCEA2,downstream_gene_variant,,ENST00000465111,;TCEA2,downstream_gene_variant,,ENST00000461072,;TCEA2,downstream_gene_variant,,ENST00000475236,;TCEA2,downstream_gene_variant,,ENST00000495168,;TCEA2,downstream_gene_variant,,ENST00000465433,;TCEA2,downstream_gene_variant,,ENST00000477783,; A ENST00000395042 Transcript stop_gained 283/1593 16/654 6/217 E/* Gag/Tag 1 -1 RGS19 HGNC HGNC:13735 protein_coding YES CCDS13555.1 ENSP00000378483 P49795 UPI0000133838 NM_005873.2 2/6 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF145 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99194 1 1 1 1 0 A 4 1 34 64076871 64076871 C A 1 0 0 0 0 0 1 0 0 13472 835 29 2 2 RGS19 20 64076871 Nonsense_Mutation SNP C C3L-02365_T 6553151 64076871 367296 341 9313 CLDN17 0 . GRCh38 21 30166353 30166353 + Missense_Mutation SNP C C A rs745577971 C3L-02365_T C3L-02365_N C C c.265G>T p.Ala89Ser p.A89S ENST00000286808 1/1 220 185 35 205 205 0 strelka-varscan-mutect CLDN17,missense_variant,p.Ala89Ser,ENST00000286808,NM_012131.2; A ENST00000286808 Transcript missense_variant 404/1193 265/675 89/224 A/S Gct/Tct rs745577971 1 -1 CLDN17 HGNC HGNC:2038 protein_coding YES CCDS13586.1 ENSP00000286808 P56750 UPI000004E655 NM_012131.2 deleterious(0.01) 1/1 Pfam_domain:PF00822,Prints_domain:PR01077,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF75,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs745577971 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 30166353 30166353 C A 1 0 0 0 0 1 0 0 0 3242 710 25 2 2 CLDN17 21 30166353 Missense_Mutation SNP C C3L-02365_T 30166353 16543630 342 9314 TIAM1 0 . GRCh38 21 31182478 31182478 + Missense_Mutation SNP C C T novel C3L-02365_T C3L-02365_N C C c.2830G>A p.Val944Met p.V944M ENST00000286827 16/29 106 88 18 91 91 0 strelka-varscan-mutect TIAM1,missense_variant,p.Val944Met,ENST00000286827,NM_003253.2;TIAM1,missense_variant,p.Val884Met,ENST00000541036,; T ENST00000286827 Transcript missense_variant 3302/7200 2830/4776 944/1591 V/M Gtg/Atg 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 tolerated(0.23) 16/29 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 34 31182478 31182478 C T 1 0 0 0 0 1 0 0 0 16324 565 20 3 3 TIAM1 21 31182478 Missense_Mutation SNP C C3L-02365_T 1016125 31182478 15527505 343 9315 TIAM1 0 . GRCh38 21 31251979 31251979 + Nonsense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.1174G>T p.Glu392Ter p.E392* ENST00000286827 6/29 395 330 65 358 355 3 strelka-varscan-mutect TIAM1,stop_gained,p.Glu392Ter,ENST00000286827,NM_003253.2;TIAM1,stop_gained,p.Glu392Ter,ENST00000541036,;TIAM1,non_coding_transcript_exon_variant,,ENST00000469412,; A ENST00000286827 Transcript stop_gained 1646/7200 1174/4776 392/1591 E/* Gag/Tag 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 6/29 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88 HIGH 1 SNV 1 1 PASS rs1490194529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 34 31251979 31251979 C A 1 0 0 0 0 0 1 0 0 16324 864 30 2 2 TIAM1 21 31251979 Nonsense_Mutation SNP C C3L-02365_T 69501 31251979 15458004 344 9316 POTEH 0 . GRCh38 22 15690224 15690224 + Silent SNP C C T rs369197112 C3L-02365_T C3L-02365_N C C c.147C>T p.= p.H49H ENST00000343518 1/11 660 578 82 456 456 0 varscan-mutect POTEH,synonymous_variant,p.=,ENST00000343518,NM_001136213.1;POTEH,synonymous_variant,p.=,ENST00000621704,;POTEH,upstream_gene_variant,,ENST00000452800,; T ENST00000343518 Transcript synonymous_variant 199/1928 147/1638 49/545 H caC/caT rs369197112 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 1/11 LOW 1 SNV 5 1 PASS rs369197112 . 2 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 15690224 15690224 C T 1 0 0 0 0 0 0 0 1 12381 535 19 1 1 POTEH 22 15690224 Silent SNP C C3L-02365_T 15690224 35128244 345 9317 CECR2 0 . GRCh38 22 17504978 17504978 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.343G>T p.Asp115Tyr p.D115Y ENST00000400585 7/19 192 100 92 160 160 0 strelka-varscan-mutect CECR2,missense_variant,p.Asp256Tyr,ENST00000612582,;CECR2,missense_variant,p.Asp278Tyr,ENST00000342247,NM_001290047.1;CECR2,missense_variant,p.Asp115Tyr,ENST00000400585,NM_001290046.1;CECR2,missense_variant,p.Asp115Tyr,ENST00000262608,; T ENST00000400585 Transcript missense_variant 781/4833 343/3903 115/1300 D/Y Gac/Tac 1 1 CECR2 HGNC HGNC:1840 protein_coding YES CCDS77646.1 ENSP00000383428 B7WPH3 UPI000198C520 NM_001290046.1 deleterious(0) 7/19 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF123 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 17504978 17504978 G T 1 0 0 0 0 1 0 0 0 2913 1174 41 2 2 CECR2 22 17504978 Missense_Mutation SNP G C3L-02365_T 1814754 17504978 33313490 346 9318 TBX1 0 . GRCh38 22 19766503 19766503 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1124G>T p.Gly375Val p.G375V ENST00000332710 9/9 106 60 46 125 125 0 strelka-varscan-mutect TBX1,missense_variant,p.Gly375Val,ENST00000332710,NM_080647.1;TBX1,intron_variant,,ENST00000359500,NM_005992.1;TBX1,intron_variant,,ENST00000329705,NM_080646.1;TBX1,intron_variant,,ENST00000621939,;TBX1,downstream_gene_variant,,ENST00000475303,;TBX1,downstream_gene_variant,,ENST00000484336,; T ENST00000332710 Transcript missense_variant 1253/2084 1124/1488 375/495 G/V gGg/gTg 1 1 TBX1 HGNC HGNC:11592 protein_coding YES CCDS13767.1 ENSP00000331791 O43435 D9ZGG0 UPI0000073068 NM_080647.1 tolerated_low_confidence(0.81) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF104 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 19766503 19766503 G T 1 0 0 0 0 1 0 0 0 16055 1232 43 2 2 TBX1 22 19766503 Missense_Mutation SNP G C3L-02365_T 2261525 19766503 31051965 347 9319 AIFM3 0 . GRCh38 22 20977999 20977999 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.1471G>T p.Ala491Ser p.A491S ENST00000399167 16/21 199 106 93 158 158 0 strelka-varscan-mutect AIFM3,missense_variant,p.Ala491Ser,ENST00000399167,NM_144704.2;AIFM3,missense_variant,p.Ala491Ser,ENST00000440238,;AIFM3,missense_variant,p.Ala497Ser,ENST00000405089,NM_001146288.1;AIFM3,missense_variant,p.Ala491Ser,ENST00000399163,NM_001018060.2;LZTR1,upstream_gene_variant,,ENST00000215739,NM_006767.3;AIFM3,downstream_gene_variant,,ENST00000434714,;AIFM3,downstream_gene_variant,,ENST00000441376,;XXbac-B135H6.18,downstream_gene_variant,,ENST00000610278,;AIFM3,non_coding_transcript_exon_variant,,ENST00000465606,;AIFM3,non_coding_transcript_exon_variant,,ENST00000483107,;LZTR1,upstream_gene_variant,,ENST00000479606,;AIFM3,downstream_gene_variant,,ENST00000468124,;AIFM3,downstream_gene_variant,,ENST00000496097,;AIFM3,non_coding_transcript_exon_variant,,ENST00000486003,;LZTR1,upstream_gene_variant,,ENST00000414985,;AIFM3,downstream_gene_variant,,ENST00000417515,;LZTR1,upstream_gene_variant,,ENST00000443265,;AIFM3,downstream_gene_variant,,ENST00000484206,;AIFM3,downstream_gene_variant,,ENST00000472575,;AIFM3,downstream_gene_variant,,ENST00000467926,;AIFM3,downstream_gene_variant,,ENST00000426113,;LZTR1,upstream_gene_variant,,ENST00000493460,; T ENST00000399167 Transcript missense_variant 1711/2387 1471/1818 491/605 A/S Gct/Tct 1 1 AIFM3 HGNC HGNC:26398 protein_coding YES CCDS13786.1 ENSP00000382120 Q96NN9 UPI0000071A61 NM_144704.2 tolerated(0.14) 16/21 Gene3D:3.50.50.60,Pfam_domain:PF07992,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF174,Superfamily_domains:SSF51905 MODERATE SNV 2 1 PASS rs1363812641 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 20977999 20977999 G T 1 0 0 0 0 1 0 0 0 505 1319 46 2 2 AIFM3 22 20977999 Missense_Mutation SNP G C3L-02365_T 1211496 20977999 29840469 348 9320 P2RX6 0 . GRCh38 22 21023516 21023516 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.788C>G p.Ser263Cys p.S263C ENST00000413302 8/12 468 420 48 169 169 0 strelka-varscan-mutect P2RX6,missense_variant,p.Ser263Cys,ENST00000413302,NM_005446.3;P2RX6,missense_variant,p.Ser237Cys,ENST00000401443,NM_001159554.1;P2RX6,3_prime_UTR_variant,,ENST00000442475,;P2RX6,3_prime_UTR_variant,,ENST00000432930,;P2RX6,3_prime_UTR_variant,,ENST00000422210,;P2RX6,non_coding_transcript_exon_variant,,ENST00000487342,;P2RX6,downstream_gene_variant,,ENST00000469722,;P2RX6,downstream_gene_variant,,ENST00000452228,; G ENST00000413302 Transcript missense_variant 936/3687 788/1326 263/441 S/C tCt/tGt 1 1 P2RX6 HGNC HGNC:8538 protein_coding YES CCDS13788.2 ENSP00000416193 O15547 UPI000013C698 NM_005446.3 tolerated(0.07) 8/12 Gene3D:3h9vA02,Pfam_domain:PF00864,PIRSF_domain:PIRSF005713,Prints_domain:PR01307,PROSITE_patterns:PS01212,hmmpanther:PTHR10125,hmmpanther:PTHR10125:SF21,TIGRFAM_domain:TIGR00863 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 21023516 21023516 C G 1 0 0 0 0 1 0 0 0 11417 913 32 4 4 P2RX6 22 21023516 Missense_Mutation SNP C C3L-02365_T 45517 21023516 29794952 349 9321 RSPH14 0 . GRCh38 22 23140277 23140277 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.144G>T p.Met48Ile p.M48I ENST00000216036 2/7 405 217 188 390 390 0 strelka-varscan-mutect RSPH14,missense_variant,p.Met48Ile,ENST00000216036,NM_014433.2;RSPH14,missense_variant,p.Met48Ile,ENST00000406876,;RSPH14,missense_variant,p.Met8Ile,ENST00000452757,;RSPH14,upstream_gene_variant,,ENST00000439064,;U7,upstream_gene_variant,,ENST00000459276,; A ENST00000216036 Transcript missense_variant 341/1291 144/1047 48/348 M/I atG/atT 1 -1 RSPH14 HGNC HGNC:13437 protein_coding YES CCDS13803.1 ENSP00000216036 Q9UHP6 UPI000004A0CE NM_014433.2 deleterious(0.04) 2/7 Gene3D:1.25.10.10,hmmpanther:PTHR15599,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 23140277 23140277 C A 1 0 0 0 0 1 0 0 0 13962 594 21 2 2 RSPH14 22 23140277 Missense_Mutation SNP C C3L-02365_T 2116761 23140277 27678191 350 9322 WWC3 0 . GRCh38 X 10126233 10126233 + Missense_Mutation SNP C C A novel C3L-02365_T C3L-02365_N C C c.2033C>A p.Ser678Tyr p.S678Y ENST00000380861 15/23 197 175 22 234 234 0 strelka-varscan-mutect WWC3,missense_variant,p.Ser678Tyr,ENST00000380861,NM_015691.3; A ENST00000380861 Transcript missense_variant 2424/6647 2033/3279 678/1092 S/Y tCc/tAc 1 1 WWC3 HGNC HGNC:29237 protein_coding YES CCDS14136.1 ENSP00000370242 Q9ULE0 UPI0000225CDE NM_015691.3 tolerated(0.61) 15/23 hmmpanther:PTHR14791:SF25,hmmpanther:PTHR14791,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 10126233 10126233 C A 1 0 0 0 0 1 0 0 0 17971 855 30 2 2 WWC3 23 10126233 Missense_Mutation SNP C C3L-02365_T 10126233 145914662 351 9323 NYX 0 . GRCh38 X 41474804 41474804 + Missense_Mutation SNP G G T C3L-02365_T C3L-02365_N G G c.1351G>T p.Val451Leu p.V451L ENST00000342595 2/2 88 66 22 109 108 1 strelka-varscan-mutect NYX,missense_variant,p.Val451Leu,ENST00000342595,NM_022567.2;NYX,missense_variant,p.Val451Leu,ENST00000378220,;NYX,downstream_gene_variant,,ENST00000486842,;RP1-169I5.4,upstream_gene_variant,,ENST00000451718,; T ENST00000342595 Transcript missense_variant 1807/2713 1351/1446 451/481 V/L Gtg/Ttg COSM1331867 1 1 NYX HGNC HGNC:8082 protein_coding YES CCDS14256.1 ENSP00000340328 Q9GZU5 UPI0000130B37 NM_022567.2 tolerated_low_confidence(0.19) 2/2 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 41474804 41474804 G T 1 0 0 0 0 1 0 0 0 10875 1261 44 2 2 NYX 23 41474804 Missense_Mutation SNP G C3L-02365_T 31348571 41474804 114566091 352 9324 AMER1 0 . GRCh38 X 64191058 64191058 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.2229G>C p.Arg743Ser p.R743S ENST00000330258 2/2 335 185 150 360 360 0 strelka-varscan-mutect AMER1,missense_variant,p.Arg743Ser,ENST00000330258,NM_152424.3;AMER1,missense_variant,p.Arg743Ser,ENST00000374869,; G ENST00000330258 Transcript missense_variant 2502/8443 2229/3408 743/1135 R/S agG/agC 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 tolerated(0.14) 2/2 hmmpanther:PTHR22237:SF0,hmmpanther:PTHR22237 MODERATE 1 SNV 1 1 PASS rs1484155916 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 64191058 64191058 C G 1 0 0 0 0 1 0 0 0 667 622 22 4 4 AMER1 23 64191058 Missense_Mutation SNP C C3L-02365_T 22716254 64191058 91849837 353 9325 HEPH 0 . GRCh38 X 66203381 66203381 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.2257T>G p.Cys753Gly p.C753G ENST00000519389 13/21 160 120 40 137 137 0 strelka-varscan-mutect HEPH,missense_variant,p.Cys753Gly,ENST00000519389,NM_138737.4;HEPH,missense_variant,p.Cys699Gly,ENST00000343002,;HEPH,missense_variant,p.Cys702Gly,ENST00000441993,NM_001130860.3;HEPH,missense_variant,p.Cys432Gly,ENST00000336279,NM_014799.3;HEPH,missense_variant,p.Cys510Gly,ENST00000419594,NM_001282141.1;HEPH,missense_variant,p.Cys656Gly,ENST00000425114,;HEPH,non_coding_transcript_exon_variant,,ENST00000471121,; G ENST00000519389 Transcript missense_variant 2436/6013 2257/3639 753/1212 C/G Tgc/Ggc 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 deleterious(0) 13/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,PROSITE_patterns:PS00079,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 66203381 66203381 T G 1 0 0 0 0 1 0 0 0 6938 1812 63 5 5 HEPH 23 66203381 Missense_Mutation SNP T C3L-02365_T 2012323 66203381 89837514 354 9326 SLC7A3 0 . GRCh38 X 70925839 70925839 + Missense_Mutation SNP C C T C3L-02365_T C3L-02365_N C C c.1834G>A p.Gly612Ser p.G612S ENST00000374299 12/12 162 127 35 203 203 0 strelka-varscan-mutect SLC7A3,missense_variant,p.Gly612Ser,ENST00000374299,;SLC7A3,missense_variant,p.Gly612Ser,ENST00000298085,NM_001048164.2,NM_032803.5; T ENST00000374299 Transcript missense_variant 1979/2236 1834/1860 612/619 G/S Ggc/Agc COSM1226577 1 -1 SLC7A3 HGNC HGNC:11061 protein_coding YES CCDS14404.1 ENSP00000363417 Q8WY07 UPI0000049F96 tolerated(0.27) 12/12 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF209 1 MODERATE 1 SNV 1 1 1 PASS rs1372449309 . 0 198 7 4 0 0 0 0 -20 0.9988161 1 1 1 0 T 3 4 34 70925839 70925839 C T 1 0 0 0 0 1 0 0 0 14981 652 23 1 1 SLC7A3 23 70925839 Missense_Mutation SNP C C3L-02365_T 4722458 70925839 85115056 355 9327 GPR174 0 . GRCh38 X 79171810 79171810 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.803G>C p.Arg268Thr p.R268T ENST00000276077 1/1 111 102 9 165 165 0 strelka-varscan-mutect GPR174,missense_variant,p.Arg268Thr,ENST00000276077,NM_032553.1; C ENST00000276077 Transcript missense_variant 839/1258 803/1002 268/333 R/T aGg/aCg 1 1 GPR174 HGNC HGNC:30245 protein_coding YES CCDS14443.1 ENSP00000276077 Q9BXC1 UPI0000050477 NM_032553.1 tolerated(0.22) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF4,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -17.90723 1 1 1 1 0 C 3 2 34 79171810 79171810 G C 1 0 0 0 0 1 0 0 0 6556 1000 35 4 4 GPR174 23 79171810 Missense_Mutation SNP G C3L-02365_T 8245971 79171810 76869085 356 9328 APOOL 0 . GRCh38 X 85046477 85046477 + Missense_Mutation SNP T T G novel C3L-02365_T C3L-02365_N T T c.47T>G p.Leu16Arg p.L16R ENST00000373173 2/9 244 224 20 323 323 0 strelka-varscan-mutect APOOL,missense_variant,p.Leu11Arg,ENST00000622540,;APOOL,missense_variant,p.Leu16Arg,ENST00000613473,;APOOL,missense_variant,p.Leu16Arg,ENST00000373173,NM_198450.5; G ENST00000373173 Transcript missense_variant 134/1279 47/807 16/268 L/R cTg/cGg 1 1 APOOL HGNC HGNC:24009 protein_coding YES CCDS48138.1 ENSP00000362268 Q6UXV4 UPI00001D6936 NM_198450.5 deleterious(0) 2/9 hmmpanther:PTHR14564,hmmpanther:PTHR14564:SF3 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999779 1 1 1 0 G 3 3 34 85046477 85046477 T G 1 0 0 0 0 1 0 0 0 936 1580 55 5 5 APOOL 23 85046477 Missense_Mutation SNP T C3L-02365_T 5874667 85046477 70994418 357 9329 ZNF711 0 . GRCh38 X 85255585 85255585 + Missense_Mutation SNP G G C novel C3L-02365_T C3L-02365_N G G c.406G>C p.Gly136Arg p.G136R ENST00000373165 4/9 178 108 70 253 253 0 strelka-varscan-mutect ZNF711,missense_variant,p.Gly136Arg,ENST00000360700,;ZNF711,missense_variant,p.Gly136Arg,ENST00000373165,NM_021998.4;ZNF711,missense_variant,p.Gly136Arg,ENST00000276123,; C ENST00000373165 Transcript missense_variant 712/4124 406/2286 136/761 G/R Ggt/Cgt 1 1 ZNF711 HGNC HGNC:13128 protein_coding YES CCDS35344.1 ENSP00000362260 Q9Y462 UPI0000212114 NM_021998.4 tolerated(0.51) 4/9 Pfam_domain:PF04704,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 34 85255585 85255585 G C 1 0 0 0 0 1 0 0 0 18691 1348 47 4 4 ZNF711 23 85255585 Missense_Mutation SNP G C3L-02365_T 209108 85255585 70785310 358 9330 H2BFWT 0 . GRCh38 X 104013227 104013227 + Missense_Mutation SNP A A T novel C3L-02365_T C3L-02365_N A A c.434T>A p.Leu145Gln p.L145Q ENST00000217926 1/3 151 93 58 169 169 0 strelka-varscan-mutect H2BFWT,missense_variant,p.Leu145Gln,ENST00000217926,NM_001002916.4;H2BFWT,missense_variant,p.Leu145Gln,ENST00000611083,; T ENST00000217926 Transcript missense_variant 461/894 434/528 145/175 L/Q cTg/cAg 1 -1 H2BFWT HGNC HGNC:27252 protein_coding YES CCDS35362.1 ENSP00000354723 Q7Z2G1 UPI000019B16C NM_001002916.4 deleterious(0) 1/3 hmmpanther:PTHR23428,hmmpanther:PTHR23428:SF27,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 104013227 104013227 A T 1 0 0 0 0 1 0 0 0 6814 188 7 4 4 H2BFWT 23 104013227 Missense_Mutation SNP A C3L-02365_T 18757642 104013227 52027668 359 9331 PAK3 0 . GRCh38 X 111146567 111146567 + Splice_Site SNP T T A novel C3L-02365_T C3L-02365_N T T c.384+2T>A p.X128_splice ENST00000360648 94 67 27 133 133 0 strelka-varscan-mutect PAK3,splice_donor_variant,,ENST00000372010,;PAK3,splice_donor_variant,,ENST00000360648,NM_001128168.1;PAK3,splice_donor_variant,,ENST00000262836,NM_001128173.1;PAK3,splice_donor_variant,,ENST00000518291,;PAK3,splice_donor_variant,,ENST00000429193,;PAK3,intron_variant,,ENST00000372007,NM_001324327.1,NM_001324326.1,NM_001324331.1,NM_001324333.1,NM_001324332.1,NM_001324334.1,NM_001324328.1,NM_001324330.1,NM_001324325.1,NM_002578.3;PAK3,intron_variant,,ENST00000519681,;PAK3,intron_variant,,ENST00000446737,NM_001128166.1;PAK3,intron_variant,,ENST00000425146,NM_001128167.1;PAK3,intron_variant,,ENST00000417227,NM_001128172.1;PAK3,intron_variant,,ENST00000620137,;PAK3,intron_variant,,ENST00000487802,; A ENST00000360648 Transcript splice_donor_variant -/2241 384/1743 128/580 1 1 PAK3 HGNC HGNC:8592 protein_coding YES CCDS48151.1 ENSP00000353864 O75914 UPI0000D61DBC NM_001128168.1 4/15 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 34 111146567 111146567 T A 1 0 0 0 0 0 0 1 0 11482 1710 59 4 4 PAK3 23 111146567 Splice_Site SNP T C3L-02365_T 7133340 111146567 44894328 360 9332 PAK3 0 . GRCh38 X 111192507 111192507 + Missense_Mutation SNP T T A novel C3L-02365_T C3L-02365_N T T c.989T>A p.Val330Glu p.V330E ENST00000360648 11/16 238 211 27 355 355 0 strelka-varscan-mutect PAK3,missense_variant,p.Val294Glu,ENST00000372007,NM_001324327.1,NM_001324326.1,NM_001324331.1,NM_001324333.1,NM_001324332.1,NM_001324334.1,NM_001324328.1,NM_001324330.1,NM_001324325.1,NM_002578.3;PAK3,missense_variant,p.Val315Glu,ENST00000519681,;PAK3,missense_variant,p.Val309Glu,ENST00000372010,;PAK3,missense_variant,p.Val294Glu,ENST00000446737,NM_001128166.1;PAK3,missense_variant,p.Val294Glu,ENST00000425146,NM_001128167.1;PAK3,missense_variant,p.Val330Glu,ENST00000360648,NM_001128168.1;PAK3,missense_variant,p.Val315Glu,ENST00000417227,NM_001128172.1;PAK3,missense_variant,p.Val309Glu,ENST00000262836,NM_001128173.1;PAK3,missense_variant,p.Val293Glu,ENST00000620137,;PAK3,missense_variant,p.Val330Glu,ENST00000518291,; A ENST00000360648 Transcript missense_variant,splice_region_variant 1016/2241 989/1743 330/580 V/E gTg/gAg 1 1 PAK3 HGNC HGNC:8592 protein_coding YES CCDS48151.1 ENSP00000353864 O75914 UPI0000D61DBC NM_001128168.1 deleterious(0) 11/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF250,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1206499470 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 111192507 111192507 T A 1 0 0 0 0 1 0 0 0 11482 1710 59 4 4 PAK3 23 111192507 Missense_Mutation SNP T C3L-02365_T 45940 111192507 44848388 361 9333 GLUD2 0 . GRCh38 X 121048417 121048417 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.733G>A p.Gly245Arg p.G245R ENST00000328078 1/1 447 272 175 472 472 0 strelka-varscan-mutect GLUD2,missense_variant,p.Gly245Arg,ENST00000328078,NM_012084.3; A ENST00000328078 Transcript missense_variant 830/2493 733/1677 245/558 G/R Ggg/Agg 1 1 GLUD2 HGNC HGNC:4336 protein_coding YES CCDS14603.1 ENSP00000327589 P49448 A0A140VK14 UPI0000129301 NM_012084.3 deleterious(0.01) 1/1 Gene3D:3.40.192.10,hmmpanther:PTHR11606,hmmpanther:PTHR11606:SF15,Superfamily_domains:SSF53223 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 121048417 121048417 G A 1 0 0 0 0 1 0 0 0 6354 1000 35 3 3 GLUD2 23 121048417 Missense_Mutation SNP G C3L-02365_T 9855910 121048417 34992478 362 9334 IGSF1 0 . GRCh38 X 131273859 131273859 + Silent SNP G G T novel C3L-02365_T C3L-02365_N G G c.3963C>A p.= p.T1321T ENST00000370903 20/20 130 81 49 189 189 0 strelka-varscan-mutect IGSF1,synonymous_variant,p.=,ENST00000370904,;IGSF1,synonymous_variant,p.=,ENST00000370903,NM_001170961.1;IGSF1,synonymous_variant,p.=,ENST00000370910,NM_001170962.1;IGSF1,synonymous_variant,p.=,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000467244,; T ENST00000370903 Transcript synonymous_variant 4246/4594 3963/4026 1321/1341 T acC/acA 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 20/20 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF102 LOW 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 34 131273859 131273859 G T 1 0 0 0 0 0 0 0 1 7503 1219 43 2 2 IGSF1 23 131273859 Silent SNP G C3L-02365_T 10225442 131273859 24767036 363 9335 MBNL3 0 . GRCh38 X 132386730 132386730 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.853C>T p.Pro285Ser p.P285S ENST00000370853 5/8 234 201 33 285 285 0 strelka-varscan-mutect MBNL3,missense_variant,p.Pro235Ser,ENST00000538204,NM_001170702.1;MBNL3,missense_variant,p.Pro189Ser,ENST00000394311,NM_001170703.1;MBNL3,missense_variant,p.Pro285Ser,ENST00000370857,;MBNL3,missense_variant,p.Pro285Ser,ENST00000370853,NM_018388.3;MBNL3,missense_variant,p.Pro189Ser,ENST00000370844,NM_001170704.1;MBNL3,missense_variant,p.Pro235Ser,ENST00000370849,NM_001170701.1;MBNL3,missense_variant,p.Pro189Ser,ENST00000421707,;MBNL3,missense_variant,p.Pro189Ser,ENST00000436215,;MBNL3,missense_variant,p.Pro66Ser,ENST00000442191,;MBNL3,intron_variant,,ENST00000370839,NM_133486.2;RAP2C-AS1,intron_variant,,ENST00000441399,;RAP2C-AS1,intron_variant,,ENST00000421483,;MBNL3,non_coding_transcript_exon_variant,,ENST00000465964,;MBNL3,downstream_gene_variant,,ENST00000473364,; A ENST00000370853 Transcript missense_variant 932/2661 853/1065 285/354 P/S Ccc/Tcc 1 -1 MBNL3 HGNC HGNC:20564 protein_coding YES CCDS14633.1 ENSP00000359890 Q9NUK0 UPI000012ED47 NM_018388.3 deleterious(0.03) 5/8 hmmpanther:PTHR12675,hmmpanther:PTHR12675:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 132386730 132386730 G A 1 0 0 0 0 1 0 0 0 9287 1174 41 3 3 MBNL3 23 132386730 Missense_Mutation SNP G C3L-02365_T 1112871 132386730 23654165 364 9336 CCDC160 0 . GRCh38 X 134244920 134244920 + Missense_Mutation SNP C C G novel C3L-02365_T C3L-02365_N C C c.120C>G p.Ser40Arg p.S40R ENST00000517294 3/3 197 132 65 286 286 0 strelka-varscan-mutect CCDC160,missense_variant,p.Ser40Arg,ENST00000517294,;CCDC160,missense_variant,p.Ser40Arg,ENST00000370809,NM_001101357.1; G ENST00000517294 Transcript missense_variant 503/1790 120/978 40/325 S/R agC/agG 1 1 CCDC160 HGNC HGNC:37286 protein_coding YES CCDS48171.1 ENSP00000427951 A6NGH7 UPI00001993FD tolerated(0.2) 3/3 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 34 134244920 134244920 C G 1 0 0 0 0 1 0 0 0 2480 709 25 4 4 CCDC160 23 134244920 Missense_Mutation SNP C C3L-02365_T 1858190 134244920 21795975 365 9337 VGLL1 0 . GRCh38 X 136548786 136548786 + Missense_Mutation SNP G G T novel C3L-02365_T C3L-02365_N G G c.412G>T p.Gly138Cys p.G138C ENST00000370634 3/5 309 180 129 344 344 0 strelka-varscan-mutect VGLL1,missense_variant,p.Gly138Cys,ENST00000370634,NM_016267.3;VGLL1,missense_variant,p.Gly103Cys,ENST00000440515,;VGLL1,intron_variant,,ENST00000456412,;MIR934,upstream_gene_variant,,ENST00000401241,;VGLL1,upstream_gene_variant,,ENST00000470358,; T ENST00000370634 Transcript missense_variant 582/1215 412/777 138/258 G/C Ggc/Tgc 1 1 VGLL1 HGNC HGNC:20985 protein_coding YES CCDS14658.1 ENSP00000359668 Q99990 UPI0000071D9A NM_016267.3 deleterious(0.01) 3/5 hmmpanther:PTHR15950,hmmpanther:PTHR15950:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 34 136548786 136548786 G T 1 0 0 0 0 1 0 0 0 17704 1232 43 2 2 VGLL1 23 136548786 Missense_Mutation SNP G C3L-02365_T 2303866 136548786 19492109 366 9338 AFF2 0 . GRCh38 X 148956566 148956566 + Missense_Mutation SNP G G A novel C3L-02365_T C3L-02365_N G G c.2521G>A p.Val841Ile p.V841I ENST00000370460 11/21 145 91 54 173 173 0 strelka-varscan-mutect AFF2,missense_variant,p.Val841Ile,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Val482Ile,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Val808Ile,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Val806Ile,ENST00000370457,NM_001169124.1,NM_001169125.1; A ENST00000370460 Transcript missense_variant 3000/13746 2521/3936 841/1311 V/I Gtc/Atc 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 tolerated(0.19) 11/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 34 148956566 148956566 G A 1 0 0 0 0 1 0 0 0 434 1377 48 3 3 AFF2 23 148956566 Missense_Mutation SNP G C3L-02365_T 12407780 148956566 7084329 367 9339 PCNX2 0 . GRCh38 1 233208583 233208583 + Missense_Mutation SNP T T C novel C3L-02508_T C3L-02508_N T T c.2798A>G p.Tyr933Cys p.Y933C ENST00000258229 13/34 378 358 20 215 215 0 strelka-varscan-mutect PCNX2,missense_variant,p.Tyr933Cys,ENST00000258229,NM_014801.3;PCNX2,missense_variant,p.Tyr66Cys,ENST00000430153,;PCNX2,missense_variant,p.Tyr66Cys,ENST00000488780,;PCNX2,missense_variant,p.Tyr102Cys,ENST00000518351,;PCNX2,missense_variant,p.Thr41Ala,ENST00000517808,;PCNX2,3_prime_UTR_variant,,ENST00000475463,;PCNX2,non_coding_transcript_exon_variant,,ENST00000324142,;PCNX2,downstream_gene_variant,,ENST00000519530,; C ENST00000258229 Transcript missense_variant 3033/7518 2798/6414 933/2137 Y/C tAc/tGc 1 -1 PCNX2 HGNC HGNC:8736 protein_coding YES CCDS44335.1 ENSP00000258229 A6NKB5 UPI0000F58F23 NM_014801.3 deleterious(0.03) 13/34 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 35 233208583 233208583 T C 1 0 0 0 0 1 0 0 0 11680 1638 57 5 5 PCNX2 1 233208583 Missense_Mutation SNP T C3L-02508_T 233208583 15747839 1 9340 TRIM54 0 . GRCh38 2 27306262 27306262 + Frame_Shift_Del DEL T T - novel C3L-02508_T C3L-02508_N T T c.1042delT p.Tyr348MetfsTer9 p.Y348Mfs*9 ENST00000296098 8/10 405 376 29 269 269 0 sindel-varindel-pindel TRIM54,frameshift_variant,p.Tyr348MetfsTer9,ENST00000296098,NM_032546.3;TRIM54,frameshift_variant,p.Tyr306MetfsTer9,ENST00000380075,NM_187841.2;MPV17,downstream_gene_variant,,ENST00000357186,;MPV17,downstream_gene_variant,,ENST00000380044,NM_002437.4;MPV17,downstream_gene_variant,,ENST00000233545,;MPV17,downstream_gene_variant,,ENST00000402310,;MPV17,downstream_gene_variant,,ENST00000405983,;MPV17,downstream_gene_variant,,ENST00000402722,;UCN,downstream_gene_variant,,ENST00000296099,NM_003353.2;MPV17,downstream_gene_variant,,ENST00000405076,;MPV17,downstream_gene_variant,,ENST00000430991,;MPV17,downstream_gene_variant,,ENST00000620797,;MPV17,downstream_gene_variant,,ENST00000616707,;MPV17,downstream_gene_variant,,ENST00000426513,;MPV17,downstream_gene_variant,,ENST00000621183,;TRIM54,downstream_gene_variant,,ENST00000485306,;MPV17,downstream_gene_variant,,ENST00000415514,;TRIM54,downstream_gene_variant,,ENST00000488321,; - ENST00000296098 Transcript frameshift_variant 1312/2027 1042/1203 348/400 Y/X Tat/at 1 1 TRIM54 HGNC HGNC:16008 protein_coding YES CCDS1745.2 ENSP00000296098 Q9BYV2 UPI000020814F NM_032546.3 8/10 PROSITE_profiles:PS51262,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF358 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 35 27306262 27306262 T - 1 0 1 0 1 0 0 0 0 17021 1522 53 0 0 TRIM54 2 27306262 Frame_Shift_Del DEL T C3L-02508_T 27306262 214887267 2 9341 STK31 0 . GRCh38 7 23769755 23769755 + Missense_Mutation SNP T T C novel C3L-02508_T C3L-02508_N T T c.1712T>C p.Val571Ala p.V571A ENST00000355870 13/24 104 95 9 80 80 0 strelka-varscan-mutect STK31,missense_variant,p.Val548Ala,ENST00000354639,NM_032944.3,NM_001260504.1;STK31,missense_variant,p.Val571Ala,ENST00000355870,NM_031414.4;STK31,missense_variant,p.Val571Ala,ENST00000433467,NM_001260505.1;STK31,splice_region_variant,,ENST00000405627,;STK31,splice_region_variant,,ENST00000478321,;STK31,splice_region_variant,,ENST00000476399,; C ENST00000355870 Transcript missense_variant,splice_region_variant 1831/3326 1712/3060 571/1019 V/A gTt/gCt 1 1 STK31 HGNC HGNC:11407 protein_coding YES CCDS5386.1 ENSP00000348132 Q9BXU1 UPI0000167B73 NM_031414.4 tolerated(0.5) 13/24 hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF3 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.41115 1 1 1 1 0 C 3 2 35 23769755 23769755 T C 1 0 0 0 0 1 0 0 0 15673 1739 60 5 5 STK31 7 23769755 Missense_Mutation SNP T C3L-02508_T 23769755 135576218 3 9342 VWC2 0 . GRCh38 7 49775772 49775772 + Missense_Mutation SNP C C A C3L-02508_T C3L-02508_N C C c.337C>A p.Pro113Thr p.P113T ENST00000340652 2/4 118 108 10 105 105 0 strelka-varscan-mutect VWC2,missense_variant,p.Pro113Thr,ENST00000340652,NM_198570.3; A ENST00000340652 Transcript missense_variant 893/11299 337/978 113/325 P/T Ccc/Acc COSM5561421 1 1 VWC2 HGNC HGNC:30200 protein_coding YES CCDS5508.1 ENSP00000341819 Q2TAL6 UPI00002373A5 NM_198570.3 deleterious_low_confidence(0.04) 2/4 1 MODERATE 1 SNV 1 1 1 PASS . . 0 201 9 0 0 0 0 0 -19.29307 0.9999794 1 1 1 0 A 3 1 35 49775772 49775772 C A 1 0 0 0 0 1 0 0 0 17802 739 26 2 2 VWC2 7 49775772 Missense_Mutation SNP C C3L-02508_T 26006017 49775772 109570201 4 9343 ACVR1B 0 . GRCh38 12 51985338 51985338 + Missense_Mutation SNP G G T novel C3L-02508_T C3L-02508_N G G c.1249G>T p.Gly417Trp p.G417W ENST00000541224 7/10 118 110 8 80 80 0 strelka-varscan-mutect ACVR1B,missense_variant,p.Gly376Trp,ENST00000257963,NM_004302.4;ACVR1B,missense_variant,p.Gly324Trp,ENST00000542485,NM_020327.3;ACVR1B,missense_variant,p.Gly417Trp,ENST00000541224,NM_020328.3;ACVR1B,missense_variant,p.Gly376Trp,ENST00000426655,;ACVR1B,missense_variant,p.Gly376Trp,ENST00000415850,;RNU6-574P,upstream_gene_variant,,ENST00000384265,;ACVR1B,non_coding_transcript_exon_variant,,ENST00000563121,; T ENST00000541224 Transcript missense_variant 1292/1791 1249/1641 417/546 G/W Ggg/Tgg 1 1 ACVR1B HGNC HGNC:172 protein_coding YES CCDS44894.2 ENSP00000442656 P36896 UPI0001915052 NM_020328.3 deleterious(0) 7/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF22,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -15.53457 0.9999976 1 1 1 0 T 3 4 35 51985338 51985338 G T 1 0 0 0 0 1 0 0 0 265 1232 43 2 2 ACVR1B 12 51985338 Missense_Mutation SNP G C3L-02508_T 51985338 81289971 5 9344 LRP1 0 . GRCh38 12 57138500 57138500 + Nonsense_Mutation SNP C C T novel C3L-02508_T C3L-02508_N C C c.109C>T p.Gln37Ter p.Q37* ENST00000243077 2/89 281 265 16 173 173 0 strelka-mutect LRP1,stop_gained,p.Gln37Ter,ENST00000243077,NM_002332.2;LRP1,stop_gained,p.Gln37Ter,ENST00000554174,;LRP1,stop_gained,p.Gln37Ter,ENST00000338962,;LRP1,stop_gained,p.Gln37Ter,ENST00000553277,; T ENST00000243077 Transcript stop_gained 575/14897 109/13635 37/4544 Q/* Caa/Taa 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 2/89 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_profiles:PS50068,SMART_domains:SM00192,Superfamily_domains:SSF57424 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 35 57138500 57138500 C T 1 0 0 0 0 0 1 0 0 8846 827 29 3 3 LRP1 12 57138500 Nonsense_Mutation SNP C C3L-02508_T 5153162 57138500 76136809 6 9345 MKL2 0 . GRCh38 16 14234155 14234155 + Missense_Mutation SNP G G T novel C3L-02508_T C3L-02508_N G G c.703G>T p.Val235Leu p.V235L ENST00000571589 9/17 161 148 13 128 128 0 strelka-varscan-mutect MKL2,missense_variant,p.Val235Leu,ENST00000571589,NM_001308142.1;MKL2,missense_variant,p.Val235Leu,ENST00000318282,;MKL2,missense_variant,p.Val235Leu,ENST00000574045,NM_014048.3;MKL2,missense_variant,p.Val224Leu,ENST00000572567,;MKL2,missense_variant,p.Val184Leu,ENST00000573051,; T ENST00000571589 Transcript missense_variant 875/8799 703/3300 235/1099 V/L Gtg/Ttg 1 1 MKL2 HGNC HGNC:29819 protein_coding YES CCDS76823.1 ENSP00000459626 Q9ULH7 UPI00001FEE5A NM_001308142.1 tolerated(0.44) 9/17 hmmpanther:PTHR22793:SF5,hmmpanther:PTHR22793 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 35 14234155 14234155 G T 1 0 0 0 0 1 0 0 0 9569 1029 36 2 2 MKL2 16 14234155 Missense_Mutation SNP G C3L-02508_T 14234155 76104190 7 9346 ATP8B3 0 . GRCh38 19 1801972 1801972 + Missense_Mutation SNP T T C novel C3L-02508_T C3L-02508_N T T c.1136A>G p.Asn379Ser p.N379S ENST00000310127 12/29 239 227 12 143 143 0 strelka-varscan-mutect ATP8B3,missense_variant,p.Asn379Ser,ENST00000310127,NM_138813.3;ATP8B3,missense_variant,p.Asn332Ser,ENST00000525591,NM_001178002.2;ATP8B3,missense_variant,p.Asn326Ser,ENST00000526092,;ATP8B3,downstream_gene_variant,,ENST00000533993,;ATP8B3,3_prime_UTR_variant,,ENST00000531925,;ATP8B3,non_coding_transcript_exon_variant,,ENST00000533107,; C ENST00000310127 Transcript missense_variant 1375/5095 1136/3903 379/1300 N/S aAc/aGc 1 -1 ATP8B3 HGNC HGNC:13535 protein_coding YES CCDS45901.1 ENSP00000311336 O60423 UPI0000074660 NM_138813.3 deleterious(0.02) 12/29 hmmpanther:PTHR24092:SF78,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Pfam_domain:PF00122,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.08836 0.9999993 1 1 1 0 C 3 2 35 1801972 1801972 T C 1 0 0 0 0 1 0 0 0 1349 1725 60 5 5 ATP8B3 19 1801972 Missense_Mutation SNP T C3L-02508_T 1801972 56815644 8 9347 UBIAD1 0 . GRCh38 1 11285679 11285679 + Missense_Mutation SNP A A T novel C3L-02549_T C3L-02549_N A A c.565A>T p.Ile189Phe p.I189F ENST00000376810 2/2 336 280 56 304 304 0 strelka-varscan-mutect UBIAD1,missense_variant,p.Ile189Phe,ENST00000376810,NM_013319.2;UBIAD1,missense_variant,p.Ile55Phe,ENST00000483738,;UBIAD1,intron_variant,,ENST00000376804,;UBIAD1,missense_variant,p.Ile70Phe,ENST00000486588,; T ENST00000376810 Transcript missense_variant 891/3646 565/1017 189/338 I/F Atc/Ttc 1 1 UBIAD1 HGNC HGNC:30791 protein_coding YES CCDS129.1 ENSP00000366006 Q9Y5Z9 UPI0000073E35 NM_013319.2 deleterious(0.01) 2/2 hmmpanther:PTHR13929:SF0,hmmpanther:PTHR13929,PIRSF_domain:PIRSF005355,Pfam_domain:PF01040 MODERATE 1 SNV 1 1 PASS rs906156643 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 11285679 11285679 A T 1 0 0 0 0 1 0 0 0 17409 217 8 4 4 UBIAD1 1 11285679 Missense_Mutation SNP A C3L-02549_T 11285679 237670743 1 9348 LRRC7 0 . GRCh38 1 69678457 69678457 + Missense_Mutation SNP C C T rs376248362 C3L-02549_T C3L-02549_N C C c.79C>T p.Arg27Trp p.R27W ENST00000370958 2/8 192 168 24 197 197 0 strelka-varscan-mutect LRRC7,missense_variant,p.Arg27Trp,ENST00000370958,;LRRC7,5_prime_UTR_variant,,ENST00000310961,; T ENST00000370958 Transcript missense_variant 269/2375 79/654 27/217 R/W Cgg/Tgg rs376248362 1 1 LRRC7 HGNC HGNC:18531 protein_coding ENSP00000359997 B1AKT2 UPI000018DB0D deleterious_low_confidence(0) 2/8 MODERATE 1 SNV 1 1 PASS rs376248362 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 69678457 69678457 C T 1 0 0 0 0 1 0 0 0 8916 875 31 1 1 LRRC7 1 69678457 Missense_Mutation SNP C C3L-02549_T 58392778 69678457 179277965 2 9349 SH3GLB1 0 . GRCh38 1 86719529 86719529 + Silent SNP T T G rs758611284 C3L-02549_T C3L-02549_N T T c.237T>G p.= p.V79V ENST00000616170 3/10 163 133 30 126 126 0 strelka-varscan-mutect SH3GLB1,synonymous_variant,p.=,ENST00000616170,NM_001206651.1;SH3GLB1,synonymous_variant,p.=,ENST00000370558,NM_016009.4;SH3GLB1,synonymous_variant,p.=,ENST00000482504,NM_001206652.1;SH3GLB1,5_prime_UTR_variant,,ENST00000535010,NM_001206653.1; G ENST00000616170 Transcript synonymous_variant 567/6456 237/1185 79/394 V gtT/gtG rs758611284 1 1 SH3GLB1 HGNC HGNC:10833 protein_coding YES CCDS72819.1 ENSP00000479919 A0A087WW40 UPI0000E05641 NM_001206651.1 3/10 PROSITE_profiles:PS51021,hmmpanther:PTHR10663:SF161,hmmpanther:PTHR10663,Pfam_domain:PF03114,Gene3D:1.20.1270.60,SMART_domains:SM00721,Superfamily_domains:SSF103657 LOW 1 SNV 1 1 PASS rs758611284 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 36 86719529 86719529 T G 1 0 0 0 0 0 0 0 1 14512 1828 64 5 5 SH3GLB1 1 86719529 Silent SNP T C3L-02549_T 17041072 86719529 162236893 3 9350 NBPF10 0 . GRCh38 1 146068153 146068153 + Missense_Mutation SNP C C T novel C3L-02549_T C3L-02549_N C C c.10885G>A p.Glu3629Lys p.E3629K ENST00000583866 88/90 55 46 9 36 36 0 varscan-mutect NBPF10,missense_variant,p.Glu3629Lys,ENST00000583866,NM_001039703.5,NM_001302371.1;NBPF10,missense_variant,p.Glu1073Lys,ENST00000617010,;NBPF10,intron_variant,,ENST00000610925,;NBPF10,intron_variant,,ENST00000622244,;NBPF10,intron_variant,,ENST00000613557,;NBPF10,intron_variant,,ENST00000616399,;NBPF10,intron_variant,,ENST00000613224,; T ENST00000583866 Transcript missense_variant 10920/13042 10885/11388 3629/3795 E/K Gag/Aag 1 -1 NBPF10 HGNC HGNC:31992 protein_coding YES CCDS76206.1 ENSP00000463957 A0A075B762 UPI00051EF319 NM_001039703.5,NM_001302371.1 tolerated(0.65) 88/90 Pfam_domain:PF06758,PROSITE_profiles:PS51316,SMART_domains:SM01148 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 146068153 146068153 C T 1 0 0 0 0 1 0 0 0 10204 835 29 3 3 NBPF10 1 146068153 Missense_Mutation SNP C C3L-02549_T 59348624 146068153 102888269 4 9351 CAPN13 0 . GRCh38 2 30754326 30754326 + Missense_Mutation SNP C C A novel C3L-02549_T C3L-02549_N C C c.905G>T p.Ser302Ile p.S302I ENST00000295055 9/23 106 87 19 97 97 0 strelka-varscan-mutect CAPN13,missense_variant,p.Ser302Ile,ENST00000295055,NM_144575.2;CAPN13,downstream_gene_variant,,ENST00000465960,;CAPN13,missense_variant,p.Ser302Ile,ENST00000458085,;CAPN13,upstream_gene_variant,,ENST00000465450,; A ENST00000295055 Transcript missense_variant 1082/2683 905/2010 302/669 S/I aGc/aTc 1 -1 CAPN13 HGNC HGNC:16663 protein_coding YES CCDS46252.1 ENSP00000295055 Q6MZZ7 UPI00000463E5 NM_144575.2 tolerated(0.09) 9/23 Pfam_domain:PF00648,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF282,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 36 30754326 30754326 C A 1 0 0 0 0 1 0 0 0 2318 797 28 2 2 CAPN13 2 30754326 Missense_Mutation SNP C C3L-02549_T 30754326 211439203 5 9352 NBEAL1 0 . GRCh38 2 203136050 203136050 + Missense_Mutation SNP A A G C3L-02549_T C3L-02549_N A A c.4100A>G p.Asn1367Ser p.N1367S ENST00000449802 27/55 130 108 22 134 134 0 strelka-varscan-mutect NBEAL1,missense_variant,p.Asn1367Ser,ENST00000449802,NM_001114132.1; G ENST00000449802 Transcript missense_variant 4433/10938 4100/8085 1367/2694 N/S aAc/aGc COSM1216712,COSM1216713 1 1 NBEAL1 HGNC HGNC:20681 protein_coding YES CCDS46495.1 ENSP00000399903 Q6ZS30 UPI000194EC27 NM_001114132.1 tolerated(1) 27/55 hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 36 203136050 203136050 A G 1 0 0 0 0 1 0 0 0 10199 43 2 5 5 NBEAL1 2 203136050 Missense_Mutation SNP A C3L-02549_T 172381724 203136050 39057479 6 9353 KIAA0232 0 . GRCh38 4 6861265 6861265 + Missense_Mutation SNP G G T C3L-02549_T C3L-02549_N G G c.883G>T p.Ala295Ser p.A295S ENST00000307659 7/10 268 226 42 229 228 1 strelka-varscan-mutect KIAA0232,missense_variant,p.Ala295Ser,ENST00000307659,NM_014743.2;KIAA0232,missense_variant,p.Ala295Ser,ENST00000425103,NM_001100590.1;KIAA0232,downstream_gene_variant,,ENST00000503069,; T ENST00000307659 Transcript missense_variant 1338/7841 883/4188 295/1395 A/S Gca/Tca COSM71289 1 1 KIAA0232 HGNC HGNC:28992 protein_coding YES CCDS43209.1 ENSP00000303928 Q92628 UPI000013EC3F NM_014743.2 tolerated(0.13) 7/10 Pfam_domain:PF15376,hmmpanther:PTHR17611,hmmpanther:PTHR17611:SF3,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 6861265 6861265 G T 1 0 0 0 0 1 0 0 0 8079 971 34 2 2 KIAA0232 4 6861265 Missense_Mutation SNP G C3L-02549_T 6861265 183353290 7 9354 SLC22A5 0 . GRCh38 5 132388954 132388954 + Missense_Mutation SNP C C A novel C3L-02549_T C3L-02549_N C C c.1057C>A p.His353Asn p.H353N ENST00000435065 7/11 316 275 41 315 315 0 strelka-varscan-mutect SLC22A5,missense_variant,p.His329Asn,ENST00000245407,NM_003060.3;SLC22A5,missense_variant,p.His353Asn,ENST00000435065,NM_001308122.1;SLC22A5,downstream_gene_variant,,ENST00000415928,;SLC22A5,non_coding_transcript_exon_variant,,ENST00000479605,;SLC22A5,missense_variant,p.His16Asn,ENST00000447841,;SLC22A5,missense_variant,p.His112Asn,ENST00000448810,;SLC22A5,3_prime_UTR_variant,,ENST00000437841,;SLC22A5,non_coding_transcript_exon_variant,,ENST00000461013,;SLC22A5,upstream_gene_variant,,ENST00000475308,; A ENST00000435065 Transcript missense_variant 1057/1746 1057/1746 353/581 H/N Cac/Aac 1 1 SLC22A5 HGNC HGNC:10969 protein_coding YES CCDS78058.1 ENSP00000402760 O76082 UPI0000EFD9B4 NM_001308122.1 tolerated(0.27) 7/11 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF283,TIGRFAM_domain:TIGR00898,Pfam_domain:PF00083,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 36 132388954 132388954 C A 1 0 0 0 0 1 0 0 0 14723 594 21 2 2 SLC22A5 5 132388954 Missense_Mutation SNP C C3L-02549_T 132388954 49149305 8 9355 C6orf203 0 . GRCh38 6 107039868 107039874 + Frame_Shift_Del DEL TACTTCC TACTTCC - novel C3L-02549_T C3L-02549_N TACTTCC TACTTCC c.124_130delACTTCCT p.Thr42GlyfsTer27 p.T42Gfs*27 ENST00000625458 3/5 289 258 31 264 264 0 sindel-varindel-pindel C6orf203,frameshift_variant,p.Thr37GlyfsTer27,ENST00000405204,NM_001142468.2;C6orf203,frameshift_variant,p.Thr42GlyfsTer27,ENST00000625458,NM_001142470.2;C6orf203,frameshift_variant,p.Thr37GlyfsTer27,ENST00000311381,NM_016487.4;C6orf203,upstream_gene_variant,,ENST00000489790,; - ENST00000625458 Transcript frameshift_variant 432-438/1146 123-129/738 41-43/245 CTS/X tgTACTTCC/tg 1 1 C6orf203 HGNC HGNC:17971 protein_coding YES CCDS78167.1 ENSP00000485698 A0A0D9SEI0 UPI0000D4EA45 NM_001142470.2 3/5 hmmpanther:PTHR13633,hmmpanther:PTHR13633:SF3 HIGH 1 deletion 3 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 36 107039868 107039868 TACTTCC - 1 0 1 0 1 0 0 0 0 2123 1644 57 0 0 C6orf203 6 107039868 Frame_Shift_Del DEL TACTTCC C3L-02549_T 107039868 63766111 9 9356 BRAF 0 . GRCh38 7 140754204 140754204 + Missense_Mutation SNP C C T novel C3L-02549_T C3L-02549_N C C c.1724G>A p.Arg575Lys p.R575K ENST00000288602 14/18 386 364 22 309 309 0 strelka-varscan-mutect BRAF,missense_variant,p.Arg183Lys,ENST00000496384,;BRAF,missense_variant,p.Arg575Lys,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Arg3Lys,ENST00000479537,;BRAF,3_prime_UTR_variant,,ENST00000497784,; T ENST00000288602 Transcript missense_variant 1785/2480 1724/2301 575/766 R/K aGa/aAa 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious(0.01) 14/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_patterns:PS00108,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF43,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 140754204 140754204 C T 1 0 0 0 0 1 0 0 0 1665 913 32 3 3 BRAF 7 140754204 Missense_Mutation SNP C C3L-02549_T 140754204 18591769 10 9357 CPSF1 0 . GRCh38 8 144400434 144400434 + Missense_Mutation SNP T T G novel C3L-02549_T C3L-02549_N T T c.746A>C p.Gln249Pro p.Q249P ENST00000616140 8/38 247 231 16 229 229 0 strelka-varscan-mutect CPSF1,missense_variant,p.Gln249Pro,ENST00000616140,NM_013291.2;CPSF1,missense_variant,p.Gln249Pro,ENST00000620219,;CPSF1,upstream_gene_variant,,ENST00000579254,;CPSF1,upstream_gene_variant,,ENST00000618543,;CPSF1,non_coding_transcript_exon_variant,,ENST00000622776,;CPSF1,non_coding_transcript_exon_variant,,ENST00000532560,;CPSF1,intron_variant,,ENST00000531042,;CPSF1,upstream_gene_variant,,ENST00000527827,;CPSF1,upstream_gene_variant,,ENST00000529288,;CPSF1,upstream_gene_variant,,ENST00000533492,;CPSF1,upstream_gene_variant,,ENST00000527916,; G ENST00000616140 Transcript missense_variant 821/4494 746/4332 249/1443 Q/P cAg/cCg 1 -1 CPSF1 HGNC HGNC:2324 protein_coding YES CCDS34966.1 ENSP00000484669 Q10570 UPI00001282EE NM_013291.2 deleterious(0.02) 8/38 Pfam_domain:PF10433,hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 36 144400434 144400434 T G 1 0 0 0 0 1 0 0 0 3620 1580 55 5 5 CPSF1 8 144400434 Missense_Mutation SNP T C3L-02549_T 144400434 738202 11 9358 OR8K5 0 . GRCh38 11 56159993 56159993 + Missense_Mutation SNP T T A novel C3L-02549_T C3L-02549_N T T c.325A>T p.Ile109Phe p.I109F ENST00000313447 1/1 219 190 29 211 211 0 strelka-varscan-mutect OR8K5,missense_variant,p.Ile109Phe,ENST00000313447,NM_001004058.2; A ENST00000313447 Transcript missense_variant 325/924 325/924 109/307 I/F Atc/Ttc 1 -1 OR8K5 HGNC HGNC:15315 protein_coding YES CCDS31521.1 ENSP00000323853 Q8NH50 UPI000004B231 NM_001004058.2 deleterious_low_confidence(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 36 56159993 56159993 T A 1 0 0 0 0 1 0 0 0 11312 1406 49 4 4 OR8K5 11 56159993 Missense_Mutation SNP T C3L-02549_T 56159993 78926629 12 9359 HSPA8 0 . GRCh38 11 123060188 123060188 + Missense_Mutation SNP A A C novel C3L-02549_T C3L-02549_N A A c.492T>G p.Ile164Met p.I164M ENST00000534624 4/9 412 357 55 346 345 1 strelka-varscan-mutect HSPA8,missense_variant,p.Ile164Met,ENST00000534624,NM_006597.5;HSPA8,missense_variant,p.Ile164Met,ENST00000532636,;HSPA8,missense_variant,p.Ile164Met,ENST00000227378,;HSPA8,missense_variant,p.Ile164Met,ENST00000453788,NM_153201.3;HSPA8,missense_variant,p.Ile145Met,ENST00000526110,;HSPA8,missense_variant,p.Ile104Met,ENST00000528292,;HSPA8,missense_variant,p.Ile164Met,ENST00000525624,;HSPA8,missense_variant,p.Ile164Met,ENST00000532182,;HSPA8,missense_variant,p.Ile164Met,ENST00000534567,;HSPA8,missense_variant,p.Ile123Met,ENST00000525463,;HSPA8,missense_variant,p.Ile164Met,ENST00000527387,;HSPA8,5_prime_UTR_variant,,ENST00000534319,;HSPA8,intron_variant,,ENST00000533540,;HSPA8,upstream_gene_variant,,ENST00000524552,;HSPA8,upstream_gene_variant,,ENST00000526686,;HSPA8,downstream_gene_variant,,ENST00000530391,;HSPA8,downstream_gene_variant,,ENST00000524590,;SNORD14C,upstream_gene_variant,,ENST00000365382,;SNORD14D,upstream_gene_variant,,ENST00000384390,;SNORD14E,upstream_gene_variant,,ENST00000364009,;HSPA8,non_coding_transcript_exon_variant,,ENST00000526862,;HSPA8,intron_variant,,ENST00000533238,;HSPA8,non_coding_transcript_exon_variant,,ENST00000532091,;HSPA8,non_coding_transcript_exon_variant,,ENST00000527983,;HSPA8,non_coding_transcript_exon_variant,,ENST00000532780,;HSPA8,non_coding_transcript_exon_variant,,ENST00000532167,;HSPA8,downstream_gene_variant,,ENST00000531063,; C ENST00000534624 Transcript missense_variant 769/2463 492/1941 164/646 I/M atT/atG 1 -1 HSPA8 HGNC HGNC:5241 protein_coding YES CCDS8440.1 ENSP00000432083 P11142 V9HW22 UPI0000000801 NM_006597.5 deleterious_low_confidence(0) 4/9 Gene3D:3.30.420.40,Pfam_domain:PF00012,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF150,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs1436365119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 36 123060188 123060188 A C 1 0 0 0 0 1 0 0 0 7312 126 5 5 5 HSPA8 11 123060188 Missense_Mutation SNP A C3L-02549_T 66900195 123060188 12026434 13 9360 ADAMTS8 0 . GRCh38 11 130405772 130405772 + Missense_Mutation SNP C C T novel C3L-02549_T C3L-02549_N C C c.2456G>A p.Ser819Asn p.S819N ENST00000257359 9/9 440 370 70 391 391 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Ser819Asn,ENST00000257359,NM_007037.4;RP11-121M22.1,downstream_gene_variant,,ENST00000602376,;RP11-121M22.1,downstream_gene_variant,,ENST00000616197,;ADAMTS8,non_coding_transcript_exon_variant,,ENST00000531752,; T ENST00000257359 Transcript missense_variant 3163/4010 2456/2670 819/889 S/N aGc/aAc 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 tolerated(0.41) 9/9 hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 130405772 130405772 C T 1 0 0 0 0 1 0 0 0 316 797 28 3 3 ADAMTS8 11 130405772 Missense_Mutation SNP C C3L-02549_T 7345584 130405772 4680850 14 9361 FGF23 0 . GRCh38 12 4370383 4370383 + Missense_Mutation SNP G G A rs7955866 C3L-02549_T C3L-02549_N G G c.716C>T p.Thr239Met p.T239M ENST00000237837 3/3 136 127 9 80 80 0 strelka-varscan-mutect FGF23,missense_variant,p.Thr239Met,ENST00000237837,NM_020638.2; A ENST00000237837 Transcript missense_variant 862/3018 716/756 239/251 T/M aCg/aTg rs7955866,CM123510 1 -1 FGF23 HGNC HGNC:3680 protein_coding YES CCDS8526.1 ENSP00000237837 Q9GZV9 UPI000003ED58 NM_020638.2 tolerated_low_confidence(0.3) 3/3 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF69 2.15659452039494e+47 MODERATE 1 SNV 1 0,1 1 PASS rs7955866 . 0 129 2 0 0 0 0 78 -5.435857 0 0 1 0 0 A 3 1 36 4370383 4370383 G A 1 0 0 0 0 1 0 0 0 5716 1145 40 1 1 FGF23 12 4370383 Missense_Mutation SNP G C3L-02549_T 4370383 128904926 15 9362 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3L-02549_T C3L-02549_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 385 309 76 326 326 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3L-02549_T 20874967 25245350 108029959 16 9363 SETD1B 0 . GRCh38 12 121809766 121809766 + Missense_Mutation SNP C C G novel C3L-02549_T C3L-02549_N C C c.821C>G p.Pro274Arg p.P274R ENST00000542440 6/18 170 142 28 179 179 0 strelka-varscan-mutect SETD1B,missense_variant,p.Pro274Arg,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Pro274Arg,ENST00000604567,;SETD1B,missense_variant,p.Pro274Arg,ENST00000619791,;SETD1B,missense_variant,p.Pro274Arg,ENST00000267197,; G ENST00000542440 Transcript missense_variant 889/8185 821/5772 274/1923 P/R cCg/cGg 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 deleterious(0) 6/18 MODERATE 1 SNV 5 1 PASS rs1310022642 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 36 121809766 121809766 C G 1 0 0 0 0 1 0 0 0 14408 652 23 4 4 SETD1B 12 121809766 Missense_Mutation SNP C C3L-02549_T 96564416 121809766 11465543 17 9364 ITGA11 0 . GRCh38 15 68321424 68321424 + Missense_Mutation SNP G G T rs145852498 C3L-02549_T C3L-02549_N G G c.2402C>A p.Thr801Lys p.T801K ENST00000315757 19/30 65 46 19 50 50 0 strelka-varscan-mutect ITGA11,missense_variant,p.Thr801Lys,ENST00000423218,;ITGA11,missense_variant,p.Thr801Lys,ENST00000315757,NM_001004439.1; T ENST00000315757 Transcript missense_variant 2498/3955 2402/3567 801/1188 T/K aCg/aAg rs145852498 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 tolerated(0.26) 19/30 Gene3D:2.60.40.1510,Pfam_domain:PF08441 MODERATE 1 SNV 1 1 PASS rs145852498 . 0 195 14 0 0 0 0 0 -20 0.9999206 1 1 1 0 T 3 4 36 68321424 68321424 G T 1 0 0 0 0 1 0 0 0 7781 1145 40 1 1 ITGA11 15 68321424 Missense_Mutation SNP G C3L-02549_T 68321424 33669765 18 9365 C16orf46 0 . GRCh38 16 81061419 81061419 + Silent SNP C C T rs76579573 C3L-02549_T C3L-02549_N C C c.930G>A p.= p.A310A ENST00000299578 4/4 175 156 19 151 151 0 strelka-varscan-mutect C16orf46,synonymous_variant,p.=,ENST00000378611,NM_001100873.1;C16orf46,synonymous_variant,p.=,ENST00000299578,NM_152337.2;C16orf46,downstream_gene_variant,,ENST00000565253,;RP11-303E16.5,downstream_gene_variant,,ENST00000562450,;RP11-303E16.8,intron_variant,,ENST00000564536,;C16orf46,downstream_gene_variant,,ENST00000444657,; T ENST00000299578 Transcript synonymous_variant 1166/1605 930/1188 310/395 A gcG/gcA rs76579573,COSM1141023,COSM1380041,COSM1380042,COSM559295 1 -1 C16orf46 HGNC HGNC:26525 protein_coding YES CCDS10932.1 ENSP00000299578 Q6P387 UPI000013E5BE NM_152337.2 4/4 hmmpanther:PTHR36869:SF1,hmmpanther:PTHR36869,Pfam_domain:PF15032 0,1,1,1,1 LOW 1 SNV 2 0,1,1,1,1 1 PASS rs76579573 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 36 81061419 81061419 C T 1 0 0 0 0 0 0 0 1 1856 523 19 1 1 C16orf46 16 81061419 Silent SNP C C3L-02549_T 81061419 9276926 19 9366 GUCY2D 0 . GRCh38 17 8012492 8012492 + Missense_Mutation SNP C C A rs746361123 C3L-02549_T C3L-02549_N C C c.1999C>A p.Leu667Met p.L667M ENST00000254854 10/20 377 322 55 323 323 0 strelka-varscan-mutect GUCY2D,missense_variant,p.Leu667Met,ENST00000254854,NM_000180.3;RP11-1099M24.9,downstream_gene_variant,,ENST00000623126,;GUCY2D,upstream_gene_variant,,ENST00000574510,; A ENST00000254854 Transcript missense_variant 2149/3698 1999/3312 667/1103 L/M Ctg/Atg rs746361123 1 1 GUCY2D HGNC HGNC:4689 protein_coding YES CCDS11127.1 ENSP00000254854 Q02846 UPI0000128C1C NM_000180.3 deleterious(0) 10/20 PROSITE_profiles:PS50011,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF228,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs746361123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 36 8012492 8012492 C A 1 0 0 0 0 1 0 0 0 6779 796 28 2 2 GUCY2D 17 8012492 Missense_Mutation SNP C C3L-02549_T 8012492 75244949 20 9367 STK11 0 . GRCh38 19 1221996 1221996 + Missense_Mutation SNP C C T rs786201090 C3L-02549_T C3L-02549_N C C c.910C>T p.Arg304Trp p.R304W ENST00000326873 7/10 234 203 31 287 287 0 strelka-varscan-mutect STK11,missense_variant,p.Arg304Trp,ENST00000586243,;STK11,missense_variant,p.Arg304Trp,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript missense_variant 1360/2611 910/1302 304/433 R/W Cgg/Tgg rs786201090,CD044169,CM981870,KinMutBase_STK11_DNA:g.16083C>T,COSM29468,COSM48789 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 7/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 pathogenic 0,0,0,0,1,1 MODERATE 1 SNV 1 1,1,1,0,1,1 1 PASS rs786201090 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 1221996 1221996 C T 1 0 0 0 0 1 0 0 0 15664 643 23 1 1 STK11 19 1221996 Missense_Mutation SNP C C3L-02549_T 1221996 57395620 21 9368 SMARCA4 0 . GRCh38 19 11021757 11021768 + In_Frame_Del DEL TCACCGCATGAA TCACCGCATGAA - novel C3L-02549_T C3L-02549_N TCACCGCATGAA TCACCGCATGAA c.2649_2660delTCACCGCATGAA p.His884_Lys887del p.H884_K887del ENST00000429416 20/36 238 192 46 248 248 0 sindel-varindel-pindel SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000429416,NM_001128844.1;SMARCA4,inframe_deletion,p.His948_Lys951del,ENST00000413806,;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000450717,NM_001128849.1;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000344626,NM_003072.3;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000590574,NM_001128847.1;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000589677,NM_001128846.1;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000541122,NM_001128845.1;SMARCA4,inframe_deletion,p.His884_Lys887del,ENST00000444061,NM_001128848.1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988,; - ENST00000429416 Transcript inframe_deletion 2930-2941/5691 2649-2660/4944 883-887/1647 GHRMK/G ggTCACCGCATGAAg/ggg 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 20/36 PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 36 11021757 11021757 TCACCGCATGAA - 1 0 1 0 1 0 0 0 0 15063 1654 58 0 0 SMARCA4 19 11021757 In_Frame_Del DEL TCACCGCATGAA C3L-02549_T 9799761 11021757 47595859 22 9369 TNNI3 0 . GRCh38 19 55156657 55156657 + Silent SNP G G T novel C3L-02549_T C3L-02549_N G G c.21C>A p.= p.I7I ENST00000588882 1/5 344 282 62 234 233 1 strelka-varscan-mutect TNNI3,synonymous_variant,p.=,ENST00000588882,;TNNI3,synonymous_variant,p.=,ENST00000586858,;TNNI3,intron_variant,,ENST00000344887,NM_000363.4;DNAAF3,downstream_gene_variant,,ENST00000455045,NM_001256716.1;DNAAF3,downstream_gene_variant,,ENST00000527223,NM_001256714.1;DNAAF3,downstream_gene_variant,,ENST00000391720,NM_178837.4;DNAAF3,downstream_gene_variant,,ENST00000524407,NM_001256715.1;DNAAF3,downstream_gene_variant,,ENST00000588076,;CTD-2587H24.5,upstream_gene_variant,,ENST00000591665,;TNNI3,intron_variant,,ENST00000590463,;TNNI3,intron_variant,,ENST00000586669,;DNAAF3,downstream_gene_variant,,ENST00000587789,;DNAAF3,downstream_gene_variant,,ENST00000527166,;DNAAF3,downstream_gene_variant,,ENST00000527292,;TNNI3,intron_variant,,ENST00000587176,;CTD-2587H24.4,intron_variant,,ENST00000587871,;DNAAF3,downstream_gene_variant,,ENST00000528412,;DNAAF3,downstream_gene_variant,,ENST00000533527,;TNNI3,upstream_gene_variant,,ENST00000585806,;DNAAF3,downstream_gene_variant,,ENST00000526959,;TNNI3,downstream_gene_variant,,ENST00000586446,;TNNI3,upstream_gene_variant,,ENST00000589864,; T ENST00000588882 Transcript synonymous_variant 69/669 21/558 7/185 I atC/atA 1 -1 TNNI3 HGNC HGNC:11947 protein_coding ENSP00000466729 K7EN02 UPI0000F06635 1/5 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 36 55156657 55156657 G T 1 0 0 0 0 0 0 0 1 16801 932 33 2 2 TNNI3 19 55156657 Silent SNP G C3L-02549_T 44134900 55156657 3460959 23 9370 ZNF470 0 . GRCh38 19 56574395 56574395 + Missense_Mutation SNP G G T novel C3L-02549_T C3L-02549_N G G c.62G>T p.Gly21Val p.G21V ENST00000330619 4/6 171 141 30 135 135 0 strelka-varscan-mutect ZNF470,missense_variant,p.Gly21Val,ENST00000330619,NM_001001668.3;ZNF470,missense_variant,p.Gly21Val,ENST00000391709,;ZNF470,missense_variant,p.Gly21Val,ENST00000601902,;ZNF470,upstream_gene_variant,,ENST00000594953,;ZNF470,intron_variant,,ENST00000601059,; T ENST00000330619 Transcript missense_variant,splice_region_variant 748/7151 62/2154 21/717 G/V gGt/gTt 1 1 ZNF470 HGNC HGNC:22220 protein_coding YES CCDS33122.1 ENSP00000333223 Q6ECI4 UPI0000D61826 NM_001001668.3 tolerated(0.15) 4/6 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF282,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 36 56574395 56574395 G T 1 0 0 0 0 1 0 0 0 18501 1275 44 2 2 ZNF470 19 56574395 Missense_Mutation SNP G C3L-02549_T 1417738 56574395 2043221 24 9371 PROCR 0 . GRCh38 20 35176431 35176431 + Missense_Mutation SNP G G A novel C3L-02549_T C3L-02549_N G G c.586G>A p.Ala196Thr p.A196T ENST00000216968 3/4 128 99 29 146 146 0 strelka-varscan-mutect PROCR,missense_variant,p.Ala196Thr,ENST00000216968,NM_006404.4;PROCR,missense_variant,p.Ala163Thr,ENST00000635377,;PROCR,missense_variant,p.Ala27Thr,ENST00000634509,;RP11-42O4.2,upstream_gene_variant,,ENST00000615962,; A ENST00000216968 Transcript missense_variant 668/1348 586/717 196/238 A/T Gcg/Acg 1 1 PROCR HGNC HGNC:9452 protein_coding YES CCDS13248.1 ENSP00000216968 Q9UNN8 UPI000012A08E NM_006404.4 tolerated(0.76) 3/4 hmmpanther:PTHR15349,Gene3D:3.30.500.10 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 36 35176431 35176431 G A 1 0 0 0 0 1 0 0 0 12681 1087 38 1 1 PROCR 20 35176431 Missense_Mutation SNP G C3L-02549_T 35176431 29267736 25 9372 SLC6A14 0 . GRCh38 X 116440973 116440973 + Frame_Shift_Del DEL C C - novel C3L-02549_T C3L-02549_N C C c.222delC p.Leu75Ter p.L75* ENST00000598581 3/14 74 51 23 73 73 0 sindel-varindel-pindel SLC6A14,frameshift_variant,p.Leu75Ter,ENST00000598581,NM_007231.4; - ENST00000598581 Transcript frameshift_variant 310/4520 222/1929 74/642 F/X ttC/tt 1 1 SLC6A14 HGNC HGNC:11047 protein_coding YES CCDS14570.1 ENSP00000470801 Q9UN76 UPI0000072E3C NM_007231.4 3/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF160,PROSITE_patterns:PS00610,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176 HIGH 1 deletion 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 36 116440973 116440973 C - 1 0 1 0 1 0 0 0 0 14960 912 32 0 0 SLC6A14 23 116440973 Frame_Shift_Del DEL C C3L-02549_T 116440973 39599922 26 9373 CNR2 0 . GRCh38 1 23875267 23875267 + Missense_Mutation SNP G G T novel C3N-00167_T C3N-00167_N G G c.351C>A p.Phe117Leu p.F117L ENST00000374472 2/2 106 79 27 147 147 0 strelka-varscan-mutect CNR2,missense_variant,p.Phe117Leu,ENST00000374472,NM_001841.2; T ENST00000374472 Transcript missense_variant 513/5254 351/1083 117/360 F/L ttC/ttA 1 -1 CNR2 HGNC HGNC:2160 protein_coding YES CCDS245.1 ENSP00000363596 P34972 A0A024RAH7 UPI000000DCA3 NM_001841.2 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 23875267 23875267 G T 1 0 0 0 0 1 0 0 0 3414 1281 45 2 2 CNR2 1 23875267 Missense_Mutation SNP G C3N-00167_T 23875267 225081155 1 9374 PSMB2 0 . GRCh38 1 35609259 35609259 + Silent SNP T T C rs768767264 C3N-00167_T C3N-00167_N T T c.435A>G p.= p.R145R ENST00000373237 4/6 78 67 11 72 72 0 strelka-varscan-mutect PSMB2,synonymous_variant,p.=,ENST00000621781,NM_001199780.1;PSMB2,synonymous_variant,p.=,ENST00000373237,NM_001199779.1,NM_002794.4;PSMB2,non_coding_transcript_exon_variant,,ENST00000630477,; C ENST00000373237 Transcript synonymous_variant 847/2701 435/606 145/201 R cgA/cgG rs768767264 1 -1 PSMB2 HGNC HGNC:9539 protein_coding YES CCDS394.1 ENSP00000362334 P49721 A0A140VJS6 UPI0000111E4C NM_001199779.1,NM_002794.4 4/6 Gene3D:3.60.20.10,Pfam_domain:PF00227,PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF6,Superfamily_domains:SSF56235 LOW 1 SNV 1 1 PASS rs768767264 . 0 208 2 0 0 0 0 0 -19.99998 1 1 1 1 0 C 2 2 37 35609259 35609259 T C 1 0 0 0 0 0 0 0 1 12828 1422 50 5 5 PSMB2 1 35609259 Silent SNP T C3N-00167_T 11733992 35609259 213347163 2 9375 CAMSAP2 0 . GRCh38 1 200848700 200848700 + Missense_Mutation SNP C C T novel C3N-00167_T C3N-00167_N C C c.1964C>T p.Ser655Phe p.S655F ENST00000236925 12/18 172 142 30 169 169 0 strelka-varscan-mutect CAMSAP2,missense_variant,p.Ser644Phe,ENST00000358823,NM_203459.2;CAMSAP2,missense_variant,p.Ser655Phe,ENST00000236925,NM_001297707.1;CAMSAP2,missense_variant,p.Ser628Phe,ENST00000413307,NM_001297708.1;CAMSAP2,intron_variant,,ENST00000447701,; T ENST00000236925 Transcript missense_variant 2013/7161 1964/4470 655/1489 S/F tCt/tTt 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 deleterious(0.02) 12/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 MODERATE 1 SNV 1 1 PASS rs1274117018 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 200848700 200848700 C T 1 0 0 0 0 1 0 0 0 2304 913 32 3 3 CAMSAP2 1 200848700 Missense_Mutation SNP C C3N-00167_T 165239441 200848700 48107722 3 9376 OBSCN 0 . GRCh38 1 228292744 228292744 + Missense_Mutation SNP G G A rs374049885 C3N-00167_T C3N-00167_N G G c.12112G>A p.Val4038Met p.V4038M ENST00000570156 45/116 432 350 82 385 385 0 strelka-varscan-mutect OBSCN,missense_variant,p.Val4038Met,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Val4038Met,ENST00000366707,;OBSCN,missense_variant,p.Val3609Met,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Val3609Met,ENST00000636875,;OBSCN,missense_variant,p.Val3609Met,ENST00000284548,NM_052843.3;OBSCN,missense_variant,p.Val885Met,ENST00000483539,;RP5-1139B12.4,downstream_gene_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000494839,; A ENST00000570156 Transcript missense_variant 12186/26925 12112/26772 4038/8923 V/M Gtg/Atg rs374049885 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.18) 45/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs374049885 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 228292744 228292744 G A 1 0 0 0 0 1 0 0 0 10889 1145 40 1 1 OBSCN 1 228292744 Missense_Mutation SNP G C3N-00167_T 27444044 228292744 20663678 4 9377 MEIS1 0 . GRCh38 2 66568740 66568740 + Missense_Mutation SNP G G T novel C3N-00167_T C3N-00167_N G G c.1098G>T p.Met366Ile p.M366I ENST00000272369 11/13 247 216 31 234 234 0 strelka-varscan MEIS1,missense_variant,p.Met366Ile,ENST00000488550,;MEIS1,missense_variant,p.Met366Ile,ENST00000272369,NM_002398.2;MEIS1,missense_variant,p.Met364Ile,ENST00000398506,;MEIS1,missense_variant,p.Met301Ile,ENST00000495021,;MEIS1,downstream_gene_variant,,ENST00000560281,;MEIS1,non_coding_transcript_exon_variant,,ENST00000409517,;MEIS1,non_coding_transcript_exon_variant,,ENST00000450027,;MEIS1,non_coding_transcript_exon_variant,,ENST00000542964,;MEIS1,downstream_gene_variant,,ENST00000475239,;MEIS1,downstream_gene_variant,,ENST00000606455,; T ENST00000272369 Transcript missense_variant 1555/4291 1098/1173 366/390 M/I atG/atT 1 1 MEIS1 HGNC HGNC:7000 protein_coding YES CCDS46309.1 ENSP00000272369 O00470 UPI000000DA5A NM_002398.2 deleterious(0.01) 11/13 hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF126 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 66568740 66568740 G T 1 0 0 0 0 1 0 0 0 9411 1348 47 2 2 MEIS1 2 66568740 Missense_Mutation SNP G C3N-00167_T 66568740 175624789 5 9378 AMER3 0 . GRCh38 2 130762473 130762473 + Missense_Mutation SNP C C A novel C3N-00167_T C3N-00167_N C C c.401C>A p.Pro134His p.P134H ENST00000423981 2/2 129 118 11 150 150 0 strelka-varscan AMER3,missense_variant,p.Pro134His,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Pro134His,ENST00000321420,NM_152698.2;AMER3,missense_variant,p.Pro134His,ENST00000458606,;AMER3,missense_variant,p.Pro134His,ENST00000431758,; A ENST00000423981 Transcript missense_variant 511/6172 401/2586 134/861 P/H cCc/cAc 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 deleterious(0) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 130762473 130762473 C A 1 0 0 0 0 1 0 0 0 669 623 22 2 2 AMER3 2 130762473 Missense_Mutation SNP C C3N-00167_T 64193733 130762473 111431056 6 9379 TIGIT 0 . GRCh38 3 114294111 114294111 + Missense_Mutation SNP C C T novel C3N-00167_T C3N-00167_N C C c.50C>T p.Pro17Leu p.P17L ENST00000486257 2/5 104 81 23 116 116 0 strelka-varscan-mutect TIGIT,missense_variant,p.Pro84Leu,ENST00000481065,;TIGIT,missense_variant,p.Pro17Leu,ENST00000486257,;TIGIT,missense_variant,p.Pro17Leu,ENST00000383671,NM_173799.3;TIGIT,intron_variant,,ENST00000461158,;TIGIT,upstream_gene_variant,,ENST00000484319,;TIGIT,non_coding_transcript_exon_variant,,ENST00000485814,; T ENST00000486257 Transcript missense_variant 307/3149 50/735 17/244 P/L cCc/cTc 1 1 TIGIT HGNC HGNC:26838 protein_coding YES CCDS2980.1 ENSP00000419085 Q495A1 UPI000013F7B8 tolerated(0.47) 2/5 PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF49,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS rs897902406 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 114294111 114294111 C T 1 0 0 0 0 1 0 0 0 16340 623 22 3 3 TIGIT 3 114294111 Missense_Mutation SNP C C3N-00167_T 114294111 84001448 7 9380 TET2 0 . GRCh38 4 105234177 105234177 + Missense_Mutation SNP A A G novel C3N-00167_T C3N-00167_N A A c.235A>G p.Thr79Ala p.T79A ENST00000540549 3/11 231 202 29 226 226 0 strelka-varscan-mutect TET2,missense_variant,p.Thr100Ala,ENST00000513237,;TET2,missense_variant,p.Thr79Ala,ENST00000540549,;TET2,missense_variant,p.Thr79Ala,ENST00000380013,NM_001127208.2;TET2,missense_variant,p.Thr79Ala,ENST00000305737,NM_017628.4;TET2,missense_variant,p.Thr79Ala,ENST00000413648,;TET2,missense_variant,p.Thr79Ala,ENST00000514870,;TET2,missense_variant,p.Thr79Ala,ENST00000265149,; G ENST00000540549 Transcript missense_variant 1095/10166 235/6009 79/2002 T/A Aca/Gca 1 1 TET2 HGNC HGNC:25941 protein_coding YES CCDS47120.1 ENSP00000442788 Q6N021 A0A158SIU0 UPI00001D75E4 tolerated(0.06) 3/11 hmmpanther:PTHR23358:SF3,hmmpanther:PTHR23358 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 37 105234177 105234177 A G 1 0 0 0 0 1 0 0 0 16191 391 14 5 5 TET2 4 105234177 Missense_Mutation SNP A C3N-00167_T 105234177 84980378 8 9381 FAT4 0 . GRCh38 4 125316928 125316928 + Missense_Mutation SNP T T A novel C3N-00167_T C3N-00167_N T T c.517T>A p.Ser173Thr p.S173T ENST00000394329 1/17 200 189 11 310 310 0 strelka-varscan-mutect FAT4,missense_variant,p.Ser173Thr,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; A ENST00000394329 Transcript missense_variant 530/16123 517/14946 173/4981 S/T Tcc/Acc 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.67) 1/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 125316928 125316928 T A 1 0 0 0 0 1 0 0 0 5552 1551 54 4 4 FAT4 4 125316928 Missense_Mutation SNP T C3N-00167_T 20082751 125316928 64897627 9 9382 NEIL3 0 . GRCh38 4 177351551 177351551 + Splice_Site SNP T T C novel C3N-00167_T C3N-00167_N T T c.1039+2T>C p.X347_splice ENST00000264596 87 82 5 98 98 0 strelka-varscan-mutect NEIL3,splice_donor_variant,,ENST00000264596,NM_018248.2;RP11-376O6.2,intron_variant,,ENST00000506895,;NEIL3,intron_variant,,ENST00000513321,; C ENST00000264596 Transcript splice_donor_variant -/2408 1039/1818 347/605 1 1 NEIL3 HGNC HGNC:24573 protein_coding YES CCDS3828.1 ENSP00000264596 Q8TAT5 UPI000013D53D NM_018248.2 7/9 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -11.14167 1 1 1 1 0 C 5 2 37 177351551 177351551 T C 1 0 0 0 0 0 0 1 0 10348 1652 57 5 5 NEIL3 4 177351551 Splice_Site SNP T C3N-00167_T 52034623 177351551 12863004 10 9383 PAPD7 0 . GRCh38 5 6746323 6746323 + Missense_Mutation SNP G G C novel C3N-00167_T C3N-00167_N G G c.605G>C p.Arg202Thr p.R202T ENST00000631941 7/13 284 244 40 217 217 0 strelka-varscan-mutect PAPD7,missense_variant,p.Arg452Thr,ENST00000230859,;PAPD7,missense_variant,p.Arg202Thr,ENST00000631941,NM_006999.4,NM_001171805.1;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,non_coding_transcript_exon_variant,,ENST00000511764,;PAPD7,upstream_gene_variant,,ENST00000505457,;PAPD7,upstream_gene_variant,,ENST00000514410,; C ENST00000631941 Transcript missense_variant 793/1902 605/1629 202/542 R/T aGa/aCa 1 1 PAPD7 HGNC HGNC:16705 protein_coding YES CCDS3871.1 ENSP00000488642 Q5XG87 UPI0000071E30 NM_006999.4,NM_001171805.1 deleterious(0) 7/13 Pfam_domain:PF03828,hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF24,Superfamily_domains:SSF81631 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 37 6746323 6746323 G C 1 0 0 0 0 1 0 0 0 11507 942 33 4 4 PAPD7 5 6746323 Missense_Mutation SNP G C3N-00167_T 6746323 174791936 11 9384 HSD17B4 0 . GRCh38 5 119541983 119541983 + Missense_Mutation SNP G G A rs751064948 C3N-00167_T C3N-00167_N G G c.2275G>A p.Ala759Thr p.A759T ENST00000504811 25/25 356 256 100 372 372 0 strelka-varscan-mutect HSD17B4,missense_variant,p.Ala759Thr,ENST00000504811,NM_001199291.2;HSD17B4,missense_variant,p.Ala734Thr,ENST00000256216,NM_000414.3;HSD17B4,missense_variant,p.Ala710Thr,ENST00000510025,NM_001292027.1;HSD17B4,missense_variant,p.Ala594Thr,ENST00000414835,NM_001292028.1;HSD17B4,missense_variant,p.Ala716Thr,ENST00000515320,NM_001199292.1;HSD17B4,missense_variant,p.Ala472Thr,ENST00000509514,;HSD17B4,missense_variant,p.Ala597Thr,ENST00000513628,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000522415,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000509951,;HSD17B4,3_prime_UTR_variant,,ENST00000442060,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000503310,;HSD17B4,non_coding_transcript_exon_variant,,ENST00000509606,;HSD17B4,intron_variant,,ENST00000515235,; A ENST00000504811 Transcript missense_variant 2459/2740 2275/2286 759/761 A/T Gcc/Acc rs751064948,COSM5003454 1 1 HSD17B4 HGNC HGNC:5213 protein_coding YES CCDS56379.1 ENSP00000420914 P51659 UPI0001AE7403 NM_001199291.2 deleterious(0.03) 25/25 Gene3D:3.30.1050.10,Coiled-coils_(Ncoils):Coil 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs751064948 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 119541983 119541983 G A 1 0 0 0 0 1 0 0 0 7281 1087 38 1 1 HSD17B4 5 119541983 Missense_Mutation SNP G C3N-00167_T 112795660 119541983 61996276 12 9385 PCDHB6 0 . GRCh38 5 141152059 141152059 + Missense_Mutation SNP C C T rs373141144 C3N-00167_T C3N-00167_N C C c.1802C>T p.Ser601Leu p.S601L ENST00000231136 1/1 492 437 55 448 448 0 varscan-mutect PCDHB6,missense_variant,p.Ser601Leu,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Ser465Leu,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; T ENST00000231136 Transcript missense_variant 2038/3266 1802/2385 601/794 S/L tCg/tTg rs373141144,COSM4901610 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 deleterious(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 0,1 1 PASS rs373141144 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 141152059 141152059 C T 1 0 0 0 0 1 0 0 0 11633 893 31 1 1 PCDHB6 5 141152059 Missense_Mutation SNP C C3N-00167_T 21610076 141152059 40386200 13 9386 GABRB2 0 . GRCh38 5 161326385 161326385 + Missense_Mutation SNP C C A rs150956270 C3N-00167_T C3N-00167_N C C c.1174G>T p.Asp392Tyr p.D392Y ENST00000274547 10/11 130 107 23 150 148 2 strelka-varscan-mutect GABRB2,missense_variant,p.Asp392Tyr,ENST00000274547,NM_021911.2;GABRB2,missense_variant,p.Asp392Tyr,ENST00000393959,;GABRB2,intron_variant,,ENST00000520240,;GABRB2,intron_variant,,ENST00000353437,NM_000813.2;GABRB2,intron_variant,,ENST00000517901,;GABRB2,intron_variant,,ENST00000517547,;GABRB2,downstream_gene_variant,,ENST00000612710,; A ENST00000274547 Transcript missense_variant 1392/7409 1174/1539 392/512 D/Y Gat/Tat rs150956270,COSM4346303,COSM449248 1 -1 GABRB2 HGNC HGNC:4082 protein_coding YES CCDS4355.1 ENSP00000274547 P47870 UPI000002AA29 NM_021911.2 deleterious(0.04) 10/11 TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs150956270 . 0 206 0 3 0 0 0 0 -20 0.9999953 1 1 1 0 A 3 1 37 161326385 161326385 C A 1 0 0 0 0 1 0 0 0 6038 884 31 1 1 GABRB2 5 161326385 Missense_Mutation SNP C C3N-00167_T 20174326 161326385 20211874 14 9387 TNFRSF21 0 . GRCh38 6 47286085 47286085 + Missense_Mutation SNP C C A novel C3N-00167_T C3N-00167_N C C c.607G>T p.Gly203Trp p.G203W ENST00000296861 2/6 388 323 65 440 440 0 strelka-varscan-mutect TNFRSF21,missense_variant,p.Gly203Trp,ENST00000296861,NM_014452.4; A ENST00000296861 Transcript missense_variant 1001/3595 607/1968 203/655 G/W Ggg/Tgg 1 -1 TNFRSF21 HGNC HGNC:13469 protein_coding YES CCDS4921.1 ENSP00000296861 O75509 A0A024RD71 UPI000004680F NM_014452.4 deleterious(0) 2/6 hmmpanther:PTHR23097:SF127,hmmpanther:PTHR23097,Pfam_domain:PF00020,SMART_domains:SM00208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 47286085 47286085 C A 1 0 0 0 0 1 0 0 0 16769 623 22 2 2 TNFRSF21 6 47286085 Missense_Mutation SNP C C3N-00167_T 47286085 123519894 15 9388 TRDN 0 . GRCh38 6 123571113 123571113 + Silent SNP T T A novel C3N-00167_T C3N-00167_N T T c.42A>T p.= p.T14T ENST00000334268 2/41 132 124 8 163 163 0 strelka-varscan TRDN,synonymous_variant,p.=,ENST00000334268,NM_006073.3;TRDN,synonymous_variant,p.=,ENST00000628709,NM_001256020.1;TRDN,synonymous_variant,p.=,ENST00000542443,NM_001256022.1;TRDN,synonymous_variant,p.=,ENST00000546248,NM_001256021.1; A ENST00000334268 Transcript synonymous_variant 360/4770 42/2190 14/729 T acA/acT 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 2/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 37 123571113 123571113 T A 1 0 0 0 0 0 0 0 1 16957 1799 63 4 4 TRDN 6 123571113 Silent SNP T C3N-00167_T 76285028 123571113 47234866 16 9389 ANKMY2 0 . GRCh38 7 16627085 16627085 + Nonsense_Mutation SNP G G A novel C3N-00167_T C3N-00167_N G G c.226C>T p.Gln76Ter p.Q76* ENST00000306999 3/10 241 170 71 155 155 0 strelka-varscan-mutect ANKMY2,stop_gained,p.Gln76Ter,ENST00000306999,NM_020319.2;ANKMY2,stop_gained,p.Gln76Ter,ENST00000628652,;ANKMY2,downstream_gene_variant,,ENST00000421746,;ANKMY2,stop_gained,p.Gln76Ter,ENST00000447802,;ANKMY2,3_prime_UTR_variant,,ENST00000453623,; A ENST00000306999 Transcript stop_gained 470/2555 226/1326 76/441 Q/* Cag/Tag 1 -1 ANKMY2 HGNC HGNC:25370 protein_coding YES CCDS5361.1 ENSP00000303570 Q8IV38 A0A024R9Z6 UPI0000035D93 NM_020319.2 3/10 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24150,hmmpanther:PTHR24150:SF9,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 37 16627085 16627085 G A 1 0 0 0 0 0 1 0 0 736 1299 45 3 3 ANKMY2 7 16627085 Nonsense_Mutation SNP G C3N-00167_T 16627085 142718888 17 9390 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-00167_T C3N-00167_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 565 357 208 547 547 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 37 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-00167_T 38547687 55174772 104171201 18 9391 ADAM18 0 . GRCh38 8 39729903 39729903 + Missense_Mutation SNP C C T C3N-00167_T C3N-00167_N C C c.2183C>T p.Ser728Leu p.S728L ENST00000265707 20/20 126 110 16 112 112 0 strelka-varscan-mutect ADAM18,missense_variant,p.Ser728Leu,ENST00000265707,NM_014237.2;ADAM18,missense_variant,p.Ser704Leu,ENST00000379866,NM_001320313.1;ADAM18,non_coding_transcript_exon_variant,,ENST00000523755,;ADAM18,3_prime_UTR_variant,,ENST00000520087,; T ENST00000265707 Transcript missense_variant 2228/2388 2183/2220 728/739 S/L tCa/tTa COSM1099762 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 tolerated(0.1) 20/20 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 39729903 39729903 C T 1 0 0 0 0 1 0 0 0 283 840 29 3 3 ADAM18 8 39729903 Missense_Mutation SNP C C3N-00167_T 39729903 105408733 19 9392 COL22A1 0 . GRCh38 8 138811885 138811885 + Missense_Mutation SNP G G T rs537744559 C3N-00167_T C3N-00167_N G G c.1363C>A p.Pro455Thr p.P455T ENST00000303045 9/65 75 70 5 78 78 0 varscan-mutect COL22A1,missense_variant,p.Pro455Thr,ENST00000303045,NM_152888.2;COL22A1,intron_variant,,ENST00000435777,; T ENST00000303045 Transcript missense_variant 1810/6346 1363/4881 455/1626 P/T Ccc/Acc rs537744559,COSM3951353 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.15) 9/65 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs537744559 . 0 169 36 5 0 0 0 0 -8.494817 0.3616521 0 1 0 0 T 3 4 37 138811885 138811885 G T 1 0 0 0 0 1 0 0 0 3469 1261 44 2 2 COL22A1 8 138811885 Missense_Mutation SNP G C3N-00167_T 99081982 138811885 6326751 20 9393 GLDC 0 . GRCh38 9 6589203 6589203 + Silent SNP C C G rs373679781 C3N-00167_T C3N-00167_N C C c.1572G>C p.= p.V524V ENST00000321612 12/25 281 218 63 417 417 0 strelka-varscan-mutect GLDC,synonymous_variant,p.=,ENST00000321612,NM_000170.2;GLDC,downstream_gene_variant,,ENST00000463305,; G ENST00000321612 Transcript synonymous_variant 1723/3767 1572/3063 524/1020 V gtG/gtC rs373679781 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 12/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,TIGRFAM_domain:TIGR00461 LOW 1 SNV 1 1 PASS rs373679781 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 37 6589203 6589203 C G 1 0 0 0 0 0 0 0 1 6311 465 17 4 4 GLDC 9 6589203 Silent SNP C C3N-00167_T 6589203 131805514 21 9394 NKX2-3 0 . GRCh38 10 99533438 99533438 + Missense_Mutation SNP G G A novel C3N-00167_T C3N-00167_N G G c.307G>A p.Glu103Lys p.E103K ENST00000344586 1/2 117 108 9 118 118 0 strelka-varscan-mutect NKX2-3,missense_variant,p.Glu103Lys,ENST00000344586,NM_145285.2;NKX2-3,missense_variant,p.Glu103Lys,ENST00000622383,;LINC01475,upstream_gene_variant,,ENST00000548010,;RP11-129J12.1,downstream_gene_variant,,ENST00000452494,; A ENST00000344586 Transcript missense_variant 506/2097 307/1095 103/364 E/K Gag/Aag 1 1 NKX2-3 HGNC HGNC:7836 protein_coding YES CCDS41558.1 ENSP00000342828 Q8TAU0 UPI00001301E8 NM_145285.2 tolerated(0.86) 1/2 hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF32,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -18.0699 1 1 1 1 0 A 3 1 37 99533438 99533438 G A 1 0 0 0 0 1 0 0 0 10487 1059 37 1 1 NKX2-3 10 99533438 Missense_Mutation SNP G C3N-00167_T 99533438 34263984 22 9395 CPXM2 0 . GRCh38 10 123770930 123770930 + Missense_Mutation SNP C C T rs768013289 C3N-00167_T C3N-00167_N C C c.1088G>A p.Gly363Glu p.G363E ENST00000241305 8/14 133 99 34 127 127 0 strelka-mutect CPXM2,missense_variant,p.Gly363Glu,ENST00000241305,NM_198148.2;CPXM2,5_prime_UTR_variant,,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; T ENST00000241305 Transcript missense_variant 1243/3554 1088/2271 363/756 G/E gGg/gAg rs768013289 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 deleterious(0) 8/14 hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs768013289 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 123770930 123770930 C T 1 0 0 0 0 1 0 0 0 3636 623 22 3 3 CPXM2 10 123770930 Missense_Mutation SNP C C3N-00167_T 24237492 123770930 10026492 23 9396 PHF21A 0 . GRCh38 11 45969820 45969820 + Missense_Mutation SNP G G A novel C3N-00167_T C3N-00167_N G G c.694C>T p.Pro232Ser p.P232S ENST00000418153 8/18 167 138 29 159 158 1 strelka-varscan-mutect PHF21A,missense_variant,p.Pro233Ser,ENST00000323180,NM_016621.3;PHF21A,missense_variant,p.Pro232Ser,ENST00000418153,NM_001101802.1;PHF21A,downstream_gene_variant,,ENST00000524497,;PHF21A,downstream_gene_variant,,ENST00000531959,;PHF21A,upstream_gene_variant,,ENST00000527753,;PHF21A,downstream_gene_variant,,ENST00000525679,;PHF21A,non_coding_transcript_exon_variant,,ENST00000527401,;PHF21A,downstream_gene_variant,,ENST00000532883,; A ENST00000418153 Transcript missense_variant 894/2730 694/2043 232/680 P/S Cca/Tca 1 -1 PHF21A HGNC HGNC:24156 protein_coding YES CCDS44578.1 ENSP00000398824 Q96BD5 UPI000006E1CB NM_001101802.1 deleterious(0.03) 8/18 hmmpanther:PTHR24102:SF6,hmmpanther:PTHR24102 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 45969820 45969820 G A 1 0 0 0 0 1 0 0 0 11919 1188 41 3 3 PHF21A 11 45969820 Missense_Mutation SNP G C3N-00167_T 45969820 89116802 24 9397 DTX4 0 . GRCh38 11 59199721 59199721 + Missense_Mutation SNP C C T novel C3N-00167_T C3N-00167_N C C c.1574C>T p.Ala525Val p.A525V ENST00000227451 8/9 293 248 45 286 286 0 strelka-varscan-mutect DTX4,missense_variant,p.Ala525Val,ENST00000227451,NM_015177.1;DTX4,missense_variant,p.Ala419Val,ENST00000532982,NM_001300727.1;DTX4,non_coding_transcript_exon_variant,,ENST00000527475,; T ENST00000227451 Transcript missense_variant 1678/5642 1574/1860 525/619 A/V gCc/gTc 1 1 DTX4 HGNC HGNC:29151 protein_coding YES CCDS44612.1 ENSP00000227451 Q9Y2E6 UPI00001C1F00 NM_015177.1 deleterious(0) 8/9 hmmpanther:PTHR12622:SF5,hmmpanther:PTHR12622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 59199721 59199721 C T 1 0 0 0 0 1 0 0 0 4620 739 26 3 3 DTX4 11 59199721 Missense_Mutation SNP C C3N-00167_T 13229901 59199721 75886901 25 9398 PPME1 0 . GRCh38 11 74230391 74230391 + Missense_Mutation SNP T T G novel C3N-00167_T C3N-00167_N T T c.545T>G p.Val182Gly p.V182G ENST00000398427 6/14 229 206 23 254 254 0 strelka-varscan-mutect PPME1,missense_variant,p.Val182Gly,ENST00000328257,NM_016147.2;PPME1,missense_variant,p.Val182Gly,ENST00000398427,NM_001271593.1;PPME1,upstream_gene_variant,,ENST00000543525,; G ENST00000398427 Transcript missense_variant 645/2496 545/1203 182/400 V/G gTt/gGt 1 1 PPME1 HGNC HGNC:30178 protein_coding YES CCDS60891.1 ENSP00000381461 Q9Y570 UPI0001639863 NM_001271593.1 deleterious(0) 6/14 hmmpanther:PTHR14189,Pfam_domain:PF12697,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF022950,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 37 74230391 74230391 T G 1 0 0 0 0 1 0 0 0 12457 1725 60 5 5 PPME1 11 74230391 Missense_Mutation SNP T C3N-00167_T 15030670 74230391 60856231 26 9399 TRPC4 0 . GRCh38 13 37783327 37783327 + Nonsense_Mutation SNP G G A novel C3N-00167_T C3N-00167_N G G c.7C>T p.Gln3Ter p.Q3* ENST00000625583 1/10 29 21 8 29 29 0 strelka-varscan-mutect TRPC4,stop_gained,p.Gln3Ter,ENST00000379705,NM_016179.2;TRPC4,stop_gained,p.Gln3Ter,ENST00000625583,NM_003306.1;TRPC4,stop_gained,p.Gln3Ter,ENST00000358477,NM_001135955.1;TRPC4,stop_gained,p.Gln3Ter,ENST00000338947,NM_001135958.1;TRPC4,stop_gained,p.Gln3Ter,ENST00000355779,NM_001135957.1;TRPC4,stop_gained,p.Gln3Ter,ENST00000379673,NM_001135956.1;TRPC4,stop_gained,p.Gln3Ter,ENST00000426868,;TRPC4,stop_gained,p.Gln3Ter,ENST00000379679,;TRPC4,stop_gained,p.Gln3Ter,ENST00000488717,; A ENST00000625583 Transcript stop_gained 7/3009 7/2949 3/982 Q/* Cag/Tag 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 1/10 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.98854 1 1 1 1 0 A 4 1 37 37783327 37783327 G A 1 0 0 0 0 0 1 0 0 17085 1299 45 3 3 TRPC4 13 37783327 Nonsense_Mutation SNP G C3N-00167_T 37783327 76581001 27 9400 FRMD6 0 . GRCh38 14 51715457 51715457 + Missense_Mutation SNP C C A novel C3N-00167_T C3N-00167_N C C c.982C>A p.Gln328Lys p.Q328K ENST00000344768 10/14 118 102 16 125 125 0 strelka-varscan-mutect FRMD6,missense_variant,p.Gln320Lys,ENST00000395718,NM_152330.3;FRMD6,missense_variant,p.Gln320Lys,ENST00000356218,NM_001042481.2;FRMD6,missense_variant,p.Gln251Lys,ENST00000554167,;FRMD6,missense_variant,p.Gln328Lys,ENST00000344768,NM_001267046.1;FRMD6,missense_variant,p.Gln58Lys,ENST00000555197,;FRMD6,upstream_gene_variant,,ENST00000553556,NM_001267047.1;FRMD6,upstream_gene_variant,,ENST00000555703,;FRMD6,non_coding_transcript_exon_variant,,ENST00000557183,;FRMD6,non_coding_transcript_exon_variant,,ENST00000557522,;FRMD6,downstream_gene_variant,,ENST00000554495,; A ENST00000344768 Transcript missense_variant 1178/2972 982/1869 328/622 Q/K Cag/Aag 1 1 FRMD6 HGNC HGNC:19839 protein_coding YES CCDS58318.1 ENSP00000343899 Q96NE9 UPI00000473F6 NM_001267046.1 tolerated(0.06) 10/14 Gene3D:2.30.29.30,Pfam_domain:PF09380,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF9,SMART_domains:SM01196,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 37 51715457 51715457 C A 1 0 0 0 0 1 0 0 0 5924 711 25 2 2 FRMD6 14 51715457 Missense_Mutation SNP C C3N-00167_T 51715457 55328261 28 9401 RTN1 0 . GRCh38 14 59727508 59727508 + Silent SNP C C T C3N-00167_T C3N-00167_N C C c.1176G>A p.= p.P392P ENST00000267484 3/9 222 173 49 251 251 0 strelka-varscan-mutect RTN1,synonymous_variant,p.=,ENST00000267484,NM_021136.2;RTN1,synonymous_variant,p.=,ENST00000611068,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,; T ENST00000267484 Transcript synonymous_variant 1512/3435 1176/2331 392/776 P ccG/ccA COSM3786358 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 3/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 1 LOW 1 SNV 1 1 1 PASS rs944737200 . 0 205 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 T 2 4 37 59727508 59727508 C T 1 0 0 0 0 0 0 0 1 13985 755 27 1 1 RTN1 14 59727508 Silent SNP C C3N-00167_T 8012051 59727508 47316210 29 9402 MYH11 0 . GRCh38 16 15724919 15724919 + Missense_Mutation SNP G G A rs185720909 C3N-00167_T C3N-00167_N G G c.3953C>T p.Ala1318Val p.A1318V ENST00000396324 30/42 434 370 64 444 443 1 strelka-varscan-mutect MYH11,missense_variant,p.Ala1318Val,ENST00000452625,NM_001040113.1;MYH11,missense_variant,p.Ala1318Val,ENST00000396324,NM_001040114.1;MYH11,missense_variant,p.Ala1311Val,ENST00000576790,NM_022844.2;MYH11,missense_variant,p.Ala1311Val,ENST00000300036,NM_002474.2;NDE1,3_prime_UTR_variant,,ENST00000396355,NM_001143979.1;NDE1,3_prime_UTR_variant,,ENST00000396354,NM_017668.2;NDE1,downstream_gene_variant,,ENST00000572967,;NDE1,downstream_gene_variant,,ENST00000573694,;AF001548.5,upstream_gene_variant,,ENST00000574212,;NDE1,downstream_gene_variant,,ENST00000572503,;MYH11,non_coding_transcript_exon_variant,,ENST00000571275,;MYH11,upstream_gene_variant,,ENST00000576164,; A ENST00000396324 Transcript missense_variant 4041/6847 3953/5940 1318/1979 A/V gCg/gTg rs185720909,COSM1608950,COSM1608951 1 -1 MYH11 HGNC HGNC:7569 protein_coding YES CCDS45423.1 ENSP00000379616 P35749 UPI00005B7237 NM_001040114.1 tolerated(0.1) 30/42 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs185720909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 37 15724919 15724919 G A 1 0 0 0 0 1 0 0 0 10031 1087 38 1 1 MYH11 16 15724919 Missense_Mutation SNP G C3N-00167_T 15724919 74613426 30 9403 TP53 0 . GRCh38 17 7674894 7674894 + Nonsense_Mutation SNP G G A rs397516436 C3N-00167_T C3N-00167_N G G c.637C>T p.Arg213Ter p.R213* ENST00000269305 6/11 345 227 118 457 457 0 strelka-varscan-mutect TP53,stop_gained,p.Arg213Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Arg213Ter,ENST00000420246,;TP53,stop_gained,p.Arg174Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Arg174Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Arg213Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Arg174Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Arg213Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Arg174Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Arg213Ter,ENST00000445888,;TP53,stop_gained,p.Arg174Ter,ENST00000619485,;TP53,stop_gained,p.Arg81Ter,ENST00000510385,NM_001126116.1;TP53,stop_gained,p.Arg54Ter,ENST00000618944,NM_001276698.1;TP53,stop_gained,p.Arg81Ter,ENST00000504290,NM_001126117.1;TP53,stop_gained,p.Arg54Ter,ENST00000610623,NM_001276699.1;TP53,stop_gained,p.Arg81Ter,ENST00000504937,NM_001126115.1;TP53,stop_gained,p.Arg54Ter,ENST00000619186,NM_001276697.1;TP53,stop_gained,p.Arg213Ter,ENST00000359597,;TP53,stop_gained,p.Arg202Ter,ENST00000615910,;TP53,stop_gained,p.Arg213Ter,ENST00000413465,;TP53,stop_gained,p.Arg81Ter,ENST00000509690,;TP53,stop_gained,p.Arg120Ter,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,stop_gained,p.Arg174Ter,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained 827/2579 637/1182 213/393 R/* Cga/Tga rs397516436,CM951226,TP53_g.12706del,TP53_g.12706C>T,TP53_g.12706C>G,TP53_g.12706C>A,COSM10654,COSM1638393,COSM3378350,COSM43798,COSM43807,COSM44102,COSM4862566,COSM4862567,COSM707888,COSM707889,COSM707890,COSM707891,COSM99615,COSM99616,COSM99617,COSM99618 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs397516436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 37 7674894 7674894 G A 1 0 0 0 0 0 1 0 0 16859 1066 37 1 1 TP53 17 7674894 Nonsense_Mutation SNP G C3N-00167_T 7674894 75582547 31 9404 SRCIN1 0 . GRCh38 17 38561950 38561950 + Missense_Mutation SNP C C T novel C3N-00167_T C3N-00167_N C C c.1213G>A p.Glu405Lys p.E405K ENST00000617146 7/19 124 95 29 100 100 0 strelka-varscan-mutect SRCIN1,missense_variant,p.Glu405Lys,ENST00000617146,NM_025248.2;SRCIN1,missense_variant,p.Glu439Lys,ENST00000621492,;SRCIN1,missense_variant,p.Glu193Lys,ENST00000622190,;SRCIN1,missense_variant,p.Glu465Lys,ENST00000612431,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000621763,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000622519,;SRCIN1,upstream_gene_variant,,ENST00000612208,; T ENST00000617146 Transcript missense_variant 1438/7058 1213/3552 405/1183 E/K Gag/Aag 1 -1 SRCIN1 HGNC HGNC:29506 protein_coding YES CCDS45660.1 ENSP00000484715 Q9C0H9 UPI0000E27F82 NM_025248.2 deleterious(0) 7/19 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF5 MODERATE 1 SNV 2 1 PASS rs1427180897 . 0 201 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 37 38561950 38561950 C T 1 0 0 0 0 1 0 0 0 15494 893 31 1 1 SRCIN1 17 38561950 Missense_Mutation SNP C C3N-00167_T 30887056 38561950 44695491 32 9405 EPG5 0 . GRCh38 18 45952431 45952431 + Silent SNP C C A novel C3N-00167_T C3N-00167_N C C c.1221G>T p.= p.L407L ENST00000282041 3/44 134 121 13 181 181 0 strelka-varscan-mutect EPG5,synonymous_variant,p.=,ENST00000282041,NM_020964.2;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,; A ENST00000282041 Transcript synonymous_variant 1256/12633 1221/7740 407/2579 L ctG/ctT 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 3/44 Low_complexity_(Seg):seg,hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 37 45952431 45952431 C A 1 0 0 0 0 0 0 0 1 5010 813 29 2 2 EPG5 18 45952431 Silent SNP C C3N-00167_T 45952431 34420854 33 9406 FOXA3 0 . GRCh38 19 45872763 45872763 + Missense_Mutation SNP C C T novel C3N-00167_T C3N-00167_N C C c.758C>T p.Pro253Leu p.P253L ENST00000302177 2/2 98 83 15 108 108 0 strelka-varscan-mutect FOXA3,missense_variant,p.Pro253Leu,ENST00000302177,NM_004497.2;FOXA3,downstream_gene_variant,,ENST00000594297,; T ENST00000302177 Transcript missense_variant 955/1989 758/1053 253/350 P/L cCc/cTc 1 1 FOXA3 HGNC HGNC:5023 protein_coding YES CCDS12677.1 ENSP00000304004 P55318 A0A024R0R3 UPI0000000DF9 NM_004497.2 tolerated(0.31) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF201,hmmpanther:PTHR11829 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 37 45872763 45872763 C T 1 0 0 0 0 1 0 0 0 5851 623 22 3 3 FOXA3 19 45872763 Missense_Mutation SNP C C3N-00167_T 45872763 12744853 34 9407 BRSK1 0 . GRCh38 19 55304776 55304776 + Missense_Mutation SNP C C T rs771561869 C3N-00167_T C3N-00167_N C C c.1573C>T p.Arg525Trp p.R525W ENST00000309383 14/19 101 85 16 110 110 0 strelka-varscan-mutect BRSK1,missense_variant,p.Arg525Trp,ENST00000309383,NM_032430.1;BRSK1,missense_variant,p.Arg541Trp,ENST00000590333,;BRSK1,missense_variant,p.Arg220Trp,ENST00000326848,;BRSK1,downstream_gene_variant,,ENST00000585418,;BRSK1,downstream_gene_variant,,ENST00000591774,;BRSK1,non_coding_transcript_exon_variant,,ENST00000588584,;BRSK1,downstream_gene_variant,,ENST00000586626,; T ENST00000309383 Transcript missense_variant 1850/3079 1573/2337 525/778 R/W Cgg/Tgg rs771561869,COSM228728 1 1 BRSK1 HGNC HGNC:18994 protein_coding YES CCDS12921.1 ENSP00000310649 Q8TDC3 UPI0000070495 NM_032430.1 deleterious(0) 14/19 Low_complexity_(Seg):seg,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF130 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771561869 . 0 205 0 4 0 0 0 0 -20 0.9999237 1 1 1 0 T 3 4 37 55304776 55304776 C T 1 0 0 0 0 1 0 0 0 1697 643 23 1 1 BRSK1 19 55304776 Missense_Mutation SNP C C3N-00167_T 9432013 55304776 3312840 35 9408 OR4F5 0 . GRCh38 1 69709 69709 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.619C>T p.= p.L207L ENST00000335137 1/1 84 77 7 129 129 0 varscan-mutect OR4F5,synonymous_variant,p.=,ENST00000335137,NM_001005484.1; T ENST00000335137 Transcript synonymous_variant 619/918 619/918 207/305 L Cta/Tta 1 1 OR4F5 HGNC HGNC:14825 protein_coding YES CCDS30547.1 ENSP00000334393 Q8NH21 UPI0000041BC1 NM_001005484.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF179,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 32 178 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 69709 69709 C T 1 0 0 0 0 0 0 0 1 11142 912 32 3 3 OR4F5 1 69709 Silent SNP C C3N-00169_T 69709 248886713 1 9409 AADACL3 0 . GRCh38 1 12716189 12716189 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.13G>T p.Ala5Ser p.A5S ENST00000359318 1/4 27 18 9 33 33 0 strelka-varscan-mutect AADACL3,missense_variant,p.Ala5Ser,ENST00000359318,NM_001103170.2;AADACL3,non_coding_transcript_exon_variant,,ENST00000620146,; T ENST00000359318 Transcript missense_variant 47/3662 13/1224 5/407 A/S Gcc/Tcc 1 1 AADACL3 HGNC HGNC:32037 protein_coding YES CCDS41253.2 ENSP00000352268 Q5VUY0 UPI0003EAEC70 NM_001103170.2 tolerated(0.4) 1/4 hmmpanther:PTHR23024,hmmpanther:PTHR23024:SF115,Transmembrane_helices:TMhelix MODERATE 1 SNV 3 1 PASS rs1183485676 . 0 206 4 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 38 12716189 12716189 G T 1 0 0 0 0 1 0 0 0 12 1203 42 2 2 AADACL3 1 12716189 Missense_Mutation SNP G C3N-00169_T 12646480 12716189 236240233 2 9410 ARHGEF10L 0 . GRCh38 1 17613131 17613131 + Missense_Mutation SNP G G T rs144936441 C3N-00169_T C3N-00169_N G G c.683G>T p.Gly228Val p.G228V ENST00000361221 8/29 141 115 26 191 190 1 strelka-varscan-mutect ARHGEF10L,missense_variant,p.Gly228Val,ENST00000361221,NM_018125.3;ARHGEF10L,intron_variant,,ENST00000375415,NM_001319837.1,NM_001011722.2;ARHGEF10L,upstream_gene_variant,,ENST00000469726,; T ENST00000361221 Transcript missense_variant 842/4488 683/3840 228/1279 G/V gGg/gTg rs144936441,COSM4143071,COSM4143072 1 1 ARHGEF10L HGNC HGNC:25540 protein_coding YES CCDS182.1 ENSP00000355060 Q9HCE6 UPI00004CA9C5 NM_018125.3 deleterious(0.03) 8/29 hmmpanther:PTHR12877,hmmpanther:PTHR12877:SF16 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs144936441 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 17613131 17613131 G T 1 0 0 0 0 1 0 0 0 1025 1232 43 2 2 ARHGEF10L 1 17613131 Missense_Mutation SNP G C3N-00169_T 4896942 17613131 231343291 3 9411 GRIK3 0 . GRCh38 1 36801891 36801891 + Missense_Mutation SNP C C G novel C3N-00169_T C3N-00169_N C C c.2720G>C p.Ser907Thr p.S907T ENST00000373091 16/16 77 60 17 108 108 0 strelka-varscan-mutect GRIK3,missense_variant,p.Ser907Thr,ENST00000373091,NM_000831.3;GRIK3,downstream_gene_variant,,ENST00000373093,; G ENST00000373091 Transcript missense_variant 2737/9101 2720/2760 907/919 S/T aGc/aCc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 tolerated_low_confidence(1) 16/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999918 1 1 1 0 G 3 3 38 36801891 36801891 C G 1 0 0 0 0 1 0 0 0 6657 797 28 4 4 GRIK3 1 36801891 Missense_Mutation SNP C C3N-00169_T 19188760 36801891 212154531 4 9412 LURAP1 0 . GRCh38 1 46220096 46220097 + Frame_Shift_Del DEL GG GG - novel C3N-00169_T C3N-00169_N GG GG c.596_597delGG p.Trp199Ter p.W199* ENST00000371980 2/2 192 157 35 310 310 0 sindel-varindel-pindel LURAP1,frameshift_variant,p.Trp199Ter,ENST00000371980,NM_001013615.2;POMGNT1,5_prime_UTR_variant,,ENST00000396420,;POMGNT1,5_prime_UTR_variant,,ENST00000371992,NM_001243766.1; - ENST00000371980 Transcript frameshift_variant 689-690/1854 596-597/720 199/239 W/X tGG/t 1 1 LURAP1 HGNC HGNC:32327 protein_coding YES CCDS30703.1 ENSP00000361048 Q96LR2 UPI0000072C34 NM_001013615.2 2/2 hmmpanther:PTHR33767 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 38 46220096 46220096 GG - 1 0 1 0 1 0 0 0 0 8993 1357 47 0 0 LURAP1 1 46220096 Frame_Shift_Del DEL GG C3N-00169_T 9418205 46220096 202736326 5 9413 CLCA4 0 . GRCh38 1 86579558 86579558 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.2327C>A p.Ala776Glu p.A776E ENST00000370563 13/14 163 143 20 197 197 0 strelka-varscan-mutect CLCA4,missense_variant,p.Ala776Glu,ENST00000370563,NM_012128.3;RP4-651E10.4,intron_variant,,ENST00000456587,; A ENST00000370563 Transcript missense_variant 2369/3211 2327/2760 776/919 A/E gCa/gAa 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 deleterious(0) 13/14 hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 MODERATE 1 SNV 1 1 PASS rs1475241410 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 86579558 86579558 C A 1 0 0 0 0 1 0 0 0 3223 710 25 2 2 CLCA4 1 86579558 Missense_Mutation SNP C C3N-00169_T 40359462 86579558 162376864 6 9414 NTNG1 0 . GRCh38 1 107324861 107324861 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.826G>T p.Val276Leu p.V276L ENST00000370068 3/8 85 66 19 106 106 0 strelka-varscan-mutect NTNG1,missense_variant,p.Val276Leu,ENST00000370067,;NTNG1,missense_variant,p.Val276Leu,ENST00000370068,;NTNG1,missense_variant,p.Val276Leu,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Val276Leu,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Val276Leu,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Val276Leu,ENST00000370065,;NTNG1,missense_variant,p.Val276Leu,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; T ENST00000370068 Transcript missense_variant 1672/4034 826/1620 276/539 V/L Gta/Tta 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.60.120.260,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 107324861 107324861 G T 1 0 0 0 0 1 0 0 0 10769 1377 48 2 2 NTNG1 1 107324861 Missense_Mutation SNP G C3N-00169_T 20745303 107324861 141631561 7 9415 FLG 0 . GRCh38 1 152307627 152307627 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.7259C>A p.Thr2420Asn p.T2420N ENST00000368799 3/3 888 574 314 538 537 1 strelka-varscan-mutect FLG,missense_variant,p.Thr2420Asn,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 7295/12747 7259/12186 2420/4061 T/N aCt/aAt 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.06) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 152307627 152307627 G T 1 0 0 0 0 1 0 0 0 5784 1029 36 2 2 FLG 1 152307627 Missense_Mutation SNP G C3N-00169_T 44982766 152307627 96648795 8 9416 PGLYRP4 0 . GRCh38 1 153341710 153341710 + Missense_Mutation SNP T T A novel C3N-00169_T C3N-00169_N T T c.542A>T p.His181Leu p.H181L ENST00000359650 6/9 333 193 140 237 236 1 strelka-varscan-mutect PGLYRP4,missense_variant,p.His177Leu,ENST00000368739,;PGLYRP4,missense_variant,p.His181Leu,ENST00000359650,NM_020393.3;PGLYRP4,downstream_gene_variant,,ENST00000490266,; A ENST00000359650 Transcript missense_variant 607/1834 542/1122 181/373 H/L cAc/cTc 1 -1 PGLYRP4 HGNC HGNC:30015 protein_coding YES CCDS30871.1 ENSP00000352672 Q96LB8 UPI000013F78A NM_020393.3 tolerated(0.12) 6/9 hmmpanther:PTHR11022:SF40,hmmpanther:PTHR11022,Gene3D:3.40.80.10,Pfam_domain:PF01510,SMART_domains:SM00701,SMART_domains:SM00644,Superfamily_domains:SSF55846 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 153341710 153341710 T A 1 0 0 0 0 1 0 0 0 11885 1696 59 4 4 PGLYRP4 1 153341710 Missense_Mutation SNP T C3N-00169_T 1034083 153341710 95614712 9 9417 TPM3 0 . GRCh38 1 154191934 154191934 + Nonsense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.85G>T p.Glu29Ter p.E29* ENST00000368530 1/10 961 563 398 697 697 0 strelka-varscan-mutect TPM3,stop_gained,p.Glu29Ter,ENST00000368530,NM_152263.3;TPM3,stop_gained,p.Glu29Ter,ENST00000271850,;TPM3,stop_gained,p.Glu29Ter,ENST00000515609,;MIR190B,downstream_gene_variant,,ENST00000401119,;TPM3,non_coding_transcript_exon_variant,,ENST00000466010,; A ENST00000368530 Transcript stop_gained 278/1523 85/858 29/285 E/* Gag/Tag 1 -1 TPM3 HGNC HGNC:12012 protein_coding YES CCDS41403.1 ENSP00000357516 P06753 UPI000013D90D NM_152263.3 1/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19269:SF38,hmmpanther:PTHR19269,Gene3D:1.20.5.340,Superfamily_domains:SSF57997 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 154191934 154191934 C A 1 0 0 0 0 0 1 0 0 16888 835 29 2 2 TPM3 1 154191934 Nonsense_Mutation SNP C C3N-00169_T 850224 154191934 94764488 10 9418 APCS 0 . GRCh38 1 159588456 159588456 + Missense_Mutation SNP G G T C3N-00169_T C3N-00169_N G G c.420G>T p.Gln140His p.Q140H ENST00000255040 2/2 347 256 91 273 272 1 strelka-varscan-mutect APCS,missense_variant,p.Gln140His,ENST00000255040,NM_001639.3; T ENST00000255040 Transcript missense_variant 517/926 420/672 140/223 Q/H caG/caT COSM1498977,COSM5580238 1 1 APCS HGNC HGNC:584 protein_coding YES CCDS1186.1 ENSP00000255040 P02743 V9HWP0 UPI0000135533 NM_001639.3 deleterious(0) 2/2 hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF99,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899,Prints_domain:PR00895 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 159588456 159588456 G T 1 0 0 0 0 1 0 0 0 887 991 35 2 2 APCS 1 159588456 Missense_Mutation SNP G C3N-00169_T 5396522 159588456 89367966 11 9419 NHLH1 0 . GRCh38 1 160370844 160370844 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.113G>T p.Gly38Val p.G38V ENST00000302101 2/2 284 204 80 209 209 0 strelka-varscan-mutect NHLH1,missense_variant,p.Gly38Val,ENST00000302101,NM_005598.3; T ENST00000302101 Transcript missense_variant 559/2563 113/402 38/133 G/V gGg/gTg 1 1 NHLH1 HGNC HGNC:7817 protein_coding YES CCDS1204.1 ENSP00000302189 Q02575 Q5T203 UPI000012C5FE NM_005598.3 tolerated(0.31) 2/2 hmmpanther:PTHR13864,hmmpanther:PTHR13864:SF20,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 160370844 160370844 G T 1 0 0 0 0 1 0 0 0 10436 1232 43 2 2 NHLH1 1 160370844 Missense_Mutation SNP G C3N-00169_T 782388 160370844 88585578 12 9420 CEP350 0 . GRCh38 1 180037040 180037040 + Missense_Mutation SNP G G T rs528631741 C3N-00169_T C3N-00169_N G G c.4061G>T p.Gly1354Val p.G1354V ENST00000367607 17/38 168 151 17 154 153 1 strelka-varscan-mutect CEP350,missense_variant,p.Gly1354Val,ENST00000367607,NM_014810.4;CEP350,upstream_gene_variant,,ENST00000418229,;CEP350,upstream_gene_variant,,ENST00000490047,; T ENST00000367607 Transcript missense_variant 4479/13491 4061/9354 1354/3117 G/V gGc/gTc rs528631741 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 deleterious(0) 17/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS rs528631741 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 180037040 180037040 G T 1 0 0 0 0 1 0 0 0 2972 1203 42 2 2 CEP350 1 180037040 Missense_Mutation SNP G C3N-00169_T 19666196 180037040 68919382 13 9421 XPR1 0 . GRCh38 1 180863766 180863766 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.1560C>T p.= p.I520I ENST00000367590 12/15 102 84 18 97 97 0 strelka-mutect XPR1,synonymous_variant,p.=,ENST00000367590,NM_004736.3;XPR1,synonymous_variant,p.=,ENST00000367589,NM_001135669.1;XPR1,non_coding_transcript_exon_variant,,ENST00000464817,;XPR1,non_coding_transcript_exon_variant,,ENST00000498177,; T ENST00000367590 Transcript synonymous_variant 1758/8474 1560/2091 520/696 I atC/atT 1 1 XPR1 HGNC HGNC:12827 protein_coding YES CCDS1340.1 ENSP00000356562 Q9UBH6 A0A024R911 UPI0000071111 NM_004736.3 12/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51380,hmmpanther:PTHR10783,hmmpanther:PTHR10783:SF40,Pfam_domain:PF03124 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 180863766 180863766 C T 1 0 0 0 0 0 0 0 1 18010 816 29 3 3 XPR1 1 180863766 Silent SNP C C3N-00169_T 826726 180863766 68092656 14 9422 COLGALT2 0 . GRCh38 1 183969454 183969454 + Frame_Shift_Del DEL G G - novel C3N-00169_T C3N-00169_N G G c.647delC p.Pro216GlnfsTer25 p.P216Qfs*25 ENST00000361927 5/12 94 67 27 85 85 0 sindel-varindel-pindel COLGALT2,frameshift_variant,p.Pro216GlnfsTer25,ENST00000361927,NM_001303420.1,NM_015101.3,NM_001303421.1;COLGALT2,upstream_gene_variant,,ENST00000367520,; - ENST00000361927 Transcript frameshift_variant 1019/5177 647/1881 216/626 P/X cCa/ca 1 -1 COLGALT2 HGNC HGNC:16790 protein_coding YES CCDS1360.1 ENSP00000354960 Q8IYK4 UPI000007423A NM_001303420.1,NM_015101.3,NM_001303421.1 5/12 hmmpanther:PTHR10730,Superfamily_domains:SSF53448 HIGH 1 deletion 1 1 PASS . . 0 198 9 3 0 0 0 0 -20 0.999522 1 1 1 0 - 7 5 38 183969454 183969454 G - 1 0 1 0 1 0 0 0 0 3504 1348 47 0 0 COLGALT2 1 183969454 Frame_Shift_Del DEL G C3N-00169_T 3105688 183969454 64986968 15 9423 ASPM 0 . GRCh38 1 197101411 197101411 + Missense_Mutation SNP C C G novel C3N-00169_T C3N-00169_N C C c.7840G>C p.Asp2614His p.D2614H ENST00000367409 18/28 495 371 124 343 343 0 strelka-varscan-mutect ASPM,missense_variant,p.Asp2614His,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Asp600His,ENST00000612785,;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000367408,; G ENST00000367409 Transcript missense_variant 8097/10887 7840/10434 2614/3477 D/H Gac/Cac 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.1) 18/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 197101411 197101411 C G 1 0 0 0 0 1 0 0 0 1203 855 30 4 4 ASPM 1 197101411 Missense_Mutation SNP C C3N-00169_T 13131957 197101411 51855011 16 9424 KIF21B 0 . GRCh38 1 201002211 201002211 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.1352G>T p.Arg451Leu p.R451L ENST00000422435 9/35 227 196 31 222 222 0 strelka-varscan-mutect KIF21B,missense_variant,p.Arg451Leu,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Arg451Leu,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Arg451Leu,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Arg451Leu,ENST00000360529,NM_001252103.1;KIF21B,non_coding_transcript_exon_variant,,ENST00000534043,; A ENST00000422435 Transcript missense_variant 1669/5519 1352/4914 451/1637 R/L cGc/cTc COSM5004691,COSM5004692 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0) 9/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs953396132 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 201002211 201002211 C A 1 0 0 0 0 1 0 0 0 8154 768 27 1 1 KIF21B 1 201002211 Missense_Mutation SNP C C3N-00169_T 3900800 201002211 47954211 17 9425 PKP1 0 . GRCh38 1 201316676 201316676 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.825G>T p.Gln275His p.Q275H ENST00000263946 4/15 304 216 88 302 302 0 strelka-varscan-mutect PKP1,missense_variant,p.Gln275His,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Gln275His,ENST00000367324,NM_001005337.2;PKP1,missense_variant,p.Gln275His,ENST00000352845,;PKP1,non_coding_transcript_exon_variant,,ENST00000475988,; T ENST00000263946 Transcript missense_variant 1076/5447 825/2244 275/747 Q/H caG/caT 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 tolerated(0.08) 4/15 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs1228086490 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 201316676 201316676 G T 1 0 0 0 0 1 0 0 0 12080 991 35 2 2 PKP1 1 201316676 Missense_Mutation SNP G C3N-00169_T 314465 201316676 47639746 18 9426 LRRN2 0 . GRCh38 1 204618022 204618022 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.1971G>T p.Lys657Asn p.K657N ENST00000367175 1/1 116 78 38 117 117 0 strelka-varscan-mutect LRRN2,missense_variant,p.Lys657Asn,ENST00000367175,;LRRN2,missense_variant,p.Lys657Asn,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Lys657Asn,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; A ENST00000367175 Transcript missense_variant 4184/5036 1971/2142 657/713 K/N aaG/aaT 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC tolerated(0.32) 1/1 MODERATE SNV 1 PASS rs1449245562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 204618022 204618022 C A 1 0 0 0 0 1 0 0 0 8941 680 24 2 2 LRRN2 1 204618022 Missense_Mutation SNP C C3N-00169_T 3301346 204618022 44338400 19 9427 RYR2 0 . GRCh38 1 237674763 237674763 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.8747C>T p.Ser2916Phe p.S2916F ENST00000366574 60/105 162 139 23 127 127 0 strelka-varscan RYR2,missense_variant,p.Ser2916Phe,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ser2900Phe,ENST00000360064,;RYR2,upstream_gene_variant,,ENST00000609119,; T ENST00000366574 Transcript missense_variant 9064/16562 8747/14904 2916/4967 S/F tCt/tTt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 60/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 237674763 237674763 C T 1 0 0 0 0 1 0 0 0 14029 913 32 3 3 RYR2 1 237674763 Missense_Mutation SNP C C3N-00169_T 33056741 237674763 11281659 20 9428 ZP4 0 . GRCh38 1 237888384 237888384 + Missense_Mutation SNP A A G novel C3N-00169_T C3N-00169_N A A c.527T>C p.Val176Ala p.V176A ENST00000611898 4/13 100 72 28 104 104 0 strelka-varscan ZP4,missense_variant,p.Val176Ala,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Val176Ala,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; G ENST00000611898 Transcript missense_variant 814/2474 527/1623 176/540 V/A gTg/gCg 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 tolerated(0.32) 4/13 Gene3D:4.10.110.10,Pfam_domain:PF00088,PROSITE_profiles:PS51448,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00018,Superfamily_domains:SSF57492 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 237888384 237888384 A G 1 0 0 0 0 1 0 0 0 18810 159 6 5 5 ZP4 1 237888384 Missense_Mutation SNP A C3N-00169_T 213621 237888384 11068038 21 9429 ZNF695 0 . GRCh38 1 246987519 246987519 + Silent SNP G G A novel C3N-00169_T C3N-00169_N G G c.996C>T p.= p.V332V ENST00000339986 4/4 55 44 11 38 38 0 strelka-varscan ZNF695,synonymous_variant,p.=,ENST00000339986,NM_020394.4;ZNF695,intron_variant,,ENST00000487338,NM_001204221.1;ZNF695,intron_variant,,ENST00000498046,;ZNF670-ZNF695,intron_variant,,ENST00000474541,;ZNF670-ZNF695,intron_variant,,ENST00000465049,;ZNF695,intron_variant,,ENST00000479214,;ZNF695,intron_variant,,ENST00000366504,;ZNF695,intron_variant,,ENST00000491337,; A ENST00000339986 Transcript synonymous_variant 1144/3340 996/1548 332/515 V gtC/gtT 1 -1 ZNF695 HGNC HGNC:30954 protein_coding YES CCDS44344.1 ENSP00000341236 Q8IW36 UPI0000F734A8 NM_020394.4 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF119,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 246987519 246987519 G A 1 0 0 0 0 0 0 0 1 18671 929 33 3 3 ZNF695 1 246987519 Silent SNP G C3N-00169_T 9099135 246987519 1968903 22 9430 OR2T33 0 . GRCh38 1 248273213 248273213 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.602G>T p.Cys201Phe p.C201F ENST00000318021 1/1 166 141 25 167 167 0 strelka-varscan OR2T33,missense_variant,p.Cys201Phe,ENST00000318021,NM_001004695.1; A ENST00000318021 Transcript missense_variant 602/963 602/963 201/320 C/F tGt/tTt COSM5665580 1 -1 OR2T33 HGNC HGNC:31255 protein_coding YES CCDS31109.1 ENSP00000324687 Q8NG76 UPI000004B237 NM_001004695.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 248273213 248273213 C A 1 0 0 0 0 1 0 0 0 11101 478 17 2 2 OR2T33 1 248273213 Missense_Mutation SNP C C3N-00169_T 1285694 248273213 683209 23 9431 DCDC2C 0 . GRCh38 2 3769373 3769373 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.916G>A p.Glu306Lys p.E306K ENST00000399143 8/11 138 118 20 184 184 0 strelka-varscan-mutect DCDC2C,missense_variant,p.Glu306Lys,ENST00000399143,NM_001287444.1;DCDC2C,missense_variant,p.Glu269Lys,ENST00000423741,;DCDC2C,non_coding_transcript_exon_variant,,ENST00000537457,; A ENST00000399143 Transcript missense_variant 1076/1480 916/1095 306/364 E/K Gag/Aag 1 1 DCDC2C HGNC HGNC:32696 protein_coding YES CCDS74481.1 ENSP00000382097 A8MYV0 UPI0002742D44 NM_001287444.1 deleterious(0) 8/11 hmmpanther:PTHR23004:SF9,hmmpanther:PTHR23004 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 3769373 3769373 G A 1 0 0 0 0 1 0 0 0 4089 943 33 3 3 DCDC2C 2 3769373 Missense_Mutation SNP G C3N-00169_T 3769373 238424156 24 9432 KIDINS220 0 . GRCh38 2 8818751 8818751 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.151C>G p.Leu51Val p.L51V ENST00000256707 3/30 156 140 16 181 181 0 strelka-varscan-mutect KIDINS220,missense_variant,p.Leu51Val,ENST00000256707,NM_020738.2;KIDINS220,missense_variant,p.Leu51Val,ENST00000473731,;KIDINS220,missense_variant,p.Leu51Val,ENST00000489024,;KIDINS220,missense_variant,p.Leu51Val,ENST00000319688,;KIDINS220,3_prime_UTR_variant,,ENST00000488729,; C ENST00000256707 Transcript missense_variant 333/7361 151/5316 51/1771 L/V Ctg/Gtg 1 -1 KIDINS220 HGNC HGNC:29508 protein_coding YES CCDS42650.1 ENSP00000256707 Q9ULH0 UPI0000208E08 NM_020738.2 tolerated(0.1) 3/30 Gene3D:1.25.40.20,Pfam_domain:PF12796,Prints_domain:PR01415,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24116,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1424027142 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 8818751 8818751 G C 1 0 0 0 0 1 0 0 0 8135 933 33 4 4 KIDINS220 2 8818751 Missense_Mutation SNP G C3N-00169_T 5049378 8818751 233374778 25 9433 HS1BP3 0 . GRCh38 2 20640857 20640857 + Silent SNP G G A novel C3N-00169_T C3N-00169_N G G c.522C>T p.= p.A174A ENST00000406618 3/3 30 25 5 23 23 0 strelka-varscan-mutect HS1BP3,synonymous_variant,p.=,ENST00000406618,;HS1BP3,intron_variant,,ENST00000402541,;HS1BP3,intron_variant,,ENST00000304031,NM_022460.3;HS1BP3,intron_variant,,ENST00000446825,;HS1BP3,upstream_gene_variant,,ENST00000458740,;HS1BP3,downstream_gene_variant,,ENST00000631166,; A ENST00000406618 Transcript synonymous_variant 543/1375 522/600 174/199 A gcC/gcT 1 -1 HS1BP3 HGNC HGNC:24979 protein_coding ENSP00000385788 B5MC96 UPI0000D4A420 3/3 LOW SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -13.86242 1 1 1 1 0 A 2 1 38 20640857 20640857 G A 1 0 0 0 0 0 0 0 1 7255 1335 47 3 3 HS1BP3 2 20640857 Silent SNP G C3N-00169_T 11822106 20640857 221552672 26 9434 THADA 0 . GRCh38 2 43505736 43505736 + Splice_Site SNP C C T novel C3N-00169_T C3N-00169_N C C c.3508-1G>A p.X1170_splice ENST00000405006 91 71 20 88 88 0 strelka-varscan THADA,splice_acceptor_variant,,ENST00000405006,NM_001083953.1;THADA,splice_acceptor_variant,,ENST00000405975,NM_022065.4;THADA,splice_acceptor_variant,,ENST00000407351,;THADA,splice_acceptor_variant,,ENST00000436947,;THADA,splice_acceptor_variant,,ENST00000462185,;THADA,splice_acceptor_variant,,ENST00000398653,;THADA,splice_acceptor_variant,,ENST00000408045,;THADA,splice_acceptor_variant,,ENST00000402796,; T ENST00000405006 Transcript splice_acceptor_variant -/6310 3508/5862 1170/1953 1 -1 THADA HGNC HGNC:19217 protein_coding YES CCDS46268.1 ENSP00000385995 Q6YHU6 UPI00001C0473 NM_001083953.1 23/37 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 38 43505736 43505736 C T 1 0 0 0 0 0 0 1 0 16272 695 24 3 3 THADA 2 43505736 Splice_Site SNP C C3N-00169_T 22864879 43505736 198687793 27 9435 AMER3 0 . GRCh38 2 130762336 130762336 + Silent SNP G G T rs771546193 C3N-00169_T C3N-00169_N G G c.264G>T p.= p.P88P ENST00000423981 2/2 64 49 15 110 110 0 strelka-varscan-mutect AMER3,synonymous_variant,p.=,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,synonymous_variant,p.=,ENST00000321420,NM_152698.2;AMER3,synonymous_variant,p.=,ENST00000458606,;AMER3,synonymous_variant,p.=,ENST00000431758,; T ENST00000423981 Transcript synonymous_variant 374/6172 264/2586 88/861 P ccG/ccT rs771546193 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 LOW 1 SNV 4 1 PASS rs771546193 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 130762336 130762336 G T 1 0 0 0 0 0 0 0 1 669 1103 39 1 1 AMER3 2 130762336 Silent SNP G C3N-00169_T 87256600 130762336 111431193 28 9436 THSD7B 0 . GRCh38 2 137618461 137618461 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.3641G>C p.Cys1214Ser p.C1214S ENST00000272643 18/27 250 206 44 234 234 0 strelka-varscan-mutect THSD7B,missense_variant,p.Cys1212Ser,ENST00000409968,NM_001316349.1;THSD7B,missense_variant,p.Cys1214Ser,ENST00000272643,;THSD7B,missense_variant,p.Cys1183Ser,ENST00000413152,NM_001080427.1; C ENST00000272643 Transcript missense_variant 3641/5939 3641/4827 1214/1608 C/S tGt/tCt 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A deleterious(0) 18/27 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,SMART_domains:SM00209 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 137618461 137618461 G C 1 0 0 0 0 1 0 0 0 16314 1377 48 4 4 THSD7B 2 137618461 Missense_Mutation SNP G C3N-00169_T 6856125 137618461 104575068 29 9437 SLC4A10 0 . GRCh38 2 161862939 161862939 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.643G>A p.Glu215Lys p.E215K ENST00000446997 6/27 129 98 31 106 106 0 strelka-varscan-mutect SLC4A10,missense_variant,p.Glu226Lys,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Glu215Lys,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Glu215Lys,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Glu215Lys,ENST00000272716,;SLC4A10,missense_variant,p.Glu215Lys,ENST00000421911,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000493021,;SLC4A10,non_coding_transcript_exon_variant,,ENST00000461456,;SLC4A10,missense_variant,p.Glu215Lys,ENST00000446228,; A ENST00000446997 Transcript missense_variant 736/5551 643/3357 215/1118 E/K Gag/Aag 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 deleterious(0.05) 6/27 hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Gene3D:1hynR00,TIGRFAM_domain:TIGR00834,Pfam_domain:PF07565,Superfamily_domains:SSF55804 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 161862939 161862939 G A 1 0 0 0 0 1 0 0 0 14928 1291 45 3 3 SLC4A10 2 161862939 Missense_Mutation SNP G C3N-00169_T 24244478 161862939 80330590 30 9438 XIRP2 0 . GRCh38 2 167242944 167242945 + Frame_Shift_Ins INS - - T novel C3N-00169_T C3N-00169_N - - c.1553dupT p.Ser519GlnfsTer2 p.S519Qfs*2 ENST00000409195 9/11 108 84 24 136 136 0 sindel-varindel XIRP2,frameshift_variant,p.Ser519GlnfsTer2,ENST00000409195,NM_152381.5;XIRP2,frameshift_variant,p.Ser297GlnfsTer2,ENST00000409273,NM_001199144.1;XIRP2,frameshift_variant,p.Ser344GlnfsTer2,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript frameshift_variant 1641-1642/12675 1552-1553/10650 518/3549 I/IX atc/aTtc 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 HIGH 1 insertion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 38 167242944 167242944 - T 1 0 1 1 0 0 0 0 0 17989 449 16 0 0 XIRP2 2 167242944 Frame_Shift_Ins INS - C3N-00169_T 5380005 167242944 74950585 31 9439 SSB 0 . GRCh38 2 169811025 169811025 + Silent SNP A A T rs779625970 C3N-00169_T C3N-00169_N A A c.978A>T p.= p.L326L ENST00000409333 10/12 138 109 29 102 102 0 strelka-varscan-mutect SSB,synonymous_variant,p.=,ENST00000409333,NM_001294145.1;SSB,synonymous_variant,p.=,ENST00000260956,NM_003142.4;METTL5,intron_variant,,ENST00000409837,;SSB,downstream_gene_variant,,ENST00000422006,;METTL5,downstream_gene_variant,,ENST00000410097,;METTL5,downstream_gene_variant,,ENST00000260953,NM_014168.3;METTL5,downstream_gene_variant,,ENST00000409965,NM_001293186.1;METTL5,downstream_gene_variant,,ENST00000392640,NM_001293187.1;METTL5,downstream_gene_variant,,ENST00000308099,;SSB,downstream_gene_variant,,ENST00000417292,;METTL5,downstream_gene_variant,,ENST00000409340,;METTL5,downstream_gene_variant,,ENST00000442181,;METTL5,downstream_gene_variant,,ENST00000538491,;SSB,non_coding_transcript_exon_variant,,ENST00000490914,;METTL5,downstream_gene_variant,,ENST00000484351,;SSB,downstream_gene_variant,,ENST00000474273,;SSB,downstream_gene_variant,,ENST00000413002,;METTL5,downstream_gene_variant,,ENST00000537825,;SSB,downstream_gene_variant,,ENST00000470621,;SSB,downstream_gene_variant,,ENST00000465871,;SSB,downstream_gene_variant,,ENST00000494051,;SSB,downstream_gene_variant,,ENST00000468600,; T ENST00000409333 Transcript synonymous_variant 1225/1782 978/1227 326/408 L ctA/ctT rs779625970 1 1 SSB HGNC HGNC:11316 protein_coding YES CCDS2237.1 ENSP00000386636 P05455 UPI000012E243 NM_001294145.1 10/12 Gene3D:3.30.70.330,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF08777,hmmpanther:PTHR22792,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS rs779625970 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 169811025 169811025 A T 1 0 0 0 0 0 0 0 1 15552 349 13 4 4 SSB 2 169811025 Silent SNP A C3N-00169_T 2568081 169811025 72382504 32 9440 SP5 0 . GRCh38 2 170716550 170716550 + Frame_Shift_Del DEL C C - rs770676571 C3N-00169_T C3N-00169_N C C c.348delC p.Ala117ProfsTer197 p.A117Pfs*197 ENST00000375281 2/2 151 131 20 212 212 0 sindel-varindel SP5,frameshift_variant,p.Ala117ProfsTer197,ENST00000375281,NM_001003845.2;LINC01124,upstream_gene_variant,,ENST00000409786,;SP5,downstream_gene_variant,,ENST00000487037,; - ENST00000375281 Transcript frameshift_variant 505/2033 343/1197 115/398 P/X Ccc/cc rs770676571,COSM5513936 1 1 SP5 HGNC HGNC:14529 protein_coding YES CCDS33322.1 ENSP00000364430 Q6BEB4 UPI000015C8D6 NM_001003845.2 2/2 0,1 HIGH 1 deletion 1 5 0,1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999914 1 1 1 0 - 7 5 38 170716550 170716550 C - 1 0 1 0 1 0 0 0 0 15293 507 18 0 0 SP5 2 170716550 Frame_Shift_Del DEL C C3N-00169_T 905525 170716550 71476979 33 9441 TTN 0 . GRCh38 2 178563003 178563004 + Frame_Shift_Ins INS - - C novel C3N-00169_T C3N-00169_N - - c.83128dupG p.Glu27710GlyfsTer9 p.E27710Gfs*9 ENST00000589042 326/363 179 135 44 176 176 0 sindel-varindel-pindel TTN,frameshift_variant,p.Glu27710GlyfsTer9,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Glu26069GlyfsTer9,ENST00000591111,;TTN,frameshift_variant,p.Glu26069GlyfsTer9,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Glu25142GlyfsTer9,ENST00000342992,NM_133378.4;TTN,frameshift_variant,p.Glu18645GlyfsTer9,ENST00000460472,NM_003319.4;TTN,frameshift_variant,p.Glu18837GlyfsTer9,ENST00000342175,NM_133437.4;TTN,frameshift_variant,p.Glu18770GlyfsTer9,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,downstream_gene_variant,,ENST00000624360,; C ENST00000589042 Transcript frameshift_variant 83353-83354/109224 83128-83129/107976 27710/35991 E/GX gaa/gGaa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 38 178563003 178563003 - C 1 0 1 1 0 0 0 0 0 17245 1783 62 0 0 TTN 2 178563003 Frame_Shift_Ins INS - C3N-00169_T 7846453 178563003 63630526 34 9442 CERKL 0 . GRCh38 2 181558633 181558654 + Frame_Shift_Del DEL AGCATTCTTCTGAGCTCTCAGA AGCATTCTTCTGAGCTCTCAGA - novel C3N-00169_T C3N-00169_N AGCATTCTTCTGAGCTCTCAGA AGCATTCTTCTGAGCTCTCAGA c.810_831delTCTGAGAGCTCAGAAGAATGCT p.Leu271GlyfsTer8 p.L271Gfs*8 ENST00000339098 6/14 408 346 62 467 467 0 sindel-pindel CERKL,frameshift_variant,p.Leu245GlyfsTer8,ENST00000410087,NM_201548.4;CERKL,frameshift_variant,p.Leu227GlyfsTer8,ENST00000409440,NM_001160277.1;CERKL,frameshift_variant,p.Leu271GlyfsTer8,ENST00000339098,NM_001030311.2;CERKL,intron_variant,,ENST00000374970,NM_001030313.2;CERKL,intron_variant,,ENST00000374969,NM_001030312.2;CERKL,non_coding_transcript_exon_variant,,ENST00000479558,;CERKL,non_coding_transcript_exon_variant,,ENST00000466715,;CERKL,3_prime_UTR_variant,,ENST00000374967,;CERKL,3_prime_UTR_variant,,ENST00000452174,;CERKL,3_prime_UTR_variant,,ENST00000421817,;CERKL,non_coding_transcript_exon_variant,,ENST00000494398,; - ENST00000339098 Transcript frameshift_variant 810-831/1677 810-831/1677 270-277/558 LLRAQKNA/X ctTCTGAGAGCTCAGAAGAATGCT/ct 1 -1 CERKL HGNC HGNC:21699 protein_coding YES CCDS42789.1 ENSP00000341159 Q49MI3 UPI000057259A NM_001030311.2 6/14 PROSITE_profiles:PS50146,hmmpanther:PTHR12358:SF26,hmmpanther:PTHR12358,Pfam_domain:PF00781,Superfamily_domains:SSF111331 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 38 181558633 181558633 AGCATTCTTCTGAGCTCTCAGA - 1 0 1 0 1 0 0 0 0 2994 175 7 0 0 CERKL 2 181558633 Frame_Shift_Del DEL AGCATTCTTCTGAGCTCTCAGA C3N-00169_T 2995630 181558633 60634896 35 9443 FSIP2 0 . GRCh38 2 185803540 185803540 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.14501C>A p.Pro4834Gln p.P4834Q ENST00000343098 17/23 81 67 14 64 64 0 strelka-varscan-mutect FSIP2,missense_variant,p.Pro4834Gln,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Pro4745Gln,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 14501/21054 14501/20991 4834/6996 P/Q cCa/cAa 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 185803540 185803540 C A 1 0 0 0 0 1 0 0 0 5949 594 21 2 2 FSIP2 2 185803540 Missense_Mutation SNP C C3N-00169_T 4244907 185803540 56389989 36 9444 GBX2 0 . GRCh38 2 236167764 236167764 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.208C>G p.Leu70Val p.L70V ENST00000306318 1/2 69 53 16 79 79 0 strelka-varscan-mutect GBX2,missense_variant,p.Leu70Val,ENST00000306318,NM_001485.3;GBX2,missense_variant,p.Leu70Val,ENST00000551105,NM_001301687.1;AC079135.1,intron_variant,,ENST00000483218,;AC079135.1,intron_variant,,ENST00000415226,;GBX2,upstream_gene_variant,,ENST00000465889,; C ENST00000306318 Transcript missense_variant 606/2123 208/1047 70/348 L/V Ctg/Gtg 1 -1 GBX2 HGNC HGNC:4186 protein_coding YES CCDS2515.1 ENSP00000302251 P52951 UPI000012B273 NM_001485.3 tolerated(0.17) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24334,hmmpanther:PTHR24334:SF3 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 236167764 236167764 G C 1 0 0 0 0 1 0 0 0 6151 962 34 4 4 GBX2 2 236167764 Missense_Mutation SNP G C3N-00169_T 50364224 236167764 6025765 37 9445 TRAF3IP1 0 . GRCh38 2 238356065 238356065 + Silent SNP C C G novel C3N-00169_T C3N-00169_N C C c.1674C>G p.= p.P558P ENST00000373327 15/17 197 157 40 180 180 0 strelka-varscan-mutect TRAF3IP1,synonymous_variant,p.=,ENST00000373327,NM_015650.3;TRAF3IP1,synonymous_variant,p.=,ENST00000391993,NM_001139490.1;TRAF3IP1,non_coding_transcript_exon_variant,,ENST00000462122,; G ENST00000373327 Transcript synonymous_variant 1896/4279 1674/2076 558/691 P ccC/ccG 1 1 TRAF3IP1 HGNC HGNC:17861 protein_coding YES CCDS33415.1 ENSP00000362424 Q8TDR0 UPI0000070E5D NM_015650.3 15/17 Pfam_domain:PF10243,hmmpanther:PTHR31363,hmmpanther:PTHR31363:SF0 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 238356065 238356065 C G 1 0 0 0 0 0 0 0 1 16923 581 21 4 4 TRAF3IP1 2 238356065 Silent SNP C C3N-00169_T 2188301 238356065 3837464 38 9446 CROCC2 0 . GRCh38 2 240963676 240963676 + Silent SNP C C A novel C3N-00169_T C3N-00169_N C C c.3214C>A p.= p.R1072R ENST00000443866 21/32 337 273 64 382 382 0 strelka-varscan-mutect CROCC2,synonymous_variant,p.=,ENST00000443866,;AC104809.4,non_coding_transcript_exon_variant,,ENST00000418218,;AC104809.4,upstream_gene_variant,,ENST00000457369,;AC104809.4,upstream_gene_variant,,ENST00000438506,; A ENST00000443866 Transcript synonymous_variant 3398/5382 3214/4968 1072/1655 R Cgg/Agg 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A 21/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 LOW SNV 5 1 PASS rs939804732 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 240963676 240963676 C A 1 0 0 0 0 0 0 0 1 3695 643 23 1 1 CROCC2 2 240963676 Silent SNP C C3N-00169_T 2607611 240963676 1229853 39 9447 THAP4 0 . GRCh38 2 241601943 241601943 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1567C>T p.His523Tyr p.H523Y ENST00000407315 5/6 171 138 33 232 232 0 strelka-varscan-mutect THAP4,missense_variant,p.His523Tyr,ENST00000407315,NM_015963.5;THAP4,missense_variant,p.His111Tyr,ENST00000402545,;THAP4,missense_variant,p.His111Tyr,ENST00000402136,NM_001164356.1;THAP4,intron_variant,,ENST00000612200,;THAP4,non_coding_transcript_exon_variant,,ENST00000497486,;THAP4,non_coding_transcript_exon_variant,,ENST00000321679,; A ENST00000407315 Transcript missense_variant 1999/2367 1567/1734 523/577 H/Y Cac/Tac 1 -1 THAP4 HGNC HGNC:23187 protein_coding YES CCDS2551.1 ENSP00000385006 Q8WY91 UPI000018DBC4 NM_015963.5 deleterious(0.01) 5/6 hmmpanther:PTHR15854,hmmpanther:PTHR15854:SF4,Pfam_domain:PF08768,Superfamily_domains:SSF50814 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 241601943 241601943 G A 1 0 0 0 0 1 0 0 0 16279 1348 47 3 3 THAP4 2 241601943 Missense_Mutation SNP G C3N-00169_T 638267 241601943 591586 40 9448 AMIGO3 0 . GRCh38 3 49718578 49718578 + Silent SNP C C T C3N-00169_T C3N-00169_N C C c.888G>A p.= p.L296L ENST00000320431 1/1 320 277 43 404 404 0 strelka-varscan-mutect AMIGO3,synonymous_variant,p.=,ENST00000320431,NM_198722.2;GMPPB,3_prime_UTR_variant,,ENST00000480687,;RNF123,intron_variant,,ENST00000327697,NM_022064.3;RNF123,intron_variant,,ENST00000433785,;GMPPB,downstream_gene_variant,,ENST00000308375,NM_013334.3;GMPPB,downstream_gene_variant,,ENST00000308388,NM_021971.2;RNF123,non_coding_transcript_exon_variant,,ENST00000497099,;RNF123,intron_variant,,ENST00000487805,;RNF123,intron_variant,,ENST00000486102,;RNF123,intron_variant,,ENST00000457726,;GMPPB,downstream_gene_variant,,ENST00000481959,;RNF123,downstream_gene_variant,,ENST00000469978,;RNF123,upstream_gene_variant,,ENST00000498376,;GMPPB,downstream_gene_variant,,ENST00000495627,;RNF123,downstream_gene_variant,,ENST00000444689,; T ENST00000320431 Transcript synonymous_variant 1118/2862 888/1515 296/504 L ctG/ctA COSM1309281 1 -1 AMIGO3 HGNC HGNC:24075 protein_coding YES CCDS33759.1 ENSP00000323096 Q86WK7 UPI00000622D6 NM_198722.2 1/1 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR24368,hmmpanther:PTHR24368:SF62,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 LOW SNV 1 1 PASS rs1466765082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 49718578 49718578 C T 1 0 0 0 0 0 0 0 1 675 813 29 3 3 AMIGO3 3 49718578 Silent SNP C C3N-00169_T 49718578 148576981 41 9449 RBM15B 0 . GRCh38 3 51392714 51392714 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1315G>A p.Asp439Asn p.D439N ENST00000563281 1/1 137 127 10 187 187 0 strelka-varscan-mutect RBM15B,missense_variant,p.Asp439Asn,ENST00000563281,NM_013286.4;DCAF1,downstream_gene_variant,,ENST00000504652,NM_001171904.1;DCAF1,downstream_gene_variant,,ENST00000423656,NM_014703.2;MANF,downstream_gene_variant,,ENST00000528157,NM_006010.5;MANF,downstream_gene_variant,,ENST00000470900,;MANF,downstream_gene_variant,,ENST00000446668,;MANF,downstream_gene_variant,,ENST00000482262,; A ENST00000563281 Transcript missense_variant 1447/6641 1315/2673 439/890 D/N Gac/Aac 1 1 RBM15B HGNC HGNC:24303 protein_coding YES CCDS33764.1 ENSP00000454545 Q8NDT2 UPI0000160BDE NM_013286.4 deleterious(0) 1/1 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF40,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 51392714 51392714 G A 1 0 0 0 0 1 0 0 0 13283 1290 45 3 3 RBM15B 3 51392714 Missense_Mutation SNP G C3N-00169_T 1674136 51392714 146902845 42 9450 ADCY5 0 . GRCh38 3 123447749 123447749 + Missense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.797T>A p.Leu266His p.L266H ENST00000462833 1/21 109 85 24 102 102 0 strelka-varscan-mutect ADCY5,missense_variant,p.Leu266His,ENST00000462833,NM_183357.2; T ENST00000462833 Transcript missense_variant 2010/7311 797/3786 266/1261 L/H cTc/cAc 1 -1 ADCY5 HGNC HGNC:236 protein_coding YES CCDS3022.1 ENSP00000419361 O95622 UPI000015E262 NM_183357.2 tolerated(0.54) 1/21 Pfam_domain:PF16214,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF332 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 123447749 123447749 A T 1 0 0 0 0 1 0 0 0 341 304 11 4 4 ADCY5 3 123447749 Missense_Mutation SNP A C3N-00169_T 72055035 123447749 74847810 43 9451 TPRA1 0 . GRCh38 3 127580058 127580058 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.89G>A p.Cys30Tyr p.C30Y ENST00000355552 2/11 237 198 39 261 261 0 strelka-varscan-mutect TPRA1,missense_variant,p.Cys30Tyr,ENST00000355552,NM_001136053.2;TPRA1,missense_variant,p.Cys30Tyr,ENST00000489960,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000450633,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000296210,NM_001142646.2;TPRA1,missense_variant,p.Cys30Tyr,ENST00000469111,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000490290,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000490643,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000462228,;MIR6825,upstream_gene_variant,,ENST00000618505,;TPRA1,upstream_gene_variant,,ENST00000465915,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000393400,;TPRA1,missense_variant,p.Cys30Tyr,ENST00000483868,; T ENST00000355552 Transcript missense_variant 466/1933 89/1122 30/373 C/Y tGc/tAc 1 -1 TPRA1 HGNC HGNC:30413 protein_coding YES CCDS3042.1 ENSP00000347748 Q86W33 UPI00000373F2 NM_001136053.2 deleterious(0) 2/11 hmmpanther:PTHR15876,hmmpanther:PTHR15876:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 127580058 127580058 C T 1 0 0 0 0 1 0 0 0 16898 710 25 3 3 TPRA1 3 127580058 Missense_Mutation SNP C C3N-00169_T 4132309 127580058 70715501 44 9452 XRN1 0 . GRCh38 3 142405053 142405053 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.1737G>T p.Glu579Asp p.E579D ENST00000264951 16/42 182 144 38 150 150 0 strelka-varscan-mutect XRN1,missense_variant,p.Glu579Asp,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Glu45Asp,ENST00000498077,;XRN1,missense_variant,p.Glu579Asp,ENST00000392981,NM_001282857.1;RNU6-1294P,downstream_gene_variant,,ENST00000515995,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,; A ENST00000264951 Transcript missense_variant 1855/10143 1737/5121 579/1706 E/D gaG/gaT 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 tolerated(0.06) 16/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 142405053 142405053 C A 1 0 0 0 0 1 0 0 0 18017 912 32 2 2 XRN1 3 142405053 Missense_Mutation SNP C C3N-00169_T 14824995 142405053 55890506 45 9453 P2RY13 0 . GRCh38 3 151328194 151328194 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.862G>T p.Asp288Tyr p.D288Y ENST00000325602 2/2 113 84 29 86 86 0 strelka-varscan-mutect P2RY13,missense_variant,p.Asp288Tyr,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; A ENST00000325602 Transcript missense_variant 882/2764 862/1065 288/354 D/Y Gac/Tac COSM1484733,COSM1484734 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 151328194 151328194 C A 1 0 0 0 0 1 0 0 0 11423 826 29 2 2 P2RY13 3 151328194 Missense_Mutation SNP C C3N-00169_T 8923141 151328194 46967365 46 9454 IGSF10 0 . GRCh38 3 151448612 151448612 + Nonsense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1369C>T p.Gln457Ter p.Q457* ENST00000282466 4/6 264 218 46 260 260 0 strelka-varscan-mutect IGSF10,stop_gained,p.Gln457Ter,ENST00000282466,NM_178822.4; A ENST00000282466 Transcript stop_gained 1369/11067 1369/7872 457/2623 Q/* Caa/Taa 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 4/6 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 151448612 151448612 G A 1 0 0 0 0 0 1 0 0 7504 1299 45 3 3 IGSF10 3 151448612 Nonsense_Mutation SNP G C3N-00169_T 120418 151448612 46846947 47 9455 IQCJ 0 . GRCh38 3 159265269 159265269 + Missense_Mutation SNP T T C novel C3N-00169_T C3N-00169_N T T c.346T>C p.Ser116Pro p.S116P ENST00000451172 5/5 157 126 31 166 166 0 strelka-varscan-mutect IQCJ,missense_variant,p.Ser89Pro,ENST00000482126,NM_001197100.1;IQCJ,missense_variant,p.Ser116Pro,ENST00000451172,NM_001042705.2;IQCJ-SCHIP1,intron_variant,,ENST00000485419,NM_001197113.1;IQCJ-SCHIP1,intron_variant,,ENST00000476809,NM_001197114.1;IQCJ,downstream_gene_variant,,ENST00000397832,NM_001042706.2;IQCJ,downstream_gene_variant,,ENST00000481796,; C ENST00000451172 Transcript missense_variant 451/885 346/480 116/159 S/P Tca/Cca 1 1 IQCJ HGNC HGNC:32406 protein_coding YES CCDS46946.1 ENSP00000402153 Q1A5X6 UPI0000D7E3A6 NM_001042705.2 tolerated_low_confidence(0.08) 5/5 Pfam_domain:PF15157,hmmpanther:PTHR35976 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 159265269 159265269 T C 1 0 0 0 0 1 0 0 0 7718 1667 58 5 5 IQCJ 3 159265269 Missense_Mutation SNP T C3N-00169_T 7816657 159265269 39030290 48 9456 ZBBX 0 . GRCh38 3 167305774 167305774 + Missense_Mutation SNP A A T rs771690201 C3N-00169_T C3N-00169_N A A c.1594T>A p.Leu532Met p.L532M ENST00000455345 16/21 168 154 14 120 120 0 strelka-varscan-mutect ZBBX,missense_variant,p.Leu532Met,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Leu532Met,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Leu532Met,ENST00000307529,;ZBBX,missense_variant,p.Leu503Met,ENST00000392767,;ZBBX,missense_variant,p.Leu503Met,ENST00000392764,NM_001199202.1; T ENST00000455345 Transcript missense_variant 1878/3185 1594/2520 532/839 L/M Ttg/Atg rs771690201 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 deleterious(0) 16/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS rs771690201 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 167305774 167305774 A T 1 0 0 0 0 1 0 0 0 18078 11 1 4 4 ZBBX 3 167305774 Missense_Mutation SNP A C3N-00169_T 8040505 167305774 30989785 49 9457 36 2 ZBBX 0 . GRCh38 3 167305776 167305776 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1592C>A p.Thr531Asn p.T531N ENST00000455345 16/21 169 156 13 115 115 0 strelka-varscan-mutect ZBBX,missense_variant,p.Thr531Asn,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Thr531Asn,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Thr531Asn,ENST00000307529,;ZBBX,missense_variant,p.Thr502Asn,ENST00000392767,;ZBBX,missense_variant,p.Thr502Asn,ENST00000392764,NM_001199202.1; T ENST00000455345 Transcript missense_variant 1876/3185 1592/2520 531/839 T/N aCt/aAt 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 tolerated(0.13) 16/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 167305776 167305776 G T 1 0 0 0 0 1 0 0 0 18078 1029 36 2 2 ZBBX 3 167305776 Missense_Mutation SNP G C3N-00169_T 2 167305776 30989783 50 9458 36 2 CCDC39 0 . GRCh38 3 180648342 180648342 + Silent SNP C C A C3N-00169_T C3N-00169_N C C c.1185G>T p.= p.L395L ENST00000442201 10/20 41 32 9 16 16 0 strelka-varscan-mutect CCDC39,synonymous_variant,p.=,ENST00000442201,NM_181426.1;CCDC39,synonymous_variant,p.=,ENST00000476379,; A ENST00000442201 Transcript synonymous_variant 1305/3279 1185/2826 395/941 L ctG/ctT COSM582773,COSM582774 1 -1 CCDC39 HGNC HGNC:25244 protein_coding YES CCDS46964.1 ENSP00000405708 Q9UFE4 UPI00015D7298 NM_181426.1 10/20 Low_complexity_(Seg):seg,hmmpanther:PTHR18962,hmmpanther:PTHR18962:SF0 1,1 LOW 1 SNV 2 1,1 1 PASS . . 1 207 2 0 0 0 0 0 -19.99941 1 1 1 1 0 A 2 1 38 180648342 180648342 C A 1 0 0 0 0 0 0 0 1 2520 813 29 2 2 CCDC39 3 180648342 Silent SNP C C3N-00169_T 13342566 180648342 17647217 51 9459 ABCC5 0 . GRCh38 3 183971790 183971790 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1534C>A p.Leu512Met p.L512M ENST00000334444 11/30 362 325 37 390 390 0 strelka-varscan ABCC5,missense_variant,p.Leu512Met,ENST00000334444,NM_005688.2;ABCC5,missense_variant,p.Leu512Met,ENST00000265586,;ABCC5,3_prime_UTR_variant,,ENST00000437205,NM_001320032.1;ABCC5,non_coding_transcript_exon_variant,,ENST00000476402,; T ENST00000334444 Transcript missense_variant 1775/5921 1534/4314 512/1437 L/M Ctg/Atg 1 -1 ABCC5 HGNC HGNC:56 protein_coding YES CCDS43176.1 ENSP00000333926 O15440 UPI000004A33C NM_005688.2 tolerated(0.11) 11/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 183971790 183971790 G T 1 0 0 0 0 1 0 0 0 60 962 34 2 2 ABCC5 3 183971790 Missense_Mutation SNP G C3N-00169_T 3323448 183971790 14323769 52 9460 TNIP2 0 . GRCh38 4 2744858 2744858 + Nonsense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.745C>T p.Gln249Ter p.Q249* ENST00000315423 4/6 187 152 35 186 186 0 strelka-varscan-mutect TNIP2,stop_gained,p.Gln142Ter,ENST00000510267,NM_001161527.1;TNIP2,stop_gained,p.Gln249Ter,ENST00000315423,NM_024309.3;TNIP2,intron_variant,,ENST00000503235,NM_001292016.1;TNIP2,non_coding_transcript_exon_variant,,ENST00000505186,;TNIP2,non_coding_transcript_exon_variant,,ENST00000502256,;TNIP2,downstream_gene_variant,,ENST00000511352,;TNIP2,downstream_gene_variant,,ENST00000507686,; A ENST00000315423 Transcript stop_gained 832/1974 745/1290 249/429 Q/* Cag/Tag 1 -1 TNIP2 HGNC HGNC:19118 protein_coding YES CCDS3362.1 ENSP00000321203 Q8NFZ5 UPI00000702D2 NM_024309.3 4/6 hmmpanther:PTHR31882 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 2744858 2744858 G A 1 0 0 0 0 0 1 0 0 16788 1328 46 3 3 TNIP2 4 2744858 Nonsense_Mutation SNP G C3N-00169_T 2744858 187469697 53 9461 PCDH7 0 . GRCh38 4 30722589 30722589 + Missense_Mutation SNP C C G novel C3N-00169_T C3N-00169_N C C c.1167C>G p.Asp389Glu p.D389E ENST00000543491 1/1 248 197 51 257 257 0 strelka-varscan-mutect PCDH7,missense_variant,p.Asp79Glu,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,missense_variant,p.Asp389Glu,ENST00000361762,NM_002589.2;PCDH7,missense_variant,p.Asp389Glu,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; G ENST00000543491 Transcript missense_variant 1737/4457 1167/3219 389/1072 D/E gaC/gaG 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 deleterious(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF321,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 30722589 30722589 C G 1 0 0 0 0 1 0 0 0 11603 506 18 4 4 PCDH7 4 30722589 Missense_Mutation SNP C C3N-00169_T 27977731 30722589 159491966 54 9462 GABRA2 0 . GRCh38 4 46250379 46250379 + Missense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.1285T>A p.Phe429Ile p.F429I ENST00000510861 10/10 174 137 37 168 168 0 strelka-varscan-mutect GABRA2,missense_variant,p.Phe429Ile,ENST00000510861,;GABRA2,missense_variant,p.Phe429Ile,ENST00000514090,;GABRA2,missense_variant,p.Phe429Ile,ENST00000356504,NM_001114175.1;GABRA2,missense_variant,p.Phe405Ile,ENST00000540012,NM_001286827.1;GABRA2,missense_variant,p.Phe429Ile,ENST00000381620,NM_000807.2;GABRA2,missense_variant,p.Phe489Ile,ENST00000507069,;GABRA2,3_prime_UTR_variant,,ENST00000630416,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;GABRA2,3_prime_UTR_variant,,ENST00000513005,; T ENST00000510861 Transcript missense_variant 1459/3411 1285/1356 429/451 F/I Ttt/Att 1 -1 GABRA2 HGNC HGNC:4076 protein_coding YES CCDS3471.1 ENSP00000421828 P47869 A0A024R9X6 UPI000013DC88 deleterious(0) 10/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF218,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00253 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 46250379 46250379 A T 1 0 0 0 0 1 0 0 0 6032 43 2 4 4 GABRA2 4 46250379 Missense_Mutation SNP A C3N-00169_T 15527790 46250379 143964176 55 9463 FRYL 0 . GRCh38 4 48623175 48623175 + Missense_Mutation SNP T T G novel C3N-00169_T C3N-00169_N T T c.125A>C p.Lys42Thr p.K42T ENST00000358350 5/64 85 65 20 62 62 0 strelka-varscan-mutect FRYL,missense_variant,p.Lys42Thr,ENST00000358350,NM_015030.1;FRYL,missense_variant,p.Lys42Thr,ENST00000503238,;FRYL,missense_variant,p.Lys42Thr,ENST00000507711,;FRYL,missense_variant,p.Lys134Thr,ENST00000505759,;FRYL,non_coding_transcript_exon_variant,,ENST00000302806,; G ENST00000358350 Transcript missense_variant 730/11706 125/9042 42/3013 K/T aAg/aCg 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 deleterious(0) 5/64 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 48623175 48623175 T G 1 0 0 0 0 1 0 0 0 5936 1623 56 5 5 FRYL 4 48623175 Missense_Mutation SNP T C3N-00169_T 2372796 48623175 141591380 56 9464 KIAA1211 0 . GRCh38 4 56314655 56314655 + Missense_Mutation SNP G G A rs78564111 C3N-00169_T C3N-00169_N G G c.1153G>A p.Ala385Thr p.A385T ENST00000504228 6/9 65 59 6 62 62 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Ala385Thr,ENST00000504228,;KIAA1211,missense_variant,p.Ala378Thr,ENST00000541073,;KIAA1211,missense_variant,p.Ala385Thr,ENST00000264229,NM_020722.1;KIAA1211,missense_variant,p.Ala385Thr,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; A ENST00000504228 Transcript missense_variant 1258/4628 1153/3702 385/1233 A/T Gcg/Acg rs78564111 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 tolerated(0.58) 6/9 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs78564111 . 0 204 6 0 0 0 0 0 -13.67507 0.9999998 1 1 1 0 A 3 1 38 56314655 56314655 G A 1 0 0 0 0 1 0 0 0 8107 1203 42 3 3 KIAA1211 4 56314655 Missense_Mutation SNP G C3N-00169_T 7691480 56314655 133899900 57 9465 ADGRL3 0 . GRCh38 4 61948192 61948192 + Silent SNP C C A C3N-00169_T C3N-00169_N C C c.2517C>A p.= p.L839L ENST00000514591 16/25 143 114 29 202 202 0 strelka-varscan-mutect ADGRL3,synonymous_variant,p.=,ENST00000512091,NM_001322246.1;ADGRL3,synonymous_variant,p.=,ENST00000514591,NM_015236.4;ADGRL3,synonymous_variant,p.=,ENST00000509896,;ADGRL3,synonymous_variant,p.=,ENST00000511324,;ADGRL3,synonymous_variant,p.=,ENST00000508693,;ADGRL3,synonymous_variant,p.=,ENST00000507164,;ADGRL3,synonymous_variant,p.=,ENST00000506720,;ADGRL3,synonymous_variant,p.=,ENST00000506746,;ADGRL3,synonymous_variant,p.=,ENST00000507625,;ADGRL3,synonymous_variant,p.=,ENST00000506700,;ADGRL3,synonymous_variant,p.=,ENST00000504896,;ADGRL3,synonymous_variant,p.=,ENST00000514157,;ADGRL3,synonymous_variant,p.=,ENST00000508946,;ADGRL3,synonymous_variant,p.=,ENST00000514996,;ADGRL3,synonymous_variant,p.=,ENST00000502815,;ADGRL3,downstream_gene_variant,,ENST00000508078,; A ENST00000514591 Transcript synonymous_variant 2846/6297 2517/4410 839/1469 L ctC/ctA COSM5668241,COSM5668242,COSM5668243,COSM5668244 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 16/25 PROSITE_profiles:PS50221,hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF01825,SMART_domains:SM00303 1,1,1,1 LOW 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 61948192 61948192 C A 1 0 0 0 0 0 0 0 1 377 842 30 2 2 ADGRL3 4 61948192 Silent SNP C C3N-00169_T 5633537 61948192 128266363 58 9466 UGT2B11 0 . GRCh38 4 69205494 69205494 + Missense_Mutation SNP T T C novel C3N-00169_T C3N-00169_N T T c.1076A>G p.Gln359Arg p.Q359R ENST00000446444 4/6 259 244 15 240 240 0 varscan-mutect UGT2B11,missense_variant,p.Gln359Arg,ENST00000446444,NM_001073.1;RP11-704M14.1,intron_variant,,ENST00000505646,;RP11-704M14.1,intron_variant,,ENST00000504301,;UGT2B11,non_coding_transcript_exon_variant,,ENST00000513315,; C ENST00000446444 Transcript missense_variant 1085/2088 1076/1590 359/529 Q/R cAg/cGg 1 -1 UGT2B11 HGNC HGNC:12545 protein_coding YES CCDS3527.1 ENSP00000387683 O75310 UPI0000137A97 NM_001073.1 deleterious(0.02) 4/6 Gene3D:3.40.50.2000,Pfam_domain:PF00201,PROSITE_patterns:PS00375,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF365,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs1459033250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 69205494 69205494 T C 1 0 0 0 0 1 0 0 0 17481 1580 55 5 5 UGT2B11 4 69205494 Missense_Mutation SNP T C3N-00169_T 7257302 69205494 121009061 59 9467 DMP1 0 . GRCh38 4 87662912 87662912 + Missense_Mutation SNP G G T rs754686792 C3N-00169_T C3N-00169_N G G c.1134G>T p.Gln378His p.Q378H ENST00000339673 6/6 227 173 54 141 141 0 strelka-varscan-mutect DMP1,missense_variant,p.Gln378His,ENST00000339673,NM_004407.3;DMP1,missense_variant,p.Gln362His,ENST00000282479,NM_001079911.2;RP11-742B18.1,intron_variant,,ENST00000506480,;RP11-742B18.1,intron_variant,,ENST00000507894,;RP11-742B18.1,upstream_gene_variant,,ENST00000506814,; T ENST00000339673 Transcript missense_variant 1233/2682 1134/1542 378/513 Q/H caG/caT rs754686792,COSM3918310 1 1 DMP1 HGNC HGNC:2932 protein_coding YES CCDS3623.1 ENSP00000340935 Q13316 UPI00001294DE NM_004407.3 deleterious(0.01) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR23400,hmmpanther:PTHR23400:SF0,Pfam_domain:PF07263 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754686792 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 87662912 87662912 G T 1 0 0 0 0 1 0 0 0 4390 991 35 2 2 DMP1 4 87662912 Missense_Mutation SNP G C3N-00169_T 18457418 87662912 102551643 60 9468 SLC9B2 0 . GRCh38 4 103044942 103044942 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.944C>G p.Ala315Gly p.A315G ENST00000394785 8/12 229 200 29 209 209 0 strelka-varscan-mutect SLC9B2,missense_variant,p.Ala315Gly,ENST00000394785,NM_178833.5;SLC9B2,missense_variant,p.Ala315Gly,ENST00000362026,;SLC9B2,missense_variant,p.Ala258Gly,ENST00000503103,NM_001300756.1;SLC9B2,missense_variant,p.Ala258Gly,ENST00000503230,NM_001300754.1;SLC9B2,missense_variant,p.Ala215Gly,ENST00000506288,;SLC9B2,non_coding_transcript_exon_variant,,ENST00000510976,;SLC9B2,downstream_gene_variant,,ENST00000515424,; C ENST00000394785 Transcript missense_variant 1576/3126 944/1614 315/537 A/G gCa/gGa 1 -1 SLC9B2 HGNC HGNC:25143 protein_coding YES CCDS3662.1 ENSP00000378265 Q86UD5 A0A024RDJ7 UPI000020B27F NM_178833.5 tolerated(0.24) 8/12 Pfam_domain:PF00999,hmmpanther:PTHR31102,hmmpanther:PTHR31102:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 103044942 103044942 G C 1 0 0 0 0 1 0 0 0 15005 1319 46 4 4 SLC9B2 4 103044942 Missense_Mutation SNP G C3N-00169_T 15382030 103044942 87169613 61 9469 HSPA4L 0 . GRCh38 4 127803796 127803796 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.831G>A p.Met277Ile p.M277I ENST00000296464 7/19 205 167 38 148 148 0 strelka-varscan-mutect HSPA4L,missense_variant,p.Met277Ile,ENST00000296464,NM_014278.2;HSPA4L,missense_variant,p.Met277Ile,ENST00000508776,;HSPA4L,missense_variant,p.Met251Ile,ENST00000505726,;HSPA4L,missense_variant,p.Met236Ile,ENST00000508549,; A ENST00000296464 Transcript missense_variant 1242/10790 831/2520 277/839 M/I atG/atA 1 1 HSPA4L HGNC HGNC:17041 protein_coding YES CCDS3734.1 ENSP00000296464 O95757 A0A140VKE7 UPI000007452A NM_014278.2 deleterious(0) 7/19 hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF161,Pfam_domain:PF00012,Gene3D:3.90.640.10,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs1444916011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 127803796 127803796 G A 1 0 0 0 0 1 0 0 0 7309 1290 45 3 3 HSPA4L 4 127803796 Missense_Mutation SNP G C3N-00169_T 24758854 127803796 62410759 62 9470 FREM3 0 . GRCh38 4 143697295 143697295 + Silent SNP T T A novel C3N-00169_T C3N-00169_N T T c.3381A>T p.= p.S1127S ENST00000329798 1/8 167 138 29 137 137 0 strelka-varscan-mutect FREM3,synonymous_variant,p.=,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; A ENST00000329798 Transcript synonymous_variant 3381/6729 3381/6420 1127/2139 S tcA/tcT 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 1/8 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 LOW SNV 5 1 PASS rs1226970332 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 143697295 143697295 T A 1 0 0 0 0 0 0 0 1 5913 1799 63 4 4 FREM3 4 143697295 Silent SNP T C3N-00169_T 15893499 143697295 46517260 63 9471 VEGFC 0 . GRCh38 4 176727904 176727904 + Missense_Mutation SNP C C A rs867744061 C3N-00169_T C3N-00169_N C C c.426G>T p.Lys142Asn p.K142N ENST00000618562 3/7 169 133 36 145 145 0 strelka-varscan-mutect VEGFC,missense_variant,p.Lys142Asn,ENST00000618562,NM_005429.4;VEGFC,non_coding_transcript_exon_variant,,ENST00000507638,; A ENST00000618562 Transcript missense_variant 842/2064 426/1260 142/419 K/N aaG/aaT rs867744061 1 -1 VEGFC HGNC HGNC:12682 protein_coding YES CCDS43285.1 ENSP00000480043 P49767 UPI0000001C2A NM_005429.4 deleterious(0) 3/7 PROSITE_profiles:PS50278,hmmpanther:PTHR12025:SF3,hmmpanther:PTHR12025,Pfam_domain:PF00341,Gene3D:2.10.90.10,SMART_domains:SM00141,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS rs867744061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 176727904 176727904 C A 1 0 0 0 0 1 0 0 0 17697 680 24 2 2 VEGFC 4 176727904 Missense_Mutation SNP C C3N-00169_T 33030609 176727904 13486651 64 9472 ADCY2 0 . GRCh38 5 7698374 7698374 + Missense_Mutation SNP A A G novel C3N-00169_T C3N-00169_N A A c.1109A>G p.Lys370Arg p.K370R ENST00000338316 7/25 385 329 56 338 338 0 strelka-varscan-mutect ADCY2,missense_variant,p.Lys370Arg,ENST00000338316,NM_020546.2;ADCY2,downstream_gene_variant,,ENST00000515681,; G ENST00000338316 Transcript missense_variant,splice_region_variant 1198/6575 1109/3276 370/1091 K/R aAg/aGg 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 tolerated(0.19) 7/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 7698374 7698374 A G 1 0 0 0 0 1 0 0 0 338 86 3 5 5 ADCY2 5 7698374 Missense_Mutation SNP A C3N-00169_T 7698374 173839885 65 9473 ZFR 0 . GRCh38 5 32419962 32419962 + Silent SNP A A G novel C3N-00169_T C3N-00169_N A A c.279T>C p.= p.A93A ENST00000265069 3/20 196 162 34 141 141 0 strelka-varscan ZFR,synonymous_variant,p.=,ENST00000265069,NM_016107.3;ZFR,non_coding_transcript_exon_variant,,ENST00000505366,;ZFR,non_coding_transcript_exon_variant,,ENST00000505204,; G ENST00000265069 Transcript synonymous_variant 382/4738 279/3225 93/1074 A gcT/gcC 1 -1 ZFR HGNC HGNC:17277 protein_coding YES CCDS34139.1 ENSP00000265069 Q96KR1 UPI00001BBB38 NM_016107.3 3/20 Low_complexity_(Seg):seg,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF87 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 32419962 32419962 A G 1 0 0 0 0 0 0 0 1 18237 291 11 5 5 ZFR 5 32419962 Silent SNP A C3N-00169_T 24721588 32419962 149118297 66 9474 RXFP3 0 . GRCh38 5 33937762 33937762 + Missense_Mutation SNP C C T rs778264518 C3N-00169_T C3N-00169_N C C c.1022C>T p.Pro341Leu p.P341L ENST00000330120 1/1 642 592 50 397 397 0 strelka-varscan RXFP3,missense_variant,p.Pro341Leu,ENST00000330120,NM_016568.3; T ENST00000330120 Transcript missense_variant 1377/1852 1022/1410 341/469 P/L cCc/cTc rs778264518 1 1 RXFP3 HGNC HGNC:24883 protein_coding YES CCDS3900.1 ENSP00000328708 Q9NSD7 UPI0000046AEB NM_016568.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF70,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 33937762 33937762 C T 1 0 0 0 0 1 0 0 0 14022 623 22 3 3 RXFP3 5 33937762 Missense_Mutation SNP C C3N-00169_T 1517800 33937762 147600497 67 9475 PRLR 0 . GRCh38 5 35084543 35084543 + Silent SNP G G T C3N-00169_T C3N-00169_N G G c.300C>A p.= p.I100I ENST00000618457 5/10 332 259 73 169 169 0 strelka-varscan PRLR,synonymous_variant,p.=,ENST00000618457,NM_000949.6;PRLR,synonymous_variant,p.=,ENST00000542609,NM_001204316.1;PRLR,synonymous_variant,p.=,ENST00000231423,;PRLR,synonymous_variant,p.=,ENST00000509140,NM_001204317.1;PRLR,synonymous_variant,p.=,ENST00000513753,;PRLR,synonymous_variant,p.=,ENST00000514088,NM_001204318.1;PRLR,synonymous_variant,p.=,ENST00000619676,NM_001204315.1;PRLR,synonymous_variant,p.=,ENST00000348262,;PRLR,synonymous_variant,p.=,ENST00000310101,;PRLR,synonymous_variant,p.=,ENST00000514206,;PRLR,synonymous_variant,p.=,ENST00000509839,;PRLR,synonymous_variant,p.=,ENST00000503330,;PRLR,intron_variant,,ENST00000620785,NM_001204314.2;PRLR,intron_variant,,ENST00000511486,;PRLR,downstream_gene_variant,,ENST00000504500,;PRLR,downstream_gene_variant,,ENST00000515839,;PRLR,non_coding_transcript_exon_variant,,ENST00000509934,;PRLR,3_prime_UTR_variant,,ENST00000618625,;PRLR,3_prime_UTR_variant,,ENST00000397391,;PRLR,intron_variant,,ENST00000508107,;CTD-2046J7.1,downstream_gene_variant,,ENST00000510160,; T ENST00000618457 Transcript synonymous_variant 727/11688 300/1869 100/622 I atC/atA COSM3615622,COSM3615623,COSM4898045 1 -1 PRLR HGNC HGNC:9446 protein_coding YES CCDS3909.1 ENSP00000482954 P16471 UPI0000132234 NM_000949.6 5/10 Gene3D:2.60.40.10,Pfam_domain:PF09067,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF86,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 35084543 35084543 G T 1 0 0 0 0 0 0 0 1 12663 1280 45 2 2 PRLR 5 35084543 Silent SNP G C3N-00169_T 1146781 35084543 146453716 68 9476 FOXD1 0 . GRCh38 5 73447831 73447831 + Missense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.532T>A p.Ser178Thr p.S178T ENST00000615637 1/1 616 509 107 674 673 1 strelka-varscan FOXD1,missense_variant,p.Ser178Thr,ENST00000615637,NM_004472.2;LINC01385,upstream_gene_variant,,ENST00000512310,;FOXD1-AS1,downstream_gene_variant,,ENST00000514661,;FOXD1,upstream_gene_variant,,ENST00000513595,; T ENST00000615637 Transcript missense_variant 697/2272 532/1398 178/465 S/T Tcg/Acg 1 -1 FOXD1 HGNC HGNC:3802 protein_coding YES CCDS75259.1 ENSP00000481581 Q16676 UPI000012ADC8 NM_004472.2 deleterious(0) 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF168,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 73447831 73447831 A T 1 0 0 0 0 1 0 0 0 5856 304 11 4 4 FOXD1 5 73447831 Missense_Mutation SNP A C3N-00169_T 38363288 73447831 108090428 69 9477 SLC25A48 0 . GRCh38 5 135888034 135888034 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.424G>T p.Gly142Cys p.G142C ENST00000412661 5/5 120 82 38 126 125 1 strelka-varscan SLC25A48,missense_variant,p.Gly142Cys,ENST00000412661,NM_145282.4;IL9,downstream_gene_variant,,ENST00000274520,NM_000590.1;SLC25A48,downstream_gene_variant,,ENST00000510147,;SLC25A48,downstream_gene_variant,,ENST00000471980,; T ENST00000412661 Transcript missense_variant,splice_region_variant 545/1148 424/474 142/157 G/C Ggt/Tgt 1 1 SLC25A48 HGNC HGNC:30451 protein_coding YES CCDS43366.2 ENSP00000413049 Q6ZT89 UPI000006FF97 NM_145282.4 tolerated(0.05) 5/5 PROSITE_profiles:PS50920,Gene3D:1okcA00,Pfam_domain:PF00153 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 135888034 135888034 G T 1 0 0 0 0 1 0 0 0 14778 1014 35 2 2 SLC25A48 5 135888034 Missense_Mutation SNP G C3N-00169_T 62440203 135888034 45650225 70 9478 PCDHAC1 0 . GRCh38 5 140928031 140928031 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1139C>T p.Ser380Phe p.S380F ENST00000253807 1/4 321 267 54 413 413 0 strelka-varscan PCDHAC1,missense_variant,p.Ser380Phe,ENST00000253807,NM_018898.3;PCDHAC1,missense_variant,p.Ser380Phe,ENST00000409700,NM_031882.3;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA13,intron_variant,,ENST00000289272,NM_018904.2;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA13,intron_variant,,ENST00000409494,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,; T ENST00000253807 Transcript missense_variant 1139/5299 1139/2892 380/963 S/F tCt/tTt 1 1 PCDHAC1 HGNC HGNC:8676 protein_coding YES CCDS4241.1 ENSP00000253807 Q9H158 UPI000013CDF7 NM_018898.3 deleterious(0.01) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF132,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 140928031 140928031 C T 1 0 0 0 0 1 0 0 0 11619 913 32 3 3 PCDHAC1 5 140928031 Missense_Mutation SNP C C3N-00169_T 5039997 140928031 40610228 71 9479 PCDHB3 0 . GRCh38 5 141101713 141101713 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.1064C>A p.Pro355His p.P355H ENST00000231130 1/1 61 33 28 91 91 0 strelka-varscan PCDHB3,missense_variant,p.Pro355His,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000194155,NM_018936.3;PCDHB2,downstream_gene_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000624513,;PCDHB2,downstream_gene_variant,,ENST00000624994,;AC005754.7,intron_variant,,ENST00000607216,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; A ENST00000231130 Transcript missense_variant 1241/3355 1064/2391 355/796 P/H cCt/cAt 1 1 PCDHB3 HGNC HGNC:8688 protein_coding YES CCDS4245.1 ENSP00000231130 Q9Y5E6 UPI0003CC25DF NM_018937.4 tolerated_low_confidence(0.09) 1/1 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 141101713 141101713 C A 1 0 0 0 0 1 0 0 0 11630 681 24 2 2 PCDHB3 5 141101713 Missense_Mutation SNP C C3N-00169_T 173682 141101713 40436546 72 9480 PCDHGB3 0 . GRCh38 5 141371666 141371666 + Silent SNP T T A novel C3N-00169_T C3N-00169_N T T c.1272T>A p.= p.A424A ENST00000576222 1/4 303 203 100 407 407 0 strelka-varscan PCDHGB3,synonymous_variant,p.=,ENST00000576222,NM_018924.4;PCDHGB3,synonymous_variant,p.=,ENST00000618934,NM_032097.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,upstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGA6,upstream_gene_variant,,ENST00000517434,NM_018919.2;PCDHGA5,downstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000576222 Transcript synonymous_variant 1403/4727 1272/2790 424/929 A gcT/gcA 1 1 PCDHGB3 HGNC HGNC:8710 protein_coding YES CCDS58980.1 ENSP00000461862 Q9Y5G1 UPI0000EE35B5 NM_018924.4 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 141371666 141371666 T A 1 0 0 0 0 0 0 0 1 11651 1509 53 4 4 PCDHGB3 5 141371666 Silent SNP T C3N-00169_T 269953 141371666 40166593 73 9481 CSF1R 0 . GRCh38 5 150070032 150070032 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.1351G>T p.Asp451Tyr p.D451Y ENST00000286301 10/22 90 60 30 92 92 0 strelka-varscan CSF1R,missense_variant,p.Asp451Tyr,ENST00000286301,NM_001288705.1,NM_005211.3;CSF1R,downstream_gene_variant,,ENST00000543093,;CSF1R,upstream_gene_variant,,ENST00000515239,;CSF1R,missense_variant,p.Asp451Tyr,ENST00000504875,;CSF1R,upstream_gene_variant,,ENST00000513609,; A ENST00000286301 Transcript missense_variant 1643/3989 1351/2919 451/972 D/Y Gat/Tat 1 -1 CSF1R HGNC HGNC:2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 UPI000004984A NM_001288705.1,NM_005211.3 tolerated(0.07) 10/22 PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF47,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000615,Pfam_domain:PF13927,Gene3D:2.60.40.10,PIRSF_domain:PIRSF500947,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 A 3 1 38 150070032 150070032 C A 1 0 0 0 0 1 0 0 0 3733 855 30 2 2 CSF1R 5 150070032 Missense_Mutation SNP C C3N-00169_T 8698366 150070032 31468227 74 9482 FAT2 0 . GRCh38 5 151568578 151568578 + Silent SNP G G A C3N-00169_T C3N-00169_N G G c.354C>T p.= p.I118I ENST00000261800 1/23 147 127 20 166 166 0 strelka-varscan FAT2,synonymous_variant,p.=,ENST00000261800,NM_001447.2; A ENST00000261800 Transcript synonymous_variant 367/14534 354/13050 118/4349 I atC/atT COSM4489908 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 1/23 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 151568578 151568578 G A 1 0 0 0 0 0 0 0 1 5550 1280 45 3 3 FAT2 5 151568578 Silent SNP G C3N-00169_T 1498546 151568578 29969681 75 9483 HAVCR2 0 . GRCh38 5 157106627 157106627 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.394G>T p.Ala132Ser p.A132S ENST00000307851 2/7 83 58 25 110 109 1 strelka-varscan HAVCR2,missense_variant,p.Ala132Ser,ENST00000307851,NM_032782.4;HAVCR2,missense_variant,p.Ala132Ser,ENST00000522593,;HAVCR2,missense_variant,p.Ala15Ser,ENST00000524219,;CTB-120L21.1,intron_variant,,ENST00000517708,;HAVCR2,downstream_gene_variant,,ENST00000517358,;HAVCR2,splice_region_variant,,ENST00000521665,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000522902,; A ENST00000307851 Transcript missense_variant,splice_region_variant 1125/2907 394/906 132/301 A/S Gcc/Tcc 1 -1 HAVCR2 HGNC HGNC:18437 protein_coding YES CCDS4333.1 ENSP00000312002 Q8TDQ0 UPI000011AAFA NM_032782.4 tolerated(0.14) 2/7 hmmpanther:PTHR15498:SF45,hmmpanther:PTHR15498,Gene3D:2.60.40.10 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 157106627 157106627 C A 1 0 0 0 0 1 0 0 0 6860 695 24 2 2 HAVCR2 5 157106627 Missense_Mutation SNP C C3N-00169_T 5538049 157106627 24431632 76 9484 F12 0 . GRCh38 5 177403304 177403304 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1481C>A p.Pro494His p.P494H ENST00000253496 12/14 481 349 132 512 511 1 strelka-varscan F12,missense_variant,p.Pro494His,ENST00000253496,NM_000505.3;GRK6,5_prime_UTR_variant,,ENST00000502598,;SLC34A1,downstream_gene_variant,,ENST00000324417,NM_003052.4;GRK6,upstream_gene_variant,,ENST00000506296,;PFN3,upstream_gene_variant,,ENST00000358571,NM_001029886.2;F12,non_coding_transcript_exon_variant,,ENST00000514943,;SLC34A1,downstream_gene_variant,,ENST00000513614,;F12,non_coding_transcript_exon_variant,,ENST00000510358,;F12,non_coding_transcript_exon_variant,,ENST00000502854,;F12,non_coding_transcript_exon_variant,,ENST00000504406,;F12,downstream_gene_variant,,ENST00000503736,; T ENST00000253496 Transcript missense_variant 1530/2049 1481/1848 494/615 P/H cCc/cAc 1 -1 F12 HGNC HGNC:3530 protein_coding YES CCDS34302.1 ENSP00000253496 P00748 UPI000048055F NM_000505.3 tolerated(0.59) 12/14 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001146,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF177,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 177403304 177403304 G T 1 0 0 0 0 1 0 0 0 5207 1232 43 2 2 F12 5 177403304 Missense_Mutation SNP G C3N-00169_T 20296677 177403304 4134955 77 9485 FAM83B 0 . GRCh38 6 54940711 54940711 + Silent SNP C C A rs371325026 C3N-00169_T C3N-00169_N C C c.1740C>A p.= p.V580V ENST00000306858 5/5 126 93 33 196 196 0 strelka-varscan FAM83B,synonymous_variant,p.=,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; A ENST00000306858 Transcript synonymous_variant 1856/3167 1740/3036 580/1011 V gtC/gtA rs371325026 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 54940711 54940711 C A 1 0 0 0 0 0 0 0 1 5492 842 30 2 2 FAM83B 6 54940711 Silent SNP C C3N-00169_T 54940711 115865268 78 9486 PHF3 0 . GRCh38 6 63712225 63712225 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.4637G>A p.Gly1546Glu p.G1546E ENST00000262043 16/16 269 226 43 218 218 0 strelka-varscan PHF3,missense_variant,p.Gly1546Glu,ENST00000262043,NM_001290259.1;PHF3,missense_variant,p.Gly1546Glu,ENST00000393387,NM_015153.3;PHF3,missense_variant,p.Gly815Glu,ENST00000515594,;PHF3,intron_variant,,ENST00000505138,;PHF3,downstream_gene_variant,,ENST00000506783,;PHF3,3_prime_UTR_variant,,ENST00000509876,; A ENST00000262043 Transcript missense_variant 4977/8233 4637/6120 1546/2039 G/E gGg/gAg 1 1 PHF3 HGNC HGNC:8921 protein_coding YES CCDS4966.1 ENSP00000262043 Q92576 UPI000007154D NM_001290259.1 tolerated(0.24) 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 63712225 63712225 G A 1 0 0 0 0 1 0 0 0 11923 1232 43 3 3 PHF3 6 63712225 Missense_Mutation SNP G C3N-00169_T 8771514 63712225 107093754 79 9487 COL19A1 0 . GRCh38 6 69936825 69936825 + Frame_Shift_Del DEL G G - novel C3N-00169_T C3N-00169_N G G c.790delG p.Val264Ter p.V264* ENST00000620364 8/51 107 86 21 147 147 0 sindel-varindel-pindel COL19A1,frameshift_variant,p.Val264Ter,ENST00000620364,NM_001858.5;COL19A1,upstream_gene_variant,,ENST00000483745,; - ENST00000620364 Transcript frameshift_variant 890/6233 788/3429 263/1142 W/X tGg/tg 1 1 COL19A1 HGNC HGNC:2196 protein_coding YES CCDS4970.1 ENSP00000480474 Q14993 UPI000004F1E3 NM_001858.5 8/51 HIGH 1 deletion 1 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 38 69936825 69936825 G - 1 0 1 0 1 0 0 0 0 3464 1357 47 0 0 COL19A1 6 69936825 Frame_Shift_Del DEL G C3N-00169_T 6224600 69936825 100869154 80 9488 SCML4 0 . GRCh38 6 107749740 107749740 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.230C>A p.Ser77Tyr p.S77Y ENST00000369020 3/8 216 161 55 262 262 0 strelka-varscan SCML4,missense_variant,p.Ser19Tyr,ENST00000369022,NM_001286408.1;SCML4,missense_variant,p.Ser48Tyr,ENST00000369021,;SCML4,missense_variant,p.Ser77Tyr,ENST00000369020,NM_198081.4;SCML4,missense_variant,p.Ser48Tyr,ENST00000440927,;SCML4,missense_variant,p.Ser19Tyr,ENST00000426221,;SCML4,non_coding_transcript_exon_variant,,ENST00000473515,;SCML4,non_coding_transcript_exon_variant,,ENST00000459992,;SCML4,non_coding_transcript_exon_variant,,ENST00000463507,; T ENST00000369020 Transcript missense_variant 476/1491 230/1245 77/414 S/Y tCc/tAc 1 -1 SCML4 HGNC HGNC:21397 protein_coding YES CCDS5060.2 ENSP00000358016 Q8N228 UPI0000EE1E57 NM_198081.4 deleterious(0) 3/8 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF85 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 107749740 107749740 G T 1 0 0 0 0 1 0 0 0 14180 1174 41 2 2 SCML4 6 107749740 Missense_Mutation SNP G C3N-00169_T 37812915 107749740 63056239 81 9489 WDR27 0 . GRCh38 6 169582842 169582842 + Silent SNP C C A rs752469238 C3N-00169_T C3N-00169_N C C c.2517G>T p.= p.A839A ENST00000448612 24/26 190 126 64 234 234 0 strelka-varscan-mutect WDR27,synonymous_variant,p.=,ENST00000448612,NM_182552.4;WDR27,synonymous_variant,p.=,ENST00000423258,NM_001202550.1;WDR27,non_coding_transcript_exon_variant,,ENST00000546525,;WDR27,non_coding_transcript_exon_variant,,ENST00000479310,; A ENST00000448612 Transcript synonymous_variant 2627/3178 2517/2688 839/895 A gcG/gcT rs752469238 1 -1 WDR27 HGNC HGNC:21248 protein_coding YES CCDS47520.2 ENSP00000416289 A2RRH5 UPI00015E06AF NM_182552.4 24/26 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF410,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs752469238 . 0 206 0 4 0 0 0 0 -20 0.9999828 1 1 1 0 A 2 1 38 169582842 169582842 C A 1 0 0 0 0 0 0 0 1 17844 755 27 1 1 WDR27 6 169582842 Silent SNP C C3N-00169_T 61833102 169582842 1223137 82 9490 GRID2IP 0 . GRCh38 7 6520719 6520719 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1127C>A p.Thr376Asn p.T376N ENST00000457091 7/22 155 121 34 192 192 0 strelka-varscan-mutect GRID2IP,missense_variant,p.Thr376Asn,ENST00000457091,NM_001145118.1;GRID2IP,missense_variant,p.Thr186Asn,ENST00000452113,;GRID2IP,missense_variant,p.Thr193Asn,ENST00000435185,; T ENST00000457091 Transcript missense_variant 1127/3636 1127/3636 376/1211 T/N aCc/aAc 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 deleterious(0.05) 7/22 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242 MODERATE 1 SNV 5 1 PASS rs1358249298 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 6520719 6520719 G T 1 0 0 0 0 1 0 0 0 6653 1261 44 2 2 GRID2IP 7 6520719 Missense_Mutation SNP G C3N-00169_T 6520719 152825254 83 9491 DFNA5 0 . GRCh38 7 24699030 24699030 + Missense_Mutation SNP G G A rs559632895 C3N-00169_T C3N-00169_N G G c.1487C>T p.Ser496Leu p.S496L ENST00000342947 10/10 392 343 49 363 363 0 strelka-mutect DFNA5,missense_variant,p.Ser496Leu,ENST00000342947,NM_004403.2;DFNA5,missense_variant,p.Ser332Leu,ENST00000419307,NM_001127454.1;DFNA5,missense_variant,p.Ser332Leu,ENST00000409970,;DFNA5,missense_variant,p.Ser496Leu,ENST00000409775,NM_001127453.1;MPP6,downstream_gene_variant,,ENST00000222644,NM_001303037.1,NM_016447.3;DFNA5,downstream_gene_variant,,ENST00000430096,;DFNA5,non_coding_transcript_exon_variant,,ENST00000479636,; A ENST00000342947 Transcript missense_variant 1913/2590 1487/1491 496/496 S/L tCa/tTa rs559632895 1 -1 DFNA5 HGNC HGNC:2810 protein_coding YES CCDS5389.1 ENSP00000339587 O60443 A0A024RA58 UPI00001291FC NM_004403.2 deleterious_low_confidence(0.02) 10/10 hmmpanther:PTHR15207,hmmpanther:PTHR15207:SF1 MODERATE 1 SNV 1 1 PASS rs559632895 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 24699030 24699030 G A 1 0 0 0 0 1 0 0 0 4262 1294 45 3 3 DFNA5 7 24699030 Missense_Mutation SNP G C3N-00169_T 18178311 24699030 134646943 84 9492 ZNF716 0 . GRCh38 7 57469649 57469649 + Silent SNP T T A novel C3N-00169_T C3N-00169_N T T c.1188T>A p.= p.T396T ENST00000420713 4/4 305 234 71 234 234 0 strelka-varscan-mutect ZNF716,synonymous_variant,p.=,ENST00000420713,NM_001159279.1; A ENST00000420713 Transcript synonymous_variant 1300/5197 1188/1488 396/495 T acT/acA 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 57469649 57469649 T A 1 0 0 0 0 0 0 0 1 18694 1596 56 4 4 ZNF716 7 57469649 Silent SNP T C3N-00169_T 32770619 57469649 101876324 85 9493 AUTS2 0 . GRCh38 7 70790439 70790439 + Silent SNP T T C novel C3N-00169_T C3N-00169_N T T c.3223T>C p.= p.L1075L ENST00000342771 19/19 91 71 20 125 125 0 strelka-varscan-mutect AUTS2,synonymous_variant,p.=,ENST00000342771,NM_015570.3;AUTS2,synonymous_variant,p.=,ENST00000406775,NM_001127231.2;AUTS2,synonymous_variant,p.=,ENST00000611706,;AUTS2,synonymous_variant,p.=,ENST00000615871,;AUTS2,downstream_gene_variant,,ENST00000418686,;AUTS2,downstream_gene_variant,,ENST00000498384,;AUTS2,downstream_gene_variant,,ENST00000449547,;AUTS2,downstream_gene_variant,,ENST00000439256,; C ENST00000342771 Transcript synonymous_variant 3544/6173 3223/3780 1075/1259 L Ttg/Ctg 1 1 AUTS2 HGNC HGNC:14262 protein_coding YES CCDS5539.1 ENSP00000344087 Q8WXX7 UPI0000126665 NM_015570.3 19/19 hmmpanther:PTHR14429,hmmpanther:PTHR14429:SF5 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 38 70790439 70790439 T C 1 0 0 0 0 0 0 0 1 1381 1606 56 5 5 AUTS2 7 70790439 Silent SNP T C3N-00169_T 13320790 70790439 88555534 86 9494 SEMA3E 0 . GRCh38 7 83368020 83368020 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1894G>A p.Val632Met p.V632M ENST00000307792 17/17 118 97 21 92 92 0 strelka-varscan-mutect SEMA3E,missense_variant,p.Val632Met,ENST00000307792,NM_012431.2;SEMA3E,missense_variant,p.Val572Met,ENST00000427262,NM_001178129.1; T ENST00000307792 Transcript missense_variant 2362/6476 1894/2328 632/775 V/M Gtg/Atg 1 -1 SEMA3E HGNC HGNC:10727 protein_coding YES CCDS34674.1 ENSP00000303212 O15041 UPI0000135A68 NM_012431.2 tolerated(0.06) 17/17 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 83368020 83368020 C T 1 0 0 0 0 1 0 0 0 14304 565 20 3 3 SEMA3E 7 83368020 Missense_Mutation SNP C C3N-00169_T 12577581 83368020 75977953 87 9495 PPP1R3A 0 . GRCh38 7 113879230 113879230 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.1862G>T p.Arg621Ile p.R621I ENST00000284601 4/4 357 288 69 298 298 0 strelka-varscan-mutect PPP1R3A,missense_variant,p.Arg621Ile,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; A ENST00000284601 Transcript missense_variant 1931/4384 1862/3369 621/1122 R/I aGa/aTa COSM2149488,COSM3411487,COSM4929283,COSM4929284 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 deleterious(0) 4/4 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 113879230 113879230 C A 1 0 0 0 0 1 0 0 0 12492 913 32 2 2 PPP1R3A 7 113879230 Missense_Mutation SNP C C3N-00169_T 30511210 113879230 45466743 88 9496 SMO 0 . GRCh38 7 129189399 129189404 + In_Frame_Del DEL TGCCCT TGCCCT - novel C3N-00169_T C3N-00169_N TGCCCT TGCCCT c.248_253delTGCCCT p.Leu83_Tyr85delinsHis p.L83_Y85delinsH ENST00000249373 1/12 315 253 62 390 390 0 sindel-varindel-pindel SMO,inframe_deletion,p.Leu83_Tyr85delinsHis,ENST00000249373,NM_005631.4; - ENST00000249373 Transcript inframe_deletion 528-533/3738 248-253/2364 83-85/787 LPY/H cTGCCCTac/cac 1 1 SMO HGNC HGNC:11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 UPI0000050447 NM_005631.4 1/12 PROSITE_profiles:PS50038,hmmpanther:PTHR11309:SF35,hmmpanther:PTHR11309,Gene3D:1ijyA00,Pfam_domain:PF01392,SMART_domains:SM00063,Superfamily_domains:SSF63501 MODERATE 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 38 129189399 129189399 TGCCCT - 1 0 1 0 1 0 0 0 0 15121 1580 55 0 0 SMO 7 129189399 In_Frame_Del DEL TGCCCT C3N-00169_T 15310169 129189399 30156574 89 9497 GIMAP4 0 . GRCh38 7 150569945 150569945 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.44C>A p.Pro15Gln p.P15Q ENST00000255945 2/3 238 188 50 249 249 0 strelka-varscan-mutect GIMAP4,missense_variant,p.Pro15Gln,ENST00000255945,NM_018326.2;GIMAP4,missense_variant,p.Pro15Gln,ENST00000461940,;GIMAP4,missense_variant,p.Pro15Gln,ENST00000479232,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000478135,;GIMAP4,intron_variant,,ENST00000494750,; A ENST00000255945 Transcript missense_variant 219/2060 44/990 15/329 P/Q cCa/cAa 1 1 GIMAP4 HGNC HGNC:21872 protein_coding YES CCDS5904.1 ENSP00000255945 Q9NUV9 A0A090N7X0 UPI0000073CB0 NM_018326.2 tolerated(0.07) 2/3 hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF57 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 150569945 150569945 C A 1 0 0 0 0 1 0 0 0 6261 594 21 2 2 GIMAP4 7 150569945 Missense_Mutation SNP C C3N-00169_T 21380546 150569945 8776028 90 9498 KCNH2 0 . GRCh38 7 150952730 150952730 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.1252G>T p.Val418Phe p.V418F ENST00000262186 6/15 373 299 74 499 499 0 strelka-varscan-mutect KCNH2,missense_variant,p.Val418Phe,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Val78Phe,ENST00000330883,NM_172057.2;KCNH2,missense_variant,p.Val302Phe,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; A ENST00000262186 Transcript missense_variant 1654/4286 1252/3480 418/1159 V/F Gtc/Ttc 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0) 6/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 150952730 150952730 C A 1 0 0 0 0 1 0 0 0 7948 507 18 2 2 KCNH2 7 150952730 Missense_Mutation SNP C C3N-00169_T 382785 150952730 8393243 91 9499 KCNU1 0 . GRCh38 8 36918876 36918876 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.2575G>C p.Val859Leu p.V859L ENST00000399881 23/27 109 93 16 106 106 0 strelka-varscan-mutect KCNU1,missense_variant,p.Val859Leu,ENST00000399881,NM_001031836.2;KCNU1,missense_variant,p.Val859Leu,ENST00000522372,; C ENST00000399881 Transcript missense_variant 2612/3695 2575/3450 859/1149 V/L Gtc/Ctc 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 deleterious(0.01) 23/27 Gene3D:3.40.50.720 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 36918876 36918876 G C 1 0 0 0 0 1 0 0 0 8009 1029 36 4 4 KCNU1 8 36918876 Missense_Mutation SNP G C3N-00169_T 36918876 108219760 92 9500 TRPS1 0 . GRCh38 8 115604992 115604992 + Missense_Mutation SNP C C G C3N-00169_T C3N-00169_N C C c.977G>C p.Gly326Ala p.G326A ENST00000395715 4/7 138 126 12 141 140 1 strelka-mutect TRPS1,missense_variant,p.Gly326Ala,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Gly313Ala,ENST00000220888,;TRPS1,missense_variant,p.Gly317Ala,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Gly267Ala,ENST00000519076,;TRPS1,missense_variant,p.Gly313Ala,ENST00000519674,;TRPS1,missense_variant,p.Gly317Ala,ENST00000517323,; G ENST00000395715 Transcript missense_variant 1555/9990 977/3885 326/1294 G/A gGt/gCt COSM1739439,COSM1739440 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 tolerated_low_confidence(0.05) 4/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 115604992 115604992 C G 1 0 0 0 0 1 0 0 0 17099 507 18 4 4 TRPS1 8 115604992 Missense_Mutation SNP C C3N-00169_T 78686116 115604992 29533644 93 9501 SQLE 0 . GRCh38 8 125009334 125009334 + Nonsense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1099C>T p.Gln367Ter p.Q367* ENST00000265896 6/11 64 56 8 57 57 0 strelka-varscan-mutect SQLE,stop_gained,p.Gln367Ter,ENST00000265896,NM_003129.3;SQLE,stop_gained,p.Gln272Ter,ENST00000523430,;SQLE,stop_gained,p.Gln19Ter,ENST00000518931,;SQLE,downstream_gene_variant,,ENST00000521232,;SQLE,upstream_gene_variant,,ENST00000520493,; T ENST00000265896 Transcript stop_gained 1997/2961 1099/1725 367/574 Q/* Caa/Taa 1 1 SQLE HGNC HGNC:11279 protein_coding YES CCDS47918.1 ENSP00000265896 Q14534 Q9UNR6 UPI0000073EEE NM_003129.3 6/11 hmmpanther:PTHR10835,Pfam_domain:PF08491 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -17.93259 0.9999972 1 1 1 0 T 4 4 38 125009334 125009334 C T 1 0 0 0 0 0 1 0 0 15487 479 17 3 3 SQLE 8 125009334 Nonsense_Mutation SNP C C3N-00169_T 9404342 125009334 20129302 94 9502 AGO2 0 . GRCh38 8 140556214 140556214 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1099G>A p.Ala367Thr p.A367T ENST00000220592 9/19 151 126 25 234 234 0 strelka-varscan-mutect AGO2,missense_variant,p.Ala367Thr,ENST00000220592,NM_012154.3;AGO2,missense_variant,p.Ala367Thr,ENST00000519980,NM_001164623.1;AGO2,3_prime_UTR_variant,,ENST00000523609,;AGO2,non_coding_transcript_exon_variant,,ENST00000521325,; T ENST00000220592 Transcript missense_variant 1212/14581 1099/2580 367/859 A/T Gcg/Acg 1 -1 AGO2 HGNC HGNC:3263 protein_coding YES CCDS6380.1 ENSP00000220592 Q9UKV8 UPI0000168652 NM_012154.3 tolerated(0.1) 9/19 HAMAP:MF_03031,hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891,SMART_domains:SM00949,Superfamily_domains:SSF101690 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 140556214 140556214 C T 1 0 0 0 0 1 0 0 0 465 797 28 3 3 AGO2 8 140556214 Missense_Mutation SNP C C3N-00169_T 15546880 140556214 4582422 95 9503 AGTPBP1 0 . GRCh38 9 85655272 85655272 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.1114C>G p.Leu372Val p.L372V ENST00000337006 10/25 166 130 36 142 142 0 strelka-varscan-mutect AGTPBP1,missense_variant,p.Leu372Val,ENST00000337006,NM_001286715.1;AGTPBP1,missense_variant,p.Leu320Val,ENST00000357081,;AGTPBP1,intron_variant,,ENST00000628899,NM_001286717.1;AGTPBP1,intron_variant,,ENST00000376083,NM_015239.2;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000376081,;AGTPBP1,downstream_gene_variant,,ENST00000491784,;AGTPBP1,downstream_gene_variant,,ENST00000376080,; C ENST00000337006 Transcript missense_variant 1181/4473 1114/3837 372/1278 L/V Ctg/Gtg 1 -1 AGTPBP1 HGNC HGNC:17258 protein_coding YES CCDS75854.1 ENSP00000338512 J3KNS1 UPI000387D56E NM_001286715.1 tolerated(0.32) 10/25 hmmpanther:PTHR12756:SF24,hmmpanther:PTHR12756 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 85655272 85655272 G C 1 0 0 0 0 1 0 0 0 479 933 33 4 4 AGTPBP1 9 85655272 Missense_Mutation SNP G C3N-00169_T 85655272 52739445 96 9504 FOXE1 0 . GRCh38 9 97854090 97854090 + Missense_Mutation SNP T T A novel C3N-00169_T C3N-00169_N T T c.176T>A p.Ile59Asn p.I59N ENST00000375123 1/1 347 288 59 326 326 0 strelka-varscan-mutect FOXE1,missense_variant,p.Ile59Asn,ENST00000375123,NM_004473.3; A ENST00000375123 Transcript missense_variant 837/3462 176/1122 59/373 I/N aTc/aAc 1 1 FOXE1 HGNC HGNC:3806 protein_coding YES CCDS35078.1 ENSP00000364265 O00358 UPI0000167B2F NM_004473.3 deleterious(0) 1/1 PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF156,PROSITE_patterns:PS00657,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785,Prints_domain:PR00053 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 97854090 97854090 T A 1 0 0 0 0 1 0 0 0 5865 1435 50 4 4 FOXE1 9 97854090 Missense_Mutation SNP T C3N-00169_T 12198818 97854090 40540627 97 9505 PSMB7 0 . GRCh38 9 124353627 124353627 + Nonsense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.805G>T p.Glu269Ter p.E269* ENST00000259457 8/8 198 160 38 223 223 0 strelka-varscan-mutect PSMB7,stop_gained,p.Glu269Ter,ENST00000259457,NM_002799.3;NEK6,downstream_gene_variant,,ENST00000373600,NM_001145001.2;NEK6,downstream_gene_variant,,ENST00000320246,NM_014397.5;NEK6,downstream_gene_variant,,ENST00000373603,;NEK6,downstream_gene_variant,,ENST00000539416,NM_001166169.1;NEK6,downstream_gene_variant,,ENST00000546191,NM_001166170.1;NEK6,downstream_gene_variant,,ENST00000540326,NM_001166167.1;NEK6,downstream_gene_variant,,ENST00000545174,NM_001166168.1;NEK6,downstream_gene_variant,,ENST00000394199,NM_001166171.1;PSMB7,non_coding_transcript_exon_variant,,ENST00000498485,; A ENST00000259457 Transcript stop_gained 819/980 805/834 269/277 E/* Gaa/Taa 1 -1 PSMB7 HGNC HGNC:9544 protein_coding YES CCDS6855.1 ENSP00000259457 Q99436 E9KL30 UPI00001325C7 NM_002799.3 8/8 Pfam_domain:PF12465 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 124353627 124353627 C A 1 0 0 0 0 0 1 0 0 12833 922 32 2 2 PSMB7 9 124353627 Nonsense_Mutation SNP C C3N-00169_T 26499537 124353627 14041090 98 9506 EHMT1 0 . GRCh38 9 137834377 137834377 + Missense_Mutation SNP G G T C3N-00169_T C3N-00169_N G G c.3569G>T p.Arg1190Leu p.R1190L ENST00000460843 26/27 407 330 77 390 390 0 strelka-varscan-mutect EHMT1,missense_variant,p.Arg1190Leu,ENST00000460843,NM_024757.4;EHMT1,missense_variant,p.Arg1159Leu,ENST00000637161,;MIR602,upstream_gene_variant,,ENST00000384960,;EHMT1,non_coding_transcript_exon_variant,,ENST00000472849,;EHMT1,downstream_gene_variant,,ENST00000637287,;EHMT1,3_prime_UTR_variant,,ENST00000637261,;EHMT1,3_prime_UTR_variant,,ENST00000637891,;EHMT1,non_coding_transcript_exon_variant,,ENST00000475564,;EHMT1,non_coding_transcript_exon_variant,,ENST00000494249,;EHMT1,non_coding_transcript_exon_variant,,ENST00000637748,;EHMT1,non_coding_transcript_exon_variant,,ENST00000475704,;EHMT1,intron_variant,,ENST00000462942,; T ENST00000460843 Transcript missense_variant 3635/5137 3569/3897 1190/1298 R/L cGg/cTg COSM3952565,COSM3952566 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 deleterious(0) 26/27 Gene3D:2.170.270.10,Pfam_domain:PF00856,PROSITE_profiles:PS50280,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF364,SMART_domains:SM00317,Superfamily_domains:SSF82199 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs886042261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 137834377 137834377 G T 1 0 0 0 0 1 0 0 0 4819 1116 39 1 1 EHMT1 9 137834377 Missense_Mutation SNP G C3N-00169_T 13480750 137834377 560340 99 9507 FBXO18 0 . GRCh38 10 5911056 5911056 + Missense_Mutation SNP T T A novel C3N-00169_T C3N-00169_N T T c.1292T>A p.Val431Asp p.V431D ENST00000379999 7/22 229 190 39 245 245 0 strelka-varscan-mutect FBXO18,missense_variant,p.Val431Asp,ENST00000379999,NM_032807.4;FBXO18,missense_variant,p.Val306Asp,ENST00000397269,NM_001258452.1,NM_001258453.1;FBXO18,missense_variant,p.Val380Asp,ENST00000362091,NM_178150.2;FBXO18,downstream_gene_variant,,ENST00000470089,;FBXO18,downstream_gene_variant,,ENST00000462507,;FBXO18,downstream_gene_variant,,ENST00000469009,;FBXO18,upstream_gene_variant,,ENST00000460453,;FBXO18,downstream_gene_variant,,ENST00000494526,; A ENST00000379999 Transcript missense_variant 1396/3702 1292/3285 431/1094 V/D gTc/gAc 1 1 FBXO18 HGNC HGNC:13620 protein_coding YES CCDS7073.1 ENSP00000369335 Q8NFZ0 UPI000019AB6F NM_032807.4 deleterious(0) 7/22 hmmpanther:PTHR11070,hmmpanther:PTHR11070:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 5911056 5911056 T A 1 0 0 0 0 1 0 0 0 5594 1667 58 4 4 FBXO18 10 5911056 Missense_Mutation SNP T C3N-00169_T 5911056 127886366 100 9508 NMT2 0 . GRCh38 10 15128444 15128444 + Nonsense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.905C>A p.Ser302Ter p.S302* ENST00000378165 8/12 161 146 15 98 98 0 strelka-varscan-mutect NMT2,stop_gained,p.Ser302Ter,ENST00000378165,NM_004808.2;NMT2,stop_gained,p.Ser289Ter,ENST00000378150,NM_001308295.1;RPP38,intron_variant,,ENST00000451677,;NMT2,downstream_gene_variant,,ENST00000478580,; T ENST00000378165 Transcript stop_gained 986/2907 905/1497 302/498 S/* tCa/tAa 1 -1 NMT2 HGNC HGNC:7858 protein_coding YES CCDS7109.1 ENSP00000367407 O60551 UPI0000130278 NM_004808.2 8/12 hmmpanther:PTHR11377,hmmpanther:PTHR11377:SF6,Gene3D:3.40.630.30,PIRSF_domain:PIRSF015892,Superfamily_domains:SSF55729 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 15128444 15128444 G T 1 0 0 0 0 0 1 0 0 10545 1294 45 2 2 NMT2 10 15128444 Nonsense_Mutation SNP G C3N-00169_T 9217388 15128444 118668978 101 9509 MRC1 0 . GRCh38 10 17873805 17873805 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.2366C>A p.Pro789Gln p.P789Q ENST00000569591 16/30 320 266 54 334 334 0 strelka-varscan-mutect MRC1,missense_variant,p.Pro789Gln,ENST00000569591,NM_002438.3; A ENST00000569591 Transcript missense_variant 2488/5198 2366/4371 789/1456 P/Q cCa/cAa 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 deleterious(0.01) 16/30 hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Gene3D:3.10.100.10,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 17873805 17873805 C A 1 0 0 0 0 1 0 0 0 9722 594 21 2 2 MRC1 10 17873805 Missense_Mutation SNP C C3N-00169_T 2745361 17873805 115923617 102 9510 SLC39A12 0 . GRCh38 10 18042792 18042792 + Missense_Mutation SNP C C T C3N-00169_T C3N-00169_N C C c.2035C>T p.Leu679Phe p.L679F ENST00000377369 13/13 201 172 29 200 200 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Leu679Phe,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Leu678Phe,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Leu642Phe,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Leu545Phe,ENST00000539911,NM_001282734.1; T ENST00000377369 Transcript missense_variant 2308/2808 2035/2076 679/691 L/F Ctc/Ttc COSM5276747,COSM5276748 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 deleterious(0) 13/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 18042792 18042792 C T 1 0 0 0 0 1 0 0 0 14893 913 32 3 3 SLC39A12 10 18042792 Missense_Mutation SNP C C3N-00169_T 168987 18042792 115754630 103 9511 ANK3 0 . GRCh38 10 60069405 60069405 + Missense_Mutation SNP C C A rs746447437 C3N-00169_T C3N-00169_N C C c.11476G>T p.Val3826Phe p.V3826F ENST00000280772 37/44 127 93 34 118 118 0 strelka-varscan-mutect ANK3,missense_variant,p.Val3826Phe,ENST00000280772,NM_020987.3;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000610321,;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000616444,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000610901,;ANK3,intron_variant,,ENST00000613207,;ANK3,intron_variant,,ENST00000511043,;ANK3,intron_variant,,ENST00000621739,; A ENST00000280772 Transcript missense_variant 11668/16874 11476/13134 3826/4377 V/F Gtc/Ttc rs746447437 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 tolerated_low_confidence(0.06) 37/44 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22 MODERATE 1 SNV 1 1 PASS rs746447437 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 60069405 60069405 C A 1 0 0 0 0 1 0 0 0 722 565 20 2 2 ANK3 10 60069405 Missense_Mutation SNP C C3N-00169_T 42026613 60069405 73728017 104 9512 CFAP58 0 . GRCh38 10 104447712 104447712 + Silent SNP C C G rs148324034 C3N-00169_T C3N-00169_N C C c.2271C>G p.= p.L757L ENST00000369704 16/18 105 83 22 141 141 0 strelka-varscan-mutect CFAP58,synonymous_variant,p.=,ENST00000369704,NM_001008723.1; G ENST00000369704 Transcript synonymous_variant 2405/3313 2271/2619 757/872 L ctC/ctG rs148324034 1 1 CFAP58 HGNC HGNC:26676 protein_coding YES CCDS31282.1 ENSP00000358718 Q5T655 UPI0000160405 NM_001008723.1 16/18 hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF31,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs148324034 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 104447712 104447712 C G 1 0 0 0 0 0 0 0 1 3027 900 32 4 4 CFAP58 10 104447712 Silent SNP C C3N-00169_T 44378307 104447712 29349710 105 9513 CFAP46 0 . GRCh38 10 132912761 132912761 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.2393G>T p.Trp798Leu p.W798L ENST00000368586 19/58 235 197 38 326 325 1 strelka-varscan-mutect CFAP46,missense_variant,p.Trp798Leu,ENST00000368586,NM_001200049.2;CFAP46,non_coding_transcript_exon_variant,,ENST00000486104,;CFAP46,upstream_gene_variant,,ENST00000466834,; A ENST00000368586 Transcript missense_variant 2494/8278 2393/8148 798/2715 W/L tGg/tTg 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 deleterious(0) 19/58 hmmpanther:PTHR15977,hmmpanther:PTHR15977:SF15 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 132912761 132912761 C A 1 0 0 0 0 1 0 0 0 3021 595 21 2 2 CFAP46 10 132912761 Missense_Mutation SNP C C3N-00169_T 28465049 132912761 884661 106 9514 B4GALNT4 0 . GRCh38 11 376682 376682 + Missense_Mutation SNP A A C novel C3N-00169_T C3N-00169_N A A c.1559A>C p.Gln520Pro p.Q520P ENST00000329962 14/20 54 42 12 102 102 0 strelka-varscan-mutect B4GALNT4,missense_variant,p.Gln520Pro,ENST00000329962,NM_178537.4;B4GALNT4,upstream_gene_variant,,ENST00000534778,;B4GALNT4,upstream_gene_variant,,ENST00000526584,;B4GALNT4,downstream_gene_variant,,ENST00000524443,;B4GALNT4,downstream_gene_variant,,ENST00000530717,; C ENST00000329962 Transcript missense_variant 1559/3444 1559/3120 520/1039 Q/P cAg/cCg 1 1 B4GALNT4 HGNC HGNC:26315 protein_coding YES CCDS7694.1 ENSP00000328277 Q76KP1 UPI00002326B6 NM_178537.4 tolerated(0.35) 14/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 3 2 38 376682 376682 A C 1 0 0 0 0 1 0 0 0 1425 188 7 5 5 B4GALNT4 11 376682 Missense_Mutation SNP A C3N-00169_T 376682 134709940 107 9515 OR51Q1 0 . GRCh38 11 5422494 5422494 + Silent SNP C C A novel C3N-00169_T C3N-00169_N C C c.294C>A p.= p.A98A ENST00000300778 1/1 193 169 24 260 259 1 strelka-varscan-mutect OR51Q1,synonymous_variant,p.=,ENST00000300778,NM_001004757.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000300778 Transcript synonymous_variant 384/1096 294/954 98/317 A gcC/gcA 1 1 OR51Q1 HGNC HGNC:14851 protein_coding YES CCDS31381.1 ENSP00000300778 Q8NH59 UPI0000041BDB NM_001004757.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF84,Superfamily_domains:SSF81321 LOW SNV 1 PASS rs1442941960 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 5422494 5422494 C A 1 0 0 0 0 0 0 0 1 11178 668 24 2 2 OR51Q1 11 5422494 Silent SNP C C3N-00169_T 5045812 5422494 129664128 108 9516 PIK3C2A 0 . GRCh38 11 17119862 17119862 + Missense_Mutation SNP G G A rs761682657 C3N-00169_T C3N-00169_N G G c.2770C>T p.Leu924Phe p.L924F ENST00000265970 15/32 173 152 21 150 150 0 strelka-varscan-mutect PIK3C2A,missense_variant,p.Leu924Phe,ENST00000265970,NM_001321378.1,NM_002645.2;RNU6-593P,upstream_gene_variant,,ENST00000364716,;PIK3C2A,intron_variant,,ENST00000531428,; A ENST00000265970 Transcript missense_variant 2770/8227 2770/5061 924/1686 L/F Ctt/Ttt rs761682657 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 deleterious(0) 15/32 Gene3D:1.25.40.70,Pfam_domain:PF00613,PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF28,SMART_domains:SM00145,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs761682657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 17119862 17119862 G A 1 0 0 0 0 1 0 0 0 12004 942 33 3 3 PIK3C2A 11 17119862 Missense_Mutation SNP G C3N-00169_T 11697368 17119862 117966760 109 9517 KIAA1549L 0 . GRCh38 11 33543392 33543392 + Missense_Mutation SNP C C T rs755961188 C3N-00169_T C3N-00169_N C C c.938C>T p.Pro313Leu p.P313L ENST00000321505 1/20 183 154 29 233 233 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Pro313Leu,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Pro313Leu,ENST00000265654,;KIAA1549L,intron_variant,,ENST00000526400,; T ENST00000321505 Transcript missense_variant 1118/11678 938/5550 313/1849 P/L cCc/cTc rs755961188 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 tolerated_low_confidence(0.09) 1/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 MODERATE 1 SNV 1 1 PASS rs755961188 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 33543392 33543392 C T 1 0 0 0 0 1 0 0 0 8121 623 22 3 3 KIAA1549L 11 33543392 Missense_Mutation SNP C C3N-00169_T 16423530 33543392 101543230 110 9518 TRAF6 0 . GRCh38 11 36490251 36490251 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.1156G>T p.Gly386Trp p.G386W ENST00000526995 7/7 177 159 18 222 222 0 strelka-varscan-mutect TRAF6,missense_variant,p.Gly386Trp,ENST00000526995,NM_004620.3;TRAF6,missense_variant,p.Gly386Trp,ENST00000348124,NM_145803.2;TRAF6,downstream_gene_variant,,ENST00000529150,; A ENST00000526995 Transcript missense_variant 1403/4627 1156/1569 386/522 G/W Ggg/Tgg COSM5473124 1 -1 TRAF6 HGNC HGNC:12036 protein_coding YES CCDS7901.1 ENSP00000433623 Q9Y4K3 UPI000000D924 NM_004620.3 deleterious(0) 7/7 PROSITE_profiles:PS50144,hmmpanther:PTHR10131:SF85,hmmpanther:PTHR10131,Gene3D:2.60.210.10,PIRSF_domain:PIRSF015614,SMART_domains:SM00061,Superfamily_domains:SSF49599 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 36490251 36490251 C A 1 0 0 0 0 1 0 0 0 16928 652 23 1 1 TRAF6 11 36490251 Missense_Mutation SNP C C3N-00169_T 2946859 36490251 98596371 111 9519 OR4C3 0 . GRCh38 11 48325478 48325478 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.538C>A p.His180Asn p.H180N ENST00000319856 1/1 106 77 29 107 107 0 strelka-varscan-mutect OR4C3,missense_variant,p.His180Asn,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.His43Asn,ENST00000611380,; A ENST00000319856 Transcript missense_variant 559/1036 538/990 180/329 H/N Cat/Aat 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1338882432 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 48325478 48325478 C A 1 0 0 0 0 1 0 0 0 11126 710 25 2 2 OR4C3 11 48325478 Missense_Mutation SNP C C3N-00169_T 11835227 48325478 86761144 112 9520 OR4A16 0 . GRCh38 11 55343560 55343560 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.360C>T p.= p.R120R ENST00000314721 1/1 208 169 39 224 224 0 strelka-varscan-mutect OR4A16,synonymous_variant,p.=,ENST00000314721,NM_001005274.1; T ENST00000314721 Transcript synonymous_variant 360/987 360/987 120/328 R cgC/cgT 1 1 OR4A16 HGNC HGNC:15153 protein_coding YES CCDS31499.1 ENSP00000325128 Q8NH70 A0A126GW87 UPI0000061EB2 NM_001005274.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF355,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 55343560 55343560 C T 1 0 0 0 0 0 0 0 1 11118 784 28 3 3 OR4A16 11 55343560 Silent SNP C C3N-00169_T 7018082 55343560 79743062 113 9521 TRIM51 0 . GRCh38 11 55885450 55885450 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.22G>T p.Val8Phe p.V8F ENST00000449290 2/7 216 177 39 210 210 0 strelka-varscan-mutect TRIM51,missense_variant,p.Val8Phe,ENST00000449290,NM_032681.3;TRIM51,upstream_gene_variant,,ENST00000244891,;RP11-738O11.9,downstream_gene_variant,,ENST00000533247,; T ENST00000449290 Transcript missense_variant 114/1629 22/1359 8/452 V/F Gtc/Ttc 1 1 TRIM51 HGNC HGNC:19023 protein_coding YES ENSP00000395086 Q9BSJ1 UPI0000DFFA1E NM_032681.3 deleterious(0.04) 2/7 hmmpanther:PTHR24103:SF302,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 55885450 55885450 G T 1 0 0 0 0 1 0 0 0 17019 1029 36 2 2 TRIM51 11 55885450 Missense_Mutation SNP G C3N-00169_T 541890 55885450 79201172 114 9522 OR8I2 0 . GRCh38 11 56093802 56093802 + Silent SNP T T C rs138372442,rs145832034 C3N-00169_T C3N-00169_N T T c.495T>C p.= p.S165S ENST00000302124 1/1 263 242 21 303 303 0 strelka-varscan-mutect OR8I2,synonymous_variant,p.=,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; C ENST00000302124 Transcript synonymous_variant 495/933 495/933 165/310 S agT/agC rs138372442,rs145832034 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs145832034 . 0 187 0 0 0 0 0 23 -8.219819 0 0 1 0 0 C 2 2 38 56093802 56093802 T C 1 0 0 0 0 0 0 0 1 11308 1722 60 5 5 OR8I2 11 56093802 Silent SNP T C3N-00169_T 208352 56093802 78992820 115 9523 TMEM151A 0 . GRCh38 11 66294406 66294406 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.160G>C p.Ala54Pro p.A54P ENST00000327259 2/2 207 180 27 233 233 0 strelka-varscan-mutect TMEM151A,missense_variant,p.Ala54Pro,ENST00000327259,NM_153266.3; C ENST00000327259 Transcript missense_variant 304/2562 160/1407 54/468 A/P Gcc/Ccc 1 1 TMEM151A HGNC HGNC:28497 protein_coding YES CCDS8133.1 ENSP00000326244 Q8N4L1 UPI0000070F9B NM_153266.3 deleterious(0.01) 2/2 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 66294406 66294406 G C 1 0 0 0 0 1 0 0 0 16512 1087 38 4 4 TMEM151A 11 66294406 Missense_Mutation SNP G C3N-00169_T 10200604 66294406 68792216 116 9524 ALDH3B2 0 . GRCh38 11 67665433 67665433 + Silent SNP G G T novel C3N-00169_T C3N-00169_N G G c.558C>A p.= p.T186T ENST00000349015 7/10 201 167 34 231 230 1 strelka-varscan-mutect ALDH3B2,synonymous_variant,p.=,ENST00000349015,NM_000695.3;ALDH3B2,synonymous_variant,p.=,ENST00000530069,NM_001031615.1;ALDH3B2,downstream_gene_variant,,ENST00000525827,;ALDH3B2,downstream_gene_variant,,ENST00000528756,;ALDH3B2,upstream_gene_variant,,ENST00000531248,;ALDH3B2,downstream_gene_variant,,ENST00000531881,;ALDH3B2,downstream_gene_variant,,ENST00000533962,;ALDH3B2,non_coding_transcript_exon_variant,,ENST00000534425,; T ENST00000349015 Transcript synonymous_variant 997/2649 558/1158 186/385 T acC/acA 1 -1 ALDH3B2 HGNC HGNC:411 protein_coding YES CCDS31622.1 ENSP00000255084 P48448 UPI000013CE83 NM_000695.3 7/10 hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF179,Pfam_domain:PF00171,Gene3D:3.40.309.10,Superfamily_domains:SSF53720 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 67665433 67665433 G T 1 0 0 0 0 0 0 0 1 600 1335 47 2 2 ALDH3B2 11 67665433 Silent SNP G C3N-00169_T 1371027 67665433 67421189 117 9525 NEU3 0 . GRCh38 11 75006262 75006262 + Nonsense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1156G>T p.Glu386Ter p.E386* ENST00000294064 3/3 219 184 35 238 237 1 strelka-varscan-mutect NEU3,stop_gained,p.Glu386Ter,ENST00000294064,NM_006656.5;NEU3,stop_gained,p.Glu386Ter,ENST00000531509,;NEU3,3_prime_UTR_variant,,ENST00000532963,;NEU3,intron_variant,,ENST00000529024,;NEU3,downstream_gene_variant,,ENST00000531619,; T ENST00000294064 Transcript stop_gained 2083/6728 1156/1386 386/461 E/* Gag/Tag 1 1 NEU3 HGNC HGNC:7760 protein_coding YES CCDS44682.1 ENSP00000294064 Q9UQ49 A0A024R5N6 UPI000015F481 NM_006656.5 3/3 hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF23,Pfam_domain:PF13088,Gene3D:2.120.10.10,Superfamily_domains:SSF50939 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 75006262 75006262 G T 1 0 0 0 0 0 1 0 0 10378 1175 41 2 2 NEU3 11 75006262 Nonsense_Mutation SNP G C3N-00169_T 7340829 75006262 60080360 118 9526 ALG8 0 . GRCh38 11 78101041 78101041 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1504G>A p.Gly502Ser p.G502S ENST00000299626 13/13 401 316 85 320 320 0 strelka-varscan-mutect ALG8,missense_variant,p.Gly502Ser,ENST00000299626,NM_024079.4;ALG8,missense_variant,p.Gly204Ser,ENST00000530608,;ALG8,missense_variant,p.Gly173Ser,ENST00000526849,;ALG8,3_prime_UTR_variant,,ENST00000376156,NM_001007027.2;ALG8,3_prime_UTR_variant,,ENST00000525783,;ALG8,downstream_gene_variant,,ENST00000615266,;ALG8,downstream_gene_variant,,ENST00000532306,;ALG8,downstream_gene_variant,,ENST00000532552,;ALG8,3_prime_UTR_variant,,ENST00000526737,;ALG8,non_coding_transcript_exon_variant,,ENST00000531213,; T ENST00000299626 Transcript missense_variant 1576/1675 1504/1581 502/526 G/S Ggc/Agc 1 -1 ALG8 HGNC HGNC:23161 protein_coding YES CCDS8258.1 ENSP00000299626 Q9BVK2 A0A024R5K5 UPI000013E5C8 NM_024079.4 deleterious(0.01) 13/13 Pfam_domain:PF03155,hmmpanther:PTHR12413,hmmpanther:PTHR12413:SF2,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 78101041 78101041 C T 1 0 0 0 0 1 0 0 0 623 681 24 3 3 ALG8 11 78101041 Missense_Mutation SNP C C3N-00169_T 3094779 78101041 56985581 119 9527 FAT3 0 . GRCh38 11 92355038 92355038 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.2476G>T p.Val826Phe p.V826F ENST00000525166 1/27 159 122 37 152 152 0 strelka-varscan-mutect FAT3,missense_variant,p.Val976Phe,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Val826Phe,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; T ENST00000525166 Transcript missense_variant 2498/18699 2476/13320 826/4439 V/F Gtc/Ttc 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.08) 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 92355038 92355038 G T 1 0 0 0 0 1 0 0 0 5551 1261 44 2 2 FAT3 11 92355038 Missense_Mutation SNP G C3N-00169_T 14253997 92355038 42731584 120 9528 FAT3 0 . GRCh38 11 92859171 92859171 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.11057C>A p.Thr3686Asn p.T3686N ENST00000525166 20/27 58 42 16 69 69 0 strelka-varscan-mutect FAT3,missense_variant,p.Thr3836Asn,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Thr3686Asn,ENST00000525166,;FAT3,missense_variant,p.Thr171Asn,ENST00000533797,; A ENST00000525166 Transcript missense_variant 11079/18699 11057/13320 3686/4439 T/N aCt/aAt 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.01) 20/27 PROSITE_profiles:PS50025,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.120.200,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 92859171 92859171 C A 1 0 0 0 0 1 0 0 0 5551 565 20 2 2 FAT3 11 92859171 Missense_Mutation SNP C C3N-00169_T 504133 92859171 42227451 121 9529 COLCA2 0 . GRCh38 11 111308295 111308295 + Nonsense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.614C>A p.Ser205Ter p.S205* ENST00000610738 5/5 337 282 55 337 337 0 strelka-varscan-mutect COLCA2,stop_gained,p.Ser108Ter,ENST00000398035,NM_001136105.2;COLCA2,stop_gained,p.Ser108Ter,ENST00000526216,;COLCA2,stop_gained,p.Ser108Ter,ENST00000614153,NM_001271457.1;COLCA2,stop_gained,p.Ser205Ter,ENST00000610738,NM_001271458.1;COLCA2,downstream_gene_variant,,ENST00000528846,;COLCA1,upstream_gene_variant,,ENST00000620864,; A ENST00000610738 Transcript stop_gained 650/1088 614/756 205/251 S/* tCg/tAg COSM3985919 1 1 COLCA2 HGNC HGNC:26978 protein_coding YES CCDS73378.1 ENSP00000484135 A8K830 UPI0002842559 NM_001271458.1 5/5 hmmpanther:PTHR36689 1 HIGH 1 SNV 1 1 1 PASS rs1197634053 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 111308295 111308295 C A 1 0 0 0 0 0 1 0 0 3499 893 31 1 1 COLCA2 11 111308295 Nonsense_Mutation SNP C C3N-00169_T 18449124 111308295 23778327 122 9530 KMT2A 0 . GRCh38 11 118472453 118472453 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1294G>A p.Glu432Lys p.E432K ENST00000534358 3/36 124 113 11 164 164 0 strelka-varscan-mutect KMT2A,missense_variant,p.Glu432Lys,ENST00000534358,NM_001197104.1;KMT2A,missense_variant,p.Glu432Lys,ENST00000389506,NM_005933.3;KMT2A,missense_variant,p.Glu465Lys,ENST00000531904,;KMT2A,intron_variant,,ENST00000533790,;KMT2A,intron_variant,,ENST00000527869,; A ENST00000534358 Transcript missense_variant 1317/16602 1294/11919 432/3972 E/K Gag/Aag 1 1 KMT2A HGNC HGNC:7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 UPI0001E5E732 NM_001197104.1 deleterious_low_confidence(0.04) 3/36 PIRSF_domain:PIRSF010354 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 118472453 118472453 G A 1 0 0 0 0 1 0 0 0 8295 1291 45 3 3 KMT2A 11 118472453 Missense_Mutation SNP G C3N-00169_T 7164158 118472453 16614169 123 9531 VWA5A 0 . GRCh38 11 124136217 124136217 + Missense_Mutation SNP T T A novel C3N-00169_T C3N-00169_N T T c.1448T>A p.Met483Lys p.M483K ENST00000456829 13/19 179 163 16 156 156 0 strelka-varscan-mutect VWA5A,missense_variant,p.Met483Lys,ENST00000456829,NM_001130142.1;VWA5A,missense_variant,p.Met483Lys,ENST00000392748,NM_014622.4; A ENST00000456829 Transcript missense_variant 1699/4388 1448/2361 483/786 M/K aTg/aAg 1 1 VWA5A HGNC HGNC:6658 protein_coding YES CCDS8444.1 ENSP00000407726 O00534 A0A024R3H3 UPI0000158B80 NM_001130142.1 tolerated(0.12) 13/19 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF100 MODERATE 1 SNV 1 1 PASS rs1201824936 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 124136217 124136217 T A 1 0 0 0 0 1 0 0 0 17796 1464 51 4 4 VWA5A 11 124136217 Missense_Mutation SNP T C3N-00169_T 5663764 124136217 10950405 124 9532 SNX19 0 . GRCh38 11 130906133 130906133 + Nonsense_Mutation SNP C C A rs756176482 C3N-00169_T C3N-00169_N C C c.2263G>T p.Glu755Ter p.E755* ENST00000265909 7/11 81 61 20 95 95 0 strelka-varscan-mutect SNX19,stop_gained,p.Glu755Ter,ENST00000265909,NM_014758.2;SNX19,stop_gained,p.Glu135Ter,ENST00000530356,;SNX19,stop_gained,p.Glu135Ter,ENST00000528555,NM_001301089.1;SNX19,splice_region_variant,,ENST00000534726,;SNX19,intron_variant,,ENST00000533214,;SNX19,splice_region_variant,,ENST00000533318,;SNX19,splice_region_variant,,ENST00000524460,;SNX19,upstream_gene_variant,,ENST00000526579,;SNX19,non_coding_transcript_exon_variant,,ENST00000527451,;SNX19,downstream_gene_variant,,ENST00000531608,; A ENST00000265909 Transcript stop_gained,splice_region_variant 2833/6535 2263/2979 755/992 E/* Gag/Tag rs756176482 1 -1 SNX19 HGNC HGNC:21532 protein_coding YES CCDS31721.1 ENSP00000265909 Q92543 UPI000013D6A5 NM_014758.2 7/11 hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF31 HIGH 1 SNV 1 1 PASS rs756176482 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 38 130906133 130906133 C A 1 0 0 0 0 0 1 0 0 15211 869 30 2 2 SNX19 11 130906133 Nonsense_Mutation SNP C C3N-00169_T 6769916 130906133 4180489 125 9533 NTM 0 . GRCh38 11 132307799 132307799 + Missense_Mutation SNP C C T C3N-00169_T C3N-00169_N C C c.637C>T p.Arg213Trp p.R213W ENST00000425719 4/8 198 168 30 203 203 0 strelka-varscan-mutect NTM,missense_variant,p.Arg213Trp,ENST00000374786,NM_016522.2;NTM,missense_variant,p.Arg213Trp,ENST00000374791,NM_001048209.1;NTM,missense_variant,p.Arg37Trp,ENST00000427481,;NTM,missense_variant,p.Arg37Trp,ENST00000539799,;NTM,missense_variant,p.Arg213Trp,ENST00000425719,NM_001144058.1;NTM,missense_variant,p.Arg213Trp,ENST00000374784,NM_001144059.1;NTM,upstream_gene_variant,,ENST00000457381,;NTM,downstream_gene_variant,,ENST00000550167,;NTM,non_coding_transcript_exon_variant,,ENST00000474900,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,non_coding_transcript_exon_variant,,ENST00000496094,;NTM,non_coding_transcript_exon_variant,,ENST00000498764,;NTM,non_coding_transcript_exon_variant,,ENST00000490356,;NTM,downstream_gene_variant,,ENST00000482316,; T ENST00000425719 Transcript missense_variant 657/1607 637/1068 213/355 R/W Cgg/Tgg COSM288344,COSM288345,COSM3782594,COSM3782595 1 1 NTM HGNC HGNC:17941 protein_coding YES CCDS44777.1 ENSP00000396722 Q9P121 UPI00001A58B9 NM_001144058.1 deleterious(0) 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF116,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs951593215 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 132307799 132307799 C T 1 0 0 0 0 1 0 0 0 10763 527 19 1 1 NTM 11 132307799 Missense_Mutation SNP C C3N-00169_T 1401666 132307799 2778823 126 9534 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-00169_T C3N-00169_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 243 174 69 324 324 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-00169_T 25245351 108029958 127 9535 SCN8A 0 . GRCh38 12 51762595 51762595 + Silent SNP C C T rs773865400 C3N-00169_T C3N-00169_N C C c.2463C>T p.= p.D821D ENST00000354534 15/27 201 156 45 215 215 0 strelka-varscan-mutect SCN8A,synonymous_variant,p.=,ENST00000354534,NM_014191.3;SCN8A,synonymous_variant,p.=,ENST00000545061,NM_001177984.2;SCN8A,synonymous_variant,p.=,ENST00000599343,;SCN8A,synonymous_variant,p.=,ENST00000627620,;SCN8A,synonymous_variant,p.=,ENST00000355133,;SCN8A,synonymous_variant,p.=,ENST00000636945,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,non_coding_transcript_exon_variant,,ENST00000550891,; T ENST00000354534 Transcript synonymous_variant 2641/11556 2463/5943 821/1980 D gaC/gaT rs773865400,COSM4042732,COSM4042733 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 15/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037,Gene3D:1.20.120.350,Pfam_domain:PF00520,Superfamily_domains:SSF81324 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs773865400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 51762595 51762595 C T 1 0 0 0 0 0 0 0 1 14193 535 19 1 1 SCN8A 12 51762595 Silent SNP C C3N-00169_T 26517244 51762595 81512714 128 9536 KRT75 0 . GRCh38 12 52431635 52431635 + Missense_Mutation SNP C C A rs769201202 C3N-00169_T C3N-00169_N C C c.778G>T p.Val260Leu p.V260L ENST00000252245 4/9 141 109 32 205 205 0 strelka-varscan-mutect KRT75,missense_variant,p.Val260Leu,ENST00000252245,NM_004693.2;RP11-1020M18.10,downstream_gene_variant,,ENST00000548135,; A ENST00000252245 Transcript missense_variant 999/2324 778/1656 260/551 V/L Gta/Tta rs769201202 1 -1 KRT75 HGNC HGNC:24431 protein_coding YES CCDS8827.1 ENSP00000252245 O95678 UPI000013CD4E NM_004693.2 deleterious(0.02) 4/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF200,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs769201202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 52431635 52431635 C A 1 0 0 0 0 1 0 0 0 8370 550 19 1 1 KRT75 12 52431635 Missense_Mutation SNP C C3N-00169_T 669040 52431635 80843674 129 9537 NTS 0 . GRCh38 12 85878483 85878483 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.274G>T p.Ala92Ser p.A92S ENST00000256010 3/4 81 58 23 133 132 1 strelka-varscan-mutect NTS,missense_variant,p.Ala92Ser,ENST00000256010,NM_006183.4;NTS,intron_variant,,ENST00000551529,;NTS,non_coding_transcript_exon_variant,,ENST00000550879,; T ENST00000256010 Transcript missense_variant 381/1237 274/513 92/170 A/S Gct/Tct 1 1 NTS HGNC HGNC:8038 protein_coding YES CCDS9029.1 ENSP00000256010 P30990 Q6FH20 UPI0000000CAD NM_006183.4 tolerated(0.52) 3/4 PD016590,Pfam_domain:PF07421,Prints_domain:PR01668,hmmpanther:PTHR15356,hmmpanther:PTHR15356:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 85878483 85878483 G T 1 0 0 0 0 1 0 0 0 10775 1319 46 2 2 NTS 12 85878483 Missense_Mutation SNP G C3N-00169_T 33446848 85878483 47396826 130 9538 DCN 0 . GRCh38 12 91172811 91172811 + Missense_Mutation SNP A A C novel C3N-00169_T C3N-00169_N A A c.269T>G p.Ile90Arg p.I90R ENST00000546745 3/3 96 75 21 99 99 0 strelka-varscan-mutect DCN,missense_variant,p.Ile90Arg,ENST00000546745,;DCN,missense_variant,p.Ile90Arg,ENST00000550099,;DCN,intron_variant,,ENST00000052754,NM_001920.3;DCN,intron_variant,,ENST00000393155,NM_133503.2;DCN,intron_variant,,ENST00000552962,;DCN,intron_variant,,ENST00000425043,NM_133505.2;DCN,intron_variant,,ENST00000549513,;DCN,intron_variant,,ENST00000547568,;DCN,intron_variant,,ENST00000420120,NM_133504.2;DCN,intron_variant,,ENST00000547937,;DCN,intron_variant,,ENST00000546391,;DCN,intron_variant,,ENST00000552145,;DCN,intron_variant,,ENST00000550563,;DCN,intron_variant,,ENST00000546370,;DCN,intron_variant,,ENST00000441303,NM_133506.2;DCN,intron_variant,,ENST00000456569,NM_133507.2;DCN,downstream_gene_variant,,ENST00000551354,; C ENST00000546745 Transcript missense_variant 357/1026 269/297 90/98 I/R aTa/aGa 1 -1 DCN HGNC HGNC:2705 protein_coding ENSP00000448857 F8VU58 UPI0000E59883 3/3 MODERATE SNV 3 1 PASS rs886187214 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 91172811 91172811 A C 1 0 0 0 0 1 0 0 0 4099 449 16 5 5 DCN 12 91172811 Missense_Mutation SNP A C3N-00169_T 5294328 91172811 42102498 131 9539 ACACB 0 . GRCh38 12 109237178 109237178 + Missense_Mutation SNP G G A rs754289848 C3N-00169_T C3N-00169_N G G c.4460G>A p.Arg1487His p.R1487H ENST00000338432 34/53 230 171 59 356 356 0 strelka-varscan-mutect ACACB,missense_variant,p.Arg1487His,ENST00000338432,;ACACB,missense_variant,p.Arg1487His,ENST00000377848,NM_001093.3;ACACB,missense_variant,p.Arg153His,ENST00000377854,;ACACB,missense_variant,p.Arg154His,ENST00000538526,;ACACB,upstream_gene_variant,,ENST00000537347,;ACACB,downstream_gene_variant,,ENST00000542524,;ACACB,upstream_gene_variant,,ENST00000534852,; A ENST00000338432 Transcript missense_variant 4579/9360 4460/7377 1487/2458 R/H cGc/cAc rs754289848,COSM1181490,COSM1181491 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB deleterious(0.03) 34/53 hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF94,Pfam_domain:PF08326 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs754289848 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 109237178 109237178 G A 1 0 0 0 0 1 0 0 0 150 1087 38 1 1 ACACB 12 109237178 Missense_Mutation SNP G C3N-00169_T 18064367 109237178 24038131 132 9540 AC127070.1 0 . GRCh38 12 132786367 132786367 + Frame_Shift_Del DEL C C - rs756151463 C3N-00169_T C3N-00169_N C C c.3095delG p.Gly1032AlafsTer38 p.G1032Afs*38 ENST00000204726 15/24 63 43 20 98 98 0 sindel-varindel-pindel GOLGA3,frameshift_variant,p.Gly1032AlafsTer38,ENST00000204726,NM_005895.3;GOLGA3,frameshift_variant,p.Gly1032AlafsTer38,ENST00000450791,;GOLGA3,frameshift_variant,p.Gly1032AlafsTer38,ENST00000456883,;AC127070.1,frameshift_variant,p.Gly1032AlafsTer38,ENST00000545875,NM_001172557.1;GOLGA3,non_coding_transcript_exon_variant,,ENST00000537452,; - ENST00000204726 Transcript frameshift_variant 3654/9252 3095/4497 1032/1498 G/X gGc/gc rs756151463 1 -1 GOLGA3 HGNC HGNC:4426 protein_coding YES CCDS9281.1 ENSP00000204726 Q08378 UPI0000190979 NM_005895.3 15/24 hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF26 HIGH deletion 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999986 1 1 1 0 - 7 5 38 132786367 132786367 C - 1 0 1 0 1 0 0 0 0 142 739 26 0 0 AC127070.1 12 132786367 Frame_Shift_Del DEL C C3N-00169_T 23549189 132786367 488942 133 9541 RNF31 0 . GRCh38 14 24147732 24147732 + Missense_Mutation SNP G G C rs370135028 C3N-00169_T C3N-00169_N G G c.34G>C p.Val12Leu p.V12L ENST00000324103 1/21 81 62 19 106 106 0 strelka-varscan-mutect RNF31,missense_variant,p.Val12Leu,ENST00000324103,NM_017999.4;RNF31,missense_variant,p.Val12Leu,ENST00000557991,;RNF31,missense_variant,p.Val12Leu,ENST00000560875,;RNF31,intron_variant,,ENST00000559275,NM_001310332.1;RNF31,intron_variant,,ENST00000559533,;RNF31,intron_variant,,ENST00000560071,;RNF31,intron_variant,,ENST00000559308,;RNF31,intron_variant,,ENST00000559260,;RNF31,upstream_gene_variant,,ENST00000560787,;PSME2,upstream_gene_variant,,ENST00000216802,NM_002818.2;PSME2,upstream_gene_variant,,ENST00000615264,;PSME2,upstream_gene_variant,,ENST00000560410,;PSME2,upstream_gene_variant,,ENST00000559056,;PSME2,upstream_gene_variant,,ENST00000630027,;PSME2,upstream_gene_variant,,ENST00000620784,;RNF31,non_coding_transcript_exon_variant,,ENST00000559882,;RNF31,intron_variant,,ENST00000557878,;RNF31,intron_variant,,ENST00000559438,;RNF31,intron_variant,,ENST00000558634,;PSME2,upstream_gene_variant,,ENST00000471700,;RNF31,upstream_gene_variant,,ENST00000559583,;PSME2,upstream_gene_variant,,ENST00000561103,;PSME2,upstream_gene_variant,,ENST00000559613,;RNF31,missense_variant,p.Val12Leu,ENST00000491351,;RNF31,non_coding_transcript_exon_variant,,ENST00000560342,;RP11-468E2.4,upstream_gene_variant,,ENST00000558468,;PSME2,upstream_gene_variant,,ENST00000558931,;RNF31,upstream_gene_variant,,ENST00000559071,;PSME2,upstream_gene_variant,,ENST00000559453,;PSME2,upstream_gene_variant,,ENST00000558273,;PSME2,upstream_gene_variant,,ENST00000560788,;RNF31,upstream_gene_variant,,ENST00000558907,;PSME2,upstream_gene_variant,,ENST00000560592,;PSME2,upstream_gene_variant,,ENST00000559493,;PSME2,upstream_gene_variant,,ENST00000559042,;PSME2,upstream_gene_variant,,ENST00000560370,;PSME2,upstream_gene_variant,,ENST00000559005,;PSME2,upstream_gene_variant,,ENST00000559359,; C ENST00000324103 Transcript missense_variant 354/3627 34/3219 12/1072 V/L Gtg/Ctg rs370135028 1 1 RNF31 HGNC HGNC:16031 protein_coding YES CCDS41931.1 ENSP00000315112 Q96EP0 UPI0000072F93 NM_017999.4 tolerated_low_confidence(0.32) 1/21 hmmpanther:PTHR16004 MODERATE 1 SNV 1 1 PASS rs370135028 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 3 2 38 24147732 24147732 G C 1 0 0 0 0 1 0 0 0 13667 1261 44 4 4 RNF31 14 24147732 Missense_Mutation SNP G C3N-00169_T 24147732 82895986 134 9542 SYT16 0 . GRCh38 14 62100456 62100456 + Missense_Mutation SNP T T C novel C3N-00169_T C3N-00169_N T T c.1687T>C p.Ser563Pro p.S563P ENST00000568344 6/6 159 131 28 199 199 0 strelka-varscan-mutect SYT16,missense_variant,p.Ser563Pro,ENST00000568344,NM_031914.2;SYT16,missense_variant,p.Ser121Pro,ENST00000430451,;RP11-355I22.2,downstream_gene_variant,,ENST00000554252,;SYT16,3_prime_UTR_variant,,ENST00000555409,; C ENST00000568344 Transcript missense_variant 1884/13978 1687/1938 563/645 S/P Tcc/Ccc 1 1 SYT16 HGNC HGNC:23142 protein_coding YES CCDS45121.1 ENSP00000478637 Q17RD7 UPI0000EE1AC0 NM_031914.2 deleterious(0) 6/6 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF113,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 62100456 62100456 T C 1 0 0 0 0 1 0 0 0 15866 1667 58 5 5 SYT16 14 62100456 Missense_Mutation SNP T C3N-00169_T 37952724 62100456 44943262 135 9543 KCNH5 0 . GRCh38 14 62981101 62981101 + Missense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.713T>A p.Phe238Tyr p.F238Y ENST00000322893 6/11 244 190 54 277 276 1 strelka-varscan-mutect KCNH5,missense_variant,p.Phe238Tyr,ENST00000322893,NM_139318.4;KCNH5,missense_variant,p.Phe238Tyr,ENST00000420622,NM_172375.2;KCNH5,missense_variant,p.Phe180Tyr,ENST00000394968,;KCNH5,non_coding_transcript_exon_variant,,ENST00000394964,; T ENST00000322893 Transcript missense_variant 982/11290 713/2967 238/988 F/Y tTc/tAc 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 deleterious(0) 6/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 62981101 62981101 A T 1 0 0 0 0 1 0 0 0 7951 246 9 4 4 KCNH5 14 62981101 Missense_Mutation SNP A C3N-00169_T 880645 62981101 44062617 136 9544 C15orf41 0 . GRCh38 15 36691706 36691706 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.368G>T p.Ser123Ile p.S123I ENST00000566621 6/11 117 89 28 118 118 0 strelka-varscan-mutect C15orf41,missense_variant,p.Ser123Ile,ENST00000566621,NM_001321759.1,NM_001321761.1,NM_001290233.1,NM_001130010.2;C15orf41,missense_variant,p.Ser25Ile,ENST00000567389,NM_032499.5;C15orf41,missense_variant,p.Ser25Ile,ENST00000338183,;C15orf41,missense_variant,p.Ser123Ile,ENST00000437989,;C15orf41,missense_variant,p.Ser123Ile,ENST00000569302,;C15orf41,missense_variant,p.Ser25Ile,ENST00000562877,NM_001290232.1;C15orf41,missense_variant,p.Ser25Ile,ENST00000566807,;C15orf41,missense_variant,p.Ser86Ile,ENST00000564586,;C15orf41,non_coding_transcript_exon_variant,,ENST00000570265,;C15orf41,upstream_gene_variant,,ENST00000565792,; T ENST00000566621 Transcript missense_variant 618/2866 368/846 123/281 S/I aGt/aTt 1 1 C15orf41 HGNC HGNC:26929 protein_coding YES CCDS45215.1 ENSP00000455397 Q9Y2V0 UPI00001FE1DF NM_001321759.1,NM_001321761.1,NM_001290233.1,NM_001130010.2 deleterious(0.02) 6/11 hmmpanther:PTHR31661,hmmpanther:PTHR31661:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 36691706 36691706 G T 1 0 0 0 0 1 0 0 0 1845 1029 36 2 2 C15orf41 15 36691706 Missense_Mutation SNP G C3N-00169_T 36691706 65299483 137 9545 SEMA6D 0 . GRCh38 15 47770997 47770997 + Missense_Mutation SNP A A G C3N-00169_T C3N-00169_N A A c.2434A>G p.Ser812Gly p.S812G ENST00000316364 19/19 279 218 61 462 462 0 strelka-varscan-mutect SEMA6D,missense_variant,p.Ser812Gly,ENST00000316364,NM_153618.1;SEMA6D,missense_variant,p.Ser750Gly,ENST00000558014,NM_001198999.1;SEMA6D,missense_variant,p.Ser756Gly,ENST00000354744,NM_153617.1;SEMA6D,missense_variant,p.Ser750Gly,ENST00000358066,NM_020858.1;SEMA6D,missense_variant,p.Ser737Gly,ENST00000389428,NM_153616.1;SEMA6D,missense_variant,p.Ser812Gly,ENST00000536845,;SEMA6D,3_prime_UTR_variant,,ENST00000355997,NM_153619.1;SEMA6D,3_prime_UTR_variant,,ENST00000558816,;SEMA6D,downstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000559064,;SEMA6D,downstream_gene_variant,,ENST00000558431,; G ENST00000316364 Transcript missense_variant 2873/6099 2434/3222 812/1073 S/G Agt/Ggt COSM1147535,COSM700399 1 1 SEMA6D HGNC HGNC:16770 protein_coding YES CCDS32225.1 ENSP00000324857 Q8NFY4 UPI000006E201 NM_153618.1 tolerated(0.35) 19/19 Low_complexity_(Seg):seg,hmmpanther:PTHR11036:SF65,hmmpanther:PTHR11036 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1483806899 . 0 208 0 0 2 0 0 0 -20 0.9984383 1 1 1 0 G 3 3 38 47770997 47770997 A G 1 0 0 0 0 1 0 0 0 14318 420 15 5 5 SEMA6D 15 47770997 Missense_Mutation SNP A C3N-00169_T 11079291 47770997 54220192 138 9546 FBN1 0 . GRCh38 15 48490026 48490026 + Silent SNP C C G novel C3N-00169_T C3N-00169_N C C c.2907G>C p.= p.L969L ENST00000316623 25/66 295 201 94 379 379 0 strelka-varscan-mutect FBN1,synonymous_variant,p.=,ENST00000316623,NM_000138.4;FBN1,intron_variant,,ENST00000537463,; G ENST00000316623 Transcript synonymous_variant 3363/11756 2907/8616 969/2871 L ctG/ctC 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 25/66 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,Superfamily_domains:SSF57581 LOW 1 SNV 1 1 PASS rs886039154 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 48490026 48490026 C G 1 0 0 0 0 0 0 0 1 5565 697 25 4 4 FBN1 15 48490026 Silent SNP C C3N-00169_T 719029 48490026 53501163 139 9547 IGDCC3 0 . GRCh38 15 65333400 65333400 + Missense_Mutation SNP C C A novel C3N-00169_T C3N-00169_N C C c.839G>T p.Gly280Val p.G280V ENST00000327987 6/14 57 43 14 104 104 0 strelka-varscan-mutect IGDCC3,missense_variant,p.Gly280Val,ENST00000327987,NM_004884.3;IGDCC3,missense_variant,p.Gly143Val,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559058,;IGDCC3,non_coding_transcript_exon_variant,,ENST00000559231,; A ENST00000327987 Transcript missense_variant 1091/4479 839/2445 280/814 G/V gGg/gTg 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 deleterious(0) 6/14 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 65333400 65333400 C A 1 0 0 0 0 1 0 0 0 7474 623 22 2 2 IGDCC3 15 65333400 Missense_Mutation SNP C C3N-00169_T 16843374 65333400 36657789 140 9548 LINGO1 0 . GRCh38 15 77614363 77614363 + Missense_Mutation SNP C C T rs752005315 C3N-00169_T C3N-00169_N C C c.1544G>A p.Arg515His p.R515H ENST00000355300 2/2 181 132 49 236 236 0 strelka-varscan-mutect LINGO1,missense_variant,p.Arg515His,ENST00000355300,NM_032808.6;LINGO1,missense_variant,p.Arg509His,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,downstream_gene_variant,,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000561686,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000564472,; T ENST00000355300 Transcript missense_variant 1719/3055 1544/1863 515/620 R/H cGc/cAc rs752005315,COSM4698083 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 tolerated(0.23) 2/2 Gene3D:2.60.40.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752005315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 77614363 77614363 C T 1 0 0 0 0 1 0 0 0 8735 768 27 1 1 LINGO1 15 77614363 Missense_Mutation SNP C C3N-00169_T 12280963 77614363 24376826 141 9549 SOX8 0 . GRCh38 16 984880 984880 + Missense_Mutation SNP G G T C3N-00169_T C3N-00169_N G G c.835G>T p.Ala279Ser p.A279S ENST00000293894 3/3 137 129 8 226 226 0 strelka-varscan-mutect SOX8,missense_variant,p.Ala279Ser,ENST00000293894,NM_014587.4;LMF1,upstream_gene_variant,,ENST00000570014,;RP11-161M6.2,upstream_gene_variant,,ENST00000565467,;RP11-161M6.2,upstream_gene_variant,,ENST00000568394,;RP11-161M6.2,upstream_gene_variant,,ENST00000562570,;RP11-161M6.2,upstream_gene_variant,,ENST00000563863,;RP11-161M6.2,upstream_gene_variant,,ENST00000565069,;RP11-161M6.2,upstream_gene_variant,,ENST00000563837,;SOX8,non_coding_transcript_exon_variant,,ENST00000566034,;LMF1,upstream_gene_variant,,ENST00000545827,; T ENST00000293894 Transcript missense_variant 950/3049 835/1341 279/446 A/S Gcc/Tcc COSM1227184 1 1 SOX8 HGNC HGNC:11203 protein_coding YES CCDS10428.1 ENSP00000293894 P57073 UPI00000015FB NM_014587.4 tolerated(0.26) 3/3 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF20 1 MODERATE 1 SNV 1 1 1 PASS rs1286616400 . 0 207 2 0 0 0 0 0 -15.48814 1 1 1 1 0 T 3 4 38 984880 984880 G T 1 0 0 0 0 1 0 0 0 15283 1087 38 1 1 SOX8 16 984880 Missense_Mutation SNP G C3N-00169_T 984880 89353465 142 9550 CACNA1H 0 . GRCh38 16 1194979 1194979 + Nonsense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.307G>T p.Glu103Ter p.E103* ENST00000348261 3/35 197 171 26 330 330 0 strelka-varscan-mutect CACNA1H,stop_gained,p.Glu103Ter,ENST00000348261,NM_021098.2;CACNA1H,stop_gained,p.Glu103Ter,ENST00000358590,NM_001005407.1;CACNA1H,stop_gained,p.Glu103Ter,ENST00000565831,;CACNA1H,upstream_gene_variant,,ENST00000564954,; T ENST00000348261 Transcript stop_gained 675/8208 307/7062 103/2353 E/* Gag/Tag 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 3/35 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192,Superfamily_domains:SSF81324 HIGH 1 SNV 1 1 PASS rs970648879 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 1194979 1194979 G T 1 0 0 0 0 0 1 0 0 2233 1059 37 1 1 CACNA1H 16 1194979 Nonsense_Mutation SNP G C3N-00169_T 210099 1194979 89143366 143 9551 IFT140 0 . GRCh38 16 1566190 1566190 + Silent SNP C C G rs775156902 C3N-00169_T C3N-00169_N C C c.1872G>C p.= p.T624T ENST00000426508 16/31 186 167 19 215 215 0 strelka-varscan-mutect IFT140,synonymous_variant,p.=,ENST00000426508,NM_014714.3;IFT140,non_coding_transcript_exon_variant,,ENST00000439987,;IFT140,3_prime_UTR_variant,,ENST00000397417,;IFT140,non_coding_transcript_exon_variant,,ENST00000565298,;IFT140,upstream_gene_variant,,ENST00000561954,; G ENST00000426508 Transcript synonymous_variant 2236/5270 1872/4389 624/1462 T acG/acC rs775156902,COSM5439103,COSM5687487 1 -1 IFT140 HGNC HGNC:29077 protein_coding YES CCDS10439.1 ENSP00000406012 Q96RY7 UPI0000073C64 NM_014714.3 16/31 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs775156902 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 1566190 1566190 C G 1 0 0 0 0 0 0 0 1 7460 755 27 4 4 IFT140 16 1566190 Silent SNP C C3N-00169_T 371211 1566190 88772155 144 9552 KIAA0430 0 . GRCh38 16 15604202 15604202 + Missense_Mutation SNP G G A C3N-00169_T C3N-00169_N G G c.4379C>T p.Thr1460Ile p.T1460I ENST00000396368 22/27 184 158 26 202 201 1 strelka-varscan-mutect KIAA0430,missense_variant,p.Thr1460Ile,ENST00000396368,NM_014647.3;KIAA0430,missense_variant,p.Thr1295Ile,ENST00000540441,;KIAA0430,missense_variant,p.Thr1460Ile,ENST00000551742,NM_001184998.1;KIAA0430,missense_variant,p.Thr1457Ile,ENST00000548025,NM_001184999.1;C16orf45,intron_variant,,ENST00000565857,;CTB-193M12.1,upstream_gene_variant,,ENST00000549756,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000547936,;KIAA0430,3_prime_UTR_variant,,ENST00000552553,;KIAA0430,upstream_gene_variant,,ENST00000552771,;KIAA0430,upstream_gene_variant,,ENST00000551878,;KIAA0430,upstream_gene_variant,,ENST00000549337,; A ENST00000396368 Transcript missense_variant 4586/7743 4379/5229 1460/1742 T/I aCc/aTc COSM1255569 1 -1 KIAA0430 HGNC HGNC:29562 protein_coding YES CCDS10562.2 ENSP00000379654 Q9Y4F3 UPI00006881BC NM_014647.3 tolerated(0.13) 22/27 Pfam_domain:PF12872,PROSITE_profiles:PS51644,hmmpanther:PTHR14379,hmmpanther:PTHR14379:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1264892329 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 15604202 15604202 G A 1 0 0 0 0 1 0 0 0 8086 1261 44 3 3 KIAA0430 16 15604202 Missense_Mutation SNP G C3N-00169_T 14038012 15604202 74734143 145 9553 XYLT1 0 . GRCh38 16 17134484 17134484 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.2016G>A p.= p.E672E ENST00000261381 9/12 136 116 20 138 138 0 strelka-varscan-mutect XYLT1,synonymous_variant,p.=,ENST00000261381,NM_022166.3;CTD-2576D5.4,upstream_gene_variant,,ENST00000567344,; T ENST00000261381 Transcript synonymous_variant 2101/9891 2016/2880 672/959 E gaG/gaA 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 9/12 hmmpanther:PTHR19297:SF91,hmmpanther:PTHR19297,Pfam_domain:PF12529 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 17134484 17134484 C T 1 0 0 0 0 0 0 0 1 18022 912 32 3 3 XYLT1 16 17134484 Silent SNP C C3N-00169_T 1530282 17134484 73203861 146 9554 ZNF469 0 . GRCh38 16 88432602 88432602 + Missense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.5048A>T p.Glu1683Val p.E1683V ENST00000437464 2/2 470 327 143 681 681 0 strelka-varscan-mutect ZNF469,missense_variant,p.Glu1711Val,ENST00000565624,;ZNF469,missense_variant,p.Glu1683Val,ENST00000437464,NM_001127464.2; T ENST00000437464 Transcript missense_variant 5048/13203 5048/11778 1683/3925 E/V gAa/gTa 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 deleterious(0.01) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 88432602 88432602 A T 1 0 0 0 0 1 0 0 0 18500 246 9 4 4 ZNF469 16 88432602 Missense_Mutation SNP A C3N-00169_T 71298118 88432602 1905743 147 9555 SGSM2 0 . GRCh38 17 2373486 2373486 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.2073C>T p.= p.I691I ENST00000268989 17/24 86 76 10 120 120 0 strelka-varscan-mutect SGSM2,synonymous_variant,p.=,ENST00000268989,NM_014853.2;SGSM2,synonymous_variant,p.=,ENST00000426855,NM_001098509.1;SGSM2,synonymous_variant,p.=,ENST00000574563,;SGSM2,upstream_gene_variant,,ENST00000573851,;RP1-59D14.5,downstream_gene_variant,,ENST00000574290,;RP1-59D14.5,downstream_gene_variant,,ENST00000573007,;SGSM2,non_coding_transcript_exon_variant,,ENST00000574857,;SGSM2,non_coding_transcript_exon_variant,,ENST00000573717,;SGSM2,upstream_gene_variant,,ENST00000572841,;SGSM2,downstream_gene_variant,,ENST00000575367,;SGSM2,downstream_gene_variant,,ENST00000574250,; T ENST00000268989 Transcript synonymous_variant 2250/4863 2073/3156 691/1051 I atC/atT 1 1 SGSM2 HGNC HGNC:29026 protein_coding YES CCDS32526.1 ENSP00000268989 O43147 UPI0000160300 NM_014853.2 17/24 PROSITE_profiles:PS50086,SMART_domains:SM00164 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.98933 1 1 1 1 0 T 2 4 38 2373486 2373486 C T 1 0 0 0 0 0 0 0 1 14481 845 30 3 3 SGSM2 17 2373486 Silent SNP C C3N-00169_T 2373486 80883955 148 9556 TP53 0 . GRCh38 17 7674217 7674217 + Missense_Mutation SNP C C A rs587782329 C3N-00169_T C3N-00169_N C C c.746G>T p.Arg249Met p.R249M ENST00000269305 7/11 197 142 55 311 311 0 strelka-varscan-mutect TP53,missense_variant,p.Arg249Met,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg249Met,ENST00000420246,;TP53,missense_variant,p.Arg210Met,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg210Met,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg249Met,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg210Met,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg249Met,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg210Met,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg249Met,ENST00000445888,;TP53,missense_variant,p.Arg210Met,ENST00000619485,;TP53,missense_variant,p.Arg117Met,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg90Met,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg117Met,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg90Met,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg117Met,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg90Met,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg249Met,ENST00000359597,;TP53,missense_variant,p.Arg238Met,ENST00000615910,;TP53,missense_variant,p.Arg249Met,ENST00000413465,;TP53,missense_variant,p.Arg117Met,ENST00000509690,;TP53,incomplete_terminal_codon_variant,p.=,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg210Met,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 936/2579 746/1182 249/393 R/M aGg/aTg rs587782329,TP53_g.13383G>T,TP53_g.13383G>C,TP53_g.13383G>A,TP53_g.13383del,COSM129832,COSM129833,COSM1649403,COSM1728798,COSM326723,COSM326724,COSM3388182,COSM3403260,COSM375642,COSM375643,COSM43665,COSM43871,COSM44091,COSM44916 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs587782329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 7674217 7674217 C A 1 0 0 0 0 1 0 0 0 16859 681 24 2 2 TP53 17 7674217 Missense_Mutation SNP C C3N-00169_T 5300731 7674217 75583224 149 9557 TBC1D26 0 . GRCh38 17 15738823 15738823 + Nonsense_Mutation SNP G G T rs749678463 C3N-00169_T C3N-00169_N G G c.490G>T p.Gly164Ter p.G164* ENST00000437605 8/15 409 339 70 511 509 2 strelka-varscan-mutect TBC1D26,stop_gained,p.Gly164Ter,ENST00000612583,;TBC1D26,stop_gained,p.Gly164Ter,ENST00000437605,NM_178571.4;TBC1D26,stop_gained,p.Gly164Ter,ENST00000579428,;TBC1D26,downstream_gene_variant,,ENST00000464963,;TBC1D26,downstream_gene_variant,,ENST00000580596,;TBC1D26,downstream_gene_variant,,ENST00000584301,;TBC1D26,downstream_gene_variant,,ENST00000578506,;AC005324.6,intron_variant,,ENST00000434017,;AC005324.6,intron_variant,,ENST00000433873,;AC005324.6,downstream_gene_variant,,ENST00000580194,;TBC1D26,downstream_gene_variant,,ENST00000585171,;TBC1D26,downstream_gene_variant,,ENST00000583675,;TBC1D26,downstream_gene_variant,,ENST00000583620,;TBC1D26,downstream_gene_variant,,ENST00000582140,;TBC1D26,downstream_gene_variant,,ENST00000582534,;TBC1D26,stop_gained,p.Gly164Ter,ENST00000469477,;TBC1D26,3_prime_UTR_variant,,ENST00000413242,;TBC1D26,non_coding_transcript_exon_variant,,ENST00000491819,;TBC1D26,non_coding_transcript_exon_variant,,ENST00000580970,;TBC1D26,downstream_gene_variant,,ENST00000412988,; T ENST00000437605 Transcript stop_gained 740/1868 490/753 164/250 G/* Gga/Tga rs749678463,COSM5633881,COSM5633882 1 1 TBC1D26 HGNC HGNC:28745 protein_coding YES CCDS42265.1 ENSP00000410111 Q86UD7 UPI0000246DD7 NM_178571.4 8/15 PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF322,hmmpanther:PTHR22957,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164,Superfamily_domains:SSF47923 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs749678463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 15738823 15738823 G T 1 0 0 0 0 0 1 0 0 16016 1117 39 1 1 TBC1D26 17 15738823 Nonsense_Mutation SNP G C3N-00169_T 8064606 15738823 67518618 150 9558 RHBDL3 0 . GRCh38 17 32321059 32321059 + Missense_Mutation SNP G G T rs372423346 C3N-00169_T C3N-00169_N G G c.1045G>T p.Val349Leu p.V349L ENST00000269051 9/9 365 289 76 453 453 0 strelka-varscan-mutect RHBDL3,missense_variant,p.Val349Leu,ENST00000269051,NM_138328.2;RHBDL3,missense_variant,p.Val251Leu,ENST00000536287,;RHBDL3,missense_variant,p.Val341Leu,ENST00000538145,;RHBDL3,missense_variant,p.Arg315Leu,ENST00000431505,;C17orf75,downstream_gene_variant,,ENST00000583104,;RP11-227G15.3,upstream_gene_variant,,ENST00000581915,;RP11-227G15.3,upstream_gene_variant,,ENST00000578389,;RHBDL3,3_prime_UTR_variant,,ENST00000578006,;RHBDL3,downstream_gene_variant,,ENST00000582967,; T ENST00000269051 Transcript missense_variant 1059/4661 1045/1215 349/404 V/L Gtg/Ttg rs372423346 1 1 RHBDL3 HGNC HGNC:16502 protein_coding YES CCDS32613.1 ENSP00000269051 P58872 UPI0000133858 NM_138328.2 deleterious(0.04) 9/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR22936,hmmpanther:PTHR22936:SF14,Gene3D:2xovA00,Pfam_domain:PF01694,PIRSF_domain:PIRSF037470,Superfamily_domains:SSF144091 MODERATE 1 SNV 1 1 PASS rs372423346 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 32321059 32321059 G T 1 0 0 0 0 1 0 0 0 13495 1145 40 1 1 RHBDL3 17 32321059 Missense_Mutation SNP G C3N-00169_T 16582236 32321059 50936382 151 9559 STRADA 0 . GRCh38 17 63714040 63714040 + Silent SNP T T A novel C3N-00169_T C3N-00169_N T T c.192A>T p.= p.P64P ENST00000336174 5/13 292 233 59 302 301 1 strelka-varscan-mutect STRADA,synonymous_variant,p.=,ENST00000245865,;STRADA,synonymous_variant,p.=,ENST00000392950,NM_153335.5;STRADA,synonymous_variant,p.=,ENST00000336174,NM_001003787.2;STRADA,synonymous_variant,p.=,ENST00000375840,NM_001003786.2,NM_001003788.2;STRADA,synonymous_variant,p.=,ENST00000579340,;STRADA,synonymous_variant,p.=,ENST00000582137,NM_001165969.1;STRADA,synonymous_variant,p.=,ENST00000617949,;STRADA,synonymous_variant,p.=,ENST00000579549,;STRADA,synonymous_variant,p.=,ENST00000582030,;STRADA,synonymous_variant,p.=,ENST00000580338,;STRADA,synonymous_variant,p.=,ENST00000584110,;STRADA,intron_variant,,ENST00000447001,NM_001165970.1;STRADA,upstream_gene_variant,,ENST00000578008,;STRADA,upstream_gene_variant,,ENST00000578801,;STRADA,downstream_gene_variant,,ENST00000580288,;STRADA,non_coding_transcript_exon_variant,,ENST00000579350,;STRADA,intron_variant,,ENST00000580039,;STRADA,intron_variant,,ENST00000581505,;RP11-51F16.8,3_prime_UTR_variant,,ENST00000580553,;STRADA,3_prime_UTR_variant,,ENST00000581243,;STRADA,non_coding_transcript_exon_variant,,ENST00000577375,;STRADA,non_coding_transcript_exon_variant,,ENST00000579318,; A ENST00000336174 Transcript synonymous_variant 305/2143 192/1296 64/431 P ccA/ccT 1 -1 STRADA HGNC HGNC:30172 protein_coding YES CCDS32703.1 ENSP00000336655 Q7RTN6 UPI000013CBBE NM_001003787.2 5/13 Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 63714040 63714040 T A 1 0 0 0 0 0 0 0 1 15705 1567 55 4 4 STRADA 17 63714040 Silent SNP T C3N-00169_T 31392981 63714040 19543401 152 9560 DDX42 0 . GRCh38 17 63787156 63787156 + Missense_Mutation SNP A A G rs746463979 C3N-00169_T C3N-00169_N A A c.107A>G p.His36Arg p.H36R ENST00000578681 3/19 473 371 102 514 514 0 strelka-varscan-mutect DDX42,missense_variant,p.His36Arg,ENST00000578681,NM_007372.3;DDX42,missense_variant,p.His36Arg,ENST00000583590,;DDX42,missense_variant,p.His36Arg,ENST00000389924,NM_203499.2;DDX42,missense_variant,p.His36Arg,ENST00000581135,;DDX42,intron_variant,,ENST00000359353,;DDX42,missense_variant,p.His36Arg,ENST00000578137,;DDX42,non_coding_transcript_exon_variant,,ENST00000580108,; G ENST00000578681 Transcript missense_variant 708/4337 107/2817 36/938 H/R cAc/cGc rs746463979 1 1 DDX42 HGNC HGNC:18676 protein_coding YES CCDS32704.1 ENSP00000464050 Q86XP3 UPI000017DA3D NM_007372.3 deleterious_low_confidence(0.01) 3/19 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs746463979 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 63787156 63787156 A G 1 0 0 0 0 1 0 0 0 4165 159 6 5 5 DDX42 17 63787156 Missense_Mutation SNP A C3N-00169_T 73116 63787156 19470285 153 9561 CCDC57 0 . GRCh38 17 82201618 82201618 + Missense_Mutation SNP C C A rs779736160 C3N-00169_T C3N-00169_N C C c.327G>T p.Glu109Asp p.E109D ENST00000389641 2/18 206 172 34 207 206 1 strelka-varscan-mutect CCDC57,missense_variant,p.Glu109Asp,ENST00000389641,;CCDC57,missense_variant,p.Glu109Asp,ENST00000392347,NM_198082.2;CCDC57,missense_variant,p.Glu109Asp,ENST00000392343,;CCDC57,upstream_gene_variant,,ENST00000578910,;CCDC57,upstream_gene_variant,,ENST00000581625,; A ENST00000389641 Transcript missense_variant 364/3000 327/2751 109/916 E/D gaG/gaT rs779736160 1 -1 CCDC57 HGNC HGNC:27564 protein_coding YES ENSP00000374292 Q2TAC2 UPI000155D557 deleterious(0.01) 2/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23161,hmmpanther:PTHR23161:SF1 MODERATE 1 SNV 5 1 PASS rs779736160 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 82201618 82201618 C A 1 0 0 0 0 1 0 0 0 2529 680 24 2 2 CCDC57 17 82201618 Missense_Mutation SNP C C3N-00169_T 18414462 82201618 1055823 154 9562 PTPRM 0 . GRCh38 18 8143738 8143738 + Silent SNP C C T rs749263983 C3N-00169_T C3N-00169_N C C c.2259C>T p.= p.F753F ENST00000580170 14/33 216 189 27 191 191 0 strelka-varscan-mutect PTPRM,synonymous_variant,p.=,ENST00000332175,NM_002845.3;PTPRM,synonymous_variant,p.=,ENST00000580170,NM_001105244.1;PTPRM,synonymous_variant,p.=,ENST00000400053,;PTPRM,synonymous_variant,p.=,ENST00000583289,;PTPRM,synonymous_variant,p.=,ENST00000577468,;PTPRM,5_prime_UTR_variant,,ENST00000400060,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,; T ENST00000580170 Transcript synonymous_variant 3296/5941 2259/4398 753/1465 F ttC/ttT rs749263983,COSM3147738,COSM4276978 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 14/33 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs749263983 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 8143738 8143738 C T 1 0 0 0 0 0 0 0 1 12960 883 31 1 1 PTPRM 18 8143738 Silent SNP C C3N-00169_T 8143738 72229547 155 9563 FHOD3 0 . GRCh38 18 36693283 36693283 + Missense_Mutation SNP G G C novel C3N-00169_T C3N-00169_N G G c.2096G>C p.Arg699Thr p.R699T ENST00000590592 17/29 323 247 76 459 459 0 strelka-varscan-mutect FHOD3,missense_variant,p.Arg524Thr,ENST00000257209,NM_025135.3;FHOD3,missense_variant,p.Arg699Thr,ENST00000590592,NM_001281740.1;FHOD3,missense_variant,p.Arg507Thr,ENST00000359247,NM_001281739.1;FHOD3,missense_variant,p.Arg285Thr,ENST00000592930,;FHOD3,intron_variant,,ENST00000591635,;FHOD3,non_coding_transcript_exon_variant,,ENST00000589114,;FHOD3,non_coding_transcript_exon_variant,,ENST00000587493,; C ENST00000590592 Transcript missense_variant 2096/4869 2096/4869 699/1622 R/T aGa/aCa 1 1 FHOD3 HGNC HGNC:26178 protein_coding YES CCDS62418.1 ENSP00000466937 Q2V2M9 UPI0002840E0A NM_001281740.1 deleterious_low_confidence(0) 17/29 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 38 36693283 36693283 G C 1 0 0 0 0 1 0 0 0 5748 942 33 4 4 FHOD3 18 36693283 Missense_Mutation SNP G C3N-00169_T 28549545 36693283 43680002 156 9564 FHOD3 0 . GRCh38 18 36709222 36709222 + Missense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.2364G>T p.Glu788Asp p.E788D ENST00000590592 18/29 309 248 61 358 358 0 strelka-varscan-mutect FHOD3,missense_variant,p.Glu613Asp,ENST00000257209,NM_025135.3;FHOD3,missense_variant,p.Glu788Asp,ENST00000590592,NM_001281740.1;FHOD3,missense_variant,p.Glu596Asp,ENST00000359247,NM_001281739.1;FHOD3,missense_variant,p.Glu374Asp,ENST00000592930,;FHOD3,intron_variant,,ENST00000591635,;FHOD3,non_coding_transcript_exon_variant,,ENST00000589114,;FHOD3,non_coding_transcript_exon_variant,,ENST00000587493,; T ENST00000590592 Transcript missense_variant 2364/4869 2364/4869 788/1622 E/D gaG/gaT 1 1 FHOD3 HGNC HGNC:26178 protein_coding YES CCDS62418.1 ENSP00000466937 Q2V2M9 UPI0002840E0A NM_001281740.1 deleterious_low_confidence(0.04) 18/29 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF213,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 36709222 36709222 G T 1 0 0 0 0 1 0 0 0 5748 962 34 2 2 FHOD3 18 36709222 Missense_Mutation SNP G C3N-00169_T 15939 36709222 43664063 157 9565 RAB27B 0 . GRCh38 18 54889281 54889281 + Silent SNP A A G novel C3N-00169_T C3N-00169_N A A c.525A>G p.= p.E175E ENST00000262094 6/6 152 104 48 142 141 1 strelka-varscan-mutect RAB27B,synonymous_variant,p.=,ENST00000262094,NM_004163.4;RAB27B,intron_variant,,ENST00000592334,;RAB27B,downstream_gene_variant,,ENST00000586570,;RP11-839G9.1,intron_variant,,ENST00000588466,;RAB27B,downstream_gene_variant,,ENST00000586594,; G ENST00000262094 Transcript synonymous_variant 1046/7281 525/657 175/218 E gaA/gaG 1 1 RAB27B HGNC HGNC:9767 protein_coding YES CCDS11958.1 ENSP00000262094 O00194 UPI0000001268 NM_004163.4 6/6 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF587,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 54889281 54889281 A G 1 0 0 0 0 0 0 0 1 13073 11 1 5 5 RAB27B 18 54889281 Silent SNP A C3N-00169_T 18180059 54889281 25484004 158 9566 ADGRE1 0 . GRCh38 19 6913742 6913742 + Silent SNP C C A novel C3N-00169_T C3N-00169_N C C c.1212C>A p.= p.V404V ENST00000312053 11/21 137 113 24 177 176 1 strelka-varscan-mutect ADGRE1,synonymous_variant,p.=,ENST00000312053,NM_001974.4;ADGRE1,synonymous_variant,p.=,ENST00000381404,NM_001256252.1;ADGRE1,synonymous_variant,p.=,ENST00000250572,NM_001256253.1;ADGRE1,synonymous_variant,p.=,ENST00000381407,NM_001256254.1;ADGRE1,synonymous_variant,p.=,ENST00000450315,NM_001256255.1;ADGRE1,downstream_gene_variant,,ENST00000595026,; A ENST00000312053 Transcript synonymous_variant 1249/3128 1212/2661 404/886 V gtC/gtA 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 11/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303 LOW 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999397 1 1 1 0 A 2 1 38 6913742 6913742 C A 1 0 0 0 0 0 0 0 1 359 900 32 2 2 ADGRE1 19 6913742 Silent SNP C C3N-00169_T 6913742 51703874 159 9567 ZNF560 0 . GRCh38 19 9468056 9468056 + Nonsense_Mutation SNP A A T novel C3N-00169_T C3N-00169_N A A c.891T>A p.Tyr297Ter p.Y297* ENST00000301480 10/10 169 131 38 162 162 0 strelka-varscan-mutect ZNF560,stop_gained,p.Tyr297Ter,ENST00000301480,NM_152476.2;ZNF560,downstream_gene_variant,,ENST00000585974,; T ENST00000301480 Transcript stop_gained 1105/2654 891/2373 297/790 Y/* taT/taA 1 -1 ZNF560 HGNC HGNC:26484 protein_coding YES CCDS12214.1 ENSP00000301480 Q96MR9 UPI000013E720 NM_152476.2 10/10 Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 9468056 9468056 A T 1 0 0 0 0 0 1 0 0 18565 224 8 4 4 ZNF560 19 9468056 Nonsense_Mutation SNP A C3N-00169_T 2554314 9468056 49149560 160 9568 ZNF254 0 . GRCh38 19 24087338 24087338 + Splice_Site SNP G G T novel C3N-00169_T C3N-00169_N G G c.30+1G>T p.X10_splice ENST00000357002 215 166 49 227 226 1 strelka-varscan-mutect ZNF254,splice_donor_variant,,ENST00000611359,NM_001278664.1;ZNF254,splice_donor_variant,,ENST00000357002,NM_203282.3;ZNF254,splice_donor_variant,,ENST00000616028,NM_001278663.1,NM_001278678.1;ZNF254,splice_donor_variant,,ENST00000339642,NM_001278665.1;ZNF254,intron_variant,,ENST00000613065,NM_001278677.1,NM_001278661.1,NM_001278662.1;ZNF254,splice_donor_variant,,ENST00000594886,;ZNF254,splice_donor_variant,,ENST00000595187,; T ENST00000357002 Transcript splice_donor_variant -/3967 30/1980 10/659 1 1 ZNF254 HGNC HGNC:13047 protein_coding YES CCDS32983.1 ENSP00000349494 O75437 UPI0000366DB6 NM_203282.3 1/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 38 24087338 24087338 G T 1 0 0 0 0 0 0 1 0 18374 1275 44 2 2 ZNF254 19 24087338 Splice_Site SNP G C3N-00169_T 14619282 24087338 34530278 161 9569 PROSER3 0 . GRCh38 19 35768444 35768444 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1342G>A p.Glu448Lys p.E448K ENST00000396908 11/11 120 105 15 167 167 0 strelka-mutect PROSER3,missense_variant,p.Glu448Lys,ENST00000396908,NM_001039887.2;PROSER3,downstream_gene_variant,,ENST00000301165,;AC002398.13,downstream_gene_variant,,ENST00000589397,;PROSER3,non_coding_transcript_exon_variant,,ENST00000536037,;PROSER3,downstream_gene_variant,,ENST00000542591,;PROSER3,downstream_gene_variant,,ENST00000544876,;PROSER3,3_prime_UTR_variant,,ENST00000620918,;PROSER3,non_coding_transcript_exon_variant,,ENST00000544158,;PROSER3,downstream_gene_variant,,ENST00000601095,; A ENST00000396908 Transcript missense_variant 1405/2149 1342/1443 448/480 E/K Gaa/Aaa 1 1 PROSER3 HGNC HGNC:25204 protein_coding YES ENSP00000380116 Q2NL68 UPI000067CA4C NM_001039887.2 tolerated(0.16) 11/11 hmmpanther:PTHR22045,hmmpanther:PTHR22045:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 35768444 35768444 G A 1 0 0 0 0 1 0 0 0 12695 1291 45 3 3 PROSER3 19 35768444 Missense_Mutation SNP G C3N-00169_T 11681106 35768444 22849172 162 9570 IRGC 0 . GRCh38 19 43719281 43719281 + Silent SNP C C T novel C3N-00169_T C3N-00169_N C C c.723C>T p.= p.R241R ENST00000244314 2/2 82 56 26 113 113 0 strelka-varscan-mutect IRGC,synonymous_variant,p.=,ENST00000244314,NM_019612.3;IRGC,downstream_gene_variant,,ENST00000596627,; T ENST00000244314 Transcript synonymous_variant 922/1662 723/1392 241/463 R cgC/cgT 1 1 IRGC HGNC HGNC:28835 protein_coding YES CCDS12629.1 ENSP00000244314 Q6NXR0 J7NNX4 UPI000011DFC0 NM_019612.3 2/2 Pfam_domain:PF05049,hmmpanther:PTHR32341,hmmpanther:PTHR32341:SF7,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 43719281 43719281 C T 1 0 0 0 0 0 0 0 1 7745 726 26 3 3 IRGC 19 43719281 Silent SNP C C3N-00169_T 7950837 43719281 14898335 163 9571 NLRP7 0 . GRCh38 19 54939604 54939604 + Silent SNP G G C rs762977273 C3N-00169_T C3N-00169_N G G c.1215C>G p.= p.G405G ENST00000588756 6/13 286 175 111 186 186 0 strelka-varscan-mutect NLRP7,synonymous_variant,p.=,ENST00000588756,;NLRP7,synonymous_variant,p.=,ENST00000328092,NM_139176.3;NLRP7,synonymous_variant,p.=,ENST00000592784,NM_001127255.1;NLRP7,synonymous_variant,p.=,ENST00000340844,NM_206828.3;NLRP7,synonymous_variant,p.=,ENST00000590030,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,downstream_gene_variant,,ENST00000587844,;NLRP7,synonymous_variant,p.=,ENST00000586379,; C ENST00000588756 Transcript synonymous_variant 1702/3826 1215/3114 405/1037 G ggC/ggG rs762977273 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 6/13 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14 LOW 1 SNV 1 1 PASS rs762977273 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 38 54939604 54939604 G C 1 0 0 0 0 0 0 0 1 10520 1074 38 4 4 NLRP7 19 54939604 Silent SNP G C3N-00169_T 11220323 54939604 3678012 164 9572 TMEM150B 0 . GRCh38 19 55312871 55312871 + Silent SNP C C A novel C3N-00169_T C3N-00169_N C C c.690G>T p.= p.P230P ENST00000326652 8/8 106 69 37 149 149 0 strelka-varscan-mutect TMEM150B,synonymous_variant,p.=,ENST00000326652,NM_001085488.2,NM_001282011.1;BRSK1,downstream_gene_variant,,ENST00000309383,NM_032430.1;BRSK1,downstream_gene_variant,,ENST00000590333,;BRSK1,downstream_gene_variant,,ENST00000326848,;TMEM150B,downstream_gene_variant,,ENST00000591570,;TMEM150B,downstream_gene_variant,,ENST00000585918,;CTD-2105E13.14,upstream_gene_variant,,ENST00000596786,;TMEM150B,3_prime_UTR_variant,,ENST00000586609,;TMEM150B,3_prime_UTR_variant,,ENST00000592603,;TMEM150B,downstream_gene_variant,,ENST00000592731,; A ENST00000326652 Transcript synonymous_variant 873/943 690/702 230/233 P ccG/ccT 1 -1 TMEM150B HGNC HGNC:34415 protein_coding YES CCDS42629.1 ENSP00000320757 A6NC51 UPI00001AF4D4 NM_001085488.2,NM_001282011.1 8/8 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs929546497 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 38 55312871 55312871 C A 1 0 0 0 0 0 0 0 1 16510 639 23 1 1 TMEM150B 19 55312871 Silent SNP C C3N-00169_T 373267 55312871 3304745 165 9573 RP5-1187M17.10 0 . GRCh38 20 3165578 3165578 + Silent SNP C C A novel C3N-00169_T C3N-00169_N C C c.1104G>T p.= p.R368R ENST00000360342 5/6 69 49 20 96 96 0 strelka-varscan-mutect RP5-1187M17.10,synonymous_variant,p.=,ENST00000329152,;RP5-1187M17.10,synonymous_variant,p.=,ENST00000337576,;RP5-1187M17.10,synonymous_variant,p.=,ENST00000360342,NM_001282533.1; A ENST00000360342 Transcript synonymous_variant 1438/4055 1104/1884 368/627 R cgG/cgT 1 -1 RP5-1187M17.10 Clone_based_vega_gene protein_coding YES CCDS63218.1 ENSP00000353496 UPI00001AE5C6 NM_001282533.1 5/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19354,hmmpanther:PTHR19354:SF6 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 38 3165578 3165578 C A 1 0 0 0 0 0 0 0 1 13781 610 22 2 2 RP5-1187M17.10 20 3165578 Silent SNP C C3N-00169_T 3165578 61278589 166 9574 PLCB1 0 . GRCh38 20 8724696 8724696 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.1622C>T p.Ser541Phe p.S541F ENST00000338037 16/32 273 219 54 210 210 0 strelka-varscan-mutect PLCB1,missense_variant,p.Ser541Phe,ENST00000378641,NM_182734.2;PLCB1,missense_variant,p.Ser541Phe,ENST00000338037,NM_015192.3;PLCB1,missense_variant,p.Ser461Phe,ENST00000612075,;PLCB1,missense_variant,p.Ser461Phe,ENST00000617005,;PLCB1,missense_variant,p.Ser440Phe,ENST00000637919,;PLCB1,missense_variant,p.Ser541Phe,ENST00000378637,;PLCB1,missense_variant,p.Ser440Phe,ENST00000625874,;PLCB1,missense_variant,p.Ser440Phe,ENST00000626966,;PLCB1,non_coding_transcript_exon_variant,,ENST00000635830,;PLCB1,non_coding_transcript_exon_variant,,ENST00000636825,;PLCB1,missense_variant,p.Ser282Phe,ENST00000487210,;PLCB1,3_prime_UTR_variant,,ENST00000636319,;PLCB1,non_coding_transcript_exon_variant,,ENST00000494924,; T ENST00000338037 Transcript missense_variant 2009/7092 1622/3651 541/1216 S/F tCt/tTt 1 1 PLCB1 HGNC HGNC:15917 protein_coding YES CCDS13102.1 ENSP00000338185 Q9NQ66 UPI0000131A8F NM_015192.3 deleterious(0) 16/32 PROSITE_profiles:PS50008,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,Gene3D:3.20.20.190,PIRSF_domain:PIRSF000956,Pfam_domain:PF00387,SMART_domains:SM00149,Superfamily_domains:SSF51695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 8724696 8724696 C T 1 0 0 0 0 1 0 0 0 12121 913 32 3 3 PLCB1 20 8724696 Missense_Mutation SNP C C3N-00169_T 5559118 8724696 55719471 167 9575 KIF3B 0 . GRCh38 20 32310597 32310597 + Missense_Mutation SNP G G T C3N-00169_T C3N-00169_N G G c.820G>T p.Ala274Ser p.A274S ENST00000375712 2/9 250 223 27 291 290 1 strelka-varscan-mutect KIF3B,missense_variant,p.Ala274Ser,ENST00000375712,NM_004798.3; T ENST00000375712 Transcript missense_variant 987/6103 820/2244 274/747 A/S Gct/Tct COSM5629398 1 1 KIF3B HGNC HGNC:6320 protein_coding YES CCDS13200.1 ENSP00000364864 O15066 UPI000012DDB1 NM_004798.3 tolerated(0.15) 2/9 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF476,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs940799632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 32310597 32310597 G T 1 0 0 0 0 1 0 0 0 8166 1087 38 1 1 KIF3B 20 32310597 Missense_Mutation SNP G C3N-00169_T 23585901 32310597 32133570 168 9576 EPB41L1 0 . GRCh38 20 36195362 36195362 + Nonsense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.1483G>T p.Glu495Ter p.E495* ENST00000338074 13/22 493 425 68 541 540 1 strelka-varscan-mutect EPB41L1,stop_gained,p.Glu495Ter,ENST00000373946,NM_001258329.1;EPB41L1,stop_gained,p.Glu495Ter,ENST00000338074,NM_012156.2;EPB41L1,stop_gained,p.Glu495Ter,ENST00000373941,;EPB41L1,intron_variant,,ENST00000441639,NM_177996.2;EPB41L1,intron_variant,,ENST00000373950,;EPB41L1,intron_variant,,ENST00000202028,NM_001258331.1;EPB41L1,intron_variant,,ENST00000628415,NM_001258330.1;EPB41L1,intron_variant,,ENST00000451082,;EPB41L1,upstream_gene_variant,,ENST00000636016,;EPB41L1,upstream_gene_variant,,ENST00000454226,; T ENST00000338074 Transcript stop_gained,splice_region_variant 1644/6266 1483/2646 495/881 E/* Gag/Tag 1 1 EPB41L1 HGNC HGNC:3378 protein_coding YES CCDS13271.1 ENSP00000337168 Q9H4G0 UPI0000129AF8 NM_012156.2 13/22 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF24,PIRSF_domain:PIRSF002304,Pfam_domain:PF04382 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 36195362 36195362 G T 1 0 0 0 0 0 1 0 0 4999 1188 41 2 2 EPB41L1 20 36195362 Nonsense_Mutation SNP G C3N-00169_T 3884765 36195362 28248805 169 9577 TNNC2 0 . GRCh38 20 45824383 45824383 + Missense_Mutation SNP C C G novel C3N-00169_T C3N-00169_N C C c.223G>C p.Glu75Gln p.E75Q ENST00000372555 4/6 180 161 19 234 234 0 strelka-varscan-mutect TNNC2,missense_variant,p.Glu60Gln,ENST00000372557,;TNNC2,missense_variant,p.Glu75Gln,ENST00000372555,NM_003279.2; G ENST00000372555 Transcript missense_variant 316/710 223/483 75/160 E/Q Gag/Cag 1 -1 TNNC2 HGNC HGNC:11944 protein_coding YES CCDS13375.1 ENSP00000361636 P02585 UPI000014A6DB NM_003279.2 deleterious(0) 4/6 Gene3D:1.10.238.10,Pfam_domain:PF13833,PROSITE_patterns:PS00018,PROSITE_profiles:PS50222,hmmpanther:PTHR23064,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 45824383 45824383 C G 1 0 0 0 0 1 0 0 0 16798 864 30 4 4 TNNC2 20 45824383 Missense_Mutation SNP C C3N-00169_T 9629021 45824383 18619784 170 9578 TCFL5 0 . GRCh38 20 62861278 62861278 + Missense_Mutation SNP C C T novel C3N-00169_T C3N-00169_N C C c.393G>A p.Met131Ile p.M131I ENST00000335351 1/6 127 113 14 74 74 0 strelka-varscan-mutect TCFL5,missense_variant,p.Met131Ile,ENST00000335351,NM_006602.3;TCFL5,missense_variant,p.Met83Ile,ENST00000217162,; T ENST00000335351 Transcript missense_variant 486/2456 393/1503 131/500 M/I atG/atA 1 -1 TCFL5 HGNC HGNC:11646 protein_coding YES CCDS13506.1 ENSP00000334294 Q9UL49 UPI0000206389 NM_006602.3 deleterious(0.01) 1/6 hmmpanther:PTHR15402:SF2,hmmpanther:PTHR15402 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 62861278 62861278 C T 1 0 0 0 0 1 0 0 0 16106 826 29 3 3 TCFL5 20 62861278 Missense_Mutation SNP C C3N-00169_T 17036895 62861278 1582889 171 9579 BHLHE23 0 . GRCh38 20 63006409 63006409 + Missense_Mutation SNP G G T rs746912203 C3N-00169_T C3N-00169_N G G c.366C>A p.Asn122Lys p.N122K ENST00000612929 1/1 242 170 72 287 287 0 strelka-varscan-mutect BHLHE23,missense_variant,p.Asn122Lys,ENST00000612929,NM_080606.3;BHLHE23,missense_variant,p.Asn106Lys,ENST00000370346,;RP11-305P22.9,upstream_gene_variant,,ENST00000607802,;RP11-305P22.9,upstream_gene_variant,,ENST00000606208,; T ENST00000612929 Transcript missense_variant 627/1109 366/726 122/241 N/K aaC/aaA rs746912203 1 -1 BHLHE23 HGNC HGNC:16093 protein_coding YES CCDS33507.2 ENSP00000480998 A0A087WXG3 UPI00024D1415 NM_080606.3 deleterious(0) 1/1 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF53,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE SNV 1 PASS rs746912203 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 63006409 63006409 G T 1 0 0 0 0 1 0 0 0 1570 1136 40 1 1 BHLHE23 20 63006409 Missense_Mutation SNP G C3N-00169_T 145131 63006409 1437758 172 9580 MRPL39 0 . GRCh38 21 25601438 25601438 + Missense_Mutation SNP C C G novel C3N-00169_T C3N-00169_N C C c.450G>C p.Met150Ile p.M150I ENST00000307301 4/11 202 182 20 160 160 0 strelka-varscan-mutect MRPL39,missense_variant,p.Met150Ile,ENST00000307301,NM_080794.3;MRPL39,missense_variant,p.Met150Ile,ENST00000352957,NM_017446.3;MRPL39,missense_variant,p.Met150Ile,ENST00000419219,; G ENST00000307301 Transcript missense_variant 492/1199 450/1062 150/353 M/I atG/atC 1 -1 MRPL39 HGNC HGNC:14027 protein_coding YES CCDS33522.1 ENSP00000305682 Q9NYK5 UPI00001AEAC0 NM_080794.3 tolerated(0.07) 4/11 Gene3D:1tkeA02,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF34,Superfamily_domains:SSF55186 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 25601438 25601438 C G 1 0 0 0 0 1 0 0 0 9777 594 21 4 4 MRPL39 21 25601438 Missense_Mutation SNP C C3N-00169_T 25601438 21108545 173 9581 TTC3 0 . GRCh38 21 37121841 37121841 + Missense_Mutation SNP C C G C3N-00169_T C3N-00169_N C C c.925C>G p.Leu309Val p.L309V ENST00000399017 12/46 138 116 22 129 129 0 strelka-varscan-mutect TTC3,missense_variant,p.Leu309Val,ENST00000399017,NM_003316.3;TTC3,missense_variant,p.Leu309Val,ENST00000354749,;TTC3,missense_variant,p.Leu309Val,ENST00000355666,NM_001001894.1;TTC3,missense_variant,p.Leu309Val,ENST00000418766,;TTC3,missense_variant,p.Leu291Val,ENST00000438055,;TTC3,missense_variant,p.Leu309Val,ENST00000450533,;TTC3,5_prime_UTR_variant,,ENST00000540756,;TTC3,non_coding_transcript_exon_variant,,ENST00000479930,;TTC3,non_coding_transcript_exon_variant,,ENST00000485402,;TTC3,non_coding_transcript_exon_variant,,ENST00000494243,;TTC3,non_coding_transcript_exon_variant,,ENST00000463216,;TTC3,non_coding_transcript_exon_variant,,ENST00000492275,;TTC3,intron_variant,,ENST00000481605,;TTC3,non_coding_transcript_exon_variant,,ENST00000476784,; G ENST00000399017 Transcript missense_variant 3672/10363 925/6078 309/2025 L/V Ctt/Gtt COSM1190352 1 1 TTC3 HGNC HGNC:12393 protein_coding YES CCDS13651.1 ENSP00000381981 P53804 UPI00001B043E NM_003316.3 deleterious(0) 12/46 Gene3D:1.25.40.10,PROSITE_profiles:PS50293,hmmpanther:PTHR17550,hmmpanther:PTHR17550:SF4,SMART_domains:SM00028,Superfamily_domains:SSF48452 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 38 37121841 37121841 C G 1 0 0 0 0 1 0 0 0 17206 913 32 4 4 TTC3 21 37121841 Missense_Mutation SNP C C3N-00169_T 11520403 37121841 9588142 174 9582 TLR7 0 . GRCh38 X 12886395 12886395 + Missense_Mutation SNP G G T rs748655746 C3N-00169_T C3N-00169_N G G c.887G>T p.Arg296Leu p.R296L ENST00000380659 3/3 100 60 40 97 97 0 strelka-varscan-mutect TLR7,missense_variant,p.Arg296Leu,ENST00000380659,NM_016562.3; T ENST00000380659 Transcript missense_variant 1026/5011 887/3150 296/1049 R/L cGt/cTt rs748655746,COSM219002 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(0.08) 3/3 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748655746 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 38 12886395 12886395 G T 1 0 0 0 0 1 0 0 0 16402 1145 40 1 1 TLR7 23 12886395 Missense_Mutation SNP G C3N-00169_T 12886395 143154500 175 9583 BMX 0 . GRCh38 X 15522494 15522494 + Nonsense_Mutation SNP C C G C3N-00169_T C3N-00169_N C C c.659C>G p.Ser220Ter p.S220* ENST00000357607 7/19 180 141 39 200 200 0 strelka-varscan-mutect BMX,stop_gained,p.Ser220Ter,ENST00000357607,;BMX,stop_gained,p.Ser220Ter,ENST00000348343,NM_001320866.1,NM_203281.2;BMX,stop_gained,p.Ser220Ter,ENST00000342014,NM_001721.6;BMX,downstream_gene_variant,,ENST00000463891,;BMX,upstream_gene_variant,,ENST00000489983,; G ENST00000357607 Transcript stop_gained 847/2598 659/2028 220/675 S/* tCa/tGa COSM5594267 1 1 BMX HGNC HGNC:1079 protein_coding YES CCDS14168.1 ENSP00000350224 P51813 UPI0000000DFF 7/19 hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF91 1 HIGH 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 38 15522494 15522494 C G 1 0 0 0 0 0 1 0 0 1629 838 29 4 4 BMX 23 15522494 Nonsense_Mutation SNP C C3N-00169_T 2636099 15522494 140518401 176 9584 MAP3K15 0 . GRCh38 X 19426317 19426317 + Missense_Mutation SNP G G A novel C3N-00169_T C3N-00169_N G G c.1193C>T p.Ser398Leu p.S398L ENST00000338883 8/29 59 31 28 40 40 0 strelka-varscan-mutect MAP3K15,missense_variant,p.Ser398Leu,ENST00000338883,NM_001001671.3;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;MAP3K15,missense_variant,p.Ser150Leu,ENST00000359173,; A ENST00000338883 Transcript missense_variant 1193/4012 1193/3942 398/1313 S/L tCa/tTa 1 -1 MAP3K15 HGNC HGNC:31689 protein_coding YES CCDS35212.2 ENSP00000345629 Q6ZN16 UPI0000E444D0 NM_001001671.3 deleterious(0) 8/29 hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363,Pfam_domain:PF13281 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 19426317 19426317 G A 1 0 0 0 0 1 0 0 0 9171 1294 45 3 3 MAP3K15 23 19426317 Missense_Mutation SNP G C3N-00169_T 3903823 19426317 136614578 177 9585 KLHL34 0 . GRCh38 X 21657000 21657000 + Silent SNP G G T novel C3N-00169_T C3N-00169_N G G c.789C>A p.= p.S263S ENST00000379499 1/1 19 7 12 20 20 0 strelka-mutect KLHL34,synonymous_variant,p.=,ENST00000379499,NM_153270.2;CNKSR2,downstream_gene_variant,,ENST00000425654,NM_001168647.1;CNKSR2,downstream_gene_variant,,ENST00000379510,NM_014927.3; T ENST00000379499 Transcript synonymous_variant 1331/3641 789/1935 263/644 S tcC/tcA 1 -1 KLHL34 HGNC HGNC:26634 protein_coding YES CCDS14199.1 ENSP00000368813 Q8N239 UPI0000072CC4 NM_153270.2 1/1 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF199 LOW SNV 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 38 21657000 21657000 G T 1 0 0 0 0 0 0 0 1 8253 1219 43 2 2 KLHL34 23 21657000 Silent SNP G C3N-00169_T 2230683 21657000 134383895 178 9586 DMD 0 . GRCh38 X 31178790 31178790 + Missense_Mutation SNP C C A C3N-00169_T C3N-00169_N C C c.10102G>T p.Asp3368Tyr p.D3368Y ENST00000357033 70/79 112 59 53 104 104 0 strelka-varscan-mutect DMD,missense_variant,p.Asp3368Tyr,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Asp3364Tyr,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Asp3367Tyr,ENST00000620040,;DMD,missense_variant,p.Asp3363Tyr,ENST00000619831,;DMD,missense_variant,p.Asp908Tyr,ENST00000378707,NM_004013.2;DMD,missense_variant,p.Asp908Tyr,ENST00000359836,NM_004022.2;DMD,missense_variant,p.Asp908Tyr,ENST00000541735,NM_004020.3,NM_004023.2;DMD,missense_variant,p.Asp1064Tyr,ENST00000358062,;DMD,missense_variant,p.Asp639Tyr,ENST00000343523,NM_004014.2;DMD,missense_variant,p.Asp908Tyr,ENST00000474231,NM_004021.2;DMD,missense_variant,p.Asp300Tyr,ENST00000378723,NM_004016.2;DMD,missense_variant,p.Asp300Tyr,ENST00000378702,NM_004015.2,NM_004017.2;DMD,missense_variant,p.Asp300Tyr,ENST00000361471,NM_004018.2;DMD,missense_variant,p.Asp300Tyr,ENST00000378680,;DMD,missense_variant,p.Asp158Tyr,ENST00000378705,;DMD,non_coding_transcript_exon_variant,,ENST00000475732,; A ENST00000357033 Transcript missense_variant 10309/13956 10102/11058 3368/3685 D/Y Gat/Tat CM070895,DMD:c.10102G>C 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0) 70/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1,0 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 31178790 31178790 C A 1 0 0 0 0 1 0 0 0 4387 913 32 2 2 DMD 23 31178790 Missense_Mutation SNP C C3N-00169_T 9521790 31178790 124862105 179 9587 CFAP47 0 . GRCh38 X 36285727 36285727 + Splice_Site SNP G G T novel C3N-00169_T C3N-00169_N G G c.7686+1G>T p.X2562_splice ENST00000378653 114 75 39 78 78 0 strelka-varscan-mutect CFAP47,splice_donor_variant,,ENST00000378653,NM_001304548.1; T ENST00000378653 Transcript splice_donor_variant -/9943 7686/9564 2562/3187 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 51/63 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 38 36285727 36285727 G T 1 0 0 0 0 0 0 1 0 3022 1275 44 2 2 CFAP47 23 36285727 Splice_Site SNP G C3N-00169_T 5106937 36285727 119755168 180 9588 TEX13A 0 . GRCh38 X 105219534 105219534 + Frame_Shift_Del DEL G G - novel C3N-00169_T C3N-00169_N G G c.660delC p.Met221TrpfsTer132 p.M221Wfs*132 ENST00000600991 3/3 107 60 47 102 102 0 sindel-varindel-pindel TEX13A,frameshift_variant,p.Met221TrpfsTer132,ENST00000600991,NM_031274.4;TEX13A,frameshift_variant,p.Met221TrpfsTer132,ENST00000609007,NM_001291277.1;IL1RAPL2,intron_variant,,ENST00000372582,NM_017416.1; - ENST00000600991 Transcript frameshift_variant 772/1377 660/1230 220/409 P/X ccC/cc 1 -1 TEX13A HGNC HGNC:11735 protein_coding YES CCDS76005.1 ENSP00000471604 Q9BXU3 UPI0000042200 NM_031274.4 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23111:SF25,hmmpanther:PTHR23111 HIGH 1 deletion 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 38 105219534 105219534 G - 1 0 1 0 1 0 0 0 0 16197 1335 47 0 0 TEX13A 23 105219534 Frame_Shift_Del DEL G C3N-00169_T 68933807 105219534 50821361 181 9589 AGTR2 0 . GRCh38 X 116173214 116173214 + Missense_Mutation SNP T T A novel C3N-00169_T C3N-00169_N T T c.934T>A p.Cys312Ser p.C312S ENST00000371906 3/3 103 53 50 45 45 0 strelka-varscan-mutect AGTR2,missense_variant,p.Cys312Ser,ENST00000371906,NM_000686.4; A ENST00000371906 Transcript missense_variant 1124/2882 934/1092 312/363 C/S Tgc/Agc 1 1 AGTR2 HGNC HGNC:338 protein_coding YES CCDS14569.1 ENSP00000360973 P50052 UPI0000125687 NM_000686.4 deleterious(0.02) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF8,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 38 116173214 116173214 T A 1 0 0 0 0 1 0 0 0 481 1580 55 4 4 AGTR2 23 116173214 Missense_Mutation SNP T C3N-00169_T 10953680 116173214 39867681 182 9590 DCAF12L2 0 . GRCh38 X 126165043 126165043 + Silent SNP T T G novel C3N-00169_T C3N-00169_N T T c.882A>C p.= p.T294T ENST00000360028 1/1 120 66 54 119 119 0 strelka-varscan-mutect DCAF12L2,synonymous_variant,p.=,ENST00000360028,NM_001013628.2; G ENST00000360028 Transcript synonymous_variant 1055/2599 882/1392 294/463 T acA/acC 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 1 PASS rs1244202599 . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 38 126165043 126165043 T G 1 0 0 0 0 0 0 0 1 4066 1683 59 5 5 DCAF12L2 23 126165043 Silent SNP T C3N-00169_T 9991829 126165043 29875852 183 9591 SLITRK2 0 . GRCh38 X 145823053 145823053 + Nonsense_Mutation SNP G G T novel C3N-00169_T C3N-00169_N G G c.628G>T p.Glu210Ter p.E210* ENST00000370490 1/1 169 101 68 169 168 1 strelka-varscan-mutect SLITRK2,stop_gained,p.Glu210Ter,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,stop_gained,p.Glu210Ter,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript stop_gained 4883/7672 628/2538 210/845 E/* Gag/Tag 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 1/1 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36,Superfamily_domains:SSF52058 HIGH 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 38 145823053 145823053 G T 1 0 0 0 0 0 1 0 0 15034 1175 41 2 2 SLITRK2 23 145823053 Nonsense_Mutation SNP G C3N-00169_T 19658010 145823053 10217842 184 9592 FAM132A 0 . GRCh38 1 1243529 1243529 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.555G>T p.= p.L185L ENST00000330388 5/8 105 88 17 136 135 1 strelka-varscan-mutect FAM132A,synonymous_variant,p.=,ENST00000330388,NM_001014980.2;FAM132A,non_coding_transcript_exon_variant,,ENST00000468365,;FAM132A,upstream_gene_variant,,ENST00000462849,;FAM132A,downstream_gene_variant,,ENST00000486627,;FAM132A,upstream_gene_variant,,ENST00000478606,; A ENST00000330388 Transcript synonymous_variant 587/1036 555/909 185/302 L ctG/ctT 1 -1 FAM132A HGNC HGNC:32308 protein_coding YES CCDS30554.1 ENSP00000329137 Q5T7M4 UPI00001D7E7A NM_001014980.2 5/8 PROSITE_profiles:PS50871,hmmpanther:PTHR24019:SF12,hmmpanther:PTHR24019,Superfamily_domains:SSF49842 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 1243529 1243529 C A 1 0 0 0 0 0 0 0 1 5292 697 25 2 2 FAM132A 1 1243529 Silent SNP C C3N-00175_T 1243529 247712893 1 9593 MEGF6 0 . GRCh38 1 3602567 3602567 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.165G>A p.= p.L55L ENST00000356575 2/37 115 89 26 152 151 1 varscan-mutect MEGF6,synonymous_variant,p.=,ENST00000356575,NM_001409.3;MEGF6,synonymous_variant,p.=,ENST00000485002,; T ENST00000356575 Transcript synonymous_variant 392/5455 165/4626 55/1541 L ctG/ctA 1 -1 MEGF6 HGNC HGNC:3232 protein_coding YES CCDS41237.1 ENSP00000348982 O75095 UPI0000DACACB NM_001409.3 2/37 PROSITE_profiles:PS51041 LOW 1 SNV 1 1 PASS rs1413824816 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 3602567 3602567 C T 1 0 0 0 0 0 0 0 1 9402 581 21 3 3 MEGF6 1 3602567 Silent SNP C C3N-00175_T 2359038 3602567 245353855 2 9594 CEP104 0 . GRCh38 1 3831164 3831164 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1718A>T p.Gln573Leu p.Q573L ENST00000378230 13/22 164 125 39 197 197 0 strelka-varscan-mutect CEP104,missense_variant,p.Gln573Leu,ENST00000378230,NM_014704.3;CEP104,upstream_gene_variant,,ENST00000461667,;CEP104,upstream_gene_variant,,ENST00000438539,;CEP104,downstream_gene_variant,,ENST00000443466,;CEP104,non_coding_transcript_exon_variant,,ENST00000460038,;CEP104,non_coding_transcript_exon_variant,,ENST00000495701,;CEP104,downstream_gene_variant,,ENST00000494653,; A ENST00000378230 Transcript missense_variant 2043/6424 1718/2778 573/925 Q/L cAg/cTg 1 -1 CEP104 HGNC HGNC:24866 protein_coding YES CCDS30571.1 ENSP00000367476 O60308 UPI0000139AA8 NM_014704.3 deleterious(0.01) 13/22 hmmpanther:PTHR13371:SF0,hmmpanther:PTHR13371,SMART_domains:SM01349,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 3831164 3831164 T A 1 0 0 0 0 1 0 0 0 2954 1580 55 4 4 CEP104 1 3831164 Missense_Mutation SNP T C3N-00175_T 228597 3831164 245125258 3 9595 GPR153 0 . GRCh38 1 6249901 6249901 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1267G>T p.Ala423Ser p.A423S ENST00000377893 6/6 15 9 6 15 15 0 strelka-varscan-mutect GPR153,missense_variant,p.Ala423Ser,ENST00000377893,NM_207370.2;HES3,downstream_gene_variant,,ENST00000377898,NM_001024598.3; A ENST00000377893 Transcript missense_variant 1527/4082 1267/1830 423/609 A/S Gcc/Tcc 1 -1 GPR153 HGNC HGNC:23618 protein_coding YES CCDS64.1 ENSP00000367125 Q6NV75 A0A0I9QQ03 UPI000040E9D7 NM_207370.2 tolerated_low_confidence(0.23) 6/6 hmmpanther:PTHR16518,hmmpanther:PTHR16518:SF5 MODERATE 1 SNV 1 1 PASS rs1241744962 . 2 205 3 0 0 0 0 0 -18.7641 1 1 1 1 0 A 3 1 39 6249901 6249901 C A 1 0 0 0 0 1 0 0 0 6545 768 27 1 1 GPR153 1 6249901 Missense_Mutation SNP C C3N-00175_T 2418737 6249901 242706521 4 9596 PLEKHG5 0 . GRCh38 1 6468282 6468282 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2791C>A p.Pro931Thr p.P931T ENST00000537245 21/22 68 61 7 100 100 0 strelka-varscan-mutect PLEKHG5,missense_variant,p.Pro929Thr,ENST00000377748,NM_198681.3;PLEKHG5,missense_variant,p.Pro931Thr,ENST00000537245,NM_001265592.1;PLEKHG5,missense_variant,p.Pro921Thr,ENST00000535355,NM_001265593.1;PLEKHG5,missense_variant,p.Pro852Thr,ENST00000340850,NM_001042664.1;PLEKHG5,missense_variant,p.Pro852Thr,ENST00000400913,NM_001042665.1;PLEKHG5,missense_variant,p.Pro889Thr,ENST00000377732,;PLEKHG5,missense_variant,p.Pro908Thr,ENST00000400915,NM_001042663.1;PLEKHG5,missense_variant,p.Pro852Thr,ENST00000377728,NM_020631.4;PLEKHG5,missense_variant,p.Pro852Thr,ENST00000377725,NM_001265594.1;PLEKHG5,intron_variant,,ENST00000377740,;TNFRSF25,upstream_gene_variant,,ENST00000377782,NM_148965.1;TNFRSF25,upstream_gene_variant,,ENST00000356876,NM_003790.2;TNFRSF25,upstream_gene_variant,,ENST00000351959,NM_148966.1;TNFRSF25,upstream_gene_variant,,ENST00000348333,NM_148967.1;TNFRSF25,upstream_gene_variant,,ENST00000481401,;TNFRSF25,upstream_gene_variant,,ENST00000351748,NM_148970.1;TNFRSF25,upstream_gene_variant,,ENST00000461703,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000487949,;TNFRSF25,upstream_gene_variant,,ENST00000513135,;TNFRSF25,upstream_gene_variant,,ENST00000485036,;TNFRSF25,upstream_gene_variant,,ENST00000480393,;TNFRSF25,upstream_gene_variant,,ENST00000473343,;TNFRSF25,upstream_gene_variant,,ENST00000414040,;TNFRSF25,upstream_gene_variant,,ENST00000510563,;TNFRSF25,upstream_gene_variant,,ENST00000453260,;TNFRSF25,upstream_gene_variant,,ENST00000502588,;TNFRSF25,upstream_gene_variant,,ENST00000502730,;TNFRSF25,upstream_gene_variant,,ENST00000469691,;TNFRSF25,upstream_gene_variant,,ENST00000453341,;TNFRSF25,upstream_gene_variant,,ENST00000515145,; T ENST00000537245 Transcript missense_variant 2856/4794 2791/3258 931/1085 P/T Cct/Act 1 -1 PLEKHG5 HGNC HGNC:29105 protein_coding YES CCDS57969.1 ENSP00000439625 O94827 UPI000206539E NM_001265592.1 tolerated_low_confidence(0.25) 21/22 Low_complexity_(Seg):seg,hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF9 MODERATE SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -15.94633 1 1 1 1 0 T 3 4 39 6468282 6468282 G T 1 0 0 0 0 1 0 0 0 12166 1232 43 2 2 PLEKHG5 1 6468282 Missense_Mutation SNP G C3N-00175_T 218381 6468282 242488140 5 9597 H6PD 0 . GRCh38 1 9263787 9263787 + Nonsense_Mutation SNP G G T rs750176902 C3N-00175_T C3N-00175_N G G c.1327G>T p.Gly443Ter p.G443* ENST00000602477 5/5 391 292 99 339 338 1 strelka-varscan-mutect H6PD,stop_gained,p.Gly432Ter,ENST00000377403,NM_004285.3;H6PD,stop_gained,p.Gly443Ter,ENST00000602477,NM_001282587.1;H6PD,upstream_gene_variant,,ENST00000495451,; T ENST00000602477 Transcript stop_gained 1479/5590 1327/2409 443/802 G/* Gga/Tga rs750176902 1 1 H6PD HGNC HGNC:4795 protein_coding YES CCDS72697.1 ENSP00000473348 R4GMU1 UPI0000D61E40 NM_001282587.1 5/5 hmmpanther:PTHR23429:SF7,hmmpanther:PTHR23429,Pfam_domain:PF02781,Gene3D:3.30.360.10,Superfamily_domains:SSF55347 HIGH 1 SNV 1 1 PASS rs750176902 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 9263787 9263787 G T 1 0 0 0 0 0 1 0 0 6818 1233 43 2 2 H6PD 1 9263787 Nonsense_Mutation SNP G C3N-00175_T 2795505 9263787 239692635 6 9598 KIF1B 0 . GRCh38 1 10304545 10304545 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3360G>T p.Gln1120His p.Q1120H ENST00000377093 21/21 107 86 21 97 96 1 strelka-varscan-mutect KIF1B,missense_variant,p.Gln1120His,ENST00000377093,NM_183416.3;KIF1B,missense_variant,p.Gln1120His,ENST00000377083,;KIF1B,intron_variant,,ENST00000377086,;KIF1B,intron_variant,,ENST00000377081,;KIF1B,intron_variant,,ENST00000620295,;KIF1B,intron_variant,,ENST00000622724,;KIF1B,intron_variant,,ENST00000263934,NM_015074.3;RN7SL731P,upstream_gene_variant,,ENST00000584329,; T ENST00000377093 Transcript missense_variant 3513/7565 3360/3462 1120/1153 Q/H caG/caT 1 1 KIF1B HGNC HGNC:16636 protein_coding CCDS112.1 ENSP00000366297 O60333 UPI0000140CB8 NM_183416.3 tolerated_low_confidence(0.37) 21/21 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 10304545 10304545 G T 1 0 0 0 0 1 0 0 0 8148 933 33 2 2 KIF1B 1 10304545 Missense_Mutation SNP G C3N-00175_T 1040758 10304545 238651877 7 9599 TARDBP 0 . GRCh38 1 11018866 11018866 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.536A>T p.Asn179Ile p.N179I ENST00000240185 4/6 581 526 55 547 547 0 strelka-varscan-mutect TARDBP,missense_variant,p.Asn179Ile,ENST00000240185,NM_007375.3;TARDBP,missense_variant,p.Asn179Ile,ENST00000315091,;TARDBP,missense_variant,p.Asn179Ile,ENST00000629725,;TARDBP,missense_variant,p.Asn179Ile,ENST00000621790,;TARDBP,missense_variant,p.Asn93Ile,ENST00000617172,;TARDBP,missense_variant,p.Asn220Ile,ENST00000476201,;TARDBP,missense_variant,p.Asn179Ile,ENST00000616545,;TARDBP,missense_variant,p.Asn179Ile,ENST00000621715,;TARDBP,missense_variant,p.Asn95Ile,ENST00000622057,;TARDBP,missense_variant,p.Asn179Ile,ENST00000473118,;TARDBP,missense_variant,p.Asn5Ile,ENST00000610369,;RP4-635E18.9,upstream_gene_variant,,ENST00000612542,;TARDBP,upstream_gene_variant,,ENST00000611008,;TARDBP,downstream_gene_variant,,ENST00000613864,;TARDBP,upstream_gene_variant,,ENST00000617757,;TARDBP,upstream_gene_variant,,ENST00000613177,;TARDBP,missense_variant,p.Asn179Ile,ENST00000473869,;RP4-635E18.9,missense_variant,p.Asn179Ile,ENST00000614757,;TARDBP,missense_variant,p.Asn59Ile,ENST00000611963,;TARDBP,missense_variant,p.Asn30Ile,ENST00000620632,;TARDBP,missense_variant,p.Asn30Ile,ENST00000619555,;TARDBP,3_prime_UTR_variant,,ENST00000439080,;TARDBP,3_prime_UTR_variant,,ENST00000472476,;TARDBP,non_coding_transcript_exon_variant,,ENST00000618606,;TARDBP,upstream_gene_variant,,ENST00000621573,;RP4-635E18.9,upstream_gene_variant,,ENST00000611136,;TARDBP,upstream_gene_variant,,ENST00000496840,;TARDBP,upstream_gene_variant,,ENST00000620505,;RP4-635E18.9,upstream_gene_variant,,ENST00000622108,;TARDBP,upstream_gene_variant,,ENST00000614494,;TARDBP,upstream_gene_variant,,ENST00000477447,; T ENST00000240185 Transcript missense_variant 892/5367 536/1245 179/414 N/I aAt/aTt 1 1 TARDBP HGNC HGNC:11571 protein_coding YES CCDS122.1 ENSP00000240185 Q13148 A0A024R4E2 UPI0000136B42 NM_007375.3 tolerated(0.13) 4/6 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF492,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 11018866 11018866 A T 1 0 0 0 0 1 0 0 0 15956 101 4 4 4 TARDBP 1 11018866 Missense_Mutation SNP A C3N-00175_T 714321 11018866 237937556 8 9600 ANGPTL7 0 . GRCh38 1 11189772 11189772 + Nonsense_Mutation SNP G G T rs779217175 C3N-00175_T C3N-00175_N G G c.193G>T p.Glu65Ter p.E65* ENST00000376819 1/5 228 206 22 258 257 1 strelka-varscan-mutect ANGPTL7,stop_gained,p.Glu65Ter,ENST00000376819,NM_021146.3;MTOR,intron_variant,,ENST00000361445,NM_004958.3;ANGPTL7,upstream_gene_variant,,ENST00000476934,; T ENST00000376819 Transcript stop_gained 432/2238 193/1041 65/346 E/* Gaa/Taa rs779217175 1 1 ANGPTL7 HGNC HGNC:24078 protein_coding YES CCDS128.1 ENSP00000366015 O43827 UPI0000035976 NM_021146.3 1/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF40 HIGH 1 SNV 1 1 PASS rs779217175 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 11189772 11189772 G T 1 0 0 0 0 0 1 0 0 717 1291 45 2 2 ANGPTL7 1 11189772 Nonsense_Mutation SNP G C3N-00175_T 170906 11189772 237766650 9 9601 DISP3 0 . GRCh38 1 11502802 11502802 + Missense_Mutation SNP C C G rs746563194 C3N-00175_T C3N-00175_N C C c.1221C>G p.Asn407Lys p.N407K ENST00000294484 3/21 244 193 51 263 263 0 strelka-varscan-mutect DISP3,missense_variant,p.Asn407Lys,ENST00000294484,NM_020780.1; G ENST00000294484 Transcript missense_variant 1359/5215 1221/4179 407/1392 N/K aaC/aaG rs746563194 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 tolerated(0.06) 3/21 hmmpanther:PTHR10796:SF125,hmmpanther:PTHR10796 MODERATE 1 SNV 1 1 PASS rs746563194 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 11502802 11502802 C G 1 0 0 0 0 1 0 0 0 4347 564 20 4 4 DISP3 1 11502802 Missense_Mutation SNP C C3N-00175_T 313030 11502802 237453620 10 9602 AADACL3 0 . GRCh38 1 12725951 12725951 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1179C>T p.= p.S393S ENST00000359318 4/4 104 74 30 131 131 0 strelka-varscan-mutect AADACL3,synonymous_variant,p.=,ENST00000359318,NM_001103170.2;AADACL3,non_coding_transcript_exon_variant,,ENST00000620146,; T ENST00000359318 Transcript synonymous_variant 1213/3662 1179/1224 393/407 S tcC/tcT 1 1 AADACL3 HGNC HGNC:32037 protein_coding YES CCDS41253.2 ENSP00000352268 Q5VUY0 UPI0003EAEC70 NM_001103170.2 4/4 Gene3D:3.40.50.1820,PIRSF_domain:PIRSF037251,hmmpanther:PTHR23024,hmmpanther:PTHR23024:SF115,Superfamily_domains:SSF53474 LOW 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 12725951 12725951 C T 1 0 0 0 0 0 0 0 1 12 581 21 3 3 AADACL3 1 12725951 Silent SNP C C3N-00175_T 1223149 12725951 236230471 11 9603 PRAMEF7 0 . GRCh38 1 12920399 12920399 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1411C>A p.His471Asn p.H471N ENST00000616979 4/4 215 189 26 254 254 0 varscan-mutect PRAMEF7,missense_variant,p.His471Asn,ENST00000616979,NM_001012277.4;PRAMEF7,missense_variant,p.His471Asn,ENST00000330881,;RNU6-1072P,upstream_gene_variant,,ENST00000384703,; A ENST00000616979 Transcript missense_variant 1509/1592 1411/1425 471/474 H/N Cac/Aac 1 1 PRAMEF7 HGNC HGNC:28415 protein_coding YES CCDS30593.1 ENSP00000484237 Q5VXH5 UPI000058F1DF NM_001012277.4 tolerated(0.08) 4/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 12920399 12920399 C A 1 0 0 0 0 1 0 0 0 12569 826 29 2 2 PRAMEF7 1 12920399 Missense_Mutation SNP C C3N-00175_T 194448 12920399 236036023 12 9604 PRAMEF27 0 . GRCh38 1 13049945 13049945 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1300G>T p.Ala434Ser p.A434S ENST00000436041 4/4 627 480 147 619 616 3 strelka-varscan-mutect PRAMEF27,missense_variant,p.Ala434Ser,ENST00000436041,NM_001300891.1; A ENST00000436041 Transcript missense_variant 1394/1863 1300/1437 434/478 A/S Gct/Tct 1 -1 PRAMEF27 HGNC HGNC:51234 protein_coding YES CCDS72704.1 ENSP00000393136 A3QJZ7 UPI000387AD89 NM_001300891.1 tolerated(0.11) 4/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19 MODERATE 1 SNV 1 1 PASS rs1196597594 . 22 188 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 13049945 13049945 C A 1 0 0 0 0 1 0 0 0 12565 710 25 2 2 PRAMEF27 1 13049945 Missense_Mutation SNP C C3N-00175_T 129546 13049945 235906477 13 9605 PRAMEF15 0 . GRCh38 1 13319940 13319940 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.862G>T p.Asp288Tyr p.D288Y ENST00000376152 3/4 337 271 66 327 325 2 strelka-varscan-mutect PRAMEF15,missense_variant,p.Asp288Tyr,ENST00000376152,NM_001098376.2;PRAMEF15,missense_variant,p.Asp286Tyr,ENST00000613530,;RP11-219C24.10,upstream_gene_variant,,ENST00000432559,; T ENST00000376152 Transcript missense_variant 956/1865 862/1437 288/478 D/Y Gac/Tac 1 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES CCDS44059.1 ENSP00000365322 Q5VWM5 UPI0000199BA7 NM_001098376.2 deleterious(0) 3/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs1283260890 . 0 202 0 0 7 0 0 0 -20 0.4807776 1 1 0 0 T 3 4 39 13319940 13319940 G T 1 0 0 0 0 1 0 0 0 12559 1174 41 2 2 PRAMEF15 1 13319940 Missense_Mutation SNP G C3N-00175_T 269995 13319940 235636482 14 9606 ZBTB17 0 . GRCh38 1 15942046 15942046 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.2356C>T p.Arg786Cys p.R786C ENST00000375733 16/16 159 140 19 149 149 0 strelka-varscan-mutect ZBTB17,missense_variant,p.Arg786Cys,ENST00000375733,NM_001287603.1;ZBTB17,missense_variant,p.Arg779Cys,ENST00000375743,NM_003443.2;ZBTB17,missense_variant,p.Arg697Cys,ENST00000537142,NM_001324137.1,NM_001287604.1,NM_001242884.1;ZBTB17,missense_variant,p.Arg186Cys,ENST00000440560,;SPEN,downstream_gene_variant,,ENST00000375759,NM_015001.2;ZBTB17,downstream_gene_variant,,ENST00000444358,;ZBTB17,non_coding_transcript_exon_variant,,ENST00000462525,;ZBTB17,downstream_gene_variant,,ENST00000479282,;ZBTB17,downstream_gene_variant,,ENST00000492834,;ZBTB17,downstream_gene_variant,,ENST00000494020,;ZBTB17,downstream_gene_variant,,ENST00000474511,;ZBTB17,downstream_gene_variant,,ENST00000490899,;ZBTB17,downstream_gene_variant,,ENST00000472658,;ZBTB17,downstream_gene_variant,,ENST00000471805,;SPEN,downstream_gene_variant,,ENST00000487496,;ZBTB17,downstream_gene_variant,,ENST00000464719,;ZBTB17,downstream_gene_variant,,ENST00000488008,;ZBTB17,downstream_gene_variant,,ENST00000487785,; A ENST00000375733 Transcript missense_variant 2595/2770 2356/2433 786/810 R/C Cgc/Tgc COSM4576515,COSM4576516 1 -1 ZBTB17 HGNC HGNC:12936 protein_coding YES CCDS72712.1 ENSP00000364885 Q13105 UPI00005054F0 NM_001287603.1 deleterious_low_confidence(0) 16/16 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF165 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1350046192 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 39 15942046 15942046 G A 1 0 0 0 0 1 0 0 0 18094 1058 37 1 1 ZBTB17 1 15942046 Missense_Mutation SNP G C3N-00175_T 2622106 15942046 233014376 15 9607 CROCC 0 . GRCh38 1 16944267 16944267 + Missense_Mutation SNP G G T rs369407665 C3N-00175_T C3N-00175_N G G c.1976G>T p.Arg659Leu p.R659L ENST00000375541 14/37 88 78 10 96 96 0 strelka-varscan-mutect CROCC,missense_variant,p.Arg659Leu,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Arg519Leu,ENST00000445545,;CROCC,missense_variant,p.Arg553Leu,ENST00000467938,;CROCC,downstream_gene_variant,,ENST00000467715,;CROCC,non_coding_transcript_exon_variant,,ENST00000492631,;CROCC,non_coding_transcript_exon_variant,,ENST00000486318,;CROCC,downstream_gene_variant,,ENST00000466256,;CROCC,upstream_gene_variant,,ENST00000477773,;CROCC,upstream_gene_variant,,ENST00000498688,;CROCC,non_coding_transcript_exon_variant,,ENST00000494191,; T ENST00000375541 Transcript missense_variant 2045/6656 1976/6054 659/2017 R/L cGg/cTg rs369407665 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 deleterious(0.03) 14/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 MODERATE 1 SNV 5 1 PASS rs369407665 . 0 203 6 0 0 0 0 0 -19.95974 0.9999999 1 1 1 0 T 3 4 39 16944267 16944267 G T 1 0 0 0 0 1 0 0 0 3694 1116 39 1 1 CROCC 1 16944267 Missense_Mutation SNP G C3N-00175_T 1002221 16944267 232012155 16 9608 KLHDC7A 0 . GRCh38 1 18483170 18483170 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2189G>T p.Arg730Leu p.R730L ENST00000400664 1/1 330 243 87 326 326 0 strelka-varscan-mutect KLHDC7A,missense_variant,p.Arg730Leu,ENST00000400664,NM_152375.2; T ENST00000400664 Transcript missense_variant 2189/5145 2189/2334 730/777 R/L cGc/cTc 1 1 KLHDC7A HGNC HGNC:26791 protein_coding YES CCDS185.2 ENSP00000383505 Q5VTJ3 UPI0000E0501F NM_152375.2 deleterious(0) 1/1 Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF242 MODERATE 1 SNV 1 PASS rs1467344706 . 0 208 0 0 2 0 0 0 -20 0.9988865 1 1 1 0 T 3 4 39 18483170 18483170 G T 1 0 0 0 0 1 0 0 0 8224 1087 38 1 1 KLHDC7A 1 18483170 Missense_Mutation SNP G C3N-00175_T 1538903 18483170 230473252 17 9609 NBL1 0 . GRCh38 1 19657028 19657028 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.550C>A p.His184Asn p.H184N ENST00000289749 4/4 70 54 16 82 82 0 strelka-varscan-mutect NBL1,missense_variant,p.His149Asn,ENST00000375136,NM_005380.7;NBL1,missense_variant,p.His183Asn,ENST00000615215,NM_001204086.2;NBL1,missense_variant,p.His149Asn,ENST00000621723,NM_001204084.2;NBL1,missense_variant,p.His149Asn,ENST00000622566,NM_001278165.1;NBL1,missense_variant,p.His149Asn,ENST00000618761,NM_001204085.1;NBL1,missense_variant,p.His149Asn,ENST00000548815,NM_001278164.1,NM_001278166.1;MINOS1-NBL1,missense_variant,p.His149Asn,ENST00000602662,NM_001204089.1;NBL1,missense_variant,p.His184Asn,ENST00000289749,NM_182744.3;NBL1,missense_variant,p.His148Asn,ENST00000427894,;NBL1,downstream_gene_variant,,ENST00000451758,;NBL1,downstream_gene_variant,,ENST00000439664,;NBL1,downstream_gene_variant,,ENST00000439278,;NBL1,downstream_gene_variant,,ENST00000428975,;NBL1,downstream_gene_variant,,ENST00000425400,;MINOS1-NBL1,downstream_gene_variant,,ENST00000602384,;MINOS1-NBL1,downstream_gene_variant,,ENST00000602293,;MINOS1-NBL1,downstream_gene_variant,,ENST00000602450,; A ENST00000289749 Transcript missense_variant 630/731 550/651 184/216 H/N Cac/Aac 1 1 NBL1 HGNC HGNC:7650 protein_coding YES CCDS41278.1 ENSP00000289749 P41271 UPI000020459F NM_182744.3 tolerated_low_confidence(0.23) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15283:SF5,hmmpanther:PTHR15283,PIRSF_domain:PIRSF018557 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19657028 19657028 C A 1 0 0 0 0 1 0 0 0 10201 594 21 2 2 NBL1 1 19657028 Missense_Mutation SNP C C3N-00175_T 1173858 19657028 229299394 18 9610 PLA2G2F 0 . GRCh38 1 20140197 20140197 + Missense_Mutation SNP G G A rs759630010 C3N-00175_T C3N-00175_N G G c.148G>A p.Val50Met p.V50M ENST00000375102 2/5 132 103 29 131 131 0 strelka-varscan-mutect PLA2G2F,missense_variant,p.Val50Met,ENST00000375102,NM_022819.3;PLA2G2F,non_coding_transcript_exon_variant,,ENST00000465062,; A ENST00000375102 Transcript missense_variant 250/2723 148/636 50/211 V/M Gtg/Atg rs759630010,COSM314198,COSM4437270 1 1 PLA2G2F HGNC HGNC:30040 protein_coding YES CCDS204.2 ENSP00000364243 Q9BZM2 UPI0000044C9D NM_022819.3 tolerated(0.2) 2/5 hmmpanther:PTHR11716,hmmpanther:PTHR11716:SF8 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs759630010 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 20140197 20140197 G A 1 0 0 0 0 1 0 0 0 12095 1145 40 1 1 PLA2G2F 1 20140197 Missense_Mutation SNP G C3N-00175_T 483169 20140197 228816225 19 9611 EIF4G3 0 . GRCh38 1 20862268 20862268 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.3011G>T p.Arg1004Met p.R1004M ENST00000400422 21/35 78 64 14 104 104 0 strelka-varscan-mutect EIF4G3,missense_variant,p.Arg974Met,ENST00000602326,NM_001198802.1;EIF4G3,missense_variant,p.Arg968Met,ENST00000264211,NM_003760.4;EIF4G3,missense_variant,p.Arg1004Met,ENST00000400422,NM_001198801.1;EIF4G3,missense_variant,p.Arg688Met,ENST00000374935,;EIF4G3,missense_variant,p.Arg1157Met,ENST00000634879,; A ENST00000400422 Transcript missense_variant 3592/5762 3011/4866 1004/1621 R/M aGg/aTg 1 -1 EIF4G3 HGNC HGNC:3298 protein_coding YES CCDS72723.1 ENSP00000383274 A0A0A0MSA7 UPI0000D4C1EC NM_001198801.1 deleterious(0) 21/35 Gene3D:1.25.40.180,Pfam_domain:PF02854,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF23,SMART_domains:SM00543,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 20862268 20862268 C A 1 0 0 0 0 1 0 0 0 4871 681 24 2 2 EIF4G3 1 20862268 Missense_Mutation SNP C C3N-00175_T 722071 20862268 228094154 20 9612 LACTBL1 0 . GRCh38 1 22953862 22953862 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.822C>A p.= p.A274A ENST00000426928 6/6 250 180 70 257 257 0 strelka-varscan-mutect LACTBL1,synonymous_variant,p.=,ENST00000426928,NM_001289974.1;LACTBL1,synonymous_variant,p.=,ENST00000618559,; T ENST00000426928 Transcript synonymous_variant 822/1641 822/1641 274/546 A gcC/gcA 1 -1 LACTBL1 HGNC HGNC:35445 protein_coding YES ENSP00000402297 H0Y608 UPI0002A47099 NM_001289974.1 6/6 hmmpanther:PTHR22935:SF64,hmmpanther:PTHR22935,Gene3D:3.40.710.10,Pfam_domain:PF00144,Superfamily_domains:SSF56601 LOW 1 SNV 5 1 PASS rs754181158 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 22953862 22953862 G T 1 0 0 0 0 0 0 0 1 8502 1103 39 1 1 LACTBL1 1 22953862 Silent SNP G C3N-00175_T 2091594 22953862 226002560 21 9613 SRSF10 0 . GRCh38 1 23971149 23971149 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.782G>A p.Gly261Asp p.G261D ENST00000492112 6/6 69 53 16 95 95 0 strelka-varscan-mutect SRSF10,missense_variant,p.Gly260Asp,ENST00000343255,NM_001191005.2;SRSF10,missense_variant,p.Gly261Asp,ENST00000492112,NM_054016.3;SRSF10,intron_variant,,ENST00000344989,NM_006625.5,NM_001300937.1;SRSF10,intron_variant,,ENST00000453840,NM_001191007.2;SRSF10,intron_variant,,ENST00000374452,NM_001191006.2;SRSF10,intron_variant,,ENST00000484146,NM_001191009.2;SRSF10,intron_variant,,ENST00000374453,NM_001300936.1;SRSF10,non_coding_transcript_exon_variant,,ENST00000338597,;SRSF10,intron_variant,,ENST00000341154,;SRSF10,downstream_gene_variant,,ENST00000473754,;SRSF10,non_coding_transcript_exon_variant,,ENST00000485841,;SRSF10,intron_variant,,ENST00000473858,;SRSF10,downstream_gene_variant,,ENST00000495785,; T ENST00000492112 Transcript missense_variant 846/1631 782/789 261/262 G/D gGc/gAc 1 -1 SRSF10 HGNC HGNC:16713 protein_coding YES CCDS30630.1 ENSP00000420195 O75494 A0A0S2Z504 UPI000005FB30 NM_054016.3 deleterious_low_confidence(0.01) 6/6 hmmpanther:PTHR23147,hmmpanther:PTHR23147:SF5 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999832 1 1 1 0 T 3 4 39 23971149 23971149 C T 1 0 0 0 0 1 0 0 0 15536 739 26 3 3 SRSF10 1 23971149 Missense_Mutation SNP C C3N-00175_T 1017287 23971149 224985273 22 9614 AIM1L 0 . GRCh38 1 26346495 26346495 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.163T>A p.Phe55Ile p.F55I ENST00000308182 2/20 111 84 27 164 163 1 strelka-varscan-mutect AIM1L,missense_variant,p.Phe55Ile,ENST00000308182,NM_001039775.3;AIM1L,missense_variant,p.Phe55Ile,ENST00000475866,;AIM1L,upstream_gene_variant,,ENST00000527815,;AIM1L,intron_variant,,ENST00000374207,; T ENST00000308182 Transcript missense_variant 313/5245 163/4986 55/1661 F/I Ttt/Att 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 deleterious_low_confidence(0.01) 2/20 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 26346495 26346495 A T 1 0 0 0 0 1 0 0 0 508 43 2 4 4 AIM1L 1 26346495 Missense_Mutation SNP A C3N-00175_T 2375346 26346495 222609927 23 9615 SLC9A1 0 . GRCh38 1 27100474 27100474 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2281G>T p.Gly761Cys p.G761C ENST00000263980 12/12 134 104 30 144 144 0 strelka-varscan-mutect SLC9A1,missense_variant,p.Gly761Cys,ENST00000263980,NM_003047.4;SLC9A1,downstream_gene_variant,,ENST00000374086,;SLC9A1,upstream_gene_variant,,ENST00000490329,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000374089,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000447808,; A ENST00000263980 Transcript missense_variant 2857/4516 2281/2448 761/815 G/C Ggc/Tgc 1 -1 SLC9A1 HGNC HGNC:11071 protein_coding YES CCDS295.1 ENSP00000263980 P19634 UPI000012FD1B NM_003047.4 deleterious(0) 12/12 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF59 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 27100474 27100474 C A 1 0 0 0 0 1 0 0 0 14993 623 22 2 2 SLC9A1 1 27100474 Missense_Mutation SNP C C3N-00175_T 753979 27100474 221855948 24 9616 COL16A1 0 . GRCh38 1 31652819 31652819 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.4647T>A p.= p.G1549G ENST00000373672 71/71 64 53 11 77 77 0 strelka-varscan-mutect COL16A1,synonymous_variant,p.=,ENST00000373672,NM_001856.3;COL16A1,downstream_gene_variant,,ENST00000440437,;RP11-73M7.6,intron_variant,,ENST00000610043,;RP11-73M7.6,intron_variant,,ENST00000591929,;RP11-73M7.6,intron_variant,,ENST00000585413,;RP11-73M7.6,intron_variant,,ENST00000609549,;RP11-73M7.6,intron_variant,,ENST00000609033,;RP11-73M7.6,intron_variant,,ENST00000589462,;RP11-73M7.6,intron_variant,,ENST00000609625,;RP11-73M7.6,intron_variant,,ENST00000607926,;RP11-73M7.6,intron_variant,,ENST00000587445,;RP11-73M7.6,intron_variant,,ENST00000585660,;RP11-73M7.6,intron_variant,,ENST00000610216,;RP11-73M7.6,intron_variant,,ENST00000623791,;RP11-73M7.6,intron_variant,,ENST00000609373,;RP11-73M7.6,intron_variant,,ENST00000608246,;RP11-73M7.6,intron_variant,,ENST00000593188,;RP11-73M7.6,intron_variant,,ENST00000623425,;RP11-73M7.6,intron_variant,,ENST00000608888,;RP11-73M7.6,intron_variant,,ENST00000624388,;RP11-73M7.6,intron_variant,,ENST00000608332,;RP11-73M7.6,intron_variant,,ENST00000591592,;RP11-73M7.6,intron_variant,,ENST00000609338,;RP11-73M7.6,upstream_gene_variant,,ENST00000623786,;RP11-73M7.6,upstream_gene_variant,,ENST00000588288,;RP11-73M7.9,downstream_gene_variant,,ENST00000581333,;RP11-73M7.6,upstream_gene_variant,,ENST00000445166,;COL16A1,downstream_gene_variant,,ENST00000461217,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488128,;COL16A1,non_coding_transcript_exon_variant,,ENST00000488897,; T ENST00000373672 Transcript synonymous_variant 5164/5736 4647/4815 1549/1604 G ggT/ggA 1 -1 COL16A1 HGNC HGNC:2193 protein_coding YES CCDS41297.1 ENSP00000362776 Q07092 UPI0000203DD1 NM_001856.3 71/71 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF372,hmmpanther:PTHR24023 LOW SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -19.99999 0.9999997 1 1 1 0 T 2 4 39 31652819 31652819 A T 1 0 0 0 0 0 0 0 1 3461 146 6 4 4 COL16A1 1 31652819 Silent SNP A C3N-00175_T 4552345 31652819 217303603 25 9617 ADGRB2 0 . GRCh38 1 31756468 31756468 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.369A>T p.= p.S123S ENST00000373655 4/33 105 85 20 140 140 0 strelka-varscan-mutect ADGRB2,synonymous_variant,p.=,ENST00000373658,;ADGRB2,synonymous_variant,p.=,ENST00000373655,NM_001294335.1;ADGRB2,synonymous_variant,p.=,ENST00000398542,;ADGRB2,synonymous_variant,p.=,ENST00000527361,NM_001294336.1;ADGRB2,synonymous_variant,p.=,ENST00000398556,;ADGRB2,synonymous_variant,p.=,ENST00000398547,;ADGRB2,synonymous_variant,p.=,ENST00000398538,;ADGRB2,synonymous_variant,p.=,ENST00000420125,;ADGRB2,synonymous_variant,p.=,ENST00000533175,;ADGRB2,downstream_gene_variant,,ENST00000436464,;MIR4254,downstream_gene_variant,,ENST00000581063,;ADGRB2,upstream_gene_variant,,ENST00000530134,; A ENST00000373655 Transcript synonymous_variant 711/5400 369/4755 123/1584 S tcA/tcT 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 4/33 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 31756468 31756468 T A 1 0 0 0 0 0 0 0 1 356 1567 55 4 4 ADGRB2 1 31756468 Silent SNP T C3N-00175_T 103649 31756468 217199954 26 9618 SPOCD1 0 . GRCh38 1 31792308 31792308 + Missense_Mutation SNP C C A rs751875735 C3N-00175_T C3N-00175_N C C c.2869G>T p.Gly957Trp p.G957W ENST00000360482 15/16 332 298 34 371 370 1 strelka-varscan-mutect SPOCD1,missense_variant,p.Gly957Trp,ENST00000360482,NM_144569.5;SPOCD1,missense_variant,p.Gly957Trp,ENST00000533231,NM_001281987.1;SPOCD1,missense_variant,p.Gly450Trp,ENST00000257100,NM_001281988.1;SPOCD1,missense_variant,p.Gly393Trp,ENST00000452755,;SPOCD1,downstream_gene_variant,,ENST00000528579,;RP11-84A19.3,downstream_gene_variant,,ENST00000527035,;SPOCD1,intron_variant,,ENST00000473361,;SPOCD1,downstream_gene_variant,,ENST00000485944,;SPOCD1,downstream_gene_variant,,ENST00000468720,;SPOCD1,downstream_gene_variant,,ENST00000460061,;SPOCD1,downstream_gene_variant,,ENST00000531039,;SPOCD1,downstream_gene_variant,,ENST00000532604,; A ENST00000360482 Transcript missense_variant 2999/3960 2869/3651 957/1216 G/W Ggg/Tgg rs751875735 1 -1 SPOCD1 HGNC HGNC:26338 protein_coding YES CCDS347.1 ENSP00000353670 Q6ZMY3 UPI000035E7DD NM_144569.5 deleterious(0) 15/16 hmmpanther:PTHR11477:SF18,hmmpanther:PTHR11477,Pfam_domain:PF07744 MODERATE 1 SNV 2 1 PASS rs751875735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 31792308 31792308 C A 1 0 0 0 0 1 0 0 0 15431 652 23 1 1 SPOCD1 1 31792308 Missense_Mutation SNP C C3N-00175_T 35840 31792308 217164114 27 9619 RBBP4 0 . GRCh38 1 32669560 32669560 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.963C>A p.Phe321Leu p.F321L ENST00000373493 8/12 43 37 6 68 68 0 strelka-varscan-mutect RBBP4,missense_variant,p.Phe321Leu,ENST00000373493,NM_005610.2;RBBP4,missense_variant,p.Phe320Leu,ENST00000414241,NM_001135255.1;RBBP4,missense_variant,p.Phe286Leu,ENST00000458695,NM_001135256.1;RBBP4,missense_variant,p.Phe321Leu,ENST00000373485,;RBBP4,missense_variant,p.Phe81Leu,ENST00000463378,;RBBP4,missense_variant,p.Phe124Leu,ENST00000475321,;RBBP4,missense_variant,p.Phe59Leu,ENST00000482190,;RBBP4,downstream_gene_variant,,ENST00000445722,;RBBP4,downstream_gene_variant,,ENST00000524393,;RBBP4,missense_variant,p.Phe76Leu,ENST00000460669,;RBBP4,3_prime_UTR_variant,,ENST00000492348,;RBBP4,downstream_gene_variant,,ENST00000401893,;RBBP4,downstream_gene_variant,,ENST00000527118,;RBBP4,downstream_gene_variant,,ENST00000526193,;RBBP4,downstream_gene_variant,,ENST00000477563,;RBBP4,downstream_gene_variant,,ENST00000531983,; A ENST00000373493 Transcript missense_variant 1122/7943 963/1278 321/425 F/L ttC/ttA COSM4514113 1 1 RBBP4 HGNC HGNC:9887 protein_coding YES CCDS366.1 ENSP00000362592 Q09028 UPI000013318C NM_005610.2 tolerated(0.54) 8/12 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF90,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.15078 1 1 1 1 0 A 3 1 39 32669560 32669560 C A 1 0 0 0 0 1 0 0 0 13262 869 30 2 2 RBBP4 1 32669560 Missense_Mutation SNP C C3N-00175_T 877252 32669560 216286862 28 9620 C1orf94 0 . GRCh38 1 34197806 34197806 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.902C>A p.Pro301His p.P301H ENST00000488417 2/7 330 255 75 383 383 0 strelka-varscan-mutect C1orf94,missense_variant,p.Pro301His,ENST00000488417,NM_001134734.1;C1orf94,missense_variant,p.Pro111His,ENST00000373374,NM_032884.4; A ENST00000488417 Transcript missense_variant 1022/2287 902/1797 301/598 P/H cCt/cAt 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 deleterious(0.02) 2/7 Low_complexity_(Seg):seg,hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1,Pfam_domain:PF15752 MODERATE 1 SNV 1 1 PASS rs1208422637 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 34197806 34197806 C A 1 0 0 0 0 1 0 0 0 2000 681 24 2 2 C1orf94 1 34197806 Missense_Mutation SNP C C3N-00175_T 1528246 34197806 214758616 29 9621 SH3D21 0 . GRCh38 1 36319483 36319483 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.625G>T p.Gly209Cys p.G209C ENST00000505871 10/13 183 144 39 252 252 0 strelka-varscan-mutect SH3D21,missense_variant,p.Gly320Cys,ENST00000453908,NM_001162530.1;SH3D21,missense_variant,p.Gly209Cys,ENST00000505871,NM_024676.4;SH3D21,missense_variant,p.Gly320Cys,ENST00000373139,;EVA1B,downstream_gene_variant,,ENST00000270824,NM_018166.2,NM_001304762.1;RP11-268J15.5,upstream_gene_variant,,ENST00000373137,;SH3D21,intron_variant,,ENST00000508854,;SH3D21,upstream_gene_variant,,ENST00000474766,;EVA1B,downstream_gene_variant,,ENST00000490466,;SH3D21,intron_variant,,ENST00000480549,; T ENST00000505871 Transcript missense_variant 789/2206 625/1938 209/645 G/C Ggc/Tgc 1 1 SH3D21 HGNC HGNC:26236 protein_coding YES CCDS30674.2 ENSP00000421294 A4FU49 UPI00017A7573 NM_024676.4 deleterious(0) 10/13 hmmpanther:PTHR14167,hmmpanther:PTHR14167:SF28 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 36319483 36319483 G T 1 0 0 0 0 1 0 0 0 14508 1348 47 2 2 SH3D21 1 36319483 Missense_Mutation SNP G C3N-00175_T 2121677 36319483 212636939 30 9622 HIVEP3 0 . GRCh38 1 41513195 41513195 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.6026G>T p.Ser2009Ile p.S2009I ENST00000372583 8/9 95 75 20 118 118 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Ser2009Ile,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Ser2009Ile,ENST00000372583,NM_024503.4;HIVEP3,non_coding_transcript_exon_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 6912/12193 6026/7221 2009/2406 S/I aGc/aTc 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 tolerated(0.1) 8/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 41513195 41513195 C A 1 0 0 0 0 1 0 0 0 7077 797 28 2 2 HIVEP3 1 41513195 Missense_Mutation SNP C C3N-00175_T 5193712 41513195 207443227 31 9623 HIVEP3 0 . GRCh38 1 41583002 41583002 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1796G>T p.Gly599Val p.G599V ENST00000372583 4/9 174 130 44 186 186 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Gly599Val,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Gly599Val,ENST00000372583,NM_024503.4;HIVEP3,upstream_gene_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 2682/12193 1796/7221 599/2406 G/V gGg/gTg 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 tolerated(0.54) 4/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 41583002 41583002 C A 1 0 0 0 0 1 0 0 0 7077 623 22 2 2 HIVEP3 1 41583002 Missense_Mutation SNP C C3N-00175_T 69807 41583002 207373420 32 9624 KLF17 0 . GRCh38 1 44130718 44130720 + In_Frame_Del DEL AAT AAT - novel C3N-00175_T C3N-00175_N AAT AAT c.1132_1134delAAT p.Asn378del p.N378del ENST00000372299 3/4 241 188 53 290 290 0 sindel-varindel-pindel KLF17,inframe_deletion,p.Asn378del,ENST00000372299,NM_173484.3;KLF17,downstream_gene_variant,,ENST00000476802,; - ENST00000372299 Transcript inframe_deletion 1190-1192/3131 1132-1134/1170 378/389 N/- AAT/- 1 1 KLF17 HGNC HGNC:18830 protein_coding YES CCDS508.1 ENSP00000361373 Q5JT82 UPI000013E95E NM_173484.3 3/4 MODERATE 1 deletion 1 1 PASS . . 0 159 0 0 48 2 0 0 -2.710076 0 0 1 0 0 - 7 5 39 44130718 44130718 AAT - 1 0 1 0 1 0 0 0 0 8210 130 5 0 0 KLF17 1 44130718 In_Frame_Del DEL AAT C3N-00175_T 2547716 44130718 204825704 33 9625 FOXD2 0 . GRCh38 1 47438486 47438486 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.351G>T p.= p.G117G ENST00000334793 1/1 169 136 33 170 170 0 strelka-varscan-mutect FOXD2,synonymous_variant,p.=,ENST00000334793,NM_004474.3;FOXD2-AS1,upstream_gene_variant,,ENST00000445551,; T ENST00000334793 Transcript synonymous_variant 2470/4675 351/1488 117/495 G ggG/ggT 1 1 FOXD2 HGNC HGNC:3803 protein_coding YES CCDS30708.1 ENSP00000335493 O60548 UPI000014153E NM_004474.3 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF168,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 47438486 47438486 G T 1 0 0 0 0 0 0 0 1 5857 1219 43 2 2 FOXD2 1 47438486 Silent SNP G C3N-00175_T 3307768 47438486 201517936 34 9626 NDC1 0 . GRCh38 1 53835602 53835602 + Missense_Mutation SNP C C A rs199526095 C3N-00175_T C3N-00175_N C C c.76G>T p.Val26Phe p.V26F ENST00000371429 2/18 90 70 20 124 124 0 strelka-varscan-mutect NDC1,missense_variant,p.Val26Phe,ENST00000371429,NM_001168551.1,NM_018087.4;NDC1,intron_variant,,ENST00000480952,; A ENST00000371429 Transcript missense_variant 675/5134 76/2025 26/674 V/F Gtt/Ttt rs199526095 1 -1 NDC1 HGNC HGNC:25525 protein_coding YES CCDS583.1 ENSP00000360483 Q9BTX1 UPI000006D8F7 NM_001168551.1,NM_018087.4 tolerated(0.09) 2/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR13269:SF6,hmmpanther:PTHR13269,Pfam_domain:PF09531 MODERATE 1 SNV 1 1 PASS rs199526095 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 53835602 53835602 C A 1 0 0 0 0 1 0 0 0 10262 565 20 2 2 NDC1 1 53835602 Missense_Mutation SNP C C3N-00175_T 6397116 53835602 195120820 35 9627 C1orf87 0 . GRCh38 1 59997639 59997639 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1450G>T p.Ala484Ser p.A484S ENST00000371201 11/12 185 124 61 256 255 1 strelka-varscan-mutect C1orf87,missense_variant,p.Ala484Ser,ENST00000371201,NM_152377.2;C1orf87,missense_variant,p.Ala255Ser,ENST00000450089,;C1orf87,non_coding_transcript_exon_variant,,ENST00000486478,;C1orf87,non_coding_transcript_exon_variant,,ENST00000488027,;C1orf87,non_coding_transcript_exon_variant,,ENST00000491817,; A ENST00000371201 Transcript missense_variant 1558/2028 1450/1641 484/546 A/S Gcc/Tcc 1 -1 C1orf87 HGNC HGNC:28547 protein_coding YES CCDS614.1 ENSP00000360244 Q8N0U7 UPI000006E066 NM_152377.2 deleterious(0.02) 11/12 Gene3D:1.10.238.10,hmmpanther:PTHR34830,hmmpanther:PTHR34830:SF1 MODERATE 1 SNV 1 1 PASS rs1269299867 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 59997639 59997639 C A 1 0 0 0 0 1 0 0 0 1999 710 25 2 2 C1orf87 1 59997639 Missense_Mutation SNP C C3N-00175_T 6162037 59997639 188958783 36 9628 PATJ 0 . GRCh38 1 61927831 61927831 + Splice_Site SNP T T G novel C3N-00175_T C3N-00175_N T T c.3670+2T>G p.X1224_splice ENST00000371158 101 71 30 118 118 0 strelka-varscan-mutect PATJ,splice_donor_variant,,ENST00000371158,NM_176877.2;PATJ,splice_donor_variant,,ENST00000494842,;PATJ,splice_donor_variant,,ENST00000490547,;PATJ,intron_variant,,ENST00000613764,;PATJ,splice_donor_variant,,ENST00000484562,;PATJ,splice_donor_variant,,ENST00000459752,;PATJ,splice_donor_variant,,ENST00000635023,;PATJ,splice_donor_variant,,ENST00000484937,;PATJ,splice_donor_variant,,ENST00000635214,; G ENST00000371158 Transcript splice_donor_variant -/8505 3670/5406 1224/1801 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 27/42 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 39 61927831 61927831 T G 1 0 0 0 0 0 0 1 0 11558 1710 59 5 5 PATJ 1 61927831 Splice_Site SNP T C3N-00175_T 1930192 61927831 187028591 37 9629 CACHD1 0 . GRCh38 1 64629481 64629481 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.491G>T p.Arg164Ile p.R164I ENST00000290039 5/27 83 57 26 109 109 0 strelka-varscan-mutect CACHD1,missense_variant,p.Arg164Ile,ENST00000290039,NM_020925.2,NM_001293274.1;CACHD1,splice_region_variant,,ENST00000495994,;CACHD1,splice_region_variant,,ENST00000470527,; T ENST00000290039 Transcript missense_variant,splice_region_variant 597/5275 491/3672 164/1223 R/I aGa/aTa 1 1 CACHD1 HGNC HGNC:29314 protein_coding YES CCDS628.2 ENSP00000290039 A0A0A0MQY7 UPI0000458A70 NM_020925.2,NM_001293274.1 deleterious(0) 5/27 Gene3D:3.30.450.20,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF40 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 64629481 64629481 G T 1 0 0 0 0 1 0 0 0 2225 1014 35 2 2 CACHD1 1 64629481 Missense_Mutation SNP G C3N-00175_T 2701650 64629481 184326941 38 9630 GBP7 0 . GRCh38 1 89150536 89150536 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.665A>T p.Glu222Val p.E222V ENST00000294671 6/11 138 90 48 198 198 0 strelka-varscan-mutect GBP7,missense_variant,p.Glu222Val,ENST00000294671,NM_207398.2;GBP2,upstream_gene_variant,,ENST00000464839,; A ENST00000294671 Transcript missense_variant 804/2454 665/1917 222/638 E/V gAg/gTg 1 -1 GBP7 HGNC HGNC:29606 protein_coding YES CCDS720.1 ENSP00000294671 Q8N8V2 UPI000013E1A3 NM_207398.2 tolerated(0.12) 6/11 PROSITE_profiles:PS51715,hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF17,Gene3D:3.40.50.300,Pfam_domain:PF02263,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 89150536 89150536 T A 1 0 0 0 0 1 0 0 0 6149 1551 54 4 4 GBP7 1 89150536 Missense_Mutation SNP T C3N-00175_T 24521055 89150536 159805886 39 9631 PLPPR4 0 . GRCh38 1 99306234 99306234 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1516C>T p.Pro506Ser p.P506S ENST00000370185 7/7 214 196 18 243 243 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Pro506Ser,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Pro448Ser,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Pro348Ser,ENST00000370184,; T ENST00000370185 Transcript missense_variant 2013/5369 1516/2292 506/763 P/S Cct/Tct 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 tolerated(0.35) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 99306234 99306234 C T 1 0 0 0 0 1 0 0 0 12212 739 26 3 3 PLPPR4 1 99306234 Missense_Mutation SNP C C3N-00175_T 10155698 99306234 149650188 40 9632 COL11A1 0 . GRCh38 1 102965518 102965518 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.2885C>T p.Pro962Leu p.P962L ENST00000370096 38/67 295 230 65 275 273 2 strelka-varscan-mutect COL11A1,missense_variant,p.Pro974Leu,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro962Leu,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro923Leu,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro846Leu,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,;COL11A1,upstream_gene_variant,,ENST00000465209,; A ENST00000370096 Transcript missense_variant 3198/7286 2885/5421 962/1806 P/L cCt/cTt COSM400821,COSM400822 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 tolerated(0.05) 38/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1192133331 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 102965518 102965518 G A 1 0 0 0 0 1 0 0 0 3455 1000 35 3 3 COL11A1 1 102965518 Missense_Mutation SNP G C3N-00175_T 3659284 102965518 145990904 41 9633 NTNG1 0 . GRCh38 1 107324738 107324738 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.703C>A p.Pro235Thr p.P235T ENST00000370068 3/8 155 122 33 158 158 0 strelka-varscan-mutect NTNG1,missense_variant,p.Pro235Thr,ENST00000370067,;NTNG1,missense_variant,p.Pro235Thr,ENST00000370068,;NTNG1,missense_variant,p.Pro235Thr,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Pro235Thr,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Pro235Thr,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Pro235Thr,ENST00000370065,;NTNG1,missense_variant,p.Pro235Thr,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; A ENST00000370068 Transcript missense_variant 1549/4034 703/1620 235/539 P/T Cct/Act 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0.03) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999967 1 1 1 0 A 3 1 39 107324738 107324738 C A 1 0 0 0 0 1 0 0 0 10769 507 18 2 2 NTNG1 1 107324738 Missense_Mutation SNP C C3N-00175_T 4359220 107324738 141631684 42 9634 WDR47 0 . GRCh38 1 108983343 108983343 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.2058A>T p.= p.T686T ENST00000400794 11/15 133 104 29 140 140 0 strelka-varscan-mutect WDR47,synonymous_variant,p.=,ENST00000369965,NM_014969.5;WDR47,synonymous_variant,p.=,ENST00000369962,NM_001142551.1;WDR47,synonymous_variant,p.=,ENST00000357672,;WDR47,synonymous_variant,p.=,ENST00000400794,NM_001142550.1;WDR47,synonymous_variant,p.=,ENST00000361054,;RP5-1065J22.2,downstream_gene_variant,,ENST00000439282,; A ENST00000400794 Transcript synonymous_variant 2192/4134 2058/2784 686/927 T acA/acT 1 -1 WDR47 HGNC HGNC:29141 protein_coding YES CCDS44186.1 ENSP00000383599 O94967 UPI0001639B05 NM_001142550.1 11/15 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19863,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 108983343 108983343 T A 1 0 0 0 0 0 0 0 1 17860 1567 55 4 4 WDR47 1 108983343 Silent SNP T C3N-00175_T 1658605 108983343 139973079 43 9635 EPS8L3 0 . GRCh38 1 109753127 109753127 + Missense_Mutation SNP G G T rs775122926 C3N-00175_T C3N-00175_N G G c.1193C>A p.Pro398His p.P398H ENST00000369805 13/19 93 68 25 104 104 0 strelka-varscan-mutect EPS8L3,missense_variant,p.Pro398His,ENST00000369805,NM_139053.2;EPS8L3,missense_variant,p.Pro397His,ENST00000361852,NM_001319952.1,NM_024526.3;EPS8L3,missense_variant,p.Pro397His,ENST00000361965,NM_133181.3;RP4-735C1.4,intron_variant,,ENST00000431955,;GSTM5,intron_variant,,ENST00000429410,;EPS8L3,upstream_gene_variant,,ENST00000475725,;EPS8L3,upstream_gene_variant,,ENST00000498743,;EPS8L3,upstream_gene_variant,,ENST00000482453,;EPS8L3,upstream_gene_variant,,ENST00000489465,;EPS8L3,3_prime_UTR_variant,,ENST00000472325,; T ENST00000369805 Transcript missense_variant 1423/2325 1193/1785 398/594 P/H cCc/cAc rs775122926 1 -1 EPS8L3 HGNC HGNC:21297 protein_coding YES CCDS815.1 ENSP00000358820 Q8TE67 UPI00001613C9 NM_139053.2 tolerated(0.07) 13/19 hmmpanther:PTHR12287:SF22,hmmpanther:PTHR12287 MODERATE 1 SNV 1 1 PASS rs775122926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 109753127 109753127 G T 1 0 0 0 0 1 0 0 0 5045 1232 43 2 2 EPS8L3 1 109753127 Missense_Mutation SNP G C3N-00175_T 769784 109753127 139203295 44 9636 EPS8L3 0 . GRCh38 1 109757544 109757544 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.909C>A p.= p.A303A ENST00000369805 11/19 149 105 44 161 161 0 strelka-varscan-mutect EPS8L3,synonymous_variant,p.=,ENST00000369805,NM_139053.2;EPS8L3,synonymous_variant,p.=,ENST00000361852,NM_001319952.1,NM_024526.3;EPS8L3,synonymous_variant,p.=,ENST00000361965,NM_133181.3;RP4-735C1.4,intron_variant,,ENST00000431955,;GSTM5,intron_variant,,ENST00000429410,;EPS8L3,downstream_gene_variant,,ENST00000494151,;EPS8L3,downstream_gene_variant,,ENST00000477568,;EPS8L3,3_prime_UTR_variant,,ENST00000472325,; T ENST00000369805 Transcript synonymous_variant 1139/2325 909/1785 303/594 A gcC/gcA 1 -1 EPS8L3 HGNC HGNC:21297 protein_coding YES CCDS815.1 ENSP00000358820 Q8TE67 UPI00001613C9 NM_139053.2 11/19 hmmpanther:PTHR12287:SF22,hmmpanther:PTHR12287 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 109757544 109757544 G T 1 0 0 0 0 0 0 0 1 5045 1335 47 2 2 EPS8L3 1 109757544 Silent SNP G C3N-00175_T 4417 109757544 139198878 45 9637 STRIP1 0 . GRCh38 1 110051725 110051725 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2104C>T p.= p.L702L ENST00000369795 20/21 256 200 56 310 310 0 strelka-varscan-mutect STRIP1,synonymous_variant,p.=,ENST00000369795,NM_033088.3;STRIP1,synonymous_variant,p.=,ENST00000369796,NM_001270768.1;STRIP1,3_prime_UTR_variant,,ENST00000485775,;STRIP1,non_coding_transcript_exon_variant,,ENST00000473429,;STRIP1,downstream_gene_variant,,ENST00000535003,;STRIP1,downstream_gene_variant,,ENST00000461054,; T ENST00000369795 Transcript synonymous_variant 2126/3265 2104/2514 702/837 L Cta/Tta 1 1 STRIP1 HGNC HGNC:25916 protein_coding YES CCDS30798.1 ENSP00000358810 Q5VSL9 UPI0000160E65 NM_033088.3 20/21 Pfam_domain:PF11882,hmmpanther:PTHR13239,hmmpanther:PTHR13239:SF5,SMART_domains:SM01293 LOW 1 SNV 1 1 PASS rs1020771142 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 110051725 110051725 C T 1 0 0 0 0 0 0 0 1 15710 680 24 3 3 STRIP1 1 110051725 Silent SNP C C3N-00175_T 294181 110051725 138904697 46 9638 OVGP1 0 . GRCh38 1 111426502 111426502 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.195G>A p.= p.Q65Q ENST00000369732 3/11 450 359 91 398 398 0 strelka-varscan-mutect OVGP1,synonymous_variant,p.=,ENST00000369732,NM_002557.3;RP11-552M11.8,downstream_gene_variant,,ENST00000564771,;OVGP1,upstream_gene_variant,,ENST00000481495,; T ENST00000369732 Transcript synonymous_variant 251/2243 195/2037 65/678 Q caG/caA 1 -1 OVGP1 HGNC HGNC:8524 protein_coding YES CCDS834.1 ENSP00000358747 Q12889 UPI0000130C53 NM_002557.3 3/11 hmmpanther:PTHR11177:SF217,hmmpanther:PTHR11177,Gene3D:3.20.20.80,Pfam_domain:PF00704,SMART_domains:SM00636,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 111426502 111426502 C T 1 0 0 0 0 0 0 0 1 11395 912 32 3 3 OVGP1 1 111426502 Silent SNP C C3N-00175_T 1374777 111426502 137529920 47 9639 SLC16A1 0 . GRCh38 1 112913950 112913950 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1444G>A p.Glu482Lys p.E482K ENST00000538576 5/5 368 317 51 330 330 0 strelka-varscan-mutect SLC16A1,missense_variant,p.Glu482Lys,ENST00000538576,NM_001166496.1;SLC16A1,missense_variant,p.Glu482Lys,ENST00000369626,NM_003051.3;SLC16A1,downstream_gene_variant,,ENST00000458229,;SLC16A1,downstream_gene_variant,,ENST00000443580,;SLC16A1,downstream_gene_variant,,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,; T ENST00000538576 Transcript missense_variant 2276/4374 1444/1503 482/500 E/K Gaa/Aaa 1 -1 SLC16A1 HGNC HGNC:10922 protein_coding YES CCDS858.1 ENSP00000441065 P53985 A0A024R0H1 UPI00000012F5 NM_001166496.1 tolerated(0.36) 5/5 hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF24 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 112913950 112913950 C T 1 0 0 0 0 1 0 0 0 14668 922 32 3 3 SLC16A1 1 112913950 Missense_Mutation SNP C C3N-00175_T 1487448 112913950 136042472 48 9640 SYCP1 0 . GRCh38 1 114913074 114913074 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.1571C>T p.Ser524Leu p.S524L ENST00000369522 19/32 133 98 35 184 184 0 strelka-varscan-mutect SYCP1,missense_variant,p.Ser524Leu,ENST00000369522,NM_003176.3,NM_001282541.1;SYCP1,missense_variant,p.Ser524Leu,ENST00000369518,;SYCP1,missense_variant,p.Ser524Leu,ENST00000618516,;SYCP1,missense_variant,p.Ser524Leu,ENST00000613524,NM_001282542.1;SYCP1,missense_variant,p.Ser524Leu,ENST00000455987,;SYCP1,non_coding_transcript_exon_variant,,ENST00000493377,;SYCP1,non_coding_transcript_exon_variant,,ENST00000482717,; T ENST00000369522 Transcript missense_variant 1811/3522 1571/2931 524/976 S/L tCa/tTa COSM3471707 1 1 SYCP1 HGNC HGNC:11487 protein_coding YES CCDS879.1 ENSP00000358535 Q15431 A0A024R0I2 UPI00001CE3B9 NM_003176.3,NM_001282541.1 tolerated(1) 19/32 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05483,hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF15 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 114913074 114913074 C T 1 0 0 0 0 1 0 0 0 15821 838 29 3 3 SYCP1 1 114913074 Missense_Mutation SNP C C3N-00175_T 1999124 114913074 134043348 49 9641 SRGAP2B 0 . GRCh38 1 144995126 144995126 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.142G>T p.Asp48Tyr p.D48Y ENST00000612199 3/10 52 42 10 28 28 0 strelka-varscan-mutect SRGAP2B,missense_variant,p.Asp48Tyr,ENST00000612199,NM_001271870.1;SRGAP2B,intron_variant,,ENST00000619678,; A ENST00000612199 Transcript missense_variant 990/7120 142/1377 48/458 D/Y Gac/Tac 1 -1 SRGAP2B HGNC HGNC:35237 protein_coding YES CCDS72854.1 ENSP00000477776 P0DMP2 UPI0002A03F43 NM_001271870.1 deleterious(0) 3/10 PROSITE_profiles:PS51741,hmmpanther:PTHR14166:SF6,hmmpanther:PTHR14166,Pfam_domain:PF00611,SMART_domains:SM00055,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99994 1 1 1 1 0 A 3 1 39 144995126 144995126 C A 1 0 0 0 0 1 0 0 0 15506 855 30 2 2 SRGAP2B 1 144995126 Missense_Mutation SNP C C3N-00175_T 30082052 144995126 103961296 50 9642 GJA5 0 . GRCh38 1 147758560 147758560 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.679T>C p.Tyr227His p.Y227H ENST00000621517 2/2 229 171 58 125 125 0 strelka-varscan-mutect GJA5,missense_variant,p.Tyr227His,ENST00000621517,NM_005266.6;GJA5,missense_variant,p.Tyr227His,ENST00000579774,NM_181703.3;GJA5,missense_variant,p.Tyr227His,ENST00000430508,;RP11-433J22.2,downstream_gene_variant,,ENST00000622634,;RP11-433J22.2,downstream_gene_variant,,ENST00000612401,; G ENST00000621517 Transcript missense_variant 823/3183 679/1077 227/358 Y/H Tac/Cac 1 -1 GJA5 HGNC HGNC:4279 protein_coding YES CCDS929.1 ENSP00000484552 P36382 X5D2H9 UPI000013D8D2 NM_005266.6 tolerated(0.06) 2/2 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF13,SMART_domains:SM01089,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 147758560 147758560 A G 1 0 0 0 0 1 0 0 0 6283 420 15 5 5 GJA5 1 147758560 Missense_Mutation SNP A C3N-00175_T 2763434 147758560 101197862 51 9643 SV2A 0 . GRCh38 1 149905951 149905951 + Frame_Shift_Del DEL A A - novel C3N-00175_T C3N-00175_N A A c.1974delT p.Phe658LeufsTer15 p.F658Lfs*15 ENST00000369146 12/13 375 293 82 288 288 0 sindel-varindel-pindel SV2A,frameshift_variant,p.Phe658LeufsTer15,ENST00000369146,NM_014849.4;SV2A,frameshift_variant,p.Phe658LeufsTer15,ENST00000369145,; - ENST00000369146 Transcript frameshift_variant 2465/4416 1974/2229 658/742 F/X ttT/tt 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 12/13 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF11,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR01299,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9984387 1 1 1 0 - 7 5 39 149905951 149905951 A - 1 0 1 0 1 0 0 0 0 15801 127 5 0 0 SV2A 1 149905951 Frame_Shift_Del DEL A C3N-00175_T 2147391 149905951 99050471 52 9644 SV2A 0 . GRCh38 1 149913352 149913352 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.489C>T p.= p.R163R ENST00000369146 2/13 444 312 132 290 290 0 strelka-varscan-mutect SV2A,synonymous_variant,p.=,ENST00000369146,NM_014849.4;SV2A,synonymous_variant,p.=,ENST00000369145,; A ENST00000369146 Transcript synonymous_variant 980/4416 489/2229 163/742 R cgC/cgT 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 2/13 hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF11,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR01299 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 149913352 149913352 G A 1 0 0 0 0 0 0 0 1 15801 958 34 3 3 SV2A 1 149913352 Silent SNP G C3N-00175_T 7401 149913352 99043070 53 9645 PLEKHO1 0 . GRCh38 1 150158907 150158907 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.614A>G p.Glu205Gly p.E205G ENST00000369124 6/6 254 185 69 188 188 0 strelka-varscan-mutect PLEKHO1,missense_variant,p.Glu205Gly,ENST00000369124,NM_016274.5;PLEKHO1,missense_variant,p.Glu22Gly,ENST00000369126,NM_001304724.1;PLEKHO1,non_coding_transcript_exon_variant,,ENST00000479194,;PLEKHO1,non_coding_transcript_exon_variant,,ENST00000441340,;PLEKHO1,upstream_gene_variant,,ENST00000502767,;PLEKHO1,non_coding_transcript_exon_variant,,ENST00000607609,;PLEKHO1,non_coding_transcript_exon_variant,,ENST00000485470,;PLEKHO1,downstream_gene_variant,,ENST00000477309,; G ENST00000369124 Transcript missense_variant 892/2050 614/1230 205/409 E/G gAg/gGg 1 1 PLEKHO1 HGNC HGNC:24310 protein_coding YES CCDS945.1 ENSP00000358120 Q53GL0 UPI000006DFAC NM_016274.5 tolerated(0.07) 6/6 hmmpanther:PTHR15871,hmmpanther:PTHR15871:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 150158907 150158907 A G 1 0 0 0 0 1 0 0 0 12177 304 11 5 5 PLEKHO1 1 150158907 Missense_Mutation SNP A C3N-00175_T 245555 150158907 98797515 54 9646 ANP32E 0 . GRCh38 1 150230605 150230605 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.293delA p.Asn98ThrfsTer3 p.N98Tfs*3 ENST00000583931 3/7 169 123 46 160 160 0 sindel-varindel-pindel ANP32E,frameshift_variant,p.Asn98ThrfsTer3,ENST00000583931,NM_001280559.1,NM_030920.4;ANP32E,frameshift_variant,p.Asn50ThrfsTer3,ENST00000616917,NM_001136479.2;ANP32E,frameshift_variant,p.Asn98ThrfsTer3,ENST00000369114,;ANP32E,frameshift_variant,p.Asn98ThrfsTer3,ENST00000533654,NM_001280560.1;ANP32E,frameshift_variant,p.Asn48ThrfsTer3,ENST00000532744,;ANP32E,intron_variant,,ENST00000629042,;ANP32E,intron_variant,,ENST00000436748,NM_001136478.3;ANP32E,intron_variant,,ENST00000369115,;ANP32E,intron_variant,,ENST00000534220,;ANP32E,upstream_gene_variant,,ENST00000534437,; - ENST00000583931 Transcript frameshift_variant 663/3451 293/807 98/268 N/X aAc/ac 1 -1 ANP32E HGNC HGNC:16673 protein_coding YES CCDS946.1 ENSP00000463154 Q9BTT0 UPI0000071679 NM_001280559.1,NM_030920.4 3/7 PROSITE_profiles:PS51450,hmmpanther:PTHR11375:SF5,hmmpanther:PTHR11375,Gene3D:3.80.10.10,Pfam_domain:PF14580,Superfamily_domains:SSF52058 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 150230605 150230605 T - 1 0 1 0 1 0 0 0 0 816 1725 60 0 0 ANP32E 1 150230605 Frame_Shift_Del DEL T C3N-00175_T 71698 150230605 98725817 55 9647 RPRD2 0 . GRCh38 1 150472486 150472486 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.3538A>T p.Ser1180Cys p.S1180C ENST00000369068 11/11 274 214 60 175 175 0 strelka-varscan-mutect RPRD2,missense_variant,p.Ser1154Cys,ENST00000401000,NM_001297674.1,NM_001297673.1;RPRD2,missense_variant,p.Ser1180Cys,ENST00000369068,NM_015203.4;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,; T ENST00000369068 Transcript missense_variant 3542/4612 3538/4386 1180/1461 S/C Agc/Tgc 1 1 RPRD2 HGNC HGNC:29039 protein_coding YES CCDS44216.1 ENSP00000358064 Q5VT52 UPI00001D7CA8 NM_015203.4 deleterious_low_confidence(0) 11/11 hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 150472486 150472486 A T 1 0 0 0 0 1 0 0 0 13871 188 7 4 4 RPRD2 1 150472486 Missense_Mutation SNP A C3N-00175_T 241881 150472486 98483936 56 9648 ADAMTSL4 0 . GRCh38 1 150558554 150558554 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.2533G>C p.Glu845Gln p.E845Q ENST00000369039 16/20 492 458 34 333 333 0 strelka-varscan-mutect ADAMTSL4,missense_variant,p.Glu845Gln,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,missense_variant,p.Glu822Gln,ENST00000271643,NM_019032.5;ADAMTSL4,missense_variant,p.Glu822Gln,ENST00000369038,;ADAMTSL4,missense_variant,p.Glu822Gln,ENST00000369041,NM_025008.4;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;RP11-54A4.2,upstream_gene_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4,non_coding_transcript_exon_variant,,ENST00000489159,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,; C ENST00000369039 Transcript missense_variant 2822/4319 2533/3294 845/1097 E/Q Gag/Cag 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 deleterious(0.01) 16/20 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 150558554 150558554 G C 1 0 0 0 0 1 0 0 0 321 1175 41 4 4 ADAMTSL4 1 150558554 Missense_Mutation SNP G C3N-00175_T 86068 150558554 98397868 57 9649 CELF3 0 . GRCh38 1 151706688 151706688 + Silent SNP C C A rs564076056 C3N-00175_T C3N-00175_N C C c.969G>T p.= p.A323A ENST00000290583 9/13 299 232 67 189 188 1 strelka-varscan-mutect CELF3,synonymous_variant,p.=,ENST00000290583,NM_001291106.1,NM_001172648.3,NM_007185.6,NM_001291107.1;CELF3,synonymous_variant,p.=,ENST00000420342,;CELF3,synonymous_variant,p.=,ENST00000290585,NM_001172649.3;RIIAD1,upstream_gene_variant,,ENST00000326413,;RP11-98D18.1,intron_variant,,ENST00000457548,;CELF3,non_coding_transcript_exon_variant,,ENST00000470688,;CELF3,downstream_gene_variant,,ENST00000478829,;CELF3,downstream_gene_variant,,ENST00000479893,;CELF3,downstream_gene_variant,,ENST00000419910,; A ENST00000290583 Transcript synonymous_variant 1763/3246 969/1398 323/465 A gcG/gcT rs564076056 1 -1 CELF3 HGNC HGNC:11967 protein_coding YES CCDS1002.1 ENSP00000290583 Q5SZQ8 UPI000013F059 NM_001291106.1,NM_001172648.3,NM_007185.6,NM_001291107.1 9/13 hmmpanther:PTHR24012:SF427,hmmpanther:PTHR24012 LOW 1 SNV 1 1 PASS rs564076056 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 151706688 151706688 C A 1 0 0 0 0 0 0 0 1 2924 639 23 1 1 CELF3 1 151706688 Silent SNP C C3N-00175_T 1148134 151706688 97249734 58 9650 RIIAD1 0 . GRCh38 1 151728790 151728790 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.233C>G p.Pro78Arg p.P78R ENST00000479191 4/5 316 278 38 208 208 0 strelka-varscan-mutect RIIAD1,missense_variant,p.Pro88Arg,ENST00000326413,;RIIAD1,missense_variant,p.Pro78Arg,ENST00000479191,NM_001144956.1;RIIAD1,non_coding_transcript_exon_variant,,ENST00000426175,;RIIAD1,non_coding_transcript_exon_variant,,ENST00000451484,;RIIAD1,non_coding_transcript_exon_variant,,ENST00000427205,;RIIAD1,non_coding_transcript_exon_variant,,ENST00000451222,; G ENST00000479191 Transcript missense_variant 233/449 233/279 78/92 P/R cCc/cGc 1 1 RIIAD1 HGNC HGNC:26686 protein_coding YES CCDS53368.1 ENSP00000419249 A6NNX1 UPI00001D7CA9 NM_001144956.1 tolerated(0.09) 4/5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 151728790 151728790 C G 1 0 0 0 0 1 0 0 0 13534 623 22 4 4 RIIAD1 1 151728790 Missense_Mutation SNP C C3N-00175_T 22102 151728790 97227632 59 9651 FLG 0 . GRCh38 1 152303433 152303433 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.11453A>T p.Gln3818Leu p.Q3818L ENST00000368799 3/3 919 714 205 577 577 0 strelka-varscan-mutect FLG,missense_variant,p.Gln3818Leu,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript missense_variant 11489/12747 11453/12186 3818/4061 Q/L cAg/cTg 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 152303433 152303433 T A 1 0 0 0 0 1 0 0 0 5784 1580 55 4 4 FLG 1 152303433 Missense_Mutation SNP T C3N-00175_T 574643 152303433 96652989 60 9652 FLG 0 . GRCh38 1 152308028 152308028 + Silent SNP G G A rs141571186 C3N-00175_T C3N-00175_N G G c.6858C>T p.= p.H2286H ENST00000368799 3/3 1146 1014 132 604 604 0 varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript synonymous_variant 6894/12747 6858/12186 2286/4061 H caC/caT rs141571186,COSM4022429 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 0,1 LOW 1 SNV 1 0,1 1 PASS rs141571186 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 152308028 152308028 G A 1 0 0 0 0 0 0 0 1 5784 1136 40 1 1 FLG 1 152308028 Silent SNP G C3N-00175_T 4595 152308028 96648394 61 9653 FLG 0 . GRCh38 1 152312315 152312315 + Silent SNP G G A rs375680393 C3N-00175_T C3N-00175_N G G c.2571C>T p.= p.H857H ENST00000368799 3/3 938 786 152 491 491 0 strelka-varscan FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; A ENST00000368799 Transcript synonymous_variant 2607/12747 2571/12186 857/4061 H caC/caT rs375680393 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 LOW 1 SNV 1 1 PASS . . 0 136 0 0 74 0 0 0 -20 0 0 1 0 0 A 2 1 39 152312315 152312315 G A 1 0 0 0 0 0 0 0 1 5784 1136 40 1 1 FLG 1 152312315 Silent SNP G C3N-00175_T 4287 152312315 96644107 62 9654 FLG 0 . GRCh38 1 152313872 152313872 + Silent SNP G G T rs578012327 C3N-00175_T C3N-00175_N G G c.1014C>A p.= p.S338S ENST00000368799 3/3 774 565 209 503 503 0 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,non_coding_transcript_exon_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript synonymous_variant 1050/12747 1014/12186 338/4061 S tcC/tcA rs578012327 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 LOW 1 SNV 1 1 PASS rs578012327 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 152313872 152313872 G T 1 0 0 0 0 0 0 0 1 5784 1219 43 2 2 FLG 1 152313872 Silent SNP G C3N-00175_T 1557 152313872 96642550 63 9655 FLG2 0 . GRCh38 1 152356335 152356335 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1451C>A p.Ser484Tyr p.S484Y ENST00000388718 3/3 503 437 66 324 323 1 strelka-varscan-mutect FLG2,missense_variant,p.Ser484Tyr,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 1524/9124 1451/7176 484/2391 S/Y tCt/tAt 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious(0.04) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 152356335 152356335 G T 1 0 0 0 0 1 0 0 0 5785 942 33 2 2 FLG2 1 152356335 Missense_Mutation SNP G C3N-00175_T 42463 152356335 96600087 64 9656 FLG2 0 . GRCh38 1 152357106 152357106 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.680C>A p.Ser227Tyr p.S227Y ENST00000388718 3/3 232 202 30 136 134 2 strelka-varscan FLG2,missense_variant,p.Ser227Tyr,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 753/9124 680/7176 227/2391 S/Y tCt/tAt 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 tolerated(0.13) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 152357106 152357106 G T 1 0 0 0 0 1 0 0 0 5785 942 33 2 2 FLG2 1 152357106 Missense_Mutation SNP G C3N-00175_T 771 152357106 96599316 65 9657 LCE3D 0 . GRCh38 1 152579792 152579792 + Missense_Mutation SNP C C T rs201921868 C3N-00175_T C3N-00175_N C C c.145G>A p.Glu49Lys p.E49K ENST00000368787 2/2 612 578 34 455 455 0 varscan-mutect LCE3D,missense_variant,p.Glu49Lys,ENST00000368787,NM_032563.1; T ENST00000368787 Transcript missense_variant 202/613 145/279 49/92 E/K Gag/Aag rs201921868,COSM1256369 1 -1 LCE3D HGNC HGNC:16615 protein_coding YES CCDS1014.1 ENSP00000357776 Q9BYE3 UPI000006EC48 NM_032563.1 tolerated_low_confidence(0.09) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF27,hmmpanther:PTHR23263,Pfam_domain:PF14672 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201921868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 152579792 152579792 C T 1 0 0 0 0 1 0 0 0 8577 893 31 1 1 LCE3D 1 152579792 Missense_Mutation SNP C C3N-00175_T 222686 152579792 96376630 66 9658 LCE1E 0 . GRCh38 1 152787644 152787644 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.345A>T p.= p.G115G ENST00000368770 2/2 95 69 26 68 68 0 strelka-varscan-mutect LCE1E,synonymous_variant,p.=,ENST00000368770,NM_178353.1;LCE1E,synonymous_variant,p.=,ENST00000368771,;LCE1E,synonymous_variant,p.=,ENST00000619588,; T ENST00000368770 Transcript synonymous_variant 398/1180 345/357 115/118 G ggA/ggT 1 1 LCE1E HGNC HGNC:29466 protein_coding YES CCDS1024.1 ENSP00000357759 Q5T753 UPI0000161050 NM_178353.1 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 152787644 152787644 A T 1 0 0 0 0 0 0 0 1 8568 291 11 4 4 LCE1E 1 152787644 Silent SNP A C3N-00175_T 207852 152787644 96168778 67 9659 IVL 0 . GRCh38 1 152910890 152910890 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1093C>A p.Leu365Ile p.L365I ENST00000368764 2/2 494 357 137 349 349 0 strelka-varscan-mutect IVL,missense_variant,p.Leu365Ile,ENST00000368764,NM_005547.2; A ENST00000368764 Transcript missense_variant 1157/2153 1093/1758 365/585 L/I Ctc/Atc 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 tolerated(0.24) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 152910890 152910890 C A 1 0 0 0 0 1 0 0 0 7835 797 28 2 2 IVL 1 152910890 Missense_Mutation SNP C C3N-00175_T 123246 152910890 96045532 68 9660 UBE2Q1 0 . GRCh38 1 154558426 154558426 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.128G>C p.Arg43Pro p.R43P ENST00000292211 1/13 345 319 26 181 181 0 strelka-varscan-mutect UBE2Q1,missense_variant,p.Arg43Pro,ENST00000292211,NM_017582.6;UBE2Q1-AS1,downstream_gene_variant,,ENST00000441613,;UBE2Q1,intron_variant,,ENST00000497453,; G ENST00000292211 Transcript missense_variant 208/3210 128/1269 43/422 R/P cGa/cCa 1 -1 UBE2Q1 HGNC HGNC:15698 protein_coding YES CCDS1069.1 ENSP00000292211 Q7Z7E8 UPI00001A36E2 NM_017582.6 tolerated(0.23) 1/13 Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 154558426 154558426 C G 1 0 0 0 0 1 0 0 0 17390 884 31 4 4 UBE2Q1 1 154558426 Missense_Mutation SNP C C3N-00175_T 1647536 154558426 94397996 69 9661 DCST2 0 . GRCh38 1 155033105 155033105 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.428A>G p.Gln143Arg p.Q143R ENST00000368424 2/15 92 42 50 77 77 0 strelka-varscan-mutect DCST2,missense_variant,p.Gln143Arg,ENST00000368424,NM_144622.2;DCST1,upstream_gene_variant,,ENST00000295542,NM_152494.3;DCST1,upstream_gene_variant,,ENST00000368419,;DCST1,upstream_gene_variant,,ENST00000423025,NM_001143687.2;DCST2,missense_variant,p.Gln143Arg,ENST00000485982,;DCST2,upstream_gene_variant,,ENST00000368423,;DCST1,upstream_gene_variant,,ENST00000525273,;DCST1,upstream_gene_variant,,ENST00000368420,; C ENST00000368424 Transcript missense_variant 487/2392 428/2322 143/773 Q/R cAa/cGa 1 -1 DCST2 HGNC HGNC:26562 protein_coding YES CCDS1082.2 ENSP00000357409 Q5T1A1 UPI0000D959B3 NM_144622.2 tolerated(0.06) 2/15 hmmpanther:PTHR21041:SF6,hmmpanther:PTHR21041 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 155033105 155033105 T C 1 0 0 0 0 1 0 0 0 4105 1812 63 5 5 DCST2 1 155033105 Missense_Mutation SNP T C3N-00175_T 474679 155033105 93923317 70 9662 DAP3 0 . GRCh38 1 155729333 155729333 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.810A>T p.= p.G270G ENST00000368336 9/13 205 154 51 152 152 0 strelka-varscan-mutect DAP3,synonymous_variant,p.=,ENST00000368336,NM_001199849.1,NM_004632.3;DAP3,synonymous_variant,p.=,ENST00000535183,NM_001199851.1;DAP3,synonymous_variant,p.=,ENST00000471642,;DAP3,synonymous_variant,p.=,ENST00000343043,NM_033657.2;DAP3,synonymous_variant,p.=,ENST00000421487,NM_001199850.1;DAP3,synonymous_variant,p.=,ENST00000471214,;DAP3,synonymous_variant,p.=,ENST00000477394,;DAP3,synonymous_variant,p.=,ENST00000497826,;DAP3,synonymous_variant,p.=,ENST00000479151,;DAP3,synonymous_variant,p.=,ENST00000490249,;DAP3,synonymous_variant,p.=,ENST00000475056,;DAP3,upstream_gene_variant,,ENST00000463295,;DAP3,downstream_gene_variant,,ENST00000463575,;DAP3,downstream_gene_variant,,ENST00000470830,;DAP3,downstream_gene_variant,,ENST00000496863,;DAP3,downstream_gene_variant,,ENST00000462002,;DAP3,non_coding_transcript_exon_variant,,ENST00000462978,;DAP3,non_coding_transcript_exon_variant,,ENST00000497433,;DAP3,downstream_gene_variant,,ENST00000471523,;DAP3,downstream_gene_variant,,ENST00000466384,; T ENST00000368336 Transcript synonymous_variant 934/2089 810/1197 270/398 G ggA/ggT 1 1 DAP3 HGNC HGNC:2673 protein_coding YES CCDS1120.1 ENSP00000357320 P51398 UPI000004ABE5 NM_001199849.1,NM_004632.3 9/13 Pfam_domain:PF10236,hmmpanther:PTHR12810,hmmpanther:PTHR12810:SF0,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 155729333 155729333 A T 1 0 0 0 0 0 0 0 1 4035 233 9 4 4 DAP3 1 155729333 Silent SNP A C3N-00175_T 696228 155729333 93227089 71 9663 GON4L 0 . GRCh38 1 155777682 155777682 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.2031T>C p.= p.V677V ENST00000368331 15/32 487 455 32 310 310 0 strelka-varscan-mutect GON4L,synonymous_variant,p.=,ENST00000368331,NM_001282860.1;GON4L,synonymous_variant,p.=,ENST00000615926,NM_001282856.1;GON4L,synonymous_variant,p.=,ENST00000437809,;GON4L,synonymous_variant,p.=,ENST00000271883,NM_001282858.1;GON4L,synonymous_variant,p.=,ENST00000620426,;GON4L,synonymous_variant,p.=,ENST00000361040,NM_001282861.1,NM_032292.5;GON4L,synonymous_variant,p.=,ENST00000622608,;GON4L,non_coding_transcript_exon_variant,,ENST00000471341,;GON4L,non_coding_transcript_exon_variant,,ENST00000482386,;GON4L,non_coding_transcript_exon_variant,,ENST00000466224,;GON4L,upstream_gene_variant,,ENST00000497369,;GON4L,upstream_gene_variant,,ENST00000490801,; G ENST00000368331 Transcript synonymous_variant 2206/7823 2031/6726 677/2241 V gtT/gtC 1 -1 GON4L HGNC HGNC:25973 protein_coding YES CCDS60296.1 ENSP00000357315 Q3T8J9 UPI0000351551 NM_001282860.1 15/32 hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 155777682 155777682 A G 1 0 0 0 0 0 0 0 1 6466 233 9 5 5 GON4L 1 155777682 Silent SNP A C3N-00175_T 48349 155777682 93178740 72 9664 PEAR1 0 . GRCh38 1 156906334 156906334 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.366T>A p.Cys122Ter p.C122* ENST00000338302 6/24 238 183 55 220 220 0 strelka-varscan-mutect PEAR1,stop_gained,p.Cys122Ter,ENST00000338302,;PEAR1,stop_gained,p.Cys122Ter,ENST00000292357,NM_001080471.1;PEAR1,stop_gained,p.Cys122Ter,ENST00000455314,;PEAR1,3_prime_UTR_variant,,ENST00000444016,;PEAR1,non_coding_transcript_exon_variant,,ENST00000469390,;PEAR1,upstream_gene_variant,,ENST00000482505,; A ENST00000338302 Transcript stop_gained 591/4970 366/3114 122/1037 C/* tgT/tgA 1 1 PEAR1 HGNC HGNC:33631 protein_coding YES CCDS30892.1 ENSP00000344465 Q5VY43 UPI000045889A 6/24 PROSITE_profiles:PS50026,hmmpanther:PTHR24052,hmmpanther:PTHR24052:SF12,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Pfam_domain:PF12661,Gene3D:2gy5A03,SMART_domains:SM00181 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 156906334 156906334 T A 1 0 0 0 0 0 1 0 0 11801 1702 59 4 4 PEAR1 1 156906334 Nonsense_Mutation SNP T C3N-00175_T 1128652 156906334 92050088 73 9665 FCRL5 0 . GRCh38 1 157544276 157544276 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.830G>T p.Trp277Leu p.W277L ENST00000361835 5/17 250 187 63 152 152 0 strelka-varscan-mutect FCRL5,missense_variant,p.Trp277Leu,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,missense_variant,p.Trp277Leu,ENST00000368189,;FCRL5,missense_variant,p.Trp277Leu,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000481082,; A ENST00000361835 Transcript missense_variant 988/5390 830/2934 277/977 W/L tGg/tTg 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(0.64) 5/17 hmmpanther:PTHR11481:SF68,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 157544276 157544276 C A 1 0 0 0 0 1 0 0 0 5660 595 21 2 2 FCRL5 1 157544276 Missense_Mutation SNP C C3N-00175_T 637942 157544276 91412146 74 9666 OR10T2 0 . GRCh38 1 158398627 158398627 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.840G>T p.= p.V280V ENST00000334438 1/1 424 389 35 268 267 1 strelka-varscan-mutect OR10T2,synonymous_variant,p.=,ENST00000334438,NM_001004475.1; A ENST00000334438 Transcript synonymous_variant 840/945 840/945 280/314 V gtG/gtT 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 158398627 158398627 C A 1 0 0 0 0 0 0 0 1 10996 581 21 2 2 OR10T2 1 158398627 Silent SNP C C3N-00175_T 854351 158398627 90557795 75 9667 OR10T2 0 . GRCh38 1 158399100 158399100 + Missense_Mutation SNP G G C rs539828963 C3N-00175_T C3N-00175_N G G c.367C>G p.Arg123Gly p.R123G ENST00000334438 1/1 309 260 49 194 194 0 strelka-varscan-mutect OR10T2,missense_variant,p.Arg123Gly,ENST00000334438,NM_001004475.1; C ENST00000334438 Transcript missense_variant 367/945 367/945 123/314 R/G Cgc/Ggc rs539828963,COSM3476043 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs539828963 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 158399100 158399100 G C 1 0 0 0 0 1 0 0 0 10996 1058 37 4 4 OR10T2 1 158399100 Missense_Mutation SNP G C3N-00175_T 473 158399100 90557322 76 9668 OR6Y1 0 . GRCh38 1 158547516 158547516 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.590C>T p.Ala197Val p.A197V ENST00000302617 1/1 249 204 45 209 209 0 strelka-varscan-mutect OR6Y1,missense_variant,p.Ala197Val,ENST00000302617,NM_001005189.1; A ENST00000302617 Transcript missense_variant 590/978 590/978 197/325 A/V gCc/gTc 1 -1 OR6Y1 HGNC HGNC:14823 protein_coding YES CCDS30899.1 ENSP00000304807 Q8NGX8 UPI000004B1E2 NM_001005189.1 tolerated(0.61) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF109,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 158547516 158547516 G A 1 0 0 0 0 1 0 0 0 11283 1203 42 3 3 OR6Y1 1 158547516 Missense_Mutation SNP G C3N-00175_T 148416 158547516 90408906 77 9669 OR6Y1 0 . GRCh38 1 158547794 158547794 + Silent SNP A A T C3N-00175_T C3N-00175_N A A c.312T>A p.= p.T104T ENST00000302617 1/1 641 491 150 441 441 0 strelka-varscan-mutect OR6Y1,synonymous_variant,p.=,ENST00000302617,NM_001005189.1; T ENST00000302617 Transcript synonymous_variant 312/978 312/978 104/325 T acT/acA COSM4023728 1 -1 OR6Y1 HGNC HGNC:14823 protein_coding YES CCDS30899.1 ENSP00000304807 Q8NGX8 UPI000004B1E2 NM_001005189.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF109,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS rs1410085182 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 158547794 158547794 A T 1 0 0 0 0 0 0 0 1 11283 291 11 4 4 OR6Y1 1 158547794 Silent SNP A C3N-00175_T 278 158547794 90408628 78 9670 SPTA1 0 . GRCh38 1 158619311 158619311 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.6441G>T p.Lys2147Asn p.K2147N ENST00000368147 45/52 691 596 95 514 514 0 strelka-varscan-mutect SPTA1,missense_variant,p.Lys2147Asn,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000481212,;SPTA1,upstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript missense_variant 6622/7999 6441/7260 2147/2419 K/N aaG/aaT 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.03) 45/52 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Gene3D:1.20.58.60,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 158619311 158619311 C A 1 0 0 0 0 1 0 0 0 15472 680 24 2 2 SPTA1 1 158619311 Missense_Mutation SNP C C3N-00175_T 71517 158619311 90337111 79 9671 37 2 SPTA1 0 . GRCh38 1 158619315 158619315 + Missense_Mutation SNP T T G rs138055271 C3N-00175_T C3N-00175_N T T c.6437A>C p.Gln2146Pro p.Q2146P ENST00000368147 45/52 686 592 94 497 496 1 strelka-varscan-mutect SPTA1,missense_variant,p.Gln2146Pro,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000481212,;SPTA1,upstream_gene_variant,,ENST00000498708,; G ENST00000368147 Transcript missense_variant 6618/7999 6437/7260 2146/2419 Q/P cAa/cCa rs138055271 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.08) 45/52 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs138055271 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 158619315 158619315 T G 1 0 0 0 0 1 0 0 0 15472 1812 63 5 5 SPTA1 1 158619315 Missense_Mutation SNP T C3N-00175_T 4 158619315 90337107 80 9672 37 2 SPTA1 0 . GRCh38 1 158648631 158648631 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3592C>A p.Gln1198Lys p.Q1198K ENST00000368147 26/52 583 457 126 418 417 1 strelka-varscan-mutect SPTA1,missense_variant,p.Gln1198Lys,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 3773/7999 3592/7260 1198/2419 Q/K Cag/Aag 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.16) 26/52 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 158648631 158648631 G T 1 0 0 0 0 1 0 0 0 15472 1328 46 2 2 SPTA1 1 158648631 Missense_Mutation SNP G C3N-00175_T 29316 158648631 90307791 81 9673 SPTA1 0 . GRCh38 1 158677781 158677781 + Missense_Mutation SNP G G C rs763960188 C3N-00175_T C3N-00175_N G G c.866C>G p.Ser289Cys p.S289C ENST00000368147 7/52 437 414 23 307 307 0 strelka-varscan-mutect SPTA1,missense_variant,p.Ser289Cys,ENST00000368147,NM_003126.2;SPTA1,missense_variant,p.Ser107Cys,ENST00000467387,; C ENST00000368147 Transcript missense_variant 1047/7999 866/7260 289/2419 S/C tCt/tGt rs763960188 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 7/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs763960188 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 158677781 158677781 G C 1 0 0 0 0 1 0 0 0 15472 942 33 4 4 SPTA1 1 158677781 Missense_Mutation SNP G C3N-00175_T 29150 158677781 90278641 82 9674 OR6K2 0 . GRCh38 1 158699701 158699701 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.952G>T p.Gly318Trp p.G318W ENST00000359610 1/1 100 70 30 66 66 0 strelka-varscan-mutect OR6K2,missense_variant,p.Gly318Trp,ENST00000359610,NM_001005279.1;OR6K1P,upstream_gene_variant,,ENST00000456766,; A ENST00000359610 Transcript missense_variant 952/975 952/975 318/324 G/W Ggg/Tgg 1 -1 OR6K2 HGNC HGNC:15029 protein_coding YES CCDS30902.1 ENSP00000352626 Q8NGY2 A0A126GV58 UPI000004B208 NM_001005279.1 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 158699701 158699701 C A 1 0 0 0 0 1 0 0 0 11271 681 24 2 2 OR6K2 1 158699701 Missense_Mutation SNP C C3N-00175_T 21920 158699701 90256721 83 9675 OR6K2 0 . GRCh38 1 158699920 158699920 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.733C>T p.His245Tyr p.H245Y ENST00000359610 1/1 432 344 88 307 307 0 strelka-varscan-mutect OR6K2,missense_variant,p.His245Tyr,ENST00000359610,NM_001005279.1;OR6K1P,upstream_gene_variant,,ENST00000456766,; A ENST00000359610 Transcript missense_variant 733/975 733/975 245/324 H/Y Cac/Tac 1 -1 OR6K2 HGNC HGNC:15029 protein_coding YES CCDS30902.1 ENSP00000352626 Q8NGY2 A0A126GV58 UPI000004B208 NM_001005279.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF68,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 158699920 158699920 G A 1 0 0 0 0 1 0 0 0 11271 1290 45 3 3 OR6K2 1 158699920 Missense_Mutation SNP G C3N-00175_T 219 158699920 90256502 84 9676 OR6K6 0 . GRCh38 1 158755678 158755678 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.863G>T p.Arg288Ile p.R288I ENST00000368144 1/1 228 170 58 175 175 0 strelka-varscan-mutect OR6K6,missense_variant,p.Arg288Ile,ENST00000368144,NM_001005184.1; T ENST00000368144 Transcript missense_variant 959/1172 863/1032 288/343 R/I aGa/aTa 1 1 OR6K6 HGNC HGNC:15033 protein_coding YES CCDS30904.1 ENSP00000357126 Q8NGW6 UPI000015F229 NM_001005184.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs915368711 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 158755678 158755678 G T 1 0 0 0 0 1 0 0 0 11273 942 33 2 2 OR6K6 1 158755678 Missense_Mutation SNP G C3N-00175_T 55758 158755678 90200744 85 9677 OR10J3 0 . GRCh38 1 159313824 159313824 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.836A>T p.Tyr279Phe p.Y279F ENST00000332217 1/1 348 287 61 221 221 0 strelka-varscan-mutect OR10J3,missense_variant,p.Tyr279Phe,ENST00000332217,NM_001004467.1; A ENST00000332217 Transcript missense_variant 836/990 836/990 279/329 Y/F tAc/tTc 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 159313824 159313824 T A 1 0 0 0 0 1 0 0 0 10988 1638 57 4 4 OR10J3 1 159313824 Missense_Mutation SNP T C3N-00175_T 558146 159313824 89642598 86 9678 OR10J1 0 . GRCh38 1 159440108 159440108 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.351delC p.Phe118LeufsTer24 p.F118Lfs*24 ENST00000423932 1/1 332 295 37 281 281 0 sindel-varindel OR10J1,frameshift_variant,p.Phe118LeufsTer24,ENST00000423932,NM_012351.2;RP11-550P17.5,intron_variant,,ENST00000431862,; - ENST00000423932 Transcript frameshift_variant 387/1090 350/963 117/320 T/X aCc/ac 1 1 OR10J1 HGNC HGNC:8175 protein_coding YES CCDS1185.1 ENSP00000399078 P30954 UPI000013E7DA NM_012351.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF417,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 159440108 159440108 C - 1 0 1 0 1 0 0 0 0 10987 507 18 0 0 OR10J1 1 159440108 Frame_Shift_Del DEL C C3N-00175_T 126284 159440108 89516314 87 9679 NCSTN 0 . GRCh38 1 160349664 160349664 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.430G>T p.Gly144Trp p.G144W ENST00000294785 4/17 707 579 128 393 392 1 strelka-varscan-mutect NCSTN,missense_variant,p.Gly124Trp,ENST00000368063,NM_001290184.1;NCSTN,missense_variant,p.Gly144Trp,ENST00000294785,NM_001290186.1,NM_015331.2;NCSTN,missense_variant,p.Gly2Trp,ENST00000424645,;NCSTN,missense_variant,p.Gly144Trp,ENST00000421914,;NCSTN,missense_variant,p.Gly177Trp,ENST00000438008,;NCSTN,upstream_gene_variant,,ENST00000435149,;NCSTN,upstream_gene_variant,,ENST00000424754,;NCSTN,downstream_gene_variant,,ENST00000437169,;NCSTN,non_coding_transcript_exon_variant,,ENST00000459963,;NCSTN,non_coding_transcript_exon_variant,,ENST00000467837,;NCSTN,non_coding_transcript_exon_variant,,ENST00000491332,;NCSTN,downstream_gene_variant,,ENST00000465223,; T ENST00000294785 Transcript missense_variant 555/2936 430/2130 144/709 G/W Ggg/Tgg 1 1 NCSTN HGNC HGNC:17091 protein_coding YES CCDS1203.1 ENSP00000294785 Q92542 UPI0000042050 NM_001290186.1,NM_015331.2 deleterious(0.01) 4/17 hmmpanther:PTHR21092:SF0,hmmpanther:PTHR21092 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 160349664 160349664 G T 1 0 0 0 0 1 0 0 0 10261 1348 47 2 2 NCSTN 1 160349664 Missense_Mutation SNP G C3N-00175_T 909556 160349664 88606758 88 9680 NHLH1 0 . GRCh38 1 160370767 160370767 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.36G>T p.= p.L12L ENST00000302101 2/2 463 355 108 269 269 0 strelka-varscan-mutect NHLH1,synonymous_variant,p.=,ENST00000302101,NM_005598.3; T ENST00000302101 Transcript synonymous_variant 482/2563 36/402 12/133 L ctG/ctT COSM4142895 1 1 NHLH1 HGNC HGNC:7817 protein_coding YES CCDS1204.1 ENSP00000302189 Q02575 Q5T203 UPI000012C5FE NM_005598.3 2/2 hmmpanther:PTHR13864,hmmpanther:PTHR13864:SF20 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 160370767 160370767 G T 1 0 0 0 0 0 0 0 1 10436 1306 46 2 2 NHLH1 1 160370767 Silent SNP G C3N-00175_T 21103 160370767 88585655 89 9681 MPZ 0 . GRCh38 1 161307271 161307271 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.221G>A p.Arg74Lys p.R74K ENST00000533357 2/6 552 524 28 367 367 0 strelka-varscan-mutect MPZ,missense_variant,p.Arg74Lys,ENST00000533357,NM_001315491.1,NM_000530.6;MPZ,5_prime_UTR_variant,,ENST00000491222,;MPZ,upstream_gene_variant,,ENST00000526189,;MPZ,missense_variant,p.Arg74Lys,ENST00000463290,;MPZ,upstream_gene_variant,,ENST00000476410,;MPZ,upstream_gene_variant,,ENST00000488271,; T ENST00000533357 Transcript missense_variant 288/1955 221/747 74/248 R/K aGa/aAa 1 -1 MPZ HGNC HGNC:7225 protein_coding YES CCDS1229.2 ENSP00000432943 P25189 UPI000012FBB1 NM_001315491.1,NM_000530.6 tolerated(0.27) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,Prints_domain:PR00213,PROSITE_profiles:PS50835,hmmpanther:PTHR13869,hmmpanther:PTHR13869:SF7,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 161307271 161307271 C T 1 0 0 0 0 1 0 0 0 9714 913 32 3 3 MPZ 1 161307271 Missense_Mutation SNP C C3N-00175_T 936504 161307271 87649151 90 9682 FCRLB 0 . GRCh38 1 161723011 161723011 + Splice_Site SNP T T G novel C3N-00175_T C3N-00175_N T T c.52+2T>G p.X18_splice ENST00000367948 253 223 30 203 203 0 strelka-varscan-mutect FCRLB,splice_donor_variant,,ENST00000367948,NM_001320241.1,NM_001002901.3;FCRLB,splice_donor_variant,,ENST00000336830,NM_001288831.1;FCRLB,splice_donor_variant,,ENST00000367946,NM_001288829.1;FCRLB,intron_variant,,ENST00000367944,NM_001288832.1;FCRLB,intron_variant,,ENST00000367945,NM_001288830.1;FCRLB,upstream_gene_variant,,ENST00000495397,; G ENST00000367948 Transcript splice_donor_variant -/1977 52/1281 18/426 1 1 FCRLB HGNC HGNC:26431 protein_coding YES CCDS30927.1 ENSP00000356925 Q6BAA4 UPI00003FF782 NM_001320241.1,NM_001002901.3 4/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 39 161723011 161723011 T G 1 0 0 0 0 0 0 1 0 5663 1710 59 5 5 FCRLB 1 161723011 Splice_Site SNP T C3N-00175_T 415740 161723011 87233411 91 9683 RGS4 0 . GRCh38 1 163074481 163074481 + Missense_Mutation SNP C C A rs368964432 C3N-00175_T C3N-00175_N C C c.830C>A p.Pro277Gln p.P277Q ENST00000421743 6/6 659 528 131 516 515 1 strelka-varscan-mutect RGS4,missense_variant,p.Pro277Gln,ENST00000421743,NM_001102445.2;RGS4,missense_variant,p.Pro180Gln,ENST00000367909,NM_005613.5;RGS4,missense_variant,p.Pro162Gln,ENST00000367906,NM_001113380.1;RGS4,missense_variant,p.Pro162Gln,ENST00000527809,;RGS4,3_prime_UTR_variant,,ENST00000367908,NM_001113381.1;RGS4,intron_variant,,ENST00000531057,;RGS4,downstream_gene_variant,,ENST00000528938,;RGS4,non_coding_transcript_exon_variant,,ENST00000491263,;RGS4,downstream_gene_variant,,ENST00000527393,;RGS4,downstream_gene_variant,,ENST00000533019,; A ENST00000421743 Transcript missense_variant 990/3311 830/909 277/302 P/Q cCg/cAg rs368964432,COSM1295390,COSM1295391 1 1 RGS4 HGNC HGNC:10000 protein_coding YES CCDS44270.1 ENSP00000397181 P49798 UPI0000E1EDBA NM_001102445.2 tolerated(0.77) 6/6 hmmpanther:PTHR10845:SF184,hmmpanther:PTHR10845,Gene3D:1.10.196.10 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs368964432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 163074481 163074481 C A 1 0 0 0 0 1 0 0 0 13478 652 23 1 1 RGS4 1 163074481 Missense_Mutation SNP C C3N-00175_T 1351470 163074481 85881941 92 9684 GPA33 0 . GRCh38 1 167068995 167068995 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.342C>T p.= p.T114T ENST00000367868 3/7 407 337 70 308 307 1 strelka-varscan-mutect GPA33,synonymous_variant,p.=,ENST00000367868,NM_005814.2;GPA33,synonymous_variant,p.=,ENST00000632571,;GPA33,non_coding_transcript_exon_variant,,ENST00000527955,;GPA33,3_prime_UTR_variant,,ENST00000534512,; A ENST00000367868 Transcript synonymous_variant 686/2802 342/960 114/319 T acC/acT 1 -1 GPA33 HGNC HGNC:4445 protein_coding YES CCDS1258.1 ENSP00000356842 Q99795 UPI000012502D NM_005814.2 3/7 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF11,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 167068995 167068995 G A 1 0 0 0 0 0 0 0 1 6481 987 35 3 3 GPA33 1 167068995 Silent SNP G C3N-00175_T 3994514 167068995 81887427 93 9685 DUSP27 0 . GRCh38 1 167128414 167128414 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.3283T>A p.Ser1095Thr p.S1095T ENST00000361200 6/6 504 438 66 362 362 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ser1095Thr,ENST00000361200,;DUSP27,missense_variant,p.Ser1095Thr,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ser1095Thr,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; A ENST00000361200 Transcript missense_variant 3449/4164 3283/3477 1095/1158 S/T Tct/Act 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10159:SF25,hmmpanther:PTHR10159 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 167128414 167128414 T A 1 0 0 0 0 1 0 0 0 4646 1667 58 4 4 DUSP27 1 167128414 Missense_Mutation SNP T C3N-00175_T 59419 167128414 81828008 94 9686 SUCO 0 . GRCh38 1 172602146 172602146 + Missense_Mutation SNP G G A rs199640710 C3N-00175_T C3N-00175_N G G c.3554G>A p.Arg1185Gln p.R1185Q ENST00000367723 20/23 230 201 29 178 178 0 strelka-varscan-mutect SUCO,missense_variant,p.Arg1185Gln,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Arg1185Gln,ENST00000608151,;SUCO,missense_variant,p.Arg1034Gln,ENST00000263688,NM_014283.4;SUCO,missense_variant,p.Arg471Gln,ENST00000616058,NM_001282751.1;SUCO,missense_variant,p.Arg663Gln,ENST00000610051,NM_001282750.1;SUCO,upstream_gene_variant,,ENST00000486569,; A ENST00000367723 Transcript missense_variant 3678/5916 3554/4218 1185/1405 R/Q cGa/cAa rs199640710,COSM899675,COSM899676 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 deleterious(0.01) 20/23 hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs199640710 . 0 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 39 172602146 172602146 G A 1 0 0 0 0 1 0 0 0 15751 1058 37 1 1 SUCO 1 172602146 Missense_Mutation SNP G C3N-00175_T 5473732 172602146 76354276 95 9687 TNN 0 . GRCh38 1 175077652 175077652 + Silent SNP C C A rs766246631 C3N-00175_T C3N-00175_N C C c.234C>A p.= p.A78A ENST00000239462 2/19 210 191 19 204 203 1 strelka-varscan-mutect TNN,synonymous_variant,p.=,ENST00000239462,NM_022093.1;TNN,synonymous_variant,p.=,ENST00000621086,;TNN,synonymous_variant,p.=,ENST00000622870,; A ENST00000239462 Transcript synonymous_variant 347/5008 234/3900 78/1299 A gcC/gcA rs766246631 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 2/19 LOW 1 SNV 2 1 PASS rs766246631 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 39 175077652 175077652 C A 1 0 0 0 0 0 0 0 1 16796 581 21 2 2 TNN 1 175077652 Silent SNP C C3N-00175_T 2475506 175077652 73878770 96 9688 TNN 0 . GRCh38 1 175079425 175079425 + Silent SNP C C A rs768377373 C3N-00175_T C3N-00175_N C C c.502C>A p.= p.R168R ENST00000239462 3/19 225 194 31 182 182 0 strelka-varscan-mutect TNN,synonymous_variant,p.=,ENST00000239462,NM_022093.1;TNN,synonymous_variant,p.=,ENST00000621086,;TNN,synonymous_variant,p.=,ENST00000622870,; A ENST00000239462 Transcript synonymous_variant 615/5008 502/3900 168/1299 R Cgg/Agg rs768377373 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 3/19 hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143 LOW 1 SNV 2 1 PASS rs768377373 . 0 207 0 3 0 0 0 0 -20 0.9999925 1 1 1 0 A 2 1 39 175079425 175079425 C A 1 0 0 0 0 0 0 0 1 16796 759 27 1 1 TNN 1 175079425 Silent SNP C C3N-00175_T 1773 175079425 73876997 97 9689 TNN 0 . GRCh38 1 175097515 175097515 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1687G>T p.Val563Leu p.V563L ENST00000239462 8/19 556 426 130 471 470 1 strelka-varscan-mutect TNN,missense_variant,p.Val563Leu,ENST00000239462,NM_022093.1;TNN,intron_variant,,ENST00000621086,;TNN,intron_variant,,ENST00000622870,; T ENST00000239462 Transcript missense_variant 1800/5008 1687/3900 563/1299 V/L Gtg/Ttg 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 tolerated(0.61) 8/19 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 175097515 175097515 G T 1 0 0 0 0 1 0 0 0 16796 1261 44 2 2 TNN 1 175097515 Missense_Mutation SNP G C3N-00175_T 18090 175097515 73858907 98 9690 TNN 0 . GRCh38 1 175123541 175123541 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.2792delT p.Val931GlyfsTer10 p.V931Gfs*10 ENST00000239462 12/19 407 369 38 402 402 0 sindel-varindel TNN,frameshift_variant,p.Val931GlyfsTer10,ENST00000239462,NM_022093.1;TNN,frameshift_variant,p.Val754GlyfsTer10,ENST00000621086,;TNN,frameshift_variant,p.Val754GlyfsTer10,ENST00000622870,; - ENST00000239462 Transcript frameshift_variant 2905/5008 2792/3900 931/1299 V/X gTg/gg 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 12/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 175123541 175123541 T - 1 0 1 0 1 0 0 0 0 16796 1696 59 0 0 TNN 1 175123541 Frame_Shift_Del DEL T C3N-00175_T 26026 175123541 73832881 99 9691 TNR 0 . GRCh38 1 175403322 175403322 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.794G>T p.Arg265Met p.R265M ENST00000367674 4/23 373 319 54 330 330 0 strelka-varscan-mutect TNR,missense_variant,p.Arg265Met,ENST00000367674,;TNR,missense_variant,p.Arg265Met,ENST00000263525,NM_003285.2;TNR,intron_variant,,ENST00000422274,; A ENST00000367674 Transcript missense_variant 1503/12949 794/4077 265/1358 R/M aGg/aTg 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0.01) 4/23 hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00181 MODERATE 1 SNV 5 1 PASS rs1204168938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 175403322 175403322 C A 1 0 0 0 0 1 0 0 0 16811 681 24 2 2 TNR 1 175403322 Missense_Mutation SNP C C3N-00175_T 279781 175403322 73553100 100 9692 PAPPA2 0 . GRCh38 1 176556603 176556603 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.281G>A p.Arg94His p.R94H ENST00000367662 2/23 333 251 82 271 271 0 strelka-varscan-mutect PAPPA2,missense_variant,p.Arg94His,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Arg94His,ENST00000367661,NM_021936.2;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,; A ENST00000367662 Transcript missense_variant 1445/9691 281/5376 94/1791 R/H cGc/cAc COSM276597,COSM276598 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated_low_confidence(0.61) 2/23 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1322260361 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 176556603 176556603 G A 1 0 0 0 0 1 0 0 0 11513 1087 38 1 1 PAPPA2 1 176556603 Missense_Mutation SNP G C3N-00175_T 1153281 176556603 72399819 101 9693 ASTN1 0 . GRCh38 1 176934184 176934184 + Missense_Mutation SNP C C A rs199937923 C3N-00175_T C3N-00175_N C C c.2639G>T p.Arg880Leu p.R880L ENST00000361833 16/23 125 118 7 108 108 0 strelka-varscan-mutect ASTN1,missense_variant,p.Arg880Leu,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Arg880Leu,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Arg880Leu,ENST00000424564,NM_207108.2;ASTN1,downstream_gene_variant,,ENST00000281881,; A ENST00000361833 Transcript missense_variant 2653/7116 2639/3885 880/1294 R/L cGa/cTa rs199937923 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious(0) 16/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS rs199937923 . 0 208 2 0 0 0 0 0 -13.96777 1 1 1 1 0 A 3 1 39 176934184 176934184 C A 1 0 0 0 0 1 0 0 0 1211 884 31 1 1 ASTN1 1 176934184 Missense_Mutation SNP C C3N-00175_T 377581 176934184 72022238 102 9694 TDRD5 0 . GRCh38 1 179618631 179618631 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.864G>T p.Gln288His p.Q288H ENST00000444136 5/18 99 87 12 144 142 2 strelka-varscan-mutect TDRD5,missense_variant,p.Gln288His,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,missense_variant,p.Gln288His,ENST00000367614,NM_001199091.1;TDRD5,missense_variant,p.Gln288His,ENST00000294848,NM_173533.3; T ENST00000444136 Transcript missense_variant 1382/3946 864/3108 288/1035 Q/H caG/caT 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 deleterious(0.03) 5/18 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 179618631 179618631 G T 1 0 0 0 0 1 0 0 0 16143 933 33 2 2 TDRD5 1 179618631 Missense_Mutation SNP G C3N-00175_T 2684447 179618631 69337791 103 9695 TDRD5 0 . GRCh38 1 179630804 179630804 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1010G>T p.Gly337Val p.G337V ENST00000444136 7/18 114 77 37 120 120 0 strelka-varscan-mutect TDRD5,missense_variant,p.Gly337Val,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,missense_variant,p.Gly337Val,ENST00000367614,NM_001199091.1;TDRD5,missense_variant,p.Gly337Val,ENST00000294848,NM_173533.3; T ENST00000444136 Transcript missense_variant 1528/3946 1010/3108 337/1035 G/V gGc/gTc 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 deleterious(0) 7/18 Pfam_domain:PF12872,PROSITE_profiles:PS51644,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 179630804 179630804 G T 1 0 0 0 0 1 0 0 0 16143 1203 42 2 2 TDRD5 1 179630804 Missense_Mutation SNP G C3N-00175_T 12173 179630804 69325618 104 9696 DHX9 0 . GRCh38 1 182878128 182878128 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.2306G>C p.Arg769Pro p.R769P ENST00000367549 20/28 228 158 70 174 174 0 strelka-varscan-mutect DHX9,missense_variant,p.Arg769Pro,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000474446,;DHX9,upstream_gene_variant,,ENST00000473076,;DHX9,downstream_gene_variant,,ENST00000490519,; C ENST00000367549 Transcript missense_variant 2416/4240 2306/3813 769/1270 R/P cGg/cCg COSM5142087 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 deleterious(0) 20/28 Gene3D:3.40.50.300,PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119,SMART_domains:SM00490,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 182878128 182878128 G C 1 0 0 0 0 1 0 0 0 4320 1116 39 4 4 DHX9 1 182878128 Missense_Mutation SNP G C3N-00175_T 3247324 182878128 66078294 105 9697 DHX9 0 . GRCh38 1 182887117 182887117 + Nonsense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.3496C>T p.Arg1166Ter p.R1166* ENST00000367549 28/28 223 196 27 175 175 0 strelka-varscan-mutect DHX9,stop_gained,p.Arg1166Ter,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000473076,; T ENST00000367549 Transcript stop_gained 3606/4240 3496/3813 1166/1270 R/* Cga/Tga COSM3479958 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 28/28 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 182887117 182887117 C T 1 0 0 0 0 0 1 0 0 4320 644 23 1 1 DHX9 1 182887117 Nonsense_Mutation SNP C C3N-00175_T 8989 182887117 66069305 106 9698 NMNAT2 0 . GRCh38 1 183290184 183290184 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.265C>A p.Gln89Lys p.Q89K ENST00000287713 4/11 186 156 30 179 179 0 strelka-varscan-mutect NMNAT2,missense_variant,p.Gln89Lys,ENST00000287713,NM_015039.3;NMNAT2,missense_variant,p.Gln84Lys,ENST00000294868,NM_170706.3;NMNAT2,non_coding_transcript_exon_variant,,ENST00000473046,; T ENST00000287713 Transcript missense_variant 600/5663 265/924 89/307 Q/K Cag/Aag 1 -1 NMNAT2 HGNC HGNC:16789 protein_coding YES CCDS1353.1 ENSP00000287713 Q9BZQ4 UPI00000706AB NM_015039.3 deleterious(0) 4/11 Gene3D:3.40.50.620,Pfam_domain:PF01467,hmmpanther:PTHR12039,hmmpanther:PTHR12039:SF2,Superfamily_domains:SSF52374 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 183290184 183290184 G T 1 0 0 0 0 1 0 0 0 10538 1357 47 2 2 NMNAT2 1 183290184 Missense_Mutation SNP G C3N-00175_T 403067 183290184 65666238 107 9699 HMCN1 0 . GRCh38 1 186128253 186128253 + Missense_Mutation SNP C C G C3N-00175_T C3N-00175_N C C c.12866C>G p.Pro4289Arg p.P4289R ENST00000271588 83/107 256 210 46 260 260 0 strelka-varscan-mutect HMCN1,missense_variant,p.Pro4289Arg,ENST00000271588,NM_031935.2; G ENST00000271588 Transcript missense_variant 13095/18208 12866/16908 4289/5635 P/R cCc/cGc COSM4913457 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 deleterious(0) 83/107 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 186128253 186128253 C G 1 0 0 0 0 1 0 0 0 7111 623 22 4 4 HMCN1 1 186128253 Missense_Mutation SNP C C3N-00175_T 2838069 186128253 62828169 108 9700 HMCN1 0 . GRCh38 1 186172112 186172112 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.15795A>G p.= p.A5265A ENST00000271588 102/107 325 292 33 269 269 0 strelka-varscan-mutect HMCN1,synonymous_variant,p.=,ENST00000271588,NM_031935.2;HMCN1,synonymous_variant,p.=,ENST00000414277,;GS1-174L6.4,downstream_gene_variant,,ENST00000428391,;HMCN1,non_coding_transcript_exon_variant,,ENST00000475585,; G ENST00000271588 Transcript synonymous_variant 16024/18208 15795/16908 5265/5635 A gcA/gcG 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 102/107 Gene3D:2.10.25.10,Pfam_domain:PF07645,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 186172112 186172112 A G 1 0 0 0 0 0 0 0 1 7111 175 7 5 5 HMCN1 1 186172112 Silent SNP A C3N-00175_T 43859 186172112 62784310 109 9701 PRG4 0 . GRCh38 1 186307061 186307061 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1342C>T p.Pro448Ser p.P448S ENST00000445192 7/13 531 477 54 353 353 0 varscan-mutect PRG4,missense_variant,p.Pro448Ser,ENST00000445192,NM_005807.4;PRG4,missense_variant,p.Pro407Ser,ENST00000367483,NM_001127708.2;PRG4,missense_variant,p.Pro405Ser,ENST00000635041,NM_001303232.1;PRG4,missense_variant,p.Pro355Ser,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,missense_variant,p.Pro314Ser,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; T ENST00000445192 Transcript missense_variant 1387/5044 1342/4215 448/1404 P/S Ccc/Tcc 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 tolerated(0.2) 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 MODERATE SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -16.39203 0.9935822 1 1 1 0 T 3 4 39 186307061 186307061 C T 1 0 0 0 0 1 0 0 0 12615 623 22 3 3 PRG4 1 186307061 Missense_Mutation SNP C C3N-00175_T 134949 186307061 62649361 110 9702 PRG4 0 . GRCh38 1 186308260 186308260 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.2541T>A p.= p.P847P ENST00000445192 7/13 381 340 41 363 363 0 strelka-varscan-mutect PRG4,synonymous_variant,p.=,ENST00000445192,NM_005807.4;PRG4,synonymous_variant,p.=,ENST00000367483,NM_001127708.2;PRG4,synonymous_variant,p.=,ENST00000635041,NM_001303232.1;PRG4,synonymous_variant,p.=,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,synonymous_variant,p.=,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; A ENST00000445192 Transcript synonymous_variant 2586/5044 2541/4215 847/1404 P ccT/ccA 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 7/13 Low_complexity_(Seg):seg LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 186308260 186308260 T A 1 0 0 0 0 0 0 0 1 12615 1567 55 4 4 PRG4 1 186308260 Silent SNP T C3N-00175_T 1199 186308260 62648162 111 9703 TPR 0 . GRCh38 1 186346271 186346271 + Missense_Mutation SNP C C T rs371802543 C3N-00175_T C3N-00175_N C C c.2960G>A p.Arg987His p.R987H ENST00000367478 23/51 67 56 11 81 81 0 strelka-varscan-mutect TPR,missense_variant,p.Arg987His,ENST00000367478,NM_003292.2;TPR,upstream_gene_variant,,ENST00000481347,; T ENST00000367478 Transcript missense_variant 3257/9708 2960/7092 987/2363 R/H cGt/cAt rs371802543,COSM677519 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 tolerated(0.09) 23/51 hmmpanther:PTHR18898 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371802543 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 186346271 186346271 C T 1 0 0 0 0 1 0 0 0 16897 536 19 1 1 TPR 1 186346271 Missense_Mutation SNP C C3N-00175_T 38011 186346271 62610151 112 9704 KCNT2 0 . GRCh38 1 196258293 196258293 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3112C>A p.Gln1038Lys p.Q1038K ENST00000294725 26/28 254 208 46 189 189 0 strelka-varscan-mutect KCNT2,missense_variant,p.Gln1014Lys,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Gln1038Lys,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Gln971Lys,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; T ENST00000294725 Transcript missense_variant 4028/4409 3112/3408 1038/1135 Q/K Cag/Aag 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious(0.03) 26/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 196258293 196258293 G T 1 0 0 0 0 1 0 0 0 8008 1357 47 2 2 KCNT2 1 196258293 Missense_Mutation SNP G C3N-00175_T 9912022 196258293 52698129 113 9705 CFH 0 . GRCh38 1 196747233 196747233 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.3616C>A p.Arg1206Ser p.R1206S ENST00000367429 22/22 560 509 51 401 400 1 varscan-mutect CFH,missense_variant,p.Arg1206Ser,ENST00000367429,NM_000186.3;CFH,non_coding_transcript_exon_variant,,ENST00000466229,; A ENST00000367429 Transcript missense_variant 3856/4127 3616/3696 1206/1231 R/S Cgt/Agt CM100539,COSM3480828 1 1 CFH HGNC HGNC:4883 protein_coding YES CCDS1385.1 ENSP00000356399 P08603 A0A024R962 UPI000013C4D1 NM_000186.3 tolerated(0.31) 22/22 Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 196747233 196747233 C A 1 0 0 0 0 1 0 0 0 3041 884 31 1 1 CFH 1 196747233 Missense_Mutation SNP C C3N-00175_T 488940 196747233 52209189 114 9706 PTPRC 0 . GRCh38 1 198694031 198694031 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.114T>A p.= p.A38A ENST00000413409 4/4 126 105 21 139 139 0 strelka-varscan-mutect PTPRC,synonymous_variant,p.=,ENST00000413409,NM_001267798.1;PTPRC,intron_variant,,ENST00000442510,NM_002838.4;PTPRC,intron_variant,,ENST00000348564,NM_080921.3;PTPRC,intron_variant,,ENST00000367367,;PTPRC,intron_variant,,ENST00000530727,;PTPRC,intron_variant,,ENST00000367379,;PTPRC,intron_variant,,ENST00000418674,;PTPRC,downstream_gene_variant,,ENST00000367364,;PTPRC,intron_variant,,ENST00000391970,;PTPRC,intron_variant,,ENST00000427110,;PTPRC,intron_variant,,ENST00000529828,;PTPRC,intron_variant,,ENST00000462363,;PTPRC,upstream_gene_variant,,ENST00000484135,; A ENST00000413409 Transcript synonymous_variant 198/1338 114/264 38/87 A gcT/gcA 1 1 PTPRC HGNC HGNC:9666 protein_coding CCDS44291.2 ENSP00000405494 M9MML4 UPI00002046F8 NM_001267798.1 4/4 LOW SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 198694031 198694031 T A 1 0 0 0 0 0 0 0 1 12951 1567 55 4 4 PTPRC 1 198694031 Silent SNP T C3N-00175_T 1946798 198694031 50262391 115 9707 KIF21B 0 . GRCh38 1 200992320 200992320 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2347G>T p.Glu783Ter p.E783* ENST00000422435 16/35 287 255 32 265 265 0 strelka-varscan-mutect KIF21B,stop_gained,p.Glu783Ter,ENST00000332129,NM_017596.3;KIF21B,stop_gained,p.Glu783Ter,ENST00000422435,NM_001252100.1;KIF21B,stop_gained,p.Glu783Ter,ENST00000461742,NM_001252102.1;KIF21B,stop_gained,p.Glu783Ter,ENST00000360529,NM_001252103.1; A ENST00000422435 Transcript stop_gained 2664/5519 2347/4914 783/1637 E/* Gag/Tag 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 16/35 hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 200992320 200992320 C A 1 0 0 0 0 0 1 0 0 8154 864 30 2 2 KIF21B 1 200992320 Nonsense_Mutation SNP C C3N-00175_T 2298289 200992320 47964102 116 9708 IGFN1 0 . GRCh38 1 201222828 201222828 + Splice_Site SNP G G A novel C3N-00175_T C3N-00175_N G G c.10290+1G>A p.X3430_splice ENST00000335211 121 105 16 105 105 0 strelka-varscan-mutect IGFN1,splice_donor_variant,,ENST00000335211,NM_001164586.1;IGFN1,splice_donor_variant,,ENST00000295591,;IGFN1,splice_donor_variant,,ENST00000412892,;RP11-567E21.3,non_coding_transcript_exon_variant,,ENST00000453155,;IGFN1,splice_donor_variant,,ENST00000437879,;IGFN1,splice_donor_variant,,ENST00000473483,; A ENST00000335211 Transcript splice_donor_variant -/11810 10290/11127 3430/3708 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 20/23 HIGH SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 201222828 201222828 G A 1 0 0 0 0 0 0 1 0 7497 1043 36 3 3 IGFN1 1 201222828 Splice_Site SNP G C3N-00175_T 230508 201222828 47733594 117 9709 LGR6 0 . GRCh38 1 202276402 202276402 + Silent SNP G G T rs375377887 C3N-00175_T C3N-00175_N G G c.525G>T p.= p.T175T ENST00000367278 5/18 223 204 19 194 194 0 strelka-varscan-mutect LGR6,synonymous_variant,p.=,ENST00000367278,NM_001017403.1;LGR6,synonymous_variant,p.=,ENST00000255432,NM_021636.2;LGR6,synonymous_variant,p.=,ENST00000423542,;LGR6,intron_variant,,ENST00000439764,NM_001017404.1;LGR6,non_coding_transcript_exon_variant,,ENST00000308543,;LGR6,non_coding_transcript_exon_variant,,ENST00000506931,;LGR6,synonymous_variant,p.=,ENST00000487787,; T ENST00000367278 Transcript synonymous_variant 614/3567 525/2904 175/967 T acG/acT rs375377887 1 1 LGR6 HGNC HGNC:19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 5/18 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs375377887 . 0 206 0 2 2 0 0 0 -6.786541 0.959765 1 1 1 0 T 2 4 39 202276402 202276402 G T 1 0 0 0 0 0 0 0 1 8668 1103 39 1 1 LGR6 1 202276402 Silent SNP G C3N-00175_T 1053574 202276402 46680020 118 9710 PPFIA4 0 . GRCh38 1 203045891 203045891 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.909G>A p.= p.K303K ENST00000447715 12/35 328 259 69 283 283 0 strelka-varscan-mutect PPFIA4,synonymous_variant,p.=,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,synonymous_variant,p.=,ENST00000447715,;PPFIA4,synonymous_variant,p.=,ENST00000600426,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;PPFIA4,non_coding_transcript_exon_variant,,ENST00000601609,; A ENST00000447715 Transcript synonymous_variant 1350/6349 909/3558 303/1185 K aaG/aaA 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 12/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 203045891 203045891 G A 1 0 0 0 0 0 0 0 1 12421 962 34 3 3 PPFIA4 1 203045891 Silent SNP G C3N-00175_T 769489 203045891 45910531 119 9711 ATP2B4 0 . GRCh38 1 203733350 203733350 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.3437A>T p.Lys1146Ile p.K1146I ENST00000367218 21/22 193 134 59 143 143 0 strelka-varscan-mutect ATP2B4,missense_variant,p.Lys1146Ile,ENST00000367218,NM_001001396.2;ATP2B4,missense_variant,p.Lys1146Ile,ENST00000341360,;ATP2B4,missense_variant,p.Lys111Ile,ENST00000356729,;ATP2B4,intron_variant,,ENST00000357681,NM_001684.4;SNORA77,downstream_gene_variant,,ENST00000408716,;ATP2B4,missense_variant,p.Lys78Ile,ENST00000484746,; T ENST00000367218 Transcript missense_variant 4334/8918 3437/3513 1146/1170 K/I aAa/aTa 1 1 ATP2B4 HGNC HGNC:817 protein_coding CCDS30977.1 ENSP00000356187 P23634 UPI000002A460 NM_001001396.2 tolerated_low_confidence(0.22) 21/22 Pfam_domain:PF12424,Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 203733350 203733350 A T 1 0 0 0 0 1 0 0 0 1295 14 1 4 4 ATP2B4 1 203733350 Missense_Mutation SNP A C3N-00175_T 687459 203733350 45223072 120 9712 NFASC 0 . GRCh38 1 204975418 204975418 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1706G>T p.Arg569Met p.R569M ENST00000339876 15/30 110 94 16 84 83 1 strelka-varscan-mutect NFASC,missense_variant,p.Arg569Met,ENST00000339876,NM_001005388.2;NFASC,missense_variant,p.Arg569Met,ENST00000401399,;NFASC,missense_variant,p.Arg580Met,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Arg580Met,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Arg563Met,ENST00000404076,;NFASC,missense_variant,p.Arg580Met,ENST00000404907,;NFASC,missense_variant,p.Arg556Met,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Arg539Met,ENST00000367173,;NFASC,missense_variant,p.Arg580Met,ENST00000513543,;NFASC,missense_variant,p.Arg569Met,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,splice_region_variant,,ENST00000404977,;NFASC,upstream_gene_variant,,ENST00000471392,;NFASC,splice_region_variant,,ENST00000512826,;NFASC,splice_region_variant,,ENST00000504476,;NFASC,downstream_gene_variant,,ENST00000514644,; T ENST00000339876 Transcript missense_variant,splice_region_variant 2034/10333 1706/3723 569/1240 R/M aGg/aTg 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 deleterious(0) 15/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 204975418 204975418 G T 1 0 0 0 0 1 0 0 0 10396 1014 35 2 2 NFASC 1 204975418 Missense_Mutation SNP G C3N-00175_T 1242068 204975418 43981004 121 9713 CNTN2 0 . GRCh38 1 205061299 205061299 + Nonsense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.852G>A p.Trp284Ter p.W284* ENST00000331830 8/23 207 183 24 153 153 0 strelka-varscan-mutect CNTN2,stop_gained,p.Trp284Ter,ENST00000331830,NM_005076.3;CNTN2,upstream_gene_variant,,ENST00000636641,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,;CNTN2,non_coding_transcript_exon_variant,,ENST00000530117,;CNTN2,downstream_gene_variant,,ENST00000532366,;CNTN2,upstream_gene_variant,,ENST00000527340,;CNTN2,upstream_gene_variant,,ENST00000530594,; A ENST00000331830 Transcript stop_gained 1209/8214 852/3123 284/1040 W/* tgG/tgA 1 1 CNTN2 HGNC HGNC:2172 protein_coding YES CCDS1449.1 ENSP00000330633 Q02246 A0A024R9B4 UPI00001266A5 NM_005076.3 8/23 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 205061299 205061299 G A 1 0 0 0 0 0 1 0 0 3422 1183 41 3 3 CNTN2 1 205061299 Nonsense_Mutation SNP G C3N-00175_T 85881 205061299 43895123 122 9714 NUCKS1 0 . GRCh38 1 205723926 205723926 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.229G>T p.Glu77Ter p.E77* ENST00000367142 4/7 207 157 50 303 303 0 strelka-varscan-mutect NUCKS1,stop_gained,p.Glu77Ter,ENST00000367142,NM_022731.4;NUCKS1,upstream_gene_variant,,ENST00000464938,; A ENST00000367142 Transcript stop_gained,splice_region_variant 532/6496 229/732 77/243 E/* Gag/Tag 1 -1 NUCKS1 HGNC HGNC:29923 protein_coding YES CCDS30987.1 ENSP00000356110 Q9H1E3 UPI000013096A NM_022731.4 4/7 Low_complexity_(Seg):seg,hmmpanther:PTHR15361 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 205723926 205723926 C A 1 0 0 0 0 0 1 0 0 10786 695 24 2 2 NUCKS1 1 205723926 Nonsense_Mutation SNP C C3N-00175_T 662627 205723926 43232496 123 9715 PM20D1 0 . GRCh38 1 205845400 205845400 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.414G>T p.= p.V138V ENST00000367136 3/13 517 482 35 468 468 0 strelka-varscan-mutect PM20D1,synonymous_variant,p.=,ENST00000367136,NM_152491.4;PM20D1,non_coding_transcript_exon_variant,,ENST00000460624,;PM20D1,upstream_gene_variant,,ENST00000461807,; A ENST00000367136 Transcript synonymous_variant 459/2152 414/1509 138/502 V gtG/gtT 1 -1 PM20D1 HGNC HGNC:26518 protein_coding YES CCDS1460.1 ENSP00000356104 Q6GTS8 UPI00003665FD NM_152491.4 3/13 hmmpanther:PTHR11014:SF16,hmmpanther:PTHR11014,Pfam_domain:PF01546,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 205845400 205845400 C A 1 0 0 0 0 0 0 0 1 12234 697 25 2 2 PM20D1 1 205845400 Silent SNP C C3N-00175_T 121474 205845400 43111022 124 9716 C1orf186 0 . GRCh38 1 206101819 206101819 + Missense_Mutation SNP C C A rs782598871 C3N-00175_T C3N-00175_N C C c.386C>A p.Pro129Gln p.P129Q ENST00000331555 6/6 345 289 56 281 281 0 strelka-varscan-mutect C1orf186,missense_variant,p.Pro129Gln,ENST00000331555,NM_001007544.3;C1orf186,missense_variant,p.Pro129Gln,ENST00000582070,;C1orf186,missense_variant,p.Pro129Gln,ENST00000603488,;C1orf186,missense_variant,p.Pro81Gln,ENST00000603378,;C1orf186,downstream_gene_variant,,ENST00000604112,; A ENST00000331555 Transcript missense_variant 1025/1665 386/519 129/172 P/Q cCg/cAg rs782598871 1 1 C1orf186 HGNC HGNC:25341 protein_coding YES CCDS73014.1 ENSP00000356093 Q6ZWK4 UPI0000039E60 NM_001007544.3 deleterious(0.03) 6/6 Pfam_domain:PF15763,hmmpanther:PTHR38491,hmmpanther:PTHR38491:SF1 MODERATE 1 SNV 1 1 PASS rs782598871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 206101819 206101819 C A 1 0 0 0 0 1 0 0 0 1976 652 23 1 1 C1orf186 1 206101819 Missense_Mutation SNP C C3N-00175_T 256419 206101819 42854603 125 9717 38 2 C1orf186 0 . GRCh38 1 206101821 206101821 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.388C>G p.Leu130Val p.L130V ENST00000331555 6/6 357 298 59 281 281 0 strelka-varscan-mutect C1orf186,missense_variant,p.Leu130Val,ENST00000331555,NM_001007544.3;C1orf186,missense_variant,p.Leu130Val,ENST00000582070,;C1orf186,missense_variant,p.Leu130Val,ENST00000603488,;C1orf186,missense_variant,p.Leu82Val,ENST00000603378,;C1orf186,downstream_gene_variant,,ENST00000604112,; G ENST00000331555 Transcript missense_variant 1027/1665 388/519 130/172 L/V Ctg/Gtg 1 1 C1orf186 HGNC HGNC:25341 protein_coding YES CCDS73014.1 ENSP00000356093 Q6ZWK4 UPI0000039E60 NM_001007544.3 tolerated(0.16) 6/6 Pfam_domain:PF15763,hmmpanther:PTHR38491,hmmpanther:PTHR38491:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 206101821 206101821 C G 1 0 0 0 0 1 0 0 0 1976 796 28 4 4 C1orf186 1 206101821 Missense_Mutation SNP C C3N-00175_T 2 206101821 42854601 126 9718 38 2 PIGR 0 . GRCh38 1 206937098 206937098 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1042G>A p.Glu348Lys p.E348K ENST00000356495 4/11 41 36 5 39 39 0 strelka-varscan-mutect PIGR,missense_variant,p.Glu348Lys,ENST00000356495,NM_002644.3;PIGR,downstream_gene_variant,,ENST00000491503,; T ENST00000356495 Transcript missense_variant 1226/4279 1042/2295 348/764 E/K Gag/Aag 1 -1 PIGR HGNC HGNC:8968 protein_coding YES CCDS1474.1 ENSP00000348888 P01833 UPI000007407E NM_002644.3 deleterious(0.04) 4/11 hmmpanther:PTHR11860:SF55,hmmpanther:PTHR11860,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs930970171 . 0 205 5 0 0 0 0 0 -12.91684 1 1 1 1 0 T 3 4 39 206937098 206937098 C T 1 0 0 0 0 1 0 0 0 11991 840 29 3 3 PIGR 1 206937098 Missense_Mutation SNP C C3N-00175_T 835277 206937098 42019324 127 9719 CR1L 0 . GRCh38 1 207717475 207717475 + Missense_Mutation SNP C C G rs374201673 C3N-00175_T C3N-00175_N C C c.1426C>G p.Pro476Ala p.P476A ENST00000508064 11/12 157 113 44 129 129 0 varscan-mutect CR1L,missense_variant,p.Pro476Ala,ENST00000508064,NM_175710.1;CR1L,3_prime_UTR_variant,,ENST00000294997,; G ENST00000508064 Transcript missense_variant 1486/1788 1426/1710 476/569 P/A Cca/Gca rs374201673 1 1 CR1L HGNC HGNC:2335 protein_coding YES CCDS44310.1 ENSP00000421736 Q2VPA4 UPI0000DD792A NM_175710.1 tolerated(0.37) 11/12 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF354,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 2 1 PASS rs374201673 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 207717475 207717475 C G 1 0 0 0 0 1 0 0 0 3639 855 30 4 4 CR1L 1 207717475 Missense_Mutation SNP C C3N-00175_T 780377 207717475 41238947 128 9720 PLXNA2 0 . GRCh38 1 208096793 208096793 + Missense_Mutation SNP C C A rs753515319 C3N-00175_T C3N-00175_N C C c.1822G>T p.Gly608Trp p.G608W ENST00000367033 7/32 309 223 86 287 286 1 strelka-varscan-mutect PLXNA2,missense_variant,p.Gly608Trp,ENST00000367033,NM_025179.3; A ENST00000367033 Transcript missense_variant 2580/11444 1822/5685 608/1894 G/W Ggg/Tgg rs753515319 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 deleterious(0.02) 7/32 hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625 MODERATE 1 SNV 1 1 PASS rs753515319 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 208096793 208096793 C A 1 0 0 0 0 1 0 0 0 12226 652 23 1 1 PLXNA2 1 208096793 Missense_Mutation SNP C C3N-00175_T 379318 208096793 40859629 129 9721 NEK2 0 . GRCh38 1 211670379 211670379 + Nonsense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.667G>T p.Glu223Ter p.E223* ENST00000366999 5/8 167 149 18 155 155 0 strelka-varscan-mutect NEK2,stop_gained,p.Glu223Ter,ENST00000366999,NM_002497.3;NEK2,stop_gained,p.Glu223Ter,ENST00000366998,NM_001204183.1;NEK2,stop_gained,p.Glu223Ter,ENST00000540251,NM_001204182.1;NEK2,non_coding_transcript_exon_variant,,ENST00000462283,;NEK2,upstream_gene_variant,,ENST00000489633,; A ENST00000366999 Transcript stop_gained 806/2131 667/1338 223/445 E/* Gaa/Taa COSM1584009,COSM4870369,COSM903495 1 -1 NEK2 HGNC HGNC:7745 protein_coding YES CCDS1500.1 ENSP00000355966 P51955 UPI000012FF27 NM_002497.3 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR24362:SF278,hmmpanther:PTHR24362,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 211670379 211670379 C A 1 0 0 0 0 0 1 0 0 10352 922 32 2 2 NEK2 1 211670379 Nonsense_Mutation SNP C C3N-00175_T 3573586 211670379 37286043 130 9722 PROX1 0 . GRCh38 1 213997088 213997088 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.553A>T p.Arg185Trp p.R185W ENST00000366958 2/5 105 99 6 95 95 0 strelka-varscan-mutect PROX1,missense_variant,p.Arg185Trp,ENST00000498508,;PROX1,missense_variant,p.Arg185Trp,ENST00000366958,NM_001270616.1;PROX1,missense_variant,p.Arg185Trp,ENST00000261454,;PROX1,missense_variant,p.Arg185Trp,ENST00000435016,NM_002763.4;PROX1,missense_variant,p.Arg185Trp,ENST00000471129,;PROX1,downstream_gene_variant,,ENST00000607425,; T ENST00000366958 Transcript missense_variant 1161/8240 553/2214 185/737 R/W Agg/Tgg 1 1 PROX1 HGNC HGNC:9459 protein_coding YES CCDS31021.1 ENSP00000355925 Q92786 UPI0000071D14 NM_001270616.1 tolerated(0.19) 2/5 hmmpanther:PTHR12198 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 213997088 213997088 A T 1 0 0 0 0 1 0 0 0 12696 63 3 4 4 PROX1 1 213997088 Missense_Mutation SNP A C3N-00175_T 2326709 213997088 34959334 131 9723 PTPN14 0 . GRCh38 1 214451920 214451920 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.229delG p.Glu77SerfsTer6 p.E77Sfs*6 ENST00000366956 3/19 171 154 17 150 150 0 sindel-varindel-pindel PTPN14,frameshift_variant,p.Glu77SerfsTer6,ENST00000366956,NM_005401.4;PTPN14,frameshift_variant,p.Glu77SerfsTer6,ENST00000543945,; - ENST00000366956 Transcript frameshift_variant 424/12985 229/3564 77/1187 E/X Gag/ag 1 -1 PTPN14 HGNC HGNC:9647 protein_coding YES CCDS1514.1 ENSP00000355923 Q15678 UPI000013DCA6 NM_005401.4 3/19 PROSITE_profiles:PS50057,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,PROSITE_patterns:PS00660,Gene3D:3.10.20.90,Pfam_domain:PF09379,PIRSF_domain:PIRSF000934,SMART_domains:SM00295,Superfamily_domains:SSF54236 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99989 0.9999998 1 1 1 0 - 7 5 39 214451920 214451920 C - 1 0 1 0 1 0 0 0 0 12936 864 30 0 0 PTPN14 1 214451920 Frame_Shift_Del DEL C C3N-00175_T 454832 214451920 34504502 132 9724 USH2A 0 . GRCh38 1 215640724 215640724 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.14802C>A p.Tyr4934Ter p.Y4934* ENST00000307340 68/72 454 404 50 376 376 0 strelka-varscan-mutect USH2A,stop_gained,p.Tyr4934Ter,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript stop_gained 15189/18883 14802/15609 4934/5202 Y/* taC/taA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 68/72 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 215640724 215640724 G T 1 0 0 0 0 0 1 0 0 17570 1256 44 2 2 USH2A 1 215640724 Nonsense_Mutation SNP G C3N-00175_T 1188804 215640724 33315698 133 9725 USH2A 0 . GRCh38 1 215650743 215650743 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.14192G>A p.Gly4731Glu p.G4731E ENST00000307340 65/72 308 279 29 240 240 0 strelka-varscan-mutect USH2A,missense_variant,p.Gly4731Glu,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 14579/18883 14192/15609 4731/5202 G/E gGg/gAg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.02) 65/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 215650743 215650743 C T 1 0 0 0 0 1 0 0 0 17570 623 22 3 3 USH2A 1 215650743 Missense_Mutation SNP C C3N-00175_T 10019 215650743 33305679 134 9726 USH2A 0 . GRCh38 1 215728043 215728043 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.12053C>T p.Ala4018Val p.A4018V ENST00000307340 61/72 301 234 67 303 302 1 strelka-varscan-mutect USH2A,missense_variant,p.Ala4018Val,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 12440/18883 12053/15609 4018/5202 A/V gCt/gTt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.07) 61/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 215728043 215728043 G A 1 0 0 0 0 1 0 0 0 17570 971 34 3 3 USH2A 1 215728043 Missense_Mutation SNP G C3N-00175_T 77300 215728043 33228379 135 9727 USH2A 0 . GRCh38 1 215999025 215999025 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.6519G>A p.= p.L2173L ENST00000307340 34/72 81 61 20 114 114 0 strelka-varscan-mutect USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript synonymous_variant 6906/18883 6519/15609 2173/5202 L ctG/ctA 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 34/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 215999025 215999025 C T 1 0 0 0 0 0 0 0 1 17570 581 21 3 3 USH2A 1 215999025 Silent SNP C C3N-00175_T 270982 215999025 32957397 136 9728 USH2A 0 . GRCh38 1 216207327 216207327 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.3262A>C p.Ser1088Arg p.S1088R ENST00000307340 16/72 344 272 72 293 293 0 strelka-varscan-mutect USH2A,missense_variant,p.Ser1088Arg,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Ser1088Arg,ENST00000366942,NM_007123.5;RP5-1099E6.3,downstream_gene_variant,,ENST00000420867,; G ENST00000307340 Transcript missense_variant 3649/18883 3262/15609 1088/5202 S/R Agt/Cgt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.72) 16/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 216207327 216207327 T G 1 0 0 0 0 1 0 0 0 17570 1580 55 5 5 USH2A 1 216207327 Missense_Mutation SNP T C3N-00175_T 208302 216207327 32749095 137 9729 SPATA17 0 . GRCh38 1 217742014 217742014 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.435A>G p.= p.E145E ENST00000366933 6/11 188 174 14 161 160 1 strelka-varscan-mutect SPATA17,synonymous_variant,p.=,ENST00000366933,NM_138796.3;SPATA17,non_coding_transcript_exon_variant,,ENST00000492747,;SPATA17,3_prime_UTR_variant,,ENST00000470448,; G ENST00000366933 Transcript synonymous_variant 490/5818 435/1086 145/361 E gaA/gaG 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 6/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22706,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 217742014 217742014 A G 1 0 0 0 0 0 0 0 1 15332 69 3 5 5 SPATA17 1 217742014 Silent SNP A C3N-00175_T 1534687 217742014 31214408 138 9730 ZC3H11B 0 . GRCh38 1 219611275 219611275 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.788C>A p.Thr263Lys p.T263K ENST00000636126 2/2 128 114 14 82 82 0 varscan-mutect ZC3H11B,missense_variant,p.Thr263Lys,ENST00000636126,;ZC3H11B,missense_variant,p.Thr263Lys,ENST00000367211,; T ENST00000636126 Transcript missense_variant 1504/4432 788/2418 263/805 T/K aCa/aAa 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C deleterious(0) 2/2 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 39 219611275 219611275 G T 1 0 0 0 0 1 0 0 0 18135 1377 48 2 2 ZC3H11B 1 219611275 Missense_Mutation SNP G C3N-00175_T 1869261 219611275 29345147 139 9731 SLC30A10 0 . GRCh38 1 219915788 219915788 + Silent SNP C C A rs200960383 C3N-00175_T C3N-00175_N C C c.1119G>T p.= p.A373A ENST00000366926 4/4 535 485 50 454 454 0 strelka-varscan-mutect SLC30A10,synonymous_variant,p.=,ENST00000366926,NM_018713.2;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484079,;SLC30A10,intron_variant,,ENST00000484239,;SLC30A10,3_prime_UTR_variant,,ENST00000356609,; A ENST00000366926 Transcript synonymous_variant 1281/1915 1119/1458 373/485 A gcG/gcT rs200960383 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 4/4 hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF14,TIGRFAM_domain:TIGR01297 LOW 1 SNV 1 1 PASS rs200960383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 219915788 219915788 C A 1 0 0 0 0 0 0 0 1 14824 639 23 1 1 SLC30A10 1 219915788 Silent SNP C C3N-00175_T 304513 219915788 29040634 140 9732 MARK1 0 . GRCh38 1 220579557 220579557 + Missense_Mutation SNP G G C rs758475266 C3N-00175_T C3N-00175_N G G c.255G>C p.Glu85Asp p.E85D ENST00000611084 2/18 123 109 14 102 102 0 strelka-varscan-mutect MARK1,missense_variant,p.Glu85Asp,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Glu85Asp,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Glu85Asp,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Glu85Asp,ENST00000366917,NM_018650.4;MARK1,downstream_gene_variant,,ENST00000485104,; C ENST00000611084 Transcript missense_variant,splice_region_variant 895/5321 255/2391 85/796 E/D gaG/gaC rs758475266 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 deleterious(0) 2/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs758475266 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 220579557 220579557 G C 1 0 0 0 0 1 0 0 0 9237 1014 35 4 4 MARK1 1 220579557 Missense_Mutation SNP G C3N-00175_T 663769 220579557 28376865 141 9733 MARK1 0 . GRCh38 1 220618709 220618709 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.863T>A p.Leu288Gln p.L288Q ENST00000611084 9/18 165 147 18 127 127 0 strelka-mutect MARK1,missense_variant,p.Leu288Gln,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Leu288Gln,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Leu266Gln,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Leu288Gln,ENST00000366917,NM_018650.4; A ENST00000611084 Transcript missense_variant 1503/5321 863/2391 288/796 L/Q cTg/cAg 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 deleterious(0) 9/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 220618709 220618709 T A 1 0 0 0 0 1 0 0 0 9237 1580 55 4 4 MARK1 1 220618709 Missense_Mutation SNP T C3N-00175_T 39152 220618709 28337713 142 9734 MIA3 0 . GRCh38 1 222621262 222621262 + Silent SNP A A T C3N-00175_T C3N-00175_N A A c.237A>T p.= p.A79A ENST00000344922 2/28 134 116 18 113 113 0 strelka-varscan-mutect MIA3,synonymous_variant,p.=,ENST00000344922,NM_001324064.1,NM_198551.3;MIA3,synonymous_variant,p.=,ENST00000344507,;MIA3,non_coding_transcript_exon_variant,,ENST00000470521,; T ENST00000344922 Transcript synonymous_variant 262/8142 237/5724 79/1907 A gcA/gcT COSM5663156 1 1 MIA3 HGNC HGNC:24008 protein_coding YES CCDS41470.1 ENSP00000340900 Q5JRA6 UPI00001D75B3 NM_001324064.1,NM_198551.3 2/28 hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF37,Pfam_domain:PF07653,Gene3D:2.30.30.40,Superfamily_domains:SSF50044 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 222621262 222621262 A T 1 0 0 0 0 0 0 0 1 9522 117 5 4 4 MIA3 1 222621262 Silent SNP A C3N-00175_T 2002553 222621262 26335160 143 9735 FBXO28 0 . GRCh38 1 224157659 224157659 + Missense_Mutation SNP G G T rs202148144 C3N-00175_T C3N-00175_N G G c.1020G>T p.Gln340His p.Q340H ENST00000366862 5/5 235 177 58 192 192 0 strelka-varscan-mutect FBXO28,missense_variant,p.Gln340His,ENST00000366862,NM_015176.3;FBXO28,3_prime_UTR_variant,,ENST00000424254,NM_001136115.2;FBXO28,3_prime_UTR_variant,,ENST00000523990,; T ENST00000366862 Transcript missense_variant 1063/5451 1020/1107 340/368 Q/H caG/caT rs202148144 1 1 FBXO28 HGNC HGNC:29046 protein_coding YES CCDS1539.1 ENSP00000355827 Q9NVF7 A0A024R3Q6 UPI000006F1C1 NM_015176.3 tolerated(0.1) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR13252 MODERATE 1 SNV 1 1 PASS rs202148144 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 224157659 224157659 G T 1 0 0 0 0 1 0 0 0 5601 933 33 2 2 FBXO28 1 224157659 Missense_Mutation SNP G C3N-00175_T 1536397 224157659 24798763 144 9736 WDR26 0 . GRCh38 1 224418413 224418413 + Missense_Mutation SNP T T C C3N-00175_T C3N-00175_N T T c.866A>G p.Tyr289Cys p.Y289C ENST00000414423 6/14 141 123 18 119 119 0 strelka-varscan-mutect WDR26,missense_variant,p.Tyr289Cys,ENST00000414423,NM_025160.6,NM_001115113.2;WDR26,downstream_gene_variant,,ENST00000445239,;WDR26,downstream_gene_variant,,ENST00000477425,;WDR26,3_prime_UTR_variant,,ENST00000486652,;WDR26,non_coding_transcript_exon_variant,,ENST00000443112,;WDR26,downstream_gene_variant,,ENST00000489825,; C ENST00000414423 Transcript missense_variant 1060/6872 866/1986 289/661 Y/C tAt/tGt COSM316519,COSM316520 1 -1 WDR26 HGNC HGNC:21208 protein_coding YES CCDS31037.2 ENSP00000408108 Q9H7D7 UPI0000203FB7 NM_025160.6,NM_001115113.2 deleterious(0) 6/14 hmmpanther:PTHR22838,hmmpanther:PTHR22838:SF0 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 224418413 224418413 T C 1 0 0 0 0 1 0 0 0 17843 1420 49 5 5 WDR26 1 224418413 Missense_Mutation SNP T C3N-00175_T 260754 224418413 24538009 145 9737 LIN9 0 . GRCh38 1 226250915 226250915 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1091G>T p.Arg364Ile p.R364I ENST00000328205 11/15 42 31 11 83 83 0 strelka-varscan-mutect LIN9,missense_variant,p.Arg364Ile,ENST00000328205,NM_173083.3;LIN9,missense_variant,p.Arg419Ile,ENST00000366808,NM_001270410.1;LIN9,missense_variant,p.Arg324Ile,ENST00000460719,NM_001270409.1;LIN9,missense_variant,p.Arg329Ile,ENST00000481685,; A ENST00000328205 Transcript missense_variant 1637/3567 1091/1677 364/558 R/I aGa/aTa 1 -1 LIN9 HGNC HGNC:30830 protein_coding YES CCDS1553.1 ENSP00000329102 Q5TKA1 UPI00001B2F3C NM_173083.3 deleterious(0) 11/15 hmmpanther:PTHR21689 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 226250915 226250915 C A 1 0 0 0 0 1 0 0 0 8721 927 32 2 2 LIN9 1 226250915 Missense_Mutation SNP C C3N-00175_T 1832502 226250915 22705507 146 9738 PARP1 0 . GRCh38 1 226365142 226365142 + Nonsense_Mutation SNP C C A rs772996633 C3N-00175_T C3N-00175_N C C c.2518G>T p.Glu840Ter p.E840* ENST00000366794 19/23 576 530 46 431 431 0 strelka-varscan-mutect PARP1,stop_gained,p.Glu840Ter,ENST00000366794,NM_001618.3;PARP1,non_coding_transcript_exon_variant,,ENST00000490921,;PARP1,non_coding_transcript_exon_variant,,ENST00000498787,;PARP1,upstream_gene_variant,,ENST00000463968,;PARP1,upstream_gene_variant,,ENST00000468608,;PARP1,upstream_gene_variant,,ENST00000491816,; A ENST00000366794 Transcript stop_gained 2662/3958 2518/3045 840/1014 E/* Gag/Tag rs772996633 1 -1 PARP1 HGNC HGNC:270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 A0A024R3T8 UPI000013D92D NM_001618.3 19/23 PROSITE_profiles:PS51059,hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF62,PIRSF_domain:PIRSF000489,Gene3D:3.90.228.10,Pfam_domain:PF00644,Superfamily_domains:SSF56399 HIGH 1 SNV 1 1 PASS rs772996633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 226365142 226365142 C A 1 0 0 0 0 0 1 0 0 11534 922 32 2 2 PARP1 1 226365142 Nonsense_Mutation SNP C C3N-00175_T 114227 226365142 22591280 147 9739 OBSCN 0 . GRCh38 1 228217154 228217154 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2519C>A p.Ser840Tyr p.S840Y ENST00000570156 8/116 385 315 70 359 358 1 strelka-varscan-mutect OBSCN,missense_variant,p.Ser840Tyr,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Ser840Tyr,ENST00000366707,;OBSCN,missense_variant,p.Ser840Tyr,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Ser840Tyr,ENST00000636875,;OBSCN,missense_variant,p.Ser840Tyr,ENST00000284548,NM_052843.3;C1orf145,upstream_gene_variant,,ENST00000295012,;OBSCN,non_coding_transcript_exon_variant,,ENST00000493977,;C1orf145,upstream_gene_variant,,ENST00000337335,;C1orf145,upstream_gene_variant,,ENST00000472613,; A ENST00000570156 Transcript missense_variant 2593/26925 2519/26772 840/8923 S/Y tCc/tAc 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0.01) 8/116 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 228217154 228217154 C A 1 0 0 0 0 1 0 0 0 10889 855 30 2 2 OBSCN 1 228217154 Missense_Mutation SNP C C3N-00175_T 1852012 228217154 20739268 148 9740 ACTA1 0 . GRCh38 1 229431636 229431636 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.997G>A p.Ala333Thr p.A333T ENST00000366684 7/7 218 207 11 274 274 0 strelka-varscan-mutect ACTA1,missense_variant,p.Ala333Thr,ENST00000366684,NM_001100.3;ACTA1,missense_variant,p.Ala210Thr,ENST00000366683,; T ENST00000366684 Transcript missense_variant 1100/1491 997/1134 333/377 A/T Gcc/Acc 1 -1 ACTA1 HGNC HGNC:129 protein_coding YES CCDS1578.1 ENSP00000355645 P68133 UPI0000000860 NM_001100.3 deleterious_low_confidence(0.03) 7/7 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF193,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 229431636 229431636 C T 1 0 0 0 0 1 0 0 0 234 768 27 1 1 ACTA1 1 229431636 Missense_Mutation SNP C C3N-00175_T 1214482 229431636 19524786 149 9741 TAF5L 0 . GRCh38 1 229594378 229594378 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1689G>C p.Met563Ile p.M563I ENST00000258281 5/5 318 285 33 275 275 0 strelka-varscan-mutect TAF5L,missense_variant,p.Met563Ile,ENST00000258281,NM_014409.3;TAF5L,missense_variant,p.Met563Ile,ENST00000366676,;TAF5L,downstream_gene_variant,,ENST00000366675,NM_001025247.1; G ENST00000258281 Transcript missense_variant 1855/3112 1689/1770 563/589 M/I atG/atC 1 -1 TAF5L HGNC HGNC:17304 protein_coding YES CCDS1581.1 ENSP00000258281 O75529 UPI0000073E93 NM_014409.3 deleterious(0.04) 5/5 hmmpanther:PTHR19879,hmmpanther:PTHR19879:SF6,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 229594378 229594378 C G 1 0 0 0 0 1 0 0 0 15925 826 29 4 4 TAF5L 1 229594378 Missense_Mutation SNP C C3N-00175_T 162742 229594378 19362044 150 9742 COA6 0 . GRCh38 1 234373791 234373791 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.73C>T p.Arg25Cys p.R25C ENST00000366613 1/3 172 127 45 172 172 0 strelka-varscan-mutect COA6,missense_variant,p.Arg25Cys,ENST00000366613,NM_001012985.2;COA6,5_prime_UTR_variant,,ENST00000366612,NM_001301733.1;COA6,intron_variant,,ENST00000366615,NM_001206641.2;COA6,intron_variant,,ENST00000619305,;RP5-827C21.6,downstream_gene_variant,,ENST00000610233,;RP5-827C21.4,upstream_gene_variant,,ENST00000451795,; T ENST00000366613 Transcript missense_variant 109/641 73/378 25/125 R/C Cgc/Tgc COSM398527 1 1 COA6 HGNC HGNC:18025 protein_coding CCDS31059.1 ENSP00000355572 Q5JTJ3 UPI000015FF99 NM_001012985.2 deleterious_low_confidence(0.03) 1/3 1 MODERATE SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 234373791 234373791 C T 1 0 0 0 0 1 0 0 0 3439 884 31 1 1 COA6 1 234373791 Missense_Mutation SNP C C3N-00175_T 4779413 234373791 14582631 151 9743 LYST 0 . GRCh38 1 235702800 235702800 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.10321G>T p.Val3441Leu p.V3441L ENST00000389793 45/53 568 519 49 387 387 0 strelka-varscan-mutect LYST,missense_variant,p.Val3441Leu,ENST00000389793,NM_000081.3,NM_001301365.1;LYST,3_prime_UTR_variant,,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000473037,; A ENST00000389793 Transcript missense_variant 10496/13480 10321/11406 3441/3801 V/L Gtg/Ttg 1 -1 LYST HGNC HGNC:1968 protein_coding YES CCDS31062.1 ENSP00000374443 Q99698 UPI000020509E NM_000081.3,NM_001301365.1 deleterious(0.02) 45/53 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF86 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 235702800 235702800 C A 1 0 0 0 0 1 0 0 0 9041 565 20 2 2 LYST 1 235702800 Missense_Mutation SNP C C3N-00175_T 1329009 235702800 13253622 152 9744 ACTN2 0 . GRCh38 1 236749162 236749162 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1554C>A p.His518Gln p.H518Q ENST00000542672 14/21 550 412 138 497 497 0 strelka-varscan-mutect ACTN2,missense_variant,p.His310Gln,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.His518Gln,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.His518Gln,ENST00000366578,NM_001103.3;ACTN2,downstream_gene_variant,,ENST00000492634,;ACTN2,upstream_gene_variant,,ENST00000461367,;ACTN2,downstream_gene_variant,,ENST00000492101,; A ENST00000542672 Transcript missense_variant 1774/4906 1554/2685 518/894 H/Q caC/caA 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.29) 14/21 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 236749162 236749162 C A 1 0 0 0 0 1 0 0 0 249 506 18 2 2 ACTN2 1 236749162 Missense_Mutation SNP C C3N-00175_T 1046362 236749162 12207260 153 9745 ACTN2 0 . GRCh38 1 236751552 236751552 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1739A>T p.Asn580Ile p.N580I ENST00000542672 15/21 413 310 103 329 329 0 strelka-varscan-mutect ACTN2,missense_variant,p.Asn372Ile,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Asn580Ile,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Asn580Ile,ENST00000366578,NM_001103.3;ACTN2,upstream_gene_variant,,ENST00000461367,;ACTN2,downstream_gene_variant,,ENST00000492101,; T ENST00000542672 Transcript missense_variant 1959/4906 1739/2685 580/894 N/I aAc/aTc 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.12) 15/21 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 236751552 236751552 A T 1 0 0 0 0 1 0 0 0 249 43 2 4 4 ACTN2 1 236751552 Missense_Mutation SNP A C3N-00175_T 2390 236751552 12204870 154 9746 RYR2 0 . GRCh38 1 237610818 237610818 + Silent SNP G G T rs79811945 C3N-00175_T C3N-00175_N G G c.4740G>T p.= p.P1580P ENST00000366574 36/105 229 204 25 156 156 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,; T ENST00000366574 Transcript synonymous_variant 5057/16562 4740/14904 1580/4967 P ccG/ccT rs79811945,COSM3677622,COSM3677623 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 36/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 0,1,1 LOW 1 SNV 1 1,1,1 1 PASS rs79811945 . 0 203 0 4 0 0 0 2 -5.823338 0 0 1 0 0 T 2 4 39 237610818 237610818 G T 1 0 0 0 0 0 0 0 1 14029 1074 38 1 1 RYR2 1 237610818 Silent SNP G C3N-00175_T 859266 237610818 11345604 155 9747 RYR2 0 . GRCh38 1 237638441 237638441 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.6877G>T p.Val2293Phe p.V2293F ENST00000366574 45/105 358 322 36 287 287 0 strelka-varscan-mutect RYR2,missense_variant,p.Val2293Phe,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Val2277Phe,ENST00000360064,; T ENST00000366574 Transcript missense_variant 7194/16562 6877/14904 2293/4967 V/F Gtt/Ttt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 45/105 Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 237638441 237638441 G T 1 0 0 0 0 1 0 0 0 14029 1029 36 2 2 RYR2 1 237638441 Missense_Mutation SNP G C3N-00175_T 27623 237638441 11317981 156 9748 RYR2 0 . GRCh38 1 237783922 237783922 + Silent SNP G G C rs757703714 C3N-00175_T C3N-00175_N G G c.12210G>C p.= p.A4070A ENST00000366574 90/105 412 341 71 281 281 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; C ENST00000366574 Transcript synonymous_variant 12527/16562 12210/14904 4070/4967 A gcG/gcC rs757703714,COSM2048971,COSM4234603,COSM4523584,COSM906259 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 90/105 Gene3D:1.10.238.10,Pfam_domain:PF13833,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Superfamily_domains:SSF47473 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS rs757703714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 237783922 237783922 G C 1 0 0 0 0 0 0 0 1 14029 1103 39 4 4 RYR2 1 237783922 Silent SNP G C3N-00175_T 145481 237783922 11172500 157 9749 RYR2 0 . GRCh38 1 237784109 237784109 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.12397C>T p.= p.L4133L ENST00000366574 90/105 220 192 28 210 210 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 12714/16562 12397/14904 4133/4967 L Ctg/Ttg 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 90/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 237784109 237784109 C T 1 0 0 0 0 0 0 0 1 14029 912 32 3 3 RYR2 1 237784109 Silent SNP C C3N-00175_T 187 237784109 11172313 158 9750 RYR2 0 . GRCh38 1 237819113 237819113 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.14511T>A p.Asp4837Glu p.D4837E ENST00000366574 101/105 206 192 14 149 149 0 strelka-varscan-mutect RYR2,missense_variant,p.Asp4837Glu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp4820Glu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,; A ENST00000366574 Transcript missense_variant 14828/16562 14511/14904 4837/4967 D/E gaT/gaA 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 101/105 Pfam_domain:PF00520,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 237819113 237819113 T A 1 0 0 0 0 1 0 0 0 14029 1461 51 4 4 RYR2 1 237819113 Missense_Mutation SNP T C3N-00175_T 35004 237819113 11137309 159 9751 CHRM3 0 . GRCh38 1 239908762 239908762 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.1311A>T p.= p.T437T ENST00000255380 5/5 417 388 29 370 370 0 strelka-varscan-mutect CHRM3,synonymous_variant,p.=,ENST00000255380,NM_000740.2;CHRM3,synonymous_variant,p.=,ENST00000615928,;CHRM3,downstream_gene_variant,,ENST00000448020,; T ENST00000255380 Transcript synonymous_variant 2090/8780 1311/1773 437/590 T acA/acT 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 5/5 Pfam_domain:PF00001,Prints_domain:PR00540,PROSITE_profiles:PS50262,SMART_domains:SM01381 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 239908762 239908762 A T 1 0 0 0 0 0 0 0 1 3138 175 7 4 4 CHRM3 1 239908762 Silent SNP A C3N-00175_T 2089649 239908762 9047660 160 9752 CEP170 0 . GRCh38 1 243165925 243165925 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2035G>T p.Glu679Ter p.E679* ENST00000366542 13/20 426 384 42 381 381 0 varscan-mutect CEP170,stop_gained,p.Glu679Ter,ENST00000366542,NM_014812.2;CEP170,stop_gained,p.Glu581Ter,ENST00000366544,NM_001042404.1;CEP170,stop_gained,p.Glu581Ter,ENST00000366543,NM_001042405.1;CEP170,stop_gained,p.Glu643Ter,ENST00000336415,;CEP170,upstream_gene_variant,,ENST00000490813,;CEP170,upstream_gene_variant,,ENST00000413359,;CEP170,upstream_gene_variant,,ENST00000464936,;CEP170,downstream_gene_variant,,ENST00000522895,;CEP170,upstream_gene_variant,,ENST00000492145,;RP11-261C10.4,intron_variant,,ENST00000437499,;RP11-261C10.4,intron_variant,,ENST00000422938,;CEP170,non_coding_transcript_exon_variant,,ENST00000451408,;CEP170,downstream_gene_variant,,ENST00000518289,;CEP170,downstream_gene_variant,,ENST00000461671,; A ENST00000366542 Transcript stop_gained 2087/6828 2035/4755 679/1584 E/* Gag/Tag 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 13/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 243165925 243165925 C A 1 0 0 0 0 0 1 0 0 2964 864 30 2 2 CEP170 1 243165925 Nonsense_Mutation SNP C C3N-00175_T 3257163 243165925 5790497 161 9753 SMYD3 0 . GRCh38 1 245764116 245764116 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1110G>T p.= p.G370G ENST00000490107 11/12 207 166 41 197 196 1 strelka-varscan-mutect SMYD3,synonymous_variant,p.=,ENST00000490107,NM_001167740.1;SMYD3,synonymous_variant,p.=,ENST00000630181,NM_022743.2;SMYD3,non_coding_transcript_exon_variant,,ENST00000366517,;SMYD3,non_coding_transcript_exon_variant,,ENST00000470510,;SMYD3,non_coding_transcript_exon_variant,,ENST00000493441,;SMYD3,non_coding_transcript_exon_variant,,ENST00000482592,;SMYD3,intron_variant,,ENST00000483072,;SMYD3,intron_variant,,ENST00000490322,;SMYD3,non_coding_transcript_exon_variant,,ENST00000366516,; A ENST00000490107 Transcript synonymous_variant 1150/1548 1110/1287 370/428 G ggG/ggT 1 -1 SMYD3 HGNC HGNC:15513 protein_coding YES CCDS53486.1 ENSP00000419184 Q9H7B4 UPI000022AFDA NM_001167740.1 11/12 PROSITE_profiles:PS51574,hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF163 LOW 1 SNV 1 1 PASS rs1387414367 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 245764116 245764116 C A 1 0 0 0 0 0 0 0 1 15144 610 22 2 2 SMYD3 1 245764116 Silent SNP C C3N-00175_T 2598191 245764116 3192306 162 9754 SMYD3 0 . GRCh38 1 246335463 246335463 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.240G>T p.Trp80Cys p.W80C ENST00000490107 3/12 249 186 63 171 170 1 strelka-varscan-mutect SMYD3,missense_variant,p.Trp80Cys,ENST00000490107,NM_001167740.1;SMYD3,missense_variant,p.Trp21Cys,ENST00000630181,NM_022743.2;SMYD3,missense_variant,p.Trp80Cys,ENST00000403792,;SMYD3,missense_variant,p.Trp21Cys,ENST00000455277,;SMYD3,missense_variant,p.Trp21Cys,ENST00000453676,;SMYD3,non_coding_transcript_exon_variant,,ENST00000470863,;SMYD3,non_coding_transcript_exon_variant,,ENST00000462422,; A ENST00000490107 Transcript missense_variant 280/1548 240/1287 80/428 W/C tgG/tgT 1 -1 SMYD3 HGNC HGNC:15513 protein_coding YES CCDS53486.1 ENSP00000419184 Q9H7B4 UPI000022AFDA NM_001167740.1 deleterious(0) 3/12 Pfam_domain:PF00856,Pfam_domain:PF01753,PROSITE_patterns:PS01360,PROSITE_profiles:PS50280,PROSITE_profiles:PS50865,PROSITE_profiles:PS51574,hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF163,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 246335463 246335463 C A 1 0 0 0 0 1 0 0 0 15144 740 26 2 2 SMYD3 1 246335463 Missense_Mutation SNP C C3N-00175_T 571347 246335463 2620959 163 9755 ZNF695 0 . GRCh38 1 246999948 246999948 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.130G>T p.Gly44Cys p.G44C ENST00000339986 2/4 225 172 53 199 198 1 strelka-varscan-mutect ZNF695,missense_variant,p.Gly44Cys,ENST00000339986,NM_020394.4;ZNF695,missense_variant,p.Gly44Cys,ENST00000487338,NM_001204221.1;ZNF695,intron_variant,,ENST00000498046,;ZNF670-ZNF695,missense_variant,p.Gly44Cys,ENST00000474541,;ZNF670-ZNF695,missense_variant,p.Gly44Cys,ENST00000465049,;ZNF695,missense_variant,p.Gly44Cys,ENST00000479214,;ZNF695,missense_variant,p.Gly44Cys,ENST00000366504,;ZNF695,missense_variant,p.Gly44Cys,ENST00000491337,; A ENST00000339986 Transcript missense_variant 278/3340 130/1548 44/515 G/C Ggt/Tgt 1 -1 ZNF695 HGNC HGNC:30954 protein_coding YES CCDS44344.1 ENSP00000341236 Q8IW36 UPI0000F734A8 NM_020394.4 deleterious(0) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF119,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 246999948 246999948 C A 1 0 0 0 0 1 0 0 0 18671 594 21 2 2 ZNF695 1 246999948 Missense_Mutation SNP C C3N-00175_T 664485 246999948 1956474 164 9756 NLRP3 0 . GRCh38 1 247425395 247425395 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.1952C>A p.Pro651His p.P651H ENST00000336119 3/9 404 313 91 308 307 1 strelka-varscan-mutect NLRP3,missense_variant,p.Pro651His,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Pro651His,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Pro651His,ENST00000366496,;NLRP3,missense_variant,p.Pro651His,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Pro651His,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Pro651His,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript missense_variant 2698/4170 1952/3111 651/1036 P/H cCc/cAc COSM4938012 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 tolerated(0.14) 3/9 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 247425395 247425395 C A 1 0 0 0 0 1 0 0 0 10516 623 22 2 2 NLRP3 1 247425395 Missense_Mutation SNP C C3N-00175_T 425447 247425395 1531027 165 9757 OR2C3 0 . GRCh38 1 247531972 247531972 + Silent SNP G G A C3N-00175_T C3N-00175_N G G c.540C>T p.= p.C180C ENST00000366487 2/2 268 221 47 260 260 0 strelka-varscan-mutect OR2C3,synonymous_variant,p.=,ENST00000366487,NM_198074.4;OR2C3,synonymous_variant,p.=,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; A ENST00000366487 Transcript synonymous_variant 902/2742 540/963 180/320 C tgC/tgT COSM4709759 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 247531972 247531972 G A 1 0 0 0 0 0 0 0 1 11072 1079 38 1 1 OR2C3 1 247531972 Silent SNP G C3N-00175_T 106577 247531972 1424450 166 9758 OR2C3 0 . GRCh38 1 247532027 247532027 + Missense_Mutation SNP G G T rs562326145 C3N-00175_T C3N-00175_N G G c.485C>A p.Thr162Lys p.T162K ENST00000366487 2/2 337 303 34 288 288 0 strelka-varscan-mutect OR2C3,missense_variant,p.Thr162Lys,ENST00000366487,NM_198074.4;OR2C3,missense_variant,p.Thr162Lys,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; T ENST00000366487 Transcript missense_variant 847/2742 485/963 162/320 T/K aCg/aAg rs562326145,COSM1473755,COSM3977411 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 deleterious(0.01) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1,1 MODERATE SNV 0,1,1 1 PASS rs562326145 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 247532027 247532027 G T 1 0 0 0 0 1 0 0 0 11072 1145 40 1 1 OR2C3 1 247532027 Missense_Mutation SNP G C3N-00175_T 55 247532027 1424395 167 9759 OR13G1 0 . GRCh38 1 247672788 247672788 + Nonsense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.254C>A p.Ser85Ter p.S85* ENST00000359688 1/1 339 315 24 239 239 0 strelka-varscan-mutect OR13G1,stop_gained,p.Ser85Ter,ENST00000359688,NM_001005487.1;RP11-634B7.4,intron_variant,,ENST00000449298,;OR3D1P,downstream_gene_variant,,ENST00000438288,; T ENST00000359688 Transcript stop_gained 254/924 254/924 85/307 S/* tCa/tAa COSM5577633 1 -1 OR13G1 HGNC HGNC:14999 protein_coding YES CCDS31094.1 ENSP00000352717 Q8NGZ3 UPI0000061E5B NM_001005487.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF237,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 247672788 247672788 G T 1 0 0 0 0 0 1 0 0 11018 1294 45 2 2 OR13G1 1 247672788 Nonsense_Mutation SNP G C3N-00175_T 140761 247672788 1283634 168 9760 OR14K1 0 . GRCh38 1 247739220 247739220 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.606C>A p.= p.V202V ENST00000283225 1/1 486 445 41 429 429 0 strelka-varscan-mutect OR14K1,synonymous_variant,p.=,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; A ENST00000283225 Transcript synonymous_variant 606/945 606/945 202/314 V gtC/gtA 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 247739220 247739220 C A 1 0 0 0 0 0 0 0 1 11026 900 32 2 2 OR14K1 1 247739220 Silent SNP C C3N-00175_T 66432 247739220 1217202 169 9761 OR11L1 0 . GRCh38 1 247841328 247841328 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.569C>A p.Ser190Tyr p.S190Y ENST00000355784 1/1 354 282 72 273 273 0 strelka-varscan-mutect OR11L1,missense_variant,p.Ser190Tyr,ENST00000355784,NM_001001959.1; T ENST00000355784 Transcript missense_variant 569/969 569/969 190/322 S/Y tCc/tAc 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 247841328 247841328 G T 1 0 0 0 0 1 0 0 0 11007 1174 41 2 2 OR11L1 1 247841328 Missense_Mutation SNP G C3N-00175_T 102108 247841328 1115094 170 9762 OR11L1 0 . GRCh38 1 247841661 247841661 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.236C>T p.Pro79Leu p.P79L ENST00000355784 1/1 251 189 62 210 210 0 strelka-varscan-mutect OR11L1,missense_variant,p.Pro79Leu,ENST00000355784,NM_001001959.1; A ENST00000355784 Transcript missense_variant 236/969 236/969 79/322 P/L cCc/cTc 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 247841661 247841661 G A 1 0 0 0 0 1 0 0 0 11007 1232 43 3 3 OR11L1 1 247841661 Missense_Mutation SNP G C3N-00175_T 333 247841661 1114761 171 9763 OR2T8 0 . GRCh38 1 247921939 247921939 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.922G>T p.Ala308Ser p.A308S ENST00000319968 1/1 163 144 19 157 157 0 strelka-varscan-mutect OR2T8,missense_variant,p.Ala308Ser,ENST00000319968,NM_001005522.1; T ENST00000319968 Transcript missense_variant 922/939 922/939 308/312 A/S Gcc/Tcc 1 1 OR2T8 HGNC HGNC:15020 protein_coding YES CCDS31100.1 ENSP00000326225 A6NH00 UPI00001999E3 NM_001005522.1 tolerated(0.83) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 247921939 247921939 G T 1 0 0 0 0 1 0 0 0 11107 1203 42 2 2 OR2T8 1 247921939 Missense_Mutation SNP G C3N-00175_T 80278 247921939 1034483 172 9764 OR2M2 0 . GRCh38 1 248180509 248180509 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.524C>T p.Ala175Val p.A175V ENST00000359682 1/1 369 292 77 284 284 0 strelka-varscan-mutect OR2M2,missense_variant,p.Ala175Val,ENST00000359682,NM_001004688.1; T ENST00000359682 Transcript missense_variant 524/1044 524/1044 175/347 A/V gCc/gTc COSM680461 1 1 OR2M2 HGNC HGNC:8268 protein_coding YES CCDS31106.1 ENSP00000352710 Q96R28 A0A126GWI7 UPI00001612E4 NM_001004688.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 248180509 248180509 C T 1 0 0 0 0 1 0 0 0 11088 739 26 3 3 OR2M2 1 248180509 Missense_Mutation SNP C C3N-00175_T 258570 248180509 775913 173 9765 OR2T33 0 . GRCh38 1 248273145 248273145 + Missense_Mutation SNP G G T rs776709960 C3N-00175_T C3N-00175_N G G c.670C>A p.Leu224Met p.L224M ENST00000318021 1/1 209 184 25 162 162 0 varscan-mutect OR2T33,missense_variant,p.Leu224Met,ENST00000318021,NM_001004695.1; T ENST00000318021 Transcript missense_variant 670/963 670/963 224/320 L/M Ctg/Atg rs776709960 1 -1 OR2T33 HGNC HGNC:31255 protein_coding YES CCDS31109.1 ENSP00000324687 Q8NG76 UPI000004B237 NM_001004695.1 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs776709960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 248273145 248273145 G T 1 0 0 0 0 1 0 0 0 11101 933 33 2 2 OR2T33 1 248273145 Missense_Mutation SNP G C3N-00175_T 92636 248273145 683277 174 9766 OR2M7 0 . GRCh38 1 248323936 248323936 + Silent SNP A A C novel C3N-00175_T C3N-00175_N A A c.633T>G p.= p.V211V ENST00000317965 1/1 476 375 101 413 413 0 strelka-varscan-mutect OR2M7,synonymous_variant,p.=,ENST00000317965,NM_001004691.1; C ENST00000317965 Transcript synonymous_variant 633/939 633/939 211/312 V gtT/gtG 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 248323936 248323936 A C 1 0 0 0 0 0 0 0 1 11092 117 5 5 5 OR2M7 1 248323936 Silent SNP A C3N-00175_T 50791 248323936 632486 175 9767 OR2T3 0 . GRCh38 1 248474079 248474079 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.729G>T p.Leu243Phe p.L243F ENST00000359594 1/1 176 147 29 160 159 1 strelka-varscan-mutect OR2T3,missense_variant,p.Leu243Phe,ENST00000359594,NM_001005495.1; T ENST00000359594 Transcript missense_variant 729/957 729/957 243/318 L/F ttG/ttT 1 1 OR2T3 HGNC HGNC:14727 protein_coding YES CCDS31117.1 ENSP00000352604 Q8NH03 A0A126GVW5 UPI00001D7CA5 NM_001005495.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF4,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 248474079 248474079 G T 1 0 0 0 0 1 0 0 0 11100 1339 47 2 2 OR2T3 1 248474079 Missense_Mutation SNP G C3N-00175_T 150143 248474079 482343 176 9768 ZNF672 0 . GRCh38 1 248847337 248847337 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.63G>A p.= p.K21K ENST00000306562 4/4 214 200 14 187 187 0 strelka-varscan-mutect ZNF672,synonymous_variant,p.=,ENST00000306562,NM_024836.2;ZNF672,synonymous_variant,p.=,ENST00000428515,;ZNF672,synonymous_variant,p.=,ENST00000423362,;ZNF692,downstream_gene_variant,,ENST00000451251,NM_001136036.2;ZNF692,downstream_gene_variant,,ENST00000306601,NM_017865.3;ZNF692,downstream_gene_variant,,ENST00000366471,NM_001193328.1;ZNF692,downstream_gene_variant,,ENST00000476503,;ZNF672,downstream_gene_variant,,ENST00000505503,;ZNF672,downstream_gene_variant,,ENST00000502697,;ZNF672,downstream_gene_variant,,ENST00000510904,;ZNF672,downstream_gene_variant,,ENST00000515369,;ZNF692,downstream_gene_variant,,ENST00000463519,;ZNF692,downstream_gene_variant,,ENST00000533927,;ZNF692,downstream_gene_variant,,ENST00000412341,;ZNF692,downstream_gene_variant,,ENST00000470787,;ZNF692,downstream_gene_variant,,ENST00000477070,;ZNF692,downstream_gene_variant,,ENST00000474351,;ZNF692,downstream_gene_variant,,ENST00000482023,;ZNF692,downstream_gene_variant,,ENST00000462037,; A ENST00000306562 Transcript synonymous_variant 809/2989 63/1359 21/452 K aaG/aaA 1 1 ZNF672 HGNC HGNC:26179 protein_coding YES CCDS1638.1 ENSP00000421915 Q499Z4 UPI0000070D6C NM_024836.2 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 248847337 248847337 G A 1 0 0 0 0 0 0 0 1 18653 933 33 3 3 ZNF672 1 248847337 Silent SNP G C3N-00175_T 373258 248847337 109085 177 9769 PXDN 0 . GRCh38 2 1643556 1643556 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.3764G>T p.Gly1255Val p.G1255V ENST00000252804 19/23 165 120 45 193 193 0 strelka-varscan-mutect PXDN,missense_variant,p.Gly1255Val,ENST00000252804,NM_012293.2;PXDN,non_coding_transcript_exon_variant,,ENST00000477093,;PXDN,non_coding_transcript_exon_variant,,ENST00000478155,;PXDN,upstream_gene_variant,,ENST00000453308,; A ENST00000252804 Transcript missense_variant 3815/6808 3764/4440 1255/1479 G/V gGg/gTg 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 deleterious(0) 19/23 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF75,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 1643556 1643556 C A 1 0 0 0 0 1 0 0 0 13001 623 22 2 2 PXDN 2 1643556 Missense_Mutation SNP C C3N-00175_T 1643556 240549973 178 9770 KIDINS220 0 . GRCh38 2 8788675 8788675 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1759G>C p.Glu587Gln p.E587Q ENST00000256707 15/30 103 91 12 145 145 0 strelka-varscan-mutect KIDINS220,missense_variant,p.Glu587Gln,ENST00000256707,NM_020738.2;KIDINS220,missense_variant,p.Glu587Gln,ENST00000473731,;KIDINS220,missense_variant,p.Glu588Gln,ENST00000489024,;KIDINS220,missense_variant,p.Glu588Gln,ENST00000319688,;KIDINS220,missense_variant,p.Glu334Gln,ENST00000496383,;KIDINS220,3_prime_UTR_variant,,ENST00000488729,;KIDINS220,downstream_gene_variant,,ENST00000474782,; G ENST00000256707 Transcript missense_variant 1941/7361 1759/5316 587/1771 E/Q Gag/Cag 1 -1 KIDINS220 HGNC HGNC:29508 protein_coding YES CCDS42650.1 ENSP00000256707 Q9ULH0 UPI0000208E08 NM_020738.2 tolerated(0.23) 15/30 Pfam_domain:PF07693,hmmpanther:PTHR24116 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -18.81212 0.9999968 1 1 1 0 G 3 3 39 8788675 8788675 C G 1 0 0 0 0 1 0 0 0 8135 922 32 4 4 KIDINS220 2 8788675 Missense_Mutation SNP C C3N-00175_T 7145119 8788675 233404854 179 9771 ASAP2 0 . GRCh38 2 9358840 9358840 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1412C>A p.Ser471Tyr p.S471Y ENST00000281419 15/28 172 125 47 192 191 1 strelka-varscan-mutect ASAP2,missense_variant,p.Ser471Tyr,ENST00000281419,NM_003887.2;ASAP2,missense_variant,p.Ser471Tyr,ENST00000315273,NM_001135191.1;ASAP2,downstream_gene_variant,,ENST00000471687,; A ENST00000281419 Transcript missense_variant 1752/5712 1412/3021 471/1006 S/Y tCc/tAc 1 1 ASAP2 HGNC HGNC:2721 protein_coding YES CCDS1661.1 ENSP00000281419 O43150 UPI0000073459 NM_003887.2 deleterious(0) 15/28 PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF238,Pfam_domain:PF01412,SMART_domains:SM00105,Superfamily_domains:SSF57863 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999981 1 1 1 0 A 3 1 39 9358840 9358840 C A 1 0 0 0 0 1 0 0 0 1153 855 30 2 2 ASAP2 2 9358840 Missense_Mutation SNP C C3N-00175_T 570165 9358840 232834689 180 9772 APOB 0 . GRCh38 2 21007255 21007255 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.9613G>C p.Asp3205His p.D3205H ENST00000233242 26/29 111 99 12 121 121 0 strelka-varscan-mutect APOB,missense_variant,p.Asp3205His,ENST00000233242,NM_000384.2; G ENST00000233242 Transcript missense_variant 9741/14121 9613/13692 3205/4563 D/H Gac/Cac 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.09) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.39634 0.9999999 1 1 1 0 G 3 3 39 21007255 21007255 C G 1 0 0 0 0 1 0 0 0 907 826 29 4 4 APOB 2 21007255 Missense_Mutation SNP C C3N-00175_T 11648415 21007255 221186274 181 9773 APOB 0 . GRCh38 2 21042386 21042386 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.212G>T p.Arg71Ile p.R71I ENST00000233242 3/29 561 436 125 547 547 0 strelka-varscan-mutect APOB,missense_variant,p.Arg71Ile,ENST00000233242,NM_000384.2;APOB,missense_variant,p.Arg71Ile,ENST00000399256,; A ENST00000233242 Transcript missense_variant 340/14121 212/13692 71/4563 R/I aGa/aTa 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 3/29 PROSITE_profiles:PS51211,hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF01347,Gene3D:1lshA01,SMART_domains:SM00638,Superfamily_domains:SSF56968 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 21042386 21042386 C A 1 0 0 0 0 1 0 0 0 907 913 32 2 2 APOB 2 21042386 Missense_Mutation SNP C C3N-00175_T 35131 21042386 221151143 182 9774 KHK 0 . GRCh38 2 27094556 27094556 + Missense_Mutation SNP G G A rs565695602 C3N-00175_T C3N-00175_N G G c.289G>A p.Ala97Thr p.A97T ENST00000260599 3/8 466 416 50 547 547 0 strelka-varscan-mutect KHK,missense_variant,p.Ala97Thr,ENST00000260599,NM_000221.2;KHK,missense_variant,p.Ala97Thr,ENST00000429697,;KHK,intron_variant,,ENST00000260598,NM_006488.2;CGREF1,downstream_gene_variant,,ENST00000402550,NM_001166240.1;KHK,non_coding_transcript_exon_variant,,ENST00000490823,;KHK,non_coding_transcript_exon_variant,,ENST00000469936,;CGREF1,downstream_gene_variant,,ENST00000440612,;KHK,upstream_gene_variant,,ENST00000464371,; A ENST00000260599 Transcript missense_variant 802/2411 289/897 97/298 A/T Gcc/Acc rs565695602 1 1 KHK HGNC HGNC:6315 protein_coding YES CCDS1734.1 ENSP00000260599 P50053 A0A140VJM6 UPI000012DE02 NM_000221.2 deleterious(0) 3/8 Gene3D:3.40.1190.20,Pfam_domain:PF00294,hmmpanther:PTHR10584,hmmpanther:PTHR10584:SF177,Superfamily_domains:SSF53613 MODERATE 1 SNV 1 1 PASS rs565695602 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 27094556 27094556 G A 1 0 0 0 0 1 0 0 0 8070 1087 38 1 1 KHK 2 27094556 Missense_Mutation SNP G C3N-00175_T 6052170 27094556 215098973 183 9775 FAM179A 0 . GRCh38 2 29002701 29002701 + Missense_Mutation SNP C C A rs376377047 C3N-00175_T C3N-00175_N C C c.593C>A p.Pro198Gln p.P198Q ENST00000379558 5/20 227 187 40 304 304 0 strelka-varscan-mutect FAM179A,missense_variant,p.Pro198Gln,ENST00000379558,NM_199280.2;FAM179A,intron_variant,,ENST00000401723,;FAM179A,downstream_gene_variant,,ENST00000420297,; A ENST00000379558 Transcript missense_variant 944/12691 593/3060 198/1019 P/Q cCg/cAg rs376377047 1 1 FAM179A HGNC HGNC:33715 protein_coding YES CCDS1769.2 ENSP00000368876 Q6ZUX3 UPI00014F7B81 NM_199280.2 tolerated(0.15) 5/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF42 MODERATE 1 SNV 5 1 PASS rs376377047 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 29002701 29002701 C A 1 0 0 0 0 1 0 0 0 5350 652 23 1 1 FAM179A 2 29002701 Missense_Mutation SNP C C3N-00175_T 1908145 29002701 213190828 184 9776 ALK 0 . GRCh38 2 29226958 29226958 + Missense_Mutation SNP C C A rs587778021 C3N-00175_T C3N-00175_N C C c.3031G>T p.Gly1011Trp p.G1011W ENST00000389048 18/29 442 344 98 440 439 1 strelka-varscan-mutect ALK,missense_variant,p.Gly1011Trp,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Gly634Trp,ENST00000618119,;ALK,upstream_gene_variant,,ENST00000431873,;ALK,upstream_gene_variant,,ENST00000453137,; A ENST00000389048 Transcript missense_variant 3938/6220 3031/4863 1011/1620 G/W Ggg/Tgg rs587778021 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 deleterious(0) 18/29 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF276 not_provided MODERATE 1 SNV 1 1 1 PASS rs587778021 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 29226958 29226958 C A 1 0 0 0 0 1 0 0 0 625 652 23 1 1 ALK 2 29226958 Missense_Mutation SNP C C3N-00175_T 224257 29226958 212966571 185 9777 CAPN14 0 . GRCh38 2 31177043 31177043 + Missense_Mutation SNP C C A rs375553136 C3N-00175_T C3N-00175_N C C c.1955G>T p.Arg652Leu p.R652L ENST00000403897 20/22 121 99 22 160 160 0 strelka-varscan-mutect CAPN14,missense_variant,p.Arg652Leu,ENST00000403897,NM_001145122.1;CAPN14,3_prime_UTR_variant,,ENST00000398824,NM_001321270.1; A ENST00000403897 Transcript missense_variant 2097/2197 1955/2055 652/684 R/L cGt/cTt rs375553136 1 -1 CAPN14 HGNC HGNC:16664 protein_coding YES CCDS46254.1 ENSP00000385247 A8MX76 UPI000173A463 NM_001145122.1 deleterious(0.02) 20/22 PROSITE_profiles:PS50222,hmmpanther:PTHR10183:SF302,hmmpanther:PTHR10183,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 2 1 PASS rs375553136 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 31177043 31177043 C A 1 0 0 0 0 1 0 0 0 2319 536 19 1 1 CAPN14 2 31177043 Missense_Mutation SNP C C3N-00175_T 1950085 31177043 211016486 186 9778 EHD3 0 . GRCh38 2 31260736 31260736 + Silent SNP C C A rs758911736 C3N-00175_T C3N-00175_N C C c.729C>A p.= p.I243I ENST00000322054 4/6 124 99 25 177 177 0 strelka-varscan-mutect EHD3,synonymous_variant,p.=,ENST00000322054,NM_014600.2; A ENST00000322054 Transcript synonymous_variant 1014/4636 729/1608 243/535 I atC/atA rs758911736,COSM3407818 1 1 EHD3 HGNC HGNC:3244 protein_coding YES CCDS1774.1 ENSP00000327116 Q9NZN3 UPI0000140D07 NM_014600.2 4/6 PROSITE_profiles:PS51718,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF67,Superfamily_domains:SSF52540 0,1 LOW 1 SNV 1 0,1 1 PASS rs758911736 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 31260736 31260736 C A 1 0 0 0 0 0 0 0 1 4815 874 31 1 1 EHD3 2 31260736 Silent SNP C C3N-00175_T 83693 31260736 210932793 187 9779 MEMO1 0 . GRCh38 2 31883408 31883408 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.635C>T p.Ser212Phe p.S212F ENST00000295065 7/9 99 84 15 175 175 0 strelka-varscan-mutect MEMO1,missense_variant,p.Ser212Phe,ENST00000295065,NM_015955.3;MEMO1,missense_variant,p.Ser215Phe,ENST00000379383,;MEMO1,missense_variant,p.Ser212Phe,ENST00000404530,NM_001301833.1;MEMO1,missense_variant,p.Ser189Phe,ENST00000426310,NM_001137602.2;DPY30,non_coding_transcript_exon_variant,,ENST00000446765,;MEMO1,intron_variant,,ENST00000490459,;MEMO1,intron_variant,,ENST00000422936,; A ENST00000295065 Transcript missense_variant 945/4505 635/894 212/297 S/F tCc/tTc 1 -1 MEMO1 HGNC HGNC:14014 protein_coding YES CCDS1776.1 ENSP00000295065 Q9Y316 UPI0000001C55 NM_015955.3 deleterious(0) 7/9 HAMAP:MF_00055,Pfam_domain:PF01875,hmmpanther:PTHR11060,hmmpanther:PTHR11060:SF0,TIGRFAM_domain:TIGR04336 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 31883408 31883408 G A 1 0 0 0 0 1 0 0 0 9416 1174 41 3 3 MEMO1 2 31883408 Missense_Mutation SNP G C3N-00175_T 622672 31883408 210310121 188 9780 HEATR5B 0 . GRCh38 2 37065755 37065755 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1333G>T p.Gly445Trp p.G445W ENST00000233099 9/36 68 56 12 76 76 0 strelka-varscan-mutect HEATR5B,missense_variant,p.Gly445Trp,ENST00000233099,NM_019024.2; A ENST00000233099 Transcript missense_variant,splice_region_variant 1429/6905 1333/6216 445/2071 G/W Ggg/Tgg 1 -1 HEATR5B HGNC HGNC:29273 protein_coding YES CCDS33181.1 ENSP00000233099 Q9P2D3 UPI0000160DCD NM_019024.2 deleterious(0) 9/36 Gene3D:1.25.10.10,hmmpanther:PTHR21663,hmmpanther:PTHR21663:SF2,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999877 1 1 1 0 A 3 1 39 37065755 37065755 C A 1 0 0 0 0 1 0 0 0 6914 695 24 2 2 HEATR5B 2 37065755 Missense_Mutation SNP C C3N-00175_T 5182347 37065755 205127774 189 9781 EIF2AK2 0 . GRCh38 2 37141623 37141623 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.319A>G p.Arg107Gly p.R107G ENST00000233057 5/17 187 147 40 229 229 0 strelka-varscan-mutect EIF2AK2,missense_variant,p.Arg107Gly,ENST00000233057,;EIF2AK2,missense_variant,p.Arg107Gly,ENST00000395127,NM_001135651.2,NM_002759.3;EIF2AK2,missense_variant,p.Arg107Gly,ENST00000405334,NM_001135652.2;EIF2AK2,missense_variant,p.Arg107Gly,ENST00000411537,;EIF2AK2,downstream_gene_variant,,ENST00000390013,;EIF2AK2,non_coding_transcript_exon_variant,,ENST00000496059,; C ENST00000233057 Transcript missense_variant 642/10042 319/1656 107/551 R/G Aga/Gga 1 -1 EIF2AK2 HGNC HGNC:9437 protein_coding YES CCDS1786.1 ENSP00000233057 P19525 UPI000000D925 deleterious(0.02) 5/17 Gene3D:3.30.160.20,Pfam_domain:PF00035,PROSITE_profiles:PS50137,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF102,SMART_domains:SM00358,Superfamily_domains:SSF54768 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 37141623 37141623 T C 1 0 0 0 0 1 0 0 0 4833 1530 53 5 5 EIF2AK2 2 37141623 Missense_Mutation SNP T C3N-00175_T 75868 37141623 205051906 190 9782 ARHGEF33 0 . GRCh38 2 38958069 38958069 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1406C>T p.Ser469Phe p.S469F ENST00000409978 15/18 165 137 28 194 194 0 strelka-varscan-mutect ARHGEF33,missense_variant,p.Ser469Phe,ENST00000409978,;ARHGEF33,missense_variant,p.Ser469Phe,ENST00000398800,NM_001145451.2;ARHGEF33,upstream_gene_variant,,ENST00000433605,;ARHGEF33,upstream_gene_variant,,ENST00000411874,;RP11-173C1.1,downstream_gene_variant,,ENST00000601251,;ARHGEF33,non_coding_transcript_exon_variant,,ENST00000483305,;ARHGEF33,upstream_gene_variant,,ENST00000430382,;ARHGEF33,non_coding_transcript_exon_variant,,ENST00000486958,; T ENST00000409978 Transcript missense_variant 1671/4484 1406/2613 469/870 S/F tCc/tTc 1 1 ARHGEF33 HGNC HGNC:37252 protein_coding YES CCDS46263.2 ENSP00000387020 A8MVX0 UPI000188157A deleterious_low_confidence(0) 15/18 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 38958069 38958069 C T 1 0 0 0 0 1 0 0 0 1038 855 30 3 3 ARHGEF33 2 38958069 Missense_Mutation SNP C C3N-00175_T 1816446 38958069 203235460 191 9783 SRBD1 0 . GRCh38 2 45562710 45562710 + Frame_Shift_Del DEL T T - C3N-00175_T C3N-00175_N T T c.1352delA p.Lys451ArgfsTer8 p.K451Rfs*8 ENST00000263736 10/21 92 77 15 93 93 0 sindel-varindel-pindel SRBD1,frameshift_variant,p.Lys451ArgfsTer8,ENST00000263736,NM_018079.4;SRBD1,non_coding_transcript_exon_variant,,ENST00000493649,; - ENST00000263736 Transcript frameshift_variant 1415/3681 1352/2988 451/995 K/X aAg/ag COSM1306824 1 -1 SRBD1 HGNC HGNC:25521 protein_coding YES CCDS1823.1 ENSP00000263736 Q8N5C6 UPI000004CC06 NM_018079.4 10/21 Superfamily_domains:0054854,Gene3D:3bzcA02,hmmpanther:PTHR10724,hmmpanther:PTHR10724:SF1 1 HIGH 1 deletion 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 45562710 45562710 T - 1 0 1 0 1 0 0 0 0 15491 1609 56 0 0 SRBD1 2 45562710 Frame_Shift_Del DEL T C3N-00175_T 6604641 45562710 196630819 192 9784 ASB3 0 . GRCh38 2 53750918 53750918 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.220A>G p.Met74Val p.M74V ENST00000263634 3/10 91 73 18 73 73 0 strelka-varscan-mutect ASB3,start_lost,p.Met1?,ENST00000406687,NM_001201965.1;ASB3,start_lost,p.Met1?,ENST00000394717,NM_145863.2;ASB3,missense_variant,p.Met67Val,ENST00000406053,;ASB3,missense_variant,p.Met74Val,ENST00000263634,NM_016115.4;GPR75-ASB3,missense_variant,p.Met112Val,ENST00000406625,NM_001164165.1;ASB3,non_coding_transcript_exon_variant,,ENST00000482829,;ASB3,non_coding_transcript_exon_variant,,ENST00000482134,;ASB3,non_coding_transcript_exon_variant,,ENST00000480522,;ASB3,non_coding_transcript_exon_variant,,ENST00000470916,;ASB3,non_coding_transcript_exon_variant,,ENST00000489508,;GPR75-ASB3,non_coding_transcript_exon_variant,,ENST00000459916,;GPR75-ASB3,intron_variant,,ENST00000498475,; C ENST00000263634 Transcript missense_variant 355/2214 220/1557 74/518 M/V Atg/Gtg 1 -1 ASB3 HGNC HGNC:16013 protein_coding YES CCDS1846.1 ENSP00000263634 Q9Y575 A0A0A6YY97 UPI00001260E7 NM_016115.4 tolerated(0.1) 3/10 PROSITE_profiles:PS50297,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF39,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 53750918 53750918 T C 1 0 0 0 0 1 0 0 0 1166 1435 50 5 5 ASB3 2 53750918 Missense_Mutation SNP T C3N-00175_T 8188208 53750918 188442611 193 9785 WDR92 0 . GRCh38 2 68157322 68157322 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.122G>T p.Arg41Leu p.R41L ENST00000295121 1/8 160 118 42 190 189 1 strelka-varscan-mutect WDR92,missense_variant,p.Arg41Leu,ENST00000295121,NM_138458.3;WDR92,missense_variant,p.Arg41Leu,ENST00000409164,NM_001256476.1;WDR92,intron_variant,,ENST00000406245,;PNO1,upstream_gene_variant,,ENST00000263657,NM_020143.2;WDR92,intron_variant,,ENST00000492039,;RP11-474G23.1,3_prime_UTR_variant,,ENST00000406334,;WDR92,non_coding_transcript_exon_variant,,ENST00000468984,;PNO1,upstream_gene_variant,,ENST00000430742,; A ENST00000295121 Transcript missense_variant 239/2626 122/1074 41/357 R/L cGg/cTg 1 -1 WDR92 HGNC HGNC:25176 protein_coding YES CCDS1884.1 ENSP00000295121 Q96MX6 A0A140VK67 UPI000006F50D NM_138458.3 deleterious(0) 1/8 Gene3D:2.130.10.10,hmmpanther:PTHR10971,hmmpanther:PTHR10971:SF2,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1417716311 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 68157322 68157322 C A 1 0 0 0 0 1 0 0 0 17895 652 23 1 1 WDR92 2 68157322 Missense_Mutation SNP C C3N-00175_T 14406404 68157322 174036207 194 9786 ANTXR1 0 . GRCh38 2 69245468 69245468 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1678C>G p.Pro560Ala p.P560A ENST00000303714 18/18 113 82 31 93 93 0 strelka-varscan-mutect ANTXR1,missense_variant,p.Pro560Ala,ENST00000303714,NM_032208.2; G ENST00000303714 Transcript missense_variant 2000/5859 1678/1695 560/564 P/A Cca/Gca 1 1 ANTXR1 HGNC HGNC:21014 protein_coding YES CCDS1892.1 ENSP00000301945 Q9H6X2 UPI0000049806 NM_032208.2 deleterious_low_confidence(0) 18/18 Prints_domain:PR01217,hmmpanther:PTHR16059,hmmpanther:PTHR16059:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 69245468 69245468 C G 1 0 0 0 0 1 0 0 0 818 855 30 4 4 ANTXR1 2 69245468 Missense_Mutation SNP C C3N-00175_T 1088146 69245468 172948061 195 9787 ATP6V1B1 0 . GRCh38 2 70958070 70958070 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.199C>T p.His67Tyr p.H67Y ENST00000234396 3/14 464 369 95 489 489 0 strelka-varscan-mutect ATP6V1B1,missense_variant,p.His67Tyr,ENST00000234396,NM_001692.3;ATP6V1B1,missense_variant,p.His67Tyr,ENST00000412314,;ATP6V1B1,missense_variant,p.His84Tyr,ENST00000454446,;ATP6V1B1,5_prime_UTR_variant,,ENST00000432098,;AC007040.11,intron_variant,,ENST00000606025,;ATP6V1B1,missense_variant,p.His67Tyr,ENST00000432367,;ATP6V1B1,non_coding_transcript_exon_variant,,ENST00000463380,;AC007040.11,intron_variant,,ENST00000453130,;ATP6V1B1,upstream_gene_variant,,ENST00000495118,;TCEB1P21,upstream_gene_variant,,ENST00000412558,; T ENST00000234396 Transcript missense_variant 272/1891 199/1542 67/513 H/Y Cac/Tac 1 1 ATP6V1B1 HGNC HGNC:853 protein_coding YES CCDS1912.1 ENSP00000234396 P15313 UPI000013C9A0 NM_001692.3 deleterious(0.02) 3/14 HAMAP:MF_00310,hmmpanther:PTHR15184,hmmpanther:PTHR15184:SF29,TIGRFAM_domain:TIGR01040,PIRSF_domain:PIRSF039114,Pfam_domain:PF02874 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 70958070 70958070 C T 1 0 0 0 0 1 0 0 0 1331 594 21 3 3 ATP6V1B1 2 70958070 Missense_Mutation SNP C C3N-00175_T 1712602 70958070 171235459 196 9788 ANKRD53 0 . GRCh38 2 70978812 70978812 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.167C>A p.Pro56His p.P56H ENST00000360589 1/6 88 65 23 114 114 0 strelka-varscan-mutect ANKRD53,missense_variant,p.Pro56His,ENST00000272421,NM_024933.3;ANKRD53,missense_variant,p.Pro56His,ENST00000441349,;ANKRD53,missense_variant,p.Pro56His,ENST00000457410,;ANKRD53,missense_variant,p.Pro56His,ENST00000360589,NM_001115116.1;AC007040.11,intron_variant,,ENST00000606025,;AC007040.11,intron_variant,,ENST00000453130,;ANKRD53,upstream_gene_variant,,ENST00000496088,;ANKRD53,upstream_gene_variant,,ENST00000460927,;ANKRD53,upstream_gene_variant,,ENST00000483334,; A ENST00000360589 Transcript missense_variant 201/1666 167/1593 56/530 P/H cCc/cAc 1 1 ANKRD53 HGNC HGNC:25691 protein_coding YES CCDS46321.1 ENSP00000353796 Q8N9V6 UPI000013D952 NM_001115116.1 deleterious_low_confidence(0) 1/6 hmmpanther:PTHR24160 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 70978812 70978812 C A 1 0 0 0 0 1 0 0 0 783 637 22 2 2 ANKRD53 2 70978812 Missense_Mutation SNP C C3N-00175_T 20742 70978812 171214717 197 9789 EXOC6B 0 . GRCh38 2 72492403 72492403 + Missense_Mutation SNP C C A rs755839202 C3N-00175_T C3N-00175_N C C c.1580G>T p.Arg527Leu p.R527L ENST00000272427 16/22 121 105 16 137 137 0 strelka-varscan-mutect EXOC6B,missense_variant,p.Arg527Leu,ENST00000272427,NM_001321729.1,NM_001321734.1,NM_015189.1;EXOC6B,missense_variant,p.Arg527Leu,ENST00000410104,;EXOC6B,missense_variant,p.Arg527Leu,ENST00000634650,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000464347,;EXOC6B,downstream_gene_variant,,ENST00000410112,; A ENST00000272427 Transcript missense_variant 1711/5918 1580/2436 527/811 R/L cGg/cTg rs755839202 1 -1 EXOC6B HGNC HGNC:17085 protein_coding YES CCDS46333.1 ENSP00000272427 Q9Y2D4 UPI000046995C NM_001321729.1,NM_001321734.1,NM_015189.1 deleterious(0) 16/22 hmmpanther:PTHR12702:SF3,hmmpanther:PTHR12702,Pfam_domain:PF04091,PIRSF_domain:PIRSF025007 MODERATE 1 SNV 2 1 PASS rs755839202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 72492403 72492403 C A 1 0 0 0 0 1 0 0 0 5177 652 23 1 1 EXOC6B 2 72492403 Missense_Mutation SNP C C3N-00175_T 1513591 72492403 169701126 198 9790 SPR 0 . GRCh38 2 72888377 72888377 + Missense_Mutation SNP A A G C3N-00175_T C3N-00175_N A A c.368A>G p.Tyr123Cys p.Y123C ENST00000234454 2/3 88 71 17 106 106 0 strelka-varscan-mutect SPR,missense_variant,p.Tyr123Cys,ENST00000234454,NM_003124.4;SPR,intron_variant,,ENST00000498749,; G ENST00000234454 Transcript missense_variant 441/1480 368/786 123/261 Y/C tAc/tGc COSM3939154 1 1 SPR HGNC HGNC:11257 protein_coding YES CCDS1920.1 ENSP00000234454 P35270 UPI000004C79D NM_003124.4 deleterious(0) 2/3 Gene3D:3.40.50.720,Pfam_domain:PF00106,hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF398,Superfamily_domains:SSF51735,TIGRFAM_domain:TIGR01500 1 MODERATE 1 SNV 1 1 1 PASS rs1024333245 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 72888377 72888377 A G 1 0 0 0 0 1 0 0 0 15445 391 14 5 5 SPR 2 72888377 Missense_Mutation SNP A C3N-00175_T 395974 72888377 169305152 199 9791 RAB11FIP5 0 . GRCh38 2 73088141 73088141 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1477G>T p.Ala493Ser p.A493S ENST00000258098 3/5 147 101 46 194 193 1 strelka-varscan-mutect RAB11FIP5,missense_variant,p.Ala493Ser,ENST00000486777,;RAB11FIP5,missense_variant,p.Ala493Ser,ENST00000258098,NM_015470.2;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000479196,;RAB11FIP5,upstream_gene_variant,,ENST00000482554,;RAB11FIP5,downstream_gene_variant,,ENST00000475951,; A ENST00000258098 Transcript missense_variant 1718/4342 1477/1962 493/653 A/S Gcc/Tcc 1 -1 RAB11FIP5 HGNC HGNC:24845 protein_coding YES CCDS1923.1 ENSP00000258098 Q9BXF6 UPI000007079C NM_015470.2 tolerated(0.68) 3/5 hmmpanther:PTHR15746:SF14,hmmpanther:PTHR15746 MODERATE 1 SNV 1 1 PASS rs1463924478 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 73088141 73088141 C A 1 0 0 0 0 1 0 0 0 13055 739 26 2 2 RAB11FIP5 2 73088141 Missense_Mutation SNP C C3N-00175_T 199764 73088141 169105388 200 9792 ALMS1 0 . GRCh38 2 73450234 73450234 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.3707C>T p.Ser1236Phe p.S1236F ENST00000613296 8/23 261 205 56 284 284 0 strelka-varscan-mutect ALMS1,missense_variant,p.Ser1236Phe,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Ser1194Phe,ENST00000484298,;ALMS1,missense_variant,p.Ser1236Phe,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; T ENST00000613296 Transcript missense_variant 3818/12925 3707/12507 1236/4168 S/F tCt/tTt 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 tolerated(0.09) 8/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 73450234 73450234 C T 1 0 0 0 0 1 0 0 0 635 913 32 3 3 ALMS1 2 73450234 Missense_Mutation SNP C C3N-00175_T 362093 73450234 168743295 201 9793 GCFC2 0 . GRCh38 2 75702340 75702340 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.478G>T p.Asp160Tyr p.D160Y ENST00000321027 3/17 319 288 31 297 297 0 strelka-varscan-mutect GCFC2,missense_variant,p.Asp160Tyr,ENST00000321027,NM_001201334.1,NM_003203.4;GCFC2,missense_variant,p.Asp160Tyr,ENST00000541687,;GCFC2,missense_variant,p.Asp160Tyr,ENST00000409857,;GCFC2,missense_variant,p.Asp160Tyr,ENST00000470503,NM_001201335.1;GCFC2,intron_variant,,ENST00000442309,;RP11-342K6.3,downstream_gene_variant,,ENST00000604464,;GCFC2,3_prime_UTR_variant,,ENST00000472230,;GCFC2,upstream_gene_variant,,ENST00000470197,; A ENST00000321027 Transcript missense_variant 612/4440 478/2346 160/781 D/Y Gat/Tat COSM5632729 1 -1 GCFC2 HGNC HGNC:1317 protein_coding YES CCDS1961.1 ENSP00000318690 P16383 UPI000013C96B NM_001201334.1,NM_003203.4 deleterious(0) 3/17 hmmpanther:PTHR12214,hmmpanther:PTHR12214:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 75702340 75702340 C A 1 0 0 0 0 1 0 0 0 6158 855 30 2 2 GCFC2 2 75702340 Missense_Mutation SNP C C3N-00175_T 2252106 75702340 166491189 202 9794 DNAH6 0 . GRCh38 2 84525688 84525688 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.349A>G p.Thr117Ala p.T117A ENST00000389394 3/77 138 109 29 197 197 0 strelka-varscan-mutect DNAH6,missense_variant,p.Thr117Ala,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Thr117Ala,ENST00000237449,;DNAH6,non_coding_transcript_exon_variant,,ENST00000468661,;DNAH6,non_coding_transcript_exon_variant,,ENST00000476689,;DNAH6,intron_variant,,ENST00000494025,; G ENST00000389394 Transcript missense_variant 486/12795 349/12477 117/4158 T/A Aca/Gca 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated_low_confidence(0.78) 3/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 84525688 84525688 A G 1 0 0 0 0 1 0 0 0 4420 159 6 5 5 DNAH6 2 84525688 Missense_Mutation SNP A C3N-00175_T 8823348 84525688 157667841 203 9795 TRIM43 0 . GRCh38 2 95594043 95594043 + Missense_Mutation SNP A A T rs755891656 C3N-00175_T C3N-00175_N A A c.20A>T p.His7Leu p.H7L ENST00000272395 2/7 259 190 69 273 273 0 strelka-varscan-mutect TRIM43,missense_variant,p.His7Leu,ENST00000272395,NM_001164464.1,NM_138800.1;RP11-440D17.5,downstream_gene_variant,,ENST00000612987,;AC009237.13,upstream_gene_variant,,ENST00000441078,; T ENST00000272395 Transcript missense_variant 156/1682 20/1341 7/446 H/L cAt/cTt rs755891656 1 1 TRIM43 HGNC HGNC:19015 protein_coding YES CCDS2015.1 ENSP00000272395 Q96BQ3 UPI000006E7BB NM_001164464.1,NM_138800.1 deleterious(0.01) 2/7 Gene3D:3.30.40.10,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF276 MODERATE 1 SNV 1 1 PASS rs755891656 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 95594043 95594043 A T 1 0 0 0 0 1 0 0 0 17008 217 8 4 4 TRIM43 2 95594043 Missense_Mutation SNP A C3N-00175_T 11068355 95594043 146599486 204 9796 ANKRD36C 0 . GRCh38 2 95891683 95891683 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2839G>T p.Gly947Ter p.G947* ENST00000456556 46/67 172 152 20 260 260 0 strelka-varscan-mutect ANKRD36C,stop_gained,p.Gly947Ter,ENST00000456556,;ANKRD36C,stop_gained,p.Gly380Ter,ENST00000295246,;ANKRD36C,3_prime_UTR_variant,,ENST00000534304,;ANKRD36C,non_coding_transcript_exon_variant,,ENST00000531153,; A ENST00000456556 Transcript stop_gained 2924/5428 2839/5337 947/1778 G/* Gga/Tga 1 -1 ANKRD36C HGNC HGNC:32946 protein_coding YES ENSP00000403302 Q5JPF3 UPI00016620F5 46/67 hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF1 HIGH 1 SNV 5 1 PASS . . 0 201 0 2 7 0 0 0 -8.624087 0.2229427 1 1 0 0 A 4 1 39 95891683 95891683 C A 1 0 0 0 0 0 1 0 0 773 603 21 2 2 ANKRD36C 2 95891683 Nonsense_Mutation SNP C C3N-00175_T 297640 95891683 146301846 205 9797 LMAN2L 0 . GRCh38 2 96739879 96739879 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.162G>A p.= p.E54E ENST00000377079 1/9 338 266 72 371 371 0 strelka-varscan-mutect LMAN2L,synonymous_variant,p.=,ENST00000264963,NM_030805.3;LMAN2L,synonymous_variant,p.=,ENST00000377079,NM_001142292.1;LMAN2L,synonymous_variant,p.=,ENST00000434524,;LMAN2L,synonymous_variant,p.=,ENST00000446780,;LMAN2L,synonymous_variant,p.=,ENST00000434865,;LMAN2L,synonymous_variant,p.=,ENST00000449221,;LMAN2L,synonymous_variant,p.=,ENST00000440610,; T ENST00000377079 Transcript synonymous_variant 186/2020 162/1080 54/359 E gaG/gaA 1 -1 LMAN2L HGNC HGNC:19263 protein_coding YES CCDS46365.1 ENSP00000366280 Q9H0V9 UPI000044099B NM_001142292.1 1/9 PROSITE_profiles:PS51328,hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF20,Gene3D:2.60.120.200,Pfam_domain:PF03388,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 96739879 96739879 C T 1 0 0 0 0 0 0 0 1 8763 796 28 3 3 LMAN2L 2 96739879 Silent SNP C C3N-00175_T 848196 96739879 145453650 206 9798 ANKRD36B 0 . GRCh38 2 97540203 97540203 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1912A>T p.Lys638Ter p.K638* ENST00000258459 29/44 140 122 18 193 193 0 strelka-varscan-mutect ANKRD36B,stop_gained,p.Lys638Ter,ENST00000258459,NM_025190.3;ANKRD36B,stop_gained,p.Lys638Ter,ENST00000359901,;ANKRD36B,intron_variant,,ENST00000438709,; A ENST00000258459 Transcript stop_gained,splice_region_variant 2192/5986 1912/4062 638/1353 K/* Aag/Tag 1 -1 ANKRD36B HGNC HGNC:29333 protein_coding YES CCDS74543.1 ENSP00000481149 Q8N2N9 UPI000155D57B NM_025190.3 29/44 hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF18 HIGH 1 SNV 5 1 PASS . . 59 150 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 97540203 97540203 T A 1 0 0 0 0 0 1 0 0 772 1797 62 4 4 ANKRD36B 2 97540203 Nonsense_Mutation SNP T C3N-00175_T 800324 97540203 144653326 207 9799 ZAP70 0 . GRCh38 2 97735263 97735263 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1096G>T p.Val366Leu p.V366L ENST00000264972 10/14 223 209 14 234 234 0 strelka-varscan-mutect ZAP70,missense_variant,p.Val366Leu,ENST00000264972,NM_001079.3;ZAP70,missense_variant,p.Val59Leu,ENST00000451498,NM_207519.1;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000487283,;ZAP70,non_coding_transcript_exon_variant,,ENST00000495754,;ZAP70,downstream_gene_variant,,ENST00000483781,;ZAP70,upstream_gene_variant,,ENST00000489250,;ZAP70,downstream_gene_variant,,ENST00000498836,; T ENST00000264972 Transcript missense_variant 1311/2437 1096/1860 366/619 V/L Gtg/Ttg 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 deleterious(0.02) 10/14 Gene3D:3.30.200.20,Pfam_domain:PF07714,PIRSF_domain:PIRSF000604,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1264869571 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 97735263 97735263 G T 1 0 0 0 0 1 0 0 0 18075 1145 40 1 1 ZAP70 2 97735263 Missense_Mutation SNP G C3N-00175_T 195060 97735263 144458266 208 9800 CNGA3 0 . GRCh38 2 98396320 98396320 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1150G>T p.Asp384Tyr p.D384Y ENST00000393504 8/8 106 82 24 88 88 0 strelka-varscan-mutect CNGA3,missense_variant,p.Asp384Tyr,ENST00000393504,NM_001298.2;CNGA3,missense_variant,p.Asp384Tyr,ENST00000272602,;CNGA3,missense_variant,p.Asp388Tyr,ENST00000409937,;CNGA3,missense_variant,p.Asp366Tyr,ENST00000436404,NM_001079878.1; T ENST00000393504 Transcript missense_variant 1567/3841 1150/2085 384/694 D/Y Gac/Tac 1 1 CNGA3 HGNC HGNC:2150 protein_coding YES CCDS2034.1 ENSP00000377140 Q16281 UPI000004717B NM_001298.2 deleterious(0) 8/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10217:SF390,hmmpanther:PTHR10217,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 98396320 98396320 G T 1 0 0 0 0 1 0 0 0 3378 942 33 2 2 CNGA3 2 98396320 Missense_Mutation SNP G C3N-00175_T 661057 98396320 143797209 209 9801 IL1R2 0 . GRCh38 2 102028288 102028288 + Missense_Mutation SNP G G A rs748144607 C3N-00175_T C3N-00175_N G G c.1093G>A p.Gly365Arg p.G365R ENST00000332549 9/9 90 82 8 115 115 0 strelka-varscan-mutect IL1R2,missense_variant,p.Gly365Arg,ENST00000332549,NM_004633.3;IL1R2,missense_variant,p.Gly365Arg,ENST00000393414,;IL1R2,downstream_gene_variant,,ENST00000441002,NM_001261419.1;IL1R2,non_coding_transcript_exon_variant,,ENST00000485335,;IL1R2,non_coding_transcript_exon_variant,,ENST00000474085,; A ENST00000332549 Transcript missense_variant 1322/1578 1093/1197 365/398 G/R Ggg/Agg rs748144607 1 1 IL1R2 HGNC HGNC:5994 protein_coding YES CCDS2054.1 ENSP00000330959 P27930 UPI0000001C78 NM_004633.3 deleterious(0) 9/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF3,Prints_domain:PR01539 MODERATE 1 SNV 1 1 PASS rs748144607 . 0 206 4 0 0 0 0 0 -16.85771 1 1 1 1 0 A 3 1 39 102028288 102028288 G A 1 0 0 0 0 1 0 0 0 7562 1232 43 3 3 IL1R2 2 102028288 Missense_Mutation SNP G C3N-00175_T 3631968 102028288 140165241 210 9802 RGPD8 0 . GRCh38 2 112389263 112389263 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.3682G>C p.Ala1228Pro p.A1228P ENST00000302558 20/23 855 707 148 731 731 0 strelka-varscan-mutect RGPD8,missense_variant,p.Ala1228Pro,ENST00000302558,NM_001164463.1;RGPD8,missense_variant,p.Ala1088Pro,ENST00000409750,;RGPD8,downstream_gene_variant,,ENST00000330575,;RGPD8,downstream_gene_variant,,ENST00000522286,; G ENST00000302558 Transcript missense_variant 3874/5576 3682/5298 1228/1765 A/P Gcc/Ccc 1 -1 RGPD8 HGNC HGNC:9849 protein_coding YES CCDS46394.1 ENSP00000306637 O14715 UPI000013E7F5 NM_001164463.1 tolerated(0.15) 20/23 hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 112389263 112389263 C G 1 0 0 0 0 1 0 0 0 13461 739 26 4 4 RGPD8 2 112389263 Missense_Mutation SNP C C3N-00175_T 10360975 112389263 129804266 211 9803 NT5DC4 0 . GRCh38 2 112724861 112724861 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.792G>T p.Glu264Asp p.E264D ENST00000327581 11/17 198 153 45 232 231 1 strelka-varscan-mutect NT5DC4,missense_variant,p.Glu264Asp,ENST00000327581,;NT5DC4,non_coding_transcript_exon_variant,,ENST00000497526,;NT5DC4,upstream_gene_variant,,ENST00000491170,;NT5DC4,upstream_gene_variant,,ENST00000462854,;NT5DC4,downstream_gene_variant,,ENST00000470675,;NT5DC4,downstream_gene_variant,,ENST00000484666,; T ENST00000327581 Transcript missense_variant 843/1767 792/1287 264/428 E/D gaG/gaT 1 1 NT5DC4 HGNC HGNC:27678 protein_coding YES ENSP00000330247 Q86YG4 UPI0000197313 deleterious(0.04) 11/17 hmmpanther:PTHR12103,hmmpanther:PTHR12103:SF18,Gene3D:3.40.50.1000,Pfam_domain:PF05761,PIRSF_domain:PIRSF017434,TIGRFAM_domain:TIGR02244,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 112724861 112724861 G T 1 0 0 0 0 1 0 0 0 10756 991 35 2 2 NT5DC4 2 112724861 Missense_Mutation SNP G C3N-00175_T 335598 112724861 129468668 212 9804 IL36B 0 . GRCh38 2 113026208 113026208 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.286G>C p.Gly96Arg p.G96R ENST00000259213 5/6 181 143 38 215 215 0 strelka-varscan-mutect IL36B,missense_variant,p.Gly96Arg,ENST00000259213,NM_014438.4;IL36B,downstream_gene_variant,,ENST00000327407,NM_173178.2; G ENST00000259213 Transcript missense_variant 394/1186 286/495 96/164 G/R Ggg/Cgg 1 -1 IL36B HGNC HGNC:15564 protein_coding YES CCDS2109.1 ENSP00000259213 Q9NZH7 UPI000003C9C0 NM_014438.4 deleterious_low_confidence(0) 5/6 Gene3D:2.80.10.50,hmmpanther:PTHR10078,hmmpanther:PTHR10078:SF24,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 113026208 113026208 C G 1 0 0 0 0 1 0 0 0 7595 681 24 4 4 IL36B 2 113026208 Missense_Mutation SNP C C3N-00175_T 301347 113026208 129167321 213 9805 IL36RN 0 . GRCh38 2 113062578 113062578 + Silent SNP G G T rs28938778 C3N-00175_T C3N-00175_N G G c.369G>T p.= p.T123T ENST00000393200 5/5 506 415 91 532 530 2 strelka-varscan-mutect IL36RN,synonymous_variant,p.=,ENST00000393200,NM_012275.2;IL36RN,synonymous_variant,p.=,ENST00000346807,NM_173170.1;IL36RN,synonymous_variant,p.=,ENST00000514072,;IL36RN,downstream_gene_variant,,ENST00000437409,; T ENST00000393200 Transcript synonymous_variant 530/2700 369/468 123/155 T acG/acT rs28938778,COSM5532696 1 1 IL36RN HGNC HGNC:15561 protein_coding YES CCDS2111.1 ENSP00000376896 Q9UBH0 A0A024R518 UPI0000034E98 NM_012275.2 5/5 hmmpanther:PTHR10078:SF7,hmmpanther:PTHR10078,PROSITE_patterns:PS00253,Gene3D:2.80.10.50,Pfam_domain:PF00340,SMART_domains:SM00125,Superfamily_domains:SSF50353,Prints_domain:PR01360,Prints_domain:PR00264 0,1 LOW 1 SNV 1 0,1 1 PASS rs28938778 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 113062578 113062578 G T 1 0 0 0 0 0 0 0 1 7597 1103 39 1 1 IL36RN 2 113062578 Silent SNP G C3N-00175_T 36370 113062578 129130951 214 9806 CNTNAP5 0 . GRCh38 2 124242317 124242317 + Nonsense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.305G>A p.Trp102Ter p.W102* ENST00000431078 3/24 223 205 18 218 218 0 strelka-varscan-mutect CNTNAP5,stop_gained,p.Trp102Ter,ENST00000431078,NM_130773.3;CNTNAP5,non_coding_transcript_exon_variant,,ENST00000470921,; A ENST00000431078 Transcript stop_gained 669/5284 305/3921 102/1306 W/* tGg/tAg 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 3/24 PROSITE_profiles:PS50022,Gene3D:2.60.120.260,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 124242317 124242317 G A 1 0 0 0 0 0 1 0 0 3432 1357 47 3 3 CNTNAP5 2 124242317 Nonsense_Mutation SNP G C3N-00175_T 11179739 124242317 117951212 215 9807 CNTNAP5 0 . GRCh38 2 124789908 124789908 + Missense_Mutation SNP C C A rs774125649 C3N-00175_T C3N-00175_N C C c.2756C>A p.Thr919Lys p.T919K ENST00000431078 18/24 90 63 27 137 137 0 strelka-varscan-mutect CNTNAP5,missense_variant,p.Thr919Lys,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 3120/5284 2756/3921 919/1306 T/K aCg/aAg rs774125649 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0.01) 18/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs774125649 . 0 205 2 3 0 0 0 0 -20 0.9999898 1 1 1 0 A 3 1 39 124789908 124789908 C A 1 0 0 0 0 1 0 0 0 3432 536 19 1 1 CNTNAP5 2 124789908 Missense_Mutation SNP C C3N-00175_T 547591 124789908 117403621 216 9808 ERCC3 0 . GRCh38 2 127280600 127280600 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1374G>T p.= p.V458V ENST00000285398 9/15 244 224 20 318 318 0 strelka-varscan-mutect ERCC3,synonymous_variant,p.=,ENST00000285398,NM_001303416.1,NM_000122.1,NM_001303418.1;ERCC3,3_prime_UTR_variant,,ENST00000445889,;ERCC3,3_prime_UTR_variant,,ENST00000426778,; A ENST00000285398 Transcript synonymous_variant 1469/2750 1374/2349 458/782 V gtG/gtT 1 -1 ERCC3 HGNC HGNC:3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 UPI000013900E NM_001303416.1,NM_000122.1,NM_001303418.1 9/15 Gene3D:3.40.50.300,Pfam_domain:PF04851,PROSITE_profiles:PS51192,hmmpanther:PTHR11274,hmmpanther:PTHR11274:SF0,SMART_domains:SM00487,Superfamily_domains:SSF52540,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00603 LOW 1 SNV 1 1 PASS rs1184073978 . 0 208 0 0 2 0 0 0 -6.723465 0.9903579 1 1 1 0 A 2 1 39 127280600 127280600 C A 1 0 0 0 0 0 0 0 1 5063 697 25 2 2 ERCC3 2 127280600 Silent SNP C C3N-00175_T 2490692 127280600 114912929 217 9809 LIMS2 0 . GRCh38 2 127657443 127657443 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.203C>A p.Ala68Asp p.A68D ENST00000324938 2/10 179 161 18 203 203 0 strelka-varscan-mutect LIMS2,missense_variant,p.Ala39Asp,ENST00000409455,;LIMS2,missense_variant,p.Ala39Asp,ENST00000410011,NM_001161404.1;LIMS2,missense_variant,p.Ala39Asp,ENST00000409808,;LIMS2,missense_variant,p.Ala68Asp,ENST00000324938,NM_017980.4;LIMS2,missense_variant,p.Ala44Asp,ENST00000355119,NM_001161403.1;LIMS2,missense_variant,p.Ala66Asp,ENST00000545738,NM_001136037.2;GPR17,downstream_gene_variant,,ENST00000544369,NM_001161415.1;GPR17,downstream_gene_variant,,ENST00000272644,NM_005291.2;GPR17,downstream_gene_variant,,ENST00000486700,;LIMS2,non_coding_transcript_exon_variant,,ENST00000466410,;LIMS2,non_coding_transcript_exon_variant,,ENST00000476932,;LIMS2,upstream_gene_variant,,ENST00000469300,; T ENST00000324938 Transcript missense_variant 361/2111 203/1098 68/365 A/D gCc/gAc 1 -1 LIMS2 HGNC HGNC:16084 protein_coding YES CCDS2147.1 ENSP00000326888 Q7Z4I7 UPI00001B5BF3 NM_017980.4 deleterious(0) 2/10 PROSITE_profiles:PS50023,hmmpanther:PTHR24210:SF10,hmmpanther:PTHR24210,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,PIRSF_domain:PIRSF038003,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 127657443 127657443 G T 1 0 0 0 0 1 0 0 0 8712 1203 42 2 2 LIMS2 2 127657443 Missense_Mutation SNP G C3N-00175_T 376843 127657443 114536086 218 9810 CFC1 0 . GRCh38 2 130598745 130598745 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.144G>C p.Gln48His p.Q48H ENST00000259216 3/6 174 164 10 176 176 0 varscan-mutect CFC1,missense_variant,p.Gln48His,ENST00000615342,NM_001270420.1;CFC1,missense_variant,p.Gln48His,ENST00000621673,NM_001270421.1;CFC1,missense_variant,p.Gln48His,ENST00000259216,NM_032545.3;Metazoa_SRP,upstream_gene_variant,,ENST00000621608,; G ENST00000259216 Transcript missense_variant 407/1046 144/672 48/223 Q/H caG/caC 1 -1 CFC1 HGNC HGNC:18292 protein_coding YES CCDS2162.1 ENSP00000259216 P0CG37 UPI0000070FF1 NM_032545.3 deleterious(0.02) 3/6 hmmpanther:PTHR14949,hmmpanther:PTHR14949:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 130598745 130598745 C G 1 0 0 0 0 1 0 0 0 3038 564 20 4 4 CFC1 2 130598745 Missense_Mutation SNP C C3N-00175_T 2941302 130598745 111594784 219 9811 AMER3 0 . GRCh38 2 130763340 130763340 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1268A>T p.Tyr423Phe p.Y423F ENST00000423981 2/2 137 101 36 206 206 0 strelka-varscan-mutect AMER3,missense_variant,p.Tyr423Phe,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Tyr423Phe,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; T ENST00000423981 Transcript missense_variant 1378/6172 1268/2586 423/861 Y/F tAc/tTc 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 deleterious(0.02) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2,Pfam_domain:PF09422 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 130763340 130763340 A T 1 0 0 0 0 1 0 0 0 669 391 14 4 4 AMER3 2 130763340 Missense_Mutation SNP A C3N-00175_T 164595 130763340 111430189 220 9812 LCT 0 . GRCh38 2 135817716 135817716 + Missense_Mutation SNP G G C rs370939537 C3N-00175_T C3N-00175_N G G c.1332C>G p.Cys444Trp p.C444W ENST00000264162 6/17 273 206 67 306 306 0 strelka-varscan-mutect LCT,missense_variant,p.Cys444Trp,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; C ENST00000264162 Transcript missense_variant 1343/6279 1332/5784 444/1927 C/W tgC/tgG rs370939537 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 deleterious(0) 6/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS rs370939537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 135817716 135817716 G C 1 0 0 0 0 1 0 0 0 8599 1079 38 4 4 LCT 2 135817716 Missense_Mutation SNP G C3N-00175_T 5054376 135817716 106375813 221 9813 NXPH2 0 . GRCh38 2 138671381 138671381 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.336T>A p.Phe112Leu p.F112L ENST00000272641 2/2 152 118 34 185 185 0 strelka-varscan-mutect NXPH2,missense_variant,p.Phe112Leu,ENST00000272641,NM_007226.2; T ENST00000272641 Transcript missense_variant 443/1052 336/795 112/264 F/L ttT/ttA 1 -1 NXPH2 HGNC HGNC:8076 protein_coding YES CCDS46421.1 ENSP00000272641 O95156 UPI000023FCD4 NM_007226.2 tolerated(0.06) 2/2 Pfam_domain:PF06312,PIRSF_domain:PIRSF038019,hmmpanther:PTHR17103,hmmpanther:PTHR17103:SF11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 138671381 138671381 A T 1 0 0 0 0 1 0 0 0 10867 127 5 4 4 NXPH2 2 138671381 Missense_Mutation SNP A C3N-00175_T 2853665 138671381 103522148 222 9814 LRP1B 0 . GRCh38 2 140322034 140322034 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.12569C>T p.Ser4190Phe p.S4190F ENST00000389484 82/91 139 121 18 200 200 0 strelka-varscan-mutect LRP1B,missense_variant,p.Ser4190Phe,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Ser422Phe,ENST00000437977,; A ENST00000389484 Transcript missense_variant 13541/16535 12569/13800 4190/4599 S/F tCt/tTt 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.09) 82/91 SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 140322034 140322034 G A 1 0 0 0 0 1 0 0 0 8850 942 33 3 3 LRP1B 2 140322034 Missense_Mutation SNP G C3N-00175_T 1650653 140322034 101871495 223 9815 LRP1B 0 . GRCh38 2 140536696 140536696 + Silent SNP G G T rs754074138 C3N-00175_T C3N-00175_N G G c.7527C>A p.= p.S2509S ENST00000389484 46/91 113 80 33 143 143 0 strelka-varscan-mutect LRP1B,synonymous_variant,p.=,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript synonymous_variant 8499/16535 7527/13800 2509/4599 S tcC/tcA rs754074138 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 46/91 PROSITE_profiles:PS50068,Pfam_domain:PF00057,Gene3D:2.10.25.10,SMART_domains:SM00192 LOW 1 SNV 1 1 PASS rs754074138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 140536696 140536696 G T 1 0 0 0 0 0 0 0 1 8850 987 35 2 2 LRP1B 2 140536696 Silent SNP G C3N-00175_T 214662 140536696 101656833 224 9816 LRP1B 0 . GRCh38 2 140951914 140951914 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.2914C>G p.Gln972Glu p.Q972E ENST00000389484 19/91 133 124 9 120 120 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gln972Glu,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Gln117Glu,ENST00000434794,; C ENST00000389484 Transcript missense_variant 3886/16535 2914/13800 972/4599 Q/E Caa/Gaa 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.15) 19/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF105,hmmpanther:PTHR10529,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 140951914 140951914 G C 1 0 0 0 0 1 0 0 0 8850 1357 47 4 4 LRP1B 2 140951914 Missense_Mutation SNP G C3N-00175_T 415218 140951914 101241615 225 9817 LRP1B 0 . GRCh38 2 141055137 141055137 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1531A>T p.Ser511Cys p.S511C ENST00000389484 10/91 152 132 20 185 185 0 strelka-varscan-mutect LRP1B,missense_variant,p.Ser511Cys,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 2503/16535 1531/13800 511/4599 S/C Agt/Tgt 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.01) 10/91 PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 141055137 141055137 T A 1 0 0 0 0 1 0 0 0 8850 1609 56 4 4 LRP1B 2 141055137 Missense_Mutation SNP T C3N-00175_T 103223 141055137 101138392 226 9818 NEB 0 . GRCh38 2 151565818 151565818 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.18159T>A p.Asn6053Lys p.N6053K ENST00000618972 115/183 110 70 40 99 99 0 strelka-varscan-mutect NEB,missense_variant,p.Asn6053Lys,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Asn6053Lys,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Asn6053Lys,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Asn6053Lys,ENST00000603639,;NEB,missense_variant,p.Asn6053Lys,ENST00000604864,;NEB,missense_variant,p.Asn4352Lys,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Asn4352Lys,ENST00000172853,;NEB,missense_variant,p.Asn783Lys,ENST00000413693,; T ENST00000618972 Transcript missense_variant,splice_region_variant 18362/26307 18159/25683 6053/8560 N/K aaT/aaA 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.19) 115/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 151565818 151565818 A T 1 0 0 0 0 1 0 0 0 10326 231 8 4 4 NEB 2 151565818 Missense_Mutation SNP A C3N-00175_T 10510681 151565818 90627711 227 9819 CACNB4 0 . GRCh38 2 151869224 151869224 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.711G>T p.Met237Ile p.M237I ENST00000539935 9/14 134 124 10 147 147 0 strelka-varscan-mutect CACNB4,missense_variant,p.Met237Ile,ENST00000539935,NM_000726.3;CACNB4,missense_variant,p.Met190Ile,ENST00000637217,NM_001320722.1;CACNB4,missense_variant,p.Met190Ile,ENST00000636598,;CACNB4,missense_variant,p.Met190Ile,ENST00000636130,;CACNB4,missense_variant,p.Met203Ile,ENST00000636901,;CACNB4,missense_variant,p.Met162Ile,ENST00000636350,;CACNB4,missense_variant,p.Met237Ile,ENST00000637309,;CACNB4,missense_variant,p.Met219Ile,ENST00000638005,NM_001005746.2;CACNB4,missense_variant,p.Met178Ile,ENST00000636442,;CACNB4,missense_variant,p.Met190Ile,ENST00000636773,;CACNB4,missense_variant,p.Met203Ile,ENST00000638091,;CACNB4,missense_variant,p.Met207Ile,ENST00000637762,;CACNB4,missense_variant,p.Met51Ile,ENST00000637284,;CACNB4,missense_variant,p.Met203Ile,ENST00000534999,NM_001005747.2;CACNB4,missense_variant,p.Met190Ile,ENST00000439467,;CACNB4,missense_variant,p.Met190Ile,ENST00000397327,;CACNB4,missense_variant,p.Met162Ile,ENST00000637418,;CACNB4,missense_variant,p.Met51Ile,ENST00000637514,;CACNB4,missense_variant,p.Met196Ile,ENST00000427385,;CACNB4,missense_variant,p.Met237Ile,ENST00000201943,NM_001145798.1;CACNB4,missense_variant,p.Met203Ile,ENST00000637216,;CACNB4,3_prime_UTR_variant,,ENST00000636947,;CACNB4,3_prime_UTR_variant,,ENST00000636129,;CACNB4,intron_variant,,ENST00000637547,;CACNB4,intron_variant,,ENST00000636617,;CACNB4,intron_variant,,ENST00000636785,;CACNB4,intron_variant,,ENST00000638040,;CACNB4,intron_variant,,ENST00000360283,;CACNB4,intron_variant,,ENST00000637779,;CACNB4,intron_variant,,ENST00000636380,;CACNB4,intron_variant,,ENST00000636108,;CACNB4,intron_variant,,ENST00000636721,;CACNB4,downstream_gene_variant,,ENST00000434468,;CACNB4,downstream_gene_variant,,ENST00000638056,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637913,;CACNB4,intron_variant,,ENST00000635803,;CACNB4,downstream_gene_variant,,ENST00000635743,;CACNB4,missense_variant,p.Asp197Tyr,ENST00000637312,;CACNB4,missense_variant,p.Met190Ile,ENST00000637828,;CACNB4,3_prime_UTR_variant,,ENST00000637436,;CACNB4,3_prime_UTR_variant,,ENST00000636762,;CTD-2021K4.1,3_prime_UTR_variant,,ENST00000637224,;CACNB4,3_prime_UTR_variant,,ENST00000635904,;CACNB4,3_prime_UTR_variant,,ENST00000637330,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637884,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637622,;CACNB4,non_coding_transcript_exon_variant,,ENST00000636834,;CACNB4,non_coding_transcript_exon_variant,,ENST00000470066,;CACNB4,non_coding_transcript_exon_variant,,ENST00000636810,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637319,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637773,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637530,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637765,;CACNB4,intron_variant,,ENST00000636831,;CACNB4,intron_variant,,ENST00000635738,;CACNB4,intron_variant,,ENST00000636507,;CACNB4,intron_variant,,ENST00000635930,;CACNB4,intron_variant,,ENST00000637232,;CACNB4,intron_variant,,ENST00000637132,;CACNB4,intron_variant,,ENST00000637550,;CACNB4,intron_variant,,ENST00000637491,;CACNB4,intron_variant,,ENST00000637535,;CACNB4,intron_variant,,ENST00000636664,;CACNB4,intron_variant,,ENST00000638150,;CACNB4,intron_variant,,ENST00000637956,;CTD-2021K4.1,intron_variant,,ENST00000637559,;CACNB4,intron_variant,,ENST00000637007,;CACNB4,intron_variant,,ENST00000636390,; A ENST00000539935 Transcript missense_variant 1175/8378 711/1563 237/520 M/I atG/atT 1 -1 CACNB4 HGNC HGNC:1404 protein_coding YES CCDS46426.1 ENSP00000438949 O00305 UPI0000208F1E NM_000726.3 deleterious(0) 9/14 Gene3D:3.40.50.300,Pfam_domain:PF00625,Prints_domain:PR01626,hmmpanther:PTHR11824,hmmpanther:PTHR11824:SF7,SMART_domains:SM00072,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 151869224 151869224 C A 1 0 0 0 0 1 0 0 0 2243 826 29 2 2 CACNB4 2 151869224 Missense_Mutation SNP C C3N-00175_T 303406 151869224 90324305 228 9820 CACNB4 0 . GRCh38 2 151870433 151870433 + Missense_Mutation SNP G G A rs762188629 C3N-00175_T C3N-00175_N G G c.695C>T p.Pro232Leu p.P232L ENST00000636947 7/7 274 244 30 349 349 0 strelka-varscan-mutect CACNB4,missense_variant,p.Pro232Leu,ENST00000636947,;CACNB4,missense_variant,p.Pro248Leu,ENST00000636129,;CACNB4,3_prime_UTR_variant,,ENST00000638056,;CACNB4,intron_variant,,ENST00000539935,NM_000726.3;CACNB4,intron_variant,,ENST00000637217,NM_001320722.1;CACNB4,intron_variant,,ENST00000636598,;CACNB4,intron_variant,,ENST00000636130,;CACNB4,intron_variant,,ENST00000636901,;CACNB4,intron_variant,,ENST00000637547,;CACNB4,intron_variant,,ENST00000636350,;CACNB4,intron_variant,,ENST00000637309,;CACNB4,intron_variant,,ENST00000636617,;CACNB4,intron_variant,,ENST00000638005,NM_001005746.2;CACNB4,intron_variant,,ENST00000636442,;CACNB4,intron_variant,,ENST00000636773,;CACNB4,intron_variant,,ENST00000638091,;CACNB4,intron_variant,,ENST00000637762,;CACNB4,intron_variant,,ENST00000636785,;CACNB4,intron_variant,,ENST00000637284,;CACNB4,intron_variant,,ENST00000534999,NM_001005747.2;CACNB4,intron_variant,,ENST00000439467,;CACNB4,intron_variant,,ENST00000397327,;CACNB4,intron_variant,,ENST00000638040,;CACNB4,intron_variant,,ENST00000637418,;CACNB4,intron_variant,,ENST00000360283,;CACNB4,intron_variant,,ENST00000637514,;CACNB4,intron_variant,,ENST00000427385,;CACNB4,intron_variant,,ENST00000637779,;CACNB4,intron_variant,,ENST00000636380,;CACNB4,intron_variant,,ENST00000636108,;CACNB4,intron_variant,,ENST00000636721,;CACNB4,intron_variant,,ENST00000201943,NM_001145798.1;CACNB4,intron_variant,,ENST00000637216,;CACNB4,downstream_gene_variant,,ENST00000434468,;CACNB4,intron_variant,,ENST00000635803,;CACNB4,intron_variant,,ENST00000637913,;CACNB4,downstream_gene_variant,,ENST00000635743,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637884,;CACNB4,non_coding_transcript_exon_variant,,ENST00000636834,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637319,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637530,;CACNB4,non_coding_transcript_exon_variant,,ENST00000637765,;CACNB4,intron_variant,,ENST00000636831,;CACNB4,intron_variant,,ENST00000635738,;CACNB4,intron_variant,,ENST00000637622,;CACNB4,intron_variant,,ENST00000636507,;CACNB4,intron_variant,,ENST00000635930,;CACNB4,intron_variant,,ENST00000470066,;CACNB4,intron_variant,,ENST00000637232,;CACNB4,intron_variant,,ENST00000637132,;CACNB4,intron_variant,,ENST00000636810,;CACNB4,intron_variant,,ENST00000637436,;CACNB4,intron_variant,,ENST00000637312,;CACNB4,intron_variant,,ENST00000636762,;CACNB4,intron_variant,,ENST00000637773,;CACNB4,intron_variant,,ENST00000637550,;CTD-2021K4.1,intron_variant,,ENST00000637224,;CACNB4,intron_variant,,ENST00000635904,;CACNB4,intron_variant,,ENST00000637330,;CACNB4,intron_variant,,ENST00000637828,;CACNB4,intron_variant,,ENST00000637491,;CACNB4,intron_variant,,ENST00000637535,;CACNB4,intron_variant,,ENST00000636664,;CACNB4,intron_variant,,ENST00000638150,;CACNB4,intron_variant,,ENST00000637956,;CTD-2021K4.1,intron_variant,,ENST00000637559,;CACNB4,intron_variant,,ENST00000637007,;CACNB4,intron_variant,,ENST00000636390,; A ENST00000636947 Transcript missense_variant 929/5575 695/924 232/307 P/L cCt/cTt rs762188629 1 -1 CACNB4 HGNC HGNC:1404 protein_coding ENSP00000490337 UPI0000E5A28D tolerated_low_confidence(0.54) 7/7 MODERATE SNV 1 PASS rs762188629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 151870433 151870433 G A 1 0 0 0 0 1 0 0 0 2243 1000 35 3 3 CACNB4 2 151870433 Missense_Mutation SNP G C3N-00175_T 1209 151870433 90323096 229 9821 BAZ2B 0 . GRCh38 2 159431148 159431148 + Missense_Mutation SNP T T A rs760395340 C3N-00175_T C3N-00175_N T T c.1909A>T p.Ser637Cys p.S637C ENST00000392783 10/37 60 44 16 65 65 0 strelka-varscan-mutect BAZ2B,missense_variant,p.Ser637Cys,ENST00000392783,NM_013450.3;BAZ2B,missense_variant,p.Ser635Cys,ENST00000392782,NM_001289975.1;BAZ2B,intron_variant,,ENST00000343439,;BAZ2B,intron_variant,,ENST00000441143,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000472953,; A ENST00000392783 Transcript missense_variant 2405/8289 1909/6507 637/2168 S/C Agt/Tgt rs760395340 1 -1 BAZ2B HGNC HGNC:963 protein_coding YES CCDS2209.2 ENSP00000376534 Q9UIF8 UPI0000D74C4A NM_013450.3 deleterious(0) 10/37 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF154,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs760395340 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 159431148 159431148 T A 1 0 0 0 0 1 0 0 0 1477 1522 53 4 4 BAZ2B 2 159431148 Missense_Mutation SNP T C3N-00175_T 7560715 159431148 82762381 230 9822 KCNH7 0 . GRCh38 2 162400226 162400226 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.2370T>A p.= p.I790I ENST00000332142 10/16 162 113 49 226 226 0 strelka-varscan-mutect KCNH7,synonymous_variant,p.=,ENST00000332142,NM_033272.3;KCNH7,synonymous_variant,p.=,ENST00000618399,; T ENST00000332142 Transcript synonymous_variant 2470/4113 2370/3591 790/1196 I atT/atA 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 10/16 PROSITE_profiles:PS50042,hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 162400226 162400226 A T 1 0 0 0 0 0 0 0 1 7953 126 5 4 4 KCNH7 2 162400226 Silent SNP A C3N-00175_T 2969078 162400226 79793303 231 9823 SCN1A 0 . GRCh38 2 166036370 166036370 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.3107A>T p.Gln1036Leu p.Q1036L ENST00000303395 18/28 40 36 4 59 59 0 strelka-varscan-mutect SCN1A,missense_variant,p.Gln1025Leu,ENST00000635776,;SCN1A,missense_variant,p.Gln1025Leu,ENST00000637988,;SCN1A,missense_variant,p.Gln1036Leu,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Gln1025Leu,ENST00000635750,;SCN1A,missense_variant,p.Gln1036Leu,ENST00000423058,;SCN1A,missense_variant,p.Gln1025Leu,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Gln1008Leu,ENST00000409050,NM_001165964.1;AC010127.3,non_coding_transcript_exon_variant,,ENST00000597623,;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;SCN1A,3_prime_UTR_variant,,ENST00000636194,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,;SCN1A,upstream_gene_variant,,ENST00000637038,;SCN1A,downstream_gene_variant,,ENST00000636759,; A ENST00000303395 Transcript missense_variant 3525/8533 3107/6030 1036/2009 Q/L cAg/cTg 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 tolerated(0.12) 18/28 Pfam_domain:PF06512,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220 MODERATE 1 SNV 5 1 PASS rs1440794053 . 1 206 3 0 0 0 0 0 -10.98341 1 1 1 1 0 A 3 1 39 166036370 166036370 T A 1 0 0 0 0 1 0 0 0 14183 1580 55 4 4 SCN1A 2 166036370 Missense_Mutation SNP T C3N-00175_T 3636144 166036370 76157159 232 9824 XIRP2 0 . GRCh38 2 167243385 167243385 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1993T>A p.Ser665Thr p.S665T ENST00000409195 9/11 225 207 18 301 301 0 strelka-varscan-mutect XIRP2,missense_variant,p.Ser665Thr,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser443Thr,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser490Thr,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; A ENST00000409195 Transcript missense_variant 2082/12675 1993/10650 665/3549 S/T Tca/Aca 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.22) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 167243385 167243385 T A 1 0 0 0 0 1 0 0 0 17989 1551 54 4 4 XIRP2 2 167243385 Missense_Mutation SNP T C3N-00175_T 1207015 167243385 74950144 233 9825 XIRP2 0 . GRCh38 2 167248474 167248474 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.7082C>T p.Ser2361Leu p.S2361L ENST00000409195 9/11 186 133 53 201 201 0 strelka-varscan-mutect XIRP2,missense_variant,p.Ser2361Leu,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser2139Leu,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser2186Leu,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; T ENST00000409195 Transcript missense_variant 7171/12675 7082/10650 2361/3549 S/L tCg/tTg COSM3425420 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious_low_confidence(0.01) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 167248474 167248474 C T 1 0 0 0 0 1 0 0 0 17989 893 31 1 1 XIRP2 2 167248474 Missense_Mutation SNP C C3N-00175_T 5089 167248474 74945055 234 9826 XIRP2 0 . GRCh38 2 167250027 167250027 + Missense_Mutation SNP A A T C3N-00175_T C3N-00175_N A A c.8635A>T p.Ser2879Cys p.S2879C ENST00000409195 9/11 232 210 22 297 297 0 strelka-varscan-mutect XIRP2,missense_variant,p.Ser2879Cys,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser2657Cys,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser2704Cys,ENST00000628543,;XIRP2,missense_variant,p.Ser293Cys,ENST00000295237,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript missense_variant 8724/12675 8635/10650 2879/3549 S/C Agt/Tgt COSM716886 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.05) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 167250027 167250027 A T 1 0 0 0 0 1 0 0 0 17989 72 3 4 4 XIRP2 2 167250027 Missense_Mutation SNP A C3N-00175_T 1553 167250027 74943502 235 9827 EVX2 0 . GRCh38 2 176083377 176083377 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.400G>A p.Ala134Thr p.A134T ENST00000308618 1/3 138 119 19 204 204 0 strelka-varscan-mutect EVX2,missense_variant,p.Ala134Thr,ENST00000308618,NM_001080458.1; T ENST00000308618 Transcript missense_variant 537/4203 400/1431 134/476 A/T Gct/Act COSM4681953 1 -1 EVX2 HGNC HGNC:3507 protein_coding YES CCDS33333.1 ENSP00000312385 Q03828 UPI000012A2AF NM_001080458.1 tolerated(0.22) 1/3 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 176083377 176083377 C T 1 0 0 0 0 1 0 0 0 5162 768 27 1 1 EVX2 2 176083377 Missense_Mutation SNP C C3N-00175_T 8833350 176083377 66110152 236 9828 TTN 0 . GRCh38 2 178712136 178712136 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.27694C>A p.Pro9232Thr p.P9232T ENST00000589042 96/363 149 101 48 167 167 0 strelka-varscan-mutect TTN,missense_variant,p.Pro9232Thr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro8915Thr,ENST00000591111,;TTN,missense_variant,p.Pro8915Thr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro7988Thr,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 27919/109224 27694/107976 9232/35991 P/T Cct/Act 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 96/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1228009511 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 178712136 178712136 G T 1 0 0 0 0 1 0 0 0 17245 1232 43 2 2 TTN 2 178712136 Missense_Mutation SNP G C3N-00175_T 2628759 178712136 63481393 237 9829 TTN 0 . GRCh38 2 178717335 178717335 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.25399C>A p.Leu8467Ile p.L8467I ENST00000589042 88/363 76 62 14 76 76 0 strelka-varscan-mutect TTN,missense_variant,p.Leu8467Ile,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu8150Ile,ENST00000591111,;TTN,missense_variant,p.Leu8150Ile,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu7223Ile,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,downstream_gene_variant,,ENST00000625536,;TTN-AS1,downstream_gene_variant,,ENST00000592630,;TTN-AS1,downstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000626117,;TTN-AS1,downstream_gene_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 25624/109224 25399/107976 8467/35991 L/I Ctt/Att COSM3573172,COSM3573173 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 88/363 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 178717335 178717335 G T 1 0 0 0 0 1 0 0 0 17245 942 33 2 2 TTN 2 178717335 Missense_Mutation SNP G C3N-00175_T 5199 178717335 63476194 238 9830 TTN 0 . GRCh38 2 178785989 178785989 + Silent SNP G G T rs746990488 C3N-00175_T C3N-00175_N G G c.2229C>A p.= p.A743A ENST00000589042 14/363 317 285 32 380 378 2 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN,synonymous_variant,p.=,ENST00000360870,NM_133379.4;TTN,downstream_gene_variant,,ENST00000436599,; T ENST00000589042 Transcript synonymous_variant 2454/109224 2229/107976 743/35991 A gcC/gcA rs746990488,COSM1482516,COSM441906,COSM441907,COSM441908,COSM441910 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 14/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 0,1,1,1,1,1 LOW 1 SNV 5 0,1,1,1,1,1 1 PASS rs746990488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 178785989 178785989 G T 1 0 0 0 0 0 0 0 1 17245 1103 39 1 1 TTN 2 178785989 Silent SNP G C3N-00175_T 68654 178785989 63407540 239 9831 FAM171B 0 . GRCh38 2 186753991 186753991 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.954G>T p.Trp318Cys p.W318C ENST00000304698 6/8 145 125 20 157 157 0 strelka-varscan-mutect FAM171B,missense_variant,p.Trp318Cys,ENST00000304698,NM_177454.3;FAM171B,downstream_gene_variant,,ENST00000612606,; T ENST00000304698 Transcript missense_variant 1157/5826 954/2481 318/826 W/C tgG/tgT 1 1 FAM171B HGNC HGNC:29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 UPI0000161631 NM_177454.3 deleterious(0) 6/8 hmmpanther:PTHR31626:SF2,hmmpanther:PTHR31626,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 186753991 186753991 G T 1 0 0 0 0 1 0 0 0 5339 1183 41 2 2 FAM171B 2 186753991 Missense_Mutation SNP G C3N-00175_T 7968002 186753991 55439538 240 9832 ZSWIM2 0 . GRCh38 2 186829730 186829730 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.1092C>A p.His364Gln p.H364Q ENST00000295131 8/9 70 61 9 84 84 0 strelka-varscan-mutect ZSWIM2,missense_variant,p.His364Gln,ENST00000295131,NM_182521.2; T ENST00000295131 Transcript missense_variant 1132/2091 1092/1902 364/633 H/Q caC/caA COSM5285900 1 -1 ZSWIM2 HGNC HGNC:30990 protein_coding YES CCDS33348.1 ENSP00000295131 Q8NEG5 UPI000013E20D NM_182521.2 deleterious(0) 8/9 PROSITE_profiles:PS50089,hmmpanther:PTHR21540,hmmpanther:PTHR21540:SF0,Pfam_domain:PF13639,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 1 MODERATE 1 SNV 1 1 1 PASS rs1218754056 . 0 204 6 0 0 0 0 0 -19.64819 0.9999999 1 1 1 0 T 3 4 39 186829730 186829730 G T 1 0 0 0 0 1 0 0 0 18842 1391 48 2 2 ZSWIM2 2 186829730 Missense_Mutation SNP G C3N-00175_T 75739 186829730 55363799 241 9833 ZSWIM2 0 . GRCh38 2 186847788 186847788 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.173T>A p.Leu58Gln p.L58Q ENST00000295131 2/9 77 71 6 136 136 0 strelka-varscan-mutect ZSWIM2,missense_variant,p.Leu58Gln,ENST00000295131,NM_182521.2;ZSWIM2,3_prime_UTR_variant,,ENST00000419862,; T ENST00000295131 Transcript missense_variant 213/2091 173/1902 58/633 L/Q cTa/cAa 1 -1 ZSWIM2 HGNC HGNC:30990 protein_coding YES CCDS33348.1 ENSP00000295131 Q8NEG5 UPI000013E20D NM_182521.2 deleterious(0) 2/9 PROSITE_profiles:PS50966,hmmpanther:PTHR21540,hmmpanther:PTHR21540:SF0,Pfam_domain:PF04434 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -13.62625 1 1 1 1 0 T 3 4 39 186847788 186847788 A T 1 0 0 0 0 1 0 0 0 18842 420 15 4 4 ZSWIM2 2 186847788 Missense_Mutation SNP A C3N-00175_T 18058 186847788 55345741 242 9834 COL3A1 0 . GRCh38 2 188999295 188999295 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.2033G>T p.Gly678Val p.G678V ENST00000304636 30/51 308 276 32 383 383 0 strelka-varscan-mutect COL3A1,missense_variant,p.Gly678Val,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Gly678Val,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000450867,;COL3A1,downstream_gene_variant,,ENST00000637672,;COL3A1,upstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript missense_variant 2203/5543 2033/4401 678/1466 G/V gGt/gTt COSM3962084,COSM3962085 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 deleterious(0) 30/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 188999295 188999295 G T 1 0 0 0 0 1 0 0 0 3477 1261 44 2 2 COL3A1 2 188999295 Missense_Mutation SNP G C3N-00175_T 2151507 188999295 53194234 243 9835 COL5A2 0 . GRCh38 2 189050638 189050638 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.2970G>T p.= p.G990G ENST00000374866 43/54 188 133 55 207 207 0 strelka-varscan-mutect COL5A2,synonymous_variant,p.=,ENST00000374866,NM_000393.3;COL5A2,synonymous_variant,p.=,ENST00000618828,; A ENST00000374866 Transcript synonymous_variant 3245/6949 2970/4500 990/1499 G ggG/ggT 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 43/54 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF539,hmmpanther:PTHR24023 LOW 1 SNV 1 1 PASS rs933589600 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 189050638 189050638 C A 1 0 0 0 0 0 0 0 1 3486 726 26 2 2 COL5A2 2 189050638 Silent SNP C C3N-00175_T 51343 189050638 53142891 244 9836 HIBCH 0 . GRCh38 2 190287620 190287620 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.404A>T p.Tyr135Phe p.Y135F ENST00000359678 6/14 162 130 32 277 277 0 strelka-varscan-mutect HIBCH,missense_variant,p.Tyr135Phe,ENST00000392332,NM_198047.2;HIBCH,missense_variant,p.Tyr135Phe,ENST00000359678,NM_014362.3;HIBCH,missense_variant,p.Tyr189Phe,ENST00000409934,;HIBCH,missense_variant,p.Tyr34Phe,ENST00000392333,; A ENST00000359678 Transcript missense_variant 699/1939 404/1161 135/386 Y/F tAt/tTt 1 -1 HIBCH HGNC HGNC:4908 protein_coding YES CCDS2304.1 ENSP00000352706 Q6NVY1 A0A140VJL0 UPI000013F16E NM_014362.3 tolerated(0.12) 6/14 Gene3D:3.90.226.10,Pfam_domain:PF16113,hmmpanther:PTHR11941,hmmpanther:PTHR11941:SF53,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 190287620 190287620 T A 1 0 0 0 0 1 0 0 0 6984 1406 49 4 4 HIBCH 2 190287620 Missense_Mutation SNP T C3N-00175_T 1236982 190287620 51905909 245 9837 GPR1 0 . GRCh38 2 206176839 206176839 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.409A>T p.Ile137Phe p.I137F ENST00000612892 4/4 201 179 22 249 249 0 strelka-varscan-mutect GPR1,missense_variant,p.Ile137Phe,ENST00000612892,NM_001261452.1,NM_001261453.1;GPR1,missense_variant,p.Ile137Phe,ENST00000407325,NM_001098199.1,NM_005279.3;GPR1,missense_variant,p.Ile137Phe,ENST00000621141,NM_001261455.1,NM_001261454.1;GPR1,missense_variant,p.Ile137Phe,ENST00000437420,;GPR1,missense_variant,p.Ile137Phe,ENST00000442134,;GPR1,missense_variant,p.Ile137Phe,ENST00000451790,;GPR1,missense_variant,p.Ile137Phe,ENST00000447845,;GPR1,downstream_gene_variant,,ENST00000411719,;GPR1,downstream_gene_variant,,ENST00000439932,;GPR1,downstream_gene_variant,,ENST00000458440,; A ENST00000612892 Transcript missense_variant 1046/2565 409/1068 137/355 I/F Atc/Ttc 1 -1 GPR1 HGNC HGNC:4463 protein_coding YES CCDS2368.1 ENSP00000480405 P46091 UPI000013C9FB NM_001261452.1,NM_001261453.1 tolerated(0.12) 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF4,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 4 1 PASS rs1186663240 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 206176839 206176839 T A 1 0 0 0 0 1 0 0 0 6523 1406 49 4 4 GPR1 2 206176839 Missense_Mutation SNP T C3N-00175_T 15889219 206176839 36016690 246 9838 ZDBF2 0 . GRCh38 2 206307180 206307180 + Silent SNP T T G rs184499250 C3N-00175_T C3N-00175_N T T c.2652T>G p.= p.T884T ENST00000374423 5/5 102 74 28 138 138 0 strelka-varscan-mutect ZDBF2,synonymous_variant,p.=,ENST00000374423,NM_020923.2;ZDBF2,synonymous_variant,p.=,ENST00000611847,NM_001285549.1; G ENST00000374423 Transcript synonymous_variant 3038/10286 2652/7065 884/2354 T acT/acG rs184499250 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 LOW 1 SNV 1 1 PASS rs184499250 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 206307180 206307180 T G 1 0 0 0 0 0 0 0 1 18174 1509 53 5 5 ZDBF2 2 206307180 Silent SNP T C3N-00175_T 130341 206307180 35886349 247 9839 UNC80 0 . GRCh38 2 209829274 209829274 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2521C>A p.Gln841Lys p.Q841K ENST00000439458 15/64 159 119 40 177 177 0 strelka-varscan-mutect UNC80,missense_variant,p.Gln841Lys,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Gln836Lys,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; A ENST00000439458 Transcript missense_variant 2601/13562 2521/9777 841/3258 Q/K Cag/Aag 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 tolerated(0.3) 15/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 209829274 209829274 C A 1 0 0 0 0 1 0 0 0 17521 711 25 2 2 UNC80 2 209829274 Missense_Mutation SNP C C3N-00175_T 3522094 209829274 32364255 248 9840 UNC80 0 . GRCh38 2 209880982 209880982 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.4004G>T p.Cys1335Phe p.C1335F ENST00000439458 25/64 156 115 41 173 173 0 strelka-varscan-mutect UNC80,missense_variant,p.Cys1335Phe,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Cys1330Phe,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; T ENST00000439458 Transcript missense_variant 4084/13562 4004/9777 1335/3258 C/F tGc/tTc 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 tolerated(0.12) 25/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS rs1407012746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 209880982 209880982 G T 1 0 0 0 0 1 0 0 0 17521 1319 46 2 2 UNC80 2 209880982 Missense_Mutation SNP G C3N-00175_T 51708 209880982 32312547 249 9841 UNC80 0 . GRCh38 2 209904869 209904869 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.4488C>A p.= p.V1496V ENST00000439458 28/64 351 305 46 364 363 1 strelka-varscan-mutect UNC80,synonymous_variant,p.=,ENST00000439458,NM_032504.1;UNC80,synonymous_variant,p.=,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; A ENST00000439458 Transcript synonymous_variant 4568/13562 4488/9777 1496/3258 V gtC/gtA 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 28/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 209904869 209904869 C A 1 0 0 0 0 0 0 0 1 17521 813 29 2 2 UNC80 2 209904869 Silent SNP C C3N-00175_T 23887 209904869 32288660 250 9842 ERBB4 0 . GRCh38 2 211705331 211705331 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1185C>A p.= p.V395V ENST00000342788 10/28 243 223 20 255 255 0 strelka-varscan-mutect ERBB4,synonymous_variant,p.=,ENST00000342788,NM_005235.2;ERBB4,synonymous_variant,p.=,ENST00000436443,NM_001042599.1;ERBB4,synonymous_variant,p.=,ENST00000402597,;ERBB4,synonymous_variant,p.=,ENST00000260943,;ERBB4,non_coding_transcript_exon_variant,,ENST00000484594,; T ENST00000342788 Transcript synonymous_variant 1496/12136 1185/3927 395/1308 V gtC/gtA 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 10/28 hmmpanther:PTHR24416:SF90,hmmpanther:PTHR24416,Pfam_domain:PF01030,Gene3D:3.80.20.20,PIRSF_domain:PIRSF000619,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 211705331 211705331 G T 1 0 0 0 0 0 0 0 1 5057 1277 45 2 2 ERBB4 2 211705331 Silent SNP G C3N-00175_T 1800462 211705331 30488198 251 9843 ABCA12 0 . GRCh38 2 215019734 215019734 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1350G>A p.= p.E450E ENST00000272895 12/53 299 257 42 366 366 0 strelka-varscan-mutect ABCA12,synonymous_variant,p.=,ENST00000272895,NM_173076.2;ABCA12,synonymous_variant,p.=,ENST00000389661,NM_015657.3;AC072062.3,intron_variant,,ENST00000617699,;AC072062.3,intron_variant,,ENST00000627811,;AC072062.3,upstream_gene_variant,,ENST00000437897,;AC072062.3,upstream_gene_variant,,ENST00000595058,;AC072062.3,upstream_gene_variant,,ENST00000419251,;AC072062.3,upstream_gene_variant,,ENST00000627336,;AC072062.3,upstream_gene_variant,,ENST00000615813,;AC072062.3,upstream_gene_variant,,ENST00000602182,; T ENST00000272895 Transcript synonymous_variant 1570/9100 1350/7788 450/2595 E gaG/gaA 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 12/53 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 215019734 215019734 C T 1 0 0 0 0 0 0 0 1 34 912 32 3 3 ABCA12 2 215019734 Silent SNP C C3N-00175_T 3314403 215019734 27173795 252 9844 MARCH4 0 . GRCh38 2 216277856 216277856 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.681C>A p.= p.A227A ENST00000273067 3/4 69 63 6 93 93 0 strelka-varscan-mutect MARCH4,synonymous_variant,p.=,ENST00000273067,NM_020814.2; T ENST00000273067 Transcript synonymous_variant 2448/4447 681/1233 227/410 A gcC/gcA 1 -1 MARCH4 HGNC HGNC:29269 protein_coding YES CCDS33376.1 ENSP00000273067 Q9P2E8 UPI00001C1DB9 NM_020814.2 3/4 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF51 LOW 1 SNV 1 1 PASS rs924412065 . 0 206 3 0 0 0 0 0 -13.7903 1 1 1 1 0 T 2 4 39 216277856 216277856 G T 1 0 0 0 0 0 0 0 1 9228 1335 47 2 2 MARCH4 2 216277856 Silent SNP G C3N-00175_T 1258122 216277856 25915673 253 9845 MARCH4 0 . GRCh38 2 216370169 216370169 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.92T>A p.Met31Lys p.M31K ENST00000273067 1/4 184 170 14 243 243 0 strelka-varscan-mutect MARCH4,missense_variant,p.Met31Lys,ENST00000273067,NM_020814.2; T ENST00000273067 Transcript missense_variant 1859/4447 92/1233 31/410 M/K aTg/aAg 1 -1 MARCH4 HGNC HGNC:29269 protein_coding YES CCDS33376.1 ENSP00000273067 Q9P2E8 UPI00001C1DB9 NM_020814.2 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF51 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 216370169 216370169 A T 1 0 0 0 0 1 0 0 0 9228 217 8 4 4 MARCH4 2 216370169 Missense_Mutation SNP A C3N-00175_T 92313 216370169 25823360 254 9846 WNT10A 0 . GRCh38 2 218882290 218882290 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.243G>T p.= p.V81V ENST00000258411 2/4 272 191 81 407 407 0 strelka-varscan-mutect WNT10A,synonymous_variant,p.=,ENST00000258411,NM_025216.2;WNT10A,synonymous_variant,p.=,ENST00000458582,;WNT10A,upstream_gene_variant,,ENST00000483911,; T ENST00000258411 Transcript synonymous_variant 876/2547 243/1254 81/417 V gtG/gtT 1 1 WNT10A HGNC HGNC:13829 protein_coding YES CCDS2426.1 ENSP00000258411 Q9GZT5 UPI0000032F2A NM_025216.2 2/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF89,SMART_domains:SM00097 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 218882290 218882290 G T 1 0 0 0 0 0 0 0 1 17938 1335 47 2 2 WNT10A 2 218882290 Silent SNP G C3N-00175_T 2512121 218882290 23311239 255 9847 ABCB6 0 . GRCh38 2 219216116 219216116 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1035G>T p.= p.V345V ENST00000265316 5/19 112 65 47 151 150 1 strelka-varscan-mutect ABCB6,synonymous_variant,p.=,ENST00000265316,NM_005689.2;ABCB6,synonymous_variant,p.=,ENST00000295750,;ATG9A,downstream_gene_variant,,ENST00000409618,;ATG9A,downstream_gene_variant,,ENST00000396761,NM_024085.4;ATG9A,downstream_gene_variant,,ENST00000361242,NM_001077198.2;ATG9A,downstream_gene_variant,,ENST00000409422,;ATG9A,3_prime_UTR_variant,,ENST00000446716,;ABCB6,3_prime_UTR_variant,,ENST00000452545,;ABCB6,non_coding_transcript_exon_variant,,ENST00000492953,;ABCB6,intron_variant,,ENST00000448398,;ABCB6,intron_variant,,ENST00000417678,;ATG9A,downstream_gene_variant,,ENST00000409033,;ABCB6,upstream_gene_variant,,ENST00000497882,;ATG9A,downstream_gene_variant,,ENST00000475339,;ABCB6,upstream_gene_variant,,ENST00000492543,;ABCB6,upstream_gene_variant,,ENST00000496984,;ABCB6,upstream_gene_variant,,ENST00000494639,; A ENST00000265316 Transcript synonymous_variant 1352/3016 1035/2529 345/842 V gtG/gtT 1 -1 ABCB6 HGNC HGNC:47 protein_coding YES CCDS2436.1 ENSP00000265316 Q9NP58 UPI000004C4BA NM_005689.2 5/19 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF18,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS . . 0 201 7 2 0 0 0 0 -20 0.9999781 1 1 1 0 A 2 1 39 219216116 219216116 C A 1 0 0 0 0 0 0 0 1 49 581 21 2 2 ABCB6 2 219216116 Silent SNP C C3N-00175_T 333826 219216116 22977413 256 9848 PTPRN 0 . GRCh38 2 219302487 219302487 + Missense_Mutation SNP C C G rs565592583 C3N-00175_T C3N-00175_N C C c.644G>C p.Gly215Ala p.G215A ENST00000295718 6/23 110 97 13 170 170 0 strelka-varscan-mutect PTPRN,missense_variant,p.Gly215Ala,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Gly215Ala,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Gly125Ala,ENST00000423636,NM_001199764.1;PTPRN,missense_variant,p.Gly125Ala,ENST00000412847,;PTPRN,incomplete_terminal_codon_variant,p.=,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,downstream_gene_variant,,ENST00000468454,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,;PTPRN,downstream_gene_variant,,ENST00000484986,; G ENST00000295718 Transcript missense_variant 885/3784 644/2940 215/979 G/A gGc/gCc rs565592583 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 tolerated(0.17) 6/23 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2 MODERATE 1 SNV 1 1 PASS rs565592583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 219302487 219302487 C G 1 0 0 0 0 1 0 0 0 12961 753 26 4 4 PTPRN 2 219302487 Missense_Mutation SNP C C3N-00175_T 86371 219302487 22891042 257 9849 SPEG 0 . GRCh38 2 219468636 219468636 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.3201A>T p.= p.T1067T ENST00000312358 11/41 126 87 39 194 194 0 strelka-varscan-mutect SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;SPEG,downstream_gene_variant,,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000396688,NM_001173476.1;SPEG,downstream_gene_variant,,ENST00000396689,;SPEG,downstream_gene_variant,,ENST00000396686,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,downstream_gene_variant,,ENST00000498378,;SPEG,downstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000496786,;SPEG,downstream_gene_variant,,ENST00000464989,;SPEG,upstream_gene_variant,,ENST00000485069,;SPEG,downstream_gene_variant,,ENST00000475921,; T ENST00000312358 Transcript synonymous_variant 3333/10782 3201/9804 1067/3267 T acA/acT 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 11/41 Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 219468636 219468636 A T 1 0 0 0 0 0 0 0 1 15387 146 6 4 4 SPEG 2 219468636 Silent SNP A C3N-00175_T 166149 219468636 22724893 258 9850 SPEG 0 . GRCh38 2 219483675 219483675 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.6212G>T p.Arg2071Leu p.R2071L ENST00000312358 30/41 168 149 19 222 222 0 strelka-varscan-mutect SPEG,missense_variant,p.Arg2071Leu,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript missense_variant 6344/10782 6212/9804 2071/3267 R/L cGc/cTc 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 219483675 219483675 G T 1 0 0 0 0 1 0 0 0 15387 1087 38 1 1 SPEG 2 219483675 Missense_Mutation SNP G C3N-00175_T 15039 219483675 22709854 259 9851 SPEG 0 . GRCh38 2 219490932 219490932 + Missense_Mutation SNP C C A rs775299831 C3N-00175_T C3N-00175_N C C c.9361C>A p.Arg3121Ser p.R3121S ENST00000312358 38/41 145 103 42 211 210 1 strelka-varscan-mutect SPEG,missense_variant,p.Arg3121Ser,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000412982,;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; A ENST00000312358 Transcript missense_variant 9493/10782 9361/9804 3121/3267 R/S Cgc/Agc rs775299831 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.16) 38/41 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 5 1 PASS rs775299831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 219490932 219490932 C A 1 0 0 0 0 1 0 0 0 15387 652 23 1 1 SPEG 2 219490932 Missense_Mutation SNP C C3N-00175_T 7257 219490932 22702597 260 9852 SLC4A3 0 . GRCh38 2 219630291 219630291 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.831G>C p.Gln277His p.Q277H ENST00000273063 6/23 129 117 12 216 216 0 strelka-varscan-mutect SLC4A3,missense_variant,p.Gln250His,ENST00000358055,NM_005070.3;SLC4A3,missense_variant,p.Gln277His,ENST00000273063,NM_001326559.1,NM_201574.2;SLC4A3,missense_variant,p.Gln250His,ENST00000373760,;SLC4A3,missense_variant,p.Gln250His,ENST00000317151,;SLC4A3,upstream_gene_variant,,ENST00000413743,;AC009955.8,upstream_gene_variant,,ENST00000455896,;SLC4A3,intron_variant,,ENST00000497589,;SLC4A3,missense_variant,p.Gln250His,ENST00000425141,;SLC4A3,upstream_gene_variant,,ENST00000416910,;SLC4A3,upstream_gene_variant,,ENST00000444906,; C ENST00000273063 Transcript missense_variant 1045/4246 831/3780 277/1259 Q/H caG/caC 1 1 SLC4A3 HGNC HGNC:11029 protein_coding YES CCDS2446.1 ENSP00000273063 P48751 UPI000022BE50 NM_001326559.1,NM_201574.2 deleterious(0.03) 6/23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.5411 0.9999998 1 1 1 0 C 3 2 39 219630291 219630291 G C 1 0 0 0 0 1 0 0 0 14932 991 35 4 4 SLC4A3 2 219630291 Missense_Mutation SNP G C3N-00175_T 139359 219630291 22563238 261 9853 PAX3 0 . GRCh38 2 222232093 222232093 + Silent SNP G G C rs773501490 C3N-00175_T C3N-00175_N G G c.777C>G p.= p.T259T ENST00000392069 5/10 406 322 84 467 467 0 strelka-varscan-mutect PAX3,synonymous_variant,p.=,ENST00000350526,NM_181457.3;PAX3,synonymous_variant,p.=,ENST00000392069,NM_181459.3;PAX3,synonymous_variant,p.=,ENST00000344493,NM_181461.3;PAX3,synonymous_variant,p.=,ENST00000392070,NM_181458.3;PAX3,synonymous_variant,p.=,ENST00000336840,NM_181460.3;PAX3,synonymous_variant,p.=,ENST00000409551,NM_001127366.2; C ENST00000392069 Transcript synonymous_variant 1143/3170 777/1518 259/505 T acC/acG rs773501490,COSM4908583,COSM4908584 1 -1 PAX3 HGNC HGNC:8617 protein_coding YES CCDS2448.1 ENSP00000375921 P23760 UPI00001A8BF0 NM_181459.3 5/10 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF307,SMART_domains:SM00389,Superfamily_domains:SSF46689 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs773501490 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 222232093 222232093 G C 1 0 0 0 0 0 0 0 1 11565 1103 39 4 4 PAX3 2 222232093 Silent SNP G C3N-00175_T 2601802 222232093 19961436 262 9854 CUL3 0 . GRCh38 2 224474378 224474378 + Splice_Site SNP T T G rs779923028 C3N-00175_T C3N-00175_N T T c.2176-2A>C p.X726_splice ENST00000264414 50 40 10 77 77 0 strelka-varscan-mutect CUL3,splice_acceptor_variant,,ENST00000264414,NM_003590.4;CUL3,splice_acceptor_variant,,ENST00000344951,NM_001257197.1;CUL3,splice_acceptor_variant,,ENST00000409777,;CUL3,splice_acceptor_variant,,ENST00000409096,NM_001257198.1;CUL3,splice_acceptor_variant,,ENST00000617432,;CUL3,splice_acceptor_variant,,ENST00000451538,;RP11-92F20.1,non_coding_transcript_exon_variant,,ENST00000622296,;RP11-92F20.1,non_coding_transcript_exon_variant,,ENST00000620050,;CUL3,downstream_gene_variant,,ENST00000536702,;CUL3,splice_acceptor_variant,,ENST00000497715,;CUL3,splice_acceptor_variant,,ENST00000454323,; G ENST00000264414 Transcript splice_acceptor_variant -/6741 2176/2307 726/768 rs779923028,COSM4855130 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 15/15 0,1 HIGH 1 SNV 1 0,1 1 PASS rs779923028 . 0 193 15 0 0 0 0 0 -19.99986 0.9997203 1 1 1 0 G 5 3 39 224474378 224474378 T G 1 0 0 0 0 0 0 1 0 3866 1536 53 5 5 CUL3 2 224474378 Splice_Site SNP T C3N-00175_T 2242285 224474378 17719151 263 9855 SP140 0 . GRCh38 2 230248885 230248885 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.893A>T p.Glu298Val p.E298V ENST00000392045 9/27 142 96 46 117 117 0 strelka-varscan-mutect SP140,missense_variant,p.Glu298Val,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Glu298Val,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Glu272Val,ENST00000343805,NM_001278452.1;SP140,missense_variant,p.Glu245Val,ENST00000417495,NM_001278453.1; T ENST00000392045 Transcript missense_variant,splice_region_variant 1007/3246 893/2604 298/867 E/V gAg/gTg 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 tolerated(0.72) 9/27 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 230248885 230248885 A T 1 0 0 0 0 1 0 0 0 15288 318 11 4 4 SP140 2 230248885 Missense_Mutation SNP A C3N-00175_T 5774507 230248885 11944644 264 9856 GIGYF2 0 . GRCh38 2 232832893 232832893 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2629G>T p.Glu877Ter p.E877* ENST00000409451 24/31 385 353 32 375 374 1 strelka-varscan-mutect GIGYF2,stop_gained,p.Glu878Ter,ENST00000629305,;GIGYF2,stop_gained,p.Glu856Ter,ENST00000409547,NM_015575.3;GIGYF2,stop_gained,p.Glu878Ter,ENST00000409480,;GIGYF2,stop_gained,p.Glu877Ter,ENST00000409451,NM_001103147.1;GIGYF2,stop_gained,p.Glu856Ter,ENST00000373563,NM_001103146.1;GIGYF2,stop_gained,p.Glu850Ter,ENST00000409196,NM_001103148.1;Y_RNA,downstream_gene_variant,,ENST00000362911,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000469843,;GIGYF2,non_coding_transcript_exon_variant,,ENST00000474312,; T ENST00000409451 Transcript stop_gained 2855/5937 2629/3963 877/1320 E/* Gaa/Taa 1 1 GIGYF2 HGNC HGNC:11960 protein_coding YES CCDS46542.1 ENSP00000387170 Q6Y7W6 UPI00003FEC8F NM_001103147.1 24/31 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14445,hmmpanther:PTHR14445:SF38,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 232832893 232832893 G T 1 0 0 0 0 0 1 0 0 6258 943 33 2 2 GIGYF2 2 232832893 Nonsense_Mutation SNP G C3N-00175_T 2584008 232832893 9360636 265 9857 INPP5D 0 . GRCh38 2 233146210 233146210 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.802C>T p.= p.L268L ENST00000445964 7/27 278 179 99 331 331 0 strelka-varscan-mutect INPP5D,synonymous_variant,p.=,ENST00000359570,NM_005541.4;INPP5D,synonymous_variant,p.=,ENST00000445964,NM_001017915.2;INPP5D,downstream_gene_variant,,ENST00000451407,; T ENST00000445964 Transcript synonymous_variant 883/4845 802/3570 268/1189 L Ctg/Ttg 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 7/27 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1224361143 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 233146210 233146210 C T 1 0 0 0 0 0 0 0 1 7659 564 20 3 3 INPP5D 2 233146210 Silent SNP C C3N-00175_T 313317 233146210 9047319 266 9858 INPP5D 0 . GRCh38 2 233198180 233198180 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2779C>A p.Leu927Met p.L927M ENST00000445964 25/27 182 167 15 177 177 0 strelka-varscan-mutect INPP5D,missense_variant,p.Leu926Met,ENST00000359570,NM_005541.4;INPP5D,missense_variant,p.Leu927Met,ENST00000445964,NM_001017915.2;INPP5D,missense_variant,p.Leu548Met,ENST00000415617,;INPP5D,missense_variant,p.Leu49Met,ENST00000417661,; A ENST00000445964 Transcript missense_variant 2860/4845 2779/3570 927/1189 L/M Ctg/Atg 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 tolerated(0.22) 25/27 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69 MODERATE 1 SNV 1 1 PASS rs1057220841 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 233198180 233198180 C A 1 0 0 0 0 1 0 0 0 7659 680 24 2 2 INPP5D 2 233198180 Missense_Mutation SNP C C3N-00175_T 51970 233198180 8995349 267 9859 UGT1A10 0 . GRCh38 2 233637045 233637045 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.523C>A p.His175Asn p.H175N ENST00000344644 1/5 204 133 71 215 214 1 strelka-varscan-mutect UGT1A10,missense_variant,p.His175Asn,ENST00000344644,NM_019075.2;UGT1A10,missense_variant,p.His175Asn,ENST00000373445,;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4; A ENST00000344644 Transcript missense_variant 592/2408 523/1593 175/530 H/N Cac/Aac 1 1 UGT1A10 HGNC HGNC:12531 protein_coding YES CCDS33403.1 ENSP00000343838 Q9HAW8 Q5DT02 UPI000006D7E8 NM_019075.2 tolerated(0.16) 1/5 Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF173,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 233637045 233637045 C A 1 0 0 0 0 1 0 0 0 17470 594 21 2 2 UGT1A10 2 233637045 Missense_Mutation SNP C C3N-00175_T 438865 233637045 8556484 268 9860 UGT1A9 0 . GRCh38 2 233672190 233672190 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.256C>G p.Leu86Val p.L86V ENST00000354728 1/5 137 125 12 148 148 0 strelka-varscan-mutect UGT1A9,missense_variant,p.Leu86Val,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A10,intron_variant,,ENST00000373445,; G ENST00000354728 Transcript missense_variant 338/2416 256/1593 86/530 L/V Ctg/Gtg 1 1 UGT1A9 HGNC HGNC:12541 protein_coding YES CCDS2505.1 ENSP00000346768 O60656 Q5DSZ5 UPI0000044213 NM_021027.2 tolerated(0.24) 1/5 hmmpanther:PTHR11926:SF173,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 233672190 233672190 C G 1 0 0 0 0 1 0 0 0 17477 912 32 4 4 UGT1A9 2 233672190 Missense_Mutation SNP C C3N-00175_T 35145 233672190 8521339 269 9861 SH3BP4 0 . GRCh38 2 235041148 235041148 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.379A>T p.Asn127Tyr p.N127Y ENST00000409212 4/6 222 150 72 217 217 0 strelka-varscan-mutect SH3BP4,missense_variant,p.Asn127Tyr,ENST00000409212,;SH3BP4,missense_variant,p.Asn127Tyr,ENST00000392011,NM_014521.2;SH3BP4,missense_variant,p.Asn127Tyr,ENST00000344528,;SH3BP4,missense_variant,p.Asn127Tyr,ENST00000446904,;SH3BP4,downstream_gene_variant,,ENST00000416021,;SH3BP4,downstream_gene_variant,,ENST00000444916,;SH3BP4,downstream_gene_variant,,ENST00000454947,; T ENST00000409212 Transcript missense_variant 886/5231 379/2892 127/963 N/Y Aat/Tat 1 1 SH3BP4 HGNC HGNC:10826 protein_coding YES CCDS2513.1 ENSP00000386862 Q9P0V3 UPI000006DA47 deleterious(0.02) 4/6 hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 235041148 235041148 A T 1 0 0 0 0 1 0 0 0 14504 362 13 4 4 SH3BP4 2 235041148 Missense_Mutation SNP A C3N-00175_T 1368958 235041148 7152381 270 9862 COL6A3 0 . GRCh38 2 237340687 237340687 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.8229G>T p.= p.L2743L ENST00000295550 38/44 364 259 105 442 442 0 strelka-varscan-mutect COL6A3,synonymous_variant,p.=,ENST00000295550,NM_004369.3;COL6A3,synonymous_variant,p.=,ENST00000353578,NM_057167.3;COL6A3,synonymous_variant,p.=,ENST00000409809,;COL6A3,synonymous_variant,p.=,ENST00000472056,NM_057166.4;COL6A3,synonymous_variant,p.=,ENST00000347401,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;COL6A3,upstream_gene_variant,,ENST00000468792,; A ENST00000295550 Transcript synonymous_variant 8682/10749 8229/9534 2743/3177 L ctG/ctT 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 38/44 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 237340687 237340687 C A 1 0 0 0 0 0 0 0 1 3490 813 29 2 2 COL6A3 2 237340687 Silent SNP C C3N-00175_T 2299539 237340687 4852842 271 9863 MLPH 0 . GRCh38 2 237552357 237552357 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1696G>C p.Asp566His p.D566H ENST00000264605 15/16 355 257 98 353 353 0 strelka-varscan-mutect MLPH,missense_variant,p.Asp566His,ENST00000264605,NM_024101.6;MLPH,missense_variant,p.Asp538His,ENST00000338530,NM_001042467.2;MLPH,missense_variant,p.Asp423His,ENST00000410032,NM_001281474.1;MLPH,missense_variant,p.Asp446His,ENST00000409373,NM_001281473.1;MLPH,missense_variant,p.Asp326His,ENST00000437893,;MLPH,missense_variant,p.Asp202His,ENST00000415753,;MLPH,missense_variant,p.Asp115His,ENST00000434770,;MLPH,missense_variant,p.Asp165His,ENST00000432475,;MLPH,non_coding_transcript_exon_variant,,ENST00000495439,;MLPH,non_coding_transcript_exon_variant,,ENST00000464123,;MLPH,non_coding_transcript_exon_variant,,ENST00000478712,;MLPH,non_coding_transcript_exon_variant,,ENST00000477457,;MLPH,non_coding_transcript_exon_variant,,ENST00000489967,; C ENST00000264605 Transcript missense_variant 1990/3823 1696/1803 566/600 D/H Gat/Cat 1 1 MLPH HGNC HGNC:29643 protein_coding YES CCDS2518.1 ENSP00000264605 Q9BV36 A0A024R492 UPI00000730BF NM_024101.6 tolerated(0.06) 15/16 hmmpanther:PTHR14555 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 237552357 237552357 G C 1 0 0 0 0 1 0 0 0 9596 1290 45 4 4 MLPH 2 237552357 Missense_Mutation SNP G C3N-00175_T 211670 237552357 4641172 272 9864 ANO7 0 . GRCh38 2 241209344 241209344 + Nonsense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.1299G>A p.Trp433Ter p.W433* ENST00000274979 12/25 190 174 16 248 248 0 strelka-varscan-mutect ANO7,stop_gained,p.Trp433Ter,ENST00000274979,NM_001001891.3;ANO7,stop_gained,p.Trp432Ter,ENST00000402430,;ANO7,upstream_gene_variant,,ENST00000471606,; A ENST00000274979 Transcript stop_gained 1402/4128 1299/2802 433/933 W/* tgG/tgA COSM1018876,COSM1592028 1 1 ANO7 HGNC HGNC:31677 protein_coding YES CCDS33423.1 ENSP00000274979 Q6IWH7 UPI0000D612DB NM_001001891.3 12/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR12308:SF22,hmmpanther:PTHR12308,Pfam_domain:PF04547 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 241209344 241209344 G A 1 0 0 0 0 0 1 0 0 809 1241 43 3 3 ANO7 2 241209344 Nonsense_Mutation SNP G C3N-00175_T 3656987 241209344 984185 273 9865 GAL3ST2 0 . GRCh38 2 241804041 241804041 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1072C>A p.Leu358Met p.L358M ENST00000192314 4/4 170 149 21 181 179 2 strelka-varscan-mutect GAL3ST2,missense_variant,p.Leu358Met,ENST00000192314,NM_022134.2;NEU4,upstream_gene_variant,,ENST00000407683,NM_001167601.2,NM_001167600.2;AC114730.3,downstream_gene_variant,,ENST00000413820,;AC114730.5,upstream_gene_variant,,ENST00000437438,; A ENST00000192314 Transcript missense_variant 1203/1370 1072/1197 358/398 L/M Ctg/Atg 1 1 GAL3ST2 HGNC HGNC:24869 protein_coding YES CCDS33427.1 ENSP00000192314 Q9H3Q3 UPI000049DF44 NM_022134.2 deleterious(0.02) 4/4 hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF55,Pfam_domain:PF06990 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 241804041 241804041 C A 1 0 0 0 0 1 0 0 0 6066 680 24 2 2 GAL3ST2 2 241804041 Missense_Mutation SNP C C3N-00175_T 594697 241804041 389488 274 9866 CHL1 0 . GRCh38 3 390814 390814 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2584C>A p.Gln862Lys p.Q862K ENST00000256509 21/28 134 104 30 139 139 0 strelka-mutect CHL1,missense_variant,p.Gln862Lys,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Gln862Lys,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Gln846Lys,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Gln49Lys,ENST00000445697,;CHL1,downstream_gene_variant,,ENST00000470880,;CHL1,splice_region_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant,splice_region_variant 3226/8023 2584/3675 862/1224 Q/K Cag/Aag 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(1) 21/28 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 390814 390814 C A 1 0 0 0 0 1 0 0 0 3108 840 29 2 2 CHL1 3 390814 Missense_Mutation SNP C C3N-00175_T 390814 197904745 275 9867 IL5RA 0 . GRCh38 3 3092320 3092320 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.898G>T p.Asp300Tyr p.D300Y ENST00000446632 9/12 171 124 47 173 173 0 strelka-varscan-mutect IL5RA,missense_variant,p.Asp300Tyr,ENST00000446632,NM_175726.3;IL5RA,missense_variant,p.Asp300Tyr,ENST00000438560,NM_001243099.1;IL5RA,missense_variant,p.Asp300Tyr,ENST00000256452,NM_000564.4;IL5RA,missense_variant,p.Asp300Tyr,ENST00000383846,NM_175728.2;IL5RA,missense_variant,p.Asp300Tyr,ENST00000430514,NM_175724.2;IL5RA,missense_variant,p.Asp300Tyr,ENST00000456302,NM_175727.2;IL5RA,missense_variant,p.Asp300Tyr,ENST00000311981,NM_175725.2;IL5RA,intron_variant,,ENST00000418488,; A ENST00000446632 Transcript missense_variant 1473/2514 898/1263 300/420 D/Y Gat/Tat COSM3592392,COSM3592393 1 -1 IL5RA HGNC HGNC:6017 protein_coding YES CCDS2559.1 ENSP00000412209 Q01344 A0A024R2C8 UPI000013C656 NM_175726.3 tolerated(0.1) 9/12 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF17,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1181321792 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 3092320 3092320 C A 1 0 0 0 0 1 0 0 0 7604 826 29 2 2 IL5RA 3 3092320 Missense_Mutation SNP C C3N-00175_T 2701506 3092320 195203239 276 9868 GRM7 0 . GRCh38 3 6861592 6861592 + Silent SNP C C G C3N-00175_T C3N-00175_N C C c.204C>G p.= p.G68G ENST00000357716 1/10 85 71 14 101 101 0 strelka-varscan-mutect GRM7,synonymous_variant,p.=,ENST00000486284,NM_181874.2;GRM7,synonymous_variant,p.=,ENST00000357716,NM_000844.3;GRM7,synonymous_variant,p.=,ENST00000389336,;GRM7,intron_variant,,ENST00000448328,;GRM7,synonymous_variant,p.=,ENST00000467425,;GRM7,synonymous_variant,p.=,ENST00000440923,;GRM7,synonymous_variant,p.=,ENST00000389335,;GRM7,intron_variant,,ENST00000443259,;GRM7,upstream_gene_variant,,ENST00000435689,; G ENST00000357716 Transcript synonymous_variant 478/4127 204/2748 68/915 G ggC/ggG COSM2784348,COSM4326860,COSM4326861 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 1/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS rs985362954 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 6861592 6861592 C G 1 0 0 0 0 0 0 0 1 6684 755 27 4 4 GRM7 3 6861592 Silent SNP C C3N-00175_T 3769272 6861592 191433967 277 9869 RAD18 0 . GRCh38 3 8939581 8939581 + Missense_Mutation SNP C C A rs368107670 C3N-00175_T C3N-00175_N C C c.677G>T p.Arg226Leu p.R226L ENST00000264926 6/13 137 101 36 136 135 1 strelka-varscan-mutect RAD18,missense_variant,p.Arg226Leu,ENST00000264926,NM_020165.3;RAD18,downstream_gene_variant,,ENST00000421052,;RAD18,downstream_gene_variant,,ENST00000413832,;RAD18,downstream_gene_variant,,ENST00000418463,;RAD18,downstream_gene_variant,,ENST00000495087,;RAD18,missense_variant,p.Arg226Leu,ENST00000415439,; A ENST00000264926 Transcript missense_variant 794/5886 677/1488 226/495 R/L cGc/cTc rs368107670 1 -1 RAD18 HGNC HGNC:18278 protein_coding YES CCDS2571.1 ENSP00000264926 Q9NS91 UPI000013D592 NM_020165.3 deleterious(0) 6/13 hmmpanther:PTHR14134,hmmpanther:PTHR14134:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs368107670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 8939581 8939581 C A 1 0 0 0 0 1 0 0 0 13140 768 27 1 1 RAD18 3 8939581 Missense_Mutation SNP C C3N-00175_T 2077989 8939581 189355978 278 9870 RPUSD3 0 . GRCh38 3 9840779 9840779 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.434C>A p.Ser145Tyr p.S145Y ENST00000383820 5/9 124 101 23 146 146 0 strelka-varscan-mutect RPUSD3,missense_variant,p.Ser145Tyr,ENST00000383820,NM_173659.3;RPUSD3,missense_variant,p.Ser130Tyr,ENST00000433535,NM_001142547.1;RPUSD3,missense_variant,p.Ser113Tyr,ENST00000424438,;RPUSD3,missense_variant,p.Ser141Tyr,ENST00000418713,;RPUSD3,missense_variant,p.Ser136Tyr,ENST00000427174,;TTLL3,intron_variant,,ENST00000455274,;TTLL3,downstream_gene_variant,,ENST00000383827,;RPUSD3,downstream_gene_variant,,ENST00000433972,;RPUSD3,downstream_gene_variant,,ENST00000433555,;RPUSD3,upstream_gene_variant,,ENST00000423108,;RPUSD3,downstream_gene_variant,,ENST00000485705,;RPUSD3,downstream_gene_variant,,ENST00000473522,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000484134,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000475470,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000464783,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000472381,;TTLL3,downstream_gene_variant,,ENST00000483051,;RPUSD3,upstream_gene_variant,,ENST00000466141,;RPUSD3,downstream_gene_variant,,ENST00000451405,;RPUSD3,downstream_gene_variant,,ENST00000460909,; T ENST00000383820 Transcript missense_variant 436/1225 434/1056 145/351 S/Y tCc/tAc 1 -1 RPUSD3 HGNC HGNC:28437 protein_coding YES CCDS2586.2 ENSP00000373331 Q6P087 UPI000066D9E0 NM_173659.3 deleterious(0) 5/9 hmmpanther:PTHR11079,hmmpanther:PTHR11079:SF93,Pfam_domain:PF00849,Superfamily_domains:SSF55120 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999959 1 1 1 0 T 3 4 39 9840779 9840779 G T 1 0 0 0 0 1 0 0 0 13923 1174 41 2 2 RPUSD3 3 9840779 Missense_Mutation SNP G C3N-00175_T 901198 9840779 188454780 279 9871 SLC6A6 0 . GRCh38 3 14478529 14478529 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1714G>T p.Val572Phe p.V572F ENST00000613060 12/15 256 205 51 306 306 0 strelka-varscan-mutect SLC6A6,missense_variant,p.Val471Phe,ENST00000622186,NM_003043.5;SLC6A6,missense_variant,p.Val572Phe,ENST00000613060,NM_001134367.3;SLC6A6,intron_variant,,ENST00000452151,;SLC6A6,3_prime_UTR_variant,,ENST00000618278,;SLC6A6,3_prime_UTR_variant,,ENST00000610642,; T ENST00000613060 Transcript missense_variant 1732/6526 1714/2166 572/721 V/F Gtt/Ttt 1 1 SLC6A6 HGNC HGNC:11052 protein_coding YES CCDS77704.1 ENSP00000481625 A0A087WY96 UPI0004449BB2 NM_001134367.3 tolerated(0.18) 12/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF171,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 14478529 14478529 G T 1 0 0 0 0 1 0 0 0 14971 1261 44 2 2 SLC6A6 3 14478529 Missense_Mutation SNP G C3N-00175_T 4637750 14478529 183817030 280 9872 C3orf20 0 . GRCh38 3 14684286 14684286 + Missense_Mutation SNP A A T rs144138671 C3N-00175_T C3N-00175_N A A c.529A>T p.Ser177Cys p.S177C ENST00000253697 4/17 149 123 26 219 219 0 strelka-varscan-mutect C3orf20,missense_variant,p.Ser177Cys,ENST00000253697,NM_032137.4;C3orf20,missense_variant,p.Ser55Cys,ENST00000435614,NM_001184958.1;C3orf20,missense_variant,p.Ser55Cys,ENST00000412910,NM_001184957.1; T ENST00000253697 Transcript missense_variant 981/3326 529/2715 177/904 S/C Agc/Tgc rs144138671 1 1 C3orf20 HGNC HGNC:25320 protein_coding YES CCDS33706.1 ENSP00000253697 Q8ND61 UPI000013CDE9 NM_032137.4 deleterious(0) 4/17 hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF16 MODERATE 1 SNV 1 1 PASS rs144138671 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 14684286 14684286 A T 1 0 0 0 0 1 0 0 0 2061 188 7 4 4 C3orf20 3 14684286 Missense_Mutation SNP A C3N-00175_T 205757 14684286 183611273 281 9873 C3orf20 0 . GRCh38 3 14703202 14703202 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.818T>A p.Leu273Gln p.L273Q ENST00000253697 6/17 212 172 40 237 237 0 strelka-varscan-mutect C3orf20,missense_variant,p.Leu273Gln,ENST00000253697,NM_032137.4;C3orf20,missense_variant,p.Leu151Gln,ENST00000435614,NM_001184958.1;C3orf20,missense_variant,p.Leu151Gln,ENST00000412910,NM_001184957.1;C3orf20,upstream_gene_variant,,ENST00000495387,; A ENST00000253697 Transcript missense_variant 1270/3326 818/2715 273/904 L/Q cTg/cAg 1 1 C3orf20 HGNC HGNC:25320 protein_coding YES CCDS33706.1 ENSP00000253697 Q8ND61 UPI000013CDE9 NM_032137.4 tolerated(0.06) 6/17 hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 14703202 14703202 T A 1 0 0 0 0 1 0 0 0 2061 1580 55 4 4 C3orf20 3 14703202 Missense_Mutation SNP T C3N-00175_T 18916 14703202 183592357 282 9874 CAPN7 0 . GRCh38 3 15217475 15217475 + Nonsense_Mutation SNP G G T rs760107220 C3N-00175_T C3N-00175_N G G c.262G>T p.Glu88Ter p.E88* ENST00000253693 3/21 124 100 24 162 162 0 strelka-varscan-mutect CAPN7,stop_gained,p.Glu88Ter,ENST00000253693,NM_014296.2;CAPN7,3_prime_UTR_variant,,ENST00000457023,;CAPN7,3_prime_UTR_variant,,ENST00000418994,; T ENST00000253693 Transcript stop_gained 515/4353 262/2442 88/813 E/* Gag/Tag rs760107220 1 1 CAPN7 HGNC HGNC:1484 protein_coding YES CCDS2624.1 ENSP00000253693 Q9Y6W3 UPI0000038A6D NM_014296.2 3/21 Gene3D:1.20.58.280,Pfam_domain:PF04212,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF22,SMART_domains:SM00745,Superfamily_domains:SSF116846 HIGH 1 SNV 1 1 PASS rs760107220 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 15217475 15217475 G T 1 0 0 0 0 0 1 0 0 2325 943 33 2 2 CAPN7 3 15217475 Nonsense_Mutation SNP G C3N-00175_T 514273 15217475 183078084 283 9875 TBC1D5 0 . GRCh38 3 17404898 17404898 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.340G>T p.Ala114Ser p.A114S ENST00000446818 7/24 42 35 7 58 58 0 strelka-varscan-mutect TBC1D5,missense_variant,p.Ala114Ser,ENST00000253692,NM_014744.2;TBC1D5,missense_variant,p.Ala114Ser,ENST00000429383,;TBC1D5,missense_variant,p.Ala114Ser,ENST00000446818,NM_001134381.1;TBC1D5,missense_variant,p.Ala66Ser,ENST00000429924,;TBC1D5,missense_variant,p.Ala114Ser,ENST00000415814,;TBC1D5,missense_variant,p.Ala114Ser,ENST00000428355,;TBC1D5,missense_variant,p.Ala114Ser,ENST00000445294,;TBC1D5,missense_variant,p.Ala114Ser,ENST00000425944,;TBC1D5,downstream_gene_variant,,ENST00000414349,;TBC1D5,downstream_gene_variant,,ENST00000507877,;TBC1D5,downstream_gene_variant,,ENST00000446863,;TBC1D5,downstream_gene_variant,,ENST00000434420,;TBC1D5,intron_variant,,ENST00000414318,;TBC1D5,downstream_gene_variant,,ENST00000443499,;TBC1D5,downstream_gene_variant,,ENST00000497531,;TBC1D5,downstream_gene_variant,,ENST00000443386,;TBC1D5,downstream_gene_variant,,ENST00000444756,;TBC1D5,3_prime_UTR_variant,,ENST00000412981,;TBC1D5,3_prime_UTR_variant,,ENST00000452492,;TBC1D5,3_prime_UTR_variant,,ENST00000430169,; A ENST00000446818 Transcript missense_variant 604/3124 340/2454 114/817 A/S Gca/Tca 1 -1 TBC1D5 HGNC HGNC:19166 protein_coding YES CCDS46770.1 ENSP00000402935 Q92609 UPI00017E10F6 NM_001134381.1 tolerated(0.42) 7/24 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF28,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 17404898 17404898 C A 1 0 0 0 0 1 0 0 0 16028 797 28 2 2 TBC1D5 3 17404898 Missense_Mutation SNP C C3N-00175_T 2187423 17404898 180890661 284 9876 KCNH8 0 . GRCh38 3 19390499 19390499 + Missense_Mutation SNP G G A rs760239055 C3N-00175_T C3N-00175_N G G c.830G>A p.Arg277Gln p.R277Q ENST00000328405 6/16 114 90 24 123 123 0 varscan-mutect KCNH8,missense_variant,p.Arg277Gln,ENST00000328405,NM_144633.2;KCNH8,non_coding_transcript_exon_variant,,ENST00000475063,;KCNH8,3_prime_UTR_variant,,ENST00000452398,; A ENST00000328405 Transcript missense_variant 1096/5137 830/3324 277/1107 R/Q cGa/cAa rs760239055,COSM5011068 1 1 KCNH8 HGNC HGNC:18864 protein_coding YES CCDS2632.1 ENSP00000328813 Q96L42 UPI0000167D12 NM_144633.2 deleterious(0.01) 6/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF380,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR01463 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760239055 . 0 206 2 2 0 0 0 0 -20 0.999999 1 1 1 0 A 3 1 39 19390499 19390499 G A 1 0 0 0 0 1 0 0 0 7954 1058 37 1 1 KCNH8 3 19390499 Missense_Mutation SNP G C3N-00175_T 1985601 19390499 178905060 285 9877 OXSM 0 . GRCh38 3 25791660 25791660 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.640C>G p.His214Asp p.H214D ENST00000280701 2/3 164 143 21 185 185 0 strelka-varscan-mutect OXSM,missense_variant,p.His214Asp,ENST00000280701,NM_017897.2;OXSM,missense_variant,p.His214Asp,ENST00000420173,NM_001145391.1;OXSM,missense_variant,p.His214Asp,ENST00000452098,;OXSM,missense_variant,p.His214Asp,ENST00000428266,;OXSM,intron_variant,,ENST00000626005,;NGLY1,upstream_gene_variant,,ENST00000417874,NM_001145294.1;OXSM,intron_variant,,ENST00000449808,;OXSM,downstream_gene_variant,,ENST00000464688,;OXSM,intron_variant,,ENST00000448177,; G ENST00000280701 Transcript missense_variant 739/1519 640/1380 214/459 H/D Cat/Gat 1 1 OXSM HGNC HGNC:26063 protein_coding YES CCDS2643.1 ENSP00000280701 Q9NWU1 A0A024R2Q9 UPI000004713F NM_017897.2 deleterious(0) 2/3 hmmpanther:PTHR11712:SF273,hmmpanther:PTHR11712,PROSITE_patterns:PS00606,TIGRFAM_domain:TIGR03150,Pfam_domain:PF00109,Gene3D:3.40.47.10,PIRSF_domain:PIRSF000447,SMART_domains:SM00825,Superfamily_domains:SSF53901 MODERATE 1 SNV 1 1 PASS rs1481250820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 25791660 25791660 C G 1 0 0 0 0 1 0 0 0 11408 826 29 4 4 OXSM 3 25791660 Missense_Mutation SNP C C3N-00175_T 6401161 25791660 172503899 286 9878 LRRC3B 0 . GRCh38 3 26709725 26709725 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.53T>C p.Leu18Pro p.L18P ENST00000396641 2/2 122 99 23 141 141 0 strelka-varscan-mutect LRRC3B,missense_variant,p.Leu18Pro,ENST00000396641,NM_052953.2;LRRC3B,missense_variant,p.Leu18Pro,ENST00000417744,NM_001317810.1;LRRC3B,missense_variant,p.Leu18Pro,ENST00000456208,NM_001317811.1;LRRC3B,missense_variant,p.Leu18Pro,ENST00000432040,;LRRC3B,missense_variant,p.Leu18Pro,ENST00000414619,;AC114877.3,upstream_gene_variant,,ENST00000446601,;LRRC3B,downstream_gene_variant,,ENST00000469437,; C ENST00000396641 Transcript missense_variant 645/1696 53/780 18/259 L/P cTa/cCa 1 1 LRRC3B HGNC HGNC:28105 protein_coding YES CCDS2644.1 ENSP00000379880 Q96PB8 A0A024R2R0 UPI000000D990 NM_052953.2 deleterious(0.01) 2/2 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF346,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs755477193 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 26709725 26709725 T C 1 0 0 0 0 1 0 0 0 8891 1522 53 5 5 LRRC3B 3 26709725 Missense_Mutation SNP T C3N-00175_T 918065 26709725 171585834 287 9879 SLC4A7 0 . GRCh38 3 27418542 27418542 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1576C>T p.Pro526Ser p.P526S ENST00000295736 11/25 190 144 46 228 228 0 strelka-varscan-mutect SLC4A7,missense_variant,p.Pro511Ser,ENST00000425128,NM_001321105.1,NM_001321106.1;SLC4A7,missense_variant,p.Pro526Ser,ENST00000295736,NM_003615.4;SLC4A7,missense_variant,p.Pro402Ser,ENST00000428386,NM_001321107.1,NM_001258380.1;SLC4A7,missense_variant,p.Pro77Ser,ENST00000419036,;SLC4A7,missense_variant,p.Pro535Ser,ENST00000454389,;SLC4A7,missense_variant,p.Pro522Ser,ENST00000440156,;SLC4A7,missense_variant,p.Pro522Ser,ENST00000445684,;SLC4A7,missense_variant,p.Pro518Ser,ENST00000446700,;SLC4A7,missense_variant,p.Pro407Ser,ENST00000455077,NM_001258379.1;SLC4A7,missense_variant,p.Pro407Ser,ENST00000437179,;SLC4A7,missense_variant,p.Pro422Ser,ENST00000428179,;SLC4A7,missense_variant,p.Pro518Ser,ENST00000438530,;SLC4A7,missense_variant,p.Pro407Ser,ENST00000457377,;SLC4A7,missense_variant,p.Pro407Ser,ENST00000437266,;SLC4A7,downstream_gene_variant,,ENST00000491211,; A ENST00000295736 Transcript missense_variant 1647/7757 1576/3645 526/1214 P/S Cca/Tca 1 -1 SLC4A7 HGNC HGNC:11033 protein_coding YES CCDS33721.1 ENSP00000295736 Q9Y6M7 UPI0000DBEEB7 NM_003615.4 deleterious(0) 11/25 Gene3D:1hynR00,Pfam_domain:PF07565,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF36,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 27418542 27418542 G A 1 0 0 0 0 1 0 0 0 14935 1174 41 3 3 SLC4A7 3 27418542 Missense_Mutation SNP G C3N-00175_T 708817 27418542 170877017 288 9880 TRANK1 0 . GRCh38 3 36857816 36857816 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1774A>T p.Lys592Ter p.K592* ENST00000429976 12/23 192 143 49 223 223 0 strelka-varscan-mutect TRANK1,stop_gained,p.Lys592Ter,ENST00000429976,NM_014831.2; A ENST00000429976 Transcript stop_gained 2022/10481 1774/8778 592/2925 K/* Aag/Tag 1 -1 TRANK1 HGNC HGNC:29011 protein_coding YES CCDS46789.2 ENSP00000416168 O15050 UPI00017BE82B NM_014831.2 12/23 hmmpanther:PTHR21529,hmmpanther:PTHR21529:SF4,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 36857816 36857816 T A 1 0 0 0 0 0 1 0 0 16937 1763 61 4 4 TRANK1 3 36857816 Nonsense_Mutation SNP T C3N-00175_T 9439274 36857816 161437743 289 9881 SCN5A 0 . GRCh38 3 38603933 38603933 + Missense_Mutation SNP G G T rs766204238 C3N-00175_T C3N-00175_N G G c.1669C>A p.His557Asn p.H557N ENST00000413689 12/28 269 221 48 298 298 0 strelka-varscan-mutect SCN5A,missense_variant,p.His557Asn,ENST00000413689,NM_001099404.1;SCN5A,missense_variant,p.His557Asn,ENST00000333535,NM_198056.2;SCN5A,missense_variant,p.His557Asn,ENST00000425664,NM_001099405.1;SCN5A,missense_variant,p.His557Asn,ENST00000423572,NM_000335.4;SCN5A,missense_variant,p.His557Asn,ENST00000451551,NM_001160161.1;SCN5A,missense_variant,p.His557Asn,ENST00000414099,;SCN5A,missense_variant,p.His557Asn,ENST00000455624,NM_001160160.1;SCN5A,missense_variant,p.His557Asn,ENST00000450102,;SCN5A,missense_variant,p.His557Asn,ENST00000449557,; T ENST00000413689 Transcript missense_variant 1863/8504 1669/6051 557/2016 H/N Cac/Aac rs766204238 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 tolerated(0.14) 12/28 Pfam_domain:PF11933,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 MODERATE 1 SNV 5 1 PASS rs766204238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 38603933 38603933 G T 1 0 0 0 0 1 0 0 0 14191 1348 47 2 2 SCN5A 3 38603933 Missense_Mutation SNP G C3N-00175_T 1746117 38603933 159691626 290 9882 XIRP1 0 . GRCh38 3 39184328 39184328 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.5118C>A p.= p.G1706G ENST00000340369 2/2 181 125 56 211 211 0 strelka-varscan-mutect XIRP1,synonymous_variant,p.=,ENST00000340369,NM_194293.2;XIRP1,synonymous_variant,p.=,ENST00000421646,;XIRP1,3_prime_UTR_variant,,ENST00000396251,NM_001198621.2; T ENST00000340369 Transcript synonymous_variant 5347/6460 5118/5532 1706/1843 G ggC/ggA 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 2/2 hmmpanther:PTHR22591 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 39184328 39184328 G T 1 0 0 0 0 0 0 0 1 17988 1190 42 2 2 XIRP1 3 39184328 Silent SNP G C3N-00175_T 580395 39184328 159111231 291 9883 XIRP1 0 . GRCh38 3 39185853 39185853 + Frame_Shift_Del DEL C C - rs773246482 C3N-00175_T C3N-00175_N C C c.3593delG p.Gly1198AlafsTer29 p.G1198Afs*29 ENST00000340369 2/2 112 91 21 127 127 0 sindel-varindel-pindel XIRP1,frameshift_variant,p.Gly1198AlafsTer29,ENST00000340369,NM_194293.2;XIRP1,intron_variant,,ENST00000396251,NM_001198621.2;XIRP1,intron_variant,,ENST00000421646,; - ENST00000340369 Transcript frameshift_variant 3822/6460 3593/5532 1198/1843 G/X gGc/gc rs773246482,COSM5136362 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 2/2 hmmpanther:PTHR22591 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999451 1 1 1 0 - 7 5 39 39185853 39185853 C - 1 0 1 0 1 0 0 0 0 17988 739 26 0 0 XIRP1 3 39185853 Frame_Shift_Del DEL C C3N-00175_T 1525 39185853 159109706 292 9884 TRAK1 0 . GRCh38 3 42184796 42184796 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.475G>T p.Glu159Ter p.E159* ENST00000327628 4/16 87 66 21 113 113 0 strelka-varscan-mutect TRAK1,stop_gained,p.Glu55Ter,ENST00000487159,;TRAK1,stop_gained,p.Glu159Ter,ENST00000327628,NM_001042646.2,NM_001265608.1;TRAK1,stop_gained,p.Glu101Ter,ENST00000396175,;TRAK1,stop_gained,p.Glu85Ter,ENST00000613405,NM_001265609.1;TRAK1,stop_gained,p.Glu101Ter,ENST00000341421,NM_014965.4;TRAK1,stop_gained,p.Glu85Ter,ENST00000449246,NM_001265610.1;TRAK1,stop_gained,p.Glu55Ter,ENST00000484786,;TRAK1,non_coding_transcript_exon_variant,,ENST00000469506,;TRAK1,downstream_gene_variant,,ENST00000418790,; T ENST00000327628 Transcript stop_gained 875/5293 475/2862 159/953 E/* Gag/Tag 1 1 TRAK1 HGNC HGNC:29947 protein_coding YES CCDS43072.1 ENSP00000328998 Q9UPV9 A0A024R2M0 UPI0000139F52 NM_001042646.2,NM_001265608.1 4/16 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF04849,hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF11 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 42184796 42184796 G T 1 0 0 0 0 0 1 0 0 16932 1188 41 2 2 TRAK1 3 42184796 Nonsense_Mutation SNP G C3N-00175_T 2998943 42184796 156110763 293 9885 ABHD5 0 . GRCh38 3 43702534 43702534 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.453G>T p.= p.G151G ENST00000458276 3/7 246 188 58 275 275 0 strelka-varscan-mutect ABHD5,synonymous_variant,p.=,ENST00000458276,NM_016006.4;ABHD5,synonymous_variant,p.=,ENST00000456453,;ABHD5,downstream_gene_variant,,ENST00000454293,;ABHD5,3_prime_UTR_variant,,ENST00000013894,;ABHD5,downstream_gene_variant,,ENST00000486764,; T ENST00000458276 Transcript synonymous_variant 576/1690 453/1050 151/349 G ggG/ggT 1 1 ABHD5 HGNC HGNC:21396 protein_coding YES CCDS2711.1 ENSP00000390849 Q8WTS1 A0A0S2Z5D6 UPI00000411E4 NM_016006.4 3/7 hmmpanther:PTHR10992:SF787,hmmpanther:PTHR10992,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474,Prints_domain:PR00111 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 43702534 43702534 G T 1 0 0 0 0 0 0 0 1 95 1190 42 2 2 ABHD5 3 43702534 Silent SNP G C3N-00175_T 1517738 43702534 154593025 294 9886 TOPAZ1 0 . GRCh38 3 44244728 44244728 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2222G>T p.Gly741Val p.G741V ENST00000309765 2/20 145 114 31 148 147 1 strelka-varscan-mutect TOPAZ1,missense_variant,p.Gly741Val,ENST00000309765,NM_001145030.1; T ENST00000309765 Transcript missense_variant 2390/5334 2222/5079 741/1692 G/V gGa/gTa 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 tolerated(0.21) 2/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44244728 44244728 G T 1 0 0 0 0 1 0 0 0 16845 1174 41 2 2 TOPAZ1 3 44244728 Missense_Mutation SNP G C3N-00175_T 542194 44244728 154050831 295 9887 ZNF501 0 . GRCh38 3 44734981 44734981 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.560A>T p.Glu187Val p.E187V ENST00000620116 3/3 165 139 26 190 190 0 strelka-varscan-mutect ZNF501,missense_variant,p.Glu187Val,ENST00000620116,NM_001258280.1;ZNF501,missense_variant,p.Glu187Val,ENST00000396048,NM_145044.3;ZNF501,downstream_gene_variant,,ENST00000491543,;KIAA1143,downstream_gene_variant,,ENST00000484437,;ZNF501,downstream_gene_variant,,ENST00000484233,;ZNF501,downstream_gene_variant,,ENST00000486486,; T ENST00000620116 Transcript missense_variant 1280/3382 560/816 187/271 E/V gAg/gTg 1 1 ZNF501 HGNC HGNC:23717 protein_coding YES CCDS2720.2 ENSP00000482632 Q96CX3 UPI00005A76A1 NM_001258280.1 deleterious_low_confidence(0.02) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF291,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44734981 44734981 A T 1 0 0 0 0 1 0 0 0 18521 304 11 4 4 ZNF501 3 44734981 Missense_Mutation SNP A C3N-00175_T 490253 44734981 153560578 296 9888 CCR3 0 . GRCh38 3 46265654 46265654 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.559C>G p.Leu187Val p.L187V ENST00000545097 3/3 171 150 21 154 154 0 strelka-varscan-mutect CCR3,missense_variant,p.Leu166Val,ENST00000357422,;CCR3,missense_variant,p.Leu187Val,ENST00000545097,NM_001164680.1,NM_178328.1;CCR3,missense_variant,p.Leu166Val,ENST00000395940,NM_178329.2,NM_001837.3;CCR3,missense_variant,p.Leu166Val,ENST00000395942,;CCR3,downstream_gene_variant,,ENST00000452454,;CCR3,downstream_gene_variant,,ENST00000457243,;CCR3,downstream_gene_variant,,ENST00000475150,;CCR3,downstream_gene_variant,,ENST00000484025,; G ENST00000545097 Transcript missense_variant 734/1786 559/1131 187/376 L/V Ctt/Gtt 1 1 CCR3 HGNC HGNC:1604 protein_coding YES CCDS54574.1 ENSP00000441600 P51677 UPI000020A60F NM_001164680.1,NM_178328.1 tolerated(0.45) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF649,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01108,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 46265654 46265654 C G 1 0 0 0 0 1 0 0 0 2642 913 32 4 4 CCR3 3 46265654 Missense_Mutation SNP C C3N-00175_T 1530673 46265654 152029905 297 9889 KLHL18 0 . GRCh38 3 47343930 47343930 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1714C>G p.Leu572Val p.L572V ENST00000232766 10/10 163 144 19 181 181 0 strelka-mutect KLHL18,missense_variant,p.Leu572Val,ENST00000232766,NM_025010.4;RP11-447D11.3,upstream_gene_variant,,ENST00000624214,;KLHL18,3_prime_UTR_variant,,ENST00000442272,; G ENST00000232766 Transcript missense_variant 1734/4620 1714/1725 572/574 L/V Ctc/Gtc 1 1 KLHL18 HGNC HGNC:29120 protein_coding YES CCDS33749.1 ENSP00000232766 O94889 A0A024R2T4 UPI00004703A5 NM_025010.4 deleterious_low_confidence(0.05) 10/10 hmmpanther:PTHR24412:SF210,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 47343930 47343930 C G 1 0 0 0 0 1 0 0 0 8237 681 24 4 4 KLHL18 3 47343930 Missense_Mutation SNP C C3N-00175_T 1078276 47343930 150951629 298 9890 MAP4 0 . GRCh38 3 47916827 47916827 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1000G>T p.Val334Leu p.V334L ENST00000360240 7/19 309 232 77 284 283 1 strelka-varscan-mutect MAP4,missense_variant,p.Val351Leu,ENST00000426837,;MAP4,missense_variant,p.Val334Leu,ENST00000395734,NM_001134364.1;MAP4,missense_variant,p.Val334Leu,ENST00000360240,NM_002375.4;MAP4,downstream_gene_variant,,ENST00000423088,;MAP4,intron_variant,,ENST00000482752,; A ENST00000360240 Transcript missense_variant 1519/5142 1000/3459 334/1152 V/L Gtg/Ttg 1 -1 MAP4 HGNC HGNC:6862 protein_coding YES CCDS33750.1 ENSP00000353375 P27816 UPI000020A6A4 NM_002375.4 tolerated(0.09) 7/19 hmmpanther:PTHR11501:SF16,hmmpanther:PTHR11501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 47916827 47916827 C A 1 0 0 0 0 1 0 0 0 9182 478 17 2 2 MAP4 3 47916827 Missense_Mutation SNP C C3N-00175_T 572897 47916827 150378732 299 9891 SLC26A6 0 . GRCh38 3 48628691 48628691 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1623G>T p.Lys541Asn p.K541N ENST00000395550 15/21 200 159 41 292 292 0 strelka-varscan-mutect SLC26A6,missense_variant,p.Lys520Asn,ENST00000358747,NM_001040454.1;SLC26A6,missense_variant,p.Lys541Asn,ENST00000420764,NM_134263.2;SLC26A6,missense_variant,p.Lys541Asn,ENST00000395550,NM_022911.2;SLC26A6,missense_variant,p.Lys541Asn,ENST00000383733,NM_134426.2;SLC26A6,missense_variant,p.Lys505Asn,ENST00000455886,NM_001281732.1;SLC26A6,missense_variant,p.Lys434Asn,ENST00000337000,NM_001281733.1;SLC26A6,downstream_gene_variant,,ENST00000421649,;SLC26A6,downstream_gene_variant,,ENST00000431739,;SLC26A6,downstream_gene_variant,,ENST00000426599,;SLC26A6,downstream_gene_variant,,ENST00000611478,;SLC26A6,downstream_gene_variant,,ENST00000482282,;SLC26A6,3_prime_UTR_variant,,ENST00000307364,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000480524,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000496469,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000462009,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000469693,;SLC26A6,intron_variant,,ENST00000489483,;SLC26A6,downstream_gene_variant,,ENST00000444531,;SLC26A6,downstream_gene_variant,,ENST00000414944,;SLC26A6,upstream_gene_variant,,ENST00000466257,;SLC26A6,downstream_gene_variant,,ENST00000485361,;SLC26A6,downstream_gene_variant,,ENST00000431213,;SLC26A6,downstream_gene_variant,,ENST00000494717,; A ENST00000395550 Transcript missense_variant 1671/2589 1623/2280 541/759 K/N aaG/aaT 1 -1 SLC26A6 HGNC HGNC:14472 protein_coding YES CCDS43087.1 ENSP00000378920 Q9BXS9 UPI0000135460 NM_022911.2 deleterious(0) 15/21 PROSITE_profiles:PS50801,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF113,Gene3D:3.30.750.24,Pfam_domain:PF01740,TIGRFAM_domain:TIGR00815,Superfamily_domains:SSF52091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 48628691 48628691 C A 1 0 0 0 0 1 0 0 0 14791 680 24 2 2 SLC26A6 3 48628691 Missense_Mutation SNP C C3N-00175_T 711864 48628691 149666868 300 9892 CCDC71 0 . GRCh38 3 49163558 49163558 + Silent SNP C C T C3N-00175_T C3N-00175_N C C c.651G>A p.= p.G217G ENST00000321895 2/2 147 135 12 197 197 0 strelka-varscan-mutect CCDC71,synonymous_variant,p.=,ENST00000321895,NM_022903.3;RP11-694I15.7,upstream_gene_variant,,ENST00000603877,; T ENST00000321895 Transcript synonymous_variant 758/1781 651/1404 217/467 G ggG/ggA COSM3595246 1 -1 CCDC71 HGNC HGNC:25760 protein_coding YES CCDS2790.1 ENSP00000319006 Q8IV32 UPI0000072BC0 NM_022903.3 2/2 Pfam_domain:PF15374,hmmpanther:PTHR14484,hmmpanther:PTHR14484:SF0 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 49163558 49163558 C T 1 0 0 0 0 0 0 0 1 2544 842 30 3 3 CCDC71 3 49163558 Silent SNP C C3N-00175_T 534867 49163558 149132001 301 9893 BSN 0 . GRCh38 3 49642609 49642609 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.975G>T p.= p.P325P ENST00000296452 3/12 63 49 14 51 51 0 strelka-varscan-mutect BSN,synonymous_variant,p.=,ENST00000296452,NM_003458.3;BSN-AS1,upstream_gene_variant,,ENST00000442384,;BSN,upstream_gene_variant,,ENST00000467456,; T ENST00000296452 Transcript synonymous_variant 1089/15955 975/11781 325/3926 P ccG/ccT 1 1 BSN HGNC HGNC:1117 protein_coding YES CCDS2800.1 ENSP00000296452 Q9UPA5 UPI000013E33C NM_003458.3 3/12 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF1,hmmpanther:PTHR14113 LOW 1 SNV 1 1 PASS rs1000511324 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 49642609 49642609 G T 1 0 0 0 0 0 0 0 1 1704 1103 39 1 1 BSN 3 49642609 Silent SNP G C3N-00175_T 479051 49642609 148652950 302 9894 LSMEM2 0 . GRCh38 3 50286522 50286522 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.110C>T p.Pro37Leu p.P37L ENST00000316436 2/4 164 131 33 174 174 0 strelka-varscan-mutect LSMEM2,missense_variant,p.Pro37Leu,ENST00000316436,NM_153215.2,NM_001304385.1;IFRD2,downstream_gene_variant,,ENST00000436390,;IFRD2,downstream_gene_variant,,ENST00000417626,NM_006764.4;IFRD2,downstream_gene_variant,,ENST00000426499,;IFRD2,downstream_gene_variant,,ENST00000484043,;IFRD2,downstream_gene_variant,,ENST00000468737,;IFRD2,downstream_gene_variant,,ENST00000474556,;IFRD2,downstream_gene_variant,,ENST00000414734,;IFRD2,downstream_gene_variant,,ENST00000489569,;IFRD2,downstream_gene_variant,,ENST00000438296,;IFRD2,downstream_gene_variant,,ENST00000464258,;IFRD2,downstream_gene_variant,,ENST00000462001,;IFRD2,downstream_gene_variant,,ENST00000483071,;IFRD2,downstream_gene_variant,,ENST00000492387,;IFRD2,downstream_gene_variant,,ENST00000486322,;IFRD2,downstream_gene_variant,,ENST00000469855,; T ENST00000316436 Transcript missense_variant 197/1494 110/495 37/164 P/L cCc/cTc 1 1 LSMEM2 HGNC HGNC:26781 protein_coding YES CCDS2814.1 ENSP00000315081 Q8N112 UPI000006DE81 NM_153215.2,NM_001304385.1 tolerated(0.1) 2/4 Pfam_domain:PF15833,hmmpanther:PTHR37333,hmmpanther:PTHR37333:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 50286522 50286522 C T 1 0 0 0 0 1 0 0 0 8969 623 22 3 3 LSMEM2 3 50286522 Missense_Mutation SNP C C3N-00175_T 643913 50286522 148009037 303 9895 LSMEM2 0 . GRCh38 3 50286753 50286753 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.252T>A p.Cys84Ter p.C84* ENST00000316436 3/4 208 169 39 249 248 1 strelka-varscan-mutect LSMEM2,stop_gained,p.Cys84Ter,ENST00000316436,NM_153215.2,NM_001304385.1;IFRD2,downstream_gene_variant,,ENST00000436390,;IFRD2,downstream_gene_variant,,ENST00000417626,NM_006764.4;IFRD2,downstream_gene_variant,,ENST00000426499,;IFRD2,downstream_gene_variant,,ENST00000484043,;IFRD2,downstream_gene_variant,,ENST00000468737,;IFRD2,downstream_gene_variant,,ENST00000474556,;IFRD2,downstream_gene_variant,,ENST00000414734,;IFRD2,downstream_gene_variant,,ENST00000489569,;IFRD2,downstream_gene_variant,,ENST00000438296,;IFRD2,downstream_gene_variant,,ENST00000464258,;IFRD2,downstream_gene_variant,,ENST00000462001,;IFRD2,downstream_gene_variant,,ENST00000483071,;IFRD2,downstream_gene_variant,,ENST00000492387,;IFRD2,downstream_gene_variant,,ENST00000486322,;IFRD2,downstream_gene_variant,,ENST00000469855,; A ENST00000316436 Transcript stop_gained 339/1494 252/495 84/164 C/* tgT/tgA 1 1 LSMEM2 HGNC HGNC:26781 protein_coding YES CCDS2814.1 ENSP00000315081 Q8N112 UPI000006DE81 NM_153215.2,NM_001304385.1 3/4 Pfam_domain:PF15833,hmmpanther:PTHR37333,hmmpanther:PTHR37333:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 50286753 50286753 T A 1 0 0 0 0 0 1 0 0 8969 1702 59 4 4 LSMEM2 3 50286753 Nonsense_Mutation SNP T C3N-00175_T 231 50286753 148008806 304 9896 DOCK3 0 . GRCh38 3 51228769 51228769 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.1756C>T p.Arg586Cys p.R586C ENST00000266037 18/53 126 102 24 167 167 0 strelka-varscan-mutect DOCK3,missense_variant,p.Arg586Cys,ENST00000266037,NM_004947.4; T ENST00000266037 Transcript missense_variant 1779/8755 1756/6093 586/2030 R/C Cgc/Tgc COSM1633236,COSM1633237 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 deleterious(0.04) 18/53 PROSITE_profiles:PS51650,hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Pfam_domain:PF14429 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 51228769 51228769 C T 1 0 0 0 0 1 0 0 0 4503 768 27 1 1 DOCK3 3 51228769 Missense_Mutation SNP C C3N-00175_T 942016 51228769 147066790 305 9897 IL17RD 0 . GRCh38 3 57098030 57098030 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1673A>T p.Asp558Val p.D558V ENST00000296318 12/13 257 200 57 296 294 2 strelka-varscan-mutect IL17RD,missense_variant,p.Asp558Val,ENST00000296318,NM_001318864.1,NM_017563.3;IL17RD,missense_variant,p.Asp414Val,ENST00000320057,;IL17RD,missense_variant,p.Asp414Val,ENST00000463523,;IL17RD,non_coding_transcript_exon_variant,,ENST00000469841,; A ENST00000296318 Transcript missense_variant 1762/8720 1673/2220 558/739 D/V gAc/gTc 1 -1 IL17RD HGNC HGNC:17616 protein_coding YES CCDS2880.2 ENSP00000296318 Q8NFM7 UPI0000047CC3 NM_001318864.1,NM_017563.3 deleterious(0) 12/13 hmmpanther:PTHR15583:SF14,hmmpanther:PTHR15583 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 57098030 57098030 T A 1 0 0 0 0 1 0 0 0 7550 1667 58 4 4 IL17RD 3 57098030 Missense_Mutation SNP T C3N-00175_T 5869261 57098030 141197529 306 9898 DNAH12 0 . GRCh38 3 57415484 57415484 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.5795delA p.Asp1932AlafsTer44 p.D1932Afs*44 ENST00000495027 38/74 194 152 42 235 235 0 sindel-varindel DNAH12,frameshift_variant,p.Asp1932AlafsTer44,ENST00000495027,NM_001291661.1;DNAH12,frameshift_variant,p.Asp1913AlafsTer44,ENST00000351747,; - ENST00000495027 Transcript frameshift_variant 5976/12146 5795/11883 1932/3960 D/X gAc/gc 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 38/74 Gene3D:3.40.50.300,Pfam_domain:PF12775,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255,SMART_domains:SM00382,Superfamily_domains:SSF52540 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 57415484 57415484 T - 1 0 1 0 1 0 0 0 0 4414 1667 58 0 0 DNAH12 3 57415484 Frame_Shift_Del DEL T C3N-00175_T 317454 57415484 140880075 307 9899 FLNB 0 . GRCh38 3 58097893 58097893 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.1063A>C p.Ser355Arg p.S355R ENST00000490882 7/47 342 271 71 354 354 0 strelka-varscan-mutect FLNB,missense_variant,p.Ser355Arg,ENST00000295956,NM_001457.3;FLNB,missense_variant,p.Ser355Arg,ENST00000429972,NM_001164318.1;FLNB,missense_variant,p.Ser355Arg,ENST00000358537,NM_001164319.1;FLNB,missense_variant,p.Ser355Arg,ENST00000490882,NM_001164317.1;FLNB,missense_variant,p.Ser186Arg,ENST00000493452,; C ENST00000490882 Transcript missense_variant 1228/8079 1063/7902 355/2633 S/R Agt/Cgt 1 1 FLNB HGNC HGNC:3755 protein_coding YES CCDS54599.1 ENSP00000420213 O75369 UPI0001765F91 NM_001164317.1 deleterious(0.03) 7/47 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF238,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 58097893 58097893 A C 1 0 0 0 0 1 0 0 0 5790 188 7 5 5 FLNB 3 58097893 Missense_Mutation SNP A C3N-00175_T 682409 58097893 140197666 308 9900 KBTBD8 0 . GRCh38 3 67003517 67003517 + Frame_Shift_Del DEL A A - novel C3N-00175_T C3N-00175_N A A c.552delA p.Glu185AsnfsTer7 p.E185Nfs*7 ENST00000417314 3/4 142 120 22 223 223 0 sindel-varindel KBTBD8,frameshift_variant,p.Glu185AsnfsTer7,ENST00000417314,NM_032505.2;KBTBD8,frameshift_variant,p.Glu108AsnfsTer7,ENST00000484414,;KBTBD8,intron_variant,,ENST00000460576,;KBTBD8,downstream_gene_variant,,ENST00000460784,;KBTBD8,intron_variant,,ENST00000469661,; - ENST00000417314 Transcript frameshift_variant 599/4680 550/1806 184/601 K/X Aaa/aa 1 1 KBTBD8 HGNC HGNC:30691 protein_coding YES CCDS2906.2 ENSP00000401878 Q8NFY9 UPI0000209974 NM_032505.2 3/4 Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF24,SMART_domains:SM00875 HIGH 1 deletion 2 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 67003517 67003517 A - 1 0 1 0 1 0 0 0 0 7915 131 5 0 0 KBTBD8 3 67003517 Frame_Shift_Del DEL A C3N-00175_T 8905624 67003517 131292042 309 9901 PDZRN3 0 . GRCh38 3 73404246 73404246 + Silent SNP C C A rs199688323 C3N-00175_T C3N-00175_N C C c.1068G>T p.= p.T356T ENST00000263666 4/10 285 221 64 297 297 0 strelka-varscan-mutect PDZRN3,synonymous_variant,p.=,ENST00000263666,NM_015009.2;PDZRN3,synonymous_variant,p.=,ENST00000462146,NM_001303141.1;PDZRN3,synonymous_variant,p.=,ENST00000479530,NM_001303142.1;PDZRN3,synonymous_variant,p.=,ENST00000466780,NM_001303140.1;PDZRN3,synonymous_variant,p.=,ENST00000492909,NM_001303139.1;PDZRN3,upstream_gene_variant,,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000308537,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000498048,;PDZRN3,upstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000477434,;PDZRN3,upstream_gene_variant,,ENST00000484487,; A ENST00000263666 Transcript synonymous_variant 1183/4248 1068/3201 356/1066 T acG/acT rs199688323 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 4/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 LOW 1 SNV 1 1 PASS rs199688323 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 73404246 73404246 C A 1 0 0 0 0 0 0 0 1 11797 639 23 1 1 PDZRN3 3 73404246 Silent SNP C C3N-00175_T 6400729 73404246 124891313 310 9902 PDZRN3 0 . GRCh38 3 73602371 73602371 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.901C>A p.His301Asn p.H301N ENST00000263666 3/10 104 83 21 107 106 1 strelka-varscan-mutect PDZRN3,missense_variant,p.His301Asn,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.His301Asn,ENST00000308537,; T ENST00000263666 Transcript missense_variant 1016/4248 901/3201 301/1066 H/N Cat/Aat 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 tolerated(0.07) 3/10 PROSITE_profiles:PS50106,hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 73602371 73602371 G T 1 0 0 0 0 1 0 0 0 11797 1290 45 2 2 PDZRN3 3 73602371 Missense_Mutation SNP G C3N-00175_T 198125 73602371 124693188 311 9903 CNTN3 0 . GRCh38 3 74365658 74365658 + Missense_Mutation SNP C C A rs756569621 C3N-00175_T C3N-00175_N C C c.991G>T p.Val331Leu p.V331L ENST00000263665 8/22 246 203 43 258 258 0 strelka-varscan-mutect CNTN3,missense_variant,p.Val331Leu,ENST00000263665,NM_020872.2; A ENST00000263665 Transcript missense_variant 1019/4948 991/3087 331/1028 V/L Gtg/Ttg rs756569621 1 -1 CNTN3 HGNC HGNC:2173 protein_coding YES CCDS33790.1 ENSP00000263665 Q9P232 UPI00001A7974 NM_020872.2 tolerated(0.18) 8/22 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF695,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs756569621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 74365658 74365658 C A 1 0 0 0 0 1 0 0 0 3423 536 19 1 1 CNTN3 3 74365658 Missense_Mutation SNP C C3N-00175_T 763287 74365658 123929901 312 9904 ZNF654 0 . GRCh38 3 88140536 88140536 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.1226T>C p.Ile409Thr p.I409T ENST00000309495 1/2 122 108 14 166 166 0 strelka-varscan-mutect ZNF654,missense_variant,p.Ile956Thr,ENST00000636215,;ZNF654,missense_variant,p.Ile409Thr,ENST00000309495,NM_018293.2;CGGBP1,intron_variant,,ENST00000462901,NM_001195308.1;CGGBP1,intron_variant,,ENST00000467332,; C ENST00000309495 Transcript missense_variant 1425/4957 1226/1746 409/581 I/T aTa/aCa 1 1 ZNF654 HGNC HGNC:25612 protein_coding YES CCDS46874.1 ENSP00000312141 Q8IZM8 UPI0000DD0307 NM_018293.2 tolerated(0.28) 1/2 hmmpanther:PTHR15507 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 88140536 88140536 T C 1 0 0 0 0 1 0 0 0 18640 1406 49 5 5 ZNF654 3 88140536 Missense_Mutation SNP T C3N-00175_T 13774878 88140536 110155023 313 9905 EPHA3 0 . GRCh38 3 89399436 89399436 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1550A>T p.Tyr517Phe p.Y517F ENST00000336596 7/17 166 134 32 160 160 0 strelka-varscan-mutect EPHA3,missense_variant,p.Tyr517Phe,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.Tyr517Phe,ENST00000494014,;EPHA3,missense_variant,p.Tyr517Phe,ENST00000452448,NM_182644.2; T ENST00000336596 Transcript missense_variant 1775/5809 1550/2952 517/983 Y/F tAt/tTt 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 tolerated(0.17) 7/17 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 89399436 89399436 A T 1 0 0 0 0 1 0 0 0 5015 449 16 4 4 EPHA3 3 89399436 Missense_Mutation SNP A C3N-00175_T 1258900 89399436 108896123 314 9906 OR5K4 0 . GRCh38 3 98354419 98354419 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.566G>T p.Cys189Phe p.C189F ENST00000354924 1/1 124 90 34 153 152 1 strelka-varscan-mutect OR5K4,missense_variant,p.Cys189Phe,ENST00000354924,NM_001005517.1;RP11-325B23.2,intron_variant,,ENST00000508616,; T ENST00000354924 Transcript missense_variant 566/966 566/966 189/321 C/F tGt/tTt 1 1 OR5K4 HGNC HGNC:31291 protein_coding YES CCDS33802.1 ENSP00000347003 A6NMS3 UPI000044D411 NM_001005517.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF198,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs1187280023 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 98354419 98354419 G T 1 0 0 0 0 1 0 0 0 11239 1377 48 2 2 OR5K4 3 98354419 Missense_Mutation SNP G C3N-00175_T 8954983 98354419 99941140 315 9907 NFKBIZ 0 . GRCh38 3 101852118 101852118 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.323G>C p.Arg108Thr p.R108T ENST00000326172 2/12 189 168 21 173 173 0 strelka-mutect NFKBIZ,missense_variant,p.Arg108Thr,ENST00000326172,NM_031419.3;NFKBIZ,missense_variant,p.Arg8Thr,ENST00000394054,NM_001005474.2;NFKBIZ,missense_variant,p.Arg108Thr,ENST00000326151,;NFKBIZ,missense_variant,p.Arg8Thr,ENST00000483180,;NFKBIZ,missense_variant,p.Arg108Thr,ENST00000461724,;NFKBIZ,missense_variant,p.Arg8Thr,ENST00000491281,;NFKBIZ,upstream_gene_variant,,ENST00000477601,;NFKBIZ,non_coding_transcript_exon_variant,,ENST00000486444,;NFKBIZ,upstream_gene_variant,,ENST00000495089,;NFKBIZ,upstream_gene_variant,,ENST00000465476,; C ENST00000326172 Transcript missense_variant 438/3923 323/2157 108/718 R/T aGa/aCa 1 1 NFKBIZ HGNC HGNC:29805 protein_coding YES CCDS2946.1 ENSP00000325663 Q9BYH8 UPI000006FBB1 NM_031419.3 deleterious_low_confidence(0) 2/12 hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 101852118 101852118 G C 1 0 0 0 0 1 0 0 0 10419 942 33 4 4 NFKBIZ 3 101852118 Missense_Mutation SNP G C3N-00175_T 3497699 101852118 96443441 316 9908 MYH15 0 . GRCh38 3 108501742 108501742 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.369G>A p.= p.L123L ENST00000273353 4/42 190 158 32 199 199 0 strelka-varscan-mutect MYH15,synonymous_variant,p.=,ENST00000273353,NM_014981.1; T ENST00000273353 Transcript synonymous_variant 426/7074 369/5841 123/1946 L ctG/ctA 1 -1 MYH15 HGNC HGNC:31073 protein_coding YES CCDS43127.1 ENSP00000273353 Q9Y2K3 UPI0000253B6F NM_014981.1 4/42 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF475,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 108501742 108501742 C T 1 0 0 0 0 0 0 0 1 10034 813 29 3 3 MYH15 3 108501742 Silent SNP C C3N-00175_T 6649624 108501742 89793817 317 9909 KIAA1524 0 . GRCh38 3 108557391 108557391 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2037G>C p.Leu679Phe p.L679F ENST00000295746 17/21 61 57 4 57 57 0 strelka-varscan-mutect KIAA1524,missense_variant,p.Leu679Phe,ENST00000295746,NM_020890.2;KIAA1524,missense_variant,p.Leu520Phe,ENST00000491772,;KIAA1524,missense_variant,p.Leu680Phe,ENST00000619684,;KIAA1524,downstream_gene_variant,,ENST00000487834,;KIAA1524,3_prime_UTR_variant,,ENST00000481530,; G ENST00000295746 Transcript missense_variant 2114/4075 2037/2718 679/905 L/F ttG/ttC 1 -1 KIAA1524 HGNC HGNC:29302 protein_coding YES CCDS33812.1 ENSP00000295746 Q8TCG1 UPI0000209EFF NM_020890.2 deleterious(0.01) 17/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23161,hmmpanther:PTHR23161:SF2 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -9.75372 0.9999996 1 1 1 0 G 3 3 39 108557391 108557391 C G 1 0 0 0 0 1 0 0 0 8119 825 29 4 4 KIAA1524 3 108557391 Missense_Mutation SNP C C3N-00175_T 55649 108557391 89738168 318 9910 TRAT1 0 . GRCh38 3 108830775 108830775 + Missense_Mutation SNP G G A rs61756221 C3N-00175_T C3N-00175_N G G c.113G>A p.Arg38Gln p.R38Q ENST00000295756 2/6 111 98 13 117 117 0 strelka-varscan-mutect TRAT1,missense_variant,p.Arg38Gln,ENST00000295756,NM_016388.2;TRAT1,intron_variant,,ENST00000426646,;TRAT1,non_coding_transcript_exon_variant,,ENST00000493604,;TRAT1,non_coding_transcript_exon_variant,,ENST00000478830,;TRAT1,non_coding_transcript_exon_variant,,ENST00000484927,; A ENST00000295756 Transcript missense_variant 343/1919 113/561 38/186 R/Q cGa/cAa rs61756221 1 1 TRAT1 HGNC HGNC:30698 protein_coding YES CCDS33813.1 ENSP00000295756 Q6PIZ9 UPI00001147D3 NM_016388.2 tolerated(0.38) 2/6 PD306446,Pfam_domain:PF15330,hmmpanther:PTHR15951 MODERATE 1 SNV 1 1 PASS rs61756221 . 0 208 0 2 0 0 0 0 -19.73716 0.9999999 1 1 1 0 A 3 1 39 108830775 108830775 G A 1 0 0 0 0 1 0 0 0 16955 1072 37 1 1 TRAT1 3 108830775 Missense_Mutation SNP G C3N-00175_T 273384 108830775 89464784 319 9911 TRAT1 0 . GRCh38 3 108847114 108847114 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.199G>A p.Asp67Asn p.D67N ENST00000295756 4/6 64 47 17 110 110 0 strelka-varscan-mutect TRAT1,missense_variant,p.Asp67Asn,ENST00000295756,NM_016388.2;TRAT1,missense_variant,p.Asp30Asn,ENST00000426646,;TRAT1,non_coding_transcript_exon_variant,,ENST00000493604,;TRAT1,non_coding_transcript_exon_variant,,ENST00000484927,; A ENST00000295756 Transcript missense_variant 429/1919 199/561 67/186 D/N Gat/Aat 1 1 TRAT1 HGNC HGNC:30698 protein_coding YES CCDS33813.1 ENSP00000295756 Q6PIZ9 UPI00001147D3 NM_016388.2 tolerated(0.61) 4/6 PD306446,Pfam_domain:PF15330,hmmpanther:PTHR15951 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 108847114 108847114 G A 1 0 0 0 0 1 0 0 0 16955 942 33 3 3 TRAT1 3 108847114 Missense_Mutation SNP G C3N-00175_T 16339 108847114 89448445 320 9912 MORC1 0 . GRCh38 3 109007083 109007083 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1713T>A p.Phe571Leu p.F571L ENST00000232603 18/28 100 79 21 87 87 0 strelka-varscan-mutect MORC1,missense_variant,p.Phe571Leu,ENST00000232603,NM_014429.3;MORC1,intron_variant,,ENST00000483760,; T ENST00000232603 Transcript missense_variant 1796/3764 1713/2955 571/984 F/L ttT/ttA 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 tolerated(0.3) 18/28 hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 109007083 109007083 A T 1 0 0 0 0 1 0 0 0 9665 359 13 4 4 MORC1 3 109007083 Missense_Mutation SNP A C3N-00175_T 159969 109007083 89288476 321 9913 CD96 0 . GRCh38 3 111545137 111545137 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.153C>A p.= p.G51G ENST00000283285 2/15 134 115 19 109 108 1 strelka-varscan-mutect CD96,synonymous_variant,p.=,ENST00000352690,NM_005816.4;CD96,synonymous_variant,p.=,ENST00000283285,NM_198196.2;CD96,synonymous_variant,p.=,ENST00000438817,NM_001318889.1;CD96,downstream_gene_variant,,ENST00000460744,;CD96,synonymous_variant,p.=,ENST00000494798,;CD96,synonymous_variant,p.=,ENST00000488054,; A ENST00000283285 Transcript synonymous_variant 284/4324 153/1758 51/585 G ggC/ggA 1 1 CD96 HGNC HGNC:16892 protein_coding YES CCDS2959.1 ENSP00000283285 P40200 UPI000013DD36 NM_198196.2 2/15 Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR15317,hmmpanther:PTHR15317:SF1,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 111545137 111545137 C A 1 0 0 0 0 0 0 0 1 2752 784 28 2 2 CD96 3 111545137 Silent SNP C C3N-00175_T 2538054 111545137 86750422 322 9914 AC026348.1 0 . GRCh38 3 113306310 113306311 + Frame_Shift_Ins INS - - AA novel C3N-00175_T C3N-00175_N - - c.4648_4649insTT p.Glu1550ValfsTer18 p.E1550Vfs*18 ENST00000393845 29/34 364 285 79 444 443 1 sindel-varindel AC026348.1,frameshift_variant,p.Glu1550ValfsTer18,ENST00000393845,NM_001164496.1;CFAP44,frameshift_variant,p.Glu687ValfsTer18,ENST00000465636,;CFAP44,frameshift_variant,p.Glu171ValfsTer18,ENST00000461734,;CFAP44,upstream_gene_variant,,ENST00000489244,;CFAP44,upstream_gene_variant,,ENST00000465510,; AA ENST00000393845 Transcript frameshift_variant 4648-4649/5565 4648-4649/5565 1550/1854 E/VX gag/gTTag 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 29/34 HIGH 1 insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 AA 7 5 39 113306310 113306310 - AA 1 0 1 1 0 0 0 0 0 128 1551 54 0 0 AC026348.1 3 113306310 Frame_Shift_Ins INS - C3N-00175_T 1761173 113306310 84989249 323 9915 AC026348.1 0 . GRCh38 3 113379475 113379475 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.2129T>G p.Leu710Arg p.L710R ENST00000393845 16/34 174 129 45 181 181 0 strelka-varscan-mutect AC026348.1,missense_variant,p.Leu710Arg,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Leu710Arg,ENST00000295868,NM_018338.3;CFAP44,downstream_gene_variant,,ENST00000475568,;CFAP44,3_prime_UTR_variant,,ENST00000488854,; C ENST00000393845 Transcript missense_variant 2129/5565 2129/5565 710/1854 L/R cTa/cGa 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 tolerated(0.14) 16/34 Low_complexity_(Seg):seg,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 113379475 113379475 A C 1 0 0 0 0 1 0 0 0 128 420 15 5 5 AC026348.1 3 113379475 Missense_Mutation SNP A C3N-00175_T 73165 113379475 84916084 324 9916 C3orf30 0 . GRCh38 3 119146792 119146792 + Missense_Mutation SNP G G T rs756123379 C3N-00175_T C3N-00175_N G G c.603G>T p.Glu201Asp p.E201D ENST00000295622 1/3 290 241 49 280 279 1 strelka-varscan-mutect C3orf30,missense_variant,p.Glu201Asp,ENST00000295622,NM_152539.2;C3orf30,missense_variant,p.Glu165Asp,ENST00000460150,;IGSF11,upstream_gene_variant,,ENST00000425327,NM_152538.2;IGSF11,upstream_gene_variant,,ENST00000441144,;C3orf30,upstream_gene_variant,,ENST00000473121,;C3orf30,upstream_gene_variant,,ENST00000492792,;RP11-484M3.5,upstream_gene_variant,,ENST00000490594,;IGSF11,upstream_gene_variant,,ENST00000494802,;C3orf30,missense_variant,p.Glu201Asp,ENST00000494105,; T ENST00000295622 Transcript missense_variant 643/1814 603/1611 201/536 E/D gaG/gaT rs756123379 1 1 C3orf30 HGNC HGNC:26553 protein_coding YES CCDS2984.1 ENSP00000295622 Q96M34 UPI000013E280 NM_152539.2 tolerated(0.07) 1/3 hmmpanther:PTHR21847,hmmpanther:PTHR21847:SF4 MODERATE 1 SNV 1 1 PASS rs756123379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 119146792 119146792 G T 1 0 0 0 0 1 0 0 0 2063 991 35 2 2 C3orf30 3 119146792 Missense_Mutation SNP G C3N-00175_T 5767317 119146792 79148767 325 9917 STXBP5L 0 . GRCh38 3 121413168 121413168 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.3031C>T p.Leu1011Phe p.L1011F ENST00000273666 25/28 69 57 12 67 67 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Leu1011Phe,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Leu987Phe,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Leu954Phe,ENST00000471262,; T ENST00000273666 Transcript missense_variant 3302/9496 3031/3561 1011/1186 L/F Ctt/Ttt 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 deleterious(0) 25/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 121413168 121413168 C T 1 0 0 0 0 1 0 0 0 15741 913 32 3 3 STXBP5L 3 121413168 Missense_Mutation SNP C C3N-00175_T 2266376 121413168 76882391 326 9918 FBXO40 0 . GRCh38 3 121622709 121622709 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1280C>T p.Ala427Val p.A427V ENST00000338040 3/4 200 165 35 232 231 1 strelka-varscan-mutect FBXO40,missense_variant,p.Ala427Val,ENST00000338040,NM_016298.3; T ENST00000338040 Transcript missense_variant 1694/5929 1280/2130 427/709 A/V gCc/gTc 1 1 FBXO40 HGNC HGNC:29816 protein_coding YES CCDS33835.1 ENSP00000337510 Q9UH90 UPI000020A046 NM_016298.3 deleterious(0) 3/4 hmmpanther:PTHR15933,hmmpanther:PTHR15933:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 121622709 121622709 C T 1 0 0 0 0 1 0 0 0 5612 739 26 3 3 FBXO40 3 121622709 Missense_Mutation SNP C C3N-00175_T 209541 121622709 76672850 327 9919 FBXO40 0 . GRCh38 3 121626698 121626698 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1918T>A p.Trp640Arg p.W640R ENST00000338040 4/4 145 102 43 155 155 0 strelka-varscan-mutect FBXO40,missense_variant,p.Trp640Arg,ENST00000338040,NM_016298.3;HCLS1,downstream_gene_variant,,ENST00000314583,NM_005335.5;HCLS1,downstream_gene_variant,,ENST00000473883,; A ENST00000338040 Transcript missense_variant 2332/5929 1918/2130 640/709 W/R Tgg/Agg 1 1 FBXO40 HGNC HGNC:29816 protein_coding YES CCDS33835.1 ENSP00000337510 Q9UH90 UPI000020A046 NM_016298.3 deleterious(0) 4/4 Gene3D:1.20.1280.50,Pfam_domain:PF15966,hmmpanther:PTHR15933,hmmpanther:PTHR15933:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 121626698 121626698 T A 1 0 0 0 0 1 0 0 0 5612 1594 55 4 4 FBXO40 3 121626698 Missense_Mutation SNP T C3N-00175_T 3989 121626698 76668861 328 9920 CASR 0 . GRCh38 3 122284997 122284997 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.3073C>T p.Pro1025Ser p.P1025S ENST00000498619 7/7 490 447 43 332 332 0 strelka-varscan-mutect CASR,missense_variant,p.Pro1025Ser,ENST00000498619,NM_001178065.1;CASR,missense_variant,p.Pro1015Ser,ENST00000490131,NM_000388.3; T ENST00000498619 Transcript missense_variant 3511/5011 3073/3267 1025/1088 P/S Ccg/Tcg 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 deleterious_low_confidence(0.01) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 122284997 122284997 C T 1 0 0 0 0 1 0 0 0 2381 623 22 3 3 CASR 3 122284997 Missense_Mutation SNP C C3N-00175_T 658299 122284997 76010562 329 9921 MYLK 0 . GRCh38 3 123725951 123725951 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1644G>T p.= p.L548L ENST00000360304 11/33 100 75 25 92 91 1 strelka-varscan-mutect MYLK,synonymous_variant,p.=,ENST00000360772,;MYLK,synonymous_variant,p.=,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,synonymous_variant,p.=,ENST00000359169,NM_053027.3;MYLK,synonymous_variant,p.=,ENST00000354792,;MYLK,synonymous_variant,p.=,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,synonymous_variant,p.=,ENST00000475616,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000514623,; A ENST00000360304 Transcript synonymous_variant 1830/7738 1644/5745 548/1914 L ctG/ctT 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 11/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 123725951 123725951 C A 1 0 0 0 0 0 0 0 1 10056 697 25 2 2 MYLK 3 123725951 Silent SNP C C3N-00175_T 1440954 123725951 74569608 330 9922 OSBPL11 0 . GRCh38 3 125552434 125552434 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1401G>T p.Glu467Asp p.E467D ENST00000296220 9/13 261 212 49 305 305 0 strelka-varscan-mutect OSBPL11,missense_variant,p.Glu467Asp,ENST00000296220,NM_022776.4; A ENST00000296220 Transcript missense_variant 1691/4191 1401/2244 467/747 E/D gaG/gaT 1 -1 OSBPL11 HGNC HGNC:16397 protein_coding YES CCDS3033.1 ENSP00000296220 Q9BXB4 A0A140VJQ6 UPI0000130E9C NM_022776.4 tolerated(0.28) 9/13 Pfam_domain:PF01237,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF46,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 125552434 125552434 C A 1 0 0 0 0 1 0 0 0 11342 680 24 2 2 OSBPL11 3 125552434 Missense_Mutation SNP C C3N-00175_T 1826483 125552434 72743125 331 9923 MCM2 0 . GRCh38 3 127604716 127604716 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.345G>T p.= p.R115R ENST00000265056 3/16 186 142 44 229 229 0 strelka-varscan-mutect MCM2,synonymous_variant,p.=,ENST00000265056,NM_004526.3;MCM2,synonymous_variant,p.=,ENST00000480910,;MCM2,upstream_gene_variant,,ENST00000491422,;MCM2,downstream_gene_variant,,ENST00000472731,;MCM2,non_coding_transcript_exon_variant,,ENST00000468659,;MCM2,synonymous_variant,p.=,ENST00000474964,;MCM2,synonymous_variant,p.=,ENST00000477668,; T ENST00000265056 Transcript synonymous_variant 589/3622 345/2715 115/904 R cgG/cgT 1 1 MCM2 HGNC HGNC:6944 protein_coding YES CCDS3043.1 ENSP00000265056 P49736 UPI00001A3E4E NM_004526.3 3/16 Low_complexity_(Seg):seg,Pfam_domain:PF12619 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 127604716 127604716 G T 1 0 0 0 0 0 0 0 1 9318 1219 43 2 2 MCM2 3 127604716 Silent SNP G C3N-00175_T 2052282 127604716 70690843 332 9924 RP11-723O4.6 0 . GRCh38 3 128932958 128932958 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1131C>A p.Asp377Glu p.D377E ENST00000508239 5/8 257 199 58 242 242 0 strelka-varscan-mutect RP11-723O4.6,missense_variant,p.Asp377Glu,ENST00000508239,;RP11-723O4.6,missense_variant,p.Asp25Glu,ENST00000637488,;KIAA1257,intron_variant,,ENST00000511438,; T ENST00000508239 Transcript missense_variant 1278/2291 1131/1719 377/572 D/E gaC/gaA 1 -1 RP11-723O4.6 Clone_based_vega_gene protein_coding YES ENSP00000424951 Q6ZUG5 UPI00001C0B67 tolerated(0.88) 5/8 hmmpanther:PTHR33667 MODERATE 1 SNV 2 1 PASS rs1393659688 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 128932958 128932958 G T 1 0 0 0 0 1 0 0 0 13759 1136 40 1 1 RP11-723O4.6 3 128932958 Missense_Mutation SNP G C3N-00175_T 1328242 128932958 69362601 333 9925 COL6A5 0 . GRCh38 3 130406150 130406150 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.4400G>T p.Gly1467Val p.G1467V ENST00000265379 16/43 206 189 17 194 193 1 strelka-varscan-mutect COL6A5,missense_variant,p.Gly1467Val,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Gly1467Val,ENST00000312481,; T ENST00000265379 Transcript missense_variant 4894/9214 4400/7836 1467/2611 G/V gGg/gTg 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0) 16/43 Low_complexity_(Seg):seg,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF01391 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 130406150 130406150 G T 1 0 0 0 0 1 0 0 0 3491 1232 43 2 2 COL6A5 3 130406150 Missense_Mutation SNP G C3N-00175_T 1473192 130406150 67889409 334 9926 COL6A6 0 . GRCh38 3 130574084 130574084 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.3106A>G p.Arg1036Gly p.R1036G ENST00000358511 7/36 261 205 56 283 283 0 strelka-varscan-mutect COL6A6,missense_variant,p.Arg1036Gly,ENST00000358511,NM_001102608.1; G ENST00000358511 Transcript missense_variant 3137/9581 3106/6792 1036/2263 R/G Aga/Gga 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 deleterious(0.02) 7/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 130574084 130574084 A G 1 0 0 0 0 1 0 0 0 3492 180 7 5 5 COL6A6 3 130574084 Missense_Mutation SNP A C3N-00175_T 167934 130574084 67721475 335 9927 CPNE4 0 . GRCh38 3 131723506 131723506 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.354C>A p.Ser118Arg p.S118R ENST00000617767 3/16 185 143 42 188 188 0 strelka-varscan-mutect CPNE4,missense_variant,p.Ser100Arg,ENST00000512055,;CPNE4,missense_variant,p.Ser100Arg,ENST00000429747,NM_130808.2;CPNE4,missense_variant,p.Ser118Arg,ENST00000617767,NM_001289112.1;CPNE4,missense_variant,p.Ser100Arg,ENST00000511604,;CPNE4,missense_variant,p.Ser118Arg,ENST00000512332,NM_153429.1;CPNE4,missense_variant,p.Ser118Arg,ENST00000502818,;CPNE4,missense_variant,p.Ser100Arg,ENST00000505881,;CPNE4,downstream_gene_variant,,ENST00000505957,;CPNE4,downstream_gene_variant,,ENST00000514999,;CPNE4,non_coding_transcript_exon_variant,,ENST00000515418,; T ENST00000617767 Transcript missense_variant 549/3556 354/1728 118/575 S/R agC/agA 1 -1 CPNE4 HGNC HGNC:2317 protein_coding YES CCDS75010.1 ENSP00000478878 Q96A23 UPI000002A6F1 NM_001289112.1 deleterious(0.05) 3/16 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF4,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 131723506 131723506 G T 1 0 0 0 0 1 0 0 0 3609 1310 46 2 2 CPNE4 3 131723506 Missense_Mutation SNP G C3N-00175_T 1149422 131723506 66572053 336 9928 SPSB4 0 . GRCh38 3 141066285 141066285 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.181C>A p.Arg61Ser p.R61S ENST00000310546 2/3 144 100 44 142 141 1 strelka-varscan-mutect SPSB4,missense_variant,p.Arg61Ser,ENST00000310546,NM_080862.2;SPSB4,upstream_gene_variant,,ENST00000508126,; A ENST00000310546 Transcript missense_variant 925/2908 181/822 61/273 R/S Cgc/Agc COSM5355711 1 1 SPSB4 HGNC HGNC:30630 protein_coding YES CCDS3115.1 ENSP00000311609 Q96A44 UPI00000734A4 NM_080862.2 tolerated(0.08) 2/3 PROSITE_profiles:PS50188,hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF3,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS rs1352282512 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 141066285 141066285 C A 1 0 0 0 0 1 0 0 0 15471 652 23 1 1 SPSB4 3 141066285 Missense_Mutation SNP C C3N-00175_T 9342779 141066285 57229274 337 9929 SPSB4 0 . GRCh38 3 141066572 141066572 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.468G>T p.Gln156His p.Q156H ENST00000310546 2/3 32 23 9 33 33 0 strelka-varscan-mutect SPSB4,missense_variant,p.Gln156His,ENST00000310546,NM_080862.2;SPSB4,upstream_gene_variant,,ENST00000508126,; T ENST00000310546 Transcript missense_variant 1212/2908 468/822 156/273 Q/H caG/caT COSM5683749 1 1 SPSB4 HGNC HGNC:30630 protein_coding YES CCDS3115.1 ENSP00000311609 Q96A44 UPI00000734A4 NM_080862.2 tolerated(0.47) 2/3 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF3,SMART_domains:SM00449,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 T 3 4 39 141066572 141066572 G T 1 0 0 0 0 1 0 0 0 15471 962 34 2 2 SPSB4 3 141066572 Missense_Mutation SNP G C3N-00175_T 287 141066572 57228987 338 9930 U2SURP 0 . GRCh38 3 143022897 143022897 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1063G>T p.Ala355Ser p.A355S ENST00000473835 12/28 110 104 6 125 125 0 strelka-varscan-mutect U2SURP,missense_variant,p.Ala355Ser,ENST00000473835,NM_001320219.1,NM_001080415.1;U2SURP,missense_variant,p.Ala354Ser,ENST00000493598,;U2SURP,missense_variant,p.Ala357Ser,ENST00000463563,;U2SURP,missense_variant,p.Ala355Ser,ENST00000488497,;U2SURP,non_coding_transcript_exon_variant,,ENST00000461591,;U2SURP,non_coding_transcript_exon_variant,,ENST00000488587,;U2SURP,upstream_gene_variant,,ENST00000480029,;U2SURP,upstream_gene_variant,,ENST00000472373,;U2SURP,downstream_gene_variant,,ENST00000470400,; T ENST00000473835 Transcript missense_variant 1153/7276 1063/3090 355/1029 A/S Gct/Tct 1 1 U2SURP HGNC HGNC:30855 protein_coding YES CCDS46928.1 ENSP00000418563 O15042 UPI0000160746 NM_001320219.1,NM_001080415.1 tolerated(0.48) 12/28 PROSITE_profiles:PS50102,hmmpanther:PTHR23140:SF1,hmmpanther:PTHR23140,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -12.52968 1 1 1 1 0 T 3 4 39 143022897 143022897 G T 1 0 0 0 0 1 0 0 0 17341 971 34 2 2 U2SURP 3 143022897 Missense_Mutation SNP G C3N-00175_T 1956325 143022897 55272662 339 9931 PLOD2 0 . GRCh38 3 146071375 146071375 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.1897C>T p.His633Tyr p.H633Y ENST00000282903 18/20 265 203 62 319 319 0 strelka-varscan-mutect PLOD2,missense_variant,p.His633Tyr,ENST00000282903,NM_182943.2;PLOD2,missense_variant,p.His612Tyr,ENST00000360060,NM_000935.2;PLOD2,missense_variant,p.His293Tyr,ENST00000461497,;PLOD2,missense_variant,p.His578Tyr,ENST00000494950,;RP11-274H2.2,intron_variant,,ENST00000480247,;RP11-274H2.3,upstream_gene_variant,,ENST00000490375,;RP11-274H2.2,downstream_gene_variant,,ENST00000494745,;PLOD2,downstream_gene_variant,,ENST00000478436,;PLOD2,upstream_gene_variant,,ENST00000495700,;PLOD2,downstream_gene_variant,,ENST00000475505,; A ENST00000282903 Transcript missense_variant 2075/3732 1897/2277 633/758 H/Y Cac/Tac COSM5398329 1 -1 PLOD2 HGNC HGNC:9082 protein_coding YES CCDS3132.1 ENSP00000282903 O00469 UPI0000049C44 NM_182943.2 deleterious(0) 18/20 hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF6,SMART_domains:SM00702 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 146071375 146071375 G A 1 0 0 0 0 1 0 0 0 12198 1348 47 3 3 PLOD2 3 146071375 Missense_Mutation SNP G C3N-00175_T 3048478 146071375 52224184 340 9932 PLSCR4 0 . GRCh38 3 146206732 146206732 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.148A>T p.Thr50Ser p.T50S ENST00000354952 4/9 185 128 57 214 214 0 strelka-varscan-mutect PLSCR4,missense_variant,p.Thr50Ser,ENST00000354952,NM_020353.2;PLSCR4,missense_variant,p.Thr50Ser,ENST00000383083,NM_001128306.1;PLSCR4,missense_variant,p.Thr35Ser,ENST00000433593,NM_001177304.1;PLSCR4,missense_variant,p.Thr50Ser,ENST00000446574,NM_001128305.1;PLSCR4,missense_variant,p.Thr50Ser,ENST00000493382,NM_001128304.1;PLSCR4,missense_variant,p.Thr50Ser,ENST00000460350,;PLSCR4,missense_variant,p.Thr50Ser,ENST00000476202,;PLSCR4,missense_variant,p.Thr50Ser,ENST00000481701,;PLSCR4,missense_variant,p.Thr50Ser,ENST00000460885,;PLSCR4,missense_variant,p.Thr50Ser,ENST00000498625,;PLSCR4,non_coding_transcript_exon_variant,,ENST00000475019,; A ENST00000354952 Transcript missense_variant 389/3303 148/990 50/329 T/S Act/Tct 1 -1 PLSCR4 HGNC HGNC:16497 protein_coding YES CCDS3133.1 ENSP00000347038 Q9NRQ2 UPI000004182E NM_020353.2 tolerated(0.1) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 146206732 146206732 T A 1 0 0 0 0 1 0 0 0 12219 1638 57 4 4 PLSCR4 3 146206732 Missense_Mutation SNP T C3N-00175_T 135357 146206732 52088827 341 9933 ZIC1 0 . GRCh38 3 147412617 147412617 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1082C>T p.Pro361Leu p.P361L ENST00000282928 2/3 206 173 33 234 234 0 strelka-varscan-mutect ZIC1,missense_variant,p.Pro361Leu,ENST00000282928,NM_003412.3;ZIC1,missense_variant,p.Pro50Leu,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,; T ENST00000282928 Transcript missense_variant 1811/5241 1082/1344 361/447 P/L cCc/cTc 1 1 ZIC1 HGNC HGNC:12872 protein_coding YES CCDS3136.1 ENSP00000282928 Q15915 UPI000013DD09 NM_003412.3 deleterious(0.01) 2/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 147412617 147412617 C T 1 0 0 0 0 1 0 0 0 18257 623 22 3 3 ZIC1 3 147412617 Missense_Mutation SNP C C3N-00175_T 1205885 147412617 50882942 342 9934 CPB1 0 . GRCh38 3 148840698 148840699 + Frame_Shift_Ins INS - - A novel C3N-00175_T C3N-00175_N - - c.287dupA p.Asn96LysfsTer11 p.N96Kfs*11 ENST00000491148 5/12 162 111 51 200 200 0 sindel-varindel-pindel CPB1,frameshift_variant,p.Asn96LysfsTer11,ENST00000491148,;CPB1,frameshift_variant,p.Asn96LysfsTer11,ENST00000282957,NM_001871.2;CPB1,frameshift_variant,p.Asn96LysfsTer11,ENST00000468341,;CPB1,frameshift_variant,p.Asn96LysfsTer?,ENST00000462345,;CPB1,non_coding_transcript_exon_variant,,ENST00000484877,;CPB1,non_coding_transcript_exon_variant,,ENST00000465718,; A ENST00000491148 Transcript frameshift_variant 619-620/1773 285-286/1254 95-96/417 -/X -/A 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD 5/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.30.70.340,Pfam_domain:PF02244,Superfamily_domains:SSF54897 HIGH 1 insertion 5 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 39 148840698 148840698 - A 1 0 1 1 0 0 0 0 0 3590 709 25 0 0 CPB1 3 148840698 Frame_Shift_Ins INS - C3N-00175_T 1428081 148840698 49454861 343 9935 HPS3 0 . GRCh38 3 149153553 149153553 + Missense_Mutation SNP G G C rs747808313 C3N-00175_T C3N-00175_N G G c.1305G>C p.Leu435Phe p.L435F ENST00000296051 7/17 270 239 31 213 212 1 strelka-varscan-mutect HPS3,missense_variant,p.Leu435Phe,ENST00000296051,NM_032383.3;HPS3,missense_variant,p.Leu270Phe,ENST00000460120,NM_001308258.1;HPS3,non_coding_transcript_exon_variant,,ENST00000462030,;HPS3,non_coding_transcript_exon_variant,,ENST00000486530,; C ENST00000296051 Transcript missense_variant 1445/4665 1305/3015 435/1004 L/F ttG/ttC rs747808313 1 1 HPS3 HGNC HGNC:15597 protein_coding YES CCDS3140.1 ENSP00000296051 Q969F9 UPI000000D989 NM_032383.3 deleterious(0.04) 7/17 hmmpanther:PTHR28633,hmmpanther:PTHR28633:SF1,Pfam_domain:PF14762,PIRSF_domain:PIRSF037473 MODERATE 1 SNV 1 1 PASS rs747808313 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 149153553 149153553 G C 1 0 0 0 0 1 0 0 0 7235 1281 45 4 4 HPS3 3 149153553 Missense_Mutation SNP G C3N-00175_T 312855 149153553 49142006 344 9936 ERICH6 0 . GRCh38 3 150680869 150680869 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.944C>G p.Thr315Ser p.T315S ENST00000295910 8/14 71 57 14 90 90 0 strelka-varscan-mutect ERICH6,missense_variant,p.Thr315Ser,ENST00000295910,NM_152394.4;ERICH6,missense_variant,p.Thr169Ser,ENST00000491361,NM_001308234.1;ERICH6,non_coding_transcript_exon_variant,,ENST00000491716,; C ENST00000295910 Transcript missense_variant 997/2052 944/1992 315/663 T/S aCc/aGc 1 -1 ERICH6 HGNC HGNC:28602 protein_coding YES CCDS3151.2 ENSP00000295910 Q7L0X2 UPI000023281A NM_152394.4 tolerated(0.43) 8/14 hmmpanther:PTHR23093 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -19.99999 0.9999964 1 1 1 0 C 3 2 39 150680869 150680869 G C 1 0 0 0 0 1 0 0 0 5086 1261 44 4 4 ERICH6 3 150680869 Missense_Mutation SNP G C3N-00175_T 1527316 150680869 47614690 345 9937 CLRN1 0 . GRCh38 3 150972595 150972595 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.114C>A p.= p.V38V ENST00000328863 1/4 439 323 116 446 445 1 strelka-varscan-mutect CLRN1,synonymous_variant,p.=,ENST00000327047,NM_174878.2;CLRN1,synonymous_variant,p.=,ENST00000328863,NM_001195794.1;CLRN1,5_prime_UTR_variant,,ENST00000468836,;CLRN1-AS1,intron_variant,,ENST00000476886,;RP11-166N6.2,intron_variant,,ENST00000469268,;CLRN1-AS1,upstream_gene_variant,,ENST00000465576,;CLRN1,non_coding_transcript_exon_variant,,ENST00000472224,; T ENST00000328863 Transcript synonymous_variant 114/738 114/738 38/245 V gtC/gtA 1 -1 CLRN1 HGNC HGNC:12605 protein_coding YES CCDS56285.1 ENSP00000329158 P58418 UPI0001E43709 NM_001195794.1 1/4 hmmpanther:PTHR31548:SF4,hmmpanther:PTHR31548 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 150972595 150972595 G T 1 0 0 0 0 0 0 0 1 3329 1161 41 2 2 CLRN1 3 150972595 Silent SNP G C3N-00175_T 291726 150972595 47322964 346 9938 IGSF10 0 . GRCh38 3 151438513 151438513 + Nonsense_Mutation SNP A A T C3N-00175_T C3N-00175_N A A c.6048T>A p.Cys2016Ter p.C2016* ENST00000282466 6/6 241 182 59 249 249 0 strelka-varscan-mutect IGSF10,stop_gained,p.Cys2016Ter,ENST00000282466,NM_178822.4;IGSF10,intron_variant,,ENST00000489791,;MED12L,downstream_gene_variant,,ENST00000474524,NM_053002.5;MED12L,downstream_gene_variant,,ENST00000273432,;IGSF10,non_coding_transcript_exon_variant,,ENST00000495443,;IGSF10,non_coding_transcript_exon_variant,,ENST00000493841,;IGSF10,upstream_gene_variant,,ENST00000497472,; T ENST00000282466 Transcript stop_gained 6048/11067 6048/7872 2016/2623 C/* tgT/tgA COSM3003586 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 6/6 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 151438513 151438513 A T 1 0 0 0 0 0 1 0 0 7504 157 6 4 4 IGSF10 3 151438513 Nonsense_Mutation SNP A C3N-00175_T 465918 151438513 46857046 347 9939 IGSF10 0 . GRCh38 3 151449018 151449018 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.963A>T p.= p.T321T ENST00000282466 4/6 174 141 33 170 170 0 strelka-varscan-mutect IGSF10,synonymous_variant,p.=,ENST00000282466,NM_178822.4; A ENST00000282466 Transcript synonymous_variant 963/11067 963/7872 321/2623 T acA/acT 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 4/6 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 151449018 151449018 T A 1 0 0 0 0 0 0 0 1 7504 1567 55 4 4 IGSF10 3 151449018 Silent SNP T C3N-00175_T 10505 151449018 46846541 348 9940 ARHGEF26 0 . GRCh38 3 154191394 154191394 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1746G>T p.= p.V582V ENST00000356448 8/15 120 79 41 107 107 0 strelka-varscan-mutect ARHGEF26,synonymous_variant,p.=,ENST00000356448,NM_001251962.1;ARHGEF26,synonymous_variant,p.=,ENST00000465093,NM_015595.3;ARHGEF26,synonymous_variant,p.=,ENST00000496710,NM_001251963.1;ARHGEF26,intron_variant,,ENST00000465817,; T ENST00000356448 Transcript synonymous_variant 2030/5254 1746/2616 582/871 V gtG/gtT 1 1 ARHGEF26 HGNC HGNC:24490 protein_coding YES CCDS46938.1 ENSP00000348828 Q96DR7 A0A140VJU4 UPI00001410D0 NM_001251962.1 8/15 PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF4,hmmpanther:PTHR12845,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 154191394 154191394 G T 1 0 0 0 0 0 0 0 1 1035 1277 45 2 2 ARHGEF26 3 154191394 Silent SNP G C3N-00175_T 2742376 154191394 44104165 349 9941 GPR149 0 . GRCh38 3 154338118 154338118 + Nonsense_Mutation SNP G G A rs774432061 C3N-00175_T C3N-00175_N G G c.1777C>T p.Arg593Ter p.R593* ENST00000389740 4/4 120 91 29 138 138 0 strelka-varscan-mutect GPR149,stop_gained,p.Arg593Ter,ENST00000389740,NM_001038705.1;RP11-316N24.2,upstream_gene_variant,,ENST00000623249,; A ENST00000389740 Transcript stop_gained 1877/2323 1777/2196 593/731 R/* Cga/Tga rs774432061,COSM1040218 1 -1 GPR149 HGNC HGNC:23627 protein_coding YES CCDS43162.1 ENSP00000374390 Q86SP6 Q2MKA6 UPI00001AEEA9 NM_001038705.1 4/4 0,1 HIGH 1 SNV 1 0,1 1 PASS rs774432061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 154338118 154338118 G A 1 0 0 0 0 0 1 0 0 6540 1066 37 1 1 GPR149 3 154338118 Nonsense_Mutation SNP G C3N-00175_T 146724 154338118 43957441 350 9942 GPR149 0 . GRCh38 3 154427547 154427547 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.1143C>T p.= p.N381N ENST00000389740 2/4 111 97 14 95 95 0 strelka-varscan-mutect GPR149,synonymous_variant,p.=,ENST00000389740,NM_001038705.1; A ENST00000389740 Transcript synonymous_variant 1243/2323 1143/2196 381/731 N aaC/aaT 1 -1 GPR149 HGNC HGNC:23627 protein_coding YES CCDS43162.1 ENSP00000374390 Q86SP6 Q2MKA6 UPI00001AEEA9 NM_001038705.1 2/4 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF32 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 154427547 154427547 G A 1 0 0 0 0 0 0 0 1 6540 1136 40 1 1 GPR149 3 154427547 Silent SNP G C3N-00175_T 89429 154427547 43868012 351 9943 IQCJ 0 . GRCh38 3 159245862 159245862 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.29A>C p.Gln10Pro p.Q10P ENST00000476809 2/10 108 84 24 131 131 0 strelka-varscan-mutect IQCJ-SCHIP1,missense_variant,p.Gln10Pro,ENST00000485419,NM_001197113.1;IQCJ-SCHIP1,missense_variant,p.Gln10Pro,ENST00000476809,NM_001197114.1;IQCJ,missense_variant,p.Gln10Pro,ENST00000397832,NM_001042706.2;IQCJ,missense_variant,p.Gln10Pro,ENST00000482126,NM_001197100.1;IQCJ,missense_variant,p.Gln10Pro,ENST00000451172,NM_001042705.2;IQCJ,non_coding_transcript_exon_variant,,ENST00000481796,; C ENST00000476809 Transcript missense_variant 29/1611 29/1611 10/536 Q/P cAg/cCg 1 1 IQCJ-SCHIP1 HGNC HGNC:38842 protein_coding YES CCDS56291.1 ENSP00000418692 UPI00016277EB NM_001197114.1 deleterious_low_confidence(0) 2/10 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 159245862 159245862 A C 1 0 0 0 0 1 0 0 0 7718 188 7 5 5 IQCJ 3 159245862 Missense_Mutation SNP A C3N-00175_T 4818315 159245862 39049697 352 9944 SLITRK3 0 . GRCh38 3 165187920 165187920 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2911G>T p.Glu971Ter p.E971* ENST00000475390 2/2 44 37 7 64 64 0 strelka-varscan-mutect SLITRK3,stop_gained,p.Glu971Ter,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,stop_gained,p.Glu971Ter,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; A ENST00000475390 Transcript stop_gained 3355/4555 2911/2934 971/977 E/* Gag/Tag 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.30311 1 1 1 1 0 A 4 1 39 165187920 165187920 C A 1 0 0 0 0 0 1 0 0 15035 864 30 2 2 SLITRK3 3 165187920 Nonsense_Mutation SNP C C3N-00175_T 5942058 165187920 33107639 353 9945 SKIL 0 . GRCh38 3 170392335 170392335 + Missense_Mutation SNP G G T rs756630039 C3N-00175_T C3N-00175_N G G c.1973G>T p.Arg658Leu p.R658L ENST00000458537 6/6 172 123 49 165 165 0 strelka-varscan-mutect SKIL,missense_variant,p.Arg658Leu,ENST00000458537,NM_005414.4,NM_001248008.1;SKIL,missense_variant,p.Arg658Leu,ENST00000259119,;SKIL,missense_variant,p.Arg638Leu,ENST00000426052,NM_001145098.2;SKIL,missense_variant,p.Arg612Leu,ENST00000413427,NM_001145097.2;SKIL,downstream_gene_variant,,ENST00000470571,; T ENST00000458537 Transcript missense_variant 2682/7182 1973/2055 658/684 R/L cGg/cTg rs756630039 1 1 SKIL HGNC HGNC:10897 protein_coding YES CCDS33890.1 ENSP00000415243 P12757 UPI000020A79D NM_005414.4,NM_001248008.1 deleterious(0) 6/6 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10005:SF3,hmmpanther:PTHR10005 MODERATE 1 SNV 1 1 PASS rs756630039 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 170392335 170392335 G T 1 0 0 0 0 1 0 0 0 14621 1116 39 1 1 SKIL 3 170392335 Missense_Mutation SNP G C3N-00175_T 5204415 170392335 27903224 354 9946 ECE2 0 . GRCh38 3 184290662 184290662 + Frame_Shift_Del DEL C C - rs772894671 C3N-00175_T C3N-00175_N C C c.2118delC p.Lys707ArgfsTer3 p.K707Rfs*3 ENST00000402825 15/19 66 38 28 102 101 1 sindel-varindel-pindel ECE2,frameshift_variant,p.Lys707ArgfsTer3,ENST00000402825,NM_014693.3;ECE2,frameshift_variant,p.Lys589ArgfsTer3,ENST00000404464,NM_001100121.1;ECE2,frameshift_variant,p.Lys560ArgfsTer3,ENST00000359140,NM_001037324.2;ECE2,frameshift_variant,p.Lys635ArgfsTer3,ENST00000357474,NM_001100120.1;ECE2,frameshift_variant,p.Lys581ArgfsTer3,ENST00000430587,;ECE2,non_coding_transcript_exon_variant,,ENST00000488401,;ECE2,non_coding_transcript_exon_variant,,ENST00000490579,; - ENST00000402825 Transcript frameshift_variant 2115/3445 2115/2652 705/883 H/X caC/ca rs772894671 1 1 ECE2 HGNC HGNC:13275 protein_coding YES CCDS3256.2 ENSP00000384223 O60344 UPI0001596888 NM_014693.3 15/19 Gene3D:3.40.390.10,Pfam_domain:PF01431,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF127,Superfamily_domains:SSF55486 HIGH 1 deletion 1 3 1 PASS . . 0 203 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 184290662 184290662 C - 1 0 1 0 1 0 0 0 0 4716 521 18 0 0 ECE2 3 184290662 Frame_Shift_Del DEL C C3N-00175_T 13898327 184290662 14004897 355 9947 ST6GAL1 0 . GRCh38 3 187042875 187042875 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.172T>C p.Ser58Pro p.S58P ENST00000169298 4/8 181 112 69 246 246 0 strelka-varscan-mutect ST6GAL1,missense_variant,p.Ser58Pro,ENST00000169298,NM_173216.2;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000448044,NM_003032.2;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000448408,;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000417392,;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000438590,;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000423451,;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000446170,;ST6GAL1,missense_variant,p.Ser58Pro,ENST00000416235,;ST6GAL1,intron_variant,,ENST00000457772,NM_173217.2;ST6GAL1,intron_variant,,ENST00000455441,;ST6GAL1,intron_variant,,ENST00000427315,;ST6GAL1,upstream_gene_variant,,ENST00000442023,;ST6GAL1,downstream_gene_variant,,ENST00000440338,;ST6GAL1,downstream_gene_variant,,ENST00000458216,;ST6GAL1,downstream_gene_variant,,ENST00000430309,;ST6GAL1,upstream_gene_variant,,ENST00000448449,;ST6GAL1,upstream_gene_variant,,ENST00000464827,; C ENST00000169298 Transcript missense_variant 846/4645 172/1221 58/406 S/P Tct/Cct 1 1 ST6GAL1 HGNC HGNC:10860 protein_coding YES CCDS3285.1 ENSP00000169298 P15907 UPI000000D97B NM_173216.2 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF55,PIRSF_domain:PIRSF005557 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 187042875 187042875 T C 1 0 0 0 0 1 0 0 0 15599 1667 58 5 5 ST6GAL1 3 187042875 Missense_Mutation SNP T C3N-00175_T 2752213 187042875 11252684 356 9948 MASP1 0 . GRCh38 3 187236404 187236404 + Silent SNP C C A rs149695036 C3N-00175_T C3N-00175_N C C c.1467G>T p.= p.A489A ENST00000296280 11/11 350 242 108 336 336 0 strelka-varscan-mutect MASP1,synonymous_variant,p.=,ENST00000296280,NM_139125.3;MASP1,synonymous_variant,p.=,ENST00000392472,;MASP1,intron_variant,,ENST00000337774,NM_001879.5;MASP1,intron_variant,,ENST00000495249,;MASP1,intron_variant,,ENST00000468121,;MASP1,non_coding_transcript_exon_variant,,ENST00000480349,; A ENST00000296280 Transcript synonymous_variant 1693/4015 1467/2187 489/728 A gcG/gcT rs149695036,COSM3781121,COSM5307671 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 11/11 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001155,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs149695036 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 187236404 187236404 C A 1 0 0 0 0 0 0 0 1 9248 523 19 1 1 MASP1 3 187236404 Silent SNP C C3N-00175_T 193529 187236404 11059155 357 9949 MASP1 0 . GRCh38 3 187253241 187253241 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.819C>G p.His273Gln p.H273Q ENST00000296280 6/11 227 172 55 342 342 0 strelka-varscan-mutect MASP1,missense_variant,p.His273Gln,ENST00000337774,NM_001879.5;MASP1,missense_variant,p.His273Gln,ENST00000296280,NM_139125.3;MASP1,missense_variant,p.His160Gln,ENST00000392472,;MASP1,missense_variant,p.His273Gln,ENST00000169293,NM_001031849.2;MASP1,missense_variant,p.His247Gln,ENST00000392470,;MASP1,downstream_gene_variant,,ENST00000392475,;MASP1,intron_variant,,ENST00000495249,;MASP1,downstream_gene_variant,,ENST00000490558,;MASP1,downstream_gene_variant,,ENST00000460839,;MASP1,upstream_gene_variant,,ENST00000483719,; C ENST00000296280 Transcript missense_variant 1045/4015 819/2187 273/728 H/Q caC/caG COSM4700768,COSM4700769,COSM4700770 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 deleterious(0) 6/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS01180,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 187253241 187253241 G C 1 0 0 0 0 1 0 0 0 9248 1368 48 4 4 MASP1 3 187253241 Missense_Mutation SNP G C3N-00175_T 16837 187253241 11042318 358 9950 ATP13A3 0 . GRCh38 3 194431149 194431149 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.2499A>G p.= p.K833K ENST00000439040 23/33 121 82 39 165 165 0 strelka-varscan-mutect ATP13A3,synonymous_variant,p.=,ENST00000439040,;ATP13A3,synonymous_variant,p.=,ENST00000256031,NM_024524.3;ATP13A3,synonymous_variant,p.=,ENST00000619199,;ATP13A3,non_coding_transcript_exon_variant,,ENST00000484023,; C ENST00000439040 Transcript synonymous_variant 3291/7720 2499/3681 833/1226 K aaA/aaG 1 -1 ATP13A3 HGNC HGNC:24113 protein_coding YES CCDS43187.1 ENSP00000416508 Q9H7F0 UPI000049DFC3 23/33 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF249,TIGRFAM_domain:TIGR01657,Gene3D:3.40.50.1000 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 194431149 194431149 T C 1 0 0 0 0 0 0 0 1 1277 1490 52 5 5 ATP13A3 3 194431149 Silent SNP T C3N-00175_T 7177908 194431149 3864410 359 9951 HTT 0 . GRCh38 4 3225721 3225721 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.7826G>T p.Ser2609Ile p.S2609I ENST00000355072 57/67 147 120 27 162 162 0 strelka-varscan-mutect HTT,missense_variant,p.Ser2609Ile,ENST00000355072,NM_002111.7;HTT,upstream_gene_variant,,ENST00000513806,;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;HTT,upstream_gene_variant,,ENST00000512068,; T ENST00000355072 Transcript missense_variant 7971/13474 7826/9429 2609/3142 S/I aGc/aTc 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 tolerated(0.11) 57/67 hmmpanther:PTHR10170,hmmpanther:PTHR10170:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 3225721 3225721 G T 1 0 0 0 0 1 0 0 0 7353 971 34 2 2 HTT 4 3225721 Missense_Mutation SNP G C3N-00175_T 3225721 186988834 360 9952 HTT 0 . GRCh38 4 3238571 3238571 + Nonsense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.9016C>T p.Gln3006Ter p.Q3006* ENST00000355072 65/67 93 81 12 106 105 1 strelka-varscan-mutect HTT,stop_gained,p.Gln3006Ter,ENST00000355072,NM_002111.7;HTT,downstream_gene_variant,,ENST00000513806,;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;HTT,downstream_gene_variant,,ENST00000508321,; T ENST00000355072 Transcript stop_gained 9161/13474 9016/9429 3006/3142 Q/* Cag/Tag 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 65/67 hmmpanther:PTHR10170,hmmpanther:PTHR10170:SF10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 3238571 3238571 C T 1 0 0 0 0 0 1 0 0 7353 711 25 3 3 HTT 4 3238571 Nonsense_Mutation SNP C C3N-00175_T 12850 3238571 186975984 361 9953 STX18 0 . GRCh38 4 4459463 4459463 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.261G>T p.Arg87Ser p.R87S ENST00000306200 3/11 151 116 35 209 209 0 strelka-varscan-mutect STX18,missense_variant,p.Arg87Ser,ENST00000306200,NM_016930.2;STX18,missense_variant,p.Arg87Ser,ENST00000505286,;STX18,missense_variant,p.Arg6Ser,ENST00000507908,;STX18,non_coding_transcript_exon_variant,,ENST00000503861,;STX18,non_coding_transcript_exon_variant,,ENST00000512195,;STX18,non_coding_transcript_exon_variant,,ENST00000512780,; A ENST00000306200 Transcript missense_variant 325/2138 261/1008 87/335 R/S agG/agT 1 -1 STX18 HGNC HGNC:15942 protein_coding YES CCDS3377.1 ENSP00000305810 Q9P2W9 UPI0000049FDD NM_016930.2 tolerated(0.27) 3/11 Pfam_domain:PF10496,hmmpanther:PTHR15959,hmmpanther:PTHR15959:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 4459463 4459463 C A 1 0 0 0 0 1 0 0 0 15725 854 30 2 2 STX18 4 4459463 Missense_Mutation SNP C C3N-00175_T 1220892 4459463 185755092 362 9954 C4orf50 0 . GRCh38 4 5959452 5959452 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.4450G>C p.Ala1484Pro p.A1484P ENST00000531445 12/12 185 161 24 248 246 2 strelka-varscan-mutect C4orf50,missense_variant,p.Ala1484Pro,ENST00000531445,;C4orf50,missense_variant,p.Ala252Pro,ENST00000324058,; G ENST00000531445 Transcript missense_variant 4526/6860 4450/4527 1484/1508 A/P Gct/Cct 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 deleterious(0.01) 12/12 hmmpanther:PTHR36866,Pfam_domain:PF15030 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 39 5959452 5959452 C G 1 0 0 0 0 1 0 0 0 2089 739 26 4 4 C4orf50 4 5959452 Missense_Mutation SNP C C3N-00175_T 1499989 5959452 184255103 363 9955 TAPT1 0 . GRCh38 4 16176219 16176219 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1007G>T p.Trp336Leu p.W336L ENST00000405303 9/14 80 74 6 113 113 0 strelka-varscan-mutect TAPT1,missense_variant,p.Trp336Leu,ENST00000405303,NM_153365.2;RP11-452J21.2,upstream_gene_variant,,ENST00000513586,;TAPT1,non_coding_transcript_exon_variant,,ENST00000488714,;TAPT1,missense_variant,p.Trp129Leu,ENST00000513782,;TAPT1,3_prime_UTR_variant,,ENST00000505603,;TAPT1,upstream_gene_variant,,ENST00000508886,;TAPT1,downstream_gene_variant,,ENST00000507425,;TAPT1,upstream_gene_variant,,ENST00000507728,;TAPT1,downstream_gene_variant,,ENST00000504281,; A ENST00000405303 Transcript missense_variant 1091/4591 1007/1704 336/567 W/L tGg/tTg 1 -1 TAPT1 HGNC HGNC:26887 protein_coding YES CCDS47030.1 ENSP00000385347 Q6NXT6 UPI0000253B29 NM_153365.2 deleterious(0.02) 9/14 hmmpanther:PTHR13317,hmmpanther:PTHR13317:SF4,Pfam_domain:PF05346 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -10.22434 0.9999733 1 1 1 0 A 3 1 39 16176219 16176219 C A 1 0 0 0 0 1 0 0 0 15953 595 21 2 2 TAPT1 4 16176219 Missense_Mutation SNP C C3N-00175_T 10216767 16176219 174038336 364 9956 KCNIP4 0 . GRCh38 4 20882616 20882616 + Missense_Mutation SNP G G C rs760840330 C3N-00175_T C3N-00175_N G G c.155C>G p.Ala52Gly p.A52G ENST00000382152 2/9 152 111 41 169 169 0 strelka-varscan-mutect KCNIP4,missense_variant,p.Ala52Gly,ENST00000382152,NM_025221.5;KCNIP4,intron_variant,,ENST00000382148,NM_001035003.1;KCNIP4,intron_variant,,ENST00000382150,NM_147183.3;KCNIP4,intron_variant,,ENST00000447367,NM_147181.3;KCNIP4,intron_variant,,ENST00000509207,NM_001035004.1;KCNIP4,intron_variant,,ENST00000382149,;KCNIP4,non_coding_transcript_exon_variant,,ENST00000515373,;KCNIP4,intron_variant,,ENST00000515786,; C ENST00000382152 Transcript missense_variant 323/1767 155/753 52/250 A/G gCt/gGt rs760840330 1 -1 KCNIP4 HGNC HGNC:30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 tolerated(0.41) 2/9 hmmpanther:PTHR23055:SF30,hmmpanther:PTHR23055 MODERATE 1 SNV 5 1 PASS rs760840330 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 20882616 20882616 G C 1 0 0 0 0 1 0 0 0 7958 971 34 4 4 KCNIP4 4 20882616 Missense_Mutation SNP G C3N-00175_T 4706397 20882616 169331939 365 9957 ADGRA3 0 . GRCh38 4 22388317 22388318 + Frame_Shift_Ins INS - - A novel C3N-00175_T C3N-00175_N - - c.3353dupT p.Leu1118PhefsTer22 p.L1118Ffs*22 ENST00000334304 19/19 114 100 14 180 180 0 sindel-varindel-pindel ADGRA3,frameshift_variant,p.Leu1118PhefsTer22,ENST00000334304,NM_145290.3;ADGRA3,non_coding_transcript_exon_variant,,ENST00000282943,;ADGRA3,downstream_gene_variant,,ENST00000504617,;ADGRA3,non_coding_transcript_exon_variant,,ENST00000499527,;ADGRA3,intron_variant,,ENST00000511051,; A ENST00000334304 Transcript frameshift_variant 3623-3624/4566 3353-3354/3966 1118/1321 L/FX ttg/ttTg 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 19/19 hmmpanther:PTHR12011:SF35,hmmpanther:PTHR12011 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 39 22388317 22388317 - A 1 0 1 1 0 0 0 0 0 354 709 25 0 0 ADGRA3 4 22388317 Frame_Shift_Ins INS - C3N-00175_T 1505701 22388317 167826238 366 9958 APBB2 0 . GRCh38 4 41013980 41013980 + Silent SNP C C A rs778240657 C3N-00175_T C3N-00175_N C C c.438G>T p.= p.S146S ENST00000508593 6/18 102 85 17 144 144 0 strelka-varscan-mutect APBB2,synonymous_variant,p.=,ENST00000295974,NM_001166050.1;APBB2,synonymous_variant,p.=,ENST00000513140,NM_173075.4;APBB2,synonymous_variant,p.=,ENST00000508593,NM_004307.1;APBB2,synonymous_variant,p.=,ENST00000506352,;APBB2,synonymous_variant,p.=,ENST00000513611,;APBB2,synonymous_variant,p.=,ENST00000509446,;APBB2,downstream_gene_variant,,ENST00000508707,;APBB2,downstream_gene_variant,,ENST00000508676,;APBB2,downstream_gene_variant,,ENST00000503503,;APBB2,downstream_gene_variant,,ENST00000503264,;APBB2,non_coding_transcript_exon_variant,,ENST00000509475,; A ENST00000508593 Transcript synonymous_variant 982/3592 438/2280 146/759 S tcG/tcT rs778240657,COSM1429703,COSM4948167 1 -1 APBB2 HGNC HGNC:582 protein_coding YES CCDS54762.1 ENSP00000427211 Q92870 UPI0001B8E1D4 NM_004307.1 6/18 hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF11 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs778240657 . 0 207 0 3 0 0 0 0 -20 0.9999949 1 1 1 0 A 2 1 39 41013980 41013980 C A 1 0 0 0 0 0 0 0 1 881 871 31 1 1 APBB2 4 41013980 Silent SNP C C3N-00175_T 18625663 41013980 149200575 367 9959 BEND4 0 . GRCh38 4 42143957 42143957 + Missense_Mutation SNP G G C rs113164208 C3N-00175_T C3N-00175_N G G c.525C>G p.Cys175Trp p.C175W ENST00000502486 3/6 24 19 5 19 19 0 strelka-varscan-mutect BEND4,missense_variant,p.Cys175Trp,ENST00000502486,NM_207406.3;BEND4,missense_variant,p.Cys171Trp,ENST00000504360,NM_001159547.1;BEND4,missense_variant,p.Cys46Trp,ENST00000611697,; C ENST00000502486 Transcript missense_variant 1105/8765 525/1605 175/534 C/W tgC/tgG rs113164208 1 -1 BEND4 HGNC HGNC:23815 protein_coding YES CCDS47048.1 ENSP00000421169 Q6ZU67 UPI00015386AF NM_207406.3 deleterious_low_confidence(0) 3/6 hmmpanther:PTHR35082 MODERATE 1 SNV 1 1 PASS rs113164208 . 0 204 6 0 0 0 0 0 -14.30292 1 1 1 1 0 C 3 2 39 42143957 42143957 G C 1 0 0 0 0 1 0 0 0 1548 1311 46 4 4 BEND4 4 42143957 Missense_Mutation SNP G C3N-00175_T 1129977 42143957 148070598 368 9960 ATP8A1 0 . GRCh38 4 42616079 42616079 + Splice_Site SNP C C A C3N-00175_T C3N-00175_N C C c.364-1G>T p.X122_splice ENST00000381668 49 41 8 134 133 1 strelka-varscan-mutect ATP8A1,splice_acceptor_variant,,ENST00000381668,NM_006095.2;ATP8A1,splice_acceptor_variant,,ENST00000264449,NM_001105529.1;ATP8A1,upstream_gene_variant,,ENST00000504024,; A ENST00000381668 Transcript splice_acceptor_variant -/8270 364/3495 122/1164 COSM733404,COSM733405 1 -1 ATP8A1 HGNC HGNC:13531 protein_coding YES CCDS3466.1 ENSP00000371084 Q9Y2Q0 UPI0000125063 NM_006095.2 4/36 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 42616079 42616079 C A 1 0 0 0 0 0 0 1 0 1345 927 32 2 2 ATP8A1 4 42616079 Splice_Site SNP C C3N-00175_T 472122 42616079 147598476 369 9961 KCTD8 0 . GRCh38 4 44175169 44175169 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1043G>T p.Ser348Ile p.S348I ENST00000360029 2/2 77 59 18 68 67 1 strelka-varscan-mutect KCTD8,missense_variant,p.Ser348Ile,ENST00000360029,NM_198353.2;KCTD8,missense_variant,p.Ser84Ile,ENST00000515268,; A ENST00000360029 Transcript missense_variant 1327/2587 1043/1422 348/473 S/I aGt/aTt 1 -1 KCTD8 HGNC HGNC:22394 protein_coding YES CCDS3467.1 ENSP00000353129 Q6ZWB6 UPI00001C08D6 NM_198353.2 deleterious(0.01) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 44175169 44175169 C A 1 0 0 0 0 1 0 0 0 8032 565 20 2 2 KCTD8 4 44175169 Missense_Mutation SNP C C3N-00175_T 1559090 44175169 146039386 370 9962 KCTD8 0 . GRCh38 4 44447816 44447816 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.708G>T p.Met236Ile p.M236I ENST00000360029 1/2 78 68 10 104 104 0 strelka-varscan-mutect KCTD8,missense_variant,p.Met236Ile,ENST00000360029,NM_198353.2;KCTD8,upstream_gene_variant,,ENST00000515268,; A ENST00000360029 Transcript missense_variant 992/2587 708/1422 236/473 M/I atG/atT 1 -1 KCTD8 HGNC HGNC:22394 protein_coding YES CCDS3467.1 ENSP00000353129 Q6ZWB6 UPI00001C08D6 NM_198353.2 tolerated(0.06) 1/2 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF68 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99303 1 1 1 1 0 A 3 1 39 44447816 44447816 C A 1 0 0 0 0 1 0 0 0 8032 594 21 2 2 KCTD8 4 44447816 Missense_Mutation SNP C C3N-00175_T 272647 44447816 145766739 371 9963 NFXL1 0 . GRCh38 4 47879096 47879096 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1938G>T p.Glu646Asp p.E646D ENST00000507489 16/23 24 17 7 95 94 1 strelka-mutect NFXL1,missense_variant,p.Glu646Asp,ENST00000507489,NM_001278624.1;NFXL1,missense_variant,p.Glu646Asp,ENST00000381538,NM_152995.5;NFXL1,missense_variant,p.Glu646Asp,ENST00000329043,NM_001278623.1;RP11-121C2.3,intron_variant,,ENST00000634611,;RP11-121C2.3,intron_variant,,ENST00000634948,;NFXL1,missense_variant,p.Glu646Asp,ENST00000464756,;NFXL1,splice_region_variant,,ENST00000507131,;NFXL1,upstream_gene_variant,,ENST00000502448,;NFXL1,upstream_gene_variant,,ENST00000508115,; A ENST00000507489 Transcript missense_variant,splice_region_variant 2115/3833 1938/2736 646/911 E/D gaG/gaT 1 -1 NFXL1 HGNC HGNC:18726 protein_coding YES CCDS3478.2 ENSP00000422037 Q6ZNB6 UPI000020BC5D NM_001278624.1 deleterious(0.01) 16/23 hmmpanther:PTHR12360 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -16.18974 0.9999954 1 1 1 0 A 3 1 39 47879096 47879096 C A 1 0 0 0 0 1 0 0 0 10424 695 24 2 2 NFXL1 4 47879096 Missense_Mutation SNP C C3N-00175_T 3431280 47879096 142335459 372 9964 CWH43 0 . GRCh38 4 48994696 48994696 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.589C>A p.Leu197Met p.L197M ENST00000226432 5/16 242 212 30 243 243 0 strelka-varscan-mutect CWH43,missense_variant,p.Leu197Met,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Leu170Met,ENST00000513409,NM_001286791.1;CWH43,missense_variant,p.Leu197Met,ENST00000514053,; A ENST00000226432 Transcript missense_variant 772/2472 589/2100 197/699 L/M Ctg/Atg 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.01) 5/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 48994696 48994696 C A 1 0 0 0 0 1 0 0 0 3883 796 28 2 2 CWH43 4 48994696 Missense_Mutation SNP C C3N-00175_T 1115600 48994696 141219859 373 9965 ERVMER34-1 0 . GRCh38 4 52744808 52744808 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.713G>T p.Gly238Val p.G238V ENST00000443173 3/3 236 204 32 291 291 0 strelka-varscan-mutect ERVMER34-1,missense_variant,p.Gly238Val,ENST00000443173,NM_001242690.1;ERVMER34-1,missense_variant,p.Gly238Val,ENST00000440542,NM_024534.5;SNORA26,upstream_gene_variant,,ENST00000391188,;ERVMER34-1,intron_variant,,ENST00000454756,; A ENST00000443173 Transcript missense_variant 1574/3830 713/1692 238/563 G/V gGc/gTc 1 -1 ERVMER34-1 HGNC HGNC:42970 protein_coding YES ENSP00000460602 Q9H9K5 UPI000006F57C NM_001242690.1 tolerated_low_confidence(0.09) 3/3 hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF42 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 52744808 52744808 C A 1 0 0 0 0 1 0 0 0 5105 739 26 2 2 ERVMER34-1 4 52744808 Missense_Mutation SNP C C3N-00175_T 3750112 52744808 137469747 374 9966 GSX2 0 . GRCh38 4 54100724 54100724 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.380A>G p.His127Arg p.H127R ENST00000326902 1/2 180 156 24 221 221 0 strelka-varscan-mutect GSX2,missense_variant,p.His127Arg,ENST00000326902,;GSX2,missense_variant,p.His127Arg,ENST00000611459,NM_133267.2;RP11-231C18.3,intron_variant,,ENST00000507166,;GSX2,intron_variant,,ENST00000503800,;GSX2,intron_variant,,ENST00000507839,;GSX2,upstream_gene_variant,,ENST00000548609,; G ENST00000326902 Transcript missense_variant 694/1812 380/915 127/304 H/R cAt/cGt 1 1 GSX2 HGNC HGNC:24959 protein_coding YES CCDS3494.1 ENSP00000319118 Q9BZM3 UPI0000141A63 deleterious_low_confidence(0.01) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF170,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 54100724 54100724 A G 1 0 0 0 0 1 0 0 0 6732 217 8 5 5 GSX2 4 54100724 Missense_Mutation SNP A C3N-00175_T 1355916 54100724 136113831 375 9967 PDGFRA 0 . GRCh38 4 54267627 54267627 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1007T>A p.Val336Asp p.V336D ENST00000257290 7/23 154 97 57 179 179 0 strelka-varscan-mutect PDGFRA,missense_variant,p.Val336Asp,ENST00000257290,NM_006206.4;RP11-231C18.3,intron_variant,,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000508170,;PDGFRA,downstream_gene_variant,,ENST00000504461,;PDGFRA,downstream_gene_variant,,ENST00000503856,;PDGFRA,downstream_gene_variant,,ENST00000512522,;PDGFRA,missense_variant,p.Val336Asp,ENST00000509490,;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092,; A ENST00000257290 Transcript missense_variant 1338/6576 1007/3270 336/1089 V/D gTt/gAt 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 tolerated(0.57) 7/23 hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000615,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 54267627 54267627 T A 1 0 0 0 0 1 0 0 0 11749 1725 60 4 4 PDGFRA 4 54267627 Missense_Mutation SNP T C3N-00175_T 166903 54267627 135946928 376 9968 KDR 0 . GRCh38 4 55094948 55094948 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.2825G>A p.Gly942Glu p.G942E ENST00000263923 21/30 224 177 47 251 250 1 strelka-varscan-mutect KDR,missense_variant,p.Gly942Glu,ENST00000263923,NM_002253.2;RP11-530I17.1,downstream_gene_variant,,ENST00000511222,;KDR,non_coding_transcript_exon_variant,,ENST00000509309,; T ENST00000263923 Transcript missense_variant 3121/5831 2825/4071 942/1356 G/E gGg/gAg COSM3301541 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0.02) 21/30 Pfam_domain:PF07714,PROSITE_profiles:PS50011,SMART_domains:SM00219,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55094948 55094948 C T 1 0 0 0 0 1 0 0 0 8059 623 22 3 3 KDR 4 55094948 Missense_Mutation SNP C C3N-00175_T 827321 55094948 135119607 377 9969 ADGRL3 0 . GRCh38 4 62037730 62037730 + Splice_Site SNP G G T C3N-00175_T C3N-00175_N G G c.3388-1G>T p.X1130_splice ENST00000514591 124 96 28 146 146 0 strelka-varscan-mutect ADGRL3,splice_acceptor_variant,,ENST00000512091,NM_001322246.1;ADGRL3,splice_acceptor_variant,,ENST00000514591,NM_015236.4;ADGRL3,splice_acceptor_variant,,ENST00000509896,;ADGRL3,splice_acceptor_variant,,ENST00000511324,;ADGRL3,splice_acceptor_variant,,ENST00000508693,;ADGRL3,splice_acceptor_variant,,ENST00000507164,;ADGRL3,splice_acceptor_variant,,ENST00000506720,;ADGRL3,splice_acceptor_variant,,ENST00000506746,;ADGRL3,splice_acceptor_variant,,ENST00000507625,;ADGRL3,splice_acceptor_variant,,ENST00000506700,;ADGRL3,splice_acceptor_variant,,ENST00000504896,;ADGRL3,splice_acceptor_variant,,ENST00000514157,;ADGRL3,splice_acceptor_variant,,ENST00000508946,;ADGRL3,splice_acceptor_variant,,ENST00000514996,;ADGRL3,splice_acceptor_variant,,ENST00000502815,; T ENST00000514591 Transcript splice_acceptor_variant -/6297 3388/4410 1130/1469 COSM3604860,COSM3604861,COSM3604862,COSM5643065 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 22/24 1,1,1,1 HIGH 1 SNV 5 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 39 62037730 62037730 G T 1 0 0 0 0 0 0 1 0 377 1014 35 2 2 ADGRL3 4 62037730 Splice_Site SNP G C3N-00175_T 6942782 62037730 128176825 378 9970 CENPC 0 . GRCh38 4 67519245 67519245 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.589A>T p.Thr197Ser p.T197S ENST00000273853 6/19 77 64 13 109 109 0 strelka-varscan-mutect CENPC,missense_variant,p.Thr197Ser,ENST00000273853,NM_001812.2;CENPC,missense_variant,p.Thr197Ser,ENST00000506882,;CENPC,missense_variant,p.Thr104Ser,ENST00000513216,;CENPC,non_coding_transcript_exon_variant,,ENST00000510189,;CENPC,upstream_gene_variant,,ENST00000506410,; A ENST00000273853 Transcript missense_variant 840/6940 589/2832 197/943 T/S Aca/Tca 1 -1 CENPC HGNC HGNC:1854 protein_coding YES CCDS47063.1 ENSP00000273853 Q03188 UPI00004135A3 NM_001812.2 deleterious(0.03) 6/19 Pfam_domain:PF15622,hmmpanther:PTHR16684 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 67519245 67519245 T A 1 0 0 0 0 1 0 0 0 2937 1638 57 4 4 CENPC 4 67519245 Missense_Mutation SNP T C3N-00175_T 5481515 67519245 122695310 379 9971 STAP1 0 . GRCh38 4 67558827 67558827 + Silent SNP C C A rs757933476 C3N-00175_T C3N-00175_N C C c.18C>A p.= p.P6P ENST00000265404 1/9 117 87 30 122 121 1 strelka-varscan-mutect STAP1,synonymous_variant,p.=,ENST00000265404,NM_012108.2;STAP1,synonymous_variant,p.=,ENST00000396225,NM_001317769.1; A ENST00000265404 Transcript synonymous_variant 100/1511 18/888 6/295 P ccC/ccA rs757933476 1 1 STAP1 HGNC HGNC:24133 protein_coding YES CCDS3515.1 ENSP00000265404 Q9ULZ2 A0A024RD91 UPI0000073E6C NM_012108.2 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR16186,hmmpanther:PTHR16186:SF10 LOW 1 SNV 1 1 PASS rs757933476 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 67558827 67558827 C A 1 0 0 0 0 0 0 0 1 15627 610 22 2 2 STAP1 4 67558827 Silent SNP C C3N-00175_T 39582 67558827 122655728 380 9972 STAP1 0 . GRCh38 4 67583594 67583594 + Missense_Mutation SNP G G T rs537318483 C3N-00175_T C3N-00175_N G G c.551G>T p.Arg184Leu p.R184L ENST00000265404 6/9 99 75 24 136 136 0 strelka-varscan-mutect STAP1,missense_variant,p.Arg184Leu,ENST00000265404,NM_012108.2;STAP1,missense_variant,p.Arg184Leu,ENST00000396225,NM_001317769.1; T ENST00000265404 Transcript missense_variant 633/1511 551/888 184/295 R/L cGg/cTg rs537318483,COSM1430590 1 1 STAP1 HGNC HGNC:24133 protein_coding YES CCDS3515.1 ENSP00000265404 Q9ULZ2 A0A024RD91 UPI0000073E6C NM_012108.2 deleterious(0) 6/9 PROSITE_profiles:PS50001,hmmpanther:PTHR16186,hmmpanther:PTHR16186:SF10,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs537318483 . 0 205 0 4 0 0 0 0 -20 0.9999666 1 1 1 0 T 3 4 39 67583594 67583594 G T 1 0 0 0 0 1 0 0 0 15627 1116 39 1 1 STAP1 4 67583594 Missense_Mutation SNP G C3N-00175_T 24767 67583594 122630961 381 9973 YTHDC1 0 . GRCh38 4 68322754 68322754 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1596G>T p.= p.V532V ENST00000344157 11/17 65 43 22 74 73 1 strelka-varscan-mutect YTHDC1,synonymous_variant,p.=,ENST00000344157,NM_001031732.2;YTHDC1,synonymous_variant,p.=,ENST00000355665,NM_133370.2;YTHDC1,synonymous_variant,p.=,ENST00000579690,;YTHDC1,upstream_gene_variant,,ENST00000507529,;YTHDC1,non_coding_transcript_exon_variant,,ENST00000506175,; A ENST00000344157 Transcript synonymous_variant 1932/6232 1596/2184 532/727 V gtG/gtT 1 -1 YTHDC1 HGNC HGNC:30626 protein_coding YES CCDS33992.1 ENSP00000339245 Q96MU7 UPI000020B86D NM_001031732.2 11/17 hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF33,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 68322754 68322754 C A 1 0 0 0 0 0 0 0 1 18057 608 21 2 2 YTHDC1 4 68322754 Silent SNP C C3N-00175_T 739160 68322754 121891801 382 9974 CABS1 0 . GRCh38 4 70335060 70335060 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.21C>A p.= p.P7P ENST00000273936 1/2 79 70 9 69 69 0 strelka-varscan-mutect CABS1,synonymous_variant,p.=,ENST00000273936,NM_033122.3; A ENST00000273936 Transcript synonymous_variant 95/1532 21/1188 7/395 P ccC/ccA 1 1 CABS1 HGNC HGNC:30710 protein_coding YES CCDS3539.1 ENSP00000273936 Q96KC9 UPI0000071735 NM_033122.3 1/2 Pfam_domain:PF15367,hmmpanther:PTHR22810 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.4042 1 1 1 1 0 A 2 1 39 70335060 70335060 C A 1 0 0 0 0 0 0 0 1 2222 581 21 2 2 CABS1 4 70335060 Silent SNP C C3N-00175_T 2012306 70335060 119879495 383 9975 ANKRD17 0 . GRCh38 4 73177501 73177501 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.426G>C p.Leu142Phe p.L142F ENST00000358602 2/34 73 56 17 102 102 0 strelka-varscan-mutect ANKRD17,missense_variant,p.Leu142Phe,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,missense_variant,p.Leu27Phe,ENST00000558247,;ANKRD17,missense_variant,p.Leu29Phe,ENST00000509867,NM_001286771.1;ANKRD17,missense_variant,p.Leu142Phe,ENST00000330838,NM_198889.1;ANKRD17,intron_variant,,ENST00000561029,;ANKRD17,non_coding_transcript_exon_variant,,ENST00000559367,; G ENST00000358602 Transcript missense_variant 543/10784 426/7812 142/2603 L/F ttG/ttC 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 deleterious_low_confidence(0) 2/34 hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 73177501 73177501 C G 1 0 0 0 0 1 0 0 0 747 593 21 4 4 ANKRD17 4 73177501 Missense_Mutation SNP C C3N-00175_T 2842441 73177501 117037054 384 9976 NUP54 0 . GRCh38 4 76144292 76144292 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.152G>T p.Gly51Val p.G51V ENST00000264883 3/12 125 85 40 142 140 2 strelka-varscan-mutect NUP54,missense_variant,p.Gly51Val,ENST00000264883,NM_017426.3;NUP54,missense_variant,p.Gly105Val,ENST00000514901,;NUP54,intron_variant,,ENST00000514987,NM_001278603.1;NUP54,splice_region_variant,,ENST00000515460,;NUP54,splice_region_variant,,ENST00000514307,;NUP54,splice_region_variant,,ENST00000506098,;NUP54,splice_region_variant,,ENST00000508583,;NUP54,splice_region_variant,,ENST00000510569,;NUP54,splice_region_variant,,ENST00000510884,;NUP54,missense_variant,p.Gly51Val,ENST00000507257,;NUP54,missense_variant,p.Asp113Tyr,ENST00000502850,;NUP54,missense_variant,p.Gly51Val,ENST00000512151,;NUP54,splice_region_variant,,ENST00000513352,;NUP54,intron_variant,,ENST00000504173,; A ENST00000264883 Transcript missense_variant,splice_region_variant 293/2367 152/1524 51/507 G/V gGa/gTa 1 -1 NUP54 HGNC HGNC:17359 protein_coding YES CCDS3576.1 ENSP00000264883 Q7Z3B4 UPI0000036166 NM_017426.3 deleterious(0.02) 3/12 hmmpanther:PTHR13000,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 202 3 4 0 0 0 0 -20 0.9998875 1 1 1 0 A 3 1 39 76144292 76144292 C A 1 0 0 0 0 1 0 0 0 10832 869 30 2 2 NUP54 4 76144292 Missense_Mutation SNP C C3N-00175_T 2966791 76144292 114070263 385 9977 AFF1 0 . GRCh38 4 87114622 87114622 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1789G>T p.Ala597Ser p.A597S ENST00000395146 12/21 172 150 22 188 188 0 strelka-varscan-mutect AFF1,missense_variant,p.Ala590Ser,ENST00000307808,NM_001313959.1,NM_005935.2;AFF1,missense_variant,p.Ala597Ser,ENST00000395146,NM_001166693.1;AFF1,missense_variant,p.Ala590Ser,ENST00000544085,;AFF1,upstream_gene_variant,,ENST00000503369,; T ENST00000395146 Transcript missense_variant 2064/9285 1789/3657 597/1218 A/S Gca/Tca 1 1 AFF1 HGNC HGNC:7135 protein_coding YES CCDS54775.1 ENSP00000378578 P51825 UPI000013EC52 NM_001166693.1 tolerated(0.15) 12/21 Pfam_domain:PF05110,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF6 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 87114622 87114622 G T 1 0 0 0 0 1 0 0 0 433 1203 42 2 2 AFF1 4 87114622 Missense_Mutation SNP G C3N-00175_T 10970330 87114622 103099933 386 9978 CCSER1 0 . GRCh38 4 90468270 90468270 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1640G>A p.Cys547Tyr p.C547Y ENST00000509176 5/11 115 102 13 149 149 0 strelka-varscan-mutect CCSER1,missense_variant,p.Cys547Tyr,ENST00000509176,NM_001145065.1;CCSER1,missense_variant,p.Cys547Tyr,ENST00000432775,NM_207491.2;CCSER1,missense_variant,p.Cys547Tyr,ENST00000505073,;CCSER1,non_coding_transcript_exon_variant,,ENST00000508086,;CCSER1,non_coding_transcript_exon_variant,,ENST00000514352,; A ENST00000509176 Transcript missense_variant 1928/5847 1640/2703 547/900 C/Y tGt/tAt 1 1 CCSER1 HGNC HGNC:29349 protein_coding YES CCDS47099.1 ENSP00000425040 Q9C0I3 UPI00005A6104 NM_001145065.1 deleterious(0) 5/11 hmmpanther:PTHR22461,hmmpanther:PTHR22461:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 90468270 90468270 G A 1 0 0 0 0 1 0 0 0 2652 1377 48 3 3 CCSER1 4 90468270 Missense_Mutation SNP G C3N-00175_T 3353648 90468270 99746285 387 9979 BMPR1B 0 . GRCh38 4 95154650 95154650 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1576G>T p.Glu526Ter p.E526* ENST00000440890 11/11 303 267 36 361 360 1 strelka-varscan-mutect BMPR1B,stop_gained,p.Glu496Ter,ENST00000515059,NM_001203.2;BMPR1B,stop_gained,p.Glu526Ter,ENST00000440890,NM_001256793.1;BMPR1B,stop_gained,p.Glu496Ter,ENST00000394931,;BMPR1B,stop_gained,p.Glu496Ter,ENST00000264568,NM_001256794.1;BMPR1B,stop_gained,p.Glu496Ter,ENST00000509540,;BMPR1B,stop_gained,p.Glu496Ter,ENST00000512312,NM_001256792.1; T ENST00000440890 Transcript stop_gained 1597/5388 1576/1599 526/532 E/* Gag/Tag 1 1 BMPR1B HGNC HGNC:1077 protein_coding YES CCDS58919.1 ENSP00000401907 O00238 UPI00017A7CB9 NM_001256793.1 11/11 hmmpanther:PTHR23255:SF62,hmmpanther:PTHR23255 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 95154650 95154650 G T 1 0 0 0 0 0 1 0 0 1625 943 33 2 2 BMPR1B 4 95154650 Nonsense_Mutation SNP G C3N-00175_T 4686380 95154650 95059905 388 9980 PDHA2 0 . GRCh38 4 95840937 95840937 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.787G>T p.Ala263Ser p.A263S ENST00000295266 1/1 308 230 78 395 394 1 strelka-varscan-mutect PDHA2,missense_variant,p.Ala263Ser,ENST00000295266,NM_005390.4; T ENST00000295266 Transcript missense_variant 919/1456 787/1167 263/388 A/S Gca/Tca COSM4713335 1 1 PDHA2 HGNC HGNC:8807 protein_coding YES CCDS3644.1 ENSP00000295266 P29803 UPI0000130C31 NM_005390.4 deleterious(0.03) 1/1 hmmpanther:PTHR11516:SF27,hmmpanther:PTHR11516,Pfam_domain:PF00676,TIGRFAM_domain:TIGR03182,Gene3D:3.40.50.970,Superfamily_domains:SSF52518 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 95840937 95840937 G T 1 0 0 0 0 1 0 0 0 11753 1203 42 2 2 PDHA2 4 95840937 Missense_Mutation SNP G C3N-00175_T 686287 95840937 94373618 389 9981 MTTP 0 . GRCh38 4 99611376 99611376 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1993T>A p.Ser665Thr p.S665T ENST00000511045 14/18 536 468 68 570 570 0 strelka-varscan-mutect MTTP,missense_variant,p.Ser638Thr,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Ser638Thr,ENST00000265517,;MTTP,missense_variant,p.Ser665Thr,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; A ENST00000511045 Transcript missense_variant 2006/3154 1993/2766 665/921 S/T Tcg/Acg 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 tolerated(0.57) 14/18 PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 99611376 99611376 T A 1 0 0 0 0 1 0 0 0 9961 1551 54 4 4 MTTP 4 99611376 Missense_Mutation SNP T C3N-00175_T 3770439 99611376 90603179 390 9982 RP11-766F14.2 0 . GRCh38 4 99654091 99654091 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.558C>A p.= p.A186A ENST00000511828 1/2 110 98 12 145 145 0 strelka-varscan-mutect RP11-766F14.2,synonymous_variant,p.=,ENST00000511828,; T ENST00000511828 Transcript synonymous_variant 558/10086 558/5382 186/1793 A gcC/gcA 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE 1/2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 99654091 99654091 G T 1 0 0 0 0 0 0 0 1 13762 987 35 2 2 RP11-766F14.2 4 99654091 Silent SNP G C3N-00175_T 42715 99654091 90560464 391 9983 MANBA 0 . GRCh38 4 102723901 102723901 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.339A>T p.Glu113Asp p.E113D ENST00000226578 3/17 137 117 20 216 216 0 strelka-varscan-mutect MANBA,missense_variant,p.Glu113Asp,ENST00000226578,NM_005908.3;MANBA,missense_variant,p.Glu113Asp,ENST00000505239,;MANBA,3_prime_UTR_variant,,ENST00000511813,;MANBA,non_coding_transcript_exon_variant,,ENST00000514430,;MANBA,upstream_gene_variant,,ENST00000506478,;KRT8P46,downstream_gene_variant,,ENST00000512037,;LRRC37A15P,downstream_gene_variant,,ENST00000514785,; A ENST00000226578 Transcript missense_variant 439/2904 339/2640 113/879 E/D gaA/gaT 1 -1 MANBA HGNC HGNC:6831 protein_coding YES CCDS3658.1 ENSP00000226578 O00462 UPI000013C8A2 NM_005908.3 tolerated(0.46) 3/17 Gene3D:2.60.120.260,hmmpanther:PTHR10066,hmmpanther:PTHR10066:SF65,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 102723901 102723901 T A 1 0 0 0 0 1 0 0 0 9140 1606 56 4 4 MANBA 4 102723901 Missense_Mutation SNP T C3N-00175_T 3069810 102723901 87490654 392 9984 LRIT3 0 . GRCh38 4 109869720 109869720 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.971G>T p.Gly324Val p.G324V ENST00000594814 4/4 44 37 7 39 39 0 strelka-varscan-mutect LRIT3,missense_variant,p.Gly141Val,ENST00000327908,;LRIT3,missense_variant,p.Gly324Val,ENST00000594814,NM_198506.4; T ENST00000594814 Transcript missense_variant 971/3566 971/2040 324/679 G/V gGg/gTg 1 1 LRIT3 HGNC HGNC:24783 protein_coding YES CCDS3688.3 ENSP00000469759 Q3SXY7 UPI0000F07E94 NM_198506.4 deleterious(0) 4/4 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF236,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 109869720 109869720 G T 1 0 0 0 0 1 0 0 0 8844 1232 43 2 2 LRIT3 4 109869720 Missense_Mutation SNP G C3N-00175_T 7145819 109869720 80344835 393 9985 ALPK1 0 . GRCh38 4 112431710 112431710 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.2164delT p.Trp722GlyfsTer25 p.W722Gfs*25 ENST00000458497 11/16 199 168 31 262 262 0 sindel-varindel-pindel ALPK1,frameshift_variant,p.Trp722GlyfsTer25,ENST00000458497,NM_025144.3,NM_001102406.1;ALPK1,frameshift_variant,p.Trp644GlyfsTer25,ENST00000504176,NM_001253884.1;ALPK1,frameshift_variant,p.Trp722GlyfsTer25,ENST00000177648,;ALPK1,downstream_gene_variant,,ENST00000508589,;ALPK1,3_prime_UTR_variant,,ENST00000509722,;ALPK1,non_coding_transcript_exon_variant,,ENST00000504745,;ALPK1,intron_variant,,ENST00000505127,;ALPK1,downstream_gene_variant,,ENST00000512847,; - ENST00000458497 Transcript frameshift_variant 2442/5410 2163/3735 721/1244 S/X tcT/tc 1 1 ALPK1 HGNC HGNC:20917 protein_coding YES CCDS3697.1 ENSP00000398048 Q96QP1 UPI000045725F NM_025144.3,NM_001102406.1 11/16 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF30,Low_complexity_(Seg):seg HIGH 1 deletion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 112431710 112431710 T - 1 0 1 0 1 0 0 0 0 644 1596 56 0 0 ALPK1 4 112431710 Frame_Shift_Del DEL T C3N-00175_T 2561990 112431710 77782845 394 9986 ZGRF1 0 . GRCh38 4 112603643 112603643 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.2857G>A p.Val953Ile p.V953I ENST00000505019 10/28 141 126 15 178 177 1 strelka-varscan-mutect ZGRF1,missense_variant,p.Val953Ile,ENST00000505019,NM_018392.4;ZGRF1,missense_variant,p.Val953Ile,ENST00000445203,;ZGRF1,missense_variant,p.Val953Ile,ENST00000309071,;ZGRF1,intron_variant,,ENST00000473015,;ZGRF1,downstream_gene_variant,,ENST00000264370,; T ENST00000505019 Transcript missense_variant 2983/6652 2857/6315 953/2104 V/I Gtc/Atc 1 -1 ZGRF1 HGNC HGNC:25654 protein_coding YES CCDS3700.2 ENSP00000424737 Q86YA3 UPI0000EE2F8F NM_018392.4 tolerated(0.34) 10/28 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 112603643 112603643 C T 1 0 0 0 0 1 0 0 0 18253 507 18 3 3 ZGRF1 4 112603643 Missense_Mutation SNP C C3N-00175_T 171933 112603643 77610912 395 9987 ZGRF1 0 . GRCh38 4 112606021 112606022 + Frame_Shift_Ins INS - - T novel C3N-00175_T C3N-00175_N - - c.2788dupA p.Thr930AsnfsTer3 p.T930Nfs*3 ENST00000505019 9/28 111 102 9 243 242 1 sindel-varindel-pindel ZGRF1,frameshift_variant,p.Thr930AsnfsTer3,ENST00000505019,NM_018392.4;ZGRF1,frameshift_variant,p.Thr930AsnfsTer3,ENST00000445203,;ZGRF1,frameshift_variant,p.Thr930AsnfsTer3,ENST00000309071,;ZGRF1,frameshift_variant,p.Thr930AsnfsTer3,ENST00000473015,;ZGRF1,non_coding_transcript_exon_variant,,ENST00000264370,;ZGRF1,downstream_gene_variant,,ENST00000514770,; T ENST00000505019 Transcript frameshift_variant 2914-2915/6652 2788-2789/6315 930/2104 T/NX acc/aAcc 1 -1 ZGRF1 HGNC HGNC:25654 protein_coding YES CCDS3700.2 ENSP00000424737 Q86YA3 UPI0000EE2F8F NM_018392.4 9/28 HIGH 1 insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 39 112606021 112606021 - T 1 0 1 1 0 0 0 0 0 18253 1261 44 0 0 ZGRF1 4 112606021 Frame_Shift_Ins INS - C3N-00175_T 2378 112606021 77608534 396 9988 ANK2 0 . GRCh38 4 113357891 113357891 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.9273G>T p.Glu3091Asp p.E3091D ENST00000357077 38/46 232 168 64 197 197 0 strelka-varscan-mutect ANK2,missense_variant,p.Glu3091Asp,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Glu3058Asp,ENST00000264366,;ANK2,missense_variant,p.Glu101Asp,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; T ENST00000357077 Transcript missense_variant 9326/14196 9273/11874 3091/3957 E/D gaG/gaT 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated(0.12) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 113357891 113357891 G T 1 0 0 0 0 1 0 0 0 721 991 35 2 2 ANK2 4 113357891 Missense_Mutation SNP G C3N-00175_T 751870 113357891 76856664 397 9989 METTL14 0 . GRCh38 4 118694471 118694471 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.448A>T p.Arg150Trp p.R150W ENST00000388822 6/11 101 86 15 190 190 0 strelka-varscan-mutect METTL14,missense_variant,p.Arg150Trp,ENST00000388822,NM_020961.3;METTL14,upstream_gene_variant,,ENST00000506780,;METTL14,3_prime_UTR_variant,,ENST00000628452,;METTL14,non_coding_transcript_exon_variant,,ENST00000502564,;METTL14,downstream_gene_variant,,ENST00000626212,; T ENST00000388822 Transcript missense_variant 615/6669 448/1371 150/456 R/W Agg/Tgg 1 1 METTL14 HGNC HGNC:29330 protein_coding YES CCDS34053.1 ENSP00000373474 Q9HCE5 UPI00000437DD NM_020961.3 deleterious(0) 6/11 PROSITE_profiles:PS51143,PROSITE_profiles:PS51592,hmmpanther:PTHR13107 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 118694471 118694471 A T 1 0 0 0 0 1 0 0 0 9440 295 11 4 4 METTL14 4 118694471 Missense_Mutation SNP A C3N-00175_T 5336580 118694471 71520084 398 9990 QRFPR 0 . GRCh38 4 121380586 121380586 + Missense_Mutation SNP G G T rs775342074 C3N-00175_T C3N-00175_N G G c.62C>A p.Thr21Lys p.T21K ENST00000394427 1/6 83 76 7 112 112 0 strelka-varscan-mutect QRFPR,missense_variant,p.Thr21Lys,ENST00000394427,NM_198179.2;QRFPR,missense_variant,p.Thr21Lys,ENST00000334383,;QRFPR,missense_variant,p.Thr21Lys,ENST00000507331,;QRFPR,non_coding_transcript_exon_variant,,ENST00000512235,; T ENST00000394427 Transcript missense_variant 474/1708 62/1296 21/431 T/K aCg/aAg rs775342074,COSM5032755 1 -1 QRFPR HGNC HGNC:15565 protein_coding YES CCDS3719.1 ENSP00000377948 Q96P65 UPI0000047B23 NM_198179.2 deleterious(0) 1/6 hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF63 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775342074 . 0 205 5 0 0 0 0 0 -15.01315 1 1 1 1 0 T 3 4 39 121380586 121380586 G T 1 0 0 0 0 1 0 0 0 13033 1145 40 1 1 QRFPR 4 121380586 Missense_Mutation SNP G C3N-00175_T 2686115 121380586 68833969 399 9991 SPATA5 0 . GRCh38 4 123056423 123056423 + Nonsense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.2116G>T p.Glu706Ter p.E706* ENST00000274008 12/16 71 64 7 124 124 0 strelka-varscan-mutect SPATA5,stop_gained,p.Glu706Ter,ENST00000274008,NM_145207.2;SPATA5,non_coding_transcript_exon_variant,,ENST00000422835,; T ENST00000274008 Transcript stop_gained 2185/8137 2116/2682 706/893 E/* Gaa/Taa COSM1309676 1 1 SPATA5 HGNC HGNC:18119 protein_coding YES CCDS3730.1 ENSP00000274008 Q8NB90 UPI000013D9E6 NM_145207.2 12/16 hmmpanther:PTHR23077:SF27,hmmpanther:PTHR23077,Pfam_domain:PF00004,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 123056423 123056423 G T 1 0 0 0 0 0 1 0 0 15355 1291 45 2 2 SPATA5 4 123056423 Nonsense_Mutation SNP G C3N-00175_T 1675837 123056423 67158132 400 9992 ANKRD50 0 . GRCh38 4 124710306 124710306 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.206C>T p.Ala69Val p.A69V ENST00000504087 2/5 149 129 20 204 203 1 strelka-varscan-mutect ANKRD50,missense_variant,p.Ala69Val,ENST00000504087,NM_020337.2;ANKRD50,intron_variant,,ENST00000515641,NM_001167882.1; A ENST00000504087 Transcript missense_variant 1244/8794 206/4290 69/1429 A/V gCt/gTt 1 -1 ANKRD50 HGNC HGNC:29223 protein_coding YES CCDS34060.1 ENSP00000425658 Q9ULJ7 UPI00002377E8 NM_020337.2 tolerated(0.23) 2/5 hmmpanther:PTHR24151,hmmpanther:PTHR24151:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 124710306 124710306 G A 1 0 0 0 0 1 0 0 0 781 971 34 3 3 ANKRD50 4 124710306 Missense_Mutation SNP G C3N-00175_T 1653883 124710306 65504249 401 9993 FAT4 0 . GRCh38 4 125318130 125318130 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.1719A>G p.= p.L573L ENST00000394329 1/17 263 202 61 331 331 0 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; G ENST00000394329 Transcript synonymous_variant 1732/16123 1719/14946 573/4981 L ctA/ctG 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 1/17 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 125318130 125318130 A G 1 0 0 0 0 0 0 0 1 5552 407 15 5 5 FAT4 4 125318130 Silent SNP A C3N-00175_T 607824 125318130 64896425 402 9994 FAT4 0 . GRCh38 4 125446420 125446420 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.7321G>C p.Gly2441Arg p.G2441R ENST00000394329 8/17 199 163 36 191 191 0 strelka-varscan-mutect FAT4,missense_variant,p.Gly2441Arg,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Gly739Arg,ENST00000335110,;FAT4,non_coding_transcript_exon_variant,,ENST00000509444,; C ENST00000394329 Transcript missense_variant 7334/16123 7321/14946 2441/4981 G/R Gga/Cga 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0) 8/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 125446420 125446420 G C 1 0 0 0 0 1 0 0 0 5552 1233 43 4 4 FAT4 4 125446420 Missense_Mutation SNP G C3N-00175_T 128290 125446420 64768135 403 9995 ABHD18 0 . GRCh38 4 128028478 128028478 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.703delG p.Asp235IlefsTer10 p.D235Ifs*10 ENST00000398965 10/11 39 31 8 45 45 0 sindel-varindel-pindel ABHD18,frameshift_variant,p.Asp187IlefsTer10,ENST00000388795,NM_001319305.1,NM_001319306.1;ABHD18,frameshift_variant,p.Asp235IlefsTer10,ENST00000398965,NM_001039717.1;ABHD18,frameshift_variant,p.Asp235IlefsTer10,ENST00000444616,;ABHD18,frameshift_variant,p.Asp142IlefsTer10,ENST00000611882,;ABHD18,3_prime_UTR_variant,,ENST00000473040,; - ENST00000398965 Transcript frameshift_variant 1021/2177 703/1245 235/414 D/X Gat/at 1 1 ABHD18 HGNC HGNC:26111 protein_coding YES CCDS47131.1 ENSP00000381937 Q0P651 UPI00006C511D NM_001039717.1 10/11 hmmpanther:PTHR13617,Pfam_domain:PF09752 HIGH 1 deletion 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.75455 1 1 1 1 0 - 7 5 39 128028478 128028478 G - 1 0 1 0 1 0 0 0 0 91 956 33 0 0 ABHD18 4 128028478 Frame_Shift_Del DEL G C3N-00175_T 2582058 128028478 62186077 404 9996 SETD7 0 . GRCh38 4 139517979 139517979 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.826G>A p.Asp276Asn p.D276N ENST00000274031 7/8 141 110 31 167 167 0 strelka-varscan-mutect SETD7,missense_variant,p.Asp276Asn,ENST00000274031,NM_030648.2;SETD7,missense_variant,p.Asp276Asn,ENST00000506866,NM_001306199.1;SETD7,non_coding_transcript_exon_variant,,ENST00000515101,; T ENST00000274031 Transcript missense_variant 1463/7365 826/1101 276/366 D/N Gat/Aat 1 -1 SETD7 HGNC HGNC:30412 protein_coding YES CCDS3748.1 ENSP00000274031 Q8WTS6 UPI0000135893 NM_030648.2 deleterious(0) 7/8 PROSITE_profiles:PS51577,PROSITE_profiles:PS50280,hmmpanther:PTHR23084:SF153,hmmpanther:PTHR23084,PIRSF_domain:PIRSF037249,Gene3D:2.170.270.10,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 139517979 139517979 C T 1 0 0 0 0 1 0 0 0 14414 826 29 3 3 SETD7 4 139517979 Missense_Mutation SNP C C3N-00175_T 11489501 139517979 50696576 405 9997 INPP4B 0 . GRCh38 4 142173706 142173706 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1285G>T p.Asp429Tyr p.D429Y ENST00000513000 17/27 200 154 46 228 226 2 strelka-varscan-mutect INPP4B,missense_variant,p.Asp429Tyr,ENST00000513000,NM_003866.2;INPP4B,missense_variant,p.Asp429Tyr,ENST00000509777,;INPP4B,missense_variant,p.Asp429Tyr,ENST00000262992,NM_001101669.1;INPP4B,missense_variant,p.Asp429Tyr,ENST00000508116,;INPP4B,missense_variant,p.Asp429Tyr,ENST00000510812,;INPP4B,missense_variant,p.Asp244Tyr,ENST00000511838,;INPP4B,missense_variant,p.Asp300Tyr,ENST00000514525,;INPP4B,3_prime_UTR_variant,,ENST00000512630,; A ENST00000513000 Transcript missense_variant 1719/8831 1285/2775 429/924 D/Y Gac/Tac 1 -1 INPP4B HGNC HGNC:6075 protein_coding YES CCDS3757.1 ENSP00000425487 O15327 UPI000013D37A NM_003866.2 deleterious(0) 17/27 hmmpanther:PTHR12187,hmmpanther:PTHR12187:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 142173706 142173706 C A 1 0 0 0 0 1 0 0 0 7656 913 32 2 2 INPP4B 4 142173706 Missense_Mutation SNP C C3N-00175_T 2655727 142173706 48040849 406 9998 FREM3 0 . GRCh38 4 143697971 143697971 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.2705A>T p.Tyr902Phe p.Y902F ENST00000329798 1/8 220 167 53 285 285 0 strelka-varscan-mutect FREM3,missense_variant,p.Tyr902Phe,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; A ENST00000329798 Transcript missense_variant 2705/6729 2705/6420 902/2139 Y/F tAc/tTc 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 deleterious(0.01) 1/8 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 143697971 143697971 T A 1 0 0 0 0 1 0 0 0 5913 1638 57 4 4 FREM3 4 143697971 Missense_Mutation SNP T C3N-00175_T 1524265 143697971 46516584 407 9999 KIAA0922 0 . GRCh38 4 153604087 153604087 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.3075C>T p.= p.A1025A ENST00000409959 25/35 306 272 34 354 354 0 strelka-varscan-mutect KIAA0922,synonymous_variant,p.=,ENST00000409663,NM_015196.3;KIAA0922,synonymous_variant,p.=,ENST00000409959,NM_001131007.1;KIAA0922,synonymous_variant,p.=,ENST00000240487,;KIAA0922,downstream_gene_variant,,ENST00000497247,; T ENST00000409959 Transcript synonymous_variant 3124/5017 3075/4833 1025/1610 A gcC/gcT 1 1 KIAA0922 HGNC HGNC:29146 protein_coding YES CCDS47148.1 ENSP00000386787 A2VDJ0 UPI00017BE9AB NM_001131007.1 25/35 hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF2 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 153604087 153604087 C T 1 0 0 0 0 0 0 0 1 8095 581 21 3 3 KIAA0922 4 153604087 Silent SNP C C3N-00175_T 9906116 153604087 36610468 408 10000 MARCH1 0 . GRCh38 4 163854042 163854042 + Silent SNP G G A rs375276624 C3N-00175_T C3N-00175_N G G c.90C>T p.= p.D30D ENST00000503008 3/8 158 143 15 168 168 0 strelka-varscan-mutect MARCH1,synonymous_variant,p.=,ENST00000503008,NM_001166373.1;MARCH1,synonymous_variant,p.=,ENST00000274056,;MARCH1,synonymous_variant,p.=,ENST00000514618,;MARCH1,synonymous_variant,p.=,ENST00000507270,;MARCH1,non_coding_transcript_exon_variant,,ENST00000503104,;MARCH1,intron_variant,,ENST00000510696,; A ENST00000503008 Transcript synonymous_variant 1067/5877 90/870 30/289 D gaC/gaT rs375276624,COSM3335337 1 -1 MARCH1 HGNC HGNC:26077 protein_coding YES CCDS54814.1 ENSP00000427223 Q8TCQ1 UPI0000037BB3 NM_001166373.1 3/8 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF53 0,1 LOW 1 SNV 1 0,1 1 PASS rs375276624 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 163854042 163854042 G A 1 0 0 0 0 0 0 0 1 9223 1136 40 1 1 MARCH1 4 163854042 Silent SNP G C3N-00175_T 10249955 163854042 26360513 409 10001 KLHL2 0 . GRCh38 4 165294455 165294455 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.653C>T p.Ser218Phe p.S218F ENST00000514860 6/15 85 77 8 122 122 0 strelka-varscan-mutect KLHL2,missense_variant,p.Ser214Phe,ENST00000226725,NM_007246.3;KLHL2,missense_variant,p.Ser126Phe,ENST00000538127,NM_001161522.1;KLHL2,missense_variant,p.Ser117Phe,ENST00000421009,;KLHL2,missense_variant,p.Ser218Phe,ENST00000514860,NM_001161521.1;KLHL2,missense_variant,p.Ser48Phe,ENST00000506761,;KLHL2,non_coding_transcript_exon_variant,,ENST00000509028,;KLHL2,non_coding_transcript_exon_variant,,ENST00000506541,;KLHL2,3_prime_UTR_variant,,ENST00000506824,; T ENST00000514860 Transcript missense_variant 903/2442 653/1794 218/597 S/F tCt/tTt 1 1 KLHL2 HGNC HGNC:6353 protein_coding YES CCDS54815.1 ENSP00000424198 O95198 UPI0000E20649 NM_001161521.1 deleterious(0) 6/15 hmmpanther:PTHR24412:SF155,hmmpanther:PTHR24412,Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,SMART_domains:SM00875 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 165294455 165294455 C T 1 0 0 0 0 1 0 0 0 8238 913 32 3 3 KLHL2 4 165294455 Missense_Mutation SNP C C3N-00175_T 1440413 165294455 24920100 410 10002 DDX60L 0 . GRCh38 4 168420319 168420319 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.2456delG p.Gly819AlafsTer17 p.G819Afs*17 ENST00000260184 18/38 120 108 12 181 181 0 sindel-varindel-pindel DDX60L,frameshift_variant,p.Gly819AlafsTer17,ENST00000511577,;DDX60L,frameshift_variant,p.Gly819AlafsTer17,ENST00000260184,NM_001012967.2;DDX60L,frameshift_variant,p.Gly819AlafsTer17,ENST00000505890,NM_001291510.1;DDX60L,frameshift_variant,p.Gly547AlafsTer17,ENST00000505863,;DDX60L,non_coding_transcript_exon_variant,,ENST00000504793,; - ENST00000260184 Transcript frameshift_variant 2677/6754 2456/5121 819/1706 G/X gGc/gc 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 18/38 PROSITE_profiles:PS51192,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -17.95363 0.9999998 1 1 1 0 - 7 5 39 168420319 168420319 C - 1 0 1 0 1 0 0 0 0 4182 739 26 0 0 DDX60L 4 168420319 Frame_Shift_Del DEL C C3N-00175_T 3125864 168420319 21794236 411 10003 DCTD 0 . GRCh38 4 182915052 182915052 + Missense_Mutation SNP C C T rs778279392 C3N-00175_T C3N-00175_N C C c.148G>A p.Ala50Thr p.A50T ENST00000357067 3/6 133 93 40 159 159 0 strelka-varscan-mutect DCTD,missense_variant,p.Ala39Thr,ENST00000438320,NM_001921.2;DCTD,missense_variant,p.Ala50Thr,ENST00000357067,NM_001012732.1;DCTD,missense_variant,p.Ala39Thr,ENST00000503988,;DCTD,missense_variant,p.Ala39Thr,ENST00000503820,;DCTD,missense_variant,p.Ala39Thr,ENST00000510370,;DCTD,missense_variant,p.Ala39Thr,ENST00000512766,;DCTD,missense_variant,p.Ala39Thr,ENST00000514754,;DCTD,missense_variant,p.Ala39Thr,ENST00000510307,;DCTD,missense_variant,p.Ala39Thr,ENST00000503182,;DCTD,downstream_gene_variant,,ENST00000508994,;DCTD,non_coding_transcript_exon_variant,,ENST00000513383,;DCTD,3_prime_UTR_variant,,ENST00000507543,;DCTD,3_prime_UTR_variant,,ENST00000513348,;DCTD,3_prime_UTR_variant,,ENST00000509218,;DCTD,3_prime_UTR_variant,,ENST00000509757,;DCTD,intron_variant,,ENST00000500813,;DCTD,intron_variant,,ENST00000507631,; T ENST00000357067 Transcript missense_variant 214/1931 148/570 50/189 A/T Gcc/Acc rs778279392,COSM291546 1 -1 DCTD HGNC HGNC:2710 protein_coding YES CCDS34108.1 ENSP00000349576 P32321 UPI00004EC28E NM_001012732.1 deleterious(0) 3/6 PROSITE_profiles:PS51747,hmmpanther:PTHR11086,Gene3D:3.40.140.10,PIRSF_domain:PIRSF006019,Pfam_domain:PF00383,Superfamily_domains:SSF53927 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778279392 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 182915052 182915052 C T 1 0 0 0 0 1 0 0 0 4108 768 27 1 1 DCTD 4 182915052 Missense_Mutation SNP C C3N-00175_T 14494733 182915052 7299503 412 10004 MTNR1A 0 . GRCh38 4 186534324 186534324 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.418A>C p.Ser140Arg p.S140R ENST00000307161 2/2 363 269 94 277 277 0 strelka-varscan-mutect MTNR1A,missense_variant,p.Ser140Arg,ENST00000307161,NM_005958.3;RP11-215A19.2,intron_variant,,ENST00000509111,; G ENST00000307161 Transcript missense_variant 620/1289 418/1053 140/350 S/R Agc/Cgc 1 -1 MTNR1A HGNC HGNC:7463 protein_coding YES CCDS3848.1 ENSP00000302811 P48039 UPI0000050407 NM_005958.3 tolerated(0.21) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF52,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00857 MODERATE 1 SNV 1 1 PASS rs1426911602 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 186534324 186534324 T G 1 0 0 0 0 1 0 0 0 9938 1580 55 5 5 MTNR1A 4 186534324 Missense_Mutation SNP T C3N-00175_T 3619272 186534324 3680231 413 10005 TRIML2 0 . GRCh38 4 188091439 188091439 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1248C>A p.Asp416Glu p.D416E ENST00000512729 7/7 124 107 17 165 165 0 strelka-varscan-mutect TRIML2,missense_variant,p.Asp416Glu,ENST00000512729,NM_173553.2;TRIML2,missense_variant,p.Asp401Glu,ENST00000326754,NM_001303419.1;TRIML2,3_prime_UTR_variant,,ENST00000503141,;TRIML2,3_prime_UTR_variant,,ENST00000503475,; T ENST00000512729 Transcript missense_variant 1473/1639 1248/1314 416/437 D/E gaC/gaA 1 -1 TRIML2 HGNC HGNC:26378 protein_coding YES ENSP00000422581 Q8N7C3 UPI000020B818 NM_173553.2 tolerated(0.1) 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF347,hmmpanther:PTHR24103,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 188091439 188091439 G T 1 0 0 0 0 1 0 0 0 17048 1368 48 2 2 TRIML2 4 188091439 Missense_Mutation SNP G C3N-00175_T 1557115 188091439 2123116 414 10006 TRIML2 0 . GRCh38 4 188097147 188097147 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.659T>A p.Leu220Gln p.L220Q ENST00000512729 6/7 159 142 17 185 185 0 strelka-varscan-mutect TRIML2,missense_variant,p.Leu220Gln,ENST00000512729,NM_173553.2;TRIML2,missense_variant,p.Leu205Gln,ENST00000326754,NM_001303419.1;TRIML2,synonymous_variant,p.=,ENST00000503141,;TRIML2,synonymous_variant,p.=,ENST00000503475,;TRIML2,downstream_gene_variant,,ENST00000511771,; T ENST00000512729 Transcript missense_variant 884/1639 659/1314 220/437 L/Q cTg/cAg 1 -1 TRIML2 HGNC HGNC:26378 protein_coding YES ENSP00000422581 Q8N7C3 UPI000020B818 NM_173553.2 deleterious(0) 6/7 hmmpanther:PTHR24103:SF347,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 188097147 188097147 A T 1 0 0 0 0 1 0 0 0 17048 188 7 4 4 TRIML2 4 188097147 Missense_Mutation SNP A C3N-00175_T 5708 188097147 2117408 415 10007 SLC9A3 0 . GRCh38 5 488468 488468 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.523C>A p.Gln175Lys p.Q175K ENST00000264938 3/17 60 49 11 71 71 0 strelka-varscan-mutect SLC9A3,missense_variant,p.Gln175Lys,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.Gln175Lys,ENST00000514375,NM_001284351.1; T ENST00000264938 Transcript missense_variant 533/2584 523/2505 175/834 Q/K Cag/Aag 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 tolerated(0.61) 3/17 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 39 488468 488468 G T 1 0 0 0 0 1 0 0 0 14995 1328 46 2 2 SLC9A3 5 488468 Missense_Mutation SNP G C3N-00175_T 488468 181049791 416 10008 SLC9A3 0 . GRCh38 5 491818 491818 + Silent SNP C C A rs146219885 C3N-00175_T C3N-00175_N C C c.465G>T p.= p.A155A ENST00000264938 2/17 81 59 22 79 79 0 strelka-varscan-mutect SLC9A3,synonymous_variant,p.=,ENST00000264938,NM_004174.2;SLC9A3,synonymous_variant,p.=,ENST00000514375,NM_001284351.1; A ENST00000264938 Transcript synonymous_variant 475/2584 465/2505 155/834 A gcG/gcT rs146219885 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 2/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 LOW 1 SNV 1 1 PASS rs146219885 . 0 200 10 0 0 0 0 0 -20 0.9999948 1 1 1 0 A 2 1 39 491818 491818 C A 1 0 0 0 0 0 0 0 1 14995 639 23 1 1 SLC9A3 5 491818 Silent SNP C C3N-00175_T 3350 491818 181046441 417 10009 NKD2 0 . GRCh38 5 1032164 1032164 + Frame_Shift_Del DEL G G - rs267600312 C3N-00175_T C3N-00175_N G G c.157delG p.Asp53ThrfsTer119 p.D53Tfs*119 ENST00000296849 4/10 197 139 58 193 193 0 sindel-varindel-pindel NKD2,frameshift_variant,p.Asp53ThrfsTer119,ENST00000296849,NM_033120.3;NKD2,frameshift_variant,p.Asp53ThrfsTer119,ENST00000274150,NM_001271082.1;NKD2,upstream_gene_variant,,ENST00000513296,;NKD2,upstream_gene_variant,,ENST00000523688,;NKD2,upstream_gene_variant,,ENST00000519933,; - ENST00000296849 Transcript frameshift_variant 383/2155 154/1356 52/451 G/X Ggg/gg rs267600312 1 1 NKD2 HGNC HGNC:17046 protein_coding YES CCDS3859.1 ENSP00000296849 Q969F2 UPI0000073E19 NM_033120.3 4/10 hmmpanther:PTHR22611:SF1,hmmpanther:PTHR22611 HIGH 1 deletion 1 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 1032164 1032164 G - 1 0 1 0 1 0 0 0 0 10477 1348 47 0 0 NKD2 5 1032164 Frame_Shift_Del DEL G C3N-00175_T 540346 1032164 180506095 418 10010 SLC12A7 0 . GRCh38 5 1052381 1052381 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.3231G>T p.Glu1077Asp p.E1077D ENST00000264930 24/24 275 215 60 195 194 1 strelka-varscan-mutect SLC12A7,missense_variant,p.Glu1077Asp,ENST00000264930,NM_006598.2;SLC12A7,missense_variant,p.Glu983Asp,ENST00000634447,;SLC12A7,downstream_gene_variant,,ENST00000514994,; A ENST00000264930 Transcript missense_variant 3275/5280 3231/3252 1077/1083 E/D gaG/gaT 1 -1 SLC12A7 HGNC HGNC:10915 protein_coding YES CCDS34129.1 ENSP00000264930 Q9Y666 UPI0000141815 NM_006598.2 deleterious(0) 24/24 Pfam_domain:PF03522,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF47,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00930 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 1052381 1052381 C A 1 0 0 0 0 1 0 0 0 14653 680 24 2 2 SLC12A7 5 1052381 Missense_Mutation SNP C C3N-00175_T 20217 1052381 180485878 419 10011 IRX4 0 . GRCh38 5 1878382 1878382 + Missense_Mutation SNP T T A C3N-00175_T C3N-00175_N T T c.1225A>T p.Thr409Ser p.T409S ENST00000613726 7/7 170 129 41 77 76 1 strelka-varscan-mutect IRX4,missense_variant,p.Thr383Ser,ENST00000505790,NM_001278634.1;IRX4,missense_variant,p.Thr409Ser,ENST00000613726,NM_001278635.1;IRX4,missense_variant,p.Thr409Ser,ENST00000622814,NM_001278633.1;IRX4,missense_variant,p.Thr383Ser,ENST00000513692,NM_001278632.1;IRX4,missense_variant,p.Thr383Ser,ENST00000231357,NM_016358.2;IRX4,downstream_gene_variant,,ENST00000511126,;IRX4,downstream_gene_variant,,ENST00000505938,;IRX4,3_prime_UTR_variant,,ENST00000508261,; A ENST00000613726 Transcript missense_variant 1448/2403 1225/1638 409/545 T/S Acc/Tcc COSM5419871,COSM5419872 1 -1 IRX4 HGNC HGNC:6129 protein_coding YES CCDS75225.1 ENSP00000482393 P78413 UPI000020BF08 NM_001278635.1 tolerated(0.09) 7/7 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF16,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1440463147 . 0 199 11 0 0 0 0 0 -20 0.9999845 1 1 1 0 A 3 1 39 1878382 1878382 T A 1 0 0 0 0 1 0 0 0 7754 1696 59 4 4 IRX4 5 1878382 Missense_Mutation SNP T C3N-00175_T 826001 1878382 179659877 420 10012 MED10 0 . GRCh38 5 6378477 6378477 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.7G>T p.Glu3Ter p.E3* ENST00000255764 1/4 144 110 34 121 121 0 strelka-varscan-mutect MED10,stop_gained,p.Glu3Ter,ENST00000255764,NM_032286.2;MED10,non_coding_transcript_exon_variant,,ENST00000504058,;MED10,upstream_gene_variant,,ENST00000503112,; A ENST00000255764 Transcript stop_gained 118/1141 7/408 3/135 E/* Gag/Tag 1 -1 MED10 HGNC HGNC:28760 protein_coding YES CCDS34134.1 ENSP00000255764 Q9BTT4 UPI000007379B NM_032286.2 1/4 hmmpanther:PTHR13345 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 4 1 39 6378477 6378477 C A 1 0 0 0 0 0 1 0 0 9365 864 30 2 2 MED10 5 6378477 Nonsense_Mutation SNP C C3N-00175_T 4500095 6378477 175159782 421 10013 ADCY2 0 . GRCh38 5 7709354 7709354 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1545C>T p.= p.S515S ENST00000338316 10/25 155 128 27 108 107 1 strelka-mutect ADCY2,synonymous_variant,p.=,ENST00000338316,NM_020546.2;RP11-711G10.1,intron_variant,,ENST00000514105,; T ENST00000338316 Transcript synonymous_variant 1634/6575 1545/3276 515/1091 S agC/agT 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 10/25 Pfam_domain:PF06327,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253 LOW 1 SNV 1 1 PASS rs1178012833 . 0 205 3 2 0 0 0 0 -20 0.9999953 1 1 1 0 T 2 4 39 7709354 7709354 C T 1 0 0 0 0 0 0 0 1 338 709 25 3 3 ADCY2 5 7709354 Silent SNP C C3N-00175_T 1330877 7709354 173828905 422 10014 ADCY2 0 . GRCh38 5 7743675 7743675 + Missense_Mutation SNP G G A rs770402477 C3N-00175_T C3N-00175_N G G c.1879G>A p.Val627Ile p.V627I ENST00000338316 15/25 269 241 28 211 211 0 strelka-varscan-mutect ADCY2,missense_variant,p.Val627Ile,ENST00000338316,NM_020546.2;RP11-711G10.1,intron_variant,,ENST00000514105,; A ENST00000338316 Transcript missense_variant 1968/6575 1879/3276 627/1091 V/I Gtc/Atc rs770402477,COSM1438705,COSM5125819 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 tolerated(0.27) 15/25 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,Transmembrane_helices:TMhelix 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770402477 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 7743675 7743675 G A 1 0 0 0 0 1 0 0 0 338 1145 40 1 1 ADCY2 5 7743675 Missense_Mutation SNP G C3N-00175_T 34321 7743675 173794584 423 10015 MARCH6 0 . GRCh38 5 10411340 10411340 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.1699delC p.His567IlefsTer61 p.H567Ifs*61 ENST00000274140 19/26 125 96 29 121 121 0 sindel-varindel-pindel MARCH6,frameshift_variant,p.His567IlefsTer61,ENST00000274140,NM_005885.3;MARCH6,frameshift_variant,p.His519IlefsTer61,ENST00000449913,NM_001270660.1;MARCH6,frameshift_variant,p.His462IlefsTer61,ENST00000503788,NM_001270661.1;MARCH6,frameshift_variant,p.His265IlefsTer61,ENST00000510792,;MARCH6,upstream_gene_variant,,ENST00000505253,;MARCH6,non_coding_transcript_exon_variant,,ENST00000511802,;MARCH6,non_coding_transcript_exon_variant,,ENST00000512449,;MARCH6,upstream_gene_variant,,ENST00000514312,; - ENST00000274140 Transcript frameshift_variant 1831/9569 1699/2733 567/910 H/X Cat/at 1 1 MARCH6 HGNC HGNC:30550 protein_coding YES CCDS34135.1 ENSP00000274140 O60337 UPI00001B94D6 NM_005885.3 19/26 hmmpanther:PTHR13145 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 10411340 10411340 C - 1 0 1 0 1 0 0 0 0 9230 826 29 0 0 MARCH6 5 10411340 Frame_Shift_Del DEL C C3N-00175_T 2667665 10411340 171126919 424 10016 ANKRD33B 0 . GRCh38 5 10618381 10618381 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.415G>C p.Ala139Pro p.A139P ENST00000296657 2/4 282 208 74 199 199 0 strelka-varscan-mutect ANKRD33B,missense_variant,p.Ala139Pro,ENST00000296657,NM_001164440.1;ANKRD33B,missense_variant,p.Ala139Pro,ENST00000504806,; C ENST00000296657 Transcript missense_variant 415/9188 415/1485 139/494 A/P Gcc/Ccc COSM5580228 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 tolerated(0.06) 2/4 PROSITE_profiles:PS50297,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 10618381 10618381 G C 1 0 0 0 0 1 0 0 0 766 1203 42 4 4 ANKRD33B 5 10618381 Missense_Mutation SNP G C3N-00175_T 207041 10618381 170919878 425 10017 TRIO 0 . GRCh38 5 14479995 14479995 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.6320A>T p.Tyr2107Phe p.Y2107F ENST00000344204 43/57 265 227 38 197 197 0 strelka-varscan-mutect TRIO,missense_variant,p.Tyr2107Phe,ENST00000344204,NM_007118.2;TRIO,missense_variant,p.Tyr1840Phe,ENST00000513206,;TRIO,missense_variant,p.Tyr187Phe,ENST00000620511,;TRIO,missense_variant,p.Tyr2048Phe,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,;TRIO,non_coding_transcript_exon_variant,,ENST00000511019,;TRIO,upstream_gene_variant,,ENST00000510281,;TRIO,downstream_gene_variant,,ENST00000506611,; T ENST00000344204 Transcript missense_variant 6344/11100 6320/9294 2107/3097 Y/F tAt/tTt 1 1 TRIO HGNC HGNC:12303 protein_coding YES CCDS3883.1 ENSP00000339299 O75962 UPI000034ECE6 NM_007118.2 deleterious(0) 43/57 PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 14479995 14479995 A T 1 0 0 0 0 1 0 0 0 17049 449 16 4 4 TRIO 5 14479995 Missense_Mutation SNP A C3N-00175_T 3861614 14479995 167058264 426 10018 FBXL7 0 . GRCh38 5 15937154 15937154 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.1444G>A p.Val482Ile p.V482I ENST00000504595 4/4 86 80 6 67 67 0 strelka-varscan-mutect FBXL7,missense_variant,p.Val482Ile,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Val440Ile,ENST00000329673,;FBXL7,missense_variant,p.Val435Ile,ENST00000510662,NM_001278317.1;MIR887,downstream_gene_variant,,ENST00000401258,; A ENST00000504595 Transcript missense_variant 1925/4562 1444/1476 482/491 V/I Gtc/Atc COSM1543028 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(1) 4/4 hmmpanther:PTHR24006,Superfamily_domains:SSF52047 1 MODERATE 1 SNV 1 1 1 PASS rs1219818114 . 0 205 5 0 0 0 0 0 -12.88698 1 1 1 1 0 A 3 1 39 15937154 15937154 G A 1 0 0 0 0 1 0 0 0 5587 1145 40 1 1 FBXL7 5 15937154 Missense_Mutation SNP G C3N-00175_T 1457159 15937154 165601105 427 10019 MARCH11 0 . GRCh38 5 16179039 16179039 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.537G>T p.Gln179His p.Q179H ENST00000332432 1/4 93 80 13 95 95 0 strelka-varscan-mutect MARCH11,missense_variant,p.Gln179His,ENST00000332432,NM_001102562.1;MARCH11,upstream_gene_variant,,ENST00000507111,;RP11-19O2.2,upstream_gene_variant,,ENST00000509037,;MARCH11,intron_variant,,ENST00000505509,; A ENST00000332432 Transcript missense_variant,splice_region_variant 737/1741 537/1209 179/402 Q/H caG/caT 1 -1 MARCH11 HGNC HGNC:33609 protein_coding YES CCDS47192.1 ENSP00000333181 A6NNE9 UPI00015B3D4A NM_001102562.1 deleterious(0.02) 1/4 PROSITE_profiles:PS51292,hmmpanther:PTHR23012:SF67,hmmpanther:PTHR23012,Gene3D:3.30.40.10,Pfam_domain:PF12906,SMART_domains:SM00744,Superfamily_domains:SSF57850 MODERATE SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999927 1 1 1 0 A 3 1 39 16179039 16179039 C A 1 0 0 0 0 1 0 0 0 9225 695 24 2 2 MARCH11 5 16179039 Missense_Mutation SNP C C3N-00175_T 241885 16179039 165359220 428 10020 PRDM9 0 . GRCh38 5 23522384 23522384 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.589C>T p.Pro197Ser p.P197S ENST00000296682 7/11 718 604 114 540 540 0 strelka-varscan-mutect PRDM9,missense_variant,p.Pro197Ser,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Pro138Ser,ENST00000635252,; T ENST00000296682 Transcript missense_variant 771/3691 589/2685 197/894 P/S Ccg/Tcg 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 7/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Pfam_domain:PF09514,Pfam_domain:PF00856 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 23522384 23522384 C T 1 0 0 0 0 1 0 0 0 12595 739 26 3 3 PRDM9 5 23522384 Missense_Mutation SNP C C3N-00175_T 7343345 23522384 158015875 429 10021 DROSHA 0 . GRCh38 5 31401509 31401509 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.4048C>A p.Gln1350Lys p.Q1350K ENST00000511367 35/35 483 396 87 341 341 0 strelka-varscan-mutect DROSHA,missense_variant,p.Gln1350Lys,ENST00000511367,NM_013235.4;DROSHA,missense_variant,p.Gln1350Lys,ENST00000344624,;DROSHA,missense_variant,p.Gln1313Lys,ENST00000442743,;DROSHA,missense_variant,p.Gln1313Lys,ENST00000513349,NM_001100412.1;DROSHA,non_coding_transcript_exon_variant,,ENST00000511778,;DROSHA,non_coding_transcript_exon_variant,,ENST00000514927,;DROSHA,downstream_gene_variant,,ENST00000512166,; T ENST00000511367 Transcript missense_variant 4293/5305 4048/4125 1350/1374 Q/K Caa/Aaa 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 tolerated(0.28) 35/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11207 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 31401509 31401509 G T 1 0 0 0 0 1 0 0 0 4584 1386 48 2 2 DROSHA 5 31401509 Missense_Mutation SNP G C3N-00175_T 7879125 31401509 150136750 430 10022 IL7R 0 . GRCh38 5 35873535 35873535 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.593C>A p.Ala198Glu p.A198E ENST00000303115 5/8 474 362 112 324 324 0 strelka-varscan-mutect IL7R,missense_variant,p.Ala198Glu,ENST00000303115,NM_002185.3;IL7R,missense_variant,p.Ala198Glu,ENST00000506850,;IL7R,missense_variant,p.Ala1Glu,ENST00000505093,;IL7R,non_coding_transcript_exon_variant,,ENST00000509668,;IL7R,intron_variant,,ENST00000514217,;IL7R,upstream_gene_variant,,ENST00000505875,; A ENST00000303115 Transcript missense_variant 722/4626 593/1380 198/459 A/E gCa/gAa 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 deleterious(0.04) 5/8 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_patterns:PS01355,PROSITE_profiles:PS50853,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 35873535 35873535 C A 1 0 0 0 0 1 0 0 0 7609 710 25 2 2 IL7R 5 35873535 Missense_Mutation SNP C C3N-00175_T 4472026 35873535 145664724 431 10023 IL7R 0 . GRCh38 5 35876038 35876038 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.932T>A p.Val311Glu p.V311E ENST00000303115 8/8 479 372 107 268 268 0 strelka-varscan-mutect IL7R,missense_variant,p.Val311Glu,ENST00000303115,NM_002185.3;IL7R,3_prime_UTR_variant,,ENST00000505093,;IL7R,downstream_gene_variant,,ENST00000506850,;IL7R,3_prime_UTR_variant,,ENST00000514217,;IL7R,non_coding_transcript_exon_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000509668,; A ENST00000303115 Transcript missense_variant 1061/4626 932/1380 311/459 V/E gTg/gAg 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 deleterious(0) 8/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 35876038 35876038 T A 1 0 0 0 0 1 0 0 0 7609 1696 59 4 4 IL7R 5 35876038 Missense_Mutation SNP T C3N-00175_T 2503 35876038 145662221 432 10024 IL7R 0 . GRCh38 5 35876052 35876052 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.946G>C p.Ala316Pro p.A316P ENST00000303115 8/8 471 365 106 297 297 0 strelka-varscan-mutect IL7R,missense_variant,p.Ala316Pro,ENST00000303115,NM_002185.3;IL7R,3_prime_UTR_variant,,ENST00000505093,;IL7R,downstream_gene_variant,,ENST00000506850,;IL7R,3_prime_UTR_variant,,ENST00000514217,;IL7R,non_coding_transcript_exon_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000509668,; C ENST00000303115 Transcript missense_variant 1075/4626 946/1380 316/459 A/P Gct/Cct 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 deleterious(0.01) 8/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 35876052 35876052 G C 1 0 0 0 0 1 0 0 0 7609 971 34 4 4 IL7R 5 35876052 Missense_Mutation SNP G C3N-00175_T 14 35876052 145662207 433 10025 UGT3A2 0 . GRCh38 5 36037947 36037947 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1145G>T p.Gly382Val p.G382V ENST00000282507 6/7 227 193 34 179 179 0 strelka-varscan-mutect UGT3A2,missense_variant,p.Gly382Val,ENST00000282507,NM_174914.3;UGT3A2,missense_variant,p.Gly348Val,ENST00000513300,NM_001168316.1;UGT3A2,downstream_gene_variant,,ENST00000504954,;UGT3A2,3_prime_UTR_variant,,ENST00000504685,; A ENST00000282507 Transcript missense_variant 1247/2355 1145/1572 382/523 G/V gGt/gTt 1 -1 UGT3A2 HGNC HGNC:27266 protein_coding YES CCDS3914.1 ENSP00000282507 Q3SY77 UPI000013DCE8 NM_174914.3 deleterious(0) 6/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF320,PROSITE_patterns:PS00375,Gene3D:3.40.50.2000,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs1352347621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 36037947 36037947 C A 1 0 0 0 0 1 0 0 0 17488 507 18 2 2 UGT3A2 5 36037947 Missense_Mutation SNP C C3N-00175_T 161895 36037947 145500312 434 10026 NIPBL 0 . GRCh38 5 37000868 37000868 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.3554A>C p.Glu1185Ala p.E1185A ENST00000282516 13/47 190 139 51 278 278 0 strelka-varscan-mutect NIPBL,missense_variant,p.Glu1185Ala,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Glu1185Ala,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,downstream_gene_variant,,ENST00000504430,;NIPBL,downstream_gene_variant,,ENST00000503274,;NIPBL,downstream_gene_variant,,ENST00000509429,; C ENST00000282516 Transcript missense_variant 4053/10435 3554/8415 1185/2804 E/A gAa/gCa 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated(0.1) 13/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 37000868 37000868 A C 1 0 0 0 0 1 0 0 0 10463 246 9 5 5 NIPBL 5 37000868 Missense_Mutation SNP A C3N-00175_T 962921 37000868 144537391 435 10027 C5orf42 0 . GRCh38 5 37187461 37187461 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.4033C>G p.Gln1345Glu p.Q1345E ENST00000425232 23/52 128 118 10 119 119 0 strelka-varscan-mutect C5orf42,missense_variant,p.Gln1345Glu,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Gln1345Glu,ENST00000508244,;C5orf42,missense_variant,p.Gln393Glu,ENST00000514429,;C5orf42,missense_variant,p.Gln350Glu,ENST00000509849,; C ENST00000425232 Transcript missense_variant 4264/11199 4033/9594 1345/3197 Q/E Cag/Gag 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0) 23/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS rs1408712462 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 37187461 37187461 G C 1 0 0 0 0 1 0 0 0 2100 1299 45 4 4 C5orf42 5 37187461 Missense_Mutation SNP G C3N-00175_T 186593 37187461 144350798 436 10028 NUP155 0 . GRCh38 5 37349172 37349172 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.903G>T p.Gln301His p.Q301H ENST00000231498 8/35 20 16 4 24 24 0 strelka-mutect NUP155,missense_variant,p.Gln301His,ENST00000231498,NM_153485.2;NUP155,missense_variant,p.Gln242His,ENST00000381843,NM_004298.3;NUP155,missense_variant,p.Gln301His,ENST00000513532,NM_001278312.1;NUP155,splice_region_variant,,ENST00000507233,; A ENST00000231498 Transcript missense_variant,splice_region_variant 1107/8143 903/4176 301/1391 Q/H caG/caT 1 -1 NUP155 HGNC HGNC:8063 protein_coding YES CCDS3921.1 ENSP00000231498 O75694 A0A024R071 UPI0000001C7F NM_153485.2 deleterious(0.01) 8/35 Pfam_domain:PF08801,hmmpanther:PTHR10350,hmmpanther:PTHR10350:SF6 MODERATE 1 SNV 1 1 PASS . . 1 201 8 0 0 0 0 0 -12.11638 0.9999989 1 1 1 0 A 3 1 39 37349172 37349172 C A 1 0 0 0 0 1 0 0 0 10821 695 24 2 2 NUP155 5 37349172 Missense_Mutation SNP C C3N-00175_T 161711 37349172 144189087 437 10029 EGFLAM 0 . GRCh38 5 38438378 38438378 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.2387G>A p.Gly796Glu p.G796E ENST00000354891 17/23 184 107 77 161 161 0 strelka-varscan-mutect EGFLAM,missense_variant,p.Gly796Glu,ENST00000322350,NM_152403.3;EGFLAM,missense_variant,p.Gly796Glu,ENST00000354891,NM_001205301.1;EGFLAM,missense_variant,p.Gly562Glu,ENST00000336740,NM_182798.2;EGFLAM,missense_variant,p.Gly162Glu,ENST00000397202,; A ENST00000354891 Transcript missense_variant 2733/3963 2387/3054 796/1017 G/E gGg/gAg 1 1 EGFLAM HGNC HGNC:26810 protein_coding YES CCDS56363.1 ENSP00000346964 Q63HQ2 UPI000022C806 NM_001205301.1 deleterious(0.04) 17/23 PROSITE_profiles:PS50026,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 38438378 38438378 G A 1 0 0 0 0 1 0 0 0 4802 1232 43 3 3 EGFLAM 5 38438378 Missense_Mutation SNP G C3N-00175_T 1089206 38438378 143099881 438 10030 CARD6 0 . GRCh38 5 40853122 40853122 + Missense_Mutation SNP A A T rs771001915 C3N-00175_T C3N-00175_N A A c.1790A>T p.Gln597Leu p.Q597L ENST00000254691 3/3 220 178 42 152 152 0 strelka-varscan-mutect CARD6,missense_variant,p.Gln597Leu,ENST00000254691,NM_032587.3;CARD6,intron_variant,,ENST00000381677,; T ENST00000254691 Transcript missense_variant 1989/4221 1790/3114 597/1037 Q/L cAg/cTg rs771001915 1 1 CARD6 HGNC HGNC:16394 protein_coding YES CCDS3935.1 ENSP00000254691 Q9BX69 UPI000013CE50 NM_032587.3 tolerated(0.12) 3/3 hmmpanther:PTHR22797,hmmpanther:PTHR22797:SF36 MODERATE 1 SNV 1 1 PASS rs771001915 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 40853122 40853122 A T 1 0 0 0 0 1 0 0 0 2346 188 7 4 4 CARD6 5 40853122 Missense_Mutation SNP A C3N-00175_T 2414744 40853122 140685137 439 10031 OXCT1 0 . GRCh38 5 41862749 41862749 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.80G>A p.Gly27Glu p.G27E ENST00000196371 2/17 420 349 71 284 282 2 strelka-varscan-mutect OXCT1,missense_variant,p.Gly27Glu,ENST00000196371,NM_000436.3; T ENST00000196371 Transcript missense_variant,splice_region_variant 241/3388 80/1563 27/520 G/E gGa/gAa 1 -1 OXCT1 HGNC HGNC:8527 protein_coding YES CCDS3937.1 ENSP00000196371 P55809 A0A024R040 UPI0000000C9A NM_000436.3 tolerated(0.26) 2/17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41862749 41862749 C T 1 0 0 0 0 1 0 0 0 11401 869 30 3 3 OXCT1 5 41862749 Missense_Mutation SNP C C3N-00175_T 1009627 41862749 139675510 440 10032 HMGCS1 0 . GRCh38 5 43297107 43297107 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.634G>C p.Glu212Gln p.E212Q ENST00000325110 5/11 214 201 13 160 160 0 strelka-varscan-mutect HMGCS1,missense_variant,p.Glu212Gln,ENST00000325110,NM_001098272.2;HMGCS1,missense_variant,p.Glu212Gln,ENST00000433297,NM_002130.7;HMGCS1,downstream_gene_variant,,ENST00000511774,;HMGCS1,downstream_gene_variant,,ENST00000507004,;HMGCS1,downstream_gene_variant,,ENST00000507293,;HMGCS1,upstream_gene_variant,,ENST00000508319,;HMGCS1,upstream_gene_variant,,ENST00000514610,; G ENST00000325110 Transcript missense_variant 841/3506 634/1563 212/520 E/Q Gaa/Caa 1 -1 HMGCS1 HGNC HGNC:5007 protein_coding YES CCDS34154.1 ENSP00000322706 Q01581 A0A024R059 UPI000012C9BC NM_001098272.2 deleterious(0) 5/11 Gene3D:3.40.47.10,Pfam_domain:PF08540,hmmpanther:PTHR11877,hmmpanther:PTHR11877:SF12,Superfamily_domains:SSF53901,TIGRFAM_domain:TIGR01833 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 43297107 43297107 C G 1 0 0 0 0 1 0 0 0 7124 835 29 4 4 HMGCS1 5 43297107 Missense_Mutation SNP C C3N-00175_T 1434358 43297107 138241152 441 10033 ITGA1 0 . GRCh38 5 52849378 52849378 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.75C>G p.Cys25Trp p.C25W ENST00000282588 2/29 105 75 30 103 103 0 strelka-varscan-mutect ITGA1,missense_variant,p.Cys25Trp,ENST00000282588,NM_181501.1; G ENST00000282588 Transcript missense_variant 533/10757 75/3540 25/1179 C/W tgC/tgG 1 1 ITGA1 HGNC HGNC:6134 protein_coding YES CCDS3955.1 ENSP00000282588 P56199 UPI00001A95E8 NM_181501.1 deleterious(0.02) 2/29 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF22,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 52849378 52849378 C G 1 0 0 0 0 1 0 0 0 7779 805 28 4 4 ITGA1 5 52849378 Missense_Mutation SNP C C3N-00175_T 9552271 52849378 128688881 442 10034 ITGA1 0 . GRCh38 5 52920423 52920423 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2247C>T p.= p.I749I ENST00000282588 17/29 83 71 12 105 105 0 strelka-varscan-mutect ITGA1,synonymous_variant,p.=,ENST00000282588,NM_181501.1;ITGA1,non_coding_transcript_exon_variant,,ENST00000504669,; T ENST00000282588 Transcript synonymous_variant 2705/10757 2247/3540 749/1179 I atC/atT 1 1 ITGA1 HGNC HGNC:6134 protein_coding YES CCDS3955.1 ENSP00000282588 P56199 UPI00001A95E8 NM_181501.1 17/29 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF22,Superfamily_domains:SSF69179 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 52920423 52920423 C T 1 0 0 0 0 0 0 0 1 7779 816 29 3 3 ITGA1 5 52920423 Silent SNP C C3N-00175_T 71045 52920423 128617836 443 10035 ITGA2 0 . GRCh38 5 53065949 53065949 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1915G>C p.Gly639Arg p.G639R ENST00000296585 15/30 435 357 78 386 386 0 strelka-varscan-mutect ITGA2,missense_variant,p.Gly639Arg,ENST00000296585,NM_002203.3;ITGA2,missense_variant,p.Gly639Arg,ENST00000510722,;ITGA2,missense_variant,p.Gly639Arg,ENST00000509814,;ITGA2,3_prime_UTR_variant,,ENST00000503810,;ITGA2,3_prime_UTR_variant,,ENST00000509960,;ITGA2,3_prime_UTR_variant,,ENST00000513685,; C ENST00000296585 Transcript missense_variant 2058/7869 1915/3546 639/1181 G/R Ggt/Cgt 1 1 ITGA2 HGNC HGNC:6137 protein_coding YES CCDS3957.1 ENSP00000296585 P17301 UPI0000169C36 NM_002203.3 deleterious(0) 15/30 PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF23,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318,Prints_domain:PR01185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 53065949 53065949 G C 1 0 0 0 0 1 0 0 0 7782 1348 47 4 4 ITGA2 5 53065949 Missense_Mutation SNP G C3N-00175_T 145526 53065949 128472310 444 10036 FST 0 . GRCh38 5 53482989 53482989 + Nonsense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.195G>A p.Trp65Ter p.W65* ENST00000256759 2/6 150 132 18 175 175 0 strelka-varscan-mutect FST,stop_gained,p.Trp65Ter,ENST00000396947,NM_006350.3;FST,stop_gained,p.Trp65Ter,ENST00000256759,NM_013409.2;FST,upstream_gene_variant,,ENST00000497789,;FST,upstream_gene_variant,,ENST00000504226,;FST,non_coding_transcript_exon_variant,,ENST00000491717,; A ENST00000256759 Transcript stop_gained 578/2519 195/1035 65/344 W/* tgG/tgA 1 1 FST HGNC HGNC:3971 protein_coding YES CCDS3959.1 ENSP00000256759 P19883 A0A024QZU6 UPI000012AC56 NM_013409.2 2/6 PROSITE_profiles:PS51364,hmmpanther:PTHR10913:SF6,hmmpanther:PTHR10913,Superfamily_domains:SSF57581 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 53482989 53482989 G A 1 0 0 0 0 0 1 0 0 5950 1183 41 3 3 FST 5 53482989 Nonsense_Mutation SNP G C3N-00175_T 417040 53482989 128055270 445 10037 FST 0 . GRCh38 5 53484145 53484145 + Silent SNP C C A rs755377992 C3N-00175_T C3N-00175_N C C c.573C>A p.= p.T191T ENST00000256759 4/6 315 250 65 324 323 1 strelka-varscan-mutect FST,synonymous_variant,p.=,ENST00000396947,NM_006350.3;FST,synonymous_variant,p.=,ENST00000256759,NM_013409.2;FST,synonymous_variant,p.=,ENST00000504226,;FST,upstream_gene_variant,,ENST00000497789,;FST,downstream_gene_variant,,ENST00000491717,; A ENST00000256759 Transcript synonymous_variant 956/2519 573/1035 191/344 T acC/acA rs755377992 1 1 FST HGNC HGNC:3971 protein_coding YES CCDS3959.1 ENSP00000256759 P19883 A0A024QZU6 UPI000012AC56 NM_013409.2 4/6 PROSITE_profiles:PS51465,hmmpanther:PTHR10913:SF6,hmmpanther:PTHR10913,Gene3D:3.30.60.30,SMART_domains:SM00280,Superfamily_domains:SSF100895 LOW 1 SNV 1 1 PASS rs755377992 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 53484145 53484145 C A 1 0 0 0 0 0 0 0 1 5950 668 24 2 2 FST 5 53484145 Silent SNP C C3N-00175_T 1156 53484145 128054114 446 10038 ADAMTS6 0 . GRCh38 5 65224926 65224926 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2189G>T p.Gly730Val p.G730V ENST00000381055 17/25 94 73 21 75 75 0 strelka-varscan-mutect ADAMTS6,missense_variant,p.Gly730Val,ENST00000381055,NM_197941.2;ADAMTS6,splice_region_variant,,ENST00000381052,;ADAMTS6,splice_region_variant,,ENST00000470597,;ADAMTS6,splice_region_variant,,ENST00000464680,; A ENST00000381055 Transcript missense_variant,splice_region_variant 3046/7311 2189/3354 730/1117 G/V gGa/gTa 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 deleterious(0.01) 17/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 65224926 65224926 C A 1 0 0 0 0 1 0 0 0 314 869 30 2 2 ADAMTS6 5 65224926 Missense_Mutation SNP C C3N-00175_T 11740781 65224926 116313333 447 10039 ADAMTS6 0 . GRCh38 5 65460183 65460183 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.618T>C p.= p.H206H ENST00000381055 4/25 117 82 35 119 119 0 strelka-varscan-mutect ADAMTS6,synonymous_variant,p.=,ENST00000381055,NM_197941.2;ADAMTS6,synonymous_variant,p.=,ENST00000381052,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000470597,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000464680,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000502886,; G ENST00000381055 Transcript synonymous_variant 1475/7311 618/3354 206/1117 H caT/caC 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 4/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 65460183 65460183 A G 1 0 0 0 0 0 0 0 1 314 98 4 5 5 ADAMTS6 5 65460183 Silent SNP A C3N-00175_T 235257 65460183 116078076 448 10040 TNPO1 0 . GRCh38 5 72882495 72882495 + Nonsense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.949A>T p.Lys317Ter p.K317* ENST00000337273 10/25 49 37 12 98 98 0 strelka-varscan-mutect TNPO1,stop_gained,p.Lys317Ter,ENST00000337273,NM_002270.3;TNPO1,stop_gained,p.Lys309Ter,ENST00000506351,NM_153188.2;TNPO1,stop_gained,p.Lys267Ter,ENST00000523768,;MIR4804,downstream_gene_variant,,ENST00000581683,;TNPO1,non_coding_transcript_exon_variant,,ENST00000508762,;TNPO1,non_coding_transcript_exon_variant,,ENST00000505082,;TNPO1,3_prime_UTR_variant,,ENST00000520850,;CTD-2339M3.1,upstream_gene_variant,,ENST00000497334,; T ENST00000337273 Transcript stop_gained 1375/11183 949/2697 317/898 K/* Aag/Tag 1 1 TNPO1 HGNC HGNC:6401 protein_coding YES CCDS43329.1 ENSP00000336712 Q92973 A0A024RAM0 UPI000020CAB6 NM_002270.3 10/25 hmmpanther:PTHR10527,hmmpanther:PTHR10527:SF21,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 72882495 72882495 A T 1 0 0 0 0 0 1 0 0 16808 247 9 4 4 TNPO1 5 72882495 Nonsense_Mutation SNP A C3N-00175_T 7422312 72882495 108655764 449 10041 TMEM171 0 . GRCh38 5 73123610 73123610 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.237C>T p.= p.S79S ENST00000454765 2/4 165 145 20 151 151 0 strelka-varscan-mutect TMEM171,synonymous_variant,p.=,ENST00000454765,NM_173490.7;TMEM171,synonymous_variant,p.=,ENST00000287773,NM_001161342.2; T ENST00000454765 Transcript synonymous_variant 710/1535 237/975 79/324 S tcC/tcT 1 1 TMEM171 HGNC HGNC:27031 protein_coding YES CCDS4017.1 ENSP00000415030 Q8WVE6 UPI000020CAC5 NM_173490.7 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR31617:SF0,hmmpanther:PTHR31617,Pfam_domain:PF15471 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 73123610 73123610 C T 1 0 0 0 0 0 0 0 1 16532 610 22 3 3 TMEM171 5 73123610 Silent SNP C C3N-00175_T 241115 73123610 108414649 450 10042 AP3B1 0 . GRCh38 5 78003009 78003009 + Missense_Mutation SNP C C A rs753428510 C3N-00175_T C3N-00175_N C C c.3178G>T p.Val1060Leu p.V1060L ENST00000255194 27/27 323 287 36 376 376 0 strelka-varscan-mutect AP3B1,missense_variant,p.Val1060Leu,ENST00000255194,NM_003664.4;AP3B1,missense_variant,p.Val1011Leu,ENST00000519295,NM_001271769.1;AP3B1,3_prime_UTR_variant,,ENST00000522901,;AP3B1,non_coding_transcript_exon_variant,,ENST00000520122,; A ENST00000255194 Transcript missense_variant 3354/5838 3178/3285 1060/1094 V/L Gtg/Ttg rs753428510 1 -1 AP3B1 HGNC HGNC:566 protein_coding YES CCDS4041.1 ENSP00000255194 O00203 A0A0S2Z5J4 UPI00001AE77D NM_003664.4 tolerated(0.7) 27/27 PIRSF_domain:PIRSF037096,SMART_domains:SM01020 MODERATE 1 SNV 1 1 PASS rs753428510 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 78003009 78003009 C A 1 0 0 0 0 1 0 0 0 860 565 20 2 2 AP3B1 5 78003009 Missense_Mutation SNP C C3N-00175_T 4879399 78003009 103535250 451 10043 HOMER1 0 . GRCh38 5 79402034 79402034 + Missense_Mutation SNP C C G C3N-00175_T C3N-00175_N C C c.549G>C p.Trp183Cys p.W183C ENST00000334082 6/9 153 119 34 149 148 1 strelka-varscan-mutect HOMER1,missense_variant,p.Trp183Cys,ENST00000334082,NM_004272.4;HOMER1,missense_variant,p.Trp9Cys,ENST00000535690,;HOMER1,intron_variant,,ENST00000508576,NM_001277078.1;HOMER1,intron_variant,,ENST00000282260,NM_001277077.1;HOMER1,upstream_gene_variant,,ENST00000460741,; G ENST00000334082 Transcript missense_variant 1992/5881 549/1065 183/354 W/C tgG/tgC COSM5403878 1 -1 HOMER1 HGNC HGNC:17512 protein_coding YES CCDS43335.1 ENSP00000334382 Q86YM7 UPI000006D8F2 NM_004272.4 deleterious(0.02) 6/9 hmmpanther:PTHR10918,hmmpanther:PTHR10918:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 79402034 79402034 C G 1 0 0 0 0 1 0 0 0 7172 624 22 4 4 HOMER1 5 79402034 Missense_Mutation SNP C C3N-00175_T 1399025 79402034 102136225 452 10044 CMYA5 0 . GRCh38 5 79729607 79729607 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.842T>A p.Val281Glu p.V281E ENST00000446378 2/13 125 96 29 142 142 0 strelka-varscan-mutect CMYA5,missense_variant,p.Val281Glu,ENST00000446378,NM_153610.4; A ENST00000446378 Transcript missense_variant 873/12847 842/12210 281/4069 V/E gTg/gAg 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 deleterious(0.01) 2/13 hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 79729607 79729607 T A 1 0 0 0 0 1 0 0 0 3368 1696 59 4 4 CMYA5 5 79729607 Missense_Mutation SNP T C3N-00175_T 327573 79729607 101808652 453 10045 FAM151B 0 . GRCh38 5 80541734 80541734 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.733A>T p.Ile245Phe p.I245F ENST00000282226 6/6 152 120 32 315 315 0 strelka-varscan-mutect FAM151B,missense_variant,p.Ile245Phe,ENST00000282226,NM_205548.2;FAM151B,non_coding_transcript_exon_variant,,ENST00000511718,; T ENST00000282226 Transcript missense_variant 888/1717 733/831 245/276 I/F Att/Ttt 1 1 FAM151B HGNC HGNC:33716 protein_coding YES CCDS4051.1 ENSP00000282226 Q6UXP7 UPI000022C849 NM_205548.2 deleterious(0.03) 6/6 hmmpanther:PTHR21184:SF3,hmmpanther:PTHR21184,Pfam_domain:PF10223 MODERATE 1 SNV 1 1 PASS rs940450147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 80541734 80541734 A T 1 0 0 0 0 1 0 0 0 5309 217 8 4 4 FAM151B 5 80541734 Missense_Mutation SNP A C3N-00175_T 812127 80541734 100996525 454 10046 VCAN 0 . GRCh38 5 83541926 83541926 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.8923C>A p.Pro2975Thr p.P2975T ENST00000265077 8/15 166 126 40 143 143 0 strelka-varscan-mutect VCAN,missense_variant,p.Pro2975Thr,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Pro1988Thr,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 9488/12625 8923/10191 2975/3396 P/T Cca/Aca 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.06) 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 83541926 83541926 C A 1 0 0 0 0 1 0 0 0 17683 739 26 2 2 VCAN 5 83541926 Missense_Mutation SNP C C3N-00175_T 3000192 83541926 97996333 455 10047 HAPLN1 0 . GRCh38 5 83652825 83652825 + Splice_Site SNP C C A novel C3N-00175_T C3N-00175_N C C c.101-1G>T p.X34_splice ENST00000274341 66 45 21 76 76 0 strelka-varscan-mutect HAPLN1,splice_acceptor_variant,,ENST00000274341,NM_001884.3;HAPLN1,splice_acceptor_variant,,ENST00000514416,;HAPLN1,splice_acceptor_variant,,ENST00000510978,;HAPLN1,splice_acceptor_variant,,ENST00000504713,;HAPLN1,splice_acceptor_variant,,ENST00000508307,;HAPLN1,splice_acceptor_variant,,ENST00000515590,;HAPLN1,splice_region_variant,,ENST00000503117,; A ENST00000274341 Transcript splice_acceptor_variant -/5607 101/1065 34/354 1 -1 HAPLN1 HGNC HGNC:2380 protein_coding YES CCDS4061.1 ENSP00000274341 P10915 A0A024RAK9 UPI0000131BFF NM_001884.3 2/4 HIGH 1 SNV 1 1 PASS rs1168098415 . 0 201 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 5 1 39 83652825 83652825 C A 1 0 0 0 0 0 0 1 0 6840 811 28 2 2 HAPLN1 5 83652825 Splice_Site SNP C C3N-00175_T 110899 83652825 97885434 456 10048 ADGRV1 0 . GRCh38 5 90711027 90711027 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.8871G>T p.= p.G2957G ENST00000405460 40/90 196 122 74 133 133 0 strelka-varscan-mutect ADGRV1,synonymous_variant,p.=,ENST00000405460,NM_032119.3;ADGRV1,synonymous_variant,p.=,ENST00000509621,; T ENST00000405460 Transcript synonymous_variant 8967/19338 8871/18921 2957/6306 G ggG/ggT 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 40/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,SMART_domains:SM00237,Superfamily_domains:SSF141072 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 90711027 90711027 G T 1 0 0 0 0 0 0 0 1 379 1219 43 2 2 ADGRV1 5 90711027 Silent SNP G C3N-00175_T 7058202 90711027 90827232 457 10049 PCSK1 0 . GRCh38 5 96397404 96397404 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1654G>A p.Asp552Asn p.D552N ENST00000311106 12/14 356 316 40 324 324 0 strelka-varscan-mutect PCSK1,missense_variant,p.Asp552Asn,ENST00000311106,NM_000439.4;PCSK1,missense_variant,p.Asp505Asn,ENST00000508626,NM_001177875.1;CTD-2337A12.1,intron_variant,,ENST00000502645,;PCSK1,non_coding_transcript_exon_variant,,ENST00000513085,; T ENST00000311106 Transcript missense_variant 1892/5086 1654/2262 552/753 D/N Gac/Aac 1 -1 PCSK1 HGNC HGNC:8743 protein_coding YES CCDS4081.1 ENSP00000308024 P29120 UPI000013F0F5 NM_000439.4 tolerated(0.06) 12/14 hmmpanther:PTHR10795:SF407,hmmpanther:PTHR10795,Gene3D:2.60.120.260,Pfam_domain:PF01483,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 96397404 96397404 C T 1 0 0 0 0 1 0 0 0 11688 855 30 3 3 PCSK1 5 96397404 Missense_Mutation SNP C C3N-00175_T 5686377 96397404 85140855 458 10050 LNPEP 0 . GRCh38 5 97003490 97003490 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1729C>T p.His577Tyr p.H577Y ENST00000231368 9/18 93 81 12 105 105 0 strelka-varscan-mutect LNPEP,missense_variant,p.His577Tyr,ENST00000231368,NM_005575.2;LNPEP,missense_variant,p.His563Tyr,ENST00000395770,NM_175920.3;LNPEP,non_coding_transcript_exon_variant,,ENST00000473914,; T ENST00000231368 Transcript missense_variant 2421/12752 1729/3078 577/1025 H/Y Cat/Tat 1 1 LNPEP HGNC HGNC:6656 protein_coding YES CCDS4087.1 ENSP00000231368 Q9UIQ6 UPI000013C94B NM_005575.2 deleterious(0.04) 9/18 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF42,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 97003490 97003490 C T 1 0 0 0 0 1 0 0 0 8791 710 25 3 3 LNPEP 5 97003490 Missense_Mutation SNP C C3N-00175_T 606086 97003490 84534769 459 10051 SLCO4C1 0 . GRCh38 5 102270679 102270679 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.747G>T p.= p.L249L ENST00000310954 3/13 196 161 35 154 153 1 strelka-varscan-mutect SLCO4C1,synonymous_variant,p.=,ENST00000310954,NM_180991.4; A ENST00000310954 Transcript synonymous_variant 1034/5334 747/2175 249/724 L ctG/ctT 1 -1 SLCO4C1 HGNC HGNC:23612 protein_coding YES CCDS34205.1 ENSP00000309741 Q6ZQN7 UPI00001C10B6 NM_180991.4 3/13 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF103,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1173813120 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 102270679 102270679 C A 1 0 0 0 0 0 0 0 1 15017 581 21 2 2 SLCO4C1 5 102270679 Silent SNP C C3N-00175_T 5267189 102270679 79267580 460 10052 EFNA5 0 . GRCh38 5 107381376 107381376 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.566A>G p.Asp189Gly p.D189G ENST00000333274 5/5 60 44 16 75 75 0 strelka-varscan-mutect EFNA5,missense_variant,p.Asp189Gly,ENST00000333274,NM_001962.2;EFNA5,missense_variant,p.Asp149Gly,ENST00000611503,;EFNA5,missense_variant,p.Asn162Ser,ENST00000509503,;EFNA5,splice_region_variant,,ENST00000510359,; C ENST00000333274 Transcript missense_variant,splice_region_variant 848/5335 566/687 189/228 D/G gAt/gGt 1 -1 EFNA5 HGNC HGNC:3225 protein_coding YES CCDS4097.1 ENSP00000328777 P52803 UPI0000129C93 NM_001962.2 deleterious(0.01) 5/5 hmmpanther:PTHR11304,hmmpanther:PTHR11304:SF33 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 107381376 107381376 T C 1 0 0 0 0 1 0 0 0 4790 1449 50 5 5 EFNA5 5 107381376 Missense_Mutation SNP T C3N-00175_T 5110697 107381376 74156883 461 10053 FER 0 . GRCh38 5 108867827 108867827 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.542T>C p.Leu181Ser p.L181S ENST00000281092 6/20 357 311 46 364 364 0 strelka-varscan-mutect FER,missense_variant,p.Leu181Ser,ENST00000281092,NM_001308028.1,NM_005246.2;FER,3_prime_UTR_variant,,ENST00000504143,; C ENST00000281092 Transcript missense_variant 926/12119 542/2469 181/822 L/S tTg/tCg 1 1 FER HGNC HGNC:3655 protein_coding YES CCDS4098.1 ENSP00000281092 P16591 W0S0X4 UPI000013DC55 NM_001308028.1,NM_005246.2 tolerated(0.05) 6/20 PIRSF_domain:PIRSF000632,PROSITE_profiles:PS51741,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF227,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 108867827 108867827 T C 1 0 0 0 0 1 0 0 0 5676 1821 63 5 5 FER 5 108867827 Missense_Mutation SNP T C3N-00175_T 1486451 108867827 72670432 462 10054 TSSK1B 0 . GRCh38 5 113434407 113434407 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.433G>T p.Asp145Tyr p.D145Y ENST00000390666 1/1 95 69 26 101 101 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Asp145Tyr,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; A ENST00000390666 Transcript missense_variant 625/2478 433/1104 145/367 D/Y Gac/Tac 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 deleterious(0) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 113434407 113434407 C A 1 0 0 0 0 1 0 0 0 17176 826 29 2 2 TSSK1B 5 113434407 Missense_Mutation SNP C C3N-00175_T 4566580 113434407 68103852 463 10055 HSD17B4 0 . GRCh38 5 119506817 119506817 + Splice_Site DEL G G - novel C3N-00175_T C3N-00175_N G G c.1337delG p.Gly446GlufsTer3 p.X446_splice ENST00000504811 104 93 11 174 174 0 sindel-varindel-pindel HSD17B4,splice_acceptor_variant,p.Gly446GlufsTer3,ENST00000504811,NM_001199291.2;HSD17B4,splice_acceptor_variant,p.Gly421GlufsTer3,ENST00000256216,NM_000414.3;HSD17B4,splice_acceptor_variant,p.Gly397GlufsTer3,ENST00000510025,NM_001292027.1;HSD17B4,splice_acceptor_variant,p.Gly281GlufsTer3,ENST00000414835,NM_001292028.1;HSD17B4,splice_acceptor_variant,p.Gly403GlufsTer3,ENST00000515320,NM_001199292.1;HSD17B4,splice_acceptor_variant,p.Gly159GlufsTer3,ENST00000509514,;HSD17B4,splice_acceptor_variant,p.Gly284GlufsTer3,ENST00000513628,;HSD17B4,splice_acceptor_variant,,ENST00000518349,;HSD17B4,splice_acceptor_variant,,ENST00000520244,;HSD17B4,upstream_gene_variant,,ENST00000522415,;HSD17B4,downstream_gene_variant,,ENST00000520216,;HSD17B4,splice_acceptor_variant,,ENST00000515235,;HSD17B4,splice_acceptor_variant,p.Gly421GlufsTer3,ENST00000442060,; - ENST00000504811 Transcript splice_acceptor_variant -/2740 1337/2286 446/761 1 1 HSD17B4 HGNC HGNC:5213 protein_coding YES CCDS56379.1 ENSP00000420914 P51659 UPI0001AE7403 NM_001199291.2 15/24 HIGH 1 deletion 2 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.11668 0.9999999 1 1 1 0 - 8 5 39 119506817 119506817 G - 1 0 1 0 1 0 0 1 0 7281 1014 35 0 0 HSD17B4 5 119506817 Splice_Site DEL G C3N-00175_T 6072410 119506817 62031442 464 10056 PRR16 0 . GRCh38 5 120686705 120686705 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.911T>A p.Val304Glu p.V304E ENST00000407149 2/2 16 10 6 14 14 0 strelka-varscan-mutect PRR16,missense_variant,p.Val281Glu,ENST00000379551,NM_016644.2;PRR16,missense_variant,p.Val304Glu,ENST00000407149,NM_001300783.1;PRR16,missense_variant,p.Val234Glu,ENST00000505123,NM_001308087.1;PRR16,missense_variant,p.Val251Glu,ENST00000446965,;PRR16,downstream_gene_variant,,ENST00000509923,; A ENST00000407149 Transcript missense_variant 1120/1747 911/915 304/304 V/E gTg/gAg 1 1 PRR16 HGNC HGNC:29654 protein_coding YES CCDS75290.1 ENSP00000385118 Q569H4 UPI00004F9C36 NM_001300783.1 deleterious(0) 2/2 Pfam_domain:PF15252,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.54453 1 1 1 1 0 A 3 1 39 120686705 120686705 T A 1 0 0 0 0 1 0 0 0 12725 1696 59 4 4 PRR16 5 120686705 Missense_Mutation SNP T C3N-00175_T 1179888 120686705 60851554 465 10057 FBN2 0 . GRCh38 5 128286817 128286817 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.6913T>C p.Cys2305Arg p.C2305R ENST00000508053 61/71 404 350 54 458 458 0 strelka-varscan-mutect FBN2,missense_variant,p.Cys2305Arg,ENST00000508053,;FBN2,missense_variant,p.Cys2305Arg,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Cys2304Arg,ENST00000619499,; G ENST00000508053 Transcript missense_variant 7888/11132 6913/8739 2305/2912 C/R Tgt/Cgt 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 61/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 128286817 128286817 A G 1 0 0 0 0 1 0 0 0 5566 188 7 5 5 FBN2 5 128286817 Missense_Mutation SNP A C3N-00175_T 7600112 128286817 53251442 466 10058 PDLIM4 0 . GRCh38 5 132266497 132266497 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.279T>C p.= p.D93D ENST00000253754 3/7 94 86 8 141 141 0 strelka-varscan-mutect PDLIM4,synonymous_variant,p.=,ENST00000253754,NM_003687.3;PDLIM4,synonymous_variant,p.=,ENST00000379018,NM_001131027.1;PDLIM4,synonymous_variant,p.=,ENST00000418373,;P4HA2,intron_variant,,ENST00000439698,;P4HA2,intron_variant,,ENST00000431054,;P4HA2,intron_variant,,ENST00000416053,;P4HA2,intron_variant,,ENST00000471826,;PDLIM4,upstream_gene_variant,,ENST00000484620,;PDLIM4,non_coding_transcript_exon_variant,,ENST00000463615,;PDLIM4,intron_variant,,ENST00000474421,;PDLIM4,upstream_gene_variant,,ENST00000462597,; C ENST00000253754 Transcript synonymous_variant 343/2282 279/993 93/330 D gaT/gaC 1 1 PDLIM4 HGNC HGNC:16501 protein_coding YES CCDS4152.1 ENSP00000253754 P50479 UPI00001338F6 NM_003687.3 3/7 hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 132266497 132266497 T C 1 0 0 0 0 0 0 0 1 11770 1461 51 5 5 PDLIM4 5 132266497 Silent SNP T C3N-00175_T 3979680 132266497 49271762 467 10059 TIFAB 0 . GRCh38 5 135449647 135449647 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.293C>A p.Pro98His p.P98H ENST00000537858 2/2 466 321 145 499 497 2 strelka-varscan-mutect TIFAB,missense_variant,p.Pro98His,ENST00000537858,NM_001099221.1;DCANP1,upstream_gene_variant,,ENST00000503143,NM_130848.2;CTB-138E5.1,upstream_gene_variant,,ENST00000510230,; T ENST00000537858 Transcript missense_variant 494/5923 293/486 98/161 P/H cCc/cAc 1 -1 TIFAB HGNC HGNC:34024 protein_coding YES CCDS43365.1 ENSP00000440509 Q6ZNK6 UPI0000603404 NM_001099221.1 deleterious(0.01) 2/2 hmmpanther:PTHR31266,hmmpanther:PTHR31266:SF3,Gene3D:2.60.200.20,Pfam_domain:PF00498,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 135449647 135449647 G T 1 0 0 0 0 1 0 0 0 16331 1232 43 2 2 TIFAB 5 135449647 Missense_Mutation SNP G C3N-00175_T 3183150 135449647 46088612 468 10060 MYOT 0 . GRCh38 5 137883567 137883567 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1000T>A p.Phe334Ile p.F334I ENST00000239926 7/10 281 190 91 310 310 0 strelka-varscan-mutect MYOT,missense_variant,p.Phe334Ile,ENST00000239926,NM_006790.2;MYOT,missense_variant,p.Phe219Ile,ENST00000515645,NM_001300911.1;MYOT,missense_variant,p.Phe150Ile,ENST00000421631,NM_001135940.1;PKD2L2,upstream_gene_variant,,ENST00000503015,;RP11-381K20.2,non_coding_transcript_exon_variant,,ENST00000508281,;RP11-381K20.2,intron_variant,,ENST00000514616,;MYOT,intron_variant,,ENST00000509812,;MYOT,non_coding_transcript_exon_variant,,ENST00000503748,;MYOT,non_coding_transcript_exon_variant,,ENST00000511254,;MYOT,upstream_gene_variant,,ENST00000508938,; A ENST00000239926 Transcript missense_variant 1374/2337 1000/1497 334/498 F/I Ttc/Atc 1 1 MYOT HGNC HGNC:12399 protein_coding YES CCDS4194.1 ENSP00000239926 A0A0C4DFM5 UPI0000073E86 NM_006790.2 deleterious(0) 7/10 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF595,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 137883567 137883567 T A 1 0 0 0 0 1 0 0 0 10095 1609 56 4 4 MYOT 5 137883567 Missense_Mutation SNP T C3N-00175_T 2433920 137883567 43654692 469 10061 EGR1 0 . GRCh38 5 138466982 138466982 + Missense_Mutation SNP C C A rs202015917 C3N-00175_T C3N-00175_N C C c.533C>A p.Ala178Glu p.A178E ENST00000239938 2/2 103 72 31 139 139 0 strelka-varscan-mutect EGR1,missense_variant,p.Ala178Glu,ENST00000239938,NM_001964.2; A ENST00000239938 Transcript missense_variant 805/3138 533/1632 178/543 A/E gCg/gAg rs202015917,COSM5548908 1 1 EGR1 HGNC HGNC:3238 protein_coding YES CCDS4206.1 ENSP00000239938 P18146 Q546S1 UPI00000008CD NM_001964.2 deleterious(0.05) 2/2 Pfam_domain:PF11928,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs202015917 . 0 204 0 5 0 0 0 0 -20 0.999874 1 1 1 0 A 3 1 39 138466982 138466982 C A 1 0 0 0 0 1 0 0 0 4807 768 27 1 1 EGR1 5 138466982 Missense_Mutation SNP C C3N-00175_T 583415 138466982 43071277 470 10062 ANKHD1 0 . GRCh38 5 140459193 140459193 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1510A>T p.Thr504Ser p.T504S ENST00000532219 9/36 120 106 14 124 124 0 strelka-varscan-mutect ANKHD1-EIF4EBP3,missense_variant,p.Thr504Ser,ENST00000532219,NM_020690.5;ANKHD1,missense_variant,p.Thr504Ser,ENST00000360839,NM_017747.2;ANKHD1,missense_variant,p.Thr504Ser,ENST00000421134,;ANKHD1,missense_variant,p.Thr504Ser,ENST00000394723,NM_024668.3;ANKHD1,missense_variant,p.Thr504Ser,ENST00000616482,NM_001197030.1;ANKHD1,missense_variant,p.Thr493Ser,ENST00000394722,NM_017978.2;ANKHD1,5_prime_UTR_variant,,ENST00000297183,;ANKHD1,upstream_gene_variant,,ENST00000246149,;ANKHD1,non_coding_transcript_exon_variant,,ENST00000490185,; T ENST00000532219 Transcript missense_variant 1570/8246 1510/7854 504/2617 T/S Act/Tct 1 1 ANKHD1-EIF4EBP3 HGNC HGNC:33530 protein_coding YES CCDS4224.1 ENSP00000432016 UPI0000074448 NM_020690.5 tolerated(0.06) 9/36 Low_complexity_(Seg):seg,PROSITE_profiles:PS50297,hmmpanther:PTHR23206:SF5,hmmpanther:PTHR23206,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE SNV 2 1 PASS rs1336433967 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 140459193 140459193 A T 1 0 0 0 0 1 0 0 0 730 43 2 4 4 ANKHD1 5 140459193 Missense_Mutation SNP A C3N-00175_T 1992211 140459193 41079066 471 10063 PCDHA1 0 . GRCh38 5 140788080 140788080 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1790T>A p.Val597Glu p.V597E ENST00000504120 1/4 468 333 135 499 499 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Val597Glu,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Val597Glu,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript missense_variant 1790/5263 1790/2853 597/950 V/E gTg/gAg 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 140788080 140788080 T A 1 0 0 0 0 1 0 0 0 11606 1696 59 4 4 PCDHA1 5 140788080 Missense_Mutation SNP T C3N-00175_T 328887 140788080 40750179 472 10064 PCDHA3 0 . GRCh38 5 140801992 140801992 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.795C>T p.= p.N265N ENST00000522353 1/4 221 190 31 242 242 0 strelka-varscan-mutect PCDHA3,synonymous_variant,p.=,ENST00000522353,NM_018906.2;PCDHA3,synonymous_variant,p.=,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; T ENST00000522353 Transcript synonymous_variant 795/5260 795/2853 265/950 N aaC/aaT 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 140801992 140801992 C T 1 0 0 0 0 0 0 0 1 11612 535 19 1 1 PCDHA3 5 140801992 Silent SNP C C3N-00175_T 13912 140801992 40736267 473 10065 PCDHA3 0 . GRCh38 5 140802120 140802120 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.923T>A p.Ile308Lys p.I308K ENST00000522353 1/4 194 131 63 197 196 1 strelka-varscan-mutect PCDHA3,missense_variant,p.Ile308Lys,ENST00000522353,NM_018906.2;PCDHA3,missense_variant,p.Ile308Lys,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; A ENST00000522353 Transcript missense_variant 923/5260 923/2853 308/950 I/K aTa/aAa 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs924147913 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 140802120 140802120 T A 1 0 0 0 0 1 0 0 0 11612 1406 49 4 4 PCDHA3 5 140802120 Missense_Mutation SNP T C3N-00175_T 128 140802120 40736139 474 10066 PCDHA5 0 . GRCh38 5 140822297 140822297 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.522C>G p.Asn174Lys p.N174K ENST00000529859 1/4 197 171 26 233 233 0 strelka-varscan-mutect PCDHA5,missense_variant,p.Asn174Lys,ENST00000529859,NM_018908.2;PCDHA5,missense_variant,p.Asn174Lys,ENST00000614258,NM_031501.1;PCDHA5,missense_variant,p.Asn174Lys,ENST00000529619,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA4,intron_variant,,ENST00000512229,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,downstream_gene_variant,,ENST00000618834,NM_031500.2;AC005609.16,upstream_gene_variant,,ENST00000624712,; G ENST00000529859 Transcript missense_variant 522/5218 522/2811 174/936 N/K aaC/aaG 1 1 PCDHA5 HGNC HGNC:8671 protein_coding YES CCDS54917.1 ENSP00000436557 Q9Y5H7 UPI00001273CD NM_018908.2 deleterious_low_confidence(0.04) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 140822297 140822297 C G 1 0 0 0 0 1 0 0 0 11614 535 19 4 4 PCDHA5 5 140822297 Missense_Mutation SNP C C3N-00175_T 20177 140822297 40715962 475 10067 PCDHA7 0 . GRCh38 5 140836256 140836256 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1873G>T p.Gly625Trp p.G625W ENST00000525929 1/4 363 274 89 445 445 0 strelka-varscan-mutect PCDHA7,missense_variant,p.Gly625Trp,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Gly625Trp,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA8,upstream_gene_variant,,ENST00000378123,NM_031856.1; T ENST00000525929 Transcript missense_variant 1873/5221 1873/2814 625/937 G/W Ggg/Tgg 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 140836256 140836256 G T 1 0 0 0 0 1 0 0 0 11616 1232 43 2 2 PCDHA7 5 140836256 Missense_Mutation SNP G C3N-00175_T 13959 140836256 40702003 476 10068 PCDHB1 0 . GRCh38 5 141053597 141053597 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2127C>G p.Ile709Met p.I709M ENST00000306549 1/1 109 74 35 137 137 0 strelka-varscan-mutect PCDHB1,missense_variant,p.Ile709Met,ENST00000306549,NM_013340.3;CTC-270D5.1,intron_variant,,ENST00000624139,;CTC-270D5.1,intron_variant,,ENST00000624778,;CTC-270D5.1,intron_variant,,ENST00000623741,;CTC-270D5.1,downstream_gene_variant,,ENST00000623109,; G ENST00000306549 Transcript missense_variant 2463/8210 2127/2457 709/818 I/M atC/atG 1 1 PCDHB1 HGNC HGNC:8680 protein_coding YES CCDS4243.1 ENSP00000307234 Q9Y5F3 UPI000013EB56 NM_013340.3 deleterious(0) 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF12,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 141053597 141053597 C G 1 0 0 0 0 1 0 0 0 11621 903 32 4 4 PCDHB1 5 141053597 Missense_Mutation SNP C C3N-00175_T 217341 141053597 40484662 477 10069 PCDHB2 0 . GRCh38 5 141094905 141094905 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.115G>C p.Glu39Gln p.E39Q ENST00000194155 1/1 98 84 14 141 141 0 strelka-varscan-mutect PCDHB2,missense_variant,p.Glu39Gln,ENST00000194155,NM_018936.3;PCDHB2,intron_variant,,ENST00000622947,;PCDHB2,intron_variant,,ENST00000624874,;PCDHB2,intron_variant,,ENST00000625033,;PCDHB2,upstream_gene_variant,,ENST00000624994,;CTC-270D5.1,intron_variant,,ENST00000623741,;CTC-270D5.1,downstream_gene_variant,,ENST00000623615,; C ENST00000194155 Transcript missense_variant 328/4126 115/2397 39/798 E/Q Gag/Cag 1 1 PCDHB2 HGNC HGNC:8687 protein_coding YES CCDS4244.1 ENSP00000194155 Q9Y5E7 UPI00001273DC NM_018936.3 deleterious_low_confidence(0) 1/1 Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77 MODERATE 1 SNV 1 PASS rs1410328083 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 141094905 141094905 G C 1 0 0 0 0 1 0 0 0 11629 1059 37 4 4 PCDHB2 5 141094905 Missense_Mutation SNP G C3N-00175_T 41308 141094905 40443354 478 10070 PCDHB9 0 . GRCh38 5 141187814 141187814 + Missense_Mutation SNP A A T rs2910320 C3N-00175_T C3N-00175_N A A c.496A>T p.Ser166Cys p.S166C ENST00000316105 1/1 223 200 23 252 252 0 strelka-varscan-mutect PCDHB9,missense_variant,p.Ser166Cys,ENST00000316105,NM_019119.4;PCDHB9,intron_variant,,ENST00000624909,;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,intron_variant,,ENST00000623266,;CH17-140K24.5,intron_variant,,ENST00000623407,; T ENST00000316105 Transcript missense_variant 688/4415 496/2394 166/797 S/C Agt/Tgt rs2910320 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 deleterious_low_confidence(0.04) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS rs2910320 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 141187814 141187814 A T 1 0 0 0 0 1 0 0 0 11636 188 7 4 4 PCDHB9 5 141187814 Missense_Mutation SNP A C3N-00175_T 92909 141187814 40350445 479 10071 PCDHB12 0 . GRCh38 5 141210920 141210920 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.2013G>T p.= p.L671L ENST00000239450 1/1 365 314 51 365 365 0 strelka-varscan-mutect PCDHB12,synonymous_variant,p.=,ENST00000239450,NM_018932.3;PCDHB12,synonymous_variant,p.=,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239450 Transcript synonymous_variant 2202/3853 2013/2388 671/795 L ctG/ctT 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 141210920 141210920 G T 1 0 0 0 0 0 0 0 1 11624 1306 46 2 2 PCDHB12 5 141210920 Silent SNP G C3N-00175_T 23106 141210920 40327339 480 10072 PCDHB12 0 . GRCh38 5 141210981 141210981 + Missense_Mutation SNP G G T rs782607224 C3N-00175_T C3N-00175_N G G c.2074G>T p.Val692Leu p.V692L ENST00000239450 1/1 495 437 58 486 486 0 strelka-varscan-mutect PCDHB12,missense_variant,p.Val692Leu,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Val355Leu,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239450 Transcript missense_variant 2263/3853 2074/2388 692/795 V/L Gtg/Ttg rs782607224,COSM735994 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Pfam_domain:PF16492,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs782607224 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 141210981 141210981 G T 1 0 0 0 0 1 0 0 0 11624 1261 44 2 2 PCDHB12 5 141210981 Missense_Mutation SNP G C3N-00175_T 61 141210981 40327278 481 10073 PCDHGA3 0 . GRCh38 5 141346256 141346256 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.2223G>T p.= p.V741V ENST00000253812 1/4 510 359 151 515 515 0 strelka-varscan-mutect PCDHGA3,synonymous_variant,p.=,ENST00000253812,NM_018916.3;PCDHGA3,synonymous_variant,p.=,ENST00000619750,NM_032011.1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,upstream_gene_variant,,ENST00000523390,NM_018922.2;PCDHGA2,downstream_gene_variant,,ENST00000528330,NM_032009.2;PCDHGB1,upstream_gene_variant,,ENST00000611598,NM_032095.1;AC005618.8,downstream_gene_variant,,ENST00000625053,;PCDHGA3,3_prime_UTR_variant,,ENST00000612467,; T ENST00000253812 Transcript synonymous_variant 2389/4771 2223/2799 741/932 V gtG/gtT 1 1 PCDHGA3 HGNC HGNC:8701 protein_coding YES CCDS47290.1 ENSP00000253812 Q9Y5H0 UPI0000161C1A NM_018916.3 1/4 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 141346256 141346256 G T 1 0 0 0 0 0 0 0 1 11642 1335 47 2 2 PCDHGA3 5 141346256 Silent SNP G C3N-00175_T 135275 141346256 40192003 482 10074 PCDHGB4 0 . GRCh38 5 141389585 141389585 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1701C>A p.= p.P567P ENST00000519479 1/4 472 431 41 685 685 0 varscan-mutect PCDHGB4,synonymous_variant,p.=,ENST00000615384,NM_032098.1;PCDHGB4,synonymous_variant,p.=,ENST00000519479,NM_003736.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000519479 Transcript synonymous_variant 1701/4578 1701/2772 567/923 P ccC/ccA 1 1 PCDHGB4 HGNC HGNC:8711 protein_coding YES CCDS54928.1 ENSP00000428288 Q9UN71 UPI000006F773 NM_003736.2 1/4 hmmpanther:PTHR24028:SF117,hmmpanther:PTHR24028,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 141389585 141389585 C A 1 0 0 0 0 0 0 0 1 11652 639 23 1 1 PCDHGB4 5 141389585 Silent SNP C C3N-00175_T 43329 141389585 40148674 483 10075 GPR151 0 . GRCh38 5 146515710 146515710 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.404T>C p.Val135Ala p.V135A ENST00000311104 1/1 175 152 23 193 193 0 strelka-varscan-mutect GPR151,missense_variant,p.Val135Ala,ENST00000311104,NM_194251.2;TCERG1,downstream_gene_variant,,ENST00000296702,NM_006706.3;TCERG1,downstream_gene_variant,,ENST00000394421,NM_001040006.1;TCERG1,downstream_gene_variant,,ENST00000506524,;TCERG1,downstream_gene_variant,,ENST00000549332,;TCERG1,downstream_gene_variant,,ENST00000511077,; G ENST00000311104 Transcript missense_variant 481/3088 404/1260 135/419 V/A gTa/gCa 1 -1 GPR151 HGNC HGNC:23624 protein_coding YES CCDS34266.1 ENSP00000308733 Q8TDV0 UPI000003BCC7 NM_194251.2 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF1,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 146515710 146515710 A G 1 0 0 0 0 1 0 0 0 6543 391 14 5 5 GPR151 5 146515710 Missense_Mutation SNP A C3N-00175_T 5126125 146515710 35022549 484 10076 DPYSL3 0 . GRCh38 5 147413642 147413642 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.836T>G p.Met279Arg p.M279R ENST00000343218 5/14 145 128 17 145 145 0 strelka-varscan-mutect DPYSL3,missense_variant,p.Met279Arg,ENST00000343218,NM_001197294.1;DPYSL3,missense_variant,p.Met165Arg,ENST00000398514,NM_001387.2;DPYSL3,downstream_gene_variant,,ENST00000512722,;DPYSL3,non_coding_transcript_exon_variant,,ENST00000519672,;DPYSL3,intron_variant,,ENST00000507309,; C ENST00000343218 Transcript missense_variant 1034/5476 836/2055 279/684 M/R aTg/aGg 1 -1 DPYSL3 HGNC HGNC:3015 protein_coding YES CCDS56387.1 ENSP00000343690 Q14195 A0A140VK07 UPI000020CF0E NM_001197294.1 tolerated(0.52) 5/14 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF57,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS rs1368258730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 147413642 147413642 A C 1 0 0 0 0 1 0 0 0 4563 217 8 5 5 DPYSL3 5 147413642 Missense_Mutation SNP A C3N-00175_T 897932 147413642 34124617 485 10077 NDST1 0 . GRCh38 5 150528029 150528029 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.739G>C p.Glu247Gln p.E247Q ENST00000261797 3/15 137 121 16 145 145 0 strelka-varscan-mutect NDST1,missense_variant,p.Glu247Gln,ENST00000261797,NM_001543.4;NDST1,missense_variant,p.Glu247Gln,ENST00000523767,NM_001301063.1; C ENST00000261797 Transcript missense_variant 1241/8030 739/2649 247/882 E/Q Gag/Cag 1 1 NDST1 HGNC HGNC:7680 protein_coding YES CCDS34277.1 ENSP00000261797 P52848 UPI000012CDA5 NM_001543.4 tolerated(0.14) 3/15 Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 150528029 150528029 G C 1 0 0 0 0 1 0 0 0 10276 1291 45 4 4 NDST1 5 150528029 Missense_Mutation SNP G C3N-00175_T 3114387 150528029 31010230 486 10078 TNIP1 0 . GRCh38 5 151062129 151062129 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.355A>T p.Ser119Cys p.S119C ENST00000315050 4/18 189 121 68 187 186 1 strelka-varscan-mutect TNIP1,missense_variant,p.Ser119Cys,ENST00000389378,NM_001252385.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000315050,NM_001252391.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000610535,NM_001258455.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000523338,NM_001252392.1;TNIP1,missense_variant,p.Ser66Cys,ENST00000520931,NM_001252386.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000610874,NM_001258456.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000521591,NM_006058.4,NM_001258454.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000522226,NM_001252390.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000518977,NM_001252393.1;TNIP1,missense_variant,p.Ser119Cys,ENST00000523200,;TNIP1,missense_variant,p.Ser119Cys,ENST00000524280,;TNIP1,missense_variant,p.Ser66Cys,ENST00000522100,;TNIP1,missense_variant,p.Ser119Cys,ENST00000520695,;TNIP1,missense_variant,p.Ser119Cys,ENST00000521001,;TNIP1,missense_variant,p.Ser66Cys,ENST00000519339,; A ENST00000315050 Transcript missense_variant,splice_region_variant 465/2785 355/1911 119/636 S/C Agt/Tgt 1 -1 TNIP1 HGNC HGNC:16903 protein_coding YES CCDS34280.1 ENSP00000317891 Q15025 UPI000000DCDC NM_001252391.1 deleterious(0.02) 4/18 hmmpanther:PTHR31882,hmmpanther:PTHR31882:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 151062129 151062129 T A 1 0 0 0 0 1 0 0 0 16787 1594 55 4 4 TNIP1 5 151062129 Missense_Mutation SNP T C3N-00175_T 534100 151062129 30476130 487 10079 GEMIN5 0 . GRCh38 5 154911877 154911877 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2017G>C p.Glu673Gln p.E673Q ENST00000285873 15/28 116 101 15 142 142 0 strelka-varscan-mutect GEMIN5,missense_variant,p.Glu673Gln,ENST00000285873,NM_001252156.1,NM_015465.4; G ENST00000285873 Transcript missense_variant 2093/5397 2017/4527 673/1508 E/Q Gag/Cag 1 -1 GEMIN5 HGNC HGNC:20043 protein_coding YES CCDS4330.1 ENSP00000285873 Q8TEQ6 UPI000020D072 NM_001252156.1,NM_015465.4 tolerated(0.07) 15/28 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF89,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 154911877 154911877 C G 1 0 0 0 0 1 0 0 0 6205 922 32 4 4 GEMIN5 5 154911877 Missense_Mutation SNP C C3N-00175_T 3849748 154911877 26626382 488 10080 GEMIN5 0 . GRCh38 5 154921369 154921369 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1436G>C p.Gly479Ala p.G479A ENST00000285873 10/28 144 122 22 148 148 0 strelka-varscan-mutect GEMIN5,missense_variant,p.Gly479Ala,ENST00000285873,NM_001252156.1,NM_015465.4; G ENST00000285873 Transcript missense_variant 1512/5397 1436/4527 479/1508 G/A gGg/gCg 1 -1 GEMIN5 HGNC HGNC:20043 protein_coding YES CCDS4330.1 ENSP00000285873 Q8TEQ6 UPI000020D072 NM_001252156.1,NM_015465.4 deleterious(0) 10/28 Gene3D:2.130.10.10,Pfam_domain:PF12894,PROSITE_profiles:PS50294,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 154921369 154921369 C G 1 0 0 0 0 1 0 0 0 6205 623 22 4 4 GEMIN5 5 154921369 Missense_Mutation SNP C C3N-00175_T 9492 154921369 26616890 489 10081 PPP1R2P3 0 . GRCh38 5 156850780 156850780 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.218C>A p.Pro73His p.P73H ENST00000522232 1/1 473 409 64 477 476 1 strelka-varscan-mutect PPP1R2P3,missense_variant,p.Pro73His,ENST00000522232,; A ENST00000522232 Transcript missense_variant 243/1991 218/618 73/205 P/H cCt/cAt 1 1 PPP1R2P3 HGNC HGNC:16318 protein_coding YES ENSP00000490297 G1AUC5 UPI000013EC9E 1/1 Pfam_domain:PF04979,hmmpanther:PTHR12398,hmmpanther:PTHR12398:SF23 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 156850780 156850780 C A 1 0 0 0 0 1 0 0 0 12486 681 24 2 2 PPP1R2P3 5 156850780 Missense_Mutation SNP C C3N-00175_T 1929411 156850780 24687479 490 10082 PPP1R2P3 0 . GRCh38 5 156851151 156851151 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.589C>A p.Gln197Lys p.Q197K ENST00000522232 1/1 194 162 32 301 300 1 strelka-varscan-mutect PPP1R2P3,missense_variant,p.Gln197Lys,ENST00000522232,; A ENST00000522232 Transcript missense_variant 614/1991 589/618 197/205 Q/K Caa/Aaa 1 1 PPP1R2P3 HGNC HGNC:16318 protein_coding YES ENSP00000490297 G1AUC5 UPI000013EC9E 1/1 hmmpanther:PTHR12398,hmmpanther:PTHR12398:SF23 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 156851151 156851151 C A 1 0 0 0 0 1 0 0 0 12486 595 21 2 2 PPP1R2P3 5 156851151 Missense_Mutation SNP C C3N-00175_T 371 156851151 24687108 491 10083 ADAM19 0 . GRCh38 5 157488285 157488285 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.2530C>G p.Pro844Ala p.P844A ENST00000257527 21/23 74 62 12 90 90 0 strelka-varscan-mutect ADAM19,missense_variant,p.Pro844Ala,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Pro844Ala,ENST00000517905,;ADAM19,missense_variant,p.Pro415Ala,ENST00000517374,;ADAM19,3_prime_UTR_variant,,ENST00000517951,; C ENST00000257527 Transcript missense_variant 2609/6481 2530/2757 844/918 P/A Cca/Gca 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 deleterious(0.03) 21/23 Low_complexity_(Seg):seg,hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 157488285 157488285 G C 1 0 0 0 0 1 0 0 0 284 1261 44 4 4 ADAM19 5 157488285 Missense_Mutation SNP G C3N-00175_T 637134 157488285 24049974 492 10084 ADAM19 0 . GRCh38 5 157509301 157509301 + Missense_Mutation SNP G G C rs775973204 C3N-00175_T C3N-00175_N G G c.905C>G p.Thr302Arg p.T302R ENST00000257527 9/23 66 59 7 66 66 0 strelka-varscan-mutect ADAM19,missense_variant,p.Thr302Arg,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Thr302Arg,ENST00000517905,;ADAM19,splice_region_variant,,ENST00000517951,; C ENST00000257527 Transcript missense_variant,splice_region_variant 984/6481 905/2757 302/918 T/R aCg/aGg rs775973204 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 deleterious(0) 9/23 PROSITE_profiles:PS50215,hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs775973204 . 0 204 6 0 0 0 0 0 -15.75242 0.9999999 1 1 1 0 C 3 2 39 157509301 157509301 G C 1 0 0 0 0 1 0 0 0 284 1159 40 4 4 ADAM19 5 157509301 Missense_Mutation SNP G C3N-00175_T 21016 157509301 24028958 493 10085 LSM11 0 . GRCh38 5 157743780 157743780 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.30G>T p.= p.S10S ENST00000286307 1/4 44 38 6 46 46 0 strelka-varscan-mutect LSM11,synonymous_variant,p.=,ENST00000286307,NM_173491.3;THG1L,downstream_gene_variant,,ENST00000231198,NM_001317825.1,NM_017872.3;THG1L,downstream_gene_variant,,ENST00000521655,;THG1L,downstream_gene_variant,,ENST00000523575,;CTC-370J7.1,downstream_gene_variant,,ENST00000518369,; T ENST00000286307 Transcript synonymous_variant 86/6584 30/1083 10/360 S tcG/tcT COSM5645496 1 1 LSM11 HGNC HGNC:30860 protein_coding YES CCDS4342.1 ENSP00000286307 P83369 UPI0000072830 NM_173491.3 1/4 Low_complexity_(Seg):seg 1 LOW 1 SNV 1 1 1 PASS rs1198522938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 157743780 157743780 G T 1 0 0 0 0 0 0 0 1 8958 1103 39 1 1 LSM11 5 157743780 Silent SNP G C3N-00175_T 234479 157743780 23794479 494 10086 PWWP2A 0 . GRCh38 5 160092615 160092615 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.2035A>T p.Ser679Cys p.S679C ENST00000307063 2/2 141 102 39 152 152 0 strelka-varscan-mutect PWWP2A,missense_variant,p.Ser679Cys,ENST00000307063,NM_001130864.1;PWWP2A,intron_variant,,ENST00000456329,NM_052927.2;PWWP2A,intron_variant,,ENST00000523662,NM_001267035.1;PWWP2A,intron_variant,,ENST00000524050,;PWWP2A,intron_variant,,ENST00000521424,;PWWP2A,downstream_gene_variant,,ENST00000520662,; A ENST00000307063 Transcript missense_variant 2070/3346 2035/2268 679/755 S/C Agc/Tgc 1 -1 PWWP2A HGNC HGNC:29406 protein_coding YES CCDS47332.1 ENSP00000305151 Q96N64 UPI0000EE3692 NM_001130864.1 deleterious(0) 2/2 PROSITE_profiles:PS50812,hmmpanther:PTHR23068,hmmpanther:PTHR23068:SF4,Gene3D:2.30.30.160,Pfam_domain:PF00855,SMART_domains:SM00293,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 160092615 160092615 T A 1 0 0 0 0 1 0 0 0 12998 1551 54 4 4 PWWP2A 5 160092615 Missense_Mutation SNP T C3N-00175_T 2348835 160092615 21445644 495 10087 ZBED8 0 . GRCh38 5 160394967 160394967 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.524A>C p.Gln175Pro p.Q175P ENST00000408953 2/2 215 193 22 238 238 0 strelka-varscan-mutect ZBED8,missense_variant,p.Gln175Pro,ENST00000408953,NM_022090.4;ZBED8,missense_variant,p.Gln175Pro,ENST00000523213,NM_001303251.1; G ENST00000408953 Transcript missense_variant 1032/2851 524/1785 175/594 Q/P cAg/cCg 1 -1 ZBED8 HGNC HGNC:30804 protein_coding YES CCDS34283.1 ENSP00000386184 Q8IZ13 UPI00000741A3 NM_022090.4 deleterious(0) 2/2 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF102 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 160394967 160394967 T G 1 0 0 0 0 1 0 0 0 18085 1580 55 5 5 ZBED8 5 160394967 Missense_Mutation SNP T C3N-00175_T 302352 160394967 21143292 496 10088 SLU7 0 . GRCh38 5 160413552 160413552 + Silent SNP T T C C3N-00175_T C3N-00175_N T T c.474A>G p.= p.Q158Q ENST00000297151 5/16 148 108 40 194 194 0 strelka-varscan-mutect SLU7,synonymous_variant,p.=,ENST00000297151,NM_006425.4;SLU7,downstream_gene_variant,,ENST00000520664,;SLU7,downstream_gene_variant,,ENST00000519349,;SLU7,downstream_gene_variant,,ENST00000521826,;SLU7,downstream_gene_variant,,ENST00000518268,;SLU7,downstream_gene_variant,,ENST00000521190,; C ENST00000297151 Transcript synonymous_variant 862/3793 474/1761 158/586 Q caA/caG COSM1754162 1 -1 SLU7 HGNC HGNC:16939 protein_coding YES CCDS4352.1 ENSP00000297151 O95391 UPI000013E3CE NM_006425.4 5/16 hmmpanther:PTHR12942,hmmpanther:PTHR12942:SF2 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 160413552 160413552 T C 1 0 0 0 0 0 0 0 1 15044 1722 60 5 5 SLU7 5 160413552 Silent SNP T C3N-00175_T 18585 160413552 21124707 497 10089 PTTG1 0 . GRCh38 5 160422782 160422782 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.165C>T p.= p.A55A ENST00000393964 2/5 271 207 64 335 335 0 strelka-varscan-mutect PTTG1,synonymous_variant,p.=,ENST00000393964,NM_001282382.1;PTTG1,synonymous_variant,p.=,ENST00000520452,NM_001282383.1;PTTG1,synonymous_variant,p.=,ENST00000352433,NM_004219.3;PTTG1,synonymous_variant,p.=,ENST00000517480,;SLU7,upstream_gene_variant,,ENST00000297151,NM_006425.4;SLU7,upstream_gene_variant,,ENST00000520664,;SLU7,upstream_gene_variant,,ENST00000519349,;SLU7,upstream_gene_variant,,ENST00000521826,;PTTG1,non_coding_transcript_exon_variant,,ENST00000519287,;PTTG1,non_coding_transcript_exon_variant,,ENST00000523659,;PTTG1,non_coding_transcript_exon_variant,,ENST00000524244,;SLU7,upstream_gene_variant,,ENST00000518268,;SLU7,upstream_gene_variant,,ENST00000521190,; T ENST00000393964 Transcript synonymous_variant 568/1070 165/609 55/202 A gcC/gcT 1 1 PTTG1 HGNC HGNC:9690 protein_coding YES CCDS4353.1 ENSP00000377536 O95997 Q6IAL9 UPI0000044DCB NM_001282382.1 2/5 hmmpanther:PTHR10418,hmmpanther:PTHR10418:SF1,Pfam_domain:PF04856 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 160422782 160422782 C T 1 0 0 0 0 0 0 0 1 12975 668 24 3 3 PTTG1 5 160422782 Silent SNP C C3N-00175_T 9230 160422782 21115477 498 10090 TENM2 0 . GRCh38 5 167952789 167952789 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.914G>C p.Trp305Ser p.W305S ENST00000518659 4/29 185 119 66 210 210 0 strelka-varscan-mutect TENM2,missense_variant,p.Trp184Ser,ENST00000519204,;TENM2,missense_variant,p.Trp305Ser,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Trp114Ser,ENST00000520394,;CTC-353G13.1,intron_variant,,ENST00000523050,;TENM2,non_coding_transcript_exon_variant,,ENST00000518693,;TENM2,non_coding_transcript_exon_variant,,ENST00000520393,;TENM2,downstream_gene_variant,,ENST00000517586,;TENM2,non_coding_transcript_exon_variant,,ENST00000522488,; C ENST00000518659 Transcript missense_variant 953/8550 914/8325 305/2774 W/S tGg/tCg 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 4/29 PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Pfam_domain:PF06484 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 167952789 167952789 G C 1 0 0 0 0 1 0 0 0 16172 1357 47 4 4 TENM2 5 167952789 Missense_Mutation SNP G C3N-00175_T 7530007 167952789 13585470 499 10091 TENM2 0 . GRCh38 5 168190449 168190449 + Silent SNP G G T rs763280815 C3N-00175_T C3N-00175_N G G c.2682G>T p.= p.T894T ENST00000518659 14/29 240 225 15 282 282 0 strelka-varscan-mutect TENM2,synonymous_variant,p.=,ENST00000519204,;TENM2,synonymous_variant,p.=,ENST00000518659,NM_001122679.1;TENM2,synonymous_variant,p.=,ENST00000520394,;CTB-178M22.1,upstream_gene_variant,,ENST00000517408,;TENM2,non_coding_transcript_exon_variant,,ENST00000521126,; T ENST00000518659 Transcript synonymous_variant 2721/8550 2682/8325 894/2774 T acG/acT rs763280815,COSM289884,COSM289885,COSM5071864,COSM5071865 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 14/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 0,1,1,1,1 LOW SNV 5 0,1,1,1,1 1 PASS rs763280815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 168190449 168190449 G T 1 0 0 0 0 0 0 0 1 16172 1103 39 1 1 TENM2 5 168190449 Silent SNP G C3N-00175_T 237660 168190449 13347810 500 10092 DOCK2 0 . GRCh38 5 170008704 170008704 + Silent SNP C C A rs772417044 C3N-00175_T C3N-00175_N C C c.3190C>A p.= p.R1064R ENST00000256935 32/52 270 236 34 286 285 1 strelka-varscan-mutect DOCK2,synonymous_variant,p.=,ENST00000256935,NM_004946.2;DOCK2,synonymous_variant,p.=,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,intron_variant,,ENST00000433448,; A ENST00000256935 Transcript synonymous_variant 3270/6097 3190/5493 1064/1830 R Cgg/Agg rs772417044,COSM3853625 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 32/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Superfamily_domains:SSF48371 0,1 LOW 1 SNV 1 0,1 1 PASS rs772417044 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 170008704 170008704 C A 1 0 0 0 0 0 0 0 1 4502 527 19 1 1 DOCK2 5 170008704 Silent SNP C C3N-00175_T 1818255 170008704 11529555 501 10093 TLX3 0 . GRCh38 5 171310358 171310358 + Silent SNP C C G rs780540255 C3N-00175_T C3N-00175_N C C c.630C>G p.= p.V210V ENST00000296921 2/3 212 188 24 257 257 0 strelka-varscan-mutect TLX3,synonymous_variant,p.=,ENST00000296921,NM_021025.2;RP11-546B8.6,upstream_gene_variant,,ENST00000619056,; G ENST00000296921 Transcript synonymous_variant 712/1493 630/876 210/291 V gtC/gtG rs780540255 1 1 TLX3 HGNC HGNC:13532 protein_coding YES CCDS34288.1 ENSP00000296921 O43711 UPI000013E3AA NM_021025.2 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,Prints_domain:PR00024,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF154,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS rs780540255 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 171310358 171310358 C G 1 0 0 0 0 0 0 0 1 16407 813 29 4 4 TLX3 5 171310358 Silent SNP C C3N-00175_T 1301654 171310358 10227901 502 10094 FGF18 0 . GRCh38 5 171449161 171449161 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.265G>C p.Glu89Gln p.E89Q ENST00000274625 4/5 225 157 68 220 220 0 strelka-varscan-mutect FGF18,missense_variant,p.Glu89Gln,ENST00000274625,NM_003862.2; C ENST00000274625 Transcript missense_variant 809/1986 265/624 89/207 E/Q Gag/Cag COSM1620051 1 1 FGF18 HGNC HGNC:3674 protein_coding YES CCDS4378.1 ENSP00000274625 O76093 UPI000003C116 NM_003862.2 deleterious(0) 4/5 Gene3D:2.80.10.50,Pfam_domain:PF00167,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF4,SMART_domains:SM00442,Superfamily_domains:SSF50353 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 171449161 171449161 G C 1 0 0 0 0 1 0 0 0 5710 1175 41 4 4 FGF18 5 171449161 Missense_Mutation SNP G C3N-00175_T 138803 171449161 10089098 503 10095 STK10 0 . GRCh38 5 172105697 172105697 + Nonsense_Mutation SNP T T A rs757545210 C3N-00175_T C3N-00175_N T T c.829A>T p.Lys277Ter p.K277* ENST00000176763 7/19 168 126 42 236 235 1 strelka-varscan-mutect STK10,stop_gained,p.Lys277Ter,ENST00000176763,NM_005990.3;STK10,non_coding_transcript_exon_variant,,ENST00000522936,;STK10,downstream_gene_variant,,ENST00000517381,;STK10,downstream_gene_variant,,ENST00000518267,;STK10,downstream_gene_variant,,ENST00000519710,;STK10,non_coding_transcript_exon_variant,,ENST00000517524,;STK10,non_coding_transcript_exon_variant,,ENST00000517527,;STK10,downstream_gene_variant,,ENST00000521322,;STK10,downstream_gene_variant,,ENST00000519441,; A ENST00000176763 Transcript stop_gained 1173/6060 829/2907 277/968 K/* Aag/Tag rs757545210,COSM13171 1 -1 STK10 HGNC HGNC:11388 protein_coding YES CCDS34290.1 ENSP00000176763 O94804 UPI0000136104 NM_005990.3 7/19 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF195,hmmpanther:PTHR24361,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 HIGH 1 SNV 1 0,1 1 PASS rs757545210 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 172105697 172105697 T A 1 0 0 0 0 0 1 0 0 15663 1763 61 4 4 STK10 5 172105697 Nonsense_Mutation SNP T C3N-00175_T 656536 172105697 9432562 504 10096 HMP19 0 . GRCh38 5 174104246 174104246 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.232C>A p.Leu78Met p.L78M ENST00000303177 4/5 206 143 63 191 191 0 strelka-varscan-mutect HMP19,missense_variant,p.Leu78Met,ENST00000303177,NM_015980.4;HMP19,missense_variant,p.Leu78Met,ENST00000519867,;HMP19,missense_variant,p.Leu78Met,ENST00000519717,;HMP19,missense_variant,p.Leu78Met,ENST00000521278,;HMP19,intron_variant,,ENST00000521585,;HMP19,non_coding_transcript_exon_variant,,ENST00000521959,;HMP19,non_coding_transcript_exon_variant,,ENST00000521146,;HMP19,3_prime_UTR_variant,,ENST00000517587,; A ENST00000303177 Transcript missense_variant 494/2452 232/516 78/171 L/M Ctg/Atg 1 1 HMP19 EntrezGene protein_coding YES CCDS4391.1 ENSP00000307722 Q9Y328 UPI000013054B NM_015980.4 tolerated(0.07) 4/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR28546,PIRSF_domain:PIRSF002383,Pfam_domain:PF06387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 174104246 174104246 C A 1 0 0 0 0 1 0 0 0 7136 680 24 2 2 HMP19 5 174104246 Missense_Mutation SNP C C3N-00175_T 1998549 174104246 7434013 505 10097 DRD1 0 . GRCh38 5 175442494 175442494 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.606C>A p.Ser202Arg p.S202R ENST00000393752 2/2 204 178 26 260 260 0 strelka-varscan-mutect DRD1,missense_variant,p.Ser202Arg,ENST00000393752,NM_000794.3; T ENST00000393752 Transcript missense_variant 1599/4054 606/1341 202/446 S/R agC/agA 1 -1 DRD1 HGNC HGNC:3020 protein_coding YES CCDS4393.1 ENSP00000377353 P21728 UPI00000503F5 NM_000794.3 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF221,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 175442494 175442494 G T 1 0 0 0 0 1 0 0 0 4575 962 34 2 2 DRD1 5 175442494 Missense_Mutation SNP G C3N-00175_T 1338248 175442494 6095765 506 10098 CDHR2 0 . GRCh38 5 176584885 176584885 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.2605delG p.Ala869ArgfsTer31 p.A869Rfs*31 ENST00000510636 19/32 255 171 84 339 339 0 sindel-varindel-pindel CDHR2,frameshift_variant,p.Ala869ArgfsTer31,ENST00000510636,NM_001171976.1;CDHR2,frameshift_variant,p.Ala869ArgfsTer31,ENST00000261944,NM_017675.4;CDHR2,frameshift_variant,p.Ala869ArgfsTer31,ENST00000506348,;CDHR2,upstream_gene_variant,,ENST00000513031,;CDHR2,upstream_gene_variant,,ENST00000508085,; - ENST00000510636 Transcript frameshift_variant 2878/4509 2604/3933 868/1310 V/X gtG/gt 1 1 CDHR2 HGNC HGNC:18231 protein_coding YES CCDS34297.1 ENSP00000424565 Q9BYE9 UPI0000DBEE8C NM_001171976.1 19/32 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF312,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 176584885 176584885 G - 1 0 1 0 1 0 0 0 0 2822 1335 47 0 0 CDHR2 5 176584885 Frame_Shift_Del DEL G C3N-00175_T 1142391 176584885 4953374 507 10099 PDLIM7 0 . GRCh38 5 177484116 177484116 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1125G>T p.= p.R375R ENST00000355841 11/13 164 145 19 283 282 1 strelka-varscan-mutect PDLIM7,synonymous_variant,p.=,ENST00000355841,NM_005451.4;PDLIM7,synonymous_variant,p.=,ENST00000359895,NM_203352.2;PDLIM7,downstream_gene_variant,,ENST00000393551,;PDLIM7,non_coding_transcript_exon_variant,,ENST00000505746,;RP11-1334A24.5,upstream_gene_variant,,ENST00000623593,;PDLIM7,3_prime_UTR_variant,,ENST00000486828,;PDLIM7,3_prime_UTR_variant,,ENST00000493815,;PDLIM7,non_coding_transcript_exon_variant,,ENST00000504380,; A ENST00000355841 Transcript synonymous_variant 1192/1689 1125/1374 375/457 R cgG/cgT 1 -1 PDLIM7 HGNC HGNC:22958 protein_coding YES CCDS4422.1 ENSP00000348099 Q9NR12 UPI0000073DEF NM_005451.4 11/13 PROSITE_profiles:PS50023,hmmpanther:PTHR24214:SF0,hmmpanther:PTHR24214,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 177484116 177484116 C A 1 0 0 0 0 0 0 0 1 11772 842 30 2 2 PDLIM7 5 177484116 Silent SNP C C3N-00175_T 899231 177484116 4054143 508 10100 TBC1D9B 0 . GRCh38 5 179875004 179875004 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2084G>T p.Gly695Val p.G695V ENST00000356834 12/22 402 299 103 476 473 3 strelka-varscan-mutect TBC1D9B,missense_variant,p.Gly695Val,ENST00000356834,NM_198868.2;TBC1D9B,missense_variant,p.Gly695Val,ENST00000355235,NM_015043.3;TBC1D9B,intron_variant,,ENST00000524222,;TBC1D9B,intron_variant,,ENST00000522472,;TBC1D9B,upstream_gene_variant,,ENST00000519746,;TBC1D9B,upstream_gene_variant,,ENST00000522180,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000518459,;TBC1D9B,upstream_gene_variant,,ENST00000521469,;TBC1D9B,upstream_gene_variant,,ENST00000520912,;TBC1D9B,upstream_gene_variant,,ENST00000519757,;TBC1D9B,upstream_gene_variant,,ENST00000521669,;TBC1D9B,upstream_gene_variant,,ENST00000522921,;TBC1D9B,downstream_gene_variant,,ENST00000518115,; A ENST00000356834 Transcript missense_variant 2122/5173 2084/3753 695/1250 G/V gGc/gTc 1 -1 TBC1D9B HGNC HGNC:29097 protein_coding YES CCDS43408.1 ENSP00000349291 Q66K14 UPI000034ECFF NM_198868.2 deleterious(0) 12/22 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF225,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS rs1338587332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 179875004 179875004 C A 1 0 0 0 0 1 0 0 0 16033 739 26 2 2 TBC1D9B 5 179875004 Missense_Mutation SNP C C3N-00175_T 2390888 179875004 1663255 509 10101 RASGEF1C 0 . GRCh38 5 180128449 180128449 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.600C>T p.= p.D200D ENST00000393371 4/13 321 220 101 386 386 0 strelka-varscan-mutect RASGEF1C,synonymous_variant,p.=,ENST00000393371,;RASGEF1C,synonymous_variant,p.=,ENST00000615330,;RASGEF1C,synonymous_variant,p.=,ENST00000361132,NM_175062.3;RASGEF1C,synonymous_variant,p.=,ENST00000522500,;RASGEF1C,non_coding_transcript_exon_variant,,ENST00000519883,;RASGEF1C,synonymous_variant,p.=,ENST00000520209,; A ENST00000393371 Transcript synonymous_variant 897/2395 600/1401 200/466 D gaC/gaT 1 -1 RASGEF1C HGNC HGNC:27400 protein_coding YES CCDS4452.1 ENSP00000377037 Q8N431 UPI0000037308 4/13 PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF186,Gene3D:2ii0A01,SMART_domains:SM00147,Superfamily_domains:0041591 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 180128449 180128449 G A 1 0 0 0 0 0 0 0 1 13232 1252 44 3 3 RASGEF1C 5 180128449 Silent SNP G C3N-00175_T 253445 180128449 1409810 510 10102 BTNL8 0 . GRCh38 5 180908707 180908707 + Silent SNP G G A rs762655217 C3N-00175_T C3N-00175_N G G c.171G>A p.= p.R57R ENST00000340184 2/8 324 232 92 403 403 0 strelka-varscan-mutect BTNL8,synonymous_variant,p.=,ENST00000231229,NM_024850.2;BTNL8,synonymous_variant,p.=,ENST00000340184,NM_001040462.2;BTNL8,synonymous_variant,p.=,ENST00000508408,NM_001159708.1;BTNL8,intron_variant,,ENST00000400707,NM_001159709.1;BTNL8,intron_variant,,ENST00000610640,;BTNL8,intron_variant,,ENST00000511704,NM_001159707.1;BTNL8,upstream_gene_variant,,ENST00000533815,NM_001159710.1;BTNL8,upstream_gene_variant,,ENST00000505126,;Y_RNA,upstream_gene_variant,,ENST00000410920,;BTNL8,upstream_gene_variant,,ENST00000514448,;BTNL8,upstream_gene_variant,,ENST00000513442,;BTNL8,upstream_gene_variant,,ENST00000503543,; A ENST00000340184 Transcript synonymous_variant 377/2071 171/1503 57/500 R agG/agA rs762655217 1 1 BTNL8 HGNC HGNC:26131 protein_coding YES CCDS43413.1 ENSP00000342197 Q6UX41 UPI00000389ED NM_001040462.2 2/8 hmmpanther:PTHR24100:SF73,hmmpanther:PTHR24100,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs762655217 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 180908707 180908707 G A 1 0 0 0 0 0 0 0 1 1743 1223 43 3 3 BTNL8 5 180908707 Silent SNP G C3N-00175_T 780258 180908707 629552 511 10103 BTNL3 0 . GRCh38 5 181005462 181005462 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.991G>T p.Val331Leu p.V331L ENST00000342868 8/8 312 273 39 328 328 0 varscan-mutect BTNL3,missense_variant,p.Val331Leu,ENST00000342868,NM_197975.2;RNU6-1036P,upstream_gene_variant,,ENST00000383959,; T ENST00000342868 Transcript missense_variant 1175/2440 991/1401 331/466 V/L Gtg/Ttg 1 1 BTNL3 HGNC HGNC:1143 protein_coding YES CCDS47358.1 ENSP00000341787 Q6UXE8 UPI00001D69EF NM_197975.2 tolerated(0.2) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24100:SF69,hmmpanther:PTHR24100,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 181005462 181005462 G T 1 0 0 0 0 1 0 0 0 1742 1261 44 2 2 BTNL3 5 181005462 Missense_Mutation SNP G C3N-00175_T 96755 181005462 532797 512 10104 LYRM4 0 . GRCh38 6 5186946 5186946 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.242A>T p.His81Leu p.H81L ENST00000500576 3/3 17 11 6 13 13 0 varscan-mutect LYRM4,missense_variant,p.His81Leu,ENST00000500576,NM_001164840.2;LYRM4,intron_variant,,ENST00000330636,NM_020408.5;LYRM4,intron_variant,,ENST00000464010,NM_001164841.2;LYRM4,intron_variant,,ENST00000468929,;LYRM4,intron_variant,,ENST00000480566,;LYRM4,intron_variant,,ENST00000463032,; A ENST00000500576 Transcript missense_variant 246/592 242/393 81/130 H/L cAt/cTt 1 -1 LYRM4 HGNC HGNC:21365 protein_coding YES CCDS54962.1 ENSP00000443900 F5H189 UPI0001B71BCB NM_001164840.2 deleterious(0.02) 3/3 hmmpanther:PTHR16213 MODERATE 1 SNV 2 1 PASS . . 4 204 2 0 0 0 0 0 -18.50838 1 1 1 1 0 A 3 1 39 5186946 5186946 T A 1 0 0 0 0 1 0 0 0 9033 1464 51 4 4 LYRM4 6 5186946 Missense_Mutation SNP T C3N-00175_T 5186946 165619033 513 10105 DSP 0 . GRCh38 6 7567792 7567792 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1152G>T p.Glu384Asp p.E384D ENST00000379802 10/24 440 331 109 501 501 0 strelka-varscan-mutect DSP,missense_variant,p.Glu384Asp,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Glu384Asp,ENST00000418664,NM_001008844.1;DSP,downstream_gene_variant,,ENST00000506617,; T ENST00000379802 Transcript missense_variant 1493/9796 1152/8616 384/2871 E/D gaG/gaT 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 tolerated(0.56) 10/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs1468028182 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 7567792 7567792 G T 1 0 0 0 0 1 0 0 0 4602 991 35 2 2 DSP 6 7567792 Missense_Mutation SNP G C3N-00175_T 2380846 7567792 163238187 514 10106 BMP6 0 . GRCh38 6 7727128 7727128 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.173C>G p.Pro58Arg p.P58R ENST00000283147 1/7 132 92 40 150 150 0 strelka-varscan-mutect BMP6,missense_variant,p.Pro58Arg,ENST00000283147,NM_001718.4; G ENST00000283147 Transcript missense_variant 332/2780 173/1542 58/513 P/R cCg/cGg 1 1 BMP6 HGNC HGNC:1073 protein_coding YES CCDS4503.1 ENSP00000283147 P22004 UPI0000126A2D NM_001718.4 tolerated_low_confidence(0.07) 1/7 Low_complexity_(Seg):seg,hmmpanther:PTHR11848:SF137,hmmpanther:PTHR11848 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 7727128 7727128 C G 1 0 0 0 0 1 0 0 0 1619 652 23 4 4 BMP6 6 7727128 Missense_Mutation SNP C C3N-00175_T 159336 7727128 163078851 515 10107 DTNBP1 0 . GRCh38 6 15627371 15627371 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.327A>G p.= p.A109A ENST00000344537 5/10 368 286 82 355 355 0 strelka-varscan-mutect DTNBP1,synonymous_variant,p.=,ENST00000338950,NM_183040.2;DTNBP1,synonymous_variant,p.=,ENST00000344537,NM_032122.4;DTNBP1,synonymous_variant,p.=,ENST00000355917,NM_001271667.1,NM_001271668.1;DTNBP1,synonymous_variant,p.=,ENST00000622898,NM_001271669.1;DTNBP1,synonymous_variant,p.=,ENST00000511762,;DTNBP1,synonymous_variant,p.=,ENST00000515875,;DTNBP1,3_prime_UTR_variant,,ENST00000506844,;DTNBP1,3_prime_UTR_variant,,ENST00000513680,;DTNBP1,3_prime_UTR_variant,,ENST00000510395,; C ENST00000344537 Transcript synonymous_variant 500/1403 327/1056 109/351 A gcA/gcG 1 -1 DTNBP1 HGNC HGNC:17328 protein_coding YES CCDS4534.1 ENSP00000341680 Q96EV8 A0A0S2Z5U8 UPI000006F968 NM_032122.4 5/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16294,hmmpanther:PTHR16294:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 15627371 15627371 T C 1 0 0 0 0 0 0 0 1 4613 1567 55 5 5 DTNBP1 6 15627371 Silent SNP T C3N-00175_T 7900243 15627371 155178608 516 10108 CAP2 0 . GRCh38 6 17513933 17513933 + Silent SNP G G T rs771675524 C3N-00175_T C3N-00175_N G G c.615G>T p.= p.T205T ENST00000229922 7/13 204 161 43 197 197 0 strelka-varscan-mutect CAP2,synonymous_variant,p.=,ENST00000229922,NM_006366.2;CAP2,synonymous_variant,p.=,ENST00000378990,;CAP2,intron_variant,,ENST00000616440,;CAP2,intron_variant,,ENST00000611958,;CAP2,intron_variant,,ENST00000489374,;CAP2,intron_variant,,ENST00000465994,;CAP2,intron_variant,,ENST00000493172,;CAP2,synonymous_variant,p.=,ENST00000479291,;CAP2,3_prime_UTR_variant,,ENST00000476263,; T ENST00000229922 Transcript synonymous_variant 1147/3316 615/1434 205/477 T acG/acT rs771675524 1 1 CAP2 HGNC HGNC:20039 protein_coding YES CCDS4539.1 ENSP00000229922 P40123 UPI0000126EC6 NM_006366.2 7/13 Superfamily_domains:0043456,Pfam_domain:PF01213,hmmpanther:PTHR10652,hmmpanther:PTHR10652:SF2 LOW 1 SNV 1 1 PASS rs771675524 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 17513933 17513933 G T 1 0 0 0 0 0 0 0 1 2312 1103 39 1 1 CAP2 6 17513933 Silent SNP G C3N-00175_T 1886562 17513933 153292046 517 10109 HIST1H4E 0 . GRCh38 6 26204666 26204666 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.22G>A p.Gly8Arg p.G8R ENST00000615164 1/1 35 25 10 100 99 1 strelka-varscan-mutect HIST1H4E,missense_variant,p.Gly8Arg,ENST00000615164,NM_003545.3;HIST1H2BF,downstream_gene_variant,,ENST00000356530,NM_003522.3;RP1-34B20.4,downstream_gene_variant,,ENST00000405418,; A ENST00000615164 Transcript missense_variant 115/1487 22/312 8/103 G/R Gga/Aga 1 1 HIST1H4E HGNC HGNC:4790 protein_coding YES CCDS4593.1 ENSP00000484789 P62805 B2R4R0 UPI000000003C NM_003545.3 deleterious_low_confidence(0.03) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR10484,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00623 MODERATE 1 SNV 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999883 1 1 1 0 A 3 1 39 26204666 26204666 G A 1 0 0 0 0 1 0 0 0 7057 1117 39 1 1 HIST1H4E 6 26204666 Missense_Mutation SNP G C3N-00175_T 8690733 26204666 144601313 518 10110 HIST1H3E 0 . GRCh38 6 26225259 26225259 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.105C>A p.= p.G35G ENST00000634733 2/2 110 89 21 135 135 0 strelka-mutect HIST1H3E,synonymous_variant,p.=,ENST00000634733,;HIST1H3E,synonymous_variant,p.=,ENST00000614911,NM_003532.2; A ENST00000634733 Transcript synonymous_variant 465/2679 105/411 35/136 G ggC/ggA 1 1 HIST1H3E HGNC HGNC:4769 protein_coding YES CCDS4596.1 ENSP00000489282 P68431 UPI00000003C7 2/2 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 26225259 26225259 C A 1 0 0 0 0 0 0 0 1 7047 755 27 1 1 HIST1H3E 6 26225259 Silent SNP C C3N-00175_T 20593 26225259 144580720 519 10111 POM121L2 0 . GRCh38 6 27309735 27309735 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2436G>C p.Met812Ile p.M812I ENST00000444565 1/1 357 304 53 376 376 0 strelka-varscan-mutect POM121L2,missense_variant,p.Met812Ile,ENST00000444565,NM_033482.3;POM121L2,intron_variant,,ENST00000429945,; G ENST00000444565 Transcript missense_variant 2436/3108 2436/3108 812/1035 M/I atG/atC 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 tolerated(0.17) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 27309735 27309735 C G 1 0 0 0 0 1 0 0 0 12353 710 25 4 4 POM121L2 6 27309735 Missense_Mutation SNP C C3N-00175_T 1084476 27309735 143496244 520 10112 OR2B2 0 . GRCh38 6 27911460 27911460 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.860C>A p.Pro287His p.P287H ENST00000303324 1/1 168 132 36 176 176 0 strelka-varscan-mutect OR2B2,missense_variant,p.Pro287His,ENST00000303324,NM_033057.2; T ENST00000303324 Transcript missense_variant 937/1212 860/1074 287/357 P/H cCc/cAc COSM5476670 1 -1 OR2B2 HGNC HGNC:13966 protein_coding YES CCDS4641.1 ENSP00000304419 Q9GZK3 A0A126GWD0 UPI000004187A NM_033057.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF254,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 27911460 27911460 G T 1 0 0 0 0 1 0 0 0 11068 1232 43 2 2 OR2B2 6 27911460 Missense_Mutation SNP G C3N-00175_T 601725 27911460 142894519 521 10113 GPX6 0 . GRCh38 6 28510881 28510881 + Silent SNP T T G novel C3N-00175_T C3N-00175_N T T c.111A>C p.= p.T37T ENST00000361902 2/5 140 99 41 140 140 0 strelka-varscan-mutect GPX6,synonymous_variant,p.=,ENST00000361902,NM_182701.1;GPX6,synonymous_variant,p.=,ENST00000612264,;GPX6,synonymous_variant,p.=,ENST00000474923,;GPX6,non_coding_transcript_exon_variant,,ENST00000483058,; G ENST00000361902 Transcript synonymous_variant 161/1712 111/666 37/221 T acA/acC 1 -1 GPX6 HGNC HGNC:4558 protein_coding YES CCDS43432.1 ENSP00000354581 P59796 UPI00001B2975 NM_182701.1 2/5 PIRSF_domain:PIRSF000303,PROSITE_profiles:PS51355,hmmpanther:PTHR11592,hmmpanther:PTHR11592:SF15 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 28510881 28510881 T G 1 0 0 0 0 0 0 0 1 6623 1567 55 5 5 GPX6 6 28510881 Silent SNP T C3N-00175_T 599421 28510881 142295098 522 10114 OR14J1 0 . GRCh38 6 29307175 29307175 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.486C>T p.= p.F162F ENST00000377160 1/1 254 194 60 267 266 1 strelka-varscan-mutect OR14J1,synonymous_variant,p.=,ENST00000377160,NM_030946.1; T ENST00000377160 Transcript synonymous_variant 486/966 486/966 162/321 F ttC/ttT 1 1 OR14J1 HGNC HGNC:13971 protein_coding YES CCDS34362.1 ENSP00000366365 Q9UGF5 A0A126GW10 UPI0000041CEC NM_030946.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF42,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 29307175 29307175 C T 1 0 0 0 0 0 0 0 1 11025 912 32 3 3 OR14J1 6 29307175 Silent SNP C C3N-00175_T 796294 29307175 141498804 523 10115 SLC44A4 0 . GRCh38 6 31864871 31864871 + Missense_Mutation SNP C C A rs150042455 C3N-00175_T C3N-00175_N C C c.1871G>T p.Gly624Val p.G624V ENST00000229729 19/21 198 162 36 265 265 0 strelka-varscan-mutect SLC44A4,missense_variant,p.Gly548Val,ENST00000544672,NM_001178045.1;SLC44A4,missense_variant,p.Gly624Val,ENST00000229729,NM_025257.2;SLC44A4,missense_variant,p.Gly582Val,ENST00000375562,NM_001178044.1;NEU1,upstream_gene_variant,,ENST00000375631,NM_000434.3;SLC44A4,downstream_gene_variant,,ENST00000414427,;SLC44A4,upstream_gene_variant,,ENST00000487680,;NEU1,upstream_gene_variant,,ENST00000495807,;NEU1,upstream_gene_variant,,ENST00000480384,;NEU1,upstream_gene_variant,,ENST00000491768,;SLC44A4,downstream_gene_variant,,ENST00000479777,;SLC44A4,downstream_gene_variant,,ENST00000475563,; A ENST00000229729 Transcript missense_variant 1892/2589 1871/2133 624/710 G/V gGg/gTg rs150042455 1 -1 SLC44A4 HGNC HGNC:13941 protein_coding YES CCDS4724.2 ENSP00000229729 Q53GD3 A0A140VJH4 UPI00004702CE NM_025257.2 tolerated(0.51) 19/21 Pfam_domain:PF04515,hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF37 MODERATE 1 SNV 1 1 PASS rs150042455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 31864871 31864871 C A 1 0 0 0 0 1 0 0 0 14915 623 22 2 2 SLC44A4 6 31864871 Missense_Mutation SNP C C3N-00175_T 2557696 31864871 138941108 524 10116 EHMT2 0 . GRCh38 6 31884765 31884765 + Missense_Mutation SNP G G T rs768152055 C3N-00175_T C3N-00175_N G G c.2552C>A p.Thr851Lys p.T851K ENST00000375528 18/26 59 48 11 69 69 0 strelka-varscan-mutect EHMT2,missense_variant,p.Thr885Lys,ENST00000395728,;EHMT2,missense_variant,p.Thr851Lys,ENST00000375528,NM_001289413.1;EHMT2,missense_variant,p.Thr828Lys,ENST00000375537,NM_006709.4;EHMT2,missense_variant,p.Thr794Lys,ENST00000375530,NM_025256.6;EHMT2,missense_variant,p.Thr159Lys,ENST00000436026,;EHMT2-AS1,downstream_gene_variant,,ENST00000434689,;EHMT2,non_coding_transcript_exon_variant,,ENST00000480912,;EHMT2,non_coding_transcript_exon_variant,,ENST00000478491,;EHMT2,non_coding_transcript_exon_variant,,ENST00000494816,;EHMT2,non_coding_transcript_exon_variant,,ENST00000461880,;EHMT2,non_coding_transcript_exon_variant,,ENST00000477678,; T ENST00000375528 Transcript missense_variant 2572/4047 2552/3702 851/1233 T/K aCg/aAg rs768152055 1 -1 EHMT2 HGNC HGNC:14129 protein_coding YES CCDS75425.1 ENSP00000364678 A2ABF8 UPI0000E5AD1F NM_001289413.1 deleterious(0.04) 18/26 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF361,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs768152055 . 0 202 8 0 0 0 0 0 -20 0.9999988 1 1 1 0 T 3 4 39 31884765 31884765 G T 1 0 0 0 0 1 0 0 0 4820 1145 40 1 1 EHMT2 6 31884765 Missense_Mutation SNP G C3N-00175_T 19894 31884765 138921214 525 10117 AGER 0 . GRCh38 6 32184212 32184212 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.11G>A p.Gly4Glu p.G4E ENST00000375069 1/11 135 115 20 166 166 0 strelka-varscan-mutect AGER,missense_variant,p.Gly4Glu,ENST00000375069,NM_001206929.1;AGER,missense_variant,p.Gly4Glu,ENST00000438221,NM_001206934.1;AGER,missense_variant,p.Gly4Glu,ENST00000375076,NM_001206932.1,NM_001136.4;AGER,missense_variant,p.Gly4Glu,ENST00000375055,NM_001206936.1,NM_001206954.1,NM_001206966.1,NM_001206940.1;AGER,missense_variant,p.Gly4Glu,ENST00000375067,NM_172197.2;AGER,missense_variant,p.Gly4Glu,ENST00000620802,;AGER,missense_variant,p.Gly4Glu,ENST00000450110,;AGER,missense_variant,p.Gly4Glu,ENST00000375056,;AGER,missense_variant,p.Gly4Glu,ENST00000538695,;AGER,5_prime_UTR_variant,,ENST00000375070,;AGER,5_prime_UTR_variant,,ENST00000375065,;PBX2,downstream_gene_variant,,ENST00000375050,NM_002586.4;RNF5,downstream_gene_variant,,ENST00000375094,NM_006913.3;MIR6833,downstream_gene_variant,,ENST00000620680,;XXbac-BPG300A18.13,downstream_gene_variant,,ENST00000559458,;RNF5,downstream_gene_variant,,ENST00000487940,;AGER,non_coding_transcript_exon_variant,,ENST00000484849,;PBX2,downstream_gene_variant,,ENST00000478678,;PBX2,downstream_gene_variant,,ENST00000496171,;AGER,upstream_gene_variant,,ENST00000473619,;PBX2,downstream_gene_variant,,ENST00000495300,;AGER,upstream_gene_variant,,ENST00000488669,;PBX2,downstream_gene_variant,,ENST00000480254,;AGER,upstream_gene_variant,,ENST00000469940,; T ENST00000375069 Transcript missense_variant 111/1538 11/1263 4/420 G/E gGa/gAa 1 -1 AGER HGNC HGNC:320 protein_coding YES CCDS75429.1 ENSP00000364210 Q15109 UPI000053E487 NM_001206929.1 tolerated_low_confidence(0.15) 1/11 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11973,hmmpanther:PTHR11973:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 32184212 32184212 C T 1 0 0 0 0 1 0 0 0 456 855 30 3 3 AGER 6 32184212 Missense_Mutation SNP C C3N-00175_T 299447 32184212 138621767 526 10118 NOTCH4 0 . GRCh38 6 32195894 32195894 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.5555C>G p.Pro1852Arg p.P1852R ENST00000375023 30/30 133 98 35 154 154 0 strelka-varscan-mutect NOTCH4,missense_variant,p.Pro1852Arg,ENST00000375023,NM_004557.3;GPSM3,upstream_gene_variant,,ENST00000375040,NM_001276501.1;GPSM3,upstream_gene_variant,,ENST00000487761,;GPSM3,upstream_gene_variant,,ENST00000375043,NM_022107.1;GPSM3,upstream_gene_variant,,ENST00000619085,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000474612,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000491215,;GPSM3,upstream_gene_variant,,ENST00000472768,; C ENST00000375023 Transcript missense_variant 5694/6745 5555/6012 1852/2003 P/R cCg/cGg 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 tolerated(0.09) 30/30 hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF64 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 32195894 32195894 G C 1 0 0 0 0 1 0 0 0 10596 1116 39 4 4 NOTCH4 6 32195894 Missense_Mutation SNP G C3N-00175_T 11682 32195894 138610085 527 10119 NOTCH4 0 . GRCh38 6 32217153 32217153 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1738G>T p.Gly580Cys p.G580C ENST00000375023 10/30 162 121 41 179 178 1 strelka-varscan-mutect NOTCH4,missense_variant,p.Gly580Cys,ENST00000375023,NM_004557.3;NOTCH4,upstream_gene_variant,,ENST00000465528,;NOTCH4,splice_region_variant,,ENST00000473562,; A ENST00000375023 Transcript missense_variant,splice_region_variant 1877/6745 1738/6012 580/2003 G/C Ggc/Tgc 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0) 10/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF64,hmmpanther:PTHR24033,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Pfam_domain:PF07645,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 32217153 32217153 C A 1 0 0 0 0 1 0 0 0 10596 695 24 2 2 NOTCH4 6 32217153 Missense_Mutation SNP C C3N-00175_T 21259 32217153 138588826 528 10120 TCP11 0 . GRCh38 6 35118414 35118414 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.1406T>C p.Ile469Thr p.I469T ENST00000311875 10/10 402 315 87 374 374 0 strelka-varscan-mutect TCP11,missense_variant,p.Ile469Thr,ENST00000311875,NM_001093728.2;TCP11,missense_variant,p.Ile393Thr,ENST00000611141,NM_001261821.1,NM_001261820.1;TCP11,missense_variant,p.Ile394Thr,ENST00000244645,NM_018679.5;TCP11,missense_variant,p.Ile394Thr,ENST00000373979,;TCP11,missense_variant,p.Ile464Thr,ENST00000444780,NM_001261817.1;TCP11,missense_variant,p.Ile418Thr,ENST00000412155,NM_001261819.1;TCP11,missense_variant,p.Ile423Thr,ENST00000373974,NM_001261818.1;TCP11,missense_variant,p.Ile456Thr,ENST00000512012,;TCP11,missense_variant,p.Ile393Thr,ENST00000418521,;TCP11,intron_variant,,ENST00000502480,;TCP11,downstream_gene_variant,,ENST00000486638,;TCP11,downstream_gene_variant,,ENST00000507706,;TCP11,downstream_gene_variant,,ENST00000492680,;TCP11,downstream_gene_variant,,ENST00000505400,;TCP11,3_prime_UTR_variant,,ENST00000504758,;TCP11,3_prime_UTR_variant,,ENST00000505911,;TCP11,3_prime_UTR_variant,,ENST00000455706,;TCP11,downstream_gene_variant,,ENST00000427376,;TCP11,downstream_gene_variant,,ENST00000469514,;TCP11,downstream_gene_variant,,ENST00000479418,;TCP11,downstream_gene_variant,,ENST00000509988,;TCP11,downstream_gene_variant,,ENST00000505335,; G ENST00000311875 Transcript missense_variant 1824/2166 1406/1551 469/516 I/T aTt/aCt 1 -1 TCP11 HGNC HGNC:11658 protein_coding YES CCDS47413.1 ENSP00000308708 Q8WWU5 A0A140VK95 UPI0000EE4D7F NM_001093728.2 deleterious(0.01) 10/10 Pfam_domain:PF05794,hmmpanther:PTHR12832,hmmpanther:PTHR12832:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 35118414 35118414 A G 1 0 0 0 0 1 0 0 0 16120 101 4 5 5 TCP11 6 35118414 Missense_Mutation SNP A C3N-00175_T 2901261 35118414 135687565 529 10121 SRPK1 0 . GRCh38 6 35869613 35869613 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1280G>T p.Cys427Phe p.C427F ENST00000373825 11/16 185 149 36 228 228 0 strelka-varscan-mutect SRPK1,missense_variant,p.Cys427Phe,ENST00000373825,NM_003137.4;SRPK1,missense_variant,p.Cys411Phe,ENST00000423325,;SRPK1,missense_variant,p.Cys443Phe,ENST00000361690,;SRPK1,downstream_gene_variant,,ENST00000510290,;SRPK1,downstream_gene_variant,,ENST00000373821,;SRPK1,non_coding_transcript_exon_variant,,ENST00000346162,;SRPK1,non_coding_transcript_exon_variant,,ENST00000502969,;SRPK1,upstream_gene_variant,,ENST00000507292,; A ENST00000373825 Transcript missense_variant 1566/4592 1280/1968 427/655 C/F tGc/tTc 1 -1 SRPK1 HGNC HGNC:11305 protein_coding YES CCDS47415.1 ENSP00000362931 Q96SB4 UPI000020DBDD NM_003137.4 deleterious(0.01) 11/16 PROSITE_profiles:PS50011,SMART_domains:SM00220 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 35869613 35869613 C A 1 0 0 0 0 1 0 0 0 15520 710 25 2 2 SRPK1 6 35869613 Missense_Mutation SNP C C3N-00175_T 751199 35869613 134936366 530 10122 PNPLA1 0 . GRCh38 6 36307588 36307588 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1471G>T p.Glu491Ter p.E491* ENST00000394571 8/8 90 77 13 73 73 0 strelka-varscan-mutect PNPLA1,stop_gained,p.Glu396Ter,ENST00000388715,NM_173676.2;PNPLA1,stop_gained,p.Glu400Ter,ENST00000636260,;PNPLA1,stop_gained,p.Glu492Ter,ENST00000457797,;PNPLA1,stop_gained,p.Glu491Ter,ENST00000394571,NM_001145717.1;PNPLA1,stop_gained,p.Glu405Ter,ENST00000312917,NM_001145716.2; T ENST00000394571 Transcript stop_gained,splice_region_variant 1471/1599 1471/1599 491/532 E/* Gag/Tag 1 1 PNPLA1 HGNC HGNC:21246 protein_coding YES CCDS54997.1 ENSP00000378072 Q8N8W4 B8XXQ3 UPI000189560E NM_001145717.1 8/8 hmmpanther:PTHR12406,hmmpanther:PTHR12406:SF23 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 36307588 36307588 G T 1 0 0 0 0 0 1 0 0 12272 1188 41 2 2 PNPLA1 6 36307588 Nonsense_Mutation SNP G C3N-00175_T 437975 36307588 134498391 531 10123 CPNE5 0 . GRCh38 6 36742383 36742383 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1667C>A p.Ser556Tyr p.S556Y ENST00000244751 21/21 184 158 26 227 227 0 strelka-varscan-mutect CPNE5,missense_variant,p.Ser556Tyr,ENST00000244751,NM_020939.1;CPNE5,missense_variant,p.Ser264Tyr,ENST00000393189,NM_001314018.1,NM_001314020.1;CPNE5,non_coding_transcript_exon_variant,,ENST00000459703,;CPNE5,non_coding_transcript_exon_variant,,ENST00000493411,;CPNE5,downstream_gene_variant,,ENST00000633929,;RP3-431A14.4,downstream_gene_variant,,ENST00000494644,; T ENST00000244751 Transcript missense_variant 2292/3897 1667/1782 556/593 S/Y tCc/tAc 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 deleterious(0) 21/21 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF51,Pfam_domain:PF07002 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 36742383 36742383 G T 1 0 0 0 0 1 0 0 0 3610 1174 41 2 2 CPNE5 6 36742383 Missense_Mutation SNP G C3N-00175_T 434795 36742383 134063596 532 10124 CMTR1 0 . GRCh38 6 37446292 37446292 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.287C>G p.Ala96Gly p.A96G ENST00000373451 4/24 98 81 17 132 132 0 strelka-varscan-mutect CMTR1,missense_variant,p.Ala96Gly,ENST00000373451,NM_015050.2;CMTR1,missense_variant,p.Ala96Gly,ENST00000455891,;CMTR1,downstream_gene_variant,,ENST00000471097,; G ENST00000373451 Transcript missense_variant,splice_region_variant 451/4033 287/2508 96/835 A/G gCc/gGc 1 1 CMTR1 HGNC HGNC:21077 protein_coding YES CCDS4835.1 ENSP00000362550 Q8N1G2 UPI00000700C2 NM_015050.2 deleterious(0.02) 4/24 PROSITE_profiles:PS50174,hmmpanther:PTHR16121:SF0,hmmpanther:PTHR16121,Pfam_domain:PF01585,SMART_domains:SM00443 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 G 3 3 39 37446292 37446292 C G 1 0 0 0 0 1 0 0 0 3366 753 26 4 4 CMTR1 6 37446292 Missense_Mutation SNP C C3N-00175_T 703909 37446292 133359687 533 10125 MDGA1 0 . GRCh38 6 37654880 37654881 + Frame_Shift_Ins INS - - T novel C3N-00175_T C3N-00175_N - - c.631dupA p.Ser211LysfsTer10 p.S211Kfs*10 ENST00000434837 5/17 204 154 50 213 213 0 sindel-varindel-pindel MDGA1,frameshift_variant,p.Ser211LysfsTer10,ENST00000434837,NM_153487.3;MDGA1,frameshift_variant,p.Ser211LysfsTer10,ENST00000505425,;MDGA1,downstream_gene_variant,,ENST00000515437,;MDGA1,downstream_gene_variant,,ENST00000508399,;MDGA1,non_coding_transcript_exon_variant,,ENST00000478143,; T ENST00000434837 Transcript frameshift_variant 1810-1811/10736 631-632/2868 211/955 S/KX agc/aAgc 1 -1 MDGA1 HGNC HGNC:19267 protein_coding YES CCDS47417.1 ENSP00000402584 Q8NFP4 UPI0000071D28 NM_153487.3 5/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF66,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF49265 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 39 37654880 37654880 - T 1 0 1 1 0 0 0 0 0 9344 797 28 0 0 MDGA1 6 37654880 Frame_Shift_Ins INS - C3N-00175_T 208588 37654880 133151099 534 10126 GLO1 0 . GRCh38 6 38677375 38677397 + Splice_Site DEL TCATTTTACCTGTAAAATGAAAA TCATTTTACCTGTAAAATGAAAA - novel C3N-00175_T C3N-00175_N TCATTTTACCTGTAAAATGAAAA TCATTTTACCTGTAAAATGAAAA c.467-14_475delTTTTCATTTTACAGGTAAAATGA p.X156_splice ENST00000373365 6/6 125 98 27 210 210 0 sindel-varindel-pindel GLO1,splice_acceptor_variant,,ENST00000373365,NM_006708.2;GLO1,splice_acceptor_variant,,ENST00000470973,; - ENST00000373365 Transcript splice_acceptor_variant,coding_sequence_variant,intron_variant ?-562/2012 ?-475/555 ?-159/184 1 -1 GLO1 HGNC HGNC:4323 protein_coding YES CCDS4837.1 ENSP00000362463 Q04760 X5DNM4 UPI0000169DF9 NM_006708.2 6/6 5/5 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 39 38677375 38677375 TCATTTTACCTGTAAAATGAAAA - 1 0 1 0 1 0 0 1 0 6328 1792 62 0 0 GLO1 6 38677375 Splice_Site DEL TCATTTTACCTGTAAAATGAAAA C3N-00175_T 1022495 38677375 132128604 535 10127 DNAH8 0 . GRCh38 6 38723014 38723014 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.205G>T p.Glu69Ter p.E69* ENST00000327475 2/93 226 168 58 240 240 0 strelka-varscan-mutect DNAH8,stop_gained,p.Glu69Ter,ENST00000327475,NM_001206927.1;DNAH8,stop_gained,p.Glu69Ter,ENST00000449981,;DNAH8,stop_gained,p.Glu69Ter,ENST00000373278,;DNAH8,upstream_gene_variant,,ENST00000359357,; T ENST00000327475 Transcript stop_gained 314/14360 205/14124 69/4707 E/* Gaa/Taa 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 2/93 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 38723014 38723014 G T 1 0 0 0 0 0 1 0 0 4422 943 33 2 2 DNAH8 6 38723014 Nonsense_Mutation SNP G C3N-00175_T 45639 38723014 132082965 536 10128 KIF6 0 . GRCh38 6 39360419 39360419 + Nonsense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.2058G>A p.Trp686Ter p.W686* ENST00000287152 18/23 125 85 40 165 165 0 strelka-varscan-mutect KIF6,stop_gained,p.Trp686Ter,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,stop_gained,p.Trp578Ter,ENST00000458470,;KIF6,stop_gained,p.Trp137Ter,ENST00000394362,;KIF6,stop_gained,p.Trp137Ter,ENST00000538893,;KIF6,stop_gained,p.Trp137Ter,ENST00000229913,NM_001289024.1; T ENST00000287152 Transcript stop_gained 2153/9082 2058/2445 686/814 W/* tgG/tgA 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 18/23 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 39360419 39360419 C T 1 0 0 0 0 0 1 0 0 8173 624 22 3 3 KIF6 6 39360419 Nonsense_Mutation SNP C C3N-00175_T 637405 39360419 131445560 537 10129 LRFN2 0 . GRCh38 6 40392271 40392271 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2042G>T p.Gly681Val p.G681V ENST00000338305 3/3 60 43 17 74 74 0 strelka-mutect LRFN2,missense_variant,p.Gly681Val,ENST00000338305,NM_020737.2; A ENST00000338305 Transcript missense_variant 2585/3270 2042/2370 681/789 G/V gGg/gTg 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 tolerated(0.06) 3/3 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25 MODERATE 1 SNV 1 1 PASS rs1307544599 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 40392271 40392271 C A 1 0 0 0 0 1 0 0 0 8832 623 22 2 2 LRFN2 6 40392271 Missense_Mutation SNP C C3N-00175_T 1031852 40392271 130413708 538 10130 CUL9 0 . GRCh38 6 43188676 43188676 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2141A>T p.Glu714Val p.E714V ENST00000252050 8/41 137 108 29 137 137 0 strelka-mutect CUL9,missense_variant,p.Glu714Val,ENST00000252050,NM_015089.3;CUL9,missense_variant,p.Glu714Val,ENST00000372647,;CUL9,non_coding_transcript_exon_variant,,ENST00000515773,;CUL9,non_coding_transcript_exon_variant,,ENST00000451399,;CUL9,non_coding_transcript_exon_variant,,ENST00000510282,; T ENST00000252050 Transcript missense_variant 2225/7780 2141/7554 714/2517 E/V gAg/gTg 1 1 CUL9 HGNC HGNC:15982 protein_coding YES CCDS4890.1 ENSP00000252050 Q8IWT3 UPI000006F22F NM_015089.3 tolerated(0.07) 8/41 hmmpanther:PTHR22771:SF2,hmmpanther:PTHR22771,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43188676 43188676 A T 1 0 0 0 0 1 0 0 0 3871 304 11 4 4 CUL9 6 43188676 Missense_Mutation SNP A C3N-00175_T 2796405 43188676 127617303 539 10131 HSP90AB1 0 . GRCh38 6 44248681 44248681 + Missense_Mutation SNP C C G rs765906022 C3N-00175_T C3N-00175_N C C c.52C>G p.Gln18Glu p.Q18E ENST00000371554 2/12 149 131 18 141 141 0 strelka-varscan-mutect HSP90AB1,missense_variant,p.Gln18Glu,ENST00000371554,;HSP90AB1,missense_variant,p.Gln18Glu,ENST00000620073,NM_001271970.1;HSP90AB1,missense_variant,p.Gln18Glu,ENST00000353801,NM_001271969.1;HSP90AB1,missense_variant,p.Gln18Glu,ENST00000371646,NM_001271971.1,NM_007355.3,NM_001271972.1; G ENST00000371554 Transcript missense_variant 266/2674 52/2175 18/724 Q/E Cag/Gag rs765906022,COSM95615 1 1 HSP90AB1 HGNC HGNC:5258 protein_coding YES CCDS4909.1 ENSP00000360609 P08238 A0A024RD80 UPI00001411EF deleterious(0.02) 2/12 Gene3D:3.30.565.10,HAMAP:MF_00505,PIRSF_domain:PIRSF002583,Prints_domain:PR00775,hmmpanther:PTHR11528,Superfamily_domains:SSF55874 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs765906022 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 44248681 44248681 C G 1 0 0 0 0 1 0 0 0 7298 827 29 4 4 HSP90AB1 6 44248681 Missense_Mutation SNP C C3N-00175_T 1060005 44248681 126557298 540 10132 TMEM151B 0 . GRCh38 6 44275829 44275829 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1003C>A p.Leu335Met p.L335M ENST00000451188 3/3 101 74 27 120 120 0 strelka-varscan-mutect TMEM151B,missense_variant,p.Leu335Met,ENST00000451188,NM_001137560.1;TMEM151B,intron_variant,,ENST00000438774,;TCTE1,downstream_gene_variant,,ENST00000371505,NM_182539.3;TCTE1,downstream_gene_variant,,ENST00000371504,;RP11-444E17.6,intron_variant,,ENST00000505802,; A ENST00000451188 Transcript missense_variant 1280/4895 1003/1701 335/566 L/M Ctg/Atg 1 1 TMEM151B HGNC HGNC:21315 protein_coding YES CCDS47437.1 ENSP00000393161 Q8IW70 UPI00006C0A4E NM_001137560.1 tolerated(0.09) 3/3 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF4,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS rs1481080724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 44275829 44275829 C A 1 0 0 0 0 1 0 0 0 16513 680 24 2 2 TMEM151B 6 44275829 Missense_Mutation SNP C C3N-00175_T 27148 44275829 126530150 541 10133 PTCHD4 0 . GRCh38 6 48068553 48068553 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.103G>T p.Gly35Cys p.G35C ENST00000339488 1/3 220 195 25 238 238 0 strelka-varscan-mutect PTCHD4,missense_variant,p.Gly35Cys,ENST00000398738,NM_207499.2;PTCHD4,missense_variant,p.Gly35Cys,ENST00000339488,NM_001013732.3; A ENST00000339488 Transcript missense_variant 137/2850 103/2541 35/846 G/C Ggt/Tgt 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 deleterious(0) 1/3 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 48068553 48068553 C A 1 0 0 0 0 1 0 0 0 12887 623 22 2 2 PTCHD4 6 48068553 Missense_Mutation SNP C C3N-00175_T 3792724 48068553 122737426 542 10134 RHAG 0 . GRCh38 6 49618152 49618152 + Silent SNP C C T rs138437733 C3N-00175_T C3N-00175_N C C c.408G>A p.= p.T136T ENST00000371175 3/10 299 238 61 330 330 0 strelka-varscan-mutect RHAG,synonymous_variant,p.=,ENST00000371175,NM_000324.2;RHAG,synonymous_variant,p.=,ENST00000229810,;RHAG,synonymous_variant,p.=,ENST00000618248,; T ENST00000371175 Transcript synonymous_variant 435/1912 408/1230 136/409 T acG/acA rs138437733,COSM1546674 1 -1 RHAG HGNC HGNC:10006 protein_coding YES CCDS4927.1 ENSP00000360217 Q02094 UPI000006D18F NM_000324.2 3/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11730:SF32,hmmpanther:PTHR11730,Pfam_domain:PF00909,Gene3D:1.10.3430.10,Superfamily_domains:0044218 0,1 LOW 1 SNV 1 0,1 1 PASS rs138437733 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 49618152 49618152 C T 1 0 0 0 0 0 0 0 1 13487 871 31 1 1 RHAG 6 49618152 Silent SNP C C3N-00175_T 1549599 49618152 121187827 543 10135 HCRTR2 0 . GRCh38 6 55263791 55263791 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.731T>C p.Leu244Pro p.L244P ENST00000615358 5/8 134 95 39 120 120 0 strelka-varscan-mutect HCRTR2,missense_variant,p.Leu244Pro,ENST00000615358,;HCRTR2,missense_variant,p.Leu244Pro,ENST00000370862,NM_001526.3; C ENST00000615358 Transcript missense_variant 1194/1936 731/1335 244/444 L/P cTg/cCg 1 1 HCRTR2 HGNC HGNC:4849 protein_coding YES CCDS4956.1 ENSP00000477548 O43614 S4X0W3 UPI000013D07A tolerated(0.11) 5/8 PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF75,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 55263791 55263791 T C 1 0 0 0 0 1 0 0 0 6889 1580 55 5 5 HCRTR2 6 55263791 Missense_Mutation SNP T C3N-00175_T 5645639 55263791 115542188 544 10136 DST 0 . GRCh38 6 56459025 56459025 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.16594G>T p.Asp5532Tyr p.D5532Y ENST00000312431 95/95 67 48 19 65 65 0 strelka-varscan-mutect DST,missense_variant,p.Asp7456Tyr,ENST00000361203,;DST,missense_variant,p.Asp5492Tyr,ENST00000421834,NM_183380.3;DST,missense_variant,p.Asp5532Tyr,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Asp5370Tyr,ENST00000370788,;DST,missense_variant,p.Asp5166Tyr,ENST00000244364,NM_015548.4;DST,missense_variant,p.Asp254Tyr,ENST00000523292,;DST,downstream_gene_variant,,ENST00000523597,;DST,non_coding_transcript_exon_variant,,ENST00000518464,;DST,non_coding_transcript_exon_variant,,ENST00000482156,;DST,non_coding_transcript_exon_variant,,ENST00000466429,; A ENST00000312431 Transcript missense_variant 16720/17756 16594/16614 5532/5537 D/Y Gac/Tac 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.06) 95/95 MODERATE 1 SNV 5 1 PASS rs956139209 . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 39 56459025 56459025 C A 1 0 0 0 0 1 0 0 0 4604 855 30 2 2 DST 6 56459025 Missense_Mutation SNP C C3N-00175_T 1195234 56459025 114346954 545 10137 DST 0 . GRCh38 6 56632006 56632006 + Silent SNP G G T rs754052746 C3N-00175_T C3N-00175_N G G c.3327C>A p.= p.I1109I ENST00000312431 26/95 182 131 51 207 207 0 strelka-varscan-mutect DST,synonymous_variant,p.=,ENST00000361203,;DST,synonymous_variant,p.=,ENST00000421834,NM_183380.3;DST,synonymous_variant,p.=,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,synonymous_variant,p.=,ENST00000370788,;DST,synonymous_variant,p.=,ENST00000244364,NM_015548.4;DST,synonymous_variant,p.=,ENST00000439203,;DST,synonymous_variant,p.=,ENST00000370765,NM_001723.5;DST,synonymous_variant,p.=,ENST00000520645,;DST,synonymous_variant,p.=,ENST00000518935,;DST,upstream_gene_variant,,ENST00000522360,; T ENST00000312431 Transcript synonymous_variant 3453/17756 3327/16614 1109/5537 I atC/atA rs754052746 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 26/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 LOW 1 SNV 5 1 PASS rs754052746 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 56632006 56632006 G T 1 0 0 0 0 0 0 0 1 4604 932 33 2 2 DST 6 56632006 Silent SNP G C3N-00175_T 172981 56632006 114173973 546 10138 DST 0 . GRCh38 6 56639610 56639610 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.2186A>G p.Asn729Ser p.N729S ENST00000312431 18/95 285 253 32 408 408 0 strelka-varscan-mutect DST,missense_variant,p.Asn689Ser,ENST00000361203,;DST,missense_variant,p.Asn689Ser,ENST00000421834,NM_183380.3;DST,missense_variant,p.Asn729Ser,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Asn689Ser,ENST00000370788,;DST,missense_variant,p.Asn363Ser,ENST00000244364,NM_015548.4;DST,missense_variant,p.Asn363Ser,ENST00000439203,;DST,missense_variant,p.Asn363Ser,ENST00000370765,NM_001723.5;DST,missense_variant,p.Asn729Ser,ENST00000520645,;DST,missense_variant,p.Asn363Ser,ENST00000518935,;DST,downstream_gene_variant,,ENST00000449297,;DST,splice_region_variant,,ENST00000521104,;DST,splice_region_variant,,ENST00000523967,;DST,downstream_gene_variant,,ENST00000518828,; C ENST00000312431 Transcript missense_variant,splice_region_variant 2312/17756 2186/16614 729/5537 N/S aAt/aGt 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.19) 18/95 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 56639610 56639610 T C 1 0 0 0 0 1 0 0 0 4604 1507 52 5 5 DST 6 56639610 Missense_Mutation SNP T C3N-00175_T 7604 56639610 114166369 547 10139 EYS 0 . GRCh38 6 64081934 64081934 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.6493C>G p.Leu2165Val p.L2165V ENST00000370621 32/44 87 79 8 182 182 0 strelka-varscan-mutect EYS,missense_variant,p.Leu2165Val,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Leu2165Val,ENST00000370621,NM_001292009.1; C ENST00000370621 Transcript missense_variant 7020/10485 6493/9498 2165/3165 L/V Ctg/Gtg 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.15) 32/44 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 203 2 4 0 0 0 0 -12.76184 0.9992701 1 1 1 0 C 3 2 39 64081934 64081934 G C 1 0 0 0 0 1 0 0 0 5200 991 35 4 4 EYS 6 64081934 Missense_Mutation SNP G C3N-00175_T 7442324 64081934 106724045 548 10140 EYS 0 . GRCh38 6 64945852 64945852 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2322G>T p.Glu774Asp p.E774D ENST00000370621 15/44 91 64 27 139 139 0 strelka-varscan-mutect EYS,missense_variant,p.Glu774Asp,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Glu774Asp,ENST00000370621,NM_001292009.1; A ENST00000370621 Transcript missense_variant 2849/10485 2322/9498 774/3165 E/D gaG/gaT 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.4) 15/44 Gene3D:2gy5A03,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 64945852 64945852 C A 1 0 0 0 0 1 0 0 0 5200 564 20 2 2 EYS 6 64945852 Missense_Mutation SNP C C3N-00175_T 863918 64945852 105860127 549 10141 RIMS1 0 . GRCh38 6 72097125 72097125 + Missense_Mutation SNP C C A rs757314703 C3N-00175_T C3N-00175_N C C c.422C>A p.Ala141Glu p.A141E ENST00000521978 3/34 299 210 89 363 363 0 strelka-varscan-mutect RIMS1,missense_variant,p.Ala141Glu,ENST00000264839,;RIMS1,missense_variant,p.Ala141Glu,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Ala141Glu,ENST00000491071,;RIMS1,missense_variant,p.Ala141Glu,ENST00000520567,;RIMS1,missense_variant,p.Ala141Glu,ENST00000517960,;RIMS1,missense_variant,p.Ala141Glu,ENST00000518273,;RIMS1,missense_variant,p.Ala141Glu,ENST00000522291,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,; A ENST00000521978 Transcript missense_variant 422/5079 422/5079 141/1692 A/E gCg/gAg rs757314703,COSM3358048 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious(0) 3/34 PROSITE_profiles:PS50178,PROSITE_profiles:PS50916,hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157,Gene3D:3.30.40.10,Pfam_domain:PF02318,Superfamily_domains:SSF57903 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757314703 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 72097125 72097125 C A 1 0 0 0 0 1 0 0 0 13542 768 27 1 1 RIMS1 6 72097125 Missense_Mutation SNP C C3N-00175_T 7151273 72097125 98708854 550 10142 COL12A1 0 . GRCh38 6 75089176 75089176 + Splice_Site SNP T T A novel C3N-00175_T C3N-00175_N T T c.8942-2A>T p.X2981_splice ENST00000322507 113 81 32 129 129 0 strelka-varscan-mutect COL12A1,splice_acceptor_variant,,ENST00000322507,NM_004370.5;COL12A1,splice_acceptor_variant,,ENST00000615798,;COL12A1,splice_acceptor_variant,,ENST00000483888,;COL12A1,splice_acceptor_variant,,ENST00000416123,;COL12A1,splice_acceptor_variant,,ENST00000345356,NM_080645.2;COL12A1,splice_acceptor_variant,,ENST00000425443,;COL12A1,splice_acceptor_variant,,ENST00000511023,; A ENST00000322507 Transcript splice_acceptor_variant -/11723 8942/9192 2981/3063 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 63/65 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 75089176 75089176 T A 1 0 0 0 0 0 0 1 0 3457 1536 53 4 4 COL12A1 6 75089176 Splice_Site SNP T C3N-00175_T 2992051 75089176 95716803 551 10143 BACH2 0 . GRCh38 6 89951122 89951122 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.984C>G p.Cys328Trp p.C328W ENST00000257749 7/9 61 38 23 97 97 0 strelka-varscan-mutect BACH2,missense_variant,p.Cys328Trp,ENST00000257749,NM_021813.3;BACH2,missense_variant,p.Cys328Trp,ENST00000537989,NM_001170794.1;BACH2,missense_variant,p.Cys328Trp,ENST00000343122,;RP3-512E2.2,intron_variant,,ENST00000445838,;RP3-512E2.2,intron_variant,,ENST00000413986,; C ENST00000257749 Transcript missense_variant 1692/9113 984/2526 328/841 C/W tgC/tgG 1 -1 BACH2 HGNC HGNC:14078 protein_coding YES CCDS5026.1 ENSP00000257749 Q9BYV9 UPI000004F8AD NM_021813.3 deleterious(0.03) 7/9 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 89951122 89951122 G C 1 0 0 0 0 1 0 0 0 1442 1195 42 4 4 BACH2 6 89951122 Missense_Mutation SNP G C3N-00175_T 14861946 89951122 80854857 552 10144 EPHA7 0 . GRCh38 6 93410558 93410558 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.775C>G p.Pro259Ala p.P259A ENST00000369303 3/17 97 64 33 142 142 0 strelka-varscan-mutect EPHA7,missense_variant,p.Pro259Ala,ENST00000369303,NM_001288629.1,NM_004440.3;EPHA7,missense_variant,p.Pro259Ala,ENST00000369297,NM_001288630.1; C ENST00000369303 Transcript missense_variant 960/6588 775/2997 259/998 P/A Ccc/Gcc 1 -1 EPHA7 HGNC HGNC:3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_001288629.1,NM_004440.3 deleterious(0.03) 3/17 Gene3D:2gy5A03,PIRSF_domain:PIRSF000666,PROSITE_patterns:PS00791,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF377 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 93410558 93410558 G C 1 0 0 0 0 1 0 0 0 5019 1203 42 4 4 EPHA7 6 93410558 Missense_Mutation SNP G C3N-00175_T 3459436 93410558 77395421 553 10145 UFL1 0 . GRCh38 6 96551513 96551513 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1899G>T p.Lys633Asn p.K633N ENST00000369278 16/19 17 9 8 58 58 0 strelka-varscan-mutect UFL1,missense_variant,p.Lys633Asn,ENST00000369278,NM_015323.4; T ENST00000369278 Transcript missense_variant,splice_region_variant 1965/4224 1899/2385 633/794 K/N aaG/aaT 1 1 UFL1 HGNC HGNC:23039 protein_coding YES CCDS5034.1 ENSP00000358283 O94874 UPI0000072D61 NM_015323.4 deleterious(0) 16/19 hmmpanther:PTHR31057,hmmpanther:PTHR31057:SF0 MODERATE 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 39 96551513 96551513 G T 1 0 0 0 0 1 0 0 0 17460 1014 35 2 2 UFL1 6 96551513 Missense_Mutation SNP G C3N-00175_T 3140955 96551513 74254466 554 10146 MMS22L 0 . GRCh38 6 97254686 97254686 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.990A>G p.= p.K330K ENST00000275053 10/25 91 84 7 159 159 0 strelka-varscan-mutect MMS22L,synonymous_variant,p.=,ENST00000275053,NM_198468.2;MMS22L,synonymous_variant,p.=,ENST00000369251,;MMS22L,synonymous_variant,p.=,ENST00000510018,;MMS22L,synonymous_variant,p.=,ENST00000482634,;MMS22L,downstream_gene_variant,,ENST00000506256,;MMS22L,downstream_gene_variant,,ENST00000484170,;MMS22L,3_prime_UTR_variant,,ENST00000509383,;MMS22L,non_coding_transcript_exon_variant,,ENST00000508976,;MMS22L,downstream_gene_variant,,ENST00000511335,; C ENST00000275053 Transcript synonymous_variant 1256/8643 990/3732 330/1243 K aaA/aaG 1 -1 MMS22L HGNC HGNC:21475 protein_coding YES CCDS5039.1 ENSP00000275053 Q6ZRQ5 UPI00003673C9 NM_198468.2 10/25 Pfam_domain:PF14910,hmmpanther:PTHR28547 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 97254686 97254686 T C 1 0 0 0 0 0 0 0 1 9636 1490 52 5 5 MMS22L 6 97254686 Silent SNP T C3N-00175_T 703173 97254686 73551293 555 10147 SOBP 0 . GRCh38 6 107634597 107634597 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1753C>A p.= p.R585R ENST00000317357 6/7 216 150 66 143 143 0 strelka-varscan-mutect SOBP,synonymous_variant,p.=,ENST00000317357,NM_018013.3;SOBP,upstream_gene_variant,,ENST00000494935,; A ENST00000317357 Transcript synonymous_variant 2412/5245 1753/2622 585/873 R Cgg/Agg 1 1 SOBP HGNC HGNC:29256 protein_coding YES CCDS43488.1 ENSP00000318900 A7XYQ1 UPI0000E6A8ED NM_018013.3 6/7 hmmpanther:PTHR23186:SF2,hmmpanther:PTHR23186 LOW 1 SNV 5 1 PASS rs1288652131 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 107634597 107634597 C A 1 0 0 0 0 0 0 0 1 15233 643 23 1 1 SOBP 6 107634597 Silent SNP C C3N-00175_T 10379911 107634597 63171382 556 10148 COL10A1 0 . GRCh38 6 116121077 116121078 + Frame_Shift_Ins INS - - T novel C3N-00175_T C3N-00175_N - - c.1038dupA p.Gly347ArgfsTer8 p.G347Rfs*8 ENST00000327673 2/2 195 140 55 216 216 0 sindel-varindel-pindel COL10A1,frameshift_variant,p.Gly347ArgfsTer8,ENST00000327673,;COL10A1,frameshift_variant,p.Gly347ArgfsTer8,ENST00000243222,NM_000493.3;NT5DC1,intron_variant,,ENST00000319550,NM_152729.2;NT5DC1,intron_variant,,ENST00000419791,;COL10A1,downstream_gene_variant,,ENST00000452729,;COL10A1,downstream_gene_variant,,ENST00000418500,;NT5DC1,intron_variant,,ENST00000460749,;NT5DC1,downstream_gene_variant,,ENST00000417846,; T ENST00000327673 Transcript frameshift_variant 1446-1447/3498 1038-1039/2043 346-347/680 -/X -/A 1 -1 COL10A1 HGNC HGNC:2185 protein_coding YES CCDS5105.1 ENSP00000327368 Q03692 UPI0000126D28 2/2 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF570,Pfam_domain:PF01391 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 7 5 39 116121077 116121077 - T 1 0 1 1 0 0 0 0 0 3454 690 24 0 0 COL10A1 6 116121077 Frame_Shift_Ins INS - C3N-00175_T 8486480 116121077 54684902 557 10149 RFX6 0 . GRCh38 6 116910970 116910970 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.708A>T p.Lys236Asn p.K236N ENST00000332958 7/19 155 119 36 267 267 0 strelka-varscan-mutect RFX6,missense_variant,p.Lys236Asn,ENST00000332958,NM_173560.3;RFX6,non_coding_transcript_exon_variant,,ENST00000471966,;RFX6,non_coding_transcript_exon_variant,,ENST00000487683,; T ENST00000332958 Transcript missense_variant 724/3460 708/2787 236/928 K/N aaA/aaT 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 deleterious(0.03) 7/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 116910970 116910970 A T 1 0 0 0 0 1 0 0 0 13441 11 1 4 4 RFX6 6 116910970 Missense_Mutation SNP A C3N-00175_T 789893 116910970 53895009 558 10150 RFX6 0 . GRCh38 6 116911034 116911034 + Nonsense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.772A>T p.Lys258Ter p.K258* ENST00000332958 7/19 126 116 10 194 193 1 strelka-varscan-mutect RFX6,stop_gained,p.Lys258Ter,ENST00000332958,NM_173560.3;RFX6,non_coding_transcript_exon_variant,,ENST00000471966,;RFX6,non_coding_transcript_exon_variant,,ENST00000487683,; T ENST00000332958 Transcript stop_gained 788/3460 772/2787 258/928 K/* Aag/Tag 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 7/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 116911034 116911034 A T 1 0 0 0 0 0 1 0 0 13441 363 13 4 4 RFX6 6 116911034 Nonsense_Mutation SNP A C3N-00175_T 64 116911034 53894945 559 10151 SMPDL3A 0 . GRCh38 6 122795784 122795784 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.220G>C p.Gly74Arg p.G74R ENST00000368440 2/8 250 173 77 330 330 0 strelka-varscan-mutect SMPDL3A,missense_variant,p.Gly74Arg,ENST00000368440,NM_006714.4;SMPDL3A,intron_variant,,ENST00000539041,NM_001286138.1;SMPDL3A,non_coding_transcript_exon_variant,,ENST00000487215,; C ENST00000368440 Transcript missense_variant 397/1851 220/1362 74/453 G/R Ggc/Cgc 1 1 SMPDL3A HGNC HGNC:17389 protein_coding YES CCDS5128.1 ENSP00000357425 Q92484 UPI00000701D1 NM_006714.4 deleterious(0) 2/8 hmmpanther:PTHR10340:SF24,hmmpanther:PTHR10340,Pfam_domain:PF00149,PIRSF_domain:PIRSF036767,Gene3D:3.60.21.10,Superfamily_domains:SSF56300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 122795784 122795784 G C 1 0 0 0 0 1 0 0 0 15129 1348 47 4 4 SMPDL3A 6 122795784 Missense_Mutation SNP G C3N-00175_T 5884750 122795784 48010195 560 10152 TRDN 0 . GRCh38 6 123267716 123267716 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1774A>T p.Ile592Leu p.I592L ENST00000334268 32/41 39 34 5 108 107 1 strelka-varscan-mutect TRDN,missense_variant,p.Ile592Leu,ENST00000334268,NM_006073.3; A ENST00000334268 Transcript missense_variant 2092/4770 1774/2190 592/729 I/L Ata/Tta 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 tolerated_low_confidence(0.13) 32/41 Low_complexity_(Seg):seg,hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 MODERATE 1 SNV 1 1 PASS rs1395576684 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 123267716 123267716 T A 1 0 0 0 0 1 0 0 0 16957 1406 49 4 4 TRDN 6 123267716 Missense_Mutation SNP T C3N-00175_T 471932 123267716 47538263 561 10153 EPB41L2 0 . GRCh38 6 130956349 130956349 + Missense_Mutation SNP C C A rs769262800 C3N-00175_T C3N-00175_N C C c.137G>T p.Gly46Val p.G46V ENST00000337057 2/20 218 166 52 325 325 0 strelka-varscan-mutect EPB41L2,missense_variant,p.Gly46Val,ENST00000337057,NM_001431.3;EPB41L2,missense_variant,p.Gly46Val,ENST00000368128,;EPB41L2,missense_variant,p.Gly46Val,ENST00000628542,;EPB41L2,missense_variant,p.Gly46Val,ENST00000527411,;EPB41L2,missense_variant,p.Gly46Val,ENST00000530481,NM_001199388.2;EPB41L2,missense_variant,p.Gly46Val,ENST00000445890,;EPB41L2,missense_variant,p.Gly46Val,ENST00000528282,NM_001252660.1;EPB41L2,missense_variant,p.Gly46Val,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,missense_variant,p.Gly46Val,ENST00000529208,;EPB41L2,missense_variant,p.Gly46Val,ENST00000525271,;EPB41L2,missense_variant,p.Gly46Val,ENST00000527659,;EPB41L2,missense_variant,p.Gly46Val,ENST00000525193,;EPB41L2,missense_variant,p.Gly46Val,ENST00000532499,;EPB41L2,missense_variant,p.Gly46Val,ENST00000531356,;EPB41L2,missense_variant,p.Gly46Val,ENST00000529709,;EPB41L2,missense_variant,p.Gly46Val,ENST00000530707,;EPB41L2,missense_variant,p.Gly46Val,ENST00000526983,;EPB41L2,intron_variant,,ENST00000530148,;EPB41L2,intron_variant,,ENST00000528179,;EPB41L2,intron_variant,,ENST00000526333,; A ENST00000337057 Transcript missense_variant 319/4457 137/3018 46/1005 G/V gGt/gTt rs769262800 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 tolerated(0.2) 2/20 PIRSF_domain:PIRSF002304 MODERATE 1 SNV 1 1 PASS rs769262800 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 130956349 130956349 C A 1 0 0 0 0 1 0 0 0 5000 507 18 2 2 EPB41L2 6 130956349 Missense_Mutation SNP C C3N-00175_T 7688633 130956349 39849630 562 10154 TAAR5 0 . GRCh38 6 132588815 132588815 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.872T>A p.Ile291Asn p.I291N ENST00000258034 1/1 209 178 31 296 296 0 strelka-varscan-mutect TAAR5,missense_variant,p.Ile291Asn,ENST00000258034,NM_003967.2; T ENST00000258034 Transcript missense_variant 872/1014 872/1014 291/337 I/N aTc/aAc 1 -1 TAAR5 HGNC HGNC:30236 protein_coding YES CCDS5156.1 ENSP00000258034 O14804 UPI000013CFAA NM_003967.2 tolerated(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF78,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 132588815 132588815 A T 1 0 0 0 0 1 0 0 0 15887 333 12 4 4 TAAR5 6 132588815 Missense_Mutation SNP A C3N-00175_T 1632466 132588815 38217164 563 10155 UTRN 0 . GRCh38 6 144473801 144473801 + Missense_Mutation SNP G G A rs748671773 C3N-00175_T C3N-00175_N G G c.3148G>A p.Ala1050Thr p.A1050T ENST00000367545 23/74 109 68 41 175 175 0 strelka-varscan-mutect UTRN,missense_variant,p.Ala1050Thr,ENST00000367545,NM_007124.2; A ENST00000367545 Transcript missense_variant 3148/12339 3148/10302 1050/3433 A/T Gca/Aca rs748671773,COSM3017294 1 1 UTRN HGNC HGNC:12635 protein_coding YES CCDS34547.1 ENSP00000356515 P46939 UPI00003673F1 NM_007124.2 deleterious(0.04) 23/74 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF225,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs748671773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 144473801 144473801 G A 1 0 0 0 0 1 0 0 0 17647 1087 38 1 1 UTRN 6 144473801 Missense_Mutation SNP G C3N-00175_T 11884986 144473801 26332178 564 10156 STXBP5 0 . GRCh38 6 147314271 147314271 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1301C>T p.Pro434Leu p.P434L ENST00000321680 13/28 183 141 42 201 201 0 strelka-varscan-mutect STXBP5,missense_variant,p.Pro434Leu,ENST00000367481,NM_139244.4;STXBP5,missense_variant,p.Pro434Leu,ENST00000321680,NM_001127715.2;STXBP5,missense_variant,p.Pro434Leu,ENST00000367480,; T ENST00000321680 Transcript missense_variant 1301/3456 1301/3456 434/1151 P/L cCc/cTc 1 1 STXBP5 HGNC HGNC:19665 protein_coding YES CCDS47499.1 ENSP00000321826 Q5T5C0 UPI0000199FE0 NM_001127715.2 deleterious(0) 13/28 hmmpanther:PTHR10241:SF22,hmmpanther:PTHR10241,SMART_domains:SM00320 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 147314271 147314271 C T 1 0 0 0 0 1 0 0 0 15740 623 22 3 3 STXBP5 6 147314271 Missense_Mutation SNP C C3N-00175_T 2840470 147314271 23491708 565 10157 SYNE1 0 . GRCh38 6 152331340 152331340 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.13345A>T p.Asn4449Tyr p.N4449Y ENST00000367255 78/146 191 132 59 265 264 1 strelka-varscan-mutect SYNE1,missense_variant,p.Asn4449Tyr,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Asn4378Tyr,ENST00000423061,NM_033071.3;SYNE1,splice_region_variant,,ENST00000341594,;SYNE1,5_prime_UTR_variant,,ENST00000448038,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,;SYNE1,downstream_gene_variant,,ENST00000471834,; A ENST00000367255 Transcript missense_variant 13947/27748 13345/26394 4449/8797 N/Y Aac/Tac 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 78/146 Gene3D:1.20.58.60,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 152331340 152331340 T A 1 0 0 0 0 1 0 0 0 15837 1841 64 4 4 SYNE1 6 152331340 Missense_Mutation SNP T C3N-00175_T 5017069 152331340 18474639 566 10158 TIAM2 0 . GRCh38 6 155179114 155179114 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2599C>A p.Pro867Thr p.P867T ENST00000461783 13/29 119 88 31 151 151 0 strelka-varscan-mutect TIAM2,missense_variant,p.Pro867Thr,ENST00000461783,;TIAM2,missense_variant,p.Pro867Thr,ENST00000318981,NM_012454.3;TIAM2,missense_variant,p.Pro891Thr,ENST00000360366,;TIAM2,missense_variant,p.Pro867Thr,ENST00000529824,;TIAM2,missense_variant,p.Pro867Thr,ENST00000528535,;TIAM2,missense_variant,p.Pro203Thr,ENST00000528391,;TIAM2,missense_variant,p.Pro179Thr,ENST00000456877,;TIAM2,upstream_gene_variant,,ENST00000543712,; A ENST00000461783 Transcript missense_variant 3872/6981 2599/5106 867/1701 P/T Cct/Act 1 1 TIAM2 HGNC HGNC:11806 protein_coding YES CCDS34558.1 ENSP00000437188 Q8IVF5 UPI00004DF8BE deleterious(0.01) 13/29 PROSITE_profiles:PS50898,SMART_domains:SM00455,Superfamily_domains:SSF50156 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 155179114 155179114 C A 1 0 0 0 0 1 0 0 0 16325 623 22 2 2 TIAM2 6 155179114 Missense_Mutation SNP C C3N-00175_T 2847774 155179114 15626865 567 10159 TULP4 0 . GRCh38 6 158502309 158502309 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2646C>T p.= p.P882P ENST00000367097 13/14 101 73 28 162 162 0 strelka-varscan-mutect TULP4,synonymous_variant,p.=,ENST00000367097,NM_020245.4;TULP4,intron_variant,,ENST00000367094,NM_001007466.2;TULP4,downstream_gene_variant,,ENST00000613390,; T ENST00000367097 Transcript synonymous_variant 4175/11295 2646/4632 882/1543 P ccC/ccT 1 1 TULP4 HGNC HGNC:15530 protein_coding YES CCDS34561.1 ENSP00000356064 Q9NRJ4 UPI000013CD76 NM_020245.4 13/14 hmmpanther:PTHR16517:SF33,hmmpanther:PTHR16517 LOW 1 SNV 1 1 PASS rs1255350529 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 158502309 158502309 C T 1 0 0 0 0 0 0 0 1 17286 610 22 3 3 TULP4 6 158502309 Silent SNP C C3N-00175_T 3323195 158502309 12303670 568 10160 PLG 0 . GRCh38 6 160731099 160731099 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1305C>A p.= p.P435P ENST00000308192 11/19 189 134 55 227 226 1 strelka-varscan-mutect PLG,synonymous_variant,p.=,ENST00000308192,NM_000301.3;PLG,non_coding_transcript_exon_variant,,ENST00000297289,;PLG,non_coding_transcript_exon_variant,,ENST00000493435,; A ENST00000308192 Transcript synonymous_variant 1368/2741 1305/2433 435/810 P ccC/ccA 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 11/19 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001150,Prints_domain:PR00018,PROSITE_patterns:PS00021,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 160731099 160731099 C A 1 0 0 0 0 0 0 0 1 12181 668 24 2 2 PLG 6 160731099 Silent SNP C C3N-00175_T 2228790 160731099 10074880 569 10161 T 0 . GRCh38 6 166164826 166164826 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.642A>G p.= p.A214A ENST00000296946 5/9 99 61 38 241 241 0 strelka-varscan-mutect T,synonymous_variant,p.=,ENST00000296946,NM_003181.3;T,synonymous_variant,p.=,ENST00000366871,NM_001270484.1;T,synonymous_variant,p.=,ENST00000366876,;T,synonymous_variant,p.=,ENST00000461348,; C ENST00000296946 Transcript synonymous_variant 1111/2436 642/1308 214/435 A gcA/gcG 1 -1 T HGNC HGNC:11515 protein_coding YES CCDS5290.1 ENSP00000296946 O15178 UPI0000126AB5 NM_003181.3 5/9 Gene3D:1h6fA00,Pfam_domain:PF00907,Prints_domain:PR00937,PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF83,SMART_domains:SM00425,Superfamily_domains:SSF49417 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 166164826 166164826 T C 1 0 0 0 0 0 0 0 1 15884 1799 63 5 5 T 6 166164826 Silent SNP T C3N-00175_T 5433727 166164826 4641153 570 10162 UNC93A 0 . GRCh38 6 167304091 167304091 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.798C>A p.Tyr266Ter p.Y266* ENST00000230256 5/8 223 168 55 264 263 1 strelka-varscan-mutect UNC93A,stop_gained,p.Tyr266Ter,ENST00000230256,NM_018974.3;UNC93A,stop_gained,p.Tyr224Ter,ENST00000366829,NM_001143947.1; A ENST00000230256 Transcript stop_gained 973/2116 798/1374 266/457 Y/* taC/taA 1 1 UNC93A HGNC HGNC:12570 protein_coding YES CCDS5300.1 ENSP00000230256 Q86WB7 UPI0000062351 NM_018974.3 5/8 Gene3D:1.20.1250.20,hmmpanther:PTHR19444,hmmpanther:PTHR19444:SF14,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 167304091 167304091 C A 1 0 0 0 0 0 1 0 0 17522 489 17 2 2 UNC93A 6 167304091 Nonsense_Mutation SNP C C3N-00175_T 1139265 167304091 3501888 571 10163 GRID2IP 0 . GRCh38 7 6509203 6509203 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1882C>A p.His628Asn p.H628N ENST00000457091 12/22 38 28 10 43 43 0 strelka-varscan-mutect GRID2IP,missense_variant,p.His628Asn,ENST00000457091,NM_001145118.1;GRID2IP,missense_variant,p.His437Asn,ENST00000452113,;GRID2IP,missense_variant,p.His444Asn,ENST00000435185,; T ENST00000457091 Transcript missense_variant 1882/3636 1882/3636 628/1211 H/N Cac/Aac 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 tolerated(1) 12/22 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 6509203 6509203 G T 1 0 0 0 0 1 0 0 0 6653 1348 47 2 2 GRID2IP 7 6509203 Missense_Mutation SNP G C3N-00175_T 6509203 152836770 572 10164 GRID2IP 0 . GRCh38 7 6521469 6521469 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1044C>A p.= p.P348P ENST00000457091 6/22 73 58 15 87 87 0 strelka-varscan-mutect GRID2IP,synonymous_variant,p.=,ENST00000457091,NM_001145118.1;GRID2IP,synonymous_variant,p.=,ENST00000452113,;GRID2IP,synonymous_variant,p.=,ENST00000435185,; T ENST00000457091 Transcript synonymous_variant 1044/3636 1044/3636 348/1211 P ccC/ccA 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 6/22 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 5 1 PASS rs1326286420 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 6521469 6521469 G T 1 0 0 0 0 0 0 0 1 6653 1335 47 2 2 GRID2IP 7 6521469 Silent SNP G C3N-00175_T 12266 6521469 152824504 573 10165 RPA3 0 . GRCh38 7 7640334 7640334 + Missense_Mutation SNP C C T rs758879887 C3N-00175_T C3N-00175_N C C c.85G>A p.Gly29Arg p.G29R ENST00000223129 5/8 390 314 76 320 320 0 strelka-varscan-mutect RPA3,missense_variant,p.Gly29Arg,ENST00000223129,NM_002947.3;RPA3,missense_variant,p.Gly29Arg,ENST00000396682,;RPA3,intron_variant,,ENST00000406109,;UMAD1,upstream_gene_variant,,ENST00000636849,NM_001302348.1,NM_001302349.1;UMAD1,upstream_gene_variant,,ENST00000482067,;UMAD1,upstream_gene_variant,,ENST00000463725,;RPA3,upstream_gene_variant,,ENST00000401447,;RP11-505D17.1,upstream_gene_variant,,ENST00000469183,;UMAD1,upstream_gene_variant,,ENST00000493246,;UMAD1,upstream_gene_variant,,ENST00000471760,;RPA3,non_coding_transcript_exon_variant,,ENST00000462723,;RPA3,intron_variant,,ENST00000463632,;RPA3,upstream_gene_variant,,ENST00000483031,; T ENST00000223129 Transcript missense_variant 1257/2020 85/366 29/121 G/R Ggg/Agg rs758879887 1 -1 RPA3 HGNC HGNC:10291 protein_coding YES CCDS5356.1 ENSP00000223129 P35244 A4D105 UPI00001122E6 NM_002947.3 deleterious(0) 5/8 hmmpanther:PTHR15114:SF1,hmmpanther:PTHR15114,Gene3D:2.40.50.140,Pfam_domain:PF08661,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS rs758879887 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 7640334 7640334 C T 1 0 0 0 0 1 0 0 0 13790 681 24 3 3 RPA3 7 7640334 Missense_Mutation SNP C C3N-00175_T 1118865 7640334 151705639 574 10166 LRRC72 0 . GRCh38 7 16526965 16526965 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.13C>A p.Pro5Thr p.P5T ENST00000401542 1/9 166 138 28 201 201 0 strelka-mutect LRRC72,missense_variant,p.Pro5Thr,ENST00000401542,NM_001195280.1;SOSTDC1,intron_variant,,ENST00000396652,;LRRC72,non_coding_transcript_exon_variant,,ENST00000482711,;LRRC72,missense_variant,p.Pro5Thr,ENST00000382124,; A ENST00000401542 Transcript missense_variant 70/1000 13/864 5/287 P/T Ccg/Acg 1 1 LRRC72 HGNC HGNC:42972 protein_coding YES CCDS56464.1 ENSP00000384971 A6NJI9 UPI000173A227 NM_001195280.1 deleterious_low_confidence(0.04) 1/9 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 16526965 16526965 C A 1 0 0 0 0 1 0 0 0 8919 623 22 2 2 LRRC72 7 16526965 Missense_Mutation SNP C C3N-00175_T 8886631 16526965 142819008 575 10167 ABCB5 0 . GRCh38 7 20651619 20651619 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.1532C>T p.Pro511Leu p.P511L ENST00000404938 13/28 145 94 51 112 112 0 strelka-varscan-mutect ABCB5,missense_variant,p.Pro511Leu,ENST00000404938,NM_001163941.1;ABCB5,missense_variant,p.Pro66Leu,ENST00000258738,NM_178559.5;ABCB5,missense_variant,p.Pro66Leu,ENST00000443026,NM_001163942.1;ABCB5,missense_variant,p.Pro66Leu,ENST00000406935,NM_001163993.2;ABCB5,non_coding_transcript_exon_variant,,ENST00000477094,; T ENST00000404938 Transcript missense_variant 2184/5811 1532/3774 511/1257 P/L cCt/cTt COSM1134283,COSM452830,COSM452831 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 deleterious(0.01) 13/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,SMART_domains:SM00382,Superfamily_domains:SSF52540 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 20651619 20651619 C T 1 0 0 0 0 1 0 0 0 48 695 24 3 3 ABCB5 7 20651619 Missense_Mutation SNP C C3N-00175_T 4124654 20651619 138694354 576 10168 DNAH11 0 . GRCh38 7 21655847 21655847 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.4960delG p.Ala1654ProfsTer65 p.A1654Pfs*65 ENST00000409508 29/82 126 92 34 101 101 0 sindel-pindel DNAH11,frameshift_variant,p.Ala1654ProfsTer65,ENST00000409508,NM_001277115.1;DNAH11,frameshift_variant,p.Ala1659ProfsTer65,ENST00000328843,;DNAH11,frameshift_variant,p.Ala1659ProfsTer65,ENST00000620169,; - ENST00000409508 Transcript frameshift_variant 4991/14167 4960/13551 1654/4516 A/X Gcc/cc 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 29/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Pfam_domain:PF08393 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 21655847 21655847 G - 1 0 1 0 1 0 0 0 0 4413 1319 46 0 0 DNAH11 7 21655847 Frame_Shift_Del DEL G C3N-00175_T 1004228 21655847 137690126 577 10169 DNAH11 0 . GRCh38 7 21710581 21710581 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.6712T>C p.Phe2238Leu p.F2238L ENST00000409508 41/82 171 121 50 195 195 0 strelka-varscan-mutect DNAH11,missense_variant,p.Phe2238Leu,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.Phe2245Leu,ENST00000328843,;DNAH11,missense_variant,p.Phe2245Leu,ENST00000620169,; C ENST00000409508 Transcript missense_variant 6743/14167 6712/13551 2238/4516 F/L Ttc/Ctc 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 tolerated(0.19) 41/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF07728,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs1375628599 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 21710581 21710581 T C 1 0 0 0 0 1 0 0 0 4413 1609 56 5 5 DNAH11 7 21710581 Missense_Mutation SNP T C3N-00175_T 54734 21710581 137635392 578 10170 DNAH11 0 . GRCh38 7 21750301 21750301 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.8877C>A p.= p.G2959G ENST00000409508 54/82 290 207 83 255 255 0 strelka-varscan-mutect DNAH11,synonymous_variant,p.=,ENST00000409508,NM_001277115.1;DNAH11,synonymous_variant,p.=,ENST00000328843,;DNAH11,synonymous_variant,p.=,ENST00000620169,; A ENST00000409508 Transcript synonymous_variant 8908/14167 8877/13551 2959/4516 G ggC/ggA 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 54/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12780,SMART_domains:SM00382 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 21750301 21750301 C A 1 0 0 0 0 0 0 0 1 4413 697 25 2 2 DNAH11 7 21750301 Silent SNP C C3N-00175_T 39720 21750301 137595672 579 10171 HOXA1 0 . GRCh38 7 27095726 27095726 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.187T>A p.Ser63Thr p.S63T ENST00000343060 1/2 167 146 21 155 155 0 strelka-mutect HOXA1,missense_variant,p.Ser63Thr,ENST00000343060,NM_005522.4;HOXA1,missense_variant,p.Ser63Thr,ENST00000355633,NM_153620.2;HOXA2,downstream_gene_variant,,ENST00000222718,NM_006735.3;HOTAIRM1,intron_variant,,ENST00000495032,;HOTAIRM1,upstream_gene_variant,,ENST00000428939,;HOTAIRM1,upstream_gene_variant,,ENST00000429611,;HOTAIRM1,upstream_gene_variant,,ENST00000434063,;HOTAIRM1,upstream_gene_variant,,ENST00000593300,;HOTAIRM1,upstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,upstream_gene_variant,,ENST00000616712,;HOTAIRM1_5,upstream_gene_variant,,ENST00000619311,;HOTAIRM1_1,upstream_gene_variant,,ENST00000622675,;HOTAIRM1_4,upstream_gene_variant,,ENST00000617934,;HOTAIRM1_3,upstream_gene_variant,,ENST00000619974,;HOXA2,downstream_gene_variant,,ENST00000612779,; T ENST00000343060 Transcript missense_variant 249/2517 187/1008 63/335 S/T Tcg/Acg 1 -1 HOXA1 HGNC HGNC:5099 protein_coding YES CCDS5401.1 ENSP00000343246 P49639 UPI000013C80E NM_005522.4 tolerated(0.64) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 27095726 27095726 A T 1 0 0 0 0 1 0 0 0 7182 246 9 4 4 HOXA1 7 27095726 Missense_Mutation SNP A C3N-00175_T 5345425 27095726 132250247 580 10172 HOXA5 0 . GRCh38 7 27143116 27143116 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.492C>A p.Ser164Arg p.S164R ENST00000222726 1/2 79 46 33 80 80 0 strelka-varscan-mutect HOXA5,missense_variant,p.Ser164Arg,ENST00000222726,NM_019102.3;HOXA3,upstream_gene_variant,,ENST00000317201,;HOXA6,downstream_gene_variant,,ENST00000222728,NM_024014.3;HOXA3,upstream_gene_variant,,ENST00000522788,;HOXA-AS3,intron_variant,,ENST00000521197,;HOXA-AS3,intron_variant,,ENST00000518848,;HOXA-AS3,upstream_gene_variant,,ENST00000518947,;HOXA-AS3,upstream_gene_variant,,ENST00000521231,;RP1-170O19.22,intron_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000518451,;HOXA6,downstream_gene_variant,,ENST00000521478,;HOXA3,upstream_gene_variant,,ENST00000521401,;RP1-170O19.23,downstream_gene_variant,,ENST00000498652,;HOXA5,upstream_gene_variant,,ENST00000520854,; T ENST00000222726 Transcript missense_variant 553/1657 492/813 164/270 S/R agC/agA COSM452918 1 -1 HOXA5 HGNC HGNC:5106 protein_coding YES CCDS5406.1 ENSP00000222726 P20719 UPI000006CEBE NM_019102.3 tolerated(0.37) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF165,hmmpanther:PTHR24326 1 MODERATE 1 SNV 1 1 1 PASS rs965111568 . 0 199 8 3 0 0 0 0 -20 0.9998359 1 1 1 0 T 3 4 39 27143116 27143116 G T 1 0 0 0 0 1 0 0 0 7189 1078 38 1 1 HOXA5 7 27143116 Missense_Mutation SNP G C3N-00175_T 47390 27143116 132202857 581 10173 HOXA9 0 . GRCh38 7 27165274 27165274 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.184G>T p.Val62Leu p.V62L ENST00000343483 1/2 71 58 13 105 105 0 strelka-varscan-mutect HOXA9,missense_variant,p.Val62Leu,ENST00000343483,NM_152739.3;HOXA9,missense_variant,p.Val62Leu,ENST00000396345,;HOXA10-HOXA9,intron_variant,,ENST00000470747,;HOXA9,downstream_gene_variant,,ENST00000384852,;HOXA10-AS,upstream_gene_variant,,ENST00000519935,;HOXA10-AS,upstream_gene_variant,,ENST00000523790,;HOXA10-AS,upstream_gene_variant,,ENST00000519694,;HOXA9,intron_variant,,ENST00000497089,;HOXA9,intron_variant,,ENST00000487384,;HOXA9,intron_variant,,ENST00000465941,;HOXA9,intron_variant,,ENST00000489695,; A ENST00000343483 Transcript missense_variant 257/2060 184/819 62/272 V/L Gtg/Ttg 1 -1 HOXA9 HGNC HGNC:5109 protein_coding YES CCDS5409.1 ENSP00000343619 P31269 UPI0000000CA4 NM_152739.3 deleterious(0.02) 1/2 hmmpanther:PTHR24326:SF226,hmmpanther:PTHR24326,PIRSF_domain:PIRSF037109,Pfam_domain:PF04617 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 27165274 27165274 C A 1 0 0 0 0 1 0 0 0 7192 507 18 2 2 HOXA9 7 27165274 Missense_Mutation SNP C C3N-00175_T 22158 27165274 132180699 582 10174 HOXA10 0 . GRCh38 7 27173584 27173584 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.723C>A p.Phe241Leu p.F241L ENST00000283921 1/2 121 92 29 112 112 0 strelka-varscan-mutect HOXA10,missense_variant,p.Phe241Leu,ENST00000283921,NM_018951.3;HOXA10,missense_variant,p.Pro120Thr,ENST00000613671,;HOXA10,intron_variant,,ENST00000396344,;HOXA10-HOXA9,intron_variant,,ENST00000470747,;HOXA9,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,downstream_gene_variant,,ENST00000519935,;HOXA10-AS,downstream_gene_variant,,ENST00000523790,;HOXA10-AS,downstream_gene_variant,,ENST00000519694,;HOXA9,intron_variant,,ENST00000465941,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA10,upstream_gene_variant,,ENST00000521421,;HOXA10,upstream_gene_variant,,ENST00000524368,;HOXA10,upstream_gene_variant,,ENST00000519593,;HOXA9,upstream_gene_variant,,ENST00000487384,;HOXA9,upstream_gene_variant,,ENST00000489695,; T ENST00000283921 Transcript missense_variant 723/2541 723/1233 241/410 F/L ttC/ttA 1 -1 HOXA10 HGNC HGNC:5100 protein_coding YES CCDS5410.2 ENSP00000283921 P31260 UPI0000EE42DA NM_018951.3 tolerated(0.45) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF52,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1413406253 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 27173584 27173584 G T 1 0 0 0 0 1 0 0 0 7183 1174 41 2 2 HOXA10 7 27173584 Missense_Mutation SNP G C3N-00175_T 8310 27173584 132172389 583 10175 CREB5 0 . GRCh38 7 28809219 28809219 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1059C>A p.= p.T353T ENST00000357727 9/11 110 90 20 92 92 0 strelka-varscan-mutect CREB5,synonymous_variant,p.=,ENST00000357727,NM_182898.3;CREB5,synonymous_variant,p.=,ENST00000396300,NM_004904.3;CREB5,synonymous_variant,p.=,ENST00000396299,NM_182899.4;CREB5,synonymous_variant,p.=,ENST00000396298,NM_001011666.2;CREB5,synonymous_variant,p.=,ENST00000409603,;CREB5,synonymous_variant,p.=,ENST00000426500,;CREB5,upstream_gene_variant,,ENST00000498316,; A ENST00000357727 Transcript synonymous_variant 1449/8532 1059/1527 353/508 T acC/acA 1 1 CREB5 HGNC HGNC:16844 protein_coding YES CCDS5417.1 ENSP00000350359 Q02930 UPI0000457534 NM_182898.3 9/11 PIRSF_domain:PIRSF003153,hmmpanther:PTHR19304,hmmpanther:PTHR19304:SF8,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999884 1 1 1 0 A 2 1 39 28809219 28809219 C A 1 0 0 0 0 0 0 0 1 3660 610 22 2 2 CREB5 7 28809219 Silent SNP C C3N-00175_T 1635635 28809219 130536754 584 10176 CREB5 0 . GRCh38 7 28809385 28809385 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1225G>A p.Glu409Lys p.E409K ENST00000357727 9/11 137 124 13 128 128 0 strelka-varscan-mutect CREB5,missense_variant,p.Glu409Lys,ENST00000357727,NM_182898.3;CREB5,missense_variant,p.Glu402Lys,ENST00000396300,NM_004904.3;CREB5,missense_variant,p.Glu376Lys,ENST00000396299,NM_182899.4;CREB5,missense_variant,p.Glu270Lys,ENST00000396298,NM_001011666.2;CREB5,missense_variant,p.Glu376Lys,ENST00000409603,;CREB5,downstream_gene_variant,,ENST00000426500,;CREB5,upstream_gene_variant,,ENST00000498316,; A ENST00000357727 Transcript missense_variant 1615/8532 1225/1527 409/508 E/K Gaa/Aaa 1 1 CREB5 HGNC HGNC:16844 protein_coding YES CCDS5417.1 ENSP00000350359 Q02930 UPI0000457534 NM_182898.3 deleterious(0) 9/11 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00170,PIRSF_domain:PIRSF003153,PROSITE_profiles:PS50217,hmmpanther:PTHR19304,hmmpanther:PTHR19304:SF8,SMART_domains:SM00338,Superfamily_domains:SSF57959 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 28809385 28809385 G A 1 0 0 0 0 1 0 0 0 3660 943 33 3 3 CREB5 7 28809385 Missense_Mutation SNP G C3N-00175_T 166 28809385 130536588 585 10177 SCRN1 0 . GRCh38 7 29926560 29926560 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1038G>T p.= p.G346G ENST00000434476 7/8 236 177 59 223 223 0 strelka-varscan-mutect SCRN1,synonymous_variant,p.=,ENST00000426154,NM_001145513.1;SCRN1,synonymous_variant,p.=,ENST00000242059,NM_014766.4;SCRN1,synonymous_variant,p.=,ENST00000409497,;SCRN1,synonymous_variant,p.=,ENST00000425819,NM_001145515.1;SCRN1,synonymous_variant,p.=,ENST00000434476,NM_001145514.1; A ENST00000434476 Transcript synonymous_variant 1087/1454 1038/1305 346/434 G ggG/ggT 1 -1 SCRN1 HGNC HGNC:22192 protein_coding YES CCDS47567.1 ENSP00000388942 Q12765 UPI000194EC2F NM_001145514.1 7/8 hmmpanther:PTHR12994:SF7,hmmpanther:PTHR12994 LOW 1 SNV 2 1 PASS rs1350725220 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 29926560 29926560 C A 1 0 0 0 0 0 0 0 1 14208 610 22 2 2 SCRN1 7 29926560 Silent SNP C C3N-00175_T 1117175 29926560 129419413 586 10178 FAM188B 0 . GRCh38 7 30875568 30875568 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1883G>T p.Gly628Val p.G628V ENST00000265299 15/18 295 267 28 258 258 0 strelka-varscan-mutect FAM188B,missense_variant,p.Gly628Val,ENST00000265299,NM_032222.2;RP5-877J2.1,missense_variant,p.Gly94Val,ENST00000509504,;INMT-FAM188B,3_prime_UTR_variant,,ENST00000458257,;FAM188B,non_coding_transcript_exon_variant,,ENST00000409881,; T ENST00000265299 Transcript missense_variant 1960/2733 1883/2274 628/757 G/V gGg/gTg 1 1 FAM188B HGNC HGNC:21916 protein_coding YES CCDS43565.1 ENSP00000265299 Q4G0A6 UPI0000D60E7B NM_032222.2 deleterious(0) 15/18 Pfam_domain:PF13898,hmmpanther:PTHR12473,hmmpanther:PTHR12473:SF4,SMART_domains:SM01174 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 30875568 30875568 G T 1 0 0 0 0 1 0 0 0 5366 1232 43 2 2 FAM188B 7 30875568 Missense_Mutation SNP G C3N-00175_T 949008 30875568 128470405 587 10179 PDE1C 0 . GRCh38 7 31828346 31828346 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1411C>G p.Pro471Ala p.P471A ENST00000396193 13/19 244 188 56 198 198 0 strelka-varscan-mutect PDE1C,missense_variant,p.Pro411Ala,ENST00000396184,NM_001322057.1,NM_001322056.1,NM_001322059.1,NM_005020.3;PDE1C,missense_variant,p.Pro471Ala,ENST00000396193,NM_001191058.2;PDE1C,missense_variant,p.Pro411Ala,ENST00000396191,NM_001191057.2;PDE1C,missense_variant,p.Pro411Ala,ENST00000321453,NM_001191059.2;PDE1C,missense_variant,p.Pro411Ala,ENST00000396182,NM_001191056.2; C ENST00000396193 Transcript missense_variant 2005/5109 1411/2310 471/769 P/A Cct/Gct 1 -1 PDE1C HGNC HGNC:8776 protein_coding YES CCDS55100.1 ENSP00000379496 A0A0A0MS69 UPI00043788D1 NM_001191058.2 deleterious(0) 13/19 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Superfamily_domains:SSF109604 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 31828346 31828346 G C 1 0 0 0 0 1 0 0 0 11723 1203 42 4 4 PDE1C 7 31828346 Missense_Mutation SNP G C3N-00175_T 952778 31828346 127517627 588 10180 FKBP9 0 . GRCh38 7 32976376 32976376 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.739G>C p.Asp247His p.D247H ENST00000538336 5/11 263 249 14 207 207 0 varscan-mutect FKBP9,missense_variant,p.Asp247His,ENST00000538336,NM_001284341.1;FKBP9,missense_variant,p.Asp194His,ENST00000242209,NM_007270.4;FKBP9,upstream_gene_variant,,ENST00000490776,NM_001284343.1;FKBP9,upstream_gene_variant,,ENST00000418354,;FKBP9,non_coding_transcript_exon_variant,,ENST00000469202,;FKBP9,non_coding_transcript_exon_variant,,ENST00000472007,;FKBP9,upstream_gene_variant,,ENST00000489038,;FKBP9,downstream_gene_variant,,ENST00000464334,;FKBP9,upstream_gene_variant,,ENST00000463443,;FKBP9,non_coding_transcript_exon_variant,,ENST00000494374,;FKBP9,non_coding_transcript_exon_variant,,ENST00000485309,; C ENST00000538336 Transcript missense_variant 909/3621 739/1872 247/623 D/H Gac/Cac 1 1 FKBP9 HGNC HGNC:3725 protein_coding YES CCDS64622.1 ENSP00000439250 O95302 UPI0001914EC6 NM_001284341.1 deleterious(0) 5/11 PROSITE_profiles:PS50059,hmmpanther:PTHR10516:SF111,hmmpanther:PTHR10516,Pfam_domain:PF00254,Gene3D:3.10.50.40,Superfamily_domains:SSF54534 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 32976376 32976376 G C 1 0 0 0 0 1 0 0 0 5778 1290 45 4 4 FKBP9 7 32976376 Missense_Mutation SNP G C3N-00175_T 1148030 32976376 126369597 589 10181 EEPD1 0 . GRCh38 7 36299077 36299077 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.1581G>A p.= p.V527V ENST00000242108 8/8 257 178 79 289 289 0 strelka-varscan-mutect EEPD1,synonymous_variant,p.=,ENST00000242108,NM_030636.2;EEPD1,synonymous_variant,p.=,ENST00000534978,;EEPD1,intron_variant,,ENST00000444777,;EEPD1,non_coding_transcript_exon_variant,,ENST00000468591,;EEPD1,downstream_gene_variant,,ENST00000487069,; A ENST00000242108 Transcript synonymous_variant 2299/4765 1581/1710 527/569 V gtG/gtA 1 1 EEPD1 HGNC HGNC:22223 protein_coding YES CCDS34619.1 ENSP00000242108 Q7L9B9 UPI000020ED9D NM_030636.2 8/8 hmmpanther:PTHR21180:SF32,hmmpanther:PTHR21180,Gene3D:3.60.10.10,Superfamily_domains:SSF56219 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 36299077 36299077 G A 1 0 0 0 0 0 0 0 1 4763 1335 47 3 3 EEPD1 7 36299077 Silent SNP G C3N-00175_T 3322701 36299077 123046896 590 10182 KIAA0895 0 . GRCh38 7 36357074 36357074 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.695C>T p.Ser232Phe p.S232F ENST00000297063 3/7 325 300 25 305 305 0 strelka-varscan-mutect KIAA0895,missense_variant,p.Ser181Phe,ENST00000317020,NM_015314.2;KIAA0895,missense_variant,p.Ser232Phe,ENST00000297063,NM_001100425.1;KIAA0895,missense_variant,p.Ser219Phe,ENST00000338533,NM_001199707.1;KIAA0895,missense_variant,p.Ser219Phe,ENST00000415803,;KIAA0895,missense_variant,p.Ser181Phe,ENST00000440378,NM_001199706.1;KIAA0895,missense_variant,p.Ser81Phe,ENST00000436884,NM_001199708.1;KIAA0895,missense_variant,p.Ser99Phe,ENST00000429651,;KIAA0895,intron_variant,,ENST00000453212,NM_001300956.1;KIAA0895,intron_variant,,ENST00000431396,;KIAA0895,intron_variant,,ENST00000480192,;KIAA0895,intron_variant,,ENST00000483526,;KIAA0895,intron_variant,,ENST00000483360,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000493327,; A ENST00000297063 Transcript missense_variant 746/4153 695/1563 232/520 S/F tCt/tTt 1 -1 KIAA0895 HGNC HGNC:22206 protein_coding YES CCDS43570.1 ENSP00000297063 Q8NCT3 UPI000013E3C0 NM_001100425.1 deleterious(0) 3/7 hmmpanther:PTHR31817,hmmpanther:PTHR31817:SF3 MODERATE 1 SNV 1 1 PASS rs1392294176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 36357074 36357074 G A 1 0 0 0 0 1 0 0 0 8092 942 33 3 3 KIAA0895 7 36357074 Missense_Mutation SNP G C3N-00175_T 57997 36357074 122988899 591 10183 NME8 0 . GRCh38 7 37884392 37884392 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1084T>A p.Cys362Ser p.C362S ENST00000199447 13/18 149 114 35 233 233 0 strelka-varscan-mutect NME8,missense_variant,p.Cys362Ser,ENST00000199447,NM_016616.4;NME8,missense_variant,p.Cys362Ser,ENST00000440017,;EPDR1,intron_variant,,ENST00000476620,;NME8,3_prime_UTR_variant,,ENST00000426106,; A ENST00000199447 Transcript missense_variant 1456/2312 1084/1767 362/588 C/S Tgc/Agc 1 1 NME8 HGNC HGNC:16473 protein_coding YES CCDS5452.1 ENSP00000199447 Q8N427 UPI00000700CB NM_016616.4 deleterious(0.03) 13/18 Gene3D:3.30.70.141,Pfam_domain:PF00334,hmmpanther:PTHR11349,hmmpanther:PTHR11349:SF65,SMART_domains:SM00562,Superfamily_domains:SSF54919 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 37884392 37884392 T A 1 0 0 0 0 1 0 0 0 10534 1696 59 4 4 NME8 7 37884392 Missense_Mutation SNP T C3N-00175_T 1527318 37884392 121461581 592 10184 C7orf25 0 . GRCh38 7 42910489 42910489 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.586G>C p.Gly196Arg p.G196R ENST00000447342 2/2 217 193 24 189 189 0 strelka-varscan-mutect C7orf25,missense_variant,p.Gly138Arg,ENST00000350427,NM_024054.2;C7orf25,missense_variant,p.Gly196Arg,ENST00000447342,NM_001099858.1;C7orf25,missense_variant,p.Gly138Arg,ENST00000438029,;C7orf25,missense_variant,p.Gly196Arg,ENST00000431882,;C7orf25,missense_variant,p.Gly138Arg,ENST00000425683,;C7orf25,downstream_gene_variant,,ENST00000432637,;RP11-111K18.1,3_prime_UTR_variant,,ENST00000442788,;RP11-111K18.1,downstream_gene_variant,,ENST00000433579,; G ENST00000447342 Transcript missense_variant 609/1823 586/1440 196/479 G/R Ggt/Cgt 1 -1 C7orf25 HGNC HGNC:21703 protein_coding YES CCDS47576.1 ENSP00000413029 Q9BPX7 UPI000159689A NM_001099858.1 deleterious(0) 2/2 Pfam_domain:PF07000,hmmpanther:PTHR13379 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 42910489 42910489 C G 1 0 0 0 0 1 0 0 0 2135 594 21 4 4 C7orf25 7 42910489 Missense_Mutation SNP C C3N-00175_T 5026097 42910489 116435484 593 10185 39 2 C7orf25 0 . GRCh38 7 42910499 42910499 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.576G>T p.Arg192Ser p.R192S ENST00000447342 2/2 203 138 65 192 192 0 strelka-varscan-mutect C7orf25,missense_variant,p.Arg134Ser,ENST00000350427,NM_024054.2;C7orf25,missense_variant,p.Arg192Ser,ENST00000447342,NM_001099858.1;C7orf25,missense_variant,p.Arg134Ser,ENST00000438029,;C7orf25,missense_variant,p.Arg192Ser,ENST00000431882,;C7orf25,missense_variant,p.Arg134Ser,ENST00000425683,;C7orf25,downstream_gene_variant,,ENST00000432637,;RP11-111K18.1,3_prime_UTR_variant,,ENST00000442788,;RP11-111K18.1,downstream_gene_variant,,ENST00000433579,; A ENST00000447342 Transcript missense_variant 599/1823 576/1440 192/479 R/S agG/agT COSM4631207,COSM4631208,COSM4784438,COSM746889 1 -1 C7orf25 HGNC HGNC:21703 protein_coding YES CCDS47576.1 ENSP00000413029 Q9BPX7 UPI000159689A NM_001099858.1 deleterious(0.02) 2/2 Pfam_domain:PF07000,hmmpanther:PTHR13379 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 42910499 42910499 C A 1 0 0 0 0 1 0 0 0 2135 622 22 2 2 C7orf25 7 42910499 Missense_Mutation SNP C C3N-00175_T 10 42910499 116435474 594 10186 39 2 HECW1 0 . GRCh38 7 43311837 43311837 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.102G>T p.= p.R34R ENST00000395891 4/30 223 158 65 210 210 0 strelka-varscan-mutect HECW1,synonymous_variant,p.=,ENST00000395891,NM_015052.4;HECW1,synonymous_variant,p.=,ENST00000453890,NM_001287059.1;HECW1,non_coding_transcript_exon_variant,,ENST00000492310,;HECW1,non_coding_transcript_exon_variant,,ENST00000464944,;HECW1,non_coding_transcript_exon_variant,,ENST00000490954,; T ENST00000395891 Transcript synonymous_variant 707/9501 102/4821 34/1606 R cgG/cgT 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 4/30 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 43311837 43311837 G T 1 0 0 0 0 0 0 0 1 6924 1248 44 2 2 HECW1 7 43311837 Silent SNP G C3N-00175_T 401338 43311837 116034136 595 10187 40 2 HECW1 0 . GRCh38 7 43311842 43311842 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.107A>T p.Lys36Met p.K36M ENST00000395891 4/30 224 158 66 214 214 0 strelka-varscan-mutect HECW1,missense_variant,p.Lys36Met,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Lys36Met,ENST00000453890,NM_001287059.1;HECW1,non_coding_transcript_exon_variant,,ENST00000492310,;HECW1,non_coding_transcript_exon_variant,,ENST00000464944,;HECW1,non_coding_transcript_exon_variant,,ENST00000490954,; T ENST00000395891 Transcript missense_variant 712/9501 107/4821 36/1606 K/M aAg/aTg 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious_low_confidence(0) 4/30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43311842 43311842 A T 1 0 0 0 0 1 0 0 0 6924 72 3 4 4 HECW1 7 43311842 Missense_Mutation SNP A C3N-00175_T 5 43311842 116034131 596 10188 40 2 HECW1 0 . GRCh38 7 43444267 43444267 + Silent SNP G G A rs763007524 C3N-00175_T C3N-00175_N G G c.1095G>A p.= p.Q365Q ENST00000395891 11/30 87 69 18 91 91 0 strelka-varscan-mutect HECW1,synonymous_variant,p.=,ENST00000395891,NM_015052.4;HECW1,synonymous_variant,p.=,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript synonymous_variant 1700/9501 1095/4821 365/1606 Q caG/caA rs763007524,COSM3929044,COSM3929045 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 11/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs763007524 . 0 201 9 0 0 0 0 0 -20 0.9999967 1 1 1 0 A 2 1 39 43444267 43444267 G A 1 0 0 0 0 0 0 0 1 6924 991 35 3 3 HECW1 7 43444267 Silent SNP G C3N-00175_T 132425 43444267 115901706 597 10189 HECW1 0 . GRCh38 7 43507168 43507168 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.3663C>A p.= p.S1221S ENST00000395891 22/30 228 178 50 207 207 0 strelka-varscan-mutect HECW1,synonymous_variant,p.=,ENST00000395891,NM_015052.4;HECW1,synonymous_variant,p.=,ENST00000453890,NM_001287059.1;HECW1,intron_variant,,ENST00000429529,;AC011738.4,downstream_gene_variant,,ENST00000436105,; A ENST00000395891 Transcript synonymous_variant 4268/9501 3663/4821 1221/1606 S tcC/tcA 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 22/30 Low_complexity_(Seg):seg,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 43507168 43507168 C A 1 0 0 0 0 0 0 0 1 6924 610 22 2 2 HECW1 7 43507168 Silent SNP C C3N-00175_T 62901 43507168 115838805 598 10190 AEBP1 0 . GRCh38 7 44110241 44110241 + Missense_Mutation SNP C C T rs757009902 C3N-00175_T C3N-00175_N C C c.1295C>T p.Ala432Val p.A432V ENST00000223357 11/21 314 279 35 390 390 0 strelka-varscan-mutect AEBP1,missense_variant,p.Ala432Val,ENST00000223357,NM_001129.4;AEBP1,upstream_gene_variant,,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,NM_001256879.1;POLD2,downstream_gene_variant,,ENST00000452185,NM_001127218.2;POLD2,downstream_gene_variant,,ENST00000610533,NM_006230.3;POLD2,downstream_gene_variant,,ENST00000223361,;AEBP1,downstream_gene_variant,,ENST00000455443,;AEBP1,downstream_gene_variant,,ENST00000449162,;AEBP1,upstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,downstream_gene_variant,,ENST00000453052,;AEBP1,upstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000489883,; T ENST00000223357 Transcript missense_variant 1600/4081 1295/3477 432/1158 A/V gCg/gTg rs757009902,COSM3881189,COSM601268 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 deleterious(0) 11/21 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_patterns:PS01285,PROSITE_profiles:PS50022,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF48,SMART_domains:SM00231,Superfamily_domains:SSF49785 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs757009902 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44110241 44110241 C T 1 0 0 0 0 1 0 0 0 424 768 27 1 1 AEBP1 7 44110241 Missense_Mutation SNP C C3N-00175_T 603073 44110241 115235732 599 10191 OGDH 0 . GRCh38 7 44647732 44647732 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.490G>A p.Asp164Asn p.D164N ENST00000222673 4/23 144 132 12 152 152 0 strelka-varscan-mutect OGDH,missense_variant,p.Asp164Asn,ENST00000222673,NM_002541.3;OGDH,missense_variant,p.Asp164Asn,ENST00000631326,;OGDH,missense_variant,p.Asp164Asn,ENST00000444676,;OGDH,missense_variant,p.Asp164Asn,ENST00000443864,NM_001003941.2;OGDH,missense_variant,p.Asp164Asn,ENST00000419661,;OGDH,intron_variant,,ENST00000449767,NM_001165036.1;OGDH,intron_variant,,ENST00000447398,;OGDH,intron_variant,,ENST00000439616,; A ENST00000222673 Transcript missense_variant 532/4181 490/3072 164/1023 D/N Gac/Aac 1 1 OGDH HGNC HGNC:8124 protein_coding YES CCDS34627.1 ENSP00000222673 Q02218 UPI000006D5FE NM_002541.3 tolerated(0.07) 4/23 PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF7,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 44647732 44647732 G A 1 0 0 0 0 1 0 0 0 10913 1290 45 3 3 OGDH 7 44647732 Missense_Mutation SNP G C3N-00175_T 537491 44647732 114698241 600 10192 ZMIZ2 0 . GRCh38 7 44759378 44759378 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.911C>T p.Ser304Phe p.S304F ENST00000309315 7/19 108 96 12 136 136 0 strelka-varscan-mutect ZMIZ2,missense_variant,p.Ser304Phe,ENST00000309315,NM_031449.3;ZMIZ2,missense_variant,p.Ser304Phe,ENST00000441627,;ZMIZ2,missense_variant,p.Ser272Phe,ENST00000433667,;ZMIZ2,missense_variant,p.Ser272Phe,ENST00000413916,NM_001300959.1;ZMIZ2,missense_variant,p.Ser304Phe,ENST00000265346,NM_174929.2;ZMIZ2,missense_variant,p.Ser304Phe,ENST00000615423,;ZMIZ2,downstream_gene_variant,,ENST00000457123,;ZMIZ2,upstream_gene_variant,,ENST00000492558,;ZMIZ2,upstream_gene_variant,,ENST00000478045,;ZMIZ2,upstream_gene_variant,,ENST00000463056,;ZMIZ2,upstream_gene_variant,,ENST00000480964,;ZMIZ2,downstream_gene_variant,,ENST00000492001,;ZMIZ2,downstream_gene_variant,,ENST00000416856,; T ENST00000309315 Transcript missense_variant 1034/5144 911/2763 304/920 S/F tCc/tTc COSM3639048 1 1 ZMIZ2 HGNC HGNC:22229 protein_coding YES CCDS43576.1 ENSP00000311778 Q8NF64 UPI00001D747B NM_031449.3 deleterious(0) 7/19 Low_complexity_(Seg):seg,hmmpanther:PTHR10782:SF38,hmmpanther:PTHR10782 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44759378 44759378 C T 1 0 0 0 0 1 0 0 0 18277 855 30 3 3 ZMIZ2 7 44759378 Missense_Mutation SNP C C3N-00175_T 111646 44759378 114586595 601 10193 TBRG4 0 . GRCh38 7 45101853 45101853 + Missense_Mutation SNP C C A rs766311842 C3N-00175_T C3N-00175_N C C c.1539G>T p.Glu513Asp p.E513D ENST00000258770 8/11 132 111 21 100 100 0 strelka-varscan-mutect TBRG4,missense_variant,p.Glu513Asp,ENST00000258770,NM_004749.3;TBRG4,missense_variant,p.Glu403Asp,ENST00000395655,;TBRG4,missense_variant,p.Glu513Asp,ENST00000494076,NM_001261834.1;TBRG4,missense_variant,p.Glu403Asp,ENST00000361278,NM_030900.3,NM_199122.2;TBRG4,missense_variant,p.Glu228Asp,ENST00000483615,;TBRG4,downstream_gene_variant,,ENST00000478532,;TBRG4,downstream_gene_variant,,ENST00000461363,;SNORA5C,downstream_gene_variant,,ENST00000364902,;SNORA5A,downstream_gene_variant,,ENST00000384111,;SNORA5B,downstream_gene_variant,,ENST00000363786,;TBRG4,non_coding_transcript_exon_variant,,ENST00000495973,;TBRG4,non_coding_transcript_exon_variant,,ENST00000478116,;TBRG4,non_coding_transcript_exon_variant,,ENST00000482482,;TBRG4,downstream_gene_variant,,ENST00000488222,;TBRG4,downstream_gene_variant,,ENST00000484326,;TBRG4,downstream_gene_variant,,ENST00000477328,; A ENST00000258770 Transcript missense_variant 1661/2243 1539/1896 513/631 E/D gaG/gaT rs766311842 1 -1 TBRG4 HGNC HGNC:17443 protein_coding YES CCDS5501.1 ENSP00000258770 Q969Z0 UPI0000071F89 NM_004749.3 tolerated(0.8) 8/11 Pfam_domain:PF08368,hmmpanther:PTHR21228,hmmpanther:PTHR21228:SF26 MODERATE 1 SNV 1 1 PASS rs766311842 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 45101853 45101853 C A 1 0 0 0 0 1 0 0 0 16054 680 24 2 2 TBRG4 7 45101853 Missense_Mutation SNP C C3N-00175_T 342475 45101853 114244120 602 10194 ADCY1 0 . GRCh38 7 45610419 45610419 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.830T>C p.Met277Thr p.M277T ENST00000297323 3/20 181 129 52 192 192 0 strelka-varscan-mutect ADCY1,missense_variant,p.Met277Thr,ENST00000297323,NM_021116.2;ADCY1,missense_variant,p.Met52Thr,ENST00000432715,NM_001281768.1;ADCY1,missense_variant,p.Met52Thr,ENST00000621543,; C ENST00000297323 Transcript missense_variant 852/12503 830/3360 277/1119 M/T aTg/aCg 1 1 ADCY1 HGNC HGNC:232 protein_coding YES CCDS34631.1 ENSP00000297323 Q08828 UPI0000199C4A NM_021116.2 deleterious(0.01) 3/20 hmmpanther:PTHR11920:SF336,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,Pfam_domain:PF16214,SMART_domains:SM00044 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 45610419 45610419 T C 1 0 0 0 0 1 0 0 0 336 1464 51 5 5 ADCY1 7 45610419 Missense_Mutation SNP T C3N-00175_T 508566 45610419 113735554 603 10195 PKD1L1 0 . GRCh38 7 47833144 47833144 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.6283C>A p.His2095Asn p.H2095N ENST00000289672 41/57 193 153 40 223 223 0 strelka-mutect PKD1L1,missense_variant,p.His2095Asn,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; T ENST00000289672 Transcript missense_variant 6334/9092 6283/8550 2095/2849 H/N Cac/Aac 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.5) 41/57 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF145 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 47833144 47833144 G T 1 0 0 0 0 1 0 0 0 12060 1348 47 2 2 PKD1L1 7 47833144 Missense_Mutation SNP G C3N-00175_T 2222725 47833144 111512829 604 10196 ABCA13 0 . GRCh38 7 48219391 48219391 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.325G>T p.Val109Phe p.V109F ENST00000435803 4/62 270 208 62 239 239 0 strelka-varscan-mutect ABCA13,missense_variant,p.Val109Phe,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Val109Phe,ENST00000417403,; T ENST00000435803 Transcript missense_variant 349/17184 325/15177 109/5058 V/F Gtc/Ttc 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.09) 4/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 48219391 48219391 G T 1 0 0 0 0 1 0 0 0 35 1029 36 2 2 ABCA13 7 48219391 Missense_Mutation SNP G C3N-00175_T 386247 48219391 111126582 605 10197 ZNF479 0 . GRCh38 7 57126029 57126029 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.251C>A p.Ala84Asp p.A84D ENST00000331162 4/5 200 169 31 216 215 1 strelka-varscan-mutect ZNF479,missense_variant,p.Ala84Asp,ENST00000331162,NM_033273.2;ZNF479,missense_variant,p.Ala84Asp,ENST00000319636,;ZNF479,missense_variant,p.Ala84Asp,ENST00000620639,; T ENST00000331162 Transcript missense_variant 522/2072 251/1575 84/524 A/D gCc/gAc 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 tolerated(0.28) 4/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 57126029 57126029 G T 1 0 0 0 0 1 0 0 0 18505 1203 42 2 2 ZNF479 7 57126029 Missense_Mutation SNP G C3N-00175_T 8906638 57126029 102219944 606 10198 WBSCR17 0 . GRCh38 7 71670084 71670084 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1379A>T p.Tyr460Phe p.Y460F ENST00000333538 8/11 278 248 30 260 260 0 strelka-varscan-mutect WBSCR17,missense_variant,p.Tyr460Phe,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Tyr381Phe,ENST00000618959,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; T ENST00000333538 Transcript missense_variant 2013/3884 1379/1797 460/598 Y/F tAc/tTc 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 tolerated(0.1) 8/11 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 71670084 71670084 A T 1 0 0 0 0 1 0 0 0 17823 391 14 4 4 WBSCR17 7 71670084 Missense_Mutation SNP A C3N-00175_T 14544055 71670084 87675889 607 10199 VPS37D 0 . GRCh38 7 73670093 73670093 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.384G>A p.= p.Q128Q ENST00000324941 3/4 209 190 19 259 259 0 strelka-varscan-mutect VPS37D,synonymous_variant,p.=,ENST00000324941,NM_001077621.1;VPS37D,intron_variant,,ENST00000451519,; A ENST00000324941 Transcript synonymous_variant 518/1624 384/756 128/251 Q caG/caA 1 1 VPS37D HGNC HGNC:18287 protein_coding YES CCDS43596.1 ENSP00000320416 Q86XT2 UPI000020E8D4 NM_001077621.1 3/4 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51314,hmmpanther:PTHR13678:SF12,hmmpanther:PTHR13678,Pfam_domain:PF07200 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 73670093 73670093 G A 1 0 0 0 0 0 0 0 1 17754 991 35 3 3 VPS37D 7 73670093 Silent SNP G C3N-00175_T 2000009 73670093 85675880 608 10200 CLIP2 0 . GRCh38 7 74338747 74338747 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.421C>A p.= p.R141R ENST00000223398 3/17 234 173 61 311 310 1 strelka-varscan-mutect CLIP2,synonymous_variant,p.=,ENST00000223398,NM_003388.4;CLIP2,synonymous_variant,p.=,ENST00000361545,NM_032421.2;CLIP2,synonymous_variant,p.=,ENST00000395060,; A ENST00000223398 Transcript synonymous_variant 748/5563 421/3141 141/1046 R Cgg/Agg 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 3/17 Gene3D:2.30.30.190,Pfam_domain:PF01302,PROSITE_profiles:PS50245,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10,SMART_domains:SM01052,Superfamily_domains:SSF74924 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 74338747 74338747 C A 1 0 0 0 0 0 0 0 1 3302 759 27 1 1 CLIP2 7 74338747 Silent SNP C C3N-00175_T 668654 74338747 85007226 609 10201 CACNA2D1 0 . GRCh38 7 81950507 81950507 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.3161A>T p.Glu1054Val p.E1054V ENST00000356860 39/39 202 151 51 242 241 1 strelka-varscan-mutect CACNA2D1,missense_variant,p.Glu1054Val,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Glu1066Val,ENST00000356253,; A ENST00000356860 Transcript missense_variant,splice_region_variant 3500/7563 3161/3276 1054/1091 E/V gAg/gTg 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 deleterious(0) 39/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 81950507 81950507 T A 1 0 0 0 0 1 0 0 0 2236 1565 54 4 4 CACNA2D1 7 81950507 Missense_Mutation SNP T C3N-00175_T 7611760 81950507 77395466 610 10202 C7orf62 0 . GRCh38 7 88794662 88794662 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.281C>A p.Thr94Asn p.T94N ENST00000297203 2/2 191 147 44 178 178 0 strelka-varscan-mutect C7orf62,missense_variant,p.Thr94Asn,ENST00000297203,NM_152706.3;ZNF804B,intron_variant,,ENST00000333190,NM_181646.3; T ENST00000297203 Transcript missense_variant 467/1023 281/762 94/253 T/N aCt/aAt 1 -1 C7orf62 HGNC HGNC:22402 protein_coding YES CCDS34678.1 ENSP00000297203 Q8TBZ9 UPI000005034C NM_152706.3 tolerated(0.08) 2/2 hmmpanther:PTHR34035,hmmpanther:PTHR34035:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 88794662 88794662 G T 1 0 0 0 0 1 0 0 0 2146 1029 36 2 2 C7orf62 7 88794662 Missense_Mutation SNP G C3N-00175_T 6844155 88794662 70551311 611 10203 CYP51A1 0 . GRCh38 7 92127631 92127631 + Missense_Mutation SNP C C A rs766245719 C3N-00175_T C3N-00175_N C C c.469G>T p.Val157Phe p.V157F ENST00000003100 4/10 161 140 21 272 271 1 strelka-varscan CYP51A1,missense_variant,p.Val157Phe,ENST00000003100,NM_000786.3;CYP51A1,missense_variant,p.Val52Phe,ENST00000450723,NM_001146152.1;CYP51A1,upstream_gene_variant,,ENST00000422867,;CYP51A1,downstream_gene_variant,,ENST00000435873,;LRRD1,splice_region_variant,,ENST00000422722,; A ENST00000003100 Transcript missense_variant,splice_region_variant 635/3210 469/1530 157/509 V/F Gtt/Ttt rs766245719 1 -1 CYP51A1 HGNC HGNC:2649 protein_coding YES CCDS5623.1 ENSP00000003100 A0A0C4DFL7 UPI000013C4D5 NM_000786.3 deleterious(0) 4/10 hmmpanther:PTHR24286:SF24,hmmpanther:PTHR24286,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 92127631 92127631 C A 1 0 0 0 0 1 0 0 0 3998 521 18 2 2 CYP51A1 7 92127631 Missense_Mutation SNP C C3N-00175_T 3332969 92127631 67218342 612 10204 KRIT1 0 . GRCh38 7 92235500 92235500 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.632G>T p.Ser211Ile p.S211I ENST00000394507 9/20 258 202 56 352 352 0 strelka-varscan-mutect KRIT1,missense_variant,p.Ser211Ile,ENST00000394507,NM_194456.1;KRIT1,missense_variant,p.Ser211Ile,ENST00000340022,NM_194455.1,NM_004912.3;KRIT1,missense_variant,p.Ser211Ile,ENST00000412043,;KRIT1,missense_variant,p.Ser211Ile,ENST00000394505,NM_194454.1;KRIT1,missense_variant,p.Ser211Ile,ENST00000394503,NM_001013406.1;KRIT1,missense_variant,p.Ser211Ile,ENST00000458177,;KRIT1,intron_variant,,ENST00000445516,;KRIT1,downstream_gene_variant,,ENST00000454017,;KRIT1,downstream_gene_variant,,ENST00000433016,;KRIT1,downstream_gene_variant,,ENST00000430102,;KRIT1,downstream_gene_variant,,ENST00000440209,;KRIT1,non_coding_transcript_exon_variant,,ENST00000486261,;KRIT1,non_coding_transcript_exon_variant,,ENST00000475770,; A ENST00000394507 Transcript missense_variant 1416/4762 632/2211 211/736 S/I aGt/aTt 1 -1 KRIT1 HGNC HGNC:1573 protein_coding YES CCDS5624.1 ENSP00000378015 O00522 A4D1F7 UPI000006F5AA NM_194456.1 tolerated(0.07) 9/20 hmmpanther:PTHR13283 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 92235500 92235500 C A 1 0 0 0 0 1 0 0 0 8327 565 20 2 2 KRIT1 7 92235500 Missense_Mutation SNP C C3N-00175_T 107869 92235500 67110473 613 10205 ERVW-1 0 . GRCh38 7 92470236 92470236 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.146C>A p.Ala49Asp p.A49D ENST00000493463 1/1 87 65 22 96 96 0 strelka-varscan-mutect ERVW-1,missense_variant,p.Ala49Asp,ENST00000493463,NM_014590.3;ERVW-1,missense_variant,p.Ala49Asp,ENST00000603053,NM_001130925.1;AC007566.10,intron_variant,,ENST00000427458,;ERVW-1,intron_variant,,ENST00000604270,;ERVW-1,intron_variant,,ENST00000603704,;ERVW-1,downstream_gene_variant,,ENST00000603252,; T ENST00000493463 Transcript missense_variant 1070/2925 146/1617 49/538 A/D gCc/gAc 1 -1 ERVW-1 HGNC HGNC:13525 protein_coding YES CCDS5626.1 ENSP00000419945 Q9UQF0 D0EYG5 UPI00000389BB NM_014590.3 tolerated_low_confidence(0.09) 1/1 hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF48 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 92470236 92470236 G T 1 0 0 0 0 1 0 0 0 5108 1203 42 2 2 ERVW-1 7 92470236 Missense_Mutation SNP G C3N-00175_T 234736 92470236 66875737 614 10206 TECPR1 0 . GRCh38 7 98225061 98225061 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2555G>T p.Gly852Val p.G852V ENST00000447648 18/26 168 131 37 176 176 0 strelka-varscan-mutect TECPR1,missense_variant,p.Gly852Val,ENST00000447648,NM_015395.2;TECPR1,non_coding_transcript_exon_variant,,ENST00000479975,;TECPR1,non_coding_transcript_exon_variant,,ENST00000476659,;TECPR1,downstream_gene_variant,,ENST00000479911,;TECPR1,upstream_gene_variant,,ENST00000462511,;TECPR1,non_coding_transcript_exon_variant,,ENST00000490842,;TECPR1,upstream_gene_variant,,ENST00000463402,;TECPR1,downstream_gene_variant,,ENST00000483740,;TECPR1,upstream_gene_variant,,ENST00000474915,; A ENST00000447648 Transcript missense_variant 2855/6564 2555/3498 852/1165 G/V gGg/gTg 1 -1 TECPR1 HGNC HGNC:22214 protein_coding YES CCDS47648.1 ENSP00000404923 Q7Z6L1 UPI0000161940 NM_015395.2 deleterious(0.03) 18/26 Pfam_domain:PF06398,hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1,SMART_domains:SM00693 MODERATE 1 SNV 1 1 PASS rs933925712 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 98225061 98225061 C A 1 0 0 0 0 1 0 0 0 16154 623 22 2 2 TECPR1 7 98225061 Missense_Mutation SNP C C3N-00175_T 5754825 98225061 61120912 615 10207 ZKSCAN1 0 . GRCh38 7 100033646 100033646 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1141G>T p.Glu381Ter p.E381* ENST00000324306 6/6 211 170 41 237 237 0 strelka-varscan-mutect ZKSCAN1,stop_gained,p.Glu381Ter,ENST00000324306,NM_003439.2;ZKSCAN1,stop_gained,p.Glu345Ter,ENST00000620510,;ZKSCAN1,stop_gained,p.Glu168Ter,ENST00000535170,NM_001287055.1;ZKSCAN1,stop_gained,p.Glu345Ter,ENST00000426572,NM_001287054.1; T ENST00000324306 Transcript stop_gained 1375/9418 1141/1692 381/563 E/* Gaa/Taa 1 1 ZKSCAN1 HGNC HGNC:13101 protein_coding YES CCDS34698.1 ENSP00000323148 P17029 UPI00000726DD NM_003439.2 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR23226,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 100033646 100033646 G T 1 0 0 0 0 0 1 0 0 18264 1291 45 2 2 ZKSCAN1 7 100033646 Nonsense_Mutation SNP G C3N-00175_T 1808585 100033646 59312327 616 10208 MBLAC1 0 . GRCh38 7 100128153 100128153 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.758A>T p.Gln253Leu p.Q253L ENST00000398075 2/2 118 85 33 142 142 0 strelka-varscan-mutect MBLAC1,missense_variant,p.Gln253Leu,ENST00000398075,NM_203397.1;CNPY4,downstream_gene_variant,,ENST00000262932,NM_152755.1;MBLAC1,downstream_gene_variant,,ENST00000421390,;RP11-506M12.1,upstream_gene_variant,,ENST00000494221,;AC073842.19,upstream_gene_variant,,ENST00000376482,;CNPY4,downstream_gene_variant,,ENST00000480692,;CNPY4,downstream_gene_variant,,ENST00000462193,; T ENST00000398075 Transcript missense_variant 1157/1502 758/801 253/266 Q/L cAg/cTg 1 1 MBLAC1 HGNC HGNC:22180 protein_coding YES CCDS43620.1 ENSP00000381150 A4D2B0 UPI000013FF40 NM_203397.1 tolerated_low_confidence(0.3) 2/2 hmmpanther:PTHR23200:SF47,hmmpanther:PTHR23200 MODERATE 1 SNV 1 1 PASS rs775928467 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 100128153 100128153 A T 1 0 0 0 0 1 0 0 0 9283 188 7 4 4 MBLAC1 7 100128153 Missense_Mutation SNP A C3N-00175_T 94507 100128153 59217820 617 10209 STAG3 0 . GRCh38 7 100200970 100200970 + Splice_Site SNP G G C novel C3N-00175_T C3N-00175_N G G c.2061+1G>C p.X687_splice ENST00000615138 129 110 19 150 150 0 strelka-varscan-mutect STAG3,splice_donor_variant,,ENST00000426455,NM_001282716.1;STAG3,splice_donor_variant,,ENST00000615138,NM_001282717.1;STAG3,splice_donor_variant,,ENST00000620100,;STAG3,splice_donor_variant,,ENST00000317296,NM_012447.3;STAG3,splice_donor_variant,,ENST00000394018,NM_001282718.1;GATS,3_prime_UTR_variant,,ENST00000436886,NM_178831.6;GATS,downstream_gene_variant,,ENST00000454084,;STAG3,upstream_gene_variant,,ENST00000412190,;STAG3,splice_donor_variant,,ENST00000440830,;STAG3,splice_donor_variant,,ENST00000491498,;GATS,downstream_gene_variant,,ENST00000440058,;GATS,downstream_gene_variant,,ENST00000414997,;GATS,downstream_gene_variant,,ENST00000437485,;STAG3,splice_donor_variant,,ENST00000496157,;STAG3,splice_donor_variant,,ENST00000479359,;GATS,3_prime_UTR_variant,,ENST00000328453,;GATS,3_prime_UTR_variant,,ENST00000543273,;STAG3,upstream_gene_variant,,ENST00000451963,;STAG3,downstream_gene_variant,,ENST00000477469,;STAG3,downstream_gene_variant,,ENST00000476057,; C ENST00000615138 Transcript splice_donor_variant -/4380 2061/3681 687/1226 1 1 STAG3 HGNC HGNC:11356 protein_coding YES CCDS75642.1 ENSP00000477973 D6W5U7 UPI000048108A NM_001282717.1 19/33 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 39 100200970 100200970 G C 1 0 0 0 0 0 0 1 0 15622 1275 44 4 4 STAG3 7 100200970 Splice_Site SNP G C3N-00175_T 72817 100200970 59145003 618 10210 NYAP1 0 . GRCh38 7 100488660 100488660 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.939G>T p.= p.G313G ENST00000300179 4/7 100 90 10 123 123 0 strelka-varscan-mutect NYAP1,synonymous_variant,p.=,ENST00000300179,NM_173564.3;NYAP1,synonymous_variant,p.=,ENST00000454988,;NYAP1,upstream_gene_variant,,ENST00000496985,;NYAP1,upstream_gene_variant,,ENST00000489641,; T ENST00000300179 Transcript synonymous_variant 1098/3581 939/2526 313/841 G ggG/ggT 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 4/7 Pfam_domain:PF15439,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -19.91755 1 1 1 1 0 T 2 4 39 100488660 100488660 G T 1 0 0 0 0 0 0 0 1 10872 1161 41 2 2 NYAP1 7 100488660 Silent SNP G C3N-00175_T 287690 100488660 58857313 619 10211 NYAP1 0 . GRCh38 7 100489569 100489569 + Missense_Mutation SNP G G T rs150286597 C3N-00175_T C3N-00175_N G G c.1848G>T p.Glu616Asp p.E616D ENST00000300179 4/7 155 120 35 195 195 0 strelka-varscan-mutect NYAP1,missense_variant,p.Glu616Asp,ENST00000300179,NM_173564.3;NYAP1,missense_variant,p.Glu559Asp,ENST00000454988,;NYAP1,upstream_gene_variant,,ENST00000496985,;NYAP1,upstream_gene_variant,,ENST00000489641,; T ENST00000300179 Transcript missense_variant 2007/3581 1848/2526 616/841 E/D gaG/gaT rs150286597,COSM5105581 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 tolerated(0.52) 4/7 Pfam_domain:PF15452,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs150286597 . 0 207 0 3 0 0 0 0 -20 0.9999972 1 1 1 0 T 3 4 39 100489569 100489569 G T 1 0 0 0 0 1 0 0 0 10872 991 35 2 2 NYAP1 7 100489569 Missense_Mutation SNP G C3N-00175_T 909 100489569 58856404 620 10212 AGFG2 0 . GRCh38 7 100555726 100555726 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.868A>T p.Thr290Ser p.T290S ENST00000300176 6/12 153 110 43 144 144 0 strelka-varscan-mutect AGFG2,missense_variant,p.Thr290Ser,ENST00000300176,NM_006076.4;AGFG2,missense_variant,p.Thr21Ser,ENST00000429987,;AGFG2,non_coding_transcript_exon_variant,,ENST00000474713,;AGFG2,3_prime_UTR_variant,,ENST00000430857,;AGFG2,non_coding_transcript_exon_variant,,ENST00000477022,; T ENST00000300176 Transcript missense_variant 990/4796 868/1446 290/481 T/S Act/Tct 1 1 AGFG2 HGNC HGNC:5177 protein_coding YES CCDS5697.1 ENSP00000300176 O95081 A4D2D6 UPI000003E7D5 NM_006076.4 tolerated(0.14) 6/12 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF233 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 100555726 100555726 A T 1 0 0 0 0 1 0 0 0 458 43 2 4 4 AGFG2 7 100555726 Missense_Mutation SNP A C3N-00175_T 66157 100555726 58790247 621 10213 FBXL13 0 . GRCh38 7 102968103 102968103 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.510C>T p.= p.L170L ENST00000313221 7/20 87 81 6 98 98 0 strelka-varscan-mutect FBXL13,synonymous_variant,p.=,ENST00000313221,NM_145032.3;FBXL13,synonymous_variant,p.=,ENST00000379308,;FBXL13,synonymous_variant,p.=,ENST00000436908,;FBXL13,synonymous_variant,p.=,ENST00000379305,NM_001287150.1;FBXL13,synonymous_variant,p.=,ENST00000455112,NM_001111038.1;FBXL13,synonymous_variant,p.=,ENST00000456695,;FBXL13,non_coding_transcript_exon_variant,,ENST00000471074,;FBXL13,non_coding_transcript_exon_variant,,ENST00000477915,;FBXL13,synonymous_variant,p.=,ENST00000448002,; A ENST00000313221 Transcript synonymous_variant 937/2744 510/2208 170/735 L ctC/ctT 1 -1 FBXL13 HGNC HGNC:21658 protein_coding YES CCDS5726.1 ENSP00000321927 Q8NEE6 UPI000020F830 NM_145032.3 7/20 Gene3D:3.80.10.10,PROSITE_profiles:PS50181,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF485,Superfamily_domains:SSF81383 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 102968103 102968103 G A 1 0 0 0 0 0 0 0 1 5573 1277 45 3 3 FBXL13 7 102968103 Silent SNP G C3N-00175_T 2412377 102968103 56377870 622 10214 SLC26A4 0 . GRCh38 7 107661741 107661742 + Frame_Shift_Ins INS - - TGTTT novel C3N-00175_T C3N-00175_N - - c.100_101insTGTTT p.Gln34LeufsTer34 p.Q34Lfs*34 ENST00000265715 2/21 278 220 58 315 315 0 sindel-varindel-pindel SLC26A4,frameshift_variant,p.Gln34LeufsTer34,ENST00000265715,NM_000441.1;SLC26A4,frameshift_variant,p.Gln34LeufsTer34,ENST00000440056,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000440512,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000629014,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000630476,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000626388,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000627161,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000449741,;SLC26A4-AS1,non_coding_transcript_exon_variant,,ENST00000587899,;SLC26A4-AS1,intron_variant,,ENST00000591896,; TGTTT ENST00000265715 Transcript frameshift_variant 324-325/4930 100-101/2343 34/780 Q/LFX caa/cTGTTTaa 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 2/21 hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF33 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 TGTTT 7 5 39 107661741 107661741 - TGTTT 1 0 1 1 0 0 0 0 0 14789 711 25 0 0 SLC26A4 7 107661741 Frame_Shift_Ins INS - C3N-00175_T 4693638 107661741 51684232 623 10215 SLC26A4 0 . GRCh38 7 107695972 107695972 + Missense_Mutation SNP G G T rs767561443 C3N-00175_T C3N-00175_N G G c.1477G>T p.Gly493Trp p.G493W ENST00000265715 13/21 381 287 94 338 337 1 strelka-varscan-mutect SLC26A4,missense_variant,p.Gly493Trp,ENST00000265715,NM_000441.1;SLC26A4,non_coding_transcript_exon_variant,,ENST00000480841,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000497446,;SLC26A4,non_coding_transcript_exon_variant,,ENST00000477350,;SLC26A4,upstream_gene_variant,,ENST00000492030,;SLC26A4,downstream_gene_variant,,ENST00000460748,; T ENST00000265715 Transcript missense_variant 1701/4930 1477/2343 493/780 G/W Ggg/Tgg rs767561443 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 deleterious(0) 13/21 hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF33,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00815,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs767561443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 107695972 107695972 G T 1 0 0 0 0 1 0 0 0 14789 1232 43 2 2 SLC26A4 7 107695972 Missense_Mutation SNP G C3N-00175_T 34231 107695972 51650001 624 10216 LAMB4 0 . GRCh38 7 108106539 108106539 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.625A>T p.Ile209Phe p.I209F ENST00000388781 7/34 92 69 23 151 151 0 strelka-varscan-mutect LAMB4,missense_variant,p.Ile209Phe,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Ile209Phe,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Ile209Phe,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; A ENST00000388781 Transcript missense_variant 709/5858 625/5286 209/1761 I/F Att/Ttt 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0) 7/34 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 108106539 108106539 T A 1 0 0 0 0 1 0 0 0 8517 1493 52 4 4 LAMB4 7 108106539 Missense_Mutation SNP T C3N-00175_T 410567 108106539 51239434 625 10217 PPP1R3A 0 . GRCh38 7 113918650 113918650 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.347A>T p.Lys116Ile p.K116I ENST00000284601 1/4 431 333 98 513 513 0 strelka-varscan-mutect PPP1R3A,missense_variant,p.Lys116Ile,ENST00000284601,NM_002711.3;PPP1R3A,intron_variant,,ENST00000449795,;PPP1R3A,intron_variant,,ENST00000284602,; A ENST00000284601 Transcript missense_variant 416/4384 347/3369 116/1122 K/I aAa/aTa 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 deleterious(0) 1/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 113918650 113918650 T A 1 0 0 0 0 1 0 0 0 12492 1841 64 4 4 PPP1R3A 7 113918650 Missense_Mutation SNP T C3N-00175_T 5812111 113918650 45427323 626 10218 FOXP2 0 . GRCh38 7 114642429 114642429 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.870G>C p.Glu290Asp p.E290D ENST00000408937 8/18 286 263 23 312 312 0 strelka-mutect FOXP2,missense_variant,p.Glu290Asp,ENST00000408937,NM_148898.3;FOXP2,missense_variant,p.Glu282Asp,ENST00000403559,NM_148900.3;FOXP2,missense_variant,p.Glu173Asp,ENST00000393491,;FOXP2,missense_variant,p.Glu262Asp,ENST00000635534,;FOXP2,missense_variant,p.Glu248Asp,ENST00000634411,;FOXP2,missense_variant,p.Glu265Asp,ENST00000393494,;FOXP2,missense_variant,p.Glu265Asp,ENST00000350908,NM_001172766.2,NM_014491.3;FOXP2,missense_variant,p.Glu244Asp,ENST00000393498,;FOXP2,missense_variant,p.Glu266Asp,ENST00000635638,;FOXP2,missense_variant,p.Glu173Asp,ENST00000393489,;FOXP2,missense_variant,p.Glu265Asp,ENST00000378237,;FOXP2,missense_variant,p.Glu245Asp,ENST00000634623,;FOXP2,missense_variant,p.Glu289Asp,ENST00000390668,NM_001172767.2;FOXP2,missense_variant,p.Glu265Asp,ENST00000360232,NM_148899.3;FOXP2,missense_variant,p.Glu119Asp,ENST00000393495,;FOXP2,missense_variant,p.Glu112Asp,ENST00000635563,;FOXP2,intron_variant,,ENST00000634372,;FOXP2,3_prime_UTR_variant,,ENST00000441290,;FOXP2,3_prime_UTR_variant,,ENST00000412402,;FOXP2,3_prime_UTR_variant,,ENST00000635109,; C ENST00000408937 Transcript missense_variant 1244/6443 870/2223 290/740 E/D gaG/gaC COSM1622235,COSM3662865,COSM3662866 1 1 FOXP2 HGNC HGNC:13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 X5D2H2 UPI000007412B NM_148898.3 tolerated(0.75) 8/18 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 114642429 114642429 G C 1 0 0 0 0 1 0 0 0 5892 933 33 4 4 FOXP2 7 114642429 Missense_Mutation SNP G C3N-00175_T 723779 114642429 44703544 627 10219 MET 0 . GRCh38 7 116771857 116771857 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.2950A>G p.Ser984Gly p.S984G ENST00000318493 14/21 433 347 86 456 456 0 strelka-varscan-mutect MET,missense_variant,p.Ser966Gly,ENST00000397752,NM_000245.2;MET,missense_variant,p.Ser984Gly,ENST00000318493,NM_001127500.1;MET,intron_variant,,ENST00000454623,;MET,downstream_gene_variant,,ENST00000422097,; G ENST00000318493 Transcript missense_variant 3137/4632 2950/4227 984/1408 S/G Agt/Ggt 1 1 MET HGNC HGNC:7029 protein_coding YES CCDS47689.1 ENSP00000317272 P08581 A0A024R728 UPI000014033E NM_001127500.1 tolerated(0.28) 14/21 hmmpanther:PTHR24416:SF332,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000617 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 116771857 116771857 A G 1 0 0 0 0 1 0 0 0 9430 188 7 5 5 MET 7 116771857 Missense_Mutation SNP A C3N-00175_T 2129428 116771857 42574116 628 10220 CTTNBP2 0 . GRCh38 7 117760694 117760694 + Silent SNP G G A rs759214218 C3N-00175_T C3N-00175_N G G c.2913C>T p.= p.P971P ENST00000160373 10/23 98 70 28 97 97 0 strelka-varscan-mutect CTTNBP2,synonymous_variant,p.=,ENST00000160373,NM_033427.2;CTTNBP2,synonymous_variant,p.=,ENST00000446636,;CTTNBP2,upstream_gene_variant,,ENST00000435233,;CTTNBP2,upstream_gene_variant,,ENST00000416239,;CTTNBP2,3_prime_UTR_variant,,ENST00000441556,;CTTNBP2,non_coding_transcript_exon_variant,,ENST00000467088,;CTTNBP2,upstream_gene_variant,,ENST00000482124,; A ENST00000160373 Transcript synonymous_variant 3005/5970 2913/4992 971/1663 P ccC/ccT rs759214218 1 -1 CTTNBP2 HGNC HGNC:15679 protein_coding YES CCDS5774.1 ENSP00000160373 Q8WZ74 Q20BG9 UPI000006E94A NM_033427.2 10/23 hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF27 LOW 1 SNV 1 1 PASS rs759214218 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 117760694 117760694 G A 1 0 0 0 0 0 0 0 1 3854 987 35 3 3 CTTNBP2 7 117760694 Silent SNP G C3N-00175_T 988837 117760694 41585279 629 10221 PTPRZ1 0 . GRCh38 7 122040974 122040974 + Missense_Mutation SNP C C G rs371838082 C3N-00175_T C3N-00175_N C C c.5796C>G p.His1932Gln p.H1932Q ENST00000393386 21/30 44 33 11 34 34 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.His1932Gln,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.His1065Gln,ENST00000449182,NM_001206839.1;PTPRZ1,downstream_gene_variant,,ENST00000468641,;PTPRZ1,downstream_gene_variant,,ENST00000470504,; G ENST00000393386 Transcript missense_variant 6207/8175 5796/6948 1932/2315 H/Q caC/caG rs371838082 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0) 21/30 PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF214,PROSITE_patterns:PS00383,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799,Prints_domain:PR00700 MODERATE 1 SNV 1 1 PASS rs371838082 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 122040974 122040974 C G 1 0 0 0 0 1 0 0 0 12969 579 20 4 4 PTPRZ1 7 122040974 Missense_Mutation SNP C C3N-00175_T 4280280 122040974 37304999 630 10222 SPAM1 0 . GRCh38 7 123953928 123953928 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.359delT p.Leu120TyrfsTer18 p.L120Yfs*18 ENST00000340011 3/7 184 141 43 207 207 0 sindel-varindel-pindel SPAM1,frameshift_variant,p.Leu120TyrfsTer18,ENST00000340011,NM_003117.4;SPAM1,frameshift_variant,p.Leu120TyrfsTer18,ENST00000439500,NM_001174046.1,NM_001174045.1;SPAM1,frameshift_variant,p.Leu120TyrfsTer18,ENST00000460182,NM_001174044.1,NM_153189.2;SPAM1,frameshift_variant,p.Leu120TyrfsTer18,ENST00000223028,;SPAM1,frameshift_variant,p.Leu120TyrfsTer18,ENST00000402183,;SPAM1,downstream_gene_variant,,ENST00000413927,; - ENST00000340011 Transcript frameshift_variant 715/2349 358/1536 120/511 L/X Tta/ta 1 1 SPAM1 HGNC HGNC:11217 protein_coding YES CCDS5790.1 ENSP00000345849 P38567 UPI0000072166 NM_003117.4 3/7 hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF20,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Gene3D:3.20.20.70,Pfam_domain:PF01630,Superfamily_domains:SSF51445,Prints_domain:PR00846 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 123953928 123953928 T - 1 0 1 0 1 0 0 0 0 15317 1606 56 0 0 SPAM1 7 123953928 Frame_Shift_Del DEL T C3N-00175_T 1912954 123953928 35392045 631 10223 SPAM1 0 . GRCh38 7 123954033 123954033 + Missense_Mutation SNP G G T rs764517940 C3N-00175_T C3N-00175_N G G c.463G>T p.Ala155Ser p.A155S ENST00000340011 3/7 218 164 54 208 208 0 strelka-varscan-mutect SPAM1,missense_variant,p.Ala155Ser,ENST00000340011,NM_003117.4;SPAM1,missense_variant,p.Ala155Ser,ENST00000439500,NM_001174046.1,NM_001174045.1;SPAM1,missense_variant,p.Ala155Ser,ENST00000460182,NM_001174044.1,NM_153189.2;SPAM1,missense_variant,p.Ala155Ser,ENST00000223028,;SPAM1,missense_variant,p.Ala155Ser,ENST00000402183,;SPAM1,downstream_gene_variant,,ENST00000413927,; T ENST00000340011 Transcript missense_variant 820/2349 463/1536 155/511 A/S Gca/Tca rs764517940 1 1 SPAM1 HGNC HGNC:11217 protein_coding YES CCDS5790.1 ENSP00000345849 P38567 UPI0000072166 NM_003117.4 tolerated(0.24) 3/7 hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF20,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Gene3D:3.20.20.70,Pfam_domain:PF01630,Superfamily_domains:SSF51445,Prints_domain:PR00846 MODERATE 1 SNV 1 1 PASS rs764517940 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 123954033 123954033 G T 1 0 0 0 0 1 0 0 0 15317 1203 42 2 2 SPAM1 7 123954033 Missense_Mutation SNP G C3N-00175_T 105 123954033 35391940 632 10224 POT1 0 . GRCh38 7 124853079 124853079 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.762G>A p.= p.E254E ENST00000357628 10/19 146 133 13 153 153 0 strelka-mutect POT1,synonymous_variant,p.=,ENST00000357628,NM_015450.2;POT1,synonymous_variant,p.=,ENST00000393329,NM_001042594.1;POT1,synonymous_variant,p.=,ENST00000610141,;POT1,synonymous_variant,p.=,ENST00000609106,;POT1,synonymous_variant,p.=,ENST00000608057,;POT1,synonymous_variant,p.=,ENST00000607932,;POT1,non_coding_transcript_exon_variant,,ENST00000608126,; T ENST00000357628 Transcript synonymous_variant 1361/4080 762/1905 254/634 E gaG/gaA 1 -1 POT1 HGNC HGNC:17284 protein_coding YES CCDS5793.1 ENSP00000350249 Q9NUX5 A0A024R739 UPI0000073E3F NM_015450.2 10/19 Gene3D:1xjvA02,Pfam_domain:PF16686,hmmpanther:PTHR14513,hmmpanther:PTHR14513:SF2,Superfamily_domains:SSF50249 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 124853079 124853079 C T 1 0 0 0 0 0 0 0 1 12374 912 32 3 3 POT1 7 124853079 Silent SNP C C3N-00175_T 899046 124853079 34492894 633 10225 FSCN3 0 . GRCh38 7 127595371 127595371 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.209A>G p.Gln70Arg p.Q70R ENST00000265825 2/7 154 129 25 182 182 0 strelka-varscan-mutect FSCN3,missense_variant,p.Gln70Arg,ENST00000265825,NM_020369.2;FSCN3,5_prime_UTR_variant,,ENST00000478821,;ARF5,downstream_gene_variant,,ENST00000000233,NM_001662.3;ARF5,downstream_gene_variant,,ENST00000415666,;FSCN3,non_coding_transcript_exon_variant,,ENST00000478328,;GCC1,upstream_gene_variant,,ENST00000497650,;GCC1,upstream_gene_variant,,ENST00000473728,;FSCN3,3_prime_UTR_variant,,ENST00000421705,;ARF5,downstream_gene_variant,,ENST00000463733,;FSCN3,upstream_gene_variant,,ENST00000469242,;ARF5,downstream_gene_variant,,ENST00000489673,; G ENST00000265825 Transcript missense_variant 428/2238 209/1497 70/498 Q/R cAg/cGg 1 1 FSCN3 HGNC HGNC:3961 protein_coding YES CCDS34746.1 ENSP00000265825 Q9NQT6 A0A140VK18 UPI000012AC5F NM_020369.2 tolerated(0.83) 2/7 hmmpanther:PTHR10551,hmmpanther:PTHR10551:SF1,PIRSF_domain:PIRSF005682,Gene3D:2.80.10.50,Pfam_domain:PF06268,Superfamily_domains:SSF50405 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 127595371 127595371 A G 1 0 0 0 0 1 0 0 0 5942 188 7 5 5 FSCN3 7 127595371 Missense_Mutation SNP A C3N-00175_T 2742292 127595371 31750602 634 10226 PRRT4 0 . GRCh38 7 128350946 128350946 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2610G>T p.Gln870His p.Q870H ENST00000446477 6/6 364 265 99 344 344 0 strelka-varscan-mutect PRRT4,missense_variant,p.Gln870His,ENST00000446477,NM_001174164.1;PRRT4,missense_variant,p.Gln870His,ENST00000535159,;PRRT4,missense_variant,p.Arg400Met,ENST00000480290,;PRRT4,3_prime_UTR_variant,,ENST00000489835,NM_001114726.2;PRRT4,downstream_gene_variant,,ENST00000489517,; A ENST00000446477 Transcript missense_variant 2924/3544 2610/2700 870/899 Q/H caG/caT 1 -1 PRRT4 HGNC HGNC:37280 protein_coding YES CCDS55160.1 ENSP00000415026 C9JH25 UPI0000DD7E1D NM_001174164.1 deleterious(0.04) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR35578,hmmpanther:PTHR35578:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 128350946 128350946 C A 1 0 0 0 0 1 0 0 0 12758 680 24 2 2 PRRT4 7 128350946 Missense_Mutation SNP C C3N-00175_T 755575 128350946 30995027 635 10227 FLNC 0 . GRCh38 7 128830976 128830976 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.339delG p.Lys113AsnfsTer5 p.K113Nfs*5 ENST00000325888 1/48 207 158 49 248 248 0 sindel-varindel-pindel FLNC,frameshift_variant,p.Lys113AsnfsTer5,ENST00000325888,NM_001458.4;FLNC,frameshift_variant,p.Lys113AsnfsTer5,ENST00000346177,NM_001127487.1; - ENST00000325888 Transcript frameshift_variant 600/9188 339/8178 113/2725 K/X aaG/aa 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 1/48 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 128830976 128830976 G - 1 0 1 0 1 0 0 0 0 5791 962 34 0 0 FLNC 7 128830976 Frame_Shift_Del DEL G C3N-00175_T 480030 128830976 30514997 636 10228 CPA5 0 . GRCh38 7 130346569 130346569 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.84G>T p.= p.L28L ENST00000485477 2/12 178 138 40 166 165 1 strelka-varscan-mutect CPA5,synonymous_variant,p.=,ENST00000485477,;CPA5,synonymous_variant,p.=,ENST00000466363,;CPA5,synonymous_variant,p.=,ENST00000474905,NM_080385.4,NM_001127441.1;CPA5,synonymous_variant,p.=,ENST00000431780,NM_001127442.1;CPA5,synonymous_variant,p.=,ENST00000461828,NM_001318223.1;CPA5,synonymous_variant,p.=,ENST00000393213,;CPA5,synonymous_variant,p.=,ENST00000463587,;CPA5,synonymous_variant,p.=,ENST00000494311,;CPA5,downstream_gene_variant,,ENST00000497503,;CPA5,non_coding_transcript_exon_variant,,ENST00000495736,; T ENST00000485477 Transcript synonymous_variant 1213/2573 84/1311 28/436 L ctG/ctT 1 1 CPA5 HGNC HGNC:15722 protein_coding YES CCDS5819.1 ENSP00000420237 Q8WXQ8 A4D1M2 UPI000000D837 2/12 hmmpanther:PTHR11705:SF16,hmmpanther:PTHR11705 LOW 1 SNV 1 1 PASS rs1199541584 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 130346569 130346569 G T 1 0 0 0 0 0 0 0 1 3587 1335 47 2 2 CPA5 7 130346569 Silent SNP G C3N-00175_T 1515593 130346569 28999404 637 10229 LRGUK 0 . GRCh38 7 134199250 134199250 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1576G>C p.Glu526Gln p.E526Q ENST00000285928 14/20 272 228 44 297 297 0 strelka-varscan-mutect LRGUK,missense_variant,p.Glu526Gln,ENST00000285928,NM_144648.1; C ENST00000285928 Transcript missense_variant 1645/3163 1576/2478 526/825 E/Q Gag/Cag 1 1 LRGUK HGNC HGNC:21964 protein_coding YES CCDS5830.1 ENSP00000285928 Q96M69 UPI0000072C76 NM_144648.1 tolerated(0.07) 14/20 PROSITE_profiles:PS50052,Gene3D:3.40.50.300,Pfam_domain:PF00625,SMART_domains:SM00072,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 134199250 134199250 G C 1 0 0 0 0 1 0 0 0 8837 1291 45 4 4 LRGUK 7 134199250 Missense_Mutation SNP G C3N-00175_T 3852681 134199250 25146723 638 10230 CTAGE6 0 . GRCh38 7 143756348 143756348 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1311C>A p.= p.A437A ENST00000470691 1/1 593 552 41 625 625 0 varscan-mutect CTAGE6,synonymous_variant,p.=,ENST00000470691,NM_178561.4;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,;RNU6-267P,upstream_gene_variant,,ENST00000516714,; T ENST00000470691 Transcript synonymous_variant 1349/2608 1311/2334 437/777 A gcC/gcA 1 -1 CTAGE6 HGNC HGNC:28644 protein_coding YES CCDS64790.1 ENSP00000474388 Q86UF2 UPI0000199826 NM_178561.4 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39 LOW 1 SNV 1 PASS rs1266061163 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 143756348 143756348 G T 1 0 0 0 0 0 0 0 1 3800 1335 47 2 2 CTAGE6 7 143756348 Silent SNP G C3N-00175_T 9557098 143756348 15589625 639 10231 SSPO 0 . GRCh38 7 149780788 149780788 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1650G>T p.Arg550Ser p.R550S ENST00000378016 12/107 191 149 42 266 266 0 strelka-varscan-mutect SSPO,missense_variant,p.Arg550Ser,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,intron_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000493502,; T ENST00000378016 Transcript missense_variant 1650/15589 1650/15453 550/5150 R/S agG/agT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 tolerated(0.16) 12/107 SMART_domains:SM00214,SMART_domains:SM00215,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 149780788 149780788 G T 1 0 0 0 0 1 0 0 0 15566 1223 43 2 2 SSPO 7 149780788 Missense_Mutation SNP G C3N-00175_T 6024440 149780788 9565185 640 10232 SSPO 0 . GRCh38 7 149791896 149791896 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.5328G>A p.= p.Q1776Q ENST00000378016 34/107 151 116 35 154 154 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,; A ENST00000378016 Transcript synonymous_variant 5328/15589 5328/15453 1776/5150 Q caG/caA 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 34/107 Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,PROSITE_profiles:PS50092,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 149791896 149791896 G A 1 0 0 0 0 0 0 0 1 15566 1020 36 3 3 SSPO 7 149791896 Silent SNP G C3N-00175_T 11108 149791896 9554077 641 10233 KCNH2 0 . GRCh38 7 150950102 150950102 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.2116C>T p.= p.L706L ENST00000430723 10/10 337 298 39 371 371 0 strelka-varscan-mutect KCNH2,synonymous_variant,p.=,ENST00000430723,NM_172056.2;KCNH2,intron_variant,,ENST00000262186,NM_000238.3;KCNH2,intron_variant,,ENST00000330883,NM_172057.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; A ENST00000430723 Transcript synonymous_variant 2445/2648 2116/2319 706/772 L Ctg/Ttg 1 -1 KCNH2 HGNC HGNC:6251 protein_coding ENSP00000387657 Q86U57 UPI0000169E05 NM_172056.2 10/10 PROSITE_profiles:PS50042,SMART_domains:SM00100 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 150950102 150950102 G A 1 0 0 0 0 0 0 0 1 7948 933 33 3 3 KCNH2 7 150950102 Silent SNP G C3N-00175_T 1158206 150950102 8395871 642 10234 ASIC3 0 . GRCh38 7 151049069 151049069 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.184G>C p.Glu62Gln p.E62Q ENST00000297512 1/11 187 164 23 240 240 0 strelka-varscan-mutect ASIC3,missense_variant,p.Glu62Gln,ENST00000357922,NM_020322.3;ASIC3,missense_variant,p.Glu62Gln,ENST00000349064,NM_004769.3;ASIC3,missense_variant,p.Glu62Gln,ENST00000297512,NM_020321.3;ABCB8,downstream_gene_variant,,ENST00000358849,NM_007188.4;ABCB8,downstream_gene_variant,,ENST00000542328,NM_001282293.1;ABCB8,downstream_gene_variant,,ENST00000297504,NM_001282291.1;ABCB8,downstream_gene_variant,,ENST00000498578,NM_001282292.1;CDK5,downstream_gene_variant,,ENST00000485972,NM_004935.3;CDK5,downstream_gene_variant,,ENST00000297518,NM_001164410.2;ASIC3,upstream_gene_variant,,ENST00000490540,;ASIC3,upstream_gene_variant,,ENST00000485929,;ASIC3,missense_variant,p.Glu62Gln,ENST00000377904,;ASIC3,missense_variant,p.Glu62Gln,ENST00000468325,;ABCB8,downstream_gene_variant,,ENST00000482899,;ABCB8,downstream_gene_variant,,ENST00000466514,;ABCB8,downstream_gene_variant,,ENST00000482309,;ASIC3,upstream_gene_variant,,ENST00000498105,;ASIC3,upstream_gene_variant,,ENST00000474135,; C ENST00000297512 Transcript missense_variant 184/1718 184/1650 62/549 E/Q Gag/Cag 1 1 ASIC3 HGNC HGNC:101 protein_coding YES CCDS5915.1 ENSP00000297512 Q9UHC3 A0A090N8Q1 UPI00000300F6 NM_020321.3 tolerated(0.11) 1/11 hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF110,Pfam_domain:PF00858 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 151049069 151049069 G C 1 0 0 0 0 1 0 0 0 1187 1291 45 4 4 ASIC3 7 151049069 Missense_Mutation SNP G C3N-00175_T 98967 151049069 8296904 643 10235 PAXIP1 0 . GRCh38 7 154946788 154946788 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2948G>C p.Gly983Ala p.G983A ENST00000404141 18/21 177 159 18 210 210 0 strelka-varscan-mutect PAXIP1,missense_variant,p.Gly983Ala,ENST00000404141,NM_007349.3;PAXIP1,missense_variant,p.Gly983Ala,ENST00000397192,;PAXIP1-AS2,non_coding_transcript_exon_variant,,ENST00000449486,;PAXIP1-AS2,non_coding_transcript_exon_variant,,ENST00000411526,;PAXIP1-AS2,downstream_gene_variant,,ENST00000397551,;RP11-5C23.1,upstream_gene_variant,,ENST00000608064,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000473219,;PAXIP1,3_prime_UTR_variant,,ENST00000457196,;PAXIP1,non_coding_transcript_exon_variant,,ENST00000464717,; G ENST00000404141 Transcript missense_variant 3103/3827 2948/3210 983/1069 G/A gGa/gCa 1 -1 PAXIP1 HGNC HGNC:8624 protein_coding YES CCDS47753.1 ENSP00000384048 Q6ZW49 UPI00004166F9 NM_007349.3 deleterious(0) 18/21 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF15,SMART_domains:SM00292 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.99999 0.9999999 1 1 1 0 G 3 3 39 154946788 154946788 C G 1 0 0 0 0 1 0 0 0 11573 855 30 4 4 PAXIP1 7 154946788 Missense_Mutation SNP C C3N-00175_T 3897719 154946788 4399185 644 10236 DNAJB6 0 . GRCh38 7 157366541 157366541 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.215G>T p.Gly72Val p.G72V ENST00000262177 4/10 222 179 43 275 274 1 strelka-varscan-mutect DNAJB6,missense_variant,p.Gly72Val,ENST00000262177,NM_058246.3;DNAJB6,missense_variant,p.Gly72Val,ENST00000429029,NM_005494.2;DNAJB6,missense_variant,p.Gly72Val,ENST00000443280,;DNAJB6,missense_variant,p.Gly72Val,ENST00000441561,;DNAJB6,missense_variant,p.Gly72Val,ENST00000634080,;DNAJB6,missense_variant,p.Gly72Val,ENST00000417758,;DNAJB6,missense_variant,p.Gly72Val,ENST00000453383,;DNAJB6,missense_variant,p.Gly72Val,ENST00000412557,;DNAJB6,downstream_gene_variant,,ENST00000437030,;DNAJB6,downstream_gene_variant,,ENST00000439402,;DNAJB6,non_coding_transcript_exon_variant,,ENST00000486083,;DNAJB6,non_coding_transcript_exon_variant,,ENST00000488001,;DNAJB6,upstream_gene_variant,,ENST00000465908,;DNAJB6,missense_variant,p.Gly72Val,ENST00000459889,;DNAJB6,missense_variant,p.Gly72Val,ENST00000441291,;DNAJB6,upstream_gene_variant,,ENST00000468928,; T ENST00000262177 Transcript missense_variant 420/2527 215/981 72/326 G/V gGa/gTa 1 1 DNAJB6 HGNC HGNC:14888 protein_coding YES CCDS5946.1 ENSP00000262177 O75190 UPI0000129436 NM_058246.3 deleterious(0) 4/10 Gene3D:1.10.287.110,Prints_domain:PR00625,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF209,Low_complexity_(Seg):seg,Superfamily_domains:SSF46565 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 157366541 157366541 G T 1 0 0 0 0 1 0 0 0 4438 1174 41 2 2 DNAJB6 7 157366541 Missense_Mutation SNP G C3N-00175_T 2419753 157366541 1979432 645 10237 MYOM2 0 . GRCh38 8 2106386 2106386 + Missense_Mutation SNP C C A rs765609218 C3N-00175_T C3N-00175_N C C c.2879C>A p.Thr960Asn p.T960N ENST00000262113 22/37 127 108 19 137 137 0 strelka-varscan-mutect MYOM2,missense_variant,p.Thr960Asn,ENST00000262113,NM_003970.3;MYOM2,missense_variant,p.Thr385Asn,ENST00000523438,;MYOM2,non_coding_transcript_exon_variant,,ENST00000518203,;MYOM2,non_coding_transcript_exon_variant,,ENST00000517520,;MYOM2,downstream_gene_variant,,ENST00000519372,;MYOM2,upstream_gene_variant,,ENST00000523443,; A ENST00000262113 Transcript missense_variant 3020/5014 2879/4398 960/1465 T/N aCc/aAc rs765609218 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 tolerated(0.06) 22/37 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs765609218 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 2106386 2106386 C A 1 0 0 0 0 1 0 0 0 10093 507 18 2 2 MYOM2 8 2106386 Missense_Mutation SNP C C3N-00175_T 2106386 143032250 646 10238 RP1L1 0 . GRCh38 8 10610952 10610952 + Missense_Mutation SNP T T A rs774835263 C3N-00175_T C3N-00175_N T T c.3146A>T p.Glu1049Val p.E1049V ENST00000382483 4/4 376 287 89 193 193 0 strelka-varscan-mutect RP1L1,missense_variant,p.Glu1049Val,ENST00000382483,NM_178857.5; A ENST00000382483 Transcript missense_variant 3370/7973 3146/7203 1049/2400 E/V gAg/gTg rs774835263 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 tolerated(0.27) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 MODERATE 1 SNV 1 1 PASS rs774835263 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 10610952 10610952 T A 1 0 0 0 0 1 0 0 0 13773 1551 54 4 4 RP1L1 8 10610952 Missense_Mutation SNP T C3N-00175_T 8504566 10610952 134527684 647 10239 XKR6 0 . GRCh38 8 10898592 10898592 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.1286G>T p.Cys429Phe p.C429F ENST00000416569 3/3 329 242 87 348 346 2 strelka-varscan-mutect XKR6,missense_variant,p.Cys429Phe,ENST00000416569,NM_173683.3;XKR6,missense_variant,p.Cys206Phe,ENST00000382461,; A ENST00000416569 Transcript missense_variant 1313/3382 1286/1926 429/641 C/F tGc/tTc COSM402968 1 -1 XKR6 HGNC HGNC:27806 protein_coding YES CCDS5978.2 ENSP00000416707 Q5GH73 UPI00004C7A9D NM_173683.3 deleterious(0) 3/3 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF7,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 10898592 10898592 C A 1 0 0 0 0 1 0 0 0 17994 710 25 2 2 XKR6 8 10898592 Missense_Mutation SNP C C3N-00175_T 287640 10898592 134240044 648 10240 GATA4 0 . GRCh38 8 11708895 11708895 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.583C>A p.= p.R195R ENST00000532059 1/6 341 313 28 194 194 0 strelka-varscan-mutect GATA4,synonymous_variant,p.=,ENST00000335135,NM_002052.3;GATA4,synonymous_variant,p.=,ENST00000622443,;GATA4,synonymous_variant,p.=,ENST00000532059,NM_001308093.1;GATA4,intron_variant,,ENST00000528712,NM_001308094.1;GATA4,intron_variant,,ENST00000526716,;GATA4,downstream_gene_variant,,ENST00000528027,;GATA4,downstream_gene_variant,,ENST00000532977,;GATA4,downstream_gene_variant,,ENST00000526974,; A ENST00000532059 Transcript synonymous_variant 663/1459 583/1332 195/443 R Cgg/Agg 1 1 GATA4 HGNC HGNC:4173 protein_coding YES CCDS78303.1 ENSP00000435712 P43694 UPI0000210221 NM_001308093.1 1/6 Pfam_domain:PF05349,PIRSF_domain:PIRSF003028,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF154 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 11708895 11708895 C A 1 0 0 0 0 0 0 0 1 6126 643 23 1 1 GATA4 8 11708895 Silent SNP C C3N-00175_T 810303 11708895 133429741 649 10241 DLC1 0 . GRCh38 8 13085921 13085921 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.4477C>G p.Pro1493Ala p.P1493A ENST00000276297 18/18 165 125 40 156 156 0 strelka-varscan-mutect DLC1,missense_variant,p.Pro1493Ala,ENST00000276297,NM_182643.2;DLC1,missense_variant,p.Pro1056Ala,ENST00000358919,NM_006094.4;DLC1,missense_variant,p.Pro1090Ala,ENST00000512044,;DLC1,missense_variant,p.Pro982Ala,ENST00000520226,NM_001164271.1;DLC1,non_coding_transcript_exon_variant,,ENST00000510318,;DLC1,downstream_gene_variant,,ENST00000521730,; C ENST00000276297 Transcript missense_variant 4887/7447 4477/4587 1493/1528 P/A Cca/Gca 1 -1 DLC1 HGNC HGNC:2897 protein_coding YES CCDS5989.1 ENSP00000276297 Q96QB1 UPI0000210275 NM_182643.2 deleterious(0) 18/18 Gene3D:3.30.530.20,Pfam_domain:PF01852,PROSITE_profiles:PS50848,hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2,SMART_domains:SM00234,Superfamily_domains:SSF55961 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 13085921 13085921 G C 1 0 0 0 0 1 0 0 0 4356 1203 42 4 4 DLC1 8 13085921 Missense_Mutation SNP G C3N-00175_T 1377026 13085921 132052715 650 10242 SGCZ 0 . GRCh38 8 14554813 14554813 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.153C>A p.Phe51Leu p.F51L ENST00000382080 2/8 145 116 29 157 157 0 strelka-mutect SGCZ,missense_variant,p.Phe51Leu,ENST00000382080,NM_139167.2;SGCZ,missense_variant,p.Phe38Leu,ENST00000421524,; T ENST00000382080 Transcript missense_variant 869/2234 153/939 51/312 F/L ttC/ttA COSM1096897 1 -1 SGCZ HGNC HGNC:14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 tolerated(1) 2/8 Pfam_domain:PF04790,hmmpanther:PTHR12939,hmmpanther:PTHR12939:SF5,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 5 1 1 PASS rs897307913 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 14554813 14554813 G T 1 0 0 0 0 1 0 0 0 14464 933 33 2 2 SGCZ 8 14554813 Missense_Mutation SNP G C3N-00175_T 1468892 14554813 130583823 651 10243 FGF20 0 . GRCh38 8 16993089 16993089 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.619C>T p.= p.L207L ENST00000180166 3/3 129 103 26 162 162 0 strelka-varscan-mutect FGF20,synonymous_variant,p.=,ENST00000180166,NM_019851.2;FGF20,synonymous_variant,p.=,ENST00000519941,; A ENST00000180166 Transcript synonymous_variant 768/1688 619/636 207/211 L Cta/Tta 1 -1 FGF20 HGNC HGNC:3677 protein_coding YES CCDS5998.1 ENSP00000180166 Q9NP95 UPI00000374AE NM_019851.2 3/3 hmmpanther:PTHR11486:SF72,hmmpanther:PTHR11486 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 16993089 16993089 G A 1 0 0 0 0 0 0 0 1 5713 991 35 3 3 FGF20 8 16993089 Silent SNP G C3N-00175_T 2438276 16993089 128145547 652 10244 STC1 0 . GRCh38 8 23854518 23854518 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.6C>A p.= p.L2L ENST00000290271 1/4 130 94 36 150 150 0 strelka-varscan-mutect STC1,synonymous_variant,p.=,ENST00000290271,NM_003155.2;STC1,upstream_gene_variant,,ENST00000524323,; T ENST00000290271 Transcript synonymous_variant 290/3883 6/744 2/247 L ctC/ctA 1 -1 STC1 HGNC HGNC:11373 protein_coding YES CCDS6043.1 ENSP00000290271 P52823 UPI00001360B4 NM_003155.2 1/4 hmmpanther:PTHR11245,hmmpanther:PTHR11245:SF1,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs1237233643 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 23854518 23854518 G T 1 0 0 0 0 0 0 0 1 15651 1161 41 2 2 STC1 8 23854518 Silent SNP G C3N-00175_T 6861429 23854518 121284118 653 10245 NEFL 0 . GRCh38 8 24952848 24952848 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1594G>T p.Gly532Cys p.G532C ENST00000610854 4/4 205 158 47 243 242 1 strelka-varscan-mutect NEFL,missense_variant,p.Gly532Cys,ENST00000610854,NM_006158.4;NEFL,3_prime_UTR_variant,,ENST00000619417,;MIR6841,downstream_gene_variant,,ENST00000637129,;CTD-2168K21.2,upstream_gene_variant,,ENST00000607735,;NEFL,downstream_gene_variant,,ENST00000615973,; A ENST00000610854 Transcript missense_variant 2189/4082 1594/1632 532/543 G/C Ggt/Tgt 1 -1 NEFL HGNC HGNC:7739 protein_coding YES CCDS75712.1 ENSP00000482169 P07196 UPI00000747CF NM_006158.4 deleterious_low_confidence(0) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF22,hmmpanther:PTHR23239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 24952848 24952848 C A 1 0 0 0 0 1 0 0 0 10343 681 24 2 2 NEFL 8 24952848 Missense_Mutation SNP C C3N-00175_T 1098330 24952848 120185788 654 10246 NEFL 0 . GRCh38 8 24953537 24953537 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1428C>A p.= p.A476A ENST00000610854 3/4 416 354 62 509 508 1 strelka-varscan-mutect NEFL,synonymous_variant,p.=,ENST00000610854,NM_006158.4;NEFL,3_prime_UTR_variant,,ENST00000619417,;MIR6841,downstream_gene_variant,,ENST00000637129,;CTD-2168K21.2,upstream_gene_variant,,ENST00000607735,;NEFL,downstream_gene_variant,,ENST00000615973,; T ENST00000610854 Transcript synonymous_variant 2023/4082 1428/1632 476/543 A gcC/gcA 1 -1 NEFL HGNC HGNC:7739 protein_coding YES CCDS75712.1 ENSP00000482169 P07196 UPI00000747CF NM_006158.4 3/4 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF22,hmmpanther:PTHR23239 LOW 1 SNV 1 1 PASS rs1455394179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 24953537 24953537 G T 1 0 0 0 0 0 0 0 1 10343 1103 39 1 1 NEFL 8 24953537 Silent SNP G C3N-00175_T 689 24953537 120185099 655 10247 DOCK5 0 . GRCh38 8 25374638 25374638 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.3800A>T p.His1267Leu p.H1267L ENST00000276440 37/52 279 247 32 294 294 0 strelka-varscan-mutect DOCK5,missense_variant,p.His1267Leu,ENST00000276440,NM_024940.6;DOCK5,missense_variant,p.His1039Leu,ENST00000444569,;DOCK5,3_prime_UTR_variant,,ENST00000467709,; T ENST00000276440 Transcript missense_variant 3844/10075 3800/5613 1267/1870 H/L cAc/cTc 1 1 DOCK5 HGNC HGNC:23476 protein_coding YES CCDS6047.1 ENSP00000276440 Q9H7D0 UPI000022D4F3 NM_024940.6 deleterious(0) 37/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF68,hmmpanther:PTHR23317,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 25374638 25374638 A T 1 0 0 0 0 1 0 0 0 4505 159 6 4 4 DOCK5 8 25374638 Missense_Mutation SNP A C3N-00175_T 421101 25374638 119763998 656 10248 UNC5D 0 . GRCh38 8 35790516 35790516 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2815C>A p.Gln939Lys p.Q939K ENST00000404895 17/17 325 235 90 351 351 0 strelka-varscan-mutect UNC5D,missense_variant,p.Gln870Lys,ENST00000287272,;UNC5D,missense_variant,p.Gln934Lys,ENST00000453357,;UNC5D,missense_variant,p.Gln944Lys,ENST00000416672,;UNC5D,missense_variant,p.Gln939Lys,ENST00000404895,NM_080872.2;UNC5D,missense_variant,p.Gln872Lys,ENST00000420357,;UNC5D,missense_variant,p.Gln515Lys,ENST00000449677,; A ENST00000404895 Transcript missense_variant 3143/3252 2815/2862 939/953 Q/K Cag/Aag 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 tolerated(0.06) 17/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 35790516 35790516 C A 1 0 0 0 0 1 0 0 0 17519 595 21 2 2 UNC5D 8 35790516 Missense_Mutation SNP C C3N-00175_T 10415878 35790516 109348120 657 10249 ADAM9 0 . GRCh38 8 39041947 39041947 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1132G>T p.Gly378Cys p.G378C ENST00000487273 12/22 217 177 40 285 285 0 strelka-varscan-mutect ADAM9,missense_variant,p.Gly378Cys,ENST00000487273,NM_003816.2;ADAM9,missense_variant,p.Gly378Cys,ENST00000379917,;ADAM9,missense_variant,p.Gly378Cys,ENST00000481873,;ADAM9,missense_variant,p.Gly378Cys,ENST00000468065,; T ENST00000487273 Transcript missense_variant,splice_region_variant 1210/3839 1132/2460 378/819 G/C Ggt/Tgt 1 1 ADAM9 HGNC HGNC:216 protein_coding YES CCDS6112.1 ENSP00000419446 Q13443 UPI0000048D87 NM_003816.2 deleterious(0) 12/22 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF136,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 39041947 39041947 G T 1 0 0 0 0 1 0 0 0 297 1246 43 2 2 ADAM9 8 39041947 Missense_Mutation SNP G C3N-00175_T 3251431 39041947 106096689 658 10250 ADAM18 0 . GRCh38 8 39648476 39648476 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1179T>A p.Cys393Ter p.C393* ENST00000265707 12/20 84 69 15 163 163 0 strelka-varscan-mutect ADAM18,stop_gained,p.Cys393Ter,ENST00000265707,NM_014237.2;ADAM18,stop_gained,p.Cys369Ter,ENST00000379866,NM_001320313.1;ADAM18,intron_variant,,ENST00000520087,; A ENST00000265707 Transcript stop_gained 1224/2388 1179/2220 393/739 C/* tgT/tgA 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 12/20 Gene3D:3.40.390.10,PROSITE_profiles:PS50214,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 39648476 39648476 T A 1 0 0 0 0 0 1 0 0 283 1702 59 4 4 ADAM18 8 39648476 Nonsense_Mutation SNP T C3N-00175_T 606529 39648476 105490160 659 10251 ANK1 0 . GRCh38 8 41693172 41693172 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.3685A>G p.Ile1229Val p.I1229V ENST00000265709 31/43 507 354 153 556 556 0 strelka-varscan-mutect ANK1,missense_variant,p.Ile1188Val,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Ile1188Val,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Ile1229Val,ENST00000265709,NM_001142446.1;ANK1,missense_variant,p.Ile510Val,ENST00000520299,;ANK1,non_coding_transcript_exon_variant,,ENST00000524227,;ANK1,non_coding_transcript_exon_variant,,ENST00000524069,;ANK1,upstream_gene_variant,,ENST00000518061,; C ENST00000265709 Transcript missense_variant 3967/6379 3685/5694 1229/1897 I/V Ata/Gta 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 tolerated(0.1) 31/43 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 41693172 41693172 T C 1 0 0 0 0 1 0 0 0 720 1464 51 5 5 ANK1 8 41693172 Missense_Mutation SNP T C3N-00175_T 2044696 41693172 103445464 660 10252 CHRNB3 0 . GRCh38 8 42708822 42708822 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.158C>A p.Thr53Asn p.T53N ENST00000289957 2/6 114 93 21 149 149 0 strelka-varscan-mutect CHRNB3,missense_variant,p.Thr53Asn,ENST00000289957,NM_000749.3;CHRNB3,5_prime_UTR_variant,,ENST00000534391,;RP11-412B14.1,intron_variant,,ENST00000527318,;CHRNB3,downstream_gene_variant,,ENST00000531610,; A ENST00000289957 Transcript missense_variant 286/2294 158/1377 53/458 T/N aCc/aAc 1 1 CHRNB3 HGNC HGNC:1963 protein_coding YES CCDS6134.1 ENSP00000289957 Q05901 UPI0000125272 NM_000749.3 tolerated(0.09) 2/6 hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS rs1335889873 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 42708822 42708822 C A 1 0 0 0 0 1 0 0 0 3152 507 18 2 2 CHRNB3 8 42708822 Missense_Mutation SNP C C3N-00175_T 1015650 42708822 102429814 661 10253 SNTG1 0 . GRCh38 8 50658601 50658601 + Missense_Mutation SNP T T A C3N-00175_T C3N-00175_N T T c.976T>A p.Trp326Arg p.W326R ENST00000522124 15/19 130 112 18 120 119 1 strelka-varscan-mutect SNTG1,missense_variant,p.Trp326Arg,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Trp326Arg,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Trp326Arg,ENST00000517473,NM_001287814.1;SNTG1,missense_variant,p.Trp326Arg,ENST00000520825,;SNTG1,missense_variant,p.Trp100Arg,ENST00000524004,; A ENST00000522124 Transcript missense_variant 1637/3504 976/1554 326/517 W/R Tgg/Agg COSM129340,COSM129341 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 tolerated(0.4) 15/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 50658601 50658601 T A 1 0 0 0 0 1 0 0 0 15194 1580 55 4 4 SNTG1 8 50658601 Missense_Mutation SNP T C3N-00175_T 7949779 50658601 94480035 662 10254 PXDNL 0 . GRCh38 8 51371878 51371878 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.3896G>T p.Cys1299Phe p.C1299F ENST00000356297 19/23 157 128 29 184 184 0 strelka-varscan-mutect PXDNL,missense_variant,p.Cys1299Phe,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.Cys373Phe,ENST00000522933,;PXDNL,missense_variant,p.Cys565Phe,ENST00000522628,; A ENST00000356297 Transcript missense_variant 3997/4805 3896/4392 1299/1463 C/F tGt/tTt COSM374843,COSM374844 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 19/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 51371878 51371878 C A 1 0 0 0 0 1 0 0 0 13002 492 17 2 2 PXDNL 8 51371878 Missense_Mutation SNP C C3N-00175_T 713277 51371878 93766758 663 10255 NSMAF 0 . GRCh38 8 58589468 58589468 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2288G>T p.Trp763Leu p.W763L ENST00000427130 26/31 61 46 15 49 49 0 varscan-mutect NSMAF,missense_variant,p.Trp732Leu,ENST00000038176,NM_003580.3;NSMAF,missense_variant,p.Trp763Leu,ENST00000427130,NM_001144772.1;NSMAF,non_coding_transcript_exon_variant,,ENST00000523177,;NSMAF,non_coding_transcript_exon_variant,,ENST00000517612,;NSMAF,non_coding_transcript_exon_variant,,ENST00000521712,;NSMAF,upstream_gene_variant,,ENST00000521972,;NSMAF,downstream_gene_variant,,ENST00000523106,;NSMAF,downstream_gene_variant,,ENST00000519166,;NSMAF,downstream_gene_variant,,ENST00000524148,;NSMAF,downstream_gene_variant,,ENST00000519174,;AC068522.4,upstream_gene_variant,,ENST00000482895,; A ENST00000427130 Transcript missense_variant 2476/3371 2288/2847 763/948 W/L tGg/tTg 1 -1 NSMAF HGNC HGNC:8017 protein_coding YES CCDS47864.1 ENSP00000411012 Q92636 UPI000192950C NM_001144772.1 deleterious(0.04) 26/31 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF53,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 58589468 58589468 C A 1 0 0 0 0 1 0 0 0 10734 595 21 2 2 NSMAF 8 58589468 Missense_Mutation SNP C C3N-00175_T 7217590 58589468 86549168 664 10256 TTPA 0 . GRCh38 8 63066018 63066018 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.438G>C p.Glu146Asp p.E146D ENST00000260116 3/5 292 212 80 278 278 0 strelka-varscan-mutect TTPA,missense_variant,p.Glu146Asp,ENST00000260116,NM_000370.3;TTPA,intron_variant,,ENST00000521138,; G ENST00000260116 Transcript missense_variant 470/2338 438/837 146/278 E/D gaG/gaC 1 -1 TTPA HGNC HGNC:12404 protein_coding YES CCDS6178.1 ENSP00000260116 P49638 UPI00001377AC NM_000370.3 tolerated(0.17) 3/5 PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF52,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS rs918456240 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 63066018 63066018 C G 1 0 0 0 0 1 0 0 0 17246 680 24 4 4 TTPA 8 63066018 Missense_Mutation SNP C C3N-00175_T 4476550 63066018 82072618 665 10257 TTPA 0 . GRCh38 8 63072959 63072959 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.334A>T p.Ser112Cys p.S112C ENST00000260116 2/5 247 209 38 252 252 0 strelka-varscan-mutect TTPA,missense_variant,p.Ser112Cys,ENST00000260116,NM_000370.3;TTPA,intron_variant,,ENST00000521138,; A ENST00000260116 Transcript missense_variant 366/2338 334/837 112/278 S/C Agc/Tgc 1 -1 TTPA HGNC HGNC:12404 protein_coding YES CCDS6178.1 ENSP00000260116 P49638 UPI00001377AC NM_000370.3 tolerated(0.13) 2/5 PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF52,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087,Prints_domain:PR00180 MODERATE 1 SNV 1 1 PASS rs1322464959 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 63072959 63072959 T A 1 0 0 0 0 1 0 0 0 17246 1580 55 4 4 TTPA 8 63072959 Missense_Mutation SNP T C3N-00175_T 6941 63072959 82065677 666 10258 TRIM55 0 . GRCh38 8 66154141 66154141 + Missense_Mutation SNP G G T rs766018012 C3N-00175_T C3N-00175_N G G c.1331G>T p.Ser444Ile p.S444I ENST00000315962 9/10 279 197 82 334 334 0 strelka-varscan-mutect TRIM55,missense_variant,p.Ser444Ile,ENST00000315962,NM_184085.1;TRIM55,missense_variant,p.Ser444Ile,ENST00000276573,NM_033058.2;TRIM55,intron_variant,,ENST00000353317,NM_184086.1;TRIM55,intron_variant,,ENST00000350034,NM_184087.1;TRIM55,intron_variant,,ENST00000517647,; T ENST00000315962 Transcript missense_variant 1704/2914 1331/1647 444/548 S/I aGt/aTt rs766018012 1 1 TRIM55 HGNC HGNC:14215 protein_coding YES CCDS6184.1 ENSP00000323913 Q9BYV6 UPI00001CE3B7 NM_184085.1 deleterious_low_confidence(0) 9/10 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF318 MODERATE 1 SNV 1 1 PASS rs766018012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 66154141 66154141 G T 1 0 0 0 0 1 0 0 0 17022 1029 36 2 2 TRIM55 8 66154141 Missense_Mutation SNP G C3N-00175_T 3081182 66154141 78984495 667 10259 SULF1 0 . GRCh38 8 69603265 69603265 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.1135G>A p.Asp379Asn p.D379N ENST00000260128 11/23 209 183 26 229 229 0 strelka-varscan-mutect SULF1,missense_variant,p.Asp379Asn,ENST00000260128,NM_015170.2;SULF1,missense_variant,p.Asp379Asn,ENST00000458141,NM_001128204.1;SULF1,missense_variant,p.Asp379Asn,ENST00000402687,NM_001128205.1;SULF1,missense_variant,p.Asp379Asn,ENST00000419716,NM_001128206.1;SULF1,missense_variant,p.Asp163Asn,ENST00000616868,;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,; A ENST00000260128 Transcript missense_variant 1852/5710 1135/2616 379/871 D/N Gat/Aat COSM3779331 1 1 SULF1 HGNC HGNC:20391 protein_coding YES CCDS6204.1 ENSP00000260128 Q8IWU6 A0A024R809 UPI000003FD82 NM_015170.2 deleterious(0.01) 11/23 hmmpanther:PTHR10342:SF210,hmmpanther:PTHR10342,PIRSF_domain:PIRSF036665,Gene3D:3.40.720.10,Superfamily_domains:SSF53649 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 69603265 69603265 G A 1 0 0 0 0 1 0 0 0 15758 1290 45 3 3 SULF1 8 69603265 Missense_Mutation SNP G C3N-00175_T 3449124 69603265 75535371 668 10260 MSC 0 . GRCh38 8 71843980 71843980 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.199G>A p.Ala67Thr p.A67T ENST00000325509 1/2 92 76 16 138 138 0 strelka-varscan-mutect MSC,missense_variant,p.Ala67Thr,ENST00000325509,NM_005098.3;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000521467,;MSC-AS1,upstream_gene_variant,,ENST00000457356,;MSC-AS1,upstream_gene_variant,,ENST00000518916,;MSC-AS1,upstream_gene_variant,,ENST00000519751,;MSC,upstream_gene_variant,,ENST00000518440,;MSC,upstream_gene_variant,,ENST00000521739,; T ENST00000325509 Transcript missense_variant 489/2023 199/621 67/206 A/T Gcg/Acg COSM5093077 1 -1 MSC HGNC HGNC:7321 protein_coding YES CCDS43746.1 ENSP00000321445 O60682 UPI000012FA29 NM_005098.3 tolerated(0.58) 1/2 hmmpanther:PTHR23349:SF62,hmmpanther:PTHR23349 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 71843980 71843980 C T 1 0 0 0 0 1 0 0 0 9851 768 27 1 1 MSC 8 71843980 Missense_Mutation SNP C C3N-00175_T 2240715 71843980 73294656 669 10261 TRPA1 0 . GRCh38 8 72055535 72055535 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.1430A>G p.Glu477Gly p.E477G ENST00000262209 12/27 307 213 94 264 264 0 strelka-varscan-mutect TRPA1,missense_variant,p.Glu477Gly,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Glu329Gly,ENST00000523582,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000457356,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000519068,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;MSC-AS1,downstream_gene_variant,,ENST00000519751,;MSC-AS1,downstream_gene_variant,,ENST00000524152,;TRPA1,non_coding_transcript_exon_variant,,ENST00000520788,; C ENST00000262209 Transcript missense_variant 1638/5223 1430/3360 477/1119 E/G gAa/gGa 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 12/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 72055535 72055535 T C 1 0 0 0 0 1 0 0 0 17082 1783 62 5 5 TRPA1 8 72055535 Missense_Mutation SNP T C3N-00175_T 211555 72055535 73083101 670 10262 SBSPON 0 . GRCh38 8 73081206 73081206 + Silent SNP C C A rs754823025 C3N-00175_T C3N-00175_N C C c.222G>T p.= p.P74P ENST00000297354 2/5 43 32 11 53 53 0 strelka-varscan-mutect SBSPON,synonymous_variant,p.=,ENST00000297354,NM_153225.3;RP11-956J14.1,downstream_gene_variant,,ENST00000442274,;SBSPON,non_coding_transcript_exon_variant,,ENST00000519697,; A ENST00000297354 Transcript synonymous_variant 427/3801 222/795 74/264 P ccG/ccT rs754823025 1 -1 SBSPON HGNC HGNC:30362 protein_coding YES CCDS43747.2 ENSP00000297354 Q8IVN8 UPI0000D47CF3 NM_153225.3 2/5 Superfamily_domains:0049461,Gene3D:2.20.100.10,PROSITE_profiles:PS50092,PROSITE_profiles:PS50958,hmmpanther:PTHR20920,hmmpanther:PTHR20920:SF2,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS rs754823025 . 0 199 11 0 0 0 0 0 -20 0.9999861 1 1 1 0 A 2 1 39 73081206 73081206 C A 1 0 0 0 0 0 0 0 1 14130 523 19 1 1 SBSPON 8 73081206 Silent SNP C C3N-00175_T 1025671 73081206 72057430 671 10263 SBSPON 0 . GRCh38 8 73092993 73092993 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.75C>A p.= p.A25A ENST00000297354 1/5 125 113 12 148 148 0 strelka-varscan-mutect SBSPON,synonymous_variant,p.=,ENST00000297354,NM_153225.3;SBSPON,intron_variant,,ENST00000519697,; T ENST00000297354 Transcript synonymous_variant 280/3801 75/795 25/264 A gcC/gcA 1 -1 SBSPON HGNC HGNC:30362 protein_coding YES CCDS43747.2 ENSP00000297354 Q8IVN8 UPI0000D47CF3 NM_153225.3 1/5 PROSITE_profiles:PS50958,hmmpanther:PTHR20920,hmmpanther:PTHR20920:SF2 LOW 1 SNV 1 1 PASS rs1046662286 . 0 208 0 2 0 0 0 0 -17.72078 0.9999998 1 1 1 0 T 2 4 39 73092993 73092993 G T 1 0 0 0 0 0 0 0 1 14130 1103 39 1 1 SBSPON 8 73092993 Silent SNP G C3N-00175_T 11787 73092993 72045643 672 10264 ZFHX4 0 . GRCh38 8 76705215 76705215 + Missense_Mutation SNP C C G rs745707914 C3N-00175_T C3N-00175_N C C c.1127C>G p.Pro376Arg p.P376R ENST00000521891 2/11 206 183 23 232 232 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Pro376Arg,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Pro376Arg,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; G ENST00000521891 Transcript missense_variant 1575/14019 1127/10851 376/3616 P/R cCg/cGg rs745707914,COSM3716038,COSM3716039 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated_low_confidence(0.49) 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs745707914 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 76705215 76705215 C G 1 0 0 0 0 1 0 0 0 18213 652 23 4 4 ZFHX4 8 76705215 Missense_Mutation SNP C C3N-00175_T 3612222 76705215 68433421 673 10265 ZFHX4 0 . GRCh38 8 76707790 76707790 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2835C>T p.= p.C945C ENST00000521891 3/11 199 172 27 309 309 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; T ENST00000521891 Transcript synonymous_variant 3283/14019 2835/10851 945/3616 C tgC/tgT 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 3/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,SMART_domains:SM00451 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 76707790 76707790 C T 1 0 0 0 0 0 0 0 1 18213 718 25 3 3 ZFHX4 8 76707790 Silent SNP C C3N-00175_T 2575 76707790 68430846 674 10266 RALYL 0 . GRCh38 8 84804791 84804791 + Missense_Mutation SNP C C G C3N-00175_T C3N-00175_N C C c.393C>G p.Phe131Leu p.F131L ENST00000517638 4/9 19 12 7 34 34 0 strelka-varscan-mutect RALYL,missense_variant,p.Phe118Leu,ENST00000521268,NM_173848.5;RALYL,missense_variant,p.Phe118Leu,ENST00000522455,NM_001100392.1;RALYL,missense_variant,p.Phe131Leu,ENST00000517638,NM_001100391.1;RALYL,missense_variant,p.Phe118Leu,ENST00000521695,NM_001100393.1;RALYL,missense_variant,p.Phe45Leu,ENST00000523850,NM_001287244.1;RALYL,missense_variant,p.Phe45Leu,ENST00000521376,;RALYL,intron_variant,,ENST00000518566,NM_001287243.1; G ENST00000517638 Transcript missense_variant 517/1972 393/915 131/304 F/L ttC/ttG COSM4492217,COSM4492218 1 1 RALYL HGNC HGNC:27036 protein_coding YES CCDS55252.1 ENSP00000430128 Q86SE5 UPI00002108E6 NM_001100391.1 tolerated(0.73) 4/9 hmmpanther:PTHR13968:SF21,hmmpanther:PTHR13968,PIRSF_domain:PIRSF037992 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 6 198 5 0 0 0 0 0 -19.88715 1 1 1 1 0 G 3 3 39 84804791 84804791 C G 1 0 0 0 0 1 0 0 0 13179 854 30 4 4 RALYL 8 84804791 Missense_Mutation SNP C C3N-00175_T 8097001 84804791 60333845 675 10267 ATP6V0D2 0 . GRCh38 8 86151509 86151509 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.860A>T p.Lys287Met p.K287M ENST00000285393 7/8 250 202 48 180 180 0 strelka-varscan-mutect ATP6V0D2,missense_variant,p.Lys287Met,ENST00000285393,NM_152565.1;CTD-3118D11.2,intron_variant,,ENST00000522679,;CTD-3118D11.2,downstream_gene_variant,,ENST00000524253,; T ENST00000285393 Transcript missense_variant 1002/2446 860/1053 287/350 K/M aAg/aTg 1 1 ATP6V0D2 HGNC HGNC:18266 protein_coding YES CCDS6241.1 ENSP00000285393 Q8N8Y2 A0A024R991 UPI0000051F69 NM_152565.1 deleterious(0.02) 7/8 Superfamily_domains:0044678,Pfam_domain:PF01992,PIRSF_domain:PIRSF018497,hmmpanther:PTHR11028,hmmpanther:PTHR11028:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 86151509 86151509 A T 1 0 0 0 0 1 0 0 0 1327 72 3 4 4 ATP6V0D2 8 86151509 Missense_Mutation SNP A C3N-00175_T 1346718 86151509 58987127 676 10268 SLC7A13 0 . GRCh38 8 86217636 86217636 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1013C>A p.Thr338Lys p.T338K ENST00000297524 3/4 197 164 33 162 162 0 strelka-varscan-mutect SLC7A13,missense_variant,p.Thr338Lys,ENST00000297524,NM_138817.2;SLC7A13,missense_variant,p.Thr329Lys,ENST00000419776,;SLC7A13,non_coding_transcript_exon_variant,,ENST00000520624,; T ENST00000297524 Transcript missense_variant 1117/1878 1013/1413 338/470 T/K aCa/aAa 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 deleterious(0.04) 3/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 86217636 86217636 G T 1 0 0 0 0 1 0 0 0 14978 1377 48 2 2 SLC7A13 8 86217636 Missense_Mutation SNP G C3N-00175_T 66127 86217636 58921000 677 10269 CPNE3 0 . GRCh38 8 86546647 86546647 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.785A>G p.Lys262Arg p.K262R ENST00000517490 10/17 163 95 68 150 150 0 strelka-varscan-mutect CPNE3,missense_variant,p.Lys262Arg,ENST00000517490,NM_003909.4;CPNE3,missense_variant,p.Lys151Arg,ENST00000517391,;CPNE3,downstream_gene_variant,,ENST00000621783,;CPNE3,non_coding_transcript_exon_variant,,ENST00000517354,;CPNE3,upstream_gene_variant,,ENST00000614678,;CPNE3,downstream_gene_variant,,ENST00000517862,;CPNE3,upstream_gene_variant,,ENST00000523588,; G ENST00000517490 Transcript missense_variant 948/4865 785/1614 262/537 K/R aAg/aGg 1 1 CPNE3 HGNC HGNC:2316 protein_coding YES CCDS6243.1 ENSP00000477590 O75131 A0A024R994 UPI0000127C13 NM_003909.4 deleterious(0.03) 10/17 Low_complexity_(Seg):seg,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 86546647 86546647 A G 1 0 0 0 0 1 0 0 0 3608 72 3 5 5 CPNE3 8 86546647 Missense_Mutation SNP A C3N-00175_T 329011 86546647 58591989 678 10270 DCAF4L2 0 . GRCh38 8 87873567 87873567 + Silent SNP C C G C3N-00175_T C3N-00175_N C C c.405G>C p.= p.L135L ENST00000319675 1/1 387 219 168 326 326 0 strelka-varscan-mutect DCAF4L2,synonymous_variant,p.=,ENST00000319675,NM_152418.3;CTB-118P15.3,downstream_gene_variant,,ENST00000613582,; G ENST00000319675 Transcript synonymous_variant 502/3326 405/1188 135/395 L ctG/ctC COSM5337802 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 1/1 Gene3D:2.130.10.10,Superfamily_domains:SSF50978 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 87873567 87873567 C G 1 0 0 0 0 0 0 0 1 4073 813 29 4 4 DCAF4L2 8 87873567 Silent SNP C C3N-00175_T 1326920 87873567 57265069 679 10271 MMP16 0 . GRCh38 8 88167894 88167894 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.484G>T p.Val162Leu p.V162L ENST00000286614 4/10 237 204 33 179 179 0 strelka-varscan-mutect MMP16,missense_variant,p.Val162Leu,ENST00000286614,NM_005941.4;MMP16,downstream_gene_variant,,ENST00000522726,;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; A ENST00000286614 Transcript missense_variant 766/11558 484/1824 162/607 V/L Gta/Tta 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 deleterious(0.01) 4/10 hmmpanther:PTHR10201:SF26,hmmpanther:PTHR10201,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00413,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 MODERATE 1 SNV 1 1 PASS rs1260245087 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 88167894 88167894 C A 1 0 0 0 0 1 0 0 0 9618 478 17 2 2 MMP16 8 88167894 Missense_Mutation SNP C C3N-00175_T 294327 88167894 56970742 680 10272 NECAB1 0 . GRCh38 8 90791970 90791970 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.84G>T p.Met28Ile p.M28I ENST00000417640 1/13 339 318 21 292 292 0 strelka-varscan-mutect NECAB1,missense_variant,p.Met28Ile,ENST00000417640,NM_022351.4;TMEM64,upstream_gene_variant,,ENST00000519519,;TMEM64,upstream_gene_variant,,ENST00000521852,;NECAB1,non_coding_transcript_exon_variant,,ENST00000521954,;TMEM64,upstream_gene_variant,,ENST00000521211,;NECAB1,non_coding_transcript_exon_variant,,ENST00000523962,;NECAB1,non_coding_transcript_exon_variant,,ENST00000522729,; T ENST00000417640 Transcript missense_variant 421/5289 84/1056 28/351 M/I atG/atT 1 1 NECAB1 HGNC HGNC:20983 protein_coding YES CCDS47889.1 ENSP00000387380 Q8N987 UPI0000070EEA NM_022351.4 tolerated(0.36) 1/13 PROSITE_profiles:PS50222,hmmpanther:PTHR12178,hmmpanther:PTHR12178:SF11 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99989 0.9999996 1 1 1 0 T 3 4 39 90791970 90791970 G T 1 0 0 0 0 1 0 0 0 10328 1377 48 2 2 NECAB1 8 90791970 Missense_Mutation SNP G C3N-00175_T 2624076 90791970 54346666 681 10273 SLC26A7 0 . GRCh38 8 91363527 91363527 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1477G>A p.Glu493Lys p.E493K ENST00000309536 13/19 30 22 8 58 58 0 strelka-varscan-mutect SLC26A7,missense_variant,p.Glu493Lys,ENST00000276609,NM_052832.3;SLC26A7,missense_variant,p.Glu493Lys,ENST00000617233,;SLC26A7,missense_variant,p.Glu192Lys,ENST00000617078,NM_001282357.1;SLC26A7,missense_variant,p.Glu493Lys,ENST00000523719,NM_001282356.1;SLC26A7,missense_variant,p.Glu493Lys,ENST00000309536,NM_134266.1;SLC26A7,non_coding_transcript_exon_variant,,ENST00000520249,;SLC26A7,non_coding_transcript_exon_variant,,ENST00000517930,;SLC26A7,3_prime_UTR_variant,,ENST00000522181,; A ENST00000309536 Transcript missense_variant 1697/2656 1477/1992 493/663 E/K Gaa/Aaa 1 1 SLC26A7 HGNC HGNC:14467 protein_coding YES CCDS6255.1 ENSP00000309504 Q8TE54 UPI0000046B1C NM_134266.1 tolerated(0.34) 13/19 PROSITE_profiles:PS50801,hmmpanther:PTHR11814:SF75,hmmpanther:PTHR11814 MODERATE 1 SNV 1 1 PASS . . 2 205 2 0 0 0 0 0 -19.9919 1 1 1 1 0 A 3 1 39 91363527 91363527 G A 1 0 0 0 0 1 0 0 0 14792 943 33 3 3 SLC26A7 8 91363527 Missense_Mutation SNP G C3N-00175_T 571557 91363527 53775109 682 10274 RAD54B 0 . GRCh38 8 94380296 94380296 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2096G>T p.Arg699Met p.R699M ENST00000336148 12/15 337 217 120 293 293 0 strelka-varscan-mutect RAD54B,missense_variant,p.Arg699Met,ENST00000336148,NM_012415.3;RAD54B,missense_variant,p.Arg515Met,ENST00000611249,NM_001205263.1;FSBP,3_prime_UTR_variant,,ENST00000517506,;RAD54B,non_coding_transcript_exon_variant,,ENST00000518358,; A ENST00000336148 Transcript missense_variant 2221/3068 2096/2733 699/910 R/M aGg/aTg 1 -1 RAD54B HGNC HGNC:17228 protein_coding YES CCDS6262.1 ENSP00000336606 Q9Y620 UPI0000070088 NM_012415.3 deleterious(0) 12/15 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF688,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 94380296 94380296 C A 1 0 0 0 0 1 0 0 0 13153 681 24 2 2 RAD54B 8 94380296 Missense_Mutation SNP C C3N-00175_T 3016769 94380296 50758340 683 10275 PLEKHF2 0 . GRCh38 8 95154222 95154222 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.178G>A p.Asp60Asn p.D60N ENST00000315367 2/2 164 149 15 126 125 1 strelka-varscan-mutect PLEKHF2,missense_variant,p.Asp60Asn,ENST00000315367,NM_024613.3;PLEKHF2,missense_variant,p.Asp60Asn,ENST00000519516,; A ENST00000315367 Transcript missense_variant 419/2881 178/750 60/249 D/N Gat/Aat 1 1 PLEKHF2 HGNC HGNC:20757 protein_coding YES CCDS6267.1 ENSP00000322373 Q9H8W4 UPI0000035DB0 NM_024613.3 deleterious(0) 2/2 PROSITE_profiles:PS50003,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 95154222 95154222 G A 1 0 0 0 0 1 0 0 0 12160 1290 45 3 3 PLEKHF2 8 95154222 Missense_Mutation SNP G C3N-00175_T 773926 95154222 49984414 684 10276 CPQ 0 . GRCh38 8 96785267 96785267 + Nonsense_Mutation SNP G G T rs760248141 C3N-00175_T C3N-00175_N G G c.370G>T p.Glu124Ter p.E124* ENST00000220763 2/8 112 92 20 90 90 0 varscan-mutect CPQ,stop_gained,p.Glu124Ter,ENST00000220763,NM_016134.3;CPQ,stop_gained,p.Glu124Ter,ENST00000521142,;CPQ,stop_gained,p.Glu124Ter,ENST00000517742,;CPQ,stop_gained,p.Glu124Ter,ENST00000519900,;CPQ,stop_gained,p.Glu124Ter,ENST00000519484,;CPQ,non_coding_transcript_exon_variant,,ENST00000525310,; T ENST00000220763 Transcript stop_gained 580/1947 370/1419 124/472 E/* Gag/Tag rs760248141 1 1 CPQ HGNC HGNC:16910 protein_coding YES CCDS6273.1 ENSP00000220763 Q9Y646 A0A024R9B8 UPI00000706B8 NM_016134.3 2/8 hmmpanther:PTHR12053,hmmpanther:PTHR12053:SF3 HIGH 1 SNV 1 1 PASS rs760248141 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 96785267 96785267 G T 1 0 0 0 0 0 1 0 0 3618 1175 41 2 2 CPQ 8 96785267 Nonsense_Mutation SNP G C3N-00175_T 1631045 96785267 48353369 685 10277 TSPYL5 0 . GRCh38 8 97277635 97277635 + Silent SNP G G A rs746850171 C3N-00175_T C3N-00175_N G G c.210C>T p.= p.L70L ENST00000322128 1/1 57 50 7 37 37 0 strelka-varscan-mutect TSPYL5,synonymous_variant,p.=,ENST00000322128,NM_033512.2; A ENST00000322128 Transcript synonymous_variant 330/4491 210/1254 70/417 L ctC/ctT rs746850171,COSM4476974 1 -1 TSPYL5 HGNC HGNC:29367 protein_coding YES CCDS34927.1 ENSP00000322802 Q86VY4 UPI0000210364 NM_033512.2 1/1 0,1 LOW 1 SNV 0,1 1 PASS rs746850171 . 0 208 2 0 0 0 0 0 -16.75767 1 1 1 1 0 A 2 1 39 97277635 97277635 G A 1 0 0 0 0 0 0 0 1 17169 1161 41 3 3 TSPYL5 8 97277635 Silent SNP G C3N-00175_T 492368 97277635 47861001 686 10278 MATN2 0 . GRCh38 8 98018067 98018067 + Nonsense_Mutation SNP C C A rs374356192 C3N-00175_T C3N-00175_N C C c.1770C>A p.Cys590Ter p.C590* ENST00000254898 12/19 274 234 40 183 182 1 strelka-varscan-mutect MATN2,stop_gained,p.Cys590Ter,ENST00000254898,NM_002380.3;MATN2,stop_gained,p.Cys590Ter,ENST00000521689,NM_030583.2;MATN2,stop_gained,p.Cys590Ter,ENST00000520016,;MATN2,stop_gained,p.Cys549Ter,ENST00000524308,;MATN2,stop_gained,p.Cys306Ter,ENST00000522025,;MATN2,stop_gained,p.Cys373Ter,ENST00000518154,;MATN2,stop_gained,p.Cys65Ter,ENST00000517321,;MATN2,stop_gained,p.Cys107Ter,ENST00000521952,;MATN2,upstream_gene_variant,,ENST00000518370,; A ENST00000254898 Transcript stop_gained 2001/4106 1770/2871 590/956 C/* tgC/tgA rs374356192 1 1 MATN2 HGNC HGNC:6908 protein_coding YES CCDS55264.1 ENSP00000254898 O00339 A0A140VKH7 UPI000021037B NM_002380.3 12/19 Gene3D:2.10.25.10,Pfam_domain:PF14670,PROSITE_patterns:PS00010,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR11132,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 HIGH 1 SNV 1 1 PASS rs374356192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 98018067 98018067 C A 1 0 0 0 0 0 1 0 0 9260 776 27 1 1 MATN2 8 98018067 Nonsense_Mutation SNP C C3N-00175_T 740432 98018067 47120569 687 10279 RGS22 0 . GRCh38 8 100072144 100072144 + Splice_Site SNP C C A novel C3N-00175_T C3N-00175_N C C c.425+1G>T p.X142_splice ENST00000360863 93 75 18 103 103 0 strelka-varscan-mutect RGS22,splice_donor_variant,,ENST00000360863,NM_015668.4;RGS22,splice_donor_variant,,ENST00000617334,;RGS22,splice_donor_variant,,ENST00000523437,NM_001286692.1;RGS22,splice_donor_variant,,ENST00000519092,;RGS22,splice_donor_variant,,ENST00000519408,;RGS22,splice_donor_variant,,ENST00000520117,;RGS22,intron_variant,,ENST00000523287,NM_001286693.1;RGS22,intron_variant,,ENST00000517828,;RGS22,splice_donor_variant,,ENST00000519725,;RGS22,splice_donor_variant,,ENST00000520923,; A ENST00000360863 Transcript splice_donor_variant -/4296 425/3795 142/1264 1 -1 RGS22 HGNC HGNC:24499 protein_coding YES CCDS43758.1 ENSP00000354109 Q8NE09 UPI0000E5AF25 NM_015668.4 5/27 HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999989 1 1 1 0 A 5 1 39 100072144 100072144 C A 1 0 0 0 0 0 0 1 0 13476 521 18 2 2 RGS22 8 100072144 Splice_Site SNP C C3N-00175_T 2054077 100072144 45066492 688 10280 SPAG1 0 . GRCh38 8 100220323 100220323 + Missense_Mutation SNP G G T rs150325048 C3N-00175_T C3N-00175_N G G c.1580G>T p.Arg527Leu p.R527L ENST00000388798 13/19 219 122 97 157 157 0 strelka-varscan-mutect SPAG1,missense_variant,p.Arg527Leu,ENST00000388798,NM_003114.4;SPAG1,missense_variant,p.Arg527Leu,ENST00000251809,NM_172218.2;SPAG1,intron_variant,,ENST00000523302,; T ENST00000388798 Transcript missense_variant 1771/3852 1580/2781 527/926 R/L cGg/cTg rs150325048,COSM3884161 1 1 SPAG1 HGNC HGNC:11212 protein_coding YES CCDS34930.1 ENSP00000373450 Q07617 UPI000016783D NM_003114.4 deleterious(0) 13/19 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR22904:SF310,hmmpanther:PTHR22904,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs150325048 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 100220323 100220323 G T 1 0 0 0 0 1 0 0 0 15306 1116 39 1 1 SPAG1 8 100220323 Missense_Mutation SNP G C3N-00175_T 148179 100220323 44918313 689 10281 DPYS 0 . GRCh38 8 104451262 104451262 + Missense_Mutation SNP G G A rs755791096 C3N-00175_T C3N-00175_N G G c.407C>T p.Thr136Met p.T136M ENST00000351513 2/10 499 473 26 376 374 2 strelka-varscan-mutect DPYS,missense_variant,p.Thr136Met,ENST00000351513,NM_001385.2;DPYS,intron_variant,,ENST00000521573,; A ENST00000351513 Transcript missense_variant 540/2127 407/1560 136/519 T/M aCg/aTg rs755791096,COSM3270909 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 deleterious(0) 2/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,TIGRFAM_domain:TIGR02033,Pfam_domain:PF01979,Gene3D:3.20.20.140,Superfamily_domains:SSF51556 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755791096 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 104451262 104451262 G A 1 0 0 0 0 1 0 0 0 4561 1145 40 1 1 DPYS 8 104451262 Missense_Mutation SNP G C3N-00175_T 4230939 104451262 40687374 690 10282 TRHR 0 . GRCh38 8 109087777 109087777 + Missense_Mutation SNP G G A rs368688599 C3N-00175_T C3N-00175_N G G c.265G>A p.Gly89Ser p.G89S ENST00000518632 2/3 490 298 192 321 321 0 strelka-varscan-mutect TRHR,missense_variant,p.Gly89Ser,ENST00000518632,;TRHR,missense_variant,p.Gly89Ser,ENST00000311762,NM_003301.5; A ENST00000518632 Transcript missense_variant 616/1660 265/1197 89/398 G/S Ggt/Agt rs368688599,COSM247969 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 tolerated(0.11) 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00751,Prints_domain:PR01846,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs368688599 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 109087777 109087777 G A 1 0 0 0 0 1 0 0 0 16969 1116 39 1 1 TRHR 8 109087777 Missense_Mutation SNP G C3N-00175_T 4636515 109087777 36050859 691 10283 TRHR 0 . GRCh38 8 109119146 109119146 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.889delC p.Gln297LysfsTer22 p.Q297Kfs*22 ENST00000518632 3/3 358 292 66 321 321 0 sindel-varindel-pindel TRHR,frameshift_variant,p.Gln297LysfsTer22,ENST00000518632,;TRHR,frameshift_variant,p.Gln297LysfsTer22,ENST00000311762,NM_003301.5; - ENST00000518632 Transcript frameshift_variant 1239/1660 888/1197 296/398 F/X ttC/tt 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00751,Prints_domain:PR01846,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115,SMART_domains:SM01381,Superfamily_domains:SSF81321 HIGH 1 deletion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 109119146 109119146 C - 1 0 1 0 1 0 0 0 0 16969 854 30 0 0 TRHR 8 109119146 Frame_Shift_Del DEL C C3N-00175_T 31369 109119146 36019490 692 10284 CSMD3 0 . GRCh38 8 112255378 112255378 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.9912C>A p.= p.G3304G ENST00000297405 62/71 436 268 168 346 345 1 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,; T ENST00000297405 Transcript synonymous_variant 10157/13212 9912/11124 3304/3707 G ggC/ggA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 62/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS rs1323355045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 112255378 112255378 G T 1 0 0 0 0 0 0 0 1 3747 1306 46 2 2 CSMD3 8 112255378 Silent SNP G C3N-00175_T 3136232 112255378 32883258 693 10285 CSMD3 0 . GRCh38 8 112666319 112666319 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2774T>A p.Ile925Asn p.I925N ENST00000297405 17/71 444 367 77 316 316 0 strelka-varscan-mutect CSMD3,missense_variant,p.Ile925Asn,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ile885Asn,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ile821Asn,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ile265Asn,ENST00000339701,; T ENST00000297405 Transcript missense_variant 3019/13212 2774/11124 925/3707 I/N aTt/aAt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 17/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs1446780743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 112666319 112666319 A T 1 0 0 0 0 1 0 0 0 3747 101 4 4 4 CSMD3 8 112666319 Missense_Mutation SNP A C3N-00175_T 410941 112666319 32472317 694 10286 DEPTOR 0 . GRCh38 8 120003043 120003043 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.857G>A p.Ser286Asn p.S286N ENST00000286234 6/9 290 188 102 297 297 0 strelka-varscan-mutect DEPTOR,missense_variant,p.Ser286Asn,ENST00000286234,NM_022783.3;DEPTOR,missense_variant,p.Ser185Asn,ENST00000523492,NM_001283012.1;DEPTOR,non_coding_transcript_exon_variant,,ENST00000518057,; A ENST00000286234 Transcript missense_variant 987/2569 857/1230 286/409 S/N aGc/aAc 1 1 DEPTOR HGNC HGNC:22953 protein_coding YES CCDS6331.1 ENSP00000286234 Q8TB45 UPI000013DE38 NM_022783.3 tolerated(0.07) 6/9 hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 120003043 120003043 G A 1 0 0 0 0 1 0 0 0 4250 971 34 3 3 DEPTOR 8 120003043 Missense_Mutation SNP G C3N-00175_T 7336724 120003043 25135593 695 10287 FER1L6 0 . GRCh38 8 123980718 123980718 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1317G>C p.Lys439Asn p.K439N ENST00000522917 11/41 287 164 123 260 260 0 strelka-varscan-mutect FER1L6,missense_variant,p.Lys439Asn,ENST00000522917,NM_001039112.2;FER1L6-AS1,downstream_gene_variant,,ENST00000518567,; C ENST00000522917 Transcript missense_variant 1523/6051 1317/5574 439/1857 K/N aaG/aaC 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 tolerated(0.07) 11/41 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1390024412 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 123980718 123980718 G C 1 0 0 0 0 1 0 0 0 5678 991 35 4 4 FER1L6 8 123980718 Missense_Mutation SNP G C3N-00175_T 3977675 123980718 21157918 696 10288 ZNF572 0 . GRCh38 8 124976994 124976994 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.726A>C p.Lys242Asn p.K242N ENST00000319286 3/3 425 345 80 287 287 0 strelka-varscan-mutect ZNF572,missense_variant,p.Lys242Asn,ENST00000319286,NM_152412.2; C ENST00000319286 Transcript missense_variant 880/3275 726/1590 242/529 K/N aaA/aaC 1 1 ZNF572 HGNC HGNC:26758 protein_coding YES CCDS6354.1 ENSP00000319305 Q7Z3I7 UPI0000140576 NM_152412.2 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 124976994 124976994 A C 1 0 0 0 0 1 0 0 0 18578 40 2 5 5 ZNF572 8 124976994 Missense_Mutation SNP A C3N-00175_T 996276 124976994 20161642 697 10289 EFR3A 0 . GRCh38 8 131955905 131955905 + Missense_Mutation SNP C C G rs759555318 C3N-00175_T C3N-00175_N C C c.776C>G p.Ala259Gly p.A259G ENST00000254624 7/23 194 156 38 138 138 0 strelka-varscan-mutect EFR3A,missense_variant,p.Ala259Gly,ENST00000254624,NM_001323553.1,NM_001323557.1,NM_015137.4;EFR3A,missense_variant,p.Ala223Gly,ENST00000519656,NM_001323553.1,NM_001323556.1,NM_001323557.1;EFR3A,missense_variant,p.Ala286Gly,ENST00000637848,;EFR3A,downstream_gene_variant,,ENST00000522709,; G ENST00000254624 Transcript missense_variant,splice_region_variant 1001/5438 776/2466 259/821 A/G gCg/gGg rs759555318 1 1 EFR3A HGNC HGNC:28970 protein_coding YES CCDS34942.2 ENSP00000254624 Q14156 UPI00001C1E8F NM_001323553.1,NM_001323557.1,NM_015137.4 tolerated(0.34) 7/23 Gene3D:1.25.10.10,hmmpanther:PTHR12444,hmmpanther:PTHR12444:SF1,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs759555318 . 0 203 3 2 2 0 0 0 -19.99721 0.9833592 1 1 1 0 G 3 3 39 131955905 131955905 C G 1 0 0 0 0 1 0 0 0 4794 782 27 4 4 EFR3A 8 131955905 Missense_Mutation SNP C C3N-00175_T 6978911 131955905 13182731 698 10290 TG 0 . GRCh38 8 133022049 133022049 + Frame_Shift_Del DEL A A - novel C3N-00175_T C3N-00175_N A A c.6936delA p.Gly2313AspfsTer31 p.G2313Dfs*31 ENST00000220616 40/48 495 317 178 383 383 0 sindel-varindel TG,frameshift_variant,p.Gly2313AspfsTer31,ENST00000220616,NM_003235.4;TG,frameshift_variant,p.Gly769AspfsTer31,ENST00000519178,;TG,frameshift_variant,p.Gly446AspfsTer31,ENST00000519543,;TG,frameshift_variant,p.Gly109AspfsTer31,ENST00000518108,;TG,downstream_gene_variant,,ENST00000522523,;TG,3_prime_UTR_variant,,ENST00000523756,; - ENST00000220616 Transcript frameshift_variant 6975/8450 6935/8307 2312/2768 E/X gAa/ga 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 40/48 Gene3D:3.40.50.1820,Pfam_domain:PF00135,PIRSF_domain:PIRSF001831,Superfamily_domains:SSF53474 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 133022049 133022049 A - 1 0 1 0 1 0 0 0 0 16246 246 9 0 0 TG 8 133022049 Frame_Shift_Del DEL A C3N-00175_T 1066144 133022049 12116587 699 10291 COL22A1 0 . GRCh38 8 138693701 138693701 + Splice_Site SNP T T A novel C3N-00175_T C3N-00175_N T T c.2701-2A>T p.X901_splice ENST00000303045 315 190 125 223 222 1 strelka-varscan-mutect COL22A1,splice_acceptor_variant,,ENST00000303045,NM_152888.2;COL22A1,splice_acceptor_variant,,ENST00000435777,;COL22A1,splice_acceptor_variant,,ENST00000341807,; A ENST00000303045 Transcript splice_acceptor_variant -/6346 2701/4881 901/1626 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 34/64 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 138693701 138693701 T A 1 0 0 0 0 0 0 1 0 3469 1594 55 4 4 COL22A1 8 138693701 Splice_Site SNP T C3N-00175_T 5671652 138693701 6444935 700 10292 ARC 0 . GRCh38 8 142613833 142613833 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.439A>T p.Thr147Ser p.T147S ENST00000356613 1/3 210 178 32 162 162 0 strelka-varscan-mutect ARC,missense_variant,p.Thr147Ser,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; A ENST00000356613 Transcript missense_variant 640/2948 439/1191 147/396 T/S Acc/Tcc 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 tolerated_low_confidence(0.34) 1/3 hmmpanther:PTHR15962 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 142613833 142613833 T A 1 0 0 0 0 1 0 0 0 963 1696 59 4 4 ARC 8 142613833 Missense_Mutation SNP T C3N-00175_T 3920132 142613833 2524803 701 10293 LY6D 0 . GRCh38 8 142785347 142785347 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.261C>A p.Cys87Ter p.C87* ENST00000301263 3/3 315 271 44 308 308 0 strelka-varscan-mutect LY6D,stop_gained,p.Cys87Ter,ENST00000301263,NM_003695.2;RP11-706C16.8,upstream_gene_variant,,ENST00000510610,;LY6D,non_coding_transcript_exon_variant,,ENST00000518434,;LY6D,non_coding_transcript_exon_variant,,ENST00000518469,;LY6D,non_coding_transcript_exon_variant,,ENST00000518884,; T ENST00000301263 Transcript stop_gained 337/804 261/387 87/128 C/* tgC/tgA 1 -1 LY6D HGNC HGNC:13348 protein_coding YES CCDS6390.1 ENSP00000301263 Q14210 UPI000002E184 NM_003695.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR16982,hmmpanther:PTHR16982:SF2,Gene3D:2.10.60.10,Pfam_domain:PF00021,SMART_domains:SM00134,Superfamily_domains:SSF57302 HIGH 1 SNV 1 1 PASS rs1462191781 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 142785347 142785347 G T 1 0 0 0 0 0 1 0 0 9000 1195 42 2 2 LY6D 8 142785347 Nonsense_Mutation SNP G C3N-00175_T 171514 142785347 2353289 702 10294 TIGD5 0 . GRCh38 8 143598299 143598299 + Missense_Mutation SNP C C A rs571709743 C3N-00175_T C3N-00175_N C C c.396C>A p.Phe132Leu p.F132L ENST00000504548 1/1 390 340 50 330 330 0 strelka-varscan-mutect TIGD5,missense_variant,p.Phe132Leu,ENST00000504548,NM_032862.4;EEF1D,intron_variant,,ENST00000533749,;EEF1D,upstream_gene_variant,,ENST00000423316,NM_001130053.2;EEF1D,upstream_gene_variant,,ENST00000618139,;EEF1D,upstream_gene_variant,,ENST00000442189,NM_032378.4;EEF1D,upstream_gene_variant,,ENST00000317198,NM_001130057.2;EEF1D,upstream_gene_variant,,ENST00000419152,NM_001130055.2;EEF1D,upstream_gene_variant,,ENST00000529272,;EEF1D,upstream_gene_variant,,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,upstream_gene_variant,,ENST00000524624,;EEF1D,upstream_gene_variant,,ENST00000534380,;EEF1D,upstream_gene_variant,,ENST00000526710,;EEF1D,upstream_gene_variant,,ENST00000526838,NM_001195203.1;EEF1D,upstream_gene_variant,,ENST00000531670,;EEF1D,upstream_gene_variant,,ENST00000528610,NM_001130056.2;EEF1D,upstream_gene_variant,,ENST00000530191,;EEF1D,upstream_gene_variant,,ENST00000533204,;EEF1D,upstream_gene_variant,,ENST00000531621,;EEF1D,upstream_gene_variant,,ENST00000531281,;EEF1D,upstream_gene_variant,,ENST00000532543,;EEF1D,upstream_gene_variant,,ENST00000531218,;EEF1D,upstream_gene_variant,,ENST00000526340,;EEF1D,upstream_gene_variant,,ENST00000532596,;EEF1D,upstream_gene_variant,,ENST00000533494,;EEF1D,upstream_gene_variant,,ENST00000534377,;EEF1D,upstream_gene_variant,,ENST00000530545,;EEF1D,upstream_gene_variant,,ENST00000531931,;EEF1D,upstream_gene_variant,,ENST00000529832,;EEF1D,upstream_gene_variant,,ENST00000530306,;EEF1D,upstream_gene_variant,,ENST00000525261,;EEF1D,upstream_gene_variant,,ENST00000528303,;EEF1D,upstream_gene_variant,,ENST00000534804,;EEF1D,upstream_gene_variant,,ENST00000534475,;EEF1D,upstream_gene_variant,,ENST00000531953,;EEF1D,upstream_gene_variant,,ENST00000529516,;EEF1D,upstream_gene_variant,,ENST00000532400,;EEF1D,upstream_gene_variant,,ENST00000526133,;EEF1D,upstream_gene_variant,,ENST00000524900,;EEF1D,upstream_gene_variant,,ENST00000531770,;EEF1D,upstream_gene_variant,,ENST00000526786,;EEF1D,upstream_gene_variant,,ENST00000524397,;EEF1D,upstream_gene_variant,,ENST00000525695,;EEF1D,upstream_gene_variant,,ENST00000529007,;EEF1D,upstream_gene_variant,,ENST00000533833,;EEF1D,upstream_gene_variant,,ENST00000534232,;EEF1D,upstream_gene_variant,,ENST00000530848,; A ENST00000504548 Transcript missense_variant 465/5390 396/1929 132/642 F/L ttC/ttA rs571709743,COSM3646083 1 1 TIGD5 HGNC HGNC:18336 protein_coding YES CCDS6406.2 ENSP00000421489 Q53EQ6 UPI0001BAE24C NM_032862.4 deleterious(0) 1/1 PROSITE_profiles:PS51253,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF283,Pfam_domain:PF03221,Gene3D:1.10.10.60,SMART_domains:SM00674,Superfamily_domains:SSF46689 0,1 MODERATE SNV 0,1 1 PASS rs571709743 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 143598299 143598299 C A 1 0 0 0 0 1 0 0 0 16337 854 30 2 2 TIGD5 8 143598299 Missense_Mutation SNP C C3N-00175_T 812952 143598299 1540337 703 10295 41 2 TIGD5 0 . GRCh38 8 143598301 143598301 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.398T>A p.Leu133Gln p.L133Q ENST00000504548 1/1 380 329 51 328 328 0 strelka-varscan-mutect TIGD5,missense_variant,p.Leu133Gln,ENST00000504548,NM_032862.4;EEF1D,intron_variant,,ENST00000533749,;EEF1D,upstream_gene_variant,,ENST00000423316,NM_001130053.2;EEF1D,upstream_gene_variant,,ENST00000618139,;EEF1D,upstream_gene_variant,,ENST00000442189,NM_032378.4;EEF1D,upstream_gene_variant,,ENST00000317198,NM_001130057.2;EEF1D,upstream_gene_variant,,ENST00000419152,NM_001130055.2;EEF1D,upstream_gene_variant,,ENST00000529272,;EEF1D,upstream_gene_variant,,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,upstream_gene_variant,,ENST00000524624,;EEF1D,upstream_gene_variant,,ENST00000534380,;EEF1D,upstream_gene_variant,,ENST00000526710,;EEF1D,upstream_gene_variant,,ENST00000526838,NM_001195203.1;EEF1D,upstream_gene_variant,,ENST00000531670,;EEF1D,upstream_gene_variant,,ENST00000528610,NM_001130056.2;EEF1D,upstream_gene_variant,,ENST00000530191,;EEF1D,upstream_gene_variant,,ENST00000533204,;EEF1D,upstream_gene_variant,,ENST00000531621,;EEF1D,upstream_gene_variant,,ENST00000531281,;EEF1D,upstream_gene_variant,,ENST00000532543,;EEF1D,upstream_gene_variant,,ENST00000531218,;EEF1D,upstream_gene_variant,,ENST00000526340,;EEF1D,upstream_gene_variant,,ENST00000532596,;EEF1D,upstream_gene_variant,,ENST00000533494,;EEF1D,upstream_gene_variant,,ENST00000534377,;EEF1D,upstream_gene_variant,,ENST00000530545,;EEF1D,upstream_gene_variant,,ENST00000531931,;EEF1D,upstream_gene_variant,,ENST00000529832,;EEF1D,upstream_gene_variant,,ENST00000530306,;EEF1D,upstream_gene_variant,,ENST00000525261,;EEF1D,upstream_gene_variant,,ENST00000528303,;EEF1D,upstream_gene_variant,,ENST00000534804,;EEF1D,upstream_gene_variant,,ENST00000534475,;EEF1D,upstream_gene_variant,,ENST00000531953,;EEF1D,upstream_gene_variant,,ENST00000529516,;EEF1D,upstream_gene_variant,,ENST00000532400,;EEF1D,upstream_gene_variant,,ENST00000526133,;EEF1D,upstream_gene_variant,,ENST00000524900,;EEF1D,upstream_gene_variant,,ENST00000531770,;EEF1D,upstream_gene_variant,,ENST00000526786,;EEF1D,upstream_gene_variant,,ENST00000524397,;EEF1D,upstream_gene_variant,,ENST00000525695,;EEF1D,upstream_gene_variant,,ENST00000529007,;EEF1D,upstream_gene_variant,,ENST00000533833,;EEF1D,upstream_gene_variant,,ENST00000534232,;EEF1D,upstream_gene_variant,,ENST00000530848,; A ENST00000504548 Transcript missense_variant 467/5390 398/1929 133/642 L/Q cTg/cAg 1 1 TIGD5 HGNC HGNC:18336 protein_coding YES CCDS6406.2 ENSP00000421489 Q53EQ6 UPI0001BAE24C NM_032862.4 deleterious(0) 1/1 PROSITE_profiles:PS51253,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF283,Pfam_domain:PF03221,Gene3D:1.10.10.60,SMART_domains:SM00674,Superfamily_domains:SSF46689 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 143598301 143598301 T A 1 0 0 0 0 1 0 0 0 16337 1580 55 4 4 TIGD5 8 143598301 Missense_Mutation SNP T C3N-00175_T 2 143598301 1540335 704 10296 41 2 CCDC166 0 . GRCh38 8 143707175 143707175 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.839C>A p.Pro280Gln p.P280Q ENST00000542437 2/2 46 33 13 26 26 0 strelka-varscan-mutect CCDC166,missense_variant,p.Pro280Gln,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; T ENST00000542437 Transcript missense_variant 839/1320 839/1320 280/439 P/Q cCg/cAg 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 deleterious(0.02) 2/2 hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 143707175 143707175 G T 1 0 0 0 0 1 0 0 0 2482 1116 39 1 1 CCDC166 8 143707175 Missense_Mutation SNP G C3N-00175_T 108874 143707175 1431461 705 10297 FAM83H 0 . GRCh38 8 143727799 143727799 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1662G>A p.= p.A554A ENST00000388913 5/5 190 173 17 51 51 0 strelka-varscan-mutect FAM83H,synonymous_variant,p.=,ENST00000388913,NM_198488.3;FAM83H,synonymous_variant,p.=,ENST00000395103,; T ENST00000388913 Transcript synonymous_variant 1788/5654 1662/3540 554/1179 A gcG/gcA 1 -1 FAM83H HGNC HGNC:24797 protein_coding YES CCDS6410.2 ENSP00000373565 Q6ZRV2 UPI00001D823F NM_198488.3 5/5 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF8,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1390924637 . 3 202 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 143727799 143727799 C T 1 0 0 0 0 0 0 0 1 5498 871 31 1 1 FAM83H 8 143727799 Silent SNP C C3N-00175_T 20624 143727799 1410837 706 10298 SLC52A2 0 . GRCh38 8 144360172 144360172 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.680G>T p.Gly227Val p.G227V ENST00000532887 3/5 458 390 68 448 448 0 strelka-varscan-mutect SLC52A2,missense_variant,p.Gly227Val,ENST00000532887,;SLC52A2,missense_variant,p.Gly227Val,ENST00000329994,NM_024531.4;SLC52A2,missense_variant,p.Gly227Val,ENST00000527078,;SLC52A2,missense_variant,p.Gly227Val,ENST00000402965,NM_001253815.1;SLC52A2,missense_variant,p.Gly227Val,ENST00000530047,NM_001253816.1;SLC52A2,missense_variant,p.Gly63Val,ENST00000526338,;SLC52A2,intron_variant,,ENST00000526752,;FBXL6,upstream_gene_variant,,ENST00000331890,NM_012162.3;FBXL6,upstream_gene_variant,,ENST00000455319,NM_024555.5;SLC52A2,downstream_gene_variant,,ENST00000534725,;SLC52A2,downstream_gene_variant,,ENST00000524541,;FBXL6,upstream_gene_variant,,ENST00000526524,;FBXL6,upstream_gene_variant,,ENST00000527000,;SLC52A2,downstream_gene_variant,,ENST00000526891,;SLC52A2,downstream_gene_variant,,ENST00000532815,;FBXL6,upstream_gene_variant,,ENST00000530687,;FBXL6,upstream_gene_variant,,ENST00000524909,;SLC52A2,missense_variant,p.Gly86Trp,ENST00000526779,;FBXL6,upstream_gene_variant,,ENST00000530142,;FBXL6,upstream_gene_variant,,ENST00000524492,;GS1-393G12.13,upstream_gene_variant,,ENST00000531225,;SLC52A2,downstream_gene_variant,,ENST00000533662,;FBXL6,upstream_gene_variant,,ENST00000529279,; T ENST00000532887 Transcript missense_variant 1263/2147 680/1338 227/445 G/V gGg/gTg 1 1 SLC52A2 HGNC HGNC:30224 protein_coding YES CCDS6423.1 ENSP00000436768 Q9HAB3 UPI000004470A tolerated(0.24) 3/5 hmmpanther:PTHR12929:SF9,hmmpanther:PTHR12929 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 144360172 144360172 G T 1 0 0 0 0 1 0 0 0 14942 1232 43 2 2 SLC52A2 8 144360172 Missense_Mutation SNP G C3N-00175_T 632373 144360172 778464 707 10299 ZNF16 0 . GRCh38 8 144932350 144932350 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.437G>T p.Gly146Val p.G146V ENST00000276816 4/4 340 319 21 233 233 0 strelka-varscan-mutect ZNF16,missense_variant,p.Gly146Val,ENST00000276816,NM_001029976.2;ZNF16,missense_variant,p.Gly146Val,ENST00000611477,NM_006958.2;ZNF16,missense_variant,p.Gly146Val,ENST00000394909,;ZNF16,missense_variant,p.Gly146Val,ENST00000532351,;ZNF16,downstream_gene_variant,,ENST00000527811,;ZNF16,non_coding_transcript_exon_variant,,ENST00000532811,;ZNF16,downstream_gene_variant,,ENST00000527512,; A ENST00000276816 Transcript missense_variant 624/2616 437/2049 146/682 G/V gGc/gTc 1 -1 ZNF16 HGNC HGNC:12947 protein_coding YES CCDS6437.1 ENSP00000276816 P17020 UPI00001E058F NM_001029976.2 tolerated(0.29) 4/4 MODERATE 1 SNV 1 1 PASS rs996427319 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 144932350 144932350 C A 1 0 0 0 0 1 0 0 0 18319 739 26 2 2 ZNF16 8 144932350 Missense_Mutation SNP C C3N-00175_T 572178 144932350 206286 708 10300 SMARCA2 0 . GRCh38 9 2033044 2033044 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.318G>T p.Met106Ile p.M106I ENST00000382203 3/34 173 131 42 167 166 1 strelka-varscan-mutect SMARCA2,missense_variant,p.Met106Ile,ENST00000637806,;SMARCA2,missense_variant,p.Met106Ile,ENST00000636559,;SMARCA2,missense_variant,p.Met106Ile,ENST00000382203,NM_001289396.1;SMARCA2,missense_variant,p.Met106Ile,ENST00000357248,NM_139045.3;SMARCA2,missense_variant,p.Met106Ile,ENST00000349721,NM_003070.4;SMARCA2,missense_variant,p.Met106Ile,ENST00000382194,;SMARCA2,missense_variant,p.Met106Ile,ENST00000637103,;SMARCA2,missense_variant,p.Met106Ile,ENST00000450198,NM_001289397.1;SMARCA2,missense_variant,p.Met106Ile,ENST00000636903,;SMARCA2,missense_variant,p.Met106Ile,ENST00000439732,;SMARCA2,missense_variant,p.Met106Ile,ENST00000457226,;SMARCA2,missense_variant,p.Met13Ile,ENST00000634287,;SMARCA2,downstream_gene_variant,,ENST00000637383,;SMARCA2,downstream_gene_variant,,ENST00000637352,;SMARCA2,downstream_gene_variant,,ENST00000636221,;SMARCA2,downstream_gene_variant,,ENST00000637097,;SMARCA2,downstream_gene_variant,,ENST00000637134,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000491574,;SMARCA2,missense_variant,p.Met106Ile,ENST00000634760,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000634536,; T ENST00000382203 Transcript missense_variant 527/5867 318/4773 106/1590 M/I atG/atT 1 1 SMARCA2 HGNC HGNC:11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 UPI00001AE8EB NM_001289396.1 tolerated_low_confidence(0.05) 3/34 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 2033044 2033044 G T 1 0 0 0 0 1 0 0 0 15062 1348 47 2 2 SMARCA2 9 2033044 Missense_Mutation SNP G C3N-00175_T 2033044 136361673 709 10301 RFX3 0 . GRCh38 9 3225050 3225050 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2242G>T p.Ala748Ser p.A748S ENST00000382004 18/18 170 143 27 185 184 1 strelka-varscan-mutect RFX3,missense_variant,p.Ala748Ser,ENST00000382004,NM_134428.2;RFX3,missense_variant,p.Ala748Ser,ENST00000617270,NM_001282116.1; A ENST00000382004 Transcript missense_variant 2554/9307 2242/2250 748/749 A/S Gca/Tca 1 -1 RFX3 HGNC HGNC:9984 protein_coding YES CCDS6449.1 ENSP00000371434 P48380 UPI0000070BFB NM_134428.2 tolerated_low_confidence(0.42) 18/18 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF20 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999944 1 1 1 0 A 3 1 39 3225050 3225050 C A 1 0 0 0 0 1 0 0 0 13438 710 25 2 2 RFX3 9 3225050 Missense_Mutation SNP C C3N-00175_T 1192006 3225050 135169667 710 10302 PTPRD 0 . GRCh38 9 8389260 8389260 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.4358T>A p.Met1453Lys p.M1453K ENST00000381196 34/43 82 71 11 105 105 0 strelka-varscan-mutect PTPRD,missense_variant,p.Met1453Lys,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Met1453Lys,ENST00000356435,;PTPRD,missense_variant,p.Met1047Lys,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Met1046Lys,ENST00000397617,;PTPRD,missense_variant,p.Met1043Lys,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Met1037Lys,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Met1453Lys,ENST00000540109,;PTPRD,missense_variant,p.Met1046Lys,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Met1046Lys,ENST00000397606,NM_001171025.1; T ENST00000381196 Transcript missense_variant 4902/9911 4358/5739 1453/1912 M/K aTg/aAg 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0) 34/43 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS rs971884436 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 8389260 8389260 A T 1 0 0 0 0 1 0 0 0 12953 217 8 4 4 PTPRD 9 8389260 Missense_Mutation SNP A C3N-00175_T 5164210 8389260 130005457 711 10303 PTPRD 0 . GRCh38 9 8436626 8436626 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.4052C>T p.Ala1351Val p.A1351V ENST00000381196 32/43 178 160 18 217 217 0 strelka-mutect PTPRD,missense_variant,p.Ala1351Val,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Ala1351Val,ENST00000356435,;PTPRD,missense_variant,p.Ala945Val,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Ala944Val,ENST00000397617,;PTPRD,missense_variant,p.Ala941Val,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Ala935Val,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Ala1351Val,ENST00000540109,;PTPRD,missense_variant,p.Ala944Val,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Ala944Val,ENST00000397606,NM_001171025.1;PTPRD,downstream_gene_variant,,ENST00000637354,; A ENST00000381196 Transcript missense_variant 4596/9911 4052/5739 1351/1912 A/V gCa/gTa 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0) 32/43 Gene3D:3.90.190.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS rs1404460582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 8436626 8436626 G A 1 0 0 0 0 1 0 0 0 12953 1319 46 3 3 PTPRD 9 8436626 Missense_Mutation SNP G C3N-00175_T 47366 8436626 129958091 712 10304 PTPRD 0 . GRCh38 9 8460539 8460539 + Silent SNP G G C rs200683418 C3N-00175_T C3N-00175_N G G c.3747C>G p.= p.P1249P ENST00000381196 30/43 168 134 34 188 188 0 strelka-varscan-mutect PTPRD,synonymous_variant,p.=,ENST00000381196,NM_002839.3;PTPRD,synonymous_variant,p.=,ENST00000356435,;PTPRD,synonymous_variant,p.=,ENST00000355233,NM_130392.3;PTPRD,synonymous_variant,p.=,ENST00000397617,;PTPRD,synonymous_variant,p.=,ENST00000397611,NM_001040712.2;PTPRD,synonymous_variant,p.=,ENST00000537002,NM_130393.3;PTPRD,synonymous_variant,p.=,ENST00000540109,;PTPRD,synonymous_variant,p.=,ENST00000486161,NM_130391.3;PTPRD,synonymous_variant,p.=,ENST00000397606,NM_001171025.1;PTPRD,synonymous_variant,p.=,ENST00000637354,; C ENST00000381196 Transcript synonymous_variant 4291/9911 3747/5739 1249/1912 P ccC/ccG rs200683418,COSM3658842,COSM3658843,COSM3658844,COSM3658845,COSM3658846,COSM3658847 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 30/43 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,Superfamily_domains:SSF49265 0,1,1,1,1,1,1 LOW 1 SNV 5 0,1,1,1,1,1,1 1 PASS rs200683418 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 8460539 8460539 G C 1 0 0 0 0 0 0 0 1 12953 1103 39 4 4 PTPRD 9 8460539 Silent SNP G C3N-00175_T 23913 8460539 129934178 713 10305 PTPRD 0 . GRCh38 9 8486265 8486265 + Missense_Mutation SNP C C A rs143196383 C3N-00175_T C3N-00175_N C C c.2552G>T p.Gly851Val p.G851V ENST00000381196 25/43 187 162 25 234 234 0 strelka-varscan-mutect PTPRD,missense_variant,p.Gly851Val,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Gly851Val,ENST00000356435,;PTPRD,missense_variant,p.Gly851Val,ENST00000540109,;PTPRD,intron_variant,,ENST00000355233,NM_130392.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,NM_130393.3;PTPRD,intron_variant,,ENST00000486161,NM_130391.3;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1;PTPRD,upstream_gene_variant,,ENST00000637354,;PTPRD,non_coding_transcript_exon_variant,,ENST00000471274,;PTPRD,upstream_gene_variant,,ENST00000477552,; A ENST00000381196 Transcript missense_variant 3096/9911 2552/5739 851/1912 G/V gGa/gTa rs143196383 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0.01) 25/43 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs143196383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 8486265 8486265 C A 1 0 0 0 0 1 0 0 0 12953 855 30 2 2 PTPRD 9 8486265 Missense_Mutation SNP C C3N-00175_T 25726 8486265 129908452 714 10306 PTPRD 0 . GRCh38 9 8518422 8518422 + Silent SNP G G C novel C3N-00175_T C3N-00175_N G G c.969C>G p.= p.P323P ENST00000381196 18/43 56 45 11 62 62 0 strelka-varscan-mutect PTPRD,synonymous_variant,p.=,ENST00000381196,NM_002839.3;PTPRD,synonymous_variant,p.=,ENST00000356435,;PTPRD,synonymous_variant,p.=,ENST00000355233,NM_130392.3;PTPRD,synonymous_variant,p.=,ENST00000397617,;PTPRD,synonymous_variant,p.=,ENST00000397611,NM_001040712.2;PTPRD,synonymous_variant,p.=,ENST00000537002,NM_130393.3;PTPRD,synonymous_variant,p.=,ENST00000540109,;PTPRD,synonymous_variant,p.=,ENST00000486161,NM_130391.3;PTPRD,synonymous_variant,p.=,ENST00000397606,NM_001171025.1; C ENST00000381196 Transcript synonymous_variant 1513/9911 969/5739 323/1912 P ccC/ccG 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 18/43 Gene3D:2.60.40.10,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00060,Superfamily_domains:SSF48726,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999758 1 1 1 0 C 2 2 39 8518422 8518422 G C 1 0 0 0 0 0 0 0 1 12953 1335 47 4 4 PTPRD 9 8518422 Silent SNP G C3N-00175_T 32157 8518422 129876295 715 10307 PTPRD 0 . GRCh38 9 8521372 8521372 + Missense_Mutation SNP A A T C3N-00175_T C3N-00175_N A A c.866T>A p.Leu289Gln p.L289Q ENST00000381196 17/43 283 248 35 227 227 0 strelka-varscan-mutect PTPRD,missense_variant,p.Leu289Gln,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Leu289Gln,ENST00000356435,;PTPRD,missense_variant,p.Leu289Gln,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Leu279Gln,ENST00000397617,;PTPRD,missense_variant,p.Leu286Gln,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Leu283Gln,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Leu289Gln,ENST00000540109,;PTPRD,missense_variant,p.Leu289Gln,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Leu279Gln,ENST00000397606,NM_001171025.1;PTPRD,downstream_gene_variant,,ENST00000488774,; T ENST00000381196 Transcript missense_variant 1410/9911 866/5739 289/1912 L/Q cTa/cAa COSM33132 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0) 17/43 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 8521372 8521372 A T 1 0 0 0 0 1 0 0 0 12953 420 15 4 4 PTPRD 9 8521372 Missense_Mutation SNP A C3N-00175_T 2950 8521372 129873345 716 10308 BNC2 0 . GRCh38 9 16419341 16419341 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2948G>T p.Gly983Val p.G983V ENST00000380672 7/7 75 62 13 70 70 0 strelka-varscan-mutect BNC2,missense_variant,p.Gly983Val,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Gly916Val,ENST00000380667,;BNC2,3_prime_UTR_variant,,ENST00000545497,;BNC2,3_prime_UTR_variant,,ENST00000418777,;BNC2,3_prime_UTR_variant,,ENST00000411752,;BNC2,3_prime_UTR_variant,,ENST00000484726,; A ENST00000380672 Transcript missense_variant 3006/12844 2948/3300 983/1099 G/V gGc/gTc 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 tolerated(0.19) 7/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 MODERATE 1 SNV 2 1 PASS rs1330774623 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 16419341 16419341 C A 1 0 0 0 0 1 0 0 0 1631 739 26 2 2 BNC2 9 16419341 Missense_Mutation SNP C C3N-00175_T 7897969 16419341 121975376 717 10309 HAUS6 0 . GRCh38 9 19058274 19058274 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2493G>T p.Gln831His p.Q831H ENST00000380502 16/17 124 99 25 157 157 0 strelka-varscan-mutect HAUS6,missense_variant,p.Gln831His,ENST00000380502,NM_001270890.1,NM_017645.4;HAUS6,missense_variant,p.Gln695His,ENST00000380496,;HAUS6,downstream_gene_variant,,ENST00000415524,; A ENST00000380502 Transcript missense_variant 2961/6536 2493/2868 831/955 Q/H caG/caT 1 -1 HAUS6 HGNC HGNC:25948 protein_coding YES CCDS6489.1 ENSP00000369871 Q7Z4H7 UPI00000740C7 NM_001270890.1,NM_017645.4 tolerated(0.11) 16/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16151 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19058274 19058274 C A 1 0 0 0 0 1 0 0 0 6856 680 24 2 2 HAUS6 9 19058274 Missense_Mutation SNP C C3N-00175_T 2638933 19058274 119336443 718 10310 IFNA6 0 . GRCh38 9 21350587 21350587 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.301G>A p.Asp101Asn p.D101N ENST00000380210 1/1 258 197 61 283 282 1 strelka-varscan-mutect IFNA6,missense_variant,p.Asp101Asn,ENST00000380210,NM_021002.2;IFNA6,missense_variant,p.Asp102Asn,ENST00000259555,; T ENST00000380210 Transcript missense_variant 792/1544 301/570 101/189 D/N Gat/Aat COSM4541538 1 -1 IFNA6 HGNC HGNC:5427 protein_coding YES CCDS6504.1 ENSP00000369558 P05013 UPI000004775F NM_021002.2 tolerated(1) 1/1 hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF27,Gene3D:1.20.1250.10,Pfam_domain:PF00143,SMART_domains:SM00076,Superfamily_domains:SSF47266,Prints_domain:PR00266 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 21350587 21350587 C T 1 0 0 0 0 1 0 0 0 7441 855 30 3 3 IFNA6 9 21350587 Missense_Mutation SNP C C3N-00175_T 2292313 21350587 117044130 719 10311 ELAVL2 0 . GRCh38 9 23731126 23731126 + Splice_Site SNP C C A novel C3N-00175_T C3N-00175_N C C c.230-1G>T p.X77_splice ENST00000397312 103 76 27 120 120 0 strelka-varscan-mutect ELAVL2,splice_acceptor_variant,,ENST00000397312,NM_004432.3;ELAVL2,splice_acceptor_variant,,ENST00000544538,;ELAVL2,splice_acceptor_variant,,ENST00000223951,NM_001171197.1,NM_001171195.1;ELAVL2,splice_acceptor_variant,,ENST00000380110,;ELAVL2,splice_acceptor_variant,,ENST00000380117,;ELAVL2,splice_acceptor_variant,,ENST00000423281,;ELAVL2,splice_acceptor_variant,,ENST00000440102,; A ENST00000397312 Transcript splice_acceptor_variant -/3805 230/1080 77/359 1 -1 ELAVL2 HGNC HGNC:3313 protein_coding YES CCDS6515.1 ENSP00000380479 Q12926 UPI000013C83F NM_004432.3 2/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 23731126 23731126 C A 1 0 0 0 0 0 0 1 0 4883 695 24 2 2 ELAVL2 9 23731126 Splice_Site SNP C C3N-00175_T 2380539 23731126 114663591 720 10312 TUSC1 0 . GRCh38 9 25677924 25677924 + Missense_Mutation SNP G G T rs566749582 C3N-00175_T C3N-00175_N G G c.398C>A p.Pro133His p.P133H ENST00000358022 1/1 341 217 124 429 429 0 strelka-varscan-mutect TUSC1,missense_variant,p.Pro133His,ENST00000358022,NM_001004125.2; T ENST00000358022 Transcript missense_variant 517/2052 398/639 133/212 P/H cCt/cAt rs566749582 1 -1 TUSC1 HGNC HGNC:31010 protein_coding YES CCDS34999.1 ENSP00000350716 Q2TAM9 UPI0000161A7E NM_001004125.2 deleterious(0) 1/1 MODERATE 1 SNV 1 PASS rs566749582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 25677924 25677924 G T 1 0 0 0 0 1 0 0 0 17288 1000 35 2 2 TUSC1 9 25677924 Missense_Mutation SNP G C3N-00175_T 1946798 25677924 112716793 721 10313 TAF1L 0 . GRCh38 9 32630976 32630976 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.4604C>T p.Thr1535Ile p.T1535I ENST00000242310 1/1 325 236 89 345 345 0 strelka-varscan-mutect TAF1L,missense_variant,p.Thr1535Ile,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; A ENST00000242310 Transcript missense_variant 4694/6216 4604/5481 1535/1826 T/I aCc/aTc 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0.01) 1/1 Gene3D:1.20.920.10,Pfam_domain:PF00439,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 32630976 32630976 G A 1 0 0 0 0 1 0 0 0 15919 1261 44 3 3 TAF1L 9 32630976 Missense_Mutation SNP G C3N-00175_T 6953052 32630976 105763741 722 10314 NOL6 0 . GRCh38 9 33466971 33466971 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1891G>C p.Glu631Gln p.E631Q ENST00000297990 15/26 104 96 8 125 125 0 strelka-varscan-mutect NOL6,missense_variant,p.Glu631Gln,ENST00000297990,NM_022917.4;NOL6,missense_variant,p.Glu631Gln,ENST00000379471,;NOL6,missense_variant,p.Glu631Gln,ENST00000353159,NM_139235.3;NOL6,upstream_gene_variant,,ENST00000379470,;MIR6851,downstream_gene_variant,,ENST00000617060,;NOL6,intron_variant,,ENST00000464829,;NOL6,downstream_gene_variant,,ENST00000496319,; G ENST00000297990 Transcript missense_variant 1979/4741 1891/3441 631/1146 E/Q Gaa/Caa 1 -1 NOL6 HGNC HGNC:19910 protein_coding YES CCDS6543.1 ENSP00000297990 Q9H6R4 UPI0000050326 NM_022917.4 tolerated(0.27) 15/26 Pfam_domain:PF03813,hmmpanther:PTHR17972 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 33466971 33466971 C G 1 0 0 0 0 1 0 0 0 10569 922 32 4 4 NOL6 9 33466971 Missense_Mutation SNP C C3N-00175_T 835995 33466971 104927746 723 10315 DNAI1 0 . GRCh38 9 34491513 34491513 + Nonsense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.652G>T p.Glu218Ter p.E218* ENST00000614641 8/20 421 311 110 506 506 0 strelka-varscan-mutect DNAI1,stop_gained,p.Glu218Ter,ENST00000614641,NM_001281428.1;DNAI1,stop_gained,p.Glu214Ter,ENST00000242317,NM_012144.3;DNAI1,stop_gained,p.Glu203Ter,ENST00000437363,;DNAI1,non_coding_transcript_exon_variant,,ENST00000488369,;DNAI1,non_coding_transcript_exon_variant,,ENST00000488790,;DNAI1,downstream_gene_variant,,ENST00000470982,; T ENST00000614641 Transcript stop_gained 906/2598 652/2112 218/703 E/* Gag/Tag COSM5603413 1 1 DNAI1 HGNC HGNC:2954 protein_coding YES CCDS75829.1 ENSP00000480538 A0A087WWV9 UPI000382F365 NM_001281428.1 8/20 hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF11 1 HIGH 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 34491513 34491513 G T 1 0 0 0 0 0 1 0 0 4424 1175 41 2 2 DNAI1 9 34491513 Nonsense_Mutation SNP G C3N-00175_T 1024542 34491513 103903204 724 10316 RUSC2 0 . GRCh38 9 35557958 35557958 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.3028C>T p.His1010Tyr p.H1010Y ENST00000455600 6/12 195 176 19 219 219 0 strelka-varscan-mutect RUSC2,missense_variant,p.His1010Tyr,ENST00000455600,NM_001135999.1;RUSC2,missense_variant,p.His1010Tyr,ENST00000361226,NM_014806.3;FAM166B,downstream_gene_variant,,ENST00000619051,NM_001287238.1,NM_001287239.1;FAM166B,downstream_gene_variant,,ENST00000399742,NM_001099951.3,NM_001164310.2;FAM166B,downstream_gene_variant,,ENST00000492890,;FAM166B,downstream_gene_variant,,ENST00000480287,;FAM166B,downstream_gene_variant,,ENST00000478246,;FAM166B,downstream_gene_variant,,ENST00000447837,; T ENST00000455600 Transcript missense_variant 3597/5636 3028/4551 1010/1516 H/Y Cat/Tat 1 1 RUSC2 HGNC HGNC:23625 protein_coding YES CCDS35008.1 ENSP00000393922 Q8N2Y8 UPI00001C1EB0 NM_001135999.1 deleterious(0.04) 6/12 Superfamily_domains:0052343,hmmpanther:PTHR15591,hmmpanther:PTHR15591:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 35557958 35557958 C T 1 0 0 0 0 1 0 0 0 14012 826 29 3 3 RUSC2 9 35557958 Missense_Mutation SNP C C3N-00175_T 1066445 35557958 102836759 725 10317 OR2S2 0 . GRCh38 9 35957189 35957189 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.910G>T p.Val304Leu p.V304L ENST00000341959 1/1 75 62 13 89 89 0 strelka-varscan-mutect OR2S2,missense_variant,p.Val304Leu,ENST00000341959,NM_019897.2; A ENST00000341959 Transcript missense_variant 966/1047 910/960 304/319 V/L Gtg/Ttg 1 -1 OR2S2 HGNC HGNC:8276 protein_coding YES CCDS6596.2 ENSP00000344040 Q9NQN1 UPI000003FF74 NM_019897.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF176,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 35957189 35957189 C A 1 0 0 0 0 1 0 0 0 11093 478 17 2 2 OR2S2 9 35957189 Missense_Mutation SNP C C3N-00175_T 399231 35957189 102437528 726 10318 FBXO10 0 . GRCh38 9 37541522 37541522 + Missense_Mutation SNP T T C C3N-00175_T C3N-00175_N T T c.247A>G p.Lys83Glu p.K83E ENST00000432825 2/11 306 267 39 366 366 0 strelka-varscan-mutect FBXO10,missense_variant,p.Lys83Glu,ENST00000432825,NM_012166.2;FBXO10,downstream_gene_variant,,ENST00000541607,;RP11-613M10.8,non_coding_transcript_exon_variant,,ENST00000544475,;RP11-613M10.8,intron_variant,,ENST00000541804,;FBXO10,missense_variant,p.Lys83Glu,ENST00000276960,;RP11-613M10.8,3_prime_UTR_variant,,ENST00000537239,; C ENST00000432825 Transcript missense_variant 296/4575 247/2871 83/956 K/E Aag/Gag COSM4139374 1 -1 FBXO10 HGNC HGNC:13589 protein_coding YES CCDS47966.1 ENSP00000403802 Q9UK96 UPI00001C1EC6 NM_012166.2 deleterious(0.01) 2/11 hmmpanther:PTHR22990:SF19,hmmpanther:PTHR22990,Gene3D:1.20.1280.50 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 37541522 37541522 T C 1 0 0 0 0 1 0 0 0 5589 1821 63 5 5 FBXO10 9 37541522 Missense_Mutation SNP T C3N-00175_T 1584333 37541522 100853195 727 10319 CNTNAP3B 0 . GRCh38 9 41964561 41964561 + Missense_Mutation SNP T T A C3N-00175_T C3N-00175_N T T c.1733A>T p.Tyr578Phe p.Y578F ENST00000377561 11/24 55 50 5 83 83 0 varscan-mutect CNTNAP3B,missense_variant,p.Tyr578Phe,ENST00000612828,;CNTNAP3B,missense_variant,p.Tyr578Phe,ENST00000377561,NM_001201380.2;CNTNAP3B,missense_variant,p.Tyr578Phe,ENST00000341990,;CNTNAP3B,intron_variant,,ENST00000617422,;CNTNAP3B,upstream_gene_variant,,ENST00000491438,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,;CNTNAP3B,intron_variant,,ENST00000619138,;CNTNAP3B,intron_variant,,ENST00000479351,; A ENST00000377561 Transcript missense_variant 2126/5379 1733/3867 578/1288 Y/F tAt/tTt COSM1331537 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 deleterious(0.02) 11/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,SMART_domains:SM00181,Superfamily_domains:SSF56496,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS rs1236403969 . 0 208 2 0 0 0 0 0 -12.52834 1 1 1 1 0 A 3 1 39 41964561 41964561 T A 1 0 0 0 0 1 0 0 0 3430 1406 49 4 4 CNTNAP3B 9 41964561 Missense_Mutation SNP T C3N-00175_T 4423039 41964561 96430156 728 10320 SPATA31A6 0 . GRCh38 9 42186342 42186342 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.640C>A p.Leu214Met p.L214M ENST00000332857 4/4 32 24 8 48 48 0 varscan-mutect SPATA31A6,missense_variant,p.Leu214Met,ENST00000332857,NM_001145196.1;SPATA31A6,non_coding_transcript_exon_variant,,ENST00000496386,; A ENST00000332857 Transcript missense_variant 669/4209 640/4032 214/1343 L/M Ctg/Atg 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(0.26) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 MODERATE 1 SNV 5 1 PASS rs1440671474 . 3 203 4 0 0 0 0 0 -19.96985 1 1 1 1 0 A 3 1 39 42186342 42186342 C A 1 0 0 0 0 1 0 0 0 15345 912 32 2 2 SPATA31A6 9 42186342 Missense_Mutation SNP C C3N-00175_T 221781 42186342 96208375 729 10321 SPATA31A7 0 . GRCh38 9 61191467 61191467 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.204G>T p.= p.R68R ENST00000619167 2/4 156 115 41 191 191 0 strelka-varscan-mutect SPATA31A7,synonymous_variant,p.=,ENST00000619167,NM_015667.2;RP11-101E5.6,downstream_gene_variant,,ENST00000611332,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000619140,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000622751,;SPATA31A7,upstream_gene_variant,,ENST00000618860,;SPATA31A7,downstream_gene_variant,,ENST00000622899,;SPATA31A7,upstream_gene_variant,,ENST00000376458,;SPATA31A7,upstream_gene_variant,,ENST00000614013,;SPATA31A7,upstream_gene_variant,,ENST00000611017,;SPATA31A7,upstream_gene_variant,,ENST00000621711,; T ENST00000619167 Transcript synonymous_variant 266/4256 204/4044 68/1347 R cgG/cgT 1 1 SPATA31A7 HGNC HGNC:32007 protein_coding YES CCDS75838.1 ENSP00000484807 Q8IWB4 UPI0000457748 NM_015667.2 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF22 LOW 1 SNV 1 1 PASS . . 23 187 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 61191467 61191467 G T 1 0 0 0 0 0 0 0 1 15346 1161 41 2 2 SPATA31A7 9 61191467 Silent SNP G C3N-00175_T 19005125 61191467 77203250 730 10322 PTAR1 0 . GRCh38 9 69750940 69750940 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.97G>T p.Gly33Cys p.G33C ENST00000340434 2/8 80 58 22 96 96 0 strelka-varscan-mutect PTAR1,missense_variant,p.Gly33Cys,ENST00000340434,NM_001099666.1;PTAR1,intron_variant,,ENST00000377200,;PTAR1,non_coding_transcript_exon_variant,,ENST00000474925,; A ENST00000340434 Transcript missense_variant 101/1417 97/1209 33/402 G/C Ggc/Tgc 1 -1 PTAR1 HGNC HGNC:30449 protein_coding YES CCDS47978.1 ENSP00000344299 Q7Z6K3 UPI00001D75C1 NM_001099666.1 deleterious(0) 2/8 hmmpanther:PTHR11129,hmmpanther:PTHR11129:SF3 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 69750940 69750940 C A 1 0 0 0 0 1 0 0 0 12876 594 21 2 2 PTAR1 9 69750940 Missense_Mutation SNP C C3N-00175_T 8559473 69750940 68643777 731 10323 TRPM6 0 . GRCh38 9 74816952 74816952 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1147G>C p.Asp383His p.D383H ENST00000360774 10/39 287 214 73 409 409 0 strelka-varscan-mutect TRPM6,missense_variant,p.Asp383His,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Asp378His,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Asp378His,ENST00000449912,NM_001177310.1;TRPM6,downstream_gene_variant,,ENST00000483186,; G ENST00000360774 Transcript missense_variant 1385/8425 1147/6069 383/2022 D/H Gat/Cat 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 tolerated(0.28) 10/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 MODERATE 1 SNV 1 1 PASS rs749988479 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 74816952 74816952 C G 1 0 0 0 0 1 0 0 0 17096 826 29 4 4 TRPM6 9 74816952 Missense_Mutation SNP C C3N-00175_T 5066012 74816952 63577765 732 10324 ZCCHC6 0 . GRCh38 9 86288722 86288722 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.4443G>A p.Met1481Ile p.M1481I ENST00000375963 27/27 113 93 20 138 138 0 strelka-varscan-mutect ZCCHC6,missense_variant,p.Met770Ile,ENST00000277141,;ZCCHC6,missense_variant,p.Met1481Ile,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,missense_variant,p.Met1245Ile,ENST00000375960,NM_001185074.1;ZCCHC6,missense_variant,p.Met381Ile,ENST00000375957,; T ENST00000375963 Transcript missense_variant 4616/5379 4443/4488 1481/1495 M/I atG/atA 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 deleterious_low_confidence(0.01) 27/27 hmmpanther:PTHR12271:SF34,hmmpanther:PTHR12271 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 86288722 86288722 C T 1 0 0 0 0 1 0 0 0 18167 826 29 3 3 ZCCHC6 9 86288722 Missense_Mutation SNP C C3N-00175_T 11471770 86288722 52105995 733 10325 CTSL 0 . GRCh38 9 87728857 87728857 + Nonsense_Mutation SNP G G A rs775431226 C3N-00175_T C3N-00175_N G G c.669G>A p.Trp223Ter p.W223* ENST00000342020 5/5 93 84 9 136 136 0 strelka-varscan-mutect CTSL,stop_gained,p.Trp223Ter,ENST00000342020,;CTSL,intron_variant,,ENST00000343150,;CTSL,intron_variant,,ENST00000340342,NM_001257972.1,NM_001257971.1,NM_001912.4,NM_145918.2;CTSL,intron_variant,,ENST00000495822,;CTSL,intron_variant,,ENST00000375894,;CTSL,intron_variant,,ENST00000482054,; A ENST00000342020 Transcript stop_gained 793/933 669/678 223/225 W/* tgG/tgA rs775431226 1 1 CTSL HGNC HGNC:2537 protein_coding ENSP00000340470 Q5T8F0 UPI000046FE25 5/5 SMART_domains:SM00645 HIGH SNV 2 1 PASS rs775431226 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 87728857 87728857 G A 1 0 0 0 0 0 1 0 0 3847 1183 41 3 3 CTSL 9 87728857 Nonsense_Mutation SNP G C3N-00175_T 1440135 87728857 50665860 734 10326 SYK 0 . GRCh38 9 90845439 90845439 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.423G>T p.Gln141His p.Q141H ENST00000375754 3/14 68 46 22 84 84 0 varscan-mutect SYK,missense_variant,p.Gln141His,ENST00000375754,NM_003177.6;SYK,missense_variant,p.Gln141His,ENST00000375746,NM_001174167.2;SYK,missense_variant,p.Gln141His,ENST00000375751,NM_001135052.3;SYK,missense_variant,p.Gln141His,ENST00000375747,NM_001174168.2;SYK,downstream_gene_variant,,ENST00000476708,; T ENST00000375754 Transcript missense_variant 571/5005 423/1908 141/635 Q/H caG/caT 1 1 SYK HGNC HGNC:11491 protein_coding YES CCDS6688.1 ENSP00000364907 P43405 A0A024R244 UPI000012E0DD NM_003177.6 tolerated(0.31) 3/14 Gene3D:2oq1A02,PIRSF_domain:PIRSF000604 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 90845439 90845439 G T 1 0 0 0 0 1 0 0 0 15828 1014 35 2 2 SYK 9 90845439 Missense_Mutation SNP G C3N-00175_T 3116582 90845439 47549278 735 10327 SYK 0 . GRCh38 9 90845452 90845452 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.436G>T p.Ala146Ser p.A146S ENST00000375754 3/14 77 50 27 102 102 0 varscan-mutect SYK,missense_variant,p.Ala146Ser,ENST00000375754,NM_003177.6;SYK,missense_variant,p.Ala146Ser,ENST00000375746,NM_001174167.2;SYK,missense_variant,p.Ala146Ser,ENST00000375751,NM_001135052.3;SYK,missense_variant,p.Ala146Ser,ENST00000375747,NM_001174168.2;SYK,downstream_gene_variant,,ENST00000476708,; T ENST00000375754 Transcript missense_variant 584/5005 436/1908 146/635 A/S Gcc/Tcc 1 1 SYK HGNC HGNC:11491 protein_coding YES CCDS6688.1 ENSP00000364907 P43405 A0A024R244 UPI000012E0DD NM_003177.6 deleterious(0.02) 3/14 Gene3D:2oq1A02,PIRSF_domain:PIRSF000604 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 90845452 90845452 G T 1 0 0 0 0 1 0 0 0 15828 1203 42 2 2 SYK 9 90845452 Missense_Mutation SNP G C3N-00175_T 13 90845452 47549265 736 10328 MFSD14B 0 . GRCh38 9 94415165 94415165 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.116G>A p.Gly39Asp p.G39D ENST00000375344 2/12 243 149 94 199 199 0 strelka-varscan-mutect MFSD14B,missense_variant,p.Gly39Asp,ENST00000375344,NM_032558.2; A ENST00000375344 Transcript missense_variant 385/3420 116/1521 39/506 G/D gGc/gAc 1 1 MFSD14B HGNC HGNC:23376 protein_coding YES CCDS6710.2 ENSP00000364493 Q5SR56 UPI000046FF5D NM_032558.2 deleterious(0) 2/12 hmmpanther:PTHR23504:SF32,hmmpanther:PTHR23504 MODERATE 1 SNV 1 1 PASS rs1311831052 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 94415165 94415165 G A 1 0 0 0 0 1 0 0 0 9485 1203 42 3 3 MFSD14B 9 94415165 Missense_Mutation SNP G C3N-00175_T 3569713 94415165 43979552 737 10329 GABBR2 0 . GRCh38 9 98708518 98708518 + Missense_Mutation SNP C C T rs868629786 C3N-00175_T C3N-00175_N C C c.220G>A p.Gly74Arg p.G74R ENST00000259455 1/19 115 73 42 128 127 1 strelka-varscan-mutect GABBR2,missense_variant,p.Gly74Arg,ENST00000259455,NM_005458.7;GABBR2,upstream_gene_variant,,ENST00000637717,; T ENST00000259455 Transcript missense_variant 680/5788 220/2826 74/941 G/R Ggg/Agg rs868629786 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 deleterious(0.01) 1/19 Gene3D:3.40.50.2300,Prints_domain:PR01176,Prints_domain:PR01178,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF40,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs868629786 . 0 205 2 3 0 0 0 0 -20 0.999993 1 1 1 0 T 3 4 39 98708518 98708518 C T 1 0 0 0 0 1 0 0 0 6027 652 23 1 1 GABBR2 9 98708518 Missense_Mutation SNP C C3N-00175_T 4293353 98708518 39686199 738 10330 GRIN3A 0 . GRCh38 9 101670497 101670497 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1915A>T p.Ser639Cys p.S639C ENST00000361820 3/9 349 215 134 435 435 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Ser639Cys,ENST00000361820,NM_133445.2; A ENST00000361820 Transcript missense_variant 2516/7770 1915/3348 639/1115 S/C Agc/Tgc 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 deleterious(0.01) 3/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Gene3D:3.40.190.10,Pfam_domain:PF10613,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 101670497 101670497 T A 1 0 0 0 0 1 0 0 0 6665 1551 54 4 4 GRIN3A 9 101670497 Missense_Mutation SNP T C3N-00175_T 2961979 101670497 36724220 739 10331 SVEP1 0 . GRCh38 9 110386031 110386031 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.10104G>T p.= p.L3368L ENST00000374469 43/48 106 61 45 152 152 0 strelka-varscan-mutect SVEP1,synonymous_variant,p.=,ENST00000401783,;SVEP1,synonymous_variant,p.=,ENST00000374469,NM_153366.3; A ENST00000374469 Transcript synonymous_variant 10299/12194 10104/10716 3368/3571 L ctG/ctT 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 43/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 110386031 110386031 C A 1 0 0 0 0 0 0 0 1 15805 697 25 2 2 SVEP1 9 110386031 Silent SNP C C3N-00175_T 8715534 110386031 28008686 740 10332 SVEP1 0 . GRCh38 9 110512951 110512951 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1278G>C p.Trp426Cys p.W426C ENST00000374469 5/48 347 215 132 337 337 0 strelka-varscan-mutect SVEP1,missense_variant,p.Trp426Cys,ENST00000401783,;SVEP1,missense_variant,p.Trp426Cys,ENST00000374469,NM_153366.3;SVEP1,missense_variant,p.Trp426Cys,ENST00000374461,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,; G ENST00000374469 Transcript missense_variant 1473/12194 1278/10716 426/3571 W/C tgG/tgC 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 deleterious(0) 5/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57184,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 110512951 110512951 C G 1 0 0 0 0 1 0 0 0 15805 508 18 4 4 SVEP1 9 110512951 Missense_Mutation SNP C C3N-00175_T 126920 110512951 27881766 741 10333 TLR4 0 . GRCh38 9 117708723 117708723 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.254T>A p.Leu85Ter p.L85* ENST00000355622 2/3 163 102 61 193 193 0 strelka-varscan-mutect TLR4,stop_gained,p.Leu85Ter,ENST00000355622,NM_138554.4;TLR4,stop_gained,p.Leu45Ter,ENST00000394487,NM_003266.3;RNU6-1082P,upstream_gene_variant,,ENST00000364574,;TLR4,non_coding_transcript_exon_variant,,ENST00000490685,;TLR4,intron_variant,,ENST00000472304,; A ENST00000355622 Transcript stop_gained 355/4844 254/2520 85/839 L/* tTa/tAa 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365:SF230,hmmpanther:PTHR24365,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 117708723 117708723 T A 1 0 0 0 0 0 1 0 0 16399 1764 61 4 4 TLR4 9 117708723 Nonsense_Mutation SNP T C3N-00175_T 7195772 117708723 20685994 742 10334 HMCN2 0 . GRCh38 9 130407636 130407636 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.12559G>T p.Gly4187Trp p.G4187W ENST00000624552 83/98 114 67 47 121 121 0 strelka-varscan-mutect HMCN2,missense_variant,p.Gly4187Trp,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,downstream_gene_variant,,ENST00000480829,; T ENST00000624552 Transcript missense_variant 12559/15610 12559/15180 4187/5059 G/W Ggg/Tgg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0) 83/98 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs916561028 . 0 202 6 2 0 0 0 0 -20 0.9999883 1 1 1 0 T 3 4 39 130407636 130407636 G T 1 0 0 0 0 1 0 0 0 7112 1116 39 1 1 HMCN2 9 130407636 Missense_Mutation SNP G C3N-00175_T 12698913 130407636 7987081 743 10335 NUP214 0 . GRCh38 9 131215334 131215334 + Silent SNP G G T rs757729764 C3N-00175_T C3N-00175_N G G c.5715G>T p.= p.S1905S ENST00000359428 31/36 78 40 38 94 94 0 strelka-varscan-mutect NUP214,synonymous_variant,p.=,ENST00000359428,NM_005085.3;NUP214,synonymous_variant,p.=,ENST00000411637,NM_001318324.1;NUP214,synonymous_variant,p.=,ENST00000451030,;NUP214,synonymous_variant,p.=,ENST00000483497,;NUP214,synonymous_variant,p.=,ENST00000453861,; T ENST00000359428 Transcript synonymous_variant 5859/7600 5715/6273 1905/2090 S tcG/tcT rs757729764 1 1 NUP214 HGNC HGNC:8064 protein_coding YES CCDS6940.1 ENSP00000352400 P35658 UPI00001BBB2F NM_005085.3 31/36 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF21,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs757729764 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 131215334 131215334 G T 1 0 0 0 0 0 0 0 1 10827 1103 39 1 1 NUP214 9 131215334 Silent SNP G C3N-00175_T 807698 131215334 7179383 744 10336 NTNG2 0 . GRCh38 9 132240981 132240981 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1294G>T p.Gly432Cys p.G432C ENST00000393229 7/8 247 138 109 312 312 0 strelka-varscan-mutect NTNG2,missense_variant,p.Gly432Cys,ENST00000393229,NM_032536.2;NTNG2,non_coding_transcript_exon_variant,,ENST00000490694,;NTNG2,upstream_gene_variant,,ENST00000483055,; T ENST00000393229 Transcript missense_variant 2070/4792 1294/1593 432/530 G/C Ggc/Tgc 1 1 NTNG2 HGNC HGNC:14288 protein_coding YES CCDS6946.1 ENSP00000376921 Q96CW9 UPI0000367698 NM_032536.2 deleterious(0) 7/8 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS00022,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 132240981 132240981 G T 1 0 0 0 0 1 0 0 0 10770 1232 43 2 2 NTNG2 9 132240981 Missense_Mutation SNP G C3N-00175_T 1025647 132240981 6153736 745 10337 CAMSAP1 0 . GRCh38 9 135821227 135821227 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.3434C>T p.Pro1145Leu p.P1145L ENST00000389532 11/17 72 39 33 125 125 0 strelka-varscan-mutect CAMSAP1,missense_variant,p.Pro1145Leu,ENST00000389532,NM_015447.3;CAMSAP1,missense_variant,p.Pro867Leu,ENST00000312405,;CAMSAP1,missense_variant,p.Pro1156Leu,ENST00000409386,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,;CAMSAP1,upstream_gene_variant,,ENST00000493088,;CAMSAP1,upstream_gene_variant,,ENST00000482664,;CAMSAP1,upstream_gene_variant,,ENST00000487868,; A ENST00000389532 Transcript missense_variant 3499/7696 3434/4809 1145/1602 P/L cCc/cTc COSM1461013,COSM4784554 1 -1 CAMSAP1 HGNC HGNC:19946 protein_coding YES CCDS35176.2 ENSP00000374183 Q5T5Y3 UPI0000EDA283 NM_015447.3 deleterious(0.04) 11/17 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 135821227 135821227 G A 1 0 0 0 0 1 0 0 0 2303 1232 43 3 3 CAMSAP1 9 135821227 Missense_Mutation SNP G C3N-00175_T 3580246 135821227 2573490 746 10338 AKR1C3 0 . GRCh38 10 5094529 5094529 + Splice_Site SNP G G A novel C3N-00175_T C3N-00175_N G G c.84+1G>A p.X28_splice ENST00000380554 233 157 76 233 233 0 strelka-varscan-mutect AKR1C3,splice_donor_variant,,ENST00000380554,NM_003739.5;AKR1C3,intron_variant,,ENST00000605149,;AKR1C3,intron_variant,,ENST00000439082,NM_001253908.1;AKR1C3,intron_variant,,ENST00000602997,;U8,upstream_gene_variant,,ENST00000459536,;AKR1C3,intron_variant,,ENST00000470862,;AKR1C3,intron_variant,,ENST00000605781,;AKR1C3,intron_variant,,ENST00000480822,;AKR1C3,splice_donor_variant,,ENST00000480697,;AKR1C3,splice_donor_variant,,ENST00000605322,;AKR1C3,upstream_gene_variant,,ENST00000603312,; A ENST00000380554 Transcript splice_donor_variant -/1807 84/972 28/323 1 1 AKR1C3 HGNC HGNC:386 protein_coding YES CCDS7063.1 ENSP00000369927 P42330 UPI0000140951 NM_003739.5 1/8 HIGH 1 SNV 1 1 PASS rs994272041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 5094529 5094529 G A 1 0 0 0 0 0 0 1 0 555 1275 44 3 3 AKR1C3 10 5094529 Splice_Site SNP G C3N-00175_T 5094529 128702893 747 10339 SFMBT2 0 . GRCh38 10 7163881 7163881 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.2574G>T p.= p.L858L ENST00000397167 21/21 132 100 32 131 131 0 strelka-varscan-mutect SFMBT2,synonymous_variant,p.=,ENST00000397167,NM_001029880.2;SFMBT2,synonymous_variant,p.=,ENST00000361972,NM_001018039.1; A ENST00000397167 Transcript synonymous_variant 2767/8024 2574/2685 858/894 L ctG/ctT 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 21/21 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF00536,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 7163881 7163881 C A 1 0 0 0 0 0 0 0 1 14436 813 29 2 2 SFMBT2 10 7163881 Silent SNP C C3N-00175_T 2069352 7163881 126633541 748 10340 ITIH5 0 . GRCh38 10 7576789 7576789 + Silent SNP G G T rs547413516 C3N-00175_T C3N-00175_N G G c.1642C>A p.= p.R548R ENST00000397146 10/14 154 124 30 183 183 0 strelka-varscan-mutect ITIH5,synonymous_variant,p.=,ENST00000397146,NM_030569.6;ITIH5,synonymous_variant,p.=,ENST00000397145,NM_001001851.2;ITIH5,synonymous_variant,p.=,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,non_coding_transcript_exon_variant,,ENST00000468389,;ITIH5,downstream_gene_variant,,ENST00000461751,;ITIH5,upstream_gene_variant,,ENST00000492668,; T ENST00000397146 Transcript synonymous_variant 1721/6721 1642/2829 548/942 R Cgg/Agg rs547413516,COSM5566377,COSM5566378 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 10/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs547413516 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 7576789 7576789 G T 1 0 0 0 0 0 0 0 1 7813 1086 38 1 1 ITIH5 10 7576789 Silent SNP G C3N-00175_T 412908 7576789 126220633 749 10341 ITIH5 0 . GRCh38 10 7576804 7576804 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1627A>T p.Thr543Ser p.T543S ENST00000397146 10/14 161 132 29 176 175 1 strelka-varscan-mutect ITIH5,missense_variant,p.Thr543Ser,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Thr543Ser,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Thr329Ser,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,non_coding_transcript_exon_variant,,ENST00000468389,;ITIH5,downstream_gene_variant,,ENST00000461751,;ITIH5,upstream_gene_variant,,ENST00000492668,; A ENST00000397146 Transcript missense_variant 1706/6721 1627/2829 543/942 T/S Aca/Tca 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 tolerated(0.05) 10/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 7576804 7576804 T A 1 0 0 0 0 1 0 0 0 7813 1667 58 4 4 ITIH5 10 7576804 Missense_Mutation SNP T C3N-00175_T 15 7576804 126220618 750 10342 ITIH2 0 . GRCh38 10 7709081 7709081 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.252G>A p.= p.R84R ENST00000358415 4/21 268 181 87 236 236 0 strelka-varscan-mutect ITIH2,synonymous_variant,p.=,ENST00000358415,NM_002216.2;ITIH2,synonymous_variant,p.=,ENST00000379587,;ITIH2,synonymous_variant,p.=,ENST00000429820,;ITIH2,intron_variant,,ENST00000480387,;ITIH2,non_coding_transcript_exon_variant,,ENST00000473227,; A ENST00000358415 Transcript synonymous_variant 418/3193 252/2841 84/946 R cgG/cgA 1 1 ITIH2 HGNC HGNC:6167 protein_coding YES CCDS31141.1 ENSP00000351190 P19823 UPI000036665E NM_002216.2 4/21 PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF14,Pfam_domain:PF08487,SMART_domains:SM00609 LOW 1 SNV 1 1 PASS rs1267311185 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 7709081 7709081 G A 1 0 0 0 0 0 0 0 1 7810 1161 41 3 3 ITIH2 10 7709081 Silent SNP G C3N-00175_T 132277 7709081 126088341 751 10343 UPF2 0 . GRCh38 10 12001691 12001691 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1639C>T p.Leu547Phe p.L547F ENST00000356352 5/21 44 36 8 67 67 0 strelka-varscan-mutect UPF2,missense_variant,p.Leu547Phe,ENST00000356352,;UPF2,missense_variant,p.Leu547Phe,ENST00000397053,NM_080599.2;UPF2,missense_variant,p.Leu547Phe,ENST00000357604,NM_015542.3; A ENST00000356352 Transcript missense_variant 2113/5569 1639/3819 547/1272 L/F Ctt/Ttt 1 -1 UPF2 HGNC HGNC:17854 protein_coding YES CCDS7086.1 ENSP00000348708 Q9HAU5 UPI0000070D5E tolerated(0.26) 5/21 hmmpanther:PTHR12839,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.57937 1 1 1 1 0 A 3 1 39 12001691 12001691 G A 1 0 0 0 0 1 0 0 0 17530 1029 36 3 3 UPF2 10 12001691 Missense_Mutation SNP G C3N-00175_T 4292610 12001691 121795731 752 10344 CDC123 0 . GRCh38 10 12215796 12215796 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.294G>T p.= p.G98G ENST00000281141 5/13 134 92 42 101 101 0 strelka-varscan-mutect CDC123,synonymous_variant,p.=,ENST00000281141,NM_006023.2;CDC123,synonymous_variant,p.=,ENST00000378900,;CDC123,synonymous_variant,p.=,ENST00000429258,;CDC123,intron_variant,,ENST00000442050,;CDC123,non_coding_transcript_exon_variant,,ENST00000455773,;CDC123,upstream_gene_variant,,ENST00000498747,; T ENST00000281141 Transcript synonymous_variant 574/1542 294/1011 98/336 G ggG/ggT 1 1 CDC123 HGNC HGNC:16827 protein_coding YES CCDS7090.1 ENSP00000281141 O75794 UPI000006FE36 NM_006023.2 5/13 hmmpanther:PTHR15323:SF6,hmmpanther:PTHR15323,PIRSF_domain:PIRSF007807,Pfam_domain:PF07065 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 12215796 12215796 G T 1 0 0 0 0 0 0 0 1 2758 1219 43 2 2 CDC123 10 12215796 Silent SNP G C3N-00175_T 214105 12215796 121581626 753 10345 MCM10 0 . GRCh38 10 13195228 13195228 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1936C>T p.Pro646Ser p.P646S ENST00000484800 14/20 184 133 51 178 177 1 strelka-varscan-mutect MCM10,missense_variant,p.Pro645Ser,ENST00000378694,;MCM10,missense_variant,p.Pro645Ser,ENST00000378714,NM_018518.4;MCM10,missense_variant,p.Pro646Ser,ENST00000484800,NM_182751.2;MCM10,non_coding_transcript_exon_variant,,ENST00000481292,;MCM10,non_coding_transcript_exon_variant,,ENST00000459751,;MCM10,upstream_gene_variant,,ENST00000485659,; T ENST00000484800 Transcript missense_variant 2039/3157 1936/2628 646/875 P/S Cca/Tca 1 1 MCM10 HGNC HGNC:18043 protein_coding YES CCDS7096.1 ENSP00000418268 Q7L590 UPI000013C5E2 NM_182751.2 deleterious(0.05) 14/20 Pfam_domain:PF09332,hmmpanther:PTHR13454,SMART_domains:SM01280 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 13195228 13195228 C T 1 0 0 0 0 1 0 0 0 9317 507 18 3 3 MCM10 10 13195228 Missense_Mutation SNP C C3N-00175_T 979432 13195228 120602194 754 10346 FAM171A1 0 . GRCh38 10 15213491 15213491 + Frame_Shift_Del DEL C C - rs780775876 C3N-00175_T C3N-00175_N C C c.2097delG p.Lys700SerfsTer45 p.K700Sfs*45 ENST00000378116 8/8 236 202 34 264 264 0 sindel-varindel FAM171A1,frameshift_variant,p.Lys700SerfsTer45,ENST00000378116,NM_001010924.1;FAM171A1,downstream_gene_variant,,ENST00000477161,; - ENST00000378116 Transcript frameshift_variant 2104/3952 2097/2673 699/890 G/X ggG/gg rs780775876 1 -1 FAM171A1 HGNC HGNC:23522 protein_coding YES CCDS31154.1 ENSP00000367356 Q5VUB5 UPI00001414CA NM_001010924.1 8/8 hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF1,Pfam_domain:PF10577 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 15213491 15213491 C - 1 0 1 0 1 0 0 0 0 5337 842 30 0 0 FAM171A1 10 15213491 Frame_Shift_Del DEL C C3N-00175_T 2018263 15213491 118583931 755 10347 ITGA8 0 . GRCh38 10 15586657 15586657 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.2299A>C p.Lys767Gln p.K767Q ENST00000378076 23/30 159 89 70 147 147 0 strelka-varscan-mutect ITGA8,missense_variant,p.Lys767Gln,ENST00000378076,NM_003638.2,NM_001291494.1; G ENST00000378076 Transcript missense_variant 2653/6755 2299/3192 767/1063 K/Q Aag/Cag 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 tolerated(0.62) 23/30 Gene3D:2.60.40.1510,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 15586657 15586657 T G 1 0 0 0 0 1 0 0 0 7789 1821 63 5 5 ITGA8 10 15586657 Missense_Mutation SNP T C3N-00175_T 373166 15586657 118210765 756 10348 PTER 0 . GRCh38 10 16484542 16484542 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.158T>G p.Val53Gly p.V53G ENST00000378000 3/6 296 202 94 276 276 0 strelka-varscan-mutect PTER,missense_variant,p.Val53Gly,ENST00000378000,NM_001001484.2;PTER,missense_variant,p.Val53Gly,ENST00000298942,NM_001261837.1;PTER,missense_variant,p.Val53Gly,ENST00000535784,NM_001261836.1,NM_030664.4;PTER,intron_variant,,ENST00000423462,NM_001261838.1;PTER,upstream_gene_variant,,ENST00000485788,; G ENST00000378000 Transcript missense_variant 404/3777 158/1050 53/349 V/G gTg/gGg 1 1 PTER HGNC HGNC:9590 protein_coding YES CCDS7111.1 ENSP00000367239 Q96BW5 UPI00000492E9 NM_001001484.2 tolerated(0.25) 3/6 Gene3D:3.20.20.140,Pfam_domain:PF02126,PROSITE_profiles:PS51347,hmmpanther:PTHR10819,hmmpanther:PTHR10819:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 16484542 16484542 T G 1 0 0 0 0 1 0 0 0 12892 1696 59 5 5 PTER 10 16484542 Missense_Mutation SNP T C3N-00175_T 897885 16484542 117312880 757 10349 MRC1 0 . GRCh38 10 17894263 17894263 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.3201G>C p.Met1067Ile p.M1067I ENST00000569591 23/30 419 362 57 409 409 0 strelka-varscan-mutect MRC1,missense_variant,p.Met1067Ile,ENST00000569591,NM_002438.3; C ENST00000569591 Transcript missense_variant 3323/5198 3201/4371 1067/1456 M/I atG/atC 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 tolerated(0.07) 23/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,PROSITE_patterns:PS00615,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 17894263 17894263 G C 1 0 0 0 0 1 0 0 0 9722 1348 47 4 4 MRC1 10 17894263 Missense_Mutation SNP G C3N-00175_T 1409721 17894263 115903159 758 10350 MRC1 0 . GRCh38 10 17910311 17910311 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.4218delC p.Ala1407ProfsTer35 p.A1407Pfs*35 ENST00000569591 30/30 764 504 260 803 803 0 sindel-varindel-pindel MRC1,frameshift_variant,p.Ala1407ProfsTer35,ENST00000569591,NM_002438.3; - ENST00000569591 Transcript frameshift_variant 4339/5198 4217/4371 1406/1456 A/X gCc/gc 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 30/30 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 17910311 17910311 C - 1 0 1 0 1 0 0 0 0 9722 739 26 0 0 MRC1 10 17910311 Frame_Shift_Del DEL C C3N-00175_T 16048 17910311 115887111 759 10351 SLC39A12 0 . GRCh38 10 18042797 18042797 + Silent SNP G G A C3N-00175_T C3N-00175_N G G c.2040G>A p.= p.L680L ENST00000377369 13/13 217 159 58 223 223 0 strelka-varscan-mutect SLC39A12,synonymous_variant,p.=,ENST00000377369,NM_001145195.1;SLC39A12,synonymous_variant,p.=,ENST00000377371,NM_001282733.1;SLC39A12,synonymous_variant,p.=,ENST00000377374,NM_152725.3;SLC39A12,synonymous_variant,p.=,ENST00000539911,NM_001282734.1; A ENST00000377369 Transcript synonymous_variant 2313/2808 2040/2076 680/691 L ctG/ctA COSM1504898,COSM5306319 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 13/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 18042797 18042797 G A 1 0 0 0 0 0 0 0 1 14893 1306 46 3 3 SLC39A12 10 18042797 Silent SNP G C3N-00175_T 132486 18042797 115754625 760 10352 NEBL 0 . GRCh38 10 20850481 20850481 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1030G>T p.Glu344Ter p.E344* ENST00000377122 11/28 160 107 53 197 197 0 strelka-varscan-mutect NEBL,stop_gained,p.Glu344Ter,ENST00000377122,NM_006393.2;NEBL,intron_variant,,ENST00000417816,NM_213569.2,NM_001173484.1;NEBL,upstream_gene_variant,,ENST00000482754,; A ENST00000377122 Transcript stop_gained 1427/9216 1030/3045 344/1014 E/* Gag/Tag 1 -1 NEBL HGNC HGNC:16932 protein_coding YES CCDS7134.1 ENSP00000366326 O76041 UPI000012FEE8 NM_006393.2 11/28 Low_complexity_(Seg):seg,PROSITE_profiles:PS51216,hmmpanther:PTHR11039,Pfam_domain:PF00880,SMART_domains:SM00227 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 20850481 20850481 C A 1 0 0 0 0 0 1 0 0 10327 835 29 2 2 NEBL 10 20850481 Nonsense_Mutation SNP C C3N-00175_T 2807684 20850481 112946941 761 10353 KIAA1217 0 . GRCh38 10 24513384 24513384 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.2127A>G p.= p.Q709Q ENST00000376454 10/21 173 122 51 154 154 0 strelka-varscan-mutect KIAA1217,synonymous_variant,p.=,ENST00000376451,;KIAA1217,synonymous_variant,p.=,ENST00000376454,NM_019590.4;KIAA1217,synonymous_variant,p.=,ENST00000376462,NM_001098500.2;KIAA1217,synonymous_variant,p.=,ENST00000376452,NM_001282767.1;KIAA1217,synonymous_variant,p.=,ENST00000458595,NM_001282768.1;KIAA1217,synonymous_variant,p.=,ENST00000430453,;KIAA1217,synonymous_variant,p.=,ENST00000396445,;KIAA1217,synonymous_variant,p.=,ENST00000307544,NM_001282769.1;KIAA1217,synonymous_variant,p.=,ENST00000376456,;KIAA1217,synonymous_variant,p.=,ENST00000396446,NM_001282770.1;KIAA1217,synonymous_variant,p.=,ENST00000438429,;KIAA1217,downstream_gene_variant,,ENST00000460373,; G ENST00000376454 Transcript synonymous_variant 2157/7381 2127/5832 709/1943 Q caA/caG 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 10/21 Pfam_domain:PF03915,hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 24513384 24513384 A G 1 0 0 0 0 0 0 0 1 8109 69 3 5 5 KIAA1217 10 24513384 Silent SNP A C3N-00175_T 3662903 24513384 109284038 762 10354 GPR158 0 . GRCh38 10 25395966 25395966 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1064A>T p.Lys355Ile p.K355I ENST00000376351 3/11 317 243 74 264 264 0 strelka-varscan-mutect GPR158,missense_variant,p.Lys355Ile,ENST00000376351,NM_020752.2;RN7SKP220,upstream_gene_variant,,ENST00000410611,; T ENST00000376351 Transcript missense_variant 1423/6959 1064/3648 355/1215 K/I aAa/aTa 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0) 3/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 25395966 25395966 A T 1 0 0 0 0 1 0 0 0 6549 14 1 4 4 GPR158 10 25395966 Missense_Mutation SNP A C3N-00175_T 882582 25395966 108401456 763 10355 GPR158 0 . GRCh38 10 25598561 25598561 + Missense_Mutation SNP C C A rs376559311 C3N-00175_T C3N-00175_N C C c.2935C>A p.Gln979Lys p.Q979K ENST00000376351 11/11 326 297 29 254 254 0 strelka-varscan-mutect GPR158,missense_variant,p.Gln979Lys,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; A ENST00000376351 Transcript missense_variant 3294/6959 2935/3648 979/1215 Q/K Caa/Aaa rs376559311 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 tolerated(0.14) 11/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS rs376559311 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 25598561 25598561 C A 1 0 0 0 0 1 0 0 0 6549 479 17 2 2 GPR158 10 25598561 Missense_Mutation SNP C C3N-00175_T 202595 25598561 108198861 764 10356 MAP3K8 0 . GRCh38 10 30451739 30451739 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.868A>T p.Thr290Ser p.T290S ENST00000263056 6/9 180 124 56 131 131 0 strelka-varscan-mutect MAP3K8,missense_variant,p.Thr290Ser,ENST00000263056,NM_005204.3;MAP3K8,missense_variant,p.Thr290Ser,ENST00000542547,NM_001244134.1;MAP3K8,missense_variant,p.Thr290Ser,ENST00000375321,;MAP3K8,downstream_gene_variant,,ENST00000415139,;MAP3K8,downstream_gene_variant,,ENST00000413724,;MAP3K8,downstream_gene_variant,,ENST00000430603,; T ENST00000263056 Transcript missense_variant 1564/3096 868/1404 290/467 T/S Aca/Tca 1 1 MAP3K8 HGNC HGNC:6860 protein_coding YES CCDS7166.1 ENSP00000263056 P41279 UPI000013D395 NM_005204.3 deleterious(0.04) 6/9 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF94,hmmpanther:PTHR24361,Pfam_domain:PF00069,Gene3D:1.10.510.10,PIRSF_domain:PIRSF038171,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 30451739 30451739 A T 1 0 0 0 0 1 0 0 0 9180 57 2 4 4 MAP3K8 10 30451739 Missense_Mutation SNP A C3N-00175_T 4853178 30451739 103345683 765 10357 ITGB1 0 . GRCh38 10 32901600 32901600 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.2367T>A p.= p.T789T ENST00000396033 16/16 159 150 9 142 142 0 varscan-mutect ITGB1,synonymous_variant,p.=,ENST00000396033,NM_133376.2;ITGB1,synonymous_variant,p.=,ENST00000302278,NM_002211.3;ITGB1,3_prime_UTR_variant,,ENST00000423113,NM_033668.2;ITGB1,3_prime_UTR_variant,,ENST00000488427,;ITGB1,3_prime_UTR_variant,,ENST00000494395,; T ENST00000396033 Transcript synonymous_variant 2503/3784 2367/2397 789/798 T acT/acA 1 -1 ITGB1 HGNC HGNC:6153 protein_coding YES CCDS7174.1 ENSP00000379350 P05556 UPI0000070EEB NM_133376.2 16/16 Gene3D:1m8oB00,Pfam_domain:PF08725,PIRSF_domain:PIRSF002512,Prints_domain:PR01186,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF28,SMART_domains:SM01241 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 32901600 32901600 A T 1 0 0 0 0 0 0 0 1 7797 175 7 4 4 ITGB1 10 32901600 Silent SNP A C3N-00175_T 2449861 32901600 100895822 766 10358 ZNF25 0 . GRCh38 10 37952511 37952511 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.987C>T p.= p.L329L ENST00000302609 6/6 142 125 17 131 131 0 strelka-varscan-mutect ZNF25,synonymous_variant,p.=,ENST00000302609,NM_145011.2;ZNF25,non_coding_transcript_exon_variant,,ENST00000374633,;ZNF25,downstream_gene_variant,,ENST00000467975,; A ENST00000302609 Transcript synonymous_variant 1200/4139 987/1371 329/456 L ctC/ctT 1 -1 ZNF25 HGNC HGNC:13043 protein_coding YES CCDS7195.1 ENSP00000302222 P17030 UPI0000071FFD NM_145011.2 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF62,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 37952511 37952511 G A 1 0 0 0 0 0 0 0 1 18370 1277 45 3 3 ZNF25 10 37952511 Silent SNP G C3N-00175_T 5050911 37952511 95844911 767 10359 RET 0 . GRCh38 10 43077286 43077286 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.28G>T p.Gly10Trp p.G10W ENST00000355710 1/20 366 248 118 292 292 0 strelka-varscan-mutect RET,missense_variant,p.Gly10Trp,ENST00000355710,NM_020975.4;RET,missense_variant,p.Gly10Trp,ENST00000615310,;RET,missense_variant,p.Gly10Trp,ENST00000340058,NM_020630.4;RET,missense_variant,p.Gly10Trp,ENST00000498820,; T ENST00000355710 Transcript missense_variant 260/5659 28/3345 10/1114 G/W Ggg/Tgg 1 1 RET HGNC HGNC:9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 A0A024R7T2 UPI00001336E1 NM_020975.4 deleterious_low_confidence(0) 1/20 PIRSF_domain:PIRSF000631,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43077286 43077286 G T 1 0 0 0 0 1 0 0 0 13406 1232 43 2 2 RET 10 43077286 Missense_Mutation SNP G C3N-00175_T 5124775 43077286 90720136 768 10360 FAM21C 0 . GRCh38 10 45765694 45765694 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1753G>A p.Gly585Ser p.G585S ENST00000374362 19/30 289 236 53 352 352 0 strelka-varscan-mutect FAM21C,missense_variant,p.Gly585Ser,ENST00000336378,;FAM21C,missense_variant,p.Gly585Ser,ENST00000374362,NM_015262.2;FAM21C,missense_variant,p.Gly585Ser,ENST00000623400,;FAM21C,missense_variant,p.Gly585Ser,ENST00000540872,NM_001169106.1;FAM21C,missense_variant,p.Gly529Ser,ENST00000359860,;FAM21C,missense_variant,p.Gly561Ser,ENST00000537517,NM_001169107.1; A ENST00000374362 Transcript missense_variant 1852/4623 1753/3963 585/1320 G/S Ggt/Agt 1 1 FAM21C HGNC HGNC:23414 protein_coding YES CCDS44374.2 ENSP00000363482 Q9Y4E1 UPI0000551BE9 NM_015262.2 tolerated(0.73) 19/30 hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 45765694 45765694 G A 1 0 0 0 0 1 0 0 0 5412 1232 43 3 3 FAM21C 10 45765694 Missense_Mutation SNP G C3N-00175_T 2688408 45765694 88031728 769 10361 MSMB 0 . GRCh38 10 46033481 46033481 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.286A>T p.Ile96Phe p.I96F ENST00000582163 4/4 165 134 31 192 192 0 strelka-varscan-mutect MSMB,missense_variant,p.Ile96Phe,ENST00000582163,NM_002443.3;MSMB,synonymous_variant,p.=,ENST00000581478,NM_138634.2;NCOA4,upstream_gene_variant,,ENST00000581486,NM_001145263.1;NCOA4,upstream_gene_variant,,ENST00000578454,NM_001145260.1;NCOA4,upstream_gene_variant,,ENST00000579039,NM_001145261.1;NCOA4,upstream_gene_variant,,ENST00000585056,;NCOA4,upstream_gene_variant,,ENST00000580070,; A ENST00000582163 Transcript missense_variant 318/488 286/345 96/114 I/F Atc/Ttc 1 -1 MSMB HGNC HGNC:7372 protein_coding YES CCDS73096.1 ENSP00000463092 P08118 UPI000012F617 NM_002443.3 deleterious(0.01) 4/4 hmmpanther:PTHR10500:SF0,hmmpanther:PTHR10500,Pfam_domain:PF05825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 46033481 46033481 T A 1 0 0 0 0 1 0 0 0 9865 1406 49 4 4 MSMB 10 46033481 Missense_Mutation SNP T C3N-00175_T 267787 46033481 87763941 770 10362 ARHGAP22 0 . GRCh38 10 48479648 48479648 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.439C>A p.Pro147Thr p.P147T ENST00000417912 4/10 138 111 27 148 148 0 strelka-varscan-mutect ARHGAP22,missense_variant,p.Pro147Thr,ENST00000249601,NM_021226.3;ARHGAP22,missense_variant,p.Pro153Thr,ENST00000435790,NM_001256025.2;ARHGAP22,missense_variant,p.Pro22Thr,ENST00000374172,;ARHGAP22,missense_variant,p.Pro147Thr,ENST00000417912,NM_001256024.1;ARHGAP22,missense_variant,p.Pro57Thr,ENST00000417247,NM_001256026.1;ARHGAP22,missense_variant,p.Pro57Thr,ENST00000374170,;ARHGAP22,intron_variant,,ENST00000471013,;ARHGAP22,upstream_gene_variant,,ENST00000515523,;ARHGAP22,missense_variant,p.Pro153Thr,ENST00000460425,; T ENST00000417912 Transcript missense_variant 595/2352 439/2145 147/714 P/T Ccg/Acg 1 -1 ARHGAP22 HGNC HGNC:30320 protein_coding YES CCDS58080.1 ENSP00000412461 Q7Z5H3 UPI0000E5BE9D NM_001256024.1 deleterious(0) 4/10 Gene3D:2.30.29.30,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF22,SMART_domains:SM00233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 48479648 48479648 G T 1 0 0 0 0 1 0 0 0 996 1232 43 2 2 ARHGAP22 10 48479648 Missense_Mutation SNP G C3N-00175_T 2446167 48479648 85317774 771 10363 LRRC18 0 . GRCh38 10 48913731 48913731 + Missense_Mutation SNP G G T rs763695309 C3N-00175_T C3N-00175_N G G c.425C>A p.Ala142Asp p.A142D ENST00000374160 1/2 59 49 10 94 94 0 strelka-varscan-mutect LRRC18,missense_variant,p.Ala142Asp,ENST00000374160,NM_001006939.3;WDFY4,intron_variant,,ENST00000325239,NM_020945.1;WDFY4,intron_variant,,ENST00000265453,;RP11-523O18.7,intron_variant,,ENST00000430438,; T ENST00000374160 Transcript missense_variant 502/1617 425/786 142/261 A/D gCc/gAc rs763695309 1 -1 LRRC18 HGNC HGNC:23199 protein_coding YES CCDS31197.1 ENSP00000363275 Q8N456 UPI00001F98A9 NM_001006939.3 tolerated(0.06) 1/2 PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF593,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs763695309 . 0 204 6 0 0 0 0 0 -19.99959 1 1 1 1 0 T 3 4 39 48913731 48913731 G T 1 0 0 0 0 1 0 0 0 8869 1203 42 2 2 LRRC18 10 48913731 Missense_Mutation SNP G C3N-00175_T 434083 48913731 84883691 772 10364 ERCC6 0 . GRCh38 10 49524771 49524771 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.659G>T p.Gly220Val p.G220V ENST00000355832 5/21 305 233 72 435 435 0 strelka-varscan-mutect ERCC6,missense_variant,p.Gly220Val,ENST00000355832,NM_000124.3;ERCC6,missense_variant,p.Gly220Val,ENST00000515869,NM_001277059.1;ERCC6,missense_variant,p.Gly220Val,ENST00000447839,NM_001277058.1;ERCC6,downstream_gene_variant,,ENST00000479652,; A ENST00000355832 Transcript missense_variant 738/8008 659/4482 220/1493 G/V gGg/gTg 1 -1 ERCC6 HGNC HGNC:3438 protein_coding YES CCDS7229.1 ENSP00000348089 Q03468 UPI000000D8DA NM_000124.3 deleterious(0.01) 5/21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 49524771 49524771 C A 1 0 0 0 0 1 0 0 0 5066 623 22 2 2 ERCC6 10 49524771 Missense_Mutation SNP C C3N-00175_T 611040 49524771 84272651 773 10365 PCDH15 0 . GRCh38 10 53823265 53823265 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.4482C>A p.= p.S1494S ENST00000373957 35/35 168 125 43 197 197 0 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000617271,NM_001142770.1;PCDH15,intron_variant,,ENST00000613657,NM_001142769.1;PCDH15,intron_variant,,ENST00000395445,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000395438,;PCDH15,intron_variant,,ENST00000612394,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,;PCDH15,upstream_gene_variant,,ENST00000476074,; T ENST00000373957 Transcript synonymous_variant 4877/7032 4482/5889 1494/1962 S tcC/tcA 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 35/35 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 53823265 53823265 G T 1 0 0 0 0 0 0 0 1 11598 1335 47 2 2 PCDH15 10 53823265 Silent SNP G C3N-00175_T 4298494 53823265 79974157 774 10366 ANK3 0 . GRCh38 10 60213413 60213413 + Missense_Mutation SNP T T A rs375976636 C3N-00175_T C3N-00175_N T T c.995A>T p.Lys332Met p.K332M ENST00000280772 9/44 69 58 11 78 78 0 strelka-varscan-mutect ANK3,missense_variant,p.Lys332Met,ENST00000280772,NM_020987.3;ANK3,missense_variant,p.Lys326Met,ENST00000373827,NM_001204403.1;ANK3,missense_variant,p.Lys315Met,ENST00000503366,NM_001204404.1;ANK3,missense_variant,p.Lys315Met,ENST00000622427,; A ENST00000280772 Transcript missense_variant,splice_region_variant 1187/16874 995/13134 332/4377 K/M aAg/aTg rs375976636 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 deleterious(0) 9/44 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs375976636 . 0 202 6 2 0 0 0 0 -19.25297 0.9999275 1 1 1 0 A 3 1 39 60213413 60213413 T A 1 0 0 0 0 1 0 0 0 722 1623 56 4 4 ANK3 10 60213413 Missense_Mutation SNP T C3N-00175_T 6390148 60213413 73584009 775 10367 PBLD 0 . GRCh38 10 68284217 68284217 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.827G>T p.Gly276Val p.G276V ENST00000358769 10/10 153 128 25 225 225 0 strelka-varscan-mutect PBLD,missense_variant,p.Gly276Val,ENST00000358769,NM_022129.3;PBLD,missense_variant,p.Gly243Val,ENST00000336578,;PBLD,missense_variant,p.Gly276Val,ENST00000309049,;PBLD,intron_variant,,ENST00000468798,;PBLD,downstream_gene_variant,,ENST00000495025,NM_001033083.1;PBLD,downstream_gene_variant,,ENST00000277795,; A ENST00000358769 Transcript missense_variant 1030/2587 827/867 276/288 G/V gGa/gTa 1 -1 PBLD HGNC HGNC:23301 protein_coding YES CCDS7277.2 ENSP00000351619 P30039 A0A024QZK5 UPI0000000DCA NM_022129.3 deleterious(0) 10/10 hmmpanther:PTHR13774:SF17,hmmpanther:PTHR13774,PIRSF_domain:PIRSF016184,Pfam_domain:PF02567,Gene3D:3.10.310.10,Superfamily_domains:SSF54506 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 68284217 68284217 C A 1 0 0 0 0 1 0 0 0 11576 855 30 2 2 PBLD 10 68284217 Missense_Mutation SNP C C3N-00175_T 8070804 68284217 65513205 776 10368 HKDC1 0 . GRCh38 10 69248545 69248545 + Missense_Mutation SNP G G T rs754621268,rs762100434 C3N-00175_T C3N-00175_N G G c.1387G>T p.Val463Leu p.V463L ENST00000354624 10/18 146 106 40 159 159 0 strelka-varscan-mutect HKDC1,missense_variant,p.Val463Leu,ENST00000354624,NM_025130.3;HKDC1,non_coding_transcript_exon_variant,,ENST00000488706,; T ENST00000354624 Transcript missense_variant 1520/3689 1387/2754 463/917 V/L Gtg/Ttg rs754621268,rs762100434 1 1 HKDC1 HGNC HGNC:23302 protein_coding YES CCDS7288.1 ENSP00000346643 Q2TB90 UPI00003666D2 NM_025130.3 tolerated(1) 10/18 hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF28,Gene3D:3.40.367.20,Superfamily_domains:SSF53067,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs762100434 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 69248545 69248545 G T 1 0 0 0 0 1 0 0 0 7082 1145 40 1 1 HKDC1 10 69248545 Missense_Mutation SNP G C3N-00175_T 964328 69248545 64548877 777 10369 TBATA 0 . GRCh38 10 70777231 70777231 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.612T>A p.= p.S204S ENST00000299290 7/11 175 138 37 202 202 0 strelka-varscan-mutect TBATA,synonymous_variant,p.=,ENST00000456372,NM_001318241.1;TBATA,synonymous_variant,p.=,ENST00000299290,NM_001318243.1,NM_152710.2;TBATA,upstream_gene_variant,,ENST00000394982,; T ENST00000299290 Transcript synonymous_variant 1002/1583 612/1056 204/351 S tcT/tcA 1 -1 TBATA HGNC HGNC:23511 protein_coding YES CCDS7308.1 ENSP00000299290 Q96M53 UPI000013E57C NM_001318243.1,NM_152710.2 7/11 Low_complexity_(Seg):seg,hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF3,Pfam_domain:PF15256 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 70777231 70777231 A T 1 0 0 0 0 0 0 0 1 15996 291 11 4 4 TBATA 10 70777231 Silent SNP A C3N-00175_T 1528686 70777231 63020191 778 10370 C10orf105 0 . GRCh38 10 71715957 71715957 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.381C>A p.Tyr127Ter p.Y127* ENST00000441508 2/2 20 16 4 32 32 0 strelka-varscan-mutect C10orf105,stop_gained,p.Tyr127Ter,ENST00000441508,NM_001164375.2;C10orf105,stop_gained,p.Tyr127Ter,ENST00000398786,NM_001168390.1;CDH23,3_prime_UTR_variant,,ENST00000442677,;CDH23,3_prime_UTR_variant,,ENST00000466757,;CDH23,intron_variant,,ENST00000224721,NM_022124.5;CDH23,intron_variant,,ENST00000622827,;CDH23,intron_variant,,ENST00000616684,NM_001171930.1;CDH23,intron_variant,,ENST00000398809,;CDH23,intron_variant,,ENST00000398792,; T ENST00000441508 Transcript stop_gained 581/4837 381/402 127/133 Y/* taC/taA 1 -1 C10orf105 HGNC HGNC:20304 protein_coding YES CCDS44430.1 ENSP00000403151 Q8TEF2 UPI00001F8E63 NM_001164375.2 2/2 hmmpanther:PTHR38325,hmmpanther:PTHR38325:SF1 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -12.24132 1 1 1 1 0 T 4 4 39 71715957 71715957 G T 1 0 0 0 0 0 1 0 0 1756 1372 48 2 2 C10orf105 10 71715957 Nonsense_Mutation SNP G C3N-00175_T 938726 71715957 62081465 779 10371 CDH23 0 . GRCh38 10 71738516 71738516 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.4243G>T p.Asp1415Tyr p.D1415Y ENST00000224721 35/70 269 227 42 308 308 0 strelka-varscan-mutect CDH23,missense_variant,p.Asp1415Tyr,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Asp1410Tyr,ENST00000622827,;C10orf105,upstream_gene_variant,,ENST00000398786,NM_001168390.1;CDH23,non_coding_transcript_exon_variant,,ENST00000398792,; T ENST00000224721 Transcript missense_variant 4633/11139 4243/10080 1415/3359 D/Y Gac/Tac 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 deleterious(0) 35/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 71738516 71738516 G T 1 0 0 0 0 1 0 0 0 2811 1174 41 2 2 CDH23 10 71738516 Missense_Mutation SNP G C3N-00175_T 22559 71738516 62058906 780 10372 ASCC1 0 . GRCh38 10 72213272 72213272 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.27A>T p.= p.I9I ENST00000342444 2/13 341 269 72 426 426 0 strelka-varscan-mutect ASCC1,synonymous_variant,p.=,ENST00000394919,NM_001198798.2;ASCC1,synonymous_variant,p.=,ENST00000342444,NM_001198799.2;ASCC1,synonymous_variant,p.=,ENST00000317168,NM_001198800.2;ASCC1,synonymous_variant,p.=,ENST00000394915,;ASCC1,synonymous_variant,p.=,ENST00000317126,;ASCC1,synonymous_variant,p.=,ENST00000533958,;ASCC1,synonymous_variant,p.=,ENST00000524829,;ASCC1,synonymous_variant,p.=,ENST00000527593,;ASCC1,synonymous_variant,p.=,ENST00000526751,;ASCC1,synonymous_variant,p.=,ENST00000531048,;ASCC1,5_prime_UTR_variant,,ENST00000530461,;ANAPC16,upstream_gene_variant,,ENST00000621663,NM_001242546.1,NM_001242547.1;ANAPC16,upstream_gene_variant,,ENST00000299381,NM_173473.3;ANAPC16,upstream_gene_variant,,ENST00000615507,NM_001242548.1;ASCC1,upstream_gene_variant,,ENST00000486689,;ASCC1,non_coding_transcript_exon_variant,,ENST00000492502,;ANAPC16,upstream_gene_variant,,ENST00000478193,;ASCC1,synonymous_variant,p.=,ENST00000532011,; A ENST00000342444 Transcript synonymous_variant 129/2270 27/1203 9/400 I atA/atT 1 -1 ASCC1 HGNC HGNC:24268 protein_coding YES CCDS55713.1 ENSP00000339404 Q8N9N2 UPI000006F7E9 NM_001198799.2 2/13 hmmpanther:PTHR13360:SF1,hmmpanther:PTHR13360,PIRSF_domain:PIRSF027019 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 72213272 72213272 T A 1 0 0 0 0 0 0 0 1 1173 1744 61 4 4 ASCC1 10 72213272 Silent SNP T C3N-00175_T 474756 72213272 61584150 781 10373 MSS51 0 . GRCh38 10 73426094 73426094 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.786A>T p.= p.G262G ENST00000299432 5/7 131 114 17 174 174 0 strelka-varscan-mutect MSS51,synonymous_variant,p.=,ENST00000299432,NM_001024593.1;MSS51,synonymous_variant,p.=,ENST00000372912,;MSS51,intron_variant,,ENST00000487126,;RP11-345K20.2,upstream_gene_variant,,ENST00000440913,; A ENST00000299432 Transcript synonymous_variant 852/2421 786/1383 262/460 G ggA/ggT 1 -1 MSS51 HGNC HGNC:21000 protein_coding YES CCDS31221.1 ENSP00000299432 Q4VC12 UPI00004CA0F2 NM_001024593.1 5/7 hmmpanther:PTHR13244,hmmpanther:PTHR13244:SF9 LOW 1 SNV 1 1 PASS rs750108481 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 73426094 73426094 T A 1 0 0 0 0 0 0 0 1 9874 1770 62 4 4 MSS51 10 73426094 Silent SNP T C3N-00175_T 1212822 73426094 60371328 782 10374 DUPD1 0 . GRCh38 10 75043888 75043888 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.330C>A p.= p.G110G ENST00000338487 2/3 341 264 77 422 422 0 strelka-varscan-mutect DUPD1,synonymous_variant,p.=,ENST00000338487,NM_001003892.1; T ENST00000338487 Transcript synonymous_variant 330/663 330/663 110/220 G ggC/ggA COSM5643197 1 -1 DUPD1 HGNC HGNC:23481 protein_coding YES CCDS31223.1 ENSP00000340609 Q68J44 UPI000003E897 NM_001003892.1 2/3 Gene3D:3.90.190.10,Pfam_domain:PF00782,Prints_domain:PR01908,Prints_domain:PR01909,PROSITE_profiles:PS50054,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF114,SMART_domains:SM00195,Superfamily_domains:SSF52799 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 75043888 75043888 G T 1 0 0 0 0 0 0 0 1 4626 1074 38 1 1 DUPD1 10 75043888 Silent SNP G C3N-00175_T 1617794 75043888 58753534 783 10375 TSPAN14 0 . GRCh38 10 80509380 80509380 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.359G>A p.Arg120Lys p.R120K ENST00000429989 5/9 195 156 39 226 226 0 strelka-varscan-mutect TSPAN14,missense_variant,p.Arg120Lys,ENST00000429989,NM_030927.2;TSPAN14,missense_variant,p.Arg103Lys,ENST00000372164,;TSPAN14,missense_variant,p.Arg103Lys,ENST00000616406,;TSPAN14,missense_variant,p.Arg120Lys,ENST00000372156,;TSPAN14,missense_variant,p.Arg120Lys,ENST00000372158,;TSPAN14,missense_variant,p.Arg90Lys,ENST00000372157,;TSPAN14,intron_variant,,ENST00000341863,;TSPAN14,intron_variant,,ENST00000481124,NM_001128309.1;TSPAN14,non_coding_transcript_exon_variant,,ENST00000469149,; A ENST00000429989 Transcript missense_variant 582/16183 359/813 120/270 R/K aGg/aAg 1 1 TSPAN14 HGNC HGNC:23303 protein_coding YES CCDS7369.1 ENSP00000396270 Q8NG11 UPI000004ACAE NM_030927.2 tolerated(1) 5/9 Superfamily_domains:0037997,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 80509380 80509380 G A 1 0 0 0 0 1 0 0 0 17143 1000 35 3 3 TSPAN14 10 80509380 Missense_Mutation SNP G C3N-00175_T 5465492 80509380 53288042 784 10376 GRID1 0 . GRCh38 10 85728010 85728010 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.1378C>A p.Pro460Thr p.P460T ENST00000327946 10/16 227 186 41 287 287 0 strelka-varscan-mutect GRID1,missense_variant,p.Pro460Thr,ENST00000327946,NM_017551.2;GRID1,missense_variant,p.Pro460Thr,ENST00000464741,; T ENST00000327946 Transcript missense_variant 1464/5834 1378/3030 460/1009 P/T Ccc/Acc COSM685156 1 -1 GRID1 HGNC HGNC:4575 protein_coding YES CCDS31236.1 ENSP00000330148 Q9ULK0 UPI00001D8051 NM_017551.2 deleterious(0.04) 10/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,SMART_domains:SM00079,SMART_domains:SM00918,Superfamily_domains:SSF53850 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 85728010 85728010 G T 1 0 0 0 0 1 0 0 0 6651 1203 42 2 2 GRID1 10 85728010 Missense_Mutation SNP G C3N-00175_T 5218630 85728010 48069412 785 10377 LIPM 0 . GRCh38 10 88802962 88802962 + Silent SNP G G A rs377287814 C3N-00175_T C3N-00175_N G G c.66G>A p.= p.L22L ENST00000404743 1/9 144 123 21 166 166 0 strelka-varscan-mutect LIPM,synonymous_variant,p.=,ENST00000404743,NM_001128215.1;LIPM,upstream_gene_variant,,ENST00000539337,; A ENST00000404743 Transcript synonymous_variant 233/1439 66/1272 22/423 L ctG/ctA rs377287814 1 1 LIPM HGNC HGNC:23455 protein_coding YES CCDS44457.1 ENSP00000383901 Q5VYY2 UPI00004B21B5 NM_001128215.1 1/9 PIRSF_domain:PIRSF000862,hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF12 LOW 1 SNV 1 1 PASS rs377287814 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 88802962 88802962 G A 1 0 0 0 0 0 0 0 1 8749 1335 47 3 3 LIPM 10 88802962 Silent SNP G C3N-00175_T 3074952 88802962 44994460 786 10378 STAMBPL1 0 . GRCh38 10 88916748 88916748 + Missense_Mutation SNP C C A rs780250922 C3N-00175_T C3N-00175_N C C c.972C>A p.Asp324Glu p.D324E ENST00000371926 8/11 106 98 8 145 144 1 strelka-varscan-mutect STAMBPL1,missense_variant,p.Asp324Glu,ENST00000371927,;STAMBPL1,missense_variant,p.Asp324Glu,ENST00000371926,NM_020799.3;STAMBPL1,missense_variant,p.Asp324Glu,ENST00000371924,;STAMBPL1,missense_variant,p.Asp158Glu,ENST00000371922,; A ENST00000371926 Transcript missense_variant 1930/2532 972/1311 324/436 D/E gaC/gaA rs780250922 1 1 STAMBPL1 HGNC HGNC:24105 protein_coding YES CCDS7391.1 ENSP00000360994 Q96FJ0 UPI000013FA61 NM_020799.3 tolerated(0.06) 8/11 hmmpanther:PTHR12947:SF7,hmmpanther:PTHR12947,Pfam_domain:PF01398,Gene3D:3.40.140.10,SMART_domains:SM00232,Superfamily_domains:0048572 MODERATE 1 SNV 1 1 PASS rs780250922 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 88916748 88916748 C A 1 0 0 0 0 1 0 0 0 15626 477 17 2 2 STAMBPL1 10 88916748 Missense_Mutation SNP C C3N-00175_T 113786 88916748 44880674 787 10379 CYP26C1 0 . GRCh38 10 93061301 93061301 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.38G>A p.Gly13Glu p.G13E ENST00000285949 1/6 92 77 15 161 161 0 strelka-varscan-mutect CYP26C1,missense_variant,p.Gly13Glu,ENST00000285949,NM_183374.2;EXOC6,downstream_gene_variant,,ENST00000260762,NM_001319195.1,NM_019053.4;EXOC6,downstream_gene_variant,,ENST00000371552,NM_001319194.1,NM_001013848.2;EXOC6,downstream_gene_variant,,ENST00000443748,NM_001319200.1;RP11-348J12.2,upstream_gene_variant,,ENST00000444965,;CYP26C1,missense_variant,p.Gly13Glu,ENST00000624358,;EXOC6,downstream_gene_variant,,ENST00000495132,; A ENST00000285949 Transcript missense_variant 38/1569 38/1569 13/522 G/E gGg/gAg 1 1 CYP26C1 HGNC HGNC:20577 protein_coding YES CCDS7425.1 ENSP00000285949 Q6V0L0 UPI00002289F0 NM_183374.2 tolerated(0.44) 1/6 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 93061301 93061301 G A 1 0 0 0 0 1 0 0 0 3960 1232 43 3 3 CYP26C1 10 93061301 Missense_Mutation SNP G C3N-00175_T 4144553 93061301 40736121 788 10380 PDE6C 0 . GRCh38 10 93613026 93613026 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.301T>C p.Cys101Arg p.C101R ENST00000371447 1/22 195 168 27 191 191 0 strelka-varscan-mutect PDE6C,missense_variant,p.Cys101Arg,ENST00000371447,NM_006204.3; C ENST00000371447 Transcript missense_variant 439/3307 301/2577 101/858 C/R Tgc/Cgc 1 1 PDE6C HGNC HGNC:8787 protein_coding YES CCDS7429.1 ENSP00000360502 P51160 UPI000013C84A NM_006204.3 tolerated(0.26) 1/22 hmmpanther:PTHR11347:SF23,hmmpanther:PTHR11347,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 93613026 93613026 T C 1 0 0 0 0 1 0 0 0 11735 1696 59 5 5 PDE6C 10 93613026 Missense_Mutation SNP T C3N-00175_T 551725 93613026 40184396 789 10381 PDE6C 0 . GRCh38 10 93625593 93625593 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.883C>A p.Pro295Thr p.P295T ENST00000371447 5/22 299 254 45 354 354 0 strelka-varscan-mutect PDE6C,missense_variant,p.Pro295Thr,ENST00000371447,NM_006204.3; A ENST00000371447 Transcript missense_variant 1021/3307 883/2577 295/858 P/T Cca/Aca 1 1 PDE6C HGNC HGNC:8787 protein_coding YES CCDS7429.1 ENSP00000360502 P51160 UPI000013C84A NM_006204.3 deleterious(0.02) 5/22 hmmpanther:PTHR11347:SF23,hmmpanther:PTHR11347,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 93625593 93625593 C A 1 0 0 0 0 1 0 0 0 11735 739 26 2 2 PDE6C 10 93625593 Missense_Mutation SNP C C3N-00175_T 12567 93625593 40171829 790 10382 LGI1 0 . GRCh38 10 93797260 93797260 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1131C>A p.Tyr377Ter p.Y377* ENST00000371418 8/8 305 244 61 369 369 0 strelka-varscan-mutect LGI1,stop_gained,p.Tyr377Ter,ENST00000371418,NM_005097.2;LGI1,stop_gained,p.Tyr353Ter,ENST00000629035,;LGI1,stop_gained,p.Tyr329Ter,ENST00000630047,;LGI1,5_prime_UTR_variant,,ENST00000637689,;LGI1,intron_variant,,ENST00000636155,;LGI1,intron_variant,,ENST00000371413,NM_001308275.1;LGI1,downstream_gene_variant,,ENST00000630184,;LGI1,non_coding_transcript_exon_variant,,ENST00000637347,;LGI1,non_coding_transcript_exon_variant,,ENST00000635804,;LGI1,upstream_gene_variant,,ENST00000636775,;LGI1,downstream_gene_variant,,ENST00000630412,;LGI1,3_prime_UTR_variant,,ENST00000637037,;LGI1,3_prime_UTR_variant,,ENST00000635953,;LGI1,3_prime_UTR_variant,,ENST00000627420,;LGI1,3_prime_UTR_variant,,ENST00000637611,;LGI1,3_prime_UTR_variant,,ENST00000636754,;LGI1,3_prime_UTR_variant,,ENST00000636232,;LGI1,3_prime_UTR_variant,,ENST00000637925,;LGI1,3_prime_UTR_variant,,ENST00000638049,;LGI1,non_coding_transcript_exon_variant,,ENST00000626307,;LGI1,intron_variant,,ENST00000636946,;LGI1,downstream_gene_variant,,ENST00000630487,;LGI1,downstream_gene_variant,,ENST00000626946,; A ENST00000371418 Transcript stop_gained 1467/2381 1131/1674 377/557 Y/* taC/taA 1 1 LGI1 HGNC HGNC:6572 protein_coding YES CCDS7431.1 ENSP00000360472 O95970 A0A0S2Z4S7 UPI0000048F03 NM_005097.2 8/8 Pfam_domain:PF03736,PROSITE_profiles:PS50912,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF17 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 93797260 93797260 C A 1 0 0 0 0 0 1 0 0 8661 489 17 2 2 LGI1 10 93797260 Nonsense_Mutation SNP C C3N-00175_T 171667 93797260 40000162 791 10383 CYP2C18 0 . GRCh38 10 94735372 94735372 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.1401T>C p.= p.I467I ENST00000285979 9/9 199 176 23 220 220 0 strelka-varscan-mutect CYP2C18,synonymous_variant,p.=,ENST00000285979,NM_000772.2;CYP2C18,synonymous_variant,p.=,ENST00000339022,NM_001128925.1;RP11-400G3.5,intron_variant,,ENST00000464755,; C ENST00000285979 Transcript synonymous_variant 1600/2418 1401/1473 467/490 I atT/atC 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 9/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs886501074 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 94735372 94735372 T C 1 0 0 0 0 0 0 0 1 3968 1800 63 5 5 CYP2C18 10 94735372 Silent SNP T C3N-00175_T 938112 94735372 39062050 792 10384 CYP2C8 0 . GRCh38 10 95069344 95069344 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.59G>T p.Trp20Leu p.W20L ENST00000371270 1/9 145 106 39 165 165 0 strelka-varscan-mutect CYP2C8,missense_variant,p.Trp20Leu,ENST00000371270,NM_000770.3;CYP2C8,5_prime_UTR_variant,,ENST00000539050,NM_001198855.1;CYP2C8,5_prime_UTR_variant,,ENST00000623108,NM_001198853.1;CYP2C8,5_prime_UTR_variant,,ENST00000535898,NM_001198854.1;CYP2C8,upstream_gene_variant,,ENST00000628935,;CYP2C8,missense_variant,p.Trp20Leu,ENST00000490994,;CYP2C8,missense_variant,p.Trp20Leu,ENST00000527420,;CYP2C8,missense_variant,p.Trp20Leu,ENST00000525991,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000527953,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000526814,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000533320,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000479946,; A ENST00000371270 Transcript missense_variant 154/1923 59/1473 20/490 W/L tGg/tTg 1 -1 CYP2C8 HGNC HGNC:2622 protein_coding YES CCDS7438.1 ENSP00000360317 P10632 UPI0000128256 NM_000770.3 deleterious(0.01) 1/9 Gene3D:1.10.630.10,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF187,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 95069344 95069344 C A 1 0 0 0 0 1 0 0 0 3970 595 21 2 2 CYP2C8 10 95069344 Missense_Mutation SNP C C3N-00175_T 333972 95069344 38728078 793 10385 PIK3AP1 0 . GRCh38 10 96626742 96626742 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1635C>A p.His545Gln p.H545Q ENST00000339364 10/17 135 105 30 190 190 0 strelka-varscan-mutect PIK3AP1,missense_variant,p.His545Gln,ENST00000339364,NM_152309.2;PIK3AP1,missense_variant,p.His367Gln,ENST00000371110,;PIK3AP1,missense_variant,p.His144Gln,ENST00000371109,;PIK3AP1,downstream_gene_variant,,ENST00000468783,; T ENST00000339364 Transcript missense_variant 1755/4803 1635/2418 545/805 H/Q caC/caA 1 -1 PIK3AP1 HGNC HGNC:30034 protein_coding YES CCDS31259.1 ENSP00000339826 Q6ZUJ8 UPI00001F947F NM_152309.2 tolerated(0.66) 10/17 hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 96626742 96626742 G T 1 0 0 0 0 1 0 0 0 12003 1252 44 2 2 PIK3AP1 10 96626742 Missense_Mutation SNP G C3N-00175_T 1557398 96626742 37170680 794 10386 PIK3AP1 0 . GRCh38 10 96709943 96709943 + Silent SNP C C A rs748663928 C3N-00175_T C3N-00175_N C C c.54G>T p.= p.P18P ENST00000339364 2/17 35 30 5 60 60 0 strelka-varscan-mutect PIK3AP1,synonymous_variant,p.=,ENST00000339364,NM_152309.2; A ENST00000339364 Transcript synonymous_variant 174/4803 54/2418 18/805 P ccG/ccT rs748663928 1 -1 PIK3AP1 HGNC HGNC:30034 protein_coding YES CCDS31259.1 ENSP00000339826 Q6ZUJ8 UPI00001F947F NM_152309.2 2/17 hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF12 LOW 1 SNV 1 1 PASS rs748663928 . 0 202 8 0 0 0 0 0 -13.14076 0.9999979 1 1 1 0 A 2 1 39 96709943 96709943 C A 1 0 0 0 0 0 0 0 1 12003 639 23 1 1 PIK3AP1 10 96709943 Silent SNP C C3N-00175_T 83201 96709943 37087479 795 10387 C10orf62 0 . GRCh38 10 97590090 97590090 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.195delG p.Ser66ValfsTer10 p.S66Vfs*10 ENST00000370640 1/1 98 85 13 138 138 0 sindel-varindel-pindel C10orf62,frameshift_variant,p.Ser66ValfsTer10,ENST00000370640,NM_001009997.2;HOGA1,intron_variant,,ENST00000370646,NM_138413.3;HOGA1,intron_variant,,ENST00000370647,NM_001134670.1;RP11-548K23.11,intron_variant,,ENST00000370649,;HOGA1,intron_variant,,ENST00000465608,; - ENST00000370640 Transcript frameshift_variant 364/1208 193/672 65/223 G/X Ggg/gg 1 1 C10orf62 HGNC HGNC:23294 protein_coding YES CCDS31261.1 ENSP00000359674 Q5T681 UPI000046FEE3 NM_001009997.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23008:SF0,hmmpanther:PTHR23008 HIGH deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 97590090 97590090 G - 1 0 1 0 1 0 0 0 0 1767 1348 47 0 0 C10orf62 10 97590090 Frame_Shift_Del DEL G C3N-00175_T 880147 97590090 36207332 796 10388 ABCC2 0 . GRCh38 10 99811599 99811599 + Missense_Mutation SNP G G T rs200976632 C3N-00175_T C3N-00175_N G G c.1964G>T p.Arg655Leu p.R655L ENST00000370449 15/32 347 271 76 412 411 1 strelka-varscan-mutect ABCC2,missense_variant,p.Arg655Leu,ENST00000370449,NM_000392.4; T ENST00000370449 Transcript missense_variant 2077/5312 1964/4638 655/1545 R/L cGa/cTa rs200976632 1 1 ABCC2 HGNC HGNC:53 protein_coding YES CCDS7484.1 ENSP00000359478 Q92887 UPI000013D6CA NM_000392.4 deleterious(0.04) 15/32 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00957 MODERATE 1 SNV 1 1 PASS rs200976632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 99811599 99811599 G T 1 0 0 0 0 1 0 0 0 57 1072 37 1 1 ABCC2 10 99811599 Missense_Mutation SNP G C3N-00175_T 2221509 99811599 33985823 797 10389 PDZD7 0 . GRCh38 10 101023987 101023987 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.308G>T p.Gly103Val p.G103V ENST00000619208 3/17 323 251 72 505 505 0 strelka-varscan-mutect PDZD7,missense_variant,p.Gly103Val,ENST00000619208,NM_001195263.1;PDZD7,missense_variant,p.Gly103Val,ENST00000370215,NM_024895.4;PDZD7,missense_variant,p.Gly103Val,ENST00000470414,;PDZD7,missense_variant,p.Gly103Val,ENST00000474125,;PDZD7,non_coding_transcript_exon_variant,,ENST00000476306,; A ENST00000619208 Transcript missense_variant 558/4135 308/3102 103/1033 G/V gGg/gTg 1 -1 PDZD7 HGNC HGNC:26257 protein_coding YES CCDS73182.1 ENSP00000480489 Q9H5P4 UPI0001D15DE5 NM_001195263.1 deleterious(0) 3/17 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF29,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 101023987 101023987 C A 1 0 0 0 0 1 0 0 0 11792 623 22 2 2 PDZD7 10 101023987 Missense_Mutation SNP C C3N-00175_T 1212388 101023987 32773435 798 10390 WBP1L 0 . GRCh38 10 102813330 102813330 + Nonstop_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.1091A>G p.Ter364TrpextTer24 p.*364Wext*24 ENST00000448841 4/4 55 48 7 75 75 0 strelka-varscan-mutect WBP1L,stop_lost,p.Ter343TrpextTer24,ENST00000369889,NM_017787.4;WBP1L,stop_lost,p.Ter364TrpextTer24,ENST00000448841,NM_001083913.1; G ENST00000448841 Transcript stop_lost 1175/4085 1091/1092 364/363 */W tAg/tGg 1 1 WBP1L HGNC HGNC:23510 protein_coding YES CCDS44473.1 ENSP00000414721 Q9NX94 UPI0000EE3B72 NM_001083913.1 4/4 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -16.88695 1 1 1 1 0 G 4 3 39 102813330 102813330 A G 1 0 0 0 0 0 0 0 0 17819 433 15 5 5 WBP1L 10 102813330 Nonstop_Mutation SNP A C3N-00175_T 1789343 102813330 30984092 799 10391 CFAP58 0 . GRCh38 10 104362088 104362088 + Silent SNP G G T rs535940421 C3N-00175_T C3N-00175_N G G c.357G>T p.= p.T119T ENST00000369704 3/18 110 84 26 159 159 0 strelka-varscan-mutect CFAP58,synonymous_variant,p.=,ENST00000369704,NM_001008723.1; T ENST00000369704 Transcript synonymous_variant 491/3313 357/2619 119/872 T acG/acT rs535940421 1 1 CFAP58 HGNC HGNC:26676 protein_coding YES CCDS31282.1 ENSP00000358718 Q5T655 UPI0000160405 NM_001008723.1 3/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF31 LOW 1 SNV 1 1 PASS rs535940421 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 104362088 104362088 G T 1 0 0 0 0 0 0 0 1 3027 1045 37 1 1 CFAP58 10 104362088 Silent SNP G C3N-00175_T 1548758 104362088 29435334 800 10392 ATRNL1 0 . GRCh38 10 115129433 115129433 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.727G>T p.Ala243Ser p.A243S ENST00000355044 5/29 188 159 29 217 216 1 strelka-varscan-mutect ATRNL1,missense_variant,p.Ala243Ser,ENST00000355044,NM_207303.4;ATRNL1,missense_variant,p.Ala243Ser,ENST00000609571,NM_001276282.3;ATRNL1,missense_variant,p.Ala243Ser,ENST00000527407,;ATRNL1,missense_variant,p.Ala176Ser,ENST00000526946,;ATRNL1,3_prime_UTR_variant,,ENST00000616894,; T ENST00000355044 Transcript missense_variant 853/8479 727/4140 243/1379 A/S Gct/Tct 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 tolerated(0.1) 5/29 PROSITE_profiles:PS50026,hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,PROSITE_patterns:PS00022,Gene3D:2gy5A03,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 115129433 115129433 G T 1 0 0 0 0 1 0 0 0 1360 971 34 2 2 ATRNL1 10 115129433 Missense_Mutation SNP G C3N-00175_T 10767345 115129433 18667989 801 10393 SLC18A2 0 . GRCh38 10 117255649 117255649 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.887T>A p.Ile296Asn p.I296N ENST00000298472 9/16 79 67 12 112 112 0 strelka-varscan-mutect SLC18A2,missense_variant,p.Ile296Asn,ENST00000298472,NM_003054.4;SLC18A2,non_coding_transcript_exon_variant,,ENST00000497497,; A ENST00000298472 Transcript missense_variant 1030/3852 887/1545 296/514 I/N aTt/aAt 1 1 SLC18A2 HGNC HGNC:10935 protein_coding YES CCDS7599.1 ENSP00000298472 Q05940 UPI00001389DE NM_003054.4 deleterious(0) 9/16 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF8,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999981 1 1 1 0 A 3 1 39 117255649 117255649 T A 1 0 0 0 0 1 0 0 0 14691 1493 52 4 4 SLC18A2 10 117255649 Missense_Mutation SNP T C3N-00175_T 2126216 117255649 16541773 802 10394 PLPP4 0 . GRCh38 10 120521039 120521039 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.389G>T p.Gly130Val p.G130V ENST00000398250 5/7 158 124 34 191 190 1 strelka-varscan-mutect PLPP4,missense_variant,p.Gly130Val,ENST00000398250,NM_001030059.1;PLPP4,missense_variant,p.Gly120Val,ENST00000369073,;PLPP4,missense_variant,p.Gly130Val,ENST00000427079,; T ENST00000398250 Transcript missense_variant 741/1521 389/816 130/271 G/V gGt/gTt 1 1 PLPP4 HGNC HGNC:23531 protein_coding YES CCDS41573.1 ENSP00000381302 Q5VZY2 UPI00001619F5 NM_001030059.1 deleterious(0) 5/7 hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF90,Pfam_domain:PF01569,Gene3D:1.20.144.10,SMART_domains:SM00014,Superfamily_domains:SSF48317 MODERATE 1 SNV 1 1 PASS rs1303568016 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 120521039 120521039 G T 1 0 0 0 0 1 0 0 0 12205 1261 44 2 2 PLPP4 10 120521039 Missense_Mutation SNP G C3N-00175_T 3265390 120521039 13276383 803 10395 TEX36 0 . GRCh38 10 125682946 125682946 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.44G>A p.Gly15Glu p.G15E ENST00000368821 1/4 216 186 30 251 251 0 strelka-varscan-mutect TEX36,missense_variant,p.Gly15Glu,ENST00000368821,NM_001128202.1;TEX36,missense_variant,p.Gly15Glu,ENST00000532135,NM_001318133.1;TEX36,missense_variant,p.Gly15Glu,ENST00000526819,;RP11-383C5.3,upstream_gene_variant,,ENST00000415305,;RP11-383C5.3,upstream_gene_variant,,ENST00000596068,;RP11-383C5.3,upstream_gene_variant,,ENST00000449693,;RP11-383C5.3,upstream_gene_variant,,ENST00000607914,; T ENST00000368821 Transcript missense_variant 199/922 44/561 15/186 G/E gGg/gAg 1 -1 TEX36 HGNC HGNC:31653 protein_coding YES CCDS44493.1 ENSP00000357811 Q5VZQ5 UPI00001D808E NM_001128202.1 deleterious(0.03) 1/4 Pfam_domain:PF15115,hmmpanther:PTHR35440,hmmpanther:PTHR35440:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 125682946 125682946 C T 1 0 0 0 0 1 0 0 0 16212 623 22 3 3 TEX36 10 125682946 Missense_Mutation SNP C C3N-00175_T 5161907 125682946 8114476 804 10396 MKI67 0 . GRCh38 10 128104695 128104695 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.7145C>T p.Ser2382Leu p.S2382L ENST00000368654 13/15 192 160 32 223 223 0 strelka-varscan-mutect MKI67,missense_variant,p.Ser2382Leu,ENST00000368654,NM_002417.4;MKI67,missense_variant,p.Ser2022Leu,ENST00000368653,NM_001145966.1;MKI67,upstream_gene_variant,,ENST00000464771,; A ENST00000368654 Transcript missense_variant 7521/12678 7145/9771 2382/3256 S/L tCa/tTa 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 tolerated(0.11) 13/15 Pfam_domain:PF08065,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM01295 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 128104695 128104695 G A 1 0 0 0 0 1 0 0 0 9566 1294 45 3 3 MKI67 10 128104695 Missense_Mutation SNP G C3N-00175_T 2421749 128104695 5692727 805 10397 ZNF511 0 . GRCh38 10 133309785 133309785 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.237G>T p.= p.A79A ENST00000361518 3/6 195 171 24 283 283 0 strelka-varscan-mutect ZNF511,synonymous_variant,p.=,ENST00000359035,;ZNF511,synonymous_variant,p.=,ENST00000361518,NM_145806.3;ZNF511-PRAP1,synonymous_variant,p.=,ENST00000368554,;TUBGCP2,upstream_gene_variant,,ENST00000543663,NM_001256617.1;TUBGCP2,upstream_gene_variant,,ENST00000368563,NM_006659.3;TUBGCP2,upstream_gene_variant,,ENST00000417178,NM_001256618.1;ZNF511,intron_variant,,ENST00000463816,;TUBGCP2,upstream_gene_variant,,ENST00000470829,;ZNF511,non_coding_transcript_exon_variant,,ENST00000482153,;TUBGCP2,intron_variant,,ENST00000482278,;TUBGCP2,upstream_gene_variant,,ENST00000480198,;TUBGCP2,upstream_gene_variant,,ENST00000487796,; T ENST00000361518 Transcript synonymous_variant 706/1520 237/759 79/252 A gcG/gcT COSM1179154,COSM1492162 1 1 ZNF511 HGNC HGNC:28445 protein_coding YES CCDS7677.1 ENSP00000355251 Q8NB15 UPI000006FF8A NM_145806.3 3/6 hmmpanther:PTHR21354,hmmpanther:PTHR21354:SF0 1,1 LOW 1 SNV 1 1,1 1 PASS rs1220991097 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 133309785 133309785 G T 1 0 0 0 0 0 0 0 1 18527 1132 40 1 1 ZNF511 10 133309785 Silent SNP G C3N-00175_T 5205090 133309785 487637 806 10398 RNH1 0 . GRCh38 11 498887 498887 + Missense_Mutation SNP C C G rs746243454 C3N-00175_T C3N-00175_N C C c.661G>C p.Gly221Arg p.G221R ENST00000534797 5/9 84 73 11 199 199 0 strelka-varscan-mutect RNH1,missense_variant,p.Gly221Arg,ENST00000534797,;RNH1,missense_variant,p.Gly221Arg,ENST00000397615,NM_203383.1,NM_002939.3;RNH1,missense_variant,p.Gly221Arg,ENST00000354420,NM_203387.2;RNH1,missense_variant,p.Gly221Arg,ENST00000397614,NM_203385.1;RNH1,missense_variant,p.Gly221Arg,ENST00000533410,NM_203386.2;RNH1,missense_variant,p.Gly221Arg,ENST00000356187,NM_203389.2;RNH1,missense_variant,p.Gly221Arg,ENST00000438658,NM_203384.1;RNH1,missense_variant,p.Gly221Arg,ENST00000397604,NM_203388.2;RNH1,missense_variant,p.Gly15Arg,ENST00000529768,;RNH1,downstream_gene_variant,,ENST00000527485,;RNH1,downstream_gene_variant,,ENST00000529306,;RNH1,downstream_gene_variant,,ENST00000529368,;RNH1,downstream_gene_variant,,ENST00000531149,;RNH1,downstream_gene_variant,,ENST00000532055,;RNH1,downstream_gene_variant,,ENST00000531540,;RNH1,downstream_gene_variant,,ENST00000533592,;RNH1,downstream_gene_variant,,ENST00000526295,;RNH1,3_prime_UTR_variant,,ENST00000525701,;RNH1,3_prime_UTR_variant,,ENST00000529115,;RNH1,non_coding_transcript_exon_variant,,ENST00000525522,;RNH1,intron_variant,,ENST00000524464,;RNH1,downstream_gene_variant,,ENST00000528713,;RNH1,downstream_gene_variant,,ENST00000524780,;RNH1,downstream_gene_variant,,ENST00000531223,; G ENST00000534797 Transcript missense_variant 2069/2973 661/1386 221/461 G/R Ggc/Cgc rs746243454 1 -1 RNH1 HGNC HGNC:10074 protein_coding YES CCDS7697.1 ENSP00000433999 P13489 A0A140VJT8 UPI0000000DE4 tolerated(0.23) 5/9 hmmpanther:PTHR24112:SF30,hmmpanther:PTHR24112,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs746243454 . 0 208 0 2 0 0 0 0 -18.25654 0.9999999 1 1 1 0 G 3 3 39 498887 498887 C G 1 0 0 0 0 1 0 0 0 13684 652 23 4 4 RNH1 11 498887 Missense_Mutation SNP C C3N-00175_T 498887 134587735 807 10399 MUC6 0 . GRCh38 11 1027408 1027408 + Frame_Shift_Del DEL G G - rs375495192 C3N-00175_T C3N-00175_N G G c.2091delC p.Val698TrpfsTer12 p.V698Wfs*12 ENST00000421673 17/33 436 378 58 669 669 0 sindel-varindel-pindel MUC6,frameshift_variant,p.Val698TrpfsTer12,ENST00000421673,NM_005961.2;MUC6,downstream_gene_variant,,ENST00000525923,; - ENST00000421673 Transcript frameshift_variant 2142/8006 2091/7320 697/2439 P/X ccC/cc rs375495192 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 17/33 hmmpanther:PTHR11339:SF264,hmmpanther:PTHR11339,Gene3D:2.10.25.10,Pfam_domain:PF01826,Superfamily_domains:SSF57567 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 1027408 1027408 G - 1 0 1 0 1 0 0 0 0 9980 1103 39 0 0 MUC6 11 1027408 Frame_Shift_Del DEL G C3N-00175_T 528521 1027408 134059214 808 10400 C11orf21 0 . GRCh38 11 2299533 2299533 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.460G>T p.Asp154Tyr p.D154Y ENST00000456145 4/5 308 240 68 445 444 1 strelka-varscan-mutect C11orf21,missense_variant,p.Asp108Tyr,ENST00000381153,;C11orf21,missense_variant,p.Asp154Tyr,ENST00000456145,NM_001142946.1;TSPAN32,upstream_gene_variant,,ENST00000182290,NM_139022.2;TSPAN32,upstream_gene_variant,,ENST00000612299,;TSPAN32,upstream_gene_variant,,ENST00000451520,;TSPAN32,upstream_gene_variant,,ENST00000381121,;TSPAN32,upstream_gene_variant,,ENST00000381117,;C11orf21,non_coding_transcript_exon_variant,,ENST00000470369,;C11orf21,non_coding_transcript_exon_variant,,ENST00000495467,;TSPAN32,upstream_gene_variant,,ENST00000483227,;TSPAN32,upstream_gene_variant,,ENST00000479508,;TSPAN32,upstream_gene_variant,,ENST00000461200,;TSPAN32,upstream_gene_variant,,ENST00000493924,;TSPAN32,upstream_gene_variant,,ENST00000446063,;TSPAN32,upstream_gene_variant,,ENST00000339046,;TSPAN32,upstream_gene_variant,,ENST00000498313,;TSPAN32,upstream_gene_variant,,ENST00000437313,;TSPAN32,upstream_gene_variant,,ENST00000484104,;TSPAN32,upstream_gene_variant,,ENST00000493948,; A ENST00000456145 Transcript missense_variant 512/1366 460/537 154/178 D/Y Gac/Tac 1 -1 C11orf21 HGNC HGNC:13231 protein_coding YES CCDS44518.1 ENSP00000406541 E9PAM5 UPI0000DD806C NM_001142946.1 deleterious_low_confidence(0.02) 4/5 Pfam_domain:PF15399 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 2299533 2299533 C A 1 0 0 0 0 1 0 0 0 1778 855 30 2 2 C11orf21 11 2299533 Missense_Mutation SNP C C3N-00175_T 1272125 2299533 132787089 809 10401 TRPM5 0 . GRCh38 11 2422174 2422174 + Missense_Mutation SNP G G A rs774051811 C3N-00175_T C3N-00175_N G G c.265C>T p.Arg89Cys p.R89C ENST00000155858 2/24 74 63 11 119 119 0 strelka-varscan-mutect TRPM5,missense_variant,p.Arg89Cys,ENST00000155858,NM_014555.3;TRPM5,missense_variant,p.Arg81Cys,ENST00000533881,;TRPM5,missense_variant,p.Arg89Cys,ENST00000533060,;TRPM5,missense_variant,p.Arg89Cys,ENST00000528453,; A ENST00000155858 Transcript missense_variant 274/3929 265/3498 89/1165 R/C Cgc/Tgc rs774051811 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 deleterious(0) 2/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 MODERATE 1 SNV 1 1 PASS rs774051811 . 0 202 8 0 0 0 0 0 -19.99996 0.9999981 1 1 1 0 A 3 1 39 2422174 2422174 G A 1 0 0 0 0 1 0 0 0 17095 1087 38 1 1 TRPM5 11 2422174 Missense_Mutation SNP G C3N-00175_T 122641 2422174 132664448 810 10402 SLC22A18AS 0 . GRCh38 11 2888582 2888582 + Frame_Shift_Del DEL C C - rs761662285 C3N-00175_T C3N-00175_N C C c.360delG p.Ser121LeufsTer47 p.S121Lfs*47 ENST00000625099 4/4 126 99 27 242 242 0 sindel-varindel-pindel SLC22A18AS,frameshift_variant,p.Ser121LeufsTer47,ENST00000625099,NM_007105.3;SLC22A18AS,frameshift_variant,p.Ser18LeufsTer47,ENST00000455942,NM_001302862.1;SLC22A18AS,frameshift_variant,p.Ser18LeufsTer47,ENST00000526203,;CDKN1C,upstream_gene_variant,,ENST00000414822,NM_000076.2;CDKN1C,upstream_gene_variant,,ENST00000440480,NM_001122630.1,NM_001122631.1;CDKN1C,upstream_gene_variant,,ENST00000430149,;CDKN1C,upstream_gene_variant,,ENST00000380725,;CDKN1C,upstream_gene_variant,,ENST00000471157,; - ENST00000625099 Transcript frameshift_variant 857/1659 360/762 120/253 G/X ggG/gg rs761662285 1 -1 SLC22A18AS HGNC HGNC:10965 protein_coding YES ENSP00000487968 Q8N1D0 UPI000013FBB8 NM_007105.3 4/4 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 2888582 2888582 C - 1 0 1 0 1 0 0 0 0 14715 494 18 0 0 SLC22A18AS 11 2888582 Frame_Shift_Del DEL C C3N-00175_T 466408 2888582 132198040 811 10403 MRGPRG 0 . GRCh38 11 3218205 3218205 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.609G>T p.= p.A203A ENST00000332314 1/1 47 41 6 89 89 0 strelka-varscan-mutect MRGPRG,synonymous_variant,p.=,ENST00000332314,NM_001164377.1;MRGPRG-AS1,upstream_gene_variant,,ENST00000420873,;MRGPRG-AS1,upstream_gene_variant,,ENST00000434798,;MRGPRG-AS1,upstream_gene_variant,,ENST00000531711,; A ENST00000332314 Transcript synonymous_variant 609/870 609/870 203/289 A gcG/gcT 1 -1 MRGPRG HGNC HGNC:24829 protein_coding YES CCDS44520.1 ENSP00000330612 Q86SM5 UPI0000047153 NM_001164377.1 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF32,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR02108 LOW SNV 1 PASS rs1407431621 . 0 202 8 0 0 0 0 0 -14.56766 0.9999973 1 1 1 0 A 2 1 39 3218205 3218205 C A 1 0 0 0 0 0 0 0 1 9732 755 27 1 1 MRGPRG 11 3218205 Silent SNP C C3N-00175_T 329623 3218205 131868417 812 10404 CHRNA10 0 . GRCh38 11 3667336 3667336 + Nonsense_Mutation SNP G G C rs750393817 C3N-00175_T C3N-00175_N G G c.791C>G p.Ser264Ter p.S264* ENST00000250699 4/5 280 211 69 296 296 0 strelka-varscan-mutect CHRNA10,stop_gained,p.Ser264Ter,ENST00000250699,NM_020402.3;CHRNA10,missense_variant,p.Gln82Glu,ENST00000534359,NM_001303034.1,NM_001303035.1;ART1,downstream_gene_variant,,ENST00000250693,NM_004314.2;NUP98,downstream_gene_variant,,ENST00000533346,;Y_RNA,upstream_gene_variant,,ENST00000364409,;Y_RNA,upstream_gene_variant,,ENST00000363331,;CHRNA10,downstream_gene_variant,,ENST00000493827,;CHRNA10,3_prime_UTR_variant,,ENST00000526599,; C ENST00000250699 Transcript stop_gained 863/1945 791/1353 264/450 S/* tCa/tGa rs750393817 1 -1 CHRNA10 HGNC HGNC:13800 protein_coding YES CCDS7745.1 ENSP00000250699 Q9GZZ6 UPI0000038CF1 NM_020402.3 4/5 hmmpanther:PTHR18945:SF566,hmmpanther:PTHR18945,Gene3D:1.20.120.370,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112 HIGH 1 SNV 1 1 PASS rs750393817 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 39 3667336 3667336 G C 1 0 0 0 0 0 1 0 0 3142 1303 45 4 4 CHRNA10 11 3667336 Nonsense_Mutation SNP G C3N-00175_T 449131 3667336 131419286 813 10405 OR52J3 0 . GRCh38 11 5047448 5047448 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.923T>A p.Phe308Tyr p.F308Y ENST00000380370 1/1 35 23 12 44 44 0 strelka-varscan-mutect OR52J3,missense_variant,p.Phe308Tyr,ENST00000380370,NM_001001916.2; A ENST00000380370 Transcript missense_variant 923/936 923/936 308/311 F/Y tTt/tAt 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 deleterious(0) 1/1 hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 197 12 0 0 0 0 0 -20 0.9999827 1 1 1 0 A 3 1 39 5047448 5047448 T A 1 0 0 0 0 1 0 0 0 11195 1841 64 4 4 OR52J3 11 5047448 Missense_Mutation SNP T C3N-00175_T 1380112 5047448 130039174 814 10406 OR51V1 0 . GRCh38 11 5200070 5200070 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.631C>A p.Leu211Met p.L211M ENST00000321255 1/1 110 93 17 189 187 2 strelka-varscan-mutect OR51V1,missense_variant,p.Leu211Met,ENST00000321255,NM_001004760.2;AC104389.16,upstream_gene_variant,,ENST00000418080,; T ENST00000321255 Transcript missense_variant 631/966 631/966 211/321 L/M Ctg/Atg COSM4710007 1 -1 OR51V1 HGNC HGNC:19597 protein_coding YES CCDS31375.1 ENSP00000321729 Q9H2C8 UPI0000140ADA NM_001004760.2 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF67,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 5200070 5200070 G T 1 0 0 0 0 1 0 0 0 11181 962 34 2 2 OR51V1 11 5200070 Missense_Mutation SNP G C3N-00175_T 152622 5200070 129886552 815 10407 OR51V1 0 . GRCh38 11 5200477 5200477 + Missense_Mutation SNP A A T rs370530643 C3N-00175_T C3N-00175_N A A c.224T>A p.Leu75Gln p.L75Q ENST00000321255 1/1 78 68 10 106 106 0 strelka-varscan-mutect OR51V1,missense_variant,p.Leu75Gln,ENST00000321255,NM_001004760.2;AC104389.16,upstream_gene_variant,,ENST00000418080,; T ENST00000321255 Transcript missense_variant 224/966 224/966 75/321 L/Q cTg/cAg rs370530643 1 -1 OR51V1 HGNC HGNC:19597 protein_coding YES CCDS31375.1 ENSP00000321729 Q9H2C8 UPI0000140ADA NM_001004760.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF67,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs370530643 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 5200477 5200477 A T 1 0 0 0 0 1 0 0 0 11181 188 7 4 4 OR51V1 11 5200477 Missense_Mutation SNP A C3N-00175_T 407 5200477 129886145 816 10408 HBD 0 . GRCh38 11 5233080 5233080 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.328G>T p.Val110Leu p.V110L ENST00000380299 3/3 384 321 63 476 476 0 strelka-varscan-mutect HBD,missense_variant,p.Val110Leu,ENST00000380299,NM_000519.3;HBD,missense_variant,p.Met35Ile,ENST00000417377,;HBD,intron_variant,,ENST00000292901,;HBD,downstream_gene_variant,,ENST00000429817,;HBB,upstream_gene_variant,,ENST00000380315,; A ENST00000380299 Transcript missense_variant 543/785 328/444 110/147 V/L Gtg/Ttg 1 -1 HBD HGNC HGNC:4829 protein_coding YES CCDS31376.1 ENSP00000369654 P02042 A0N071 UPI0000161DC2 NM_000519.3 tolerated(0.11) 3/3 PROSITE_profiles:PS01033,hmmpanther:PTHR11442:SF50,hmmpanther:PTHR11442,Pfam_domain:PF00042,Gene3D:1.10.490.10,Superfamily_domains:SSF46458 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 5233080 5233080 C A 1 0 0 0 0 1 0 0 0 6865 478 17 2 2 HBD 11 5233080 Missense_Mutation SNP C C3N-00175_T 32603 5233080 129853542 817 10409 OR52E6 0 . GRCh38 11 5841537 5841537 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.361G>T p.Ala121Ser p.A121S ENST00000329322 1/1 88 65 23 112 112 0 strelka-varscan-mutect OR52E6,missense_variant,p.Ala121Ser,ENST00000329322,NM_001005167.1;OR52E6,missense_variant,p.Ala125Ser,ENST00000379946,;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000329322 Transcript missense_variant 361/970 361/942 121/313 A/S Gcc/Tcc 1 -1 OR52E6 HGNC HGNC:15215 protein_coding YES CCDS53597.1 ENSP00000328878 Q96RD3 A0A126GVK5 UPI00000015AE NM_001005167.1 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF175,hmmpanther:PTHR26450,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 5841537 5841537 C A 1 0 0 0 0 1 0 0 0 11190 739 26 2 2 OR52E6 11 5841537 Missense_Mutation SNP C C3N-00175_T 608457 5841537 129245085 818 10410 SMPD1 0 . GRCh38 11 6394325 6394325 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1614C>T p.= p.L538L ENST00000342245 6/6 117 105 12 151 151 0 strelka-varscan-mutect SMPD1,synonymous_variant,p.=,ENST00000342245,NM_001318087.1,NM_000543.4;SMPD1,synonymous_variant,p.=,ENST00000527275,NM_001007593.2;SMPD1,synonymous_variant,p.=,ENST00000526280,;APBB1,downstream_gene_variant,,ENST00000389906,;APBB1,downstream_gene_variant,,ENST00000609360,NM_001164.4;APBB1,downstream_gene_variant,,ENST00000299402,;APBB1,downstream_gene_variant,,ENST00000311051,NM_145689.2;APBB1,downstream_gene_variant,,ENST00000610474,;APBB1,downstream_gene_variant,,ENST00000608394,NM_001257321.2;APBB1,downstream_gene_variant,,ENST00000618005,;APBB1,downstream_gene_variant,,ENST00000608704,NM_001257320.2;APBB1,downstream_gene_variant,,ENST00000608645,NM_001257326.2;APBB1,downstream_gene_variant,,ENST00000608655,NM_001257319.2;APBB1,downstream_gene_variant,,ENST00000621678,;APBB1,downstream_gene_variant,,ENST00000530885,NM_001257323.2;APBB1,downstream_gene_variant,,ENST00000609331,NM_001257325.2;APBB1,downstream_gene_variant,,ENST00000529519,;SMPD1,downstream_gene_variant,,ENST00000530395,;APBB1,downstream_gene_variant,,ENST00000526240,;SMPD1,downstream_gene_variant,,ENST00000533196,;SMPD1,3_prime_UTR_variant,,ENST00000534405,NM_001318088.1;SMPD1,3_prime_UTR_variant,,ENST00000533123,;SMPD1,3_prime_UTR_variant,,ENST00000531303,;SMPD1,non_coding_transcript_exon_variant,,ENST00000531336,;APBB1,downstream_gene_variant,,ENST00000608435,;APBB1,downstream_gene_variant,,ENST00000524626,;SMPD1,downstream_gene_variant,,ENST00000532367,; T ENST00000342245 Transcript synonymous_variant 1782/2452 1614/1896 538/631 L ctC/ctT 1 1 SMPD1 HGNC HGNC:11120 protein_coding YES CCDS44531.1 ENSP00000340409 P17405 UPI000013E592 NM_001318087.1,NM_000543.4 6/6 PIRSF_domain:PIRSF000948,hmmpanther:PTHR10340,hmmpanther:PTHR10340:SF34 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 6394325 6394325 C T 1 0 0 0 0 0 0 0 1 15125 900 32 3 3 SMPD1 11 6394325 Silent SNP C C3N-00175_T 552788 6394325 128692297 819 10411 TRIM66 0 . GRCh38 11 8621223 8621223 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2913G>A p.= p.V971V ENST00000402157 17/22 259 202 57 314 314 0 strelka-varscan-mutect TRIM66,synonymous_variant,p.=,ENST00000402157,;TRIM66,synonymous_variant,p.=,ENST00000299550,NM_014818.1;TRIM66,synonymous_variant,p.=,ENST00000530502,;TRIM66,non_coding_transcript_exon_variant,,ENST00000481014,;TRIM66,upstream_gene_variant,,ENST00000529211,;TRIM66,upstream_gene_variant,,ENST00000525788,; T ENST00000402157 Transcript synonymous_variant 3354/10086 2913/3738 971/1245 V gtG/gtA 1 -1 TRIM66 HGNC HGNC:29005 protein_coding YES ENSP00000384876 B5MCJ9 UPI00016113E8 17/22 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 8621223 8621223 C T 1 0 0 0 0 0 0 0 1 17035 581 21 3 3 TRIM66 11 8621223 Silent SNP C C3N-00175_T 2226898 8621223 126465399 820 10412 NRIP3 0 . GRCh38 11 9003839 9003839 + Missense_Mutation SNP C C A rs779140807 C3N-00175_T C3N-00175_N C C c.97G>T p.Val33Leu p.V33L ENST00000309166 1/7 119 90 29 177 177 0 strelka-varscan-mutect NRIP3,missense_variant,p.Val33Leu,ENST00000309166,NM_020645.2;NRIP3,missense_variant,p.Val33Leu,ENST00000531090,;NRIP3,missense_variant,p.Val33Leu,ENST00000525100,;RP11-467K18.2,upstream_gene_variant,,ENST00000531592,; A ENST00000309166 Transcript missense_variant 211/3809 97/726 33/241 V/L Gtg/Ttg rs779140807 1 -1 NRIP3 HGNC HGNC:1167 protein_coding YES CCDS31422.1 ENSP00000310205 Q9NQ35 UPI000004B7A9 NM_020645.2 deleterious(0.03) 1/7 hmmpanther:PTHR12917:SF2,hmmpanther:PTHR12917 MODERATE 1 SNV 1 1 PASS rs779140807 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 9003839 9003839 C A 1 0 0 0 0 1 0 0 0 10712 507 18 2 2 NRIP3 11 9003839 Missense_Mutation SNP C C3N-00175_T 382616 9003839 126082783 821 10413 DKK3 0 . GRCh38 11 12008474 12008474 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.109delG p.Ala37LeufsTer21 p.A37Lfs*21 ENST00000396505 2/8 156 146 10 198 198 0 sindel-varindel-pindel DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000396505,NM_015881.5;DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000326932,NM_001018057.1,NM_013253.4;DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000525493,;DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000533813,;DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000534511,;DKK3,frameshift_variant,p.Ala37LeufsTer21,ENST00000529338,;DKK3,non_coding_transcript_exon_variant,,ENST00000527132,;DKK3,non_coding_transcript_exon_variant,,ENST00000526218,;DKK3,non_coding_transcript_exon_variant,,ENST00000533900,;DKK3,non_coding_transcript_exon_variant,,ENST00000530694,;DKK3,intron_variant,,ENST00000532873,;DKK3,non_coding_transcript_exon_variant,,ENST00000534479,; - ENST00000396505 Transcript frameshift_variant 348/2650 109/1053 37/350 A/X Gct/ct 1 -1 DKK3 HGNC HGNC:2893 protein_coding YES CCDS7808.1 ENSP00000379762 Q9UBP4 UPI00001694CA NM_015881.5 2/8 HIGH 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.54913 0.9999996 1 1 1 0 - 7 5 39 12008474 12008474 C - 1 0 1 0 1 0 0 0 0 4352 739 26 0 0 DKK3 11 12008474 Frame_Shift_Del DEL C C3N-00175_T 3004635 12008474 123078148 822 10414 COPB1 0 . GRCh38 11 14480853 14480853 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.1118A>G p.His373Arg p.H373R ENST00000249923 10/22 151 128 23 228 228 0 strelka-varscan-mutect COPB1,missense_variant,p.His373Arg,ENST00000249923,NM_016451.4;COPB1,missense_variant,p.His373Arg,ENST00000439561,NM_001144061.1,NM_001144062.1;COPB1,missense_variant,p.His373Arg,ENST00000534234,;RNU7-49P,downstream_gene_variant,,ENST00000516182,;COPB1,upstream_gene_variant,,ENST00000526191,; C ENST00000249923 Transcript missense_variant 1419/3481 1118/2862 373/953 H/R cAt/cGt 1 -1 COPB1 HGNC HGNC:2231 protein_coding YES CCDS7815.1 ENSP00000249923 P53618 UPI000000103D NM_016451.4 tolerated(0.41) 10/22 hmmpanther:PTHR10635,Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF005727,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 14480853 14480853 T C 1 0 0 0 0 1 0 0 0 3520 1464 51 5 5 COPB1 11 14480853 Missense_Mutation SNP T C3N-00175_T 2472379 14480853 120605769 823 10415 LUZP2 0 . GRCh38 11 25078572 25078572 + Missense_Mutation SNP T T A C3N-00175_T C3N-00175_N T T c.955T>A p.Cys319Ser p.C319S ENST00000336930 12/12 123 94 29 187 187 0 strelka-varscan-mutect LUZP2,missense_variant,p.Cys233Ser,ENST00000533227,NM_001252008.1;LUZP2,missense_variant,p.Cys233Ser,ENST00000620308,;LUZP2,missense_variant,p.Cys319Ser,ENST00000336930,NM_001252010.1,NM_001009909.3; A ENST00000336930 Transcript missense_variant 1021/3553 955/1041 319/346 C/S Tgc/Agc COSM3446430 1 1 LUZP2 HGNC HGNC:23206 protein_coding YES CCDS31446.1 ENSP00000336817 Q86TE4 UPI000019816C NM_001252010.1,NM_001009909.3 tolerated_low_confidence(0.09) 12/12 hmmpanther:PTHR22414 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 25078572 25078572 T A 1 0 0 0 0 1 0 0 0 8996 1812 63 4 4 LUZP2 11 25078572 Missense_Mutation SNP T C3N-00175_T 10597719 25078572 110008050 824 10416 MPPED2 0 . GRCh38 11 30536036 30536036 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.268C>T p.= p.L90L ENST00000358117 2/6 82 63 19 68 67 1 strelka-varscan-mutect MPPED2,synonymous_variant,p.=,ENST00000448418,NM_001145399.1;MPPED2,synonymous_variant,p.=,ENST00000358117,NM_001584.2;MPPED2,downstream_gene_variant,,ENST00000528686,;MPPED2,non_coding_transcript_exon_variant,,ENST00000525519,;MPPED2,synonymous_variant,p.=,ENST00000526437,;MPPED2,non_coding_transcript_exon_variant,,ENST00000524636,; A ENST00000358117 Transcript synonymous_variant 391/2405 268/885 90/294 L Ctg/Ttg 1 -1 MPPED2 HGNC HGNC:1180 protein_coding YES CCDS7870.1 ENSP00000350833 Q15777 UPI0000124E87 NM_001584.2 2/6 Gene3D:3.60.21.10,Pfam_domain:PF00149,PIRSF_domain:PIRSF035808,hmmpanther:PTHR12905,hmmpanther:PTHR12905:SF12,Superfamily_domains:SSF56300 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 30536036 30536036 G A 1 0 0 0 0 0 0 0 1 9708 962 34 3 3 MPPED2 11 30536036 Silent SNP G C3N-00175_T 5457464 30536036 104550586 825 10417 NAT10 0 . GRCh38 11 34134554 34134554 + Missense_Mutation SNP G G T rs769422131 C3N-00175_T C3N-00175_N G G c.1879G>T p.Val627Phe p.V627F ENST00000257829 18/29 201 168 33 242 241 1 strelka-varscan-mutect NAT10,missense_variant,p.Val627Phe,ENST00000257829,NM_024662.2;NAT10,missense_variant,p.Val555Phe,ENST00000531159,NM_001144030.1;NAT10,missense_variant,p.Val474Phe,ENST00000615292,;NAT10,intron_variant,,ENST00000527971,;NAT10,upstream_gene_variant,,ENST00000530017,; T ENST00000257829 Transcript missense_variant 2085/4002 1879/3078 627/1025 V/F Gtt/Ttt rs769422131 1 1 NAT10 HGNC HGNC:29830 protein_coding YES CCDS7889.1 ENSP00000257829 Q9H0A0 UPI000013CF8E NM_024662.2 deleterious(0) 18/29 PROSITE_profiles:PS51186,hmmpanther:PTHR10925,Pfam_domain:PF13718,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS rs769422131 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 34134554 34134554 G T 1 0 0 0 0 1 0 0 0 10183 1145 40 1 1 NAT10 11 34134554 Missense_Mutation SNP G C3N-00175_T 3598518 34134554 100952068 826 10418 ELF5 0 . GRCh38 11 34493608 34493608 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.256T>A p.Cys86Ser p.C86S ENST00000312319 3/7 318 289 29 410 409 1 strelka-varscan-mutect ELF5,missense_variant,p.Cys86Ser,ENST00000312319,NM_198381.1;ELF5,missense_variant,p.Cys76Ser,ENST00000532417,;ELF5,missense_variant,p.Cys76Ser,ENST00000257832,NM_001422.3;ELF5,intron_variant,,ENST00000620316,NM_001243081.1;ELF5,intron_variant,,ENST00000429939,NM_001243080.1;ELF5,intron_variant,,ENST00000528709,; T ENST00000312319 Transcript missense_variant 486/2450 256/798 86/265 C/S Tgc/Agc 1 -1 ELF5 HGNC HGNC:3320 protein_coding YES CCDS7892.1 ENSP00000311010 Q9UKW6 UPI000006EFE4 NM_198381.1 tolerated(0.41) 3/7 PROSITE_profiles:PS51433,hmmpanther:PTHR11849:SF15,hmmpanther:PTHR11849,Pfam_domain:PF02198,Gene3D:1.10.150.50,SMART_domains:SM00251,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 34493608 34493608 A T 1 0 0 0 0 1 0 0 0 4890 130 5 4 4 ELF5 11 34493608 Missense_Mutation SNP A C3N-00175_T 359054 34493608 100593014 827 10419 CD44 0 . GRCh38 11 35211414 35211414 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1775G>C p.Gly592Ala p.G592A ENST00000428726 14/18 260 234 26 315 315 0 strelka-varscan-mutect CD44,missense_variant,p.Gly592Ala,ENST00000428726,NM_000610.3;CD44,missense_variant,p.Gly549Ala,ENST00000415148,NM_001001389.1;CD44,missense_variant,p.Gly343Ala,ENST00000433892,NM_001001390.1;CD44,missense_variant,p.Gly279Ala,ENST00000434472,NM_001202555.1;CD44,missense_variant,p.Gly226Ala,ENST00000526000,;CD44,intron_variant,,ENST00000263398,NM_001001391.1;CD44,intron_variant,,ENST00000442151,NM_001202557.1;CD44,intron_variant,,ENST00000352818,NM_001202556.1;CD44,intron_variant,,ENST00000526669,;CD44,intron_variant,,ENST00000279452,;CD44,intron_variant,,ENST00000278385,;CD44,intron_variant,,ENST00000525688,;CD44,intron_variant,,ENST00000278386,NM_001001392.1;CD44,downstream_gene_variant,,ENST00000531110,;CD44,downstream_gene_variant,,ENST00000525685,;CD44,downstream_gene_variant,,ENST00000528672,;CD44,downstream_gene_variant,,ENST00000531873,;CD44,downstream_gene_variant,,ENST00000533222,;CD44,downstream_gene_variant,,ENST00000526553,;CD44,downstream_gene_variant,,ENST00000527889,;RP1-68D18.4,intron_variant,,ENST00000528869,;RP1-68D18.2,upstream_gene_variant,,ENST00000510619,;CD44,downstream_gene_variant,,ENST00000528086,;CD44,non_coding_transcript_exon_variant,,ENST00000525293,;CD44,intron_variant,,ENST00000425428,;CD44,upstream_gene_variant,,ENST00000527326,;CD44,downstream_gene_variant,,ENST00000532339,; C ENST00000428726 Transcript missense_variant 1898/3046 1775/2229 592/742 G/A gGa/gCa 1 1 CD44 HGNC HGNC:1681 protein_coding YES CCDS7897.1 ENSP00000398632 P16070 UPI000013D3FE NM_000610.3 tolerated(0.4) 14/18 hmmpanther:PTHR10225,hmmpanther:PTHR10225:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 35211414 35211414 G C 1 0 0 0 0 1 0 0 0 2721 1174 41 4 4 CD44 11 35211414 Missense_Mutation SNP G C3N-00175_T 717806 35211414 99875208 828 10420 RAG2 0 . GRCh38 11 36592830 36592830 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.1339T>G p.Ser447Ala p.S447A ENST00000618712 3/3 370 277 93 457 454 3 strelka-varscan-mutect RAG2,missense_variant,p.Ser447Ala,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,missense_variant,p.Ser447Ala,ENST00000311485,NM_000536.3;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000529083,;RAG2,downstream_gene_variant,,ENST00000527033,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,intron_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; C ENST00000618712 Transcript missense_variant 1933/2818 1339/1584 447/527 S/A Tct/Gct 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 deleterious(0) 3/3 Pfam_domain:PF13341,hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0,Superfamily_domains:SSF57903 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 36592830 36592830 A C 1 0 0 0 0 1 0 0 0 13165 304 11 5 5 RAG2 11 36592830 Missense_Mutation SNP A C3N-00175_T 1381416 36592830 98493792 829 10421 LRRC4C 0 . GRCh38 11 40114972 40114972 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1321C>A p.Leu441Met p.L441M ENST00000278198 2/2 142 111 31 192 192 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Leu441Met,ENST00000278198,;LRRC4C,missense_variant,p.Leu441Met,ENST00000527150,;LRRC4C,missense_variant,p.Leu441Met,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Leu441Met,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Leu441Met,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript missense_variant 3285/4054 1321/1923 441/640 L/M Ctg/Atg 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious(0) 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 40114972 40114972 G T 1 0 0 0 0 1 0 0 0 8903 991 35 2 2 LRRC4C 11 40114972 Missense_Mutation SNP G C3N-00175_T 3522142 40114972 94971650 830 10422 CREB3L1 0 . GRCh38 11 46307898 46307898 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.414G>T p.= p.V138V ENST00000621158 3/12 161 136 25 166 166 0 strelka-varscan-mutect CREB3L1,synonymous_variant,p.=,ENST00000621158,NM_052854.3;CREB3L1,synonymous_variant,p.=,ENST00000534787,;CREB3L1,upstream_gene_variant,,ENST00000530518,;CREB3L1,upstream_gene_variant,,ENST00000527342,; T ENST00000621158 Transcript synonymous_variant 865/2687 414/1560 138/519 V gtG/gtT 1 1 CREB3L1 HGNC HGNC:18856 protein_coding YES CCDS53620.1 ENSP00000481956 Q96BA8 UPI000004ABFF NM_052854.3 3/12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 46307898 46307898 G T 1 0 0 0 0 0 0 0 1 3656 1335 47 2 2 CREB3L1 11 46307898 Silent SNP G C3N-00175_T 6192926 46307898 88778724 831 10423 MADD 0 . GRCh38 11 47282886 47282886 + Silent SNP C C T rs755965991 C3N-00175_T C3N-00175_N C C c.1779C>T p.= p.R593R ENST00000311027 10/36 199 182 17 267 267 0 strelka-varscan-mutect MADD,synonymous_variant,p.=,ENST00000342922,NM_130470.2;MADD,synonymous_variant,p.=,ENST00000311027,NM_003682.3;MADD,synonymous_variant,p.=,ENST00000395336,NM_130475.2;MADD,synonymous_variant,p.=,ENST00000349238,NM_130473.2;MADD,synonymous_variant,p.=,ENST00000402192,NM_130476.2;MADD,synonymous_variant,p.=,ENST00000407859,NM_130471.2;MADD,synonymous_variant,p.=,ENST00000402799,NM_130472.2,NM_001135943.1;MADD,synonymous_variant,p.=,ENST00000406482,NM_130474.2;MADD,synonymous_variant,p.=,ENST00000395344,NM_001135944.1;MADD,downstream_gene_variant,,ENST00000428807,;MADD,downstream_gene_variant,,ENST00000489415,;MADD,upstream_gene_variant,,ENST00000524686,;MADD,upstream_gene_variant,,ENST00000524530,; T ENST00000311027 Transcript synonymous_variant 1944/5990 1779/4944 593/1647 R cgC/cgT rs755965991,COSM4426176 1 1 MADD HGNC HGNC:6766 protein_coding YES CCDS7930.1 ENSP00000310933 Q8WXG6 UPI000013E874 NM_003682.3 10/36 hmmpanther:PTHR13008 0,1 LOW 1 SNV 1 0,1 1 PASS rs755965991 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 47282886 47282886 C T 1 0 0 0 0 0 0 0 1 9068 755 27 1 1 MADD 11 47282886 Silent SNP C C3N-00175_T 974988 47282886 87803736 832 10424 OR4X1 0 . GRCh38 11 48264456 48264456 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.596C>A p.Thr199Asn p.T199N ENST00000320048 1/1 228 169 59 235 235 0 strelka-varscan-mutect OR4X1,missense_variant,p.Thr199Asn,ENST00000320048,NM_001004726.1; A ENST00000320048 Transcript missense_variant 596/918 596/918 199/305 T/N aCc/aAc 1 1 OR4X1 HGNC HGNC:14854 protein_coding YES CCDS31487.1 ENSP00000321506 Q8NH49 UPI0000041BDE NM_001004726.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF271,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 48264456 48264456 C A 1 0 0 0 0 1 0 0 0 11160 507 18 2 2 OR4X1 11 48264456 Missense_Mutation SNP C C3N-00175_T 981570 48264456 86822166 833 10425 OR4S1 0 . GRCh38 11 48306309 48306309 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.87C>G p.Phe29Leu p.F29L ENST00000319988 1/1 210 175 35 228 228 0 strelka-varscan-mutect OR4S1,missense_variant,p.Phe29Leu,ENST00000319988,NM_001004725.1; G ENST00000319988 Transcript missense_variant 87/930 87/930 29/309 F/L ttC/ttG 1 1 OR4S1 HGNC HGNC:14705 protein_coding YES CCDS31488.1 ENSP00000321447 Q8NGB4 A0A126GVU1 UPI0000041B2E NM_001004725.1 deleterious(0) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26451:SF226,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 48306309 48306309 C G 1 0 0 0 0 1 0 0 0 11158 912 32 4 4 OR4S1 11 48306309 Missense_Mutation SNP C C3N-00175_T 41853 48306309 86780313 834 10426 OR4A16 0 . GRCh38 11 55343540 55343540 + Missense_Mutation SNP G G T rs762002982 C3N-00175_T C3N-00175_N G G c.340G>T p.Val114Leu p.V114L ENST00000314721 1/1 179 145 34 228 228 0 strelka-varscan-mutect OR4A16,missense_variant,p.Val114Leu,ENST00000314721,NM_001005274.1; T ENST00000314721 Transcript missense_variant 340/987 340/987 114/328 V/L Gtg/Ttg rs762002982 1 1 OR4A16 HGNC HGNC:15153 protein_coding YES CCDS31499.1 ENSP00000325128 Q8NH70 A0A126GW87 UPI0000061EB2 NM_001005274.1 tolerated_low_confidence(0.25) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF355,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs762002982 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55343540 55343540 G T 1 0 0 0 0 1 0 0 0 11118 1261 44 2 2 OR4A16 11 55343540 Missense_Mutation SNP G C3N-00175_T 7037231 55343540 79743082 835 10427 OR4S2 0 . GRCh38 11 55651240 55651240 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.337C>A p.Leu113Ile p.L113I ENST00000312422 1/1 65 28 37 65 65 0 strelka-varscan-mutect OR4S2,missense_variant,p.Leu113Ile,ENST00000312422,NM_001004059.2; A ENST00000312422 Transcript missense_variant 337/936 337/936 113/311 L/I Ctt/Att 1 1 OR4S2 HGNC HGNC:15183 protein_coding YES CCDS31505.1 ENSP00000310337 Q8NH73 A0A126GVG1 UPI00001D77D2 NM_001004059.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 23 186 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 55651240 55651240 C A 1 0 0 0 0 1 0 0 0 11159 681 24 2 2 OR4S2 11 55651240 Missense_Mutation SNP C C3N-00175_T 307700 55651240 79435382 836 10428 OR5W2 0 . GRCh38 11 55914049 55914049 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.534C>T p.= p.F178F ENST00000344514 1/1 78 71 7 82 82 0 strelka-varscan-mutect OR5W2,synonymous_variant,p.=,ENST00000344514,NM_001001960.1; A ENST00000344514 Transcript synonymous_variant 534/933 534/933 178/310 F ttC/ttT 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -15.45604 1 1 1 1 0 A 2 1 39 55914049 55914049 G A 1 0 0 0 0 0 0 0 1 11253 933 33 3 3 OR5W2 11 55914049 Silent SNP G C3N-00175_T 262809 55914049 79172573 837 10429 OR5F1 0 . GRCh38 11 55994297 55994297 + Missense_Mutation SNP G G T rs765749853 C3N-00175_T C3N-00175_N G G c.329C>A p.Thr110Asn p.T110N ENST00000278409 1/1 194 164 30 195 195 0 strelka-varscan-mutect OR5F1,missense_variant,p.Thr110Asn,ENST00000278409,NM_003697.1; T ENST00000278409 Transcript missense_variant 329/945 329/945 110/314 T/N aCc/aAc rs765749853 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs765749853 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55994297 55994297 G T 1 0 0 0 0 1 0 0 0 11228 1261 44 2 2 OR5F1 11 55994297 Missense_Mutation SNP G C3N-00175_T 80248 55994297 79092325 838 10430 OR5J2 0 . GRCh38 11 56177203 56177203 + Nonsense_Mutation SNP G G T rs755600455 C3N-00175_T C3N-00175_N G G c.586G>T p.Glu196Ter p.E196* ENST00000312298 1/1 237 206 31 231 231 0 strelka-varscan-mutect OR5J2,stop_gained,p.Glu196Ter,ENST00000312298,NM_001005492.1; T ENST00000312298 Transcript stop_gained 586/939 586/939 196/312 E/* Gag/Tag rs755600455 1 1 OR5J2 HGNC HGNC:19612 protein_coding YES CCDS31522.1 ENSP00000310788 Q8NH18 A0A126GVP0 UPI000004B232 NM_001005492.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF343,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS rs755600455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 56177203 56177203 G T 1 0 0 0 0 0 1 0 0 11235 1291 45 2 2 OR5J2 11 56177203 Nonsense_Mutation SNP G C3N-00175_T 182906 56177203 78909419 839 10431 OR8H1 0 . GRCh38 11 56290782 56290782 + Missense_Mutation SNP A A T rs764171124 C3N-00175_T C3N-00175_N A A c.281T>A p.Met94Lys p.M94K ENST00000313022 1/1 165 140 25 203 203 0 strelka-varscan-mutect OR8H1,missense_variant,p.Met94Lys,ENST00000313022,NM_001005199.1;OR8H1,missense_variant,p.Met90Lys,ENST00000610894,; T ENST00000313022 Transcript missense_variant 309/1038 281/936 94/311 M/K aTg/aAg rs764171124 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 tolerated(0.18) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs764171124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 56290782 56290782 A T 1 0 0 0 0 1 0 0 0 11305 217 8 4 4 OR8H1 11 56290782 Missense_Mutation SNP A C3N-00175_T 113579 56290782 78795840 840 10432 OR5M3 0 . GRCh38 11 56469924 56469924 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.574G>T p.Val192Leu p.V192L ENST00000312240 1/1 119 101 18 138 138 0 strelka-varscan-mutect OR5M3,missense_variant,p.Val192Leu,ENST00000312240,NM_001004742.2; A ENST00000312240 Transcript missense_variant 574/924 574/924 192/307 V/L Gta/Tta 1 -1 OR5M3 HGNC HGNC:14806 protein_coding YES CCDS31532.1 ENSP00000312208 Q8NGP4 UPI0000041BAA NM_001004742.2 tolerated(0.29) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF17,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1401618880 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 56469924 56469924 C A 1 0 0 0 0 1 0 0 0 11244 478 17 2 2 OR5M3 11 56469924 Missense_Mutation SNP C C3N-00175_T 179142 56469924 78616698 841 10433 CLP1 0 . GRCh38 11 57660881 57660881 + Frame_Shift_Del DEL T T - novel C3N-00175_T C3N-00175_N T T c.723delT p.Leu242TrpfsTer25 p.L242Wfs*25 ENST00000533682 3/3 163 120 43 205 205 0 sindel-varindel-pindel CLP1,frameshift_variant,p.Leu242TrpfsTer25,ENST00000533682,;CLP1,frameshift_variant,p.Leu253TrpfsTer25,ENST00000529430,;CLP1,frameshift_variant,p.Leu178TrpfsTer25,ENST00000302731,NM_001142597.1;CLP1,frameshift_variant,p.Leu242TrpfsTer25,ENST00000525602,NM_006831.2;CLP1,downstream_gene_variant,,ENST00000529773,;CLP1,downstream_gene_variant,,ENST00000533905,; - ENST00000533682 Transcript frameshift_variant 1448/2435 723/1278 241/425 A/X gcT/gc 1 1 CLP1 HGNC HGNC:16999 protein_coding YES CCDS7964.1 ENSP00000434995 Q92989 UPI000012754A 3/3 HAMAP:MF_03035,hmmpanther:PTHR12755,Pfam_domain:PF16575,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 57660881 57660881 T - 1 0 1 0 1 0 0 0 0 3320 1538 54 0 0 CLP1 11 57660881 Frame_Shift_Del DEL T C3N-00175_T 1190957 57660881 77425741 842 10434 MS4A4A 0 . GRCh38 11 60302599 60302599 + Missense_Mutation SNP T T A rs749978296 C3N-00175_T C3N-00175_N T T c.428T>A p.Leu143Gln p.L143Q ENST00000337908 5/7 179 127 52 209 209 0 strelka-varscan-mutect MS4A4A,missense_variant,p.Leu143Gln,ENST00000337908,NM_148975.2,NM_024021.3;MS4A4A,intron_variant,,ENST00000532114,NM_001243266.1;MS4A4A,3_prime_UTR_variant,,ENST00000343968,;MS4A4A,3_prime_UTR_variant,,ENST00000527056,;MS4A4A,3_prime_UTR_variant,,ENST00000529950,;MS4A4A,upstream_gene_variant,,ENST00000529991,; A ENST00000337908 Transcript missense_variant 518/1604 428/720 143/239 L/Q cTg/cAg rs749978296 1 1 MS4A4A HGNC HGNC:13371 protein_coding YES CCDS7982.1 ENSP00000338648 Q96JQ5 UPI0000055AE7 NM_148975.2,NM_024021.3 deleterious(0.01) 5/7 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF59,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs749978296 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 60302599 60302599 T A 1 0 0 0 0 1 0 0 0 9840 1580 55 4 4 MS4A4A 11 60302599 Missense_Mutation SNP T C3N-00175_T 2641718 60302599 74784023 843 10435 MS4A4A 0 . GRCh38 11 60302697 60302697 + Missense_Mutation SNP G G T rs752297993 C3N-00175_T C3N-00175_N G G c.526G>T p.Gly176Trp p.G176W ENST00000337908 5/7 124 106 18 144 144 0 strelka-varscan-mutect MS4A4A,missense_variant,p.Gly176Trp,ENST00000337908,NM_148975.2,NM_024021.3;MS4A4A,intron_variant,,ENST00000532114,NM_001243266.1;MS4A4A,3_prime_UTR_variant,,ENST00000343968,;MS4A4A,3_prime_UTR_variant,,ENST00000527056,;MS4A4A,upstream_gene_variant,,ENST00000529991,;MS4A4A,downstream_gene_variant,,ENST00000529950,; T ENST00000337908 Transcript missense_variant 616/1604 526/720 176/239 G/W Ggg/Tgg rs752297993 1 1 MS4A4A HGNC HGNC:13371 protein_coding YES CCDS7982.1 ENSP00000338648 Q96JQ5 UPI0000055AE7 NM_148975.2,NM_024021.3 tolerated(0.05) 5/7 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF59 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 60302697 60302697 G T 1 0 0 0 0 1 0 0 0 9840 1348 47 2 2 MS4A4A 11 60302697 Missense_Mutation SNP G C3N-00175_T 98 60302697 74783925 844 10436 MS4A14 0 . GRCh38 11 60416966 60416966 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.2097C>A p.= p.P699P ENST00000531783 6/6 99 76 23 122 122 0 strelka-varscan-mutect MS4A14,synonymous_variant,p.=,ENST00000395001,NM_001261827.1;MS4A14,synonymous_variant,p.=,ENST00000300187,NM_032597.4;MS4A14,synonymous_variant,p.=,ENST00000531783,NM_001261828.1;MS4A14,synonymous_variant,p.=,ENST00000395005,NM_001079692.2;MS4A14,synonymous_variant,p.=,ENST00000531787,;MS4A14,3_prime_UTR_variant,,ENST00000530662,;MS4A14,3_prime_UTR_variant,,ENST00000527841,;MS4A14,3_prime_UTR_variant,,ENST00000525397,; A ENST00000531783 Transcript synonymous_variant 2188/2910 2097/2139 699/712 P ccC/ccA 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 6/6 LOW 1 SNV 5 1 PASS rs1318162527 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 60416966 60416966 C A 1 0 0 0 0 0 0 0 1 9835 581 21 2 2 MS4A14 11 60416966 Silent SNP C C3N-00175_T 114269 60416966 74669656 845 10437 RAB3IL1 0 . GRCh38 11 61908114 61908114 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.204C>A p.= p.S68S ENST00000394836 2/10 150 133 17 186 186 0 strelka-varscan-mutect RAB3IL1,synonymous_variant,p.=,ENST00000394836,NM_013401.3;RAB3IL1,synonymous_variant,p.=,ENST00000301773,NM_001271686.1;RAB3IL1,synonymous_variant,p.=,ENST00000531922,;RAB3IL1,upstream_gene_variant,,ENST00000530888,; T ENST00000394836 Transcript synonymous_variant 362/2284 204/1149 68/382 S tcC/tcA 1 -1 RAB3IL1 HGNC HGNC:9780 protein_coding YES CCDS8014.1 ENSP00000378313 Q8TBN0 UPI000007260E NM_013401.3 2/10 hmmpanther:PTHR14430:SF1,hmmpanther:PTHR14430,Superfamily_domains:0053574 LOW 1 SNV 1 1 PASS rs1323996451 . 0 206 0 3 0 0 0 0 -19.99999 0.9999882 1 1 1 0 T 2 4 39 61908114 61908114 G T 1 0 0 0 0 0 0 0 1 13096 1335 47 2 2 RAB3IL1 11 61908114 Silent SNP G C3N-00175_T 1491148 61908114 73178508 846 10438 AHNAK 0 . GRCh38 11 62518317 62518317 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.16100G>T p.Gly5367Val p.G5367V ENST00000378024 5/5 154 111 43 162 160 2 strelka-varscan-mutect AHNAK,missense_variant,p.Gly5367Val,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; A ENST00000378024 Transcript missense_variant 16375/18787 16100/17673 5367/5890 G/V gGa/gTa 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0.03) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 62518317 62518317 C A 1 0 0 0 0 1 0 0 0 491 855 30 2 2 AHNAK 11 62518317 Missense_Mutation SNP C C3N-00175_T 610203 62518317 72568305 847 10439 RNASEH2C 0 . GRCh38 11 65720710 65720710 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.49C>A p.Arg17Ser p.R17S ENST00000308418 1/4 338 309 29 300 300 0 strelka-varscan-mutect RNASEH2C,missense_variant,p.Arg17Ser,ENST00000308418,NM_032193.3;RNASEH2C,missense_variant,p.Arg17Ser,ENST00000527610,;RNASEH2C,5_prime_UTR_variant,,ENST00000528220,;KAT5,downstream_gene_variant,,ENST00000341318,NM_182710.2;KAT5,downstream_gene_variant,,ENST00000377046,NM_006388.3;KAT5,downstream_gene_variant,,ENST00000352980,NM_182709.2;KAT5,downstream_gene_variant,,ENST00000534650,;KAT5,downstream_gene_variant,,ENST00000530446,NM_001206833.1;KAT5,downstream_gene_variant,,ENST00000533596,;RNASEH2C,missense_variant,p.Arg11Ser,ENST00000531596,;RNASEH2C,non_coding_transcript_exon_variant,,ENST00000530192,;RNASEH2C,upstream_gene_variant,,ENST00000534482,;KAT5,downstream_gene_variant,,ENST00000533441,;RNASEH2C,upstream_gene_variant,,ENST00000533698,;KAT5,downstream_gene_variant,,ENST00000525600,; T ENST00000308418 Transcript missense_variant 238/2794 49/495 17/164 R/S Cgc/Agc 1 -1 RNASEH2C HGNC HGNC:24116 protein_coding YES CCDS8111.1 ENSP00000308193 Q8TDP1 A0A024R5B3 UPI000000D799 NM_032193.3 deleterious(0.03) 1/4 hmmpanther:PTHR21726 MODERATE 1 SNV 1 1 PASS rs772074076 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 65720710 65720710 G T 1 0 0 0 0 1 0 0 0 13593 1087 38 1 1 RNASEH2C 11 65720710 Missense_Mutation SNP G C3N-00175_T 3202393 65720710 69365912 848 10440 SART1 0 . GRCh38 11 65965219 65965219 + Splice_Site SNP G G T novel C3N-00175_T C3N-00175_N G G c.554+1G>T p.X185_splice ENST00000312397 94 75 19 119 119 0 strelka-varscan-mutect SART1,splice_donor_variant,,ENST00000312397,NM_005146.4;SART1,downstream_gene_variant,,ENST00000528573,;SART1,splice_donor_variant,,ENST00000529532,;SART1,splice_donor_variant,,ENST00000530251,;SART1,downstream_gene_variant,,ENST00000532333,; T ENST00000312397 Transcript splice_donor_variant -/3293 554/2403 185/800 1 1 SART1 HGNC HGNC:10538 protein_coding YES CCDS31611.1 ENSP00000310448 O43290 UPI00000732D5 NM_005146.4 4/19 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 39 65965219 65965219 G T 1 0 0 0 0 0 0 1 0 14107 1275 44 2 2 SART1 11 65965219 Splice_Site SNP G C3N-00175_T 244509 65965219 69121403 849 10441 PACS1 0 . GRCh38 11 66230815 66230815 + Missense_Mutation SNP G G T rs770845874 C3N-00175_T C3N-00175_N G G c.1501G>T p.Gly501Trp p.G501W ENST00000320580 13/24 335 266 69 291 291 0 strelka-varscan-mutect PACS1,missense_variant,p.Gly501Trp,ENST00000320580,NM_018026.3;PACS1,missense_variant,p.Gly37Trp,ENST00000529757,;PACS1,upstream_gene_variant,,ENST00000528935,;PACS1,upstream_gene_variant,,ENST00000529795,; T ENST00000320580 Transcript missense_variant 1534/4392 1501/2892 501/963 G/W Ggg/Tgg rs770845874 1 1 PACS1 HGNC HGNC:30032 protein_coding YES CCDS8129.1 ENSP00000316454 Q6VY07 A0A024R5H6 UPI0000190973 NM_018026.3 deleterious(0) 13/24 hmmpanther:PTHR13280,hmmpanther:PTHR13280:SF16 MODERATE 1 SNV 1 1 PASS rs770845874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 66230815 66230815 G T 1 0 0 0 0 1 0 0 0 11450 1232 43 2 2 PACS1 11 66230815 Missense_Mutation SNP G C3N-00175_T 265596 66230815 68855807 850 10442 SYT12 0 . GRCh38 11 67039861 67039861 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.279C>T p.= p.S93S ENST00000393946 7/11 155 118 37 149 149 0 strelka-varscan-mutect SYT12,synonymous_variant,p.=,ENST00000393946,;SYT12,synonymous_variant,p.=,ENST00000525457,NM_001177880.1;SYT12,synonymous_variant,p.=,ENST00000527043,NM_177963.3;SYT12,synonymous_variant,p.=,ENST00000533427,;SYT12,non_coding_transcript_exon_variant,,ENST00000526281,;SYT12,non_coding_transcript_exon_variant,,ENST00000525149,; T ENST00000393946 Transcript synonymous_variant 1441/4534 279/1266 93/421 S agC/agT 1 1 SYT12 HGNC HGNC:18381 protein_coding YES CCDS8154.1 ENSP00000377520 Q8IV01 UPI00000746CD 7/11 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF252 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 67039861 67039861 C T 1 0 0 0 0 0 0 0 1 15862 738 26 3 3 SYT12 11 67039861 Silent SNP C C3N-00175_T 809046 67039861 68046761 851 10443 CARNS1 0 . GRCh38 11 67419038 67419038 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.647C>A p.Thr216Lys p.T216K ENST00000445895 4/9 180 145 35 249 249 0 strelka-varscan-mutect CARNS1,missense_variant,p.Thr216Lys,ENST00000445895,NM_001166222.1;CARNS1,missense_variant,p.Thr93Lys,ENST00000307823,NM_020811.1;CARNS1,missense_variant,p.Thr216Lys,ENST00000531040,;PPP1CA,intron_variant,,ENST00000542876,;PPP1CA,intron_variant,,ENST00000546202,;CARNS1,downstream_gene_variant,,ENST00000529925,;CARNS1,downstream_gene_variant,,ENST00000525907,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531958,; A ENST00000445895 Transcript missense_variant 761/3971 647/2853 216/950 T/K aCa/aAa 1 1 CARNS1 HGNC HGNC:29268 protein_coding YES CCDS53667.1 ENSP00000389009 A5YM72 UPI0001B99E02 NM_001166222.1 deleterious(0.01) 4/9 Low_complexity_(Seg):seg,Gene3D:3.30.470.20 MODERATE 1 SNV 5 1 PASS rs1316270837 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 67419038 67419038 C A 1 0 0 0 0 1 0 0 0 2355 478 17 2 2 CARNS1 11 67419038 Missense_Mutation SNP C C3N-00175_T 379177 67419038 67667584 852 10444 RNF121 0 . GRCh38 11 71994770 71994770 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.679G>T p.Ala227Ser p.A227S ENST00000361756 7/9 225 194 31 220 220 0 strelka-varscan-mutect RNF121,missense_variant,p.Ala227Ser,ENST00000361756,NM_018320.4;RNF121,missense_variant,p.Ala195Ser,ENST00000530137,;RNF121,missense_variant,p.Ala67Ser,ENST00000533380,;RNF121,intron_variant,,ENST00000393713,NM_001300926.1;IL18BP,upstream_gene_variant,,ENST00000497194,NM_005699.3;IL18BP,upstream_gene_variant,,ENST00000404792,NM_173042.2;IL18BP,upstream_gene_variant,,ENST00000393703,NM_001039660.1;IL18BP,upstream_gene_variant,,ENST00000337131,;IL18BP,upstream_gene_variant,,ENST00000620017,NM_173044.2;IL18BP,upstream_gene_variant,,ENST00000393705,NM_001039659.1;IL18BP,upstream_gene_variant,,ENST00000260049,NM_001145057.1;IL18BP,upstream_gene_variant,,ENST00000531053,;RNF121,non_coding_transcript_exon_variant,,ENST00000490867,;IL18BP,upstream_gene_variant,,ENST00000525932,;IL18BP,upstream_gene_variant,,ENST00000531777,;IL18BP,upstream_gene_variant,,ENST00000414358,;RNF121,downstream_gene_variant,,ENST00000525176,;RNF121,missense_variant,p.Cys135Phe,ENST00000525243,;RNF121,3_prime_UTR_variant,,ENST00000526549,;RNF121,3_prime_UTR_variant,,ENST00000530655,;IL18BP,upstream_gene_variant,,ENST00000343898,;IL18BP,upstream_gene_variant,,ENST00000534583,;RNF121,downstream_gene_variant,,ENST00000528683,;RNF121,upstream_gene_variant,,ENST00000532379,;RNF121,downstream_gene_variant,,ENST00000530058,; T ENST00000361756 Transcript missense_variant 1040/2625 679/984 227/327 A/S Gct/Tct 1 1 RNF121 HGNC HGNC:21070 protein_coding YES CCDS8203.1 ENSP00000354571 Q9H920 UPI000006FB75 NM_018320.4 tolerated(0.05) 7/9 PROSITE_profiles:PS50089,hmmpanther:PTHR13407,hmmpanther:PTHR13407:SF1,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -14.32265 0.996248 1 1 1 0 T 3 4 39 71994770 71994770 G T 1 0 0 0 0 1 0 0 0 13609 1319 46 2 2 RNF121 11 71994770 Missense_Mutation SNP G C3N-00175_T 4575732 71994770 63091852 853 10445 FOLR3 0 . GRCh38 11 72136104 72136104 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.152A>T p.Asp51Val p.D51V ENST00000611028 2/5 149 109 40 175 175 0 strelka-varscan-mutect FOLR3,missense_variant,p.Asp51Val,ENST00000611028,NM_000804.2;FOLR3,missense_variant,p.Asp49Val,ENST00000442948,;FOLR3,missense_variant,p.Asp51Val,ENST00000622388,;FOLR3,missense_variant,p.Asp49Val,ENST00000546166,;FOLR3,missense_variant,p.Asp51Val,ENST00000612844,NM_001318045.1;FOLR3,upstream_gene_variant,,ENST00000545379,;RPEP6,downstream_gene_variant,,ENST00000546228,; T ENST00000611028 Transcript missense_variant 175/820 152/738 51/245 D/V gAc/gTc 1 1 FOLR3 HGNC HGNC:3795 protein_coding YES CCDS73344.1 ENSP00000481114 A0A087WXL1 UPI0000D4B12C NM_000804.2 deleterious(0) 2/5 hmmpanther:PTHR10517:SF17,hmmpanther:PTHR10517,Pfam_domain:PF03024 MODERATE 1 SNV 1 1 PASS rs1224266770 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 72136104 72136104 A T 1 0 0 0 0 1 0 0 0 5843 275 10 4 4 FOLR3 11 72136104 Missense_Mutation SNP A C3N-00175_T 141334 72136104 62950518 854 10446 CHRDL2 0 . GRCh38 11 74713461 74713461 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.214T>A p.Tyr72Asn p.Y72N ENST00000263671 3/12 203 165 38 122 122 0 strelka-varscan-mutect CHRDL2,missense_variant,p.Tyr72Asn,ENST00000376332,NM_001278473.2;CHRDL2,missense_variant,p.Tyr72Asn,ENST00000263671,NM_015424.5,NM_001304391.1,NM_001304390.1;CHRDL2,missense_variant,p.Tyr72Asn,ENST00000528789,;CHRDL2,5_prime_UTR_variant,,ENST00000622063,;CHRDL2,non_coding_transcript_exon_variant,,ENST00000534159,;CHRDL2,missense_variant,p.Tyr52Asn,ENST00000534276,;CHRDL2,intron_variant,,ENST00000376324,NM_001304416.1;CHRDL2,intron_variant,,ENST00000528471,; T ENST00000263671 Transcript missense_variant 501/1712 214/1356 72/451 Y/N Tac/Aac 1 -1 CHRDL2 HGNC HGNC:24168 protein_coding YES CCDS8234.1 ENSP00000263671 Q6WN34 UPI0000034E41 NM_015424.5,NM_001304391.1,NM_001304390.1 tolerated(0.52) 3/12 PROSITE_profiles:PS50184,hmmpanther:PTHR11339,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS rs1345252301 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 74713461 74713461 A T 1 0 0 0 0 1 0 0 0 3134 362 13 4 4 CHRDL2 11 74713461 Missense_Mutation SNP A C3N-00175_T 2577357 74713461 60373161 855 10447 THAP12 0 . GRCh38 11 76365967 76365967 + Missense_Mutation SNP T T A rs780565256 C3N-00175_T C3N-00175_N T T c.95A>T p.Gln32Leu p.Q32L ENST00000260045 2/5 106 80 26 118 118 0 strelka-varscan-mutect THAP12,missense_variant,p.Gln32Leu,ENST00000260045,NM_004705.3;THAP12,non_coding_transcript_exon_variant,,ENST00000531878,;THAP12,missense_variant,p.Gln32Leu,ENST00000528993,;THAP12,upstream_gene_variant,,ENST00000525277,; A ENST00000260045 Transcript missense_variant 201/3300 95/2286 32/761 Q/L cAg/cTg rs780565256 1 -1 THAP12 HGNC HGNC:9440 protein_coding YES CCDS8243.1 ENSP00000260045 O43422 A0A140VJQ7 UPI0000131030 NM_004705.3 deleterious(0.02) 2/5 Pfam_domain:PF05485,PROSITE_profiles:PS50950,hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF104,SMART_domains:SM00692,SMART_domains:SM00980,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS rs780565256 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 76365967 76365967 T A 1 0 0 0 0 1 0 0 0 16276 1594 55 4 4 THAP12 11 76365967 Missense_Mutation SNP T C3N-00175_T 1652506 76365967 58720655 856 10448 CLNS1A 0 . GRCh38 11 77625816 77625816 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.265G>T p.Glu89Ter p.E89* ENST00000525428 3/7 76 40 36 90 90 0 strelka-varscan-mutect CLNS1A,stop_gained,p.Glu89Ter,ENST00000525428,NM_001293.2;CLNS1A,stop_gained,p.Glu89Ter,ENST00000525064,NM_001311201.1;CLNS1A,stop_gained,p.Glu89Ter,ENST00000528364,NM_001311199.1;CLNS1A,intron_variant,,ENST00000263309,NM_001311200.1;CLNS1A,intron_variant,,ENST00000532069,;CLNS1A,missense_variant,p.Arg43Ile,ENST00000527133,;CLNS1A,upstream_gene_variant,,ENST00000526009,;CLNS1A,upstream_gene_variant,,ENST00000527265,;CLNS1A,upstream_gene_variant,,ENST00000527299,;CLNS1A,upstream_gene_variant,,ENST00000525359,; A ENST00000525428 Transcript stop_gained,splice_region_variant 356/2993 265/714 89/237 E/* Gaa/Taa 1 -1 CLNS1A HGNC HGNC:2080 protein_coding YES CCDS8252.1 ENSP00000433919 P54105 UPI0000044777 NM_001293.2 3/7 Low_complexity_(Seg):seg,hmmpanther:PTHR21399,Pfam_domain:PF03517 HIGH 1 SNV 1 1 PASS rs1284777048 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 77625816 77625816 C A 1 0 0 0 0 0 1 0 0 3318 927 32 2 2 CLNS1A 11 77625816 Nonsense_Mutation SNP C C3N-00175_T 1259849 77625816 57460806 857 10449 INTS4 0 . GRCh38 11 77991153 77991153 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.201A>T p.Glu67Asp p.E67D ENST00000534064 2/23 180 121 59 145 145 0 strelka-varscan-mutect INTS4,missense_variant,p.Glu67Asp,ENST00000534064,NM_033547.3;INTS4,missense_variant,p.Glu67Asp,ENST00000529807,;INTS4,missense_variant,p.Glu67Asp,ENST00000527522,;INTS4,missense_variant,p.Glu67Asp,ENST00000433818,;INTS4,missense_variant,p.Glu67Asp,ENST00000534408,;INTS4,missense_variant,p.Glu67Asp,ENST00000524766,; A ENST00000534064 Transcript missense_variant 236/3156 201/2892 67/963 E/D gaA/gaT 1 -1 INTS4 HGNC HGNC:25048 protein_coding YES CCDS31644.1 ENSP00000434466 Q96HW7 UPI00001FB00A NM_033547.3 tolerated(0.22) 2/23 hmmpanther:PTHR20938:SF0,hmmpanther:PTHR20938,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 77991153 77991153 T A 1 0 0 0 0 1 0 0 0 7682 1838 64 4 4 INTS4 11 77991153 Missense_Mutation SNP T C3N-00175_T 365337 77991153 57095469 858 10450 DLG2 0 . GRCh38 11 83962948 83962948 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.1277C>A p.Pro426His p.P426H ENST00000376104 14/28 360 285 75 254 254 0 strelka-varscan-mutect DLG2,missense_variant,p.Pro321His,ENST00000398309,NM_001364.3;DLG2,missense_variant,p.Pro360His,ENST00000280241,NM_001206769.1;DLG2,missense_variant,p.Pro426His,ENST00000376104,NM_001142699.1;DLG2,missense_variant,p.Pro270His,ENST00000418306,NM_001142700.1;DLG2,missense_variant,p.Pro288His,ENST00000531015,;DLG2,missense_variant,p.Pro321His,ENST00000532653,NM_001300983.1;DLG2,missense_variant,p.Pro321His,ENST00000524982,;DLG2,missense_variant,p.Pro260His,ENST00000330014,;DLG2,missense_variant,p.Pro360His,ENST00000398301,;DLG2,downstream_gene_variant,,ENST00000398299,;DLG2,non_coding_transcript_exon_variant,,ENST00000529111,; T ENST00000376104 Transcript missense_variant 1589/5139 1277/2928 426/975 P/H cCc/cAc COSM140667 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 deleterious(0.01) 14/28 hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119,PIRSF_domain:PIRSF001741,Pfam_domain:PF10600 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 83962948 83962948 G T 1 0 0 0 0 1 0 0 0 4362 1232 43 2 2 DLG2 11 83962948 Missense_Mutation SNP G C3N-00175_T 5971795 83962948 51123674 859 10451 DLG2 0 . GRCh38 11 84317096 84317096 + Missense_Mutation SNP C C A rs781269823 C3N-00175_T C3N-00175_N C C c.50G>T p.Gly17Val p.G17V ENST00000280241 1/22 180 122 58 183 183 0 strelka-varscan-mutect DLG2,missense_variant,p.Gly17Val,ENST00000280241,NM_001206769.1;DLG2,missense_variant,p.Gly17Val,ENST00000398301,;DLG2,intron_variant,,ENST00000398309,NM_001364.3;DLG2,intron_variant,,ENST00000376104,NM_001142699.1;DLG2,intron_variant,,ENST00000532653,NM_001300983.1;DLG2,intron_variant,,ENST00000524982,;DLG2,intron_variant,,ENST00000527466,;DLG2,intron_variant,,ENST00000529111,; A ENST00000280241 Transcript missense_variant 244/7730 50/2730 17/909 G/V gGg/gTg rs781269823,COSM3687687 1 -1 DLG2 HGNC HGNC:2901 protein_coding CCDS55782.1 ENSP00000280241 Q15700 UPI0000577A76 NM_001206769.1 tolerated_low_confidence(0.1) 1/22 0,1 MODERATE SNV 5 0,1 1 PASS rs781269823 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 84317096 84317096 C A 1 0 0 0 0 1 0 0 0 4362 623 22 2 2 DLG2 11 84317096 Missense_Mutation SNP C C3N-00175_T 354148 84317096 50769526 860 10452 CTSC 0 . GRCh38 11 88294499 88294499 + Missense_Mutation SNP C C G C3N-00175_T C3N-00175_N C C c.899G>C p.Gly300Ala p.G300A ENST00000227266 7/7 281 218 63 287 287 0 strelka-varscan-mutect CTSC,missense_variant,p.Gly300Ala,ENST00000227266,NM_001814.4;CTSC,downstream_gene_variant,,ENST00000527018,;CTSC,non_coding_transcript_exon_variant,,ENST00000533897,; G ENST00000227266 Transcript missense_variant 1014/1921 899/1392 300/463 G/A gGc/gCc CM010202 1 -1 CTSC HGNC HGNC:2528 protein_coding YES CCDS8282.1 ENSP00000227266 P53634 UPI000006D22D NM_001814.4 deleterious(0) 7/7 hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF354,Pfam_domain:PF00112,Gene3D:3.90.70.10,SMART_domains:SM00645,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 88294499 88294499 C G 1 0 0 0 0 1 0 0 0 3840 739 26 4 4 CTSC 11 88294499 Missense_Mutation SNP C C3N-00175_T 3977403 88294499 46792123 861 10453 GRM5 0 . GRCh38 11 89047387 89047387 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.486C>A p.= p.L162L ENST00000305447 1/9 204 173 31 179 179 0 strelka-varscan-mutect GRM5,synonymous_variant,p.=,ENST00000455756,NM_000842.4;GRM5,synonymous_variant,p.=,ENST00000305447,NM_001143831.2;GRM5,synonymous_variant,p.=,ENST00000305432,;GRM5,synonymous_variant,p.=,ENST00000393294,;GRM5,upstream_gene_variant,,ENST00000449371,; T ENST00000305447 Transcript synonymous_variant 636/4571 486/3639 162/1212 L ctC/ctA 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 1/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,PROSITE_patterns:PS00979,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 89047387 89047387 G T 1 0 0 0 0 0 0 0 1 6682 1161 41 2 2 GRM5 11 89047387 Silent SNP G C3N-00175_T 752888 89047387 46039235 862 10454 GRM5 0 . GRCh38 11 89047665 89047665 + Nonsense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.208G>T p.Glu70Ter p.E70* ENST00000305447 1/9 501 391 110 417 417 0 strelka-varscan-mutect GRM5,stop_gained,p.Glu70Ter,ENST00000455756,NM_000842.4;GRM5,stop_gained,p.Glu70Ter,ENST00000305447,NM_001143831.2;GRM5,stop_gained,p.Glu70Ter,ENST00000305432,;GRM5,stop_gained,p.Glu70Ter,ENST00000393294,;GRM5,upstream_gene_variant,,ENST00000449371,; A ENST00000305447 Transcript stop_gained 358/4571 208/3639 70/1212 E/* Gag/Tag COSM5553710,COSM5553711 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 1/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 89047665 89047665 C A 1 0 0 0 0 0 1 0 0 6682 864 30 2 2 GRM5 11 89047665 Nonsense_Mutation SNP C C3N-00175_T 278 89047665 46038957 863 10455 NAALAD2 0 . GRCh38 11 90134764 90134764 + Silent SNP G G C rs770197026 C3N-00175_T C3N-00175_N G G c.6G>C p.= p.A2A ENST00000534061 1/19 250 223 27 226 226 0 strelka-varscan-mutect NAALAD2,synonymous_variant,p.=,ENST00000534061,NM_005467.3;NAALAD2,synonymous_variant,p.=,ENST00000321955,NM_001300930.1;NAALAD2,synonymous_variant,p.=,ENST00000525171,;NAALAD2,synonymous_variant,p.=,ENST00000375944,;NAALAD2,synonymous_variant,p.=,ENST00000525497,;NAALAD2,upstream_gene_variant,,ENST00000526637,;NAALAD2,synonymous_variant,p.=,ENST00000527493,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000524501,;NAALAD2,non_coding_transcript_exon_variant,,ENST00000529090,; C ENST00000534061 Transcript synonymous_variant 236/3600 6/2223 2/740 A gcG/gcC rs770197026 1 1 NAALAD2 HGNC HGNC:14526 protein_coding YES CCDS8288.1 ENSP00000432481 Q9Y3Q0 UPI0000031A85 NM_005467.3 1/19 hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF38 LOW 1 SNV 1 1 PASS rs770197026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 90134764 90134764 G C 1 0 0 0 0 0 0 0 1 10132 1103 39 4 4 NAALAD2 11 90134764 Silent SNP G C3N-00175_T 1087099 90134764 44951858 864 10456 FAT3 0 . GRCh38 11 92810072 92810072 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.9027C>A p.Asp3009Glu p.D3009E ENST00000525166 12/27 114 85 29 94 94 0 strelka-varscan-mutect FAT3,missense_variant,p.Asp3159Glu,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Asp3009Glu,ENST00000525166,; A ENST00000525166 Transcript missense_variant 9049/18699 9027/13320 3009/4439 D/E gaC/gaA 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 12/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 92810072 92810072 C A 1 0 0 0 0 1 0 0 0 5551 492 17 2 2 FAT3 11 92810072 Missense_Mutation SNP C C3N-00175_T 2675308 92810072 42276550 865 10457 FAT3 0 . GRCh38 11 92831708 92831708 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.9118G>C p.Glu3040Gln p.E3040Q ENST00000525166 13/27 233 170 63 223 223 0 strelka-varscan-mutect FAT3,missense_variant,p.Glu3190Gln,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Glu3040Gln,ENST00000525166,; C ENST00000525166 Transcript missense_variant 9140/18699 9118/13320 3040/4439 E/Q Gag/Cag 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.01) 13/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 92831708 92831708 G C 1 0 0 0 0 1 0 0 0 5551 1175 41 4 4 FAT3 11 92831708 Missense_Mutation SNP G C3N-00175_T 21636 92831708 42254914 866 10458 FAT3 0 . GRCh38 11 92840583 92840583 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.9940A>T p.Ser3314Cys p.S3314C ENST00000525166 17/27 132 100 32 88 88 0 strelka-varscan-mutect FAT3,missense_variant,p.Ser3464Cys,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ser3314Cys,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000533797,; T ENST00000525166 Transcript missense_variant 9962/18699 9940/13320 3314/4439 S/C Agc/Tgc 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 17/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 92840583 92840583 A T 1 0 0 0 0 1 0 0 0 5551 188 7 4 4 FAT3 11 92840583 Missense_Mutation SNP A C3N-00175_T 8875 92840583 42246039 867 10459 FAT3 0 . GRCh38 11 92844478 92844478 + Missense_Mutation SNP C C A rs187335351 C3N-00175_T C3N-00175_N C C c.10661C>A p.Ala3554Glu p.A3554E ENST00000525166 18/27 293 205 88 277 277 0 strelka-varscan-mutect FAT3,missense_variant,p.Ala3704Glu,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ala3554Glu,ENST00000525166,;FAT3,missense_variant,p.Ala39Glu,ENST00000533797,; A ENST00000525166 Transcript missense_variant 10683/18699 10661/13320 3554/4439 A/E gCg/gAg rs187335351 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.09) 18/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 MODERATE 1 SNV 5 1 PASS rs187335351 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 92844478 92844478 C A 1 0 0 0 0 1 0 0 0 5551 768 27 1 1 FAT3 11 92844478 Missense_Mutation SNP C C3N-00175_T 3895 92844478 42242144 868 10460 PANX1 0 . GRCh38 11 94129493 94129493 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.181G>C p.Gly61Arg p.G61R ENST00000227638 1/5 66 49 17 65 65 0 strelka-varscan-mutect PANX1,missense_variant,p.Gly61Arg,ENST00000227638,NM_015368.3;PANX1,missense_variant,p.Gly61Arg,ENST00000436171,; C ENST00000227638 Transcript missense_variant,splice_region_variant 566/2769 181/1281 61/426 G/R Ggt/Cgt 1 1 PANX1 HGNC HGNC:8599 protein_coding YES CCDS8296.1 ENSP00000227638 Q96RD7 A0A024R397 UPI000004C63F NM_015368.3 deleterious(0.03) 1/5 Pfam_domain:PF00876,PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF5 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 39 94129493 94129493 G C 1 0 0 0 0 1 0 0 0 11501 1362 47 4 4 PANX1 11 94129493 Missense_Mutation SNP G C3N-00175_T 1285015 94129493 40957129 869 10461 SESN3 0 . GRCh38 11 95230835 95230835 + Nonsense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.26C>A p.Ser9Ter p.S9* ENST00000536441 1/10 286 254 32 230 230 0 strelka-varscan-mutect SESN3,stop_gained,p.Ser9Ter,ENST00000536441,NM_144665.3;SESN3,stop_gained,p.Ser9Ter,ENST00000416495,;SESN3,intron_variant,,ENST00000278499,NM_001271594.1;SESN3,intron_variant,,ENST00000634898,;SESN3,intron_variant,,ENST00000542176,;RP11-712B9.2,intron_variant,,ENST00000543150,;RP11-712B9.2,intron_variant,,ENST00000536683,;RP11-712B9.2,intron_variant,,ENST00000534891,;RP11-712B9.2,upstream_gene_variant,,ENST00000540692,;RP11-712B9.2,upstream_gene_variant,,ENST00000543573,;SESN3,intron_variant,,ENST00000537480,; T ENST00000536441 Transcript stop_gained 363/9558 26/1479 9/492 S/* tCg/tAg COSM3368612,COSM3368613 1 -1 SESN3 HGNC HGNC:23060 protein_coding YES CCDS8303.1 ENSP00000441927 P58005 UPI0000135891 NM_144665.3 1/10 hmmpanther:PTHR12474:SF4,hmmpanther:PTHR12474 1,1 HIGH 1 SNV 2 1,1 1 PASS rs1318902387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 95230835 95230835 G T 1 0 0 0 0 0 1 0 0 14403 1059 37 1 1 SESN3 11 95230835 Nonsense_Mutation SNP G C3N-00175_T 1101342 95230835 39855787 870 10462 ANGPTL5 0 . GRCh38 11 101900467 101900467 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.624G>T p.Leu208Phe p.L208F ENST00000334289 7/9 168 129 39 310 310 0 strelka-varscan-mutect ANGPTL5,missense_variant,p.Leu208Phe,ENST00000334289,NM_178127.4;ANGPTL5,missense_variant,p.Leu143Phe,ENST00000534527,; A ENST00000334289 Transcript missense_variant 1220/2368 624/1167 208/388 L/F ttG/ttT 1 -1 ANGPTL5 HGNC HGNC:19705 protein_coding YES CCDS8312.1 ENSP00000335255 Q86XS5 UPI000015F945 NM_178127.4 tolerated(0.05) 7/9 Gene3D:3.90.215.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF185,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS rs1309081164 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 101900467 101900467 C A 1 0 0 0 0 1 0 0 0 715 477 17 2 2 ANGPTL5 11 101900467 Missense_Mutation SNP C C3N-00175_T 6669632 101900467 33186155 871 10463 MMP20 0 . GRCh38 11 102606539 102606539 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.949G>T p.Asp317Tyr p.D317Y ENST00000260228 6/10 429 377 52 541 540 1 strelka-varscan-mutect MMP20,missense_variant,p.Asp317Tyr,ENST00000260228,NM_004771.3;RP11-817J15.2,upstream_gene_variant,,ENST00000542119,;RP11-817J15.2,upstream_gene_variant,,ENST00000544115,;MMP20,non_coding_transcript_exon_variant,,ENST00000544938,; A ENST00000260228 Transcript missense_variant 962/1956 949/1452 317/483 D/Y Gac/Tac 1 -1 MMP20 HGNC HGNC:7167 protein_coding YES CCDS8318.1 ENSP00000260228 O60882 UPI000013D0B3 NM_004771.3 deleterious(0) 6/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201:SF125,hmmpanther:PTHR10201,PIRSF_domain:PIRSF001191,Gene3D:2.110.10.10,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 102606539 102606539 C A 1 0 0 0 0 1 0 0 0 9622 869 30 2 2 MMP20 11 102606539 Missense_Mutation SNP C C3N-00175_T 706072 102606539 32480083 872 10464 MMP8 0 . GRCh38 11 102721475 102721475 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.548C>A p.Ala183Asp p.A183D ENST00000236826 4/10 175 131 44 235 234 1 strelka-varscan-mutect MMP8,missense_variant,p.Ala183Asp,ENST00000236826,NM_002424.2,NM_001304441.1,NM_001304442.1;MMP8,missense_variant,p.Ala159Asp,ENST00000438475,;MMP8,3_prime_UTR_variant,,ENST00000528662,;MMP8,3_prime_UTR_variant,,ENST00000533258,;MMP8,downstream_gene_variant,,ENST00000532799,;MMP8,downstream_gene_variant,,ENST00000531168,; T ENST00000236826 Transcript missense_variant 647/3056 548/1404 183/467 A/D gCc/gAc 1 -1 MMP8 HGNC HGNC:7175 protein_coding YES CCDS8320.1 ENSP00000236826 P22894 UPI00000422BB NM_002424.2,NM_001304441.1,NM_001304442.1 deleterious(0) 4/10 Gene3D:3.40.390.10,Pfam_domain:PF00413,PIRSF_domain:PIRSF001191,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF137,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs1215016736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 102721475 102721475 G T 1 0 0 0 0 1 0 0 0 9631 1203 42 2 2 MMP8 11 102721475 Missense_Mutation SNP G C3N-00175_T 114936 102721475 32365147 873 10465 ATM 0 . GRCh38 11 108316030 108316030 + Missense_Mutation SNP G G A rs864622251 C3N-00175_T C3N-00175_N G G c.6115G>A p.Glu2039Lys p.E2039K ENST00000278616 42/63 315 222 93 449 447 2 strelka-varscan-mutect ATM,missense_variant,p.Glu2039Lys,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Glu2039Lys,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,non_coding_transcript_exon_variant,,ENST00000532765,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; A ENST00000278616 Transcript missense_variant 6500/13147 6115/9171 2039/3056 E/K Gaa/Aaa rs864622251,CM094668,COSM1561120,COSM200671 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 deleterious(0) 42/63 PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF72,hmmpanther:PTHR11139 uncertain_significance 0,0,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs864622251 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 108316030 108316030 G A 1 0 0 0 0 1 0 0 0 1261 1059 37 1 1 ATM 11 108316030 Missense_Mutation SNP G C3N-00175_T 5594555 108316030 26770592 874 10466 SIDT2 0 . GRCh38 11 117182567 117182567 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.565G>T p.Val189Leu p.V189L ENST00000324225 5/26 184 143 41 301 301 0 strelka-varscan-mutect SIDT2,missense_variant,p.Val189Leu,ENST00000324225,NM_001040455.1;SIDT2,missense_variant,p.Val189Leu,ENST00000620360,;SIDT2,missense_variant,p.Val189Leu,ENST00000431081,;SIDT2,missense_variant,p.Val189Leu,ENST00000278951,;SIDT2,missense_variant,p.Val189Leu,ENST00000628876,;SIDT2,missense_variant,p.Val39Leu,ENST00000524842,;SIDT2,missense_variant,p.Val88Leu,ENST00000531353,;SIDT2,downstream_gene_variant,,ENST00000532960,;SIDT2,non_coding_transcript_exon_variant,,ENST00000530948,;SIDT2,intron_variant,,ENST00000525339,;SIDT2,non_coding_transcript_exon_variant,,ENST00000531255,;SIDT2,upstream_gene_variant,,ENST00000529441,;SIDT2,downstream_gene_variant,,ENST00000528397,; T ENST00000324225 Transcript missense_variant 1096/4406 565/2499 189/832 V/L Gtg/Ttg COSM126166,COSM4617081,COSM4617082 1 1 SIDT2 HGNC HGNC:24272 protein_coding YES CCDS31682.1 ENSP00000314023 Q8NBJ9 UPI000004BA68 NM_001040455.1 deleterious(0) 5/26 hmmpanther:PTHR12185,hmmpanther:PTHR12185:SF16,Pfam_domain:PF13965 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1309515919 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 117182567 117182567 G T 1 0 0 0 0 1 0 0 0 14567 1261 44 2 2 SIDT2 11 117182567 Missense_Mutation SNP G C3N-00175_T 8866537 117182567 17904055 875 10467 TMPRSS4 0 . GRCh38 11 118094849 118094849 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.37A>T p.Ser13Cys p.S13C ENST00000618855 2/13 158 118 40 245 245 0 strelka-varscan-mutect TMPRSS4,missense_variant,p.Ser11Cys,ENST00000534111,NM_001173551.1;TMPRSS4,missense_variant,p.Ser13Cys,ENST00000618855,NM_019894.3,NM_001290094.1;TMPRSS4,missense_variant,p.Ser13Cys,ENST00000616579,;TMPRSS4,missense_variant,p.Ser13Cys,ENST00000437212,;TMPRSS4,missense_variant,p.Ser13Cys,ENST00000522824,NM_001083947.1;TMPRSS4,missense_variant,p.Ser11Cys,ENST00000523251,NM_001173552.1;TMPRSS4,missense_variant,p.Ser11Cys,ENST00000522151,;TMPRSS4,5_prime_UTR_variant,,ENST00000522307,NM_001290096.1;TMPRSS4,upstream_gene_variant,,ENST00000517544,;TMPRSS4,missense_variant,p.Ser11Cys,ENST00000517483,;TMPRSS4,missense_variant,p.Ser11Cys,ENST00000519236,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000519126,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000522462,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000520063,; T ENST00000618855 Transcript missense_variant 328/3531 37/1314 13/437 S/C Agc/Tgc 1 1 TMPRSS4 HGNC HGNC:11878 protein_coding YES CCDS31684.1 ENSP00000477949 Q9NRS4 UPI00001FA467 NM_019894.3,NM_001290094.1 tolerated(0.05) 2/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 118094849 118094849 A T 1 0 0 0 0 1 0 0 0 16725 188 7 4 4 TMPRSS4 11 118094849 Missense_Mutation SNP A C3N-00175_T 912282 118094849 16991773 876 10468 ROBO3 0 . GRCh38 11 124879250 124879250 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.3594T>A p.= p.R1198R ENST00000397801 24/28 90 65 25 136 136 0 strelka-varscan-mutect ROBO3,synonymous_variant,p.=,ENST00000397801,NM_022370.3;ROBO3,synonymous_variant,p.=,ENST00000538940,;ROBO3,5_prime_UTR_variant,,ENST00000543966,;ROBO4,downstream_gene_variant,,ENST00000306534,NM_019055.5;RP11-664I21.5,upstream_gene_variant,,ENST00000524453,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525482,;ROBO3,non_coding_transcript_exon_variant,,ENST00000528820,;ROBO3,non_coding_transcript_exon_variant,,ENST00000528144,;ROBO3,non_coding_transcript_exon_variant,,ENST00000531075,;ROBO3,downstream_gene_variant,,ENST00000526551,;ROBO3,downstream_gene_variant,,ENST00000532472,;ROBO3,downstream_gene_variant,,ENST00000531545,;ROBO3,non_coding_transcript_exon_variant,,ENST00000527245,;ROBO3,non_coding_transcript_exon_variant,,ENST00000529658,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525448,;ROBO3,non_coding_transcript_exon_variant,,ENST00000527196,;ROBO3,non_coding_transcript_exon_variant,,ENST00000524971,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525304,;ROBO4,downstream_gene_variant,,ENST00000534407,;ROBO3,downstream_gene_variant,,ENST00000534598,;ROBO3,downstream_gene_variant,,ENST00000528068,;ROBO3,downstream_gene_variant,,ENST00000531888,;ROBO3,downstream_gene_variant,,ENST00000530647,;ROBO3,downstream_gene_variant,,ENST00000531119,; A ENST00000397801 Transcript synonymous_variant 3786/4569 3594/4161 1198/1386 R cgT/cgA 1 1 ROBO3 HGNC HGNC:13433 protein_coding YES CCDS44755.1 ENSP00000380903 Q96MS0 UPI000035AA82 NM_022370.3 24/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF724 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 124879250 124879250 T A 1 0 0 0 0 0 0 0 1 13693 1683 59 4 4 ROBO3 11 124879250 Silent SNP T C3N-00175_T 6784401 124879250 10207372 877 10469 PKNOX2 0 . GRCh38 11 125411843 125411843 + Missense_Mutation SNP C C T rs780034819 C3N-00175_T C3N-00175_N C C c.914C>T p.Ser305Phe p.S305F ENST00000298282 10/13 160 136 24 244 244 0 strelka-varscan-mutect PKNOX2,missense_variant,p.Ser305Phe,ENST00000298282,NM_022062.2;PKNOX2,non_coding_transcript_exon_variant,,ENST00000530517,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000531116,;PKNOX2,3_prime_UTR_variant,,ENST00000532623,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000526955,; T ENST00000298282 Transcript missense_variant 1185/3687 914/1419 305/472 S/F tCt/tTt rs780034819,COSM924518 1 1 PKNOX2 HGNC HGNC:16714 protein_coding YES CCDS41730.1 ENSP00000298282 Q96KN3 UPI000023271E NM_022062.2 deleterious(0) 10/13 PROSITE_profiles:PS50071,hmmpanther:PTHR11850:SF53,hmmpanther:PTHR11850,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780034819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 125411843 125411843 C T 1 0 0 0 0 1 0 0 0 12079 913 32 3 3 PKNOX2 11 125411843 Missense_Mutation SNP C C3N-00175_T 532593 125411843 9674779 878 10470 ARHGAP32 0 . GRCh38 11 128971108 128971108 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.4063G>T p.Asp1355Tyr p.D1355Y ENST00000310343 22/22 59 37 22 91 91 0 strelka-varscan-mutect ARHGAP32,missense_variant,p.Asp1355Tyr,ENST00000310343,NM_001142685.1;ARHGAP32,missense_variant,p.Asp1006Tyr,ENST00000392657,NM_014715.3;ARHGAP32,missense_variant,p.Asp1006Tyr,ENST00000527272,;ARHGAP32,3_prime_UTR_variant,,ENST00000524655,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000526162,; A ENST00000310343 Transcript missense_variant 4063/10111 4063/6264 1355/2087 D/Y Gat/Tat 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 deleterious_low_confidence(0.02) 22/22 hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 128971108 128971108 C A 1 0 0 0 0 1 0 0 0 1006 855 30 2 2 ARHGAP32 11 128971108 Missense_Mutation SNP C C3N-00175_T 3559265 128971108 6115514 879 10471 ADAMTS8 0 . GRCh38 11 130405883 130405883 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.2345T>G p.Leu782Trp p.L782W ENST00000257359 9/9 116 78 38 182 182 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Leu782Trp,ENST00000257359,NM_007037.4;RP11-121M22.1,downstream_gene_variant,,ENST00000602376,;RP11-121M22.1,downstream_gene_variant,,ENST00000616197,;ADAMTS8,non_coding_transcript_exon_variant,,ENST00000531752,; C ENST00000257359 Transcript missense_variant 3052/4010 2345/2670 782/889 L/W tTg/tGg 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 deleterious(0) 9/9 hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS rs1279586383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 130405883 130405883 A C 1 0 0 0 0 1 0 0 0 316 131 5 5 5 ADAMTS8 11 130405883 Missense_Mutation SNP A C3N-00175_T 1434775 130405883 4680739 880 10472 IQSEC3 0 . GRCh38 12 138966 138966 + Silent SNP C C A rs201912061 C3N-00175_T C3N-00175_N C C c.1603C>A p.= p.R535R ENST00000538872 4/14 65 60 5 79 79 0 strelka-varscan-mutect IQSEC3,synonymous_variant,p.=,ENST00000538872,NM_001170738.1;IQSEC3,synonymous_variant,p.=,ENST00000382841,NM_015232.1;RP11-598F7.4,intron_variant,,ENST00000505893,;RP11-598F7.4,downstream_gene_variant,,ENST00000508953,; A ENST00000538872 Transcript synonymous_variant 1721/7094 1603/3549 535/1182 R Cgg/Agg rs201912061 1 1 IQSEC3 HGNC HGNC:29193 protein_coding YES CCDS53728.1 ENSP00000437554 Q9UPP2 UPI0000DBEEF0 NM_001170738.1 4/14 LOW SNV 5 1 PASS rs201912061 . 0 197 11 0 0 0 0 0 -11.34479 0.9998351 1 1 1 0 A 2 1 39 138966 138966 C A 1 0 0 0 0 0 0 0 1 7725 759 27 1 1 IQSEC3 12 138966 Silent SNP C C3N-00175_T 138966 133136343 881 10473 ERC1 0 . GRCh38 12 1183317 1183317 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2053C>T p.= p.L685L ENST00000589028 10/18 171 108 63 135 135 0 strelka-varscan-mutect ERC1,synonymous_variant,p.=,ENST00000543086,NM_178039.3;ERC1,synonymous_variant,p.=,ENST00000589028,NM_178040.3;ERC1,synonymous_variant,p.=,ENST00000397203,;ERC1,synonymous_variant,p.=,ENST00000355446,NM_001301248.1;ERC1,synonymous_variant,p.=,ENST00000360905,;ERC1,synonymous_variant,p.=,ENST00000546231,;ERC1,synonymous_variant,p.=,ENST00000611180,;ERC1,non_coding_transcript_exon_variant,,ENST00000536573,;ERC1,synonymous_variant,p.=,ENST00000440394,;ERC1,synonymous_variant,p.=,ENST00000347735,;ERC1,synonymous_variant,p.=,ENST00000542302,;ERC1,synonymous_variant,p.=,ENST00000545948,;ERC1,non_coding_transcript_exon_variant,,ENST00000538971,; T ENST00000589028 Transcript synonymous_variant 2210/9202 2053/3351 685/1116 L Ctg/Ttg 1 1 ERC1 HGNC HGNC:17072 protein_coding YES CCDS8508.1 ENSP00000468263 Q8IUD2 UPI000007479C NM_178040.3 10/18 Pfam_domain:PF10174,hmmpanther:PTHR18861,hmmpanther:PTHR18861:SF1 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 1183317 1183317 C T 1 0 0 0 0 0 0 0 1 5059 912 32 3 3 ERC1 12 1183317 Silent SNP C C3N-00175_T 1044351 1183317 132091992 882 10474 CACNA2D4 0 . GRCh38 12 1844489 1844489 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2383C>A p.Leu795Met p.L795M ENST00000382722 25/38 143 124 19 135 135 0 strelka-varscan-mutect CACNA2D4,missense_variant,p.Leu795Met,ENST00000382722,NM_172364.4;CACNA2D4,missense_variant,p.Leu770Met,ENST00000587995,;CACNA2D4,missense_variant,p.Leu795Met,ENST00000586184,;CACNA2D4,missense_variant,p.Leu731Met,ENST00000588077,;CACNA2D4,missense_variant,p.Leu731Met,ENST00000585708,;CACNA2D4,missense_variant,p.Leu656Met,ENST00000585732,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000539048,;CACNA2D4,missense_variant,p.Leu76Met,ENST00000537784,;CACNA2D4,3_prime_UTR_variant,,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,; T ENST00000382722 Transcript missense_variant 2746/5475 2383/3414 795/1137 L/M Ctg/Atg 1 -1 CACNA2D4 HGNC HGNC:20202 protein_coding YES CCDS44785.1 ENSP00000372169 Q7Z3S7 UPI0000E593D9 NM_172364.4 tolerated(0.78) 25/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF26,Pfam_domain:PF08473 MODERATE 1 SNV 1 1 PASS rs1404930260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 1844489 1844489 G T 1 0 0 0 0 1 0 0 0 2239 991 35 2 2 CACNA2D4 12 1844489 Missense_Mutation SNP G C3N-00175_T 661172 1844489 131430820 883 10475 CACNA1C 0 . GRCh38 12 2115304 2115304 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.130C>A p.Pro44Thr p.P44T ENST00000347598 2/49 127 88 39 128 128 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Pro44Thr,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000406454,;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000335762,;CACNA1C,missense_variant,p.Pro44Thr,ENST00000480911,;CACNA1C,missense_variant,p.Pro44Thr,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Pro44Thr,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Pro44Thr,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Pro74Thr,ENST00000543114,; A ENST00000347598 Transcript missense_variant 130/6655 130/6561 44/2186 P/T Ccc/Acc 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious_low_confidence(0.01) 2/49 Prints_domain:PR01635,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 MODERATE 1 SNV 1 1 PASS rs1057518456 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 2115304 2115304 C A 1 0 0 0 0 1 0 0 0 2228 623 22 2 2 CACNA1C 12 2115304 Missense_Mutation SNP C C3N-00175_T 270815 2115304 131160005 884 10476 CACNA1C 0 . GRCh38 12 2664842 2664842 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.4394C>A p.Ala1465Asp p.A1465D ENST00000347598 37/49 61 39 22 59 59 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000406454,;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Ala1442Asp,ENST00000335762,;CACNA1C,missense_variant,p.Ala1465Asp,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Ala1439Asp,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Ala1445Asp,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Ala1437Asp,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Ala1434Asp,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Ala1406Asp,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Ala1406Asp,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Ala1404Asp,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Ala1417Asp,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Ala108Asp,ENST00000616390,;CACNA1C-AS2,downstream_gene_variant,,ENST00000545526,;CACNA1C,upstream_gene_variant,,ENST00000465934,;AC007618.3,downstream_gene_variant,,ENST00000366455,; A ENST00000347598 Transcript missense_variant 4394/6655 4394/6561 1465/2186 A/D gCc/gAc 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0.02) 37/49 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999849 1 1 1 0 A 3 1 39 2664842 2664842 C A 1 0 0 0 0 1 0 0 0 2228 739 26 2 2 CACNA1C 12 2664842 Missense_Mutation SNP C C3N-00175_T 549538 2664842 130610467 885 10477 FGF6 0 . GRCh38 12 4445472 4445472 + Silent SNP G G T rs761583325 C3N-00175_T C3N-00175_N G G c.99C>A p.= p.G33G ENST00000228837 1/3 203 176 27 255 255 0 strelka-varscan-mutect FGF6,synonymous_variant,p.=,ENST00000228837,NM_020996.2;FGF6,upstream_gene_variant,,ENST00000543077,; T ENST00000228837 Transcript synonymous_variant 143/743 99/627 33/208 G ggC/ggA rs761583325 1 -1 FGF6 HGNC HGNC:3684 protein_coding YES CCDS8527.1 ENSP00000228837 P10767 UPI00000411BF NM_020996.2 1/3 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF25,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs761583325 . 0 206 0 3 0 0 0 0 -20 0.9999915 1 1 1 0 T 2 4 39 4445472 4445472 G T 1 0 0 0 0 0 0 0 1 5720 1306 46 2 2 FGF6 12 4445472 Silent SNP G C3N-00175_T 1780630 4445472 128829837 886 10478 DYRK4 0 . GRCh38 12 4593151 4593151 + Missense_Mutation SNP G G T rs371271508 C3N-00175_T C3N-00175_N G G c.268G>T p.Gly90Cys p.G90C ENST00000540757 4/13 119 101 18 107 107 0 strelka-varscan-mutect DYRK4,missense_variant,p.Gly90Cys,ENST00000540757,NM_003845.2;DYRK4,missense_variant,p.Gly205Cys,ENST00000543431,;DYRK4,missense_variant,p.Gly90Cys,ENST00000010132,;DYRK4,downstream_gene_variant,,ENST00000536645,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536157,;DYRK4,downstream_gene_variant,,ENST00000539309,;DYRK4,downstream_gene_variant,,ENST00000542905,;DYRK4,downstream_gene_variant,,ENST00000539701,;DYRK4,downstream_gene_variant,,ENST00000537719,;DYRK4,downstream_gene_variant,,ENST00000538520,; T ENST00000540757 Transcript missense_variant 428/3272 268/1563 90/520 G/C Ggc/Tgc rs371271508 1 1 DYRK4 HGNC HGNC:3095 protein_coding YES CCDS8530.1 ENSP00000441755 Q9NR20 UPI000006E05C NM_003845.2 deleterious(0.01) 4/13 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF22 MODERATE 1 SNV 1 1 PASS rs371271508 . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 39 4593151 4593151 G T 1 0 0 0 0 1 0 0 0 4682 1348 47 2 2 DYRK4 12 4593151 Missense_Mutation SNP G C3N-00175_T 147679 4593151 128682158 887 10479 AKAP3 0 . GRCh38 12 4638115 4638115 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.82C>A p.Gln28Lys p.Q28K ENST00000228850 4/6 192 138 54 248 247 1 strelka-varscan-mutect AKAP3,missense_variant,p.Gln28Lys,ENST00000228850,NM_001278309.1;AKAP3,missense_variant,p.Gln28Lys,ENST00000545990,NM_006422.3;AKAP3,missense_variant,p.Gln28Lys,ENST00000540967,;AKAP3,missense_variant,p.Gln28Lys,ENST00000536414,;AKAP3,downstream_gene_variant,,ENST00000544636,;AKAP3,downstream_gene_variant,,ENST00000541484,;RP11-500M8.7,intron_variant,,ENST00000536588,;RP11-500M8.6,upstream_gene_variant,,ENST00000537929,; T ENST00000228850 Transcript missense_variant 629/3339 82/2562 28/853 Q/K Cag/Aag COSM2068389,COSM2068390 1 -1 AKAP3 HGNC HGNC:373 protein_coding YES CCDS8531.1 ENSP00000228850 O75969 V9HWD4 UPI000013C8DF NM_001278309.1 tolerated(0.09) 4/6 hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF9,SMART_domains:SM00807 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 4638115 4638115 G T 1 0 0 0 0 1 0 0 0 536 1357 47 2 2 AKAP3 12 4638115 Missense_Mutation SNP G C3N-00175_T 44964 4638115 128637194 888 10480 ANO2 0 . GRCh38 12 5732551 5732551 + Missense_Mutation SNP A A C rs373654644 C3N-00175_T C3N-00175_N A A c.1517T>G p.Leu506Trp p.L506W ENST00000356134 16/27 60 52 8 86 86 0 strelka-varscan-mutect ANO2,missense_variant,p.Leu506Trp,ENST00000327087,;ANO2,missense_variant,p.Leu506Trp,ENST00000356134,NM_001278597.1,NM_001278596.1;ANO2,missense_variant,p.Leu510Trp,ENST00000546188,;ANO2,missense_variant,p.Leu65Trp,ENST00000545860,;ANO2,non_coding_transcript_exon_variant,,ENST00000538154,;ANO2,non_coding_transcript_exon_variant,,ENST00000542326,;ANO2,non_coding_transcript_exon_variant,,ENST00000540543,; C ENST00000356134 Transcript missense_variant 1589/3717 1517/3000 506/999 L/W tTg/tGg rs373654644 1 -1 ANO2 HGNC HGNC:1183 protein_coding YES CCDS44807.2 ENSP00000348453 Q9NQ90 UPI00000715DF NM_001278597.1,NM_001278596.1 tolerated(0.19) 16/27 Pfam_domain:PF04547 MODERATE 1 SNV 5 1 PASS rs373654644 . 0 206 2 2 0 0 0 0 -14.54902 0.9999976 1 1 1 0 C 3 2 39 5732551 5732551 A C 1 0 0 0 0 1 0 0 0 804 131 5 5 5 ANO2 12 5732551 Missense_Mutation SNP A C3N-00175_T 1094436 5732551 127542758 889 10481 SLC2A14 0 . GRCh38 12 7821248 7821248 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1056G>T p.= p.V352V ENST00000539924 7/10 189 168 21 206 205 1 strelka-mutect SLC2A14,synonymous_variant,p.=,ENST00000543909,NM_001286233.1;SLC2A14,synonymous_variant,p.=,ENST00000340749,NM_001286235.1;SLC2A14,synonymous_variant,p.=,ENST00000431042,NM_001286234.1;SLC2A14,synonymous_variant,p.=,ENST00000616981,;SLC2A14,synonymous_variant,p.=,ENST00000542546,;SLC2A14,synonymous_variant,p.=,ENST00000396589,NM_153449.3;SLC2A14,synonymous_variant,p.=,ENST00000539924,NM_001286237.1;SLC2A14,synonymous_variant,p.=,ENST00000535295,NM_001286236.1;SLC2A14,5_prime_UTR_variant,,ENST00000542505,; A ENST00000539924 Transcript synonymous_variant 1077/1873 1056/1608 352/535 V gtG/gtT 1 -1 SLC2A14 HGNC HGNC:18301 protein_coding YES CCDS66302.1 ENSP00000445929 Q8TDB8 UPI0001915325 NM_001286237.1 7/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF23,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 7821248 7821248 C A 1 0 0 0 0 0 0 0 1 14813 581 21 2 2 SLC2A14 12 7821248 Silent SNP C C3N-00175_T 2088697 7821248 125454061 890 10482 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C G rs121913529 C3N-00175_T C3N-00175_N C C c.35G>C p.Gly12Ala p.G12A ENST00000256078 2/6 265 188 77 348 348 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Ala,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Ala,ENST00000556131,;KRAS,missense_variant,p.Gly12Ala,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Ala,ENST00000557334,; G ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/A gGt/gCt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.02) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 25245350 25245350 C G 1 0 0 0 0 1 0 0 0 8318 507 18 4 4 KRAS 12 25245350 Missense_Mutation SNP C C3N-00175_T 17424102 25245350 108029959 891 10483 SMCO2 0 . GRCh38 12 27501959 27501959 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.870C>T p.= p.V290V ENST00000416383 9/9 58 42 16 70 70 0 strelka-varscan-mutect SMCO2,synonymous_variant,p.=,ENST00000416383,NM_001145010.1;SMCO2,synonymous_variant,p.=,ENST00000298876,;SMCO2,synonymous_variant,p.=,ENST00000535986,;SMCO2,non_coding_transcript_exon_variant,,ENST00000541168,;RARSP1,downstream_gene_variant,,ENST00000542842,; T ENST00000416383 Transcript synonymous_variant 1046/1272 870/1032 290/343 V gtC/gtT 1 1 SMCO2 HGNC HGNC:34448 protein_coding YES CCDS44852.1 ENSP00000387617 A6NFE2 UPI000166275D NM_001145010.1 9/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR22422:SF5,hmmpanther:PTHR22422,Pfam_domain:PF14992 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 27501959 27501959 C T 1 0 0 0 0 0 0 0 1 15083 842 30 3 3 SMCO2 12 27501959 Silent SNP C C3N-00175_T 2256609 27501959 105773350 892 10484 OVCH1 0 . GRCh38 12 29455406 29455406 + Splice_Site SNP C C A novel C3N-00175_T C3N-00175_N C C c.2281-1G>T p.X761_splice ENST00000318184 88 79 9 76 76 0 strelka-varscan-mutect OVCH1,splice_acceptor_variant,,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;OVCH1-AS1,intron_variant,,ENST00000550906,; A ENST00000318184 Transcript splice_acceptor_variant -/3405 2281/3405 761/1134 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 19/27 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.25907 1 1 1 1 0 A 5 1 39 29455406 29455406 C A 1 0 0 0 0 0 0 1 0 11393 695 24 2 2 OVCH1 12 29455406 Splice_Site SNP C C3N-00175_T 1953447 29455406 103819903 893 10485 DNM1L 0 . GRCh38 12 32733752 32733752 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.1523A>G p.Asn508Ser p.N508S ENST00000553257 14/21 217 185 32 309 309 0 strelka-varscan-mutect DNM1L,missense_variant,p.Asn495Ser,ENST00000452533,NM_012063.3;DNM1L,missense_variant,p.Asn508Ser,ENST00000381000,NM_001278465.1;DNM1L,missense_variant,p.Asn292Ser,ENST00000414834,NM_001278466.1;DNM1L,missense_variant,p.Asn508Ser,ENST00000358214,;DNM1L,missense_variant,p.Asn495Ser,ENST00000266481,NM_005690.4;DNM1L,missense_variant,p.Asn508Ser,ENST00000553257,NM_001278464.1;DNM1L,missense_variant,p.Asn495Ser,ENST00000549701,NM_012062.4;DNM1L,missense_variant,p.Asn495Ser,ENST00000547312,NM_001278463.1;RP11-278C7.3,upstream_gene_variant,,ENST00000620472,;RP11-278C7.5,downstream_gene_variant,,ENST00000620106,;YARS2,intron_variant,,ENST00000551673,;DNM1L,3_prime_UTR_variant,,ENST00000546757,;DNM1L,3_prime_UTR_variant,,ENST00000546649,;DNM1L,3_prime_UTR_variant,,ENST00000547078,;DNM1L,non_coding_transcript_exon_variant,,ENST00000552743,;DNM1L,non_coding_transcript_exon_variant,,ENST00000550093,;DNM1L,non_coding_transcript_exon_variant,,ENST00000548151,;DNM1L,downstream_gene_variant,,ENST00000413295,;DNM1L,downstream_gene_variant,,ENST00000434676,;DNM1L,upstream_gene_variant,,ENST00000549157,; G ENST00000553257 Transcript missense_variant 1600/2699 1523/2250 508/749 N/S aAc/aGc 1 1 DNM1L HGNC HGNC:2973 protein_coding YES CCDS61095.1 ENSP00000449089 O00429 UPI00017A7CB6 NM_001278464.1 deleterious(0) 14/21 hmmpanther:PTHR11566:SF39,hmmpanther:PTHR11566,Pfam_domain:PF01031 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 32733752 32733752 A G 1 0 0 0 0 1 0 0 0 4484 43 2 5 5 DNM1L 12 32733752 Missense_Mutation SNP A C3N-00175_T 3278346 32733752 100541557 894 10486 PKP2 0 . GRCh38 12 32877890 32877890 + Frame_Shift_Del DEL C C - rs749862514 C3N-00175_T C3N-00175_N C C c.990delG p.Asn331IlefsTer21 p.N331Ifs*21 ENST00000070846 3/14 177 115 62 199 199 0 sindel-varindel-pindel PKP2,frameshift_variant,p.Asn331IlefsTer21,ENST00000340811,NM_001005242.2;PKP2,frameshift_variant,p.Asn331IlefsTer21,ENST00000070846,NM_004572.3; - ENST00000070846 Transcript frameshift_variant 1015/4241 990/2646 330/881 G/X ggG/gg rs749862514 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 3/14 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 32877890 32877890 C - 1 0 1 0 1 0 0 0 0 12081 842 30 0 0 PKP2 12 32877890 Frame_Shift_Del DEL C C3N-00175_T 144138 32877890 100397419 895 10487 ABCD2 0 . GRCh38 12 39617089 39617089 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1019A>T p.Tyr340Phe p.Y340F ENST00000308666 2/10 138 122 16 158 158 0 strelka-varscan-mutect ABCD2,missense_variant,p.Tyr340Phe,ENST00000308666,NM_005164.3; A ENST00000308666 Transcript missense_variant 1155/6238 1019/2223 340/740 Y/F tAc/tTc 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 tolerated(0.13) 2/10 PROSITE_profiles:PS50929,hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24,Pfam_domain:PF06472,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 39617089 39617089 T A 1 0 0 0 0 1 0 0 0 65 1638 57 4 4 ABCD2 12 39617089 Missense_Mutation SNP T C3N-00175_T 6739199 39617089 93658220 896 10488 ABCD2 0 . GRCh38 12 39619520 39619520 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.96T>A p.= p.A32A ENST00000308666 1/10 291 252 39 272 271 1 strelka-varscan-mutect ABCD2,synonymous_variant,p.=,ENST00000308666,NM_005164.3; T ENST00000308666 Transcript synonymous_variant 232/6238 96/2223 32/740 A gcT/gcA 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 39619520 39619520 A T 1 0 0 0 0 0 0 0 1 65 291 11 4 4 ABCD2 12 39619520 Silent SNP A C3N-00175_T 2431 39619520 93655789 897 10489 C12orf40 0 . GRCh38 12 39721140 39721140 + Silent SNP A A C novel C3N-00175_T C3N-00175_N A A c.1848A>C p.= p.L616L ENST00000324616 13/13 284 254 30 343 343 0 strelka-varscan-mutect C12orf40,synonymous_variant,p.=,ENST00000324616,NM_001031748.2;C12orf40,intron_variant,,ENST00000468200,; C ENST00000324616 Transcript synonymous_variant 2002/2776 1848/1959 616/652 L ctA/ctC 1 1 C12orf40 HGNC HGNC:26846 protein_coding YES CCDS41770.1 ENSP00000317671 Q86WS4 UPI000069A925 NM_001031748.2 13/13 hmmpanther:PTHR35158:SF1,hmmpanther:PTHR35158,Pfam_domain:PF15089 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 39721140 39721140 A C 1 0 0 0 0 0 0 0 1 1809 349 13 5 5 C12orf40 12 39721140 Silent SNP A C3N-00175_T 101620 39721140 93554169 898 10490 PDZRN4 0 . GRCh38 12 41563620 41563620 + Missense_Mutation SNP G G T rs751304304 C3N-00175_T C3N-00175_N G G c.1438G>T p.Val480Leu p.V480L ENST00000402685 8/10 147 116 31 147 147 0 strelka-varscan-mutect PDZRN4,missense_variant,p.Val220Leu,ENST00000298919,;PDZRN4,missense_variant,p.Val480Leu,ENST00000402685,NM_001164595.1;PDZRN4,missense_variant,p.Val222Leu,ENST00000539469,NM_013377.3;PDZRN4,non_coding_transcript_exon_variant,,ENST00000548316,; T ENST00000402685 Transcript missense_variant 1446/3347 1438/3111 480/1036 V/L Gtg/Ttg rs751304304 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 tolerated(0.3) 8/10 Gene3D:2.30.42.10,Pfam_domain:PF00595,hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF6,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 2 1 PASS rs751304304 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41563620 41563620 G T 1 0 0 0 0 1 0 0 0 11798 1145 40 1 1 PDZRN4 12 41563620 Missense_Mutation SNP G C3N-00175_T 1842480 41563620 91711689 899 10491 YAF2 0 . GRCh38 12 42235844 42235844 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.306G>T p.Arg102Ser p.R102S ENST00000555248 3/3 360 320 40 424 424 0 strelka-varscan-mutect YAF2,missense_variant,p.Arg102Ser,ENST00000555248,NM_001190980.1;YAF2,intron_variant,,ENST00000327791,NM_001190979.1;YAF2,intron_variant,,ENST00000534854,NM_005748.4;YAF2,intron_variant,,ENST00000380790,NM_001190977.1;YAF2,intron_variant,,ENST00000548917,;PPHLN1,upstream_gene_variant,,ENST00000549190,;YAF2,non_coding_transcript_exon_variant,,ENST00000541702,;YAF2,intron_variant,,ENST00000547622,;YAF2,intron_variant,,ENST00000547724,;YAF2,non_coding_transcript_exon_variant,,ENST00000546782,;YAF2,intron_variant,,ENST00000552109,;YAF2,intron_variant,,ENST00000547351,;YAF2,intron_variant,,ENST00000551268,;YAF2,intron_variant,,ENST00000546726,;YAF2,intron_variant,,ENST00000547254,;YAF2,intron_variant,,ENST00000552928,;YAF2,intron_variant,,ENST00000548661,; A ENST00000555248 Transcript missense_variant 475/5095 306/354 102/117 R/S agG/agT 1 -1 YAF2 HGNC HGNC:17363 protein_coding CCDS53780.1 ENSP00000451626 Q8IY57 UPI000022934E NM_001190980.1 tolerated_low_confidence(0.16) 3/3 MODERATE SNV 2 1 PASS rs1373017382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 42235844 42235844 C A 1 0 0 0 0 1 0 0 0 18025 622 22 2 2 YAF2 12 42235844 Missense_Mutation SNP C C3N-00175_T 672224 42235844 91039465 900 10492 ZCRB1 0 . GRCh38 12 42313158 42313158 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.563G>C p.Ser188Thr p.S188T ENST00000266529 8/8 94 67 27 162 162 0 strelka-varscan-mutect ZCRB1,missense_variant,p.Ser188Thr,ENST00000266529,NM_033114.3;ZCRB1,missense_variant,p.Ser147Thr,ENST00000552673,;PPHLN1,intron_variant,,ENST00000549190,;ZCRB1,downstream_gene_variant,,ENST00000552235,; G ENST00000266529 Transcript missense_variant 747/1827 563/654 188/217 S/T aGt/aCt 1 -1 ZCRB1 HGNC HGNC:29620 protein_coding YES CCDS8740.1 ENSP00000266529 Q8TBF4 A0A024R106 UPI00000467ED NM_033114.3 tolerated(0.36) 8/8 hmmpanther:PTHR23139 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 42313158 42313158 C G 1 0 0 0 0 1 0 0 0 18171 565 20 4 4 ZCRB1 12 42313158 Missense_Mutation SNP C C3N-00175_T 77314 42313158 90962151 901 10493 ZCRB1 0 . GRCh38 12 42313183 42313183 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.538G>T p.Glu180Ter p.E180* ENST00000266529 8/8 75 61 14 114 114 0 strelka-mutect ZCRB1,stop_gained,p.Glu180Ter,ENST00000266529,NM_033114.3;ZCRB1,stop_gained,p.Glu139Ter,ENST00000552673,;PPHLN1,intron_variant,,ENST00000549190,;ZCRB1,downstream_gene_variant,,ENST00000552235,; A ENST00000266529 Transcript stop_gained 722/1827 538/654 180/217 E/* Gaa/Taa 1 -1 ZCRB1 HGNC HGNC:29620 protein_coding YES CCDS8740.1 ENSP00000266529 Q8TBF4 A0A024R106 UPI00000467ED NM_033114.3 8/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23139 HIGH 1 SNV 1 1 PASS rs1288153232 . 0 200 3 5 2 0 0 0 -10.16394 0.9305889 1 1 1 0 A 4 1 39 42313183 42313183 C A 1 0 0 0 0 0 1 0 0 18171 922 32 2 2 ZCRB1 12 42313183 Nonsense_Mutation SNP C C3N-00175_T 25 42313183 90962126 902 10494 ADAMTS20 0 . GRCh38 12 43551001 43551001 + Missense_Mutation SNP C C A rs767895763 C3N-00175_T C3N-00175_N C C c.361G>T p.Ala121Ser p.A121S ENST00000389420 2/39 128 111 17 178 178 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Ala121Ser,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Ala121Ser,ENST00000395541,;ADAMTS20,missense_variant,p.Ala121Ser,ENST00000553158,; A ENST00000389420 Transcript missense_variant 361/6076 361/5733 121/1910 A/S Gca/Tca rs767895763 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(0.64) 2/39 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS rs767895763 . 0 206 0 3 0 0 0 0 -20 0.9999915 1 1 1 0 A 3 1 39 43551001 43551001 C A 1 0 0 0 0 1 0 0 0 310 768 27 1 1 ADAMTS20 12 43551001 Missense_Mutation SNP C C3N-00175_T 1237818 43551001 89724308 903 10495 DHH 0 . GRCh38 12 49089987 49089987 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1063C>A p.Arg355Ser p.R355S ENST00000266991 3/3 158 113 45 188 188 0 strelka-varscan-mutect DHH,missense_variant,p.Arg355Ser,ENST00000266991,NM_021044.2;RP11-386G11.8,upstream_gene_variant,,ENST00000553174,;RP11-386G11.8,upstream_gene_variant,,ENST00000548030,; T ENST00000266991 Transcript missense_variant 1370/1936 1063/1191 355/396 R/S Cgc/Agc 1 -1 DHH HGNC HGNC:2865 protein_coding YES CCDS8779.1 ENSP00000266991 O43323 UPI0000035884 NM_021044.2 deleterious(0.05) 3/3 hmmpanther:PTHR11889,hmmpanther:PTHR11889:SF56,PIRSF_domain:PIRSF009400,Pfam_domain:PF01079,Prints_domain:PR00632 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -20 0.9998653 1 1 1 0 T 3 4 39 49089987 49089987 G T 1 0 0 0 0 1 0 0 0 4288 1116 39 1 1 DHH 12 49089987 Missense_Mutation SNP G C3N-00175_T 5538986 49089987 84185322 904 10496 FAIM2 0 . GRCh38 12 49887405 49887405 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.782G>T p.Gly261Val p.G261V ENST00000320634 11/12 221 193 28 257 257 0 strelka-varscan-mutect FAIM2,missense_variant,p.Gly261Val,ENST00000320634,NM_012306.3;FAIM2,missense_variant,p.Gly215Val,ENST00000550890,;FAIM2,missense_variant,p.Gly219Val,ENST00000552669,;FAIM2,intron_variant,,ENST00000552863,;FAIM2,downstream_gene_variant,,ENST00000550635,;FAIM2,downstream_gene_variant,,ENST00000547871,;FAIM2,3_prime_UTR_variant,,ENST00000550195,; A ENST00000320634 Transcript missense_variant 877/4654 782/951 261/316 G/V gGa/gTa 1 -1 FAIM2 HGNC HGNC:17067 protein_coding YES CCDS8791.1 ENSP00000321951 Q9BWQ8 UPI0000072B0C NM_012306.3 deleterious(0.02) 11/12 Pfam_domain:PF01027,hmmpanther:PTHR23291,hmmpanther:PTHR23291:SF18,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 49887405 49887405 C A 1 0 0 0 0 1 0 0 0 5248 855 30 2 2 FAIM2 12 49887405 Missense_Mutation SNP C C3N-00175_T 797418 49887405 83387904 905 10497 SLC4A8 0 . GRCh38 12 51450991 51450991 + Missense_Mutation SNP G G T rs763980383 C3N-00175_T C3N-00175_N G G c.246G>T p.Gln82His p.Q82H ENST00000453097 3/25 60 37 23 60 60 0 strelka-varscan-mutect SLC4A8,missense_variant,p.Gln82His,ENST00000453097,NM_001039960.2;SLC4A8,missense_variant,p.Gln29His,ENST00000358657,NM_001258401.2;SLC4A8,missense_variant,p.Gln29His,ENST00000514353,NM_001258403.1;SLC4A8,missense_variant,p.Gln29His,ENST00000535225,NM_001267615.1,NM_001258402.1;SLC4A8,non_coding_transcript_exon_variant,,ENST00000548352,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000551071,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000604314,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000319957,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000547697,;SLC4A8,non_coding_transcript_exon_variant,,ENST00000552001,; T ENST00000453097 Transcript missense_variant 463/11824 246/3282 82/1093 Q/H caG/caT rs763980383 1 1 SLC4A8 HGNC HGNC:11034 protein_coding YES CCDS44890.1 ENSP00000405812 Q2Y0W8 UPI00005E6FB4 NM_001039960.2 tolerated(0.1) 3/25 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF37 MODERATE 1 SNV 1 1 PASS rs763980383 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 51450991 51450991 G T 1 0 0 0 0 1 0 0 0 14936 991 35 2 2 SLC4A8 12 51450991 Missense_Mutation SNP G C3N-00175_T 1563586 51450991 81824318 906 10498 AMHR2 0 . GRCh38 12 53430266 53430266 + Missense_Mutation SNP G G T rs201339353 C3N-00175_T C3N-00175_N G G c.1409G>T p.Trp470Leu p.W470L ENST00000257863 10/11 406 365 41 418 418 0 strelka-varscan-mutect AMHR2,missense_variant,p.Trp470Leu,ENST00000257863,NM_020547.2;AMHR2,missense_variant,p.Gly469Cys,ENST00000550311,NM_001164690.1;AMHR2,missense_variant,p.Trp167Leu,ENST00000550839,;AMHR2,intron_variant,,ENST00000379791,NM_001164691.1;AMHR2,non_coding_transcript_exon_variant,,ENST00000552233,;AMHR2,downstream_gene_variant,,ENST00000548303,; T ENST00000257863 Transcript missense_variant 1489/1863 1409/1722 470/573 W/L tGg/tTg rs201339353 1 1 AMHR2 HGNC HGNC:465 protein_coding YES CCDS8858.1 ENSP00000257863 Q16671 UPI0000125970 NM_020547.2 deleterious(0) 10/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF037392,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF49,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs201339353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 53430266 53430266 G T 1 0 0 0 0 1 0 0 0 672 1357 47 2 2 AMHR2 12 53430266 Missense_Mutation SNP G C3N-00175_T 1979275 53430266 79845043 907 10499 TESPA1 0 . GRCh38 12 54962961 54962961 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.937G>T p.Asp313Tyr p.D313Y ENST00000449076 9/11 137 99 38 193 193 0 strelka-varscan-mutect TESPA1,missense_variant,p.Asp175Tyr,ENST00000524622,NM_001261844.1,NM_014796.2;TESPA1,missense_variant,p.Asp313Tyr,ENST00000449076,NM_001136030.2;TESPA1,missense_variant,p.Asp175Tyr,ENST00000532804,;TESPA1,missense_variant,p.Asp313Tyr,ENST00000316577,NM_001098815.2;TESPA1,missense_variant,p.Asp175Tyr,ENST00000531122,;TESPA1,intron_variant,,ENST00000532757,;TESPA1,downstream_gene_variant,,ENST00000524668,;TESPA1,downstream_gene_variant,,ENST00000526532,;TESPA1,upstream_gene_variant,,ENST00000528240,;TESPA1,downstream_gene_variant,,ENST00000533446,;TESPA1,downstream_gene_variant,,ENST00000524959,;TESPA1,3_prime_UTR_variant,,ENST00000524923,;TESPA1,downstream_gene_variant,,ENST00000525978,; A ENST00000449076 Transcript missense_variant 1070/2010 937/1566 313/521 D/Y Gac/Tac 1 -1 TESPA1 HGNC HGNC:29109 protein_coding YES CCDS44913.1 ENSP00000400892 A2RU30 A0A024RB73 UPI00001FC438 NM_001136030.2 deleterious(0.01) 9/11 hmmpanther:PTHR17469 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 54962961 54962961 C A 1 0 0 0 0 1 0 0 0 16189 855 30 2 2 TESPA1 12 54962961 Missense_Mutation SNP C C3N-00175_T 1532695 54962961 78312348 908 10500 OR6C65 0 . GRCh38 12 55401111 55401111 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.583C>A p.Leu195Ile p.L195I ENST00000379665 1/1 132 84 48 172 172 0 strelka-varscan-mutect OR6C65,missense_variant,p.Leu195Ile,ENST00000379665,NM_001005518.1;OR6C73P,downstream_gene_variant,,ENST00000546432,; A ENST00000379665 Transcript missense_variant 682/1076 583/939 195/312 L/I Ctt/Att 1 1 OR6C65 HGNC HGNC:31295 protein_coding YES CCDS31821.1 ENSP00000368986 A6NJZ3 A0A126GW71 UPI000044D410 NM_001005518.1 tolerated_low_confidence(0.12) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 55401111 55401111 C A 1 0 0 0 0 1 0 0 0 11263 797 28 2 2 OR6C65 12 55401111 Missense_Mutation SNP C C3N-00175_T 438150 55401111 77874198 909 10501 PAN2 0 . GRCh38 12 56332883 56332883 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.212A>C p.Glu71Ala p.E71A ENST00000425394 2/26 193 171 22 198 198 0 strelka-varscan-mutect PAN2,missense_variant,p.Glu71Ala,ENST00000425394,NM_001127460.2;PAN2,missense_variant,p.Glu71Ala,ENST00000610546,;PAN2,missense_variant,p.Glu71Ala,ENST00000548043,;PAN2,missense_variant,p.Glu71Ala,ENST00000440411,NM_014871.4;PAN2,missense_variant,p.Glu71Ala,ENST00000257931,NM_001166279.1;PAN2,intron_variant,,ENST00000547572,;IL23A,upstream_gene_variant,,ENST00000619177,;IL23A,upstream_gene_variant,,ENST00000622119,;PAN2,non_coding_transcript_exon_variant,,ENST00000551359,;PAN2,non_coding_transcript_exon_variant,,ENST00000547994,;PAN2,non_coding_transcript_exon_variant,,ENST00000549964,;PAN2,upstream_gene_variant,,ENST00000547518,; G ENST00000425394 Transcript missense_variant 589/5372 212/3609 71/1202 E/A gAa/gCa 1 -1 PAN2 HGNC HGNC:20074 protein_coding YES CCDS44922.1 ENSP00000401721 Q504Q3 UPI0000577D0A NM_001127460.2 deleterious(0.01) 2/26 HAMAP:MF_03182,hmmpanther:PTHR15728,hmmpanther:PTHR15728:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 56332883 56332883 T G 1 0 0 0 0 1 0 0 0 11495 1783 62 5 5 PAN2 12 56332883 Missense_Mutation SNP T C3N-00175_T 931772 56332883 76942426 910 10502 GLI1 0 . GRCh38 12 57471341 57471341 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2601G>T p.Gln867His p.Q867H ENST00000228682 12/12 41 29 12 49 49 0 strelka-varscan-mutect GLI1,missense_variant,p.Gln867His,ENST00000228682,NM_005269.2;GLI1,missense_variant,p.Gln826His,ENST00000546141,NM_001167609.1;GLI1,missense_variant,p.Gln739His,ENST00000543426,NM_001160045.1;GLI1,missense_variant,p.Gln826His,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;ARHGAP9,downstream_gene_variant,,ENST00000548139,;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000550130,;ARHGAP9,downstream_gene_variant,,ENST00000550454,;MARS,upstream_gene_variant,,ENST00000549133,;ARHGAP9,downstream_gene_variant,,ENST00000547200,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;ARHGAP9,downstream_gene_variant,,ENST00000548148,;ARHGAP9,downstream_gene_variant,,ENST00000550440,;ARHGAP9,downstream_gene_variant,,ENST00000546704,; T ENST00000228682 Transcript missense_variant 2692/3613 2601/3321 867/1106 Q/H caG/caT 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 tolerated(0.17) 12/12 hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818 MODERATE 1 SNV 1 1 PASS . . 0 191 18 0 0 0 0 0 -20 0.999523 1 1 1 0 T 3 4 39 57471341 57471341 G T 1 0 0 0 0 1 0 0 0 6315 962 34 2 2 GLI1 12 57471341 Missense_Mutation SNP G C3N-00175_T 1138458 57471341 75803968 911 10503 OS9 0 . GRCh38 12 57695995 57695995 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.437G>T p.Gly146Val p.G146V ENST00000315970 4/15 248 219 29 242 242 0 strelka-varscan-mutect OS9,missense_variant,p.Gly146Val,ENST00000315970,NM_006812.3;OS9,missense_variant,p.Gly146Val,ENST00000257966,NM_001261420.1;OS9,missense_variant,p.Gly146Val,ENST00000389142,NM_001017957.2;OS9,missense_variant,p.Gly146Val,ENST00000551035,NM_001261421.1;OS9,missense_variant,p.Gly146Val,ENST00000552285,NM_001017956.2;OS9,missense_variant,p.Gly146Val,ENST00000389146,NM_001017958.2;OS9,missense_variant,p.Gly87Val,ENST00000439210,NM_001261423.1;OS9,intron_variant,,ENST00000435406,NM_001261422.1;OS9,intron_variant,,ENST00000413095,;OS9,intron_variant,,ENST00000547079,;OS9,intron_variant,,ENST00000550372,;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,3_prime_UTR_variant,,ENST00000552423,;OS9,3_prime_UTR_variant,,ENST00000551285,;OS9,3_prime_UTR_variant,,ENST00000550848,;OS9,non_coding_transcript_exon_variant,,ENST00000549307,;OS9,non_coding_transcript_exon_variant,,ENST00000553208,;OS9,non_coding_transcript_exon_variant,,ENST00000550793,;OS9,intron_variant,,ENST00000552787,;OS9,downstream_gene_variant,,ENST00000549897,; T ENST00000315970 Transcript missense_variant 478/2691 437/2004 146/667 G/V gGc/gTc 1 1 OS9 HGNC HGNC:16994 protein_coding YES CCDS31843.1 ENSP00000318165 Q13438 UPI0000130EAC NM_006812.3 deleterious(0) 4/15 Pfam_domain:PF07915,hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 57695995 57695995 G T 1 0 0 0 0 1 0 0 0 11338 1203 42 2 2 OS9 12 57695995 Missense_Mutation SNP G C3N-00175_T 224654 57695995 75579314 912 10504 HELB 0 . GRCh38 12 66306489 66306489 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.752A>T p.His251Leu p.H251L ENST00000247815 3/13 61 53 8 102 102 0 strelka-varscan-mutect HELB,missense_variant,p.His251Leu,ENST00000247815,NM_033647.3;HELB,missense_variant,p.His251Leu,ENST00000545134,;HELB,missense_variant,p.His251Leu,ENST00000542394,;HELB,missense_variant,p.His251Leu,ENST00000440906,; T ENST00000247815 Transcript missense_variant 811/12866 752/3264 251/1087 H/L cAt/cTt 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 deleterious(0.01) 3/13 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -18.71174 1 1 1 1 0 T 3 4 39 66306489 66306489 A T 1 0 0 0 0 1 0 0 0 6927 217 8 4 4 HELB 12 66306489 Missense_Mutation SNP A C3N-00175_T 8610494 66306489 66968820 913 10505 DYRK2 0 . GRCh38 12 67658479 67658479 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1572G>T p.Met524Ile p.M524I ENST00000344096 3/3 44 37 7 52 52 0 strelka-varscan-mutect DYRK2,missense_variant,p.Met524Ile,ENST00000344096,NM_006482.2;DYRK2,missense_variant,p.Met451Ile,ENST00000393555,NM_003583.3;DYRK2,downstream_gene_variant,,ENST00000543747,;DYRK2,downstream_gene_variant,,ENST00000319833,;DYRK2,downstream_gene_variant,,ENST00000542503,;RP11-335O4.3,downstream_gene_variant,,ENST00000425371,; T ENST00000344096 Transcript missense_variant 1985/8912 1572/1806 524/601 M/I atG/atT 1 1 DYRK2 HGNC HGNC:3093 protein_coding YES CCDS8978.1 ENSP00000342105 Q92630 UPI000006E92B NM_006482.2 tolerated(0.11) 3/3 PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF51,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -17.3998 1 1 1 1 0 T 3 4 39 67658479 67658479 G T 1 0 0 0 0 1 0 0 0 4680 1290 45 2 2 DYRK2 12 67658479 Missense_Mutation SNP G C3N-00175_T 1351990 67658479 65616830 914 10506 TRHDE 0 . GRCh38 12 72272824 72272824 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.46T>A p.Ser16Thr p.S16T ENST00000261180 1/19 67 61 6 88 88 0 strelka-varscan-mutect TRHDE,missense_variant,p.Ser16Thr,ENST00000261180,NM_013381.2;TRHDE,upstream_gene_variant,,ENST00000547300,;TRHDE-AS1,non_coding_transcript_exon_variant,,ENST00000426250,;TRHDE-AS1,upstream_gene_variant,,ENST00000435350,;TRHDE-AS1,upstream_gene_variant,,ENST00000550334,;TRHDE,intron_variant,,ENST00000548156,;TRHDE,upstream_gene_variant,,ENST00000552503,; A ENST00000261180 Transcript missense_variant 142/10733 46/3075 16/1024 S/T Tcc/Acc 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious_low_confidence(0.03) 1/19 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -13.88176 1 1 1 1 0 A 3 1 39 72272824 72272824 T A 1 0 0 0 0 1 0 0 0 16968 1551 54 4 4 TRHDE 12 72272824 Missense_Mutation SNP T C3N-00175_T 4614345 72272824 61002485 915 10507 TRHDE 0 . GRCh38 12 72575512 72575512 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2156G>T p.Gly719Val p.G719V ENST00000261180 12/19 272 196 76 300 299 1 strelka-varscan-mutect TRHDE,missense_variant,p.Gly719Val,ENST00000261180,NM_013381.2;TRHDE,non_coding_transcript_exon_variant,,ENST00000549138,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549401,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549922,; T ENST00000261180 Transcript missense_variant 2252/10733 2156/3075 719/1024 G/V gGc/gTc 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0.05) 12/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 MODERATE 1 SNV 1 1 PASS rs1032850885 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 72575512 72575512 G T 1 0 0 0 0 1 0 0 0 16968 1203 42 2 2 TRHDE 12 72575512 Missense_Mutation SNP G C3N-00175_T 302688 72575512 60699797 916 10508 TRHDE 0 . GRCh38 12 72618980 72618980 + Missense_Mutation SNP G G T rs745307313 C3N-00175_T C3N-00175_N G G c.2276G>T p.Arg759Leu p.R759L ENST00000261180 13/19 119 92 27 135 135 0 strelka-varscan-mutect TRHDE,missense_variant,p.Arg759Leu,ENST00000261180,NM_013381.2;TRHDE,downstream_gene_variant,,ENST00000549138,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549922,; T ENST00000261180 Transcript missense_variant 2372/10733 2276/3075 759/1024 R/L cGa/cTa rs745307313,COSM1606622 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0.01) 13/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs745307313 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 72618980 72618980 G T 1 0 0 0 0 1 0 0 0 16968 1058 37 1 1 TRHDE 12 72618980 Missense_Mutation SNP G C3N-00175_T 43468 72618980 60656329 917 10509 GLIPR1L2 0 . GRCh38 12 75422951 75422951 + Missense_Mutation SNP G G A rs144813686 C3N-00175_T C3N-00175_N G G c.632G>A p.Arg211Gln p.R211Q ENST00000550916 4/6 270 205 65 238 238 0 strelka-varscan-mutect GLIPR1L2,missense_variant,p.Arg211Gln,ENST00000550916,NM_001270396.1;GLIPR1L2,missense_variant,p.Arg104Gln,ENST00000378692,;GLIPR1L2,missense_variant,p.Arg211Gln,ENST00000320460,NM_152436.2;GLIPR1L2,downstream_gene_variant,,ENST00000547164,; A ENST00000550916 Transcript missense_variant 679/2609 632/1035 211/344 R/Q cGa/cAa rs144813686,COSM431849,COSM70910 1 1 GLIPR1L2 HGNC HGNC:28592 protein_coding YES CCDS58258.1 ENSP00000448248 Q4G1C9 UPI00001408B2 NM_001270396.1 tolerated(0.9) 4/6 hmmpanther:PTHR10334:SF236,hmmpanther:PTHR10334,Gene3D:3.40.33.10 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs144813686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 75422951 75422951 G A 1 0 0 0 0 1 0 0 0 6321 1058 37 1 1 GLIPR1L2 12 75422951 Missense_Mutation SNP G C3N-00175_T 2803971 75422951 57852358 918 10510 NAV3 0 . GRCh38 12 78128862 78128862 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.4437C>A p.Asn1479Lys p.N1479K ENST00000397909 18/40 81 60 21 96 96 0 strelka-varscan-mutect NAV3,missense_variant,p.Asn1479Lys,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Asn1479Lys,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Asn374Lys,ENST00000552895,;NAV3,missense_variant,p.Asn108Lys,ENST00000550788,;RP11-136F16.2,downstream_gene_variant,,ENST00000418757,; A ENST00000397909 Transcript missense_variant 4610/9821 4437/7158 1479/2385 N/K aaC/aaA 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0.01) 18/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 78128862 78128862 C A 1 0 0 0 0 1 0 0 0 10194 579 20 2 2 NAV3 12 78128862 Missense_Mutation SNP C C3N-00175_T 2705911 78128862 55146447 919 10511 NAV3 0 . GRCh38 12 78148857 78148857 + Silent SNP C C A rs770148138 C3N-00175_T C3N-00175_N C C c.4723C>A p.= p.R1575R ENST00000397909 22/40 170 152 18 201 201 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000552895,;NAV3,synonymous_variant,p.=,ENST00000550788,; A ENST00000397909 Transcript synonymous_variant 4896/9821 4723/7158 1575/2385 R Cgg/Agg rs770148138,COSM1648995,COSM1992647,COSM431876,COSM5233412,COSM5272842,COSM550018 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 22/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 0,1,1,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1,1,1 1 PASS rs770148138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 78148857 78148857 C A 1 0 0 0 0 0 0 0 1 10194 759 27 1 1 NAV3 12 78148857 Silent SNP C C3N-00175_T 19995 78148857 55126452 920 10512 MYF6 0 . GRCh38 12 80707987 80707987 + Missense_Mutation SNP G G C C3N-00175_T C3N-00175_N G G c.268G>C p.Ala90Pro p.A90P ENST00000228641 1/3 477 406 71 508 508 0 strelka-varscan-mutect MYF6,missense_variant,p.Ala90Pro,ENST00000228641,NM_002469.2; C ENST00000228641 Transcript missense_variant 490/1465 268/729 90/242 A/P Gcc/Ccc COSM313015 1 1 MYF6 HGNC HGNC:7566 protein_coding YES CCDS9019.1 ENSP00000228641 P23409 UPI0000001050 NM_002469.2 deleterious(0.02) 1/3 hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4,Pfam_domain:PF01586,Gene3D:4.10.280.10,SMART_domains:SM00520 1 MODERATE 1 SNV 1 1 1 PASS rs768710318 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 80707987 80707987 G C 1 0 0 0 0 1 0 0 0 10028 1319 46 4 4 MYF6 12 80707987 Missense_Mutation SNP G C3N-00175_T 2559130 80707987 52567322 921 10513 PPFIA2 0 . GRCh38 12 81754110 81754110 + Missense_Mutation SNP T T C rs375272875 C3N-00175_T C3N-00175_N T T c.112A>G p.Met38Val p.M38V ENST00000549396 3/33 413 286 127 403 403 0 strelka-varscan-mutect PPFIA2,missense_variant,p.Met38Val,ENST00000550584,NM_001220473.2;PPFIA2,missense_variant,p.Met38Val,ENST00000549396,NM_003625.4;PPFIA2,missense_variant,p.Met38Val,ENST00000549325,NM_001220474.2;PPFIA2,missense_variant,p.Met38Val,ENST00000548586,NM_001220476.2;PPFIA2,missense_variant,p.Met38Val,ENST00000552948,NM_001220475.2;PPFIA2,missense_variant,p.Met38Val,ENST00000551442,;PPFIA2,missense_variant,p.Met38Val,ENST00000547623,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000550798,; C ENST00000549396 Transcript missense_variant 273/5363 112/3774 38/1257 M/V Atg/Gtg rs375272875 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 tolerated(0.08) 3/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 MODERATE 1 SNV 1 1 PASS rs375272875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 81754110 81754110 T C 1 0 0 0 0 1 0 0 0 12419 1406 49 5 5 PPFIA2 12 81754110 Missense_Mutation SNP T C3N-00175_T 1046123 81754110 51521199 922 10514 LRRIQ1 0 . GRCh38 12 85137925 85137925 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.4285G>T p.Glu1429Ter p.E1429* ENST00000393217 19/27 29 17 12 84 84 0 strelka-mutect LRRIQ1,stop_gained,p.Glu1429Ter,ENST00000393217,NM_001079910.1; T ENST00000393217 Transcript stop_gained 4346/5394 4285/5169 1429/1722 E/* Gaa/Taa 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 19/27 HIGH 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 85137925 85137925 G T 1 0 0 0 0 0 1 0 0 8935 1291 45 2 2 LRRIQ1 12 85137925 Nonsense_Mutation SNP G C3N-00175_T 3383815 85137925 48137384 923 10515 MGAT4C 0 . GRCh38 12 85979507 85979507 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1219C>A p.His407Asn p.H407N ENST00000611864 4/4 209 153 56 262 261 1 strelka-varscan-mutect MGAT4C,missense_variant,p.His407Asn,ENST00000611864,;MGAT4C,missense_variant,p.His407Asn,ENST00000620241,;MGAT4C,missense_variant,p.His407Asn,ENST00000621808,NM_013244.3;MGAT4C,missense_variant,p.His407Asn,ENST00000548651,;MGAT4C,missense_variant,p.His407Asn,ENST00000552808,;MGAT4C,downstream_gene_variant,,ENST00000547225,;MGAT4C,downstream_gene_variant,,ENST00000552435,; T ENST00000611864 Transcript missense_variant 1275/25116 1219/1437 407/478 H/N Cat/Aat 1 -1 MGAT4C HGNC HGNC:30871 protein_coding YES CCDS9030.1 ENSP00000481096 Q9UBM8 UPI00001B002C tolerated(0.19) 4/4 hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF14 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 85979507 85979507 G T 1 0 0 0 0 1 0 0 0 9507 1319 46 2 2 MGAT4C 12 85979507 Missense_Mutation SNP G C3N-00175_T 841582 85979507 47295802 924 10516 CEP290 0 . GRCh38 12 88106739 88106739 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.2753A>T p.Lys918Met p.K918M ENST00000552810 25/54 65 46 19 215 215 0 strelka-varscan-mutect CEP290,missense_variant,p.Lys918Met,ENST00000552810,NM_025114.3;CEP290,missense_variant,p.Lys920Met,ENST00000309041,;CEP290,missense_variant,p.Lys671Met,ENST00000604024,;CEP290,upstream_gene_variant,,ENST00000547691,;CEP290,downstream_gene_variant,,ENST00000397838,;CEP290,downstream_gene_variant,,ENST00000547926,; A ENST00000552810 Transcript missense_variant 3097/7948 2753/7440 918/2479 K/M aAg/aTg 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 deleterious(0) 25/54 hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 88106739 88106739 T A 1 0 0 0 0 1 0 0 0 2969 1609 56 4 4 CEP290 12 88106739 Missense_Mutation SNP T C3N-00175_T 2127232 88106739 45168570 925 10517 CFAP54 0 . GRCh38 12 96684721 96684721 + Silent SNP C C T rs375064372 C3N-00175_T C3N-00175_N C C c.5790C>T p.= p.F1930F ENST00000524981 41/68 116 108 8 164 164 0 strelka-varscan-mutect CFAP54,synonymous_variant,p.=,ENST00000524981,NM_001306084.1;CFAP54,synonymous_variant,p.=,ENST00000637336,;CFAP54,non_coding_transcript_exon_variant,,ENST00000342887,; T ENST00000524981 Transcript synonymous_variant 5813/9766 5790/9291 1930/3096 F ttC/ttT rs375064372,COSM3466695 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 41/68 hmmpanther:PTHR33487,hmmpanther:PTHR33487:SF2,Gene3D:1.25.40.10 0,1 LOW 1 SNV 5 0,1 1 PASS rs375064372 . 0 208 0 2 0 0 0 0 -11.93683 0.9999997 1 1 1 0 T 2 4 39 96684721 96684721 C T 1 0 0 0 0 0 0 0 1 3025 883 31 1 1 CFAP54 12 96684721 Silent SNP C C3N-00175_T 8577982 96684721 36590588 926 10518 CFAP54 0 . GRCh38 12 96753742 96753742 + Splice_Site SNP G G C novel C3N-00175_T C3N-00175_N G G c.7685-1G>C p.X2562_splice ENST00000524981 94 82 12 96 96 0 strelka-varscan-mutect CFAP54,splice_acceptor_variant,,ENST00000524981,NM_001306084.1;CFAP54,splice_acceptor_variant,,ENST00000637336,;CFAP54,splice_acceptor_variant,,ENST00000342887,; C ENST00000524981 Transcript splice_acceptor_variant -/9766 7685/9291 2562/3096 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 55/67 HIGH 1 SNV 5 1 PASS . . 0 194 11 3 2 0 0 0 -7.275299 0.8438172 1 1 1 0 C 5 2 39 96753742 96753742 G C 1 0 0 0 0 0 0 1 0 3025 1014 35 4 4 CFAP54 12 96753742 Splice_Site SNP G C3N-00175_T 69021 96753742 36521567 927 10519 ANKS1B 0 . GRCh38 12 98832044 98832044 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.2871G>T p.= p.R957R ENST00000547776 18/26 238 210 28 228 228 0 strelka-varscan-mutect ANKS1B,synonymous_variant,p.=,ENST00000547776,NM_152788.4;ANKS1B,synonymous_variant,p.=,ENST00000550693,NM_001204069.1;ANKS1B,synonymous_variant,p.=,ENST00000549493,NM_181670.3;ANKS1B,synonymous_variant,p.=,ENST00000547010,;ANKS1B,synonymous_variant,p.=,ENST00000549558,NM_020140.3;ANKS1B,synonymous_variant,p.=,ENST00000550778,;ANKS1B,synonymous_variant,p.=,ENST00000547446,NM_001204067.1;ANKS1B,synonymous_variant,p.=,ENST00000546960,NM_001204068.1;ANKS1B,synonymous_variant,p.=,ENST00000546568,NM_001204070.1;ANKS1B,5_prime_UTR_variant,,ENST00000341752,NM_001204081.1;ANKS1B,5_prime_UTR_variant,,ENST00000333732,NM_001204079.1,NM_001204080.1,NM_001204065.1;ANKS1B,5_prime_UTR_variant,,ENST00000546364,;ANKS1B,5_prime_UTR_variant,,ENST00000549797,;ANKS1B,5_prime_UTR_variant,,ENST00000551560,;ANKS1B,5_prime_UTR_variant,,ENST00000552407,;ANKS1B,5_prime_UTR_variant,,ENST00000552748,;ANKS1B,5_prime_UTR_variant,,ENST00000551613,;ANKS1B,5_prime_UTR_variant,,ENST00000548447,;ANKS1B,intron_variant,,ENST00000549025,NM_001204066.1;ANKS1B,non_coding_transcript_exon_variant,,ENST00000551830,;ANKS1B,5_prime_UTR_variant,,ENST00000547362,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000552245,; A ENST00000547776 Transcript synonymous_variant 2871/3885 2871/3747 957/1248 R cgG/cgT 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 18/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 98832044 98832044 C A 1 0 0 0 0 0 0 0 1 795 494 18 2 2 ANKS1B 12 98832044 Silent SNP C C3N-00175_T 2078302 98832044 34443265 928 10520 UHRF1BP1L 0 . GRCh38 12 100050290 100050290 + Missense_Mutation SNP C C G rs761777651 C3N-00175_T C3N-00175_N C C c.3596G>C p.Gly1199Ala p.G1199A ENST00000279907 17/21 109 94 15 91 91 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Gly1199Ala,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Gly849Ala,ENST00000545232,;UHRF1BP1L,upstream_gene_variant,,ENST00000548712,;UHRF1BP1L,non_coding_transcript_exon_variant,,ENST00000547504,; G ENST00000279907 Transcript missense_variant 3809/5168 3596/4395 1199/1464 G/A gGt/gCt rs761777651 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 tolerated(0.19) 17/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS rs761777651 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 100050290 100050290 C G 1 0 0 0 0 1 0 0 0 17493 507 18 4 4 UHRF1BP1L 12 100050290 Missense_Mutation SNP C C3N-00175_T 1218246 100050290 33225019 929 10521 UHRF1BP1L 0 . GRCh38 12 100072807 100072807 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.1414A>G p.Thr472Ala p.T472A ENST00000279907 12/21 138 116 22 126 126 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Thr472Ala,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Thr122Ala,ENST00000545232,;UHRF1BP1L,missense_variant,p.Thr472Ala,ENST00000356828,NM_001006947.1;UHRF1BP1L,missense_variant,p.Thr122Ala,ENST00000551973,;UHRF1BP1L,missense_variant,p.Thr61Ala,ENST00000550544,;UHRF1BP1L,missense_variant,p.Thr61Ala,ENST00000548045,; C ENST00000279907 Transcript missense_variant 1627/5168 1414/4395 472/1464 T/A Aca/Gca 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 deleterious(0.04) 12/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 100072807 100072807 T C 1 0 0 0 0 1 0 0 0 17493 1638 57 5 5 UHRF1BP1L 12 100072807 Missense_Mutation SNP T C3N-00175_T 22517 100072807 33202502 930 10522 SLC17A8 0 . GRCh38 12 100401815 100401815 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.715G>T p.Gly239Trp p.G239W ENST00000323346 6/12 394 262 132 416 416 0 strelka-varscan-mutect SLC17A8,missense_variant,p.Gly239Trp,ENST00000323346,NM_139319.2;SLC17A8,missense_variant,p.Gly239Trp,ENST00000392989,NM_001145288.1;SLC17A8,upstream_gene_variant,,ENST00000547922,; T ENST00000323346 Transcript missense_variant 1028/3983 715/1770 239/589 G/W Ggg/Tgg 1 1 SLC17A8 HGNC HGNC:20151 protein_coding YES CCDS9077.1 ENSP00000316909 Q8NDX2 UPI0000073B9B NM_139319.2 deleterious(0) 6/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF207,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 100401815 100401815 G T 1 0 0 0 0 1 0 0 0 14688 1348 47 2 2 SLC17A8 12 100401815 Missense_Mutation SNP G C3N-00175_T 329008 100401815 32873494 931 10523 UTP20 0 . GRCh38 12 101363692 101363692 + Silent SNP C C A rs752695607 C3N-00175_T C3N-00175_N C C c.5907C>A p.= p.G1969G ENST00000261637 45/62 126 116 10 133 133 0 strelka-varscan-mutect UTP20,synonymous_variant,p.=,ENST00000261637,NM_014503.2; A ENST00000261637 Transcript synonymous_variant 6081/9025 5907/8358 1969/2785 G ggC/ggA rs752695607 1 1 UTP20 HGNC HGNC:17897 protein_coding YES CCDS9081.1 ENSP00000261637 O75691 UPI00001FB38B NM_014503.2 45/62 hmmpanther:PTHR17695,hmmpanther:PTHR17695:SF11,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs752695607 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 101363692 101363692 C A 1 0 0 0 0 0 0 0 1 17642 697 25 2 2 UTP20 12 101363692 Silent SNP C C3N-00175_T 961877 101363692 31911617 932 10524 POLR3B 0 . GRCh38 12 106433860 106433860 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1769G>T p.Gly590Val p.G590V ENST00000228347 16/28 84 74 10 147 147 0 strelka-varscan-mutect POLR3B,missense_variant,p.Gly590Val,ENST00000228347,NM_018082.5;POLR3B,missense_variant,p.Gly532Val,ENST00000539066,NM_001160708.1; T ENST00000228347 Transcript missense_variant 1991/4273 1769/3402 590/1133 G/V gGa/gTa 1 1 POLR3B HGNC HGNC:30348 protein_coding YES CCDS9105.1 ENSP00000228347 Q9NW08 UPI000000DB67 NM_018082.5 deleterious(0) 16/28 Pfam_domain:PF04566,hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF8,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 106433860 106433860 G T 1 0 0 0 0 1 0 0 0 12340 1174 41 2 2 POLR3B 12 106433860 Missense_Mutation SNP G C3N-00175_T 5070168 106433860 26841449 933 10525 RFX4 0 . GRCh38 12 106750676 106750676 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.1845T>C p.= p.Y615Y ENST00000357881 17/18 70 66 4 81 81 0 varscan-mutect RFX4,synonymous_variant,p.=,ENST00000392842,NM_213594.2;RFX4,synonymous_variant,p.=,ENST00000229387,NM_032491.5;RFX4,synonymous_variant,p.=,ENST00000357881,NM_001206691.1;RP11-144F15.1,intron_variant,,ENST00000551505,;RP11-144F15.1,intron_variant,,ENST00000549203,; C ENST00000357881 Transcript synonymous_variant 1985/2565 1845/2235 615/744 Y taT/taC 1 1 RFX4 HGNC HGNC:9985 protein_coding YES CCDS55880.1 ENSP00000350552 Q33E94 UPI00001FB460 NM_001206691.1 17/18 Low_complexity_(Seg):seg,hmmpanther:PTHR12619:SF25,hmmpanther:PTHR12619 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -9.629429 1 1 1 1 0 C 2 2 39 106750676 106750676 T C 1 0 0 0 0 0 0 0 1 13439 1471 51 5 5 RFX4 12 106750676 Silent SNP T C3N-00175_T 316816 106750676 26524633 934 10526 ASCL4 0 . GRCh38 12 107775381 107775381 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.166G>T p.Ala56Ser p.A56S ENST00000342331 1/1 175 157 18 262 262 0 strelka-varscan-mutect ASCL4,missense_variant,p.Ala56Ser,ENST00000342331,NM_203436.2; T ENST00000342331 Transcript missense_variant 997/2260 166/522 56/173 A/S Gca/Tca COSM4645097 1 1 ASCL4 HGNC HGNC:24311 protein_coding YES CCDS31894.2 ENSP00000345420 Q6XD76 UPI00001973FA NM_203436.2 tolerated(0.49) 1/1 hmmpanther:PTHR13935,hmmpanther:PTHR13935:SF51 1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 107775381 107775381 G T 1 0 0 0 0 1 0 0 0 1178 1087 38 1 1 ASCL4 12 107775381 Missense_Mutation SNP G C3N-00175_T 1024705 107775381 25499928 935 10527 CMKLR1 0 . GRCh38 12 108291938 108291938 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1025C>G p.Thr342Arg p.T342R ENST00000312143 3/3 246 169 77 241 241 0 strelka-varscan-mutect CMKLR1,missense_variant,p.Thr342Arg,ENST00000312143,NM_001142344.1;CMKLR1,missense_variant,p.Thr342Arg,ENST00000412676,NM_001142345.1;CMKLR1,missense_variant,p.Thr342Arg,ENST00000550402,NM_001142343.1;CMKLR1,missense_variant,p.Thr340Arg,ENST00000552995,NM_004072.2;CMKLR1,downstream_gene_variant,,ENST00000550573,;CMKLR1,downstream_gene_variant,,ENST00000549466,; C ENST00000312143 Transcript missense_variant 1389/5283 1025/1122 342/373 T/R aCa/aGa 1 -1 CMKLR1 HGNC HGNC:2121 protein_coding YES CCDS44965.1 ENSP00000311733 Q99788 UPI0000127BD4 NM_001142344.1 deleterious(0.01) 3/3 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF696,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01126 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 108291938 108291938 G C 1 0 0 0 0 1 0 0 0 3354 1377 48 4 4 CMKLR1 12 108291938 Missense_Mutation SNP G C3N-00175_T 516557 108291938 24983371 936 10528 CUX2 0 . GRCh38 12 111310670 111310670 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1888G>C p.Val630Leu p.V630L ENST00000261726 15/22 35 30 5 55 55 0 strelka-varscan-mutect CUX2,missense_variant,p.Val630Leu,ENST00000261726,NM_015267.3; C ENST00000261726 Transcript missense_variant 2042/6844 1888/4461 630/1486 V/L Gtg/Ctg 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 tolerated(0.47) 15/22 PROSITE_profiles:PS51042,hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5,SMART_domains:SM01109 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -13.56672 1 1 1 1 0 C 3 2 39 111310670 111310670 G C 1 0 0 0 0 1 0 0 0 3875 1029 36 4 4 CUX2 12 111310670 Missense_Mutation SNP G C3N-00175_T 3018732 111310670 21964639 937 10529 ALDH2 0 . GRCh38 12 111790506 111790506 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.625A>G p.Lys209Glu p.K209E ENST00000261733 6/13 270 237 33 314 314 0 strelka-varscan-mutect ALDH2,missense_variant,p.Lys209Glu,ENST00000261733,NM_000690.3;ALDH2,missense_variant,p.Lys162Glu,ENST00000416293,NM_001204889.1;RP11-162P23.2,missense_variant,p.Lys204Glu,ENST00000546840,;ALDH2,3_prime_UTR_variant,,ENST00000548536,;ALDH2,upstream_gene_variant,,ENST00000549106,; G ENST00000261733 Transcript missense_variant 686/9569 625/1554 209/517 K/E Aag/Gag 1 1 ALDH2 HGNC HGNC:404 protein_coding YES CCDS9155.1 ENSP00000261733 P05091 UPI0000129293 NM_000690.3 deleterious(0) 6/13 Gene3D:3.40.605.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF211,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 111790506 111790506 A G 1 0 0 0 0 1 0 0 0 596 247 9 5 5 ALDH2 12 111790506 Missense_Mutation SNP A C3N-00175_T 479836 111790506 21484803 938 10530 TBX5 0 . GRCh38 12 114355702 114355702 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.1387C>A p.His463Asn p.H463N ENST00000310346 9/9 169 113 56 200 200 0 strelka-varscan-mutect TBX5,missense_variant,p.His463Asn,ENST00000310346,NM_000192.3;TBX5,missense_variant,p.His413Asn,ENST00000349716,NM_080717.2;TBX5,missense_variant,p.His463Asn,ENST00000405440,NM_181486.2; T ENST00000310346 Transcript missense_variant 2054/3825 1387/1557 463/518 H/N Cac/Aac COSM3456499 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 tolerated_low_confidence(0.09) 9/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 114355702 114355702 G T 1 0 0 0 0 1 0 0 0 16065 1348 47 2 2 TBX5 12 114355702 Missense_Mutation SNP G C3N-00175_T 2565196 114355702 18919607 939 10531 MED13L 0 . GRCh38 12 115991135 115991135 + Silent SNP C C A rs542711978 C3N-00175_T C3N-00175_N C C c.3819G>T p.= p.T1273T ENST00000281928 17/31 435 388 47 421 421 0 strelka-varscan-mutect MED13L,synonymous_variant,p.=,ENST00000281928,NM_015335.4; A ENST00000281928 Transcript synonymous_variant 4026/14234 3819/6633 1273/2210 T acG/acT rs542711978 1 -1 MED13L HGNC HGNC:22962 protein_coding YES CCDS9177.1 ENSP00000281928 Q71F56 UPI0000241C1E NM_015335.4 17/31 hmmpanther:PTHR10791,hmmpanther:PTHR10791:SF64 LOW 1 SNV 1 1 PASS rs542711978 . 0 208 0 0 0 0 0 2 -8.767275 0 0 1 0 0 A 2 1 39 115991135 115991135 C A 1 0 0 0 0 0 0 0 1 9370 639 23 1 1 MED13L 12 115991135 Silent SNP C C3N-00175_T 1635433 115991135 17284174 940 10532 GCN1 0 . GRCh38 12 120173655 120173655 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1364G>T p.Arg455Leu p.R455L ENST00000300648 14/58 49 42 7 60 60 0 strelka-varscan-mutect GCN1,missense_variant,p.Arg455Leu,ENST00000300648,NM_006836.1;GCN1,downstream_gene_variant,,ENST00000548821,; A ENST00000300648 Transcript missense_variant,splice_region_variant 1377/8675 1364/8016 455/2671 R/L cGg/cTg 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 deleterious(0.04) 14/58 hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs909142137 . 0 203 7 0 0 0 0 0 -16.76321 0.9999995 1 1 1 0 A 3 1 39 120173655 120173655 C A 1 0 0 0 0 1 0 0 0 6169 666 23 1 1 GCN1 12 120173655 Missense_Mutation SNP C C3N-00175_T 4182520 120173655 13101654 941 10533 SETD1B 0 . GRCh38 12 121814235 121814235 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2020G>T p.Val674Leu p.V674L ENST00000542440 7/18 94 81 13 94 94 0 strelka-varscan-mutect SETD1B,missense_variant,p.Val674Leu,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Val674Leu,ENST00000604567,;SETD1B,missense_variant,p.Val674Leu,ENST00000619791,;SETD1B,missense_variant,p.Val674Leu,ENST00000267197,; T ENST00000542440 Transcript missense_variant 2088/8185 2020/5772 674/1923 V/L Gtg/Ttg 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 tolerated_low_confidence(0.19) 7/18 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999925 1 1 1 0 T 3 4 39 121814235 121814235 G T 1 0 0 0 0 1 0 0 0 14408 1377 48 2 2 SETD1B 12 121814235 Missense_Mutation SNP G C3N-00175_T 1640580 121814235 11461074 942 10534 CLIP1 0 . GRCh38 12 122274063 122274063 + Missense_Mutation SNP C C A rs201297279 C3N-00175_T C3N-00175_N C C c.4066G>T p.Gly1356Trp p.G1356W ENST00000620786 25/26 119 108 11 122 121 1 strelka-varscan-mutect CLIP1,missense_variant,p.Gly1356Trp,ENST00000620786,NM_001247997.1;CLIP1,missense_variant,p.Gly1345Trp,ENST00000358808,NM_002956.2;CLIP1,missense_variant,p.Gly1345Trp,ENST00000302528,;CLIP1,missense_variant,p.Gly1234Trp,ENST00000361654,;CLIP1,missense_variant,p.Gly1310Trp,ENST00000537178,NM_198240.1;CLIP1,missense_variant,p.Gly931Trp,ENST00000545889,;CLIP1,missense_variant,p.Gly1356Trp,ENST00000540338,;CLIP1,missense_variant,p.Gly35Trp,ENST00000540539,;CLIP1,non_coding_transcript_exon_variant,,ENST00000536634,;CLIP1,non_coding_transcript_exon_variant,,ENST00000538120,;CLIP1,non_coding_transcript_exon_variant,,ENST00000501271,;CLIP1,downstream_gene_variant,,ENST00000543205,; A ENST00000620786 Transcript missense_variant 4221/5913 4066/4317 1356/1438 G/W Ggg/Tgg rs201297279 1 -1 CLIP1 HGNC HGNC:10461 protein_coding YES CCDS58285.1 ENSP00000479322 P30622 UPI0000E00D4E NM_001247997.1 deleterious(0) 25/26 Low_complexity_(Seg):seg,hmmpanther:PTHR18916:SF44,hmmpanther:PTHR18916 MODERATE 1 SNV 5 1 PASS rs201297279 . 0 208 0 2 0 0 0 0 -16.40262 0.9999998 1 1 1 0 A 3 1 39 122274063 122274063 C A 1 0 0 0 0 1 0 0 0 3301 652 23 1 1 CLIP1 12 122274063 Missense_Mutation SNP C C3N-00175_T 459828 122274063 11001246 943 10535 PITPNM2 0 . GRCh38 12 122986102 122986102 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.3975G>C p.Met1325Ile p.M1325I ENST00000320201 25/25 52 42 10 72 72 0 strelka-mutect PITPNM2,missense_variant,p.Met1319Ile,ENST00000280562,NM_001300801.1;PITPNM2,missense_variant,p.Met1325Ile,ENST00000320201,NM_020845.2;PITPNM2,missense_variant,p.Met1325Ile,ENST00000542749,;ABCB9,upstream_gene_variant,,ENST00000542678,;ARL6IP4,downstream_gene_variant,,ENST00000315580,NM_018694.3;ARL6IP4,downstream_gene_variant,,ENST00000543566,NM_001278379.1,NM_016638.3;ARL6IP4,downstream_gene_variant,,ENST00000453766,NM_001278378.1,NM_001002251.2;ARL6IP4,downstream_gene_variant,,ENST00000392435,NM_001002252.2;ARL6IP4,downstream_gene_variant,,ENST00000454885,NM_001278380.1;ARL6IP4,downstream_gene_variant,,ENST00000542099,;ARL6IP4,downstream_gene_variant,,ENST00000426960,;ARL6IP4,downstream_gene_variant,,ENST00000412505,;ARL6IP4,downstream_gene_variant,,ENST00000413381,;ARL6IP4,downstream_gene_variant,,ENST00000439686,;ARL6IP4,downstream_gene_variant,,ENST00000456762,;ARL6IP4,downstream_gene_variant,,ENST00000357866,;RP11-197N18.2,downstream_gene_variant,,ENST00000540866,;ARL6IP4,downstream_gene_variant,,ENST00000540708,;ARL6IP4,downstream_gene_variant,,ENST00000539576,;ARL6IP4,downstream_gene_variant,,ENST00000540382,;ARL6IP4,downstream_gene_variant,,ENST00000392433,;ARL6IP4,downstream_gene_variant,,ENST00000539770,;ARL6IP4,downstream_gene_variant,,ENST00000536502,;ARL6IP4,downstream_gene_variant,,ENST00000442210,;ARL6IP4,downstream_gene_variant,,ENST00000536073,; G ENST00000320201 Transcript missense_variant 4114/6736 3975/4050 1325/1349 M/I atG/atC 1 -1 PITPNM2 HGNC HGNC:21044 protein_coding YES CCDS9242.1 ENSP00000322218 Q9BZ72 UPI0000070D27 NM_020845.2 deleterious_low_confidence(0.02) 25/25 MODERATE SNV 5 1 PASS rs977855119 . 0 204 6 0 0 0 0 0 -19.99991 1 1 1 1 0 G 3 3 39 122986102 122986102 C G 1 0 0 0 0 1 0 0 0 12047 826 29 4 4 PITPNM2 12 122986102 Missense_Mutation SNP C C3N-00175_T 712039 122986102 10289207 944 10536 DNAH10 0 . GRCh38 12 123871459 123871459 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.7288C>T p.His2430Tyr p.H2430Y ENST00000638045 44/78 90 69 21 114 114 0 strelka-varscan-mutect DNAH10,missense_variant,p.His2491Tyr,ENST00000409039,;DNAH10,missense_variant,p.His2430Tyr,ENST00000638045,NM_207437.3;DNAH10,intron_variant,,ENST00000497783,; T ENST00000638045 Transcript missense_variant,splice_region_variant 7313/13678 7288/13416 2430/4471 H/Y Cac/Tac 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0) 44/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF12775 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 123871459 123871459 C T 1 0 0 0 0 1 0 0 0 4411 840 29 3 3 DNAH10 12 123871459 Missense_Mutation SNP C C3N-00175_T 885357 123871459 9403850 945 10537 TMEM132D 0 . GRCh38 12 129073978 129073978 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.3197T>A p.Val1066Glu p.V1066E ENST00000422113 9/9 70 47 23 81 81 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Val1066Glu,ENST00000422113,NM_133448.2;TMEM132D,missense_variant,p.Val604Glu,ENST00000389441,; T ENST00000422113 Transcript missense_variant 3524/5776 3197/3300 1066/1099 V/E gTg/gAg 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 deleterious(0.01) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 129073978 129073978 A T 1 0 0 0 0 1 0 0 0 16492 159 6 4 4 TMEM132D 12 129073978 Missense_Mutation SNP A C3N-00175_T 5202519 129073978 4201331 946 10538 TUBA3C 0 . GRCh38 13 19177061 19177061 + Missense_Mutation SNP G G A rs780474312 C3N-00175_T C3N-00175_N G G c.922C>T p.Arg308Cys p.R308C ENST00000400113 4/5 272 240 32 373 372 1 strelka-varscan-mutect TUBA3C,missense_variant,p.Arg308Cys,ENST00000400113,NM_006001.2;TUBA3C,missense_variant,p.Arg308Cys,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; A ENST00000400113 Transcript missense_variant 1027/1551 922/1353 308/450 R/C Cgc/Tgc rs780474312 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 deleterious_low_confidence(0) 4/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.30.1330.20,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307 MODERATE 1 SNV 5 1 PASS rs780474312 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19177061 19177061 G A 1 0 0 0 0 1 0 0 0 17256 1058 37 1 1 TUBA3C 13 19177061 Missense_Mutation SNP G C3N-00175_T 19177061 95187267 947 10539 TUBA3C 0 . GRCh38 13 19177540 19177540 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.443G>T p.Gly148Val p.G148V ENST00000400113 4/5 57 33 24 67 67 0 strelka-varscan-mutect TUBA3C,missense_variant,p.Gly148Val,ENST00000400113,NM_006001.2;TUBA3C,missense_variant,p.Gly148Val,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; A ENST00000400113 Transcript missense_variant 548/1551 443/1353 148/450 G/V gGg/gTg 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 deleterious_low_confidence(0) 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,PROSITE_patterns:PS00227,Gene3D:3.40.50.1440,Pfam_domain:PF00091,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01162,Prints_domain:PR01161 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19177540 19177540 C A 1 0 0 0 0 1 0 0 0 17256 623 22 2 2 TUBA3C 13 19177540 Missense_Mutation SNP C C3N-00175_T 479 19177540 95186788 948 10540 RNF17 0 . GRCh38 13 24789348 24789348 + Missense_Mutation SNP A A T C3N-00175_T C3N-00175_N A A c.784A>T p.Ile262Phe p.I262F ENST00000255324 8/36 75 58 17 118 118 0 strelka-varscan-mutect RNF17,missense_variant,p.Ile262Phe,ENST00000255324,NM_031277.2,NM_001184993.1;RNF17,missense_variant,p.Ile262Phe,ENST00000255325,;RNF17,splice_region_variant,,ENST00000255326,; T ENST00000255324 Transcript missense_variant,splice_region_variant 836/5119 784/4872 262/1623 I/F Att/Ttt COSM946194,COSM946195 1 1 RNF17 HGNC HGNC:10060 protein_coding YES CCDS9308.2 ENSP00000255324 Q9BXT8 UPI00001FC8BA NM_031277.2,NM_001184993.1 deleterious(0) 8/36 hmmpanther:PTHR16442 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 24789348 24789348 A T 1 0 0 0 0 1 0 0 0 13638 347 12 4 4 RNF17 13 24789348 Missense_Mutation SNP A C3N-00175_T 5611808 24789348 89574980 949 10541 RNF17 0 . GRCh38 13 24859076 24859076 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.3686G>T p.Trp1229Leu p.W1229L ENST00000255324 26/36 93 85 8 131 131 0 strelka-varscan-mutect RNF17,missense_variant,p.Trp1229Leu,ENST00000255324,NM_031277.2,NM_001184993.1;RNF17,missense_variant,p.Trp553Leu,ENST00000418120,;RNF17,missense_variant,p.Trp281Leu,ENST00000339524,; T ENST00000255324 Transcript missense_variant 3738/5119 3686/4872 1229/1623 W/L tGg/tTg COSM3467921 1 1 RNF17 HGNC HGNC:10060 protein_coding YES CCDS9308.2 ENSP00000255324 Q9BXT8 UPI00001FC8BA NM_031277.2,NM_001184993.1 deleterious(0) 26/36 PROSITE_profiles:PS50304,hmmpanther:PTHR16442,Pfam_domain:PF00567,Gene3D:2.30.30.140,SMART_domains:SM00333,Superfamily_domains:SSF63748 1 MODERATE 1 SNV 2 1 1 PASS . . 0 206 0 3 0 0 0 0 -12.62391 0.9999791 1 1 1 0 T 3 4 39 24859076 24859076 G T 1 0 0 0 0 1 0 0 0 13638 1357 47 2 2 RNF17 13 24859076 Missense_Mutation SNP G C3N-00175_T 69728 24859076 89505252 950 10542 ATP8A2 0 . GRCh38 13 25578880 25578880 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.1848G>T p.= p.L616L ENST00000381655 21/37 150 136 14 257 255 2 strelka-varscan-mutect ATP8A2,synonymous_variant,p.=,ENST00000381655,NM_016529.4;ATP8A2,intron_variant,,ENST00000255283,;ATP8A2,non_coding_transcript_exon_variant,,ENST00000491840,;ATP8A2,synonymous_variant,p.=,ENST00000281620,; T ENST00000381655 Transcript synonymous_variant 1990/9575 1848/3567 616/1188 L ctG/ctT 1 1 ATP8A2 HGNC HGNC:13533 protein_coding YES CCDS41873.1 ENSP00000371070 Q9NTI2 UPI0000229592 NM_016529.4 21/37 hmmpanther:PTHR24092:SF66,hmmpanther:PTHR24092,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 25578880 25578880 G T 1 0 0 0 0 0 0 0 1 1346 1335 47 2 2 ATP8A2 13 25578880 Silent SNP G C3N-00175_T 719804 25578880 88785448 951 10543 FLT3 0 . GRCh38 13 28027089 28027089 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.2206A>C p.Ser736Arg p.S736R ENST00000241453 17/24 62 46 16 75 75 0 strelka-varscan-mutect FLT3,missense_variant,p.Ser736Arg,ENST00000241453,NM_004119.2;FLT3,missense_variant,p.Ser736Arg,ENST00000380987,; G ENST00000241453 Transcript missense_variant,splice_region_variant 2288/3842 2206/2982 736/993 S/R Agc/Cgc 1 -1 FLT3 HGNC HGNC:3765 protein_coding YES CCDS31953.1 ENSP00000241453 P36888 UPI00001FC90B NM_004119.2 tolerated(0.86) 17/24 PROSITE_profiles:PS50011,Pfam_domain:PF07714,SMART_domains:SM00219 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 28027089 28027089 T G 1 0 0 0 0 1 0 0 0 5798 1594 55 5 5 FLT3 13 28027089 Missense_Mutation SNP T C3N-00175_T 2448209 28027089 86337239 952 10544 FRY 0 . GRCh38 13 32244086 32244086 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.6732G>C p.Gln2244His p.Q2244H ENST00000542859 47/61 241 207 34 309 309 0 strelka-varscan-mutect FRY,missense_variant,p.Gln2244His,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Gln2243His,ENST00000380250,; C ENST00000542859 Transcript missense_variant 7228/13200 6732/9042 2244/3013 Q/H caG/caC 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0.02) 47/61 Pfam_domain:PF14225,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS rs1301046018 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 32244086 32244086 G C 1 0 0 0 0 1 0 0 0 5935 991 35 4 4 FRY 13 32244086 Missense_Mutation SNP G C3N-00175_T 4216997 32244086 82120242 953 10545 BRCA2 0 . GRCh38 13 32326564 32326564 + Missense_Mutation SNP G G T rs80358810 C3N-00175_T C3N-00175_N G G c.582G>T p.Trp194Cys p.W194C ENST00000380152 7/27 150 131 19 186 186 0 strelka-varscan-mutect BRCA2,missense_variant,p.Trp194Cys,ENST00000380152,;BRCA2,missense_variant,p.Trp194Cys,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,;BRCA2,non_coding_transcript_exon_variant,,ENST00000530893,; T ENST00000380152 Transcript missense_variant 815/11986 582/10257 194/3418 W/C tgG/tgT rs80358810 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC deleterious(0) 7/27 Low_complexity_(Seg):seg,hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 not_provided,pathogenic MODERATE 1 SNV 5 1 1 PASS rs80358810 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 32326564 32326564 G T 1 0 0 0 0 1 0 0 0 1669 1270 44 2 2 BRCA2 13 32326564 Missense_Mutation SNP G C3N-00175_T 82478 32326564 82037764 954 10546 NBEA 0 . GRCh38 13 34942933 34942933 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.113G>T p.Gly38Val p.G38V ENST00000400445 1/58 44 40 4 52 52 0 strelka-varscan-mutect NBEA,missense_variant,p.Gly38Val,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Gly38Val,ENST00000310336,;NBEA,missense_variant,p.Gly38Val,ENST00000629018,;NBEA,missense_variant,p.Gly38Val,ENST00000379939,; T ENST00000400445 Transcript missense_variant 647/11119 113/8841 38/2946 G/V gGg/gTg 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 tolerated_low_confidence(0.1) 1/58 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -10.64765 1 1 1 1 0 T 3 4 39 34942933 34942933 G T 1 0 0 0 0 1 0 0 0 10198 1232 43 2 2 NBEA 13 34942933 Missense_Mutation SNP G C3N-00175_T 2616369 34942933 79421395 955 10547 DCLK1 0 . GRCh38 13 35839146 35839146 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1066C>G p.Leu356Val p.L356V ENST00000255448 7/18 134 121 13 207 207 0 strelka-varscan-mutect DCLK1,missense_variant,p.Leu356Val,ENST00000360631,;DCLK1,missense_variant,p.Leu49Val,ENST00000615680,NM_001195415.1;DCLK1,missense_variant,p.Leu356Val,ENST00000255448,NM_004734.4;DCLK1,missense_variant,p.Leu49Val,ENST00000379893,NM_001195416.1; C ENST00000255448 Transcript missense_variant 1278/5703 1066/2190 356/729 L/V Ctt/Gtt 1 -1 DCLK1 HGNC HGNC:2700 protein_coding YES CCDS9354.1 ENSP00000255448 O15075 UPI000002A7C2 NM_004734.4 tolerated(0.56) 7/18 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF122 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 35839146 35839146 G C 1 0 0 0 0 1 0 0 0 4093 1029 36 4 4 DCLK1 13 35839146 Missense_Mutation SNP G C3N-00175_T 896213 35839146 78525182 956 10548 LHFP 0 . GRCh38 13 39378483 39378483 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.429G>T p.Trp143Cys p.W143C ENST00000379589 3/4 160 132 28 193 192 1 strelka-varscan-mutect LHFP,missense_variant,p.Trp143Cys,ENST00000379589,NM_005780.2; A ENST00000379589 Transcript missense_variant 892/2110 429/603 143/200 W/C tgG/tgT 1 -1 LHFP HGNC HGNC:6586 protein_coding YES CCDS9369.1 ENSP00000368908 Q9Y693 A0A024RDR1 UPI000006D140 NM_005780.2 deleterious(0) 3/4 Pfam_domain:PF10242,hmmpanther:PTHR12489,hmmpanther:PTHR12489:SF12,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 39378483 39378483 C A 1 0 0 0 0 1 0 0 0 8672 624 22 2 2 LHFP 13 39378483 Missense_Mutation SNP C C3N-00175_T 3539337 39378483 74985845 957 10549 ELF1 0 . GRCh38 13 40934026 40934026 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1259C>G p.Thr420Ser p.T420S ENST00000239882 9/9 75 69 6 97 97 0 strelka-varscan-mutect ELF1,missense_variant,p.Thr420Ser,ENST00000239882,NM_172373.3;ELF1,missense_variant,p.Thr162Ser,ENST00000442101,;ELF1,missense_variant,p.Thr420Ser,ENST00000635415,;ELF1,missense_variant,p.Thr396Ser,ENST00000625359,NM_001145353.1;ELF1,splice_region_variant,,ENST00000498824,; C ENST00000239882 Transcript missense_variant,splice_region_variant 1574/3566 1259/1860 420/619 T/S aCt/aGt 1 -1 ELF1 HGNC HGNC:3316 protein_coding YES CCDS9374.1 ENSP00000239882 P32519 A0A024RDU6 UPI000007071F NM_172373.3 tolerated(0.29) 9/9 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF156 MODERATE 1 SNV 1 1 PASS rs1467314988 . 0 207 3 0 0 0 0 0 -13.53163 1 1 1 1 0 C 3 2 39 40934026 40934026 G C 1 0 0 0 0 1 0 0 0 4886 1043 36 4 4 ELF1 13 40934026 Missense_Mutation SNP G C3N-00175_T 1555543 40934026 73430302 958 10550 MTRF1 0 . GRCh38 13 41217228 41217228 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1225G>T p.Glu409Ter p.E409* ENST00000379480 10/10 99 82 17 141 141 0 strelka-varscan-mutect MTRF1,stop_gained,p.Glu409Ter,ENST00000379480,NM_004294.2;MTRF1,stop_gained,p.Glu409Ter,ENST00000379477,;RP11-74J13.8,intron_variant,,ENST00000619407,;MTRF1,splice_region_variant,,ENST00000473492,; A ENST00000379480 Transcript stop_gained,splice_region_variant 1326/2185 1225/1338 409/445 E/* Gaa/Taa 1 -1 MTRF1 HGNC HGNC:7469 protein_coding YES CCDS9378.1 ENSP00000368793 O75570 A0A024RDT1 UPI0000035FC6 NM_004294.2 10/10 hmmpanther:PTHR11075,hmmpanther:PTHR11075:SF44,Superfamily_domains:SSF75620 HIGH 1 SNV 1 1 PASS rs1292042060 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 41217228 41217228 C A 1 0 0 0 0 0 1 0 0 9945 869 30 2 2 MTRF1 13 41217228 Nonsense_Mutation SNP C C3N-00175_T 283202 41217228 73147100 959 10551 DGKH 0 . GRCh38 13 42190504 42190504 + Missense_Mutation SNP G G C rs113799173 C3N-00175_T C3N-00175_N G G c.2014G>C p.Gly672Arg p.G672R ENST00000337343 16/30 134 106 28 154 154 0 strelka-varscan-mutect DGKH,missense_variant,p.Gly672Arg,ENST00000261491,NM_152910.5;DGKH,missense_variant,p.Gly672Arg,ENST00000337343,NM_178009.4;DGKH,missense_variant,p.Gly672Arg,ENST00000379274,NM_001204504.2;DGKH,missense_variant,p.Gly536Arg,ENST00000536612,NM_001204505.2;DGKH,missense_variant,p.Gly536Arg,ENST00000628433,NM_001297429.1,NM_001204506.2;DGKH,non_coding_transcript_exon_variant,,ENST00000498255,;DGKH,missense_variant,p.Gly536Arg,ENST00000627777,;DGKH,3_prime_UTR_variant,,ENST00000626247,; C ENST00000337343 Transcript missense_variant 2035/4246 2014/3663 672/1220 G/R Ggt/Cgt rs113799173 1 1 DGKH HGNC HGNC:2854 protein_coding YES CCDS9381.1 ENSP00000337572 Q86XP1 UPI000017DA47 NM_178009.4 tolerated(0.49) 16/30 MODERATE 1 SNV 1 1 PASS rs113799173 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 42190504 42190504 G C 1 0 0 0 0 1 0 0 0 4276 1348 47 4 4 DGKH 13 42190504 Missense_Mutation SNP G C3N-00175_T 973276 42190504 72173824 960 10552 ZC3H13 0 . GRCh38 13 45967629 45967629 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.4196A>T p.Glu1399Val p.E1399V ENST00000282007 15/17 89 77 12 118 118 0 strelka-mutect ZC3H13,missense_variant,p.Glu1399Val,ENST00000242848,;ZC3H13,missense_variant,p.Glu1399Val,ENST00000282007,NM_015070.4; A ENST00000282007 Transcript missense_variant 4267/6412 4196/4695 1399/1564 E/V gAa/gTa 1 -1 ZC3H13 HGNC HGNC:20368 protein_coding YES CCDS9400.1 ENSP00000282007 Q5T200 UPI0000366969 NM_015070.4 deleterious_low_confidence(0) 15/17 hmmpanther:PTHR13585,hmmpanther:PTHR13585:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 45967629 45967629 T A 1 0 0 0 0 1 0 0 0 18140 1783 62 4 4 ZC3H13 13 45967629 Missense_Mutation SNP T C3N-00175_T 3777125 45967629 68396699 961 10553 KIAA0226L 0 . GRCh38 13 46372000 46372000 + Missense_Mutation SNP T T A rs764713697 C3N-00175_T C3N-00175_N T T c.476A>T p.Tyr159Phe p.Y159F ENST00000429979 3/15 129 117 12 163 163 0 strelka-varscan-mutect KIAA0226L,missense_variant,p.Tyr159Phe,ENST00000429979,NM_025113.3;KIAA0226L,missense_variant,p.Tyr159Phe,ENST00000389908,NM_001286761.1;KIAA0226L,missense_variant,p.Tyr159Phe,ENST00000378787,NM_001286762.1;KIAA0226L,missense_variant,p.Tyr92Phe,ENST00000378784,NM_001286763.1;KIAA0226L,missense_variant,p.Tyr24Phe,ENST00000631139,NM_001286764.1;KIAA0226L,missense_variant,p.Tyr159Phe,ENST00000439642,;KIAA0226L,missense_variant,p.Tyr24Phe,ENST00000417405,;KIAA0226L,intron_variant,,ENST00000378781,NM_001286765.1;KIAA0226L,intron_variant,,ENST00000378797,NM_001286766.1;KIAA0226L,intron_variant,,ENST00000409879,;RNU2-6P,downstream_gene_variant,,ENST00000411404,;KIAA0226L,missense_variant,p.Tyr159Phe,ENST00000441284,; A ENST00000429979 Transcript missense_variant 1081/3979 476/1989 159/662 Y/F tAt/tTt rs764713697,COSM5632862,COSM5632863,COSM5632864 1 -1 KIAA0226L HGNC HGNC:20420 protein_coding YES CCDS31970.2 ENSP00000396935 Q9H714 UPI00001FCD59 NM_025113.3 tolerated(0.7) 3/15 hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF14 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs764713697 . 0 208 0 2 0 0 0 0 -17.5411 0.9999998 1 1 1 0 A 3 1 39 46372000 46372000 T A 1 0 0 0 0 1 0 0 0 8078 1406 49 4 4 KIAA0226L 13 46372000 Missense_Mutation SNP T C3N-00175_T 404371 46372000 67992328 962 10554 ATP7B 0 . GRCh38 13 51937531 51937531 + Missense_Mutation SNP G G T rs767380632 C3N-00175_T C3N-00175_N G G c.3848C>A p.Ala1283Asp p.A1283D ENST00000242839 18/21 378 303 75 545 545 0 strelka-varscan-mutect ATP7B,missense_variant,p.Ala1283Asp,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Ala1205Asp,ENST00000448424,;ATP7B,missense_variant,p.Ala1172Asp,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Ala1076Asp,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Ala1235Asp,ENST00000634844,;ATP7B,missense_variant,p.Ala1218Asp,ENST00000418097,;ATP7B,missense_variant,p.Ala853Asp,ENST00000400370,;ATP7B,upstream_gene_variant,,ENST00000634519,;ATP7B,3_prime_UTR_variant,,ENST00000634308,;ATP7B,3_prime_UTR_variant,,ENST00000634296,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634810,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634620,; T ENST00000242839 Transcript missense_variant 4005/6638 3848/4398 1283/1465 A/D gCc/gAc rs767380632 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 deleterious(0) 18/21 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,TIGRFAM_domain:TIGR01494,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01525,Superfamily_domains:SSF56784,Prints_domain:PR00119 MODERATE 1 SNV 1 1 PASS rs767380632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 51937531 51937531 G T 1 0 0 0 0 1 0 0 0 1344 1203 42 2 2 ATP7B 13 51937531 Missense_Mutation SNP G C3N-00175_T 5565531 51937531 62426797 963 10555 DACH1 0 . GRCh38 13 71475181 71475181 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.2043C>T p.= p.D681D ENST00000613252 10/11 226 182 44 298 298 0 strelka-varscan-mutect DACH1,synonymous_variant,p.=,ENST00000613252,NM_080759.5;DACH1,synonymous_variant,p.=,ENST00000611519,NM_080760.5;DACH1,synonymous_variant,p.=,ENST00000620444,NM_004392.6;DACH1,synonymous_variant,p.=,ENST00000619232,; A ENST00000613252 Transcript synonymous_variant 2466/5233 2043/2121 681/706 D gaC/gaT 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 10/11 hmmpanther:PTHR12577:SF14,hmmpanther:PTHR12577 LOW 1 SNV 1 1 PASS rs984740479 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 71475181 71475181 G A 1 0 0 0 0 0 0 0 1 4021 1252 44 3 3 DACH1 13 71475181 Silent SNP G C3N-00175_T 19537650 71475181 42889147 964 10556 DACH1 0 . GRCh38 13 71557023 71557023 + Splice_Site SNP C C A novel C3N-00175_T C3N-00175_N C C c.1570+1G>T p.X524_splice ENST00000613252 72 63 9 80 80 0 strelka-varscan-mutect DACH1,splice_donor_variant,,ENST00000613252,NM_080759.5;DACH1,splice_donor_variant,,ENST00000619232,;DACH1,intron_variant,,ENST00000611519,NM_080760.5;DACH1,intron_variant,,ENST00000620444,NM_004392.6; A ENST00000613252 Transcript splice_donor_variant -/5233 1570/2121 524/706 1 -1 DACH1 HGNC HGNC:2663 protein_coding YES CCDS41899.1 ENSP00000482245 Q9UI36 UPI000007308B NM_080759.5 6/10 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.73561 1 1 1 1 0 A 5 1 39 71557023 71557023 C A 1 0 0 0 0 0 0 1 0 4021 521 18 2 2 DACH1 13 71557023 Splice_Site SNP C C3N-00175_T 81842 71557023 42807305 965 10557 EDNRB 0 . GRCh38 13 77903293 77903293 + Missense_Mutation SNP T T C C3N-00175_T C3N-00175_N T T c.934A>G p.Ile312Val p.I312V ENST00000377211 4/8 232 200 32 240 240 0 strelka-varscan-mutect EDNRB,missense_variant,p.Ile312Val,ENST00000377211,NM_001201397.1;EDNRB,missense_variant,p.Ile222Val,ENST00000334286,NM_000115.3,NM_001122659.2;EDNRB,missense_variant,p.Ile222Val,ENST00000626030,NM_003991.3; C ENST00000377211 Transcript missense_variant 1087/4471 934/1599 312/532 I/V Att/Gtt COSM4048585,COSM4048586,COSM4048587 1 -1 EDNRB HGNC HGNC:3180 protein_coding YES CCDS55902.1 ENSP00000366416 P24530 A0A024R638 UPI0000046D5C NM_001201397.1 tolerated(0.3) 4/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF30,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 77903293 77903293 T C 1 0 0 0 0 1 0 0 0 4748 1493 52 5 5 EDNRB 13 77903293 Missense_Mutation SNP T C3N-00175_T 6346270 77903293 36461035 966 10558 RNF219 0 . GRCh38 13 78616171 78616171 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1590G>T p.Met530Ile p.M530I ENST00000282003 6/6 228 196 32 301 300 1 strelka-varscan-mutect RNF219,missense_variant,p.Met530Ile,ENST00000282003,NM_024546.3;RNF219-AS1,non_coding_transcript_exon_variant,,ENST00000606429,;RNF219-AS1,non_coding_transcript_exon_variant,,ENST00000560584,;RNF219-AS1,downstream_gene_variant,,ENST00000560209,; A ENST00000282003 Transcript missense_variant 1649/3529 1590/2181 530/726 M/I atG/atT 1 -1 RNF219 HGNC HGNC:20308 protein_coding YES CCDS31997.1 ENSP00000282003 Q5W0B1 UPI0000458868 NM_024546.3 deleterious(0) 6/6 hmmpanther:PTHR14609,hmmpanther:PTHR14609:SF1 MODERATE 1 SNV 1 1 PASS rs954109961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 78616171 78616171 C A 1 0 0 0 0 1 0 0 0 13661 594 21 2 2 RNF219 13 78616171 Missense_Mutation SNP C C3N-00175_T 712878 78616171 35748157 967 10559 DCT 0 . GRCh38 13 94465682 94465682 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.814C>T p.= p.L272L ENST00000446125 4/10 198 175 23 224 224 0 strelka-varscan-mutect DCT,synonymous_variant,p.=,ENST00000377028,NM_001922.3;DCT,synonymous_variant,p.=,ENST00000446125,NM_001129889.1;DCT,non_coding_transcript_exon_variant,,ENST00000490854,;DCT,synonymous_variant,p.=,ENST00000483392,;DCT,non_coding_transcript_exon_variant,,ENST00000472871,; A ENST00000446125 Transcript synonymous_variant 1241/2395 814/1659 272/552 L Ctg/Ttg 1 -1 DCT HGNC HGNC:2709 protein_coding YES CCDS45060.1 ENSP00000392762 P40126 UPI0000E13F02 NM_001129889.1 4/10 Gene3D:1.10.1280.10,Pfam_domain:PF00264,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF4,Superfamily_domains:SSF48056 LOW 1 SNV 1 1 PASS rs775382645 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 94465682 94465682 G A 1 0 0 0 0 0 0 0 1 4107 933 33 3 3 DCT 13 94465682 Silent SNP G C3N-00175_T 15849511 94465682 19898646 968 10560 ABCC4 0 . GRCh38 13 95074299 95074299 + Silent SNP C C A rs781637371 C3N-00175_T C3N-00175_N C C c.2832G>T p.= p.T944T ENST00000376887 23/31 122 107 15 159 159 0 strelka-varscan-mutect ABCC4,synonymous_variant,p.=,ENST00000376887,NM_005845.4,NM_001301829.1;ABCC4,non_coding_transcript_exon_variant,,ENST00000467685,;ABCC4,upstream_gene_variant,,ENST00000474158,; A ENST00000376887 Transcript synonymous_variant 2947/5839 2832/3978 944/1325 T acG/acT rs781637371 1 -1 ABCC4 HGNC HGNC:55 protein_coding YES CCDS9474.1 ENSP00000366084 O15439 UPI00001A36E6 NM_005845.4,NM_001301829.1 23/31 PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF237,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS rs781637371 . 0 207 0 3 0 0 0 0 -19.99907 0.9999905 1 1 1 0 A 2 1 39 95074299 95074299 C A 1 0 0 0 0 0 0 0 1 59 523 19 1 1 ABCC4 13 95074299 Silent SNP C C3N-00175_T 608617 95074299 19290029 969 10561 CLYBL 0 . GRCh38 13 99606710 99606710 + Silent SNP G G C novel C3N-00175_T C3N-00175_N G G c.15G>C p.= p.L5L ENST00000376355 1/8 60 51 9 73 73 0 strelka-varscan-mutect CLYBL,synonymous_variant,p.=,ENST00000376355,;CLYBL,synonymous_variant,p.=,ENST00000339105,NM_206808.3;CLYBL,synonymous_variant,p.=,ENST00000376354,; C ENST00000376355 Transcript synonymous_variant 42/6771 15/1023 5/340 L ctG/ctC 1 1 CLYBL HGNC HGNC:18355 protein_coding YES CCDS32002.1 ENSP00000365533 Q8N0X4 UPI0000071ADE 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR11105:SF0,hmmpanther:PTHR11105 LOW 1 SNV 2 1 PASS rs1222420781 . 0 202 7 0 0 0 0 0 -19.89043 0.9999995 1 1 1 0 C 2 2 39 99606710 99606710 G C 1 0 0 0 0 0 0 0 1 3346 1306 46 4 4 CLYBL 13 99606710 Silent SNP G C3N-00175_T 4532411 99606710 14757618 970 10562 TMTC4 0 . GRCh38 13 100656409 100656409 + Silent SNP G G A rs775686914 C3N-00175_T C3N-00175_N G G c.612C>T p.= p.F204F ENST00000342624 6/19 94 87 7 140 140 0 strelka-varscan-mutect TMTC4,synonymous_variant,p.=,ENST00000342624,NM_032813.3;TMTC4,synonymous_variant,p.=,ENST00000376234,NM_001079669.2;TMTC4,synonymous_variant,p.=,ENST00000328767,NM_001286453.1; A ENST00000342624 Transcript synonymous_variant 871/3602 612/2283 204/760 F ttC/ttT rs775686914 1 -1 TMTC4 HGNC HGNC:25904 protein_coding YES CCDS9497.2 ENSP00000343871 Q5T4D3 UPI000004B63E NM_032813.3 6/19 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF440,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS rs775686914 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 100656409 100656409 G A 1 0 0 0 0 0 0 0 1 16737 1165 41 3 3 TMTC4 13 100656409 Silent SNP G C3N-00175_T 1049699 100656409 13707919 971 10563 NALCN 0 . GRCh38 13 101074594 101074594 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.4023C>A p.= p.G1341G ENST00000251127 36/44 157 145 12 187 186 1 strelka-varscan-mutect NALCN,synonymous_variant,p.=,ENST00000251127,NM_052867.2; T ENST00000251127 Transcript synonymous_variant 4105/6818 4023/5217 1341/1738 G ggC/ggA 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 36/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 101074594 101074594 G T 1 0 0 0 0 0 0 0 1 10155 1306 46 2 2 NALCN 13 101074594 Silent SNP G C3N-00175_T 418185 101074594 13289734 972 10564 NALCN 0 . GRCh38 13 101124642 101124642 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.2158C>T p.= p.L720L ENST00000251127 18/44 149 120 29 205 205 0 strelka-varscan-mutect NALCN,synonymous_variant,p.=,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000467264,; A ENST00000251127 Transcript synonymous_variant 2240/6818 2158/5217 720/1738 L Ctg/Ttg 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 18/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 101124642 101124642 G A 1 0 0 0 0 0 0 0 1 10155 933 33 3 3 NALCN 13 101124642 Silent SNP G C3N-00175_T 50048 101124642 13239686 973 10565 CCDC168 0 . GRCh38 13 102730470 102730470 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.20227G>A p.Glu6743Lys p.E6743K ENST00000322527 4/4 124 111 13 178 178 0 strelka-varscan-mutect CCDC168,missense_variant,p.Glu6743Lys,ENST00000322527,NM_001146197.1; T ENST00000322527 Transcript missense_variant 20365/21466 20227/21246 6743/7081 E/K Gaa/Aaa 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(1) 4/4 hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 MODERATE 1 SNV 3 1 PASS . . 0 208 0 0 2 0 0 0 -6.611334 0.9939388 1 1 1 0 T 3 4 39 102730470 102730470 C T 1 0 0 0 0 1 0 0 0 2484 835 29 3 3 CCDC168 13 102730470 Missense_Mutation SNP C C3N-00175_T 1605828 102730470 11633858 974 10566 EFNB2 0 . GRCh38 13 106493419 106493419 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.623C>G p.Thr208Arg p.T208R ENST00000245323 5/5 43 39 4 48 48 0 strelka-varscan-mutect EFNB2,missense_variant,p.Thr208Arg,ENST00000245323,NM_004093.3; C ENST00000245323 Transcript missense_variant 773/4461 623/1002 208/333 T/R aCa/aGa 1 -1 EFNB2 HGNC HGNC:3227 protein_coding YES CCDS9507.1 ENSP00000245323 P52799 UPI0000129C9B NM_004093.3 tolerated(0.51) 5/5 hmmpanther:PTHR11304:SF18,hmmpanther:PTHR11304 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.69844 1 1 1 1 0 C 3 2 39 106493419 106493419 G C 1 0 0 0 0 1 0 0 0 4792 1377 48 4 4 EFNB2 13 106493419 Missense_Mutation SNP G C3N-00175_T 3762949 106493419 7870909 975 10567 LIG4 0 . GRCh38 13 108210589 108210589 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.680A>T p.Gln227Leu p.Q227L ENST00000611712 3/3 131 105 26 206 206 0 strelka-varscan-mutect LIG4,missense_variant,p.Gln227Leu,ENST00000611712,;LIG4,missense_variant,p.Gln227Leu,ENST00000356922,NM_002312.3;LIG4,missense_variant,p.Gln227Leu,ENST00000405925,NM_001098268.1;LIG4,missense_variant,p.Gln227Leu,ENST00000442234,NM_206937.1;LIG4,missense_variant,p.Gln160Leu,ENST00000614526,; A ENST00000611712 Transcript missense_variant 1030/4180 680/2736 227/911 Q/L cAa/cTa 1 -1 LIG4 HGNC HGNC:6601 protein_coding YES CCDS9508.1 ENSP00000484288 P49917 A0A024RE06 UPI00000742BF tolerated(0.23) 3/3 hmmpanther:PTHR10459:SF7,hmmpanther:PTHR10459,TIGRFAM_domain:TIGR00574,Superfamily_domains:SSF56091,Superfamily_domains:0050884 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 108210589 108210589 T A 1 0 0 0 0 1 0 0 0 8692 1812 63 4 4 LIG4 13 108210589 Missense_Mutation SNP T C3N-00175_T 1717170 108210589 6153739 976 10568 TUBGCP3 0 . GRCh38 13 112554987 112554987 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.740A>T p.Glu247Val p.E247V ENST00000261965 7/22 104 90 14 124 124 0 strelka-mutect TUBGCP3,missense_variant,p.Glu247Val,ENST00000261965,NM_006322.5,NM_001286277.1;TUBGCP3,missense_variant,p.Glu247Val,ENST00000375669,NM_001286278.1;TUBGCP3,missense_variant,p.Glu247Val,ENST00000464139,NM_001286279.1;TUBGCP3,downstream_gene_variant,,ENST00000483532,; A ENST00000261965 Transcript missense_variant 927/3899 740/2724 247/907 E/V gAa/gTa 1 -1 TUBGCP3 HGNC HGNC:18598 protein_coding YES CCDS9525.1 ENSP00000261965 Q96CW5 UPI000000DB88 NM_006322.5,NM_001286277.1 deleterious(0) 7/22 hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF14 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 112554987 112554987 T A 1 0 0 0 0 1 0 0 0 17277 1783 62 4 4 TUBGCP3 13 112554987 Missense_Mutation SNP T C3N-00175_T 4344398 112554987 1809341 977 10569 OR4Q3 0 . GRCh38 14 19747996 19747996 + Frame_Shift_Del DEL G G - rs190796594 C3N-00175_T C3N-00175_N G G c.569delG p.Cys190SerfsTer7 p.C190Sfs*7 ENST00000331723 1/1 388 337 51 397 397 0 sindel-varindel-pindel OR4Q3,frameshift_variant,p.Cys190SerfsTer7,ENST00000331723,NM_172194.1;OR4N2,intron_variant,,ENST00000557414,; - ENST00000331723 Transcript frameshift_variant 569/942 569/942 190/313 C/X tGc/tc rs190796594 1 1 OR4Q3 HGNC HGNC:15426 protein_coding YES CCDS32020.1 ENSP00000330049 Q8NH05 A0A126GW32 UPI0000061EF0 NM_172194.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF208,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 19747996 19747996 G - 1 0 1 0 1 0 0 0 0 11157 1319 46 0 0 OR4Q3 14 19747996 Frame_Shift_Del DEL G C3N-00175_T 19747996 87295722 978 10570 OR4K5 0 . GRCh38 14 19920776 19920776 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.170C>A p.Ser57Tyr p.S57Y ENST00000315915 1/1 328 241 87 289 288 1 strelka-varscan-mutect OR4K5,missense_variant,p.Ser57Tyr,ENST00000315915,NM_001005483.1; A ENST00000315915 Transcript missense_variant 195/1078 170/972 57/323 S/Y tCc/tAc 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19920776 19920776 C A 1 0 0 0 0 1 0 0 0 11150 855 30 2 2 OR4K5 14 19920776 Missense_Mutation SNP C C3N-00175_T 172780 19920776 87122942 979 10571 OR4K5 0 . GRCh38 14 19921031 19921031 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.425C>A p.Thr142Asn p.T142N ENST00000315915 1/1 514 486 28 456 456 0 strelka-varscan-mutect OR4K5,missense_variant,p.Thr142Asn,ENST00000315915,NM_001005483.1; A ENST00000315915 Transcript missense_variant 450/1078 425/972 142/323 T/N aCt/aAt 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 tolerated(0.07) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19921031 19921031 C A 1 0 0 0 0 1 0 0 0 11150 565 20 2 2 OR4K5 14 19921031 Missense_Mutation SNP C C3N-00175_T 255 19921031 87122687 980 10572 TEP1 0 . GRCh38 14 20406288 20406288 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.680C>T p.Ser227Phe p.S227F ENST00000262715 3/55 260 233 27 246 246 0 strelka-varscan-mutect TEP1,missense_variant,p.Ser227Phe,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Ser227Phe,ENST00000556935,;TEP1,downstream_gene_variant,,ENST00000556549,;TEP1,missense_variant,p.Ser227Phe,ENST00000555727,;TEP1,upstream_gene_variant,,ENST00000557627,; A ENST00000262715 Transcript missense_variant 721/10695 680/7884 227/2627 S/F tCt/tTt 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 tolerated(0.77) 3/55 PROSITE_profiles:PS50988,Pfam_domain:PF05731 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 20406288 20406288 G A 1 0 0 0 0 1 0 0 0 16175 942 33 3 3 TEP1 14 20406288 Missense_Mutation SNP G C3N-00175_T 485257 20406288 86637430 981 10573 RPGRIP1 0 . GRCh38 14 21301044 21301044 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.297G>T p.Glu99Asp p.E99D ENST00000400017 3/24 330 175 155 398 398 0 strelka-varscan-mutect RPGRIP1,missense_variant,p.Glu99Asp,ENST00000400017,NM_020366.3;RPGRIP1,missense_variant,p.Glu99Asp,ENST00000557771,;RPGRIP1,missense_variant,p.Glu99Asp,ENST00000556336,;RPGRIP1,upstream_gene_variant,,ENST00000554750,; T ENST00000400017 Transcript missense_variant 297/3940 297/3861 99/1286 E/D gaG/gaT 1 1 RPGRIP1 HGNC HGNC:13436 protein_coding YES CCDS45080.1 ENSP00000382895 Q96KN7 UPI0000071B81 NM_020366.3 tolerated(0.21) 3/24 hmmpanther:PTHR14240:SF3,hmmpanther:PTHR14240 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 21301044 21301044 G T 1 0 0 0 0 1 0 0 0 13801 933 33 2 2 RPGRIP1 14 21301044 Missense_Mutation SNP G C3N-00175_T 894756 21301044 85742674 982 10574 MYH6 0 . GRCh38 14 23404809 23404809 + Missense_Mutation SNP C C G rs763305936 C3N-00175_T C3N-00175_N C C c.544G>C p.Ala182Pro p.A182P ENST00000405093 7/39 374 193 181 429 429 0 strelka-varscan-mutect MYH6,missense_variant,p.Ala182Pro,ENST00000405093,NM_002471.3;MYH6,missense_variant,p.Ala182Pro,ENST00000356287,;MYH6,non_coding_transcript_exon_variant,,ENST00000557461,; G ENST00000405093 Transcript missense_variant 615/5941 544/5820 182/1939 A/P Gcg/Ccg rs763305936 1 -1 MYH6 HGNC HGNC:7576 protein_coding YES CCDS9600.1 ENSP00000386041 P13533 UPI0000160969 NM_002471.3 deleterious(0) 7/39 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs763305936 . 0 208 0 0 2 0 0 0 -20 0.9996218 1 1 1 0 G 3 3 39 23404809 23404809 C G 1 0 0 0 0 1 0 0 0 10038 739 26 4 4 MYH6 14 23404809 Missense_Mutation SNP C C3N-00175_T 2103765 23404809 83638909 983 10575 JPH4 0 . GRCh38 14 23571188 23571188 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1543G>T p.Glu515Ter p.E515* ENST00000397118 6/7 166 129 37 188 188 0 strelka-varscan-mutect JPH4,stop_gained,p.Glu515Ter,ENST00000397118,NM_032452.2;JPH4,stop_gained,p.Glu515Ter,ENST00000356300,NM_001146028.1;JPH4,stop_gained,p.Glu516Ter,ENST00000622501,;JPH4,stop_gained,p.Glu180Ter,ENST00000544177,;AP1G2,upstream_gene_variant,,ENST00000308724,NM_001282475.1;AP1G2,upstream_gene_variant,,ENST00000397120,NM_001282474.1,NM_003917.4;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000556843,;RP11-66N24.3,downstream_gene_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000460049,;AP1G2,upstream_gene_variant,,ENST00000465445,;AP1G2,upstream_gene_variant,,ENST00000535852,;JPH4,downstream_gene_variant,,ENST00000553505,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000554312,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000554816,; A ENST00000397118 Transcript stop_gained 2446/4386 1543/1887 515/628 E/* Gag/Tag 1 -1 JPH4 HGNC HGNC:20156 protein_coding YES CCDS9603.1 ENSP00000380307 Q96JJ6 UPI00001C1F68 NM_032452.2 6/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF14,PIRSF_domain:PIRSF037387 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 23571188 23571188 C A 1 0 0 0 0 0 1 0 0 7875 835 29 2 2 JPH4 14 23571188 Nonsense_Mutation SNP C C3N-00175_T 166379 23571188 83472530 984 10576 NYNRIN 0 . GRCh38 14 24409372 24409373 + Frame_Shift_Ins INS - - G novel C3N-00175_T C3N-00175_N - - c.1584dupG p.Leu529AlafsTer14 p.L529Afs*14 ENST00000382554 4/9 151 119 32 207 207 0 sindel-varindel-pindel NYNRIN,frameshift_variant,p.Leu529AlafsTer14,ENST00000382554,NM_025081.2;NYNRIN,upstream_gene_variant,,ENST00000554505,; G ENST00000382554 Transcript frameshift_variant 1896-1897/7857 1578-1579/5697 526-527/1898 -/X -/G 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 4/9 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2 HIGH 1 insertion 5 6 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 39 24409372 24409372 - G 1 0 1 1 0 0 0 0 0 10874 69 3 0 0 NYNRIN 14 24409372 Frame_Shift_Ins INS - C3N-00175_T 838184 24409372 82634346 985 10577 G2E3 0 . GRCh38 14 30589385 30589385 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.138G>T p.Leu46Phe p.L46F ENST00000206595 4/15 38 30 8 84 84 0 strelka-varscan-mutect G2E3,missense_variant,p.Leu46Phe,ENST00000206595,NM_017769.3;G2E3,missense_variant,p.Leu76Phe,ENST00000553504,;G2E3,missense_variant,p.Leu46Phe,ENST00000547532,;G2E3,missense_variant,p.Leu46Phe,ENST00000550944,;G2E3,missense_variant,p.Leu46Phe,ENST00000554714,;G2E3,missense_variant,p.Leu46Phe,ENST00000555429,;G2E3,splice_region_variant,,ENST00000438909,NM_001308097.1;G2E3,upstream_gene_variant,,ENST00000552515,;G2E3,splice_region_variant,,ENST00000544007,;G2E3,splice_region_variant,,ENST00000552488,;G2E3,upstream_gene_variant,,ENST00000549553,; T ENST00000206595 Transcript missense_variant,splice_region_variant 292/5804 138/2121 46/706 L/F ttG/ttT 1 1 G2E3 HGNC HGNC:20338 protein_coding YES CCDS9638.1 ENSP00000206595 Q7L622 UPI000013F3A8 NM_017769.3 deleterious(0) 4/15 hmmpanther:PTHR12420,hmmpanther:PTHR12420:SF26,Pfam_domain:PF13771 MODERATE 1 SNV 1 1 PASS . . 1 204 3 2 0 0 0 0 -16.43602 0.9999967 1 1 1 0 T 3 4 39 30589385 30589385 G T 1 0 0 0 0 1 0 0 0 6011 1304 45 2 2 G2E3 14 30589385 Missense_Mutation SNP G C3N-00175_T 6180013 30589385 76454333 986 10578 AKAP6 0 . GRCh38 14 32823136 32823136 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.5323G>A p.Asp1775Asn p.D1775N ENST00000280979 13/14 191 100 91 208 208 0 strelka-varscan-mutect AKAP6,missense_variant,p.Asp1775Asn,ENST00000280979,NM_004274.4;AKAP6,intron_variant,,ENST00000557272,; A ENST00000280979 Transcript missense_variant 5493/15006 5323/6960 1775/2319 D/N Gac/Aac 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 deleterious(0) 13/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 32823136 32823136 G A 1 0 0 0 0 1 0 0 0 539 1290 45 3 3 AKAP6 14 32823136 Missense_Mutation SNP G C3N-00175_T 2233751 32823136 74220582 987 10579 NPAS3 0 . GRCh38 14 33800867 33800867 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.2560G>A p.Val854Met p.V854M ENST00000356141 12/12 433 382 51 400 400 0 strelka-varscan-mutect NPAS3,missense_variant,p.Val822Met,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Val824Met,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Val859Met,ENST00000551492,;NPAS3,missense_variant,p.Val854Met,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Val841Met,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Val828Met,ENST00000551634,; A ENST00000356141 Transcript missense_variant 2560/2802 2560/2802 854/933 V/M Gtg/Atg 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 tolerated_low_confidence(0.29) 12/12 hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 33800867 33800867 G A 1 0 0 0 0 1 0 0 0 10612 1145 40 1 1 NPAS3 14 33800867 Missense_Mutation SNP G C3N-00175_T 977731 33800867 73242851 988 10580 MIA2 0 . GRCh38 14 39247895 39247895 + Frame_Shift_Del DEL A A - rs545679883 C3N-00175_T C3N-00175_N A A c.1322delA p.Lys441ArgfsTer17 p.K441Rfs*17 ENST00000553728 4/28 50 38 12 92 92 0 sindel-varindel-pindel RP11-407N17.3,frameshift_variant,p.Lys441ArgfsTer17,ENST00000553728,;MIA2,frameshift_variant,p.Lys441ArgfsTer17,ENST00000280082,NM_054024.3;MIA2,non_coding_transcript_exon_variant,,ENST00000556784,; - ENST00000553728 Transcript frameshift_variant 1534/4392 1321/4020 441/1339 K/X Aag/ag rs545679883 1 1 RP11-407N17.3 Clone_based_vega_gene protein_coding YES ENSP00000452252 G3V599 UPI00021CF1EF 4/28 Low_complexity_(Seg):seg,hmmpanther:PTHR23158:SF38,hmmpanther:PTHR23158 HIGH deletion 5 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 39247895 39247895 A - 1 0 1 0 1 0 0 0 0 9521 131 5 0 0 MIA2 14 39247895 Frame_Shift_Del DEL A C3N-00175_T 5447028 39247895 67795823 989 10581 LRFN5 0 . GRCh38 14 41891394 41891394 + Frame_Shift_Del DEL G G - rs181411518 C3N-00175_T C3N-00175_N G G c.1531delG p.Glu511AsnfsTer19 p.E511Nfs*19 ENST00000298119 4/6 227 119 108 283 283 0 sindel-varindel-pindel LRFN5,frameshift_variant,p.Glu511AsnfsTer19,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; - ENST00000298119 Transcript frameshift_variant 2719/3723 1530/2160 510/719 T/X acG/ac rs181411518,COSM5517008 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 41891394 41891394 G - 1 0 1 0 1 0 0 0 0 8835 1103 39 0 0 LRFN5 14 41891394 Frame_Shift_Del DEL G C3N-00175_T 2643499 41891394 65152324 990 10582 MDGA2 0 . GRCh38 14 47218074 47218074 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.335C>A p.Ala112Glu p.A112E ENST00000399232 3/17 144 115 29 140 140 0 strelka-varscan-mutect MDGA2,missense_variant,p.Ala112Glu,ENST00000399232,NM_001113498.2;MDGA2,missense_variant,p.Ala136Glu,ENST00000486952,;MDGA2,5_prime_UTR_variant,,ENST00000426342,;MDGA2,5_prime_UTR_variant,,ENST00000357362,NM_182830.4;MDGA2,5_prime_UTR_variant,,ENST00000557238,;MDGA2,5_prime_UTR_variant,,ENST00000482848,; T ENST00000399232 Transcript missense_variant 700/5075 335/2871 112/956 A/E gCa/gAa 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 deleterious(0) 3/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 47218074 47218074 G T 1 0 0 0 0 1 0 0 0 9345 1319 46 2 2 MDGA2 14 47218074 Missense_Mutation SNP G C3N-00175_T 5326680 47218074 59825644 991 10583 C14orf37 0 . GRCh38 14 58138997 58138997 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.362C>A p.Ser121Ter p.S121* ENST00000267485 2/8 126 98 28 169 169 0 strelka-varscan-mutect C14orf37,stop_gained,p.Ser121Ter,ENST00000267485,NM_001001872.2;C14orf37,non_coding_transcript_exon_variant,,ENST00000334342,;C14orf37,non_coding_transcript_exon_variant,,ENST00000557175,;C14orf37,downstream_gene_variant,,ENST00000554218,;UBA52P3,upstream_gene_variant,,ENST00000491303,; T ENST00000267485 Transcript stop_gained 557/6495 362/2325 121/774 S/* tCa/tAa 1 -1 C14orf37 HGNC HGNC:19846 protein_coding YES CCDS32089.1 ENSP00000267485 Q86TY3 UPI000000CC37 NM_001001872.2 2/8 hmmpanther:PTHR21585,hmmpanther:PTHR21585:SF0,Pfam_domain:PF15767 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 58138997 58138997 G T 1 0 0 0 0 0 1 0 0 1838 1294 45 2 2 C14orf37 14 58138997 Nonsense_Mutation SNP G C3N-00175_T 10920923 58138997 48904721 992 10584 DACT1 0 . GRCh38 14 58646566 58646566 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1943G>C p.Gly648Ala p.G648A ENST00000335867 4/4 65 53 12 64 64 0 strelka-varscan-mutect DACT1,missense_variant,p.Gly611Ala,ENST00000395153,NM_001079520.1;DACT1,missense_variant,p.Gly367Ala,ENST00000541264,;DACT1,missense_variant,p.Gly648Ala,ENST00000335867,NM_016651.5;DACT1,missense_variant,p.Gly367Ala,ENST00000556859,;DACT1,downstream_gene_variant,,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,; C ENST00000335867 Transcript missense_variant 1967/2571 1943/2511 648/836 G/A gGc/gCc 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 tolerated(0.34) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 58646566 58646566 G C 1 0 0 0 0 1 0 0 0 4023 1203 42 4 4 DACT1 14 58646566 Missense_Mutation SNP G C3N-00175_T 507569 58646566 48397152 993 10585 SYNE2 0 . GRCh38 14 63954758 63954758 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.630G>T p.Trp210Cys p.W210C ENST00000358025 8/116 213 119 94 214 214 0 strelka-varscan-mutect SYNE2,missense_variant,p.Trp210Cys,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Trp210Cys,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Trp210Cys,ENST00000357395,;SYNE2,missense_variant,p.Trp210Cys,ENST00000554584,;SYNE2,missense_variant,p.Trp210Cys,ENST00000341472,; T ENST00000358025 Transcript missense_variant 842/21842 630/20724 210/6907 W/C tgG/tgT 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0) 8/116 PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF317,hmmpanther:PTHR11915,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 63954758 63954758 G T 1 0 0 0 0 1 0 0 0 15838 1183 41 2 2 SYNE2 14 63954758 Missense_Mutation SNP G C3N-00175_T 5308192 63954758 43088960 994 10586 SMOC1 0 . GRCh38 14 70023343 70023343 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1187A>T p.Lys396Met p.K396M ENST00000361956 11/12 354 303 51 416 416 0 strelka-varscan-mutect SMOC1,missense_variant,p.Lys396Met,ENST00000381280,NM_022137.5;SMOC1,missense_variant,p.Lys396Met,ENST00000361956,NM_001034852.2; T ENST00000361956 Transcript missense_variant 1450/2040 1187/1308 396/435 K/M aAg/aTg 1 1 SMOC1 HGNC HGNC:20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF NM_001034852.2 deleterious(0) 11/12 Low_complexity_(Seg):seg,hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF13,Gene3D:1.10.238.10,Pfam_domain:PF10591,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 70023343 70023343 A T 1 0 0 0 0 1 0 0 0 15122 72 3 4 4 SMOC1 14 70023343 Missense_Mutation SNP A C3N-00175_T 6068585 70023343 37020375 995 10587 MED6 0 . GRCh38 14 70584848 70584848 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.706A>T p.Lys236Ter p.K236* ENST00000615788 8/9 229 136 93 196 196 0 strelka-varscan-mutect MED6,stop_gained,p.Lys236Ter,ENST00000256379,NM_005466.3;MED6,stop_gained,p.Lys236Ter,ENST00000615788,NM_001284211.1;MED6,stop_gained,p.Lys243Ter,ENST00000430055,NM_001284209.1;MED6,stop_gained,p.Lys236Ter,ENST00000554963,;MED6,3_prime_UTR_variant,,ENST00000440435,NM_001284210.1;MED6,non_coding_transcript_exon_variant,,ENST00000555296,; A ENST00000615788 Transcript stop_gained 759/1700 706/774 236/257 K/* Aaa/Taa 1 -1 MED6 HGNC HGNC:19970 protein_coding YES CCDS73649.1 ENSP00000481920 A0A087WYL7 UPI0001EF1523 NM_001284211.1 8/9 hmmpanther:PTHR13104,PIRSF_domain:PIRSF023869 HIGH 1 SNV 5 1 PASS rs1296304750 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 70584848 70584848 T A 1 0 0 0 0 0 1 0 0 9390 1763 61 4 4 MED6 14 70584848 Nonsense_Mutation SNP T C3N-00175_T 561505 70584848 36458870 996 10588 RGS6 0 . GRCh38 14 72352183 72352183 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.173G>C p.Ser58Thr p.S58T ENST00000553525 3/18 94 58 36 109 109 0 strelka-varscan-mutect RGS6,missense_variant,p.Ser58Thr,ENST00000553530,NM_001204418.1,NM_004296.5,NM_001204420.1,NM_001204422.1;RGS6,missense_variant,p.Ser23Thr,ENST00000622468,;RGS6,missense_variant,p.Ser23Thr,ENST00000402788,NM_001204423.1;RGS6,missense_variant,p.Ser23Thr,ENST00000343854,;RGS6,missense_variant,p.Ser58Thr,ENST00000553525,NM_001204424.1;RGS6,missense_variant,p.Ser58Thr,ENST00000555571,;RGS6,missense_variant,p.Ser58Thr,ENST00000556437,NM_001204417.1,NM_001204421.1,NM_001204419.1,NM_001204416.1;RGS6,missense_variant,p.Ser58Thr,ENST00000355512,;RGS6,missense_variant,p.Ser58Thr,ENST00000404301,;RGS6,missense_variant,p.Ser58Thr,ENST00000407322,;RGS6,missense_variant,p.Ser58Thr,ENST00000406236,;RGS6,missense_variant,p.Ser58Thr,ENST00000554474,; C ENST00000553525 Transcript missense_variant 696/2005 173/1473 58/490 S/T aGt/aCt 1 1 RGS6 HGNC HGNC:10002 protein_coding YES CCDS55924.1 ENSP00000451030 P49758 UPI00001698D0 NM_001204424.1 deleterious(0.05) 3/18 PROSITE_profiles:PS50186,hmmpanther:PTHR10845:SF27,hmmpanther:PTHR10845,Gene3D:1.10.10.10,Pfam_domain:PF00610,SMART_domains:SM00049,Superfamily_domains:SSF46785 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 72352183 72352183 G C 1 0 0 0 0 1 0 0 0 13480 1029 36 4 4 RGS6 14 72352183 Missense_Mutation SNP G C3N-00175_T 1767335 72352183 34691535 997 10589 ENTPD5 0 . GRCh38 14 73988059 73988059 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.44C>T p.Ser15Phe p.S15F ENST00000334696 4/16 216 162 54 282 282 0 strelka-varscan-mutect ENTPD5,missense_variant,p.Ser15Phe,ENST00000334696,NM_001249.2;ENTPD5,missense_variant,p.Ser15Phe,ENST00000557325,;ENTPD5,missense_variant,p.Ser15Phe,ENST00000556242,;ENTPD5,missense_variant,p.Ser15Phe,ENST00000553284,;ENTPD5,downstream_gene_variant,,ENST00000554664,; A ENST00000334696 Transcript missense_variant 364/5842 44/1287 15/428 S/F tCc/tTc 1 -1 ENTPD5 HGNC HGNC:3367 protein_coding YES CCDS9825.1 ENSP00000335246 O75356 A0A024R6D3 UPI0000052B69 NM_001249.2 deleterious_low_confidence(0) 4/16 hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF35,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 73988059 73988059 G A 1 0 0 0 0 1 0 0 0 4987 1174 41 3 3 ENTPD5 14 73988059 Missense_Mutation SNP G C3N-00175_T 1635876 73988059 33055659 998 10590 UNC79 0 . GRCh38 14 93577866 93577866 + Nonsense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1705C>T p.Arg569Ter p.R569* ENST00000256339 18/50 148 118 30 169 169 0 strelka-varscan-mutect UNC79,stop_gained,p.Arg746Ter,ENST00000553484,;UNC79,stop_gained,p.Arg746Ter,ENST00000555664,;UNC79,stop_gained,p.Arg569Ter,ENST00000256339,NM_020818.3;UNC79,stop_gained,p.Arg746Ter,ENST00000393151,;UNC79,stop_gained,p.Arg569Ter,ENST00000621021,; T ENST00000256339 Transcript stop_gained 2360/8400 1705/7377 569/2458 R/* Cga/Tga 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 18/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 93577866 93577866 C T 1 0 0 0 0 0 1 0 0 17520 644 23 1 1 UNC79 14 93577866 Nonsense_Mutation SNP C C3N-00175_T 19589807 93577866 13465852 999 10591 PPP4R4 0 . GRCh38 14 94242386 94242386 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1244C>A p.Thr415Asn p.T415N ENST00000304338 11/25 144 118 26 162 162 0 strelka-varscan-mutect PPP4R4,missense_variant,p.Thr415Asn,ENST00000304338,NM_058237.1; A ENST00000304338 Transcript missense_variant 1398/3868 1244/2622 415/873 T/N aCt/aAt 1 1 PPP4R4 HGNC HGNC:23788 protein_coding YES CCDS9921.1 ENSP00000305924 Q6NUP7 UPI000016223B NM_058237.1 deleterious(0.01) 11/25 Gene3D:1.25.10.10,hmmpanther:PTHR21467,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 94242386 94242386 C A 1 0 0 0 0 1 0 0 0 12530 565 20 2 2 PPP4R4 14 94242386 Missense_Mutation SNP C C3N-00175_T 664520 94242386 12801332 1000 10592 SERPINA6 0 . GRCh38 14 94314327 94314327 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.322G>T p.Gly108Cys p.G108C ENST00000341584 2/5 446 281 165 483 482 1 strelka-varscan-mutect SERPINA6,missense_variant,p.Gly108Cys,ENST00000341584,NM_001756.3;SERPINA6,missense_variant,p.Gly108Cys,ENST00000557225,;SERPINA6,missense_variant,p.Gly108Cys,ENST00000555056,; A ENST00000341584 Transcript missense_variant 469/1534 322/1218 108/405 G/C Ggt/Tgt 1 -1 SERPINA6 HGNC HGNC:1540 protein_coding YES CCDS9924.1 ENSP00000342850 P08185 UPI0000127182 NM_001756.3 deleterious(0) 2/5 hmmpanther:PTHR11461:SF34,hmmpanther:PTHR11461,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 94314327 94314327 C A 1 0 0 0 0 1 0 0 0 14369 623 22 2 2 SERPINA6 14 94314327 Missense_Mutation SNP C C3N-00175_T 71941 94314327 12729391 1001 10593 SERPINA11 0 . GRCh38 14 94446381 94446381 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.867T>A p.= p.A289A ENST00000334708 3/5 182 154 28 190 190 0 strelka-varscan-mutect SERPINA11,synonymous_variant,p.=,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; T ENST00000334708 Transcript synonymous_variant 932/1476 867/1269 289/422 A gcT/gcA 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 3/5 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 94446381 94446381 A T 1 0 0 0 0 0 0 0 1 14364 175 7 4 4 SERPINA11 14 94446381 Silent SNP A C3N-00175_T 132054 94446381 12597337 1002 10594 SERPINA5 0 . GRCh38 14 94590305 94590305 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.884A>C p.Lys295Thr p.K295T ENST00000329597 4/6 18 15 3 40 40 0 strelka-mutect SERPINA5,missense_variant,p.Lys295Thr,ENST00000329597,NM_000624.5;SERPINA5,missense_variant,p.Lys295Thr,ENST00000554866,;SERPINA5,missense_variant,p.Lys295Thr,ENST00000554276,;SERPINA5,missense_variant,p.Lys295Thr,ENST00000553780,;SERPINA5,missense_variant,p.Lys295Thr,ENST00000554760,;SERPINA5,downstream_gene_variant,,ENST00000556775,;SERPINA5,downstream_gene_variant,,ENST00000555681,;SERPINA5,downstream_gene_variant,,ENST00000557598,;SERPINA5,downstream_gene_variant,,ENST00000554220,;SERPINA5,downstream_gene_variant,,ENST00000553511,;SERPINA5,downstream_gene_variant,,ENST00000554633,;SERPINA5,downstream_gene_variant,,ENST00000556064,;SERPINA5,non_coding_transcript_exon_variant,,ENST00000556730,;SERPINA3,upstream_gene_variant,,ENST00000553947,; C ENST00000329597 Transcript missense_variant 1119/2337 884/1221 295/406 K/T aAa/aCa 1 1 SERPINA5 HGNC HGNC:8723 protein_coding YES CCDS9928.1 ENSP00000333203 P05154 A0A024R6N9 UPI000013E52C NM_000624.5 tolerated(0.65) 4/6 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF176,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 94590305 94590305 A C 1 0 0 0 0 1 0 0 0 14368 14 1 5 5 SERPINA5 14 94590305 Missense_Mutation SNP A C3N-00175_T 143924 94590305 12453413 1003 10595 EML1 0 . GRCh38 14 99907706 99907706 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1134G>T p.Gln378His p.Q378H ENST00000334192 11/23 204 172 32 220 220 0 strelka-varscan-mutect EML1,missense_variant,p.Gln359His,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Gln378His,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Gln347His,ENST00000327921,;EML1,missense_variant,p.Gln346His,ENST00000554479,;EML1,intron_variant,,ENST00000554386,;EML1,non_coding_transcript_exon_variant,,ENST00000555812,;EML1,missense_variant,p.Gln101His,ENST00000554553,;EML1,non_coding_transcript_exon_variant,,ENST00000554111,; T ENST00000334192 Transcript missense_variant 1268/4064 1134/2505 378/834 Q/H caG/caT 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 deleterious(0.01) 11/23 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 99907706 99907706 G T 1 0 0 0 0 1 0 0 0 4939 933 33 2 2 EML1 14 99907706 Missense_Mutation SNP G C3N-00175_T 5317401 99907706 7136012 1004 10596 MOK 0 . GRCh38 14 102263574 102263574 + Missense_Mutation SNP C C T rs536673850 C3N-00175_T C3N-00175_N C C c.255G>A p.Met85Ile p.M85I ENST00000361847 4/12 64 59 5 135 135 0 strelka-mutect MOK,missense_variant,p.Met85Ile,ENST00000361847,NM_014226.2;MOK,missense_variant,p.Met85Ile,ENST00000522874,;MOK,missense_variant,p.Met85Ile,ENST00000193029,;MOK,missense_variant,p.Met55Ile,ENST00000524214,NM_001272011.1;MOK,non_coding_transcript_exon_variant,,ENST00000524019,;MOK,non_coding_transcript_exon_variant,,ENST00000521966,;MOK,intron_variant,,ENST00000521493,;MOK,missense_variant,p.Met85Ile,ENST00000517537,;MOK,3_prime_UTR_variant,,ENST00000520238,;MOK,3_prime_UTR_variant,,ENST00000524207,;MOK,non_coding_transcript_exon_variant,,ENST00000518686,;MOK,non_coding_transcript_exon_variant,,ENST00000523485,;MOK,non_coding_transcript_exon_variant,,ENST00000519569,;MOK,intron_variant,,ENST00000521766,;MOK,intron_variant,,ENST00000521388,;MOK,intron_variant,,ENST00000562292,;MOK,intron_variant,,ENST00000518399,;MOK,intron_variant,,ENST00000518482,;MOK,intron_variant,,ENST00000519877,;MOK,intron_variant,,ENST00000522093,; T ENST00000361847 Transcript missense_variant 487/1940 255/1260 85/419 M/I atG/atA rs536673850 1 -1 MOK HGNC HGNC:9833 protein_coding YES CCDS9971.1 ENSP00000355304 Q9UQ07 UPI0000035B77 NM_014226.2 deleterious(0) 4/12 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF72,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 102263574 102263574 C T 1 0 0 0 0 1 0 0 0 9661 594 21 3 3 MOK 14 102263574 Missense_Mutation SNP C C3N-00175_T 2355868 102263574 4780144 1005 10597 ASPG 0 . GRCh38 14 104097585 104097585 + Missense_Mutation SNP G G T rs765497573 C3N-00175_T C3N-00175_N G G c.461G>T p.Arg154Leu p.R154L ENST00000551177 5/16 137 83 54 225 225 0 strelka-varscan-mutect ASPG,missense_variant,p.Arg154Leu,ENST00000551177,NM_001080464.2;ASPG,missense_variant,p.Arg154Leu,ENST00000546892,;ASPG,missense_variant,p.Arg91Leu,ENST00000551170,;ASPG,non_coding_transcript_exon_variant,,ENST00000548372,; T ENST00000551177 Transcript missense_variant 553/4851 461/1722 154/573 R/L cGt/cTt rs765497573 1 1 ASPG HGNC HGNC:20123 protein_coding YES CCDS45170.2 ENSP00000450040 Q86U10 UPI00001D7B76 NM_001080464.2 deleterious(0.02) 5/16 PROSITE_profiles:PS51732,hmmpanther:PTHR11707:SF28,hmmpanther:PTHR11707,TIGRFAM_domain:TIGR00519,PIRSF_domain:PIRSF001220,Gene3D:3.40.50.1170,Pfam_domain:PF00710,PIRSF_domain:PIRSF500176,SMART_domains:SM00870,Superfamily_domains:SSF53774 MODERATE 1 SNV 1 1 PASS rs765497573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 104097585 104097585 G T 1 0 0 0 0 1 0 0 0 1199 1145 40 1 1 ASPG 14 104097585 Missense_Mutation SNP G C3N-00175_T 1834011 104097585 2946133 1006 10598 AHNAK2 0 . GRCh38 14 104948099 104948099 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.7352T>A p.Val2451Glu p.V2451E ENST00000333244 7/7 318 247 71 363 361 2 strelka-varscan-mutect AHNAK2,missense_variant,p.Val2451Glu,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; T ENST00000333244 Transcript missense_variant 7472/18254 7352/17388 2451/5795 V/E gTg/gAg 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0.04) 7/7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 104948099 104948099 A T 1 0 0 0 0 1 0 0 0 492 159 6 4 4 AHNAK2 14 104948099 Missense_Mutation SNP A C3N-00175_T 850514 104948099 2095619 1007 10599 AHNAK2 0 . GRCh38 14 104950446 104950446 + Missense_Mutation SNP C C G rs199554131 C3N-00175_T C3N-00175_N C C c.5005G>C p.Gly1669Arg p.G1669R ENST00000333244 7/7 702 427 275 763 763 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Gly1669Arg,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; G ENST00000333244 Transcript missense_variant 5125/18254 5005/17388 1669/5795 G/R Ggg/Cgg rs199554131 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0) 7/7 hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348 MODERATE 1 SNV 5 1 PASS rs199554131 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 104950446 104950446 C G 1 0 0 0 0 1 0 0 0 492 594 21 4 4 AHNAK2 14 104950446 Missense_Mutation SNP C C3N-00175_T 2347 104950446 2093272 1008 10600 AHNAK2 0 . GRCh38 14 104951606 104951606 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.3845T>C p.Val1282Ala p.V1282A ENST00000333244 7/7 260 186 74 341 340 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Val1282Ala,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; G ENST00000333244 Transcript missense_variant 3965/18254 3845/17388 1282/5795 V/A gTg/gCg 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0.01) 7/7 MODERATE 1 SNV 5 1 PASS . . 22 188 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 104951606 104951606 A G 1 0 0 0 0 1 0 0 0 492 159 6 5 5 AHNAK2 14 104951606 Missense_Mutation SNP A C3N-00175_T 1160 104951606 2092112 1009 10601 BTBD6 0 . GRCh38 14 105249083 105249083 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.213G>C p.Glu71Asp p.E71D ENST00000392554 1/4 90 76 14 93 93 0 strelka-varscan-mutect BTBD6,missense_variant,p.Glu71Asp,ENST00000392554,NM_033271.2;BTBD6,missense_variant,p.Glu71Asp,ENST00000536364,;BTBD6,missense_variant,p.Glu71Asp,ENST00000537513,;BTBD6,splice_region_variant,,ENST00000327471,;BTBD6,5_prime_UTR_variant,,ENST00000463376,;BRF1,intron_variant,,ENST00000547530,NM_001519.3;BRF1,intron_variant,,ENST00000379937,NM_001242788.1;BRF1,intron_variant,,ENST00000446501,NM_001242789.1;BRF1,intron_variant,,ENST00000440513,NM_001242786.1;BRF1,intron_variant,,ENST00000327359,NM_001242787.1;BRF1,intron_variant,,ENST00000619151,;BRF1,intron_variant,,ENST00000552127,;BRF1,intron_variant,,ENST00000546417,;BRF1,upstream_gene_variant,,ENST00000392557,NM_145685.2;BRF1,upstream_gene_variant,,ENST00000550375,;BRF1,upstream_gene_variant,,ENST00000550208,;BRF1,upstream_gene_variant,,ENST00000379932,;BRF1,upstream_gene_variant,,ENST00000551787,;BRF1,downstream_gene_variant,,ENST00000550692,;BTBD6,upstream_gene_variant,,ENST00000392553,; C ENST00000392554 Transcript missense_variant,splice_region_variant 510/2176 213/1458 71/485 E/D gaG/gaC 1 1 BTBD6 HGNC HGNC:19897 protein_coding YES CCDS10002.2 ENSP00000376337 Q96KE9 UPI00001FDD27 NM_033271.2 tolerated(0.06) 1/4 Gene3D:3.30.710.10,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF4,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 105249083 105249083 G C 1 0 0 0 0 1 0 0 0 1721 956 33 4 4 BTBD6 14 105249083 Missense_Mutation SNP G C3N-00175_T 297477 105249083 1794635 1010 10602 GOLGA6L2 0 . GRCh38 15 23443915 23443915 + Silent SNP A A G novel C3N-00175_T C3N-00175_N A A c.453T>C p.= p.P151P ENST00000567107 5/8 238 159 79 311 311 0 strelka-varscan-mutect GOLGA6L2,synonymous_variant,p.=,ENST00000567107,NM_001304388.1;GOLGA6L2,synonymous_variant,p.=,ENST00000312015,;GOLGA6L2,5_prime_UTR_variant,,ENST00000345070,;GOLGA6L2,synonymous_variant,p.=,ENST00000566571,; G ENST00000567107 Transcript synonymous_variant 506/3030 453/2730 151/909 P ccT/ccC 1 -1 GOLGA6L2 HGNC HGNC:26695 protein_coding YES CCDS76728.1 ENSP00000454407 H3BMJ4 UPI00024672CE NM_001304388.1 5/8 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 23443915 23443915 A G 1 0 0 0 0 0 0 0 1 6440 59 3 5 5 GOLGA6L2 15 23443915 Silent SNP A C3N-00175_T 23443915 78547274 1011 10603 NPAP1 0 . GRCh38 15 24678132 24678132 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.2265A>T p.= p.A755A ENST00000329468 1/1 202 135 67 309 309 0 strelka-varscan-mutect NPAP1,synonymous_variant,p.=,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript synonymous_variant 2265/7526 2265/3471 755/1156 A gcA/gcT 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 24678132 24678132 A T 1 0 0 0 0 0 0 0 1 10609 146 6 4 4 NPAP1 15 24678132 Silent SNP A C3N-00175_T 1234217 24678132 77313057 1012 10604 HERC2 0 . GRCh38 15 28234276 28234276 + Nonsense_Mutation SNP G G A rs768276777 C3N-00175_T C3N-00175_N G G c.4012C>T p.Gln1338Ter p.Q1338* ENST00000261609 27/93 349 305 44 424 424 0 varscan-mutect HERC2,stop_gained,p.Gln1338Ter,ENST00000261609,NM_004667.5;HERC2,upstream_gene_variant,,ENST00000569335,; A ENST00000261609 Transcript stop_gained 4121/15337 4012/14505 1338/4834 Q/* Cag/Tag rs768276777 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 27/93 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF325 HIGH 1 SNV 1 1 PASS rs768276777 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 28234276 28234276 G A 1 0 0 0 0 0 1 0 0 6942 1299 45 3 3 HERC2 15 28234276 Nonsense_Mutation SNP G C3N-00175_T 3556144 28234276 73756913 1013 10605 STARD9 0 . GRCh38 15 42692551 42692551 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.10973T>G p.Phe3658Cys p.F3658C ENST00000290607 23/33 135 115 20 191 191 0 strelka-varscan-mutect STARD9,missense_variant,p.Phe3658Cys,ENST00000290607,NM_020759.2;STARD9,missense_variant,p.Phe986Cys,ENST00000562619,; G ENST00000290607 Transcript missense_variant 11030/15567 10973/14103 3658/4700 F/C tTt/tGt 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 tolerated(0.17) 23/33 hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF48 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 42692551 42692551 T G 1 0 0 0 0 1 0 0 0 15639 1841 64 5 5 STARD9 15 42692551 Missense_Mutation SNP T C3N-00175_T 14458275 42692551 59298638 1014 10606 B2M 0 . GRCh38 15 44715461 44715461 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.106G>T p.Glu36Ter p.E36* ENST00000558401 2/4 272 174 98 376 375 1 strelka-varscan-mutect B2M,stop_gained,p.Glu36Ter,ENST00000558401,NM_004048.2;B2M,stop_gained,p.Glu36Ter,ENST00000559916,;B2M,splice_region_variant,,ENST00000544417,;B2M,non_coding_transcript_exon_variant,,ENST00000559907,;B2M,intron_variant,,ENST00000559220,;PATL2,upstream_gene_variant,,ENST00000558573,;B2M,upstream_gene_variant,,ENST00000560556,;B2M,stop_gained,p.Glu36Ter,ENST00000561424,;B2M,missense_variant,p.Arg32Ile,ENST00000557901,;B2M,non_coding_transcript_exon_variant,,ENST00000559720,;B2M,non_coding_transcript_exon_variant,,ENST00000560681,;B2M,intron_variant,,ENST00000349264,;B2M,downstream_gene_variant,,ENST00000632133,;B2M,upstream_gene_variant,,ENST00000623550,;B2M,upstream_gene_variant,,ENST00000561139,; T ENST00000558401 Transcript stop_gained 176/1715 106/360 36/119 E/* Gag/Tag 1 1 B2M HGNC HGNC:914 protein_coding YES CCDS10113.1 ENSP00000452780 P61769 UPI000000D892 NM_004048.2 2/4 PROSITE_profiles:PS50835,hmmpanther:PTHR19944:SF62,hmmpanther:PTHR19944,Pfam_domain:PF07654,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS rs1204151497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 44715461 44715461 G T 1 0 0 0 0 0 1 0 0 1401 956 33 2 2 B2M 15 44715461 Nonsense_Mutation SNP G C3N-00175_T 2022910 44715461 57275728 1015 10607 SEMA6D 0 . GRCh38 15 47765995 47765995 + Nonsense_Mutation SNP T T A rs112152715 C3N-00175_T C3N-00175_N T T c.1554T>A p.Tyr518Ter p.Y518* ENST00000316364 14/19 25 18 7 27 27 0 strelka-varscan-mutect SEMA6D,stop_gained,p.Tyr518Ter,ENST00000316364,NM_153618.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000558014,NM_001198999.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000354744,NM_153617.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000358066,NM_020858.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000355997,NM_153619.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000389428,NM_153616.1;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000558816,;SEMA6D,stop_gained,p.Tyr518Ter,ENST00000536845,;SEMA6D,downstream_gene_variant,,ENST00000389425,NM_024966.2;SEMA6D,downstream_gene_variant,,ENST00000559196,;SEMA6D,upstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000561133,;SEMA6D,upstream_gene_variant,,ENST00000559064,;SEMA6D,non_coding_transcript_exon_variant,,ENST00000558431,; A ENST00000316364 Transcript stop_gained 1993/6099 1554/3222 518/1073 Y/* taT/taA rs112152715 1 1 SEMA6D HGNC HGNC:16770 protein_coding YES CCDS32225.1 ENSP00000324857 Q8NFY4 UPI000006E201 NM_153618.1 14/19 hmmpanther:PTHR11036:SF65,hmmpanther:PTHR11036,Gene3D:3.30.1680.10,Pfam_domain:PF01437,SMART_domains:SM00423,Superfamily_domains:SSF101912,Superfamily_domains:SSF103575 HIGH 1 SNV 1 1 PASS rs112152715 . 0 207 2 0 0 0 0 0 -19.60831 1 1 1 1 0 A 4 1 39 47765995 47765995 T A 1 0 0 0 0 0 1 0 0 14318 1471 51 4 4 SEMA6D 15 47765995 Nonsense_Mutation SNP T C3N-00175_T 3050534 47765995 54225194 1016 10608 NOX5 0 . GRCh38 15 69047464 69047464 + Nonsense_Mutation SNP G G T rs565188759 C3N-00175_T C3N-00175_N G G c.1744G>T p.Glu582Ter p.E582* ENST00000388866 12/16 124 86 38 136 136 0 strelka-varscan-mutect NOX5,stop_gained,p.Glu564Ter,ENST00000260364,;NOX5,stop_gained,p.Glu582Ter,ENST00000388866,NM_024505.3;NOX5,stop_gained,p.Glu536Ter,ENST00000448182,;NOX5,stop_gained,p.Glu554Ter,ENST00000530406,NM_001184779.1;NOX5,stop_gained,p.Glu547Ter,ENST00000455873,NM_001184780.1;RP11-809H16.4,upstream_gene_variant,,ENST00000559495,;NOX5,non_coding_transcript_exon_variant,,ENST00000525163,;NOX5,3_prime_UTR_variant,,ENST00000525143,;NOX5,non_coding_transcript_exon_variant,,ENST00000527315,;NOX5,non_coding_transcript_exon_variant,,ENST00000529367,; T ENST00000388866 Transcript stop_gained 1785/2804 1744/2298 582/765 E/* Gag/Tag rs565188759 1 1 NOX5 HGNC HGNC:14874 protein_coding YES CCDS32276.2 ENSP00000373518 Q96PH1 UPI000006DDBD NM_024505.3 12/16 hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF58,Gene3D:3.40.50.80,Superfamily_domains:SSF52343 HIGH 1 SNV 1 1 PASS rs565188759 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 69047464 69047464 G T 1 0 0 0 0 0 1 0 0 10605 1291 45 2 2 NOX5 15 69047464 Nonsense_Mutation SNP G C3N-00175_T 21281469 69047464 32943725 1017 10609 PEAK1 0 . GRCh38 15 77114275 77114275 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.5122G>C p.Glu1708Gln p.E1708Q ENST00000560626 7/7 193 169 24 258 258 0 strelka-varscan-mutect PEAK1,missense_variant,p.Glu1708Gln,ENST00000560626,;PEAK1,missense_variant,p.Glu1708Gln,ENST00000312493,NM_024776.3; G ENST00000560626 Transcript missense_variant 5598/19217 5122/5241 1708/1746 E/Q Gag/Cag 1 -1 PEAK1 HGNC HGNC:29431 protein_coding YES CCDS42062.1 ENSP00000452796 Q9H792 UPI00002378D0 deleterious(0) 7/7 hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5 MODERATE 1 SNV 5 1 PASS rs1193818609 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 77114275 77114275 C G 1 0 0 0 0 1 0 0 0 11800 835 29 4 4 PEAK1 15 77114275 Missense_Mutation SNP C C3N-00175_T 8066811 77114275 24876914 1018 10610 MEX3B 0 . GRCh38 15 82044253 82044253 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.617A>G p.Glu206Gly p.E206G ENST00000329713 2/2 90 60 30 162 162 0 strelka-varscan-mutect MEX3B,missense_variant,p.Glu206Gly,ENST00000329713,NM_032246.4;MEX3B,3_prime_UTR_variant,,ENST00000558133,; C ENST00000329713 Transcript missense_variant 1053/3528 617/1710 206/569 E/G gAg/gGg 1 -1 MEX3B HGNC HGNC:25297 protein_coding YES CCDS10319.1 ENSP00000329918 Q6ZN04 UPI00001982CC NM_032246.4 deleterious(0) 2/2 PROSITE_profiles:PS50084,hmmpanther:PTHR23285,hmmpanther:PTHR23285:SF5,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 82044253 82044253 T C 1 0 0 0 0 1 0 0 0 9463 1551 54 5 5 MEX3B 15 82044253 Missense_Mutation SNP T C3N-00175_T 4929978 82044253 19946936 1019 10611 ZSCAN2 0 . GRCh38 15 84604213 84604213 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.286G>T p.Glu96Ter p.E96* ENST00000448803 2/3 141 95 46 276 276 0 strelka-varscan-mutect ZSCAN2,stop_gained,p.Glu96Ter,ENST00000448803,NM_181877.3;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000327179,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000546148,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000538076,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000334141,NM_017894.5;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000541040,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000485222,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000379358,NM_001007072.1;ZSCAN2,intron_variant,,ENST00000358472,;ZSCAN2,intron_variant,,ENST00000540936,;ZSCAN2,downstream_gene_variant,,ENST00000502939,;ZSCAN2,downstream_gene_variant,,ENST00000442073,;ZSCAN2,downstream_gene_variant,,ENST00000546275,;RP11-182J1.18,intron_variant,,ENST00000618330,;ZSCAN2,stop_gained,p.Glu96Ter,ENST00000540894,; T ENST00000448803 Transcript stop_gained 578/3813 286/1845 96/614 E/* Gag/Tag 1 1 ZSCAN2 HGNC HGNC:20994 protein_coding YES CCDS10329.2 ENSP00000410198 Q7Z7L9 UPI000021D4BC NM_181877.3 2/3 PROSITE_profiles:PS50804,hmmpanther:PTHR24387:SF9,hmmpanther:PTHR24387,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 84604213 84604213 G T 1 0 0 0 0 0 1 0 0 18825 1175 41 2 2 ZSCAN2 15 84604213 Nonsense_Mutation SNP G C3N-00175_T 2559960 84604213 17386976 1020 10612 NTRK3 0 . GRCh38 15 88135399 88135399 + Splice_Site SNP T T A novel C3N-00175_T C3N-00175_N T T c.908-2A>T p.X303_splice ENST00000360948 204 153 51 280 280 0 strelka-varscan-mutect NTRK3,splice_acceptor_variant,,ENST00000394480,NM_002530.3;NTRK3,splice_acceptor_variant,,ENST00000558676,;NTRK3,splice_acceptor_variant,,ENST00000317501,;NTRK3,splice_acceptor_variant,,ENST00000360948,NM_001012338.2;NTRK3,splice_acceptor_variant,,ENST00000357724,;NTRK3,splice_acceptor_variant,,ENST00000355254,NM_001243101.1;NTRK3,splice_acceptor_variant,,ENST00000626019,;NTRK3,splice_acceptor_variant,,ENST00000629765,;NTRK3,splice_acceptor_variant,,ENST00000557856,;NTRK3,splice_acceptor_variant,,ENST00000542733,NM_001320135.1;NTRK3,splice_acceptor_variant,,ENST00000540489,NM_001007156.2;NTRK3,intron_variant,,ENST00000560017,;NTRK3,downstream_gene_variant,,ENST00000559188,;NTRK3,splice_acceptor_variant,,ENST00000559764,; A ENST00000360948 Transcript splice_acceptor_variant -/3004 908/2520 303/839 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 9/19 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 88135399 88135399 T A 1 0 0 0 0 0 0 1 0 10774 1594 55 4 4 NTRK3 15 88135399 Splice_Site SNP T C3N-00175_T 3531186 88135399 13855790 1021 10613 ANPEP 0 . GRCh38 15 89792451 89792451 + Splice_Site SNP C C A rs761569899 C3N-00175_T C3N-00175_N C C c.2360+1G>T p.X787_splice ENST00000300060 99 73 26 168 168 0 strelka-varscan-mutect ANPEP,splice_donor_variant,,ENST00000300060,NM_001150.2;ANPEP,splice_donor_variant,,ENST00000558740,;ANPEP,downstream_gene_variant,,ENST00000559761,; A ENST00000300060 Transcript splice_donor_variant -/3678 2360/2904 787/967 rs761569899 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 17/20 HIGH 1 SNV 1 1 PASS rs761569899 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 89792451 89792451 C A 1 0 0 0 0 0 0 1 0 817 550 19 1 1 ANPEP 15 89792451 Splice_Site SNP C C3N-00175_T 1657052 89792451 12198738 1022 10614 IQGAP1 0 . GRCh38 15 90491520 90491520 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.4436A>T p.Gln1479Leu p.Q1479L ENST00000268182 34/38 141 109 32 209 208 1 strelka-varscan-mutect IQGAP1,missense_variant,p.Gln1479Leu,ENST00000268182,NM_003870.3;IQGAP1,missense_variant,p.Gln907Leu,ENST00000560738,;IQGAP1,3_prime_UTR_variant,,ENST00000633485,;IQGAP1,non_coding_transcript_exon_variant,,ENST00000561461,;IQGAP1,non_coding_transcript_exon_variant,,ENST00000561132,;IQGAP1,non_coding_transcript_exon_variant,,ENST00000559031,;IQGAP1,non_coding_transcript_exon_variant,,ENST00000559674,;IQGAP1,upstream_gene_variant,,ENST00000558957,;IQGAP1,downstream_gene_variant,,ENST00000558491,; T ENST00000268182 Transcript missense_variant 4560/7233 4436/4974 1479/1657 Q/L cAg/cTg 1 1 IQGAP1 HGNC HGNC:6110 protein_coding YES CCDS10362.1 ENSP00000268182 P46940 A0A024RC65 UPI000012D863 NM_003870.3 deleterious(0.01) 34/38 hmmpanther:PTHR14149:SF15,hmmpanther:PTHR14149,Pfam_domain:PF03836 MODERATE 1 SNV 1 1 PASS rs1321297541 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 90491520 90491520 A T 1 0 0 0 0 1 0 0 0 7720 188 7 4 4 IQGAP1 15 90491520 Missense_Mutation SNP A C3N-00175_T 699069 90491520 11499669 1023 10615 IFT140 0 . GRCh38 16 1584355 1584355 + Silent SNP C C A rs761080545 C3N-00175_T C3N-00175_N C C c.1221G>T p.= p.R407R ENST00000426508 11/31 269 211 58 354 354 0 strelka-varscan-mutect IFT140,synonymous_variant,p.=,ENST00000426508,NM_014714.3;LA16c-395F10.2,intron_variant,,ENST00000563162,;LA16c-425C2.1,upstream_gene_variant,,ENST00000568149,;IFT140,non_coding_transcript_exon_variant,,ENST00000439987,;IFT140,missense_variant,p.Gly132Cys,ENST00000397417,;IFT140,upstream_gene_variant,,ENST00000565298,; A ENST00000426508 Transcript synonymous_variant 1585/5270 1221/4389 407/1462 R cgG/cgT rs761080545 1 -1 IFT140 HGNC HGNC:29077 protein_coding YES CCDS10439.1 ENSP00000406012 Q96RY7 UPI0000073C64 NM_014714.3 11/31 hmmpanther:PTHR15722,Superfamily_domains:SSF50978 LOW SNV 5 1 PASS rs761080545 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 1584355 1584355 C A 1 0 0 0 0 0 0 0 1 7460 610 22 2 2 IFT140 16 1584355 Silent SNP C C3N-00175_T 1584355 88753990 1024 10616 RPL3L 0 . GRCh38 16 1947042 1947042 + Missense_Mutation SNP G G T rs758361406 C3N-00175_T C3N-00175_N G G c.745C>A p.Arg249Ser p.R249S ENST00000268661 6/10 174 138 36 252 252 0 strelka-varscan-mutect RPL3L,missense_variant,p.Arg249Ser,ENST00000268661,NM_005061.2;MSRB1,upstream_gene_variant,,ENST00000361871,NM_016332.2;MSRB1,upstream_gene_variant,,ENST00000622125,;MSRB1,upstream_gene_variant,,ENST00000399753,;MSRB1,upstream_gene_variant,,ENST00000564908,;MSRB1,upstream_gene_variant,,ENST00000473663,; T ENST00000268661 Transcript missense_variant 840/2182 745/1224 249/407 R/S Cgc/Agc rs758361406,COSM346441 1 -1 RPL3L HGNC HGNC:10351 protein_coding YES CCDS10450.1 ENSP00000268661 Q92901 UPI0000161C28 NM_005061.2 deleterious(0.02) 6/10 hmmpanther:PTHR11363,hmmpanther:PTHR11363:SF7,Pfam_domain:PF00297,Gene3D:2.40.30.10,Superfamily_domains:SSF50447 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758361406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 1947042 1947042 G T 1 0 0 0 0 1 0 0 0 13847 1087 38 1 1 RPL3L 16 1947042 Missense_Mutation SNP G C3N-00175_T 362687 1947042 88391303 1025 10617 RAB26 0 . GRCh38 16 2153374 2153374 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.724G>A p.Asp242Asn p.D242N ENST00000210187 9/9 183 163 20 204 204 0 strelka-varscan-mutect RAB26,missense_variant,p.Asp242Asn,ENST00000210187,NM_014353.4;RAB26,missense_variant,p.Asp176Asn,ENST00000541451,NM_001308053.1;RAB26,intron_variant,,ENST00000566724,;TRAF7,upstream_gene_variant,,ENST00000326181,NM_032271.2;TRAF7,upstream_gene_variant,,ENST00000565383,;TRAF7,upstream_gene_variant,,ENST00000567653,;SNHG19,downstream_gene_variant,,ENST00000563192,;SNORD60,downstream_gene_variant,,ENST00000383903,;snoR1,downstream_gene_variant,,ENST00000628177,;RAB26,non_coding_transcript_exon_variant,,ENST00000564426,;RAB26,non_coding_transcript_exon_variant,,ENST00000562735,;RAB26,non_coding_transcript_exon_variant,,ENST00000561600,;RAB26,non_coding_transcript_exon_variant,,ENST00000567145,;TRAF7,upstream_gene_variant,,ENST00000564067,;RAB26,downstream_gene_variant,,ENST00000565592,;TRAF7,upstream_gene_variant,,ENST00000569686,; A ENST00000210187 Transcript missense_variant 884/1675 724/771 242/256 D/N Gat/Aat 1 1 RAB26 HGNC HGNC:14259 protein_coding YES CCDS10460.1 ENSP00000210187 Q9ULW5 UPI00003584E3 NM_014353.4 deleterious(0.01) 9/9 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF531,hmmpanther:PTHR24073,Gene3D:3.40.50.300,SMART_domains:SM00176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 2153374 2153374 G A 1 0 0 0 0 1 0 0 0 13071 1290 45 3 3 RAB26 16 2153374 Missense_Mutation SNP G C3N-00175_T 206332 2153374 88184971 1026 10618 GRIN2A 0 . GRCh38 16 9937958 9937958 + Splice_Site SNP C C G rs397518465 C3N-00175_T C3N-00175_N C C c.1007+1G>C p.X336_splice ENST00000396573 296 239 57 268 268 0 strelka-varscan-mutect GRIN2A,splice_donor_variant,,ENST00000396573,NM_000833.4;GRIN2A,splice_donor_variant,,ENST00000396575,;GRIN2A,splice_donor_variant,,ENST00000330684,NM_001134407.2;GRIN2A,splice_donor_variant,,ENST00000562109,NM_001134408.2;GRIN2A,splice_donor_variant,,ENST00000535259,;GRIN2A,synonymous_variant,p.=,ENST00000637393,;GRIN2A,splice_donor_variant,,ENST00000636273,;GRIN2A,splice_donor_variant,,ENST00000461292,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000568247,;GRIN2A,intron_variant,,ENST00000566683,;GRIN2A,downstream_gene_variant,,ENST00000566670,; G ENST00000396573 Transcript splice_donor_variant -/14450 1007/4395 336/1464 rs397518465 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 4/13 pathogenic HIGH 1 SNV 1 1 1 PASS rs397518465 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 39 9937958 9937958 C G 1 0 0 0 0 0 0 1 0 6661 550 19 4 4 GRIN2A 16 9937958 Splice_Site SNP C C3N-00175_T 7784584 9937958 80400387 1027 10619 CLEC16A 0 . GRCh38 16 11120638 11120638 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2140A>T p.Thr714Ser p.T714S ENST00000409790 20/24 48 31 17 48 48 0 strelka-mutect CLEC16A,missense_variant,p.Thr714Ser,ENST00000409790,NM_015226.2;CLEC16A,missense_variant,p.Thr696Ser,ENST00000409552,NM_001243403.1;CLEC16A,upstream_gene_variant,,ENST00000261657,;CLEC16A,upstream_gene_variant,,ENST00000428742,;CLEC16A,upstream_gene_variant,,ENST00000436973,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000465491,; T ENST00000409790 Transcript missense_variant 2370/6891 2140/3162 714/1053 T/S Aca/Tca 1 1 CLEC16A HGNC HGNC:29013 protein_coding YES CCDS45409.1 ENSP00000387122 Q2KHT3 UPI0000253BAD NM_015226.2 tolerated(0.11) 20/24 hmmpanther:PTHR21481,hmmpanther:PTHR21481:SF0 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 11120638 11120638 A T 1 0 0 0 0 1 0 0 0 3266 391 14 4 4 CLEC16A 16 11120638 Missense_Mutation SNP A C3N-00175_T 1182680 11120638 79217707 1028 10620 CCP110 0 . GRCh38 16 19536782 19536782 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.1113G>A p.Met371Ile p.M371I ENST00000381396 4/15 412 380 32 414 414 0 strelka-varscan-mutect CCP110,missense_variant,p.Met371Ile,ENST00000396212,NM_001323572.1,NM_001323571.1,NM_014711.4;CCP110,missense_variant,p.Met371Ile,ENST00000381396,NM_001323569.1,NM_001199022.1;CCP110,missense_variant,p.Met371Ile,ENST00000396208,;CCP110,downstream_gene_variant,,ENST00000561888,;CCP110,intron_variant,,ENST00000562083,; A ENST00000381396 Transcript missense_variant 1360/5446 1113/3039 371/1012 M/I atG/atA 1 1 CCP110 HGNC HGNC:24342 protein_coding YES CCDS55992.1 ENSP00000370803 O43303 UPI0000D619A9 NM_001323569.1,NM_001199022.1 tolerated(0.21) 4/15 hmmpanther:PTHR13594 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19536782 19536782 G A 1 0 0 0 0 1 0 0 0 2637 1290 45 3 3 CCP110 16 19536782 Missense_Mutation SNP G C3N-00175_T 8416144 19536782 70801563 1029 10621 KNOP1 0 . GRCh38 16 19714359 19714359 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.677C>T p.Pro226Leu p.P226L ENST00000219837 2/5 145 130 15 168 168 0 varscan-mutect KNOP1,missense_variant,p.Pro226Leu,ENST00000219837,NM_001012991.2;KNOP1,missense_variant,p.Pro74Leu,ENST00000567367,;IQCK,upstream_gene_variant,,ENST00000320394,NM_153208.1;KNOP1,upstream_gene_variant,,ENST00000568230,;KNOP1,downstream_gene_variant,,ENST00000564480,;IQCK,upstream_gene_variant,,ENST00000564186,;AC002550.5,intron_variant,,ENST00000565916,;KNOP1,non_coding_transcript_exon_variant,,ENST00000565844,;IQCK,upstream_gene_variant,,ENST00000308214,;IQCK,upstream_gene_variant,,ENST00000568300,;IQCK,upstream_gene_variant,,ENST00000568126,;IQCK,upstream_gene_variant,,ENST00000561839,;IQCK,upstream_gene_variant,,ENST00000564955,;IQCK,upstream_gene_variant,,ENST00000561935,;IQCK,upstream_gene_variant,,ENST00000564515,;IQCK,upstream_gene_variant,,ENST00000566312,; A ENST00000219837 Transcript missense_variant 756/6432 677/1377 226/458 P/L cCa/cTa 1 -1 KNOP1 HGNC HGNC:34404 protein_coding YES CCDS42127.1 ENSP00000219837 Q1ED39 UPI00001982F5 NM_001012991.2 tolerated(1) 2/5 hmmpanther:PTHR22426 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 19714359 19714359 G A 1 0 0 0 0 1 0 0 0 8306 1348 47 3 3 KNOP1 16 19714359 Missense_Mutation SNP G C3N-00175_T 177577 19714359 70623986 1030 10622 IQCK 0 . GRCh38 16 19827064 19827064 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.729G>T p.Trp243Cys p.W243C ENST00000320394 9/10 237 178 59 247 247 0 strelka-varscan-mutect IQCK,missense_variant,p.Trp243Cys,ENST00000320394,NM_153208.1;IQCK,missense_variant,p.Trp243Cys,ENST00000564186,;IQCK,missense_variant,p.Ala1Ser,ENST00000568061,;IQCK,non_coding_transcript_exon_variant,,ENST00000562762,;IQCK,3_prime_UTR_variant,,ENST00000308214,;IQCK,3_prime_UTR_variant,,ENST00000561839,;IQCK,3_prime_UTR_variant,,ENST00000564955,;IQCK,3_prime_UTR_variant,,ENST00000561935,;IQCK,non_coding_transcript_exon_variant,,ENST00000568300,; T ENST00000320394 Transcript missense_variant 1428/3482 729/864 243/287 W/C tgG/tgT 1 1 IQCK HGNC HGNC:28556 protein_coding YES CCDS10580.1 ENSP00000324901 Q8N0W5 UPI0000072C5C NM_153208.1 deleterious(0) 9/10 hmmpanther:PTHR34927 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 19827064 19827064 G T 1 0 0 0 0 1 0 0 0 7719 1212 42 2 2 IQCK 16 19827064 Missense_Mutation SNP G C3N-00175_T 112705 19827064 70511281 1031 10623 ACSM2A 0 . GRCh38 16 20469554 20469554 + Frame_Shift_Del DEL A A - novel C3N-00175_T C3N-00175_N A A c.431delA p.Asp144AlafsTer34 p.D144Afs*34 ENST00000573854 4/14 138 113 25 162 162 0 sindel-varindel ACSM2A,frameshift_variant,p.Asp144AlafsTer34,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,frameshift_variant,p.Asp144AlafsTer34,ENST00000396104,;ACSM2A,frameshift_variant,p.Asp144AlafsTer34,ENST00000575690,;ACSM2A,frameshift_variant,p.Asp144AlafsTer34,ENST00000219054,;ACSM2A,frameshift_variant,p.Asp65AlafsTer34,ENST00000417235,NM_001308169.1;ACSM2A,downstream_gene_variant,,ENST00000571894,;ACSM2A,downstream_gene_variant,,ENST00000576361,;ACSM2A,downstream_gene_variant,,ENST00000574251,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,upstream_gene_variant,,ENST00000572921,;ACSM2A,frameshift_variant,p.Asp144AlafsTer34,ENST00000574692,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,; - ENST00000573854 Transcript frameshift_variant 545/2837 431/1734 144/577 D/X gAc/gc 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 4/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 20469554 20469554 A - 1 0 1 0 1 0 0 0 0 225 275 10 0 0 ACSM2A 16 20469554 Frame_Shift_Del DEL A C3N-00175_T 642490 20469554 69868791 1032 10624 ACSM1 0 . GRCh38 16 20685274 20685274 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.322C>A p.Leu108Ile p.L108I ENST00000307493 2/13 486 379 107 459 458 1 strelka-varscan-mutect ACSM1,missense_variant,p.Leu108Ile,ENST00000307493,NM_001318890.1,NM_052956.2;ACSM1,missense_variant,p.Leu108Ile,ENST00000520010,;ACSM1,missense_variant,p.Leu108Ile,ENST00000523065,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;ACSM3,downstream_gene_variant,,ENST00000614721,;ACSM1,missense_variant,p.Leu108Ile,ENST00000519745,; T ENST00000307493 Transcript missense_variant 390/2051 322/1734 108/577 L/I Cta/Ata 1 -1 ACSM1 HGNC HGNC:18049 protein_coding YES CCDS10587.1 ENSP00000301956 Q08AH1 UPI00000558D0 NM_001318890.1,NM_052956.2 tolerated(0.13) 2/13 hmmpanther:PTHR24095:SF150,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 20685274 20685274 G T 1 0 0 0 0 1 0 0 0 224 991 35 2 2 ACSM1 16 20685274 Missense_Mutation SNP G C3N-00175_T 215720 20685274 69653071 1033 10625 DNAH3 0 . GRCh38 16 20959219 20959219 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.10786G>T p.Glu3596Ter p.E3596* ENST00000261383 54/62 279 200 79 304 303 1 strelka-varscan-mutect DNAH3,stop_gained,p.Glu3596Ter,ENST00000261383,NM_017539.2; A ENST00000261383 Transcript stop_gained 10786/12394 10786/12351 3596/4116 E/* Gag/Tag 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 54/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF03028 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 20959219 20959219 C A 1 0 0 0 0 0 1 0 0 4418 835 29 2 2 DNAH3 16 20959219 Nonsense_Mutation SNP C C3N-00175_T 273945 20959219 69379126 1034 10626 DNAH3 0 . GRCh38 16 20963976 20963976 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.9908C>A p.Thr3303Asn p.T3303N ENST00000261383 53/62 176 122 54 224 223 1 strelka-varscan-mutect DNAH3,missense_variant,p.Thr3303Asn,ENST00000261383,NM_017539.2; T ENST00000261383 Transcript missense_variant 9908/12394 9908/12351 3303/4116 T/N aCc/aAc 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0.03) 53/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 20963976 20963976 G T 1 0 0 0 0 1 0 0 0 4418 1261 44 2 2 DNAH3 16 20963976 Missense_Mutation SNP G C3N-00175_T 4757 20963976 69374369 1035 10627 DNAH3 0 . GRCh38 16 21127770 21127770 + Silent SNP C C A rs373634011 C3N-00175_T C3N-00175_N C C c.1125G>T p.= p.A375A ENST00000261383 8/62 234 194 40 242 241 1 strelka-varscan-mutect DNAH3,synonymous_variant,p.=,ENST00000261383,NM_017539.2;CTC-508F8.1,intron_variant,,ENST00000575612,;DNAH3,non_coding_transcript_exon_variant,,ENST00000396036,; A ENST00000261383 Transcript synonymous_variant 1125/12394 1125/12351 375/4116 A gcG/gcT rs373634011 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 8/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676 LOW 1 SNV 1 1 PASS rs373634011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 21127770 21127770 C A 1 0 0 0 0 0 0 0 1 4418 639 23 1 1 DNAH3 16 21127770 Silent SNP C C3N-00175_T 163794 21127770 69210575 1036 10628 OTOA 0 . GRCh38 16 21736320 21736320 + Missense_Mutation SNP A A T C3N-00175_T C3N-00175_N A A c.2361A>T p.Glu787Asp p.E787D ENST00000388958 21/28 484 384 100 456 456 0 strelka-varscan-mutect OTOA,missense_variant,p.Glu787Asp,ENST00000388958,NM_144672.3;OTOA,missense_variant,p.Glu801Asp,ENST00000286149,;OTOA,missense_variant,p.Glu708Asp,ENST00000388956,NM_001161683.1;OTOA,missense_variant,p.Glu463Asp,ENST00000388957,NM_170664.2;OTOA,non_coding_transcript_exon_variant,,ENST00000563871,;OTOA,non_coding_transcript_exon_variant,,ENST00000563506,; T ENST00000388958 Transcript missense_variant 2362/3610 2361/3420 787/1139 E/D gaA/gaT COSM5646666,COSM5646667,COSM5646668 1 1 OTOA HGNC HGNC:16378 protein_coding YES CCDS10600.2 ENSP00000373610 Q7RTW8 UPI00005C8607 NM_144672.3 tolerated(0.09) 21/28 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF18 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 21736320 21736320 A T 1 0 0 0 0 1 0 0 0 11368 98 4 4 4 OTOA 16 21736320 Missense_Mutation SNP A C3N-00175_T 608550 21736320 68602025 1037 10629 VWA3A 0 . GRCh38 16 22138493 22138493 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.2273T>A p.Val758Asp p.V758D ENST00000389398 22/34 189 143 46 164 164 0 strelka-varscan-mutect VWA3A,missense_variant,p.Val758Asp,ENST00000389398,NM_173615.4;VWA3A,missense_variant,p.Val140Asp,ENST00000563389,;VWA3A,downstream_gene_variant,,ENST00000568328,;VWA3A,missense_variant,p.Val368Asp,ENST00000299840,;VWA3A,downstream_gene_variant,,ENST00000566668,; A ENST00000389398 Transcript missense_variant 2369/4600 2273/3555 758/1184 V/D gTc/gAc 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 deleterious(0.02) 22/34 MODERATE 1 SNV 5 1 PASS . . 0 206 0 2 2 0 0 0 -20 0.9937609 1 1 1 0 A 3 1 39 22138493 22138493 T A 1 0 0 0 0 1 0 0 0 17794 1667 58 4 4 VWA3A 16 22138493 Missense_Mutation SNP T C3N-00175_T 402173 22138493 68199852 1038 10630 EEF2K 0 . GRCh38 16 22257679 22257679 + Missense_Mutation SNP C C T rs777214457 C3N-00175_T C3N-00175_N C C c.938C>T p.Ala313Val p.A313V ENST00000263026 9/18 166 134 32 165 165 0 strelka-varscan-mutect EEF2K,missense_variant,p.Ala313Val,ENST00000263026,NM_013302.3;EEF2K,missense_variant,p.Ala313Val,ENST00000568269,;EEF2K,non_coding_transcript_exon_variant,,ENST00000563555,; T ENST00000263026 Transcript missense_variant 1412/7388 938/2178 313/725 A/V gCc/gTc rs777214457 1 1 EEF2K HGNC HGNC:24615 protein_coding YES CCDS10604.1 ENSP00000263026 O00418 UPI000013D387 NM_013302.3 tolerated(0.8) 9/18 PROSITE_profiles:PS51158,hmmpanther:PTHR14187,Pfam_domain:PF02816,PIRSF_domain:PIRSF038139,SMART_domains:SM00811,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs777214457 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 22257679 22257679 C T 1 0 0 0 0 1 0 0 0 4760 739 26 3 3 EEF2K 16 22257679 Missense_Mutation SNP C C3N-00175_T 119186 22257679 68080666 1039 10631 HS3ST2 0 . GRCh38 16 22814641 22814641 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.31C>T p.Pro11Ser p.P11S ENST00000261374 1/2 130 94 36 155 155 0 strelka-varscan-mutect HS3ST2,missense_variant,p.Pro11Ser,ENST00000261374,NM_006043.1;CTC-591M7.1,upstream_gene_variant,,ENST00000636354,;CTC-591M7.1,upstream_gene_variant,,ENST00000636266,;HS3ST2,missense_variant,p.Pro11Ser,ENST00000473392,; T ENST00000261374 Transcript missense_variant 465/2314 31/1104 11/367 P/S Cca/Tca 1 1 HS3ST2 HGNC HGNC:5195 protein_coding YES CCDS10606.1 ENSP00000261374 Q9Y278 UPI000004C63A NM_006043.1 deleterious_low_confidence(0.01) 1/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS51257,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF10 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999982 1 1 1 0 T 3 4 39 22814641 22814641 C T 1 0 0 0 0 1 0 0 0 7258 739 26 3 3 HS3ST2 16 22814641 Missense_Mutation SNP C C3N-00175_T 556962 22814641 67523704 1040 10632 SCNN1G 0 . GRCh38 16 23186488 23186488 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.217C>T p.Leu73Phe p.L73F ENST00000300061 2/13 439 352 87 509 509 0 strelka-varscan-mutect SCNN1G,missense_variant,p.Leu73Phe,ENST00000300061,NM_001039.3; T ENST00000300061 Transcript missense_variant 360/3507 217/1950 73/649 L/F Ctc/Ttc 1 1 SCNN1G HGNC HGNC:10602 protein_coding YES CCDS10608.1 ENSP00000300061 P51170 A5X2V1 UPI0000070D86 NM_001039.3 deleterious(0.02) 2/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF19,Pfam_domain:PF00858,TIGRFAM_domain:TIGR00859 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 23186488 23186488 C T 1 0 0 0 0 1 0 0 0 14199 681 24 3 3 SCNN1G 16 23186488 Missense_Mutation SNP C C3N-00175_T 371847 23186488 67151857 1041 10633 ERN2 0 . GRCh38 16 23700591 23700591 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.1617G>A p.= p.Q539Q ENST00000634482 13/22 106 85 21 103 103 0 strelka-varscan-mutect ERN2,synonymous_variant,p.=,ENST00000634482,NM_033266.3;ERN2,synonymous_variant,p.=,ENST00000256797,;ERN2,synonymous_variant,p.=,ENST00000457008,NM_001308220.1;CTD-2196E14.8,upstream_gene_variant,,ENST00000624143,;ERN2,3_prime_UTR_variant,,ENST00000562562,; T ENST00000634482 Transcript synonymous_variant 1786/3616 1617/2925 539/974 Q caG/caA 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 13/22 hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15,Gene3D:3.30.200.20 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 23700591 23700591 C T 1 0 0 0 0 0 0 0 1 5096 912 32 3 3 ERN2 16 23700591 Silent SNP C C3N-00175_T 514103 23700591 66637754 1042 10634 ERN2 0 . GRCh38 16 23701099 23701099 + Silent SNP G G T rs200049259 C3N-00175_T C3N-00175_N G G c.1363C>A p.= p.R455R ENST00000634482 12/22 100 70 30 101 101 0 strelka-varscan-mutect ERN2,synonymous_variant,p.=,ENST00000634482,NM_033266.3;ERN2,synonymous_variant,p.=,ENST00000256797,;ERN2,intron_variant,,ENST00000457008,NM_001308220.1;CTD-2196E14.8,upstream_gene_variant,,ENST00000624143,;ERN2,3_prime_UTR_variant,,ENST00000562562,; T ENST00000634482 Transcript synonymous_variant 1532/3616 1363/2925 455/974 R Cga/Aga rs200049259 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 12/22 hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15 LOW 1 SNV 1 1 PASS rs200049259 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 23701099 23701099 G T 1 0 0 0 0 0 0 0 1 5096 1124 39 1 1 ERN2 16 23701099 Silent SNP G C3N-00175_T 508 23701099 66637246 1043 10635 ITGAL 0 . GRCh38 16 30496506 30496506 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1772T>A p.Leu591His p.L591H ENST00000356798 15/31 177 131 46 181 181 0 strelka-varscan-mutect ITGAL,missense_variant,p.Leu591His,ENST00000356798,NM_002209.2;ITGAL,missense_variant,p.Leu508His,ENST00000358164,NM_001114380.1;ITGAL,intron_variant,,ENST00000433423,;RP11-297C4.1,downstream_gene_variant,,ENST00000563751,;ITGAL,downstream_gene_variant,,ENST00000568012,;ITGAL,non_coding_transcript_exon_variant,,ENST00000568987,;ITGAL,intron_variant,,ENST00000568926,;ITGAL,downstream_gene_variant,,ENST00000564935,;ITGAL,upstream_gene_variant,,ENST00000563615,; A ENST00000356798 Transcript missense_variant 1952/5213 1772/3513 591/1170 L/H cTt/cAt 1 1 ITGAL HGNC HGNC:6148 protein_coding YES CCDS32433.1 ENSP00000349252 P20701 UPI000013C4FF NM_002209.2 deleterious(0) 15/31 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF84,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 30496506 30496506 T A 1 0 0 0 0 1 0 0 0 7793 1609 56 4 4 ITGAL 16 30496506 Missense_Mutation SNP T C3N-00175_T 6795407 30496506 59841839 1044 10636 ITGAL 0 . GRCh38 16 30499078 30499078 + Silent SNP C C A C3N-00175_T C3N-00175_N C C c.1837C>A p.= p.R613R ENST00000356798 16/31 89 57 32 115 115 0 strelka-varscan-mutect ITGAL,synonymous_variant,p.=,ENST00000356798,NM_002209.2;ITGAL,synonymous_variant,p.=,ENST00000358164,NM_001114380.1;ITGAL,intron_variant,,ENST00000433423,;MIR4518,upstream_gene_variant,,ENST00000580665,;RP11-297C4.1,non_coding_transcript_exon_variant,,ENST00000563751,;ITGAL,downstream_gene_variant,,ENST00000568012,;ITGAL,intron_variant,,ENST00000568926,;ITGAL,intron_variant,,ENST00000568987,;ITGAL,downstream_gene_variant,,ENST00000564935,;ITGAL,upstream_gene_variant,,ENST00000563615,; A ENST00000356798 Transcript synonymous_variant 2017/5213 1837/3513 613/1170 R Cgg/Agg COSM240256 1 1 ITGAL HGNC HGNC:6148 protein_coding YES CCDS32433.1 ENSP00000349252 P20701 UPI000013C4FF NM_002209.2 16/31 Gene3D:3nigC00,Pfam_domain:PF08441,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF84,SMART_domains:SM00191,Superfamily_domains:SSF69318 1 LOW 1 SNV 1 1 1 PASS rs1428037729 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 30499078 30499078 C A 1 0 0 0 0 0 0 0 1 7793 666 23 1 1 ITGAL 16 30499078 Silent SNP C C3N-00175_T 2572 30499078 59839267 1045 10637 ITGAX 0 . GRCh38 16 31371147 31371147 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1774C>G p.Gln592Glu p.Q592E ENST00000562522 15/31 110 84 26 121 121 0 strelka-varscan-mutect ITGAX,missense_variant,p.Gln592Glu,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Gln592Glu,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,upstream_gene_variant,,ENST00000562138,; G ENST00000562522 Transcript missense_variant 1807/3990 1774/3510 592/1169 Q/E Caa/Gaa 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.01) 15/31 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 31371147 31371147 C G 1 0 0 0 0 1 0 0 0 7796 827 29 4 4 ITGAX 16 31371147 Missense_Mutation SNP C C3N-00175_T 872069 31371147 58967198 1046 10638 ITGAX 0 . GRCh38 16 31377265 31377265 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.2789G>T p.Ser930Ile p.S930I ENST00000562522 23/31 141 105 36 129 128 1 strelka-varscan-mutect ITGAX,missense_variant,p.Ser930Ile,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Ser930Ile,ENST00000562522,NM_001286375.1;ITGAX,splice_region_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000562138,; T ENST00000562522 Transcript missense_variant,splice_region_variant 2822/3990 2789/3510 930/1169 S/I aGc/aTc COSM703156 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0.01) 23/31 Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 31377265 31377265 G T 1 0 0 0 0 1 0 0 0 7796 1014 35 2 2 ITGAX 16 31377265 Missense_Mutation SNP G C3N-00175_T 6118 31377265 58961080 1047 10639 SHCBP1 0 . GRCh38 16 46621332 46621332 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.28G>T p.Gly10Cys p.G10C ENST00000303383 1/13 124 101 23 148 148 0 strelka-varscan-mutect SHCBP1,missense_variant,p.Gly10Cys,ENST00000303383,NM_024745.4;RP11-46D6.1,downstream_gene_variant,,ENST00000574180,;RP11-46D6.1,downstream_gene_variant,,ENST00000562549,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000564272,;SHCBP1,non_coding_transcript_exon_variant,,ENST00000566016,; A ENST00000303383 Transcript missense_variant 295/3461 28/2019 10/672 G/C Ggt/Tgt 1 -1 SHCBP1 HGNC HGNC:29547 protein_coding YES CCDS10720.1 ENSP00000306473 Q8NEM2 UPI000013E898 NM_024745.4 deleterious_low_confidence(0.04) 1/13 hmmpanther:PTHR14695:SF8,hmmpanther:PTHR14695 MODERATE 1 SNV 1 1 PASS rs1363863229 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 46621332 46621332 C A 1 0 0 0 0 1 0 0 0 14533 652 23 1 1 SHCBP1 16 46621332 Missense_Mutation SNP C C3N-00175_T 15244067 46621332 43717013 1048 10640 ABCC11 0 . GRCh38 16 48196245 48196245 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.2391C>A p.= p.I797I ENST00000394747 17/29 213 142 71 174 174 0 strelka-varscan-mutect ABCC11,synonymous_variant,p.=,ENST00000394747,NM_033151.3;ABCC11,synonymous_variant,p.=,ENST00000356608,;ABCC11,synonymous_variant,p.=,ENST00000394748,NM_032583.3;ABCC11,synonymous_variant,p.=,ENST00000353782,NM_145186.2;ABCC11,non_coding_transcript_exon_variant,,ENST00000569172,; T ENST00000394747 Transcript synonymous_variant 2741/4862 2391/4149 797/1382 I atC/atA 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 17/29 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 48196245 48196245 G T 1 0 0 0 0 0 0 0 1 55 1164 41 2 2 ABCC11 16 48196245 Silent SNP G C3N-00175_T 1574913 48196245 42142100 1049 10641 ZNF423 0 . GRCh38 16 49523645 49523645 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3804C>A p.Phe1268Leu p.F1268L ENST00000561648 8/9 209 151 58 205 204 1 strelka-varscan-mutect ZNF423,missense_variant,p.Phe1268Leu,ENST00000561648,;ZNF423,missense_variant,p.Phe1208Leu,ENST00000563137,;ZNF423,missense_variant,p.Phe1268Leu,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Phe1208Leu,ENST00000562871,;ZNF423,missense_variant,p.Phe1151Leu,ENST00000535559,;ZNF423,missense_variant,p.Phe1208Leu,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Phe1151Leu,ENST00000567169,; T ENST00000561648 Transcript missense_variant 4105/7907 3804/3855 1268/1284 F/L ttC/ttA 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC deleterious(0) 8/9 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 49523645 49523645 G T 1 0 0 0 0 1 0 0 0 18470 933 33 2 2 ZNF423 16 49523645 Missense_Mutation SNP G C3N-00175_T 1327400 49523645 40814700 1050 10642 ADCY7 0 . GRCh38 16 50291795 50291795 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.435G>T p.= p.R145R ENST00000394697 4/26 254 183 71 326 326 0 strelka-varscan-mutect ADCY7,synonymous_variant,p.=,ENST00000394697,;ADCY7,synonymous_variant,p.=,ENST00000254235,NM_001114.4;ADCY7,synonymous_variant,p.=,ENST00000566433,NM_001286057.1;ADCY7,synonymous_variant,p.=,ENST00000537579,;ADCY7,downstream_gene_variant,,ENST00000566761,;ADCY7,downstream_gene_variant,,ENST00000564965,;ADCY7,downstream_gene_variant,,ENST00000569265,;MIR6771,upstream_gene_variant,,ENST00000619793,;ADCY7,intron_variant,,ENST00000564044,;ADCY7,intron_variant,,ENST00000563677,;ADCY7,downstream_gene_variant,,ENST00000562623,;ADCY7,downstream_gene_variant,,ENST00000568933,;ADCY7,synonymous_variant,p.=,ENST00000567277,; T ENST00000394697 Transcript synonymous_variant 775/6213 435/3243 145/1080 R cgG/cgT 1 1 ADCY7 HGNC HGNC:238 protein_coding YES CCDS10741.1 ENSP00000378187 P51828 UPI000004C5DB 4/26 hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF273,Pfam_domain:PF16214,PIRSF_domain:PIRSF039050 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 50291795 50291795 G T 1 0 0 0 0 0 0 0 1 343 1219 43 2 2 ADCY7 16 50291795 Silent SNP G C3N-00175_T 768150 50291795 40046550 1051 10643 NKD1 0 . GRCh38 16 50625568 50625568 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.450G>T p.Lys150Asn p.K150N ENST00000268459 6/10 223 177 46 283 283 0 strelka-varscan-mutect NKD1,missense_variant,p.Lys150Asn,ENST00000268459,NM_033119.4;NKD1,non_coding_transcript_exon_variant,,ENST00000566396,; T ENST00000268459 Transcript missense_variant 674/17105 450/1413 150/470 K/N aaG/aaT 1 1 NKD1 HGNC HGNC:17045 protein_coding YES CCDS10743.1 ENSP00000268459 Q969G9 UPI0000073F02 NM_033119.4 deleterious(0) 6/10 PROSITE_profiles:PS50222,hmmpanther:PTHR22611:SF2,hmmpanther:PTHR22611,PROSITE_patterns:PS00018,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 50625568 50625568 G T 1 0 0 0 0 1 0 0 0 10476 991 35 2 2 NKD1 16 50625568 Missense_Mutation SNP G C3N-00175_T 333773 50625568 39712777 1052 10644 MMP2 0 . GRCh38 16 55491945 55491945 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1325A>T p.Gln442Leu p.Q442L ENST00000219070 8/13 239 196 43 219 219 0 strelka-varscan-mutect MMP2,missense_variant,p.Gln442Leu,ENST00000219070,NM_004530.5;MMP2,missense_variant,p.Gln366Leu,ENST00000570308,;MMP2,missense_variant,p.Gln392Leu,ENST00000437642,NM_001127891.2;MMP2,missense_variant,p.Gln366Leu,ENST00000543485,NM_001302508.1,NM_001302510.1,NM_001302509.1;MMP2,missense_variant,p.Gln67Leu,ENST00000570283,;RP11-212I21.3,downstream_gene_variant,,ENST00000623886,; T ENST00000219070 Transcript missense_variant 1834/3741 1325/1983 442/660 Q/L cAg/cTg 1 1 MMP2 HGNC HGNC:7166 protein_coding YES CCDS10752.1 ENSP00000219070 P08253 A0A024R6R4 UPI00000422C4 NM_004530.5 deleterious(0) 8/13 Gene3D:3.40.390.10,Pfam_domain:PF00413,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF29,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs1412312873 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55491945 55491945 A T 1 0 0 0 0 1 0 0 0 9621 188 7 4 4 MMP2 16 55491945 Missense_Mutation SNP A C3N-00175_T 4866377 55491945 34846400 1053 10645 SLC6A2 0 . GRCh38 16 55700287 55700287 + Missense_Mutation SNP C C T rs148686754 C3N-00175_T C3N-00175_N C C c.1739C>T p.Thr580Met p.T580M ENST00000219833 12/14 120 107 13 144 144 0 strelka-varscan-mutect SLC6A2,missense_variant,p.Thr580Met,ENST00000379906,NM_001043.3;SLC6A2,missense_variant,p.Thr475Met,ENST00000567238,NM_001172502.1;SLC6A2,missense_variant,p.Thr580Met,ENST00000219833,NM_001172504.1;SLC6A2,missense_variant,p.Thr580Met,ENST00000568943,NM_001172501.1;SLC6A2,missense_variant,p.Thr580Met,ENST00000561820,;SLC6A2,missense_variant,p.Thr535Met,ENST00000566163,;SLC6A2,synonymous_variant,p.=,ENST00000574918,;SLC6A2,intron_variant,,ENST00000414754,;RP11-481F24.3,upstream_gene_variant,,ENST00000624017,; T ENST00000219833 Transcript missense_variant 1790/2858 1739/1887 580/628 T/M aCg/aTg rs148686754,COSM323447,COSM323448,COSM336061,COSM336062 1 1 SLC6A2 HGNC HGNC:11048 protein_coding YES CCDS54011.1 ENSP00000219833 P23975 UPI00000734FD NM_001172504.1 tolerated(0.13) 12/14 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF37 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs148686754 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55700287 55700287 C T 1 0 0 0 0 1 0 0 0 14966 536 19 1 1 SLC6A2 16 55700287 Missense_Mutation SNP C C3N-00175_T 208342 55700287 34638058 1054 10646 NLRC5 0 . GRCh38 16 57037247 57037247 + Frame_Shift_Del DEL G G - rs779817822 C3N-00175_T C3N-00175_N G G c.2764delG p.Val922Ter p.V922* ENST00000262510 15/49 269 224 45 322 322 0 sindel-varindel-pindel NLRC5,frameshift_variant,p.Val922Ter,ENST00000262510,;NLRC5,frameshift_variant,p.Val922Ter,ENST00000436936,NM_032206.4;NLRC5,frameshift_variant,p.Val922Ter,ENST00000539144,;NLRC5,frameshift_variant,p.Val675Ter,ENST00000538805,;NLRC5,frameshift_variant,p.Val429Ter,ENST00000538110,;NLRC5,frameshift_variant,p.Val221Ter,ENST00000543030,;NLRC5,frameshift_variant,p.Val650Ter,ENST00000545081,;NLRC5,frameshift_variant,p.Val73Ter,ENST00000538453,;NLRC5,3_prime_UTR_variant,,ENST00000539881,;NLRC5,upstream_gene_variant,,ENST00000540182,;NLRC5,upstream_gene_variant,,ENST00000538930,;NLRC5,upstream_gene_variant,,ENST00000538778,;NLRC5,upstream_gene_variant,,ENST00000541020,; - ENST00000262510 Transcript frameshift_variant 2989/6822 2764/5601 922/1866 V/X Gtg/tg rs779817822 1 1 NLRC5 HGNC HGNC:29933 protein_coding YES CCDS10773.1 ENSP00000262510 Q86WI3 UPI00001AEE94 15/49 Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 HIGH 1 deletion 5 1 PASS . . 0 208 0 0 2 0 0 0 -19.99899 0.9974541 1 1 1 0 - 7 5 39 57037247 57037247 G - 1 0 1 0 1 0 0 0 0 10507 1145 40 0 0 NLRC5 16 57037247 Frame_Shift_Del DEL G C3N-00175_T 1336960 57037247 33301098 1055 10647 CCDC102A 0 . GRCh38 16 57525923 57525923 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.790A>T p.Lys264Ter p.K264* ENST00000258214 3/9 165 122 43 201 201 0 strelka-varscan-mutect CCDC102A,stop_gained,p.Lys264Ter,ENST00000258214,NM_033212.3; A ENST00000258214 Transcript stop_gained 1037/2463 790/1653 264/550 K/* Aag/Tag 1 -1 CCDC102A HGNC HGNC:28097 protein_coding YES CCDS10784.1 ENSP00000258214 Q96A19 UPI000013CFBA NM_033212.3 3/9 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF479 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 57525923 57525923 T A 1 0 0 0 0 0 1 0 0 2434 1792 62 4 4 CCDC102A 16 57525923 Nonsense_Mutation SNP T C3N-00175_T 488676 57525923 32812422 1056 10648 RP11-457D20.2 0 . GRCh38 16 60358557 60358557 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.924C>A p.Asn308Lys p.N308K ENST00000614215 1/1 96 78 18 95 94 1 strelka-varscan-mutect RP11-457D20.2,missense_variant,p.Asn308Lys,ENST00000614215,NM_001282301.1;RP11-354I13.2,upstream_gene_variant,,ENST00000565506,;RP11-354I13.2,upstream_gene_variant,,ENST00000565133,;RP11-457D20.1,downstream_gene_variant,,ENST00000563482,; T ENST00000614215 Transcript missense_variant 924/1026 924/1026 308/341 N/K aaC/aaA 1 -1 RP11-457D20.2 Clone_based_vega_gene protein_coding YES ENSP00000482925 A8MU76 UPI00017616FE NM_001282301.1 tolerated_low_confidence(0.09) 1/1 hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF76 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 60358557 60358557 G T 1 0 0 0 0 1 0 0 0 13744 1368 48 2 2 RP11-457D20.2 16 60358557 Missense_Mutation SNP G C3N-00175_T 2832634 60358557 29979788 1057 10649 CDH8 0 . GRCh38 16 61654094 61654094 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1914G>T p.= p.V638V ENST00000577390 12/12 71 43 28 86 86 0 strelka-varscan-mutect CDH8,synonymous_variant,p.=,ENST00000577390,NM_001796.4;CDH8,synonymous_variant,p.=,ENST00000577730,;CDH8,synonymous_variant,p.=,ENST00000299345,;CDH8,downstream_gene_variant,,ENST00000583483,;CDH8,3_prime_UTR_variant,,ENST00000585315,; A ENST00000577390 Transcript synonymous_variant 2869/9721 1914/2400 638/799 V gtG/gtT 1 -1 CDH8 HGNC HGNC:1767 protein_coding YES CCDS10802.1 ENSP00000462701 P55286 UPI0000126D9F NM_001796.4 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF273,hmmpanther:PTHR24027,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1262284212 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 61654094 61654094 C A 1 0 0 0 0 0 0 0 1 2819 581 21 2 2 CDH8 16 61654094 Silent SNP C C3N-00175_T 1295537 61654094 28684251 1058 10650 RRAD 0 . GRCh38 16 66923688 66923688 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.477G>T p.Met159Ile p.M159I ENST00000299759 4/5 157 118 39 251 251 0 strelka-varscan-mutect RRAD,missense_variant,p.Met159Ile,ENST00000299759,;RRAD,missense_variant,p.Met159Ile,ENST00000420652,NM_004165.2,NM_001128850.1;RRAD,missense_variant,p.Met84Ile,ENST00000566577,;RRAD,intron_variant,,ENST00000568915,;CDH16,upstream_gene_variant,,ENST00000299752,NM_004062.3;CDH16,upstream_gene_variant,,ENST00000394055,NM_001204744.1;CDH16,upstream_gene_variant,,ENST00000565796,NM_001204745.1;CDH16,upstream_gene_variant,,ENST00000570262,;CDH16,upstream_gene_variant,,ENST00000568632,NM_001204746.1;CDH16,upstream_gene_variant,,ENST00000565235,;RRAD,non_coding_transcript_exon_variant,,ENST00000567791,;CDH16,upstream_gene_variant,,ENST00000567269,;CDH16,upstream_gene_variant,,ENST00000568698,; A ENST00000299759 Transcript missense_variant 728/1569 477/927 159/308 M/I atG/atT 1 -1 RRAD HGNC HGNC:10446 protein_coding YES CCDS10824.1 ENSP00000299759 P55042 A0A024R6X0 UPI0000072F9C deleterious(0.04) 4/5 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF74,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,PIRSF_domain:PIRSF038017,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 66923688 66923688 C A 1 0 0 0 0 1 0 0 0 13925 594 21 2 2 RRAD 16 66923688 Missense_Mutation SNP C C3N-00175_T 5269594 66923688 23414657 1059 10651 CARMIL2 0 . GRCh38 16 67646965 67646965 + Silent SNP C C A rs761787480 C3N-00175_T C3N-00175_N C C c.603C>A p.= p.L201L ENST00000334583 8/38 135 94 41 228 228 0 strelka-varscan-mutect CARMIL2,synonymous_variant,p.=,ENST00000334583,NM_001013838.1;CARMIL2,synonymous_variant,p.=,ENST00000545661,NM_001317026.1;CARMIL2,3_prime_UTR_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602321,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602742,;CARMIL2,upstream_gene_variant,,ENST00000602931,;CARMIL2,downstream_gene_variant,,ENST00000602467,; A ENST00000334583 Transcript synonymous_variant 931/4687 603/4308 201/1435 L ctC/ctA rs761787480 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 8/38 hmmpanther:PTHR24112:SF32,hmmpanther:PTHR24112,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS rs761787480 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 67646965 67646965 C A 1 0 0 0 0 0 0 0 1 2352 871 31 1 1 CARMIL2 16 67646965 Silent SNP C C3N-00175_T 723277 67646965 22691380 1060 10652 GFOD2 0 . GRCh38 16 67685691 67685691 + Missense_Mutation SNP C C A rs371418821 C3N-00175_T C3N-00175_N C C c.25G>T p.Val9Leu p.V9L ENST00000268797 2/3 71 48 23 92 92 0 strelka-varscan-mutect GFOD2,missense_variant,p.Val9Leu,ENST00000602279,NM_001243650.1;GFOD2,missense_variant,p.Val9Leu,ENST00000268797,NM_030819.3;GFOD2,missense_variant,p.Val9Leu,ENST00000602377,;GFOD2,missense_variant,p.Val9Leu,ENST00000602855,;GFOD2,upstream_gene_variant,,ENST00000602627,;GFOD2,missense_variant,p.Val9Leu,ENST00000602496,; A ENST00000268797 Transcript missense_variant 371/2126 25/1158 9/385 V/L Gtg/Ttg rs371418821 1 -1 GFOD2 HGNC HGNC:28159 protein_coding YES CCDS10845.1 ENSP00000268797 Q3B7J2 UPI000013D7DD NM_030819.3 tolerated(0.11) 2/3 Gene3D:3.40.50.720,Pfam_domain:PF01408,hmmpanther:PTHR22604,hmmpanther:PTHR22604:SF90,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs371418821 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 67685691 67685691 C A 1 0 0 0 0 1 0 0 0 6218 536 19 1 1 GFOD2 16 67685691 Missense_Mutation SNP C C3N-00175_T 38726 67685691 22652654 1061 10653 CLEC18B 0 . GRCh38 16 74411674 74411674 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.979T>A p.Cys327Ser p.C327S ENST00000339953 8/13 197 181 16 301 301 0 varscan-mutect CLEC18B,missense_variant,p.Cys327Ser,ENST00000617101,;CLEC18B,missense_variant,p.Cys327Ser,ENST00000619275,;CLEC18B,missense_variant,p.Cys327Ser,ENST00000339953,NM_001011880.2;CLEC18B,3_prime_UTR_variant,,ENST00000620745,;CLEC18B,non_coding_transcript_exon_variant,,ENST00000564842,;CLEC18B,downstream_gene_variant,,ENST00000425714,; T ENST00000339953 Transcript missense_variant 1101/1865 979/1368 327/455 C/S Tgt/Agt 1 -1 CLEC18B HGNC HGNC:33849 protein_coding YES CCDS32484.1 ENSP00000341051 Q6UXF7 UPI000025210E NM_001011880.2 deleterious_low_confidence(0) 8/13 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs745609847 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 74411674 74411674 A T 1 0 0 0 0 1 0 0 0 3269 231 8 4 4 CLEC18B 16 74411674 Missense_Mutation SNP A C3N-00175_T 6725983 74411674 15926671 1062 10654 GABARAPL2 0 . GRCh38 16 75568135 75568135 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.189C>G p.Ile63Met p.I63M ENST00000037243 3/4 196 179 17 216 216 0 strelka-varscan-mutect GABARAPL2,missense_variant,p.Ile63Met,ENST00000037243,NM_007285.6;GABARAPL2,missense_variant,p.Ile3Met,ENST00000568455,;GABARAPL2,missense_variant,p.Ile63Met,ENST00000565057,;GABARAPL2,intron_variant,,ENST00000563744,;RP11-490B18.6,downstream_gene_variant,,ENST00000611726,;RP11-77K12.8,intron_variant,,ENST00000564489,; G ENST00000037243 Transcript missense_variant 325/1002 189/354 63/117 I/M atC/atG 1 1 GABARAPL2 HGNC HGNC:13291 protein_coding YES CCDS10921.1 ENSP00000037243 P60520 UPI0000023921 NM_007285.6 deleterious(0.03) 3/4 Gene3D:3.10.20.90,Pfam_domain:PF02991,hmmpanther:PTHR10969,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.99865 0.9999998 1 1 1 0 G 3 3 39 75568135 75568135 C G 1 0 0 0 0 1 0 0 0 6025 816 29 4 4 GABARAPL2 16 75568135 Missense_Mutation SNP C C3N-00175_T 1156461 75568135 14770210 1063 10655 ZNF469 0 . GRCh38 16 88436487 88436487 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.8933C>A p.Ala2978Asp p.A2978D ENST00000437464 2/2 145 88 57 249 248 1 strelka-varscan-mutect ZNF469,missense_variant,p.Ala3006Asp,ENST00000565624,;ZNF469,missense_variant,p.Ala2978Asp,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 8933/13203 8933/11778 2978/3925 A/D gCc/gAc 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.1) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS rs931171498 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 88436487 88436487 C A 1 0 0 0 0 1 0 0 0 18500 739 26 2 2 ZNF469 16 88436487 Missense_Mutation SNP C C3N-00175_T 12868352 88436487 1901858 1064 10656 TRAPPC2L 0 . GRCh38 16 88860219 88860219 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.621G>T p.Leu207Phe p.L207F ENST00000565504 4/4 186 135 51 246 246 0 strelka-varscan-mutect TRAPPC2L,missense_variant,p.Leu207Phe,ENST00000565504,;TRAPPC2L,intron_variant,,ENST00000301021,NM_001318524.1,NM_001318525.1,NM_001318528.1,NM_001318530.1,NM_016209.3;TRAPPC2L,intron_variant,,ENST00000564365,;TRAPPC2L,intron_variant,,ENST00000567895,;TRAPPC2L,intron_variant,,ENST00000568583,;TRAPPC2L,intron_variant,,ENST00000561840,;TRAPPC2L,intron_variant,,ENST00000567312,;GALNS,upstream_gene_variant,,ENST00000268695,NM_000512.4;PABPN1L,downstream_gene_variant,,ENST00000419291,NM_001080487.2;PABPN1L,downstream_gene_variant,,ENST00000411789,NM_001294328.1;PABPN1L,downstream_gene_variant,,ENST00000547152,;GALNS,upstream_gene_variant,,ENST00000569433,;GALNS,upstream_gene_variant,,ENST00000568311,;GALNS,upstream_gene_variant,,ENST00000562831,;TRAPPC2L,downstream_gene_variant,,ENST00000625770,;GALNS,upstream_gene_variant,,ENST00000565364,;TRAPPC2L,intron_variant,,ENST00000565205,;TRAPPC2L,intron_variant,,ENST00000564404,;TRAPPC2L,intron_variant,,ENST00000562125,;TRAPPC2L,intron_variant,,ENST00000563514,;GALNS,upstream_gene_variant,,ENST00000567525,;GALNS,upstream_gene_variant,,ENST00000568613,;TRAPPC2L,downstream_gene_variant,,ENST00000564547,;TRAPPC2L,downstream_gene_variant,,ENST00000565309,;TRAPPC2L,downstream_gene_variant,,ENST00000562792,; T ENST00000565504 Transcript missense_variant 645/3102 621/726 207/241 L/F ttG/ttT 1 1 TRAPPC2L HGNC HGNC:30887 protein_coding ENSP00000455100 H3BP13 UPI000059D3DD 4/4 MODERATE SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 88860219 88860219 G T 1 0 0 0 0 1 0 0 0 16946 1339 47 2 2 TRAPPC2L 16 88860219 Missense_Mutation SNP G C3N-00175_T 423732 88860219 1478126 1065 10657 WDR81 0 . GRCh38 17 1725916 1725916 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.957G>T p.= p.V319V ENST00000409644 1/10 69 48 21 118 118 0 strelka-varscan-mutect WDR81,synonymous_variant,p.=,ENST00000409644,NM_001163809.1;WDR81,intron_variant,,ENST00000309182,NM_152348.3;WDR81,intron_variant,,ENST00000419248,NM_001163811.1;WDR81,intron_variant,,ENST00000437219,NM_001163673.1;WDR81,intron_variant,,ENST00000446363,;WDR81,intron_variant,,ENST00000418841,;WDR81,intron_variant,,ENST00000455636,;WDR81,intron_variant,,ENST00000468539,;WDR81,upstream_gene_variant,,ENST00000575206,;RP11-961A15.1,splice_region_variant,,ENST00000576540,;WDR81,intron_variant,,ENST00000492901,;WDR81,upstream_gene_variant,,ENST00000464528,;WDR81,upstream_gene_variant,,ENST00000479966,;WDR81,upstream_gene_variant,,ENST00000474958,; T ENST00000409644 Transcript synonymous_variant 957/6733 957/5826 319/1941 V gtG/gtT 1 1 WDR81 HGNC HGNC:26600 protein_coding YES CCDS54062.1 ENSP00000386609 Q562E7 UPI0001881A85 NM_001163809.1 1/10 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 1725916 1725916 G T 1 0 0 0 0 0 0 0 1 17885 1335 47 2 2 WDR81 17 1725916 Silent SNP G C3N-00175_T 1725916 81531525 1066 10658 ASPA 0 . GRCh38 17 3494384 3494384 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.669T>C p.= p.Y223Y ENST00000263080 5/6 248 185 63 352 352 0 strelka-varscan-mutect ASPA,synonymous_variant,p.=,ENST00000263080,NM_000049.2;ASPA,synonymous_variant,p.=,ENST00000456349,NM_001128085.1;SPATA22,intron_variant,,ENST00000541913,NM_001321336.1;SPATA22,intron_variant,,ENST00000570318,; C ENST00000263080 Transcript synonymous_variant 827/5431 669/942 223/313 Y taT/taC 1 1 ASPA HGNC HGNC:756 protein_coding YES CCDS11028.1 ENSP00000263080 P45381 Q6FH48 UPI00000012D1 NM_000049.2 5/6 HAMAP:MF_00704,hmmpanther:PTHR15162,hmmpanther:PTHR15162:SF9,PIRSF_domain:PIRSF018001,Pfam_domain:PF04952,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 3494384 3494384 T C 1 0 0 0 0 0 0 0 1 1197 1413 49 5 5 ASPA 17 3494384 Silent SNP T C3N-00175_T 1768468 3494384 79763057 1067 10659 ITGAE 0 . GRCh38 17 3751861 3751861 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1682C>G p.Ser561Cys p.S561C ENST00000263087 15/31 96 85 11 169 169 0 strelka-varscan-mutect ITGAE,missense_variant,p.Ser561Cys,ENST00000263087,NM_002208.4;ITGAE,downstream_gene_variant,,ENST00000572121,; C ENST00000263087 Transcript missense_variant 1781/3858 1682/3540 561/1179 S/C tCc/tGc 1 -1 ITGAE HGNC HGNC:6147 protein_coding YES CCDS32531.1 ENSP00000263087 P38570 UPI000049DE2D NM_002208.4 deleterious(0) 15/31 Gene3D:3nigC00,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF79,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 3751861 3751861 G C 1 0 0 0 0 1 0 0 0 7792 1174 41 4 4 ITGAE 17 3751861 Missense_Mutation SNP G C3N-00175_T 257477 3751861 79505580 1068 10660 CAMKK1 0 . GRCh38 17 3885598 3885598 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.90G>T p.Glu30Asp p.E30D ENST00000158166 2/16 198 139 59 313 313 0 strelka-varscan-mutect CAMKK1,missense_variant,p.Glu30Asp,ENST00000348335,NM_172206.1,NM_032294.2;CAMKK1,missense_variant,p.Glu57Asp,ENST00000381769,;CAMKK1,missense_variant,p.Glu30Asp,ENST00000158166,NM_172207.2;CAMKK1,non_coding_transcript_exon_variant,,ENST00000573483,; A ENST00000158166 Transcript missense_variant 239/2459 90/1563 30/520 E/D gaG/gaT 1 -1 CAMKK1 HGNC HGNC:1469 protein_coding YES CCDS11039.1 ENSP00000158166 Q8N5S9 UPI0000141119 NM_172207.2 tolerated_low_confidence(0.16) 2/16 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF232 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 3885598 3885598 C A 1 0 0 0 0 1 0 0 0 2297 680 24 2 2 CAMKK1 17 3885598 Missense_Mutation SNP C C3N-00175_T 133737 3885598 79371843 1069 10661 C17orf107 0 . GRCh38 17 4900049 4900049 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.180G>A p.= p.K60K ENST00000381365 2/3 46 42 4 87 87 0 varscan-mutect C17orf107,synonymous_variant,p.=,ENST00000381365,NM_001145536.1;C17orf107,synonymous_variant,p.=,ENST00000521575,;CHRNE,intron_variant,,ENST00000293780,NM_000080.3;MINK1,downstream_gene_variant,,ENST00000355280,NM_153827.4,NM_015716.4;MINK1,downstream_gene_variant,,ENST00000347992,NM_170663.4;MINK1,downstream_gene_variant,,ENST00000453408,NM_001024937.3;MINK1,downstream_gene_variant,,ENST00000576037,;CHRNE,downstream_gene_variant,,ENST00000575637,;CHRNE,intron_variant,,ENST00000572438,;MINK1,downstream_gene_variant,,ENST00000572330,;MINK1,downstream_gene_variant,,ENST00000574453,NM_001321236.1;MINK1,downstream_gene_variant,,ENST00000571207,;MINK1,downstream_gene_variant,,ENST00000574871,;MINK1,downstream_gene_variant,,ENST00000575511,; A ENST00000381365 Transcript synonymous_variant 407/3199 180/573 60/190 K aaG/aaA 1 1 C17orf107 HGNC HGNC:37238 protein_coding YES CCDS45591.1 ENSP00000370770 Q6ZR85 UPI00001C0FE1 NM_001145536.1 2/3 hmmpanther:PTHR38506,hmmpanther:PTHR38506:SF1 LOW SNV 2 1 PASS . . 0 196 0 0 0 0 0 14 -2.717852 0 0 1 0 0 A 2 1 39 4900049 4900049 G A 1 0 0 0 0 0 0 0 1 1878 933 33 3 3 C17orf107 17 4900049 Silent SNP G C3N-00175_T 1014451 4900049 78357392 1070 10662 USP6 0 . GRCh38 17 5137144 5137144 + Missense_Mutation SNP G G T rs766182812 C3N-00175_T C3N-00175_N G G c.783G>T p.Gln261His p.Q261H ENST00000574788 19/38 290 194 96 397 397 0 strelka-varscan-mutect USP6,missense_variant,p.Gln261His,ENST00000574788,NM_001304284.1;USP6,missense_variant,p.Gln261His,ENST00000250066,NM_004505.3;USP6,downstream_gene_variant,,ENST00000572429,;USP6,missense_variant,p.Gln261His,ENST00000575709,;USP6,missense_variant,p.Gln261His,ENST00000572949,;USP6,downstream_gene_variant,,ENST00000357482,; T ENST00000574788 Transcript missense_variant 3013/8464 783/4221 261/1406 Q/H caG/caT rs766182812 1 1 USP6 HGNC HGNC:12629 protein_coding YES CCDS11069.2 ENSP00000460380 P35125 UPI000006226F NM_001304284.1 deleterious_low_confidence(0.02) 19/38 Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF233,SMART_domains:SM00164 MODERATE 1 SNV 1 1 PASS rs766182812 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 5137144 5137144 G T 1 0 0 0 0 1 0 0 0 17629 1020 36 2 2 USP6 17 5137144 Missense_Mutation SNP G C3N-00175_T 237095 5137144 78120297 1071 10663 RABEP1 0 . GRCh38 17 5350629 5350629 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.963G>T p.Gln321His p.Q321H ENST00000537505 7/18 144 111 33 257 257 0 strelka-varscan-mutect RABEP1,missense_variant,p.Gln321His,ENST00000537505,NM_004703.5,NM_001291581.1;RABEP1,missense_variant,p.Gln321His,ENST00000341923,NM_001083585.2;RABEP1,upstream_gene_variant,,ENST00000574568,;RABEP1,splice_region_variant,,ENST00000575475,; T ENST00000537505 Transcript missense_variant,splice_region_variant 1150/5365 963/2589 321/862 Q/H caG/caT 1 1 RABEP1 HGNC HGNC:17677 protein_coding YES CCDS45592.1 ENSP00000445408 Q15276 UPI00000745A5 NM_004703.5,NM_001291581.1 deleterious(0.01) 7/18 Low_complexity_(Seg):seg,hmmpanther:PTHR31179:SF5,hmmpanther:PTHR31179,Pfam_domain:PF03528 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 5350629 5350629 G T 1 0 0 0 0 1 0 0 0 13120 1014 35 2 2 RABEP1 17 5350629 Missense_Mutation SNP G C3N-00175_T 213485 5350629 77906812 1072 10664 GUCY2D 0 . GRCh38 17 8014015 8014015 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2399A>T p.His800Leu p.H800L ENST00000254854 12/20 298 257 41 432 431 1 strelka-varscan-mutect GUCY2D,missense_variant,p.His800Leu,ENST00000254854,NM_000180.3;RP11-1099M24.9,non_coding_transcript_exon_variant,,ENST00000623126,;GUCY2D,upstream_gene_variant,,ENST00000574510,; T ENST00000254854 Transcript missense_variant 2549/3698 2399/3312 800/1103 H/L cAc/cTc 1 1 GUCY2D HGNC HGNC:4689 protein_coding YES CCDS11127.1 ENSP00000254854 Q02846 UPI0000128C1C NM_000180.3 deleterious(0.04) 12/20 PROSITE_profiles:PS50011,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF228,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 8014015 8014015 A T 1 0 0 0 0 1 0 0 0 6779 159 6 4 4 GUCY2D 17 8014015 Missense_Mutation SNP A C3N-00175_T 2663386 8014015 75243426 1073 10665 PFAS 0 . GRCh38 17 8263932 8263932 + Missense_Mutation SNP G G T rs142452570 C3N-00175_T C3N-00175_N G G c.1787G>T p.Arg596Leu p.R596L ENST00000314666 15/28 36 26 10 87 87 0 strelka-varscan-mutect PFAS,missense_variant,p.Arg596Leu,ENST00000314666,NM_012393.2;PFAS,intron_variant,,ENST00000583059,;PFAS,upstream_gene_variant,,ENST00000546020,;PFAS,non_coding_transcript_exon_variant,,ENST00000585319,;PFAS,3_prime_UTR_variant,,ENST00000580356,;PFAS,non_coding_transcript_exon_variant,,ENST00000581288,;PFAS,upstream_gene_variant,,ENST00000578979,;PFAS,upstream_gene_variant,,ENST00000580251,; T ENST00000314666 Transcript missense_variant 1920/5371 1787/4017 596/1338 R/L cGg/cTg rs142452570 1 1 PFAS HGNC HGNC:8863 protein_coding YES CCDS11136.1 ENSP00000313490 O15067 UPI00001A95E5 NM_012393.2 tolerated(0.06) 15/28 HAMAP:MF_00419,hmmpanther:PTHR10099,hmmpanther:PTHR10099:SF1,TIGRFAM_domain:TIGR01735,Pfam_domain:PF02769,Superfamily_domains:SSF56042 MODERATE 1 SNV 1 1 PASS rs142452570 . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 39 8263932 8263932 G T 1 0 0 0 0 1 0 0 0 11844 1130 39 1 1 PFAS 17 8263932 Missense_Mutation SNP G C3N-00175_T 249917 8263932 74993509 1074 10666 PIK3R5 0 . GRCh38 17 8888256 8888256 + Missense_Mutation SNP C C A rs769606668 C3N-00175_T C3N-00175_N C C c.1531G>T p.Asp511Tyr p.D511Y ENST00000447110 10/19 221 174 47 309 308 1 strelka-varscan-mutect PIK3R5,missense_variant,p.Asp511Tyr,ENST00000447110,NM_001142633.2;PIK3R5,missense_variant,p.Asp125Tyr,ENST00000616147,NM_001251852.1;PIK3R5,missense_variant,p.Asp125Tyr,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,missense_variant,p.Asp125Tyr,ENST00000623421,NM_001251855.1;PIK3R5,missense_variant,p.Asp511Tyr,ENST00000581552,NM_014308.3;PIK3R5,missense_variant,p.Asp511Tyr,ENST00000584803,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,; A ENST00000447110 Transcript missense_variant 1661/4495 1531/2643 511/880 D/Y Gat/Tat rs769606668 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 deleterious(0) 10/19 Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS rs769606668 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 8888256 8888256 C A 1 0 0 0 0 1 0 0 0 12017 855 30 2 2 PIK3R5 17 8888256 Missense_Mutation SNP C C3N-00175_T 624324 8888256 74369185 1075 10667 MYH13 0 . GRCh38 17 10345346 10345346 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1440C>G p.Ile480Met p.I480M ENST00000418404 14/41 406 365 41 458 458 0 varscan-mutect MYH13,missense_variant,p.Ile480Met,ENST00000418404,;MYH13,missense_variant,p.Ile480Met,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Ile480Met,ENST00000621918,;RP11-401O9.3,downstream_gene_variant,,ENST00000577743,; C ENST00000418404 Transcript missense_variant 1604/6296 1440/5817 480/1938 I/M atC/atG 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0) 14/41 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 10345346 10345346 G C 1 0 0 0 0 1 0 0 0 10032 1280 45 4 4 MYH13 17 10345346 Missense_Mutation SNP G C3N-00175_T 1457090 10345346 72912095 1076 10668 MYH1 0 . GRCh38 17 10505221 10505221 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2377C>A p.Gln793Lys p.Q793K ENST00000226207 21/40 192 127 65 230 230 0 strelka-varscan-mutect MYH1,missense_variant,p.Gln793Lys,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript missense_variant 2472/6024 2377/5820 793/1939 Q/K Cag/Aag 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 21/40 Gene3D:1wdcA00,PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 10505221 10505221 G T 1 0 0 0 0 1 0 0 0 10029 1357 47 2 2 MYH1 17 10505221 Missense_Mutation SNP G C3N-00175_T 159875 10505221 72752220 1077 10669 ZNF287 0 . GRCh38 17 16552568 16552568 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.1574A>G p.Gln525Arg p.Q525R ENST00000395824 6/6 85 56 29 155 155 0 strelka-varscan-mutect ZNF287,missense_variant,p.Gln525Arg,ENST00000395824,;ZNF287,missense_variant,p.Gln525Arg,ENST00000395825,NM_020653.2;ZNF287,downstream_gene_variant,,ENST00000498796,; C ENST00000395824 Transcript missense_variant 2192/3373 1574/2286 525/761 Q/R cAg/cGg 1 -1 ZNF287 HGNC HGNC:13502 protein_coding YES CCDS11179.2 ENSP00000379168 Q9HBT7 UPI0000200A57 tolerated(0.54) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF236,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs768193322 . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 C 3 2 39 16552568 16552568 T C 1 0 0 0 0 1 0 0 0 18401 1580 55 5 5 ZNF287 17 16552568 Missense_Mutation SNP T C3N-00175_T 6047347 16552568 66704873 1078 10670 CCDC144A 0 . GRCh38 17 16735251 16735251 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2980G>T p.Gly994Ter p.G994* ENST00000360524 12/18 44 30 14 89 89 0 strelka-varscan-mutect CCDC144A,stop_gained,p.Gly994Ter,ENST00000399273,;CCDC144A,stop_gained,p.Gly994Ter,ENST00000360524,NM_014695.2;CCDC144A,downstream_gene_variant,,ENST00000456009,;RP11-219A15.1,stop_gained,p.Gly994Ter,ENST00000448331,;CCDC144A,3_prime_UTR_variant,,ENST00000360495,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000470068,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000328495,; T ENST00000360524 Transcript stop_gained 3056/5830 2980/4284 994/1427 G/* Gga/Tga 1 1 CCDC144A HGNC HGNC:29072 protein_coding YES CCDS45621.1 ENSP00000353717 A2RUR9 UPI0000F095D0 NM_014695.2 12/18 hmmpanther:PTHR22245:SF0,hmmpanther:PTHR22245,Pfam_domain:PF14915 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 16735251 16735251 G T 1 0 0 0 0 0 1 0 0 2465 1349 47 2 2 CCDC144A 17 16735251 Nonsense_Mutation SNP G C3N-00175_T 182683 16735251 66522190 1079 10671 MYO15A 0 . GRCh38 17 18151502 18151502 + Silent SNP C C A rs778098806 C3N-00175_T C3N-00175_N C C c.7762C>A p.= p.R2588R ENST00000205890 40/66 417 340 77 421 421 0 strelka-varscan-mutect MYO15A,synonymous_variant,p.=,ENST00000205890,NM_016239.3;MYO15A,synonymous_variant,p.=,ENST00000615845,;MYO15A,upstream_gene_variant,,ENST00000418233,;MYO15A,upstream_gene_variant,,ENST00000445289,;MYO15A,downstream_gene_variant,,ENST00000578999,;MYO15A,upstream_gene_variant,,ENST00000536811,;MYO15A,upstream_gene_variant,,ENST00000585180,; A ENST00000205890 Transcript synonymous_variant 8100/11863 7762/10593 2588/3530 R Cgg/Agg rs778098806,COSM1216307 1 1 MYO15A HGNC HGNC:7594 protein_coding YES CCDS42271.1 ENSP00000205890 Q9UKN7 UPI0000E59E6E NM_016239.3 40/66 0,1 LOW 1 SNV 5 0,1 1 PASS rs778098806 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 18151502 18151502 C A 1 0 0 0 0 0 0 0 1 10063 643 23 1 1 MYO15A 17 18151502 Silent SNP C C3N-00175_T 1416251 18151502 65105939 1080 10672 ZNF286B 0 . GRCh38 17 18662608 18662608 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.898G>C p.Glu300Gln p.E300Q ENST00000545289 5/5 192 180 12 205 205 0 varscan-mutect ZNF286B,missense_variant,p.Glu300Gln,ENST00000545289,NM_001145045.1;ZNF286B,3_prime_UTR_variant,,ENST00000285274,;TBC1D28,upstream_gene_variant,,ENST00000570881,; G ENST00000545289 Transcript missense_variant 1149/5328 898/1569 300/522 E/Q Gaa/Caa 1 -1 ZNF286B HGNC HGNC:33241 protein_coding YES CCDS58523.1 ENSP00000461413 P0CG31 UPI000192A2F2 NM_001145045.1 deleterious(0.01) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF217,hmmpanther:PTHR24377,Gene3D:3.30.160.60,SMART_domains:SM00355 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 18662608 18662608 C G 1 0 0 0 0 1 0 0 0 18400 835 29 4 4 ZNF286B 17 18662608 Missense_Mutation SNP C C3N-00175_T 511106 18662608 64594833 1081 10673 SLC47A2 0 . GRCh38 17 19714777 19714777 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.238T>A p.Cys80Ser p.C80S ENST00000325411 3/17 290 198 92 267 267 0 strelka-varscan-mutect SLC47A2,missense_variant,p.Cys80Ser,ENST00000350657,NM_001256663.1;SLC47A2,missense_variant,p.Cys80Ser,ENST00000325411,NM_001099646.1,NM_152908.3;SLC47A2,missense_variant,p.Cys80Ser,ENST00000433844,;RP11-311F12.1,upstream_gene_variant,,ENST00000577087,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000463318,;SLC47A2,missense_variant,p.Cys80Ser,ENST00000574239,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000467379,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000467609,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000483510,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000574220,;SLC47A2,downstream_gene_variant,,ENST00000456947,; T ENST00000325411 Transcript missense_variant 289/2258 238/1809 80/602 C/S Tgc/Agc 1 -1 SLC47A2 HGNC HGNC:26439 protein_coding YES CCDS11211.1 ENSP00000326671 Q86VL8 UPI0000190813 NM_001099646.1,NM_152908.3 tolerated(0.11) 3/17 Pfam_domain:PF01554,hmmpanther:PTHR11206,hmmpanther:PTHR11206:SF81,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 19714777 19714777 A T 1 0 0 0 0 1 0 0 0 14925 188 7 4 4 SLC47A2 17 19714777 Missense_Mutation SNP A C3N-00175_T 1052169 19714777 63542664 1082 10674 ALDH3A1 0 . GRCh38 17 19740434 19740434 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.851G>C p.Arg284Thr p.R284T ENST00000457500 6/10 199 185 14 185 185 0 strelka-varscan-mutect ALDH3A1,missense_variant,p.Arg284Thr,ENST00000457500,NM_001135168.1;ALDH3A1,missense_variant,p.Arg284Thr,ENST00000225740,NM_000691.4;ALDH3A1,missense_variant,p.Arg284Thr,ENST00000444455,NM_001135167.1;ALDH3A1,missense_variant,p.Arg211Thr,ENST00000494157,;ALDH3A1,missense_variant,p.Arg284Thr,ENST00000439102,;ALDH3A1,intron_variant,,ENST00000395555,;ALDH3A1,downstream_gene_variant,,ENST00000574162,;ALDH3A1,downstream_gene_variant,,ENST00000426645,;ALDH3A1,downstream_gene_variant,,ENST00000570414,;ALDH3A1,downstream_gene_variant,,ENST00000573368,;RP11-311F12.2,downstream_gene_variant,,ENST00000580884,;ALDH3A1,downstream_gene_variant,,ENST00000485231,;ALDH3A1,missense_variant,p.Arg284Thr,ENST00000468746,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000479677,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000485472,;ALDH3A1,non_coding_transcript_exon_variant,,ENST00000487650,;ALDH3A1,downstream_gene_variant,,ENST00000575860,;ALDH3A1,downstream_gene_variant,,ENST00000575103,; G ENST00000457500 Transcript missense_variant 1181/1925 851/1362 284/453 R/T aGa/aCa 1 -1 ALDH3A1 HGNC HGNC:405 protein_coding YES CCDS11212.1 ENSP00000411821 P30838 UPI000013C87C NM_001135168.1 deleterious(0) 6/10 hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF105,PIRSF_domain:PIRSF036492,Pfam_domain:PF00171,Gene3D:3.40.309.10,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS rs1223928903 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 19740434 19740434 C G 1 0 0 0 0 1 0 0 0 597 913 32 4 4 ALDH3A1 17 19740434 Missense_Mutation SNP C C3N-00175_T 25657 19740434 63517007 1083 10675 CDRT15L2 0 . GRCh38 17 20579909 20579909 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.166C>A p.Leu56Ile p.L56I ENST00000399044 1/2 251 207 44 206 206 0 strelka-varscan-mutect CDRT15L2,missense_variant,p.Leu56Ile,ENST00000399044,NM_001190790.1;RP11-434D2.12,upstream_gene_variant,,ENST00000580931,;ZSWIM5P2,downstream_gene_variant,,ENST00000420212,; A ENST00000399044 Transcript missense_variant 186/1048 166/846 56/281 L/I Cta/Ata COSM5310194 1 1 CDRT15L2 HGNC HGNC:34075 protein_coding YES CCDS54096.1 ENSP00000382000 A8MXV6 UPI00001D7A81 NM_001190790.1 deleterious_low_confidence(0.05) 1/2 hmmpanther:PTHR16471,hmmpanther:PTHR16471:SF0 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 20579909 20579909 C A 1 0 0 0 0 1 0 0 0 2881 680 24 2 2 CDRT15L2 17 20579909 Missense_Mutation SNP C C3N-00175_T 839475 20579909 62677532 1084 10676 MAP2K3 0 . GRCh38 17 21304494 21304494 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.637G>T p.Gly213Cys p.G213C ENST00000342679 8/12 453 379 74 351 351 0 strelka-varscan-mutect MAP2K3,missense_variant,p.Gly213Cys,ENST00000342679,NM_145109.2;MAP2K3,missense_variant,p.Gly184Cys,ENST00000361818,NM_002756.4;MAP2K3,missense_variant,p.Gly184Cys,ENST00000613338,;MAP2K3,missense_variant,p.Gly184Cys,ENST00000316920,;MAP2K3,downstream_gene_variant,,ENST00000526076,;MAP2K3,3_prime_UTR_variant,,ENST00000395491,NM_001316332.1;MAP2K3,3_prime_UTR_variant,,ENST00000496046,;MAP2K3,downstream_gene_variant,,ENST00000583508,;MAP2K3,downstream_gene_variant,,ENST00000479129,; T ENST00000342679 Transcript missense_variant 886/2303 637/1044 213/347 G/C Ggc/Tgc 1 1 MAP2K3 HGNC HGNC:6843 protein_coding YES CCDS11217.1 ENSP00000345083 P46734 Q6FI23 UPI000012F48C NM_145109.2 deleterious(0) 8/12 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF191,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 21304494 21304494 G T 1 0 0 0 0 1 0 0 0 9160 1348 47 2 2 MAP2K3 17 21304494 Missense_Mutation SNP G C3N-00175_T 724585 21304494 61952947 1085 10677 NOS2 0 . GRCh38 17 27765673 27765673 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2290G>T p.Gly764Cys p.G764C ENST00000313735 20/27 143 80 63 110 110 0 strelka-varscan-mutect NOS2,missense_variant,p.Gly764Cys,ENST00000313735,NM_000625.4;NOS2,missense_variant,p.Gly725Cys,ENST00000621962,; A ENST00000313735 Transcript missense_variant 2524/4176 2290/3462 764/1153 G/C Ggc/Tgc 1 -1 NOS2 HGNC HGNC:7873 protein_coding YES CCDS11223.1 ENSP00000327251 P35228 UPI000011D645 NM_000625.4 deleterious(0.02) 20/27 PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF56,Pfam_domain:PF00667,Gene3D:2.40.30.10,Superfamily_domains:SSF63380 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 27765673 27765673 C A 1 0 0 0 0 1 0 0 0 10588 681 24 2 2 NOS2 17 27765673 Missense_Mutation SNP C C3N-00175_T 6461179 27765673 55491768 1086 10678 NUFIP2 0 . GRCh38 17 29293796 29293796 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.264G>A p.= p.P88P ENST00000225388 1/4 43 39 4 51 51 0 strelka-varscan-mutect NUFIP2,synonymous_variant,p.=,ENST00000225388,NM_020772.2;NUFIP2,synonymous_variant,p.=,ENST00000579665,; T ENST00000225388 Transcript synonymous_variant 323/10850 264/2088 88/695 P ccG/ccA 1 -1 NUFIP2 HGNC HGNC:17634 protein_coding YES CCDS32600.1 ENSP00000225388 Q7Z417 A1L3A7 UPI00001B078D NM_020772.2 1/4 hmmpanther:PTHR28333,hmmpanther:PTHR28333:SF2 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -10.82338 1 1 1 1 0 T 2 4 39 29293796 29293796 C T 1 0 0 0 0 0 0 0 1 10813 871 31 1 1 NUFIP2 17 29293796 Silent SNP C C3N-00175_T 1528123 29293796 53963645 1087 10679 ABHD15 0 . GRCh38 17 29566706 29566706 + Silent SNP C C G novel C3N-00175_T C3N-00175_N C C c.261G>C p.= p.L87L ENST00000307201 1/2 158 123 35 192 192 0 strelka-varscan-mutect ABHD15,synonymous_variant,p.=,ENST00000307201,NM_198147.2;TP53I13,upstream_gene_variant,,ENST00000301057,NM_138349.2;TP53I13,upstream_gene_variant,,ENST00000578749,;TP53I13,upstream_gene_variant,,ENST00000581411,;TP53I13,upstream_gene_variant,,ENST00000580183,;TP53I13,upstream_gene_variant,,ENST00000582829,;TP53I13,upstream_gene_variant,,ENST00000583940,;ABHD15-AS1,intron_variant,,ENST00000581474,;RP11-68I3.4,upstream_gene_variant,,ENST00000579050,;TP53I13,intron_variant,,ENST00000584522,;TP53I13,intron_variant,,ENST00000578073,;TP53I13,upstream_gene_variant,,ENST00000579674,;TP53I13,upstream_gene_variant,,ENST00000577934,;TP53I13,upstream_gene_variant,,ENST00000580132,; G ENST00000307201 Transcript synonymous_variant 432/3592 261/1407 87/468 L ctG/ctC 1 -1 ABHD15 HGNC HGNC:26971 protein_coding YES CCDS32602.1 ENSP00000302657 Q6UXT9 UPI00001C1FC9 NM_198147.2 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10794:SF39,hmmpanther:PTHR10794 LOW 1 SNV 1 1 PASS rs1448924957 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 29566706 29566706 C G 1 0 0 0 0 0 0 0 1 85 697 25 4 4 ABHD15 17 29566706 Silent SNP C C3N-00175_T 272910 29566706 53690735 1088 10680 CORO6 0 . GRCh38 17 29615827 29615827 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1324G>T p.Glu442Ter p.E442* ENST00000345068 11/11 117 111 6 128 128 0 strelka-varscan-mutect CORO6,stop_gained,p.Glu442Ter,ENST00000345068,;CORO6,stop_gained,p.Glu442Ter,ENST00000388767,NM_032854.3;CORO6,stop_gained,p.Glu402Ter,ENST00000580212,;CORO6,stop_gained,p.Glu441Ter,ENST00000584969,;ANKRD13B,downstream_gene_variant,,ENST00000394859,NM_152345.4;ANKRD13B,downstream_gene_variant,,ENST00000614878,;CORO6,downstream_gene_variant,,ENST00000492276,;CORO6,downstream_gene_variant,,ENST00000584602,;ANKRD13B,downstream_gene_variant,,ENST00000579719,;ABHD15-AS1,intron_variant,,ENST00000581474,;CORO6,downstream_gene_variant,,ENST00000577909,;CORO6,3_prime_UTR_variant,,ENST00000480954,;CORO6,non_coding_transcript_exon_variant,,ENST00000459686,;CORO6,non_coding_transcript_exon_variant,,ENST00000467534,;CORO6,non_coding_transcript_exon_variant,,ENST00000469090,;CORO6,non_coding_transcript_exon_variant,,ENST00000579388,;ANKRD13B,downstream_gene_variant,,ENST00000487527,;ANKRD13B,downstream_gene_variant,,ENST00000488766,;ANKRD13B,downstream_gene_variant,,ENST00000493506,; A ENST00000345068 Transcript stop_gained 1538/2603 1324/1419 442/472 E/* Gag/Tag 1 -1 CORO6 HGNC HGNC:21356 protein_coding YES CCDS11252.2 ENSP00000344562 Q6QEF8 UPI0000DA4C55 11/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF23 HIGH SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -9.086 0.9999993 1 1 1 0 A 4 1 39 29615827 29615827 C A 1 0 0 0 0 0 1 0 0 3552 922 32 2 2 CORO6 17 29615827 Nonsense_Mutation SNP C C3N-00175_T 49121 29615827 53641614 1089 10681 SSH2 0 . GRCh38 17 29632478 29632478 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2716C>A p.Gln906Lys p.Q906K ENST00000540801 16/16 264 154 110 276 276 0 strelka-varscan-mutect SSH2,missense_variant,p.Gln879Lys,ENST00000269033,NM_033389.3;SSH2,missense_variant,p.Gln906Lys,ENST00000540801,NM_001282129.1;SSH2,upstream_gene_variant,,ENST00000577991,;ABHD15-AS1,intron_variant,,ENST00000581474,; T ENST00000540801 Transcript missense_variant 2809/4538 2716/4353 906/1450 Q/K Cag/Aag 1 -1 SSH2 HGNC HGNC:30580 protein_coding YES CCDS74024.1 ENSP00000444743 F5H527 UPI0002065A97 NM_001282129.1 deleterious_low_confidence(0) 16/16 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 29632478 29632478 G T 1 0 0 0 0 1 0 0 0 15561 1328 46 2 2 SSH2 17 29632478 Missense_Mutation SNP G C3N-00175_T 16651 29632478 53624963 1090 10682 NSRP1 0 . GRCh38 17 30185210 30185210 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1213A>T p.Ser405Cys p.S405C ENST00000247026 7/7 172 142 30 175 175 0 strelka-varscan-mutect NSRP1,missense_variant,p.Ser405Cys,ENST00000247026,NM_032141.3;NSRP1,missense_variant,p.Ser351Cys,ENST00000612959,NM_001261467.1;NSRP1,downstream_gene_variant,,ENST00000580103,;NSRP1,non_coding_transcript_exon_variant,,ENST00000540900,;NSRP1,downstream_gene_variant,,ENST00000577289,;NSRP1,3_prime_UTR_variant,,ENST00000394826,;NSRP1,downstream_gene_variant,,ENST00000475652,; T ENST00000247026 Transcript missense_variant 1276/2541 1213/1677 405/558 S/C Agt/Tgt 1 1 NSRP1 HGNC HGNC:25305 protein_coding YES CCDS11255.1 ENSP00000247026 Q9H0G5 UPI000006E653 NM_032141.3 deleterious(0) 7/7 hmmpanther:PTHR31938 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 30185210 30185210 A T 1 0 0 0 0 1 0 0 0 10740 188 7 4 4 NSRP1 17 30185210 Missense_Mutation SNP A C3N-00175_T 552732 30185210 53072231 1091 10683 RAB11FIP4 0 . GRCh38 17 31531625 31531625 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.1807G>T p.Ala603Ser p.A603S ENST00000621161 15/15 137 81 56 140 140 0 strelka-varscan-mutect RAB11FIP4,missense_variant,p.Ala603Ser,ENST00000621161,NM_032932.5;RAB11FIP4,missense_variant,p.Ala501Ser,ENST00000394744,NM_001303542.2;RAB11FIP4,upstream_gene_variant,,ENST00000579485,;RAB11FIP4,non_coding_transcript_exon_variant,,ENST00000578148,;RP1-41C23.2,downstream_gene_variant,,ENST00000624452,;RAB11FIP4,downstream_gene_variant,,ENST00000585058,;RAB11FIP4,downstream_gene_variant,,ENST00000581460,; T ENST00000621161 Transcript missense_variant 2036/8628 1807/1914 603/637 A/S Gcc/Tcc COSM4890616 1 1 RAB11FIP4 HGNC HGNC:30267 protein_coding YES CCDS11267.1 ENSP00000482620 Q86YS3 UPI000000D857 NM_032932.5 deleterious(0) 15/15 PROSITE_profiles:PS51511,hmmpanther:PTHR15726,hmmpanther:PTHR15726:SF5,Pfam_domain:PF09457,Superfamily_domains:SSF144270 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 31531625 31531625 G T 1 0 0 0 0 1 0 0 0 13054 971 34 2 2 RAB11FIP4 17 31531625 Missense_Mutation SNP G C3N-00175_T 1346415 31531625 51725816 1092 10684 CCT6B 0 . GRCh38 17 34961330 34961330 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.64G>T p.Val22Phe p.V22F ENST00000314144 1/14 98 86 12 101 101 0 strelka-varscan-mutect CCT6B,missense_variant,p.Val22Phe,ENST00000314144,NM_006584.3;CCT6B,missense_variant,p.Val22Phe,ENST00000421975,NM_001193529.2;CCT6B,missense_variant,p.Val22Phe,ENST00000436961,NM_001193530.1;CCT6B,intron_variant,,ENST00000585073,;ZNF830,upstream_gene_variant,,ENST00000361952,NM_052857.3;ZNF830,upstream_gene_variant,,ENST00000578339,; A ENST00000314144 Transcript missense_variant 180/1838 64/1593 22/530 V/F Gtc/Ttc 1 -1 CCT6B HGNC HGNC:1621 protein_coding YES CCDS32617.1 ENSP00000327191 Q92526 UPI000013F740 NM_006584.3 deleterious(0.01) 1/14 Low_complexity_(Seg):seg,hmmpanther:PTHR11353:SF58,hmmpanther:PTHR11353,TIGRFAM_domain:TIGR02347,Gene3D:1.10.560.10,Superfamily_domains:SSF48592 MODERATE 1 SNV 1 1 PASS rs948722321 . 0 203 6 0 0 0 0 0 -19.99999 0.9999999 1 1 1 0 A 3 1 39 34961330 34961330 C A 1 0 0 0 0 1 0 0 0 2659 478 17 2 2 CCT6B 17 34961330 Missense_Mutation SNP C C3N-00175_T 3429705 34961330 48296111 1093 10685 TAF15 0 . GRCh38 17 35844522 35844522 + Missense_Mutation SNP G G T rs376580614 C3N-00175_T C3N-00175_N G G c.1223G>T p.Arg408Leu p.R408L ENST00000605844 15/16 98 62 36 101 101 0 strelka-varscan-mutect TAF15,missense_variant,p.Arg408Leu,ENST00000605844,NM_139215.2;TAF15,missense_variant,p.Arg405Leu,ENST00000604841,NM_003487.3;TAF15,missense_variant,p.Arg317Leu,ENST00000603777,;TAF15,missense_variant,p.Arg73Leu,ENST00000604694,;TAF15,upstream_gene_variant,,ENST00000603967,;TAF15,downstream_gene_variant,,ENST00000603393,;TAF15,downstream_gene_variant,,ENST00000603346,; T ENST00000605844 Transcript missense_variant 1338/2191 1223/1779 408/592 R/L cGt/cTt rs376580614 1 1 TAF15 HGNC HGNC:11547 protein_coding YES CCDS32623.1 ENSP00000474096 Q92804 UPI000013317D NM_139215.2 tolerated_low_confidence(0.06) 15/16 hmmpanther:PTHR23238,hmmpanther:PTHR23238:SF25,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs376580614 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 35844522 35844522 G T 1 0 0 0 0 1 0 0 0 15914 1145 40 1 1 TAF15 17 35844522 Missense_Mutation SNP G C3N-00175_T 883192 35844522 47412919 1094 10686 MYO19 0 . GRCh38 17 36528095 36528095 + Silent SNP G G C novel C3N-00175_T C3N-00175_N G G c.120C>G p.= p.L40L ENST00000614623 4/26 146 131 15 139 139 0 strelka-varscan-mutect MYO19,synonymous_variant,p.=,ENST00000614623,NM_001163735.1;MYO19,synonymous_variant,p.=,ENST00000610930,NM_025109.5;MYO19,synonymous_variant,p.=,ENST00000621344,NM_001033580.2;MYO19,synonymous_variant,p.=,ENST00000616159,;MYO19,synonymous_variant,p.=,ENST00000622055,;MYO19,synonymous_variant,p.=,ENST00000616207,;MYO19,synonymous_variant,p.=,ENST00000613551,;MYO19,intron_variant,,ENST00000620640,;MYO19,downstream_gene_variant,,ENST00000620644,;MYO19,synonymous_variant,p.=,ENST00000610992,;MYO19,synonymous_variant,p.=,ENST00000621550,; C ENST00000614623 Transcript synonymous_variant 643/4054 120/2913 40/970 L ctC/ctG 1 -1 MYO19 HGNC HGNC:26234 protein_coding YES CCDS54112.1 ENSP00000479518 Q96H55 UPI000173AA19 NM_001163735.1 4/26 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF289,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 36528095 36528095 G C 1 0 0 0 0 0 0 0 1 10068 1277 45 4 4 MYO19 17 36528095 Silent SNP G C3N-00175_T 683573 36528095 46729346 1095 10687 STAC2 0 . GRCh38 17 39217931 39217931 + Missense_Mutation SNP G G T rs138657621 C3N-00175_T C3N-00175_N G G c.333C>A p.His111Gln p.H111Q ENST00000333461 2/11 240 200 40 236 236 0 strelka-varscan-mutect STAC2,missense_variant,p.His111Gln,ENST00000333461,NM_198993.3;STAC2,intron_variant,,ENST00000584501,; T ENST00000333461 Transcript missense_variant 703/3362 333/1236 111/411 H/Q caC/caA rs138657621 1 -1 STAC2 HGNC HGNC:23990 protein_coding YES CCDS11335.1 ENSP00000327509 Q6ZMT1 D0IN09 UPI0000223E4D NM_198993.3 deleterious(0.02) 2/11 Gene3D:3.30.60.20,Pfam_domain:PF00130,PROSITE_patterns:PS00479,PROSITE_profiles:PS50081,hmmpanther:PTHR15135,hmmpanther:PTHR15135:SF5,SMART_domains:SM00109,Superfamily_domains:SSF57889 MODERATE 1 SNV 1 1 PASS rs138657621 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 39217931 39217931 G T 1 0 0 0 0 1 0 0 0 15618 1368 48 2 2 STAC2 17 39217931 Missense_Mutation SNP G C3N-00175_T 2689836 39217931 44039510 1096 10688 PNMT 0 . GRCh38 17 39670119 39670119 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.579C>A p.Ser193Arg p.S193R ENST00000269582 3/3 280 260 20 278 277 1 strelka-varscan-mutect PNMT,missense_variant,p.Ser193Arg,ENST00000269582,NM_002686.4;PNMT,missense_variant,p.Ser95Arg,ENST00000394246,;PGAP3,downstream_gene_variant,,ENST00000300658,NM_033419.4;PGAP3,downstream_gene_variant,,ENST00000378011,NM_001291726.1;PGAP3,downstream_gene_variant,,ENST00000579146,NM_001291733.1;TCAP,downstream_gene_variant,,ENST00000309889,NM_003673.3;PGAP3,downstream_gene_variant,,ENST00000619169,;PGAP3,downstream_gene_variant,,ENST00000429199,NM_001291728.1;PNMT,downstream_gene_variant,,ENST00000581428,;TCAP,downstream_gene_variant,,ENST00000578283,;PGAP3,downstream_gene_variant,,ENST00000309862,;PGAP3,downstream_gene_variant,,ENST00000584620,;PGAP3,downstream_gene_variant,,ENST00000577337,;PGAP3,downstream_gene_variant,,ENST00000580898,;PGAP3,downstream_gene_variant,,ENST00000582276,; A ENST00000269582 Transcript missense_variant 897/1253 579/849 193/282 S/R agC/agA 1 1 PNMT HGNC HGNC:9160 protein_coding YES CCDS11343.1 ENSP00000269582 P11086 UPI0000111BE4 NM_002686.4 deleterious(0) 3/3 PROSITE_profiles:PS51681,hmmpanther:PTHR10867,hmmpanther:PTHR10867:SF18,Gene3D:3.40.50.150,PIRSF_domain:PIRSF000384,Pfam_domain:PF01234,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 39670119 39670119 C A 1 0 0 0 0 1 0 0 0 12267 796 28 2 2 PNMT 17 39670119 Missense_Mutation SNP C C3N-00175_T 452188 39670119 43587322 1097 10689 42 2 PNMT 0 . GRCh38 17 39670123 39670123 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.583C>A p.Gln195Lys p.Q195K ENST00000269582 3/3 275 257 18 281 280 1 strelka-varscan-mutect PNMT,missense_variant,p.Gln195Lys,ENST00000269582,NM_002686.4;PNMT,missense_variant,p.Gln97Lys,ENST00000394246,;PGAP3,downstream_gene_variant,,ENST00000300658,NM_033419.4;PGAP3,downstream_gene_variant,,ENST00000378011,NM_001291726.1;PGAP3,downstream_gene_variant,,ENST00000579146,NM_001291733.1;TCAP,downstream_gene_variant,,ENST00000309889,NM_003673.3;PGAP3,downstream_gene_variant,,ENST00000619169,;PGAP3,downstream_gene_variant,,ENST00000429199,NM_001291728.1;PNMT,downstream_gene_variant,,ENST00000581428,;TCAP,downstream_gene_variant,,ENST00000578283,;PGAP3,downstream_gene_variant,,ENST00000309862,;PGAP3,downstream_gene_variant,,ENST00000584620,;PGAP3,downstream_gene_variant,,ENST00000577337,;PGAP3,downstream_gene_variant,,ENST00000580898,;PGAP3,downstream_gene_variant,,ENST00000582276,; A ENST00000269582 Transcript missense_variant 901/1253 583/849 195/282 Q/K Cag/Aag 1 1 PNMT HGNC HGNC:9160 protein_coding YES CCDS11343.1 ENSP00000269582 P11086 UPI0000111BE4 NM_002686.4 tolerated(0.31) 3/3 PROSITE_profiles:PS51681,hmmpanther:PTHR10867,hmmpanther:PTHR10867:SF18,Gene3D:3.40.50.150,PIRSF_domain:PIRSF000384,Pfam_domain:PF01234,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 39670123 39670123 C A 1 0 0 0 0 1 0 0 0 12267 827 29 2 2 PNMT 17 39670123 Missense_Mutation SNP C C3N-00175_T 4 39670123 43587318 1098 10690 42 2 KRTAP4-9 0 . GRCh38 17 41105495 41105495 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.107G>T p.Arg36Met p.R36M ENST00000391415 1/1 345 214 131 324 324 0 strelka-varscan-mutect KRTAP4-9,missense_variant,p.Arg36Met,ENST00000391415,NM_001146041.1;KRTAP4-9,missense_variant,p.Arg36Met,ENST00000617453,;KRTAP4-7,intron_variant,,ENST00000612231,;KRTAP4-16,upstream_gene_variant,,ENST00000440582,; T ENST00000391415 Transcript missense_variant 164/1157 107/633 36/210 R/M aGg/aTg COSM3517232 1 1 KRTAP4-9 HGNC HGNC:18910 protein_coding YES CCDS54124.1 ENSP00000375234 Q9BYQ8 UPI000021D2D3 NM_001146041.1 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF1,Pfam_domain:PF01500 1 MODERATE 1 SNV 1 1 PASS rs1265504276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41105495 41105495 G T 1 0 0 0 0 1 0 0 0 8452 1000 35 2 2 KRTAP4-9 17 41105495 Missense_Mutation SNP G C3N-00175_T 1435372 41105495 42151946 1099 10691 KRTAP4-6 0 . GRCh38 17 41140397 41140397 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.91T>A p.Cys31Ser p.C31S ENST00000345847 1/1 351 299 52 299 299 0 strelka-varscan-mutect KRTAP4-6,missense_variant,p.Cys31Ser,ENST00000345847,NM_030976.1; T ENST00000345847 Transcript missense_variant 91/1055 91/618 31/205 C/S Tgc/Agc 1 -1 KRTAP4-6 HGNC HGNC:18909 protein_coding YES CCDS54125.1 ENSP00000328270 Q9BYQ5 UPI00006C17B9 NM_030976.1 deleterious(0.03) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF60,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs1322824012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41140397 41140397 A T 1 0 0 0 0 1 0 0 0 8449 188 7 4 4 KRTAP4-6 17 41140397 Missense_Mutation SNP A C3N-00175_T 34902 41140397 42117044 1100 10692 KRTAP9-4 0 . GRCh38 17 41250181 41250181 + Missense_Mutation SNP G G T rs751541274 C3N-00175_T C3N-00175_N G G c.461G>T p.Cys154Phe p.C154F ENST00000334109 1/1 240 145 95 217 216 1 strelka-varscan-mutect KRTAP9-4,missense_variant,p.Cys154Phe,ENST00000334109,NM_033191.2; T ENST00000334109 Transcript missense_variant 495/967 461/465 154/154 C/F tGc/tTc rs751541274 1 1 KRTAP9-4 HGNC HGNC:18902 protein_coding YES CCDS11386.1 ENSP00000334922 Q9BYQ2 UPI000013F6DA NM_033191.2 deleterious(0) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF65,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS rs751541274 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41250181 41250181 G T 1 0 0 0 0 1 0 0 0 8472 1319 46 2 2 KRTAP9-4 17 41250181 Missense_Mutation SNP G C3N-00175_T 109784 41250181 42007260 1101 10693 KRTAP9-7 0 . GRCh38 17 41275926 41275926 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.229A>G p.Ser77Gly p.S77G ENST00000391354 1/1 419 281 138 390 390 0 strelka-varscan-mutect KRTAP9-7,missense_variant,p.Ser77Gly,ENST00000391354,NM_001277332.1;KRTAP9-11P,downstream_gene_variant,,ENST00000431013,;KRTAP9-10P,upstream_gene_variant,,ENST00000435672,; G ENST00000391354 Transcript missense_variant 268/1039 229/510 77/169 S/G Agc/Ggc 1 1 KRTAP9-7 HGNC HGNC:18915 protein_coding YES CCDS59287.1 ENSP00000375149 A8MTY7 UPI0000DD83F7 NM_001277332.1 tolerated(0.37) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF56,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs1260108062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 41275926 41275926 A G 1 0 0 0 0 1 0 0 0 8474 188 7 5 5 KRTAP9-7 17 41275926 Missense_Mutation SNP A C3N-00175_T 25745 41275926 41981515 1102 10694 KRT13 0 . GRCh38 17 41505106 41505106 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.445G>A p.Glu149Lys p.E149K ENST00000246635 1/8 219 186 33 205 205 0 strelka-varscan-mutect KRT13,missense_variant,p.Glu149Lys,ENST00000246635,NM_153490.2;KRT13,missense_variant,p.Glu149Lys,ENST00000336861,NM_002274.3;KRT13,missense_variant,p.Glu149Lys,ENST00000587544,;KRT13,missense_variant,p.Glu42Lys,ENST00000590425,;KRT13,intron_variant,,ENST00000587435,;AC019349.5,downstream_gene_variant,,ENST00000411759,;KRT13,upstream_gene_variant,,ENST00000587118,;KRT13,upstream_gene_variant,,ENST00000475217,;KRT13,3_prime_UTR_variant,,ENST00000464634,;KRT13,non_coding_transcript_exon_variant,,ENST00000468313,; T ENST00000246635 Transcript missense_variant 492/1699 445/1377 149/458 E/K Gag/Aag 1 -1 KRT13 HGNC HGNC:6415 protein_coding YES CCDS11396.1 ENSP00000246635 P13646 UPI000013CBF6 NM_153490.2 tolerated(0.68) 1/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF121,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41505106 41505106 C T 1 0 0 0 0 1 0 0 0 8332 835 29 3 3 KRT13 17 41505106 Missense_Mutation SNP C C3N-00175_T 229180 41505106 41752335 1103 10695 ACLY 0 . GRCh38 17 41867819 41867819 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.3297G>C p.Met1099Ile p.M1099I ENST00000352035 29/29 145 136 9 99 99 0 strelka-varscan-mutect ACLY,missense_variant,p.Met1099Ile,ENST00000352035,NM_001303274.1,NM_001096.2;ACLY,missense_variant,p.Met1089Ile,ENST00000353196,NM_001303275.1,NM_198830.1;ACLY,missense_variant,p.Met1099Ile,ENST00000590151,;ACLY,missense_variant,p.Met1089Ile,ENST00000393896,;ACLY,missense_variant,p.Met828Ile,ENST00000537919,;KLHL11,upstream_gene_variant,,ENST00000319121,NM_018143.2;RP11-229E13.4,downstream_gene_variant,,ENST00000619176,;ACLY,non_coding_transcript_exon_variant,,ENST00000588779,; G ENST00000352035 Transcript missense_variant 3428/4339 3297/3306 1099/1101 M/I atG/atC 1 -1 ACLY HGNC HGNC:115 protein_coding YES CCDS11412.1 ENSP00000253792 P53396 A0A024R1T9 UPI000013CDF3 NM_001303274.1,NM_001096.2 deleterious_low_confidence(0.03) 29/29 PIRSF_domain:PIRSF036511,hmmpanther:PTHR23118 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 41867819 41867819 C G 1 0 0 0 0 1 0 0 0 185 826 29 4 4 ACLY 17 41867819 Missense_Mutation SNP C C3N-00175_T 362713 41867819 41389622 1104 10696 CCR10 0 . GRCh38 17 42679706 42679706 + Silent SNP G G A rs761722420 C3N-00175_T C3N-00175_N G G c.936C>T p.= p.F312F ENST00000332438 2/2 46 38 8 40 40 0 strelka-varscan-mutect CCR10,synonymous_variant,p.=,ENST00000591765,;CCR10,synonymous_variant,p.=,ENST00000332438,NM_016602.2;CNTNAP1,upstream_gene_variant,,ENST00000264638,NM_003632.2;PLEKHH3,upstream_gene_variant,,ENST00000293349,;PLEKHH3,upstream_gene_variant,,ENST00000591022,NM_024927.4;PLEKHH3,upstream_gene_variant,,ENST00000587627,;CCR10,downstream_gene_variant,,ENST00000591568,;CTD-3193K9.3,downstream_gene_variant,,ENST00000592440,;CTD-3193K9.4,upstream_gene_variant,,ENST00000593139,;PLEKHH3,upstream_gene_variant,,ENST00000456950,;PLEKHH3,upstream_gene_variant,,ENST00000591544,;CNTNAP1,upstream_gene_variant,,ENST00000591662,;PLEKHH3,upstream_gene_variant,,ENST00000591490,;PLEKHH3,upstream_gene_variant,,ENST00000591196,; A ENST00000332438 Transcript synonymous_variant 956/1773 936/1089 312/362 F ttC/ttT rs761722420 1 -1 CCR10 HGNC HGNC:4474 protein_coding YES CCDS11435.1 ENSP00000332504 P46092 UPI0000212EE9 NM_016602.2 2/2 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF726,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00657,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs761722420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 42679706 42679706 G A 1 0 0 0 0 0 0 0 1 2640 1165 41 3 3 CCR10 17 42679706 Silent SNP G C3N-00175_T 811887 42679706 40577735 1105 10697 CD300LG 0 . GRCh38 17 43857138 43857138 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.867G>T p.Lys289Asn p.K289N ENST00000317310 6/7 262 168 94 254 254 0 strelka-varscan-mutect CD300LG,missense_variant,p.Lys289Asn,ENST00000317310,NM_145273.3;CD300LG,missense_variant,p.Lys289Asn,ENST00000539718,NM_001168322.1;CD300LG,missense_variant,p.Lys255Asn,ENST00000377203,NM_001168323.1;CD300LG,missense_variant,p.Lys204Asn,ENST00000293396,NM_001168324.1;CD300LG,missense_variant,p.Lys204Asn,ENST00000586233,;CD300LG,downstream_gene_variant,,ENST00000589212,; T ENST00000317310 Transcript missense_variant 908/2758 867/999 289/332 K/N aaG/aaT COSM979810 1 1 CD300LG HGNC HGNC:30455 protein_coding YES CCDS11470.1 ENSP00000321005 Q6UXG3 UPI000013E104 NM_145273.3 deleterious(0.04) 6/7 hmmpanther:PTHR11860,hmmpanther:PTHR11860:SF22 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43857138 43857138 G T 1 0 0 0 0 1 0 0 0 2706 1020 36 2 2 CD300LG 17 43857138 Missense_Mutation SNP G C3N-00175_T 1177432 43857138 39400303 1106 10698 ITGA2B 0 . GRCh38 17 44380647 44380647 + Splice_Site SNP T T C novel C3N-00175_T C3N-00175_N T T c.1394-2A>G p.X465_splice ENST00000262407 685 430 255 706 706 0 strelka-varscan-mutect ITGA2B,splice_acceptor_variant,,ENST00000262407,NM_000419.3;ITGA2B,upstream_gene_variant,,ENST00000587295,;ITGA2B,splice_acceptor_variant,,ENST00000592462,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592226,;ITGA2B,downstream_gene_variant,,ENST00000589645,;ITGA2B,downstream_gene_variant,,ENST00000591990,;ITGA2B,downstream_gene_variant,,ENST00000592944,;ITGA2B,downstream_gene_variant,,ENST00000592253,;ITGA2B,downstream_gene_variant,,ENST00000592075,; C ENST00000262407 Transcript splice_acceptor_variant -/3333 1394/3120 465/1039 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 13/29 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 39 44380647 44380647 T C 1 0 0 0 0 0 0 1 0 7783 1536 53 5 5 ITGA2B 17 44380647 Splice_Site SNP T C3N-00175_T 523509 44380647 38876794 1107 10699 GPATCH8 0 . GRCh38 17 44401218 44401218 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.859A>G p.Ile287Val p.I287V ENST00000591680 8/8 244 157 87 172 172 0 strelka-varscan-mutect GPATCH8,missense_variant,p.Ile287Val,ENST00000591680,NM_001304939.1,NM_001002909.3;GPATCH8,downstream_gene_variant,,ENST00000585614,;GPATCH8,3_prime_UTR_variant,,ENST00000587228,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000335500,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000635257,;GPATCH8,downstream_gene_variant,,ENST00000590041,; C ENST00000591680 Transcript missense_variant 890/4692 859/4509 287/1502 I/V Att/Gtt 1 -1 GPATCH8 HGNC HGNC:29066 protein_coding YES CCDS32666.1 ENSP00000467556 Q9UKJ3 UPI0000237985 NM_001304939.1,NM_001002909.3 tolerated(0.25) 8/8 hmmpanther:PTHR17614:SF11,hmmpanther:PTHR17614 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 44401218 44401218 T C 1 0 0 0 0 1 0 0 0 6495 1464 51 5 5 GPATCH8 17 44401218 Missense_Mutation SNP T C3N-00175_T 20571 44401218 38856223 1108 10700 GPATCH8 0 . GRCh38 17 44464508 44464508 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.157T>A p.Trp53Arg p.W53R ENST00000591680 3/8 475 309 166 389 389 0 strelka-varscan-mutect GPATCH8,missense_variant,p.Trp53Arg,ENST00000591680,NM_001304939.1,NM_001002909.3;GPATCH8,missense_variant,p.Trp28Arg,ENST00000585614,;GPATCH8,3_prime_UTR_variant,,ENST00000587228,;GPATCH8,3_prime_UTR_variant,,ENST00000590041,;GPATCH8,3_prime_UTR_variant,,ENST00000592746,;GPATCH8,3_prime_UTR_variant,,ENST00000586037,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000335500,; T ENST00000591680 Transcript missense_variant 188/4692 157/4509 53/1502 W/R Tgg/Agg 1 -1 GPATCH8 HGNC HGNC:29066 protein_coding YES CCDS32666.1 ENSP00000467556 Q9UKJ3 UPI0000237985 NM_001304939.1,NM_001002909.3 deleterious_low_confidence(0) 3/8 Low_complexity_(Seg):seg,PROSITE_profiles:PS50174,hmmpanther:PTHR17614:SF11,hmmpanther:PTHR17614,Pfam_domain:PF01585,SMART_domains:SM00443 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44464508 44464508 A T 1 0 0 0 0 1 0 0 0 6495 159 6 4 4 GPATCH8 17 44464508 Missense_Mutation SNP A C3N-00175_T 63290 44464508 38792933 1109 10701 TBX21 0 . GRCh38 17 47744970 47744970 + Missense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.1212G>A p.Met404Ile p.M404I ENST00000177694 6/6 316 297 19 340 340 0 strelka-varscan-mutect TBX21,missense_variant,p.Met404Ile,ENST00000177694,NM_013351.1;TBX21,downstream_gene_variant,,ENST00000581328,; A ENST00000177694 Transcript missense_variant 1423/2572 1212/1608 404/535 M/I atG/atA COSM5204040 1 1 TBX21 HGNC HGNC:11599 protein_coding YES CCDS11514.1 ENSP00000177694 Q9UL17 UPI0000001C88 NM_013351.1 tolerated(0.08) 6/6 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF125 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 47744970 47744970 G A 1 0 0 0 0 1 0 0 0 16062 1290 45 3 3 TBX21 17 47744970 Missense_Mutation SNP G C3N-00175_T 3280462 47744970 35512471 1110 10702 OSBPL7 0 . GRCh38 17 47808343 47808343 + Missense_Mutation SNP C C A rs774434828 C3N-00175_T C3N-00175_N C C c.2477G>T p.Arg826Met p.R826M ENST00000007414 23/23 214 123 91 202 202 0 strelka-varscan-mutect OSBPL7,missense_variant,p.Arg826Met,ENST00000007414,NM_145798.2;OSBPL7,missense_variant,p.Arg826Met,ENST00000392507,;OSBPL7,3_prime_UTR_variant,,ENST00000613735,;OSBPL7,3_prime_UTR_variant,,ENST00000579728,;OSBPL7,3_prime_UTR_variant,,ENST00000578461,;OSBPL7,non_coding_transcript_exon_variant,,ENST00000583167,; A ENST00000007414 Transcript missense_variant 2669/3640 2477/2529 826/842 R/M aGg/aTg rs774434828 1 -1 OSBPL7 HGNC HGNC:16387 protein_coding YES CCDS11515.1 ENSP00000007414 Q9BZF2 UPI0000130E98 NM_145798.2 deleterious(0.03) 23/23 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF85,Superfamily_domains:0051579 MODERATE 1 SNV 1 1 PASS rs774434828 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 47808343 47808343 C A 1 0 0 0 0 1 0 0 0 11348 681 24 2 2 OSBPL7 17 47808343 Missense_Mutation SNP C C3N-00175_T 63373 47808343 35449098 1111 10703 OSBPL7 0 . GRCh38 17 47808586 47808586 + Missense_Mutation SNP C C A rs201378531 C3N-00175_T C3N-00175_N C C c.2372G>T p.Arg791Leu p.R791L ENST00000007414 22/23 177 112 65 178 177 1 strelka-varscan-mutect OSBPL7,missense_variant,p.Arg791Leu,ENST00000007414,NM_145798.2;OSBPL7,missense_variant,p.Arg791Leu,ENST00000392507,;OSBPL7,3_prime_UTR_variant,,ENST00000613735,;OSBPL7,3_prime_UTR_variant,,ENST00000579728,;OSBPL7,3_prime_UTR_variant,,ENST00000578461,;OSBPL7,non_coding_transcript_exon_variant,,ENST00000583167,; A ENST00000007414 Transcript missense_variant 2564/3640 2372/2529 791/842 R/L cGc/cTc rs201378531 1 -1 OSBPL7 HGNC HGNC:16387 protein_coding YES CCDS11515.1 ENSP00000007414 Q9BZF2 UPI0000130E98 NM_145798.2 deleterious(0) 22/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF85,Pfam_domain:PF01237,Superfamily_domains:0051579 MODERATE 1 SNV 1 1 PASS rs201378531 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 47808586 47808586 C A 1 0 0 0 0 1 0 0 0 11348 768 27 1 1 OSBPL7 17 47808586 Missense_Mutation SNP C C3N-00175_T 243 47808586 35448855 1112 10704 ABI3 0 . GRCh38 17 49217857 49217857 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.404C>A p.Pro135His p.P135H ENST00000225941 3/8 129 103 26 121 121 0 strelka-varscan-mutect ABI3,missense_variant,p.Pro135His,ENST00000225941,NM_016428.2;ABI3,missense_variant,p.Pro129His,ENST00000419580,NM_001135186.1;ABI3,upstream_gene_variant,,ENST00000571035,;ABI3,upstream_gene_variant,,ENST00000573347,; A ENST00000225941 Transcript missense_variant 902/2109 404/1101 135/366 P/H cCc/cAc 1 1 ABI3 HGNC HGNC:29859 protein_coding YES CCDS11546.1 ENSP00000225941 Q9P2A4 UPI000013C888 NM_016428.2 tolerated(0.06) 3/8 hmmpanther:PTHR10460:SF7,hmmpanther:PTHR10460,Pfam_domain:PF07815 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 49217857 49217857 C A 1 0 0 0 0 1 0 0 0 100 623 22 2 2 ABI3 17 49217857 Missense_Mutation SNP C C3N-00175_T 1409271 49217857 34039584 1113 10705 SPATA20 0 . GRCh38 17 50554426 50554426 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.2133A>T p.= p.S711S ENST00000006658 15/17 369 306 63 341 340 1 strelka-varscan-mutect SPATA20,synonymous_variant,p.=,ENST00000619622,NM_001258373.1;SPATA20,synonymous_variant,p.=,ENST00000006658,NM_022827.3;SPATA20,synonymous_variant,p.=,ENST00000356488,NM_001258372.1;SPATA20,synonymous_variant,p.=,ENST00000634597,;CACNA1G-AS1,downstream_gene_variant,,ENST00000505793,;CACNA1G-AS1,downstream_gene_variant,,ENST00000505495,;CACNA1G-AS1,downstream_gene_variant,,ENST00000508920,;SPATA20,3_prime_UTR_variant,,ENST00000504334,;SPATA20,3_prime_UTR_variant,,ENST00000503127,;SPATA20,3_prime_UTR_variant,,ENST00000511937,;SPATA20,non_coding_transcript_exon_variant,,ENST00000503063,;SPATA20,downstream_gene_variant,,ENST00000635113,;SPATA20,downstream_gene_variant,,ENST00000505559,;SPATA20,downstream_gene_variant,,ENST00000512181,;SPATA20,downstream_gene_variant,,ENST00000511347,;SPATA20,downstream_gene_variant,,ENST00000505656,;SPATA20,downstream_gene_variant,,ENST00000504265,;SPATA20,downstream_gene_variant,,ENST00000515619,;SPATA20,downstream_gene_variant,,ENST00000504271,;SPATA20,downstream_gene_variant,,ENST00000513618,;SPATA20,downstream_gene_variant,,ENST00000508528,; T ENST00000006658 Transcript synonymous_variant 2253/2719 2133/2409 711/802 S tcA/tcT 1 1 SPATA20 HGNC HGNC:26125 protein_coding YES CCDS11571.1 ENSP00000006658 Q8TB22 UPI000006CE23 NM_022827.3 15/17 PIRSF_domain:PIRSF006402,hmmpanther:PTHR12145,hmmpanther:PTHR12145:SF11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 50554426 50554426 A T 1 0 0 0 0 0 0 0 1 15336 175 7 4 4 SPATA20 17 50554426 Silent SNP A C3N-00175_T 1336569 50554426 32703015 1114 10706 CACNA1G 0 . GRCh38 17 50572038 50572038 + Splice_Site SNP G G A novel C3N-00175_T C3N-00175_N G G c.746+1G>A p.X249_splice ENST00000359106 87 73 14 56 56 0 strelka-varscan-mutect CACNA1G,splice_donor_variant,,ENST00000354983,NM_198396.2;CACNA1G,splice_donor_variant,,ENST00000352832,NM_198387.2;CACNA1G,splice_donor_variant,,ENST00000359106,NM_018896.4;CACNA1G,splice_donor_variant,,ENST00000360761,NM_198382.2;CACNA1G,splice_donor_variant,,ENST00000442258,NM_198388.2;CACNA1G,splice_donor_variant,,ENST00000429973,NM_198386.2;CACNA1G,splice_donor_variant,,ENST00000507336,NM_198377.2;CACNA1G,splice_donor_variant,,ENST00000358244,NM_198376.2;CACNA1G,splice_donor_variant,,ENST00000507510,NM_198385.2;CACNA1G,splice_donor_variant,,ENST00000515765,NM_198380.2;CACNA1G,splice_donor_variant,,ENST00000515411,NM_001256324.1;CACNA1G,splice_donor_variant,,ENST00000502264,NM_198383.2;CACNA1G,splice_donor_variant,,ENST00000510115,NM_198379.2;CACNA1G,splice_donor_variant,,ENST00000514079,NM_001256325.1;CACNA1G,splice_donor_variant,,ENST00000513689,NM_001256326.1;CACNA1G,splice_donor_variant,,ENST00000515165,NM_198384.2;CACNA1G,splice_donor_variant,,ENST00000507609,NM_001256327.1;CACNA1G,splice_donor_variant,,ENST00000512389,NM_198378.2;CACNA1G,splice_donor_variant,,ENST00000514181,NM_001256328.1;CACNA1G,splice_donor_variant,,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,splice_donor_variant,,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,splice_donor_variant,,ENST00000510366,NM_001256331.1;CACNA1G,splice_donor_variant,,ENST00000514717,NM_001256332.1;CACNA1G,splice_donor_variant,,ENST00000505165,NM_001256333.1;CACNA1G,splice_donor_variant,,ENST00000507896,NM_001256334.1;CACNA1G,splice_donor_variant,,ENST00000416767,;CACNA1G,splice_donor_variant,,ENST00000570567,;CACNA1G,splice_donor_variant,,ENST00000506406,;CACNA1G,splice_donor_variant,,ENST00000504076,;CACNA1G,splice_donor_variant,,ENST00000511765,;CACNA1G,splice_donor_variant,,ENST00000503436,;CACNA1G,splice_donor_variant,,ENST00000511768,;CACNA1G,splice_donor_variant,,ENST00000503607,; A ENST00000359106 Transcript splice_donor_variant -/7648 746/7134 249/2377 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 5/37 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 39 50572038 50572038 G A 1 0 0 0 0 0 0 1 0 2232 1391 48 3 3 CACNA1G 17 50572038 Splice_Site SNP G C3N-00175_T 17612 50572038 32685403 1115 10707 KIF2B 0 . GRCh38 17 53824880 53824880 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.1847C>A p.Ser616Tyr p.S616Y ENST00000268919 1/1 140 107 33 133 133 0 strelka-varscan-mutect KIF2B,missense_variant,p.Ser616Tyr,ENST00000268919,NM_032559.4; A ENST00000268919 Transcript missense_variant 1980/2313 1847/2022 616/673 S/Y tCt/tAt COSM5013205 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 deleterious(0) 1/1 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524 1 MODERATE 1 SNV 1 1 PASS rs1457271736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 53824880 53824880 C A 1 0 0 0 0 1 0 0 0 8163 913 32 2 2 KIF2B 17 53824880 Missense_Mutation SNP C C3N-00175_T 3252842 53824880 29432561 1116 10708 TEX14 0 . GRCh38 17 58599129 58599129 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2234C>A p.Thr745Lys p.T745K ENST00000240361 14/33 440 369 71 399 398 1 strelka-varscan-mutect TEX14,missense_variant,p.Thr739Lys,ENST00000389934,NM_198393.3;TEX14,missense_variant,p.Thr745Lys,ENST00000240361,NM_001201457.1;TEX14,missense_variant,p.Thr739Lys,ENST00000349033,NM_031272.4;TEX14,3_prime_UTR_variant,,ENST00000582740,; T ENST00000240361 Transcript missense_variant 2320/4911 2234/4494 745/1497 T/K aCa/aAa 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 tolerated(0.05) 14/33 hmmpanther:PTHR23060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 58599129 58599129 G T 1 0 0 0 0 1 0 0 0 16200 1377 48 2 2 TEX14 17 58599129 Missense_Mutation SNP G C3N-00175_T 4774249 58599129 24658312 1117 10709 TUBD1 0 . GRCh38 17 59866648 59866648 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1036G>T p.Val346Phe p.V346F ENST00000325752 7/9 170 111 59 161 161 0 strelka-varscan-mutect TUBD1,missense_variant,p.Val346Phe,ENST00000325752,NM_016261.3;TUBD1,missense_variant,p.Val291Phe,ENST00000340993,NM_001193609.1,NM_001193612.1;TUBD1,missense_variant,p.Val346Phe,ENST00000394239,NM_001193610.1;TUBD1,missense_variant,p.Val92Phe,ENST00000346141,;TUBD1,missense_variant,p.Val346Phe,ENST00000592426,;TUBD1,missense_variant,p.Val130Phe,ENST00000539018,NM_001193613.1;TUBD1,intron_variant,,ENST00000613721,NM_001193611.1;TUBD1,intron_variant,,ENST00000376094,;TUBD1,3_prime_UTR_variant,,ENST00000591548,;TUBD1,3_prime_UTR_variant,,ENST00000593110,;TUBD1,non_coding_transcript_exon_variant,,ENST00000588009,; A ENST00000325752 Transcript missense_variant 1324/2490 1036/1362 346/453 V/F Gtc/Ttc 1 -1 TUBD1 HGNC HGNC:16811 protein_coding YES CCDS11620.1 ENSP00000320797 Q9UJT1 UPI000013D7FA NM_016261.3 tolerated(0.06) 7/9 hmmpanther:PTHR11588:SF4,hmmpanther:PTHR11588,Superfamily_domains:SSF55307 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 59866648 59866648 C A 1 0 0 0 0 1 0 0 0 17272 507 18 2 2 TUBD1 17 59866648 Missense_Mutation SNP C C3N-00175_T 1267519 59866648 23390793 1118 10710 TACO1 0 . GRCh38 17 63604559 63604559 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.306C>G p.Asn102Lys p.N102K ENST00000258975 2/5 537 336 201 446 446 0 strelka-varscan-mutect TACO1,missense_variant,p.Asn102Lys,ENST00000258975,NM_016360.3;TACO1,non_coding_transcript_exon_variant,,ENST00000581120,; G ENST00000258975 Transcript missense_variant 518/1469 306/894 102/297 N/K aaC/aaG 1 1 TACO1 HGNC HGNC:24316 protein_coding YES CCDS11640.1 ENSP00000258975 Q9BSH4 UPI0000042223 NM_016360.3 deleterious(0) 2/5 HAMAP:MF_00693,hmmpanther:PTHR12532:SF5,hmmpanther:PTHR12532,Pfam_domain:PF01709,Gene3D:1.10.10.200,Superfamily_domains:SSF75625 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 63604559 63604559 C G 1 0 0 0 0 1 0 0 0 15900 477 17 4 4 TACO1 17 63604559 Missense_Mutation SNP C C3N-00175_T 3737911 63604559 19652882 1119 10711 CEP95 0 . GRCh38 17 64530981 64530981 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1502T>A p.Ile501Asn p.I501N ENST00000556440 13/20 91 82 9 85 85 0 strelka-varscan-mutect CEP95,missense_variant,p.Ile501Asn,ENST00000556440,NM_138363.1;CEP95,missense_variant,p.Ile436Asn,ENST00000553412,;CEP95,intron_variant,,ENST00000583457,;CEP95,non_coding_transcript_exon_variant,,ENST00000577476,;CEP95,3_prime_UTR_variant,,ENST00000553956,;CEP95,non_coding_transcript_exon_variant,,ENST00000579117,;CEP95,non_coding_transcript_exon_variant,,ENST00000584857,;CEP95,non_coding_transcript_exon_variant,,ENST00000579478,;CEP95,non_coding_transcript_exon_variant,,ENST00000579637,;CEP95,upstream_gene_variant,,ENST00000581885,;CEP95,upstream_gene_variant,,ENST00000580285,;CEP95,upstream_gene_variant,,ENST00000582698,; A ENST00000556440 Transcript missense_variant 2012/3139 1502/2466 501/821 I/N aTt/aAt 1 1 CEP95 HGNC HGNC:25141 protein_coding YES CCDS45763.1 ENSP00000450461 Q96GE4 UPI000006F4B3 NM_138363.1 tolerated(0.08) 13/20 hmmpanther:PTHR22545,hmmpanther:PTHR22545:SF0 MODERATE 1 SNV 1 1 PASS rs1221751011 . 0 208 0 2 0 0 0 0 -14.48917 0.9999998 1 1 1 0 A 3 1 39 64530981 64530981 T A 1 0 0 0 0 1 0 0 0 2988 1493 52 4 4 CEP95 17 64530981 Missense_Mutation SNP T C3N-00175_T 926422 64530981 18726460 1120 10712 RGS9 0 . GRCh38 17 65225359 65225359 + Missense_Mutation SNP G G T rs201578421 C3N-00175_T C3N-00175_N G G c.1765G>T p.Gly589Cys p.G589C ENST00000262406 18/19 439 289 150 339 339 0 strelka-varscan-mutect RGS9,missense_variant,p.Gly586Cys,ENST00000449996,NM_001081955.2;RGS9,missense_variant,p.Gly589Cys,ENST00000262406,NM_003835.3;RGS9,missense_variant,p.Gly589Cys,ENST00000635833,;RGS9,missense_variant,p.Gly586Cys,ENST00000443584,NM_001165933.1;RGS9,3_prime_UTR_variant,,ENST00000584234,;RGS9,non_coding_transcript_exon_variant,,ENST00000577595,; T ENST00000262406 Transcript missense_variant 1832/2375 1765/2025 589/674 G/C Ggc/Tgc rs201578421 1 1 RGS9 HGNC HGNC:10004 protein_coding YES CCDS42373.1 ENSP00000262406 O75916 UPI000013382A NM_003835.3 deleterious_low_confidence(0) 18/19 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF170 MODERATE 1 SNV 1 1 PASS rs201578421 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 65225359 65225359 G T 1 0 0 0 0 1 0 0 0 13484 1000 35 2 2 RGS9 17 65225359 Missense_Mutation SNP G C3N-00175_T 694378 65225359 18032082 1121 10713 ABCA6 0 . GRCh38 17 69087377 69087377 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.3795T>A p.= p.A1265A ENST00000284425 29/39 203 133 70 190 190 0 strelka-varscan-mutect ABCA6,synonymous_variant,p.=,ENST00000284425,NM_080284.2;ABCA6,non_coding_transcript_exon_variant,,ENST00000446604,;ABCA6,non_coding_transcript_exon_variant,,ENST00000589482,; T ENST00000284425 Transcript synonymous_variant 3970/5300 3795/4854 1265/1617 A gcT/gcA 1 -1 ABCA6 HGNC HGNC:36 protein_coding YES CCDS11683.1 ENSP00000284425 Q8N139 UPI000013DD9D NM_080284.2 29/39 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 69087377 69087377 A T 1 0 0 0 0 0 0 0 1 40 291 11 4 4 ABCA6 17 69087377 Silent SNP A C3N-00175_T 3862018 69087377 14170064 1122 10714 SDK2 0 . GRCh38 17 73438044 73438044 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.836C>A p.Ala279Asp p.A279D ENST00000392650 7/45 199 103 96 190 190 0 strelka-varscan-mutect SDK2,missense_variant,p.Ala279Asp,ENST00000392650,NM_001144952.1;SDK2,upstream_gene_variant,,ENST00000479356,; T ENST00000392650 Transcript missense_variant 837/10723 836/6519 279/2172 A/D gCc/gAc 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 deleterious(0.01) 7/45 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 73438044 73438044 G T 1 0 0 0 0 1 0 0 0 14244 1203 42 2 2 SDK2 17 73438044 Missense_Mutation SNP G C3N-00175_T 4350667 73438044 9819397 1123 10715 GPR142 0 . GRCh38 17 74371991 74371991 + Silent SNP G G T rs762918019 C3N-00175_T C3N-00175_N G G c.780G>T p.= p.L260L ENST00000335666 4/4 145 78 67 154 154 0 strelka-varscan-mutect GPR142,synonymous_variant,p.=,ENST00000335666,NM_181790.1;GPR142,3_prime_UTR_variant,,ENST00000582579,;GPR142,downstream_gene_variant,,ENST00000585308,; T ENST00000335666 Transcript synonymous_variant 828/1437 780/1389 260/462 L ctG/ctT rs762918019 1 1 GPR142 HGNC HGNC:20088 protein_coding YES CCDS11698.1 ENSP00000335158 Q7Z601 UPI00001AA7F1 NM_181790.1 4/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF48,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs762918019 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 74371991 74371991 G T 1 0 0 0 0 0 0 0 1 6536 1364 48 2 2 GPR142 17 74371991 Silent SNP G C3N-00175_T 933947 74371991 8885450 1124 10716 SLC9A3R1 0 . GRCh38 17 74763420 74763420 + Silent SNP C C T rs147104235 C3N-00175_T C3N-00175_N C C c.657C>T p.= p.I219I ENST00000262613 3/6 182 172 10 144 144 0 strelka-varscan-mutect SLC9A3R1,synonymous_variant,p.=,ENST00000262613,NM_004252.4;SLC9A3R1,synonymous_variant,p.=,ENST00000413388,;SLC9A3R1,intron_variant,,ENST00000583369,;SLC9A3R1,non_coding_transcript_exon_variant,,ENST00000578958,;SLC9A3R1,upstream_gene_variant,,ENST00000581356,; T ENST00000262613 Transcript synonymous_variant 852/1969 657/1077 219/358 I atC/atT rs147104235,COSM1522375 1 1 SLC9A3R1 HGNC HGNC:11075 protein_coding YES CCDS11705.1 ENSP00000262613 O14745 UPI0000072521 NM_004252.4 3/6 Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF037866,PROSITE_profiles:PS50106,hmmpanther:PTHR14191,hmmpanther:PTHR14191:SF7,SMART_domains:SM00228,Superfamily_domains:SSF50156 0,1 LOW 1 SNV 1 0,1 1 PASS rs147104235 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 74763420 74763420 C T 1 0 0 0 0 0 0 0 1 14996 816 29 3 3 SLC9A3R1 17 74763420 Silent SNP C C3N-00175_T 391429 74763420 8494021 1125 10717 LLGL2 0 . GRCh38 17 75563805 75563805 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.880G>T p.Gly294Trp p.G294W ENST00000392550 9/26 306 269 37 256 256 0 strelka-varscan-mutect LLGL2,missense_variant,p.Gly294Trp,ENST00000392550,NM_001031803.1;LLGL2,missense_variant,p.Gly294Trp,ENST00000167462,NM_004524.2;LLGL2,missense_variant,p.Gly294Trp,ENST00000577200,;LLGL2,missense_variant,p.Gly294Trp,ENST00000578363,;LLGL2,missense_variant,p.Gly294Trp,ENST00000375227,NM_001015002.1;LLGL2,downstream_gene_variant,,ENST00000581713,;LLGL2,downstream_gene_variant,,ENST00000580578,;LLGL2,downstream_gene_variant,,ENST00000583658,;LLGL2,missense_variant,p.Gly12Trp,ENST00000578638,;LLGL2,splice_region_variant,,ENST00000545227,;LLGL2,splice_region_variant,,ENST00000580027,;LLGL2,upstream_gene_variant,,ENST00000577500,;LLGL2,downstream_gene_variant,,ENST00000582860,; T ENST00000392550 Transcript missense_variant,splice_region_variant 997/3509 880/3063 294/1020 G/W Ggg/Tgg 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 deleterious(0) 9/26 Pfam_domain:PF08366,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 75563805 75563805 G T 1 0 0 0 0 1 0 0 0 8758 1246 43 2 2 LLGL2 17 75563805 Missense_Mutation SNP G C3N-00175_T 800385 75563805 7693636 1126 10718 FBF1 0 . GRCh38 17 75920397 75920397 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1662G>T p.= p.L554L ENST00000627351 16/28 117 103 14 126 126 0 strelka-varscan-mutect FBF1,synonymous_variant,p.=,ENST00000586717,NM_001319193.1;FBF1,synonymous_variant,p.=,ENST00000319129,;FBF1,synonymous_variant,p.=,ENST00000636174,;FBF1,synonymous_variant,p.=,ENST00000592193,;FBF1,synonymous_variant,p.=,ENST00000627351,NM_001080542.1;FBF1,3_prime_UTR_variant,,ENST00000586838,;FBF1,non_coding_transcript_exon_variant,,ENST00000585990,;RP11-552F3.12,non_coding_transcript_exon_variant,,ENST00000593156,;FBF1,upstream_gene_variant,,ENST00000588283,; A ENST00000627351 Transcript synonymous_variant 1662/3402 1662/3402 554/1133 L ctG/ctT 1 -1 FBF1 HGNC HGNC:24674 protein_coding YES CCDS45779.1 ENSP00000486708 Q8TES7 UPI0000DD841F NM_001080542.1 16/28 hmmpanther:PTHR33689,hmmpanther:PTHR33689:SF1 LOW 1 SNV 5 1 PASS rs1340764605 . 0 204 3 3 0 0 0 0 -19.97655 0.9998724 1 1 1 0 A 2 1 39 75920397 75920397 C A 1 0 0 0 0 0 0 0 1 5557 697 25 2 2 FBF1 17 75920397 Silent SNP C C3N-00175_T 356592 75920397 7337044 1127 10719 UBE2O 0 . GRCh38 17 76390977 76390977 + Missense_Mutation SNP T T C novel C3N-00175_T C3N-00175_N T T c.3845A>G p.Glu1282Gly p.E1282G ENST00000319380 18/18 63 49 14 74 74 0 strelka-varscan-mutect UBE2O,missense_variant,p.Glu1282Gly,ENST00000319380,NM_022066.3;UBE2O,missense_variant,p.Glu797Gly,ENST00000587127,;SPHK1,downstream_gene_variant,,ENST00000545180,;SPHK1,downstream_gene_variant,,ENST00000323374,NM_182965.2;SPHK1,downstream_gene_variant,,ENST00000590959,NM_021972.3;SPHK1,downstream_gene_variant,,ENST00000592299,NM_001142601.1;SPHK1,downstream_gene_variant,,ENST00000392496,NM_001142602.1;SPHK1,downstream_gene_variant,,ENST00000588682,;SPHK1,downstream_gene_variant,,ENST00000590379,;SPHK1,downstream_gene_variant,,ENST00000591651,;UBE2O,downstream_gene_variant,,ENST00000586409,;SPHK1,downstream_gene_variant,,ENST00000591762,;SPHK1,downstream_gene_variant,,ENST00000587167,; C ENST00000319380 Transcript missense_variant 3910/5436 3845/3879 1282/1292 E/G gAg/gGg 1 -1 UBE2O HGNC HGNC:29554 protein_coding YES CCDS32742.1 ENSP00000323687 Q9C0C9 UPI000020032F NM_022066.3 tolerated_low_confidence(0.48) 18/18 hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF150 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 76390977 76390977 T C 1 0 0 0 0 1 0 0 0 17389 1551 54 5 5 UBE2O 17 76390977 Missense_Mutation SNP T C3N-00175_T 470580 76390977 6866464 1128 10720 BIRC5 0 . GRCh38 17 78223567 78223567 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.324G>T p.= p.R108R ENST00000374948 3/3 201 139 62 170 170 0 strelka-varscan-mutect BIRC5,synonymous_variant,p.=,ENST00000374948,NM_001012270.1;BIRC5,3_prime_UTR_variant,,ENST00000301633,NM_001012271.1;BIRC5,3_prime_UTR_variant,,ENST00000350051,NM_001168.2;BIRC5,downstream_gene_variant,,ENST00000587746,;BIRC5,downstream_gene_variant,,ENST00000592734,;BIRC5,non_coding_transcript_exon_variant,,ENST00000589892,;BIRC5,downstream_gene_variant,,ENST00000592115,;BIRC5,downstream_gene_variant,,ENST00000590925,;BIRC5,downstream_gene_variant,,ENST00000586192,;BIRC5,downstream_gene_variant,,ENST00000591800,; T ENST00000374948 Transcript synonymous_variant 377/2446 324/414 108/137 R cgG/cgT 1 1 BIRC5 HGNC HGNC:593 protein_coding CCDS32751.1 ENSP00000364086 O15392 UPI000006E9D2 NM_001012270.1 3/3 LOW SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 78223567 78223567 G T 1 0 0 0 0 0 0 0 1 1588 1161 41 2 2 BIRC5 17 78223567 Silent SNP G C3N-00175_T 1832590 78223567 5033874 1129 10721 RNF213 0 . GRCh38 17 80298513 80298513 + Silent SNP A A T C3N-00175_T C3N-00175_N A A c.2205A>T p.= p.L735L ENST00000582970 11/68 289 234 55 312 312 0 strelka-varscan-mutect RNF213,synonymous_variant,p.=,ENST00000582970,NM_001256071.2;RNF213,synonymous_variant,p.=,ENST00000508628,;RNF213,synonymous_variant,p.=,ENST00000319921,NM_020954.3;RNF213,non_coding_transcript_exon_variant,,ENST00000559070,;RNF213,non_coding_transcript_exon_variant,,ENST00000574060,; T ENST00000582970 Transcript synonymous_variant 2348/21055 2205/15624 735/5207 L ctA/ctT COSM5023876,COSM5023877,COSM5023878 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 11/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 80298513 80298513 A T 1 0 0 0 0 0 0 0 1 13656 434 15 4 4 RNF213 17 80298513 Silent SNP A C3N-00175_T 2074946 80298513 2958928 1130 10722 CEP131 0 . GRCh38 17 81193978 81193978 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2269G>T p.Glu757Ter p.E757* ENST00000450824 18/26 69 46 23 84 84 0 strelka-varscan-mutect CEP131,stop_gained,p.Glu760Ter,ENST00000269392,NM_001319228.1;CEP131,stop_gained,p.Glu757Ter,ENST00000450824,NM_014984.2;CEP131,stop_gained,p.Glu757Ter,ENST00000374782,NM_001319229.1,NM_001009811.2;CEP131,stop_gained,p.Glu760Ter,ENST00000575907,;CEP131,stop_gained,p.Glu196Ter,ENST00000573053,;CEP131,stop_gained,p.Glu18Ter,ENST00000570817,;CEP131,upstream_gene_variant,,ENST00000571292,;RP11-455O6.2,upstream_gene_variant,,ENST00000571085,; A ENST00000450824 Transcript stop_gained 2448/3543 2269/3243 757/1080 E/* Gag/Tag 1 -1 CEP131 HGNC HGNC:29511 protein_coding YES CCDS45808.1 ENSP00000393583 Q9UPN4 UPI00002017B6 NM_014984.2 18/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31540,hmmpanther:PTHR31540:SF1,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 81193978 81193978 C A 1 0 0 0 0 0 1 0 0 2959 864 30 2 2 CEP131 17 81193978 Nonsense_Mutation SNP C C3N-00175_T 895465 81193978 2063463 1131 10723 BAHCC1 0 . GRCh38 17 81443540 81443540 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2191G>T p.Gly731Cys p.G731C ENST00000584436 5/29 26 17 9 34 34 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Gly731Cys,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Gly731Cys,ENST00000307745,;BAHCC1,non_coding_transcript_exon_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 2558/10801 2191/7920 731/2639 G/C Ggc/Tgc 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0) 5/29 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 81443540 81443540 G T 1 0 0 0 0 1 0 0 0 1451 1232 43 2 2 BAHCC1 17 81443540 Missense_Mutation SNP G C3N-00175_T 249562 81443540 1813901 1132 10724 BAHCC1 0 . GRCh38 17 81447206 81447206 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.3427A>T p.Arg1143Trp p.R1143W ENST00000584436 12/29 72 50 22 89 89 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Arg1143Trp,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Arg1112Trp,ENST00000307745,;MIR3186,downstream_gene_variant,,ENST00000577404,;BAHCC1,downstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 3794/10801 3427/7920 1143/2639 R/W Agg/Tgg 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0.01) 12/29 hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 39 81447206 81447206 A T 1 0 0 0 0 1 0 0 0 1451 179 7 4 4 BAHCC1 17 81447206 Missense_Mutation SNP A C3N-00175_T 3666 81447206 1810235 1133 10725 NPLOC4 0 . GRCh38 17 81597276 81597276 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.962G>A p.Arg321Gln p.R321Q ENST00000331134 10/17 275 239 36 244 244 0 strelka-varscan-mutect NPLOC4,missense_variant,p.Arg321Gln,ENST00000374747,;NPLOC4,missense_variant,p.Arg321Gln,ENST00000331134,NM_017921.3;NPLOC4,non_coding_transcript_exon_variant,,ENST00000572351,;NPLOC4,3_prime_UTR_variant,,ENST00000574897,; T ENST00000331134 Transcript missense_variant 1178/4415 962/1827 321/608 R/Q cGa/cAa 1 -1 NPLOC4 HGNC HGNC:18261 protein_coding YES CCDS45812.1 ENSP00000331487 Q8TAT6 A0A024R8R4 UPI0000070BDD NM_017921.3 tolerated(0.51) 10/17 Pfam_domain:PF05021,PIRSF_domain:PIRSF010052,hmmpanther:PTHR12710 MODERATE 1 SNV 1 1 PASS rs1378278966 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 81597276 81597276 C T 1 0 0 0 0 1 0 0 0 10642 884 31 1 1 NPLOC4 17 81597276 Missense_Mutation SNP C C3N-00175_T 150070 81597276 1660165 1134 10726 CSNK1D 0 . GRCh38 17 82253111 82253111 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.470G>T p.Arg157Leu p.R157L ENST00000314028 4/9 613 393 220 677 677 0 strelka-varscan-mutect CSNK1D,missense_variant,p.Arg157Leu,ENST00000314028,NM_001893.4;CSNK1D,missense_variant,p.Arg157Leu,ENST00000392334,NM_139062.2;CSNK1D,missense_variant,p.Arg157Leu,ENST00000398519,;CSNK1D,missense_variant,p.Arg120Leu,ENST00000580446,;SLC16A3,intron_variant,,ENST00000583025,;CSNK1D,non_coding_transcript_exon_variant,,ENST00000578904,;CSNK1D,non_coding_transcript_exon_variant,,ENST00000582844,;RP13-516M14.8,downstream_gene_variant,,ENST00000624920,;CSNK1D,downstream_gene_variant,,ENST00000584472,;CSNK1D,downstream_gene_variant,,ENST00000578194,;CSNK1D,upstream_gene_variant,,ENST00000580565,;CSNK1D,missense_variant,p.Arg75Leu,ENST00000269361,;CSNK1D,non_coding_transcript_exon_variant,,ENST00000581241,;CSNK1D,non_coding_transcript_exon_variant,,ENST00000584377,;CSNK1D,intron_variant,,ENST00000403276,;CSNK1D,upstream_gene_variant,,ENST00000578501,;CSNK1D,upstream_gene_variant,,ENST00000580784,;CSNK1D,downstream_gene_variant,,ENST00000579316,;CSNK1D,upstream_gene_variant,,ENST00000581737,;CSNK1D,downstream_gene_variant,,ENST00000581660,;CSNK1D,upstream_gene_variant,,ENST00000581108,;CSNK1D,downstream_gene_variant,,ENST00000580061,;CSNK1D,downstream_gene_variant,,ENST00000585026,;CSNK1D,upstream_gene_variant,,ENST00000584672,;RP13-516M14.8,downstream_gene_variant,,ENST00000622924,; A ENST00000314028 Transcript missense_variant 820/3712 470/1248 157/415 R/L cGg/cTg 1 -1 CSNK1D HGNC HGNC:2452 protein_coding YES CCDS11805.1 ENSP00000324464 P48730 UPI000012DC64 NM_001893.4 deleterious_low_confidence(0) 4/9 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF175,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 82253111 82253111 C A 1 0 0 0 0 1 0 0 0 3752 652 23 1 1 CSNK1D 17 82253111 Missense_Mutation SNP C C3N-00175_T 655835 82253111 1004330 1135 10727 LAMA1 0 . GRCh38 18 6986187 6986187 + Frame_Shift_Del DEL C C - C3N-00175_T C3N-00175_N C C c.5329delG p.Glu1777LysfsTer13 p.E1777Kfs*13 ENST00000389658 37/63 284 192 92 306 306 0 sindel-varindel-pindel LAMA1,frameshift_variant,p.Glu1777LysfsTer13,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; - ENST00000389658 Transcript frameshift_variant 5423/9657 5329/9228 1777/3075 E/X Gaa/aa COSM3527439 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 37/63 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06008 1 HIGH 1 deletion 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 6986187 6986187 C - 1 0 1 0 1 0 0 0 0 8509 864 30 0 0 LAMA1 18 6986187 Frame_Shift_Del DEL C C3N-00175_T 6986187 73387098 1136 10728 LAMA1 0 . GRCh38 18 7037690 7037690 + Missense_Mutation SNP T T A rs760132767 C3N-00175_T C3N-00175_N T T c.1625A>T p.Gln542Leu p.Q542L ENST00000389658 12/63 438 325 113 498 498 0 strelka-varscan-mutect LAMA1,missense_variant,p.Gln542Leu,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,downstream_gene_variant,,ENST00000585178,; A ENST00000389658 Transcript missense_variant 1719/9657 1625/9228 542/3075 Q/L cAg/cTg rs760132767 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 tolerated(0.11) 12/63 PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299 MODERATE 1 SNV 2 1 PASS rs760132767 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 7037690 7037690 T A 1 0 0 0 0 1 0 0 0 8509 1580 55 4 4 LAMA1 18 7037690 Missense_Mutation SNP T C3N-00175_T 51503 7037690 73335595 1137 10729 LAMA1 0 . GRCh38 18 7042219 7042219 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1187C>A p.Pro396His p.P396H ENST00000389658 9/63 245 206 39 260 260 0 strelka-varscan-mutect LAMA1,missense_variant,p.Pro396His,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,upstream_gene_variant,,ENST00000585178,; T ENST00000389658 Transcript missense_variant 1281/9657 1187/9228 396/3075 P/H cCc/cAc 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 9/63 Gene3D:2.10.25.10,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 7042219 7042219 G T 1 0 0 0 0 1 0 0 0 8509 1232 43 2 2 LAMA1 18 7042219 Missense_Mutation SNP G C3N-00175_T 4529 7042219 73331066 1138 10730 LDLRAD4 0 . GRCh38 18 13643385 13643385 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.363C>G p.Ser121Arg p.S121R ENST00000359446 5/6 33 23 10 36 36 0 strelka-varscan-mutect LDLRAD4,missense_variant,p.Ser121Arg,ENST00000359446,NM_181481.4;LDLRAD4,missense_variant,p.Ser84Arg,ENST00000587757,NM_001003674.3;LDLRAD4,missense_variant,p.Ser44Arg,ENST00000585931,NM_001276249.1;LDLRAD4,missense_variant,p.Ser23Arg,ENST00000592991,NM_001276251.1;LDLRAD4,intron_variant,,ENST00000399848,NM_181482.4;LDLRAD4,intron_variant,,ENST00000586765,NM_001003675.3;RP11-701H16.4,downstream_gene_variant,,ENST00000588397,;LDLRAD4,non_coding_transcript_exon_variant,,ENST00000586207,;LDLRAD4,non_coding_transcript_exon_variant,,ENST00000361303,;LDLRAD4,intron_variant,,ENST00000435606,; G ENST00000359446 Transcript missense_variant 831/8486 363/921 121/306 S/R agC/agG 1 1 LDLRAD4 HGNC HGNC:1224 protein_coding YES CCDS32793.1 ENSP00000352420 O15165 UPI0000126BCF NM_181481.4 deleterious(0.04) 5/6 hmmpanther:PTHR16514:SF4,hmmpanther:PTHR16514 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 13643385 13643385 C G 1 0 0 0 0 1 0 0 0 8615 767 27 4 4 LDLRAD4 18 13643385 Missense_Mutation SNP C C3N-00175_T 6601166 13643385 66729900 1139 10731 KLHL14 0 . GRCh38 18 32677277 32677277 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1642C>A p.Gln548Lys p.Q548K ENST00000359358 8/9 148 133 15 160 160 0 strelka-varscan-mutect KLHL14,missense_variant,p.Gln548Lys,ENST00000359358,NM_020805.1; T ENST00000359358 Transcript missense_variant 2081/4312 1642/1887 548/628 Q/K Cag/Aag 1 -1 KLHL14 HGNC HGNC:29266 protein_coding YES CCDS32813.1 ENSP00000352314 Q9P2G3 UPI00001C1FF2 NM_020805.1 deleterious(0.01) 8/9 Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 32677277 32677277 G T 1 0 0 0 0 1 0 0 0 8234 1357 47 2 2 KLHL14 18 32677277 Missense_Mutation SNP G C3N-00175_T 19033892 32677277 47696008 1140 10732 NOL4 0 . GRCh38 18 33943086 33943086 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1521G>T p.Arg507Ser p.R507S ENST00000261592 9/11 120 100 20 174 172 2 strelka-varscan-mutect NOL4,missense_variant,p.Arg507Ser,ENST00000261592,NM_003787.4;NOL4,missense_variant,p.Arg433Ser,ENST00000538587,NM_001198547.1;NOL4,missense_variant,p.Arg427Ser,ENST00000590712,NM_001198546.1;NOL4,missense_variant,p.Arg222Ser,ENST00000535384,NM_001198549.1;NOL4,missense_variant,p.Arg192Ser,ENST00000586553,;NOL4,intron_variant,,ENST00000589544,NM_001198548.1;NOL4,3_prime_UTR_variant,,ENST00000586314,; A ENST00000261592 Transcript missense_variant 1819/3957 1521/1917 507/638 R/S agG/agT 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 deleterious(0.01) 9/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 33943086 33943086 C A 1 0 0 0 0 1 0 0 0 10567 854 30 2 2 NOL4 18 33943086 Missense_Mutation SNP C C3N-00175_T 1265809 33943086 46430199 1141 10733 DTNA 0 . GRCh38 18 34812111 34812111 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.601C>A p.Gln201Lys p.Q201K ENST00000598334 7/20 208 169 39 262 262 0 strelka-varscan-mutect DTNA,missense_variant,p.Gln201Lys,ENST00000283365,NM_032975.3;DTNA,missense_variant,p.Gln201Lys,ENST00000399121,NM_001198939.1;DTNA,missense_variant,p.Gln201Lys,ENST00000444659,NM_001390.4;DTNA,missense_variant,p.Gln201Lys,ENST00000595022,NM_001198940.1;DTNA,missense_variant,p.Gln201Lys,ENST00000348997,NM_032978.6,NM_001391.5;DTNA,missense_variant,p.Gln201Lys,ENST00000598334,NM_001198938.1;DTNA,missense_variant,p.Gln201Lys,ENST00000598142,;DTNA,missense_variant,p.Gln201Lys,ENST00000598774,NM_032979.4;DTNA,missense_variant,p.Gln201Lys,ENST00000399113,;DTNA,missense_variant,p.Gln201Lys,ENST00000597599,NM_001198941.1;DTNA,missense_variant,p.Gln201Lys,ENST00000315456,NM_001392.4;DTNA,missense_variant,p.Gln201Lys,ENST00000554864,NM_001128175.1;DTNA,missense_variant,p.Gln201Lys,ENST00000596745,NM_001198945.1;DTNA,upstream_gene_variant,,ENST00000592114,;DTNA,downstream_gene_variant,,ENST00000585446,; A ENST00000598334 Transcript missense_variant,splice_region_variant 927/3201 601/2175 201/724 Q/K Cag/Aag 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 deleterious(0.04) 7/20 hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,Gene3D:1.10.238.10,Pfam_domain:PF09069,PIRSF_domain:PIRSF038204,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 34812111 34812111 C A 1 0 0 0 0 1 0 0 0 4611 492 17 2 2 DTNA 18 34812111 Missense_Mutation SNP C C3N-00175_T 869025 34812111 45561174 1142 10734 PIK3C3 0 . GRCh38 18 42027516 42027516 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1558G>T p.Val520Leu p.V520L ENST00000262039 14/25 106 88 18 154 154 0 strelka-varscan-mutect PIK3C3,missense_variant,p.Val520Leu,ENST00000262039,NM_002647.2;PIK3C3,missense_variant,p.Val457Leu,ENST00000398870,NM_001308020.1;PIK3C3,non_coding_transcript_exon_variant,,ENST00000590013,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000593098,; T ENST00000262039 Transcript missense_variant 1644/9443 1558/2664 520/887 V/L Gta/Tta 1 1 PIK3C3 HGNC HGNC:8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 UPI00000708CE NM_002647.2 deleterious(0.03) 14/25 Gene3D:1.25.40.70,Pfam_domain:PF00613,PIRSF_domain:PIRSF000587,PROSITE_profiles:PS51545,hmmpanther:PTHR10048,SMART_domains:SM00145,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1428544886 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 42027516 42027516 G T 1 0 0 0 0 1 0 0 0 12007 1145 40 1 1 PIK3C3 18 42027516 Missense_Mutation SNP G C3N-00175_T 7215405 42027516 38345769 1143 10735 LOXHD1 0 . GRCh38 18 46547007 46547007 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.69G>T p.Gln23His p.Q23H ENST00000300591 4/24 190 158 32 251 251 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Gln1134His,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Gln928His,ENST00000441551,;LOXHD1,missense_variant,p.Gln23His,ENST00000300591,NM_001145472.2;LOXHD1,missense_variant,p.Gln23His,ENST00000582408,;LOXHD1,missense_variant,p.Gln23His,ENST00000419859,;LOXHD1,5_prime_UTR_variant,,ENST00000579038,NM_001308013.1;LOXHD1,missense_variant,p.Gln36His,ENST00000536111,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; A ENST00000300591 Transcript missense_variant 483/3970 69/3345 23/1114 Q/H caG/caT 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 deleterious(0) 4/24 PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 46547007 46547007 C A 1 0 0 0 0 1 0 0 0 8801 796 28 2 2 LOXHD1 18 46547007 Missense_Mutation SNP C C3N-00175_T 4519491 46547007 33826278 1144 10736 LOXHD1 0 . GRCh38 18 46657013 46657013 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.21G>C p.Arg7Ser p.R7S ENST00000536736 1/40 169 157 12 226 226 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Arg7Ser,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Arg7Ser,ENST00000441551,; G ENST00000536736 Transcript missense_variant 21/6848 21/6636 7/2211 R/S agG/agC 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 deleterious_low_confidence(0.01) 1/40 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 46657013 46657013 C G 1 0 0 0 0 1 0 0 0 8801 738 26 4 4 LOXHD1 18 46657013 Missense_Mutation SNP C C3N-00175_T 110006 46657013 33716272 1145 10737 DCC 0 . GRCh38 18 53410607 53410607 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3091G>T p.Gly1031Trp p.G1031W ENST00000442544 20/29 262 238 24 345 343 2 strelka-varscan-mutect DCC,missense_variant,p.Gly1031Trp,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Gly1008Trp,ENST00000412726,;DCC,missense_variant,p.Gly666Trp,ENST00000581580,;DCC,missense_variant,p.Gly170Trp,ENST00000579941,;DCC,3_prime_UTR_variant,,ENST00000304775,; T ENST00000442544 Transcript missense_variant 3707/10206 3091/4344 1031/1447 G/W Ggg/Tgg 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 deleterious(0) 20/29 Gene3D:2.60.40.10,Pfam_domain:PF00041,Prints_domain:PR00014,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 53410607 53410607 G T 1 0 0 0 0 1 0 0 0 4084 1232 43 2 2 DCC 18 53410607 Missense_Mutation SNP G C3N-00175_T 6753594 53410607 26962678 1146 10738 POLI 0 . GRCh38 18 54293765 54293765 + Silent SNP A A T novel C3N-00175_T C3N-00175_N A A c.1521A>T p.= p.T507T ENST00000579534 10/10 78 74 4 135 135 0 varscan-mutect POLI,synonymous_variant,p.=,ENST00000579534,NM_007195.2;POLI,synonymous_variant,p.=,ENST00000579434,;POLI,synonymous_variant,p.=,ENST00000217800,;POLI,synonymous_variant,p.=,ENST00000406285,;POLI,intron_variant,,ENST00000579823,;POLI,non_coding_transcript_exon_variant,,ENST00000582366,;POLI,3_prime_UTR_variant,,ENST00000585023,;POLI,non_coding_transcript_exon_variant,,ENST00000577727,;POLI,non_coding_transcript_exon_variant,,ENST00000577361,;POLI,downstream_gene_variant,,ENST00000581950,; T ENST00000579534 Transcript synonymous_variant 1664/6133 1521/2223 507/740 T acA/acT 1 1 POLI HGNC HGNC:9182 protein_coding YES CCDS11954.2 ENSP00000462664 Q9UNA4 UPI00004DDD95 NM_007195.2 10/10 hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 54293765 54293765 A T 1 0 0 0 0 0 0 0 1 12313 117 5 4 4 POLI 18 54293765 Silent SNP A C3N-00175_T 883158 54293765 26079520 1147 10739 WDR7 0 . GRCh38 18 56695155 56695155 + Silent SNP G G C rs749535701 C3N-00175_T C3N-00175_N G G c.1314G>C p.= p.T438T ENST00000254442 11/28 116 94 22 138 138 0 strelka-mutect WDR7,synonymous_variant,p.=,ENST00000254442,NM_015285.2;WDR7,synonymous_variant,p.=,ENST00000357574,NM_052834.2;WDR7,intron_variant,,ENST00000615645,;WDR7,intron_variant,,ENST00000589935,;WDR7,non_coding_transcript_exon_variant,,ENST00000585754,; C ENST00000254442 Transcript synonymous_variant 1525/14083 1314/4473 438/1490 T acG/acC rs749535701 1 1 WDR7 HGNC HGNC:13490 protein_coding YES CCDS11962.1 ENSP00000254442 Q9Y4E6 UPI000013CE33 NM_015285.2 11/28 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF409,Superfamily_domains:SSF50998 LOW 1 SNV 1 1 PASS rs749535701 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 56695155 56695155 G C 1 0 0 0 0 0 0 0 1 17876 1103 39 4 4 WDR7 18 56695155 Silent SNP G C3N-00175_T 2401390 56695155 23678130 1148 10740 ST8SIA3 0 . GRCh38 18 57357183 57357183 + Silent SNP C C T rs376754702 C3N-00175_T C3N-00175_N C C c.573C>T p.= p.F191F ENST00000324000 3/4 166 135 31 192 191 1 strelka-varscan-mutect ST8SIA3,synonymous_variant,p.=,ENST00000324000,NM_015879.2;ST8SIA3,synonymous_variant,p.=,ENST00000586360,; T ENST00000324000 Transcript synonymous_variant 2607/11833 573/1143 191/380 F ttC/ttT rs376754702,COSM709293 1 1 ST8SIA3 HGNC HGNC:14269 protein_coding YES CCDS32834.1 ENSP00000320431 O43173 UPI000014126D NM_015879.2 3/4 hmmpanther:PTHR11987:SF36,hmmpanther:PTHR11987,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557 0,1 LOW 1 SNV 1 0,1 1 PASS rs376754702 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 57357183 57357183 C T 1 0 0 0 0 0 0 0 1 15611 883 31 1 1 ST8SIA3 18 57357183 Silent SNP C C3N-00175_T 662028 57357183 23016102 1149 10741 ALPK2 0 . GRCh38 18 58517099 58517099 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.5749C>G p.Gln1917Glu p.Q1917E ENST00000361673 9/13 246 207 39 350 350 0 strelka-varscan-mutect ALPK2,missense_variant,p.Gln1917Glu,ENST00000361673,NM_052947.3;RP11-1151B14.5,upstream_gene_variant,,ENST00000610389,; C ENST00000361673 Transcript missense_variant 5963/7303 5749/6513 1917/2170 Q/E Cag/Gag 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0) 9/13 PROSITE_profiles:PS51158,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,SMART_domains:SM00811,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 58517099 58517099 G C 1 0 0 0 0 1 0 0 0 645 1299 45 4 4 ALPK2 18 58517099 Missense_Mutation SNP G C3N-00175_T 1159916 58517099 21856186 1150 10742 43 2 ALPK2 0 . GRCh38 18 58517105 58517105 + Missense_Mutation SNP G G T rs754653638 C3N-00175_T C3N-00175_N G G c.5743C>A p.Arg1915Ser p.R1915S ENST00000361673 9/13 227 190 37 324 324 0 strelka-varscan-mutect ALPK2,missense_variant,p.Arg1915Ser,ENST00000361673,NM_052947.3;RP11-1151B14.5,upstream_gene_variant,,ENST00000610389,; T ENST00000361673 Transcript missense_variant 5957/7303 5743/6513 1915/2170 R/S Cgt/Agt rs754653638 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0) 9/13 PROSITE_profiles:PS51158,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,SMART_domains:SM00811,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs754653638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 58517105 58517105 G T 1 0 0 0 0 1 0 0 0 645 1087 38 1 1 ALPK2 18 58517105 Missense_Mutation SNP G C3N-00175_T 6 58517105 21856180 1151 10743 43 2 SERPINB11 0 . GRCh38 18 63710220 63710220 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.27T>A p.= p.V9V ENST00000623262 1/5 86 77 9 112 112 0 strelka-varscan-mutect SERPINB11,synonymous_variant,p.=,ENST00000382749,NM_080475.3;SERPINB11,synonymous_variant,p.=,ENST00000544088,;SERPINB11,synonymous_variant,p.=,ENST00000489748,;SERPINB11,synonymous_variant,p.=,ENST00000623262,NM_001291278.1;SERPINB11,synonymous_variant,p.=,ENST00000624518,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000467649,;SERPINB11,synonymous_variant,p.=,ENST00000536691,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000610304,;SERPINB11,downstream_gene_variant,,ENST00000613567,; A ENST00000623262 Transcript synonymous_variant 27/918 27/918 9/305 V gtT/gtA 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 1/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Gene3D:1jjoA00,Pfam_domain:PF00079,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.19867 1 1 1 1 0 A 2 1 39 63710220 63710220 T A 1 0 0 0 0 0 0 0 1 14374 1799 63 4 4 SERPINB11 18 63710220 Silent SNP T C3N-00175_T 5193115 63710220 16663065 1152 10744 FAM69C 0 . GRCh38 18 74436579 74436579 + Silent SNP T T C novel C3N-00175_T C3N-00175_N T T c.1182A>G p.= p.R394R ENST00000343998 4/4 158 136 22 206 206 0 strelka-varscan-mutect FAM69C,synonymous_variant,p.=,ENST00000343998,NM_001044369.2;FAM69C,synonymous_variant,p.=,ENST00000400291,; C ENST00000343998 Transcript synonymous_variant 1191/3671 1182/1260 394/419 R agA/agG 1 -1 FAM69C HGNC HGNC:31729 protein_coding YES CCDS42445.2 ENSP00000344331 Q0P6D2 UPI000041AA52 NM_001044369.2 4/4 hmmpanther:PTHR21093,hmmpanther:PTHR21093:SF2 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 74436579 74436579 T C 1 0 0 0 0 0 0 0 1 5470 1548 54 5 5 FAM69C 18 74436579 Silent SNP T C3N-00175_T 10726359 74436579 5936706 1153 10745 FAM69C 0 . GRCh38 18 74447199 74447199 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.283C>A p.Leu95Met p.L95M ENST00000343998 2/4 125 111 14 158 158 0 strelka-mutect FAM69C,missense_variant,p.Leu95Met,ENST00000343998,NM_001044369.2;FAM69C,intron_variant,,ENST00000400291,; T ENST00000343998 Transcript missense_variant 292/3671 283/1260 95/419 L/M Ctg/Atg 1 -1 FAM69C HGNC HGNC:31729 protein_coding YES CCDS42445.2 ENSP00000344331 Q0P6D2 UPI000041AA52 NM_001044369.2 deleterious(0) 2/4 hmmpanther:PTHR21093,hmmpanther:PTHR21093:SF2,Pfam_domain:PF14875,SMART_domains:SM01299 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 74447199 74447199 G T 1 0 0 0 0 1 0 0 0 5470 991 35 2 2 FAM69C 18 74447199 Missense_Mutation SNP G C3N-00175_T 10620 74447199 5926086 1154 10746 FAM69C 0 . GRCh38 18 74447254 74447254 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.228C>A p.= p.A76A ENST00000343998 2/4 64 57 7 73 73 0 strelka-varscan-mutect FAM69C,synonymous_variant,p.=,ENST00000343998,NM_001044369.2;FAM69C,intron_variant,,ENST00000400291,; T ENST00000343998 Transcript synonymous_variant 237/3671 228/1260 76/419 A gcC/gcA COSM4979206 1 -1 FAM69C HGNC HGNC:31729 protein_coding YES CCDS42445.2 ENSP00000344331 Q0P6D2 UPI000041AA52 NM_001044369.2 2/4 hmmpanther:PTHR21093,hmmpanther:PTHR21093:SF2,Pfam_domain:PF14875,SMART_domains:SM01299 1 LOW 1 SNV 5 1 1 PASS rs1156374401 . 0 202 8 0 0 0 0 0 -15.73805 0.9999963 1 1 1 0 T 2 4 39 74447254 74447254 G T 1 0 0 0 0 0 0 0 1 5470 1103 39 1 1 FAM69C 18 74447254 Silent SNP G C3N-00175_T 55 74447254 5926031 1155 10747 ZNF407 0 . GRCh38 18 74633228 74633228 + Nonsense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2209A>T p.Lys737Ter p.K737* ENST00000299687 1/8 100 75 25 191 191 0 strelka-varscan-mutect ZNF407,stop_gained,p.Lys737Ter,ENST00000299687,NM_017757.2;ZNF407,stop_gained,p.Lys737Ter,ENST00000577538,NM_001146189.1;ZNF407,stop_gained,p.Lys737Ter,ENST00000582337,;ZNF407,stop_gained,p.Lys737Ter,ENST00000309902,NM_001146190.1; T ENST00000299687 Transcript stop_gained 2209/7948 2209/6747 737/2248 K/* Aaa/Taa 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 1/8 SMART_domains:SM00355,SMART_domains:SM00451 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 74633228 74633228 A T 1 0 0 0 0 0 1 0 0 18459 363 13 4 4 ZNF407 18 74633228 Nonsense_Mutation SNP A C3N-00175_T 185974 74633228 5740057 1156 10748 ZNF236 0 . GRCh38 18 76910135 76910135 + Silent SNP G G T rs753514687 C3N-00175_T C3N-00175_N G G c.2619G>T p.= p.A873A ENST00000320610 15/31 75 62 13 155 155 0 strelka-varscan-mutect ZNF236,synonymous_variant,p.=,ENST00000253159,NM_007345.3;ZNF236,synonymous_variant,p.=,ENST00000320610,NM_001306089.1;ZNF236,synonymous_variant,p.=,ENST00000543926,; T ENST00000320610 Transcript synonymous_variant 2620/7124 2619/5544 873/1847 A gcG/gcT rs753514687 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 15/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396 LOW 1 SNV 1 1 PASS rs753514687 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 76910135 76910135 G T 1 0 0 0 0 0 0 0 1 18366 1074 38 1 1 ZNF236 18 76910135 Silent SNP G C3N-00175_T 2276907 76910135 3463150 1157 10749 ZNF236 0 . GRCh38 18 76959739 76959739 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.5165G>T p.Arg1722Ile p.R1722I ENST00000320610 29/31 97 80 17 124 124 0 strelka-varscan-mutect ZNF236,missense_variant,p.Arg1720Ile,ENST00000253159,NM_007345.3;ZNF236,missense_variant,p.Arg1722Ile,ENST00000320610,NM_001306089.1;ZNF236,3_prime_UTR_variant,,ENST00000543926,; T ENST00000320610 Transcript missense_variant 5166/7124 5165/5544 1722/1847 R/I aGa/aTa 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 deleterious(0) 29/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 76959739 76959739 G T 1 0 0 0 0 1 0 0 0 18366 942 33 2 2 ZNF236 18 76959739 Missense_Mutation SNP G C3N-00175_T 49604 76959739 3413546 1158 10750 SALL3 0 . GRCh38 18 78994098 78994098 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2107G>T p.Gly703Trp p.G703W ENST00000537592 2/3 123 93 30 204 204 0 strelka-varscan-mutect SALL3,missense_variant,p.Gly703Trp,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Gly570Trp,ENST00000536229,;SALL3,missense_variant,p.Gly703Trp,ENST00000575389,;SALL3,missense_variant,p.Gly435Trp,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript missense_variant 2107/6555 2107/3903 703/1300 G/W Ggg/Tgg 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 deleterious(0) 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 78994098 78994098 G T 1 0 0 0 0 1 0 0 0 14071 1232 43 2 2 SALL3 18 78994098 Missense_Mutation SNP G C3N-00175_T 2034359 78994098 1379187 1159 10751 MIER2 0 . GRCh38 19 311931 311931 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.898T>A p.Cys300Ser p.C300S ENST00000264819 10/14 190 162 28 234 233 1 strelka-varscan-mutect MIER2,missense_variant,p.Cys300Ser,ENST00000264819,NM_017550.1;MIER2,upstream_gene_variant,,ENST00000619835,; T ENST00000264819 Transcript missense_variant 898/6884 898/1638 300/545 C/S Tgt/Agt 1 -1 MIER2 HGNC HGNC:29210 protein_coding YES CCDS32855.1 ENSP00000264819 Q8N344 UPI00001AE8C2 NM_017550.1 tolerated(0.1) 10/14 PROSITE_profiles:PS51293,hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF27,SMART_domains:SM00717 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 311931 311931 A T 1 0 0 0 0 1 0 0 0 9544 188 7 4 4 MIER2 19 311931 Missense_Mutation SNP A C3N-00175_T 311931 58305685 1160 10752 APC2 0 . GRCh38 19 1470071 1470071 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.6770C>G p.Pro2257Arg p.P2257R ENST00000535453 14/14 112 103 9 201 201 0 strelka-varscan-mutect APC2,missense_variant,p.Pro2257Arg,ENST00000535453,;APC2,missense_variant,p.Pro2257Arg,ENST00000233607,NM_005883.2;C19orf25,intron_variant,,ENST00000588427,;C19orf25,downstream_gene_variant,,ENST00000436106,;APC2,downstream_gene_variant,,ENST00000238483,;APC2,downstream_gene_variant,,ENST00000590469,;C19orf25,downstream_gene_variant,,ENST00000588871,;C19orf25,downstream_gene_variant,,ENST00000585675,NM_152482.2;C19orf25,downstream_gene_variant,,ENST00000588849,;C19orf25,downstream_gene_variant,,ENST00000427685,;C19orf25,downstream_gene_variant,,ENST00000592872,;C19orf25,downstream_gene_variant,,ENST00000586564,;C19orf25,downstream_gene_variant,,ENST00000590621,;APC2,downstream_gene_variant,,ENST00000593146,;C19orf25,downstream_gene_variant,,ENST00000592486,; G ENST00000535453 Transcript missense_variant 8483/11656 6770/6912 2257/2303 P/R cCc/cGc 1 1 APC2 HGNC HGNC:24036 protein_coding YES CCDS12068.1 ENSP00000442954 O95996 UPI0000073D85 deleterious(0.04) 14/14 hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 1470071 1470071 C G 1 0 0 0 0 1 0 0 0 884 623 22 4 4 APC2 19 1470071 Missense_Mutation SNP C C3N-00175_T 1158140 1470071 57147545 1161 10753 PCSK4 0 . GRCh38 19 1482176 1482176 + Missense_Mutation SNP C C A rs554107508 C3N-00175_T C3N-00175_N C C c.1851G>T p.Gln617His p.Q617H ENST00000300954 15/15 69 54 15 112 112 0 strelka-varscan-mutect PCSK4,missense_variant,p.Gln617His,ENST00000300954,NM_017573.4;C19orf25,upstream_gene_variant,,ENST00000436106,;C19orf25,upstream_gene_variant,,ENST00000588871,;C19orf25,upstream_gene_variant,,ENST00000585675,NM_152482.2;C19orf25,upstream_gene_variant,,ENST00000588849,;C19orf25,upstream_gene_variant,,ENST00000427685,;C19orf25,upstream_gene_variant,,ENST00000592872,;C19orf25,upstream_gene_variant,,ENST00000586564,;C19orf25,upstream_gene_variant,,ENST00000590621,;C19orf25,upstream_gene_variant,,ENST00000588427,;C19orf25,upstream_gene_variant,,ENST00000591027,;C19orf25,upstream_gene_variant,,ENST00000592605,;PCSK4,3_prime_UTR_variant,,ENST00000591201,;PCSK4,non_coding_transcript_exon_variant,,ENST00000586616,;PCSK4,non_coding_transcript_exon_variant,,ENST00000441747,;PCSK4,non_coding_transcript_exon_variant,,ENST00000586074,;PCSK4,downstream_gene_variant,,ENST00000588195,;PCSK4,downstream_gene_variant,,ENST00000586002,;PCSK4,downstream_gene_variant,,ENST00000591303,;C19orf25,upstream_gene_variant,,ENST00000589421,; A ENST00000300954 Transcript missense_variant 1913/2661 1851/2268 617/755 Q/H caG/caT rs554107508 1 -1 PCSK4 HGNC HGNC:8746 protein_coding YES CCDS12069.2 ENSP00000300954 Q6UW60 A0A140VJQ9 UPI000014E136 NM_017573.4 tolerated(0.55) 15/15 hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF386,Gene3D:2.10.220.10,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs554107508 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 39 1482176 1482176 C A 1 0 0 0 0 1 0 0 0 11690 796 28 2 2 PCSK4 19 1482176 Missense_Mutation SNP C C3N-00175_T 12105 1482176 57135440 1162 10754 MEX3D 0 . GRCh38 19 1556399 1556399 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1120G>T p.Ala374Ser p.A374S ENST00000402693 2/2 76 68 8 107 107 0 strelka-varscan-mutect MEX3D,missense_variant,p.Ala374Ser,ENST00000402693,NM_203304.3,NM_001174118.1;MEX3D,missense_variant,p.Ala198Ser,ENST00000605173,; A ENST00000402693 Transcript missense_variant 1120/2850 1120/1956 374/651 A/S Gcc/Tcc 1 -1 MEX3D HGNC HGNC:16734 protein_coding YES CCDS32865.2 ENSP00000384398 Q86XN8 UPI000059D61B NM_203304.3,NM_001174118.1 tolerated(1) 2/2 hmmpanther:PTHR23285,hmmpanther:PTHR23285:SF3 MODERATE 1 SNV 1 1 PASS rs1270769445 . 0 200 9 0 0 0 0 0 -17.1862 0.9999863 1 1 1 0 A 3 1 39 1556399 1556399 C A 1 0 0 0 0 1 0 0 0 9465 739 26 2 2 MEX3D 19 1556399 Missense_Mutation SNP C C3N-00175_T 74223 1556399 57061217 1163 10755 LMNB2 0 . GRCh38 19 2434901 2434901 + Nonsense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.868A>T p.Lys290Ter p.K290* ENST00000325327 6/12 171 136 35 210 210 0 strelka-varscan-mutect LMNB2,stop_gained,p.Lys290Ter,ENST00000325327,NM_032737.3;LMNB2,downstream_gene_variant,,ENST00000614319,;LMNB2,non_coding_transcript_exon_variant,,ENST00000527409,;LMNB2,upstream_gene_variant,,ENST00000475819,;LMNB2,upstream_gene_variant,,ENST00000532465,;LMNB2,downstream_gene_variant,,ENST00000534495,;LMNB2,non_coding_transcript_exon_variant,,ENST00000490554,; A ENST00000325327 Transcript stop_gained 931/4671 868/1863 290/620 K/* Aag/Tag 1 -1 LMNB2 HGNC HGNC:6638 protein_coding YES CCDS12090.2 ENSP00000327054 Q03252 J9JID7 UPI000059D625 NM_032737.3 6/12 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF152,SMART_domains:SM01391 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 2434901 2434901 T A 1 0 0 0 0 0 1 0 0 8774 1821 63 4 4 LMNB2 19 2434901 Nonsense_Mutation SNP T C3N-00175_T 878502 2434901 56182715 1164 10756 SLC39A3 0 . GRCh38 19 2733271 2733272 + Frame_Shift_Del DEL CG CG - novel C3N-00175_T C3N-00175_N CG CG c.424_425delCG p.Arg142GlyfsTer42 p.R142Gfs*42 ENST00000269740 3/3 72 56 16 108 108 0 sindel-varindel-pindel SLC39A3,frameshift_variant,p.Arg142GlyfsTer42,ENST00000269740,NM_144564.4;SLC39A3,frameshift_variant,p.Arg142GlyfsTer42,ENST00000545664,;AC006538.4,intron_variant,,ENST00000586572,;SLC39A3,downstream_gene_variant,,ENST00000455372,NM_213568.1;SLC39A3,downstream_gene_variant,,ENST00000589363,;SLC39A3,downstream_gene_variant,,ENST00000589166,;AC006538.1,upstream_gene_variant,,ENST00000567905,;SLC39A3,downstream_gene_variant,,ENST00000590875,; - ENST00000269740 Transcript frameshift_variant 754-755/1502 424-425/945 142/314 R/X CGg/g 1 -1 SLC39A3 HGNC HGNC:17128 protein_coding YES CCDS12093.1 ENSP00000269740 Q9BRY0 UPI00001B216E NM_144564.4 3/3 hmmpanther:PTHR11040:SF64,hmmpanther:PTHR11040,Pfam_domain:PF02535 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 2733271 2733271 CG - 1 0 1 0 1 0 0 0 0 14897 652 23 0 0 SLC39A3 19 2733271 Frame_Shift_Del DEL CG C3N-00175_T 298370 2733271 55884345 1165 10757 ZNF57 0 . GRCh38 19 2917415 2917415 + Missense_Mutation SNP C C T rs371789463 C3N-00175_T C3N-00175_N C C c.794C>T p.Ser265Leu p.S265L ENST00000306908 4/4 225 200 25 244 244 0 strelka-varscan-mutect ZNF57,missense_variant,p.Ser265Leu,ENST00000306908,NM_001319083.1,NM_173480.2;ZNF57,missense_variant,p.Ser267Leu,ENST00000614108,;ZNF57,missense_variant,p.Ser233Leu,ENST00000523428,;ZNF57,downstream_gene_variant,,ENST00000522294,;ZNF57,downstream_gene_variant,,ENST00000590305,;AC006277.2,intron_variant,,ENST00000520090,; T ENST00000306908 Transcript missense_variant 942/2003 794/1668 265/555 S/L tCg/tTg rs371789463,COSM4076527 1 1 ZNF57 HGNC HGNC:13125 protein_coding YES CCDS12098.1 ENSP00000303696 Q68EA5 A5HJR3 UPI000006FE5C NM_001319083.1,NM_173480.2 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF9,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371789463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 2917415 2917415 C T 1 0 0 0 0 1 0 0 0 18575 893 31 1 1 ZNF57 19 2917415 Missense_Mutation SNP C C3N-00175_T 184144 2917415 55700201 1166 10758 GNA15 0 . GRCh38 19 3151745 3151745 + Missense_Mutation SNP A A G C3N-00175_T C3N-00175_N A A c.524A>G p.Tyr175Cys p.Y175C ENST00000262958 4/7 79 74 5 100 100 0 strelka-mutect GNA15,missense_variant,p.Tyr175Cys,ENST00000262958,NM_002068.3;AC005264.2,intron_variant,,ENST00000587587,;GNA15,3_prime_UTR_variant,,ENST00000592455,;GNA15,non_coding_transcript_exon_variant,,ENST00000586082,; G ENST00000262958 Transcript missense_variant 782/2133 524/1125 175/374 Y/C tAc/tGc COSM3959885 1 1 GNA15 HGNC HGNC:4383 protein_coding YES CCDS12104.1 ENSP00000262958 P30679 UPI000003BBCB NM_002068.3 deleterious(0) 4/7 Gene3D:1.10.400.10,Pfam_domain:PF00503,Prints_domain:PR00318,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF217,SMART_domains:SM00275,Superfamily_domains:SSF47895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.26985 1 1 1 1 0 G 3 3 39 3151745 3151745 A G 1 0 0 0 0 1 0 0 0 6383 391 14 5 5 GNA15 19 3151745 Missense_Mutation SNP A C3N-00175_T 234330 3151745 55465871 1167 10759 NFIC 0 . GRCh38 19 3381797 3381797 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.116G>T p.Arg39Leu p.R39L ENST00000443272 2/11 285 242 43 382 382 0 strelka-varscan-mutect NFIC,missense_variant,p.Arg30Leu,ENST00000589123,NM_205843.2;NFIC,missense_variant,p.Arg30Leu,ENST00000395111,NM_001245005.1;NFIC,missense_variant,p.Arg39Leu,ENST00000443272,NM_001245002.1;NFIC,missense_variant,p.Arg39Leu,ENST00000341919,NM_005597.3;NFIC,missense_variant,p.Arg39Leu,ENST00000590282,NM_001245004.1;NFIC,missense_variant,p.Arg30Leu,ENST00000586919,; T ENST00000443272 Transcript missense_variant 167/1716 116/1527 39/508 R/L cGc/cTc 1 1 NFIC HGNC HGNC:7786 protein_coding YES CCDS59330.1 ENSP00000396843 P08651 UPI000012FFC8 NM_001245002.1 deleterious(0) 2/11 PROSITE_profiles:PS51080,hmmpanther:PTHR11492,PROSITE_patterns:PS00349,Pfam_domain:PF10524 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 3381797 3381797 G T 1 0 0 0 0 1 0 0 0 10409 1087 38 1 1 NFIC 19 3381797 Missense_Mutation SNP G C3N-00175_T 230052 3381797 55235819 1168 10760 MATK 0 . GRCh38 19 3779792 3779792 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.751C>A p.Leu251Met p.L251M ENST00000395045 9/14 194 146 48 231 231 0 strelka-varscan-mutect MATK,missense_variant,p.Leu250Met,ENST00000310132,NM_139355.2;MATK,missense_variant,p.Leu251Met,ENST00000395045,NM_002378.3;MATK,missense_variant,p.Leu250Met,ENST00000585778,;MATK,missense_variant,p.Leu209Met,ENST00000395040,NM_139354.2;MATK,missense_variant,p.Leu251Met,ENST00000619596,;MATK,missense_variant,p.Leu165Met,ENST00000590493,;MATK,missense_variant,p.Leu131Met,ENST00000587180,;MATK,missense_variant,p.Leu157Met,ENST00000588983,;MATK,downstream_gene_variant,,ENST00000590028,;MATK,downstream_gene_variant,,ENST00000590849,;AC005777.3,upstream_gene_variant,,ENST00000588332,; T ENST00000395045 Transcript missense_variant 1089/2073 751/1527 251/508 L/M Ctg/Atg 1 -1 MATK HGNC HGNC:6906 protein_coding YES CCDS12113.1 ENSP00000378485 P42679 UPI000013FB32 NM_002378.3 tolerated(0.37) 9/14 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF268,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Superfamily_domains:SSF55550 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 3779792 3779792 G T 1 0 0 0 0 1 0 0 0 9258 1014 35 2 2 MATK 19 3779792 Missense_Mutation SNP G C3N-00175_T 397995 3779792 54837824 1169 10761 DAPK3 0 . GRCh38 19 3964896 3964896 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.158G>T p.Arg53Leu p.R53L ENST00000545797 3/9 220 172 48 304 304 0 strelka-varscan-mutect DAPK3,missense_variant,p.Arg53Leu,ENST00000545797,NM_001348.2;DAPK3,missense_variant,p.Arg53Leu,ENST00000301264,;DAPK3,missense_variant,p.Arg53Leu,ENST00000596311,;DAPK3,missense_variant,p.Arg53Leu,ENST00000593844,;DAPK3,missense_variant,p.Arg53Leu,ENST00000601824,;DAPK3,upstream_gene_variant,,ENST00000594894,;DAPK3,upstream_gene_variant,,ENST00000385000,;DAPK3,upstream_gene_variant,,ENST00000595279,; A ENST00000545797 Transcript missense_variant 402/2257 158/1365 53/454 R/L cGg/cTg 1 -1 DAPK3 HGNC HGNC:2676 protein_coding YES CCDS12116.1 ENSP00000442973 O43293 UPI000006F7FA NM_001348.2 deleterious(0.03) 3/9 Low_complexity_(Seg):seg,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS rs1196349982 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 3964896 3964896 C A 1 0 0 0 0 1 0 0 0 4038 652 23 1 1 DAPK3 19 3964896 Missense_Mutation SNP C C3N-00175_T 185104 3964896 54652720 1170 10762 ANKRD24 0 . GRCh38 19 4217793 4217793 + Frame_Shift_Del DEL G G - novel C3N-00175_T C3N-00175_N G G c.2635delG p.Asp879ThrfsTer131 p.D879Tfs*131 ENST00000600132 18/22 36 30 6 37 37 0 sindel-pindel ANKRD24,frameshift_variant,p.Asp879ThrfsTer131,ENST00000600132,NM_133475.1;ANKRD24,frameshift_variant,p.Asp879ThrfsTer131,ENST00000318934,;ANKRD24,frameshift_variant,p.Asp969ThrfsTer131,ENST00000262970,;ANKRD24,downstream_gene_variant,,ENST00000597689,;ANKRD24,downstream_gene_variant,,ENST00000595096,; - ENST00000600132 Transcript frameshift_variant 2909/4026 2633/3441 878/1146 R/X cGg/cg 1 1 ANKRD24 HGNC HGNC:29424 protein_coding YES CCDS45925.1 ENSP00000471252 Q8TF21 UPI000041F5A9 NM_133475.1 18/22 Low_complexity_(Seg):seg,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF16 HIGH 1 deletion 5 2 1 PASS . . 0 199 10 0 0 0 0 0 -15.32097 0.9999856 1 1 1 0 - 7 5 39 4217793 4217793 G - 1 0 1 0 1 0 0 0 0 756 1116 39 0 0 ANKRD24 19 4217793 Frame_Shift_Del DEL G C3N-00175_T 252897 4217793 54399823 1171 10763 CHAF1A 0 . GRCh38 19 4409357 4409357 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.558G>T p.Glu186Asp p.E186D ENST00000301280 3/15 260 185 75 295 294 1 strelka-varscan-mutect CHAF1A,missense_variant,p.Glu186Asp,ENST00000301280,NM_005483.2;CHAF1A,upstream_gene_variant,,ENST00000587739,;CHAF1A,downstream_gene_variant,,ENST00000585854,;CHAF1A,downstream_gene_variant,,ENST00000587580,; T ENST00000301280 Transcript missense_variant 659/3339 558/2871 186/956 E/D gaG/gaT 1 1 CHAF1A HGNC HGNC:1910 protein_coding YES CCDS32875.1 ENSP00000301280 Q13111 UPI000034E58B NM_005483.2 tolerated(0.29) 3/15 Pfam_domain:PF15557,hmmpanther:PTHR15272,hmmpanther:PTHR15272:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 4409357 4409357 G T 1 0 0 0 0 1 0 0 0 3070 991 35 2 2 CHAF1A 19 4409357 Missense_Mutation SNP G C3N-00175_T 191564 4409357 54208259 1172 10764 TICAM1 0 . GRCh38 19 4817661 4817661 + Silent SNP C C G novel C3N-00175_T C3N-00175_N C C c.717G>C p.= p.V239V ENST00000248244 2/2 37 31 6 54 54 0 strelka-varscan-mutect TICAM1,synonymous_variant,p.=,ENST00000248244,NM_182919.3;TICAM1,synonymous_variant,p.=,ENST00000621756,; G ENST00000248244 Transcript synonymous_variant 947/2676 717/2139 239/712 V gtG/gtC 1 -1 TICAM1 HGNC HGNC:18348 protein_coding YES CCDS12136.1 ENSP00000248244 Q8IUC6 UPI000000D72E NM_182919.3 2/2 PIRSF_domain:PIRSF037744 LOW 1 SNV 1 1 PASS rs1202295243 . 0 207 3 0 0 0 0 0 -15.75579 1 1 1 1 0 G 2 3 39 4817661 4817661 C G 1 0 0 0 0 0 0 0 1 16326 697 25 4 4 TICAM1 19 4817661 Silent SNP C C3N-00175_T 408304 4817661 53799955 1173 10765 LONP1 0 . GRCh38 19 5692091 5692091 + Missense_Mutation SNP C C T rs146338629 C3N-00175_T C3N-00175_N C C c.2821G>A p.Glu941Lys p.E941K ENST00000360614 18/18 106 93 13 173 173 0 strelka-mutect LONP1,missense_variant,p.Glu941Lys,ENST00000360614,NM_004793.3;LONP1,missense_variant,p.Glu745Lys,ENST00000540670,NM_001276480.1;LONP1,missense_variant,p.Glu877Lys,ENST00000593119,NM_001276479.1;LONP1,missense_variant,p.Glu827Lys,ENST00000585374,;LONP1,missense_variant,p.Glu811Lys,ENST00000590729,;LONP1,missense_variant,p.Gly232Glu,ENST00000589473,;HSD11B1L,downstream_gene_variant,,ENST00000581521,;HSD11B1L,downstream_gene_variant,,ENST00000581773,;HSD11B1L,downstream_gene_variant,,ENST00000339423,NM_198706.2;HSD11B1L,downstream_gene_variant,,ENST00000342970,NM_198707.2;HSD11B1L,downstream_gene_variant,,ENST00000616276,NM_001267868.1;HSD11B1L,downstream_gene_variant,,ENST00000577917,NM_001267871.1;HSD11B1L,downstream_gene_variant,,ENST00000581893,NM_001267869.1,NM_198708.2;HSD11B1L,downstream_gene_variant,,ENST00000423665,NM_198533.2;HSD11B1L,downstream_gene_variant,,ENST00000301382,NM_198705.2;HSD11B1L,downstream_gene_variant,,ENST00000411793,NM_198704.2;HSD11B1L,downstream_gene_variant,,ENST00000583928,;HSD11B1L,downstream_gene_variant,,ENST00000577257,;RPL36,downstream_gene_variant,,ENST00000577222,;HSD11B1L,downstream_gene_variant,,ENST00000578046,;LONP1,downstream_gene_variant,,ENST00000590206,;RPL36,downstream_gene_variant,,ENST00000347512,NM_033643.2;HSD11B1L,downstream_gene_variant,,ENST00000579559,NM_001267870.1;RPL36,downstream_gene_variant,,ENST00000394580,NM_015414.3;RPL36,downstream_gene_variant,,ENST00000579446,;RPL36,downstream_gene_variant,,ENST00000579649,;RPL36,downstream_gene_variant,,ENST00000582463,;RPL36,downstream_gene_variant,,ENST00000582380,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;HSD11B1L,downstream_gene_variant,,ENST00000578167,;HSD11B1L,downstream_gene_variant,,ENST00000579562,;HSD11B1L,downstream_gene_variant,,ENST00000577920,;RPL36,downstream_gene_variant,,ENST00000590786,;HSD11B1L,downstream_gene_variant,,ENST00000582346,;HSD11B1L,downstream_gene_variant,,ENST00000584904,;HSD11B1L,downstream_gene_variant,,ENST00000581423,;HSD11B1L,downstream_gene_variant,,ENST00000578832,; T ENST00000360614 Transcript missense_variant 2979/3236 2821/2880 941/959 E/K Gag/Aag rs146338629 1 -1 LONP1 HGNC HGNC:9479 protein_coding YES CCDS12148.1 ENSP00000353826 P36776 UPI000012E7EF NM_004793.3 tolerated(0.06) 18/18 Gene3D:3.30.230.10,HAMAP:MF_03120,Pfam_domain:PF05362,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF50,Superfamily_domains:SSF54211,TIGRFAM_domain:TIGR00763 MODERATE 1 SNV 1 1 PASS rs146338629 . 0 207 0 3 0 0 0 0 -19.78506 0.9999904 1 1 1 0 T 3 4 39 5692091 5692091 C T 1 0 0 0 0 1 0 0 0 8794 864 30 3 3 LONP1 19 5692091 Missense_Mutation SNP C C3N-00175_T 874430 5692091 52925525 1174 10766 TUBB4A 0 . GRCh38 19 6495771 6495771 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.728C>A p.Pro243Gln p.P243Q ENST00000264071 4/4 620 528 92 669 669 0 strelka-varscan-mutect TUBB4A,missense_variant,p.Pro243Gln,ENST00000264071,NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1;TUBB4A,missense_variant,p.Pro139Gln,ENST00000594276,;TUBB4A,downstream_gene_variant,,ENST00000597686,NM_001289127.1;TUBB4A,downstream_gene_variant,,ENST00000601152,;TUBB4A,downstream_gene_variant,,ENST00000594075,;TUBB4A,downstream_gene_variant,,ENST00000598006,;TUBB4A,downstream_gene_variant,,ENST00000598635,NM_001289123.1;TUBB4A,downstream_gene_variant,,ENST00000596926,;TUBB4A,downstream_gene_variant,,ENST00000596291,;TUBB4A,downstream_gene_variant,,ENST00000601640,;TUBB4A,downstream_gene_variant,,ENST00000600216,;CTD-2396E7.10,downstream_gene_variant,,ENST00000596027,;CTD-2396E7.9,downstream_gene_variant,,ENST00000599292,;TUBB4A,downstream_gene_variant,,ENST00000595324,;TUBB4A,downstream_gene_variant,,ENST00000594290,; T ENST00000264071 Transcript missense_variant 1100/2552 728/1335 243/444 P/Q cCg/cAg COSM5141771 1 -1 TUBB4A HGNC HGNC:20774 protein_coding YES CCDS12168.1 ENSP00000264071 P04350 UPI000005FC27 NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1 deleterious_low_confidence(0) 4/4 Gene3D:3.40.50.1440,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF121,SMART_domains:SM00864,Superfamily_domains:SSF52490 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 6495771 6495771 G T 1 0 0 0 0 1 0 0 0 17268 1116 39 1 1 TUBB4A 19 6495771 Missense_Mutation SNP G C3N-00175_T 803680 6495771 52121845 1175 10767 VAV1 0 . GRCh38 19 6833925 6833925 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.1749G>A p.= p.R583R ENST00000602142 19/27 242 189 53 261 261 0 strelka-varscan-mutect VAV1,synonymous_variant,p.=,ENST00000304076,NM_001258206.1;VAV1,synonymous_variant,p.=,ENST00000596764,NM_001258207.1;VAV1,synonymous_variant,p.=,ENST00000599806,;VAV1,synonymous_variant,p.=,ENST00000539284,;VAV1,synonymous_variant,p.=,ENST00000602142,NM_005428.3;VAV1,downstream_gene_variant,,ENST00000601452,;VAV1,upstream_gene_variant,,ENST00000598270,;VAV1,downstream_gene_variant,,ENST00000600396,;VAV1,downstream_gene_variant,,ENST00000597967,; A ENST00000602142 Transcript synonymous_variant 1831/2620 1749/2538 583/845 R agG/agA 1 1 VAV1 HGNC HGNC:12657 protein_coding YES CCDS12174.1 ENSP00000472929 P15498 UPI0000138213 NM_005428.3 19/27 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 6833925 6833925 G A 1 0 0 0 0 0 0 0 1 17676 1223 43 3 3 VAV1 19 6833925 Silent SNP G C3N-00175_T 338154 6833925 51783691 1176 10768 ADGRE1 0 . GRCh38 19 6913731 6913731 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1201C>A p.Leu401Met p.L401M ENST00000312053 11/21 108 94 14 142 142 0 strelka-varscan-mutect ADGRE1,missense_variant,p.Leu401Met,ENST00000312053,NM_001974.4;ADGRE1,missense_variant,p.Leu349Met,ENST00000381404,NM_001256252.1;ADGRE1,missense_variant,p.Leu401Met,ENST00000250572,NM_001256253.1;ADGRE1,missense_variant,p.Leu260Met,ENST00000381407,NM_001256254.1;ADGRE1,missense_variant,p.Leu224Met,ENST00000450315,NM_001256255.1;ADGRE1,missense_variant,p.Leu318Met,ENST00000595026,; A ENST00000312053 Transcript missense_variant 1238/3128 1201/2661 401/886 L/M Ctg/Atg 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 deleterious(0.05) 11/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 6913731 6913731 C A 1 0 0 0 0 1 0 0 0 359 680 24 2 2 ADGRE1 19 6913731 Missense_Mutation SNP C C3N-00175_T 79806 6913731 51703885 1177 10769 ZNF414 0 . GRCh38 19 8513215 8513215 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.130G>C p.Glu44Gln p.E44Q ENST00000393927 2/8 241 203 38 293 293 0 strelka-varscan-mutect ZNF414,missense_variant,p.Glu44Gln,ENST00000393927,NM_001146175.1;ZNF414,missense_variant,p.Glu44Gln,ENST00000255616,NM_032370.2;ZNF414,upstream_gene_variant,,ENST00000596772,;ZNF414,upstream_gene_variant,,ENST00000593661,;ZNF414,upstream_gene_variant,,ENST00000594748,;ZNF414,non_coding_transcript_exon_variant,,ENST00000600906,;ZNF414,intron_variant,,ENST00000599379,;ZNF414,upstream_gene_variant,,ENST00000602128,;ZNF414,upstream_gene_variant,,ENST00000595348,; G ENST00000393927 Transcript missense_variant 244/2300 130/1173 44/390 E/Q Gag/Cag 1 -1 ZNF414 HGNC HGNC:20630 protein_coding YES CCDS54211.1 ENSP00000377504 Q96IQ9 UPI000059D659 NM_001146175.1 deleterious_low_confidence(0.02) 2/8 hmmpanther:PTHR21695,hmmpanther:PTHR21695:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1305563601 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 8513215 8513215 C G 1 0 0 0 0 1 0 0 0 18463 864 30 4 4 ZNF414 19 8513215 Missense_Mutation SNP C C3N-00175_T 1599484 8513215 50104401 1178 10770 ADAMTS10 0 . GRCh38 19 8585608 8585608 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2713C>A p.Arg905Ser p.R905S ENST00000270328 22/25 110 87 23 123 123 0 strelka-varscan-mutect ADAMTS10,missense_variant,p.Arg905Ser,ENST00000270328,;ADAMTS10,missense_variant,p.Arg905Ser,ENST00000597188,NM_030957.3;ADAMTS10,missense_variant,p.Arg392Ser,ENST00000595838,NM_001282352.1;AC130469.2,downstream_gene_variant,,ENST00000597256,;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,;ADAMTS10,downstream_gene_variant,,ENST00000603221,;ADAMTS10,downstream_gene_variant,,ENST00000593826,;ADAMTS10,downstream_gene_variant,,ENST00000596911,;ADAMTS10,downstream_gene_variant,,ENST00000596236,; T ENST00000270328 Transcript missense_variant 2944/4194 2713/3312 905/1103 R/S Cgc/Agc 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 deleterious(0.03) 22/25 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26,Low_complexity_(Seg):seg,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 8585608 8585608 G T 1 0 0 0 0 1 0 0 0 300 1087 38 1 1 ADAMTS10 19 8585608 Missense_Mutation SNP G C3N-00175_T 72393 8585608 50032008 1179 10771 ADAMTS10 0 . GRCh38 19 8597121 8597121 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.906G>A p.= p.E302E ENST00000270328 7/25 262 239 23 323 323 0 strelka-varscan-mutect ADAMTS10,synonymous_variant,p.=,ENST00000270328,;ADAMTS10,synonymous_variant,p.=,ENST00000597188,NM_030957.3;ADAMTS10,upstream_gene_variant,,ENST00000595838,NM_001282352.1;ADAMTS10,downstream_gene_variant,,ENST00000596709,;ADAMTS10,downstream_gene_variant,,ENST00000596466,;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000601163,;ADAMTS10,upstream_gene_variant,,ENST00000603221,;ADAMTS10,upstream_gene_variant,,ENST00000593826,;ADAMTS10,upstream_gene_variant,,ENST00000601872,;ADAMTS10,upstream_gene_variant,,ENST00000596236,; T ENST00000270328 Transcript synonymous_variant 1137/4194 906/3312 302/1103 E gaG/gaA 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 7/25 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26,Superfamily_domains:SSF55486 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 8597121 8597121 C T 1 0 0 0 0 0 0 0 1 300 912 32 3 3 ADAMTS10 19 8597121 Silent SNP C C3N-00175_T 11513 8597121 50020495 1180 10772 ACTL9 0 . GRCh38 19 8697516 8697516 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.1186T>C p.Cys396Arg p.C396R ENST00000324436 1/1 84 74 10 124 124 0 strelka-mutect ACTL9,missense_variant,p.Cys396Arg,ENST00000324436,NM_178525.4;ACTL9,missense_variant,p.Cys396Arg,ENST00000612068,;AC093230.2,upstream_gene_variant,,ENST00000623340,; G ENST00000324436 Transcript missense_variant 1307/1426 1186/1251 396/416 C/R Tgc/Cgc 1 -1 ACTL9 HGNC HGNC:28494 protein_coding YES CCDS12207.1 ENSP00000316674 Q8TC94 UPI000000DB15 NM_178525.4 tolerated(0.09) 1/1 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF194,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -19.9878 1 1 1 1 0 G 3 3 39 8697516 8697516 A G 1 0 0 0 0 1 0 0 0 247 188 7 5 5 ACTL9 19 8697516 Missense_Mutation SNP A C3N-00175_T 100395 8697516 49920100 1181 10773 MUC16 0 . GRCh38 19 8923049 8923049 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.36212C>G p.Pro12071Arg p.P12071R ENST00000397910 9/84 161 121 40 145 145 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro12071Arg,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 36416/43816 36212/43524 12071/14507 P/R cCa/cGa 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 9/84 hmmpanther:PTHR14672,Gene3D:1ivzA00,SMART_domains:SM00200,Superfamily_domains:0047452 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 8923049 8923049 G C 1 0 0 0 0 1 0 0 0 9972 1348 47 4 4 MUC16 19 8923049 Missense_Mutation SNP G C3N-00175_T 225533 8923049 49694567 1182 10774 OR7D4 0 . GRCh38 19 9214255 9214255 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.583A>T p.Asn195Tyr p.N195Y ENST00000308682 1/1 287 240 47 297 296 1 strelka-varscan-mutect OR7D4,missense_variant,p.Asn195Tyr,ENST00000308682,NM_001005191.2; A ENST00000308682 Transcript missense_variant 617/1022 583/939 195/312 N/Y Aat/Tat 1 -1 OR7D4 HGNC HGNC:8380 protein_coding YES CCDS32901.1 ENSP00000310488 Q8NG98 A0A126GVR1 UPI00000472B5 NM_001005191.2 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF371,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 9214255 9214255 T A 1 0 0 0 0 1 0 0 0 11290 1812 63 4 4 OR7D4 19 9214255 Missense_Mutation SNP T C3N-00175_T 291206 9214255 49403361 1183 10775 OR7D4 0 . GRCh38 19 9214420 9214420 + Missense_Mutation SNP G G T rs368945619 C3N-00175_T C3N-00175_N G G c.418C>A p.Leu140Ile p.L140I ENST00000308682 1/1 289 213 76 355 354 1 strelka-varscan-mutect OR7D4,missense_variant,p.Leu140Ile,ENST00000308682,NM_001005191.2; T ENST00000308682 Transcript missense_variant 452/1022 418/939 140/312 L/I Ctc/Atc rs368945619 1 -1 OR7D4 HGNC HGNC:8380 protein_coding YES CCDS32901.1 ENSP00000310488 Q8NG98 A0A126GVR1 UPI00000472B5 NM_001005191.2 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF371,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs368945619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 9214420 9214420 G T 1 0 0 0 0 1 0 0 0 11290 1000 35 2 2 OR7D4 19 9214420 Missense_Mutation SNP G C3N-00175_T 165 9214420 49403196 1184 10776 ZNF699 0 . GRCh38 19 9296383 9296384 + Frame_Shift_Ins INS - - A novel C3N-00175_T C3N-00175_N - - c.1020dupT p.Gly341TrpfsTer5 p.G341Wfs*5 ENST00000591998 6/6 82 70 12 130 130 0 sindel-varindel-pindel ZNF699,frameshift_variant,p.Gly341TrpfsTer5,ENST00000591998,;ZNF699,frameshift_variant,p.Gly341TrpfsTer5,ENST00000308650,NM_198535.1;CTC-325H20.4,downstream_gene_variant,,ENST00000591336,; A ENST00000591998 Transcript frameshift_variant 1249-1250/3358 1020-1021/1929 340-341/642 -/X -/T 1 -1 ZNF699 HGNC HGNC:24750 protein_coding YES CCDS42495.1 ENSP00000467723 Q32M78 UPI00001D825F 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF132,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 39 9296383 9296383 - A 1 0 1 1 0 0 0 0 0 18674 594 21 0 0 ZNF699 19 9296383 Frame_Shift_Ins INS - C3N-00175_T 81963 9296383 49321233 1185 10777 CNN1 0 . GRCh38 19 11538964 11538964 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.37G>A p.Gly13Arg p.G13R ENST00000252456 1/7 56 41 15 95 95 0 strelka-mutect CNN1,missense_variant,p.Gly13Arg,ENST00000252456,NM_001299.4;CNN1,5_prime_UTR_variant,,ENST00000592923,NM_001308341.1,NM_001308342.1;CNN1,5_prime_UTR_variant,,ENST00000535659,;CNN1,upstream_gene_variant,,ENST00000586059,;CNN1,upstream_gene_variant,,ENST00000585869,;CNN1,upstream_gene_variant,,ENST00000587087,;CNN1,non_coding_transcript_exon_variant,,ENST00000588468,; A ENST00000252456 Transcript missense_variant 248/1633 37/894 13/297 G/R Ggg/Agg 1 1 CNN1 HGNC HGNC:2155 protein_coding YES CCDS12263.1 ENSP00000252456 P51911 V9HWA5 UPI0000127AE3 NM_001299.4 tolerated(0.13) 1/7 hmmpanther:PTHR18959,hmmpanther:PTHR18959:SF43,Superfamily_domains:SSF47576,Prints_domain:PR00888 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 11538964 11538964 G A 1 0 0 0 0 1 0 0 0 3389 1116 39 1 1 CNN1 19 11538964 Missense_Mutation SNP G C3N-00175_T 2242581 11538964 47078652 1186 10778 CASP14 0 . GRCh38 19 15053570 15053570 + Missense_Mutation SNP T T A rs750592871 C3N-00175_T C3N-00175_N T T c.116T>A p.Leu39Gln p.L39Q ENST00000427043 3/7 312 240 72 339 338 1 strelka-varscan-mutect CASP14,missense_variant,p.Leu39Gln,ENST00000427043,NM_012114.2;CASP14,upstream_gene_variant,,ENST00000598738,; A ENST00000427043 Transcript missense_variant 424/3241 116/729 39/242 L/Q cTg/cAg rs750592871 1 1 CASP14 HGNC HGNC:1502 protein_coding YES CCDS12323.1 ENSP00000393417 P31944 B2CIS9 UPI0000044176 NM_012114.2 deleterious(0) 3/7 PROSITE_profiles:PS50208,hmmpanther:PTHR10454:SF131,hmmpanther:PTHR10454,Gene3D:3.40.50.1460,Pfam_domain:PF00656,SMART_domains:SM00115,Superfamily_domains:SSF52129,Prints_domain:PR00376 MODERATE 1 SNV 1 1 PASS rs750592871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 15053570 15053570 T A 1 0 0 0 0 1 0 0 0 2370 1580 55 4 4 CASP14 19 15053570 Missense_Mutation SNP T C3N-00175_T 3514606 15053570 43564046 1187 10779 NWD1 0 . GRCh38 19 16773240 16773240 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2525C>G p.Ala842Gly p.A842G ENST00000524140 11/19 389 309 80 398 398 0 strelka-varscan-mutect NWD1,missense_variant,p.Ala842Gly,ENST00000524140,NM_001007525.3;NWD1,missense_variant,p.Ala842Gly,ENST00000379808,;NWD1,missense_variant,p.Ala842Gly,ENST00000552788,NM_001290355.1;NWD1,missense_variant,p.Ala842Gly,ENST00000549814,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; G ENST00000524140 Transcript missense_variant 2943/7641 2525/4299 842/1432 A/G gCa/gGa 1 1 NWD1 HGNC HGNC:27619 protein_coding YES CCDS32945.2 ENSP00000428579 Q149M9 UPI0000D6173E NM_001007525.3 deleterious(0.04) 11/19 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF472 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 16773240 16773240 C G 1 0 0 0 0 1 0 0 0 10854 710 25 4 4 NWD1 19 16773240 Missense_Mutation SNP C C3N-00175_T 1719670 16773240 41844376 1188 10780 SIN3B 0 . GRCh38 19 16877587 16877587 + Missense_Mutation SNP G G T rs566655086 C3N-00175_T C3N-00175_N G G c.2998G>T p.Ala1000Ser p.A1000S ENST00000379803 18/20 215 180 35 328 327 1 strelka-varscan-mutect SIN3B,missense_variant,p.Ala1000Ser,ENST00000379803,NM_015260.3;SIN3B,missense_variant,p.Ala968Ser,ENST00000248054,NM_001297595.1;SIN3B,missense_variant,p.Ala558Ser,ENST00000595541,NM_001297597.1;SIN3B,non_coding_transcript_exon_variant,,ENST00000594235,;SIN3B,downstream_gene_variant,,ENST00000595900,;SIN3B,non_coding_transcript_exon_variant,,ENST00000601141,;SIN3B,non_coding_transcript_exon_variant,,ENST00000595049,; T ENST00000379803 Transcript missense_variant 3012/5129 2998/3489 1000/1162 A/S Gcg/Tcg rs566655086,COSM4580763 1 1 SIN3B HGNC HGNC:19354 protein_coding YES CCDS32946.1 ENSP00000369131 O75182 UPI0000425EFA NM_015260.3 tolerated(0.33) 18/20 hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF1,Pfam_domain:PF16879 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs566655086 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 16877587 16877587 G T 1 0 0 0 0 1 0 0 0 14590 1087 38 1 1 SIN3B 19 16877587 Missense_Mutation SNP G C3N-00175_T 104347 16877587 41740029 1189 10781 SLC5A5 0 . GRCh38 19 17872406 17872406 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.87C>A p.= p.G29G ENST00000222248 1/15 76 61 15 116 116 0 strelka-varscan-mutect SLC5A5,synonymous_variant,p.=,ENST00000222248,NM_000453.2;AC005796.2,upstream_gene_variant,,ENST00000623214,; A ENST00000222248 Transcript synonymous_variant 434/3576 87/1932 29/643 G ggC/ggA 1 1 SLC5A5 HGNC HGNC:11040 protein_coding YES CCDS12368.1 ENSP00000222248 Q92911 UPI00001359F6 NM_000453.2 1/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF18 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 17872406 17872406 C A 1 0 0 0 0 0 0 0 1 14951 697 25 2 2 SLC5A5 19 17872406 Silent SNP C C3N-00175_T 994819 17872406 40745210 1190 10782 IL12RB1 0 . GRCh38 19 18082249 18082249 + Missense_Mutation SNP G G T rs756640017 C3N-00175_T C3N-00175_N G G c.140C>A p.Pro47His p.P47H ENST00000600835 4/18 403 359 44 448 447 1 strelka-varscan-mutect IL12RB1,missense_variant,p.Pro47His,ENST00000600835,NM_001290024.1;IL12RB1,missense_variant,p.Pro47His,ENST00000593993,NM_001290023.1,NM_005535.2;IL12RB1,missense_variant,p.Pro47His,ENST00000322153,NM_153701.2;IL12RB1,missense_variant,p.Pro47His,ENST00000598019,;IL12RB1,missense_variant,p.Pro47His,ENST00000594176,;IL12RB1,missense_variant,p.Pro51His,ENST00000430026,;IL12RB1,downstream_gene_variant,,ENST00000597416,; T ENST00000600835 Transcript missense_variant 439/2901 140/1989 47/662 P/H cCt/cAt rs756640017 1 -1 IL12RB1 HGNC HGNC:5971 protein_coding YES CCDS54232.1 ENSP00000470788 P42701 UPI00000502CE NM_001290024.1 deleterious(0) 4/18 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF51,hmmpanther:PTHR23036 MODERATE 1 SNV 1 1 PASS rs756640017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 18082249 18082249 G T 1 0 0 0 0 1 0 0 0 7534 1000 35 2 2 IL12RB1 19 18082249 Missense_Mutation SNP G C3N-00175_T 209843 18082249 40535367 1191 10783 TMEM59L 0 . GRCh38 19 18613106 18613106 + Missense_Mutation SNP G G T rs11538357 C3N-00175_T C3N-00175_N G G c.148G>T p.Asp50Tyr p.D50Y ENST00000600490 2/9 23 19 4 23 23 0 strelka-mutect TMEM59L,missense_variant,p.Asp50Tyr,ENST00000600490,;TMEM59L,missense_variant,p.Asp50Tyr,ENST00000262817,NM_012109.2;TMEM59L,upstream_gene_variant,,ENST00000594709,;TMEM59L,non_coding_transcript_exon_variant,,ENST00000598660,;TMEM59L,non_coding_transcript_exon_variant,,ENST00000594859,; T ENST00000600490 Transcript missense_variant 333/1717 148/1029 50/342 D/Y Gac/Tac rs11538357 1 1 TMEM59L HGNC HGNC:13237 protein_coding YES CCDS12383.1 ENSP00000470879 Q9UK28 A0A024R7L4 UPI0000034024 tolerated(1) 2/9 hmmpanther:PTHR28652:SF1,hmmpanther:PTHR28652 MODERATE 1 SNV 5 1 PASS rs11538357 . 1 203 6 0 0 0 0 0 -11.92252 1 1 1 1 0 T 3 4 39 18613106 18613106 G T 1 0 0 0 0 1 0 0 0 16662 1058 37 1 1 TMEM59L 19 18613106 Missense_Mutation SNP G C3N-00175_T 530857 18613106 40004510 1192 10784 ZNF66 0 . GRCh38 19 20806717 20806717 + Nonsense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1117G>T p.Glu373Ter p.E373* ENST00000344519 4/4 84 65 19 134 134 0 strelka-varscan-mutect ZNF66,stop_gained,p.Glu373Ter,ENST00000344519,; T ENST00000344519 Transcript stop_gained 1140/1745 1117/1722 373/573 E/* Gaa/Taa 1 1 ZNF66 HGNC HGNC:13135 protein_coding YES ENSP00000461425 Q6ZN08 UPI00025A2C0A 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF105,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 20806717 20806717 G T 1 0 0 0 0 0 1 0 0 18643 943 33 2 2 ZNF66 19 20806717 Nonsense_Mutation SNP G C3N-00175_T 2193611 20806717 37810899 1193 10785 ZNF431 0 . GRCh38 19 21143608 21143608 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.61G>A p.Glu21Lys p.E21K ENST00000311048 2/5 179 163 16 183 183 0 strelka-varscan-mutect ZNF431,missense_variant,p.Glu21Lys,ENST00000311048,NM_133473.2;ZNF431,missense_variant,p.Glu21Lys,ENST00000600692,;ZNF431,missense_variant,p.Glu21Lys,ENST00000598331,;ZNF431,missense_variant,p.Glu21Lys,ENST00000594425,;ZNF431,missense_variant,p.Glu21Lys,ENST00000599296,; A ENST00000311048 Transcript missense_variant 205/13894 61/1731 21/576 E/K Gag/Aag 1 1 ZNF431 HGNC HGNC:20809 protein_coding YES CCDS32979.1 ENSP00000308578 Q8TF32 A0A024R7Q8 UPI0000191EAC NM_133473.2 tolerated_low_confidence(0.52) 2/5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 21143608 21143608 G A 1 0 0 0 0 1 0 0 0 18477 1291 45 3 3 ZNF431 19 21143608 Missense_Mutation SNP G C3N-00175_T 336891 21143608 37474008 1194 10786 ZNF100 0 . GRCh38 19 21726677 21726677 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1628G>T p.Cys543Phe p.C543F ENST00000608416 6/8 44 37 7 48 48 0 strelka-varscan-mutect ZNF100,missense_variant,p.Cys543Phe,ENST00000608416,;ZNF100,3_prime_UTR_variant,,ENST00000358296,NM_173531.3;ZNF100,3_prime_UTR_variant,,ENST00000305570,;ZNF100,downstream_gene_variant,,ENST00000594401,; A ENST00000608416 Transcript missense_variant 1697/1840 1628/1701 543/566 C/F tGt/tTt 1 -1 ZNF100 HGNC HGNC:12880 protein_coding ENSP00000476534 A0A075B7G6 UPI0004E4CA8A deleterious(0.01) 6/8 PROSITE_profiles:PS50157,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -17.52438 1 1 1 1 0 A 3 1 39 21726677 21726677 C A 1 0 0 0 0 1 0 0 0 18292 478 17 2 2 ZNF100 19 21726677 Missense_Mutation SNP C C3N-00175_T 583069 21726677 36890939 1195 10787 ZNF729 0 . GRCh38 19 22313862 22313862 + Missense_Mutation SNP A A C novel C3N-00175_T C3N-00175_N A A c.445A>C p.Thr149Pro p.T149P ENST00000601693 4/4 46 30 16 69 69 0 strelka-varscan-mutect ZNF729,missense_variant,p.Thr149Pro,ENST00000601693,NM_001242680.1; C ENST00000601693 Transcript missense_variant 563/3877 445/3759 149/1252 T/P Acc/Ccc 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 tolerated(0.1) 4/4 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 22313862 22313862 A C 1 0 0 0 0 1 0 0 0 18703 391 14 5 5 ZNF729 19 22313862 Missense_Mutation SNP A C3N-00175_T 587185 22313862 36303754 1196 10788 ZNF98 0 . GRCh38 19 22391748 22391748 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.1487G>A p.Gly496Asp p.G496D ENST00000357774 4/4 183 150 33 202 201 1 strelka-varscan-mutect ZNF98,missense_variant,p.Gly496Asp,ENST00000357774,NM_001098626.1;ZNF98,downstream_gene_variant,,ENST00000593657,; T ENST00000357774 Transcript missense_variant 1609/2338 1487/1719 496/572 G/D gGc/gAc COSM1271942,COSM1271943 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 tolerated(0.05) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 3 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 22391748 22391748 C T 1 0 0 0 0 1 0 0 0 18796 739 26 3 3 ZNF98 19 22391748 Missense_Mutation SNP C C3N-00175_T 77886 22391748 36225868 1197 10789 VSTM2B 0 . GRCh38 19 29528454 29528454 + Nonsense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.289A>T p.Lys97Ter p.K97* ENST00000335523 3/5 165 135 30 222 222 0 strelka-varscan-mutect VSTM2B,stop_gained,p.Lys97Ter,ENST00000335523,NM_001146339.1;CTC-525D6.1,upstream_gene_variant,,ENST00000582581,;CTC-525D6.2,upstream_gene_variant,,ENST00000579268,;CTC-525D6.1,upstream_gene_variant,,ENST00000577849,; T ENST00000335523 Transcript stop_gained 374/1488 289/858 97/285 K/* Aaa/Taa 1 1 VSTM2B HGNC HGNC:33595 protein_coding YES CCDS46034.1 ENSP00000335038 A6NLU5 UPI00001D8158 NM_001146339.1 3/5 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF23,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 29528454 29528454 A T 1 0 0 0 0 0 1 0 0 17781 363 13 4 4 VSTM2B 19 29528454 Nonsense_Mutation SNP A C3N-00175_T 7136706 29528454 29089162 1198 10790 ZNF536 0 . GRCh38 19 30549437 30549437 + Missense_Mutation SNP C C A rs866481206 C3N-00175_T C3N-00175_N C C c.3818C>A p.Ser1273Tyr p.S1273Y ENST00000355537 4/5 21 14 7 27 27 0 strelka-varscan-mutect ZNF536,missense_variant,p.Ser1273Tyr,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Ser31Tyr,ENST00000592773,;ZNF536,downstream_gene_variant,,ENST00000585628,;CTD-2001J20.1,upstream_gene_variant,,ENST00000623331,; A ENST00000355537 Transcript missense_variant 3965/4945 3818/3903 1273/1300 S/Y tCt/tAt rs866481206 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious_low_confidence(0) 4/5 MODERATE 1 SNV 1 1 PASS rs866481206 . 0 206 4 0 0 0 0 0 -19.79546 1 1 1 1 0 A 3 1 39 30549437 30549437 C A 1 0 0 0 0 1 0 0 0 18547 913 32 2 2 ZNF536 19 30549437 Missense_Mutation SNP C C3N-00175_T 1020983 30549437 28068179 1199 10791 DPY19L3 0 . GRCh38 19 32480419 32480419 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1851G>T p.Lys617Asn p.K617N ENST00000342179 18/19 88 66 22 109 109 0 strelka-varscan-mutect DPY19L3,missense_variant,p.Lys617Asn,ENST00000342179,NM_207325.2;DPY19L3,missense_variant,p.Lys617Asn,ENST00000392250,NM_001172774.1;DPY19L3,missense_variant,p.Lys617Asn,ENST00000586987,;DPY19L3,3_prime_UTR_variant,,ENST00000588648,;DPY19L3,3_prime_UTR_variant,,ENST00000592832,;DPY19L3,non_coding_transcript_exon_variant,,ENST00000592142,;DPY19L3,non_coding_transcript_exon_variant,,ENST00000608291,; T ENST00000342179 Transcript missense_variant 2066/6015 1851/2151 617/716 K/N aaG/aaT 1 1 DPY19L3 HGNC HGNC:27120 protein_coding YES CCDS12422.1 ENSP00000344937 Q6ZPD9 UPI00001C10BE NM_207325.2 tolerated(0.07) 18/19 hmmpanther:PTHR31488:SF4,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 32480419 32480419 G T 1 0 0 0 0 1 0 0 0 4557 933 33 2 2 DPY19L3 19 32480419 Missense_Mutation SNP G C3N-00175_T 1930982 32480419 26137197 1200 10792 CHST8 0 . GRCh38 19 33689292 33689292 + Missense_Mutation SNP G G T rs754261375 C3N-00175_T C3N-00175_N G G c.31G>T p.Ala11Ser p.A11S ENST00000262622 2/4 75 58 17 91 91 0 strelka-varscan-mutect CHST8,missense_variant,p.Ala11Ser,ENST00000262622,NM_022467.3;CHST8,missense_variant,p.Ala11Ser,ENST00000434302,NM_001127895.1;CHST8,missense_variant,p.Ala11Ser,ENST00000438847,NM_001127896.1;CHST8,missense_variant,p.Ala11Ser,ENST00000591231,;CHST8,non_coding_transcript_exon_variant,,ENST00000604556,; T ENST00000262622 Transcript missense_variant 789/2479 31/1275 11/424 A/S Gcc/Tcc rs754261375 1 1 CHST8 HGNC HGNC:15993 protein_coding YES CCDS12433.1 ENSP00000262622 Q9H2A9 UPI000006F966 NM_022467.3 tolerated(0.27) 2/4 hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF7,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs754261375 . 0 203 5 2 0 0 0 0 -20 0.9999825 1 1 1 0 T 3 4 39 33689292 33689292 G T 1 0 0 0 0 1 0 0 0 3170 1203 42 2 2 CHST8 19 33689292 Missense_Mutation SNP G C3N-00175_T 1208873 33689292 24928324 1201 10793 KMT2B 0 . GRCh38 19 35721548 35721548 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2201A>T p.Gln734Leu p.Q734L ENST00000420124 3/37 185 137 48 195 195 0 strelka-varscan-mutect KMT2B,missense_variant,p.Gln734Leu,ENST00000420124,NM_014727.2;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,NM_014383.1;KMT2B,downstream_gene_variant,,ENST00000606995,;ZBTB32,downstream_gene_variant,,ENST00000481182,; T ENST00000420124 Transcript missense_variant 2201/8469 2201/8148 734/2715 Q/L cAg/cTg 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 tolerated_low_confidence(0.21) 3/37 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999979 1 1 1 0 T 3 4 39 35721548 35721548 A T 1 0 0 0 0 1 0 0 0 8296 188 7 4 4 KMT2B 19 35721548 Missense_Mutation SNP A C3N-00175_T 2032256 35721548 22896068 1202 10794 KMT2B 0 . GRCh38 19 35733396 35733396 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.6847A>T p.Thr2283Ser p.T2283S ENST00000420124 28/37 170 150 20 211 211 0 strelka-varscan-mutect KMT2B,missense_variant,p.Thr2283Ser,ENST00000420124,NM_014727.2;KMT2B,non_coding_transcript_exon_variant,,ENST00000592092,;KMT2B,upstream_gene_variant,,ENST00000585476,;KMT2B,upstream_gene_variant,,ENST00000586308,; T ENST00000420124 Transcript missense_variant 6847/8469 6847/8148 2283/2715 T/S Act/Tct 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 tolerated(0.74) 28/37 MODERATE 1 SNV 1 1 PASS rs1434829009 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 35733396 35733396 A T 1 0 0 0 0 1 0 0 0 8296 159 6 4 4 KMT2B 19 35733396 Missense_Mutation SNP A C3N-00175_T 11848 35733396 22884220 1203 10795 NPHS1 0 . GRCh38 19 35841713 35841713 + Splice_Site SNP A A G C3N-00175_T C3N-00175_N A A c.2815+2T>C p.X939_splice ENST00000378910 338 272 66 346 346 0 strelka-varscan-mutect NPHS1,splice_donor_variant,,ENST00000378910,NM_004646.3;NPHS1,splice_donor_variant,,ENST00000353632,;NPHS1,downstream_gene_variant,,ENST00000585400,; G ENST00000378910 Transcript splice_donor_variant -/4276 2815/3726 939/1241 CS044966 1 -1 NPHS1 HGNC HGNC:7908 protein_coding YES CCDS32996.1 ENSP00000368190 O60500 UPI000004EF61 NM_004646.3 20/28 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 39 35841713 35841713 A G 1 0 0 0 0 0 0 1 0 10630 405 14 5 5 NPHS1 19 35841713 Splice_Site SNP A C3N-00175_T 108317 35841713 22775903 1204 10796 CATSPERG 0 . GRCh38 19 38337396 38337396 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.162G>C p.Lys54Asn p.K54N ENST00000409235 2/29 338 251 87 527 527 0 strelka-varscan-mutect CATSPERG,missense_variant,p.Lys54Asn,ENST00000409235,NM_021185.4;CATSPERG,missense_variant,p.Lys54Asn,ENST00000410018,;CATSPERG,missense_variant,p.Lys54Asn,ENST00000409410,;CATSPERG,missense_variant,p.Lys54Asn,ENST00000471517,;CATSPERG,missense_variant,p.Lys54Asn,ENST00000312265,;CATSPERG,missense_variant,p.Lys54Asn,ENST00000475343,;CATSPERG,non_coding_transcript_exon_variant,,ENST00000477793,; C ENST00000409235 Transcript missense_variant 277/3746 162/3480 54/1159 K/N aaG/aaC 1 1 CATSPERG HGNC HGNC:25243 protein_coding YES CCDS12514.2 ENSP00000386962 Q6ZRH7 UPI000022A813 NM_021185.4 tolerated(0.13) 2/29 Pfam_domain:PF15064,hmmpanther:PTHR14327 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 38337396 38337396 G C 1 0 0 0 0 1 0 0 0 2393 933 33 4 4 CATSPERG 19 38337396 Missense_Mutation SNP G C3N-00175_T 2495683 38337396 20280220 1205 10797 ACP7 0 . GRCh38 19 39106975 39106975 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1142C>A p.Ala381Asp p.A381D ENST00000331256 12/13 153 102 51 220 220 0 strelka-varscan-mutect ACP7,missense_variant,p.Ala381Asp,ENST00000331256,NM_001004318.2;ACP7,intron_variant,,ENST00000594229,;ACP7,intron_variant,,ENST00000601531,;ACP7,3_prime_UTR_variant,,ENST00000601575,; A ENST00000331256 Transcript missense_variant 1416/2966 1142/1317 381/438 A/D gCt/gAt 1 1 ACP7 HGNC HGNC:33781 protein_coding YES CCDS33018.1 ENSP00000327557 Q6ZNF0 UPI000041AA68 NM_001004318.2 tolerated(0.64) 12/13 Gene3D:3.60.21.10,Pfam_domain:PF14008,hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF9,Superfamily_domains:SSF56300 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 39106975 39106975 C A 1 0 0 0 0 1 0 0 0 208 797 28 2 2 ACP7 19 39106975 Missense_Mutation SNP C C3N-00175_T 769579 39106975 19510641 1206 10798 SUPT5H 0 . GRCh38 19 39469351 39469351 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1327G>T p.Val443Leu p.V443L ENST00000599117 17/31 174 125 49 285 285 0 strelka-varscan-mutect SUPT5H,missense_variant,p.Val443Leu,ENST00000599117,NM_001319990.1;SUPT5H,missense_variant,p.Val439Leu,ENST00000359191,NM_001319991.1;SUPT5H,missense_variant,p.Val443Leu,ENST00000598725,NM_001319990.1,NM_003169.3;SUPT5H,missense_variant,p.Val443Leu,ENST00000432763,NM_001111020.2,NM_001130824.1;SUPT5H,missense_variant,p.Val439Leu,ENST00000402194,NM_001130825.1;SUPT5H,downstream_gene_variant,,ENST00000593727,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000599335,;SUPT5H,upstream_gene_variant,,ENST00000598117,;SUPT5H,downstream_gene_variant,,ENST00000599907,;SUPT5H,downstream_gene_variant,,ENST00000598520,;SUPT5H,upstream_gene_variant,,ENST00000596208,; T ENST00000599117 Transcript missense_variant 1694/3902 1327/3264 443/1087 V/L Gtg/Ttg 1 1 SUPT5H HGNC HGNC:11469 protein_coding YES CCDS12536.1 ENSP00000470252 O00267 UPI000006D81A NM_001319990.1 deleterious(0.01) 17/31 hmmpanther:PTHR11125,PIRSF_domain:PIRSF036945,SMART_domains:SM00739 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 39469351 39469351 G T 1 0 0 0 0 1 0 0 0 15786 1145 40 1 1 SUPT5H 19 39469351 Missense_Mutation SNP G C3N-00175_T 362376 39469351 19148265 1207 10799 ATP1A3 0 . GRCh38 19 41985869 41985869 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.640T>A p.Cys214Ser p.C214S ENST00000545399 6/23 143 97 46 198 198 0 strelka-varscan-mutect ATP1A3,missense_variant,p.Cys214Ser,ENST00000545399,NM_001256214.1;ATP1A3,missense_variant,p.Cys201Ser,ENST00000302102,NM_152296.4;ATP1A3,missense_variant,p.Cys171Ser,ENST00000602133,;ATP1A3,missense_variant,p.Cys212Ser,ENST00000543770,NM_001256213.1;ATP1A3,missense_variant,p.Cys171Ser,ENST00000473086,;ATP1A3,downstream_gene_variant,,ENST00000636197,;ATP1A3,downstream_gene_variant,,ENST00000468774,;ATP1A3,downstream_gene_variant,,ENST00000636258,;ATP1A3,downstream_gene_variant,,ENST00000636282,;ATP1A3,downstream_gene_variant,,ENST00000637406,;ATP1A3,missense_variant,p.Cys201Ser,ENST00000441343,;ATP1A3,upstream_gene_variant,,ENST00000485672,;ATP1A3,downstream_gene_variant,,ENST00000465007,; T ENST00000545399 Transcript missense_variant 824/3618 640/3081 214/1026 C/S Tgc/Agc 1 -1 ATP1A3 HGNC HGNC:801 protein_coding YES CCDS58664.1 ENSP00000444688 P13637 UPI0001914BDE NM_001256214.1 deleterious(0.01) 6/23 Superfamily_domains:0049471,Gene3D:2.70.150.10,Pfam_domain:PF00122,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01106,TIGRFAM_domain:TIGR01494 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 41985869 41985869 A T 1 0 0 0 0 1 0 0 0 1282 202 7 4 4 ATP1A3 19 41985869 Missense_Mutation SNP A C3N-00175_T 2516518 41985869 16631747 1208 10800 PSG1 0 . GRCh38 19 42871835 42871835 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.641C>A p.Pro214His p.P214H ENST00000312439 3/6 220 148 72 252 252 0 strelka-varscan-mutect PSG1,missense_variant,p.Pro214His,ENST00000244296,NM_006905.2;PSG1,missense_variant,p.Pro214His,ENST00000436291,NM_001184825.1;PSG1,missense_variant,p.Pro214His,ENST00000595356,NM_001184826.1;PSG1,missense_variant,p.Pro214His,ENST00000312439,NM_001297773.1;PSG1,missense_variant,p.Pro143His,ENST00000595930,;PSG1,missense_variant,p.Pro135His,ENST00000597058,;PSG1,intron_variant,,ENST00000403380,;PSG1,intron_variant,,ENST00000595124,;PSG1,downstream_gene_variant,,ENST00000601073,;PSG1,downstream_gene_variant,,ENST00000601456,;PSG1,upstream_gene_variant,,ENST00000602039,; T ENST00000312439 Transcript missense_variant 727/1882 641/1287 214/428 P/H cCc/cAc 1 -1 PSG1 HGNC HGNC:9514 protein_coding YES CCDS74380.1 ENSP00000308970 P11464 UPI000006DB43 NM_001297773.1 deleterious(0.04) 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 42871835 42871835 G T 1 0 0 0 0 1 0 0 0 12804 1232 43 2 2 PSG1 19 42871835 Missense_Mutation SNP G C3N-00175_T 885966 42871835 15745781 1209 10801 PSG6 0 . GRCh38 19 42910839 42910839 + Silent SNP G G T rs761435971 C3N-00175_T C3N-00175_N G G c.447C>A p.= p.S149S ENST00000292125 3/6 81 54 27 97 96 1 strelka-varscan-mutect PSG6,synonymous_variant,p.=,ENST00000187910,NM_001031850.3;PSG6,synonymous_variant,p.=,ENST00000402603,;PSG6,synonymous_variant,p.=,ENST00000292125,NM_002782.4;PSG6,synonymous_variant,p.=,ENST00000594375,;PSG7,intron_variant,,ENST00000617049,;PSG6,downstream_gene_variant,,ENST00000601833,;PSG6,non_coding_transcript_exon_variant,,ENST00000402456,;PSG6,non_coding_transcript_exon_variant,,ENST00000595062,;PSG6,non_coding_transcript_exon_variant,,ENST00000484292,;PSG6,upstream_gene_variant,,ENST00000599753,; T ENST00000292125 Transcript synonymous_variant 492/1391 447/1308 149/435 S tcC/tcA rs761435971 1 -1 PSG6 HGNC HGNC:9523 protein_coding YES CCDS12613.1 ENSP00000292125 Q00889 UPI00001327A1 NM_002782.4 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs761435971 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 42910839 42910839 G T 1 0 0 0 0 0 0 0 1 12810 1335 47 2 2 PSG6 19 42910839 Silent SNP G C3N-00175_T 39004 42910839 15706777 1210 10802 PSG6 0 . GRCh38 19 42916454 42916454 + Missense_Mutation SNP G G T rs374758763 C3N-00175_T C3N-00175_N G G c.98C>A p.Thr33Asn p.T33N ENST00000292125 2/6 103 65 38 110 110 0 strelka-varscan-mutect PSG6,missense_variant,p.Thr33Asn,ENST00000187910,NM_001031850.3;PSG6,missense_variant,p.Thr33Asn,ENST00000402603,;PSG6,missense_variant,p.Thr33Asn,ENST00000292125,NM_002782.4;PSG6,5_prime_UTR_variant,,ENST00000601833,;PSG7,intron_variant,,ENST00000617049,;PSG6,intron_variant,,ENST00000594375,;PSG6,non_coding_transcript_exon_variant,,ENST00000402456,;PSG6,intron_variant,,ENST00000484292,;PSG6,upstream_gene_variant,,ENST00000595062,; T ENST00000292125 Transcript missense_variant 143/1391 98/1308 33/435 T/N aCt/aAt rs374758763 1 -1 PSG6 HGNC HGNC:9523 protein_coding YES CCDS12613.1 ENSP00000292125 Q00889 UPI00001327A1 NM_002782.4 deleterious(0) 2/6 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs374758763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 42916454 42916454 G T 1 0 0 0 0 1 0 0 0 12810 1029 36 2 2 PSG6 19 42916454 Missense_Mutation SNP G C3N-00175_T 5615 42916454 15701162 1211 10803 CD177 0 . GRCh38 19 43360395 43360395 + Silent SNP C C G novel C3N-00175_T C3N-00175_N C C c.750C>G p.= p.L250L ENST00000618265 6/9 69 40 29 121 121 0 strelka-varscan-mutect CD177,synonymous_variant,p.=,ENST00000618265,NM_020406.3;CTC-490G23.4,downstream_gene_variant,,ENST00000607109,;CD177,3_prime_UTR_variant,,ENST00000378012,; G ENST00000618265 Transcript synonymous_variant 806/2222 750/1314 250/437 L ctC/ctG 1 1 CD177 HGNC HGNC:30072 protein_coding YES CCDS62700.1 ENSP00000479536 A0A087WVM2 UPI0000DB6A71 NM_020406.3 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR16529,hmmpanther:PTHR16529:SF8 LOW 1 SNV 1 1 PASS rs1243676731 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 43360395 43360395 C G 1 0 0 0 0 0 0 0 1 2674 842 30 4 4 CD177 19 43360395 Silent SNP C C3N-00175_T 443941 43360395 15257221 1212 10804 PLAUR 0 . GRCh38 19 43670110 43670110 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.11C>A p.Pro4Gln p.P4Q ENST00000340093 1/7 136 89 47 197 195 2 strelka-varscan-mutect PLAUR,missense_variant,p.Pro4Gln,ENST00000221264,NM_001005377.2;PLAUR,missense_variant,p.Pro4Gln,ENST00000340093,NM_002659.3;PLAUR,missense_variant,p.Pro4Gln,ENST00000339082,NM_001005376.2;PLAUR,missense_variant,p.Pro4Gln,ENST00000601723,NM_001301037.1;PLAUR,upstream_gene_variant,,ENST00000593939,;PLAUR,upstream_gene_variant,,ENST00000599892,;PLAUR,upstream_gene_variant,,ENST00000599546,;PLAUR,upstream_gene_variant,,ENST00000602141,;PLAUR,upstream_gene_variant,,ENST00000593714,;PLAUR,missense_variant,p.Pro4Gln,ENST00000597107,;PLAUR,non_coding_transcript_exon_variant,,ENST00000601876,;PLAUR,non_coding_transcript_exon_variant,,ENST00000598875,; T ENST00000340093 Transcript missense_variant 241/1548 11/1008 4/335 P/Q cCg/cAg 1 -1 PLAUR HGNC HGNC:9053 protein_coding YES CCDS12628.1 ENSP00000339328 Q03405 UPI000000D8C1 NM_002659.3 deleterious_low_confidence(0.03) 1/7 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43670110 43670110 G T 1 0 0 0 0 1 0 0 0 12117 1116 39 1 1 PLAUR 19 43670110 Missense_Mutation SNP G C3N-00175_T 309715 43670110 14947506 1213 10805 LYPD5 0 . GRCh38 19 43798929 43798929 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.253C>A p.Gln85Lys p.Q85K ENST00000377950 3/5 139 73 66 148 148 0 strelka-varscan-mutect LYPD5,missense_variant,p.Gln85Lys,ENST00000377950,NM_001031749.2;LYPD5,missense_variant,p.Gln42Lys,ENST00000414615,NM_182573.2;LYPD5,missense_variant,p.Gln42Lys,ENST00000594013,NM_001288763.1;LYPD5,missense_variant,p.Gln42Lys,ENST00000602179,;LYPD5,missense_variant,p.Gln42Lys,ENST00000594049,;AC115522.3,upstream_gene_variant,,ENST00000595680,;LYPD5,non_coding_transcript_exon_variant,,ENST00000601224,;LYPD5,upstream_gene_variant,,ENST00000595666,; T ENST00000377950 Transcript missense_variant 334/2499 253/756 85/251 Q/K Cag/Aag 1 -1 LYPD5 HGNC HGNC:26397 protein_coding YES CCDS46096.1 ENSP00000367185 Q6UWN5 UPI00006A77F6 NM_001031749.2 tolerated(0.59) 3/5 hmmpanther:PTHR10624,Superfamily_domains:SSF57302 MODERATE 1 SNV 1 1 PASS rs1459165809 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 43798929 43798929 G T 1 0 0 0 0 1 0 0 0 9024 1357 47 2 2 LYPD5 19 43798929 Missense_Mutation SNP G C3N-00175_T 128819 43798929 14818687 1214 10806 ZNF229 0 . GRCh38 19 44429713 44429713 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.1068G>T p.Lys356Asn p.K356N ENST00000614049 6/6 145 100 45 180 179 1 strelka-varscan-mutect ZNF229,missense_variant,p.Lys350Asn,ENST00000613197,NM_001278510.2;ZNF229,missense_variant,p.Lys356Asn,ENST00000614049,NM_014518.3;ZNF229,downstream_gene_variant,,ENST00000592308,;CTC-512J12.4,intron_variant,,ENST00000588655,;ZNF229,intron_variant,,ENST00000591289,;ZNF229,3_prime_UTR_variant,,ENST00000620012,; A ENST00000614049 Transcript missense_variant 1502/4507 1068/2478 356/825 K/N aaG/aaT COSM3535585 1 -1 ZNF229 HGNC HGNC:13022 protein_coding YES CCDS42574.1 ENSP00000479884 Q9UJW7 UPI0001747B51 NM_014518.3 deleterious(0.05) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF348,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS rs1443576409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 44429713 44429713 C A 1 0 0 0 0 1 0 0 0 18359 680 24 2 2 ZNF229 19 44429713 Missense_Mutation SNP C C3N-00175_T 630784 44429713 14187903 1215 10807 PRKD2 0 . GRCh38 19 46691745 46691745 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.1692G>T p.= p.V564V ENST00000433867 13/19 179 135 44 249 249 0 strelka-varscan-mutect PRKD2,synonymous_variant,p.=,ENST00000433867,NM_016457.4,NM_001079880.1,NM_001079881.1;PRKD2,synonymous_variant,p.=,ENST00000291281,;PRKD2,synonymous_variant,p.=,ENST00000595515,;PRKD2,synonymous_variant,p.=,ENST00000600194,NM_001079882.1;PRKD2,synonymous_variant,p.=,ENST00000601806,;RN7SL364P,upstream_gene_variant,,ENST00000473668,;PRKD2,synonymous_variant,p.=,ENST00000597390,;PRKD2,non_coding_transcript_exon_variant,,ENST00000599019,;PRKD2,non_coding_transcript_exon_variant,,ENST00000597589,;PRKD2,non_coding_transcript_exon_variant,,ENST00000599464,;PRKD2,upstream_gene_variant,,ENST00000602155,; A ENST00000433867 Transcript synonymous_variant 2170/3321 1692/2637 564/878 V gtG/gtT 1 -1 PRKD2 HGNC HGNC:17293 protein_coding YES CCDS12689.1 ENSP00000393978 Q9BZL6 UPI0000049BFA NM_016457.4,NM_001079880.1,NM_001079881.1 13/19 PROSITE_profiles:PS50011,hmmpanther:PTHR22968,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000552,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9987367 1 1 1 0 A 2 1 39 46691745 46691745 C A 1 0 0 0 0 0 0 0 1 12652 581 21 2 2 PRKD2 19 46691745 Silent SNP C C3N-00175_T 2262032 46691745 11925871 1216 10808 ARHGAP35 0 . GRCh38 19 46920743 46920743 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.2068G>T p.Asp690Tyr p.D690Y ENST00000404338 1/6 125 102 23 147 147 0 strelka-varscan-mutect ARHGAP35,missense_variant,p.Asp690Tyr,ENST00000404338,NM_004491.4;ARHGAP35,missense_variant,p.Asp690Tyr,ENST00000614079,;ARHGAP35,missense_variant,p.Asp690Tyr,ENST00000615647,; T ENST00000404338 Transcript missense_variant 2068/8889 2068/4500 690/1499 D/Y Gat/Tat COSM1177603,COSM1177604 1 1 ARHGAP35 HGNC HGNC:4591 protein_coding YES CCDS46127.1 ENSP00000385720 Q9NRY4 UPI0000163F71 NM_004491.4 deleterious(0) 1/6 hmmpanther:PTHR23176:SF26,hmmpanther:PTHR23176 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1271615780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 46920743 46920743 G T 1 0 0 0 0 1 0 0 0 1008 1174 41 2 2 ARHGAP35 19 46920743 Missense_Mutation SNP G C3N-00175_T 228998 46920743 11696873 1217 10809 SCAF1 0 . GRCh38 19 49654850 49654850 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.3598G>T p.Gly1200Cys p.G1200C ENST00000360565 9/11 34 22 12 81 80 1 strelka-varscan-mutect SCAF1,missense_variant,p.Gly1200Cys,ENST00000360565,NM_021228.2;IRF3,downstream_gene_variant,,ENST00000597198,;IRF3,downstream_gene_variant,,ENST00000309877,;IRF3,downstream_gene_variant,,ENST00000600911,;IRF3,downstream_gene_variant,,ENST00000377139,NM_001571.5;IRF3,downstream_gene_variant,,ENST00000601291,NM_001197122.1;IRF3,downstream_gene_variant,,ENST00000593922,NM_001197123.1;IRF3,downstream_gene_variant,,ENST00000598808,;IRF3,downstream_gene_variant,,ENST00000377135,NM_001197125.1;IRF3,downstream_gene_variant,,ENST00000599144,NM_001197126.1;IRF3,downstream_gene_variant,,ENST00000599223,NM_001197124.1;IRF3,downstream_gene_variant,,ENST00000596756,;IRF3,downstream_gene_variant,,ENST00000600022,NM_001197127.1;IRF3,downstream_gene_variant,,ENST00000596822,;IRF3,downstream_gene_variant,,ENST00000596765,NM_001197128.1;SCAF1,downstream_gene_variant,,ENST00000598359,;IRF3,downstream_gene_variant,,ENST00000599680,;IRF3,downstream_gene_variant,,ENST00000597636,;IRF3,downstream_gene_variant,,ENST00000596644,; T ENST00000360565 Transcript missense_variant 3722/4306 3598/3939 1200/1312 G/C Ggc/Tgc 1 1 SCAF1 HGNC HGNC:30403 protein_coding YES CCDS33074.1 ENSP00000353769 Q9H7N4 UPI0000071891 NM_021228.2 deleterious_low_confidence(0) 9/11 Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 49654850 49654850 G T 1 0 0 0 0 1 0 0 0 14132 1232 43 2 2 SCAF1 19 49654850 Missense_Mutation SNP G C3N-00175_T 2734107 49654850 8962766 1218 10810 SIGLEC11 0 . GRCh38 19 49960685 49960685 + Silent SNP G G T rs147865552 C3N-00175_T C3N-00175_N G G c.327C>A p.= p.P109P ENST00000447370 2/11 124 90 34 198 197 1 strelka-varscan-mutect SIGLEC11,synonymous_variant,p.=,ENST00000447370,NM_052884.2;SIGLEC11,synonymous_variant,p.=,ENST00000426971,NM_001135163.1;SIGLEC11,upstream_gene_variant,,ENST00000426296,;CTC-326K19.6,upstream_gene_variant,,ENST00000451973,; T ENST00000447370 Transcript synonymous_variant 418/3173 327/2097 109/698 P ccC/ccA rs147865552 1 -1 SIGLEC11 HGNC HGNC:15622 protein_coding YES CCDS12790.2 ENSP00000412361 Q96RL6 UPI00018131F5 NM_052884.2 2/11 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF44,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs147865552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 49960685 49960685 G T 1 0 0 0 0 0 0 0 1 14571 1103 39 1 1 SIGLEC11 19 49960685 Silent SNP G C3N-00175_T 305835 49960685 8656931 1219 10811 VRK3 0 . GRCh38 19 50007799 50007799 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.317A>C p.Lys106Thr p.K106T ENST00000599538 5/15 277 189 88 355 355 0 strelka-varscan-mutect VRK3,missense_variant,p.Lys106Thr,ENST00000599538,;VRK3,missense_variant,p.Lys106Thr,ENST00000593919,;VRK3,missense_variant,p.Lys106Thr,ENST00000316763,NM_016440.3;VRK3,missense_variant,p.Lys106Thr,ENST00000594948,;VRK3,missense_variant,p.Lys106Thr,ENST00000594092,NM_001308420.1;VRK3,missense_variant,p.Lys56Thr,ENST00000601341,;VRK3,missense_variant,p.Lys56Thr,ENST00000377011,NM_001025778.1;VRK3,missense_variant,p.Lys56Thr,ENST00000601912,;VRK3,missense_variant,p.Lys106Thr,ENST00000596445,;VRK3,missense_variant,p.Lys106Thr,ENST00000597215,;VRK3,missense_variant,p.Lys56Thr,ENST00000600137,;VRK3,missense_variant,p.Lys74Thr,ENST00000600259,;VRK3,missense_variant,p.Lys106Thr,ENST00000601324,;VRK3,non_coding_transcript_exon_variant,,ENST00000424804,;VRK3,downstream_gene_variant,,ENST00000599138,;VRK3,missense_variant,p.Lys56Thr,ENST00000596814,;VRK3,missense_variant,p.Lys106Thr,ENST00000596121,;VRK3,3_prime_UTR_variant,,ENST00000594090,;VRK3,3_prime_UTR_variant,,ENST00000599342,; G ENST00000599538 Transcript missense_variant 982/2126 317/1425 106/474 K/T aAa/aCa 1 -1 VRK3 HGNC HGNC:18996 protein_coding YES CCDS12791.1 ENSP00000469880 Q8IV63 A0A024QZI4 UPI0000035BA6 tolerated(0.13) 5/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 50007799 50007799 T G 1 0 0 0 0 1 0 0 0 17770 1841 64 5 5 VRK3 19 50007799 Missense_Mutation SNP T C3N-00175_T 47114 50007799 8609817 1220 10812 SHANK1 0 . GRCh38 19 50704438 50704438 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1154A>T p.Gln385Leu p.Q385L ENST00000293441 8/23 108 74 34 159 159 0 strelka-varscan-mutect SHANK1,missense_variant,p.Gln385Leu,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Gln385Leu,ENST00000391814,;SHANK1,missense_variant,p.Gln385Leu,ENST00000359082,;SHANK1,splice_region_variant,,ENST00000461154,; A ENST00000293441 Transcript missense_variant,splice_region_variant 1173/6643 1154/6486 385/2161 Q/L cAg/cTg 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 deleterious(0) 8/23 PROSITE_profiles:PS50297,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 50704438 50704438 T A 1 0 0 0 0 1 0 0 0 14523 1594 55 4 4 SHANK1 19 50704438 Missense_Mutation SNP T C3N-00175_T 696639 50704438 7913178 1221 10813 SIGLEC12 0 . GRCh38 19 51499585 51499585 + Missense_Mutation SNP C C A rs201888334 C3N-00175_T C3N-00175_N C C c.940G>T p.Val314Leu p.V314L ENST00000291707 3/8 71 48 23 122 122 0 strelka-varscan-mutect SIGLEC12,missense_variant,p.Val314Leu,ENST00000291707,NM_053003.3;SIGLEC12,missense_variant,p.Val196Leu,ENST00000598614,NM_033329.2;SIGLEC12,3_prime_UTR_variant,,ENST00000596742,; A ENST00000291707 Transcript missense_variant 996/2121 940/1788 314/595 V/L Gtg/Ttg rs201888334,COSM4080624 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 tolerated(1) 3/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF53,hmmpanther:PTHR12035,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201888334 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 51499585 51499585 C A 1 0 0 0 0 1 0 0 0 14572 536 19 1 1 SIGLEC12 19 51499585 Missense_Mutation SNP C C3N-00175_T 795147 51499585 7118031 1222 10814 ZNF160 0 . GRCh38 19 53069356 53069356 + Missense_Mutation SNP C C T novel C3N-00175_T C3N-00175_N C C c.1178G>A p.Gly393Glu p.G393E ENST00000429604 7/7 79 56 23 119 119 0 strelka-varscan-mutect ZNF160,missense_variant,p.Gly357Glu,ENST00000601421,;ZNF160,missense_variant,p.Gly393Glu,ENST00000429604,NM_001322132.1,NM_001322129.1,NM_001322138.1,NM_001322134.1,NM_001322131.1,NM_001322133.1,NM_198893.2,NM_001102603.1;ZNF160,missense_variant,p.Gly393Glu,ENST00000599056,NM_001322138.1;ZNF160,missense_variant,p.Gly393Glu,ENST00000418871,NM_001322135.1,NM_001322128.1,NM_001322138.1,NM_001322136.1,NM_033288.3;ZNF160,missense_variant,p.Gly393Glu,ENST00000599247,;ZNF160,downstream_gene_variant,,ENST00000355147,NM_001322126.1;ZNF160,downstream_gene_variant,,ENST00000601982,; T ENST00000429604 Transcript missense_variant 1594/4336 1178/2457 393/818 G/E gGa/gAa 1 -1 ZNF160 HGNC HGNC:12948 protein_coding YES CCDS12859.1 ENSP00000406201 Q9HCG1 A0A024R4Q2 UPI0000202B37 NM_001322132.1,NM_001322129.1,NM_001322138.1,NM_001322134.1,NM_001322131.1,NM_001322133.1,NM_198893.2,NM_001102603.1 deleterious(0.02) 7/7 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF132,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 53069356 53069356 C T 1 0 0 0 0 1 0 0 0 18320 855 30 3 3 ZNF160 19 53069356 Missense_Mutation SNP C C3N-00175_T 1569771 53069356 5548260 1223 10815 BIRC8 0 . GRCh38 19 53290234 53290234 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.141C>A p.= p.A47A ENST00000426466 1/1 174 125 49 211 211 0 strelka-varscan-mutect BIRC8,synonymous_variant,p.=,ENST00000426466,NM_033341.4; T ENST00000426466 Transcript synonymous_variant 1393/2026 141/711 47/236 A gcC/gcA 1 -1 BIRC8 HGNC HGNC:14878 protein_coding YES CCDS12863.1 ENSP00000412957 Q96P09 UPI000003966A NM_033341.4 1/1 Gene3D:1.10.1170.10,Pfam_domain:PF00653,PROSITE_patterns:PS01282,PROSITE_profiles:PS50143,hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF102,SMART_domains:SM00238,Superfamily_domains:SSF57924 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 53290234 53290234 G T 1 0 0 0 0 0 0 0 1 1591 1335 47 2 2 BIRC8 19 53290234 Silent SNP G C3N-00175_T 220878 53290234 5327382 1224 10816 PRKCG 0 . GRCh38 19 53900689 53900689 + Silent SNP C C T rs780647467 C3N-00175_T C3N-00175_N C C c.1515C>T p.= p.N505N ENST00000263431 14/18 298 257 41 466 465 1 strelka-varscan-mutect PRKCG,synonymous_variant,p.=,ENST00000263431,NM_002739.3; T ENST00000263431 Transcript synonymous_variant 1797/3133 1515/2094 505/697 N aaC/aaT rs780647467,COSM1646960,COSM713832 1 1 PRKCG HGNC HGNC:9402 protein_coding YES CCDS12867.1 ENSP00000263431 P05129 UPI000000DC69 NM_002739.3 14/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF162,hmmpanther:PTHR24356,PIRSF_domain:PIRSF000550,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs780647467 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 53900689 53900689 C T 1 0 0 0 0 0 0 0 1 12645 535 19 1 1 PRKCG 19 53900689 Silent SNP C C3N-00175_T 610455 53900689 4716927 1225 10817 LILRB4 0 . GRCh38 19 54664373 54664373 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.543C>A p.= p.P181P ENST00000391736 6/14 172 127 45 255 255 0 strelka-varscan-mutect LILRB4,synonymous_variant,p.=,ENST00000391736,NM_001278426.3;LILRB4,synonymous_variant,p.=,ENST00000430952,NM_001278427.3;LILRB4,synonymous_variant,p.=,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,synonymous_variant,p.=,ENST00000391734,;LILRB4,synonymous_variant,p.=,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000470943,; A ENST00000391736 Transcript synonymous_variant 858/4002 543/1347 181/448 P ccC/ccA 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 6/14 PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Pfam_domain:PF00047,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 54664373 54664373 C A 1 0 0 0 0 0 0 0 1 8701 581 21 2 2 LILRB4 19 54664373 Silent SNP C C3N-00175_T 763684 54664373 3953243 1226 10818 FCAR 0 . GRCh38 19 54889793 54889793 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.794A>T p.Glu265Val p.E265V ENST00000355524 5/5 268 182 86 339 339 0 strelka-varscan-mutect FCAR,missense_variant,p.Glu265Val,ENST00000355524,NM_002000.3;FCAR,missense_variant,p.Glu243Val,ENST00000391725,NM_133269.3;FCAR,missense_variant,p.Glu253Val,ENST00000359272,NM_133272.3;FCAR,missense_variant,p.Glu231Val,ENST00000391724,NM_133278.3;FCAR,missense_variant,p.Glu157Val,ENST00000391726,NM_133273.3;FCAR,missense_variant,p.Glu169Val,ENST00000345937,NM_133271.3;FCAR,missense_variant,p.Glu156Val,ENST00000353758,NM_133277.3;FCAR,3_prime_UTR_variant,,ENST00000391723,NM_133274.3;FCAR,downstream_gene_variant,,ENST00000469767,;CTB-61M7.2,upstream_gene_variant,,ENST00000594721,;FCAR,non_coding_transcript_exon_variant,,ENST00000482092,;FCAR,non_coding_transcript_exon_variant,,ENST00000471750,;FCAR,non_coding_transcript_exon_variant,,ENST00000472634,;FCAR,downstream_gene_variant,,ENST00000488066,; T ENST00000355524 Transcript missense_variant 804/1483 794/864 265/287 E/V gAa/gTa 1 1 FCAR HGNC HGNC:3608 protein_coding YES CCDS12907.1 ENSP00000347714 P24071 UPI000011B429 NM_002000.3 deleterious(0.01) 5/5 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 54889793 54889793 A T 1 0 0 0 0 1 0 0 0 5636 246 9 4 4 FCAR 19 54889793 Missense_Mutation SNP A C3N-00175_T 225420 54889793 3727823 1227 10819 SHISA7 0 . GRCh38 19 55442446 55442446 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.418C>T p.Pro140Ser p.P140S ENST00000376325 1/4 212 198 14 290 290 0 strelka-varscan-mutect SHISA7,missense_variant,p.Pro140Ser,ENST00000376325,NM_001145176.1;SHISA7,upstream_gene_variant,,ENST00000416792,; A ENST00000376325 Transcript missense_variant 418/6033 418/1617 140/538 P/S Ccg/Tcg 1 -1 SHISA7 HGNC HGNC:35409 protein_coding YES CCDS46193.1 ENSP00000365503 A6NL88 UPI000193055E NM_001145176.1 tolerated(0.14) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF2,Pfam_domain:PF13908 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 55442446 55442446 G A 1 0 0 0 0 1 0 0 0 14545 1203 42 3 3 SHISA7 19 55442446 Missense_Mutation SNP G C3N-00175_T 552653 55442446 3175170 1228 10820 U2AF2 0 . GRCh38 19 55662541 55662541 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.526G>T p.Gly176Trp p.G176W ENST00000308924 6/12 82 49 33 129 129 0 strelka-varscan-mutect U2AF2,missense_variant,p.Gly176Trp,ENST00000450554,NM_001012478.1;U2AF2,missense_variant,p.Gly176Trp,ENST00000308924,NM_007279.2;U2AF2,missense_variant,p.Gly12Trp,ENST00000590551,;CTD-2537I9.12,intron_variant,,ENST00000589456,;CTD-2537I9.12,intron_variant,,ENST00000585940,;U2AF2,3_prime_UTR_variant,,ENST00000592874,;U2AF2,non_coding_transcript_exon_variant,,ENST00000587275,;U2AF2,downstream_gene_variant,,ENST00000587196,;U2AF2,downstream_gene_variant,,ENST00000588850,;U2AF2,downstream_gene_variant,,ENST00000592867,; T ENST00000308924 Transcript missense_variant 566/1698 526/1428 176/475 G/W Ggg/Tgg 1 1 U2AF2 HGNC HGNC:23156 protein_coding YES CCDS12933.1 ENSP00000307863 P26368 UPI0000137924 NM_007279.2 tolerated(0.16) 6/12 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR23139,SMART_domains:SM00360,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01642 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 55662541 55662541 G T 1 0 0 0 0 1 0 0 0 17340 1232 43 2 2 U2AF2 19 55662541 Missense_Mutation SNP G C3N-00175_T 220095 55662541 2955075 1229 10821 NLRP9 0 . GRCh38 19 55733310 55733310 + Nonsense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.521T>A p.Leu174Ter p.L174* ENST00000332836 2/9 153 104 49 191 191 0 strelka-varscan-mutect NLRP9,stop_gained,p.Leu174Ter,ENST00000332836,NM_176820.3;NLRP9,stop_gained,p.Leu174Ter,ENST00000590200,;RN7SKP109,upstream_gene_variant,,ENST00000410592,; T ENST00000332836 Transcript stop_gained 549/3484 521/2976 174/991 L/* tTa/tAa 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 2/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 39 55733310 55733310 A T 1 0 0 0 0 0 1 0 0 10522 372 13 4 4 NLRP9 19 55733310 Nonsense_Mutation SNP A C3N-00175_T 70769 55733310 2884306 1230 10822 ZNF667 0 . GRCh38 19 56441332 56441332 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1663T>A p.Tyr555Asn p.Y555N ENST00000504904 7/7 130 85 45 211 211 0 strelka-varscan-mutect ZNF667,missense_variant,p.Tyr555Asn,ENST00000504904,NM_001321356.1;ZNF667,missense_variant,p.Tyr555Asn,ENST00000292069,NM_022103.3;ZNF667,missense_variant,p.Tyr337Asn,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; T ENST00000504904 Transcript missense_variant 2383/4390 1663/1833 555/610 Y/N Tat/Aat 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs767720252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 56441332 56441332 A T 1 0 0 0 0 1 0 0 0 18648 420 15 4 4 ZNF667 19 56441332 Missense_Mutation SNP A C3N-00175_T 708022 56441332 2176284 1231 10823 DUXA 0 . GRCh38 19 57155272 57155272 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.539T>A p.Leu180Gln p.L180Q ENST00000554048 5/6 196 154 42 241 241 0 strelka-varscan-mutect DUXA,missense_variant,p.Leu180Gln,ENST00000554048,NM_001012729.1;CTC-360J11.5,downstream_gene_variant,,ENST00000604851,;CTC-360J11.6,upstream_gene_variant,,ENST00000604182,; T ENST00000554048 Transcript missense_variant 539/1006 539/615 180/204 L/Q cTg/cAg 1 -1 DUXA HGNC HGNC:32179 protein_coding YES CCDS33126.1 ENSP00000452398 A6NLW8 UPI0000198B7E NM_001012729.1 tolerated(0.32) 5/6 MODERATE 1 SNV 5 1 PASS rs1184189843 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 57155272 57155272 A T 1 0 0 0 0 1 0 0 0 4656 202 7 4 4 DUXA 19 57155272 Missense_Mutation SNP A C3N-00175_T 713940 57155272 1462344 1232 10824 ZNF606 0 . GRCh38 19 58000587 58000587 + Missense_Mutation SNP C C A rs774934695 C3N-00175_T C3N-00175_N C C c.184G>T p.Gly62Cys p.G62C ENST00000552184 3/3 123 73 50 134 133 1 strelka-varscan-mutect ZNF606,missense_variant,p.Gly62Cys,ENST00000552184,;ZNF606,missense_variant,p.Gly62Cys,ENST00000546715,;ZNF606,intron_variant,,ENST00000341164,NM_025027.3;ZNF606,intron_variant,,ENST00000547828,;ZNF606,intron_variant,,ENST00000551380,;ZNF606,intron_variant,,ENST00000547121,;CTD-2368P22.1,upstream_gene_variant,,ENST00000550135,;CTD-2368P22.1,upstream_gene_variant,,ENST00000546949,;CTD-2368P22.1,upstream_gene_variant,,ENST00000313957,;CTD-2368P22.1,upstream_gene_variant,,ENST00000553254,;CTD-2368P22.1,upstream_gene_variant,,ENST00000547364,;ZNF606,intron_variant,,ENST00000552579,;ZNF606,intron_variant,,ENST00000550599,;CTD-2368P22.1,upstream_gene_variant,,ENST00000546956,;ZNF606,downstream_gene_variant,,ENST00000550560,; A ENST00000552184 Transcript missense_variant 635/651 184/200 62/66 G/C Ggc/Tgc rs774934695 1 -1 ZNF606 HGNC HGNC:25879 protein_coding ENSP00000447075 F8W1H2 UPI0003F47CCC deleterious_low_confidence(0) 3/3 MODERATE SNV 2 1 PASS rs774934695 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 58000587 58000587 C A 1 0 0 0 0 1 0 0 0 18607 623 22 2 2 ZNF606 19 58000587 Missense_Mutation SNP C C3N-00175_T 845315 58000587 617029 1233 10825 DEFB125 0 . GRCh38 20 96269 96269 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.323G>T p.Gly108Val p.G108V ENST00000382410 2/2 140 117 23 190 189 1 strelka-varscan-mutect DEFB125,missense_variant,p.Gly108Val,ENST00000382410,NM_153325.3;DEFB125,non_coding_transcript_exon_variant,,ENST00000608838,; T ENST00000382410 Transcript missense_variant 323/587 323/471 108/156 G/V gGa/gTa 1 1 DEFB125 HGNC HGNC:18105 protein_coding YES CCDS12989.2 ENSP00000371847 Q8N687 UPI00001A36DE NM_153325.3 tolerated(0.09) 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF4 MODERATE 1 SNV 1 1 PASS rs1458481985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 96269 96269 G T 1 0 0 0 0 1 0 0 0 4214 1174 41 2 2 DEFB125 20 96269 Missense_Mutation SNP G C3N-00175_T 96269 64347898 1234 10826 FAM110A 0 . GRCh38 20 845633 845633 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.829G>T p.Val277Leu p.V277L ENST00000304189 3/3 227 181 46 340 340 0 strelka-varscan-mutect FAM110A,missense_variant,p.Val277Leu,ENST00000304189,NM_001289145.1;FAM110A,missense_variant,p.Val277Leu,ENST00000381941,NM_001289146.1,NM_001042353.2;FAM110A,missense_variant,p.Val277Leu,ENST00000381939,;FAM110A,missense_variant,p.Val277Leu,ENST00000246100,NM_207121.4,NM_031424.5;FAM110A,missense_variant,p.Val277Leu,ENST00000541082,NM_001289147.1;FAM110A,missense_variant,p.Val171Leu,ENST00000505691,; T ENST00000304189 Transcript missense_variant 1210/1856 829/888 277/295 V/L Gtg/Ttg COSM1029305 1 1 FAM110A HGNC HGNC:16188 protein_coding YES CCDS13008.1 ENSP00000354163 Q9BQ89 UPI00001285E4 NM_001289145.1 deleterious(0.01) 3/3 hmmpanther:PTHR14758:SF4,hmmpanther:PTHR14758,Pfam_domain:PF14160 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 845633 845633 G T 1 0 0 0 0 1 0 0 0 5260 1145 40 1 1 FAM110A 20 845633 Missense_Mutation SNP G C3N-00175_T 749364 845633 63598534 1235 10827 TGM3 0 . GRCh38 20 2328130 2328130 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1098G>T p.Gln366His p.Q366H ENST00000381458 9/13 118 97 21 186 186 0 strelka-varscan-mutect TGM3,missense_variant,p.Gln366His,ENST00000381458,NM_003245.3;TGM3,downstream_gene_variant,,ENST00000463090,; T ENST00000381458 Transcript missense_variant 1161/2642 1098/2082 366/693 Q/H caG/caT 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 tolerated(0.07) 9/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 2328130 2328130 G T 1 0 0 0 0 1 0 0 0 16264 1020 36 2 2 TGM3 20 2328130 Missense_Mutation SNP G C3N-00175_T 1482497 2328130 62116037 1236 10828 SNRPB 0 . GRCh38 20 2463136 2463136 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.512G>T p.Gly171Val p.G171V ENST00000438552 5/7 48 42 6 72 72 0 strelka-varscan-mutect SNRPB,missense_variant,p.Gly171Val,ENST00000381342,NM_003091.3;SNRPB,missense_variant,p.Gly171Val,ENST00000438552,NM_198216.1;SNRPB,3_prime_UTR_variant,,ENST00000474384,;RP4-734P14.4,downstream_gene_variant,,ENST00000461548,; A ENST00000438552 Transcript missense_variant 675/1008 512/723 171/240 G/V gGc/gTc 1 -1 SNRPB HGNC HGNC:11153 protein_coding YES CCDS13026.1 ENSP00000412566 P14678 UPI00001351FF NM_198216.1 tolerated(0.11) 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR10701:SF3,hmmpanther:PTHR10701,PIRSF_domain:PIRSF037187 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -14.40418 0.9999743 1 1 1 0 A 3 1 39 2463136 2463136 C A 1 0 0 0 0 1 0 0 0 15181 739 26 2 2 SNRPB 20 2463136 Missense_Mutation SNP C C3N-00175_T 135006 2463136 61981031 1237 10829 TMC2 0 . GRCh38 20 2641279 2641279 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.2649T>A p.= p.S883S ENST00000358864 20/20 185 164 21 260 260 0 strelka-varscan-mutect TMC2,synonymous_variant,p.=,ENST00000358864,NM_080751.2; A ENST00000358864 Transcript synonymous_variant 2664/3169 2649/2721 883/906 S tcT/tcA 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 20/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 2641279 2641279 T A 1 0 0 0 0 0 0 0 1 16431 1567 55 4 4 TMC2 20 2641279 Silent SNP T C3N-00175_T 178143 2641279 61802888 1238 10830 PLCB1 0 . GRCh38 20 8765319 8765319 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.2891C>A p.Ala964Asp p.A964D ENST00000338037 26/32 113 101 12 185 185 0 strelka-varscan-mutect PLCB1,missense_variant,p.Ala964Asp,ENST00000378641,NM_182734.2;PLCB1,missense_variant,p.Ala964Asp,ENST00000338037,NM_015192.3;PLCB1,missense_variant,p.Ala884Asp,ENST00000612075,;PLCB1,missense_variant,p.Ala884Asp,ENST00000617005,;PLCB1,missense_variant,p.Ala863Asp,ENST00000637919,;PLCB1,missense_variant,p.Ala964Asp,ENST00000378637,;PLCB1,missense_variant,p.Ala863Asp,ENST00000625874,;PLCB1,missense_variant,p.Ala863Asp,ENST00000626966,;PLCB1,missense_variant,p.Ala51Asp,ENST00000628239,;PLCB1,non_coding_transcript_exon_variant,,ENST00000635830,;PLCB1,non_coding_transcript_exon_variant,,ENST00000636825,;PLCB1,missense_variant,p.Ala705Asp,ENST00000487210,;PLCB1,missense_variant,p.Ala21Asp,ENST00000635929,;PLCB1,non_coding_transcript_exon_variant,,ENST00000494924,; A ENST00000338037 Transcript missense_variant 3278/7092 2891/3651 964/1216 A/D gCc/gAc 1 1 PLCB1 HGNC HGNC:15917 protein_coding YES CCDS13102.1 ENSP00000338185 Q9NQ66 UPI0000131A8F NM_015192.3 tolerated(0.25) 26/32 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,PIRSF_domain:PIRSF000956 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 8765319 8765319 C A 1 0 0 0 0 1 0 0 0 12121 739 26 2 2 PLCB1 20 8765319 Missense_Mutation SNP C C3N-00175_T 6124040 8765319 55678848 1239 10831 PLCB1 0 . GRCh38 20 8774666 8774666 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.3058C>T p.Arg1020Trp p.R1020W ENST00000338037 27/32 89 77 12 125 125 0 strelka-varscan-mutect PLCB1,missense_variant,p.Arg1020Trp,ENST00000378641,NM_182734.2;PLCB1,missense_variant,p.Arg1020Trp,ENST00000338037,NM_015192.3;PLCB1,missense_variant,p.Arg940Trp,ENST00000612075,;PLCB1,missense_variant,p.Arg940Trp,ENST00000617005,;PLCB1,missense_variant,p.Arg919Trp,ENST00000637919,;PLCB1,missense_variant,p.Arg1020Trp,ENST00000378637,;PLCB1,missense_variant,p.Arg919Trp,ENST00000625874,;PLCB1,missense_variant,p.Arg919Trp,ENST00000626966,;PLCB1,missense_variant,p.Arg107Trp,ENST00000628239,;PLCB1,non_coding_transcript_exon_variant,,ENST00000635830,;PLCB1,non_coding_transcript_exon_variant,,ENST00000636825,;PLCB1,missense_variant,p.Arg761Trp,ENST00000487210,;PLCB1,missense_variant,p.Arg77Trp,ENST00000635929,;PLCB1,non_coding_transcript_exon_variant,,ENST00000494924,; T ENST00000338037 Transcript missense_variant 3445/7092 3058/3651 1020/1216 R/W Cgg/Tgg COSM3549446,COSM3549447 1 1 PLCB1 HGNC HGNC:15917 protein_coding YES CCDS13102.1 ENSP00000338185 Q9NQ66 UPI0000131A8F NM_015192.3 tolerated(0.08) 27/32 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,Gene3D:1jadA00,PIRSF_domain:PIRSF000956,Pfam_domain:PF08703,Superfamily_domains:0053448 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1023330264 . 0 202 6 2 0 0 0 0 -19.52097 0.9998993 1 1 1 0 T 3 4 39 8774666 8774666 C T 1 0 0 0 0 1 0 0 0 12121 875 31 1 1 PLCB1 20 8774666 Missense_Mutation SNP C C3N-00175_T 9347 8774666 55669501 1240 10832 JAG1 0 . GRCh38 20 10647006 10647006 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.1818G>C p.Lys606Asn p.K606N ENST00000254958 14/26 376 340 36 613 613 0 strelka-varscan-mutect JAG1,missense_variant,p.Lys606Asn,ENST00000254958,NM_000214.2;JAG1,missense_variant,p.Lys56Asn,ENST00000613518,;MIR6870,downstream_gene_variant,,ENST00000615931,;JAG1,non_coding_transcript_exon_variant,,ENST00000423891,;JAG1,non_coding_transcript_exon_variant,,ENST00000612857,;JAG1,upstream_gene_variant,,ENST00000488480,;JAG1,downstream_gene_variant,,ENST00000617965,;JAG1,downstream_gene_variant,,ENST00000620743,;JAG1,downstream_gene_variant,,ENST00000622545,; G ENST00000254958 Transcript missense_variant 2395/6048 1818/3657 606/1218 K/N aaG/aaC 1 -1 JAG1 HGNC HGNC:6188 protein_coding YES CCDS13112.1 ENSP00000254958 P78504 UPI00000498B5 NM_000214.2 deleterious(0.03) 14/26 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF269,SMART_domains:SM00179,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 10647006 10647006 C G 1 0 0 0 0 1 0 0 0 7847 912 32 4 4 JAG1 20 10647006 Missense_Mutation SNP C C3N-00175_T 1872340 10647006 53797161 1241 10833 KIF16B 0 . GRCh38 20 16507992 16507992 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.665G>T p.Arg222Met p.R222M ENST00000408042 7/23 143 129 14 223 223 0 strelka-mutect KIF16B,missense_variant,p.Arg222Met,ENST00000354981,NM_024704.4;KIF16B,missense_variant,p.Arg222Met,ENST00000636835,NM_001199865.1;KIF16B,missense_variant,p.Arg222Met,ENST00000408042,NM_001199866.1; A ENST00000408042 Transcript missense_variant 823/4640 665/4179 222/1392 R/M aGg/aTg 1 -1 KIF16B HGNC HGNC:15869 protein_coding YES CCDS56178.1 ENSP00000384164 Q96L93 UPI00003BF77C NM_001199866.1 deleterious(0) 7/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF400,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 16507992 16507992 C A 1 0 0 0 0 1 0 0 0 8142 681 24 2 2 KIF16B 20 16507992 Missense_Mutation SNP C C3N-00175_T 5860986 16507992 47936175 1242 10834 CFAP61 0 . GRCh38 20 20277396 20277396 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2734C>G p.Pro912Ala p.P912A ENST00000245957 22/27 134 116 18 198 198 0 strelka-varscan-mutect CFAP61,missense_variant,p.Pro912Ala,ENST00000245957,NM_015585.3;CFAP61,intron_variant,,ENST00000488640,;CFAP61,missense_variant,p.Pro268Ala,ENST00000377308,; G ENST00000245957 Transcript missense_variant 2810/4082 2734/3714 912/1237 P/A Cca/Gca 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 tolerated(0.05) 22/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 20277396 20277396 C G 1 0 0 0 0 1 0 0 0 3028 623 22 4 4 CFAP61 20 20277396 Missense_Mutation SNP C C3N-00175_T 3769404 20277396 44166771 1243 10835 CFAP61 0 . GRCh38 20 20298270 20298270 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.3306C>G p.Cys1102Trp p.C1102W ENST00000245957 25/27 297 241 56 379 379 0 strelka-varscan-mutect CFAP61,missense_variant,p.Cys1102Trp,ENST00000245957,NM_015585.3;CFAP61,non_coding_transcript_exon_variant,,ENST00000469994,;CFAP61,3_prime_UTR_variant,,ENST00000377308,; G ENST00000245957 Transcript missense_variant 3382/4082 3306/3714 1102/1237 C/W tgC/tgG 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 deleterious(0) 25/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 20298270 20298270 C G 1 0 0 0 0 1 0 0 0 3028 747 26 4 4 CFAP61 20 20298270 Missense_Mutation SNP C C3N-00175_T 20874 20298270 44145897 1244 10836 ENTPD6 0 . GRCh38 20 25217538 25217538 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.835G>T p.Ala279Ser p.A279S ENST00000376652 9/15 206 162 44 256 256 0 strelka-varscan-mutect ENTPD6,missense_variant,p.Ala278Ser,ENST00000360031,;ENTPD6,missense_variant,p.Ala279Ser,ENST00000376652,NM_001247.2;ENTPD6,missense_variant,p.Ala262Ser,ENST00000354989,NM_001114089.1;ENTPD6,missense_variant,p.Ala279Ser,ENST00000433259,;ENTPD6,missense_variant,p.Ala103Ser,ENST00000376666,;ENTPD6,missense_variant,p.Ala261Ser,ENST00000439162,;ENTPD6,missense_variant,p.Ala231Ser,ENST00000425813,;ENTPD6,missense_variant,p.Ala200Ser,ENST00000433417,;ENTPD6,missense_variant,p.Ala172Ser,ENST00000447877,;ENTPD6,missense_variant,p.Ala213Ser,ENST00000417467,;ENTPD6,missense_variant,p.Ala137Ser,ENST00000427553,;ENTPD6,downstream_gene_variant,,ENST00000435520,;ENTPD6,downstream_gene_variant,,ENST00000418890,;Y_RNA,downstream_gene_variant,,ENST00000365544,;ENTPD6,non_coding_transcript_exon_variant,,ENST00000471478,;ENTPD6,upstream_gene_variant,,ENST00000485936,;ENTPD6,upstream_gene_variant,,ENST00000481322,; T ENST00000376652 Transcript missense_variant 998/2750 835/1455 279/484 A/S Gca/Tca 1 1 ENTPD6 HGNC HGNC:3368 protein_coding YES CCDS13170.1 ENSP00000365840 O75354 UPI0000052B67 NM_001247.2 tolerated(1) 9/15 hmmpanther:PTHR11782:SF36,hmmpanther:PTHR11782,Pfam_domain:PF01150 MODERATE 1 SNV 1 1 PASS rs896560972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 25217538 25217538 G T 1 0 0 0 0 1 0 0 0 4988 1203 42 2 2 ENTPD6 20 25217538 Missense_Mutation SNP G C3N-00175_T 4919268 25217538 39226629 1245 10837 DEFB121 0 . GRCh38 20 31405049 31405049 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.95C>A p.Thr32Lys p.T32K ENST00000376314 2/2 78 55 23 112 112 0 strelka-varscan-mutect DEFB121,missense_variant,p.Thr32Lys,ENST00000376314,NM_001011878.2;DEFB121,non_coding_transcript_exon_variant,,ENST00000376312,; T ENST00000376314 Transcript missense_variant 209/389 95/231 32/76 T/K aCa/aAa 1 -1 DEFB121 HGNC HGNC:18101 protein_coding YES CCDS33456.1 ENSP00000417128 Q5J5C9 UPI00004A06B0 NM_001011878.2 tolerated(0.85) 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF30,Pfam_domain:PF13841,PD866254 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 31405049 31405049 G T 1 0 0 0 0 1 0 0 0 4211 1377 48 2 2 DEFB121 20 31405049 Missense_Mutation SNP G C3N-00175_T 6187511 31405049 33039118 1246 10838 EFCAB8 0 . GRCh38 20 32961223 32961223 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.3481C>A p.Gln1161Lys p.Q1161K ENST00000400522 27/27 115 98 17 156 156 0 strelka-varscan-mutect EFCAB8,missense_variant,p.Gln1161Lys,ENST00000400522,; A ENST00000400522 Transcript missense_variant 3575/3961 3481/3867 1161/1288 Q/K Cag/Aag 1 1 EFCAB8 HGNC HGNC:34532 protein_coding YES ENSP00000383366 A0A096LNH2 UPI00018E24E9 tolerated_low_confidence(0.07) 27/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 32961223 32961223 C A 1 0 0 0 0 1 0 0 0 4775 595 21 2 2 EFCAB8 20 32961223 Missense_Mutation SNP C C3N-00175_T 1556174 32961223 31482944 1247 10839 BPIFB6 0 . GRCh38 20 33033038 33033039 + Frame_Shift_Ins INS - - A novel C3N-00175_T C3N-00175_N - - c.153dupA p.Gly52ArgfsTer74 p.G52Rfs*74 ENST00000349552 2/15 135 115 20 187 187 0 sindel-varindel-pindel BPIFB6,frameshift_variant,p.Gly52ArgfsTer74,ENST00000349552,NM_174897.2;BPIFB6,frameshift_variant,p.Gly53ArgfsTer16,ENST00000542375,; A ENST00000349552 Transcript frameshift_variant 152-153/1362 152-153/1362 51/453 A/AX gca/gcAa 1 1 BPIFB6 HGNC HGNC:16504 protein_coding YES CCDS13211.1 ENSP00000344929 Q8NFQ5 UPI000003C8F3 NM_174897.2 2/15 hmmpanther:PTHR10504:SF71,hmmpanther:PTHR10504,Pfam_domain:PF01273 HIGH 1 insertion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 39 33033038 33033038 - A 1 0 1 1 0 0 0 0 0 1661 710 25 0 0 BPIFB6 20 33033038 Frame_Shift_Ins INS - C3N-00175_T 71815 33033038 31411129 1248 10840 BPIFB1 0 . GRCh38 20 33288775 33288775 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.150C>T p.= p.T50T ENST00000253354 3/16 176 137 39 194 194 0 strelka-varscan-mutect BPIFB1,synonymous_variant,p.=,ENST00000253354,NM_033197.2;BPIFB1,synonymous_variant,p.=,ENST00000423645,; T ENST00000253354 Transcript synonymous_variant 311/1727 150/1455 50/484 T acC/acT 1 1 BPIFB1 HGNC HGNC:16108 protein_coding YES CCDS13218.1 ENSP00000253354 Q8TDL5 UPI000006EEF9 NM_033197.2 3/16 hmmpanther:PTHR10504:SF21,hmmpanther:PTHR10504,PIRSF_domain:PIRSF037186,Pfam_domain:PF01273,SMART_domains:SM00328 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 33288775 33288775 C T 1 0 0 0 0 0 0 0 1 1657 581 21 3 3 BPIFB1 20 33288775 Silent SNP C C3N-00175_T 255737 33288775 31155392 1249 10841 NCOA6 0 . GRCh38 20 34741119 34741119 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.5137G>T p.Val1713Leu p.V1713L ENST00000374796 12/16 302 273 29 292 292 0 strelka-varscan-mutect NCOA6,missense_variant,p.Val1713Leu,ENST00000374796,NM_001318240.1;NCOA6,missense_variant,p.Val1713Leu,ENST00000359003,NM_014071.3;NCOA6,intron_variant,,ENST00000612493,NM_001242539.1;NCOA6,intron_variant,,ENST00000616167,;NCOA6,intron_variant,,ENST00000628752,; A ENST00000374796 Transcript missense_variant 7708/9311 5137/6192 1713/2063 V/L Gta/Tta COSM4979052 1 -1 NCOA6 HGNC HGNC:15936 protein_coding YES CCDS13241.1 ENSP00000363929 Q14686 UPI000013C634 NM_001318240.1 tolerated_low_confidence(0.08) 12/16 Low_complexity_(Seg):seg,hmmpanther:PTHR15690,hmmpanther:PTHR15690:SF0 1 MODERATE 1 SNV 1 1 1 PASS rs1174960530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 34741119 34741119 C A 1 0 0 0 0 1 0 0 0 10252 478 17 2 2 NCOA6 20 34741119 Missense_Mutation SNP C C3N-00175_T 1452344 34741119 29703048 1250 10842 44 2 NCOA6 0 . GRCh38 20 34741121 34741121 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.5135C>T p.Pro1712Leu p.P1712L ENST00000374796 12/16 295 266 29 297 297 0 strelka-varscan-mutect NCOA6,missense_variant,p.Pro1712Leu,ENST00000374796,NM_001318240.1;NCOA6,missense_variant,p.Pro1712Leu,ENST00000359003,NM_014071.3;NCOA6,intron_variant,,ENST00000612493,NM_001242539.1;NCOA6,intron_variant,,ENST00000616167,;NCOA6,intron_variant,,ENST00000628752,; A ENST00000374796 Transcript missense_variant 7706/9311 5135/6192 1712/2063 P/L cCt/cTt 1 -1 NCOA6 HGNC HGNC:15936 protein_coding YES CCDS13241.1 ENSP00000363929 Q14686 UPI000013C634 NM_001318240.1 deleterious_low_confidence(0) 12/16 Low_complexity_(Seg):seg,hmmpanther:PTHR15690,hmmpanther:PTHR15690:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 34741121 34741121 G A 1 0 0 0 0 1 0 0 0 10252 1000 35 3 3 NCOA6 20 34741121 Missense_Mutation SNP G C3N-00175_T 2 34741121 29703046 1251 10843 44 2 MYL9 0 . GRCh38 20 36548162 36548162 + Missense_Mutation SNP C C A rs7273824 C3N-00175_T C3N-00175_N C C c.315C>A p.Asn105Lys p.N105K ENST00000279022 3/4 75 67 8 110 110 0 strelka-varscan-mutect MYL9,missense_variant,p.Asn105Lys,ENST00000279022,NM_006097.4;MYL9,intron_variant,,ENST00000346786,NM_181526.2;DLGAP4-AS1,intron_variant,,ENST00000439595,;DLGAP4-AS1,intron_variant,,ENST00000425233,; A ENST00000279022 Transcript missense_variant 419/2821 315/519 105/172 N/K aaC/aaA rs7273824,COSM3693464 1 1 MYL9 HGNC HGNC:15754 protein_coding YES CCDS13276.1 ENSP00000279022 P24844 UPI00000012F1 NM_006097.4 deleterious(0.01) 3/4 PROSITE_profiles:PS50222,hmmpanther:PTHR23049,hmmpanther:PTHR23049:SF37,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs7273824 . 0 206 4 0 0 0 0 0 -17.59094 1 1 1 1 0 A 3 1 39 36548162 36548162 C A 1 0 0 0 0 1 0 0 0 10054 535 19 1 1 MYL9 20 36548162 Missense_Mutation SNP C C3N-00175_T 1807041 36548162 27896005 1252 10844 PTPRT 0 . GRCh38 20 42315785 42315785 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.2077C>G p.Pro693Ala p.P693A ENST00000373198 12/32 206 178 28 221 221 0 strelka-varscan-mutect PTPRT,missense_variant,p.Pro693Ala,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Pro693Ala,ENST00000373193,;PTPRT,missense_variant,p.Pro693Ala,ENST00000373201,;PTPRT,missense_variant,p.Pro693Ala,ENST00000373190,;PTPRT,missense_variant,p.Pro693Ala,ENST00000373184,;PTPRT,missense_variant,p.Pro693Ala,ENST00000356100,;PTPRT,missense_variant,p.Pro693Ala,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Pro311Ala,ENST00000612229,;PTPRT,missense_variant,p.Pro309Ala,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; C ENST00000373198 Transcript missense_variant 2313/12746 2077/4383 693/1460 P/A Cct/Gct 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 tolerated(0.63) 12/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 42315785 42315785 G C 1 0 0 0 0 1 0 0 0 12967 1232 43 4 4 PTPRT 20 42315785 Missense_Mutation SNP G C3N-00175_T 5767623 42315785 22128382 1253 10845 L3MBTL1 0 . GRCh38 20 43536123 43536123 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1886G>T p.Gly629Val p.G629V ENST00000418998 18/22 236 202 34 282 282 0 strelka-varscan-mutect L3MBTL1,missense_variant,p.Gly347Val,ENST00000422861,;L3MBTL1,missense_variant,p.Gly629Val,ENST00000418998,NM_032107.4;L3MBTL1,missense_variant,p.Gly561Val,ENST00000373135,NM_015478.6;L3MBTL1,missense_variant,p.Gly629Val,ENST00000427442,;L3MBTL1,missense_variant,p.Gly566Val,ENST00000373134,;L3MBTL1,upstream_gene_variant,,ENST00000471977,;L3MBTL1,3_prime_UTR_variant,,ENST00000445228,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000373133,;L3MBTL1,upstream_gene_variant,,ENST00000494117,;L3MBTL1,downstream_gene_variant,,ENST00000497347,;RP1-138B7.6,upstream_gene_variant,,ENST00000621802,;L3MBTL1,downstream_gene_variant,,ENST00000485334,;L3MBTL1,downstream_gene_variant,,ENST00000483547,; T ENST00000418998 Transcript missense_variant 1962/3365 1886/2523 629/840 G/V gGc/gTc 1 1 L3MBTL1 HGNC HGNC:15905 protein_coding YES CCDS46602.2 ENSP00000398516 Q9Y468 UPI0001E18E26 NM_032107.4 deleterious(0.01) 18/22 hmmpanther:PTHR12247:SF69,hmmpanther:PTHR12247,Pfam_domain:PF01530,Superfamily_domains:0042508,Superfamily_domains:SSF63748 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 43536123 43536123 G T 1 0 0 0 0 1 0 0 0 8493 1203 42 2 2 L3MBTL1 20 43536123 Missense_Mutation SNP G C3N-00175_T 1220338 43536123 20908044 1254 10846 KCNK15 0 . GRCh38 20 44746047 44746047 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.137G>T p.Gly46Val p.G46V ENST00000372861 1/2 58 35 23 71 71 0 strelka-varscan-mutect KCNK15,missense_variant,p.Gly46Val,ENST00000372861,NM_022358.3;RP4-781B1.5,upstream_gene_variant,,ENST00000611368,;KCNK15-AS1,upstream_gene_variant,,ENST00000427303,;KCNK15-AS1,upstream_gene_variant,,ENST00000445420,; T ENST00000372861 Transcript missense_variant 268/2599 137/993 46/330 G/V gGc/gTc 1 1 KCNK15 HGNC HGNC:13814 protein_coding YES CCDS13337.1 ENSP00000361952 Q9H427 UPI000003EA1C NM_022358.3 tolerated(0.17) 1/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF18,PIRSF_domain:PIRSF038061 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 44746047 44746047 G T 1 0 0 0 0 1 0 0 0 7979 1203 42 2 2 KCNK15 20 44746047 Missense_Mutation SNP G C3N-00175_T 1209924 44746047 19698120 1255 10847 KCNK15 0 . GRCh38 20 44750608 44750608 + Missense_Mutation SNP G G A rs367808576 C3N-00175_T C3N-00175_N G G c.763G>A p.Glu255Lys p.E255K ENST00000372861 2/2 140 106 34 177 177 0 strelka-varscan-mutect KCNK15,missense_variant,p.Glu255Lys,ENST00000372861,NM_022358.3;RIMS4,downstream_gene_variant,,ENST00000372851,NM_182970.3;RP4-781B1.5,downstream_gene_variant,,ENST00000611368,;KCNK15-AS1,upstream_gene_variant,,ENST00000427303,;KCNK15-AS1,upstream_gene_variant,,ENST00000445420,; A ENST00000372861 Transcript missense_variant 894/2599 763/993 255/330 E/K Gag/Aag rs367808576 1 1 KCNK15 HGNC HGNC:13814 protein_coding YES CCDS13337.1 ENSP00000361952 Q9H427 UPI000003EA1C NM_022358.3 tolerated(0.56) 2/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF18,PIRSF_domain:PIRSF038061,Prints_domain:PR01690 MODERATE 1 SNV 1 1 PASS rs367808576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 44750608 44750608 G A 1 0 0 0 0 1 0 0 0 7979 1059 37 1 1 KCNK15 20 44750608 Missense_Mutation SNP G C3N-00175_T 4561 44750608 19693559 1256 10848 SEMG1 0 . GRCh38 20 45208519 45208519 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1222G>T p.Gly408Cys p.G408C ENST00000372781 2/3 121 96 25 167 167 0 strelka-varscan-mutect SEMG1,missense_variant,p.Gly408Cys,ENST00000372781,NM_003007.3; T ENST00000372781 Transcript missense_variant 1279/1662 1222/1389 408/462 G/C Ggc/Tgc 1 1 SEMG1 HGNC HGNC:10742 protein_coding YES CCDS13345.1 ENSP00000361867 P04279 UPI0000135844 NM_003007.3 tolerated(0.08) 2/3 hmmpanther:PTHR10547:SF4,hmmpanther:PTHR10547,Pfam_domain:PF05474 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 45208519 45208519 G T 1 0 0 0 0 1 0 0 0 14320 1348 47 2 2 SEMG1 20 45208519 Missense_Mutation SNP G C3N-00175_T 457911 45208519 19235648 1257 10849 RBPJL 0 . GRCh38 20 45316707 45316707 + Nonsense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.1302C>A p.Cys434Ter p.C434* ENST00000343694 12/12 95 77 18 133 133 0 strelka-varscan-mutect RBPJL,stop_gained,p.Cys434Ter,ENST00000343694,NM_014276.3;RBPJL,stop_gained,p.Cys433Ter,ENST00000372743,NM_001281449.1;RBPJL,missense_variant,p.Arg438Ser,ENST00000372741,NM_001281448.1;RBPJL,missense_variant,p.Arg151Ser,ENST00000464504,;RBPJL,non_coding_transcript_exon_variant,,ENST00000622729,; A ENST00000343694 Transcript stop_gained 1374/2489 1302/1554 434/517 C/* tgC/tgA COSM1412048 1 1 RBPJL HGNC HGNC:13761 protein_coding YES CCDS13349.1 ENSP00000341243 Q9UBG7 UPI0000047297 NM_014276.3 12/12 Gene3D:2.60.40.10,hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,Superfamily_domains:SSF81296 1 HIGH 1 SNV 2 1 1 PASS rs1333952891 . 0 203 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 45316707 45316707 C A 1 0 0 0 0 0 1 0 0 13330 777 27 1 1 RBPJL 20 45316707 Nonsense_Mutation SNP C C3N-00175_T 108188 45316707 19127460 1258 10850 TP53TG5 0 . GRCh38 20 45375370 45375370 + Missense_Mutation SNP G G T rs778649036 C3N-00175_T C3N-00175_N G G c.437C>A p.Ala146Glu p.A146E ENST00000372726 4/5 475 411 64 523 522 1 strelka-varscan-mutect TP53TG5,missense_variant,p.Ala146Glu,ENST00000372726,NM_014477.2;SYS1,3_prime_UTR_variant,,ENST00000426004,NM_001099791.2;SYS1-DBNDD2,intron_variant,,ENST00000475242,;TP53TG5,downstream_gene_variant,,ENST00000494455,;TP53TG5,downstream_gene_variant,,ENST00000488588,;SYS1-DBNDD2,intron_variant,,ENST00000419593,;SYS1-DBNDD2,intron_variant,,ENST00000452133,;SYS1-DBNDD2,intron_variant,,ENST00000458187,; T ENST00000372726 Transcript missense_variant 594/2374 437/873 146/290 A/E gCg/gAg rs778649036,COSM1027225 1 -1 TP53TG5 HGNC HGNC:15856 protein_coding YES CCDS13352.1 ENSP00000361811 Q9Y2B4 UPI000000165C NM_014477.2 tolerated(0.73) 4/5 hmmpanther:PTHR15562,hmmpanther:PTHR15562:SF0,Pfam_domain:PF15331 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778649036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 45375370 45375370 G T 1 0 0 0 0 1 0 0 0 16870 1087 38 1 1 TP53TG5 20 45375370 Missense_Mutation SNP G C3N-00175_T 58663 45375370 19068797 1259 10851 ZSWIM3 0 . GRCh38 20 45877565 45877565 + Missense_Mutation SNP G G T rs763424614 C3N-00175_T C3N-00175_N G G c.1007G>T p.Arg336Leu p.R336L ENST00000255152 2/2 175 127 48 239 239 0 strelka-varscan-mutect ZSWIM3,missense_variant,p.Arg336Leu,ENST00000255152,NM_080752.3;ZSWIM1,upstream_gene_variant,,ENST00000372523,NM_080603.4;ZSWIM1,upstream_gene_variant,,ENST00000372520,; T ENST00000255152 Transcript missense_variant 1216/2773 1007/2091 336/696 R/L cGg/cTg rs763424614,COSM352096 1 1 ZSWIM3 HGNC HGNC:16157 protein_coding YES CCDS13381.1 ENSP00000255152 Q96MP5 UPI00000736E4 NM_080752.3 deleterious(0.01) 2/2 hmmpanther:PTHR31569:SF3,hmmpanther:PTHR31569 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763424614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 45877565 45877565 G T 1 0 0 0 0 1 0 0 0 18843 1116 39 1 1 ZSWIM3 20 45877565 Missense_Mutation SNP G C3N-00175_T 502195 45877565 18566602 1260 10852 ZNF335 0 . GRCh38 20 45965755 45965755 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.975A>T p.= p.P325P ENST00000322927 7/28 93 76 17 94 94 0 strelka-varscan-mutect ZNF335,synonymous_variant,p.=,ENST00000322927,NM_022095.3;ZNF335,non_coding_transcript_exon_variant,,ENST00000476822,;ZNF335,downstream_gene_variant,,ENST00000494955,;ZNF335,upstream_gene_variant,,ENST00000475002,; A ENST00000322927 Transcript synonymous_variant 1076/4430 975/4029 325/1342 P ccA/ccT 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 7/28 hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF36 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 45965755 45965755 T A 1 0 0 0 0 0 0 0 1 18424 1567 55 4 4 ZNF335 20 45965755 Silent SNP T C3N-00175_T 88190 45965755 18478412 1261 10853 PREX1 0 . GRCh38 20 48692672 48692672 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1036G>T p.Ala346Ser p.A346S ENST00000371941 8/40 137 120 17 148 148 0 strelka-varscan-mutect PREX1,missense_variant,p.Ala346Ser,ENST00000371941,NM_020820.3;PREX1,missense_variant,p.Gly5Cys,ENST00000620554,; A ENST00000371941 Transcript missense_variant,splice_region_variant 1059/6636 1036/4980 346/1659 A/S Gcg/Tcg 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 tolerated(0.12) 8/40 PROSITE_profiles:PS50003,hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 48692672 48692672 C A 1 0 0 0 0 1 0 0 0 12610 695 24 2 2 PREX1 20 48692672 Missense_Mutation SNP C C3N-00175_T 2726917 48692672 15751495 1262 10854 SLC9A8 0 . GRCh38 20 49887895 49887895 + Missense_Mutation SNP G G T rs371568441 C3N-00175_T C3N-00175_N G G c.1753G>T p.Gly585Cys p.G585C ENST00000417961 16/16 152 103 49 176 176 0 strelka-varscan-mutect SLC9A8,missense_variant,p.Gly585Cys,ENST00000417961,NM_001260491.1;SLC9A8,missense_variant,p.Gly569Cys,ENST00000361573,NM_015266.2;SLC9A8,non_coding_transcript_exon_variant,,ENST00000490250,; T ENST00000417961 Transcript missense_variant 1963/6309 1753/1794 585/597 G/C Ggc/Tgc rs371568441 1 1 SLC9A8 HGNC HGNC:20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 UPI00017A7E08 NM_001260491.1 tolerated(0.05) 16/16 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF122 MODERATE 1 SNV 2 1 PASS rs371568441 . 0 207 0 3 0 0 0 0 -20 0.9999986 1 1 1 0 T 3 4 39 49887895 49887895 G T 1 0 0 0 0 1 0 0 0 15002 1232 43 2 2 SLC9A8 20 49887895 Missense_Mutation SNP G C3N-00175_T 1195223 49887895 14556272 1263 10855 SPATA2 0 . GRCh38 20 49906099 49906099 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1083A>T p.Arg361Ser p.R361S ENST00000422556 3/3 73 59 14 117 117 0 strelka-varscan-mutect SPATA2,missense_variant,p.Arg361Ser,ENST00000422556,NM_001135773.1;SPATA2,missense_variant,p.Arg361Ser,ENST00000289431,NM_006038.3; A ENST00000422556 Transcript missense_variant 1433/4138 1083/1563 361/520 R/S agA/agT 1 -1 SPATA2 HGNC HGNC:14681 protein_coding YES CCDS13422.1 ENSP00000416799 Q9UM82 UPI000013557F NM_001135773.1 tolerated(0.11) 3/3 hmmpanther:PTHR15326,hmmpanther:PTHR15326:SF8 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 49906099 49906099 T A 1 0 0 0 0 1 0 0 0 15335 1780 62 4 4 SPATA2 20 49906099 Missense_Mutation SNP T C3N-00175_T 18204 49906099 14538068 1264 10856 ZFP64 0 . GRCh38 20 52085010 52085010 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1485G>T p.Glu495Asp p.E495D ENST00000361387 9/9 109 81 28 104 104 0 strelka-varscan-mutect ZFP64,missense_variant,p.Glu495Asp,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.Glu276Asp,ENST00000371523,NM_001319146.1;ZFP64,3_prime_UTR_variant,,ENST00000456175,;ZFP64,intron_variant,,ENST00000371518,;ZFP64,downstream_gene_variant,,ENST00000395989,;ZFP64,downstream_gene_variant,,ENST00000477786,;ZFP64,downstream_gene_variant,,ENST00000467811,; A ENST00000361387 Transcript missense_variant 1546/2545 1485/1938 495/645 E/D gaG/gaT 1 -1 ZFP64 HGNC HGNC:15940 protein_coding CCDS13439.1 ENSP00000355179 Q9NTW7 UPI000013C56C NM_199427.2 tolerated(0.2) 9/9 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF34,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 52085010 52085010 C A 1 0 0 0 0 1 0 0 0 18228 912 32 2 2 ZFP64 20 52085010 Missense_Mutation SNP C C3N-00175_T 2178911 52085010 12359157 1265 10857 BMP7 0 . GRCh38 20 57173175 57173175 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.1171G>T p.Val391Leu p.V391L ENST00000450594 6/6 300 215 85 354 354 0 strelka-varscan-mutect BMP7,missense_variant,p.Val391Leu,ENST00000450594,;BMP7,intron_variant,,ENST00000395863,NM_001719.2;BMP7,intron_variant,,ENST00000395864,;BMP7,downstream_gene_variant,,ENST00000433911,;BMP7,intron_variant,,ENST00000460817,;BMP7,downstream_gene_variant,,ENST00000463939,;BMP7,intron_variant,,ENST00000476877,; A ENST00000450594 Transcript missense_variant 1678/1857 1171/1239 391/412 V/L Gtg/Ttg 1 -1 BMP7 HGNC HGNC:1074 protein_coding ENSP00000398687 B1AL00 UPI0000E5A357 tolerated_low_confidence(0.29) 6/6 PROSITE_profiles:PS51362,SMART_domains:SM00204 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 57173175 57173175 C A 1 0 0 0 0 1 0 0 0 1620 478 17 2 2 BMP7 20 57173175 Missense_Mutation SNP C C3N-00175_T 5088165 57173175 7270992 1266 10858 APCDD1L 0 . GRCh38 20 58467445 58467445 + Silent SNP G G T C3N-00175_T C3N-00175_N G G c.402C>A p.= p.I134I ENST00000371149 3/4 97 69 28 117 117 0 strelka-varscan-mutect APCDD1L,synonymous_variant,p.=,ENST00000371149,NM_153360.2;APCDD1L,downstream_gene_variant,,ENST00000425773,; T ENST00000371149 Transcript synonymous_variant 633/3426 402/1506 134/501 I atC/atA COSM3548213,COSM4893573 1 -1 APCDD1L HGNC HGNC:26892 protein_coding YES CCDS13467.1 ENSP00000360191 Q8NCL9 UPI000006F69F NM_153360.2 3/4 Pfam_domain:PF14921,hmmpanther:PTHR31021,hmmpanther:PTHR31021:SF3,SMART_domains:SM01352 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 58467445 58467445 G T 1 0 0 0 0 0 0 0 1 886 1048 37 1 1 APCDD1L 20 58467445 Silent SNP G C3N-00175_T 1294270 58467445 5976722 1267 10859 LAMA5 0 . GRCh38 20 62322345 62322345 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.6270C>T p.= p.C2090C ENST00000252999 47/80 105 86 19 159 159 0 strelka-varscan-mutect LAMA5,synonymous_variant,p.=,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000497363,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000481120,; A ENST00000252999 Transcript synonymous_variant 6337/11426 6270/11088 2090/3695 C tgC/tgT 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 47/80 PROSITE_profiles:PS50027,PROSITE_patterns:PS01248,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 62322345 62322345 G A 1 0 0 0 0 0 0 0 1 8513 1195 42 3 3 LAMA5 20 62322345 Silent SNP G C3N-00175_T 3854900 62322345 2121822 1268 10860 OGFR 0 . GRCh38 20 62808281 62808281 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.275C>G p.Pro92Arg p.P92R ENST00000290291 3/7 153 113 40 214 214 0 strelka-varscan-mutect OGFR,missense_variant,p.Pro40Arg,ENST00000370461,;OGFR,missense_variant,p.Pro92Arg,ENST00000290291,NM_007346.2;OGFR,missense_variant,p.Pro92Arg,ENST00000621591,;OGFR,missense_variant,p.Pro33Arg,ENST00000450048,;OGFR-AS1,upstream_gene_variant,,ENST00000431361,; G ENST00000290291 Transcript missense_variant 300/2410 275/2034 92/677 P/R cCa/cGa 1 1 OGFR HGNC HGNC:15768 protein_coding YES CCDS13504.1 ENSP00000290291 Q9NZT2 UPI000013F107 NM_007346.2 tolerated(0.27) 3/7 Pfam_domain:PF04664,hmmpanther:PTHR14015,hmmpanther:PTHR14015:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 62808281 62808281 C G 1 0 0 0 0 1 0 0 0 10918 594 21 4 4 OGFR 20 62808281 Missense_Mutation SNP C C3N-00175_T 485936 62808281 1635886 1269 10861 OGFR 0 . GRCh38 20 62812634 62812634 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1019G>T p.Arg340Met p.R340M ENST00000290291 7/7 217 157 60 264 264 0 strelka-varscan-mutect OGFR,missense_variant,p.Arg288Met,ENST00000370461,;OGFR,missense_variant,p.Arg340Met,ENST00000290291,NM_007346.2;OGFR,intron_variant,,ENST00000621591,;COL9A3,upstream_gene_variant,,ENST00000343916,NM_001853.3;OGFR,downstream_gene_variant,,ENST00000450048,;COL9A3,upstream_gene_variant,,ENST00000489045,;COL9A3,upstream_gene_variant,,ENST00000477612,; T ENST00000290291 Transcript missense_variant 1044/2410 1019/2034 340/677 R/M aGg/aTg 1 1 OGFR HGNC HGNC:15768 protein_coding YES CCDS13504.1 ENSP00000290291 Q9NZT2 UPI000013F107 NM_007346.2 tolerated(0.06) 7/7 hmmpanther:PTHR14015,hmmpanther:PTHR14015:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 62812634 62812634 G T 1 0 0 0 0 1 0 0 0 10918 1000 35 2 2 OGFR 20 62812634 Missense_Mutation SNP G C3N-00175_T 4353 62812634 1631533 1270 10862 COL20A1 0 . GRCh38 20 63310492 63310492 + Silent SNP C C A rs535665257 C3N-00175_T C3N-00175_N C C c.1375C>A p.= p.R459R ENST00000358894 11/36 123 109 14 151 151 0 strelka-mutect COL20A1,synonymous_variant,p.=,ENST00000422202,;COL20A1,synonymous_variant,p.=,ENST00000358894,NM_020882.2;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,; A ENST00000358894 Transcript synonymous_variant 1475/4172 1375/3855 459/1284 R Cgg/Agg rs535665257 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 11/36 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,Low_complexity_(Seg):seg,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs535665257 . 0 202 6 2 0 0 0 0 -19.96649 0.9998591 1 1 1 0 A 2 1 39 63310492 63310492 C A 1 0 0 0 0 0 0 0 1 3467 759 27 1 1 COL20A1 20 63310492 Silent SNP C C3N-00175_T 497858 63310492 1133675 1271 10863 CHRNA4 0 . GRCh38 20 63356372 63356372 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.272A>C p.Gln91Pro p.Q91P ENST00000370263 3/6 336 296 40 396 396 0 strelka-varscan-mutect CHRNA4,missense_variant,p.Gln91Pro,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,splice_region_variant,,ENST00000615287,;RP11-261N11.8,upstream_gene_variant,,ENST00000370257,;CHRNA4,splice_region_variant,,ENST00000467563,;CHRNA4,splice_region_variant,,ENST00000628665,;CHRNA4,intron_variant,,ENST00000463705,;CHRNA4,upstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000636481,;CHRNA4,downstream_gene_variant,,ENST00000637443,;CHRNA4,downstream_gene_variant,,ENST00000636726,;CHRNA4,upstream_gene_variant,,ENST00000637628,;CHRNA4,upstream_gene_variant,,ENST00000637243,;CHRNA4,missense_variant,p.Gln91Pro,ENST00000627000,;CHRNA4,missense_variant,p.Gln66Pro,ENST00000498043,;CHRNA4,upstream_gene_variant,,ENST00000627869,;CHRNA4,downstream_gene_variant,,ENST00000626188,;CHRNA4,downstream_gene_variant,,ENST00000628606,; G ENST00000370263 Transcript missense_variant,splice_region_variant 450/5577 272/1884 91/627 Q/P cAg/cCg 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 deleterious(0) 3/6 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR00252,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 63356372 63356372 T G 1 0 0 0 0 1 0 0 0 3145 1594 55 5 5 CHRNA4 20 63356372 Missense_Mutation SNP T C3N-00175_T 45880 63356372 1087795 1272 10864 ZBTB46 0 . GRCh38 20 63747062 63747062 + Silent SNP C C T rs757444968 C3N-00175_T C3N-00175_N C C c.1638G>A p.= p.E546E ENST00000395104 4/4 225 209 16 344 344 0 strelka-varscan-mutect ZBTB46,synonymous_variant,p.=,ENST00000395104,NM_025224.3;ZBTB46,synonymous_variant,p.=,ENST00000245663,;ZBTB46,synonymous_variant,p.=,ENST00000302995,;SLC2A4RG,downstream_gene_variant,,ENST00000266077,NM_020062.3;RP4-583P15.10,downstream_gene_variant,,ENST00000447343,;RP4-583P15.10,downstream_gene_variant,,ENST00000433905,;SLC2A4RG,downstream_gene_variant,,ENST00000493772,;SLC2A4RG,downstream_gene_variant,,ENST00000473157,;SLC2A4RG,downstream_gene_variant,,ENST00000491109,;SLC2A4RG,downstream_gene_variant,,ENST00000474248,;SLC2A4RG,downstream_gene_variant,,ENST00000482718,;SLC2A4RG,downstream_gene_variant,,ENST00000485897,;SLC2A4RG,downstream_gene_variant,,ENST00000496425,; T ENST00000395104 Transcript synonymous_variant 1804/5198 1638/1770 546/589 E gaG/gaA rs757444968,COSM4529731 1 -1 ZBTB46 HGNC HGNC:16094 protein_coding YES CCDS13538.1 ENSP00000378536 Q86UZ6 UPI0000206406 NM_025224.3 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR19303:SF270,hmmpanther:PTHR19303 0,1 LOW SNV 2 0,1 1 PASS rs757444968 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 63747062 63747062 C T 1 0 0 0 0 0 0 0 1 18117 680 24 3 3 ZBTB46 20 63747062 Silent SNP C C3N-00175_T 390690 63747062 697105 1273 10865 APP 0 . GRCh38 21 26170590 26170590 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.31G>T p.Ala11Ser p.A11S ENST00000346798 1/18 273 214 59 294 294 0 strelka-varscan-mutect APP,missense_variant,p.Ala11Ser,ENST00000357903,NM_201413.2,NM_001204302.1;APP,missense_variant,p.Ala11Ser,ENST00000346798,NM_000484.3;APP,missense_variant,p.Ala11Ser,ENST00000348990,NM_201414.2,NM_001204303.1;APP,missense_variant,p.Ala11Ser,ENST00000354192,NM_001136129.2;APP,missense_variant,p.Ala11Ser,ENST00000439274,NM_001136130.2;APP,missense_variant,p.Ala11Ser,ENST00000358918,NM_001204301.1;APP,intron_variant,,ENST00000359726,NM_001136131.2;AP000230.1,upstream_gene_variant,,ENST00000608591,;AP000230.1,upstream_gene_variant,,ENST00000609365,;AP001439.2,intron_variant,,ENST00000455275,;APP,non_coding_transcript_exon_variant,,ENST00000474136,;APP,upstream_gene_variant,,ENST00000466453,; A ENST00000346798 Transcript missense_variant 65/3467 31/2313 11/770 A/S Gcc/Tcc 1 -1 APP HGNC HGNC:620 protein_coding YES CCDS13576.1 ENSP00000284981 P05067 A0A140VJC8 UPI000002DB1C NM_000484.3 tolerated(0.52) 1/18 hmmpanther:PTHR23103,hmmpanther:PTHR23103:SF7,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1180882911 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 26170590 26170590 C A 1 0 0 0 0 1 0 0 0 938 739 26 2 2 APP 21 26170590 Missense_Mutation SNP C C3N-00175_T 26170590 20539393 1274 10866 KRTAP6-1 0 . GRCh38 21 30613857 30613857 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.48G>A p.= p.G16G ENST00000329122 1/1 246 189 57 278 277 1 strelka-varscan-mutect KRTAP6-1,synonymous_variant,p.=,ENST00000329122,NM_181602.1;KRTAP20-1,upstream_gene_variant,,ENST00000334664,NM_181615.1; T ENST00000329122 Transcript synonymous_variant 74/500 48/216 16/71 G ggG/ggA 1 -1 KRTAP6-1 HGNC HGNC:18931 protein_coding YES CCDS13602.1 ENSP00000332690 Q3LI64 UPI00001A9E58 NM_181602.1 1/1 hmmpanther:PTHR31678,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 30613857 30613857 C T 1 0 0 0 0 0 0 0 1 8464 494 18 3 3 KRTAP6-1 21 30613857 Silent SNP C C3N-00175_T 4443267 30613857 16096126 1275 10867 URB1 0 . GRCh38 21 32337432 32337432 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.4593G>T p.= p.G1531G ENST00000382751 27/39 131 105 26 153 152 1 strelka-varscan-mutect URB1,synonymous_variant,p.=,ENST00000382751,NM_014825.2;URB1,upstream_gene_variant,,ENST00000492603,;URB1,upstream_gene_variant,,ENST00000480196,; A ENST00000382751 Transcript synonymous_variant 4709/10832 4593/6816 1531/2271 G ggG/ggT 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 27/39 hmmpanther:PTHR13500 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 32337432 32337432 C A 1 0 0 0 0 0 0 0 1 17554 610 22 2 2 URB1 21 32337432 Silent SNP C C3N-00175_T 1723575 32337432 14372551 1276 10868 C21orf59 0 . GRCh38 21 32604133 32604133 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.526G>C p.Gly176Arg p.G176R ENST00000290155 4/7 75 59 16 73 73 0 strelka-varscan-mutect C21orf59,missense_variant,p.Gly176Arg,ENST00000382549,;C21orf59,missense_variant,p.Gly176Arg,ENST00000290155,NM_021254.2;C21orf59,missense_variant,p.Gly176Arg,ENST00000440966,;AP000275.65,missense_variant,p.Gly176Arg,ENST00000553001,;AP000275.65,missense_variant,p.Gly144Arg,ENST00000431216,;C21orf59,missense_variant,p.Gly24Arg,ENST00000425336,;C21orf59,missense_variant,p.Gly159Arg,ENST00000458138,;C21orf59,upstream_gene_variant,,ENST00000431599,;C21orf59,3_prime_UTR_variant,,ENST00000300260,;C21orf59,non_coding_transcript_exon_variant,,ENST00000483315,; G ENST00000290155 Transcript missense_variant 1149/1692 526/873 176/290 G/R Gga/Cga 1 -1 C21orf59 HGNC HGNC:1301 protein_coding YES CCDS13617.1 ENSP00000290155 P57076 UPI00001286B0 NM_021254.2 deleterious(0) 4/7 hmmpanther:PTHR13238 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 32604133 32604133 C G 1 0 0 0 0 1 0 0 0 2014 632 22 4 4 C21orf59 21 32604133 Missense_Mutation SNP C C3N-00175_T 266701 32604133 14105850 1277 10869 ITSN1 0 . GRCh38 21 33772230 33772230 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.1212A>T p.Lys404Asn p.K404N ENST00000381318 12/40 434 368 66 460 460 0 strelka-varscan-mutect ITSN1,missense_variant,p.Lys404Asn,ENST00000381318,NM_003024.2;ITSN1,missense_variant,p.Lys367Asn,ENST00000381285,;ITSN1,missense_variant,p.Lys404Asn,ENST00000399367,;ITSN1,missense_variant,p.Lys404Asn,ENST00000381291,NM_001001132.1;ITSN1,missense_variant,p.Lys404Asn,ENST00000399352,;ITSN1,missense_variant,p.Lys404Asn,ENST00000399349,;ITSN1,missense_variant,p.Lys404Asn,ENST00000399355,;ITSN1,missense_variant,p.Lys367Asn,ENST00000399353,;ITSN1,missense_variant,p.Lys404Asn,ENST00000399338,;ITSN1,missense_variant,p.Lys344Asn,ENST00000381283,;ITSN1,3_prime_UTR_variant,,ENST00000379960,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,non_coding_transcript_exon_variant,,ENST00000488166,;ITSN1,upstream_gene_variant,,ENST00000474132,; T ENST00000381318 Transcript missense_variant 1500/17015 1212/5166 404/1721 K/N aaA/aaT 1 1 ITSN1 HGNC HGNC:6183 protein_coding YES CCDS33545.1 ENSP00000370719 Q15811 UPI00001403C6 NM_003024.2 deleterious(0) 12/40 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF68 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 33772230 33772230 A T 1 0 0 0 0 1 0 0 0 7832 11 1 4 4 ITSN1 21 33772230 Missense_Mutation SNP A C3N-00175_T 1168097 33772230 12937753 1278 10870 UMODL1 0 . GRCh38 21 42076168 42076168 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.240G>T p.= p.L80L ENST00000408989 2/22 356 274 82 363 362 1 strelka-varscan-mutect UMODL1,synonymous_variant,p.=,ENST00000400424,NM_001199528.2;UMODL1,synonymous_variant,p.=,ENST00000400427,NM_001199527.1;UMODL1,synonymous_variant,p.=,ENST00000408989,NM_173568.3;UMODL1,synonymous_variant,p.=,ENST00000408910,NM_001004416.2; T ENST00000408989 Transcript synonymous_variant 240/5262 240/4341 80/1446 L ctG/ctT 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42935.1 ENSP00000386126 Q5DID0 UPI0000D6254B NM_173568.3 2/22 PROSITE_profiles:PS51041,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF262 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 42076168 42076168 G T 1 0 0 0 0 0 0 0 1 17504 1335 47 2 2 UMODL1 21 42076168 Silent SNP G C3N-00175_T 8303938 42076168 4633815 1279 10871 UMODL1 0 . GRCh38 21 42084186 42084186 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.422G>A p.Gly141Glu p.G141E ENST00000408989 3/22 195 169 26 219 219 0 strelka-varscan-mutect UMODL1,missense_variant,p.Gly69Glu,ENST00000400424,NM_001199528.2;UMODL1,missense_variant,p.Gly69Glu,ENST00000400427,NM_001199527.1;UMODL1,missense_variant,p.Gly141Glu,ENST00000408989,NM_173568.3;UMODL1,missense_variant,p.Gly141Glu,ENST00000408910,NM_001004416.2;UMODL1,upstream_gene_variant,,ENST00000491559,;UMODL1,upstream_gene_variant,,ENST00000466434,;UMODL1,upstream_gene_variant,,ENST00000400421,;UMODL1,upstream_gene_variant,,ENST00000468982,;UMODL1,upstream_gene_variant,,ENST00000485357,;UMODL1,upstream_gene_variant,,ENST00000497243,; A ENST00000408989 Transcript missense_variant 422/5262 422/4341 141/1446 G/E gGa/gAa 1 1 UMODL1 HGNC HGNC:12560 protein_coding YES CCDS42935.1 ENSP00000386126 Q5DID0 UPI0000D6254B NM_173568.3 tolerated(0.06) 3/22 Gene3D:4.10.75.10,Pfam_domain:PF00095,PROSITE_profiles:PS51390,SMART_domains:SM00217,Superfamily_domains:SSF57256 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 42084186 42084186 G A 1 0 0 0 0 1 0 0 0 17504 1174 41 3 3 UMODL1 21 42084186 Missense_Mutation SNP G C3N-00175_T 8018 42084186 4625797 1280 10872 WDR4 0 . GRCh38 21 42862353 42862353 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.495G>T p.= p.R165R ENST00000398208 5/11 182 144 38 216 216 0 strelka-varscan-mutect WDR4,synonymous_variant,p.=,ENST00000398208,NM_001260474.1,NM_001260476.1,NM_018669.5,NM_001260475.1;WDR4,synonymous_variant,p.=,ENST00000330317,NM_033661.4;WDR4,non_coding_transcript_exon_variant,,ENST00000492742,;WDR4,non_coding_transcript_exon_variant,,ENST00000476326,;WDR4,non_coding_transcript_exon_variant,,ENST00000470658,;WDR4,non_coding_transcript_exon_variant,,ENST00000479429,;WDR4,non_coding_transcript_exon_variant,,ENST00000463902,; A ENST00000398208 Transcript synonymous_variant 555/2122 495/1239 165/412 R cgG/cgT 1 -1 WDR4 HGNC HGNC:12756 protein_coding YES CCDS13691.1 ENSP00000381266 P57081 UPI00000372F0 NM_001260474.1,NM_001260476.1,NM_018669.5,NM_001260475.1 5/11 PROSITE_profiles:PS50294,HAMAP:MF_03056,hmmpanther:PTHR16288:SF0,hmmpanther:PTHR16288,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs977219340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 42862353 42862353 C A 1 0 0 0 0 0 0 0 1 17853 610 22 2 2 WDR4 21 42862353 Silent SNP C C3N-00175_T 778167 42862353 3847630 1281 10873 KRTAP10-4 0 . GRCh38 21 44573914 44573914 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.157delC p.Leu53Ter p.L53* ENST00000400374 1/1 395 337 58 502 502 0 sindel-varindel-pindel KRTAP10-4,frameshift_variant,p.Leu53Ter,ENST00000400374,NM_198687.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,upstream_gene_variant,,ENST00000397916,; - ENST00000400374 Transcript frameshift_variant 186/1643 156/1206 52/401 C/X tgC/tg 1 1 KRTAP10-4 HGNC HGNC:20521 protein_coding YES CCDS42957.1 ENSP00000383225 P60372 UPI00003D4D6E NM_198687.2 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72,Low_complexity_(Seg):seg HIGH deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 44573914 44573914 C - 1 0 1 0 1 0 0 0 0 8394 747 26 0 0 KRTAP10-4 21 44573914 Frame_Shift_Del DEL C C3N-00175_T 1711561 44573914 2136069 1282 10874 KRTAP10-7 0 . GRCh38 21 44600891 44600891 + Nonsense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.270C>A p.Cys90Ter p.C90* ENST00000609664 1/1 637 547 90 705 704 1 varscan-mutect KRTAP10-7,stop_gained,p.Cys90Ter,ENST00000609664,NM_198689.2;KRTAP10-7,stop_gained,p.Cys85Ter,ENST00000616689,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; A ENST00000609664 Transcript stop_gained 295/1578 270/1113 90/370 C/* tgC/tgA 1 1 KRTAP10-7 HGNC HGNC:22970 protein_coding YES CCDS74803.1 ENSP00000476821 P60409 UPI000021C43E NM_198689.2 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72,Low_complexity_(Seg):seg HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 44600891 44600891 C A 1 0 0 0 0 0 1 0 0 8397 747 26 2 2 KRTAP10-7 21 44600891 Nonsense_Mutation SNP C C3N-00175_T 26977 44600891 2109092 1283 10875 ITGB2 0 . GRCh38 21 44886742 44886742 + Frame_Shift_Del DEL C C - rs868212330 C3N-00175_T C3N-00175_N C C c.2241delG p.Trp747Ter p.W747* ENST00000397850 16/17 412 322 90 530 530 0 sindel-varindel-pindel ITGB2,frameshift_variant,p.Trp747Ter,ENST00000397850,;ITGB2,frameshift_variant,p.Trp747Ter,ENST00000302347,NM_001303238.1,NM_000211.4;ITGB2,frameshift_variant,p.Trp747Ter,ENST00000355153,NM_001127491.2;ITGB2,frameshift_variant,p.Trp747Ter,ENST00000397857,;ITGB2,frameshift_variant,p.Trp747Ter,ENST00000397852,;ITGB2,frameshift_variant,p.Trp690Ter,ENST00000397854,;ITGB2,3_prime_UTR_variant,,ENST00000523323,;ITGB2,non_coding_transcript_exon_variant,,ENST00000498666,;ITGB2,non_coding_transcript_exon_variant,,ENST00000475170,;ITGB2,non_coding_transcript_exon_variant,,ENST00000479202,; - ENST00000397850 Transcript frameshift_variant 2694/3178 2241/2310 747/769 W/X tgG/tg rs868212330,COSM3551540 1 -1 ITGB2 HGNC HGNC:6155 protein_coding YES CCDS13716.1 ENSP00000380948 P05107 UPI0000000C70 16/17 Gene3D:1.20.5.100,Pfam_domain:PF08725,PIRSF_domain:PIRSF002512,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF15,SMART_domains:SM01241 0,1 HIGH 1 deletion 5 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 44886742 44886742 C - 1 0 1 0 1 0 0 0 0 7800 856 30 0 0 ITGB2 21 44886742 Frame_Shift_Del DEL C C3N-00175_T 285851 44886742 1823241 1284 10876 ADARB1 0 . GRCh38 21 45185091 45185091 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.1685G>T p.Arg562Leu p.R562L ENST00000360697 7/10 72 53 19 72 72 0 strelka-varscan-mutect ADARB1,missense_variant,p.Arg522Leu,ENST00000348831,NM_001112.3;ADARB1,missense_variant,p.Arg562Leu,ENST00000360697,;ADARB1,missense_variant,p.Arg562Leu,ENST00000437626,NM_015833.3;ADARB1,missense_variant,p.Arg550Leu,ENST00000629643,;ADARB1,missense_variant,p.Arg562Leu,ENST00000389863,NM_001160230.1,NM_015834.3;ADARB1,splice_region_variant,,ENST00000389861,;ADARB1,downstream_gene_variant,,ENST00000631642,;ADARB1,missense_variant,p.Arg562Leu,ENST00000496664,;ADARB1,missense_variant,p.Arg522Leu,ENST00000492414,; T ENST00000360697 Transcript missense_variant,splice_region_variant 1700/6604 1685/2226 562/741 R/L cGc/cTc 1 1 ADARB1 HGNC HGNC:226 protein_coding YES CCDS33589.1 ENSP00000353920 P78563 UPI0000133622 deleterious(0) 7/10 Pfam_domain:PF02137,PROSITE_profiles:PS50141,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF58,SMART_domains:SM00552 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 39 45185091 45185091 G T 1 0 0 0 0 1 0 0 0 326 1130 39 1 1 ADARB1 21 45185091 Missense_Mutation SNP G C3N-00175_T 298349 45185091 1524892 1285 10877 ADARB1 0 . GRCh38 21 45222098 45222098 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.2127G>A p.= p.Q709Q ENST00000360697 10/10 136 98 38 158 157 1 strelka-varscan-mutect ADARB1,synonymous_variant,p.=,ENST00000348831,NM_001112.3;ADARB1,synonymous_variant,p.=,ENST00000360697,;ADARB1,synonymous_variant,p.=,ENST00000437626,NM_015833.3;ADARB1,synonymous_variant,p.=,ENST00000629643,;ADARB1,synonymous_variant,p.=,ENST00000389863,NM_001160230.1,NM_015834.3;ADARB1,non_coding_transcript_exon_variant,,ENST00000389861,;ADARB1,synonymous_variant,p.=,ENST00000496664,;ADARB1,synonymous_variant,p.=,ENST00000492414,; A ENST00000360697 Transcript synonymous_variant 2142/6604 2127/2226 709/741 Q caG/caA 1 1 ADARB1 HGNC HGNC:226 protein_coding YES CCDS33589.1 ENSP00000353920 P78563 UPI0000133622 10/10 Pfam_domain:PF02137,PROSITE_profiles:PS50141,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF58,SMART_domains:SM00552 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 45222098 45222098 G A 1 0 0 0 0 0 0 0 1 326 991 35 3 3 ADARB1 21 45222098 Silent SNP G C3N-00175_T 37007 45222098 1487885 1286 10878 COL6A1 0 . GRCh38 21 46003485 46003485 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.2559G>T p.Lys853Asn p.K853N ENST00000361866 35/35 198 148 50 247 247 0 strelka-varscan-mutect COL6A1,missense_variant,p.Lys853Asn,ENST00000361866,NM_001848.2;COL6A1,missense_variant,p.Lys851Asn,ENST00000612273,;COL6A1,non_coding_transcript_exon_variant,,ENST00000498614,;COL6A1,non_coding_transcript_exon_variant,,ENST00000486023,;COL6A1,downstream_gene_variant,,ENST00000463060,;COL6A1,downstream_gene_variant,,ENST00000466285,; T ENST00000361866 Transcript missense_variant 2673/4238 2559/3087 853/1028 K/N aaG/aaT 1 1 COL6A1 HGNC HGNC:2211 protein_coding YES CCDS13727.1 ENSP00000355180 P12109 UPI000019B179 NM_001848.2 deleterious(0.02) 35/35 PROSITE_profiles:PS50234,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF390,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs1227702618 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 46003485 46003485 G T 1 0 0 0 0 1 0 0 0 3488 962 34 2 2 COL6A1 21 46003485 Missense_Mutation SNP G C3N-00175_T 781387 46003485 706498 1287 10879 COL6A2 0 . GRCh38 21 46119053 46119053 + Silent SNP C C A rs769165553 C3N-00175_T C3N-00175_N C C c.1203C>A p.= p.A401A ENST00000300527 14/28 286 221 65 307 306 1 strelka-varscan-mutect COL6A2,synonymous_variant,p.=,ENST00000300527,NM_001849.3;COL6A2,synonymous_variant,p.=,ENST00000310645,NM_058175.2;COL6A2,synonymous_variant,p.=,ENST00000409416,;COL6A2,synonymous_variant,p.=,ENST00000397763,NM_058174.2;COL6A2,upstream_gene_variant,,ENST00000413758,;COL6A2,downstream_gene_variant,,ENST00000485591,; A ENST00000300527 Transcript synonymous_variant 1307/3461 1203/3060 401/1019 A gcC/gcA rs769165553 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 14/28 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF119,hmmpanther:PTHR24023 LOW 1 SNV 1 1 PASS rs769165553 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 46119053 46119053 C A 1 0 0 0 0 0 0 0 1 3489 610 22 2 2 COL6A2 21 46119053 Silent SNP C C3N-00175_T 115568 46119053 590930 1288 10880 FTCD 0 . GRCh38 21 46138640 46138640 + Silent SNP C C G novel C3N-00175_T C3N-00175_N C C c.1311G>C p.= p.T437T ENST00000291670 12/15 282 225 57 332 332 0 strelka-varscan-mutect FTCD,missense_variant,p.Gly423Arg,ENST00000397743,;FTCD,synonymous_variant,p.=,ENST00000397748,NM_001320412.1;FTCD,synonymous_variant,p.=,ENST00000291670,NM_006657.2;FTCD,synonymous_variant,p.=,ENST00000397746,NM_206965.1;FTCD,upstream_gene_variant,,ENST00000446405,;FTCD,non_coding_transcript_exon_variant,,ENST00000498355,;FTCD,non_coding_transcript_exon_variant,,ENST00000460011,;FTCD,non_coding_transcript_exon_variant,,ENST00000494498,;FTCD,non_coding_transcript_exon_variant,,ENST00000488577,;FTCD,upstream_gene_variant,,ENST00000483568,; G ENST00000291670 Transcript synonymous_variant 1355/1905 1311/1626 437/541 T acG/acC 1 -1 FTCD HGNC HGNC:3974 protein_coding YES CCDS13731.1 ENSP00000291670 O95954 UPI000012AC75 NM_006657.2 12/15 Superfamily_domains:0041691,Pfam_domain:PF04961,hmmpanther:PTHR12234,hmmpanther:PTHR12234:SF0 LOW 1 SNV 1 1 PASS rs1413956976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 46138640 46138640 C G 1 0 0 0 0 0 0 0 1 5955 652 23 4 4 FTCD 21 46138640 Silent SNP C C3N-00175_T 19587 46138640 571343 1289 10881 DIP2A 0 . GRCh38 21 46547011 46547011 + Missense_Mutation SNP G G T rs765372886 C3N-00175_T C3N-00175_N G G c.2491G>T p.Val831Leu p.V831L ENST00000417564 21/38 193 157 36 221 221 0 strelka-varscan-mutect DIP2A,missense_variant,p.Val827Leu,ENST00000400274,NM_001146116.1;DIP2A,missense_variant,p.Val831Leu,ENST00000417564,NM_015151.3;DIP2A,missense_variant,p.Val831Leu,ENST00000457905,NM_206889.2;DIP2A,missense_variant,p.Val831Leu,ENST00000435722,NM_206891.2,NM_206890.2;DIP2A,missense_variant,p.Val788Leu,ENST00000466639,NM_001146115.1;DIP2A,downstream_gene_variant,,ENST00000473752,;DIP2A,non_coding_transcript_exon_variant,,ENST00000480553,;DIP2A,downstream_gene_variant,,ENST00000494435,; T ENST00000417564 Transcript missense_variant 2512/6967 2491/4716 831/1571 V/L Gtg/Ttg rs765372886,COSM5519778,COSM5519779,COSM5519780,COSM5519781 1 1 DIP2A HGNC HGNC:17217 protein_coding YES CCDS46655.1 ENSP00000392066 Q14689 UPI00001B2E47 NM_015151.3 deleterious(0) 21/38 hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF24,Superfamily_domains:SSF56801 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs765372886 . 0 206 0 3 0 0 0 0 -20 0.9999957 1 1 1 0 T 3 4 39 46547011 46547011 G T 1 0 0 0 0 1 0 0 0 4332 1145 40 1 1 DIP2A 21 46547011 Missense_Mutation SNP G C3N-00175_T 408371 46547011 162972 1290 10882 OR11H1 0 . GRCh38 22 15528900 15528900 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.742G>C p.Gly248Arg p.G248R ENST00000252835 1/1 571 472 99 456 456 0 strelka-varscan-mutect OR11H1,missense_variant,p.Gly248Arg,ENST00000252835,NM_001005239.1; C ENST00000252835 Transcript missense_variant 743/982 742/981 248/326 G/R Ggg/Cgg 1 1 OR11H1 HGNC HGNC:15404 protein_coding YES CCDS74807.1 ENSP00000252835 Q8NG94 UPI000004B1CF NM_001005239.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1254271205 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 15528900 15528900 G C 1 0 0 0 0 1 0 0 0 11002 1348 47 4 4 OR11H1 22 15528900 Missense_Mutation SNP G C3N-00175_T 15528900 35289568 1291 10883 POTEH 0 . GRCh38 22 15690171 15690171 + Frame_Shift_Del DEL T T - rs773123715 C3N-00175_T C3N-00175_N T T c.95delT p.Phe32SerfsTer23 p.F32Sfs*23 ENST00000343518 1/11 839 770 69 705 705 0 sindel-varindel-pindel POTEH,frameshift_variant,p.Phe32SerfsTer23,ENST00000343518,NM_001136213.1;POTEH,frameshift_variant,p.Phe32SerfsTer23,ENST00000621704,;POTEH,upstream_gene_variant,,ENST00000452800,; - ENST00000343518 Transcript frameshift_variant 146/1928 94/1638 32/545 F/X Ttc/tc rs773123715 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 1/11 HIGH 1 deletion 5 1 1 PASS . . 8 202 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 15690171 15690171 T - 1 0 1 0 1 0 0 0 0 12381 1609 56 0 0 POTEH 22 15690171 Frame_Shift_Del DEL T C3N-00175_T 161271 15690171 35128297 1292 10884 XKR3 0 . GRCh38 22 16808021 16808021 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.53C>T p.Ser18Phe p.S18F ENST00000331428 2/4 86 73 13 99 99 0 strelka-varscan-mutect XKR3,missense_variant,p.Ser18Phe,ENST00000331428,NM_001318251.1,NM_175878.3; A ENST00000331428 Transcript missense_variant 156/1690 53/1380 18/459 S/F tCt/tTt 1 -1 XKR3 HGNC HGNC:28778 protein_coding YES CCDS42975.1 ENSP00000331704 Q5GH77 UPI000013EFAE NM_001318251.1,NM_175878.3 deleterious(0.01) 2/4 hmmpanther:PTHR14297:SF7,hmmpanther:PTHR14297 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 39 16808021 16808021 G A 1 0 0 0 0 1 0 0 0 17991 942 33 3 3 XKR3 22 16808021 Missense_Mutation SNP G C3N-00175_T 1117850 16808021 34010447 1293 10885 IL17RA 0 . GRCh38 22 17105869 17105869 + Nonsense_Mutation SNP G G A rs758399114 C3N-00175_T C3N-00175_N G G c.960G>A p.Trp320Ter p.W320* ENST00000319363 11/13 552 468 84 611 611 0 strelka-varscan-mutect IL17RA,stop_gained,p.Trp320Ter,ENST00000319363,NM_014339.6;IL17RA,intron_variant,,ENST00000612619,NM_001289905.1; A ENST00000319363 Transcript stop_gained 1093/8607 960/2601 320/866 W/* tgG/tgA rs758399114 1 1 IL17RA HGNC HGNC:5985 protein_coding YES CCDS13739.1 ENSP00000320936 Q96F46 UPI000005031F NM_014339.6 11/13 hmmpanther:PTHR15583,hmmpanther:PTHR15583:SF13,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS rs758399114 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 17105869 17105869 G A 1 0 0 0 0 0 1 0 0 7547 1241 43 3 3 IL17RA 22 17105869 Nonsense_Mutation SNP G C3N-00175_T 297848 17105869 33712599 1294 10886 PI4KA 0 . GRCh38 22 20752907 20752907 + Missense_Mutation SNP C C G rs771454034 C3N-00175_T C3N-00175_N C C c.2983G>C p.Asp995His p.D995H ENST00000255882 25/55 140 132 8 119 119 0 varscan-mutect PI4KA,missense_variant,p.Asp995His,ENST00000255882,NM_058004.3;PI4KA,downstream_gene_variant,,ENST00000466162,;PI4KA,upstream_gene_variant,,ENST00000475414,; G ENST00000255882 Transcript missense_variant 3070/6752 2983/6309 995/2102 D/H Gat/Cat rs771454034 1 -1 PI4KA HGNC HGNC:8983 protein_coding YES CCDS33603.2 ENSP00000255882 P42356 J3KN10 UPI0000E06BD6 NM_058004.3 deleterious(0) 25/55 hmmpanther:PTHR10048:SF58,hmmpanther:PTHR10048,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs771454034 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 20752907 20752907 C G 1 0 0 0 0 1 0 0 0 11962 869 30 4 4 PI4KA 22 20752907 Missense_Mutation SNP C C3N-00175_T 3647038 20752907 30065561 1295 10887 ZNF280A 0 . GRCh38 22 22514048 22514048 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.1583T>C p.Met528Thr p.M528T ENST00000302097 2/2 87 61 26 122 122 0 strelka-varscan-mutect ZNF280A,missense_variant,p.Met528Thr,ENST00000302097,NM_080740.4;ZNF280B,upstream_gene_variant,,ENST00000626650,NM_080764.3; G ENST00000302097 Transcript missense_variant 1836/2148 1583/1629 528/542 M/T aTg/aCg 1 -1 ZNF280A HGNC HGNC:18597 protein_coding YES CCDS13800.1 ENSP00000302855 P59817 UPI000011B50C NM_080740.4 tolerated(0.35) 2/2 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF294 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 22514048 22514048 A G 1 0 0 0 0 1 0 0 0 18390 217 8 5 5 ZNF280A 22 22514048 Missense_Mutation SNP A C3N-00175_T 1761141 22514048 28304420 1296 10888 CABIN1 0 . GRCh38 22 24072383 24072383 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.2505G>A p.= p.E835E ENST00000398319 18/37 332 240 92 418 418 0 strelka-varscan-mutect CABIN1,synonymous_variant,p.=,ENST00000398319,NM_001199281.1;CABIN1,synonymous_variant,p.=,ENST00000263119,NM_012295.3;CABIN1,synonymous_variant,p.=,ENST00000617531,NM_001201429.1;CABIN1,synonymous_variant,p.=,ENST00000405822,;CABIN1,downstream_gene_variant,,ENST00000484593,; A ENST00000398319 Transcript synonymous_variant 2890/7480 2505/6663 835/2220 E gaG/gaA 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 18/37 hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 24072383 24072383 G A 1 0 0 0 0 0 0 0 1 2214 991 35 3 3 CABIN1 22 24072383 Silent SNP G C3N-00175_T 1558335 24072383 26746085 1297 10889 CABIN1 0 . GRCh38 22 24087652 24087652 + Nonsense_Mutation SNP C C G C3N-00175_T C3N-00175_N C C c.3464C>G p.Ser1155Ter p.S1155* ENST00000398319 23/37 182 159 23 264 264 0 strelka-varscan-mutect CABIN1,stop_gained,p.Ser1155Ter,ENST00000398319,NM_001199281.1;CABIN1,stop_gained,p.Ser1155Ter,ENST00000263119,NM_012295.3;CABIN1,stop_gained,p.Ser1105Ter,ENST00000617531,NM_001201429.1;CABIN1,stop_gained,p.Ser1105Ter,ENST00000405822,;CABIN1,non_coding_transcript_exon_variant,,ENST00000496016,; G ENST00000398319 Transcript stop_gained 3849/7480 3464/6663 1155/2220 S/* tCa/tGa COSM726156 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 23/37 Gene3D:1.25.40.10,hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 39 24087652 24087652 C G 1 0 0 0 0 0 1 0 0 2214 838 29 4 4 CABIN1 22 24087652 Nonsense_Mutation SNP C C3N-00175_T 15269 24087652 26730816 1298 10890 MYO18B 0 . GRCh38 22 25902705 25902705 + Nonsense_Mutation SNP G G A C3N-00175_T C3N-00175_N G G c.4916G>A p.Trp1639Ter p.W1639* ENST00000335473 30/44 126 89 37 170 170 0 strelka-varscan-mutect MYO18B,stop_gained,p.Trp1639Ter,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,stop_gained,p.Trp1640Ter,ENST00000407587,;MYO18B,stop_gained,p.Trp1639Ter,ENST00000536101,;CTA-125H2.2,intron_variant,,ENST00000609889,;CTA-125H2.2,intron_variant,,ENST00000608257,;CTA-125H2.2,upstream_gene_variant,,ENST00000453457,;CTA-125H2.2,upstream_gene_variant,,ENST00000600211,;CTA-125H2.2,upstream_gene_variant,,ENST00000609275,;CTA-125H2.2,upstream_gene_variant,,ENST00000597284,;CTA-125H2.2,upstream_gene_variant,,ENST00000609157,;CTA-125H2.2,upstream_gene_variant,,ENST00000608507,;CTA-125H2.2,upstream_gene_variant,,ENST00000595093,;CTA-125H2.2,upstream_gene_variant,,ENST00000608115,;CTA-125H2.2,upstream_gene_variant,,ENST00000597548,;CTA-125H2.2,upstream_gene_variant,,ENST00000594585,;CTA-125H2.2,upstream_gene_variant,,ENST00000595102,;CTA-125H2.2,upstream_gene_variant,,ENST00000594856,;CTA-125H2.2,upstream_gene_variant,,ENST00000599080,;CTA-125H2.2,upstream_gene_variant,,ENST00000594542,;CTA-125H2.2,upstream_gene_variant,,ENST00000600269,;CTA-125H2.2,upstream_gene_variant,,ENST00000609570,;CTA-125H2.2,upstream_gene_variant,,ENST00000600903,;CTA-125H2.2,upstream_gene_variant,,ENST00000599792,;CTA-125H2.2,upstream_gene_variant,,ENST00000609823,;CTA-125H2.2,upstream_gene_variant,,ENST00000607895,;MYO18B,non_coding_transcript_exon_variant,,ENST00000536204,;MYO18B,non_coding_transcript_exon_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript stop_gained 5166/8565 4916/7704 1639/2567 W/* tGg/tAg COSM4550091 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 30/44 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 39 25902705 25902705 G A 1 0 0 0 0 0 1 0 0 10067 1357 47 3 3 MYO18B 22 25902705 Nonsense_Mutation SNP G C3N-00175_T 1815053 25902705 24915763 1299 10891 RASL10A 0 . GRCh38 22 29315208 29315208 + Silent SNP C C A novel C3N-00175_T C3N-00175_N C C c.39G>T p.= p.P13P ENST00000216101 1/3 130 104 26 148 148 0 strelka-varscan-mutect RASL10A,synonymous_variant,p.=,ENST00000401450,;RASL10A,synonymous_variant,p.=,ENST00000216101,NM_006477.4;GAS2L1,downstream_gene_variant,,ENST00000618518,;GAS2L1,downstream_gene_variant,,ENST00000616432,;GAS2L1,downstream_gene_variant,,ENST00000621062,NM_006478.4;GAS2L1,downstream_gene_variant,,ENST00000611648,NM_152236.2;GAS2L1,downstream_gene_variant,,ENST00000610653,;GAS2L1,downstream_gene_variant,,ENST00000406549,NM_001278730.1;AC002059.10,downstream_gene_variant,,ENST00000608014,;RASL10A,intron_variant,,ENST00000608559,;RASL10A,upstream_gene_variant,,ENST00000474590,;GAS2L1,downstream_gene_variant,,ENST00000491016,; A ENST00000216101 Transcript synonymous_variant 549/1490 39/612 13/203 P ccG/ccT 1 -1 RASL10A HGNC HGNC:16954 protein_coding YES CCDS13854.1 ENSP00000216101 Q92737 A0A024R1C8 UPI00001348FD NM_006477.4 1/3 PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF65,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 29315208 29315208 C A 1 0 0 0 0 0 0 0 1 13240 639 23 1 1 RASL10A 22 29315208 Silent SNP C C3N-00175_T 3412503 29315208 21503260 1300 10892 RFPL1 0 . GRCh38 22 29438961 29438961 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.170G>T p.Cys57Phe p.C57F ENST00000354373 1/2 218 151 67 338 337 1 strelka-varscan-mutect RFPL1,missense_variant,p.Cys57Phe,ENST00000354373,NM_021026.2;RFPL1S,non_coding_transcript_exon_variant,,ENST00000461286,;RFPL4AP6,downstream_gene_variant,,ENST00000616792,;RFPL1S,downstream_gene_variant,,ENST00000539579,;AC000041.10,downstream_gene_variant,,ENST00000619824,; T ENST00000354373 Transcript missense_variant 379/1496 170/954 57/317 C/F tGc/tTc 1 1 RFPL1 HGNC HGNC:9977 protein_coding YES CCDS13857.2 ENSP00000346342 O75677 UPI000013CC65 NM_021026.2 tolerated(0.33) 1/2 Gene3D:3.30.40.10,Pfam_domain:PF15227,PROSITE_profiles:PS50089,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF225,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 29438961 29438961 G T 1 0 0 0 0 1 0 0 0 13424 1319 46 2 2 RFPL1 22 29438961 Missense_Mutation SNP G C3N-00175_T 123753 29438961 21379507 1301 10893 CSF2RB 0 . GRCh38 22 36938008 36938008 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2200C>G p.Leu734Val p.L734V ENST00000403662 14/14 361 290 71 458 458 0 strelka-varscan-mutect CSF2RB,missense_variant,p.Leu734Val,ENST00000403662,NM_000395.2;CSF2RB,missense_variant,p.Leu734Val,ENST00000262825,;CSF2RB,missense_variant,p.Leu740Val,ENST00000406230,; G ENST00000403662 Transcript missense_variant 2422/4863 2200/2694 734/897 L/V Ctg/Gtg 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 tolerated(0.14) 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF22,PIRSF_domain:PIRSF001956 MODERATE 1 SNV 5 1 PASS rs1406704383 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 36938008 36938008 C G 1 0 0 0 0 1 0 0 0 3736 912 32 4 4 CSF2RB 22 36938008 Missense_Mutation SNP C C3N-00175_T 7499047 36938008 13880460 1302 10894 CBX6 0 . GRCh38 22 38871928 38871928 + Silent SNP C C G novel C3N-00175_T C3N-00175_N C C c.87G>C p.= p.L29L ENST00000407418 2/5 43 32 11 71 71 0 strelka-varscan-mutect CBX6,synonymous_variant,p.=,ENST00000407418,NM_014292.4;CBX6,synonymous_variant,p.=,ENST00000216083,NM_001303494.1;CBX6,non_coding_transcript_exon_variant,,ENST00000469420,; G ENST00000407418 Transcript synonymous_variant 211/6122 87/1239 29/412 L ctG/ctC 1 -1 CBX6 HGNC HGNC:1556 protein_coding YES CCDS13980.1 ENSP00000384490 O95503 UPI00001271FD NM_014292.4 2/5 PROSITE_profiles:PS50013,hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF8,PROSITE_patterns:PS00598,Pfam_domain:PF00385,Gene3D:2.40.50.40,SMART_domains:SM00298,Superfamily_domains:SSF54160,Prints_domain:PR00504 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 39 38871928 38871928 C G 1 0 0 0 0 0 0 0 1 2422 581 21 4 4 CBX6 22 38871928 Silent SNP C C3N-00175_T 1933920 38871928 11946540 1303 10895 NLGN4X 0 . GRCh38 X 6151089 6151089 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.378C>T p.= p.I126I ENST00000381095 2/6 221 138 83 263 262 1 strelka-varscan-mutect NLGN4X,synonymous_variant,p.=,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,synonymous_variant,p.=,ENST00000381093,NM_001282146.1;NLGN4X,synonymous_variant,p.=,ENST00000275857,NM_020742.3;NLGN4X,synonymous_variant,p.=,ENST00000381092,;NLGN4X,synonymous_variant,p.=,ENST00000538097,;NLGN4X,non_coding_transcript_exon_variant,,ENST00000469740,;NLGN4X,downstream_gene_variant,,ENST00000483337,; A ENST00000381095 Transcript synonymous_variant 1006/5870 378/2451 126/816 I atC/atT 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 2/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 6151089 6151089 G A 1 0 0 0 0 0 0 0 1 10501 932 33 3 3 NLGN4X 23 6151089 Silent SNP G C3N-00175_T 6151089 149889806 1304 10896 FAM9A 0 . GRCh38 X 8795259 8795259 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.650T>C p.Ile217Thr p.I217T ENST00000543214 7/10 66 37 29 83 83 0 strelka-varscan-mutect FAM9A,missense_variant,p.Ile217Thr,ENST00000543214,NM_001171186.1;FAM9A,missense_variant,p.Ile217Thr,ENST00000381003,NM_174951.3; G ENST00000543214 Transcript missense_variant 786/1544 650/999 217/332 I/T aTa/aCa 1 -1 FAM9A HGNC HGNC:18403 protein_coding YES CCDS14131.1 ENSP00000440163 Q8IZU1 UPI000012A418 NM_001171186.1 deleterious_low_confidence(0.01) 7/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 8795259 8795259 A G 1 0 0 0 0 1 0 0 0 5517 449 16 5 5 FAM9A 23 8795259 Missense_Mutation SNP A C3N-00175_T 2644170 8795259 147245636 1305 10897 TLR7 0 . GRCh38 X 12888270 12888270 + Missense_Mutation SNP A A G novel C3N-00175_T C3N-00175_N A A c.2762A>G p.Glu921Gly p.E921G ENST00000380659 3/3 64 38 26 74 74 0 strelka-varscan-mutect TLR7,missense_variant,p.Glu921Gly,ENST00000380659,NM_016562.3; G ENST00000380659 Transcript missense_variant 2901/5011 2762/3150 921/1049 E/G gAg/gGg 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(0.13) 3/3 Gene3D:3.40.50.10140,Pfam_domain:PF01582,PROSITE_profiles:PS50104,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 12888270 12888270 A G 1 0 0 0 0 1 0 0 0 16402 304 11 5 5 TLR7 23 12888270 Missense_Mutation SNP A C3N-00175_T 4093011 12888270 143152625 1306 10898 BMX 0 . GRCh38 X 15556088 15556088 + Frame_Shift_Del DEL C C - novel C3N-00175_T C3N-00175_N C C c.1971delC p.Thr658HisfsTer50 p.T658Hfs*50 ENST00000357607 19/19 76 55 21 90 90 0 sindel-varindel-pindel BMX,frameshift_variant,p.Thr658HisfsTer50,ENST00000357607,;BMX,frameshift_variant,p.Thr658HisfsTer50,ENST00000348343,NM_001320866.1,NM_203281.2;BMX,frameshift_variant,p.Thr658HisfsTer50,ENST00000342014,NM_001721.6;ACE2,downstream_gene_variant,,ENST00000427411,NM_021804.2;ACE2,downstream_gene_variant,,ENST00000252519,;ACE2,downstream_gene_variant,,ENST00000471548,; - ENST00000357607 Transcript frameshift_variant 2157/2598 1969/2028 657/675 P/X Ccc/cc 1 1 BMX HGNC HGNC:1079 protein_coding YES CCDS14168.1 ENSP00000350224 P51813 UPI0000000DFF 19/19 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF91,SMART_domains:SM00219,Superfamily_domains:SSF56112 HIGH deletion 2 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 15556088 15556088 C - 1 0 1 0 1 0 0 0 0 1629 855 30 0 0 BMX 23 15556088 Frame_Shift_Del DEL C C3N-00175_T 2667818 15556088 140484807 1307 10899 CDKL5 0 . GRCh38 X 18579893 18579893 + Missense_Mutation SNP G G A novel C3N-00175_T C3N-00175_N G G c.328G>A p.Glu110Lys p.E110K ENST00000379989 7/22 128 119 9 165 164 1 strelka-varscan-mutect CDKL5,missense_variant,p.Glu110Lys,ENST00000623535,;CDKL5,missense_variant,p.Glu110Lys,ENST00000635828,;CDKL5,missense_variant,p.Glu110Lys,ENST00000379989,NM_001037343.1;CDKL5,missense_variant,p.Glu110Lys,ENST00000379996,NM_003159.2;CDKL5,missense_variant,p.Glu110Lys,ENST00000463994,;CDKL5,missense_variant,p.Glu110Lys,ENST00000637881,;CDKL5,downstream_gene_variant,,ENST00000624700,;CDKL5,downstream_gene_variant,,ENST00000623364,; A ENST00000379989 Transcript missense_variant 613/3463 328/3093 110/1030 E/K Gag/Aag 1 1 CDKL5 HGNC HGNC:11411 protein_coding YES CCDS14186.1 ENSP00000369325 O76039 UPI0000136103 NM_001037343.1 deleterious_low_confidence(0.03) 7/22 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF111,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 18579893 18579893 G A 1 0 0 0 0 1 0 0 0 2861 1291 45 3 3 CDKL5 23 18579893 Missense_Mutation SNP G C3N-00175_T 3023805 18579893 137461002 1308 10900 ZNF645 0 . GRCh38 X 22273432 22273432 + Missense_Mutation SNP C C A rs749058196 C3N-00175_T C3N-00175_N C C c.441C>A p.Ser147Arg p.S147R ENST00000323684 1/1 70 42 28 76 76 0 strelka-varscan-mutect ZNF645,missense_variant,p.Ser147Arg,ENST00000323684,NM_152577.3;PTCHD1-AS,intron_variant,,ENST00000608254,; A ENST00000323684 Transcript missense_variant 490/1519 441/1278 147/425 S/R agC/agA rs749058196,COSM756517 1 1 ZNF645 HGNC HGNC:26371 protein_coding YES CCDS14205.1 ENSP00000323348 Q8N7E2 UPI0000073BD5 NM_152577.3 tolerated(0.11) 1/1 hmmpanther:PTHR13480,hmmpanther:PTHR13480:SF1 0,1 MODERATE 1 SNV 0,1 1 PASS rs749058196 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 22273432 22273432 C A 1 0 0 0 0 1 0 0 0 18634 767 27 1 1 ZNF645 23 22273432 Missense_Mutation SNP C C3N-00175_T 3693539 22273432 133767463 1309 10901 POLA1 0 . GRCh38 X 24723243 24723243 + Silent SNP G G A C3N-00175_T C3N-00175_N G G c.1158G>A p.= p.T386T ENST00000379059 11/37 96 60 36 102 102 0 strelka-varscan-mutect POLA1,synonymous_variant,p.=,ENST00000379068,;POLA1,synonymous_variant,p.=,ENST00000379059,NM_016937.3;POLA1,synonymous_variant,p.=,ENST00000611764,;POLA1,upstream_gene_variant,,ENST00000493342,; A ENST00000379059 Transcript synonymous_variant 1173/5440 1158/4389 386/1462 T acG/acA COSM4933508,COSM4933509 1 1 POLA1 HGNC HGNC:9173 protein_coding YES CCDS14214.1 ENSP00000368349 P09884 UPI000014D383 NM_016937.3 11/37 hmmpanther:PTHR10322:SF21,hmmpanther:PTHR10322,TIGRFAM_domain:TIGR00592,Pfam_domain:PF03104 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 24723243 24723243 G A 1 0 0 0 0 0 0 0 1 12297 1074 38 1 1 POLA1 23 24723243 Silent SNP G C3N-00175_T 2449811 24723243 131317652 1310 10902 NR0B1 0 . GRCh38 X 30304812 30304812 + Missense_Mutation SNP G G C novel C3N-00175_T C3N-00175_N G G c.1180C>G p.Leu394Val p.L394V ENST00000378970 2/2 124 69 55 164 164 0 strelka-varscan-mutect NR0B1,missense_variant,p.Leu394Val,ENST00000378970,NM_000475.4;NR0B1,downstream_gene_variant,,ENST00000378963,; C ENST00000378970 Transcript missense_variant 1415/2021 1180/1413 394/470 L/V Ctg/Gtg 1 -1 NR0B1 HGNC HGNC:7960 protein_coding YES CCDS14223.1 ENSP00000368253 P51843 F1D8P4 UPI0000128ED4 NM_000475.4 deleterious(0.01) 2/2 hmmpanther:PTHR24081:SF1,hmmpanther:PTHR24081,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 30304812 30304812 G C 1 0 0 0 0 1 0 0 0 10669 991 35 4 4 NR0B1 23 30304812 Missense_Mutation SNP G C3N-00175_T 5581569 30304812 125736083 1311 10903 FAM47A 0 . GRCh38 X 34131894 34131894 + Missense_Mutation SNP G G T C3N-00175_T C3N-00175_N G G c.385C>A p.His129Asn p.H129N ENST00000346193 1/1 58 34 24 51 51 0 strelka-varscan-mutect FAM47A,missense_variant,p.His129Asn,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.His129Asn,ENST00000613251,; T ENST00000346193 Transcript missense_variant 418/2556 385/2376 129/791 H/N Cat/Aat COSM3965179 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 deleterious(0.05) 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 1 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 34131894 34131894 G T 1 0 0 0 0 1 0 0 0 5447 1319 46 2 2 FAM47A 23 34131894 Missense_Mutation SNP G C3N-00175_T 3827082 34131894 121909001 1312 10904 FAM47B 0 . GRCh38 X 34942919 34942919 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.88T>A p.Phe30Ile p.F30I ENST00000329357 1/1 86 58 28 105 105 0 strelka-varscan-mutect FAM47B,missense_variant,p.Phe30Ile,ENST00000329357,NM_152631.2; A ENST00000329357 Transcript missense_variant 124/2120 88/1938 30/645 F/I Ttc/Atc 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 tolerated(0.17) 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 34942919 34942919 T A 1 0 0 0 0 1 0 0 0 5448 1609 56 4 4 FAM47B 23 34942919 Missense_Mutation SNP T C3N-00175_T 811025 34942919 121097976 1313 10905 CFAP47 0 . GRCh38 X 35975886 35975886 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.2686A>T p.Ile896Leu p.I896L ENST00000297866 15/16 94 65 29 134 134 0 strelka-varscan-mutect CFAP47,missense_variant,p.Ile896Leu,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Ile896Leu,ENST00000297866,NM_152632.3;CFAP47,3_prime_UTR_variant,,ENST00000493930,; T ENST00000297866 Transcript missense_variant 2752/3608 2686/2931 896/976 I/L Ata/Tta 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 deleterious(0.04) 15/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 35975886 35975886 A T 1 0 0 0 0 1 0 0 0 3022 333 12 4 4 CFAP47 23 35975886 Missense_Mutation SNP A C3N-00175_T 1032967 35975886 120065009 1314 10906 FAM47C 0 . GRCh38 X 37008983 37008983 + Silent SNP C C A rs782508474 C3N-00175_T C3N-00175_N C C c.573C>A p.= p.P191P ENST00000358047 1/1 94 47 47 98 98 0 strelka-varscan-mutect FAM47C,synonymous_variant,p.=,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript synonymous_variant 587/3270 573/3108 191/1035 P ccC/ccA rs782508474 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 LOW 1 SNV 1 PASS rs782508474 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 37008983 37008983 C A 1 0 0 0 0 0 0 0 1 5449 639 23 1 1 FAM47C 23 37008983 Silent SNP C C3N-00175_T 1033097 37008983 119031912 1315 10907 PPP1R3F 0 . GRCh38 X 49287044 49287044 + Missense_Mutation SNP C C G novel C3N-00175_T C3N-00175_N C C c.2354C>G p.Ser785Cys p.S785C ENST00000055335 4/4 117 98 19 124 124 0 strelka-varscan-mutect PPP1R3F,missense_variant,p.Ser785Cys,ENST00000055335,NM_033215.4;PPP1R3F,missense_variant,p.Ser439Cys,ENST00000376188,;PPP1R3F,missense_variant,p.Ser439Cys,ENST00000466508,;PPP1R3F,missense_variant,p.Ser439Cys,ENST00000495799,NM_001184745.1;PPP1R3F,intron_variant,,ENST00000471261,; G ENST00000055335 Transcript missense_variant 2370/3421 2354/2400 785/799 S/C tCc/tGc 1 1 PPP1R3F HGNC HGNC:14944 protein_coding YES CCDS35254.1 ENSP00000055335 Q6ZSY5 UPI00001D7BA8 NM_033215.4 deleterious_low_confidence(0) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR12307:SF5,hmmpanther:PTHR12307,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 49287044 49287044 C G 1 0 0 0 0 1 0 0 0 12496 855 30 4 4 PPP1R3F 23 49287044 Missense_Mutation SNP C C3N-00175_T 12278061 49287044 106753851 1316 10908 SHROOM4 0 . GRCh38 X 50607620 50607620 + Silent SNP G G A novel C3N-00175_T C3N-00175_N G G c.3522C>T p.= p.L1174L ENST00000376020 6/9 147 92 55 133 133 0 strelka-varscan-mutect SHROOM4,synonymous_variant,p.=,ENST00000376020,NM_020717.3;SHROOM4,synonymous_variant,p.=,ENST00000460112,;SHROOM4,synonymous_variant,p.=,ENST00000289292,; A ENST00000376020 Transcript synonymous_variant 3548/9556 3522/4482 1174/1493 L ctC/ctT 1 -1 SHROOM4 HGNC HGNC:29215 protein_coding YES CCDS35277.1 ENSP00000365188 Q9ULL8 UPI00001C2068 NM_020717.3 6/9 hmmpanther:PTHR15012:SF35,hmmpanther:PTHR15012 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 50607620 50607620 G A 1 0 0 0 0 0 0 0 1 14559 1277 45 3 3 SHROOM4 23 50607620 Silent SNP G C3N-00175_T 1320576 50607620 105433275 1317 10909 ALAS2 0 . GRCh38 X 55013545 55013545 + Missense_Mutation SNP T T G novel C3N-00175_T C3N-00175_N T T c.1541A>C p.Glu514Ala p.E514A ENST00000330807 10/11 70 50 20 78 78 0 strelka-varscan-mutect ALAS2,missense_variant,p.Glu514Ala,ENST00000330807,NM_000032.4;ALAS2,missense_variant,p.Glu501Ala,ENST00000396198,NM_001037968.3;ALAS2,missense_variant,p.Glu477Ala,ENST00000335854,NM_001037967.3;APEX2,downstream_gene_variant,,ENST00000374987,NM_014481.3;ALAS2,intron_variant,,ENST00000498636,;ALAS2,downstream_gene_variant,,ENST00000463868,;ALAS2,downstream_gene_variant,,ENST00000477869,; G ENST00000330807 Transcript missense_variant 1679/2027 1541/1764 514/587 E/A gAg/gCg 1 -1 ALAS2 HGNC HGNC:397 protein_coding YES CCDS14366.1 ENSP00000332369 P22557 UPI000012C3FE NM_000032.4 deleterious(0) 10/11 hmmpanther:PTHR13693:SF58,hmmpanther:PTHR13693,Gene3D:3.90.1150.10,TIGRFAM_domain:TIGR01821,Pfam_domain:PF00155,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 55013545 55013545 T G 1 0 0 0 0 1 0 0 0 585 1551 54 5 5 ALAS2 23 55013545 Missense_Mutation SNP T C3N-00175_T 4405925 55013545 101027350 1318 10910 HEPH 0 . GRCh38 X 66172566 66172566 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.541C>A p.Pro181Thr p.P181T ENST00000519389 3/21 30 17 13 37 37 0 strelka-varscan-mutect HEPH,missense_variant,p.Pro181Thr,ENST00000519389,NM_138737.4;HEPH,missense_variant,p.Pro127Thr,ENST00000343002,;HEPH,missense_variant,p.Pro130Thr,ENST00000441993,NM_001130860.3;HEPH,missense_variant,p.Pro130Thr,ENST00000419594,NM_001282141.1;HEPH,missense_variant,p.Pro127Thr,ENST00000425114,;HEPH,missense_variant,p.Pro127Thr,ENST00000458621,;HEPH,5_prime_UTR_variant,,ENST00000336279,NM_014799.3;HEPH,downstream_gene_variant,,ENST00000429547,; A ENST00000519389 Transcript missense_variant 720/6013 541/3639 181/1212 P/T Cct/Act COSM3562777,COSM3562778 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 deleterious(0.02) 3/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Pfam_domain:PF07732,Superfamily_domains:SSF49503 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1188793883 . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 39 66172566 66172566 C A 1 0 0 0 0 1 0 0 0 6938 623 22 2 2 HEPH 23 66172566 Missense_Mutation SNP C C3N-00175_T 11159021 66172566 89868329 1319 10911 TBX22 0 . GRCh38 X 80022314 80022314 + Missense_Mutation SNP G G T rs367771247 C3N-00175_T C3N-00175_N G G c.45G>T p.Leu15Phe p.L15F ENST00000373296 2/9 212 123 89 212 212 0 strelka-varscan-mutect TBX22,missense_variant,p.Leu15Phe,ENST00000373296,NM_001109878.1,NM_001109879.1;TBX22,missense_variant,p.Leu15Phe,ENST00000373294,NM_016954.2,NM_001303475.1;TBX22,upstream_gene_variant,,ENST00000626877,;TBX22,missense_variant,p.Leu15Phe,ENST00000626498,;TBX22,non_coding_transcript_exon_variant,,ENST00000476373,; T ENST00000373296 Transcript missense_variant 179/2355 45/1563 15/520 L/F ttG/ttT rs367771247 1 1 TBX22 HGNC HGNC:11600 protein_coding YES CCDS14445.1 ENSP00000362393 Q9Y458 UPI00001377ED NM_001109878.1,NM_001109879.1 deleterious(0) 2/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF116 MODERATE 1 SNV 5 1 PASS rs367771247 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 80022314 80022314 G T 1 0 0 0 0 1 0 0 0 16063 1339 47 2 2 TBX22 23 80022314 Missense_Mutation SNP G C3N-00175_T 13849748 80022314 76018581 1320 10912 TBX22 0 . GRCh38 X 80023141 80023141 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.257G>T p.Ser86Ile p.S86I ENST00000373296 3/9 151 83 68 153 153 0 strelka-varscan-mutect TBX22,missense_variant,p.Ser86Ile,ENST00000373296,NM_001109878.1,NM_001109879.1;TBX22,missense_variant,p.Ser86Ile,ENST00000373294,NM_016954.2,NM_001303475.1;TBX22,non_coding_transcript_exon_variant,,ENST00000626877,;TBX22,missense_variant,p.Ser86Ile,ENST00000626498,;TBX22,downstream_gene_variant,,ENST00000476373,; T ENST00000373296 Transcript missense_variant 391/2355 257/1563 86/520 S/I aGt/aTt 1 1 TBX22 HGNC HGNC:11600 protein_coding YES CCDS14445.1 ENSP00000362393 Q9Y458 UPI00001377ED NM_001109878.1,NM_001109879.1 deleterious(0.04) 3/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF116 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 80023141 80023141 G T 1 0 0 0 0 1 0 0 0 16063 1029 36 2 2 TBX22 23 80023141 Missense_Mutation SNP G C3N-00175_T 827 80023141 76017754 1321 10913 TGIF2LX 0 . GRCh38 X 89922582 89922582 + Missense_Mutation SNP A A T novel C3N-00175_T C3N-00175_N A A c.497A>T p.Gln166Leu p.Q166L ENST00000561129 1/1 263 154 109 267 266 1 strelka-varscan-mutect TGIF2LX,missense_variant,p.Gln166Leu,ENST00000561129,;TGIF2LX,missense_variant,p.Gln166Leu,ENST00000283891,NM_138960.3; T ENST00000561129 Transcript missense_variant 627/928 497/726 166/241 Q/L cAg/cTg 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 tolerated(0.07) 1/1 hmmpanther:PTHR11850:SF16,hmmpanther:PTHR11850 MODERATE 1 SNV 1 PASS rs1447352316 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 89922582 89922582 A T 1 0 0 0 0 1 0 0 0 16260 188 7 4 4 TGIF2LX 23 89922582 Missense_Mutation SNP A C3N-00175_T 9899441 89922582 66118313 1322 10914 PABPC5 0 . GRCh38 X 91436133 91436133 + Missense_Mutation SNP C C T C3N-00175_T C3N-00175_N C C c.556C>T p.Arg186Trp p.R186W ENST00000312600 2/2 140 115 25 200 200 0 strelka-varscan-mutect PABPC5,missense_variant,p.Arg186Trp,ENST00000312600,NM_080832.2;PABPC5,missense_variant,p.Arg22Trp,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; T ENST00000312600 Transcript missense_variant 770/3221 556/1149 186/382 R/W Cgg/Tgg COSM1126344 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 deleterious(0) 2/2 Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01628 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 91436133 91436133 C T 1 0 0 0 0 1 0 0 0 11445 759 27 1 1 PABPC5 23 91436133 Missense_Mutation SNP C C3N-00175_T 1513551 91436133 64604762 1323 10915 BEX4 0 . GRCh38 X 103216193 103216193 + Missense_Mutation SNP G G T novel C3N-00175_T C3N-00175_N G G c.40G>T p.Gly14Trp p.G14W ENST00000372695 3/3 19 4 15 12 12 0 strelka-varscan-mutect BEX4,missense_variant,p.Gly14Trp,ENST00000372695,NM_001080425.3;BEX4,missense_variant,p.Gly14Trp,ENST00000372691,NM_001127688.2; T ENST00000372695 Transcript missense_variant 275/1328 40/363 14/120 G/W Ggg/Tgg 1 1 BEX4 HGNC HGNC:25475 protein_coding YES CCDS35355.1 ENSP00000361780 Q9NWD9 UPI0000038D5E NM_001080425.3 deleterious(0.01) 3/3 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF008633,hmmpanther:PTHR13987,hmmpanther:PTHR13987:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 15 190 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 103216193 103216193 G T 1 0 0 0 0 1 0 0 0 1560 1116 39 1 1 BEX4 23 103216193 Missense_Mutation SNP G C3N-00175_T 11780060 103216193 52824702 1324 10916 BEX2 0 . GRCh38 X 103310415 103310415 + Missense_Mutation SNP A A C rs3184865 C3N-00175_T C3N-00175_N A A c.34T>G p.Cys12Gly p.C12G ENST00000536889 2/3 111 62 49 145 145 0 strelka-varscan-mutect BEX2,missense_variant,p.Cys12Gly,ENST00000536889,NM_001168400.1,NM_001168399.1;BEX2,5_prime_UTR_variant,,ENST00000372677,NM_032621.3;BEX2,5_prime_UTR_variant,,ENST00000449185,;BEX2,5_prime_UTR_variant,,ENST00000372674,NM_001168401.1; C ENST00000536889 Transcript missense_variant 392/1077 34/483 12/160 C/G Tgc/Ggc rs3184865 1 -1 BEX2 HGNC HGNC:30933 protein_coding YES CCDS55467.1 ENSP00000442521 Q9BXY8 UPI0000D4D907 NM_001168400.1,NM_001168399.1 tolerated_low_confidence(0.54) 2/3 MODERATE 1 SNV 2 1 PASS rs3184865 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 39 103310415 103310415 A C 1 0 0 0 0 1 0 0 0 1559 130 5 5 5 BEX2 23 103310415 Missense_Mutation SNP A C3N-00175_T 94222 103310415 52730480 1325 10917 H2BFWT 0 . GRCh38 X 104013640 104013640 + Silent SNP G G T novel C3N-00175_T C3N-00175_N G G c.21C>A p.= p.P7P ENST00000217926 1/3 51 34 17 65 65 0 strelka-varscan-mutect H2BFWT,synonymous_variant,p.=,ENST00000217926,NM_001002916.4;H2BFWT,synonymous_variant,p.=,ENST00000611083,; T ENST00000217926 Transcript synonymous_variant 48/894 21/528 7/175 P ccC/ccA 1 -1 H2BFWT HGNC HGNC:27252 protein_coding YES CCDS35362.1 ENSP00000354723 Q7Z2G1 UPI000019B16C NM_001002916.4 1/3 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 104013640 104013640 G T 1 0 0 0 0 0 0 0 1 6814 1219 43 2 2 H2BFWT 23 104013640 Silent SNP G C3N-00175_T 703225 104013640 52027255 1326 10918 ACSL4 0 . GRCh38 X 109659506 109659506 + Missense_Mutation SNP T T A novel C3N-00175_T C3N-00175_N T T c.1826A>T p.Gln609Leu p.Q609L ENST00000340800 16/17 88 54 34 104 104 0 strelka-mutect ACSL4,missense_variant,p.Gln609Leu,ENST00000340800,NM_001318509.1,NM_022977.2;ACSL4,missense_variant,p.Gln609Leu,ENST00000469796,;ACSL4,missense_variant,p.Gln568Leu,ENST00000348502,NM_001318510.1,NM_004458.2;ACSL4,non_coding_transcript_exon_variant,,ENST00000505075,;ACSL4,intron_variant,,ENST00000514500,; A ENST00000340800 Transcript missense_variant 2331/5333 1826/2136 609/711 Q/L cAg/cTg 1 -1 ACSL4 HGNC HGNC:3571 protein_coding YES CCDS14548.1 ENSP00000339787 O60488 UPI000012E293 NM_001318509.1,NM_022977.2 deleterious(0.02) 16/17 Gene3D:3.30.300.30,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF241,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 109659506 109659506 T A 1 0 0 0 0 1 0 0 0 221 1594 55 4 4 ACSL4 23 109659506 Missense_Mutation SNP T C3N-00175_T 5645866 109659506 46381389 1327 10919 KIAA1210 0 . GRCh38 X 119088110 119088110 + Silent SNP A A C novel C3N-00175_T C3N-00175_N A A c.3120T>G p.= p.V1040V ENST00000402510 11/14 125 82 43 130 130 0 strelka-varscan-mutect KIAA1210,synonymous_variant,p.=,ENST00000402510,NM_020721.1; C ENST00000402510 Transcript synonymous_variant 3120/7824 3120/5130 1040/1709 V gtT/gtG 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 11/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 39 119088110 119088110 A C 1 0 0 0 0 0 0 0 1 8106 117 5 5 5 KIAA1210 23 119088110 Silent SNP A C3N-00175_T 9428604 119088110 36952785 1328 10920 USP26 0 . GRCh38 X 133027191 133027191 + Silent SNP G G T rs764088622 C3N-00175_T C3N-00175_N G G c.1030C>A p.= p.R344R ENST00000511190 6/6 107 58 49 107 107 0 strelka-varscan-mutect USP26,synonymous_variant,p.=,ENST00000511190,;USP26,synonymous_variant,p.=,ENST00000370832,NM_031907.1; T ENST00000511190 Transcript synonymous_variant 1500/3665 1030/2742 344/913 R Cgg/Agg rs764088622,COSM1664913 1 -1 USP26 HGNC HGNC:13485 protein_coding YES CCDS14635.1 ENSP00000423390 Q9BXU7 UPI00000421FD 6/6 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF390,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 0,1 LOW 1 SNV 2 0,1 1 PASS rs764088622 . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 133027191 133027191 G T 1 0 0 0 0 0 0 0 1 17598 1144 40 1 1 USP26 23 133027191 Silent SNP G C3N-00175_T 13939081 133027191 23013704 1329 10921 ADGRG4 0 . GRCh38 X 136348647 136348647 + Silent SNP T T A novel C3N-00175_T C3N-00175_N T T c.4941T>A p.= p.S1647S ENST00000394143 6/26 125 64 61 118 118 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; A ENST00000394143 Transcript synonymous_variant 5232/9931 4941/9243 1647/3080 S tcT/tcA 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 39 136348647 136348647 T A 1 0 0 0 0 0 0 0 1 371 1538 54 4 4 ADGRG4 23 136348647 Silent SNP T C3N-00175_T 3321456 136348647 19692248 1330 10922 F9 0 . GRCh38 X 139537098 139537098 + Frame_Shift_Del DEL C C - rs139089559 C3N-00175_T C3N-00175_N C C c.178delC p.Glu61ArgfsTer43 p.E61Rfs*43 ENST00000218099 2/8 60 36 24 125 125 0 sindel-varindel-pindel F9,frameshift_variant,p.Glu61ArgfsTer43,ENST00000218099,NM_000133.3;F9,frameshift_variant,p.Glu61ArgfsTer34,ENST00000394090,;F9,non_coding_transcript_exon_variant,,ENST00000479617,; - ENST00000218099 Transcript frameshift_variant 184/2780 177/1386 59/461 N/X aaC/aa rs139089559,COSM3379532 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 2/8 Gene3D:4.10.740.10,Pfam_domain:PF00594,PIRSF_domain:PIRSF001143,Prints_domain:PR00001,PROSITE_profiles:PS50998,SMART_domains:SM00069,Superfamily_domains:SSF57630 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 39 139537098 139537098 C - 1 0 1 0 1 0 0 0 0 5220 506 18 0 0 F9 23 139537098 Frame_Shift_Del DEL C C3N-00175_T 3188451 139537098 16503797 1331 10923 MAGEC2 0 . GRCh38 X 142203603 142203603 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.385G>T p.Gly129Cys p.G129C ENST00000247452 3/3 67 50 17 73 73 0 strelka-varscan-mutect MAGEC2,missense_variant,p.Gly129Cys,ENST00000247452,NM_016249.3; A ENST00000247452 Transcript missense_variant 733/1991 385/1122 129/373 G/C Ggc/Tgc 1 -1 MAGEC2 HGNC HGNC:13574 protein_coding YES CCDS14678.1 ENSP00000354660 Q9UBF1 UPI000012F059 NM_016249.3 deleterious(0.04) 3/3 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 142203603 142203603 C A 1 0 0 0 0 1 0 0 0 9099 623 22 2 2 MAGEC2 23 142203603 Missense_Mutation SNP C C3N-00175_T 2666505 142203603 13837292 1332 10924 HSFX2 0 . GRCh38 X 149594454 149594454 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.247G>T p.Asp83Tyr p.D83Y ENST00000598963 1/2 22 14 8 29 29 0 strelka-varscan-mutect HSFX2,missense_variant,p.Asp83Tyr,ENST00000598963,NM_001164415.2;TMEM185A,downstream_gene_variant,,ENST00000600449,NM_032508.3;TMEM185A,downstream_gene_variant,,ENST00000611119,NM_001174092.2;TMEM185A,downstream_gene_variant,,ENST00000613273,;TMEM185A,downstream_gene_variant,,ENST00000502858,;TMEM185A,downstream_gene_variant,,ENST00000616857,;TMEM185A,downstream_gene_variant,,ENST00000612022,; A ENST00000598963 Transcript missense_variant 263/1365 247/1272 83/423 D/Y Gac/Tac 1 -1 HSFX2 HGNC HGNC:32701 protein_coding YES CCDS48179.1 ENSP00000469223 Q9UBD0 A0A140VK21 UPI000007033B NM_001164415.2 tolerated(0.11) 1/2 hmmpanther:PTHR10015,hmmpanther:PTHR10015:SF163 MODERATE 1 SNV 1 1 PASS . . 25 182 3 0 0 0 0 0 -19.9995 1 1 1 1 0 A 3 1 39 149594454 149594454 C A 1 0 0 0 0 1 0 0 0 7295 826 29 2 2 HSFX2 23 149594454 Missense_Mutation SNP C C3N-00175_T 7390851 149594454 6446441 1333 10925 MAGEA11 0 . GRCh38 X 149714554 149714554 + Missense_Mutation SNP C C A novel C3N-00175_T C3N-00175_N C C c.170C>A p.Ser57Tyr p.S57Y ENST00000355220 3/5 78 49 29 91 91 0 strelka-varscan-mutect MAGEA11,missense_variant,p.Ser57Tyr,ENST00000355220,NM_005366.4;MAGEA11,missense_variant,p.Ser28Tyr,ENST00000333104,NM_001011544.1;MAGEA11,missense_variant,p.Ser28Tyr,ENST00000412632,;MAGEA11,non_coding_transcript_exon_variant,,ENST00000518694,; A ENST00000355220 Transcript missense_variant 272/1864 170/1290 57/429 S/Y tCc/tAc 1 1 MAGEA11 HGNC HGNC:6798 protein_coding YES CCDS48180.1 ENSP00000347358 P43364 UPI0000211BB0 NM_005366.4 deleterious_low_confidence(0) 3/5 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF71 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 149714554 149714554 C A 1 0 0 0 0 1 0 0 0 9081 855 30 2 2 MAGEA11 23 149714554 Missense_Mutation SNP C C3N-00175_T 120100 149714554 6326341 1334 10926 MAGEA8 0 . GRCh38 X 149884508 149884508 + Missense_Mutation SNP T T A rs782690283 C3N-00175_T C3N-00175_N T T c.236T>A p.Leu79Gln p.L79Q ENST00000535454 4/4 85 45 40 97 97 0 strelka-varscan-mutect MAGEA8,missense_variant,p.Leu79Gln,ENST00000535454,NM_001166400.1;MAGEA8,missense_variant,p.Leu79Gln,ENST00000542674,NM_001166401.1;MAGEA8,missense_variant,p.Leu79Gln,ENST00000286482,NM_005364.4;LINC00850,downstream_gene_variant,,ENST00000629221,;MAGEA8-AS1,upstream_gene_variant,,ENST00000427671,;MAGEA8,non_coding_transcript_exon_variant,,ENST00000493910,;MAGEA8,non_coding_transcript_exon_variant,,ENST00000345830,; A ENST00000535454 Transcript missense_variant 785/2112 236/957 79/318 L/Q cTg/cAg rs782690283 1 1 MAGEA8 HGNC HGNC:6806 protein_coding YES CCDS14692.1 ENSP00000438293 P43361 UPI0000071C79 NM_001166400.1 tolerated(0.3) 4/4 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF65,Pfam_domain:PF12440,SMART_domains:SM01392 MODERATE SNV 3 1 PASS rs782690283 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 149884508 149884508 T A 1 0 0 0 0 1 0 0 0 9086 1580 55 4 4 MAGEA8 23 149884508 Missense_Mutation SNP T C3N-00175_T 169954 149884508 6156387 1335 10927 CXorf40B 0 . GRCh38 X 149933757 149933757 + Missense_Mutation SNP C C G rs372900564 C3N-00175_T C3N-00175_N C C c.118G>C p.Ala40Pro p.A40P ENST00000370406 4/5 178 89 89 190 190 0 strelka-varscan-mutect CXorf40B,missense_variant,p.Ala40Pro,ENST00000370406,;CXorf40B,missense_variant,p.Ala40Pro,ENST00000462691,;CXorf40B,missense_variant,p.Ala40Pro,ENST00000370404,NM_001013845.1;CXorf40B,missense_variant,p.Ala40Pro,ENST00000370409,;CXorf40B,missense_variant,p.Ala40Pro,ENST00000355203,;CXorf40B,missense_variant,p.Ala40Pro,ENST00000483447,;XX-FW81066F1.2,downstream_gene_variant,,ENST00000457775,;LINC00894,upstream_gene_variant,,ENST00000449111,;CXorf40B,downstream_gene_variant,,ENST00000497550,; G ENST00000370406 Transcript missense_variant 947/1653 118/477 40/158 A/P Gcc/Ccc rs372900564,COSM4107424,COSM4107425 1 -1 CXorf40B HGNC HGNC:17402 protein_coding YES CCDS35426.1 ENSP00000359434 Q96DE9 UPI0000072E4A deleterious(0) 4/5 Gene3D:2.30.130.30,hmmpanther:PTHR31666,hmmpanther:PTHR31666:SF0,SMART_domains:SM01022,Superfamily_domains:SSF88697 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs372900564 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 39 149933757 149933757 C G 1 0 0 0 0 1 0 0 0 3915 768 27 4 4 CXorf40B 23 149933757 Missense_Mutation SNP C C3N-00175_T 49249 149933757 6107138 1336 10928 CNGA2 0 . GRCh38 X 151742570 151742570 + Missense_Mutation SNP C C A C3N-00175_T C3N-00175_N C C c.517C>A p.Leu173Met p.L173M ENST00000329903 5/6 83 43 40 88 87 1 strelka-varscan-mutect CNGA2,missense_variant,p.Leu173Met,ENST00000329903,NM_005140.1; A ENST00000329903 Transcript missense_variant 550/2834 517/1995 173/664 L/M Ctg/Atg COSM3559173 1 1 CNGA2 HGNC HGNC:2149 protein_coding YES CCDS14701.1 ENSP00000328478 Q16280 UPI000003E7AE NM_005140.1 tolerated(0.55) 5/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217:SF389,hmmpanther:PTHR10217,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 39 151742570 151742570 C A 1 0 0 0 0 1 0 0 0 3377 680 24 2 2 CNGA2 23 151742570 Missense_Mutation SNP C C3N-00175_T 1808813 151742570 4298325 1337 10929 L1CAM 0 . GRCh38 X 153864015 153864015 + Missense_Mutation SNP G G T rs147688847 C3N-00175_T C3N-00175_N G G c.3325C>A p.Arg1109Ser p.R1109S ENST00000370060 26/29 158 96 62 219 219 0 strelka-varscan-mutect L1CAM,missense_variant,p.Arg1109Ser,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,missense_variant,p.Arg1104Ser,ENST00000361981,NM_001143963.2;L1CAM,missense_variant,p.Arg1104Ser,ENST00000370055,;L1CAM,missense_variant,p.Arg1109Ser,ENST00000361699,NM_024003.3;L1CAM,intron_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000455590,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000484652,; T ENST00000370060 Transcript missense_variant,splice_region_variant 3515/5113 3325/3774 1109/1257 R/S Cgc/Agc rs147688847 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 tolerated(0.56) 26/29 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS rs147688847 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 39 153864015 153864015 G T 1 0 0 0 0 1 0 0 0 8489 1130 39 1 1 L1CAM 23 153864015 Missense_Mutation SNP G C3N-00175_T 2121445 153864015 2176880 1338 10930 L1CAM 0 . GRCh38 X 153867081 153867081 + Silent SNP C C T novel C3N-00175_T C3N-00175_N C C c.2181G>A p.= p.E727E ENST00000370060 18/29 210 119 91 271 271 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,synonymous_variant,p.=,ENST00000455590,;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000484652,; T ENST00000370060 Transcript synonymous_variant 2371/5113 2181/3774 727/1257 E gaG/gaA 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 18/29 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 39 153867081 153867081 C T 1 0 0 0 0 0 0 0 1 8489 912 32 3 3 L1CAM 23 153867081 Silent SNP C C3N-00175_T 3066 153867081 2173814 1339 10931 L1CAM 0 . GRCh38 X 153870234 153870234 + Silent SNP C C G rs201381558 C3N-00175_T C3N-00175_N C C c.813G>C p.= p.T271T ENST00000370060 9/29 39 25 14 83 83 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,downstream_gene_variant,,ENST00000458029,;L1CAM,downstream_gene_variant,,ENST00000407935,;L1CAM,upstream_gene_variant,,ENST00000455590,;L1CAM,downstream_gene_variant,,ENST00000420165,;L1CAM,downstream_gene_variant,,ENST00000464967,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,upstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000460553,;L1CAM,upstream_gene_variant,,ENST00000484652,; G ENST00000370060 Transcript synonymous_variant 1003/5113 813/3774 271/1257 T acG/acC rs201381558,COSM4697131,COSM4935096 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 9/29 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs201381558 . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 G 2 3 39 153870234 153870234 C G 1 0 0 0 0 0 0 0 1 8489 755 27 4 4 L1CAM 23 153870234 Silent SNP C C3N-00175_T 3153 153870234 2170661 1340 10932 PTPRU 0 . GRCh38 1 29258632 29258632 + Silent SNP G G C novel C3N-00180_T C3N-00180_N G G c.333G>C p.= p.G111G ENST00000345512 3/31 203 111 92 309 309 0 strelka-varscan-mutect PTPRU,synonymous_variant,p.=,ENST00000373779,NM_133178.3;PTPRU,synonymous_variant,p.=,ENST00000428026,NM_001195001.1;PTPRU,synonymous_variant,p.=,ENST00000460170,NM_133177.3;PTPRU,synonymous_variant,p.=,ENST00000345512,NM_005704.4;PTPRU,upstream_gene_variant,,ENST00000527027,; C ENST00000345512 Transcript synonymous_variant 462/4470 333/4341 111/1446 G ggG/ggC 1 1 PTPRU HGNC HGNC:9683 protein_coding YES CCDS334.1 ENSP00000334941 Q92729 UPI000013C57E NM_005704.4 3/31 PROSITE_profiles:PS50060,hmmpanther:PTHR19134:SF207,hmmpanther:PTHR19134,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1303749627 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 29258632 29258632 G C 1 0 0 0 0 0 0 0 1 12968 1190 42 4 4 PTPRU 1 29258632 Silent SNP G C3N-00180_T 29258632 219697790 1 10933 CSMD2 0 . GRCh38 1 33533795 33533795 + Splice_Site SNP C C T C3N-00180_T C3N-00180_N C C c.9991+1G>A p.X3331_splice ENST00000373381 109 56 53 183 183 0 strelka-varscan-mutect CSMD2,splice_donor_variant,,ENST00000373381,NM_001281956.1;CSMD2,splice_donor_variant,,ENST00000619121,;CSMD2,splice_donor_variant,,ENST00000373388,NM_052896.4;CSMD2,splice_donor_variant,,ENST00000241312,; T ENST00000373381 Transcript splice_donor_variant -/13698 9991/10896 3331/3631 COSM1732300,COSM1732301 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 63/70 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 5 4 40 33533795 33533795 C T 1 0 0 0 0 0 0 1 0 3746 550 19 1 1 CSMD2 1 33533795 Splice_Site SNP C C3N-00180_T 4275163 33533795 215422627 2 10934 LRRC40 0 . GRCh38 1 70205525 70205525 + Silent SNP G G T novel C3N-00180_T C3N-00180_N G G c.16C>A p.= p.R6R ENST00000370952 1/15 100 58 42 110 110 0 strelka-varscan-mutect LRRC40,synonymous_variant,p.=,ENST00000370952,NM_017768.4;SRSF11,upstream_gene_variant,,ENST00000370950,NM_004768.3;SRSF11,upstream_gene_variant,,ENST00000370951,NM_001190987.1;SRSF11,upstream_gene_variant,,ENST00000463877,; T ENST00000370952 Transcript synonymous_variant 96/2884 16/1809 6/602 R Cgg/Agg 1 -1 LRRC40 HGNC HGNC:26004 protein_coding YES CCDS646.1 ENSP00000359990 Q9H9A6 A0A140VJN3 UPI000004A0A0 NM_017768.4 1/15 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 70205525 70205525 G T 1 0 0 0 0 0 0 0 1 8894 1086 38 1 1 LRRC40 1 70205525 Silent SNP G C3N-00180_T 36671730 70205525 178750897 3 10935 AMY2A 0 . GRCh38 1 103619018 103619018 + Silent SNP T T C novel C3N-00180_T C3N-00180_N T T c.423T>C p.= p.F141F ENST00000622339 4/11 21 16 5 20 20 0 varscan-mutect AMY2A,synonymous_variant,p.=,ENST00000622339,;AMY2A,synonymous_variant,p.=,ENST00000414303,NM_000699.3;AMY2A,synonymous_variant,p.=,ENST00000423678,;AMY2A,upstream_gene_variant,,ENST00000497748,; C ENST00000622339 Transcript synonymous_variant 718/1862 423/1536 141/511 F ttT/ttC 1 1 AMY2A HGNC HGNC:477 protein_coding YES CCDS783.1 ENSP00000481450 P04746 UPI0000000C80 4/11 Gene3D:3.20.20.80,Pfam_domain:PF00128,hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF161,SMART_domains:SM00642,Superfamily_domains:SSF51445 LOW 1 SNV 5 1 PASS rs1336382319 . 6 202 2 0 0 0 0 0 -15.15433 1 1 1 1 0 C 2 2 40 103619018 103619018 T C 1 0 0 0 0 0 0 0 1 691 1780 62 5 5 AMY2A 1 103619018 Silent SNP T C3N-00180_T 33413493 103619018 145337404 4 10936 FCRL5 0 . GRCh38 1 157521250 157521250 + Missense_Mutation SNP G G A novel C3N-00180_T C3N-00180_N G G c.2282C>T p.Thr761Ile p.T761I ENST00000361835 11/17 173 112 61 134 134 0 strelka-mutect FCRL5,missense_variant,p.Thr761Ile,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,downstream_gene_variant,,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000461387,;FCRL5,non_coding_transcript_exon_variant,,ENST00000497286,;FCRL5,upstream_gene_variant,,ENST00000483875,; A ENST00000361835 Transcript missense_variant 2440/5390 2282/2934 761/977 T/I aCc/aTc 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 deleterious(0.02) 11/17 PROSITE_profiles:PS50835,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs900884937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 157521250 157521250 G A 1 0 0 0 0 1 0 0 0 5660 1261 44 3 3 FCRL5 1 157521250 Missense_Mutation SNP G C3N-00180_T 53902232 157521250 91435172 5 10937 FASLG 0 . GRCh38 1 172660127 172660127 + Frame_Shift_Del DEL G G - novel C3N-00180_T C3N-00180_N G G c.382delG p.Glu128ArgfsTer4 p.E128Rfs*4 ENST00000367721 2/4 289 113 176 379 379 0 sindel-varindel-pindel FASLG,frameshift_variant,p.Glu128ArgfsTer4,ENST00000367721,NM_000639.2;FASLG,intron_variant,,ENST00000340030,NM_001302746.1; - ENST00000367721 Transcript frameshift_variant 565/1888 381/846 127/281 L/X ttG/tt 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 2/4 hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF33 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 40 172660127 172660127 G - 1 0 1 0 1 0 0 0 0 5542 1339 47 0 0 FASLG 1 172660127 Frame_Shift_Del DEL G C3N-00180_T 15138877 172660127 76296295 6 10938 TNR 0 . GRCh38 1 175323466 175323466 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.3968G>T p.Trp1323Leu p.W1323L ENST00000367674 23/23 164 120 44 151 151 0 strelka-varscan-mutect TNR,missense_variant,p.Trp1323Leu,ENST00000367674,;TNR,missense_variant,p.Trp1323Leu,ENST00000263525,NM_003285.2;RP3-518E13.2,intron_variant,,ENST00000569593,; A ENST00000367674 Transcript missense_variant 4677/12949 3968/4077 1323/1358 W/L tGg/tTg 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0) 23/23 Gene3D:4.10.530.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 40 175323466 175323466 C A 1 0 0 0 0 1 0 0 0 16811 595 21 2 2 TNR 1 175323466 Missense_Mutation SNP C C3N-00180_T 2663339 175323466 73632956 7 10939 ASTN1 0 . GRCh38 1 177023565 177023565 + Missense_Mutation SNP C C A rs750249282 C3N-00180_T C3N-00180_N C C c.1277G>T p.Arg426Leu p.R426L ENST00000361833 7/23 40 19 21 52 52 0 strelka-varscan-mutect ASTN1,missense_variant,p.Arg426Leu,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Arg426Leu,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Arg426Leu,ENST00000424564,NM_207108.2;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;ASTN1,intron_variant,,ENST00000473640,; A ENST00000361833 Transcript missense_variant 1291/7116 1277/3885 426/1294 R/L cGc/cTc rs750249282,COSM4872669,COSM4947414,COSM73755,COSM900056 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious(0.01) 7/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs750249282 . 0 194 16 0 0 0 0 0 -20 0.9999293 1 1 1 0 A 3 1 40 177023565 177023565 C A 1 0 0 0 0 1 0 0 0 1211 768 27 1 1 ASTN1 1 177023565 Missense_Mutation SNP C C3N-00180_T 1700099 177023565 71932857 8 10940 F13B 0 . GRCh38 1 197060442 197060442 + Missense_Mutation SNP T T A C3N-00180_T C3N-00180_N T T c.729A>T p.Glu243Asp p.E243D ENST00000367412 5/12 52 42 10 135 135 0 strelka-mutect F13B,missense_variant,p.Glu243Asp,ENST00000367412,NM_001994.2; A ENST00000367412 Transcript missense_variant 773/2217 729/1986 243/661 E/D gaA/gaT COSM4682191 1 -1 F13B HGNC HGNC:3534 protein_coding YES CCDS1388.1 ENSP00000356382 P05160 UPI000013D8E0 NM_001994.2 tolerated(0.05) 5/12 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF314,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 197060442 197060442 T A 1 0 0 0 0 1 0 0 0 5209 1838 64 4 4 F13B 1 197060442 Missense_Mutation SNP T C3N-00180_T 20036877 197060442 51895980 9 10941 DNAH14 0 . GRCh38 1 225305048 225305048 + Silent SNP A A C novel C3N-00180_T C3N-00180_N A A c.8685A>C p.= p.A2895A ENST00000430092 56/84 127 90 37 262 261 1 strelka-varscan-mutect DNAH14,synonymous_variant,p.=,ENST00000430092,NM_001373.1;DNAH14,synonymous_variant,p.=,ENST00000439375,;DNAH14,synonymous_variant,p.=,ENST00000445597,;DNAH14,synonymous_variant,p.=,ENST00000327794,; C ENST00000430092 Transcript synonymous_variant 8900/13763 8685/13548 2895/4515 A gcA/gcC 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 56/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676,Pfam_domain:PF12780 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 225305048 225305048 A C 1 0 0 0 0 0 0 0 1 4415 146 6 5 5 DNAH14 1 225305048 Silent SNP A C3N-00180_T 28244606 225305048 23651374 10 10942 OBSCN 0 . GRCh38 1 228282079 228282079 + Missense_Mutation SNP C C T novel C3N-00180_T C3N-00180_N C C c.9631C>T p.Arg3211Cys p.R3211C ENST00000570156 36/116 324 170 154 452 452 0 strelka-varscan-mutect OBSCN,missense_variant,p.Arg3211Cys,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Arg3211Cys,ENST00000366707,;OBSCN,missense_variant,p.Arg2782Cys,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Arg2782Cys,ENST00000636875,;OBSCN,missense_variant,p.Arg2782Cys,ENST00000284548,NM_052843.3;OBSCN,missense_variant,p.Arg58Cys,ENST00000483539,;OBSCN,missense_variant,p.Arg630Cys,ENST00000366706,;OBSCN,non_coding_transcript_exon_variant,,ENST00000366704,; T ENST00000570156 Transcript missense_variant 9705/26925 9631/26772 3211/8923 R/C Cgc/Tgc 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0.01) 36/116 Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1041621354 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 228282079 228282079 C T 1 0 0 0 0 1 0 0 0 10889 652 23 1 1 OBSCN 1 228282079 Missense_Mutation SNP C C3N-00180_T 2977031 228282079 20674343 11 10943 OR2G2 0 . GRCh38 1 247588786 247588786 + Missense_Mutation SNP C C G rs764488449 C3N-00180_T C3N-00180_N C C c.427C>G p.Leu143Val p.L143V ENST00000320065 1/1 282 226 56 350 350 0 strelka-varscan-mutect OR2G2,missense_variant,p.Leu143Val,ENST00000320065,NM_001001915.1;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; G ENST00000320065 Transcript missense_variant 427/954 427/954 143/317 L/V Ctc/Gtc rs764488449,COSM5536089 1 1 OR2G2 HGNC HGNC:15007 protein_coding YES CCDS31092.1 ENSP00000326349 Q8NGZ5 UPI0000061EB9 NM_001001915.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF132,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE SNV 0,1 1 PASS rs764488449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 247588786 247588786 C G 1 0 0 0 0 1 0 0 0 11076 913 32 4 4 OR2G2 1 247588786 Missense_Mutation SNP C C3N-00180_T 19306707 247588786 1367636 12 10944 EPCAM 0 . GRCh38 2 47379910 47379910 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.799G>T p.Gly267Cys p.G267C ENST00000263735 7/9 683 455 228 612 612 0 strelka-varscan EPCAM,missense_variant,p.Gly267Cys,ENST00000263735,NM_002354.2;EPCAM,missense_variant,p.Gly295Cys,ENST00000405271,;MIR559,downstream_gene_variant,,ENST00000385188,;Metazoa_SRP,upstream_gene_variant,,ENST00000622819,;EPCAM,missense_variant,p.Gly295Cys,ENST00000456133,;EPCAM,non_coding_transcript_exon_variant,,ENST00000490733,;EPCAM,downstream_gene_variant,,ENST00000474691,; T ENST00000263735 Transcript missense_variant 1157/1724 799/945 267/314 G/C Ggt/Tgt 1 1 EPCAM HGNC HGNC:11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 deleterious(0) 7/9 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14168:SF2,hmmpanther:PTHR14168 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 47379910 47379910 G T 1 0 0 0 0 1 0 0 0 5008 1348 47 2 2 EPCAM 2 47379910 Missense_Mutation SNP G C3N-00180_T 47379910 194813619 13 10945 OTX1 0 . GRCh38 2 63054101 63054101 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.152A>G p.Asp51Gly p.D51G ENST00000282549 4/5 135 80 55 204 204 0 strelka-varscan OTX1,missense_variant,p.Asp51Gly,ENST00000282549,NM_014562.3;OTX1,missense_variant,p.Asp51Gly,ENST00000366671,NM_001199770.1;OTX1,synonymous_variant,p.=,ENST00000405984,;OTX1,downstream_gene_variant,,ENST00000484066,;OTX1,downstream_gene_variant,,ENST00000477348,;OTX1,downstream_gene_variant,,ENST00000476383,; G ENST00000282549 Transcript missense_variant 428/2861 152/1065 51/354 D/G gAc/gGc 1 1 OTX1 HGNC HGNC:8521 protein_coding YES CCDS1873.1 ENSP00000282549 P32242 UPI0000130F36 NM_014562.3 deleterious(0.02) 4/5 PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF310,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 63054101 63054101 A G 1 0 0 0 0 1 0 0 0 11390 275 10 5 5 OTX1 2 63054101 Missense_Mutation SNP A C3N-00180_T 15674191 63054101 179139428 14 10946 DYSF 0 . GRCh38 2 71520802 71520802 + Silent SNP C C A C3N-00180_T C3N-00180_N C C c.1047C>A p.= p.L349L ENST00000410020 12/56 521 304 217 587 587 0 strelka-varscan DYSF,synonymous_variant,p.=,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,synonymous_variant,p.=,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,synonymous_variant,p.=,ENST00000413539,NM_001130979.1;DYSF,synonymous_variant,p.=,ENST00000429174,NM_001130978.1;DYSF,synonymous_variant,p.=,ENST00000409762,NM_001130980.1;DYSF,synonymous_variant,p.=,ENST00000410020,NM_001130987.1;DYSF,synonymous_variant,p.=,ENST00000409651,NM_001130982.1;DYSF,synonymous_variant,p.=,ENST00000409366,NM_001130983.1;DYSF,synonymous_variant,p.=,ENST00000410041,NM_001130985.1;DYSF,synonymous_variant,p.=,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,synonymous_variant,p.=,ENST00000394120,NM_001130455.1; A ENST00000410020 Transcript synonymous_variant 1188/6657 1047/6360 349/2119 L ctC/ctA COSM1149220,COSM721915 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 12/56 Gene3D:2.60.40.150,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33,SMART_domains:SM00239,SMART_domains:SM01202,Superfamily_domains:SSF49562 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 40 71520802 71520802 C A 1 0 0 0 0 0 0 0 1 4683 813 29 2 2 DYSF 2 71520802 Silent SNP C C3N-00180_T 8466701 71520802 170672727 15 10947 CFAP221 0 . GRCh38 2 119652059 119652059 + Missense_Mutation SNP A A T novel C3N-00180_T C3N-00180_N A A c.2404A>T p.Arg802Trp p.R802W ENST00000413369 23/24 138 77 61 139 139 0 strelka-varscan CFAP221,missense_variant,p.Arg361Trp,ENST00000443972,;CFAP221,missense_variant,p.Arg802Trp,ENST00000413369,NM_001271049.1;CFAP221,downstream_gene_variant,,ENST00000434869,;CFAP221,upstream_gene_variant,,ENST00000464578,;CFAP221,3_prime_UTR_variant,,ENST00000295220,; T ENST00000413369 Transcript missense_variant 2491/2801 2404/2523 802/840 R/W Agg/Tgg 1 1 CFAP221 HGNC HGNC:33720 protein_coding YES CCDS33282.2 ENSP00000393222 Q4G0U5 UPI0001D322F9 NM_001271049.1 deleterious(0) 23/24 hmmpanther:PTHR23053 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 119652059 119652059 A T 1 0 0 0 0 1 0 0 0 3016 179 7 4 4 CFAP221 2 119652059 Missense_Mutation SNP A C3N-00180_T 48131257 119652059 122541470 16 10948 AMER3 0 . GRCh38 2 130763837 130763837 + Missense_Mutation SNP A A T novel C3N-00180_T C3N-00180_N A A c.1765A>T p.Thr589Ser p.T589S ENST00000423981 2/2 161 105 56 118 118 0 strelka-varscan AMER3,missense_variant,p.Thr589Ser,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Thr589Ser,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; T ENST00000423981 Transcript missense_variant 1875/6172 1765/2586 589/861 T/S Aca/Tca 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 tolerated(0.69) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 MODERATE 1 SNV 4 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 130763837 130763837 A T 1 0 0 0 0 1 0 0 0 669 159 6 4 4 AMER3 2 130763837 Missense_Mutation SNP A C3N-00180_T 11111778 130763837 111429692 17 10949 THSD7B 0 . GRCh38 2 137572454 137572454 + Silent SNP G G T novel C3N-00180_T C3N-00180_N G G c.3327G>T p.= p.L1109L ENST00000272643 16/27 201 123 78 178 178 0 strelka-varscan THSD7B,synonymous_variant,p.=,ENST00000409968,NM_001316349.1;THSD7B,synonymous_variant,p.=,ENST00000272643,;THSD7B,synonymous_variant,p.=,ENST00000413152,NM_001080427.1; T ENST00000272643 Transcript synonymous_variant 3327/5939 3327/4827 1109/1608 L ctG/ctT 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A 16/27 Gene3D:2.20.100.10,PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 137572454 137572454 G T 1 0 0 0 0 0 0 0 1 16314 1364 48 2 2 THSD7B 2 137572454 Silent SNP G C3N-00180_T 6808617 137572454 104621075 18 10950 RFTN2 0 . GRCh38 2 197617874 197617874 + Missense_Mutation SNP C C T novel C3N-00180_T C3N-00180_N C C c.976G>A p.Glu326Lys p.E326K ENST00000295049 6/9 135 105 30 215 215 0 strelka-varscan RFTN2,missense_variant,p.Glu326Lys,ENST00000295049,NM_144629.2;RFTN2,missense_variant,p.Glu8Lys,ENST00000454447,;RFTN2,non_coding_transcript_exon_variant,,ENST00000494346,; T ENST00000295049 Transcript missense_variant 1513/5827 976/1506 326/501 E/K Gaa/Aaa 1 -1 RFTN2 HGNC HGNC:26402 protein_coding YES CCDS2323.1 ENSP00000295049 Q52LD8 UPI000013E1F9 NM_144629.2 tolerated(0.32) 6/9 hmmpanther:PTHR17601,hmmpanther:PTHR17601:SF1,Pfam_domain:PF15250 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 197617874 197617874 C T 1 0 0 0 0 1 0 0 0 13433 922 32 3 3 RFTN2 2 197617874 Missense_Mutation SNP C C3N-00180_T 60045420 197617874 44575655 19 10951 TMEM237 0 . GRCh38 2 201629771 201629771 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.635G>T p.Trp212Leu p.W212L ENST00000409883 8/13 164 99 65 321 320 1 strelka-varscan TMEM237,missense_variant,p.Trp204Leu,ENST00000409444,NM_152388.3;TMEM237,missense_variant,p.Trp212Leu,ENST00000409883,NM_001044385.2;TMEM237,missense_variant,p.Trp204Leu,ENST00000621467,;TMEM237,non_coding_transcript_exon_variant,,ENST00000466839,;TMEM237,non_coding_transcript_exon_variant,,ENST00000466641,;TMEM237,upstream_gene_variant,,ENST00000471318,;TMEM237,downstream_gene_variant,,ENST00000489550,;TMEM237,3_prime_UTR_variant,,ENST00000286196,;TMEM237,3_prime_UTR_variant,,ENST00000432684,;TMEM237,3_prime_UTR_variant,,ENST00000444047,;TMEM237,upstream_gene_variant,,ENST00000495329,; A ENST00000409883 Transcript missense_variant 752/5415 635/1227 212/408 W/L tGg/tTg 1 -1 TMEM237 HGNC HGNC:14432 protein_coding YES CCDS46489.1 ENSP00000386264 Q96Q45 UPI0000DD5A47 NM_001044385.2 tolerated(0.06) 8/13 hmmpanther:PTHR28388,hmmpanther:PTHR28388:SF1,Pfam_domain:PF15383 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 201629771 201629771 C A 1 0 0 0 0 1 0 0 0 16598 595 21 2 2 TMEM237 2 201629771 Missense_Mutation SNP C C3N-00180_T 4011897 201629771 40563758 20 10952 ALPI 0 . GRCh38 2 232456254 232456254 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.55G>T p.Gly19Cys p.G19C ENST00000295463 1/11 413 261 152 454 453 1 strelka-varscan-mutect ALPI,missense_variant,p.Gly19Cys,ENST00000295463,NM_001631.4;ALPI,missense_variant,p.Gly19Cys,ENST00000457560,; T ENST00000295463 Transcript missense_variant 132/2550 55/1587 19/528 G/C Ggc/Tgc 1 1 ALPI HGNC HGNC:437 protein_coding YES CCDS2492.1 ENSP00000295463 P09923 A0A024R4A2 UPI0000131FFE NM_001631.4 tolerated(0.11) 1/11 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11596:SF31,hmmpanther:PTHR11596 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 232456254 232456254 G T 1 0 0 0 0 1 0 0 0 643 1232 43 2 2 ALPI 2 232456254 Missense_Mutation SNP G C3N-00180_T 30826483 232456254 9737275 21 10953 ALS2CL 0 . GRCh38 3 46689337 46689337 + Splice_Site SNP C C A novel C3N-00180_T C3N-00180_N C C c.103+1G>T p.X35_splice ENST00000318962 162 68 94 333 333 0 strelka-varscan-mutect ALS2CL,splice_donor_variant,,ENST00000318962,NM_147129.3;ALS2CL,splice_donor_variant,,ENST00000415953,NM_001190707.1;ALS2CL,splice_donor_variant,,ENST00000450172,;ALS2CL,splice_donor_variant,,ENST00000431015,;ALS2CL,splice_donor_variant,,ENST00000434140,;ALS2CL,upstream_gene_variant,,ENST00000423707,; A ENST00000318962 Transcript splice_donor_variant -/4741 103/2862 35/953 1 -1 ALS2CL HGNC HGNC:20605 protein_coding YES CCDS2743.1 ENSP00000313670 Q60I27 A0A024R2U1 UPI00001B5641 NM_147129.3 2/25 HIGH 1 SNV 1 1 PASS rs1157881315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 40 46689337 46689337 C A 1 0 0 0 0 0 0 1 0 651 521 18 2 2 ALS2CL 3 46689337 Splice_Site SNP C C3N-00180_T 46689337 151606222 22 10954 NFKBIZ 0 . GRCh38 3 101849717 101849717 + Missense_Mutation SNP T T G novel C3N-00180_T C3N-00180_N T T c.89T>G p.Leu30Arg p.L30R ENST00000326172 1/12 30 12 18 72 72 0 strelka-varscan-mutect NFKBIZ,missense_variant,p.Leu30Arg,ENST00000326172,NM_031419.3;NFKBIZ,missense_variant,p.Leu30Arg,ENST00000326151,;NFKBIZ,missense_variant,p.Leu30Arg,ENST00000461724,;NFKBIZ,intron_variant,,ENST00000394054,NM_001005474.2;NFKBIZ,intron_variant,,ENST00000483180,;NFKBIZ,upstream_gene_variant,,ENST00000491281,;NFKBIZ,non_coding_transcript_exon_variant,,ENST00000486444,;NFKBIZ,upstream_gene_variant,,ENST00000465476,; G ENST00000326172 Transcript missense_variant 204/3923 89/2157 30/718 L/R cTc/cGc 1 1 NFKBIZ HGNC HGNC:29805 protein_coding YES CCDS2946.1 ENSP00000325663 Q9BYH8 UPI000006FBB1 NM_031419.3 deleterious_low_confidence(0) 1/12 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 101849717 101849717 T G 1 0 0 0 0 1 0 0 0 10419 1551 54 5 5 NFKBIZ 3 101849717 Missense_Mutation SNP T C3N-00180_T 55160380 101849717 96445842 23 10955 OPA1 0 . GRCh38 3 193659505 193659505 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.2410G>T p.Val804Leu p.V804L ENST00000361908 24/30 165 72 93 329 329 0 strelka-varscan-mutect OPA1,missense_variant,p.Val822Leu,ENST00000361510,NM_130837.2;OPA1,missense_variant,p.Val804Leu,ENST00000361908,NM_130836.2;OPA1,missense_variant,p.Val786Leu,ENST00000361715,NM_130835.2;OPA1,missense_variant,p.Val785Leu,ENST00000361828,NM_130832.2,NM_130834.2;OPA1,missense_variant,p.Val767Leu,ENST00000392438,NM_015560.2;OPA1,missense_variant,p.Val768Leu,ENST00000361150,NM_130833.2,NM_130831.2;OPA1,upstream_gene_variant,,ENST00000445863,;OPA1,non_coding_transcript_exon_variant,,ENST00000482865,; T ENST00000361908 Transcript missense_variant 2644/6439 2410/2994 804/997 V/L Gtg/Ttg 1 1 OPA1 HGNC HGNC:8140 protein_coding YES CCDS33917.1 ENSP00000354681 O60313 E5KLJ7 UPI0000422960 NM_130836.2 tolerated(0.58) 24/30 hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF67 MODERATE 1 SNV 1 1 PASS rs1440910404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 193659505 193659505 G T 1 0 0 0 0 1 0 0 0 10948 1261 44 2 2 OPA1 3 193659505 Missense_Mutation SNP G C3N-00180_T 91809788 193659505 4636054 24 10956 GAK 0 . GRCh38 4 888860 888860 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.1192C>A p.Gln398Lys p.Q398K ENST00000314167 11/28 181 121 60 278 278 0 strelka-varscan-mutect GAK,missense_variant,p.Gln398Lys,ENST00000314167,NM_005255.2;GAK,missense_variant,p.Gln319Lys,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,intron_variant,,ENST00000618573,;GAK,non_coding_transcript_exon_variant,,ENST00000504435,;GAK,downstream_gene_variant,,ENST00000505819,;GAK,upstream_gene_variant,,ENST00000504947,; T ENST00000314167 Transcript missense_variant 1303/4442 1192/3936 398/1311 Q/K Cag/Aag 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 deleterious(0) 11/28 hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 888860 888860 G T 1 0 0 0 0 1 0 0 0 6063 1357 47 2 2 GAK 4 888860 Missense_Mutation SNP G C3N-00180_T 888860 189325695 25 10957 ADGRL3 0 . GRCh38 4 62070603 62070603 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.4105G>T p.Asp1369Tyr p.D1369Y ENST00000514591 25/25 392 263 129 347 347 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Asp1369Tyr,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Asp1480Tyr,ENST00000506720,;ADGRL3,missense_variant,p.Asp1471Tyr,ENST00000506746,;ADGRL3,missense_variant,p.Asp1428Tyr,ENST00000507625,;ADGRL3,missense_variant,p.Asp1412Tyr,ENST00000508946,;ADGRL3,missense_variant,p.Asp1403Tyr,ENST00000514996,;ADGRL3,missense_variant,p.Asp818Tyr,ENST00000502815,;ADGRL3,3_prime_UTR_variant,,ENST00000512091,NM_001322246.1;ADGRL3,3_prime_UTR_variant,,ENST00000509896,;ADGRL3,3_prime_UTR_variant,,ENST00000511324,;ADGRL3,3_prime_UTR_variant,,ENST00000508693,;ADGRL3,3_prime_UTR_variant,,ENST00000507164,;ADGRL3,3_prime_UTR_variant,,ENST00000506700,;ADGRL3,3_prime_UTR_variant,,ENST00000504896,;ADGRL3,3_prime_UTR_variant,,ENST00000514157,;ADGRL3-AS1,downstream_gene_variant,,ENST00000506704,;ADGRL3-AS1,downstream_gene_variant,,ENST00000504135,;ADGRL3-AS1,downstream_gene_variant,,ENST00000509461,; T ENST00000514591 Transcript missense_variant 4434/6297 4105/4410 1369/1469 D/Y Gat/Tat 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious_low_confidence(0.02) 25/25 Pfam_domain:PF02354 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 62070603 62070603 G T 1 0 0 0 0 1 0 0 0 377 942 33 2 2 ADGRL3 4 62070603 Missense_Mutation SNP G C3N-00180_T 61181743 62070603 128143952 26 10958 USO1 0 . GRCh38 4 75787087 75787087 + Missense_Mutation SNP C C T C3N-00180_T C3N-00180_N C C c.893C>T p.Thr298Ile p.T298I ENST00000264904 11/26 99 62 37 117 117 0 strelka-varscan-mutect USO1,missense_variant,p.Thr298Ile,ENST00000264904,NM_001290049.1;USO1,missense_variant,p.Thr294Ile,ENST00000514213,NM_003715.3; T ENST00000264904 Transcript missense_variant 1115/4135 893/2922 298/973 T/I aCc/aTc COSM1486095,COSM1486096 1 1 USO1 HGNC HGNC:30904 protein_coding YES CCDS77929.1 ENSP00000264904 O60763 UPI0001D1479E NM_001290049.1 tolerated(0.09) 11/26 hmmpanther:PTHR10013 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 75787087 75787087 C T 1 0 0 0 0 1 0 0 0 17573 507 18 3 3 USO1 4 75787087 Missense_Mutation SNP C C3N-00180_T 13716484 75787087 114427468 27 10959 FRAS1 0 . GRCh38 4 78540634 78540634 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.11549G>T p.Arg3850Leu p.R3850L ENST00000512123 74/74 47 26 21 27 27 0 strelka-varscan-mutect FRAS1,missense_variant,p.Arg3850Leu,ENST00000512123,NM_025074.6; T ENST00000512123 Transcript missense_variant 11989/15624 11549/12039 3850/4012 R/L cGc/cTc 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 deleterious(0) 74/74 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29 MODERATE 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.999998 1 1 1 0 T 3 4 40 78540634 78540634 G T 1 0 0 0 0 1 0 0 0 5908 1087 38 1 1 FRAS1 4 78540634 Missense_Mutation SNP G C3N-00180_T 2753547 78540634 111673921 28 10960 RP11-766F14.2 0 . GRCh38 4 99650164 99650164 + Silent SNP G G C novel C3N-00180_T C3N-00180_N G G c.4485C>G p.= p.P1495P ENST00000511828 1/2 169 110 59 163 163 0 strelka-varscan-mutect RP11-766F14.2,synonymous_variant,p.=,ENST00000511828,; C ENST00000511828 Transcript synonymous_variant 4485/10086 4485/5382 1495/1793 P ccC/ccG 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE 1/2 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 99650164 99650164 G C 1 0 0 0 0 0 0 0 1 13762 1219 43 4 4 RP11-766F14.2 4 99650164 Silent SNP G C3N-00180_T 21109530 99650164 90564391 29 10961 CENPE 0 . GRCh38 4 103120228 103120228 + Missense_Mutation SNP T T C novel C3N-00180_T C3N-00180_N T T c.7249A>G p.Ile2417Val p.I2417V ENST00000265148 44/49 128 77 51 259 259 0 strelka-varscan-mutect CENPE,missense_variant,p.Ile2417Val,ENST00000265148,NM_001813.2;CENPE,missense_variant,p.Ile2380Val,ENST00000611174,;CENPE,missense_variant,p.Ile2296Val,ENST00000380026,NM_001286734.1;CENPE,non_coding_transcript_exon_variant,,ENST00000509823,; C ENST00000265148 Transcript missense_variant 7339/8612 7249/8106 2417/2701 I/V Ata/Gta 1 -1 CENPE HGNC HGNC:1856 protein_coding YES CCDS34042.1 ENSP00000265148 Q02224 UPI000020B28A NM_001813.2 tolerated(0.89) 44/49 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 40 103120228 103120228 T C 1 0 0 0 0 1 0 0 0 2938 1464 51 5 5 CENPE 4 103120228 Missense_Mutation SNP T C3N-00180_T 3470064 103120228 87094327 30 10962 NDST3 0 . GRCh38 4 118054337 118054337 + Missense_Mutation SNP G G A C3N-00180_T C3N-00180_N G G c.427G>A p.Asp143Asn p.D143N ENST00000296499 2/14 135 84 51 153 153 0 strelka-varscan-mutect NDST3,missense_variant,p.Asp143Asn,ENST00000296499,NM_004784.2;NDST3,non_coding_transcript_exon_variant,,ENST00000394488,; A ENST00000296499 Transcript missense_variant 830/5961 427/2622 143/873 D/N Gat/Aat COSM124699 1 1 NDST3 HGNC HGNC:7682 protein_coding YES CCDS3708.1 ENSP00000296499 O95803 UPI0000071C44 NM_004784.2 tolerated(0.08) 2/14 Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF29 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 118054337 118054337 G A 1 0 0 0 0 1 0 0 0 10278 1174 41 3 3 NDST3 4 118054337 Missense_Mutation SNP G C3N-00180_T 14934109 118054337 72160218 31 10963 RXFP1 0 . GRCh38 4 158633459 158633459 + Silent SNP G G T rs577414448 C3N-00180_T C3N-00180_N G G c.1035G>T p.= p.L345L ENST00000423548 12/18 100 83 17 162 162 0 strelka-varscan RXFP1,synonymous_variant,p.=,ENST00000423548,NM_001253727.1;RXFP1,synonymous_variant,p.=,ENST00000448688,NM_001253733.1,NM_001253732.1;RXFP1,synonymous_variant,p.=,ENST00000307765,NM_021634.3;RXFP1,synonymous_variant,p.=,ENST00000613319,NM_001253730.1;RXFP1,synonymous_variant,p.=,ENST00000460056,;RXFP1,synonymous_variant,p.=,ENST00000470033,NM_001253728.1;RXFP1,intron_variant,,ENST00000343542,NM_001253729.1;RXFP1,3_prime_UTR_variant,,ENST00000342048,;RXFP1,3_prime_UTR_variant,,ENST00000471616,; T ENST00000423548 Transcript synonymous_variant 1298/3930 1035/2355 345/784 L ctG/ctT rs577414448 1 1 RXFP1 HGNC HGNC:19718 protein_coding YES CCDS75204.1 ENSP00000405841 B4DGP2 UPI00017A6DBF NM_001253727.1 12/18 Gene3D:3.80.10.10,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF18,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 158633459 158633459 G T 1 0 0 0 0 0 0 0 1 14020 1277 45 2 2 RXFP1 4 158633459 Silent SNP G C3N-00180_T 40579122 158633459 31581096 32 10964 ZDHHC11 0 . GRCh38 5 825185 825185 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.1002G>T p.Gln334His p.Q334H ENST00000283441 8/13 336 275 61 260 260 0 strelka-varscan-mutect ZDHHC11,missense_variant,p.Gln334His,ENST00000283441,NM_024786.2;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000503758,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000508951,;ZDHHC11,missense_variant,p.Gln195His,ENST00000507800,; A ENST00000283441 Transcript missense_variant 1386/2604 1002/1239 334/412 Q/H caG/caT 1 -1 ZDHHC11 HGNC HGNC:19158 protein_coding YES CCDS3857.1 ENSP00000283441 Q9H8X9 UPI000013C384 NM_024786.2 tolerated_low_confidence(0.2) 8/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 825185 825185 C A 1 0 0 0 0 1 0 0 0 18176 680 24 2 2 ZDHHC11 5 825185 Missense_Mutation SNP C C3N-00180_T 825185 180713074 33 10965 C7 0 . GRCh38 5 40964817 40964817 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.1826C>A p.Pro609Gln p.P609Q ENST00000313164 14/18 174 119 55 312 312 0 strelka-varscan-mutect C7,missense_variant,p.Pro609Gln,ENST00000313164,NM_000587.2;C7,non_coding_transcript_exon_variant,,ENST00000486779,;RP11-301A5.2,downstream_gene_variant,,ENST00000504890,; A ENST00000313164 Transcript missense_variant 2185/4257 1826/2532 609/843 P/Q cCa/cAa 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 14/18 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 40964817 40964817 C A 1 0 0 0 0 1 0 0 0 2134 594 21 2 2 C7 5 40964817 Missense_Mutation SNP C C3N-00180_T 40139632 40964817 140573442 34 10966 HCN1 0 . GRCh38 5 45262426 45262426 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.2168C>A p.Thr723Asn p.T723N ENST00000303230 8/8 133 85 48 92 92 0 strelka-varscan-mutect HCN1,missense_variant,p.Thr723Asn,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; T ENST00000303230 Transcript missense_variant 2409/9885 2168/2673 723/890 T/N aCc/aAc 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated_low_confidence(0.16) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 45262426 45262426 G T 1 0 0 0 0 1 0 0 0 6883 1261 44 2 2 HCN1 5 45262426 Missense_Mutation SNP G C3N-00180_T 4297609 45262426 136275833 35 10967 BDP1 0 . GRCh38 5 71467476 71467476 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.908G>T p.Trp303Leu p.W303L ENST00000358731 6/39 169 96 73 213 213 0 strelka-varscan-mutect BDP1,missense_variant,p.Trp303Leu,ENST00000358731,NM_018429.2;BDP1,missense_variant,p.Trp303Leu,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,; T ENST00000358731 Transcript missense_variant 1171/11073 908/7875 303/2624 W/L tGg/tTg 1 1 BDP1 HGNC HGNC:13652 protein_coding YES CCDS43328.1 ENSP00000351575 A6H8Y1 UPI000020CA90 NM_018429.2 deleterious(0) 6/39 hmmpanther:PTHR22929:SF1,hmmpanther:PTHR22929,Pfam_domain:PF15963,SMART_domains:SM00717,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 71467476 71467476 G T 1 0 0 0 0 1 0 0 0 1542 1357 47 2 2 BDP1 5 71467476 Missense_Mutation SNP G C3N-00180_T 26205050 71467476 110070783 36 10968 MAP1B 0 . GRCh38 5 72186666 72186666 + Missense_Mutation SNP G G T rs763276687 C3N-00180_T C3N-00180_N G G c.422G>T p.Gly141Val p.G141V ENST00000296755 4/7 200 115 85 217 217 0 strelka-varscan-mutect MAP1B,missense_variant,p.Gly141Val,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,missense_variant,p.Gly15Val,ENST00000504492,;MAP1B,missense_variant,p.Gly141Val,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000512974,;MAP1B,3_prime_UTR_variant,,ENST00000513526,; T ENST00000296755 Transcript missense_variant 720/12036 422/7407 141/2468 G/V gGg/gTg rs763276687 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 deleterious(0) 4/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 MODERATE 1 SNV 2 1 PASS rs763276687 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 72186666 72186666 G T 1 0 0 0 0 1 0 0 0 9151 1232 43 2 2 MAP1B 5 72186666 Missense_Mutation SNP G C3N-00180_T 719190 72186666 109351593 37 10969 KIAA0825 0 . GRCh38 5 94520580 94520580 + Missense_Mutation SNP T T A C3N-00180_T C3N-00180_N T T c.638A>T p.Gln213Leu p.Q213L ENST00000329378 5/5 94 67 27 109 109 0 strelka-varscan-mutect KIAA0825,missense_variant,p.Gln213Leu,ENST00000513200,NM_001145678.1;KIAA0825,missense_variant,p.Gln213Leu,ENST00000329378,NM_173665.2; A ENST00000329378 Transcript missense_variant 888/2262 638/975 213/324 Q/L cAa/cTa COSM3661999,COSM3662000,COSM3662001 1 -1 KIAA0825 HGNC HGNC:28532 protein_coding YES CCDS4070.1 ENSP00000331385 Q8IV33 UPI00000746AF NM_173665.2 deleterious(0) 5/5 hmmpanther:PTHR33960:SF1,hmmpanther:PTHR33960 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 94520580 94520580 T A 1 0 0 0 0 1 0 0 0 8091 1812 63 4 4 KIAA0825 5 94520580 Missense_Mutation SNP T C3N-00180_T 22333914 94520580 87017679 38 10970 DMXL1 0 . GRCh38 5 119170217 119170217 + Missense_Mutation SNP C C T novel C3N-00180_T C3N-00180_N C C c.5426C>T p.Thr1809Ile p.T1809I ENST00000539542 24/44 66 49 17 83 83 0 strelka-varscan-mutect DMXL1,missense_variant,p.Thr1809Ile,ENST00000539542,NM_001290321.2;DMXL1,missense_variant,p.Thr1809Ile,ENST00000311085,NM_001290322.2,NM_005509.5;DMXL1,non_coding_transcript_exon_variant,,ENST00000504497,;DMXL1,upstream_gene_variant,,ENST00000507552,; T ENST00000539542 Transcript missense_variant 5607/11236 5426/9147 1809/3048 T/I aCa/aTa 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 tolerated(0.22) 24/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12,Pfam_domain:PF12234 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 119170217 119170217 C T 1 0 0 0 0 1 0 0 0 4403 478 17 3 3 DMXL1 5 119170217 Missense_Mutation SNP C C3N-00180_T 24649637 119170217 62368042 39 10971 PCDHA10 0 . GRCh38 5 140857664 140857664 + Missense_Mutation SNP G G C rs201104305 C3N-00180_T C3N-00180_N G G c.1616G>C p.Gly539Ala p.G539A ENST00000307360 1/4 989 546 443 896 896 0 strelka-varscan-mutect PCDHA10,missense_variant,p.Gly539Ala,ENST00000562220,NM_031859.2;PCDHA10,missense_variant,p.Gly539Ala,ENST00000307360,NM_018901.3;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; C ENST00000307360 Transcript missense_variant 1616/5254 1616/2847 539/948 G/A gGg/gCg rs201104305,COSM1645878,COSM336806 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 tolerated_low_confidence(1) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs201104305 . 2 97 0 0 90 21 0 0 -20 0 0 1 0 0 C 3 2 40 140857664 140857664 G C 1 0 0 0 0 1 0 0 0 11607 1232 43 4 4 PCDHA10 5 140857664 Missense_Mutation SNP G C3N-00180_T 21687447 140857664 40680595 40 10972 JAKMIP2 0 . GRCh38 5 147620693 147620693 + Silent SNP T T C novel C3N-00180_T C3N-00180_N T T c.2115A>G p.= p.R705R ENST00000616793 18/22 119 75 44 217 217 0 strelka-varscan-mutect JAKMIP2,synonymous_variant,p.=,ENST00000616793,NM_001270941.1;JAKMIP2,synonymous_variant,p.=,ENST00000265272,NM_014790.4;JAKMIP2,synonymous_variant,p.=,ENST00000507386,NM_001270934.1;JAKMIP2,synonymous_variant,p.=,ENST00000333010,NM_001282282.1;JAKMIP2-AS1,intron_variant,,ENST00000626945,;JAKMIP2-AS1,intron_variant,,ENST00000627433,;JAKMIP2-AS1,intron_variant,,ENST00000630514,; C ENST00000616793 Transcript synonymous_variant 2656/9272 2115/2463 705/820 R agA/agG 1 -1 JAKMIP2 HGNC HGNC:29067 protein_coding YES CCDS75352.1 ENSP00000479248 Q96AA8 UPI0000E5AC9B NM_001270941.1 18/22 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 147620693 147620693 T C 1 0 0 0 0 0 0 0 1 7854 1780 62 5 5 JAKMIP2 5 147620693 Silent SNP T C3N-00180_T 6763029 147620693 33917566 41 10973 ZNF300 0 . GRCh38 5 150896651 150896651 + Silent SNP T T G rs763622160 C3N-00180_T C3N-00180_N T T c.636A>C p.= p.P212P ENST00000446148 7/7 175 118 57 165 165 0 strelka-varscan-mutect ZNF300,synonymous_variant,p.=,ENST00000446148,NM_001172831.1;ZNF300,synonymous_variant,p.=,ENST00000274599,NM_052860.2;ZNF300,synonymous_variant,p.=,ENST00000394226,;ZNF300,synonymous_variant,p.=,ENST00000418587,NM_001172832.1;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,; G ENST00000446148 Transcript synonymous_variant 1064/3323 636/1863 212/620 P ccA/ccC rs763622160 1 -1 ZNF300 HGNC HGNC:13091 protein_coding YES CCDS54940.1 ENSP00000397178 Q96RE9 UPI0001AE74AD NM_001172831.1 7/7 hmmpanther:PTHR24377:SF320,hmmpanther:PTHR24377 LOW 1 SNV 1 1 PASS rs763622160 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 40 150896651 150896651 T G 1 0 0 0 0 0 0 0 1 18406 1799 63 5 5 ZNF300 5 150896651 Silent SNP T C3N-00180_T 3275958 150896651 30641608 42 10974 EYS 0 . GRCh38 6 64813378 64813378 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.3443G>T p.Arg1148Ile p.R1148I ENST00000370621 22/44 51 26 25 183 183 0 strelka-mutect EYS,missense_variant,p.Arg1148Ile,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Arg1148Ile,ENST00000370621,NM_001292009.1; A ENST00000370621 Transcript missense_variant,splice_region_variant 3970/10485 3443/9498 1148/3165 R/I aGa/aTa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.46) 22/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1334016191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 64813378 64813378 C A 1 0 0 0 0 1 0 0 0 5200 695 24 2 2 EYS 6 64813378 Missense_Mutation SNP C C3N-00180_T 64813378 105992601 43 10975 MAP3K4 0 . GRCh38 6 161111858 161111858 + Silent SNP A A C novel C3N-00180_T C3N-00180_N A A c.4419A>C p.= p.S1473S ENST00000392142 24/27 139 86 53 159 159 0 strelka-varscan-mutect MAP3K4,synonymous_variant,p.=,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,synonymous_variant,p.=,ENST00000366920,NM_001301072.1;MAP3K4,synonymous_variant,p.=,ENST00000366919,NM_006724.3;MAP3K4,synonymous_variant,p.=,ENST00000348824,;MAP3K4,3_prime_UTR_variant,,ENST00000490904,;MAP3K4,3_prime_UTR_variant,,ENST00000544041,;MAP3K4,non_coding_transcript_exon_variant,,ENST00000536852,;MAP3K4,downstream_gene_variant,,ENST00000541901,;MAP3K4,downstream_gene_variant,,ENST00000544733,;MAP3K4,downstream_gene_variant,,ENST00000539610,; C ENST00000392142 Transcript synonymous_variant 4567/5490 4419/4827 1473/1608 S tcA/tcC 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 24/27 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF365,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 161111858 161111858 A C 1 0 0 0 0 0 0 0 1 9175 204 8 5 5 MAP3K4 6 161111858 Silent SNP A C3N-00180_T 96298480 161111858 9694121 44 10976 NUPL2 0 . GRCh38 7 23182124 23182124 + Silent SNP C C A rs775237329 C3N-00180_T C3N-00180_N C C c.39C>A p.= p.R13R ENST00000258742 1/7 287 184 103 259 259 0 strelka-varscan-mutect NUPL2,synonymous_variant,p.=,ENST00000258742,NM_007342.2;NUPL2,synonymous_variant,p.=,ENST00000413919,;NUPL2,synonymous_variant,p.=,ENST00000410002,;KLHL7,downstream_gene_variant,,ENST00000339077,NM_001031710.2;NUPL2,non_coding_transcript_exon_variant,,ENST00000487595,;NUPL2,synonymous_variant,p.=,ENST00000438012,;NUPL2,synonymous_variant,p.=,ENST00000437140,;NUPL2,non_coding_transcript_exon_variant,,ENST00000485250,;NUPL2,non_coding_transcript_exon_variant,,ENST00000497500,;NUPL2,upstream_gene_variant,,ENST00000486136,; A ENST00000258742 Transcript synonymous_variant 298/1795 39/1272 13/423 R cgC/cgA rs775237329 1 1 NUPL2 HGNC HGNC:17010 protein_coding YES CCDS5379.1 ENSP00000258742 O15504 UPI0000072A3C NM_007342.2 1/7 PROSITE_profiles:PS50103,hmmpanther:PTHR21495,hmmpanther:PTHR21495:SF45,SMART_domains:SM00356 LOW 1 SNV 1 1 PASS rs775237329 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 40 23182124 23182124 C A 1 0 0 0 0 0 0 0 1 10840 784 28 2 2 NUPL2 7 23182124 Silent SNP C C3N-00180_T 23182124 136163849 45 10977 POM121L12 0 . GRCh38 7 53036247 53036247 + Missense_Mutation SNP C C G rs762091356 C3N-00180_T C3N-00180_N C C c.576C>G p.Phe192Leu p.F192L ENST00000408890 1/1 366 240 126 323 323 0 strelka-varscan-mutect POM121L12,missense_variant,p.Phe192Leu,ENST00000408890,NM_182595.3; G ENST00000408890 Transcript missense_variant 606/1283 576/891 192/296 F/L ttC/ttG rs762091356,COSM3639636 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.46) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 0,1 MODERATE 1 SNV 0,1 1 PASS rs762091356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 53036247 53036247 C G 1 0 0 0 0 1 0 0 0 12352 883 31 4 4 POM121L12 7 53036247 Missense_Mutation SNP C C3N-00180_T 29854123 53036247 106309726 46 10978 PCLO 0 . GRCh38 7 82916308 82916308 + Missense_Mutation SNP G G C novel C3N-00180_T C3N-00180_N G G c.11678C>G p.Pro3893Arg p.P3893R ENST00000333891 7/25 246 152 94 199 199 0 strelka-varscan-mutect PCLO,missense_variant,p.Pro3893Arg,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Pro3893Arg,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Pro613Arg,ENST00000437081,; C ENST00000333891 Transcript missense_variant 12016/20329 11678/15429 3893/5142 P/R cCt/cGt 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0) 7/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 40 82916308 82916308 G C 1 0 0 0 0 1 0 0 0 11671 1000 35 4 4 PCLO 7 82916308 Missense_Mutation SNP G C3N-00180_T 29880061 82916308 76429665 47 10979 LRCH4 0 . GRCh38 7 100576002 100576002 + Nonsense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.1645G>T p.Glu549Ter p.E549* ENST00000310300 16/18 104 66 38 122 122 0 strelka-varscan-mutect LRCH4,stop_gained,p.Glu549Ter,ENST00000310300,NM_002319.4,NM_001289934.1;LRCH4,stop_gained,p.Glu9Ter,ENST00000619071,;LRCH4,stop_gained,p.Glu97Ter,ENST00000497245,;LRCH4,stop_gained,p.Glu74Ter,ENST00000485554,;SAP25,upstream_gene_variant,,ENST00000622764,;SAP25,upstream_gene_variant,,ENST00000614631,;SAP25,upstream_gene_variant,,ENST00000538735,NM_001168682.1;LRCH4,non_coding_transcript_exon_variant,,ENST00000467201,;RP11-44M6.7,non_coding_transcript_exon_variant,,ENST00000485071,;LRCH4,non_coding_transcript_exon_variant,,ENST00000476881,;LRCH4,non_coding_transcript_exon_variant,,ENST00000490359,;LRCH4,downstream_gene_variant,,ENST00000498539,;LRCH4,downstream_gene_variant,,ENST00000487697,;SAP25,upstream_gene_variant,,ENST00000611464,;RP11-44M6.3,downstream_gene_variant,,ENST00000223076,; A ENST00000310300 Transcript stop_gained 1698/2552 1645/2052 549/683 E/* Gag/Tag 1 -1 LRCH4 HGNC HGNC:6691 protein_coding YES CCDS34706.1 ENSP00000309689 O75427 UPI00000714CE NM_002319.4,NM_001289934.1 16/18 PROSITE_profiles:PS50021,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 100576002 100576002 C A 1 0 0 0 0 0 1 0 0 8829 835 29 2 2 LRCH4 7 100576002 Nonsense_Mutation SNP C C3N-00180_T 17659694 100576002 58769971 48 10980 DOCK4 0 . GRCh38 7 111877145 111877145 + Silent SNP G G C novel C3N-00180_T C3N-00180_N G G c.1629C>G p.= p.L543L ENST00000437633 17/52 72 54 18 123 123 0 strelka-varscan-mutect DOCK4,synonymous_variant,p.=,ENST00000428084,;DOCK4,synonymous_variant,p.=,ENST00000437633,NM_014705.3;DOCK4,synonymous_variant,p.=,ENST00000445943,;DOCK4,synonymous_variant,p.=,ENST00000494651,;DOCK4,upstream_gene_variant,,ENST00000423057,;DOCK4,non_coding_transcript_exon_variant,,ENST00000476846,;DOCK4,upstream_gene_variant,,ENST00000492532,; C ENST00000437633 Transcript synonymous_variant 1886/6212 1629/5901 543/1966 L ctC/ctG 1 -1 DOCK4 HGNC HGNC:19192 protein_coding YES CCDS47688.1 ENSP00000404179 Q8N1I0 UPI0000D5BB0D NM_014705.3 17/52 PROSITE_profiles:PS51650,hmmpanther:PTHR23317:SF75,hmmpanther:PTHR23317,Pfam_domain:PF14429 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 111877145 111877145 G C 1 0 0 0 0 0 0 0 1 4504 1277 45 4 4 DOCK4 7 111877145 Silent SNP G C3N-00180_T 11301143 111877145 47468828 49 10981 KCND2 0 . GRCh38 7 120275186 120275186 + Missense_Mutation SNP T T A novel C3N-00180_T C3N-00180_N T T c.554T>A p.Leu185Gln p.L185Q ENST00000331113 1/6 196 108 88 134 134 0 strelka-varscan-mutect KCND2,missense_variant,p.Leu185Gln,ENST00000331113,NM_012281.2; A ENST00000331113 Transcript missense_variant 1519/5331 554/1893 185/630 L/Q cTg/cAg 1 1 KCND2 HGNC HGNC:6238 protein_coding YES CCDS5776.1 ENSP00000333496 Q9NZV8 A4D0V9 UPI0000073D37 NM_012281.2 tolerated(0.17) 1/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF159,Gene3D:1.20.120.350,Superfamily_domains:SSF81324,Prints_domain:PR00169,Prints_domain:PR01497 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 120275186 120275186 T A 1 0 0 0 0 1 0 0 0 7935 1580 55 4 4 KCND2 7 120275186 Missense_Mutation SNP T C3N-00180_T 8398041 120275186 39070787 50 10982 ERICH1 0 . GRCh38 8 673427 673427 + Missense_Mutation SNP C C A rs750406908 C3N-00180_T C3N-00180_N C C c.925G>T p.Ala309Ser p.A309S ENST00000262109 4/6 350 228 122 480 480 0 strelka-varscan-mutect ERICH1,missense_variant,p.Ala78Ser,ENST00000522893,;ERICH1,missense_variant,p.Ala309Ser,ENST00000262109,NM_207332.2;ERICH1,missense_variant,p.Ala215Ser,ENST00000522706,;ERICH1,non_coding_transcript_exon_variant,,ENST00000518895,;ERICH1,downstream_gene_variant,,ENST00000518277,;ERICH1,downstream_gene_variant,,ENST00000524138,;ERICH1,downstream_gene_variant,,ENST00000518313,;ERICH1,upstream_gene_variant,,ENST00000523415,;ERICH1,upstream_gene_variant,,ENST00000523053,; A ENST00000262109 Transcript missense_variant 1003/1813 925/1332 309/443 A/S Gct/Tct rs750406908 1 -1 ERICH1 HGNC HGNC:27234 protein_coding YES CCDS5955.1 ENSP00000262109 Q86X53 UPI000000DB6B NM_207332.2 tolerated(0.42) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR22444:SF1,hmmpanther:PTHR22444 MODERATE 1 SNV 1 1 PASS rs750406908 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 673427 673427 C A 1 0 0 0 0 1 0 0 0 5081 739 26 2 2 ERICH1 8 673427 Missense_Mutation SNP C C3N-00180_T 673427 144465209 51 10983 ZFHX4 0 . GRCh38 8 76852805 76852805 + Nonsense_Mutation SNP A A T novel C3N-00180_T C3N-00180_N A A c.5884A>T p.Lys1962Ter p.K1962* ENST00000521891 10/11 96 66 30 124 124 0 strelka-varscan-mutect ZFHX4,stop_gained,p.Lys1962Ter,ENST00000521891,NM_024721.4;ZFHX4,stop_gained,p.Lys1936Ter,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; T ENST00000521891 Transcript stop_gained 6332/14019 5884/10851 1962/3616 K/* Aag/Tag 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 40 76852805 76852805 A T 1 0 0 0 0 0 1 0 0 18213 15 1 4 4 ZFHX4 8 76852805 Nonsense_Mutation SNP A C3N-00180_T 76179378 76852805 68285831 52 10984 PEX2 0 . GRCh38 8 76984086 76984086 + Silent SNP C C T novel C3N-00180_T C3N-00180_N C C c.93G>A p.= p.Q31Q ENST00000357039 4/4 100 62 38 67 67 0 strelka-varscan-mutect PEX2,synonymous_variant,p.=,ENST00000357039,NM_000318.2,NM_001172086.1;PEX2,synonymous_variant,p.=,ENST00000522527,NM_001079867.1;PEX2,synonymous_variant,p.=,ENST00000520103,NM_001172087.1;PEX2,synonymous_variant,p.=,ENST00000518986,;PEX2,downstream_gene_variant,,ENST00000519956,;PEX2,downstream_gene_variant,,ENST00000520203,; T ENST00000357039 Transcript synonymous_variant 489/4317 93/918 31/305 Q caG/caA 1 -1 PEX2 HGNC HGNC:9717 protein_coding YES CCDS6221.1 ENSP00000349543 P28328 UPI000013E3FB NM_000318.2,NM_001172086.1 4/4 PD124462,Pfam_domain:PF04757 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 76984086 76984086 C T 1 0 0 0 0 0 0 0 1 11835 796 28 3 3 PEX2 8 76984086 Silent SNP C C3N-00180_T 131281 76984086 68154550 53 10985 SPATC1 0 . GRCh38 8 144041264 144041264 + Missense_Mutation SNP G G T rs367672859 C3N-00180_T C3N-00180_N G G c.1339G>T p.Gly447Cys p.G447C ENST00000377470 4/5 174 117 57 224 224 0 strelka-varscan-mutect SPATC1,missense_variant,p.Gly447Cys,ENST00000377470,NM_198572.2;SPATC1,intron_variant,,ENST00000447830,NM_001134374.1; T ENST00000377470 Transcript missense_variant 1441/2007 1339/1776 447/591 G/C Ggt/Tgt rs367672859 1 1 SPATC1 HGNC HGNC:30510 protein_coding YES CCDS6413.2 ENSP00000366690 Q76KD6 UPI00001D8243 NM_198572.2 deleterious(0) 4/5 Pfam_domain:PF15059,hmmpanther:PTHR22192,hmmpanther:PTHR22192:SF16 MODERATE 1 SNV 1 1 PASS rs367672859 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 144041264 144041264 G T 1 0 0 0 0 1 0 0 0 15362 1232 43 2 2 SPATC1 8 144041264 Missense_Mutation SNP G C3N-00180_T 67057178 144041264 1097372 54 10986 PTCHD3 0 . GRCh38 10 27398781 27398781 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.1817T>C p.Val606Ala p.V606A ENST00000438700 4/4 219 127 92 281 281 0 strelka-varscan-mutect PTCHD3,missense_variant,p.Val606Ala,ENST00000438700,NM_001034842.3;PTCHD3,intron_variant,,ENST00000622555,; G ENST00000438700 Transcript missense_variant 1935/2529 1817/2304 606/767 V/A gTc/gCc 1 -1 PTCHD3 HGNC HGNC:24776 protein_coding YES CCDS31173.1 ENSP00000417658 Q3KNS1 UPI000004E892 NM_001034842.3 deleterious(0) 4/4 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF60,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 27398781 27398781 A G 1 0 0 0 0 1 0 0 0 12886 275 10 5 5 PTCHD3 10 27398781 Missense_Mutation SNP A C3N-00180_T 27398781 106398641 55 10987 FAM21C 0 . GRCh38 10 45759354 45759354 + Nonsense_Mutation SNP G G T rs782615615 C3N-00180_T C3N-00180_N G G c.1588G>T p.Glu530Ter p.E530* ENST00000374362 17/30 278 211 67 366 366 0 strelka-varscan-mutect FAM21C,stop_gained,p.Glu530Ter,ENST00000336378,;FAM21C,stop_gained,p.Glu530Ter,ENST00000374362,NM_015262.2;FAM21C,stop_gained,p.Glu530Ter,ENST00000623400,;FAM21C,stop_gained,p.Glu530Ter,ENST00000540872,NM_001169106.1;FAM21C,stop_gained,p.Glu474Ter,ENST00000359860,;FAM21C,stop_gained,p.Glu506Ter,ENST00000537517,NM_001169107.1; T ENST00000374362 Transcript stop_gained 1687/4623 1588/3963 530/1320 E/* Gaa/Taa rs782615615 1 1 FAM21C HGNC HGNC:23414 protein_coding YES CCDS44374.2 ENSP00000363482 Q9Y4E1 UPI0000551BE9 NM_015262.2 17/30 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 40 45759354 45759354 G T 1 0 0 0 0 0 1 0 0 5412 943 33 2 2 FAM21C 10 45759354 Nonsense_Mutation SNP G C3N-00180_T 18360573 45759354 88038068 56 10988 SORCS1 0 . GRCh38 10 106597444 106597444 + Nonsense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.3172G>T p.Glu1058Ter p.E1058* ENST00000263054 24/26 249 154 95 213 213 0 strelka-varscan-mutect SORCS1,stop_gained,p.Glu1058Ter,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,stop_gained,p.Glu816Ter,ENST00000612154,;SORCS1,stop_gained,p.Glu816Ter,ENST00000622431,;SORCS1,stop_gained,p.Glu816Ter,ENST00000344440,;SORCS1,stop_gained,p.Glu593Ter,ENST00000369698,;SORCS1,stop_gained,p.Glu73Ter,ENST00000452214,;SORCS1,downstream_gene_variant,,ENST00000478809,;SORCS1,non_coding_transcript_exon_variant,,ENST00000473866,; A ENST00000263054 Transcript stop_gained 3180/7272 3172/3507 1058/1168 E/* Gaa/Taa 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 24/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 106597444 106597444 C A 1 0 0 0 0 0 1 0 0 15252 922 32 2 2 SORCS1 10 106597444 Nonsense_Mutation SNP C C3N-00180_T 60838090 106597444 27199978 57 10989 PIDD1 0 . GRCh38 11 801298 801299 + Frame_Shift_Ins INS - - G novel C3N-00180_T C3N-00180_N - - c.1549dupC p.Leu517ProfsTer50 p.L517Pfs*50 ENST00000347755 9/16 33 29 4 97 97 0 sindel-pindel PIDD1,frameshift_variant,p.Leu517ProfsTer50,ENST00000347755,NM_145886.3;PIDD1,frameshift_variant,p.Leu517ProfsTer50,ENST00000411829,NM_145887.3;SLC25A22,upstream_gene_variant,,ENST00000628067,NM_001191061.1;SLC25A22,upstream_gene_variant,,ENST00000531214,NM_001191060.1;PANO1,downstream_gene_variant,,ENST00000620120,NM_001293167.1;SLC25A22,upstream_gene_variant,,ENST00000532484,;SLC25A22,upstream_gene_variant,,ENST00000531437,;SLC25A22,upstream_gene_variant,,ENST00000530360,;PIDD1,intron_variant,,ENST00000527812,;PIDD1,downstream_gene_variant,,ENST00000534649,;PIDD1,downstream_gene_variant,,ENST00000530911,;PIDD1,downstream_gene_variant,,ENST00000528122,;PIDD1,frameshift_variant,p.Leu234ProfsTer50,ENST00000531286,;PIDD1,3_prime_UTR_variant,,ENST00000524486,;PIDD1,3_prime_UTR_variant,,ENST00000525028,;PIDD1,non_coding_transcript_exon_variant,,ENST00000527357,;PIDD1,non_coding_transcript_exon_variant,,ENST00000534525,;SLC25A22,upstream_gene_variant,,ENST00000529351,;SLC25A22,upstream_gene_variant,,ENST00000531514,;SLC25A22,upstream_gene_variant,,ENST00000524891,; G ENST00000347755 Transcript frameshift_variant 1691-1692/2998 1549-1550/2733 517/910 L/PX ctg/cCtg 1 -1 PIDD1 HGNC HGNC:16491 protein_coding YES CCDS7716.1 ENSP00000337797 Q9HB75 UPI000045644A NM_145886.3 9/16 Pfam_domain:PF00791,PROSITE_profiles:PS51145 HIGH 1 insertion 1 1 PASS . . 0 204 6 0 0 0 0 0 -11.11012 0.9999999 1 1 1 0 G 7 5 40 801298 801298 - G 1 0 1 1 0 0 0 0 0 11973 188 7 0 0 PIDD1 11 801298 Frame_Shift_Ins INS - C3N-00180_T 801298 134285324 58 10990 MUC5B 0 . GRCh38 11 1245035 1245035 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.8155C>A p.Leu2719Met p.L2719M ENST00000529681 31/49 252 238 14 367 367 0 varscan-mutect MUC5B,missense_variant,p.Leu2719Met,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; A ENST00000529681 Transcript missense_variant 8213/17911 8155/17289 2719/5762 L/M Ctg/Atg 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.09) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs781567544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 1245035 1245035 C A 1 0 0 0 0 1 0 0 0 9979 796 28 2 2 MUC5B 11 1245035 Missense_Mutation SNP C C3N-00180_T 443737 1245035 133841587 59 10991 MUC5B 0 . GRCh38 11 1248806 1248806 + Missense_Mutation SNP C C A rs562058210 C3N-00180_T C3N-00180_N C C c.11926C>A p.Leu3976Met p.L3976M ENST00000529681 31/49 167 66 101 262 262 0 strelka-varscan-mutect MUC5B,missense_variant,p.Leu3976Met,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; A ENST00000529681 Transcript missense_variant 11984/17911 11926/17289 3976/5762 L/M Ctg/Atg rs562058210 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.19) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs562058210 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 1248806 1248806 C A 1 0 0 0 0 1 0 0 0 9979 796 28 2 2 MUC5B 11 1248806 Missense_Mutation SNP C C3N-00180_T 3771 1248806 133837816 60 10992 TRPM5 0 . GRCh38 11 2423009 2423009 + Nonsense_Mutation SNP C C A rs139404126 C3N-00180_T C3N-00180_N C C c.28G>T p.Gly10Ter p.G10* ENST00000155858 1/24 100 39 61 261 261 0 strelka-varscan-mutect TRPM5,stop_gained,p.Gly10Ter,ENST00000155858,NM_014555.3;TRPM5,stop_gained,p.Gly2Ter,ENST00000533881,;TRPM5,stop_gained,p.Gly10Ter,ENST00000533060,;TRPM5,stop_gained,p.Gly10Ter,ENST00000528453,; A ENST00000155858 Transcript stop_gained 37/3929 28/3498 10/1165 G/* Gga/Tga rs139404126 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 1/24 HIGH 1 SNV 1 1 PASS rs139404126 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 2423009 2423009 C A 1 0 0 0 0 0 1 0 0 17095 661 23 1 1 TRPM5 11 2423009 Nonsense_Mutation SNP C C3N-00180_T 1174203 2423009 132663613 61 10993 RRP8 0 . GRCh38 11 6601465 6601465 + Nonsense_Mutation SNP T T A rs763055185 C3N-00180_T C3N-00180_N T T c.601A>T p.Lys201Ter p.K201* ENST00000254605 3/7 622 146 476 355 355 0 strelka-varscan-mutect RRP8,stop_gained,p.Lys201Ter,ENST00000254605,NM_015324.3;RRP8,intron_variant,,ENST00000534343,;ILK,upstream_gene_variant,,ENST00000396751,NM_001014795.2;ILK,upstream_gene_variant,,ENST00000299421,NM_001014794.2,NM_004517.3;ILK,upstream_gene_variant,,ENST00000537806,;ILK,upstream_gene_variant,,ENST00000420936,;ILK,upstream_gene_variant,,ENST00000532063,NM_001278442.1;ILK,upstream_gene_variant,,ENST00000528995,NM_001278441.1;ILK,upstream_gene_variant,,ENST00000526318,;ILK,upstream_gene_variant,,ENST00000627400,;RP11-732A19.8,downstream_gene_variant,,ENST00000527191,;ILK,upstream_gene_variant,,ENST00000534565,;RRP8,stop_gained,p.Lys201Ter,ENST00000533907,;RRP8,3_prime_UTR_variant,,ENST00000530762,;TAF10,downstream_gene_variant,,ENST00000616342,;ILK,upstream_gene_variant,,ENST00000530016,;ILK,upstream_gene_variant,,ENST00000526711,;RRP8,upstream_gene_variant,,ENST00000526352,;ILK,upstream_gene_variant,,ENST00000527121,;ILK,upstream_gene_variant,,ENST00000526114,; A ENST00000254605 Transcript stop_gained 719/6560 601/1371 201/456 K/* Aag/Tag rs763055185 1 -1 RRP8 HGNC HGNC:29030 protein_coding YES CCDS31411.1 ENSP00000254605 O43159 UPI00001580F8 NM_015324.3 3/7 hmmpanther:PTHR12787,hmmpanther:PTHR12787:SF0,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs763055185 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 6601465 6601465 T A 1 0 0 0 0 0 1 0 0 13946 1821 63 4 4 RRP8 11 6601465 Nonsense_Mutation SNP T C3N-00180_T 4178456 6601465 128485157 62 10994 FBXO3 0 . GRCh38 11 33768870 33768870 + Silent SNP C C A novel C3N-00180_T C3N-00180_N C C c.339G>T p.= p.R113R ENST00000265651 3/11 124 76 48 128 128 0 strelka-varscan-mutect FBXO3,synonymous_variant,p.=,ENST00000530401,;FBXO3,synonymous_variant,p.=,ENST00000534136,;FBXO3,synonymous_variant,p.=,ENST00000265651,NM_012175.3;FBXO3,synonymous_variant,p.=,ENST00000448981,NM_033406.2;FBXO3,5_prime_UTR_variant,,ENST00000526785,;FBXO3,non_coding_transcript_exon_variant,,ENST00000533103,;FBXO3,non_coding_transcript_exon_variant,,ENST00000526952,;FBXO3,synonymous_variant,p.=,ENST00000532927,;FBXO3,synonymous_variant,p.=,ENST00000529137,;FBXO3,non_coding_transcript_exon_variant,,ENST00000530013,; A ENST00000265651 Transcript synonymous_variant 358/2397 339/1416 113/471 R cgG/cgT 1 -1 FBXO3 HGNC HGNC:13582 protein_coding YES CCDS7887.1 ENSP00000265651 Q9UK99 UPI000000DB30 NM_012175.3 3/11 hmmpanther:PTHR14289,hmmpanther:PTHR14289:SF16,Superfamily_domains:SSF160631 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 40 33768870 33768870 C A 1 0 0 0 0 0 0 0 1 5602 842 30 2 2 FBXO3 11 33768870 Silent SNP C C3N-00180_T 27167405 33768870 101317752 63 10995 FAT3 0 . GRCh38 11 92524787 92524787 + Missense_Mutation SNP C C T novel C3N-00180_T C3N-00180_N C C c.2996C>T p.Ser999Leu p.S999L ENST00000525166 2/27 531 96 435 425 425 0 strelka-varscan-mutect FAT3,missense_variant,p.Ser1149Leu,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ser999Leu,ENST00000525166,;FAT3,non_coding_transcript_exon_variant,,ENST00000528921,; T ENST00000525166 Transcript missense_variant 3018/18699 2996/13320 999/4439 S/L tCa/tTa 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.02) 2/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 92524787 92524787 C T 1 0 0 0 0 1 0 0 0 5551 838 29 3 3 FAT3 11 92524787 Missense_Mutation SNP C C3N-00180_T 58755917 92524787 42561835 64 10996 SORL1 0 . GRCh38 11 121545423 121545423 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.2045A>G p.Tyr682Cys p.Y682C ENST00000260197 14/48 203 36 167 117 117 0 strelka-varscan-mutect SORL1,missense_variant,p.Tyr682Cys,ENST00000260197,NM_003105.5;SORL1,non_coding_transcript_exon_variant,,ENST00000532451,; G ENST00000260197 Transcript missense_variant 2174/10904 2045/6645 682/2214 Y/C tAt/tGt 1 1 SORL1 HGNC HGNC:11185 protein_coding YES CCDS8436.1 ENSP00000260197 Q92673 UPI000013D0B1 NM_003105.5 deleterious(0) 14/48 Pfam_domain:PF15901,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF20,SMART_domains:SM00602 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 121545423 121545423 A G 1 0 0 0 0 1 0 0 0 15256 449 16 5 5 SORL1 11 121545423 Missense_Mutation SNP A C3N-00180_T 29020636 121545423 13541199 65 10997 OR8B3 0 . GRCh38 11 124397195 124397195 + Missense_Mutation SNP A A T novel C3N-00180_T C3N-00180_N A A c.157T>A p.Ser53Thr p.S53T ENST00000354597 1/1 328 148 180 203 203 0 strelka-varscan-mutect OR8B3,missense_variant,p.Ser53Thr,ENST00000354597,NM_001005467.1; T ENST00000354597 Transcript missense_variant 174/987 157/942 53/313 S/T Tct/Act 1 -1 OR8B3 HGNC HGNC:8472 protein_coding YES CCDS31709.1 ENSP00000346611 Q8NGG8 UPI000004B9C9 NM_001005467.1 deleterious_low_confidence(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF258,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 124397195 124397195 A T 1 0 0 0 0 1 0 0 0 11298 246 9 4 4 OR8B3 11 124397195 Missense_Mutation SNP A C3N-00180_T 2851772 124397195 10689427 66 10998 B3GAT1 0 . GRCh38 11 134384099 134384099 + Missense_Mutation SNP G G T C3N-00180_T C3N-00180_N G G c.202C>A p.Arg68Ser p.R68S ENST00000524765 3/6 212 30 182 80 80 0 strelka-mutect B3GAT1,missense_variant,p.Arg68Ser,ENST00000524765,;B3GAT1,missense_variant,p.Arg68Ser,ENST00000312527,NM_054025.2;B3GAT1,missense_variant,p.Arg68Ser,ENST00000392580,NM_018644.3;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531510,;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531778,; T ENST00000524765 Transcript missense_variant 4747/5737 202/1005 68/334 R/S Cgc/Agc COSM1352790,COSM3738963 1 -1 B3GAT1 HGNC HGNC:921 protein_coding YES CCDS8500.1 ENSP00000433847 Q9P2W7 UPI0000073281 deleterious(0.01) 3/6 hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF21 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 40 134384099 134384099 G T 1 0 0 0 0 1 0 0 0 1409 1087 38 1 1 B3GAT1 11 134384099 Missense_Mutation SNP G C3N-00180_T 9986904 134384099 702523 67 10999 SLCO1C1 0 . GRCh38 12 20699608 20699608 + Nonsense_Mutation SNP T T A novel C3N-00180_T C3N-00180_N T T c.32T>A p.Leu11Ter p.L11* ENST00000545604 3/16 124 78 46 192 192 0 strelka-varscan-mutect SLCO1C1,stop_gained,p.Leu11Ter,ENST00000266509,NM_017435.4;SLCO1C1,stop_gained,p.Leu11Ter,ENST00000545604,NM_001145946.1;SLCO1C1,stop_gained,p.Leu11Ter,ENST00000540354,NM_001145945.1;SLCO1C1,intron_variant,,ENST00000545102,NM_001145944.1;SLCO1C1,downstream_gene_variant,,ENST00000535609,;SLCO1C1,downstream_gene_variant,,ENST00000534996,;SLCO1C1,downstream_gene_variant,,ENST00000539443,;SLCO1C1,stop_gained,p.Leu11Ter,ENST00000539415,;SLCO1C1,non_coding_transcript_exon_variant,,ENST00000497911,; A ENST00000545604 Transcript stop_gained 262/2557 32/2193 11/730 L/* tTg/tAg 1 1 SLCO1C1 HGNC HGNC:13819 protein_coding YES CCDS53757.1 ENSP00000444149 Q9NYB5 UPI00004C3E1B NM_001145946.1 3/16 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF99 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 20699608 20699608 T A 1 0 0 0 0 0 1 0 0 15012 1821 63 4 4 SLCO1C1 12 20699608 Nonsense_Mutation SNP T C3N-00180_T 20699608 112575701 68 11000 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C A rs121913529 C3N-00180_T C3N-00180_N C C c.35G>T p.Gly12Val p.G12V ENST00000256078 2/6 325 214 111 368 367 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Val,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Val,ENST00000556131,;KRAS,missense_variant,p.Gly12Val,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Val,ENST00000557334,; A ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/V gGt/gTt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 25245350 25245350 C A 1 0 0 0 0 1 0 0 0 8318 507 18 2 2 KRAS 12 25245350 Missense_Mutation SNP C C3N-00180_T 4545742 25245350 108029959 69 11001 TMTC1 0 . GRCh38 12 29506897 29506897 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.2598G>T p.Leu866Phe p.L866F ENST00000539277 18/18 265 194 71 226 225 1 strelka-varscan-mutect TMTC1,missense_variant,p.Leu758Phe,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Leu928Phe,ENST00000551659,;TMTC1,missense_variant,p.Leu890Phe,ENST00000552618,;TMTC1,missense_variant,p.Leu866Phe,ENST00000539277,NM_001193451.1;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,non_coding_transcript_exon_variant,,ENST00000552925,; A ENST00000539277 Transcript missense_variant 2657/2758 2598/2649 866/882 L/F ttG/ttT 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 deleterious(0) 18/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00386 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 29506897 29506897 C A 1 0 0 0 0 1 0 0 0 16734 593 21 2 2 TMTC1 12 29506897 Missense_Mutation SNP C C3N-00180_T 4261547 29506897 103768412 70 11002 ESPL1 0 . GRCh38 12 53290435 53290435 + Missense_Mutation SNP G G C novel C3N-00180_T C3N-00180_N G G c.5330G>C p.Trp1777Ser p.W1777S ENST00000257934 24/31 238 169 69 233 233 0 strelka-varscan-mutect ESPL1,missense_variant,p.Trp1777Ser,ENST00000257934,NM_012291.4;ESPL1,missense_variant,p.Trp1777Ser,ENST00000552462,;PFDN5,upstream_gene_variant,,ENST00000551018,NM_002624.3;ESPL1,3_prime_UTR_variant,,ENST00000552671,;ESPL1,non_coding_transcript_exon_variant,,ENST00000549154,;ESPL1,downstream_gene_variant,,ENST00000553016,;ESPL1,downstream_gene_variant,,ENST00000535123,;ESPL1,downstream_gene_variant,,ENST00000552600,; C ENST00000257934 Transcript missense_variant 5421/6623 5330/6363 1777/2120 W/S tGg/tCg 1 1 ESPL1 HGNC HGNC:16856 protein_coding YES CCDS8852.1 ENSP00000257934 Q14674 UPI00003668C3 NM_012291.4 deleterious(0) 24/31 hmmpanther:PTHR12792,Pfam_domain:PF03568 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 40 53290435 53290435 G C 1 0 0 0 0 1 0 0 0 5115 1357 47 4 4 ESPL1 12 53290435 Missense_Mutation SNP G C3N-00180_T 23783538 53290435 79984874 71 11003 ZDHHC17 0 . GRCh38 12 76764282 76764282 + Missense_Mutation SNP G G A rs762609140 C3N-00180_T C3N-00180_N G G c.46G>A p.Asp16Asn p.D16N ENST00000426126 1/17 165 119 46 182 182 0 strelka-varscan-mutect ZDHHC17,missense_variant,p.Asp16Asn,ENST00000426126,NM_015336.2;ZDHHC17,5_prime_UTR_variant,,ENST00000550876,;ZDHHC17,upstream_gene_variant,,ENST00000549682,;ZDHHC17,missense_variant,p.Asp16Asn,ENST00000546778,;ZDHHC17,missense_variant,p.Asp14Asn,ENST00000552453,;ZDHHC17,missense_variant,p.Asp11Asn,ENST00000547620,;ZDHHC17,missense_variant,p.Asp9Asn,ENST00000551407,;ZDHHC17,missense_variant,p.Asp9Asn,ENST00000547604,;ZDHHC17,upstream_gene_variant,,ENST00000550163,; A ENST00000426126 Transcript missense_variant 695/5259 46/1899 16/632 D/N Gat/Aat rs762609140 1 1 ZDHHC17 HGNC HGNC:18412 protein_coding YES CCDS44946.1 ENSP00000403397 Q8IUH5 UPI0000051F55 NM_015336.2 tolerated_low_confidence(0.19) 1/17 hmmpanther:PTHR24161:SF18,hmmpanther:PTHR24161 MODERATE 1 SNV 1 1 PASS rs762609140 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 76764282 76764282 G A 1 0 0 0 0 1 0 0 0 18183 1174 41 3 3 ZDHHC17 12 76764282 Missense_Mutation SNP G C3N-00180_T 23473847 76764282 56511027 72 11004 TMEM119 0 . GRCh38 12 108591621 108591621 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.763G>T p.Gly255Trp p.G255W ENST00000392806 2/2 148 100 48 168 168 0 strelka-varscan-mutect TMEM119,missense_variant,p.Gly255Trp,ENST00000392806,NM_181724.2;TMEM119,downstream_gene_variant,,ENST00000549031,;TMEM119,downstream_gene_variant,,ENST00000549447,;TMEM119,downstream_gene_variant,,ENST00000547567,; A ENST00000392806 Transcript missense_variant 932/2707 763/852 255/283 G/W Ggg/Tgg 1 -1 TMEM119 HGNC HGNC:27884 protein_coding YES CCDS9119.1 ENSP00000376553 Q4V9L6 UPI0000049333 NM_181724.2 deleterious_low_confidence(0.03) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR28645,hmmpanther:PTHR28645:SF1,Pfam_domain:PF15724 MODERATE 1 SNV 1 1 PASS rs748388228 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 108591621 108591621 C A 1 0 0 0 0 1 0 0 0 16476 681 24 2 2 TMEM119 12 108591621 Missense_Mutation SNP C C3N-00180_T 31827339 108591621 24683688 73 11005 DNAH10 0 . GRCh38 12 123787844 123787844 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.1279A>G p.Arg427Gly p.R427G ENST00000638045 10/78 204 127 77 318 318 0 strelka-varscan-mutect DNAH10,missense_variant,p.Arg488Gly,ENST00000409039,;DNAH10,missense_variant,p.Arg427Gly,ENST00000638045,NM_207437.3;DNAH10,missense_variant,p.Arg245Gly,ENST00000614082,;DNAH10,non_coding_transcript_exon_variant,,ENST00000467219,;DNAH10,non_coding_transcript_exon_variant,,ENST00000447853,; G ENST00000638045 Transcript missense_variant 1304/13678 1279/13416 427/4471 R/G Agg/Ggg 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0.03) 10/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF08385 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 123787844 123787844 A G 1 0 0 0 0 1 0 0 0 4411 179 7 5 5 DNAH10 12 123787844 Missense_Mutation SNP A C3N-00180_T 15196223 123787844 9487465 74 11006 EP400 0 . GRCh38 12 132045741 132045741 + Silent SNP A A G novel C3N-00180_T C3N-00180_N A A c.7041A>G p.= p.L2347L ENST00000389562 38/52 115 78 37 130 130 0 strelka-varscan-mutect EP400,synonymous_variant,p.=,ENST00000389562,;EP400,synonymous_variant,p.=,ENST00000389561,NM_015409.4;EP400,non_coding_transcript_exon_variant,,ENST00000611841,; G ENST00000389562 Transcript synonymous_variant 7076/12836 7041/9372 2347/3123 L ttA/ttG 1 1 EP400 HGNC HGNC:11958 protein_coding YES CCDS31929.2 ENSP00000374213 Q96L91 UPI00004566BC 38/52 PROSITE_profiles:PS50090 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 40 132045741 132045741 A G 1 0 0 0 0 0 0 0 1 4995 388 14 5 5 EP400 12 132045741 Silent SNP A C3N-00180_T 8257897 132045741 1229568 75 11007 PCDH8 0 . GRCh38 13 52846409 52846409 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.2028C>A p.Asp676Glu p.D676E ENST00000377942 1/3 93 24 69 134 134 0 strelka-varscan-mutect PCDH8,missense_variant,p.Asp676Glu,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Asp676Glu,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; T ENST00000377942 Transcript missense_variant 2232/5088 2028/3213 676/1070 D/E gaC/gaA 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 tolerated(0.93) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 52846409 52846409 G T 1 0 0 0 0 1 0 0 0 11604 1252 44 2 2 PCDH8 13 52846409 Missense_Mutation SNP G C3N-00180_T 52846409 61517919 76 11008 NEDD8 0 . GRCh38 14 24218169 24218169 + Missense_Mutation SNP G G C rs74744808 C3N-00180_T C3N-00180_N G G c.113C>G p.Pro38Arg p.P38R ENST00000250495 3/4 159 120 39 185 185 0 strelka-varscan-mutect NEDD8,missense_variant,p.Pro38Arg,ENST00000250495,NM_006156.2;NEDD8,missense_variant,p.Pro38Arg,ENST00000524927,;NEDD8-MDP1,missense_variant,p.Pro38Arg,ENST00000534348,NM_001199823.1;RP11-468E2.1,upstream_gene_variant,,ENST00000530611,;CHMP4A,upstream_gene_variant,,ENST00000347519,NM_014169.3;CHMP4A,upstream_gene_variant,,ENST00000530996,;CHMP4A,upstream_gene_variant,,ENST00000609024,;MDP1,upstream_gene_variant,,ENST00000288087,NM_001199822.1,NM_138476.3;MDP1,upstream_gene_variant,,ENST00000396833,NM_001199821.1;NEDD8,non_coding_transcript_exon_variant,,ENST00000527046,;NEDD8-MDP1,non_coding_transcript_exon_variant,,ENST00000604306,;NEDD8,non_coding_transcript_exon_variant,,ENST00000531430,;NEDD8,intron_variant,,ENST00000526430,;MDP1,upstream_gene_variant,,ENST00000532557,;MDP1,upstream_gene_variant,,ENST00000525696,;NEDD8-MDP1,missense_variant,p.Pro38Arg,ENST00000605847,;NEDD8,missense_variant,p.Pro38Arg,ENST00000396828,;NEDD8-MDP1,missense_variant,p.Pro38Arg,ENST00000530579,;NEDD8,non_coding_transcript_exon_variant,,ENST00000560427,;AL136419.6,upstream_gene_variant,,ENST00000565988,;AL136419.6,upstream_gene_variant,,ENST00000528804,;CHMP4A,upstream_gene_variant,,ENST00000533523,;MDP1,upstream_gene_variant,,ENST00000530222,;MDP1,upstream_gene_variant,,ENST00000466422,;MDP1,upstream_gene_variant,,ENST00000532742,;MDP1,upstream_gene_variant,,ENST00000533536,;CHMP4A,upstream_gene_variant,,ENST00000527154,;MDP1,upstream_gene_variant,,ENST00000528849,;MDP1,upstream_gene_variant,,ENST00000531553,;CHMP4A,upstream_gene_variant,,ENST00000534106,; C ENST00000250495 Transcript missense_variant 300/708 113/246 38/81 P/R cCa/cGa rs74744808 1 -1 NEDD8 HGNC HGNC:7732 protein_coding YES CCDS9621.1 ENSP00000250495 Q15843 UPI00000009A5 NM_006156.2 deleterious(0) 3/4 PROSITE_profiles:PS50053,hmmpanther:PTHR10666,PROSITE_patterns:PS00299,Pfam_domain:PF00240,Gene3D:3.10.20.90,SMART_domains:SM00213,Superfamily_domains:SSF54236,Prints_domain:PR00348 MODERATE 1 SNV 1 1 PASS rs74744808 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 40 24218169 24218169 G C 1 0 0 0 0 1 0 0 0 10340 1348 47 4 4 NEDD8 14 24218169 Missense_Mutation SNP G C3N-00180_T 24218169 82825549 77 11009 RTN1 0 . GRCh38 14 59746173 59746173 + Missense_Mutation SNP C C A C3N-00180_T C3N-00180_N C C c.550G>T p.Asp184Tyr p.D184Y ENST00000267484 2/9 111 85 26 60 60 0 strelka-varscan-mutect RTN1,missense_variant,p.Asp184Tyr,ENST00000267484,NM_021136.2;RTN1,missense_variant,p.Asp110Tyr,ENST00000611068,; A ENST00000267484 Transcript missense_variant 886/3435 550/2331 184/776 D/Y Gac/Tac COSM4552152,COSM4802485 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 deleterious(0) 2/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 59746173 59746173 C A 1 0 0 0 0 1 0 0 0 13985 913 32 2 2 RTN1 14 59746173 Missense_Mutation SNP C C3N-00180_T 35528004 59746173 47297545 78 11010 VASH1 0 . GRCh38 14 76778050 76778050 + Missense_Mutation SNP G G A rs762287715 C3N-00180_T C3N-00180_N G G c.1004G>A p.Arg335Lys p.R335K ENST00000167106 6/7 83 41 42 87 87 0 strelka-varscan-mutect VASH1,missense_variant,p.Arg335Lys,ENST00000167106,NM_014909.4;VASH1,5_prime_UTR_variant,,ENST00000554743,;VASH1,downstream_gene_variant,,ENST00000554237,;RP11-488C13.5,downstream_gene_variant,,ENST00000556072,;RP11-488C13.5,downstream_gene_variant,,ENST00000554058,;RP11-488C13.7,upstream_gene_variant,,ENST00000553758,;RP11-488C13.6,intron_variant,,ENST00000556368,;RP11-488C13.6,downstream_gene_variant,,ENST00000553507,;VASH1,downstream_gene_variant,,ENST00000556038,;VASH1,downstream_gene_variant,,ENST00000553518,; A ENST00000167106 Transcript missense_variant 1637/5728 1004/1098 335/365 R/K aGg/aAg rs762287715 1 1 VASH1 HGNC HGNC:19964 protein_coding YES CCDS9851.1 ENSP00000167106 Q7L8A9 UPI0000073F7C NM_014909.4 tolerated(0.08) 6/7 hmmpanther:PTHR15750:SF3,hmmpanther:PTHR15750 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 76778050 76778050 G A 1 0 0 0 0 1 0 0 0 17670 1000 35 3 3 VASH1 14 76778050 Missense_Mutation SNP G C3N-00180_T 17031877 76778050 30265668 79 11011 NDN 0 . GRCh38 15 23686372 23686372 + Silent SNP G G T novel C3N-00180_T C3N-00180_N G G c.846C>A p.= p.V282V ENST00000331837 1/1 60 50 10 51 51 0 strelka-mutect NDN,synonymous_variant,p.=,ENST00000331837,NM_002487.2; T ENST00000331837 Transcript synonymous_variant 959/1931 846/966 282/321 V gtC/gtA 1 -1 NDN HGNC HGNC:7675 protein_coding YES CCDS10014.1 ENSP00000332643 Q99608 X5D982 UPI000012FEF1 NM_002487.2 1/1 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF10 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -19.99983 1 1 1 1 0 T 2 4 40 23686372 23686372 G T 1 0 0 0 0 0 0 0 1 10268 929 33 2 2 NDN 15 23686372 Silent SNP G C3N-00180_T 23686372 78304817 80 11012 ARNT2 0 . GRCh38 15 80593600 80593600 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.2056G>T p.Asp686Tyr p.D686Y ENST00000303329 19/19 137 80 57 115 115 0 strelka-varscan-mutect ARNT2,missense_variant,p.Asp675Tyr,ENST00000533983,;ARNT2,missense_variant,p.Asp686Tyr,ENST00000303329,NM_014862.3;ARNT2,missense_variant,p.Asp686Tyr,ENST00000622346,;ARNT2,missense_variant,p.Asp675Tyr,ENST00000527771,; T ENST00000303329 Transcript missense_variant,splice_region_variant 2221/6558 2056/2154 686/717 D/Y Gac/Tac 1 1 ARNT2 HGNC HGNC:16876 protein_coding YES CCDS32307.1 ENSP00000307479 Q9HBZ2 X5DQN9 UPI00001FEA05 NM_014862.3 deleterious_low_confidence(0) 19/19 hmmpanther:PTHR23042,hmmpanther:PTHR23042:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 80593600 80593600 G T 1 0 0 0 0 1 0 0 0 1108 1188 41 2 2 ARNT2 15 80593600 Missense_Mutation SNP G C3N-00180_T 56907228 80593600 21397589 81 11013 C16orf59 0 . GRCh38 16 2460663 2460663 + Missense_Mutation SNP C C G novel C3N-00180_T C3N-00180_N C C c.166C>G p.Pro56Ala p.P56A ENST00000361837 3/10 143 100 43 227 227 0 strelka-varscan-mutect C16orf59,missense_variant,p.Pro56Ala,ENST00000569496,;C16orf59,missense_variant,p.Pro56Ala,ENST00000563531,;C16orf59,missense_variant,p.Pro56Ala,ENST00000361837,NM_025108.2;C16orf59,missense_variant,p.Pro23Ala,ENST00000567489,;C16orf59,5_prime_UTR_variant,,ENST00000483320,;C16orf59,5_prime_UTR_variant,,ENST00000568753,;CCNF,downstream_gene_variant,,ENST00000397066,NM_001761.2;RP11-715J22.4,upstream_gene_variant,,ENST00000566085,;RP11-715J22.4,upstream_gene_variant,,ENST00000565827,;MIR6768,upstream_gene_variant,,ENST00000610734,;RP11-715J22.2,downstream_gene_variant,,ENST00000563775,;C16orf59,non_coding_transcript_exon_variant,,ENST00000569994,;C16orf59,non_coding_transcript_exon_variant,,ENST00000569664,;C16orf59,non_coding_transcript_exon_variant,,ENST00000562253,;C16orf59,non_coding_transcript_exon_variant,,ENST00000569665,;C16orf59,non_coding_transcript_exon_variant,,ENST00000565537,;CCNF,downstream_gene_variant,,ENST00000293968,NM_001323538.1;C16orf59,upstream_gene_variant,,ENST00000565716,;C16orf59,upstream_gene_variant,,ENST00000566580,; G ENST00000361837 Transcript missense_variant 231/1662 166/1302 56/433 P/A Cca/Gca 1 1 C16orf59 HGNC HGNC:25849 protein_coding YES CCDS10468.2 ENSP00000355022 Q7L2K0 UPI000059D2F3 NM_025108.2 deleterious(0.02) 3/10 hmmpanther:PTHR14870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 2460663 2460663 C G 1 0 0 0 0 1 0 0 0 1860 739 26 4 4 C16orf59 16 2460663 Missense_Mutation SNP C C3N-00180_T 2460663 87877682 82 11014 HS3ST4 0 . GRCh38 16 26135888 26135888 + Silent SNP G G T rs540523376 C3N-00180_T C3N-00180_N G G c.1011G>T p.= p.A337A ENST00000331351 2/2 402 280 122 448 447 1 strelka-varscan-mutect HS3ST4,synonymous_variant,p.=,ENST00000331351,NM_006040.2;HS3ST4,non_coding_transcript_exon_variant,,ENST00000475436,; T ENST00000331351 Transcript synonymous_variant 1403/3203 1011/1371 337/456 A gcG/gcT rs540523376 1 1 HS3ST4 HGNC HGNC:5200 protein_coding YES CCDS53995.1 ENSP00000330606 Q9Y661 UPI000040938A NM_006040.2 2/2 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF11,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs540523376 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 26135888 26135888 G T 1 0 0 0 0 0 0 0 1 7261 1074 38 1 1 HS3ST4 16 26135888 Silent SNP G C3N-00180_T 23675225 26135888 64202457 83 11015 CYLD 0 . GRCh38 16 50751758 50751758 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.659G>T p.Gly220Val p.G220V ENST00000427738 3/18 427 285 142 427 426 1 strelka-varscan-mutect CYLD,missense_variant,p.Gly220Val,ENST00000427738,;CYLD,missense_variant,p.Gly220Val,ENST00000311559,NM_015247.2;CYLD,missense_variant,p.Gly220Val,ENST00000398568,NM_001042412.1;CYLD,missense_variant,p.Gly220Val,ENST00000569418,NM_001042355.1;CYLD,missense_variant,p.Gly220Val,ENST00000568704,;CYLD,missense_variant,p.Gly220Val,ENST00000564326,;CYLD,missense_variant,p.Gly220Val,ENST00000566206,;CYLD,missense_variant,p.Gly220Val,ENST00000566679,;CYLD,downstream_gene_variant,,ENST00000569681,;CYLD,downstream_gene_variant,,ENST00000564634,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,; T ENST00000427738 Transcript missense_variant 864/8503 659/2871 220/956 G/V gGg/gTg 1 1 CYLD HGNC HGNC:2584 protein_coding YES CCDS45482.1 ENSP00000392025 Q9NQC7 UPI0000073A15 tolerated(0.29) 3/18 hmmpanther:PTHR11830:SF3,hmmpanther:PTHR11830,Superfamily_domains:SSF74924 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 50751758 50751758 G T 1 0 0 0 0 1 0 0 0 3946 1232 43 2 2 CYLD 16 50751758 Missense_Mutation SNP G C3N-00180_T 24615870 50751758 39586587 84 11016 CHD9 0 . GRCh38 16 53273743 53273743 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.4835A>G p.Gln1612Arg p.Q1612R ENST00000447540 23/39 96 66 30 147 147 0 strelka-varscan-mutect CHD9,missense_variant,p.Gln1612Arg,ENST00000566029,NM_025134.4;CHD9,missense_variant,p.Gln1612Arg,ENST00000447540,NM_001308319.1;CHD9,missense_variant,p.Gln1612Arg,ENST00000564845,;CHD9,missense_variant,p.Gln1612Arg,ENST00000398510,;CHD9,5_prime_UTR_variant,,ENST00000615216,;CHD9,5_prime_UTR_variant,,ENST00000622617,;CHD9,non_coding_transcript_exon_variant,,ENST00000219084,; G ENST00000447540 Transcript missense_variant 5044/11509 4835/8694 1612/2897 Q/R cAa/cGa 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 deleterious(0.04) 23/39 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 53273743 53273743 A G 1 0 0 0 0 1 0 0 0 3091 130 5 5 5 CHD9 16 53273743 Missense_Mutation SNP A C3N-00180_T 2521985 53273743 37064602 85 11017 MINK1 0 . GRCh38 17 4893552 4893552 + Missense_Mutation SNP G G C novel C3N-00180_T C3N-00180_N G G c.2519G>C p.Gly840Ala p.G840A ENST00000355280 21/32 30 13 17 66 66 0 strelka-mutect MINK1,missense_variant,p.Gly840Ala,ENST00000355280,NM_153827.4,NM_015716.4;MINK1,missense_variant,p.Gly811Ala,ENST00000347992,NM_170663.4;MINK1,missense_variant,p.Gly820Ala,ENST00000453408,NM_001024937.3;CHRNE,downstream_gene_variant,,ENST00000293780,NM_000080.3;MINK1,upstream_gene_variant,,ENST00000576037,;MINK1,3_prime_UTR_variant,,ENST00000574453,NM_001321236.1;MINK1,3_prime_UTR_variant,,ENST00000571207,;MINK1,non_coding_transcript_exon_variant,,ENST00000572330,;MINK1,non_coding_transcript_exon_variant,,ENST00000572629,;MINK1,non_coding_transcript_exon_variant,,ENST00000571526,;MINK1,upstream_gene_variant,,ENST00000574871,;CHRNE,downstream_gene_variant,,ENST00000572438,;MINK1,upstream_gene_variant,,ENST00000575511,;MINK1,upstream_gene_variant,,ENST00000572304,; C ENST00000355280 Transcript missense_variant 2715/4961 2519/3999 840/1332 G/A gGc/gCc 1 1 MINK1 HGNC HGNC:17565 protein_coding YES CCDS45588.1 ENSP00000347427 Q8N4C8 UPI00001678BB NM_153827.4,NM_015716.4 tolerated(0.1) 21/32 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 40 4893552 4893552 G C 1 0 0 0 0 1 0 0 0 9551 1203 42 4 4 MINK1 17 4893552 Missense_Mutation SNP G C3N-00180_T 4893552 78363889 86 11018 TP53 0 . GRCh38 17 7673790 7673790 + Missense_Mutation SNP C C A rs763098116 C3N-00180_T C3N-00180_N C C c.830G>T p.Cys277Phe p.C277F ENST00000269305 8/11 479 184 295 798 798 0 strelka-varscan-mutect TP53,missense_variant,p.Cys277Phe,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Cys277Phe,ENST00000420246,;TP53,missense_variant,p.Cys238Phe,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Cys238Phe,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Cys277Phe,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Cys238Phe,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Cys277Phe,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Cys238Phe,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Cys277Phe,ENST00000445888,;TP53,missense_variant,p.Cys238Phe,ENST00000619485,;TP53,missense_variant,p.Cys145Phe,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Cys118Phe,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Cys145Phe,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Cys118Phe,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Cys145Phe,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Cys118Phe,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Cys277Phe,ENST00000359597,;TP53,missense_variant,p.Cys266Phe,ENST00000615910,;TP53,missense_variant,p.Cys145Phe,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Cys238Phe,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 1020/2579 830/1182 277/393 C/F tGt/tTt rs763098116,CM078491,TP53_g.13810G>T,TP53_g.13810G>A,TP53_g.13810G>C,COSM10749,COSM1649337,COSM4271761,COSM43737,COSM44992,COSM562338 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic 0,0,0,0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1 1 PASS rs763098116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 7673790 7673790 C A 1 0 0 0 0 1 0 0 0 16859 478 17 2 2 TP53 17 7673790 Missense_Mutation SNP C C3N-00180_T 2780238 7673790 75583651 87 11019 ATAD5 0 . GRCh38 17 30835658 30835658 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.1577A>G p.Glu526Gly p.E526G ENST00000321990 2/23 76 38 38 102 102 0 strelka-varscan-mutect ATAD5,missense_variant,p.Glu526Gly,ENST00000321990,NM_024857.4;CTD-2349P21.11,intron_variant,,ENST00000580873,;ATAD5,missense_variant,p.Glu526Gly,ENST00000578295,;ATAD5,non_coding_transcript_exon_variant,,ENST00000585133,;CTD-2349P21.1,downstream_gene_variant,,ENST00000490847,; G ENST00000321990 Transcript missense_variant 1955/6869 1577/5535 526/1844 E/G gAg/gGg 1 1 ATAD5 HGNC HGNC:25752 protein_coding YES CCDS11260.1 ENSP00000313171 Q96QE3 UPI0000071E9E NM_024857.4 tolerated(0.11) 2/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 30835658 30835658 A G 1 0 0 0 0 1 0 0 0 1224 304 11 5 5 ATAD5 17 30835658 Missense_Mutation SNP A C3N-00180_T 23161868 30835658 52421783 88 11020 STARD3 0 . GRCh38 17 39660254 39660254 + Missense_Mutation SNP G G A novel C3N-00180_T C3N-00180_N G G c.839G>A p.Gly280Asp p.G280D ENST00000336308 10/15 247 182 65 350 350 0 strelka-varscan-mutect STARD3,missense_variant,p.Gly280Asp,ENST00000336308,NM_006804.3;STARD3,missense_variant,p.Gly254Asp,ENST00000580611,;STARD3,missense_variant,p.Gly262Asp,ENST00000394250,NM_001165938.1;STARD3,missense_variant,p.Gly280Asp,ENST00000544210,NM_001165937.1;TCAP,upstream_gene_variant,,ENST00000309889,NM_003673.3;STARD3,downstream_gene_variant,,ENST00000443521,;STARD3,downstream_gene_variant,,ENST00000581894,;STARD3,downstream_gene_variant,,ENST00000583419,;STARD3,downstream_gene_variant,,ENST00000577248,;STARD3,downstream_gene_variant,,ENST00000579479,;STARD3,downstream_gene_variant,,ENST00000580331,;STARD3,downstream_gene_variant,,ENST00000583718,;STARD3,non_coding_transcript_exon_variant,,ENST00000583639,;STARD3,downstream_gene_variant,,ENST00000578232,;STARD3,downstream_gene_variant,,ENST00000582874,;STARD3,downstream_gene_variant,,ENST00000460894,;STARD3,downstream_gene_variant,,ENST00000585214,;STARD3,downstream_gene_variant,,ENST00000578254,;STARD3,missense_variant,p.Ala258Thr,ENST00000578577,;STARD3,3_prime_UTR_variant,,ENST00000583884,;STARD3,non_coding_transcript_exon_variant,,ENST00000481171,;STARD3,non_coding_transcript_exon_variant,,ENST00000584850,;STARD3,non_coding_transcript_exon_variant,,ENST00000488876,;STARD3,non_coding_transcript_exon_variant,,ENST00000471896,;STARD3,non_coding_transcript_exon_variant,,ENST00000585269,;STARD3,non_coding_transcript_exon_variant,,ENST00000578384,;STARD3,downstream_gene_variant,,ENST00000583582,;STARD3,downstream_gene_variant,,ENST00000484773,;STARD3,upstream_gene_variant,,ENST00000578686,;STARD3,downstream_gene_variant,,ENST00000580551,; A ENST00000336308 Transcript missense_variant 1057/2132 839/1338 280/445 G/D gGc/gAc 1 1 STARD3 HGNC HGNC:17579 protein_coding YES CCDS11341.1 ENSP00000337446 Q14849 UPI000013CE10 NM_006804.3 deleterious(0) 10/15 PROSITE_profiles:PS50848,hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF51,Gene3D:3.30.530.20,Pfam_domain:PF01852,SMART_domains:SM00234,Superfamily_domains:SSF55961 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 39660254 39660254 G A 1 0 0 0 0 1 0 0 0 15632 1203 42 3 3 STARD3 17 39660254 Missense_Mutation SNP G C3N-00180_T 8824596 39660254 43597187 89 11021 NACA2 0 . GRCh38 17 61590695 61590695 + Silent SNP T T C novel C3N-00180_T C3N-00180_N T T c.486A>G p.= p.V162V ENST00000521764 1/1 536 316 220 452 452 0 strelka-varscan-mutect NACA2,synonymous_variant,p.=,ENST00000521764,NM_199290.3; C ENST00000521764 Transcript synonymous_variant 508/777 486/648 162/215 V gtA/gtG 1 -1 NACA2 HGNC HGNC:23290 protein_coding YES CCDS11630.1 ENSP00000427802 Q9H009 UPI0000070B04 NM_199290.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR21713,hmmpanther:PTHR21713:SF2,PIRSF_domain:PIRSF015901 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 61590695 61590695 T C 1 0 0 0 0 0 0 0 1 10140 1625 57 5 5 NACA2 17 61590695 Silent SNP T C3N-00180_T 21930441 61590695 21666746 90 11022 SDK2 0 . GRCh38 17 73401979 73401979 + Missense_Mutation SNP T T A novel C3N-00180_T C3N-00180_N T T c.2647A>T p.Ser883Cys p.S883C ENST00000392650 19/45 107 57 50 153 153 0 strelka-varscan-mutect SDK2,missense_variant,p.Ser883Cys,ENST00000392650,NM_001144952.1;SDK2,missense_variant,p.Ser59Cys,ENST00000424778,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; A ENST00000392650 Transcript missense_variant 2648/10723 2647/6519 883/2172 S/C Agc/Tgc 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 deleterious(0) 19/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 73401979 73401979 T A 1 0 0 0 0 1 0 0 0 14244 1580 55 4 4 SDK2 17 73401979 Missense_Mutation SNP T C3N-00180_T 11811284 73401979 9855462 91 11023 L3MBTL4 0 . GRCh38 18 6241435 6241435 + Nonsense_Mutation SNP T T A novel C3N-00180_T C3N-00180_N T T c.475A>T p.Lys159Ter p.K159* ENST00000400105 8/20 47 10 37 154 154 0 strelka-varscan-mutect L3MBTL4,stop_gained,p.Lys159Ter,ENST00000400104,;L3MBTL4,stop_gained,p.Lys159Ter,ENST00000317931,;L3MBTL4,stop_gained,p.Lys159Ter,ENST00000400105,NM_173464.3;L3MBTL4,stop_gained,p.Lys159Ter,ENST00000583054,;L3MBTL4,downstream_gene_variant,,ENST00000581231,;L3MBTL4,downstream_gene_variant,,ENST00000583809,; A ENST00000400105 Transcript stop_gained 635/3546 475/1872 159/623 K/* Aaa/Taa 1 -1 L3MBTL4 HGNC HGNC:26677 protein_coding YES CCDS11839.2 ENSP00000382976 Q8NA19 UPI000013DDC0 NM_173464.3 8/20 hmmpanther:PTHR12247:SF78,hmmpanther:PTHR12247,Gene3D:2.30.30.160,Superfamily_domains:SSF63748 HIGH 1 SNV 2 1 PASS rs1281211736 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 40 6241435 6241435 T A 1 0 0 0 0 0 1 0 0 8496 1763 61 4 4 L3MBTL4 18 6241435 Nonsense_Mutation SNP T C3N-00180_T 6241435 74131850 92 11024 MYO5B 0 . GRCh38 18 49902721 49902721 + Missense_Mutation SNP C C A rs201920924 C3N-00180_T C3N-00180_N C C c.2684G>T p.Arg895Leu p.R895L ENST00000285039 21/40 426 125 301 589 589 0 strelka-varscan-mutect MYO5B,missense_variant,p.Arg895Leu,ENST00000285039,NM_001080467.2;MYO5B,missense_variant,p.Arg38Leu,ENST00000324581,; A ENST00000285039 Transcript missense_variant 2984/9505 2684/5547 895/1848 R/L cGg/cTg rs201920924,COSM3526176 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 deleterious(0) 21/40 Pfam_domain:PF00612,PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356,SMART_domains:SM00015,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201920924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 49902721 49902721 C A 1 0 0 0 0 1 0 0 0 10080 652 23 1 1 MYO5B 18 49902721 Missense_Mutation SNP C C3N-00180_T 43661286 49902721 30470564 93 11025 CDH20 0 . GRCh38 18 61554398 61554398 + Silent SNP C C A rs139351388 C3N-00180_T C3N-00180_N C C c.2109C>A p.= p.P703P ENST00000262717 12/12 148 40 108 184 184 0 strelka-varscan-mutect CDH20,synonymous_variant,p.=,ENST00000262717,;CDH20,synonymous_variant,p.=,ENST00000536675,NM_031891.2;CDH20,synonymous_variant,p.=,ENST00000538374,;CDH20,downstream_gene_variant,,ENST00000587582,; A ENST00000262717 Transcript synonymous_variant 2507/3882 2109/2406 703/801 P ccC/ccA rs139351388,COSM392893,COSM5388322 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D 12/12 hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Pfam_domain:PF01049 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs139351388 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 40 61554398 61554398 C A 1 0 0 0 0 0 0 0 1 2809 639 23 1 1 CDH20 18 61554398 Silent SNP C C3N-00180_T 11651677 61554398 18818887 94 11026 STK11 0 . GRCh38 19 1220693 1220693 + Missense_Mutation SNP A A T novel C3N-00180_T C3N-00180_N A A c.710A>T p.Asp237Val p.D237V ENST00000326873 5/10 57 28 29 147 147 0 strelka-varscan-mutect STK11,missense_variant,p.Asp237Val,ENST00000586243,;STK11,missense_variant,p.Asp237Val,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript missense_variant 1160/2611 710/1302 237/433 D/V gAc/gTc 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 5/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 1220693 1220693 A T 1 0 0 0 0 1 0 0 0 15664 275 10 4 4 STK11 19 1220693 Missense_Mutation SNP A C3N-00180_T 1220693 57396923 95 11027 ZNF99 0 . GRCh38 19 22757663 22757663 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.2246C>A p.Thr749Asn p.T749N ENST00000596209 4/4 178 70 108 274 274 0 strelka-varscan-mutect ZNF99,missense_variant,p.Thr749Asn,ENST00000596209,NM_001080409.2;ZNF99,missense_variant,p.Thr658Asn,ENST00000397104,; T ENST00000596209 Transcript missense_variant 2337/7817 2246/2595 749/864 T/N aCt/aAt 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 tolerated(0.22) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs757387389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 22757663 22757663 G T 1 0 0 0 0 1 0 0 0 18797 1029 36 2 2 ZNF99 19 22757663 Missense_Mutation SNP G C3N-00180_T 21536970 22757663 35859953 96 11028 ZNF541 0 . GRCh38 19 47549430 47549430 + Silent SNP G G C novel C3N-00180_T C3N-00180_N G G c.363C>G p.= p.T121T ENST00000391901 2/15 408 239 169 411 411 0 strelka-varscan-mutect ZNF541,synonymous_variant,p.=,ENST00000314121,;ZNF541,synonymous_variant,p.=,ENST00000391901,NM_001277075.1;ZNF541,upstream_gene_variant,,ENST00000595558,;ZNF541,upstream_gene_variant,,ENST00000263351,; C ENST00000391901 Transcript synonymous_variant 363/4580 363/4041 121/1346 T acC/acG 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 2/15 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 40 47549430 47549430 G C 1 0 0 0 0 0 0 0 1 18549 987 35 4 4 ZNF541 19 47549430 Silent SNP G C3N-00180_T 24791767 47549430 11068186 97 11029 RPS9 0 . GRCh38 19 54201579 54201579 + Missense_Mutation SNP G G A novel C3N-00180_T C3N-00180_N G G c.190G>A p.Asp64Asn p.D64N ENST00000302907 3/5 168 113 55 220 220 0 strelka-varscan-mutect RPS9,missense_variant,p.Asp64Asn,ENST00000402367,;RPS9,missense_variant,p.Asp64Asn,ENST00000441429,;RPS9,missense_variant,p.Asp64Asn,ENST00000302907,NM_001013.3;RPS9,missense_variant,p.Asp64Asn,ENST00000391752,NM_001321702.1;RPS9,missense_variant,p.Asp64Asn,ENST00000391753,;RPS9,missense_variant,p.Asp64Asn,ENST00000391751,NM_001321706.1;RPS9,missense_variant,p.Asp64Asn,ENST00000626547,;AC012314.20,upstream_gene_variant,,ENST00000426213,;RPS9,missense_variant,p.Asp64Asn,ENST00000448962,;RPS9,missense_variant,p.Asp64Asn,ENST00000445961,;RPS9,missense_variant,p.Asp64Asn,ENST00000436445,;RPS9,non_coding_transcript_exon_variant,,ENST00000495002,;RPS9,non_coding_transcript_exon_variant,,ENST00000484121,;RPS9,non_coding_transcript_exon_variant,,ENST00000460761,; A ENST00000302907 Transcript missense_variant 362/829 190/585 64/194 D/N Gat/Aat 1 1 RPS9 HGNC HGNC:10442 protein_coding YES CCDS12884.1 ENSP00000302896 P46781 UPI00000040B2 NM_001013.3 tolerated(0.06) 3/5 hmmpanther:PTHR11831,hmmpanther:PTHR11831:SF10,TIGRFAM_domain:TIGR01018,SMART_domains:SM01390,Superfamily_domains:SSF55174 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 54201579 54201579 G A 1 0 0 0 0 1 0 0 0 13917 1290 45 3 3 RPS9 19 54201579 Missense_Mutation SNP G C3N-00180_T 6652149 54201579 4416037 98 11030 ZNF530 0 . GRCh38 19 57605991 57605991 + Missense_Mutation SNP A A G novel C3N-00180_T C3N-00180_N A A c.466A>G p.Met156Val p.M156V ENST00000332854 3/3 329 226 103 334 334 0 strelka-varscan-mutect ZNF530,missense_variant,p.Met156Val,ENST00000332854,NM_020880.3;ZNF530,intron_variant,,ENST00000597864,;ZNF530,downstream_gene_variant,,ENST00000597700,;ZNF530,missense_variant,p.Met156Val,ENST00000600619,;ZNF530,non_coding_transcript_exon_variant,,ENST00000598297,; G ENST00000332854 Transcript missense_variant 686/2962 466/1800 156/599 M/V Atg/Gtg 1 1 ZNF530 HGNC HGNC:29297 protein_coding YES CCDS12955.1 ENSP00000332861 Q6P9A1 UPI0000199017 NM_020880.3 tolerated(1) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 40 57605991 57605991 A G 1 0 0 0 0 1 0 0 0 18544 449 16 5 5 ZNF530 19 57605991 Missense_Mutation SNP A C3N-00180_T 3404412 57605991 1011625 99 11031 ZNF135 0 . GRCh38 19 58061601 58061601 + Missense_Mutation SNP G G T rs751598990 C3N-00180_T C3N-00180_N G G c.91G>T p.Val31Leu p.V31L ENST00000401053 2/4 117 87 30 166 165 1 strelka-mutect ZNF135,missense_variant,p.Val31Leu,ENST00000401053,NM_001164529.1,NM_007134.1;ZNF135,missense_variant,p.Val19Leu,ENST00000313434,NM_001289401.1;ZNF135,missense_variant,p.Val19Leu,ENST00000511556,NM_003436.3;ZNF135,missense_variant,p.Val31Leu,ENST00000359978,NM_001164530.1;ZNF135,5_prime_UTR_variant,,ENST00000506786,NM_001289402.1;ZNF135,missense_variant,p.Val19Leu,ENST00000515535,; T ENST00000401053 Transcript missense_variant 94/3346 91/2049 31/682 V/L Gtg/Ttg rs751598990 1 1 ZNF135 HGNC HGNC:12919 protein_coding YES CCDS54329.1 ENSP00000441410 P52742 UPI0001B3CB2A NM_001164529.1,NM_007134.1 deleterious(0) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF250,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS rs751598990 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 58061601 58061601 G T 1 0 0 0 0 1 0 0 0 18306 1145 40 1 1 ZNF135 19 58061601 Missense_Mutation SNP G C3N-00180_T 455610 58061601 556015 100 11032 LAMA5 0 . GRCh38 20 62323527 62323528 + Frame_Shift_Del DEL GT GT - novel C3N-00180_T C3N-00180_N GT GT c.5992_5993delAC p.Thr1998HisfsTer54 p.T1998Hfs*54 ENST00000252999 45/80 98 59 39 127 127 0 sindel-varindel-pindel LAMA5,frameshift_variant,p.Thr1998HisfsTer54,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000497363,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000481120,; - ENST00000252999 Transcript frameshift_variant 6059-6060/11426 5992-5993/11088 1998/3695 T/X ACc/c 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 45/80 PROSITE_profiles:PS50027,PROSITE_patterns:PS01248,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 HIGH 1 deletion 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 40 62323527 62323527 GT - 1 0 1 0 1 0 0 0 0 8513 1261 44 0 0 LAMA5 20 62323527 Frame_Shift_Del DEL GT C3N-00180_T 62323527 2120640 101 11033 NPBWR2 0 . GRCh38 20 64106399 64106399 + Missense_Mutation SNP C C T novel C3N-00180_T C3N-00180_N C C c.433G>A p.Val145Met p.V145M ENST00000369768 1/1 227 124 103 203 203 0 strelka-varscan-mutect NPBWR2,missense_variant,p.Val145Met,ENST00000369768,NM_005286.2; T ENST00000369768 Transcript missense_variant 773/1352 433/1002 145/333 V/M Gtg/Atg 1 -1 NPBWR2 HGNC HGNC:4530 protein_coding YES CCDS13557.1 ENSP00000358783 P48146 UPI000013CBB3 NM_005286.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF18,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 64106399 64106399 C T 1 0 0 0 0 1 0 0 0 10617 507 18 3 3 NPBWR2 20 64106399 Missense_Mutation SNP C C3N-00180_T 1782872 64106399 337768 102 11034 TPTE 0 . GRCh38 21 10567731 10567731 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.508C>A p.Leu170Met p.L170M ENST00000618007 11/24 71 56 15 448 447 1 strelka-varscan-mutect TPTE,missense_variant,p.Leu152Met,ENST00000622113,NM_199259.3;TPTE,missense_variant,p.Leu170Met,ENST00000618007,NM_199261.3;TPTE,missense_variant,p.Leu132Met,ENST00000427445,NM_199260.3;TPTE,missense_variant,p.Leu32Met,ENST00000612746,NM_001290224.1;TPTE,downstream_gene_variant,,ENST00000612957,;AL078471.5,non_coding_transcript_exon_variant,,ENST00000612267,; A ENST00000618007 Transcript missense_variant 838/2150 508/1656 170/551 L/M Ctg/Atg 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 deleterious(0.03) 11/24 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12305:SF56,hmmpanther:PTHR12305,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 10567731 10567731 C A 1 0 0 0 0 1 0 0 0 16911 912 32 2 2 TPTE 21 10567731 Missense_Mutation SNP C C3N-00180_T 10567731 36142252 103 11035 LTN1 0 . GRCh38 21 28982360 28982360 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.723G>T p.Gln241His p.Q241H ENST00000614971 5/30 151 109 42 187 187 0 strelka-varscan-mutect LTN1,missense_variant,p.Gln241His,ENST00000614971,NM_015565.2;LTN1,missense_variant,p.Gln241His,ENST00000389194,;LTN1,missense_variant,p.Gln195His,ENST00000361371,;LTN1,missense_variant,p.Gln241His,ENST00000389195,;LTN1,missense_variant,p.Gln124His,ENST00000483326,; A ENST00000614971 Transcript missense_variant 736/7756 723/5439 241/1812 Q/H caG/caT 1 -1 LTN1 HGNC HGNC:13082 protein_coding YES CCDS33527.2 ENSP00000478783 O94822 UPI000049DF6C NM_015565.2 tolerated(0.17) 5/30 hmmpanther:PTHR12389 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 28982360 28982360 C A 1 0 0 0 0 1 0 0 0 8987 680 24 2 2 LTN1 21 28982360 Missense_Mutation SNP C C3N-00180_T 18414629 28982360 17727623 104 11036 NDUFV3 0 . GRCh38 21 42893363 42893363 + Silent SNP A A G novel C3N-00180_T C3N-00180_N A A c.30A>G p.= p.G10G ENST00000354250 1/4 308 191 117 418 418 0 strelka-varscan-mutect NDUFV3,synonymous_variant,p.=,ENST00000340344,NM_001001503.1;NDUFV3,synonymous_variant,p.=,ENST00000354250,NM_021075.3;NDUFV3,non_coding_transcript_exon_variant,,ENST00000460740,;NDUFV3,intron_variant,,ENST00000460259,; G ENST00000354250 Transcript synonymous_variant 99/1575 30/1422 10/473 G ggA/ggG 1 1 NDUFV3 HGNC HGNC:7719 protein_coding YES CCDS33572.1 ENSP00000346196 P56181 UPI000037848B NM_021075.3 1/4 hmmpanther:PTHR17117:SF1,hmmpanther:PTHR17117 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 40 42893363 42893363 A G 1 0 0 0 0 0 0 0 1 10325 262 10 5 5 NDUFV3 21 42893363 Silent SNP A C3N-00180_T 13911003 42893363 3816620 105 11037 GAB4 0 . GRCh38 22 16963822 16963822 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.1484C>A p.Ala495Glu p.A495E ENST00000400588 9/10 251 159 92 301 301 0 strelka-varscan-mutect GAB4,missense_variant,p.Ala495Glu,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,downstream_gene_variant,,ENST00000523144,;GAB4,downstream_gene_variant,,ENST00000520505,;GAB4,3_prime_UTR_variant,,ENST00000465611,; T ENST00000400588 Transcript missense_variant 1592/2630 1484/1725 495/574 A/E gCa/gAa 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 tolerated(0.14) 9/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 40 16963822 16963822 G T 1 0 0 0 0 1 0 0 0 6022 1319 46 2 2 GAB4 22 16963822 Missense_Mutation SNP G C3N-00180_T 16963822 33854646 106 11038 LRRC74B 0 . GRCh38 22 21048958 21048958 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.423C>A p.Asp141Glu p.D141E ENST00000442047 4/9 170 101 69 164 163 1 strelka-varscan-mutect LRRC74B,missense_variant,p.Asp141Glu,ENST00000442047,NM_001291006.1;AC002472.11,downstream_gene_variant,,ENST00000450652,;P2RX6P,upstream_gene_variant,,ENST00000439119,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000497328,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000473769,;P2RX6P,upstream_gene_variant,,ENST00000450626,; A ENST00000442047 Transcript missense_variant 423/1179 423/1179 141/392 D/E gaC/gaA 1 1 LRRC74B HGNC HGNC:34301 protein_coding YES CCDS77654.1 ENSP00000394078 Q6ZQY2 UPI000436DF24 NM_001291006.1 deleterious(0) 4/9 Gene3D:3.80.10.10,Pfam_domain:PF13516,hmmpanther:PTHR24114,hmmpanther:PTHR24114:SF21,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE SNV 5 1 PASS rs1399856924 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 21048958 21048958 C A 1 0 0 0 0 1 0 0 0 8922 506 18 2 2 LRRC74B 22 21048958 Missense_Mutation SNP C C3N-00180_T 4085136 21048958 29769510 107 11039 SLC5A4 0 . GRCh38 22 32218688 32218688 + Silent SNP A A T novel C3N-00180_T C3N-00180_N A A c.1806T>A p.= p.A602A ENST00000266086 15/15 217 114 103 380 380 0 strelka-varscan-mutect SLC5A4,synonymous_variant,p.=,ENST00000266086,NM_014227.2;RP1-90G24.10,intron_variant,,ENST00000434942,; T ENST00000266086 Transcript synonymous_variant 1818/2030 1806/1980 602/659 A gcT/gcA 1 -1 SLC5A4 HGNC HGNC:11039 protein_coding YES CCDS13903.1 ENSP00000266086 Q9NY91 UPI00001359F4 NM_014227.2 15/15 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 40 32218688 32218688 A T 1 0 0 0 0 0 0 0 1 14950 59 3 4 4 SLC5A4 22 32218688 Silent SNP A C3N-00180_T 11169730 32218688 18599780 108 11040 BRWD3 0 . GRCh38 X 80722788 80722788 + Splice_Site SNP C C A novel C3N-00180_T C3N-00180_N C C c.1651-1G>T p.X551_splice ENST00000373275 122 26 96 169 169 0 strelka-varscan-mutect BRWD3,splice_acceptor_variant,,ENST00000373275,NM_153252.4;BRWD3,upstream_gene_variant,,ENST00000473691,;BRWD3,upstream_gene_variant,,ENST00000497335,; A ENST00000373275 Transcript splice_acceptor_variant -/11381 1651/5409 551/1802 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 16/40 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 40 80722788 80722788 C A 1 0 0 0 0 0 0 1 0 1700 927 32 2 2 BRWD3 23 80722788 Splice_Site SNP C C3N-00180_T 80722788 75318107 109 11041 ARMCX4 0 . GRCh38 X 101490344 101490344 + Missense_Mutation SNP G G T novel C3N-00180_T C3N-00180_N G G c.1755G>T p.Arg585Ser p.R585S ENST00000423738 2/2 94 28 66 77 77 0 strelka-varscan-mutect ARMCX4,missense_variant,p.Arg585Ser,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; T ENST00000423738 Transcript missense_variant 1957/7424 1755/6873 585/2290 R/S agG/agT 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 tolerated(0.23) 2/2 MODERATE 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 40 101490344 101490344 G T 1 0 0 0 0 1 0 0 0 1102 1223 43 2 2 ARMCX4 23 101490344 Missense_Mutation SNP G C3N-00180_T 20767556 101490344 54550551 110 11042 GPRASP1 0 . GRCh38 X 102657394 102657394 + Missense_Mutation SNP T T A novel C3N-00180_T C3N-00180_N T T c.3481T>A p.Leu1161Ile p.L1161I ENST00000537097 6/6 132 23 109 130 130 0 strelka-varscan-mutect GPRASP1,missense_variant,p.Leu1161Ile,ENST00000537097,NM_001184727.1;GPRASP1,missense_variant,p.Leu1161Ile,ENST00000361600,NM_014710.4;GPRASP1,missense_variant,p.Leu1161Ile,ENST00000415986,NM_001099410.1;GPRASP1,missense_variant,p.Leu1161Ile,ENST00000444152,NM_001099411.1;RP4-769N13.7,intron_variant,,ENST00000602441,;ARMCX5-GPRASP2,intron_variant,,ENST00000486740,;ARMCX5-GPRASP2,intron_variant,,ENST00000602366,;ARMCX5-GPRASP2,intron_variant,,ENST00000602463,;GPRASP1,downstream_gene_variant,,ENST00000466098,; A ENST00000537097 Transcript missense_variant 4294/5980 3481/4188 1161/1395 L/I Tta/Ata 1 1 GPRASP1 HGNC HGNC:24834 protein_coding YES CCDS35352.1 ENSP00000445683 Q5JY77 UPI0000073B80 NM_001184727.1 tolerated(0.06) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR15712:SF22,hmmpanther:PTHR15712,Pfam_domain:PF04826 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 102657394 102657394 T A 1 0 0 0 0 1 0 0 0 6601 1838 64 4 4 GPRASP1 23 102657394 Missense_Mutation SNP T C3N-00180_T 1167050 102657394 53383501 111 11043 TENM1 0 . GRCh38 X 124380937 124380937 + Missense_Mutation SNP C C A novel C3N-00180_T C3N-00180_N C C c.7798G>T p.Gly2600Trp p.G2600W ENST00000422452 32/32 99 21 78 105 105 0 strelka-varscan-mutect TENM1,missense_variant,p.Gly2600Trp,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Gly2593Trp,ENST00000371130,NM_014253.3;STAG2,intron_variant,,ENST00000469481,; A ENST00000422452 Transcript missense_variant 7862/12891 7798/8199 2600/2732 G/W Ggg/Tgg 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 32/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 40 124380937 124380937 C A 1 0 0 0 0 1 0 0 0 16171 623 22 2 2 TENM1 23 124380937 Missense_Mutation SNP C C3N-00180_T 21723543 124380937 31659958 112 11044 AJAP1 0 . GRCh38 1 4712426 4712426 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.556A>T p.Thr186Ser p.T186S ENST00000378191 2/6 93 78 15 68 68 0 strelka-varscan-mutect AJAP1,missense_variant,p.Thr186Ser,ENST00000378191,NM_018836.3;AJAP1,missense_variant,p.Thr186Ser,ENST00000378190,NM_001042478.1;AJAP1,downstream_gene_variant,,ENST00000466761,; T ENST00000378191 Transcript missense_variant 937/11666 556/1236 186/411 T/S Acg/Tcg 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 deleterious(0) 2/6 hmmpanther:PTHR32422,Pfam_domain:PF15298 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999292 1 1 1 0 T 3 4 41 4712426 4712426 A T 1 0 0 0 0 1 0 0 0 516 159 6 4 4 AJAP1 1 4712426 Missense_Mutation SNP A C3N-00199_T 4712426 244243996 1 11045 AJAP1 0 . GRCh38 1 4772394 4772394 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.1032G>T p.= p.L344L ENST00000378191 4/6 580 387 193 482 482 0 strelka-varscan-mutect AJAP1,synonymous_variant,p.=,ENST00000378191,NM_018836.3;AJAP1,synonymous_variant,p.=,ENST00000378190,NM_001042478.1; T ENST00000378191 Transcript synonymous_variant 1413/11666 1032/1236 344/411 L ctG/ctT 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 4/6 hmmpanther:PTHR32422,Pfam_domain:PF15298 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 4772394 4772394 G T 1 0 0 0 0 0 0 0 1 516 1335 47 2 2 AJAP1 1 4772394 Silent SNP G C3N-00199_T 59968 4772394 244184028 2 11046 HES2 0 . GRCh38 1 6419026 6419026 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.369G>T p.= p.A123A ENST00000377834 4/4 124 101 23 63 63 0 strelka-varscan-mutect HES2,synonymous_variant,p.=,ENST00000377834,NM_019089.4;HES2,3_prime_UTR_variant,,ENST00000487437,;HES2,3_prime_UTR_variant,,ENST00000489730,;HES2,intron_variant,,ENST00000377837,;HES2,intron_variant,,ENST00000377836,;HES2,upstream_gene_variant,,ENST00000471190,; A ENST00000377834 Transcript synonymous_variant 468/4262 369/522 123/173 A gcG/gcT 1 -1 HES2 HGNC HGNC:16005 protein_coding YES CCDS30574.1 ENSP00000367065 Q9Y543 UPI000012C617 NM_019089.4 4/4 Superfamily_domains:0053813,Pfam_domain:PF07527,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF15,SMART_domains:SM00511 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 6419026 6419026 C A 1 0 0 0 0 0 0 0 1 6950 639 23 1 1 HES2 1 6419026 Silent SNP C C3N-00199_T 1646632 6419026 242537396 3 11047 KIF1B 0 . GRCh38 1 10365614 10365614 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.4580G>C p.Ser1527Thr p.S1527T ENST00000263934 41/47 478 443 35 596 596 0 strelka-varscan-mutect KIF1B,missense_variant,p.Ser1573Thr,ENST00000377086,;KIF1B,missense_variant,p.Ser1573Thr,ENST00000377081,;KIF1B,missense_variant,p.Ser1559Thr,ENST00000620295,;KIF1B,missense_variant,p.Ser1547Thr,ENST00000622724,;KIF1B,missense_variant,p.Ser1527Thr,ENST00000263934,NM_015074.3;KIF1B,missense_variant,p.Ser255Thr,ENST00000635499,;KIF1B,downstream_gene_variant,,ENST00000465635,;KIF1B,non_coding_transcript_exon_variant,,ENST00000470616,;KIF1B,downstream_gene_variant,,ENST00000483340,; C ENST00000263934 Transcript missense_variant 4733/6816 4580/5313 1527/1770 S/T aGc/aCc 1 1 KIF1B HGNC HGNC:16636 protein_coding YES CCDS111.1 ENSP00000263934 O60333 UPI000013EE7E NM_015074.3 tolerated(0.68) 41/47 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 10365614 10365614 G C 1 0 0 0 0 1 0 0 0 8148 971 34 4 4 KIF1B 1 10365614 Missense_Mutation SNP G C3N-00199_T 3946588 10365614 238590808 4 11048 KIF17 0 . GRCh38 1 20682880 20682880 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.2236C>A p.Gln746Lys p.Q746K ENST00000247986 11/15 185 142 43 168 168 0 strelka-varscan-mutect KIF17,missense_variant,p.Gln746Lys,ENST00000247986,NM_020816.3;KIF17,missense_variant,p.Gln746Lys,ENST00000400463,NM_001122819.2;KIF17,missense_variant,p.Gln646Lys,ENST00000375044,NM_001287212.1;KIF17,non_coding_transcript_exon_variant,,ENST00000490034,;KIF17,non_coding_transcript_exon_variant,,ENST00000477167,;KIF17,non_coding_transcript_exon_variant,,ENST00000462858,;KIF17,non_coding_transcript_exon_variant,,ENST00000498225,; T ENST00000247986 Transcript missense_variant 2547/3969 2236/3090 746/1029 Q/K Cag/Aag 1 -1 KIF17 HGNC HGNC:19167 protein_coding YES CCDS213.1 ENSP00000247986 Q9P2E2 UPI0000185F1A NM_020816.3 tolerated(0.12) 11/15 hmmpanther:PTHR24115:SF355,hmmpanther:PTHR24115 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 20682880 20682880 G T 1 0 0 0 0 1 0 0 0 8143 1333 46 2 2 KIF17 1 20682880 Missense_Mutation SNP G C3N-00199_T 10317266 20682880 228273542 5 11049 ECE1 0 . GRCh38 1 21279290 21279290 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.181G>T p.Ala61Ser p.A61S ENST00000374893 3/19 570 419 151 585 585 0 strelka-varscan-mutect ECE1,missense_variant,p.Ala45Ser,ENST00000415912,NM_001113348.1;ECE1,missense_variant,p.Ala49Ser,ENST00000357071,NM_001113347.1;ECE1,missense_variant,p.Ala61Ser,ENST00000374893,NM_001397.2;ECE1,missense_variant,p.Ala58Ser,ENST00000264205,NM_001113349.1;ECE1,missense_variant,p.Ala61Ser,ENST00000436918,;ECE1,missense_variant,p.Ala44Ser,ENST00000527991,;ECE1,missense_variant,p.Ala47Ser,ENST00000481130,;ECE1,5_prime_UTR_variant,,ENST00000473505,;ECE1,non_coding_transcript_exon_variant,,ENST00000463334,;ECE1,non_coding_transcript_exon_variant,,ENST00000526194,; A ENST00000374893 Transcript missense_variant 256/2484 181/2313 61/770 A/S Gca/Tca 1 -1 ECE1 HGNC HGNC:3146 protein_coding YES CCDS215.1 ENSP00000364028 P42892 A0A024RAF7 UPI0000129B5E NM_001397.2 tolerated(1) 3/19 hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF130 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 21279290 21279290 C A 1 0 0 0 0 1 0 0 0 4715 710 25 2 2 ECE1 1 21279290 Missense_Mutation SNP C C3N-00199_T 596410 21279290 227677132 6 11050 SEPN1 0 . GRCh38 1 25811729 25811735 + Frame_Shift_Del DEL GATCCTG GATCCTG - novel C3N-00199_T C3N-00199_N GATCCTG GATCCTG c.1134_1140delCCTGGAT p.Ile378MetfsTer? p.I378Mfs*? ENST00000361547 9/13 310 227 83 327 327 0 sindel-varindel-pindel SEPN1,frameshift_variant,p.Ile378MetfsTer?,ENST00000361547,NM_020451.2;SEPN1,frameshift_variant,p.Ile344MetfsTer6,ENST00000354177,;SEPN1,frameshift_variant,p.Ile344MetfsTer6,ENST00000374315,NM_206926.1;SEPN1,upstream_gene_variant,,ENST00000630065,;SEPN1,upstream_gene_variant,,ENST00000494537,;RP1-317E23.6,non_coding_transcript_exon_variant,,ENST00000559265,;RP1-317E23.6,upstream_gene_variant,,ENST00000527604,; - ENST00000361547 Transcript frameshift_variant 1186-1192/4334 1131-1137/1773 377-379/590 VIL/X gtGATCCTG/gt 1 1 SEPN1 HGNC HGNC:15999 protein_coding YES CCDS41282.1 ENSP00000355141 Q9NZV5 UPI00003761B2 NM_020451.2 9/13 hmmpanther:PTHR16213,hmmpanther:PTHR16213:SF78 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 41 25811729 25811729 GATCCTG - 1 0 1 0 1 0 0 0 0 14332 1277 45 0 0 SEPN1 1 25811729 Frame_Shift_Del DEL GATCCTG C3N-00199_T 4532439 25811729 223144693 7 11051 GPATCH3 0 . GRCh38 1 26892434 26892434 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.1338C>T p.= p.H446H ENST00000361720 6/7 243 178 65 191 191 0 strelka-varscan-mutect GPATCH3,synonymous_variant,p.=,ENST00000361720,NM_022078.2;GPATCH3,synonymous_variant,p.=,ENST00000450844,;GPATCH3,intron_variant,,ENST00000445019,;GPN2,upstream_gene_variant,,ENST00000374135,NM_018066.3;GPN2,upstream_gene_variant,,ENST00000431781,;GPN2,upstream_gene_variant,,ENST00000461282,; A ENST00000361720 Transcript synonymous_variant 1362/2123 1338/1578 446/525 H caC/caT 1 -1 GPATCH3 HGNC HGNC:25720 protein_coding YES CCDS290.1 ENSP00000354645 Q96I76 UPI000003E830 NM_022078.2 6/7 Pfam_domain:PF01585,PROSITE_profiles:PS50174,hmmpanther:PTHR14390,hmmpanther:PTHR14390:SF2,SMART_domains:SM00443 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 26892434 26892434 G A 1 0 0 0 0 0 0 0 1 6493 1252 44 3 3 GPATCH3 1 26892434 Silent SNP G C3N-00199_T 1080705 26892434 222063988 8 11052 ZSCAN20 0 . GRCh38 1 33491526 33491526 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.1268A>T p.Glu423Val p.E423V ENST00000361328 6/8 124 105 19 124 124 0 strelka-varscan-mutect ZSCAN20,missense_variant,p.Glu423Val,ENST00000361328,NM_145238.3;ZSCAN20,missense_variant,p.Glu369Val,ENST00000373413,;ZSCAN20,downstream_gene_variant,,ENST00000480917,; T ENST00000361328 Transcript missense_variant 1421/4316 1268/3132 423/1043 E/V gAg/gTg 1 1 ZSCAN20 HGNC HGNC:13093 protein_coding YES CCDS41300.1 ENSP00000355053 P17040 UPI0000D61EC5 NM_145238.3 deleterious(0.02) 6/8 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 33491526 33491526 A T 1 0 0 0 0 1 0 0 0 18826 304 11 4 4 ZSCAN20 1 33491526 Missense_Mutation SNP A C3N-00199_T 6599092 33491526 215464896 9 11053 DLGAP3 0 . GRCh38 1 34899709 34899709 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1346G>T p.Ser449Ile p.S449I ENST00000373347 5/12 321 207 114 260 260 0 strelka-varscan-mutect DLGAP3,missense_variant,p.Ser449Ile,ENST00000373347,NM_001080418.2;DLGAP3,missense_variant,p.Ser449Ile,ENST00000235180,; A ENST00000373347 Transcript missense_variant 1615/3856 1346/2940 449/979 S/I aGc/aTc 1 -1 DLGAP3 HGNC HGNC:30368 protein_coding YES CCDS30670.1 ENSP00000362444 O95886 UPI00003D4D81 NM_001080418.2 deleterious(0) 5/12 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF4 MODERATE 1 SNV 5 1 PASS rs1415973124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 34899709 34899709 C A 1 0 0 0 0 1 0 0 0 4368 797 28 2 2 DLGAP3 1 34899709 Missense_Mutation SNP C C3N-00199_T 1408183 34899709 214056713 10 11054 COL8A2 0 . GRCh38 1 36098403 36098403 + Missense_Mutation SNP C C G novel C3N-00199_T C3N-00199_N C C c.1278G>C p.Lys426Asn p.K426N ENST00000397799 4/4 541 438 103 570 570 0 strelka-varscan-mutect COL8A2,missense_variant,p.Lys426Asn,ENST00000397799,NM_005202.3;COL8A2,missense_variant,p.Lys426Asn,ENST00000303143,;COL8A2,missense_variant,p.Lys361Asn,ENST00000481785,NM_001294347.1;COL8A2,intron_variant,,ENST00000615990,;ADPRHL2,downstream_gene_variant,,ENST00000373178,NM_017825.2; G ENST00000397799 Transcript missense_variant 1503/4670 1278/2112 426/703 K/N aaG/aaC 1 -1 COL8A2 HGNC HGNC:2216 protein_coding YES CCDS403.1 ENSP00000380901 P25067 UPI00001B2F2D NM_005202.3 deleterious(0.02) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF584 MODERATE SNV 5 1 PASS rs1296516994 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 36098403 36098403 C G 1 0 0 0 0 1 0 0 0 3495 680 24 4 4 COL8A2 1 36098403 Missense_Mutation SNP C C3N-00199_T 1198694 36098403 212858019 11 11055 KDM4A 0 . GRCh38 1 43669296 43669296 + Missense_Mutation SNP C C T novel C3N-00199_T C3N-00199_N C C c.1360C>T p.Pro454Ser p.P454S ENST00000372396 10/22 223 171 52 227 227 0 strelka-varscan-mutect KDM4A,missense_variant,p.Pro454Ser,ENST00000372396,NM_014663.2;KDM4A,downstream_gene_variant,,ENST00000463151,;KDM4A,downstream_gene_variant,,ENST00000485249,;KDM4A,downstream_gene_variant,,ENST00000472265,; T ENST00000372396 Transcript missense_variant 1494/4474 1360/3195 454/1064 P/S Cca/Tca 1 1 KDM4A HGNC HGNC:22978 protein_coding YES CCDS491.1 ENSP00000361473 O75164 UPI000013D35A NM_014663.2 tolerated(0.07) 10/22 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF32 MODERATE 1 SNV 1 1 PASS rs1301506786 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 43669296 43669296 C T 1 0 0 0 0 1 0 0 0 8046 637 22 3 3 KDM4A 1 43669296 Missense_Mutation SNP C C3N-00199_T 7570893 43669296 205287126 12 11056 C8A 0 . GRCh38 1 56867621 56867621 + Silent SNP G G A C3N-00199_T C3N-00199_N G G c.90G>A p.= p.R30R ENST00000361249 2/11 326 265 61 390 390 0 strelka-varscan-mutect C8A,synonymous_variant,p.=,ENST00000361249,NM_000562.2; A ENST00000361249 Transcript synonymous_variant 186/2356 90/1755 30/584 R cgG/cgA COSM352926 1 1 C8A HGNC HGNC:1352 protein_coding YES CCDS606.1 ENSP00000354458 P07357 UPI0000127C5A NM_000562.2 2/11 Low_complexity_(Seg):seg,hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325 1 LOW 1 SNV 1 1 1 PASS rs1267332754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 56867621 56867621 G A 1 0 0 0 0 0 0 0 1 2150 1219 43 3 3 C8A 1 56867621 Silent SNP G C3N-00199_T 13198325 56867621 192088801 13 11057 L1TD1 0 . GRCh38 1 62207071 62207071 + Missense_Mutation SNP A A G novel C3N-00199_T C3N-00199_N A A c.443A>G p.Asn148Ser p.N148S ENST00000498273 3/4 68 47 21 227 227 0 strelka-varscan-mutect L1TD1,missense_variant,p.Asn148Ser,ENST00000498273,NM_001164835.1,NM_019079.4;Y_RNA,upstream_gene_variant,,ENST00000363304,;RP5-1155K23.4,downstream_gene_variant,,ENST00000450606,; G ENST00000498273 Transcript missense_variant 738/3849 443/2598 148/865 N/S aAc/aGc 1 1 L1TD1 HGNC HGNC:25595 protein_coding YES CCDS619.1 ENSP00000419901 Q5T7N2 UPI000013E18E NM_001164835.1,NM_019079.4 deleterious(0.02) 3/4 MODERATE 1 SNV 1 1 PASS rs1337737887 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 62207071 62207071 A G 1 0 0 0 0 1 0 0 0 8490 43 2 5 5 L1TD1 1 62207071 Missense_Mutation SNP A C3N-00199_T 5339450 62207071 186749351 14 11058 DNAJC6 0 . GRCh38 1 65405984 65405984 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.2342A>T p.Gln781Leu p.Q781L ENST00000371069 16/19 345 298 47 312 312 0 strelka-varscan-mutect DNAJC6,missense_variant,p.Gln711Leu,ENST00000263441,NM_001256865.1;DNAJC6,missense_variant,p.Gln724Leu,ENST00000395325,NM_014787.3;DNAJC6,missense_variant,p.Gln781Leu,ENST00000371069,NM_001256864.1; T ENST00000371069 Transcript missense_variant 2543/5365 2342/2913 781/970 Q/L cAg/cTg 1 1 DNAJC6 HGNC HGNC:15469 protein_coding YES CCDS58004.1 ENSP00000360108 O75061 UPI000022AE8A NM_001256864.1 tolerated(0.06) 16/19 Low_complexity_(Seg):seg,hmmpanther:PTHR23172:SF4,hmmpanther:PTHR23172 MODERATE 1 SNV 1 1 PASS rs1453709743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 65405984 65405984 A T 1 0 0 0 0 1 0 0 0 4466 188 7 4 4 DNAJC6 1 65405984 Missense_Mutation SNP A C3N-00199_T 3198913 65405984 183550438 15 11059 TTLL7 0 . GRCh38 1 83947125 83947125 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.505G>T p.Gly169Trp p.G169W ENST00000260505 6/21 39 31 8 137 137 0 strelka-varscan-mutect TTLL7,missense_variant,p.Gly169Trp,ENST00000260505,NM_024686.4;TTLL7,missense_variant,p.Gly169Trp,ENST00000610996,;TTLL7,splice_region_variant,,ENST00000477524,;TTLL7,splice_region_variant,,ENST00000472688,;TTLL7,splice_region_variant,,ENST00000488014,;TTLL7,intron_variant,,ENST00000482783,;TTLL7,downstream_gene_variant,,ENST00000467670,;TTLL7,missense_variant,p.Gly169Trp,ENST00000480174,;TTLL7,missense_variant,p.Gly53Trp,ENST00000485638,;TTLL7,intron_variant,,ENST00000474957,; A ENST00000260505 Transcript missense_variant,splice_region_variant 883/7976 505/2664 169/887 G/W Ggg/Tgg 1 -1 TTLL7 HGNC HGNC:26242 protein_coding YES CCDS690.2 ENSP00000260505 Q6ZT98 UPI000020391D NM_024686.4 deleterious(0) 6/21 Pfam_domain:PF03133,PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF102,Superfamily_domains:SSF56059 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -19.86016 1 1 1 1 0 A 3 1 41 83947125 83947125 C A 1 0 0 0 0 1 0 0 0 17243 608 21 2 2 TTLL7 1 83947125 Missense_Mutation SNP C C3N-00199_T 18541141 83947125 165009297 16 11060 LPAR3 0 . GRCh38 1 84865506 84865506 + Silent SNP C C A rs370676637 C3N-00199_T C3N-00199_N C C c.615G>T p.= p.V205V ENST00000440886 1/2 294 226 68 347 347 0 strelka-varscan-mutect LPAR3,synonymous_variant,p.=,ENST00000440886,;LPAR3,synonymous_variant,p.=,ENST00000370611,NM_012152.2;LPAR3,non_coding_transcript_exon_variant,,ENST00000491034,; A ENST00000440886 Transcript synonymous_variant 654/3345 615/1062 205/353 V gtG/gtT rs370676637 1 -1 LPAR3 HGNC HGNC:14298 protein_coding YES CCDS700.1 ENSP00000395389 Q9UBY5 UPI000003CAC0 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF21,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs370676637 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 84865506 84865506 C A 1 0 0 0 0 0 0 0 1 8809 465 17 2 2 LPAR3 1 84865506 Silent SNP C C3N-00199_T 918381 84865506 164090916 17 11061 CLCA2 0 . GRCh38 1 86447581 86447581 + Missense_Mutation SNP G G T rs372198099 C3N-00199_T C3N-00199_N G G c.1787G>T p.Arg596Leu p.R596L ENST00000370565 11/14 360 271 89 396 396 0 strelka-varscan-mutect CLCA2,missense_variant,p.Arg596Leu,ENST00000370565,NM_006536.5;CLCA2,upstream_gene_variant,,ENST00000498802,;CLCA2,downstream_gene_variant,,ENST00000490884,; T ENST00000370565 Transcript missense_variant 1949/4025 1787/2832 596/943 R/L cGc/cTc rs372198099 1 1 CLCA2 HGNC HGNC:2016 protein_coding YES CCDS708.1 ENSP00000359596 Q9UQC9 UPI0000035838 NM_006536.5 deleterious(0) 11/14 Pfam_domain:PF08434,hmmpanther:PTHR10579,hmmpanther:PTHR10579:SF66,TIGRFAM_domain:TIGR00868 MODERATE 1 SNV 1 1 PASS rs372198099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 86447581 86447581 G T 1 0 0 0 0 1 0 0 0 3222 1087 38 1 1 CLCA2 1 86447581 Missense_Mutation SNP G C3N-00199_T 1582075 86447581 162508841 18 11062 STRIP1 0 . GRCh38 1 110051843 110051843 + Missense_Mutation SNP A A T rs767414666 C3N-00199_T C3N-00199_N A A c.2222A>T p.Gln741Leu p.Q741L ENST00000369795 20/21 292 251 41 286 286 0 strelka-varscan-mutect STRIP1,missense_variant,p.Gln741Leu,ENST00000369795,NM_033088.3;STRIP1,missense_variant,p.Gln646Leu,ENST00000369796,NM_001270768.1;STRIP1,3_prime_UTR_variant,,ENST00000485775,;STRIP1,non_coding_transcript_exon_variant,,ENST00000473429,;STRIP1,downstream_gene_variant,,ENST00000461054,; T ENST00000369795 Transcript missense_variant 2244/3265 2222/2514 741/837 Q/L cAg/cTg rs767414666 1 1 STRIP1 HGNC HGNC:25916 protein_coding YES CCDS30798.1 ENSP00000358810 Q5VSL9 UPI0000160E65 NM_033088.3 deleterious(0.01) 20/21 Pfam_domain:PF11882,hmmpanther:PTHR13239,hmmpanther:PTHR13239:SF5,SMART_domains:SM01293 MODERATE 1 SNV 1 1 PASS rs767414666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 110051843 110051843 A T 1 0 0 0 0 1 0 0 0 15710 188 7 4 4 STRIP1 1 110051843 Missense_Mutation SNP A C3N-00199_T 23604262 110051843 138904579 19 11063 GJA8 0 . GRCh38 1 147908159 147908159 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.204G>T p.Glu68Asp p.E68D ENST00000369235 1/1 592 374 218 393 393 0 strelka-varscan-mutect GJA8,missense_variant,p.Glu68Asp,ENST00000369235,NM_005267.4; T ENST00000369235 Transcript missense_variant 204/1302 204/1302 68/433 E/D gaG/gaT 1 1 GJA8 HGNC HGNC:4281 protein_coding YES CCDS30834.1 ENSP00000358238 P48165 X5D7G1 UPI0000049BA0 NM_005267.4 deleterious(0.02) 1/1 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF19,SMART_domains:SM00037 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 147908159 147908159 G T 1 0 0 0 0 1 0 0 0 6284 991 35 2 2 GJA8 1 147908159 Missense_Mutation SNP G C3N-00199_T 37856316 147908159 101048263 20 11064 LYSMD1 0 . GRCh38 1 151160956 151160956 + Missense_Mutation SNP C C A rs147702548 C3N-00199_T C3N-00199_N C C c.610G>T p.Gly204Cys p.G204C ENST00000368908 3/3 332 208 124 212 211 1 strelka-varscan-mutect LYSMD1,missense_variant,p.Gly204Cys,ENST00000368908,NM_212551.4;LYSMD1,missense_variant,p.Gly156Cys,ENST00000440902,NM_001136543.1;SCNM1,intron_variant,,ENST00000602841,NM_001204848.1;TNFAIP8L2,downstream_gene_variant,,ENST00000368910,NM_024575.4; A ENST00000368908 Transcript missense_variant 1271/2479 610/684 204/227 G/C Ggt/Tgt rs147702548 1 -1 LYSMD1 HGNC HGNC:32070 protein_coding YES CCDS986.1 ENSP00000357904 Q96S90 UPI000007311C NM_212551.4 deleterious(0) 3/3 hmmpanther:PTHR20932:SF2,hmmpanther:PTHR20932 MODERATE 1 SNV 1 1 PASS rs147702548 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 151160956 151160956 C A 1 0 0 0 0 1 0 0 0 9037 681 24 2 2 LYSMD1 1 151160956 Missense_Mutation SNP C C3N-00199_T 3252797 151160956 97795466 21 11065 LCE5A 0 . GRCh38 1 152511885 152511885 + Nonsense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.351C>A p.Cys117Ter p.C117* ENST00000334269 2/2 136 77 59 104 104 0 strelka-varscan-mutect LCE5A,stop_gained,p.Cys117Ter,ENST00000334269,NM_178438.4;AL135842.1,intron_variant,,ENST00000624892,;CRCT1,upstream_gene_variant,,ENST00000368790,NM_019060.2; A ENST00000334269 Transcript stop_gained 527/819 351/357 117/118 C/* tgC/tgA 1 1 LCE5A HGNC HGNC:16614 protein_coding YES CCDS1011.1 ENSP00000333952 Q5TCM9 UPI00001615D7 NM_178438.4 2/2 hmmpanther:PTHR23263,Low_complexity_(Seg):seg HIGH SNV 3 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 152511885 152511885 C A 1 0 0 0 0 0 1 0 0 8580 805 28 2 2 LCE5A 1 152511885 Nonsense_Mutation SNP C C3N-00199_T 1350929 152511885 96444537 22 11066 DENND4B 0 . GRCh38 1 153932382 153932382 + Missense_Mutation SNP C C A rs367917095 C3N-00199_T C3N-00199_N C C c.3818G>T p.Arg1273Leu p.R1273L ENST00000361217 24/28 409 308 101 248 248 0 strelka-varscan-mutect DENND4B,missense_variant,p.Arg1273Leu,ENST00000361217,NM_014856.2;DENND4B,downstream_gene_variant,,ENST00000368646,;DENND4B,intron_variant,,ENST00000474386,;DENND4B,non_coding_transcript_exon_variant,,ENST00000480340,;DENND4B,non_coding_transcript_exon_variant,,ENST00000492898,;DENND4B,non_coding_transcript_exon_variant,,ENST00000462423,;DENND4B,downstream_gene_variant,,ENST00000531748,;DENND4B,downstream_gene_variant,,ENST00000477746,; A ENST00000361217 Transcript missense_variant 4237/5706 3818/4491 1273/1496 R/L cGt/cTt rs367917095 1 -1 DENND4B HGNC HGNC:29044 protein_coding YES CCDS44228.1 ENSP00000354597 O75064 UPI000047EA3E NM_014856.2 tolerated(0.07) 24/28 hmmpanther:PTHR12296:SF18,hmmpanther:PTHR12296 MODERATE 1 SNV 1 1 PASS rs367917095 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 153932382 153932382 C A 1 0 0 0 0 1 0 0 0 4238 536 19 1 1 DENND4B 1 153932382 Missense_Mutation SNP C C3N-00199_T 1420497 153932382 95024040 23 11067 CHRNB2 0 . GRCh38 1 154575889 154575889 + Missense_Mutation SNP C C A rs754372558 C3N-00199_T C3N-00199_N C C c.1466C>A p.Thr489Asn p.T489N ENST00000368476 6/6 1007 771 236 685 684 1 strelka-varscan-mutect CHRNB2,missense_variant,p.Thr489Asn,ENST00000368476,NM_000748.2;CHRNB2,missense_variant,p.Thr491Asn,ENST00000637900,;RP11-61L14.6,downstream_gene_variant,,ENST00000421866,;CHRNB2,upstream_gene_variant,,ENST00000635876,;CHRNB2,missense_variant,p.Thr489Asn,ENST00000636034,; A ENST00000368476 Transcript missense_variant 1730/5867 1466/1509 489/502 T/N aCc/aAc rs754372558 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 tolerated(0.55) 6/6 MODERATE 1 SNV 1 1 PASS rs754372558 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 154575889 154575889 C A 1 0 0 0 0 1 0 0 0 3151 507 18 2 2 CHRNB2 1 154575889 Missense_Mutation SNP C C3N-00199_T 643507 154575889 94380533 24 11068 DUSP27 0 . GRCh38 1 167126465 167126465 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.1334G>T p.Ser445Ile p.S445I ENST00000361200 6/6 166 104 62 121 121 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ser445Ile,ENST00000361200,;DUSP27,missense_variant,p.Ser445Ile,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ser445Ile,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; T ENST00000361200 Transcript missense_variant 1500/4164 1334/3477 445/1158 S/I aGc/aTc COSM4024783 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 6/6 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 167126465 167126465 G T 1 0 0 0 0 1 0 0 0 4646 971 34 2 2 DUSP27 1 167126465 Missense_Mutation SNP G C3N-00199_T 12550576 167126465 81829957 25 11069 MROH9 0 . GRCh38 1 171062140 171062140 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.2290G>T p.Ala764Ser p.A764S ENST00000367759 21/22 75 62 13 146 146 0 strelka-varscan-mutect MROH9,missense_variant,p.Ala764Ser,ENST00000367759,NM_001163629.1; T ENST00000367759 Transcript missense_variant 2444/3165 2290/2586 764/861 A/S Gca/Tca 1 1 MROH9 HGNC HGNC:26287 protein_coding YES CCDS53429.1 ENSP00000356733 Q5TGP6 UPI0001B09232 NM_001163629.1 deleterious(0.04) 21/22 Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 171062140 171062140 G T 1 0 0 0 0 1 0 0 0 9748 1203 42 2 2 MROH9 1 171062140 Missense_Mutation SNP G C3N-00199_T 3935675 171062140 77894282 26 11070 TNR 0 . GRCh38 1 175359720 175359720 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.2866C>A p.Pro956Thr p.P956T ENST00000367674 15/23 131 77 54 144 144 0 strelka-varscan-mutect TNR,missense_variant,p.Pro956Thr,ENST00000367674,;TNR,missense_variant,p.Pro956Thr,ENST00000263525,NM_003285.2; T ENST00000367674 Transcript missense_variant 3575/12949 2866/4077 956/1358 P/T Cct/Act 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0) 15/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 175359720 175359720 G T 1 0 0 0 0 1 0 0 0 16811 1232 43 2 2 TNR 1 175359720 Missense_Mutation SNP G C3N-00199_T 4297580 175359720 73596702 27 11071 PAPPA2 0 . GRCh38 1 176556442 176556442 + Silent SNP G G A C3N-00199_T C3N-00199_N G G c.120G>A p.= p.L40L ENST00000367662 2/23 397 266 131 306 306 0 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2;PAPPA2,synonymous_variant,p.=,ENST00000367661,NM_021936.2;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,; A ENST00000367662 Transcript synonymous_variant 1284/9691 120/5376 40/1791 L ctG/ctA COSM4430003,COSM4430004 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 2/23 1,1 LOW 1 SNV 1 1,1 1 PASS rs1245048813 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 176556442 176556442 G A 1 0 0 0 0 0 0 0 1 11513 1277 45 3 3 PAPPA2 1 176556442 Silent SNP G C3N-00199_T 1196722 176556442 72399980 28 11072 ASTN1 0 . GRCh38 1 177023566 177023566 + Missense_Mutation SNP G G T rs201453556 C3N-00199_T C3N-00199_N G G c.1276C>A p.Arg426Ser p.R426S ENST00000361833 7/23 118 83 35 55 55 0 strelka-varscan-mutect ASTN1,missense_variant,p.Arg426Ser,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Arg426Ser,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Arg426Ser,ENST00000424564,NM_207108.2;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;ASTN1,intron_variant,,ENST00000473640,; T ENST00000361833 Transcript missense_variant 1290/7116 1276/3885 426/1294 R/S Cgc/Agc rs201453556 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 tolerated(0.77) 7/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 MODERATE 1 SNV 1 1 PASS rs201453556 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 177023566 177023566 G T 1 0 0 0 0 1 0 0 0 1211 1130 39 1 1 ASTN1 1 177023566 Missense_Mutation SNP G C3N-00199_T 467124 177023566 71932856 29 11073 HMCN1 0 . GRCh38 1 186108513 186108513 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.10905G>T p.= p.R3635R ENST00000271588 71/107 325 280 45 537 537 0 strelka-varscan-mutect HMCN1,synonymous_variant,p.=,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript synonymous_variant 11134/18208 10905/16908 3635/5635 R cgG/cgT 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 71/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 186108513 186108513 G T 1 0 0 0 0 0 0 0 1 7111 1161 41 2 2 HMCN1 1 186108513 Silent SNP G C3N-00199_T 9084947 186108513 62847909 30 11074 LHX9 0 . GRCh38 1 197929095 197929095 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1030G>T p.Ala344Ser p.A344S ENST00000367387 5/5 721 345 376 381 381 0 strelka-varscan-mutect LHX9,missense_variant,p.Ala344Ser,ENST00000367387,NM_020204.2;LHX9,missense_variant,p.Ala335Ser,ENST00000367390,NM_001014434.1;LHX9,intron_variant,,ENST00000561173,;LHX9,intron_variant,,ENST00000367391,; T ENST00000367387 Transcript missense_variant 1455/7836 1030/1194 344/397 A/S Gcc/Tcc 1 1 LHX9 HGNC HGNC:14222 protein_coding YES CCDS1393.1 ENSP00000356357 Q9NQ69 UPI00001B6453 NM_020204.2 tolerated(1) 5/5 hmmpanther:PTHR24208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 197929095 197929095 G T 1 0 0 0 0 1 0 0 0 8686 1203 42 2 2 LHX9 1 197929095 Missense_Mutation SNP G C3N-00199_T 11820582 197929095 51027327 31 11075 DYRK3 0 . GRCh38 1 206648059 206648059 + Silent SNP C C G novel C3N-00199_T C3N-00199_N C C c.861C>G p.= p.A287A ENST00000367109 3/3 200 92 108 251 251 0 strelka-varscan-mutect DYRK3,synonymous_variant,p.=,ENST00000367106,;DYRK3,synonymous_variant,p.=,ENST00000367108,NM_001004023.1;DYRK3,synonymous_variant,p.=,ENST00000367109,NM_003582.2;DYRK3,downstream_gene_variant,,ENST00000441486,;DYRK3,intron_variant,,ENST00000489878,; G ENST00000367109 Transcript synonymous_variant 1029/2163 861/1767 287/588 A gcC/gcG 1 1 DYRK3 HGNC HGNC:3094 protein_coding YES CCDS30999.1 ENSP00000356076 O43781 UPI0000071267 NM_003582.2 3/3 PROSITE_profiles:PS50011,hmmpanther:PTHR24058:SF35,hmmpanther:PTHR24058,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9996879 1 1 1 0 G 2 3 41 206648059 206648059 C G 1 0 0 0 0 0 0 0 1 4681 668 24 4 4 DYRK3 1 206648059 Silent SNP C C3N-00199_T 8718964 206648059 42308363 32 11076 TRAF3IP3 0 . GRCh38 1 209763073 209763073 + Missense_Mutation SNP G G A C3N-00199_T C3N-00199_N G G c.557G>A p.Gly186Glu p.G186E ENST00000367024 6/17 177 157 20 243 243 0 strelka-varscan-mutect TRAF3IP3,missense_variant,p.Gly186Glu,ENST00000367024,NM_001320143.1;TRAF3IP3,missense_variant,p.Gly186Glu,ENST00000367025,NM_025228.3;TRAF3IP3,missense_variant,p.Gly166Glu,ENST00000367026,NM_001320144.1;TRAF3IP3,missense_variant,p.Gly166Glu,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000479796,;TRAF3IP3,downstream_gene_variant,,ENST00000468672,;TRAF3IP3,missense_variant,p.Gly186Glu,ENST00000478359,; A ENST00000367024 Transcript missense_variant 1073/2331 557/1656 186/551 G/E gGa/gAa COSM5677586,COSM5677587 1 1 TRAF3IP3 HGNC HGNC:30766 protein_coding YES CCDS1490.2 ENSP00000355991 Q9Y228 UPI00005190E1 NM_001320143.1 deleterious(0) 6/17 hmmpanther:PTHR15715:SF21,hmmpanther:PTHR15715 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 209763073 209763073 G A 1 0 0 0 0 1 0 0 0 16925 1188 41 3 3 TRAF3IP3 1 209763073 Missense_Mutation SNP G C3N-00199_T 3115014 209763073 39193349 33 11077 RD3 0 . GRCh38 1 211479152 211479152 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.472C>A p.Arg158Ser p.R158S ENST00000367002 3/3 340 255 85 265 265 0 strelka-varscan-mutect RD3,missense_variant,p.Arg158Ser,ENST00000367002,NM_001164688.1,NM_183059.2;RD3,non_coding_transcript_exon_variant,,ENST00000484910,; T ENST00000367002 Transcript missense_variant 1636/4266 472/588 158/195 R/S Cgc/Agc 1 -1 RD3 HGNC HGNC:19689 protein_coding YES CCDS1498.1 ENSP00000355969 Q7Z3Z2 UPI00001BB29F NM_001164688.1,NM_183059.2 deleterious(0) 3/3 hmmpanther:PTHR28489,hmmpanther:PTHR28489:SF1,PD822638 MODERATE 1 SNV 1 1 PASS rs1047786307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 211479152 211479152 G T 1 0 0 0 0 1 0 0 0 13357 1087 38 1 1 RD3 1 211479152 Missense_Mutation SNP G C3N-00199_T 1716079 211479152 37477270 34 11078 BATF3 0 . GRCh38 1 212699695 212699695 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.68C>T p.Pro23Leu p.P23L ENST00000243440 1/3 72 63 9 26 26 0 strelka-mutect BATF3,missense_variant,p.Pro23Leu,ENST00000243440,NM_018664.2;BATF3,upstream_gene_variant,,ENST00000478275,; A ENST00000243440 Transcript missense_variant 291/980 68/384 23/127 P/L cCg/cTg 1 -1 BATF3 HGNC HGNC:28915 protein_coding YES CCDS1508.1 ENSP00000243440 Q9NR55 UPI000006F080 NM_018664.2 deleterious_low_confidence(0.03) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23351:SF13,hmmpanther:PTHR23351 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 212699695 212699695 G A 1 0 0 0 0 1 0 0 0 1472 1116 39 1 1 BATF3 1 212699695 Missense_Mutation SNP G C3N-00199_T 1220543 212699695 36256727 35 11079 ZC3H11B 0 . GRCh38 1 219611129 219611129 + Nonsense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.934G>T p.Glu312Ter p.E312* ENST00000636126 2/2 202 159 43 450 450 0 strelka-varscan-mutect ZC3H11B,stop_gained,p.Glu312Ter,ENST00000636126,;ZC3H11B,stop_gained,p.Glu312Ter,ENST00000367211,; A ENST00000636126 Transcript stop_gained 1650/4432 934/2418 312/805 E/* Gaa/Taa 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C 2/2 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 219611129 219611129 C A 1 0 0 0 0 0 1 0 0 18135 835 29 2 2 ZC3H11B 1 219611129 Nonsense_Mutation SNP C C3N-00199_T 6911434 219611129 29345293 36 11080 H3F3A 0 . GRCh38 1 226065808 226065808 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.281A>T p.Gln94Leu p.Q94L ENST00000366813 2/3 123 89 34 189 189 0 strelka-varscan-mutect H3F3A,missense_variant,p.Gln94Leu,ENST00000366814,;H3F3A,missense_variant,p.Gln94Leu,ENST00000366813,;H3F3A,missense_variant,p.Gln94Leu,ENST00000366815,NM_002107.4;H3F3A,missense_variant,p.Gln94Leu,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; T ENST00000366813 Transcript missense_variant,splice_region_variant 656/1308 281/411 94/136 Q/L cAg/cTg 1 1 H3F3A HGNC HGNC:4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 B2R4P9 UPI00000007B0 deleterious_low_confidence(0.02) 2/3 hmmpanther:PTHR11426,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 226065808 226065808 A T 1 0 0 0 0 1 0 0 0 6815 202 7 4 4 H3F3A 1 226065808 Missense_Mutation SNP A C3N-00199_T 6454679 226065808 22890614 37 11081 AGT 0 . GRCh38 1 230706091 230706091 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.966G>T p.Trp322Cys p.W322C ENST00000366667 3/5 472 359 113 475 475 0 strelka-varscan-mutect AGT,missense_variant,p.Trp322Cys,ENST00000366667,NM_000029.3;RP11-99J16__A.2,downstream_gene_variant,,ENST00000412344,; A ENST00000366667 Transcript missense_variant 1181/2291 966/1458 322/485 W/C tgG/tgT 1 -1 AGT HGNC HGNC:333 protein_coding YES CCDS1585.1 ENSP00000355627 P01019 B0ZBE2 UPI0000125B13 NM_000029.3 deleterious(0.01) 3/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF13,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 230706091 230706091 C A 1 0 0 0 0 1 0 0 0 478 856 30 2 2 AGT 1 230706091 Missense_Mutation SNP C C3N-00199_T 4640283 230706091 18250331 38 11082 LYST 0 . GRCh38 1 235733842 235733842 + Missense_Mutation SNP T T A C3N-00199_T C3N-00199_N T T c.8600A>T p.Asn2867Ile p.N2867I ENST00000389793 33/53 71 48 23 172 172 0 strelka-varscan-mutect LYST,missense_variant,p.Asn2867Ile,ENST00000389793,NM_000081.3,NM_001301365.1;LYST,3_prime_UTR_variant,,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000473037,;LYST,downstream_gene_variant,,ENST00000461526,;LDHAP2,upstream_gene_variant,,ENST00000437325,; A ENST00000389793 Transcript missense_variant 8775/13480 8600/11406 2867/3801 N/I aAt/aTt COSM1601940 1 -1 LYST HGNC HGNC:1968 protein_coding YES CCDS31062.1 ENSP00000374443 Q99698 UPI000020509E NM_000081.3,NM_001301365.1 tolerated(0.08) 33/53 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF86 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 235733842 235733842 T A 1 0 0 0 0 1 0 0 0 9041 1493 52 4 4 LYST 1 235733842 Missense_Mutation SNP T C3N-00199_T 5027751 235733842 13222580 39 11083 RYR2 0 . GRCh38 1 237700334 237700334 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.9234C>A p.= p.G3078G ENST00000366574 65/105 280 229 51 361 360 1 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript synonymous_variant 9551/16562 9234/14904 3078/4967 G ggC/ggA 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 65/105 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 237700334 237700334 C A 1 0 0 0 0 0 0 0 1 14029 726 26 2 2 RYR2 1 237700334 Silent SNP C C3N-00199_T 1966492 237700334 11256088 40 11084 PLD5 0 . GRCh38 1 242265439 242265439 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.505C>A p.Leu169Ile p.L169I ENST00000536534 4/10 75 54 21 170 170 0 strelka-varscan-mutect PLD5,missense_variant,p.Leu169Ile,ENST00000536534,;PLD5,missense_variant,p.Leu169Ile,ENST00000442594,NM_001320272.1,NM_152666.2;PLD5,missense_variant,p.Leu107Ile,ENST00000427495,NM_001195812.1,NM_001195811.1;PLD5,missense_variant,p.Leu107Ile,ENST00000459864,;PLD5,upstream_gene_variant,,ENST00000474177,;PLD5,missense_variant,p.Leu169Ile,ENST00000467561,;PLD5,3_prime_UTR_variant,,ENST00000314833,;PLD5,3_prime_UTR_variant,,ENST00000366545,; T ENST00000536534 Transcript missense_variant 747/8721 505/1611 169/536 L/I Ctt/Att COSM1584326,COSM4868403,COSM906545 1 -1 PLD5 HGNC HGNC:26879 protein_coding YES CCDS1621.2 ENSP00000440896 Q8N7P1 UPI000040E1A4 tolerated(0.58) 4/10 hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 242265439 242265439 G T 1 0 0 0 0 1 0 0 0 12143 942 33 2 2 PLD5 1 242265439 Missense_Mutation SNP G C3N-00199_T 4565105 242265439 6690983 41 11085 OR1C1 0 . GRCh38 1 247758249 247758249 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.158C>A p.Ser53Tyr p.S53Y ENST00000408896 1/1 182 128 54 345 345 0 strelka-varscan-mutect OR1C1,missense_variant,p.Ser53Tyr,ENST00000408896,NM_012353.2; T ENST00000408896 Transcript missense_variant 158/945 158/945 53/314 S/Y tCt/tAt 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0.03) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1182521036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 247758249 247758249 G T 1 0 0 0 0 1 0 0 0 11029 942 33 2 2 OR1C1 1 247758249 Missense_Mutation SNP G C3N-00199_T 5492810 247758249 1198173 42 11086 OR2W3 0 . GRCh38 1 247895801 247895801 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.215G>T p.Ser72Ile p.S72I ENST00000360358 1/1 254 191 63 231 231 0 strelka-varscan-mutect OR2W3,missense_variant,p.Ser72Ile,ENST00000360358,NM_001001957.2; T ENST00000360358 Transcript missense_variant 215/945 215/945 72/314 S/I aGt/aTt 1 1 OR2W3 HGNC HGNC:15021 protein_coding YES CCDS31099.1 ENSP00000353516 Q7Z3T1 UPI0000061EA8 NM_001001957.2 deleterious(0) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF223,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 247895801 247895801 G T 1 0 0 0 0 1 0 0 0 11111 1029 36 2 2 OR2W3 1 247895801 Missense_Mutation SNP G C3N-00199_T 137552 247895801 1060621 43 11087 OR2W3 0 . GRCh38 1 247896431 247896431 + Frame_Shift_Del DEL C C - C3N-00199_T C3N-00199_N C C c.850delC p.Leu284SerfsTer14 p.L284Sfs*14 ENST00000360358 1/1 210 157 53 222 222 0 sindel-varindel-pindel OR2W3,frameshift_variant,p.Leu284SerfsTer14,ENST00000360358,NM_001001957.2; - ENST00000360358 Transcript frameshift_variant 845/945 845/945 282/314 T/X aCc/ac COSM293658 1 1 OR2W3 HGNC HGNC:15021 protein_coding YES CCDS31099.1 ENSP00000353516 Q7Z3T1 UPI0000061EA8 NM_001001957.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF223,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 HIGH 1 deletion 5 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 41 247896431 247896431 C - 1 0 1 0 1 0 0 0 0 11111 507 18 0 0 OR2W3 1 247896431 Frame_Shift_Del DEL C C3N-00199_T 630 247896431 1059991 44 11088 OR2AK2 0 . GRCh38 1 247966117 247966117 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.786G>T p.= p.V262V ENST00000366480 1/1 162 122 40 306 306 0 strelka-varscan-mutect OR2AK2,synonymous_variant,p.=,ENST00000366480,NM_001004491.1; T ENST00000366480 Transcript synonymous_variant 885/1107 786/1008 262/335 V gtG/gtT 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 247966117 247966117 G T 1 0 0 0 0 0 0 0 1 11064 1335 47 2 2 OR2AK2 1 247966117 Silent SNP G C3N-00199_T 69686 247966117 990305 45 11089 OR2L2 0 . GRCh38 1 248038386 248038386 + Missense_Mutation SNP G G T rs553489526 C3N-00199_T C3N-00199_N G G c.119G>T p.Gly40Val p.G40V ENST00000366479 1/1 95 72 23 253 253 0 strelka-varscan-mutect OR2L2,missense_variant,p.Gly40Val,ENST00000366479,NM_001004686.2; T ENST00000366479 Transcript missense_variant 119/939 119/939 40/312 G/V gGa/gTa rs553489526,COSM425901 1 1 OR2L2 HGNC HGNC:8266 protein_coding YES CCDS31103.1 ENSP00000355435 Q8NH16 A0A126GW34 UPI0000061EAA NM_001004686.2 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF189,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs553489526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 248038386 248038386 G T 1 0 0 0 0 1 0 0 0 11085 1174 41 2 2 OR2L2 1 248038386 Missense_Mutation SNP G C3N-00199_T 72269 248038386 918036 46 11090 GREB1 0 . GRCh38 2 11615280 11615280 + Silent SNP G G T rs752937124 C3N-00199_T C3N-00199_N G G c.3312G>T p.= p.L1104L ENST00000381486 20/33 123 97 26 158 158 0 strelka-varscan-mutect GREB1,synonymous_variant,p.=,ENST00000381486,NM_014668.3;GREB1,synonymous_variant,p.=,ENST00000234142,;GREB1,synonymous_variant,p.=,ENST00000396123,;GREB1,downstream_gene_variant,,ENST00000432985,;GREB1,non_coding_transcript_exon_variant,,ENST00000472040,; T ENST00000381486 Transcript synonymous_variant 3612/8484 3312/5850 1104/1949 L ctG/ctT rs752937124 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 20/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 LOW 1 SNV 5 1 PASS rs752937124 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 11615280 11615280 G T 1 0 0 0 0 0 0 0 1 6639 1335 47 2 2 GREB1 2 11615280 Silent SNP G C3N-00199_T 11615280 230578249 47 11091 OSR1 0 . GRCh38 2 19353369 19353369 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.437G>T p.Gly146Val p.G146V ENST00000272223 2/3 364 299 65 414 414 0 strelka-varscan-mutect OSR1,missense_variant,p.Gly146Val,ENST00000272223,NM_145260.2;MIR4757,downstream_gene_variant,,ENST00000584244,;OSR1,downstream_gene_variant,,ENST00000498844,;OSR1,non_coding_transcript_exon_variant,,ENST00000487581,; A ENST00000272223 Transcript missense_variant 782/1936 437/801 146/266 G/V gGg/gTg 1 -1 OSR1 HGNC HGNC:8111 protein_coding YES CCDS1694.1 ENSP00000272223 Q8TAX0 UPI000006EA6A NM_145260.2 tolerated(0.37) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR14196,hmmpanther:PTHR14196:SF5 MODERATE 1 SNV 1 1 PASS rs1179360144 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 19353369 19353369 C A 1 0 0 0 0 1 0 0 0 11360 623 22 2 2 OSR1 2 19353369 Missense_Mutation SNP C C3N-00199_T 7738089 19353369 222840160 48 11092 C2orf70 0 . GRCh38 2 26577614 26577615 + Frame_Shift_Ins INS - - G novel C3N-00199_T C3N-00199_N - - c.447_448insG p.Leu150AlafsTer49 p.L150Afs*49 ENST00000329615 3/4 107 88 19 93 93 0 sindel-pindel C2orf70,frameshift_variant,p.Pro137ArgfsTer18,ENST00000409392,NM_001322426.1;C2orf70,frameshift_variant,p.Leu150AlafsTer49,ENST00000329615,NM_001105519.1;C2orf70,frameshift_variant,p.Pro51ArgfsTer75,ENST00000453368,;CIB4,downstream_gene_variant,,ENST00000288861,NM_001029881.1;CIB4,downstream_gene_variant,,ENST00000405346,;CIB4,downstream_gene_variant,,ENST00000403670,;C2orf70,non_coding_transcript_exon_variant,,ENST00000479453,; G ENST00000329615 Transcript frameshift_variant 478-479/731 447-448/606 149-150/201 -/X -/G 1 1 C2orf70 HGNC HGNC:27938 protein_coding YES CCDS42661.1 ENSP00000332875 A6NJV1 UPI00001AFA74 NM_001105519.1 3/4 hmmpanther:PTHR34924:SF1,hmmpanther:PTHR34924 HIGH insertion 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 41 26577614 26577614 - G 1 0 1 1 0 0 0 0 0 2044 623 22 0 0 C2orf70 2 26577614 Frame_Shift_Ins INS - C3N-00199_T 7224245 26577614 215615915 49 11093 SUPT7L 0 . GRCh38 2 27661236 27661236 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.167C>T p.Pro56Leu p.P56L ENST00000337768 3/6 94 74 20 125 125 0 strelka-varscan-mutect SUPT7L,missense_variant,p.Pro56Leu,ENST00000337768,NM_014860.2,NM_001282729.1;SUPT7L,missense_variant,p.Pro54Leu,ENST00000406540,;SUPT7L,missense_variant,p.Pro54Leu,ENST00000464789,;SUPT7L,missense_variant,p.Pro54Leu,ENST00000405491,NM_001282731.1,NM_001282730.1;SUPT7L,intron_variant,,ENST00000404798,NM_001282732.1;SLC4A1AP,upstream_gene_variant,,ENST00000613058,NM_018158.2;SLC4A1AP,upstream_gene_variant,,ENST00000326019,;SLC4A1AP,upstream_gene_variant,,ENST00000618046,;SLC4A1AP,upstream_gene_variant,,ENST00000613517,;SLC4A1AP,upstream_gene_variant,,ENST00000427424,; A ENST00000337768 Transcript missense_variant 737/4488 167/1245 56/414 P/L cCc/cTc 1 -1 SUPT7L HGNC HGNC:30632 protein_coding YES CCDS42667.1 ENSP00000336750 O94864 UPI000013607D NM_014860.2,NM_001282729.1 deleterious(0) 3/6 hmmpanther:PTHR28598,hmmpanther:PTHR28598:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 27661236 27661236 G A 1 0 0 0 0 1 0 0 0 15787 1232 43 3 3 SUPT7L 2 27661236 Missense_Mutation SNP G C3N-00199_T 1083622 27661236 214532293 50 11094 FOXN2 0 . GRCh38 2 48346512 48346512 + Missense_Mutation SNP T T A rs764474426 C3N-00199_T C3N-00199_N T T c.298T>A p.Cys100Ser p.C100S ENST00000340553 3/7 57 48 9 161 161 0 strelka-varscan-mutect FOXN2,missense_variant,p.Cys100Ser,ENST00000340553,NM_002158.3;FOXN2,missense_variant,p.Cys100Ser,ENST00000413569,;FOXN2,synonymous_variant,p.=,ENST00000616844,; A ENST00000340553 Transcript missense_variant 559/5408 298/1296 100/431 C/S Tgc/Agc rs764474426 1 1 FOXN2 HGNC HGNC:5281 protein_coding YES CCDS1838.1 ENSP00000343633 P32314 UPI0000226321 NM_002158.3 tolerated(0.43) 3/7 hmmpanther:PTHR13962:SF19,hmmpanther:PTHR13962 MODERATE 1 SNV 1 1 PASS rs764474426 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 48346512 48346512 T A 1 0 0 0 0 1 0 0 0 5884 1812 63 4 4 FOXN2 2 48346512 Missense_Mutation SNP T C3N-00199_T 20685276 48346512 193847017 51 11095 WDPCP 0 . GRCh38 2 63174750 63174750 + Silent SNP T T C novel C3N-00199_T C3N-00199_N T T c.1998A>G p.= p.S666S ENST00000272321 15/18 90 67 23 271 271 0 strelka-varscan-mutect WDPCP,synonymous_variant,p.=,ENST00000409120,;WDPCP,synonymous_variant,p.=,ENST00000272321,NM_015910.5;WDPCP,synonymous_variant,p.=,ENST00000409199,;WDPCP,synonymous_variant,p.=,ENST00000398544,NM_001042692.2;WDPCP,3_prime_UTR_variant,,ENST00000409354,; C ENST00000272321 Transcript synonymous_variant 2526/3392 1998/2241 666/746 S tcA/tcG 1 -1 WDPCP HGNC HGNC:28027 protein_coding YES CCDS42688.1 ENSP00000272321 O95876 UPI000013D946 NM_015910.5 15/18 hmmpanther:PTHR13667:SF5,hmmpanther:PTHR13667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 41 63174750 63174750 T C 1 0 0 0 0 0 0 0 1 17833 1451 51 5 5 WDPCP 2 63174750 Silent SNP T C3N-00199_T 14828238 63174750 179018779 52 11096 REG1A 0 . GRCh38 2 79121591 79121591 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.94G>C p.Ala32Pro p.A32P ENST00000233735 3/6 313 245 68 366 366 0 strelka-varscan-mutect REG1A,missense_variant,p.Ala32Pro,ENST00000233735,NM_002909.4;REG1A,non_coding_transcript_exon_variant,,ENST00000488524,;REG1A,non_coding_transcript_exon_variant,,ENST00000485184,;REG1A,non_coding_transcript_exon_variant,,ENST00000461579,; C ENST00000233735 Transcript missense_variant 197/808 94/501 32/166 A/P Gcc/Ccc 1 1 REG1A HGNC HGNC:9951 protein_coding YES CCDS1964.1 ENSP00000233735 P05451 UPI000012E72D NM_002909.4 tolerated(0.77) 3/6 hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF55,Gene3D:3.10.100.10,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 79121591 79121591 G C 1 0 0 0 0 1 0 0 0 13380 1203 42 4 4 REG1A 2 79121591 Missense_Mutation SNP G C3N-00199_T 15946841 79121591 163071938 53 11097 RGPD3 0 . GRCh38 2 106468248 106468248 + Nonsense_Mutation SNP G G T rs753903388 C3N-00199_T C3N-00199_N G G c.41C>A p.Ser14Ter p.S14* ENST00000409886 1/23 477 422 55 363 363 0 strelka-varscan-mutect RGPD3,stop_gained,p.Ser14Ter,ENST00000409886,NM_001144013.1;RGPD3,stop_gained,p.Ser14Ter,ENST00000304514,;AC108868.3,downstream_gene_variant,,ENST00000437031,; T ENST00000409886 Transcript stop_gained 129/5594 41/5277 14/1758 S/* tCg/tAg rs753903388,COSM1004944,COSM1004945 1 -1 RGPD3 HGNC HGNC:32416 protein_coding YES CCDS46379.1 ENSP00000386588 A6NKT7 UPI00006C049F NM_001144013.1 1/23 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs753903388 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 41 106468248 106468248 G T 1 0 0 0 0 0 1 0 0 13459 1059 37 1 1 RGPD3 2 106468248 Nonsense_Mutation SNP G C3N-00199_T 27346657 106468248 135725281 54 11098 CYP27C1 0 . GRCh38 2 127203487 127203487 + Missense_Mutation SNP T T G novel C3N-00199_T C3N-00199_N T T c.63A>C p.Glu21Asp p.E21D ENST00000335247 2/8 107 78 29 317 317 0 strelka-varscan-mutect CYP27C1,missense_variant,p.Glu21Asp,ENST00000335247,NM_001001665.3;CYP27C1,missense_variant,p.Glu21Asp,ENST00000409327,; G ENST00000335247 Transcript missense_variant 194/4401 63/1119 21/372 E/D gaA/gaC 1 -1 CYP27C1 HGNC HGNC:33480 protein_coding YES CCDS33285.1 ENSP00000334128 Q4G0S4 A0A024RAI7 UPI00001995F8 NM_001001665.3 tolerated(0.52) 2/8 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF9,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 127203487 127203487 T G 1 0 0 0 0 1 0 0 0 3963 1606 56 5 5 CYP27C1 2 127203487 Missense_Mutation SNP T C3N-00199_T 20735239 127203487 114990042 55 11099 ERCC3 0 . GRCh38 2 127293584 127293584 + Nonsense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.163G>T p.Glu55Ter p.E55* ENST00000285398 2/15 304 251 53 342 341 1 strelka-varscan-mutect ERCC3,stop_gained,p.Glu55Ter,ENST00000285398,NM_001303416.1,NM_000122.1,NM_001303418.1;ERCC3,upstream_gene_variant,,ENST00000456257,;ERCC3,3_prime_UTR_variant,,ENST00000445889,;ERCC3,3_prime_UTR_variant,,ENST00000426778,;ERCC3,non_coding_transcript_exon_variant,,ENST00000494464,;ERCC3,non_coding_transcript_exon_variant,,ENST00000462306,;ERCC3,non_coding_transcript_exon_variant,,ENST00000490062,;ERCC3,upstream_gene_variant,,ENST00000460485,; A ENST00000285398 Transcript stop_gained 258/2750 163/2349 55/782 E/* Gaa/Taa 1 -1 ERCC3 HGNC HGNC:3435 protein_coding YES CCDS2144.1 ENSP00000285398 P19447 UPI000013900E NM_001303416.1,NM_000122.1,NM_001303418.1 2/15 hmmpanther:PTHR11274,hmmpanther:PTHR11274:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 127293584 127293584 C A 1 0 0 0 0 0 1 0 0 5063 835 29 2 2 ERCC3 2 127293584 Nonsense_Mutation SNP C C3N-00199_T 90097 127293584 114899945 56 11100 AMER3 0 . GRCh38 2 130764494 130764494 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.2422C>A p.His808Asn p.H808N ENST00000423981 2/2 267 220 47 265 265 0 strelka-varscan-mutect AMER3,missense_variant,p.His808Asn,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.His808Asn,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; A ENST00000423981 Transcript missense_variant 2532/6172 2422/2586 808/861 H/N Cac/Aac 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 tolerated_low_confidence(0.23) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 130764494 130764494 C A 1 0 0 0 0 1 0 0 0 669 594 21 2 2 AMER3 2 130764494 Missense_Mutation SNP C C3N-00199_T 3470910 130764494 111429035 57 11101 LRP1B 0 . GRCh38 2 140495684 140495684 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.8915G>T p.Cys2972Phe p.C2972F ENST00000389484 56/91 75 62 13 188 188 0 strelka-varscan-mutect LRP1B,missense_variant,p.Cys2972Phe,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 9887/16535 8915/13800 2972/4599 C/F tGc/tTc 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.01) 56/91 PROSITE_profiles:PS50026,PROSITE_patterns:PS01187,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 140495684 140495684 C A 1 0 0 0 0 1 0 0 0 8850 710 25 2 2 LRP1B 2 140495684 Missense_Mutation SNP C C3N-00199_T 9731190 140495684 101697845 58 11102 LRP1B 0 . GRCh38 2 140841075 140841075 + Missense_Mutation SNP C C G novel C3N-00199_T C3N-00199_N C C c.4957G>C p.Gly1653Arg p.G1653R ENST00000389484 30/91 42 31 11 101 101 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gly1653Arg,ENST00000389484,NM_018557.2; G ENST00000389484 Transcript missense_variant 5929/16535 4957/13800 1653/4599 G/R Ggg/Cgg 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 30/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 140841075 140841075 C G 1 0 0 0 0 1 0 0 0 8850 681 24 4 4 LRP1B 2 140841075 Missense_Mutation SNP C C3N-00199_T 345391 140841075 101352454 59 11103 LRP1B 0 . GRCh38 2 141049178 141049178 + Nonsense_Mutation SNP C C A C3N-00199_T C3N-00199_N C C c.1597G>T p.Gly533Ter p.G533* ENST00000389484 11/91 85 73 12 224 224 0 varscan-mutect LRP1B,stop_gained,p.Gly533Ter,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript stop_gained 2569/16535 1597/13800 533/4599 G/* Gga/Tga COSM5369486 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 11/91 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 141049178 141049178 C A 1 0 0 0 0 0 1 0 0 8850 690 24 2 2 LRP1B 2 141049178 Nonsense_Mutation SNP C C3N-00199_T 208103 141049178 101144351 60 11104 KIF5C 0 . GRCh38 2 148981488 148981488 + Missense_Mutation SNP A A G novel C3N-00199_T C3N-00199_N A A c.1496A>G p.Asp499Gly p.D499G ENST00000435030 14/26 133 125 8 185 185 0 strelka-varscan-mutect KIF5C,missense_variant,p.Asp499Gly,ENST00000435030,NM_004522.2;KIF5C,non_coding_transcript_exon_variant,,ENST00000464066,;KIF5C,non_coding_transcript_exon_variant,,ENST00000460377,; G ENST00000435030 Transcript missense_variant 1864/6931 1496/2874 499/957 D/G gAc/gGc 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 deleterious(0.01) 14/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 148981488 148981488 A G 1 0 0 0 0 1 0 0 0 8172 275 10 5 5 KIF5C 2 148981488 Missense_Mutation SNP A C3N-00199_T 7932310 148981488 93212041 61 11105 GALNT3 0 . GRCh38 2 165757148 165757148 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1291G>T p.Val431Leu p.V431L ENST00000392701 7/11 174 141 33 490 490 0 strelka-varscan-mutect GALNT3,missense_variant,p.Val431Leu,ENST00000392701,NM_004482.3;GALNT3,missense_variant,p.Val169Leu,ENST00000409882,;GALNT3,missense_variant,p.Val431Leu,ENST00000412248,;GALNT3,3_prime_UTR_variant,,ENST00000437849,;GALNT3,downstream_gene_variant,,ENST00000463254,; A ENST00000392701 Transcript missense_variant 2067/3868 1291/1902 431/633 V/L Gtg/Ttg 1 -1 GALNT3 HGNC HGNC:4125 protein_coding YES CCDS2226.1 ENSP00000376465 Q14435 UPI000013C989 NM_004482.3 deleterious(0) 7/11 hmmpanther:PTHR11675:SF33,hmmpanther:PTHR11675,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 165757148 165757148 C A 1 0 0 0 0 1 0 0 0 6085 507 18 2 2 GALNT3 2 165757148 Missense_Mutation SNP C C3N-00199_T 16775660 165757148 76436381 62 11106 XIRP2 0 . GRCh38 2 167243694 167243694 + Missense_Mutation SNP A A G C3N-00199_T C3N-00199_N A A c.2302A>G p.Arg768Gly p.R768G ENST00000409195 9/11 64 46 18 158 157 1 strelka-varscan-mutect XIRP2,missense_variant,p.Arg768Gly,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Arg546Gly,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Arg593Gly,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; G ENST00000409195 Transcript missense_variant 2391/12675 2302/10650 768/3549 R/G Aga/Gga COSM1564707 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 Pfam_domain:PF08043,PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 167243694 167243694 A G 1 0 0 0 0 1 0 0 0 17989 64 3 5 5 XIRP2 2 167243694 Missense_Mutation SNP A C3N-00199_T 1486546 167243694 74949835 63 11107 G6PC2 0 . GRCh38 2 168907929 168907929 + Silent SNP C C T rs139331128 C3N-00199_T C3N-00199_N C C c.918C>T p.= p.L306L ENST00000375363 5/5 273 222 51 539 539 0 strelka-varscan-mutect G6PC2,synonymous_variant,p.=,ENST00000375363,NM_021176.2;SPC25,intron_variant,,ENST00000451987,;G6PC2,downstream_gene_variant,,ENST00000429379,NM_001081686.1;G6PC2,downstream_gene_variant,,ENST00000421979,;G6PC2,non_coding_transcript_exon_variant,,ENST00000461586,;SPC25,intron_variant,,ENST00000472216,;G6PC2,3_prime_UTR_variant,,ENST00000282075,; T ENST00000375363 Transcript synonymous_variant 1010/1214 918/1068 306/355 L ctC/ctT rs139331128 1 1 G6PC2 HGNC HGNC:28906 protein_coding YES CCDS2230.1 ENSP00000364512 Q9NQR9 UPI0000048D51 NM_021176.2 5/5 PIRSF_domain:PIRSF000905,hmmpanther:PTHR12591,hmmpanther:PTHR12591:SF1,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs139331128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 168907929 168907929 C T 1 0 0 0 0 0 0 0 1 6015 900 32 3 3 G6PC2 2 168907929 Silent SNP C C3N-00199_T 1664235 168907929 73285600 64 11108 WIPF1 0 . GRCh38 2 174571622 174571622 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1183C>A p.Pro395Thr p.P395T ENST00000409415 5/5 265 198 67 333 333 0 strelka-varscan-mutect WIPF1,missense_variant,p.Pro395Thr,ENST00000409415,;WIPF1,intron_variant,,ENST00000392547,NM_003387.4;WIPF1,intron_variant,,ENST00000272746,;WIPF1,intron_variant,,ENST00000409891,;WIPF1,intron_variant,,ENST00000392546,;WIPF1,intron_variant,,ENST00000359761,NM_001077269.1;WIPF1,downstream_gene_variant,,ENST00000410117,;WIPF1,downstream_gene_variant,,ENST00000455428,;WIPF1,downstream_gene_variant,,ENST00000436221,;AC018890.6,intron_variant,,ENST00000442996,;AC018890.6,intron_variant,,ENST00000412835,;AC010894.5,upstream_gene_variant,,ENST00000454203,;WIPF1,upstream_gene_variant,,ENST00000467149,; T ENST00000409415 Transcript missense_variant 1319/1772 1183/1212 395/403 P/T Cca/Aca 1 -1 WIPF1 HGNC HGNC:12736 protein_coding ENSP00000387150 E9PB87 UPI0001881868 deleterious_low_confidence(0) 5/5 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 174571622 174571622 G T 1 0 0 0 0 1 0 0 0 17923 1261 44 2 2 WIPF1 2 174571622 Missense_Mutation SNP G C3N-00199_T 5663693 174571622 67621907 65 11109 PDE11A 0 . GRCh38 2 177629456 177629456 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.2753C>A p.Ala918Asp p.A918D ENST00000286063 20/20 311 250 61 537 536 1 strelka-varscan-mutect PDE11A,missense_variant,p.Ala918Asp,ENST00000286063,NM_016953.3;PDE11A,missense_variant,p.Ala668Asp,ENST00000358450,NM_001077197.1;PDE11A,missense_variant,p.Ala560Asp,ENST00000409504,NM_001077358.1;PDE11A,missense_variant,p.Ala474Asp,ENST00000389683,NM_001077196.1;PDE11A,missense_variant,p.Ala121Asp,ENST00000436700,;PDE11A,non_coding_transcript_exon_variant,,ENST00000488399,;PDE11A,non_coding_transcript_exon_variant,,ENST00000478646,; T ENST00000286063 Transcript missense_variant 3071/9275 2753/2802 918/933 A/D gCc/gAc COSM4947124,COSM75887 1 -1 PDE11A HGNC HGNC:8773 protein_coding YES CCDS33334.1 ENSP00000286063 Q9HCR9 UPI00001402C1 NM_016953.3 tolerated_low_confidence(0.41) 20/20 Low_complexity_(Seg):seg,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF130 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 177629456 177629456 G T 1 0 0 0 0 1 0 0 0 11719 1203 42 2 2 PDE11A 2 177629456 Missense_Mutation SNP G C3N-00199_T 3057834 177629456 64564073 66 11110 TTN 0 . GRCh38 2 178564281 178564281 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.81851T>A p.Val27284Asp p.V27284D ENST00000589042 326/363 176 166 10 520 520 0 strelka-varscan-mutect TTN,missense_variant,p.Val27284Asp,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Val25643Asp,ENST00000591111,;TTN,missense_variant,p.Val25643Asp,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Val24716Asp,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Val18219Asp,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Val18411Asp,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Val18344Asp,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,; T ENST00000589042 Transcript missense_variant 82076/109224 81851/107976 27284/35991 V/D gTc/gAc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 178564281 178564281 A T 1 0 0 0 0 1 0 0 0 17245 275 10 4 4 TTN 2 178564281 Missense_Mutation SNP A C3N-00199_T 934825 178564281 63629248 67 11111 DNAH7 0 . GRCh38 2 195926432 195926432 + Frame_Shift_Del DEL C C - rs767015854 C3N-00199_T C3N-00199_N C C c.3606delG p.Ile1203Ter p.I1203* ENST00000312428 22/65 25 22 3 91 91 0 varindel-pindel DNAH7,frameshift_variant,p.Ile1203Ter,ENST00000312428,NM_018897.2; - ENST00000312428 Transcript frameshift_variant 3707/12394 3606/12075 1202/4024 G/X ggG/gg rs767015854,COSM4544618 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 22/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 197 12 0 0 0 0 0 -9.076041 0.9998682 1 1 1 0 - 7 5 41 195926432 195926432 C - 1 0 1 0 1 0 0 0 0 4421 842 30 0 0 DNAH7 2 195926432 Frame_Shift_Del DEL C C3N-00199_T 17362151 195926432 46267097 68 11112 PLCD4 0 . GRCh38 2 218618693 218618693 + Missense_Mutation SNP G G A C3N-00199_T C3N-00199_N G G c.296G>A p.Arg99His p.R99H ENST00000450993 4/16 440 338 102 401 400 1 strelka-varscan-mutect PLCD4,missense_variant,p.Arg99His,ENST00000450993,NM_032726.3;PLCD4,missense_variant,p.Arg99His,ENST00000432688,;PLCD4,missense_variant,p.Arg99His,ENST00000417849,;PLCD4,incomplete_terminal_codon_variant,p.=,ENST00000415854,;PLCD4,missense_variant,p.Ala65Thr,ENST00000444453,;PLCD4,missense_variant,p.Ala65Thr,ENST00000446503,;PLCD4,non_coding_transcript_exon_variant,,ENST00000473443,;PLCD4,non_coding_transcript_exon_variant,,ENST00000483685,;PLCD4,non_coding_transcript_exon_variant,,ENST00000469493,;PLCD4,non_coding_transcript_exon_variant,,ENST00000465713,;PLCD4,upstream_gene_variant,,ENST00000459791,; A ENST00000450993 Transcript missense_variant 635/3232 296/2289 99/762 R/H cGc/cAc COSM3838598 1 1 PLCD4 HGNC HGNC:9062 protein_coding YES CCDS46516.1 ENSP00000388631 Q9BRC7 UPI0000044279 NM_032726.3 deleterious(0) 4/16 PROSITE_profiles:PS50003,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF31,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 1 MODERATE 1 SNV 1 1 1 PASS rs998141297 . 0 208 0 0 2 0 0 0 -20 0.9985955 1 1 1 0 A 3 1 41 218618693 218618693 G A 1 0 0 0 0 1 0 0 0 12127 1087 38 1 1 PLCD4 2 218618693 Missense_Mutation SNP G C3N-00199_T 22692261 218618693 23574836 69 11113 IHH 0 . GRCh38 2 219060355 219060355 + Missense_Mutation SNP C C G C3N-00199_T C3N-00199_N C C c.113G>C p.Arg38Pro p.R38P ENST00000295731 1/3 218 175 43 170 170 0 strelka-varscan-mutect IHH,missense_variant,p.Arg38Pro,ENST00000295731,NM_002181.3;MIR3131,upstream_gene_variant,,ENST00000583592,; G ENST00000295731 Transcript missense_variant 113/2023 113/1236 38/411 R/P cGg/cCg COSM1191629 1 -1 IHH HGNC HGNC:5956 protein_coding YES CCDS33380.1 ENSP00000295731 Q14623 UPI0000035883 NM_002181.3 tolerated(0.1) 1/3 Pfam_domain:PF01085,PIRSF_domain:PIRSF009400,hmmpanther:PTHR11889,hmmpanther:PTHR11889:SF39,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 219060355 219060355 C G 1 0 0 0 0 1 0 0 0 7515 652 23 4 4 IHH 2 219060355 Missense_Mutation SNP C C3N-00199_T 441662 219060355 23133174 70 11114 CHRND 0 . GRCh38 2 232529944 232529944 + Missense_Mutation SNP G G A rs766740341 C3N-00199_T C3N-00199_N G G c.625G>A p.Gly209Arg p.G209R ENST00000258385 7/12 141 118 23 136 136 0 strelka-varscan-mutect CHRND,missense_variant,p.Gly194Arg,ENST00000543200,NM_001256657.1;CHRND,missense_variant,p.Gly209Arg,ENST00000258385,NM_000751.2;PRSS56,downstream_gene_variant,,ENST00000617714,NM_001195129.1;PRSS56,downstream_gene_variant,,ENST00000449534,;CHRND,downstream_gene_variant,,ENST00000449596,;CHRND,missense_variant,p.Arg172Gln,ENST00000441621,;CHRND,3_prime_UTR_variant,,ENST00000446616,;CHRND,intron_variant,,ENST00000412233,; A ENST00000258385 Transcript missense_variant 657/2112 625/1554 209/517 G/R Ggg/Agg rs766740341 1 1 CHRND HGNC HGNC:1965 protein_coding YES CCDS2494.1 ENSP00000258385 Q07001 UPI000012525E NM_000751.2 deleterious(0) 7/12 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF61,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs766740341 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 232529944 232529944 G A 1 0 0 0 0 1 0 0 0 3154 1130 39 1 1 CHRND 2 232529944 Missense_Mutation SNP G C3N-00199_T 13469589 232529944 9663585 71 11115 SAG 0 . GRCh38 2 233335053 233335053 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.898G>A p.Asp300Asn p.D300N ENST00000409110 11/16 102 79 23 133 133 0 strelka-varscan-mutect SAG,missense_variant,p.Asp300Asn,ENST00000409110,NM_000541.4;SAG,non_coding_transcript_exon_variant,,ENST00000476500,;SAG,non_coding_transcript_exon_variant,,ENST00000469222,;SAG,non_coding_transcript_exon_variant,,ENST00000471884,;SAG,non_coding_transcript_exon_variant,,ENST00000412969,;SAG,non_coding_transcript_exon_variant,,ENST00000483231,;SAG,non_coding_transcript_exon_variant,,ENST00000473771,;SAG,upstream_gene_variant,,ENST00000474220,; A ENST00000409110 Transcript missense_variant 1128/1591 898/1218 300/405 D/N Gat/Aat 1 1 SAG HGNC HGNC:10521 protein_coding YES CCDS46545.1 ENSP00000386444 P10523 UPI000013CD8D NM_000541.4 deleterious(0.02) 11/16 hmmpanther:PTHR11792:SF15,hmmpanther:PTHR11792,Gene3D:1g4mB02,Pfam_domain:PF02752,SMART_domains:SM01017,Superfamily_domains:SSF81296,Prints_domain:PR00309 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 233335053 233335053 G A 1 0 0 0 0 1 0 0 0 14067 1174 41 3 3 SAG 2 233335053 Missense_Mutation SNP G C3N-00199_T 805109 233335053 8858476 72 11116 MLPH 0 . GRCh38 2 237518627 237518627 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.534G>T p.Gln178His p.Q178H ENST00000264605 5/16 383 295 88 382 382 0 strelka-varscan-mutect MLPH,missense_variant,p.Gln178His,ENST00000264605,NM_024101.6;MLPH,missense_variant,p.Gln178His,ENST00000338530,NM_001042467.2;MLPH,missense_variant,p.Gln178His,ENST00000410032,NM_001281474.1;MLPH,missense_variant,p.Gln178His,ENST00000409373,NM_001281473.1;MLPH,upstream_gene_variant,,ENST00000437893,;MLPH,non_coding_transcript_exon_variant,,ENST00000468178,;MLPH,upstream_gene_variant,,ENST00000485956,;MLPH,downstream_gene_variant,,ENST00000477501,;MLPH,non_coding_transcript_exon_variant,,ENST00000495439,;MLPH,non_coding_transcript_exon_variant,,ENST00000464123,;MLPH,non_coding_transcript_exon_variant,,ENST00000478712,;MLPH,non_coding_transcript_exon_variant,,ENST00000494110,; T ENST00000264605 Transcript missense_variant 828/3823 534/1803 178/600 Q/H caG/caT 1 1 MLPH HGNC HGNC:29643 protein_coding YES CCDS2518.1 ENSP00000264605 Q9BV36 A0A024R492 UPI00000730BF NM_024101.6 deleterious(0.02) 5/16 hmmpanther:PTHR14555 MODERATE 1 SNV 1 1 PASS rs1265900279 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 237518627 237518627 G T 1 0 0 0 0 1 0 0 0 9596 991 35 2 2 MLPH 2 237518627 Missense_Mutation SNP G C3N-00199_T 4183574 237518627 4674902 73 11117 GRM7 0 . GRCh38 3 7461582 7461582 + Splice_Site SNP G G T novel C3N-00199_T C3N-00199_N G G c.1376-1G>T p.X459_splice ENST00000357716 98 67 31 184 184 0 varscan-mutect GRM7,splice_acceptor_variant,,ENST00000486284,NM_181874.2;GRM7,splice_acceptor_variant,,ENST00000357716,NM_000844.3;GRM7,splice_acceptor_variant,,ENST00000389336,;GRM7,splice_acceptor_variant,,ENST00000402647,;GRM7,splice_acceptor_variant,,ENST00000445087,;GRM7,splice_acceptor_variant,,ENST00000458641,;GRM7,splice_acceptor_variant,,ENST00000463676,;GRM7,splice_acceptor_variant,,ENST00000467425,;GRM7,splice_acceptor_variant,,ENST00000440923,;GRM7,splice_acceptor_variant,,ENST00000389335,; T ENST00000357716 Transcript splice_acceptor_variant -/4127 1376/2748 459/915 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 6/9 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 41 7461582 7461582 G T 1 0 0 0 0 0 0 1 0 6684 1014 35 2 2 GRM7 3 7461582 Splice_Site SNP G C3N-00199_T 7461582 190833977 74 11118 ARPP21 0 . GRCh38 3 35707014 35707014 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.727G>T p.Gly243Cys p.G243C ENST00000417925 9/19 33 26 7 156 156 0 strelka-mutect ARPP21,missense_variant,p.Gly243Cys,ENST00000187397,NM_016300.4;ARPP21,missense_variant,p.Gly243Cys,ENST00000444190,NM_001267617.1;ARPP21,missense_variant,p.Gly243Cys,ENST00000417925,NM_001267619.1;ARPP21,intron_variant,,ENST00000425289,;ARPP21,intron_variant,,ENST00000476327,;ARPP21,missense_variant,p.Gly106Cys,ENST00000446068,;ARPP21,non_coding_transcript_exon_variant,,ENST00000494494,;ARPP21,intron_variant,,ENST00000427590,; T ENST00000417925 Transcript missense_variant 941/3086 727/2442 243/813 G/C Ggt/Tgt 1 1 ARPP21 HGNC HGNC:16968 protein_coding YES CCDS58823.1 ENSP00000412326 Q9UBL0 UPI0000209B3D NM_001267619.1 tolerated(0.11) 9/19 PROSITE_profiles:PS51673,hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF14,Superfamily_domains:SSF82708 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 35707014 35707014 G T 1 0 0 0 0 1 0 0 0 1121 1000 35 2 2 ARPP21 3 35707014 Missense_Mutation SNP G C3N-00199_T 28245432 35707014 162588545 75 11119 EPHA6 0 . GRCh38 3 96987483 96987483 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.604C>A p.Leu202Ile p.L202I ENST00000389672 3/18 77 61 16 216 216 0 strelka-varscan-mutect EPHA6,missense_variant,p.Leu202Ile,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Leu202Ile,ENST00000470610,;EPHA6,missense_variant,p.Leu147Ile,ENST00000506569,NM_001278301.1; A ENST00000389672 Transcript missense_variant 642/3971 604/3393 202/1130 L/I Cta/Ata 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 96987483 96987483 C A 1 0 0 0 0 1 0 0 0 5018 564 20 2 2 EPHA6 3 96987483 Missense_Mutation SNP C C3N-00199_T 61280469 96987483 101308076 76 11120 SIDT1 0 . GRCh38 3 113607093 113607093 + Missense_Mutation SNP C C T rs774292168 C3N-00199_T C3N-00199_N C C c.1457C>T p.Ala486Val p.A486V ENST00000393830 15/26 122 97 25 194 194 0 strelka-varscan-mutect SIDT1,missense_variant,p.Ala486Val,ENST00000264852,NM_001322294.1,NM_001322299.1,NM_017699.2;SIDT1,missense_variant,p.Ala486Val,ENST00000393830,NM_001308350.1;SIDT1,intron_variant,,ENST00000463226,;SIDT1,non_coding_transcript_exon_variant,,ENST00000492863,;SIDT1,downstream_gene_variant,,ENST00000480746,;SIDT1,downstream_gene_variant,,ENST00000465803,;SIDT1,downstream_gene_variant,,ENST00000468728,; T ENST00000393830 Transcript missense_variant 1496/2572 1457/2499 486/832 A/V gCt/gTt rs774292168 1 1 SIDT1 HGNC HGNC:25967 protein_coding YES CCDS77790.1 ENSP00000377416 Q9NXL6 UPI0000DA58D9 NM_001308350.1 deleterious(0.01) 15/26 Pfam_domain:PF13965,hmmpanther:PTHR12185,hmmpanther:PTHR12185:SF15 MODERATE 1 SNV 1 1 PASS rs774292168 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 113607093 113607093 C T 1 0 0 0 0 1 0 0 0 14566 797 28 3 3 SIDT1 3 113607093 Missense_Mutation SNP C C3N-00199_T 16619610 113607093 84688466 77 11121 C3orf30 0 . GRCh38 3 119147083 119147083 + Silent SNP T T A novel C3N-00199_T C3N-00199_N T T c.894T>A p.= p.V298V ENST00000295622 1/3 120 97 23 254 254 0 strelka-varscan-mutect C3orf30,synonymous_variant,p.=,ENST00000295622,NM_152539.2;C3orf30,synonymous_variant,p.=,ENST00000460150,;C3orf30,synonymous_variant,p.=,ENST00000473121,;C3orf30,synonymous_variant,p.=,ENST00000492792,;IGSF11,upstream_gene_variant,,ENST00000425327,NM_152538.2;IGSF11,upstream_gene_variant,,ENST00000441144,;RP11-484M3.5,upstream_gene_variant,,ENST00000490594,;IGSF11,upstream_gene_variant,,ENST00000494802,;C3orf30,synonymous_variant,p.=,ENST00000494105,; A ENST00000295622 Transcript synonymous_variant 934/1814 894/1611 298/536 V gtT/gtA 1 1 C3orf30 HGNC HGNC:26553 protein_coding YES CCDS2984.1 ENSP00000295622 Q96M34 UPI000013E280 NM_152539.2 1/3 hmmpanther:PTHR21847,hmmpanther:PTHR21847:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 119147083 119147083 T A 1 0 0 0 0 0 0 0 1 2063 1799 63 4 4 C3orf30 3 119147083 Silent SNP T C3N-00199_T 5539990 119147083 79148476 78 11122 HCLS1 0 . GRCh38 3 121631920 121631920 + Missense_Mutation SNP C C T rs559028635 C3N-00199_T C3N-00199_N C C c.1387G>A p.Glu463Lys p.E463K ENST00000314583 14/14 303 259 44 307 307 0 strelka-varscan-mutect HCLS1,missense_variant,p.Glu463Lys,ENST00000314583,NM_005335.5;HCLS1,missense_variant,p.Glu426Lys,ENST00000428394,NM_001292041.1;FBXO40,downstream_gene_variant,,ENST00000338040,NM_016298.3;HCLS1,non_coding_transcript_exon_variant,,ENST00000473883,;HCLS1,downstream_gene_variant,,ENST00000495491,; T ENST00000314583 Transcript missense_variant 1479/2000 1387/1461 463/486 E/K Gag/Aag rs559028635,COSM5591232,COSM5591233 1 -1 HCLS1 HGNC HGNC:4844 protein_coding YES CCDS3003.1 ENSP00000320176 P14317 UPI000013F884 NM_005335.5 deleterious(0) 14/14 Gene3D:2.30.30.40,Pfam_domain:PF00018,Prints_domain:PR00452,Prints_domain:PR00499,PROSITE_profiles:PS50002,hmmpanther:PTHR10829,hmmpanther:PTHR10829:SF5,SMART_domains:SM00326,Superfamily_domains:SSF50044 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs559028635 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 121631920 121631920 C T 1 0 0 0 0 1 0 0 0 6882 893 31 1 1 HCLS1 3 121631920 Missense_Mutation SNP C C3N-00199_T 2484837 121631920 76663639 79 11123 ALG1L 0 . GRCh38 3 125931638 125931638 + Missense_Mutation SNP C C T rs766790697 C3N-00199_T C3N-00199_N C C c.335G>A p.Cys112Tyr p.C112Y ENST00000611639 4/6 356 284 72 359 359 0 strelka-varscan-mutect ALG1L,missense_variant,p.Cys92Tyr,ENST00000340333,NM_001015050.2;ALG1L,missense_variant,p.Cys112Tyr,ENST00000611639,NM_001195223.1;FAM86JP,downstream_gene_variant,,ENST00000485843,;FAM86JP,downstream_gene_variant,,ENST00000467239,;FAM86JP,downstream_gene_variant,,ENST00000486431,;FAM86JP,downstream_gene_variant,,ENST00000484500,; T ENST00000611639 Transcript missense_variant,splice_region_variant 335/701 335/624 112/207 C/Y tGt/tAt rs766790697 1 -1 ALG1L HGNC HGNC:33721 protein_coding YES CCDS74998.1 ENSP00000482705 A0A087WZJ8 UPI0000160B1B NM_001195223.1 deleterious(0) 4/6 hmmpanther:PTHR13036:SF1,hmmpanther:PTHR13036,Superfamily_domains:SSF53756 MODERATE SNV 3 1 PASS rs766790697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 125931638 125931638 C T 1 0 0 0 0 1 0 0 0 617 608 21 3 3 ALG1L 3 125931638 Missense_Mutation SNP C C3N-00199_T 4299718 125931638 72363921 80 11124 PLXNA1 0 . GRCh38 3 127022270 127022270 + Silent SNP C C G rs779534849 C3N-00199_T C3N-00199_N C C c.4224C>G p.= p.L1408L ENST00000393409 21/31 255 206 49 263 263 0 strelka-varscan-mutect PLXNA1,synonymous_variant,p.=,ENST00000393409,NM_032242.3;PLXNA1,upstream_gene_variant,,ENST00000503234,; G ENST00000393409 Transcript synonymous_variant 4224/9066 4224/5691 1408/1896 L ctC/ctG rs779534849 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 21/31 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS rs779534849 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 41 127022270 127022270 C G 1 0 0 0 0 0 0 0 1 12225 813 29 4 4 PLXNA1 3 127022270 Silent SNP C C3N-00199_T 1090632 127022270 71273289 81 11125 SI 0 . GRCh38 3 165049848 165049848 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1540C>A p.Gln514Lys p.Q514K ENST00000264382 14/48 59 50 9 137 137 0 strelka-varscan-mutect SI,missense_variant,p.Gln514Lys,ENST00000264382,NM_001041.3; T ENST00000264382 Transcript missense_variant 1603/6011 1540/5484 514/1827 Q/K Caa/Aaa 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.3) 14/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF01055 MODERATE 1 SNV 1 1 PASS rs1166926043 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 165049848 165049848 G T 1 0 0 0 0 1 0 0 0 14561 1299 45 2 2 SI 3 165049848 Missense_Mutation SNP G C3N-00199_T 38027578 165049848 33245711 82 11126 NAALADL2 0 . GRCh38 3 175627291 175627291 + Missense_Mutation SNP G G C rs761944758 C3N-00199_T C3N-00199_N G G c.1801G>C p.Gly601Arg p.G601R ENST00000454872 11/14 101 83 18 287 287 0 strelka-varscan-mutect NAALADL2,missense_variant,p.Gly601Arg,ENST00000454872,NM_207015.2;NAALADL2,splice_region_variant,,ENST00000489299,; C ENST00000454872 Transcript missense_variant,splice_region_variant 1929/9865 1801/2388 601/795 G/R Ggt/Cgt rs761944758 1 1 NAALADL2 HGNC HGNC:23219 protein_coding YES CCDS46960.1 ENSP00000404705 Q58DX5 UPI0000161608 NM_207015.2 tolerated(0.42) 11/14 hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs761944758 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 175627291 175627291 G C 1 0 0 0 0 1 0 0 0 10134 1246 43 4 4 NAALADL2 3 175627291 Missense_Mutation SNP G C3N-00199_T 10577443 175627291 22668268 83 11127 GNB4 0 . GRCh38 3 179413492 179413492 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.619T>A p.Ser207Thr p.S207T ENST00000232564 8/10 173 135 38 389 389 0 strelka-varscan-mutect GNB4,missense_variant,p.Ser207Thr,ENST00000232564,NM_021629.3;GNB4,missense_variant,p.Ser207Thr,ENST00000468623,;GNB4,missense_variant,p.Ser130Thr,ENST00000466899,;GNB4,downstream_gene_variant,,ENST00000497513,;GNB4,non_coding_transcript_exon_variant,,ENST00000465153,; T ENST00000232564 Transcript missense_variant 906/6434 619/1023 207/340 S/T Tct/Act 1 -1 GNB4 HGNC HGNC:20731 protein_coding YES CCDS3230.1 ENSP00000232564 Q9HAV0 UPI000012B21A NM_021629.3 tolerated(0.98) 8/10 Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,Prints_domain:PR00320,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,hmmpanther:PTHR19850:SF28,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 179413492 179413492 A T 1 0 0 0 0 1 0 0 0 6399 304 11 4 4 GNB4 3 179413492 Missense_Mutation SNP A C3N-00199_T 3786201 179413492 18882067 84 11128 RTP2 0 . GRCh38 3 187701973 187701973 + Silent SNP G G T rs764392777 C3N-00199_T C3N-00199_N G G c.156C>A p.= p.A52A ENST00000358241 1/2 52 45 7 46 46 0 strelka-varscan-mutect RTP2,synonymous_variant,p.=,ENST00000358241,NM_001004312.2;RP11-211G3.3,upstream_gene_variant,,ENST00000449623,;RP11-211G3.3,upstream_gene_variant,,ENST00000437407,; T ENST00000358241 Transcript synonymous_variant 585/1346 156/678 52/225 A gcC/gcA rs764392777 1 -1 RTP2 HGNC HGNC:32486 protein_coding YES CCDS33911.1 ENSP00000350976 Q5QGT7 UPI00001D801A NM_001004312.2 1/2 hmmpanther:PTHR14402:SF18,hmmpanther:PTHR14402,Pfam_domain:PF13695,SMART_domains:SM01328 LOW 1 SNV 1 1 PASS rs764392777 . 0 206 4 0 0 0 0 0 -16.78968 1 1 1 1 0 T 2 4 41 187701973 187701973 G T 1 0 0 0 0 0 0 0 1 13994 987 35 2 2 RTP2 3 187701973 Silent SNP G C3N-00199_T 8288481 187701973 10593586 85 11129 ADD1 0 . GRCh38 4 2894069 2894069 + Silent SNP C C T novel C3N-00199_T C3N-00199_N C C c.567C>T p.= p.Y189Y ENST00000264758 5/15 92 72 20 159 159 0 strelka-varscan-mutect ADD1,synonymous_variant,p.=,ENST00000355842,NM_001286645.1;ADD1,synonymous_variant,p.=,ENST00000398125,NM_176801.2;ADD1,synonymous_variant,p.=,ENST00000264758,NM_014189.3;ADD1,synonymous_variant,p.=,ENST00000398129,NM_001119.4;ADD1,synonymous_variant,p.=,ENST00000446856,;ADD1,synonymous_variant,p.=,ENST00000503455,;ADD1,synonymous_variant,p.=,ENST00000513328,NM_014190.3;ADD1,synonymous_variant,p.=,ENST00000398123,;ADD1,synonymous_variant,p.=,ENST00000508277,;ADD1,upstream_gene_variant,,ENST00000514940,;ADD1,3_prime_UTR_variant,,ENST00000510101,;ADD1,non_coding_transcript_exon_variant,,ENST00000506157,;ADD1,non_coding_transcript_exon_variant,,ENST00000508684,;ADD1,non_coding_transcript_exon_variant,,ENST00000503169,;ADD1,non_coding_transcript_exon_variant,,ENST00000509039,;ADD1,non_coding_transcript_exon_variant,,ENST00000534870,; T ENST00000264758 Transcript synonymous_variant 755/4045 567/2307 189/768 Y taC/taT 1 1 ADD1 HGNC HGNC:243 protein_coding YES CCDS3363.1 ENSP00000264758 P35611 UPI000002A35E NM_014189.3 5/15 hmmpanther:PTHR10672:SF4,hmmpanther:PTHR10672,Pfam_domain:PF00596,Gene3D:3.40.225.10,SMART_domains:SM01007,Superfamily_domains:SSF53639 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 2894069 2894069 C T 1 0 0 0 0 0 0 0 1 348 489 17 3 3 ADD1 4 2894069 Silent SNP C C3N-00199_T 2894069 187320486 86 11130 OTOP1 0 . GRCh38 4 4197624 4197624 + Missense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.1210A>T p.Ile404Phe p.I404F ENST00000296358 5/6 184 163 21 173 173 0 strelka-varscan-mutect OTOP1,missense_variant,p.Ile404Phe,ENST00000296358,NM_177998.1; A ENST00000296358 Transcript missense_variant 1235/1864 1210/1839 404/612 I/F Atc/Ttc 1 -1 OTOP1 HGNC HGNC:19656 protein_coding YES CCDS3372.1 ENSP00000296358 Q7RTM1 UPI0000186945 NM_177998.1 deleterious(0.01) 5/6 Pfam_domain:PF03189,hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF19 MODERATE 1 SNV 1 1 PASS rs888869662 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 4197624 4197624 T A 1 0 0 0 0 1 0 0 0 11373 1406 49 4 4 OTOP1 4 4197624 Missense_Mutation SNP T C3N-00199_T 1303555 4197624 186016931 87 11131 WFS1 0 . GRCh38 4 6301658 6301658 + Silent SNP G G T rs779337227 C3N-00199_T C3N-00199_N G G c.1863G>T p.= p.V621V ENST00000226760 8/8 257 230 27 218 218 0 strelka-varscan-mutect WFS1,synonymous_variant,p.=,ENST00000226760,NM_001145853.1,NM_006005.3;WFS1,synonymous_variant,p.=,ENST00000503569,;WFS1,downstream_gene_variant,,ENST00000506362,;WFS1,non_coding_transcript_exon_variant,,ENST00000507765,;WFS1,downstream_gene_variant,,ENST00000513395,; T ENST00000226760 Transcript synonymous_variant 2033/3640 1863/2673 621/890 V gtG/gtT rs779337227 1 1 WFS1 HGNC HGNC:12762 protein_coding YES CCDS3386.1 ENSP00000226760 O76024 A0A0S2Z4V6 UPI00000715C3 NM_001145853.1,NM_006005.3 8/8 Prints_domain:PR02061,hmmpanther:PTHR13098 LOW 1 SNV 1 1 PASS rs779337227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 6301658 6301658 G T 1 0 0 0 0 0 0 0 1 17917 1335 47 2 2 WFS1 4 6301658 Silent SNP G C3N-00199_T 2104034 6301658 183912897 88 11132 CCDC96 0 . GRCh38 4 7041603 7041603 + Missense_Mutation SNP C C T novel C3N-00199_T C3N-00199_N C C c.1336G>A p.Val446Met p.V446M ENST00000310085 1/1 196 157 39 243 242 1 strelka-varscan-mutect CCDC96,missense_variant,p.Val446Met,ENST00000310085,NM_153376.2;TADA2B,upstream_gene_variant,,ENST00000310074,NM_152293.2;TADA2B,upstream_gene_variant,,ENST00000512388,;TADA2B,upstream_gene_variant,,ENST00000506692,;RP11-367J11.2,intron_variant,,ENST00000500031,; T ENST00000310085 Transcript missense_variant 1337/2091 1336/1668 446/555 V/M Gtg/Atg 1 -1 CCDC96 HGNC HGNC:26900 protein_coding YES CCDS3395.1 ENSP00000309285 Q2M329 UPI00000705C9 NM_153376.2 deleterious(0) 1/1 hmmpanther:PTHR15654:SF1,hmmpanther:PTHR15654,Pfam_domain:PF13870 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 7041603 7041603 C T 1 0 0 0 0 1 0 0 0 2572 536 19 1 1 CCDC96 4 7041603 Missense_Mutation SNP C C3N-00199_T 739945 7041603 183172952 89 11133 ADGRL3 0 . GRCh38 4 61909667 61909667 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1791G>T p.Gln597His p.Q597H ENST00000514591 11/25 150 136 14 297 297 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Gln597His,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.Gln597His,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Gln665His,ENST00000509896,;ADGRL3,missense_variant,p.Gln665His,ENST00000511324,;ADGRL3,missense_variant,p.Gln665His,ENST00000508693,;ADGRL3,missense_variant,p.Gln665His,ENST00000507164,;ADGRL3,missense_variant,p.Gln665His,ENST00000506720,;ADGRL3,missense_variant,p.Gln665His,ENST00000506746,;ADGRL3,missense_variant,p.Gln665His,ENST00000507625,;ADGRL3,missense_variant,p.Gln597His,ENST00000506700,;ADGRL3,missense_variant,p.Gln597His,ENST00000504896,;ADGRL3,missense_variant,p.Gln597His,ENST00000514157,;ADGRL3,missense_variant,p.Gln597His,ENST00000508946,;ADGRL3,missense_variant,p.Gln597His,ENST00000514996,;ADGRL3,missense_variant,p.Gln68His,ENST00000502815,;Y_RNA,downstream_gene_variant,,ENST00000365299,; T ENST00000514591 Transcript missense_variant 2120/6297 1791/4410 597/1469 Q/H caG/caT 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0.01) 11/25 hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF16489 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 61909667 61909667 G T 1 0 0 0 0 1 0 0 0 377 962 34 2 2 ADGRL3 4 61909667 Missense_Mutation SNP G C3N-00199_T 54868064 61909667 128304888 90 11134 LIN54 0 . GRCh38 4 82984798 82984798 + Missense_Mutation SNP A A G novel C3N-00199_T C3N-00199_N A A c.47T>C p.Ile16Thr p.I16T ENST00000340417 2/13 57 53 4 161 161 0 varscan-mutect LIN54,missense_variant,p.Ile16Thr,ENST00000340417,NM_194282.3;LIN54,missense_variant,p.Ile16Thr,ENST00000506560,NM_001288996.1;LIN54,missense_variant,p.Ile16Thr,ENST00000505397,;LIN54,intron_variant,,ENST00000442461,NM_001115008.2;LIN54,intron_variant,,ENST00000446851,NM_001288997.1;LIN54,intron_variant,,ENST00000510557,NM_001115007.2;LIN54,intron_variant,,ENST00000509748,;LIN54,missense_variant,p.Ile16Thr,ENST00000508171,;LIN54,intron_variant,,ENST00000510877,; G ENST00000340417 Transcript missense_variant 425/6127 47/2250 16/749 I/T aTa/aCa 1 -1 LIN54 HGNC HGNC:25397 protein_coding YES CCDS3599.1 ENSP00000341947 Q6MZP7 A0A024RDD8 UPI00001D75DE NM_194282.3 deleterious_low_confidence(0) 2/13 hmmpanther:PTHR12446,hmmpanther:PTHR12446:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 82984798 82984798 A G 1 0 0 0 0 1 0 0 0 8717 449 16 5 5 LIN54 4 82984798 Missense_Mutation SNP A C3N-00199_T 21075131 82984798 107229757 91 11135 DSPP 0 . GRCh38 4 87613020 87613020 + Missense_Mutation SNP G G C rs764046745 C3N-00199_T C3N-00199_N G G c.834G>C p.Lys278Asn p.K278N ENST00000399271 4/5 157 143 14 470 470 0 strelka-varscan-mutect DSPP,missense_variant,p.Lys278Asn,ENST00000399271,NM_014208.3;DSPP,missense_variant,p.Lys278Asn,ENST00000282478,;RP11-742B18.1,intron_variant,,ENST00000506480,; C ENST00000399271 Transcript missense_variant 954/4331 834/3906 278/1301 K/N aaG/aaC rs764046745 1 1 DSPP HGNC HGNC:3054 protein_coding YES CCDS43248.1 ENSP00000382213 Q9NZW4 UPI00006BFF57 NM_014208.3 tolerated_low_confidence(0.29) 4/5 hmmpanther:PTHR32093,hmmpanther:PTHR32093:SF9 MODERATE SNV 5 1 PASS rs764046745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 87613020 87613020 G C 1 0 0 0 0 1 0 0 0 4603 991 35 4 4 DSPP 4 87613020 Missense_Mutation SNP G C3N-00199_T 4628222 87613020 102601535 92 11136 RP11-766F14.2 0 . GRCh38 4 99650585 99650585 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.4064G>T p.Arg1355Met p.R1355M ENST00000511828 1/2 166 149 17 255 255 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Arg1355Met,ENST00000511828,; A ENST00000511828 Transcript missense_variant 4064/10086 4064/5382 1355/1793 R/M aGg/aTg 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE deleterious(0.01) 1/2 MODERATE 1 SNV 1 1 PASS rs1225866777 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 99650585 99650585 C A 1 0 0 0 0 1 0 0 0 13762 681 24 2 2 RP11-766F14.2 4 99650585 Missense_Mutation SNP C C3N-00199_T 12037565 99650585 90563970 93 11137 EMCN 0 . GRCh38 4 100421308 100421308 + Missense_Mutation SNP T T A C3N-00199_T C3N-00199_N T T c.638A>T p.Tyr213Phe p.Y213F ENST00000296420 8/12 125 113 12 363 362 1 strelka-varscan-mutect EMCN,missense_variant,p.Tyr213Phe,ENST00000296420,NM_016242.3;EMCN,missense_variant,p.Tyr200Phe,ENST00000511970,NM_001159694.1;EMCN,missense_variant,p.Tyr162Phe,ENST00000502569,;EMCN,intron_variant,,ENST00000305864,;EMCN,intron_variant,,ENST00000506300,; A ENST00000296420 Transcript missense_variant 817/4037 638/786 213/261 Y/F tAc/tTc COSM4120995 1 -1 EMCN HGNC HGNC:16041 protein_coding YES CCDS3655.1 ENSP00000296420 Q9ULC0 Q4W5J1 UPI000003777D NM_016242.3 deleterious(0) 8/12 Pfam_domain:PF07010,hmmpanther:PTHR15869,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS rs1304158155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 100421308 100421308 T A 1 0 0 0 0 1 0 0 0 4930 1638 57 4 4 EMCN 4 100421308 Missense_Mutation SNP T C3N-00199_T 770723 100421308 89793247 94 11138 USP38 0 . GRCh38 4 143220368 143220368 + Missense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.3041T>A p.Phe1014Tyr p.F1014Y ENST00000307017 10/10 154 140 14 259 259 0 strelka-varscan-mutect USP38,missense_variant,p.Phe1014Tyr,ENST00000307017,NM_001290326.1,NM_032557.6;USP38,downstream_gene_variant,,ENST00000510377,NM_001290325.1;USP38,3_prime_UTR_variant,,ENST00000511739,; A ENST00000307017 Transcript missense_variant 3547/7009 3041/3129 1014/1042 F/Y tTt/tAt 1 1 USP38 HGNC HGNC:20067 protein_coding YES CCDS3758.1 ENSP00000303434 Q8NB14 UPI0000047AF9 NM_001290326.1,NM_032557.6 tolerated(0.14) 10/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 143220368 143220368 T A 1 0 0 0 0 1 0 0 0 17611 1841 64 4 4 USP38 4 143220368 Missense_Mutation SNP T C3N-00199_T 42799060 143220368 46994187 95 11139 GUCY1A3 0 . GRCh38 4 155708295 155708295 + Splice_Site SNP G G T novel C3N-00199_T C3N-00199_N G G c.376+1G>T p.X126_splice ENST00000296518 27 22 5 71 71 0 strelka-varscan-mutect GUCY1A3,splice_donor_variant,,ENST00000296518,;GUCY1A3,splice_donor_variant,,ENST00000393832,NM_001130685.2;GUCY1A3,splice_donor_variant,,ENST00000511108,NM_000856.5;GUCY1A3,splice_donor_variant,,ENST00000506455,NM_001130682.2;GUCY1A3,splice_donor_variant,,ENST00000513574,NM_001130684.2;GUCY1A3,splice_donor_variant,,ENST00000455639,NM_001256449.1,NM_001130683.3;GUCY1A3,splice_donor_variant,,ENST00000511507,NM_001130687.2;GUCY1A3,splice_donor_variant,,ENST00000621234,;GUCY1A3,splice_donor_variant,,ENST00000515602,;GUCY1A3,splice_donor_variant,,ENST00000443668,;GUCY1A3,splice_donor_variant,,ENST00000512983,;GUCY1A3,splice_donor_variant,,ENST00000515201,;GUCY1A3,intron_variant,,ENST00000509901,; T ENST00000296518 Transcript splice_donor_variant -/4400 376/2073 126/690 1 1 GUCY1A3 HGNC HGNC:4685 protein_coding YES CCDS34085.1 ENSP00000296518 Q02108 UPI0000033343 5/9 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 41 155708295 155708295 G T 1 0 0 0 0 0 0 1 0 6776 1275 44 2 2 GUCY1A3 4 155708295 Splice_Site SNP G C3N-00199_T 12487927 155708295 34506260 96 11140 SLC9A3 0 . GRCh38 5 476347 476347 + Missense_Mutation SNP G G T rs372661265 C3N-00199_T C3N-00199_N G G c.1922C>A p.Thr641Lys p.T641K ENST00000264938 13/17 277 223 54 276 276 0 strelka-varscan-mutect SLC9A3,missense_variant,p.Thr641Lys,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.Thr632Lys,ENST00000514375,NM_001284351.1;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000607286,;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000606319,;PP7080,upstream_gene_variant,,ENST00000342584,;PP7080,upstream_gene_variant,,ENST00000510604,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606288,;PP7080,upstream_gene_variant,,ENST00000510714,;PP7080,upstream_gene_variant,,ENST00000502511,;CTD-2228K2.7,upstream_gene_variant,,ENST00000607005,;EXOC3,downstream_gene_variant,,ENST00000509294,;EXOC3,downstream_gene_variant,,ENST00000515601,;EXOC3,downstream_gene_variant,,ENST00000503889,;CTD-2228K2.7,upstream_gene_variant,,ENST00000534918,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606074,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606107,;SLC9A3,downstream_gene_variant,,ENST00000507407,; T ENST00000264938 Transcript missense_variant 1932/2584 1922/2505 641/834 T/K aCg/aAg rs372661265 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 tolerated(0.27) 13/17 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840 MODERATE 1 SNV 1 1 PASS rs372661265 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 476347 476347 G T 1 0 0 0 0 1 0 0 0 14995 1145 40 1 1 SLC9A3 5 476347 Missense_Mutation SNP G C3N-00199_T 476347 181061912 97 11141 CDH12 0 . GRCh38 5 22078458 22078458 + Missense_Mutation SNP C C A C3N-00199_T C3N-00199_N C C c.219G>T p.Gln73His p.Q73H ENST00000382254 5/15 100 75 25 249 249 0 strelka-varscan-mutect CDH12,missense_variant,p.Gln73His,ENST00000382254,NM_004061.3;CDH12,missense_variant,p.Gln73His,ENST00000504376,;CDH12,missense_variant,p.Gln73His,ENST00000522262,;CDH12,downstream_gene_variant,,ENST00000518209,;CDH12,downstream_gene_variant,,ENST00000521745,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; A ENST00000382254 Transcript missense_variant 1306/4164 219/2385 73/794 Q/H caG/caT COSM737291 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 tolerated(0.18) 5/15 Pfam_domain:PF00028,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 22078458 22078458 C A 1 0 0 0 0 1 0 0 0 2801 564 20 2 2 CDH12 5 22078458 Missense_Mutation SNP C C3N-00199_T 21602111 22078458 159459801 98 11142 PRDM9 0 . GRCh38 5 23527649 23527649 + Missense_Mutation SNP A A T rs775988761 C3N-00199_T C3N-00199_N A A c.2561A>T p.His854Leu p.H854L ENST00000296682 11/11 455 376 79 515 515 0 strelka-varscan-mutect PRDM9,missense_variant,p.His854Leu,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; T ENST00000296682 Transcript missense_variant 2743/3691 2561/2685 854/894 H/L cAc/cTc rs775988761 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 11/11 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs775988761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 23527649 23527649 A T 1 0 0 0 0 1 0 0 0 12595 159 6 4 4 PRDM9 5 23527649 Missense_Mutation SNP A C3N-00199_T 1449191 23527649 158010610 99 11143 ADAMTS6 0 . GRCh38 5 65300021 65300021 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.1334C>T p.Ser445Phe p.S445F ENST00000381055 10/25 64 58 6 182 182 0 strelka-varscan-mutect ADAMTS6,missense_variant,p.Ser445Phe,ENST00000381055,NM_197941.2;ADAMTS6,3_prime_UTR_variant,,ENST00000381052,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000470597,;ADAMTS6,non_coding_transcript_exon_variant,,ENST00000464680,; A ENST00000381055 Transcript missense_variant 2191/7311 1334/3354 445/1117 S/F tCt/tTt 1 -1 ADAMTS6 HGNC HGNC:222 protein_coding YES CCDS3983.2 ENSP00000370443 Q9UKP5 UPI000050D3F1 NM_197941.2 deleterious(0.01) 10/25 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF27,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 65300021 65300021 G A 1 0 0 0 0 1 0 0 0 314 942 33 3 3 ADAMTS6 5 65300021 Missense_Mutation SNP G C3N-00199_T 41772372 65300021 116238238 100 11144 MAP1B 0 . GRCh38 5 72199678 72199678 + Missense_Mutation SNP A A G novel C3N-00199_T C3N-00199_N A A c.6323A>G p.Glu2108Gly p.E2108G ENST00000296755 5/7 80 73 7 175 175 0 strelka-varscan-mutect MAP1B,missense_variant,p.Glu2108Gly,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; G ENST00000296755 Transcript missense_variant 6621/12036 6323/7407 2108/2468 E/G gAg/gGg 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 deleterious(0.02) 5/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 72199678 72199678 A G 1 0 0 0 0 1 0 0 0 9151 304 11 5 5 MAP1B 5 72199678 Missense_Mutation SNP A C3N-00199_T 6899657 72199678 109338581 101 11145 RAD50 0 . GRCh38 5 132604808 132604812 + Frame_Shift_Del DEL TCTAG TCTAG - novel C3N-00199_T C3N-00199_N TCTAG TCTAG c.2528_2532delCTAGT p.Ser843Ter p.S843* ENST00000378823 16/25 65 50 15 218 218 0 sindel-varindel-pindel RAD50,frameshift_variant,p.Ser843Ter,ENST00000378823,NM_005732.3;RAD50,downstream_gene_variant,,ENST00000496204,;RAD50,splice_region_variant,,ENST00000533482,;RAD50,splice_region_variant,,ENST00000423956,; - ENST00000378823 Transcript frameshift_variant,splice_region_variant 2914-2918/8306 2527-2531/3939 843-844/1312 SS/X TCTAGt/t 1 1 RAD50 HGNC HGNC:9816 protein_coding YES CCDS34233.1 ENSP00000368100 Q92878 UPI000006E9ED NM_005732.3 16/25 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18867,hmmpanther:PTHR18867:SF12,TIGRFAM_domain:TIGR00606 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 41 132604808 132604808 TCTAG - 1 0 1 0 1 0 0 0 0 13145 1797 62 0 0 RAD50 5 132604808 Frame_Shift_Del DEL TCTAG C3N-00199_T 60405130 132604808 48933451 102 11146 SPATA24 0 . GRCh38 5 139401788 139401788 + Missense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.352A>T p.Ser118Cys p.S118C ENST00000450845 4/6 197 167 30 184 184 0 strelka-varscan-mutect SPATA24,missense_variant,p.Ser118Cys,ENST00000302091,;SPATA24,missense_variant,p.Ser118Cys,ENST00000450845,NM_194296.1;SPATA24,missense_variant,p.Ser118Cys,ENST00000451821,;SPATA24,missense_variant,p.Ser96Cys,ENST00000509959,;SPATA24,missense_variant,p.Ser115Cys,ENST00000507779,;SPATA24,missense_variant,p.Ser66Cys,ENST00000512761,;SPATA24,missense_variant,p.Ser115Cys,ENST00000514983,; A ENST00000450845 Transcript missense_variant 360/659 352/618 118/205 S/C Agc/Tgc 1 -1 SPATA24 HGNC HGNC:27322 protein_coding YES CCDS47274.1 ENSP00000414920 Q86W54 UPI0000198A05 NM_194296.1 deleterious(0.01) 4/6 hmmpanther:PTHR35155,Pfam_domain:PF15175 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 139401788 139401788 T A 1 0 0 0 0 1 0 0 0 15339 1580 55 4 4 SPATA24 5 139401788 Missense_Mutation SNP T C3N-00199_T 6796980 139401788 42136471 103 11147 PCDHA4 0 . GRCh38 5 140809038 140809038 + Silent SNP C C T rs370669259 C3N-00199_T C3N-00199_N C C c.1851C>T p.= p.G617G ENST00000530339 1/4 449 369 80 395 395 0 strelka-varscan-mutect PCDHA4,synonymous_variant,p.=,ENST00000618834,NM_031500.2;PCDHA4,synonymous_variant,p.=,ENST00000530339,NM_018907.3;PCDHA4,synonymous_variant,p.=,ENST00000512229,;PCDHA4,synonymous_variant,p.=,ENST00000378125,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,downstream_gene_variant,,ENST00000532566,NM_031497.1;PCDHA2,downstream_gene_variant,,ENST00000520672,NM_031496.1;AC005609.16,intron_variant,,ENST00000624712,; T ENST00000530339 Transcript synonymous_variant 1851/5251 1851/2844 617/947 G ggC/ggT rs370669259,COSM1061952,COSM1061953 1 1 PCDHA4 HGNC HGNC:8670 protein_coding YES CCDS54916.1 ENSP00000435300 Q9UN74 UPI00001273CC NM_018907.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs370669259 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 140809038 140809038 C T 1 0 0 0 0 0 0 0 1 11613 755 27 1 1 PCDHA4 5 140809038 Silent SNP C C3N-00199_T 1407250 140809038 40729221 104 11148 PCDHA6 0 . GRCh38 5 140829250 140829250 + Missense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.1159T>A p.Cys387Ser p.C387S ENST00000529310 1/4 401 353 48 477 477 0 strelka-varscan-mutect PCDHA6,missense_variant,p.Cys387Ser,ENST00000529310,NM_018909.3;PCDHA6,missense_variant,p.Cys387Ser,ENST00000378126,NM_031848.2;PCDHA6,missense_variant,p.Cys387Ser,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA5,downstream_gene_variant,,ENST00000614258,NM_031501.1;PCDHA7,upstream_gene_variant,,ENST00000356878,NM_031852.1; A ENST00000529310 Transcript missense_variant 1273/5374 1159/2853 387/950 C/S Tgc/Agc 1 1 PCDHA6 HGNC HGNC:8672 protein_coding YES CCDS47281.1 ENSP00000433378 Q9UN73 UPI00001273CE NM_018909.3 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF131,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 140829250 140829250 T A 1 0 0 0 0 1 0 0 0 11615 1580 55 4 4 PCDHA6 5 140829250 Missense_Mutation SNP T C3N-00199_T 20212 140829250 40709009 105 11149 PCDHA10 0 . GRCh38 5 140856191 140856191 + Missense_Mutation SNP C C T rs773891459 C3N-00199_T C3N-00199_N C C c.143C>T p.Ala48Val p.A48V ENST00000307360 1/4 702 618 84 527 526 1 strelka-varscan-mutect PCDHA10,missense_variant,p.Ala48Val,ENST00000562220,NM_031859.2;PCDHA10,missense_variant,p.Ala48Val,ENST00000307360,NM_018901.3;PCDHA10,missense_variant,p.Ala48Val,ENST00000506939,NM_031860.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4; T ENST00000307360 Transcript missense_variant 143/5254 143/2847 48/948 A/V gCg/gTg rs773891459,COSM3409837,COSM3409838,COSM3409839 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 deleterious_low_confidence(0.01) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs773891459 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 140856191 140856191 C T 1 0 0 0 0 1 0 0 0 11607 768 27 1 1 PCDHA10 5 140856191 Missense_Mutation SNP C C3N-00199_T 26941 140856191 40682068 106 11150 PCDHB6 0 . GRCh38 5 141150858 141150858 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.601C>A p.Arg201Ser p.R201S ENST00000231136 1/1 270 203 67 221 221 0 strelka-varscan-mutect PCDHB6,missense_variant,p.Arg201Ser,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Arg65Ser,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; A ENST00000231136 Transcript missense_variant 837/3266 601/2385 201/794 R/S Cgc/Agc 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 141150858 141150858 C A 1 0 0 0 0 1 0 0 0 11633 652 23 1 1 PCDHB6 5 141150858 Missense_Mutation SNP C C3N-00199_T 294667 141150858 40387401 107 11151 PCDHB9 0 . GRCh38 5 141188287 141188287 + Silent SNP C C T rs782033630 C3N-00199_T C3N-00199_N C C c.969C>T p.= p.D323D ENST00000316105 1/1 87 78 9 249 248 1 strelka-varscan-mutect PCDHB9,synonymous_variant,p.=,ENST00000316105,NM_019119.4;PCDHB9,5_prime_UTR_variant,,ENST00000624909,;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,intron_variant,,ENST00000623266,;CH17-140K24.5,intron_variant,,ENST00000623407,; T ENST00000316105 Transcript synonymous_variant 1161/4415 969/2394 323/797 D gaC/gaT rs782033630 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW SNV 1 PASS rs782033630 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 141188287 141188287 C T 1 0 0 0 0 0 0 0 1 11636 535 19 1 1 PCDHB9 5 141188287 Silent SNP C C3N-00199_T 37429 141188287 40349972 108 11152 PCDHGA2 0 . GRCh38 5 141340457 141340457 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1486G>T p.Val496Phe p.V496F ENST00000394576 1/4 224 155 69 261 261 0 strelka-varscan-mutect PCDHGA2,missense_variant,p.Val496Phe,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Val496Phe,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; T ENST00000394576 Transcript missense_variant 1486/4605 1486/2799 496/932 V/F Gtt/Ttt 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 tolerated_low_confidence(0.18) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 141340457 141340457 G T 1 0 0 0 0 1 0 0 0 11641 1377 48 2 2 PCDHGA2 5 141340457 Missense_Mutation SNP G C3N-00199_T 152170 141340457 40197802 109 11153 PCDHGA4 0 . GRCh38 5 141356726 141356726 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1619C>A p.Ser540Tyr p.S540Y ENST00000571252 1/4 221 191 30 367 367 0 strelka-varscan-mutect PCDHGA4,missense_variant,p.Ser540Tyr,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Ser540Tyr,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000571252 Transcript missense_variant 1702/4778 1619/2889 540/962 S/Y tCc/tAc 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1209862693 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 141356726 141356726 C A 1 0 0 0 0 1 0 0 0 11643 855 30 2 2 PCDHGA4 5 141356726 Missense_Mutation SNP C C3N-00199_T 16269 141356726 40181533 110 11154 GABRA6 0 . GRCh38 5 161689044 161689044 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.321G>C p.Met107Ile p.M107I ENST00000274545 4/9 233 181 52 497 497 0 strelka-varscan-mutect GABRA6,missense_variant,p.Met97Ile,ENST00000523217,;GABRA6,missense_variant,p.Met107Ile,ENST00000274545,NM_000811.2;GABRA6,missense_variant,p.Met47Ile,ENST00000520000,;GABRA6,missense_variant,p.Met2Ile,ENST00000523691,;GABRA6,missense_variant,p.Met54Ile,ENST00000517823,;RP11-348M17.2,intron_variant,,ENST00000521984,;GABRA6,downstream_gene_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,non_coding_transcript_exon_variant,,ENST00000524220,;GABRA6,upstream_gene_variant,,ENST00000521520,; C ENST00000274545 Transcript missense_variant 754/2128 321/1362 107/453 M/I atG/atC 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 deleterious(0) 4/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 161689044 161689044 G C 1 0 0 0 0 1 0 0 0 6036 1348 47 4 4 GABRA6 5 161689044 Missense_Mutation SNP G C3N-00199_T 20332318 161689044 19849215 111 11155 GABRA1 0 . GRCh38 5 161873185 161873185 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.324G>A p.Met108Ile p.M108I ENST00000393943 5/10 245 182 63 401 401 0 strelka-varscan-mutect GABRA1,missense_variant,p.Met108Ile,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Met108Ile,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Met123Ile,ENST00000638159,;GABRA1,missense_variant,p.Met108Ile,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Met108Ile,ENST00000638112,;GABRA1,missense_variant,p.Met108Ile,ENST00000636573,;GABRA1,missense_variant,p.Met108Ile,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Met108Ile,ENST00000637827,;GABRA1,missense_variant,p.Met108Ile,ENST00000635880,;GABRA1,missense_variant,p.Met108Ile,ENST00000634335,;GABRA1,missense_variant,p.Met108Ile,ENST00000519621,;GABRA1,downstream_gene_variant,,ENST00000522651,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,non_coding_transcript_exon_variant,,ENST00000635916,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,; A ENST00000393943 Transcript missense_variant 1107/4686 324/1371 108/456 M/I atG/atA 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 tolerated(0.5) 5/10 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 161873185 161873185 G A 1 0 0 0 0 1 0 0 0 6031 1290 45 3 3 GABRA1 5 161873185 Missense_Mutation SNP G C3N-00199_T 184141 161873185 19665074 112 11156 TENM2 0 . GRCh38 5 167375331 167375331 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.360G>T p.Glu120Asp p.E120D ENST00000518659 2/29 587 386 201 420 419 1 strelka-varscan-mutect TENM2,missense_variant,p.Glu120Asp,ENST00000518659,NM_001122679.1; T ENST00000518659 Transcript missense_variant 399/8550 360/8325 120/2774 E/D gaG/gaT COSM5424874,COSM5424875 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 tolerated_low_confidence(0.45) 2/29 PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Pfam_domain:PF06484 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs918452735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 167375331 167375331 G T 1 0 0 0 0 1 0 0 0 16172 991 35 2 2 TENM2 5 167375331 Missense_Mutation SNP G C3N-00199_T 5502146 167375331 14162928 113 11157 ADAMTS2 0 . GRCh38 5 179154074 179154074 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1357C>A p.Gln453Lys p.Q453K ENST00000251582 8/22 465 318 147 343 342 1 strelka-varscan-mutect ADAMTS2,missense_variant,p.Gln453Lys,ENST00000251582,NM_014244.4;ADAMTS2,missense_variant,p.Gln453Lys,ENST00000274609,NM_021599.2; T ENST00000251582 Transcript missense_variant 1459/6754 1357/3636 453/1211 Q/K Cag/Aag 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 tolerated(1) 8/22 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 179154074 179154074 G T 1 0 0 0 0 1 0 0 0 309 1357 47 2 2 ADAMTS2 5 179154074 Missense_Mutation SNP G C3N-00199_T 11778743 179154074 2384185 114 11158 TNXB 0 . GRCh38 6 32042607 32042607 + Splice_Site SNP C C A novel C3N-00199_T C3N-00199_N C C c.1346-1G>T p.X449_splice ENST00000451343 518 416 102 435 435 0 strelka-varscan-mutect TNXB,splice_acceptor_variant,,ENST00000375244,NM_019105.6;TNXB,splice_acceptor_variant,,ENST00000611016,;TNXB,splice_acceptor_variant,,ENST00000451343,NM_032470.3;CYP21A2,downstream_gene_variant,,ENST00000418967,NM_000500.7;CYP21A2,downstream_gene_variant,,ENST00000435122,NM_001128590.3;CYP21A2,downstream_gene_variant,,ENST00000478281,;CYP21A2,downstream_gene_variant,,ENST00000471671,;TNXB,splice_acceptor_variant,,ENST00000490077,;TNXB,splice_acceptor_variant,,ENST00000498094,;CYP21A2,downstream_gene_variant,,ENST00000479074,;CYP21A2,downstream_gene_variant,,ENST00000479730,;CYP21A2,downstream_gene_variant,,ENST00000486063,;CYP21A2,downstream_gene_variant,,ENST00000483041,;CYP21A2,downstream_gene_variant,,ENST00000466779,;CYP21A2,downstream_gene_variant,,ENST00000466879,;CYP21A2,downstream_gene_variant,,ENST00000480027,;CYP21A2,downstream_gene_variant,,ENST00000488465,;CYP21A2,downstream_gene_variant,,ENST00000464325,;CYP21A2,downstream_gene_variant,,ENST00000469053,;CYP21A2,downstream_gene_variant,,ENST00000462278,; A ENST00000451343 Transcript splice_acceptor_variant -/3125 1346/2022 449/673 1 -1 TNXB HGNC HGNC:11976 protein_coding YES CCDS4736.1 ENSP00000407685 P22105 UPI0000000E8E NM_032470.3 8/12 HIGH 1 SNV 1 1 PASS rs1194542776 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 41 32042607 32042607 C A 1 0 0 0 0 0 0 1 0 16820 695 24 2 2 TNXB 6 32042607 Splice_Site SNP C C3N-00199_T 32042607 138763372 115 11159 FAM83B 0 . GRCh38 6 54870595 54870595 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.349G>T p.Gly117Trp p.G117W ENST00000306858 2/5 138 107 31 287 287 0 strelka-varscan-mutect FAM83B,missense_variant,p.Gly117Trp,ENST00000306858,NM_001010872.2; T ENST00000306858 Transcript missense_variant 465/3167 349/3036 117/1011 G/W Ggg/Tgg 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 deleterious(0.01) 2/5 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF4,Pfam_domain:PF07894 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 54870595 54870595 G T 1 0 0 0 0 1 0 0 0 5492 1000 35 2 2 FAM83B 6 54870595 Missense_Mutation SNP G C3N-00199_T 22827988 54870595 115935384 116 11160 GFRAL 0 . GRCh38 6 55327577 55327577 + Splice_Site SNP G G A novel C3N-00199_T C3N-00199_N G G c.22+1G>A p.X8_splice ENST00000340465 66 50 16 168 168 0 strelka-varscan-mutect GFRAL,splice_donor_variant,,ENST00000340465,NM_207410.2; A ENST00000340465 Transcript splice_donor_variant -/1911 22/1185 8/394 1 1 GFRAL HGNC HGNC:32789 protein_coding YES CCDS4957.1 ENSP00000343636 Q6UXV0 UPI000023780D NM_207410.2 1/8 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 41 55327577 55327577 G A 1 0 0 0 0 0 0 1 0 6225 1275 44 3 3 GFRAL 6 55327577 Splice_Site SNP G C3N-00199_T 456982 55327577 115478402 117 11161 BACH2 0 . GRCh38 6 89951592 89951592 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.514G>T p.Asp172Tyr p.D172Y ENST00000257749 7/9 483 389 94 433 430 3 strelka-varscan-mutect BACH2,missense_variant,p.Asp172Tyr,ENST00000257749,NM_021813.3;BACH2,missense_variant,p.Asp172Tyr,ENST00000537989,NM_001170794.1;BACH2,missense_variant,p.Asp172Tyr,ENST00000343122,;RP3-512E2.2,intron_variant,,ENST00000445838,;RP3-512E2.2,intron_variant,,ENST00000413986,; A ENST00000257749 Transcript missense_variant 1222/9113 514/2526 172/841 D/Y Gat/Tat 1 -1 BACH2 HGNC HGNC:14078 protein_coding YES CCDS5026.1 ENSP00000257749 Q9BYV9 UPI000004F8AD NM_021813.3 deleterious(0.01) 7/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 89951592 89951592 C A 1 0 0 0 0 1 0 0 0 1442 855 30 2 2 BACH2 6 89951592 Missense_Mutation SNP C C3N-00199_T 34624015 89951592 80854387 118 11162 UFL1 0 . GRCh38 6 96549484 96549484 + Silent SNP G G T rs139773222 C3N-00199_T C3N-00199_N G G c.1593G>T p.= p.T531T ENST00000369278 14/19 45 32 13 144 144 0 strelka-varscan-mutect UFL1,synonymous_variant,p.=,ENST00000369278,NM_015323.4; T ENST00000369278 Transcript synonymous_variant 1659/4224 1593/2385 531/794 T acG/acT rs139773222 1 1 UFL1 HGNC HGNC:23039 protein_coding YES CCDS5034.1 ENSP00000358283 O94874 UPI0000072D61 NM_015323.4 14/19 hmmpanther:PTHR31057,hmmpanther:PTHR31057:SF0 LOW 1 SNV 1 1 PASS rs139773222 . 0 196 14 0 0 0 0 0 -20 0.9999217 1 1 1 0 T 2 4 41 96549484 96549484 G T 1 0 0 0 0 0 0 0 1 17460 1103 39 1 1 UFL1 6 96549484 Silent SNP G C3N-00199_T 6597892 96549484 74256495 119 11163 UNC93A 0 . GRCh38 6 167294570 167294570 + Silent SNP T T C novel C3N-00199_T C3N-00199_N T T c.141T>C p.= p.Y47Y ENST00000230256 2/8 322 264 58 245 245 0 strelka-varscan-mutect UNC93A,synonymous_variant,p.=,ENST00000230256,NM_018974.3;UNC93A,synonymous_variant,p.=,ENST00000366829,NM_001143947.1;UNC93A,synonymous_variant,p.=,ENST00000503433,;UNC93A,non_coding_transcript_exon_variant,,ENST00000366830,;UNC93A,non_coding_transcript_exon_variant,,ENST00000504706,; C ENST00000230256 Transcript synonymous_variant 316/2116 141/1374 47/457 Y taT/taC 1 1 UNC93A HGNC HGNC:12570 protein_coding YES CCDS5300.1 ENSP00000230256 Q86WB7 UPI0000062351 NM_018974.3 2/8 Gene3D:1.20.1250.20,Pfam_domain:PF05978,hmmpanther:PTHR19444,hmmpanther:PTHR19444:SF14,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 41 167294570 167294570 T C 1 0 0 0 0 0 0 0 1 17522 1471 51 5 5 UNC93A 6 167294570 Silent SNP T C3N-00199_T 70745086 167294570 3511409 120 11164 ELFN1 0 . GRCh38 7 1746052 1746052 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1456G>T p.Gly486Cys p.G486C ENST00000424383 3/3 179 98 81 129 129 0 strelka-varscan-mutect ELFN1,missense_variant,p.Gly486Cys,ENST00000424383,;ELFN1,missense_variant,p.Gly486Cys,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; T ENST00000424383 Transcript missense_variant 1943/3845 1456/2487 486/828 G/C Ggc/Tgc 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 deleterious(0.01) 3/3 hmmpanther:PTHR24367:SF34,hmmpanther:PTHR24367 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 1746052 1746052 G T 1 0 0 0 0 1 0 0 0 4891 1232 43 2 2 ELFN1 7 1746052 Missense_Mutation SNP G C3N-00199_T 1746052 157599921 121 11165 HOXA2 0 . GRCh38 7 27101235 27101235 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.622C>A p.Gln208Lys p.Q208K ENST00000222718 2/2 577 381 196 678 678 0 strelka-varscan-mutect HOXA2,missense_variant,p.Gln208Lys,ENST00000222718,NM_006735.3;HOXA3,downstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA3,downstream_gene_variant,,ENST00000396352,NM_030661.4;HOTAIRM1,downstream_gene_variant,,ENST00000428939,;HOTAIRM1,downstream_gene_variant,,ENST00000429611,;HOTAIRM1,downstream_gene_variant,,ENST00000434063,;HOTAIRM1,downstream_gene_variant,,ENST00000593300,;HOTAIRM1,downstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,downstream_gene_variant,,ENST00000616712,;HOTAIRM1,downstream_gene_variant,,ENST00000495032,;HOTAIRM1_5,downstream_gene_variant,,ENST00000619311,;HOTAIRM1_1,downstream_gene_variant,,ENST00000622675,;HOTAIRM1_4,downstream_gene_variant,,ENST00000617934,;HOTAIRM1_3,downstream_gene_variant,,ENST00000619974,;HOXA2,non_coding_transcript_exon_variant,,ENST00000612779,; T ENST00000222718 Transcript missense_variant 933/1814 622/1131 208/376 Q/K Caa/Aaa 1 -1 HOXA2 HGNC HGNC:5103 protein_coding YES CCDS5403.1 ENSP00000222718 O43364 UPI0000049C49 NM_006735.3 tolerated(0.93) 2/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF179 MODERATE 1 SNV 1 1 PASS rs760839440 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 27101235 27101235 G T 1 0 0 0 0 1 0 0 0 7186 1357 47 2 2 HOXA2 7 27101235 Missense_Mutation SNP G C3N-00199_T 25355183 27101235 132244738 122 11166 PPP1R17 0 . GRCh38 7 31697107 31697107 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.378C>A p.= p.P126P ENST00000342032 4/5 85 54 31 122 122 0 strelka-varscan-mutect PPP1R17,synonymous_variant,p.=,ENST00000342032,NM_006658.4;PPP1R17,synonymous_variant,p.=,ENST00000409146,NM_001145123.2;PPP1R17,non_coding_transcript_exon_variant,,ENST00000498609,; A ENST00000342032 Transcript synonymous_variant 1006/2268 378/468 126/155 P ccC/ccA 1 1 PPP1R17 HGNC HGNC:16973 protein_coding YES CCDS5436.1 ENSP00000340125 O96001 A0A090N8N7 UPI000006D182 NM_006658.4 4/5 hmmpanther:PTHR15387,hmmpanther:PTHR15387:SF0 LOW 1 SNV 1 1 PASS rs959754348 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 31697107 31697107 C A 1 0 0 0 0 0 0 0 1 12477 668 24 2 2 PPP1R17 7 31697107 Silent SNP C C3N-00199_T 4595872 31697107 127648866 123 11167 CAMK2B 0 . GRCh38 7 44220653 44220653 + Silent SNP A A T novel C3N-00199_T C3N-00199_N A A c.1731T>A p.= p.V577V ENST00000395749 22/24 230 184 46 174 174 0 strelka-varscan-mutect CAMK2B,synonymous_variant,p.=,ENST00000395749,NM_001220.4;CAMK2B,synonymous_variant,p.=,ENST00000457475,NM_172079.2;CAMK2B,synonymous_variant,p.=,ENST00000350811,NM_001293170.1;CAMK2B,synonymous_variant,p.=,ENST00000440254,NM_172078.2;CAMK2B,synonymous_variant,p.=,ENST00000358707,NM_172081.2;CAMK2B,synonymous_variant,p.=,ENST00000258682,NM_172080.2;CAMK2B,synonymous_variant,p.=,ENST00000353625,NM_172083.2;CAMK2B,synonymous_variant,p.=,ENST00000395747,;CAMK2B,synonymous_variant,p.=,ENST00000346990,NM_172084.2;CAMK2B,synonymous_variant,p.=,ENST00000425809,;CAMK2B,intron_variant,,ENST00000347193,NM_172082.2;CAMK2B,non_coding_transcript_exon_variant,,ENST00000489429,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000497584,;CAMK2B,3_prime_UTR_variant,,ENST00000523845,;CAMK2B,3_prime_UTR_variant,,ENST00000353185,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000466584,; T ENST00000395749 Transcript synonymous_variant 1808/4447 1731/2001 577/666 V gtT/gtA 1 -1 CAMK2B HGNC HGNC:1461 protein_coding YES CCDS5483.1 ENSP00000379098 Q13554 A4D2J9 UPI0000164A3E NM_001220.4 22/24 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF107,Gene3D:3.10.450.50,Pfam_domain:PF08332,Superfamily_domains:SSF54427 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 44220653 44220653 A T 1 0 0 0 0 0 0 0 1 2291 117 5 4 4 CAMK2B 7 44220653 Silent SNP A C3N-00199_T 12523546 44220653 115125320 124 11168 ZPBP 0 . GRCh38 7 49983465 49983465 + Missense_Mutation SNP G G A rs778999986 C3N-00199_T C3N-00199_N G G c.838C>T p.Arg280Cys p.R280C ENST00000046087 7/8 130 123 7 256 256 0 strelka-mutect ZPBP,missense_variant,p.Arg280Cys,ENST00000046087,NM_007009.2;ZPBP,missense_variant,p.Arg279Cys,ENST00000419417,NM_001159878.1;ZPBP,non_coding_transcript_exon_variant,,ENST00000491129,; A ENST00000046087 Transcript missense_variant 908/1213 838/1056 280/351 R/C Cgt/Tgt rs778999986,COSM1313157 1 -1 ZPBP HGNC HGNC:15662 protein_coding YES CCDS5509.1 ENSP00000046087 Q9BS86 UPI0000073BD0 NM_007009.2 tolerated(0.05) 7/8 Pfam_domain:PF07354,hmmpanther:PTHR15443,hmmpanther:PTHR15443:SF5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778999986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 49983465 49983465 G A 1 0 0 0 0 1 0 0 0 18811 1145 40 1 1 ZPBP 7 49983465 Missense_Mutation SNP G C3N-00199_T 5762812 49983465 109362508 125 11169 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-00199_T C3N-00199_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 872 405 467 537 537 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-00199_T 5208357 55191822 104154151 126 11170 SEPT14 0 . GRCh38 7 55834442 55834442 + Missense_Mutation SNP C C T novel C3N-00199_T C3N-00199_N C C c.703G>A p.Ala235Thr p.A235T ENST00000388975 6/10 74 58 16 94 94 0 varscan-mutect SEPT14,missense_variant,p.Ala235Thr,ENST00000388975,NM_207366.2; T ENST00000388975 Transcript missense_variant 820/3785 703/1299 235/432 A/T Gcg/Acg 1 -1 SEPT14 HGNC HGNC:33280 protein_coding YES CCDS5519.2 ENSP00000373627 Q6ZU15 UPI0000E0AB69 NM_207366.2 tolerated(0.2) 6/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884:SF51,hmmpanther:PTHR18884,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 55834442 55834442 C T 1 0 0 0 0 1 0 0 0 14339 797 28 3 3 SEPT14 7 55834442 Missense_Mutation SNP C C3N-00199_T 642620 55834442 103511531 127 11171 SLC25A13 0 . GRCh38 7 96234903 96234903 + Missense_Mutation SNP T T C novel C3N-00199_T C3N-00199_N T T c.227A>G p.Gln76Arg p.Q76R ENST00000416240 4/18 97 80 17 270 270 0 strelka-varscan-mutect SLC25A13,missense_variant,p.Gln76Arg,ENST00000416240,NM_001160210.1;SLC25A13,missense_variant,p.Gln76Arg,ENST00000265631,NM_014251.2;SLC25A13,intron_variant,,ENST00000472162,; C ENST00000416240 Transcript missense_variant 418/3192 227/2031 76/676 Q/R cAa/cGa 1 -1 SLC25A13 HGNC HGNC:10983 protein_coding YES CCDS55130.1 ENSP00000400101 Q9UJS0 UPI0000001663 NM_001160210.1 tolerated(0.35) 4/18 Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 96234903 96234903 T C 1 0 0 0 0 1 0 0 0 14740 1812 63 5 5 SLC25A13 7 96234903 Missense_Mutation SNP T C3N-00199_T 40400461 96234903 63111070 128 11172 RELN 0 . GRCh38 7 103511005 103511005 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.8120T>A p.Val2707Glu p.V2707E ENST00000428762 51/65 194 164 30 321 321 0 strelka-varscan-mutect RELN,missense_variant,p.Val2707Glu,ENST00000424685,;RELN,missense_variant,p.Val2707Glu,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Val2707Glu,ENST00000343529,NM_173054.2;CTB-107G13.1,intron_variant,,ENST00000422488,; T ENST00000428762 Transcript missense_variant,splice_region_variant 8280/11571 8120/10383 2707/3460 V/E gTg/gAg 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0.01) 51/65 hmmpanther:PTHR11841 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 103511005 103511005 A T 1 0 0 0 0 1 0 0 0 13390 173 6 4 4 RELN 7 103511005 Missense_Mutation SNP A C3N-00199_T 7276102 103511005 55834968 129 11173 RELN 0 . GRCh38 7 103551067 103551067 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.6302G>T p.Gly2101Val p.G2101V ENST00000428762 41/65 572 446 126 693 692 1 strelka-varscan-mutect RELN,missense_variant,p.Gly2101Val,ENST00000424685,;RELN,missense_variant,p.Gly2101Val,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Gly2101Val,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant,splice_region_variant 6462/11571 6302/10383 2101/3460 G/V gGa/gTa 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0) 41/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 103551067 103551067 C A 1 0 0 0 0 1 0 0 0 13390 637 22 2 2 RELN 7 103551067 Missense_Mutation SNP C C3N-00199_T 40062 103551067 55794906 130 11174 RELN 0 . GRCh38 7 103572219 103572219 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.4553G>T p.Gly1518Val p.G1518V ENST00000428762 31/65 127 108 19 392 391 1 strelka-varscan-mutect RELN,missense_variant,p.Gly1518Val,ENST00000424685,;RELN,missense_variant,p.Gly1518Val,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Gly1518Val,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 4713/11571 4553/10383 1518/3460 G/V gGc/gTc 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0.05) 31/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 103572219 103572219 C A 1 0 0 0 0 1 0 0 0 13390 739 26 2 2 RELN 7 103572219 Missense_Mutation SNP C C3N-00199_T 21152 103572219 55773754 131 11175 COG5 0 . GRCh38 7 107548164 107548164 + Missense_Mutation SNP C C A rs759063795 C3N-00199_T C3N-00199_N C C c.457G>T p.Val153Phe p.V153F ENST00000297135 5/22 122 104 18 441 440 1 strelka-varscan-mutect COG5,missense_variant,p.Val153Phe,ENST00000393603,NM_001161520.1;COG5,missense_variant,p.Val153Phe,ENST00000347053,NM_181733.2;COG5,missense_variant,p.Val153Phe,ENST00000297135,NM_006348.3;COG5,missense_variant,p.Val122Phe,ENST00000605888,;COG5,non_coding_transcript_exon_variant,,ENST00000475638,;COG5,non_coding_transcript_exon_variant,,ENST00000469503,; A ENST00000297135 Transcript missense_variant 982/4060 457/2583 153/860 V/F Gtt/Ttt rs759063795 1 -1 COG5 HGNC HGNC:14857 protein_coding YES CCDS5742.1 ENSP00000297135 Q9UP83 UPI0000246D05 NM_006348.3 tolerated(0.05) 5/22 Pfam_domain:PF10392,hmmpanther:PTHR13228,hmmpanther:PTHR13228:SF3 MODERATE 1 SNV 1 1 PASS rs759063795 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 107548164 107548164 C A 1 0 0 0 0 1 0 0 0 3449 478 17 2 2 COG5 7 107548164 Missense_Mutation SNP C C3N-00199_T 3975945 107548164 51797809 132 11176 FLNC 0 . GRCh38 7 128855225 128855225 + Frame_Shift_Del DEL A A - novel C3N-00199_T C3N-00199_N A A c.7163delA p.Asn2388MetfsTer36 p.N2388Mfs*36 ENST00000325888 43/48 385 361 24 383 383 0 varindel-pindel FLNC,frameshift_variant,p.Asn2388MetfsTer36,ENST00000325888,NM_001458.4;FLNC,frameshift_variant,p.Asn2355MetfsTer36,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; - ENST00000325888 Transcript frameshift_variant 7423/9188 7162/8178 2388/2725 N/X Aat/at 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 43/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 2 0 0 0 -5.504239 0.983751 1 1 1 0 - 7 5 41 128855225 128855225 A - 1 0 1 0 1 0 0 0 0 5791 130 5 0 0 FLNC 7 128855225 Frame_Shift_Del DEL A C3N-00199_T 21307061 128855225 30490748 133 11177 TRPV5 0 . GRCh38 7 142914960 142914960 + Missense_Mutation SNP A A G novel C3N-00199_T C3N-00199_N A A c.1373T>C p.Leu458Pro p.L458P ENST00000265310 11/15 201 171 30 223 223 0 strelka-varscan-mutect TRPV5,missense_variant,p.Leu458Pro,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Leu403Pro,ENST00000439304,; G ENST00000265310 Transcript missense_variant 1722/2952 1373/2190 458/729 L/P cTg/cCg 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 deleterious(0) 11/15 Pfam_domain:PF00520,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 142914960 142914960 A G 1 0 0 0 0 1 0 0 0 17105 188 7 5 5 TRPV5 7 142914960 Missense_Mutation SNP A C3N-00199_T 14059735 142914960 16431013 134 11178 CTAGE15 0 . GRCh38 7 143573050 143573050 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.1233G>A p.= p.E411E ENST00000420911 1/1 192 157 35 538 538 0 strelka-varscan-mutect CTAGE15,synonymous_variant,p.=,ENST00000420911,NM_001008747.2;RNU6-162P,upstream_gene_variant,,ENST00000516228,; A ENST00000420911 Transcript synonymous_variant 1250/2587 1233/2334 411/777 E gaG/gaA 1 1 CTAGE15 HGNC HGNC:37295 protein_coding YES CCDS64788.1 ENSP00000474204 A4D2H0 UPI0000199821 NM_001008747.2 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 21 189 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 143573050 143573050 G A 1 0 0 0 0 0 0 0 1 3797 991 35 3 3 CTAGE15 7 143573050 Silent SNP G C3N-00199_T 658090 143573050 15772923 135 11179 TPK1 0 . GRCh38 7 144682909 144682909 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.185G>T p.Ser62Ile p.S62I ENST00000360057 4/9 75 60 15 147 146 1 strelka-varscan-mutect TPK1,missense_variant,p.Ser62Ile,ENST00000360057,NM_022445.3;TPK1,missense_variant,p.Ser62Ile,ENST00000378099,NM_001042482.1;TPK1,missense_variant,p.Ala17Ser,ENST00000538212,;TPK1,missense_variant,p.Ser62Ile,ENST00000552881,;TPK1,splice_region_variant,,ENST00000546806,;TPK1,missense_variant,p.Asp17Tyr,ENST00000482940,;TPK1,missense_variant,p.Ser62Ile,ENST00000378098,;TPK1,missense_variant,p.Ala17Ser,ENST00000489798,;TPK1,splice_region_variant,,ENST00000481645,; A ENST00000360057 Transcript missense_variant,splice_region_variant 288/2439 185/732 62/243 S/I aGc/aTc 1 -1 TPK1 HGNC HGNC:17358 protein_coding YES CCDS5888.1 ENSP00000353165 Q9H3S4 A0A090N8Y0 UPI000004FD50 NM_022445.3 deleterious(0.02) 4/9 hmmpanther:PTHR13622,Pfam_domain:PF04263,PIRSF_domain:PIRSF031057,TIGRFAM_domain:TIGR01378,Gene3D:3.40.50.10240,Superfamily_domains:SSF63999 MODERATE 1 SNV 1 1 PASS rs757877655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 144682909 144682909 C A 1 0 0 0 0 1 0 0 0 16885 695 24 2 2 TPK1 7 144682909 Missense_Mutation SNP C C3N-00199_T 1109859 144682909 14663064 136 11180 SSPO 0 . GRCh38 7 149776410 149776410 + Silent SNP C C T novel C3N-00199_T C3N-00199_N C C c.115C>T p.= p.L39L ENST00000378016 2/107 220 193 27 212 212 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;ZNF467,upstream_gene_variant,,ENST00000302017,NM_207336.1;ZNF467,upstream_gene_variant,,ENST00000484747,;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,upstream_gene_variant,,ENST00000486824,; T ENST00000378016 Transcript synonymous_variant 115/15589 115/15453 39/5150 L Ctg/Ttg 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 2/107 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 149776410 149776410 C T 1 0 0 0 0 0 0 0 1 15566 680 24 3 3 SSPO 7 149776410 Silent SNP C C3N-00199_T 5093501 149776410 9569563 137 11181 SSPO 0 . GRCh38 7 149779049 149779049 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1016G>T p.Gly339Val p.G339V ENST00000378016 8/107 63 43 20 83 83 0 strelka-varscan-mutect SSPO,missense_variant,p.Gly339Val,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,intron_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000493502,; T ENST00000378016 Transcript missense_variant 1016/15589 1016/15453 339/5150 G/V gGa/gTa 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 8/107 Pfam_domain:PF00094,SMART_domains:SM00216,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 149779049 149779049 G T 1 0 0 0 0 1 0 0 0 15566 1174 41 2 2 SSPO 7 149779049 Missense_Mutation SNP G C3N-00199_T 2639 149779049 9566924 138 11182 KCNH2 0 . GRCh38 7 150945450 150945450 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.3395C>G p.Pro1132Arg p.P1132R ENST00000262186 15/15 178 134 44 166 166 0 strelka-varscan-mutect KCNH2,missense_variant,p.Pro1132Arg,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Pro792Arg,ENST00000330883,NM_172057.2;KCNH2,downstream_gene_variant,,ENST00000430723,NM_172056.2;KCNH2,downstream_gene_variant,,ENST00000532957,;KCNH2,downstream_gene_variant,,ENST00000473610,;KCNH2,downstream_gene_variant,,ENST00000461280,; C ENST00000262186 Transcript missense_variant 3797/4286 3395/3480 1132/1159 P/R cCc/cGc 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious_low_confidence(0.02) 15/15 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 150945450 150945450 G C 1 0 0 0 0 1 0 0 0 7948 1232 43 4 4 KCNH2 7 150945450 Missense_Mutation SNP G C3N-00199_T 1166401 150945450 8400523 139 11183 GALNTL5 0 . GRCh38 7 151983019 151983019 + Silent SNP G G A rs766808347 C3N-00199_T C3N-00199_N G G c.402G>A p.= p.P134P ENST00000616416 5/10 306 285 21 422 422 0 strelka-varscan-mutect GALNTL5,synonymous_variant,p.=,ENST00000616416,;GALNTL5,synonymous_variant,p.=,ENST00000392800,NM_145292.3;GALNTL5,synonymous_variant,p.=,ENST00000431418,;GALNTL5,non_coding_transcript_exon_variant,,ENST00000468278,;GALNTL5,3_prime_UTR_variant,,ENST00000416269,;GALNTL5,3_prime_UTR_variant,,ENST00000414073,;GALNTL5,3_prime_UTR_variant,,ENST00000426341,;GALNTL5,intron_variant,,ENST00000448366,;GALNTL5,intron_variant,,ENST00000416062,; A ENST00000616416 Transcript synonymous_variant 708/1763 402/1332 134/443 P ccG/ccA rs766808347,COSM366683 1 1 GALNTL5 HGNC HGNC:21725 protein_coding YES CCDS5929.1 ENSP00000479207 Q7Z4T8 UPI000013C82E 5/10 hmmpanther:PTHR11675:SF17,hmmpanther:PTHR11675,Superfamily_domains:SSF53448 0,1 LOW 1 SNV 5 0,1 1 PASS rs766808347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 151983019 151983019 G A 1 0 0 0 0 0 0 0 1 6092 1045 37 1 1 GALNTL5 7 151983019 Silent SNP G C3N-00199_T 1037569 151983019 7362954 140 11184 WRN 0 . GRCh38 8 31141447 31141447 + Silent SNP C C A rs150095039 C3N-00199_T C3N-00199_N C C c.2985C>A p.= p.A995A ENST00000298139 25/35 166 157 9 436 434 2 strelka-varscan-mutect WRN,synonymous_variant,p.=,ENST00000298139,NM_000553.4;WRN,non_coding_transcript_exon_variant,,ENST00000521620,; A ENST00000298139 Transcript synonymous_variant 3234/5215 2985/4299 995/1432 A gcC/gcA rs150095039 1 1 WRN HGNC HGNC:12791 protein_coding YES CCDS6082.1 ENSP00000298139 Q14191 UPI000013E49D NM_000553.4 25/35 hmmpanther:PTHR13710:SF87,hmmpanther:PTHR13710,Gene3D:1.10.10.10,TIGRFAM_domain:TIGR00614,Pfam_domain:PF09382,SMART_domains:SM00956,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS rs150095039 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 31141447 31141447 C A 1 0 0 0 0 0 0 0 1 17959 639 23 1 1 WRN 8 31141447 Silent SNP C C3N-00199_T 31141447 113997189 141 11185 MMP16 0 . GRCh38 8 88116529 88116529 + Missense_Mutation SNP C C G rs138174209 C3N-00199_T C3N-00199_N C C c.1061G>C p.Arg354Pro p.R354P ENST00000286614 6/10 133 95 38 176 176 0 strelka-varscan-mutect MMP16,missense_variant,p.Arg354Pro,ENST00000286614,NM_005941.4;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; G ENST00000286614 Transcript missense_variant 1343/11558 1061/1824 354/607 R/P cGt/cCt rs138174209,COSM1569518,COSM3738387 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 deleterious(0) 6/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,SMART_domains:SM00120,Superfamily_domains:SSF50923 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs138174209 . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 88116529 88116529 C G 1 0 0 0 0 1 0 0 0 9618 536 19 4 4 MMP16 8 88116529 Missense_Mutation SNP C C3N-00199_T 56975082 88116529 57022107 142 11186 KCNS2 0 . GRCh38 8 98428595 98428595 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.616C>A p.Leu206Ile p.L206I ENST00000287042 2/2 391 280 111 410 410 0 strelka-varscan-mutect KCNS2,missense_variant,p.Leu206Ile,ENST00000287042,NM_020697.2;KCNS2,missense_variant,p.Leu206Ile,ENST00000521839,;STK3,intron_variant,,ENST00000517832,; A ENST00000287042 Transcript missense_variant 966/5219 616/1434 206/477 L/I Ctc/Atc 1 1 KCNS2 HGNC HGNC:6301 protein_coding YES CCDS6279.1 ENSP00000287042 Q9ULS6 UPI0000001653 NM_020697.2 tolerated(0.78) 2/2 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF60,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 98428595 98428595 C A 1 0 0 0 0 1 0 0 0 8005 681 24 2 2 KCNS2 8 98428595 Missense_Mutation SNP C C3N-00199_T 10312066 98428595 46710041 143 11187 ADCK5 0 . GRCh38 8 144391810 144391810 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.958G>T p.Gly320Cys p.G320C ENST00000308860 9/15 326 216 110 321 321 0 strelka-varscan-mutect ADCK5,missense_variant,p.Gly320Cys,ENST00000308860,NM_174922.4;CPSF1,downstream_gene_variant,,ENST00000616140,NM_013291.2;CPSF1,downstream_gene_variant,,ENST00000620219,;CPSF1,downstream_gene_variant,,ENST00000531727,;CPSF1,downstream_gene_variant,,ENST00000532935,;CPSF1,downstream_gene_variant,,ENST00000401314,;ADCK5,downstream_gene_variant,,ENST00000526231,;ADCK5,downstream_gene_variant,,ENST00000534714,;ADCK5,3_prime_UTR_variant,,ENST00000529654,;ADCK5,downstream_gene_variant,,ENST00000533715,;CPSF1,downstream_gene_variant,,ENST00000531480,;CPSF1,downstream_gene_variant,,ENST00000526271,;ADCK5,downstream_gene_variant,,ENST00000526833,;CPSF1,downstream_gene_variant,,ENST00000527827,;CPSF1,downstream_gene_variant,,ENST00000532725,;ADCK5,downstream_gene_variant,,ENST00000532190,;CPSF1,downstream_gene_variant,,ENST00000529288,;CPSF1,downstream_gene_variant,,ENST00000531042,; T ENST00000308860 Transcript missense_variant 1002/1949 958/1743 320/580 G/C Ggc/Tgc 1 1 ADCK5 HGNC HGNC:21738 protein_coding YES CCDS34965.2 ENSP00000310547 Q3MIX3 UPI00005B7249 NM_174922.4 deleterious(0) 9/15 hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF59,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1337257231 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 144391810 144391810 G T 1 0 0 0 0 1 0 0 0 335 1116 39 1 1 ADCK5 8 144391810 Missense_Mutation SNP G C3N-00199_T 45963215 144391810 746826 144 11188 FREM1 0 . GRCh38 9 14775976 14775976 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.4670T>A p.Leu1557Gln p.L1557Q ENST00000422223 26/38 490 226 264 351 351 0 strelka-varscan-mutect FREM1,missense_variant,p.Leu1557Gln,ENST00000422223,NM_144966.5;FREM1,missense_variant,p.Leu1557Gln,ENST00000380880,;FREM1,missense_variant,p.Leu93Gln,ENST00000380894,NM_001177704.1;FREM1,non_coding_transcript_exon_variant,,ENST00000466679,;FREM1,non_coding_transcript_exon_variant,,ENST00000485068,;FREM1,upstream_gene_variant,,ENST00000486223,;FREM1,intron_variant,,ENST00000380875,;FREM1,upstream_gene_variant,,ENST00000427623,; T ENST00000422223 Transcript missense_variant 5486/10086 4670/6540 1557/2179 L/Q cTg/cAg 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 deleterious(0.02) 26/38 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 14775976 14775976 A T 1 0 0 0 0 1 0 0 0 5911 188 7 4 4 FREM1 9 14775976 Missense_Mutation SNP A C3N-00199_T 14775976 123618741 145 11189 DENND4C 0 . GRCh38 9 19342743 19342743 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.2968G>T p.Gly990Cys p.G990C ENST00000602925 21/32 98 50 48 208 208 0 strelka-varscan-mutect DENND4C,missense_variant,p.Gly990Cys,ENST00000602925,NM_017925.6;DENND4C,missense_variant,p.Gly1039Cys,ENST00000434457,;DENND4C,missense_variant,p.Gly26Cys,ENST00000380427,;DENND4C,upstream_gene_variant,,ENST00000361024,;DENND4C,upstream_gene_variant,,ENST00000380424,;DENND4C,3_prime_UTR_variant,,ENST00000494124,;DENND4C,non_coding_transcript_exon_variant,,ENST00000380437,;DENND4C,downstream_gene_variant,,ENST00000602442,; T ENST00000602925 Transcript missense_variant 3384/6831 2968/5730 990/1909 G/C Ggt/Tgt 1 1 DENND4C HGNC HGNC:26079 protein_coding YES CCDS6491.3 ENSP00000473565 R4GNB2 UPI0000EE421F NM_017925.6 deleterious(0.03) 21/32 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 19342743 19342743 G T 1 0 0 0 0 1 0 0 0 4239 1348 47 2 2 DENND4C 9 19342743 Missense_Mutation SNP G C3N-00199_T 4566767 19342743 119051974 146 11190 IFNA6 0 . GRCh38 9 21350704 21350704 + Missense_Mutation SNP G G A C3N-00199_T C3N-00199_N G G c.184C>T p.Pro62Ser p.P62S ENST00000380210 1/1 216 204 12 233 233 0 strelka-varscan-mutect IFNA6,missense_variant,p.Pro62Ser,ENST00000380210,NM_021002.2;IFNA6,missense_variant,p.Pro63Ser,ENST00000259555,; A ENST00000380210 Transcript missense_variant 675/1544 184/570 62/189 P/S Ccc/Tcc COSM3656590 1 -1 IFNA6 HGNC HGNC:5427 protein_coding YES CCDS6504.1 ENSP00000369558 P05013 UPI000004775F NM_021002.2 deleterious(0.02) 1/1 hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF27,Gene3D:1.20.1250.10,Pfam_domain:PF00143,SMART_domains:SM00076,Superfamily_domains:SSF47266,Prints_domain:PR00266 1 MODERATE 1 SNV 1 1 PASS rs1181102432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 21350704 21350704 G A 1 0 0 0 0 1 0 0 0 7441 1174 41 3 3 IFNA6 9 21350704 Missense_Mutation SNP G C3N-00199_T 2007961 21350704 117044013 147 11191 LINGO2 0 . GRCh38 9 27950063 27950063 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.609C>A p.= p.L203L ENST00000379992 6/6 151 71 80 214 214 0 strelka-varscan-mutect LINGO2,synonymous_variant,p.=,ENST00000379992,NM_152570.2,NM_001258282.1;LINGO2,synonymous_variant,p.=,ENST00000308675,;LINGO2,synonymous_variant,p.=,ENST00000613945,; T ENST00000379992 Transcript synonymous_variant 1059/3044 609/1821 203/606 L ctC/ctA 1 -1 LINGO2 HGNC HGNC:21207 protein_coding YES CCDS6524.1 ENSP00000369328 Q7L985 UPI000004C7CD NM_152570.2,NM_001258282.1 6/6 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF38,Low_complexity_(Seg):seg,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 27950063 27950063 G T 1 0 0 0 0 0 0 0 1 8736 1277 45 2 2 LINGO2 9 27950063 Silent SNP G C3N-00199_T 6599359 27950063 110444654 148 11192 PRUNE2 0 . GRCh38 9 76644886 76644886 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.8581G>T p.Gly2861Cys p.G2861C ENST00000376718 12/19 69 62 7 115 115 0 strelka-varscan-mutect PRUNE2,missense_variant,p.Gly2861Cys,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Gly2503Cys,ENST00000428286,;PRUNE2,missense_variant,p.Gly2861Cys,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,missense_variant,p.Gly2183Cys,ENST00000426088,;PRUNE2,missense_variant,p.Gly126Cys,ENST00000376717,NM_001308050.1;PRUNE2,missense_variant,p.Gly96Cys,ENST00000223609,;PRUNE2,missense_variant,p.Gly31Cys,ENST00000424866,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000466266,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000488346,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000494975,; A ENST00000376718 Transcript missense_variant 8705/12584 8581/9267 2861/3088 G/C Ggc/Tgc 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 deleterious(0) 12/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112,Pfam_domain:PF12496 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -16.07009 1 1 1 1 0 A 3 1 41 76644886 76644886 C A 1 0 0 0 0 1 0 0 0 12791 594 21 2 2 PRUNE2 9 76644886 Missense_Mutation SNP C C3N-00199_T 48694823 76644886 61749831 149 11193 SVEP1 0 . GRCh38 9 110407825 110407825 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.7775C>A p.Ala2592Asp p.A2592D ENST00000374469 38/48 97 69 28 233 233 0 strelka-varscan-mutect SVEP1,missense_variant,p.Ala2595Asp,ENST00000401783,;SVEP1,missense_variant,p.Ala2592Asp,ENST00000374469,NM_153366.3; T ENST00000374469 Transcript missense_variant 7970/12194 7775/10716 2592/3571 A/D gCc/gAc 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 tolerated(0.54) 38/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 110407825 110407825 G T 1 0 0 0 0 1 0 0 0 15805 1203 42 2 2 SVEP1 9 110407825 Missense_Mutation SNP G C3N-00199_T 33762939 110407825 27986892 150 11194 COL27A1 0 . GRCh38 9 114252925 114252925 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.3134G>T p.Gly1045Val p.G1045V ENST00000356083 27/61 108 101 7 126 126 0 strelka-varscan-mutect COL27A1,missense_variant,p.Gly1045Val,ENST00000356083,NM_032888.3;COL27A1,3_prime_UTR_variant,,ENST00000494090,; T ENST00000356083 Transcript missense_variant 3525/7790 3134/5583 1045/1860 G/V gGa/gTa COSM5201764 1 1 COL27A1 HGNC HGNC:22986 protein_coding YES CCDS6802.1 ENSP00000348385 Q8IZC6 UPI0000062271 NM_032888.3 27/61 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF549,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.17946 1 1 1 1 0 T 3 4 41 114252925 114252925 G T 1 0 0 0 0 1 0 0 0 3474 1174 41 2 2 COL27A1 9 114252925 Missense_Mutation SNP G C3N-00199_T 3845100 114252925 24141792 151 11195 HMCN2 0 . GRCh38 9 130418896 130418896 + Silent SNP C C A rs61743633 C3N-00199_T C3N-00199_N C C c.13026C>A p.= p.P4342P ENST00000624552 86/98 95 63 32 89 89 0 strelka-varscan-mutect HMCN2,synonymous_variant,p.=,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,; A ENST00000624552 Transcript synonymous_variant 13026/15610 13026/15180 4342/5059 P ccC/ccA rs61743633 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 86/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS rs61743633 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 130418896 130418896 C A 1 0 0 0 0 0 0 0 1 7112 668 24 2 2 HMCN2 9 130418896 Silent SNP C C3N-00199_T 16165971 130418896 7975821 152 11196 RAPGEF1 0 . GRCh38 9 131628047 131628047 + Missense_Mutation SNP T T C novel C3N-00199_T C3N-00199_N T T c.1070A>G p.His357Arg p.H357R ENST00000372190 9/24 141 99 42 151 151 0 varscan-mutect RAPGEF1,missense_variant,p.His356Arg,ENST00000372195,NM_001304275.1;RAPGEF1,missense_variant,p.His339Arg,ENST00000372189,NM_005312.3;RAPGEF1,missense_variant,p.His357Arg,ENST00000372190,NM_198679.1;RAPGEF1,upstream_gene_variant,,ENST00000419442,;RAPGEF1,non_coding_transcript_exon_variant,,ENST00000481260,; C ENST00000372190 Transcript missense_variant 1108/6045 1070/3288 357/1095 H/R cAc/cGc 1 -1 RAPGEF1 HGNC HGNC:4568 protein_coding YES CCDS48048.1 ENSP00000361264 Q13905 UPI0000074689 NM_198679.1 tolerated_low_confidence(0.12) 9/24 MODERATE 1 SNV 1 1 PASS rs1165391734 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 131628047 131628047 T C 1 0 0 0 0 1 0 0 0 13202 1696 59 5 5 RAPGEF1 9 131628047 Missense_Mutation SNP T C3N-00199_T 1209151 131628047 6766670 153 11197 SEC16A 0 . GRCh38 9 136474524 136474524 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.3092G>T p.Gly1031Val p.G1031V ENST00000313050 1/30 248 180 68 268 268 0 strelka-varscan-mutect SEC16A,missense_variant,p.Gly1031Val,ENST00000290037,NM_001276418.1;SEC16A,missense_variant,p.Gly1031Val,ENST00000313050,NM_014866.1;SEC16A,missense_variant,p.Gly853Val,ENST00000371706,;SEC16A,missense_variant,p.Gly853Val,ENST00000431893,; A ENST00000313050 Transcript missense_variant 3166/8806 3092/7074 1031/2357 G/V gGg/gTg 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 deleterious(0.02) 1/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 136474524 136474524 C A 1 0 0 0 0 1 0 0 0 14263 623 22 2 2 SEC16A 9 136474524 Missense_Mutation SNP C C3N-00199_T 4846477 136474524 1920193 154 11198 EHMT1 0 . GRCh38 9 137814501 137814501 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.3251A>T p.Tyr1084Phe p.Y1084F ENST00000460843 22/27 570 517 53 525 525 0 strelka-varscan-mutect EHMT1,missense_variant,p.Tyr1084Phe,ENST00000460843,NM_024757.4;EHMT1,missense_variant,p.Tyr1053Phe,ENST00000637161,;EHMT1,downstream_gene_variant,,ENST00000636027,;EHMT1,non_coding_transcript_exon_variant,,ENST00000488242,;EHMT1,non_coding_transcript_exon_variant,,ENST00000636163,;EHMT1,non_coding_transcript_exon_variant,,ENST00000637407,;EHMT1,upstream_gene_variant,,ENST00000635741,;EHMT1,upstream_gene_variant,,ENST00000635987,;EHMT1,upstream_gene_variant,,ENST00000636463,;EHMT1,upstream_gene_variant,,ENST00000636472,;EHMT1,upstream_gene_variant,,ENST00000636495,;EHMT1,upstream_gene_variant,,ENST00000636526,;EHMT1,upstream_gene_variant,,ENST00000637400,;EHMT1,upstream_gene_variant,,ENST00000637784,;EHMT1,upstream_gene_variant,,ENST00000637912,;EHMT1,upstream_gene_variant,,ENST00000638024,;EHMT1,missense_variant,p.Tyr703Phe,ENST00000462942,;EHMT1,3_prime_UTR_variant,,ENST00000637261,;EHMT1,3_prime_UTR_variant,,ENST00000637891,;EHMT1,non_coding_transcript_exon_variant,,ENST00000483653,;EHMT1,upstream_gene_variant,,ENST00000475564,;EHMT1,upstream_gene_variant,,ENST00000494249,;EHMT1,upstream_gene_variant,,ENST00000637748,;EHMT1,downstream_gene_variant,,ENST00000486164,;EHMT1,downstream_gene_variant,,ENST00000637949,; T ENST00000460843 Transcript missense_variant 3317/5137 3251/3897 1084/1298 Y/F tAc/tTc 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 deleterious(0) 22/27 Gene3D:2.170.270.10,Pfam_domain:PF05033,PROSITE_profiles:PS50867,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF364,SMART_domains:SM00468,Superfamily_domains:SSF82199 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 137814501 137814501 A T 1 0 0 0 0 1 0 0 0 4819 391 14 4 4 EHMT1 9 137814501 Missense_Mutation SNP A C3N-00199_T 1339977 137814501 580216 155 11199 ITIH5 0 . GRCh38 10 7637475 7637475 + Silent SNP C C T rs749252937 C3N-00199_T C3N-00199_N C C c.405G>A p.= p.E135E ENST00000397146 5/14 148 139 9 148 148 0 strelka-varscan-mutect ITIH5,synonymous_variant,p.=,ENST00000397146,NM_030569.6;ITIH5,synonymous_variant,p.=,ENST00000397145,NM_001001851.2;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,; T ENST00000397146 Transcript synonymous_variant 484/6721 405/2829 135/942 E gaG/gaA rs749252937,COSM1255077,COSM3440638,COSM3440639 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 5/14 Low_complexity_(Seg):seg,PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,Pfam_domain:PF08487,SMART_domains:SM00609 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs749252937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 7637475 7637475 C T 1 0 0 0 0 0 0 0 1 7813 927 32 3 3 ITIH5 10 7637475 Silent SNP C C3N-00199_T 7637475 126159947 156 11200 OLAH 0 . GRCh38 10 15056935 15056935 + Missense_Mutation SNP C C G rs770856312 C3N-00199_T C3N-00199_N C C c.275C>G p.Pro92Arg p.P92R ENST00000378217 4/9 126 97 29 109 109 0 strelka-varscan-mutect OLAH,missense_variant,p.Pro92Arg,ENST00000378217,NM_018324.2;OLAH,missense_variant,p.Pro92Arg,ENST00000413672,;OLAH,intron_variant,,ENST00000378228,NM_001039702.2;OLAH,intron_variant,,ENST00000378225,;OLAH,intron_variant,,ENST00000429028,;OLAH,intron_variant,,ENST00000428897,;OLAH,intron_variant,,ENST00000493912,; G ENST00000378217 Transcript missense_variant 462/1767 275/957 92/318 P/R cCg/cGg rs770856312 1 1 OLAH HGNC HGNC:25625 protein_coding YES CCDS7106.1 ENSP00000367462 Q9NV23 UPI000007139E NM_018324.2 tolerated_low_confidence(0.11) 4/9 MODERATE 1 SNV 2 1 PASS rs770856312 . 0 198 11 0 0 0 0 0 -20 0.9999823 1 1 1 0 G 3 3 41 15056935 15056935 C G 1 0 0 0 0 1 0 0 0 10926 652 23 4 4 OLAH 10 15056935 Missense_Mutation SNP C C3N-00199_T 7419460 15056935 118740487 157 11201 CUBN 0 . GRCh38 10 17100182 17100182 + Nonsense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1588G>T p.Glu530Ter p.E530* ENST00000377833 14/67 141 78 63 439 439 0 strelka-varscan-mutect CUBN,stop_gained,p.Glu530Ter,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript stop_gained 1654/11949 1588/10872 530/3623 E/* Gag/Tag 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 14/67 PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 1 1 PASS rs1261796321 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 17100182 17100182 C A 1 0 0 0 0 0 1 0 0 3861 893 31 1 1 CUBN 10 17100182 Nonsense_Mutation SNP C C3N-00199_T 2043247 17100182 116697240 158 11202 ST8SIA6 0 . GRCh38 10 17321245 17321245 + Missense_Mutation SNP G G T rs748029727 C3N-00199_T C3N-00199_N G G c.830C>A p.Thr277Lys p.T277K ENST00000377602 8/8 104 96 8 273 273 0 strelka-varscan-mutect ST8SIA6,missense_variant,p.Thr277Lys,ENST00000377602,NM_001004470.1;ST8SIA6,missense_variant,p.Thr98Lys,ENST00000440449,; T ENST00000377602 Transcript missense_variant 905/2276 830/1197 277/398 T/K aCg/aAg rs748029727,COSM3397028,COSM3397029 1 -1 ST8SIA6 HGNC HGNC:23317 protein_coding YES CCDS31158.1 ENSP00000366827 P61647 UPI0000359594 NM_001004470.1 deleterious(0) 8/8 hmmpanther:PTHR11987:SF29,hmmpanther:PTHR11987,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748029727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 17321245 17321245 G T 1 0 0 0 0 1 0 0 0 15614 1145 40 1 1 ST8SIA6 10 17321245 Missense_Mutation SNP G C3N-00199_T 221063 17321245 116476177 159 11203 GDF10 0 . GRCh38 10 47310422 47310422 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.946C>A p.Gln316Lys p.Q316K ENST00000580279 2/3 194 181 13 184 184 0 strelka-varscan-mutect GDF10,missense_variant,p.Gln316Lys,ENST00000580279,NM_004962.3; A ENST00000580279 Transcript missense_variant 1212/2458 946/1437 316/478 Q/K Cag/Aag 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 tolerated(0.88) 2/3 PIRSF_domain:PIRSF037403 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.47287 0.9999661 1 1 1 0 A 3 1 41 47310422 47310422 C A 1 0 0 0 0 1 0 0 0 6184 479 17 2 2 GDF10 10 47310422 Missense_Mutation SNP C C3N-00199_T 29989177 47310422 86487000 160 11204 MBL2 0 . GRCh38 10 52768314 52768314 + Silent SNP C C T novel C3N-00199_T C3N-00199_N C C c.570G>A p.= p.K190K ENST00000373968 4/4 69 60 9 156 156 0 strelka-varscan-mutect MBL2,synonymous_variant,p.=,ENST00000373968,NM_000242.2; T ENST00000373968 Transcript synonymous_variant 635/3569 570/747 190/248 K aaG/aaA 1 -1 MBL2 HGNC HGNC:6922 protein_coding YES CCDS7247.1 ENSP00000363079 P11226 UPI0000035011 NM_000242.2 4/4 PROSITE_profiles:PS50041,hmmpanther:PTHR24020,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs1257704240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 52768314 52768314 C T 1 0 0 0 0 0 0 0 1 9282 912 32 3 3 MBL2 10 52768314 Silent SNP C C3N-00199_T 5457892 52768314 81029108 161 11205 NRBF2 0 . GRCh38 10 63153579 63153579 + Nonsense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.225G>A p.Trp75Ter p.W75* ENST00000277746 4/4 64 57 7 115 115 0 strelka-varscan-mutect NRBF2,stop_gained,p.Trp75Ter,ENST00000277746,NM_030759.4;NRBF2,stop_gained,p.Trp65Ter,ENST00000435510,NM_001282405.1; A ENST00000277746 Transcript stop_gained 406/1853 225/864 75/287 W/* tgG/tgA 1 1 NRBF2 HGNC HGNC:19692 protein_coding YES CCDS7268.1 ENSP00000277746 Q96F24 UPI000006D398 NM_030759.4 4/4 Superfamily_domains:0052258,Pfam_domain:PF17169,hmmpanther:PTHR14964,hmmpanther:PTHR14964:SF2 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -12.39117 0.9999879 1 1 1 0 A 4 1 41 63153579 63153579 G A 1 0 0 0 0 0 1 0 0 10697 1183 41 3 3 NRBF2 10 63153579 Nonsense_Mutation SNP G C3N-00199_T 10385265 63153579 70643843 162 11206 ZSWIM8 0 . GRCh38 10 73791083 73791083 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.1050G>A p.= p.L350L ENST00000398706 8/26 219 196 23 219 219 0 strelka-varscan-mutect ZSWIM8,synonymous_variant,p.=,ENST00000604729,;ZSWIM8,synonymous_variant,p.=,ENST00000398706,NM_015037.3;ZSWIM8,synonymous_variant,p.=,ENST00000605216,NM_001242487.1;ZSWIM8,synonymous_variant,p.=,ENST00000603114,NM_001242488.1;ZSWIM8,synonymous_variant,p.=,ENST00000604524,;ZSWIM8,upstream_gene_variant,,ENST00000603187,;ZSWIM8,upstream_gene_variant,,ENST00000412198,;ZSWIM8,upstream_gene_variant,,ENST00000604754,;ZSWIM8,upstream_gene_variant,,ENST00000431225,;ZSWIM8,upstream_gene_variant,,ENST00000489234,;ZSWIM8,upstream_gene_variant,,ENST00000425051,;ZSWIM8,downstream_gene_variant,,ENST00000451629,;RP11-574K11.26,upstream_gene_variant,,ENST00000623633,;ZSWIM8,synonymous_variant,p.=,ENST00000433366,;ZSWIM8,upstream_gene_variant,,ENST00000492395,;ZSWIM8,downstream_gene_variant,,ENST00000446546,; A ENST00000398706 Transcript synonymous_variant 1305/6062 1050/5529 350/1842 L ctG/ctA 1 1 ZSWIM8 HGNC HGNC:23528 protein_coding YES CCDS44440.1 ENSP00000381693 A7E2V4 UPI0000ED938E NM_015037.3 8/26 hmmpanther:PTHR22619 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 73791083 73791083 G A 1 0 0 0 0 0 0 0 1 18848 1306 46 3 3 ZSWIM8 10 73791083 Silent SNP G C3N-00199_T 10637504 73791083 60006339 163 11207 1 8 3 3 1021 G 3.66252e-05 ZSWIM8 0 . GRCh38 10 73791153 73791153 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.1120G>A p.Asp374Asn p.D374N ENST00000398706 8/26 103 93 10 117 117 0 strelka-varscan-mutect ZSWIM8,missense_variant,p.Asp374Asn,ENST00000604729,;ZSWIM8,missense_variant,p.Asp374Asn,ENST00000398706,NM_015037.3;ZSWIM8,missense_variant,p.Asp374Asn,ENST00000605216,NM_001242487.1;ZSWIM8,missense_variant,p.Asp374Asn,ENST00000603114,NM_001242488.1;ZSWIM8,missense_variant,p.Asp374Asn,ENST00000604524,;ZSWIM8,upstream_gene_variant,,ENST00000603187,;ZSWIM8,upstream_gene_variant,,ENST00000412198,;ZSWIM8,upstream_gene_variant,,ENST00000604754,;ZSWIM8,upstream_gene_variant,,ENST00000431225,;ZSWIM8,upstream_gene_variant,,ENST00000489234,;ZSWIM8,upstream_gene_variant,,ENST00000425051,;ZSWIM8,downstream_gene_variant,,ENST00000451629,;RP11-574K11.26,upstream_gene_variant,,ENST00000623633,;ZSWIM8,missense_variant,p.Asp374Asn,ENST00000433366,;ZSWIM8,upstream_gene_variant,,ENST00000492395,;ZSWIM8,downstream_gene_variant,,ENST00000446546,; A ENST00000398706 Transcript missense_variant 1375/6062 1120/5529 374/1842 D/N Gac/Aac 1 1 ZSWIM8 HGNC HGNC:23528 protein_coding YES CCDS44440.1 ENSP00000381693 A7E2V4 UPI0000ED938E NM_015037.3 deleterious(0) 8/26 hmmpanther:PTHR22619 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.8275 1 1 1 1 0 A 3 1 41 73791153 73791153 G A 1 0 0 0 0 1 0 0 0 18848 1290 45 3 3 ZSWIM8 10 73791153 Missense_Mutation SNP G C3N-00199_T 70 73791153 60006269 164 11208 1 8 3 3 1021 G 3.66252e-05 ZSWIM8 0 . GRCh38 10 73792103 73792103 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.1564G>A p.Gly522Arg p.G522R ENST00000398706 10/26 82 72 10 77 77 0 strelka-varscan-mutect ZSWIM8,missense_variant,p.Gly522Arg,ENST00000604729,;ZSWIM8,missense_variant,p.Gly522Arg,ENST00000398706,NM_015037.3;ZSWIM8,missense_variant,p.Gly522Arg,ENST00000605216,NM_001242487.1;ZSWIM8,missense_variant,p.Gly522Arg,ENST00000603114,NM_001242488.1;ZSWIM8,missense_variant,p.Gly522Arg,ENST00000604524,;ZSWIM8,upstream_gene_variant,,ENST00000603187,;ZSWIM8,upstream_gene_variant,,ENST00000412198,;ZSWIM8,upstream_gene_variant,,ENST00000604754,;ZSWIM8-AS1,downstream_gene_variant,,ENST00000456638,;ZSWIM8,non_coding_transcript_exon_variant,,ENST00000431225,;ZSWIM8,upstream_gene_variant,,ENST00000489234,;ZSWIM8,upstream_gene_variant,,ENST00000425051,;ZSWIM8,upstream_gene_variant,,ENST00000487278,;ZSWIM8,downstream_gene_variant,,ENST00000451629,;RP11-574K11.26,downstream_gene_variant,,ENST00000623633,;ZSWIM8,missense_variant,p.Gly522Arg,ENST00000433366,;ZSWIM8,missense_variant,p.Gly141Arg,ENST00000492395,;RP11-574K11.31,downstream_gene_variant,,ENST00000603027,; A ENST00000398706 Transcript missense_variant 1819/6062 1564/5529 522/1842 G/R Ggg/Agg 1 1 ZSWIM8 HGNC HGNC:23528 protein_coding YES CCDS44440.1 ENSP00000381693 A7E2V4 UPI0000ED938E NM_015037.3 tolerated_low_confidence(0.3) 10/26 hmmpanther:PTHR22619 MODERATE SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -19.97866 0.9999993 1 1 1 0 A 3 1 41 73792103 73792103 G A 1 0 0 0 0 1 0 0 0 18848 1348 47 3 3 ZSWIM8 10 73792103 Missense_Mutation SNP G C3N-00199_T 950 73792103 60005319 165 11209 1 8 3 3 1021 G 3.66252e-05 ADK 0 . GRCh38 10 74394260 74394260 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.393G>A p.= p.E131E ENST00000286621 5/11 125 80 45 374 374 0 strelka-varscan-mutect ADK,synonymous_variant,p.=,ENST00000541550,NM_001202449.1;ADK,synonymous_variant,p.=,ENST00000372734,NM_001123.3;ADK,synonymous_variant,p.=,ENST00000539909,NM_001202450.1;ADK,synonymous_variant,p.=,ENST00000286621,NM_006721.3; A ENST00000286621 Transcript synonymous_variant 443/1169 393/1089 131/362 E gaG/gaA 1 1 ADK HGNC HGNC:257 protein_coding YES CCDS7343.1 ENSP00000286621 P55263 UPI00001255EA NM_006721.3 5/11 Gene3D:3.40.1190.20,Pfam_domain:PF00294,hmmpanther:PTHR10584,hmmpanther:PTHR10584:SF24,Superfamily_domains:SSF53613 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 74394260 74394260 G A 1 0 0 0 0 0 0 0 1 394 962 34 3 3 ADK 10 74394260 Silent SNP G C3N-00199_T 602157 74394260 59403162 166 11210 VWA2 0 . GRCh38 10 114286328 114286328 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1387G>T p.Gly463Cys p.G463C ENST00000392982 11/14 79 65 14 97 97 0 strelka-varscan-mutect VWA2,missense_variant,p.Gly463Cys,ENST00000392982,NM_001272046.1;VWA2,missense_variant,p.Gly159Cys,ENST00000603594,;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,; T ENST00000392982 Transcript missense_variant 1637/2794 1387/2268 463/755 G/C Ggc/Tgc 1 1 VWA2 HGNC HGNC:24709 protein_coding YES CCDS7589.2 ENSP00000376708 Q5GFL6 UPI00004C7AA3 NM_001272046.1 tolerated(0.12) 11/14 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF117,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 114286328 114286328 G T 1 0 0 0 0 1 0 0 0 17793 1232 43 2 2 VWA2 10 114286328 Missense_Mutation SNP G C3N-00199_T 39892068 114286328 19511094 167 11211 GFRA1 0 . GRCh38 10 116093753 116093753 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.964C>T p.= p.L322L ENST00000355422 8/11 217 197 20 450 450 0 strelka-varscan-mutect GFRA1,synonymous_variant,p.=,ENST00000439649,NM_001145453.1;GFRA1,synonymous_variant,p.=,ENST00000369236,NM_145793.3;GFRA1,synonymous_variant,p.=,ENST00000355422,NM_005264.4;GFRA1,synonymous_variant,p.=,ENST00000369234,; A ENST00000355422 Transcript synonymous_variant 1515/2583 964/1398 322/465 L Cta/Tta 1 -1 GFRA1 HGNC HGNC:4243 protein_coding YES CCDS44481.1 ENSP00000347591 P56159 UPI000012B3A8 NM_005264.4 8/11 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF3,Pfam_domain:PF02351,PIRSF_domain:PIRSF038071,SMART_domains:SM00907,Superfamily_domains:0042655,Prints_domain:PR01316 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 116093753 116093753 G A 1 0 0 0 0 0 0 0 1 6221 991 35 3 3 GFRA1 10 116093753 Silent SNP G C3N-00199_T 1807425 116093753 17703669 168 11212 HSPA12A 0 . GRCh38 10 116675330 116675330 + Silent SNP C C A rs782001720 C3N-00199_T C3N-00199_N C C c.1479G>T p.= p.A493A ENST00000369209 12/12 112 93 19 187 187 0 strelka-varscan-mutect HSPA12A,synonymous_variant,p.=,ENST00000635765,;HSPA12A,synonymous_variant,p.=,ENST00000369209,NM_025015.2;RP11-498B4.5,downstream_gene_variant,,ENST00000433600,; A ENST00000369209 Transcript synonymous_variant 1584/5722 1479/2028 493/675 A gcG/gcT rs782001720 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 12/12 Gene3D:3.30.420.40,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS rs782001720 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 41 116675330 116675330 C A 1 0 0 0 0 0 0 0 1 7300 639 23 1 1 HSPA12A 10 116675330 Silent SNP C C3N-00199_T 581577 116675330 17122092 169 11213 MKI67 0 . GRCh38 10 128112373 128112373 + Missense_Mutation SNP C C T C3N-00199_T C3N-00199_N C C c.1729G>A p.Val577Ile p.V577I ENST00000368654 9/15 120 103 17 299 299 0 strelka-varscan-mutect MKI67,missense_variant,p.Val577Ile,ENST00000368654,NM_002417.4;MKI67,missense_variant,p.Val217Ile,ENST00000368653,NM_001145966.1;MKI67,non_coding_transcript_exon_variant,,ENST00000484853,;MKI67,downstream_gene_variant,,ENST00000478293,; T ENST00000368654 Transcript missense_variant 2105/12678 1729/9771 577/3256 V/I Gtt/Att COSM4798309 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 tolerated(0.58) 9/15 hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17 1 MODERATE 1 SNV 2 1 1 PASS rs1167658826 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 128112373 128112373 C T 1 0 0 0 0 1 0 0 0 9566 507 18 3 3 MKI67 10 128112373 Missense_Mutation SNP C C3N-00199_T 11437043 128112373 5685049 170 11214 KNDC1 0 . GRCh38 10 133198784 133198784 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.2276C>A p.Pro759His p.P759H ENST00000304613 14/30 78 69 9 81 81 0 strelka-varscan-mutect KNDC1,missense_variant,p.Pro759His,ENST00000304613,NM_152643.6;KNDC1,missense_variant,p.Pro694His,ENST00000368571,; A ENST00000304613 Transcript missense_variant 2297/6793 2276/5250 759/1749 P/H cCc/cAc 1 1 KNDC1 HGNC HGNC:29374 protein_coding YES CCDS7674.1 ENSP00000304437 Q76NI1 UPI00003529F7 NM_152643.6 deleterious(0.01) 14/30 Low_complexity_(Seg):seg,hmmpanther:PTHR21560,hmmpanther:PTHR21560:SF0 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.37452 1 1 1 1 0 A 3 1 41 133198784 133198784 C A 1 0 0 0 0 1 0 0 0 8304 623 22 2 2 KNDC1 10 133198784 Missense_Mutation SNP C C3N-00199_T 5086411 133198784 598638 171 11215 MUC5AC 0 . GRCh38 11 1198927 1198927 + Silent SNP G G T rs760904372 C3N-00199_T C3N-00199_N G G c.16227G>T p.= p.P5409P ENST00000621226 44/49 270 169 101 266 265 1 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript synonymous_variant 16274/17448 16227/16965 5409/5654 P ccG/ccT rs760904372 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 44/49 PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,SMART_domains:SM00214 LOW 1 SNV 5 1 PASS rs760904372 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 1198927 1198927 G T 1 0 0 0 0 0 0 0 1 9978 1103 39 1 1 MUC5AC 11 1198927 Silent SNP G C3N-00199_T 1198927 133887695 172 11216 OR51E2 0 . GRCh38 11 4682556 4682556 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.156C>A p.= p.R52R ENST00000396950 2/2 203 127 76 273 273 0 strelka-varscan-mutect OR51E2,synonymous_variant,p.=,ENST00000396950,NM_030774.3;OR51E2,synonymous_variant,p.=,ENST00000532598,; T ENST00000396950 Transcript synonymous_variant 396/2781 156/963 52/320 R cgC/cgA 1 -1 OR51E2 HGNC HGNC:15195 protein_coding YES CCDS7751.1 ENSP00000380153 Q9H255 A0A126GVK0 UPI000003B49B NM_030774.3 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF92,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 4682556 4682556 G T 1 0 0 0 0 0 0 0 1 11169 1306 46 2 2 OR51E2 11 4682556 Silent SNP G C3N-00199_T 3483629 4682556 130404066 173 11217 CYB5R2 0 . GRCh38 11 7665435 7665435 + Missense_Mutation SNP G G T rs146956666 C3N-00199_T C3N-00199_N G G c.770C>A p.Thr257Lys p.T257K ENST00000533558 9/9 109 61 48 103 103 0 strelka-varscan-mutect CYB5R2,missense_variant,p.Thr257Lys,ENST00000533558,NM_001302826.1;CYB5R2,missense_variant,p.Thr257Lys,ENST00000299498,NM_001302827.1,NM_016229.4;CYB5R2,3_prime_UTR_variant,,ENST00000524790,;CYB5R2,downstream_gene_variant,,ENST00000531096,;CYB5R2,downstream_gene_variant,,ENST00000524608,;CYB5R2,downstream_gene_variant,,ENST00000527542,;CYB5R2,downstream_gene_variant,,ENST00000436351,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000528585,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000534698,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000526084,;CYB5R2,non_coding_transcript_exon_variant,,ENST00000532621,;CYB5R2,downstream_gene_variant,,ENST00000534443,;CYB5R2,downstream_gene_variant,,ENST00000532920,; T ENST00000533558 Transcript missense_variant 1327/1658 770/831 257/276 T/K aCg/aAg rs146956666,COSM1357068 1 -1 CYB5R2 HGNC HGNC:24376 protein_coding YES CCDS7780.1 ENSP00000437041 Q6BCY4 UPI000013E5AB NM_001302826.1 deleterious(0.03) 9/9 hmmpanther:PTHR19370:SF108,hmmpanther:PTHR19370,Pfam_domain:PF00175,Gene3D:3.40.50.80,Superfamily_domains:SSF52343 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs146956666 . 0 204 3 2 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 41 7665435 7665435 G T 1 0 0 0 0 1 0 0 0 3931 1145 40 1 1 CYB5R2 11 7665435 Missense_Mutation SNP G C3N-00199_T 2982879 7665435 127421187 174 11218 OTOG 0 . GRCh38 11 17596998 17596998 + Missense_Mutation SNP C C T C3N-00199_T C3N-00199_N C C c.3709C>T p.Arg1237Cys p.R1237C ENST00000399391 29/55 128 121 7 154 154 0 strelka-mutect OTOG,missense_variant,p.Arg1225Cys,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Arg1237Cys,ENST00000399391,NM_001277269.1;OTOG,missense_variant,p.Arg252Cys,ENST00000342528,; T ENST00000399391 Transcript missense_variant 3709/8778 3709/8778 1237/2925 R/C Cgc/Tgc COSM4790173 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 29/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Pfam_domain:PF08742,SMART_domains:SM00832,Superfamily_domains:0050434 1 MODERATE 1 SNV 5 1 1 PASS rs1037786055 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 17596998 17596998 C T 1 0 0 0 0 1 0 0 0 11370 652 23 1 1 OTOG 11 17596998 Missense_Mutation SNP C C3N-00199_T 9931563 17596998 117489624 175 11219 PAMR1 0 . GRCh38 11 35451907 35451907 + Silent SNP C C A rs772690955 C3N-00199_T C3N-00199_N C C c.852G>T p.= p.A284A ENST00000622144 7/12 38 28 10 112 112 0 strelka-varscan-mutect PAMR1,synonymous_variant,p.=,ENST00000622144,NM_015430.3;PAMR1,synonymous_variant,p.=,ENST00000527605,;PAMR1,intron_variant,,ENST00000619888,NM_001001991.2;PAMR1,intron_variant,,ENST00000621476,NM_001282675.1;PAMR1,intron_variant,,ENST00000615849,NM_001282676.1;PAMR1,intron_variant,,ENST00000611014,;PAMR1,intron_variant,,ENST00000529303,;PAMR1,non_coding_transcript_exon_variant,,ENST00000534803,; A ENST00000622144 Transcript synonymous_variant 890/2785 852/2214 284/737 A gcG/gcT rs772690955 1 -1 PAMR1 HGNC HGNC:24554 protein_coding YES CCDS7898.1 ENSP00000482899 Q6UXH9 UPI000013DB70 NM_015430.3 7/12 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs772690955 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 35451907 35451907 C A 1 0 0 0 0 0 0 0 1 11494 523 19 1 1 PAMR1 11 35451907 Silent SNP C C3N-00199_T 17854909 35451907 99634715 176 11220 CHST1 0 . GRCh38 11 45649744 45649744 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1180C>A p.Leu394Met p.L394M ENST00000308064 4/4 88 45 43 59 59 0 strelka-varscan-mutect CHST1,missense_variant,p.Leu394Met,ENST00000308064,NM_003654.5;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,upstream_gene_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,; T ENST00000308064 Transcript missense_variant 1851/2718 1180/1236 394/411 L/M Ctg/Atg 1 -1 CHST1 HGNC HGNC:1969 protein_coding YES CCDS7913.1 ENSP00000309270 O43916 UPI0000073EA0 NM_003654.5 deleterious(0) 4/4 hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF36,PIRSF_domain:PIRSF005883 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 41 45649744 45649744 G T 1 0 0 0 0 1 0 0 0 3157 962 34 2 2 CHST1 11 45649744 Missense_Mutation SNP G C3N-00199_T 10197837 45649744 89436878 177 11221 BTBD18 0 . GRCh38 11 57745927 57745927 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.346C>T p.Arg116Cys p.R116C ENST00000422652 3/3 178 121 57 200 200 0 strelka-varscan-mutect BTBD18,missense_variant,p.Arg116Cys,ENST00000422652,NM_001145101.1;BTBD18,missense_variant,p.Arg116Cys,ENST00000436147,;TMX2,downstream_gene_variant,,ENST00000278422,NM_015959.3;TMX2,downstream_gene_variant,,ENST00000378312,NM_001144012.2;C11orf31,downstream_gene_variant,,ENST00000622257,;C11orf31,downstream_gene_variant,,ENST00000388857,;C11orf31,downstream_gene_variant,,ENST00000534355,NM_170746.2;BTBD18,downstream_gene_variant,,ENST00000527995,;C11orf31,downstream_gene_variant,,ENST00000528798,;C11orf31,downstream_gene_variant,,ENST00000623303,;TMX2-CTNND1,intron_variant,,ENST00000528395,;RP11-691N7.6,intron_variant,,ENST00000531074,;TMX2,downstream_gene_variant,,ENST00000529403,;C11orf31,downstream_gene_variant,,ENST00000533321,;C11orf31,downstream_gene_variant,,ENST00000534386,; A ENST00000422652 Transcript missense_variant 635/3044 346/2139 116/712 R/C Cgt/Tgt 1 -1 BTBD18 HGNC HGNC:37214 protein_coding YES CCDS44603.1 ENSP00000394472 B2RXH4 UPI00006C113A NM_001145101.1 deleterious(0.02) 3/3 hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 57745927 57745927 G A 1 0 0 0 0 1 0 0 0 1717 1116 39 1 1 BTBD18 11 57745927 Missense_Mutation SNP G C3N-00199_T 12096183 57745927 77340695 178 11222 MS4A5 0 . GRCh38 11 60430856 60430856 + Silent SNP T T C C3N-00199_T C3N-00199_N T T c.214T>C p.= p.L72L ENST00000300190 2/5 47 25 22 172 172 0 strelka-varscan-mutect MS4A5,synonymous_variant,p.=,ENST00000300190,NM_023945.2;MS4A5,synonymous_variant,p.=,ENST00000528905,;MS4A5,intron_variant,,ENST00000528093,;MS4A5,intron_variant,,ENST00000534071,;MS4A5,synonymous_variant,p.=,ENST00000533885,;MS4A5,intron_variant,,ENST00000531403,; C ENST00000300190 Transcript synonymous_variant 300/722 214/603 72/200 L Ttg/Ctg COSM543995 1 1 MS4A5 HGNC HGNC:13374 protein_coding YES CCDS7987.1 ENSP00000300190 Q9H3V2 UPI0000043670 NM_023945.2 2/5 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF54 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 41 60430856 60430856 T C 1 0 0 0 0 0 0 0 1 9842 1606 56 5 5 MS4A5 11 60430856 Silent SNP T C3N-00199_T 2684929 60430856 74655766 179 11223 FAT3 0 . GRCh38 11 92800787 92800787 + Missense_Mutation SNP G G C C3N-00199_T C3N-00199_N G G c.7324G>C p.Asp2442His p.D2442H ENST00000525166 9/27 122 70 52 275 275 0 strelka-varscan-mutect FAT3,missense_variant,p.Asp2592His,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Asp2442His,ENST00000525166,; C ENST00000525166 Transcript missense_variant 7346/18699 7324/13320 2442/4439 D/H Gat/Cat COSM4558698,COSM4558699,COSM5551932,COSM5551933 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 92800787 92800787 G C 1 0 0 0 0 1 0 0 0 5551 1174 41 4 4 FAT3 11 92800787 Missense_Mutation SNP G C3N-00199_T 32369931 92800787 42285835 180 11224 MTNR1B 0 . GRCh38 11 92981571 92981571 + Missense_Mutation SNP C C G rs200944330 C3N-00199_T C3N-00199_N C C c.348C>G p.Ser116Arg p.S116R ENST00000257068 2/2 407 246 161 458 458 0 strelka-varscan-mutect MTNR1B,missense_variant,p.Ser116Arg,ENST00000257068,NM_005959.3;MTNR1B,intron_variant,,ENST00000528076,;MTNR1B,3_prime_UTR_variant,,ENST00000532482,; G ENST00000257068 Transcript missense_variant 354/1565 348/1089 116/362 S/R agC/agG rs200944330 1 1 MTNR1B HGNC HGNC:7464 protein_coding YES CCDS8290.1 ENSP00000257068 P49286 UPI0000050408 NM_005959.3 deleterious(0) 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF262,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs200944330 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 92981571 92981571 C G 1 0 0 0 0 1 0 0 0 9939 767 27 4 4 MTNR1B 11 92981571 Missense_Mutation SNP C C3N-00199_T 180784 92981571 42105051 181 11225 CASP1 0 . GRCh38 11 105030425 105030425 + Nonsense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.532A>T p.Arg178Ter p.R178* ENST00000533400 5/9 99 71 28 257 257 0 strelka-varscan-mutect CASP1,stop_gained,p.Arg178Ter,ENST00000533400,NM_001257118.2;CASP1,stop_gained,p.Arg141Ter,ENST00000527979,;CASP1,stop_gained,p.Arg178Ter,ENST00000436863,NM_033292.3;CASP1,stop_gained,p.Arg139Ter,ENST00000528974,;CASP1,stop_gained,p.Arg157Ter,ENST00000525825,NM_001223.4,NM_001257119.2;CASP1,stop_gained,p.Arg85Ter,ENST00000526568,NM_033293.3;CASP1,stop_gained,p.Arg85Ter,ENST00000446369,NM_033294.3;CASP1,stop_gained,p.Arg85Ter,ENST00000534497,;CASP1,stop_gained,p.Arg27Ter,ENST00000532439,;CASP1,intron_variant,,ENST00000353247,NM_033295.3;CASP1,intron_variant,,ENST00000531166,;CASP1,3_prime_UTR_variant,,ENST00000529871,;CASP1,downstream_gene_variant,,ENST00000526511,;CASP1,downstream_gene_variant,,ENST00000528424,;CASP1,downstream_gene_variant,,ENST00000532520,;CASP1,upstream_gene_variant,,ENST00000527625,; A ENST00000533400 Transcript stop_gained 568/2001 532/1215 178/404 R/* Aga/Tga 1 -1 CASP1 HGNC HGNC:1499 protein_coding YES CCDS8330.1 ENSP00000433138 P29466 UPI000003AEF8 NM_001257118.2 5/9 Gene3D:3.40.50.1460,Pfam_domain:PF00656,PIRSF_domain:PIRSF038001,PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF34,SMART_domains:SM00115,Superfamily_domains:SSF52129 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 105030425 105030425 T A 1 0 0 0 0 0 1 0 0 2368 1530 53 4 4 CASP1 11 105030425 Nonsense_Mutation SNP T C3N-00199_T 12048854 105030425 30056197 182 11226 NLRX1 0 . GRCh38 11 119174596 119174596 + Missense_Mutation SNP C C G rs552633626 C3N-00199_T C3N-00199_N C C c.993C>G p.Cys331Trp p.C331W ENST00000409109 6/10 357 242 115 394 394 0 strelka-varscan-mutect NLRX1,missense_variant,p.Cys331Trp,ENST00000409109,NM_001282144.1;NLRX1,missense_variant,p.Cys331Trp,ENST00000292199,NM_024618.3;NLRX1,missense_variant,p.Cys331Trp,ENST00000409991,NM_001282143.1;NLRX1,missense_variant,p.Cys331Trp,ENST00000409265,NM_001282358.1;NLRX1,missense_variant,p.Cys331Trp,ENST00000525863,;NLRX1,downstream_gene_variant,,ENST00000454811,;NLRX1,downstream_gene_variant,,ENST00000449394,;NLRX1,downstream_gene_variant,,ENST00000422249,;NLRX1,downstream_gene_variant,,ENST00000474751,;NLRX1,upstream_gene_variant,,ENST00000469103,;NLRX1,downstream_gene_variant,,ENST00000468765,;NLRX1,downstream_gene_variant,,ENST00000482180,;NLRX1,non_coding_transcript_exon_variant,,ENST00000481860,;NLRX1,non_coding_transcript_exon_variant,,ENST00000524562,; G ENST00000409109 Transcript missense_variant 1580/4092 993/2928 331/975 C/W tgC/tgG rs552633626 1 1 NLRX1 HGNC HGNC:29890 protein_coding YES CCDS8416.1 ENSP00000387334 Q86UT6 UPI0000161217 NM_001282144.1 deleterious_low_confidence(0) 6/10 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF152 MODERATE 1 SNV 1 1 PASS rs552633626 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 119174596 119174596 C G 1 0 0 0 0 1 0 0 0 10523 776 27 4 4 NLRX1 11 119174596 Missense_Mutation SNP C C3N-00199_T 14144171 119174596 15912026 183 11227 FOXJ2 0 . GRCh38 12 8044053 8044053 + Missense_Mutation SNP T T C novel C3N-00199_T C3N-00199_N T T c.580T>C p.Ser194Pro p.S194P ENST00000162391 5/11 42 31 11 52 52 0 strelka-varscan-mutect FOXJ2,missense_variant,p.Ser194Pro,ENST00000162391,NM_018416.2;FOXJ2,missense_variant,p.Ser194Pro,ENST00000428177,; C ENST00000162391 Transcript missense_variant 1725/5523 580/1725 194/574 S/P Tca/Cca 1 1 FOXJ2 HGNC HGNC:24818 protein_coding YES CCDS8587.1 ENSP00000162391 Q9P0K8 UPI000012ADE1 NM_018416.2 tolerated(0.35) 5/11 hmmpanther:PTHR11829:SF103,hmmpanther:PTHR11829 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 8044053 8044053 T C 1 0 0 0 0 1 0 0 0 5875 1667 58 5 5 FOXJ2 12 8044053 Missense_Mutation SNP T C3N-00199_T 8044053 125231256 184 11228 CAPZA3 0 . GRCh38 12 18738410 18738410 + Missense_Mutation SNP G G T rs757316928 C3N-00199_T C3N-00199_N G G c.142G>T p.Gly48Cys p.G48C ENST00000317658 1/1 76 54 22 279 279 0 strelka-varscan-mutect CAPZA3,missense_variant,p.Gly48Cys,ENST00000317658,NM_033328.2;PLCZ1,upstream_gene_variant,,ENST00000266505,NM_033123.3;PLCZ1,upstream_gene_variant,,ENST00000539875,;PLCZ1,upstream_gene_variant,,ENST00000543242,;PLCZ1,upstream_gene_variant,,ENST00000541966,;PLCZ1,upstream_gene_variant,,ENST00000539072,;RP11-361I14.2,downstream_gene_variant,,ENST00000536931,;PLCZ1,upstream_gene_variant,,ENST00000545129,;PLCZ1,upstream_gene_variant,,ENST00000541109,;PLCZ1,upstream_gene_variant,,ENST00000318197,;PLCZ1,upstream_gene_variant,,ENST00000539207,;PLCZ1,upstream_gene_variant,,ENST00000544849,;PLCZ1,upstream_gene_variant,,ENST00000535429,; T ENST00000317658 Transcript missense_variant 310/1087 142/900 48/299 G/C Ggt/Tgt rs757316928 1 1 CAPZA3 HGNC HGNC:24205 protein_coding YES CCDS8681.1 ENSP00000326238 Q96KX2 A0A140VKF6 UPI00001270FE NM_033328.2 deleterious(0.01) 1/1 hmmpanther:PTHR10653,hmmpanther:PTHR10653:SF6,Pfam_domain:PF01267,Superfamily_domains:SSF90096 MODERATE SNV 1 PASS rs757316928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 18738410 18738410 G T 1 0 0 0 0 1 0 0 0 2337 1000 35 2 2 CAPZA3 12 18738410 Missense_Mutation SNP G C3N-00199_T 10694357 18738410 114536899 185 11229 PKP2 0 . GRCh38 12 32841085 32841085 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1631C>A p.Pro544Gln p.P544Q ENST00000070846 7/14 108 73 35 244 244 0 strelka-varscan-mutect PKP2,missense_variant,p.Pro500Gln,ENST00000340811,NM_001005242.2;PKP2,missense_variant,p.Pro544Gln,ENST00000070846,NM_004572.3; T ENST00000070846 Transcript missense_variant 1656/4241 1631/2646 544/881 P/Q cCa/cAa 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 deleterious(0) 7/14 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1318070848 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 32841085 32841085 G T 1 0 0 0 0 1 0 0 0 12081 1348 47 2 2 PKP2 12 32841085 Missense_Mutation SNP G C3N-00199_T 14102675 32841085 100434224 186 11230 NCKAP5L 0 . GRCh38 12 49801960 49801960 + Missense_Mutation SNP C C A rs374619177 C3N-00199_T C3N-00199_N C C c.239G>T p.Arg80Leu p.R80L ENST00000335999 6/13 157 113 44 185 185 0 strelka-varscan-mutect NCKAP5L,missense_variant,p.Arg80Leu,ENST00000335999,NM_001037806.3;NCKAP5L,upstream_gene_variant,,ENST00000433948,;NCKAP5L,downstream_gene_variant,,ENST00000480927,;NCKAP5L,downstream_gene_variant,,ENST00000477361,;NCKAP5L,downstream_gene_variant,,ENST00000491441,; A ENST00000335999 Transcript missense_variant 441/4900 239/4005 80/1334 R/L cGa/cTa rs374619177 1 -1 NCKAP5L HGNC HGNC:29321 protein_coding YES CCDS41781.2 ENSP00000337998 Q9HCH0 UPI00006C1298 NM_001037806.3 deleterious(0) 6/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21740 MODERATE 1 SNV 5 1 PASS rs374619177 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 49801960 49801960 C A 1 0 0 0 0 1 0 0 0 10242 884 31 1 1 NCKAP5L 12 49801960 Missense_Mutation SNP C C3N-00199_T 16960875 49801960 83473349 187 11231 MYRFL 0 . GRCh38 12 69936569 69936569 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.2161G>C p.Val721Leu p.V721L ENST00000552032 19/25 67 50 17 171 171 0 strelka-varscan-mutect MYRFL,missense_variant,p.Val710Leu,ENST00000547771,;MYRFL,missense_variant,p.Val721Leu,ENST00000552032,NM_182530.2;MYRFL,missense_variant,p.Val186Leu,ENST00000548892,;MYRFL,missense_variant,p.Val86Leu,ENST00000535034,;MYRFL,missense_variant,p.Val86Leu,ENST00000299350,;LINC01481,intron_variant,,ENST00000549419,; C ENST00000552032 Transcript missense_variant 2375/3139 2161/2733 721/910 V/L Gtc/Ctc 1 1 MYRFL HGNC HGNC:26316 protein_coding YES CCDS76577.1 ENSP00000448753 Q96LU7 UPI00016627C0 NM_182530.2 tolerated(0.4) 19/25 hmmpanther:PTHR13029,hmmpanther:PTHR13029:SF17 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 69936569 69936569 G C 1 0 0 0 0 1 0 0 0 10102 1029 36 4 4 MYRFL 12 69936569 Missense_Mutation SNP G C3N-00199_T 20134609 69936569 63338740 188 11232 POLR3B 0 . GRCh38 12 106459364 106459364 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.2566A>T p.Ile856Leu p.I856L ENST00000228347 22/28 178 136 42 515 515 0 strelka-varscan-mutect POLR3B,missense_variant,p.Ile856Leu,ENST00000228347,NM_018082.5;POLR3B,missense_variant,p.Ile798Leu,ENST00000539066,NM_001160708.1; T ENST00000228347 Transcript missense_variant 2788/4273 2566/3402 856/1133 I/L Ata/Tta 1 1 POLR3B HGNC HGNC:30348 protein_coding YES CCDS9105.1 ENSP00000228347 Q9NW08 UPI000000DB67 NM_018082.5 tolerated(0.88) 22/28 Gene3D:2.40.50.150,Pfam_domain:PF00562,hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF8,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 106459364 106459364 A T 1 0 0 0 0 1 0 0 0 12340 231 8 4 4 POLR3B 12 106459364 Missense_Mutation SNP A C3N-00199_T 36522795 106459364 26815945 189 11233 TBX5 0 . GRCh38 12 114366205 114366205 + Silent SNP G G T C3N-00199_T C3N-00199_N G G c.942C>A p.= p.P314P ENST00000310346 8/9 184 139 45 231 230 1 strelka-varscan-mutect TBX5,synonymous_variant,p.=,ENST00000310346,NM_000192.3;TBX5,synonymous_variant,p.=,ENST00000349716,NM_080717.2;TBX5,synonymous_variant,p.=,ENST00000405440,NM_181486.2;TBX5,synonymous_variant,p.=,ENST00000526441,; T ENST00000310346 Transcript synonymous_variant 1609/3825 942/1557 314/518 P ccC/ccA COSM5268581,COSM5268582 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 114366205 114366205 G T 1 0 0 0 0 0 0 0 1 16065 1219 43 2 2 TBX5 12 114366205 Silent SNP G C3N-00199_T 7906841 114366205 18909104 190 11234 DNAH10 0 . GRCh38 12 123841387 123841387 + Silent SNP G G A C3N-00199_T C3N-00199_N G G c.4848G>A p.= p.A1616A ENST00000638045 29/78 350 304 46 421 421 0 strelka-varscan-mutect DNAH10,synonymous_variant,p.=,ENST00000409039,;DNAH10,synonymous_variant,p.=,ENST00000638045,NM_207437.3;DNAH10,synonymous_variant,p.=,ENST00000497783,; A ENST00000638045 Transcript synonymous_variant 4873/13678 4848/13416 1616/4471 A gcG/gcA COSM4549853,COSM4549854 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 29/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF08393 1,1 LOW 1 SNV 1,1 1 PASS rs984373122 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 123841387 123841387 G A 1 0 0 0 0 0 0 0 1 4411 1045 37 1 1 DNAH10 12 123841387 Silent SNP G C3N-00199_T 9475182 123841387 9433922 191 11235 TMEM132C 0 . GRCh38 12 128415202 128415202 + Missense_Mutation SNP C C T rs557263376 C3N-00199_T C3N-00199_N C C c.556C>T p.Arg186Trp p.R186W ENST00000435159 2/9 241 215 26 293 293 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Arg186Trp,ENST00000435159,NM_001136103.2; T ENST00000435159 Transcript missense_variant 556/4947 556/3327 186/1108 R/W Cgg/Tgg rs557263376,COSM1476318 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0) 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs557263376 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 128415202 128415202 C T 1 0 0 0 0 1 0 0 0 16491 643 23 1 1 TMEM132C 12 128415202 Missense_Mutation SNP C C3N-00199_T 4573815 128415202 4860107 192 11236 TMEM132C 0 . GRCh38 12 128705137 128705137 + Silent SNP G G T rs754749450 C3N-00199_T C3N-00199_N G G c.2169G>T p.= p.T723T ENST00000435159 9/9 77 71 6 90 90 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; T ENST00000435159 Transcript synonymous_variant 2169/4947 2169/3327 723/1108 T acG/acT rs754749450 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 LOW 1 SNV 5 1 PASS rs754749450 . 0 196 13 0 0 0 0 0 -12.81334 0.9994162 1 1 1 0 T 2 4 41 128705137 128705137 G T 1 0 0 0 0 0 0 0 1 16491 1074 38 1 1 TMEM132C 12 128705137 Silent SNP G C3N-00199_T 289935 128705137 4570172 193 11237 SLC15A4 0 . GRCh38 12 128814983 128814983 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.634G>T p.Gly212Cys p.G212C ENST00000266771 2/8 260 235 25 315 315 0 strelka-varscan-mutect SLC15A4,missense_variant,p.Gly212Cys,ENST00000266771,NM_145648.3;SLC15A4,upstream_gene_variant,,ENST00000614634,;SLC15A4,non_coding_transcript_exon_variant,,ENST00000539703,;SLC15A4,non_coding_transcript_exon_variant,,ENST00000535272,;RP11-21K12.2,upstream_gene_variant,,ENST00000623017,;SLC15A4,missense_variant,p.Gly158Cys,ENST00000376744,;SLC15A4,missense_variant,p.Gly72Cys,ENST00000376740,;SLC15A4,non_coding_transcript_exon_variant,,ENST00000366292,;SLC15A4,upstream_gene_variant,,ENST00000544112,; A ENST00000266771 Transcript missense_variant 674/2779 634/1734 212/577 G/C Ggc/Tgc 1 -1 SLC15A4 HGNC HGNC:23090 protein_coding YES CCDS9264.1 ENSP00000266771 Q8N697 UPI000006F120 NM_145648.3 deleterious(0.03) 2/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF80,Pfam_domain:PF00854,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 128814983 128814983 C A 1 0 0 0 0 1 0 0 0 14666 594 21 2 2 SLC15A4 12 128814983 Missense_Mutation SNP C C3N-00199_T 109846 128814983 4460326 194 11238 MMP17 0 . GRCh38 12 131840591 131840591 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.441G>T p.= p.R147R ENST00000360564 4/10 41 27 14 45 45 0 strelka-varscan-mutect MMP17,synonymous_variant,p.=,ENST00000360564,NM_016155.4;MMP17,synonymous_variant,p.=,ENST00000535291,;MMP17,synonymous_variant,p.=,ENST00000545671,;MMP17,synonymous_variant,p.=,ENST00000545790,;MMP17,5_prime_UTR_variant,,ENST00000534865,;MMP17,upstream_gene_variant,,ENST00000535004,;MMP17,upstream_gene_variant,,ENST00000542648,;MMP17,upstream_gene_variant,,ENST00000535182,;MMP17,upstream_gene_variant,,ENST00000542142,;MMP17,upstream_gene_variant,,ENST00000537848,; T ENST00000360564 Transcript synonymous_variant 543/2411 441/1812 147/603 R cgG/cgT 1 1 MMP17 HGNC HGNC:7163 protein_coding YES CCDS31927.1 ENSP00000353767 Q9ULZ9 UPI00001AF305 NM_016155.4 4/10 Gene3D:3.40.390.10,Pfam_domain:PF00413,PIRSF_domain:PIRSF001191,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF21,SMART_domains:SM00235,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 131840591 131840591 G T 1 0 0 0 0 0 0 0 1 9619 1219 43 2 2 MMP17 12 131840591 Silent SNP G C3N-00199_T 3025608 131840591 1434718 195 11239 ATP7B 0 . GRCh38 13 51939161 51939161 + Missense_Mutation SNP C C T rs758025913 C3N-00199_T C3N-00199_N C C c.3589G>A p.Ala1197Thr p.A1197T ENST00000242839 17/21 599 536 63 601 600 1 strelka-varscan-mutect ATP7B,missense_variant,p.Ala1197Thr,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Ala1119Thr,ENST00000448424,;ATP7B,missense_variant,p.Ala1086Thr,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Ala990Thr,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Ala1149Thr,ENST00000634844,;ATP7B,missense_variant,p.Ala1132Thr,ENST00000418097,;ATP7B,missense_variant,p.Ala767Thr,ENST00000400370,;ATP7B,upstream_gene_variant,,ENST00000634519,;ATP7B,downstream_gene_variant,,ENST00000466629,;ATP7B,3_prime_UTR_variant,,ENST00000634308,;ATP7B,3_prime_UTR_variant,,ENST00000634296,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634810,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634620,; T ENST00000242839 Transcript missense_variant 3746/6638 3589/4398 1197/1465 A/T Gct/Act rs758025913,CM994114,COSM4664512 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 tolerated(1) 17/21 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,TIGRFAM_domain:TIGR01494,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01525,Pfam_domain:PF00702,Superfamily_domains:SSF56784,Prints_domain:PR00119 0,0,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs758025913 . 0 208 0 0 0 0 0 2 -11.56731 0 0 1 0 0 T 3 4 41 51939161 51939161 C T 1 0 0 0 0 1 0 0 0 1344 768 27 1 1 ATP7B 13 51939161 Missense_Mutation SNP C C3N-00199_T 51939161 62425167 196 11240 PCDH17 0 . GRCh38 13 57724684 57724684 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.2870A>T p.Gln957Leu p.Q957L ENST00000377918 4/4 80 61 19 168 168 0 strelka-varscan-mutect PCDH17,missense_variant,p.Gln957Leu,ENST00000377918,NM_001040429.2;PCDH17,missense_variant,p.Gln344Leu,ENST00000612954,;PCDH17,missense_variant,p.Gln163Leu,ENST00000615375,;PCDH17,3_prime_UTR_variant,,ENST00000484979,; T ENST00000377918 Transcript missense_variant 3605/8232 2870/3480 957/1159 Q/L cAg/cTg 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 deleterious(0.03) 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 57724684 57724684 A T 1 0 0 0 0 1 0 0 0 11599 188 7 4 4 PCDH17 13 57724684 Missense_Mutation SNP A C3N-00199_T 5785523 57724684 56639644 197 11241 SLITRK1 0 . GRCh38 13 83880803 83880803 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.705G>T p.= p.L235L ENST00000377084 1/1 267 226 41 390 390 0 strelka-varscan-mutect SLITRK1,synonymous_variant,p.=,ENST00000377084,NM_052910.2,NM_001281503.1; A ENST00000377084 Transcript synonymous_variant 1591/5189 705/2091 235/696 L ctG/ctT 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 1/1 SMART_domains:SM00082,Superfamily_domains:SSF52058 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 83880803 83880803 C A 1 0 0 0 0 0 0 0 1 15033 813 29 2 2 SLITRK1 13 83880803 Silent SNP C C3N-00199_T 26156119 83880803 30483525 198 11242 SLITRK5 0 . GRCh38 13 87676762 87676762 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1374C>A p.Asn458Lys p.N458K ENST00000325089 2/2 151 125 26 207 207 0 strelka-varscan-mutect SLITRK5,missense_variant,p.Asn458Lys,ENST00000325089,NM_015567.1; A ENST00000325089 Transcript missense_variant 1593/21103 1374/2877 458/958 N/K aaC/aaA 1 1 SLITRK5 HGNC HGNC:20295 protein_coding YES CCDS9465.1 ENSP00000366283 O94991 UPI000015F6F7 NM_015567.1 deleterious(0.01) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF10,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs1328526399 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 87676762 87676762 C A 1 0 0 0 0 1 0 0 0 15037 506 18 2 2 SLITRK5 13 87676762 Missense_Mutation SNP C C3N-00199_T 3795959 87676762 26687566 199 11243 CCDC168 0 . GRCh38 13 102736665 102736665 + Nonsense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.14032G>T p.Glu4678Ter p.E4678* ENST00000322527 4/4 50 37 13 169 169 0 strelka-varscan-mutect CCDC168,stop_gained,p.Glu4678Ter,ENST00000322527,NM_001146197.1; A ENST00000322527 Transcript stop_gained 14170/21466 14032/21246 4678/7081 E/* Gaa/Taa 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 Pfam_domain:PF15804,hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 HIGH 1 SNV 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 41 102736665 102736665 C A 1 0 0 0 0 0 1 0 0 2484 864 30 2 2 CCDC168 13 102736665 Nonsense_Mutation SNP C C3N-00199_T 15059903 102736665 11627663 200 11244 KCNK10 0 . GRCh38 14 88263229 88263229 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.375C>T p.= p.S125S ENST00000319231 2/7 126 82 44 134 134 0 strelka-varscan-mutect KCNK10,synonymous_variant,p.=,ENST00000340700,NM_021161.4;KCNK10,synonymous_variant,p.=,ENST00000319231,NM_138317.2;KCNK10,synonymous_variant,p.=,ENST00000312350,NM_138318.2;KCNK10,synonymous_variant,p.=,ENST00000556282,; A ENST00000319231 Transcript synonymous_variant 826/2725 375/1632 125/543 S agC/agT 1 -1 KCNK10 HGNC HGNC:6273 protein_coding YES CCDS9881.1 ENSP00000312811 P57789 UPI000002A697 NM_138317.2 2/7 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF32,Prints_domain:PR01499 LOW 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 41 88263229 88263229 G A 1 0 0 0 0 0 0 0 1 7976 1194 42 3 3 KCNK10 14 88263229 Silent SNP G C3N-00199_T 88263229 18780489 201 11245 SERPINA3 0 . GRCh38 14 94614882 94614882 + Silent SNP C C A C3N-00199_T C3N-00199_N C C c.441C>A p.= p.L147L ENST00000467132 2/5 363 293 70 344 344 0 strelka-varscan-mutect SERPINA3,synonymous_variant,p.=,ENST00000467132,;SERPINA3,synonymous_variant,p.=,ENST00000393078,NM_001085.4;SERPINA3,synonymous_variant,p.=,ENST00000393080,;SERPINA3,synonymous_variant,p.=,ENST00000555820,;SERPINA3,upstream_gene_variant,,ENST00000482740,;SERPINA3,upstream_gene_variant,,ENST00000621603,;SERPINA3,intron_variant,,ENST00000556388,;SERPINA3,downstream_gene_variant,,ENST00000485588,;SERPINA3,synonymous_variant,p.=,ENST00000556968,;SERPINA3,3_prime_UTR_variant,,ENST00000553947,; A ENST00000467132 Transcript synonymous_variant 1589/2660 441/1272 147/423 L ctC/ctA COSM699765 1 1 SERPINA3 HGNC HGNC:16 protein_coding YES CCDS32150.1 ENSP00000450540 P01011 A0A024R6P0 UPI000012509B 2/5 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF145,SMART_domains:SM00093,Superfamily_domains:SSF56574 1 LOW SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 94614882 94614882 C A 1 0 0 0 0 0 0 0 1 14366 813 29 2 2 SERPINA3 14 94614882 Silent SNP C C3N-00199_T 6351653 94614882 12428836 202 11246 DIO3 0 . GRCh38 14 101561727 101561727 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.231G>T p.= p.R77R ENST00000510508 1/1 289 226 63 208 208 0 strelka-varscan-mutect DIO3,synonymous_variant,p.=,ENST00000510508,NM_001362.3;DIO3OS,upstream_gene_variant,,ENST00000554735,;DIO3OS,upstream_gene_variant,,ENST00000557661,;DIO3OS,upstream_gene_variant,,ENST00000555174,;DIO3OS,upstream_gene_variant,,ENST00000554441,;DIO3OS,upstream_gene_variant,,ENST00000554694,;DIO3OS,upstream_gene_variant,,ENST00000555882,;DIO3OS,upstream_gene_variant,,ENST00000557532,;DIO3OS,upstream_gene_variant,,ENST00000557109,;DIO3OS,upstream_gene_variant,,ENST00000553729,;DIO3OS,upstream_gene_variant,,ENST00000556266,;DIO3OS,upstream_gene_variant,,ENST00000408206,; T ENST00000510508 Transcript synonymous_variant 377/2102 231/915 77/304 R cgG/cgT 1 1 DIO3 HGNC HGNC:2885 protein_coding YES CCDS41992.2 ENSP00000427336 P55073 UPI0001B1A4B2 NM_001362.3 1/1 Pfam_domain:PF00837,PIRSF_domain:PIRSF001330,PIRSF_domain:PIRSF500144,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF4 LOW SNV 1 PASS rs1377981069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 101561727 101561727 G T 1 0 0 0 0 0 0 0 1 4331 1219 43 2 2 DIO3 14 101561727 Silent SNP G C3N-00199_T 6946845 101561727 5481991 203 11247 TRPM1 0 . GRCh38 15 31040294 31040294 + Missense_Mutation SNP C C T C3N-00199_T C3N-00199_N C C c.2191G>A p.Glu731Lys p.E731K ENST00000542188 17/27 448 403 45 620 620 0 strelka-varscan-mutect TRPM1,missense_variant,p.Glu731Lys,ENST00000542188,NM_001252020.1;TRPM1,missense_variant,p.Glu692Lys,ENST00000397795,NM_002420.5;TRPM1,missense_variant,p.Glu714Lys,ENST00000256552,NM_001252024.1;TRPM1,missense_variant,p.Glu615Lys,ENST00000558768,;TRPM1,missense_variant,p.Glu692Lys,ENST00000558445,;TRPM1,intron_variant,,ENST00000559177,;RP11-348B17.1,intron_variant,,ENST00000561299,;RP11-348B17.1,downstream_gene_variant,,ENST00000558755,;TRPM1,3_prime_UTR_variant,,ENST00000560801,; T ENST00000542188 Transcript missense_variant 2505/6004 2191/4929 731/1642 E/K Gag/Aag COSM5633045 1 -1 TRPM1 HGNC HGNC:7146 protein_coding YES CCDS58347.1 ENSP00000437849 Q7Z4N2 UPI0001DBB3A9 NM_001252020.1 deleterious(0) 17/27 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF13 1 MODERATE 1 SNV 1 1 1 PASS rs1355796117 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 31040294 31040294 C T 1 0 0 0 0 1 0 0 0 17091 893 31 1 1 TRPM1 15 31040294 Missense_Mutation SNP C C3N-00199_T 31040294 70950895 204 11248 FMN1 0 . GRCh38 15 32969288 32969288 + Missense_Mutation SNP C C A rs770280947 C3N-00199_T C3N-00199_N C C c.2413G>T p.Val805Phe p.V805F ENST00000616417 8/21 160 142 18 301 300 1 strelka-varscan-mutect FMN1,missense_variant,p.Val805Phe,ENST00000616417,NM_001277313.1;FMN1,missense_variant,p.Val582Phe,ENST00000334528,NM_001103184.3;FMN1,missense_variant,p.Val805Phe,ENST00000559047,;FMN1,missense_variant,p.Val707Phe,ENST00000561249,;SNORD77,upstream_gene_variant,,ENST00000391113,; A ENST00000616417 Transcript missense_variant 2917/13529 2413/4260 805/1419 V/F Gtc/Ttc rs770280947 1 -1 FMN1 HGNC HGNC:3768 protein_coding YES CCDS61581.1 ENSP00000479134 Q68DA7 UPI0001AE68B4 NM_001277313.1 deleterious(0) 8/21 hmmpanther:PTHR13037:SF11,hmmpanther:PTHR13037,Prints_domain:PR00828 MODERATE 1 SNV 5 1 PASS rs770280947 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 32969288 32969288 C A 1 0 0 0 0 1 0 0 0 5805 536 19 1 1 FMN1 15 32969288 Missense_Mutation SNP C C3N-00199_T 1928994 32969288 69021901 205 11249 FAM98B 0 . GRCh38 15 38464075 38464075 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.115G>T p.Ala39Ser p.A39S ENST00000397609 2/8 55 50 5 178 178 0 strelka-mutect FAM98B,missense_variant,p.Ala39Ser,ENST00000397609,NM_173611.3;FAM98B,missense_variant,p.Ala39Ser,ENST00000491535,;FAM98B,upstream_gene_variant,,ENST00000559431,;FAM98B,upstream_gene_variant,,ENST00000305752,;AC109631.1,upstream_gene_variant,,ENST00000559695,; T ENST00000397609 Transcript missense_variant 150/4388 115/1302 39/433 A/S Gca/Tca 1 1 FAM98B HGNC HGNC:26773 protein_coding YES CCDS10047.2 ENSP00000380734 Q52LJ0 UPI0000DA182F NM_173611.3 tolerated(0.05) 2/8 hmmpanther:PTHR31353,hmmpanther:PTHR31353:SF11,Pfam_domain:PF10239 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -9.703485 0.9999998 1 1 1 0 T 3 4 41 38464075 38464075 G T 1 0 0 0 0 1 0 0 0 5515 1203 42 2 2 FAM98B 15 38464075 Missense_Mutation SNP G C3N-00199_T 5494787 38464075 63527114 206 11250 RASGRP1 0 . GRCh38 15 38512895 38512895 + Missense_Mutation SNP C C T C3N-00199_T C3N-00199_N C C c.737G>A p.Arg246Gln p.R246Q ENST00000310803 7/17 118 108 10 153 153 0 strelka-varscan-mutect RASGRP1,missense_variant,p.Arg246Gln,ENST00000310803,NM_005739.3;RASGRP1,missense_variant,p.Arg246Gln,ENST00000539159,;RASGRP1,missense_variant,p.Arg260Gln,ENST00000558432,;RASGRP1,missense_variant,p.Arg297Gln,ENST00000561180,;RASGRP1,missense_variant,p.Arg246Gln,ENST00000450598,NM_001128602.1;RASGRP1,missense_variant,p.Arg246Gln,ENST00000559830,NM_001306086.1;RASGRP1,missense_variant,p.Arg246Gln,ENST00000558164,;RASGRP1,missense_variant,p.Arg246Gln,ENST00000414708,;RASGRP1,upstream_gene_variant,,ENST00000560425,; T ENST00000310803 Transcript missense_variant 915/5023 737/2394 246/797 R/Q cGa/cAa COSM215604 1 -1 RASGRP1 HGNC HGNC:9878 protein_coding YES CCDS45222.1 ENSP00000310244 O95267 UPI000006FE1C NM_005739.3 deleterious(0) 7/17 Superfamily_domains:0041591,Gene3D:2ii0A02,Pfam_domain:PF00617,PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF174,SMART_domains:SM00147 1 MODERATE 1 SNV 1 1 1 PASS rs1330653682 . 0 208 2 0 0 0 0 0 -19.7191 1 1 1 1 0 T 3 4 41 38512895 38512895 C T 1 0 0 0 0 1 0 0 0 13235 884 31 1 1 RASGRP1 15 38512895 Missense_Mutation SNP C C3N-00199_T 48820 38512895 63478294 207 11251 SLC28A2 0 . GRCh38 15 45263994 45263994 + Missense_Mutation SNP T T A novel C3N-00199_T C3N-00199_N T T c.560T>A p.Leu187His p.L187H ENST00000347644 6/18 51 45 6 102 102 0 strelka-varscan-mutect SLC28A2,missense_variant,p.Leu187His,ENST00000347644,NM_004212.3;SLC28A2,missense_variant,p.Leu175His,ENST00000560438,;CTD-2651B20.3,intron_variant,,ENST00000560344,;CTD-2651B20.3,intron_variant,,ENST00000561404,;SLC28A2,intron_variant,,ENST00000559924,; A ENST00000347644 Transcript missense_variant 625/4374 560/1977 187/658 L/H cTc/cAc 1 1 SLC28A2 HGNC HGNC:11002 protein_coding YES CCDS10121.1 ENSP00000315006 O43868 UPI000013D0D5 NM_004212.3 deleterious(0) 6/18 Pfam_domain:PF01773,hmmpanther:PTHR10590,hmmpanther:PTHR10590:SF11,TIGRFAM_domain:TIGR00804,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1023142556 . 0 207 2 0 0 0 0 0 -14.91188 1 1 1 1 0 A 3 1 41 45263994 45263994 T A 1 0 0 0 0 1 0 0 0 14802 1551 54 4 4 SLC28A2 15 45263994 Missense_Mutation SNP T C3N-00199_T 6751099 45263994 56727195 208 11252 ATP8B4 0 . GRCh38 15 49862366 49862366 + Missense_Mutation SNP C C G rs146911077 C3N-00199_T C3N-00199_N C C c.3176G>C p.Arg1059Pro p.R1059P ENST00000284509 27/28 34 28 6 86 86 0 strelka-mutect ATP8B4,missense_variant,p.Arg1059Pro,ENST00000284509,NM_024837.3;ATP8B4,missense_variant,p.Arg1059Pro,ENST00000559829,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000558498,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000560479,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,3_prime_UTR_variant,,ENST00000558906,;ATP8B4,3_prime_UTR_variant,,ENST00000557955,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000558203,;ATP8B4,non_coding_transcript_exon_variant,,ENST00000560354,; G ENST00000284509 Transcript missense_variant 3318/5676 3176/3579 1059/1192 R/P cGa/cCa rs146911077 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 tolerated(0.13) 27/28 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF80,Pfam_domain:PF16212,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473 MODERATE 1 SNV 5 1 PASS rs146911077 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 41 49862366 49862366 C G 1 0 0 0 0 1 0 0 0 1350 884 31 4 4 ATP8B4 15 49862366 Missense_Mutation SNP C C3N-00199_T 4598372 49862366 52128823 209 11253 NTRK3 0 . GRCh38 15 87929286 87929286 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.2038C>A p.Leu680Met p.L680M ENST00000360948 17/20 344 301 43 476 476 0 strelka-varscan-mutect NTRK3,missense_variant,p.Leu680Met,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Leu672Met,ENST00000558676,;NTRK3,missense_variant,p.Leu680Met,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Leu672Met,ENST00000357724,;NTRK3,missense_variant,p.Leu672Met,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Leu680Met,ENST00000626019,;NTRK3,missense_variant,p.Leu680Met,ENST00000629765,;NTRK3,missense_variant,p.Leu672Met,ENST00000557856,;NTRK3,missense_variant,p.Leu582Met,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Leu77Met,ENST00000558576,;NTRK3,downstream_gene_variant,,ENST00000559680,; T ENST00000360948 Transcript missense_variant 2344/3004 2038/2520 680/839 L/M Ctg/Atg 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 tolerated(0.08) 17/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_patterns:PS00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 87929286 87929286 G T 1 0 0 0 0 1 0 0 0 10774 991 35 2 2 NTRK3 15 87929286 Missense_Mutation SNP G C3N-00199_T 38066920 87929286 14061903 210 11254 TICRR 0 . GRCh38 15 89575850 89575850 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.264C>A p.= p.A88A ENST00000268138 1/22 201 173 28 244 243 1 strelka-varscan-mutect TICRR,synonymous_variant,p.=,ENST00000268138,NM_152259.3;TICRR,synonymous_variant,p.=,ENST00000560985,NM_001308025.1;RP11-429B14.1,intron_variant,,ENST00000559041,;RP11-429B14.3,downstream_gene_variant,,ENST00000560477,; A ENST00000268138 Transcript synonymous_variant 369/6775 264/5733 88/1910 A gcC/gcA 1 1 TICRR HGNC HGNC:28704 protein_coding YES CCDS10352.2 ENSP00000268138 Q7Z2Z1 UPI0000D61399 NM_152259.3 1/22 Low_complexity_(Seg):seg,hmmpanther:PTHR21556 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 89575850 89575850 C A 1 0 0 0 0 0 0 0 1 16328 610 22 2 2 TICRR 15 89575850 Silent SNP C C3N-00199_T 1646564 89575850 12415339 211 11255 MESP2 0 . GRCh38 15 89777239 89777239 + Nonsense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.882G>A p.Trp294Ter p.W294* ENST00000341735 1/2 80 70 10 115 115 0 strelka-varscan-mutect MESP2,stop_gained,p.Trp294Ter,ENST00000341735,NM_001039958.1;MESP2,intron_variant,,ENST00000560219,;MESP2,intron_variant,,ENST00000558723,; A ENST00000341735 Transcript stop_gained 882/1552 882/1194 294/397 W/* tgG/tgA 1 1 MESP2 HGNC HGNC:29659 protein_coding YES CCDS42078.1 ENSP00000342392 Q0VG99 UPI00006E232B NM_001039958.1 1/2 hmmpanther:PTHR20937,hmmpanther:PTHR20937:SF6 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.993 1 1 1 1 0 A 4 1 41 89777239 89777239 G A 1 0 0 0 0 0 1 0 0 9428 1183 41 3 3 MESP2 15 89777239 Nonsense_Mutation SNP G C3N-00199_T 201389 89777239 12213950 212 11256 NPRL3 0 . GRCh38 16 86759 86759 + Silent SNP C C T novel C3N-00199_T C3N-00199_N C C c.1656G>A p.= p.V552V ENST00000620134 14/15 321 181 140 219 219 0 strelka-varscan-mutect NPRL3,synonymous_variant,p.=,ENST00000620134,;NPRL3,synonymous_variant,p.=,ENST00000611875,NM_001077350.2,NM_001243247.1;NPRL3,synonymous_variant,p.=,ENST00000399953,NM_001243248.1,NM_001039476.2,NM_001243249.1;MPG,downstream_gene_variant,,ENST00000356432,NM_001015052.2;MPG,downstream_gene_variant,,ENST00000219431,NM_002434.3;MPG,downstream_gene_variant,,ENST00000397817,NM_001015054.2;MPG,downstream_gene_variant,,ENST00000436333,;Z69720.2,upstream_gene_variant,,ENST00000601483,;NPRL3,3_prime_UTR_variant,,ENST00000622194,;NPRL3,3_prime_UTR_variant,,ENST00000621703,;NPRL3,non_coding_transcript_exon_variant,,ENST00000610509,; T ENST00000620134 Transcript synonymous_variant 1942/3203 1656/1710 552/569 V gtG/gtA 1 -1 NPRL3 HGNC HGNC:14124 protein_coding YES CCDS73795.1 ENSP00000483814 Q12980 UPI000013790E 14/15 hmmpanther:PTHR13153 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 86759 86759 C T 1 0 0 0 0 0 0 0 1 10654 581 21 3 3 NPRL3 16 86759 Silent SNP C C3N-00199_T 86759 90251586 213 11257 FLYWCH1 0 . GRCh38 16 2930733 2930733 + Missense_Mutation SNP G G C novel C3N-00199_T C3N-00199_N G G c.649G>C p.Glu217Gln p.E217Q ENST00000253928 4/10 350 283 67 230 230 0 strelka-varscan-mutect FLYWCH1,missense_variant,p.Glu217Gln,ENST00000253928,NM_001308068.1;FLYWCH1,missense_variant,p.Glu216Gln,ENST00000416288,NM_032296.2,NM_020912.1;FLYWCH1,upstream_gene_variant,,ENST00000344592,;FLYWCH1,upstream_gene_variant,,ENST00000573564,;FLYWCH1,downstream_gene_variant,,ENST00000570425,;FLYWCH1,downstream_gene_variant,,ENST00000573525,;FLYWCH1,upstream_gene_variant,,ENST00000571580,;FLYWCH1,upstream_gene_variant,,ENST00000570752,;FLYWCH1,upstream_gene_variant,,ENST00000575604,; C ENST00000253928 Transcript missense_variant 1054/5037 649/2151 217/716 E/Q Gag/Cag 1 1 FLYWCH1 HGNC HGNC:25404 protein_coding YES CCDS76809.1 ENSP00000253928 Q4VC44 UPI000013CE05 NM_001308068.1 tolerated_low_confidence(0.07) 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR31665,hmmpanther:PTHR31665:SF3 MODERATE 1 SNV 1 1 PASS rs1260074383 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 2930733 2930733 G C 1 0 0 0 0 1 0 0 0 5803 1175 41 4 4 FLYWCH1 16 2930733 Missense_Mutation SNP G C3N-00199_T 2843974 2930733 87407612 214 11258 ATP2A1 0 . GRCh38 16 28903132 28903132 + Silent SNP T T C novel C3N-00199_T C3N-00199_N T T c.2847T>C p.= p.Y949Y ENST00000357084 20/22 663 539 124 474 474 0 strelka-varscan-mutect ATP2A1,synonymous_variant,p.=,ENST00000395503,NM_004320.4;ATP2A1,synonymous_variant,p.=,ENST00000357084,NM_173201.3;ATP2A1,synonymous_variant,p.=,ENST00000536376,NM_001286075.1;RABEP2,downstream_gene_variant,,ENST00000358201,NM_024816.2;RABEP2,downstream_gene_variant,,ENST00000357573,;RABEP2,downstream_gene_variant,,ENST00000544477,;ATP2A1,upstream_gene_variant,,ENST00000564112,;ATP2A1,downstream_gene_variant,,ENST00000564732,; C ENST00000357084 Transcript synonymous_variant 3114/3532 2847/3006 949/1001 Y taT/taC 1 1 ATP2A1 HGNC HGNC:811 protein_coding YES CCDS10643.1 ENSP00000349595 O14983 UPI000003B461 NM_173201.3 20/22 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF335,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 41 28903132 28903132 T C 1 0 0 0 0 0 0 0 1 1289 1471 51 5 5 ATP2A1 16 28903132 Silent SNP T C3N-00199_T 25972399 28903132 61435213 215 11259 CD19 0 . GRCh38 16 28933240 28933240 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.566C>A p.Thr189Asn p.T189N ENST00000538922 4/15 613 500 113 420 420 0 strelka-varscan-mutect CD19,missense_variant,p.Thr189Asn,ENST00000538922,NM_001178098.1;CD19,missense_variant,p.Thr189Asn,ENST00000324662,NM_001770.5;CD19,missense_variant,p.Thr189Asn,ENST00000567541,;RABEP2,intron_variant,,ENST00000566762,;CD19,non_coding_transcript_exon_variant,,ENST00000565089,;CD19,non_coding_transcript_exon_variant,,ENST00000566890,;CD19,upstream_gene_variant,,ENST00000567368,; A ENST00000538922 Transcript missense_variant 628/1957 566/1674 189/557 T/N aCc/aAc 1 1 CD19 HGNC HGNC:1633 protein_coding YES CCDS53998.1 ENSP00000437940 P15391 UPI0000E02929 NM_001178098.1 deleterious(0.04) 4/15 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR16674,hmmpanther:PTHR16674:SF2,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 28933240 28933240 C A 1 0 0 0 0 1 0 0 0 2676 507 18 2 2 CD19 16 28933240 Missense_Mutation SNP C C3N-00199_T 30108 28933240 61405105 216 11260 FAM57B 0 . GRCh38 16 30025666 30025666 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.450C>A p.= p.T150T ENST00000564806 3/3 520 456 64 342 342 0 strelka-varscan-mutect FAM57B,synonymous_variant,p.=,ENST00000564806,;FAM57B,intron_variant,,ENST00000380495,NM_031478.4;FAM57B,intron_variant,,ENST00000279389,NM_001318504.1;C16orf92,intron_variant,,ENST00000569198,;C16orf92,intron_variant,,ENST00000567847,;FAM57B,downstream_gene_variant,,ENST00000561666,;C16orf92,downstream_gene_variant,,ENST00000300575,NM_001109659.1,NM_001109660.1;DOC2A,upstream_gene_variant,,ENST00000574405,;DOC2A,upstream_gene_variant,,ENST00000567824,;DOC2A,upstream_gene_variant,,ENST00000572637,;DOC2A,upstream_gene_variant,,ENST00000570194,;DOC2A,upstream_gene_variant,,ENST00000564075,;FAM57B,downstream_gene_variant,,ENST00000569508,;C16orf92,downstream_gene_variant,,ENST00000561910,; T ENST00000564806 Transcript synonymous_variant 496/1710 450/513 150/170 T acC/acA 1 -1 FAM57B HGNC HGNC:25295 protein_coding ENSP00000457769 H3BUS2 UPI0002466F9E 3/3 PROSITE_profiles:PS50922 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 30025666 30025666 G T 1 0 0 0 0 0 0 0 1 5459 987 35 2 2 FAM57B 16 30025666 Silent SNP G C3N-00199_T 1092426 30025666 60312679 217 11261 ITGAM 0 . GRCh38 16 31324668 31324668 + Silent SNP A A T novel C3N-00199_T C3N-00199_N A A c.2178A>T p.= p.P726P ENST00000544665 18/30 80 49 31 66 66 0 strelka-varscan-mutect ITGAM,synonymous_variant,p.=,ENST00000544665,NM_001145808.1;ITGAM,synonymous_variant,p.=,ENST00000287497,NM_000632.3;ITGAM,downstream_gene_variant,,ENST00000567031,;ITGAM,upstream_gene_variant,,ENST00000561838,;ITGAM,upstream_gene_variant,,ENST00000569746,;ITGAM,upstream_gene_variant,,ENST00000567178,; T ENST00000544665 Transcript synonymous_variant 2249/4718 2178/3462 726/1153 P ccA/ccT 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 18/30 Gene3D:1jv2A02,Pfam_domain:PF08441,Prints_domain:PR01185,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 31324668 31324668 A T 1 0 0 0 0 0 0 0 1 7794 175 7 4 4 ITGAM 16 31324668 Silent SNP A C3N-00199_T 1299002 31324668 59013677 218 11262 TP53 0 . GRCh38 17 7674292 7674292 + Splice_Site SNP T T C C3N-00199_T C3N-00199_N T T c.673-2A>G p.X225_splice ENST00000269305 342 224 118 373 373 0 strelka-varscan-mutect TP53,splice_acceptor_variant,,ENST00000617185,NM_001126114.2;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000622645,NM_001276696.1;TP53,splice_acceptor_variant,,ENST00000610292,NM_001126118.1;TP53,splice_acceptor_variant,,ENST00000455263,NM_001126113.2;TP53,splice_acceptor_variant,,ENST00000610538,NM_001276695.1;TP53,splice_acceptor_variant,,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,splice_acceptor_variant,,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000619485,;TP53,splice_acceptor_variant,,ENST00000510385,NM_001126116.1;TP53,splice_acceptor_variant,,ENST00000618944,NM_001276698.1;TP53,splice_acceptor_variant,,ENST00000504290,NM_001126117.1;TP53,splice_acceptor_variant,,ENST00000610623,NM_001276699.1;TP53,splice_acceptor_variant,,ENST00000504937,NM_001126115.1;TP53,splice_acceptor_variant,,ENST00000619186,NM_001276697.1;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000615910,;TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,splice_acceptor_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; C ENST00000269305 Transcript splice_acceptor_variant -/2579 673/1182 225/393 CS109519,TP53_g.13308A>G,TP53_g.13308A>T,TP53_g.13308A>C,COSM12559,COSM25225,COSM2744671,COSM323937,COSM323938,COSM323939,COSM33649,COSM41575,COSM4271842,COSM6908,COSM98015 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 6/10 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,0,0,0,1,1,1,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 41 7674292 7674292 T C 1 0 0 0 0 0 0 1 0 16859 1536 53 5 5 TP53 17 7674292 Splice_Site SNP T C3N-00199_T 7674292 75583149 219 11263 MYH8 0 . GRCh38 17 10400721 10400721 + Missense_Mutation SNP G G A novel C3N-00199_T C3N-00199_N G G c.3404C>T p.Ala1135Val p.A1135V ENST00000403437 27/40 286 163 123 313 313 0 strelka-varscan-mutect MYH8,missense_variant,p.Ala1135Val,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript missense_variant 3499/6041 3404/5814 1135/1937 A/V gCg/gTg 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 tolerated(1) 27/40 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 10400721 10400721 G A 1 0 0 0 0 1 0 0 0 10041 1087 38 1 1 MYH8 17 10400721 Missense_Mutation SNP G C3N-00199_T 2726429 10400721 72856720 220 11264 TMEM11 0 . GRCh38 17 21198678 21198678 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.225C>T p.= p.I75I ENST00000317635 2/2 194 135 59 211 211 0 strelka-varscan-mutect TMEM11,synonymous_variant,p.=,ENST00000317635,NM_003876.2;TMEM11,non_coding_transcript_exon_variant,,ENST00000584432,;TMEM11,non_coding_transcript_exon_variant,,ENST00000577419,;TMEM11,non_coding_transcript_exon_variant,,ENST00000584732,;TMEM11,non_coding_transcript_exon_variant,,ENST00000583929,;TMEM11,non_coding_transcript_exon_variant,,ENST00000583264,; A ENST00000317635 Transcript synonymous_variant 697/2095 225/579 75/192 I atC/atT 1 -1 TMEM11 HGNC HGNC:16823 protein_coding YES CCDS11216.1 ENSP00000319992 P17152 UPI0000131C88 NM_003876.2 2/2 Pfam_domain:PF14972,hmmpanther:PTHR15099,hmmpanther:PTHR15099:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 21198678 21198678 G A 1 0 0 0 0 0 0 0 1 16470 1280 45 3 3 TMEM11 17 21198678 Silent SNP G C3N-00199_T 10797957 21198678 62058763 221 11265 UNC119 0 . GRCh38 17 28547830 28547830 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.457G>T p.Asp153Tyr p.D153Y ENST00000335765 4/5 118 84 34 158 158 0 strelka-varscan-mutect UNC119,missense_variant,p.Asp58Tyr,ENST00000484980,;UNC119,missense_variant,p.Asp58Tyr,ENST00000470125,;UNC119,missense_variant,p.Asp153Tyr,ENST00000301032,NM_054035.2;UNC119,missense_variant,p.Asp153Tyr,ENST00000335765,NM_005148.3;UNC119,missense_variant,p.Asp146Tyr,ENST00000444148,;UNC119,missense_variant,p.Glu78Asp,ENST00000581945,;UNC119,non_coding_transcript_exon_variant,,ENST00000487844,;RP11-192H23.4,intron_variant,,ENST00000481916,;UNC119,downstream_gene_variant,,ENST00000578434,; A ENST00000335765 Transcript missense_variant 568/1424 457/723 153/240 D/Y Gac/Tac 1 -1 UNC119 HGNC HGNC:12565 protein_coding YES CCDS11233.1 ENSP00000337040 Q13432 UPI00000012A7 NM_005148.3 deleterious(0) 4/5 hmmpanther:PTHR12951:SF2,hmmpanther:PTHR12951,Gene3D:1kshB00,Pfam_domain:PF05351,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 28547830 28547830 C A 1 0 0 0 0 1 0 0 0 17506 913 32 2 2 UNC119 17 28547830 Missense_Mutation SNP C C3N-00199_T 7349152 28547830 54709611 222 11266 TMEM132E 0 . GRCh38 17 34632820 34632820 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.1329G>T p.Trp443Cys p.W443C ENST00000321639 7/10 573 523 50 646 644 2 strelka-varscan-mutect TMEM132E,missense_variant,p.Trp533Cys,ENST00000631683,NM_001304438.1;TMEM132E,missense_variant,p.Trp443Cys,ENST00000321639,;TMEM132E,upstream_gene_variant,,ENST00000577271,; T ENST00000321639 Transcript missense_variant 1657/4369 1329/2955 443/984 W/C tgG/tgT 1 1 TMEM132E HGNC HGNC:26991 protein_coding YES ENSP00000316532 Q6IEE7 UPI000035960F deleterious(0) 7/10 Pfam_domain:PF16070,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 34632820 34632820 G T 1 0 0 0 0 1 0 0 0 16493 1241 43 2 2 TMEM132E 17 34632820 Missense_Mutation SNP G C3N-00199_T 6084990 34632820 48624621 223 11267 UNC45B 0 . GRCh38 17 35186446 35186446 + Missense_Mutation SNP C C A C3N-00199_T C3N-00199_N C C c.2683C>A p.Leu895Met p.L895M ENST00000268876 20/20 444 326 118 557 557 0 strelka-varscan-mutect UNC45B,missense_variant,p.Leu895Met,ENST00000268876,NM_173167.2;UNC45B,missense_variant,p.Leu893Met,ENST00000394570,NM_001267052.1,NM_001033576.1;UNC45B,missense_variant,p.Leu814Met,ENST00000591048,NM_001308281.1;RP11-799D4.2,upstream_gene_variant,,ENST00000590144,;RP11-799D4.1,upstream_gene_variant,,ENST00000592961,; A ENST00000268876 Transcript missense_variant 2780/5679 2683/2796 895/931 L/M Ctg/Atg COSM3516200 1 1 UNC45B HGNC HGNC:14304 protein_coding YES CCDS11292.1 ENSP00000268876 Q8IWX7 UPI0000074455 NM_173167.2 deleterious(0.03) 20/20 Gene3D:1.25.10.10,Superfamily_domains:SSF48371 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 35186446 35186446 C A 1 0 0 0 0 1 0 0 0 17513 680 24 2 2 UNC45B 17 35186446 Missense_Mutation SNP C C3N-00199_T 553626 35186446 48070995 224 11268 LHX1 0 . GRCh38 17 36942974 36942974 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1064C>A p.Pro355His p.P355H ENST00000614239 5/5 223 159 64 218 217 1 strelka-varscan-mutect LHX1,missense_variant,p.Pro355His,ENST00000614239,NM_005568.4;LHX1,intron_variant,,ENST00000621767,;RP11-445F12.2,intron_variant,,ENST00000614759,;LHX1,downstream_gene_variant,,ENST00000619939,;LHX1,downstream_gene_variant,,ENST00000616237,; A ENST00000614239 Transcript missense_variant 1787/3425 1064/1221 355/406 P/H cCc/cAc 1 1 LHX1 HGNC HGNC:6593 protein_coding YES CCDS11316.1 ENSP00000477829 P48742 UPI000013CE37 NM_005568.4 deleterious(0) 5/5 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF106,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 36942974 36942974 C A 1 0 0 0 0 1 0 0 0 8679 623 22 2 2 LHX1 17 36942974 Missense_Mutation SNP C C3N-00199_T 1756528 36942974 46314467 225 11269 AARSD1 0 . GRCh38 17 42955908 42955908 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1250G>T p.Gly417Val p.G417V ENST00000421990 12/17 109 85 24 220 220 0 strelka-varscan-mutect PTGES3L-AARSD1,missense_variant,p.Gly417Val,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,missense_variant,p.Gly417Val,ENST00000409399,;PTGES3L-AARSD1,missense_variant,p.Gly356Val,ENST00000360221,NM_025267.3;PTGES3L-AARSD1,missense_variant,p.Gly326Val,ENST00000409103,;AARSD1,missense_variant,p.Gly243Val,ENST00000427569,NM_001261434.1;AARSD1,missense_variant,p.Gly138Val,ENST00000430739,;AARSD1,downstream_gene_variant,,ENST00000416949,;AARSD1,missense_variant,p.Gly14Val,ENST00000591096,;AARSD1,3_prime_UTR_variant,,ENST00000450475,;PTGES3L-AARSD1,3_prime_UTR_variant,,ENST00000423601,;AARSD1,non_coding_transcript_exon_variant,,ENST00000441280,;AARSD1,non_coding_transcript_exon_variant,,ENST00000491665,;AARSD1,non_coding_transcript_exon_variant,,ENST00000486664,;AARSD1,non_coding_transcript_exon_variant,,ENST00000478040,;AARSD1,downstream_gene_variant,,ENST00000483774,;AARSD1,downstream_gene_variant,,ENST00000591910,;AARSD1,downstream_gene_variant,,ENST00000436545,;AARSD1,upstream_gene_variant,,ENST00000593123,;AARSD1,upstream_gene_variant,,ENST00000474578,;AARSD1,upstream_gene_variant,,ENST00000587023,;AARSD1,upstream_gene_variant,,ENST00000592136,;AARSD1,upstream_gene_variant,,ENST00000483535,;AARSD1,upstream_gene_variant,,ENST00000486493,; A ENST00000421990 Transcript missense_variant 1596/2150 1250/1761 417/586 G/V gGg/gTg 1 -1 PTGES3L-AARSD1 HGNC HGNC:43946 protein_coding YES CCDS45691.1 ENSP00000409924 Q9BTE6 UPI0000D4E5DF NM_001136042.2 deleterious(0) 12/17 PROSITE_profiles:PS50860,hmmpanther:PTHR11777 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 42955908 42955908 C A 1 0 0 0 0 1 0 0 0 25 623 22 2 2 AARSD1 17 42955908 Missense_Mutation SNP C C3N-00199_T 6012934 42955908 40301533 226 11270 ERN1 0 . GRCh38 17 64049129 64049129 + Frame_Shift_Del DEL C C - novel C3N-00199_T C3N-00199_N C C c.2327delG p.Gly776AlafsTer33 p.G776Afs*33 ENST00000433197 18/22 87 61 26 70 70 0 sindel-varindel-pindel ERN1,frameshift_variant,p.Gly776AlafsTer33,ENST00000433197,NM_001433.3;ERN1,downstream_gene_variant,,ENST00000583077,; - ENST00000433197 Transcript frameshift_variant 2423/7876 2327/2934 776/977 G/X gGc/gc 1 -1 ERN1 HGNC HGNC:3449 protein_coding YES CCDS45762.1 ENSP00000401445 O75460 UPI0000201263 NM_001433.3 18/22 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF7,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 deletion 1 1 PASS . . 0 202 5 3 0 0 0 0 -20 0.9999265 1 1 1 0 - 7 5 41 64049129 64049129 C - 1 0 1 0 1 0 0 0 0 5095 739 26 0 0 ERN1 17 64049129 Frame_Shift_Del DEL C C3N-00199_T 21093221 64049129 19208312 227 11271 SLC25A10 0 . GRCh38 17 81712476 81712476 + Frame_Shift_Del DEL C C - novel C3N-00199_T C3N-00199_N C C c.51delC p.Cys18AlafsTer23 p.C18Afs*23 ENST00000545862 1/11 32 25 7 20 20 0 sindel-varindel-pindel SLC25A10,frameshift_variant,p.Cys18AlafsTer23,ENST00000331531,NM_001270888.1;SLC25A10,frameshift_variant,p.Cys18AlafsTer23,ENST00000545862,NM_001270953.1;SLC25A10,frameshift_variant,p.Cys18AlafsTer23,ENST00000350690,NM_012140.4;RP13-1032I1.10,intron_variant,,ENST00000571730,;MRPL12,downstream_gene_variant,,ENST00000333676,NM_002949.3;SLC25A10,frameshift_variant,p.Cys18AlafsTer60,ENST00000574129,;SLC25A10,upstream_gene_variant,,ENST00000573246,;SLC25A10,upstream_gene_variant,,ENST00000574884,;SLC25A10,upstream_gene_variant,,ENST00000570310,;SLC25A10,upstream_gene_variant,,ENST00000571876,; - ENST00000545862 Transcript frameshift_variant 241/1911 50/1221 17/406 S/X tCc/tc 1 1 SLC25A10 HGNC HGNC:10980 protein_coding YES CCDS74176.1 ENSP00000446242 F6RGN5 UPI00027A7714 NM_001270953.1 1/11 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF39 HIGH deletion 2 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.85598 1 1 1 1 0 - 7 5 41 81712476 81712476 C - 1 0 1 0 1 0 0 0 0 14737 855 30 0 0 SLC25A10 17 81712476 Frame_Shift_Del DEL C C3N-00199_T 17663347 81712476 1544965 228 11272 CTAGE1 0 . GRCh38 18 22415593 22415593 + Missense_Mutation SNP G G A C3N-00199_T C3N-00199_N G G c.2219C>T p.Pro740Leu p.P740L ENST00000391403 1/1 27 18 9 66 66 0 strelka-varscan-mutect CTAGE1,missense_variant,p.Pro740Leu,ENST00000391403,NM_172241.2;CTAGE1,upstream_gene_variant,,ENST00000525417,;RP11-863N1.4,downstream_gene_variant,,ENST00000603437,; A ENST00000391403 Transcript missense_variant 2323/4313 2219/2238 740/745 P/L cCc/cTc COSM708330,COSM708331 1 -1 CTAGE1 HGNC HGNC:24346 protein_coding YES CCDS45837.1 ENSP00000375220 Q96RT6 UPI00000721F4 NM_172241.2 tolerated(0.09) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 41 22415593 22415593 G A 1 0 0 0 0 1 0 0 0 3796 1232 43 3 3 CTAGE1 18 22415593 Missense_Mutation SNP G C3N-00199_T 22415593 57957692 229 11273 LAMA3 0 . GRCh38 18 23949813 23949813 + Missense_Mutation SNP G G A rs139393524 C3N-00199_T C3N-00199_N G G c.9400G>A p.Asp3134Asn p.D3134N ENST00000313654 71/75 229 217 12 463 462 1 strelka-varscan-mutect LAMA3,missense_variant,p.Asp3134Asn,ENST00000313654,NM_198129.2;LAMA3,missense_variant,p.Asp3078Asn,ENST00000399516,NM_001127717.2;LAMA3,missense_variant,p.Asp1525Asn,ENST00000269217,NM_000227.4;LAMA3,missense_variant,p.Asp1469Asn,ENST00000587184,NM_001127718.2;LAMA3,upstream_gene_variant,,ENST00000588004,;LAMA3,downstream_gene_variant,,ENST00000590104,;LAMA3,non_coding_transcript_exon_variant,,ENST00000588770,; A ENST00000313654 Transcript missense_variant 9641/10661 9400/10002 3134/3333 D/N Gat/Aat rs139393524 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 tolerated(1) 71/75 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs139393524 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 23949813 23949813 G A 1 0 0 0 0 1 0 0 0 8511 1174 41 3 3 LAMA3 18 23949813 Missense_Mutation SNP G C3N-00199_T 1534220 23949813 56423472 230 11274 ZNF521 0 . GRCh38 18 25062720 25062720 + Missense_Mutation SNP T T C novel C3N-00199_T C3N-00199_N T T c.3928A>G p.Ser1310Gly p.S1310G ENST00000361524 8/8 67 47 20 192 192 0 strelka-varscan-mutect ZNF521,missense_variant,p.Ser1310Gly,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Ser1090Gly,ENST00000584787,NM_001308225.1;ZNF521,missense_variant,p.Ser1310Gly,ENST00000538137,;ZNF521,3_prime_UTR_variant,,ENST00000399425,; C ENST00000361524 Transcript missense_variant 4077/4871 3928/3936 1310/1311 S/G Agc/Ggc 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 tolerated_low_confidence(0.11) 8/8 PROSITE_profiles:PS50157 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 25062720 25062720 T C 1 0 0 0 0 1 0 0 0 18537 1580 55 5 5 ZNF521 18 25062720 Missense_Mutation SNP T C3N-00199_T 1112907 25062720 55310565 231 11275 SETBP1 0 . GRCh38 18 44950207 44950207 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.867G>T p.= p.V289V ENST00000282030 4/6 271 150 121 306 306 0 strelka-varscan-mutect SETBP1,synonymous_variant,p.=,ENST00000282030,NM_015559.2; T ENST00000282030 Transcript synonymous_variant 1163/9899 867/4791 289/1596 V gtG/gtT 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 44950207 44950207 G T 1 0 0 0 0 0 0 0 1 14406 1335 47 2 2 SETBP1 18 44950207 Silent SNP G C3N-00199_T 19887487 44950207 35423078 232 11276 NFATC1 0 . GRCh38 18 79410549 79410549 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.274G>T p.Ala92Ser p.A92S ENST00000427363 2/10 274 142 132 233 233 0 strelka-varscan-mutect NFATC1,missense_variant,p.Ala92Ser,ENST00000591814,NM_172390.2;NFATC1,missense_variant,p.Ala92Ser,ENST00000253506,NM_006162.4;NFATC1,missense_variant,p.Ala79Ser,ENST00000329101,NM_172387.2;NFATC1,missense_variant,p.Ala79Ser,ENST00000318065,NM_172389.2;NFATC1,missense_variant,p.Ala92Ser,ENST00000427363,NM_001278669.1;NFATC1,missense_variant,p.Ala79Ser,ENST00000592223,NM_001278675.1;NFATC1,missense_variant,p.Ala92Ser,ENST00000587635,;NFATC1,missense_variant,p.Ala92Ser,ENST00000542384,NM_001278670.1;NFATC1,missense_variant,p.Ala79Ser,ENST00000586434,NM_001278672.1;NFATC1,intron_variant,,ENST00000545796,NM_001278673.1;NFATC1,intron_variant,,ENST00000397790,NM_172388.2;NFATC1,intron_variant,,ENST00000590313,; T ENST00000427363 Transcript missense_variant 274/2832 274/2832 92/943 A/S Gct/Tct 1 1 NFATC1 HGNC HGNC:7775 protein_coding YES CCDS62467.1 ENSP00000389377 O95644 UPI000012FFB5 NM_001278669.1 tolerated(0.57) 2/10 hmmpanther:PTHR12533:SF5,hmmpanther:PTHR12533 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 79410549 79410549 G T 1 0 0 0 0 1 0 0 0 10398 971 34 2 2 NFATC1 18 79410549 Missense_Mutation SNP G C3N-00199_T 34460342 79410549 962736 233 11277 WIZ 0 . GRCh38 19 15437131 15437131 + Splice_Site SNP T T A novel C3N-00199_T C3N-00199_N T T c.206-2A>T p.X69_splice ENST00000263381 91 46 45 119 119 0 strelka-varscan-mutect WIZ,splice_acceptor_variant,,ENST00000263381,NM_021241.2;WIZ,splice_acceptor_variant,,ENST00000596159,;WIZ,upstream_gene_variant,,ENST00000599910,;WIZ,upstream_gene_variant,,ENST00000599686,;WIZ,splice_acceptor_variant,,ENST00000595214,; A ENST00000263381 Transcript splice_acceptor_variant -/5695 206/2385 69/794 1 -1 WIZ HGNC HGNC:30917 protein_coding YES CCDS42516.1 ENSP00000263381 O95785 UPI000041F888 NM_021241.2 2/7 HIGH 1 SNV 2 1 PASS . . 0 197 13 0 0 0 0 0 -20 0.9999839 1 1 1 0 A 5 1 41 15437131 15437131 T A 1 0 0 0 0 0 0 1 0 17931 1594 55 4 4 WIZ 19 15437131 Splice_Site SNP T C3N-00199_T 15437131 43180485 234 11278 WDR88 0 . GRCh38 19 33137780 33137780 + Missense_Mutation SNP A A T novel C3N-00199_T C3N-00199_N A A c.380A>T p.Lys127Met p.K127M ENST00000355868 2/11 162 105 57 203 203 0 strelka-varscan-mutect WDR88,missense_variant,p.Lys127Met,ENST00000361680,;WDR88,missense_variant,p.Lys127Met,ENST00000355868,NM_173479.3;WDR88,missense_variant,p.Lys127Met,ENST00000592765,; T ENST00000355868 Transcript missense_variant 456/1718 380/1419 127/472 K/M aAg/aTg 1 1 WDR88 HGNC HGNC:26999 protein_coding YES CCDS12429.1 ENSP00000348129 Q6ZMY6 UPI0000456C8B NM_173479.3 deleterious(0) 2/11 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF418,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998,Prints_domain:PR00320 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 33137780 33137780 A T 1 0 0 0 0 1 0 0 0 17891 86 3 4 4 WDR88 19 33137780 Missense_Mutation SNP A C3N-00199_T 17700649 33137780 25479836 235 11279 LRFN1 0 . GRCh38 19 39308044 39308044 + Silent SNP C C G novel C3N-00199_T C3N-00199_N C C c.1905G>C p.= p.P635P ENST00000248668 2/2 68 42 26 70 70 0 strelka-varscan-mutect LRFN1,synonymous_variant,p.=,ENST00000248668,NM_020862.1; G ENST00000248668 Transcript synonymous_variant 1905/3381 1905/2316 635/771 P ccG/ccC 1 -1 LRFN1 HGNC HGNC:29290 protein_coding YES CCDS46071.1 ENSP00000248668 Q9P244 UPI00001A5C55 NM_020862.1 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF34 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 41 39308044 39308044 C G 1 0 0 0 0 0 0 0 1 8831 639 23 4 4 LRFN1 19 39308044 Silent SNP C C3N-00199_T 6170264 39308044 19309572 236 11280 KLK7 0 . GRCh38 19 50981912 50981912 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.76C>A p.Gln26Lys p.Q26K ENST00000391807 3/6 122 88 34 135 133 2 strelka-varscan-mutect KLK7,missense_variant,p.Gln26Lys,ENST00000391807,NM_139277.2;KLK7,missense_variant,p.Gln26Lys,ENST00000595820,NM_005046.3;KLK7,splice_region_variant,,ENST00000597707,NM_001207053.1;KLK7,splice_region_variant,,ENST00000593904,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK7,downstream_gene_variant,,ENST00000595638,;KLK7,intron_variant,,ENST00000304045,NM_001243126.1; T ENST00000391807 Transcript missense_variant,splice_region_variant 178/1912 76/762 26/253 Q/K Cag/Aag 1 -1 KLK7 HGNC HGNC:6368 protein_coding YES CCDS12812.1 ENSP00000375683 P49862 A0A024R4H6 UPI0000001BC4 NM_139277.2 tolerated(0.39) 3/6 hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF231,Superfamily_domains:SSF50494 MODERATE SNV 5 1 PASS rs1253902860 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 50981912 50981912 G T 1 0 0 0 0 1 0 0 0 8278 1362 47 2 2 KLK7 19 50981912 Missense_Mutation SNP G C3N-00199_T 11673868 50981912 7635704 237 11281 FAM110A 0 . GRCh38 20 845605 845605 + Silent SNP C C T C3N-00199_T C3N-00199_N C C c.801C>T p.= p.G267G ENST00000304189 3/3 447 332 115 277 277 0 strelka-varscan-mutect FAM110A,synonymous_variant,p.=,ENST00000304189,NM_001289145.1;FAM110A,synonymous_variant,p.=,ENST00000381941,NM_001289146.1,NM_001042353.2;FAM110A,synonymous_variant,p.=,ENST00000381939,;FAM110A,synonymous_variant,p.=,ENST00000246100,NM_207121.4,NM_031424.5;FAM110A,synonymous_variant,p.=,ENST00000541082,NM_001289147.1;FAM110A,synonymous_variant,p.=,ENST00000505691,; T ENST00000304189 Transcript synonymous_variant 1182/1856 801/888 267/295 G ggC/ggT COSM1413288 1 1 FAM110A HGNC HGNC:16188 protein_coding YES CCDS13008.1 ENSP00000354163 Q9BQ89 UPI00001285E4 NM_001289145.1 3/3 hmmpanther:PTHR14758:SF4,hmmpanther:PTHR14758,Pfam_domain:PF14160 1 LOW 1 SNV 2 1 1 PASS rs1220405799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 845605 845605 C T 1 0 0 0 0 0 0 0 1 5260 755 27 1 1 FAM110A 20 845605 Silent SNP C C3N-00199_T 845605 63598562 238 11282 RAD21L1 0 . GRCh38 20 1228525 1228525 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.72G>T p.Glu24Asp p.E24D ENST00000409241 2/14 105 75 30 190 190 0 strelka-varscan-mutect RAD21L1,missense_variant,p.Glu24Asp,ENST00000409241,NM_001136566.2;RAD21L1,missense_variant,p.Glu24Asp,ENST00000402452,;RAD21L1,missense_variant,p.Glu24Asp,ENST00000246108,;RAD21L1,upstream_gene_variant,,ENST00000477283,; T ENST00000409241 Transcript missense_variant 165/1808 72/1671 24/556 E/D gaG/gaT 1 1 RAD21L1 HGNC HGNC:16271 protein_coding YES CCDS46568.1 ENSP00000386414 Q9H4I0 UPI000188152B NM_001136566.2 tolerated(0.29) 2/14 Pfam_domain:PF04825,hmmpanther:PTHR12585,hmmpanther:PTHR12585:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 1228525 1228525 G T 1 0 0 0 0 1 0 0 0 13142 933 33 2 2 RAD21L1 20 1228525 Missense_Mutation SNP G C3N-00199_T 382920 1228525 63215642 239 11283 MYH7B 0 . GRCh38 20 34979721 34979721 + Nonsense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.385G>T p.Glu129Ter p.E129* ENST00000262873 5/43 384 361 23 238 238 0 strelka-varscan-mutect MYH7B,stop_gained,p.Glu129Ter,ENST00000262873,NM_020884.4;MYH7B,stop_gained,p.Glu128Ter,ENST00000618182,;MYH7B,upstream_gene_variant,,ENST00000481922,;MYH7B,non_coding_transcript_exon_variant,,ENST00000470929,; T ENST00000262873 Transcript stop_gained 477/6293 385/5952 129/1983 E/* Gag/Tag COSM3545608 1 1 MYH7B HGNC HGNC:15906 protein_coding YES CCDS42869.1 ENSP00000262873 A7E2Y1 UPI000046D367 NM_020884.4 5/43 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF358,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 41 34979721 34979721 G T 1 0 0 0 0 0 1 0 0 10040 1175 41 2 2 MYH7B 20 34979721 Nonsense_Mutation SNP G C3N-00199_T 33751196 34979721 29464446 240 11284 PROCR 0 . GRCh38 20 35176798 35176798 + Silent SNP T T A novel C3N-00199_T C3N-00199_N T T c.702T>A p.= p.G234G ENST00000216968 4/4 719 462 257 580 580 0 strelka-varscan-mutect PROCR,synonymous_variant,p.=,ENST00000216968,NM_006404.4;PROCR,intron_variant,,ENST00000635377,;PROCR,intron_variant,,ENST00000634509,;RP11-42O4.2,upstream_gene_variant,,ENST00000615962,; A ENST00000216968 Transcript synonymous_variant 784/1348 702/717 234/238 G ggT/ggA 1 1 PROCR HGNC HGNC:9452 protein_coding YES CCDS13248.1 ENSP00000216968 Q9UNN8 UPI000012A08E NM_006404.4 4/4 hmmpanther:PTHR15349 LOW 1 SNV 1 1 PASS rs1023443790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 35176798 35176798 T A 1 0 0 0 0 0 0 0 1 12681 1683 59 4 4 PROCR 20 35176798 Silent SNP T C3N-00199_T 197077 35176798 29267369 241 11285 JPH2 0 . GRCh38 20 44160115 44160115 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.672C>T p.= p.G224G ENST00000372980 2/6 525 322 203 311 311 0 strelka-varscan-mutect JPH2,synonymous_variant,p.=,ENST00000372980,NM_020433.4; A ENST00000372980 Transcript synonymous_variant 1545/4787 672/2091 224/696 G ggC/ggT 1 -1 JPH2 HGNC HGNC:14202 protein_coding YES CCDS13325.1 ENSP00000362071 Q9BR39 UPI000012DAC2 NM_020433.4 2/6 hmmpanther:PTHR23085:SF5,hmmpanther:PTHR23085,PIRSF_domain:PIRSF037387 LOW 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999997 1 1 1 0 A 2 1 41 44160115 44160115 G A 1 0 0 0 0 0 0 0 1 7873 1074 38 1 1 JPH2 20 44160115 Silent SNP G C3N-00199_T 8983317 44160115 20284052 242 11286 VAPB 0 . GRCh38 20 58440997 58440997 + Missense_Mutation SNP G G T C3N-00199_T C3N-00199_N G G c.487G>T p.Asp163Tyr p.D163Y ENST00000475243 5/6 158 109 49 319 319 0 strelka-varscan-mutect VAPB,missense_variant,p.Asp163Tyr,ENST00000475243,NM_004738.4;VAPB,intron_variant,,ENST00000395802,NM_001195677.1;VAPB,non_coding_transcript_exon_variant,,ENST00000265619,;VAPB,non_coding_transcript_exon_variant,,ENST00000463370,;VAPB,3_prime_UTR_variant,,ENST00000520497,;VAPB,non_coding_transcript_exon_variant,,ENST00000476395,; T ENST00000475243 Transcript missense_variant 825/7936 487/732 163/243 D/Y Gac/Tac COSM5187568 1 1 VAPB HGNC HGNC:12649 protein_coding YES CCDS33498.1 ENSP00000417175 O95292 Q53XM7 UPI0000048ED2 NM_004738.4 deleterious(0) 5/6 hmmpanther:PTHR10809:SF12,hmmpanther:PTHR10809,PIRSF_domain:PIRSF019693 1 MODERATE 1 SNV 1 1 1 PASS rs892724485 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 58440997 58440997 G T 1 0 0 0 0 1 0 0 0 17667 1290 45 2 2 VAPB 20 58440997 Missense_Mutation SNP G C3N-00199_T 14280882 58440997 6003170 243 11287 PHACTR3 0 . GRCh38 20 59755361 59755361 + Missense_Mutation SNP G G T novel C3N-00199_T C3N-00199_N G G c.538G>T p.Ala180Ser p.A180S ENST00000371015 4/13 244 194 50 197 197 0 strelka-varscan-mutect PHACTR3,missense_variant,p.Ala180Ser,ENST00000371015,NM_080672.4;PHACTR3,missense_variant,p.Ala139Ser,ENST00000395636,NM_183244.1;PHACTR3,missense_variant,p.Ala139Ser,ENST00000541461,NM_001281507.1;PHACTR3,missense_variant,p.Ala177Ser,ENST00000359926,NM_001199505.1;PHACTR3,missense_variant,p.Ala139Ser,ENST00000355648,NM_001199506.1;PHACTR3,missense_variant,p.Ala139Ser,ENST00000361300,NM_183246.1; T ENST00000371015 Transcript missense_variant 1005/2728 538/1680 180/559 A/S Gca/Tca 1 1 PHACTR3 HGNC HGNC:15833 protein_coding YES CCDS13480.1 ENSP00000360054 Q96KR7 UPI000006D452 NM_080672.4 tolerated(0.73) 4/13 hmmpanther:PTHR12751:SF7,hmmpanther:PTHR12751 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 59755361 59755361 G T 1 0 0 0 0 1 0 0 0 11900 1333 46 2 2 PHACTR3 20 59755361 Missense_Mutation SNP G C3N-00199_T 1314364 59755361 4688806 244 11288 KRTAP24-1 0 . GRCh38 21 30282630 30282630 + Silent SNP G G T novel C3N-00199_T C3N-00199_N G G c.303C>A p.= p.G101G ENST00000340345 1/1 44 31 13 62 62 0 strelka-varscan-mutect KRTAP24-1,synonymous_variant,p.=,ENST00000340345,NM_001085455.2; T ENST00000340345 Transcript synonymous_variant 329/1650 303/765 101/254 G ggC/ggA 1 -1 KRTAP24-1 HGNC HGNC:33902 protein_coding YES CCDS42915.1 ENSP00000339238 Q3LI83 UPI00005C50F3 NM_001085455.2 1/1 Pfam_domain:PF05287,hmmpanther:PTHR23260,hmmpanther:PTHR23260:SF2 LOW 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 30282630 30282630 G T 1 0 0 0 0 0 0 0 1 8433 1190 42 2 2 KRTAP24-1 21 30282630 Silent SNP G C3N-00199_T 30282630 16427353 245 11289 CECR6 0 . GRCh38 22 17119472 17119472 + Silent SNP G G A novel C3N-00199_T C3N-00199_N G G c.1656C>T p.= p.S552S ENST00000331437 1/1 651 592 59 564 563 1 strelka-varscan-mutect CECR6,synonymous_variant,p.=,ENST00000331437,NM_031890.3;CECR6,synonymous_variant,p.=,ENST00000399875,NM_001163079.1;IL17RA,downstream_gene_variant,,ENST00000319363,NM_014339.6;IL17RA,downstream_gene_variant,,ENST00000612619,NM_001289905.1;AC006946.15,upstream_gene_variant,,ENST00000441544,;AC006946.15,upstream_gene_variant,,ENST00000428078,; A ENST00000331437 Transcript synonymous_variant 1782/4954 1656/1737 552/578 S tcC/tcT 1 -1 CECR6 HGNC HGNC:1844 protein_coding YES CCDS13740.1 ENSP00000329318 Q9BXQ6 UPI0000127513 NM_031890.3 1/1 hmmpanther:PTHR22146,hmmpanther:PTHR22146:SF1,Low_complexity_(Seg):seg LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 17119472 17119472 G A 1 0 0 0 0 0 0 0 1 2915 1219 43 3 3 CECR6 22 17119472 Silent SNP G C3N-00199_T 17119472 33698996 246 11290 CECR2 0 . GRCh38 22 17542812 17542812 + Missense_Mutation SNP A A T rs865863983 C3N-00199_T C3N-00199_N A A c.2180A>T p.Gln727Leu p.Q727L ENST00000400585 16/19 168 154 14 145 145 0 strelka-varscan-mutect CECR2,missense_variant,p.Gln868Leu,ENST00000612582,;CECR2,missense_variant,p.Gln910Leu,ENST00000342247,NM_001290047.1;CECR2,missense_variant,p.Gln727Leu,ENST00000400585,NM_001290046.1;CECR2,missense_variant,p.Gln727Leu,ENST00000262608,; T ENST00000400585 Transcript missense_variant 2618/4833 2180/3903 727/1300 Q/L cAg/cTg rs865863983 1 1 CECR2 HGNC HGNC:1840 protein_coding YES CCDS77646.1 ENSP00000383428 B7WPH3 UPI000198C520 NM_001290046.1 deleterious(0) 16/19 MODERATE 1 SNV 1 1 PASS rs865863983 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 17542812 17542812 A T 1 0 0 0 0 1 0 0 0 2913 188 7 4 4 CECR2 22 17542812 Missense_Mutation SNP A C3N-00199_T 423340 17542812 33275656 247 11291 CBX6 0 . GRCh38 22 38866963 38866963 + Missense_Mutation SNP C C T C3N-00199_T C3N-00199_N C C c.485G>A p.Arg162His p.R162H ENST00000407418 5/5 142 133 9 115 115 0 strelka-varscan-mutect CBX6,missense_variant,p.Arg162His,ENST00000407418,NM_014292.4;CBX6,missense_variant,p.Arg144His,ENST00000216083,NM_001303494.1;CBX6,downstream_gene_variant,,ENST00000469420,; T ENST00000407418 Transcript missense_variant 609/6122 485/1239 162/412 R/H cGc/cAc COSM1199737 1 -1 CBX6 HGNC HGNC:1556 protein_coding YES CCDS13980.1 ENSP00000384490 O95503 UPI00001271FD NM_014292.4 deleterious(0.04) 5/5 hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF8 1 MODERATE 1 SNV 1 1 1 PASS rs1003303920 . 0 204 5 0 0 0 0 0 -16.82167 1 1 1 1 0 T 3 4 41 38866963 38866963 C T 1 0 0 0 0 1 0 0 0 2422 768 27 1 1 CBX6 22 38866963 Missense_Mutation SNP C C3N-00199_T 21324151 38866963 11951505 248 11292 DCAF8L2 0 . GRCh38 X 27748382 27748382 + Missense_Mutation SNP T T C novel C3N-00199_T C3N-00199_N T T c.1487T>C p.Phe496Ser p.F496S ENST00000451261 5/5 62 35 27 135 135 0 strelka-varscan-mutect DCAF8L2,missense_variant,p.Phe496Ser,ENST00000451261,;DCAF8L2,missense_variant,p.Phe496Ser,ENST00000545306,NM_001136533.1;DCAF8L2,downstream_gene_variant,,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,; C ENST00000451261 Transcript missense_variant 1886/2295 1487/1896 496/631 F/S tTc/tCc 1 1 DCAF8L2 HGNC HGNC:31811 protein_coding YES CCDS59162.1 ENSP00000462745 P0C7V8 UPI000183CBD9 deleterious(0) 5/5 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF42,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 41 27748382 27748382 T C 1 0 0 0 0 1 0 0 0 4079 1783 62 5 5 DCAF8L2 23 27748382 Missense_Mutation SNP T C3N-00199_T 27748382 128292513 249 11293 DCAF8L2 0 . GRCh38 X 27748521 27748521 + Silent SNP C C A novel C3N-00199_T C3N-00199_N C C c.1626C>A p.= p.P542P ENST00000451261 5/5 84 48 36 142 142 0 strelka-varscan-mutect DCAF8L2,synonymous_variant,p.=,ENST00000451261,;DCAF8L2,synonymous_variant,p.=,ENST00000545306,NM_001136533.1;DCAF8L2,downstream_gene_variant,,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,; A ENST00000451261 Transcript synonymous_variant 2025/2295 1626/1896 542/631 P ccC/ccA 1 1 DCAF8L2 HGNC HGNC:31811 protein_coding YES CCDS59162.1 ENSP00000462745 P0C7V8 UPI000183CBD9 5/5 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF42 LOW 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 27748521 27748521 C A 1 0 0 0 0 0 0 0 1 4079 581 21 2 2 DCAF8L2 23 27748521 Silent SNP C C3N-00199_T 139 27748521 128292374 250 11294 MAGEB2 0 . GRCh38 X 30218802 30218802 + Silent SNP G G T rs200872475 C3N-00199_T C3N-00199_N G G c.222G>T p.= p.A74A ENST00000378988 2/2 110 59 51 113 113 0 strelka-varscan-mutect MAGEB2,synonymous_variant,p.=,ENST00000378988,NM_002364.4; T ENST00000378988 Transcript synonymous_variant 323/1610 222/960 74/319 A gcG/gcT rs200872475 1 1 MAGEB2 HGNC HGNC:6809 protein_coding YES CCDS14219.1 ENSP00000368273 O15479 UPI000013C683 NM_002364.4 2/2 Pfam_domain:PF12440,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF22,Low_complexity_(Seg):seg,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS rs200872475 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 41 30218802 30218802 G T 1 0 0 0 0 0 0 0 1 9092 1103 39 1 1 MAGEB2 23 30218802 Silent SNP G C3N-00199_T 2470281 30218802 125822093 251 11295 CACNA1F 0 . GRCh38 X 49217925 49217925 + Silent SNP G G A C3N-00199_T C3N-00199_N G G c.3042C>T p.= p.F1014F ENST00000376265 25/48 392 350 42 302 302 0 strelka-varscan-mutect CACNA1F,synonymous_variant,p.=,ENST00000376265,NM_005183.3;CACNA1F,synonymous_variant,p.=,ENST00000323022,NM_001256789.2;CACNA1F,synonymous_variant,p.=,ENST00000376251,NM_001256790.2;CACNA1F,downstream_gene_variant,,ENST00000480889,; A ENST00000376265 Transcript synonymous_variant 3104/6070 3042/5934 1014/1977 F ttC/ttT COSM3780506 1 -1 CACNA1F HGNC HGNC:1393 protein_coding YES CCDS35253.1 ENSP00000365441 O60840 UPI0000072854 NM_005183.3 25/48 hmmpanther:PTHR10037:SF184,hmmpanther:PTHR10037,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 41 49217925 49217925 G A 1 0 0 0 0 0 0 0 1 2231 1049 37 1 1 CACNA1F 23 49217925 Silent SNP G C3N-00199_T 18999123 49217925 106822970 252 11296 CACNA1F 0 . GRCh38 X 49224927 49224927 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.1744G>T p.Gly582Cys p.G582C ENST00000376265 14/48 360 143 217 254 254 0 strelka-varscan-mutect CACNA1F,missense_variant,p.Gly582Cys,ENST00000376265,NM_005183.3;CACNA1F,missense_variant,p.Gly571Cys,ENST00000323022,NM_001256789.2;CACNA1F,missense_variant,p.Gly517Cys,ENST00000376251,NM_001256790.2;CACNA1F,upstream_gene_variant,,ENST00000480889,; A ENST00000376265 Transcript missense_variant 1806/6070 1744/5934 582/1977 G/C Ggt/Tgt 1 -1 CACNA1F HGNC HGNC:1393 protein_coding YES CCDS35253.1 ENSP00000365441 O60840 UPI0000072854 NM_005183.3 tolerated(0.05) 14/48 hmmpanther:PTHR10037:SF184,hmmpanther:PTHR10037,Gene3D:1.20.120.350,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1198536265 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 49224927 49224927 C A 1 0 0 0 0 1 0 0 0 2231 652 23 1 1 CACNA1F 23 49224927 Missense_Mutation SNP C C3N-00199_T 7002 49224927 106815968 253 11297 IQSEC2 0 . GRCh38 X 53248781 53248781 + Missense_Mutation SNP C C A rs150014892 C3N-00199_T C3N-00199_N C C c.2399G>T p.Arg800Leu p.R800L ENST00000396435 6/15 176 74 102 129 129 0 strelka-varscan-mutect IQSEC2,missense_variant,p.Arg800Leu,ENST00000396435,NM_001111125.2;IQSEC2,missense_variant,p.Arg595Leu,ENST00000375365,NM_015075.1; A ENST00000396435 Transcript missense_variant 2600/6011 2399/4467 800/1488 R/L cGg/cTg rs150014892 1 -1 IQSEC2 HGNC HGNC:29059 protein_coding YES CCDS48130.1 ENSP00000379712 Q5JU85 UPI00001C207D NM_001111125.2 deleterious(0.01) 6/15 PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF61,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.220.20,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 1 1 PASS rs150014892 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 53248781 53248781 C A 1 0 0 0 0 1 0 0 0 7724 652 23 1 1 IQSEC2 23 53248781 Missense_Mutation SNP C C3N-00199_T 4023854 53248781 102792114 254 11298 FGD1 0 . GRCh38 X 54456523 54456523 + Missense_Mutation SNP C C T novel C3N-00199_T C3N-00199_N C C c.1681G>A p.Ala561Thr p.A561T ENST00000375135 9/18 117 98 19 55 55 0 strelka-varscan-mutect FGD1,missense_variant,p.Ala561Thr,ENST00000375135,NM_004463.2; T ENST00000375135 Transcript missense_variant 2415/4275 1681/2886 561/961 A/T Gcc/Acc 1 -1 FGD1 HGNC HGNC:3663 protein_coding YES CCDS14359.1 ENSP00000364277 P98174 A0A024R9Y5 UPI000012A705 NM_004463.2 tolerated(0.06) 9/18 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF79,Gene3D:1.20.900.10,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 54456523 54456523 C T 1 0 0 0 0 1 0 0 0 5696 710 25 3 3 FGD1 23 54456523 Missense_Mutation SNP C C3N-00199_T 1207742 54456523 101584372 255 11299 KLHL4 0 . GRCh38 X 87633856 87633856 + Missense_Mutation SNP G G T rs755871530 C3N-00199_T C3N-00199_N G G c.1657G>T p.Val553Leu p.V553L ENST00000373114 8/11 30 15 15 80 80 0 strelka-varscan-mutect KLHL4,missense_variant,p.Val553Leu,ENST00000373119,NM_019117.4;KLHL4,missense_variant,p.Val553Leu,ENST00000373114,NM_057162.2; T ENST00000373114 Transcript missense_variant 1737/2445 1657/2163 553/720 V/L Gta/Tta rs755871530,COSM1132251,COSM1132252 1 1 KLHL4 HGNC HGNC:6355 protein_coding YES CCDS14456.1 ENSP00000362206 Q9C0H6 UPI000002ACC4 NM_057162.2 tolerated(0.05) 8/11 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,Prints_domain:PR00501,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF74,SMART_domains:SM00612 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs755871530 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 87633856 87633856 G T 1 0 0 0 0 1 0 0 0 8257 1145 40 1 1 KLHL4 23 87633856 Missense_Mutation SNP G C3N-00199_T 33177333 87633856 68407039 256 11300 DCAF12L1 0 . GRCh38 X 126551774 126551774 + Missense_Mutation SNP C C A novel C3N-00199_T C3N-00199_N C C c.835G>T p.Ala279Ser p.A279S ENST00000371126 1/2 172 29 143 95 95 0 strelka-varscan-mutect DCAF12L1,missense_variant,p.Ala279Ser,ENST00000371126,NM_178470.4; A ENST00000371126 Transcript missense_variant 1078/3382 835/1392 279/463 A/S Gcg/Tcg 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 tolerated(0.18) 1/2 Gene3D:2.130.10.10,hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 126551774 126551774 C A 1 0 0 0 0 1 0 0 0 4065 797 28 2 2 DCAF12L1 23 126551774 Missense_Mutation SNP C C3N-00199_T 38917918 126551774 29489121 257 11301 FRMD7 0 . GRCh38 X 132097281 132097281 + Missense_Mutation SNP C C T rs747452860 C3N-00199_T C3N-00199_N C C c.269G>A p.Arg90Gln p.R90Q ENST00000298542 4/12 149 48 101 164 164 0 strelka-varscan-mutect FRMD7,missense_variant,p.Arg90Gln,ENST00000298542,NM_194277.2;FRMD7,missense_variant,p.Arg75Gln,ENST00000464296,NM_001306193.1;FRMD7,upstream_gene_variant,,ENST00000370879,; T ENST00000298542 Transcript missense_variant 445/3198 269/2145 90/714 R/Q cGg/cAg rs747452860 1 -1 FRMD7 HGNC HGNC:8079 protein_coding YES CCDS35397.1 ENSP00000298542 Q6ZUT3 UPI00001C0AED NM_194277.2 tolerated(0.94) 4/12 Gene3D:1.20.80.10,Pfam_domain:PF00373,PROSITE_profiles:PS50057,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF112,SMART_domains:SM00295,Superfamily_domains:SSF47031 MODERATE 1 SNV 1 1 PASS rs747452860 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 41 132097281 132097281 C T 1 0 0 0 0 1 0 0 0 5925 652 23 1 1 FRMD7 23 132097281 Missense_Mutation SNP C C3N-00199_T 5545507 132097281 23943614 258 11302 CNGA2 0 . GRCh38 X 151743287 151743287 + Missense_Mutation SNP C C T rs747754116 C3N-00199_T C3N-00199_N C C c.784C>T p.Arg262Trp p.R262W ENST00000329903 6/6 121 110 11 93 93 0 strelka-varscan-mutect CNGA2,missense_variant,p.Arg262Trp,ENST00000329903,NM_005140.1; T ENST00000329903 Transcript missense_variant 817/2834 784/1995 262/664 R/W Cgg/Tgg rs747754116,COSM310163,COSM5412218 1 1 CNGA2 HGNC HGNC:2149 protein_coding YES CCDS14701.1 ENSP00000328478 Q16280 UPI000003E7AE NM_005140.1 deleterious(0) 6/6 hmmpanther:PTHR10217:SF389,hmmpanther:PTHR10217,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747754116 . 0 207 3 0 0 0 0 0 -19.99278 1 1 1 1 0 T 3 4 41 151743287 151743287 C T 1 0 0 0 0 1 0 0 0 3377 643 23 1 1 CNGA2 23 151743287 Missense_Mutation SNP C C3N-00199_T 19646006 151743287 4297608 259 11303 MAGEA6 0 . GRCh38 X 152766854 152766854 + Missense_Mutation SNP G G A rs781930988 C3N-00199_T C3N-00199_N G G c.797C>T p.Pro266Leu p.P266L ENST00000616035 3/3 258 225 33 218 218 0 strelka-varscan-mutect MAGEA6,missense_variant,p.Pro266Leu,ENST00000616035,NM_175868.1;MAGEA6,missense_variant,p.Pro266Leu,ENST00000329342,NM_005363.2;MAGEA6,downstream_gene_variant,,ENST00000457643,;MAGEA6,downstream_gene_variant,,ENST00000412733,; A ENST00000616035 Transcript missense_variant 1055/1762 797/945 266/314 P/L cCt/cTt rs781930988,COSM367545 1 -1 MAGEA6 HGNC HGNC:6804 protein_coding YES CCDS76050.1 ENSP00000480637 P43360 UPI000000D9B0 NM_175868.1 deleterious(0.01) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs781930988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 41 152766854 152766854 G A 1 0 0 0 0 1 0 0 0 9085 1000 35 3 3 MAGEA6 23 152766854 Missense_Mutation SNP G C3N-00199_T 1023567 152766854 3274041 260 11304 PRAMEF12 0 . GRCh38 1 12777546 12777546 + Missense_Mutation SNP C C A rs754343116 C3N-00203_T C3N-00203_N C C c.1399C>A p.Leu467Met p.L467M ENST00000357726 3/3 274 209 65 247 247 0 strelka-varscan-mutect PRAMEF12,missense_variant,p.Leu467Met,ENST00000357726,NM_001080830.4; A ENST00000357726 Transcript missense_variant 1426/1786 1399/1452 467/483 L/M Ctg/Atg rs754343116 1 1 PRAMEF12 HGNC HGNC:22125 protein_coding YES CCDS41254.1 ENSP00000350358 O95522 UPI0000EE6E0A NM_001080830.4 tolerated(0.18) 3/3 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF31,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 2 1 PASS rs754343116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 12777546 12777546 C A 1 0 0 0 0 1 0 0 0 12557 680 24 2 2 PRAMEF12 1 12777546 Missense_Mutation SNP C C3N-00203_T 12777546 236178876 1 11305 PAX7 0 . GRCh38 1 18735749 18735749 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1273C>A p.Gln425Lys p.Q425K ENST00000375375 8/8 451 409 42 291 291 0 strelka-varscan-mutect PAX7,missense_variant,p.Gln425Lys,ENST00000420770,NM_001135254.1;PAX7,missense_variant,p.Gln425Lys,ENST00000375375,NM_002584.2;PAX7,missense_variant,p.Gln423Lys,ENST00000400661,NM_013945.2; A ENST00000375375 Transcript missense_variant 1871/2260 1273/1563 425/520 Q/K Cag/Aag 1 1 PAX7 HGNC HGNC:8621 protein_coding YES CCDS186.1 ENSP00000364524 P23759 UPI000004A132 NM_002584.2 deleterious_low_confidence(0.01) 8/8 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF248 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 18735749 18735749 C A 1 0 0 0 0 1 0 0 0 11569 595 21 2 2 PAX7 1 18735749 Missense_Mutation SNP C C3N-00203_T 5958203 18735749 230220673 2 11306 MYOM3 0 . GRCh38 1 24068288 24068288 + Nonsense_Mutation SNP G G T rs759894942 C3N-00203_T C3N-00203_N G G c.3230C>A p.Ser1077Ter p.S1077* ENST00000374434 26/37 268 216 52 250 250 0 strelka-varscan-mutect MYOM3,stop_gained,p.Ser1077Ter,ENST00000374434,NM_152372.3;MYOM3,upstream_gene_variant,,ENST00000338909,;RP11-293P20.4,intron_variant,,ENST00000429191,;RP11-293P20.2,intron_variant,,ENST00000439239,;MYOM3,intron_variant,,ENST00000448831,; T ENST00000374434 Transcript stop_gained 3393/5804 3230/4314 1077/1437 S/* tCg/tAg rs759894942 1 -1 MYOM3 HGNC HGNC:26679 protein_coding YES CCDS41281.1 ENSP00000363557 Q5VTT5 UPI0000203A5D NM_152372.3 26/37 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS rs759894942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 24068288 24068288 G T 1 0 0 0 0 0 1 0 0 10094 1059 37 1 1 MYOM3 1 24068288 Nonsense_Mutation SNP G C3N-00203_T 5332539 24068288 224888134 3 11307 MATN1 0 . GRCh38 1 30718819 30718819 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.580G>C p.Glu194Gln p.E194Q ENST00000373765 3/8 156 119 37 107 107 0 strelka-varscan-mutect MATN1,missense_variant,p.Glu194Gln,ENST00000373765,NM_002379.3;MATN1-AS1,non_coding_transcript_exon_variant,,ENST00000414532,;MATN1-AS1,non_coding_transcript_exon_variant,,ENST00000454613,;MATN1-AS1,non_coding_transcript_exon_variant,,ENST00000414763,;MATN1,non_coding_transcript_exon_variant,,ENST00000477320,;MATN1,upstream_gene_variant,,ENST00000494561,; G ENST00000373765 Transcript missense_variant 616/3832 580/1491 194/496 E/Q Gag/Cag 1 -1 MATN1 HGNC HGNC:6907 protein_coding YES CCDS336.1 ENSP00000362870 P21941 UPI000004F1ED NM_002379.3 tolerated(0.17) 3/8 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF91,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs1329564412 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 30718819 30718819 C G 1 0 0 0 0 1 0 0 0 9259 893 31 4 4 MATN1 1 30718819 Missense_Mutation SNP C C3N-00203_T 6650531 30718819 218237603 4 11308 CSMD2 0 . GRCh38 1 33716314 33716314 + Silent SNP T T G rs369448490 C3N-00203_T C3N-00203_N T T c.3189A>C p.= p.S1063S ENST00000373381 20/71 267 228 39 218 218 0 strelka-varscan-mutect CSMD2,synonymous_variant,p.=,ENST00000373381,NM_001281956.1;CSMD2,synonymous_variant,p.=,ENST00000619121,;CSMD2,synonymous_variant,p.=,ENST00000373388,NM_052896.4;CSMD2,synonymous_variant,p.=,ENST00000241312,; G ENST00000373381 Transcript synonymous_variant 3366/13698 3189/10896 1063/3631 S tcA/tcC rs369448490 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 20/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS rs369448490 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 42 33716314 33716314 T G 1 0 0 0 0 0 0 0 1 3746 1451 51 5 5 CSMD2 1 33716314 Silent SNP T C3N-00203_T 2997495 33716314 215240108 5 11309 CSMD2 0 . GRCh38 1 33935768 33935768 + Missense_Mutation SNP G G A C3N-00203_T C3N-00203_N G G c.704C>T p.Ser235Phe p.S235F ENST00000373381 4/71 64 47 17 57 57 0 strelka-varscan-mutect CSMD2,missense_variant,p.Ser235Phe,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Ser195Phe,ENST00000619121,;CSMD2,missense_variant,p.Ser195Phe,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Ser195Phe,ENST00000241312,; A ENST00000373381 Transcript missense_variant 881/13698 704/10896 235/3631 S/F tCc/tTc COSM4901816,COSM4901817 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 tolerated(1) 4/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 42 33935768 33935768 G A 1 0 0 0 0 1 0 0 0 3746 1174 41 3 3 CSMD2 1 33935768 Missense_Mutation SNP G C3N-00203_T 219454 33935768 215020654 6 11310 GRIK3 0 . GRCh38 1 36825717 36825717 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1640C>A p.Pro547His p.P547H ENST00000373091 11/16 163 143 20 144 143 1 strelka-varscan-mutect GRIK3,missense_variant,p.Pro547His,ENST00000373091,NM_000831.3;GRIK3,missense_variant,p.Pro547His,ENST00000373093,; T ENST00000373091 Transcript missense_variant 1657/9101 1640/2760 547/919 P/H cCc/cAc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 deleterious(0) 11/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS rs1454572099 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 36825717 36825717 G T 1 0 0 0 0 1 0 0 0 6657 1232 43 2 2 GRIK3 1 36825717 Missense_Mutation SNP G C3N-00203_T 2889949 36825717 212130705 7 11311 HIVEP3 0 . GRCh38 1 41513336 41513336 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.5885C>T p.Pro1962Leu p.P1962L ENST00000372583 8/9 199 172 27 144 144 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Pro1962Leu,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Pro1962Leu,ENST00000372583,NM_024503.4;HIVEP3,non_coding_transcript_exon_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 6771/12193 5885/7221 1962/2406 P/L cCt/cTt 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 tolerated(0.49) 8/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 41513336 41513336 G A 1 0 0 0 0 1 0 0 0 7077 1000 35 3 3 HIVEP3 1 41513336 Missense_Mutation SNP G C3N-00203_T 4687619 41513336 207443086 8 11312 FAAH 0 . GRCh38 1 46408511 46408511 + Missense_Mutation SNP A A C novel C3N-00203_T C3N-00203_N A A c.1004A>C p.Tyr335Ser p.Y335S ENST00000243167 8/15 512 394 118 420 419 1 strelka-varscan-mutect FAAH,missense_variant,p.Tyr335Ser,ENST00000243167,NM_001441.2;FAAH,downstream_gene_variant,,ENST00000468718,;FAAH,missense_variant,p.Ile43Leu,ENST00000484697,;FAAH,non_coding_transcript_exon_variant,,ENST00000493735,;FAAH,non_coding_transcript_exon_variant,,ENST00000489366,;FAAH,upstream_gene_variant,,ENST00000493636,; C ENST00000243167 Transcript missense_variant 1088/2094 1004/1740 335/579 Y/S tAt/tCt 1 1 FAAH HGNC HGNC:3553 protein_coding YES CCDS535.1 ENSP00000243167 O00519 UPI000013C9E7 NM_001441.2 deleterious(0) 8/15 Gene3D:3.90.1300.10,Pfam_domain:PF01425,PIRSF_domain:PIRSF001221,hmmpanther:PTHR11895,hmmpanther:PTHR11895:SF91,Superfamily_domains:SSF75304 MODERATE 1 SNV 1 1 PASS rs1343198051 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 46408511 46408511 A C 1 0 0 0 0 1 0 0 0 5222 449 16 5 5 FAAH 1 46408511 Missense_Mutation SNP A C3N-00203_T 4895175 46408511 202547911 9 11313 SCP2 0 . GRCh38 1 53039003 53039003 + Frame_Shift_Del DEL G G - novel C3N-00203_T C3N-00203_N G G c.1426delG p.Val476TrpfsTer3 p.V476Wfs*3 ENST00000371514 14/16 281 242 39 241 241 0 sindel-varindel-pindel SCP2,frameshift_variant,p.Val476TrpfsTer3,ENST00000371514,NM_002979.4;SCP2,frameshift_variant,p.Val452TrpfsTer3,ENST00000407246,NM_001193599.1;SCP2,frameshift_variant,p.Val395TrpfsTer3,ENST00000528311,NM_001193617.1;SCP2,frameshift_variant,p.Val432TrpfsTer3,ENST00000371509,NM_001193600.1;SCP2,frameshift_variant,p.Val91TrpfsTer3,ENST00000478274,;SCP2,frameshift_variant,p.Val69TrpfsTer3,ENST00000430330,NM_001007100.2;SCP2,frameshift_variant,p.Val72TrpfsTer3,ENST00000435345,NM_001007099.2;SCP2,intron_variant,,ENST00000488965,;SCP2,intron_variant,,ENST00000408941,NM_001007250.2;SCP2,intron_variant,,ENST00000484100,;SCP2,3_prime_UTR_variant,,ENST00000478631,;SCP2,3_prime_UTR_variant,,ENST00000533119,; - ENST00000371514 Transcript frameshift_variant 1593/2811 1425/1644 475/547 V/X gtG/gt 1 1 SCP2 HGNC HGNC:10606 protein_coding YES CCDS572.1 ENSP00000360569 P22307 UPI0000130258 NM_002979.4 14/16 hmmpanther:PTHR24314,hmmpanther:PTHR24314:SF13,Gene3D:3.30.1050.10,Pfam_domain:PF02036,Superfamily_domains:SSF55718 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 53039003 53039003 G - 1 0 1 0 1 0 0 0 0 14203 1335 47 0 0 SCP2 1 53039003 Frame_Shift_Del DEL G C3N-00203_T 6630492 53039003 195917419 10 11314 ANKRD13C 0 . GRCh38 1 70292405 70292405 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.1198A>G p.Met400Val p.M400V ENST00000370944 9/13 110 98 12 124 124 0 strelka-varscan-mutect ANKRD13C,missense_variant,p.Met400Val,ENST00000370944,NM_030816.4;ANKRD13C,missense_variant,p.Met365Val,ENST00000262346,;ANKRD13C,non_coding_transcript_exon_variant,,ENST00000490846,; C ENST00000370944 Transcript missense_variant 1512/4069 1198/1626 400/541 M/V Atg/Gtg 1 -1 ANKRD13C HGNC HGNC:25374 protein_coding YES CCDS648.2 ENSP00000359982 Q8N6S4 UPI0000140CE0 NM_030816.4 tolerated(0.72) 9/13 hmmpanther:PTHR12447,Pfam_domain:PF11904 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 70292405 70292405 T C 1 0 0 0 0 1 0 0 0 744 1493 52 5 5 ANKRD13C 1 70292405 Missense_Mutation SNP T C3N-00203_T 17253402 70292405 178664017 11 11315 NEGR1 0 . GRCh38 1 71611106 71611106 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.708C>T p.= p.T236T ENST00000357731 5/7 190 165 25 199 199 0 strelka-varscan-mutect NEGR1,synonymous_variant,p.=,ENST00000357731,NM_173808.2;NEGR1,synonymous_variant,p.=,ENST00000306821,; A ENST00000357731 Transcript synonymous_variant 948/12811 708/1065 236/354 T acC/acT 1 -1 NEGR1 HGNC HGNC:17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 UPI00000477EE NM_173808.2 5/7 Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF132,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1222993912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 71611106 71611106 G A 1 0 0 0 0 0 0 0 1 10345 1219 43 3 3 NEGR1 1 71611106 Silent SNP G C3N-00203_T 1318701 71611106 177345316 12 11316 TNNI3K 0 . GRCh38 1 74463475 74463475 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.2046C>A p.= p.I682I ENST00000326637 21/25 272 228 44 232 232 0 strelka-varscan-mutect TNNI3K,synonymous_variant,p.=,ENST00000326637,NM_015978.2;FPGT-TNNI3K,synonymous_variant,p.=,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,synonymous_variant,p.=,ENST00000370899,NM_001199327.1;RP4-650F12.2,upstream_gene_variant,,ENST00000442876,;TNNI3K,non_coding_transcript_exon_variant,,ENST00000370889,; A ENST00000326637 Transcript synonymous_variant 2097/3001 2046/2508 682/835 I atC/atA 1 1 TNNI3K HGNC HGNC:19661 protein_coding YES CCDS664.1 ENSP00000322251 Q59H18 UPI0000035B8F NM_015978.2 21/25 PROSITE_profiles:PS50011,hmmpanther:PTHR23257:SF477,hmmpanther:PTHR23257,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 74463475 74463475 C A 1 0 0 0 0 0 0 0 1 16802 816 29 2 2 TNNI3K 1 74463475 Silent SNP C C3N-00203_T 2852369 74463475 174492947 13 11317 ERICH3 0 . GRCh38 1 74620851 74620851 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.883G>T p.Gly295Trp p.G295W ENST00000326665 8/15 186 153 33 214 213 1 strelka-varscan-mutect ERICH3,missense_variant,p.Gly295Trp,ENST00000326665,NM_001002912.4;ERICH3,missense_variant,p.Gly98Trp,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,;ERICH3,3_prime_UTR_variant,,ENST00000479666,; A ENST00000326665 Transcript missense_variant 1102/7159 883/4593 295/1530 G/W Ggg/Tgg 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0) 8/15 hmmpanther:PTHR23034 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 74620851 74620851 C A 1 0 0 0 0 1 0 0 0 5083 623 22 2 2 ERICH3 1 74620851 Missense_Mutation SNP C C3N-00203_T 157376 74620851 174335571 14 11318 MSH4 0 . GRCh38 1 75867571 75867571 + Missense_Mutation SNP C C A rs760280278 C3N-00203_T C3N-00203_N C C c.1288C>A p.Leu430Ile p.L430I ENST00000263187 9/20 126 109 17 179 179 0 strelka-varscan-mutect MSH4,missense_variant,p.Leu430Ile,ENST00000263187,NM_002440.3; A ENST00000263187 Transcript missense_variant 1392/3266 1288/2811 430/936 L/I Ctt/Att rs760280278 1 1 MSH4 HGNC HGNC:7327 protein_coding YES CCDS670.1 ENSP00000263187 O15457 UPI000006D934 NM_002440.3 tolerated(0.05) 9/20 Gene3D:1.10.1420.10,Pfam_domain:PF05192,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF21,SMART_domains:SM00533,Superfamily_domains:SSF48334 MODERATE 1 SNV 1 1 PASS rs760280278 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 75867571 75867571 C A 1 0 0 0 0 1 0 0 0 9855 565 20 2 2 MSH4 1 75867571 Missense_Mutation SNP C C3N-00203_T 1246720 75867571 173088851 15 11319 GBP6 0 . GRCh38 1 89369584 89369584 + Missense_Mutation SNP G G C rs770541907 C3N-00203_T C3N-00203_N G G c.229G>C p.Gly77Arg p.G77R ENST00000370456 3/11 138 111 27 126 126 0 strelka-varscan-mutect GBP6,missense_variant,p.Gly77Arg,ENST00000370456,NM_198460.2; C ENST00000370456 Transcript missense_variant 322/2987 229/1902 77/633 G/R Ggc/Cgc rs770541907 1 1 GBP6 HGNC HGNC:25395 protein_coding YES CCDS723.1 ENSP00000359485 Q6ZN66 UPI00001D7DF5 NM_198460.2 deleterious(0) 3/11 PROSITE_profiles:PS51715,hmmpanther:PTHR10751:SF48,hmmpanther:PTHR10751,Pfam_domain:PF02263,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs770541907 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 89369584 89369584 G C 1 0 0 0 0 1 0 0 0 6148 1232 43 4 4 GBP6 1 89369584 Missense_Mutation SNP G C3N-00203_T 13502013 89369584 159586838 16 11320 SETSIP 0 . GRCh38 1 92075311 92075311 + Missense_Mutation SNP G G T rs569444534 C3N-00203_T C3N-00203_N G G c.131C>A p.Pro44Gln p.P44Q ENST00000596516 1/1 261 195 66 294 294 0 strelka-varscan-mutect SETSIP,missense_variant,p.Pro44Gln,ENST00000596516,NM_001287737.1;SETSIP,missense_variant,p.Pro34Gln,ENST00000485873,;BTBD8,upstream_gene_variant,,ENST00000636805,;BTBD8,upstream_gene_variant,,ENST00000635934,;BTBD8,upstream_gene_variant,,ENST00000370382,; T ENST00000596516 Transcript missense_variant 131/909 131/909 44/302 P/Q cCg/cAg rs569444534 1 -1 SETSIP HGNC HGNC:42937 protein_coding YES CCDS72821.1 ENSP00000480946 P0DME0 UPI000016114F NM_001287737.1 deleterious(0.03) 1/1 hmmpanther:PTHR11875:SF74,hmmpanther:PTHR11875,Superfamily_domains:SSF143113 MODERATE 1 SNV 1 PASS rs569444534 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 92075311 92075311 G T 1 0 0 0 0 1 0 0 0 14419 1116 39 1 1 SETSIP 1 92075311 Missense_Mutation SNP G C3N-00203_T 2705727 92075311 156881111 17 11321 OLFM3 0 . GRCh38 1 101806157 101806157 + Silent SNP T T A novel C3N-00203_T C3N-00203_N T T c.678A>T p.= p.T226T ENST00000338858 5/6 225 183 42 192 192 0 strelka-varscan-mutect OLFM3,synonymous_variant,p.=,ENST00000370103,NM_058170.3;OLFM3,synonymous_variant,p.=,ENST00000338858,NM_001288821.1;OLFM3,3_prime_UTR_variant,,ENST00000536598,;OLFM3,non_coding_transcript_exon_variant,,ENST00000462354,;OLFM3,non_coding_transcript_exon_variant,,ENST00000465523,; A ENST00000338858 Transcript synonymous_variant 678/2189 678/1437 226/478 T acA/acT 1 -1 OLFM3 HGNC HGNC:17990 protein_coding YES CCDS72832.1 ENSP00000345192 Q96PB7 Q6IMJ0 UPI000004C626 NM_001288821.1 5/6 Pfam_domain:PF02191,PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF36,SMART_domains:SM00284 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 101806157 101806157 T A 1 0 0 0 0 0 0 0 1 10929 1567 55 4 4 OLFM3 1 101806157 Silent SNP T C3N-00203_T 9730846 101806157 147150265 18 11322 AKNAD1 0 . GRCh38 1 108851937 108851937 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.728C>T p.Ser243Leu p.S243L ENST00000370001 2/16 237 186 51 198 198 0 strelka-varscan-mutect AKNAD1,missense_variant,p.Ser243Leu,ENST00000370001,NM_152763.4;AKNAD1,missense_variant,p.Ser243Leu,ENST00000369995,;AKNAD1,missense_variant,p.Ser243Leu,ENST00000369994,;RP11-475E11.9,intron_variant,,ENST00000357393,;AKNAD1,missense_variant,p.Ser243Leu,ENST00000474186,;AKNAD1,missense_variant,p.Ser243Leu,ENST00000461774,;AKNAD1,missense_variant,p.Ser243Leu,ENST00000472781,; A ENST00000370001 Transcript missense_variant 997/3053 728/2511 243/836 S/L tCa/tTa 1 -1 AKNAD1 HGNC HGNC:28398 protein_coding YES CCDS791.2 ENSP00000359018 Q5T1N1 UPI00004700A0 NM_152763.4 deleterious(0.02) 2/16 hmmpanther:PTHR21510,hmmpanther:PTHR21510:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 108851937 108851937 G A 1 0 0 0 0 1 0 0 0 548 1294 45 3 3 AKNAD1 1 108851937 Missense_Mutation SNP G C3N-00203_T 7045780 108851937 140104485 19 11323 SORT1 0 . GRCh38 1 109336272 109336272 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.1339G>C p.Glu447Gln p.E447Q ENST00000256637 11/20 312 260 52 267 267 0 strelka-varscan-mutect SORT1,missense_variant,p.Glu447Gln,ENST00000256637,NM_002959.5;SORT1,missense_variant,p.Glu310Gln,ENST00000538502,NM_001205228.1;SORT1,non_coding_transcript_exon_variant,,ENST00000466471,; G ENST00000256637 Transcript missense_variant 1398/7028 1339/2496 447/831 E/Q Gaa/Caa 1 -1 SORT1 HGNC HGNC:11186 protein_coding YES CCDS798.1 ENSP00000256637 Q99523 UPI0000074182 NM_002959.5 tolerated(0.49) 11/20 Gene3D:2.130.10.140,Pfam_domain:PF15902,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF23,SMART_domains:SM00602,Superfamily_domains:SSF110296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 109336272 109336272 C G 1 0 0 0 0 1 0 0 0 15257 835 29 4 4 SORT1 1 109336272 Missense_Mutation SNP C C3N-00203_T 484335 109336272 139620150 20 11324 NRAS 0 . GRCh38 1 114713909 114713909 + Missense_Mutation SNP G G T rs121913254 C3N-00203_T C3N-00203_N G G c.181C>A p.Gln61Lys p.Q61K ENST00000369535 3/7 107 82 25 79 79 0 strelka-varscan-mutect NRAS,missense_variant,p.Gln61Lys,ENST00000369535,NM_002524.4;CSDE1,downstream_gene_variant,,ENST00000610726,NM_001242891.1;CSDE1,downstream_gene_variant,,ENST00000438362,;CSDE1,downstream_gene_variant,,ENST00000358528,NM_001007553.2;CSDE1,downstream_gene_variant,,ENST00000339438,NM_007158.5;CSDE1,downstream_gene_variant,,ENST00000369530,NM_001130523.2;CSDE1,downstream_gene_variant,,ENST00000530886,;CSDE1,downstream_gene_variant,,ENST00000261443,NM_001242893.1;CSDE1,downstream_gene_variant,,ENST00000534699,NM_001242892.1;CSDE1,downstream_gene_variant,,ENST00000483407,; T ENST00000369535 Transcript missense_variant 435/4449 181/570 61/189 Q/K Caa/Aaa rs121913254,COSM580,COSM581 1 -1 NRAS HGNC HGNC:7989 protein_coding YES CCDS877.1 ENSP00000358548 P01111 Q5U091 UPI0000001254 NM_002524.4 deleterious(0.01) 3/7 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF189,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs121913254 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 114713909 114713909 G T 1 0 0 0 0 1 0 0 0 10696 1386 48 2 2 NRAS 1 114713909 Missense_Mutation SNP G C3N-00203_T 5377637 114713909 134242513 21 11325 FAM72B 0 . GRCh38 1 121177334 121177334 + Splice_Site SNP T T C novel C3N-00203_T C3N-00203_N T T c.231-2A>G p.X77_splice ENST00000369390 132 100 32 101 101 0 strelka-varscan-mutect FAM72B,splice_acceptor_variant,,ENST00000369390,NM_001100910.1;FAM72B,splice_acceptor_variant,,ENST00000355228,NM_001320149.1;FAM72B,splice_acceptor_variant,,ENST00000452190,;FAM72B,splice_acceptor_variant,,ENST00000471903,;FAM72B,intron_variant,,ENST00000619376,;FAM72B,splice_acceptor_variant,,ENST00000468129,; C ENST00000369390 Transcript splice_acceptor_variant -/2396 231/450 77/149 1 -1 FAM72B HGNC HGNC:24805 protein_coding YES CCDS72848.1 ENSP00000358397 Q86X60 UPI000046FF4E NM_001100910.1 2/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 42 121177334 121177334 T C 1 0 0 0 0 0 0 1 0 5480 1536 53 5 5 FAM72B 1 121177334 Splice_Site SNP T C3N-00203_T 6463425 121177334 127779088 22 11326 ADAMTSL4 0 . GRCh38 1 150556767 150556768 + In_Frame_Ins INS - - CCA novel C3N-00203_T C3N-00203_N - - c.1798_1800dupACC p.Thr600dup p.T600dup ENST00000369039 11/20 132 112 20 100 100 0 sindel-varindel ADAMTSL4,inframe_insertion,p.Thr600dup,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,inframe_insertion,p.Thr577dup,ENST00000271643,NM_019032.5;ADAMTSL4,inframe_insertion,p.Thr577dup,ENST00000369038,;ADAMTSL4,inframe_insertion,p.Thr577dup,ENST00000369041,NM_025008.4;MIR4257,downstream_gene_variant,,ENST00000581735,;RP11-54A4.2,intron_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;ADAMTSL4,downstream_gene_variant,,ENST00000483335,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,;ADAMTSL4,upstream_gene_variant,,ENST00000489159,; CCA ENST00000369039 Transcript inframe_insertion 2081-2082/4319 1792-1793/3294 598/1097 P/PT ccc/cCCAcc 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 11/20 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144,Pfam_domain:PF05986 MODERATE 1 insertion 5 8 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 CCA 7 5 42 150556767 150556767 - CCA 1 0 1 1 0 0 0 0 0 321 623 22 0 0 ADAMTSL4 1 150556767 In_Frame_Ins INS - C3N-00203_T 29379433 150556767 98399655 23 11327 HRNR 0 . GRCh38 1 152218440 152218440 + Nonsense_Mutation SNP G G T rs141737935 C3N-00203_T C3N-00203_N G G c.3189C>A p.Tyr1063Ter p.Y1063* ENST00000368801 3/3 648 514 134 499 498 1 strelka-varscan-mutect HRNR,stop_gained,p.Tyr1063Ter,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368801 Transcript stop_gained 3265/9623 3189/8553 1063/2850 Y/* taC/taA rs141737935,COSM1472638,COSM3369284 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs141737935 . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 152218440 152218440 G T 1 0 0 0 0 0 1 0 0 7254 1140 40 1 1 HRNR 1 152218440 Nonsense_Mutation SNP G C3N-00203_T 1661673 152218440 96737982 24 11328 FLG 0 . GRCh38 1 152307453 152307453 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.7433A>G p.Tyr2478Cys p.Y2478C ENST00000368799 3/3 552 390 162 396 396 0 strelka-varscan-mutect FLG,missense_variant,p.Tyr2478Cys,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENST00000368799 Transcript missense_variant 7469/12747 7433/12186 2478/4061 Y/C tAc/tGc 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.08) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 152307453 152307453 T C 1 0 0 0 0 1 0 0 0 5784 1638 57 5 5 FLG 1 152307453 Missense_Mutation SNP T C3N-00203_T 89013 152307453 96648969 25 11329 FLG 0 . GRCh38 1 152313689 152313689 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.1197C>A p.= p.A399A ENST00000368799 3/3 474 354 120 358 357 1 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,non_coding_transcript_exon_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript synonymous_variant 1233/12747 1197/12186 399/4061 A gcC/gcA 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 LOW 1 SNV 1 1 PASS rs1242002570 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 152313689 152313689 G T 1 0 0 0 0 0 0 0 1 5784 1335 47 2 2 FLG 1 152313689 Silent SNP G C3N-00203_T 6236 152313689 96642733 26 11330 FLG2 0 . GRCh38 1 152354574 152354574 + Nonsense_Mutation SNP G G T rs760212702 C3N-00203_T C3N-00203_N G G c.3212C>A p.Ser1071Ter p.S1071* ENST00000388718 3/3 539 421 118 448 448 0 strelka-varscan-mutect FLG2,stop_gained,p.Ser1071Ter,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript stop_gained 3285/9124 3212/7176 1071/2391 S/* tCa/tAa rs760212702 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 HIGH SNV 5 1 PASS rs760212702 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 152354574 152354574 G T 1 0 0 0 0 0 1 0 0 5785 1294 45 2 2 FLG2 1 152354574 Nonsense_Mutation SNP G C3N-00203_T 40885 152354574 96601848 27 11331 KCNN3 0 . GRCh38 1 154725989 154725989 + Missense_Mutation SNP G G T rs758516858 C3N-00203_T C3N-00203_N G G c.1673C>A p.Ala558Asp p.A558D ENST00000618040 6/9 255 223 32 203 203 0 strelka-varscan-mutect KCNN3,missense_variant,p.Ala558Asp,ENST00000618040,NM_001204087.1;KCNN3,missense_variant,p.Ala543Asp,ENST00000271915,NM_002249.5;KCNN3,missense_variant,p.Ala238Asp,ENST00000361147,NM_170782.2;KCNN3,missense_variant,p.Ala230Asp,ENST00000358505,; T ENST00000618040 Transcript missense_variant 1987/13057 1673/2241 558/746 A/D gCc/gAc rs758516858 1 -1 KCNN3 HGNC HGNC:6292 protein_coding YES CCDS72928.1 ENSP00000481848 A0A087WYJ0 UPI0001F936D2 NM_001204087.1 deleterious(0) 6/9 Gene3D:1.10.287.70,Pfam_domain:PF07885,hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF40,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs758516858 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 154725989 154725989 G T 1 0 0 0 0 1 0 0 0 7996 1203 42 2 2 KCNN3 1 154725989 Missense_Mutation SNP G C3N-00203_T 2371415 154725989 94230433 28 11332 ASH1L 0 . GRCh38 1 155478951 155478951 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.3919A>T p.Ser1307Cys p.S1307C ENST00000392403 3/28 254 181 73 192 192 0 strelka-varscan-mutect ASH1L,missense_variant,p.Ser1307Cys,ENST00000368346,;ASH1L,missense_variant,p.Ser1307Cys,ENST00000392403,NM_018489.2;ASH1L,downstream_gene_variant,,ENST00000548830,; A ENST00000392403 Transcript missense_variant 4398/10979 3919/8895 1307/2964 S/C Agt/Tgt 1 -1 ASH1L HGNC HGNC:19088 protein_coding YES CCDS1113.2 ENSP00000376204 Q9NR48 UPI0000DACAC8 NM_018489.2 deleterious_low_confidence(0) 3/28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 155478951 155478951 T A 1 0 0 0 0 1 0 0 0 1183 1609 56 4 4 ASH1L 1 155478951 Missense_Mutation SNP T C3N-00203_T 752962 155478951 93477471 29 11333 NES 0 . GRCh38 1 156673081 156673081 + Silent SNP T T A rs774118029 C3N-00203_T C3N-00203_N T T c.1107A>T p.= p.P369P ENST00000368223 4/4 62 46 16 57 57 0 strelka-varscan-mutect NES,synonymous_variant,p.=,ENST00000368223,NM_006617.1; A ENST00000368223 Transcript synonymous_variant 1240/5558 1107/4866 369/1621 P ccA/ccT rs774118029,COSM5124273 1 -1 NES HGNC HGNC:7756 protein_coding YES CCDS1151.1 ENSP00000357206 P48681 UPI0000213DC0 NM_006617.1 4/4 hmmpanther:PTHR23239:SF131,hmmpanther:PTHR23239 0,1 LOW 1 SNV 1 0,1 1 PASS rs774118029 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 156673081 156673081 T A 1 0 0 0 0 0 0 0 1 10372 1567 55 4 4 NES 1 156673081 Silent SNP T C3N-00203_T 1194130 156673081 92283341 30 11334 FCRL2 0 . GRCh38 1 157767524 157767524 + Missense_Mutation SNP G G T rs777058693 C3N-00203_T C3N-00203_N G G c.110C>A p.Pro37His p.P37H ENST00000469986 1/2 312 245 67 309 309 0 strelka-varscan-mutect FCRL2,missense_variant,p.Pro37His,ENST00000469986,;FCRL2,intron_variant,,ENST00000361516,NM_030764.3;FCRL2,intron_variant,,ENST00000368181,;FCRL2,non_coding_transcript_exon_variant,,ENST00000368178,;FCRL2,downstream_gene_variant,,ENST00000462774,; T ENST00000469986 Transcript missense_variant 251/902 110/579 37/192 P/H cCt/cAt rs777058693 1 -1 FCRL2 HGNC HGNC:14875 protein_coding ENSP00000417393 Q96LA5 UPI000006D16A deleterious(0.03) 1/2 MODERATE SNV 1 1 PASS rs777058693 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 157767524 157767524 G T 1 0 0 0 0 1 0 0 0 5658 1000 35 2 2 FCRL2 1 157767524 Missense_Mutation SNP G C3N-00203_T 1094443 157767524 91188898 31 11335 CD1A 0 . GRCh38 1 158256991 158256991 + Silent SNP T T A novel C3N-00203_T C3N-00203_N T T c.810T>A p.= p.A270A ENST00000289429 4/6 131 105 26 120 120 0 strelka-varscan-mutect CD1A,synonymous_variant,p.=,ENST00000289429,NM_001763.2; A ENST00000289429 Transcript synonymous_variant 1343/2096 810/984 270/327 A gcT/gcA 1 1 CD1A HGNC HGNC:1634 protein_coding YES CCDS1174.1 ENSP00000289429 P06126 UPI0000161A54 NM_001763.2 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF160,SMART_domains:SM00407,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 158256991 158256991 T A 1 0 0 0 0 0 0 0 1 2677 1567 55 4 4 CD1A 1 158256991 Silent SNP T C3N-00203_T 489467 158256991 90699431 32 11336 OR6Y1 0 . GRCh38 1 158547158 158547158 + Silent SNP C C A rs774241495 C3N-00203_T C3N-00203_N C C c.948G>T p.= p.G316G ENST00000302617 1/1 147 113 34 110 110 0 strelka-varscan-mutect OR6Y1,synonymous_variant,p.=,ENST00000302617,NM_001005189.1; A ENST00000302617 Transcript synonymous_variant 948/978 948/978 316/325 G ggG/ggT rs774241495 1 -1 OR6Y1 HGNC HGNC:14823 protein_coding YES CCDS30899.1 ENSP00000304807 Q8NGX8 UPI000004B1E2 NM_001005189.1 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF109 LOW 1 SNV 1 PASS rs774241495 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 158547158 158547158 C A 1 0 0 0 0 0 0 0 1 11283 726 26 2 2 OR6Y1 1 158547158 Silent SNP C C3N-00203_T 290167 158547158 90409264 33 11337 OR6Y1 0 . GRCh38 1 158547723 158547723 + Missense_Mutation SNP T T A rs751744042 C3N-00203_T C3N-00203_N T T c.383A>T p.Tyr128Phe p.Y128F ENST00000302617 1/1 432 337 95 335 335 0 strelka-varscan-mutect OR6Y1,missense_variant,p.Tyr128Phe,ENST00000302617,NM_001005189.1; A ENST00000302617 Transcript missense_variant 383/978 383/978 128/325 Y/F tAt/tTt rs751744042,COSM5641414 1 -1 OR6Y1 HGNC HGNC:14823 protein_coding YES CCDS30899.1 ENSP00000304807 Q8NGX8 UPI000004B1E2 NM_001005189.1 tolerated(0.07) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF109,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs751744042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 158547723 158547723 T A 1 0 0 0 0 1 0 0 0 11283 1406 49 4 4 OR6Y1 1 158547723 Missense_Mutation SNP T C3N-00203_T 565 158547723 90408699 34 11338 OR10J3 0 . GRCh38 1 159314532 159314532 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.128A>T p.Asn43Ile p.N43I ENST00000332217 1/1 405 290 115 389 389 0 strelka-varscan-mutect OR10J3,missense_variant,p.Asn43Ile,ENST00000332217,NM_001004467.1; A ENST00000332217 Transcript missense_variant 128/990 128/990 43/329 N/I aAt/aTt 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 159314532 159314532 T A 1 0 0 0 0 1 0 0 0 10988 1493 52 4 4 OR10J3 1 159314532 Missense_Mutation SNP T C3N-00203_T 766809 159314532 89641890 35 11339 45 2 OR10J3 0 . GRCh38 1 159314534 159314534 + Silent SNP G G C novel C3N-00203_T C3N-00203_N G G c.126C>G p.= p.G42G ENST00000332217 1/1 401 286 115 386 386 0 strelka-varscan-mutect OR10J3,synonymous_variant,p.=,ENST00000332217,NM_001004467.1; C ENST00000332217 Transcript synonymous_variant 126/990 126/990 42/329 G ggC/ggG 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 159314534 159314534 G C 1 0 0 0 0 0 0 0 1 10988 1306 46 4 4 OR10J3 1 159314534 Silent SNP G C3N-00203_T 2 159314534 89641888 36 11340 45 2 FCRL6 0 . GRCh38 1 159809110 159809110 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.469C>G p.Gln157Glu p.Q157E ENST00000368106 4/10 309 278 31 159 159 0 strelka-varscan-mutect FCRL6,missense_variant,p.Gln164Glu,ENST00000321935,NM_001284217.1;FCRL6,missense_variant,p.Gln157Glu,ENST00000339348,;FCRL6,missense_variant,p.Gln157Glu,ENST00000368106,NM_001004310.2;FCRL6,intron_variant,,ENST00000392235,;FCRL6,intron_variant,,ENST00000536257,;FCRL6,non_coding_transcript_exon_variant,,ENST00000540741,;FCRL6,downstream_gene_variant,,ENST00000541729,; G ENST00000368106 Transcript missense_variant 470/1306 469/1305 157/434 Q/E Cag/Gag 1 1 FCRL6 HGNC HGNC:31910 protein_coding YES CCDS30912.1 ENSP00000357086 Q6DN72 UPI0000D62020 NM_001004310.2 deleterious(0.02) 4/10 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF62,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999855 1 1 1 0 G 3 3 42 159809110 159809110 C G 1 0 0 0 0 1 0 0 0 5661 711 25 4 4 FCRL6 1 159809110 Missense_Mutation SNP C C3N-00203_T 494576 159809110 89147312 37 11341 FCGR2B 0 . GRCh38 1 161673151 161673151 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.568C>A p.His190Asn p.H190N ENST00000358671 4/8 206 163 43 226 226 0 strelka-varscan-mutect FCGR2B,missense_variant,p.His190Asn,ENST00000358671,NM_004001.4,NM_001002275.2;FCGR2B,missense_variant,p.His183Asn,ENST00000367961,NM_001190828.1;FCGR2B,missense_variant,p.His190Asn,ENST00000236937,NM_001002274.2,NM_001002273.2;RP11-25K21.1,intron_variant,,ENST00000453111,;RP11-25K21.1,downstream_gene_variant,,ENST00000626340,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000480308,;FCGR2B,non_coding_transcript_exon_variant,,ENST00000485778,; A ENST00000358671 Transcript missense_variant 649/2115 568/933 190/310 H/N Cac/Aac 1 1 FCGR2B HGNC HGNC:3618 protein_coding YES CCDS30924.1 ENSP00000351497 P31994 UPI0000001600 NM_004001.4,NM_001002275.2 deleterious(0.03) 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF51,hmmpanther:PTHR11481,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 161673151 161673151 C A 1 0 0 0 0 1 0 0 0 5645 826 29 2 2 FCGR2B 1 161673151 Missense_Mutation SNP C C3N-00203_T 1864041 161673151 87283271 38 11342 SOAT1 0 . GRCh38 1 179337847 179337847 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.340G>T p.Ala114Ser p.A114S ENST00000367619 5/16 89 66 23 80 80 0 strelka-varscan-mutect SOAT1,missense_variant,p.Ala56Ser,ENST00000540564,NM_001252511.1;SOAT1,missense_variant,p.Ala114Ser,ENST00000367619,NM_003101.5;SOAT1,missense_variant,p.Ala49Ser,ENST00000539888,NM_001252512.1;SOAT1,missense_variant,p.Ala114Ser,ENST00000426956,; T ENST00000367619 Transcript missense_variant 483/6835 340/1653 114/550 A/S Gca/Tca 1 1 SOAT1 HGNC HGNC:11177 protein_coding YES CCDS1330.1 ENSP00000356591 P35610 UPI0000071233 NM_003101.5 tolerated(0.61) 5/16 hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF6,PIRSF_domain:PIRSF500230,PIRSF_domain:PIRSF000439 MODERATE 1 SNV 1 1 PASS rs1272007528 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 179337847 179337847 G T 1 0 0 0 0 1 0 0 0 15231 971 34 2 2 SOAT1 1 179337847 Missense_Mutation SNP G C3N-00203_T 17664696 179337847 69618575 39 11343 AXDND1 0 . GRCh38 1 179445052 179445052 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.1646A>G p.Gln549Arg p.Q549R ENST00000367618 16/26 284 256 28 303 303 0 strelka-varscan-mutect AXDND1,missense_variant,p.Gln549Arg,ENST00000367618,NM_144696.5;AXDND1,missense_variant,p.Gln483Arg,ENST00000434088,;AXDND1,intron_variant,,ENST00000617277,;AXDND1,non_coding_transcript_exon_variant,,ENST00000461179,;AXDND1,intron_variant,,ENST00000511157,;HNRNPA1P54,downstream_gene_variant,,ENST00000411857,;MEF2AP1,downstream_gene_variant,,ENST00000454867,; G ENST00000367618 Transcript missense_variant 2033/3642 1646/3039 549/1012 Q/R cAg/cGg 1 1 AXDND1 HGNC HGNC:26564 protein_coding YES CCDS30948.1 ENSP00000356590 Q5T1B0 UPI000022AC91 NM_144696.5 deleterious(0.02) 16/26 hmmpanther:PTHR23052 MODERATE 1 SNV 1 1 PASS rs1459327798 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 179445052 179445052 A G 1 0 0 0 0 1 0 0 0 1392 188 7 5 5 AXDND1 1 179445052 Missense_Mutation SNP A C3N-00203_T 107205 179445052 69511370 40 11344 TDRD5 0 . GRCh38 1 179635666 179635666 + Splice_Site SNP G G T novel C3N-00203_T C3N-00203_N G G c.1300-1G>T p.X434_splice ENST00000444136 129 86 43 121 120 1 strelka-varscan-mutect TDRD5,splice_acceptor_variant,,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,splice_acceptor_variant,,ENST00000367614,NM_001199091.1;TDRD5,splice_acceptor_variant,,ENST00000294848,NM_173533.3;TDRD5,upstream_gene_variant,,ENST00000417329,; T ENST00000444136 Transcript splice_acceptor_variant -/3946 1300/3108 434/1035 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 8/17 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 179635666 179635666 G T 1 0 0 0 0 0 0 1 0 16143 985 34 2 2 TDRD5 1 179635666 Splice_Site SNP G C3N-00203_T 190614 179635666 69320756 41 11345 CACNA1E 0 . GRCh38 1 181720831 181720831 + Silent SNP T T A C3N-00203_T C3N-00203_N T T c.1932T>A p.= p.P644P ENST00000367573 15/48 246 222 24 202 202 0 strelka-varscan-mutect CACNA1E,synonymous_variant,p.=,ENST00000621791,NM_001205294.1;CACNA1E,synonymous_variant,p.=,ENST00000621551,;CACNA1E,synonymous_variant,p.=,ENST00000367567,;CACNA1E,synonymous_variant,p.=,ENST00000358338,;CACNA1E,synonymous_variant,p.=,ENST00000367570,NM_000721.3;CACNA1E,synonymous_variant,p.=,ENST00000367573,NM_001205293.1;CACNA1E,synonymous_variant,p.=,ENST00000357570,;CACNA1E,synonymous_variant,p.=,ENST00000360108,;CACNA1E,downstream_gene_variant,,ENST00000524607,; A ENST00000367573 Transcript synonymous_variant 1932/7067 1932/6942 644/2313 P ccT/ccA COSM4941887,COSM4941888,COSM4941889,COSM4941890 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 15/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00167 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 181720831 181720831 T A 1 0 0 0 0 0 0 0 1 2230 1567 55 4 4 CACNA1E 1 181720831 Silent SNP T C3N-00203_T 2085165 181720831 67235591 42 11346 RGSL1 0 . GRCh38 1 182474306 182474306 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1195C>A p.Leu399Ile p.L399I ENST00000294854 6/22 346 305 41 326 326 0 strelka-varscan-mutect RGSL1,missense_variant,p.Leu399Ile,ENST00000294854,NM_001137669.1;RGSL1,downstream_gene_variant,,ENST00000437548,;RGSL1,downstream_gene_variant,,ENST00000634679,;RGSL1,downstream_gene_variant,,ENST00000634723,;RGSL1,downstream_gene_variant,,ENST00000447374,;RGSL1,downstream_gene_variant,,ENST00000634626,;RGSL1,downstream_gene_variant,,ENST00000634758,;RGSL1,downstream_gene_variant,,ENST00000426890,;RGSL1,missense_variant,p.Leu434Ile,ENST00000443996,;RGSL1,non_coding_transcript_exon_variant,,ENST00000367561,;RGSL1,intron_variant,,ENST00000422241,;RGSL1,intron_variant,,ENST00000416676,;RGSL1,upstream_gene_variant,,ENST00000415960,;RGSL1,downstream_gene_variant,,ENST00000635407,;RGSL1,downstream_gene_variant,,ENST00000444367,; A ENST00000294854 Transcript missense_variant 1215/3696 1195/3231 399/1076 L/I Ctt/Att 1 1 RGSL1 HGNC HGNC:18636 protein_coding YES CCDS58049.1 ENSP00000457748 A5PLK6 UPI000156571A NM_001137669.1 deleterious(0) 6/22 hmmpanther:PTHR10845:SF173,hmmpanther:PTHR10845,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS rs1250316282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 182474306 182474306 C A 1 0 0 0 0 1 0 0 0 13486 565 20 2 2 RGSL1 1 182474306 Missense_Mutation SNP C C3N-00203_T 753475 182474306 66482116 43 11347 TPR 0 . GRCh38 1 186327605 186327605 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.5744C>G p.Ser1915Cys p.S1915C ENST00000367478 40/51 368 279 89 333 333 0 strelka-varscan-mutect TPR,missense_variant,p.Ser1915Cys,ENST00000367478,NM_003292.2;TPR,upstream_gene_variant,,ENST00000467810,;TPR,upstream_gene_variant,,ENST00000492973,; C ENST00000367478 Transcript missense_variant 6041/9708 5744/7092 1915/2363 S/C tCt/tGt 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 deleterious(0) 40/51 hmmpanther:PTHR18898 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 186327605 186327605 G C 1 0 0 0 0 1 0 0 0 16897 942 33 4 4 TPR 1 186327605 Missense_Mutation SNP G C3N-00203_T 3853299 186327605 62628817 44 11348 CRB1 0 . GRCh38 1 197427836 197427836 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2511C>A p.Asp837Glu p.D837E ENST00000367400 7/12 458 338 120 398 398 0 strelka-varscan-mutect CRB1,missense_variant,p.Asp218Glu,ENST00000367397,;CRB1,missense_variant,p.Asp768Glu,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Asp837Glu,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Asp725Glu,ENST00000367399,NM_001193640.1;CRB1,intron_variant,,ENST00000538660,NM_001257966.1;CRB1,non_coding_transcript_exon_variant,,ENST00000480086,;CRB1,missense_variant,p.Asp837Glu,ENST00000484075,; A ENST00000367400 Transcript missense_variant 2646/4932 2511/4221 837/1406 D/E gaC/gaA 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 tolerated(0.18) 7/12 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24049,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1485255522 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 197427836 197427836 C A 1 0 0 0 0 1 0 0 0 3648 477 17 2 2 CRB1 1 197427836 Missense_Mutation SNP C C3N-00203_T 11100231 197427836 51528586 45 11349 KIF14 0 . GRCh38 1 200618001 200618001 + Missense_Mutation SNP C C G rs748610123 C3N-00203_T C3N-00203_N C C c.723G>C p.Gln241His p.Q241H ENST00000367350 2/30 236 143 93 162 162 0 strelka-varscan-mutect KIF14,missense_variant,p.Gln241His,ENST00000367350,NM_014875.2;KIF14,missense_variant,p.Gln241His,ENST00000614960,; G ENST00000367350 Transcript missense_variant 1162/7274 723/4947 241/1648 Q/H caG/caC rs748610123 1 -1 KIF14 HGNC HGNC:19181 protein_coding YES CCDS30963.1 ENSP00000356319 Q15058 UPI000012DDA3 NM_014875.2 tolerated(0.06) 2/30 MODERATE 1 SNV 1 1 PASS rs748610123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 200618001 200618001 C G 1 0 0 0 0 1 0 0 0 8140 912 32 4 4 KIF14 1 200618001 Missense_Mutation SNP C C3N-00203_T 3190165 200618001 48338421 46 11350 KIF21B 0 . GRCh38 1 200988785 200988785 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.3279C>A p.= p.L1093L ENST00000422435 22/35 101 58 43 72 72 0 strelka-varscan-mutect KIF21B,synonymous_variant,p.=,ENST00000332129,NM_017596.3;KIF21B,synonymous_variant,p.=,ENST00000422435,NM_001252100.1;KIF21B,synonymous_variant,p.=,ENST00000461742,NM_001252102.1;KIF21B,synonymous_variant,p.=,ENST00000360529,NM_001252103.1; T ENST00000422435 Transcript synonymous_variant 3596/5519 3279/4914 1093/1637 L ctC/ctA 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 22/35 hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115,Superfamily_domains:SSF46579 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 200988785 200988785 G T 1 0 0 0 0 0 0 0 1 8154 1277 45 2 2 KIF21B 1 200988785 Silent SNP G C3N-00203_T 370784 200988785 47967637 47 11351 IPO9 0 . GRCh38 1 201874852 201874852 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.2854G>C p.Glu952Gln p.E952Q ENST00000361565 22/24 177 123 54 159 159 0 strelka-varscan-mutect IPO9,missense_variant,p.Glu952Gln,ENST00000361565,NM_018085.4;IPO9,missense_variant,p.Glu27Gln,ENST00000456707,; C ENST00000361565 Transcript missense_variant 2923/11435 2854/3126 952/1041 E/Q Gag/Cag 1 1 IPO9 HGNC HGNC:19425 protein_coding YES CCDS1415.1 ENSP00000354742 Q96P70 UPI000007304B NM_018085.4 deleterious(0.04) 22/24 hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF9,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 201874852 201874852 G C 1 0 0 0 0 1 0 0 0 7702 1175 41 4 4 IPO9 1 201874852 Missense_Mutation SNP G C3N-00203_T 886067 201874852 47081570 48 11352 PTPN7 0 . GRCh38 1 202150310 202150310 + Splice_Site SNP C C T C3N-00203_T C3N-00203_N C C c.1304+1G>A p.X435_splice ENST00000309017 177 95 82 111 111 0 strelka-varscan-mutect PTPN7,splice_donor_variant,,ENST00000309017,NM_002832.3;PTPN7,splice_donor_variant,,ENST00000367279,NM_080588.2;PTPN7,splice_donor_variant,,ENST00000477554,NM_001199797.1;PTPN7,downstream_gene_variant,,ENST00000477625,;PTPN7,downstream_gene_variant,,ENST00000476061,;PTPN7,downstream_gene_variant,,ENST00000629151,;PTPN7,non_coding_transcript_exon_variant,,ENST00000492977,;PTPN7,downstream_gene_variant,,ENST00000479092,;PTPN7,splice_donor_variant,,ENST00000495688,;PTPN7,splice_donor_variant,,ENST00000496197,;PTPN7,splice_donor_variant,,ENST00000480836,;PTPN7,splice_donor_variant,,ENST00000462815,; T ENST00000309017 Transcript splice_donor_variant -/3765 1304/1398 435/465 COSM4868178,COSM902294 1 -1 PTPN7 HGNC HGNC:9659 protein_coding YES CCDS1423.2 ENSP00000309116 P35236 UPI00004701F6 NM_002832.3 9/9 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 202150310 202150310 C T 1 0 0 0 0 0 0 1 0 12947 521 18 3 3 PTPN7 1 202150310 Splice_Site SNP C C3N-00203_T 275458 202150310 46806112 49 11353 REN 0 . GRCh38 1 204159399 204159399 + Missense_Mutation SNP C C A rs121917742 C3N-00203_T C3N-00203_N C C c.689G>T p.Arg230Ile p.R230I ENST00000272190 5/10 473 430 43 305 304 1 strelka-varscan-mutect REN,missense_variant,p.Arg192Ile,ENST00000638118,;REN,missense_variant,p.Arg230Ile,ENST00000272190,NM_000537.3; A ENST00000272190 Transcript missense_variant,splice_region_variant 718/1447 689/1221 230/406 R/I aGa/aTa rs121917742,CM053392 1 -1 REN HGNC HGNC:9958 protein_coding YES CCDS30981.1 ENSP00000272190 P00797 UPI000000091F NM_000537.3 deleterious(0) 5/10 Gene3D:2.40.70.10,Pfam_domain:PF00026,PROSITE_profiles:PS51767,hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF77,Superfamily_domains:SSF50630 pathogenic MODERATE 1 SNV 1 1,1 1 PASS rs121917742 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 204159399 204159399 C A 1 0 0 0 0 1 0 0 0 13394 695 24 2 2 REN 1 204159399 Missense_Mutation SNP C C3N-00203_T 2009089 204159399 44797023 50 11354 MDM4 0 . GRCh38 1 204544617 204544617 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.755G>T p.Gly252Val p.G252V ENST00000367182 9/11 153 122 31 164 164 0 strelka-varscan MDM4,missense_variant,p.Gly252Val,ENST00000367182,NM_002393.4;MDM4,missense_variant,p.Gly154Val,ENST00000614459,NM_001278517.1;MDM4,missense_variant,p.Gly137Val,ENST00000367179,;MDM4,3_prime_UTR_variant,,ENST00000391947,NM_001278516.1;MDM4,3_prime_UTR_variant,,ENST00000621032,;MDM4,intron_variant,,ENST00000454264,NM_001204171.1;MDM4,intron_variant,,ENST00000616250,NM_001278518.1;MDM4,intron_variant,,ENST00000612738,NM_001278519.1;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,intron_variant,,ENST00000444261,;MDM4,intron_variant,,ENST00000507825,;MDM4,non_coding_transcript_exon_variant,,ENST00000463049,;MDM4,non_coding_transcript_exon_variant,,ENST00000470908,;MDM4,downstream_gene_variant,,ENST00000462012,;MDM4,downstream_gene_variant,,ENST00000471783,; T ENST00000367182 Transcript missense_variant 917/10073 755/1473 252/490 G/V gGa/gTa 1 1 MDM4 HGNC HGNC:6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 A0A024R990 UPI000007467F NM_002393.4 tolerated(0.14) 9/11 hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF20,PIRSF_domain:PIRSF006748,PIRSF_domain:PIRSF500699 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 204544617 204544617 G T 1 0 0 0 0 1 0 0 0 9352 1174 41 2 2 MDM4 1 204544617 Missense_Mutation SNP G C3N-00203_T 385218 204544617 44411805 51 11355 RBBP5 0 . GRCh38 1 205099751 205099751 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.968A>G p.Gln323Arg p.Q323R ENST00000264515 9/14 132 117 15 109 109 0 strelka-varscan RBBP5,missense_variant,p.Gln323Arg,ENST00000264515,NM_001193273.1,NM_005057.3;RBBP5,missense_variant,p.Gln323Arg,ENST00000367164,NM_001193272.1; C ENST00000264515 Transcript missense_variant 1110/4404 968/1617 323/538 Q/R cAg/cGg 1 -1 RBBP5 HGNC HGNC:9888 protein_coding YES CCDS30983.1 ENSP00000264515 Q15291 A0A024R9B5 UPI00001A9CA5 NM_001193273.1,NM_005057.3 deleterious(0.02) 9/14 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF433,Superfamily_domains:SSF117289 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 205099751 205099751 T C 1 0 0 0 0 1 0 0 0 13263 1580 55 5 5 RBBP5 1 205099751 Missense_Mutation SNP T C3N-00203_T 555134 205099751 43856671 52 11356 PLXNA2 0 . GRCh38 1 208042346 208042346 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.4038G>T p.Gln1346His p.Q1346H ENST00000367033 22/32 98 86 12 127 127 0 strelka-varscan PLXNA2,missense_variant,p.Gln1346His,ENST00000367033,NM_025179.3;PLXNA2,upstream_gene_variant,,ENST00000463510,; A ENST00000367033 Transcript missense_variant 4796/11444 4038/5685 1346/1894 Q/H caG/caT 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 tolerated(0.13) 22/32 hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Pfam_domain:PF08337 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 208042346 208042346 C A 1 0 0 0 0 1 0 0 0 12226 796 28 2 2 PLXNA2 1 208042346 Missense_Mutation SNP C C3N-00203_T 2942595 208042346 40914076 53 11357 DNAH14 0 . GRCh38 1 225140923 225140923 + Silent SNP A A T novel C3N-00203_T C3N-00203_N A A c.4359A>T p.= p.I1453I ENST00000430092 27/84 349 270 79 282 282 0 strelka-varscan-mutect DNAH14,synonymous_variant,p.=,ENST00000430092,NM_001373.1;DNAH14,synonymous_variant,p.=,ENST00000439375,;DNAH14,synonymous_variant,p.=,ENST00000445597,;DNAH14,synonymous_variant,p.=,ENST00000328556,;DNAH14,intron_variant,,ENST00000495456,; T ENST00000430092 Transcript synonymous_variant 4574/13763 4359/13548 1453/4515 I atA/atT 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 27/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254 LOW SNV 5 1 PASS rs1033755281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 225140923 225140923 A T 1 0 0 0 0 0 0 0 1 4415 381 14 4 4 DNAH14 1 225140923 Silent SNP A C3N-00203_T 17098577 225140923 23815499 54 11358 RYR2 0 . GRCh38 1 237614367 237614367 + Missense_Mutation SNP G G C C3N-00203_T C3N-00203_N G G c.5239G>C p.Gly1747Arg p.G1747R ENST00000366574 37/105 297 240 57 274 274 0 strelka-varscan-mutect RYR2,missense_variant,p.Gly1747Arg,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly1731Arg,ENST00000360064,; C ENST00000366574 Transcript missense_variant 5556/16562 5239/14904 1747/4967 G/R Ggc/Cgc COSM358351 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.17) 37/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 237614367 237614367 G C 1 0 0 0 0 1 0 0 0 14029 1116 39 4 4 RYR2 1 237614367 Missense_Mutation SNP G C3N-00203_T 12473444 237614367 11342055 55 11359 RYR2 0 . GRCh38 1 237627848 237627848 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.6208G>T p.Ala2070Ser p.A2070S ENST00000366574 41/105 135 113 22 128 128 0 strelka-varscan-mutect RYR2,missense_variant,p.Ala2070Ser,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ala2054Ser,ENST00000360064,; T ENST00000366574 Transcript missense_variant 6525/16562 6208/14904 2070/4967 A/S Gct/Tct 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.07) 41/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 237627848 237627848 G T 1 0 0 0 0 1 0 0 0 14029 1203 42 2 2 RYR2 1 237627848 Missense_Mutation SNP G C3N-00203_T 13481 237627848 11328574 56 11360 RGS7 0 . GRCh38 1 240816358 240816358 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.742C>A p.Pro248Thr p.P248T ENST00000366565 11/18 360 273 87 325 325 0 strelka-varscan-mutect RGS7,missense_variant,p.Pro248Thr,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Pro248Thr,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Pro248Thr,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Pro195Thr,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Pro79Thr,ENST00000440928,; T ENST00000366565 Transcript missense_variant 1124/2494 742/1464 248/487 P/T Cca/Aca 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 tolerated(0.14) 11/18 Low_complexity_(Seg):seg,Gene3D:4.10.260.10,Superfamily_domains:SSF48670 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 240816358 240816358 G T 1 0 0 0 0 1 0 0 0 13481 1261 44 2 2 RGS7 1 240816358 Missense_Mutation SNP G C3N-00203_T 3188510 240816358 8140064 57 11361 NLRP3 0 . GRCh38 1 247424564 247424564 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.1121C>A p.Ser374Tyr p.S374Y ENST00000336119 3/9 355 317 38 313 312 1 strelka-varscan NLRP3,missense_variant,p.Ser374Tyr,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Ser374Tyr,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Ser374Tyr,ENST00000366496,;NLRP3,missense_variant,p.Ser374Tyr,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Ser374Tyr,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Ser374Tyr,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript missense_variant 1867/4170 1121/3111 374/1036 S/Y tCc/tAc COSM355549 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 deleterious(0) 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Pfam_domain:PF05729,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 247424564 247424564 C A 1 0 0 0 0 1 0 0 0 10516 855 30 2 2 NLRP3 1 247424564 Missense_Mutation SNP C C3N-00203_T 6608206 247424564 1531858 58 11362 OR2G3 0 . GRCh38 1 247605982 247605982 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.397G>T p.Val133Leu p.V133L ENST00000320002 1/1 210 184 26 190 188 2 strelka-varscan OR2G3,missense_variant,p.Val133Leu,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; T ENST00000320002 Transcript missense_variant 397/930 397/930 133/309 V/L Gta/Tta 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 tolerated(0.12) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 42 247605982 247605982 G T 1 0 0 0 0 1 0 0 0 11077 1377 48 2 2 OR2G3 1 247605982 Missense_Mutation SNP G C3N-00203_T 181418 247605982 1350440 59 11363 OR14A2 0 . GRCh38 1 247723324 247723324 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.720C>A p.Phe240Leu p.F240L ENST00000366485 1/1 270 250 20 282 280 2 strelka-varscan OR14A2,missense_variant,p.Phe240Leu,ENST00000366485,;RP11-634B7.5,intron_variant,,ENST00000426444,;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; T ENST00000366485 Transcript missense_variant 720/945 720/945 240/314 F/L ttC/ttA 1 -1 OR14A2 HGNC HGNC:15024 protein_coding YES ENSP00000355441 Q96R54 A0A126GWG8 UPI000004A5E7 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF346,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 247723324 247723324 G T 1 0 0 0 0 1 0 0 0 11022 1165 41 2 2 OR14A2 1 247723324 Missense_Mutation SNP G C3N-00203_T 117342 247723324 1233098 60 11364 OR2W3 0 . GRCh38 1 247895676 247895676 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.90C>A p.= p.V30V ENST00000360358 1/1 226 199 27 225 225 0 strelka-varscan OR2W3,synonymous_variant,p.=,ENST00000360358,NM_001001957.2; A ENST00000360358 Transcript synonymous_variant 90/945 90/945 30/314 V gtC/gtA 1 1 OR2W3 HGNC HGNC:15021 protein_coding YES CCDS31099.1 ENSP00000353516 Q7Z3T1 UPI0000061EA8 NM_001001957.2 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26453:SF223,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 247895676 247895676 C A 1 0 0 0 0 0 0 0 1 11111 813 29 2 2 OR2W3 1 247895676 Silent SNP C C3N-00203_T 172352 247895676 1060746 61 11365 OR2L13 0 . GRCh38 1 248099402 248099402 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.27T>A p.Asn9Lys p.N9K ENST00000358120 2/2 94 69 25 111 111 0 strelka-varscan OR2L13,missense_variant,p.Asn9Lys,ENST00000358120,NM_001304535.1,NM_175911.3; A ENST00000358120 Transcript missense_variant 172/1692 27/939 9/312 N/K aaT/aaA 1 1 OR2L13 HGNC HGNC:19578 protein_coding YES CCDS1637.1 ENSP00000350836 Q8N349 A0A126GW96 UPI0000043517 NM_001304535.1,NM_175911.3 tolerated(0.07) 2/2 hmmpanther:PTHR26453:SF102,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 248099402 248099402 T A 1 0 0 0 0 1 0 0 0 11084 1461 51 4 4 OR2L13 1 248099402 Missense_Mutation SNP T C3N-00203_T 203726 248099402 857020 62 11366 GREB1 0 . GRCh38 2 11633015 11633015 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.4943G>A p.Cys1648Tyr p.C1648Y ENST00000381486 28/33 304 238 66 214 214 0 strelka-varscan-mutect GREB1,missense_variant,p.Cys1648Tyr,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Cys1648Tyr,ENST00000234142,;GREB1,missense_variant,p.Cys646Tyr,ENST00000396123,; A ENST00000381486 Transcript missense_variant 5243/8484 4943/5850 1648/1949 C/Y tGc/tAc 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 deleterious(0) 28/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 11633015 11633015 G A 1 0 0 0 0 1 0 0 0 6639 1319 46 3 3 GREB1 2 11633015 Missense_Mutation SNP G C3N-00203_T 11633015 230560514 63 11367 FAM84A 0 . GRCh38 2 14634365 14634365 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.386T>C p.Leu129Pro p.L129P ENST00000295092 2/2 66 53 13 52 52 0 strelka-varscan-mutect FAM84A,missense_variant,p.Leu129Pro,ENST00000295092,NM_145175.2;FAM84A,missense_variant,p.Leu129Pro,ENST00000331243,;AC011897.2,downstream_gene_variant,,ENST00000450715,;AC011897.2,downstream_gene_variant,,ENST00000418481,;FAM84A,upstream_gene_variant,,ENST00000497769,;FAM84A,upstream_gene_variant,,ENST00000464947,; C ENST00000295092 Transcript missense_variant 674/6355 386/879 129/292 L/P cTg/cCg 1 1 FAM84A HGNC HGNC:20743 protein_coding YES CCDS1684.1 ENSP00000295092 Q96KN4 UPI000013E203 NM_145175.2 deleterious(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR13943:SF38,hmmpanther:PTHR13943,Pfam_domain:PF04970 MODERATE 1 SNV 1 1 PASS rs1356905557 . 0 194 16 0 0 0 0 0 -20 0.999574 1 1 1 0 C 3 2 42 14634365 14634365 T C 1 0 0 0 0 1 0 0 0 5499 1580 55 5 5 FAM84A 2 14634365 Missense_Mutation SNP T C3N-00203_T 3001350 14634365 227559164 64 11368 APOB 0 . GRCh38 2 21029939 21029939 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.1429G>A p.Asp477Asn p.D477N ENST00000233242 11/29 643 517 126 437 437 0 strelka-varscan APOB,missense_variant,p.Asp477Asn,ENST00000233242,NM_000384.2;APOB,missense_variant,p.Asp477Asn,ENST00000399256,; T ENST00000233242 Transcript missense_variant 1557/14121 1429/13692 477/4563 D/N Gac/Aac 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.06) 11/29 PROSITE_profiles:PS51211,hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF01347,Gene3D:1lshA02,SMART_domains:SM00638,Superfamily_domains:0040642 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 21029939 21029939 C T 1 0 0 0 0 1 0 0 0 907 826 29 3 3 APOB 2 21029939 Missense_Mutation SNP C C3N-00203_T 6395574 21029939 221163590 65 11369 OTOF 0 . GRCh38 2 26516524 26516524 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.403G>T p.Gly135Ter p.G135* ENST00000272371 5/47 409 313 96 310 310 0 strelka-varscan OTOF,stop_gained,p.Gly135Ter,ENST00000272371,NM_194248.2;OTOF,stop_gained,p.Gly135Ter,ENST00000403946,NM_001287489.1; A ENST00000272371 Transcript stop_gained 530/7156 403/5994 135/1997 G/* Gga/Tga 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 5/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 26516524 26516524 C A 1 0 0 0 0 0 1 0 0 11369 632 22 2 2 OTOF 2 26516524 Nonsense_Mutation SNP C C3N-00203_T 5486585 26516524 215677005 66 11370 ATRAID 0 . GRCh38 2 27213180 27213180 + Missense_Mutation SNP T T A rs758303600 C3N-00203_T C3N-00203_N T T c.268T>A p.Cys90Ser p.C90S ENST00000611786 2/7 187 133 54 113 113 0 strelka-varscan ATRAID,missense_variant,p.Cys90Ser,ENST00000611786,NM_080592.3;ATRAID,missense_variant,p.Cys90Ser,ENST00000380171,;ATRAID,missense_variant,p.Cys35Ser,ENST00000606999,NM_001170795.1;ATRAID,5_prime_UTR_variant,,ENST00000405489,NM_016085.4;ATRAID,5_prime_UTR_variant,,ENST00000419744,;CAD,upstream_gene_variant,,ENST00000264705,NM_004341.3;CAD,upstream_gene_variant,,ENST00000403525,NM_001306079.1;SLC5A6,upstream_gene_variant,,ENST00000310574,NM_021095.2;SLC5A6,upstream_gene_variant,,ENST00000408041,;SLC5A6,upstream_gene_variant,,ENST00000412471,;SLC5A6,upstream_gene_variant,,ENST00000414408,;SLC5A6,upstream_gene_variant,,ENST00000401463,;SLC5A6,upstream_gene_variant,,ENST00000432106,;SLC5A6,upstream_gene_variant,,ENST00000426119,;SLC5A6,upstream_gene_variant,,ENST00000430186,;SLC5A6,upstream_gene_variant,,ENST00000428518,;SLC5A6,upstream_gene_variant,,ENST00000442731,;ATRAID,non_coding_transcript_exon_variant,,ENST00000484646,;SLC5A6,upstream_gene_variant,,ENST00000488743,;SLC5A6,upstream_gene_variant,,ENST00000445802,;ATRAID,upstream_gene_variant,,ENST00000472515,;ATRAID,upstream_gene_variant,,ENST00000491220,; A ENST00000611786 Transcript missense_variant 441/1256 268/855 90/284 C/S Tgc/Agc rs758303600 1 1 ATRAID HGNC HGNC:24090 protein_coding YES CCDS1741.1 ENSP00000484228 Q6UW56 UPI0000456D96 NM_080592.3 deleterious(0) 2/7 hmmpanther:PTHR15926 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 27213180 27213180 T A 1 0 0 0 0 1 0 0 0 1357 1478 51 4 4 ATRAID 2 27213180 Missense_Mutation SNP T C3N-00203_T 696656 27213180 214980349 67 11371 C2orf71 0 . GRCh38 2 29073226 29073226 + Missense_Mutation SNP A A C novel C3N-00203_T C3N-00203_N A A c.1036T>G p.Cys346Gly p.C346G ENST00000331664 1/2 124 92 32 106 106 0 strelka-varscan C2orf71,missense_variant,p.Cys346Gly,ENST00000331664,NM_001029883.2; C ENST00000331664 Transcript missense_variant 1036/7044 1036/3867 346/1288 C/G Tgc/Ggc 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.07) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 29073226 29073226 A C 1 0 0 0 0 1 0 0 0 2045 217 8 5 5 C2orf71 2 29073226 Missense_Mutation SNP A C3N-00203_T 1860046 29073226 213120303 68 11372 MSH6 0 . GRCh38 2 47800519 47800519 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2536G>T p.Glu846Ter p.E846* ENST00000234420 4/10 145 111 34 129 129 0 strelka-varscan MSH6,stop_gained,p.Glu846Ter,ENST00000234420,NM_000179.2;MSH6,stop_gained,p.Glu544Ter,ENST00000614496,NM_001281493.1;MSH6,stop_gained,p.Glu544Ter,ENST00000538136,NM_001281494.1;MSH6,stop_gained,p.Glu716Ter,ENST00000540021,NM_001281492.1;MSH6,stop_gained,p.Glu845Ter,ENST00000616033,;MSH6,5_prime_UTR_variant,,ENST00000622629,;FBXO11,intron_variant,,ENST00000405808,;MSH6,downstream_gene_variant,,ENST00000455383,;MSH6,downstream_gene_variant,,ENST00000411819,;MSH6,downstream_gene_variant,,ENST00000420813,;MSH6,3_prime_UTR_variant,,ENST00000445503,;FBXO11,intron_variant,,ENST00000434234,;MSH6,downstream_gene_variant,,ENST00000456246,;RPL36AP15,upstream_gene_variant,,ENST00000444514,; T ENST00000234420 Transcript stop_gained 2688/7476 2536/4083 846/1360 E/* Gaa/Taa 1 1 MSH6 HGNC HGNC:7329 protein_coding YES CCDS1836.1 ENSP00000234420 P52701 UPI00000405F8 NM_000179.2 4/10 Gene3D:1.10.1420.10,Pfam_domain:PF05192,PIRSF_domain:PIRSF037677,SMART_domains:SM00533,Superfamily_domains:SSF48334 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 47800519 47800519 G T 1 0 0 0 0 0 1 0 0 9857 1291 45 2 2 MSH6 2 47800519 Nonsense_Mutation SNP G C3N-00203_T 18727293 47800519 194393010 69 11373 NRXN1 0 . GRCh38 2 50497662 50497662 + Frame_Shift_Del DEL G G - novel C3N-00203_T C3N-00203_N G G c.2670delC p.Ile891SerfsTer22 p.I891Sfs*22 ENST00000404971 15/24 148 137 11 123 122 1 varindel-pindel NRXN1,frameshift_variant,p.Ile851SerfsTer22,ENST00000406316,NM_004801.4;NRXN1,frameshift_variant,p.Ile843SerfsTer22,ENST00000625672,;NRXN1,frameshift_variant,p.Ile891SerfsTer22,ENST00000404971,NM_001135659.1;NRXN1,frameshift_variant,p.Ile851SerfsTer22,ENST00000401669,;NRXN1,frameshift_variant,p.Ile839SerfsTer22,ENST00000405472,;NRXN1,frameshift_variant,p.Ile843SerfsTer22,ENST00000630543,;NRXN1,frameshift_variant,p.Ile581SerfsTer22,ENST00000406859,;NRXN1,frameshift_variant,p.Ile566SerfsTer22,ENST00000402717,;NRXN1,upstream_gene_variant,,ENST00000625320,;NRXN1,downstream_gene_variant,,ENST00000495871,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,upstream_gene_variant,,ENST00000637889,;NRXN1,frameshift_variant,p.Ile569SerfsTer22,ENST00000331040,;NRXN1,non_coding_transcript_exon_variant,,ENST00000474354,;NRXN1,downstream_gene_variant,,ENST00000462791,;NRXN1,upstream_gene_variant,,ENST00000626192,; - ENST00000404971 Transcript frameshift_variant 4010/7578 2670/4644 890/1547 G/X ggC/gg 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 15/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 50497662 50497662 G - 1 0 1 0 1 0 0 0 0 10724 1306 46 0 0 NRXN1 2 50497662 Frame_Shift_Del DEL G C3N-00203_T 2697143 50497662 191695867 70 11374 CLHC1 0 . GRCh38 2 55177641 55177641 + Missense_Mutation SNP C C T C3N-00203_T C3N-00203_N C C c.1525G>A p.Gly509Ser p.G509S ENST00000401408 12/13 112 94 18 89 89 0 strelka-varscan CLHC1,missense_variant,p.Gly509Ser,ENST00000401408,NM_152385.2;CLHC1,missense_variant,p.Gly509Ser,ENST00000407122,;CLHC1,missense_variant,p.Gly387Ser,ENST00000406076,NM_001135598.1;CLHC1,non_coding_transcript_exon_variant,,ENST00000494539,;CLHC1,downstream_gene_variant,,ENST00000487320,;CLHC1,3_prime_UTR_variant,,ENST00000428621,;CLHC1,3_prime_UTR_variant,,ENST00000411884,; T ENST00000401408 Transcript missense_variant 1871/2248 1525/1761 509/586 G/S Ggc/Agc COSM3972279,COSM3972280 1 -1 CLHC1 HGNC HGNC:26453 protein_coding YES CCDS33201.1 ENSP00000384869 Q8NHS4 UPI00004DEC65 NM_152385.2 deleterious(0.04) 12/13 Gene3D:1bpoA02,PIRSF_domain:PIRSF037469,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF11 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 1 202 5 2 0 0 0 0 -20 0.9999641 1 1 1 0 T 3 4 42 55177641 55177641 C T 1 0 0 0 0 1 0 0 0 3293 594 21 3 3 CLHC1 2 55177641 Missense_Mutation SNP C C3N-00203_T 4679979 55177641 187015888 71 11375 REG3G 0 . GRCh38 2 79027146 79027146 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.308G>T p.Trp103Leu p.W103L ENST00000272324 4/6 183 144 39 158 158 0 strelka-varscan REG3G,missense_variant,p.Trp103Leu,ENST00000272324,NM_001008387.2;REG3G,missense_variant,p.Trp103Leu,ENST00000393897,NM_198448.3;REG3G,intron_variant,,ENST00000409471,NM_001270040.1;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,downstream_gene_variant,,ENST00000498312,; T ENST00000272324 Transcript missense_variant 492/938 308/528 103/175 W/L tGg/tTg 1 1 REG3G HGNC HGNC:29595 protein_coding YES CCDS1962.1 ENSP00000272324 Q6UW15 UPI0000048F1E NM_001008387.2 deleterious(0) 4/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF60,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 79027146 79027146 G T 1 0 0 0 0 1 0 0 0 13383 1357 47 2 2 REG3G 2 79027146 Missense_Mutation SNP G C3N-00203_T 23849505 79027146 163166383 72 11376 REG3A 0 . GRCh38 2 79158417 79158417 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.242G>T p.Ser81Ile p.S81I ENST00000393878 3/5 244 204 40 213 213 0 strelka-varscan REG3A,missense_variant,p.Ser81Ile,ENST00000393878,NM_138938.2;REG3A,missense_variant,p.Ser81Ile,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,missense_variant,p.Ser81Ile,ENST00000305165,;AC011754.1,non_coding_transcript_exon_variant,,ENST00000415201,;REG3A,downstream_gene_variant,,ENST00000464746,;REG3A,downstream_gene_variant,,ENST00000490901,; A ENST00000393878 Transcript missense_variant 590/1095 242/528 81/175 S/I aGt/aTt 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 deleterious(0) 3/5 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 79158417 79158417 C A 1 0 0 0 0 1 0 0 0 13382 565 20 2 2 REG3A 2 79158417 Missense_Mutation SNP C C3N-00203_T 131271 79158417 163035112 73 11377 DNAH6 0 . GRCh38 2 84525605 84525605 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.266A>T p.Tyr89Phe p.Y89F ENST00000389394 3/77 413 276 137 352 352 0 strelka-varscan DNAH6,missense_variant,p.Tyr89Phe,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Tyr89Phe,ENST00000237449,;DNAH6,non_coding_transcript_exon_variant,,ENST00000468661,;DNAH6,non_coding_transcript_exon_variant,,ENST00000476689,;DNAH6,intron_variant,,ENST00000494025,; T ENST00000389394 Transcript missense_variant 403/12795 266/12477 89/4158 Y/F tAc/tTc 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 deleterious_low_confidence(0.01) 3/77 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 84525605 84525605 A T 1 0 0 0 0 1 0 0 0 4420 391 14 4 4 DNAH6 2 84525605 Missense_Mutation SNP A C3N-00203_T 5367188 84525605 157667924 74 11378 DNAH6 0 . GRCh38 2 84707660 84707660 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.8992A>T p.Ile2998Leu p.I2998L ENST00000389394 54/77 198 161 37 180 180 0 strelka-varscan DNAH6,missense_variant,p.Ile2998Leu,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Ile2998Leu,ENST00000237449,; T ENST00000389394 Transcript missense_variant 9129/12795 8992/12477 2998/4158 I/L Ata/Tta 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated(0.32) 54/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF12777 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 84707660 84707660 A T 1 0 0 0 0 1 0 0 0 4420 217 8 4 4 DNAH6 2 84707660 Missense_Mutation SNP A C3N-00203_T 182055 84707660 157485869 75 11379 CHMP3 0 . GRCh38 2 86542291 86542291 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.67A>T p.Ile23Leu p.I23L ENST00000263856 2/6 241 191 50 257 257 0 strelka-varscan CHMP3,missense_variant,p.Ile23Leu,ENST00000263856,NM_016079.3;CHMP3,missense_variant,p.Ile23Leu,ENST00000409727,NM_001193517.1;RNF103-CHMP3,missense_variant,p.Ile52Leu,ENST00000604011,NM_001198954.1;RNF103-CHMP3,missense_variant,p.Ile130Leu,ENST00000440757,;CHMP3,intron_variant,,ENST00000409225,NM_001005753.2;CHMP3,non_coding_transcript_exon_variant,,ENST00000485465,;CHMP3,non_coding_transcript_exon_variant,,ENST00000393773,;CHMP3,non_coding_transcript_exon_variant,,ENST00000486404,;CHMP3,non_coding_transcript_exon_variant,,ENST00000409810,;CHMP3,non_coding_transcript_exon_variant,,ENST00000466032,; A ENST00000263856 Transcript missense_variant 196/3171 67/669 23/222 I/L Ata/Tta 1 -1 CHMP3 HGNC HGNC:29865 protein_coding YES CCDS33236.1 ENSP00000263856 Q9Y3E7 UPI000006E953 NM_016079.3 tolerated(1) 2/6 Pfam_domain:PF03357,hmmpanther:PTHR10476,hmmpanther:PTHR10476:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 86542291 86542291 T A 1 0 0 0 0 1 0 0 0 3115 1435 50 4 4 CHMP3 2 86542291 Missense_Mutation SNP T C3N-00203_T 1834631 86542291 155651238 76 11380 TXNDC9 0 . GRCh38 2 99322189 99322189 + Missense_Mutation SNP T T G novel C3N-00203_T C3N-00203_N T T c.329A>C p.His110Pro p.H110P ENST00000264255 4/5 174 135 39 137 137 0 strelka-varscan TXNDC9,missense_variant,p.His110Pro,ENST00000264255,NM_005783.3;TXNDC9,missense_variant,p.His110Pro,ENST00000409434,;TXNDC9,missense_variant,p.His110Pro,ENST00000409705,;TXNDC9,3_prime_UTR_variant,,ENST00000434323,;RP11-111H13.1,intron_variant,,ENST00000465095,;TXNDC9,3_prime_UTR_variant,,ENST00000422767,;TXNDC9,3_prime_UTR_variant,,ENST00000438680,;TXNDC9,non_coding_transcript_exon_variant,,ENST00000463385,;RP11-111H13.1,intron_variant,,ENST00000424491,; G ENST00000264255 Transcript missense_variant 585/1637 329/681 110/226 H/P cAt/cCt 1 -1 TXNDC9 HGNC HGNC:24110 protein_coding YES CCDS2044.1 ENSP00000264255 O14530 UPI0000124E09 NM_005783.3 deleterious(0) 4/5 hmmpanther:PTHR21148,Pfam_domain:PF00085,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 99322189 99322189 T G 1 0 0 0 0 1 0 0 0 17316 1464 51 5 5 TXNDC9 2 99322189 Missense_Mutation SNP T C3N-00203_T 12779898 99322189 142871340 77 11381 IL18RAP 0 . GRCh38 2 102451976 102451976 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.1595G>A p.Arg532Lys p.R532K ENST00000264260 12/12 174 136 38 140 140 0 strelka-varscan IL18RAP,missense_variant,p.Arg532Lys,ENST00000264260,NM_003853.3;IL18RAP,missense_variant,p.Arg390Lys,ENST00000409369,; A ENST00000264260 Transcript missense_variant 2184/2773 1595/1800 532/599 R/K aGg/aAg 1 1 IL18RAP HGNC HGNC:5989 protein_coding YES CCDS2061.1 ENSP00000264260 O95256 UPI0000071CAF NM_003853.3 tolerated(0.14) 12/12 Gene3D:3.40.50.10140,Pfam_domain:PF01582,Prints_domain:PR01537,PROSITE_profiles:PS50104,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF23,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 102451976 102451976 G A 1 0 0 0 0 1 0 0 0 7556 1000 35 3 3 IL18RAP 2 102451976 Missense_Mutation SNP G C3N-00203_T 3129787 102451976 139741553 78 11382 MRPS9 0 . GRCh38 2 105088988 105088989 + Frame_Shift_Del DEL TA TA - novel C3N-00203_T C3N-00203_N TA TA c.497_498delAT p.Tyr166TrpfsTer36 p.Y166Wfs*36 ENST00000258455 6/11 127 105 22 107 107 0 sindel-varindel-pindel MRPS9,frameshift_variant,p.Tyr166TrpfsTer36,ENST00000258455,NM_182640.2;MRPS9,upstream_gene_variant,,ENST00000472220,;MRPS9,upstream_gene_variant,,ENST00000413583,; - ENST00000258455 Transcript frameshift_variant 604-605/1500 494-495/1191 165/396 V/X gTA/g 1 1 MRPS9 HGNC HGNC:14501 protein_coding YES CCDS2065.1 ENSP00000258455 P82933 UPI00000467F9 NM_182640.2 6/11 hmmpanther:PTHR21569,hmmpanther:PTHR21569:SF1 HIGH 1 deletion 1 3 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 105088988 105088988 TA - 1 0 1 0 1 0 0 0 0 9826 1652 57 0 0 MRPS9 2 105088988 Frame_Shift_Del DEL TA C3N-00203_T 2637012 105088988 137104541 79 11383 CCDC93 0 . GRCh38 2 118000913 118000913 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.271G>T p.Val91Phe p.V91F ENST00000376300 4/24 244 211 33 169 169 0 strelka-varscan CCDC93,missense_variant,p.Val91Phe,ENST00000376300,NM_019044.4;CCDC93,missense_variant,p.Val91Phe,ENST00000319432,;AC009303.1,intron_variant,,ENST00000627670,;AC009303.1,intron_variant,,ENST00000588042,;AC009303.1,intron_variant,,ENST00000590516,;AC009303.1,intron_variant,,ENST00000627106,;AC009303.1,downstream_gene_variant,,ENST00000585381,;AC009303.1,downstream_gene_variant,,ENST00000588733,;RP11-98C1.2,downstream_gene_variant,,ENST00000591103,;AC009303.1,downstream_gene_variant,,ENST00000630241,;AC009303.1,downstream_gene_variant,,ENST00000629927,;AC009303.1,downstream_gene_variant,,ENST00000627378,;AC009303.1,downstream_gene_variant,,ENST00000413179,;CCDC93,upstream_gene_variant,,ENST00000460781,;CCDC93,non_coding_transcript_exon_variant,,ENST00000474006,; A ENST00000376300 Transcript missense_variant 409/6899 271/1896 91/631 V/F Gtc/Ttc 1 -1 CCDC93 HGNC HGNC:25611 protein_coding YES CCDS2121.2 ENSP00000365477 Q567U6 UPI0000207DEC NM_019044.4 deleterious(0) 4/24 Pfam_domain:PF09762,hmmpanther:PTHR16441 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 42 118000913 118000913 C A 1 0 0 0 0 1 0 0 0 2570 478 17 2 2 CCDC93 2 118000913 Missense_Mutation SNP C C3N-00203_T 12911925 118000913 124192616 80 11384 CNTNAP5 0 . GRCh38 2 124763696 124763696 + Silent SNP C C A rs753128638 C3N-00203_T C3N-00203_N C C c.2256C>A p.= p.S752S ENST00000431078 15/24 222 120 102 181 181 0 strelka-varscan CNTNAP5,synonymous_variant,p.=,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript synonymous_variant 2620/5284 2256/3921 752/1306 S tcC/tcA rs753128638 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 124763696 124763696 C A 1 0 0 0 0 0 0 0 1 3432 668 24 2 2 CNTNAP5 2 124763696 Silent SNP C C3N-00203_T 6762783 124763696 117429833 81 11385 POTEI 0 . GRCh38 2 130509018 130509018 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.218G>T p.Arg73Met p.R73M ENST00000451531 1/15 820 642 178 665 664 1 strelka-varscan POTEI,missense_variant,p.Arg73Met,ENST00000451531,NM_001277406.1;POTEI,missense_variant,p.Arg73Met,ENST00000631234,;POTEI,missense_variant,p.Arg73Met,ENST00000615053,; A ENST00000451531 Transcript missense_variant 649/7020 218/3228 73/1075 R/M aGg/aTg 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0) 1/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 130509018 130509018 C A 1 0 0 0 0 1 0 0 0 12382 681 24 2 2 POTEI 2 130509018 Missense_Mutation SNP C C3N-00203_T 5745322 130509018 111684511 82 11386 LCT 0 . GRCh38 2 135808896 135808896 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.3451C>A p.Leu1151Met p.L1151M ENST00000264162 8/17 145 113 32 98 98 0 strelka-varscan LCT,missense_variant,p.Leu1151Met,ENST00000264162,NM_002299.2;Y_RNA,downstream_gene_variant,,ENST00000363794,;LCT,missense_variant,p.Leu583Met,ENST00000452974,; T ENST00000264162 Transcript missense_variant 3462/6279 3451/5784 1151/1927 L/M Ctg/Atg 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 tolerated(0.08) 8/17 hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF38,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 135808896 135808896 G T 1 0 0 0 0 1 0 0 0 8599 991 35 2 2 LCT 2 135808896 Missense_Mutation SNP G C3N-00203_T 5299878 135808896 106384633 83 11387 SLC4A10 0 . GRCh38 2 161947680 161947680 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.2218T>C p.Ser740Pro p.S740P ENST00000446997 17/27 278 210 68 223 223 0 strelka-varscan SLC4A10,missense_variant,p.Ser721Pro,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Ser710Pro,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Ser740Pro,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Ser710Pro,ENST00000272716,;SLC4A10,missense_variant,p.Ser740Pro,ENST00000421911,;SLC4A10,3_prime_UTR_variant,,ENST00000446228,; C ENST00000446997 Transcript missense_variant 2311/5551 2218/3357 740/1118 S/P Tca/Cca 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 deleterious(0) 17/27 Transmembrane_helices:TMhelix,hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 161947680 161947680 T C 1 0 0 0 0 1 0 0 0 14928 1667 58 5 5 SLC4A10 2 161947680 Missense_Mutation SNP T C3N-00203_T 26138784 161947680 80245849 84 11388 DPP4 0 . GRCh38 2 162018729 162018729 + Missense_Mutation SNP C C A rs201959805 C3N-00203_T C3N-00203_N C C c.1420G>T p.Gly474Cys p.G474C ENST00000360534 16/26 100 82 18 105 104 1 strelka-varscan DPP4,missense_variant,p.Gly474Cys,ENST00000360534,NM_001935.3;DPP4,splice_region_variant,,ENST00000468903,;DPP4,upstream_gene_variant,,ENST00000491591,;DPP4,splice_region_variant,,ENST00000434918,;DPP4,splice_region_variant,,ENST00000490286,;DPP4,upstream_gene_variant,,ENST00000494507,; A ENST00000360534 Transcript missense_variant,splice_region_variant 1981/3904 1420/2301 474/766 G/C Ggt/Tgt rs201959805 1 -1 DPP4 HGNC HGNC:3009 protein_coding YES CCDS2216.1 ENSP00000353731 P27487 UPI000004F7BF NM_001935.3 deleterious(0) 16/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF128,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999724 1 1 1 0 A 3 1 42 162018729 162018729 C A 1 0 0 0 0 1 0 0 0 4544 666 23 1 1 DPP4 2 162018729 Missense_Mutation SNP C C3N-00203_T 71049 162018729 80174800 85 11389 KCNH7 0 . GRCh38 2 162446124 162446124 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1448G>T p.Ser483Ile p.S483I ENST00000332142 7/16 306 246 60 250 250 0 strelka-varscan KCNH7,missense_variant,p.Ser483Ile,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Ser383Ile,ENST00000618399,;KCNH7,missense_variant,p.Ser476Ile,ENST00000328032,NM_173162.2;KCNH7,missense_variant,p.Ser374Ile,ENST00000621889,; A ENST00000332142 Transcript missense_variant 1548/4113 1448/3591 483/1196 S/I aGt/aTt 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 deleterious(0) 7/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 162446124 162446124 C A 1 0 0 0 0 1 0 0 0 7953 565 20 2 2 KCNH7 2 162446124 Missense_Mutation SNP C C3N-00203_T 427395 162446124 79747405 86 11390 ITGA6 0 . GRCh38 2 172491266 172491266 + Missense_Mutation SNP C C T rs765042466 C3N-00203_T C3N-00203_N C C c.2824C>T p.Arg942Trp p.R942W ENST00000409080 22/25 646 419 227 380 380 0 strelka-varscan ITGA6,missense_variant,p.Arg942Trp,ENST00000264107,NM_000210.2;ITGA6,missense_variant,p.Arg942Trp,ENST00000409080,NM_001079818.1;ITGA6,missense_variant,p.Arg823Trp,ENST00000409532,;ITGA6,missense_variant,p.Arg981Trp,ENST00000442250,;ITGA6,missense_variant,p.Arg937Trp,ENST00000458358,;ITGA6,missense_variant,p.Arg109Trp,ENST00000416789,;AC093818.1,intron_variant,,ENST00000442417,;ITGA6,non_coding_transcript_exon_variant,,ENST00000475302,;ITGA6,downstream_gene_variant,,ENST00000469534,;ITGA6,downstream_gene_variant,,ENST00000470259,; T ENST00000409080 Transcript missense_variant 2824/5306 2824/3276 942/1091 R/W Cgg/Tgg rs765042466 1 1 ITGA6 HGNC HGNC:6142 protein_coding YES CCDS46451.1 ENSP00000386896 P23229 UPI0000EA87E5 NM_001079818.1 tolerated(0.12) 22/25 Gene3D:1jv2A04,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF9,Superfamily_domains:SSF69179 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 172491266 172491266 C T 1 0 0 0 0 1 0 0 0 7787 759 27 1 1 ITGA6 2 172491266 Missense_Mutation SNP C C3N-00203_T 10045142 172491266 69702263 87 11391 HNRNPA3 0 . GRCh38 2 177215869 177215869 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.315G>T p.= p.V105V ENST00000392524 3/11 130 72 58 92 92 0 strelka-varscan HNRNPA3,synonymous_variant,p.=,ENST00000411529,;HNRNPA3,synonymous_variant,p.=,ENST00000392524,NM_194247.2;HNRNPA3,synonymous_variant,p.=,ENST00000435711,;HNRNPA3,upstream_gene_variant,,ENST00000432457,;HNRNPA3,downstream_gene_variant,,ENST00000581696,;AC079305.8,upstream_gene_variant,,ENST00000455416,;HNRNPA3,upstream_gene_variant,,ENST00000483137,; T ENST00000392524 Transcript synonymous_variant 552/2067 315/1137 105/378 V gtG/gtT 1 1 HNRNPA3 HGNC HGNC:24941 protein_coding YES CCDS2273.1 ENSP00000376309 P51991 UPI00001BE8DE NM_194247.2 3/11 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF392,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 177215869 177215869 G T 1 0 0 0 0 0 0 0 1 7151 1335 47 2 2 HNRNPA3 2 177215869 Silent SNP G C3N-00203_T 4724603 177215869 64977660 88 11392 RBM45 0 . GRCh38 2 178112671 178112671 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.125G>T p.Arg42Met p.R42M ENST00000286070 1/10 522 427 95 343 343 0 strelka-varscan RBM45,missense_variant,p.Arg42Met,ENST00000616198,;RBM45,missense_variant,p.Arg42Met,ENST00000286070,NM_152945.2;PDE11A,upstream_gene_variant,,ENST00000358450,NM_001077197.1;RBM45,non_coding_transcript_exon_variant,,ENST00000424000,; T ENST00000286070 Transcript missense_variant 217/1785 125/1425 42/474 R/M aGg/aTg 1 1 RBM45 HGNC HGNC:24468 protein_coding YES CCDS33335.1 ENSP00000286070 Q8IUH3 UPI00001AEAD8 NM_152945.2 deleterious(0) 1/10 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF389,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 178112671 178112671 G T 1 0 0 0 0 1 0 0 0 13305 1000 35 2 2 RBM45 2 178112671 Missense_Mutation SNP G C3N-00203_T 896802 178112671 64080858 89 11393 TTN 0 . GRCh38 2 178565707 178565707 + Missense_Mutation SNP C C A rs369941201 C3N-00203_T C3N-00203_N C C c.80425G>T p.Gly26809Cys p.G26809C ENST00000589042 326/363 436 280 156 293 291 2 strelka-varscan TTN,missense_variant,p.Gly26809Cys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gly25168Cys,ENST00000591111,;TTN,missense_variant,p.Gly25168Cys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gly24241Cys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Gly17744Cys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Gly17936Cys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Gly17869Cys,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,; A ENST00000589042 Transcript missense_variant 80650/109224 80425/107976 26809/35991 G/C Ggt/Tgt rs369941201 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 uncertain_significance MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 178565707 178565707 C A 1 0 0 0 0 1 0 0 0 17245 652 23 1 1 TTN 2 178565707 Missense_Mutation SNP C C3N-00203_T 453036 178565707 63627822 90 11394 TTN 0 . GRCh38 2 178574326 178574326 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.71806A>T p.Ile23936Phe p.I23936F ENST00000589042 326/363 202 139 63 145 145 0 strelka-varscan TTN,missense_variant,p.Ile23936Phe,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ile22295Phe,ENST00000591111,;TTN,missense_variant,p.Ile22295Phe,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ile21368Phe,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ile14871Phe,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ile15063Phe,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ile14996Phe,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-171I2.2,upstream_gene_variant,,ENST00000603521,;RP11-171I2.5,upstream_gene_variant,,ENST00000604215,; A ENST00000589042 Transcript missense_variant 72031/109224 71806/107976 23936/35991 I/F Att/Ttt 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 178574326 178574326 T A 1 0 0 0 0 1 0 0 0 17245 1406 49 4 4 TTN 2 178574326 Missense_Mutation SNP T C3N-00203_T 8619 178574326 63619203 91 11395 TTN 0 . GRCh38 2 178675050 178675050 + Missense_Mutation SNP A A T rs376836503 C3N-00203_T C3N-00203_N A A c.34601T>A p.Leu11534Gln p.L11534Q ENST00000589042 150/363 214 185 29 165 165 0 strelka-varscan TTN,missense_variant,p.Leu11534Gln,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu11160Gln,ENST00000591111,;TTN,missense_variant,p.Leu11160Gln,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu10233Gln,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN,upstream_gene_variant,,ENST00000448510,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 34826/109224 34601/107976 11534/35991 L/Q cTa/cAa rs376836503 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 150/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 likely_benign MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 178675050 178675050 A T 1 0 0 0 0 1 0 0 0 17245 420 15 4 4 TTN 2 178675050 Missense_Mutation SNP A C3N-00203_T 100724 178675050 63518479 92 11396 TTN 0 . GRCh38 2 178724490 178724490 + Missense_Mutation SNP C C G rs531296995 C3N-00203_T C3N-00203_N C C c.20885G>C p.Gly6962Ala p.G6962A ENST00000589042 72/363 144 117 27 103 102 1 strelka-varscan TTN,missense_variant,p.Gly6962Ala,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gly6645Ala,ENST00000591111,;TTN,missense_variant,p.Gly6645Ala,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gly5718Ala,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;RP11-171I2.1,non_coding_transcript_exon_variant,,ENST00000590024,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,; G ENST00000589042 Transcript missense_variant 21110/109224 20885/107976 6962/35991 G/A gGa/gCa rs531296995 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 72/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 178724490 178724490 C G 1 0 0 0 0 1 0 0 0 17245 855 30 4 4 TTN 2 178724490 Missense_Mutation SNP C C3N-00203_T 49440 178724490 63469039 93 11397 TTN 0 . GRCh38 2 178733650 178733650 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.15739G>T p.Gly5247Ter p.G5247* ENST00000589042 53/363 135 109 26 100 100 0 strelka-varscan TTN,stop_gained,p.Gly5247Ter,ENST00000589042,NM_001267550.2;TTN,stop_gained,p.Gly4930Ter,ENST00000591111,;TTN,stop_gained,p.Gly4930Ter,ENST00000615779,NM_001256850.1;TTN,stop_gained,p.Gly4003Ter,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,upstream_gene_variant,,ENST00000627661,;TTN-AS1,upstream_gene_variant,,ENST00000590773,;TTN-AS1,upstream_gene_variant,,ENST00000631319,; A ENST00000589042 Transcript stop_gained 15964/109224 15739/107976 5247/35991 G/* Gga/Tga 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 53/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999962 1 1 1 0 A 4 1 42 178733650 178733650 C A 1 0 0 0 0 0 1 0 0 17245 603 21 2 2 TTN 2 178733650 Nonsense_Mutation SNP C C3N-00203_T 9160 178733650 63459879 94 11398 TTN 0 . GRCh38 2 178740666 178740666 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.12567G>C p.Met4189Ile p.M4189I ENST00000589042 48/363 449 319 130 332 332 0 strelka-varscan TTN,missense_variant,p.Met4189Ile,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Met3872Ile,ENST00000591111,;TTN,missense_variant,p.Met3872Ile,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Met3826Ile,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Met4018Ile,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Met3951Ile,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000342992,NM_133378.4;TTN,downstream_gene_variant,,ENST00000360870,NM_133379.4;TTN-AS1,intron_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000627661,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000631319,;TTN-AS1,upstream_gene_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000625480,; G ENST00000589042 Transcript missense_variant 12792/109224 12567/107976 4189/35991 M/I atG/atC 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 48/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 178740666 178740666 C G 1 0 0 0 0 1 0 0 0 17245 478 17 4 4 TTN 2 178740666 Missense_Mutation SNP C C3N-00203_T 7016 178740666 63452863 95 11399 FAM171B 0 . GRCh38 2 186762666 186762666 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2324C>A p.Pro775His p.P775H ENST00000304698 8/8 378 322 56 234 234 0 strelka-varscan-mutect FAM171B,missense_variant,p.Pro775His,ENST00000304698,NM_177454.3; A ENST00000304698 Transcript missense_variant 2527/5826 2324/2481 775/826 P/H cCt/cAt 1 1 FAM171B HGNC HGNC:29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 UPI0000161631 NM_177454.3 tolerated(0.59) 8/8 hmmpanther:PTHR31626:SF2,hmmpanther:PTHR31626,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 186762666 186762666 C A 1 0 0 0 0 1 0 0 0 5339 681 24 2 2 FAM171B 2 186762666 Missense_Mutation SNP C C3N-00203_T 8022000 186762666 55430863 96 11400 CALCRL 0 . GRCh38 2 187359211 187359211 + Splice_Site SNP C C T novel C3N-00203_T C3N-00203_N C C c.842+1G>A p.X281_splice ENST00000409998 171 155 16 119 119 0 strelka-varscan-mutect CALCRL,splice_donor_variant,,ENST00000409998,;CALCRL,splice_donor_variant,,ENST00000392370,NM_005795.5;CALCRL,splice_donor_variant,,ENST00000410068,NM_001271751.1;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; T ENST00000409998 Transcript splice_donor_variant -/5223 842/1386 281/461 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF 12/15 HIGH 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 187359211 187359211 C T 1 0 0 0 0 0 0 1 0 2270 579 20 3 3 CALCRL 2 187359211 Splice_Site SNP C C3N-00203_T 596545 187359211 54834318 97 11401 NBEAL1 0 . GRCh38 2 203122306 203122306 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.2558G>C p.Arg853Thr p.R853T ENST00000449802 18/55 134 110 24 159 159 0 strelka-varscan-mutect NBEAL1,missense_variant,p.Arg853Thr,ENST00000449802,NM_001114132.1; C ENST00000449802 Transcript missense_variant 2891/10938 2558/8085 853/2694 R/T aGa/aCa 1 1 NBEAL1 HGNC HGNC:20681 protein_coding YES CCDS46495.1 ENSP00000399903 Q6ZS30 UPI000194EC27 NM_001114132.1 tolerated(0.11) 18/55 hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 203122306 203122306 G C 1 0 0 0 0 1 0 0 0 10199 942 33 4 4 NBEAL1 2 203122306 Missense_Mutation SNP G C3N-00203_T 15763095 203122306 39071223 98 11402 PIKFYVE 0 . GRCh38 2 208273716 208273716 + Missense_Mutation SNP G G T rs758117456 C3N-00203_T C3N-00203_N G G c.305G>T p.Arg102Leu p.R102L ENST00000264380 3/42 539 424 115 401 401 0 strelka-varscan-mutect PIKFYVE,missense_variant,p.Arg102Leu,ENST00000264380,NM_015040.3;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000452564,;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000392202,NM_152671.3;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000407449,NM_001178000.1;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000308862,;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000422495,;PIKFYVE,missense_variant,p.Arg102Leu,ENST00000443896,;MYL6BP1,upstream_gene_variant,,ENST00000429485,; T ENST00000264380 Transcript missense_variant 463/9901 305/6297 102/2098 R/L cGg/cTg rs758117456 1 1 PIKFYVE HGNC HGNC:23785 protein_coding YES CCDS2382.1 ENSP00000264380 Q9Y2I7 UPI0000366FD6 NM_015040.3 deleterious(0.04) 3/42 MODERATE 1 SNV 1 1 PASS rs758117456 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 208273716 208273716 G T 1 0 0 0 0 1 0 0 0 12019 1116 39 1 1 PIKFYVE 2 208273716 Missense_Mutation SNP G C3N-00203_T 5151410 208273716 33919813 99 11403 CXCR1 0 . GRCh38 2 218164703 218164703 + Missense_Mutation SNP G G T rs777099652 C3N-00203_T C3N-00203_N G G c.509C>A p.Pro170His p.P170H ENST00000295683 2/2 570 424 146 449 448 1 strelka-varscan-mutect CXCR1,missense_variant,p.Pro170His,ENST00000295683,NM_000634.2; T ENST00000295683 Transcript missense_variant 630/2488 509/1053 170/350 P/H cCc/cAc rs777099652 1 -1 CXCR1 HGNC HGNC:6026 protein_coding YES CCDS2409.1 ENSP00000295683 P25024 UPI0000050457 NM_000634.2 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF689,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs777099652 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 218164703 218164703 G T 1 0 0 0 0 1 0 0 0 3901 1232 43 2 2 CXCR1 2 218164703 Missense_Mutation SNP G C3N-00203_T 9890987 218164703 24028826 100 11404 SPHKAP 0 . GRCh38 2 228019227 228019227 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1627G>T p.Gly543Ter p.G543* ENST00000392056 7/12 265 248 17 243 243 0 strelka-varscan-mutect SPHKAP,stop_gained,p.Gly543Ter,ENST00000392056,NM_001142644.1;SPHKAP,stop_gained,p.Gly543Ter,ENST00000344657,NM_030623.3; A ENST00000392056 Transcript stop_gained 1674/6917 1627/5103 543/1700 G/* Gga/Tga 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 HIGH 1 SNV 1 1 PASS rs1416078052 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 228019227 228019227 C A 1 0 0 0 0 0 1 0 0 15399 690 24 2 2 SPHKAP 2 228019227 Nonsense_Mutation SNP C C3N-00203_T 9854524 228019227 14174302 101 11405 TRIP12 0 . GRCh38 2 229789616 229789616 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.4609T>C p.Tyr1537His p.Y1537H ENST00000389044 31/42 124 95 29 76 76 0 strelka-varscan-mutect TRIP12,missense_variant,p.Tyr1489His,ENST00000283943,NM_001284215.1,NM_004238.2;TRIP12,missense_variant,p.Tyr1537His,ENST00000389044,NM_001284214.1;TRIP12,missense_variant,p.Tyr1219His,ENST00000389045,NM_001284216.1;TRIP12,downstream_gene_variant,,ENST00000495322,;TRIP12,downstream_gene_variant,,ENST00000470302,; G ENST00000389044 Transcript missense_variant 4778/6405 4609/6123 1537/2040 Y/H Tat/Cat 1 -1 TRIP12 HGNC HGNC:12306 protein_coding YES CCDS63146.1 ENSP00000373696 Q14669 UPI0000DA6BE7 NM_001284214.1 deleterious(0.04) 31/42 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF73 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 229789616 229789616 A G 1 0 0 0 0 1 0 0 0 17053 405 14 5 5 TRIP12 2 229789616 Missense_Mutation SNP A C3N-00203_T 1770389 229789616 12403913 102 11406 KLHL30 0 . GRCh38 2 238141483 238141483 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.729G>A p.= p.Q243Q ENST00000409223 2/8 50 37 13 31 31 0 strelka-varscan-mutect KLHL30,synonymous_variant,p.=,ENST00000409223,NM_198582.3; A ENST00000409223 Transcript synonymous_variant 836/3726 729/1737 243/578 Q caG/caA 1 1 KLHL30 HGNC HGNC:24770 protein_coding YES CCDS46555.2 ENSP00000386389 Q0D2K2 UPI00001D7DA5 NM_198582.3 2/8 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF9 LOW 1 SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 238141483 238141483 G A 1 0 0 0 0 0 0 0 1 8249 991 35 3 3 KLHL30 2 238141483 Silent SNP G C3N-00203_T 8351867 238141483 4052046 103 11407 C3orf20 0 . GRCh38 3 14757541 14757541 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2111C>A p.Pro704His p.P704H ENST00000253697 13/17 518 423 95 331 330 1 strelka-varscan-mutect C3orf20,missense_variant,p.Pro704His,ENST00000253697,NM_032137.4;C3orf20,missense_variant,p.Pro582His,ENST00000435614,NM_001184958.1;C3orf20,missense_variant,p.Pro582His,ENST00000412910,NM_001184957.1; A ENST00000253697 Transcript missense_variant 2563/3326 2111/2715 704/904 P/H cCc/cAc 1 1 C3orf20 HGNC HGNC:25320 protein_coding YES CCDS33706.1 ENSP00000253697 Q8ND61 UPI000013CDE9 NM_032137.4 deleterious(0) 13/17 hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 14757541 14757541 C A 1 0 0 0 0 1 0 0 0 2061 623 22 2 2 C3orf20 3 14757541 Missense_Mutation SNP C C3N-00203_T 14757541 183538018 104 11408 SLC4A7 0 . GRCh38 3 27394516 27394516 + Splice_Site SNP A A T novel C3N-00203_T C3N-00203_N A A c.3090+2T>A p.X1030_splice ENST00000295736 138 108 30 124 124 0 strelka-varscan-mutect SLC4A7,splice_donor_variant,,ENST00000425128,NM_001321105.1,NM_001321106.1;SLC4A7,splice_donor_variant,,ENST00000295736,NM_003615.4;SLC4A7,splice_donor_variant,,ENST00000428386,NM_001321107.1,NM_001258380.1;SLC4A7,splice_donor_variant,,ENST00000419036,;SLC4A7,splice_donor_variant,,ENST00000454389,;SLC4A7,splice_donor_variant,,ENST00000440156,;SLC4A7,splice_donor_variant,,ENST00000445684,;SLC4A7,splice_donor_variant,,ENST00000446700,;SLC4A7,splice_donor_variant,,ENST00000455077,NM_001258379.1;SLC4A7,splice_donor_variant,,ENST00000437179,;SLC4A7,splice_donor_variant,,ENST00000428179,;SLC4A7,splice_donor_variant,,ENST00000438530,;SLC4A7,splice_donor_variant,,ENST00000457377,;SLC4A7,splice_donor_variant,,ENST00000437266,;SLC4A7,downstream_gene_variant,,ENST00000475120,;SLC4A7,upstream_gene_variant,,ENST00000465487,; T ENST00000295736 Transcript splice_donor_variant -/7757 3090/3645 1030/1214 1 -1 SLC4A7 HGNC HGNC:11033 protein_coding YES CCDS33721.1 ENSP00000295736 Q9Y6M7 UPI0000DBEEB7 NM_003615.4 20/24 HIGH 1 SNV 1 1 PASS rs1352606094 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 27394516 27394516 A T 1 0 0 0 0 0 0 1 0 14935 405 14 4 4 SLC4A7 3 27394516 Splice_Site SNP A C3N-00203_T 12636975 27394516 170901043 105 11409 SCN11A 0 . GRCh38 3 38950197 38950197 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.166C>T p.= p.L56L ENST00000302328 1/26 428 383 45 308 308 0 strelka-varscan-mutect SCN11A,synonymous_variant,p.=,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,synonymous_variant,p.=,ENST00000444237,;SCN11A,synonymous_variant,p.=,ENST00000456224,; A ENST00000302328 Transcript synonymous_variant 365/6500 166/5376 56/1791 L Cta/Tta 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 1/26 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 38950197 38950197 G A 1 0 0 0 0 0 0 0 1 14182 991 35 3 3 SCN11A 3 38950197 Silent SNP G C3N-00203_T 11555681 38950197 159345362 106 11410 XIRP1 0 . GRCh38 3 39188015 39188015 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.1431G>A p.= p.Q477Q ENST00000340369 2/2 290 192 98 206 206 0 strelka-varscan-mutect XIRP1,synonymous_variant,p.=,ENST00000340369,NM_194293.2;XIRP1,synonymous_variant,p.=,ENST00000396251,NM_001198621.2;XIRP1,intron_variant,,ENST00000421646,; T ENST00000340369 Transcript synonymous_variant 1660/6460 1431/5532 477/1843 Q caG/caA 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 2/2 hmmpanther:PTHR22591 LOW 1 SNV 1 1 PASS rs1219306727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 39188015 39188015 C T 1 0 0 0 0 0 0 0 1 17988 680 24 3 3 XIRP1 3 39188015 Silent SNP C C3N-00203_T 237818 39188015 159107544 107 11411 TMEM158 0 . GRCh38 3 45225830 45225830 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.198G>A p.= p.E66E ENST00000503771 1/1 49 44 5 54 54 0 strelka-varscan TMEM158,synonymous_variant,p.=,ENST00000503771,NM_015444.2; T ENST00000503771 Transcript synonymous_variant 449/1813 198/903 66/300 E gaG/gaA 1 -1 TMEM158 HGNC HGNC:30293 protein_coding YES CCDS54573.1 ENSP00000422431 Q8WZ71 UPI0000E5DD5E NM_015444.2 1/1 hmmpanther:PTHR38324,hmmpanther:PTHR38324:SF1,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 45225830 45225830 C T 1 0 0 0 0 0 0 0 1 16517 680 24 3 3 TMEM158 3 45225830 Silent SNP C C3N-00203_T 6037815 45225830 153069729 108 11412 SLC26A6 0 . GRCh38 3 48632053 48632053 + Missense_Mutation SNP C C A rs768584325 C3N-00203_T C3N-00203_N C C c.473G>T p.Arg158Leu p.R158L ENST00000455886 5/20 147 102 45 88 88 0 strelka-varscan-mutect SLC26A6,missense_variant,p.Arg158Leu,ENST00000455886,NM_001281732.1;SLC26A6,missense_variant,p.Arg158Leu,ENST00000426599,;SLC26A6,intron_variant,,ENST00000358747,NM_001040454.1;SLC26A6,intron_variant,,ENST00000420764,NM_134263.2;SLC26A6,intron_variant,,ENST00000395550,NM_022911.2;SLC26A6,intron_variant,,ENST00000383733,NM_134426.2;SLC26A6,intron_variant,,ENST00000337000,NM_001281733.1;SLC26A6,intron_variant,,ENST00000421649,;SLC26A6,intron_variant,,ENST00000431739,;CELSR3,downstream_gene_variant,,ENST00000164024,NM_001407.2;SLC26A6,downstream_gene_variant,,ENST00000611478,;SLC26A6,intron_variant,,ENST00000482282,;SLC26A6,non_coding_transcript_exon_variant,,ENST00000489483,;SLC26A6,intron_variant,,ENST00000480524,;SLC26A6,intron_variant,,ENST00000307364,;SLC26A6,intron_variant,,ENST00000444531,;SLC26A6,intron_variant,,ENST00000414944,;SLC26A6,intron_variant,,ENST00000431213,;CELSR3,downstream_gene_variant,,ENST00000498057,;CELSR3,downstream_gene_variant,,ENST00000461362,;SLC26A6,upstream_gene_variant,,ENST00000496469,;SLC26A6,upstream_gene_variant,,ENST00000462009,;SLC26A6,upstream_gene_variant,,ENST00000466257,;SLC26A6,upstream_gene_variant,,ENST00000485361,;SLC26A6,upstream_gene_variant,,ENST00000469693,;SLC26A6,upstream_gene_variant,,ENST00000494717,; A ENST00000455886 Transcript missense_variant 521/2460 473/2172 158/723 R/L cGc/cTc rs768584325 1 -1 SLC26A6 HGNC HGNC:14472 protein_coding CCDS63628.1 ENSP00000401066 Q9BXS9 UPI00017A794B NM_001281732.1 tolerated(0.13) 5/20 Low_complexity_(Seg):seg,hmmpanther:PTHR11814:SF113,hmmpanther:PTHR11814 MODERATE SNV 2 1 PASS rs768584325 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 48632053 48632053 C A 1 0 0 0 0 1 0 0 0 14791 768 27 1 1 SLC26A6 3 48632053 Missense_Mutation SNP C C3N-00203_T 3406223 48632053 149663506 109 11413 LAMB2 0 . GRCh38 3 49123490 49123490 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.3939G>T p.Gln1313His p.Q1313H ENST00000418109 26/33 597 451 146 475 475 0 strelka-varscan-mutect LAMB2,missense_variant,p.Gln1313His,ENST00000418109,NM_002292.3;LAMB2,missense_variant,p.Gln1313His,ENST00000305544,;USP19,upstream_gene_variant,,ENST00000453664,NM_001199162.1;USP19,upstream_gene_variant,,ENST00000417901,NM_001199161.1;USP19,upstream_gene_variant,,ENST00000434032,NM_001199160.1;USP19,upstream_gene_variant,,ENST00000398892,;USP19,upstream_gene_variant,,ENST00000398888,NM_006677.2;USP19,upstream_gene_variant,,ENST00000398898,;USP19,upstream_gene_variant,,ENST00000306026,;USP19,upstream_gene_variant,,ENST00000488993,;USP19,upstream_gene_variant,,ENST00000491859,;LAMB2,downstream_gene_variant,,ENST00000464891,;USP19,upstream_gene_variant,,ENST00000465902,;LAMB2,downstream_gene_variant,,ENST00000486298,;LAMB2,non_coding_transcript_exon_variant,,ENST00000469665,;LAMB2,non_coding_transcript_exon_variant,,ENST00000477225,;LAMB2,upstream_gene_variant,,ENST00000498377,;LAMB2,upstream_gene_variant,,ENST00000467506,;LAMB2,downstream_gene_variant,,ENST00000493571,;LAMB2,downstream_gene_variant,,ENST00000542580,;LAMB2,downstream_gene_variant,,ENST00000538659,;LAMB2,downstream_gene_variant,,ENST00000480640,;LAMB2,downstream_gene_variant,,ENST00000477701,;LAMB2,downstream_gene_variant,,ENST00000483057,;LAMB2,downstream_gene_variant,,ENST00000462930,;LAMB2,upstream_gene_variant,,ENST00000484713,;LAMB2,downstream_gene_variant,,ENST00000488638,; A ENST00000418109 Transcript missense_variant 4104/5674 3939/5397 1313/1798 Q/H caG/caT 1 -1 LAMB2 HGNC HGNC:6487 protein_coding YES CCDS2789.1 ENSP00000388325 P55268 A0A024R319 UPI000013EA62 NM_002292.3 tolerated(0.14) 26/33 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF36 MODERATE 1 SNV 1 1 PASS rs1164022460 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 49123490 49123490 C A 1 0 0 0 0 1 0 0 0 8515 796 28 2 2 LAMB2 3 49123490 Missense_Mutation SNP C C3N-00203_T 491437 49123490 149172069 110 11414 APEH 0 . GRCh38 3 49675298 49675298 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.261G>T p.Glu87Asp p.E87D ENST00000296456 3/22 268 208 60 175 175 0 strelka-varscan-mutect APEH,missense_variant,p.Glu87Asp,ENST00000296456,NM_001640.3;APEH,missense_variant,p.Glu87Asp,ENST00000438011,;APEH,missense_variant,p.Glu84Asp,ENST00000457042,;APEH,intron_variant,,ENST00000442186,;APEH,intron_variant,,ENST00000449966,;BSN,downstream_gene_variant,,ENST00000296452,NM_003458.3;APEH,non_coding_transcript_exon_variant,,ENST00000483715,;APEH,non_coding_transcript_exon_variant,,ENST00000462439,;APEH,non_coding_transcript_exon_variant,,ENST00000463616,;APEH,intron_variant,,ENST00000463995,;APEH,intron_variant,,ENST00000447436,;APEH,intron_variant,,ENST00000446089,;APEH,intron_variant,,ENST00000491799,;APEH,upstream_gene_variant,,ENST00000482301,;APEH,upstream_gene_variant,,ENST00000469362,;APEH,upstream_gene_variant,,ENST00000447541,; T ENST00000296456 Transcript missense_variant 661/3220 261/2199 87/732 E/D gaG/gaT 1 1 APEH HGNC HGNC:586 protein_coding YES CCDS2801.1 ENSP00000296456 P13798 A0A024R2U9 UPI00000735A1 NM_001640.3 tolerated(0.14) 3/22 hmmpanther:PTHR11731:SF7,hmmpanther:PTHR11731,Superfamily_domains:SSF50993 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 49675298 49675298 G T 1 0 0 0 0 1 0 0 0 888 933 33 2 2 APEH 3 49675298 Missense_Mutation SNP G C3N-00203_T 551808 49675298 148620261 111 11415 CADPS 0 . GRCh38 3 62592749 62592749 + Splice_Site SNP C C G novel C3N-00203_T C3N-00203_N C C c.1326-1G>C p.X442_splice ENST00000383710 122 88 34 82 82 0 strelka-varscan-mutect CADPS,splice_acceptor_variant,,ENST00000383710,NM_003716.3;CADPS,splice_acceptor_variant,,ENST00000612439,;CADPS,splice_acceptor_variant,,ENST00000357948,NM_183393.2;CADPS,splice_acceptor_variant,,ENST00000283269,NM_183394.2; G ENST00000383710 Transcript splice_acceptor_variant -/5471 1326/4062 442/1353 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 6/29 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 42 62592749 62592749 C G 1 0 0 0 0 0 0 1 0 2260 811 28 4 4 CADPS 3 62592749 Splice_Site SNP C C3N-00203_T 12917451 62592749 135702810 112 11416 FOXP1 0 . GRCh38 3 70976969 70976969 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.1502A>G p.Tyr501Cys p.Y501C ENST00000615603 17/21 441 374 67 260 260 0 strelka-varscan-mutect FOXP1,missense_variant,p.Tyr501Cys,ENST00000615603,NM_001244810.1;FOXP1,missense_variant,p.Tyr501Cys,ENST00000318789,NM_032682.5;FOXP1,missense_variant,p.Tyr401Cys,ENST00000614176,NM_001244813.1;FOXP1,missense_variant,p.Tyr501Cys,ENST00000475937,NM_001244816.1;FOXP1,missense_variant,p.Tyr500Cys,ENST00000493089,NM_001244808.1;FOXP1,missense_variant,p.Tyr501Cys,ENST00000498215,NM_001244814.1;FOXP1,missense_variant,p.Tyr503Cys,ENST00000491238,NM_001244815.1;FOXP1,missense_variant,p.Tyr425Cys,ENST00000484350,NM_001244812.1;FOXP1,missense_variant,p.Tyr501Cys,ENST00000468577,;FOXP1,missense_variant,p.Tyr397Cys,ENST00000497355,;FOXP1,non_coding_transcript_exon_variant,,ENST00000614183,;FOXP1,missense_variant,p.Tyr501Cys,ENST00000327590,; C ENST00000615603 Transcript missense_variant 2028/7140 1502/2082 501/693 Y/C tAc/tGc 1 -1 FOXP1 HGNC HGNC:3823 protein_coding YES CCDS74964.1 ENSP00000484803 A0A087X299 UPI00022AEF64 NM_001244810.1 deleterious(0) 17/21 PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF176,hmmpanther:PTHR11829,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785,Prints_domain:PR00053 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 70976969 70976969 T C 1 0 0 0 0 1 0 0 0 5891 1638 57 5 5 FOXP1 3 70976969 Missense_Mutation SNP T C3N-00203_T 8384220 70976969 127318590 113 11417 SHQ1 0 . GRCh38 3 72815405 72815405 + Splice_Site SNP T T A rs745678979 C3N-00203_T C3N-00203_N T T c.883-2A>T p.X295_splice ENST00000325599 154 136 18 178 178 0 strelka-varscan-mutect SHQ1,splice_acceptor_variant,,ENST00000325599,NM_018130.2;SHQ1,splice_acceptor_variant,,ENST00000463369,;SHQ1,splice_acceptor_variant,,ENST00000475558,;SHQ1,splice_acceptor_variant,,ENST00000468347,;SHQ1,splice_acceptor_variant,,ENST00000444040,; A ENST00000325599 Transcript splice_acceptor_variant -/2879 883/1734 295/577 rs745678979 1 -1 SHQ1 HGNC HGNC:25543 protein_coding YES CCDS33788.1 ENSP00000315182 Q6PI26 UPI00001416C5 NM_018130.2 7/10 HIGH 1 SNV 1 1 PASS rs745678979 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 42 72815405 72815405 T A 1 0 0 0 0 0 0 1 0 14555 1623 56 4 4 SHQ1 3 72815405 Splice_Site SNP T C3N-00203_T 1838436 72815405 125480154 114 11418 CADM2 0 . GRCh38 3 85883443 85883443 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.370G>T p.Gly124Cys p.G124C ENST00000405615 3/10 84 66 18 78 78 0 strelka-varscan-mutect CADM2,missense_variant,p.Gly131Cys,ENST00000383699,NM_001256504.1,NM_001256505.1,NM_001167675.1;CADM2,missense_variant,p.Gly122Cys,ENST00000407528,NM_001167674.1;CADM2,missense_variant,p.Gly124Cys,ENST00000405615,NM_153184.3; T ENST00000405615 Transcript missense_variant,splice_region_variant 370/1314 370/1314 124/437 G/C Ggt/Tgt 1 1 CADM2 HGNC HGNC:29849 protein_coding YES CCDS33792.1 ENSP00000384193 Q8N3J6 UPI000013F077 NM_153184.3 deleterious(0.01) 3/10 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF56,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 85883443 85883443 G T 1 0 0 0 0 1 0 0 0 2257 1246 43 2 2 CADM2 3 85883443 Missense_Mutation SNP G C3N-00203_T 13068038 85883443 112412116 115 11419 EPHA6 0 . GRCh38 3 97532453 97532453 + Silent SNP C C A rs139774071 C3N-00203_T C3N-00203_N C C c.2296C>A p.= p.R766R ENST00000389672 11/18 281 221 60 185 185 0 strelka-varscan-mutect EPHA6,synonymous_variant,p.=,ENST00000389672,NM_001080448.2;EPHA6,synonymous_variant,p.=,ENST00000514100,NM_001278300.1;EPHA6,synonymous_variant,p.=,ENST00000502694,NM_173655.3;EPHA6,synonymous_variant,p.=,ENST00000477384,;EPHA6,synonymous_variant,p.=,ENST00000503760,;EPHA6,synonymous_variant,p.=,ENST00000508345,; A ENST00000389672 Transcript synonymous_variant 2334/3971 2296/3393 766/1130 R Cgg/Agg rs139774071,COSM95852 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 11/18 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1 LOW 1 SNV 2 0,1 1 PASS rs139774071 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 97532453 97532453 C A 1 0 0 0 0 0 0 0 1 5018 875 31 1 1 EPHA6 3 97532453 Silent SNP C C3N-00203_T 11649010 97532453 100763106 116 11420 SENP7 0 . GRCh38 3 101417596 101417596 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.479A>T p.Glu160Val p.E160V ENST00000394095 5/24 217 173 44 164 164 0 varscan-mutect SENP7,missense_variant,p.Glu160Val,ENST00000394095,NM_020654.4;SENP7,missense_variant,p.Glu160Val,ENST00000394094,NM_001077203.2;SENP7,missense_variant,p.Glu127Val,ENST00000348610,NM_001282802.1;SENP7,intron_variant,,ENST00000314261,NM_001282801.1;SENP7,intron_variant,,ENST00000394091,NM_001282803.1;RP11-144C15.1,downstream_gene_variant,,ENST00000468519,; A ENST00000394095 Transcript missense_variant 533/4945 479/3153 160/1050 E/V gAa/gTa 1 -1 SENP7 HGNC HGNC:30402 protein_coding YES CCDS2941.2 ENSP00000377655 Q9BQF6 UPI0000E56ED1 NM_020654.4 deleterious(0) 5/24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 101417596 101417596 T A 1 0 0 0 0 1 0 0 0 14327 1797 62 4 4 SENP7 3 101417596 Missense_Mutation SNP T C3N-00203_T 3885143 101417596 96877963 117 11421 C3orf30 0 . GRCh38 3 119147428 119147428 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1239G>T p.Gln413His p.Q413H ENST00000295622 1/3 304 239 65 276 275 1 strelka-varscan-mutect C3orf30,missense_variant,p.Gln413His,ENST00000295622,NM_152539.2;C3orf30,missense_variant,p.Gln377His,ENST00000460150,;C3orf30,missense_variant,p.Gln206His,ENST00000473121,;C3orf30,missense_variant,p.Gln148His,ENST00000492792,;RP11-484M3.5,missense_variant,p.Gln4His,ENST00000490594,;IGSF11,upstream_gene_variant,,ENST00000425327,NM_152538.2;IGSF11,upstream_gene_variant,,ENST00000441144,;IGSF11,upstream_gene_variant,,ENST00000494802,;C3orf30,missense_variant,p.Gln413His,ENST00000494105,; T ENST00000295622 Transcript missense_variant 1279/1814 1239/1611 413/536 Q/H caG/caT 1 1 C3orf30 HGNC HGNC:26553 protein_coding YES CCDS2984.1 ENSP00000295622 Q96M34 UPI000013E280 NM_152539.2 deleterious(0.01) 1/3 hmmpanther:PTHR21847,hmmpanther:PTHR21847:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 119147428 119147428 G T 1 0 0 0 0 1 0 0 0 2063 933 33 2 2 C3orf30 3 119147428 Missense_Mutation SNP G C3N-00203_T 17729832 119147428 79148131 118 11422 DIRC2 0 . GRCh38 3 122872500 122872500 + Silent SNP C C A C3N-00203_T C3N-00203_N C C c.1224C>A p.= p.V408V ENST00000261038 8/9 284 217 67 300 300 0 strelka-varscan-mutect DIRC2,synonymous_variant,p.=,ENST00000261038,NM_032839.2;DIRC2,3_prime_UTR_variant,,ENST00000477647,; A ENST00000261038 Transcript synonymous_variant 1622/3596 1224/1437 408/478 V gtC/gtA COSM1536210 1 1 DIRC2 HGNC HGNC:16628 protein_coding YES CCDS3018.1 ENSP00000261038 Q96SL1 UPI0000073CC7 NM_032839.2 8/9 Gene3D:1.20.1250.20,hmmpanther:PTHR10924,hmmpanther:PTHR10924:SF0,Superfamily_domains:SSF103473 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 122872500 122872500 C A 1 0 0 0 0 0 0 0 1 4339 900 32 2 2 DIRC2 3 122872500 Silent SNP C C3N-00203_T 3725072 122872500 75423059 119 11423 ZNF148 0 . GRCh38 3 125234251 125234251 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.746A>T p.His249Leu p.H249L ENST00000360647 8/9 207 179 28 235 235 0 strelka-varscan-mutect ZNF148,missense_variant,p.His249Leu,ENST00000360647,NM_021964.2;ZNF148,missense_variant,p.His249Leu,ENST00000485866,;ZNF148,missense_variant,p.His249Leu,ENST00000484491,;ZNF148,missense_variant,p.His249Leu,ENST00000492394,;ZNF148,intron_variant,,ENST00000468369,;ZNF148,non_coding_transcript_exon_variant,,ENST00000497929,;ZNF148,upstream_gene_variant,,ENST00000496732,; A ENST00000360647 Transcript missense_variant 1232/9651 746/2385 249/794 H/L cAt/cTt 1 -1 ZNF148 HGNC HGNC:12933 protein_coding YES CCDS3031.1 ENSP00000353863 Q9UQR1 UPI000013C2FF NM_021964.2 deleterious(0) 8/9 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF65,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 125234251 125234251 T A 1 0 0 0 0 1 0 0 0 18315 1464 51 4 4 ZNF148 3 125234251 Missense_Mutation SNP T C3N-00203_T 2361751 125234251 73061308 120 11424 PODXL2 0 . GRCh38 3 127660476 127660476 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.448A>T p.Asn150Tyr p.N150Y ENST00000342480 3/8 275 176 99 198 198 0 strelka-varscan-mutect PODXL2,missense_variant,p.Asn150Tyr,ENST00000342480,NM_015720.3; T ENST00000342480 Transcript missense_variant 487/2186 448/1818 150/605 N/Y Aat/Tat 1 1 PODXL2 HGNC HGNC:17936 protein_coding YES CCDS3044.1 ENSP00000345359 Q9NZ53 UPI000006FC4B NM_015720.3 deleterious(0.03) 3/8 hmmpanther:PTHR15594 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 127660476 127660476 A T 1 0 0 0 0 1 0 0 0 12290 246 9 4 4 PODXL2 3 127660476 Missense_Mutation SNP A C3N-00203_T 2426225 127660476 70635083 121 11425 HMCES 0 . GRCh38 3 129290709 129290709 + Missense_Mutation SNP G G T rs756205892 C3N-00203_T C3N-00203_N G G c.358G>T p.Val120Phe p.V120F ENST00000383463 4/7 298 188 110 182 182 0 strelka-varscan-mutect HMCES,missense_variant,p.Val120Phe,ENST00000383463,NM_020187.2;HMCES,missense_variant,p.Val120Phe,ENST00000502878,;HMCES,missense_variant,p.Val120Phe,ENST00000389735,NM_001006109.1;HMCES,missense_variant,p.Val72Phe,ENST00000509042,;HMCES,missense_variant,p.Val120Phe,ENST00000509551,;HMCES,intron_variant,,ENST00000417226,;HMCES,intron_variant,,ENST00000511665,;HMCES,intron_variant,,ENST00000510314,; T ENST00000383463 Transcript missense_variant 447/2515 358/1065 120/354 V/F Gtt/Ttt rs756205892 1 1 HMCES HGNC HGNC:24446 protein_coding YES CCDS33852.1 ENSP00000372955 Q96FZ2 UPI000006FF4D NM_020187.2 deleterious(0) 4/7 Gene3D:2icuA00,Pfam_domain:PF02586,hmmpanther:PTHR13604,hmmpanther:PTHR13604:SF0,Superfamily_domains:SSF143081 MODERATE 1 SNV 1 1 PASS rs756205892 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 129290709 129290709 G T 1 0 0 0 0 1 0 0 0 7110 1145 40 1 1 HMCES 3 129290709 Missense_Mutation SNP G C3N-00203_T 1630233 129290709 69004850 122 11426 COL6A6 0 . GRCh38 3 130574517 130574517 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.3539G>T p.Gly1180Val p.G1180V ENST00000358511 7/36 101 75 26 100 100 0 strelka-varscan-mutect COL6A6,missense_variant,p.Gly1180Val,ENST00000358511,NM_001102608.1; T ENST00000358511 Transcript missense_variant 3570/9581 3539/6792 1180/2263 G/V gGt/gTt 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 tolerated(0.12) 7/36 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 130574517 130574517 G T 1 0 0 0 0 1 0 0 0 3492 1261 44 2 2 COL6A6 3 130574517 Missense_Mutation SNP G C3N-00203_T 1283808 130574517 67721042 123 11427 CPNE4 0 . GRCh38 3 131723530 131723530 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.330G>T p.= p.R110R ENST00000617767 3/16 309 285 24 240 240 0 strelka-varscan-mutect CPNE4,synonymous_variant,p.=,ENST00000512055,;CPNE4,synonymous_variant,p.=,ENST00000429747,NM_130808.2;CPNE4,synonymous_variant,p.=,ENST00000617767,NM_001289112.1;CPNE4,synonymous_variant,p.=,ENST00000511604,;CPNE4,synonymous_variant,p.=,ENST00000512332,NM_153429.1;CPNE4,synonymous_variant,p.=,ENST00000502818,;CPNE4,synonymous_variant,p.=,ENST00000505881,;CPNE4,downstream_gene_variant,,ENST00000505957,;CPNE4,downstream_gene_variant,,ENST00000514999,;CPNE4,non_coding_transcript_exon_variant,,ENST00000515418,; A ENST00000617767 Transcript synonymous_variant 525/3556 330/1728 110/575 R cgG/cgT 1 -1 CPNE4 HGNC HGNC:2317 protein_coding YES CCDS75010.1 ENSP00000478878 Q96A23 UPI000002A6F1 NM_001289112.1 3/16 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF4,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 2 1 PASS rs1168412024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 131723530 131723530 C A 1 0 0 0 0 0 0 0 1 3609 494 18 2 2 CPNE4 3 131723530 Silent SNP C C3N-00203_T 1149013 131723530 66572029 124 11428 NPHP3 0 . GRCh38 3 132699967 132699967 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.1838G>T p.Arg613Leu p.R613L ENST00000337331 12/27 405 372 33 313 312 1 strelka-varscan-mutect NPHP3,missense_variant,p.Arg613Leu,ENST00000337331,NM_153240.4;NPHP3-ACAD11,missense_variant,p.Arg613Leu,ENST00000471702,;NPHP3,missense_variant,p.Arg515Leu,ENST00000465756,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,;NPHP3,downstream_gene_variant,,ENST00000469232,;NPHP3,upstream_gene_variant,,ENST00000515289,; A ENST00000337331 Transcript missense_variant 1925/4362 1838/3993 613/1330 R/L cGt/cTt COSM4113657 1 -1 NPHP3 HGNC HGNC:7907 protein_coding YES CCDS3078.1 ENSP00000338766 Q7Z494 UPI00001B6B30 NM_153240.4 deleterious(0) 12/27 hmmpanther:PTHR19959:SF153,hmmpanther:PTHR19959,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs937330869 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 132699967 132699967 C A 1 0 0 0 0 1 0 0 0 10628 536 19 1 1 NPHP3 3 132699967 Missense_Mutation SNP C C3N-00203_T 976437 132699967 65595592 125 11429 PRR23C 0 . GRCh38 3 139044482 139044482 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.139G>A p.Asp47Asn p.D47N ENST00000413199 1/1 148 140 8 120 119 1 strelka-varscan-mutect PRR23C,missense_variant,p.Asp47Asn,ENST00000413199,NM_001134657.1;MRPS22,intron_variant,,ENST00000495075,; T ENST00000413199 Transcript missense_variant 411/2791 139/789 47/262 D/N Gac/Aac 1 -1 PRR23C HGNC HGNC:37173 protein_coding YES CCDS46924.1 ENSP00000396648 Q6ZRP0 UPI00001C0F48 NM_001134657.1 tolerated(0.67) 1/1 hmmpanther:PTHR31813:SF6,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 139044482 139044482 C T 1 0 0 0 0 1 0 0 0 12731 913 32 3 3 PRR23C 3 139044482 Missense_Mutation SNP C C3N-00203_T 6344515 139044482 59251077 126 11430 CLSTN2 0 . GRCh38 3 140448518 140448518 + Splice_Site SNP G G A novel C3N-00203_T C3N-00203_N G G c.788-1G>A p.X263_splice ENST00000458420 135 120 15 72 72 0 strelka-varscan-mutect CLSTN2,splice_acceptor_variant,,ENST00000458420,NM_022131.2;RP11-68L1.2,downstream_gene_variant,,ENST00000509191,;RP11-68L1.2,downstream_gene_variant,,ENST00000502712,;RP11-68L1.2,downstream_gene_variant,,ENST00000503357,;CLSTN2,splice_acceptor_variant,,ENST00000511524,; A ENST00000458420 Transcript splice_acceptor_variant -/14202 788/2868 263/955 1 1 CLSTN2 HGNC HGNC:17448 protein_coding YES CCDS3112.1 ENSP00000402460 Q9H4D0 UPI00001B0051 NM_022131.2 5/16 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 5 1 42 140448518 140448518 G A 1 0 0 0 0 0 0 1 0 3334 956 33 3 3 CLSTN2 3 140448518 Splice_Site SNP G C3N-00203_T 1404036 140448518 57847041 127 11431 KPNA4 0 . GRCh38 3 160531515 160531515 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.330A>G p.= p.L110L ENST00000334256 6/17 186 150 36 157 157 0 strelka-varscan-mutect KPNA4,synonymous_variant,p.=,ENST00000334256,NM_002268.4; C ENST00000334256 Transcript synonymous_variant 636/8981 330/1566 110/521 L ttA/ttG 1 -1 KPNA4 HGNC HGNC:6397 protein_coding YES CCDS3191.1 ENSP00000334373 O00629 UPI0000001648 NM_002268.4 6/17 hmmpanther:PTHR23316:SF7,hmmpanther:PTHR23316,Pfam_domain:PF00514,Gene3D:1.25.10.10,PIRSF_domain:PIRSF005673,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 160531515 160531515 T C 1 0 0 0 0 0 0 0 1 8312 1751 61 5 5 KPNA4 3 160531515 Silent SNP T C3N-00203_T 20082997 160531515 37764044 128 11432 ZNF595 0 . GRCh38 4 59436 59436 + Missense_Mutation SNP G G T C3N-00203_T C3N-00203_N G G c.10G>T p.Val4Leu p.V4L ENST00000610261 2/4 295 277 18 314 314 0 varscan-mutect ZNF595,missense_variant,p.Val4Leu,ENST00000610261,NM_182524.3;ZNF595,missense_variant,p.Val4Leu,ENST00000609518,NM_001286052.1;ZNF595,missense_variant,p.Val4Leu,ENST00000509152,;ZNF595,intron_variant,,ENST00000608255,NM_001286053.1,NM_001286054.1;ZNF595,non_coding_transcript_exon_variant,,ENST00000502981,; T ENST00000610261 Transcript missense_variant 214/2911 10/1947 4/648 V/L Gta/Tta COSM384440 1 1 ZNF595 HGNC HGNC:27196 protein_coding YES CCDS75075.1 ENSP00000477392 Q7Z3I0 UPI00001A9D0D NM_182524.3 tolerated(1) 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF303,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 59436 59436 G T 1 0 0 0 0 1 0 0 0 18600 1145 40 1 1 ZNF595 4 59436 Missense_Mutation SNP G C3N-00203_T 59436 190155119 129 11433 GAK 0 . GRCh38 4 888915 888915 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.1137G>T p.= p.R379R ENST00000314167 11/28 338 258 80 219 219 0 strelka-varscan-mutect GAK,synonymous_variant,p.=,ENST00000314167,NM_005255.2;GAK,synonymous_variant,p.=,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,intron_variant,,ENST00000618573,;GAK,non_coding_transcript_exon_variant,,ENST00000504435,;GAK,downstream_gene_variant,,ENST00000505819,;GAK,upstream_gene_variant,,ENST00000504947,; A ENST00000314167 Transcript synonymous_variant 1248/4442 1137/3936 379/1311 R cgG/cgT 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 11/28 hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 888915 888915 C A 1 0 0 0 0 0 0 0 1 6063 610 22 2 2 GAK 4 888915 Silent SNP C C3N-00203_T 829479 888915 189325640 130 11434 KCNIP4 0 . GRCh38 4 20758834 20758834 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.345C>T p.= p.F115F ENST00000382152 4/9 248 215 33 173 173 0 strelka-varscan-mutect KCNIP4,synonymous_variant,p.=,ENST00000382148,NM_001035003.1;KCNIP4,synonymous_variant,p.=,ENST00000359001,NM_147182.3;KCNIP4,synonymous_variant,p.=,ENST00000382152,NM_025221.5;KCNIP4,synonymous_variant,p.=,ENST00000382150,NM_147183.3;KCNIP4,synonymous_variant,p.=,ENST00000447367,NM_147181.3;KCNIP4,synonymous_variant,p.=,ENST00000509207,NM_001035004.1;KCNIP4,non_coding_transcript_exon_variant,,ENST00000382149,;KCNIP4,3_prime_UTR_variant,,ENST00000515786,; A ENST00000382152 Transcript synonymous_variant 513/1767 345/753 115/250 F ttC/ttT 1 -1 KCNIP4 HGNC HGNC:30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 4/9 hmmpanther:PTHR23055:SF30,hmmpanther:PTHR23055,Gene3D:1.10.238.10,Pfam_domain:PF13833,Superfamily_domains:SSF47473 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 20758834 20758834 G A 1 0 0 0 0 0 0 0 1 7958 933 33 3 3 KCNIP4 4 20758834 Silent SNP G C3N-00203_T 19869919 20758834 169455721 131 11435 CORIN 0 . GRCh38 4 47665264 47665264 + Splice_Site SNP C C T novel C3N-00203_T C3N-00203_N C C c.1358-1G>A p.X453_splice ENST00000273857 137 115 22 142 142 0 strelka-varscan-mutect CORIN,splice_acceptor_variant,,ENST00000273857,NM_006587.3;CORIN,splice_acceptor_variant,,ENST00000610355,NM_001278585.1;CORIN,splice_acceptor_variant,,ENST00000508498,;CORIN,splice_acceptor_variant,,ENST00000502252,;CORIN,splice_acceptor_variant,,ENST00000505909,;CORIN,splice_acceptor_variant,,ENST00000504584,NM_001278586.1;CORIN,splice_acceptor_variant,,ENST00000503821,;CORIN,upstream_gene_variant,,ENST00000505754,; T ENST00000273857 Transcript splice_acceptor_variant -/4852 1358/3129 453/1042 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 10/21 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 47665264 47665264 C T 1 0 0 0 0 0 0 1 0 3546 695 24 3 3 CORIN 4 47665264 Splice_Site SNP C C3N-00203_T 26906430 47665264 142549291 132 11436 CWH43 0 . GRCh38 4 49003982 49003982 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.1050T>A p.Asp350Glu p.D350E ENST00000226432 7/16 117 90 27 72 72 0 strelka-varscan-mutect CWH43,missense_variant,p.Asp350Glu,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Asp323Glu,ENST00000513409,NM_001286791.1;CWH43,non_coding_transcript_exon_variant,,ENST00000506221,;CWH43,intron_variant,,ENST00000514053,; A ENST00000226432 Transcript missense_variant 1233/2472 1050/2100 350/699 D/E gaT/gaA 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.03) 7/16 hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 49003982 49003982 T A 1 0 0 0 0 1 0 0 0 3883 1461 51 4 4 CWH43 4 49003982 Missense_Mutation SNP T C3N-00203_T 1338718 49003982 141210573 133 11437 KDR 0 . GRCh38 4 55088953 55088953 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.3425G>T p.Cys1142Phe p.C1142F ENST00000263923 26/30 395 302 93 368 368 0 strelka-varscan-mutect KDR,missense_variant,p.Cys1142Phe,ENST00000263923,NM_002253.2;RP11-530I17.1,intron_variant,,ENST00000511222,; A ENST00000263923 Transcript missense_variant 3721/5831 3425/4071 1142/1356 C/F tGc/tTc 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0) 26/30 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 55088953 55088953 C A 1 0 0 0 0 1 0 0 0 8059 710 25 2 2 KDR 4 55088953 Missense_Mutation SNP C C3N-00203_T 6084971 55088953 135125602 134 11438 NOA1 0 . GRCh38 4 56976524 56976524 + Silent SNP G G C novel C3N-00203_T C3N-00203_N G G c.1062C>G p.= p.L354L ENST00000264230 1/7 240 184 56 172 172 0 strelka-varscan-mutect NOA1,synonymous_variant,p.=,ENST00000264230,NM_032313.2;POLR2B,upstream_gene_variant,,ENST00000381227,;POLR2B,upstream_gene_variant,,ENST00000441246,NM_001303269.1;POLR2B,upstream_gene_variant,,ENST00000314595,NM_000938.2;POLR2B,upstream_gene_variant,,ENST00000431623,NM_001303268.1;POLR2B,upstream_gene_variant,,ENST00000450656,;POLR2B,upstream_gene_variant,,ENST00000433463,;POLR2B,upstream_gene_variant,,ENST00000497845,;POLR2B,upstream_gene_variant,,ENST00000495311,; C ENST00000264230 Transcript synonymous_variant 2300/3415 1062/2097 354/698 L ctC/ctG 1 -1 NOA1 HGNC HGNC:28473 protein_coding YES CCDS3510.1 ENSP00000264230 Q8NC60 UPI000006DAEE NM_032313.2 1/7 PROSITE_profiles:PS51721,hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF3,Gene3D:3.40.50.300,Pfam_domain:PF01926,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 56976524 56976524 G C 1 0 0 0 0 0 0 0 1 10552 929 33 4 4 NOA1 4 56976524 Silent SNP G C3N-00203_T 1887571 56976524 133238031 135 11439 NAAA 0 . GRCh38 4 75921090 75921090 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.700G>T p.Val234Phe p.V234F ENST00000286733 6/11 93 71 22 75 75 0 strelka-varscan-mutect NAAA,missense_variant,p.Val234Phe,ENST00000286733,NM_014435.3;NAAA,missense_variant,p.Val133Phe,ENST00000505594,;NAAA,missense_variant,p.Val234Phe,ENST00000507956,;NAAA,missense_variant,p.Val109Phe,ENST00000602782,;NAAA,upstream_gene_variant,,ENST00000511606,;NAAA,missense_variant,p.Val39Phe,ENST00000513045,; A ENST00000286733 Transcript missense_variant 802/1900 700/1080 234/359 V/F Gtt/Ttt 1 -1 NAAA HGNC HGNC:736 protein_coding YES CCDS43239.1 ENSP00000286733 Q02083 UPI00001AEAEE NM_014435.3 deleterious(0.04) 6/11 Pfam_domain:PF02275,PIRSF_domain:PIRSF017632,hmmpanther:PTHR28583,hmmpanther:PTHR28583:SF4 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 75921090 75921090 C A 1 0 0 0 0 1 0 0 0 10131 478 17 2 2 NAAA 4 75921090 Missense_Mutation SNP C C3N-00203_T 18944566 75921090 114293465 136 11440 PRDM8 0 . GRCh38 4 80203327 80203327 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1865C>A p.Pro622His p.P622H ENST00000339711 10/10 416 328 88 400 399 1 strelka-varscan-mutect PRDM8,missense_variant,p.Pro622His,ENST00000339711,NM_020226.3;PRDM8,missense_variant,p.Pro622His,ENST00000504452,;PRDM8,missense_variant,p.Pro622His,ENST00000415738,NM_001099403.1;PRDM8,downstream_gene_variant,,ENST00000515013,; A ENST00000339711 Transcript missense_variant 3096/4095 1865/2070 622/689 P/H cCc/cAc 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 deleterious(0) 10/10 hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF7,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 80203327 80203327 C A 1 0 0 0 0 1 0 0 0 12594 623 22 2 2 PRDM8 4 80203327 Missense_Mutation SNP C C3N-00203_T 4282237 80203327 110011228 137 11441 SPP1 0 . GRCh38 4 87980401 87980401 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.183G>A p.= p.V61V ENST00000395080 5/7 273 207 66 215 215 0 strelka-varscan-mutect SPP1,synonymous_variant,p.=,ENST00000614857,NM_001251830.1;SPP1,synonymous_variant,p.=,ENST00000395080,NM_001040058.1;SPP1,synonymous_variant,p.=,ENST00000360804,NM_001040060.1;SPP1,intron_variant,,ENST00000237623,NM_000582.2;SPP1,intron_variant,,ENST00000508233,NM_001251829.1;SPP1,non_coding_transcript_exon_variant,,ENST00000509659,;SPP1,non_coding_transcript_exon_variant,,ENST00000513981,;SPP1,intron_variant,,ENST00000509334,;SPP1,non_coding_transcript_exon_variant,,ENST00000508002,;SPP1,downstream_gene_variant,,ENST00000504310,;SPP1,downstream_gene_variant,,ENST00000505146,; A ENST00000395080 Transcript synonymous_variant 310/1473 183/945 61/314 V gtG/gtA 1 1 SPP1 HGNC HGNC:11255 protein_coding YES CCDS43250.1 ENSP00000378517 P10451 A0A024RDE2 UPI0000000E0B NM_001040058.1 5/7 hmmpanther:PTHR10607:SF1,hmmpanther:PTHR10607,Pfam_domain:PF00865,SMART_domains:SM00017,Prints_domain:PR00216 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 87980401 87980401 G A 1 0 0 0 0 0 0 0 1 15439 1364 48 3 3 SPP1 4 87980401 Silent SNP G C3N-00203_T 7777074 87980401 102234154 138 11442 MMRN1 0 . GRCh38 4 89936262 89936262 + Missense_Mutation SNP G G A rs778039444 C3N-00203_T C3N-00203_N G G c.2582G>A p.Arg861Gln p.R861Q ENST00000394980 7/9 153 124 29 147 146 1 strelka-varscan-mutect MMRN1,missense_variant,p.Arg861Gln,ENST00000394980,;MMRN1,missense_variant,p.Arg861Gln,ENST00000264790,NM_007351.2;MMRN1,missense_variant,p.Arg603Gln,ENST00000508372,; A ENST00000394980 Transcript missense_variant 2901/5217 2582/3687 861/1228 R/Q cGg/cAg rs778039444,COSM2957873 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 tolerated(0.08) 7/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs778039444 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 89936262 89936262 G A 1 0 0 0 0 1 0 0 0 9633 1116 39 1 1 MMRN1 4 89936262 Missense_Mutation SNP G C3N-00203_T 1955861 89936262 100278293 139 11443 GRID2 0 . GRCh38 4 93515378 93515378 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.2160C>G p.Asn720Lys p.N720K ENST00000282020 13/16 156 109 47 130 130 0 strelka-varscan-mutect GRID2,missense_variant,p.Asn720Lys,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Asn639Lys,ENST00000611049,;GRID2,missense_variant,p.Asn625Lys,ENST00000510992,NM_001286838.1; G ENST00000282020 Transcript missense_variant 3195/6117 2160/3024 720/1007 N/K aaC/aaG 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 deleterious(0.01) 13/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 93515378 93515378 C G 1 0 0 0 0 1 0 0 0 6652 477 17 4 4 GRID2 4 93515378 Missense_Mutation SNP C C3N-00203_T 3579116 93515378 96699177 140 11444 LAMTOR3 0 . GRCh38 4 99885656 99885656 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.123A>G p.= p.P41P ENST00000499666 5/7 316 257 59 236 236 0 strelka-varscan-mutect LAMTOR3,splice_acceptor_variant,,ENST00000226522,NM_001243736.1;LAMTOR3,synonymous_variant,p.=,ENST00000499666,NM_021970.3;LAMTOR3,non_coding_transcript_exon_variant,,ENST00000515100,; C ENST00000499666 Transcript synonymous_variant 316/4226 123/375 41/124 P ccA/ccG 1 -1 LAMTOR3 HGNC HGNC:15606 protein_coding YES CCDS3652.1 ENSP00000424183 Q9UHA4 UPI000012F194 NM_021970.3 5/7 Gene3D:3.30.450.30,Pfam_domain:PF08923,hmmpanther:PTHR13378,SMART_domains:SM01278,Superfamily_domains:SSF103196 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 99885656 99885656 T C 1 0 0 0 0 0 0 0 1 8527 1594 55 5 5 LAMTOR3 4 99885656 Silent SNP T C3N-00203_T 6370278 99885656 90328899 141 11445 SLC9B2 0 . GRCh38 4 103044927 103044927 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.959T>C p.Leu320Pro p.L320P ENST00000394785 8/12 289 235 54 262 261 1 strelka-varscan-mutect SLC9B2,missense_variant,p.Leu320Pro,ENST00000394785,NM_178833.5;SLC9B2,missense_variant,p.Leu320Pro,ENST00000362026,;SLC9B2,missense_variant,p.Leu263Pro,ENST00000503103,NM_001300756.1;SLC9B2,missense_variant,p.Leu263Pro,ENST00000503230,NM_001300754.1;SLC9B2,missense_variant,p.Leu220Pro,ENST00000506288,;SLC9B2,non_coding_transcript_exon_variant,,ENST00000510976,;SLC9B2,downstream_gene_variant,,ENST00000515424,; G ENST00000394785 Transcript missense_variant 1591/3126 959/1614 320/537 L/P cTt/cCt 1 -1 SLC9B2 HGNC HGNC:25143 protein_coding YES CCDS3662.1 ENSP00000378265 Q86UD5 A0A024RDJ7 UPI000020B27F NM_178833.5 deleterious(0) 8/12 Pfam_domain:PF00999,hmmpanther:PTHR31102,hmmpanther:PTHR31102:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs993336465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 103044927 103044927 A G 1 0 0 0 0 1 0 0 0 15005 72 3 5 5 SLC9B2 4 103044927 Missense_Mutation SNP A C3N-00203_T 3159271 103044927 87169628 142 11446 ANK2 0 . GRCh38 4 113277932 113277932 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.1779G>A p.= p.G593G ENST00000357077 16/46 485 404 81 378 378 0 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000506722,NM_001127493.1;ANK2,synonymous_variant,p.=,ENST00000394537,NM_020977.3;ANK2,synonymous_variant,p.=,ENST00000504454,;ANK2,synonymous_variant,p.=,ENST00000503423,;ANK2,synonymous_variant,p.=,ENST00000634436,;ANK2,synonymous_variant,p.=,ENST00000503271,; A ENST00000357077 Transcript synonymous_variant 1832/14196 1779/11874 593/3957 G ggG/ggA 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 16/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 113277932 113277932 G A 1 0 0 0 0 0 0 0 1 721 1188 41 3 3 ANK2 4 113277932 Silent SNP G C3N-00203_T 10233005 113277932 76936623 143 11447 KIAA1109 0 . GRCh38 4 122333749 122333749 + Silent SNP A A C novel C3N-00203_T C3N-00203_N A A c.11586A>C p.= p.L3862L ENST00000264501 68/86 419 333 86 357 357 0 strelka-varscan-mutect KIAA1109,synonymous_variant,p.=,ENST00000264501,;KIAA1109,synonymous_variant,p.=,ENST00000388738,NM_015312.3;KIAA1109,synonymous_variant,p.=,ENST00000438707,;KIAA1109,synonymous_variant,p.=,ENST00000306802,;KIAA1109,upstream_gene_variant,,ENST00000483357,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000480651,; C ENST00000264501 Transcript synonymous_variant 11959/15896 11586/15018 3862/5005 L ctA/ctC 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 68/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 122333749 122333749 A C 1 0 0 0 0 0 0 0 1 8101 378 14 5 5 KIAA1109 4 122333749 Silent SNP A C3N-00203_T 9055817 122333749 67880806 144 11448 MFSD8 0 . GRCh38 4 127943935 127943935 + Missense_Mutation SNP C C A rs552923962 C3N-00203_T C3N-00203_N C C c.256G>T p.Gly86Cys p.G86C ENST00000296468 5/13 437 337 100 334 334 0 strelka-varscan-mutect MFSD8,missense_variant,p.Gly86Cys,ENST00000296468,NM_152778.2;MFSD8,missense_variant,p.Gly41Cys,ENST00000513559,;MFSD8,non_coding_transcript_exon_variant,,ENST00000515130,;MFSD8,non_coding_transcript_exon_variant,,ENST00000505284,;MFSD8,non_coding_transcript_exon_variant,,ENST00000508441,;MFSD8,missense_variant,p.Gly41Cys,ENST00000509826,; A ENST00000296468 Transcript missense_variant 384/4510 256/1557 86/518 G/C Ggc/Tgc rs552923962 1 -1 MFSD8 HGNC HGNC:28486 protein_coding YES CCDS3736.1 ENSP00000296468 Q8NHS3 UPI000004DAF1 NM_152778.2 deleterious(0.02) 5/13 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23510,hmmpanther:PTHR23510:SF3,Gene3D:1.20.1250.20,Pfam_domain:PF07690,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs552923962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 127943935 127943935 C A 1 0 0 0 0 1 0 0 0 9496 594 21 2 2 MFSD8 4 127943935 Missense_Mutation SNP C C3N-00203_T 5610186 127943935 62270620 145 11449 TRIM61 0 . GRCh38 4 164969858 164969858 + Missense_Mutation SNP C C T C3N-00203_T C3N-00203_N C C c.145G>A p.Asp49Asn p.D49N ENST00000329314 3/5 695 612 83 581 581 0 varscan-mutect TRIM61,missense_variant,p.Asp49Asn,ENST00000329314,NM_001012414.2;RP11-366M4.11,non_coding_transcript_exon_variant,,ENST00000508856,; T ENST00000329314 Transcript missense_variant 758/1582 145/630 49/209 D/N Gat/Aat COSM3601660 1 -1 TRIM61 HGNC HGNC:24339 protein_coding YES CCDS34093.1 ENSP00000332288 Q5EBN2 UPI00004CEC1B NM_001012414.2 tolerated(0.1) 3/5 PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF304,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Pfam_domain:PF15227,SMART_domains:SM00184,Superfamily_domains:SSF57850 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 164969858 164969858 C T 1 0 0 0 0 1 0 0 0 17028 826 29 3 3 TRIM61 4 164969858 Missense_Mutation SNP C C3N-00203_T 37025923 164969858 25244697 146 11450 SPOCK3 0 . GRCh38 4 166912713 166912713 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.390G>C p.Gln130His p.Q130H ENST00000357154 6/12 191 156 35 182 182 0 strelka-varscan-mutect SPOCK3,missense_variant,p.Gln79His,ENST00000421836,NM_001204352.1;SPOCK3,missense_variant,p.Gln130His,ENST00000357154,NM_016950.2;SPOCK3,missense_variant,p.Gln130His,ENST00000506886,;SPOCK3,missense_variant,p.Gln127His,ENST00000357545,NM_001040159.1;SPOCK3,missense_variant,p.Gln130His,ENST00000511531,;SPOCK3,missense_variant,p.Gln127His,ENST00000504953,;SPOCK3,missense_variant,p.Gln10His,ENST00000541354,NM_001204355.1,NM_001204353.1;SPOCK3,missense_variant,p.Gln130His,ENST00000502330,;SPOCK3,missense_variant,p.Gln38His,ENST00000535728,NM_001204354.1;SPOCK3,missense_variant,p.Gln127His,ENST00000510741,NM_001204356.1;SPOCK3,missense_variant,p.Gln127His,ENST00000511269,;SPOCK3,missense_variant,p.Gln127His,ENST00000512648,NM_001204358.1;SPOCK3,missense_variant,p.Gln127His,ENST00000509854,;SPOCK3,intron_variant,,ENST00000512681,NM_001251967.1;SPOCK3,intron_variant,,ENST00000510403,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;SPOCK3,3_prime_UTR_variant,,ENST00000511226,;SPOCK3,3_prime_UTR_variant,,ENST00000515316,;SPOCK3,intron_variant,,ENST00000502741,;SPOCK3,intron_variant,,ENST00000507086,;SPOCK3,intron_variant,,ENST00000515143,; G ENST00000357154 Transcript missense_variant 528/2986 390/1311 130/436 Q/H caG/caC 1 -1 SPOCK3 HGNC HGNC:13565 protein_coding YES CCDS54817.1 ENSP00000349677 Q9BQ16 UPI000004BA60 NM_016950.2 tolerated(0.47) 6/12 hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF10,Superfamily_domains:SSF100895 MODERATE 1 SNV 5 1 PASS rs1355513406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 166912713 166912713 C G 1 0 0 0 0 1 0 0 0 15434 564 20 4 4 SPOCK3 4 166912713 Missense_Mutation SNP C C3N-00203_T 1942855 166912713 23301842 147 11451 DDX60L 0 . GRCh38 4 168406063 168406063 + Nonsense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.3100G>T p.Glu1034Ter p.E1034* ENST00000260184 24/38 191 148 43 154 154 0 strelka-varscan-mutect DDX60L,stop_gained,p.Glu1034Ter,ENST00000511577,;DDX60L,stop_gained,p.Glu1034Ter,ENST00000260184,NM_001012967.2;DDX60L,stop_gained,p.Glu1034Ter,ENST00000505890,NM_001291510.1;DDX60L,stop_gained,p.Glu730Ter,ENST00000505863,; A ENST00000260184 Transcript stop_gained 3321/6754 3100/5121 1034/1706 E/* Gaa/Taa COSM5400835,COSM5400836 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 24/38 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 168406063 168406063 C A 1 0 0 0 0 0 1 0 0 4182 864 30 2 2 DDX60L 4 168406063 Nonsense_Mutation SNP C C3N-00203_T 1493350 168406063 21808492 148 11452 NEK1 0 . GRCh38 4 169599177 169599177 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.235G>T p.Val79Leu p.V79L ENST00000507142 5/36 226 183 43 228 228 0 strelka-varscan-mutect NEK1,missense_variant,p.Val79Leu,ENST00000439128,NM_012224.2;NEK1,missense_variant,p.Val79Leu,ENST00000507142,NM_001199397.1;NEK1,missense_variant,p.Val79Leu,ENST00000511633,NM_001199398.1;NEK1,missense_variant,p.Val79Leu,ENST00000510533,NM_001199400.1;NEK1,missense_variant,p.Val79Leu,ENST00000512193,NM_001199399.1;NEK1,stop_lost,p.Ter46TyrextTer1,ENST00000510108,;NEK1,upstream_gene_variant,,ENST00000509912,; A ENST00000507142 Transcript missense_variant 815/5556 235/3861 79/1286 V/L Gta/Tta 1 -1 NEK1 HGNC HGNC:7744 protein_coding YES CCDS56351.1 ENSP00000424757 Q96PY6 UPI00001D76CA NM_001199397.1 deleterious(0) 5/36 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF36,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1367769528 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 169599177 169599177 C A 1 0 0 0 0 1 0 0 0 10349 565 20 2 2 NEK1 4 169599177 Missense_Mutation SNP C C3N-00203_T 1193114 169599177 20615378 149 11453 FAT1 0 . GRCh38 4 186636069 186636069 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.4139T>A p.Ile1380Lys p.I1380K ENST00000441802 6/27 320 248 72 292 292 0 strelka-varscan-mutect FAT1,missense_variant,p.Ile1380Lys,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Ile1380Lys,ENST00000614102,; T ENST00000441802 Transcript missense_variant 4349/14786 4139/13767 1380/4588 I/K aTa/aAa 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0) 6/27 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 186636069 186636069 A T 1 0 0 0 0 1 0 0 0 5549 449 16 4 4 FAT1 4 186636069 Missense_Mutation SNP A C3N-00203_T 17036892 186636069 3578486 150 11454 ADAMTS16 0 . GRCh38 5 5209236 5209236 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.1595A>T p.Asp532Val p.D532V ENST00000274181 10/23 124 91 33 88 87 1 strelka-varscan-mutect ADAMTS16,missense_variant,p.Asp532Val,ENST00000274181,NM_139056.2;ADAMTS16,missense_variant,p.Asp532Val,ENST00000511368,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 1733/4979 1595/3675 532/1224 D/V gAc/gTc 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 10/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 5209236 5209236 A T 1 0 0 0 0 1 0 0 0 305 275 10 4 4 ADAMTS16 5 5209236 Missense_Mutation SNP A C3N-00203_T 5209236 176329023 151 11455 ADCY2 0 . GRCh38 5 7695795 7695795 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.913G>T p.Asp305Tyr p.D305Y ENST00000338316 6/25 217 178 39 220 220 0 strelka-varscan-mutect ADCY2,missense_variant,p.Asp305Tyr,ENST00000338316,NM_020546.2;ADCY2,missense_variant,p.Asp94Tyr,ENST00000515681,;ADCY2,downstream_gene_variant,,ENST00000513693,; T ENST00000338316 Transcript missense_variant 1002/6575 913/3276 305/1091 D/Y Gac/Tac 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0) 6/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 7695795 7695795 G T 1 0 0 0 0 1 0 0 0 338 1290 45 2 2 ADCY2 5 7695795 Missense_Mutation SNP G C3N-00203_T 2486559 7695795 173842464 152 11456 NPR3 0 . GRCh38 5 32782898 32782898 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.1296T>C p.= p.I432I ENST00000265074 6/8 99 73 26 86 86 0 strelka-varscan-mutect NPR3,synonymous_variant,p.=,ENST00000265074,NM_001204375.1;NPR3,synonymous_variant,p.=,ENST00000326958,NM_001204376.1;NPR3,synonymous_variant,p.=,ENST00000434067,;NPR3,synonymous_variant,p.=,ENST00000415167,NM_000908.3;NPR3,synonymous_variant,p.=,ENST00000509104,;NPR3,non_coding_transcript_exon_variant,,ENST00000506712,; C ENST00000265074 Transcript synonymous_variant 1639/7344 1296/1626 432/541 I atT/atC 1 1 NPR3 HGNC HGNC:7945 protein_coding YES CCDS56357.1 ENSP00000265074 P17342 UPI0000125B46 NM_001204375.1 6/8 hmmpanther:PTHR11920:SF302,hmmpanther:PTHR11920,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 32782898 32782898 T C 1 0 0 0 0 0 0 0 1 10652 1826 63 5 5 NPR3 5 32782898 Silent SNP T C3N-00203_T 25087103 32782898 148755361 153 11457 CAPSL 0 . GRCh38 5 35909933 35909933 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.458G>T p.Trp153Leu p.W153L ENST00000397367 4/5 230 191 39 209 209 0 strelka-varscan-mutect CAPSL,missense_variant,p.Trp153Leu,ENST00000397367,NM_144647.3;CAPSL,missense_variant,p.Trp153Leu,ENST00000397366,NM_001042625.1;CAPSL,missense_variant,p.Trp153Leu,ENST00000513623,;CAPSL,missense_variant,p.Trp153Leu,ENST00000514524,; A ENST00000397367 Transcript missense_variant 585/1004 458/627 153/208 W/L tGg/tTg 1 -1 CAPSL HGNC HGNC:28375 protein_coding YES CCDS3912.2 ENSP00000380524 Q8WWF8 UPI0000149B20 NM_144647.3 tolerated(0.37) 4/5 Gene3D:1.10.238.10,Pfam_domain:PF13499,hmmpanther:PTHR10891,hmmpanther:PTHR10891:SF551,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 35909933 35909933 C A 1 0 0 0 0 1 0 0 0 2334 595 21 2 2 CAPSL 5 35909933 Missense_Mutation SNP C C3N-00203_T 3127035 35909933 145628326 154 11458 NIPBL 0 . GRCh38 5 36958124 36958124 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.251G>C p.Gly84Ala p.G84A ENST00000282516 4/47 412 347 65 354 354 0 strelka-varscan-mutect NIPBL,missense_variant,p.Gly84Ala,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Gly84Ala,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000505998,;NIPBL,upstream_gene_variant,,ENST00000504430,; C ENST00000282516 Transcript missense_variant 750/10435 251/8415 84/2804 G/A gGc/gCc 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 tolerated(0.18) 4/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 36958124 36958124 G C 1 0 0 0 0 1 0 0 0 10463 1203 42 4 4 NIPBL 5 36958124 Missense_Mutation SNP G C3N-00203_T 1048191 36958124 144580135 155 11459 OSMR 0 . GRCh38 5 38903985 38903985 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.1095G>C p.Leu365Phe p.L365F ENST00000274276 8/18 305 247 58 320 320 0 strelka-varscan-mutect OSMR,missense_variant,p.Leu365Phe,ENST00000274276,NM_001323505.1,NM_001323506.1,NM_003999.2;OSMR,upstream_gene_variant,,ENST00000513831,; C ENST00000274276 Transcript missense_variant 1497/5539 1095/2940 365/979 L/F ttG/ttC 1 1 OSMR HGNC HGNC:8507 protein_coding YES CCDS3928.1 ENSP00000274276 Q99650 UPI000004CAC3 NM_001323505.1,NM_001323506.1,NM_003999.2 tolerated(0.05) 8/18 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF95,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 38903985 38903985 G C 1 0 0 0 0 1 0 0 0 11359 1368 48 4 4 OSMR 5 38903985 Missense_Mutation SNP G C3N-00203_T 1945861 38903985 142634274 156 11460 FYB 0 . GRCh38 5 39134350 39134350 + Splice_Site SNP C C T novel C3N-00203_T C3N-00203_N C C c.1706-1G>A p.X569_splice ENST00000512982 78 72 6 56 56 0 strelka-mutect FYB,splice_acceptor_variant,,ENST00000351578,NM_199335.3;FYB,splice_acceptor_variant,,ENST00000505428,NM_001465.4;FYB,splice_acceptor_variant,,ENST00000512982,NM_001243093.1;FYB,splice_acceptor_variant,,ENST00000515010,; T ENST00000512982 Transcript splice_acceptor_variant -/2747 1706/2520 569/839 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 8/18 HIGH 1 SNV 2 1 PASS . . 0 180 29 0 0 0 0 0 -12.42497 0.9141835 0 1 1 0 T 5 4 42 39134350 39134350 C T 1 0 0 0 0 0 0 1 0 5995 927 32 3 3 FYB 5 39134350 Splice_Site SNP C C3N-00203_T 230365 39134350 142403909 157 11461 HCN1 0 . GRCh38 5 45262205 45262205 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.2389G>A p.Val797Met p.V797M ENST00000303230 8/8 246 210 36 204 204 0 strelka-varscan-mutect HCN1,missense_variant,p.Val797Met,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; T ENST00000303230 Transcript missense_variant 2630/9885 2389/2673 797/890 V/M Gtg/Atg 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated_low_confidence(0.08) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 45262205 45262205 C T 1 0 0 0 0 1 0 0 0 6883 507 18 3 3 HCN1 5 45262205 Missense_Mutation SNP C C3N-00203_T 6127855 45262205 136276054 158 11462 HMGCR 0 . GRCh38 5 75351078 75351078 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.952A>G p.Met318Val p.M318V ENST00000287936 10/20 153 107 46 166 166 0 strelka-varscan-mutect HMGCR,missense_variant,p.Met318Val,ENST00000287936,NM_000859.2;HMGCR,missense_variant,p.Met318Val,ENST00000343975,NM_001130996.1;HMGCR,missense_variant,p.Met318Val,ENST00000511206,;HMGCR,non_coding_transcript_exon_variant,,ENST00000504466,;HMGCR,upstream_gene_variant,,ENST00000515776,;HMGCR,upstream_gene_variant,,ENST00000508070,; G ENST00000287936 Transcript missense_variant 1108/4585 952/2667 318/888 M/V Atg/Gtg 1 1 HMGCR HGNC HGNC:5006 protein_coding YES CCDS4027.1 ENSP00000287936 P04035 A0A024RAP2 UPI000012C9E2 NM_000859.2 tolerated(0.71) 10/20 hmmpanther:PTHR10572,hmmpanther:PTHR10572:SF2,TIGRFAM_domain:TIGR00920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 75351078 75351078 A G 1 0 0 0 0 1 0 0 0 7123 217 8 5 5 HMGCR 5 75351078 Missense_Mutation SNP A C3N-00203_T 30088873 75351078 106187181 159 11463 AC113404.1 0 . GRCh38 5 76173666 76173666 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.518G>A p.Gly173Glu p.G173E ENST00000631802 1/2 368 284 84 395 395 0 strelka-varscan-mutect AC113404.1,missense_variant,p.Gly173Glu,ENST00000631802,;AC113404.1,missense_variant,p.Gly154Glu,ENST00000506621,;SV2C,intron_variant,,ENST00000502798,NM_014979.3;SV2C,intron_variant,,ENST00000322285,NM_001297716.1;RP11-466P24.5,downstream_gene_variant,,ENST00000507884,; T ENST00000631802 Transcript missense_variant 666/1917 518/555 173/184 G/E gGg/gAg 1 -1 AC113404.1 Clone_based_ensembl_gene protein_coding YES ENSP00000488821 A6NIZ1 UPI0000140E7F tolerated(0.25) 1/2 PROSITE_profiles:PS51421,hmmpanther:PTHR24070 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 76173666 76173666 C T 1 0 0 0 0 1 0 0 0 140 623 22 3 3 AC113404.1 5 76173666 Missense_Mutation SNP C C3N-00203_T 822588 76173666 105364593 160 11464 POU5F2 0 . GRCh38 5 93741481 93741481 + Missense_Mutation SNP C C A rs753162634 C3N-00203_T C3N-00203_N C C c.83G>T p.Arg28Leu p.R28L ENST00000606183 1/1 118 77 41 106 105 1 strelka-varscan-mutect POU5F2,missense_variant,p.Arg28Leu,ENST00000606183,NM_153216.1;FAM172A,intron_variant,,ENST00000395965,NM_032042.5;FAM172A,intron_variant,,ENST00000505869,NM_001163418.1;FAM172A,intron_variant,,ENST00000509163,NM_001163417.1;FAM172A,intron_variant,,ENST00000509739,;RP11-185E12.2,upstream_gene_variant,,ENST00000606528,;FAM172A,intron_variant,,ENST00000502503,; A ENST00000606183 Transcript missense_variant 157/8418 83/987 28/328 R/L cGg/cTg rs753162634 1 -1 POU5F2 HGNC HGNC:26367 protein_coding YES CCDS59489.1 ENSP00000489796 Q8N7G0 UPI0000135E4C NM_153216.1 tolerated(0.06) 1/1 hmmpanther:PTHR11636:SF14,hmmpanther:PTHR11636 MODERATE SNV 1 PASS rs753162634 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 93741481 93741481 C A 1 0 0 0 0 1 0 0 0 12399 652 23 1 1 POU5F2 5 93741481 Missense_Mutation SNP C C3N-00203_T 17567815 93741481 87796778 161 11465 PRR16 0 . GRCh38 5 120686706 120686706 + Silent SNP G G C novel C3N-00203_T C3N-00203_N G G c.912G>C p.= p.V304V ENST00000407149 2/2 23 16 7 36 36 0 strelka-varscan-mutect PRR16,synonymous_variant,p.=,ENST00000379551,NM_016644.2;PRR16,synonymous_variant,p.=,ENST00000407149,NM_001300783.1;PRR16,synonymous_variant,p.=,ENST00000505123,NM_001308087.1;PRR16,synonymous_variant,p.=,ENST00000446965,;PRR16,downstream_gene_variant,,ENST00000509923,; C ENST00000407149 Transcript synonymous_variant 1121/1747 912/915 304/304 V gtG/gtC 1 1 PRR16 HGNC HGNC:29654 protein_coding YES CCDS75290.1 ENSP00000385118 Q569H4 UPI00004F9C36 NM_001300783.1 2/2 Pfam_domain:PF15252,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0 LOW 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -19.77197 1 1 1 1 0 C 2 2 42 120686706 120686706 G C 1 0 0 0 0 0 0 0 1 12725 1364 48 4 4 PRR16 5 120686706 Silent SNP G C3N-00203_T 26945225 120686706 60851553 162 11466 TGFBI 0 . GRCh38 5 136054775 136054775 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.1324G>C p.Asp442His p.D442H ENST00000442011 10/17 369 285 84 376 376 0 strelka-varscan-mutect TGFBI,missense_variant,p.Asp442His,ENST00000442011,NM_000358.2;TGFBI,missense_variant,p.Asp160His,ENST00000514554,;TGFBI,missense_variant,p.Asp186His,ENST00000604555,;TGFBI,missense_variant,p.Asp181His,ENST00000508767,;TGFBI,upstream_gene_variant,,ENST00000508076,;TGFBI,upstream_gene_variant,,ENST00000503087,;TGFBI,3_prime_UTR_variant,,ENST00000507018,;TGFBI,3_prime_UTR_variant,,ENST00000509485,;TGFBI,non_coding_transcript_exon_variant,,ENST00000515433,;TGFBI,non_coding_transcript_exon_variant,,ENST00000506699,;TGFBI,upstream_gene_variant,,ENST00000513497,;TGFBI,upstream_gene_variant,,ENST00000514242,;TGFBI,downstream_gene_variant,,ENST00000509749,; C ENST00000442011 Transcript missense_variant 1485/2804 1324/2052 442/683 D/H Gac/Cac 1 1 TGFBI HGNC HGNC:11771 protein_coding YES CCDS47266.1 ENSP00000416330 Q15582 A0A0S2Z4Q2 UPI0000000C6A NM_000358.2 tolerated(0.12) 10/17 Gene3D:2.30.180.10,Pfam_domain:PF02469,PIRSF_domain:PIRSF016553,PROSITE_profiles:PS50213,hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF82,SMART_domains:SM00554,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 136054775 136054775 G C 1 0 0 0 0 1 0 0 0 16253 942 33 4 4 TGFBI 5 136054775 Missense_Mutation SNP G C3N-00203_T 15368069 136054775 45483484 163 11467 PCDHA1 0 . GRCh38 5 140787161 140787161 + Missense_Mutation SNP G G C C3N-00203_T C3N-00203_N G G c.871G>C p.Glu291Gln p.E291Q ENST00000504120 1/4 86 62 24 106 106 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Glu291Gln,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Glu291Gln,ENST00000378133,NM_031410.2;PCDHA1,missense_variant,p.Glu291Gln,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; C ENST00000504120 Transcript missense_variant 871/5263 871/2853 291/950 E/Q Gaa/Caa COSM1219535,COSM1219536 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 tolerated_low_confidence(0.33) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999981 1 1 1 0 C 3 2 42 140787161 140787161 G C 1 0 0 0 0 1 0 0 0 11606 943 33 4 4 PCDHA1 5 140787161 Missense_Mutation SNP G C3N-00203_T 4732386 140787161 40751098 164 11468 CAMK2A 0 . GRCh38 5 150251995 150251995 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.585C>A p.Asp195Glu p.D195E ENST00000398376 8/19 163 111 52 158 157 1 strelka-varscan-mutect CAMK2A,missense_variant,p.Asp195Glu,ENST00000348628,NM_171825.2;CAMK2A,missense_variant,p.Asp195Glu,ENST00000398376,NM_015981.3;CAMK2A,downstream_gene_variant,,ENST00000515758,;CAMK2A,non_coding_transcript_exon_variant,,ENST00000508662,; T ENST00000398376 Transcript missense_variant 589/1493 585/1470 195/489 D/E gaC/gaA 1 -1 CAMK2A HGNC HGNC:1460 protein_coding YES CCDS43387.1 ENSP00000381412 Q9UQM7 A8K161 UPI0000161115 NM_015981.3 deleterious_low_confidence(0) 8/19 PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF226,hmmpanther:PTHR24347,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 150251995 150251995 G T 1 0 0 0 0 1 0 0 0 2290 1252 44 2 2 CAMK2A 5 150251995 Missense_Mutation SNP G C3N-00203_T 9464834 150251995 31286264 165 11469 ADAM19 0 . GRCh38 5 157488436 157488436 + Silent SNP G G T C3N-00203_T C3N-00203_N G G c.2379C>A p.= p.P793P ENST00000257527 21/23 76 60 16 92 92 0 strelka-varscan-mutect ADAM19,synonymous_variant,p.=,ENST00000257527,NM_033274.4;ADAM19,synonymous_variant,p.=,ENST00000517905,;ADAM19,synonymous_variant,p.=,ENST00000517374,;ADAM19,3_prime_UTR_variant,,ENST00000517951,; T ENST00000257527 Transcript synonymous_variant 2458/6481 2379/2757 793/918 P ccC/ccA COSM1143739,COSM5269846,COSM5269847,COSM591069 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 21/23 Low_complexity_(Seg):seg,hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 157488436 157488436 G T 1 0 0 0 0 0 0 0 1 284 1219 43 2 2 ADAM19 5 157488436 Silent SNP G C3N-00203_T 7236441 157488436 24049823 166 11470 GABRA1 0 . GRCh38 5 161854232 161854232 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.149T>A p.Leu50Gln p.L50Q ENST00000393943 3/10 240 189 51 306 306 0 strelka-varscan-mutect GABRA1,missense_variant,p.Leu50Gln,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Leu50Gln,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Leu65Gln,ENST00000638159,;GABRA1,missense_variant,p.Leu50Gln,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Leu50Gln,ENST00000638112,;GABRA1,missense_variant,p.Leu50Gln,ENST00000636573,;GABRA1,missense_variant,p.Leu50Gln,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Leu50Gln,ENST00000637827,;GABRA1,missense_variant,p.Leu50Gln,ENST00000635880,;GABRA1,missense_variant,p.Leu50Gln,ENST00000634335,;GABRA1,missense_variant,p.Leu71Gln,ENST00000522651,;GABRA1,missense_variant,p.Leu50Gln,ENST00000519621,;GABRA1,missense_variant,p.Leu50Gln,ENST00000521339,;GABRA1,downstream_gene_variant,,ENST00000635096,;GABRA1,downstream_gene_variant,,ENST00000637620,;GABRA1,stop_lost,p.Ter71LysextTer7,ENST00000636340,;GABRA1,missense_variant,p.Leu50Gln,ENST00000637044,; A ENST00000393943 Transcript missense_variant 932/4686 149/1371 50/456 L/Q cTa/cAa 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 deleterious(0) 3/10 Superfamily_domains:0038932,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 161854232 161854232 T A 1 0 0 0 0 1 0 0 0 6031 1522 53 4 4 GABRA1 5 161854232 Missense_Mutation SNP T C3N-00203_T 4365796 161854232 19684027 167 11471 ADAMTS2 0 . GRCh38 5 179137784 179137784 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.1936C>T p.His646Tyr p.H646Y ENST00000251582 12/22 273 228 45 166 166 0 strelka-varscan-mutect ADAMTS2,missense_variant,p.His646Tyr,ENST00000251582,NM_014244.4; A ENST00000251582 Transcript missense_variant 2038/6754 1936/3636 646/1211 H/Y Cac/Tac 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 tolerated(1) 12/22 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 179137784 179137784 G A 1 0 0 0 0 1 0 0 0 309 1348 47 3 3 ADAMTS2 5 179137784 Missense_Mutation SNP G C3N-00203_T 17283552 179137784 2400475 168 11472 BMP6 0 . GRCh38 6 7862409 7862409 + Missense_Mutation SNP C C A rs778340100 C3N-00203_T C3N-00203_N C C c.1115C>A p.Thr372Asn p.T372N ENST00000283147 4/7 722 452 270 415 415 0 strelka-varscan-mutect BMP6,missense_variant,p.Thr372Asn,ENST00000283147,NM_001718.4; A ENST00000283147 Transcript missense_variant 1274/2780 1115/1542 372/513 T/N aCc/aAc rs778340100 1 1 BMP6 HGNC HGNC:1073 protein_coding YES CCDS4503.1 ENSP00000283147 P22004 UPI0000126A2D NM_001718.4 tolerated(0.05) 4/7 Low_complexity_(Seg):seg,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF137 MODERATE 1 SNV 1 1 PASS rs778340100 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 7862409 7862409 C A 1 0 0 0 0 1 0 0 0 1619 507 18 2 2 BMP6 6 7862409 Missense_Mutation SNP C C3N-00203_T 7862409 162943570 169 11473 HIST1H2AA 0 . GRCh38 6 25726431 25726431 + Missense_Mutation SNP G G A C3N-00203_T C3N-00203_N G G c.97C>T p.Arg33Cys p.R33C ENST00000297012 1/1 236 195 41 182 182 0 strelka-varscan HIST1H2AA,missense_variant,p.Arg33Cys,ENST00000297012,NM_170745.3;HIST1H2BA,upstream_gene_variant,,ENST00000274764,NM_170610.2; A ENST00000297012 Transcript missense_variant 97/396 97/396 33/131 R/C Cgt/Tgt COSM5404923 1 -1 HIST1H2AA HGNC HGNC:18729 protein_coding YES CCDS4562.1 ENSP00000297012 Q96QV6 UPI0000073CDD NM_170745.3 deleterious_low_confidence(0.03) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00620,hmmpanther:PTHR23430,SMART_domains:SM00414,Superfamily_domains:SSF47113 1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 25726431 25726431 G A 1 0 0 0 0 1 0 0 0 7016 1058 37 1 1 HIST1H2AA 6 25726431 Missense_Mutation SNP G C3N-00203_T 17864022 25726431 145079548 170 11474 ZNF311 0 . GRCh38 6 28995907 28995907 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.1095G>T p.= p.G365G ENST00000377179 7/7 274 211 63 289 289 0 strelka-varscan ZNF311,synonymous_variant,p.=,ENST00000377179,NM_001010877.2;ZNF311,non_coding_transcript_exon_variant,,ENST00000483450,; A ENST00000377179 Transcript synonymous_variant 1608/2730 1095/2001 365/666 G ggG/ggT 1 -1 ZNF311 HGNC HGNC:13847 protein_coding YES CCDS34357.1 ENSP00000366384 Q5JNZ3 UPI000020D71E NM_001010877.2 7/7 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF273,SMART_domains:SM00355 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 28995907 28995907 C A 1 0 0 0 0 0 0 0 1 18409 842 30 2 2 ZNF311 6 28995907 Silent SNP C C3N-00203_T 3269476 28995907 141810072 171 11475 OR2W1 0 . GRCh38 6 29044864 29044864 + Nonsense_Mutation SNP G G C C3N-00203_T C3N-00203_N G G c.312C>G p.Tyr104Ter p.Y104* ENST00000377175 1/1 224 178 46 216 216 0 strelka-varscan OR2W1,stop_gained,p.Tyr104Ter,ENST00000377175,NM_030903.3;XXbac-BPG258E24.10,intron_variant,,ENST00000623334,;XXbac-BPG258E24.10,intron_variant,,ENST00000623946,; C ENST00000377175 Transcript stop_gained 377/1028 312/963 104/320 Y/* taC/taG COSM3623893 1 -1 OR2W1 HGNC HGNC:8281 protein_coding YES CCDS4656.1 ENSP00000366380 Q9Y3N9 A0A126GVA1 UPI000003FF8A NM_030903.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF169,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 42 29044864 29044864 G C 1 0 0 0 0 0 1 0 0 11110 1372 48 4 4 OR2W1 6 29044864 Nonsense_Mutation SNP G C3N-00203_T 48957 29044864 141761115 172 11476 UHRF1BP1 0 . GRCh38 6 34857437 34857437 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1540G>T p.Glu514Ter p.E514* ENST00000192788 12/21 275 213 62 177 176 1 strelka-varscan-mutect UHRF1BP1,stop_gained,p.Glu514Ter,ENST00000192788,NM_017754.3;UHRF1BP1,stop_gained,p.Glu514Ter,ENST00000452449,; T ENST00000192788 Transcript stop_gained 1711/9570 1540/4323 514/1440 E/* Gag/Tag 1 1 UHRF1BP1 HGNC HGNC:21216 protein_coding YES CCDS43455.1 ENSP00000192788 Q6BDS2 UPI00001B654C NM_017754.3 12/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF15 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 34857437 34857437 G T 1 0 0 0 0 0 1 0 0 17492 943 33 2 2 UHRF1BP1 6 34857437 Nonsense_Mutation SNP G C3N-00203_T 5812573 34857437 135948542 173 11477 CLPS 0 . GRCh38 6 35797253 35797253 + Silent SNP G G C novel C3N-00203_T C3N-00203_N G G c.36C>G p.= p.L12L ENST00000259938 1/3 253 232 21 191 191 0 strelka-varscan-mutect CLPS,synonymous_variant,p.=,ENST00000259938,NM_001832.3;CLPS,synonymous_variant,p.=,ENST00000616014,NM_001252598.1;CLPS,upstream_gene_variant,,ENST00000622413,NM_001252597.1;CLPSL1,downstream_gene_variant,,ENST00000428710,; C ENST00000259938 Transcript synonymous_variant 59/526 36/339 12/112 L ctC/ctG 1 -1 CLPS HGNC HGNC:2085 protein_coding YES CCDS4811.1 ENSP00000259938 P04118 UPI0000127E78 NM_001832.3 1/3 hmmpanther:PTHR10041,hmmpanther:PTHR10041:SF8,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 35797253 35797253 G C 1 0 0 0 0 0 0 0 1 3323 929 33 4 4 CLPS 6 35797253 Silent SNP G C3N-00203_T 939816 35797253 135008726 174 11478 CPNE5 0 . GRCh38 6 36794616 36794616 + Silent SNP G G T C3N-00203_T C3N-00203_N G G c.438C>A p.= p.G146G ENST00000244751 7/21 357 285 72 251 251 0 strelka-varscan-mutect CPNE5,synonymous_variant,p.=,ENST00000244751,NM_020939.1;CPNE5,synonymous_variant,p.=,ENST00000633136,;CPNE5,synonymous_variant,p.=,ENST00000633280,; T ENST00000244751 Transcript synonymous_variant 1063/3897 438/1782 146/593 G ggC/ggA COSM4674392 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 7/21 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 36794616 36794616 G T 1 0 0 0 0 0 0 0 1 3610 1306 46 2 2 CPNE5 6 36794616 Silent SNP G C3N-00203_T 997363 36794616 134011363 175 11479 DAAM2 0 . GRCh38 6 39865016 39865016 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.370G>C p.Glu124Gln p.E124Q ENST00000398904 5/25 336 293 43 194 193 1 strelka-varscan-mutect DAAM2,missense_variant,p.Glu124Gln,ENST00000538976,NM_015345.3;DAAM2,missense_variant,p.Glu124Gln,ENST00000398904,;DAAM2,missense_variant,p.Glu124Gln,ENST00000274867,NM_001201427.1;DAAM2,missense_variant,p.Glu124Gln,ENST00000633794,;DAAM2,downstream_gene_variant,,ENST00000405961,;DAAM2,3_prime_UTR_variant,,ENST00000494405,;DAAM2,non_coding_transcript_exon_variant,,ENST00000491083,;DAAM2,downstream_gene_variant,,ENST00000475489,;DAAM2,upstream_gene_variant,,ENST00000632657,; C ENST00000398904 Transcript missense_variant 552/6224 370/3207 124/1068 E/Q Gag/Cag 1 1 DAAM2 HGNC HGNC:18143 protein_coding YES CCDS56426.1 ENSP00000381876 Q86T65 UPI000020DC88 tolerated(0.14) 5/25 PROSITE_profiles:PS51232,Gene3D:1.25.10.10,Pfam_domain:PF06371,SMART_domains:SM01140,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 39865016 39865016 G C 1 0 0 0 0 1 0 0 0 4017 1175 41 4 4 DAAM2 6 39865016 Missense_Mutation SNP G C3N-00203_T 3070400 39865016 130940963 176 11480 PTK7 0 . GRCh38 6 43143524 43143524 + Missense_Mutation SNP G G T rs534728368 C3N-00203_T C3N-00203_N G G c.2179G>T p.Val727Leu p.V727L ENST00000481273 14/20 497 403 94 276 276 0 strelka-varscan-mutect PTK7,missense_variant,p.Val719Leu,ENST00000230419,NM_002821.4;PTK7,missense_variant,p.Val679Leu,ENST00000345201,NM_152880.3;PTK7,missense_variant,p.Val663Leu,ENST00000352931,NM_152882.3;PTK7,missense_variant,p.Val589Leu,ENST00000349241,NM_152881.3;PTK7,missense_variant,p.Val727Leu,ENST00000481273,NM_001270398.1;PTK7,intron_variant,,ENST00000489707,;PTK7,upstream_gene_variant,,ENST00000473339,;PTK7,downstream_gene_variant,,ENST00000481946,;PTK7,missense_variant,p.Val719Leu,ENST00000230418,;PTK7,3_prime_UTR_variant,,ENST00000470019,;PTK7,3_prime_UTR_variant,,ENST00000497957,;PTK7,3_prime_UTR_variant,,ENST00000494146,;PTK7,3_prime_UTR_variant,,ENST00000461100,;PTK7,non_coding_transcript_exon_variant,,ENST00000487673,;PTK7,non_coding_transcript_exon_variant,,ENST00000493339,;PTK7,upstream_gene_variant,,ENST00000461389,;PTK7,downstream_gene_variant,,ENST00000470471,; T ENST00000481273 Transcript missense_variant 2249/3436 2179/3237 727/1078 V/L Gtg/Ttg rs534728368 1 1 PTK7 HGNC HGNC:9618 protein_coding YES CCDS59021.1 ENSP00000418754 Q13308 UPI0001B79423 NM_001270398.1 deleterious(0.01) 14/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR26391,hmmpanther:PTHR26391:SF15,Gene3D:3.30.200.20 MODERATE 1 SNV 2 1 PASS rs534728368 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 43143524 43143524 G T 1 0 0 0 0 1 0 0 0 12921 1145 40 1 1 PTK7 6 43143524 Missense_Mutation SNP G C3N-00203_T 3278508 43143524 127662455 177 11481 CRISP2 0 . GRCh38 6 49698458 49698458 + Missense_Mutation SNP C C G rs762980390 C3N-00203_T C3N-00203_N C C c.321G>C p.Trp107Cys p.W107C ENST00000339139 7/10 185 145 40 177 177 0 strelka-varscan-mutect CRISP2,missense_variant,p.Trp107Cys,ENST00000618917,;CRISP2,missense_variant,p.Trp107Cys,ENST00000339139,NM_001142417.2,NM_001142408.2,NM_003296.3;CRISP2,missense_variant,p.Trp107Cys,ENST00000616725,NM_001142407.2,NM_001261822.1,NM_001142435.2; G ENST00000339139 Transcript missense_variant 558/1382 321/732 107/243 W/C tgG/tgC rs762980390 1 -1 CRISP2 HGNC HGNC:12024 protein_coding YES CCDS4928.1 ENSP00000339155 P16562 A0A024RD74 UPI000013728C NM_001142417.2,NM_001142408.2,NM_003296.3 deleterious(0) 7/10 hmmpanther:PTHR10334:SF228,hmmpanther:PTHR10334,Gene3D:3.40.33.10,Pfam_domain:PF00188,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS rs762980390 . 0 207 0 3 0 0 0 0 -20 0.999997 1 1 1 0 G 3 3 42 49698458 49698458 C G 1 0 0 0 0 1 0 0 0 3681 508 18 4 4 CRISP2 6 49698458 Missense_Mutation SNP C C3N-00203_T 6554934 49698458 121107521 178 11482 KLHL31 0 . GRCh38 6 53651817 53651817 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.1686G>T p.= p.A562A ENST00000370905 3/3 548 358 190 323 322 1 strelka-varscan-mutect KLHL31,synonymous_variant,p.=,ENST00000370905,NM_001003760.4;KLHL31,synonymous_variant,p.=,ENST00000407079,; A ENST00000370905 Transcript synonymous_variant 1827/5743 1686/1905 562/634 A gcG/gcT 1 -1 KLHL31 HGNC HGNC:21353 protein_coding YES CCDS34478.1 ENSP00000359942 Q9H511 UPI000006D624 NM_001003760.4 3/3 hmmpanther:PTHR24412:SF247,hmmpanther:PTHR24412,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 53651817 53651817 C A 1 0 0 0 0 0 0 0 1 8250 755 27 1 1 KLHL31 6 53651817 Silent SNP C C3N-00203_T 3953359 53651817 117154162 179 11483 RIMS1 0 . GRCh38 6 72400641 72400641 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.5006T>A p.Leu1669His p.L1669H ENST00000521978 34/34 159 103 56 196 195 1 strelka-varscan RIMS1,missense_variant,p.Leu1518His,ENST00000264839,;RIMS1,missense_variant,p.Leu1669His,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Leu1458His,ENST00000491071,;RIMS1,missense_variant,p.Leu1319His,ENST00000520567,;RIMS1,missense_variant,p.Leu1452His,ENST00000517960,;RIMS1,missense_variant,p.Leu1348His,ENST00000518273,;RIMS1,missense_variant,p.Leu1268His,ENST00000522291,;RIMS1,missense_variant,p.Leu989His,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Leu1015His,ENST00000517433,;RIMS1,missense_variant,p.Leu794His,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Leu803His,ENST00000517827,NM_001168410.1;RIMS1,missense_variant,p.Leu737His,ENST00000425662,NM_001168409.1;RIMS1,missense_variant,p.Leu587His,ENST00000522211,;RIMS1,missense_variant,p.Leu717His,ENST00000370420,;RIMS1,missense_variant,p.Leu196His,ENST00000414192,NM_001168411.1;RIMS1,downstream_gene_variant,,ENST00000453976,;RIMS1,non_coding_transcript_exon_variant,,ENST00000431478,;RIMS1,non_coding_transcript_exon_variant,,ENST00000463023,; A ENST00000521978 Transcript missense_variant 5006/5079 5006/5079 1669/1692 L/H cTc/cAc 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious(0) 34/34 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 72400641 72400641 T A 1 0 0 0 0 1 0 0 0 13542 1551 54 4 4 RIMS1 6 72400641 Missense_Mutation SNP T C3N-00203_T 18748824 72400641 98405338 180 11484 MYO6 0 . GRCh38 6 75891292 75891292 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.2932G>A p.Glu978Lys p.E978K ENST00000369977 27/35 318 253 65 292 292 0 strelka-varscan MYO6,missense_variant,p.Glu978Lys,ENST00000369981,;MYO6,missense_variant,p.Glu978Lys,ENST00000369985,NM_001300899.1;MYO6,missense_variant,p.Glu978Lys,ENST00000369977,NM_004999.3;MYO6,missense_variant,p.Glu978Lys,ENST00000369975,;MYO6,missense_variant,p.Glu978Lys,ENST00000627432,;MYO6,missense_variant,p.Glu978Lys,ENST00000615563,;MYO6,missense_variant,p.Glu41Lys,ENST00000430435,; A ENST00000369977 Transcript missense_variant 3071/5597 2932/3858 978/1285 E/K Gaa/Aaa 1 1 MYO6 HGNC HGNC:7605 protein_coding YES CCDS34487.1 ENSP00000358994 Q9UM54 UPI00000727CF NM_004999.3 tolerated(0.25) 27/35 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF483 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 75891292 75891292 G A 1 0 0 0 0 1 0 0 0 10082 1291 45 3 3 MYO6 6 75891292 Missense_Mutation SNP G C3N-00203_T 3490651 75891292 94914687 181 11485 SNAP91 0 . GRCh38 6 83605698 83605698 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.1128C>A p.= p.A376A ENST00000439399 14/30 246 177 69 242 241 1 strelka-varscan SNAP91,synonymous_variant,p.=,ENST00000521485,;SNAP91,synonymous_variant,p.=,ENST00000439399,NM_014841.2;SNAP91,synonymous_variant,p.=,ENST00000369694,NM_001242792.1;SNAP91,synonymous_variant,p.=,ENST00000195649,NM_001256718.1;SNAP91,synonymous_variant,p.=,ENST00000521743,;SNAP91,synonymous_variant,p.=,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,synonymous_variant,p.=,ENST00000520213,NM_001242794.1;SNAP91,synonymous_variant,p.=,ENST00000521931,;SNAP91,synonymous_variant,p.=,ENST00000369691,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,; T ENST00000439399 Transcript synonymous_variant 1445/4452 1128/2724 376/907 A gcC/gcA 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 14/30 Low_complexity_(Seg):seg,hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 83605698 83605698 G T 1 0 0 0 0 0 0 0 1 15154 1335 47 2 2 SNAP91 6 83605698 Silent SNP G C3N-00203_T 7714406 83605698 87200281 182 11486 ZNF292 0 . GRCh38 6 87255305 87255305 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.1676A>T p.His559Leu p.H559L ENST00000369577 8/8 265 199 66 309 308 1 strelka-varscan ZNF292,missense_variant,p.His559Leu,ENST00000369577,NM_015021.1;ZNF292,missense_variant,p.His554Leu,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,; T ENST00000369577 Transcript missense_variant 1719/10610 1676/8172 559/2723 H/L cAt/cTt 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 deleterious(0) 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14,SMART_domains:SM00355 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 87255305 87255305 A T 1 0 0 0 0 1 0 0 0 18402 217 8 4 4 ZNF292 6 87255305 Missense_Mutation SNP A C3N-00203_T 3649607 87255305 83550674 183 11487 GPRC6A 0 . GRCh38 6 116829005 116829005 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.9C>G p.Phe3Leu p.F3L ENST00000310357 1/6 64 43 21 68 68 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Phe3Leu,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Phe3Leu,ENST00000368549,NM_001286355.1;GPRC6A,missense_variant,p.Phe3Leu,ENST00000530250,NM_001286354.1; C ENST00000310357 Transcript missense_variant 31/2860 9/2781 3/926 F/L ttC/ttG 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated_low_confidence(1) 1/6 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1347039890 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 116829005 116829005 G C 1 0 0 0 0 1 0 0 0 6607 933 33 4 4 GPRC6A 6 116829005 Missense_Mutation SNP G C3N-00203_T 29573700 116829005 53976974 184 11488 TBC1D32 0 . GRCh38 6 121112530 121112530 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.3299T>A p.Leu1100His p.L1100H ENST00000398212 29/32 152 110 42 157 157 0 strelka-varscan-mutect TBC1D32,missense_variant,p.Leu1141His,ENST00000275159,;TBC1D32,missense_variant,p.Leu1100His,ENST00000398212,NM_152730.5;TBC1D32,non_coding_transcript_exon_variant,,ENST00000398197,;TBC1D32,non_coding_transcript_exon_variant,,ENST00000368464,;TBC1D32,3_prime_UTR_variant,,ENST00000464622,;TBC1D32,3_prime_UTR_variant,,ENST00000509492,; T ENST00000398212 Transcript missense_variant 3349/3824 3299/3774 1100/1257 L/H cTt/cAt 1 -1 TBC1D32 HGNC HGNC:21485 protein_coding YES CCDS43501.1 ENSP00000381270 Q96NH3 UPI0000E67203 NM_152730.5 deleterious(0) 29/32 Pfam_domain:PF14961,hmmpanther:PTHR13465,hmmpanther:PTHR13465:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 121112530 121112530 A T 1 0 0 0 0 1 0 0 0 16022 72 3 4 4 TBC1D32 6 121112530 Missense_Mutation SNP A C3N-00203_T 4283525 121112530 49693449 185 11489 PTPRK 0 . GRCh38 6 127998764 127998764 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.2683C>G p.Leu895Val p.L895V ENST00000532331 18/33 63 45 18 55 55 0 strelka-varscan-mutect PTPRK,missense_variant,p.Leu879Val,ENST00000368226,NM_002844.3;PTPRK,missense_variant,p.Leu879Val,ENST00000368213,NM_001135648.2;PTPRK,missense_variant,p.Leu895Val,ENST00000532331,NM_001291981.1;PTPRK,missense_variant,p.Leu891Val,ENST00000368210,;PTPRK,missense_variant,p.Leu905Val,ENST00000368207,;PTPRK,missense_variant,p.Leu878Val,ENST00000368215,NM_001291984.1;PTPRK,missense_variant,p.Leu172Val,ENST00000415046,;PTPRK,missense_variant,p.Leu138Val,ENST00000415055,;PTPRK,downstream_gene_variant,,ENST00000524481,;PTPRK,downstream_gene_variant,,ENST00000531050,; C ENST00000532331 Transcript missense_variant 2801/5757 2683/4389 895/1462 L/V Ctc/Gtc 1 -1 PTPRK HGNC HGNC:9674 protein_coding YES CCDS78179.1 ENSP00000432973 Q15262 UPI000189A90C NM_001291981.1 deleterious(0.01) 18/33 hmmpanther:PTHR19134:SF209,hmmpanther:PTHR19134,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 127998764 127998764 G C 1 0 0 0 0 1 0 0 0 12959 942 33 4 4 PTPRK 6 127998764 Missense_Mutation SNP G C3N-00203_T 6886234 127998764 42807215 186 11490 TMEM200A 0 . GRCh38 6 130441007 130441008 + Frame_Shift_Ins INS - - C novel C3N-00203_T C3N-00203_N - - c.586dupC p.Gln196ProfsTer35 p.Q196Pfs*35 ENST00000392429 2/2 113 81 32 149 149 0 sindel-varindel-pindel TMEM200A,frameshift_variant,p.Gln196ProfsTer35,ENST00000392429,NM_052913.2;TMEM200A,frameshift_variant,p.Gln196ProfsTer35,ENST00000296978,NM_001258277.1;TMEM200A,frameshift_variant,p.Gln196ProfsTer35,ENST00000545622,NM_001258278.1;TMEM200A,frameshift_variant,p.Gln196ProfsTer35,ENST00000617887,NM_001258276.1; C ENST00000392429 Transcript frameshift_variant 2963-2964/5017 585-586/1476 195-196/491 -/X -/C 1 1 TMEM200A HGNC HGNC:21075 protein_coding YES CCDS5140.1 ENSP00000376224 Q86VY9 A8K2A1 UPI000000DA85 NM_052913.2 2/2 hmmpanther:PTHR31815:SF0,hmmpanther:PTHR31815 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 42 130441007 130441007 - C 1 0 1 1 0 0 0 0 0 16562 40 2 0 0 TMEM200A 6 130441007 Frame_Shift_Ins INS - C3N-00203_T 2442243 130441007 40364972 187 11491 TMEM200A 0 . GRCh38 6 130441874 130441874 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1452G>T p.Arg484Ser p.R484S ENST00000392429 2/2 62 47 15 81 80 1 strelka-varscan TMEM200A,missense_variant,p.Arg484Ser,ENST00000392429,NM_052913.2;TMEM200A,missense_variant,p.Arg484Ser,ENST00000296978,NM_001258277.1;TMEM200A,missense_variant,p.Arg484Ser,ENST00000545622,NM_001258278.1;TMEM200A,missense_variant,p.Arg484Ser,ENST00000617887,NM_001258276.1; T ENST00000392429 Transcript missense_variant 3830/5017 1452/1476 484/491 R/S agG/agT 1 1 TMEM200A HGNC HGNC:21075 protein_coding YES CCDS5140.1 ENSP00000376224 Q86VY9 A8K2A1 UPI000000DA85 NM_052913.2 deleterious_low_confidence(0) 2/2 hmmpanther:PTHR31815:SF0,hmmpanther:PTHR31815 MODERATE 1 SNV 1 1 PASS . . 0 193 15 2 0 0 0 0 -20 0.9982317 1 1 1 0 T 3 4 42 130441874 130441874 G T 1 0 0 0 0 1 0 0 0 16562 1223 43 2 2 TMEM200A 6 130441874 Missense_Mutation SNP G C3N-00203_T 867 130441874 40364105 188 11492 ADGB 0 . GRCh38 6 146721406 146721406 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.1996T>A p.Ser666Thr p.S666T ENST00000397944 17/36 98 68 30 85 84 1 strelka-varscan ADGB,missense_variant,p.Ser666Thr,ENST00000397944,NM_024694.3;ADGB,missense_variant,p.Ser86Thr,ENST00000480328,;ADGB,3_prime_UTR_variant,,ENST00000493950,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,; A ENST00000397944 Transcript missense_variant 2072/5325 1996/5004 666/1667 S/T Tca/Aca 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 tolerated(0.57) 17/36 hmmpanther:PTHR10183:SF304,hmmpanther:PTHR10183 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 146721406 146721406 T A 1 0 0 0 0 1 0 0 0 351 1565 54 4 4 ADGB 6 146721406 Missense_Mutation SNP T C3N-00203_T 16279532 146721406 24084573 189 11493 ADGB 0 . GRCh38 6 146763945 146763945 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.3595C>A p.Gln1199Lys p.Q1199K ENST00000397944 28/36 123 92 31 132 132 0 strelka-varscan ADGB,missense_variant,p.Gln1199Lys,ENST00000397944,NM_024694.3;ADGB,intron_variant,,ENST00000367490,;ADGB,3_prime_UTR_variant,,ENST00000493950,;ADGB,intron_variant,,ENST00000480328,; A ENST00000397944 Transcript missense_variant 3671/5325 3595/5004 1199/1667 Q/K Caa/Aaa 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 tolerated(0.82) 28/36 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 146763945 146763945 C A 1 0 0 0 0 1 0 0 0 351 711 25 2 2 ADGB 6 146763945 Missense_Mutation SNP C C3N-00203_T 42539 146763945 24042034 190 11494 TCP10 0 . GRCh38 6 167376051 167376051 + Silent SNP C C A rs781755099 C3N-00203_T C3N-00203_N C C c.603G>T p.= p.P201P ENST00000397829 6/8 161 121 40 159 159 0 strelka-varscan TCP10,synonymous_variant,p.=,ENST00000366827,;TCP10,synonymous_variant,p.=,ENST00000617120,;TCP10,synonymous_variant,p.=,ENST00000397829,NM_004610.3;TCP10,3_prime_UTR_variant,,ENST00000460930,;TCP10,downstream_gene_variant,,ENST00000476779,;TCP10,non_coding_transcript_exon_variant,,ENST00000508373,;TCP10,non_coding_transcript_exon_variant,,ENST00000463894,;TCP10,upstream_gene_variant,,ENST00000514083,;TCP10,downstream_gene_variant,,ENST00000491085,; A ENST00000397829 Transcript synonymous_variant 771/2141 603/981 201/326 P ccG/ccT rs781755099 1 -1 TCP10 HGNC HGNC:11656 protein_coding YES CCDS43527.1 ENSP00000380929 D1MPS5 UPI0000D820CE NM_004610.3 6/8 hmmpanther:PTHR10331 LOW 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -20 0.9987225 1 1 1 0 A 2 1 42 167376051 167376051 C A 1 0 0 0 0 0 0 0 1 16117 755 27 1 1 TCP10 6 167376051 Silent SNP C C3N-00203_T 20612106 167376051 3429928 191 11495 TTYH3 0 . GRCh38 7 2656128 2656128 + Missense_Mutation SNP A A C novel C3N-00203_T C3N-00203_N A A c.1057A>C p.Thr353Pro p.T353P ENST00000258796 10/14 150 132 18 95 94 1 strelka-varscan-mutect TTYH3,missense_variant,p.Thr353Pro,ENST00000258796,NM_025250.2;TTYH3,missense_variant,p.Thr321Pro,ENST00000407643,;TTYH3,missense_variant,p.Thr182Pro,ENST00000403167,;TTYH3,missense_variant,p.Thr13Pro,ENST00000429448,;TTYH3,non_coding_transcript_exon_variant,,ENST00000498454,; C ENST00000258796 Transcript missense_variant 1262/4840 1057/1572 353/523 T/P Acg/Ccg 1 1 TTYH3 HGNC HGNC:22222 protein_coding YES CCDS34588.1 ENSP00000258796 Q9C0H2 A0A024R816 UPI000020E9F9 NM_025250.2 deleterious(0) 10/14 Pfam_domain:PF04906,hmmpanther:PTHR12424,hmmpanther:PTHR12424:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 2656128 2656128 A C 1 0 0 0 0 1 0 0 0 17251 159 6 5 5 TTYH3 7 2656128 Missense_Mutation SNP A C3N-00203_T 2656128 156689845 192 11496 SDK1 0 . GRCh38 7 4049444 4049444 + Missense_Mutation SNP G G T rs774536015 C3N-00203_T C3N-00203_N G G c.2699G>T p.Gly900Val p.G900V ENST00000404826 18/45 247 182 65 173 171 2 strelka-varscan-mutect SDK1,missense_variant,p.Gly900Val,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Gly900Val,ENST00000615806,;SDK1,missense_variant,p.Gly900Val,ENST00000389531,; T ENST00000404826 Transcript missense_variant 2838/10397 2699/6642 900/2213 G/V gGc/gTc rs774536015 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0) 18/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs774536015 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 4049444 4049444 G T 1 0 0 0 0 1 0 0 0 14243 1203 42 2 2 SDK1 7 4049444 Missense_Mutation SNP G C3N-00203_T 1393316 4049444 155296529 193 11497 HOXA2 0 . GRCh38 7 27102301 27102301 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.200A>G p.His67Arg p.H67R ENST00000222718 1/2 279 216 63 222 222 0 strelka-varscan HOXA2,missense_variant,p.His67Arg,ENST00000222718,NM_006735.3;HOXA3,downstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA3,downstream_gene_variant,,ENST00000396352,NM_030661.4;HOXA3,downstream_gene_variant,,ENST00000317201,;HOTAIRM1,downstream_gene_variant,,ENST00000428939,;HOTAIRM1,downstream_gene_variant,,ENST00000429611,;HOTAIRM1,downstream_gene_variant,,ENST00000434063,;HOTAIRM1,downstream_gene_variant,,ENST00000593300,;HOTAIRM1,downstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,downstream_gene_variant,,ENST00000616712,;HOTAIRM1_5,downstream_gene_variant,,ENST00000619311,;HOTAIRM1_4,downstream_gene_variant,,ENST00000617934,;HOTAIRM1_3,downstream_gene_variant,,ENST00000619974,;HOXA2,non_coding_transcript_exon_variant,,ENST00000612779,; C ENST00000222718 Transcript missense_variant 511/1814 200/1131 67/376 H/R cAc/cGc 1 -1 HOXA2 HGNC HGNC:5103 protein_coding YES CCDS5403.1 ENSP00000222718 O43364 UPI0000049C49 NM_006735.3 tolerated(0.12) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF179 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 27102301 27102301 T C 1 0 0 0 0 1 0 0 0 7186 1696 59 5 5 HOXA2 7 27102301 Missense_Mutation SNP T C3N-00203_T 23052857 27102301 132243672 194 11498 GLI3 0 . GRCh38 7 42076810 42076810 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.415G>T p.Ala139Ser p.A139S ENST00000395925 4/15 387 300 87 317 317 0 strelka-varscan GLI3,missense_variant,p.Ala139Ser,ENST00000395925,NM_000168.5;GLI3,missense_variant,p.Ala139Ser,ENST00000448703,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,; A ENST00000395925 Transcript missense_variant 500/8208 415/4743 139/1580 A/S Gcc/Tcc COSM3881029 1 -1 GLI3 HGNC HGNC:4319 protein_coding YES CCDS5465.1 ENSP00000379258 P10071 UPI000020EE4C NM_000168.5 tolerated(0.09) 4/15 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF5 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 42076810 42076810 C A 1 0 0 0 0 1 0 0 0 6317 710 25 2 2 GLI3 7 42076810 Missense_Mutation SNP C C3N-00203_T 14974509 42076810 117269163 195 11499 PSMA2 0 . GRCh38 7 42932142 42932142 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.17A>G p.Tyr6Cys p.Y6C ENST00000223321 1/8 406 329 77 306 306 0 strelka-varscan PSMA2,missense_variant,p.Tyr6Cys,ENST00000223321,NM_002787.4;PSMA2,missense_variant,p.Tyr6Cys,ENST00000445517,;MRPL32,upstream_gene_variant,,ENST00000223324,NM_031903.2;MRPL32,upstream_gene_variant,,ENST00000496564,;PSMA2,missense_variant,p.Tyr6Cys,ENST00000411875,;RP11-111K18.1,missense_variant,p.Tyr6Cys,ENST00000442788,;PSMA2,missense_variant,p.Tyr5Cys,ENST00000436986,;RP11-111K18.1,missense_variant,p.Tyr6Cys,ENST00000433579,;MRPL32,upstream_gene_variant,,ENST00000432845,;PSMA2,upstream_gene_variant,,ENST00000457444,;MRPL32,upstream_gene_variant,,ENST00000413995,; C ENST00000223321 Transcript missense_variant 82/1487 17/705 6/234 Y/C tAc/tGc 1 -1 PSMA2 HGNC HGNC:9531 protein_coding YES CCDS5467.1 ENSP00000223321 P25787 UPI000004D00F NM_002787.4 deleterious(0) 1/8 hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF16,PROSITE_patterns:PS00388,Gene3D:3.60.20.10,Pfam_domain:PF10584,SMART_domains:SM00948,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 42932142 42932142 T C 1 0 0 0 0 1 0 0 0 12818 1638 57 5 5 PSMA2 7 42932142 Missense_Mutation SNP T C3N-00203_T 855332 42932142 116413831 196 11500 ADCY1 0 . GRCh38 7 45703423 45703423 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2502G>T p.Arg834Ser p.R834S ENST00000297323 15/20 299 231 68 228 227 1 strelka-varscan ADCY1,missense_variant,p.Arg834Ser,ENST00000297323,NM_021116.2; T ENST00000297323 Transcript missense_variant 2524/12503 2502/3360 834/1119 R/S agG/agT 1 1 ADCY1 HGNC HGNC:232 protein_coding YES CCDS34631.1 ENSP00000297323 Q08828 UPI0000199C4A NM_021116.2 tolerated(0.05) 15/20 hmmpanther:PTHR11920:SF336,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,SMART_domains:SM00044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 45703423 45703423 G T 1 0 0 0 0 1 0 0 0 336 1194 42 2 2 ADCY1 7 45703423 Missense_Mutation SNP G C3N-00203_T 2771281 45703423 113642550 197 11501 EGFR 0 . GRCh38 7 55160276 55160276 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.1436A>T p.Lys479Ile p.K479I ENST00000275493 12/28 273 215 58 220 220 0 strelka-varscan EGFR,missense_variant,p.Lys479Ile,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Lys434Ile,ENST00000454757,;EGFR,missense_variant,p.Lys434Ile,ENST00000455089,;EGFR,missense_variant,p.Lys479Ile,ENST00000344576,NM_201284.1;EGFR,missense_variant,p.Lys479Ile,ENST00000342916,NM_201282.1;EGFR,downstream_gene_variant,,ENST00000420316,NM_201283.1; T ENST00000275493 Transcript missense_variant 1613/9821 1436/3633 479/1210 K/I aAa/aTa 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 tolerated(0.08) 12/28 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Pfam_domain:PF01030,PIRSF_domain:PIRSF000619,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 55160276 55160276 A T 1 0 0 0 0 1 0 0 0 4803 14 1 4 4 EGFR 7 55160276 Missense_Mutation SNP A C3N-00203_T 9456853 55160276 104185697 198 11502 WBSCR17 0 . GRCh38 7 71665410 71665410 + Splice_Site SNP G G A novel C3N-00203_T C3N-00203_N G G c.1081-1G>A p.X361_splice ENST00000333538 104 86 18 90 90 0 strelka-varscan WBSCR17,splice_acceptor_variant,,ENST00000333538,NM_022479.2;WBSCR17,splice_acceptor_variant,,ENST00000618959,;WBSCR17,splice_acceptor_variant,,ENST00000498380,;WBSCR17,splice_acceptor_variant,,ENST00000467723,; A ENST00000333538 Transcript splice_acceptor_variant -/3884 1081/1797 361/598 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 6/10 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 42 71665410 71665410 G A 1 0 0 0 0 0 0 1 0 17823 1014 35 3 3 WBSCR17 7 71665410 Splice_Site SNP G C3N-00203_T 16505134 71665410 87680563 199 11503 FKBP6 0 . GRCh38 7 73328584 73328584 + Nonsense_Mutation SNP G G T rs545404821 C3N-00203_T C3N-00203_N G G c.67G>T p.Glu23Ter p.E23* ENST00000252037 2/9 304 254 50 241 241 0 strelka-varscan FKBP6,stop_gained,p.Glu23Ter,ENST00000413573,NM_001281304.1;FKBP6,stop_gained,p.Glu23Ter,ENST00000252037,NM_003602.4;FKBP6,stop_gained,p.Glu18Ter,ENST00000431982,NM_001135211.2;FKBP6,stop_gained,p.Glu18Ter,ENST00000442793,;TRIM50,upstream_gene_variant,,ENST00000333149,NM_178125.3,NM_001281450.1;TRIM50,upstream_gene_variant,,ENST00000453152,NM_001281451.1;TRIM50,upstream_gene_variant,,ENST00000493498,;FKBP6,stop_gained,p.Glu23Ter,ENST00000445032,;FKBP6,stop_gained,p.Glu23Ter,ENST00000429879,;FKBP6,non_coding_transcript_exon_variant,,ENST00000437013,; T ENST00000252037 Transcript stop_gained 136/1500 67/984 23/327 E/* Gag/Tag rs545404821 1 1 FKBP6 HGNC HGNC:3722 protein_coding YES CCDS43595.1 ENSP00000252037 O75344 UPI000000165F NM_003602.4 2/9 Gene3D:3.10.50.40,hmmpanther:PTHR10516,hmmpanther:PTHR10516:SF10,Superfamily_domains:SSF54534 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 73328584 73328584 G T 1 0 0 0 0 0 1 0 0 5776 1059 37 1 1 FKBP6 7 73328584 Nonsense_Mutation SNP G C3N-00203_T 1663174 73328584 86017389 200 11504 GPC2 0 . GRCh38 7 100176265 100176265 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.267G>T p.= p.V89V ENST00000292377 2/10 369 225 144 246 245 1 strelka-varscan-mutect GPC2,synonymous_variant,p.=,ENST00000292377,NM_152742.2;STAG3,upstream_gene_variant,,ENST00000426455,NM_001282716.1;STAG3,upstream_gene_variant,,ENST00000615138,NM_001282717.1;STAG3,upstream_gene_variant,,ENST00000620100,;STAG3,upstream_gene_variant,,ENST00000317296,NM_012447.3;STAG3,upstream_gene_variant,,ENST00000394018,NM_001282718.1;STAG3,upstream_gene_variant,,ENST00000439782,;STAG3,upstream_gene_variant,,ENST00000416412,;STAG3,upstream_gene_variant,,ENST00000422690,;GPC2,upstream_gene_variant,,ENST00000490629,;GPC2,synonymous_variant,p.=,ENST00000480087,;GPC2,non_coding_transcript_exon_variant,,ENST00000471717,;STAG3,upstream_gene_variant,,ENST00000496157,;GPC2,upstream_gene_variant,,ENST00000486702,;STAG3,upstream_gene_variant,,ENST00000482546,; A ENST00000292377 Transcript synonymous_variant 435/2532 267/1740 89/579 V gtG/gtT 1 -1 GPC2 HGNC HGNC:4450 protein_coding YES CCDS5689.1 ENSP00000292377 Q8N158 UPI000005340D NM_152742.2 2/10 hmmpanther:PTHR10822:SF24,hmmpanther:PTHR10822,Pfam_domain:PF01153 LOW 1 SNV 1 1 PASS rs1349286268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 100176265 100176265 C A 1 0 0 0 0 0 0 0 1 6500 581 21 2 2 GPC2 7 100176265 Silent SNP C C3N-00203_T 26847681 100176265 59169708 201 11505 PCOLCE 0 . GRCh38 7 100604073 100604073 + Missense_Mutation SNP C C T rs143607884 C3N-00203_T C3N-00203_N C C c.319C>T p.Arg107Trp p.R107W ENST00000223061 3/9 798 653 145 414 414 0 strelka-varscan-mutect PCOLCE,missense_variant,p.Arg107Trp,ENST00000223061,NM_002593.3;FBXO24,downstream_gene_variant,,ENST00000241071,NM_033506.2;FBXO24,downstream_gene_variant,,ENST00000427939,NM_012172.4;FBXO24,downstream_gene_variant,,ENST00000468962,NM_001163499.1;PCOLCE-AS1,non_coding_transcript_exon_variant,,ENST00000446022,;PCOLCE-AS1,upstream_gene_variant,,ENST00000442166,;PCOLCE,non_coding_transcript_exon_variant,,ENST00000496269,;PCOLCE,upstream_gene_variant,,ENST00000486440,;PCOLCE,non_coding_transcript_exon_variant,,ENST00000487172,;PCOLCE,non_coding_transcript_exon_variant,,ENST00000462260,;PCOLCE,non_coding_transcript_exon_variant,,ENST00000482863,;FBXO24,downstream_gene_variant,,ENST00000488079,;PCOLCE,upstream_gene_variant,,ENST00000472348,;PCOLCE,upstream_gene_variant,,ENST00000468214,;PCOLCE,upstream_gene_variant,,ENST00000460002,;PCOLCE,upstream_gene_variant,,ENST00000490909,; T ENST00000223061 Transcript missense_variant 599/1702 319/1350 107/449 R/W Cgg/Tgg rs143607884 1 1 PCOLCE HGNC HGNC:8738 protein_coding YES CCDS5700.1 ENSP00000223061 Q15113 UPI0000131428 NM_002593.3 deleterious(0) 3/9 PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF628,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs143607884 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 100604073 100604073 C T 1 0 0 0 0 1 0 0 0 11683 759 27 1 1 PCOLCE 7 100604073 Missense_Mutation SNP C C3N-00203_T 427808 100604073 58741900 202 11506 TRIM56 0 . GRCh38 7 101087395 101087395 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.83T>A p.Leu28Gln p.L28Q ENST00000306085 3/3 320 204 116 149 149 0 strelka-varscan-mutect TRIM56,missense_variant,p.Leu28Gln,ENST00000306085,NM_030961.2;TRIM56,missense_variant,p.Leu28Gln,ENST00000412507,;TRIM56,missense_variant,p.Leu28Gln,ENST00000467847,;TRIM56,upstream_gene_variant,,ENST00000487252,; A ENST00000306085 Transcript missense_variant 380/10952 83/2268 28/755 L/Q cTg/cAg 1 1 TRIM56 HGNC HGNC:19028 protein_coding YES CCDS43625.1 ENSP00000305161 Q9BRZ2 UPI0000171C4A NM_030961.2 deleterious(0) 3/3 PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF331,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Pfam_domain:PF13445,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9993699 1 1 1 0 A 3 1 42 101087395 101087395 T A 1 0 0 0 0 1 0 0 0 17023 1580 55 4 4 TRIM56 7 101087395 Missense_Mutation SNP T C3N-00203_T 483322 101087395 58258578 203 11507 LRRN3 0 . GRCh38 7 111123692 111123692 + Missense_Mutation SNP A A G rs758915597 C3N-00203_T C3N-00203_N A A c.920A>G p.Asn307Ser p.N307S ENST00000451085 4/4 339 290 49 218 218 0 strelka-varscan-mutect LRRN3,missense_variant,p.Asn307Ser,ENST00000451085,NM_001099660.1;LRRN3,missense_variant,p.Asn307Ser,ENST00000422987,NM_018334.4;LRRN3,missense_variant,p.Asn307Ser,ENST00000308478,NM_001099658.1;IMMP2L,intron_variant,,ENST00000405709,NM_032549.3;IMMP2L,intron_variant,,ENST00000331762,NM_001244606.1;IMMP2L,intron_variant,,ENST00000447215,;IMMP2L,intron_variant,,ENST00000452895,;IMMP2L,intron_variant,,ENST00000450877,;LRRN3,downstream_gene_variant,,ENST00000421101,;IMMP2L,intron_variant,,ENST00000489381,; G ENST00000451085 Transcript missense_variant 1966/3725 920/2127 307/708 N/S aAc/aGc rs758915597 1 1 LRRN3 HGNC HGNC:17200 protein_coding YES CCDS5754.1 ENSP00000397312 Q9H3W5 A4D0T1 UPI0000037517 NM_001099660.1 deleterious(0.02) 4/4 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF7,Superfamily_domains:SSF52058 MODERATE SNV 2 1 PASS rs758915597 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 111123692 111123692 A G 1 0 0 0 0 1 0 0 0 8942 43 2 5 5 LRRN3 7 111123692 Missense_Mutation SNP A C3N-00203_T 10036297 111123692 48222281 204 11508 CTTNBP2 0 . GRCh38 7 117725254 117725254 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.4059G>T p.Trp1353Cys p.W1353C ENST00000160373 18/23 427 241 186 209 209 0 strelka-varscan-mutect CTTNBP2,missense_variant,p.Trp1353Cys,ENST00000160373,NM_033427.2;CTTNBP2,missense_variant,p.Trp841Cys,ENST00000446636,;CTTNBP2,3_prime_UTR_variant,,ENST00000441556,;CTTNBP2,intron_variant,,ENST00000445366,; A ENST00000160373 Transcript missense_variant 4151/5970 4059/4992 1353/1663 W/C tgG/tgT 1 -1 CTTNBP2 HGNC HGNC:15679 protein_coding YES CCDS5774.1 ENSP00000160373 Q8WZ74 Q20BG9 UPI000006E94A NM_033427.2 deleterious(0) 18/23 hmmpanther:PTHR24166:SF27,hmmpanther:PTHR24166 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9995448 1 1 1 0 A 3 1 42 117725254 117725254 C A 1 0 0 0 0 1 0 0 0 3854 869 30 2 2 CTTNBP2 7 117725254 Missense_Mutation SNP C C3N-00203_T 6601562 117725254 41620719 205 11509 CPED1 0 . GRCh38 7 121244291 121244291 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.2263G>C p.Gly755Arg p.G755R ENST00000310396 18/23 493 334 159 342 342 0 strelka-varscan-mutect CPED1,missense_variant,p.Gly755Arg,ENST00000310396,NM_024913.4;CPED1,missense_variant,p.Gly755Arg,ENST00000450913,NM_001105533.1;CPED1,missense_variant,p.Gly535Arg,ENST00000423795,;CPED1,non_coding_transcript_exon_variant,,ENST00000466055,; C ENST00000310396 Transcript missense_variant 2730/5340 2263/3081 755/1026 G/R Ggt/Cgt 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 tolerated(0.19) 18/23 hmmpanther:PTHR14776 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 121244291 121244291 G C 1 0 0 0 0 1 0 0 0 3598 1348 47 4 4 CPED1 7 121244291 Missense_Mutation SNP G C3N-00203_T 3519037 121244291 38101682 206 11510 SLC13A1 0 . GRCh38 7 123169305 123169305 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.396C>T p.= p.A132A ENST00000194130 4/15 188 160 28 123 123 0 strelka-varscan-mutect SLC13A1,synonymous_variant,p.=,ENST00000194130,NM_022444.3;SLC13A1,synonymous_variant,p.=,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; A ENST00000194130 Transcript synonymous_variant 436/3815 396/1788 132/595 A gcC/gcT 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 4/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283,Pfam_domain:PF00939 LOW 1 SNV 1 1 PASS rs1276746627 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 123169305 123169305 G A 1 0 0 0 0 0 0 0 1 14656 987 35 3 3 SLC13A1 7 123169305 Silent SNP G C3N-00203_T 1925014 123169305 36176668 207 11511 GPR37 0 . GRCh38 7 124764630 124764630 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.347C>G p.Pro116Arg p.P116R ENST00000303921 1/2 73 59 14 59 59 0 strelka-varscan-mutect GPR37,missense_variant,p.Pro116Arg,ENST00000303921,NM_005302.3; C ENST00000303921 Transcript missense_variant 998/3021 347/1842 116/613 P/R cCa/cGa 1 -1 GPR37 HGNC HGNC:4494 protein_coding YES CCDS5792.1 ENSP00000306449 O15354 UPI0000001C92 NM_005302.3 tolerated_low_confidence(0.24) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1230885802 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 124764630 124764630 G C 1 0 0 0 0 1 0 0 0 6576 1348 47 4 4 GPR37 7 124764630 Missense_Mutation SNP G C3N-00203_T 1595325 124764630 34581343 208 11512 KCP 0 . GRCh38 7 128910665 128910665 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.12C>T p.= p.V4V ENST00000610776 1/40 196 170 26 92 92 0 strelka-varscan-mutect KCP,synonymous_variant,p.=,ENST00000610776,;KCP,synonymous_variant,p.=,ENST00000613019,;KCP,synonymous_variant,p.=,ENST00000620378,NM_001135914.1;KCP,non_coding_transcript_exon_variant,,ENST00000612224,;KCP,synonymous_variant,p.=,ENST00000611280,;RP11-309L24.6,downstream_gene_variant,,ENST00000469533,; A ENST00000610776 Transcript synonymous_variant 55/5108 12/4887 4/1628 V gtC/gtT 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 1/40 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 42 128910665 128910665 G A 1 0 0 0 0 0 0 0 1 8012 1045 37 1 1 KCP 7 128910665 Silent SNP G C3N-00203_T 4146035 128910665 30435308 209 11513 RP11-286H14.4 0 . GRCh38 7 129127053 129127053 + Missense_Mutation SNP G G T rs757791946 C3N-00203_T C3N-00203_N G G c.536G>T p.Gly179Val p.G179V ENST00000467614 1/2 803 528 275 511 511 0 strelka-varscan-mutect RP11-286H14.4,missense_variant,p.Gly179Val,ENST00000467614,; T ENST00000467614 Transcript missense_variant 536/1263 536/1218 179/405 G/V gGc/gTc rs757791946 1 1 RP11-286H14.4 Clone_based_vega_gene protein_coding YES ENSP00000490163 deleterious(0) 1/2 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF314,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 PASS rs757791946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 129127053 129127053 G T 1 0 0 0 0 1 0 0 0 13725 1203 42 2 2 RP11-286H14.4 7 129127053 Missense_Mutation SNP G C3N-00203_T 216388 129127053 30218920 210 11514 CEP41 0 . GRCh38 7 130416935 130416935 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.129C>T p.= p.L43L ENST00000223208 3/11 362 216 146 310 309 1 strelka-varscan-mutect CEP41,synonymous_variant,p.=,ENST00000223208,NM_018718.2;CEP41,synonymous_variant,p.=,ENST00000343969,NM_001257158.1;CEP41,synonymous_variant,p.=,ENST00000472739,;CEP41,synonymous_variant,p.=,ENST00000492389,;CEP41,synonymous_variant,p.=,ENST00000475282,;CEP41,synonymous_variant,p.=,ENST00000477003,;CEP41,synonymous_variant,p.=,ENST00000469826,;CEP41,intron_variant,,ENST00000541543,NM_001257159.1;CEP41,downstream_gene_variant,,ENST00000616628,NM_001257160.1;CEP41,downstream_gene_variant,,ENST00000489512,;CEP41,downstream_gene_variant,,ENST00000495702,;CEP41,downstream_gene_variant,,ENST00000334451,;CEP41,synonymous_variant,p.=,ENST00000484549,;CEP41,3_prime_UTR_variant,,ENST00000471201,;CEP41,non_coding_transcript_exon_variant,,ENST00000498527,;CEP41,non_coding_transcript_exon_variant,,ENST00000482730,; A ENST00000223208 Transcript synonymous_variant 400/6513 129/1122 43/373 L ctC/ctT 1 -1 CEP41 HGNC HGNC:12370 protein_coding YES CCDS5821.1 ENSP00000223208 Q9BYV8 UPI000006D546 NM_018718.2 3/11 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 130416935 130416935 G A 1 0 0 0 0 0 0 0 1 2973 1045 37 1 1 CEP41 7 130416935 Silent SNP G C3N-00203_T 1289882 130416935 28929038 211 11515 WEE2 0 . GRCh38 7 141709074 141709074 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.316C>A p.Pro106Thr p.P106T ENST00000397541 1/12 156 111 45 116 116 0 strelka-varscan-mutect WEE2,missense_variant,p.Pro106Thr,ENST00000397541,NM_001105558.1;WEE2-AS1,intron_variant,,ENST00000488785,;WEE2-AS1,intron_variant,,ENST00000478332,;WEE2-AS1,intron_variant,,ENST00000462383,;WEE2-AS1,intron_variant,,ENST00000495800,;WEE2-AS1,intron_variant,,ENST00000465110,;WEE2-AS1,intron_variant,,ENST00000471512,;WEE2-AS1,intron_variant,,ENST00000459753,; A ENST00000397541 Transcript missense_variant 722/3061 316/1704 106/567 P/T Ccc/Acc 1 1 WEE2 HGNC HGNC:19684 protein_coding YES CCDS43660.1 ENSP00000380675 P0C1S8 UPI000004E9D3 NM_001105558.1 tolerated(0.19) 1/12 hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF75,PIRSF_domain:PIRSF037281 MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 141709074 141709074 C A 1 0 0 0 0 1 0 0 0 17902 739 26 2 2 WEE2 7 141709074 Missense_Mutation SNP C C3N-00203_T 11292139 141709074 17636899 212 11516 MGAM2 0 . GRCh38 7 142198656 142198656 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.4965G>A p.= p.K1655K ENST00000477922 44/48 298 199 99 155 155 0 strelka-varscan-mutect MGAM2,synonymous_variant,p.=,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript synonymous_variant 5019/7867 4965/7548 1655/2515 K aaG/aaA 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 44/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51011 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 142198656 142198656 G A 1 0 0 0 0 0 0 0 1 9500 991 35 3 3 MGAM2 7 142198656 Silent SNP G C3N-00203_T 489582 142198656 17147317 213 11517 KRBA1 0 . GRCh38 7 149723786 149723786 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.927T>C p.= p.C309C ENST00000496259 8/17 453 400 53 170 170 0 strelka-varscan-mutect KRBA1,synonymous_variant,p.=,ENST00000319551,NM_032534.3;KRBA1,synonymous_variant,p.=,ENST00000496259,NM_001290187.1;KRBA1,synonymous_variant,p.=,ENST00000485033,;KRBA1,downstream_gene_variant,,ENST00000467333,;KRBA1,downstream_gene_variant,,ENST00000486744,;KRBA1,downstream_gene_variant,,ENST00000497895,;KRBA1,synonymous_variant,p.=,ENST00000621069,;KRBA1,non_coding_transcript_exon_variant,,ENST00000496080,; C ENST00000496259 Transcript synonymous_variant 971/3763 927/3195 309/1064 C tgT/tgC 1 1 KRBA1 HGNC HGNC:22228 protein_coding YES CCDS78285.1 ENSP00000418647 A0A0C4DH65 UPI0003F48BD7 NM_001290187.1 8/17 Pfam_domain:PF15287,hmmpanther:PTHR22740,SMART_domains:SM01258 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 149723786 149723786 T C 1 0 0 0 0 0 0 0 1 8319 1673 58 5 5 KRBA1 7 149723786 Silent SNP T C3N-00203_T 7525130 149723786 9622187 214 11518 CRYGN 0 . GRCh38 7 151436245 151436245 + Silent SNP G G C rs781681564 C3N-00203_T C3N-00203_N G G c.351C>G p.= p.P117P ENST00000337323 3/4 86 75 11 46 46 0 strelka-varscan-mutect CRYGN,synonymous_variant,p.=,ENST00000337323,NM_144727.1;CRYGN,intron_variant,,ENST00000491928,NM_001308292.1;MIR3907,upstream_gene_variant,,ENST00000579424,;RP4-555L14.4,intron_variant,,ENST00000465549,;CRYGN,non_coding_transcript_exon_variant,,ENST00000476631,;CRYGN,non_coding_transcript_exon_variant,,ENST00000462809,;CRYGN,non_coding_transcript_exon_variant,,ENST00000478106,; C ENST00000337323 Transcript synonymous_variant 478/754 351/549 117/182 P ccC/ccG rs781681564 1 -1 CRYGN HGNC HGNC:20458 protein_coding YES CCDS5926.1 ENSP00000338613 Q8WXF5 A0A090N8I5 UPI000006F59A NM_144727.1 3/4 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF22,Gene3D:2.60.20.10,Pfam_domain:PF00030,Superfamily_domains:SSF49695 LOW 1 SNV 1 1 PASS rs781681564 . 0 207 3 0 0 0 0 0 -19.9999 1 1 1 1 0 C 2 2 42 151436245 151436245 G C 1 0 0 0 0 0 0 0 1 3720 987 35 4 4 CRYGN 7 151436245 Silent SNP G C3N-00203_T 1712459 151436245 7909728 215 11519 MNX1 0 . GRCh38 7 157005848 157005848 + Missense_Mutation SNP C C G C3N-00203_T C3N-00203_N C C c.878G>C p.Arg293Pro p.R293P ENST00000252971 3/3 612 523 89 309 309 0 strelka-varscan-mutect MNX1,missense_variant,p.Arg293Pro,ENST00000252971,NM_005515.3;MNX1,missense_variant,p.Arg81Pro,ENST00000543409,NM_001165255.1;MNX1,missense_variant,p.Arg81Pro,ENST00000428439,;MNX1,synonymous_variant,p.=,ENST00000425745,;MNX1,intron_variant,,ENST00000469500,;MNX1,intron_variant,,ENST00000479817,;MNX1-AS1,upstream_gene_variant,,ENST00000480284,;MNX1-AS2,upstream_gene_variant,,ENST00000429228,;MNX1,3_prime_UTR_variant,,ENST00000474448,;MNX1,downstream_gene_variant,,ENST00000605400,; G ENST00000252971 Transcript missense_variant 1179/2174 878/1206 293/401 R/P cGg/cCg CM003828,COSM5005014,COSM5005015 1 -1 MNX1 HGNC HGNC:4979 protein_coding YES CCDS34788.1 ENSP00000252971 P50219 UPI000020E726 NM_005515.3 deleterious(0) 3/3 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50071,hmmpanther:PTHR24335,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 157005848 157005848 C G 1 0 0 0 0 1 0 0 0 9643 652 23 4 4 MNX1 7 157005848 Missense_Mutation SNP C C3N-00203_T 5569603 157005848 2340125 216 11520 PRSS55 0 . GRCh38 8 10538753 10538753 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.1019G>A p.Cys340Tyr p.C340Y ENST00000328655 5/5 55 43 12 88 88 0 strelka-varscan-mutect PRSS55,missense_variant,p.Cys340Tyr,ENST00000328655,NM_198464.3;PRSS51,intron_variant,,ENST00000637190,;PRSS55,intron_variant,,ENST00000522210,NM_001197020.1;PRSS55,intron_variant,,ENST00000518641,;PRSS51,intron_variant,,ENST00000523024,; A ENST00000328655 Transcript missense_variant 1059/1124 1019/1059 340/352 C/Y tGt/tAt 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 tolerated(0.36) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 10538753 10538753 G A 1 0 0 0 0 1 0 0 0 12783 1377 48 3 3 PRSS55 8 10538753 Missense_Mutation SNP G C3N-00203_T 10538753 134599883 217 11521 PCM1 0 . GRCh38 8 17960100 17960100 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.2127T>C p.= p.N709N ENST00000325083 14/39 151 126 25 168 168 0 strelka-varscan-mutect PCM1,synonymous_variant,p.=,ENST00000327578,NM_001315508.1;PCM1,synonymous_variant,p.=,ENST00000325083,NM_006197.3;PCM1,synonymous_variant,p.=,ENST00000519253,;PCM1,synonymous_variant,p.=,ENST00000524226,;PCM1,synonymous_variant,p.=,ENST00000517730,;PCM1,downstream_gene_variant,,ENST00000518537,;PCM1,non_coding_transcript_exon_variant,,ENST00000518762,;PCM1,non_coding_transcript_exon_variant,,ENST00000517836,;PCM1,upstream_gene_variant,,ENST00000524356,; C ENST00000325083 Transcript synonymous_variant 2566/6820 2127/6075 709/2024 N aaT/aaC 1 1 PCM1 HGNC HGNC:8727 protein_coding YES CCDS47812.1 ENSP00000327077 Q15154 UPI0000210A25 NM_006197.3 14/39 hmmpanther:PTHR14164,hmmpanther:PTHR14164:SF12 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 42 17960100 17960100 T C 1 0 0 0 0 0 0 0 1 11672 1490 52 5 5 PCM1 8 17960100 Silent SNP T C3N-00203_T 7421347 17960100 127178536 218 11522 EBF2 0 . GRCh38 8 25850616 25850616 + Missense_Mutation SNP G G C rs751209442 C3N-00203_T C3N-00203_N G G c.1674C>G p.Ser558Arg p.S558R ENST00000520164 15/16 51 41 10 72 72 0 strelka-varscan-mutect EBF2,missense_variant,p.Ser558Arg,ENST00000520164,NM_022659.3;EBF2,missense_variant,p.Ser410Arg,ENST00000408929,;EBF2,3_prime_UTR_variant,,ENST00000535548,; C ENST00000520164 Transcript missense_variant 2212/5145 1674/1728 558/575 S/R agC/agG rs751209442,COSM3899132,COSM3899133 1 -1 EBF2 HGNC HGNC:19090 protein_coding YES CCDS43726.1 ENSP00000430241 Q9HAK2 UPI0000DD7EC9 NM_022659.3 tolerated_low_confidence(0.21) 15/16 hmmpanther:PTHR10747 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs751209442 . 0 199 11 0 0 0 0 0 -19.99987 0.9999767 1 1 1 0 C 3 2 42 25850616 25850616 G C 1 0 0 0 0 1 0 0 0 4705 1078 38 4 4 EBF2 8 25850616 Missense_Mutation SNP G C3N-00203_T 7890516 25850616 119288020 219 11523 ADAM18 0 . GRCh38 8 39668063 39668063 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.1392C>G p.Cys464Trp p.C464W ENST00000265707 14/20 427 366 61 314 314 0 strelka-varscan-mutect ADAM18,missense_variant,p.Cys464Trp,ENST00000265707,NM_014237.2;ADAM18,missense_variant,p.Cys440Trp,ENST00000379866,NM_001320313.1;ADAM18,3_prime_UTR_variant,,ENST00000520087,; G ENST00000265707 Transcript missense_variant 1437/2388 1392/2220 464/739 C/W tgC/tgG 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 deleterious(0) 14/20 Gene3D:4.10.70.10,Pfam_domain:PF00200,PROSITE_profiles:PS50214,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,SMART_domains:SM00050,Superfamily_domains:SSF57552 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 39668063 39668063 C G 1 0 0 0 0 1 0 0 0 283 718 25 4 4 ADAM18 8 39668063 Missense_Mutation SNP C C3N-00203_T 13817447 39668063 105470573 220 11524 ANK1 0 . GRCh38 8 41696483 41696483 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2963C>A p.Thr988Asn p.T988N ENST00000265709 27/43 380 341 39 356 356 0 strelka-varscan-mutect ANK1,missense_variant,p.Thr947Asn,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Thr947Asn,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Thr988Asn,ENST00000265709,NM_001142446.1;ANK1,missense_variant,p.Thr269Asn,ENST00000520299,;ANK1,non_coding_transcript_exon_variant,,ENST00000524227,;ANK1,upstream_gene_variant,,ENST00000524069,; T ENST00000265709 Transcript missense_variant 3245/6379 2963/5694 988/1897 T/N aCc/aAc 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 deleterious(0) 27/43 Pfam_domain:PF00791,PROSITE_profiles:PS51145,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,SMART_domains:SM00218 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 41696483 41696483 G T 1 0 0 0 0 1 0 0 0 720 1261 44 2 2 ANK1 8 41696483 Missense_Mutation SNP G C3N-00203_T 2028420 41696483 103442153 221 11525 C8orf22 0 . GRCh38 8 49074121 49074121 + Missense_Mutation SNP G G A C3N-00203_T C3N-00203_N G G c.118G>A p.Asp40Asn p.D40N ENST00000303202 3/5 196 169 27 237 237 0 strelka-varscan-mutect C8orf22,missense_variant,p.Asp40Asn,ENST00000303202,NM_001256598.1;C8orf22,missense_variant,p.Asp40Asn,ENST00000399653,NM_001007176.4;C8orf22,missense_variant,p.Asp40Asn,ENST00000517663,NM_001256596.1;C8orf22,missense_variant,p.Asp40Asn,ENST00000522267,NM_001256597.1; A ENST00000303202 Transcript missense_variant 291/1499 118/255 40/84 D/N Gac/Aac COSM243409 1 1 C8orf22 HGNC HGNC:31745 protein_coding YES CCDS59101.1 ENSP00000304926 Q8WWR9 UPI0000070316 NM_001256598.1 tolerated(0.06) 3/5 hmmpanther:PTHR14572:SF1,hmmpanther:PTHR14572,Pfam_domain:PF15060 1 MODERATE 1 SNV 1 1 1 PASS rs1212695465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 49074121 49074121 G A 1 0 0 0 0 1 0 0 0 2153 1058 37 1 1 C8orf22 8 49074121 Missense_Mutation SNP G C3N-00203_T 7377638 49074121 96064515 222 11526 TCEA1 0 . GRCh38 8 54010493 54010493 + Splice_Site SNP C C G novel C3N-00203_T C3N-00203_N C C c.64-1G>C p.X22_splice ENST00000521604 214 153 61 221 221 0 strelka-varscan-mutect TCEA1,splice_acceptor_variant,,ENST00000521604,NM_006756.3;TCEA1,splice_acceptor_variant,,ENST00000522635,;TCEA1,splice_acceptor_variant,,ENST00000520534,;TCEA1,splice_acceptor_variant,,ENST00000518784,;TCEA1,intron_variant,,ENST00000396401,NM_201437.2;TCEA1,splice_acceptor_variant,,ENST00000521086,;TCEA1,splice_acceptor_variant,,ENST00000522397,;TCEA1,splice_acceptor_variant,,ENST00000521836,;TCEA1,splice_acceptor_variant,,ENST00000517351,;TCEA1,splice_acceptor_variant,,ENST00000518310,;TCEA1,splice_acceptor_variant,,ENST00000519704,; G ENST00000521604 Transcript splice_acceptor_variant -/2858 64/906 22/301 1 -1 TCEA1 HGNC HGNC:11612 protein_coding YES CCDS47858.1 ENSP00000428426 P23193 UPI0000136ABE NM_006756.3 1/9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 42 54010493 54010493 C G 1 0 0 0 0 0 0 1 0 16074 695 24 4 4 TCEA1 8 54010493 Splice_Site SNP C C3N-00203_T 4936372 54010493 91128143 223 11527 PREX2 0 . GRCh38 8 68109451 68109451 + Missense_Mutation SNP A A T rs760875810 C3N-00203_T C3N-00203_N A A c.2974A>T p.Ile992Phe p.I992F ENST00000288368 25/40 226 201 25 197 197 0 strelka-varscan-mutect PREX2,missense_variant,p.Ile992Phe,ENST00000288368,NM_024870.2;PREX2,non_coding_transcript_exon_variant,,ENST00000517617,;PREX2,downstream_gene_variant,,ENST00000529398,; T ENST00000288368 Transcript missense_variant 3251/10750 2974/4821 992/1606 I/F Atc/Ttc rs760875810 1 1 PREX2 HGNC HGNC:22950 protein_coding YES CCDS6201.1 ENSP00000288368 Q70Z35 UPI0000375435 NM_024870.2 tolerated_low_confidence(0.05) 25/40 hmmpanther:PTHR22829:SF1,hmmpanther:PTHR22829 MODERATE 1 SNV 1 1 PASS rs760875810 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 68109451 68109451 A T 1 0 0 0 0 1 0 0 0 12611 217 8 4 4 PREX2 8 68109451 Missense_Mutation SNP A C3N-00203_T 14098958 68109451 77029185 224 11528 KCNB2 0 . GRCh38 8 72567752 72567752 + Silent SNP C C A C3N-00203_T C3N-00203_N C C c.18C>A p.= p.P6P ENST00000523207 2/3 60 51 9 47 47 0 strelka-varscan-mutect KCNB2,synonymous_variant,p.=,ENST00000523207,NM_004770.2; A ENST00000523207 Transcript synonymous_variant 606/3582 18/2736 6/911 P ccC/ccA COSM4957828 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 2/3 1 LOW 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.96578 1 1 1 1 0 A 2 1 42 72567752 72567752 C A 1 0 0 0 0 0 0 0 1 7929 610 22 2 2 KCNB2 8 72567752 Silent SNP C C3N-00203_T 4458301 72567752 72570884 225 11529 ZBTB10 0 . GRCh38 8 80499519 80499519 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.998G>T p.Gly333Val p.G333V ENST00000430430 3/7 105 86 19 100 100 0 strelka-varscan-mutect ZBTB10,missense_variant,p.Gly333Val,ENST00000430430,;ZBTB10,missense_variant,p.Gly333Val,ENST00000426744,NM_023929.4;ZBTB10,missense_variant,p.Gly333Val,ENST00000455036,NM_001105539.2;ZBTB10,missense_variant,p.Gly160Val,ENST00000610895,;ZBTB10,missense_variant,p.Gly41Val,ENST00000379091,NM_001277145.1; T ENST00000430430 Transcript missense_variant 1777/10132 998/2616 333/871 G/V gGg/gTg 1 1 ZBTB10 HGNC HGNC:30953 protein_coding YES CCDS47880.1 ENSP00000387462 Q96DT7 UPI0000E5AEF3 tolerated(0.08) 3/7 hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF27 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 80499519 80499519 G T 1 0 0 0 0 1 0 0 0 18089 1232 43 2 2 ZBTB10 8 80499519 Missense_Mutation SNP G C3N-00203_T 7931767 80499519 64639117 226 11530 DCAF4L2 0 . GRCh38 8 87873841 87873841 + Missense_Mutation SNP C C A rs780860993 C3N-00203_T C3N-00203_N C C c.131G>T p.Arg44Leu p.R44L ENST00000319675 1/1 479 428 51 385 385 0 strelka-varscan-mutect DCAF4L2,missense_variant,p.Arg44Leu,ENST00000319675,NM_152418.3; A ENST00000319675 Transcript missense_variant 228/3326 131/1188 44/395 R/L cGt/cTt rs780860993 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 deleterious(0) 1/1 hmmpanther:PTHR22847:SF457,hmmpanther:PTHR22847 MODERATE 1 SNV 1 PASS rs780860993 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 87873841 87873841 C A 1 0 0 0 0 1 0 0 0 4073 536 19 1 1 DCAF4L2 8 87873841 Missense_Mutation SNP C C3N-00203_T 7374322 87873841 57264795 227 11531 CDH17 0 . GRCh38 8 94151959 94151959 + Missense_Mutation SNP G G T rs769518455 C3N-00203_T C3N-00203_N G G c.1705C>A p.His569Asn p.H569N ENST00000027335 13/18 530 482 48 428 428 0 strelka-varscan-mutect CDH17,missense_variant,p.His569Asn,ENST00000027335,NM_004063.3;CDH17,missense_variant,p.His569Asn,ENST00000450165,NM_001144663.1;CDH17,missense_variant,p.His355Asn,ENST00000441892,;CDH17,intron_variant,,ENST00000520952,; T ENST00000027335 Transcript missense_variant 1830/3693 1705/2499 569/832 H/N Cac/Aac rs769518455 1 -1 CDH17 HGNC HGNC:1756 protein_coding YES CCDS6260.1 ENSP00000027335 Q12864 UPI000013C546 NM_004063.3 tolerated(0.51) 13/18 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF292,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs769518455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 94151959 94151959 G T 1 0 0 0 0 1 0 0 0 2805 1377 48 2 2 CDH17 8 94151959 Missense_Mutation SNP G C3N-00203_T 6278118 94151959 50986677 228 11532 RIMS2 0 . GRCh38 8 103885929 103885929 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.1330G>A p.Asp444Asn p.D444N ENST00000504942 4/24 350 323 27 250 250 0 strelka-varscan-mutect RIMS2,missense_variant,p.Asp252Asn,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Asp222Asn,ENST00000436393,;RIMS2,missense_variant,p.Asp444Asn,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Asp386Asn,ENST00000626043,;RIMS2,missense_variant,p.Asp252Asn,ENST00000408894,;RIMS2,missense_variant,p.Asp252Asn,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Asp448Asn,ENST00000632716,;RIMS2,missense_variant,p.Asp252Asn,ENST00000515551,; A ENST00000504942 Transcript missense_variant 1469/4228 1330/4050 444/1349 D/N Gat/Aat 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0.01) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 103885929 103885929 G A 1 0 0 0 0 1 0 0 0 13543 942 33 3 3 RIMS2 8 103885929 Missense_Mutation SNP G C3N-00203_T 9733970 103885929 41252707 229 11533 ZFPM2 0 . GRCh38 8 105801345 105801345 + Silent SNP C C A rs768549497 C3N-00203_T C3N-00203_N C C c.1263C>A p.= p.P421P ENST00000407775 8/8 736 416 320 504 503 1 strelka-varscan-mutect ZFPM2,synonymous_variant,p.=,ENST00000407775,NM_012082.3;ZFPM2,synonymous_variant,p.=,ENST00000520492,;ZFPM2,synonymous_variant,p.=,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; A ENST00000407775 Transcript synonymous_variant 1513/4700 1263/3456 421/1151 P ccC/ccA rs768549497 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 LOW 1 SNV 1 1 PASS rs768549497 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 105801345 105801345 C A 1 0 0 0 0 0 0 0 1 18236 610 22 2 2 ZFPM2 8 105801345 Silent SNP C C3N-00203_T 1915416 105801345 39337291 230 11534 PKHD1L1 0 . GRCh38 8 109459692 109459692 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.7102G>T p.Gly2368Ter p.G2368* ENST00000378402 47/78 307 277 30 286 286 0 strelka-varscan-mutect PKHD1L1,stop_gained,p.Gly2368Ter,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript stop_gained 7206/13076 7102/12732 2368/4243 G/* Gga/Tga 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 47/78 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 109459692 109459692 G T 1 0 0 0 0 0 1 0 0 12068 1001 35 2 2 PKHD1L1 8 109459692 Nonsense_Mutation SNP G C3N-00203_T 3658347 109459692 35678944 231 11535 CSMD3 0 . GRCh38 8 112306035 112306035 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.8043C>A p.Ser2681Arg p.S2681R ENST00000297405 51/71 350 232 118 327 327 0 strelka-varscan-mutect CSMD3,missense_variant,p.Ser2681Arg,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser2641Arg,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser2577Arg,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser1951Arg,ENST00000339701,;CSMD3,downstream_gene_variant,,ENST00000492692,; T ENST00000297405 Transcript missense_variant 8288/13212 8043/11124 2681/3707 S/R agC/agA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 51/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 112306035 112306035 G T 1 0 0 0 0 1 0 0 0 3747 1310 46 2 2 CSMD3 8 112306035 Missense_Mutation SNP G C3N-00203_T 2846343 112306035 32832601 232 11536 CSMD3 0 . GRCh38 8 112682628 112682628 + Missense_Mutation SNP G G T rs775939123 C3N-00203_T C3N-00203_N G G c.2491C>A p.His831Asn p.H831N ENST00000297405 16/71 223 207 16 256 255 1 strelka-varscan-mutect CSMD3,missense_variant,p.His831Asn,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.His791Asn,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.His727Asn,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.His171Asn,ENST00000339701,; T ENST00000297405 Transcript missense_variant 2736/13212 2491/11124 831/3707 H/N Cat/Aat rs775939123,COSM1551627,COSM1551628 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.02) 16/71 Superfamily_domains:SSF49854 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs775939123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 112682628 112682628 G T 1 0 0 0 0 1 0 0 0 3747 1377 48 2 2 CSMD3 8 112682628 Missense_Mutation SNP G C3N-00203_T 376593 112682628 32456008 233 11537 CSMD3 0 . GRCh38 8 112689878 112689878 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.2145C>A p.= p.P715P ENST00000297405 14/71 171 160 11 185 185 0 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,; T ENST00000297405 Transcript synonymous_variant 2390/13212 2145/11124 715/3707 P ccC/ccA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 14/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 112689878 112689878 G T 1 0 0 0 0 0 0 0 1 3747 1335 47 2 2 CSMD3 8 112689878 Silent SNP G C3N-00203_T 7250 112689878 32448758 234 11538 ZFAT 0 . GRCh38 8 134520905 134520906 + Frame_Shift_Ins INS - - T novel C3N-00203_T C3N-00203_N - - c.3211dupA p.Ile1071AsnfsTer2 p.I1071Nfs*2 ENST00000377838 13/16 220 200 20 131 131 0 varindel-pindel ZFAT,frameshift_variant,p.Ile1059AsnfsTer2,ENST00000520727,NM_001029939.3,NM_001289394.1;ZFAT,frameshift_variant,p.Ile1071AsnfsTer2,ENST00000377838,NM_020863.3;ZFAT,frameshift_variant,p.Ile1059AsnfsTer2,ENST00000429442,;ZFAT,frameshift_variant,p.Ile1059AsnfsTer2,ENST00000520214,NM_001167583.2;ZFAT,frameshift_variant,p.Ile1059AsnfsTer2,ENST00000520356,NM_001174158.1;ZFAT,frameshift_variant,p.Ile1009AsnfsTer2,ENST00000523399,NM_001174157.1;ZFAT,non_coding_transcript_exon_variant,,ENST00000517307,;ZFAT,3_prime_UTR_variant,,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000518408,; T ENST00000377838 Transcript frameshift_variant 3386-3387/4597 3211-3212/3732 1071/1243 I/NX att/aAtt 1 -1 ZFAT HGNC HGNC:19899 protein_coding YES CCDS47924.1 ENSP00000367069 Q9P243 UPI0000210061 NM_020863.3 13/16 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF218 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 42 134520905 134520905 - T 1 0 1 1 0 0 0 0 0 18209 101 4 0 0 ZFAT 8 134520905 Frame_Shift_Ins INS - C3N-00203_T 21831027 134520905 10617731 235 11539 FAM135B 0 . GRCh38 8 138152671 138152671 + Nonsense_Mutation SNP G G A C3N-00203_T C3N-00203_N G G c.1804C>T p.Gln602Ter p.Q602* ENST00000395297 13/20 233 124 109 188 188 0 strelka-varscan-mutect FAM135B,stop_gained,p.Gln602Ter,ENST00000395297,NM_015912.3;FAM135B,stop_gained,p.Gln602Ter,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript stop_gained 1975/6962 1804/4221 602/1406 Q/* Caa/Taa COSM749144,COSM749145 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 13/20 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 138152671 138152671 G A 1 0 0 0 0 0 1 0 0 5299 1357 47 3 3 FAM135B 8 138152671 Nonsense_Mutation SNP G C3N-00203_T 3631766 138152671 6985965 236 11540 DMRT3 0 . GRCh38 9 990149 990149 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.563G>C p.Gly188Ala p.G188A ENST00000190165 2/2 223 171 52 236 236 0 strelka-varscan-mutect DMRT3,missense_variant,p.Gly188Ala,ENST00000190165,NM_021240.3;DMRT3,missense_variant,p.Gly51Ala,ENST00000417254,; C ENST00000190165 Transcript missense_variant 601/2183 563/1419 188/472 G/A gGc/gCc 1 1 DMRT3 HGNC HGNC:13909 protein_coding YES CCDS6443.1 ENSP00000190165 Q9NQL9 UPI0000073634 NM_021240.3 tolerated(0.2) 2/2 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF73 MODERATE 1 SNV 1 1 PASS rs1189691657 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 990149 990149 G C 1 0 0 0 0 1 0 0 0 4394 1203 42 4 4 DMRT3 9 990149 Missense_Mutation SNP G C3N-00203_T 990149 137404568 237 11541 KCNV2 0 . GRCh38 9 2718467 2718467 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.728G>A p.Arg243Gln p.R243Q ENST00000382082 1/2 205 164 41 124 124 0 strelka-varscan-mutect KCNV2,missense_variant,p.Arg243Gln,ENST00000382082,NM_133497.3;PUM3,downstream_gene_variant,,ENST00000490444,; A ENST00000382082 Transcript missense_variant 966/2186 728/1638 243/545 R/Q cGg/cAg 1 1 KCNV2 HGNC HGNC:19698 protein_coding YES CCDS6447.1 ENSP00000371514 Q8TDN2 UPI0000048D8E NM_133497.3 deleterious(0.03) 1/2 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF40,Gene3D:1.20.120.350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 2718467 2718467 G A 1 0 0 0 0 1 0 0 0 8011 1116 39 1 1 KCNV2 9 2718467 Missense_Mutation SNP G C3N-00203_T 1728318 2718467 135676250 238 11542 ARID3C 0 . GRCh38 9 34623913 34623913 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.526C>T p.Leu176Phe p.L176F ENST00000378909 3/7 196 162 34 138 138 0 strelka-varscan-mutect ARID3C,missense_variant,p.Leu176Phe,ENST00000378909,NM_001017363.1;DCTN3,upstream_gene_variant,,ENST00000378913,;DCTN3,upstream_gene_variant,,ENST00000341694,NM_024348.3,NM_001281426.1;DCTN3,upstream_gene_variant,,ENST00000259632,NM_007234.4;DCTN3,upstream_gene_variant,,ENST00000378916,NM_001281425.1;DCTN3,upstream_gene_variant,,ENST00000477738,NM_001281427.1;DCTN3,upstream_gene_variant,,ENST00000421919,;DCTN3,upstream_gene_variant,,ENST00000378911,; A ENST00000378909 Transcript missense_variant 619/1411 526/1239 176/412 L/F Ctc/Ttc 1 -1 ARID3C HGNC HGNC:21209 protein_coding YES CCDS35006.1 ENSP00000368189 A6NKF2 UPI0000509F06 NM_001017363.1 deleterious(0) 3/7 Gene3D:1.10.150.60,Pfam_domain:PF01388,PROSITE_profiles:PS51011,hmmpanther:PTHR15348,hmmpanther:PTHR15348:SF2,SMART_domains:SM00501,SMART_domains:SM01014,Superfamily_domains:SSF46774 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 34623913 34623913 G A 1 0 0 0 0 1 0 0 0 1054 1000 35 3 3 ARID3C 9 34623913 Missense_Mutation SNP G C3N-00203_T 31905446 34623913 103770804 239 11543 CCIN 0 . GRCh38 9 36169968 36169968 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.466A>T p.Ile156Phe p.I156F ENST00000335119 1/1 283 247 36 241 241 0 strelka-varscan-mutect CCIN,missense_variant,p.Ile156Phe,ENST00000335119,NM_005893.2; T ENST00000335119 Transcript missense_variant 575/1941 466/1767 156/588 I/F Att/Ttt 1 1 CCIN HGNC HGNC:1568 protein_coding YES CCDS6599.1 ENSP00000334996 Q13939 Q8WX35 UPI000006EB8E NM_005893.2 deleterious(0.01) 1/1 hmmpanther:PTHR24412:SF163,hmmpanther:PTHR24412,Pfam_domain:PF07707,SMART_domains:SM00875 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 36169968 36169968 A T 1 0 0 0 0 1 0 0 0 2576 217 8 4 4 CCIN 9 36169968 Missense_Mutation SNP A C3N-00203_T 1546055 36169968 102224749 240 11544 ZBTB5 0 . GRCh38 9 37441896 37441896 + Missense_Mutation SNP G G A C3N-00203_T C3N-00203_N G G c.656C>T p.Pro219Leu p.P219L ENST00000307750 2/2 224 177 47 169 168 1 strelka-varscan-mutect ZBTB5,missense_variant,p.Pro219Leu,ENST00000307750,NM_014872.2;GRHPR,downstream_gene_variant,,ENST00000318158,NM_012203.1;GRHPR,downstream_gene_variant,,ENST00000497693,;GRHPR,downstream_gene_variant,,ENST00000480596,;GRHPR,downstream_gene_variant,,ENST00000494290,; A ENST00000307750 Transcript missense_variant 845/4627 656/2034 219/677 P/L cCg/cTg COSM2775610 1 -1 ZBTB5 HGNC HGNC:23836 protein_coding YES CCDS6610.1 ENSP00000307604 O15062 Q5T942 UPI000006FAE2 NM_014872.2 deleterious(0.01) 2/2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 A 3 1 42 37441896 37441896 G A 1 0 0 0 0 1 0 0 0 18121 1116 39 1 1 ZBTB5 9 37441896 Missense_Mutation SNP G C3N-00203_T 1271928 37441896 100952821 241 11545 CNTNAP3 0 . GRCh38 9 39109213 39109213 + Missense_Mutation SNP C C G rs757220529 C3N-00203_T C3N-00203_N C C c.2312G>C p.Arg771Pro p.R771P ENST00000297668 15/24 227 168 59 236 236 0 strelka-varscan-mutect CNTNAP3,missense_variant,p.Arg771Pro,ENST00000297668,NM_033655.3;CNTNAP3,missense_variant,p.Arg770Pro,ENST00000377656,;CNTNAP3,missense_variant,p.Arg683Pro,ENST00000358144,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000495573,;CNTNAP3,intron_variant,,ENST00000448573,;CNTNAP3,3_prime_UTR_variant,,ENST00000443583,; G ENST00000297668 Transcript missense_variant 2386/5064 2312/3867 771/1288 R/P cGa/cCa rs757220529,COSM1109164 1 -1 CNTNAP3 HGNC HGNC:13834 protein_coding YES CCDS6616.1 ENSP00000297668 Q9BZ76 UPI000013E43B NM_033655.3 deleterious(0) 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757220529 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 39109213 39109213 C G 1 0 0 0 0 1 0 0 0 3429 884 31 4 4 CNTNAP3 9 39109213 Missense_Mutation SNP C C3N-00203_T 1667317 39109213 99285504 242 11546 SPATA31A3 0 . GRCh38 9 66991076 66991076 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.245G>T p.Arg82Ile p.R82I ENST00000428649 2/4 108 84 24 138 137 1 strelka-varscan-mutect SPATA31A3,missense_variant,p.Arg82Ile,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; A ENST00000428649 Transcript missense_variant,splice_region_variant 307/4256 245/4044 82/1347 R/I aGa/aTa 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 deleterious(0) 2/4 Pfam_domain:PF15371,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 66991076 66991076 C A 1 0 0 0 0 1 0 0 0 15344 927 32 2 2 SPATA31A3 9 66991076 Missense_Mutation SNP C C3N-00203_T 27881863 66991076 71403641 243 11547 DAPK1 0 . GRCh38 9 87646495 87646495 + Missense_Mutation SNP G G T rs570212877 C3N-00203_T C3N-00203_N G G c.1166G>T p.Cys389Phe p.C389F ENST00000408954 13/26 282 220 62 229 229 0 strelka-varscan-mutect DAPK1,missense_variant,p.Cys389Phe,ENST00000469640,;DAPK1,missense_variant,p.Cys389Phe,ENST00000408954,NM_004938.3;DAPK1,missense_variant,p.Cys389Phe,ENST00000622514,NM_001288729.1;DAPK1,missense_variant,p.Cys389Phe,ENST00000472284,NM_001288730.1;DAPK1,missense_variant,p.Cys389Phe,ENST00000358077,NM_001288731.1;DAPK1,missense_variant,p.Cys389Phe,ENST00000491893,;DAPK1,upstream_gene_variant,,ENST00000495281,;DAPK1,upstream_gene_variant,,ENST00000494010,;DAPK1,3_prime_UTR_variant,,ENST00000489291,;DAPK1,non_coding_transcript_exon_variant,,ENST00000469067,;DAPK1,upstream_gene_variant,,ENST00000475804,; T ENST00000408954 Transcript missense_variant 1501/5892 1166/4293 389/1430 C/F tGt/tTt rs570212877 1 1 DAPK1 HGNC HGNC:2674 protein_coding YES CCDS43842.1 ENSP00000386135 P53355 UPI0000210C2F NM_004938.3 tolerated(0.65) 13/26 Gene3D:1.25.40.20,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF699,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs570212877 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 87646495 87646495 G T 1 0 0 0 0 1 0 0 0 4036 1377 48 2 2 DAPK1 9 87646495 Missense_Mutation SNP G C3N-00203_T 20655419 87646495 50748222 244 11548 TBC1D2 0 . GRCh38 9 98255237 98255237 + Missense_Mutation SNP C C A rs550202423 C3N-00203_T C3N-00203_N C C c.305G>T p.Cys102Phe p.C102F ENST00000465784 1/13 193 144 49 180 180 0 strelka-varscan-mutect TBC1D2,missense_variant,p.Cys102Phe,ENST00000465784,NM_001267571.1;TBC1D2,missense_variant,p.Cys102Phe,ENST00000375066,NM_018421.3;TBC1D2,missense_variant,p.Cys102Phe,ENST00000375064,;TBC1D2,5_prime_UTR_variant,,ENST00000342112,; A ENST00000465784 Transcript missense_variant 485/3349 305/2787 102/928 C/F tGt/tTt rs550202423 1 -1 TBC1D2 HGNC HGNC:18026 protein_coding YES CCDS75865.1 ENSP00000481721 Q9BYX2 UPI000022D946 NM_001267571.1 tolerated(0.72) 1/13 PROSITE_profiles:PS50003,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs550202423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 98255237 98255237 C A 1 0 0 0 0 1 0 0 0 16008 478 17 2 2 TBC1D2 9 98255237 Missense_Mutation SNP C C3N-00203_T 10608742 98255237 40139480 245 11549 ANKS6 0 . GRCh38 9 98780228 98780228 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1329G>T p.Trp443Cys p.W443C ENST00000353234 6/15 326 247 79 295 294 1 strelka-varscan-mutect ANKS6,missense_variant,p.Trp443Cys,ENST00000353234,NM_173551.3;ANKS6,missense_variant,p.Trp142Cys,ENST00000375019,;ANKS6,upstream_gene_variant,,ENST00000444472,;ANKS6,non_coding_transcript_exon_variant,,ENST00000634393,;ANKS6,downstream_gene_variant,,ENST00000486778,;ANKS6,downstream_gene_variant,,ENST00000466120,; A ENST00000353234 Transcript missense_variant 1377/7164 1329/2616 443/871 W/C tgG/tgT 1 -1 ANKS6 HGNC HGNC:26724 protein_coding YES CCDS43856.1 ENSP00000297837 Q68DC2 UPI0000530317 NM_173551.3 tolerated(0.14) 6/15 hmmpanther:PTHR10627:SF39,hmmpanther:PTHR10627 MODERATE 1 SNV 1 1 PASS rs915544649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 98780228 98780228 C A 1 0 0 0 0 1 0 0 0 798 856 30 2 2 ANKS6 9 98780228 Missense_Mutation SNP C C3N-00203_T 524991 98780228 39614489 246 11550 WHRN 0 . GRCh38 9 114426215 114426215 + Missense_Mutation SNP C C G rs774944578 C3N-00203_T C3N-00203_N C C c.1162G>C p.Ala388Pro p.A388P ENST00000362057 4/12 399 354 45 317 317 0 strelka-varscan-mutect WHRN,missense_variant,p.Ala388Pro,ENST00000362057,NM_015404.3,NM_001173425.1;WHRN,missense_variant,p.Ala5Pro,ENST00000265134,NM_001083885.2;WHRN,upstream_gene_variant,,ENST00000374059,; G ENST00000362057 Transcript missense_variant 1331/3566 1162/2724 388/907 A/P Gca/Cca rs774944578 1 -1 WHRN HGNC HGNC:16361 protein_coding YES CCDS6806.1 ENSP00000354623 A0A0C4DFT9 UPI00003519A7 NM_015404.3,NM_001173425.1 tolerated(0.16) 4/12 hmmpanther:PTHR23116:SF37,hmmpanther:PTHR23116 MODERATE 1 SNV 1 1 PASS rs774944578 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 114426215 114426215 C G 1 0 0 0 0 1 0 0 0 17919 753 26 4 4 WHRN 9 114426215 Missense_Mutation SNP C C3N-00203_T 15645987 114426215 23968502 247 11551 TNC 0 . GRCh38 9 115024124 115024124 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.6344C>A p.Ala2115Asp p.A2115D ENST00000350763 27/28 85 73 12 44 44 0 strelka-varscan-mutect TNC,missense_variant,p.Ala2115Asp,ENST00000350763,NM_002160.3;TNC,missense_variant,p.Ala1752Asp,ENST00000535648,;TNC,missense_variant,p.Ala1933Asp,ENST00000341037,;TNC,missense_variant,p.Ala1842Asp,ENST00000423613,;TNC,missense_variant,p.Ala1752Asp,ENST00000542877,;TNC,missense_variant,p.Ala1478Asp,ENST00000537320,; T ENST00000350763 Transcript missense_variant 6756/7641 6344/6606 2115/2201 A/D gCc/gAc 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 deleterious(0.04) 27/28 PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF38,hmmpanther:PTHR19143,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 115024124 115024124 G T 1 0 0 0 0 1 0 0 0 16744 1203 42 2 2 TNC 9 115024124 Missense_Mutation SNP G C3N-00203_T 597909 115024124 23370593 248 11552 PAPPA 0 . GRCh38 9 116211641 116211641 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1627G>T p.Gly543Cys p.G543C ENST00000328252 4/22 129 102 27 116 116 0 strelka-varscan-mutect PAPPA,missense_variant,p.Gly543Cys,ENST00000328252,NM_002581.3; T ENST00000328252 Transcript missense_variant,splice_region_variant 1996/10959 1627/4884 543/1627 G/C Ggc/Tgc 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 4/22 Gene3D:3.40.390.10,Pfam_domain:PF05572,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 116211641 116211641 G T 1 0 0 0 0 1 0 0 0 11512 1362 47 2 2 PAPPA 9 116211641 Missense_Mutation SNP G C3N-00203_T 1187517 116211641 22183076 249 11553 ASTN2 0 . GRCh38 9 117414584 117414584 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.355C>G p.Leu119Val p.L119V ENST00000361209 1/22 168 134 34 143 143 0 strelka-varscan-mutect ASTN2,missense_variant,p.Leu119Val,ENST00000313400,;ASTN2,missense_variant,p.Leu119Val,ENST00000361209,NM_014010.4;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; C ENST00000361209 Transcript missense_variant 487/4622 355/3867 119/1288 L/V Ctc/Gtc 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 deleterious_low_confidence(0) 1/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 117414584 117414584 G C 1 0 0 0 0 1 0 0 0 1212 1000 35 4 4 ASTN2 9 117414584 Missense_Mutation SNP G C3N-00203_T 1202943 117414584 20980133 250 11554 CDK5RAP2 0 . GRCh38 9 120539040 120539040 + Splice_Site SNP C C A novel C3N-00203_T C3N-00203_N C C c.507+1G>T p.X169_splice ENST00000349780 388 287 101 373 372 1 strelka-varscan-mutect CDK5RAP2,splice_donor_variant,,ENST00000349780,NM_018249.5;CDK5RAP2,splice_donor_variant,,ENST00000360190,NM_001011649.2;CDK5RAP2,splice_donor_variant,,ENST00000360822,NM_001272039.1;CDK5RAP2,splice_donor_variant,,ENST00000472883,;CDK5RAP2,splice_donor_variant,,ENST00000473282,;CDK5RAP2,splice_donor_variant,,ENST00000480112,;CDK5RAP2,splice_donor_variant,,ENST00000481266,;CDK5RAP2,upstream_gene_variant,,ENST00000483412,; A ENST00000349780 Transcript splice_donor_variant -/6228 507/5682 169/1893 1 -1 CDK5RAP2 HGNC HGNC:18672 protein_coding YES CCDS6823.1 ENSP00000343818 Q96SN8 UPI0000367673 NM_018249.5 6/37 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 42 120539040 120539040 C A 1 0 0 0 0 0 0 1 0 2850 753 26 2 2 CDK5RAP2 9 120539040 Splice_Site SNP C C3N-00203_T 3124456 120539040 17855677 251 11555 TTLL11 0 . GRCh38 9 121870642 121870642 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.1858A>G p.Ile620Val p.I620V ENST00000321582 7/9 231 181 50 191 191 0 strelka-varscan-mutect TTLL11,missense_variant,p.Ile620Val,ENST00000321582,NM_001139442.1;TTLL11,3_prime_UTR_variant,,ENST00000474723,;TTLL11,3_prime_UTR_variant,,ENST00000373778,; C ENST00000321582 Transcript missense_variant 2046/3250 1858/2403 620/800 I/V Att/Gtt 1 -1 TTLL11 HGNC HGNC:18113 protein_coding YES CCDS48012.1 ENSP00000321346 Q8NHH1 UPI0000E0BF7B NM_001139442.1 deleterious(0.02) 7/9 hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF107 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 121870642 121870642 T C 1 0 0 0 0 1 0 0 0 17236 1464 51 5 5 TTLL11 9 121870642 Missense_Mutation SNP T C3N-00203_T 1331602 121870642 16524075 252 11556 C9orf78 0 . GRCh38 9 129828208 129828208 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.823G>T p.Asp275Tyr p.D275Y ENST00000372447 9/9 281 257 24 255 255 0 strelka-varscan-mutect C9orf78,missense_variant,p.Asp275Tyr,ENST00000372447,NM_016520.2;TOR1A,upstream_gene_variant,,ENST00000351698,NM_000113.2;C9orf78,non_coding_transcript_exon_variant,,ENST00000461349,;C9orf78,downstream_gene_variant,,ENST00000461762,;C9orf78,downstream_gene_variant,,ENST00000480023,;TOR1A,upstream_gene_variant,,ENST00000473084,;TOR1A,upstream_gene_variant,,ENST00000473604,;C9orf78,downstream_gene_variant,,ENST00000461539,;C9orf78,downstream_gene_variant,,ENST00000492991,;C9orf78,downstream_gene_variant,,ENST00000495934,; A ENST00000372447 Transcript missense_variant 877/1795 823/870 275/289 D/Y Gat/Tat 1 -1 C9orf78 HGNC HGNC:24932 protein_coding YES CCDS6931.1 ENSP00000361524 Q9NZ63 UPI000006F0CA NM_016520.2 deleterious(0) 9/9 hmmpanther:PTHR13486:SF2,hmmpanther:PTHR13486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 129828208 129828208 C A 1 0 0 0 0 1 0 0 0 2191 826 29 2 2 C9orf78 9 129828208 Missense_Mutation SNP C C3N-00203_T 7957566 129828208 8566509 253 11557 ABCA2 0 . GRCh38 9 137016448 137016448 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2947G>T p.Glu983Ter p.E983* ENST00000341511 21/49 209 187 22 144 143 1 strelka-varscan-mutect ABCA2,stop_gained,p.Glu983Ter,ENST00000265662,;ABCA2,stop_gained,p.Glu982Ter,ENST00000371605,;ABCA2,stop_gained,p.Glu1013Ter,ENST00000614293,;ABCA2,stop_gained,p.Glu983Ter,ENST00000341511,NM_001606.4,NM_212533.2;ABCA2,stop_gained,p.Glu333Ter,ENST00000479446,;ABCA2,stop_gained,p.Glu330Ter,ENST00000488535,;ABCA2,3_prime_UTR_variant,,ENST00000487109,;ABCA2,non_coding_transcript_exon_variant,,ENST00000459850,;ABCA2,downstream_gene_variant,,ENST00000464876,;ABCA2,downstream_gene_variant,,ENST00000492260,;ABCA2,downstream_gene_variant,,ENST00000494046,;ABCA2,upstream_gene_variant,,ENST00000431584,;ABCA2,downstream_gene_variant,,ENST00000470535,;ABCA2,downstream_gene_variant,,ENST00000466707,;ABCA2,downstream_gene_variant,,ENST00000467624,; A ENST00000341511 Transcript stop_gained 2997/8063 2947/7311 983/2436 E/* Gag/Tag 1 -1 ABCA2 HGNC HGNC:32 protein_coding YES CCDS43909.1 ENSP00000344155 Q9BZC7 UPI0000049F97 NM_001606.4,NM_212533.2 21/49 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF116 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 137016448 137016448 C A 1 0 0 0 0 0 1 0 0 36 864 30 2 2 ABCA2 9 137016448 Nonsense_Mutation SNP C C3N-00203_T 7188240 137016448 1378269 254 11558 KIAA1217 0 . GRCh38 10 24543531 24543531 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.4261G>T p.Glu1421Ter p.E1421* ENST00000376454 19/21 276 215 61 282 281 1 strelka-varscan-mutect KIAA1217,stop_gained,p.Glu1104Ter,ENST00000376451,;KIAA1217,stop_gained,p.Glu1421Ter,ENST00000376454,NM_019590.4;KIAA1217,stop_gained,p.Glu304Ter,ENST00000635163,;KIAA1217,intron_variant,,ENST00000376462,NM_001098500.2;KIAA1217,intron_variant,,ENST00000376452,NM_001282767.1;KIAA1217,intron_variant,,ENST00000458595,NM_001282768.1;KIAA1217,intron_variant,,ENST00000430453,;KIAA1217,intron_variant,,ENST00000396445,;KIAA1217,intron_variant,,ENST00000307544,NM_001282769.1;KIAA1217,intron_variant,,ENST00000396446,NM_001282770.1;KIAA1217,non_coding_transcript_exon_variant,,ENST00000492009,; T ENST00000376454 Transcript stop_gained 4291/7381 4261/5832 1421/1943 E/* Gag/Tag 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 19/21 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 24543531 24543531 G T 1 0 0 0 0 0 1 0 0 8109 943 33 2 2 KIAA1217 10 24543531 Nonsense_Mutation SNP G C3N-00203_T 24543531 109253891 255 11559 MPP7 0 . GRCh38 10 28059698 28059698 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.1250A>T p.Tyr417Phe p.Y417F ENST00000337532 15/18 312 253 59 271 271 0 strelka-varscan-mutect MPP7,missense_variant,p.Tyr417Phe,ENST00000337532,NM_001318170.1,NM_173496.3;MPP7,missense_variant,p.Tyr417Phe,ENST00000375732,;MPP7,missense_variant,p.Tyr417Phe,ENST00000375719,;MPP7,missense_variant,p.Tyr178Phe,ENST00000441595,;MPP7,missense_variant,p.Tyr417Phe,ENST00000496637,; A ENST00000337532 Transcript missense_variant 1527/5080 1250/1731 417/576 Y/F tAc/tTc 1 -1 MPP7 HGNC HGNC:26542 protein_coding YES CCDS7158.1 ENSP00000337907 Q5T2T1 UPI00000558E1 NM_001318170.1,NM_173496.3 deleterious(0) 15/18 PROSITE_profiles:PS50052,hmmpanther:PTHR23122:SF39,hmmpanther:PTHR23122,PROSITE_patterns:PS00856,Gene3D:3.30.63.10,Pfam_domain:PF00625,SMART_domains:SM00072,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 28059698 28059698 T A 1 0 0 0 0 1 0 0 0 9705 1638 57 4 4 MPP7 10 28059698 Missense_Mutation SNP T C3N-00203_T 3516167 28059698 105737724 256 11560 EPC1 0 . GRCh38 10 32292991 32292991 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.663A>G p.= p.R221R ENST00000263062 4/15 163 128 35 135 135 0 strelka-varscan-mutect EPC1,synonymous_variant,p.=,ENST00000319778,NM_001272019.2,NM_001272004.1;EPC1,synonymous_variant,p.=,ENST00000375110,NM_001282391.1;EPC1,synonymous_variant,p.=,ENST00000263062,NM_025209.3;EPC1,non_coding_transcript_exon_variant,,ENST00000495790,; C ENST00000263062 Transcript synonymous_variant 933/2913 663/2511 221/836 R cgA/cgG 1 -1 EPC1 HGNC HGNC:19876 protein_coding YES CCDS7172.1 ENSP00000263062 Q9H2F5 UPI000006F77F NM_025209.3 4/15 hmmpanther:PTHR14898,hmmpanther:PTHR14898:SF6 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 32292991 32292991 T C 1 0 0 0 0 0 0 0 1 5006 1797 62 5 5 EPC1 10 32292991 Silent SNP T C3N-00203_T 4233293 32292991 101504431 257 11561 FZD8 0 . GRCh38 10 35640771 35640771 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.659C>A p.Pro220His p.P220H ENST00000374694 1/1 24 16 8 25 25 0 strelka-varscan-mutect FZD8,missense_variant,p.Pro220His,ENST00000374694,NM_031866.2;FZD8,downstream_gene_variant,,ENST00000579659,; T ENST00000374694 Transcript missense_variant 1508/4030 659/2085 220/694 P/H cCc/cAc 1 -1 FZD8 HGNC HGNC:4046 protein_coding YES CCDS7192.1 ENSP00000363826 Q9H461 UPI0000047F3B NM_031866.2 tolerated(0.06) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 206 3 0 0 0 0 0 -19.99875 1 1 1 1 0 T 3 4 42 35640771 35640771 G T 1 0 0 0 0 1 0 0 0 6007 1232 43 2 2 FZD8 10 35640771 Missense_Mutation SNP G C3N-00203_T 3347780 35640771 98156651 258 11562 PRKG1 0 . GRCh38 10 52280815 52280815 + Missense_Mutation SNP G G T C3N-00203_T C3N-00203_N G G c.1430G>T p.Arg477Ile p.R477I ENST00000373980 13/18 353 191 162 304 304 0 strelka-varscan-mutect PRKG1,missense_variant,p.Arg477Ile,ENST00000373980,NM_006258.3;PRKG1,missense_variant,p.Arg462Ile,ENST00000373985,NM_001098512.2;PRKG1,missense_variant,p.Arg250Ile,ENST00000401604,;PRKG1-AS1,intron_variant,,ENST00000426785,;PRKG1-AS1,intron_variant,,ENST00000452247,;PRKG1,non_coding_transcript_exon_variant,,ENST00000373975,; T ENST00000373980 Transcript missense_variant 1847/6928 1430/2061 477/686 R/I aGa/aTa COSM2146593,COSM2146594 1 1 PRKG1 HGNC HGNC:9414 protein_coding YES CCDS7244.1 ENSP00000363092 Q13976 UPI000012DDCD NM_006258.3 deleterious(0) 13/18 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000559,PROSITE_profiles:PS50011,hmmpanther:PTHR24353,hmmpanther:PTHR24353:SF68,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 52280815 52280815 G T 1 0 0 0 0 1 0 0 0 12655 942 33 2 2 PRKG1 10 52280815 Missense_Mutation SNP G C3N-00203_T 16640044 52280815 81516607 259 11563 KCNMA1 0 . GRCh38 10 77086560 77086560 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.1368C>T p.= p.F456F ENST00000286628 11/28 541 322 219 431 431 0 strelka-varscan-mutect KCNMA1,synonymous_variant,p.=,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,synonymous_variant,p.=,ENST00000286627,NM_002247.3;KCNMA1,synonymous_variant,p.=,ENST00000286628,NM_001161352.1;KCNMA1,synonymous_variant,p.=,ENST00000354353,;KCNMA1,synonymous_variant,p.=,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,synonymous_variant,p.=,ENST00000372443,;KCNMA1,synonymous_variant,p.=,ENST00000372440,NM_001014797.2;KCNMA1,synonymous_variant,p.=,ENST00000404771,;KCNMA1,synonymous_variant,p.=,ENST00000457953,;KCNMA1,synonymous_variant,p.=,ENST00000626620,NM_001161353.1;KCNMA1,synonymous_variant,p.=,ENST00000372437,;KCNMA1,synonymous_variant,p.=,ENST00000372421,;KCNMA1,synonymous_variant,p.=,ENST00000372408,;KCNMA1,synonymous_variant,p.=,ENST00000372403,;KCNMA1,synonymous_variant,p.=,ENST00000404857,NM_001271518.1;KCNMA1,synonymous_variant,p.=,ENST00000434208,;KCNMA1,upstream_gene_variant,,ENST00000484507,; A ENST00000286628 Transcript synonymous_variant 1368/6100 1368/3711 456/1236 F ttC/ttT 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 11/28 Gene3D:3.40.50.720,Prints_domain:PR01449,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 77086560 77086560 G A 1 0 0 0 0 0 0 0 1 7990 1281 45 3 3 KCNMA1 10 77086560 Silent SNP G C3N-00203_T 24805745 77086560 56710862 260 11564 MYOF 0 . GRCh38 10 93392937 93392937 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.1436C>G p.Thr479Ser p.T479S ENST00000359263 17/54 243 146 97 182 182 0 strelka-varscan-mutect MYOF,missense_variant,p.Thr479Ser,ENST00000359263,NM_013451.3;MYOF,intron_variant,,ENST00000358334,NM_133337.2;MYOF,downstream_gene_variant,,ENST00000371489,; C ENST00000359263 Transcript missense_variant 1436/6719 1436/6186 479/2061 T/S aCt/aGt 1 -1 MYOF HGNC HGNC:3656 protein_coding YES CCDS41551.1 ENSP00000352208 Q9NZM1 UPI000012FBA1 NM_013451.3 tolerated(0.86) 17/54 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 93392937 93392937 G C 1 0 0 0 0 1 0 0 0 10090 1029 36 4 4 MYOF 10 93392937 Missense_Mutation SNP G C3N-00203_T 16306377 93392937 40404485 261 11565 DNMBP 0 . GRCh38 10 99955806 99955806 + Silent SNP C C A rs749330402 C3N-00203_T C3N-00203_N C C c.1668G>T p.= p.L556L ENST00000324109 4/17 313 171 142 249 249 0 strelka-varscan-mutect DNMBP,synonymous_variant,p.=,ENST00000324109,NM_015221.2;DNMBP-AS1,non_coding_transcript_exon_variant,,ENST00000434409,; A ENST00000324109 Transcript synonymous_variant 1760/6400 1668/4734 556/1577 L ctG/ctT rs749330402 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 4/17 hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834 LOW 1 SNV 1 1 PASS rs749330402 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 99955806 99955806 C A 1 0 0 0 0 0 0 0 1 4487 813 29 2 2 DNMBP 10 99955806 Silent SNP C C3N-00203_T 6562869 99955806 33841616 262 11566 TLX1 0 . GRCh38 10 101131576 101131576 + Missense_Mutation SNP G G T rs547819047 C3N-00203_T C3N-00203_N G G c.35G>T p.Gly12Val p.G12V ENST00000370196 1/3 90 84 6 82 82 0 strelka-varscan-mutect TLX1,missense_variant,p.Gly12Val,ENST00000370196,NM_005521.3;TLX1,missense_variant,p.Gly12Val,ENST00000467928,NM_001195517.1;TLX1,upstream_gene_variant,,ENST00000463716,;TLX1NB,upstream_gene_variant,,ENST00000445873,;TLX1NB,upstream_gene_variant,,ENST00000425505,;TLX1,upstream_gene_variant,,ENST00000533319,;TLX1,upstream_gene_variant,,ENST00000525019,; T ENST00000370196 Transcript missense_variant 1072/2906 35/993 12/330 G/V gGt/gTt rs547819047 1 1 TLX1 HGNC HGNC:5056 protein_coding YES CCDS7510.1 ENSP00000359215 P31314 UPI000013705F NM_005521.3 tolerated(0.09) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF120,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS rs547819047 . 0 204 2 4 0 0 0 0 -9.567982 0.9986622 1 1 1 0 T 3 4 42 101131576 101131576 G T 1 0 0 0 0 1 0 0 0 16405 1261 44 2 2 TLX1 10 101131576 Missense_Mutation SNP G C3N-00203_T 1175770 101131576 32665846 263 11567 SORCS3 0 . GRCh38 10 105139416 105139416 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1232C>A p.Ala411Asp p.A411D ENST00000369701 8/27 105 73 32 97 97 0 strelka-varscan-mutect SORCS3,missense_variant,p.Ala411Asp,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Ala411Asp,ENST00000369699,; A ENST00000369701 Transcript missense_variant 1459/5757 1232/3669 411/1222 A/D gCc/gAc 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0.02) 8/27 Pfam_domain:PF15902,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,SMART_domains:SM00602 MODERATE 1 SNV 1 1 PASS rs1163237794 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 105139416 105139416 C A 1 0 0 0 0 1 0 0 0 15254 739 26 2 2 SORCS3 10 105139416 Missense_Mutation SNP C C3N-00203_T 4007840 105139416 28658006 264 11568 TACC2 0 . GRCh38 10 122085467 122085467 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.2967G>T p.= p.G989G ENST00000369005 4/23 439 249 190 321 321 0 strelka-varscan-mutect TACC2,synonymous_variant,p.=,ENST00000369005,NM_206862.3;TACC2,synonymous_variant,p.=,ENST00000334433,;TACC2,synonymous_variant,p.=,ENST00000515273,NM_001291877.1;TACC2,synonymous_variant,p.=,ENST00000453444,;TACC2,synonymous_variant,p.=,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; T ENST00000369005 Transcript synonymous_variant 3307/9673 2967/8847 989/2948 G ggG/ggT 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 4/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 122085467 122085467 G T 1 0 0 0 0 0 0 0 1 15898 1190 42 2 2 TACC2 10 122085467 Silent SNP G C3N-00203_T 16946051 122085467 11711955 265 11569 CFAP46 0 . GRCh38 10 132847074 132847074 + Missense_Mutation SNP G G T rs372515344 C3N-00203_T C3N-00203_N G G c.6125C>A p.Ala2042Glu p.A2042E ENST00000368586 43/58 104 56 48 80 80 0 strelka-varscan-mutect CFAP46,missense_variant,p.Ala2042Glu,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript missense_variant 6226/8278 6125/8148 2042/2715 A/E gCg/gAg rs372515344 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 deleterious(0) 43/58 hmmpanther:PTHR15977,hmmpanther:PTHR15977:SF15 MODERATE 1 SNV 5 1 PASS rs372515344 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 132847074 132847074 G T 1 0 0 0 0 1 0 0 0 3021 1087 38 1 1 CFAP46 10 132847074 Missense_Mutation SNP G C3N-00203_T 10761607 132847074 950348 266 11570 TRPM5 0 . GRCh38 11 2421188 2421188 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.309C>T p.= p.I103I ENST00000155858 3/24 210 150 60 183 183 0 strelka-varscan-mutect TRPM5,synonymous_variant,p.=,ENST00000155858,NM_014555.3;TRPM5,synonymous_variant,p.=,ENST00000533881,;TRPM5,synonymous_variant,p.=,ENST00000533060,;TRPM5,synonymous_variant,p.=,ENST00000528453,; A ENST00000155858 Transcript synonymous_variant 318/3929 309/3498 103/1165 I atC/atT 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 3/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 LOW 1 SNV 1 1 PASS rs1337463471 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 2421188 2421188 G A 1 0 0 0 0 0 0 0 1 17095 1164 41 3 3 TRPM5 11 2421188 Silent SNP G C3N-00203_T 2421188 132665434 267 11571 OR52J3 0 . GRCh38 11 5046855 5046855 + Silent SNP T T A novel C3N-00203_T C3N-00203_N T T c.330T>A p.= p.T110T ENST00000380370 1/1 200 147 53 207 207 0 strelka-varscan-mutect OR52J3,synonymous_variant,p.=,ENST00000380370,NM_001001916.2; A ENST00000380370 Transcript synonymous_variant 330/936 330/936 110/311 T acT/acA 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 5046855 5046855 T A 1 0 0 0 0 0 0 0 1 11195 1567 55 4 4 OR52J3 11 5046855 Silent SNP T C3N-00203_T 2625667 5046855 130039767 268 11572 OR51B5 0 . GRCh38 11 5343513 5343513 + Missense_Mutation SNP G G T rs201732422 C3N-00203_T C3N-00203_N G G c.12C>A p.Ser4Arg p.S4R ENST00000300773 1/1 34 23 11 65 65 0 strelka-varscan-mutect OR51B5,missense_variant,p.Ser4Arg,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300773 Transcript missense_variant 12/939 12/939 4/312 S/R agC/agA rs201732422 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76 MODERATE SNV 1 PASS rs201732422 . 0 200 10 0 0 0 0 0 -20 0.9999963 1 1 1 0 T 3 4 42 5343513 5343513 G T 1 0 0 0 0 1 0 0 0 11165 1078 38 1 1 OR51B5 11 5343513 Missense_Mutation SNP G C3N-00203_T 296658 5343513 129743109 269 11573 OR51J1 0 . GRCh38 11 5403114 5403114 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.518G>T p.Trp173Leu p.W173L ENST00000332043 1/1 200 144 56 214 213 1 strelka-varscan-mutect OR51J1,missense_variant,p.Trp173Leu,ENST00000332043,;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000332043 Transcript missense_variant 518/951 518/951 173/316 W/L tGg/tTg 1 1 OR51J1 HGNC HGNC:14856 protein_coding YES ENSP00000332473 Q9H342 UPI00001AFFE3 tolerated(1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF81,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 5403114 5403114 G T 1 0 0 0 0 1 0 0 0 11175 1357 47 2 2 OR51J1 11 5403114 Missense_Mutation SNP G C3N-00203_T 59601 5403114 129683508 270 11574 MPPED2 0 . GRCh38 11 30580332 30580332 + Silent SNP C C G rs771565862 C3N-00203_T C3N-00203_N C C c.42G>C p.= p.T14T ENST00000358117 1/6 211 146 65 196 196 0 strelka-varscan-mutect MPPED2,synonymous_variant,p.=,ENST00000448418,NM_001145399.1;MPPED2,synonymous_variant,p.=,ENST00000358117,NM_001584.2;MPPED2,synonymous_variant,p.=,ENST00000528686,;RP5-1024C24.1,upstream_gene_variant,,ENST00000531002,;RP5-1024C24.1,upstream_gene_variant,,ENST00000525871,;MPPED2,synonymous_variant,p.=,ENST00000526437,; G ENST00000358117 Transcript synonymous_variant 165/2405 42/885 14/294 T acG/acC rs771565862 1 -1 MPPED2 HGNC HGNC:1180 protein_coding YES CCDS7870.1 ENSP00000350833 Q15777 UPI0000124E87 NM_001584.2 1/6 PIRSF_domain:PIRSF035808,hmmpanther:PTHR12905,hmmpanther:PTHR12905:SF12 LOW 1 SNV 1 1 PASS rs771565862 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 42 30580332 30580332 C G 1 0 0 0 0 0 0 0 1 9708 639 23 4 4 MPPED2 11 30580332 Silent SNP C C3N-00203_T 25177218 30580332 104506290 271 11575 LARGE2 0 . GRCh38 11 45928274 45928274 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1852C>A p.Pro618Thr p.P618T ENST00000531526 13/14 334 236 98 312 312 0 strelka-varscan-mutect LARGE2,missense_variant,p.Pro618Thr,ENST00000531526,NM_152312.4;LARGE2,missense_variant,p.Pro618Thr,ENST00000325468,;LARGE2,missense_variant,p.Pro618Thr,ENST00000401752,NM_001300721.1;LARGE2,missense_variant,p.Pro587Thr,ENST00000529052,NM_001300722.1;LARGE2,intron_variant,,ENST00000531847,;PHF21A,downstream_gene_variant,,ENST00000323180,NM_016621.3;LARGE2,downstream_gene_variant,,ENST00000534410,;LARGE2,non_coding_transcript_exon_variant,,ENST00000528236,;LARGE2,non_coding_transcript_exon_variant,,ENST00000530437,;PHF21A,downstream_gene_variant,,ENST00000527401,;LARGE2,downstream_gene_variant,,ENST00000414027,;LARGE2,downstream_gene_variant,,ENST00000525609,; A ENST00000531526 Transcript missense_variant 1963/2528 1852/2166 618/721 P/T Ccc/Acc 1 1 LARGE2 HGNC HGNC:16522 protein_coding YES CCDS31473.1 ENSP00000432869 Q8N3Y3 UPI000004B639 NM_152312.4 deleterious(0) 13/14 Pfam_domain:PF13896,hmmpanther:PTHR12270,hmmpanther:PTHR12270:SF23 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 45928274 45928274 C A 1 0 0 0 0 1 0 0 0 8538 507 18 2 2 LARGE2 11 45928274 Missense_Mutation SNP C C3N-00203_T 15347942 45928274 89158348 272 11576 OR5B2 0 . GRCh38 11 58422414 58422414 + Missense_Mutation SNP A A T rs201040273 C3N-00203_T C3N-00203_N A A c.848T>A p.Leu283Gln p.L283Q ENST00000302581 1/1 206 151 55 221 220 1 strelka-varscan-mutect OR5B2,missense_variant,p.Leu283Gln,ENST00000302581,NM_001005566.2; T ENST00000302581 Transcript missense_variant 900/1049 848/930 283/309 L/Q cTg/cAg rs201040273 1 -1 OR5B2 HGNC HGNC:8323 protein_coding YES CCDS31550.1 ENSP00000303076 Q96R09 UPI000004B227 NM_001005566.2 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF3,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs201040273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 58422414 58422414 A T 1 0 0 0 0 1 0 0 0 11221 188 7 4 4 OR5B2 11 58422414 Missense_Mutation SNP A C3N-00203_T 12494140 58422414 76664208 273 11577 OR5B12 0 . GRCh38 11 58439403 58439403 + Frame_Shift_Del DEL T T - novel C3N-00203_T C3N-00203_N T T c.749delA p.Tyr250LeufsTer29 p.Y250Lfs*29 ENST00000302572 1/1 138 96 42 156 156 0 sindel-varindel-pindel OR5B12,frameshift_variant,p.Tyr250LeufsTer29,ENST00000302572,NM_001004733.2; - ENST00000302572 Transcript frameshift_variant 771/1054 749/945 250/314 Y/X tAt/tt 1 -1 OR5B12 HGNC HGNC:15432 protein_coding YES CCDS31551.1 ENSP00000306657 Q96R08 UPI00000015B2 NM_001004733.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 58439403 58439403 T - 1 0 1 0 1 0 0 0 0 11219 1406 49 0 0 OR5B12 11 58439403 Frame_Shift_Del DEL T C3N-00203_T 16989 58439403 76647219 274 11578 MS4A6E 0 . GRCh38 11 60337944 60337944 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.351G>T p.= p.L117L ENST00000300182 2/4 174 131 43 183 182 1 strelka-varscan-mutect MS4A6E,synonymous_variant,p.=,ENST00000300182,NM_139249.2;MS4A6E,synonymous_variant,p.=,ENST00000532756,;MS4A6E,intron_variant,,ENST00000530509,; T ENST00000300182 Transcript synonymous_variant 416/711 351/444 117/147 L ctG/ctT 1 1 MS4A6E HGNC HGNC:14285 protein_coding YES CCDS7984.1 ENSP00000300182 Q96DS6 UPI0000073D4C NM_139249.2 2/4 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF46 LOW 1 SNV 1 1 PASS rs1185862934 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 60337944 60337944 G T 1 0 0 0 0 0 0 0 1 9844 1362 47 2 2 MS4A6E 11 60337944 Silent SNP G C3N-00203_T 1898541 60337944 74748678 275 11579 PGA5 0 . GRCh38 11 61251178 61251178 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1064C>A p.Thr355Asn p.T355N ENST00000312403 9/9 633 487 146 494 493 1 strelka-varscan-mutect PGA5,missense_variant,p.Thr355Asn,ENST00000312403,NM_014224.3;PGA5,missense_variant,p.Thr201Asn,ENST00000451616,;PGA5,missense_variant,p.Thr95Asn,ENST00000541528,;CTD-2331C18.5,downstream_gene_variant,,ENST00000537594,; A ENST00000312403 Transcript missense_variant 1249/1519 1064/1167 355/388 T/N aCc/aAc 1 1 PGA5 HGNC HGNC:8887 protein_coding YES CCDS8001.1 ENSP00000309542 P0DJD9 UPI000006CE33 NM_014224.3 tolerated(0.5) 9/9 Gene3D:2.40.70.10,Pfam_domain:PF00026,PROSITE_profiles:PS51767,hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF239,Superfamily_domains:SSF50630 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 61251178 61251178 C A 1 0 0 0 0 1 0 0 0 11862 507 18 2 2 PGA5 11 61251178 Missense_Mutation SNP C C3N-00203_T 913234 61251178 73835444 276 11580 SLC22A24 0 . GRCh38 11 63096099 63096099 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.962G>T p.Arg321Ile p.R321I ENST00000612278 6/10 189 147 42 151 151 0 strelka-varscan-mutect SLC22A24,missense_variant,p.Arg321Ile,ENST00000612278,NM_001136506.2;SLC22A24,missense_variant,p.Arg321Ile,ENST00000417740,; A ENST00000612278 Transcript missense_variant 1404/2101 962/1659 321/552 R/I aGa/aTa 1 -1 SLC22A24 HGNC HGNC:28542 protein_coding YES CCDS73308.1 ENSP00000480336 A0A087WWM3 UPI000004DAF7 NM_001136506.2 deleterious(0.03) 6/10 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF208,Pfam_domain:PF00083,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 63096099 63096099 C A 1 0 0 0 0 1 0 0 0 14718 913 32 2 2 SLC22A24 11 63096099 Missense_Mutation SNP C C3N-00203_T 1844921 63096099 71990523 277 11581 PACS1 0 . GRCh38 11 66070525 66070525 + Silent SNP C C G novel C3N-00203_T C3N-00203_N C C c.39C>G p.= p.G13G ENST00000320580 1/24 59 50 9 73 73 0 strelka-varscan-mutect PACS1,synonymous_variant,p.=,ENST00000320580,NM_018026.3;SF3B2,downstream_gene_variant,,ENST00000528302,;SF3B2,downstream_gene_variant,,ENST00000322535,NM_006842.2;SF3B2,downstream_gene_variant,,ENST00000530981,;RP11-1167A19.2,upstream_gene_variant,,ENST00000529036,;PACS1,non_coding_transcript_exon_variant,,ENST00000527224,;SF3B2,downstream_gene_variant,,ENST00000534765,; G ENST00000320580 Transcript synonymous_variant 72/4392 39/2892 13/963 G ggC/ggG 1 1 PACS1 HGNC HGNC:30032 protein_coding YES CCDS8129.1 ENSP00000316454 Q6VY07 A0A024R5H6 UPI0000190973 NM_018026.3 1/24 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -19.95746 1 1 1 1 0 G 2 3 42 66070525 66070525 C G 1 0 0 0 0 0 0 0 1 11450 755 27 4 4 PACS1 11 66070525 Silent SNP C C3N-00203_T 2974426 66070525 69016097 278 11582 PPP6R3 0 . GRCh38 11 68554189 68554189 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.663G>T p.= p.L221L ENST00000393801 7/25 230 186 44 172 171 1 strelka-varscan-mutect PPP6R3,synonymous_variant,p.=,ENST00000393800,NM_001164161.1;PPP6R3,synonymous_variant,p.=,ENST00000393801,NM_001164160.1;PPP6R3,synonymous_variant,p.=,ENST00000527403,;PPP6R3,synonymous_variant,p.=,ENST00000265636,NM_018312.4;PPP6R3,synonymous_variant,p.=,ENST00000265637,;PPP6R3,synonymous_variant,p.=,ENST00000524904,NM_001164162.1;PPP6R3,synonymous_variant,p.=,ENST00000529710,NM_001164164.1;PPP6R3,synonymous_variant,p.=,ENST00000524845,NM_001164163.1;PPP6R3,synonymous_variant,p.=,ENST00000529907,;PPP6R3,intron_variant,,ENST00000534534,;PPP6R3,upstream_gene_variant,,ENST00000534190,;PPP6R3,downstream_gene_variant,,ENST00000531244,;PPP6R3,upstream_gene_variant,,ENST00000531432,;PPP6R3,downstream_gene_variant,,ENST00000527069,;PPP6R3,downstream_gene_variant,,ENST00000525050,;PPP6R3,downstream_gene_variant,,ENST00000529172,; T ENST00000393801 Transcript synonymous_variant 878/5069 663/2640 221/879 L ctG/ctT 1 1 PPP6R3 HGNC HGNC:1173 protein_coding YES CCDS53671.1 ENSP00000377390 Q5H9R7 UPI0000688150 NM_001164160.1 7/25 hmmpanther:PTHR12634:SF12,hmmpanther:PTHR12634,Pfam_domain:PF04499,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 68554189 68554189 G T 1 0 0 0 0 0 0 0 1 12536 1277 45 2 2 PPP6R3 11 68554189 Silent SNP G C3N-00203_T 2483664 68554189 66532433 279 11583 FGF3 0 . GRCh38 11 69810334 69810334 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.691G>T p.Gly231Cys p.G231C ENST00000334134 3/3 90 54 36 40 40 0 strelka-varscan-mutect FGF3,missense_variant,p.Gly231Cys,ENST00000334134,NM_005247.2; A ENST00000334134 Transcript missense_variant 782/892 691/720 231/239 G/C Ggc/Tgc 1 -1 FGF3 HGNC HGNC:3681 protein_coding YES CCDS8195.1 ENSP00000334122 P11487 UPI0000040661 NM_005247.2 deleterious_low_confidence(0.02) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 69810334 69810334 C A 1 0 0 0 0 1 0 0 0 5717 623 22 2 2 FGF3 11 69810334 Missense_Mutation SNP C C3N-00203_T 1256145 69810334 65276288 280 11584 FGF3 0 . GRCh38 11 69816370 69816370 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.274T>A p.Phe92Ile p.F92I ENST00000334134 2/3 556 418 138 395 395 0 strelka-varscan-mutect FGF3,missense_variant,p.Phe92Ile,ENST00000334134,NM_005247.2; T ENST00000334134 Transcript missense_variant 365/892 274/720 92/239 F/I Ttc/Atc 1 -1 FGF3 HGNC HGNC:3681 protein_coding YES CCDS8195.1 ENSP00000334122 P11487 UPI0000040661 NM_005247.2 deleterious(0.04) 2/3 hmmpanther:PTHR11486:SF26,hmmpanther:PTHR11486,Pfam_domain:PF00167,Gene3D:2.80.10.50,SMART_domains:SM00442,Superfamily_domains:SSF50353,Prints_domain:PR00262 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 69816370 69816370 A T 1 0 0 0 0 1 0 0 0 5717 72 3 4 4 FGF3 11 69816370 Missense_Mutation SNP A C3N-00203_T 6036 69816370 65270252 281 11585 TMEM135 0 . GRCh38 11 87038095 87038095 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.50A>G p.His17Arg p.H17R ENST00000305494 1/15 455 363 92 367 367 0 strelka-varscan-mutect TMEM135,missense_variant,p.His17Arg,ENST00000340353,NM_001168724.1;TMEM135,missense_variant,p.His17Arg,ENST00000305494,NM_022918.3;TMEM135,missense_variant,p.His17Arg,ENST00000525018,;TMEM135,missense_variant,p.His17Arg,ENST00000526733,;TMEM135,splice_region_variant,,ENST00000532959,;TMEM135,non_coding_transcript_exon_variant,,ENST00000529023,; G ENST00000305494 Transcript missense_variant 89/2433 50/1377 17/458 H/R cAc/cGc 1 1 TMEM135 HGNC HGNC:26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 UPI00001FB0C7 NM_022918.3 deleterious(0) 1/15 hmmpanther:PTHR12459,hmmpanther:PTHR12459:SF3,Pfam_domain:PF15982 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 87038095 87038095 A G 1 0 0 0 0 1 0 0 0 16496 173 6 5 5 TMEM135 11 87038095 Missense_Mutation SNP A C3N-00203_T 17221725 87038095 48048527 282 11586 CASP4 0 . GRCh38 11 104949720 104949720 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.604A>T p.Ser202Cys p.S202C ENST00000444739 5/9 508 323 185 332 332 0 strelka-varscan-mutect CASP4,missense_variant,p.Ser202Cys,ENST00000444739,NM_001225.3;CASP4,missense_variant,p.Ser146Cys,ENST00000393150,NM_033306.2;CASP4,downstream_gene_variant,,ENST00000417440,;CASP4,upstream_gene_variant,,ENST00000533252,;CASP4,non_coding_transcript_exon_variant,,ENST00000531333,;CASP4,non_coding_transcript_exon_variant,,ENST00000529183,;CASP4,non_coding_transcript_exon_variant,,ENST00000529565,;CASP4,non_coding_transcript_exon_variant,,ENST00000533730,;CASP4,non_coding_transcript_exon_variant,,ENST00000524843,;CASP4,downstream_gene_variant,,ENST00000531546,;CASP4,upstream_gene_variant,,ENST00000534356,;CASP4,upstream_gene_variant,,ENST00000525116,;CASP4,upstream_gene_variant,,ENST00000530309,; A ENST00000444739 Transcript missense_variant 1515/2158 604/1134 202/377 S/C Agc/Tgc 1 -1 CASP4 HGNC HGNC:1505 protein_coding YES CCDS8327.1 ENSP00000388566 P49662 UPI000003AEFA NM_001225.3 deleterious(0) 5/9 Gene3D:3.40.50.1460,Pfam_domain:PF00656,PROSITE_patterns:PS01121,PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF149,SMART_domains:SM00115,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 104949720 104949720 T A 1 0 0 0 0 1 0 0 0 2373 1580 55 4 4 CASP4 11 104949720 Missense_Mutation SNP T C3N-00203_T 17911625 104949720 30136902 283 11587 MSANTD4 0 . GRCh38 11 106010515 106010515 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.403G>T p.Gly135Cys p.G135C ENST00000301919 2/3 210 182 28 129 128 1 strelka-varscan-mutect MSANTD4,missense_variant,p.Gly135Cys,ENST00000301919,NM_032424.1;MSANTD4,missense_variant,p.Gly135Cys,ENST00000530788,;MSANTD4,missense_variant,p.Gly23Cys,ENST00000617528,;MSANTD4,downstream_gene_variant,,ENST00000530108,;MSANTD4,downstream_gene_variant,,ENST00000534458,;MSANTD4,upstream_gene_variant,,ENST00000529805,; A ENST00000301919 Transcript missense_variant 1819/4087 403/1038 135/345 G/C Ggt/Tgt 1 -1 MSANTD4 HGNC HGNC:29383 protein_coding YES CCDS31663.1 ENSP00000304713 Q8NCY6 UPI0000073CF1 NM_032424.1 deleterious(0.01) 2/3 hmmpanther:PTHR21732 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 106010515 106010515 C A 1 0 0 0 0 1 0 0 0 9850 681 24 2 2 MSANTD4 11 106010515 Missense_Mutation SNP C C3N-00203_T 1060795 106010515 29076107 284 11588 TECTA 0 . GRCh38 11 121129796 121129796 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2526C>A p.Phe842Leu p.F842L ENST00000392793 10/24 434 354 80 343 343 0 strelka-varscan-mutect TECTA,missense_variant,p.Phe842Leu,ENST00000392793,;TECTA,missense_variant,p.Phe842Leu,ENST00000264037,NM_005422.2; A ENST00000392793 Transcript missense_variant 2797/7426 2526/6468 842/2155 F/L ttC/ttA 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D tolerated(0.53) 10/24 PROSITE_profiles:PS51233,Pfam_domain:PF00094,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 121129796 121129796 C A 1 0 0 0 0 1 0 0 0 16158 825 29 2 2 TECTA 11 121129796 Missense_Mutation SNP C C3N-00203_T 15119281 121129796 13956826 285 11589 OR10G4 0 . GRCh38 11 124016168 124016168 + Silent SNP C C T C3N-00203_T C3N-00203_N C C c.594C>T p.= p.I198I ENST00000320891 1/1 290 234 56 256 256 0 strelka-varscan-mutect OR10G4,synonymous_variant,p.=,ENST00000320891,NM_001004462.1; T ENST00000320891 Transcript synonymous_variant 594/936 594/936 198/311 I atC/atT COSM313479 1 1 OR10G4 HGNC HGNC:14809 protein_coding YES CCDS31702.1 ENSP00000325076 Q8NGN3 A0A126GWS5 UPI0000041BAD NM_001004462.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF6,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 124016168 124016168 C T 1 0 0 0 0 0 0 0 1 10977 903 32 3 3 OR10G4 11 124016168 Silent SNP C C3N-00203_T 2886372 124016168 11070454 286 11590 OR8G5 0 . GRCh38 11 124265456 124265456 + Frame_Shift_Del DEL C C - novel C3N-00203_T C3N-00203_N C C c.631delC p.His211IlefsTer10 p.H211Ifs*10 ENST00000524943 1/1 196 153 43 234 234 0 sindel-varindel-pindel OR8G5,frameshift_variant,p.His211IlefsTer10,ENST00000524943,NM_001005198.1; - ENST00000524943 Transcript frameshift_variant 630/1041 630/1041 210/346 N/X aaC/aa 1 1 OR8G5 HGNC HGNC:19622 protein_coding YES CCDS66256.1 ENSP00000477014 Q8NG78 A0A126GVX5 UPI00003B286B NM_001005198.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 124265456 124265456 C - 1 0 1 0 1 0 0 0 0 11304 506 18 0 0 OR8G5 11 124265456 Frame_Shift_Del DEL C C3N-00203_T 249288 124265456 10821166 287 11591 OR8B3 0 . GRCh38 11 124397050 124397050 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.302T>A p.Leu101Gln p.L101Q ENST00000354597 1/1 336 278 58 356 356 0 strelka-varscan-mutect OR8B3,missense_variant,p.Leu101Gln,ENST00000354597,NM_001005467.1; T ENST00000354597 Transcript missense_variant 319/987 302/942 101/313 L/Q cTg/cAg 1 -1 OR8B3 HGNC HGNC:8472 protein_coding YES CCDS31709.1 ENSP00000346611 Q8NGG8 UPI000004B9C9 NM_001005467.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF258,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 124397050 124397050 A T 1 0 0 0 0 1 0 0 0 11298 188 7 4 4 OR8B3 11 124397050 Missense_Mutation SNP A C3N-00203_T 131594 124397050 10689572 288 11592 PRDM10 0 . GRCh38 11 129914739 129914739 + Missense_Mutation SNP G G C C3N-00203_T C3N-00203_N G G c.2818C>G p.Gln940Glu p.Q940E ENST00000358825 18/22 267 198 69 245 245 0 strelka-varscan-mutect PRDM10,missense_variant,p.Gln940Glu,ENST00000358825,NM_020228.2;PRDM10,missense_variant,p.Gln936Glu,ENST00000360871,NM_199437.1;PRDM10,missense_variant,p.Gln910Glu,ENST00000528746,;PRDM10,missense_variant,p.Gln854Glu,ENST00000423662,NM_199438.1;PRDM10,missense_variant,p.Gln850Glu,ENST00000304538,NM_199439.1;PRDM10,missense_variant,p.Gln854Glu,ENST00000526082,;PRDM10,missense_variant,p.Gln653Glu,ENST00000533431,; C ENST00000358825 Transcript missense_variant 3050/6322 2818/3483 940/1160 Q/E Cag/Gag COSM3935380 1 -1 PRDM10 HGNC HGNC:13995 protein_coding YES CCDS44771.1 ENSP00000351686 Q9NQV6 UPI00002371B3 NM_020228.2 deleterious_low_confidence(0.02) 18/22 Low_complexity_(Seg):seg,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF30 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 129914739 129914739 G C 1 0 0 0 0 1 0 0 0 12582 1299 45 4 4 PRDM10 11 129914739 Missense_Mutation SNP G C3N-00203_T 5517689 129914739 5171883 289 11593 ADAMTS8 0 . GRCh38 11 130414619 130414619 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.1478T>A p.Leu493Gln p.L493Q ENST00000257359 5/9 161 126 35 153 153 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Leu493Gln,ENST00000257359,NM_007037.4;ADAMTS8,upstream_gene_variant,,ENST00000531752,; T ENST00000257359 Transcript missense_variant 2185/4010 1478/2670 493/889 L/Q cTg/cAg 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 deleterious(0) 5/9 hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 130414619 130414619 A T 1 0 0 0 0 1 0 0 0 316 188 7 4 4 ADAMTS8 11 130414619 Missense_Mutation SNP A C3N-00203_T 499880 130414619 4672003 290 11594 WNK1 0 . GRCh38 12 894602 894602 + Silent SNP A A T novel C3N-00203_T C3N-00203_N A A c.6306A>T p.= p.S2102S ENST00000340908 23/28 827 648 179 464 464 0 strelka-varscan-mutect WNK1,synonymous_variant,p.=,ENST00000530271,;WNK1,synonymous_variant,p.=,ENST00000537687,NM_001184985.1;WNK1,synonymous_variant,p.=,ENST00000340908,NM_213655.4;WNK1,synonymous_variant,p.=,ENST00000315939,NM_018979.3;WNK1,synonymous_variant,p.=,ENST00000535572,NM_014823.2;WNK1,upstream_gene_variant,,ENST00000542424,; T ENST00000340908 Transcript synonymous_variant 6949/11208 6306/7905 2102/2634 S tcA/tcT 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 23/28 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 894602 894602 A T 1 0 0 0 0 0 0 0 1 17933 175 7 4 4 WNK1 12 894602 Silent SNP A C3N-00203_T 894602 132380707 291 11595 GRIN2B 0 . GRCh38 12 13564458 13564458 + Missense_Mutation SNP C C T rs199677214 C3N-00203_T C3N-00203_N C C c.2780G>A p.Arg927Gln p.R927Q ENST00000609686 13/13 438 354 84 379 379 0 strelka-varscan-mutect GRIN2B,missense_variant,p.Arg927Gln,ENST00000609686,NM_000834.3;GRIN2B,intron_variant,,ENST00000637214,;GRIN2B,non_coding_transcript_exon_variant,,ENST00000628166,;GRIN2B,upstream_gene_variant,,ENST00000636207,; T ENST00000609686 Transcript missense_variant 3234/30355 2780/4455 927/1484 R/Q cGg/cAg rs199677214,COSM244810 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 tolerated(0.11) 13/13 Pfam_domain:PF10565 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199677214 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 13564458 13564458 C T 1 0 0 0 0 1 0 0 0 6662 652 23 1 1 GRIN2B 12 13564458 Missense_Mutation SNP C C3N-00203_T 12669856 13564458 119710851 292 11596 GOLT1B 0 . GRCh38 12 21507942 21507942 + Splice_Site SNP A A G novel C3N-00203_T C3N-00203_N A A c.118-2A>G p.X40_splice ENST00000631252 261 217 44 166 166 0 strelka-varscan-mutect GOLT1B,splice_acceptor_variant,,ENST00000631252,;GOLT1B,intron_variant,,ENST00000229314,NM_016072.4;GOLT1B,intron_variant,,ENST00000540141,;GOLT1B,intron_variant,,ENST00000542038,;GOLT1B,intron_variant,,ENST00000535593,;GOLT1B,intron_variant,,ENST00000545093,;GOLT1B,splice_acceptor_variant,,ENST00000539025,;GOLT1B,splice_acceptor_variant,,ENST00000539663,;GOLT1B,intron_variant,,ENST00000542194,;GOLT1B,downstream_gene_variant,,ENST00000545113,; G ENST00000631252 Transcript splice_acceptor_variant -/223 118/129 40/42 1 1 GOLT1B HGNC HGNC:20175 protein_coding ENSP00000486919 F5GXH6 UPI000204ABFD 2/2 HIGH SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 42 21507942 21507942 A G 1 0 0 0 0 0 0 1 0 6465 434 15 5 5 GOLT1B 12 21507942 Splice_Site SNP A C3N-00203_T 7943484 21507942 111767367 293 11597 TM7SF3 0 . GRCh38 12 26999651 26999651 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.272C>A p.Thr91Lys p.T91K ENST00000343028 3/12 240 153 87 120 118 2 strelka-varscan-mutect TM7SF3,missense_variant,p.Thr91Lys,ENST00000343028,NM_016551.2;TM7SF3,missense_variant,p.Thr70Lys,ENST00000512808,;TM7SF3,missense_variant,p.Thr96Lys,ENST00000545600,;TM7SF3,splice_region_variant,,ENST00000539741,;TM7SF3,5_prime_UTR_variant,,ENST00000543088,;TM7SF3,5_prime_UTR_variant,,ENST00000535423,;TM7SF3,intron_variant,,ENST00000535819,;TM7SF3,intron_variant,,ENST00000543803,;TM7SF3,intron_variant,,ENST00000543655,;TM7SF3,upstream_gene_variant,,ENST00000545303,;TM7SF3,non_coding_transcript_exon_variant,,ENST00000542667,;TM7SF3,downstream_gene_variant,,ENST00000539399,;TM7SF3,missense_variant,p.Asn39Lys,ENST00000542019,;TM7SF3,upstream_gene_variant,,ENST00000535260,;TM7SF3,upstream_gene_variant,,ENST00000543882,; T ENST00000343028 Transcript missense_variant 498/2709 272/1713 91/570 T/K aCa/aAa 1 -1 TM7SF3 HGNC HGNC:23049 protein_coding YES CCDS8710.1 ENSP00000342322 Q9NS93 UPI0000136849 NM_016551.2 deleterious(0.01) 3/12 hmmpanther:PTHR15937 MODERATE 1 SNV 1 1 PASS rs1222894123 . 0 207 0 3 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 42 26999651 26999651 G T 1 0 0 0 0 1 0 0 0 16420 1377 48 2 2 TM7SF3 12 26999651 Missense_Mutation SNP G C3N-00203_T 5491709 26999651 106275658 294 11598 TSPAN11 0 . GRCh38 12 30982573 30982573 + Frame_Shift_Del DEL C C - rs777669603 C3N-00203_T C3N-00203_N C C c.498delC p.His166GlnfsTer141 p.H166Qfs*141 ENST00000261177 6/8 133 92 41 79 79 0 sindel-varindel-pindel TSPAN11,frameshift_variant,p.His166GlnfsTer141,ENST00000261177,NM_001080509.2;TSPAN11,frameshift_variant,p.His166GlnfsTer141,ENST00000546076,;TSPAN11,frameshift_variant,p.His95GlnfsTer141,ENST00000535215,;RP11-551L14.4,intron_variant,,ENST00000613860,;RP11-551L14.4,upstream_gene_variant,,ENST00000612219,;RP11-551L14.4,downstream_gene_variant,,ENST00000625497,; - ENST00000261177 Transcript frameshift_variant 557/5505 498/762 166/253 H/X caC/ca rs777669603,COSM2205208 1 1 TSPAN11 HGNC HGNC:30795 protein_coding YES CCDS31765.1 ENSP00000261177 A1L157 UPI00001AE7E4 NM_001080509.2 6/8 hmmpanther:PTHR19282:SF198,hmmpanther:PTHR19282,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Superfamily_domains:0037997 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 30982573 30982573 C - 1 0 1 0 1 0 0 0 0 17140 477 17 0 0 TSPAN11 12 30982573 Frame_Shift_Del DEL C C3N-00203_T 3982922 30982573 102292736 295 11599 KIAA1551 0 . GRCh38 12 31983824 31983824 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.2869G>C p.Asp957His p.D957H ENST00000312561 4/6 287 216 71 185 185 0 strelka-varscan-mutect KIAA1551,missense_variant,p.Asp957His,ENST00000312561,NM_018169.3;KIAA1551,downstream_gene_variant,,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,;KIAA1551,upstream_gene_variant,,ENST00000543763,; C ENST00000312561 Transcript missense_variant 3283/6230 2869/5244 957/1747 D/H Gat/Cat 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 deleterious(0) 4/6 Pfam_domain:PF15395,hmmpanther:PTHR21604 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 31983824 31983824 G C 1 0 0 0 0 1 0 0 0 8122 942 33 4 4 KIAA1551 12 31983824 Missense_Mutation SNP G C3N-00203_T 1001251 31983824 101291485 296 11600 TMEM117 0 . GRCh38 12 43844842 43844842 + Frame_Shift_Del DEL G G - novel C3N-00203_T C3N-00203_N G G c.192delG p.Trp64Ter p.W64* ENST00000266534 2/8 258 204 54 261 261 0 sindel-varindel-pindel TMEM117,frameshift_variant,p.Trp64Ter,ENST00000266534,NM_032256.2;TMEM117,frameshift_variant,p.Trp64Ter,ENST00000551577,NM_001286211.1;TMEM117,upstream_gene_variant,,ENST00000550495,NM_001286213.1;TMEM117,frameshift_variant,p.Trp64Ter,ENST00000546868,;TMEM117,non_coding_transcript_exon_variant,,ENST00000546387,; - ENST00000266534 Transcript frameshift_variant 318/2758 191/1545 64/514 W/X tGg/tg 1 1 TMEM117 HGNC HGNC:25308 protein_coding YES CCDS8745.1 ENSP00000266534 Q9H0C3 UPI0000037D18 NM_032256.2 2/8 Pfam_domain:PF15113,hmmpanther:PTHR31226 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 43844842 43844842 G - 1 0 1 0 1 0 0 0 0 16475 1357 47 0 0 TMEM117 12 43844842 Frame_Shift_Del DEL G C3N-00203_T 11861018 43844842 89430467 297 11601 NELL2 0 . GRCh38 12 44815997 44815997 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.474C>G p.His158Gln p.H158Q ENST00000437801 4/21 238 186 52 227 227 0 strelka-varscan-mutect NELL2,missense_variant,p.His108Gln,ENST00000429094,NM_001145108.1;NELL2,missense_variant,p.His158Gln,ENST00000437801,NM_001145107.1;NELL2,missense_variant,p.His107Gln,ENST00000395487,NM_001145109.1;NELL2,missense_variant,p.His108Gln,ENST00000452445,NM_006159.2;NELL2,missense_variant,p.His107Gln,ENST00000551601,;NELL2,missense_variant,p.His107Gln,ENST00000549027,;NELL2,missense_variant,p.His131Gln,ENST00000333837,NM_001145110.1;NELL2,missense_variant,p.His108Gln,ENST00000552993,;NELL2,missense_variant,p.His107Gln,ENST00000548531,;NELL2,missense_variant,p.His105Gln,ENST00000553120,;NELL2,missense_variant,p.His108Gln,ENST00000548826,;NELL2,non_coding_transcript_exon_variant,,ENST00000547172,;NELL2,non_coding_transcript_exon_variant,,ENST00000547751,; C ENST00000437801 Transcript missense_variant 846/3279 474/2601 158/866 H/Q caC/caG 1 -1 NELL2 HGNC HGNC:7751 protein_coding YES CCDS44863.1 ENSP00000416341 Q99435 UPI000191537D NM_001145107.1 tolerated(0.11) 4/21 hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF0,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,SMART_domains:SM00210,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 44815997 44815997 G C 1 0 0 0 0 1 0 0 0 10365 1020 36 4 4 NELL2 12 44815997 Missense_Mutation SNP G C3N-00203_T 971155 44815997 88459312 298 11602 DBX2 0 . GRCh38 12 45016470 45016470 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.836T>C p.Ile279Thr p.I279T ENST00000332700 4/4 165 124 41 136 136 0 strelka-varscan-mutect DBX2,missense_variant,p.Ile279Thr,ENST00000332700,NM_001004329.2; G ENST00000332700 Transcript missense_variant 1008/2806 836/1020 279/339 I/T aTa/aCa 1 -1 DBX2 HGNC HGNC:33186 protein_coding YES CCDS31781.1 ENSP00000331470 Q6ZNG2 UPI000041A784 NM_001004329.2 deleterious(0.01) 4/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 45016470 45016470 A G 1 0 0 0 0 1 0 0 0 4060 449 16 5 5 DBX2 12 45016470 Missense_Mutation SNP A C3N-00203_T 200473 45016470 88258839 299 11603 OR8S1 0 . GRCh38 12 48526431 48526431 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.800C>T p.Pro267Leu p.P267L ENST00000310194 1/2 323 261 62 271 270 1 strelka-varscan-mutect OR8S1,missense_variant,p.Pro267Leu,ENST00000310194,NM_001005203.2;OR8S1,intron_variant,,ENST00000551654,; T ENST00000310194 Transcript missense_variant 800/1080 800/1080 267/359 P/L cCc/cTc 1 1 OR8S1 HGNC HGNC:19628 protein_coding YES CCDS31789.1 ENSP00000310632 Q8NH09 UPI000013EFC1 NM_001005203.2 tolerated(0.26) 1/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF379,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 48526431 48526431 C T 1 0 0 0 0 1 0 0 0 11313 623 22 3 3 OR8S1 12 48526431 Missense_Mutation SNP C C3N-00203_T 3509961 48526431 84748878 300 11604 SCN8A 0 . GRCh38 12 51807034 51807034 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.5548G>C p.Ala1850Pro p.A1850P ENST00000354534 27/27 504 396 108 360 360 0 strelka-varscan-mutect SCN8A,missense_variant,p.Ala1850Pro,ENST00000354534,NM_014191.3;SCN8A,missense_variant,p.Ala1809Pro,ENST00000545061,NM_001177984.2;SCN8A,missense_variant,p.Ala1861Pro,ENST00000599343,;SCN8A,missense_variant,p.Ala1850Pro,ENST00000627620,;SCN8A,missense_variant,p.Ala1809Pro,ENST00000355133,;RP11-923I11.3,downstream_gene_variant,,ENST00000565518,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,3_prime_UTR_variant,,ENST00000636945,; C ENST00000354534 Transcript missense_variant 5726/11556 5548/5943 1850/1980 A/P Gcc/Ccc 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 deleterious(0) 27/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037 MODERATE 1 SNV 1 1 PASS . . 0 206 0 0 4 0 0 0 -20 0.9296274 1 1 1 0 C 3 2 42 51807034 51807034 G C 1 0 0 0 0 1 0 0 0 14193 1319 46 4 4 SCN8A 12 51807034 Missense_Mutation SNP G C3N-00203_T 3280603 51807034 81468275 301 11605 LRP1 0 . GRCh38 12 57199379 57199379 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.9844C>T p.His3282Tyr p.H3282Y ENST00000243077 61/89 174 138 36 115 115 0 strelka-varscan-mutect LRP1,missense_variant,p.His3282Tyr,ENST00000243077,NM_002332.2;LRP1,upstream_gene_variant,,ENST00000555124,;MIR1228,downstream_gene_variant,,ENST00000408438,;LRP1,upstream_gene_variant,,ENST00000556356,;LRP1,upstream_gene_variant,,ENST00000451724,;LRP1,upstream_gene_variant,,ENST00000556247,;LRP1,upstream_gene_variant,,ENST00000555941,; T ENST00000243077 Transcript missense_variant 10310/14897 9844/13635 3282/4544 H/Y Cat/Tat 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 deleterious(0.01) 61/89 Gene3D:2.120.10.30,PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF100,Superfamily_domains:SSF57184,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 57199379 57199379 C T 1 0 0 0 0 1 0 0 0 8846 594 21 3 3 LRP1 12 57199379 Missense_Mutation SNP C C3N-00203_T 5392345 57199379 76075930 302 11606 GLI1 0 . GRCh38 12 57467394 57467394 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.974A>G p.His325Arg p.H325R ENST00000228682 9/12 154 129 25 106 106 0 strelka-varscan-mutect GLI1,missense_variant,p.His325Arg,ENST00000228682,NM_005269.2;GLI1,missense_variant,p.His284Arg,ENST00000546141,NM_001167609.1;GLI1,missense_variant,p.His197Arg,ENST00000543426,NM_001160045.1;GLI1,missense_variant,p.His284Arg,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;GLI1,downstream_gene_variant,,ENST00000528432,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; G ENST00000228682 Transcript missense_variant 1065/3613 974/3321 325/1106 H/R cAc/cGc 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 deleterious(0) 9/12 PROSITE_profiles:PS50157,hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 57467394 57467394 A G 1 0 0 0 0 1 0 0 0 6315 159 6 5 5 GLI1 12 57467394 Missense_Mutation SNP A C3N-00203_T 268015 57467394 75807915 303 11607 IL26 0 . GRCh38 12 68202018 68202018 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.429G>T p.Arg143Ser p.R143S ENST00000229134 4/5 104 84 20 116 115 1 strelka-varscan-mutect IL26,missense_variant,p.Arg143Ser,ENST00000229134,NM_018402.1;IFNG-AS1,intron_variant,,ENST00000536914,; A ENST00000229134 Transcript missense_variant,splice_region_variant 494/1075 429/516 143/171 R/S agG/agT 1 -1 IL26 HGNC HGNC:17119 protein_coding YES CCDS8981.1 ENSP00000229134 Q9NPH9 UPI0000035828 NM_018402.1 tolerated(0.08) 4/5 Gene3D:1.20.1250.10,Pfam_domain:PF00726,hmmpanther:PTHR11585,hmmpanther:PTHR11585:SF11,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 42 68202018 68202018 C A 1 0 0 0 0 1 0 0 0 7582 637 22 2 2 IL26 12 68202018 Missense_Mutation SNP C C3N-00203_T 10734624 68202018 65073291 304 11608 NAV3 0 . GRCh38 12 77941106 77941106 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.387T>C p.= p.N129N ENST00000397909 3/40 99 80 19 88 88 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,synonymous_variant,p.=,ENST00000550042,;NAV3,non_coding_transcript_exon_variant,,ENST00000549369,;NAV3,non_coding_transcript_exon_variant,,ENST00000551277,; C ENST00000397909 Transcript synonymous_variant 560/9821 387/7158 129/2385 N aaT/aaC 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 3/40 PROSITE_profiles:PS50021,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 77941106 77941106 T C 1 0 0 0 0 0 0 0 1 10194 1461 51 5 5 NAV3 12 77941106 Silent SNP T C3N-00203_T 9739088 77941106 55334203 305 11609 NAV3 0 . GRCh38 12 78175308 78175308 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.4984C>A p.Leu1662Ile p.L1662I ENST00000397909 25/40 168 128 40 126 125 1 strelka-varscan-mutect NAV3,missense_variant,p.Leu1662Ile,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Leu1662Ile,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Leu557Ile,ENST00000552895,;NAV3,missense_variant,p.Leu291Ile,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000548948,; A ENST00000397909 Transcript missense_variant,splice_region_variant 5157/9821 4984/7158 1662/2385 L/I Ctt/Att 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0.01) 25/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 78175308 78175308 C A 1 0 0 0 0 1 0 0 0 10194 927 32 2 2 NAV3 12 78175308 Missense_Mutation SNP C C3N-00203_T 234202 78175308 55100001 306 11610 MGAT4C 0 . GRCh38 12 85980130 85980130 + Missense_Mutation SNP C C A rs770702724 C3N-00203_T C3N-00203_N C C c.596G>T p.Arg199Leu p.R199L ENST00000611864 4/4 207 178 29 227 226 1 strelka-varscan-mutect MGAT4C,missense_variant,p.Arg199Leu,ENST00000611864,;MGAT4C,missense_variant,p.Arg199Leu,ENST00000620241,;MGAT4C,missense_variant,p.Arg199Leu,ENST00000621808,NM_013244.3;MGAT4C,missense_variant,p.Arg199Leu,ENST00000548651,;MGAT4C,missense_variant,p.Arg199Leu,ENST00000552808,;MGAT4C,missense_variant,p.Arg199Leu,ENST00000547225,;MGAT4C,intron_variant,,ENST00000552435,; A ENST00000611864 Transcript missense_variant 652/25116 596/1437 199/478 R/L cGt/cTt rs770702724,COSM3399161,COSM3466175,COSM4781811,COSM4897753 1 -1 MGAT4C HGNC HGNC:30871 protein_coding YES CCDS9030.1 ENSP00000481096 Q9UBM8 UPI00001B002C deleterious(0) 4/4 Pfam_domain:PF04666,hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF14 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs770702724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 85980130 85980130 C A 1 0 0 0 0 1 0 0 0 9507 536 19 1 1 MGAT4C 12 85980130 Missense_Mutation SNP C C3N-00203_T 7804822 85980130 47295179 307 11611 C12orf74 0 . GRCh38 12 92706792 92706792 + Nonsense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.161T>A p.Leu54Ter p.L54* ENST00000397833 2/3 288 218 70 237 237 0 strelka-varscan-mutect C12orf74,stop_gained,p.Leu54Ter,ENST00000544406,NM_001178097.2;C12orf74,stop_gained,p.Leu54Ter,ENST00000397833,NM_001037671.3; A ENST00000397833 Transcript stop_gained 612/1856 161/573 54/190 L/* tTa/tAa 1 1 C12orf74 HGNC HGNC:27887 protein_coding YES CCDS41819.1 ENSP00000380933 Q32Q52 UPI00005DB386 NM_001037671.3 2/3 Pfam_domain:PF15720,hmmpanther:PTHR41399,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs1253814082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 92706792 92706792 T A 1 0 0 0 0 0 1 0 0 1823 1764 61 4 4 C12orf74 12 92706792 Nonsense_Mutation SNP T C3N-00203_T 6726662 92706792 40568517 308 11612 EEA1 0 . GRCh38 12 92864865 92864865 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.240G>T p.Leu80Phe p.L80F ENST00000322349 3/29 120 92 28 113 113 0 strelka-varscan-mutect EEA1,missense_variant,p.Leu80Phe,ENST00000322349,NM_003566.3;EEA1,non_coding_transcript_exon_variant,,ENST00000547833,;EEA1,3_prime_UTR_variant,,ENST00000553019,;EEA1,intron_variant,,ENST00000418984,; A ENST00000322349 Transcript missense_variant 505/9875 240/4236 80/1411 L/F ttG/ttT 1 -1 EEA1 HGNC HGNC:3185 protein_coding YES CCDS31874.1 ENSP00000317955 Q15075 UPI000013C754 NM_003566.3 tolerated(0.06) 3/29 hmmpanther:PTHR23164:SF6,hmmpanther:PTHR23164 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 92864865 92864865 C A 1 0 0 0 0 1 0 0 0 4750 840 29 2 2 EEA1 12 92864865 Missense_Mutation SNP C C3N-00203_T 158073 92864865 40410444 309 11613 SOCS2 0 . GRCh38 12 93574720 93574720 + Splice_Site SNP A A T novel C3N-00203_T C3N-00203_N A A c.140-2A>T p.X47_splice ENST00000622746 89 75 14 85 85 0 strelka-varscan-mutect SOCS2,splice_acceptor_variant,,ENST00000622746,NM_001270469.1,NM_001270470.1;SOCS2,splice_acceptor_variant,,ENST00000340600,NM_003877.4,NM_001270471.1;SOCS2,splice_acceptor_variant,,ENST00000549122,;SOCS2,splice_acceptor_variant,,ENST00000549206,NM_001270467.1;SOCS2,splice_acceptor_variant,,ENST00000551556,;SOCS2,splice_acceptor_variant,,ENST00000536696,NM_001270468.1;SOCS2,splice_acceptor_variant,,ENST00000549887,;SOCS2,splice_acceptor_variant,,ENST00000548091,;SOCS2,3_prime_UTR_variant,,ENST00000548537,;SOCS2,upstream_gene_variant,,ENST00000551883,;SOCS2,upstream_gene_variant,,ENST00000549510,;SOCS2,downstream_gene_variant,,ENST00000547229,;SOCS2-AS1,upstream_gene_variant,,ENST00000499137,;SOCS2-AS1,upstream_gene_variant,,ENST00000500986,;SOCS2-AS1,upstream_gene_variant,,ENST00000551626,; T ENST00000622746 Transcript splice_acceptor_variant -/2881 140/597 47/198 1 1 SOCS2 HGNC HGNC:19382 protein_coding YES CCDS9047.1 ENSP00000481249 O14508 A0A024RBD2 UPI0000135B63 NM_001270469.1,NM_001270470.1 2/2 HIGH SNV 3 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 93574720 93574720 A T 1 0 0 0 0 0 0 1 0 15235 202 7 4 4 SOCS2 12 93574720 Splice_Site SNP A C3N-00203_T 709855 93574720 39700589 310 11614 CEP83 0 . GRCh38 12 94333553 94333553 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1506G>T p.Met502Ile p.M502I ENST00000397809 13/17 315 268 47 247 247 0 strelka-varscan-mutect CEP83,missense_variant,p.Met502Ile,ENST00000397809,NM_016122.2;CEP83,missense_variant,p.Met502Ile,ENST00000339839,NM_001042399.1;CEP83,missense_variant,p.Met373Ile,ENST00000397807,;CEP83,upstream_gene_variant,,ENST00000552632,;CEP83,non_coding_transcript_exon_variant,,ENST00000546587,;CEP83,missense_variant,p.Met469Ile,ENST00000547232,; A ENST00000397809 Transcript missense_variant 2056/3773 1506/2106 502/701 M/I atG/atT 1 -1 CEP83 HGNC HGNC:17966 protein_coding YES CCDS41820.1 ENSP00000380911 J3KNW7 UPI0000D4BD6F NM_016122.2 tolerated(0.37) 13/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23170,hmmpanther:PTHR23170:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 94333553 94333553 C A 1 0 0 0 0 1 0 0 0 2984 594 21 2 2 CEP83 12 94333553 Missense_Mutation SNP C C3N-00203_T 758833 94333553 38941756 311 11615 TMPO 0 . GRCh38 12 98527993 98527993 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.387G>T p.= p.V129V ENST00000266732 2/4 374 288 86 382 380 2 strelka-varscan-mutect TMPO,synonymous_variant,p.=,ENST00000556029,NM_001032283.2;TMPO,synonymous_variant,p.=,ENST00000266732,NM_003276.2;TMPO,synonymous_variant,p.=,ENST00000343315,NM_001307975.1;TMPO,synonymous_variant,p.=,ENST00000393053,NM_001032284.2;TMPO,synonymous_variant,p.=,ENST00000261210,;TMPO,synonymous_variant,p.=,ENST00000556678,;TMPO,non_coding_transcript_exon_variant,,ENST00000547214,;TMPO,non_coding_transcript_exon_variant,,ENST00000549938,;TMPO,non_coding_transcript_exon_variant,,ENST00000546828,;TMPO,non_coding_transcript_exon_variant,,ENST00000548911,;TMPO,non_coding_transcript_exon_variant,,ENST00000552831,; T ENST00000266732 Transcript synonymous_variant 625/3615 387/2085 129/694 V gtG/gtT 1 1 TMPO HGNC HGNC:11875 protein_coding YES CCDS9064.1 ENSP00000266732 P42166 UPI000013D709 NM_003276.2 2/4 PROSITE_profiles:PS50954,hmmpanther:PTHR12019:SF10,hmmpanther:PTHR12019,Gene3D:1.10.720.40,Pfam_domain:PF03020,SMART_domains:SM00540,Superfamily_domains:SSF63451 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 98527993 98527993 G T 1 0 0 0 0 0 0 0 1 16713 1277 45 2 2 TMPO 12 98527993 Silent SNP G C3N-00203_T 4194440 98527993 34747316 312 11616 NR1H4 0 . GRCh38 12 100532557 100532557 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.575G>T p.Cys192Phe p.C192F ENST00000551379 3/9 330 270 60 275 275 0 strelka-varscan-mutect NR1H4,missense_variant,p.Cys182Phe,ENST00000548884,NM_005123.3;NR1H4,missense_variant,p.Cys182Phe,ENST00000392986,NM_001206979.1,NM_001206977.1;NR1H4,missense_variant,p.Cys192Phe,ENST00000188403,NM_001206992.1;NR1H4,missense_variant,p.Cys192Phe,ENST00000551379,NM_001206993.1;NR1H4,intron_variant,,ENST00000549996,NM_001206978.1;NR1H4,missense_variant,p.Cys182Phe,ENST00000321046,; T ENST00000551379 Transcript missense_variant 603/1489 575/1461 192/486 C/F tGt/tTt 1 1 NR1H4 HGNC HGNC:7967 protein_coding YES CCDS55876.1 ENSP00000447149 Q96RI1 UPI000006E701 NM_001206993.1 deleterious(0) 3/9 PROSITE_profiles:PS51030,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF155,Gene3D:3.30.50.10,Pfam_domain:PF00105,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 MODERATE 1 SNV 1 1 PASS rs1197605464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 100532557 100532557 G T 1 0 0 0 0 1 0 0 0 10675 1377 48 2 2 NR1H4 12 100532557 Missense_Mutation SNP G C3N-00203_T 2004564 100532557 32742752 313 11617 UTP20 0 . GRCh38 12 101299725 101299725 + Nonsense_Mutation SNP G G T rs765120524 C3N-00203_T C3N-00203_N G G c.1474G>T p.Glu492Ter p.E492* ENST00000261637 13/62 67 53 14 109 109 0 strelka-varscan-mutect UTP20,stop_gained,p.Glu492Ter,ENST00000261637,NM_014503.2; T ENST00000261637 Transcript stop_gained 1648/9025 1474/8358 492/2785 E/* Gaa/Taa rs765120524,COSM2063214 1 1 UTP20 HGNC HGNC:17897 protein_coding YES CCDS9081.1 ENSP00000261637 O75691 UPI00001FB38B NM_014503.2 13/62 hmmpanther:PTHR17695,hmmpanther:PTHR17695:SF11,Superfamily_domains:SSF48371 0,1 HIGH 1 SNV 1 0,1 1 PASS rs765120524 . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 4 4 42 101299725 101299725 G T 1 0 0 0 0 0 1 0 0 17642 1059 37 1 1 UTP20 12 101299725 Nonsense_Mutation SNP G C3N-00203_T 767168 101299725 31975584 314 11618 TMEM119 0 . GRCh38 12 108591898 108591898 + Silent SNP G G T rs748122455 C3N-00203_T C3N-00203_N G G c.486C>A p.= p.P162P ENST00000392806 2/2 114 90 24 99 99 0 strelka-varscan-mutect TMEM119,synonymous_variant,p.=,ENST00000392806,NM_181724.2;TMEM119,downstream_gene_variant,,ENST00000549031,;TMEM119,downstream_gene_variant,,ENST00000549447,;TMEM119,downstream_gene_variant,,ENST00000547567,; T ENST00000392806 Transcript synonymous_variant 655/2707 486/852 162/283 P ccC/ccA rs748122455,COSM1267996 1 -1 TMEM119 HGNC HGNC:27884 protein_coding YES CCDS9119.1 ENSP00000376553 Q4V9L6 UPI0000049333 NM_181724.2 2/2 hmmpanther:PTHR28645,hmmpanther:PTHR28645:SF1,Pfam_domain:PF15724 0,1 LOW 1 SNV 1 0,1 1 PASS rs748122455 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 108591898 108591898 G T 1 0 0 0 0 0 0 0 1 16476 1103 39 1 1 TMEM119 12 108591898 Silent SNP G C3N-00203_T 7292173 108591898 24683411 315 11619 CCDC63 0 . GRCh38 12 110853472 110853472 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.77A>T p.Gln26Leu p.Q26L ENST00000308208 3/12 289 219 70 183 183 0 strelka-varscan-mutect CCDC63,missense_variant,p.Gln26Leu,ENST00000308208,NM_152591.2;CCDC63,5_prime_UTR_variant,,ENST00000545036,NM_001286243.1;CCDC63,intron_variant,,ENST00000552694,NM_001286244.1;CCDC63,intron_variant,,ENST00000550317,; T ENST00000308208 Transcript missense_variant 319/1993 77/1692 26/563 Q/L cAg/cTg 1 1 CCDC63 HGNC HGNC:26669 protein_coding YES CCDS9151.1 ENSP00000312399 Q8NA47 UPI000006F794 NM_152591.2 tolerated(1) 3/12 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21694,hmmpanther:PTHR21694:SF20 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 110853472 110853472 A T 1 0 0 0 0 1 0 0 0 2536 188 7 4 4 CCDC63 12 110853472 Missense_Mutation SNP A C3N-00203_T 2261574 110853472 22421837 316 11620 CUX2 0 . GRCh38 12 111312113 111312113 + Silent SNP G G T rs575614068 C3N-00203_T C3N-00203_N G G c.1914G>T p.= p.P638P ENST00000261726 16/22 94 82 12 71 71 0 strelka-varscan-mutect CUX2,synonymous_variant,p.=,ENST00000261726,NM_015267.3; T ENST00000261726 Transcript synonymous_variant 2068/6844 1914/4461 638/1486 P ccG/ccT rs575614068 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 16/22 hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 LOW 1 SNV 1 1 PASS rs575614068 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 42 111312113 111312113 G T 1 0 0 0 0 0 0 0 1 3875 1045 37 1 1 CUX2 12 111312113 Silent SNP G C3N-00203_T 458641 111312113 21963196 317 11621 MAPKAPK5 0 . GRCh38 12 111890048 111890048 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1231G>T p.Glu411Ter p.E411* ENST00000551404 13/14 196 141 55 143 143 0 strelka-varscan-mutect MAPKAPK5,stop_gained,p.Glu409Ter,ENST00000550735,NM_003668.3;MAPKAPK5,stop_gained,p.Glu411Ter,ENST00000551404,NM_139078.2;MAPKAPK5,stop_gained,p.Glu262Ter,ENST00000549875,;MAPKAPK5,non_coding_transcript_exon_variant,,ENST00000547067,;MAPKAPK5,non_coding_transcript_exon_variant,,ENST00000547915,;MAPKAPK5,non_coding_transcript_exon_variant,,ENST00000552111,;MAPKAPK5,downstream_gene_variant,,ENST00000553053,; T ENST00000551404 Transcript stop_gained 1339/1630 1231/1422 411/473 E/* Gaa/Taa 1 1 MAPKAPK5 HGNC HGNC:6889 protein_coding YES CCDS44975.1 ENSP00000449381 Q8IW41 UPI0000161429 NM_139078.2 13/14 hmmpanther:PTHR24349 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 111890048 111890048 G T 1 0 0 0 0 0 1 0 0 9215 1291 45 2 2 MAPKAPK5 12 111890048 Nonsense_Mutation SNP G C3N-00203_T 577935 111890048 21385261 318 11622 TMEM132B 0 . GRCh38 12 125644231 125644231 + Silent SNP C C A rs758226132 C3N-00203_T C3N-00203_N C C c.1578C>A p.= p.T526T ENST00000299308 6/9 257 207 50 241 239 2 strelka-varscan-mutect TMEM132B,synonymous_variant,p.=,ENST00000299308,NM_052907.3;TMEM132B,synonymous_variant,p.=,ENST00000613307,NM_001286219.1;TMEM132B,non_coding_transcript_exon_variant,,ENST00000535886,; A ENST00000299308 Transcript synonymous_variant 1586/10906 1578/3237 526/1078 T acC/acA rs758226132 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 6/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388,Pfam_domain:PF16070 LOW 1 SNV 5 1 PASS rs758226132 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 125644231 125644231 C A 1 0 0 0 0 0 0 0 1 16490 639 23 1 1 TMEM132B 12 125644231 Silent SNP C C3N-00203_T 13754183 125644231 7631078 319 11623 TMEM132C 0 . GRCh38 12 128415454 128415454 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.808G>T p.Gly270Cys p.G270C ENST00000435159 2/9 149 120 29 123 123 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Gly270Cys,ENST00000435159,NM_001136103.2; T ENST00000435159 Transcript missense_variant 808/4947 808/3327 270/1108 G/C Ggc/Tgc 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0) 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 MODERATE 1 SNV 5 1 PASS rs955800347 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 128415454 128415454 G T 1 0 0 0 0 1 0 0 0 16491 1116 39 1 1 TMEM132C 12 128415454 Missense_Mutation SNP G C3N-00203_T 2771223 128415454 4859855 320 11624 TMEM132D 0 . GRCh38 12 129699809 129699809 + Splice_Site SNP C C A novel C3N-00203_T C3N-00203_N C C c.968+1G>T p.X323_splice ENST00000422113 89 68 21 89 89 0 strelka-varscan-mutect TMEM132D,splice_donor_variant,,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript splice_donor_variant -/5776 968/3300 323/1099 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 2/8 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 42 129699809 129699809 C A 1 0 0 0 0 0 0 1 0 16492 521 18 2 2 TMEM132D 12 129699809 Splice_Site SNP C C3N-00203_T 1284355 129699809 3575500 321 11625 RIMBP2 0 . GRCh38 12 130414250 130414250 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2527C>A p.Pro843Thr p.P843T ENST00000261655 14/19 77 64 13 82 82 0 strelka-varscan-mutect RIMBP2,missense_variant,p.Pro843Thr,ENST00000261655,NM_015347.4;RIMBP2,5_prime_UTR_variant,,ENST00000536632,; T ENST00000261655 Transcript missense_variant 2691/6321 2527/3159 843/1052 P/T Cct/Act 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 tolerated(0.1) 14/19 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.999986 1 1 1 0 T 3 4 42 130414250 130414250 G T 1 0 0 0 0 1 0 0 0 13538 1232 43 2 2 RIMBP2 12 130414250 Missense_Mutation SNP G C3N-00203_T 714441 130414250 2861059 322 11626 GALNT9 0 . GRCh38 12 132197225 132197225 + Frame_Shift_Del DEL C C - rs745851728 C3N-00203_T C3N-00203_N C C c.596delG p.Gly199AlafsTer29 p.G199Afs*29 ENST00000397325 7/7 208 165 43 131 131 0 sindel-varindel-pindel GALNT9,frameshift_variant,p.Gly565AlafsTer29,ENST00000328957,;GALNT9,frameshift_variant,p.Gly199AlafsTer29,ENST00000397325,NM_021808.3;GALNT9,frameshift_variant,p.Gly338AlafsTer29,ENST00000411988,;GALNT9,frameshift_variant,p.Gly199AlafsTer29,ENST00000541995,NM_001122636.1;GALNT9,downstream_gene_variant,,ENST00000538356,;RP13-977J11.3,upstream_gene_variant,,ENST00000623965,; - ENST00000397325 Transcript frameshift_variant 874/1727 596/714 199/237 G/X gGc/gc rs745851728 1 -1 GALNT9 HGNC HGNC:4131 protein_coding YES CCDS41866.1 ENSP00000380488 Q9HCQ5 UPI000006CCBE NM_021808.3 7/7 PROSITE_profiles:PS50231,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF28,Gene3D:2.80.10.50,Pfam_domain:PF00652,SMART_domains:SM00458,Superfamily_domains:SSF50370 HIGH 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 132197225 132197225 C - 1 0 1 0 1 0 0 0 0 6091 739 26 0 0 GALNT9 12 132197225 Frame_Shift_Del DEL C C3N-00203_T 1782975 132197225 1078084 323 11627 SACS 0 . GRCh38 13 23334413 23334413 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.9463C>G p.Leu3155Val p.L3155V ENST00000382292 9/9 176 129 47 215 215 0 strelka-varscan-mutect SACS,missense_variant,p.Leu3155Val,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Leu2405Val,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; C ENST00000382292 Transcript missense_variant 9737/15324 9463/13740 3155/4579 L/V Ctt/Gtt 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 deleterious(0) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 23334413 23334413 G C 1 0 0 0 0 1 0 0 0 14063 1000 35 4 4 SACS 13 23334413 Missense_Mutation SNP G C3N-00203_T 23334413 91029915 324 11628 ATP12A 0 . GRCh38 13 24688457 24688457 + Missense_Mutation SNP G G T rs149324896 C3N-00203_T C3N-00203_N G G c.367G>T p.Ala123Ser p.A123S ENST00000218548 4/23 83 64 19 82 82 0 strelka-varscan-mutect ATP12A,missense_variant,p.Ala123Ser,ENST00000381946,NM_001676.5;ATP12A,missense_variant,p.Ala123Ser,ENST00000218548,NM_001185085.1; T ENST00000218548 Transcript missense_variant 700/3732 367/3138 123/1045 A/S Gcc/Tcc rs149324896,COSM2266842 1 1 ATP12A HGNC HGNC:13816 protein_coding YES CCDS53858.1 ENSP00000218548 P54707 UPI000006D1DE NM_001185085.1 tolerated(0.21) 4/23 hmmpanther:PTHR24093:SF282,hmmpanther:PTHR24093,Pfam_domain:PF00690,TIGRFAM_domain:TIGR01106,SMART_domains:SM00831,Superfamily_domains:0049473,Prints_domain:PR00121,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs149324896 . 0 196 14 0 0 0 0 0 -20 0.9998788 1 1 1 0 T 3 4 42 24688457 24688457 G T 1 0 0 0 0 1 0 0 0 1274 1087 38 1 1 ATP12A 13 24688457 Missense_Mutation SNP G C3N-00203_T 1354044 24688457 89675871 325 11629 PDS5B 0 . GRCh38 13 32775043 32775043 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.4335A>T p.Glu1445Asp p.E1445D ENST00000315596 35/35 240 178 62 242 241 1 strelka-varscan-mutect PDS5B,missense_variant,p.Glu1445Asp,ENST00000315596,NM_015032.3;PDS5B,downstream_gene_variant,,ENST00000447833,;PDS5B,3_prime_UTR_variant,,ENST00000450460,;PDS5B,downstream_gene_variant,,ENST00000474274,; T ENST00000315596 Transcript missense_variant 4521/7497 4335/4344 1445/1447 E/D gaA/gaT 1 1 PDS5B HGNC HGNC:20418 protein_coding YES CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 NM_015032.3 tolerated_low_confidence(0.06) 35/35 hmmpanther:PTHR12663,hmmpanther:PTHR12663:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 32775043 32775043 A T 1 0 0 0 0 1 0 0 0 11780 40 2 4 4 PDS5B 13 32775043 Missense_Mutation SNP A C3N-00203_T 8086586 32775043 81589285 326 11630 SLITRK1 0 . GRCh38 13 83880777 83880777 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.731C>A p.Pro244His p.P244H ENST00000377084 1/1 316 251 65 295 294 1 strelka-varscan-mutect SLITRK1,missense_variant,p.Pro244His,ENST00000377084,NM_052910.2,NM_001281503.1; T ENST00000377084 Transcript missense_variant 1617/5189 731/2091 244/696 P/H cCc/cAc 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 deleterious(0) 1/1 SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 83880777 83880777 G T 1 0 0 0 0 1 0 0 0 15033 1232 43 2 2 SLITRK1 13 83880777 Missense_Mutation SNP G C3N-00203_T 51105734 83880777 30483551 327 11631 MBNL2 0 . GRCh38 13 97391423 97391423 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.1096A>G p.Ile366Val p.I366V ENST00000376673 8/8 293 229 64 255 255 0 strelka-varscan-mutect MBNL2,missense_variant,p.Ile366Val,ENST00000376673,NM_001306070.1;MBNL2,missense_variant,p.Ile354Val,ENST00000343600,NM_207304.2;MBNL2,missense_variant,p.Ile354Val,ENST00000397601,;MBNL2,3_prime_UTR_variant,,ENST00000345429,NM_144778.3;MBNL2,3_prime_UTR_variant,,ENST00000449284,;MBNL2,3_prime_UTR_variant,,ENST00000469707,; G ENST00000376673 Transcript missense_variant 1936/4632 1096/1122 366/373 I/V Ata/Gta 1 1 MBNL2 HGNC HGNC:16746 protein_coding YES CCDS76644.1 ENSP00000365861 Q5VZF2 UPI00005B72AD NM_001306070.1 tolerated_low_confidence(0.75) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 97391423 97391423 A G 1 0 0 0 0 1 0 0 0 9286 101 4 5 5 MBNL2 13 97391423 Missense_Mutation SNP A C3N-00203_T 13510646 97391423 16972905 328 11632 SLC15A1 0 . GRCh38 13 98702529 98702529 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1417G>T p.Val473Leu p.V473L ENST00000376503 18/23 177 127 50 159 159 0 strelka-varscan-mutect SLC15A1,missense_variant,p.Val473Leu,ENST00000376503,NM_005073.3; A ENST00000376503 Transcript missense_variant,splice_region_variant 1473/3106 1417/2127 473/708 V/L Gta/Tta 1 -1 SLC15A1 HGNC HGNC:10920 protein_coding YES CCDS9489.1 ENSP00000365686 P46059 B2CQT6 UPI000013166F NM_005073.3 tolerated(0.38) 18/23 TIGRFAM_domain:TIGR00926 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 98702529 98702529 C A 1 0 0 0 0 1 0 0 0 14663 521 18 2 2 SLC15A1 13 98702529 Missense_Mutation SNP C C3N-00203_T 1311106 98702529 15661799 329 11633 KDELC1 0 . GRCh38 13 102798593 102798593 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.78G>A p.= p.Q26Q ENST00000376004 1/10 135 114 21 115 115 0 strelka-varscan-mutect KDELC1,synonymous_variant,p.=,ENST00000376004,NM_024089.2;BIVM,upstream_gene_variant,,ENST00000257336,NM_017693.3;BIVM,upstream_gene_variant,,ENST00000448849,NM_001159596.1;KDELC1,non_coding_transcript_exon_variant,,ENST00000460338,;BIVM,upstream_gene_variant,,ENST00000491929,;BIVM,upstream_gene_variant,,ENST00000481069,;KDELC1,upstream_gene_variant,,ENST00000486540,; T ENST00000376004 Transcript synonymous_variant 415/2060 78/1509 26/502 Q caG/caA 1 -1 KDELC1 HGNC HGNC:19350 protein_coding YES CCDS9504.1 ENSP00000365172 Q6UW63 UPI000004C663 NM_024089.2 1/10 PROSITE_profiles:PS50194,hmmpanther:PTHR12203,hmmpanther:PTHR12203:SF21 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 102798593 102798593 C T 1 0 0 0 0 0 0 0 1 8034 796 28 3 3 KDELC1 13 102798593 Silent SNP C C3N-00203_T 4096064 102798593 11565735 330 11634 OR4K2 0 . GRCh38 14 19877045 19877045 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.778T>A p.Trp260Arg p.W260R ENST00000298642 1/1 745 672 73 670 670 0 strelka-varscan-mutect OR4K2,missense_variant,p.Trp260Arg,ENST00000298642,NM_001005501.1; A ENST00000298642 Transcript missense_variant 814/1078 778/945 260/314 W/R Tgg/Agg 1 1 OR4K2 HGNC HGNC:14728 protein_coding YES CCDS32023.1 ENSP00000298642 Q8NGD2 A0A126GVP5 UPI0000041B4D NM_001005501.1 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF260,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 19877045 19877045 T A 1 0 0 0 0 1 0 0 0 11149 1696 59 4 4 OR4K2 14 19877045 Missense_Mutation SNP T C3N-00203_T 19877045 87166673 331 11635 MYH7 0 . GRCh38 14 23429283 23429283 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.1203C>G p.His401Gln p.H401Q ENST00000355349 13/40 531 491 40 346 346 0 strelka-varscan-mutect MYH7,missense_variant,p.His401Gln,ENST00000355349,NM_000257.3; C ENST00000355349 Transcript missense_variant 1366/6087 1203/5808 401/1935 H/Q caC/caG 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 tolerated(0.06) 13/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 23429283 23429283 G C 1 0 0 0 0 1 0 0 0 10039 1252 44 4 4 MYH7 14 23429283 Missense_Mutation SNP G C3N-00203_T 3552238 23429283 83614435 332 11636 MYH7 0 . GRCh38 14 23433705 23433706 + Frame_Shift_Ins INS - - A novel C3N-00203_T C3N-00203_N - - c.27dupT p.Gly10TrpfsTer23 p.G10Wfs*23 ENST00000355349 3/40 335 296 39 225 225 0 sindel-varindel-pindel MYH7,frameshift_variant,p.Gly10TrpfsTer23,ENST00000355349,NM_000257.3; A ENST00000355349 Transcript frameshift_variant 190-191/6087 27-28/5808 9-10/1935 -/X -/T 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 3/40 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 42 23433705 23433705 - A 1 0 1 1 0 0 0 0 0 10039 594 21 0 0 MYH7 14 23433705 Frame_Shift_Ins INS - C3N-00203_T 4422 23433705 83610013 333 11637 AP1G2 0 . GRCh38 14 23564644 23564644 + Missense_Mutation SNP T T G novel C3N-00203_T C3N-00203_N T T c.839A>C p.Asp280Ala p.D280A ENST00000308724 8/21 163 125 38 127 127 0 strelka-varscan-mutect AP1G2,missense_variant,p.Asp280Ala,ENST00000308724,NM_001282475.1;AP1G2,missense_variant,p.Asp280Ala,ENST00000397120,NM_001282474.1,NM_003917.4;JPH4,downstream_gene_variant,,ENST00000397118,NM_032452.2;JPH4,downstream_gene_variant,,ENST00000356300,NM_001146028.1;JPH4,downstream_gene_variant,,ENST00000622501,;THTPA,downstream_gene_variant,,ENST00000288014,;JPH4,downstream_gene_variant,,ENST00000544177,;AP1G2,downstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000554477,;AP1G2,downstream_gene_variant,,ENST00000556843,;RP11-66N24.3,intron_variant,,ENST00000555968,;RP11-66N24.4,downstream_gene_variant,,ENST00000553985,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000555510,;AP1G2,upstream_gene_variant,,ENST00000555118,;AP1G2,non_coding_transcript_exon_variant,,ENST00000460049,;AP1G2,non_coding_transcript_exon_variant,,ENST00000465445,;AP1G2,non_coding_transcript_exon_variant,,ENST00000535852,;AP1G2,non_coding_transcript_exon_variant,,ENST00000556152,;AP1G2,non_coding_transcript_exon_variant,,ENST00000554977,;AP1G2,upstream_gene_variant,,ENST00000554554,;AP1G2,downstream_gene_variant,,ENST00000556743,;AP1G2,downstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000556966,;AP1G2,downstream_gene_variant,,ENST00000557619,;AP1G2,downstream_gene_variant,,ENST00000555896,;AP1G2,downstream_gene_variant,,ENST00000554069,;AP1G2,downstream_gene_variant,,ENST00000556943,;AP1G2,downstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000554982,;AP1G2,upstream_gene_variant,,ENST00000554892,;AP1G2,downstream_gene_variant,,ENST00000553756,;AP1G2,downstream_gene_variant,,ENST00000554312,;AP1G2,downstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000557162,;AP1G2,upstream_gene_variant,,ENST00000557132,;AP1G2,upstream_gene_variant,,ENST00000557391,;AP1G2,upstream_gene_variant,,ENST00000556741,;AP1G2,upstream_gene_variant,,ENST00000555974,;AP1G2,upstream_gene_variant,,ENST00000555789,;AP1G2,downstream_gene_variant,,ENST00000554816,; G ENST00000308724 Transcript missense_variant 1595/3298 839/2358 280/785 D/A gAc/gCc 1 -1 AP1G2 HGNC HGNC:556 protein_coding YES CCDS9602.1 ENSP00000312442 O75843 UPI0000124FE8 NM_001282475.1 deleterious(0) 8/21 Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF037094,hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF28,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 23564644 23564644 T G 1 0 0 0 0 1 0 0 0 849 1667 58 5 5 AP1G2 14 23564644 Missense_Mutation SNP T C3N-00203_T 130939 23564644 83479074 334 11638 FOXG1 0 . GRCh38 14 28768489 28768489 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.1210C>G p.Pro404Ala p.P404A ENST00000313071 1/1 336 273 63 247 247 0 strelka-varscan-mutect FOXG1,missense_variant,p.Pro404Ala,ENST00000313071,NM_005249.4;LINC01551,upstream_gene_variant,,ENST00000399387,;LINC01551,upstream_gene_variant,,ENST00000552957,;LINC01551,upstream_gene_variant,,ENST00000548213,;FOXG1-AS1,upstream_gene_variant,,ENST00000551395,;FOXG1-AS1,upstream_gene_variant,,ENST00000546560,;FOXG1-AS1,upstream_gene_variant,,ENST00000549487,;FOXG1,downstream_gene_variant,,ENST00000637817,;FOXG1,downstream_gene_variant,,ENST00000636893,;FOXG1,downstream_gene_variant,,ENST00000636353,;FOXG1,downstream_gene_variant,,ENST00000637220,;FOXG1,downstream_gene_variant,,ENST00000636346,;FOXG1,downstream_gene_variant,,ENST00000636604,;FOXG1,downstream_gene_variant,,ENST00000637351,; G ENST00000313071 Transcript missense_variant 3102/4890 1210/1470 404/489 P/A Ccc/Gcc 1 1 FOXG1 HGNC HGNC:3811 protein_coding YES CCDS9636.1 ENSP00000339004 P55316 UPI00001AE46C NM_005249.4 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF165 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 28768489 28768489 C G 1 0 0 0 0 1 0 0 0 5869 623 22 4 4 FOXG1 14 28768489 Missense_Mutation SNP C C3N-00203_T 5203845 28768489 78275229 335 11639 AKAP6 0 . GRCh38 14 32824260 32824260 + Missense_Mutation SNP G G T rs747689365 C3N-00203_T C3N-00203_N G G c.6447G>T p.Lys2149Asn p.K2149N ENST00000280979 13/14 317 233 84 307 306 1 strelka-varscan-mutect AKAP6,missense_variant,p.Lys2149Asn,ENST00000280979,NM_004274.4;AKAP6,intron_variant,,ENST00000557272,; T ENST00000280979 Transcript missense_variant 6617/15006 6447/6960 2149/2319 K/N aaG/aaT rs747689365 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 tolerated_low_confidence(0.11) 13/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2 MODERATE 1 SNV 1 1 PASS rs747689365 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 32824260 32824260 G T 1 0 0 0 0 1 0 0 0 539 991 35 2 2 AKAP6 14 32824260 Missense_Mutation SNP G C3N-00203_T 4055771 32824260 74219458 336 11640 TMX1 0 . GRCh38 14 51249507 51249507 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.529G>T p.Val177Leu p.V177L ENST00000457354 6/8 237 179 58 213 213 0 strelka-varscan-mutect TMX1,missense_variant,p.Val177Leu,ENST00000457354,NM_030755.4;Y_RNA,downstream_gene_variant,,ENST00000364950,;TMX1,3_prime_UTR_variant,,ENST00000556683,;TMX1,downstream_gene_variant,,ENST00000555574,; T ENST00000457354 Transcript missense_variant 654/3995 529/843 177/280 V/L Gtg/Ttg 1 1 TMX1 HGNC HGNC:15487 protein_coding YES CCDS41953.1 ENSP00000393316 Q9H3N1 UPI0000048EB4 NM_030755.4 deleterious(0.05) 6/8 hmmpanther:PTHR18929:SF72,hmmpanther:PTHR18929 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 51249507 51249507 G T 1 0 0 0 0 1 0 0 0 16740 1029 36 2 2 TMX1 14 51249507 Missense_Mutation SNP G C3N-00203_T 18425247 51249507 55794211 337 11641 ISM2 0 . GRCh38 14 77482523 77482527 + Frame_Shift_Del DEL TTTCC TTTCC - novel C3N-00203_T C3N-00203_N TTTCC TTTCC c.768_772delGGAAA p.Glu257ArgfsTer25 p.E257Rfs*25 ENST00000342219 4/7 194 179 15 137 137 0 sindel-varindel-pindel ISM2,frameshift_variant,p.Glu257ArgfsTer25,ENST00000342219,NM_199296.2;ISM2,frameshift_variant,p.Glu176ArgfsTer?,ENST00000554801,;ISM2,intron_variant,,ENST00000493585,NM_182509.3;ISM2,3_prime_UTR_variant,,ENST00000216481,;ISM2,non_coding_transcript_exon_variant,,ENST00000487738,;ISM2,downstream_gene_variant,,ENST00000472744,;ISM2,downstream_gene_variant,,ENST00000480979,;ISM2,downstream_gene_variant,,ENST00000471734,; - ENST00000342219 Transcript frameshift_variant 825-829/2971 768-772/1716 256-258/571 EEK/EX gaGGAAAaa/gaaa 1 -1 ISM2 HGNC HGNC:23176 protein_coding YES CCDS9864.1 ENSP00000341490 Q6H9L7 UPI000019950C NM_199296.2 4/7 hmmpanther:PTHR10239:SF28,hmmpanther:PTHR10239 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 77482523 77482523 TTTCC - 1 0 1 0 1 0 0 0 0 7768 1850 64 0 0 ISM2 14 77482523 Frame_Shift_Del DEL TTTCC C3N-00203_T 26233016 77482523 29561195 338 11642 NRXN3 0 . GRCh38 14 78243709 78243709 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.616C>A p.Pro206Thr p.P206T ENST00000634499 2/20 160 141 19 150 150 0 strelka-varscan-mutect NRXN3,missense_variant,p.Pro206Thr,ENST00000634499,;NRXN3,missense_variant,p.Pro206Thr,ENST00000635466,;NRXN3,missense_variant,p.Pro206Thr,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556088,; A ENST00000634499 Transcript missense_variant 1621/6069 616/4995 206/1664 P/T Ccc/Acc 1 1 NRXN3 HGNC HGNC:8010 protein_coding ENSP00000488920 A0A0U1RQC5 UPI000719A152 2/20 Gene3D:2.60.120.200,PROSITE_profiles:PS50026,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 78243709 78243709 C A 1 0 0 0 0 1 0 0 0 10726 855 30 2 2 NRXN3 14 78243709 Missense_Mutation SNP C C3N-00203_T 761186 78243709 28800009 339 11643 FLRT2 0 . GRCh38 14 85622091 85622091 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.577G>T p.Ala193Ser p.A193S ENST00000330753 2/2 216 199 17 208 208 0 strelka-varscan-mutect FLRT2,missense_variant,p.Ala193Ser,ENST00000330753,NM_013231.4;FLRT2,missense_variant,p.Ala193Ser,ENST00000554746,;FLRT2,upstream_gene_variant,,ENST00000553650,; T ENST00000330753 Transcript missense_variant 1344/33679 577/1983 193/660 A/S Gct/Tct 1 1 FLRT2 HGNC HGNC:3761 protein_coding YES CCDS9877.1 ENSP00000332879 O43155 UPI0000049E10 NM_013231.4 tolerated(1) 2/2 hmmpanther:PTHR24369:SF23,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 85622091 85622091 G T 1 0 0 0 0 1 0 0 0 5795 1319 46 2 2 FLRT2 14 85622091 Missense_Mutation SNP G C3N-00203_T 7378382 85622091 21421627 340 11644 GOLGA5 0 . GRCh38 14 92811735 92811735 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.1301A>G p.Lys434Arg p.K434R ENST00000163416 6/13 214 156 58 175 174 1 strelka-varscan-mutect GOLGA5,missense_variant,p.Lys434Arg,ENST00000163416,NM_005113.3;GOLGA5,downstream_gene_variant,,ENST00000555793,; G ENST00000163416 Transcript missense_variant 1557/2969 1301/2196 434/731 K/R aAa/aGa 1 1 GOLGA5 HGNC HGNC:4428 protein_coding YES CCDS9905.1 ENSP00000163416 Q8TBA6 UPI000013C5AA NM_005113.3 deleterious(0) 6/13 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF09787,hmmpanther:PTHR13815,hmmpanther:PTHR13815:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 92811735 92811735 A G 1 0 0 0 0 1 0 0 0 6434 14 1 5 5 GOLGA5 14 92811735 Missense_Mutation SNP A C3N-00203_T 7189644 92811735 14231983 341 11645 SERPINA1 0 . GRCh38 14 94382974 94382974 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.264C>T p.= p.L88L ENST00000448921 4/7 56 50 6 59 59 0 strelka-varscan-mutect SERPINA1,synonymous_variant,p.=,ENST00000448921,NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1;SERPINA1,synonymous_variant,p.=,ENST00000437397,NM_001127706.1,NM_001127707.1,NM_001127702.1;SERPINA1,synonymous_variant,p.=,ENST00000355814,NM_001002235.2,NM_001127700.1;SERPINA1,synonymous_variant,p.=,ENST00000440909,;SERPINA1,synonymous_variant,p.=,ENST00000393088,;SERPINA1,synonymous_variant,p.=,ENST00000404814,;SERPINA1,synonymous_variant,p.=,ENST00000393087,NM_000295.4;SERPINA1,synonymous_variant,p.=,ENST00000449399,;SERPINA1,synonymous_variant,p.=,ENST00000636712,;SERPINA1,synonymous_variant,p.=,ENST00000402629,;SERPINA1,synonymous_variant,p.=,ENST00000557492,;SERPINA1,synonymous_variant,p.=,ENST00000556091,;SERPINA1,synonymous_variant,p.=,ENST00000553327,;SERPINA1,synonymous_variant,p.=,ENST00000556955,;SERPINA1,synonymous_variant,p.=,ENST00000554720,;SERPINA1,downstream_gene_variant,,ENST00000557118,;SERPINA1,downstream_gene_variant,,ENST00000555289,;SERPINA1,synonymous_variant,p.=,ENST00000489769,; A ENST00000448921 Transcript synonymous_variant 837/3532 264/1257 88/418 L ctC/ctT 1 -1 SERPINA1 HGNC HGNC:8941 protein_coding YES CCDS9925.1 ENSP00000416066 P01009 E9KL23 UPI000000CBEC NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1 4/7 hmmpanther:PTHR11461:SF165,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.61795 1 1 1 1 0 A 2 1 42 94382974 94382974 G A 1 0 0 0 0 0 0 0 1 14362 929 33 3 3 SERPINA1 14 94382974 Silent SNP G C3N-00203_T 1571239 94382974 12660744 342 11646 NPAP1 0 . GRCh38 15 24677264 24677264 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.1397C>A p.Pro466His p.P466H ENST00000329468 1/1 279 231 48 280 279 1 strelka-varscan-mutect NPAP1,missense_variant,p.Pro466His,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1397/7526 1397/3471 466/1156 P/H cCt/cAt COSM333559 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.14) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 24677264 24677264 C A 1 0 0 0 0 1 0 0 0 10609 681 24 2 2 NPAP1 15 24677264 Missense_Mutation SNP C C3N-00203_T 24677264 77313925 343 11647 GABRB3 0 . GRCh38 15 26772444 26772444 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.198C>A p.Asn66Lys p.N66K ENST00000311550 3/9 361 315 46 370 370 0 strelka-varscan-mutect GABRB3,missense_variant,p.Asn122Lys,ENST00000541819,;GABRB3,missense_variant,p.Asn66Lys,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Asn66Lys,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Asn33Lys,ENST00000638099,;GABRB3,5_prime_UTR_variant,,ENST00000622697,NM_001278631.1;GABRB3,upstream_gene_variant,,ENST00000636466,;GABRB3,non_coding_transcript_exon_variant,,ENST00000557641,;GABRB3,non_coding_transcript_exon_variant,,ENST00000554722,;GABRB3,missense_variant,p.Asn66Lys,ENST00000555632,;GABRB3,missense_variant,p.Asn66Lys,ENST00000554556,; T ENST00000311550 Transcript missense_variant 310/5781 198/1422 66/473 N/K aaC/aaA 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 tolerated(0.19) 3/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 26772444 26772444 G T 1 0 0 0 0 1 0 0 0 6039 1368 48 2 2 GABRB3 15 26772444 Missense_Mutation SNP G C3N-00203_T 2095180 26772444 75218745 344 11648 RYR3 0 . GRCh38 15 33646501 33646501 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.3916C>A p.Leu1306Met p.L1306M ENST00000634891 29/104 103 73 30 77 77 0 strelka-varscan-mutect RYR3,missense_variant,p.Leu1306Met,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Leu1306Met,ENST00000622037,;RYR3,missense_variant,p.Leu1306Met,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Leu1306Met,ENST00000389232,;RYR3,missense_variant,p.Leu1306Met,ENST00000634418,;RYR3,intron_variant,,ENST00000636583,; A ENST00000634891 Transcript missense_variant 4017/15591 3916/14613 1306/4870 L/M Ctg/Atg 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.06) 29/104 PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS rs1396287727 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 33646501 33646501 C A 1 0 0 0 0 1 0 0 0 14030 912 32 2 2 RYR3 15 33646501 Missense_Mutation SNP C C3N-00203_T 6874057 33646501 68344688 345 11649 RYR3 0 . GRCh38 15 33669388 33669388 + Missense_Mutation SNP A A C novel C3N-00203_T C3N-00203_N A A c.5654A>C p.Asn1885Thr p.N1885T ENST00000634891 37/104 327 263 64 286 286 0 strelka-varscan-mutect RYR3,missense_variant,p.Asn1885Thr,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Asn1885Thr,ENST00000622037,;RYR3,missense_variant,p.Asn1885Thr,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Asn1885Thr,ENST00000389232,;RYR3,missense_variant,p.Asn1885Thr,ENST00000634418,; C ENST00000634891 Transcript missense_variant 5755/15591 5654/14613 1885/4870 N/T aAc/aCc 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.08) 37/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 33669388 33669388 A C 1 0 0 0 0 1 0 0 0 14030 43 2 5 5 RYR3 15 33669388 Missense_Mutation SNP A C3N-00203_T 22887 33669388 68321801 346 11650 C15orf41 0 . GRCh38 15 36808367 36808367 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.760G>C p.Glu254Gln p.E254Q ENST00000566621 11/11 218 174 44 162 162 0 strelka-varscan-mutect C15orf41,missense_variant,p.Glu254Gln,ENST00000566621,NM_001321759.1,NM_001321761.1,NM_001290233.1,NM_001130010.2;C15orf41,missense_variant,p.Glu156Gln,ENST00000567389,NM_032499.5;C15orf41,missense_variant,p.Glu156Gln,ENST00000338183,;C15orf41,missense_variant,p.Glu254Gln,ENST00000437989,;C15orf41,missense_variant,p.Glu260Gln,ENST00000569302,;C15orf41,missense_variant,p.Gly16Ala,ENST00000563167,;C15orf41,missense_variant,p.Glu156Gln,ENST00000562877,NM_001290232.1;C15orf41,missense_variant,p.Glu78Gln,ENST00000562489,;C15orf41,non_coding_transcript_exon_variant,,ENST00000565792,;C15orf41,non_coding_transcript_exon_variant,,ENST00000566932,;CSNK1A1P1,intron_variant,,ENST00000430593,;C15orf41,non_coding_transcript_exon_variant,,ENST00000566677,; C ENST00000566621 Transcript missense_variant 1010/2866 760/846 254/281 E/Q Gag/Cag 1 1 C15orf41 HGNC HGNC:26929 protein_coding YES CCDS45215.1 ENSP00000455397 Q9Y2V0 UPI00001FE1DF NM_001321759.1,NM_001321761.1,NM_001290233.1,NM_001130010.2 deleterious(0.03) 11/11 Pfam_domain:PF14811,hmmpanther:PTHR31661,hmmpanther:PTHR31661:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 36808367 36808367 G C 1 0 0 0 0 1 0 0 0 1845 1175 41 4 4 C15orf41 15 36808367 Missense_Mutation SNP G C3N-00203_T 3138979 36808367 65182822 347 11651 SPRED1 0 . GRCh38 15 38299420 38299420 + Nonsense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.80C>A p.Ser27Ter p.S27* ENST00000299084 2/7 419 314 105 358 357 1 strelka-varscan-mutect SPRED1,stop_gained,p.Ser27Ter,ENST00000299084,NM_152594.2;SPRED1,stop_gained,p.Ser6Ter,ENST00000561317,;SPRED1,non_coding_transcript_exon_variant,,ENST00000561205,; A ENST00000299084 Transcript stop_gained 940/7780 80/1335 27/444 S/* tCa/tAa COSM126941 1 1 SPRED1 HGNC HGNC:20249 protein_coding YES CCDS32193.1 ENSP00000299084 Q7Z699 UPI0000072FBD NM_152594.2 2/7 Low_complexity_(Seg):seg,PROSITE_profiles:PS50229,hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF18,Gene3D:2.30.29.30,Pfam_domain:PF00568,SMART_domains:SM00461,Superfamily_domains:SSF50729 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 38299420 38299420 C A 1 0 0 0 0 0 1 0 0 15446 838 29 2 2 SPRED1 15 38299420 Nonsense_Mutation SNP C C3N-00203_T 1491053 38299420 63691769 348 11652 WDR76 0 . GRCh38 15 43835069 43835069 + Silent SNP G G T rs149899666 C3N-00203_T C3N-00203_N G G c.471G>T p.= p.S157S ENST00000263795 3/13 218 150 68 162 161 1 strelka-varscan-mutect WDR76,synonymous_variant,p.=,ENST00000263795,NM_024908.3;WDR76,synonymous_variant,p.=,ENST00000381246,NM_001167941.1;WDR76,synonymous_variant,p.=,ENST00000452115,; T ENST00000263795 Transcript synonymous_variant 541/3978 471/1881 157/626 S tcG/tcT rs149899666,COSM4054892 1 1 WDR76 HGNC HGNC:25773 protein_coding YES CCDS10106.1 ENSP00000263795 Q9H967 UPI000013D462 NM_024908.3 3/13 hmmpanther:PTHR14773:SF0,hmmpanther:PTHR14773 0,1 LOW 1 SNV 1 0,1 1 PASS rs149899666 . 0 207 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 T 2 4 42 43835069 43835069 G T 1 0 0 0 0 0 0 0 1 17882 1103 39 1 1 WDR76 15 43835069 Silent SNP G C3N-00203_T 5535649 43835069 58156120 349 11653 UNC13C 0 . GRCh38 15 54013420 54013420 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.517C>A p.Leu173Ile p.L173I ENST00000260323 1/32 170 139 31 161 161 0 strelka-varscan-mutect UNC13C,missense_variant,p.Leu173Ile,ENST00000260323,NM_001080534.1; A ENST00000260323 Transcript missense_variant 517/12946 517/6645 173/2214 L/I Cta/Ata 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0.02) 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 54013420 54013420 C A 1 0 0 0 0 1 0 0 0 17510 912 32 2 2 UNC13C 15 54013420 Missense_Mutation SNP C C3N-00203_T 10178351 54013420 47977769 350 11654 PML 0 . GRCh38 15 74023372 74023372 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.1147C>T p.= p.L383L ENST00000268058 3/9 212 169 43 204 204 0 strelka-varscan-mutect PML,synonymous_variant,p.=,ENST00000565898,;PML,synonymous_variant,p.=,ENST00000268058,NM_033238.2;PML,synonymous_variant,p.=,ENST00000563500,;PML,synonymous_variant,p.=,ENST00000435786,NM_033240.2;PML,synonymous_variant,p.=,ENST00000268059,NM_033239.2;PML,synonymous_variant,p.=,ENST00000436891,NM_033244.3;PML,synonymous_variant,p.=,ENST00000354026,NM_033250.2;PML,synonymous_variant,p.=,ENST00000569477,;PML,synonymous_variant,p.=,ENST00000395135,NM_002675.3;PML,synonymous_variant,p.=,ENST00000569965,;PML,synonymous_variant,p.=,ENST00000567606,;PML,synonymous_variant,p.=,ENST00000564428,NM_033249.2;PML,synonymous_variant,p.=,ENST00000395132,NM_033247.2;PML,synonymous_variant,p.=,ENST00000359928,NM_033246.2;PML,synonymous_variant,p.=,ENST00000567543,;PML,synonymous_variant,p.=,ENST00000566068,;PML,synonymous_variant,p.=,ENST00000565239,;PML,upstream_gene_variant,,ENST00000562086,;PML,splice_region_variant,,ENST00000569161,;PML,non_coding_transcript_exon_variant,,ENST00000564725,; T ENST00000268058 Transcript synonymous_variant 1243/4508 1147/2649 383/882 L Ctg/Ttg 1 1 PML HGNC HGNC:9113 protein_coding YES CCDS10255.1 ENSP00000268058 P29590 UPI000013D78F NM_033238.2 3/9 Pfam_domain:PF12126,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF374 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 74023372 74023372 C T 1 0 0 0 0 0 0 0 1 12242 680 24 3 3 PML 15 74023372 Silent SNP C C3N-00203_T 20009952 74023372 27967817 351 11655 ISLR2 0 . GRCh38 15 74133886 74133886 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1132C>A p.Pro378Thr p.P378T ENST00000361742 4/4 222 167 55 178 178 0 strelka-varscan-mutect ISLR2,missense_variant,p.Pro378Thr,ENST00000361742,NM_001130136.1;ISLR2,missense_variant,p.Pro378Thr,ENST00000435464,NM_001130138.1;ISLR2,missense_variant,p.Pro378Thr,ENST00000565159,NM_001130137.1;ISLR2,missense_variant,p.Pro378Thr,ENST00000453268,NM_020851.2;ISLR2,missense_variant,p.Pro378Thr,ENST00000565540,;ISLR2,intron_variant,,ENST00000419208,;ISLR2,downstream_gene_variant,,ENST00000569886,;ISLR2,downstream_gene_variant,,ENST00000561740,;ISLR2,downstream_gene_variant,,ENST00000567206,;ISLR2,downstream_gene_variant,,ENST00000565332,;RP11-247C2.2,upstream_gene_variant,,ENST00000514871,;ISLR2,intron_variant,,ENST00000561975,;ISLR2,downstream_gene_variant,,ENST00000565068,; A ENST00000361742 Transcript missense_variant 1901/4817 1132/2238 378/745 P/T Cca/Aca 1 1 ISLR2 HGNC HGNC:29286 protein_coding YES CCDS10259.1 ENSP00000355402 Q6UXK2 UPI000004C60F NM_001130136.1 tolerated(0.17) 4/4 hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 74133886 74133886 C A 1 0 0 0 0 1 0 0 0 7766 623 22 2 2 ISLR2 15 74133886 Missense_Mutation SNP C C3N-00203_T 110514 74133886 27857303 352 11656 ANKRD34C 0 . GRCh38 15 79294289 79294289 + Missense_Mutation SNP A A C novel C3N-00203_T C3N-00203_N A A c.1005A>C p.Lys335Asn p.K335N ENST00000421388 1/1 196 159 37 230 230 0 strelka-varscan-mutect ANKRD34C,missense_variant,p.Lys335Asn,ENST00000421388,NM_001146341.1; C ENST00000421388 Transcript missense_variant 1005/4951 1005/1608 335/535 K/N aaA/aaC 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 tolerated(0.14) 1/1 hmmpanther:PTHR24157 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 79294289 79294289 A C 1 0 0 0 0 1 0 0 0 769 69 3 5 5 ANKRD34C 15 79294289 Missense_Mutation SNP A C3N-00203_T 5160403 79294289 22696900 353 11657 ADAMTSL3 0 . GRCh38 15 83870869 83870869 + Silent SNP C C A rs143597327 C3N-00203_T C3N-00203_N C C c.870C>A p.= p.L290L ENST00000286744 9/30 265 226 39 259 259 0 strelka-varscan-mutect ADAMTSL3,synonymous_variant,p.=,ENST00000286744,NM_207517.2;ADAMTSL3,synonymous_variant,p.=,ENST00000567476,NM_001301110.1;ADAMTSL3,upstream_gene_variant,,ENST00000567663,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,; A ENST00000286744 Transcript synonymous_variant 1094/7336 870/5076 290/1691 L ctC/ctA rs143597327 1 1 ADAMTSL3 HGNC HGNC:14633 protein_coding YES CCDS10326.1 ENSP00000286744 P82987 UPI00001615A5 NM_207517.2 9/30 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF169 LOW 1 SNV 1 1 PASS rs143597327 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 83870869 83870869 C A 1 0 0 0 0 0 0 0 1 320 871 31 1 1 ADAMTSL3 15 83870869 Silent SNP C C3N-00203_T 4576580 83870869 18120320 354 11658 SLC28A1 0 . GRCh38 15 84905628 84905628 + Missense_Mutation SNP C C A rs768211693 C3N-00203_T C3N-00203_N C C c.693C>A p.Phe231Leu p.F231L ENST00000394573 8/19 509 394 115 408 408 0 strelka-varscan-mutect SLC28A1,missense_variant,p.Phe231Leu,ENST00000394573,NM_004213.4;SLC28A1,missense_variant,p.Phe231Leu,ENST00000286749,NM_001287762.1;SLC28A1,missense_variant,p.Phe231Leu,ENST00000538177,NM_001287761.1; A ENST00000394573 Transcript missense_variant 916/2769 693/1950 231/649 F/L ttC/ttA rs768211693 1 1 SLC28A1 HGNC HGNC:11001 protein_coding YES CCDS10334.1 ENSP00000378074 O00337 UPI000013DE67 NM_004213.4 deleterious(0.05) 8/19 hmmpanther:PTHR10590:SF16,hmmpanther:PTHR10590,Pfam_domain:PF01773,TIGRFAM_domain:TIGR00804 MODERATE 1 SNV 1 1 PASS rs768211693 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 84905628 84905628 C A 1 0 0 0 0 1 0 0 0 14801 883 31 1 1 SLC28A1 15 84905628 Missense_Mutation SNP C C3N-00203_T 1034759 84905628 17085561 355 11659 AGBL1 0 . GRCh38 15 86266450 86266450 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1744G>T p.Glu582Ter p.E582* ENST00000441037 12/25 79 61 18 75 75 0 strelka-varscan-mutect AGBL1,stop_gained,p.Glu582Ter,ENST00000441037,;AGBL1,stop_gained,p.Glu536Ter,ENST00000635782,NM_152336.2;AGBL1,stop_gained,p.Glu536Ter,ENST00000421325,;AGBL1,non_coding_transcript_exon_variant,,ENST00000567715,;AGBL1,non_coding_transcript_exon_variant,,ENST00000568785,; T ENST00000441037 Transcript stop_gained 1744/3551 1744/3339 582/1112 E/* Gag/Tag 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 12/25 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5 HIGH 1 SNV 5 1 PASS rs1425281552 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 86266450 86266450 G T 1 0 0 0 0 0 1 0 0 451 1291 45 2 2 AGBL1 15 86266450 Nonsense_Mutation SNP G C3N-00203_T 1360822 86266450 15724739 356 11660 ACAN 0 . GRCh38 15 88845525 88845525 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.1072C>A p.Pro358Thr p.P358T ENST00000439576 7/18 68 52 16 62 62 0 strelka-varscan-mutect ACAN,missense_variant,p.Pro358Thr,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Pro358Thr,ENST00000617301,;ACAN,missense_variant,p.Pro358Thr,ENST00000559004,;ACAN,missense_variant,p.Pro358Thr,ENST00000561243,;ACAN,missense_variant,p.Pro358Thr,ENST00000352105,NM_001135.3;ACAN,missense_variant,p.Pro358Thr,ENST00000558207,; A ENST00000439576 Transcript missense_variant 1446/8840 1072/7593 358/2530 P/T Cca/Aca COSM3887706,COSM3887707 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0.03) 7/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 88845525 88845525 C A 1 0 0 0 0 1 0 0 0 160 623 22 2 2 ACAN 15 88845525 Missense_Mutation SNP C C3N-00203_T 2579075 88845525 13145664 357 11661 WDR93 0 . GRCh38 15 89738124 89738124 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1849C>A p.Leu617Ile p.L617I ENST00000268130 16/17 178 153 25 138 138 0 strelka-varscan-mutect WDR93,missense_variant,p.Leu617Ile,ENST00000268130,NM_020212.1;WDR93,missense_variant,p.Leu589Ile,ENST00000560294,NM_001284395.1;WDR93,non_coding_transcript_exon_variant,,ENST00000444934,; A ENST00000268130 Transcript missense_variant 1950/2409 1849/2061 617/686 L/I Ctc/Atc 1 1 WDR93 HGNC HGNC:26924 protein_coding YES CCDS32326.1 ENSP00000268130 Q6P2C0 UPI00001D77A7 NM_020212.1 deleterious(0) 16/17 hmmpanther:PTHR12219:SF17,hmmpanther:PTHR12219 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 89738124 89738124 C A 1 0 0 0 0 1 0 0 0 17896 565 20 2 2 WDR93 15 89738124 Missense_Mutation SNP C C3N-00203_T 892599 89738124 12253065 358 11662 SRRM2 0 . GRCh38 16 2763348 2763348 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2820G>T p.Arg940Ser p.R940S ENST00000301740 11/15 206 131 75 177 176 1 strelka-varscan-mutect SRRM2,missense_variant,p.Arg940Ser,ENST00000301740,NM_016333.3;SRRM2,missense_variant,p.Arg940Ser,ENST00000576924,;SRRM2,missense_variant,p.Arg844Ser,ENST00000571378,;SRRM2,intron_variant,,ENST00000630499,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,upstream_gene_variant,,ENST00000573311,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000573451,; T ENST00000301740 Transcript missense_variant 3369/9353 2820/8259 940/2752 R/S agG/agT 1 1 SRRM2 HGNC HGNC:16639 protein_coding YES CCDS32373.1 ENSP00000301740 Q9UQ35 A0A140VK53 UPI000049DDFC NM_016333.3 deleterious_low_confidence(0) 11/15 Low_complexity_(Seg):seg,hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9993748 1 1 1 0 T 3 4 42 2763348 2763348 G T 1 0 0 0 0 1 0 0 0 15530 1223 43 2 2 SRRM2 16 2763348 Missense_Mutation SNP G C3N-00203_T 2763348 87574997 359 11663 MEFV 0 . GRCh38 16 3254550 3254550 + Frame_Shift_Del DEL C C - novel C3N-00203_T C3N-00203_N C C c.518delG p.Gly173AlafsTer22 p.G173Afs*22 ENST00000219596 2/10 50 28 22 55 55 0 sindel-varindel-pindel MEFV,frameshift_variant,p.Gly173AlafsTer22,ENST00000219596,NM_000243.2;MEFV,intron_variant,,ENST00000339854,;MEFV,intron_variant,,ENST00000541159,NM_001198536.1;MEFV,intron_variant,,ENST00000536379,;MEFV,frameshift_variant,p.Gly173AlafsTer22,ENST00000542898,;MEFV,frameshift_variant,p.Gly173AlafsTer22,ENST00000537682,;MEFV,frameshift_variant,p.Gly173AlafsTer22,ENST00000538326,;MEFV,frameshift_variant,p.Gly173AlafsTer22,ENST00000570511,;MEFV,intron_variant,,ENST00000536980,;MEFV,intron_variant,,ENST00000539145,;MEFV,intron_variant,,ENST00000576315,;MEFV,intron_variant,,ENST00000574583,;MEFV,intron_variant,,ENST00000572244,; - ENST00000219596 Transcript frameshift_variant 558/3499 518/2346 173/781 G/X gGc/gc 1 -1 MEFV HGNC HGNC:6998 protein_coding YES CCDS10498.1 ENSP00000219596 O15553 UPI000004C0CA NM_000243.2 2/10 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 3254550 3254550 C - 1 0 1 0 1 0 0 0 0 9399 739 26 0 0 MEFV 16 3254550 Frame_Shift_Del DEL C C3N-00203_T 491202 3254550 87083795 360 11664 FAM57B 0 . GRCh38 16 30030487 30030487 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.41G>T p.Gly14Val p.G14V ENST00000380495 1/5 48 29 19 48 48 0 strelka-varscan-mutect FAM57B,missense_variant,p.Gly14Val,ENST00000380495,NM_031478.4;FAM57B,intron_variant,,ENST00000561666,;FAM57B,upstream_gene_variant,,ENST00000564806,;FAM57B,upstream_gene_variant,,ENST00000279389,NM_001318504.1;FAM57B,downstream_gene_variant,,ENST00000571269,;C16orf92,downstream_gene_variant,,ENST00000569198,;C16orf92,downstream_gene_variant,,ENST00000567847,;FAM57B,downstream_gene_variant,,ENST00000567037,;FAM57B,intron_variant,,ENST00000569508,; A ENST00000380495 Transcript missense_variant 773/2313 41/825 14/274 G/V gGa/gTa 1 -1 FAM57B HGNC HGNC:25295 protein_coding YES CCDS10667.2 ENSP00000369863 Q71RH2 F1T0F5 UPI000022EE26 NM_031478.4 tolerated(0.05) 1/5 hmmpanther:PTHR13439,hmmpanther:PTHR13439:SF15 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 30030487 30030487 C A 1 0 0 0 0 1 0 0 0 5459 855 30 2 2 FAM57B 16 30030487 Missense_Mutation SNP C C3N-00203_T 26775937 30030487 60307858 361 11665 ABCC11 0 . GRCh38 16 48214980 48214980 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1149G>T p.Gln383His p.Q383H ENST00000394747 8/29 265 209 56 202 200 2 strelka-varscan-mutect ABCC11,missense_variant,p.Gln383His,ENST00000394747,NM_033151.3;ABCC11,missense_variant,p.Gln383His,ENST00000356608,;ABCC11,missense_variant,p.Gln383His,ENST00000394748,NM_032583.3;ABCC11,missense_variant,p.Gln383His,ENST00000353782,NM_145186.2;ABCC11,downstream_gene_variant,,ENST00000565487,;ABCC11,non_coding_transcript_exon_variant,,ENST00000567385,; A ENST00000394747 Transcript missense_variant 1499/4862 1149/4149 383/1382 Q/H caG/caT 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 deleterious(0) 8/29 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 48214980 48214980 C A 1 0 0 0 0 1 0 0 0 55 912 32 2 2 ABCC11 16 48214980 Missense_Mutation SNP C C3N-00203_T 18184493 48214980 42123365 362 11666 CES5A 0 . GRCh38 16 55871654 55871654 + Missense_Mutation SNP C C A rs772066729 C3N-00203_T C3N-00203_N C C c.475G>T p.Ala159Ser p.A159S ENST00000521992 4/14 254 203 51 183 182 1 strelka-varscan-mutect CES5A,missense_variant,p.Ala159Ser,ENST00000521992,NM_001190158.1;CES5A,missense_variant,p.Ala24Ser,ENST00000518005,;CES5A,missense_variant,p.Ala130Ser,ENST00000290567,NM_001143685.1;CES5A,missense_variant,p.Ala130Ser,ENST00000319165,NM_145024.2;CES5A,missense_variant,p.Ala24Ser,ENST00000536025,;CES5A,intron_variant,,ENST00000520435,;CES5A,intron_variant,,ENST00000541580,;CES5A,intron_variant,,ENST00000544479,;CES5A,missense_variant,p.Ala24Ser,ENST00000521228,; A ENST00000521992 Transcript missense_variant 621/2258 475/1815 159/604 A/S Gcc/Tcc rs772066729 1 -1 CES5A HGNC HGNC:26459 protein_coding YES CCDS54012.1 ENSP00000428864 Q6NT32 UPI0001914B41 NM_001190158.1 deleterious(0.03) 4/14 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF43,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS rs772066729 . 0 207 0 0 2 0 0 0 -20 0.9981209 1 1 1 0 A 3 1 42 55871654 55871654 C A 1 0 0 0 0 1 0 0 0 3005 710 25 2 2 CES5A 16 55871654 Missense_Mutation SNP C C3N-00203_T 7656674 55871654 34466691 363 11667 ADGRG3 0 . GRCh38 16 57676261 57676261 + Missense_Mutation SNP C C G rs200028157,rs781349146 C3N-00203_T C3N-00203_N C C c.268C>G p.Pro90Ala p.P90A ENST00000333493 3/12 280 233 47 195 195 0 strelka-varscan-mutect ADGRG3,missense_variant,p.Pro90Ala,ENST00000333493,NM_170776.4;ADGRG3,intron_variant,,ENST00000450388,NM_001308360.1;RP11-405F3.4,downstream_gene_variant,,ENST00000563062,;ADGRG3,missense_variant,p.Pro90Ala,ENST00000567991,;ADGRG3,3_prime_UTR_variant,,ENST00000568245,;ADGRG3,non_coding_transcript_exon_variant,,ENST00000565579,;ADGRG3,intron_variant,,ENST00000565902,;ADGRG3,upstream_gene_variant,,ENST00000569977,; G ENST00000333493 Transcript missense_variant 429/2728 268/1650 90/549 P/A Cct/Gct rs200028157,rs781349146,COSM5385062 1 1 ADGRG3 HGNC HGNC:13728 protein_coding YES CCDS10786.1 ENSP00000332900 Q86Y34 UPI000003C9E1 NM_170776.4 tolerated(0.34) 3/12 hmmpanther:PTHR12011:SF285,hmmpanther:PTHR12011 0,0,1 MODERATE 1 SNV 1 0,0,1 1 PASS rs200028157 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 57676261 57676261 C G 1 0 0 0 0 1 0 0 0 370 739 26 4 4 ADGRG3 16 57676261 Missense_Mutation SNP C C3N-00203_T 1804607 57676261 32662084 364 11668 DYNC1LI2 0 . GRCh38 16 66727745 66727745 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.1204A>T p.Ser402Cys p.S402C ENST00000258198 11/13 183 135 48 162 162 0 strelka-varscan-mutect DYNC1LI2,missense_variant,p.Ser402Cys,ENST00000258198,NM_006141.2;DYNC1LI2,missense_variant,p.Ser325Cys,ENST00000443351,NM_001286157.1;DYNC1LI2,missense_variant,p.Ser77Cys,ENST00000569320,;DYNC1LI2,intron_variant,,ENST00000563628,;DYNC1LI2,downstream_gene_variant,,ENST00000440564,;RP11-63M22.2,intron_variant,,ENST00000569274,;DYNC1LI2,downstream_gene_variant,,ENST00000570201,;DYNC1LI2,missense_variant,p.Ser28Cys,ENST00000564559,;DYNC1LI2,non_coding_transcript_exon_variant,,ENST00000567499,;DYNC1LI2,non_coding_transcript_exon_variant,,ENST00000564833,;DYNC1LI2,intron_variant,,ENST00000568453,;DYNC1LI2,downstream_gene_variant,,ENST00000565532,; A ENST00000258198 Transcript missense_variant 1411/4515 1204/1479 402/492 S/C Agt/Tgt 1 -1 DYNC1LI2 HGNC HGNC:2966 protein_coding YES CCDS10818.1 ENSP00000258198 O43237 A0A024R6Z0 UPI0000129A0D NM_006141.2 deleterious(0.01) 11/13 Pfam_domain:PF05783,hmmpanther:PTHR12688,hmmpanther:PTHR12688:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1213933201 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 66727745 66727745 T A 1 0 0 0 0 1 0 0 0 4669 1580 55 4 4 DYNC1LI2 16 66727745 Missense_Mutation SNP T C3N-00203_T 9051484 66727745 23610600 365 11669 PMFBP1 0 . GRCh38 16 72129089 72129089 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1927G>T p.Glu643Ter p.E643* ENST00000237353 13/21 184 153 31 137 137 0 strelka-varscan-mutect PMFBP1,stop_gained,p.Glu648Ter,ENST00000537465,;PMFBP1,stop_gained,p.Glu643Ter,ENST00000237353,NM_031293.2;PMFBP1,stop_gained,p.Glu498Ter,ENST00000355636,NM_001160213.1;PMFBP1,upstream_gene_variant,,ENST00000537792,;PMFBP1,stop_gained,p.Glu446Ter,ENST00000537392,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,; A ENST00000237353 Transcript stop_gained 2189/3527 1927/3024 643/1007 E/* Gaa/Taa 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 13/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 HIGH 1 SNV 1 1 PASS rs1393701267 . 0 206 0 3 0 0 0 0 -20 0.9999948 1 1 1 0 A 4 1 42 72129089 72129089 C A 1 0 0 0 0 0 1 0 0 12241 864 30 2 2 PMFBP1 16 72129089 Nonsense_Mutation SNP C C3N-00203_T 5401344 72129089 18209256 366 11670 ZFHX3 0 . GRCh38 16 72950751 72950751 + Silent SNP C C G rs371914920 C3N-00203_T C3N-00203_N C C c.2934G>C p.= p.A978A ENST00000268489 3/10 309 266 43 240 240 0 strelka-varscan-mutect ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,synonymous_variant,p.=,ENST00000397992,NM_001164766.1; G ENST00000268489 Transcript synonymous_variant 3607/16064 2934/11112 978/3703 A gcG/gcC rs371914920 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 3/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 LOW 1 SNV 1 1 PASS rs371914920 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 42 72950751 72950751 C G 1 0 0 0 0 0 0 0 1 18212 639 23 4 4 ZFHX3 16 72950751 Silent SNP C C3N-00203_T 821662 72950751 17387594 367 11671 GSE1 0 . GRCh38 16 85666154 85666154 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.2937C>A p.= p.A979A ENST00000253458 13/16 506 404 102 385 385 0 strelka-varscan-mutect GSE1,synonymous_variant,p.=,ENST00000253458,NM_014615.3;GSE1,synonymous_variant,p.=,ENST00000393243,NM_001278184.1;GSE1,synonymous_variant,p.=,ENST00000412692,;GSE1,synonymous_variant,p.=,ENST00000405402,NM_001134473.2;GSE1,synonymous_variant,p.=,ENST00000438180,;GSE1,non_coding_transcript_exon_variant,,ENST00000469381,;GSE1,non_coding_transcript_exon_variant,,ENST00000562659,;GSE1,downstream_gene_variant,,ENST00000479488,;GSE1,downstream_gene_variant,,ENST00000495192,;GSE1,upstream_gene_variant,,ENST00000496345,; A ENST00000253458 Transcript synonymous_variant 3113/7495 2937/3654 979/1217 A gcC/gcA 1 1 GSE1 HGNC HGNC:28979 protein_coding YES CCDS10952.1 ENSP00000253458 Q14687 UPI0000185F04 NM_014615.3 13/16 hmmpanther:PTHR17608 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 85666154 85666154 C A 1 0 0 0 0 0 0 0 1 6702 610 22 2 2 GSE1 16 85666154 Silent SNP C C3N-00203_T 12715403 85666154 4672191 368 11672 CA5A 0 . GRCh38 16 87904806 87904806 + Missense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.439G>T p.Gly147Cys p.G147C ENST00000309893 3/7 219 162 57 169 169 0 strelka-varscan-mutect CA5A,missense_variant,p.Gly147Cys,ENST00000309893,NM_001739.1; A ENST00000309893 Transcript missense_variant 505/7567 439/918 147/305 G/C Ggc/Tgc COSM974657 1 -1 CA5A HGNC HGNC:1377 protein_coding YES CCDS10965.1 ENSP00000309649 P35218 UPI0000126DF3 NM_001739.1 deleterious(0.04) 3/7 Gene3D:3.10.200.10,Pfam_domain:PF00194,PROSITE_patterns:PS00162,PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF89,SMART_domains:SM01057,Superfamily_domains:SSF51069 1 MODERATE 1 SNV 1 1 1 PASS rs1226444061 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 87904806 87904806 C A 1 0 0 0 0 1 0 0 0 2205 652 23 1 1 CA5A 16 87904806 Missense_Mutation SNP C C3N-00203_T 2238652 87904806 2433539 369 11673 ZC3H18 0 . GRCh38 16 88611464 88611464 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1475G>T p.Arg492Leu p.R492L ENST00000452588 9/19 353 271 82 248 248 0 strelka-varscan-mutect ZC3H18,missense_variant,p.Arg468Leu,ENST00000301011,NM_144604.3;ZC3H18,missense_variant,p.Arg492Leu,ENST00000452588,NM_001294340.1;ZC3H18,intron_variant,,ENST00000567085,;ZC3H18,non_coding_transcript_exon_variant,,ENST00000564161,;ZC3H18,downstream_gene_variant,,ENST00000568072,; T ENST00000452588 Transcript missense_variant 1653/3211 1475/2934 492/977 R/L cGt/cTt 1 1 ZC3H18 HGNC HGNC:25091 protein_coding YES CCDS73924.1 ENSP00000416951 E7ERS3 UPI0001AE683F NM_001294340.1 tolerated_low_confidence(0.07) 9/19 Low_complexity_(Seg):seg,hmmpanther:PTHR12506,hmmpanther:PTHR12506:SF22 MODERATE 1 SNV 2 1 PASS rs1445841130 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 88611464 88611464 G T 1 0 0 0 0 1 0 0 0 18143 1145 40 1 1 ZC3H18 16 88611464 Missense_Mutation SNP G C3N-00203_T 706658 88611464 1726881 370 11674 RP11-566K11.2 0 . GRCh38 16 89919308 89919308 + Frame_Shift_Del DEL C C - rs746774948 C3N-00203_T C3N-00203_N C C c.54delC p.Thr19GlnfsTer33 p.T19Qfs*33 ENST00000555147 1/1 91 66 25 84 84 0 sindel-varindel-pindel MC1R,frameshift_variant,p.Thr19GlnfsTer33,ENST00000555427,;MC1R,frameshift_variant,p.Thr19GlnfsTer33,ENST00000555147,NM_002386.3;RP11-566K11.2,frameshift_variant,p.Thr19GlnfsTer33,ENST00000556922,;TUBB3,upstream_gene_variant,,ENST00000554444,NM_001197181.1;TUBB3,upstream_gene_variant,,ENST00000315491,NM_006086.3;TUBB3,upstream_gene_variant,,ENST00000554336,;TUBB3,upstream_gene_variant,,ENST00000555810,;TUBB3,upstream_gene_variant,,ENST00000553967,;TUBB3,upstream_gene_variant,,ENST00000555576,;TUBB3,upstream_gene_variant,,ENST00000625617,;TUBB3,upstream_gene_variant,,ENST00000556565,;RP11-566K11.4,downstream_gene_variant,,ENST00000554623,;TUBB3,upstream_gene_variant,,ENST00000554116,;MC1R,downstream_gene_variant,,ENST00000539976,;TUBB3,upstream_gene_variant,,ENST00000555609,;TUBB3,upstream_gene_variant,,ENST00000556536,;TUBB3,upstream_gene_variant,,ENST00000557262,;TUBB3,upstream_gene_variant,,ENST00000557490,;TUBB3,upstream_gene_variant,,ENST00000554927,;RP11-566K11.7,downstream_gene_variant,,ENST00000570217,;TUBB3,upstream_gene_variant,,ENST00000553656,; - ENST00000555147 Transcript frameshift_variant 1430/3099 50/954 17/317 T/X aCc/ac rs746774948 1 1 MC1R HGNC HGNC:6929 protein_coding YES CCDS56011.1 ENSP00000451605 Q01726 Q1JUL4 UPI00000622C3 NM_002386.3 1/1 Prints_domain:PR00536 HIGH deletion 4 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 89919308 89919308 C - 1 0 1 0 1 0 0 0 0 13753 507 18 0 0 RP11-566K11.2 16 89919308 Frame_Shift_Del DEL C C3N-00203_T 1307844 89919308 419037 371 11675 SCARF1 0 . GRCh38 17 1635251 1635251 + Missense_Mutation SNP C C T C3N-00203_T C3N-00203_N C C c.2000G>A p.Gly667Asp p.G667D ENST00000263071 11/11 134 70 64 97 97 0 strelka-varscan-mutect SCARF1,missense_variant,p.Gly667Asp,ENST00000263071,NM_003693.3;SCARF1,missense_variant,p.Gly581Asp,ENST00000348987,;SCARF1,3_prime_UTR_variant,,ENST00000571272,NM_145350.2;SCARF1,3_prime_UTR_variant,,ENST00000434376,;SCARF1,3_prime_UTR_variant,,ENST00000573852,;SCARF1,non_coding_transcript_exon_variant,,ENST00000576012,;SCARF1,downstream_gene_variant,,ENST00000570902,; T ENST00000263071 Transcript missense_variant 2050/3443 2000/2493 667/830 G/D gGc/gAc COSM4723893 1 -1 SCARF1 HGNC HGNC:16820 protein_coding YES CCDS11007.1 ENSP00000263071 Q14162 UPI00001AE868 NM_003693.3 tolerated(0.2) 11/11 hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF0 1 MODERATE 1 SNV 1 1 1 PASS rs1175465160 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 1635251 1635251 C T 1 0 0 0 0 1 0 0 0 14149 739 26 3 3 SCARF1 17 1635251 Missense_Mutation SNP C C3N-00203_T 1635251 81622190 372 11676 WSCD1 0 . GRCh38 17 6080893 6080893 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.235C>A p.Pro79Thr p.P79T ENST00000574946 2/9 208 145 63 206 205 1 strelka-varscan-mutect WSCD1,missense_variant,p.Pro79Thr,ENST00000574946,;WSCD1,missense_variant,p.Pro79Thr,ENST00000317744,NM_015253.1;WSCD1,missense_variant,p.Pro79Thr,ENST00000539421,;WSCD1,missense_variant,p.Pro79Thr,ENST00000574232,;WSCD1,missense_variant,p.Pro79Thr,ENST00000576083,;WSCD1,missense_variant,p.Pro79Thr,ENST00000571973,;WSCD1,intron_variant,,ENST00000573634,;WSCD1,downstream_gene_variant,,ENST00000573619,;WSCD1,downstream_gene_variant,,ENST00000576233,;WSCD1,upstream_gene_variant,,ENST00000576947,;WSCD1,downstream_gene_variant,,ENST00000572764,;WSCD1,missense_variant,p.Pro51Thr,ENST00000571494,; A ENST00000574946 Transcript missense_variant 625/5884 235/1728 79/575 P/T Cca/Aca 1 1 WSCD1 HGNC HGNC:29060 protein_coding YES CCDS32538.1 ENSP00000460825 Q658N2 UPI0000197208 tolerated(0.43) 2/9 MODERATE 1 SNV 2 1 PASS rs1299813039 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 6080893 6080893 C A 1 0 0 0 0 1 0 0 0 17963 623 22 2 2 WSCD1 17 6080893 Missense_Mutation SNP C C3N-00203_T 4445642 6080893 77176548 373 11677 TP53 0 . GRCh38 17 7675076 7675076 + Missense_Mutation SNP T T C C3N-00203_T C3N-00203_N T T c.536A>G p.His179Arg p.H179R ENST00000269305 5/11 338 212 126 340 340 0 strelka-varscan-mutect TP53,missense_variant,p.His179Arg,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.His179Arg,ENST00000420246,;TP53,missense_variant,p.His140Arg,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.His140Arg,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.His179Arg,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.His140Arg,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.His179Arg,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.His140Arg,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.His179Arg,ENST00000445888,;TP53,missense_variant,p.His140Arg,ENST00000619485,;TP53,missense_variant,p.His47Arg,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.His20Arg,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.His47Arg,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.His20Arg,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.His47Arg,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.His20Arg,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.His179Arg,ENST00000359597,;TP53,missense_variant,p.His168Arg,ENST00000615910,;TP53,missense_variant,p.His179Arg,ENST00000413465,;TP53,missense_variant,p.His47Arg,ENST00000509690,;TP53,missense_variant,p.His86Arg,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.His140Arg,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 726/2579 536/1182 179/393 H/R cAt/cGt TP53_g.12524A>G,TP53_g.12524A>C,TP53_g.12524del,TP53_g.12524A>T,COSM10889,COSM129844,COSM129845,COSM129846,COSM129847,COSM1645241,COSM1731642,COSM214222,COSM214223,COSM214224,COSM214225,COSM3396280,COSM3980298,COSM43635,COSM44218,COSM44627 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1057519991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 7675076 7675076 T C 1 0 0 0 0 1 0 0 0 16859 1464 51 5 5 TP53 17 7675076 Missense_Mutation SNP T C3N-00203_T 1594183 7675076 75582365 374 11678 BORCS6 0 . GRCh38 17 8189428 8189428 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.713C>G p.Pro238Arg p.P238R ENST00000389017 1/1 74 48 26 88 88 0 strelka-varscan-mutect BORCS6,missense_variant,p.Pro238Arg,ENST00000389017,NM_017622.2;AC129492.1,missense_variant,p.Gly60Arg,ENST00000622992,;MIR4521,downstream_gene_variant,,ENST00000635897,; C ENST00000389017 Transcript missense_variant 1480/2575 713/1074 238/357 P/R cCt/cGt 1 -1 BORCS6 HGNC HGNC:25939 protein_coding YES CCDS11133.2 ENSP00000373669 Q96GS4 UPI000022A2C3 NM_017622.2 deleterious(0.03) 1/1 Pfam_domain:PF10157,hmmpanther:PTHR13440,hmmpanther:PTHR13440:SF7,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 8189428 8189428 G C 1 0 0 0 0 1 0 0 0 1648 1000 35 4 4 BORCS6 17 8189428 Missense_Mutation SNP G C3N-00203_T 514352 8189428 75068013 375 11679 46 2 BORCS6 0 . GRCh38 17 8189431 8189431 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.710C>G p.Ala237Gly p.A237G ENST00000389017 1/1 74 49 25 85 85 0 strelka-varscan-mutect BORCS6,missense_variant,p.Ala237Gly,ENST00000389017,NM_017622.2;AC129492.1,missense_variant,p.Ala61Pro,ENST00000622992,;MIR4521,downstream_gene_variant,,ENST00000635897,; C ENST00000389017 Transcript missense_variant 1477/2575 710/1074 237/357 A/G gCc/gGc 1 -1 BORCS6 HGNC HGNC:25939 protein_coding YES CCDS11133.2 ENSP00000373669 Q96GS4 UPI000022A2C3 NM_017622.2 deleterious(0.05) 1/1 Pfam_domain:PF10157,hmmpanther:PTHR13440,hmmpanther:PTHR13440:SF7,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs989491329 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 8189431 8189431 G C 1 0 0 0 0 1 0 0 0 1648 1203 42 4 4 BORCS6 17 8189431 Missense_Mutation SNP G C3N-00203_T 3 8189431 75068010 376 11680 46 2 MYH8 0 . GRCh38 17 10400538 10400538 + Missense_Mutation SNP C C T C3N-00203_T C3N-00203_N C C c.3587G>A p.Arg1196Gln p.R1196Q ENST00000403437 27/40 336 264 72 384 384 0 strelka-mutect MYH8,missense_variant,p.Arg1196Gln,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript missense_variant 3682/6041 3587/5814 1196/1937 R/Q cGg/cAg COSM4704678 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0.01) 27/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576 1 MODERATE SNV 5 1 1 PASS rs1340594495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 10400538 10400538 C T 1 0 0 0 0 1 0 0 0 10041 652 23 1 1 MYH8 17 10400538 Missense_Mutation SNP C C3N-00203_T 2211107 10400538 72856903 377 11681 47 3 MYH8 0 . GRCh38 17 10400539 10400539 + Silent SNP G G T rs765916450 C3N-00203_T C3N-00203_N G G c.3586C>A p.= p.R1196R ENST00000403437 27/40 331 264 67 394 394 0 strelka-mutect MYH8,synonymous_variant,p.=,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript synonymous_variant 3681/6041 3586/5814 1196/1937 R Cgg/Agg rs765916450 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 27/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576 LOW SNV 5 1 PASS rs765916450 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 10400539 10400539 G T 1 0 0 0 0 0 0 0 1 10041 1057 37 1 1 MYH8 17 10400539 Silent SNP G C3N-00203_T 1 10400539 72856902 378 11682 47 3 MYH8 0 . GRCh38 17 10400540 10400540 + Silent SNP A A T novel C3N-00203_T C3N-00203_N A A c.3585T>A p.= p.L1195L ENST00000403437 27/40 328 260 68 397 396 1 strelka-mutect MYH8,synonymous_variant,p.=,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript synonymous_variant 3680/6041 3585/5814 1195/1937 L ctT/ctA 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 27/40 hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 10400540 10400540 A T 1 0 0 0 0 0 0 0 1 10041 233 9 4 4 MYH8 17 10400540 Silent SNP A C3N-00203_T 1 10400540 72856901 379 11683 47 3 MYH2 0 . GRCh38 17 10528956 10528956 + Missense_Mutation SNP C C A rs781461127 C3N-00203_T C3N-00203_N C C c.3478G>T p.Gly1160Cys p.G1160C ENST00000245503 27/40 501 348 153 492 492 0 strelka-varscan-mutect MYH2,missense_variant,p.Gly1160Cys,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.Gly1160Cys,ENST00000397183,NM_001100112.1;MYH2,intron_variant,,ENST00000532183,;MYH2,intron_variant,,ENST00000622564,;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000245503 Transcript missense_variant 3863/6339 3478/5826 1160/1941 G/C Ggt/Tgt rs781461127 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 deleterious(0) 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS rs781461127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 10528956 10528956 C A 1 0 0 0 0 1 0 0 0 10035 652 23 1 1 MYH2 17 10528956 Missense_Mutation SNP C C3N-00203_T 128416 10528956 72728485 380 11684 NCOR1 0 . GRCh38 17 16139119 16139119 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1241G>T p.Arg414Leu p.R414L ENST00000268712 12/46 174 139 35 184 183 1 strelka-varscan-mutect NCOR1,missense_variant,p.Arg414Leu,ENST00000268712,NM_006311.3;NCOR1,missense_variant,p.Arg305Leu,ENST00000395857,;NCOR1,missense_variant,p.Arg414Leu,ENST00000395851,NM_001190440.1;NCOR1,missense_variant,p.Arg305Leu,ENST00000395848,NM_001190438.1;NCOR1,missense_variant,p.Arg423Leu,ENST00000436828,;NCOR1,missense_variant,p.Arg414Leu,ENST00000411510,;NCOR1,missense_variant,p.Arg423Leu,ENST00000582357,;RNU6-862P,upstream_gene_variant,,ENST00000362804,;NCOR1,3_prime_UTR_variant,,ENST00000460276,; A ENST00000268712 Transcript missense_variant 1499/10720 1241/7323 414/2440 R/L cGa/cTa 1 -1 NCOR1 HGNC HGNC:7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 A0A024RD47 UPI000013D7D5 NM_006311.3 deleterious(0) 12/46 hmmpanther:PTHR13992:SF5,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 16139119 16139119 C A 1 0 0 0 0 1 0 0 0 10254 884 31 1 1 NCOR1 17 16139119 Missense_Mutation SNP C C3N-00203_T 5610163 16139119 67118322 381 11685 GRAP 0 . GRCh38 17 19021951 19021951 + Missense_Mutation SNP C C A rs766873552 C3N-00203_T C3N-00203_N C C c.493G>T p.Gly165Cys p.G165C ENST00000573099 4/4 29 19 10 18 18 0 strelka-varscan-mutect GRAP,missense_variant,p.Gly165Cys,ENST00000573099,;SLC5A10,3_prime_UTR_variant,,ENST00000317977,NM_001282417.1;GRAP,3_prime_UTR_variant,,ENST00000284154,NM_006613.3;GRAP,3_prime_UTR_variant,,ENST00000395635,;SLC5A10,downstream_gene_variant,,ENST00000395647,NM_152351.4;SLC5A10,downstream_gene_variant,,ENST00000395645,NM_001042450.2;SLC5A10,downstream_gene_variant,,ENST00000417251,NM_001270649.1;SLC5A10,downstream_gene_variant,,ENST00000395643,NM_001270648.1;GRAP,3_prime_UTR_variant,,ENST00000583020,;SLC5A10,downstream_gene_variant,,ENST00000584658,; A ENST00000573099 Transcript missense_variant 564/846 493/618 165/205 G/C Ggc/Tgc rs766873552 1 -1 GRAP HGNC HGNC:4562 protein_coding ENSP00000459833 I3L2P9 UPI0000E59E8D deleterious_low_confidence(0.01) 4/4 MODERATE SNV 3 1 PASS rs766873552 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 19021951 19021951 C A 1 0 0 0 0 1 0 0 0 6632 652 23 1 1 GRAP 17 19021951 Missense_Mutation SNP C C3N-00203_T 2882832 19021951 64235490 382 11686 TNFAIP1 0 . GRCh38 17 28339623 28339623 + Frame_Shift_Del DEL G G - novel C3N-00203_T C3N-00203_N G G c.104delG p.Gly35AlafsTer12 p.G35Afs*12 ENST00000226225 2/7 183 163 20 140 140 0 varindel-pindel TNFAIP1,frameshift_variant,p.Gly35AlafsTer12,ENST00000226225,NM_021137.4;TNFAIP1,frameshift_variant,p.Gly35AlafsTer12,ENST00000582302,;TNFAIP1,frameshift_variant,p.Gly35AlafsTer12,ENST00000578158,;TNFAIP1,intron_variant,,ENST00000544907,;IFT20,upstream_gene_variant,,ENST00000585089,NM_001267774.1;IFT20,upstream_gene_variant,,ENST00000357896,NM_174887.3;IFT20,upstream_gene_variant,,ENST00000585313,NM_001267775.1;IFT20,upstream_gene_variant,,ENST00000578122,;IFT20,upstream_gene_variant,,ENST00000578985,;IFT20,upstream_gene_variant,,ENST00000395418,NM_001267776.1;IFT20,upstream_gene_variant,,ENST00000579419,NM_001267777.1;IFT20,upstream_gene_variant,,ENST00000588477,NM_001267778.1;IFT20,upstream_gene_variant,,ENST00000577498,;TNFAIP1,upstream_gene_variant,,ENST00000577535,;TNFAIP1,intron_variant,,ENST00000583213,;IFT20,upstream_gene_variant,,ENST00000582797,;IFT20,upstream_gene_variant,,ENST00000578547,;IFT20,upstream_gene_variant,,ENST00000322326,;IFT20,upstream_gene_variant,,ENST00000580357,;IFT20,upstream_gene_variant,,ENST00000580991,; - ENST00000226225 Transcript frameshift_variant 369/3627 102/951 34/316 V/X gtG/gt 1 1 TNFAIP1 HGNC HGNC:11894 protein_coding YES CCDS11227.1 ENSP00000226225 Q13829 UPI00001370D5 NM_021137.4 2/7 Gene3D:3.30.710.10,Pfam_domain:PF02214,PROSITE_profiles:PS50097,hmmpanther:PTHR11145,hmmpanther:PTHR11145:SF17,SMART_domains:SM00225,Superfamily_domains:SSF54695 HIGH 1 deletion 1 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 42 28339623 28339623 G - 1 0 1 0 1 0 0 0 0 16746 1335 47 0 0 TNFAIP1 17 28339623 Frame_Shift_Del DEL G C3N-00203_T 9317672 28339623 54917818 383 11687 ARL5C 0 . GRCh38 17 39161303 39161303 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.304A>T p.Thr102Ser p.T102S ENST00000269586 4/6 343 200 143 306 306 0 strelka-varscan-mutect ARL5C,missense_variant,p.Thr102Ser,ENST00000269586,NM_001143968.1;RP5-906A24.1,upstream_gene_variant,,ENST00000623613,;ARL5C,downstream_gene_variant,,ENST00000583123,;ARL5C,missense_variant,p.Thr25Ser,ENST00000578912,;ARL5C,downstream_gene_variant,,ENST00000581554,;ARL5C,downstream_gene_variant,,ENST00000581255,; A ENST00000269586 Transcript missense_variant 304/540 304/540 102/179 T/S Act/Tct 1 -1 ARL5C HGNC HGNC:31111 protein_coding YES CCDS45664.1 ENSP00000269586 A6NH57 UPI00001600CC NM_001143968.1 tolerated(0.27) 4/6 Gene3D:3.40.50.300,Pfam_domain:PF00025,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF148,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 39161303 39161303 T A 1 0 0 0 0 1 0 0 0 1080 1696 59 4 4 ARL5C 17 39161303 Missense_Mutation SNP T C3N-00203_T 10821680 39161303 44096138 384 11688 KRT28 0 . GRCh38 17 40799627 40799627 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.267C>A p.= p.T89T ENST00000306658 1/8 356 244 112 337 337 0 strelka-varscan-mutect KRT28,synonymous_variant,p.=,ENST00000306658,NM_181535.3;RP11-605F20.1,upstream_gene_variant,,ENST00000582101,; T ENST00000306658 Transcript synonymous_variant 333/1685 267/1395 89/464 T acC/acA 1 -1 KRT28 HGNC HGNC:30842 protein_coding YES CCDS11376.1 ENSP00000305263 Q7Z3Y7 UPI0000246D70 NM_181535.3 1/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF215,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS rs1184386216 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 40799627 40799627 G T 1 0 0 0 0 0 0 0 1 8347 1335 47 2 2 KRT28 17 40799627 Silent SNP G C3N-00203_T 1638324 40799627 42457814 385 11689 JUP 0 . GRCh38 17 41771736 41771736 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.119A>G p.Lys40Arg p.K40R ENST00000393931 2/14 654 394 260 546 546 0 strelka-varscan-mutect JUP,missense_variant,p.Lys40Arg,ENST00000393931,NM_002230.2;JUP,missense_variant,p.Lys40Arg,ENST00000393930,;JUP,missense_variant,p.Lys40Arg,ENST00000310706,NM_021991.2;JUP,missense_variant,p.Lys40Arg,ENST00000449889,;JUP,missense_variant,p.Lys40Arg,ENST00000437187,;JUP,missense_variant,p.Lys40Arg,ENST00000424457,;JUP,missense_variant,p.Lys40Arg,ENST00000420370,;JUP,missense_variant,p.Lys40Arg,ENST00000437369,;JUP,missense_variant,p.Lys40Arg,ENST00000591690,;JUP,downstream_gene_variant,,ENST00000465293,;JUP,non_coding_transcript_exon_variant,,ENST00000589036,; C ENST00000393931 Transcript missense_variant 238/3497 119/2238 40/745 K/R aAg/aGg 1 -1 JUP HGNC HGNC:6207 protein_coding YES CCDS11407.1 ENSP00000377508 P14923 A0A0S2Z487 UPI0000073ED4 NM_002230.2 tolerated(0.22) 2/14 MODERATE 1 SNV 1 1 PASS rs113994176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 41771736 41771736 T C 1 0 0 0 0 1 0 0 0 7882 1609 56 5 5 JUP 17 41771736 Missense_Mutation SNP T C3N-00203_T 972109 41771736 41485705 386 11690 TLK2 0 . GRCh38 17 62574410 62574410 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1187G>T p.Arg396Met p.R396M ENST00000326270 13/23 256 160 96 218 216 2 strelka-varscan-mutect TLK2,missense_variant,p.Arg396Met,ENST00000326270,NM_001284333.1;TLK2,intron_variant,,ENST00000582809,;TLK2,intron_variant,,ENST00000346027,NM_006852.3;TLK2,intron_variant,,ENST00000343388,NM_001284363.1;TLK2,intron_variant,,ENST00000581041,;TLK2,intron_variant,,ENST00000578697,;TLK2,intron_variant,,ENST00000584367,; T ENST00000326270 Transcript missense_variant,splice_region_variant 1455/3512 1187/2319 396/772 R/M aGg/aTg 1 1 TLK2 HGNC HGNC:11842 protein_coding YES CCDS62283.1 ENSP00000316512 Q86UE8 UPI00001B6B0E NM_001284333.1 tolerated(0.07) 13/23 hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF20 MODERATE 1 SNV 1 1 PASS rs1284424623 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 62574410 62574410 G T 1 0 0 0 0 1 0 0 0 16390 1014 35 2 2 TLK2 17 62574410 Missense_Mutation SNP G C3N-00203_T 20802674 62574410 20683031 387 11691 COLEC12 0 . GRCh38 18 335114 335114 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1444G>T p.Gly482Cys p.G482C ENST00000400256 6/10 221 159 62 193 191 2 strelka-varscan-mutect COLEC12,missense_variant,p.Gly482Cys,ENST00000400256,NM_130386.2;COLEC12,non_coding_transcript_exon_variant,,ENST00000582147,; A ENST00000400256 Transcript missense_variant 1652/5742 1444/2229 482/742 G/C Ggt/Tgt 1 -1 COLEC12 HGNC HGNC:16016 protein_coding YES CCDS32782.1 ENSP00000383115 Q5KU26 UPI00002018EC NM_130386.2 deleterious(0) 6/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF597,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 335114 335114 C A 1 0 0 0 0 1 0 0 0 3502 623 22 2 2 COLEC12 18 335114 Missense_Mutation SNP C C3N-00203_T 335114 80038171 388 11692 DLGAP1 0 . GRCh38 18 3729312 3729312 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1414G>T p.Glu472Ter p.E472* ENST00000315677 7/13 256 198 58 163 163 0 strelka-varscan-mutect DLGAP1,stop_gained,p.Glu472Ter,ENST00000315677,NM_004746.3;DLGAP1,stop_gained,p.Glu178Ter,ENST00000400150,NM_001308390.1;DLGAP1,stop_gained,p.Glu184Ter,ENST00000515196,NM_001242763.1;DLGAP1,stop_gained,p.Glu170Ter,ENST00000400147,NM_001003809.2;DLGAP1,stop_gained,p.Glu178Ter,ENST00000400155,NM_001242764.1;DLGAP1,stop_gained,p.Glu180Ter,ENST00000400149,;DLGAP1,stop_gained,p.Glu472Ter,ENST00000581527,NM_001242761.1;DLGAP1,stop_gained,p.Glu170Ter,ENST00000539435,NM_001242766.1;DLGAP1,stop_gained,p.Glu184Ter,ENST00000534970,NM_001242762.1;DLGAP1,stop_gained,p.Glu178Ter,ENST00000581699,;DLGAP1,stop_gained,p.Glu170Ter,ENST00000400145,NM_001242765.1;DLGAP1,non_coding_transcript_exon_variant,,ENST00000478161,;DLGAP1,non_coding_transcript_exon_variant,,ENST00000498188,;DLGAP1,non_coding_transcript_exon_variant,,ENST00000485480,;DLGAP1,non_coding_transcript_exon_variant,,ENST00000486430,; A ENST00000315677 Transcript stop_gained 2010/6683 1414/2934 472/977 E/* Gag/Tag 1 -1 DLGAP1 HGNC HGNC:2905 protein_coding YES CCDS11836.1 ENSP00000316377 O14490 UPI0000129490 NM_004746.3 7/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF7 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 3729312 3729312 C A 1 0 0 0 0 0 1 0 0 4366 864 30 2 2 DLGAP1 18 3729312 Nonsense_Mutation SNP C C3N-00203_T 3394198 3729312 76643973 389 11693 EPB41L3 0 . GRCh38 18 5428441 5428441 + Missense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.937T>A p.Leu313Ile p.L313I ENST00000341928 9/23 217 162 55 183 183 0 strelka-varscan-mutect EPB41L3,missense_variant,p.Leu313Ile,ENST00000341928,NM_012307.3;EPB41L3,missense_variant,p.Leu313Ile,ENST00000342933,;EPB41L3,missense_variant,p.Leu171Ile,ENST00000400111,;EPB41L3,missense_variant,p.Leu313Ile,ENST00000544123,NM_001281533.1;EPB41L3,missense_variant,p.Leu313Ile,ENST00000540638,NM_001281534.1;EPB41L3,missense_variant,p.Leu204Ile,ENST00000545076,NM_001281535.1;EPB41L3,intron_variant,,ENST00000584670,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000542652,;EPB41L3,downstream_gene_variant,,ENST00000581757,;EPB41L3,downstream_gene_variant,,ENST00000578432,;EPB41L3,missense_variant,p.Leu204Ile,ENST00000637651,; T ENST00000341928 Transcript missense_variant 1278/4706 937/3264 313/1087 L/I Tta/Ata 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 deleterious(0) 9/23 PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF20,Pfam_domain:PF09380,Gene3D:2.30.29.30,SMART_domains:SM01196,Superfamily_domains:SSF50729,Prints_domain:PR00661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 5428441 5428441 A T 1 0 0 0 0 1 0 0 0 5001 40 2 4 4 EPB41L3 18 5428441 Missense_Mutation SNP A C3N-00203_T 1699129 5428441 74944844 390 11694 LAMA1 0 . GRCh38 18 6956749 6956749 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.7981A>T p.Ser2661Cys p.S2661C ENST00000389658 56/63 418 330 88 356 356 0 strelka-varscan-mutect LAMA1,missense_variant,p.Ser2661Cys,ENST00000389658,NM_005559.3;RP11-781P6.1,non_coding_transcript_exon_variant,,ENST00000584722,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488089,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488064,;LAMA1,upstream_gene_variant,,ENST00000492048,; A ENST00000389658 Transcript missense_variant 8075/9657 7981/9228 2661/3075 S/C Agt/Tgt 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0.03) 56/63 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,Superfamily_domains:SSF49899 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 6956749 6956749 T A 1 0 0 0 0 1 0 0 0 8509 1580 55 4 4 LAMA1 18 6956749 Missense_Mutation SNP T C3N-00203_T 1528308 6956749 73416536 391 11695 LAMA1 0 . GRCh38 18 7009307 7009307 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.3933G>A p.Met1311Ile p.M1311I ENST00000389658 27/63 489 403 86 439 439 0 strelka-varscan-mutect LAMA1,missense_variant,p.Met1311Ile,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; T ENST00000389658 Transcript missense_variant 4027/9657 3933/9228 1311/3075 M/I atG/atA 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 27/63 Pfam_domain:PF00052,PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00281 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 7009307 7009307 C T 1 0 0 0 0 1 0 0 0 8509 478 17 3 3 LAMA1 18 7009307 Missense_Mutation SNP C C3N-00203_T 52558 7009307 73363978 392 11696 PIEZO2 0 . GRCh38 18 10691296 10691296 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.6939C>T p.= p.G2313G ENST00000503781 44/52 295 250 45 219 218 1 strelka-varscan-mutect PIEZO2,synonymous_variant,p.=,ENST00000383408,;PIEZO2,synonymous_variant,p.=,ENST00000302079,;PIEZO2,synonymous_variant,p.=,ENST00000580640,;PIEZO2,synonymous_variant,p.=,ENST00000503781,NM_022068.3;PIEZO2,synonymous_variant,p.=,ENST00000538948,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; A ENST00000503781 Transcript synonymous_variant 6939/8259 6939/8259 2313/2752 G ggC/ggT 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 44/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 10691296 10691296 G A 1 0 0 0 0 0 0 0 1 11975 958 34 3 3 PIEZO2 18 10691296 Silent SNP G C3N-00203_T 3681989 10691296 69681989 393 11697 SLC35G4 0 . GRCh38 18 11609847 11609847 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.252C>A p.= p.A84A ENST00000636911 1/2 408 343 65 373 371 2 strelka-varscan-mutect SLC35G4,synonymous_variant,p.=,ENST00000636911,;SLC35G4,synonymous_variant,p.=,ENST00000588001,NM_001282300.1; A ENST00000636911 Transcript synonymous_variant 373/1201 252/1017 84/338 A gcC/gcA 1 1 SLC35G4 HGNC HGNC:31043 protein_coding YES ENSP00000489773 UPI0001AE65E0 1/2 Superfamily_domains:0043518,hmmpanther:PTHR22911,hmmpanther:PTHR22911:SF32 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 11609847 11609847 C A 1 0 0 0 0 0 0 0 1 14868 610 22 2 2 SLC35G4 18 11609847 Silent SNP C C3N-00203_T 918551 11609847 68763438 394 11698 ANKRD62 0 . GRCh38 18 12097758 12097758 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.733G>A p.Val245Ile p.V245I ENST00000587848 5/14 171 125 46 121 121 0 strelka-varscan-mutect ANKRD62,missense_variant,p.Val245Ile,ENST00000587848,NM_001277333.1;RNU6-324P,upstream_gene_variant,,ENST00000363957,;ANKRD62,upstream_gene_variant,,ENST00000418274,;RP11-815J4.5,upstream_gene_variant,,ENST00000589352,;SDHDP1,downstream_gene_variant,,ENST00000588055,; A ENST00000587848 Transcript missense_variant 898/2919 733/2754 245/917 V/I Gtt/Att 1 1 ANKRD62 HGNC HGNC:35241 protein_coding YES CCDS67439.1 ENSP00000467740 A6NC57 UPI0000DD848C NM_001277333.1 tolerated(0.48) 5/14 PROSITE_profiles:PS50297,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF29,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 12097758 12097758 G A 1 0 0 0 0 1 0 0 0 789 1377 48 3 3 ANKRD62 18 12097758 Missense_Mutation SNP G C3N-00203_T 487911 12097758 68275527 395 11699 MYO5B 0 . GRCh38 18 49929558 49929558 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2044G>T p.Gly682Trp p.G682W ENST00000285039 17/40 322 248 74 273 273 0 strelka-varscan-mutect MYO5B,missense_variant,p.Gly682Trp,ENST00000285039,NM_001080467.2; A ENST00000285039 Transcript missense_variant 2344/9505 2044/5547 682/1848 G/W Ggg/Tgg 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 deleterious(0) 17/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1401138978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 49929558 49929558 C A 1 0 0 0 0 1 0 0 0 10080 652 23 1 1 MYO5B 18 49929558 Missense_Mutation SNP C C3N-00203_T 37831800 49929558 30443727 396 11700 PLIN4 0 . GRCh38 19 4510734 4510734 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.3184G>A p.Gly1062Ser p.G1062S ENST00000301286 3/6 29 18 11 18 18 0 strelka-varscan-mutect PLIN4,missense_variant,p.Gly1077Ser,ENST00000633942,;PLIN4,missense_variant,p.Gly1062Ser,ENST00000301286,NM_001080400.1; T ENST00000301286 Transcript missense_variant 3184/6353 3184/4074 1062/1357 G/S Ggt/Agt 1 -1 PLIN4 HGNC HGNC:29393 protein_coding YES CCDS45927.1 ENSP00000301286 Q96Q06 UPI00001D822A NM_001080400.1 tolerated(0.13) 3/6 hmmpanther:PTHR14024,hmmpanther:PTHR14024:SF31 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 4510734 4510734 C T 1 0 0 0 0 1 0 0 0 12188 594 21 3 3 PLIN4 19 4510734 Missense_Mutation SNP C C3N-00203_T 4510734 54106882 397 11701 CATSPERD 0 . GRCh38 19 5771035 5771035 + Missense_Mutation SNP G G T rs374184519 C3N-00203_T C3N-00203_N G G c.1726G>T p.Val576Phe p.V576F ENST00000381624 19/22 217 164 53 145 145 0 strelka-varscan-mutect CATSPERD,missense_variant,p.Val576Phe,ENST00000381624,NM_152784.3;CATSPERD,non_coding_transcript_exon_variant,,ENST00000309164,;CATSPERD,upstream_gene_variant,,ENST00000448307,; T ENST00000381624 Transcript missense_variant 1787/2516 1726/2397 576/798 V/F Gtc/Ttc rs374184519,COSM76755 1 1 CATSPERD HGNC HGNC:28598 protein_coding YES CCDS12149.2 ENSP00000371037 Q86XM0 UPI000059D641 NM_152784.3 deleterious(0) 19/22 Pfam_domain:PF15020,hmmpanther:PTHR33722,hmmpanther:PTHR33722:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374184519 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 5771035 5771035 G T 1 0 0 0 0 1 0 0 0 2392 1145 40 1 1 CATSPERD 19 5771035 Missense_Mutation SNP G C3N-00203_T 1260301 5771035 52846581 398 11702 ZNF426 0 . GRCh38 19 9533905 9533905 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.179A>T p.Asp60Val p.D60V ENST00000253115 5/8 257 181 76 177 177 0 strelka-varscan-mutect ZNF426,missense_variant,p.Asp60Val,ENST00000253115,NM_001318055.1,NM_001318056.1,NM_024106.1;ZNF426,missense_variant,p.Asp22Val,ENST00000593003,NM_001300883.1;ZNF426,missense_variant,p.Asp60Val,ENST00000535489,;ZNF426,missense_variant,p.Asp60Val,ENST00000589289,;CTC-543D15.8,upstream_gene_variant,,ENST00000619671,;CTC-543D15.8,upstream_gene_variant,,ENST00000613560,;ZNF426,intron_variant,,ENST00000635810,; A ENST00000253115 Transcript missense_variant 443/7085 179/1665 60/554 D/V gAc/gTc 1 -1 ZNF426 HGNC HGNC:20725 protein_coding YES CCDS12215.1 ENSP00000253115 Q9BUY5 A0A024R7D7 UPI0000072122 NM_001318055.1,NM_001318056.1,NM_024106.1 deleterious(0) 5/8 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF85,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS rs1311729034 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 9533905 9533905 T A 1 0 0 0 0 1 0 0 0 18472 1667 58 4 4 ZNF426 19 9533905 Missense_Mutation SNP T C3N-00203_T 3762870 9533905 49083711 399 11703 RNASEH2A 0 . GRCh38 19 12810387 12810387 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.620G>T p.Gly207Val p.G207V ENST00000221486 6/8 650 509 141 483 481 2 strelka-varscan-mutect RNASEH2A,missense_variant,p.Gly207Val,ENST00000221486,NM_006397.2;HOOK2,intron_variant,,ENST00000589765,;RNASEH2A,non_coding_transcript_exon_variant,,ENST00000593017,;RNASEH2A,downstream_gene_variant,,ENST00000590121,;RNASEH2A,downstream_gene_variant,,ENST00000590279,; T ENST00000221486 Transcript missense_variant 714/1165 620/900 207/299 G/V gGc/gTc 1 1 RNASEH2A HGNC HGNC:18518 protein_coding YES CCDS12282.1 ENSP00000221486 O75792 UPI00001343E6 NM_006397.2 deleterious(0) 6/8 hmmpanther:PTHR10954,hmmpanther:PTHR10954:SF7,Gene3D:1.10.10.460,Pfam_domain:PF01351,TIGRFAM_domain:TIGR00729,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 12810387 12810387 G T 1 0 0 0 0 1 0 0 0 13591 1203 42 2 2 RNASEH2A 19 12810387 Missense_Mutation SNP G C3N-00203_T 3276482 12810387 45807229 400 11704 CACNA1A 0 . GRCh38 19 13208878 13208880 + In_Frame_Del DEL GAT GAT - rs749638821 C3N-00203_T C3N-00203_N GAT GAT c.6656_6658delATC p.His2219del p.H2219del ENST00000360228 46/47 103 97 6 111 110 1 varindel-pindel CACNA1A,inframe_deletion,p.His2220del,ENST00000638009,NM_001127221.1;CACNA1A,inframe_deletion,p.His2220del,ENST00000635895,;CACNA1A,inframe_deletion,p.His2220del,ENST00000637769,;CACNA1A,inframe_deletion,p.His2219del,ENST00000360228,NM_001127222.1;CACNA1A,inframe_deletion,p.His2225del,ENST00000614285,;CACNA1A,inframe_deletion,p.His2173del,ENST00000637736,;CACNA1A,inframe_deletion,p.His2220del,ENST00000636389,;CACNA1A,inframe_deletion,p.His2225del,ENST00000638029,NM_023035.2;CACNA1A,inframe_deletion,p.His2225del,ENST00000637432,NM_000068.3;CACNA1A,inframe_deletion,p.His2221del,ENST00000573710,;CACNA1A,inframe_deletion,p.His2220del,ENST00000635727,;CACNA1A,inframe_deletion,p.His2208del,ENST00000636012,;CACNA1A,inframe_deletion,p.His2208del,ENST00000637276,;CACNA1A,inframe_deletion,p.His2221del,ENST00000637927,;CACNA1A,inframe_deletion,p.His2222del,ENST00000636549,NM_001174080.1;CACNA1A,inframe_deletion,p.His694del,ENST00000587525,;CACNA1A,inframe_deletion,p.His594del,ENST00000585802,;CACNA1A,inframe_deletion,p.His509del,ENST00000636473,;CACNA1A,downstream_gene_variant,,ENST00000637819,;CACNA1A,downstream_gene_variant,,ENST00000636610,;CACNA1A,downstream_gene_variant,,ENST00000635988,;CACNA1A,downstream_gene_variant,,ENST00000636074,;CACNA1A,downstream_gene_variant,,ENST00000636768,;CACNA1A,downstream_gene_variant,,ENST00000638114,; - ENST00000360228 Transcript inframe_deletion 6891-6893/8627 6656-6658/7521 2219-2220/2506 HP/P cATCcc/ccc rs749638821,COSM1390728,COSM1390729,COSM1390730,COSM1390731 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 46/47 Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59 0,1,1,1,1 MODERATE 1 deletion 1 0,1,1,1,1 1 PASS . . 0 10 0 0 0 0 0 199 -4.419474 0 0 1 0 0 - 7 5 42 13208878 13208878 GAT - 1 0 1 0 1 0 0 0 0 2226 1174 41 0 0 CACNA1A 19 13208878 In_Frame_Del DEL GAT C3N-00203_T 398491 13208878 45408738 401 11705 CILP2 0 . GRCh38 19 19544877 19544877 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.2332T>A p.Trp778Arg p.W778R ENST00000291495 8/8 119 87 32 85 85 0 strelka-varscan-mutect CILP2,missense_variant,p.Trp784Arg,ENST00000586018,;CILP2,missense_variant,p.Trp778Arg,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; A ENST00000291495 Transcript missense_variant 2417/4199 2332/3471 778/1156 W/R Tgg/Agg 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 deleterious(0) 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 MODERATE 1 SNV 1 1 PASS rs762645493 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 19544877 19544877 T A 1 0 0 0 0 1 0 0 0 3192 1580 55 4 4 CILP2 19 19544877 Missense_Mutation SNP T C3N-00203_T 6335999 19544877 39072739 402 11706 ZNF493 0 . GRCh38 19 21423806 21423806 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1147G>T p.Gly383Cys p.G383C ENST00000392288 4/4 261 214 47 286 286 0 strelka-varscan-mutect ZNF493,missense_variant,p.Gly383Cys,ENST00000392288,NM_001076678.2;ZNF493,missense_variant,p.Gly255Cys,ENST00000355504,NM_175910.6;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,; T ENST00000392288 Transcript missense_variant 1256/5023 1147/2325 383/774 G/C Ggc/Tgc 1 1 ZNF493 HGNC HGNC:23708 protein_coding YES CCDS42536.1 ENSP00000376110 Q6ZR52 UPI000022ABBF NM_001076678.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF247,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 21423806 21423806 G T 1 0 0 0 0 1 0 0 0 18517 1348 47 2 2 ZNF493 19 21423806 Missense_Mutation SNP G C3N-00203_T 1878929 21423806 37193810 403 11707 MAG 0 . GRCh38 19 35299831 35299831 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.693C>A p.Tyr231Ter p.Y231* ENST00000392213 5/11 84 46 38 43 43 0 strelka-varscan-mutect MAG,stop_gained,p.Tyr231Ter,ENST00000361922,NM_080600.2;MAG,stop_gained,p.Tyr231Ter,ENST00000392213,NM_002361.3;MAG,stop_gained,p.Tyr206Ter,ENST00000537831,NM_001199216.1;MAG,downstream_gene_variant,,ENST00000595791,;MAG,downstream_gene_variant,,ENST00000600291,;MAG,downstream_gene_variant,,ENST00000597035,; A ENST00000392213 Transcript stop_gained 852/2390 693/1881 231/626 Y/* taC/taA 1 1 MAG HGNC HGNC:6783 protein_coding YES CCDS12455.1 ENSP00000376048 P20916 UPI000012EB2F NM_002361.3 5/11 Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF54,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 35299831 35299831 C A 1 0 0 0 0 0 1 0 0 9078 547 19 1 1 MAG 19 35299831 Nonsense_Mutation SNP C C3N-00203_T 13876025 35299831 23317785 404 11708 DMKN 0 . GRCh38 19 35513317 35513317 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.159G>T p.Lys53Asn p.K53N ENST00000339686 1/16 705 372 333 363 363 0 strelka-varscan-mutect DMKN,missense_variant,p.Lys53Asn,ENST00000339686,NM_033317.4;DMKN,missense_variant,p.Lys53Asn,ENST00000447113,NM_001190348.1;DMKN,missense_variant,p.Lys53Asn,ENST00000419602,NM_001126056.2;DMKN,missense_variant,p.Lys53Asn,ENST00000429837,NM_001190347.1;DMKN,missense_variant,p.Lys53Asn,ENST00000424570,NM_001126057.2;DMKN,missense_variant,p.Lys53Asn,ENST00000418261,NM_001126058.2;DMKN,missense_variant,p.Lys53Asn,ENST00000451297,NM_001190349.1;DMKN,upstream_gene_variant,,ENST00000402589,NM_001308380.1;DMKN,upstream_gene_variant,,ENST00000434389,;DMKN,upstream_gene_variant,,ENST00000414866,NM_001126059.2;DMKN,upstream_gene_variant,,ENST00000436012,NM_001308383.1;DMKN,upstream_gene_variant,,ENST00000443640,;DMKN,upstream_gene_variant,,ENST00000467637,;DMKN,upstream_gene_variant,,ENST00000602781,;DMKN,upstream_gene_variant,,ENST00000480502,;DMKN,upstream_gene_variant,,ENST00000492341,;DMKN,upstream_gene_variant,,ENST00000472252,;DMKN,upstream_gene_variant,,ENST00000474928,;DMKN,upstream_gene_variant,,ENST00000461300,;DMKN,upstream_gene_variant,,ENST00000602679,;DMKN,upstream_gene_variant,,ENST00000458071,;DMKN,upstream_gene_variant,,ENST00000392206,;DMKN,upstream_gene_variant,,ENST00000488892,;DMKN,upstream_gene_variant,,ENST00000450261,;DMKN,upstream_gene_variant,,ENST00000462126,;DMKN,upstream_gene_variant,,ENST00000476051,;DMKN,upstream_gene_variant,,ENST00000474992,;DMKN,upstream_gene_variant,,ENST00000489395,;DMKN,upstream_gene_variant,,ENST00000490622,;DMKN,upstream_gene_variant,,ENST00000488542,;DMKN,upstream_gene_variant,,ENST00000462721,;DMKN,upstream_gene_variant,,ENST00000465927,;DMKN,upstream_gene_variant,,ENST00000467532,;DMKN,upstream_gene_variant,,ENST00000482321,;DMKN,upstream_gene_variant,,ENST00000464709,;DMKN,upstream_gene_variant,,ENST00000464894,;DMKN,upstream_gene_variant,,ENST00000471786,;DMKN,upstream_gene_variant,,ENST00000476246,;DMKN,upstream_gene_variant,,ENST00000488762,;DMKN,upstream_gene_variant,,ENST00000498211,;DMKN,upstream_gene_variant,,ENST00000493979,;DMKN,upstream_gene_variant,,ENST00000463292,;DMKN,upstream_gene_variant,,ENST00000597212,;DMKN,upstream_gene_variant,,ENST00000460051,;DMKN,upstream_gene_variant,,ENST00000498593,;DMKN,upstream_gene_variant,,ENST00000483855,;DMKN,upstream_gene_variant,,ENST00000486450,;DMKN,upstream_gene_variant,,ENST00000462538,;DMKN,upstream_gene_variant,,ENST00000470857,;DMKN,upstream_gene_variant,,ENST00000493517,;DMKN,upstream_gene_variant,,ENST00000480507,;DMKN,upstream_gene_variant,,ENST00000472065,;DMKN,upstream_gene_variant,,ENST00000498269,;DMKN,upstream_gene_variant,,ENST00000470746,;DMKN,upstream_gene_variant,,ENST00000595571,; A ENST00000339686 Transcript missense_variant 336/1927 159/1431 53/476 K/N aaG/aaT 1 -1 DMKN HGNC HGNC:25063 protein_coding YES CCDS12463.1 ENSP00000342012 Q6E0U4 UPI00002020EB NM_033317.4 tolerated(0.08) 1/16 hmmpanther:PTHR36881,hmmpanther:PTHR36881:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 35513317 35513317 C A 1 0 0 0 0 1 0 0 0 4389 680 24 2 2 DMKN 19 35513317 Missense_Mutation SNP C C3N-00203_T 213486 35513317 23104299 405 11709 HSPB6 0 . GRCh38 19 35755669 35755669 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.336C>T p.= p.F112F ENST00000592984 4/4 164 136 28 116 116 0 strelka-varscan-mutect HSPB6,synonymous_variant,p.=,ENST00000592984,;HSPB6,synonymous_variant,p.=,ENST00000004982,NM_144617.2;HSPB6,3_prime_UTR_variant,,ENST00000587965,;PROSER3,upstream_gene_variant,,ENST00000396908,NM_001039887.2;PROSER3,upstream_gene_variant,,ENST00000536950,;LIN37,downstream_gene_variant,,ENST00000301159,NM_019104.2;PROSER3,upstream_gene_variant,,ENST00000301165,;PROSER3,upstream_gene_variant,,ENST00000537459,;PROSER3,upstream_gene_variant,,ENST00000421853,;PROSER3,upstream_gene_variant,,ENST00000545674,;PROSER3,upstream_gene_variant,,ENST00000444637,;LIN37,downstream_gene_variant,,ENST00000591163,;PROSER3,upstream_gene_variant,,ENST00000542134,;LIN37,downstream_gene_variant,,ENST00000587751,;AC002398.11,upstream_gene_variant,,ENST00000591091,;AC002398.12,downstream_gene_variant,,ENST00000587767,;PROSER3,upstream_gene_variant,,ENST00000544876,;LIN37,downstream_gene_variant,,ENST00000591076,;PROSER3,upstream_gene_variant,,ENST00000620918,;PROSER3,upstream_gene_variant,,ENST00000600988,;LIN37,downstream_gene_variant,,ENST00000595455,;LIN37,downstream_gene_variant,,ENST00000587108,;LIN37,downstream_gene_variant,,ENST00000590706,;AC002398.9,downstream_gene_variant,,ENST00000591613,;PROSER3,upstream_gene_variant,,ENST00000601095,;LIN37,downstream_gene_variant,,ENST00000590890,;LIN37,downstream_gene_variant,,ENST00000592871,;PROSER3,upstream_gene_variant,,ENST00000539771,; A ENST00000592984 Transcript synonymous_variant 533/1634 336/483 112/160 F ttC/ttT 1 -1 HSPB6 HGNC HGNC:26511 protein_coding YES CCDS12475.1 ENSP00000468057 O14558 V9HWB6 UPI000012CCD5 4/4 Gene3D:2.60.40.790,Pfam_domain:PF00011,Prints_domain:PR00299,PROSITE_profiles:PS01031,hmmpanther:PTHR11527,hmmpanther:PTHR11527:SF109,Superfamily_domains:SSF49764 LOW SNV 4 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 35755669 35755669 G A 1 0 0 0 0 0 0 0 1 7318 1049 37 1 1 HSPB6 19 35755669 Silent SNP G C3N-00203_T 242352 35755669 22861947 406 11710 ZNF573 0 . GRCh38 19 37739107 37739107 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1383G>T p.Gln461His p.Q461H ENST00000536220 5/5 206 168 38 165 164 1 strelka-varscan-mutect ZNF573,missense_variant,p.Gln374His,ENST00000392138,;ZNF573,missense_variant,p.Gln461His,ENST00000536220,NM_001172691.1,NM_001172690.1;ZNF573,missense_variant,p.Gln461His,ENST00000590414,;ZNF573,missense_variant,p.Gln373His,ENST00000357309,NM_001172692.1,NM_001172689.1;ZNF573,missense_variant,p.Gln403His,ENST00000339503,NM_152360.3;ZNF573,downstream_gene_variant,,ENST00000378445,;ZNF573,downstream_gene_variant,,ENST00000585724,;ZNF573,intron_variant,,ENST00000590674,;ZNF573,3_prime_UTR_variant,,ENST00000589632,;ZNF573,3_prime_UTR_variant,,ENST00000586155,;ZNF573,downstream_gene_variant,,ENST00000489148,;ZNF573,downstream_gene_variant,,ENST00000591516,; A ENST00000536220 Transcript missense_variant 1452/2257 1383/1998 461/665 Q/H caG/caT 1 -1 ZNF573 HGNC HGNC:26420 protein_coding YES CCDS59381.1 ENSP00000440464 Q86YE8 UPI000059D70C NM_001172691.1,NM_001172690.1 tolerated(0.1) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF159,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 37739107 37739107 C A 1 0 0 0 0 1 0 0 0 18579 912 32 2 2 ZNF573 19 37739107 Missense_Mutation SNP C C3N-00203_T 1983438 37739107 20878509 407 11711 RYR1 0 . GRCh38 19 38494484 38494484 + Missense_Mutation SNP G G T rs530885842 C3N-00203_T C3N-00203_N G G c.6407G>T p.Arg2136Leu p.R2136L ENST00000359596 39/106 550 408 142 424 424 0 strelka-varscan-mutect RYR1,missense_variant,p.Arg2136Leu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Arg2136Leu,ENST00000359596,NM_000540.2;RYR1,upstream_gene_variant,,ENST00000594335,; T ENST00000359596 Transcript missense_variant 6407/15117 6407/15117 2136/5038 R/L cGt/cTt rs530885842 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.02) 39/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS rs530885842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 38494484 38494484 G T 1 0 0 0 0 1 0 0 0 14028 1145 40 1 1 RYR1 19 38494484 Missense_Mutation SNP G C3N-00203_T 755377 38494484 20123132 408 11712 DLL3 0 . GRCh38 19 39507223 39507223 + Frame_Shift_Del DEL C C - novel C3N-00203_T C3N-00203_N C C c.1279delC p.Arg427AlafsTer121 p.R427Afs*121 ENST00000205143 7/8 90 61 29 124 124 0 sindel-varindel-pindel DLL3,frameshift_variant,p.Arg427AlafsTer121,ENST00000205143,NM_016941.3;DLL3,frameshift_variant,p.Arg427AlafsTer121,ENST00000356433,NM_203486.2;DLL3,frameshift_variant,p.Arg199AlafsTer?,ENST00000596614,;DLL3,downstream_gene_variant,,ENST00000600437,; - ENST00000205143 Transcript frameshift_variant 1285/2332 1278/1857 426/618 C/X tgC/tg 1 1 DLL3 HGNC HGNC:2909 protein_coding YES CCDS12538.1 ENSP00000205143 Q9NYJ7 UPI0000051041 NM_016941.3 7/8 PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF308,hmmpanther:PTHR24044,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 HIGH 1 deletion 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 39507223 39507223 C - 1 0 1 0 1 0 0 0 0 4374 747 26 0 0 DLL3 19 39507223 Frame_Shift_Del DEL C C3N-00203_T 1012739 39507223 19110393 409 11713 SPTBN4 0 . GRCh38 19 40557056 40557056 + Missense_Mutation SNP G G C rs769990152 C3N-00203_T C3N-00203_N G G c.5323G>C p.Glu1775Gln p.E1775Q ENST00000352632 26/36 56 43 13 34 34 0 strelka-varscan-mutect SPTBN4,missense_variant,p.Glu1775Gln,ENST00000338932,;SPTBN4,missense_variant,p.Glu1775Gln,ENST00000352632,;SPTBN4,missense_variant,p.Glu1775Gln,ENST00000392025,;SPTBN4,missense_variant,p.Glu1775Gln,ENST00000598249,NM_020971.2;SPTBN4,missense_variant,p.Glu1775Gln,ENST00000595535,;SPTBN4,missense_variant,p.Glu451Gln,ENST00000392023,NM_025213.2;SPTBN4,3_prime_UTR_variant,,ENST00000597389,;SPTBN4,downstream_gene_variant,,ENST00000596900,; C ENST00000352632 Transcript missense_variant 5409/8676 5323/7695 1775/2564 E/Q Gag/Cag rs769990152 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB deleterious(0) 26/36 Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150 MODERATE 1 SNV 5 1 PASS rs769990152 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 40557056 40557056 G C 1 0 0 0 0 1 0 0 0 15477 1059 37 4 4 SPTBN4 19 40557056 Missense_Mutation SNP G C3N-00203_T 1049833 40557056 18060560 410 11714 TEX101 0 . GRCh38 19 43416101 43416101 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.121G>C p.Gly41Arg p.G41R ENST00000602198 5/8 94 75 19 70 70 0 strelka-varscan-mutect TEX101,missense_variant,p.Gly41Arg,ENST00000602198,NM_031451.4;TEX101,missense_variant,p.Gly23Arg,ENST00000598265,NM_001130011.1;TEX101,splice_region_variant,,ENST00000601707,; C ENST00000602198 Transcript missense_variant,splice_region_variant 563/1446 121/804 41/267 G/R Ggc/Cgc 1 1 TEX101 HGNC HGNC:30722 protein_coding YES CCDS12619.1 ENSP00000472308 Q9BY14 A0A024R0T7 UPI000013CDD3 NM_031451.4 tolerated(0.15) 5/8 hmmpanther:PTHR16529,hmmpanther:PTHR16529:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999906 1 1 1 0 C 3 2 42 43416101 43416101 G C 1 0 0 0 0 1 0 0 0 16194 1246 43 4 4 TEX101 19 43416101 Missense_Mutation SNP G C3N-00203_T 2859045 43416101 15201515 411 11715 DACT3 0 . GRCh38 19 46649469 46649469 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.903C>T p.= p.P301P ENST00000391916 4/4 25 21 4 37 37 0 strelka-mutect DACT3,synonymous_variant,p.=,ENST00000391916,NM_145056.2;DACT3,synonymous_variant,p.=,ENST00000300875,NM_001301046.1;DACT3,downstream_gene_variant,,ENST00000410105,; A ENST00000391916 Transcript synonymous_variant 977/2834 903/1890 301/629 P ccC/ccT 1 -1 DACT3 HGNC HGNC:30745 protein_coding YES CCDS12688.2 ENSP00000375783 Q96B18 UPI0000202707 NM_145056.2 4/4 hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF1 LOW 1 SNV 5 1 PASS rs1263070754 . 0 208 2 0 0 0 0 0 -12.2107 1 1 1 1 0 A 2 1 42 46649469 46649469 G A 1 0 0 0 0 0 0 0 1 4025 1103 39 1 1 DACT3 19 46649469 Silent SNP G C3N-00203_T 3233368 46649469 11968147 412 11716 SIGLEC12 0 . GRCh38 19 51501360 51501360 + Missense_Mutation SNP C C A rs762995704 C3N-00203_T C3N-00203_N C C c.374G>T p.Arg125Ile p.R125I ENST00000291707 1/8 195 137 58 224 224 0 strelka-varscan-mutect SIGLEC12,missense_variant,p.Arg125Ile,ENST00000291707,NM_053003.3;SIGLEC12,upstream_gene_variant,,ENST00000598614,NM_033329.2;SIGLEC12,missense_variant,p.Arg125Ile,ENST00000596742,;CTD-3073N11.7,downstream_gene_variant,,ENST00000594712,; A ENST00000291707 Transcript missense_variant 430/2121 374/1788 125/595 R/I aGa/aTa rs762995704 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 deleterious(0) 1/8 PROSITE_profiles:PS50835,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs762995704 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 51501360 51501360 C A 1 0 0 0 0 1 0 0 0 14572 913 32 2 2 SIGLEC12 19 51501360 Missense_Mutation SNP C C3N-00203_T 4851891 51501360 7116256 413 11717 PRKCG 0 . GRCh38 19 53892644 53892644 + Splice_Site SNP G G T novel C3N-00203_T C3N-00203_N G G c.821+1G>T p.X274_splice ENST00000263431 63 45 18 81 81 0 strelka-varscan-mutect PRKCG,splice_donor_variant,,ENST00000263431,NM_002739.3;PRKCG,downstream_gene_variant,,ENST00000474397,;PRKCG,downstream_gene_variant,,ENST00000479081,;PRKCG,downstream_gene_variant,,ENST00000419486,; T ENST00000263431 Transcript splice_donor_variant -/3133 821/2094 274/697 1 1 PRKCG HGNC HGNC:9402 protein_coding YES CCDS12867.1 ENSP00000263431 P05129 UPI000000DC69 NM_002739.3 7/17 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 42 53892644 53892644 G T 1 0 0 0 0 0 0 1 0 12645 1275 44 2 2 PRKCG 19 53892644 Splice_Site SNP G C3N-00203_T 2391284 53892644 4724972 414 11718 KIR2DL3 0 . GRCh38 19 54751690 54751690 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.757G>A p.Val253Ile p.V253I ENST00000342376 6/8 362 263 99 423 423 0 strelka-varscan-mutect KIR2DL3,missense_variant,p.Val253Ile,ENST00000342376,NM_015868.2;CTB-61M7.1,intron_variant,,ENST00000400864,;KIR2DP1,upstream_gene_variant,,ENST00000415311,; A ENST00000342376 Transcript missense_variant 788/1590 757/1026 253/341 V/I Gtc/Atc 1 1 KIR2DL3 HGNC HGNC:6331 protein_coding YES CCDS33107.1 ENSP00000342215 P43628 E3NZD8 UPI000012DB1C NM_015868.2 deleterious(0.03) 6/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11738:SF119,hmmpanther:PTHR11738 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 54751690 54751690 G A 1 0 0 0 0 1 0 0 0 8182 1261 44 3 3 KIR2DL3 19 54751690 Missense_Mutation SNP G C3N-00203_T 859046 54751690 3865926 415 11719 NLRP7 0 . GRCh38 19 54939971 54939971 + Missense_Mutation SNP A A G novel C3N-00203_T C3N-00203_N A A c.848T>C p.Leu283Pro p.L283P ENST00000588756 6/13 311 234 77 326 326 0 strelka-varscan-mutect NLRP7,missense_variant,p.Leu283Pro,ENST00000588756,;NLRP7,missense_variant,p.Leu283Pro,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Leu283Pro,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Leu283Pro,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Leu283Pro,ENST00000590030,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,downstream_gene_variant,,ENST00000587844,;NLRP7,missense_variant,p.Leu283Pro,ENST00000586379,; G ENST00000588756 Transcript missense_variant 1335/3826 848/3114 283/1037 L/P cTg/cCg 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 deleterious(0) 6/13 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14,Pfam_domain:PF05729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 54939971 54939971 A G 1 0 0 0 0 1 0 0 0 10520 188 7 5 5 NLRP7 19 54939971 Missense_Mutation SNP A C3N-00203_T 188281 54939971 3677645 416 11720 TNNT1 0 . GRCh38 19 55138026 55138026 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.436G>A p.Asp146Asn p.D146N ENST00000588981 10/14 578 429 149 587 587 0 strelka-varscan-mutect TNNT1,missense_variant,p.Asp146Asn,ENST00000588981,NM_003283.5;TNNT1,missense_variant,p.Asp76Asn,ENST00000587465,;TNNT1,missense_variant,p.Asp135Asn,ENST00000587758,NM_001291774.1;TNNT1,missense_variant,p.Asp76Asn,ENST00000585321,;TNNT1,missense_variant,p.Asp146Asn,ENST00000291901,NM_001126132.2;TNNT1,missense_variant,p.Asp135Asn,ENST00000356783,NM_001126133.2;TNNT1,missense_variant,p.Asp76Asn,ENST00000536926,;TNNT1,missense_variant,p.Asp146Asn,ENST00000593046,;TNNT1,missense_variant,p.Asp94Asn,ENST00000593194,;TNNT1,missense_variant,p.Asp43Asn,ENST00000588426,;TNNT1,missense_variant,p.Asp135Asn,ENST00000589226,;TNNT1,missense_variant,p.Asp31Asn,ENST00000589745,;TNNT1,missense_variant,p.Asp142Asn,ENST00000588147,;TNNT1,upstream_gene_variant,,ENST00000586649,;TNNT1,non_coding_transcript_exon_variant,,ENST00000592920,;TNNT1,3_prime_UTR_variant,,ENST00000587089,; T ENST00000588981 Transcript missense_variant 641/1163 436/837 146/278 D/N Gat/Aat 1 -1 TNNT1 HGNC HGNC:11948 protein_coding YES CCDS12917.1 ENSP00000467176 P13805 UPI000016A37B NM_003283.5 deleterious(0) 10/14 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11521,hmmpanther:PTHR11521:SF6,Pfam_domain:PF00992 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 55138026 55138026 C T 1 0 0 0 0 1 0 0 0 16803 855 30 3 3 TNNT1 19 55138026 Missense_Mutation SNP C C3N-00203_T 198055 55138026 3479590 417 11721 ZNF628 0 . GRCh38 19 55482249 55482249 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.1056C>T p.= p.P352P ENST00000598519 3/3 95 90 5 114 114 0 varscan-mutect ZNF628,synonymous_variant,p.=,ENST00000598519,NM_033113.2;ZNF628,synonymous_variant,p.=,ENST00000391718,;NAT14,upstream_gene_variant,,ENST00000205194,NM_020378.3;NAT14,upstream_gene_variant,,ENST00000591590,;NAT14,upstream_gene_variant,,ENST00000588985,;ZNF628,downstream_gene_variant,,ENST00000591164,;NAT14,upstream_gene_variant,,ENST00000587400,;NAT14,upstream_gene_variant,,ENST00000592719,; T ENST00000598519 Transcript synonymous_variant 1609/3847 1056/3180 352/1059 P ccC/ccT 1 1 ZNF628 HGNC HGNC:28054 protein_coding YES CCDS33116.3 ENSP00000469591 Q5EBL2 UPI00026B9C6E NM_033113.2 3/3 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 55482249 55482249 C T 1 0 0 0 0 0 0 0 1 18627 639 23 1 1 ZNF628 19 55482249 Silent SNP C C3N-00203_T 344223 55482249 3135367 418 11722 ZNF814 0 . GRCh38 19 57873899 57873899 + Nonsense_Mutation SNP A A T novel C3N-00203_T C3N-00203_N A A c.1491T>A p.Cys497Ter p.C497* ENST00000435989 3/3 161 114 47 224 224 0 strelka-varscan-mutect ZNF814,stop_gained,p.Cys497Ter,ENST00000435989,NM_001144989.1;ZNF814,stop_gained,p.Cys331Ter,ENST00000614383,;ZNF814,intron_variant,,ENST00000597832,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000600634,;ZNF814,intron_variant,,ENST00000595048,;ZNF814,downstream_gene_variant,,ENST00000597807,;ZNF814,intron_variant,,ENST00000594629,;ZNF814,intron_variant,,ENST00000597348,;ZNF814,intron_variant,,ENST00000595894,;ZNF814,upstream_gene_variant,,ENST00000594159,;CTD-2583A14.9,downstream_gene_variant,,ENST00000602124,; T ENST00000435989 Transcript stop_gained 1726/3146 1491/2568 497/855 C/* tgT/tgA 1 -1 ZNF814 HGNC HGNC:33258 protein_coding YES CCDS46212.1 ENSP00000410545 B7Z6K7 UPI0001662BAD NM_001144989.1 3/3 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 57873899 57873899 A T 1 0 0 0 0 0 1 0 0 18762 157 6 4 4 ZNF814 19 57873899 Nonsense_Mutation SNP A C3N-00203_T 2391650 57873899 743717 419 11723 SOX12 0 . GRCh38 20 326272 326272 + Frame_Shift_Del DEL G G - C3N-00203_T C3N-00203_N G G c.352delG p.Ala118ArgfsTer181 p.A118Rfs*181 ENST00000342665 1/1 68 43 25 55 55 0 sindel-varindel-pindel SOX12,frameshift_variant,p.Ala118ArgfsTer181,ENST00000342665,NM_006943.3;NRSN2-AS1,intron_variant,,ENST00000442637,;NRSN2-AS1,upstream_gene_variant,,ENST00000414676,; - ENST00000342665 Transcript frameshift_variant 678/4630 348/948 116/315 K/X aaG/aa COSM3545190 1 1 SOX12 HGNC HGNC:11198 protein_coding YES CCDS12995.1 ENSP00000347646 O15370 UPI0000167B9D NM_006943.3 1/1 Gene3D:1.10.30.10,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF221,Low_complexity_(Seg):seg 1 HIGH deletion 4 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 326272 326272 G - 1 0 1 0 1 0 0 0 0 15269 991 35 0 0 SOX12 20 326272 Frame_Shift_Del DEL G C3N-00203_T 326272 64117895 420 11724 IDH3B 0 . GRCh38 20 2663706 2663706 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.170A>G p.Asp57Gly p.D57G ENST00000380843 3/12 595 474 121 405 405 0 strelka-varscan-mutect IDH3B,missense_variant,p.Asp57Gly,ENST00000380843,NM_006899.3;IDH3B,missense_variant,p.Asp57Gly,ENST00000613370,NM_001258384.1;IDH3B,missense_variant,p.Asp57Gly,ENST00000474315,;IDH3B,missense_variant,p.Asp57Gly,ENST00000380851,NM_174855.2;RP4-686C3.7,upstream_gene_variant,,ENST00000418739,;IDH3B,non_coding_transcript_exon_variant,,ENST00000488299,;IDH3B,non_coding_transcript_exon_variant,,ENST00000462967,;IDH3B,non_coding_transcript_exon_variant,,ENST00000491065,;IDH3B,upstream_gene_variant,,ENST00000492240,;IDH3B,upstream_gene_variant,,ENST00000466494,;IDH3B,upstream_gene_variant,,ENST00000477689,;IDH3B,upstream_gene_variant,,ENST00000466999,;IDH3B,upstream_gene_variant,,ENST00000479376,; C ENST00000380843 Transcript missense_variant 201/1545 170/1158 57/385 D/G gAc/gGc 1 -1 IDH3B HGNC HGNC:5385 protein_coding YES CCDS13032.1 ENSP00000370223 O43837 UPI000013CBC6 NM_006899.3 deleterious(0) 3/12 Gene3D:3.40.718.10,Pfam_domain:PF00180,hmmpanther:PTHR11835,hmmpanther:PTHR11835:SF42,SMART_domains:SM01329,Superfamily_domains:SSF53659,TIGRFAM_domain:TIGR00175 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 2663706 2663706 T C 1 0 0 0 0 1 0 0 0 7397 1667 58 5 5 IDH3B 20 2663706 Missense_Mutation SNP T C3N-00203_T 2337434 2663706 61780461 421 11725 SIGLEC1 0 . GRCh38 20 3694525 3694525 + Silent SNP T T C novel C3N-00203_T C3N-00203_N T T c.2952A>G p.= p.P984P ENST00000344754 12/21 35 28 7 32 32 0 strelka-varscan-mutect SIGLEC1,synonymous_variant,p.=,ENST00000344754,NM_023068.3;SIGLEC1,upstream_gene_variant,,ENST00000419548,; C ENST00000344754 Transcript synonymous_variant 2952/6720 2952/5130 984/1709 P ccA/ccG 1 -1 SIGLEC1 HGNC HGNC:11127 protein_coding YES CCDS13060.1 ENSP00000341141 Q9BZZ2 UPI0000049BA6 NM_023068.3 12/21 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs746977518 . 0 208 2 0 0 0 0 0 -18.53595 1 1 1 1 0 C 2 2 42 3694525 3694525 T C 1 0 0 0 0 0 0 0 1 14569 1683 59 5 5 SIGLEC1 20 3694525 Silent SNP T C3N-00203_T 1030819 3694525 60749642 422 11726 COMMD7 0 . GRCh38 20 32728091 32728091 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.136G>C p.Glu46Gln p.E46Q ENST00000278980 2/9 222 197 25 205 205 0 strelka-varscan-mutect COMMD7,missense_variant,p.Glu46Gln,ENST00000278980,NM_053041.2;COMMD7,missense_variant,p.Glu45Gln,ENST00000446419,NM_001099339.1;COMMD7,missense_variant,p.Glu46Gln,ENST00000474815,;COMMD7,splice_region_variant,,ENST00000610160,; G ENST00000278980 Transcript missense_variant,splice_region_variant 742/1900 136/603 46/200 E/Q Gag/Cag 1 -1 COMMD7 HGNC HGNC:16223 protein_coding YES CCDS42864.1 ENSP00000278980 Q86VX2 UPI000006D145 NM_053041.2 tolerated(0.1) 2/9 hmmpanther:PTHR16231,hmmpanther:PTHR16231:SF2,Pfam_domain:PF07258 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 42 32728091 32728091 C G 1 0 0 0 0 1 0 0 0 3513 927 32 4 4 COMMD7 20 32728091 Missense_Mutation SNP C C3N-00203_T 29033566 32728091 31716076 423 11727 MMP24 0 . GRCh38 20 35251996 35251996 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.487T>C p.Trp163Arg p.W163R ENST00000246186 3/9 248 211 37 196 196 0 strelka-varscan-mutect MMP24,missense_variant,p.Trp163Arg,ENST00000246186,NM_006690.3;MMP24-AS1,intron_variant,,ENST00000635104,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000433764,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,downstream_gene_variant,,ENST00000453892,; C ENST00000246186 Transcript missense_variant 572/4414 487/1938 163/645 W/R Tgg/Cgg 1 1 MMP24 HGNC HGNC:7172 protein_coding YES CCDS46593.1 ENSP00000246186 Q9Y5R2 UPI000012F259 NM_006690.3 deleterious(0) 3/9 hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 204 0 4 2 0 0 0 -17.5569 0.9558358 1 1 1 0 C 3 2 42 35251996 35251996 T C 1 0 0 0 0 1 0 0 0 9624 1696 59 5 5 MMP24 20 35251996 Missense_Mutation SNP T C3N-00203_T 2523905 35251996 29192171 424 11728 PI3 0 . GRCh38 20 45176105 45176105 + Silent SNP T T C C3N-00203_T C3N-00203_N T T c.324T>C p.= p.S108S ENST00000243924 2/3 208 186 22 179 179 0 strelka-varscan-mutect PI3,synonymous_variant,p.=,ENST00000243924,NM_002638.3; C ENST00000243924 Transcript synonymous_variant 371/577 324/354 108/117 S tcT/tcC COSM443885 1 1 PI3 HGNC HGNC:8947 protein_coding YES CCDS13344.1 ENSP00000243924 P19957 UPI0000000CAE NM_002638.3 2/3 PROSITE_profiles:PS51390,hmmpanther:PTHR19441,hmmpanther:PTHR19441:SF30,Pfam_domain:PF00095,Gene3D:4.10.75.10,SMART_domains:SM00217,Superfamily_domains:SSF57256,Prints_domain:PR00003 1 LOW 1 SNV 1 1 1 PASS rs1029241821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 45176105 45176105 T C 1 0 0 0 0 0 0 0 1 11959 1596 56 5 5 PI3 20 45176105 Silent SNP T C3N-00203_T 9924109 45176105 19268062 425 11729 NCOA3 0 . GRCh38 20 47622278 47622278 + Silent SNP C C T novel C3N-00203_T C3N-00203_N C C c.31C>T p.= p.L11L ENST00000371998 3/23 128 107 21 100 100 0 strelka-varscan-mutect NCOA3,synonymous_variant,p.=,ENST00000372004,NM_006534.3;NCOA3,synonymous_variant,p.=,ENST00000371997,NM_001174088.1;NCOA3,synonymous_variant,p.=,ENST00000371998,NM_001174087.1,NM_181659.2;NCOA3,upstream_gene_variant,,ENST00000497292,;NCOA3,upstream_gene_variant,,ENST00000490248,; T ENST00000371998 Transcript synonymous_variant 222/4668 31/4275 11/1424 L Ctg/Ttg 1 1 NCOA3 HGNC HGNC:7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 UPI000012FE45 NM_001174087.1,NM_181659.2 3/23 hmmpanther:PTHR10684:SF3,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 47622278 47622278 C T 1 0 0 0 0 0 0 0 1 10249 564 20 3 3 NCOA3 20 47622278 Silent SNP C C3N-00203_T 2446173 47622278 16821889 426 11730 ARFGEF2 0 . GRCh38 20 48994460 48994460 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.2983T>C p.Cys995Arg p.C995R ENST00000371917 22/39 541 469 72 449 449 0 strelka-varscan-mutect ARFGEF2,missense_variant,p.Cys995Arg,ENST00000371917,NM_006420.2;ARFGEF2,upstream_gene_variant,,ENST00000493140,; C ENST00000371917 Transcript missense_variant 2983/8852 2983/5358 995/1785 C/R Tgc/Cgc 1 1 ARFGEF2 HGNC HGNC:15853 protein_coding YES CCDS13411.1 ENSP00000360985 Q9Y6D5 UPI000013D378 NM_006420.2 deleterious(0) 22/39 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 48994460 48994460 T C 1 0 0 0 0 1 0 0 0 976 1464 51 5 5 ARFGEF2 20 48994460 Missense_Mutation SNP T C3N-00203_T 1372182 48994460 15449707 427 11731 KCNB1 0 . GRCh38 20 49374837 49374837 + Silent SNP G G T novel C3N-00203_T C3N-00203_N G G c.723C>A p.= p.T241T ENST00000371741 2/2 121 89 32 119 119 0 strelka-varscan-mutect KCNB1,synonymous_variant,p.=,ENST00000371741,NM_004975.2;KCNB1,synonymous_variant,p.=,ENST00000635465,;KCNB1,intron_variant,,ENST00000635878,;KCNB1,non_coding_transcript_exon_variant,,ENST00000635210,;RP4-791K14.2,intron_variant,,ENST00000637341,;KCNB1,upstream_gene_variant,,ENST00000636838,;RP4-791K14.2,downstream_gene_variant,,ENST00000637091,;RP4-791K14.2,downstream_gene_variant,,ENST00000637575,;KCNB1,upstream_gene_variant,,ENST00000637131,; T ENST00000371741 Transcript synonymous_variant 919/11879 723/2577 241/858 T acC/acA 1 -1 KCNB1 HGNC HGNC:6231 protein_coding YES CCDS13418.1 ENSP00000360806 Q14721 UPI000012DC80 NM_004975.2 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR11537:SF134,hmmpanther:PTHR11537,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324,Prints_domain:PR00169 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 42 49374837 49374837 G T 1 0 0 0 0 0 0 0 1 7928 1335 47 2 2 KCNB1 20 49374837 Silent SNP G C3N-00203_T 380377 49374837 15069330 428 11732 MOCS3 0 . GRCh38 20 50959746 50959746 + Nonsense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.904G>T p.Glu302Ter p.E302* ENST00000244051 1/1 186 161 25 162 162 0 strelka-varscan-mutect MOCS3,stop_gained,p.Glu302Ter,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; T ENST00000244051 Transcript stop_gained 921/5106 904/1383 302/460 E/* Gaa/Taa 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 1/1 HAMAP:MF_03049,hmmpanther:PTHR10953,Superfamily_domains:SSF69572 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 42 50959746 50959746 G T 1 0 0 0 0 0 1 0 0 9655 1175 41 2 2 MOCS3 20 50959746 Nonsense_Mutation SNP G C3N-00203_T 1584909 50959746 13484421 429 11733 MC3R 0 . GRCh38 20 56249485 56249485 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.642G>A p.= p.A214A ENST00000243911 1/1 346 299 47 333 333 0 strelka-varscan-mutect MC3R,synonymous_variant,p.=,ENST00000243911,NM_019888.3; A ENST00000243911 Transcript synonymous_variant 754/1084 642/972 214/323 A gcG/gcA 1 1 MC3R HGNC HGNC:6931 protein_coding YES CCDS13449.2 ENSP00000243911 P41968 UPI0000E5A34B NM_019888.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF4,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 56249485 56249485 G A 1 0 0 0 0 0 0 0 1 9298 1074 38 1 1 MC3R 20 56249485 Silent SNP G C3N-00203_T 5289739 56249485 8194682 430 11734 HELZ2 0 . GRCh38 20 63562317 63562317 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.6368G>T p.Gly2123Val p.G2123V ENST00000467148 9/19 77 67 10 63 62 1 strelka-varscan-mutect HELZ2,missense_variant,p.Gly2123Val,ENST00000467148,NM_001037335.2;HELZ2,missense_variant,p.Gly1554Val,ENST00000427522,NM_033405.3;HELZ2,upstream_gene_variant,,ENST00000478861,; A ENST00000467148 Transcript missense_variant 6438/8064 6368/7950 2123/2649 G/V gGc/gTc 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 deleterious(0) 9/19 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF376 MODERATE 1 SNV 1 1 PASS rs1304596570 . 0 203 6 0 0 0 0 0 -19.99102 0.9999999 1 1 1 0 A 3 1 42 63562317 63562317 C A 1 0 0 0 0 1 0 0 0 6932 739 26 2 2 HELZ2 20 63562317 Missense_Mutation SNP C C3N-00203_T 7312832 63562317 881850 431 11735 MYT1 0 . GRCh38 20 64208105 64208105 + Silent SNP G G A C3N-00203_T C3N-00203_N G G c.909G>A p.= p.E303E ENST00000328439 7/23 120 96 24 99 99 0 strelka-varscan-mutect MYT1,synonymous_variant,p.=,ENST00000536311,;MYT1,synonymous_variant,p.=,ENST00000328439,NM_004535.2;MYT1,intron_variant,,ENST00000622439,;MYT1,intron_variant,,ENST00000360149,; A ENST00000328439 Transcript synonymous_variant 1273/5535 909/3366 303/1121 E gaG/gaA COSM4100602,COSM4100603 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 7/23 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS rs1169280249 . 0 199 5 6 0 0 0 0 -20 0.9956695 1 1 1 0 A 2 1 42 64208105 64208105 G A 1 0 0 0 0 0 0 0 1 10105 991 35 3 3 MYT1 20 64208105 Silent SNP G C3N-00203_T 645788 64208105 236062 432 11736 LIPI 0 . GRCh38 21 14189385 14189385 + Silent SNP T T G novel C3N-00203_T C3N-00203_N T T c.144A>C p.= p.L48L ENST00000344577 2/10 130 108 22 122 122 0 strelka-varscan-mutect LIPI,synonymous_variant,p.=,ENST00000344577,NM_198996.3;LIPI,synonymous_variant,p.=,ENST00000536861,NM_001303000.1,NM_001302998.1;LIPI,synonymous_variant,p.=,ENST00000614229,NM_001302999.1;LIPI,upstream_gene_variant,,ENST00000400211,; G ENST00000344577 Transcript synonymous_variant 170/1652 144/1446 48/481 L ctA/ctC 1 -1 LIPI HGNC HGNC:18821 protein_coding YES CCDS13564.1 ENSP00000343331 Q6XZB0 UPI000462096D NM_198996.3 2/10 hmmpanther:PTHR11610:SF103,hmmpanther:PTHR11610,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 42 14189385 14189385 T G 1 0 0 0 0 0 0 0 1 8746 1741 61 5 5 LIPI 21 14189385 Silent SNP T C3N-00203_T 14189385 32520598 433 11737 C21orf91 0 . GRCh38 21 17796787 17796787 + Silent SNP G G C novel C3N-00203_T C3N-00203_N G G c.459C>G p.= p.G153G ENST00000284881 3/5 287 259 28 280 280 0 strelka-varscan-mutect C21orf91,synonymous_variant,p.=,ENST00000284881,NM_001100420.1;C21orf91,synonymous_variant,p.=,ENST00000400559,NM_017447.3;C21orf91,synonymous_variant,p.=,ENST00000400558,NM_001100421.1;C21orf91,synonymous_variant,p.=,ENST00000405964,;C21orf91-OT1,upstream_gene_variant,,ENST00000430815,;C21orf91-OT1,upstream_gene_variant,,ENST00000439392,;C21orf91-OT1,upstream_gene_variant,,ENST00000430401,;AL109761.5,intron_variant,,ENST00000428689,;C21orf91,non_coding_transcript_exon_variant,,ENST00000493464,; C ENST00000284881 Transcript synonymous_variant 550/5433 459/894 153/297 G ggC/ggG 1 -1 C21orf91 HGNC HGNC:16459 protein_coding YES CCDS42907.1 ENSP00000284881 Q9NYK6 UPI000004A0E1 NM_001100420.1 3/5 Pfam_domain:PF06937,hmmpanther:PTHR15961 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 42 17796787 17796787 G C 1 0 0 0 0 0 0 0 1 2016 1306 46 4 4 C21orf91 21 17796787 Silent SNP G C3N-00203_T 3607402 17796787 28913196 434 11738 RIPK4 0 . GRCh38 21 41756645 41756645 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.354G>T p.= p.R118R ENST00000332512 2/8 416 312 104 365 365 0 strelka-varscan-mutect RIPK4,synonymous_variant,p.=,ENST00000352483,;RIPK4,synonymous_variant,p.=,ENST00000332512,NM_020639.2; A ENST00000332512 Transcript synonymous_variant 419/3889 354/2355 118/784 R cgG/cgT 1 -1 RIPK4 HGNC HGNC:496 protein_coding YES CCDS13675.1 ENSP00000332454 P57078 UPI000002A3C9 NM_020639.2 2/8 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF65,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 41756645 41756645 C A 1 0 0 0 0 0 0 0 1 13557 494 18 2 2 RIPK4 21 41756645 Silent SNP C C3N-00203_T 23959858 41756645 4953338 435 11739 TRPM2 0 . GRCh38 21 44441804 44441804 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.4499G>A p.Gly1500Glu p.G1500E ENST00000397928 32/32 85 59 26 60 60 0 strelka-varscan-mutect TRPM2,missense_variant,p.Gly1500Glu,ENST00000397928,NM_003307.3;TRPM2,missense_variant,p.Gly1500Glu,ENST00000300482,;TRPM2,missense_variant,p.Gly1446Glu,ENST00000300481,;TRPM2,missense_variant,p.Gly1550Glu,ENST00000397932,;TRPM2,missense_variant,p.Gly244Glu,ENST00000621064,;snoZ6,downstream_gene_variant,,ENST00000583496,;snoZ6,downstream_gene_variant,,ENST00000581669,;TRPM2,non_coding_transcript_exon_variant,,ENST00000498430,;TRPM2,non_coding_transcript_exon_variant,,ENST00000490982,; A ENST00000397928 Transcript missense_variant 4944/6221 4499/4512 1500/1503 G/E gGg/gAg 1 1 TRPM2 HGNC HGNC:12339 protein_coding YES CCDS13710.1 ENSP00000381023 O94759 UPI0000169D60 NM_003307.3 tolerated(0.15) 32/32 hmmpanther:PTHR13800:SF2,hmmpanther:PTHR13800,Gene3D:3.90.79.10,Superfamily_domains:SSF55811 MODERATE 1 SNV 1 1 PASS rs1290493135 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 44441804 44441804 G A 1 0 0 0 0 1 0 0 0 17092 1232 43 3 3 TRPM2 21 44441804 Missense_Mutation SNP G C3N-00203_T 2685159 44441804 2268179 436 11740 ELFN2 0 . GRCh38 22 37374631 37374631 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.904C>A p.His302Asn p.H302N ENST00000402918 3/3 117 81 36 133 132 1 strelka-varscan-mutect ELFN2,missense_variant,p.His302Asn,ENST00000402918,NM_052906.4;ELFN2,missense_variant,p.His302Asn,ENST00000613079,;ELFN2,intron_variant,,ENST00000430883,;ELFN2,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000451509,;ELFN2,downstream_gene_variant,,ENST00000424973,; T ENST00000402918 Transcript missense_variant 1690/8361 904/2463 302/820 H/N Cac/Aac 1 -1 ELFN2 HGNC HGNC:29396 protein_coding YES CCDS33642.1 ENSP00000385277 Q5R3F8 UPI000004E87D NM_052906.4 deleterious(0.04) 3/3 hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367 MODERATE SNV 4 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 37374631 37374631 G T 1 0 0 0 0 1 0 0 0 4892 1319 46 2 2 ELFN2 22 37374631 Missense_Mutation SNP G C3N-00203_T 37374631 13443837 437 11741 CARD10 0 . GRCh38 22 37495946 37495946 + Missense_Mutation SNP G G T rs779872538 C3N-00203_T C3N-00203_N G G c.2117C>A p.Pro706His p.P706H ENST00000403299 15/21 232 157 75 253 253 0 strelka-varscan-mutect CARD10,missense_variant,p.Pro706His,ENST00000403299,;CARD10,missense_variant,p.Pro706His,ENST00000251973,NM_014550.3;CARD10,missense_variant,p.Pro420His,ENST00000406271,;CARD10,missense_variant,p.Pro347His,ENST00000437756,;CARD10,missense_variant,p.Pro178His,ENST00000433485,;CARD10,non_coding_transcript_exon_variant,,ENST00000486118,;CARD10,non_coding_transcript_exon_variant,,ENST00000488141,;CARD10,upstream_gene_variant,,ENST00000467812,; T ENST00000403299 Transcript missense_variant 2334/4113 2117/3099 706/1032 P/H cCc/cAc rs779872538 1 -1 CARD10 HGNC HGNC:16422 protein_coding YES CCDS13948.1 ENSP00000384570 Q9BWT7 UPI0000044645 deleterious(0) 15/21 hmmpanther:PTHR14559,hmmpanther:PTHR14559:SF12 MODERATE 1 SNV 5 1 PASS rs779872538 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 37495946 37495946 G T 1 0 0 0 0 1 0 0 0 2339 1232 43 2 2 CARD10 22 37495946 Missense_Mutation SNP G C3N-00203_T 121315 37495946 13322522 438 11742 CACNA1I 0 . GRCh38 22 39663816 39663816 + Missense_Mutation SNP G G T rs769347392 C3N-00203_T C3N-00203_N G G c.3572G>T p.Arg1191Leu p.R1191L ENST00000402142 19/37 158 119 39 138 138 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Arg1191Leu,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Arg1156Leu,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Arg1191Leu,ENST00000401624,;CACNA1I,missense_variant,p.Arg1156Leu,ENST00000407673,; T ENST00000402142 Transcript missense_variant 3572/10004 3572/6672 1191/2223 R/L cGg/cTg rs769347392 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0) 19/37 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs769347392 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 39663816 39663816 G T 1 0 0 0 0 1 0 0 0 2234 1116 39 1 1 CACNA1I 22 39663816 Missense_Mutation SNP G C3N-00203_T 2167870 39663816 11154652 439 11743 MAPK8IP2 0 . GRCh38 22 50604649 50604649 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.1350G>T p.Trp450Cys p.W450C ENST00000329492 5/12 97 68 29 104 104 0 strelka-varscan-mutect MAPK8IP2,missense_variant,p.Trp450Cys,ENST00000329492,NM_012324.4;CHKB,upstream_gene_variant,,ENST00000463053,;MAPK8IP2,non_coding_transcript_exon_variant,,ENST00000008876,; T ENST00000329492 Transcript missense_variant 1484/3381 1350/2475 450/824 W/C tgG/tgT 1 1 MAPK8IP2 HGNC HGNC:6883 protein_coding YES CCDS74886.1 ENSP00000330572 Q13387 UPI000012DAB7 NM_012324.4 deleterious_low_confidence(0.03) 5/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 50604649 50604649 G T 1 0 0 0 0 1 0 0 0 9209 1241 43 2 2 MAPK8IP2 22 50604649 Missense_Mutation SNP G C3N-00203_T 10940833 50604649 213819 440 11744 P2RY8 0 . GRCh38 X 1466454 1466454 + Silent SNP C C A C3N-00203_T C3N-00203_N C C c.105G>T p.= p.A35A ENST00000381297 2/2 403 326 77 298 298 0 strelka-varscan-mutect P2RY8,synonymous_variant,p.=,ENST00000381297,NM_178129.4;P2RY8,synonymous_variant,p.=,ENST00000460672,; A ENST00000381297 Transcript synonymous_variant 316/4198 105/1080 35/359 A gcG/gcT COSM4909610,COSM4909611 1 -1 P2RY8 HGNC HGNC:15524 protein_coding YES CCDS14115.1 ENSP00000370697 Q86VZ1 UPI000000DA6D NM_178129.4 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF25,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 1466454 1466454 C A 1 0 0 0 0 0 0 0 1 11428 639 23 1 1 P2RY8 23 1466454 Silent SNP C C3N-00203_T 1466454 154574441 441 11745 FANCB 0 . GRCh38 X 14864576 14864576 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.935G>T p.Trp312Leu p.W312L ENST00000398334 3/10 185 87 98 124 124 0 strelka-varscan-mutect FANCB,missense_variant,p.Trp312Leu,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Trp312Leu,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Trp312Leu,ENST00000452869,;FANCB,downstream_gene_variant,,ENST00000489126,; A ENST00000398334 Transcript missense_variant 1203/3008 935/2580 312/859 W/L tGg/tTg 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 tolerated(0.17) 3/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 14864576 14864576 C A 1 0 0 0 0 1 0 0 0 5522 595 21 2 2 FANCB 23 14864576 Missense_Mutation SNP C C3N-00203_T 13398122 14864576 141176319 442 11746 GRPR 0 . GRCh38 X 16123984 16123985 + Frame_Shift_Ins INS - - C novel C3N-00203_T C3N-00203_N - - c.31_32insC p.Leu11SerfsTer23 p.L11Sfs*23 ENST00000380289 1/3 106 59 47 100 100 0 sindel-varindel-pindel GRPR,frameshift_variant,p.Leu11SerfsTer23,ENST00000380289,NM_005314.2; C ENST00000380289 Transcript frameshift_variant 429-430/1929 31-32/1155 11/384 L/SX ttg/tCtg 1 1 GRPR HGNC HGNC:4609 protein_coding YES CCDS14174.1 ENSP00000369643 P30550 X5D7H2 UPI00000503FE NM_005314.2 1/3 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF116,Prints_domain:PR00640 HIGH 1 insertion 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.999998 1 1 1 0 C 7 5 42 16123984 16123984 - C 1 0 1 1 0 0 0 0 0 6690 1606 56 0 0 GRPR 23 16123984 Frame_Shift_Ins INS - C3N-00203_T 1259408 16123984 139916911 443 11747 TAB3 0 . GRCh38 X 30854521 30854521 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.1144A>G p.Arg382Gly p.R382G ENST00000378933 7/12 124 78 46 109 109 0 strelka-varscan-mutect TAB3,missense_variant,p.Arg382Gly,ENST00000378933,NM_152787.4;TAB3,missense_variant,p.Arg382Gly,ENST00000378930,;TAB3,missense_variant,p.Arg382Gly,ENST00000378932,;TAB3,downstream_gene_variant,,ENST00000288422,;TAB3-AS2,non_coding_transcript_exon_variant,,ENST00000445240,;TAB3,upstream_gene_variant,,ENST00000378928,;TAB3,missense_variant,p.Arg382Gly,ENST00000467136,; C ENST00000378933 Transcript missense_variant 1691/6671 1144/2139 382/712 R/G Agg/Ggg 1 -1 TAB3 HGNC HGNC:30681 protein_coding YES CCDS14226.1 ENSP00000368215 Q8N5C8 UPI0000071648 NM_152787.4 deleterious(0.01) 7/12 hmmpanther:PTHR10351:SF45,hmmpanther:PTHR10351 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 30854521 30854521 T C 1 0 0 0 0 1 0 0 0 15893 1521 53 5 5 TAB3 23 30854521 Missense_Mutation SNP T C3N-00203_T 14730537 30854521 125186374 444 11748 CFAP47 0 . GRCh38 X 35989322 35989322 + Missense_Mutation SNP C C T novel C3N-00203_T C3N-00203_N C C c.2717C>T p.Thr906Ile p.T906I ENST00000297866 16/16 87 58 29 82 82 0 strelka-varscan-mutect CFAP47,missense_variant,p.Thr906Ile,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Thr906Ile,ENST00000297866,NM_152632.3;CFAP47,3_prime_UTR_variant,,ENST00000493930,; T ENST00000297866 Transcript missense_variant 2783/3608 2717/2931 906/976 T/I aCt/aTt 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 tolerated(0.63) 16/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 MODERATE 1 SNV 2 1 PASS rs1437998142 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 35989322 35989322 C T 1 0 0 0 0 1 0 0 0 3022 579 20 3 3 CFAP47 23 35989322 Missense_Mutation SNP C C3N-00203_T 5134801 35989322 120051573 445 11749 CFAP47 0 . GRCh38 X 36353584 36353584 + Silent SNP G G A novel C3N-00203_T C3N-00203_N G G c.8754G>A p.= p.L2918L ENST00000378653 60/64 201 101 100 168 168 0 strelka-varscan-mutect CFAP47,synonymous_variant,p.=,ENST00000378653,NM_001304548.1; A ENST00000378653 Transcript synonymous_variant 8820/9943 8754/9564 2918/3187 L ctG/ctA 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 60/64 hmmpanther:PTHR23053 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 36353584 36353584 G A 1 0 0 0 0 0 0 0 1 3022 1277 45 3 3 CFAP47 23 36353584 Silent SNP G C3N-00203_T 364262 36353584 119687311 446 11750 UBA1 0 . GRCh38 X 47212997 47212997 + Missense_Mutation SNP T T G novel C3N-00203_T C3N-00203_N T T c.2654T>G p.Leu885Arg p.L885R ENST00000335972 23/26 185 117 68 157 157 0 strelka-varscan-mutect UBA1,missense_variant,p.Leu885Arg,ENST00000335972,NM_003334.3;UBA1,missense_variant,p.Leu885Arg,ENST00000377351,NM_153280.2;UBA1,missense_variant,p.Leu333Arg,ENST00000377269,;CDK16,upstream_gene_variant,,ENST00000517997,; G ENST00000335972 Transcript missense_variant 2837/3559 2654/3177 885/1058 L/R cTg/cGg 1 1 UBA1 HGNC HGNC:12469 protein_coding YES CCDS14275.1 ENSP00000338413 P22314 A0A024R1A3 UPI0000137946 NM_003334.3 tolerated(0.56) 23/26 hmmpanther:PTHR10953:SF144,hmmpanther:PTHR10953,Gene3D:1y8qD02,Pfam_domain:PF00899,TIGRFAM_domain:TIGR01408,Superfamily_domains:SSF69572 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 47212997 47212997 T G 1 0 0 0 0 1 0 0 0 17346 1580 55 5 5 UBA1 23 47212997 Missense_Mutation SNP T C3N-00203_T 10859413 47212997 108827898 447 11751 FTSJ1 0 . GRCh38 X 48481681 48481681 + Silent SNP G G A rs782597073 C3N-00203_T C3N-00203_N G G c.621G>A p.= p.P207P ENST00000348411 9/13 298 164 134 248 248 0 strelka-varscan-mutect FTSJ1,synonymous_variant,p.=,ENST00000019019,NM_177439.2;FTSJ1,synonymous_variant,p.=,ENST00000348411,NM_012280.3;FTSJ1,synonymous_variant,p.=,ENST00000396894,NM_001282157.1;FTSJ1,non_coding_transcript_exon_variant,,ENST00000496365,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000490202,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000467954,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000489599,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000466371,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000473235,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000492562,;FTSJ1,non_coding_transcript_exon_variant,,ENST00000475806,;FTSJ1,downstream_gene_variant,,ENST00000487353,;FTSJ1,downstream_gene_variant,,ENST00000485486,; A ENST00000348411 Transcript synonymous_variant 944/1892 621/990 207/329 P ccG/ccA rs782597073,COSM2966328 1 1 FTSJ1 HGNC HGNC:13254 protein_coding YES CCDS14294.1 ENSP00000326948 Q9UET6 A0A024QYX5 UPI0000001C19 NM_012280.3 9/13 HAMAP:MF_03162,hmmpanther:PTHR10920,hmmpanther:PTHR10920:SF12 0,1 LOW 1 SNV 1 0,1 1 PASS rs782597073 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 48481681 48481681 G A 1 0 0 0 0 0 0 0 1 5961 1103 39 1 1 FTSJ1 23 48481681 Silent SNP G C3N-00203_T 1268684 48481681 107559214 448 11752 ITIH6 0 . GRCh38 X 54791051 54791051 + Frame_Shift_Del DEL G G - novel C3N-00203_T C3N-00203_N G G c.402delC p.Ser135AlafsTer8 p.S135Afs*8 ENST00000218436 4/13 145 68 77 108 108 0 sindel-varindel-pindel ITIH6,frameshift_variant,p.Ser135AlafsTer8,ENST00000218436,NM_198510.2;ITIH6,upstream_gene_variant,,ENST00000498398,; - ENST00000218436 Transcript frameshift_variant 432/4968 402/3942 134/1313 T/X acC/ac 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 4/13 Pfam_domain:PF08487,PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10,SMART_domains:SM00609 HIGH 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 42 54791051 54791051 G - 1 0 1 0 1 0 0 0 0 7814 1335 47 0 0 ITIH6 23 54791051 Frame_Shift_Del DEL G C3N-00203_T 6309370 54791051 101249844 449 11753 DGAT2L6 0 . GRCh38 X 70199828 70199828 + Silent SNP T T A novel C3N-00203_T C3N-00203_N T T c.213T>A p.= p.A71A ENST00000333026 3/7 100 61 39 101 101 0 strelka-varscan-mutect DGAT2L6,synonymous_variant,p.=,ENST00000333026,NM_198512.2; A ENST00000333026 Transcript synonymous_variant 313/1553 213/1014 71/337 A gcT/gcA 1 1 DGAT2L6 HGNC HGNC:23250 protein_coding YES CCDS14397.1 ENSP00000328036 Q6ZPD8 UPI00001C10BF NM_198512.2 3/7 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF19 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 70199828 70199828 T A 1 0 0 0 0 0 0 0 1 4266 1596 56 4 4 DGAT2L6 23 70199828 Silent SNP T C3N-00203_T 15408777 70199828 85841067 450 11754 TAF1 0 . GRCh38 X 71381741 71381741 + Splice_Site SNP A A G novel C3N-00203_T C3N-00203_N A A c.1421-2A>G p.X474_splice ENST00000423759 75 39 36 60 60 0 strelka-varscan-mutect TAF1,splice_acceptor_variant,,ENST00000423759,NM_001286074.1;TAF1,splice_acceptor_variant,,ENST00000373790,NM_138923.3;TAF1,splice_acceptor_variant,,ENST00000276072,NM_004606.4;TAF1,downstream_gene_variant,,ENST00000483365,; G ENST00000423759 Transcript splice_acceptor_variant -/7722 1421/5688 474/1895 1 1 TAF1 HGNC HGNC:11535 protein_coding YES CCDS69783.1 ENSP00000406549 P21675 UPI000171708A NM_001286074.1 8/38 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 42 71381741 71381741 A G 1 0 0 0 0 0 0 1 0 15909 434 15 5 5 TAF1 23 71381741 Splice_Site SNP A C3N-00203_T 1181913 71381741 84659154 451 11755 HDAC8 0 . GRCh38 X 72572709 72572709 + Missense_Mutation SNP T T C novel C3N-00203_T C3N-00203_N T T c.53A>G p.Tyr18Cys p.Y18C ENST00000373573 1/11 84 46 38 59 59 0 strelka-varscan-mutect HDAC8,missense_variant,p.Tyr18Cys,ENST00000439122,NM_001166419.1;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373571,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373573,NM_018486.2;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373589,NM_001166418.1;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373568,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000415409,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373554,NM_001166420.1;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373560,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373556,NM_001166422.1;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373559,NM_001166448.1;HDAC8,missense_variant,p.Tyr18Cys,ENST00000373583,;HDAC8,upstream_gene_variant,,ENST00000421523,;HDAC8,non_coding_transcript_exon_variant,,ENST00000478743,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000436675,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000412342,;HDAC8,missense_variant,p.Tyr18Cys,ENST00000444609,;HDAC8,non_coding_transcript_exon_variant,,ENST00000486704,; C ENST00000373573 Transcript missense_variant 395/2014 53/1134 18/377 Y/C tAt/tGt 1 -1 HDAC8 HGNC HGNC:13315 protein_coding YES CCDS14420.1 ENSP00000362674 Q9BY41 UPI00000411E6 NM_018486.2 deleterious(0) 1/11 Gene3D:3.40.800.20,PIRSF_domain:PIRSF037913,hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF125,Superfamily_domains:SSF52768 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 72572709 72572709 T C 1 0 0 0 0 1 0 0 0 6900 1406 49 5 5 HDAC8 23 72572709 Missense_Mutation SNP T C3N-00203_T 1190968 72572709 83468186 452 11756 ZCCHC13 0 . GRCh38 X 74304519 74304519 + Missense_Mutation SNP C C G rs746589997 C3N-00203_T C3N-00203_N C C c.253C>G p.Arg85Gly p.R85G ENST00000339534 1/1 191 121 70 179 179 0 strelka-varscan-mutect ZCCHC13,missense_variant,p.Arg85Gly,ENST00000339534,NM_203303.2; G ENST00000339534 Transcript missense_variant 330/842 253/501 85/166 R/G Cga/Gga rs746589997,COSM4742358 1 1 ZCCHC13 HGNC HGNC:31749 protein_coding YES CCDS14425.1 ENSP00000345633 Q8WW36 UPI0000070721 NM_203303.2 deleterious(0.01) 1/1 hmmpanther:PTHR23002,hmmpanther:PTHR23002:SF53 0,1 MODERATE 1 SNV 0,1 1 PASS rs746589997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 74304519 74304519 C G 1 0 0 0 0 1 0 0 0 18157 528 19 4 4 ZCCHC13 23 74304519 Missense_Mutation SNP C C3N-00203_T 1731810 74304519 81736376 453 11757 PGAM4 0 . GRCh38 X 77969551 77969551 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.88C>A p.Leu30Met p.L30M ENST00000458128 1/1 162 76 86 106 106 0 strelka-varscan-mutect PGAM4,missense_variant,p.Leu30Met,ENST00000458128,NM_001029891.2;ATP7A,intron_variant,,ENST00000341514,NM_000052.6;ATP7A,intron_variant,,ENST00000343533,NM_001282224.1;RP5-1000K24.2,downstream_gene_variant,,ENST00000602791,; T ENST00000458128 Transcript missense_variant 88/765 88/765 30/254 L/M Ctg/Atg 1 -1 PGAM4 HGNC HGNC:21731 protein_coding YES CCDS35338.1 ENSP00000412189 Q8N0Y7 UPI0000131CD2 NM_001029891.2 deleterious(0) 1/1 HAMAP:MF_01039,hmmpanther:PTHR11931:SF14,hmmpanther:PTHR11931,Gene3D:3.40.50.1240,Pfam_domain:PF00300,TIGRFAM_domain:TIGR01258,SMART_domains:SM00855,Superfamily_domains:SSF53254 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 77969551 77969551 G T 1 0 0 0 0 1 0 0 0 11865 933 33 2 2 PGAM4 23 77969551 Missense_Mutation SNP G C3N-00203_T 3665032 77969551 78071344 454 11758 DACH2 0 . GRCh38 X 86148981 86148981 + Missense_Mutation SNP G G A novel C3N-00203_T C3N-00203_N G G c.361G>A p.Val121Met p.V121M ENST00000373125 1/12 159 142 17 72 72 0 strelka-varscan-mutect DACH2,missense_variant,p.Val121Met,ENST00000373131,NM_001139514.1;DACH2,missense_variant,p.Val121Met,ENST00000373125,NM_053281.3;DACH2,missense_variant,p.Val121Met,ENST00000461604,;DACH2,missense_variant,p.Val121Met,ENST00000506327,; A ENST00000373125 Transcript missense_variant 361/2232 361/1800 121/599 V/M Gtg/Atg 1 1 DACH2 HGNC HGNC:16814 protein_coding YES CCDS14455.1 ENSP00000362217 Q96NX9 UPI00000717B4 NM_053281.3 deleterious(0) 1/12 Gene3D:3.10.260.20,Pfam_domain:PF02437,hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7,Superfamily_domains:SSF46955 MODERATE 1 SNV 1 1 PASS rs1184913396 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 86148981 86148981 G A 1 0 0 0 0 1 0 0 0 4022 1145 40 1 1 DACH2 23 86148981 Missense_Mutation SNP G C3N-00203_T 8179430 86148981 69891914 455 11759 DRP2 0 . GRCh38 X 101258409 101258409 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.2491C>A p.Arg831Ser p.R831S ENST00000395209 22/24 532 117 415 161 161 0 strelka-varscan-mutect DRP2,missense_variant,p.Arg831Ser,ENST00000395209,NM_001939.2;DRP2,missense_variant,p.Arg831Ser,ENST00000402866,;DRP2,missense_variant,p.Arg831Ser,ENST00000538510,;DRP2,missense_variant,p.Arg753Ser,ENST00000541709,NM_001171184.1; A ENST00000395209 Transcript missense_variant 3018/7277 2491/2874 831/957 R/S Cgc/Agc 1 1 DRP2 HGNC HGNC:3032 protein_coding YES CCDS14480.2 ENSP00000378635 Q13474 A0A024RCH3 UPI000013D388 NM_001939.2 tolerated(0.17) 22/24 hmmpanther:PTHR11915,PIRSF_domain:PIRSF038205 MODERATE 1 SNV 1 1 PASS rs1333006621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 101258409 101258409 C A 1 0 0 0 0 1 0 0 0 4585 652 23 1 1 DRP2 23 101258409 Missense_Mutation SNP C C3N-00203_T 15109428 101258409 54782486 456 11760 ZMAT1 0 . GRCh38 X 101884658 101884658 + Nonsense_Mutation SNP C C A C3N-00203_T C3N-00203_N C C c.769G>T p.Glu257Ter p.E257* ENST00000372782 7/7 461 397 64 157 157 0 strelka-varscan-mutect ZMAT1,stop_gained,p.Glu257Ter,ENST00000372782,NM_001011657.3;ZMAT1,stop_gained,p.Glu257Ter,ENST00000540921,;ZMAT1,non_coding_transcript_exon_variant,,ENST00000494068,;ZMAT1,non_coding_transcript_exon_variant,,ENST00000458570,;ZMAT1,non_coding_transcript_exon_variant,,ENST00000488347,;ZMAT1,downstream_gene_variant,,ENST00000490757,; A ENST00000372782 Transcript stop_gained 817/3185 769/1917 257/638 E/* Gaa/Taa COSM1112027,COSM1112028 1 -1 ZMAT1 HGNC HGNC:29377 protein_coding YES CCDS35348.1 ENSP00000361868 Q5H9K5 UPI0001DD37FB NM_001011657.3 7/7 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 101884658 101884658 C A 1 0 0 0 0 0 1 0 0 18271 922 32 2 2 ZMAT1 23 101884658 Nonsense_Mutation SNP C C3N-00203_T 626249 101884658 54156237 457 11761 GPRASP1 0 . GRCh38 X 102654110 102654110 + Missense_Mutation SNP T T A novel C3N-00203_T C3N-00203_N T T c.197T>A p.Val66Asp p.V66D ENST00000537097 6/6 123 82 41 94 94 0 strelka-varscan-mutect GPRASP1,missense_variant,p.Val66Asp,ENST00000537097,NM_001184727.1;GPRASP1,missense_variant,p.Val66Asp,ENST00000361600,NM_014710.4;GPRASP1,missense_variant,p.Val66Asp,ENST00000415986,NM_001099410.1;GPRASP1,missense_variant,p.Val66Asp,ENST00000444152,NM_001099411.1;RP4-769N13.7,intron_variant,,ENST00000602441,;ARMCX5-GPRASP2,intron_variant,,ENST00000486740,;ARMCX5-GPRASP2,intron_variant,,ENST00000602366,;ARMCX5-GPRASP2,intron_variant,,ENST00000602463,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000466616,;GPRASP1,downstream_gene_variant,,ENST00000466098,; A ENST00000537097 Transcript missense_variant 1010/5980 197/4188 66/1395 V/D gTt/gAt 1 1 GPRASP1 HGNC HGNC:24834 protein_coding YES CCDS35352.1 ENSP00000445683 Q5JY77 UPI0000073B80 NM_001184727.1 deleterious(0.01) 6/6 hmmpanther:PTHR15712:SF22,hmmpanther:PTHR15712 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 42 102654110 102654110 T A 1 0 0 0 0 1 0 0 0 6601 1725 60 4 4 GPRASP1 23 102654110 Missense_Mutation SNP T C3N-00203_T 769452 102654110 53386785 458 11762 GLRA4 0 . GRCh38 X 103719246 103719246 + Missense_Mutation SNP C C G novel C3N-00203_T C3N-00203_N C C c.744G>C p.Lys248Asn p.K248N ENST00000372617 7/9 90 34 56 55 55 0 strelka-varscan-mutect GLRA4,missense_variant,p.Lys248Asn,ENST00000372617,NM_001024452.2;GLRA4,downstream_gene_variant,,ENST00000469567,;GLRA4,non_coding_transcript_exon_variant,,ENST00000480725,;GLRA4,intron_variant,,ENST00000436213,; G ENST00000372617 Transcript missense_variant 1165/1795 744/1254 248/417 K/N aaG/aaC 1 -1 GLRA4 HGNC HGNC:31715 protein_coding YES CCDS43980.2 ENSP00000361700 Q5JXX5 UPI000188140C NM_001024452.2 tolerated(0.19) 7/9 hmmpanther:PTHR18945:SF211,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE 1 SNV 5 1 PASS rs1309556677 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 42 103719246 103719246 C G 1 0 0 0 0 1 0 0 0 6336 564 20 4 4 GLRA4 23 103719246 Missense_Mutation SNP C C3N-00203_T 1065136 103719246 52321649 459 11763 RGAG1 0 . GRCh38 X 110452708 110452708 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.2091G>T p.Met697Ile p.M697I ENST00000465301 3/4 278 198 80 155 155 0 strelka-varscan-mutect RGAG1,missense_variant,p.Met697Ile,ENST00000465301,NM_020769.2;RGAG1,missense_variant,p.Met697Ile,ENST00000540313,;RGAG1,downstream_gene_variant,,ENST00000520821,; T ENST00000465301 Transcript missense_variant 2337/5426 2091/4167 697/1388 M/I atG/atT 1 1 RGAG1 HGNC HGNC:29245 protein_coding YES CCDS14552.1 ENSP00000419786 Q8NET4 UPI000006F841 NM_020769.2 tolerated(0.19) 3/4 hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF48 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 110452708 110452708 G T 1 0 0 0 0 1 0 0 0 13446 1290 45 2 2 RGAG1 23 110452708 Missense_Mutation SNP G C3N-00203_T 6733462 110452708 45588187 460 11764 SMARCA1 0 . GRCh38 X 129515758 129515758 + Missense_Mutation SNP G G C novel C3N-00203_T C3N-00203_N G G c.559C>G p.Gln187Glu p.Q187E ENST00000371121 5/25 284 103 181 178 178 0 strelka-varscan-mutect SMARCA1,missense_variant,p.Gln187Glu,ENST00000371122,NM_003069.4;SMARCA1,missense_variant,p.Gln187Glu,ENST00000371123,NM_001282875.1;SMARCA1,missense_variant,p.Gln187Glu,ENST00000371121,NM_001282874.1;SNORD112,upstream_gene_variant,,ENST00000516361,;SMARCA1,non_coding_transcript_exon_variant,,ENST00000478420,;SMARCA1,non_coding_transcript_exon_variant,,ENST00000617310,; C ENST00000371121 Transcript missense_variant 594/3564 559/3213 187/1070 Q/E Cag/Gag 1 -1 SMARCA1 HGNC HGNC:11097 protein_coding YES CCDS76019.1 ENSP00000360162 B7ZLQ5 UPI00004258DE NM_001282874.1 deleterious(0) 5/25 hmmpanther:PTHR10799:SF691,hmmpanther:PTHR10799,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 42 129515758 129515758 G C 1 0 0 0 0 1 0 0 0 15061 1299 45 4 4 SMARCA1 23 129515758 Missense_Mutation SNP G C3N-00203_T 19063050 129515758 26525137 461 11765 F9 0 . GRCh38 X 139551218 139551218 + Missense_Mutation SNP G G T rs137852241 C3N-00203_T C3N-00203_N G G c.677G>T p.Arg226Leu p.R226L ENST00000218099 6/8 342 141 201 213 213 0 strelka-varscan-mutect F9,missense_variant,p.Arg226Leu,ENST00000218099,NM_000133.3;F9,missense_variant,p.Arg188Leu,ENST00000394090,;F9,downstream_gene_variant,,ENST00000479617,; T ENST00000218099 Transcript missense_variant 684/2780 677/1386 226/461 R/L cGg/cTg rs137852241,CM940541,CM940542,CM940543,COSM1556441 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 deleterious(0) 6/8 PIRSF_domain:PIRSF001143,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF135,SMART_domains:SM00020,Superfamily_domains:SSF50494 pathogenic 0,0,0,0,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs137852241 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 139551218 139551218 G T 1 0 0 0 0 1 0 0 0 5220 1116 39 1 1 F9 23 139551218 Missense_Mutation SNP G C3N-00203_T 10035460 139551218 16489677 462 11766 MAGEC1 0 . GRCh38 X 141906939 141906939 + Missense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1535C>A p.Ser512Tyr p.S512Y ENST00000285879 4/4 237 169 68 151 151 0 strelka-varscan-mutect MAGEC1,missense_variant,p.Ser512Tyr,ENST00000285879,NM_005462.4;MAGEC1,intron_variant,,ENST00000406005,; A ENST00000285879 Transcript missense_variant 1821/4270 1535/3429 512/1142 S/Y tCt/tAt 1 1 MAGEC1 HGNC HGNC:6812 protein_coding YES CCDS35417.1 ENSP00000285879 O60732 UPI000006F2FD NM_005462.4 deleterious_low_confidence(0) 4/4 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 42 141906939 141906939 C A 1 0 0 0 0 1 0 0 0 9098 913 32 2 2 MAGEC1 23 141906939 Missense_Mutation SNP C C3N-00203_T 2355721 141906939 14133956 463 11767 MAGEA6 0 . GRCh38 X 152767355 152767355 + Missense_Mutation SNP G G T novel C3N-00203_T C3N-00203_N G G c.296C>A p.Pro99His p.P99H ENST00000616035 3/3 323 139 184 190 190 0 strelka-varscan-mutect MAGEA6,missense_variant,p.Pro99His,ENST00000616035,NM_175868.1;MAGEA6,missense_variant,p.Pro99His,ENST00000329342,NM_005363.2;MAGEA6,missense_variant,p.Pro99His,ENST00000457643,;MAGEA6,missense_variant,p.Pro99His,ENST00000412733,; T ENST00000616035 Transcript missense_variant 554/1762 296/945 99/314 P/H cCt/cAt 1 -1 MAGEA6 HGNC HGNC:6804 protein_coding YES CCDS76050.1 ENSP00000480637 P43360 UPI000000D9B0 NM_175868.1 deleterious(0) 3/3 hmmpanther:PTHR11736:SF60,hmmpanther:PTHR11736 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 42 152767355 152767355 G T 1 0 0 0 0 1 0 0 0 9085 1000 35 2 2 MAGEA6 23 152767355 Missense_Mutation SNP G C3N-00203_T 10860416 152767355 3273540 464 11768 IL9R 0 . GRCh38 X 156002886 156002886 + Silent SNP C C A novel C3N-00203_T C3N-00203_N C C c.150C>A p.= p.P50P ENST00000369423 3/9 253 154 99 180 180 0 strelka-varscan-mutect IL9R,synonymous_variant,p.=,ENST00000369423,NM_176786.1;IL9R,intron_variant,,ENST00000244174,NM_002186.2;IL9R,intron_variant,,ENST00000489233,;IL9R,upstream_gene_variant,,ENST00000494962,;AJ271736.10,upstream_gene_variant,,ENST00000483543,; A ENST00000369423 Transcript synonymous_variant 188/2032 150/1029 50/342 P ccC/ccA 1 1 IL9R HGNC HGNC:6030 protein_coding CCDS59180.1 ENSP00000358431 Q01113 UPI00001AF535 NM_176786.1 3/9 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 42 156002886 156002886 C A 1 0 0 0 0 0 0 0 1 7611 695 24 2 2 IL9R 23 156002886 Silent SNP C C3N-00203_T 3235531 156002886 38009 465 11769 KDM5D 0 . GRCh38 Y 19716374 19716374 + Nonsense_Mutation SNP C C A novel C3N-00203_T C3N-00203_N C C c.1936G>T p.Glu646Ter p.E646* ENST00000317961 15/27 245 128 117 222 222 0 strelka-varscan-mutect KDM5D,stop_gained,p.Glu677Ter,ENST00000541639,NM_001146705.1;KDM5D,stop_gained,p.Glu646Ter,ENST00000317961,NM_004653.4;KDM5D,stop_gained,p.Glu589Ter,ENST00000382806,NM_001146706.1;KDM5D,stop_gained,p.Glu605Ter,ENST00000440077,;KDM5D,downstream_gene_variant,,ENST00000447300,;KDM5D,non_coding_transcript_exon_variant,,ENST00000469599,;KDM5D,non_coding_transcript_exon_variant,,ENST00000492117,;KDM5D,upstream_gene_variant,,ENST00000478891,; A ENST00000317961 Transcript stop_gained 2208/5472 1936/4620 646/1539 E/* Gag/Tag 1 -1 KDM5D HGNC HGNC:11115 protein_coding YES CCDS14794.1 ENSP00000322408 Q9BY66 UPI0000135A93 NM_004653.4 15/27 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF47 HIGH 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 42 19716374 19716374 C A 1 0 0 0 0 0 1 0 0 8054 922 32 2 2 KDM5D 24 19716374 Nonsense_Mutation SNP C C3N-00203_T 19716374 37511041 466 11770 CHD5 0 . GRCh38 1 6109909 6109909 + Missense_Mutation SNP C C T rs373083783 C3N-00217_T C3N-00217_N C C c.5464G>A p.Ala1822Thr p.A1822T ENST00000262450 38/42 98 90 8 82 82 0 strelka-varscan-mutect CHD5,missense_variant,p.Ala1822Thr,ENST00000262450,NM_015557.2;CHD5,upstream_gene_variant,,ENST00000475121,;CHD5,3_prime_UTR_variant,,ENST00000496404,;CHD5,3_prime_UTR_variant,,ENST00000462991,;CHD5,3_prime_UTR_variant,,ENST00000377999,; T ENST00000262450 Transcript missense_variant 5564/9646 5464/5865 1822/1954 A/T Gcc/Acc rs373083783,COSM2237724,COSM4239989 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 deleterious(0.04) 38/42 Pfam_domain:PF08074 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs373083783 . 0 200 8 2 0 0 0 0 -12.59426 0.9991077 1 1 1 0 T 3 4 43 6109909 6109909 C T 1 0 0 0 0 1 0 0 0 3087 768 27 1 1 CHD5 1 6109909 Missense_Mutation SNP C C3N-00217_T 6109909 242846513 1 11771 CLCN6 0 . GRCh38 1 11807152 11807152 + Nonsense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.109G>T p.Glu37Ter p.E37* ENST00000346436 2/23 144 123 21 200 200 0 strelka-varscan-mutect CLCN6,stop_gained,p.Glu37Ter,ENST00000312413,NM_001256959.1;CLCN6,stop_gained,p.Glu37Ter,ENST00000346436,NM_001286.3;CLCN6,stop_gained,p.Glu37Ter,ENST00000376496,;CLCN6,stop_gained,p.Glu37Ter,ENST00000376497,;MTHFR,upstream_gene_variant,,ENST00000376592,;MTHFR,upstream_gene_variant,,ENST00000376583,;MTHFR,upstream_gene_variant,,ENST00000376590,NM_005957.4;MTHFR,upstream_gene_variant,,ENST00000376585,;MTHFR,upstream_gene_variant,,ENST00000423400,;MTHFR,upstream_gene_variant,,ENST00000376486,;MTHFR,upstream_gene_variant,,ENST00000418034,;MTHFR,upstream_gene_variant,,ENST00000431243,;MTHFR,upstream_gene_variant,,ENST00000413656,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376492,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376490,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376491,; T ENST00000346436 Transcript stop_gained 161/5583 109/2610 37/869 E/* Gag/Tag 1 1 CLCN6 HGNC HGNC:2024 protein_coding YES CCDS138.1 ENSP00000234488 P51797 UPI000013F2D3 NM_001286.3 2/23 hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF59 HIGH 1 SNV 1 1 PASS rs1372498907 . 0 205 0 3 2 0 0 0 -11.30342 0.9722318 1 1 1 0 T 4 4 43 11807152 11807152 G T 1 0 0 0 0 0 1 0 0 3231 1175 41 2 2 CLCN6 1 11807152 Nonsense_Mutation SNP G C3N-00217_T 5697243 11807152 237149270 2 11772 KIAA2013 0 . GRCh38 1 11925989 11925989 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.249A>G p.= p.V83V ENST00000376572 1/3 247 213 34 251 251 0 strelka-varscan-mutect KIAA2013,synonymous_variant,p.=,ENST00000376572,NM_138346.2;KIAA2013,synonymous_variant,p.=,ENST00000376576,;KIAA2013,synonymous_variant,p.=,ENST00000616327,; C ENST00000376572 Transcript synonymous_variant 435/2815 249/1905 83/634 V gtA/gtG 1 -1 KIAA2013 HGNC HGNC:28513 protein_coding YES CCDS141.1 ENSP00000365756 Q8IYS2 UPI00000741FB NM_138346.2 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR31386:SF2,hmmpanther:PTHR31386,Pfam_domain:PF10222 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 11925989 11925989 T C 1 0 0 0 0 0 0 0 1 8132 1625 57 5 5 KIAA2013 1 11925989 Silent SNP T C3N-00217_T 118837 11925989 237030433 3 11773 PRAMEF8 0 . GRCh38 1 13281816 13281816 + Missense_Mutation SNP C C A rs150974181 C3N-00217_T C3N-00217_N C C c.980G>T p.Arg327Met p.R327M ENST00000357367 4/4 535 397 138 470 470 0 strelka-varscan-mutect PRAMEF8,missense_variant,p.Arg327Met,ENST00000357367,NM_001012276.3;PRAMEF8,missense_variant,p.Arg327Met,ENST00000621519,;PRAMEF8,missense_variant,p.Arg327Met,ENST00000614831,;RNU6-443P,upstream_gene_variant,,ENST00000384780,; A ENST00000357367 Transcript missense_variant 1063/1844 980/1425 327/474 R/M aGg/aTg rs150974181 1 -1 PRAMEF8 HGNC HGNC:24074 protein_coding YES CCDS72709.1 ENSP00000349931 Q5VWM4 UPI000191706C NM_001012276.3 deleterious(0.03) 4/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs1325969803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 13281816 13281816 C A 1 0 0 0 0 1 0 0 0 12570 681 24 2 2 PRAMEF8 1 13281816 Missense_Mutation SNP C C3N-00217_T 1355827 13281816 235674606 4 11774 PRAMEF8 0 . GRCh38 1 13283962 13283962 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.130T>A p.Phe44Ile p.F44I ENST00000357367 2/4 482 389 93 491 490 1 strelka-varscan-mutect PRAMEF8,missense_variant,p.Phe44Ile,ENST00000357367,NM_001012276.3;PRAMEF8,missense_variant,p.Phe44Ile,ENST00000621519,;PRAMEF8,missense_variant,p.Phe44Ile,ENST00000614831,;RNU6-443P,upstream_gene_variant,,ENST00000384780,; T ENST00000357367 Transcript missense_variant 213/1844 130/1425 44/474 F/I Ttc/Atc 1 -1 PRAMEF8 HGNC HGNC:24074 protein_coding YES CCDS72709.1 ENSP00000349931 Q5VWM4 UPI000191706C NM_001012276.3 deleterious(0.04) 2/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 13283962 13283962 A T 1 0 0 0 0 1 0 0 0 12570 72 3 4 4 PRAMEF8 1 13283962 Missense_Mutation SNP A C3N-00217_T 2146 13283962 235672460 5 11775 CROCC 0 . GRCh38 1 16936737 16936737 + Missense_Mutation SNP G G T rs759919596 C3N-00217_T C3N-00217_N G G c.1057G>T p.Ala353Ser p.A353S ENST00000375541 9/37 252 221 31 216 216 0 strelka-varscan-mutect CROCC,missense_variant,p.Ala353Ser,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Ala213Ser,ENST00000445545,;CROCC,missense_variant,p.Ala247Ser,ENST00000467938,;CROCC,upstream_gene_variant,,ENST00000467715,;CROCC,non_coding_transcript_exon_variant,,ENST00000466256,;CROCC,intron_variant,,ENST00000492631,;CROCC,upstream_gene_variant,,ENST00000494191,; T ENST00000375541 Transcript missense_variant 1126/6656 1057/6054 353/2017 A/S Gcc/Tcc rs759919596 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 tolerated(0.27) 9/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs759919596 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 16936737 16936737 G T 1 0 0 0 0 1 0 0 0 3694 1203 42 2 2 CROCC 1 16936737 Missense_Mutation SNP G C3N-00217_T 3652775 16936737 232019685 6 11776 FAM46B 0 . GRCh38 1 27006309 27006309 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.913A>C p.Met305Leu p.M305L ENST00000289166 2/2 110 86 24 89 89 0 strelka-varscan-mutect FAM46B,missense_variant,p.Met305Leu,ENST00000289166,NM_052943.3; G ENST00000289166 Transcript missense_variant 1079/2368 913/1278 305/425 M/L Atg/Ctg 1 -1 FAM46B HGNC HGNC:28273 protein_coding YES CCDS294.2 ENSP00000289166 Q96A09 UPI0000374A6A NM_052943.3 deleterious(0) 2/2 Pfam_domain:PF07984,hmmpanther:PTHR12974,hmmpanther:PTHR12974:SF46,SMART_domains:SM01153 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 27006309 27006309 T G 1 0 0 0 0 1 0 0 0 5444 1464 51 5 5 FAM46B 1 27006309 Missense_Mutation SNP T C3N-00217_T 10069572 27006309 221950113 7 11777 SPOCD1 0 . GRCh38 1 31796595 31796595 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.2266C>T p.= p.L756L ENST00000360482 10/16 558 291 267 411 411 0 strelka-varscan-mutect SPOCD1,splice_region_variant,p.=,ENST00000452755,;SPOCD1,synonymous_variant,p.=,ENST00000360482,NM_144569.5;SPOCD1,synonymous_variant,p.=,ENST00000533231,NM_001281987.1;SPOCD1,synonymous_variant,p.=,ENST00000257100,NM_001281988.1;SPOCD1,intron_variant,,ENST00000528579,;SPOCD1,downstream_gene_variant,,ENST00000529396,;SPOCD1,downstream_gene_variant,,ENST00000528791,;SPOCD1,downstream_gene_variant,,ENST00000525930,;SPOCD1,non_coding_transcript_exon_variant,,ENST00000485944,;SPOCD1,non_coding_transcript_exon_variant,,ENST00000468720,;SPOCD1,non_coding_transcript_exon_variant,,ENST00000460061,;SPOCD1,non_coding_transcript_exon_variant,,ENST00000531039,;SPOCD1,intron_variant,,ENST00000473361,;SPOCD1,intron_variant,,ENST00000532604,; A ENST00000360482 Transcript synonymous_variant 2396/3960 2266/3651 756/1216 L Ctg/Ttg 1 -1 SPOCD1 HGNC HGNC:26338 protein_coding YES CCDS347.1 ENSP00000353670 Q6ZMY3 UPI000035E7DD NM_144569.5 10/16 hmmpanther:PTHR11477:SF18,hmmpanther:PTHR11477 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 31796595 31796595 G A 1 0 0 0 0 0 0 0 1 15431 956 33 3 3 SPOCD1 1 31796595 Silent SNP G C3N-00217_T 4790286 31796595 217159827 8 11778 AGO1 0 . GRCh38 1 35906956 35906956 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.1419G>T p.= p.R473R ENST00000373204 12/19 86 81 5 73 73 0 strelka-varscan-mutect AGO1,synonymous_variant,p.=,ENST00000373204,NM_012199.2;AGO1,synonymous_variant,p.=,ENST00000373206,;AGO1,3_prime_UTR_variant,,ENST00000635259,; T ENST00000373204 Transcript synonymous_variant 1632/13708 1419/2574 473/857 R cgG/cgT 1 1 AGO1 HGNC HGNC:3262 protein_coding YES CCDS398.1 ENSP00000362300 Q9UL18 UPI000012D07D NM_012199.2 12/19 hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891,Gene3D:3.40.50.2300,Pfam_domain:PF16487 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -11.34806 1 1 1 1 0 T 2 4 43 35906956 35906956 G T 1 0 0 0 0 0 0 0 1 464 1161 41 2 2 AGO1 1 35906956 Silent SNP G C3N-00217_T 4110361 35906956 213049466 9 11779 EPHA10 0 . GRCh38 1 37761756 37761756 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.499G>T p.Gly167Cys p.G167C ENST00000373048 3/17 185 95 90 118 118 0 strelka-varscan-mutect EPHA10,missense_variant,p.Gly167Cys,ENST00000373048,NM_001099439.1;EPHA10,missense_variant,p.Gly167Cys,ENST00000427468,;EPHA10,missense_variant,p.Gly167Cys,ENST00000319637,NM_173641.2; A ENST00000373048 Transcript missense_variant 499/5425 499/3027 167/1008 G/C Ggt/Tgt 1 -1 EPHA10 HGNC HGNC:19987 protein_coding YES CCDS41305.1 ENSP00000362139 Q5JZY3 UPI00001A41BD NM_001099439.1 deleterious(0) 3/17 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF258,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 37761756 37761756 C A 1 0 0 0 0 1 0 0 0 5013 623 22 2 2 EPHA10 1 37761756 Missense_Mutation SNP C C3N-00217_T 1854800 37761756 211194666 10 11780 MUTYH 0 . GRCh38 1 45332241 45332241 + Silent SNP C C A rs771290019 C3N-00217_T C3N-00217_N C C c.849G>T p.= p.G283G ENST00000372098 10/16 485 395 90 522 522 0 strelka-varscan-mutect MUTYH,synonymous_variant,p.=,ENST00000450313,NM_001128425.1;MUTYH,synonymous_variant,p.=,ENST00000372115,NM_001048171.1;MUTYH,synonymous_variant,p.=,ENST00000372098,NM_012222.2;MUTYH,synonymous_variant,p.=,ENST00000372104,NM_001293195.1;MUTYH,synonymous_variant,p.=,ENST00000372110,NM_001293190.1;MUTYH,synonymous_variant,p.=,ENST00000355498,NM_001293196.1,NM_001293192.1,NM_001048173.1;MUTYH,synonymous_variant,p.=,ENST00000354383,NM_001048172.1;MUTYH,synonymous_variant,p.=,ENST00000448481,NM_001293191.1;MUTYH,synonymous_variant,p.=,ENST00000456914,NM_001048174.1;MUTYH,synonymous_variant,p.=,ENST00000528013,;MUTYH,synonymous_variant,p.=,ENST00000435155,;MUTYH,synonymous_variant,p.=,ENST00000412971,;MUTYH,synonymous_variant,p.=,ENST00000529892,;MUTYH,intron_variant,,ENST00000529984,;MUTYH,intron_variant,,ENST00000488731,;MUTYH,intron_variant,,ENST00000531105,;HPDL,downstream_gene_variant,,ENST00000334815,NM_032756.2;MUTYH,downstream_gene_variant,,ENST00000483127,;MUTYH,synonymous_variant,p.=,ENST00000467459,;MUTYH,3_prime_UTR_variant,,ENST00000481571,;MUTYH,3_prime_UTR_variant,,ENST00000475516,;MUTYH,3_prime_UTR_variant,,ENST00000533178,;MUTYH,3_prime_UTR_variant,,ENST00000467940,;MUTYH,3_prime_UTR_variant,,ENST00000461495,;MUTYH,3_prime_UTR_variant,,ENST00000470256,;MUTYH,non_coding_transcript_exon_variant,,ENST00000462388,;MUTYH,non_coding_transcript_exon_variant,,ENST00000478796,;MUTYH,non_coding_transcript_exon_variant,,ENST00000466231,;MUTYH,downstream_gene_variant,,ENST00000483642,;MUTYH,downstream_gene_variant,,ENST00000481139,;MUTYH,downstream_gene_variant,,ENST00000492494,;MUTYH,downstream_gene_variant,,ENST00000479746,;MUTYH,downstream_gene_variant,,ENST00000476789,;MUTYH,upstream_gene_variant,,ENST00000482094,;MUTYH,downstream_gene_variant,,ENST00000462387,;MUTYH,downstream_gene_variant,,ENST00000485484,;MUTYH,downstream_gene_variant,,ENST00000534453,;MUTYH,downstream_gene_variant,,ENST00000525160,;MUTYH,downstream_gene_variant,,ENST00000474703,;MUTYH,upstream_gene_variant,,ENST00000485271,; A ENST00000372098 Transcript synonymous_variant 983/1839 849/1641 283/546 G ggG/ggT rs771290019 1 -1 MUTYH HGNC HGNC:7527 protein_coding YES CCDS520.1 ENSP00000361170 Q9UIF7 E5KP26 UPI000006EB4F NM_012222.2 10/16 hmmpanther:PTHR10359,Gene3D:1.10.1670.10,SMART_domains:SM00478,Superfamily_domains:SSF48150 LOW 1 SNV 1 1 PASS rs771290019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 45332241 45332241 C A 1 0 0 0 0 0 0 0 1 9990 610 22 2 2 MUTYH 1 45332241 Silent SNP C C3N-00217_T 7570485 45332241 203624181 11 11781 FAM151A 0 . GRCh38 1 54611726 54611726 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.820C>A p.Gln274Lys p.Q274K ENST00000302250 6/8 136 107 29 121 121 0 strelka-varscan-mutect FAM151A,missense_variant,p.Gln274Lys,ENST00000302250,NM_176782.2;FAM151A,missense_variant,p.Gln274Lys,ENST00000371304,;ACOT11,intron_variant,,ENST00000371316,NM_015547.3;ACOT11,downstream_gene_variant,,ENST00000343744,NM_147161.3;ACOT11,downstream_gene_variant,,ENST00000481208,; T ENST00000302250 Transcript missense_variant 981/2005 820/1758 274/585 Q/K Cag/Aag 1 -1 FAM151A HGNC HGNC:25032 protein_coding YES CCDS594.1 ENSP00000306888 Q8WW52 UPI000003776D NM_176782.2 deleterious(0) 6/8 Pfam_domain:PF10223,hmmpanther:PTHR21184,hmmpanther:PTHR21184:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 54611726 54611726 G T 1 0 0 0 0 1 0 0 0 5308 1328 46 2 2 FAM151A 1 54611726 Missense_Mutation SNP G C3N-00217_T 9279485 54611726 194344696 12 11782 MROH7 0 . GRCh38 1 54701253 54701253 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.3216G>T p.= p.R1072R ENST00000421030 19/24 80 70 10 82 82 0 strelka-varscan-mutect MROH7,synonymous_variant,p.=,ENST00000421030,NM_001039464.3;MROH7,synonymous_variant,p.=,ENST00000409996,NM_001291332.1;MROH7,downstream_gene_variant,,ENST00000339553,;MROH7,downstream_gene_variant,,ENST00000395690,;MROH7-TTC4,synonymous_variant,p.=,ENST00000414150,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000606515,;MROH7,3_prime_UTR_variant,,ENST00000413188,;MROH7,3_prime_UTR_variant,,ENST00000422659,;MROH7,3_prime_UTR_variant,,ENST00000440047,;MROH7,3_prime_UTR_variant,,ENST00000440217,;MROH7,non_coding_transcript_exon_variant,,ENST00000371287,;MROH7-TTC4,non_coding_transcript_exon_variant,,ENST00000460155,;MROH7,downstream_gene_variant,,ENST00000438846,; T ENST00000421030 Transcript synonymous_variant 3501/4329 3216/3972 1072/1323 R cgG/cgT 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 19/24 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF17,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 2 1 PASS rs1340940404 . 0 208 2 0 0 0 0 0 -19.99532 1 1 1 1 0 T 2 4 43 54701253 54701253 G T 1 0 0 0 0 0 0 0 1 9747 1219 43 2 2 MROH7 1 54701253 Silent SNP G C3N-00217_T 89527 54701253 194255169 13 11783 FPGT 0 . GRCh38 1 74205431 74205431 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.1423A>G p.Arg475Gly p.R475G ENST00000370898 4/4 141 115 26 248 248 0 strelka-varscan-mutect FPGT,missense_variant,p.Arg475Gly,ENST00000370898,NM_003838.4;FPGT,missense_variant,p.Arg208Gly,ENST00000534056,NM_001199328.2;FPGT,3_prime_UTR_variant,,ENST00000370894,NM_001199329.2;FPGT-TNNI3K,intron_variant,,ENST00000370895,;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,intron_variant,,ENST00000370899,NM_001199327.1;FPGT-TNNI3K,intron_variant,,ENST00000370893,;FPGT-TNNI3K,intron_variant,,ENST00000534632,;FPGT,downstream_gene_variant,,ENST00000467578,;FPGT,downstream_gene_variant,,ENST00000482102,;FPGT,downstream_gene_variant,,ENST00000472069,;FPGT,intron_variant,,ENST00000524915,;FPGT-TNNI3K,intron_variant,,ENST00000533006,;FPGT,downstream_gene_variant,,ENST00000529485,; G ENST00000370898 Transcript missense_variant 1451/3254 1423/1824 475/607 R/G Aga/Gga 1 1 FPGT HGNC HGNC:3825 protein_coding YES CCDS663.2 ENSP00000359935 A0A0A0MRP2 UPI0003348FC3 NM_003838.4 tolerated(1) 4/4 Pfam_domain:PF07959,PIRSF_domain:PIRSF036640,hmmpanther:PTHR15045 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 74205431 74205431 A G 1 0 0 0 0 1 0 0 0 5903 412 15 5 5 FPGT 1 74205431 Missense_Mutation SNP A C3N-00217_T 19504178 74205431 174750991 14 11784 ERICH3 0 . GRCh38 1 74620883 74620883 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.851A>G p.His284Arg p.H284R ENST00000326665 8/15 71 45 26 108 108 0 strelka-varscan-mutect ERICH3,missense_variant,p.His284Arg,ENST00000326665,NM_001002912.4;ERICH3,missense_variant,p.His87Arg,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,;ERICH3,3_prime_UTR_variant,,ENST00000479666,; C ENST00000326665 Transcript missense_variant 1070/7159 851/4593 284/1530 H/R cAt/cGt 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 tolerated(0.1) 8/15 hmmpanther:PTHR23034 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 74620883 74620883 T C 1 0 0 0 0 1 0 0 0 5083 1464 51 5 5 ERICH3 1 74620883 Missense_Mutation SNP T C3N-00217_T 415452 74620883 174335539 15 11785 ADGRL2 0 . GRCh38 1 81951085 81951085 + Missense_Mutation SNP C C A rs750558783 C3N-00217_T C3N-00217_N C C c.1560C>A p.Asn520Lys p.N520K ENST00000319517 7/20 119 108 11 146 146 0 strelka-varscan-mutect ADGRL2,missense_variant,p.Asn520Lys,ENST00000370728,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370730,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370717,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000627151,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370715,NM_001297705.1;ADGRL2,missense_variant,p.Asn520Lys,ENST00000319517,NM_012302.3;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370713,NM_001297706.1;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370725,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370723,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000370727,;ADGRL2,missense_variant,p.Asn458Lys,ENST00000370721,;ADGRL2,missense_variant,p.Asn520Lys,ENST00000359929,NM_001297704.1;ADGRL2,missense_variant,p.Asn388Lys,ENST00000449420,;ADGRL2,intron_variant,,ENST00000469377,;ADGRL2,upstream_gene_variant,,ENST00000468283,; A ENST00000319517 Transcript missense_variant 1776/5479 1560/4212 520/1403 N/K aaC/aaA rs750558783 1 1 ADGRL2 HGNC HGNC:18582 protein_coding YES CCDS689.1 ENSP00000322270 O95490 UPI000005046B NM_012302.3 deleterious(0.01) 7/20 PROSITE_profiles:PS50227,hmmpanther:PTHR12011:SF61,hmmpanther:PTHR12011,Pfam_domain:PF02793,SMART_domains:SM00008,Superfamily_domains:SSF111418 MODERATE 1 SNV 1 1 PASS rs750558783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 81951085 81951085 C A 1 0 0 0 0 1 0 0 0 376 564 20 2 2 ADGRL2 1 81951085 Missense_Mutation SNP C C3N-00217_T 7330202 81951085 167005337 16 11786 LPAR3 0 . GRCh38 1 84813880 84813880 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1028G>T p.Ser343Ile p.S343I ENST00000440886 2/2 116 75 41 139 139 0 strelka-varscan-mutect LPAR3,missense_variant,p.Ser343Ile,ENST00000440886,;LPAR3,missense_variant,p.Ser343Ile,ENST00000370611,NM_012152.2;LPAR3,downstream_gene_variant,,ENST00000491034,; A ENST00000440886 Transcript missense_variant 1067/3345 1028/1062 343/353 S/I aGc/aTc 1 -1 LPAR3 HGNC HGNC:14298 protein_coding YES CCDS700.1 ENSP00000395389 Q9UBY5 UPI000003CAC0 tolerated(0.25) 2/2 PD334079,Prints_domain:PR01560,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF21 MODERATE 1 SNV 1 1 PASS rs962900293 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 84813880 84813880 C A 1 0 0 0 0 1 0 0 0 8809 797 28 2 2 LPAR3 1 84813880 Missense_Mutation SNP C C3N-00217_T 2862795 84813880 164142542 17 11787 EVI5 0 . GRCh38 1 92607607 92607607 + Missense_Mutation SNP G G A C3N-00217_T C3N-00217_N G G c.1933C>T p.Arg645Cys p.R645C ENST00000540033 16/19 66 42 24 134 134 0 strelka-varscan-mutect EVI5,missense_variant,p.Arg645Cys,ENST00000540033,NM_001308248.1;EVI5,missense_variant,p.Arg634Cys,ENST00000370331,NM_005665.4;EVI5,missense_variant,p.Arg252Cys,ENST00000491940,;EVI5,non_coding_transcript_exon_variant,,ENST00000492513,;EVI5,downstream_gene_variant,,ENST00000468580,; A ENST00000540033 Transcript missense_variant 1943/7436 1933/2466 645/821 R/C Cgt/Tgt COSM1344921,COSM4783216 1 -1 EVI5 HGNC HGNC:3501 protein_coding YES CCDS76179.1 ENSP00000440826 O60447 UPI0002065028 NM_001308248.1 deleterious(0) 16/19 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1311854813 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 92607607 92607607 G A 1 0 0 0 0 1 0 0 0 5156 1087 38 1 1 EVI5 1 92607607 Missense_Mutation SNP G C3N-00217_T 7793727 92607607 156348815 18 11788 SNX7 0 . GRCh38 1 98685023 98685024 + Frame_Shift_Ins INS - - TT novel C3N-00217_T C3N-00217_N - - c.320_321dupTT p.Thr108LeufsTer4 p.T108Lfs*4 ENST00000306121 2/9 34 24 10 50 50 0 sindel-varindel SNX7,frameshift_variant,p.Thr108LeufsTer4,ENST00000306121,NM_015976.4;SNX7,frameshift_variant,p.Thr108LeufsTer4,ENST00000529992,NM_152238.3;SNX7,frameshift_variant,p.Thr44LeufsTer4,ENST00000454199,;SNX7,3_prime_UTR_variant,,ENST00000528824,; TT ENST00000306121 Transcript frameshift_variant 328-329/1734 319-320/1356 107/451 V/VX gtt/gTTtt 1 1 SNX7 HGNC HGNC:14971 protein_coding YES CCDS755.2 ENSP00000304429 Q9UNH6 UPI0000205396 NM_015976.4 2/9 PROSITE_profiles:PS50195,hmmpanther:PTHR10555:SF21,hmmpanther:PTHR10555,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268 HIGH 1 insertion 1 2 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 TT 7 5 43 98685023 98685023 - TT 1 0 1 1 0 0 0 0 0 15228 1377 48 0 0 SNX7 1 98685023 Frame_Shift_Ins INS - C3N-00217_T 6077416 98685023 150271399 19 11789 PSRC1 0 . GRCh38 1 109281915 109281915 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.223G>A p.Glu75Lys p.E75K ENST00000369909 4/8 41 26 15 39 39 0 strelka-varscan-mutect PSRC1,missense_variant,p.Glu75Lys,ENST00000409138,;PSRC1,missense_variant,p.Glu75Lys,ENST00000369909,NM_001032291.2,NM_032636.7;PSRC1,missense_variant,p.Glu75Lys,ENST00000409267,;PSRC1,missense_variant,p.Glu75Lys,ENST00000369907,;PSRC1,missense_variant,p.Glu75Lys,ENST00000369903,;PSRC1,missense_variant,p.Glu75Lys,ENST00000369904,NM_001005290.3;PSRC1,missense_variant,p.Glu75Lys,ENST00000418914,;PSRC1,missense_variant,p.Glu75Lys,ENST00000429031,;PSRC1,upstream_gene_variant,,ENST00000474126,;PSRC1,non_coding_transcript_exon_variant,,ENST00000492431,;PSRC1,non_coding_transcript_exon_variant,,ENST00000459765,;PSRC1,non_coding_transcript_exon_variant,,ENST00000471740,; T ENST00000369909 Transcript missense_variant 367/1742 223/1002 75/333 E/K Gag/Aag 1 -1 PSRC1 HGNC HGNC:24472 protein_coding YES CCDS797.1 ENSP00000358925 Q6PGN9 A0A024R099 UPI0000073C97 NM_001032291.2,NM_032636.7 deleterious(0) 4/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF1,Pfam_domain:PF15259 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 109281915 109281915 C T 1 0 0 0 0 1 0 0 0 12871 864 30 3 3 PSRC1 1 109281915 Missense_Mutation SNP C C3N-00217_T 10596892 109281915 139674507 20 11790 KCNA10 0 . GRCh38 1 110517308 110517308 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.1480A>G p.Thr494Ala p.T494A ENST00000369771 1/1 102 80 22 145 145 0 strelka-varscan-mutect KCNA10,missense_variant,p.Thr494Ala,ENST00000369771,NM_005549.2; C ENST00000369771 Transcript missense_variant 1868/1959 1480/1536 494/511 T/A Aca/Gca 1 -1 KCNA10 HGNC HGNC:6219 protein_coding YES CCDS826.1 ENSP00000358786 Q16322 UPI0000071B2B NM_005549.2 tolerated_low_confidence(0.35) 1/1 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF44 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 110517308 110517308 T C 1 0 0 0 0 1 0 0 0 7918 1696 59 5 5 KCNA10 1 110517308 Missense_Mutation SNP T C3N-00217_T 1235393 110517308 138439114 21 11791 PDE4DIP 0 . GRCh38 1 149005004 149005004 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.3982G>A p.Glu1328Lys p.E1328K ENST00000369356 27/44 200 172 28 148 148 0 varscan-mutect PDE4DIP,missense_variant,p.Glu1464Lys,ENST00000585156,;PDE4DIP,missense_variant,p.Glu1328Lys,ENST00000369356,NM_001198834.3;PDE4DIP,missense_variant,p.Glu1464Lys,ENST00000524974,;PDE4DIP,missense_variant,p.Glu1328Lys,ENST00000369354,NM_014644.5;PDE4DIP,missense_variant,p.Glu1284Lys,ENST00000618462,NM_001198832.2;RP4-791M13.5,downstream_gene_variant,,ENST00000531288,;PDE4DIP,intron_variant,,ENST00000530062,;PDE4DIP,upstream_gene_variant,,ENST00000479369,; A ENST00000369356 Transcript missense_variant 4273/8307 3982/7089 1328/2362 E/K Gag/Aag 1 1 PDE4DIP HGNC HGNC:15580 protein_coding YES CCDS72892.1 ENSP00000358363 A0A0A0MRM1 UPI000292EFC6 NM_001198834.3 tolerated(0.85) 27/44 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 43 149005004 149005004 G A 1 0 0 0 0 1 0 0 0 11731 1291 45 3 3 PDE4DIP 1 149005004 Missense_Mutation SNP G C3N-00217_T 38487696 149005004 99951418 22 11792 OTUD7B 0 . GRCh38 1 149944805 149944805 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.1584G>C p.Lys528Asn p.K528N ENST00000581312 12/12 442 387 55 227 227 0 strelka-mutect OTUD7B,missense_variant,p.Lys528Asn,ENST00000581312,NM_020205.3;OTUD7B,downstream_gene_variant,,ENST00000417191,; G ENST00000581312 Transcript missense_variant 1879/8872 1584/2532 528/843 K/N aaG/aaC 1 -1 OTUD7B HGNC HGNC:16683 protein_coding YES CCDS72903.1 ENSP00000462729 Q6GQQ9 UPI000020415D NM_020205.3 deleterious(0) 12/12 hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 149944805 149944805 C G 1 0 0 0 0 1 0 0 0 11388 680 24 4 4 OTUD7B 1 149944805 Missense_Mutation SNP C C3N-00217_T 939801 149944805 99011617 23 11793 ADAMTSL4 0 . GRCh38 1 150557212 150557212 + Missense_Mutation SNP C C A rs768995007 C3N-00217_T C3N-00217_N C C c.1993C>A p.Leu665Ile p.L665I ENST00000369039 13/20 312 249 63 124 124 0 strelka-varscan-mutect ADAMTSL4,missense_variant,p.Leu665Ile,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,missense_variant,p.Leu642Ile,ENST00000271643,NM_019032.5;ADAMTSL4,missense_variant,p.Leu642Ile,ENST00000369038,;ADAMTSL4,missense_variant,p.Leu642Ile,ENST00000369041,NM_025008.4;RP11-54A4.2,intron_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,;ADAMTSL4,upstream_gene_variant,,ENST00000489159,; A ENST00000369039 Transcript missense_variant 2282/4319 1993/3294 665/1097 L/I Ctc/Atc rs768995007 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 tolerated(0.08) 13/20 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs768995007 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 150557212 150557212 C A 1 0 0 0 0 1 0 0 0 321 681 24 2 2 ADAMTSL4 1 150557212 Missense_Mutation SNP C C3N-00217_T 612407 150557212 98399210 24 11794 ADAMTSL4 0 . GRCh38 1 150559457 150559457 + Silent SNP C C G novel C3N-00217_T C3N-00217_N C C c.3003C>G p.= p.P1001P ENST00000369039 18/20 306 241 65 138 138 0 strelka-varscan-mutect ADAMTSL4,synonymous_variant,p.=,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,synonymous_variant,p.=,ENST00000271643,NM_019032.5;ADAMTSL4,synonymous_variant,p.=,ENST00000369038,;ADAMTSL4,downstream_gene_variant,,ENST00000369041,NM_025008.4;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;RP11-54A4.2,upstream_gene_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4,non_coding_transcript_exon_variant,,ENST00000489159,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,; G ENST00000369039 Transcript synonymous_variant 3292/4319 3003/3294 1001/1097 P ccC/ccG 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 18/20 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 150559457 150559457 C G 1 0 0 0 0 0 0 0 1 321 668 24 4 4 ADAMTSL4 1 150559457 Silent SNP C C3N-00217_T 2245 150559457 98396965 25 11795 ADAMTSL4 0 . GRCh38 1 150560083 150560083 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.3181C>G p.Pro1061Ala p.P1061A ENST00000369039 20/20 790 645 145 325 325 0 strelka-varscan-mutect ADAMTSL4,missense_variant,p.Pro1061Ala,ENST00000369039,NM_001288608.1,NM_001288607.1;ADAMTSL4,missense_variant,p.Pro1038Ala,ENST00000271643,NM_019032.5;ADAMTSL4,missense_variant,p.Pro1038Ala,ENST00000369038,;ADAMTSL4,downstream_gene_variant,,ENST00000369041,NM_025008.4;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000617352,;RP11-54A4.2,upstream_gene_variant,,ENST00000442435,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000369035,;ADAMTSL4,non_coding_transcript_exon_variant,,ENST00000489159,;ADAMTSL4-AS1,downstream_gene_variant,,ENST00000615012,; G ENST00000369039 Transcript missense_variant 3470/4319 3181/3294 1061/1097 P/A Cca/Gca 1 1 ADAMTSL4 HGNC HGNC:19706 protein_coding YES CCDS72908.1 ENSP00000358035 Q6UY14 UPI0001AE7902 NM_001288608.1,NM_001288607.1 tolerated(0.28) 20/20 PROSITE_profiles:PS50900,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF144,Pfam_domain:PF08686 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 150560083 150560083 C G 1 0 0 0 0 1 0 0 0 321 855 30 4 4 ADAMTSL4 1 150560083 Missense_Mutation SNP C C3N-00217_T 626 150560083 98396339 26 11796 ENSA 0 . GRCh38 1 150627523 150627523 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.127A>T p.Ser43Cys p.S43C ENST00000339643 2/5 441 277 164 232 232 0 strelka-varscan-mutect ENSA,missense_variant,p.Ser43Cys,ENST00000271690,NM_207044.1;ENSA,missense_variant,p.Ser43Cys,ENST00000356527,;ENSA,missense_variant,p.Ser43Cys,ENST00000369014,NM_004436.2;ENSA,missense_variant,p.Ser39Cys,ENST00000513281,NM_207047.1;ENSA,missense_variant,p.Ser43Cys,ENST00000369016,;ENSA,missense_variant,p.Ser43Cys,ENST00000503345,;ENSA,missense_variant,p.Ser39Cys,ENST00000361532,NM_207046.1;ENSA,missense_variant,p.Ser39Cys,ENST00000361631,NM_207045.1;ENSA,missense_variant,p.Ser43Cys,ENST00000362052,NM_207168.1;ENSA,missense_variant,p.Ser43Cys,ENST00000339643,NM_207042.1;ENSA,missense_variant,p.Ser43Cys,ENST00000503241,NM_207043.1;ENSA,non_coding_transcript_exon_variant,,ENST00000354702,;ENSA,intron_variant,,ENST00000505321,;ENSA,missense_variant,p.Ser43Cys,ENST00000509582,; A ENST00000339643 Transcript missense_variant 233/633 127/414 43/137 S/C Agc/Tgc 1 -1 ENSA HGNC HGNC:3360 protein_coding YES CCDS959.1 ENSP00000341743 O43768 UPI00001C1A8D NM_207042.1 deleterious(0.02) 2/5 hmmpanther:PTHR10358,hmmpanther:PTHR10358:SF5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 150627523 150627523 T A 1 0 0 0 0 1 0 0 0 4981 1609 56 4 4 ENSA 1 150627523 Missense_Mutation SNP T C3N-00217_T 67440 150627523 98328899 27 11797 CHRNB2 0 . GRCh38 1 154572129 154572129 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1306G>T p.Asp436Tyr p.D436Y ENST00000368476 5/6 132 83 49 47 47 0 strelka-varscan-mutect CHRNB2,missense_variant,p.Asp436Tyr,ENST00000368476,NM_000748.2;CHRNB2,missense_variant,p.Asp438Tyr,ENST00000637900,;CHRNB2,upstream_gene_variant,,ENST00000635876,;CHRNB2,missense_variant,p.Asp436Tyr,ENST00000636034,;CHRNB2,downstream_gene_variant,,ENST00000636695,; T ENST00000368476 Transcript missense_variant 1570/5867 1306/1509 436/502 D/Y Gac/Tac 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 deleterious(0) 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF80,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 154572129 154572129 G T 1 0 0 0 0 1 0 0 0 3151 942 33 2 2 CHRNB2 1 154572129 Missense_Mutation SNP G C3N-00217_T 3944606 154572129 94384293 28 11798 TRIM46 0 . GRCh38 1 155181923 155181923 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.1660G>A p.Ala554Thr p.A554T ENST00000334634 9/10 384 264 120 196 196 0 strelka-varscan-mutect TRIM46,missense_variant,p.Ala512Thr,ENST00000392451,NM_001256600.1;TRIM46,missense_variant,p.Ala531Thr,ENST00000368382,NM_001256599.1;TRIM46,missense_variant,p.Ala541Thr,ENST00000611379,NM_001256601.1;TRIM46,missense_variant,p.Ala554Thr,ENST00000334634,NM_025058.4;TRIM46,missense_variant,p.Ala428Thr,ENST00000545012,NM_001282378.1;TRIM46,missense_variant,p.Ala554Thr,ENST00000368383,;MUC1,downstream_gene_variant,,ENST00000611571,;TRIM46,downstream_gene_variant,,ENST00000368385,NM_001282379.1;MUC1,downstream_gene_variant,,ENST00000612778,NM_001204286.1;MUC1,downstream_gene_variant,,ENST00000620103,NM_001204285.1;TRIM46,downstream_gene_variant,,ENST00000543729,;MUC1,downstream_gene_variant,,ENST00000462215,;MUC1,downstream_gene_variant,,ENST00000457295,;MUC1,downstream_gene_variant,,ENST00000462317,;MUC1,downstream_gene_variant,,ENST00000338684,NM_001204289.1,NM_001204291.1;MUC1,downstream_gene_variant,,ENST00000610359,NM_001204292.1;MUC1,downstream_gene_variant,,ENST00000614519,;MUC1,downstream_gene_variant,,ENST00000368392,NM_001018016.2,NM_001204288.1;MUC1,downstream_gene_variant,,ENST00000611577,;MUC1,downstream_gene_variant,,ENST00000615517,NM_001204295.1;MUC1,downstream_gene_variant,,ENST00000368393,NM_001204293.1;MUC1,downstream_gene_variant,,ENST00000438413,NM_001204290.1;MUC1,downstream_gene_variant,,ENST00000337604,NM_001204287.1,NM_002456.5;MUC1,downstream_gene_variant,,ENST00000368390,NM_001018017.2;MUC1,downstream_gene_variant,,ENST00000368398,NM_001204294.1;MUC1,downstream_gene_variant,,ENST00000485118,;MUC1,downstream_gene_variant,,ENST00000343256,NM_001044390.2,NM_001204296.1;MUC1,downstream_gene_variant,,ENST00000471283,NM_001044393.2;MUC1,downstream_gene_variant,,ENST00000368389,NM_001204297.1;MUC1,downstream_gene_variant,,ENST00000342482,;MUC1,downstream_gene_variant,,ENST00000368396,NM_001044392.2,NM_001044391.2;TRIM46,non_coding_transcript_exon_variant,,ENST00000468878,;TRIM46,non_coding_transcript_exon_variant,,ENST00000474430,;TRIM46,downstream_gene_variant,,ENST00000464760,;RP11-201K10.3,intron_variant,,ENST00000473363,;MUC1,downstream_gene_variant,,ENST00000610468,;MUC1,downstream_gene_variant,,ENST00000468978,;MUC1,downstream_gene_variant,,ENST00000498431,;MUC1,downstream_gene_variant,,ENST00000467134,; A ENST00000334634 Transcript missense_variant 1660/3061 1660/2280 554/759 A/T Gca/Aca 1 1 TRIM46 HGNC HGNC:19019 protein_coding YES CCDS1097.1 ENSP00000334657 Q7Z4K8 UPI000022B316 NM_025058.4 tolerated(0.43) 9/10 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF27,hmmpanther:PTHR24103,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 155181923 155181923 G A 1 0 0 0 0 1 0 0 0 17011 971 34 3 3 TRIM46 1 155181923 Missense_Mutation SNP G C3N-00217_T 609794 155181923 93774499 29 11799 BCAN 0 . GRCh38 1 156647081 156647081 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.372G>T p.= p.L124L ENST00000329117 3/14 112 44 68 79 79 0 strelka-varscan-mutect BCAN,synonymous_variant,p.=,ENST00000329117,NM_021948.4;BCAN,synonymous_variant,p.=,ENST00000361588,NM_198427.1;BCAN,synonymous_variant,p.=,ENST00000457777,;BCAN,synonymous_variant,p.=,ENST00000441358,;BCAN,intron_variant,,ENST00000424639,;RP11-284F21.7,non_coding_transcript_exon_variant,,ENST00000448869,;RP11-284F21.10,upstream_gene_variant,,ENST00000605886,;BCAN,synonymous_variant,p.=,ENST00000479949,;BCAN,upstream_gene_variant,,ENST00000491823,; T ENST00000329117 Transcript synonymous_variant 708/3466 372/2736 124/911 L ctG/ctT 1 1 BCAN HGNC HGNC:23059 protein_coding YES CCDS1149.1 ENSP00000331210 Q96GW7 UPI000006F0E9 NM_021948.4 3/14 PROSITE_profiles:PS50835,hmmpanther:PTHR22804,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 156647081 156647081 G T 1 0 0 0 0 0 0 0 1 1492 1277 45 2 2 BCAN 1 156647081 Silent SNP G C3N-00217_T 1465158 156647081 92309341 30 11800 CD1C 0 . GRCh38 1 158291345 158291345 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.273C>A p.Tyr91Ter p.Y91* ENST00000368170 2/6 253 118 135 226 225 1 strelka-varscan-mutect CD1C,stop_gained,p.Tyr91Ter,ENST00000368170,NM_001765.2;CD1C,stop_gained,p.Tyr26Ter,ENST00000443761,; A ENST00000368170 Transcript stop_gained 552/1435 273/1002 91/333 Y/* taC/taA 1 1 CD1C HGNC HGNC:1636 protein_coding YES CCDS1175.1 ENSP00000357152 P29017 UPI000013DF78 NM_001765.2 2/6 hmmpanther:PTHR16675:SF155,hmmpanther:PTHR16675,Pfam_domain:PF16497,Gene3D:3.30.500.10,Superfamily_domains:SSF54452 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 158291345 158291345 C A 1 0 0 0 0 0 1 0 0 2679 518 18 2 2 CD1C 1 158291345 Nonsense_Mutation SNP C C3N-00217_T 1644264 158291345 90665077 31 11801 CADM3 0 . GRCh38 1 159200901 159200901 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.1278C>T p.= p.D426D ENST00000368124 10/10 77 68 9 65 64 1 strelka-varscan-mutect CADM3,synonymous_variant,p.=,ENST00000368125,NM_001127173.1;CADM3,synonymous_variant,p.=,ENST00000368124,NM_021189.3;ACKR1,upstream_gene_variant,,ENST00000537147,;ACKR1,upstream_gene_variant,,ENST00000368122,NM_002036.3;ACKR1,upstream_gene_variant,,ENST00000368121,NM_001122951.2;CADM3,downstream_gene_variant,,ENST00000416746,;ACKR1,upstream_gene_variant,,ENST00000435307,;CADM3-AS1,non_coding_transcript_exon_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; T ENST00000368124 Transcript synonymous_variant 1435/2546 1278/1299 426/432 D gaC/gaT 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 10/10 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -19.35856 0.9999999 1 1 1 0 T 2 4 43 159200901 159200901 C T 1 0 0 0 0 0 0 0 1 2258 477 17 3 3 CADM3 1 159200901 Silent SNP C C3N-00217_T 909556 159200901 89755521 32 11802 OR10J3 0 . GRCh38 1 159314422 159314422 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.238C>A p.Pro80Thr p.P80T ENST00000332217 1/1 411 365 46 317 316 1 strelka-varscan-mutect OR10J3,missense_variant,p.Pro80Thr,ENST00000332217,NM_001004467.1; T ENST00000332217 Transcript missense_variant 238/990 238/990 80/329 P/T Ccc/Acc COSM1688897 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 159314422 159314422 G T 1 0 0 0 0 1 0 0 0 10988 1174 41 2 2 OR10J3 1 159314422 Missense_Mutation SNP G C3N-00217_T 113521 159314422 89642000 33 11803 KCNJ9 0 . GRCh38 1 160084834 160084834 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.804C>T p.= p.D268D ENST00000368088 2/3 105 37 68 71 71 0 strelka-varscan-mutect KCNJ9,synonymous_variant,p.=,ENST00000368088,NM_004983.2; T ENST00000368088 Transcript synonymous_variant 1046/4170 804/1182 268/393 D gaC/gaT 1 1 KCNJ9 HGNC HGNC:6270 protein_coding YES CCDS1194.1 ENSP00000357067 Q92806 UPI000013E1B3 NM_004983.2 2/3 hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF17,Pfam_domain:PF01007,PIRSF_domain:PIRSF005465,Gene3D:2.60.40.1400,Superfamily_domains:SSF81296,Prints_domain:PR01329 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 160084834 160084834 C T 1 0 0 0 0 0 0 0 1 7974 535 19 1 1 KCNJ9 1 160084834 Silent SNP C C3N-00217_T 770412 160084834 88871588 34 11804 OLFML2B 0 . GRCh38 1 162000265 162000265 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.800C>A p.Pro267His p.P267H ENST00000367940 5/8 269 122 147 201 201 0 strelka-varscan-mutect OLFML2B,missense_variant,p.Pro266His,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Pro267His,ENST00000367940,NM_001297713.1; T ENST00000367940 Transcript missense_variant 1010/2685 800/2256 267/751 P/H cCc/cAc 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 tolerated(0.74) 5/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37 MODERATE 1 SNV 2 1 PASS rs1468140412 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 162000265 162000265 G T 1 0 0 0 0 1 0 0 0 10933 1232 43 2 2 OLFML2B 1 162000265 Missense_Mutation SNP G C3N-00217_T 1915431 162000265 86956157 35 11805 F5 0 . GRCh38 1 169541130 169541130 + Silent SNP G G C novel C3N-00217_T C3N-00217_N G G c.3960C>G p.= p.P1320P ENST00000367797 13/25 593 550 43 388 388 0 varscan-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4; C ENST00000367797 Transcript synonymous_variant 4162/7024 3960/6675 1320/2224 P ccC/ccG 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 13/25 PIRSF_domain:PIRSF000354 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 169541130 169541130 G C 1 0 0 0 0 0 0 0 1 5216 1335 47 4 4 F5 1 169541130 Silent SNP G C3N-00217_T 7540865 169541130 79415292 36 11806 F5 0 . GRCh38 1 169541265 169541265 + Silent SNP G G C novel C3N-00217_T C3N-00217_N G G c.3825C>G p.= p.P1275P ENST00000367797 13/25 365 225 140 310 310 0 strelka-varscan-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4; C ENST00000367797 Transcript synonymous_variant 4027/7024 3825/6675 1275/2224 P ccC/ccG 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 13/25 PIRSF_domain:PIRSF000354 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 169541265 169541265 G C 1 0 0 0 0 0 0 0 1 5216 1219 43 4 4 F5 1 169541265 Silent SNP G C3N-00217_T 135 169541265 79415157 37 11807 SLC9C2 0 . GRCh38 1 173576685 173576685 + Missense_Mutation SNP G G T rs540891244 C3N-00217_T C3N-00217_N G G c.878C>A p.Pro293Gln p.P293Q ENST00000367714 8/28 112 100 12 99 99 0 strelka-varscan-mutect SLC9C2,missense_variant,p.Pro293Gln,ENST00000367714,NM_178527.3;RP3-436N22.3,intron_variant,,ENST00000431459,;SLC9C2,non_coding_transcript_exon_variant,,ENST00000466087,; T ENST00000367714 Transcript missense_variant 1301/4428 878/3375 293/1124 P/Q cCg/cAg rs540891244,COSM378899 1 -1 SLC9C2 HGNC HGNC:28664 protein_coding YES CCDS1308.1 ENSP00000356687 Q5TAH2 UPI0000197379 NM_178527.3 deleterious(0) 8/28 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF91,Pfam_domain:PF00999 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs540891244 . 0 205 3 2 0 0 0 0 -18.34569 0.9999873 1 1 1 0 T 3 4 43 173576685 173576685 G T 1 0 0 0 0 1 0 0 0 15007 1116 39 1 1 SLC9C2 1 173576685 Missense_Mutation SNP G C3N-00217_T 4035420 173576685 75379737 38 11808 TNN 0 . GRCh38 1 175098516 175098516 + Silent SNP G G T rs769031710 C3N-00217_T C3N-00217_N G G c.2040G>T p.= p.P680P ENST00000239462 9/19 477 433 44 296 295 1 strelka-varscan-mutect TNN,synonymous_variant,p.=,ENST00000239462,NM_022093.1;TNN,intron_variant,,ENST00000621086,;TNN,intron_variant,,ENST00000622870,; T ENST00000239462 Transcript synonymous_variant 2153/5008 2040/3900 680/1299 P ccG/ccT rs769031710,COSM4534032 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 9/19 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 LOW 1 SNV 2 0,1 1 PASS rs769031710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 175098516 175098516 G T 1 0 0 0 0 0 0 0 1 16796 1103 39 1 1 TNN 1 175098516 Silent SNP G C3N-00217_T 1521831 175098516 73857906 39 11809 PAPPA2 0 . GRCh38 1 176557063 176557063 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.741C>T p.= p.S247S ENST00000367662 2/23 454 397 57 272 271 1 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2;PAPPA2,synonymous_variant,p.=,ENST00000367661,NM_021936.2;PAPPA2,downstream_gene_variant,,ENST00000486075,;PAPPA2,downstream_gene_variant,,ENST00000493665,; T ENST00000367662 Transcript synonymous_variant 1905/9691 741/5376 247/1791 S tcC/tcT 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 2/23 Gene3D:2.60.120.200,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 176557063 176557063 C T 1 0 0 0 0 0 0 0 1 11513 668 24 3 3 PAPPA2 1 176557063 Silent SNP C C3N-00217_T 1458547 176557063 72399359 40 11810 RASAL2 0 . GRCh38 1 178466024 178466024 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.3492G>C p.Lys1164Asn p.K1164N ENST00000367649 16/18 258 242 16 182 182 0 strelka-varscan-mutect RASAL2,missense_variant,p.Lys1023Asn,ENST00000462775,NM_004841.3;RASAL2,missense_variant,p.Lys1164Asn,ENST00000367649,NM_170692.2;RASAL2,missense_variant,p.Lys574Asn,ENST00000433130,; C ENST00000367649 Transcript missense_variant 3844/4378 3492/3843 1164/1280 K/N aaG/aaC 1 1 RASAL2 HGNC HGNC:9874 protein_coding YES CCDS1321.2 ENSP00000356621 Q9UJF2 UPI00019B254F NM_170692.2 deleterious(0) 16/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF12004,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 178466024 178466024 G C 1 0 0 0 0 1 0 0 0 13225 962 34 4 4 RASAL2 1 178466024 Missense_Mutation SNP G C3N-00217_T 1908961 178466024 70490398 41 11811 CACNA1E 0 . GRCh38 1 181798735 181798735 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.6843G>T p.= p.G2281G ENST00000367573 48/48 99 90 9 35 35 0 strelka-varscan-mutect CACNA1E,synonymous_variant,p.=,ENST00000621791,NM_001205294.1;CACNA1E,synonymous_variant,p.=,ENST00000621551,;CACNA1E,synonymous_variant,p.=,ENST00000367567,;CACNA1E,synonymous_variant,p.=,ENST00000358338,;CACNA1E,synonymous_variant,p.=,ENST00000367570,NM_000721.3;CACNA1E,synonymous_variant,p.=,ENST00000367573,NM_001205293.1;CACNA1E,synonymous_variant,p.=,ENST00000357570,;CACNA1E,synonymous_variant,p.=,ENST00000360108,; T ENST00000367573 Transcript synonymous_variant 6843/7067 6843/6942 2281/2313 G ggG/ggT 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 48/48 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.33187 0.9999998 1 1 1 0 T 2 4 43 181798735 181798735 G T 1 0 0 0 0 0 0 0 1 2230 1190 42 2 2 CACNA1E 1 181798735 Silent SNP G C3N-00217_T 3332711 181798735 67157687 42 11812 ZNF648 0 . GRCh38 1 182057448 182057448 + Missense_Mutation SNP G G T rs778261209 C3N-00217_T C3N-00217_N G G c.563C>A p.Ser188Tyr p.S188Y ENST00000339948 2/2 478 413 65 311 309 2 strelka-varscan-mutect ZNF648,missense_variant,p.Ser188Tyr,ENST00000339948,NM_001009992.1; T ENST00000339948 Transcript missense_variant 771/3649 563/1707 188/568 S/Y tCt/tAt rs778261209,COSM900610 1 -1 ZNF648 HGNC HGNC:18190 protein_coding YES CCDS30952.1 ENSP00000344129 Q5T619 UPI0000161414 NM_001009992.1 deleterious(0.02) 2/2 hmmpanther:PTHR24376:SF1,hmmpanther:PTHR24376 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778261209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 182057448 182057448 G T 1 0 0 0 0 1 0 0 0 18636 942 33 2 2 ZNF648 1 182057448 Missense_Mutation SNP G C3N-00217_T 258713 182057448 66898974 43 11813 HMCN1 0 . GRCh38 1 185911698 185911698 + Missense_Mutation SNP G G T rs763207902 C3N-00217_T C3N-00217_N G G c.818G>T p.Gly273Val p.G273V ENST00000271588 6/107 428 386 42 388 388 0 strelka-varscan-mutect HMCN1,missense_variant,p.Gly273Val,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript missense_variant 1047/18208 818/16908 273/5635 G/V gGc/gTc rs763207902 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 deleterious(0) 6/107 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678 MODERATE 1 SNV 1 1 PASS rs763207902 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 185911698 185911698 G T 1 0 0 0 0 1 0 0 0 7111 1203 42 2 2 HMCN1 1 185911698 Missense_Mutation SNP G C3N-00217_T 3854250 185911698 63044724 44 11814 RGS2 0 . GRCh38 1 192811480 192811480 + Nonsense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.520C>T p.Gln174Ter p.Q174* ENST00000235382 5/5 256 223 33 241 241 0 strelka-varscan-mutect RGS2,stop_gained,p.Gln174Ter,ENST00000235382,NM_002923.3;RGS2,downstream_gene_variant,,ENST00000483295,;RGS2,downstream_gene_variant,,ENST00000464302,;RGS2,downstream_gene_variant,,ENST00000487236,; T ENST00000235382 Transcript stop_gained 551/1354 520/636 174/211 Q/* Cag/Tag 1 1 RGS2 HGNC HGNC:9998 protein_coding YES CCDS1377.1 ENSP00000235382 P41220 A0A024R939 UPI0000044575 NM_002923.3 5/5 PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF43,hmmpanther:PTHR10845,Pfam_domain:PF00615,Gene3D:1.10.167.10,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 192811480 192811480 C T 1 0 0 0 0 0 1 0 0 13473 595 21 3 3 RGS2 1 192811480 Nonsense_Mutation SNP C C3N-00217_T 6899782 192811480 56144942 45 11815 DDX59 0 . GRCh38 1 200648548 200648548 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1487A>T p.Tyr496Phe p.Y496F ENST00000331314 7/8 144 125 19 123 123 0 strelka-varscan-mutect DDX59,missense_variant,p.Tyr496Phe,ENST00000447706,;DDX59,missense_variant,p.Tyr496Phe,ENST00000331314,NM_001031725.4;DDX59,missense_variant,p.Tyr134Phe,ENST00000413408,;DDX59,missense_variant,p.Tyr139Phe,ENST00000433235,;DDX59,missense_variant,p.Tyr74Phe,ENST00000429498,;DDX59,missense_variant,p.Tyr33Phe,ENST00000452560,;DDX59,downstream_gene_variant,,ENST00000453944,; A ENST00000331314 Transcript missense_variant 1701/2289 1487/1860 496/619 Y/F tAt/tTt 1 -1 DDX59 HGNC HGNC:25360 protein_coding YES CCDS30964.1 ENSP00000330460 Q5T1V6 UPI00001AFE4C NM_001031725.4 tolerated(0.35) 7/8 PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF42,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1331418211 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 200648548 200648548 T A 1 0 0 0 0 1 0 0 0 4179 1406 49 4 4 DDX59 1 200648548 Missense_Mutation SNP T C3N-00217_T 7837068 200648548 48307874 46 11816 C1orf106 0 . GRCh38 1 200911496 200911496 + Missense_Mutation SNP G G T rs745954951 C3N-00217_T C3N-00217_N G G c.1003G>T p.Ala335Ser p.A335S ENST00000413687 9/10 143 119 24 79 79 0 strelka-varscan-mutect C1orf106,missense_variant,p.Ala420Ser,ENST00000367342,NM_018265.3;C1orf106,missense_variant,p.Ala335Ser,ENST00000413687,NM_001142569.2;C1orf106,non_coding_transcript_exon_variant,,ENST00000526172,;C1orf106,upstream_gene_variant,,ENST00000465162,;C1orf106,downstream_gene_variant,,ENST00000531649,; T ENST00000413687 Transcript missense_variant 1364/2197 1003/1737 335/578 A/S Gcc/Tcc rs745954951 1 1 C1orf106 HGNC HGNC:25599 protein_coding YES CCDS44292.1 ENSP00000392105 Q3KP66 UPI0000204714 NM_001142569.2 tolerated(0.2) 9/10 hmmpanther:PTHR16093,hmmpanther:PTHR16093:SF4 MODERATE 1 SNV 2 1 PASS rs745954951 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 200911496 200911496 G T 1 0 0 0 0 1 0 0 0 1956 1087 38 1 1 C1orf106 1 200911496 Missense_Mutation SNP G C3N-00217_T 262948 200911496 48044926 47 11817 CACNA1S 0 . GRCh38 1 201087903 201087903 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.927G>T p.Trp309Cys p.W309C ENST00000362061 7/44 378 182 196 259 259 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Trp309Cys,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Trp309Cys,ENST00000367338,; A ENST00000362061 Transcript missense_variant 1154/6166 927/5622 309/1873 W/C tgG/tgT 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 deleterious(0) 7/44 Pfam_domain:PF00520,Prints_domain:PR00167,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 201087903 201087903 C A 1 0 0 0 0 1 0 0 0 2235 740 26 2 2 CACNA1S 1 201087903 Missense_Mutation SNP C C3N-00217_T 176407 201087903 47868519 48 11818 PPP1R15B 0 . GRCh38 1 204409714 204409714 + Nonsense_Mutation SNP G G T rs779920714 C3N-00217_T C3N-00217_N G G c.1698C>A p.Tyr566Ter p.Y566* ENST00000367188 1/2 252 217 35 204 204 0 strelka-varscan-mutect PPP1R15B,stop_gained,p.Tyr566Ter,ENST00000367188,NM_032833.4;RP11-739N20.2,intron_variant,,ENST00000443515,; T ENST00000367188 Transcript stop_gained 2078/5227 1698/2142 566/713 Y/* taC/taA rs779920714 1 -1 PPP1R15B HGNC HGNC:14951 protein_coding YES CCDS1445.1 ENSP00000356156 Q5SWA1 UPI0000EE3EB3 NM_032833.4 1/2 hmmpanther:PTHR16489,hmmpanther:PTHR16489:SF11,Pfam_domain:PF10488 HIGH 1 SNV 1 1 PASS rs779920714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 204409714 204409714 G T 1 0 0 0 0 0 1 0 0 12474 1372 48 2 2 PPP1R15B 1 204409714 Nonsense_Mutation SNP G C3N-00217_T 3321811 204409714 44546708 49 11819 CR2 0 . GRCh38 1 207469764 207469764 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.887C>A p.Ser296Ter p.S296* ENST00000367057 6/20 190 82 108 156 156 0 strelka-varscan-mutect CR2,stop_gained,p.Ser296Ter,ENST00000367057,NM_001006658.2;CR2,stop_gained,p.Ser296Ter,ENST00000367058,NM_001877.4;CR2,stop_gained,p.Ser296Ter,ENST00000367059,;CR2,non_coding_transcript_exon_variant,,ENST00000485707,;CR2,downstream_gene_variant,,ENST00000479186,;CR2,upstream_gene_variant,,ENST00000475194,; A ENST00000367057 Transcript stop_gained 1076/4240 887/3279 296/1092 S/* tCa/tAa 1 1 CR2 HGNC HGNC:2336 protein_coding YES CCDS31007.1 ENSP00000356024 P20023 UPI0000366600 NM_001006658.2 6/20 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF391,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 207469764 207469764 C A 1 0 0 0 0 0 1 0 0 3640 838 29 2 2 CR2 1 207469764 Nonsense_Mutation SNP C C3N-00217_T 3060050 207469764 41486658 50 11820 CENPF 0 . GRCh38 1 214645582 214645582 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.6012G>T p.= p.V2004V ENST00000366955 13/20 288 260 28 203 202 1 strelka-varscan-mutect CENPF,synonymous_variant,p.=,ENST00000366955,NM_016343.3;CENPF,upstream_gene_variant,,ENST00000614578,;CENPF,upstream_gene_variant,,ENST00000467765,; T ENST00000366955 Transcript synonymous_variant 6180/10307 6012/9345 2004/3114 V gtG/gtT 1 1 CENPF HGNC HGNC:1857 protein_coding YES CCDS31023.1 ENSP00000355922 P49454 UPI00001AE985 NM_016343.3 13/20 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10473,hmmpanther:PTHR18874 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 214645582 214645582 G T 1 0 0 0 0 0 0 0 1 2939 1335 47 2 2 CENPF 1 214645582 Silent SNP G C3N-00217_T 7175818 214645582 34310840 51 11821 LEFTY1 0 . GRCh38 1 225886841 225886841 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.987C>A p.Ser329Arg p.S329R ENST00000272134 4/4 418 205 213 239 238 1 strelka-varscan LEFTY1,missense_variant,p.Ser329Arg,ENST00000272134,NM_020997.3;RP4-559A3.7,3_prime_UTR_variant,,ENST00000432920,;TMEM63A,upstream_gene_variant,,ENST00000366835,NM_014698.2;LEFTY1,downstream_gene_variant,,ENST00000492457,; T ENST00000272134 Transcript missense_variant 1067/1626 987/1101 329/366 S/R agC/agA 1 -1 LEFTY1 HGNC HGNC:6552 protein_coding YES CCDS1548.1 ENSP00000272134 O75610 UPI000003721B NM_020997.3 tolerated(0.15) 4/4 PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF167,hmmpanther:PTHR11848,Gene3D:2.10.90.10,PIRSF_domain:PIRSF037402,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501,Prints_domain:PR01427 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 225886841 225886841 G T 1 0 0 0 0 1 0 0 0 8623 1310 46 2 2 LEFTY1 1 225886841 Missense_Mutation SNP G C3N-00217_T 11241259 225886841 23069581 52 11822 PYCR2 0 . GRCh38 1 225921857 225921857 + Splice_Site SNP C C T novel C3N-00217_T C3N-00217_N C C c.540+1G>A p.X180_splice ENST00000343818 230 91 139 153 153 0 strelka-varscan PYCR2,splice_donor_variant,,ENST00000343818,NM_013328.3;PYCR2,splice_donor_variant,,ENST00000612651,;PYCR2,splice_donor_variant,,ENST00000489681,;RP4-559A3.7,intron_variant,,ENST00000432920,;PYCR2,intron_variant,,ENST00000612039,NM_001271681.1;PYCR2,downstream_gene_variant,,ENST00000472798,;PYCR2,downstream_gene_variant,,ENST00000618782,;PYCR2,splice_donor_variant,,ENST00000478402,;PYCR2,splice_donor_variant,,ENST00000446534,;PYCR2,splice_donor_variant,,ENST00000466127,;PYCR2,downstream_gene_variant,,ENST00000467298,; T ENST00000343818 Transcript splice_donor_variant -/1689 540/963 180/320 1 -1 PYCR2 HGNC HGNC:30262 protein_coding YES CCDS31043.1 ENSP00000342502 Q96C36 A0A0S2Z5U6 UPI000006F2BB NM_013328.3 4/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 225921857 225921857 C T 1 0 0 0 0 0 0 1 0 13011 492 17 3 3 PYCR2 1 225921857 Splice_Site SNP C C3N-00217_T 35016 225921857 23034565 53 11823 SIPA1L2 0 . GRCh38 1 232403516 232403516 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.4872G>T p.= p.L1624L ENST00000366630 20/22 189 164 25 113 113 0 strelka-varscan SIPA1L2,synonymous_variant,p.=,ENST00000366630,;SIPA1L2,synonymous_variant,p.=,ENST00000262861,NM_020808.3;SIPA1L2,synonymous_variant,p.=,ENST00000308942,;SIPA1L2,upstream_gene_variant,,ENST00000494056,;SIPA1L2,downstream_gene_variant,,ENST00000495863,; A ENST00000366630 Transcript synonymous_variant 5231/6690 4872/5169 1624/1722 L ctG/ctT 1 -1 SIPA1L2 HGNC HGNC:23800 protein_coding YES CCDS41474.1 ENSP00000355589 Q9P2F8 UPI00001D7D6A 20/22 hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711,Pfam_domain:PF11881 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 232403516 232403516 C A 1 0 0 0 0 0 0 0 1 14593 581 21 2 2 SIPA1L2 1 232403516 Silent SNP C C3N-00217_T 6481659 232403516 16552906 54 11824 GPR137B 0 . GRCh38 1 236178502 236178502 + Missense_Mutation SNP T T A C3N-00217_T C3N-00217_N T T c.553T>A p.Trp185Arg p.W185R ENST00000366592 3/7 377 333 44 284 283 1 strelka-varscan-mutect GPR137B,missense_variant,p.Trp185Arg,ENST00000366592,NM_003272.3;GPR137B,missense_variant,p.Trp49Arg,ENST00000454895,;GPR137B,stop_gained,p.Leu168Ter,ENST00000419162,;GPR137B,intron_variant,,ENST00000366591,; A ENST00000366592 Transcript missense_variant 644/2042 553/1200 185/399 W/R Tgg/Agg COSM425652 1 1 GPR137B HGNC HGNC:11862 protein_coding YES CCDS1609.1 ENSP00000355551 O60478 UPI0000050441 NM_003272.3 tolerated(0.35) 3/7 hmmpanther:PTHR15146:SF0,hmmpanther:PTHR15146 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 236178502 236178502 T A 1 0 0 0 0 1 0 0 0 6532 1812 63 4 4 GPR137B 1 236178502 Missense_Mutation SNP T C3N-00217_T 3774986 236178502 12777920 55 11825 ACTN2 0 . GRCh38 1 236761075 236761075 + Missense_Mutation SNP A A C novel C3N-00217_T C3N-00217_N A A c.2428A>C p.Thr810Pro p.T810P ENST00000542672 20/21 860 362 498 569 569 0 strelka-varscan-mutect ACTN2,missense_variant,p.Thr602Pro,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Thr810Pro,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Thr810Pro,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; C ENST00000542672 Transcript missense_variant 2648/4906 2428/2685 810/894 T/P Acc/Ccc 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.11) 20/21 Gene3D:1.10.238.10,Pfam_domain:PF13833,PROSITE_profiles:PS50222,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 236761075 236761075 A C 1 0 0 0 0 1 0 0 0 249 159 6 5 5 ACTN2 1 236761075 Missense_Mutation SNP A C3N-00217_T 582573 236761075 12195347 56 11826 MTR 0 . GRCh38 1 236895414 236895414 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.3462C>T p.= p.G1154G ENST00000366577 31/33 512 466 46 346 346 0 strelka-varscan-mutect MTR,synonymous_variant,p.=,ENST00000366577,NM_000254.2;MTR,synonymous_variant,p.=,ENST00000535889,NM_001291939.1;MTR,synonymous_variant,p.=,ENST00000366576,NM_001291940.1;MTR,non_coding_transcript_exon_variant,,ENST00000470570,; T ENST00000366577 Transcript synonymous_variant 3856/10529 3462/3798 1154/1265 G ggC/ggT 1 1 MTR HGNC HGNC:7468 protein_coding YES CCDS1614.1 ENSP00000355536 Q99707 UPI0000036BC4 NM_000254.2 31/33 PROSITE_profiles:PS50974,Gene3D:2o2kA01,Pfam_domain:PF02965,TIGRFAM_domain:TIGR02082,PIRSF_domain:PIRSF000381,Superfamily_domains:SSF56507 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 236895414 236895414 C T 1 0 0 0 0 0 0 0 1 9944 697 25 3 3 MTR 1 236895414 Silent SNP C C3N-00217_T 134339 236895414 12061008 57 11827 ZP4 0 . GRCh38 1 237885574 237885574 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.977A>T p.Asn326Ile p.N326I ENST00000611898 8/13 124 106 18 93 92 1 strelka-varscan-mutect ZP4,missense_variant,p.Asn326Ile,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Asn326Ile,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; A ENST00000611898 Transcript missense_variant 1264/2474 977/1623 326/540 N/I aAc/aTc 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 tolerated(0.11) 8/13 Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 43 237885574 237885574 T A 1 0 0 0 0 1 0 0 0 18810 1725 60 4 4 ZP4 1 237885574 Missense_Mutation SNP T C3N-00217_T 990160 237885574 11070848 58 11828 WDR64 0 . GRCh38 1 241674660 241674660 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.396T>C p.= p.D132D ENST00000366552 4/27 110 97 13 98 98 0 strelka-varscan-mutect WDR64,synonymous_variant,p.=,ENST00000366552,NM_144625.4;WDR64,non_coding_transcript_exon_variant,,ENST00000461971,;WDR64,non_coding_transcript_exon_variant,,ENST00000496914,;OPN3,intron_variant,,ENST00000463155,; C ENST00000366552 Transcript synonymous_variant 603/4371 396/3246 132/1081 D gaT/gaC 1 1 WDR64 HGNC HGNC:26570 protein_coding YES ENSP00000355510 B1ANS9 UPI0000519142 NM_144625.4 4/27 Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 241674660 241674660 T C 1 0 0 0 0 0 0 0 1 17874 1461 51 5 5 WDR64 1 241674660 Silent SNP T C3N-00217_T 3789086 241674660 7281762 59 11829 KIF26B 0 . GRCh38 1 245367189 245367189 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.821G>T p.Ser274Ile p.S274I ENST00000407071 3/15 380 335 45 275 275 0 strelka-varscan-mutect KIF26B,missense_variant,p.Ser274Ile,ENST00000407071,NM_018012.3;KIF26B,non_coding_transcript_exon_variant,,ENST00000479506,; T ENST00000407071 Transcript missense_variant 1261/7287 821/6327 274/2108 S/I aGc/aTc 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 tolerated(0.43) 3/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 245367189 245367189 G T 1 0 0 0 0 1 0 0 0 8160 971 34 2 2 KIF26B 1 245367189 Missense_Mutation SNP G C3N-00217_T 3692529 245367189 3589233 60 11830 TRIM58 0 . GRCh38 1 247875963 247875963 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.935G>A p.Ser312Asn p.S312N ENST00000366481 6/6 242 219 23 139 139 0 strelka-varscan-mutect TRIM58,missense_variant,p.Ser312Asn,ENST00000366481,NM_015431.3; A ENST00000366481 Transcript missense_variant 983/3225 935/1461 312/486 S/N aGt/aAt 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0.04) 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 247875963 247875963 G A 1 0 0 0 0 1 0 0 0 17024 1029 36 3 3 TRIM58 1 247875963 Missense_Mutation SNP G C3N-00217_T 2508774 247875963 1080459 61 11831 OR2L3 0 . GRCh38 1 248061209 248061209 + Missense_Mutation SNP C C G rs761253989 C3N-00217_T C3N-00217_N C C c.528C>G p.Phe176Leu p.F176L ENST00000359959 1/1 196 152 44 197 197 0 strelka-varscan-mutect OR2L3,missense_variant,p.Phe176Leu,ENST00000359959,NM_001004687.1; G ENST00000359959 Transcript missense_variant 528/939 528/939 176/312 F/L ttC/ttG rs761253989 1 1 OR2L3 HGNC HGNC:15009 protein_coding YES CCDS31104.1 ENSP00000353044 Q8NG85 UPI0000061EB8 NM_001004687.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF166,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs761253989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 248061209 248061209 C G 1 0 0 0 0 1 0 0 0 11086 912 32 4 4 OR2L3 1 248061209 Missense_Mutation SNP C C3N-00217_T 185246 248061209 895213 62 11832 OR2T2 0 . GRCh38 1 248453623 248453623 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.826T>A p.Ser276Thr p.S276T ENST00000342927 1/1 137 112 25 147 147 0 strelka-varscan-mutect OR2T2,missense_variant,p.Ser276Thr,ENST00000342927,NM_001004136.1; A ENST00000342927 Transcript missense_variant 826/975 826/975 276/324 S/T Tct/Act 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 248453623 248453623 T A 1 0 0 0 0 1 0 0 0 11097 1667 58 4 4 OR2T2 1 248453623 Missense_Mutation SNP T C3N-00217_T 392414 248453623 502799 63 11833 OR2T34 0 . GRCh38 1 248573916 248573916 + Missense_Mutation SNP G G T rs779981033 C3N-00217_T C3N-00217_N G G c.842C>A p.Ala281Asp p.A281D ENST00000328782 1/1 69 62 7 47 47 0 varscan-mutect OR2T34,missense_variant,p.Ala281Asp,ENST00000328782,NM_001001821.1; T ENST00000328782 Transcript missense_variant 842/957 842/957 281/318 A/D gCc/gAc rs779981033 1 -1 OR2T34 HGNC HGNC:31256 protein_coding YES CCDS31120.1 ENSP00000330904 Q8NGX1 UPI0000061ED4 NM_001001821.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF4,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs779981033 . 0 202 8 0 0 0 0 0 -15.46807 0.9999957 1 1 1 0 T 3 4 43 248573916 248573916 G T 1 0 0 0 0 1 0 0 0 11102 1203 42 2 2 OR2T34 1 248573916 Missense_Mutation SNP G C3N-00217_T 120293 248573916 382506 64 11834 OR2T10 0 . GRCh38 1 248593758 248593758 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.11C>A p.Ala4Asp p.A4D ENST00000330500 1/1 105 41 64 93 93 0 strelka-varscan-mutect OR2T10,missense_variant,p.Ala4Asp,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; T ENST00000330500 Transcript missense_variant 11/939 11/939 4/312 A/D gCc/gAc 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 tolerated(0.34) 1/1 hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1243389136 . 4 202 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 248593758 248593758 G T 1 0 0 0 0 1 0 0 0 11095 1203 42 2 2 OR2T10 1 248593758 Missense_Mutation SNP G C3N-00217_T 19842 248593758 362664 65 11835 TMEM18 0 . GRCh38 2 677340 677340 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.6G>T p.= p.P2P ENST00000281017 1/5 275 192 83 230 230 0 strelka-varscan-mutect TMEM18,synonymous_variant,p.=,ENST00000281017,NM_152834.2;TMEM18,upstream_gene_variant,,ENST00000355654,;TMEM18,upstream_gene_variant,,ENST00000405941,;AC092159.2,non_coding_transcript_exon_variant,,ENST00000445418,;AC092159.2,upstream_gene_variant,,ENST00000435573,;TMEM18,synonymous_variant,p.=,ENST00000432667,;TMEM18,upstream_gene_variant,,ENST00000477202,;TMEM18,upstream_gene_variant,,ENST00000461640,;TMEM18,upstream_gene_variant,,ENST00000418447,; A ENST00000281017 Transcript synonymous_variant 100/2762 6/423 2/140 P ccG/ccT 1 -1 TMEM18 HGNC HGNC:25257 protein_coding YES CCDS33141.1 ENSP00000281017 Q96B42 UPI0000208A7D NM_152834.2 1/5 Low_complexity_(Seg):seg,hmmpanther:PTHR22593 LOW 1 SNV 1 1 PASS rs1205828241 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 677340 677340 C A 1 0 0 0 0 0 0 0 1 16543 523 19 1 1 TMEM18 2 677340 Silent SNP C C3N-00217_T 677340 241516189 66 11836 SNTG2 0 . GRCh38 2 1173100 1173100 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.508G>T p.Gly170Trp p.G170W ENST00000308624 8/17 147 101 46 140 139 1 strelka-varscan-mutect SNTG2,missense_variant,p.Gly170Trp,ENST00000308624,NM_018968.3;SNTG2,intron_variant,,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000467759,;SNTG2,non_coding_transcript_exon_variant,,ENST00000463442,;SNTG2,non_coding_transcript_exon_variant,,ENST00000494178,;SNTG2,non_coding_transcript_exon_variant,,ENST00000475201,; T ENST00000308624 Transcript missense_variant 637/1888 508/1620 170/539 G/W Ggg/Tgg 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 deleterious(0) 8/17 Gene3D:2.30.42.10,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,Low_complexity_(Seg):seg,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 1173100 1173100 G T 1 0 0 0 0 1 0 0 0 15195 1000 35 2 2 SNTG2 2 1173100 Missense_Mutation SNP G C3N-00217_T 495760 1173100 241020429 67 11837 SNTG2 0 . GRCh38 2 1239767 1239767 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.879T>A p.= p.P293P ENST00000308624 11/17 236 172 64 224 224 0 strelka-varscan-mutect SNTG2,synonymous_variant,p.=,ENST00000308624,NM_018968.3;SNTG2,synonymous_variant,p.=,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000494178,; A ENST00000308624 Transcript synonymous_variant 1008/1888 879/1620 293/539 P ccT/ccA 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 11/17 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 1239767 1239767 T A 1 0 0 0 0 0 0 0 1 15195 1596 56 4 4 SNTG2 2 1239767 Silent SNP T C3N-00217_T 66667 1239767 240953762 68 11838 CMPK2 0 . GRCh38 2 6865454 6865454 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.243G>A p.= p.P81P ENST00000256722 1/5 25 14 11 26 26 0 strelka-mutect CMPK2,synonymous_variant,p.=,ENST00000256722,NM_207315.3;CMPK2,synonymous_variant,p.=,ENST00000404168,NM_001256477.1;CMPK2,synonymous_variant,p.=,ENST00000458098,NM_001256478.1;RSAD2,upstream_gene_variant,,ENST00000442639,;CMPK2,intron_variant,,ENST00000478738,;CMPK2,intron_variant,,ENST00000465619,;CMPK2,intron_variant,,ENST00000470479,;RSAD2,upstream_gene_variant,,ENST00000474872,;CMPK2,upstream_gene_variant,,ENST00000491738,; T ENST00000256722 Transcript synonymous_variant 243/2884 243/1350 81/449 P ccG/ccA 1 -1 CMPK2 HGNC HGNC:27015 protein_coding YES CCDS42648.1 ENSP00000256722 Q5EBM0 UPI000016014D NM_207315.3 1/5 hmmpanther:PTHR10344:SF3,hmmpanther:PTHR10344,PIRSF_domain:PIRSF019736 LOW 1 SNV 1 1 PASS . . 15 193 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 6865454 6865454 C T 1 0 0 0 0 0 0 0 1 3356 639 23 1 1 CMPK2 2 6865454 Silent SNP C C3N-00217_T 5625687 6865454 235328075 69 11839 APOB 0 . GRCh38 2 21002808 21002808 + Missense_Mutation SNP G G T rs375471570 C3N-00217_T C3N-00217_N G G c.12614C>A p.Pro4205Gln p.P4205Q ENST00000233242 29/29 52 38 14 74 74 0 strelka-varscan-mutect APOB,missense_variant,p.Pro4205Gln,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; T ENST00000233242 Transcript missense_variant 12742/14121 12614/13692 4205/4563 P/Q cCg/cAg rs375471570,COSM2715949 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 29/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs375471570 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 43 21002808 21002808 G T 1 0 0 0 0 1 0 0 0 907 1116 39 1 1 APOB 2 21002808 Missense_Mutation SNP G C3N-00217_T 14137354 21002808 221190721 70 11840 APOB 0 . GRCh38 2 21007083 21007083 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.9785C>A p.Pro3262Gln p.P3262Q ENST00000233242 26/29 327 220 107 347 346 1 strelka-varscan-mutect APOB,missense_variant,p.Pro3262Gln,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 9913/14121 9785/13692 3262/4563 P/Q cCa/cAa 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.05) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 21007083 21007083 G T 1 0 0 0 0 1 0 0 0 907 1348 47 2 2 APOB 2 21007083 Missense_Mutation SNP G C3N-00217_T 4275 21007083 221186446 71 11841 CAD 0 . GRCh38 2 27233809 27233809 + Splice_Site SNP G G C novel C3N-00217_T C3N-00217_N G G c.3399+1G>C p.X1133_splice ENST00000264705 113 80 33 93 93 0 strelka-varscan CAD,splice_donor_variant,,ENST00000264705,NM_004341.3;CAD,splice_donor_variant,,ENST00000403525,NM_001306079.1;CAD,upstream_gene_variant,,ENST00000458503,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,splice_donor_variant,,ENST00000475695,;CAD,downstream_gene_variant,,ENST00000491891,;CAD,upstream_gene_variant,,ENST00000479002,; C ENST00000264705 Transcript splice_donor_variant -/7265 3399/6678 1133/2225 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 21/43 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 43 27233809 27233809 G C 1 0 0 0 0 0 0 1 0 2255 1275 44 4 4 CAD 2 27233809 Splice_Site SNP G C3N-00217_T 6226726 27233809 214959720 72 11842 CAD 0 . GRCh38 2 27235274 27235274 + Silent SNP G G T rs749232399 C3N-00217_T C3N-00217_N G G c.3816G>T p.= p.A1272A ENST00000264705 24/44 100 76 24 74 74 0 strelka-varscan CAD,synonymous_variant,p.=,ENST00000264705,NM_004341.3;CAD,synonymous_variant,p.=,ENST00000403525,NM_001306079.1;CAD,upstream_gene_variant,,ENST00000456311,;CAD,upstream_gene_variant,,ENST00000458503,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,upstream_gene_variant,,ENST00000491461,;CAD,non_coding_transcript_exon_variant,,ENST00000479002,;CAD,upstream_gene_variant,,ENST00000487239,;CAD,downstream_gene_variant,,ENST00000475695,;CAD,downstream_gene_variant,,ENST00000491891,; T ENST00000264705 Transcript synonymous_variant 3978/7265 3816/6678 1272/2225 A gcG/gcT rs749232399 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 24/44 Gene3D:3.30.470.20,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF5,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01369 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 T 2 4 43 27235274 27235274 G T 1 0 0 0 0 0 0 0 1 2255 1103 39 1 1 CAD 2 27235274 Silent SNP G C3N-00217_T 1465 27235274 214958255 73 11843 IFT172 0 . GRCh38 2 27446356 27446356 + Splice_Site SNP C C T novel C3N-00217_T C3N-00217_N C C c.4660-1G>A p.X1554_splice ENST00000260570 152 142 10 118 118 0 strelka-varscan IFT172,splice_acceptor_variant,,ENST00000260570,NM_015662.2;KRTCAP3,3_prime_UTR_variant,,ENST00000543753,NM_001168364.1;KRTCAP3,3_prime_UTR_variant,,ENST00000452499,;NRBP1,downstream_gene_variant,,ENST00000233557,NM_001321357.1;NRBP1,downstream_gene_variant,,ENST00000379863,NM_001321359.1,NM_001321361.1,NM_001321358.1;NRBP1,downstream_gene_variant,,ENST00000379852,NM_013392.2;KRTCAP3,downstream_gene_variant,,ENST00000407293,;KRTCAP3,downstream_gene_variant,,ENST00000288873,NM_001321325.1,NM_173853.3;IFT172,splice_acceptor_variant,,ENST00000507184,;IFT172,splice_acceptor_variant,,ENST00000509128,;IFT172,splice_acceptor_variant,,ENST00000420854,;IFT172,splice_acceptor_variant,,ENST00000480892,;NRBP1,downstream_gene_variant,,ENST00000460499,;NRBP1,downstream_gene_variant,,ENST00000486701,;IFT172,downstream_gene_variant,,ENST00000450564,;KRTCAP3,downstream_gene_variant,,ENST00000464699,;KRTCAP3,downstream_gene_variant,,ENST00000453171,;IFT172,upstream_gene_variant,,ENST00000494163,;KRTCAP3,downstream_gene_variant,,ENST00000494572,;IFT172,upstream_gene_variant,,ENST00000479419,; T ENST00000260570 Transcript splice_acceptor_variant -/5415 4660/5250 1554/1749 1 -1 IFT172 HGNC HGNC:30391 protein_coding YES CCDS1755.1 ENSP00000260570 Q9UG01 UPI0000353ABB NM_015662.2 42/47 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 27446356 27446356 C T 1 0 0 0 0 0 0 1 0 7461 695 24 3 3 IFT172 2 27446356 Splice_Site SNP C C3N-00217_T 211082 27446356 214747173 74 11844 C2orf16 0 . GRCh38 2 27577318 27577318 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.746G>A p.Gly249Glu p.G249E ENST00000408964 1/1 171 122 49 167 167 0 strelka-varscan C2orf16,missense_variant,p.Gly249Glu,ENST00000408964,NM_032266.3; A ENST00000408964 Transcript missense_variant 797/6199 746/5955 249/1984 G/E gGg/gAg 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 tolerated(0.49) 1/1 hmmpanther:PTHR33888 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 27577318 27577318 G A 1 0 0 0 0 1 0 0 0 2032 1232 43 3 3 C2orf16 2 27577318 Missense_Mutation SNP G C3N-00217_T 130962 27577318 214616211 75 11845 C2orf16 0 . GRCh38 2 27581852 27581852 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.5280T>C p.= p.S1760S ENST00000408964 1/1 625 527 98 507 507 0 strelka-varscan C2orf16,synonymous_variant,p.=,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; C ENST00000408964 Transcript synonymous_variant 5331/6199 5280/5955 1760/1984 S agT/agC 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 1/1 hmmpanther:PTHR33888,Low_complexity_(Seg):seg LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 27581852 27581852 T C 1 0 0 0 0 0 0 0 1 2032 1664 58 5 5 C2orf16 2 27581852 Silent SNP T C3N-00217_T 4534 27581852 214611677 76 11846 GALNT14 0 . GRCh38 2 30955690 30955690 + Silent SNP A A T novel C3N-00217_T C3N-00217_N A A c.597T>A p.= p.T199T ENST00000324589 7/16 209 147 62 178 178 0 strelka-varscan GALNT14,synonymous_variant,p.=,ENST00000349752,NM_024572.3;GALNT14,synonymous_variant,p.=,ENST00000406653,NM_001253827.1;GALNT14,synonymous_variant,p.=,ENST00000324589,NM_001253826.1;GALNT14,synonymous_variant,p.=,ENST00000430167,;GALNT14,non_coding_transcript_exon_variant,,ENST00000464038,;GALNT14,non_coding_transcript_exon_variant,,ENST00000481023,;GALNT14,upstream_gene_variant,,ENST00000486564,;GALNT14,downstream_gene_variant,,ENST00000496397,;GALNT14,downstream_gene_variant,,ENST00000461193,;GALNT14,3_prime_UTR_variant,,ENST00000455477,;GALNT14,3_prime_UTR_variant,,ENST00000424136,; T ENST00000324589 Transcript synonymous_variant 658/2169 597/1674 199/557 T acT/acA 1 -1 GALNT14 HGNC HGNC:22946 protein_coding YES CCDS58706.1 ENSP00000314500 Q96FL9 UPI0000073A6F NM_001253826.1 7/16 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF8,Pfam_domain:PF00535,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 30955690 30955690 A T 1 0 0 0 0 0 0 0 1 6080 291 11 4 4 GALNT14 2 30955690 Silent SNP A C3N-00217_T 3373838 30955690 211237839 77 11847 BIRC6 0 . GRCh38 2 32401162 32401162 + Splice_Site SNP G G T novel C3N-00217_T C3N-00217_N G G c.1035-1G>T p.X345_splice ENST00000421745 154 99 55 141 141 0 strelka-varscan BIRC6,splice_acceptor_variant,,ENST00000421745,NM_016252.3;BIRC6,splice_acceptor_variant,,ENST00000466527,; T ENST00000421745 Transcript splice_acceptor_variant -/15703 1035/14574 345/4857 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 6/73 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 32401162 32401162 G T 1 0 0 0 0 0 0 1 0 1589 1014 35 2 2 BIRC6 2 32401162 Splice_Site SNP G C3N-00217_T 1445472 32401162 209792367 78 11848 LTBP1 0 . GRCh38 2 33300507 33300507 + Nonsense_Mutation SNP G G T rs148779103 C3N-00217_T C3N-00217_N G G c.3292G>T p.Glu1098Ter p.E1098* ENST00000404816 21/34 217 152 65 180 180 0 strelka-varscan LTBP1,stop_gained,p.Glu1098Ter,ENST00000404816,NM_206943.2;LTBP1,stop_gained,p.Glu772Ter,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,stop_gained,p.Glu719Ter,ENST00000404525,NM_001166265.1;LTBP1,stop_gained,p.Glu772Ter,ENST00000407925,NM_000627.3;LTBP1,stop_gained,p.Glu719Ter,ENST00000402934,;LTBP1,stop_gained,p.Glu65Ter,ENST00000415140,;LTBP1,upstream_gene_variant,,ENST00000422669,;LTBP1,non_coding_transcript_exon_variant,,ENST00000498013,;LTBP1,upstream_gene_variant,,ENST00000489740,; T ENST00000404816 Transcript stop_gained 3645/6333 3292/5166 1098/1721 E/* Gag/Tag rs148779103 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 21/34 Gene3D:2.10.25.10,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 33300507 33300507 G T 1 0 0 0 0 0 1 0 0 8979 1059 37 1 1 LTBP1 2 33300507 Nonsense_Mutation SNP G C3N-00217_T 899345 33300507 208893022 79 11849 SLC8A1 0 . GRCh38 2 40428637 40428637 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.1644T>A p.His548Gln p.H548Q ENST00000403092 2/11 160 110 50 142 142 0 strelka-varscan SLC8A1,missense_variant,p.His548Gln,ENST00000406785,;SLC8A1,missense_variant,p.His548Gln,ENST00000403092,;SLC8A1,missense_variant,p.His548Gln,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.His548Gln,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.His548Gln,ENST00000405269,;SLC8A1,missense_variant,p.His548Gln,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.His548Gln,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.His548Gln,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,missense_variant,p.His545Gln,ENST00000407929,; T ENST00000403092 Transcript missense_variant 1678/3178 1644/2922 548/973 H/Q caT/caA 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 tolerated(0.46) 2/11 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,SMART_domains:SM00237,Superfamily_domains:SSF141072,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 40428637 40428637 A T 1 0 0 0 0 1 0 0 0 14989 214 8 4 4 SLC8A1 2 40428637 Missense_Mutation SNP A C3N-00217_T 7128130 40428637 201764892 80 11850 FSHR 0 . GRCh38 2 48963178 48963178 + Missense_Mutation SNP C C A rs368367400 C3N-00217_T C3N-00217_N C C c.1643G>T p.Cys548Phe p.C548F ENST00000406846 10/10 280 207 73 299 297 2 strelka-varscan FSHR,missense_variant,p.Cys548Phe,ENST00000406846,NM_000145.3;FSHR,missense_variant,p.Cys522Phe,ENST00000304421,NM_181446.2;FSHR,downstream_gene_variant,,ENST00000454032,;RP11-460M2.1,intron_variant,,ENST00000634588,; A ENST00000406846 Transcript missense_variant 1763/2784 1643/2088 548/695 C/F tGc/tTc rs368367400 1 -1 FSHR HGNC HGNC:3969 protein_coding YES CCDS1843.1 ENSP00000384708 UPI000013E97A NM_000145.3 deleterious(0) 10/10 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF5,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48963178 48963178 C A 1 0 0 0 0 1 0 0 0 5947 710 25 2 2 FSHR 2 48963178 Missense_Mutation SNP C C3N-00217_T 8534541 48963178 193230351 81 11851 NRXN1 0 . GRCh38 2 50053571 50053571 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.3948C>A p.Phe1316Leu p.F1316L ENST00000404971 22/24 265 187 78 322 320 2 strelka-varscan NRXN1,missense_variant,p.Phe1246Leu,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Phe1268Leu,ENST00000625672,;NRXN1,missense_variant,p.Phe1316Leu,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Phe1276Leu,ENST00000401669,;NRXN1,missense_variant,p.Phe1264Leu,ENST00000405472,;NRXN1,missense_variant,p.Phe1268Leu,ENST00000630543,;NRXN1,missense_variant,p.Phe211Leu,ENST00000342183,NM_138735.2;NRXN1,missense_variant,p.Phe241Leu,ENST00000401710,;NRXN1,missense_variant,p.Phe241Leu,ENST00000628364,;NRXN1,5_prime_UTR_variant,,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,3_prime_UTR_variant,,ENST00000637906,; T ENST00000404971 Transcript missense_variant 5288/7578 3948/4644 1316/1547 F/L ttC/ttA 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 22/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 50053571 50053571 G T 1 0 0 0 0 1 0 0 0 10724 1281 45 2 2 NRXN1 2 50053571 Missense_Mutation SNP G C3N-00217_T 1090393 50053571 192139958 82 11852 NRXN1 0 . GRCh38 2 50236813 50236813 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.3642G>C p.Leu1214Phe p.L1214F ENST00000404971 19/24 308 221 87 343 343 0 strelka-varscan NRXN1,missense_variant,p.Leu1174Phe,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Leu1166Phe,ENST00000625672,;NRXN1,missense_variant,p.Leu1214Phe,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Leu1174Phe,ENST00000401669,;NRXN1,missense_variant,p.Leu1162Phe,ENST00000405472,;NRXN1,missense_variant,p.Leu1166Phe,ENST00000630543,;NRXN1,missense_variant,p.Leu139Phe,ENST00000342183,NM_138735.2;NRXN1,missense_variant,p.Leu139Phe,ENST00000401710,;NRXN1,missense_variant,p.Leu139Phe,ENST00000628364,;NRXN1,5_prime_UTR_variant,,ENST00000611589,;NRXN1,downstream_gene_variant,,ENST00000625320,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636736,;NRXN1,downstream_gene_variant,,ENST00000636818,;NRXN1,missense_variant,p.Leu892Phe,ENST00000331040,;NRXN1,missense_variant,p.Leu100Phe,ENST00000637906,; G ENST00000404971 Transcript missense_variant 4982/7578 3642/4644 1214/1547 L/F ttG/ttC 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 19/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 50236813 50236813 C G 1 0 0 0 0 1 0 0 0 10724 593 21 4 4 NRXN1 2 50236813 Missense_Mutation SNP C C3N-00217_T 183242 50236813 191956716 83 11853 DYSF 0 . GRCh38 2 71564200 71564200 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2552C>A p.Thr851Lys p.T851K ENST00000410020 24/56 423 369 54 407 407 0 strelka-varscan DYSF,missense_variant,p.Thr833Lys,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Thr850Lys,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Thr864Lys,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Thr833Lys,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Thr850Lys,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Thr851Lys,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Thr865Lys,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Thr834Lys,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Thr851Lys,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Thr820Lys,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Thr834Lys,ENST00000394120,NM_001130455.1; A ENST00000410020 Transcript missense_variant 2693/6657 2552/6360 851/2119 T/K aCa/aAa 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0) 24/56 Pfam_domain:PF08150,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33,SMART_domains:SM01201 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 71564200 71564200 C A 1 0 0 0 0 1 0 0 0 4683 478 17 2 2 DYSF 2 71564200 Missense_Mutation SNP C C3N-00217_T 21327387 71564200 170629329 84 11854 DQX1 0 . GRCh38 2 74519695 74519695 + Nonsense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.1667T>A p.Leu556Ter p.L556* ENST00000404568 10/12 234 158 76 186 185 1 strelka-varscan DQX1,stop_gained,p.Leu556Ter,ENST00000404568,NM_133637.2;DQX1,stop_gained,p.Leu556Ter,ENST00000393951,;TLX2,downstream_gene_variant,,ENST00000233638,NM_016170.4;TLX2,downstream_gene_variant,,ENST00000621092,;DQX1,downstream_gene_variant,,ENST00000451518,;TLX2,downstream_gene_variant,,ENST00000497238,;DQX1,downstream_gene_variant,,ENST00000495597,;DQX1,downstream_gene_variant,,ENST00000498552,;DQX1,3_prime_UTR_variant,,ENST00000418139,;DQX1,non_coding_transcript_exon_variant,,ENST00000473508,;DQX1,non_coding_transcript_exon_variant,,ENST00000483555,; T ENST00000404568 Transcript stop_gained 1887/2689 1667/2154 556/717 L/* tTg/tAg 1 -1 DQX1 HGNC HGNC:20410 protein_coding YES CCDS1949.2 ENSP00000384621 Q8TE96 UPI0000208758 NM_133637.2 10/12 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF108 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 74519695 74519695 A T 1 0 0 0 0 0 1 0 0 4566 131 5 4 4 DQX1 2 74519695 Nonsense_Mutation SNP A C3N-00217_T 2955495 74519695 167673834 85 11855 DNAH6 0 . GRCh38 2 84816057 84816057 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.12347C>T p.Ala4116Val p.A4116V ENST00000389394 76/77 166 112 54 150 150 0 strelka-varscan DNAH6,missense_variant,p.Ala4116Val,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Ala4116Val,ENST00000237449,; T ENST00000389394 Transcript missense_variant 12484/12795 12347/12477 4116/4158 A/V gCc/gTc 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated(0.74) 76/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF03028 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 84816057 84816057 C T 1 0 0 0 0 1 0 0 0 4420 739 26 3 3 DNAH6 2 84816057 Missense_Mutation SNP C C3N-00217_T 10296362 84816057 157377472 86 11856 KCNIP3 0 . GRCh38 2 95382453 95382453 + Missense_Mutation SNP C C A C3N-00217_T C3N-00217_N C C c.632C>A p.Pro211Gln p.P211Q ENST00000295225 7/9 91 74 17 55 54 1 strelka-varscan KCNIP3,missense_variant,p.Pro211Gln,ENST00000295225,NM_013434.4;KCNIP3,missense_variant,p.Pro211Gln,ENST00000360990,;KCNIP3,missense_variant,p.Pro185Gln,ENST00000468529,NM_001034914.1;KCNIP3,non_coding_transcript_exon_variant,,ENST00000377181,; A ENST00000295225 Transcript missense_variant 767/2940 632/771 211/256 P/Q cCg/cAg COSM4999375,COSM4999376,COSM4999377 1 1 KCNIP3 HGNC HGNC:15523 protein_coding YES CCDS2013.1 ENSP00000295225 Q9Y2W7 A0A024RE22 UPI0000000CCD NM_013434.4 deleterious(0.01) 7/9 PROSITE_profiles:PS50222,hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF61,Gene3D:1.10.238.10,Pfam_domain:PF13499,Superfamily_domains:SSF47473 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 199 7 4 0 0 0 0 -20 0.9985018 1 1 1 0 A 3 1 43 95382453 95382453 C A 1 0 0 0 0 1 0 0 0 7957 652 23 1 1 KCNIP3 2 95382453 Missense_Mutation SNP C C3N-00217_T 10566396 95382453 146811076 87 11857 FER1L5 0 . GRCh38 2 96642869 96642869 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.33T>A p.= p.I11I ENST00000624922 1/53 174 121 53 125 125 0 strelka-varscan FER1L5,synonymous_variant,p.=,ENST00000623019,;FER1L5,synonymous_variant,p.=,ENST00000624922,NM_001293083.1;FER1L5,synonymous_variant,p.=,ENST00000622983,;FER1L5,5_prime_UTR_variant,,ENST00000623246,;KANSL3,upstream_gene_variant,,ENST00000431828,NM_001115016.2;KANSL3,upstream_gene_variant,,ENST00000448075,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;KANSL3,upstream_gene_variant,,ENST00000487070,;KANSL3,upstream_gene_variant,,ENST00000475820,;FER1L5,non_coding_transcript_exon_variant,,ENST00000505256,;KANSL3,upstream_gene_variant,,ENST00000354204,;KANSL3,upstream_gene_variant,,ENST00000420155,;KANSL3,upstream_gene_variant,,ENST00000597150,;KANSL3,upstream_gene_variant,,ENST00000444759,;KANSL3,upstream_gene_variant,,ENST00000452268,;KANSL3,upstream_gene_variant,,ENST00000418735,;KANSL3,upstream_gene_variant,,ENST00000416138,;KANSL3,upstream_gene_variant,,ENST00000478492,; A ENST00000624922 Transcript synonymous_variant 33/6367 33/6174 11/2057 I atT/atA 1 1 FER1L5 HGNC HGNC:19044 protein_coding YES CCDS77438.1 ENSP00000485238 A0A096LNV2 UPI00046B3755 NM_001293083.1 1/53 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 96642869 96642869 T A 1 0 0 0 0 0 0 0 1 5677 1800 63 4 4 FER1L5 2 96642869 Silent SNP T C3N-00217_T 1260416 96642869 145550660 88 11858 ST6GAL2 0 . GRCh38 2 106843527 106843527 + Missense_Mutation SNP G G T rs201546993 C3N-00217_T C3N-00217_N G G c.451C>A p.Pro151Thr p.P151T ENST00000409382 2/6 135 92 43 122 122 0 strelka-varscan ST6GAL2,missense_variant,p.Pro151Thr,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Pro151Thr,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Pro151Thr,ENST00000409087,NM_001142352.1;ST6GAL2,downstream_gene_variant,,ENST00000419159,;AC016994.2,downstream_gene_variant,,ENST00000425419,; T ENST00000409382 Transcript missense_variant 1062/7275 451/1590 151/529 P/T Cct/Act rs201546993,COSM3564868,COSM3564869 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 2/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 106843527 106843527 G T 1 0 0 0 0 1 0 0 0 15600 1232 43 2 2 ST6GAL2 2 106843527 Missense_Mutation SNP G C3N-00217_T 10200658 106843527 135350002 89 11859 IL1A 0 . GRCh38 2 112778033 112778033 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.569A>T p.Gln190Leu p.Q190L ENST00000263339 6/7 158 107 51 191 191 0 strelka-varscan IL1A,missense_variant,p.Gln190Leu,ENST00000263339,NM_000575.3; A ENST00000263339 Transcript missense_variant 725/2124 569/816 190/271 Q/L cAa/cTa 1 -1 IL1A HGNC HGNC:5991 protein_coding YES CCDS2101.1 ENSP00000263339 P01583 UPI0000000CCF NM_000575.3 tolerated(0.16) 6/7 hmmpanther:PTHR10078:SF26,hmmpanther:PTHR10078,Gene3D:2.80.10.50,Pfam_domain:PF00340,SMART_domains:SM00125,Superfamily_domains:SSF50353,Prints_domain:PR01357,Prints_domain:PR00264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 112778033 112778033 T A 1 0 0 0 0 1 0 0 0 7558 1812 63 4 4 IL1A 2 112778033 Missense_Mutation SNP T C3N-00217_T 5934506 112778033 129415496 90 11860 EN1 0 . GRCh38 2 118847140 118847140 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.28A>C p.Ser10Arg p.S10R ENST00000295206 1/2 213 185 28 158 158 0 strelka-varscan EN1,missense_variant,p.Ser10Arg,ENST00000295206,NM_001426.3;EN1,upstream_gene_variant,,ENST00000546667,; G ENST00000295206 Transcript missense_variant 539/2457 28/1179 10/392 S/R Agt/Cgt 1 -1 EN1 HGNC HGNC:3342 protein_coding YES CCDS2123.1 ENSP00000295206 Q05925 UPI000013E21D NM_001426.3 deleterious_low_confidence(0) 1/2 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 118847140 118847140 T G 1 0 0 0 0 1 0 0 0 4951 1609 56 5 5 EN1 2 118847140 Missense_Mutation SNP T C3N-00217_T 6069107 118847140 123346389 91 11861 TMEM185B 0 . GRCh38 2 120222799 120222799 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.178G>T p.Val60Leu p.V60L ENST00000426077 1/1 87 58 29 58 58 0 strelka-varscan TMEM185B,missense_variant,p.Val60Leu,ENST00000426077,NM_024121.2; A ENST00000426077 Transcript missense_variant 610/2131 178/1053 60/350 V/L Gtg/Ttg 1 -1 TMEM185B HGNC HGNC:18896 protein_coding YES CCDS58722.1 ENSP00000453399 Q9H7F4 UPI0000074167 NM_024121.2 deleterious(0.03) 1/1 Pfam_domain:PF10269,hmmpanther:PTHR13568,hmmpanther:PTHR13568:SF5,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 120222799 120222799 C A 1 0 0 0 0 1 0 0 0 16551 536 19 1 1 TMEM185B 2 120222799 Missense_Mutation SNP C C3N-00217_T 1375659 120222799 121970730 92 11862 RALB 0 . GRCh38 2 120285937 120285937 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.178G>C p.Glu60Gln p.E60Q ENST00000272519 3/5 311 226 85 257 257 0 strelka-varscan RALB,missense_variant,p.Glu60Gln,ENST00000272519,NM_002881.2;RALB,missense_variant,p.Glu60Gln,ENST00000420510,;RALB,missense_variant,p.Glu60Gln,ENST00000412383,;RALB,missense_variant,p.Glu60Gln,ENST00000449649,;RALB,missense_variant,p.Glu82Gln,ENST00000447591,;AC012363.1,downstream_gene_variant,,ENST00000631153,;RALB,intron_variant,,ENST00000470417,;RALB,3_prime_UTR_variant,,ENST00000431732,; C ENST00000272519 Transcript missense_variant 448/2344 178/621 60/206 E/Q Gaa/Caa COSM1527636,COSM5270391 1 1 RALB HGNC HGNC:9840 protein_coding YES CCDS2131.1 ENSP00000272519 P11234 A0A024RAG3 UPI000000124F NM_002881.2 tolerated(0.1) 3/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF199,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 120285937 120285937 G C 1 0 0 0 0 1 0 0 0 13170 1175 41 4 4 RALB 2 120285937 Missense_Mutation SNP G C3N-00217_T 63138 120285937 121907592 93 11863 CNTNAP5 0 . GRCh38 2 124504536 124504536 + Missense_Mutation SNP G G A C3N-00217_T C3N-00217_N G G c.1304G>A p.Arg435His p.R435H ENST00000431078 8/24 151 131 20 135 135 0 strelka-varscan CNTNAP5,missense_variant,p.Arg435His,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 1668/5284 1304/3921 435/1306 R/H cGc/cAc COSM441066 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 tolerated(0.22) 8/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 124504536 124504536 G A 1 0 0 0 0 1 0 0 0 3432 1087 38 1 1 CNTNAP5 2 124504536 Missense_Mutation SNP G C3N-00217_T 4218599 124504536 117688993 94 11864 MYO7B 0 . GRCh38 2 127622014 127622014 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.3480G>T p.= p.A1160A ENST00000428314 27/47 299 210 89 276 275 1 strelka-varscan MYO7B,synonymous_variant,p.=,ENST00000428314,NM_001080527.1;MYO7B,synonymous_variant,p.=,ENST00000409816,;MYO7B,synonymous_variant,p.=,ENST00000409090,;MYO7B,synonymous_variant,p.=,ENST00000437387,;RP11-286H15.1,downstream_gene_variant,,ENST00000609697,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,; T ENST00000428314 Transcript synonymous_variant 3533/6715 3480/6351 1160/2116 A gcG/gcT 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 27/47 Pfam_domain:PF00784,PROSITE_profiles:PS51016,SMART_domains:SM00139 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 127622014 127622014 G T 1 0 0 0 0 0 0 0 1 10084 1045 37 1 1 MYO7B 2 127622014 Silent SNP G C3N-00217_T 3117478 127622014 114571515 95 11865 ARHGEF4 0 . GRCh38 2 131045441 131045441 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1916C>A p.Pro639His p.P639H ENST00000326016 13/14 194 142 52 194 194 0 strelka-varscan ARHGEF4,missense_variant,p.Pro1765His,ENST00000409359,;ARHGEF4,missense_variant,p.Pro639His,ENST00000525839,NM_032995.2;ARHGEF4,missense_variant,p.Pro664His,ENST00000392953,;ARHGEF4,missense_variant,p.Pro639His,ENST00000326016,NM_015320.3;ARHGEF4,missense_variant,p.Pro579His,ENST00000611048,;ARHGEF4,missense_variant,p.Pro516His,ENST00000409303,;ARHGEF4,missense_variant,p.Pro568His,ENST00000355771,;ARHGEF4,missense_variant,p.Pro256His,ENST00000532720,;ARHGEF4,intron_variant,,ENST00000428230,;ARHGEF4,intron_variant,,ENST00000438985,;FAM168B,downstream_gene_variant,,ENST00000409185,NM_001321746.1,NM_001321744.1,NM_001321747.1,NM_001321745.1,NM_001321748.1,NM_001009993.2;ARHGEF4,downstream_gene_variant,,ENST00000439368,;ARHGEF4,3_prime_UTR_variant,,ENST00000636987,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000490728,;ARHGEF4,downstream_gene_variant,,ENST00000525092,;ARHGEF4,downstream_gene_variant,,ENST00000527365,; A ENST00000326016 Transcript missense_variant 2435/3666 1916/2073 639/690 P/H cCc/cAc 1 1 ARHGEF4 HGNC HGNC:684 protein_coding YES CCDS2165.1 ENSP00000316845 Q9NR80 UPI00001417F6 NM_015320.3 deleterious(0.01) 13/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 131045441 131045441 C A 1 0 0 0 0 1 0 0 0 1043 637 22 2 2 ARHGEF4 2 131045441 Missense_Mutation SNP C C3N-00217_T 3423427 131045441 111148088 96 11866 CCDC74A 0 . GRCh38 2 131530704 131530704 + Silent SNP C C A rs149664658 C3N-00217_T C3N-00217_N C C c.421C>A p.= p.R141R ENST00000295171 3/8 310 271 39 272 272 0 strelka-varscan CCDC74A,synonymous_variant,p.=,ENST00000295171,NM_138770.2,NM_001258304.1;CCDC74A,synonymous_variant,p.=,ENST00000467992,NM_001258305.1;CCDC74A,intron_variant,,ENST00000409856,NM_001258306.1;CCDC74A,intron_variant,,ENST00000434330,;CCDC74A,downstream_gene_variant,,ENST00000478665,;CCDC74A,3_prime_UTR_variant,,ENST00000454549,;CCDC74A,downstream_gene_variant,,ENST00000465939,;CCDC74A,downstream_gene_variant,,ENST00000468650,;MED15P4,downstream_gene_variant,,ENST00000417579,; A ENST00000295171 Transcript synonymous_variant 559/1543 421/1137 141/378 R Cgg/Agg rs149664658 1 1 CCDC74A HGNC HGNC:25197 protein_coding YES CCDS2167.1 ENSP00000295171 Q96AQ1 UPI000006E43A NM_138770.2,NM_001258304.1 3/8 hmmpanther:PTHR14882,hmmpanther:PTHR14882:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 131530704 131530704 C A 1 0 0 0 0 0 0 0 1 2547 527 19 1 1 CCDC74A 2 131530704 Silent SNP C C3N-00217_T 485263 131530704 110662825 97 11867 LRP1B 0 . GRCh38 2 141062251 141062251 + Missense_Mutation SNP C C A rs763797972 C3N-00217_T C3N-00217_N C C c.1036G>T p.Gly346Trp p.G346W ENST00000389484 8/91 99 71 28 115 115 0 strelka-varscan LRP1B,missense_variant,p.Gly346Trp,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 2008/16535 1036/13800 346/4599 G/W Ggg/Tgg rs763797972 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 8/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 141062251 141062251 C A 1 0 0 0 0 1 0 0 0 8850 652 23 1 1 LRP1B 2 141062251 Missense_Mutation SNP C C3N-00217_T 9531547 141062251 101131278 98 11868 GRB14 0 . GRCh38 2 164493054 164493054 + Missense_Mutation SNP A A C rs112309467 C3N-00217_T C3N-00217_N A A c.1605T>G p.Cys535Trp p.C535W ENST00000263915 14/14 142 121 21 159 159 0 strelka-varscan GRB14,missense_variant,p.Cys535Trp,ENST00000263915,NM_004490.2;GRB14,downstream_gene_variant,,ENST00000446413,;GRB14,non_coding_transcript_exon_variant,,ENST00000497306,;GRB14,non_coding_transcript_exon_variant,,ENST00000488342,; C ENST00000263915 Transcript missense_variant 2144/2382 1605/1623 535/540 C/W tgT/tgG rs112309467 1 -1 GRB14 HGNC HGNC:4565 protein_coding YES CCDS2222.1 ENSP00000263915 Q14449 UPI000013D489 NM_004490.2 deleterious(0) 14/14 PROSITE_profiles:PS50001,hmmpanther:PTHR11243:SF22,hmmpanther:PTHR11243,Gene3D:3.30.505.10,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 164493054 164493054 A C 1 0 0 0 0 1 0 0 0 6636 157 6 5 5 GRB14 2 164493054 Missense_Mutation SNP A C3N-00217_T 23430803 164493054 77700475 99 11869 XIRP2 0 . GRCh38 2 167210883 167210883 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.711C>A p.Ser237Arg p.S237R ENST00000409195 4/11 117 75 42 125 125 0 strelka-varscan XIRP2,missense_variant,p.Ser237Arg,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser15Arg,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser62Arg,ENST00000628543,;XIRP2,missense_variant,p.Ser270Arg,ENST00000409728,NM_001199143.1;XIRP2,missense_variant,p.Ser237Arg,ENST00000409043,NM_001079810.3;XIRP2,missense_variant,p.Ser15Arg,ENST00000409605,NM_001199145.1; A ENST00000409195 Transcript missense_variant 800/12675 711/10650 237/3549 S/R agC/agA 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.01) 4/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 167210883 167210883 C A 1 0 0 0 0 1 0 0 0 17989 796 28 2 2 XIRP2 2 167210883 Missense_Mutation SNP C C3N-00217_T 2717829 167210883 74982646 100 11870 XIRP2 0 . GRCh38 2 167243548 167243548 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2156G>T p.Arg719Met p.R719M ENST00000409195 9/11 185 140 45 254 254 0 strelka-varscan XIRP2,missense_variant,p.Arg719Met,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Arg497Met,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Arg544Met,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript missense_variant 2245/12675 2156/10650 719/3549 R/M aGg/aTg 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 167243548 167243548 G T 1 0 0 0 0 1 0 0 0 17989 1000 35 2 2 XIRP2 2 167243548 Missense_Mutation SNP G C3N-00217_T 32665 167243548 74949981 101 11871 XIRP2 0 . GRCh38 2 167248217 167248217 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.6825C>A p.Asn2275Lys p.N2275K ENST00000409195 9/11 199 149 50 255 255 0 strelka-varscan XIRP2,missense_variant,p.Asn2275Lys,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Asn2053Lys,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Asn2100Lys,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 6914/12675 6825/10650 2275/3549 N/K aaC/aaA 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated_low_confidence(0.26) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 167248217 167248217 C A 1 0 0 0 0 1 0 0 0 17989 564 20 2 2 XIRP2 2 167248217 Missense_Mutation SNP C C3N-00217_T 4669 167248217 74945312 102 11872 MYO3B 0 . GRCh38 2 170466518 170466518 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2821G>T p.Asp941Tyr p.D941Y ENST00000408978 25/35 167 117 50 153 153 0 strelka-varscan MYO3B,missense_variant,p.Asp941Tyr,ENST00000408978,NM_138995.4;MYO3B,missense_variant,p.Asp941Tyr,ENST00000409044,NM_001083615.3;MYO3B,missense_variant,p.Asp950Tyr,ENST00000484338,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,intron_variant,,ENST00000602629,;MYO3B,missense_variant,p.Asp941Tyr,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; T ENST00000408978 Transcript missense_variant 2964/5529 2821/4026 941/1341 D/Y Gac/Tac 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 deleterious(0) 25/35 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF476,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 170466518 170466518 G T 1 0 0 0 0 1 0 0 0 10078 1174 41 2 2 MYO3B 2 170466518 Missense_Mutation SNP G C3N-00217_T 3218301 170466518 71727011 103 11873 RBM45 0 . GRCh38 2 178126108 178126108 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1357G>T p.Val453Leu p.V453L ENST00000286070 9/10 128 103 25 189 189 0 strelka-varscan RBM45,missense_variant,p.Val114Leu,ENST00000455903,;RBM45,missense_variant,p.Val455Leu,ENST00000616198,;RBM45,missense_variant,p.Val453Leu,ENST00000286070,NM_152945.2;RBM45,missense_variant,p.Val52Leu,ENST00000424099,;RBM45,upstream_gene_variant,,ENST00000464647,;RBM45,non_coding_transcript_exon_variant,,ENST00000424000,;RBM45,downstream_gene_variant,,ENST00000493048,; T ENST00000286070 Transcript missense_variant 1449/1785 1357/1425 453/474 V/L Gtg/Ttg 1 1 RBM45 HGNC HGNC:24468 protein_coding YES CCDS33335.1 ENSP00000286070 Q8IUH3 UPI00001AEAD8 NM_152945.2 deleterious(0.02) 9/10 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF389,hmmpanther:PTHR24012,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 178126108 178126108 G T 1 0 0 0 0 1 0 0 0 13305 1261 44 2 2 RBM45 2 178126108 Missense_Mutation SNP G C3N-00217_T 7659590 178126108 64067421 104 11874 ITGA4 0 . GRCh38 2 181493415 181493415 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1244C>A p.Ser415Ter p.S415* ENST00000397033 11/28 107 82 25 113 113 0 strelka-varscan ITGA4,stop_gained,p.Ser415Ter,ENST00000397033,NM_000885.4;ITGA4,stop_gained,p.Ser415Ter,ENST00000233573,;ITGA4,non_coding_transcript_exon_variant,,ENST00000473002,;ITGA4,upstream_gene_variant,,ENST00000490435,; A ENST00000397033 Transcript stop_gained 1674/4189 1244/3099 415/1032 S/* tCa/tAa 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 11/28 hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,Gene3D:3nigC00,SMART_domains:SM00191,Superfamily_domains:SSF69318 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 181493415 181493415 C A 1 0 0 0 0 0 1 0 0 7785 840 29 2 2 ITGA4 2 181493415 Nonsense_Mutation SNP C C3N-00217_T 3367307 181493415 60700114 105 11875 NEUROD1 0 . GRCh38 2 181678465 181678465 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.396T>C p.= p.S132S ENST00000295108 2/2 358 281 77 309 309 0 strelka-varscan NEUROD1,synonymous_variant,p.=,ENST00000295108,NM_002500.4;AC013733.3,upstream_gene_variant,,ENST00000440371,;CERKL,intron_variant,,ENST00000479558,;CERKL,intron_variant,,ENST00000497337,;NEUROD1,intron_variant,,ENST00000496876,; G ENST00000295108 Transcript synonymous_variant 854/2852 396/1071 132/356 S tcT/tcC 1 -1 NEUROD1 HGNC HGNC:7762 protein_coding YES CCDS2283.1 ENSP00000295108 Q13562 A0A0S2Z493 UPI000013E207 NM_002500.4 2/2 Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,PROSITE_profiles:PS50888,hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF88,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 181678465 181678465 A G 1 0 0 0 0 0 0 0 1 10385 407 15 5 5 NEUROD1 2 181678465 Silent SNP A C3N-00217_T 185050 181678465 60515064 106 11876 FSIP2 0 . GRCh38 2 185801190 185801190 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.12151C>A p.His4051Asn p.H4051N ENST00000343098 17/23 125 91 34 224 224 0 strelka-varscan FSIP2,missense_variant,p.His4051Asn,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.His3962Asn,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 12151/21054 12151/20991 4051/6996 H/N Cat/Aat 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 tolerated(0.08) 17/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 185801190 185801190 C A 1 0 0 0 0 1 0 0 0 5949 478 17 2 2 FSIP2 2 185801190 Missense_Mutation SNP C C3N-00217_T 4122725 185801190 56392339 107 11877 FSIP2 0 . GRCh38 2 185803487 185803487 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.14448T>A p.= p.A4816A ENST00000343098 17/23 62 45 17 92 92 0 strelka-varscan FSIP2,synonymous_variant,p.=,ENST00000343098,NM_173651.2;FSIP2,synonymous_variant,p.=,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript synonymous_variant 14448/21054 14448/20991 4816/6996 A gcT/gcA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 LOW SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 185803487 185803487 T A 1 0 0 0 0 0 0 0 1 5949 1567 55 4 4 FSIP2 2 185803487 Silent SNP T C3N-00217_T 2297 185803487 56390042 108 11878 DNAH7 0 . GRCh38 2 195888263 195888263 + Missense_Mutation SNP T T C C3N-00217_T C3N-00217_N T T c.5401A>G p.Thr1801Ala p.T1801A ENST00000312428 33/65 113 79 34 144 144 0 strelka-varscan DNAH7,missense_variant,p.Thr1801Ala,ENST00000312428,NM_018897.2;DNAH7,downstream_gene_variant,,ENST00000475293,; C ENST00000312428 Transcript missense_variant 5502/12394 5401/12075 1801/4024 T/A Aca/Gca COSM2904917 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 tolerated(0.1) 33/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 195888263 195888263 T C 1 0 0 0 0 1 0 0 0 4421 1652 57 5 5 DNAH7 2 195888263 Missense_Mutation SNP T C3N-00217_T 10084776 195888263 46305266 109 11879 NRP2 0 . GRCh38 2 205792244 205792244 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2450C>T p.Pro817Leu p.P817L ENST00000360409 16/17 170 130 40 219 219 0 strelka-varscan NRP2,missense_variant,p.Pro817Leu,ENST00000360409,NM_201266.1;NRP2,missense_variant,p.Pro812Leu,ENST00000357785,NM_003872.2;NRP2,intron_variant,,ENST00000412873,NM_201279.1;NRP2,non_coding_transcript_exon_variant,,ENST00000467850,; T ENST00000360409 Transcript missense_variant 3241/6662 2450/2796 817/931 P/L cCa/cTa 1 1 NRP2 HGNC HGNC:8005 protein_coding YES CCDS2364.1 ENSP00000353582 X5D2Q8 UPI0000000A04 NM_201266.1 deleterious(0.03) 16/17 PIRSF_domain:PIRSF036960 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 205792244 205792244 C T 1 0 0 0 0 1 0 0 0 10719 594 21 3 3 NRP2 2 205792244 Missense_Mutation SNP C C3N-00217_T 9903981 205792244 36401285 110 11880 DES 0 . GRCh38 2 219418814 219418814 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.352C>G p.Arg118Gly p.R118G ENST00000373960 1/9 338 249 89 305 305 0 strelka-varscan DES,missense_variant,p.Arg118Gly,ENST00000373960,NM_001927.3;DES,upstream_gene_variant,,ENST00000477226,;DES,upstream_gene_variant,,ENST00000492726,; G ENST00000373960 Transcript missense_variant 438/2248 352/1413 118/470 R/G Cgc/Ggc 1 1 DES HGNC HGNC:2770 protein_coding YES CCDS33383.1 ENSP00000363071 P17661 Q53SB5 UPI0000001603 NM_001927.3 deleterious(0) 1/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF28,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 219418814 219418814 C G 1 0 0 0 0 1 0 0 0 4255 652 23 4 4 DES 2 219418814 Missense_Mutation SNP C C3N-00217_T 13626570 219418814 22774715 111 11881 SPEG 0 . GRCh38 2 219483305 219483305 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.5842G>C p.Val1948Leu p.V1948L ENST00000312358 30/41 90 63 27 47 47 0 strelka-varscan SPEG,missense_variant,p.Val1948Leu,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; C ENST00000312358 Transcript missense_variant 5974/10782 5842/9804 1948/3267 V/L Gtg/Ctg 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.05) 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 219483305 219483305 G C 1 0 0 0 0 1 0 0 0 15387 1261 44 4 4 SPEG 2 219483305 Missense_Mutation SNP G C3N-00217_T 64491 219483305 22710224 112 11882 DNER 0 . GRCh38 2 229367090 229367090 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.1885G>C p.Glu629Gln p.E629Q ENST00000341772 12/13 248 169 79 198 198 0 strelka-varscan DNER,missense_variant,p.Glu629Gln,ENST00000341772,NM_139072.3; G ENST00000341772 Transcript missense_variant 2020/3260 1885/2214 629/737 E/Q Gag/Cag 1 -1 DNER HGNC HGNC:24456 protein_coding YES CCDS33390.1 ENSP00000345229 Q8NFT8 UPI0000048EB8 NM_139072.3 deleterious(0.01) 12/13 hmmpanther:PTHR24044:SF275,hmmpanther:PTHR24044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 229367090 229367090 C G 1 0 0 0 0 1 0 0 0 4480 864 30 4 4 DNER 2 229367090 Missense_Mutation SNP C C3N-00217_T 9883785 229367090 12826439 113 11883 AGAP1 0 . GRCh38 2 235744770 235744770 + Missense_Mutation SNP C C A rs141449009 C3N-00217_T C3N-00217_N C C c.469C>A p.His157Asn p.H157N ENST00000304032 5/18 225 184 41 211 211 0 strelka-varscan AGAP1,missense_variant,p.His157Asn,ENST00000304032,NM_001037131.2;AGAP1,missense_variant,p.His103Asn,ENST00000428334,;AGAP1,missense_variant,p.His103Asn,ENST00000614409,;AGAP1,missense_variant,p.His422Asn,ENST00000409538,;AGAP1,missense_variant,p.His157Asn,ENST00000336665,NM_014914.4;AGAP1,missense_variant,p.His157Asn,ENST00000409457,NM_001244888.1;AGAP1,missense_variant,p.His103Asn,ENST00000619456,;AGAP1,missense_variant,p.His104Asn,ENST00000402604,;AGAP1,3_prime_UTR_variant,,ENST00000635100,; A ENST00000304032 Transcript missense_variant 1049/10832 469/2574 157/857 H/N Cac/Aac rs141449009,COSM5138612 1 1 AGAP1 HGNC HGNC:16922 protein_coding YES CCDS33408.1 ENSP00000307634 Q9UPQ3 UPI00005E1AE1 NM_001037131.2 tolerated(1) 5/18 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51419,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF226,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 5 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 235744770 235744770 C A 1 0 0 0 0 1 0 0 0 443 594 21 2 2 AGAP1 2 235744770 Missense_Mutation SNP C C3N-00217_T 6377680 235744770 6448759 114 11884 KIF1A 0 . GRCh38 2 240797720 240797720 + Silent SNP C C A rs765920658 C3N-00217_T C3N-00217_N C C c.33G>T p.= p.R11R ENST00000498729 2/49 116 69 47 108 108 0 strelka-varscan-mutect KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,synonymous_variant,p.=,ENST00000404283,;KIF1A,synonymous_variant,p.=,ENST00000448728,; A ENST00000498729 Transcript synonymous_variant 280/9223 33/5376 11/1791 R cgG/cgT rs765920658 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 2/49 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs765920658 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 240797720 240797720 C A 1 0 0 0 0 0 0 0 1 8147 610 22 2 2 KIF1A 2 240797720 Silent SNP C C3N-00217_T 5052950 240797720 1395809 115 11885 OXTR 0 . GRCh38 3 8768134 8768134 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.54C>A p.= p.A18A ENST00000316793 3/4 28 13 15 65 65 0 strelka-varscan-mutect OXTR,synonymous_variant,p.=,ENST00000316793,NM_000916.3;OXTR,synonymous_variant,p.=,ENST00000431493,;OXTR,synonymous_variant,p.=,ENST00000449615,;CAV3,intron_variant,,ENST00000472766,;OXTR,downstream_gene_variant,,ENST00000474615,; T ENST00000316793 Transcript synonymous_variant 679/4364 54/1170 18/389 A gcC/gcA 1 -1 OXTR HGNC HGNC:8529 protein_coding YES CCDS2570.1 ENSP00000324270 P30559 B2R9L7 UPI000013FEA9 NM_000916.3 3/4 Prints_domain:PR00665,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF19,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 8768134 8768134 G T 1 0 0 0 0 0 0 0 1 11411 1103 39 1 1 OXTR 3 8768134 Silent SNP G C3N-00217_T 8768134 189527425 116 11886 SLC6A11 0 . GRCh38 3 10938316 10938316 + Frame_Shift_Del DEL C C - rs752171053 C3N-00217_T C3N-00217_N C C c.1813delC p.Arg605GlyfsTer3 p.R605Gfs*3 ENST00000254488 14/14 45 33 12 72 72 0 sindel-varindel SLC6A11,frameshift_variant,p.Arg605GlyfsTer3,ENST00000254488,NM_014229.1;SLC6A11,downstream_gene_variant,,ENST00000464828,; - ENST00000254488 Transcript frameshift_variant 1879/4296 1813/1899 605/632 R/X Cgg/gg rs752171053 1 1 SLC6A11 HGNC HGNC:11044 protein_coding YES CCDS2602.1 ENSP00000254488 P48066 UPI00001354A6 NM_014229.1 14/14 Prints_domain:PR01197,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF124 HIGH 1 deletion 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 10938316 10938316 C - 1 0 1 0 1 0 0 0 0 14957 527 19 0 0 SLC6A11 3 10938316 Frame_Shift_Del DEL C C3N-00217_T 2170182 10938316 187357243 117 11887 GALNT15 0 . GRCh38 3 16175461 16175461 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.310G>T p.Ala104Ser p.A104S ENST00000339732 1/10 82 47 35 119 119 0 strelka-varscan-mutect GALNT15,missense_variant,p.Ala104Ser,ENST00000339732,NM_054110.4;GALNT15,missense_variant,p.Ala104Ser,ENST00000437509,;GALNT15,non_coding_transcript_exon_variant,,ENST00000470031,;GALNT15,upstream_gene_variant,,ENST00000430410,; T ENST00000339732 Transcript missense_variant 813/4669 310/1920 104/639 A/S Gcc/Tcc COSM5548345 1 1 GALNT15 HGNC HGNC:21531 protein_coding YES CCDS33711.1 ENSP00000344260 Q8N3T1 UPI0000048F0D NM_054110.4 tolerated(0.1) 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF36 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 16175461 16175461 G T 1 0 0 0 0 1 0 0 0 6081 1203 42 2 2 GALNT15 3 16175461 Missense_Mutation SNP G C3N-00217_T 5237145 16175461 182120098 118 11888 TMEM89 0 . GRCh38 3 48621634 48621634 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.123G>T p.Gln41His p.Q41H ENST00000330862 1/2 198 149 49 201 201 0 strelka-varscan-mutect TMEM89,missense_variant,p.Gln41His,ENST00000330862,NM_001008269.1;SLC26A6,downstream_gene_variant,,ENST00000358747,NM_001040454.1;SLC26A6,downstream_gene_variant,,ENST00000420764,NM_134263.2;SLC26A6,downstream_gene_variant,,ENST00000395550,NM_022911.2;SLC26A6,downstream_gene_variant,,ENST00000383733,NM_134426.2;SLC26A6,downstream_gene_variant,,ENST00000455886,NM_001281732.1;SLC26A6,downstream_gene_variant,,ENST00000337000,NM_001281733.1;SLC26A6,downstream_gene_variant,,ENST00000489483,;SLC26A6,downstream_gene_variant,,ENST00000480524,;SLC26A6,downstream_gene_variant,,ENST00000307364,; A ENST00000330862 Transcript missense_variant 222/662 123/480 41/159 Q/H caG/caT 1 -1 TMEM89 HGNC HGNC:32372 protein_coding YES CCDS33751.1 ENSP00000329557 A2RUT3 UPI000006214F NM_001008269.1 deleterious(0.02) 1/2 Pfam_domain:PF15098,hmmpanther:PTHR37869,hmmpanther:PTHR37869:SF1 MODERATE 1 SNV 1 1 PASS rs1266800926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48621634 48621634 C A 1 0 0 0 0 1 0 0 0 16690 796 28 2 2 TMEM89 3 48621634 Missense_Mutation SNP C C3N-00217_T 32446173 48621634 149673925 119 11889 PRICKLE2 0 . GRCh38 3 64099432 64099432 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.2154A>T p.Arg718Ser p.R718S ENST00000295902 8/8 23 16 7 57 57 0 strelka-varscan-mutect PRICKLE2,missense_variant,p.Arg718Ser,ENST00000295902,NM_198859.3;PRICKLE2,missense_variant,p.Arg774Ser,ENST00000564377,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000476308,;PRICKLE2-AS2,upstream_gene_variant,,ENST00000484703,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,; A ENST00000295902 Transcript missense_variant 2740/8305 2154/2535 718/844 R/S agA/agT 1 -1 PRICKLE2 HGNC HGNC:20340 protein_coding YES CCDS2902.1 ENSP00000295902 Q7Z3G6 A0A024R368 UPI0000160A8B NM_198859.3 tolerated(0.34) 8/8 hmmpanther:PTHR24211:SF18,hmmpanther:PTHR24211 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.69126 1 1 1 1 0 A 3 1 43 64099432 64099432 T A 1 0 0 0 0 1 0 0 0 12619 1548 54 4 4 PRICKLE2 3 64099432 Missense_Mutation SNP T C3N-00217_T 15477798 64099432 134196127 120 11890 EPHA3 0 . GRCh38 3 89431173 89431173 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.2160C>T p.= p.V720V ENST00000336596 13/17 177 118 59 159 159 0 strelka-varscan-mutect EPHA3,synonymous_variant,p.=,ENST00000336596,NM_005233.5;EPHA3,synonymous_variant,p.=,ENST00000494014,; T ENST00000336596 Transcript synonymous_variant 2385/5809 2160/2952 720/983 V gtC/gtT 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 13/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 89431173 89431173 C T 1 0 0 0 0 0 0 0 1 5015 813 29 3 3 EPHA3 3 89431173 Silent SNP C C3N-00217_T 25331741 89431173 108864386 121 11891 MYH15 0 . GRCh38 3 108454119 108454119 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.2346G>A p.= p.L782L ENST00000273353 22/42 84 71 13 82 82 0 strelka-varscan-mutect MYH15,synonymous_variant,p.=,ENST00000273353,NM_014981.1;MYH15,downstream_gene_variant,,ENST00000495753,;MYH15,non_coding_transcript_exon_variant,,ENST00000478998,; T ENST00000273353 Transcript synonymous_variant 2403/7074 2346/5841 782/1946 L ctG/ctA 1 -1 MYH15 HGNC HGNC:31073 protein_coding YES CCDS43127.1 ENSP00000273353 Q9Y2K3 UPI0000253B6F NM_014981.1 22/42 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF475,hmmpanther:PTHR13140,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 43 108454119 108454119 C T 1 0 0 0 0 0 0 0 1 10034 581 21 3 3 MYH15 3 108454119 Silent SNP C C3N-00217_T 19022946 108454119 89841440 122 11892 CCDC80 0 . GRCh38 3 112638191 112638191 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1715C>A p.Ser572Tyr p.S572Y ENST00000206423 2/8 258 165 93 311 309 2 strelka-varscan-mutect CCDC80,missense_variant,p.Ser572Tyr,ENST00000206423,NM_199511.2;CCDC80,missense_variant,p.Ser572Tyr,ENST00000439685,NM_199512.2;CCDC80,upstream_gene_variant,,ENST00000461431,;CCDC80,downstream_gene_variant,,ENST00000475181,;CCDC80,downstream_gene_variant,,ENST00000480275,;CCDC80,downstream_gene_variant,,ENST00000469554,;CCDC80,downstream_gene_variant,,ENST00000473959,; T ENST00000206423 Transcript missense_variant 2669/12430 1715/2853 572/950 S/Y tCt/tAt 1 -1 CCDC80 HGNC HGNC:30649 protein_coding YES CCDS2968.1 ENSP00000206423 Q76M96 UPI000004EE7F NM_199511.2 deleterious(0.02) 2/8 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 112638191 112638191 G T 1 0 0 0 0 1 0 0 0 2552 942 33 2 2 CCDC80 3 112638191 Missense_Mutation SNP G C3N-00217_T 4184072 112638191 85657368 123 11893 USF3 0 . GRCh38 3 113659315 113659315 + Missense_Mutation SNP G G T rs747143801 C3N-00217_T C3N-00217_N G G c.2367C>A p.Asn789Lys p.N789K ENST00000316407 7/7 263 195 68 262 262 0 strelka-varscan-mutect USF3,missense_variant,p.Asn789Lys,ENST00000316407,NM_001009899.3;USF3,missense_variant,p.Asn789Lys,ENST00000478658,;USF3,intron_variant,,ENST00000491165,;USF3,non_coding_transcript_exon_variant,,ENST00000496826,; T ENST00000316407 Transcript missense_variant 2778/13708 2367/6738 789/2245 N/K aaC/aaA rs747143801 1 -1 USF3 HGNC HGNC:30494 protein_coding YES CCDS43133.1 ENSP00000320794 Q68DE3 UPI0004438052 NM_001009899.3 tolerated_low_confidence(0.09) 7/7 MODERATE 1 SNV 5 1 PASS rs747143801 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 113659315 113659315 G T 1 0 0 0 0 1 0 0 0 17567 1368 48 2 2 USF3 3 113659315 Missense_Mutation SNP G C3N-00217_T 1021124 113659315 84636244 124 11894 PLA1A 0 . GRCh38 3 119609529 119609529 + Missense_Mutation SNP G G T rs751075487 C3N-00217_T C3N-00217_N G G c.515G>T p.Gly172Val p.G172V ENST00000273371 4/11 222 155 67 198 197 1 strelka-varscan-mutect PLA1A,missense_variant,p.Gly172Val,ENST00000273371,NM_015900.3;PLA1A,missense_variant,p.Gly156Val,ENST00000494440,NM_001293225.1;PLA1A,missense_variant,p.Gly156Val,ENST00000495992,NM_001206960.1;PLA1A,missense_variant,p.Gly38Val,ENST00000475963,;PLA1A,5_prime_UTR_variant,,ENST00000488919,NM_001206961.1;PLA1A,downstream_gene_variant,,ENST00000472126,; T ENST00000273371 Transcript missense_variant 587/1786 515/1371 172/456 G/V gGg/gTg rs751075487 1 1 PLA1A HGNC HGNC:17661 protein_coding YES CCDS2991.1 ENSP00000273371 Q53H76 UPI0000073F97 NM_015900.3 deleterious(0) 4/11 hmmpanther:PTHR11610:SF111,hmmpanther:PTHR11610,Pfam_domain:PF00151,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474,Prints_domain:PR00821 MODERATE 1 SNV 1 1 PASS rs751075487 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 119609529 119609529 G T 1 0 0 0 0 1 0 0 0 12084 1232 43 2 2 PLA1A 3 119609529 Missense_Mutation SNP G C3N-00217_T 5950214 119609529 78686030 125 11895 PLA1A 0 . GRCh38 3 119613032 119613032 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.578G>T p.Gly193Val p.G193V ENST00000273371 5/11 83 57 26 90 90 0 strelka-varscan-mutect PLA1A,missense_variant,p.Gly193Val,ENST00000273371,NM_015900.3;PLA1A,missense_variant,p.Gly177Val,ENST00000494440,NM_001293225.1;PLA1A,missense_variant,p.Gly177Val,ENST00000495992,NM_001206960.1;PLA1A,missense_variant,p.Gly20Val,ENST00000488919,NM_001206961.1;PLA1A,missense_variant,p.Gly59Val,ENST00000475963,; T ENST00000273371 Transcript missense_variant 650/1786 578/1371 193/456 G/V gGa/gTa 1 1 PLA1A HGNC HGNC:17661 protein_coding YES CCDS2991.1 ENSP00000273371 Q53H76 UPI0000073F97 NM_015900.3 deleterious(0) 5/11 hmmpanther:PTHR11610:SF111,hmmpanther:PTHR11610,Pfam_domain:PF00151,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000865,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 119613032 119613032 G T 1 0 0 0 0 1 0 0 0 12084 1174 41 2 2 PLA1A 3 119613032 Missense_Mutation SNP G C3N-00217_T 3503 119613032 78682527 126 11896 MAATS1 0 . GRCh38 3 119740569 119740569 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1554G>T p.Lys518Asn p.K518N ENST00000273390 13/18 163 107 56 136 136 0 strelka-varscan-mutect MAATS1,missense_variant,p.Lys518Asn,ENST00000273390,NM_001320318.1,NM_001320316.1,NM_033364.3;RP11-169N13.4,downstream_gene_variant,,ENST00000489428,;MAATS1,3_prime_UTR_variant,,ENST00000482573,NM_001320318.1,NM_001320317.1;MAATS1,3_prime_UTR_variant,,ENST00000482927,;MAATS1,3_prime_UTR_variant,,ENST00000475093,;MAATS1,non_coding_transcript_exon_variant,,ENST00000483134,;MAATS1,non_coding_transcript_exon_variant,,ENST00000468630,;MAATS1,downstream_gene_variant,,ENST00000461322,; T ENST00000273390 Transcript missense_variant 1631/4433 1554/2304 518/767 K/N aaG/aaT 1 1 MAATS1 HGNC HGNC:24010 protein_coding YES CCDS2994.1 ENSP00000273390 Q7Z4T9 UPI00001C1DFE NM_001320318.1,NM_001320316.1,NM_033364.3 tolerated(0.15) 13/18 hmmpanther:PTHR22455,hmmpanther:PTHR22455:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 119740569 119740569 G T 1 0 0 0 0 1 0 0 0 9055 962 34 2 2 MAATS1 3 119740569 Missense_Mutation SNP G C3N-00217_T 127537 119740569 78554990 127 11897 ARGFX 0 . GRCh38 3 121570721 121570721 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.8A>G p.Asn3Ser p.N3S ENST00000334384 1/4 121 84 37 102 102 0 strelka-varscan-mutect ARGFX,missense_variant,p.Asn3Ser,ENST00000334384,NM_001012659.1; G ENST00000334384 Transcript missense_variant 18/992 8/948 3/315 N/S aAc/aGc 1 1 ARGFX HGNC HGNC:30146 protein_coding YES CCDS33834.1 ENSP00000335578 A6NJG6 UPI00004ED62C NM_001012659.1 tolerated(0.1) 1/4 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 121570721 121570721 A G 1 0 0 0 0 1 0 0 0 983 43 2 5 5 ARGFX 3 121570721 Missense_Mutation SNP A C3N-00217_T 1830152 121570721 76724838 128 11898 ITGB5 0 . GRCh38 3 124764506 124764506 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2189G>T p.Ser730Ile p.S730I ENST00000296181 14/15 98 64 34 98 98 0 strelka-varscan-mutect ITGB5,missense_variant,p.Ser730Ile,ENST00000296181,NM_002213.4;ITGB5,downstream_gene_variant,,ENST00000481591,;ITGB5,non_coding_transcript_exon_variant,,ENST00000461306,;ITGB5,non_coding_transcript_exon_variant,,ENST00000460797,; A ENST00000296181 Transcript missense_variant 2486/4372 2189/2400 730/799 S/I aGc/aTc 1 -1 ITGB5 HGNC HGNC:6160 protein_coding YES CCDS3030.1 ENSP00000296181 P18084 L7RT22 UPI000012DA10 NM_002213.4 deleterious(0.03) 14/15 Gene3D:1.20.5.100,PIRSF_domain:PIRSF002512,Prints_domain:PR01186,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF26,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 43 124764506 124764506 C A 1 0 0 0 0 1 0 0 0 7804 797 28 2 2 ITGB5 3 124764506 Missense_Mutation SNP C C3N-00217_T 3193785 124764506 73531053 129 11899 UROC1 0 . GRCh38 3 126505954 126505954 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.660T>A p.His220Gln p.H220Q ENST00000383579 7/21 318 223 95 313 313 0 strelka-varscan-mutect UROC1,missense_variant,p.His220Gln,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.His220Gln,ENST00000383579,NM_001165974.1; T ENST00000383579 Transcript missense_variant 694/2735 660/2211 220/736 H/Q caT/caA 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 deleterious(0) 7/21 HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 MODERATE 1 SNV 1 1 PASS rs1211889706 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 126505954 126505954 A T 1 0 0 0 0 1 0 0 0 17560 214 8 4 4 UROC1 3 126505954 Missense_Mutation SNP A C3N-00217_T 1741448 126505954 71789605 130 11900 COL6A5 0 . GRCh38 3 130440648 130440648 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.6298G>T p.Ala2100Ser p.A2100S ENST00000265379 36/43 167 122 45 207 207 0 strelka-varscan-mutect COL6A5,missense_variant,p.Ala2100Ser,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Ala356Ser,ENST00000512836,;COL6A5,missense_variant,p.Ala47Ser,ENST00000373157,;COL6A5,upstream_gene_variant,,ENST00000512482,;COL6A5,missense_variant,p.Ala2104Ser,ENST00000312481,; T ENST00000265379 Transcript missense_variant 6792/9214 6298/7836 2100/2611 A/S Gct/Tct COSM3060702,COSM3060703,COSM4319033 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0) 36/43 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 130440648 130440648 G T 1 0 0 0 0 1 0 0 0 3491 1203 42 2 2 COL6A5 3 130440648 Missense_Mutation SNP G C3N-00217_T 3934694 130440648 67854911 131 11901 IL20RB 0 . GRCh38 3 136980589 136980589 + Missense_Mutation SNP A A T C3N-00217_T C3N-00217_N A A c.212A>T p.Gln71Leu p.Q71L ENST00000329582 2/7 168 113 55 190 190 0 strelka-varscan-mutect IL20RB,missense_variant,p.Gln71Leu,ENST00000329582,NM_144717.3;IL20RB-AS1,intron_variant,,ENST00000462176,;IL20RB,intron_variant,,ENST00000484501,;IL20RB,missense_variant,p.Gln39Leu,ENST00000475972,;IL20RB,3_prime_UTR_variant,,ENST00000469964,;IL20RB,3_prime_UTR_variant,,ENST00000491483,; T ENST00000329582 Transcript missense_variant 461/2047 212/936 71/311 Q/L cAg/cTg COSM4113881,COSM4113882 1 1 IL20RB HGNC HGNC:6004 protein_coding YES CCDS3093.1 ENSP00000328133 Q6UXL0 UPI000003E7F6 NM_144717.3 deleterious(0) 2/7 PROSITE_profiles:PS50853,hmmpanther:PTHR20859:SF48,hmmpanther:PTHR20859,Pfam_domain:PF01108,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs771839384 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 136980589 136980589 A T 1 0 0 0 0 1 0 0 0 7572 202 7 4 4 IL20RB 3 136980589 Missense_Mutation SNP A C3N-00217_T 6539941 136980589 61314970 132 11902 SPSB4 0 . GRCh38 3 141066589 141066589 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.485C>A p.Pro162Gln p.P162Q ENST00000310546 2/3 31 22 9 25 25 0 strelka-varscan-mutect SPSB4,missense_variant,p.Pro162Gln,ENST00000310546,NM_080862.2;SPSB4,upstream_gene_variant,,ENST00000508126,; A ENST00000310546 Transcript missense_variant 1229/2908 485/822 162/273 P/Q cCg/cAg 1 1 SPSB4 HGNC HGNC:30630 protein_coding YES CCDS3115.1 ENSP00000311609 Q96A44 UPI00000734A4 NM_080862.2 deleterious(0) 2/3 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF3,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1222450992 . 0 204 6 0 0 0 0 0 -19.99992 1 1 1 1 0 A 3 1 43 141066589 141066589 C A 1 0 0 0 0 1 0 0 0 15471 652 23 1 1 SPSB4 3 141066589 Missense_Mutation SNP C C3N-00217_T 4086000 141066589 57228970 133 11903 RASA2 0 . GRCh38 3 141512253 141512253 + Missense_Mutation SNP G G A rs759141778 C3N-00217_T C3N-00217_N G G c.224G>A p.Arg75His p.R75H ENST00000286364 2/24 128 109 19 186 186 0 strelka-varscan-mutect RASA2,missense_variant,p.Arg75His,ENST00000286364,NM_001303246.1,NM_001303245.1,NM_006506.3;RASA2,missense_variant,p.Arg75His,ENST00000452898,;RASA2,3_prime_UTR_variant,,ENST00000515549,; A ENST00000286364 Transcript missense_variant 259/5614 224/2550 75/849 R/H cGt/cAt rs759141778,COSM3124692,COSM76170 1 1 RASA2 HGNC HGNC:9872 protein_coding YES CCDS3117.1 ENSP00000286364 Q15283 UPI00001351F5 NM_001303246.1,NM_001303245.1,NM_006506.3 deleterious(0) 2/24 PROSITE_profiles:PS50004,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF21,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs759141778 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 141512253 141512253 G A 1 0 0 0 0 1 0 0 0 13220 1145 40 1 1 RASA2 3 141512253 Missense_Mutation SNP G C3N-00217_T 445664 141512253 56783306 134 11904 TSC22D2 0 . GRCh38 3 150411059 150411059 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.1709C>G p.Thr570Arg p.T570R ENST00000361875 1/4 207 139 68 180 180 0 strelka-varscan-mutect TSC22D2,missense_variant,p.Thr570Arg,ENST00000361875,NM_014779.3;TSC22D2,missense_variant,p.Thr18Arg,ENST00000466814,;TSC22D2,missense_variant,p.Thr31Arg,ENST00000480589,;TSC22D2,upstream_gene_variant,,ENST00000485421,; G ENST00000361875 Transcript missense_variant 2725/11154 1709/2343 570/780 T/R aCa/aGa 1 1 TSC22D2 HGNC HGNC:29095 protein_coding YES CCDS3149.1 ENSP00000354543 O75157 UPI00000722E0 NM_014779.3 tolerated(0.13) 1/4 hmmpanther:PTHR12348,hmmpanther:PTHR12348:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 150411059 150411059 C G 1 0 0 0 0 1 0 0 0 17114 478 17 4 4 TSC22D2 3 150411059 Missense_Mutation SNP C C3N-00217_T 8898806 150411059 47884500 135 11905 IL1RAP 0 . GRCh38 3 190656470 190656470 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.1927A>G p.Lys643Glu p.K643E ENST00000317757 12/12 243 219 24 196 196 0 strelka-varscan-mutect IL1RAP,missense_variant,p.Lys643Glu,ENST00000317757,NM_001167931.1;IL1RAP,missense_variant,p.Lys643Glu,ENST00000443369,;IL1RAP,downstream_gene_variant,,ENST00000412504,;IL1RAP,downstream_gene_variant,,ENST00000447382,NM_002182.3;IL1RAP,downstream_gene_variant,,ENST00000072516,NM_001167929.1;RP11-268E23.2,upstream_gene_variant,,ENST00000609508,;IL1RAP,downstream_gene_variant,,ENST00000413869,;IL1RAP,downstream_gene_variant,,ENST00000342550,; G ENST00000317757 Transcript missense_variant 2133/5413 1927/2064 643/687 K/E Aag/Gag 1 1 IL1RAP HGNC HGNC:5995 protein_coding YES CCDS54696.1 ENSP00000314807 Q9NPH3 UPI000020A9C1 NM_001167931.1 deleterious_low_confidence(0.01) 12/12 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 G 3 3 43 190656470 190656470 A G 1 0 0 0 0 1 0 0 0 7563 363 13 5 5 IL1RAP 3 190656470 Missense_Mutation SNP A C3N-00217_T 40245411 190656470 7639089 136 11906 PIGG 0 . GRCh38 4 523652 523652 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1808G>T p.Gly603Val p.G603V ENST00000453061 9/13 241 172 69 234 234 0 strelka-varscan-mutect PIGG,missense_variant,p.Gly603Val,ENST00000453061,NM_001127178.2;PIGG,missense_variant,p.Gly595Val,ENST00000310340,NM_017733.4;PIGG,missense_variant,p.Gly514Val,ENST00000504346,NM_001289051.1;PIGG,missense_variant,p.Gly470Val,ENST00000383028,NM_001289052.1;PIGG,downstream_gene_variant,,ENST00000509768,NM_001289053.1;PIGG,downstream_gene_variant,,ENST00000503111,NM_001289057.1;PIGG,upstream_gene_variant,,ENST00000510235,;PIGG,non_coding_transcript_exon_variant,,ENST00000511247,;PIGG,non_coding_transcript_exon_variant,,ENST00000508562,;PIGG,downstream_gene_variant,,ENST00000506898,;PIGG,downstream_gene_variant,,ENST00000507493,;PIGG,upstream_gene_variant,,ENST00000503261,;PIGG,downstream_gene_variant,,ENST00000513679,;PIGG,downstream_gene_variant,,ENST00000506402,;PIGG,downstream_gene_variant,,ENST00000504187,;PIGG,upstream_gene_variant,,ENST00000511666,;PIGG,upstream_gene_variant,,ENST00000508669,; T ENST00000453061 Transcript missense_variant 1914/3218 1808/2952 603/983 G/V gGt/gTt 1 1 PIGG HGNC HGNC:25985 protein_coding YES CCDS46992.1 ENSP00000415203 Q5H8A4 UPI00004C7A82 NM_001127178.2 tolerated(0.49) 9/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 523652 523652 G T 1 0 0 0 0 1 0 0 0 11982 1261 44 2 2 PIGG 4 523652 Missense_Mutation SNP G C3N-00217_T 523652 189690903 137 11907 CLRN2 0 . GRCh38 4 17515290 17515290 + Silent SNP G G T rs759541960 C3N-00217_T C3N-00217_N G G c.24G>T p.= p.A8A ENST00000511148 1/3 151 103 48 131 131 0 strelka-varscan-mutect CLRN2,synonymous_variant,p.=,ENST00000511148,NM_001079827.2;QDPR,upstream_gene_variant,,ENST00000281243,NM_000320.2;QDPR,upstream_gene_variant,,ENST00000428702,NM_001306140.1;QDPR,upstream_gene_variant,,ENST00000513615,;QDPR,upstream_gene_variant,,ENST00000505710,;QDPR,upstream_gene_variant,,ENST00000508623,;QDPR,upstream_gene_variant,,ENST00000507439,;QDPR,upstream_gene_variant,,ENST00000514300,; T ENST00000511148 Transcript synonymous_variant 126/823 24/699 8/232 A gcG/gcT rs759541960 1 1 CLRN2 HGNC HGNC:33939 protein_coding YES CCDS47032.1 ENSP00000424711 A0PK11 UPI0000D6154A NM_001079827.2 1/3 hmmpanther:PTHR31548,hmmpanther:PTHR31548:SF5 LOW 1 SNV 1 1 PASS rs759541960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 17515290 17515290 G T 1 0 0 0 0 0 0 0 1 3330 1132 40 1 1 CLRN2 4 17515290 Silent SNP G C3N-00217_T 16991638 17515290 172699265 138 11908 ADGRA3 0 . GRCh38 4 22454865 22454865 + Splice_Site SNP C C A novel C3N-00217_T C3N-00217_N C C c.473+1G>T p.X158_splice ENST00000334304 152 118 34 203 202 1 strelka-varscan-mutect ADGRA3,splice_donor_variant,,ENST00000334304,NM_145290.3;ADGRA3,splice_donor_variant,,ENST00000502482,;ADGRA3,splice_donor_variant,,ENST00000514129,;ADGRA3,splice_donor_variant,,ENST00000282943,;ADGRA3,splice_donor_variant,,ENST00000513385,;ADGRA3,splice_donor_variant,,ENST00000514749,;ADGRA3,intron_variant,,ENST00000506133,; A ENST00000334304 Transcript splice_donor_variant -/4566 473/3966 158/1321 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 4/18 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 43 22454865 22454865 C A 1 0 0 0 0 0 0 1 0 354 492 17 2 2 ADGRA3 4 22454865 Splice_Site SNP C C3N-00217_T 4939575 22454865 167759690 139 11909 TLR10 0 . GRCh38 4 38774319 38774319 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.1272C>A p.= p.V424V ENST00000308973 4/4 60 41 19 87 87 0 strelka-varscan-mutect TLR10,synonymous_variant,p.=,ENST00000308973,NM_030956.3;TLR10,synonymous_variant,p.=,ENST00000613579,NM_001195108.1,NM_001195106.1;TLR10,synonymous_variant,p.=,ENST00000622002,NM_001195107.1;TLR10,synonymous_variant,p.=,ENST00000361424,NM_001017388.2;TLR10,synonymous_variant,p.=,ENST00000506111,;TLR10,synonymous_variant,p.=,ENST00000508334,;TLR10,downstream_gene_variant,,ENST00000502321,;TLR10,downstream_gene_variant,,ENST00000507953,; T ENST00000308973 Transcript synonymous_variant 1878/3958 1272/2436 424/811 V gtC/gtA 1 -1 TLR10 HGNC HGNC:15634 protein_coding YES CCDS3445.1 ENSP00000308925 Q9BXR5 A0A024R9W4 UPI0000048F1C NM_030956.3 4/4 hmmpanther:PTHR24365:SF131,hmmpanther:PTHR24365,PIRSF_domain:PIRSF037595,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 38774319 38774319 G T 1 0 0 0 0 0 0 0 1 16396 1277 45 2 2 TLR10 4 38774319 Silent SNP G C3N-00217_T 16319454 38774319 151440236 140 11910 KDR 0 . GRCh38 4 55102397 55102397 + Nonsense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.2099G>A p.Trp700Ter p.W700* ENST00000263923 14/30 269 193 76 301 301 0 strelka-varscan-mutect KDR,stop_gained,p.Trp700Ter,ENST00000263923,NM_002253.2;KDR,downstream_gene_variant,,ENST00000512566,; T ENST00000263923 Transcript stop_gained 2395/5831 2099/4071 700/1356 W/* tGg/tAg COSM4992136 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 14/30 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 55102397 55102397 C T 1 0 0 0 0 0 1 0 0 8059 595 21 3 3 KDR 4 55102397 Nonsense_Mutation SNP C C3N-00217_T 16328078 55102397 135112158 141 11911 KIAA1211 0 . GRCh38 4 56314928 56314928 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1426C>A p.Arg476Ser p.R476S ENST00000504228 6/9 263 187 76 227 227 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Arg476Ser,ENST00000504228,;KIAA1211,missense_variant,p.Arg469Ser,ENST00000541073,;KIAA1211,missense_variant,p.Arg476Ser,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; A ENST00000504228 Transcript missense_variant 1531/4628 1426/3702 476/1233 R/S Cgt/Agt 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 tolerated(0.11) 6/9 MODERATE 1 SNV 5 1 PASS rs1407907307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 56314928 56314928 C A 1 0 0 0 0 1 0 0 0 8107 884 31 1 1 KIAA1211 4 56314928 Missense_Mutation SNP C C3N-00217_T 1212531 56314928 133899627 142 11912 TECRL 0 . GRCh38 4 64309848 64309848 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.635C>G p.Thr212Arg p.T212R ENST00000381210 6/12 157 133 24 249 249 0 strelka-varscan-mutect TECRL,missense_variant,p.Thr212Arg,ENST00000381210,NM_001010874.4;TECRL,missense_variant,p.Thr212Arg,ENST00000507440,;TECRL,non_coding_transcript_exon_variant,,ENST00000513125,;TECRL,non_coding_transcript_exon_variant,,ENST00000511356,; C ENST00000381210 Transcript missense_variant 746/3573 635/1092 212/363 T/R aCa/aGa COSM1267605 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 deleterious(0.01) 6/12 Pfam_domain:PF02544,hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 64309848 64309848 G C 1 0 0 0 0 1 0 0 0 16157 1377 48 4 4 TECRL 4 64309848 Missense_Mutation SNP G C3N-00217_T 7994920 64309848 125904707 143 11913 TMPRSS11B 0 . GRCh38 4 68227964 68227964 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.1198T>C p.Tyr400His p.Y400H ENST00000332644 10/10 111 99 12 161 161 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Tyr400His,ENST00000332644,NM_182502.3;TMPRSS11B,downstream_gene_variant,,ENST00000502365,;TMPRSS11B,downstream_gene_variant,,ENST00000510856,; G ENST00000332644 Transcript missense_variant 1360/2671 1198/1251 400/416 Y/H Tat/Cat 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 deleterious(0) 10/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF171,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.39634 0.9999999 1 1 1 0 G 3 3 43 68227964 68227964 A G 1 0 0 0 0 1 0 0 0 16716 420 15 5 5 TMPRSS11B 4 68227964 Missense_Mutation SNP A C3N-00217_T 3918116 68227964 121986591 144 11914 TMPRSS11B 0 . GRCh38 4 68229281 68229281 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.922G>T p.Gly308Cys p.G308C ENST00000332644 8/10 71 50 21 92 92 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Gly308Cys,ENST00000332644,NM_182502.3;TMPRSS11B,non_coding_transcript_exon_variant,,ENST00000510856,;TMPRSS11B,downstream_gene_variant,,ENST00000502365,; A ENST00000332644 Transcript missense_variant 1084/2671 922/1251 308/416 G/C Ggt/Tgt 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 deleterious(0) 8/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF171,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 43 68229281 68229281 C A 1 0 0 0 0 1 0 0 0 16716 681 24 2 2 TMPRSS11B 4 68229281 Missense_Mutation SNP C C3N-00217_T 1317 68229281 121985274 145 11915 UGT2B7 0 . GRCh38 4 69098632 69098632 + Missense_Mutation SNP C C G rs544218603 C3N-00217_T C3N-00217_N C C c.814C>G p.Pro272Ala p.P272A ENST00000305231 2/6 202 175 27 240 240 0 strelka-varscan-mutect UGT2B7,missense_variant,p.Pro272Ala,ENST00000305231,NM_001074.2;UGT2B7,missense_variant,p.Pro272Ala,ENST00000508661,;UGT2B7,missense_variant,p.Pro272Ala,ENST00000622664,;UGT2B7,missense_variant,p.Pro23Ala,ENST00000502942,;UGT2B7,non_coding_transcript_exon_variant,,ENST00000509763,; G ENST00000305231 Transcript missense_variant 860/1887 814/1590 272/529 P/A Cca/Gca rs544218603 1 1 UGT2B7 HGNC HGNC:12554 protein_coding YES CCDS3526.1 ENSP00000304811 P16662 UPI00000015EC NM_001074.2 deleterious(0) 2/6 hmmpanther:PTHR11926:SF382,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs544218603 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 69098632 69098632 C G 1 0 0 0 0 1 0 0 0 17486 507 18 4 4 UGT2B7 4 69098632 Missense_Mutation SNP C C3N-00217_T 869351 69098632 121115923 146 11916 UGT2B4 0 . GRCh38 4 69495754 69495754 + Nonsense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.108G>A p.Trp36Ter p.W36* ENST00000305107 1/6 120 88 32 119 119 0 strelka-varscan-mutect UGT2B4,stop_gained,p.Trp36Ter,ENST00000305107,NM_021139.2;UGT2B4,stop_gained,p.Trp36Ter,ENST00000512583,NM_001297615.1;UGT2B4,stop_gained,p.Trp36Ter,ENST00000510114,;UGT2B4,non_coding_transcript_exon_variant,,ENST00000506580,;UGT2B4,intron_variant,,ENST00000502655,;UGT2B4,intron_variant,,ENST00000503836,; T ENST00000305107 Transcript stop_gained 155/2103 108/1587 36/528 W/* tgG/tgA COSM587866 1 -1 UGT2B4 HGNC HGNC:12553 protein_coding YES CCDS43234.1 ENSP00000305221 P06133 UPI000000087F NM_021139.2 1/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF198,Pfam_domain:PF00201,Superfamily_domains:SSF53756 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 69495754 69495754 C T 1 0 0 0 0 0 1 0 0 17485 856 30 3 3 UGT2B4 4 69495754 Nonsense_Mutation SNP C C3N-00217_T 397122 69495754 120718801 147 11917 CSN2 0 . GRCh38 4 69957567 69957567 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.382C>A p.Pro128Thr p.P128T ENST00000353151 5/7 363 266 97 381 380 1 strelka-varscan-mutect CSN2,missense_variant,p.Pro128Thr,ENST00000353151,NM_001302770.1,NM_001891.3; T ENST00000353151 Transcript missense_variant 394/1066 382/681 128/226 P/T Cct/Act COSM1540955 1 -1 CSN2 HGNC HGNC:2447 protein_coding YES CCDS3532.1 ENSP00000341030 P05814 W5RWE1 UPI0000126FDB NM_001302770.1,NM_001891.3 tolerated(0.24) 5/7 hmmpanther:PTHR11500:SF0,hmmpanther:PTHR11500,PIRSF_domain:PIRSF002372 1 MODERATE 1 SNV 1 1 1 PASS rs1003669682 . 0 207 0 0 3 0 0 0 -20 0.9883043 1 1 1 0 T 3 4 43 69957567 69957567 G T 1 0 0 0 0 1 0 0 0 3748 1232 43 2 2 CSN2 4 69957567 Missense_Mutation SNP G C3N-00217_T 461813 69957567 120256988 148 11918 NUP54 0 . GRCh38 4 76144293 76144293 + Splice_Site SNP C C T novel C3N-00217_T C3N-00217_N C C c.152-1G>A p.X51_splice ENST00000264883 122 84 38 140 140 0 strelka-varscan-mutect NUP54,splice_acceptor_variant,,ENST00000264883,NM_017426.3;NUP54,splice_acceptor_variant,,ENST00000514901,;NUP54,intron_variant,,ENST00000514987,NM_001278603.1;NUP54,splice_acceptor_variant,,ENST00000515460,;NUP54,splice_acceptor_variant,,ENST00000514307,;NUP54,splice_acceptor_variant,,ENST00000506098,;NUP54,splice_acceptor_variant,,ENST00000508583,;NUP54,splice_acceptor_variant,,ENST00000510569,;NUP54,splice_acceptor_variant,,ENST00000510884,;NUP54,splice_acceptor_variant,,ENST00000507257,;NUP54,splice_acceptor_variant,,ENST00000502850,;NUP54,splice_acceptor_variant,,ENST00000512151,;NUP54,splice_acceptor_variant,,ENST00000513352,;NUP54,intron_variant,,ENST00000504173,; T ENST00000264883 Transcript splice_acceptor_variant -/2367 152/1524 51/507 1 -1 NUP54 HGNC HGNC:17359 protein_coding YES CCDS3576.1 ENSP00000264883 Q7Z3B4 UPI0000036166 NM_017426.3 2/11 HIGH 1 SNV 1 1 PASS rs1180314955 . 0 204 2 4 0 0 0 0 -20 0.999932 1 1 1 0 T 5 4 43 76144293 76144293 C T 1 0 0 0 0 0 0 1 0 10832 695 24 3 3 NUP54 4 76144293 Splice_Site SNP C C3N-00217_T 6186726 76144293 114070262 149 11919 GK2 0 . GRCh38 4 79407683 79407683 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.518C>A p.Ala173Asp p.A173D ENST00000358842 1/1 196 146 50 247 247 0 strelka-varscan-mutect GK2,missense_variant,p.Ala173Asp,ENST00000358842,NM_033214.2; T ENST00000358842 Transcript missense_variant 611/1942 518/1662 173/553 A/D gCt/gAt 1 -1 GK2 HGNC HGNC:4291 protein_coding YES CCDS3585.1 ENSP00000351706 Q14410 A0A140VKG0 UPI000011E629 NM_033214.2 deleterious(0.01) 1/1 hmmpanther:PTHR10196:SF46,hmmpanther:PTHR10196,TIGRFAM_domain:TIGR01311,Pfam_domain:PF00370,Gene3D:3.30.420.40,PIRSF_domain:PIRSF000538,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 79407683 79407683 G T 1 0 0 0 0 1 0 0 0 6299 971 34 2 2 GK2 4 79407683 Missense_Mutation SNP G C3N-00217_T 3263390 79407683 110806872 150 11920 HERC5 0 . GRCh38 4 88494199 88494199 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2312G>T p.Gly771Val p.G771V ENST00000264350 18/23 162 100 62 165 163 2 strelka-varscan HERC5,missense_variant,p.Gly771Val,ENST00000264350,NM_016323.3;HERC5,missense_variant,p.Gly409Val,ENST00000508159,;HERC5,non_coding_transcript_exon_variant,,ENST00000510223,;HERC5,non_coding_transcript_exon_variant,,ENST00000502913,; T ENST00000264350 Transcript missense_variant 2465/3513 2312/3075 771/1024 G/V gGg/gTg 1 1 HERC5 HGNC HGNC:24368 protein_coding YES CCDS3630.1 ENSP00000264350 Q9UII4 UPI000013D500 NM_016323.3 deleterious(0) 18/23 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF344,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 125 2 31 48 4 0 0 -9.200608 0 0 1 0 0 T 3 4 43 88494199 88494199 G T 1 0 0 0 0 1 0 0 0 6945 1232 43 2 2 HERC5 4 88494199 Missense_Mutation SNP G C3N-00217_T 9086516 88494199 101720356 151 11921 RP11-766F14.2 0 . GRCh38 4 99652703 99652703 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1946C>A p.Ser649Tyr p.S649Y ENST00000511828 1/2 192 129 63 164 164 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Ser649Tyr,ENST00000511828,; T ENST00000511828 Transcript missense_variant 1946/10086 1946/5382 649/1793 S/Y tCc/tAc 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE deleterious(0) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 99652703 99652703 G T 1 0 0 0 0 1 0 0 0 13762 1174 41 2 2 RP11-766F14.2 4 99652703 Missense_Mutation SNP G C3N-00217_T 11158504 99652703 90561852 152 11922 PPP3CA 0 . GRCh38 4 101061147 101061147 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1096G>T p.Val366Leu p.V366L ENST00000394854 10/14 159 119 40 271 271 0 strelka-varscan-mutect PPP3CA,missense_variant,p.Val366Leu,ENST00000394854,NM_000944.4;PPP3CA,missense_variant,p.Val324Leu,ENST00000323055,NM_001130692.1;PPP3CA,missense_variant,p.Val134Leu,ENST00000512215,;PPP3CA,missense_variant,p.Val366Leu,ENST00000394853,NM_001130691.1;PPP3CA,missense_variant,p.Val268Leu,ENST00000507176,; A ENST00000394854 Transcript missense_variant 1780/4685 1096/1566 366/521 V/L Gta/Tta 1 -1 PPP3CA HGNC HGNC:9314 protein_coding YES CCDS34037.1 ENSP00000378323 Q08209 A0A0S2Z4C6 UPI0000110660 NM_000944.4 tolerated(0.23) 10/14 hmmpanther:PTHR11668:SF261,hmmpanther:PTHR11668,Gene3D:3.60.21.10,Superfamily_domains:SSF56300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 101061147 101061147 C A 1 0 0 0 0 1 0 0 0 12519 507 18 2 2 PPP3CA 4 101061147 Missense_Mutation SNP C C3N-00217_T 1408444 101061147 89153408 153 11923 LARP7 0 . GRCh38 4 112646955 112646955 + Missense_Mutation SNP G G T rs199621386 C3N-00217_T C3N-00217_N G G c.573G>T p.Glu191Asp p.E191D ENST00000509061 7/15 69 46 23 96 96 0 strelka-mutect LARP7,missense_variant,p.Glu191Asp,ENST00000509061,NM_001267039.1;LARP7,missense_variant,p.Glu184Asp,ENST00000344442,NM_016648.3;LARP7,missense_variant,p.Glu184Asp,ENST00000324052,NM_015454.2;LARP7,missense_variant,p.Glu184Asp,ENST00000505034,;LARP7,intron_variant,,ENST00000513553,;LARP7,upstream_gene_variant,,ENST00000511529,;LARP7,downstream_gene_variant,,ENST00000507443,;LARP7,downstream_gene_variant,,ENST00000508577,;MIR302B,downstream_gene_variant,,ENST00000362188,;MIR302A,downstream_gene_variant,,ENST00000385192,;MIR302C,downstream_gene_variant,,ENST00000362232,;MIR302D,downstream_gene_variant,,ENST00000362275,;MIR367,downstream_gene_variant,,ENST00000362299,;MIR302B,non_coding_transcript_exon_variant,,ENST00000510655,;MIR302B,non_coding_transcript_exon_variant,,ENST00000509938,;MIR302B,non_coding_transcript_exon_variant,,ENST00000505215,;LARP7,splice_region_variant,,ENST00000503316,;LARP7,splice_region_variant,,ENST00000509622,;LARP7,downstream_gene_variant,,ENST00000512589,;LARP7,downstream_gene_variant,,ENST00000505216,; T ENST00000509061 Transcript missense_variant,splice_region_variant 876/2332 573/1770 191/589 E/D gaG/gaT rs199621386 1 1 LARP7 HGNC HGNC:24912 protein_coding YES CCDS58924.1 ENSP00000422626 Q4G0J3 UPI000020B34C NM_001267039.1 tolerated(0.06) 7/15 PROSITE_profiles:PS50102,hmmpanther:PTHR22792,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs199621386 . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 43 112646955 112646955 G T 1 0 0 0 0 1 0 0 0 8544 1014 35 2 2 LARP7 4 112646955 Missense_Mutation SNP G C3N-00217_T 11585808 112646955 77567600 154 11924 KIAA1109 0 . GRCh38 4 122349913 122349913 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.13688G>A p.Arg4563Lys p.R4563K ENST00000264501 80/86 209 159 50 249 249 0 strelka-varscan-mutect KIAA1109,missense_variant,p.Arg4563Lys,ENST00000264501,;KIAA1109,missense_variant,p.Arg4563Lys,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Arg1232Lys,ENST00000438707,;KIAA1109,missense_variant,p.Arg939Lys,ENST00000306802,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000491933,; A ENST00000264501 Transcript missense_variant 14061/15896 13688/15018 4563/5005 R/K aGg/aAg 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 tolerated(0.75) 80/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640,Pfam_domain:PF10479,SMART_domains:SM01220 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 122349913 122349913 G A 1 0 0 0 0 1 0 0 0 8101 1000 35 3 3 KIAA1109 4 122349913 Missense_Mutation SNP G C3N-00217_T 9702958 122349913 67864642 155 11925 KIAA1109 0 . GRCh38 4 122356725 122356725 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.14605G>T p.Val4869Leu p.V4869L ENST00000264501 84/86 169 116 53 178 176 2 strelka-varscan-mutect KIAA1109,missense_variant,p.Val4869Leu,ENST00000264501,;KIAA1109,missense_variant,p.Val4869Leu,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Val1538Leu,ENST00000438707,;KIAA1109,missense_variant,p.Val1245Leu,ENST00000306802,; T ENST00000264501 Transcript missense_variant 14978/15896 14605/15018 4869/5005 V/L Gta/Tta 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 deleterious(0.01) 84/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640,Pfam_domain:PF10479,SMART_domains:SM01220 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 122356725 122356725 G T 1 0 0 0 0 1 0 0 0 8101 1029 36 2 2 KIAA1109 4 122356725 Missense_Mutation SNP G C3N-00217_T 6812 122356725 67857830 156 11926 FAT4 0 . GRCh38 4 125319628 125319628 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.3217T>G p.Ser1073Ala p.S1073A ENST00000394329 1/17 61 53 8 101 101 0 strelka-varscan-mutect FAT4,missense_variant,p.Ser1073Ala,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; G ENST00000394329 Transcript missense_variant 3230/16123 3217/14946 1073/4981 S/A Tct/Gct 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.33) 1/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 125319628 125319628 T G 1 0 0 0 0 1 0 0 0 5552 1783 62 5 5 FAT4 4 125319628 Missense_Mutation SNP T C3N-00217_T 2962903 125319628 64894927 157 11927 FAT4 0 . GRCh38 4 125449109 125449109 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.8093G>T p.Gly2698Val p.G2698V ENST00000394329 9/17 194 147 47 316 316 0 strelka-varscan-mutect FAT4,missense_variant,p.Gly2698Val,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Gly996Val,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; T ENST00000394329 Transcript missense_variant 8106/16123 8093/14946 2698/4981 G/V gGa/gTa 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.01) 9/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 125449109 125449109 G T 1 0 0 0 0 1 0 0 0 5552 1174 41 2 2 FAT4 4 125449109 Missense_Mutation SNP G C3N-00217_T 129481 125449109 64765446 158 11928 FAT4 0 . GRCh38 4 125449773 125449773 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.8757G>T p.Arg2919Ser p.R2919S ENST00000394329 9/17 73 54 19 140 140 0 strelka-varscan-mutect FAT4,missense_variant,p.Arg2919Ser,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Arg1217Ser,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; T ENST00000394329 Transcript missense_variant 8770/16123 8757/14946 2919/4981 R/S agG/agT 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.42) 9/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 125449773 125449773 G T 1 0 0 0 0 1 0 0 0 5552 1165 41 2 2 FAT4 4 125449773 Missense_Mutation SNP G C3N-00217_T 664 125449773 64764782 159 11929 PCDH18 0 . GRCh38 4 137532083 137532083 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.6C>A p.His2Gln p.H2Q ENST00000344876 1/4 43 31 12 63 63 0 strelka-varscan-mutect PCDH18,missense_variant,p.His2Gln,ENST00000344876,NM_019035.4;PCDH18,missense_variant,p.His2Gln,ENST00000412923,NM_001300828.1;PCDH18,intron_variant,,ENST00000507846,;PCDH18,intron_variant,,ENST00000510305,;PCDH18,intron_variant,,ENST00000511115,;PCDH18,intron_variant,,ENST00000611581,;PCDH18,upstream_gene_variant,,ENST00000620262,;PCDH18,upstream_gene_variant,,ENST00000617302,; T ENST00000344876 Transcript missense_variant 393/5906 6/3408 2/1135 H/Q caC/caA 1 -1 PCDH18 HGNC HGNC:14268 protein_coding YES CCDS34064.1 ENSP00000355082 Q9HCL0 UPI0000047A88 NM_019035.4 tolerated_low_confidence(0.3) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF9,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 137532083 137532083 G T 1 0 0 0 0 1 0 0 0 11600 1252 44 2 2 PCDH18 4 137532083 Missense_Mutation SNP G C3N-00217_T 12082310 137532083 52682472 160 11930 FBXW7 0 . GRCh38 4 152337912 152337912 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.751C>G p.Leu251Val p.L251V ENST00000281708 5/12 109 93 16 132 132 0 strelka-varscan-mutect FBXW7,missense_variant,p.Leu251Val,ENST00000281708,NM_033632.3;FBXW7,missense_variant,p.Leu171Val,ENST00000263981,NM_018315.4;FBXW7,missense_variant,p.Leu133Val,ENST00000296555,NM_001013415.1;FBXW7,missense_variant,p.Leu251Val,ENST00000603548,;FBXW7,missense_variant,p.Leu251Val,ENST00000603841,;FBXW7,missense_variant,p.Leu75Val,ENST00000393956,;DEAR,non_coding_transcript_exon_variant,,ENST00000605147,; C ENST00000281708 Transcript missense_variant 1981/4976 751/2124 251/707 L/V Ctt/Gtt 1 -1 FBXW7 HGNC HGNC:16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 UPI000007007E NM_033632.3 tolerated(0.17) 5/12 hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF217 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 152337912 152337912 G C 1 0 0 0 0 1 0 0 0 5632 971 34 4 4 FBXW7 4 152337912 Missense_Mutation SNP G C3N-00217_T 14805829 152337912 37876643 161 11931 TRIM2 0 . GRCh38 4 153315529 153315529 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1555G>T p.Val519Leu p.V519L ENST00000338700 7/12 116 77 39 128 128 0 strelka-varscan-mutect TRIM2,missense_variant,p.Val519Leu,ENST00000338700,NM_015271.4;TRIM2,missense_variant,p.Val492Leu,ENST00000437508,NM_001130067.1; T ENST00000338700 Transcript missense_variant 1620/6735 1555/2316 519/771 V/L Gta/Tta 1 1 TRIM2 HGNC HGNC:15974 protein_coding YES CCDS3781.2 ENSP00000339659 Q9C040 UPI00005A60C0 NM_015271.4 tolerated(0.15) 7/12 Gene3D:2.120.10.30,Pfam_domain:PF01436,PROSITE_profiles:PS51125,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF2,Superfamily_domains:SSF101898 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 153315529 153315529 G T 1 0 0 0 0 1 0 0 0 16983 1261 44 2 2 TRIM2 4 153315529 Missense_Mutation SNP G C3N-00217_T 977617 153315529 36899026 162 11932 DDX60 0 . GRCh38 4 168236345 168236345 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.4440G>T p.Met1480Ile p.M1480I ENST00000393743 33/38 94 66 28 132 132 0 strelka-varscan-mutect DDX60,missense_variant,p.Met1480Ile,ENST00000393743,NM_017631.5;DDX60,upstream_gene_variant,,ENST00000511317,;DDX60,non_coding_transcript_exon_variant,,ENST00000507815,; A ENST00000393743 Transcript missense_variant 4732/6071 4440/5139 1480/1712 M/I atG/atT 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 deleterious(0.02) 33/38 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 168236345 168236345 C A 1 0 0 0 0 1 0 0 0 4181 594 21 2 2 DDX60 4 168236345 Missense_Mutation SNP C C3N-00217_T 14920816 168236345 21978210 163 11933 STOX2 0 . GRCh38 4 184009771 184009771 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.933G>T p.Glu311Asp p.E311D ENST00000308497 3/4 287 209 78 274 274 0 strelka-varscan-mutect STOX2,missense_variant,p.Glu311Asp,ENST00000308497,NM_020225.1;STOX2,upstream_gene_variant,,ENST00000506529,;RP11-739P1.3,upstream_gene_variant,,ENST00000636429,;STOX2,intron_variant,,ENST00000513034,;STOX2,downstream_gene_variant,,ENST00000512520,; T ENST00000308497 Transcript missense_variant 2368/10458 933/2781 311/926 E/D gaG/gaT 1 1 STOX2 HGNC HGNC:25450 protein_coding YES CCDS47167.1 ENSP00000311257 Q9P2F5 UPI00001C1E11 NM_020225.1 deleterious(0) 3/4 hmmpanther:PTHR22437,hmmpanther:PTHR22437:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 184009771 184009771 G T 1 0 0 0 0 1 0 0 0 15698 933 33 2 2 STOX2 4 184009771 Missense_Mutation SNP G C3N-00217_T 15773426 184009771 6204784 164 11934 FAT1 0 . GRCh38 4 186620073 186620073 + Silent SNP C C A rs372725093 C3N-00217_T C3N-00217_N C C c.6513G>T p.= p.P2171P ENST00000441802 10/27 197 133 64 214 213 1 strelka-varscan-mutect FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,; A ENST00000441802 Transcript synonymous_variant 6723/14786 6513/13767 2171/4588 P ccG/ccT rs372725093 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 10/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS rs372725093 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 186620073 186620073 C A 1 0 0 0 0 0 0 0 1 5549 871 31 1 1 FAT1 4 186620073 Silent SNP C C3N-00217_T 2610302 186620073 3594482 165 11935 IRX4 0 . GRCh38 5 1878009 1878009 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.1598T>A p.Leu533His p.L533H ENST00000613726 7/7 45 28 17 42 42 0 strelka-varscan-mutect IRX4,missense_variant,p.Leu507His,ENST00000505790,NM_001278634.1;IRX4,missense_variant,p.Leu533His,ENST00000613726,NM_001278635.1;IRX4,missense_variant,p.Leu533His,ENST00000622814,NM_001278633.1;IRX4,missense_variant,p.Leu507His,ENST00000513692,NM_001278632.1;IRX4,missense_variant,p.Leu507His,ENST00000231357,NM_016358.2;IRX4,downstream_gene_variant,,ENST00000511126,;IRX4,downstream_gene_variant,,ENST00000505938,;IRX4,3_prime_UTR_variant,,ENST00000508261,; T ENST00000613726 Transcript missense_variant 1821/2403 1598/1638 533/545 L/H cTc/cAc 1 -1 IRX4 HGNC HGNC:6129 protein_coding YES CCDS75225.1 ENSP00000482393 P78413 UPI000020BF08 NM_001278635.1 deleterious_low_confidence(0) 7/7 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF16,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 1878009 1878009 A T 1 0 0 0 0 1 0 0 0 7754 304 11 4 4 IRX4 5 1878009 Missense_Mutation SNP A C3N-00217_T 1878009 179660250 166 11936 ADCY2 0 . GRCh38 5 7709307 7709307 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.1498T>C p.Ser500Pro p.S500P ENST00000338316 10/25 193 159 34 159 159 0 strelka-varscan-mutect ADCY2,missense_variant,p.Ser500Pro,ENST00000338316,NM_020546.2;RP11-711G10.1,intron_variant,,ENST00000514105,; C ENST00000338316 Transcript missense_variant 1587/6575 1498/3276 500/1091 S/P Tcc/Ccc 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0.01) 10/25 Pfam_domain:PF06327,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 7709307 7709307 T C 1 0 0 0 0 1 0 0 0 338 1667 58 5 5 ADCY2 5 7709307 Missense_Mutation SNP T C3N-00217_T 5831298 7709307 173828952 167 11937 DNAH5 0 . GRCh38 5 13866227 13866227 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.4109T>C p.Met1370Thr p.M1370T ENST00000265104 26/79 257 237 20 306 306 0 strelka-varscan-mutect DNAH5,missense_variant,p.Met1370Thr,ENST00000265104,NM_001369.2;CTB-51A17.1,intron_variant,,ENST00000637153,;CTB-51A17.1,intron_variant,,ENST00000503244,; G ENST00000265104 Transcript missense_variant 4214/15633 4109/13875 1370/4624 M/T aTg/aCg 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 tolerated(0.12) 26/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 13866227 13866227 A G 1 0 0 0 0 1 0 0 0 4419 217 8 5 5 DNAH5 5 13866227 Missense_Mutation SNP A C3N-00217_T 6156920 13866227 167672032 168 11938 CDH12 0 . GRCh38 5 21842199 21842199 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.776T>A p.Leu259His p.L259H ENST00000382254 8/15 144 100 44 161 161 0 strelka-varscan-mutect CDH12,missense_variant,p.Leu259His,ENST00000382254,NM_004061.3;CDH12,missense_variant,p.Leu259His,ENST00000504376,;CDH12,missense_variant,p.Leu219His,ENST00000522262,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript missense_variant 1863/4164 776/2385 259/794 L/H cTc/cAc 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 deleterious(0) 8/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 21842199 21842199 A T 1 0 0 0 0 1 0 0 0 2801 304 11 4 4 CDH12 5 21842199 Missense_Mutation SNP A C3N-00217_T 7975972 21842199 159696060 169 11939 PRDM9 0 . GRCh38 5 23509938 23509938 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.212C>T p.Pro71Leu p.P71L ENST00000296682 4/11 349 251 98 327 327 0 strelka-varscan-mutect PRDM9,missense_variant,p.Pro71Leu,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Pro12Leu,ENST00000635252,;PRDM9,missense_variant,p.Pro71Leu,ENST00000502755,; T ENST00000296682 Transcript missense_variant 394/3691 212/2685 71/894 P/L cCa/cTa 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious_low_confidence(0) 4/11 PROSITE_profiles:PS50806,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 23509938 23509938 C T 1 0 0 0 0 1 0 0 0 12595 594 21 3 3 PRDM9 5 23509938 Missense_Mutation SNP C C3N-00217_T 1667739 23509938 158028321 170 11940 PRDM9 0 . GRCh38 5 23526464 23526464 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1376G>T p.Arg459Met p.R459M ENST00000296682 11/11 425 295 130 448 448 0 strelka-varscan-mutect PRDM9,missense_variant,p.Arg459Met,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Arg400Met,ENST00000635252,; T ENST00000296682 Transcript missense_variant 1558/3691 1376/2685 459/894 R/M aGg/aTg 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 tolerated(0.13) 11/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10 MODERATE 1 SNV 1 1 PASS rs1327487744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 23526464 23526464 G T 1 0 0 0 0 1 0 0 0 12595 1000 35 2 2 PRDM9 5 23526464 Missense_Mutation SNP G C3N-00217_T 16526 23526464 158011795 171 11941 RXFP3 0 . GRCh38 5 33936896 33936896 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.156G>T p.= p.L52L ENST00000330120 1/1 47 42 5 40 40 0 strelka-varscan-mutect RXFP3,synonymous_variant,p.=,ENST00000330120,NM_016568.3; T ENST00000330120 Transcript synonymous_variant 511/1852 156/1410 52/469 L ctG/ctT 1 1 RXFP3 HGNC HGNC:24883 protein_coding YES CCDS3900.1 ENSP00000328708 Q9NSD7 UPI0000046AEB NM_016568.3 1/1 LOW 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -12.47081 0.9999999 1 1 1 0 T 2 4 43 33936896 33936896 G T 1 0 0 0 0 0 0 0 1 14022 1335 47 2 2 RXFP3 5 33936896 Silent SNP G C3N-00217_T 10410432 33936896 147601363 172 11942 DAB2 0 . GRCh38 5 39390473 39390473 + Nonsense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.433C>T p.Gln145Ter p.Q145* ENST00000320816 5/15 196 131 65 174 174 0 strelka-varscan-mutect DAB2,stop_gained,p.Gln145Ter,ENST00000545653,NM_001244871.1;DAB2,stop_gained,p.Gln145Ter,ENST00000320816,NM_001343.3;DAB2,stop_gained,p.Gln145Ter,ENST00000339788,;DAB2,stop_gained,p.Gln145Ter,ENST00000509337,;DAB2,downstream_gene_variant,,ENST00000515700,;DAB2,downstream_gene_variant,,ENST00000503513,;DAB2,downstream_gene_variant,,ENST00000511792,;DAB2,non_coding_transcript_exon_variant,,ENST00000512525,;C9,intron_variant,,ENST00000483232,;DAB2,downstream_gene_variant,,ENST00000513052,;DAB2,downstream_gene_variant,,ENST00000515269,;DAB2,3_prime_UTR_variant,,ENST00000507539,;DAB2,upstream_gene_variant,,ENST00000505968,; A ENST00000320816 Transcript stop_gained 901/4534 433/2313 145/770 Q/* Cag/Tag 1 -1 DAB2 HGNC HGNC:2662 protein_coding YES CCDS34149.1 ENSP00000313391 P98082 A0A024R036 UPI0000169E27 NM_001343.3 5/15 Gene3D:2.30.29.30,Pfam_domain:PF00640,PROSITE_profiles:PS01179,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF30,SMART_domains:SM00462,Superfamily_domains:SSF50729 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 39390473 39390473 G A 1 0 0 0 0 0 1 0 0 4019 1299 45 3 3 DAB2 5 39390473 Nonsense_Mutation SNP G C3N-00217_T 5453577 39390473 142147786 173 11943 C6 0 . GRCh38 5 41161818 41161818 + Missense_Mutation SNP G G C rs778044260 C3N-00217_T C3N-00217_N G G c.1333C>G p.Arg445Gly p.R445G ENST00000263413 10/18 188 128 60 224 224 0 strelka-varscan-mutect C6,missense_variant,p.Arg445Gly,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Arg445Gly,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000475349,;C6,non_coding_transcript_exon_variant,,ENST00000473450,;C6,upstream_gene_variant,,ENST00000511470,; C ENST00000263413 Transcript missense_variant 1598/3661 1333/2805 445/934 R/G Cga/Gga rs778044260,COSM1685973 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 deleterious(0) 10/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Pfam_domain:PF01823,SMART_domains:SM00457 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778044260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 41161818 41161818 G C 1 0 0 0 0 1 0 0 0 2111 1066 37 4 4 C6 5 41161818 Missense_Mutation SNP G C3N-00217_T 1771345 41161818 140376441 174 11944 PLCXD3 0 . GRCh38 5 41382106 41382106 + Frame_Shift_Del DEL C C - C3N-00217_T C3N-00217_N C C c.532delG p.Glu178LysfsTer4 p.E178Kfs*4 ENST00000377801 2/3 214 141 73 266 266 0 sindel-varindel-pindel PLCXD3,frameshift_variant,p.Glu178LysfsTer4,ENST00000377801,;PLCXD3,frameshift_variant,p.Glu178LysfsTer4,ENST00000328457,NM_001005473.2; - ENST00000377801 Transcript frameshift_variant 607/7704 532/966 178/321 E/X Gaa/aa COSM3920107 1 -1 PLCXD3 HGNC HGNC:31822 protein_coding YES CCDS34150.1 ENSP00000367032 Q63HM9 UPI0000049DBB 2/3 Gene3D:3.20.20.190,hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF33,SMART_domains:SM00148,Superfamily_domains:SSF51695 1 HIGH 1 deletion 2 1 1 PASS . . 0 199 0 0 11 0 0 0 -20 0.283947 1 1 0 0 - 7 5 43 41382106 41382106 C - 1 0 1 0 1 0 0 0 0 12137 864 30 0 0 PLCXD3 5 41382106 Frame_Shift_Del DEL C C3N-00217_T 220288 41382106 140156153 175 11945 MAP3K1 0 . GRCh38 5 56859910 56859910 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.829G>A p.Val277Met p.V277M ENST00000399503 3/20 392 275 117 397 397 0 strelka-varscan-mutect MAP3K1,missense_variant,p.Val277Met,ENST00000399503,NM_005921.1;AC008937.2,non_coding_transcript_exon_variant,,ENST00000415589,; A ENST00000399503 Transcript missense_variant 829/7011 829/4539 277/1512 V/M Gtg/Atg 1 1 MAP3K1 HGNC HGNC:6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 deleterious_low_confidence(0.05) 3/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 56859910 56859910 G A 1 0 0 0 0 1 0 0 0 9165 1043 36 3 3 MAP3K1 5 56859910 Missense_Mutation SNP G C3N-00217_T 15477804 56859910 124678349 176 11946 MAP1B 0 . GRCh38 5 72198203 72198203 + Silent SNP G G T rs368998959 C3N-00217_T C3N-00217_N G G c.4848G>T p.= p.P1616P ENST00000296755 5/7 183 152 31 215 215 0 strelka-varscan-mutect MAP1B,synonymous_variant,p.=,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; T ENST00000296755 Transcript synonymous_variant 5146/12036 4848/7407 1616/2468 P ccG/ccT rs368998959 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 5/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 LOW 1 SNV 2 1 PASS rs368998959 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 72198203 72198203 G T 1 0 0 0 0 0 0 0 1 9151 1045 37 1 1 MAP1B 5 72198203 Silent SNP G C3N-00217_T 15338293 72198203 109340056 177 11947 VCAN 0 . GRCh38 5 83519383 83519383 + Silent SNP C C A rs746239661 C3N-00217_T C3N-00217_N C C c.1077C>A p.= p.L359L ENST00000265077 7/15 118 86 32 123 123 0 strelka-varscan-mutect VCAN,synonymous_variant,p.=,ENST00000265077,NM_004385.4;VCAN,synonymous_variant,p.=,ENST00000342785,NM_001164098.1;VCAN,synonymous_variant,p.=,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; A ENST00000265077 Transcript synonymous_variant 1642/12625 1077/10191 359/3396 L ctC/ctA rs746239661,COSM5269061 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 0,1 LOW 1 SNV 1 0,1 1 PASS rs746239661 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 83519383 83519383 C A 1 0 0 0 0 0 0 0 1 17683 871 31 1 1 VCAN 5 83519383 Silent SNP C C3N-00217_T 11321180 83519383 98018876 178 11948 GPR150 0 . GRCh38 5 95620725 95620725 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.450G>T p.= p.A150A ENST00000380007 1/1 36 18 18 43 43 0 strelka-varscan-mutect GPR150,synonymous_variant,p.=,ENST00000380007,NM_199243.1; T ENST00000380007 Transcript synonymous_variant 648/2065 450/1305 150/434 A gcG/gcT 1 1 GPR150 HGNC HGNC:23628 protein_coding YES CCDS4074.1 ENSP00000369344 Q8NGU9 G4XH61 UPI000003BCD0 NM_199243.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF650,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 95620725 95620725 G T 1 0 0 0 0 0 0 0 1 6542 1103 39 1 1 GPR150 5 95620725 Silent SNP G C3N-00217_T 12101342 95620725 85917534 179 11949 SLCO4C1 0 . GRCh38 5 102258039 102258039 + Missense_Mutation SNP A A C C3N-00217_T C3N-00217_N A A c.1177T>G p.Ser393Ala p.S393A ENST00000310954 7/13 102 68 34 108 108 0 strelka-varscan-mutect SLCO4C1,missense_variant,p.Ser393Ala,ENST00000310954,NM_180991.4; C ENST00000310954 Transcript missense_variant 1464/5334 1177/2175 393/724 S/A Tca/Gca COSM4568497 1 -1 SLCO4C1 HGNC HGNC:23612 protein_coding YES CCDS34205.1 ENSP00000309741 Q6ZQN7 UPI00001C10B6 NM_180991.4 deleterious(0.04) 7/13 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF103,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 102258039 102258039 A C 1 0 0 0 0 1 0 0 0 15017 246 9 5 5 SLCO4C1 5 102258039 Missense_Mutation SNP A C3N-00217_T 6637314 102258039 79280220 180 11950 SLCO6A1 0 . GRCh38 5 102498485 102498485 + Splice_Site SNP A A C C3N-00217_T C3N-00217_N A A c.358+2T>G p.X120_splice ENST00000506729 67 54 13 74 74 0 strelka-varscan-mutect SLCO6A1,splice_donor_variant,,ENST00000506729,NM_001289002.1,NM_173488.4;SLCO6A1,splice_donor_variant,,ENST00000379807,;SLCO6A1,splice_donor_variant,,ENST00000389019,NM_001289004.1;SLCO6A1,splice_donor_variant,,ENST00000513675,NM_001308014.1;RP11-58B2.1,upstream_gene_variant,,ENST00000502494,;SLCO6A1,splice_donor_variant,,ENST00000514551,;SLCO6A1,splice_donor_variant,,ENST00000505407,; C ENST00000506729 Transcript splice_donor_variant -/2689 358/2160 120/719 COSM1059241 1 -1 SLCO6A1 HGNC HGNC:23613 protein_coding YES CCDS34206.1 ENSP00000421339 Q86UG4 A0A140VJU7 UPI000020C392 NM_001289002.1,NM_173488.4 1/13 1 HIGH 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 43 102498485 102498485 A C 1 0 0 0 0 0 0 1 0 15019 173 6 5 5 SLCO6A1 5 102498485 Splice_Site SNP A C3N-00217_T 240446 102498485 79039774 181 11951 PRR16 0 . GRCh38 5 120464612 120464612 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.126C>A p.= p.G42G ENST00000407149 1/2 119 80 39 117 117 0 strelka-varscan-mutect PRR16,synonymous_variant,p.=,ENST00000407149,NM_001300783.1;PRR16,5_prime_UTR_variant,,ENST00000379551,NM_016644.2;PRR16,upstream_gene_variant,,ENST00000509923,; A ENST00000407149 Transcript synonymous_variant 335/1747 126/915 42/304 G ggC/ggA 1 1 PRR16 HGNC HGNC:29654 protein_coding YES CCDS75290.1 ENSP00000385118 Q569H4 UPI00004F9C36 NM_001300783.1 1/2 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0 LOW 1 SNV 1 1 PASS rs1240670107 . 0 206 0 2 2 0 0 0 -20 0.9962826 1 1 1 0 A 2 1 43 120464612 120464612 C A 1 0 0 0 0 0 0 0 1 12725 755 27 1 1 PRR16 5 120464612 Silent SNP C C3N-00217_T 17966127 120464612 61073647 182 11952 RAPGEF6 0 . GRCh38 5 131455950 131455950 + Missense_Mutation SNP T T G C3N-00217_T C3N-00217_N T T c.2927A>C p.Tyr976Ser p.Y976S ENST00000296859 20/29 142 106 36 198 198 0 strelka-varscan-mutect RAPGEF6,missense_variant,p.Tyr976Ser,ENST00000509018,NM_016340.5;CTC-432M15.3,missense_variant,p.Tyr1026Ser,ENST00000514667,;RAPGEF6,missense_variant,p.Tyr981Ser,ENST00000507093,NM_001164387.1;RAPGEF6,missense_variant,p.Tyr976Ser,ENST00000296859,NM_001164386.1;RAPGEF6,missense_variant,p.Tyr976Ser,ENST00000627212,NM_001164388.1;RAPGEF6,missense_variant,p.Tyr976Ser,ENST00000308008,NM_001164389.1;RAPGEF6,missense_variant,p.Tyr691Ser,ENST00000512052,;RAPGEF6,missense_variant,p.Tyr976Ser,ENST00000515170,; G ENST00000296859 Transcript missense_variant 3008/5618 2927/4830 976/1609 Y/S tAc/tCc COSM4141406,COSM4141407,COSM4141408,COSM4141409 1 -1 RAPGEF6 HGNC HGNC:20655 protein_coding YES CCDS54900.1 ENSP00000296859 Q8TEU7 UPI000189A836 NM_001164386.1 deleterious(0) 20/29 Superfamily_domains:0041591,Gene3D:2ii0A02,Pfam_domain:PF00617,PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF222,SMART_domains:SM00147 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 131455950 131455950 T G 1 0 0 0 0 1 0 0 0 13207 1638 57 5 5 RAPGEF6 5 131455950 Missense_Mutation SNP T C3N-00217_T 10991338 131455950 50082309 183 11953 RAPGEF6 0 . GRCh38 5 131508200 131508200 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.813G>T p.Leu271Phe p.L271F ENST00000296859 9/29 118 78 40 127 127 0 strelka-varscan-mutect RAPGEF6,missense_variant,p.Leu271Phe,ENST00000509018,NM_016340.5;CTC-432M15.3,missense_variant,p.Leu321Phe,ENST00000514667,;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000507093,NM_001164387.1;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000296859,NM_001164386.1;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000627212,NM_001164388.1;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000308008,NM_001164389.1;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000510071,NM_001164390.1;RAPGEF6,missense_variant,p.Leu99Phe,ENST00000513227,;RAPGEF6,missense_variant,p.Leu124Phe,ENST00000504575,;RAPGEF6,missense_variant,p.Leu124Phe,ENST00000504039,;RAPGEF6,upstream_gene_variant,,ENST00000512052,;RAPGEF6,missense_variant,p.Leu271Phe,ENST00000515170,;RAPGEF6,non_coding_transcript_exon_variant,,ENST00000514179,; A ENST00000296859 Transcript missense_variant 894/5618 813/4830 271/1609 L/F ttG/ttT 1 -1 RAPGEF6 HGNC HGNC:20655 protein_coding YES CCDS54900.1 ENSP00000296859 Q8TEU7 UPI000189A836 NM_001164386.1 deleterious(0) 9/29 Gene3D:2.60.120.10,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF222,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 131508200 131508200 C A 1 0 0 0 0 1 0 0 0 13207 709 25 2 2 RAPGEF6 5 131508200 Missense_Mutation SNP C C3N-00217_T 52250 131508200 50030059 184 11954 PCDHA3 0 . GRCh38 5 140802051 140802051 + Missense_Mutation SNP T T G rs781808156 C3N-00217_T C3N-00217_N T T c.854T>G p.Met285Arg p.M285R ENST00000522353 1/4 245 223 22 255 255 0 strelka-varscan-mutect PCDHA3,missense_variant,p.Met285Arg,ENST00000522353,NM_018906.2;PCDHA3,missense_variant,p.Met285Arg,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; G ENST00000522353 Transcript missense_variant 854/5260 854/2853 285/950 M/R aTg/aGg rs781808156 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs781808156 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 140802051 140802051 T G 1 0 0 0 0 1 0 0 0 11612 1464 51 5 5 PCDHA3 5 140802051 Missense_Mutation SNP T C3N-00217_T 9293851 140802051 40736208 185 11955 PCDHA5 0 . GRCh38 5 140823383 140823383 + Silent SNP G G T rs201301158 C3N-00217_T C3N-00217_N G G c.1608G>T p.= p.A536A ENST00000529859 1/4 758 514 244 572 571 1 strelka-varscan-mutect PCDHA5,synonymous_variant,p.=,ENST00000529859,NM_018908.2;PCDHA5,synonymous_variant,p.=,ENST00000614258,NM_031501.1;PCDHA5,synonymous_variant,p.=,ENST00000529619,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA4,intron_variant,,ENST00000512229,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA6,upstream_gene_variant,,ENST00000529310,NM_018909.3;PCDHA6,upstream_gene_variant,,ENST00000378126,NM_031848.2;PCDHA6,upstream_gene_variant,,ENST00000527624,NM_031849.2;AC005609.16,upstream_gene_variant,,ENST00000624712,; T ENST00000529859 Transcript synonymous_variant 1608/5218 1608/2811 536/936 A gcG/gcT rs201301158,COSM1433821,COSM1433822,COSM3409821 1 1 PCDHA5 HGNC HGNC:8671 protein_coding YES CCDS54917.1 ENSP00000436557 Q9Y5H7 UPI00001273CD NM_018908.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs201301158 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 140823383 140823383 G T 1 0 0 0 0 0 0 0 1 11614 1074 38 1 1 PCDHA5 5 140823383 Silent SNP G C3N-00217_T 21332 140823383 40714876 186 11956 PCDHA7 0 . GRCh38 5 140835461 140835461 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1078C>A p.Pro360Thr p.P360T ENST00000525929 1/4 229 160 69 282 282 0 strelka-varscan-mutect PCDHA7,missense_variant,p.Pro360Thr,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Pro360Thr,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA6,downstream_gene_variant,,ENST00000378126,NM_031848.2; A ENST00000525929 Transcript missense_variant 1078/5221 1078/2814 360/937 P/T Cca/Aca 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 tolerated_low_confidence(0.07) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 140835461 140835461 C A 1 0 0 0 0 1 0 0 0 11616 855 30 2 2 PCDHA7 5 140835461 Missense_Mutation SNP C C3N-00217_T 12078 140835461 40702798 187 11957 1 9 3 3 526 N G_C 6.123227e-05 PCDHA7 0 . GRCh38 5 140835626 140835626 + Missense_Mutation SNP C C A rs782043218 C3N-00217_T C3N-00217_N C C c.1243C>A p.Arg415Ser p.R415S ENST00000525929 1/4 406 278 128 360 359 1 strelka-varscan-mutect PCDHA7,missense_variant,p.Arg415Ser,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Arg415Ser,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA6,downstream_gene_variant,,ENST00000378126,NM_031848.2; A ENST00000525929 Transcript missense_variant 1243/5221 1243/2814 415/937 R/S Cgc/Agc rs782043218,COSM1433875,COSM1433876 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 deleterious_low_confidence(0.01) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782043218 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 140835626 140835626 C A 1 0 0 0 0 1 0 0 0 11616 652 23 1 1 PCDHA7 5 140835626 Missense_Mutation SNP C C3N-00217_T 165 140835626 40702633 188 11958 1 9 3 3 526 N G_C 6.123227e-05 PCDHA7 0 . GRCh38 5 140835986 140835986 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.1603G>C p.Val535Leu p.V535L ENST00000525929 1/4 825 582 243 631 631 0 strelka-varscan-mutect PCDHA7,missense_variant,p.Val535Leu,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Val535Leu,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA6,downstream_gene_variant,,ENST00000378126,NM_031848.2; C ENST00000525929 Transcript missense_variant 1603/5221 1603/2814 535/937 V/L Gtg/Ctg COSM5242636,COSM5242637 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 deleterious_low_confidence(0.03) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 140835986 140835986 G C 1 0 0 0 0 1 0 0 0 11616 1261 44 4 4 PCDHA7 5 140835986 Missense_Mutation SNP G C3N-00217_T 360 140835986 40702273 189 11959 1 9 3 3 526 N G_C 6.123227e-05 PCDHB10 0 . GRCh38 5 141194473 141194473 + Missense_Mutation SNP G G T rs782602590 C3N-00217_T C3N-00217_N G G c.1921G>T p.Val641Leu p.V641L ENST00000239446 1/1 427 360 67 289 289 0 strelka-varscan-mutect PCDHB10,missense_variant,p.Val641Leu,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,upstream_gene_variant,,ENST00000625144,; T ENST00000239446 Transcript missense_variant 2121/3290 1921/2403 641/800 V/L Gtg/Ttg rs782602590 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 tolerated_low_confidence(1) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS rs782602590 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 141194473 141194473 G T 1 0 0 0 0 1 0 0 0 11622 1145 40 1 1 PCDHB10 5 141194473 Missense_Mutation SNP G C3N-00217_T 358487 141194473 40343786 190 11960 PCDHB11 0 . GRCh38 5 141199849 141199849 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.75G>T p.Gln25His p.Q25H ENST00000354757 1/1 258 165 93 234 233 1 strelka-varscan-mutect PCDHB11,missense_variant,p.Gln25His,ENST00000354757,NM_018931.2;PCDHB11,intron_variant,,ENST00000624887,;PCDHB10,downstream_gene_variant,,ENST00000239446,NM_018930.3;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000354757 Transcript missense_variant 268/4198 75/2394 25/797 Q/H caG/caT 1 1 PCDHB11 HGNC HGNC:8682 protein_coding YES CCDS4253.1 ENSP00000346802 Q9Y5F2 UPI00001273E6 NM_018931.2 tolerated_low_confidence(0.51) 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF91,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 141199849 141199849 G T 1 0 0 0 0 1 0 0 0 11623 991 35 2 2 PCDHB11 5 141199849 Missense_Mutation SNP G C3N-00217_T 5376 141199849 40338410 191 11961 PCDHB13 0 . GRCh38 5 141214277 141214277 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.154G>T p.Asp52Tyr p.D52Y ENST00000341948 1/1 82 57 25 98 98 0 strelka-varscan-mutect PCDHB13,missense_variant,p.Asp52Tyr,ENST00000341948,NM_018933.3;PCDHB12,downstream_gene_variant,,ENST00000239450,NM_018932.3;PCDHB12,downstream_gene_variant,,ENST00000622978,;PCDHB12,downstream_gene_variant,,ENST00000624949,;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000341948 Transcript missense_variant 359/5061 154/2397 52/798 D/Y Gac/Tac 1 1 PCDHB13 HGNC HGNC:8684 protein_coding YES CCDS4255.1 ENSP00000345491 Q9Y5F0 UPI0000047816 NM_018933.3 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF129,Pfam_domain:PF08266,SMART_domains:SM00112 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 141214277 141214277 G T 1 0 0 0 0 1 0 0 0 11625 1174 41 2 2 PCDHB13 5 141214277 Missense_Mutation SNP G C3N-00217_T 14428 141214277 40323982 192 11962 PCDHGA1 0 . GRCh38 5 141331908 141331908 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.1224A>G p.= p.R408R ENST00000517417 1/4 257 210 47 302 302 0 strelka-varscan-mutect PCDHGA1,synonymous_variant,p.=,ENST00000517417,NM_018912.2;PCDHGA1,synonymous_variant,p.=,ENST00000378105,NM_031993.1;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,; G ENST00000517417 Transcript synonymous_variant 1224/4604 1224/2796 408/931 R agA/agG 1 1 PCDHGA1 HGNC HGNC:8696 protein_coding YES CCDS54922.1 ENSP00000431083 Q9Y5H4 UPI0000070596 NM_018912.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF108,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 141331908 141331908 A G 1 0 0 0 0 0 0 0 1 11637 243 9 5 5 PCDHGA1 5 141331908 Silent SNP A C3N-00217_T 117631 141331908 40206351 193 11963 PCDHGA2 0 . GRCh38 5 141339453 141339453 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.482A>T p.Asp161Val p.D161V ENST00000394576 1/4 263 184 79 222 222 0 strelka-varscan-mutect PCDHGA2,missense_variant,p.Asp161Val,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Asp161Val,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA1,downstream_gene_variant,,ENST00000378105,NM_031993.1;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; T ENST00000394576 Transcript missense_variant 482/4605 482/2799 161/932 D/V gAc/gTc 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 141339453 141339453 A T 1 0 0 0 0 1 0 0 0 11641 275 10 4 4 PCDHGA2 5 141339453 Missense_Mutation SNP A C3N-00217_T 7545 141339453 40198806 194 11964 PCDHGA2 0 . GRCh38 5 141339546 141339546 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.575C>A p.Pro192Gln p.P192Q ENST00000394576 1/4 167 118 49 138 138 0 strelka-varscan-mutect PCDHGA2,missense_variant,p.Pro192Gln,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Pro192Gln,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA1,downstream_gene_variant,,ENST00000378105,NM_031993.1;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; A ENST00000394576 Transcript missense_variant 575/4605 575/2799 192/932 P/Q cCa/cAa 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 141339546 141339546 C A 1 0 0 0 0 1 0 0 0 11641 594 21 2 2 PCDHGA2 5 141339546 Missense_Mutation SNP C C3N-00217_T 93 141339546 40198713 195 11965 PCDH12 0 . GRCh38 5 141955075 141955075 + Nonsense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.2777C>G p.Ser926Ter p.S926* ENST00000231484 1/4 312 233 79 237 237 0 strelka-varscan-mutect PCDH12,stop_gained,p.Ser926Ter,ENST00000231484,NM_016580.3;RNF14,upstream_gene_variant,,ENST00000511961,;RNF14,upstream_gene_variant,,ENST00000506822,;PCDH12,downstream_gene_variant,,ENST00000510041,;AC005740.6,downstream_gene_variant,,ENST00000607378,;PCDH12,downstream_gene_variant,,ENST00000512221,; C ENST00000231484 Transcript stop_gained 3988/6562 2777/3555 926/1184 S/* tCa/tGa 1 -1 PCDH12 HGNC HGNC:8657 protein_coding YES CCDS4269.1 ENSP00000231484 Q9NPG4 UPI00001313B4 NM_016580.3 1/4 hmmpanther:PTHR24028:SF42,hmmpanther:PTHR24028 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 43 141955075 141955075 G C 1 0 0 0 0 0 1 0 0 11597 1294 45 4 4 PCDH12 5 141955075 Nonsense_Mutation SNP G C3N-00217_T 615529 141955075 39583184 196 11966 JAKMIP2 0 . GRCh38 5 147660956 147660956 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.619C>A p.= p.R207R ENST00000616793 3/22 121 81 40 119 119 0 strelka-varscan-mutect JAKMIP2,synonymous_variant,p.=,ENST00000616793,NM_001270941.1;JAKMIP2,synonymous_variant,p.=,ENST00000265272,NM_014790.4;JAKMIP2,synonymous_variant,p.=,ENST00000507386,NM_001270934.1;JAKMIP2,synonymous_variant,p.=,ENST00000333010,NM_001282282.1;JAKMIP2-AS1,non_coding_transcript_exon_variant,,ENST00000626945,;JAKMIP2-AS1,downstream_gene_variant,,ENST00000627433,;JAKMIP2-AS1,downstream_gene_variant,,ENST00000630514,;JAKMIP2-AS1,downstream_gene_variant,,ENST00000630801,;JAKMIP2,non_coding_transcript_exon_variant,,ENST00000507343,; T ENST00000616793 Transcript synonymous_variant 1160/9272 619/2463 207/820 R Cgg/Agg 1 -1 JAKMIP2 HGNC HGNC:29067 protein_coding YES CCDS75352.1 ENSP00000479248 Q96AA8 UPI0000E5AC9B NM_001270941.1 3/22 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 147660956 147660956 G T 1 0 0 0 0 0 0 0 1 7854 1057 37 1 1 JAKMIP2 5 147660956 Silent SNP G C3N-00217_T 5705881 147660956 33877303 197 11967 HTR4 0 . GRCh38 5 148509955 148509955 + Missense_Mutation SNP C C G rs751138733 C3N-00217_T C3N-00217_N C C c.577G>C p.Ala193Pro p.A193P ENST00000360693 6/8 212 153 59 178 178 0 strelka-varscan-mutect HTR4,missense_variant,p.Ala193Pro,ENST00000360693,;HTR4,missense_variant,p.Ala193Pro,ENST00000362016,NM_001040173.2;HTR4,missense_variant,p.Ala193Pro,ENST00000377888,NM_000870.6;HTR4,missense_variant,p.Ala193Pro,ENST00000521530,NM_001040169.2;HTR4,missense_variant,p.Ala193Pro,ENST00000521735,NM_199453.3;HTR4,missense_variant,p.Ala193Pro,ENST00000520514,NM_001286410.1;HTR4,missense_variant,p.Ala193Pro,ENST00000631296,;HTR4,missense_variant,p.Ala193Pro,ENST00000517929,NM_001040172.2;HTR4,missense_variant,p.Ala193Pro,ENST00000524063,;HTR4,missense_variant,p.Ala193Pro,ENST00000522588,;HTR4,non_coding_transcript_exon_variant,,ENST00000521124,; G ENST00000360693 Transcript missense_variant 716/3082 577/1287 193/428 A/P Gcc/Ccc rs751138733 1 -1 HTR4 HGNC HGNC:5299 protein_coding YES CCDS34272.1 ENSP00000353915 Q13639 UPI00002323B1 deleterious(0) 6/8 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF33,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 5 1 PASS rs751138733 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 148509955 148509955 C G 1 0 0 0 0 1 0 0 0 7345 768 27 4 4 HTR4 5 148509955 Missense_Mutation SNP C C3N-00217_T 848999 148509955 33028304 198 11968 ADAM19 0 . GRCh38 5 157491891 157491891 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1930A>T p.Arg644Trp p.R644W ENST00000257527 17/23 279 211 68 227 227 0 strelka-varscan-mutect ADAM19,missense_variant,p.Arg644Trp,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Arg644Trp,ENST00000517905,;ADAM19,missense_variant,p.Arg215Trp,ENST00000517374,;ADAM19,3_prime_UTR_variant,,ENST00000517951,; A ENST00000257527 Transcript missense_variant 2009/6481 1930/2757 644/918 R/W Agg/Tgg 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 deleterious(0) 17/23 hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 157491891 157491891 T A 1 0 0 0 0 1 0 0 0 284 1579 55 4 4 ADAM19 5 157491891 Missense_Mutation SNP T C3N-00217_T 8981936 157491891 24046368 199 11969 TENM2 0 . GRCh38 5 168204621 168204621 + Missense_Mutation SNP G G T rs754860654 C3N-00217_T C3N-00217_N G G c.3824G>T p.Arg1275Leu p.R1275L ENST00000518659 19/29 83 53 30 75 74 1 strelka-varscan-mutect TENM2,missense_variant,p.Arg1154Leu,ENST00000519204,;TENM2,missense_variant,p.Arg1275Leu,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Arg1043Leu,ENST00000520394,; T ENST00000518659 Transcript missense_variant,splice_region_variant 3863/8550 3824/8325 1275/2774 R/L cGa/cTa rs754860654 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 19/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2.120.10.30,Superfamily_domains:SSF101898 MODERATE 1 SNV 5 1 PASS rs754860654 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 168204621 168204621 G T 1 0 0 0 0 1 0 0 0 16172 1130 39 1 1 TENM2 5 168204621 Missense_Mutation SNP G C3N-00217_T 10712730 168204621 13333638 200 11970 SLIT3 0 . GRCh38 5 168762601 168762601 + Silent SNP C C A rs778742275 C3N-00217_T C3N-00217_N C C c.1548G>T p.= p.V516V ENST00000332966 15/36 186 144 42 154 153 1 strelka-varscan-mutect SLIT3,synonymous_variant,p.=,ENST00000519560,NM_003062.3;SLIT3,synonymous_variant,p.=,ENST00000404867,;SLIT3,synonymous_variant,p.=,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000519486,; A ENST00000332966 Transcript synonymous_variant 1621/4895 1548/4593 516/1530 V gtG/gtT rs778742275 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 15/36 SMART_domains:SM00013,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs778742275 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 168762601 168762601 C A 1 0 0 0 0 0 0 0 1 15032 581 21 2 2 SLIT3 5 168762601 Silent SNP C C3N-00217_T 557980 168762601 12775658 201 11971 C5orf58 0 . GRCh38 5 170235021 170235021 + Missense_Mutation SNP A A C novel C3N-00217_T C3N-00217_N A A c.108A>C p.Lys36Asn p.K36N ENST00000593851 3/4 86 79 7 146 146 0 strelka-varscan-mutect C5orf58,missense_variant,p.Lys15Asn,ENST00000521850,;C5orf58,missense_variant,p.Lys15Asn,ENST00000524171,;C5orf58,missense_variant,p.Lys15Asn,ENST00000517575,;C5orf58,missense_variant,p.Lys36Asn,ENST00000593851,NM_001102609.1;C5orf58,missense_variant,p.Lys15Asn,ENST00000421269,;C5orf58,upstream_gene_variant,,ENST00000518395,; C ENST00000593851 Transcript missense_variant 191/509 108/309 36/102 K/N aaA/aaC 1 1 C5orf58 HGNC HGNC:37272 protein_coding YES ENSP00000490013 C9J3I9 UPI0000160413 NM_001102609.1 tolerated(0.07) 3/4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 170235021 170235021 A C 1 0 0 0 0 1 0 0 0 2108 69 3 5 5 C5orf58 5 170235021 Missense_Mutation SNP A C3N-00217_T 1472420 170235021 11303238 202 11972 LCP2 0 . GRCh38 5 170287990 170287990 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.168G>A p.= p.K56K ENST00000046794 3/21 291 259 32 262 262 0 strelka-varscan-mutect LCP2,synonymous_variant,p.=,ENST00000046794,NM_005565.3;LCP2,synonymous_variant,p.=,ENST00000628092,;LCP2,non_coding_transcript_exon_variant,,ENST00000522760,;LCP2,non_coding_transcript_exon_variant,,ENST00000519594,;LCP2,non_coding_transcript_exon_variant,,ENST00000522823,;LCP2,non_coding_transcript_exon_variant,,ENST00000519149,; T ENST00000046794 Transcript synonymous_variant 784/4678 168/1602 56/533 K aaG/aaA 1 -1 LCP2 HGNC HGNC:6529 protein_coding YES CCDS47339.1 ENSP00000046794 Q13094 UPI000012E2AE NM_005565.3 3/21 Gene3D:1.10.150.50,Pfam_domain:PF07647,SMART_domains:SM00454,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 170287990 170287990 C T 1 0 0 0 0 0 0 0 1 8598 564 20 3 3 LCP2 5 170287990 Silent SNP C C3N-00217_T 52969 170287990 11250269 203 11973 MSX2 0 . GRCh38 5 174724845 174724845 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.186G>T p.= p.A62A ENST00000239243 1/2 219 159 60 206 206 0 strelka-varscan-mutect MSX2,synonymous_variant,p.=,ENST00000239243,NM_002449.4;MSX2,synonymous_variant,p.=,ENST00000507785,; T ENST00000239243 Transcript synonymous_variant 313/2241 186/804 62/267 A gcG/gcT 1 1 MSX2 HGNC HGNC:7392 protein_coding YES CCDS4392.1 ENSP00000239243 P35548 UPI000013CA79 NM_002449.4 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24338:SF10,hmmpanther:PTHR24338 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 174724845 174724845 G T 1 0 0 0 0 0 0 0 1 9880 1132 40 1 1 MSX2 5 174724845 Silent SNP G C3N-00217_T 4436855 174724845 6813414 204 11974 FAM153B 0 . GRCh38 5 176099030 176099030 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.316G>T p.Gly106Cys p.G106C ENST00000515817 9/20 196 150 46 180 180 0 strelka-varscan-mutect FAM153B,missense_variant,p.Gly106Cys,ENST00000515817,NM_001265615.1;FAM153B,missense_variant,p.Gly183Cys,ENST00000253490,;FAM153B,missense_variant,p.Gly106Cys,ENST00000510151,;FAM153B,missense_variant,p.Gly95Cys,ENST00000503724,;FAM153B,intron_variant,,ENST00000512862,;FAM153B,intron_variant,,ENST00000611539,;FAM153B,non_coding_transcript_exon_variant,,ENST00000393522,;FAM153B,downstream_gene_variant,,ENST00000503533,;FAM153B,missense_variant,p.Gly106Cys,ENST00000508296,; T ENST00000515817 Transcript missense_variant 600/1966 316/933 106/310 G/C Ggc/Tgc 1 1 FAM153B HGNC HGNC:27323 protein_coding YES CCDS43401.2 ENSP00000427684 D6RF84 UPI00001D7EF3 NM_001265615.1 tolerated_low_confidence(0.13) 9/20 Pfam_domain:PF15722,hmmpanther:PTHR40712,hmmpanther:PTHR40712:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 176099030 176099030 G T 1 0 0 0 0 1 0 0 0 5311 1000 35 2 2 FAM153B 5 176099030 Missense_Mutation SNP G C3N-00217_T 1374185 176099030 5439229 205 11975 PPP1R3G 0 . GRCh38 6 5086089 5086089 + Nonsense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.604C>T p.Gln202Ter p.Q202* ENST00000405617 1/1 157 125 32 112 112 0 strelka-varscan-mutect PPP1R3G,stop_gained,p.Gln202Ter,ENST00000405617,NM_001145115.2; T ENST00000405617 Transcript stop_gained 1509/4907 604/1077 202/358 Q/* Cag/Tag 1 1 PPP1R3G HGNC HGNC:14945 protein_coding YES CCDS47366.1 ENSP00000393832 B7ZBB8 UPI0000237382 NM_001145115.2 1/1 hmmpanther:PTHR12307:SF7,hmmpanther:PTHR12307 HIGH 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 5086089 5086089 C T 1 0 0 0 0 0 1 0 0 12497 595 21 3 3 PPP1R3G 6 5086089 Nonsense_Mutation SNP C C3N-00217_T 5086089 165719890 206 11976 LYRM4 0 . GRCh38 6 5186969 5186969 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.219C>A p.His73Gln p.H73Q ENST00000500576 3/3 14 10 4 13 13 0 strelka-mutect LYRM4,missense_variant,p.His73Gln,ENST00000500576,NM_001164840.2;LYRM4,intron_variant,,ENST00000330636,NM_020408.5;LYRM4,intron_variant,,ENST00000464010,NM_001164841.2;LYRM4,intron_variant,,ENST00000468929,;LYRM4,intron_variant,,ENST00000480566,;LYRM4,intron_variant,,ENST00000463032,; T ENST00000500576 Transcript missense_variant 223/592 219/393 73/130 H/Q caC/caA 1 -1 LYRM4 HGNC HGNC:21365 protein_coding YES CCDS54962.1 ENSP00000443900 F5H189 UPI0001B71BCB NM_001164840.2 tolerated(0.31) 3/3 hmmpanther:PTHR16213 MODERATE 1 SNV 2 1 PASS . . 25 184 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 5186969 5186969 G T 1 0 0 0 0 1 0 0 0 9033 1020 36 2 2 LYRM4 6 5186969 Missense_Mutation SNP G C3N-00217_T 100880 5186969 165619010 207 11977 POM121L2 0 . GRCh38 6 27310030 27310030 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.2141C>G p.Pro714Arg p.P714R ENST00000444565 1/1 333 234 99 318 317 1 strelka-varscan-mutect POM121L2,missense_variant,p.Pro714Arg,ENST00000444565,NM_033482.3;POM121L2,intron_variant,,ENST00000429945,; C ENST00000444565 Transcript missense_variant 2141/3108 2141/3108 714/1035 P/R cCt/cGt 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 deleterious(0) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 27310030 27310030 G C 1 0 0 0 0 1 0 0 0 12353 1000 35 4 4 POM121L2 6 27310030 Missense_Mutation SNP G C3N-00217_T 22123061 27310030 143495949 208 11978 MDC1 0 . GRCh38 6 30712532 30712532 + Silent SNP G G C C3N-00217_T C3N-00217_N G G c.1410C>G p.= p.V470V ENST00000376406 5/15 201 165 36 136 136 0 strelka-varscan-mutect MDC1,synonymous_variant,p.=,ENST00000376406,NM_014641.2;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000613547,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;MDC1,upstream_gene_variant,,ENST00000492462,; C ENST00000376406 Transcript synonymous_variant 2058/7576 1410/6270 470/2089 V gtC/gtG COSM3251977,COSM3251978 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 5/15 Low_complexity_(Seg):seg,hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 1,1 LOW SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 30712532 30712532 G C 1 0 0 0 0 0 0 0 1 9341 1161 41 4 4 MDC1 6 30712532 Silent SNP G C3N-00217_T 3402502 30712532 140093447 209 11979 LY6G6E 0 . GRCh38 6 31712721 31712721 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.121C>A p.Pro41Thr p.P41T ENST00000461287 2/22 273 101 172 110 110 0 strelka-varscan-mutect XXbac-BPG32J3.20,missense_variant,p.Pro41Thr,ENST00000461287,;LY6G6E,missense_variant,p.Pro66Thr,ENST00000409239,;LY6G6E,missense_variant,p.Pro41Thr,ENST00000399142,;LY6G6E,missense_variant,p.Pro41Thr,ENST00000450147,;LY6G6E,missense_variant,p.Pro41Thr,ENST00000383418,;XXbac-BPG32J3.19,intron_variant,,ENST00000503322,;LY6G6F,downstream_gene_variant,,ENST00000375832,NM_001003693.1;LY6G6D,upstream_gene_variant,,ENST00000375824,;LY6G6D,upstream_gene_variant,,ENST00000375825,NM_021246.2;LY6G6D,upstream_gene_variant,,ENST00000479334,; T ENST00000461287 Transcript missense_variant 381/2332 121/192 41/63 P/T Cct/Act 1 -1 XXbac-BPG32J3.20 Clone_based_vega_gene protein_coding YES ENSP00000475702 U3KQA8 UPI00018814AC deleterious_low_confidence(0) 2/22 hmmpanther:PTHR14569 MODERATE SNV 2 1 PASS rs1368894859 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 31712721 31712721 G T 1 0 0 0 0 1 0 0 0 9006 1232 43 2 2 LY6G6E 6 31712721 Missense_Mutation SNP G C3N-00217_T 1000189 31712721 139093258 210 11980 SKIV2L 0 . GRCh38 6 31967788 31967788 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.2657A>T p.Gln886Leu p.Q886L ENST00000375394 22/28 359 244 115 222 222 0 strelka-varscan-mutect SKIV2L,missense_variant,p.Gln886Leu,ENST00000375394,NM_006929.4;DXO,downstream_gene_variant,,ENST00000375349,;STK19,upstream_gene_variant,,ENST00000375331,NM_004197.1;DXO,downstream_gene_variant,,ENST00000337523,NM_005510.3;STK19,upstream_gene_variant,,ENST00000375333,NM_032454.1;DXO,downstream_gene_variant,,ENST00000375356,;SKIV2L,upstream_gene_variant,,ENST00000491994,;DXO,downstream_gene_variant,,ENST00000495340,;STK19,upstream_gene_variant,,ENST00000460018,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000461915,;DXO,downstream_gene_variant,,ENST00000478221,;DXO,downstream_gene_variant,,ENST00000474587,;DXO,downstream_gene_variant,,ENST00000487914,;SKIV2L,upstream_gene_variant,,ENST00000471818,;STK19,upstream_gene_variant,,ENST00000463823,;STK19,upstream_gene_variant,,ENST00000466336,;SKIV2L,upstream_gene_variant,,ENST00000470453,;SKIV2L,missense_variant,p.Gln11Leu,ENST00000483553,;SKIV2L,3_prime_UTR_variant,,ENST00000474839,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000465703,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000484835,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000494058,;DXO,downstream_gene_variant,,ENST00000477826,;DXO,downstream_gene_variant,,ENST00000473976,;STK19,upstream_gene_variant,,ENST00000473983,;STK19,upstream_gene_variant,,ENST00000466132,;DXO,downstream_gene_variant,,ENST00000485557,;DXO,downstream_gene_variant,,ENST00000498357,;DXO,downstream_gene_variant,,ENST00000492946,;STK19,upstream_gene_variant,,ENST00000492583,;DXO,downstream_gene_variant,,ENST00000491327,;STK19,upstream_gene_variant,,ENST00000479644,;DXO,downstream_gene_variant,,ENST00000480240,;SKIV2L,downstream_gene_variant,,ENST00000461073,;STK19,upstream_gene_variant,,ENST00000491861,;STK19,upstream_gene_variant,,ENST00000519179,;STK19,upstream_gene_variant,,ENST00000483801,;STK19,upstream_gene_variant,,ENST00000469907,;STK19,upstream_gene_variant,,ENST00000478486,;DXO,downstream_gene_variant,,ENST00000460058,;SKIV2L,upstream_gene_variant,,ENST00000485349,;STK19,upstream_gene_variant,,ENST00000484540,;SKIV2L,downstream_gene_variant,,ENST00000466290,;STK19,upstream_gene_variant,,ENST00000471028,; T ENST00000375394 Transcript missense_variant 2770/3894 2657/3741 886/1246 Q/L cAg/cTg 1 1 SKIV2L HGNC HGNC:10898 protein_coding YES CCDS4731.1 ENSP00000364543 Q15477 UPI000045740B NM_006929.4 tolerated(0.23) 22/28 Pfam_domain:PF13234,PIRSF_domain:PIRSF005198 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 31967788 31967788 A T 1 0 0 0 0 1 0 0 0 14622 188 7 4 4 SKIV2L 6 31967788 Missense_Mutation SNP A C3N-00217_T 255067 31967788 138838191 211 11981 ZFAND3 0 . GRCh38 6 38116677 38116677 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.467G>T p.Arg156Leu p.R156L ENST00000287218 5/6 167 114 53 114 114 0 strelka-varscan-mutect ZFAND3,missense_variant,p.Arg156Leu,ENST00000287218,NM_021943.2;ZFAND3,missense_variant,p.Arg134Leu,ENST00000373391,;ZFAND3,missense_variant,p.Arg133Leu,ENST00000373389,;ZFAND3,downstream_gene_variant,,ENST00000474522,;ZFAND3,non_coding_transcript_exon_variant,,ENST00000440482,; T ENST00000287218 Transcript missense_variant 914/3366 467/684 156/227 R/L cGg/cTg 1 1 ZFAND3 HGNC HGNC:18019 protein_coding YES CCDS4836.1 ENSP00000287218 Q9H8U3 A0A024RD12 UPI000006E3A4 NM_021943.2 deleterious(0) 5/6 Gene3D:4.10.1110.10,PROSITE_profiles:PS51039,hmmpanther:PTHR10634,hmmpanther:PTHR10634:SF28,Low_complexity_(Seg):seg,Superfamily_domains:SSF118310 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.99998 1 1 1 0 T 3 4 43 38116677 38116677 G T 1 0 0 0 0 1 0 0 0 18205 1116 39 1 1 ZFAND3 6 38116677 Missense_Mutation SNP G C3N-00217_T 6148889 38116677 132689302 212 11982 DNAH8 0 . GRCh38 6 38823601 38823601 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.3760T>A p.Ser1254Thr p.S1254T ENST00000327475 28/93 135 107 28 141 140 1 strelka-varscan-mutect DNAH8,missense_variant,p.Ser1254Thr,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Ser1037Thr,ENST00000359357,;DNAH8,missense_variant,p.Ser1254Thr,ENST00000449981,;SNORA8,upstream_gene_variant,,ENST00000391284,; A ENST00000327475 Transcript missense_variant 3869/14360 3760/14124 1254/4707 S/T Tca/Aca 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 tolerated(0.29) 28/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 38823601 38823601 T A 1 0 0 0 0 1 0 0 0 4422 1435 50 4 4 DNAH8 6 38823601 Missense_Mutation SNP T C3N-00217_T 706924 38823601 131982378 213 11983 GUCA1B 0 . GRCh38 6 42188732 42188732 + Splice_Site SNP C C A novel C3N-00217_T C3N-00217_N C C c.208-1G>T p.X70_splice ENST00000230361 502 448 54 348 348 0 strelka-varscan-mutect GUCA1B,splice_acceptor_variant,,ENST00000230361,NM_002098.5; A ENST00000230361 Transcript splice_acceptor_variant -/1113 208/603 70/200 1 -1 GUCA1B HGNC HGNC:4679 protein_coding YES CCDS4865.1 ENSP00000230361 Q9UMX6 UPI000013C92C NM_002098.5 1/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 43 42188732 42188732 C A 1 0 0 0 0 0 0 1 0 6770 695 24 2 2 GUCA1B 6 42188732 Splice_Site SNP C C3N-00217_T 3365131 42188732 128617247 214 11984 TFAP2D 0 . GRCh38 6 50715599 50715599 + Missense_Mutation SNP G G T rs765913790 C3N-00217_T C3N-00217_N G G c.523G>T p.Ala175Ser p.A175S ENST00000008391 2/8 60 46 14 60 60 0 strelka-varscan-mutect TFAP2D,missense_variant,p.Ala175Ser,ENST00000008391,NM_172238.3;TFAP2D,upstream_gene_variant,,ENST00000492804,; T ENST00000008391 Transcript missense_variant 751/1711 523/1359 175/452 A/S Gca/Tca rs765913790,COSM190932 1 1 TFAP2D HGNC HGNC:15581 protein_coding YES CCDS4933.1 ENSP00000008391 Q7Z6R9 UPI00001A3A89 NM_172238.3 tolerated(0.87) 2/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10812:SF5,hmmpanther:PTHR10812 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765913790 . 0 202 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 43 50715599 50715599 G T 1 0 0 0 0 1 0 0 0 16223 971 34 2 2 TFAP2D 6 50715599 Missense_Mutation SNP G C3N-00217_T 8526867 50715599 120090380 215 11985 RIMS1 0 . GRCh38 6 72398295 72398295 + Silent SNP G G T rs375475877 C3N-00217_T C3N-00217_N G G c.4665G>T p.= p.V1555V ENST00000521978 32/34 104 90 14 177 175 2 strelka-varscan-mutect RIMS1,synonymous_variant,p.=,ENST00000264839,;RIMS1,synonymous_variant,p.=,ENST00000521978,NM_014989.5;RIMS1,synonymous_variant,p.=,ENST00000520567,;RIMS1,synonymous_variant,p.=,ENST00000517960,;RIMS1,synonymous_variant,p.=,ENST00000518273,;RIMS1,synonymous_variant,p.=,ENST00000522291,;RIMS1,synonymous_variant,p.=,ENST00000401910,NM_001168407.1;RIMS1,synonymous_variant,p.=,ENST00000517433,;RIMS1,synonymous_variant,p.=,ENST00000523963,NM_001168408.1;RIMS1,synonymous_variant,p.=,ENST00000517827,NM_001168410.1;RIMS1,synonymous_variant,p.=,ENST00000425662,NM_001168409.1;RIMS1,synonymous_variant,p.=,ENST00000453976,;RIMS1,synonymous_variant,p.=,ENST00000522211,;RIMS1,synonymous_variant,p.=,ENST00000370420,;RIMS1,synonymous_variant,p.=,ENST00000414192,NM_001168411.1;RIMS1,intron_variant,,ENST00000491071,;RIMS1,non_coding_transcript_exon_variant,,ENST00000431478,;RIMS1,non_coding_transcript_exon_variant,,ENST00000463023,; T ENST00000521978 Transcript synonymous_variant 4665/5079 4665/5079 1555/1692 V gtG/gtT rs375475877 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 32/34 PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF19,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS rs375475877 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 72398295 72398295 G T 1 0 0 0 0 0 0 0 1 13542 1335 47 2 2 RIMS1 6 72398295 Silent SNP G C3N-00217_T 21682696 72398295 98407684 216 11986 CEP162 0 . GRCh38 6 84149703 84149703 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.3630G>T p.Arg1210Ser p.R1210S ENST00000403245 24/27 30 18 12 69 69 0 strelka-varscan-mutect CEP162,missense_variant,p.Arg1210Ser,ENST00000403245,NM_014895.3;CEP162,missense_variant,p.Arg1134Ser,ENST00000617909,;CEP162,missense_variant,p.Arg1134Ser,ENST00000257766,NM_001286206.1;CEP162,splice_region_variant,,ENST00000461137,;CEP162,splice_region_variant,,ENST00000487999,; A ENST00000403245 Transcript missense_variant,splice_region_variant 3745/5156 3630/4212 1210/1403 R/S agG/agT 1 -1 CEP162 HGNC HGNC:21107 protein_coding YES CCDS34494.2 ENSP00000385215 Q5TB80 UPI0001533DAA NM_014895.3 deleterious(0) 24/27 hmmpanther:PTHR34031 MODERATE 1 SNV 5 1 PASS rs1332370074 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 84149703 84149703 C A 1 0 0 0 0 1 0 0 0 2962 637 22 2 2 CEP162 6 84149703 Missense_Mutation SNP C C3N-00217_T 11751408 84149703 86656276 217 11987 GABRR2 0 . GRCh38 6 89267768 89267768 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.647C>A p.Ser216Tyr p.S216Y ENST00000402938 6/9 123 96 27 162 162 0 strelka-varscan-mutect GABRR2,missense_variant,p.Ser216Tyr,ENST00000402938,NM_002043.3;GABRR2,downstream_gene_variant,,ENST00000602808,;GABRR2,non_coding_transcript_exon_variant,,ENST00000602432,; T ENST00000402938 Transcript missense_variant 781/1682 647/1398 216/465 S/Y tCc/tAc 1 -1 GABRR2 HGNC HGNC:4091 protein_coding YES CCDS5020.3 ENSP00000386029 P28476 UPI000012B0DB NM_002043.3 deleterious(0) 6/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF197,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs894421622 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 89267768 89267768 G T 1 0 0 0 0 1 0 0 0 6048 1174 41 2 2 GABRR2 6 89267768 Missense_Mutation SNP G C3N-00217_T 5118065 89267768 81538211 218 11988 FUT9 0 . GRCh38 6 96203419 96203419 + Missense_Mutation SNP C C G C3N-00217_T C3N-00217_N C C c.264C>G p.Ile88Met p.I88M ENST00000302103 3/3 42 34 8 52 52 0 strelka-varscan-mutect FUT9,missense_variant,p.Ile88Met,ENST00000302103,NM_006581.3; G ENST00000302103 Transcript missense_variant 590/12783 264/1080 88/359 I/M atC/atG COSM3630646 1 1 FUT9 HGNC HGNC:4020 protein_coding YES CCDS5033.1 ENSP00000302599 Q9Y231 UPI000013E792 NM_006581.3 deleterious(0.04) 3/3 Pfam_domain:PF17039,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF10,Superfamily_domains:SSF53756 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.69 1 1 1 1 0 G 3 3 43 96203419 96203419 C G 1 0 0 0 0 1 0 0 0 5983 845 30 4 4 FUT9 6 96203419 Missense_Mutation SNP C C3N-00217_T 6935651 96203419 74602560 219 11989 SIM1 0 . GRCh38 6 100393813 100393813 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1244C>A p.Ala415Asp p.A415D ENST00000369208 11/12 57 48 9 71 70 1 strelka-varscan-mutect SIM1,missense_variant,p.Ala415Asp,ENST00000369208,;SIM1,missense_variant,p.Ala415Asp,ENST00000262901,NM_005068.2;SIM1,non_coding_transcript_exon_variant,,ENST00000505753,; T ENST00000369208 Transcript missense_variant 2027/8430 1244/2301 415/766 A/D gCc/gAc 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 deleterious(0) 11/12 Pfam_domain:PF06621,PROSITE_profiles:PS51302,hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.96053 1 1 1 1 0 T 3 4 43 100393813 100393813 G T 1 0 0 0 0 1 0 0 0 14586 1203 42 2 2 SIM1 6 100393813 Missense_Mutation SNP G C3N-00217_T 4190394 100393813 70412166 220 11990 SERINC1 0 . GRCh38 6 122471734 122471734 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.4G>T p.Gly2Trp p.G2W ENST00000339697 1/10 165 114 51 191 191 0 strelka-varscan-mutect SERINC1,missense_variant,p.Gly2Trp,ENST00000339697,NM_020755.2;PKIB,upstream_gene_variant,,ENST00000615438,NM_001270394.1;PKIB,upstream_gene_variant,,ENST00000392491,NM_001270393.1,NM_181794.2;RP3-425C14.5,upstream_gene_variant,,ENST00000624363,;PKIB,upstream_gene_variant,,ENST00000607474,;PKIB,upstream_gene_variant,,ENST00000608895,; A ENST00000339697 Transcript missense_variant 89/3137 4/1362 2/453 G/W Ggg/Tgg 1 -1 SERINC1 HGNC HGNC:13464 protein_coding YES CCDS5125.1 ENSP00000342962 Q9NRX5 UPI000004E6A2 NM_020755.2 deleterious(0) 1/10 Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR10383:SF15,hmmpanther:PTHR10383 MODERATE 1 SNV 1 1 PASS rs1182271335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 122471734 122471734 C A 1 0 0 0 0 1 0 0 0 14355 623 22 2 2 SERINC1 6 122471734 Missense_Mutation SNP C C3N-00217_T 22077921 122471734 48334245 221 11991 ARHGAP18 0 . GRCh38 6 129629380 129629380 + Missense_Mutation SNP C C G rs745580689 C3N-00217_T C3N-00217_N C C c.759G>C p.Lys253Asn p.K253N ENST00000368149 5/15 114 75 39 143 143 0 strelka-varscan-mutect ARHGAP18,missense_variant,p.Lys253Asn,ENST00000368149,NM_033515.2; G ENST00000368149 Transcript missense_variant 848/4462 759/1992 253/663 K/N aaG/aaC rs745580689,COSM4855615 1 -1 ARHGAP18 HGNC HGNC:21035 protein_coding YES CCDS34535.1 ENSP00000357131 Q8N392 UPI000020E208 NM_033515.2 tolerated(0.25) 5/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF6,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs745580689 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 129629380 129629380 C G 1 0 0 0 0 1 0 0 0 992 912 32 4 4 ARHGAP18 6 129629380 Missense_Mutation SNP C C3N-00217_T 7157646 129629380 41176599 222 11992 VNN1 0 . GRCh38 6 132693205 132693205 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.645C>A p.= p.L215L ENST00000367928 4/7 124 92 32 192 191 1 strelka-varscan-mutect VNN1,synonymous_variant,p.=,ENST00000367928,NM_004666.2; T ENST00000367928 Transcript synonymous_variant 659/3106 645/1542 215/513 L ctC/ctA 1 -1 VNN1 HGNC HGNC:12705 protein_coding YES CCDS5159.1 ENSP00000356905 O95497 UPI000013C91E NM_004666.2 4/7 PROSITE_profiles:PS50263,hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF16,PIRSF_domain:PIRSF011861,Pfam_domain:PF00795,Gene3D:3.60.110.10,Superfamily_domains:SSF56317 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 132693205 132693205 G T 1 0 0 0 0 0 0 0 1 17729 929 33 2 2 VNN1 6 132693205 Silent SNP G C3N-00217_T 3063825 132693205 38112774 223 11993 SGK1 0 . GRCh38 6 134262078 134262078 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.140G>T p.Gly47Val p.G47V ENST00000367858 2/14 44 38 6 63 63 0 strelka-varscan-mutect SGK1,missense_variant,p.Gly47Val,ENST00000367858,NM_001143676.1;SGK1,missense_variant,p.Gly47Val,ENST00000524929,;SGK1,missense_variant,p.Gly47Val,ENST00000533224,;SGK1,missense_variant,p.Gly16Val,ENST00000461976,;SGK1,upstream_gene_variant,,ENST00000460769,;RNA5SP218,downstream_gene_variant,,ENST00000363188,;SGK1,upstream_gene_variant,,ENST00000484353,; A ENST00000367858 Transcript missense_variant 738/3201 140/1581 47/526 G/V gGc/gTc 1 -1 SGK1 HGNC HGNC:10810 protein_coding YES CCDS47476.1 ENSP00000356832 O00141 UPI000013CA0E NM_001143676.1 tolerated_low_confidence(0.14) 2/14 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.07774 1 1 1 1 0 A 3 1 43 134262078 134262078 C A 1 0 0 0 0 1 0 0 0 14467 739 26 2 2 SGK1 6 134262078 Missense_Mutation SNP C C3N-00217_T 1568873 134262078 36543901 224 11994 SHPRH 0 . GRCh38 6 145910508 145910508 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.4455A>G p.= p.K1485K ENST00000367505 25/30 111 88 23 109 109 0 strelka-varscan-mutect SHPRH,synonymous_variant,p.=,ENST00000629427,;SHPRH,synonymous_variant,p.=,ENST00000367505,;SHPRH,synonymous_variant,p.=,ENST00000438092,NM_173082.3;SHPRH,synonymous_variant,p.=,ENST00000275233,NM_001042683.2;SHPRH,3_prime_UTR_variant,,ENST00000433355,; C ENST00000367505 Transcript synonymous_variant 4720/7201 4455/5052 1485/1683 K aaA/aaG 1 -1 SHPRH HGNC HGNC:19336 protein_coding YES CCDS43513.2 ENSP00000356475 Q149N8 UPI0000458A24 25/30 Gene3D:3.30.40.10 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 145910508 145910508 T C 1 0 0 0 0 0 0 0 1 14554 1606 56 5 5 SHPRH 6 145910508 Silent SNP T C3N-00217_T 11648430 145910508 24895471 225 11995 GRM1 0 . GRCh38 6 146159379 146159379 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.732C>T p.= p.F244F ENST00000361719 3/9 254 200 54 327 326 1 strelka-varscan-mutect GRM1,synonymous_variant,p.=,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,synonymous_variant,p.=,ENST00000361719,;GRM1,synonymous_variant,p.=,ENST00000282753,NM_001278064.1;GRM1,synonymous_variant,p.=,ENST00000355289,NM_001278067.1;GRM1,synonymous_variant,p.=,ENST00000507907,;GRM1,non_coding_transcript_exon_variant,,ENST00000502405,;GRM1,non_coding_transcript_exon_variant,,ENST00000507005,; T ENST00000361719 Transcript synonymous_variant 1099/6754 732/3585 244/1194 F ttC/ttT 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD 3/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00248 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 146159379 146159379 C T 1 0 0 0 0 0 0 0 1 6678 825 29 3 3 GRM1 6 146159379 Silent SNP C C3N-00217_T 248871 146159379 24646600 226 11996 GRM1 0 . GRCh38 6 146386931 146386931 + Silent SNP G G T rs141287468 C3N-00217_T C3N-00217_N G G c.1644G>T p.= p.T548T ENST00000361719 7/9 310 228 82 370 370 0 strelka-varscan-mutect GRM1,synonymous_variant,p.=,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,synonymous_variant,p.=,ENST00000361719,;GRM1,synonymous_variant,p.=,ENST00000282753,NM_001278064.1;GRM1,synonymous_variant,p.=,ENST00000355289,NM_001278067.1;GRM1,synonymous_variant,p.=,ENST00000507907,; T ENST00000361719 Transcript synonymous_variant 2011/6754 1644/3585 548/1194 T acG/acT rs141287468 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD 7/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,PROSITE_patterns:PS00980,Pfam_domain:PF07562 LOW 1 SNV 5 1 PASS rs141287468 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 146386931 146386931 G T 1 0 0 0 0 0 0 0 1 6678 1103 39 1 1 GRM1 6 146386931 Silent SNP G C3N-00217_T 227552 146386931 24419048 227 11997 ADGB 0 . GRCh38 6 146736544 146736544 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.2841G>C p.Trp947Cys p.W947C ENST00000397944 23/36 89 73 16 178 178 0 strelka-varscan-mutect ADGB,missense_variant,p.Trp947Cys,ENST00000397944,NM_024694.3;ADGB,missense_variant,p.Trp9Cys,ENST00000367490,;ADGB,missense_variant,p.Trp367Cys,ENST00000480328,;ADGB,3_prime_UTR_variant,,ENST00000493950,; C ENST00000397944 Transcript missense_variant 2917/5325 2841/5004 947/1667 W/C tgG/tgC 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 deleterious(0) 23/36 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 146736544 146736544 G C 1 0 0 0 0 1 0 0 0 351 1241 43 4 4 ADGB 6 146736544 Missense_Mutation SNP G C3N-00217_T 349613 146736544 24069435 228 11998 SYNE1 0 . GRCh38 6 152510216 152510216 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.558G>T p.Lys186Asn p.K186N ENST00000367255 8/146 259 198 61 418 418 0 strelka-varscan-mutect SYNE1,missense_variant,p.Lys186Asn,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Lys193Asn,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Lys169Asn,ENST00000341594,;SYNE1,missense_variant,p.Lys193Asn,ENST00000367248,;SYNE1,missense_variant,p.Lys186Asn,ENST00000367253,;SYNE1,missense_variant,p.Lys186Asn,ENST00000413186,;SYNE1,missense_variant,p.Lys186Asn,ENST00000537750,;SYNE1,missense_variant,p.Lys186Asn,ENST00000466159,;SYNE1,missense_variant,p.Lys176Asn,ENST00000610489,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; A ENST00000367255 Transcript missense_variant 1160/27748 558/26394 186/8797 K/N aaG/aaT 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 8/146 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 152510216 152510216 C A 1 0 0 0 0 1 0 0 0 15837 564 20 2 2 SYNE1 6 152510216 Missense_Mutation SNP C C3N-00217_T 5773672 152510216 18295763 229 11999 FNDC1 0 . GRCh38 6 159234010 159234010 + Silent SNP C C A rs749069803 C3N-00217_T C3N-00217_N C C c.3498C>A p.= p.P1166P ENST00000297267 11/23 151 123 28 185 185 0 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,synonymous_variant,p.=,ENST00000329629,; A ENST00000297267 Transcript synonymous_variant 3698/6552 3498/5685 1166/1894 P ccC/ccA rs749069803 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 11/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 LOW 1 SNV 1 1 PASS rs749069803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 159234010 159234010 C A 1 0 0 0 0 0 0 0 1 5824 610 22 2 2 FNDC1 6 159234010 Silent SNP C C3N-00217_T 6723794 159234010 11571969 230 12000 PLG 0 . GRCh38 6 160753040 160753040 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2412G>T p.Glu804Asp p.E804D ENST00000308192 19/19 123 94 29 195 195 0 strelka-varscan-mutect PLG,missense_variant,p.Glu804Asp,ENST00000308192,NM_000301.3;PLG,non_coding_transcript_exon_variant,,ENST00000461414,;PLG,downstream_gene_variant,,ENST00000467466,;RP1-81D8.5,downstream_gene_variant,,ENST00000612111,; T ENST00000308192 Transcript missense_variant 2475/2741 2412/2433 804/810 E/D gaG/gaT 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 tolerated(0.16) 19/19 Gene3D:2.40.10.10,PIRSF_domain:PIRSF001150,PROSITE_profiles:PS50240,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 160753040 160753040 G T 1 0 0 0 0 1 0 0 0 12181 991 35 2 2 PLG 6 160753040 Missense_Mutation SNP G C3N-00217_T 1519030 160753040 10052939 231 12001 UNC93A 0 . GRCh38 6 167304060 167304060 + Missense_Mutation SNP G G T rs372539280 C3N-00217_T C3N-00217_N G G c.767G>T p.Arg256Leu p.R256L ENST00000230256 5/8 223 168 55 308 307 1 strelka-varscan-mutect UNC93A,missense_variant,p.Arg256Leu,ENST00000230256,NM_018974.3;UNC93A,missense_variant,p.Arg214Leu,ENST00000366829,NM_001143947.1; T ENST00000230256 Transcript missense_variant 942/2116 767/1374 256/457 R/L cGt/cTt rs372539280 1 1 UNC93A HGNC HGNC:12570 protein_coding YES CCDS5300.1 ENSP00000230256 Q86WB7 UPI0000062351 NM_018974.3 deleterious(0) 5/8 Gene3D:1.20.1250.20,hmmpanther:PTHR19444,hmmpanther:PTHR19444:SF14,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs372539280 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 167304060 167304060 G T 1 0 0 0 0 1 0 0 0 17522 1145 40 1 1 UNC93A 6 167304060 Missense_Mutation SNP G C3N-00217_T 6551020 167304060 3501919 232 12002 INTS1 0 . GRCh38 7 1479506 1479506 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.4253G>T p.Gly1418Val p.G1418V ENST00000404767 31/48 145 117 28 136 135 1 strelka-varscan-mutect INTS1,missense_variant,p.Gly1418Val,ENST00000404767,NM_001080453.2;INTS1,downstream_gene_variant,,ENST00000468115,;INTS1,upstream_gene_variant,,ENST00000482994,; A ENST00000404767 Transcript missense_variant 4339/6959 4253/6573 1418/2190 G/V gGc/gTc 1 -1 INTS1 HGNC HGNC:24555 protein_coding YES CCDS47526.1 ENSP00000385722 Q8N201 UPI0000D7211C NM_001080453.2 tolerated(0.26) 31/48 hmmpanther:PTHR21224:SF1,hmmpanther:PTHR21224,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs1415588701 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 1479506 1479506 C A 1 0 0 0 0 1 0 0 0 7677 739 26 2 2 INTS1 7 1479506 Missense_Mutation SNP C C3N-00217_T 1479506 157866467 233 12003 FAM220A 0 . GRCh38 7 6330669 6330669 + Silent SNP C C A rs142897377 C3N-00217_T C3N-00217_N C C c.486G>T p.= p.P162P ENST00000313324 2/2 255 195 60 343 341 2 strelka-varscan-mutect FAM220A,synonymous_variant,p.=,ENST00000313324,NM_001037163.1;FAM220A,synonymous_variant,p.=,ENST00000616824,;FAM220A,downstream_gene_variant,,ENST00000530143,;FAM220A,downstream_gene_variant,,ENST00000524898,;FAM220A,downstream_gene_variant,,ENST00000578372,;FAM220A,downstream_gene_variant,,ENST00000533877,; A ENST00000313324 Transcript synonymous_variant 954/2214 486/780 162/259 P ccG/ccT rs142897377 1 -1 FAM220A HGNC HGNC:22422 protein_coding YES CCDS34599.1 ENSP00000317289 Q7Z4H9 UPI000013F4F0 NM_001037163.1 2/2 Pfam_domain:PF15487,hmmpanther:PTHR31980,hmmpanther:PTHR31980:SF2 LOW 1 SNV 1 1 PASS rs142897377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 6330669 6330669 C A 1 0 0 0 0 0 0 0 1 5413 639 23 1 1 FAM220A 7 6330669 Silent SNP C C3N-00217_T 4851163 6330669 153015304 234 12004 DNAH11 0 . GRCh38 7 21571892 21571892 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.1512C>T p.= p.V504V ENST00000409508 8/82 57 44 13 117 117 0 strelka-varscan-mutect DNAH11,synonymous_variant,p.=,ENST00000409508,NM_001277115.1;DNAH11,synonymous_variant,p.=,ENST00000328843,;DNAH11,synonymous_variant,p.=,ENST00000620169,;DNAH11,downstream_gene_variant,,ENST00000496218,; T ENST00000409508 Transcript synonymous_variant 1543/14167 1512/13551 504/4516 V gtC/gtT 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 8/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Pfam_domain:PF08385 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 21571892 21571892 C T 1 0 0 0 0 0 0 0 1 4413 842 30 3 3 DNAH11 7 21571892 Silent SNP C C3N-00217_T 15241223 21571892 137774081 235 12005 EVX1 0 . GRCh38 7 27243163 27243163 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.133C>A p.Arg45Ser p.R45S ENST00000496902 1/3 187 157 30 223 223 0 strelka-varscan-mutect EVX1,missense_variant,p.Arg45Ser,ENST00000496902,NM_001989.4,NM_001304519.1;EVX1,missense_variant,p.Arg45Ser,ENST00000222761,;EVX1,upstream_gene_variant,,ENST00000580535,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000519218,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1,upstream_gene_variant,,ENST00000518886,; A ENST00000496902 Transcript missense_variant 464/2955 133/1224 45/407 R/S Cgt/Agt 1 1 EVX1 HGNC HGNC:3506 protein_coding YES CCDS5413.1 ENSP00000419266 P49640 UPI000012A2AD NM_001989.4,NM_001304519.1 tolerated(0.35) 1/3 MODERATE 1 SNV 1 1 PASS rs1044643048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 27243163 27243163 C A 1 0 0 0 0 1 0 0 0 5161 652 23 1 1 EVX1 7 27243163 Missense_Mutation SNP C C3N-00217_T 5671271 27243163 132102810 236 12006 ELMO1 0 . GRCh38 7 37222671 37222671 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.724T>A p.Tyr242Asn p.Y242N ENST00000310758 10/22 108 90 18 177 177 0 strelka-varscan ELMO1,missense_variant,p.Tyr242Asn,ENST00000310758,NM_001206480.2,NM_014800.10;ELMO1,missense_variant,p.Tyr242Asn,ENST00000442504,NM_001206482.1;ELMO1,missense_variant,p.Tyr242Asn,ENST00000448602,;ELMO1,missense_variant,p.Tyr7Asn,ENST00000433246,;ELMO1,non_coding_transcript_exon_variant,,ENST00000487336,; T ENST00000310758 Transcript missense_variant 1372/4022 724/2184 242/727 Y/N Tat/Aat 1 -1 ELMO1 HGNC HGNC:16286 protein_coding YES CCDS5449.1 ENSP00000312185 Q92556 A4D1X5 UPI000006F687 NM_001206480.2,NM_014800.10 tolerated(0.54) 10/22 Gene3D:1.25.10.10,Pfam_domain:PF11841,hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF23,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 37222671 37222671 A T 1 0 0 0 0 1 0 0 0 4899 420 15 4 4 ELMO1 7 37222671 Missense_Mutation SNP A C3N-00217_T 9979508 37222671 122123302 237 12007 NPC1L1 0 . GRCh38 7 44539710 44539710 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.687G>T p.= p.V229V ENST00000289547 2/20 91 68 23 127 127 0 strelka-varscan NPC1L1,synonymous_variant,p.=,ENST00000289547,NM_013389.2;NPC1L1,synonymous_variant,p.=,ENST00000546276,;NPC1L1,synonymous_variant,p.=,ENST00000381160,NM_001101648.1;NPC1L1,synonymous_variant,p.=,ENST00000423141,NM_001300967.1; A ENST00000289547 Transcript synonymous_variant 743/5048 687/4080 229/1359 V gtG/gtT 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 2/20 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89,Pfam_domain:PF16414 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 44539710 44539710 C A 1 0 0 0 0 0 0 0 1 10619 581 21 2 2 NPC1L1 7 44539710 Silent SNP C C3N-00217_T 7317039 44539710 114806263 238 12008 ABCA13 0 . GRCh38 7 48376529 48376529 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.11292C>A p.Ser3764Arg p.S3764R ENST00000435803 35/62 154 126 28 274 274 0 strelka-varscan ABCA13,missense_variant,p.Ser3764Arg,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Ser1071Arg,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,missense_variant,p.Ser30Arg,ENST00000453246,;ABCA13,non_coding_transcript_exon_variant,,ENST00000484268,; A ENST00000435803 Transcript missense_variant 11316/17184 11292/15177 3764/5058 S/R agC/agA 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.05) 35/62 Transmembrane_helices:TMhelix,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Pfam_domain:PF12698 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48376529 48376529 C A 1 0 0 0 0 1 0 0 0 35 738 26 2 2 ABCA13 7 48376529 Missense_Mutation SNP C C3N-00217_T 3836819 48376529 110969444 239 12009 ZNF679 0 . GRCh38 7 64266039 64266039 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.406G>C p.Val136Leu p.V136L ENST00000421025 5/5 114 77 37 336 336 0 strelka-varscan ZNF679,missense_variant,p.Val136Leu,ENST00000421025,NM_153363.2;ZNF679,missense_variant,p.Val136Leu,ENST00000255746,; C ENST00000421025 Transcript missense_variant 675/1567 406/1236 136/411 V/L Gtg/Ctg 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 tolerated(0.16) 5/5 hmmpanther:PTHR24384:SF91,hmmpanther:PTHR24384 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 64266039 64266039 G C 1 0 0 0 0 1 0 0 0 18659 1261 44 4 4 ZNF679 7 64266039 Missense_Mutation SNP G C3N-00217_T 15889510 64266039 95079934 240 12010 PCLO 0 . GRCh38 7 82953104 82953104 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.7849G>T p.Glu2617Ter p.E2617* ENST00000333891 5/25 148 94 54 182 182 0 strelka-varscan PCLO,stop_gained,p.Glu2617Ter,ENST00000333891,NM_033026.5;PCLO,stop_gained,p.Glu2617Ter,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript stop_gained 8187/20329 7849/15429 2617/5142 E/* Gaa/Taa 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 82953104 82953104 C A 1 0 0 0 0 0 1 0 0 11671 835 29 2 2 PCLO 7 82953104 Nonsense_Mutation SNP C C3N-00217_T 18687065 82953104 76392869 241 12011 SEMA3E 0 . GRCh38 7 83367650 83367650 + Missense_Mutation SNP T T A C3N-00217_T C3N-00217_N T T c.2264A>T p.Gln755Leu p.Q755L ENST00000307792 17/17 265 157 108 273 273 0 strelka-varscan SEMA3E,missense_variant,p.Gln755Leu,ENST00000307792,NM_012431.2;SEMA3E,missense_variant,p.Gln695Leu,ENST00000427262,NM_001178129.1; A ENST00000307792 Transcript missense_variant 2732/6476 2264/2328 755/775 Q/L cAg/cTg COSM323254 1 -1 SEMA3E HGNC HGNC:10727 protein_coding YES CCDS34674.1 ENSP00000303212 O15041 UPI0000135A68 NM_012431.2 tolerated(0.32) 17/17 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 83367650 83367650 T A 1 0 0 0 0 1 0 0 0 14304 1580 55 4 4 SEMA3E 7 83367650 Missense_Mutation SNP T C3N-00217_T 414546 83367650 75978323 242 12012 ZNF804B 0 . GRCh38 7 89335031 89335031 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2049C>A p.Ser683Arg p.S683R ENST00000333190 4/4 123 102 21 200 200 0 strelka-varscan ZNF804B,missense_variant,p.Ser683Arg,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Ser600Arg,ENST00000611114,; A ENST00000333190 Transcript missense_variant 2658/4659 2049/4050 683/1349 S/R agC/agA 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 tolerated(0.1) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 89335031 89335031 C A 1 0 0 0 0 1 0 0 0 18756 709 25 2 2 ZNF804B 7 89335031 Missense_Mutation SNP C C3N-00217_T 5967381 89335031 70010942 243 12013 SAMD9 0 . GRCh38 7 93105020 93105020 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.1078A>G p.Arg360Gly p.R360G ENST00000379958 3/3 130 102 28 236 235 1 strelka-varscan SAMD9,missense_variant,p.Arg360Gly,ENST00000379958,NM_017654.3;SAMD9,missense_variant,p.Arg360Gly,ENST00000620985,NM_001193307.1;SAMD9,missense_variant,p.Arg360Gly,ENST00000446617,; C ENST00000379958 Transcript missense_variant 1348/6852 1078/4770 360/1589 R/G Aga/Gga 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 tolerated(0.05) 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 93105020 93105020 T C 1 0 0 0 0 1 0 0 0 14086 1588 55 5 5 SAMD9 7 93105020 Missense_Mutation SNP T C3N-00217_T 3769989 93105020 66240953 244 12014 MUC17 0 . GRCh38 7 101037957 101037957 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.6541C>A p.Leu2181Ile p.L2181I ENST00000306151 3/13 69 43 26 95 95 0 strelka-varscan MUC17,missense_variant,p.Leu2181Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Leu2181Ile,ENST00000379439,; A ENST00000306151 Transcript missense_variant 6605/14247 6541/13482 2181/4493 L/I Ctt/Att 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.28) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 101037957 101037957 C A 1 0 0 0 0 1 0 0 0 9973 681 24 2 2 MUC17 7 101037957 Missense_Mutation SNP C C3N-00217_T 7932937 101037957 58308016 245 12015 MUC17 0 . GRCh38 7 101040965 101040965 + Silent SNP C C T rs750778755 C3N-00217_T C3N-00217_N C C c.9549C>T p.= p.T3183T ENST00000306151 3/13 122 71 51 133 133 0 strelka-varscan MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; T ENST00000306151 Transcript synonymous_variant 9613/14247 9549/13482 3183/4493 T acC/acT rs750778755,COSM1330226 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999991 1 1 1 0 T 2 4 43 101040965 101040965 C T 1 0 0 0 0 0 0 0 1 9973 610 22 3 3 MUC17 7 101040965 Silent SNP C C3N-00217_T 3008 101040965 58305008 246 12016 RELN 0 . GRCh38 7 103635429 103635429 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.2461C>G p.Pro821Ala p.P821A ENST00000428762 19/65 140 82 58 207 207 0 strelka-varscan RELN,missense_variant,p.Pro821Ala,ENST00000424685,;RELN,missense_variant,p.Pro821Ala,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Pro821Ala,ENST00000343529,NM_173054.2; C ENST00000428762 Transcript missense_variant 2621/11571 2461/10383 821/3460 P/A Ccc/Gcc COSM598294 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0.04) 19/65 hmmpanther:PTHR11841,Gene3D:2.120.10.10,Superfamily_domains:SSF50939 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 103635429 103635429 G C 1 0 0 0 0 1 0 0 0 13390 1217 42 4 4 RELN 7 103635429 Missense_Mutation SNP G C3N-00217_T 2594464 103635429 55710544 247 12017 NAMPT 0 . GRCh38 7 106268471 106268471 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.736G>T p.Glu246Ter p.E246* ENST00000222553 6/11 65 38 27 98 98 0 strelka-varscan NAMPT,stop_gained,p.Glu246Ter,ENST00000222553,NM_005746.2;NAMPT,stop_gained,p.Glu246Ter,ENST00000354289,;NAMPT,non_coding_transcript_exon_variant,,ENST00000467730,;NAMPT,downstream_gene_variant,,ENST00000484527,;NAMPT,downstream_gene_variant,,ENST00000393618,;NAMPT,downstream_gene_variant,,ENST00000441045,;NAMPT,downstream_gene_variant,,ENST00000489358,;NAMPT,non_coding_transcript_exon_variant,,ENST00000491027,;NAMPT,downstream_gene_variant,,ENST00000486949,; A ENST00000222553 Transcript stop_gained 1044/4582 736/1476 246/491 E/* Gaa/Taa 1 -1 NAMPT HGNC HGNC:30092 protein_coding YES CCDS5737.1 ENSP00000222553 P43490 A0A024R718 UPI0000131383 NM_005746.2 6/11 Gene3D:3.20.140.10,Pfam_domain:PF04095,PIRSF_domain:PIRSF005943,hmmpanther:PTHR11098,hmmpanther:PTHR11098:SF15,Superfamily_domains:SSF51690 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 106268471 106268471 C A 1 0 0 0 0 0 1 0 0 10156 922 32 2 2 NAMPT 7 106268471 Nonsense_Mutation SNP C C3N-00217_T 2633042 106268471 53077502 248 12018 PTPRZ1 0 . GRCh38 7 122012505 122012505 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.3459T>A p.= p.S1153S ENST00000393386 12/30 131 103 28 160 160 0 strelka-varscan PTPRZ1,synonymous_variant,p.=,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; A ENST00000393386 Transcript synonymous_variant 3870/8175 3459/6948 1153/2315 S tcT/tcA 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 12/30 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 122012505 122012505 T A 1 0 0 0 0 0 0 0 1 12969 1567 55 4 4 PTPRZ1 7 122012505 Silent SNP T C3N-00217_T 15744034 122012505 37333468 249 12019 TAS2R16 0 . GRCh38 7 122995500 122995500 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.135G>A p.= p.V45V ENST00000249284 1/1 102 61 41 105 105 0 strelka-varscan TAS2R16,synonymous_variant,p.=,ENST00000249284,NM_016945.2; T ENST00000249284 Transcript synonymous_variant 201/997 135/876 45/291 V gtG/gtA 1 -1 TAS2R16 HGNC HGNC:14921 protein_coding YES CCDS5785.1 ENSP00000249284 Q9NYV7 UPI0000038B18 NM_016945.2 1/1 Pfam_domain:PF05296,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF68,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 122995500 122995500 C T 1 0 0 0 0 0 0 0 1 15968 581 21 3 3 TAS2R16 7 122995500 Silent SNP C C3N-00217_T 982995 122995500 36350473 250 12020 GRM8 0 . GRCh38 7 126533502 126533502 + Missense_Mutation SNP G G T rs142400397 C3N-00217_T C3N-00217_N G G c.1880C>A p.Thr627Lys p.T627K ENST00000339582 9/11 214 132 82 258 257 1 strelka-varscan GRM8,missense_variant,p.Thr627Lys,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Thr627Lys,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Thr135Lys,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Thr627Lys,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; T ENST00000339582 Transcript missense_variant 2689/4057 1880/2727 627/908 T/K aCg/aAg rs142400397,COSM2768128,COSM4359498 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.1) 9/11 Pfam_domain:PF00003,Prints_domain:PR00248,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Transmembrane_helices:TMhelix 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 126533502 126533502 G T 1 0 0 0 0 1 0 0 0 6685 1145 40 1 1 GRM8 7 126533502 Missense_Mutation SNP G C3N-00217_T 3538002 126533502 32812471 251 12021 FLNC 0 . GRCh38 7 128853750 128853750 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.6397C>A p.Arg2133Ser p.R2133S ENST00000325888 39/48 577 486 91 387 386 1 strelka-varscan FLNC,missense_variant,p.Arg2133Ser,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Arg2100Ser,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; A ENST00000325888 Transcript missense_variant 6658/9188 6397/8178 2133/2725 R/S Cgc/Agc 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 deleterious(0.01) 39/48 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 128853750 128853750 C A 1 0 0 0 0 1 0 0 0 5791 652 23 1 1 FLNC 7 128853750 Missense_Mutation SNP C C3N-00217_T 2320248 128853750 30492223 252 12022 FLNC 0 . GRCh38 7 128856846 128856846 + Missense_Mutation SNP G G T rs200295337 C3N-00217_T C3N-00217_N G G c.7486G>T p.Val2496Phe p.V2496F ENST00000325888 45/48 348 190 158 300 300 0 strelka-varscan FLNC,missense_variant,p.Val2496Phe,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Val2463Phe,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; T ENST00000325888 Transcript missense_variant 7747/9188 7486/8178 2496/2725 V/F Gtt/Ttt rs200295337 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 deleterious(0) 45/48 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 128856846 128856846 G T 1 0 0 0 0 1 0 0 0 5791 1145 40 1 1 FLNC 7 128856846 Missense_Mutation SNP G C3N-00217_T 3096 128856846 30489127 253 12023 TSGA13 0 . GRCh38 7 130669071 130669071 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.771C>A p.= p.A257A ENST00000456951 9/9 282 242 40 203 203 0 strelka-varscan TSGA13,synonymous_variant,p.=,ENST00000456951,NM_001304968.1;TSGA13,synonymous_variant,p.=,ENST00000356588,NM_052933.3;COPG2,upstream_gene_variant,,ENST00000425248,NM_012133.5;COPG2,upstream_gene_variant,,ENST00000330992,NM_001290033.1; T ENST00000456951 Transcript synonymous_variant 1623/2046 771/828 257/275 A gcC/gcA 1 -1 TSGA13 HGNC HGNC:12369 protein_coding YES CCDS5824.1 ENSP00000406047 Q96PP4 A0A024R769 UPI0000073CFB NM_001304968.1 9/9 Pfam_domain:PF14994,hmmpanther:PTHR37352 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 130669071 130669071 G T 1 0 0 0 0 0 0 0 1 17125 987 35 2 2 TSGA13 7 130669071 Silent SNP G C3N-00217_T 1812225 130669071 28676902 254 12024 DGKI 0 . GRCh38 7 137552431 137552431 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.2085G>T p.= p.L695L ENST00000288490 20/34 302 260 42 275 275 0 strelka-varscan DGKI,synonymous_variant,p.=,ENST00000453654,;DGKI,synonymous_variant,p.=,ENST00000424189,;DGKI,synonymous_variant,p.=,ENST00000446122,;DGKI,synonymous_variant,p.=,ENST00000288490,NM_004717.2;DGKI,synonymous_variant,p.=,ENST00000614521,;DGKI,non_coding_transcript_exon_variant,,ENST00000460662,; A ENST00000288490 Transcript synonymous_variant 2086/3895 2085/3198 695/1065 L ctG/ctT 1 -1 DGKI HGNC HGNC:2855 protein_coding YES CCDS5845.1 ENSP00000288490 O75912 UPI000012DD23 NM_004717.2 20/34 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41,Superfamily_domains:SSF111331 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 137552431 137552431 C A 1 0 0 0 0 0 0 0 1 4277 813 29 2 2 DGKI 7 137552431 Silent SNP C C3N-00217_T 6883360 137552431 21793542 255 12025 PRSS37 0 . GRCh38 7 141836519 141836519 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.584C>A p.Thr195Asn p.T195N ENST00000350549 5/5 161 91 70 137 137 0 strelka-varscan PRSS37,missense_variant,p.Thr195Asn,ENST00000350549,NM_001008270.2,NM_001171951.1;PRSS37,missense_variant,p.Thr195Asn,ENST00000438520,;PRSS37,3_prime_UTR_variant,,ENST00000419085,;PRSS37,3_prime_UTR_variant,,ENST00000452758,; T ENST00000350549 Transcript missense_variant 956/1189 584/708 195/235 T/N aCt/aAt 1 -1 PRSS37 HGNC HGNC:29211 protein_coding YES CCDS34764.1 ENSP00000297767 A4D1T9 UPI000004223A NM_001008270.2,NM_001171951.1 deleterious(0) 5/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF244,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 141836519 141836519 G T 1 0 0 0 0 1 0 0 0 12773 1029 36 2 2 PRSS37 7 141836519 Missense_Mutation SNP G C3N-00217_T 4284088 141836519 17509454 256 12026 MGAM2 0 . GRCh38 7 142133981 142133981 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.576G>T p.Leu192Phe p.L192F ENST00000477922 7/48 76 40 36 60 60 0 strelka-varscan MGAM2,missense_variant,p.Leu192Phe,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Leu192Phe,ENST00000550469,; T ENST00000477922 Transcript missense_variant,splice_region_variant 630/7867 576/7548 192/2515 L/F ttG/ttT 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.02) 7/48 Pfam_domain:PF16863,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF74650 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 142133981 142133981 G T 1 0 0 0 0 1 0 0 0 9500 1275 44 2 2 MGAM2 7 142133981 Missense_Mutation SNP G C3N-00217_T 297462 142133981 17211992 257 12027 GIMAP4 0 . GRCh38 7 150569942 150569942 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.41C>A p.Thr14Lys p.T14K ENST00000255945 2/3 203 132 71 211 211 0 strelka-varscan GIMAP4,missense_variant,p.Thr14Lys,ENST00000255945,NM_018326.2;GIMAP4,missense_variant,p.Thr14Lys,ENST00000461940,;GIMAP4,missense_variant,p.Thr14Lys,ENST00000479232,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000478135,;GIMAP4,intron_variant,,ENST00000494750,; A ENST00000255945 Transcript missense_variant 216/2060 41/990 14/329 T/K aCa/aAa 1 1 GIMAP4 HGNC HGNC:21872 protein_coding YES CCDS5904.1 ENSP00000255945 Q9NUV9 A0A090N7X0 UPI0000073CB0 NM_018326.2 tolerated(0.88) 2/3 hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF57 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 150569942 150569942 C A 1 0 0 0 0 1 0 0 0 6261 478 17 2 2 GIMAP4 7 150569942 Missense_Mutation SNP C C3N-00217_T 8435961 150569942 8776031 258 12028 GIMAP4 0 . GRCh38 7 150572913 150572913 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.843G>T p.Lys281Asn p.K281N ENST00000255945 3/3 255 212 43 302 302 0 strelka-varscan GIMAP4,missense_variant,p.Lys281Asn,ENST00000255945,NM_018326.2;GIMAP4,missense_variant,p.Lys295Asn,ENST00000461940,;GIMAP4,downstream_gene_variant,,ENST00000479232,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000494750,;GIMAP4,downstream_gene_variant,,ENST00000478135,; T ENST00000255945 Transcript missense_variant 1018/2060 843/990 281/329 K/N aaG/aaT COSM1087241,COSM3636026 1 1 GIMAP4 HGNC HGNC:21872 protein_coding YES CCDS5904.1 ENSP00000255945 Q9NUV9 A0A090N7X0 UPI0000073CB0 NM_018326.2 deleterious(0.04) 3/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF57,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 150572913 150572913 G T 1 0 0 0 0 1 0 0 0 6261 933 33 2 2 GIMAP4 7 150572913 Missense_Mutation SNP G C3N-00217_T 2971 150572913 8773060 259 12029 DLGAP2 0 . GRCh38 8 1668331 1668331 + Missense_Mutation SNP G G C rs376920234 C3N-00217_T C3N-00217_N G G c.1573G>C p.Val525Leu p.V525L ENST00000612087 6/11 17 5 12 36 36 0 strelka-varscan-mutect DLGAP2,missense_variant,p.Val525Leu,ENST00000612087,NM_001277161.1;DLGAP2,missense_variant,p.Val542Leu,ENST00000520901,;DLGAP2,missense_variant,p.Val605Leu,ENST00000637795,;DLGAP2,missense_variant,p.Val604Leu,ENST00000421627,;DLGAP2,missense_variant,p.Val525Leu,ENST00000637152,NM_004745.4; C ENST00000612087 Transcript missense_variant,splice_region_variant 1707/10088 1573/2886 525/961 V/L Gtc/Ctc rs376920234 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 tolerated(0.67) 6/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3 MODERATE 1 SNV 5 1 PASS rs376920234 . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 1668331 1668331 G C 1 0 0 0 0 1 0 0 0 4367 1391 48 4 4 DLGAP2 8 1668331 Missense_Mutation SNP G C3N-00217_T 1668331 143470305 260 12030 CSMD1 0 . GRCh38 8 2974607 2974607 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.8587C>T p.Pro2863Ser p.P2863S ENST00000520002 57/71 113 82 31 114 114 0 strelka-mutect CSMD1,missense_variant,p.Pro2724Ser,ENST00000537824,;CSMD1,missense_variant,p.Pro2280Ser,ENST00000335551,;CSMD1,missense_variant,p.Pro2863Ser,ENST00000520002,;CSMD1,missense_variant,p.Pro2863Ser,ENST00000602557,;CSMD1,missense_variant,p.Pro2862Ser,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Pro2805Ser,ENST00000400186,;CSMD1,missense_variant,p.Pro2805Ser,ENST00000602723,; A ENST00000520002 Transcript missense_variant 9143/11740 8587/10698 2863/3565 P/S Cca/Tca 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.01) 57/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999949 1 1 1 0 A 3 1 43 2974607 2974607 G A 1 0 0 0 0 1 0 0 0 3745 1232 43 3 3 CSMD1 8 2974607 Missense_Mutation SNP G C3N-00217_T 1306276 2974607 142164029 261 12031 CSMD1 0 . GRCh38 8 3108607 3108607 + Missense_Mutation SNP G G T rs752350985 C3N-00217_T C3N-00217_N G G c.6753C>A p.Phe2251Leu p.F2251L ENST00000520002 45/71 124 91 33 128 128 0 strelka-varscan-mutect CSMD1,missense_variant,p.Phe2112Leu,ENST00000537824,;CSMD1,missense_variant,p.Phe1731Leu,ENST00000335551,;CSMD1,missense_variant,p.Phe2251Leu,ENST00000520002,;CSMD1,missense_variant,p.Phe2251Leu,ENST00000602557,;CSMD1,missense_variant,p.Phe2250Leu,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Phe2251Leu,ENST00000400186,;CSMD1,missense_variant,p.Phe2251Leu,ENST00000602723,;CSMD1,downstream_gene_variant,,ENST00000520561,;CSMD1,upstream_gene_variant,,ENST00000523062,; T ENST00000520002 Transcript missense_variant 7309/11740 6753/10698 2251/3565 F/L ttC/ttA rs752350985,COSM4674958,COSM4674959 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.01) 45/71 PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs752350985 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 3108607 3108607 G T 1 0 0 0 0 1 0 0 0 3745 1188 41 2 2 CSMD1 8 3108607 Missense_Mutation SNP G C3N-00217_T 134000 3108607 142030029 262 12032 UNC5D 0 . GRCh38 8 35568097 35568097 + Splice_Site SNP G G C C3N-00217_T C3N-00217_N G G c.323-1G>C p.X108_splice ENST00000404895 105 82 23 107 107 0 strelka-varscan UNC5D,splice_acceptor_variant,,ENST00000287272,;UNC5D,splice_acceptor_variant,,ENST00000453357,;UNC5D,splice_acceptor_variant,,ENST00000416672,;UNC5D,splice_acceptor_variant,,ENST00000404895,NM_080872.2;UNC5D,splice_acceptor_variant,,ENST00000420357,; C ENST00000404895 Transcript splice_acceptor_variant -/3252 323/2862 108/953 COSM3648614,COSM3648615 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 2/16 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 43 35568097 35568097 G C 1 0 0 0 0 0 0 1 0 17519 1014 35 4 4 UNC5D 8 35568097 Splice_Site SNP G C3N-00217_T 32459490 35568097 109570539 263 12033 UNC5D 0 . GRCh38 8 35568163 35568163 + Missense_Mutation SNP G G C rs758449590 C3N-00217_T C3N-00217_N G G c.388G>C p.Glu130Gln p.E130Q ENST00000404895 3/17 228 172 56 199 199 0 strelka-varscan UNC5D,missense_variant,p.Glu130Gln,ENST00000287272,;UNC5D,missense_variant,p.Glu125Gln,ENST00000453357,;UNC5D,missense_variant,p.Glu130Gln,ENST00000416672,;UNC5D,missense_variant,p.Glu130Gln,ENST00000404895,NM_080872.2;UNC5D,missense_variant,p.Glu130Gln,ENST00000420357,; C ENST00000404895 Transcript missense_variant 716/3252 388/2862 130/953 E/Q Gag/Cag rs758449590 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 deleterious(0) 3/17 Gene3D:2.60.40.10,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 35568163 35568163 G C 1 0 0 0 0 1 0 0 0 17519 1059 37 4 4 UNC5D 8 35568163 Missense_Mutation SNP G C3N-00217_T 66 35568163 109570473 264 12034 ADGRA2 0 . GRCh38 8 37834032 37834032 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.1512G>T p.= p.L504L ENST00000412232 11/19 823 770 53 118 118 0 strelka-varscan ADGRA2,synonymous_variant,p.=,ENST00000315215,;ADGRA2,synonymous_variant,p.=,ENST00000412232,NM_032777.9;ADGRA2,downstream_gene_variant,,ENST00000428068,; T ENST00000412232 Transcript synonymous_variant 1525/5651 1512/4017 504/1338 L ctG/ctT 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 11/19 hmmpanther:PTHR12011:SF33,hmmpanther:PTHR12011 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 37834032 37834032 G T 1 0 0 0 0 0 0 0 1 353 1335 47 2 2 ADGRA2 8 37834032 Silent SNP G C3N-00217_T 2265869 37834032 107304604 265 12035 XKR4 0 . GRCh38 8 55102759 55102759 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.271G>C p.Ala91Pro p.A91P ENST00000327381 1/3 60 45 15 31 31 0 strelka-varscan XKR4,missense_variant,p.Ala91Pro,ENST00000327381,NM_052898.1;XKR4,missense_variant,p.Ala91Pro,ENST00000622811,; C ENST00000327381 Transcript missense_variant 371/19880 271/1953 91/650 A/P Gcg/Ccg 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 tolerated(0.32) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 55102759 55102759 G C 1 0 0 0 0 1 0 0 0 17992 1203 42 4 4 XKR4 8 55102759 Missense_Mutation SNP G C3N-00217_T 17268727 55102759 90035877 266 12036 CLVS1 0 . GRCh38 8 61376718 61376718 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.569C>T p.Ser190Phe p.S190F ENST00000519846 4/7 192 175 17 135 135 0 strelka-varscan CLVS1,missense_variant,p.Ser190Phe,ENST00000519846,;CLVS1,missense_variant,p.Ser190Phe,ENST00000325897,NM_173519.2;CLVS1,5_prime_UTR_variant,,ENST00000518592,;CLVS1,5_prime_UTR_variant,,ENST00000524095,;CLVS1,5_prime_UTR_variant,,ENST00000520712,;CLVS1,non_coding_transcript_exon_variant,,ENST00000521189,; T ENST00000519846 Transcript missense_variant 1041/3622 569/1065 190/354 S/F tCc/tTc COSM4500599 1 1 CLVS1 HGNC HGNC:23139 protein_coding YES CCDS6176.1 ENSP00000428402 Q8IUQ0 UPI000007472D deleterious(0) 4/7 Gene3D:3.40.525.10,Pfam_domain:PF00650,PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF72,SMART_domains:SM00516,Superfamily_domains:SSF52087 1 MODERATE 1 SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99907 0.9999998 1 1 1 0 T 3 4 43 61376718 61376718 C T 1 0 0 0 0 1 0 0 0 3344 855 30 3 3 CLVS1 8 61376718 Missense_Mutation SNP C C3N-00217_T 6273959 61376718 83761918 267 12037 C8orf46 0 . GRCh38 8 66505419 66505419 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.171G>T p.= p.L57L ENST00000305454 3/6 128 107 21 78 78 0 strelka-varscan C8orf46,synonymous_variant,p.=,ENST00000305454,NM_152765.3;C8orf46,synonymous_variant,p.=,ENST00000522977,;C8orf46,synonymous_variant,p.=,ENST00000480005,;C8orf46,synonymous_variant,p.=,ENST00000521495,;RNU6-1324P,upstream_gene_variant,,ENST00000384222,;C8orf46,non_coding_transcript_exon_variant,,ENST00000482608,;C8orf46,non_coding_transcript_exon_variant,,ENST00000519702,;C8orf46,non_coding_transcript_exon_variant,,ENST00000485639,;C8orf46,non_coding_transcript_exon_variant,,ENST00000470796,;C8orf46,downstream_gene_variant,,ENST00000521813,;C8orf46,3_prime_UTR_variant,,ENST00000460144,;C8orf46,3_prime_UTR_variant,,ENST00000450307,;C8orf46,non_coding_transcript_exon_variant,,ENST00000484919,; T ENST00000305454 Transcript synonymous_variant 612/3513 171/624 57/207 L ctG/ctT 1 1 C8orf46 HGNC HGNC:28498 protein_coding YES CCDS6191.2 ENSP00000302260 Q8TAG6 UPI00003750A4 NM_152765.3 3/6 Pfam_domain:PF15505,hmmpanther:PTHR31520 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 2 4 43 66505419 66505419 G T 1 0 0 0 0 0 0 0 1 2159 1306 46 2 2 C8orf46 8 66505419 Silent SNP G C3N-00217_T 5128701 66505419 78633217 268 12038 TRPA1 0 . GRCh38 8 72057783 72057783 + Missense_Mutation SNP G G T rs372548303 C3N-00217_T C3N-00217_N G G c.1027C>A p.Arg343Ser p.R343S ENST00000262209 9/27 330 177 153 265 265 0 strelka-varscan TRPA1,missense_variant,p.Arg343Ser,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Arg195Ser,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,downstream_gene_variant,,ENST00000457356,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;TRPA1,upstream_gene_variant,,ENST00000520788,; T ENST00000262209 Transcript missense_variant 1235/5223 1027/3360 343/1119 R/S Cgc/Agc rs372548303 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0.03) 9/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 72057783 72057783 G T 1 0 0 0 0 1 0 0 0 17082 1145 40 1 1 TRPA1 8 72057783 Missense_Mutation SNP G C3N-00217_T 5552364 72057783 73080853 269 12039 CNGB3 0 . GRCh38 8 86604196 86604197 + Frame_Shift_Del DEL CC CC - novel C3N-00217_T C3N-00217_N CC CC c.1677_1678delGG p.Glu560AsnfsTer16 p.E560Nfs*16 ENST00000320005 15/18 242 224 18 191 191 0 varindel-pindel CNGB3,frameshift_variant,p.Glu560AsnfsTer16,ENST00000320005,NM_019098.4; - ENST00000320005 Transcript frameshift_variant 1725-1726/4347 1677-1678/2430 559-560/809 KE/KX aaGGaa/aaaa 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 15/18 PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385,PROSITE_patterns:PS00888,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 86604196 86604196 CC - 1 0 1 0 1 0 0 0 0 3381 864 30 0 0 CNGB3 8 86604196 Frame_Shift_Del DEL CC C3N-00217_T 14546413 86604196 58534440 270 12040 MMP16 0 . GRCh38 8 88167886 88167886 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.492T>C p.= p.P164P ENST00000286614 4/10 279 229 50 191 191 0 strelka-varscan MMP16,synonymous_variant,p.=,ENST00000286614,NM_005941.4;MMP16,downstream_gene_variant,,ENST00000522726,;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; G ENST00000286614 Transcript synonymous_variant 774/11558 492/1824 164/607 P ccT/ccC 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 4/10 hmmpanther:PTHR10201:SF26,hmmpanther:PTHR10201,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00413,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 88167886 88167886 A G 1 0 0 0 0 0 0 0 1 9618 291 11 5 5 MMP16 8 88167886 Silent SNP A C3N-00217_T 1563690 88167886 56970750 271 12041 RIMS2 0 . GRCh38 8 103697232 103697232 + Missense_Mutation SNP G G A C3N-00217_T C3N-00217_N G G c.323G>A p.Cys108Tyr p.C108Y ENST00000504942 2/24 409 163 246 366 365 1 strelka-varscan RIMS2,missense_variant,p.Cys108Tyr,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Cys50Tyr,ENST00000626043,;RIMS2,missense_variant,p.Cys108Tyr,ENST00000632716,; A ENST00000504942 Transcript missense_variant 462/4228 323/4050 108/1349 C/Y tGt/tAt COSM1150810,COSM3643490,COSM3643491,COSM748965 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 2/24 Gene3D:3.30.40.10,Pfam_domain:PF02318,PROSITE_profiles:PS50178,PROSITE_profiles:PS50916,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Superfamily_domains:SSF57903 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 103697232 103697232 G A 1 0 0 0 0 1 0 0 0 13543 1377 48 3 3 RIMS2 8 103697232 Missense_Mutation SNP G C3N-00217_T 15529346 103697232 41441404 272 12042 RIMS2 0 . GRCh38 8 103766393 103766393 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.554A>T p.Glu185Val p.E185V ENST00000504942 3/24 557 261 296 408 408 0 strelka-varscan RIMS2,missense_variant,p.Glu185Val,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Glu127Val,ENST00000626043,;RIMS2,missense_variant,p.Glu189Val,ENST00000632716,;RIMS2,non_coding_transcript_exon_variant,,ENST00000395361,;RP11-771F20.1,upstream_gene_variant,,ENST00000481577,; T ENST00000504942 Transcript missense_variant 693/4228 554/4050 185/1349 E/V gAg/gTg 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0.01) 3/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 103766393 103766393 A T 1 0 0 0 0 1 0 0 0 13543 304 11 4 4 RIMS2 8 103766393 Missense_Mutation SNP A C3N-00217_T 69161 103766393 41372243 273 12043 DCSTAMP 0 . GRCh38 8 104348636 104348636 + Frame_Shift_Del DEL C C - novel C3N-00217_T C3N-00217_N C C c.84delC p.Phe29LeufsTer31 p.F29Lfs*31 ENST00000297581 2/4 444 176 268 274 274 0 sindel-varindel-pindel DCSTAMP,frameshift_variant,p.Phe29LeufsTer31,ENST00000297581,NM_030788.3;DCSTAMP,frameshift_variant,p.Phe29LeufsTer31,ENST00000622554,NM_001257317.1;DCSTAMP,frameshift_variant,p.Phe29LeufsTer31,ENST00000517991,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000518023,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000517364,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000519562,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,upstream_gene_variant,,ENST00000518051,; - ENST00000297581 Transcript frameshift_variant 133/1953 84/1413 28/470 D/X gaC/ga 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 2/4 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 104348636 104348636 C - 1 0 1 0 1 0 0 0 0 4106 564 20 0 0 DCSTAMP 8 104348636 Frame_Shift_Del DEL C C3N-00217_T 582243 104348636 40790000 274 12044 DCSTAMP 0 . GRCh38 8 104348851 104348851 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.299C>A p.Ala100Glu p.A100E ENST00000297581 2/4 387 344 43 262 262 0 strelka-varscan DCSTAMP,missense_variant,p.Ala100Glu,ENST00000297581,NM_030788.3;DCSTAMP,missense_variant,p.Ala100Glu,ENST00000622554,NM_001257317.1;DCSTAMP,missense_variant,p.Ala100Glu,ENST00000517991,;DCSTAMP,non_coding_transcript_exon_variant,,ENST00000518023,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,upstream_gene_variant,,ENST00000518051,;DCSTAMP,downstream_gene_variant,,ENST00000517364,;DCSTAMP,downstream_gene_variant,,ENST00000519562,; A ENST00000297581 Transcript missense_variant 348/1953 299/1413 100/470 A/E gCa/gAa 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 deleterious(0.03) 2/4 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 104348851 104348851 C A 1 0 0 0 0 1 0 0 0 4106 710 25 2 2 DCSTAMP 8 104348851 Missense_Mutation SNP C C3N-00217_T 215 104348851 40789785 275 12045 CSMD3 0 . GRCh38 8 112224843 112224843 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.11052C>A p.= p.T3684T ENST00000297405 71/71 512 463 49 391 391 0 strelka-varscan CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,; T ENST00000297405 Transcript synonymous_variant 11297/13212 11052/11124 3684/3707 T acC/acA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 71/71 hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 112224843 112224843 G T 1 0 0 0 0 0 0 0 1 3747 1335 47 2 2 CSMD3 8 112224843 Silent SNP G C3N-00217_T 7875992 112224843 32913793 276 12046 CSMD3 0 . GRCh38 8 112301897 112301897 + Nonsense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.8336C>G p.Ser2779Ter p.S2779* ENST00000297405 53/71 363 331 32 301 301 0 strelka-varscan CSMD3,stop_gained,p.Ser2779Ter,ENST00000297405,NM_198123.1;CSMD3,stop_gained,p.Ser2739Ter,ENST00000343508,NM_198124.1;CSMD3,stop_gained,p.Ser2610Ter,ENST00000455883,NM_052900.2;CSMD3,stop_gained,p.Ser2049Ter,ENST00000339701,; C ENST00000297405 Transcript stop_gained 8581/13212 8336/11124 2779/3707 S/* tCa/tGa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 53/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 43 112301897 112301897 G C 1 0 0 0 0 0 1 0 0 3747 1294 45 4 4 CSMD3 8 112301897 Nonsense_Mutation SNP G C3N-00217_T 77054 112301897 32836739 277 12047 KHDRBS3 0 . GRCh38 8 135582036 135582036 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.770C>T p.Pro257Leu p.P257L ENST00000355849 6/9 98 88 10 75 75 0 strelka-varscan KHDRBS3,missense_variant,p.Pro257Leu,ENST00000355849,NM_006558.2;KHDRBS3,missense_variant,p.Pro229Leu,ENST00000524199,;KHDRBS3,missense_variant,p.Pro172Leu,ENST00000524282,;KHDRBS3,intron_variant,,ENST00000520981,;KHDRBS3,non_coding_transcript_exon_variant,,ENST00000522079,;KHDRBS3,missense_variant,p.Pro182Leu,ENST00000517859,; T ENST00000355849 Transcript missense_variant 1180/1977 770/1041 257/346 P/L cCa/cTa 1 1 KHDRBS3 HGNC HGNC:18117 protein_coding YES CCDS6374.1 ENSP00000348108 O75525 UPI0000073E6F NM_006558.2 tolerated(0.21) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF29 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.89386 1 1 1 1 0 T 3 4 43 135582036 135582036 C T 1 0 0 0 0 1 0 0 0 8069 594 21 3 3 KHDRBS3 8 135582036 Missense_Mutation SNP C C3N-00217_T 23280139 135582036 9556600 278 12048 FAM135B 0 . GRCh38 8 138141289 138141289 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.3699C>A p.Phe1233Leu p.F1233L ENST00000395297 17/20 360 158 202 257 257 0 strelka-varscan FAM135B,missense_variant,p.Phe1233Leu,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,;FAM135B,downstream_gene_variant,,ENST00000467365,;FAM135B,downstream_gene_variant,,ENST00000395295,; T ENST00000395297 Transcript missense_variant 3870/6962 3699/4221 1233/1406 F/L ttC/ttA COSM3951318,COSM3951319,COSM4400007,COSM4400008 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0.01) 17/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482,Gene3D:3.40.50.1820,Pfam_domain:PF05057,Superfamily_domains:SSF53474 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 138141289 138141289 G T 1 0 0 0 0 1 0 0 0 5299 1165 41 2 2 FAM135B 8 138141289 Missense_Mutation SNP G C3N-00217_T 2559253 138141289 6997347 279 12049 ADGRB1 0 . GRCh38 8 142464834 142464834 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.636C>A p.= p.P212P ENST00000517894 2/31 187 77 110 122 122 0 strelka-varscan ADGRB1,synonymous_variant,p.=,ENST00000517894,;ADGRB1,synonymous_variant,p.=,ENST00000323289,NM_001702.2;ADGRB1,synonymous_variant,p.=,ENST00000521208,; A ENST00000517894 Transcript synonymous_variant 1530/6241 636/4755 212/1584 P ccC/ccA 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 2/31 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 142464834 142464834 C A 1 0 0 0 0 0 0 0 1 355 668 24 2 2 ADGRB1 8 142464834 Silent SNP C C3N-00217_T 4323545 142464834 2673802 280 12050 ADGRB1 0 . GRCh38 8 142477149 142477149 + Missense_Mutation SNP G G T rs570235746 C3N-00217_T C3N-00217_N G G c.1093G>T p.Val365Leu p.V365L ENST00000517894 5/31 67 30 37 52 52 0 strelka-varscan ADGRB1,missense_variant,p.Val365Leu,ENST00000517894,;ADGRB1,missense_variant,p.Val365Leu,ENST00000323289,NM_001702.2;ADGRB1,missense_variant,p.Val365Leu,ENST00000521208,;ADGRB1,upstream_gene_variant,,ENST00000518820,; T ENST00000517894 Transcript missense_variant 1987/6241 1093/4755 365/1584 V/L Gtg/Ttg rs570235746 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 tolerated(0.11) 5/31 PROSITE_profiles:PS50092,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS . . 0 196 10 4 0 0 0 0 -20 0.9994474 1 1 1 0 T 3 4 43 142477149 142477149 G T 1 0 0 0 0 1 0 0 0 355 1145 40 1 1 ADGRB1 8 142477149 Missense_Mutation SNP G C3N-00217_T 12315 142477149 2661487 281 12051 JRK 0 . GRCh38 8 142666024 142666024 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.35G>T p.Gly12Val p.G12V ENST00000612905 2/2 303 271 32 154 154 0 strelka-varscan JRK,missense_variant,p.Gly12Val,ENST00000612905,NM_003724.3;JRK,missense_variant,p.Gly12Val,ENST00000614134,;JRK,missense_variant,p.Gly12Val,ENST00000615982,NM_001279352.1;JRK,missense_variant,p.Gly12Val,ENST00000571961,NM_001077527.2;JRK,missense_variant,p.Gly12Val,ENST00000503272,;PSCA,upstream_gene_variant,,ENST00000505305,;PSCA,upstream_gene_variant,,ENST00000510969,;JRK,downstream_gene_variant,,ENST00000591357,;JRK,upstream_gene_variant,,ENST00000506774,; A ENST00000612905 Transcript missense_variant 560/9124 35/1707 12/568 G/V gGg/gTg 1 -1 JRK HGNC HGNC:6199 protein_coding YES CCDS75796.1 ENSP00000482410 Q86XJ5 UPI000000DA37 NM_003724.3 deleterious(0.03) 2/2 PROSITE_profiles:PS50960,hmmpanther:PTHR19303:SF191,hmmpanther:PTHR19303 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 142666024 142666024 C A 1 0 0 0 0 1 0 0 0 7876 623 22 2 2 JRK 8 142666024 Missense_Mutation SNP C C3N-00217_T 188875 142666024 2472612 282 12052 TIGD5 0 . GRCh38 8 143598574 143598574 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.671C>T p.Pro224Leu p.P224L ENST00000504548 1/1 80 24 56 37 37 0 strelka-varscan TIGD5,missense_variant,p.Pro224Leu,ENST00000504548,NM_032862.4;EEF1D,intron_variant,,ENST00000533749,;EEF1D,upstream_gene_variant,,ENST00000423316,NM_001130053.2;EEF1D,upstream_gene_variant,,ENST00000618139,;EEF1D,upstream_gene_variant,,ENST00000442189,NM_032378.4;EEF1D,upstream_gene_variant,,ENST00000317198,NM_001130057.2;EEF1D,upstream_gene_variant,,ENST00000419152,NM_001130055.2;EEF1D,upstream_gene_variant,,ENST00000529272,;EEF1D,upstream_gene_variant,,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,upstream_gene_variant,,ENST00000524624,;EEF1D,upstream_gene_variant,,ENST00000534380,;EEF1D,upstream_gene_variant,,ENST00000526710,;EEF1D,upstream_gene_variant,,ENST00000526838,NM_001195203.1;EEF1D,upstream_gene_variant,,ENST00000531670,;EEF1D,upstream_gene_variant,,ENST00000528610,NM_001130056.2;EEF1D,upstream_gene_variant,,ENST00000530191,;EEF1D,upstream_gene_variant,,ENST00000533204,;EEF1D,upstream_gene_variant,,ENST00000531621,;EEF1D,upstream_gene_variant,,ENST00000531281,;EEF1D,upstream_gene_variant,,ENST00000532543,;EEF1D,upstream_gene_variant,,ENST00000531218,;EEF1D,upstream_gene_variant,,ENST00000526340,;EEF1D,upstream_gene_variant,,ENST00000532596,;EEF1D,upstream_gene_variant,,ENST00000533494,;EEF1D,upstream_gene_variant,,ENST00000534377,;EEF1D,upstream_gene_variant,,ENST00000530545,;EEF1D,upstream_gene_variant,,ENST00000531931,;EEF1D,upstream_gene_variant,,ENST00000529832,;EEF1D,upstream_gene_variant,,ENST00000530306,;EEF1D,upstream_gene_variant,,ENST00000525261,;EEF1D,upstream_gene_variant,,ENST00000528303,;EEF1D,upstream_gene_variant,,ENST00000534804,;EEF1D,upstream_gene_variant,,ENST00000534475,;EEF1D,upstream_gene_variant,,ENST00000531953,;EEF1D,upstream_gene_variant,,ENST00000529516,;EEF1D,upstream_gene_variant,,ENST00000532400,;EEF1D,upstream_gene_variant,,ENST00000526133,;EEF1D,upstream_gene_variant,,ENST00000524900,;EEF1D,upstream_gene_variant,,ENST00000531770,;EEF1D,upstream_gene_variant,,ENST00000526786,;EEF1D,upstream_gene_variant,,ENST00000524397,;EEF1D,upstream_gene_variant,,ENST00000525695,;EEF1D,upstream_gene_variant,,ENST00000529007,;EEF1D,upstream_gene_variant,,ENST00000533833,;EEF1D,upstream_gene_variant,,ENST00000534232,;EEF1D,upstream_gene_variant,,ENST00000530848,; T ENST00000504548 Transcript missense_variant 740/5390 671/1929 224/642 P/L cCg/cTg 1 1 TIGD5 HGNC HGNC:18336 protein_coding YES CCDS6406.2 ENSP00000421489 Q53EQ6 UPI0001BAE24C NM_032862.4 tolerated(0.38) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF283 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 143598574 143598574 C T 1 0 0 0 0 1 0 0 0 16337 652 23 1 1 TIGD5 8 143598574 Missense_Mutation SNP C C3N-00217_T 932550 143598574 1540062 283 12053 FBXL6 0 . GRCh38 8 144356450 144356450 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1075G>T p.Glu359Ter p.E359* ENST00000331890 7/9 462 413 49 260 260 0 strelka-varscan FBXL6,stop_gained,p.Glu359Ter,ENST00000331890,NM_012162.3;FBXL6,stop_gained,p.Glu353Ter,ENST00000455319,NM_024555.5;SLC52A2,intron_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532887,;SLC52A2,upstream_gene_variant,,ENST00000329994,NM_024531.4;SLC52A2,upstream_gene_variant,,ENST00000527078,;SLC52A2,upstream_gene_variant,,ENST00000402965,NM_001253815.1;SLC52A2,upstream_gene_variant,,ENST00000530047,NM_001253816.1;TMEM249,upstream_gene_variant,,ENST00000565365,NM_001252402.2,NM_001280561.1;SLC52A2,upstream_gene_variant,,ENST00000534725,;TMEM249,upstream_gene_variant,,ENST00000562477,NM_001252404.2;SLC52A2,upstream_gene_variant,,ENST00000526752,;SLC52A2,upstream_gene_variant,,ENST00000526338,;FBXL6,non_coding_transcript_exon_variant,,ENST00000526524,;FBXL6,non_coding_transcript_exon_variant,,ENST00000527000,;FBXL6,non_coding_transcript_exon_variant,,ENST00000524909,;SLC52A2,intron_variant,,ENST00000532815,;SLC52A2,upstream_gene_variant,,ENST00000526891,;FBXL6,downstream_gene_variant,,ENST00000530687,;FBXL6,non_coding_transcript_exon_variant,,ENST00000530142,;FBXL6,non_coding_transcript_exon_variant,,ENST00000524492,;TMEM249,upstream_gene_variant,,ENST00000561638,;GS1-393G12.13,upstream_gene_variant,,ENST00000531225,;SLC52A2,upstream_gene_variant,,ENST00000533662,;SLC52A2,upstream_gene_variant,,ENST00000526779,;FBXL6,downstream_gene_variant,,ENST00000529279,; A ENST00000331890 Transcript stop_gained 1140/1785 1075/1620 359/539 E/* Gag/Tag 1 -1 FBXL6 HGNC HGNC:13603 protein_coding YES CCDS6422.1 ENSP00000330098 Q8N531 UPI0002064E15 NM_012162.3 7/9 Gene3D:3.80.10.10,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF479,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 144356450 144356450 C A 1 0 0 0 0 0 1 0 0 5586 922 32 2 2 FBXL6 8 144356450 Nonsense_Mutation SNP C C3N-00217_T 757876 144356450 782186 284 12054 PTPRD 0 . GRCh38 9 8521314 8521314 + Silent SNP C C A rs778129787 C3N-00217_T C3N-00217_N C C c.924G>T p.= p.L308L ENST00000381196 17/43 133 109 24 165 165 0 strelka-varscan-mutect PTPRD,synonymous_variant,p.=,ENST00000381196,NM_002839.3;PTPRD,synonymous_variant,p.=,ENST00000356435,;PTPRD,synonymous_variant,p.=,ENST00000355233,NM_130392.3;PTPRD,synonymous_variant,p.=,ENST00000397617,;PTPRD,synonymous_variant,p.=,ENST00000397611,NM_001040712.2;PTPRD,synonymous_variant,p.=,ENST00000537002,NM_130393.3;PTPRD,synonymous_variant,p.=,ENST00000540109,;PTPRD,synonymous_variant,p.=,ENST00000486161,NM_130391.3;PTPRD,synonymous_variant,p.=,ENST00000397606,NM_001171025.1;PTPRD,downstream_gene_variant,,ENST00000488774,; A ENST00000381196 Transcript synonymous_variant 1468/9911 924/5739 308/1912 L ctG/ctT rs778129787,COSM351897,COSM351898 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 17/43 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs778129787 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 8521314 8521314 C A 1 0 0 0 0 0 0 0 1 12953 581 21 2 2 PTPRD 9 8521314 Silent SNP C C3N-00217_T 8521314 129873403 285 12055 IFNA17 0 . GRCh38 9 21227798 21227798 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.376G>A p.Glu126Lys p.E126K ENST00000413767 1/1 331 278 53 413 413 0 strelka-varscan-mutect IFNA17,missense_variant,p.Glu126Lys,ENST00000413767,NM_021268.2;IFNWP5,downstream_gene_variant,,ENST00000445100,; T ENST00000413767 Transcript missense_variant 425/980 376/570 126/189 E/K Gag/Aag 1 -1 IFNA17 HGNC HGNC:5422 protein_coding YES CCDS6500.1 ENSP00000411940 P01571 UPI0000052AF9 NM_021268.2 tolerated(0.1) 1/1 Gene3D:1.20.1250.10,Pfam_domain:PF00143,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF29,SMART_domains:SM00076,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 21227798 21227798 C T 1 0 0 0 0 1 0 0 0 7436 864 30 3 3 IFNA17 9 21227798 Missense_Mutation SNP C C3N-00217_T 12706484 21227798 117166919 286 12056 FAM205A 0 . GRCh38 9 34725124 34725124 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2116G>A p.Gly706Arg p.G706R ENST00000378788 4/4 243 201 42 224 224 0 strelka-varscan-mutect FAM205A,missense_variant,p.Gly706Arg,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript missense_variant 2156/4225 2116/4008 706/1335 G/R Ggg/Agg 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 tolerated(0.1) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 34725124 34725124 C T 1 0 0 0 0 1 0 0 0 5386 594 21 3 3 FAM205A 9 34725124 Missense_Mutation SNP C C3N-00217_T 13497326 34725124 103669593 287 12057 TLN1 0 . GRCh38 9 35719176 35719176 + Silent SNP C C G novel C3N-00217_T C3N-00217_N C C c.1794G>C p.= p.L598L ENST00000314888 16/57 179 113 66 206 206 0 strelka-varscan-mutect TLN1,synonymous_variant,p.=,ENST00000314888,NM_006289.3;TLN1,downstream_gene_variant,,ENST00000378192,; G ENST00000314888 Transcript synonymous_variant 2148/8823 1794/7626 598/2541 L ctG/ctC 1 -1 TLN1 HGNC HGNC:11845 protein_coding YES CCDS35009.1 ENSP00000316029 Q9Y490 UPI0000211375 NM_006289.3 16/57 hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF7,Gene3D:1sj7B00,Pfam_domain:PF09141,Superfamily_domains:0043634 LOW 1 SNV 1 1 PASS rs1046474968 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 35719176 35719176 C G 1 0 0 0 0 0 0 0 1 16393 581 21 4 4 TLN1 9 35719176 Silent SNP C C3N-00217_T 994052 35719176 102675541 288 12058 FRMPD1 0 . GRCh38 9 37745177 37745177 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.3145C>A p.His1049Asn p.H1049N ENST00000539465 16/16 231 156 75 272 272 0 strelka-varscan-mutect FRMPD1,missense_variant,p.His1049Asn,ENST00000539465,;FRMPD1,missense_variant,p.His1049Asn,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; A ENST00000539465 Transcript missense_variant 3738/5465 3145/4737 1049/1578 H/N Cat/Aat 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC tolerated_low_confidence(0.05) 16/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 37745177 37745177 C A 1 0 0 0 0 1 0 0 0 5927 594 21 2 2 FRMPD1 9 37745177 Missense_Mutation SNP C C3N-00217_T 2026001 37745177 100649540 289 12059 SPATA31A6 0 . GRCh38 9 42187518 42187518 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1816C>A p.His606Asn p.H606N ENST00000332857 4/4 268 252 16 312 312 0 varscan-mutect SPATA31A6,missense_variant,p.His606Asn,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; A ENST00000332857 Transcript missense_variant 1845/4209 1816/4032 606/1343 H/N Cac/Aac 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 deleterious(0.01) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS . . 12 196 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 42187518 42187518 C A 1 0 0 0 0 1 0 0 0 15345 478 17 2 2 SPATA31A6 9 42187518 Missense_Mutation SNP C C3N-00217_T 4442341 42187518 96207199 290 12060 SPATA31A7 0 . GRCh38 9 61193914 61193914 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1828C>A p.His610Asn p.H610N ENST00000619167 4/4 72 62 10 80 80 0 varscan-mutect SPATA31A7,missense_variant,p.His610Asn,ENST00000619167,NM_015667.2;RP11-101E5.6,downstream_gene_variant,,ENST00000611332,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000621711,;SPATA31A7,downstream_gene_variant,,ENST00000618860,;SPATA31A7,downstream_gene_variant,,ENST00000619140,;SPATA31A7,downstream_gene_variant,,ENST00000622899,;SPATA31A7,downstream_gene_variant,,ENST00000622751,;SPATA31A7,downstream_gene_variant,,ENST00000376458,;SPATA31A7,downstream_gene_variant,,ENST00000614013,;SPATA31A7,downstream_gene_variant,,ENST00000611017,; A ENST00000619167 Transcript missense_variant 1890/4256 1828/4044 610/1347 H/N Cac/Aac 1 1 SPATA31A7 HGNC HGNC:32007 protein_coding YES CCDS75838.1 ENSP00000484807 Q8IWB4 UPI0000457748 NM_015667.2 deleterious(0.01) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF22,Pfam_domain:PF14650 MODERATE 1 SNV 1 1 PASS . . 6 202 2 0 0 0 0 0 -19.99861 1 1 1 1 0 A 3 1 43 61193914 61193914 C A 1 0 0 0 0 1 0 0 0 15346 478 17 2 2 SPATA31A7 9 61193914 Missense_Mutation SNP C C3N-00217_T 19006396 61193914 77200803 291 12061 PRKACG 0 . GRCh38 9 69013426 69013426 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.667T>A p.Trp223Arg p.W223R ENST00000377276 1/1 378 237 141 401 400 1 strelka-varscan-mutect PRKACG,missense_variant,p.Trp223Arg,ENST00000377276,NM_002732.3;PIP5K1B,downstream_gene_variant,,ENST00000541509,NM_001278253.1;PIP5K1B,downstream_gene_variant,,ENST00000265382,NM_003558.3;PIP5K1B,downstream_gene_variant,,ENST00000478500,; T ENST00000377276 Transcript missense_variant 688/1585 667/1056 223/351 W/R Tgg/Agg 1 -1 PRKACG HGNC HGNC:9382 protein_coding YES CCDS6625.1 ENSP00000366488 P22612 UPI000013E448 NM_002732.3 deleterious(0) 1/1 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24353,hmmpanther:PTHR24353:SF53,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 69013426 69013426 A T 1 0 0 0 0 1 0 0 0 12632 159 6 4 4 PRKACG 9 69013426 Missense_Mutation SNP A C3N-00217_T 7819512 69013426 69381291 292 12062 TRPM6 0 . GRCh38 9 74739434 74739434 + Nonsense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.5503A>T p.Arg1835Ter p.R1835* ENST00000360774 35/39 294 238 56 354 354 0 strelka-varscan-mutect TRPM6,stop_gained,p.Arg1835Ter,ENST00000360774,NM_017662.4;TRPM6,stop_gained,p.Arg1830Ter,ENST00000361255,NM_001177311.1;TRPM6,stop_gained,p.Arg1830Ter,ENST00000449912,NM_001177310.1; A ENST00000360774 Transcript stop_gained 5741/8425 5503/6069 1835/2022 R/* Aga/Tga 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 35/39 Gene3D:3.30.200.20,Pfam_domain:PF02816,PROSITE_profiles:PS51158,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15,SMART_domains:SM00811,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 74739434 74739434 T A 1 0 0 0 0 0 1 0 0 17096 1617 56 4 4 TRPM6 9 74739434 Nonsense_Mutation SNP T C3N-00217_T 5726008 74739434 63655283 293 12063 TLE4 0 . GRCh38 9 79704807 79704807 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.634A>T p.Ser212Cys p.S212C ENST00000376537 9/21 176 111 65 174 174 0 strelka-varscan-mutect TLE4,missense_variant,p.Ser212Cys,ENST00000376544,NM_001282753.1;TLE4,missense_variant,p.Ser212Cys,ENST00000376552,NM_007005.4,NM_001282760.1;TLE4,missense_variant,p.Ser212Cys,ENST00000376537,NM_001282748.1;TLE4,missense_variant,p.Ser187Cys,ENST00000265284,NM_001282749.1;TLE4,missense_variant,p.Ser3Cys,ENST00000496114,;TLE4,missense_variant,p.Ser197Cys,ENST00000428713,;TLE4,missense_variant,p.Ser82Cys,ENST00000490347,;TLE4,missense_variant,p.Ser9Cys,ENST00000467142,;TLE4,downstream_gene_variant,,ENST00000435650,;TLE4,upstream_gene_variant,,ENST00000417836,;TLE4,non_coding_transcript_exon_variant,,ENST00000463431,;TLE4,upstream_gene_variant,,ENST00000478290,;TLE4,missense_variant,p.Gln255Leu,ENST00000462803,;TLE4,3_prime_UTR_variant,,ENST00000470872,;TLE4,non_coding_transcript_exon_variant,,ENST00000495170,; T ENST00000376537 Transcript missense_variant 810/2793 634/2418 212/805 S/C Agt/Tgt 1 1 TLE4 HGNC HGNC:11840 protein_coding YES CCDS65069.1 ENSP00000365720 Q04727 UPI000056D4A8 NM_001282748.1 deleterious(0.01) 9/21 hmmpanther:PTHR10814,hmmpanther:PTHR10814:SF21,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 79704807 79704807 A T 1 0 0 0 0 1 0 0 0 16387 188 7 4 4 TLE4 9 79704807 Missense_Mutation SNP A C3N-00217_T 4965373 79704807 58689910 294 12064 DIRAS2 0 . GRCh38 9 90613516 90613516 + Silent SNP G G T C3N-00217_T C3N-00217_N G G c.312C>A p.= p.I104I ENST00000375765 2/2 448 362 86 445 445 0 strelka-varscan-mutect DIRAS2,synonymous_variant,p.=,ENST00000375765,NM_017594.4;DIRAS2,synonymous_variant,p.=,ENST00000636786,;DIRAS2,downstream_gene_variant,,ENST00000637905,; T ENST00000375765 Transcript synonymous_variant 702/4386 312/600 104/199 I atC/atA COSM456216 1 -1 DIRAS2 HGNC HGNC:19323 protein_coding YES CCDS6687.1 ENSP00000364919 Q96HU8 UPI000004D253 NM_017594.4 2/2 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF178,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 90613516 90613516 G T 1 0 0 0 0 0 0 0 1 4336 932 33 2 2 DIRAS2 9 90613516 Silent SNP G C3N-00217_T 10908709 90613516 47781201 295 12065 ROR2 0 . GRCh38 9 91724833 91724833 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1661G>A p.Ser554Asn p.S554N ENST00000375708 9/9 51 41 10 41 41 0 strelka-varscan-mutect ROR2,missense_variant,p.Ser554Asn,ENST00000375708,NM_004560.3;ROR2,missense_variant,p.Ser414Asn,ENST00000375715,;ROR2,non_coding_transcript_exon_variant,,ENST00000550066,; T ENST00000375708 Transcript missense_variant 1860/4096 1661/2832 554/943 S/N aGc/aAc 1 -1 ROR2 HGNC HGNC:10257 protein_coding YES CCDS6691.1 ENSP00000364860 Q01974 UPI000013E8CA NM_004560.3 deleterious(0.03) 9/9 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000624,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF132,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99994 1 1 1 1 0 T 3 4 43 91724833 91724833 C T 1 0 0 0 0 1 0 0 0 13704 797 28 3 3 ROR2 9 91724833 Missense_Mutation SNP C C3N-00217_T 1111317 91724833 46669884 296 12066 ROR2 0 . GRCh38 9 91733316 91733316 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.743C>A p.Pro248Gln p.P248Q ENST00000375708 6/9 152 128 24 153 151 2 strelka-varscan-mutect ROR2,missense_variant,p.Pro248Gln,ENST00000375708,NM_004560.3;ROR2,missense_variant,p.Pro108Gln,ENST00000375715,;ROR2,non_coding_transcript_exon_variant,,ENST00000550066,; T ENST00000375708 Transcript missense_variant 942/4096 743/2832 248/943 P/Q cCg/cAg COSM3908829,COSM4926158 1 -1 ROR2 HGNC HGNC:10257 protein_coding YES CCDS6691.1 ENSP00000364860 Q01974 UPI000013E8CA NM_004560.3 tolerated(0.18) 6/9 Gene3D:2.40.20.10,Pfam_domain:PF01392,PIRSF_domain:PIRSF000624,PROSITE_profiles:PS50038,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF132 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1363164502 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 91733316 91733316 G T 1 0 0 0 0 1 0 0 0 13704 1116 39 1 1 ROR2 9 91733316 Missense_Mutation SNP G C3N-00217_T 8483 91733316 46661401 297 12067 FBP2 0 . GRCh38 9 94593699 94593699 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.28G>T p.Asp10Tyr p.D10Y ENST00000375337 1/7 143 75 68 161 161 0 strelka-varscan-mutect FBP2,missense_variant,p.Asp10Tyr,ENST00000375337,NM_003837.3; A ENST00000375337 Transcript missense_variant 95/1305 28/1020 10/339 D/Y Gac/Tac 1 -1 FBP2 HGNC HGNC:3607 protein_coding YES CCDS6711.1 ENSP00000364486 O00757 UPI000013CDC2 NM_003837.3 deleterious(0) 1/7 PIRSF_domain:PIRSF000904,PIRSF_domain:PIRSF500210,hmmpanther:PTHR11556,hmmpanther:PTHR11556:SF13,Superfamily_domains:SSF56655 MODERATE 1 SNV 1 1 PASS rs1417966414 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 94593699 94593699 C A 1 0 0 0 0 1 0 0 0 5569 884 31 1 1 FBP2 9 94593699 Missense_Mutation SNP C C3N-00217_T 2860383 94593699 43801018 298 12068 GRIN3A 0 . GRCh38 9 101613516 101613516 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2626G>A p.Gly876Ser p.G876S ENST00000361820 6/9 327 273 54 364 364 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Gly876Ser,ENST00000361820,NM_133445.2;GRIN3A,non_coding_transcript_exon_variant,,ENST00000479772,; T ENST00000361820 Transcript missense_variant 3227/7770 2626/3348 876/1115 G/S Ggc/Agc 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 deleterious(0) 6/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 101613516 101613516 C T 1 0 0 0 0 1 0 0 0 6665 594 21 3 3 GRIN3A 9 101613516 Missense_Mutation SNP C C3N-00217_T 7019817 101613516 36781201 299 12069 OR13C5 0 . GRCh38 9 104598717 104598717 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.697G>T p.Gly233Trp p.G233W ENST00000374779 1/1 237 195 42 326 326 0 strelka-varscan-mutect OR13C5,missense_variant,p.Gly233Trp,ENST00000374779,NM_001004482.1; A ENST00000374779 Transcript missense_variant 697/957 697/957 233/318 G/W Ggg/Tgg 1 -1 OR13C5 HGNC HGNC:15100 protein_coding YES CCDS35091.1 ENSP00000363911 Q8NGS8 UPI0000041D12 NM_001004482.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF121,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1324469059 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 104598717 104598717 C A 1 0 0 0 0 1 0 0 0 11013 623 22 2 2 OR13C5 9 104598717 Missense_Mutation SNP C C3N-00217_T 2985201 104598717 33796000 300 12070 OR1Q1 0 . GRCh38 9 122615062 122615062 + Missense_Mutation SNP G G A rs764018659 C3N-00217_T C3N-00217_N G G c.325G>A p.Val109Ile p.V109I ENST00000297913 1/1 237 193 44 267 267 0 strelka-varscan-mutect OR1Q1,missense_variant,p.Val109Ile,ENST00000297913,NM_012364.1;RP11-64P14.7,intron_variant,,ENST00000431442,;RP11-64P14.7,upstream_gene_variant,,ENST00000419604,; A ENST00000297913 Transcript missense_variant 325/945 325/945 109/314 V/I Gtc/Atc rs764018659,COSM4709721 1 1 OR1Q1 HGNC HGNC:8223 protein_coding YES CCDS35125.1 ENSP00000297913 Q15612 UPI000003CACD NM_012364.1 tolerated(0.55) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE SNV 0,1 1 PASS rs764018659 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 122615062 122615062 G A 1 0 0 0 0 1 0 0 0 11049 1145 40 1 1 OR1Q1 9 122615062 Missense_Mutation SNP G C3N-00217_T 18016345 122615062 15779655 301 12071 CRB2 0 . GRCh38 9 123370248 123370248 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.1195G>A p.Gly399Ser p.G399S ENST00000373631 7/13 176 146 30 149 147 2 strelka-varscan-mutect CRB2,missense_variant,p.Gly399Ser,ENST00000373631,NM_173689.6;CRB2,missense_variant,p.Gly399Ser,ENST00000359999,;CRB2,missense_variant,p.Gly67Ser,ENST00000460253,; A ENST00000373631 Transcript missense_variant 1196/5550 1195/3858 399/1285 G/S Ggc/Agc 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 deleterious(0) 7/13 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 123370248 123370248 G A 1 0 0 0 0 1 0 0 0 3649 1348 47 3 3 CRB2 9 123370248 Missense_Mutation SNP G C3N-00217_T 755186 123370248 15024469 302 12072 LHX2 0 . GRCh38 9 124032641 124032641 + Silent SNP G G C novel C3N-00217_T C3N-00217_N G G c.1155G>C p.= p.V385V ENST00000373615 5/5 141 89 52 105 105 0 strelka-varscan-mutect LHX2,synonymous_variant,p.=,ENST00000373615,NM_004789.3;LHX2,synonymous_variant,p.=,ENST00000446480,;LHX2,3_prime_UTR_variant,,ENST00000488674,;RP11-85O21.5,upstream_gene_variant,,ENST00000429482,; C ENST00000373615 Transcript synonymous_variant 1894/2554 1155/1221 385/406 V gtG/gtC 1 1 LHX2 HGNC HGNC:6594 protein_coding YES CCDS6853.1 ENSP00000362717 P50458 UPI000012E659 NM_004789.3 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF90 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 124032641 124032641 G C 1 0 0 0 0 0 0 0 1 8680 1306 46 4 4 LHX2 9 124032641 Silent SNP G C3N-00217_T 662393 124032641 14362076 303 12073 OBP2B 0 . GRCh38 9 133205348 133205348 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.644G>T p.Gly215Val p.G215V ENST00000372032 8/8 91 77 14 82 82 0 strelka-varscan-mutect OBP2B,missense_variant,p.Gly215Val,ENST00000372032,;OBP2B,3_prime_UTR_variant,,ENST00000618116,NM_001288987.1;OBP2B,3_prime_UTR_variant,,ENST00000372034,NM_014581.3;OBP2B,non_coding_transcript_exon_variant,,ENST00000461961,;OBP2B,3_prime_UTR_variant,,ENST00000473737,; A ENST00000372032 Transcript missense_variant 672/702 644/663 215/220 G/V gGa/gTa 1 -1 OBP2B HGNC HGNC:23381 protein_coding ENSP00000361102 C9J395 UPI0004E4CBE6 deleterious_low_confidence(0) 8/8 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 133205348 133205348 C A 1 0 0 0 0 1 0 0 0 10888 855 30 2 2 OBP2B 9 133205348 Missense_Mutation SNP C C3N-00217_T 9172707 133205348 5189369 304 12074 OLFM1 0 . GRCh38 9 135119611 135119611 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.891C>T p.= p.P297P ENST00000371793 6/6 193 131 62 185 185 0 strelka-varscan-mutect OLFM1,synonymous_variant,p.=,ENST00000252854,NM_014279.4;OLFM1,synonymous_variant,p.=,ENST00000371796,NM_001282612.1;OLFM1,synonymous_variant,p.=,ENST00000371793,NM_001282611.1;OLFM1,synonymous_variant,p.=,ENST00000539877,;OLFM1,3_prime_UTR_variant,,ENST00000545657,;OLFM1,non_coding_transcript_exon_variant,,ENST00000483042,; T ENST00000371793 Transcript synonymous_variant 1142/2444 891/1458 297/485 P ccC/ccT 1 1 OLFM1 HGNC HGNC:17187 protein_coding YES CCDS65184.1 ENSP00000360858 Q99784 UPI000013DB05 NM_001282611.1 6/6 PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF34,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 135119611 135119611 C T 1 0 0 0 0 0 0 0 1 10927 668 24 3 3 OLFM1 9 135119611 Silent SNP C C3N-00217_T 1914263 135119611 3275106 305 12075 OBP2A 0 . GRCh38 9 135549900 135549900 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.643G>T p.Asp215Tyr p.D215Y ENST00000340780 7/7 110 102 8 116 116 0 varscan-mutect OBP2A,missense_variant,p.Asp215Tyr,ENST00000340780,NM_001293189.1;OBP2A,missense_variant,p.Gly215Val,ENST00000619164,;OBP2A,3_prime_UTR_variant,,ENST00000539850,;OBP2A,3_prime_UTR_variant,,ENST00000371776,NM_014582.2;OBP2A,3_prime_UTR_variant,,ENST00000342114,NM_001293193.1;OBP2A,3_prime_UTR_variant,,ENST00000471886,;OBP2A,3_prime_UTR_variant,,ENST00000537747,; T ENST00000340780 Transcript missense_variant 685/741 643/687 215/228 D/Y Gac/Tac 1 1 OBP2A HGNC HGNC:23380 protein_coding YES CCDS78455.1 ENSP00000342097 Q5T8A5 UPI00003676A5 NM_001293189.1 deleterious_low_confidence(0) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 135549900 135549900 G T 1 0 0 0 0 1 0 0 0 10887 1174 41 2 2 OBP2A 9 135549900 Missense_Mutation SNP G C3N-00217_T 430289 135549900 2844817 306 12076 NOTCH1 0 . GRCh38 9 136500740 136500740 + Frame_Shift_Del DEL G G - novel C3N-00217_T C3N-00217_N G G c.5746delC p.Gln1916ArgfsTer65 p.Q1916Rfs*65 ENST00000277541 31/34 302 189 113 309 309 0 sindel-varindel-pindel NOTCH1,frameshift_variant,p.Gln1916ArgfsTer65,ENST00000277541,NM_017617.3;NOTCH1,downstream_gene_variant,,ENST00000494783,; - ENST00000277541 Transcript frameshift_variant 5822/9371 5746/7668 1916/2555 Q/X Cag/ag 1 -1 NOTCH1 HGNC HGNC:7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 UPI0000210F68 NM_017617.3 31/34 Gene3D:1.25.40.20,Pfam_domain:PF12796,PIRSF_domain:PIRSF002279,PROSITE_profiles:PS50297,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF69,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 136500740 136500740 G - 1 0 1 0 1 0 0 0 0 10592 1357 47 0 0 NOTCH1 9 136500740 Frame_Shift_Del DEL G C3N-00217_T 950840 136500740 1893977 307 12077 FUT7 0 . GRCh38 9 137031089 137031089 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.650C>G p.Pro217Arg p.P217R ENST00000314412 2/2 286 184 102 254 254 0 strelka-varscan-mutect FUT7,missense_variant,p.Pro217Arg,ENST00000314412,NM_004479.3;ABCA2,upstream_gene_variant,,ENST00000265662,;ABCA2,upstream_gene_variant,,ENST00000371605,;ABCA2,upstream_gene_variant,,ENST00000614293,;ABCA2,upstream_gene_variant,,ENST00000341511,NM_001606.4,NM_212533.2;ABCA2,upstream_gene_variant,,ENST00000625103,;C9orf139,intron_variant,,ENST00000623196,;ABCA2,upstream_gene_variant,,ENST00000459850,;ABCA2,upstream_gene_variant,,ENST00000487109,;ABCA2,upstream_gene_variant,,ENST00000464876,;ABCA2,upstream_gene_variant,,ENST00000492260,;ABCA2,upstream_gene_variant,,ENST00000494046,;ABCA2,upstream_gene_variant,,ENST00000476211,;ABCA2,upstream_gene_variant,,ENST00000398207,;RP11-229P13.27,downstream_gene_variant,,ENST00000622933,;RP11-229P13.27,downstream_gene_variant,,ENST00000625047,;ABCA2,upstream_gene_variant,,ENST00000425423,; C ENST00000314412 Transcript missense_variant 1669/2584 650/1029 217/342 P/R cCc/cGc 1 -1 FUT7 HGNC HGNC:4018 protein_coding YES CCDS7022.1 ENSP00000318142 Q11130 UPI000012ADAF NM_004479.3 deleterious(0.01) 2/2 hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF12,Pfam_domain:PF00852,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 137031089 137031089 G C 1 0 0 0 0 1 0 0 0 5981 1232 43 4 4 FUT7 9 137031089 Missense_Mutation SNP G C3N-00217_T 530349 137031089 1363628 308 12078 TAF3 0 . GRCh38 10 7964797 7964797 + Silent SNP G G T rs778165372 C3N-00217_T C3N-00217_N G G c.1287G>T p.= p.P429P ENST00000344293 3/7 191 146 45 214 214 0 strelka-varscan-mutect TAF3,synonymous_variant,p.=,ENST00000344293,NM_031923.3; T ENST00000344293 Transcript synonymous_variant 1493/4872 1287/2790 429/929 P ccG/ccT rs778165372 1 1 TAF3 HGNC HGNC:17303 protein_coding YES CCDS41487.1 ENSP00000340271 Q5VWG9 UPI00004588FA NM_031923.3 3/7 LOW 1 SNV 2 1 PASS rs778165372 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 7964797 7964797 G T 1 0 0 0 0 0 0 0 1 15921 1103 39 1 1 TAF3 10 7964797 Silent SNP G C3N-00217_T 7964797 125832625 309 12079 TAF3 0 . GRCh38 10 7965079 7965079 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.1569G>C p.Lys523Asn p.K523N ENST00000344293 3/7 198 154 44 254 254 0 strelka-varscan-mutect TAF3,missense_variant,p.Lys523Asn,ENST00000344293,NM_031923.3; C ENST00000344293 Transcript missense_variant 1775/4872 1569/2790 523/929 K/N aaG/aaC 1 1 TAF3 HGNC HGNC:17303 protein_coding YES CCDS41487.1 ENSP00000340271 Q5VWG9 UPI00004588FA NM_031923.3 deleterious_low_confidence(0) 3/7 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 2 1 PASS . . 0 195 0 2 13 0 0 0 -20 0.08785784 1 1 0 0 C 3 2 43 7965079 7965079 G C 1 0 0 0 0 1 0 0 0 15921 933 33 4 4 TAF3 10 7965079 Missense_Mutation SNP G C3N-00217_T 282 7965079 125832343 310 12080 CCDC3 0 . GRCh38 10 13001297 13001297 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.274G>T p.Glu92Ter p.E92* ENST00000378825 1/3 242 177 65 189 189 0 strelka-varscan-mutect CCDC3,stop_gained,p.Glu92Ter,ENST00000378825,NM_031455.3;CCDC3,intron_variant,,ENST00000378839,NM_001282658.1; A ENST00000378825 Transcript stop_gained 401/2731 274/813 92/270 E/* Gag/Tag 1 -1 CCDC3 HGNC HGNC:23813 protein_coding YES CCDS7093.1 ENSP00000368102 Q9BQI4 UPI000006E69C NM_031455.3 1/3 hmmpanther:PTHR31663,hmmpanther:PTHR31663:SF4 HIGH 1 SNV 1 1 PASS rs1379657760 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 13001297 13001297 C A 1 0 0 0 0 0 1 0 0 2514 864 30 2 2 CCDC3 10 13001297 Nonsense_Mutation SNP C C3N-00217_T 5036218 13001297 120796125 311 12081 MRC1 0 . GRCh38 10 17875251 17875251 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.2548T>A p.Tyr850Asn p.Y850N ENST00000569591 17/30 124 93 31 191 191 0 strelka-varscan-mutect MRC1,missense_variant,p.Tyr850Asn,ENST00000569591,NM_002438.3; A ENST00000569591 Transcript missense_variant,splice_region_variant 2670/5198 2548/4371 850/1456 Y/N Tat/Aat 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 tolerated(0.06) 17/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 17875251 17875251 T A 1 0 0 0 0 1 0 0 0 9722 1420 49 4 4 MRC1 10 17875251 Missense_Mutation SNP T C3N-00217_T 4873954 17875251 115922171 312 12082 PTF1A 0 . GRCh38 10 23193716 23193716 + Missense_Mutation SNP C C G C3N-00217_T C3N-00217_N C C c.797C>G p.Pro266Arg p.P266R ENST00000376504 2/2 382 256 126 335 335 0 strelka-varscan-mutect PTF1A,missense_variant,p.Pro266Arg,ENST00000376504,NM_178161.2; G ENST00000376504 Transcript missense_variant 1001/1537 797/987 266/328 P/R cCc/cGc COSM5666979 1 1 PTF1A HGNC HGNC:23734 protein_coding YES CCDS7143.1 ENSP00000365687 Q7RTS3 UPI000018F612 NM_178161.2 deleterious(0) 2/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF59 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 23193716 23193716 C G 1 0 0 0 0 1 0 0 0 12893 623 22 4 4 PTF1A 10 23193716 Missense_Mutation SNP C C3N-00217_T 5318465 23193716 110603706 313 12083 MYO3A 0 . GRCh38 10 26143561 26143561 + Missense_Mutation SNP A A T rs758480848 C3N-00217_T C3N-00217_N A A c.2376A>T p.Glu792Asp p.E792D ENST00000265944 21/35 313 215 98 325 325 0 strelka-varscan-mutect MYO3A,missense_variant,p.Glu792Asp,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; T ENST00000265944 Transcript missense_variant 2542/5581 2376/4851 792/1616 E/D gaA/gaT rs758480848 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0) 21/35 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs758480848 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 26143561 26143561 A T 1 0 0 0 0 1 0 0 0 10077 69 3 4 4 MYO3A 10 26143561 Missense_Mutation SNP A C3N-00217_T 2949845 26143561 107653861 314 12084 BMS1 0 . GRCh38 10 42796733 42796733 + Missense_Mutation SNP G G T rs758829653 C3N-00217_T C3N-00217_N G G c.1489G>T p.Asp497Tyr p.D497Y ENST00000374518 10/23 360 251 109 338 338 0 strelka-varscan-mutect BMS1,missense_variant,p.Asp497Tyr,ENST00000374518,NM_014753.3; T ENST00000374518 Transcript missense_variant 1552/7753 1489/3849 497/1282 D/Y Gat/Tat rs758829653 1 1 BMS1 HGNC HGNC:23505 protein_coding YES CCDS7199.1 ENSP00000363642 Q14692 UPI0000126A3E NM_014753.3 deleterious(0) 10/23 hmmpanther:PTHR12858:SF2,hmmpanther:PTHR12858 MODERATE 1 SNV 1 1 PASS rs758829653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 42796733 42796733 G T 1 0 0 0 0 1 0 0 0 1627 1174 41 2 2 BMS1 10 42796733 Missense_Mutation SNP G C3N-00217_T 16653172 42796733 91000689 315 12085 ZNF485 0 . GRCh38 10 43616971 43616971 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.928A>T p.Ser310Cys p.S310C ENST00000361807 5/5 135 94 41 184 183 1 strelka-varscan-mutect ZNF485,missense_variant,p.Ser310Cys,ENST00000361807,NM_001318141.1,NM_145312.3;ZNF485,missense_variant,p.Ser310Cys,ENST00000374435,NM_001318140.1;ZNF485,downstream_gene_variant,,ENST00000430885,; T ENST00000361807 Transcript missense_variant 1122/2054 928/1326 310/441 S/C Agc/Tgc 1 1 ZNF485 HGNC HGNC:23440 protein_coding YES CCDS7205.2 ENSP00000354694 Q8NCK3 A0A024R7T5 UPI00000717FE NM_001318141.1,NM_145312.3 tolerated(0.08) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF14,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 43616971 43616971 A T 1 0 0 0 0 1 0 0 0 18510 304 11 4 4 ZNF485 10 43616971 Missense_Mutation SNP A C3N-00217_T 820238 43616971 90180451 316 12086 FRMPD2 0 . GRCh38 10 48232150 48232150 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1133A>T p.Glu378Val p.E378V ENST00000374201 10/29 382 264 118 362 362 0 strelka-varscan-mutect FRMPD2,missense_variant,p.Glu378Val,ENST00000374201,NM_001018071.3;FRMPD2,missense_variant,p.Glu354Val,ENST00000305531,NM_001318191.1;FRMPD2,missense_variant,p.Glu378Val,ENST00000636244,;FRMPD2,3_prime_UTR_variant,,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,; A ENST00000374201 Transcript missense_variant 1436/4997 1133/3930 378/1309 E/V gAg/gTg 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 tolerated(0.56) 10/29 PROSITE_profiles:PS50057,hmmpanther:PTHR19964:SF42,hmmpanther:PTHR19964,Gene3D:3.10.20.90,Pfam_domain:PF09379,SMART_domains:SM00295,Superfamily_domains:SSF54236,Prints_domain:PR00935 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48232150 48232150 T A 1 0 0 0 0 1 0 0 0 5928 1551 54 4 4 FRMPD2 10 48232150 Missense_Mutation SNP T C3N-00217_T 4615179 48232150 85565272 317 12087 WDFY4 0 . GRCh38 10 48867328 48867328 + Nonsense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.6727A>T p.Lys2243Ter p.K2243* ENST00000325239 39/61 90 64 26 119 119 0 strelka-varscan-mutect WDFY4,stop_gained,p.Lys2243Ter,ENST00000325239,NM_020945.1;WDFY4,stop_gained,p.Lys330Ter,ENST00000265453,; T ENST00000325239 Transcript stop_gained 6727/9555 6727/9555 2243/3184 K/* Aaa/Taa 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 39/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 48867328 48867328 A T 1 0 0 0 0 0 1 0 0 17831 131 5 4 4 WDFY4 10 48867328 Nonsense_Mutation SNP A C3N-00217_T 635178 48867328 84930094 318 12088 ERCC6 0 . GRCh38 10 49482715 49482715 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2141G>T p.Gly714Val p.G714V ENST00000355832 10/21 126 84 42 161 160 1 strelka-varscan-mutect ERCC6,missense_variant,p.Gly714Val,ENST00000355832,NM_000124.3;ERCC6,non_coding_transcript_exon_variant,,ENST00000623115,;ERCC6,downstream_gene_variant,,ENST00000623318,;ERCC6,downstream_gene_variant,,ENST00000475116,;ERCC6,non_coding_transcript_exon_variant,,ENST00000623073,; A ENST00000355832 Transcript missense_variant 2220/8008 2141/4482 714/1493 G/V gGg/gTg 1 -1 ERCC6 HGNC HGNC:3438 protein_coding YES CCDS7229.1 ENSP00000348089 Q03468 UPI000000D8DA NM_000124.3 deleterious(0) 10/21 hmmpanther:PTHR10799:SF752,hmmpanther:PTHR10799,Pfam_domain:PF00176,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 49482715 49482715 C A 1 0 0 0 0 1 0 0 0 5066 623 22 2 2 ERCC6 10 49482715 Missense_Mutation SNP C C3N-00217_T 615387 49482715 84314707 319 12089 PCDH15 0 . GRCh38 10 53831534 53831534 + Splice_Site SNP C C A C3N-00217_T C3N-00217_N C C c.3999-1G>T p.X1333_splice ENST00000373957 183 134 49 207 207 0 strelka-varscan-mutect PCDH15,splice_acceptor_variant,,ENST00000614895,;PCDH15,splice_acceptor_variant,,ENST00000373965,NM_001142772.1;PCDH15,splice_acceptor_variant,,ENST00000414778,;PCDH15,splice_acceptor_variant,,ENST00000617051,;PCDH15,splice_acceptor_variant,,ENST00000373957,NM_001142763.1;PCDH15,splice_acceptor_variant,,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,splice_acceptor_variant,,ENST00000395430,NM_001142766.1;PCDH15,splice_acceptor_variant,,ENST00000395433,NM_001142773.1;PCDH15,splice_acceptor_variant,,ENST00000395432,NM_001142767.1;PCDH15,splice_acceptor_variant,,ENST00000320301,NM_033056.3;PCDH15,splice_acceptor_variant,,ENST00000622048,;PCDH15,splice_acceptor_variant,,ENST00000437009,NM_001142765.1;PCDH15,splice_acceptor_variant,,ENST00000617271,NM_001142770.1;PCDH15,splice_acceptor_variant,,ENST00000613657,NM_001142769.1;PCDH15,splice_acceptor_variant,,ENST00000395445,;PCDH15,splice_acceptor_variant,,ENST00000616114,;PCDH15,splice_acceptor_variant,,ENST00000395438,;PCDH15,splice_acceptor_variant,,ENST00000612394,;PCDH15,splice_acceptor_variant,,ENST00000621708,NM_001142771.1;PCDH15,splice_acceptor_variant,,ENST00000409834,;PCDH15,splice_acceptor_variant,,ENST00000495484,;PCDH15,splice_acceptor_variant,,ENST00000618301,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,splice_acceptor_variant,,ENST00000463095,;PCDH15,splice_acceptor_variant,,ENST00000448885,;PCDH15,splice_acceptor_variant,,ENST00000373956,;PCDH15,splice_acceptor_variant,,ENST00000414367,; A ENST00000373957 Transcript splice_acceptor_variant -/7032 3999/5889 1333/1962 COSM1585010,COSM3438852,COSM3438853,COSM3438854,COSM3438855,COSM918954,COSM918955,COSM918956 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 30/34 1,1,1,1,1,1,1,1 HIGH 1 SNV 5 1,1,1,1,1,1,1,1 1 PASS rs1057520709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 43 53831534 53831534 C A 1 0 0 0 0 0 0 1 0 11598 927 32 2 2 PCDH15 10 53831534 Splice_Site SNP C C3N-00217_T 4348819 53831534 79965888 320 12090 ZNF365 0 . GRCh38 10 62666181 62666181 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1273C>A p.Gln425Lys p.Q425K ENST00000410046 7/8 138 106 32 183 183 0 strelka-varscan-mutect ZNF365,missense_variant,p.Gln425Lys,ENST00000410046,NM_199451.2;ZNF365,missense_variant,p.Gln179Lys,ENST00000395251,NM_199452.3;ZNF365,missense_variant,p.Gln179Lys,ENST00000614806,;ZNF365,missense_variant,p.Gln31Lys,ENST00000395249,;ZNF365,3_prime_UTR_variant,,ENST00000373784,;ZNF365,intron_variant,,ENST00000344640,; A ENST00000410046 Transcript missense_variant 1553/3379 1273/1389 425/462 Q/K Caa/Aaa 1 1 ZNF365 HGNC HGNC:18194 protein_coding YES CCDS7264.1 ENSP00000387091 Q70YC5 UPI00002323B9 NM_199451.2 tolerated_low_confidence(0.15) 7/8 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 62666181 62666181 C A 1 0 0 0 0 1 0 0 0 18441 479 17 2 2 ZNF365 10 62666181 Missense_Mutation SNP C C3N-00217_T 8834647 62666181 71131241 321 12091 PRF1 0 . GRCh38 10 70598326 70598326 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.1395G>T p.= p.L465L ENST00000441259 3/3 263 171 92 259 259 0 strelka-varscan-mutect PRF1,synonymous_variant,p.=,ENST00000441259,NM_001083116.1,NM_005041.4;PRF1,synonymous_variant,p.=,ENST00000373209,; A ENST00000441259 Transcript synonymous_variant 1556/2533 1395/1668 465/555 L ctG/ctT 1 -1 PRF1 HGNC HGNC:9360 protein_coding YES CCDS7305.1 ENSP00000398568 P14222 UPI000013162B NM_001083116.1,NM_005041.4 3/3 PROSITE_profiles:PS50004,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF3,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 70598326 70598326 C A 1 0 0 0 0 0 0 0 1 12612 581 21 2 2 PRF1 10 70598326 Silent SNP C C3N-00217_T 7932145 70598326 63199096 322 12092 CDH23 0 . GRCh38 10 71643859 71643859 + Splice_Site SNP A A G novel C3N-00217_T C3N-00217_N A A c.1150-2A>G p.X384_splice ENST00000224721 131 96 35 115 115 0 strelka-varscan-mutect CDH23,splice_acceptor_variant,,ENST00000224721,NM_022124.5;CDH23,splice_acceptor_variant,,ENST00000616684,NM_001171930.1;CDH23,splice_acceptor_variant,,ENST00000398809,;CDH23,splice_acceptor_variant,,ENST00000466757,;CDH23,splice_acceptor_variant,,ENST00000299366,NM_001171931.1;CDH23,splice_acceptor_variant,,ENST00000461841,NM_052836.3;CDH23,intron_variant,,ENST00000622827,;CDH23,intron_variant,,ENST00000398842,;CDH23,intron_variant,,ENST00000470494,;CDH23,upstream_gene_variant,,ENST00000442677,; G ENST00000224721 Transcript splice_acceptor_variant -/11139 1150/10080 384/3359 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 11/69 HIGH SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 43 71643859 71643859 A G 1 0 0 0 0 0 0 1 0 2811 202 7 5 5 CDH23 10 71643859 Splice_Site SNP A C3N-00217_T 1045533 71643859 62153563 323 12093 CDH23 0 . GRCh38 10 71709170 71709170 + Missense_Mutation SNP G G T rs536438868 C3N-00217_T C3N-00217_N G G c.3194G>T p.Arg1065Leu p.R1065L ENST00000224721 27/70 161 130 31 128 127 1 strelka-varscan-mutect CDH23,missense_variant,p.Arg1065Leu,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Arg1060Leu,ENST00000622827,;CDH23,missense_variant,p.Arg652Leu,ENST00000442677,;CDH23,missense_variant,p.Arg1060Leu,ENST00000616684,NM_001171930.1;CDH23,missense_variant,p.Arg1060Leu,ENST00000398809,;CDH23,missense_variant,p.Arg871Leu,ENST00000466757,;C10orf105,downstream_gene_variant,,ENST00000441508,NM_001164375.2;C10orf105,downstream_gene_variant,,ENST00000398786,NM_001168390.1;CDH23,downstream_gene_variant,,ENST00000299366,NM_001171931.1;CDH23,upstream_gene_variant,,ENST00000398792,; T ENST00000224721 Transcript missense_variant 3584/11139 3194/10080 1065/3359 R/L cGg/cTg rs536438868,COSM273631,COSM5120671 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 deleterious(0.04) 27/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF277,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs536438868 . 0 205 0 4 0 0 0 0 -20 0.9999478 1 1 1 0 T 3 4 43 71709170 71709170 G T 1 0 0 0 0 1 0 0 0 2811 1116 39 1 1 CDH23 10 71709170 Missense_Mutation SNP G C3N-00217_T 65311 71709170 62088252 324 12094 CDHR1 0 . GRCh38 10 84202979 84202979 + Splice_Site SNP G G T novel C3N-00217_T C3N-00217_N G G c.640-1G>T p.X214_splice ENST00000623527 407 311 96 324 323 1 strelka-varscan-mutect CDHR1,splice_acceptor_variant,,ENST00000623527,NM_033100.3;CDHR1,splice_acceptor_variant,,ENST00000372117,;CDHR1,splice_acceptor_variant,,ENST00000332904,NM_001171971.2;CDHR1,upstream_gene_variant,,ENST00000624091,; T ENST00000623527 Transcript splice_acceptor_variant -/6781 640/2580 214/859 1 1 CDHR1 HGNC HGNC:14550 protein_coding YES CCDS7372.1 ENSP00000485478 Q96JP9 F1T0L2 UPI0000161C2F NM_033100.3 7/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 84202979 84202979 G T 1 0 0 0 0 0 0 1 0 2821 1014 35 2 2 CDHR1 10 84202979 Splice_Site SNP G C3N-00217_T 12493809 84202979 49594443 325 12095 TNKS2 0 . GRCh38 10 91859534 91859534 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.3167G>T p.Gly1056Val p.G1056V ENST00000371627 25/27 150 117 33 193 193 0 strelka-varscan-mutect TNKS2,missense_variant,p.Gly1056Val,ENST00000371627,NM_025235.3; T ENST00000371627 Transcript missense_variant 3546/6157 3167/3501 1056/1166 G/V gGa/gTa 1 1 TNKS2 HGNC HGNC:15677 protein_coding YES CCDS7417.1 ENSP00000360689 Q9H2K2 UPI00000362BE NM_025235.3 deleterious(0.01) 25/27 Gene3D:3.90.228.10,Pfam_domain:PF00644,PROSITE_profiles:PS51059,hmmpanther:PTHR24180,hmmpanther:PTHR24180:SF11,Superfamily_domains:SSF56399 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 91859534 91859534 G T 1 0 0 0 0 1 0 0 0 16794 1174 41 2 2 TNKS2 10 91859534 Missense_Mutation SNP G C3N-00217_T 7656555 91859534 41937888 326 12096 LCOR 0 . GRCh38 10 96983770 96983770 + Nonsense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2380G>T p.Glu794Ter p.E794* ENST00000286067 1/1 295 210 85 230 230 0 strelka-varscan-mutect LCOR,stop_gained,p.Glu1076Ter,ENST00000421806,;LCOR,stop_gained,p.Glu794Ter,ENST00000286067,NM_015652.2; T ENST00000286067 Transcript stop_gained 2487/4542 2380/3744 794/1247 E/* Gag/Tag 1 1 LCOR HGNC HGNC:29503 protein_coding YES CCDS7452.1 ENSP00000286067 Q8N655 UPI000006F242 NM_015652.2 1/1 Pfam_domain:PF15090,hmmpanther:PTHR14931,hmmpanther:PTHR14931:SF2 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 96983770 96983770 G T 1 0 0 0 0 0 1 0 0 8595 1291 45 2 2 LCOR 10 96983770 Nonsense_Mutation SNP G C3N-00217_T 5124236 96983770 36813652 327 12097 DNMBP 0 . GRCh38 10 99955762 99955762 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1712A>T p.Asp571Val p.D571V ENST00000324109 4/17 202 136 66 210 210 0 strelka-varscan-mutect DNMBP,missense_variant,p.Asp571Val,ENST00000324109,NM_015221.2;DNMBP-AS1,non_coding_transcript_exon_variant,,ENST00000434409,; A ENST00000324109 Transcript missense_variant 1804/6400 1712/4734 571/1577 D/V gAt/gTt 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 deleterious_low_confidence(0) 4/17 hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 99955762 99955762 T A 1 0 0 0 0 1 0 0 0 4487 1435 50 4 4 DNMBP 10 99955762 Missense_Mutation SNP T C3N-00217_T 2971992 99955762 33841660 328 12098 SEC31B 0 . GRCh38 10 100490731 100490731 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2625G>T p.Leu875Phe p.L875F ENST00000370345 20/26 54 39 15 47 47 0 strelka-varscan-mutect SEC31B,missense_variant,p.Leu875Phe,ENST00000370345,NM_015490.3;SEC31B,3_prime_UTR_variant,,ENST00000479697,;SEC31B,3_prime_UTR_variant,,ENST00000462434,;SEC31B,3_prime_UTR_variant,,ENST00000469546,;SEC31B,3_prime_UTR_variant,,ENST00000482456,;SEC31B,downstream_gene_variant,,ENST00000484848,;SEC31B,upstream_gene_variant,,ENST00000492667,;SEC31B,upstream_gene_variant,,ENST00000485800,; A ENST00000370345 Transcript missense_variant 2723/4612 2625/3540 875/1179 L/F ttG/ttT 1 -1 SEC31B HGNC HGNC:23197 protein_coding YES CCDS7495.1 ENSP00000359370 Q9NQW1 UPI0000070A8E NM_015490.3 tolerated(0.31) 20/26 hmmpanther:PTHR13923:SF22,hmmpanther:PTHR13923 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999982 1 1 1 0 A 3 1 43 100490731 100490731 C A 1 0 0 0 0 1 0 0 0 14276 709 25 2 2 SEC31B 10 100490731 Missense_Mutation SNP C C3N-00217_T 534969 100490731 33306691 329 12099 CFAP46 0 . GRCh38 10 132835325 132835325 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.6723C>T p.= p.D2241D ENST00000368586 47/58 157 93 64 135 135 0 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2;CFAP46,synonymous_variant,p.=,ENST00000448925,;CFAP46,non_coding_transcript_exon_variant,,ENST00000476633,; A ENST00000368586 Transcript synonymous_variant 6824/8278 6723/8148 2241/2715 D gaC/gaT 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 47/58 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 132835325 132835325 G A 1 0 0 0 0 0 0 0 1 3021 1368 48 3 3 CFAP46 10 132835325 Silent SNP G C3N-00217_T 32344594 132835325 962097 330 12100 OR51E2 0 . GRCh38 11 4682047 4682047 + Missense_Mutation SNP C C A rs565364663 C3N-00217_T C3N-00217_N C C c.665G>T p.Arg222Leu p.R222L ENST00000396950 2/2 361 222 139 307 307 0 strelka-varscan-mutect OR51E2,missense_variant,p.Arg222Leu,ENST00000396950,NM_030774.3;OR51E2,downstream_gene_variant,,ENST00000532598,; A ENST00000396950 Transcript missense_variant 905/2781 665/963 222/320 R/L cGa/cTa rs565364663,COSM1353976,COSM4574388 1 -1 OR51E2 HGNC HGNC:15195 protein_coding YES CCDS7751.1 ENSP00000380153 Q9H255 A0A126GVK0 UPI000003B49B NM_030774.3 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF92,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs565364663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 4682047 4682047 C A 1 0 0 0 0 1 0 0 0 11169 884 31 1 1 OR51E2 11 4682047 Missense_Mutation SNP C C3N-00217_T 4682047 130404575 331 12101 OR51G2 0 . GRCh38 11 4915167 4915167 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.497T>C p.Phe166Ser p.F166S ENST00000322013 1/1 277 192 85 254 254 0 strelka-varscan-mutect OR51G2,missense_variant,p.Phe166Ser,ENST00000322013,NM_001005238.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; G ENST00000322013 Transcript missense_variant 497/945 497/945 166/314 F/S tTt/tCt 1 -1 OR51G2 HGNC HGNC:15198 protein_coding YES CCDS31365.1 ENSP00000322593 Q8NGK0 UPI0000041C2F NM_001005238.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF133,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 4915167 4915167 A G 1 0 0 0 0 1 0 0 0 11171 14 1 5 5 OR51G2 11 4915167 Missense_Mutation SNP A C3N-00217_T 233120 4915167 130171455 332 12102 OR51G2 0 . GRCh38 11 4915256 4915256 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.408C>A p.His136Gln p.H136Q ENST00000322013 1/1 166 128 38 149 148 1 strelka-varscan-mutect OR51G2,missense_variant,p.His136Gln,ENST00000322013,NM_001005238.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322013 Transcript missense_variant 408/945 408/945 136/314 H/Q caC/caA 1 -1 OR51G2 HGNC HGNC:15198 protein_coding YES CCDS31365.1 ENSP00000322593 Q8NGK0 UPI0000041C2F NM_001005238.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF133,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 4915256 4915256 G T 1 0 0 0 0 1 0 0 0 11171 1020 36 2 2 OR51G2 11 4915256 Missense_Mutation SNP G C3N-00217_T 89 4915256 130171366 333 12103 OR52E2 0 . GRCh38 11 5059092 5059092 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.536C>A p.Thr179Asn p.T179N ENST00000321522 1/1 68 41 27 71 71 0 strelka-varscan-mutect OR52E2,missense_variant,p.Thr179Asn,ENST00000321522,NM_001005164.2; T ENST00000321522 Transcript missense_variant 536/978 536/978 179/325 T/N aCc/aAc 1 -1 OR52E2 HGNC HGNC:14769 protein_coding YES CCDS31371.1 ENSP00000322088 Q8NGJ4 UPI0000046AE3 NM_001005164.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF169,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1226206074 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 5059092 5059092 G T 1 0 0 0 0 1 0 0 0 11187 1261 44 2 2 OR52E2 11 5059092 Missense_Mutation SNP G C3N-00217_T 143836 5059092 130027530 334 12104 OR52A5 0 . GRCh38 11 5132137 5132137 + Frame_Shift_Del DEL A A - novel C3N-00217_T C3N-00217_N A A c.506delT p.Leu169ArgfsTer20 p.L169Rfs*20 ENST00000307388 1/1 179 114 65 201 201 0 sindel-varindel-pindel OR52A5,frameshift_variant,p.Leu169ArgfsTer20,ENST00000307388,NM_001005160.2; - ENST00000307388 Transcript frameshift_variant 506/951 506/951 169/316 L/X cTg/cg 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321 HIGH 1 deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 5132137 5132137 A - 1 0 1 0 1 0 0 0 0 11183 188 7 0 0 OR52A5 11 5132137 Frame_Shift_Del DEL A C3N-00217_T 73045 5132137 129954485 335 12105 OR51B5 0 . GRCh38 11 5343244 5343244 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.281C>A p.Ala94Asp p.A94D ENST00000300773 1/1 182 102 80 129 129 0 strelka-varscan-mutect OR51B5,missense_variant,p.Ala94Asp,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300773 Transcript missense_variant 281/939 281/939 94/312 A/D gCc/gAc 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 5343244 5343244 G T 1 0 0 0 0 1 0 0 0 11165 1203 42 2 2 OR51B5 11 5343244 Missense_Mutation SNP G C3N-00217_T 211107 5343244 129743378 336 12106 PSMA1 0 . GRCh38 11 14510925 14510925 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.589G>C p.Gly197Arg p.G197R ENST00000418988 9/11 113 81 32 150 150 0 strelka-varscan-mutect PSMA1,missense_variant,p.Gly166Arg,ENST00000530457,;PSMA1,missense_variant,p.Gly191Arg,ENST00000396394,NM_002786.3;PSMA1,missense_variant,p.Gly197Arg,ENST00000418988,NM_148976.2;PSMA1,non_coding_transcript_exon_variant,,ENST00000524606,;RP11-140L24.4,3_prime_UTR_variant,,ENST00000555531,;PSMA1,non_coding_transcript_exon_variant,,ENST00000528307,;PSMA1,non_coding_transcript_exon_variant,,ENST00000527632,;PSMA1,non_coding_transcript_exon_variant,,ENST00000531023,;PSMA1,downstream_gene_variant,,ENST00000529524,;PSMA1,downstream_gene_variant,,ENST00000533331,;PSMA1,downstream_gene_variant,,ENST00000531156,;PSMA1,downstream_gene_variant,,ENST00000526443,; G ENST00000418988 Transcript missense_variant 917/1266 589/810 197/269 G/R Ggt/Cgt 1 -1 PSMA1 HGNC HGNC:9530 protein_coding YES CCDS31431.1 ENSP00000414359 P25786 UPI000002B1AC NM_148976.2 deleterious(0) 9/11 PROSITE_profiles:PS51475,hmmpanther:PTHR11599:SF12,hmmpanther:PTHR11599,Gene3D:3.60.20.10,Pfam_domain:PF00227,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 14510925 14510925 C G 1 0 0 0 0 1 0 0 0 12817 594 21 4 4 PSMA1 11 14510925 Missense_Mutation SNP C C3N-00217_T 9167681 14510925 120575697 337 12107 SLC17A6 0 . GRCh38 11 22374864 22374864 + Missense_Mutation SNP T T A C3N-00217_T C3N-00217_N T T c.1151T>A p.Val384Glu p.V384E ENST00000263160 9/12 66 39 27 110 110 0 strelka-varscan-mutect SLC17A6,missense_variant,p.Val384Glu,ENST00000263160,NM_020346.2; A ENST00000263160 Transcript missense_variant 1588/3949 1151/1749 384/582 V/E gTg/gAg COSM378957 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 deleterious(0) 9/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 22374864 22374864 T A 1 0 0 0 0 1 0 0 0 14686 1696 59 4 4 SLC17A6 11 22374864 Missense_Mutation SNP T C3N-00217_T 7863939 22374864 112711758 338 12108 SLC17A6 0 . GRCh38 11 22377654 22377654 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.1663C>T p.Pro555Ser p.P555S ENST00000263160 12/12 198 138 60 174 174 0 strelka-varscan-mutect SLC17A6,missense_variant,p.Pro555Ser,ENST00000263160,NM_020346.2; T ENST00000263160 Transcript missense_variant 2100/3949 1663/1749 555/582 P/S Cct/Tct COSM4651918 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 tolerated(0.28) 12/12 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 22377654 22377654 C T 1 0 0 0 0 1 0 0 0 14686 739 26 3 3 SLC17A6 11 22377654 Missense_Mutation SNP C C3N-00217_T 2790 22377654 112708968 339 12109 KIAA1549L 0 . GRCh38 11 33543539 33543539 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1085C>T p.Ser362Phe p.S362F ENST00000321505 1/20 199 109 90 181 181 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Ser362Phe,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Ser362Phe,ENST00000265654,;KIAA1549L,intron_variant,,ENST00000526400,; T ENST00000321505 Transcript missense_variant 1265/11678 1085/5550 362/1849 S/F tCt/tTt 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 deleterious_low_confidence(0) 1/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 33543539 33543539 C T 1 0 0 0 0 1 0 0 0 8121 913 32 3 3 KIAA1549L 11 33543539 Missense_Mutation SNP C C3N-00217_T 11165885 33543539 101543083 340 12110 LRRC4C 0 . GRCh38 11 40115858 40115858 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.435A>G p.= p.V145V ENST00000278198 2/2 255 222 33 274 274 0 strelka-varscan-mutect LRRC4C,synonymous_variant,p.=,ENST00000278198,;LRRC4C,synonymous_variant,p.=,ENST00000527150,;LRRC4C,synonymous_variant,p.=,ENST00000530763,NM_020929.2;LRRC4C,synonymous_variant,p.=,ENST00000528697,NM_001258419.1;LRRC4C,synonymous_variant,p.=,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; C ENST00000278198 Transcript synonymous_variant 2399/4054 435/1923 145/640 V gtA/gtG 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Gene3D:3.80.10.10,Pfam_domain:PF13306,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 40115858 40115858 T C 1 0 0 0 0 0 0 0 1 8903 1393 49 5 5 LRRC4C 11 40115858 Silent SNP T C3N-00217_T 6572319 40115858 94970764 341 12111 SYT13 0 . GRCh38 11 45252552 45252552 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.715C>A p.Leu239Met p.L239M ENST00000020926 4/6 210 124 86 131 131 0 strelka-varscan-mutect SYT13,missense_variant,p.Leu239Met,ENST00000020926,NM_020826.2;SYT13,downstream_gene_variant,,ENST00000528101,;CTD-2560E9.5,upstream_gene_variant,,ENST00000534342,;CTD-2560E9.5,upstream_gene_variant,,ENST00000531663,;SYT13,3_prime_UTR_variant,,ENST00000533332,; T ENST00000020926 Transcript missense_variant 827/5144 715/1281 239/426 L/M Ctg/Atg 1 -1 SYT13 HGNC HGNC:14962 protein_coding YES CCDS31470.1 ENSP00000020926 Q7L8C5 UPI000003AC01 NM_020826.2 deleterious(0.01) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF250,Pfam_domain:PF00168,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 45252552 45252552 G T 1 0 0 0 0 1 0 0 0 15863 991 35 2 2 SYT13 11 45252552 Missense_Mutation SNP G C3N-00217_T 5136694 45252552 89834070 342 12112 SYT13 0 . GRCh38 11 45254363 45254363 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.451G>C p.Glu151Gln p.E151Q ENST00000020926 3/6 131 96 35 115 115 0 strelka-varscan-mutect SYT13,missense_variant,p.Glu151Gln,ENST00000020926,NM_020826.2;SYT13,missense_variant,p.Glu111Gln,ENST00000528101,;CTD-2560E9.5,non_coding_transcript_exon_variant,,ENST00000531663,;CTD-2560E9.5,intron_variant,,ENST00000534342,;SYT13,3_prime_UTR_variant,,ENST00000533332,; G ENST00000020926 Transcript missense_variant 563/5144 451/1281 151/426 E/Q Gag/Cag 1 -1 SYT13 HGNC HGNC:14962 protein_coding YES CCDS31470.1 ENSP00000020926 Q7L8C5 UPI000003AC01 NM_020826.2 tolerated(0.06) 3/6 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF250,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs1314970772 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 45254363 45254363 C G 1 0 0 0 0 1 0 0 0 15863 922 32 4 4 SYT13 11 45254363 Missense_Mutation SNP C C3N-00217_T 1811 45254363 89832259 343 12113 CREB3L1 0 . GRCh38 11 46320283 46320283 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.1278A>G p.= p.L426L ENST00000621158 11/12 79 56 23 63 63 0 strelka-varscan-mutect CREB3L1,synonymous_variant,p.=,ENST00000621158,NM_052854.3;CREB3L1,downstream_gene_variant,,ENST00000530518,;CREB3L1,non_coding_transcript_exon_variant,,ENST00000534616,;CREB3L1,non_coding_transcript_exon_variant,,ENST00000616094,; G ENST00000621158 Transcript synonymous_variant 1729/2687 1278/1560 426/519 L ctA/ctG 1 1 CREB3L1 HGNC HGNC:18856 protein_coding YES CCDS53620.1 ENSP00000481956 Q96BA8 UPI000004ABFF NM_052854.3 11/12 hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF24 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 46320283 46320283 A G 1 0 0 0 0 0 0 0 1 3656 436 16 5 5 CREB3L1 11 46320283 Silent SNP A C3N-00217_T 1065920 46320283 88766339 344 12114 OR4C5 0 . GRCh38 11 48365970 48365970 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.496G>T p.Val166Leu p.V166L ENST00000319813 1/1 281 194 87 269 269 0 strelka-varscan-mutect OR4C5,missense_variant,p.Val166Leu,ENST00000319813,; A ENST00000319813 Transcript missense_variant 496/981 496/981 166/326 V/L Gtg/Ttg 1 -1 OR4C5 HGNC HGNC:14702 protein_coding YES ENSP00000321338 Q8NGB2 UPI0000061EE9 tolerated_low_confidence(0.53) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF9,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1158789817 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48365970 48365970 C A 1 0 0 0 0 1 0 0 0 11128 507 18 2 2 OR4C5 11 48365970 Missense_Mutation SNP C C3N-00217_T 2045687 48365970 86720652 345 12115 OR9G4 0 . GRCh38 11 56743215 56743215 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.597G>T p.Leu199Phe p.L199F ENST00000302957 1/1 162 96 66 226 225 1 strelka-varscan-mutect OR9G4,missense_variant,p.Leu199Phe,ENST00000302957,NM_001005284.1;MIR6128,upstream_gene_variant,,ENST00000615528,;OR9G3P,downstream_gene_variant,,ENST00000525553,; A ENST00000302957 Transcript missense_variant 597/985 597/984 199/327 L/F ttG/ttT 1 -1 OR9G4 HGNC HGNC:15322 protein_coding YES CCDS31537.1 ENSP00000307515 Q8NGQ1 UPI00001D77DB NM_001005284.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF141,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs992888582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 56743215 56743215 C A 1 0 0 0 0 1 0 0 0 11318 593 21 2 2 OR9G4 11 56743215 Missense_Mutation SNP C C3N-00217_T 8377245 56743215 78343407 346 12116 INCENP 0 . GRCh38 11 62148757 62148757 + Missense_Mutation SNP G G T rs186337901 C3N-00217_T C3N-00217_N G G c.2302G>T p.Ala768Ser p.A768S ENST00000394818 17/19 37 12 25 36 36 0 strelka-varscan-mutect INCENP,missense_variant,p.Ala768Ser,ENST00000394818,NM_001040694.1;INCENP,missense_variant,p.Ala764Ser,ENST00000278849,NM_020238.2;INCENP,upstream_gene_variant,,ENST00000531099,; T ENST00000394818 Transcript missense_variant 2504/3964 2302/2757 768/918 A/S Gct/Tct rs186337901 1 1 INCENP HGNC HGNC:6058 protein_coding YES CCDS44624.1 ENSP00000378295 Q9NQS7 UPI0000D7D6F3 NM_001040694.1 tolerated(0.07) 17/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13142:SF1,hmmpanther:PTHR13142 MODERATE 1 SNV 1 1 PASS rs186337901 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 62148757 62148757 G T 1 0 0 0 0 1 0 0 0 7635 1203 42 2 2 INCENP 11 62148757 Missense_Mutation SNP G C3N-00217_T 5405542 62148757 72937865 347 12117 AHNAK 0 . GRCh38 11 62517501 62517501 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.16916G>T p.Gly5639Val p.G5639V ENST00000378024 5/5 168 75 93 167 167 0 strelka-varscan-mutect AHNAK,missense_variant,p.Gly5639Val,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; A ENST00000378024 Transcript missense_variant 17191/18787 16916/17673 5639/5890 G/V gGg/gTg 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 62517501 62517501 C A 1 0 0 0 0 1 0 0 0 491 623 22 2 2 AHNAK 11 62517501 Missense_Mutation SNP C C3N-00217_T 368744 62517501 72569121 348 12118 FLRT1 0 . GRCh38 11 64117358 64117358 + Missense_Mutation SNP G G C rs767022154 C3N-00217_T C3N-00217_N G G c.1091G>C p.Arg364Pro p.R364P ENST00000246841 2/2 65 39 26 104 104 0 strelka-varscan-mutect FLRT1,missense_variant,p.Arg364Pro,ENST00000246841,NM_013280.4;MACROD1,intron_variant,,ENST00000255681,NM_014067.3;RP11-21A7A.3,downstream_gene_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000545464,; C ENST00000246841 Transcript missense_variant 2134/3949 1091/2025 364/674 R/P cGg/cCg rs767022154,COSM4887990 1 1 FLRT1 HGNC HGNC:3760 protein_coding YES CCDS8057.1 ENSP00000246841 Q9NZU1 UPI0000039F94 NM_013280.4 deleterious(0) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF30,SMART_domains:SM00082,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs767022154 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 64117358 64117358 G C 1 0 0 0 0 1 0 0 0 5794 1116 39 4 4 FLRT1 11 64117358 Missense_Mutation SNP G C3N-00217_T 1599857 64117358 70969264 349 12119 NRXN2 0 . GRCh38 11 64661020 64661020 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.1918C>A p.Pro640Thr p.P640T ENST00000265459 10/23 117 87 30 107 107 0 strelka-varscan-mutect NRXN2,missense_variant,p.Pro640Thr,ENST00000265459,NM_015080.3;NRXN2,missense_variant,p.Pro609Thr,ENST00000377559,NM_138732.2;NRXN2,missense_variant,p.Pro633Thr,ENST00000409571,;NRXN2,missense_variant,p.Pro640Thr,ENST00000377551,;AP001092.4,downstream_gene_variant,,ENST00000433606,;NRXN2,non_coding_transcript_exon_variant,,ENST00000496291,;NRXN2,upstream_gene_variant,,ENST00000486057,; T ENST00000265459 Transcript missense_variant 2380/6621 1918/5139 640/1712 P/T Ccc/Acc COSM5373213 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 tolerated(0.36) 10/23 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF593,SMART_domains:SM00282,Superfamily_domains:SSF49899 1 MODERATE SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 64661020 64661020 G T 1 0 0 0 0 1 0 0 0 10725 1203 42 2 2 NRXN2 11 64661020 Missense_Mutation SNP G C3N-00217_T 543662 64661020 70425602 350 12120 NAALADL1 0 . GRCh38 11 65058470 65058470 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.52G>C p.Gly18Arg p.G18R ENST00000358658 1/18 106 60 46 83 83 0 strelka-varscan-mutect NAALADL1,missense_variant,p.Gly18Arg,ENST00000358658,NM_005468.2;NAALADL1,missense_variant,p.Gly18Arg,ENST00000340252,;NAALADL1,missense_variant,p.Gly18Arg,ENST00000356632,;NAALADL1,missense_variant,p.Gly18Arg,ENST00000355721,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000529274,;NAALADL1,non_coding_transcript_exon_variant,,ENST00000528977,; G ENST00000358658 Transcript missense_variant 80/2699 52/2223 18/740 G/R Ggg/Cgg 1 -1 NAALADL1 HGNC HGNC:23536 protein_coding YES CCDS31604.1 ENSP00000351484 Q9UQQ1 UPI000013E761 NM_005468.2 tolerated(0.1) 1/18 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF50 MODERATE 1 SNV 1 1 PASS rs1390754962 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 65058470 65058470 C G 1 0 0 0 0 1 0 0 0 10133 623 22 4 4 NAALADL1 11 65058470 Missense_Mutation SNP C C3N-00217_T 397450 65058470 70028152 351 12121 SNX32 0 . GRCh38 11 65850510 65850510 + Missense_Mutation SNP C C G rs764719974 C3N-00217_T C3N-00217_N C C c.454C>G p.Arg152Gly p.R152G ENST00000308342 5/13 218 173 45 178 178 0 strelka-varscan-mutect SNX32,missense_variant,p.Arg152Gly,ENST00000308342,NM_152760.2;CFL1,downstream_gene_variant,,ENST00000525451,;CFL1,downstream_gene_variant,,ENST00000308162,NM_005507.2;CFL1,downstream_gene_variant,,ENST00000531407,;CFL1,downstream_gene_variant,,ENST00000527344,;CFL1,downstream_gene_variant,,ENST00000524553,;CFL1,downstream_gene_variant,,ENST00000532134,;CFL1,downstream_gene_variant,,ENST00000534769,;CFL1,downstream_gene_variant,,ENST00000530413,;CFL1,downstream_gene_variant,,ENST00000531413,;CFL1,intron_variant,,ENST00000527752,;SNX32,downstream_gene_variant,,ENST00000531795,;SNX32,non_coding_transcript_exon_variant,,ENST00000530101,;SNX32,non_coding_transcript_exon_variant,,ENST00000526972,;SNX32,non_coding_transcript_exon_variant,,ENST00000533298,;SNX32,non_coding_transcript_exon_variant,,ENST00000533236,;SNX32,non_coding_transcript_exon_variant,,ENST00000534387,;CFL1,downstream_gene_variant,,ENST00000530945,;SNX32,downstream_gene_variant,,ENST00000531503,;SNX32,downstream_gene_variant,,ENST00000524729,; G ENST00000308342 Transcript missense_variant 879/2003 454/1212 152/403 R/G Cgt/Ggt rs764719974,COSM930513 1 1 SNX32 HGNC HGNC:26423 protein_coding YES CCDS8113.2 ENSP00000310620 Q86XE0 UPI000000DAEA NM_152760.2 deleterious(0.03) 5/13 PROSITE_profiles:PS50195,hmmpanther:PTHR10555:SF137,hmmpanther:PTHR10555,Gene3D:3.30.1520.10,Pfam_domain:PF00787,PIRSF_domain:PIRSF036924,Superfamily_domains:SSF64268 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764719974 . 0 207 0 3 0 0 0 0 -20 0.9999967 1 1 1 0 G 3 3 43 65850510 65850510 C G 1 0 0 0 0 1 0 0 0 15223 768 27 4 4 SNX32 11 65850510 Missense_Mutation SNP C C3N-00217_T 792040 65850510 69236112 352 12122 ANKRD13D 0 . GRCh38 11 67292043 67292043 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.594G>T p.= p.V198V ENST00000511455 6/15 63 36 27 24 24 0 strelka-varscan-mutect ANKRD13D,synonymous_variant,p.=,ENST00000447274,;ANKRD13D,synonymous_variant,p.=,ENST00000308440,;ANKRD13D,synonymous_variant,p.=,ENST00000511455,NM_207354.2;ANKRD13D,synonymous_variant,p.=,ENST00000514166,;ANKRD13D,downstream_gene_variant,,ENST00000514779,;ANKRD13D,non_coding_transcript_exon_variant,,ENST00000506531,;ANKRD13D,non_coding_transcript_exon_variant,,ENST00000504729,;ANKRD13D,downstream_gene_variant,,ENST00000512101,;ANKRD13D,upstream_gene_variant,,ENST00000504186,;ANKRD13D,downstream_gene_variant,,ENST00000513460,; T ENST00000511455 Transcript synonymous_variant 764/2139 594/1818 198/605 V gtG/gtT 1 1 ANKRD13D HGNC HGNC:27880 protein_coding YES CCDS31616.2 ENSP00000427130 Q6ZTN6 UPI00001981D2 NM_207354.2 6/15 Pfam_domain:PF11904,hmmpanther:PTHR12447,hmmpanther:PTHR12447:SF2 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 67292043 67292043 G T 1 0 0 0 0 0 0 0 1 745 1335 47 2 2 ANKRD13D 11 67292043 Silent SNP G C3N-00217_T 1441533 67292043 67794579 353 12123 ANO1 0 . GRCh38 11 70161240 70161240 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1658C>T p.Ser553Phe p.S553F ENST00000355303 17/26 322 206 116 331 331 0 strelka-varscan-mutect ANO1,missense_variant,p.Ser553Phe,ENST00000355303,NM_018043.5;ANO1,missense_variant,p.Ser262Phe,ENST00000531349,;ANO1,missense_variant,p.Ser407Phe,ENST00000530676,;ANO1,missense_variant,p.Ser495Phe,ENST00000316296,;ANO1,missense_variant,p.Ser104Phe,ENST00000531300,;ANO1,upstream_gene_variant,,ENST00000529636,; T ENST00000355303 Transcript missense_variant 1963/4790 1658/2961 553/986 S/F tCc/tTc 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 tolerated(0.68) 17/26 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 70161240 70161240 C T 1 0 0 0 0 1 0 0 0 802 855 30 3 3 ANO1 11 70161240 Missense_Mutation SNP C C3N-00217_T 2869197 70161240 64925382 354 12124 SHANK2 0 . GRCh38 11 70502241 70502241 + Missense_Mutation SNP C C A C3N-00217_T C3N-00217_N C C c.479G>T p.Arg160Leu p.R160L ENST00000338508 4/11 246 202 44 208 208 0 strelka-varscan-mutect SHANK2,missense_variant,p.Arg159Leu,ENST00000409161,;SHANK2,missense_variant,p.Arg748Leu,ENST00000601538,NM_012309.4;SHANK2,missense_variant,p.Arg160Leu,ENST00000449833,;SHANK2,missense_variant,p.Arg160Leu,ENST00000338508,NM_133266.4;SHANK2,missense_variant,p.Arg37Leu,ENST00000424924,;SHANK2,missense_variant,p.Arg160Leu,ENST00000409530,;SHANK2,missense_variant,p.Arg159Leu,ENST00000412252,;SHANK2,missense_variant,p.Arg147Leu,ENST00000357171,;SHANK2,missense_variant,p.Arg160Leu,ENST00000449116,;SHANK2,intron_variant,,ENST00000426687,; A ENST00000338508 Transcript missense_variant 530/7271 479/3786 160/1261 R/L cGc/cTc COSM4618969,COSM4618970,COSM4618971,COSM4618972 1 -1 SHANK2 HGNC HGNC:14295 protein_coding YES CCDS76448.1 ENSP00000345193 A6NHU9 UPI0001B09234 NM_133266.4 deleterious(0) 4/11 hmmpanther:PTHR24135:SF17,hmmpanther:PTHR24135 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs932534804 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 70502241 70502241 C A 1 0 0 0 0 1 0 0 0 14524 768 27 1 1 SHANK2 11 70502241 Missense_Mutation SNP C C3N-00217_T 341001 70502241 64584381 355 12125 UBTFL1 0 . GRCh38 11 90086987 90086987 + Silent SNP A A C novel C3N-00217_T C3N-00217_N A A c.1038A>C p.= p.A346A ENST00000530464 1/1 18 9 9 17 17 0 strelka-varscan-mutect UBTFL1,synonymous_variant,p.=,ENST00000530464,NM_001143975.1; C ENST00000530464 Transcript synonymous_variant 1038/1182 1038/1182 346/393 A gcA/gcC 1 1 UBTFL1 HGNC HGNC:14533 protein_coding YES ENSP00000485108 P0CB47 UPI0000185F50 NM_001143975.1 1/1 Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 8 195 6 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 90086987 90086987 A C 1 0 0 0 0 0 0 0 1 17434 175 7 5 5 UBTFL1 11 90086987 Silent SNP A C3N-00217_T 19584746 90086987 44999635 356 12126 48 2 UBTFL1 0 . GRCh38 11 90086989 90086989 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1040G>T p.Gly347Val p.G347V ENST00000530464 1/1 18 10 8 18 18 0 strelka-varscan-mutect UBTFL1,missense_variant,p.Gly347Val,ENST00000530464,NM_001143975.1; T ENST00000530464 Transcript missense_variant 1040/1182 1040/1182 347/393 G/V gGa/gTa 1 1 UBTFL1 HGNC HGNC:14533 protein_coding YES ENSP00000485108 P0CB47 UPI0000185F50 NM_001143975.1 tolerated(0.06) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 8 198 4 0 0 0 0 0 -19.99992 1 1 1 1 0 T 3 4 43 90086989 90086989 G T 1 0 0 0 0 1 0 0 0 17434 1174 41 2 2 UBTFL1 11 90086989 Missense_Mutation SNP G C3N-00217_T 2 90086989 44999633 357 12127 48 2 FAT3 0 . GRCh38 11 92354372 92354372 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.1810G>C p.Asp604His p.D604H ENST00000525166 1/27 106 63 43 234 234 0 strelka-varscan-mutect FAT3,missense_variant,p.Asp754His,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Asp604His,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; C ENST00000525166 Transcript missense_variant 1832/18699 1810/13320 604/4439 D/H Gac/Cac COSM3772109,COSM933058,COSM933059 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs1408408990 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 92354372 92354372 G C 1 0 0 0 0 1 0 0 0 5551 1058 37 4 4 FAT3 11 92354372 Missense_Mutation SNP G C3N-00217_T 2267383 92354372 42732250 358 12128 ABCG4 0 . GRCh38 11 119158607 119158607 + Silent SNP C C T rs145578285 C3N-00217_T C3N-00217_N C C c.1218C>T p.= p.I406I ENST00000619701 11/15 186 111 75 245 243 2 strelka-varscan-mutect ABCG4,synonymous_variant,p.=,ENST00000619701,NM_022169.4;ABCG4,synonymous_variant,p.=,ENST00000622721,;ABCG4,synonymous_variant,p.=,ENST00000615496,NM_001142505.1;ABCG4,downstream_gene_variant,,ENST00000524604,;ABCG4,non_coding_transcript_exon_variant,,ENST00000533694,;ABCG4,downstream_gene_variant,,ENST00000534402,; T ENST00000619701 Transcript synonymous_variant 1582/3852 1218/1941 406/646 I atC/atT rs145578285,COSM2106515 1 1 ABCG4 HGNC HGNC:13884 protein_coding YES CCDS8415.1 ENSP00000481728 Q9H172 UPI000000D999 NM_022169.4 11/15 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF211,Pfam_domain:PF01061 0,1 LOW 1 SNV 1 0,1 1 PASS rs145578285 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 119158607 119158607 C T 1 0 0 0 0 0 0 0 1 74 874 31 1 1 ABCG4 11 119158607 Silent SNP C C3N-00217_T 26804235 119158607 15928015 359 12129 ZNF202 0 . GRCh38 11 123726468 123726468 + Nonsense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1476G>A p.Trp492Ter p.W492* ENST00000336139 8/8 130 123 7 190 190 0 varscan-mutect ZNF202,stop_gained,p.Trp492Ter,ENST00000336139,NM_001301779.1;ZNF202,stop_gained,p.Trp492Ter,ENST00000530393,NM_003455.3;ZNF202,stop_gained,p.Trp492Ter,ENST00000529691,NM_001301819.1,NM_001301780.1;ZNF202,downstream_gene_variant,,ENST00000533463,;ZNF202,downstream_gene_variant,,ENST00000526252,;ZNF202,downstream_gene_variant,,ENST00000528306,;ZNF202,downstream_gene_variant,,ENST00000530944,;ZNF202,downstream_gene_variant,,ENST00000529250,; T ENST00000336139 Transcript stop_gained 1839/4130 1476/1947 492/648 W/* tgG/tgA 1 -1 ZNF202 HGNC HGNC:12994 protein_coding YES CCDS8443.1 ENSP00000337724 O95125 A0A024R3M3 UPI000013E581 NM_001301779.1 8/8 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF219,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 123726468 123726468 C T 1 0 0 0 0 0 1 0 0 18340 856 30 3 3 ZNF202 11 123726468 Nonsense_Mutation SNP C C3N-00217_T 4567861 123726468 11360154 360 12130 HEPACAM 0 . GRCh38 11 124923916 124923916 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.522C>A p.= p.T174T ENST00000298251 3/7 300 181 119 355 355 0 strelka-varscan-mutect HEPACAM,synonymous_variant,p.=,ENST00000298251,NM_152722.4;HEPN1,downstream_gene_variant,,ENST00000408930,NM_001037558.2;HEPACAM,non_coding_transcript_exon_variant,,ENST00000526273,;HEPACAM,downstream_gene_variant,,ENST00000528971,; T ENST00000298251 Transcript synonymous_variant 928/3602 522/1251 174/416 T acC/acA 1 -1 HEPACAM HGNC HGNC:26361 protein_coding YES CCDS8456.1 ENSP00000298251 Q14CZ8 UPI000013E4B5 NM_152722.4 3/7 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12080,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 124923916 124923916 G T 1 0 0 0 0 0 0 0 1 6936 1335 47 2 2 HEPACAM 11 124923916 Silent SNP G C3N-00217_T 1197448 124923916 10162706 361 12131 FLI1 0 . GRCh38 11 128810478 128810478 + Silent SNP G G T C3N-00217_T C3N-00217_N G G c.849G>T p.= p.L283L ENST00000527786 9/9 140 75 65 158 158 0 strelka-varscan-mutect FLI1,synonymous_variant,p.=,ENST00000281428,NM_001271010.1;FLI1,synonymous_variant,p.=,ENST00000527786,NM_002017.4;FLI1,synonymous_variant,p.=,ENST00000534087,NM_001167681.2;FLI1,synonymous_variant,p.=,ENST00000344954,NM_001271012.1;FLI1,3_prime_UTR_variant,,ENST00000429175,;FLI1,3_prime_UTR_variant,,ENST00000608303,;FLI1,non_coding_transcript_exon_variant,,ENST00000528790,; T ENST00000527786 Transcript synonymous_variant 1338/4127 849/1359 283/452 L ctG/ctT COSM81190 1 1 FLI1 HGNC HGNC:3749 protein_coding YES CCDS44768.1 ENSP00000433488 Q01543 A0A024R3M5 UPI000012A972 NM_002017.4 9/9 Gene3D:1.10.10.10,Pfam_domain:PF00178,Prints_domain:PR00454,PROSITE_patterns:PS00345,PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF161,SMART_domains:SM00413,Superfamily_domains:SSF46785 1 LOW 1 SNV 1 1 1 PASS rs1179005819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 128810478 128810478 G T 1 0 0 0 0 0 0 0 1 5786 1364 48 2 2 FLI1 11 128810478 Silent SNP G C3N-00217_T 3886562 128810478 6276144 362 12132 CACNA1C 0 . GRCh38 12 2566528 2566528 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1615C>T p.Leu539Phe p.L539F ENST00000347598 12/49 122 109 13 146 146 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Leu539Phe,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000406454,;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Leu564Phe,ENST00000335762,;CACNA1C,missense_variant,p.Leu539Phe,ENST00000480911,;CACNA1C,missense_variant,p.Leu539Phe,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Leu539Phe,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Leu539Phe,ENST00000399644,NM_001129841.1;CACNA1C,non_coding_transcript_exon_variant,,ENST00000491104,; T ENST00000347598 Transcript missense_variant 1615/6655 1615/6561 539/2186 L/F Ctc/Ttc 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0.02) 12/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.37276 0.9999999 1 1 1 0 T 3 4 43 2566528 2566528 C T 1 0 0 0 0 1 0 0 0 2228 797 28 3 3 CACNA1C 12 2566528 Missense_Mutation SNP C C3N-00217_T 2566528 130708781 363 12133 KCNA1 0 . GRCh38 12 4911937 4911937 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.559G>C p.Glu187Gln p.E187Q ENST00000382545 2/2 132 118 14 120 120 0 strelka-varscan-mutect KCNA1,missense_variant,p.Glu187Gln,ENST00000382545,NM_000217.2;KCNA1,intron_variant,,ENST00000543874,;KCNA1,intron_variant,,ENST00000541095,; C ENST00000382545 Transcript missense_variant 1666/7976 559/1488 187/495 E/Q Gag/Cag 1 1 KCNA1 HGNC HGNC:6218 protein_coding YES CCDS8535.1 ENSP00000371985 Q09470 UPI000013C8E0 NM_000217.2 deleterious(0) 2/2 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,Prints_domain:PR01496,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF24,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 4911937 4911937 G C 1 0 0 0 0 1 0 0 0 7917 1175 41 4 4 KCNA1 12 4911937 Missense_Mutation SNP G C3N-00217_T 2345409 4911937 128363372 364 12134 KCNA5 0 . GRCh38 12 5044351 5044351 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.204T>A p.= p.P68P ENST00000252321 1/1 51 36 15 52 52 0 strelka-varscan-mutect KCNA5,synonymous_variant,p.=,ENST00000252321,NM_002234.3; A ENST00000252321 Transcript synonymous_variant 363/2800 204/1842 68/613 P ccT/ccA 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 1/1 Prints_domain:PR01512,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 5044351 5044351 T A 1 0 0 0 0 0 0 0 1 7922 1538 54 4 4 KCNA5 12 5044351 Silent SNP T C3N-00217_T 132414 5044351 128230958 365 12135 VWF 0 . GRCh38 12 6013512 6013513 + Frame_Shift_Ins INS - - A novel C3N-00217_T C3N-00217_N - - c.5588dupT p.Leu1863PhefsTer15 p.L1863Ffs*15 ENST00000261405 32/52 426 290 136 414 414 0 sindel-varindel-pindel VWF,frameshift_variant,p.Leu1863PhefsTer15,ENST00000261405,NM_000552.3;VWF,intron_variant,,ENST00000538635,; A ENST00000261405 Transcript frameshift_variant 5843-5844/8838 5588-5589/8442 1863/2813 L/FX ttg/ttTg 1 -1 VWF HGNC HGNC:12726 protein_coding YES CCDS8539.1 ENSP00000261405 P04275 UPI00001AE7EE NM_000552.3 32/52 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,PIRSF_domain:PIRSF002495,SMART_domains:SM00327,Superfamily_domains:SSF53300 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 43 6013512 6013512 - A 1 0 1 1 0 0 0 0 0 17806 593 21 0 0 VWF 12 6013512 Frame_Shift_Ins INS - C3N-00217_T 969161 6013512 127261797 366 12136 CD163 0 . GRCh38 12 7481160 7481160 + Splice_Site SNP C C T novel C3N-00217_T C3N-00217_N C C c.3343+1G>A p.X1115_splice ENST00000359156 87 63 24 71 71 0 strelka-varscan-mutect CD163,splice_donor_variant,,ENST00000359156,NM_004244.5;CD163,splice_donor_variant,,ENST00000396620,;CD163,splice_donor_variant,,ENST00000432237,NM_203416.3;CD163,splice_donor_variant,,ENST00000541972,;CD163,intron_variant,,ENST00000537626,;CD163,intron_variant,,ENST00000542280,;CD163L1,upstream_gene_variant,,ENST00000543276,;CD163,downstream_gene_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;CD163,downstream_gene_variant,,ENST00000538840,; T ENST00000359156 Transcript splice_donor_variant -/4268 3343/3471 1115/1156 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 15/16 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 7481160 7481160 C T 1 0 0 0 0 0 0 1 0 2670 521 18 3 3 CD163 12 7481160 Splice_Site SNP C C3N-00217_T 1467648 7481160 125794149 367 12137 A2M 0 . GRCh38 12 9072369 9072369 + Frame_Shift_Del DEL G G - novel C3N-00217_T C3N-00217_N G G c.4093delC p.Leu1365Ter p.L1365* ENST00000318602 31/36 193 150 43 224 224 0 sindel-varindel-pindel A2M,frameshift_variant,p.Leu1365Ter,ENST00000318602,NM_000014.4;A2M-AS1,downstream_gene_variant,,ENST00000499762,;A2M,intron_variant,,ENST00000543436,;A2M,downstream_gene_variant,,ENST00000545828,;A2M,upstream_gene_variant,,ENST00000495442,;A2M,upstream_gene_variant,,ENST00000495709,; - ENST00000318602 Transcript frameshift_variant 4401/4844 4093/4425 1365/1474 L/X Cta/ta 1 -1 A2M HGNC HGNC:7 protein_coding YES CCDS44827.1 ENSP00000323929 P01023 UPI000014038F NM_000014.4 31/36 Gene3D:1ayoA00,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF103,Superfamily_domains:SSF49410 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 9072369 9072369 G - 1 0 1 0 1 0 0 0 0 3 991 35 0 0 A2M 12 9072369 Frame_Shift_Del DEL G C3N-00217_T 1591209 9072369 124202940 368 12138 MANSC1 0 . GRCh38 12 12330862 12330862 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.461C>T p.Ala154Val p.A154V ENST00000535902 4/4 130 97 33 151 151 0 strelka-varscan-mutect MANSC1,missense_variant,p.Ala154Val,ENST00000535902,NM_018050.2;MANSC1,missense_variant,p.Ala120Val,ENST00000396349,;MANSC1,missense_variant,p.Ala73Val,ENST00000545735,; A ENST00000535902 Transcript missense_variant 1025/5831 461/1296 154/431 A/V gCc/gTc 1 -1 MANSC1 HGNC HGNC:25505 protein_coding YES CCDS8648.1 ENSP00000438205 Q9H8J5 UPI0000049E05 NM_018050.2 tolerated(1) 4/4 hmmpanther:PTHR16021,hmmpanther:PTHR16021:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 12330862 12330862 G A 1 0 0 0 0 1 0 0 0 9145 1203 42 3 3 MANSC1 12 12330862 Missense_Mutation SNP G C3N-00217_T 3258493 12330862 120944447 369 12139 PDE3A 0 . GRCh38 12 20637223 20637223 + Missense_Mutation SNP C C A rs373818809 C3N-00217_T C3N-00217_N C C c.2125C>A p.Arg709Ser p.R709S ENST00000359062 9/16 61 44 17 104 104 0 strelka-varscan-mutect PDE3A,missense_variant,p.Arg709Ser,ENST00000359062,NM_000921.4,NM_001244683.1;PDE3A,non_coding_transcript_exon_variant,,ENST00000544307,; A ENST00000359062 Transcript missense_variant 2165/7576 2125/3426 709/1141 R/S Cgt/Agt rs373818809,COSM283903 1 1 PDE3A HGNC HGNC:8778 protein_coding YES CCDS31754.1 ENSP00000351957 Q14432 UPI000014175F NM_000921.4,NM_001244683.1 deleterious(0.01) 9/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF104,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373818809 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 20637223 20637223 C A 1 0 0 0 0 1 0 0 0 11725 652 23 1 1 PDE3A 12 20637223 Missense_Mutation SNP C C3N-00217_T 8306361 20637223 112638086 370 12140 ABCC9 0 . GRCh38 12 21895293 21895293 + Frame_Shift_Del DEL G G - novel C3N-00217_T C3N-00217_N G G c.1641delC p.Ile548Ter p.I548* ENST00000261200 11/38 79 60 19 169 169 0 sindel-varindel-pindel ABCC9,frameshift_variant,p.Ile548Ter,ENST00000261200,NM_020297.3;ABCC9,frameshift_variant,p.Ile548Ter,ENST00000261201,NM_005691.3;ABCC9,frameshift_variant,p.Ile211Ter,ENST00000544039,; - ENST00000261200 Transcript frameshift_variant 1641/8293 1641/4650 547/1549 P/X ccC/cc 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 11/38 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 21895293 21895293 G - 1 0 1 0 1 0 0 0 0 63 1335 47 0 0 ABCC9 12 21895293 Frame_Shift_Del DEL G C3N-00217_T 1258070 21895293 111380016 371 12141 SYT10 0 . GRCh38 12 33426263 33426263 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.384G>T p.Glu128Asp p.E128D ENST00000228567 2/7 291 211 80 296 294 2 strelka-varscan-mutect SYT10,missense_variant,p.Glu128Asp,ENST00000228567,NM_198992.3;SYT10,upstream_gene_variant,,ENST00000567656,;SYT10,missense_variant,p.Glu128Asp,ENST00000539102,; A ENST00000228567 Transcript missense_variant 681/4461 384/1572 128/523 E/D gaG/gaT 1 -1 SYT10 HGNC HGNC:19266 protein_coding YES CCDS8732.1 ENSP00000228567 Q6XYQ8 UPI0000052B30 NM_198992.3 tolerated(0.15) 2/7 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 33426263 33426263 C A 1 0 0 0 0 1 0 0 0 15860 796 28 2 2 SYT10 12 33426263 Missense_Mutation SNP C C3N-00217_T 11530970 33426263 99849046 372 12142 DDN 0 . GRCh38 12 48997767 48997767 + Missense_Mutation SNP C C G rs773498346 C3N-00217_T C3N-00217_N C C c.1109G>C p.Gly370Ala p.G370A ENST00000421952 2/2 49 30 19 34 34 0 strelka-mutect DDN,missense_variant,p.Gly370Ala,ENST00000421952,NM_015086.1;PRKAG1,downstream_gene_variant,,ENST00000548065,NM_002733.4;PRKAG1,downstream_gene_variant,,ENST00000316299,NM_001206709.1;PRKAG1,downstream_gene_variant,,ENST00000547306,;PRKAG1,downstream_gene_variant,,ENST00000552212,NM_001206710.1;PRKAG1,downstream_gene_variant,,ENST00000551770,;PRKAG1,downstream_gene_variant,,ENST00000548362,;RP11-386G11.5,upstream_gene_variant,,ENST00000547866,;RP11-386G11.5,upstream_gene_variant,,ENST00000552933,;RP11-386G11.5,upstream_gene_variant,,ENST00000552284,;RP11-386G11.5,upstream_gene_variant,,ENST00000547395,;RP11-386G11.3,downstream_gene_variant,,ENST00000549516,;PRKAG1,downstream_gene_variant,,ENST00000546531,; G ENST00000421952 Transcript missense_variant 1131/3749 1109/2136 370/711 G/A gGc/gCc rs773498346 1 -1 DDN HGNC HGNC:24458 protein_coding YES CCDS31791.2 ENSP00000390590 O94850 UPI000019821C NM_015086.1 deleterious_low_confidence(0.01) 2/2 Pfam_domain:PF15498,hmmpanther:PTHR16757 MODERATE 1 SNV 1 1 PASS rs773498346 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 48997767 48997767 C G 1 0 0 0 0 1 0 0 0 4137 739 26 4 4 DDN 12 48997767 Missense_Mutation SNP C C3N-00217_T 15571504 48997767 84277542 373 12143 KMT2D 0 . GRCh38 12 49032024 49032024 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.12681G>T p.Met4227Ile p.M4227I ENST00000301067 39/54 67 51 16 62 61 1 strelka-varscan-mutect KMT2D,missense_variant,p.Met4227Ile,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,; A ENST00000301067 Transcript missense_variant 12681/19419 12681/16614 4227/5537 M/I atG/atT 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 tolerated_low_confidence(0.11) 39/54 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 49032024 49032024 C A 1 0 0 0 0 1 0 0 0 8298 710 25 2 2 KMT2D 12 49032024 Missense_Mutation SNP C C3N-00217_T 34257 49032024 84243285 374 12144 AQP6 0 . GRCh38 12 49973512 49973512 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.339G>A p.= p.V113V ENST00000615425 1/5 164 136 28 138 138 0 strelka-varscan-mutect AQP6,synonymous_variant,p.=,ENST00000615425,NM_001652.3;AQP6,synonymous_variant,p.=,ENST00000315520,;AQP6,synonymous_variant,p.=,ENST00000618286,;AQP6,intron_variant,,ENST00000551733,;RACGAP1,downstream_gene_variant,,ENST00000548961,;AQP6,non_coding_transcript_exon_variant,,ENST00000489786,; A ENST00000615425 Transcript synonymous_variant 339/2245 339/849 113/282 V gtG/gtA 1 1 AQP6 HGNC HGNC:639 protein_coding YES CCDS31798.1 ENSP00000477688 Q13520 UPI000013EBD8 NM_001652.3 1/5 Gene3D:1.20.1080.10,Pfam_domain:PF00230,Prints_domain:PR00783,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF113,Superfamily_domains:SSF81338,TIGRFAM_domain:TIGR00861,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 49973512 49973512 G A 1 0 0 0 0 0 0 0 1 953 1335 47 3 3 AQP6 12 49973512 Silent SNP G C3N-00217_T 941488 49973512 83301797 375 12145 TFCP2 0 . GRCh38 12 51104179 51104179 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.942A>G p.= p.P314P ENST00000257915 9/15 133 87 46 153 152 1 strelka-varscan-mutect TFCP2,synonymous_variant,p.=,ENST00000257915,NM_001173452.1,NM_005653.4;TFCP2,synonymous_variant,p.=,ENST00000548115,NM_001173453.1;TFCP2,synonymous_variant,p.=,ENST00000548108,;TFCP2,intron_variant,,ENST00000549867,;TFCP2,upstream_gene_variant,,ENST00000546822,;RP11-416A17.1,upstream_gene_variant,,ENST00000469738,; C ENST00000257915 Transcript synonymous_variant 1401/3546 942/1509 314/502 P ccA/ccG 1 -1 TFCP2 HGNC HGNC:11748 protein_coding YES CCDS8808.1 ENSP00000257915 Q12800 A0A024R120 UPI0000071CCA NM_001173452.1,NM_005653.4 9/15 hmmpanther:PTHR11037,hmmpanther:PTHR11037:SF11,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 51104179 51104179 T C 1 0 0 0 0 0 0 0 1 16228 1567 55 5 5 TFCP2 12 51104179 Silent SNP T C3N-00217_T 1130667 51104179 82171130 376 12146 GALNT6 0 . GRCh38 12 51379495 51379495 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.287C>A p.Pro96Gln p.P96Q ENST00000543196 2/11 200 178 22 184 184 0 strelka-varscan-mutect GALNT6,missense_variant,p.Pro96Gln,ENST00000543196,;GALNT6,missense_variant,p.Pro96Gln,ENST00000356317,NM_007210.3;GALNT6,missense_variant,p.Pro96Gln,ENST00000604381,;GALNT6,missense_variant,p.Pro96Gln,ENST00000604847,;GALNT6,downstream_gene_variant,,ENST00000603563,;GALNT6,downstream_gene_variant,,ENST00000605138,;GALNT6,downstream_gene_variant,,ENST00000605617,;GALNT6,downstream_gene_variant,,ENST00000603188,;GALNT6,downstream_gene_variant,,ENST00000604506,;GALNT6,downstream_gene_variant,,ENST00000605055,;GALNT6,downstream_gene_variant,,ENST00000604426,;GALNT6,downstream_gene_variant,,ENST00000603203,;GALNT6,downstream_gene_variant,,ENST00000605089,;GALNT6,downstream_gene_variant,,ENST00000605822,;GALNT6,downstream_gene_variant,,ENST00000605367,;GALNT6,downstream_gene_variant,,ENST00000605720,;GALNT6,downstream_gene_variant,,ENST00000603482,;GALNT6,missense_variant,p.Pro96Gln,ENST00000603641,; T ENST00000543196 Transcript missense_variant 493/5207 287/1869 96/622 P/Q cCa/cAa 1 -1 GALNT6 HGNC HGNC:4128 protein_coding YES CCDS8813.1 ENSP00000444171 Q8NCL4 UPI000013D726 tolerated(0.38) 2/11 hmmpanther:PTHR11675:SF58,hmmpanther:PTHR11675 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 51379495 51379495 G T 1 0 0 0 0 1 0 0 0 6088 1348 47 2 2 GALNT6 12 51379495 Missense_Mutation SNP G C3N-00217_T 275316 51379495 81895814 377 12147 KRT6B 0 . GRCh38 12 52447830 52447830 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1372C>A p.Leu458Met p.L458M ENST00000252252 7/9 570 392 178 514 513 1 strelka-varscan-mutect KRT6B,missense_variant,p.Leu458Met,ENST00000252252,NM_005555.3; T ENST00000252252 Transcript missense_variant 1420/2282 1372/1695 458/564 L/M Ctg/Atg 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 deleterious(0) 7/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Gene3D:1.20.5.170,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs1206313527 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 52447830 52447830 G T 1 0 0 0 0 1 0 0 0 8363 991 35 2 2 KRT6B 12 52447830 Missense_Mutation SNP G C3N-00217_T 1068335 52447830 80827479 378 12148 ESPL1 0 . GRCh38 12 53288307 53288307 + Silent SNP C C A C3N-00217_T C3N-00217_N C C c.4512C>A p.= p.I1504I ENST00000257934 19/31 107 73 34 88 88 0 strelka-varscan-mutect ESPL1,synonymous_variant,p.=,ENST00000257934,NM_012291.4;ESPL1,synonymous_variant,p.=,ENST00000552462,;ESPL1,3_prime_UTR_variant,,ENST00000552671,;ESPL1,non_coding_transcript_exon_variant,,ENST00000549154,;ESPL1,non_coding_transcript_exon_variant,,ENST00000553016,;ESPL1,non_coding_transcript_exon_variant,,ENST00000535123,;ESPL1,non_coding_transcript_exon_variant,,ENST00000552600,; A ENST00000257934 Transcript synonymous_variant 4603/6623 4512/6363 1504/2120 I atC/atA COSM4495326 1 1 ESPL1 HGNC HGNC:16856 protein_coding YES CCDS8852.1 ENSP00000257934 Q14674 UPI00003668C3 NM_012291.4 19/31 hmmpanther:PTHR12792 1 LOW 1 SNV 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 53288307 53288307 C A 1 0 0 0 0 0 0 0 1 5115 845 30 2 2 ESPL1 12 53288307 Silent SNP C C3N-00217_T 840477 53288307 79987002 379 12149 LRP1 0 . GRCh38 12 57194646 57194646 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.8138G>T p.Trp2713Leu p.W2713L ENST00000243077 50/89 95 65 30 69 69 0 strelka-varscan-mutect LRP1,missense_variant,p.Trp2713Leu,ENST00000243077,NM_002332.2;LRP1,downstream_gene_variant,,ENST00000554118,;MIR1228,downstream_gene_variant,,ENST00000408438,; T ENST00000243077 Transcript missense_variant 8604/14897 8138/13635 2713/4544 W/L tGg/tTg 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 deleterious(0) 50/89 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 57194646 57194646 G T 1 0 0 0 0 1 0 0 0 8846 1357 47 2 2 LRP1 12 57194646 Missense_Mutation SNP G C3N-00217_T 3906339 57194646 76080663 380 12150 SLC6A15 0 . GRCh38 12 84870659 84870659 + Silent SNP C C G novel C3N-00217_T C3N-00217_N C C c.1314G>C p.= p.G438G ENST00000266682 9/12 89 61 28 65 65 0 strelka-varscan-mutect SLC6A15,synonymous_variant,p.=,ENST00000266682,NM_182767.5;SLC6A15,synonymous_variant,p.=,ENST00000309283,;SLC6A15,synonymous_variant,p.=,ENST00000552192,NM_001146335.2;SLC6A15,downstream_gene_variant,,ENST00000551612,;SLC6A15,non_coding_transcript_exon_variant,,ENST00000551818,;SLC6A15,downstream_gene_variant,,ENST00000551388,;SLC6A15,upstream_gene_variant,,ENST00000548267,; G ENST00000266682 Transcript synonymous_variant 1856/4879 1314/2193 438/730 G ggG/ggC 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 9/12 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 84870659 84870659 C G 1 0 0 0 0 0 0 0 1 14961 842 30 4 4 SLC6A15 12 84870659 Silent SNP C C3N-00217_T 27676013 84870659 48404650 381 12151 ATP2B1 0 . GRCh38 12 89591259 89591259 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.3388G>A p.Glu1130Lys p.E1130K ENST00000428670 21/21 114 75 39 135 135 0 strelka-varscan-mutect ATP2B1,missense_variant,p.Glu1130Lys,ENST00000428670,;ATP2B1,missense_variant,p.Glu1130Lys,ENST00000261173,NM_001682.2;ATP2B1,missense_variant,p.Glu873Lys,ENST00000393164,;ATP2B1,missense_variant,p.Glu210Lys,ENST00000635033,;ATP2B1,missense_variant,p.Glu111Lys,ENST00000550716,;ATP2B1,3_prime_UTR_variant,,ENST00000359142,NM_001001323.1;RP11-981P6.1,intron_variant,,ENST00000552778,; T ENST00000428670 Transcript missense_variant 3845/7032 3388/3663 1130/1220 E/K Gaa/Aaa 1 -1 ATP2B1 HGNC HGNC:814 protein_coding YES CCDS9035.1 ENSP00000392043 P20020 A0A024RBC7 UPI000002A436 deleterious(0.04) 21/21 Pfam_domain:PF12424 MODERATE SNV 5 1 PASS rs922455554 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 89591259 89591259 C T 1 0 0 0 0 1 0 0 0 1292 835 29 3 3 ATP2B1 12 89591259 Missense_Mutation SNP C C3N-00217_T 4720600 89591259 43684050 382 12152 VEZT 0 . GRCh38 12 95257213 95257213 + Nonsense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.232A>T p.Lys78Ter p.K78* ENST00000436874 3/12 101 69 32 130 130 0 strelka-varscan-mutect VEZT,stop_gained,p.Lys78Ter,ENST00000436874,NM_017599.3;VEZT,stop_gained,p.Lys30Ter,ENST00000397792,;VEZT,stop_gained,p.Lys97Ter,ENST00000551472,;VEZT,stop_gained,p.Lys30Ter,ENST00000551311,;VEZT,stop_gained,p.Lys69Ter,ENST00000552821,;VEZT,intron_variant,,ENST00000549002,;VEZT,intron_variant,,ENST00000546445,;VEZT,non_coding_transcript_exon_variant,,ENST00000356859,;VEZT,non_coding_transcript_exon_variant,,ENST00000550106,;VEZT,non_coding_transcript_exon_variant,,ENST00000546398,;VEZT,non_coding_transcript_exon_variant,,ENST00000552626,;VEZT,non_coding_transcript_exon_variant,,ENST00000546409,;VEZT,non_coding_transcript_exon_variant,,ENST00000551746,;VEZT,non_coding_transcript_exon_variant,,ENST00000553063,;VEZT,non_coding_transcript_exon_variant,,ENST00000546365,;VEZT,non_coding_transcript_exon_variant,,ENST00000547894,;VEZT,non_coding_transcript_exon_variant,,ENST00000552031,;VEZT,intron_variant,,ENST00000551695,;VEZT,intron_variant,,ENST00000551356,;VEZT,intron_variant,,ENST00000551902,;VEZT,downstream_gene_variant,,ENST00000549589,;VEZT,stop_gained,p.Lys78Ter,ENST00000548245,;VEZT,3_prime_UTR_variant,,ENST00000547997,;VEZT,3_prime_UTR_variant,,ENST00000552660,;VEZT,3_prime_UTR_variant,,ENST00000551994,;VEZT,3_prime_UTR_variant,,ENST00000548455,;VEZT,3_prime_UTR_variant,,ENST00000550803,;VEZT,3_prime_UTR_variant,,ENST00000548822,;VEZT,3_prime_UTR_variant,,ENST00000551039,;VEZT,3_prime_UTR_variant,,ENST00000549624,;VEZT,3_prime_UTR_variant,,ENST00000547484,;VEZT,non_coding_transcript_exon_variant,,ENST00000549192,;VEZT,intron_variant,,ENST00000548838,;VEZT,intron_variant,,ENST00000547611,;VEZT,intron_variant,,ENST00000546557,;VEZT,intron_variant,,ENST00000548371,;VEZT,downstream_gene_variant,,ENST00000551792,; T ENST00000436874 Transcript stop_gained 337/4562 232/2340 78/779 K/* Aag/Tag 1 1 VEZT HGNC HGNC:18258 protein_coding YES CCDS44954.1 ENSP00000410083 Q9HBM0 UPI00001FB2EC NM_017599.3 3/12 hmmpanther:PTHR15989:SF5,hmmpanther:PTHR15989 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 95257213 95257213 A T 1 0 0 0 0 0 1 0 0 17702 363 13 4 4 VEZT 12 95257213 Nonsense_Mutation SNP A C3N-00217_T 5665954 95257213 38018096 383 12153 GAS2L3 0 . GRCh38 12 100624646 100624646 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1841C>T p.Ser614Phe p.S614F ENST00000547754 10/10 271 228 43 259 259 0 strelka-varscan-mutect GAS2L3,missense_variant,p.Ser510Phe,ENST00000537247,NM_001303131.1;GAS2L3,missense_variant,p.Ser614Phe,ENST00000547754,NM_174942.2;GAS2L3,missense_variant,p.Ser614Phe,ENST00000539410,;GAS2L3,missense_variant,p.Ser614Phe,ENST00000266754,NM_001303130.1;GAS2L3,missense_variant,p.Ser311Phe,ENST00000552854,; T ENST00000547754 Transcript missense_variant 2067/2340 1841/2085 614/694 S/F tCc/tTc 1 1 GAS2L3 HGNC HGNC:27475 protein_coding YES CCDS9079.1 ENSP00000448955 Q86XJ1 A0A024RBF4 UPI000000DA3B NM_174942.2 deleterious(0) 10/10 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 100624646 100624646 C T 1 0 0 0 0 1 0 0 0 6118 855 30 3 3 GAS2L3 12 100624646 Missense_Mutation SNP C C3N-00217_T 5367433 100624646 32650663 384 12154 DAO 0 . GRCh38 12 108897087 108897087 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.694G>T p.Gly232Trp p.G232W ENST00000228476 8/11 384 292 92 335 333 2 strelka-varscan-mutect DAO,missense_variant,p.Gly232Trp,ENST00000228476,NM_001917.4;DAO,missense_variant,p.Gly166Trp,ENST00000551281,;DAO,missense_variant,p.Gly109Trp,ENST00000547768,;DAO,downstream_gene_variant,,ENST00000547166,;DAO,splice_region_variant,,ENST00000549215,;DAO,splice_region_variant,,ENST00000547122,;DAO,upstream_gene_variant,,ENST00000546552,; T ENST00000228476 Transcript missense_variant,splice_region_variant 898/1756 694/1044 232/347 G/W Ggg/Tgg 1 1 DAO HGNC HGNC:2671 protein_coding YES CCDS9122.1 ENSP00000228476 P14920 A0A024RBI1 UPI0000130F5F NM_001917.4 deleterious(0) 8/11 Gene3D:3.30.9.10,Pfam_domain:PF01266,PIRSF_domain:PIRSF000189,hmmpanther:PTHR11530,hmmpanther:PTHR11530:SF11,Superfamily_domains:SSF54373 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 108897087 108897087 G T 1 0 0 0 0 1 0 0 0 4032 1014 35 2 2 DAO 12 108897087 Missense_Mutation SNP G C3N-00217_T 8272441 108897087 24378222 385 12155 MVK 0 . GRCh38 12 109579890 109579890 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.315G>T p.Glu105Asp p.E105D ENST00000539575 3/10 567 400 167 488 487 1 strelka-varscan-mutect MVK,missense_variant,p.Glu105Asp,ENST00000539575,;MVK,missense_variant,p.Glu105Asp,ENST00000625889,;MVK,missense_variant,p.Glu105Asp,ENST00000228510,NM_000431.3,NM_001114185.2;MVK,missense_variant,p.Glu105Asp,ENST00000392727,NM_001301182.1;MVK,missense_variant,p.Glu105Asp,ENST00000546277,;MVK,missense_variant,p.Glu105Asp,ENST00000539335,;MVK,intron_variant,,ENST00000636996,;MVK,intron_variant,,ENST00000629016,;MVK,intron_variant,,ENST00000539696,;MVK,intron_variant,,ENST00000535044,;MVK,3_prime_UTR_variant,,ENST00000537237,;MVK,intron_variant,,ENST00000447878,;MVK,intron_variant,,ENST00000636529,;MVK,intron_variant,,ENST00000545774,;MVK,upstream_gene_variant,,ENST00000545516,; T ENST00000539575 Transcript missense_variant 331/2747 315/1191 105/396 E/D gaG/gaT 1 1 MVK HGNC HGNC:7530 protein_coding YES CCDS9132.1 ENSP00000443551 Q03426 B2RDU6 UPI000012DE5B tolerated(0.09) 3/10 hmmpanther:PTHR10457,hmmpanther:PTHR10457:SF4,Gene3D:3.30.230.10,TIGRFAM_domain:TIGR00549,Superfamily_domains:SSF54211 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 109579890 109579890 G T 1 0 0 0 0 1 0 0 0 9994 962 34 2 2 MVK 12 109579890 Missense_Mutation SNP G C3N-00217_T 682803 109579890 23695419 386 12156 RPH3A 0 . GRCh38 12 112868562 112868562 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.577G>C p.Glu193Gln p.E193Q ENST00000389385 8/22 148 95 53 111 111 0 strelka-varscan-mutect RPH3A,missense_variant,p.Glu193Gln,ENST00000389385,NM_001143854.1;RPH3A,missense_variant,p.Glu193Gln,ENST00000415485,;RPH3A,missense_variant,p.Glu189Gln,ENST00000551052,NM_014954.3;RPH3A,missense_variant,p.Glu193Gln,ENST00000543106,;RPH3A,missense_variant,p.Glu144Gln,ENST00000548866,;RPH3A,downstream_gene_variant,,ENST00000551593,;RPH3A,downstream_gene_variant,,ENST00000547728,;RPH3A,downstream_gene_variant,,ENST00000550901,;RPH3A,downstream_gene_variant,,ENST00000551198,;RPH3A,downstream_gene_variant,,ENST00000552667,;RPH3A,downstream_gene_variant,,ENST00000548197,;RPH3A,downstream_gene_variant,,ENST00000553114,;RPH3A,downstream_gene_variant,,ENST00000546703,;RPH3A,downstream_gene_variant,,ENST00000547840,;RPH3A,downstream_gene_variant,,ENST00000551748,;RPH3A,downstream_gene_variant,,ENST00000549769,;RPH3A,downstream_gene_variant,,ENST00000547686,;RPH3A,non_coding_transcript_exon_variant,,ENST00000549913,;RPH3A,non_coding_transcript_exon_variant,,ENST00000547222,;RPH3A,downstream_gene_variant,,ENST00000552679,;RPH3A,downstream_gene_variant,,ENST00000547099,; C ENST00000389385 Transcript missense_variant 1074/4679 577/2085 193/694 E/Q Gag/Cag 1 1 RPH3A HGNC HGNC:17056 protein_coding YES CCDS44979.1 ENSP00000374036 Q9Y2J0 UPI000013456D NM_001143854.1 tolerated(0.14) 8/22 Low_complexity_(Seg):seg,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 112868562 112868562 G C 1 0 0 0 0 1 0 0 0 13803 1291 45 4 4 RPH3A 12 112868562 Missense_Mutation SNP G C3N-00217_T 3288672 112868562 20406747 387 12157 RPH3A 0 . GRCh38 12 112883356 112883356 + Missense_Mutation SNP G G T rs35555961 C3N-00217_T C3N-00217_N G G c.1390G>T p.Val464Leu p.V464L ENST00000389385 16/22 304 226 78 273 271 2 strelka-varscan-mutect RPH3A,missense_variant,p.Val464Leu,ENST00000389385,NM_001143854.1;RPH3A,missense_variant,p.Val464Leu,ENST00000415485,;RPH3A,missense_variant,p.Val460Leu,ENST00000551052,NM_014954.3;RPH3A,missense_variant,p.Val464Leu,ENST00000543106,;RPH3A,missense_variant,p.Val415Leu,ENST00000548866,;RPH3A,non_coding_transcript_exon_variant,,ENST00000549913,;RPH3A,downstream_gene_variant,,ENST00000552755,;RPH3A,upstream_gene_variant,,ENST00000546687,; T ENST00000389385 Transcript missense_variant 1887/4679 1390/2085 464/694 V/L Gtg/Ttg rs35555961,COSM4978270 1 1 RPH3A HGNC HGNC:17056 protein_coding YES CCDS44979.1 ENSP00000374036 Q9Y2J0 UPI000013456D NM_001143854.1 deleterious(0.02) 16/22 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs35555961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 112883356 112883356 G T 1 0 0 0 0 1 0 0 0 13803 1145 40 1 1 RPH3A 12 112883356 Missense_Mutation SNP G C3N-00217_T 14794 112883356 20391953 388 12158 GJA3 0 . GRCh38 13 20142941 20142941 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.348G>A p.= p.K116K ENST00000241125 2/2 301 203 98 210 210 0 strelka-varscan-mutect GJA3,synonymous_variant,p.=,ENST00000241125,NM_021954.3; T ENST00000241125 Transcript synonymous_variant 525/5211 348/1308 116/435 K aaG/aaA 1 -1 GJA3 HGNC HGNC:4277 protein_coding YES CCDS9289.1 ENSP00000241125 Q9Y6H8 UPI0000052BDE NM_021954.3 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11984:SF12,hmmpanther:PTHR11984,Gene3D:2zw3A00,Pfam_domain:PF00029 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 20142941 20142941 C T 1 0 0 0 0 0 0 0 1 6282 912 32 3 3 GJA3 13 20142941 Silent SNP C C3N-00217_T 20142941 94221387 389 12159 SACS 0 . GRCh38 13 23371117 23371117 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.220C>T p.Leu74Phe p.L74F ENST00000382292 3/9 65 61 4 71 71 0 varscan-mutect SACS,missense_variant,p.Leu74Phe,ENST00000382292,NM_014363.5;SACS,intron_variant,,ENST00000402364,NM_001278055.1;SACS,upstream_gene_variant,,ENST00000455470,;RPLP1P13,upstream_gene_variant,,ENST00000434567,; A ENST00000382292 Transcript missense_variant 494/15324 220/13740 74/4579 L/F Ctt/Ttt 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 deleterious_low_confidence(0.01) 3/9 MODERATE 1 SNV 5 1 PASS rs1176497702 . 0 208 2 0 0 0 0 0 -10.09207 1 1 1 1 0 A 3 1 43 23371117 23371117 G A 1 0 0 0 0 1 0 0 0 14063 942 33 3 3 SACS 13 23371117 Missense_Mutation SNP G C3N-00217_T 3228176 23371117 90993211 390 12160 ATP8A2 0 . GRCh38 13 25540334 25540334 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.597G>A p.Met199Ile p.M199I ENST00000381655 8/37 151 107 44 197 197 0 strelka-varscan-mutect ATP8A2,missense_variant,p.Met199Ile,ENST00000381655,NM_016529.4;ATP8A2,missense_variant,p.Met159Ile,ENST00000255283,;ATP8A2,missense_variant,p.Met39Ile,ENST00000281620,; A ENST00000381655 Transcript missense_variant 739/9575 597/3567 199/1188 M/I atG/atA 1 1 ATP8A2 HGNC HGNC:13533 protein_coding YES CCDS41873.1 ENSP00000371070 Q9NTI2 UPI0000229592 NM_016529.4 tolerated(0.08) 8/37 hmmpanther:PTHR24092:SF66,hmmpanther:PTHR24092,Gene3D:2.70.150.10,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049471 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 25540334 25540334 G A 1 0 0 0 0 1 0 0 0 1346 1377 48 3 3 ATP8A2 13 25540334 Missense_Mutation SNP G C3N-00217_T 2169217 25540334 88823994 391 12161 INTS6 0 . GRCh38 13 51374270 51374270 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2042G>A p.Gly681Glu p.G681E ENST00000311234 15/18 361 298 63 330 330 0 strelka-mutect INTS6,missense_variant,p.Gly668Glu,ENST00000398119,NM_001039937.1;INTS6,missense_variant,p.Gly681Glu,ENST00000311234,NM_012141.2;INTS6,missense_variant,p.Gly503Glu,ENST00000497989,NM_001306091.1;INTS6,missense_variant,p.Gly365Glu,ENST00000490542,;INTS6,3_prime_UTR_variant,,ENST00000469430,;INTS6,non_coding_transcript_exon_variant,,ENST00000483441,; T ENST00000311234 Transcript missense_variant 2515/3662 2042/2664 681/887 G/E gGa/gAa 1 -1 INTS6 HGNC HGNC:14879 protein_coding YES CCDS9428.1 ENSP00000310260 Q9UL03 A0A024RDU0 UPI0000030C84 NM_012141.2 tolerated(0.41) 15/18 hmmpanther:PTHR12957:SF23,hmmpanther:PTHR12957 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 51374270 51374270 C T 1 0 0 0 0 1 0 0 0 7684 855 30 3 3 INTS6 13 51374270 Missense_Mutation SNP C C3N-00217_T 25833936 51374270 62990058 392 12162 ATP7B 0 . GRCh38 13 51974999 51974999 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.221A>T p.Lys74Met p.K74M ENST00000242839 2/21 270 136 134 118 118 0 strelka-varscan-mutect ATP7B,missense_variant,p.Lys74Met,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Lys74Met,ENST00000448424,;ATP7B,missense_variant,p.Lys74Met,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Lys74Met,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Lys74Met,ENST00000634844,;ATP7B,missense_variant,p.Lys74Met,ENST00000418097,;ATP7B,missense_variant,p.Lys74Met,ENST00000400370,;ATP7B,non_coding_transcript_exon_variant,,ENST00000482841,;ATP7B,intron_variant,,ENST00000635406,;ATP7B,upstream_gene_variant,,ENST00000483772,;ATP7B,missense_variant,p.Lys74Met,ENST00000634308,;ATP7B,upstream_gene_variant,,ENST00000634620,; A ENST00000242839 Transcript missense_variant 378/6638 221/4398 74/1465 K/M aAg/aTg 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 tolerated(0.05) 2/21 PROSITE_profiles:PS50846,PROSITE_patterns:PS01047,Pfam_domain:PF00403,Gene3D:3.30.70.100,TIGRFAM_domain:TIGR00003,Superfamily_domains:SSF55008 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 51974999 51974999 T A 1 0 0 0 0 1 0 0 0 1344 1609 56 4 4 ATP7B 13 51974999 Missense_Mutation SNP T C3N-00217_T 600729 51974999 62389329 393 12163 NEK3 0 . GRCh38 13 52151371 52151371 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.415G>A p.Gly139Arg p.G139R ENST00000618534 6/16 267 218 49 258 258 0 strelka-varscan-mutect NEK3,missense_variant,p.Gly139Arg,ENST00000618534,NM_152720.2;NEK3,missense_variant,p.Gly139Arg,ENST00000610828,NM_002498.2;NEK3,missense_variant,p.Gly139Arg,ENST00000611833,NM_001146099.1;NEK3,missense_variant,p.Gly139Arg,ENST00000620675,;NEK3,downstream_gene_variant,,ENST00000550841,;NEK3,downstream_gene_variant,,ENST00000629912,;NEK3,missense_variant,p.Gly139Arg,ENST00000617054,;NEK3,3_prime_UTR_variant,,ENST00000551355,;NEK3,non_coding_transcript_exon_variant,,ENST00000552973,; T ENST00000618534 Transcript missense_variant 810/2414 415/1521 139/506 G/R Gga/Aga 1 -1 NEK3 HGNC HGNC:7746 protein_coding YES CCDS73576.1 ENSP00000484443 P51956 UPI000012FF28 NM_152720.2 deleterious(0) 6/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24362:SF7,hmmpanther:PTHR24362,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 52151371 52151371 C T 1 0 0 0 0 1 0 0 0 10353 603 21 3 3 NEK3 13 52151371 Missense_Mutation SNP C C3N-00217_T 176372 52151371 62212957 394 12164 PCDH17 0 . GRCh38 13 57724754 57724754 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.2940T>A p.= p.A980A ENST00000377918 4/4 327 174 153 273 273 0 strelka-varscan-mutect PCDH17,synonymous_variant,p.=,ENST00000377918,NM_001040429.2;PCDH17,synonymous_variant,p.=,ENST00000612954,;PCDH17,downstream_gene_variant,,ENST00000615375,;PCDH17,3_prime_UTR_variant,,ENST00000484979,; A ENST00000377918 Transcript synonymous_variant 3675/8232 2940/3480 980/1159 A gcT/gcA 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41 LOW 1 SNV 1 1 PASS rs969507075 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 57724754 57724754 T A 1 0 0 0 0 0 0 0 1 11599 1509 53 4 4 PCDH17 13 57724754 Silent SNP T C3N-00217_T 5573383 57724754 56639574 395 12165 KLF12 0 . GRCh38 13 73846307 73846307 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.190G>T p.Glu64Ter p.E64* ENST00000377669 3/7 290 146 144 206 204 2 strelka-varscan-mutect KLF12,stop_gained,p.Glu64Ter,ENST00000377669,NM_007249.4;RP11-157H4.1,upstream_gene_variant,,ENST00000625150,;KLF12,non_coding_transcript_exon_variant,,ENST00000472022,; A ENST00000377669 Transcript stop_gained 217/10637 190/1209 64/402 E/* Gag/Tag 1 -1 KLF12 HGNC HGNC:6346 protein_coding YES CCDS9449.1 ENSP00000366897 Q9Y4X4 UPI000013D144 NM_007249.4 3/7 hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF60 HIGH 1 SNV 1 1 PASS rs1173461029 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 73846307 73846307 C A 1 0 0 0 0 0 1 0 0 8205 864 30 2 2 KLF12 13 73846307 Nonsense_Mutation SNP C C3N-00217_T 16121553 73846307 40518021 396 12166 SLITRK1 0 . GRCh38 13 83880082 83880082 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.1426C>G p.Leu476Val p.L476V ENST00000377084 1/1 166 79 87 154 154 0 strelka-varscan-mutect SLITRK1,missense_variant,p.Leu476Val,ENST00000377084,NM_052910.2,NM_001281503.1; C ENST00000377084 Transcript missense_variant 2312/5189 1426/2091 476/696 L/V Ctc/Gtc COSM1706886,COSM4048655 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 deleterious(0.04) 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,Low_complexity_(Seg):seg,SMART_domains:SM00369,Superfamily_domains:SSF52058 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 83880082 83880082 G C 1 0 0 0 0 1 0 0 0 15033 1000 35 4 4 SLITRK1 13 83880082 Missense_Mutation SNP G C3N-00217_T 10033775 83880082 30484246 397 12167 HS6ST3 0 . GRCh38 13 96091064 96091064 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.202C>A p.= p.R68R ENST00000376705 1/2 52 16 36 24 24 0 strelka-varscan-mutect HS6ST3,synonymous_variant,p.=,ENST00000376705,NM_153456.3; A ENST00000376705 Transcript synonymous_variant 226/7804 202/1416 68/471 R Cgg/Agg 1 1 HS6ST3 HGNC HGNC:19134 protein_coding YES CCDS9481.1 ENSP00000365895 Q8IZP7 UPI00001AF933 NM_153456.3 1/2 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 2 201 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 96091064 96091064 C A 1 0 0 0 0 0 0 0 1 7266 759 27 1 1 HS6ST3 13 96091064 Silent SNP C C3N-00217_T 12210982 96091064 18273264 398 12168 TMTC4 0 . GRCh38 13 100635072 100635072 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.1326G>T p.= p.V442V ENST00000342624 11/19 178 134 44 134 134 0 strelka-varscan-mutect TMTC4,synonymous_variant,p.=,ENST00000342624,NM_032813.3;TMTC4,synonymous_variant,p.=,ENST00000376234,NM_001079669.2;TMTC4,synonymous_variant,p.=,ENST00000328767,NM_001286453.1;TMTC4,non_coding_transcript_exon_variant,,ENST00000462211,;TMTC4,non_coding_transcript_exon_variant,,ENST00000478272,;TMTC4,non_coding_transcript_exon_variant,,ENST00000496511,;TMTC4,non_coding_transcript_exon_variant,,ENST00000489713,; A ENST00000342624 Transcript synonymous_variant 1585/3602 1326/2283 442/760 V gtG/gtT 1 -1 TMTC4 HGNC HGNC:25904 protein_coding YES CCDS9497.2 ENSP00000343871 Q5T4D3 UPI000004B63E NM_032813.3 11/19 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF440,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 100635072 100635072 C A 1 0 0 0 0 0 0 0 1 16737 697 25 2 2 TMTC4 13 100635072 Silent SNP C C3N-00217_T 4544008 100635072 13729256 399 12169 NALCN 0 . GRCh38 13 101283956 101283956 + Missense_Mutation SNP C C G rs780182598 C3N-00217_T C3N-00217_N C C c.1111G>C p.Gly371Arg p.G371R ENST00000251127 10/44 143 114 29 174 174 0 strelka-varscan-mutect NALCN,missense_variant,p.Gly371Arg,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; G ENST00000251127 Transcript missense_variant 1193/6818 1111/5217 371/1738 G/R Gga/Cga rs780182598 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 deleterious(0.03) 10/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214 MODERATE 1 SNV 1 1 PASS rs780182598 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 101283956 101283956 C G 1 0 0 0 0 1 0 0 0 10155 632 22 4 4 NALCN 13 101283956 Missense_Mutation SNP C C3N-00217_T 648884 101283956 13080372 400 12170 NALCN 0 . GRCh38 13 101395221 101395221 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.253G>T p.Glu85Ter p.E85* ENST00000251127 3/44 92 72 20 141 140 1 strelka-varscan-mutect NALCN,stop_gained,p.Glu85Ter,ENST00000251127,NM_052867.2;NALCN,stop_gained,p.Glu85Ter,ENST00000376200,;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; A ENST00000251127 Transcript stop_gained 335/6818 253/5217 85/1738 E/* Gag/Tag 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 3/44 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 101395221 101395221 C A 1 0 0 0 0 0 1 0 0 10155 922 32 2 2 NALCN 13 101395221 Nonsense_Mutation SNP C C3N-00217_T 111265 101395221 12969107 401 12171 CCDC168 0 . GRCh38 13 102749094 102749094 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1603G>A p.Asp535Asn p.D535N ENST00000322527 4/4 80 42 38 84 84 0 strelka-varscan-mutect CCDC168,missense_variant,p.Asp535Asn,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; T ENST00000322527 Transcript missense_variant 1741/21466 1603/21246 535/7081 D/N Gat/Aat 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.17) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 102749094 102749094 C T 1 0 0 0 0 1 0 0 0 2484 913 32 3 3 CCDC168 13 102749094 Missense_Mutation SNP C C3N-00217_T 1353873 102749094 11615234 402 12172 SLC10A2 0 . GRCh38 13 103051309 103051309 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.709G>T p.Gly237Cys p.G237C ENST00000245312 4/6 469 349 120 326 325 1 strelka-varscan-mutect SLC10A2,missense_variant,p.Gly237Cys,ENST00000245312,NM_000452.2; A ENST00000245312 Transcript missense_variant 1306/3779 709/1047 237/348 G/C Ggt/Tgt 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 deleterious(0) 4/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 103051309 103051309 C A 1 0 0 0 0 1 0 0 0 14639 623 22 2 2 SLC10A2 13 103051309 Missense_Mutation SNP C C3N-00217_T 302215 103051309 11313019 403 12173 MYO16 0 . GRCh38 13 108806801 108806801 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.864C>A p.= p.G288G ENST00000457511 7/35 201 153 48 173 173 0 strelka-varscan-mutect MYO16,synonymous_variant,p.=,ENST00000457511,NM_001198950.1;MYO16,synonymous_variant,p.=,ENST00000356711,NM_015011.1;MYO16,synonymous_variant,p.=,ENST00000357550,;MYO16,synonymous_variant,p.=,ENST00000251041,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,; A ENST00000457511 Transcript synonymous_variant 1486/7436 864/5643 288/1880 G ggC/ggA 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 7/35 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999669 1 1 1 0 A 2 1 43 108806801 108806801 C A 1 0 0 0 0 0 0 0 1 10065 753 26 2 2 MYO16 13 108806801 Silent SNP C C3N-00217_T 5755492 108806801 5557527 404 12174 COL4A1 0 . GRCh38 13 110167215 110167215 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.3892C>A p.Pro1298Thr p.P1298T ENST00000375820 44/52 522 394 128 368 367 1 strelka-varscan-mutect COL4A1,missense_variant,p.Pro1298Thr,ENST00000375820,NM_001845.5;COL4A1,upstream_gene_variant,,ENST00000467182,;COL4A1,upstream_gene_variant,,ENST00000474391,; T ENST00000375820 Transcript missense_variant 4014/6532 3892/5010 1298/1669 P/T Cca/Aca 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0) 44/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 110167215 110167215 G T 1 0 0 0 0 1 0 0 0 3478 1174 41 2 2 COL4A1 13 110167215 Missense_Mutation SNP G C3N-00217_T 1360414 110167215 4197113 405 12175 COL4A1 0 . GRCh38 13 110173968 110173968 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.3437C>G p.Pro1146Arg p.P1146R ENST00000375820 40/52 466 283 183 314 314 0 strelka-varscan-mutect COL4A1,missense_variant,p.Pro1146Arg,ENST00000375820,NM_001845.5; C ENST00000375820 Transcript missense_variant 3559/6532 3437/5010 1146/1669 P/R cCa/cGa 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 tolerated(0.06) 40/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 110173968 110173968 G C 1 0 0 0 0 1 0 0 0 3478 1348 47 4 4 COL4A1 13 110173968 Missense_Mutation SNP G C3N-00217_T 6753 110173968 4190360 406 12176 OR4K13 0 . GRCh38 14 20034086 20034086 + Missense_Mutation SNP C C A rs767834956 C3N-00217_T C3N-00217_N C C c.673G>T p.Val225Phe p.V225F ENST00000315693 1/1 354 159 195 336 335 1 strelka-varscan-mutect OR4K13,missense_variant,p.Val225Phe,ENST00000315693,NM_001004714.1; A ENST00000315693 Transcript missense_variant 675/917 673/915 225/304 V/F Gtt/Ttt rs767834956 1 -1 OR4K13 HGNC HGNC:15351 protein_coding YES CCDS32028.1 ENSP00000319322 Q8NH42 A0A126GVS2 UPI0000041CEB NM_001004714.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF123,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs767834956 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 20034086 20034086 C A 1 0 0 0 0 1 0 0 0 11145 565 20 2 2 OR4K13 14 20034086 Missense_Mutation SNP C C3N-00217_T 20034086 87009632 407 12177 OR11G2 0 . GRCh38 14 20198275 20198275 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.940C>G p.Leu314Val p.L314V ENST00000357366 1/1 147 129 18 160 160 0 strelka-varscan-mutect OR11G2,missense_variant,p.Leu314Val,ENST00000357366,NM_001005503.1; G ENST00000357366 Transcript missense_variant 940/1111 940/1038 314/345 L/V Ctg/Gtg 1 1 OR11G2 HGNC HGNC:15346 protein_coding YES CCDS32032.1 ENSP00000349930 Q8NGC1 UPI000015F241 NM_001005503.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF183,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1220683434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 20198275 20198275 C G 1 0 0 0 0 1 0 0 0 11001 912 32 4 4 OR11G2 14 20198275 Missense_Mutation SNP C C3N-00217_T 164189 20198275 86845443 408 12178 CHD8 0 . GRCh38 14 21393945 21393945 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.5850G>A p.Met1950Ile p.M1950I ENST00000399982 31/37 209 148 61 194 194 0 strelka-varscan-mutect CHD8,missense_variant,p.Met1950Ile,ENST00000399982,NM_001170629.1;CHD8,missense_variant,p.Met1950Ile,ENST00000557364,;CHD8,missense_variant,p.Met1671Ile,ENST00000430710,NM_020920.3;CHD8,upstream_gene_variant,,ENST00000553870,;SNORD8,downstream_gene_variant,,ENST00000363915,;SNORD9,upstream_gene_variant,,ENST00000362566,;CHD8,downstream_gene_variant,,ENST00000555962,;CHD8,non_coding_transcript_exon_variant,,ENST00000555301,;CHD8,downstream_gene_variant,,ENST00000557329,;RP11-689J19.1,upstream_gene_variant,,ENST00000480068,; T ENST00000399982 Transcript missense_variant 5915/8229 5850/7746 1950/2581 M/I atG/atA 1 -1 CHD8 HGNC HGNC:20153 protein_coding YES CCDS53885.1 ENSP00000382863 Q9HCK8 UPI00002375B9 NM_001170629.1 deleterious(0.01) 31/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 21393945 21393945 C T 1 0 0 0 0 1 0 0 0 3090 710 25 3 3 CHD8 14 21393945 Missense_Mutation SNP C C3N-00217_T 1195670 21393945 85649773 409 12179 NPAS3 0 . GRCh38 14 33215320 33215320 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.279C>T p.= p.I93I ENST00000356141 3/12 451 359 92 322 322 0 strelka-varscan-mutect NPAS3,synonymous_variant,p.=,ENST00000346562,NM_022123.2;NPAS3,synonymous_variant,p.=,ENST00000548645,NM_001165893.1;NPAS3,synonymous_variant,p.=,ENST00000551492,;NPAS3,synonymous_variant,p.=,ENST00000356141,NM_001164749.1;NPAS3,synonymous_variant,p.=,ENST00000357798,NM_173159.2;NPAS3,synonymous_variant,p.=,ENST00000551634,;NPAS3,synonymous_variant,p.=,ENST00000546849,;NPAS3,5_prime_UTR_variant,,ENST00000547068,;NPAS3,5_prime_UTR_variant,,ENST00000551008,;NPAS3,non_coding_transcript_exon_variant,,ENST00000549770,; T ENST00000356141 Transcript synonymous_variant 279/2802 279/2802 93/933 I atC/atT 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 3/12 PROSITE_profiles:PS50888,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 33215320 33215320 C T 1 0 0 0 0 0 0 0 1 10612 816 29 3 3 NPAS3 14 33215320 Silent SNP C C3N-00217_T 11821375 33215320 73828398 410 12180 VRTN 0 . GRCh38 14 74357180 74357180 + Missense_Mutation SNP G G T rs773509797 C3N-00217_T C3N-00217_N G G c.397G>T p.Val133Leu p.V133L ENST00000256362 2/2 141 111 30 71 71 0 strelka-varscan-mutect VRTN,missense_variant,p.Val133Leu,ENST00000256362,NM_018228.2;VRTN,downstream_gene_variant,,ENST00000557177,; T ENST00000256362 Transcript missense_variant 638/3466 397/2109 133/702 V/L Gtg/Ttg rs773509797,COSM32986 1 1 VRTN HGNC HGNC:20223 protein_coding YES CCDS9830.1 ENSP00000256362 Q9H8Y1 UPI00000737D5 NM_018228.2 tolerated(0.1) 2/2 hmmpanther:PTHR16081,hmmpanther:PTHR16081:SF0 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773509797 . 0 196 12 2 0 0 0 0 -20 0.999173 1 1 1 0 T 3 4 43 74357180 74357180 G T 1 0 0 0 0 1 0 0 0 17771 1145 40 1 1 VRTN 14 74357180 Missense_Mutation SNP G C3N-00217_T 41141860 74357180 32686538 411 12181 STON2 0 . GRCh38 14 81278066 81278066 + Missense_Mutation SNP G G C rs562599312 C3N-00217_T C3N-00217_N G G c.1245C>G p.His415Gln p.H415Q ENST00000555447 6/8 374 135 239 215 214 1 strelka-varscan-mutect STON2,missense_variant,p.His415Gln,ENST00000555447,NM_001256430.1;STON2,missense_variant,p.His415Gln,ENST00000267540,NM_033104.3;STON2,missense_variant,p.His415Gln,ENST00000614646,;STON2,upstream_gene_variant,,ENST00000553821,;STON2,downstream_gene_variant,,ENST00000556280,;STON2,non_coding_transcript_exon_variant,,ENST00000555284,; C ENST00000555447 Transcript missense_variant 1658/4302 1245/2763 415/920 H/Q caC/caG rs562599312 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 tolerated(0.29) 6/8 PIRSF_domain:PIRSF037099 MODERATE 1 SNV 1 1 PASS rs562599312 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 81278066 81278066 G C 1 0 0 0 0 1 0 0 0 15696 1252 44 4 4 STON2 14 81278066 Missense_Mutation SNP G C3N-00217_T 6920886 81278066 25765652 412 12182 GALC 0 . GRCh38 14 87968348 87968348 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.895G>T p.Gly299Cys p.G299C ENST00000261304 8/17 178 66 112 118 117 1 strelka-varscan-mutect GALC,missense_variant,p.Gly299Cys,ENST00000261304,NM_000153.3;GALC,missense_variant,p.Gly273Cys,ENST00000393569,NM_001201402.1;GALC,missense_variant,p.Gly243Cys,ENST00000544807,;GALC,missense_variant,p.Gly276Cys,ENST00000393568,NM_001201401.1;GALC,missense_variant,p.Gly296Cys,ENST00000622264,;GALC,upstream_gene_variant,,ENST00000557520,;GALC,missense_variant,p.Gly88Cys,ENST00000555000,;GALC,3_prime_UTR_variant,,ENST00000557316,;GALC,non_coding_transcript_exon_variant,,ENST00000474294,;GALC,downstream_gene_variant,,ENST00000477716,; A ENST00000261304 Transcript missense_variant 1002/3883 895/2058 299/685 G/C Ggc/Tgc 1 -1 GALC HGNC HGNC:4115 protein_coding YES CCDS9878.2 ENSP00000261304 A0A0A0MQV0 UPI00001FD982 NM_000153.3 deleterious(0) 8/17 Gene3D:3.20.20.80,Pfam_domain:PF02057,hmmpanther:PTHR15172,hmmpanther:PTHR15172:SF1,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 43 87968348 87968348 C A 1 0 0 0 0 1 0 0 0 6069 594 21 2 2 GALC 14 87968348 Missense_Mutation SNP C C3N-00217_T 6690282 87968348 19075370 413 12183 LGMN 0 . GRCh38 14 92704680 92704680 + Missense_Mutation SNP C C A rs149227402 C3N-00217_T C3N-00217_N C C c.1219G>T p.Val407Leu p.V407L ENST00000393218 14/15 161 150 11 123 123 0 strelka-varscan-mutect LGMN,missense_variant,p.Val407Leu,ENST00000393218,NM_001008530.2;LGMN,missense_variant,p.Val407Leu,ENST00000334869,NM_005606.6;LGMN,missense_variant,p.Val350Leu,ENST00000557434,;LGMN,intron_variant,,ENST00000555699,;LGMN,intron_variant,,ENST00000555169,;LGMN,3_prime_UTR_variant,,ENST00000557609,;LGMN,non_coding_transcript_exon_variant,,ENST00000556790,;LGMN,downstream_gene_variant,,ENST00000557725,; A ENST00000393218 Transcript missense_variant 1557/2115 1219/1302 407/433 V/L Gtg/Ttg rs149227402 1 -1 LGMN HGNC HGNC:9472 protein_coding YES CCDS9904.1 ENSP00000376911 Q99538 Q53XC6 UPI000000CC65 NM_001008530.2 tolerated(0.07) 14/15 hmmpanther:PTHR12000:SF3,hmmpanther:PTHR12000,PIRSF_domain:PIRSF500139,PIRSF_domain:PIRSF019663 MODERATE 1 SNV 1 1 PASS rs149227402 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 92704680 92704680 C A 1 0 0 0 0 1 0 0 0 8665 536 19 1 1 LGMN 14 92704680 Missense_Mutation SNP C C3N-00217_T 4736332 92704680 14339038 414 12184 AHNAK2 0 . GRCh38 14 104944612 104944612 + Silent SNP G G T rs768951245 C3N-00217_T C3N-00217_N G G c.10839C>A p.= p.A3613A ENST00000333244 7/7 616 212 404 403 402 1 strelka-varscan-mutect AHNAK2,synonymous_variant,p.=,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; T ENST00000333244 Transcript synonymous_variant 10959/18254 10839/17388 3613/5795 A gcC/gcA rs768951245 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 LOW 1 SNV 5 1 PASS rs768951245 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 104944612 104944612 G T 1 0 0 0 0 0 0 0 1 492 1335 47 2 2 AHNAK2 14 104944612 Silent SNP G C3N-00217_T 12239932 104944612 2099106 415 12185 AHNAK2 0 . GRCh38 14 104950755 104950755 + Missense_Mutation SNP C C A rs776678150 C3N-00217_T C3N-00217_N C C c.4696G>T p.Val1566Leu p.V1566L ENST00000333244 7/7 825 726 99 461 461 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Val1566Leu,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; A ENST00000333244 Transcript missense_variant 4816/18254 4696/17388 1566/5795 V/L Gtg/Ttg rs776678150 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.66) 7/7 MODERATE 1 SNV 5 1 PASS rs776678150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 104950755 104950755 C A 1 0 0 0 0 1 0 0 0 492 478 17 2 2 AHNAK2 14 104950755 Missense_Mutation SNP C C3N-00217_T 6143 104950755 2092963 416 12186 UBE3A 0 . GRCh38 15 25375499 25375499 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.336A>C p.Lys112Asn p.K112N ENST00000397954 6/14 157 128 29 226 226 0 strelka-varscan-mutect UBE3A,missense_variant,p.Lys89Asn,ENST00000635914,;UBE3A,missense_variant,p.Lys89Asn,ENST00000638155,;UBE3A,missense_variant,p.Lys89Asn,ENST00000438097,;UBE3A,missense_variant,p.Lys89Asn,ENST00000638011,;UBE3A,missense_variant,p.Lys109Asn,ENST00000614096,NM_130839.2;UBE3A,missense_variant,p.Lys109Asn,ENST00000637886,;UBE3A,missense_variant,p.Lys89Asn,ENST00000630424,;UBE3A,missense_variant,p.Lys89Asn,ENST00000232165,NM_130838.1;UBE3A,missense_variant,p.Lys89Asn,ENST00000625778,;UBE3A,missense_variant,p.Lys89Asn,ENST00000566215,;UBE3A,missense_variant,p.Lys89Asn,ENST00000428984,;UBE3A,missense_variant,p.Lys112Asn,ENST00000397954,NM_000462.3;UBE3A,missense_variant,p.Lys109Asn,ENST00000630907,;UBE3A,missense_variant,p.Lys116Asn,ENST00000626068,;UBE3A,missense_variant,p.Lys109Asn,ENST00000628733,;UBE3A,downstream_gene_variant,,ENST00000630607,;UBE3A,downstream_gene_variant,,ENST00000629252,;UBE3A,downstream_gene_variant,,ENST00000628267,;UBE3A,downstream_gene_variant,,ENST00000629886,;UBE3A,downstream_gene_variant,,ENST00000628890,;SNHG14,intron_variant,,ENST00000554726,;SNHG14,downstream_gene_variant,,ENST00000453082,;UBE3A,non_coding_transcript_exon_variant,,ENST00000626793,; G ENST00000397954 Transcript missense_variant 581/2873 336/2628 112/875 K/N aaA/aaC 1 -1 UBE3A HGNC HGNC:12496 protein_coding YES CCDS45192.1 ENSP00000381045 Q05086 UPI0000161F3B NM_000462.3 tolerated(0.27) 6/14 hmmpanther:PTHR11254,PIRSF_domain:PIRSF037201 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 25375499 25375499 T G 1 0 0 0 0 1 0 0 0 17402 1838 64 5 5 UBE3A 15 25375499 Missense_Mutation SNP T C3N-00217_T 25375499 76615690 417 12187 GABRB3 0 . GRCh38 15 26621319 26621319 + Silent SNP C C T C3N-00217_T C3N-00217_N C C c.456G>A p.= p.G152G ENST00000311550 4/9 380 321 59 411 411 0 strelka-varscan-mutect GABRB3,synonymous_variant,p.=,ENST00000541819,;GABRB3,synonymous_variant,p.=,ENST00000622697,NM_001278631.1;GABRB3,synonymous_variant,p.=,ENST00000311550,NM_000814.5;GABRB3,synonymous_variant,p.=,ENST00000628124,NM_001191320.1;GABRB3,synonymous_variant,p.=,ENST00000636466,;GABRB3,synonymous_variant,p.=,ENST00000299267,NM_021912.4;GABRB3,synonymous_variant,p.=,ENST00000638099,;GABRB3,synonymous_variant,p.=,ENST00000400188,NM_001191321.2;GABRB3,synonymous_variant,p.=,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000556166,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,non_coding_transcript_exon_variant,,ENST00000636690,;GABRB3,synonymous_variant,p.=,ENST00000635994,;GABRB3,synonymous_variant,p.=,ENST00000556636,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;GABRB3,intron_variant,,ENST00000554556,; T ENST00000311550 Transcript synonymous_variant 568/5781 456/1422 152/473 G ggG/ggA COSM1152816,COSM1152817,COSM3401653,COSM3401654,COSM3401655,COSM960023 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 4/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 1,1,1,1,1,1 LOW 1 SNV 1 1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 26621319 26621319 C T 1 0 0 0 0 0 0 0 1 6039 753 26 3 3 GABRB3 15 26621319 Silent SNP C C3N-00217_T 1245820 26621319 75369870 418 12188 GABRA5 0 . GRCh38 15 26939956 26939956 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.756C>A p.His252Gln p.H252Q ENST00000335625 9/11 123 97 26 149 149 0 strelka-varscan-mutect GABRA5,missense_variant,p.His252Gln,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.His252Gln,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.His252Gln,ENST00000355395,;GABRB3,upstream_gene_variant,,ENST00000541819,;GABRA5,downstream_gene_variant,,ENST00000555182,; A ENST00000335625 Transcript missense_variant 1644/3251 756/1389 252/462 H/Q caC/caA 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0.03) 9/11 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR00252,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 26939956 26939956 C A 1 0 0 0 0 1 0 0 0 6035 506 18 2 2 GABRA5 15 26939956 Missense_Mutation SNP C C3N-00217_T 318637 26939956 75051233 419 12189 GABRG3 0 . GRCh38 15 27532814 27532814 + Missense_Mutation SNP G G T rs779933664 C3N-00217_T C3N-00217_N G G c.1337G>T p.Arg446Leu p.R446L ENST00000615808 10/10 249 194 55 229 229 0 strelka-varscan-mutect GABRG3,missense_variant,p.Arg446Leu,ENST00000615808,NM_033223.4;GABRG3,missense_variant,p.Arg267Leu,ENST00000333743,;GABRG3,downstream_gene_variant,,ENST00000451330,;RP11-100M12.3,intron_variant,,ENST00000556642,;RP11-100M12.3,downstream_gene_variant,,ENST00000557170,; T ENST00000615808 Transcript missense_variant 1591/10768 1337/1404 446/467 R/L cGg/cTg rs779933664 1 1 GABRG3 HGNC HGNC:4088 protein_coding YES CCDS45195.1 ENSP00000479113 Q99928 UPI000012AFCB NM_033223.4 deleterious(0) 10/10 Gene3D:1.20.58.390,Pfam_domain:PF02932,Prints_domain:PR00253,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF195,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs779933664 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 27532814 27532814 G T 1 0 0 0 0 1 0 0 0 6044 1116 39 1 1 GABRG3 15 27532814 Missense_Mutation SNP G C3N-00217_T 592858 27532814 74458375 420 12190 HERC2 0 . GRCh38 15 28144206 28144206 + Missense_Mutation SNP C C G rs149280444 C3N-00217_T C3N-00217_N C C c.11170G>C p.Val3724Leu p.V3724L ENST00000261609 73/93 175 152 23 191 191 0 strelka-mutect HERC2,missense_variant,p.Val3724Leu,ENST00000261609,NM_004667.5;HERC2,upstream_gene_variant,,ENST00000564519,; G ENST00000261609 Transcript missense_variant 11279/15337 11170/14505 3724/4834 V/L Gtc/Ctc rs149280444,COSM3732752 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 deleterious(0.04) 73/93 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs149280444 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 28144206 28144206 C G 1 0 0 0 0 1 0 0 0 6942 536 19 4 4 HERC2 15 28144206 Missense_Mutation SNP C C3N-00217_T 611392 28144206 73846983 421 12191 GOLGA8F 0 . GRCh38 15 28384158 28384158 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.639C>G p.Ser213Arg p.S213R ENST00000532622 9/19 76 30 46 69 69 0 strelka-varscan-mutect GOLGA8F,missense_variant,p.Ser213Arg,ENST00000532622,;GOLGA8F,5_prime_UTR_variant,,ENST00000526619,;RN7SL238P,upstream_gene_variant,,ENST00000613832,;GOLGA8F,downstream_gene_variant,,ENST00000568250,;GOLGA8F,downstream_gene_variant,,ENST00000568913,;GOLGA8F,downstream_gene_variant,,ENST00000565126,;GOLGA8F,downstream_gene_variant,,ENST00000564114,; G ENST00000532622 Transcript missense_variant 701/2009 639/1947 213/648 S/R agC/agG 1 1 GOLGA8F HGNC HGNC:32378 protein_coding YES ENSP00000454322 H3BMC3 UPI00024672FE deleterious(0.03) 9/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881 MODERATE 1 SNV 5 1 PASS . . 74 134 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 28384158 28384158 C G 1 0 0 0 0 1 0 0 0 6449 738 26 4 4 GOLGA8F 15 28384158 Missense_Mutation SNP C C3N-00217_T 239952 28384158 73607031 422 12192 FMN1 0 . GRCh38 15 32910498 32910498 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.3264G>T p.Glu1088Asp p.E1088D ENST00000616417 11/21 163 129 34 182 181 1 strelka-varscan-mutect FMN1,missense_variant,p.Glu1088Asp,ENST00000616417,NM_001277313.1;FMN1,missense_variant,p.Glu865Asp,ENST00000334528,NM_001103184.3;FMN1,missense_variant,p.Glu1088Asp,ENST00000559047,;FMN1,missense_variant,p.Glu990Asp,ENST00000561249,;FMN1,missense_variant,p.Glu42Asp,ENST00000560317,;FMN1,non_coding_transcript_exon_variant,,ENST00000558628,; A ENST00000616417 Transcript missense_variant 3768/13529 3264/4260 1088/1419 E/D gaG/gaT 1 -1 FMN1 HGNC HGNC:3768 protein_coding YES CCDS61581.1 ENSP00000479134 Q68DA7 UPI0001AE68B4 NM_001277313.1 tolerated(0.05) 11/21 PROSITE_profiles:PS51444,hmmpanther:PTHR13037:SF11,hmmpanther:PTHR13037,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447,Prints_domain:PR00828 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 32910498 32910498 C A 1 0 0 0 0 1 0 0 0 5805 912 32 2 2 FMN1 15 32910498 Missense_Mutation SNP C C3N-00217_T 4526340 32910498 69080691 423 12193 RYR3 0 . GRCh38 15 33636410 33636410 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.3416G>T p.Gly1139Val p.G1139V ENST00000634891 27/104 235 147 88 306 306 0 strelka-varscan-mutect RYR3,missense_variant,p.Gly1139Val,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Gly1139Val,ENST00000622037,;RYR3,missense_variant,p.Gly1139Val,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Gly1139Val,ENST00000389232,;RYR3,missense_variant,p.Gly1139Val,ENST00000634418,; T ENST00000634891 Transcript missense_variant 3517/15591 3416/14613 1139/4870 G/V gGg/gTg 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 27/104 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 33636410 33636410 G T 1 0 0 0 0 1 0 0 0 14030 1232 43 2 2 RYR3 15 33636410 Missense_Mutation SNP G C3N-00217_T 725912 33636410 68354779 424 12194 RYR3 0 . GRCh38 15 33670551 33670551 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.5855G>T p.Cys1952Phe p.C1952F ENST00000634891 38/104 40 35 5 76 76 0 strelka-varscan-mutect RYR3,missense_variant,p.Cys1952Phe,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Cys1952Phe,ENST00000622037,;RYR3,missense_variant,p.Cys1952Phe,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Cys1952Phe,ENST00000389232,;RYR3,missense_variant,p.Cys1952Phe,ENST00000634418,; T ENST00000634891 Transcript missense_variant 5956/15591 5855/14613 1952/4870 C/F tGc/tTc 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.71) 38/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -13.38136 1 1 1 1 0 T 3 4 43 33670551 33670551 G T 1 0 0 0 0 1 0 0 0 14030 1333 46 2 2 RYR3 15 33670551 Missense_Mutation SNP G C3N-00217_T 34141 33670551 68320638 425 12195 SLC12A6 0 . GRCh38 15 34245377 34245377 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.1851G>A p.= p.G617G ENST00000354181 15/26 438 355 83 407 407 0 strelka-varscan-mutect SLC12A6,synonymous_variant,p.=,ENST00000290209,NM_005135.2;SLC12A6,synonymous_variant,p.=,ENST00000354181,;SLC12A6,synonymous_variant,p.=,ENST00000458406,NM_001042494.1;SLC12A6,synonymous_variant,p.=,ENST00000560611,NM_133647.1;SLC12A6,synonymous_variant,p.=,ENST00000397707,NM_001042497.1;SLC12A6,synonymous_variant,p.=,ENST00000397702,NM_001042495.1;SLC12A6,synonymous_variant,p.=,ENST00000558589,NM_001042496.1;SLC12A6,synonymous_variant,p.=,ENST00000560164,;SLC12A6,synonymous_variant,p.=,ENST00000558667,;SLC12A6,synonymous_variant,p.=,ENST00000561080,;SLC12A6,synonymous_variant,p.=,ENST00000559664,;SLC12A6,synonymous_variant,p.=,ENST00000559523,;SLC12A6,upstream_gene_variant,,ENST00000558950,;SLC12A6,upstream_gene_variant,,ENST00000560023,; T ENST00000354181 Transcript synonymous_variant 2344/4568 1851/3453 617/1150 G ggG/ggA 1 -1 SLC12A6 HGNC HGNC:10914 protein_coding YES CCDS58352.1 ENSP00000346112 Q9UHW9 A0A024R9I5 UPI0000135427 15/26 Pfam_domain:PF00324,Prints_domain:PR01081,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF66,TIGRFAM_domain:TIGR00930 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 34245377 34245377 C T 1 0 0 0 0 0 0 0 1 14652 610 22 3 3 SLC12A6 15 34245377 Silent SNP C C3N-00217_T 574826 34245377 67745812 426 12196 TMCO5A 0 . GRCh38 15 37951153 37951153 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.786G>T p.= p.L262L ENST00000319669 11/11 245 151 94 270 270 0 strelka-varscan-mutect TMCO5A,synonymous_variant,p.=,ENST00000319669,NM_152453.3;TMCO5A,intron_variant,,ENST00000559502,;TMCO5A,3_prime_UTR_variant,,ENST00000560653,; T ENST00000319669 Transcript synonymous_variant 888/1274 786/867 262/288 L ctG/ctT 1 1 TMCO5A HGNC HGNC:28558 protein_coding YES CCDS10046.1 ENSP00000327234 Q8N6Q1 A0A024R9I9 UPI00001BBFD2 NM_152453.3 11/11 hmmpanther:PTHR22422:SF7,hmmpanther:PTHR22422,Pfam_domain:PF14992 LOW 1 SNV 1 1 PASS rs1425678244 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 37951153 37951153 G T 1 0 0 0 0 0 0 0 1 16445 1335 47 2 2 TMCO5A 15 37951153 Silent SNP G C3N-00217_T 3705776 37951153 64040036 427 12197 MAP1A 0 . GRCh38 15 43524511 43524511 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.3038C>A p.Ser1013Tyr p.S1013Y ENST00000300231 4/6 257 204 53 244 244 0 strelka-varscan-mutect MAP1A,missense_variant,p.Ser1251Tyr,ENST00000382031,;MAP1A,missense_variant,p.Ser1013Tyr,ENST00000300231,NM_002373.5; A ENST00000300231 Transcript missense_variant 3488/10258 3038/8412 1013/2803 S/Y tCc/tAc 1 1 MAP1A HGNC HGNC:6835 protein_coding YES CCDS42031.1 ENSP00000300231 P78559 UPI000013E63C NM_002373.5 deleterious(0) 4/6 hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 43524511 43524511 C A 1 0 0 0 0 1 0 0 0 9150 855 30 2 2 MAP1A 15 43524511 Missense_Mutation SNP C C3N-00217_T 5573358 43524511 58466678 428 12198 STRC 0 . GRCh38 15 43617694 43617694 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.727G>T p.Val243Leu p.V243L ENST00000450892 2/29 29 25 4 36 36 0 varscan-mutect STRC,missense_variant,p.Val243Leu,ENST00000450892,NM_153700.2;STRC,missense_variant,p.Val183Leu,ENST00000432436,;STRC,5_prime_UTR_variant,,ENST00000541030,;STRC,missense_variant,p.Val243Leu,ENST00000428650,;STRC,missense_variant,p.Val243Leu,ENST00000440125,;STRC,upstream_gene_variant,,ENST00000485556,;STRC,upstream_gene_variant,,ENST00000471703,;STRC,upstream_gene_variant,,ENST00000448437,;STRC,upstream_gene_variant,,ENST00000455136,;STRC,upstream_gene_variant,,ENST00000483250,;STRC,upstream_gene_variant,,ENST00000470279,; A ENST00000450892 Transcript missense_variant 805/5680 727/5328 243/1775 V/L Gtg/Ttg 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 tolerated(0.09) 2/29 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -11.57538 1 1 1 1 0 A 3 1 43 43617694 43617694 C A 1 0 0 0 0 1 0 0 0 15709 565 20 2 2 STRC 15 43617694 Missense_Mutation SNP C C3N-00217_T 93183 43617694 58373495 429 12199 DUOX2 0 . GRCh38 15 45108085 45108085 + Silent SNP C C A rs752704146 C3N-00217_T C3N-00217_N C C c.1536G>T p.= p.R512R ENST00000603300 13/34 364 238 126 274 274 0 strelka-varscan-mutect DUOX2,synonymous_variant,p.=,ENST00000389039,;DUOX2,synonymous_variant,p.=,ENST00000603300,NM_014080.4;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,; A ENST00000603300 Transcript synonymous_variant 1739/6345 1536/4647 512/1548 R cgG/cgT rs752704146 1 -1 DUOX2 HGNC HGNC:13273 protein_coding YES CCDS10117.1 ENSP00000475084 Q9NRD8 UPI000013D775 NM_014080.4 13/34 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,Superfamily_domains:SSF48113 LOW 1 SNV 1 1 PASS rs752704146 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 45108085 45108085 C A 1 0 0 0 0 0 0 0 1 4623 610 22 2 2 DUOX2 15 45108085 Silent SNP C C3N-00217_T 1490391 45108085 56883104 430 12200 ONECUT1 0 . GRCh38 15 52757816 52757816 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.1137G>C p.Lys379Asn p.K379N ENST00000305901 2/2 108 61 47 130 130 0 strelka-varscan-mutect ONECUT1,missense_variant,p.Lys379Asn,ENST00000305901,NM_004498.2;ONECUT1,missense_variant,p.Arg20Thr,ENST00000560699,;ONECUT1,non_coding_transcript_exon_variant,,ENST00000561401,; G ENST00000305901 Transcript missense_variant 1265/2092 1137/1398 379/465 K/N aaG/aaC 1 -1 ONECUT1 HGNC HGNC:8138 protein_coding YES CCDS10150.1 ENSP00000302630 Q9UBC0 UPI000012CA91 NM_004498.2 tolerated(0.05) 2/2 hmmpanther:PTHR14057:SF9,hmmpanther:PTHR14057,Gene3D:1.10.10.60 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 52757816 52757816 C G 1 0 0 0 0 1 0 0 0 10943 681 24 4 4 ONECUT1 15 52757816 Missense_Mutation SNP C C3N-00217_T 7649731 52757816 49233373 431 12201 PRTG 0 . GRCh38 15 55740610 55740610 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.169G>A p.Val57Ile p.V57I ENST00000389286 2/20 195 163 32 245 245 0 strelka-varscan-mutect PRTG,missense_variant,p.Val57Ile,ENST00000389286,NM_173814.5;PRTG,missense_variant,p.Val57Ile,ENST00000561292,;PRTG,5_prime_UTR_variant,,ENST00000558349,;PRTG,upstream_gene_variant,,ENST00000623053,; T ENST00000389286 Transcript missense_variant 217/11967 169/3453 57/1150 V/I Gtt/Att 1 -1 PRTG HGNC HGNC:26373 protein_coding YES CCDS42040.1 ENSP00000373937 Q2VWP7 UPI00001555A7 NM_173814.5 tolerated(0.31) 2/20 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF661,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1445356691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 55740610 55740610 C T 1 0 0 0 0 1 0 0 0 12788 536 19 1 1 PRTG 15 55740610 Missense_Mutation SNP C C3N-00217_T 2982794 55740610 46250579 432 12202 NEDD4 0 . GRCh38 15 55834053 55834053 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.3672A>G p.Ile1224Met p.I1224M ENST00000508342 22/25 72 59 13 100 100 0 strelka-varscan-mutect NEDD4,missense_variant,p.Ile1224Met,ENST00000508342,NM_001284338.1;NEDD4,missense_variant,p.Ile1152Met,ENST00000338963,NM_198400.3;NEDD4,missense_variant,p.Ile1208Met,ENST00000506154,NM_001284339.1;NEDD4,missense_variant,p.Ile805Met,ENST00000435532,NM_006154.3;NEDD4,missense_variant,p.Ile815Met,ENST00000508871,NM_001284340.1;NEDD4,3_prime_UTR_variant,,ENST00000503468,; C ENST00000508342 Transcript missense_variant 3972/7235 3672/3960 1224/1319 I/M atA/atG 1 -1 NEDD4 HGNC HGNC:7727 protein_coding YES CCDS61644.1 ENSP00000424827 P46934 UPI00001FE52D NM_001284338.1 deleterious(0.01) 22/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF282,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 55834053 55834053 T C 1 0 0 0 0 1 0 0 0 10338 1628 57 5 5 NEDD4 15 55834053 Missense_Mutation SNP T C3N-00217_T 93443 55834053 46157136 433 12203 USP3 0 . GRCh38 15 63537128 63537128 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.256A>T p.Met86Leu p.M86L ENST00000380324 3/15 97 75 22 150 150 0 strelka-varscan-mutect USP3,missense_variant,p.Met64Leu,ENST00000268049,;USP3,missense_variant,p.Met86Leu,ENST00000380324,NM_006537.3;USP3,missense_variant,p.Met69Leu,ENST00000558285,;USP3,missense_variant,p.Met64Leu,ENST00000559771,;USP3,missense_variant,p.Met117Leu,ENST00000561442,;USP3,intron_variant,,ENST00000540797,NM_001256702.1;USP3,intron_variant,,ENST00000560070,;USP3,downstream_gene_variant,,ENST00000559276,;USP3,intron_variant,,ENST00000561326,;USP3,missense_variant,p.Met9Leu,ENST00000559257,;USP3,3_prime_UTR_variant,,ENST00000559192,;USP3,3_prime_UTR_variant,,ENST00000558157,;USP3,3_prime_UTR_variant,,ENST00000557884,;USP3,intron_variant,,ENST00000559873,;USP3,upstream_gene_variant,,ENST00000538686,; T ENST00000380324 Transcript missense_variant 385/2333 256/1563 86/520 M/L Atg/Ttg 1 1 USP3 HGNC HGNC:12626 protein_coding YES CCDS32265.1 ENSP00000369681 Q9Y6I4 UPI0000071F2D NM_006537.3 tolerated(0.23) 3/15 PROSITE_profiles:PS50271,Gene3D:3.30.40.10,Pfam_domain:PF02148,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 63537128 63537128 A T 1 0 0 0 0 1 0 0 0 17602 449 16 4 4 USP3 15 63537128 Missense_Mutation SNP A C3N-00217_T 7703075 63537128 38454061 434 12204 IGDCC3 0 . GRCh38 15 65334842 65334842 + Nonsense_Mutation SNP C C A rs770319633 C3N-00217_T C3N-00217_N C C c.709G>T p.Glu237Ter p.E237* ENST00000327987 5/14 94 54 40 103 103 0 strelka-varscan-mutect IGDCC3,stop_gained,p.Glu237Ter,ENST00000327987,NM_004884.3;IGDCC3,stop_gained,p.Glu100Ter,ENST00000558354,;IGDCC3,stop_gained,p.Glu114Ter,ENST00000559058,;IGDCC3,upstream_gene_variant,,ENST00000559231,; A ENST00000327987 Transcript stop_gained 961/4479 709/2445 237/814 E/* Gag/Tag rs770319633 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 5/14 Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 65334842 65334842 C A 1 0 0 0 0 0 1 0 0 7474 864 30 2 2 IGDCC3 15 65334842 Nonsense_Mutation SNP C C3N-00217_T 1797714 65334842 36656347 435 12205 IGDCC4 0 . GRCh38 15 65392212 65392212 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2044G>T p.Gly682Cys p.G682C ENST00000352385 11/20 115 67 48 68 68 0 strelka-varscan-mutect IGDCC4,missense_variant,p.Gly682Cys,ENST00000352385,NM_020962.2;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,; A ENST00000352385 Transcript missense_variant 2254/6508 2044/3753 682/1250 G/C Ggc/Tgc 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 deleterious(0) 11/20 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 65392212 65392212 C A 1 0 0 0 0 1 0 0 0 7475 623 22 2 2 IGDCC4 15 65392212 Missense_Mutation SNP C C3N-00217_T 57370 65392212 36598977 436 12206 NOX5 0 . GRCh38 15 69033172 69033172 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.750G>A p.= p.V250V ENST00000388866 5/16 176 139 37 140 140 0 strelka-varscan-mutect NOX5,synonymous_variant,p.=,ENST00000260364,;NOX5,synonymous_variant,p.=,ENST00000388866,NM_024505.3;NOX5,synonymous_variant,p.=,ENST00000448182,;NOX5,synonymous_variant,p.=,ENST00000530406,NM_001184779.1;NOX5,synonymous_variant,p.=,ENST00000455873,NM_001184780.1;RP11-809H16.4,downstream_gene_variant,,ENST00000559495,;NOX5,synonymous_variant,p.=,ENST00000525143,;NOX5,non_coding_transcript_exon_variant,,ENST00000527315,;RP11-809H16.2,downstream_gene_variant,,ENST00000557966,; A ENST00000388866 Transcript synonymous_variant 791/2804 750/2298 250/765 V gtG/gtA 1 1 NOX5 HGNC HGNC:14874 protein_coding YES CCDS32276.2 ENSP00000373518 Q96PH1 UPI000006DDBD NM_024505.3 5/16 hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF58,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 69033172 69033172 G A 1 0 0 0 0 0 0 0 1 10605 1306 46 3 3 NOX5 15 69033172 Silent SNP G C3N-00217_T 3640960 69033172 32958017 437 12207 NEO1 0 . GRCh38 15 73270024 73270024 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.2509G>T p.Asp837Tyr p.D837Y ENST00000339362 18/30 161 140 21 166 166 0 varscan-mutect NEO1,missense_variant,p.Asp837Tyr,ENST00000339362,;NEO1,missense_variant,p.Asp837Tyr,ENST00000261908,NM_002499.3;NEO1,missense_variant,p.Asp837Tyr,ENST00000558964,NM_001172624.1;NEO1,missense_variant,p.Asp837Tyr,ENST00000560262,NM_001172623.1;NEO1,intron_variant,,ENST00000560328,; T ENST00000339362 Transcript missense_variant 2956/7342 2509/4386 837/1461 D/Y Gat/Tat COSM434251 1 1 NEO1 HGNC HGNC:7754 protein_coding YES CCDS10247.1 ENSP00000341198 Q92859 UPI000013D221 deleterious(0) 18/30 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 73270024 73270024 G T 1 0 0 0 0 1 0 0 0 10370 1290 45 2 2 NEO1 15 73270024 Missense_Mutation SNP G C3N-00217_T 4236852 73270024 28721165 438 12208 NEO1 0 . GRCh38 15 73302646 73302646 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.4336G>T p.Ala1446Ser p.A1446S ENST00000339362 30/30 153 91 62 225 225 0 strelka-varscan-mutect NEO1,missense_variant,p.Ala1446Ser,ENST00000339362,;NEO1,missense_variant,p.Ala1446Ser,ENST00000261908,NM_002499.3;NEO1,missense_variant,p.Ala1115Ser,ENST00000560328,;NEO1,missense_variant,p.Ala1435Ser,ENST00000558964,NM_001172624.1;NEO1,missense_variant,p.Ala1393Ser,ENST00000560262,NM_001172623.1;NEO1,non_coding_transcript_exon_variant,,ENST00000560808,;NEO1,downstream_gene_variant,,ENST00000558886,; T ENST00000339362 Transcript missense_variant 4783/7342 4336/4386 1446/1461 A/S Gcc/Tcc 1 1 NEO1 HGNC HGNC:7754 protein_coding YES CCDS10247.1 ENSP00000341198 Q92859 UPI000013D221 deleterious(0) 30/30 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF55,Pfam_domain:PF06583 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 73302646 73302646 G T 1 0 0 0 0 1 0 0 0 10370 1203 42 2 2 NEO1 15 73302646 Missense_Mutation SNP G C3N-00217_T 32622 73302646 28688543 439 12209 ISLR2 0 . GRCh38 15 74134282 74134282 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1528G>T p.Gly510Cys p.G510C ENST00000361742 4/4 90 70 20 100 100 0 strelka-varscan-mutect ISLR2,missense_variant,p.Gly510Cys,ENST00000361742,NM_001130136.1;ISLR2,missense_variant,p.Gly510Cys,ENST00000435464,NM_001130138.1;ISLR2,missense_variant,p.Gly510Cys,ENST00000565159,NM_001130137.1;ISLR2,missense_variant,p.Gly510Cys,ENST00000453268,NM_020851.2;ISLR2,missense_variant,p.Gly510Cys,ENST00000565540,;ISLR2,intron_variant,,ENST00000419208,;ISLR2,downstream_gene_variant,,ENST00000569886,;ISLR2,downstream_gene_variant,,ENST00000561740,;ISLR2,downstream_gene_variant,,ENST00000567206,;ISLR2,downstream_gene_variant,,ENST00000565332,;ISLR2,intron_variant,,ENST00000561975,;ISLR2,downstream_gene_variant,,ENST00000565068,; T ENST00000361742 Transcript missense_variant 2297/4817 1528/2238 510/745 G/C Ggc/Tgc 1 1 ISLR2 HGNC HGNC:29286 protein_coding YES CCDS10259.1 ENSP00000355402 Q6UXK2 UPI000004C60F NM_001130136.1 deleterious(0.01) 4/4 hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF15,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1260108878 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 74134282 74134282 G T 1 0 0 0 0 1 0 0 0 7766 1232 43 2 2 ISLR2 15 74134282 Missense_Mutation SNP G C3N-00217_T 831636 74134282 27856907 440 12210 ISLR 0 . GRCh38 15 74175703 74175703 + Missense_Mutation SNP G G A rs762884175 C3N-00217_T C3N-00217_N G G c.845G>A p.Ser282Asn p.S282N ENST00000249842 2/2 111 94 17 98 98 0 strelka-varscan-mutect ISLR,missense_variant,p.Ser282Asn,ENST00000249842,NM_005545.3;ISLR,missense_variant,p.Ser282Asn,ENST00000395118,NM_201526.1;STRA6,downstream_gene_variant,,ENST00000323940,NM_001142617.1;STRA6,downstream_gene_variant,,ENST00000616000,NM_001142618.1;STRA6,downstream_gene_variant,,ENST00000395105,NM_022369.3;STRA6,downstream_gene_variant,,ENST00000423167,NM_001142619.1;STRA6,downstream_gene_variant,,ENST00000416286,;STRA6,downstream_gene_variant,,ENST00000449139,;STRA6,downstream_gene_variant,,ENST00000535552,NM_001199040.1;STRA6,downstream_gene_variant,,ENST00000563965,NM_001199042.1;STRA6,downstream_gene_variant,,ENST00000574278,NM_001199041.1;STRA6,downstream_gene_variant,,ENST00000572785,;ISLR,downstream_gene_variant,,ENST00000560862,;ISLR,downstream_gene_variant,,ENST00000559510,;RP11-665J16.1,intron_variant,,ENST00000561647,;STRA6,downstream_gene_variant,,ENST00000574439,;STRA6,downstream_gene_variant,,ENST00000545137,; A ENST00000249842 Transcript missense_variant 1202/2371 845/1287 282/428 S/N aGc/aAc rs762884175,COSM1210942 1 1 ISLR HGNC HGNC:6133 protein_coding YES CCDS10260.1 ENSP00000249842 O14498 A0A146E5L3 UPI0000049E09 NM_005545.3 tolerated(0.49) 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF14,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762884175 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 74175703 74175703 G A 1 0 0 0 0 1 0 0 0 7765 971 34 3 3 ISLR 15 74175703 Missense_Mutation SNP G C3N-00217_T 41421 74175703 27815486 441 12211 SIN3A 0 . GRCh38 15 75412951 75412951 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.568T>A p.Tyr190Asn p.Y190N ENST00000394947 5/21 173 133 40 185 185 0 strelka-varscan-mutect SIN3A,missense_variant,p.Tyr190Asn,ENST00000394947,NM_001145358.1;SIN3A,missense_variant,p.Tyr190Asn,ENST00000360439,NM_001145357.1;SIN3A,missense_variant,p.Tyr190Asn,ENST00000394949,NM_015477.2;SIN3A,downstream_gene_variant,,ENST00000564778,;SIN3A,downstream_gene_variant,,ENST00000562776,;SIN3A,downstream_gene_variant,,ENST00000568431,;CTD-2562G15.2,upstream_gene_variant,,ENST00000569073,; T ENST00000394947 Transcript missense_variant 883/6737 568/3822 190/1273 Y/N Tac/Aac 1 -1 SIN3A HGNC HGNC:19353 protein_coding YES CCDS10279.1 ENSP00000378402 Q96ST3 UPI000013EAD4 NM_001145358.1 deleterious(0) 5/21 hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 75412951 75412951 A T 1 0 0 0 0 1 0 0 0 14589 420 15 4 4 SIN3A 15 75412951 Missense_Mutation SNP A C3N-00217_T 1237248 75412951 26578238 442 12212 ACSBG1 0 . GRCh38 15 78174437 78174437 + Missense_Mutation SNP G G T rs776603338 C3N-00217_T C3N-00217_N G G c.1790C>A p.Ala597Asp p.A597D ENST00000258873 12/14 254 194 60 252 252 0 strelka-varscan-mutect ACSBG1,missense_variant,p.Ala597Asp,ENST00000258873,NM_001199377.1,NM_015162.4;ACSBG1,missense_variant,p.Ala355Asp,ENST00000560817,;IDH3A,downstream_gene_variant,,ENST00000299518,NM_005530.2;IDH3A,downstream_gene_variant,,ENST00000558554,;IDH3A,downstream_gene_variant,,ENST00000558535,;ACSBG1,3_prime_UTR_variant,,ENST00000560124,;ACSBG1,non_coding_transcript_exon_variant,,ENST00000560183,;IDH3A,downstream_gene_variant,,ENST00000559889,;IDH3A,downstream_gene_variant,,ENST00000558602,;IDH3A,downstream_gene_variant,,ENST00000560667,;ACSBG1,downstream_gene_variant,,ENST00000559707,;ACSBG1,downstream_gene_variant,,ENST00000558301,;IDH3A,downstream_gene_variant,,ENST00000557960,; T ENST00000258873 Transcript missense_variant 1996/6357 1790/2175 597/724 A/D gCc/gAc rs776603338,COSM4757910 1 -1 ACSBG1 HGNC HGNC:29567 protein_coding YES CCDS10298.1 ENSP00000258873 Q96GR2 UPI000006E955 NM_001199377.1,NM_015162.4 deleterious(0) 12/14 hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF184,Superfamily_domains:SSF56801 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776603338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 78174437 78174437 G T 1 0 0 0 0 1 0 0 0 215 1203 42 2 2 ACSBG1 15 78174437 Missense_Mutation SNP G C3N-00217_T 2761486 78174437 23816752 443 12213 ANPEP 0 . GRCh38 15 89804261 89804261 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1171G>T p.Ala391Ser p.A391S ENST00000300060 6/21 108 89 19 120 120 0 strelka-varscan-mutect ANPEP,missense_variant,p.Ala391Ser,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,non_coding_transcript_exon_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000560030,;ANPEP,downstream_gene_variant,,ENST00000560028,;ANPEP,upstream_gene_variant,,ENST00000559761,; A ENST00000300060 Transcript missense_variant 1485/3678 1171/2904 391/967 A/S Gcc/Tcc 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 deleterious(0) 6/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Pfam_domain:PF01433,Superfamily_domains:SSF55486,Prints_domain:PR00756 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 89804261 89804261 C A 1 0 0 0 0 1 0 0 0 817 739 26 2 2 ANPEP 15 89804261 Missense_Mutation SNP C C3N-00217_T 11629824 89804261 12186928 444 12214 TXNDC11 0 . GRCh38 16 11691912 11691912 + Silent SNP A A T novel C3N-00217_T C3N-00217_N A A c.1359T>A p.= p.T453T ENST00000356957 9/13 125 100 25 93 93 0 strelka-varscan-mutect TXNDC11,synonymous_variant,p.=,ENST00000356957,NM_001303447.1;TXNDC11,synonymous_variant,p.=,ENST00000283033,NM_015914.6;TXNDC11,downstream_gene_variant,,ENST00000575591,;TXNDC11,upstream_gene_variant,,ENST00000570917,;TXNDC11,non_coding_transcript_exon_variant,,ENST00000572732,;TXNDC11,downstream_gene_variant,,ENST00000576969,;TXNDC11,downstream_gene_variant,,ENST00000571882,;TXNDC11,upstream_gene_variant,,ENST00000575349,; T ENST00000356957 Transcript synonymous_variant 1467/3178 1359/2958 453/985 T acT/acA 1 -1 TXNDC11 HGNC HGNC:28030 protein_coding YES CCDS76822.1 ENSP00000349439 Q6PKC3 UPI000041D75B NM_001303447.1 9/13 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 11691912 11691912 A T 1 0 0 0 0 0 0 0 1 17308 175 7 4 4 TXNDC11 16 11691912 Silent SNP A C3N-00217_T 11691912 78646433 445 12215 PARN 0 . GRCh38 16 14446943 14446943 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1809G>T p.Glu603Asp p.E603D ENST00000437198 23/24 209 156 53 152 152 0 strelka-varscan-mutect PARN,missense_variant,p.Glu603Asp,ENST00000437198,NM_002582.3;PARN,missense_variant,p.Glu557Asp,ENST00000420015,NM_001242992.1;PARN,missense_variant,p.Glu542Asp,ENST00000341484,NM_001134477.2;PARN,missense_variant,p.Glu428Asp,ENST00000539279,;PARN,downstream_gene_variant,,ENST00000564882,; A ENST00000437198 Transcript missense_variant 1951/3078 1809/1920 603/639 E/D gaG/gaT 1 -1 PARN HGNC HGNC:8609 protein_coding YES CCDS45419.1 ENSP00000387911 O95453 UPI0000031F7A NM_002582.3 tolerated_low_confidence(0.23) 23/24 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999977 1 1 1 0 A 3 1 43 14446943 14446943 C A 1 0 0 0 0 1 0 0 0 11533 680 24 2 2 PARN 16 14446943 Missense_Mutation SNP C C3N-00217_T 2755031 14446943 75891402 446 12216 CCP110 0 . GRCh38 16 19537401 19537401 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.1732G>T p.Asp578Tyr p.D578Y ENST00000381396 4/15 128 111 17 141 141 0 strelka-varscan-mutect CCP110,missense_variant,p.Asp578Tyr,ENST00000396212,NM_001323572.1,NM_001323571.1,NM_014711.4;CCP110,missense_variant,p.Asp578Tyr,ENST00000381396,NM_001323569.1,NM_001199022.1;CCP110,missense_variant,p.Asp578Tyr,ENST00000396208,;CCP110,downstream_gene_variant,,ENST00000561888,;CCP110,intron_variant,,ENST00000562083,; T ENST00000381396 Transcript missense_variant 1979/5446 1732/3039 578/1012 D/Y Gat/Tat COSM3506752 1 1 CCP110 HGNC HGNC:24342 protein_coding YES CCDS55992.1 ENSP00000370803 O43303 UPI0000D619A9 NM_001323569.1,NM_001199022.1 deleterious(0.01) 4/15 hmmpanther:PTHR13594 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 19537401 19537401 G T 1 0 0 0 0 1 0 0 0 2637 1174 41 2 2 CCP110 16 19537401 Missense_Mutation SNP G C3N-00217_T 5090458 19537401 70800944 447 12217 GPRC5B 0 . GRCh38 16 19872456 19872456 + Silent SNP G G C rs771810976 C3N-00217_T C3N-00217_N G G c.390C>G p.= p.G130G ENST00000300571 2/4 187 110 77 162 162 0 strelka-varscan-mutect GPRC5B,synonymous_variant,p.=,ENST00000300571,NM_016235.2;GPRC5B,synonymous_variant,p.=,ENST00000569479,;GPRC5B,synonymous_variant,p.=,ENST00000569847,;GPRC5B,synonymous_variant,p.=,ENST00000535671,;GPRC5B,synonymous_variant,p.=,ENST00000562469,;GPRC5B,synonymous_variant,p.=,ENST00000566822,;GPRC5B,downstream_gene_variant,,ENST00000564449,;GPRC5B,downstream_gene_variant,,ENST00000568214,;GPRC5B,downstream_gene_variant,,ENST00000570142,; C ENST00000300571 Transcript synonymous_variant 582/5213 390/1212 130/403 G ggC/ggG rs771810976 1 -1 GPRC5B HGNC HGNC:13308 protein_coding YES CCDS10581.1 ENSP00000300571 Q9NZH0 A0A024QYX2 UPI0000032747 NM_016235.2 2/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR14511,hmmpanther:PTHR14511:SF9,Pfam_domain:PF00003 LOW 1 SNV 1 1 PASS rs771810976 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 19872456 19872456 G C 1 0 0 0 0 0 0 0 1 6604 1074 38 4 4 GPRC5B 16 19872456 Silent SNP G C3N-00217_T 335055 19872456 70465889 448 12218 ACSM2B 0 . GRCh38 16 20552160 20552160 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.878C>A p.Pro293Gln p.P293Q ENST00000329697 6/14 83 51 32 71 71 0 strelka-varscan-mutect ACSM2B,missense_variant,p.Pro293Gln,ENST00000329697,NM_001105069.1;ACSM2B,missense_variant,p.Pro293Gln,ENST00000414188,;ACSM2B,missense_variant,p.Pro293Gln,ENST00000565232,;ACSM2B,missense_variant,p.Pro293Gln,ENST00000567001,NM_182617.3;ACSM2B,missense_variant,p.Pro214Gln,ENST00000565322,;ACSM2B,missense_variant,p.Pro62Gln,ENST00000567288,;ACSM2B,missense_variant,p.Pro103Gln,ENST00000569163,;ACSM2B,downstream_gene_variant,,ENST00000568882,;ACSM2B,3_prime_UTR_variant,,ENST00000569327,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,;ACSM2B,upstream_gene_variant,,ENST00000569131,;ACSM2B,upstream_gene_variant,,ENST00000566998,; T ENST00000329697 Transcript missense_variant 1047/2935 878/1734 293/577 P/Q cCa/cAa 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 deleterious(0) 6/14 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF188,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 20552160 20552160 G T 1 0 0 0 0 1 0 0 0 226 1348 47 2 2 ACSM2B 16 20552160 Missense_Mutation SNP G C3N-00217_T 679704 20552160 69786185 449 12219 DNAH3 0 . GRCh38 16 20982872 20982872 + Missense_Mutation SNP C C A rs769980991 C3N-00217_T C3N-00217_N C C c.7708G>T p.Gly2570Trp p.G2570W ENST00000261383 49/62 178 122 56 130 130 0 strelka-varscan-mutect DNAH3,missense_variant,p.Gly2570Trp,ENST00000261383,NM_017539.2; A ENST00000261383 Transcript missense_variant 7708/12394 7708/12351 2570/4116 G/W Ggg/Tgg rs769980991 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0) 49/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12780,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs769980991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 20982872 20982872 C A 1 0 0 0 0 1 0 0 0 4418 681 24 2 2 DNAH3 16 20982872 Missense_Mutation SNP C C3N-00217_T 430712 20982872 69355473 450 12220 ATXN2L 0 . GRCh38 16 28834086 28834086 + Missense_Mutation SNP A A G rs571133202 C3N-00217_T C3N-00217_N A A c.2047A>G p.Thr683Ala p.T683A ENST00000395547 16/24 215 184 31 136 136 0 strelka-mutect ATXN2L,missense_variant,p.Thr683Ala,ENST00000336783,NM_007245.3;ATXN2L,missense_variant,p.Thr683Ala,ENST00000395547,NM_148414.2;ATXN2L,missense_variant,p.Thr683Ala,ENST00000340394,NM_148415.2;ATXN2L,missense_variant,p.Thr683Ala,ENST00000325215,NM_145714.2;ATXN2L,missense_variant,p.Thr683Ala,ENST00000382686,NM_148416.2;ATXN2L,missense_variant,p.Thr683Ala,ENST00000570200,NM_017492.3;ATXN2L,missense_variant,p.Thr689Ala,ENST00000564304,NM_001308230.1;ATXN2L,missense_variant,p.Thr8Ala,ENST00000566946,;ATXN2L,downstream_gene_variant,,ENST00000568266,;ATXN2L,upstream_gene_variant,,ENST00000564162,;ATXN2L,upstream_gene_variant,,ENST00000569318,;ATXN2L,upstream_gene_variant,,ENST00000567024,;ATXN2L,upstream_gene_variant,,ENST00000566007,;RP11-24N18.1,intron_variant,,ENST00000563565,;ATXN2L,non_coding_transcript_exon_variant,,ENST00000565845,;ATXN2L,downstream_gene_variant,,ENST00000570284,;ATXN2L,missense_variant,p.Thr8Ala,ENST00000562583,;ATXN2L,3_prime_UTR_variant,,ENST00000565971,;ATXN2L,non_coding_transcript_exon_variant,,ENST00000563314,;ATXN2L,non_coding_transcript_exon_variant,,ENST00000564035,;ATXN2L,upstream_gene_variant,,ENST00000561732,;ATXN2L,downstream_gene_variant,,ENST00000564284,;ATXN2L,upstream_gene_variant,,ENST00000562686,; G ENST00000395547 Transcript missense_variant 2214/3981 2047/3294 683/1097 T/A Act/Gct rs571133202,COSM5252706,COSM5252707,COSM557514,COSM557515 1 1 ATXN2L HGNC HGNC:31326 protein_coding YES CCDS10640.1 ENSP00000378917 Q8WWM7 UPI000016783F NM_148414.2 tolerated(0.05) 16/24 Low_complexity_(Seg):seg,hmmpanther:PTHR12854:SF8,hmmpanther:PTHR12854 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs571133202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 28834086 28834086 A G 1 0 0 0 0 1 0 0 0 1366 43 2 5 5 ATXN2L 16 28834086 Missense_Mutation SNP A C3N-00217_T 7851214 28834086 61504259 451 12221 CDIPT 0 . GRCh38 16 29860596 29860596 + Missense_Mutation SNP G G C rs762669095 C3N-00217_T C3N-00217_N G G c.399C>G p.Ile133Met p.I133M ENST00000219789 4/6 197 178 19 121 121 0 strelka-varscan-mutect CDIPT,missense_variant,p.Ile133Met,ENST00000219789,NM_006319.4;CDIPT,missense_variant,p.Ile157Met,ENST00000561555,NM_001286586.1;CDIPT,missense_variant,p.Ile88Met,ENST00000566113,NM_001286585.1;CDIPT,missense_variant,p.Ile133Met,ENST00000569956,;CDIPT,missense_variant,p.Ile133Met,ENST00000570016,;CDIPT,missense_variant,p.Ile133Met,ENST00000563415,;CTD-2574D22.7,upstream_gene_variant,,ENST00000611923,;CDIPT-AS1,upstream_gene_variant,,ENST00000398859,;CDIPT-AS1,upstream_gene_variant,,ENST00000565014,;CDIPT,upstream_gene_variant,,ENST00000567459,;CDIPT,3_prime_UTR_variant,,ENST00000564296,;CDIPT,non_coding_transcript_exon_variant,,ENST00000563893,;CDIPT,non_coding_transcript_exon_variant,,ENST00000562041,;CDIPT-AS1,upstream_gene_variant,,ENST00000638164,; C ENST00000219789 Transcript missense_variant 1278/2353 399/642 133/213 I/M atC/atG rs762669095 1 -1 CDIPT HGNC HGNC:1769 protein_coding YES CCDS10657.1 ENSP00000219789 O14735 A8K3L7 UPI0000131B1C NM_006319.4 deleterious(0.02) 4/6 PIRSF_domain:PIRSF000848,hmmpanther:PTHR15362,hmmpanther:PTHR15362:SF4 MODERATE 1 SNV 1 1 PASS rs762669095 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 29860596 29860596 G C 1 0 0 0 0 1 0 0 0 2827 932 33 4 4 CDIPT 16 29860596 Missense_Mutation SNP G C3N-00217_T 1026510 29860596 60477749 452 12222 MAPK3 0 . GRCh38 16 30121897 30121897 + Missense_Mutation SNP G G A C3N-00217_T C3N-00217_N G G c.280C>T p.Arg94Cys p.R94C ENST00000263025 2/9 385 363 22 280 279 1 strelka-varscan-mutect MAPK3,missense_variant,p.Arg94Cys,ENST00000263025,NM_002746.2;MAPK3,missense_variant,p.Arg94Cys,ENST00000322266,NM_001109891.1;MAPK3,missense_variant,p.Arg94Cys,ENST00000395199,NM_001040056.2;MAPK3,missense_variant,p.Arg94Cys,ENST00000395202,;MAPK3,missense_variant,p.Arg65Cys,ENST00000395200,;MAPK3,5_prime_UTR_variant,,ENST00000484663,;MAPK3,5_prime_UTR_variant,,ENST00000478356,;MAPK3,5_prime_UTR_variant,,ENST00000481230,;MAPK3,missense_variant,p.Arg94Cys,ENST00000466521,;MAPK3,missense_variant,p.Arg94Cys,ENST00000490298,;MAPK3,non_coding_transcript_exon_variant,,ENST00000483869,;MAPK3,upstream_gene_variant,,ENST00000461737,;MAPK3,upstream_gene_variant,,ENST00000473431,; A ENST00000263025 Transcript missense_variant 365/1861 280/1140 94/379 R/C Cgc/Tgc COSM471620,COSM4857281,COSM4857282 1 -1 MAPK3 HGNC HGNC:6877 protein_coding YES CCDS10672.1 ENSP00000263025 P27361 L7RXH5 UPI0000000DD7 NM_002746.2 deleterious(0.01) 2/9 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF203,PROSITE_patterns:PS01351,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 30121897 30121897 G A 1 0 0 0 0 1 0 0 0 9203 1087 38 1 1 MAPK3 16 30121897 Missense_Mutation SNP G C3N-00217_T 261301 30121897 60216448 453 12223 ITGAM 0 . GRCh38 16 31326890 31326890 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.2666A>T p.Lys889Met p.K889M ENST00000544665 22/30 240 189 51 160 160 0 strelka-varscan-mutect ITGAM,missense_variant,p.Lys889Met,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Lys888Met,ENST00000287497,NM_000632.3;ITGAM,upstream_gene_variant,,ENST00000565142,;ITGAM,downstream_gene_variant,,ENST00000567031,;ITGAM,non_coding_transcript_exon_variant,,ENST00000561838,;ITGAM,upstream_gene_variant,,ENST00000569746,;ITGAM,upstream_gene_variant,,ENST00000567178,; T ENST00000544665 Transcript missense_variant 2737/4718 2666/3462 889/1153 K/M aAg/aTg 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0.04) 22/30 Gene3D:2.60.40.1510,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 31326890 31326890 A T 1 0 0 0 0 1 0 0 0 7794 72 3 4 4 ITGAM 16 31326890 Missense_Mutation SNP A C3N-00217_T 1204993 31326890 59011455 454 12224 NETO2 0 . GRCh38 16 47083501 47083501 + Frame_Shift_Del DEL C C - novel C3N-00217_T C3N-00217_N C C c.1298delG p.Arg433ProfsTer39 p.R433Pfs*39 ENST00000562435 9/9 240 171 69 231 231 0 sindel-varindel-pindel NETO2,frameshift_variant,p.Arg433ProfsTer39,ENST00000562435,NM_018092.4;NETO2,frameshift_variant,p.Arg426ProfsTer39,ENST00000303155,NM_001201477.1;NETO2,frameshift_variant,p.Arg273ProfsTer39,ENST00000562559,;NETO2,frameshift_variant,p.Arg136ProfsTer39,ENST00000564667,;NETO2,downstream_gene_variant,,ENST00000563078,; - ENST00000562435 Transcript frameshift_variant 1683/7481 1298/1578 433/525 R/X cGc/cc 1 -1 NETO2 HGNC HGNC:14644 protein_coding YES CCDS10727.1 ENSP00000455169 Q8NC67 UPI000003C718 NM_018092.4 9/9 hmmpanther:PTHR10127:SF314,hmmpanther:PTHR10127 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 47083501 47083501 C - 1 0 1 0 1 0 0 0 0 10375 768 27 0 0 NETO2 16 47083501 Frame_Shift_Del DEL C C3N-00217_T 15756611 47083501 43254844 455 12225 ZNF423 0 . GRCh38 16 49637850 49637850 + Silent SNP C C A rs16947743 C3N-00217_T C3N-00217_N C C c.1302G>T p.= p.A434A ENST00000561648 5/9 324 152 172 198 198 0 strelka-varscan-mutect ZNF423,synonymous_variant,p.=,ENST00000561648,;ZNF423,synonymous_variant,p.=,ENST00000563137,;ZNF423,synonymous_variant,p.=,ENST00000262383,NM_015069.3;ZNF423,synonymous_variant,p.=,ENST00000562871,;ZNF423,synonymous_variant,p.=,ENST00000535559,;ZNF423,synonymous_variant,p.=,ENST00000562520,NM_001271620.1;ZNF423,synonymous_variant,p.=,ENST00000567169,; A ENST00000561648 Transcript synonymous_variant 1603/7907 1302/3855 434/1284 A gcG/gcT rs16947743,COSM3771954,COSM3771955 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC 5/9 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs16947743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 49637850 49637850 C A 1 0 0 0 0 0 0 0 1 18470 639 23 1 1 ZNF423 16 49637850 Silent SNP C C3N-00217_T 2554349 49637850 40700495 456 12226 OGFOD1 0 . GRCh38 16 56475565 56475565 + Missense_Mutation SNP G G C rs768611899 C3N-00217_T C3N-00217_N G G c.1467G>C p.Glu489Asp p.E489D ENST00000566157 12/13 254 189 65 252 252 0 strelka-varscan-mutect OGFOD1,missense_variant,p.Glu489Asp,ENST00000566157,NM_018233.3;OGFOD1,missense_variant,p.Glu446Asp,ENST00000568397,;BBS2,intron_variant,,ENST00000564459,;BBS2,intron_variant,,ENST00000564123,;OGFOD1,splice_region_variant,,ENST00000336111,; C ENST00000566157 Transcript missense_variant,splice_region_variant 1590/4647 1467/1629 489/542 E/D gaG/gaC rs768611899 1 1 OGFOD1 HGNC HGNC:25585 protein_coding YES CCDS10761.2 ENSP00000457258 Q8N543 UPI0000049DA2 NM_018233.3 deleterious(0.01) 12/13 hmmpanther:PTHR12117,Pfam_domain:PF10637 MODERATE 1 SNV 1 1 PASS rs768611899 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 56475565 56475565 G C 1 0 0 0 0 1 0 0 0 10915 1014 35 4 4 OGFOD1 16 56475565 Missense_Mutation SNP G C3N-00217_T 6837715 56475565 33862780 457 12227 MT2A 0 . GRCh38 16 56609049 56609049 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.86G>T p.Cys29Phe p.C29F ENST00000245185 2/3 375 245 130 278 278 0 strelka-varscan-mutect MT2A,missense_variant,p.Cys29Phe,ENST00000245185,NM_005953.3;MT2A,missense_variant,p.Cys29Phe,ENST00000561491,;RP11-249C24.10,downstream_gene_variant,,ENST00000569778,;MT2A,non_coding_transcript_exon_variant,,ENST00000563985,;MT2A,non_coding_transcript_exon_variant,,ENST00000567300,;MT2A,non_coding_transcript_exon_variant,,ENST00000562017,; T ENST00000245185 Transcript missense_variant 543/786 86/186 29/61 C/F tGc/tTc 1 1 MT2A HGNC HGNC:7406 protein_coding YES CCDS10763.1 ENSP00000245185 P02795 UPI000012F71A NM_005953.3 deleterious(0.04) 2/3 Gene3D:4mt2A00,Pfam_domain:PF00131,Prints_domain:PR00860,PROSITE_patterns:PS00203,hmmpanther:PTHR23299,Low_complexity_(Seg):seg,Superfamily_domains:SSF57868 MODERATE 1 SNV 1 1 PASS rs1339841313 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 56609049 56609049 G T 1 0 0 0 0 1 0 0 0 9890 1319 46 2 2 MT2A 16 56609049 Missense_Mutation SNP G C3N-00217_T 133484 56609049 33729296 458 12228 CDH5 0 . GRCh38 16 66402995 66402995 + Silent SNP G G T rs746556861 C3N-00217_T C3N-00217_N G G c.2181G>T p.= p.T727T ENST00000341529 12/12 621 307 314 325 325 0 strelka-varscan-mutect CDH5,synonymous_variant,p.=,ENST00000341529,NM_001795.3;CDH5,synonymous_variant,p.=,ENST00000614547,;CDH5,synonymous_variant,p.=,ENST00000539168,;CDH5,3_prime_UTR_variant,,ENST00000565334,; T ENST00000341529 Transcript synonymous_variant 2329/4120 2181/2355 727/784 T acG/acT rs746556861,COSM558524 1 1 CDH5 HGNC HGNC:1764 protein_coding YES CCDS10804.1 ENSP00000344115 P33151 UPI000016B272 NM_001795.3 12/12 hmmpanther:PTHR24027:SF89,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 0,1 LOW 1 SNV 1 0,1 1 PASS rs746556861 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 66402995 66402995 G T 1 0 0 0 0 0 0 0 1 2816 1074 38 1 1 CDH5 16 66402995 Silent SNP G C3N-00217_T 9793946 66402995 23935350 459 12229 COG4 0 . GRCh38 16 70497371 70497371 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.1331C>T p.Thr444Ile p.T444I ENST00000323786 11/19 624 497 127 396 396 0 strelka-varscan-mutect COG4,missense_variant,p.Thr444Ile,ENST00000323786,NM_015386.2;COG4,missense_variant,p.Thr444Ile,ENST00000393612,NM_001195139.1;COG4,3_prime_UTR_variant,,ENST00000564415,;COG4,3_prime_UTR_variant,,ENST00000482252,;COG4,non_coding_transcript_exon_variant,,ENST00000530314,;COG4,non_coding_transcript_exon_variant,,ENST00000526700,;COG4,upstream_gene_variant,,ENST00000564315,;COG4,downstream_gene_variant,,ENST00000567244,; A ENST00000323786 Transcript missense_variant 1353/2833 1331/2370 444/789 T/I aCc/aTc 1 -1 COG4 HGNC HGNC:18620 protein_coding YES CCDS10892.2 ENSP00000315775 J3KNI1 UPI000059D3B0 NM_015386.2 tolerated(0.1) 11/19 hmmpanther:PTHR24016:SF0,hmmpanther:PTHR24016,Pfam_domain:PF08318,SMART_domains:SM00762 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 70497371 70497371 G A 1 0 0 0 0 1 0 0 0 3448 1261 44 3 3 COG4 16 70497371 Missense_Mutation SNP G C3N-00217_T 4094376 70497371 19840974 460 12230 VAC14 0 . GRCh38 16 70762963 70762963 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.1223T>A p.Leu408His p.L408H ENST00000261776 11/19 467 390 77 262 262 0 strelka-varscan-mutect VAC14,missense_variant,p.Leu408His,ENST00000261776,NM_018052.3;VAC14-AS1,intron_variant,,ENST00000562507,;VAC14-AS1,intron_variant,,ENST00000398177,;VAC14,3_prime_UTR_variant,,ENST00000568548,;VAC14,intron_variant,,ENST00000568886,;VAC14,upstream_gene_variant,,ENST00000563662,; T ENST00000261776 Transcript missense_variant 1484/3099 1223/2349 408/782 L/H cTc/cAc 1 -1 VAC14 HGNC HGNC:25507 protein_coding YES CCDS10896.1 ENSP00000261776 Q08AM6 UPI00001A832B NM_018052.3 deleterious(0) 11/19 hmmpanther:PTHR16023,hmmpanther:PTHR16023:SF0,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 70762963 70762963 A T 1 0 0 0 0 1 0 0 0 17656 304 11 4 4 VAC14 16 70762963 Missense_Mutation SNP A C3N-00217_T 265592 70762963 19575382 461 12231 PKD1L3 0 . GRCh38 16 71953076 71953076 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2827G>T p.Ala943Ser p.A943S ENST00000620267 18/30 101 62 39 85 85 0 strelka-varscan-mutect PKD1L3,missense_variant,p.Ala943Ser,ENST00000620267,NM_181536.1; A ENST00000620267 Transcript missense_variant 2827/5199 2827/5199 943/1732 A/S Gcc/Tcc 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 deleterious(0.01) 18/30 Transmembrane_helices:TMhelix,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 71953076 71953076 C A 1 0 0 0 0 1 0 0 0 12061 739 26 2 2 PKD1L3 16 71953076 Missense_Mutation SNP C C3N-00217_T 1190113 71953076 18385269 462 12232 PKD1L3 0 . GRCh38 16 71954290 71954290 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2624C>A p.Ser875Tyr p.S875Y ENST00000620267 17/30 102 65 37 71 71 0 strelka-varscan-mutect PKD1L3,missense_variant,p.Ser875Tyr,ENST00000620267,NM_181536.1; T ENST00000620267 Transcript missense_variant 2624/5199 2624/5199 875/1732 S/Y tCc/tAc 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 tolerated(0.21) 17/30 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 71954290 71954290 G T 1 0 0 0 0 1 0 0 0 12061 1174 41 2 2 PKD1L3 16 71954290 Missense_Mutation SNP G C3N-00217_T 1214 71954290 18384055 463 12233 PLCG2 0 . GRCh38 16 81891479 81891479 + Missense_Mutation SNP C C A rs772003833 C3N-00217_T C3N-00217_N C C c.875C>A p.Thr292Lys p.T292K ENST00000564138 11/33 149 93 56 128 128 0 strelka-varscan-mutect PLCG2,missense_variant,p.Thr292Lys,ENST00000564138,NM_002661.4;PLCG2,missense_variant,p.Thr292Lys,ENST00000359376,;PLCG2,missense_variant,p.Thr62Lys,ENST00000563193,;PLCG2,non_coding_transcript_exon_variant,,ENST00000562605,;PLCG2,non_coding_transcript_exon_variant,,ENST00000567980,;PLCG2,upstream_gene_variant,,ENST00000570198,;PLCG2,upstream_gene_variant,,ENST00000563375,; A ENST00000564138 Transcript missense_variant 1089/8707 875/3798 292/1265 T/K aCg/aAg rs772003833 1 1 PLCG2 HGNC HGNC:9066 protein_coding YES CCDS42204.1 ENSP00000482457 P16885 UPI00001411F7 NM_002661.4 tolerated(0.39) 11/33 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF25,PIRSF_domain:PIRSF000952,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs772003833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 81891479 81891479 C A 1 0 0 0 0 1 0 0 0 12130 536 19 1 1 PLCG2 16 81891479 Missense_Mutation SNP C C3N-00217_T 9937189 81891479 8446866 464 12234 IRF8 0 . GRCh38 16 85918723 85918723 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.908C>A p.Ala303Asp p.A303D ENST00000268638 7/9 284 173 111 199 199 0 strelka-varscan-mutect IRF8,missense_variant,p.Ala303Asp,ENST00000268638,NM_002163.2;IRF8,missense_variant,p.Ala303Asp,ENST00000564803,;IRF8,missense_variant,p.Ala99Asp,ENST00000562492,;IRF8,missense_variant,p.Ala99Asp,ENST00000569607,;IRF8,intron_variant,,ENST00000566369,;IRF8,downstream_gene_variant,,ENST00000569145,;MIR6774,downstream_gene_variant,,ENST00000614651,; A ENST00000268638 Transcript missense_variant 1330/3030 908/1281 303/426 A/D gCc/gAc 1 1 IRF8 HGNC HGNC:5358 protein_coding YES CCDS10956.1 ENSP00000268638 Q02556 UPI000012D188 NM_002163.2 tolerated(0.62) 7/9 hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF7,Gene3D:2.60.200.10,Pfam_domain:PF10401,SMART_domains:SM01243,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 85918723 85918723 C A 1 0 0 0 0 1 0 0 0 7743 739 26 2 2 IRF8 16 85918723 Missense_Mutation SNP C C3N-00217_T 4027244 85918723 4419622 465 12235 TP53 0 . GRCh38 17 7675145 7675145 + Missense_Mutation SNP C C G rs371524413 C3N-00217_T C3N-00217_N C C c.467G>C p.Arg156Pro p.R156P ENST00000269305 5/11 184 87 97 216 216 0 strelka-varscan-mutect TP53,missense_variant,p.Arg156Pro,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg156Pro,ENST00000420246,;TP53,missense_variant,p.Arg117Pro,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg117Pro,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg156Pro,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg117Pro,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg156Pro,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg117Pro,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg156Pro,ENST00000445888,;TP53,missense_variant,p.Arg117Pro,ENST00000619485,;TP53,missense_variant,p.Arg24Pro,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg24Pro,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg24Pro,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg156Pro,ENST00000359597,;TP53,missense_variant,p.Arg145Pro,ENST00000615910,;TP53,missense_variant,p.Arg156Pro,ENST00000413465,;TP53,missense_variant,p.Arg24Pro,ENST00000509690,;TP53,missense_variant,p.Arg156Pro,ENST00000508793,;TP53,missense_variant,p.Arg63Pro,ENST00000514944,;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg117Pro,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 657/2579 467/1182 156/393 R/P cGc/cCc rs371524413,CM984589,TP53_g.12455G>A,TP53_g.12455del,TP53_g.12455G>C,TP53_g.12455G>T,COSM10760,COSM1522489,COSM1522490,COSM1522491,COSM1522492,COSM2744905,COSM3712457,COSM3970367,COSM3970368,COSM3970369,COSM3970370,COSM3970371,COSM3970372,COSM43548,COSM43739,COSM45530 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 tolerated(0.22) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs371524413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 7675145 7675145 C G 1 0 0 0 0 1 0 0 0 16859 768 27 4 4 TP53 17 7675145 Missense_Mutation SNP C C3N-00217_T 7675145 75582296 466 12236 ALOXE3 0 . GRCh38 17 8112110 8112110 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1163A>T p.His388Leu p.H388L ENST00000318227 7/16 236 135 101 330 330 0 strelka-varscan-mutect ALOXE3,missense_variant,p.His412Leu,ENST00000380149,;ALOXE3,missense_variant,p.His256Leu,ENST00000448843,NM_021628.2;ALOXE3,missense_variant,p.His388Leu,ENST00000318227,NM_001165960.1; A ENST00000318227 Transcript missense_variant 1432/3053 1163/2532 388/843 H/L cAt/cTt 1 -1 ALOXE3 HGNC HGNC:13743 protein_coding YES CCDS54084.1 ENSP00000314879 Q9BYJ1 UPI0000EE63AA NM_001165960.1 tolerated(0.22) 7/16 PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF62,Superfamily_domains:SSF48484 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 8112110 8112110 T A 1 0 0 0 0 1 0 0 0 642 1464 51 4 4 ALOXE3 17 8112110 Missense_Mutation SNP T C3N-00217_T 436965 8112110 75145331 467 12237 MYH13 0 . GRCh38 17 10333122 10333122 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2126G>A p.Cys709Tyr p.C709Y ENST00000418404 18/41 108 67 41 109 109 0 strelka-varscan-mutect MYH13,missense_variant,p.Cys709Tyr,ENST00000418404,;MYH13,missense_variant,p.Cys709Tyr,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Cys709Tyr,ENST00000621918,;RP11-401O9.3,intron_variant,,ENST00000577743,; T ENST00000418404 Transcript missense_variant 2290/6296 2126/5817 709/1938 C/Y tGc/tAc 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0.03) 18/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS rs931730352 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 10333122 10333122 C T 1 0 0 0 0 1 0 0 0 10032 710 25 3 3 MYH13 17 10333122 Missense_Mutation SNP C C3N-00217_T 2221012 10333122 72924319 468 12238 MYH1 0 . GRCh38 17 10516592 10516592 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.51C>A p.= p.L17L ENST00000226207 3/40 201 124 77 276 275 1 strelka-varscan-mutect MYH1,synonymous_variant,p.=,ENST00000226207,NM_005963.3;MYH2,downstream_gene_variant,,ENST00000245503,NM_017534.5;MYH2,downstream_gene_variant,,ENST00000397183,NM_001100112.1;MYH2,downstream_gene_variant,,ENST00000532183,;MYH2,downstream_gene_variant,,ENST00000622564,;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript synonymous_variant 146/6024 51/5820 17/1939 L ctC/ctA 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 3/40 LOW SNV 5 1 PASS rs1351101332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 10516592 10516592 G T 1 0 0 0 0 0 0 0 1 10029 1161 41 2 2 MYH1 17 10516592 Silent SNP G C3N-00217_T 183470 10516592 72740849 469 12239 MYH3 0 . GRCh38 17 10631822 10631822 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.5151G>T p.= p.L1717L ENST00000583535 35/41 346 200 146 492 492 0 strelka-varscan-mutect MYH3,synonymous_variant,p.=,ENST00000583535,NM_002470.3;MYH3,upstream_gene_variant,,ENST00000577963,;MYH3,upstream_gene_variant,,ENST00000579928,; A ENST00000583535 Transcript synonymous_variant 5239/6037 5151/5823 1717/1940 L ctG/ctT 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 35/41 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF427,Pfam_domain:PF01576,Superfamily_domains:SSF57997 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 10631822 10631822 C A 1 0 0 0 0 0 0 0 1 10036 697 25 2 2 MYH3 17 10631822 Silent SNP C C3N-00217_T 115230 10631822 72625619 470 12240 NCOR1 0 . GRCh38 17 16153388 16153388 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.740C>T p.Ala247Val p.A247V ENST00000268712 7/46 59 44 15 108 108 0 strelka-varscan-mutect NCOR1,missense_variant,p.Ala247Val,ENST00000268712,NM_006311.3;NCOR1,missense_variant,p.Ala138Val,ENST00000395857,;NCOR1,missense_variant,p.Ala247Val,ENST00000395851,NM_001190440.1;NCOR1,missense_variant,p.Ala138Val,ENST00000395848,NM_001190438.1;NCOR1,missense_variant,p.Ala247Val,ENST00000436828,;NCOR1,missense_variant,p.Ala247Val,ENST00000411510,;NCOR1,missense_variant,p.Ala247Val,ENST00000582357,;NCOR1,3_prime_UTR_variant,,ENST00000460276,; A ENST00000268712 Transcript missense_variant 998/10720 740/7323 247/2440 A/V gCa/gTa 1 -1 NCOR1 HGNC HGNC:7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 A0A024RD47 UPI000013D7D5 NM_006311.3 deleterious(0) 7/46 hmmpanther:PTHR13992:SF5,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 16153388 16153388 G A 1 0 0 0 0 1 0 0 0 10254 1319 46 3 3 NCOR1 17 16153388 Missense_Mutation SNP G C3N-00217_T 5521566 16153388 67104053 471 12241 CCDC144A 0 . GRCh38 17 16732601 16732601 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.2353C>G p.Gln785Glu p.Q785E ENST00000360524 11/18 77 50 27 165 165 0 strelka-varscan-mutect CCDC144A,missense_variant,p.Gln785Glu,ENST00000399273,;CCDC144A,missense_variant,p.Gln785Glu,ENST00000360524,NM_014695.2;CCDC144A,downstream_gene_variant,,ENST00000456009,;RP11-219A15.1,missense_variant,p.Gln785Glu,ENST00000448331,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000470068,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000328495,;CCDC144A,intron_variant,,ENST00000360495,;CCDC144A,downstream_gene_variant,,ENST00000463809,; G ENST00000360524 Transcript missense_variant 2429/5830 2353/4284 785/1427 Q/E Caa/Gaa 1 1 CCDC144A HGNC HGNC:29072 protein_coding YES CCDS45621.1 ENSP00000353717 A2RUR9 UPI0000F095D0 NM_014695.2 deleterious(0) 11/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 16732601 16732601 C G 1 0 0 0 0 1 0 0 0 2465 479 17 4 4 CCDC144A 17 16732601 Missense_Mutation SNP C C3N-00217_T 579213 16732601 66524840 472 12242 TVP23B 0 . GRCh38 17 18797633 18797633 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.295G>T p.Asp99Tyr p.D99Y ENST00000307767 4/7 48 27 21 99 99 0 strelka-varscan-mutect TVP23B,missense_variant,p.Asp35Tyr,ENST00000476139,NM_001316919.1;TVP23B,missense_variant,p.Asp99Tyr,ENST00000307767,NM_001316921.1,NM_016078.4;TVP23B,missense_variant,p.Asp35Tyr,ENST00000581733,;TVP23B,missense_variant,p.Asp99Tyr,ENST00000574226,;TVP23B,missense_variant,p.Asp35Tyr,ENST00000575261,;TVP23B,3_prime_UTR_variant,,ENST00000574294,;TVP23B,3_prime_UTR_variant,,ENST00000571018,;TVP23B,non_coding_transcript_exon_variant,,ENST00000482741,;TVP23B,non_coding_transcript_exon_variant,,ENST00000572845,; T ENST00000307767 Transcript missense_variant 594/2064 295/618 99/205 D/Y Gat/Tat 1 1 TVP23B HGNC HGNC:20399 protein_coding YES CCDS42274.1 ENSP00000305654 Q9NYZ1 UPI00000713C4 NM_001316921.1,NM_016078.4 deleterious(0) 4/7 hmmpanther:PTHR13019,hmmpanther:PTHR13019:SF9,Pfam_domain:PF05832 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 18797633 18797633 G T 1 0 0 0 0 1 0 0 0 17294 942 33 2 2 TVP23B 17 18797633 Missense_Mutation SNP G C3N-00217_T 2065032 18797633 64459808 473 12243 SLC5A10 0 . GRCh38 17 19019447 19019447 + Silent SNP C C G rs775065880 C3N-00217_T C3N-00217_N C C c.1314C>G p.= p.G438G ENST00000395647 12/15 86 43 43 93 93 0 strelka-varscan-mutect SLC5A10,synonymous_variant,p.=,ENST00000317977,NM_001282417.1;SLC5A10,synonymous_variant,p.=,ENST00000395647,NM_152351.4;SLC5A10,synonymous_variant,p.=,ENST00000395645,NM_001042450.2;SLC5A10,synonymous_variant,p.=,ENST00000417251,NM_001270649.1;SLC5A10,synonymous_variant,p.=,ENST00000395643,NM_001270648.1;GRAP,downstream_gene_variant,,ENST00000284154,NM_006613.3;GRAP,downstream_gene_variant,,ENST00000573099,;GRAP,downstream_gene_variant,,ENST00000395635,;SLC5A10,non_coding_transcript_exon_variant,,ENST00000584658,;GRAP,downstream_gene_variant,,ENST00000583020,; G ENST00000395647 Transcript synonymous_variant 1355/2140 1314/1839 438/612 G ggC/ggG rs775065880 1 1 SLC5A10 HGNC HGNC:23155 protein_coding YES CCDS11201.2 ENSP00000379008 A0PJK1 UPI00001401D2 NM_152351.4 12/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF128,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS rs775065880 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 19019447 19019447 C G 1 0 0 0 0 0 0 0 1 14945 755 27 4 4 SLC5A10 17 19019447 Silent SNP C C3N-00217_T 221814 19019447 64237994 474 12244 KIAA0100 0 . GRCh38 17 28644999 28644999 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.58T>C p.Phe20Leu p.F20L ENST00000528896 1/39 324 202 122 266 266 0 strelka-varscan-mutect KIAA0100,missense_variant,p.Phe20Leu,ENST00000528896,NM_014680.3;KIAA0100,intron_variant,,ENST00000544884,;KIAA0100,intron_variant,,ENST00000389003,;SDF2,downstream_gene_variant,,ENST00000247020,NM_006923.3;SDF2,downstream_gene_variant,,ENST00000587788,;SDF2,downstream_gene_variant,,ENST00000592250,;SDF2,downstream_gene_variant,,ENST00000585749,;SDF2,downstream_gene_variant,,ENST00000587629,;SDF2,downstream_gene_variant,,ENST00000588472,;SDF2,downstream_gene_variant,,ENST00000587338,;KIAA0100,missense_variant,p.Phe20Leu,ENST00000583403,;KIAA0100,non_coding_transcript_exon_variant,,ENST00000577417,;KIAA0100,non_coding_transcript_exon_variant,,ENST00000580882,;SDF2,downstream_gene_variant,,ENST00000589788,;SDF2,downstream_gene_variant,,ENST00000591903,;KIAA0100,upstream_gene_variant,,ENST00000577580,;KIAA0100,upstream_gene_variant,,ENST00000582901,;KIAA0100,upstream_gene_variant,,ENST00000581267,;KIAA0100,upstream_gene_variant,,ENST00000579253,; G ENST00000528896 Transcript missense_variant 133/7407 58/6708 20/2235 F/L Ttt/Ctt 1 -1 KIAA0100 HGNC HGNC:28960 protein_coding YES CCDS32595.1 ENSP00000436773 Q14667 UPI00004B4130 NM_014680.3 tolerated(0.72) 1/39 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR15678 MODERATE 1 SNV 1 1 PASS rs1474763375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 28644999 28644999 A G 1 0 0 0 0 1 0 0 0 8074 72 3 5 5 KIAA0100 17 28644999 Missense_Mutation SNP A C3N-00217_T 9625552 28644999 54612442 475 12245 CCL23 0 . GRCh38 17 36013299 36013299 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.312C>A p.= p.T104T ENST00000615050 4/4 133 88 45 118 118 0 strelka-varscan-mutect CCL23,synonymous_variant,p.=,ENST00000615050,NM_005064.5;CCL23,synonymous_variant,p.=,ENST00000612516,NM_145898.3;RP11-104J23.2,downstream_gene_variant,,ENST00000617747,;RP11-104J23.1,downstream_gene_variant,,ENST00000617328,;RP11-104J23.1,downstream_gene_variant,,ENST00000619334,;CCL23,3_prime_UTR_variant,,ENST00000613876,; T ENST00000615050 Transcript synonymous_variant 383/624 312/414 104/137 T acC/acA 1 -1 CCL23 HGNC HGNC:10622 protein_coding YES CCDS11305.1 ENSP00000481357 P55773 UPI000002B480 NM_005064.5 4/4 hmmpanther:PTHR12015:SF77,hmmpanther:PTHR12015,PROSITE_patterns:PS00472,Pfam_domain:PF00048,Gene3D:2.40.50.40,SMART_domains:SM00199,Superfamily_domains:SSF54117 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 36013299 36013299 G T 1 0 0 0 0 0 0 0 1 2593 1335 47 2 2 CCL23 17 36013299 Silent SNP G C3N-00217_T 7368300 36013299 47244142 476 12246 CCL23 0 . GRCh38 17 36013745 36013745 + Missense_Mutation SNP T T A rs778736599 C3N-00217_T C3N-00217_N T T c.301A>T p.Ile101Phe p.I101F ENST00000615050 3/4 114 72 42 73 73 0 strelka-varscan-mutect CCL23,missense_variant,p.Ile101Phe,ENST00000615050,NM_005064.5;CCL23,missense_variant,p.Ile84Phe,ENST00000612516,NM_145898.3;RP11-104J23.2,downstream_gene_variant,,ENST00000617747,;RP11-104J23.1,downstream_gene_variant,,ENST00000617328,;RP11-104J23.1,downstream_gene_variant,,ENST00000619334,;CCL23,missense_variant,p.Met13Leu,ENST00000613876,; A ENST00000615050 Transcript missense_variant,splice_region_variant 372/624 301/414 101/137 I/F Atc/Ttc rs778736599 1 -1 CCL23 HGNC HGNC:10622 protein_coding YES CCDS11305.1 ENSP00000481357 P55773 UPI000002B480 NM_005064.5 deleterious(0) 3/4 hmmpanther:PTHR12015:SF77,hmmpanther:PTHR12015,PROSITE_patterns:PS00472,Pfam_domain:PF00048,Gene3D:2.40.50.40,SMART_domains:SM00199,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS rs778736599 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 36013745 36013745 T A 1 0 0 0 0 1 0 0 0 2593 1478 51 4 4 CCL23 17 36013745 Missense_Mutation SNP T C3N-00217_T 446 36013745 47243696 477 12247 ARHGAP23 0 . GRCh38 17 38510943 38510943 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.4447G>T p.Ala1483Ser p.A1483S ENST00000622683 24/24 145 101 44 110 110 0 strelka-varscan-mutect ARHGAP23,missense_variant,p.Ala1483Ser,ENST00000622683,NM_001199417.1;ARHGAP23,downstream_gene_variant,,ENST00000620417,;ARHGAP23,downstream_gene_variant,,ENST00000620329,;ARHGAP23,downstream_gene_variant,,ENST00000618325,; T ENST00000622683 Transcript missense_variant 4515/5964 4447/4476 1483/1491 A/S Gcc/Tcc 1 1 ARHGAP23 HGNC HGNC:29293 protein_coding YES CCDS56027.1 ENSP00000481862 Q9P227 UPI0000F3BE51 NM_001199417.1 tolerated_low_confidence(0.09) 24/24 hmmpanther:PTHR23175:SF5,hmmpanther:PTHR23175 MODERATE 1 SNV 5 1 PASS rs1427166342 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 38510943 38510943 G T 1 0 0 0 0 1 0 0 0 997 1203 42 2 2 ARHGAP23 17 38510943 Missense_Mutation SNP G C3N-00217_T 2497198 38510943 44746498 478 12248 MLLT6 0 . GRCh38 17 38717544 38717544 + Silent SNP G G T rs765344795 C3N-00217_T C3N-00217_N G G c.1764G>T p.= p.L588L ENST00000621332 11/20 155 119 36 84 84 0 strelka-varscan-mutect MLLT6,synonymous_variant,p.=,ENST00000621332,NM_005937.3;MLLT6,synonymous_variant,p.=,ENST00000615858,;MLLT6,downstream_gene_variant,,ENST00000620609,;MIR4726,upstream_gene_variant,,ENST00000615971,;CTB-58E17.9,intron_variant,,ENST00000620144,;MLLT6,non_coding_transcript_exon_variant,,ENST00000612066,;MLLT6,upstream_gene_variant,,ENST00000619356,;MLLT6,downstream_gene_variant,,ENST00000620482,;MLLT6,downstream_gene_variant,,ENST00000618652,; T ENST00000621332 Transcript synonymous_variant 1855/7578 1764/3282 588/1093 L ctG/ctT rs765344795 1 1 MLLT6 HGNC HGNC:7138 protein_coding YES CCDS11327.1 ENSP00000479910 A0A087WW39 UPI00004B412B NM_005937.3 11/20 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF90,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs765344795 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 38717544 38717544 G T 1 0 0 0 0 0 0 0 1 9593 1306 46 2 2 MLLT6 17 38717544 Silent SNP G C3N-00217_T 206601 38717544 44539897 479 12249 KRTAP2-4 0 . GRCh38 17 41065553 41065553 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.293G>T p.Cys98Phe p.C98F ENST00000394015 1/1 53 48 5 79 79 0 varscan-mutect KRTAP2-4,missense_variant,p.Cys98Phe,ENST00000394015,NM_033184.3; A ENST00000394015 Transcript missense_variant 327/764 293/387 98/128 C/F tGc/tTc 1 -1 KRTAP2-4 HGNC HGNC:18891 protein_coding YES CCDS32648.1 ENSP00000377583 Q9BYR9 UPI000006EB3A NM_033184.3 deleterious(0) 1/1 hmmpanther:PTHR23262:SF6,hmmpanther:PTHR23262,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS rs1468860840 . 0 206 4 0 0 0 0 0 -12.32595 1 1 1 1 0 A 3 1 43 41065553 41065553 C A 1 0 0 0 0 1 0 0 0 8422 710 25 2 2 KRTAP2-4 17 41065553 Missense_Mutation SNP C C3N-00217_T 2348009 41065553 42191888 480 12250 WNK4 0 . GRCh38 17 42796258 42796258 + Silent SNP C C A rs769688931 C3N-00217_T C3N-00217_N C C c.3567C>A p.= p.L1189L ENST00000246914 17/19 138 99 39 121 121 0 strelka-varscan-mutect WNK4,synonymous_variant,p.=,ENST00000246914,NM_032387.4;CNTD1,upstream_gene_variant,,ENST00000588408,NM_173478.2;CNTD1,upstream_gene_variant,,ENST00000588527,;COA3,downstream_gene_variant,,ENST00000328434,NM_001040431.2;CNTD1,upstream_gene_variant,,ENST00000585355,;WNK4,downstream_gene_variant,,ENST00000587745,;CNTD1,upstream_gene_variant,,ENST00000591559,;WNK4,3_prime_UTR_variant,,ENST00000591448,NM_001321299.1;COA3,intron_variant,,ENST00000586680,;WNK4,downstream_gene_variant,,ENST00000592072,;CNTD1,upstream_gene_variant,,ENST00000592166,; A ENST00000246914 Transcript synonymous_variant 3588/4001 3567/3732 1189/1243 L ctC/ctA rs769688931 1 1 WNK4 HGNC HGNC:14544 protein_coding YES CCDS11439.1 ENSP00000246914 Q96J92 UPI000006FC0F NM_032387.4 17/19 hmmpanther:PTHR13902:SF52,hmmpanther:PTHR13902 LOW 1 SNV 1 1 PASS rs769688931 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 42796258 42796258 C A 1 0 0 0 0 0 0 0 1 17936 900 32 2 2 WNK4 17 42796258 Silent SNP C C3N-00217_T 1730705 42796258 40461183 481 12251 FAM171A2 0 . GRCh38 17 44360074 44360074 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.177C>A p.= p.A59A ENST00000293443 2/8 202 141 61 172 171 1 strelka-varscan-mutect FAM171A2,synonymous_variant,p.=,ENST00000293443,NM_198475.2;FAM171A2,synonymous_variant,p.=,ENST00000589407,;FAM171A2,synonymous_variant,p.=,ENST00000588067,;FAM171A2,non_coding_transcript_exon_variant,,ENST00000592560,;RPL7L1P5,downstream_gene_variant,,ENST00000590816,; T ENST00000293443 Transcript synonymous_variant 338/3160 177/2481 59/826 A gcC/gcA 1 -1 FAM171A2 HGNC HGNC:30480 protein_coding YES CCDS45701.1 ENSP00000293443 A8MVW0 UPI0000E59FC0 NM_198475.2 2/8 Pfam_domain:PF10577,hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 44360074 44360074 G T 1 0 0 0 0 0 0 0 1 5338 987 35 2 2 FAM171A2 17 44360074 Silent SNP G C3N-00217_T 1563816 44360074 38897367 482 12252 CCDC103 0 . GRCh38 17 44901142 44901142 + Splice_Site SNP G G T novel C3N-00217_T C3N-00217_N G G c.143+1G>T p.X48_splice ENST00000412523 313 227 86 262 262 0 strelka-varscan-mutect FAM187A,splice_donor_variant,,ENST00000331733,;CCDC103,splice_donor_variant,,ENST00000417826,;FAM187A,splice_donor_variant,,ENST00000412523,NM_001258399.1,NM_001258396.1,NM_213607.2,NM_001258395.1;CCDC103,splice_donor_variant,,ENST00000410006,;CCDC103,splice_donor_variant,,ENST00000357776,NM_001258398.1;CCDC103,splice_donor_variant,,ENST00000577339,;CCDC103,splice_donor_variant,,ENST00000410027,NM_001258397.1;EFTUD2,upstream_gene_variant,,ENST00000426333,NM_004247.3;EFTUD2,upstream_gene_variant,,ENST00000591382,NM_001258353.1;EFTUD2,upstream_gene_variant,,ENST00000592576,NM_001258354.1;GFAP,downstream_gene_variant,,ENST00000253408,NM_002055.4;EFTUD2,upstream_gene_variant,,ENST00000402521,NM_001142605.1;EFTUD2,upstream_gene_variant,,ENST00000592701,;EFTUD2,upstream_gene_variant,,ENST00000593072,;AC015936.3,downstream_gene_variant,,ENST00000441312,;GFAP,downstream_gene_variant,,ENST00000592065,;EFTUD2,upstream_gene_variant,,ENST00000589825,;EFTUD2,upstream_gene_variant,,ENST00000592408,;EFTUD2,upstream_gene_variant,,ENST00000590105,; T ENST00000412523 Transcript splice_donor_variant -/1748 143/729 48/242 1 1 FAM187A HGNC HGNC:35153 protein_coding YES CCDS11490.1 ENSP00000391869 UPI0000074564 NM_001258399.1,NM_001258396.1,NM_213607.2,NM_001258395.1 2/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 44901142 44901142 G T 1 0 0 0 0 0 0 1 0 2436 1275 44 2 2 CCDC103 17 44901142 Splice_Site SNP G C3N-00217_T 541068 44901142 38356299 483 12253 GOSR2 0 . GRCh38 17 46923217 46923217 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.25C>A p.His9Asn p.H9N ENST00000225567 1/7 275 254 21 185 184 1 strelka-varscan-mutect GOSR2,missense_variant,p.His9Asn,ENST00000415811,NM_001012511.1;GOSR2,missense_variant,p.His9Asn,ENST00000576910,;GOSR2,missense_variant,p.His9Asn,ENST00000225567,NM_054022.2;GOSR2,missense_variant,p.His9Asn,ENST00000393456,NM_004287.3;GOSR2,missense_variant,p.His9Asn,ENST00000575949,;GOSR2,missense_variant,p.His8Asn,ENST00000570879,;GOSR2,5_prime_UTR_variant,,ENST00000572403,;RP11-63A1.1,upstream_gene_variant,,ENST00000572349,;RNU6ATAC3P,downstream_gene_variant,,ENST00000387974,;RP11-156P1.2,missense_variant,p.His9Asn,ENST00000571841,;GOSR2,non_coding_transcript_exon_variant,,ENST00000571048,;GOSR2,non_coding_transcript_exon_variant,,ENST00000571658,; A ENST00000225567 Transcript missense_variant 56/855 25/642 9/213 H/N Cac/Aac 1 1 GOSR2 HGNC HGNC:4431 protein_coding YES CCDS11507.1 ENSP00000225567 O14653 UPI000002AACF NM_054022.2 tolerated(1) 1/7 PIRSF_domain:PIRSF028865,hmmpanther:PTHR21230,hmmpanther:PTHR21230:SF1,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS rs1345998860 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 46923217 46923217 C A 1 0 0 0 0 1 0 0 0 6472 724 25 2 2 GOSR2 17 46923217 Missense_Mutation SNP C C3N-00217_T 2022075 46923217 36334224 484 12254 HOXB13 0 . GRCh38 17 48728196 48728196 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.398A>T p.Tyr133Phe p.Y133F ENST00000290295 1/2 490 403 87 405 404 1 strelka-varscan-mutect HOXB13,missense_variant,p.Tyr133Phe,ENST00000290295,NM_006361.5;PRAC2,downstream_gene_variant,,ENST00000422730,NM_001282275.1;PRAC2,downstream_gene_variant,,ENST00000432056,NM_001282276.1;CTD-2377D24.4,upstream_gene_variant,,ENST00000495536,;MIR3185,upstream_gene_variant,,ENST00000583892,;HOXB13-AS1_1,downstream_gene_variant,,ENST00000613209,;HOXB13-AS1_2,downstream_gene_variant,,ENST00000612962,; A ENST00000290295 Transcript missense_variant 983/3467 398/855 133/284 Y/F tAt/tTt 1 -1 HOXB13 HGNC HGNC:5112 protein_coding YES CCDS11536.1 ENSP00000290295 Q92826 UPI000006F288 NM_006361.5 tolerated(0.27) 1/2 hmmpanther:PTHR24326:SF47,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 48728196 48728196 T A 1 0 0 0 0 1 0 0 0 7194 1406 49 4 4 HOXB13 17 48728196 Missense_Mutation SNP T C3N-00217_T 1804979 48728196 34529245 485 12255 SCN4A 0 . GRCh38 17 63944727 63944727 + Silent SNP G G T rs538933926 C3N-00217_T C3N-00217_N G G c.3858C>A p.= p.T1286T ENST00000435607 21/24 166 119 47 201 201 0 strelka-varscan-mutect SCN4A,synonymous_variant,p.=,ENST00000435607,NM_000334.4;SCN4A,synonymous_variant,p.=,ENST00000578147,;SCN4A,downstream_gene_variant,,ENST00000584310,; T ENST00000435607 Transcript synonymous_variant 3935/7805 3858/5511 1286/1836 T acC/acA rs538933926 1 -1 SCN4A HGNC HGNC:10591 protein_coding YES CCDS45761.1 ENSP00000396320 P35499 UPI0000201254 NM_000334.4 21/24 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF223,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs538933926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 63944727 63944727 G T 1 0 0 0 0 0 0 0 1 14189 1219 43 2 2 SCN4A 17 63944727 Silent SNP G C3N-00217_T 15216531 63944727 19312714 486 12256 ABCA6 0 . GRCh38 17 69134722 69134722 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.481G>A p.Gly161Ser p.G161S ENST00000284425 5/39 201 146 55 221 221 0 strelka-varscan-mutect ABCA6,missense_variant,p.Gly161Ser,ENST00000284425,NM_080284.2;ABCA6,downstream_gene_variant,,ENST00000590645,; T ENST00000284425 Transcript missense_variant 656/5300 481/4854 161/1617 G/S Ggt/Agt 1 -1 ABCA6 HGNC HGNC:36 protein_coding YES CCDS11683.1 ENSP00000284425 Q8N139 UPI000013DD9D NM_080284.2 tolerated(0.91) 5/39 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 69134722 69134722 C T 1 0 0 0 0 1 0 0 0 40 594 21 3 3 ABCA6 17 69134722 Missense_Mutation SNP C C3N-00217_T 5189995 69134722 14122719 487 12257 ABCA5 0 . GRCh38 17 69270680 69270680 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.2963G>A p.Ser988Asn p.S988N ENST00000392676 22/39 51 40 11 69 69 0 strelka-varscan-mutect ABCA5,missense_variant,p.Ser988Asn,ENST00000392676,NM_172232.3;ABCA5,missense_variant,p.Ser988Asn,ENST00000588877,NM_018672.4;ABCA5,downstream_gene_variant,,ENST00000593153,;ABCA5,upstream_gene_variant,,ENST00000586811,;ABCA5,3_prime_UTR_variant,,ENST00000586995,;ABCA5,3_prime_UTR_variant,,ENST00000591234,; T ENST00000392676 Transcript missense_variant 3028/8220 2963/4929 988/1642 S/N aGt/aAt 1 -1 ABCA5 HGNC HGNC:35 protein_coding YES CCDS11685.1 ENSP00000376443 Q8WWZ7 UPI000013DD9E NM_172232.3 deleterious(0) 22/39 Transmembrane_helices:TMhelix,hmmpanther:PTHR19229:SF100,hmmpanther:PTHR19229,Pfam_domain:PF12698 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 69270680 69270680 C T 1 0 0 0 0 1 0 0 0 39 565 20 3 3 ABCA5 17 69270680 Missense_Mutation SNP C C3N-00217_T 135958 69270680 13986761 488 12258 OTOP3 0 . GRCh38 17 74941552 74941552 + Missense_Mutation SNP G G A rs745958249 C3N-00217_T C3N-00217_N G G c.233G>A p.Arg78Gln p.R78Q ENST00000328801 2/7 100 63 37 61 61 0 strelka-varscan-mutect OTOP3,missense_variant,p.Arg78Gln,ENST00000328801,NM_001272005.1,NM_178233.2;OTOP3,3_prime_UTR_variant,,ENST00000580749,; A ENST00000328801 Transcript missense_variant 233/2363 233/1791 78/596 R/Q cGg/cAg rs745958249,COSM1610742 1 1 OTOP3 HGNC HGNC:19658 protein_coding YES CCDS11709.1 ENSP00000328090 Q7RTS5 UPI000019097F NM_001272005.1,NM_178233.2 tolerated(0.51) 2/7 hmmpanther:PTHR21522:SF36,hmmpanther:PTHR21522 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs745958249 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 74941552 74941552 G A 1 0 0 0 0 1 0 0 0 11375 1116 39 1 1 OTOP3 17 74941552 Missense_Mutation SNP G C3N-00217_T 5670872 74941552 8315889 489 12259 LLGL2 0 . GRCh38 17 75569254 75569254 + Missense_Mutation SNP C C T rs781542922 C3N-00217_T C3N-00217_N C C c.1510C>T p.Arg504Trp p.R504W ENST00000392550 14/26 191 144 47 149 149 0 strelka-varscan-mutect LLGL2,missense_variant,p.Arg504Trp,ENST00000392550,NM_001031803.1;LLGL2,missense_variant,p.Arg504Trp,ENST00000167462,NM_004524.2;LLGL2,missense_variant,p.Arg504Trp,ENST00000577200,;LLGL2,downstream_gene_variant,,ENST00000578363,;LLGL2,downstream_gene_variant,,ENST00000375227,NM_001015002.1;LLGL2,synonymous_variant,p.=,ENST00000578719,;LLGL2,3_prime_UTR_variant,,ENST00000578638,;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227,;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500,;LLGL2,downstream_gene_variant,,ENST00000580027,;LLGL2,upstream_gene_variant,,ENST00000579092,;LLGL2,upstream_gene_variant,,ENST00000582393,;LLGL2,upstream_gene_variant,,ENST00000577211,;LLGL2,upstream_gene_variant,,ENST00000578034,;LLGL2,upstream_gene_variant,,ENST00000583514,; T ENST00000392550 Transcript missense_variant 1627/3509 1510/3063 504/1020 R/W Cgg/Tgg rs781542922,COSM4467855,COSM4467856 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 deleterious(0) 14/26 Gene3D:2.130.10.10,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF20,Superfamily_domains:SSF50978,Superfamily_domains:SSF50978 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs781542922 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 75569254 75569254 C T 1 0 0 0 0 1 0 0 0 8758 643 23 1 1 LLGL2 17 75569254 Missense_Mutation SNP C C3N-00217_T 627702 75569254 7688187 490 12260 RNF157 0 . GRCh38 17 76159465 76159465 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1174G>T p.Gly392Cys p.G392C ENST00000269391 12/19 145 108 37 144 144 0 strelka-varscan-mutect RNF157,missense_variant,p.Gly392Cys,ENST00000269391,NM_052916.2;RNF157,missense_variant,p.Gly392Cys,ENST00000319945,;RNF157,downstream_gene_variant,,ENST00000591615,;RNF157,upstream_gene_variant,,ENST00000591355,;RP11-449J21.5,downstream_gene_variant,,ENST00000586661,;RP11-449J21.5,downstream_gene_variant,,ENST00000592748,;RNF157,upstream_gene_variant,,ENST00000592869,;RNF157,downstream_gene_variant,,ENST00000593155,; A ENST00000269391 Transcript missense_variant 1307/4955 1174/2040 392/679 G/C Ggc/Tgc 1 -1 RNF157 HGNC HGNC:29402 protein_coding YES CCDS32740.1 ENSP00000269391 Q96PX1 UPI00001C1FDD NM_052916.2 tolerated(0.08) 12/19 hmmpanther:PTHR22996:SF1,hmmpanther:PTHR22996 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 76159465 76159465 C A 1 0 0 0 0 1 0 0 0 13632 594 21 2 2 RNF157 17 76159465 Missense_Mutation SNP C C3N-00217_T 590211 76159465 7097976 491 12261 RNF213 0 . GRCh38 17 80346557 80346557 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.8222C>G p.Thr2741Ser p.T2741S ENST00000582970 29/68 516 447 69 400 400 0 strelka-varscan-mutect RNF213,missense_variant,p.Thr2741Ser,ENST00000582970,NM_001256071.2;RNF213,missense_variant,p.Thr2790Ser,ENST00000508628,;CTD-2047H16.3,downstream_gene_variant,,ENST00000622931,; G ENST00000582970 Transcript missense_variant 8365/21055 8222/15624 2741/5207 T/S aCc/aGc 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 deleterious(0.01) 29/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 80346557 80346557 C G 1 0 0 0 0 1 0 0 0 13656 507 18 4 4 RNF213 17 80346557 Missense_Mutation SNP C C3N-00217_T 4187092 80346557 2910884 492 12262 EMILIN2 0 . GRCh38 18 2891042 2891042 + Silent SNP G G T rs114420829 C3N-00217_T C3N-00217_N G G c.915G>T p.= p.T305T ENST00000254528 4/8 379 252 127 324 323 1 strelka-varscan-mutect EMILIN2,synonymous_variant,p.=,ENST00000254528,NM_032048.2; T ENST00000254528 Transcript synonymous_variant 1074/5910 915/3162 305/1053 T acG/acT rs114420829 1 1 EMILIN2 HGNC HGNC:19881 protein_coding YES CCDS11828.1 ENSP00000254528 Q9BXX0 UPI000013CE3E NM_032048.2 4/8 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF5 LOW 1 SNV 1 1 PASS rs114420829 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 2891042 2891042 G T 1 0 0 0 0 0 0 0 1 4937 1103 39 1 1 EMILIN2 18 2891042 Silent SNP G C3N-00217_T 2891042 77482243 493 12263 LAMA1 0 . GRCh38 18 6978295 6978295 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.6091G>T p.Gly2031Trp p.G2031W ENST00000389658 43/63 432 317 115 329 328 1 strelka-varscan-mutect LAMA1,missense_variant,p.Gly2031Trp,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript missense_variant 6185/9657 6091/9228 2031/3075 G/W Ggg/Tgg 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 43/63 Pfam_domain:PF06009,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 6978295 6978295 C A 1 0 0 0 0 1 0 0 0 8509 623 22 2 2 LAMA1 18 6978295 Missense_Mutation SNP C C3N-00217_T 4087253 6978295 73394990 494 12264 AFG3L2 0 . GRCh38 18 12329765 12329765 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2194G>T p.Glu732Ter p.E732* ENST00000269143 17/17 254 176 78 237 236 1 strelka-varscan-mutect AFG3L2,stop_gained,p.Glu732Ter,ENST00000269143,NM_006796.2;TUBB6,3_prime_UTR_variant,,ENST00000591909,NM_001303525.1;TUBB6,intron_variant,,ENST00000590967,;TUBB6,intron_variant,,ENST00000586691,;TUBB6,downstream_gene_variant,,ENST00000317702,NM_001303524.1,NM_032525.2,NM_001303529.1;TUBB6,downstream_gene_variant,,ENST00000591208,;TUBB6,downstream_gene_variant,,ENST00000590103,NM_001303526.1;TUBB6,downstream_gene_variant,,ENST00000586653,;TUBB6,downstream_gene_variant,,ENST00000590693,;TUBB6,downstream_gene_variant,,ENST00000591463,;TUBB6,downstream_gene_variant,,ENST00000592683,;TUBB6,downstream_gene_variant,,ENST00000417736,;TUBB6,downstream_gene_variant,,ENST00000586810,;TUBB6,downstream_gene_variant,,ENST00000590388,; A ENST00000269143 Transcript stop_gained 2426/3247 2194/2394 732/797 E/* Gaa/Taa 1 -1 AFG3L2 HGNC HGNC:315 protein_coding YES CCDS11859.1 ENSP00000269143 Q9Y4W6 UPI000013D7FF NM_006796.2 17/17 Low_complexity_(Seg):seg,HAMAP:MF_01458,hmmpanther:PTHR23076,hmmpanther:PTHR23076:SF45,Pfam_domain:PF01434,TIGRFAM_domain:TIGR01241,Superfamily_domains:SSF140990 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 12329765 12329765 C A 1 0 0 0 0 0 1 0 0 437 922 32 2 2 AFG3L2 18 12329765 Nonsense_Mutation SNP C C3N-00217_T 5351470 12329765 68043520 495 12265 GATA6 0 . GRCh38 18 22171171 22171172 + Frame_Shift_Ins INS - - T novel C3N-00217_T C3N-00217_N - - c.29dupT p.Leu10PhefsTer108 p.L10Ffs*108 ENST00000269216 2/7 175 129 46 101 101 0 sindel-varindel-pindel GATA6,frameshift_variant,p.Leu10PhefsTer108,ENST00000269216,NM_005257.5;GATA6,frameshift_variant,p.Leu10PhefsTer108,ENST00000581694,;GATA6-AS1,upstream_gene_variant,,ENST00000583490,;GATA6-AS1,upstream_gene_variant,,ENST00000584373,;GATA6-AS1,upstream_gene_variant,,ENST00000579431,;GATA6-AS1,upstream_gene_variant,,ENST00000584201,;RP11-627G18.2,downstream_gene_variant,,ENST00000578504,; T ENST00000269216 Transcript frameshift_variant 304-305/3770 27-28/1788 9-10/595 -/X -/T 1 1 GATA6 HGNC HGNC:4174 protein_coding YES CCDS11872.1 ENSP00000269216 Q92908 UPI0000201AC8 NM_005257.5 2/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF23 HIGH 1 insertion 1 2 1 PASS . . 0 204 3 2 0 0 0 0 -20 0.9999979 1 1 1 0 T 7 5 43 22171171 22171171 - T 1 0 1 1 0 0 0 0 0 6128 805 28 0 0 GATA6 18 22171171 Frame_Shift_Ins INS - C3N-00217_T 9841406 22171171 58202114 496 12266 DSC3 0 . GRCh38 18 30997005 30997005 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2279G>T p.Ser760Ile p.S760I ENST00000360428 15/16 343 263 80 323 323 0 strelka-varscan-mutect DSC3,missense_variant,p.Ser760Ile,ENST00000434452,NM_024423.3;DSC3,missense_variant,p.Ser760Ile,ENST00000360428,NM_001941.4;DSC3,missense_variant,p.Ser135Ile,ENST00000584980,; A ENST00000360428 Transcript missense_variant 2360/6939 2279/2691 760/896 S/I aGc/aTc 1 -1 DSC3 HGNC HGNC:3037 protein_coding YES CCDS32810.1 ENSP00000353608 Q14574 UPI000004CAAD NM_001941.4 deleterious(0.03) 15/16 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 30997005 30997005 C A 1 0 0 0 0 1 0 0 0 4588 797 28 2 2 DSC3 18 30997005 Missense_Mutation SNP C C3N-00217_T 8825834 30997005 49376280 497 12267 DSC3 0 . GRCh38 18 31008468 31008468 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1321G>T p.Ala441Ser p.A441S ENST00000360428 10/16 391 294 97 324 324 0 strelka-varscan-mutect DSC3,missense_variant,p.Ala441Ser,ENST00000434452,NM_024423.3;DSC3,missense_variant,p.Ala441Ser,ENST00000360428,NM_001941.4;DSC3,upstream_gene_variant,,ENST00000584980,; A ENST00000360428 Transcript missense_variant 1402/6939 1321/2691 441/896 A/S Gcg/Tcg 1 -1 DSC3 HGNC HGNC:3037 protein_coding YES CCDS32810.1 ENSP00000353608 Q14574 UPI000004CAAD NM_001941.4 deleterious(0) 10/16 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF12,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1212344002 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 31008468 31008468 C A 1 0 0 0 0 1 0 0 0 4588 797 28 2 2 DSC3 18 31008468 Missense_Mutation SNP C C3N-00217_T 11463 31008468 49364817 498 12268 DSC2 0 . GRCh38 18 31069067 31069067 + Missense_Mutation SNP C C G rs139290300 C3N-00217_T C3N-00217_N C C c.2335G>C p.Gly779Arg p.G779R ENST00000280904 15/16 456 411 45 359 359 0 strelka-varscan-mutect DSC2,missense_variant,p.Gly779Arg,ENST00000280904,NM_024422.4;DSC2,missense_variant,p.Gly779Arg,ENST00000251081,NM_004949.4; G ENST00000280904 Transcript missense_variant 2779/12325 2335/2706 779/901 G/R Gga/Cga rs139290300,COSM1711081,COSM1711082 1 -1 DSC2 HGNC HGNC:3036 protein_coding YES CCDS11892.1 ENSP00000280904 Q02487 UPI00001298F9 NM_024422.4 deleterious(0.02) 15/16 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF0 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs139290300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 31069067 31069067 C G 1 0 0 0 0 1 0 0 0 4587 661 23 4 4 DSC2 18 31069067 Missense_Mutation SNP C C3N-00217_T 60599 31069067 49304218 499 12269 DSG1 0 . GRCh38 18 31343462 31343462 + Nonsense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1700T>A p.Leu567Ter p.L567* ENST00000257192 12/15 612 464 148 427 427 0 strelka-varscan-mutect DSG1,stop_gained,p.Leu567Ter,ENST00000257192,NM_001942.3;DSG1,upstream_gene_variant,,ENST00000462981,;RNU6-167P,downstream_gene_variant,,ENST00000384292,;DSG1-AS1,non_coding_transcript_exon_variant,,ENST00000581856,;DSG1-AS1,non_coding_transcript_exon_variant,,ENST00000578119,;DSG1-AS1,downstream_gene_variant,,ENST00000578477,; A ENST00000257192 Transcript stop_gained 1912/5045 1700/3150 567/1049 L/* tTg/tAg 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 12/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 31343462 31343462 T A 1 0 0 0 0 0 1 0 0 4597 1821 63 4 4 DSG1 18 31343462 Nonsense_Mutation SNP T C3N-00217_T 274395 31343462 49029823 500 12270 KIAA1328 0 . GRCh38 18 36959326 36959326 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.467G>T p.Arg156Ile p.R156I ENST00000280020 6/10 144 90 54 192 191 1 strelka-varscan-mutect KIAA1328,missense_variant,p.Arg152Ile,ENST00000591619,;KIAA1328,missense_variant,p.Arg156Ile,ENST00000280020,NM_020776.1;KIAA1328,missense_variant,p.Arg144Ile,ENST00000587139,;KIAA1328,intron_variant,,ENST00000586135,;KIAA1328,intron_variant,,ENST00000591911,;KIAA1328,downstream_gene_variant,,ENST00000590456,;KIAA1328,3_prime_UTR_variant,,ENST00000590617,;KIAA1328,3_prime_UTR_variant,,ENST00000592611,; T ENST00000280020 Transcript missense_variant 489/4853 467/1734 156/577 R/I aGa/aTa 1 1 KIAA1328 HGNC HGNC:29248 protein_coding YES CCDS45855.1 ENSP00000280020 Q86T90 UPI00001C1FF0 NM_020776.1 deleterious(0.01) 6/10 Pfam_domain:PF15369,hmmpanther:PTHR28375,hmmpanther:PTHR28375:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 36959326 36959326 G T 1 0 0 0 0 1 0 0 0 8113 942 33 2 2 KIAA1328 18 36959326 Missense_Mutation SNP G C3N-00217_T 5615864 36959326 43413959 501 12271 SYT4 0 . GRCh38 18 43274062 43274062 + Missense_Mutation SNP G G T rs746536919 C3N-00217_T C3N-00217_N G G c.367C>A p.Pro123Thr p.P123T ENST00000255224 2/4 266 145 121 223 223 0 strelka-varscan-mutect SYT4,missense_variant,p.Pro123Thr,ENST00000255224,NM_020783.3;SYT4,missense_variant,p.Pro105Thr,ENST00000590752,;SYT4,intron_variant,,ENST00000596867,;SYT4,intron_variant,,ENST00000593720,;SYT4,non_coding_transcript_exon_variant,,ENST00000591820,;SYT4,intron_variant,,ENST00000586678,;SYT4,intron_variant,,ENST00000585604,;SYT4,upstream_gene_variant,,ENST00000589479,; T ENST00000255224 Transcript missense_variant 736/4110 367/1278 123/425 P/T Ccg/Acg rs746536919,COSM5299669,COSM5299670 1 -1 SYT4 HGNC HGNC:11512 protein_coding YES CCDS11922.1 ENSP00000255224 Q9H2B2 UPI000013669E NM_020783.3 tolerated(0.21) 2/4 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs746536919 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 43274062 43274062 G T 1 0 0 0 0 1 0 0 0 15870 1232 43 2 2 SYT4 18 43274062 Missense_Mutation SNP G C3N-00217_T 6314736 43274062 37099223 502 12272 SETBP1 0 . GRCh38 18 44952368 44952368 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.3028A>G p.Thr1010Ala p.T1010A ENST00000282030 4/6 476 356 120 453 453 0 strelka-varscan-mutect SETBP1,missense_variant,p.Thr1010Ala,ENST00000282030,NM_015559.2; G ENST00000282030 Transcript missense_variant 3324/9899 3028/4791 1010/1596 T/A Act/Gct 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 tolerated(0.11) 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 44952368 44952368 A G 1 0 0 0 0 1 0 0 0 14406 275 10 5 5 SETBP1 18 44952368 Missense_Mutation SNP A C3N-00217_T 1678306 44952368 35420917 503 12273 ATP5A1 0 . GRCh38 18 46086391 46086391 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1280A>T p.Lys427Met p.K427M ENST00000398752 9/12 260 193 67 205 205 0 strelka-varscan-mutect ATP5A1,missense_variant,p.Lys427Met,ENST00000398752,NM_004046.5;ATP5A1,missense_variant,p.Lys377Met,ENST00000593152,NM_001001935.2,NM_001257335.1;ATP5A1,missense_variant,p.Lys427Met,ENST00000282050,NM_001001937.1;ATP5A1,missense_variant,p.Lys405Met,ENST00000590665,NM_001257334.1;ATP5A1,downstream_gene_variant,,ENST00000589869,;ATP5A1,downstream_gene_variant,,ENST00000590324,;ATP5A1,downstream_gene_variant,,ENST00000590406,;ATP5A1,downstream_gene_variant,,ENST00000589252,;ATP5A1,downstream_gene_variant,,ENST00000592989,;ATP5A1,3_prime_UTR_variant,,ENST00000586592,;ATP5A1,3_prime_UTR_variant,,ENST00000590156,;ATP5A1,3_prime_UTR_variant,,ENST00000592364,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000586523,;ATP5A1,non_coding_transcript_exon_variant,,ENST00000587902,;ATP5A1,downstream_gene_variant,,ENST00000589611,;ATP5A1,downstream_gene_variant,,ENST00000590448,;ATP5A1,downstream_gene_variant,,ENST00000591981,;ATP5A1,downstream_gene_variant,,ENST00000585650,; A ENST00000398752 Transcript missense_variant 1402/5818 1280/1662 427/553 K/M aAg/aTg 1 -1 ATP5A1 HGNC HGNC:823 protein_coding YES CCDS11927.1 ENSP00000381736 P25705 V9HW26 UPI000006221A NM_004046.5 deleterious_low_confidence(0) 9/12 HAMAP:MF_01346,hmmpanther:PTHR15184:SF3,hmmpanther:PTHR15184,Gene3D:2ck3A03,Pfam_domain:PF00306,TIGRFAM_domain:TIGR00962,PIRSF_domain:PIRSF039088,Superfamily_domains:SSF47917 MODERATE 1 SNV 1 1 PASS rs1414605468 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 46086391 46086391 T A 1 0 0 0 0 1 0 0 0 1300 1623 56 4 4 ATP5A1 18 46086391 Missense_Mutation SNP T C3N-00217_T 1134023 46086391 34286894 504 12274 POLI 0 . GRCh38 18 54282943 54282943 + Silent SNP A A T C3N-00217_T C3N-00217_N A A c.903A>T p.= p.S301S ENST00000579534 6/10 135 80 55 152 152 0 strelka-varscan-mutect POLI,synonymous_variant,p.=,ENST00000579534,NM_007195.2;POLI,synonymous_variant,p.=,ENST00000579434,;POLI,synonymous_variant,p.=,ENST00000217800,;POLI,synonymous_variant,p.=,ENST00000406285,;POLI,synonymous_variant,p.=,ENST00000579823,;POLI,downstream_gene_variant,,ENST00000583136,;POLI,downstream_gene_variant,,ENST00000577612,;POLI,downstream_gene_variant,,ENST00000580880,;POLI,upstream_gene_variant,,ENST00000582366,;POLI,downstream_gene_variant,,ENST00000580905,;POLI,synonymous_variant,p.=,ENST00000585023,;POLI,synonymous_variant,p.=,ENST00000581950,;POLI,downstream_gene_variant,,ENST00000577971,;POLI,upstream_gene_variant,,ENST00000577361,;POLI,upstream_gene_variant,,ENST00000583576,; T ENST00000579534 Transcript synonymous_variant 1046/6133 903/2223 301/740 S tcA/tcT COSM988961,COSM988962 1 1 POLI HGNC HGNC:9182 protein_coding YES CCDS11954.2 ENSP00000462664 Q9UNA4 UPI00004DDD95 NM_007195.2 6/10 Gene3D:1.10.150.20,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF10,Superfamily_domains:SSF56672 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 54282943 54282943 A T 1 0 0 0 0 0 0 0 1 12313 175 7 4 4 POLI 18 54282943 Silent SNP A C3N-00217_T 8196552 54282943 26090342 505 12275 TCF4 0 . GRCh38 18 55631312 55631312 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.272C>A p.Thr91Asn p.T91N ENST00000398339 2/21 95 85 10 74 74 0 strelka-varscan-mutect TCF4,missense_variant,p.Thr91Asn,ENST00000398339,NM_001243226.2;TCF4,intron_variant,,ENST00000568169,;TCF4,intron_variant,,ENST00000565124,;TCF4,intron_variant,,ENST00000628391,;TCF4,missense_variant,p.Thr91Asn,ENST00000627320,;TCF4,missense_variant,p.Thr90Asn,ENST00000569357,;TCF4,missense_variant,p.Thr18Asn,ENST00000565393,;TCF4,intron_variant,,ENST00000630224,;RPL21P126,upstream_gene_variant,,ENST00000470049,; T ENST00000398339 Transcript missense_variant 402/2551 272/2322 91/773 T/N aCt/aAt 1 -1 TCF4 HGNC HGNC:11634 protein_coding YES CCDS58631.1 ENSP00000381382 E9PH57 UPI0000EE5B9B NM_001243226.2 deleterious_low_confidence(0.01) 2/21 MODERATE 1 SNV 1 1 PASS rs1306347941 . 0 198 12 0 0 0 0 0 -19.83382 0.9998353 1 1 1 0 T 3 4 43 55631312 55631312 G T 1 0 0 0 0 1 0 0 0 16102 1029 36 2 2 TCF4 18 55631312 Missense_Mutation SNP G C3N-00217_T 1348369 55631312 24741973 506 12276 PHLPP1 0 . GRCh38 18 62895073 62895073 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.2129T>A p.Val710Asp p.V710D ENST00000262719 5/17 177 114 63 140 140 0 strelka-varscan-mutect PHLPP1,missense_variant,p.Val710Asp,ENST00000262719,NM_194449.3;PHLPP1,non_coding_transcript_exon_variant,,ENST00000487409,; A ENST00000262719 Transcript missense_variant 2363/6390 2129/5154 710/1717 V/D gTc/gAc 1 1 PHLPP1 HGNC HGNC:20610 protein_coding YES CCDS45881.2 ENSP00000262719 O60346 UPI000051AE2E NM_194449.3 deleterious(0) 5/17 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF252,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 62895073 62895073 T A 1 0 0 0 0 1 0 0 0 11942 1667 58 4 4 PHLPP1 18 62895073 Missense_Mutation SNP T C3N-00217_T 7263761 62895073 17478212 507 12277 CDH7 0 . GRCh38 18 65843899 65843899 + Missense_Mutation SNP C C A C3N-00217_T C3N-00217_N C C c.1069C>A p.Pro357Thr p.P357T ENST00000397968 7/12 123 89 34 108 108 0 strelka-varscan-mutect CDH7,missense_variant,p.Pro357Thr,ENST00000397968,NM_004361.2;CDH7,missense_variant,p.Pro357Thr,ENST00000536984,NM_001317214.1;CDH7,missense_variant,p.Pro357Thr,ENST00000323011,NM_033646.1; A ENST00000397968 Transcript missense_variant 1495/12231 1069/2358 357/785 P/T Ccg/Acg COSM3527224,COSM3527225 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 tolerated(0.11) 7/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 65843899 65843899 C A 1 0 0 0 0 1 0 0 0 2818 855 30 2 2 CDH7 18 65843899 Missense_Mutation SNP C C3N-00217_T 2948826 65843899 14529386 508 12278 ZNF407 0 . GRCh38 18 74631500 74631500 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.481G>T p.Asp161Tyr p.D161Y ENST00000299687 1/8 288 184 104 303 303 0 strelka-varscan-mutect ZNF407,missense_variant,p.Asp161Tyr,ENST00000299687,NM_017757.2;ZNF407,missense_variant,p.Asp161Tyr,ENST00000577538,NM_001146189.1;ZNF407,missense_variant,p.Asp161Tyr,ENST00000582337,;ZNF407,missense_variant,p.Asp161Tyr,ENST00000309902,NM_001146190.1; T ENST00000299687 Transcript missense_variant 481/7948 481/6747 161/2248 D/Y Gat/Tat 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 tolerated(1) 1/8 hmmpanther:PTHR24402:SF5,hmmpanther:PTHR24402 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9993656 1 1 1 0 T 3 4 43 74631500 74631500 G T 1 0 0 0 0 1 0 0 0 18459 1290 45 2 2 ZNF407 18 74631500 Missense_Mutation SNP G C3N-00217_T 8787601 74631500 5741785 509 12279 ZNF407 0 . GRCh38 18 74634102 74634102 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.3083C>G p.Ser1028Cys p.S1028C ENST00000299687 1/8 250 209 41 202 202 0 strelka-varscan-mutect ZNF407,missense_variant,p.Ser1028Cys,ENST00000299687,NM_017757.2;ZNF407,missense_variant,p.Ser1028Cys,ENST00000577538,NM_001146189.1;ZNF407,missense_variant,p.Ser1028Cys,ENST00000582337,;ZNF407,missense_variant,p.Ser1028Cys,ENST00000309902,NM_001146190.1; G ENST00000299687 Transcript missense_variant 3083/7948 3083/6747 1028/2248 S/C tCc/tGc 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 deleterious(0) 1/8 SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 74634102 74634102 C G 1 0 0 0 0 1 0 0 0 18459 855 30 4 4 ZNF407 18 74634102 Missense_Mutation SNP C C3N-00217_T 2602 74634102 5739183 510 12280 SALL3 0 . GRCh38 18 78992088 78992088 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.97G>T p.Gly33Cys p.G33C ENST00000537592 2/3 52 34 18 43 43 0 strelka-varscan-mutect SALL3,missense_variant,p.Gly33Cys,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Gly33Cys,ENST00000575389,;SALL3,missense_variant,p.Gly33Cys,ENST00000616649,;SALL3,5_prime_UTR_variant,,ENST00000536229,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,non_coding_transcript_exon_variant,,ENST00000572928,; T ENST00000537592 Transcript missense_variant 97/6555 97/3903 33/1300 G/C Ggt/Tgt 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 deleterious(0.03) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 78992088 78992088 G T 1 0 0 0 0 1 0 0 0 14071 1000 35 2 2 SALL3 18 78992088 Missense_Mutation SNP G C3N-00217_T 4357986 78992088 1381197 511 12281 SALL3 0 . GRCh38 18 78992129 78992129 + Silent SNP G G T rs780511868 C3N-00217_T C3N-00217_N G G c.138G>T p.= p.G46G ENST00000537592 2/3 84 57 27 66 66 0 strelka-varscan-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,synonymous_variant,p.=,ENST00000616649,;SALL3,5_prime_UTR_variant,,ENST00000536229,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,non_coding_transcript_exon_variant,,ENST00000572928,; T ENST00000537592 Transcript synonymous_variant 138/6555 138/3903 46/1300 G ggG/ggT rs780511868 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 LOW 1 SNV 5 1 PASS rs780511868 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 78992129 78992129 G T 1 0 0 0 0 0 0 0 1 14071 1219 43 2 2 SALL3 18 78992129 Silent SNP G C3N-00217_T 41 78992129 1381156 512 12282 STK11 0 . GRCh38 19 1222988 1222988 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.924G>T p.Trp308Cys p.W308C ENST00000326873 8/10 50 26 24 63 63 0 strelka-varscan-mutect STK11,missense_variant,p.Trp308Cys,ENST00000586243,;STK11,missense_variant,p.Trp308Cys,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript missense_variant 1374/2611 924/1302 308/433 W/C tgG/tgT CM981871,KinMutBase_STK11_DNA:g.17075G>T 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 8/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1,0 1 PASS rs1057520042 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 1222988 1222988 G T 1 0 0 0 0 1 0 0 0 15664 1275 44 2 2 STK11 19 1222988 Missense_Mutation SNP G C3N-00217_T 1222988 57394628 513 12283 DOHH 0 . GRCh38 19 3491761 3491761 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.640G>C p.Gly214Arg p.G214R ENST00000427575 5/5 73 36 37 73 73 0 strelka-varscan-mutect DOHH,missense_variant,p.Gly214Arg,ENST00000427575,NM_001145165.1;DOHH,missense_variant,p.Gly214Arg,ENST00000250937,NM_031304.4;DOHH,missense_variant,p.Gly214Arg,ENST00000592858,;DOHH,downstream_gene_variant,,ENST00000587122,;DOHH,non_coding_transcript_exon_variant,,ENST00000586906,; G ENST00000427575 Transcript missense_variant 1092/2031 640/909 214/302 G/R Gga/Cga 1 -1 DOHH HGNC HGNC:28662 protein_coding YES CCDS12108.1 ENSP00000398882 Q9BU89 UPI0000071C59 NM_001145165.1 deleterious(0) 5/5 HAMAP:MF_03101,hmmpanther:PTHR12697,Pfam_domain:PF13646,Gene3D:1.25.10.10,SMART_domains:SM00567,Superfamily_domains:SSF48371 MODERATE 1 SNV 3 1 PASS . . 0 202 7 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 3491761 3491761 C G 1 0 0 0 0 1 0 0 0 4510 632 22 4 4 DOHH 19 3491761 Missense_Mutation SNP C C3N-00217_T 2268773 3491761 55125855 514 12284 CD70 0 . GRCh38 19 6590899 6590899 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.104T>C p.Val35Ala p.V35A ENST00000245903 1/3 75 47 28 109 108 1 strelka-varscan-mutect CD70,missense_variant,p.Val35Ala,ENST00000245903,NM_001252.4;CD70,missense_variant,p.Val35Ala,ENST00000423145,;CD70,missense_variant,p.Val35Ala,ENST00000597430,;RPL7P50,upstream_gene_variant,,ENST00000600588,; G ENST00000245903 Transcript missense_variant 254/913 104/582 35/193 V/A gTg/gCg 1 -1 CD70 HGNC HGNC:11937 protein_coding YES CCDS12170.1 ENSP00000245903 P32970 A0A0U5JA32 UPI00001370B6 NM_001252.4 tolerated(0.59) 1/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR15152:SF0,hmmpanther:PTHR15152 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 6590899 6590899 A G 1 0 0 0 0 1 0 0 0 2737 159 6 5 5 CD70 19 6590899 Missense_Mutation SNP A C3N-00217_T 3099138 6590899 52026717 515 12285 ZNF358 0 . GRCh38 19 7520550 7520550 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.1308C>T p.= p.S436S ENST00000597229 2/2 133 72 61 172 172 0 strelka-varscan-mutect ZNF358,synonymous_variant,p.=,ENST00000597229,NM_018083.4;MCOLN1,upstream_gene_variant,,ENST00000264079,NM_020533.2;MCOLN1,upstream_gene_variant,,ENST00000601003,;ZNF358,downstream_gene_variant,,ENST00000596712,;CTD-2207O23.12,downstream_gene_variant,,ENST00000599312,;CTD-2207O23.11,upstream_gene_variant,,ENST00000602083,;MCOLN1,upstream_gene_variant,,ENST00000394321,;MCOLN1,upstream_gene_variant,,ENST00000596390,;CTD-2207O23.12,downstream_gene_variant,,ENST00000597384,; T ENST00000597229 Transcript synonymous_variant 1478/1954 1308/1707 436/568 S tcC/tcT 1 1 ZNF358 HGNC HGNC:16838 protein_coding YES CCDS32890.2 ENSP00000472305 Q9NW07 UPI0000201F0C NM_018083.4 2/2 LOW SNV 2 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999993 1 1 1 0 T 2 4 43 7520550 7520550 C T 1 0 0 0 0 0 0 0 1 18439 610 22 3 3 ZNF358 19 7520550 Silent SNP C C3N-00217_T 929651 7520550 51097066 516 12286 CAMSAP3 0 . GRCh38 19 7610553 7610553 + Missense_Mutation SNP C C A rs762865565 C3N-00217_T C3N-00217_N C C c.919C>A p.Arg307Ser p.R307S ENST00000446248 8/19 134 77 57 147 147 0 strelka-varscan-mutect CAMSAP3,missense_variant,p.Arg307Ser,ENST00000446248,NM_001080429.2;CAMSAP3,missense_variant,p.Arg280Ser,ENST00000160298,NM_020902.1;CAMSAP3,upstream_gene_variant,,ENST00000595692,; A ENST00000446248 Transcript missense_variant 1020/4179 919/3831 307/1276 R/S Cgc/Agc rs762865565 1 1 CAMSAP3 HGNC HGNC:29307 protein_coding YES CCDS45947.1 ENSP00000416797 Q9P1Y5 UPI0000161861 NM_001080429.2 tolerated(0.61) 8/19 hmmpanther:PTHR21595:SF2,hmmpanther:PTHR21595,Pfam_domain:PF11971,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs762865565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 7610553 7610553 C A 1 0 0 0 0 1 0 0 0 2305 884 31 1 1 CAMSAP3 19 7610553 Missense_Mutation SNP C C3N-00217_T 90003 7610553 51007063 517 12287 KEAP1 0 . GRCh38 19 10491872 10491872 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1030G>T p.Ala344Ser p.A344S ENST00000171111 3/6 149 79 70 199 199 0 strelka-varscan-mutect KEAP1,missense_variant,p.Ala344Ser,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Ala344Ser,ENST00000393623,NM_012289.3;KEAP1,upstream_gene_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,missense_variant,p.Ala4Ser,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENST00000171111 Transcript missense_variant 1578/2955 1030/1875 344/624 A/S Gct/Tct 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 tolerated(0.09) 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 10491872 10491872 C A 1 0 0 0 0 1 0 0 0 8061 739 26 2 2 KEAP1 19 10491872 Missense_Mutation SNP C C3N-00217_T 2881319 10491872 48125744 518 12288 ZNF709 0 . GRCh38 19 12464592 12464592 + Missense_Mutation SNP C C T novel C3N-00217_T C3N-00217_N C C c.1330G>A p.Gly444Arg p.G444R ENST00000397732 4/4 61 39 22 140 140 0 strelka-varscan-mutect ZNF709,missense_variant,p.Gly444Arg,ENST00000397732,NM_152601.3;CTD-2192J16.17,missense_variant,p.Gly444Arg,ENST00000428311,;ZNF709,downstream_gene_variant,,ENST00000455490,;CTD-3105H18.7,downstream_gene_variant,,ENST00000420038,;CTD-3105H18.18,intron_variant,,ENST00000598753,; T ENST00000397732 Transcript missense_variant 1502/4910 1330/1926 444/641 G/R Gga/Aga 1 -1 ZNF709 HGNC HGNC:20629 protein_coding YES CCDS42504.1 ENSP00000380840 Q8N972 UPI000006CF50 NM_152601.3 deleterious(0.03) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 12464592 12464592 C T 1 0 0 0 0 1 0 0 0 18688 603 21 3 3 ZNF709 19 12464592 Missense_Mutation SNP C C3N-00217_T 1972720 12464592 46153024 519 12289 CYP4F22 0 . GRCh38 19 15548150 15548150 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1179G>T p.Lys393Asn p.K393N ENST00000269703 11/14 364 218 146 521 520 1 strelka-varscan-mutect CYP4F22,missense_variant,p.Lys393Asn,ENST00000269703,NM_173483.3;CYP4F22,missense_variant,p.Lys393Asn,ENST00000601005,; T ENST00000269703 Transcript missense_variant 1378/2641 1179/1596 393/531 K/N aaG/aaT 1 1 CYP4F22 HGNC HGNC:26820 protein_coding YES CCDS12331.1 ENSP00000269703 Q6NT55 UPI000013D84B NM_173483.3 deleterious(0) 11/14 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00385,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF53,Superfamily_domains:SSF48264 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 15548150 15548150 G T 1 0 0 0 0 1 0 0 0 3992 991 35 2 2 CYP4F22 19 15548150 Missense_Mutation SNP G C3N-00217_T 3083558 15548150 43069466 520 12290 TMEM38A 0 . GRCh38 19 16661301 16661301 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.84T>G p.Ser28Arg p.S28R ENST00000187762 1/6 133 104 29 140 140 0 strelka-varscan-mutect TMEM38A,missense_variant,p.Ser28Arg,ENST00000187762,NM_024074.1;TMEM38A,missense_variant,p.Ser14Arg,ENST00000599479,;SMIM7,upstream_gene_variant,,ENST00000487416,NM_024104.3;SMIM7,upstream_gene_variant,,ENST00000627144,;SMIM7,upstream_gene_variant,,ENST00000597711,;SMIM7,upstream_gene_variant,,ENST00000358726,NM_001300925.1;CTC-429P9.4,upstream_gene_variant,,ENST00000593459,;SMIM7,upstream_gene_variant,,ENST00000397349,;SMIM7,upstream_gene_variant,,ENST00000461364,;CTC-429P9.4,upstream_gene_variant,,ENST00000593962,;SMIM7,upstream_gene_variant,,ENST00000594507,;TMEM38A,non_coding_transcript_exon_variant,,ENST00000595452,;SMIM7,upstream_gene_variant,,ENST00000487803,;SMIM7,upstream_gene_variant,,ENST00000593409,;SMIM7,upstream_gene_variant,,ENST00000465250,;SMIM7,upstream_gene_variant,,ENST00000481671,;SMIM7,upstream_gene_variant,,ENST00000599310,;SMIM7,upstream_gene_variant,,ENST00000594662,;SMIM7,upstream_gene_variant,,ENST00000593404,;SMIM7,upstream_gene_variant,,ENST00000597781,;CTC-429P9.4,upstream_gene_variant,,ENST00000600705,;SMIM7,upstream_gene_variant,,ENST00000598278,;SMIM7,upstream_gene_variant,,ENST00000463051,;SMIM7,upstream_gene_variant,,ENST00000600740,;SMIM7,upstream_gene_variant,,ENST00000461488,;CTC-429P9.4,upstream_gene_variant,,ENST00000593991,;SMIM7,upstream_gene_variant,,ENST00000602194,;CTC-429P9.4,upstream_gene_variant,,ENST00000594509,;CTC-429P9.4,upstream_gene_variant,,ENST00000601636,;CTC-429P9.4,upstream_gene_variant,,ENST00000595505,; G ENST00000187762 Transcript missense_variant 175/2649 84/900 28/299 S/R agT/agG 1 1 TMEM38A HGNC HGNC:28462 protein_coding YES CCDS12349.1 ENSP00000187762 Q9H6F2 UPI000006E0B9 NM_024074.1 deleterious(0) 1/6 hmmpanther:PTHR12454,hmmpanther:PTHR12454:SF3,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 16661301 16661301 T G 1 0 0 0 0 1 0 0 0 16636 1722 60 5 5 TMEM38A 19 16661301 Missense_Mutation SNP T C3N-00217_T 1113151 16661301 41956315 521 12291 NCAN 0 . GRCh38 19 19228255 19228255 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2635G>T p.Gly879Trp p.G879W ENST00000252575 8/15 112 63 49 145 144 1 strelka-varscan-mutect NCAN,missense_variant,p.Gly879Trp,ENST00000252575,NM_004386.2;RNU6-1028P,upstream_gene_variant,,ENST00000517164,;NCAN,non_coding_transcript_exon_variant,,ENST00000590187,; T ENST00000252575 Transcript missense_variant 2734/6387 2635/3966 879/1321 G/W Ggg/Tgg 1 1 NCAN HGNC HGNC:2465 protein_coding YES CCDS12397.1 ENSP00000252575 O14594 A0A024R7M3 UPI000013CD70 NM_004386.2 deleterious(0.01) 8/15 hmmpanther:PTHR22804:SF24,hmmpanther:PTHR22804 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 19228255 19228255 G T 1 0 0 0 0 1 0 0 0 10220 1232 43 2 2 NCAN 19 19228255 Missense_Mutation SNP G C3N-00217_T 2566954 19228255 39389361 522 12292 ZNF99 0 . GRCh38 19 22758882 22758882 + Missense_Mutation SNP A A C novel C3N-00217_T C3N-00217_N A A c.1027T>G p.Cys343Gly p.C343G ENST00000596209 4/4 112 72 40 305 305 0 strelka-varscan-mutect ZNF99,missense_variant,p.Cys343Gly,ENST00000596209,NM_001080409.2;ZNF99,missense_variant,p.Cys252Gly,ENST00000397104,; C ENST00000596209 Transcript missense_variant 1118/7817 1027/2595 343/864 C/G Tgt/Ggt 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 22758882 22758882 A C 1 0 0 0 0 1 0 0 0 18797 217 8 5 5 ZNF99 19 22758882 Missense_Mutation SNP A C3N-00217_T 3530627 22758882 35858734 523 12293 ZNF730 0 . GRCh38 19 23134175 23134175 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.99G>T p.Met33Ile p.M33I ENST00000597761 2/4 86 54 32 143 143 0 strelka-varscan-mutect ZNF730,start_lost,p.Met1?,ENST00000593635,;ZNF730,missense_variant,p.Met33Ile,ENST00000597761,NM_001277403.1;ZNF730,upstream_gene_variant,,ENST00000599195,; T ENST00000597761 Transcript missense_variant 298/2374 99/1512 33/503 M/I atG/atT COSM994052 1 1 ZNF730 HGNC HGNC:32470 protein_coding YES CCDS59371.1 ENSP00000472959 Q6ZMV8 UPI000035E7F4 NM_001277403.1 deleterious(0.03) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF110,SMART_domains:SM00349 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 23134175 23134175 G T 1 0 0 0 0 1 0 0 0 18704 1377 48 2 2 ZNF730 19 23134175 Missense_Mutation SNP G C3N-00217_T 375293 23134175 35483441 524 12294 TSHZ3 0 . GRCh38 19 31277575 31277575 + Missense_Mutation SNP A A G novel C3N-00217_T C3N-00217_N A A c.2218T>C p.Ser740Pro p.S740P ENST00000240587 2/2 36 19 17 28 28 0 strelka-varscan-mutect TSHZ3,missense_variant,p.Ser740Pro,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; G ENST00000240587 Transcript missense_variant 2546/5176 2218/3246 740/1081 S/P Tcc/Ccc 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 tolerated(0.12) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 31277575 31277575 A G 1 0 0 0 0 1 0 0 0 17130 304 11 5 5 TSHZ3 19 31277575 Missense_Mutation SNP A C3N-00217_T 8143400 31277575 27340041 525 12295 ZNF599 0 . GRCh38 19 34760534 34760534 + Silent SNP T T C novel C3N-00217_T C3N-00217_N T T c.267A>G p.= p.T89T ENST00000329285 4/4 118 84 34 99 99 0 strelka-varscan-mutect ZNF599,synonymous_variant,p.=,ENST00000329285,NM_001007248.2;ZNF599,downstream_gene_variant,,ENST00000587354,; C ENST00000329285 Transcript synonymous_variant 641/3099 267/1767 89/588 T acA/acG 1 -1 ZNF599 HGNC HGNC:26408 protein_coding YES CCDS32991.1 ENSP00000333802 Q96NL3 UPI0000071186 NM_001007248.2 4/4 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF20 LOW 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 43 34760534 34760534 T C 1 0 0 0 0 0 0 0 1 18604 1567 55 5 5 ZNF599 19 34760534 Silent SNP T C3N-00217_T 3482959 34760534 23857082 526 12296 HPN 0 . GRCh38 19 35060805 35060805 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.799C>T p.= p.L267L ENST00000262626 9/13 43 32 11 37 37 0 strelka-varscan-mutect HPN,synonymous_variant,p.=,ENST00000262626,NM_182983.2;HPN,synonymous_variant,p.=,ENST00000392226,NM_002151.2;HPN,synonymous_variant,p.=,ENST00000597419,;HPN,downstream_gene_variant,,ENST00000600390,;HPN-AS1,intron_variant,,ENST00000392227,;HPN,downstream_gene_variant,,ENST00000600675,;HPN,non_coding_transcript_exon_variant,,ENST00000593305,;HPN,non_coding_transcript_exon_variant,,ENST00000599363,;HPN,non_coding_transcript_exon_variant,,ENST00000541345,;HPN,downstream_gene_variant,,ENST00000596662,; T ENST00000262626 Transcript synonymous_variant 1624/2363 799/1254 267/417 L Ctg/Ttg 1 1 HPN HGNC HGNC:5155 protein_coding YES CCDS32993.1 ENSP00000262626 P05981 A0A140VJK9 UPI000003FE67 NM_182983.2 9/13 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF130,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 35060805 35060805 C T 1 0 0 0 0 0 0 0 1 7231 680 24 3 3 HPN 19 35060805 Silent SNP C C3N-00217_T 300271 35060805 23556811 527 12297 ZNF568 0 . GRCh38 19 36997282 36997282 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.1591G>T p.Gly531Trp p.G531W ENST00000617745 8/8 140 92 48 168 168 0 strelka-varscan-mutect ZNF568,missense_variant,p.Gly531Trp,ENST00000617745,NM_001204838.1;ZNF568,missense_variant,p.Gly467Trp,ENST00000455427,NM_001204839.1;ZNF568,missense_variant,p.Gly531Trp,ENST00000444991,;ZNF568,downstream_gene_variant,,ENST00000433993,;ZNF568,downstream_gene_variant,,ENST00000455817,;ZNF568,downstream_gene_variant,,ENST00000588596,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,; T ENST00000617745 Transcript missense_variant 1791/2441 1591/1908 531/635 G/W Ggg/Tgg COSM3734961 1 1 ZNF568 HGNC HGNC:25392 protein_coding CCDS74351.1 ENSP00000482444 A0A087WZ84 UPI0001FD28F8 NM_001204838.1 deleterious(0) 8/8 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF107,Low_complexity_(Seg):seg,Superfamily_domains:SSF57667 1 MODERATE SNV 5 1 1 PASS rs1261514973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 36997282 36997282 G T 1 0 0 0 0 1 0 0 0 18573 1348 47 2 2 ZNF568 19 36997282 Missense_Mutation SNP G C3N-00217_T 1936477 36997282 21620334 528 12298 CATSPERG 0 . GRCh38 19 38356843 38356843 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.1297G>A p.Val433Met p.V433M ENST00000409235 11/29 140 96 44 101 101 0 strelka-varscan-mutect CATSPERG,missense_variant,p.Val433Met,ENST00000409235,NM_021185.4;CATSPERG,missense_variant,p.Val433Met,ENST00000409410,;CATSPERG,intron_variant,,ENST00000410018,;CATSPERG,intron_variant,,ENST00000489693,;AC005625.1,downstream_gene_variant,,ENST00000590304,;CATSPERG,intron_variant,,ENST00000466060,;CATSPERG,3_prime_UTR_variant,,ENST00000471517,;CATSPERG,3_prime_UTR_variant,,ENST00000312265,;CATSPERG,3_prime_UTR_variant,,ENST00000412458,;CATSPERG,upstream_gene_variant,,ENST00000470292,;CATSPERG,upstream_gene_variant,,ENST00000585424,; A ENST00000409235 Transcript missense_variant 1412/3746 1297/3480 433/1159 V/M Gtg/Atg 1 1 CATSPERG HGNC HGNC:25243 protein_coding YES CCDS12514.2 ENSP00000386962 Q6ZRH7 UPI000022A813 NM_021185.4 tolerated(0.05) 11/29 Pfam_domain:PF15064,hmmpanther:PTHR14327 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 38356843 38356843 G A 1 0 0 0 0 1 0 0 0 2393 1261 44 3 3 CATSPERG 19 38356843 Missense_Mutation SNP G C3N-00217_T 1359561 38356843 20260773 529 12299 GGN 0 . GRCh38 19 38386456 38386456 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.806G>T p.Gly269Val p.G269V ENST00000334928 3/4 243 183 60 205 205 0 strelka-varscan-mutect GGN,missense_variant,p.Gly269Val,ENST00000334928,NM_152657.3;SPRED3,upstream_gene_variant,,ENST00000338502,NM_001042522.2;PSMD8,downstream_gene_variant,,ENST00000592035,;PSMD8,downstream_gene_variant,,ENST00000215071,;SPRED3,upstream_gene_variant,,ENST00000587013,;PSMD8,downstream_gene_variant,,ENST00000620216,NM_002812.4;SPRED3,upstream_gene_variant,,ENST00000586301,;PSMD8,downstream_gene_variant,,ENST00000602911,;PSMD8,downstream_gene_variant,,ENST00000592561,;SPRED3,upstream_gene_variant,,ENST00000587947,;PSMD8,downstream_gene_variant,,ENST00000585598,;GGN,downstream_gene_variant,,ENST00000587676,;GGN,downstream_gene_variant,,ENST00000586599,;AC005789.9,intron_variant,,ENST00000585411,;GGN,intron_variant,,ENST00000591809,;SPRED3,upstream_gene_variant,,ENST00000587564,;GGN,missense_variant,p.Gly186Val,ENST00000585737,;SPRED3,upstream_gene_variant,,ENST00000586958,;PSMD8,downstream_gene_variant,,ENST00000590331,; A ENST00000334928 Transcript missense_variant 939/2239 806/1959 269/652 G/V gGg/gTg 1 -1 GGN HGNC HGNC:18869 protein_coding YES CCDS12516.1 ENSP00000334940 Q86UU5 UPI0000073CAB NM_152657.3 deleterious_low_confidence(0.04) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR22979,hmmpanther:PTHR22979:SF24,Pfam_domain:PF15685 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 38386456 38386456 C A 1 0 0 0 0 1 0 0 0 6234 623 22 2 2 GGN 19 38386456 Missense_Mutation SNP C C3N-00217_T 29613 38386456 20231160 530 12300 AKT2 0 . GRCh38 19 40233917 40233917 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.1401G>A p.= p.R467R ENST00000392038 14/14 122 83 39 90 90 0 strelka-varscan-mutect AKT2,synonymous_variant,p.=,ENST00000392038,NM_001626.5;AKT2,synonymous_variant,p.=,ENST00000424901,;AKT2,synonymous_variant,p.=,ENST00000311278,;AKT2,3_prime_UTR_variant,,ENST00000476247,;AKT2,3_prime_UTR_variant,,ENST00000497948,;AKT2,downstream_gene_variant,,ENST00000579047,NM_001243027.2,NM_001243028.2;AKT2,downstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000391845,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,3_prime_UTR_variant,,ENST00000391844,;AKT2,3_prime_UTR_variant,,ENST00000584288,;AKT2,3_prime_UTR_variant,,ENST00000489375,;AKT2,non_coding_transcript_exon_variant,,ENST00000483166,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,non_coding_transcript_exon_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000578282,; T ENST00000392038 Transcript synonymous_variant 1700/5300 1401/1446 467/481 R cgG/cgA 1 -1 AKT2 HGNC HGNC:392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 UPI0000049EDB NM_001626.5 14/14 Pfam_domain:PF00433,PROSITE_profiles:PS51285,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF176,SMART_domains:SM00133 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 40233917 40233917 C T 1 0 0 0 0 0 0 0 1 563 842 30 3 3 AKT2 19 40233917 Silent SNP C C3N-00217_T 1847461 40233917 18383699 531 12301 AKT2 0 . GRCh38 19 40242626 40242626 + Nonsense_Mutation SNP C C A rs148339167 C3N-00217_T C3N-00217_N C C c.349G>T p.Glu117Ter p.E117* ENST00000392038 5/14 291 195 96 217 217 0 strelka-varscan-mutect AKT2,stop_gained,p.Glu117Ter,ENST00000392038,NM_001626.5;AKT2,stop_gained,p.Glu117Ter,ENST00000424901,;AKT2,stop_gained,p.Glu55Ter,ENST00000579047,NM_001243027.2,NM_001243028.2;AKT2,stop_gained,p.Glu117Ter,ENST00000311278,;AKT2,stop_gained,p.Glu117Ter,ENST00000416362,;AKT2,stop_gained,p.Glu117Ter,ENST00000441941,;AKT2,stop_gained,p.Glu117Ter,ENST00000423127,;AKT2,stop_gained,p.Glu117Ter,ENST00000392037,;AKT2,stop_gained,p.Glu117Ter,ENST00000486368,;AKT2,stop_gained,p.Glu117Ter,ENST00000596634,;AKT2,stop_gained,p.Glu117Ter,ENST00000452077,;AKT2,stop_gained,p.Glu117Ter,ENST00000578123,;AKT2,upstream_gene_variant,,ENST00000578615,;AKT2,downstream_gene_variant,,ENST00000456441,;AKT2,downstream_gene_variant,,ENST00000583859,;AKT2,downstream_gene_variant,,ENST00000358335,;AKT2,upstream_gene_variant,,ENST00000578310,;AKT2,upstream_gene_variant,,ENST00000391845,;AKT2,upstream_gene_variant,,ENST00000480878,;AKT2,stop_gained,p.Glu28Ter,ENST00000601166,;AKT2,missense_variant,p.Arg58Leu,ENST00000391844,;AKT2,missense_variant,p.Arg58Leu,ENST00000584288,;AKT2,missense_variant,p.Arg58Leu,ENST00000492463,;AKT2,3_prime_UTR_variant,,ENST00000491778,;AKT2,non_coding_transcript_exon_variant,,ENST00000578975,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,non_coding_transcript_exon_variant,,ENST00000537834,;AKT2,non_coding_transcript_exon_variant,,ENST00000487537,;AKT2,upstream_gene_variant,,ENST00000483166,;AKT2,upstream_gene_variant,,ENST00000496089,;AKT2,upstream_gene_variant,,ENST00000580878,;AKT2,upstream_gene_variant,,ENST00000579345,;AKT2,upstream_gene_variant,,ENST00000578282,; A ENST00000392038 Transcript stop_gained 648/5300 349/1446 117/481 E/* Gag/Tag rs148339167 1 -1 AKT2 HGNC HGNC:392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 UPI0000049EDB NM_001626.5 5/14 hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF176 HIGH 1 SNV 1 1 PASS rs148339167 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 40242626 40242626 C A 1 0 0 0 0 0 1 0 0 563 893 31 1 1 AKT2 19 40242626 Nonsense_Mutation SNP C C3N-00217_T 8709 40242626 18374990 532 12302 NUMBL 0 . GRCh38 19 40673346 40673346 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.1034C>T p.Thr345Ile p.T345I ENST00000252891 8/10 54 34 20 56 56 0 strelka-varscan-mutect NUMBL,missense_variant,p.Thr345Ile,ENST00000252891,NM_004756.4;NUMBL,missense_variant,p.Thr304Ile,ENST00000598779,NM_001289979.1;NUMBL,missense_variant,p.Thr304Ile,ENST00000540131,NM_001289980.1;NUMBL,downstream_gene_variant,,ENST00000598773,;NUMBL,downstream_gene_variant,,ENST00000600967,;NUMBL,downstream_gene_variant,,ENST00000593367,; A ENST00000252891 Transcript missense_variant,splice_region_variant 1202/3561 1034/1830 345/609 T/I aCa/aTa 1 -1 NUMBL HGNC HGNC:8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 UPI000003032B NM_004756.4 tolerated(0.05) 8/10 Pfam_domain:PF06311,PIRSF_domain:PIRSF017607,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF32 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 40673346 40673346 G A 1 0 0 0 0 1 0 0 0 10817 1391 48 3 3 NUMBL 19 40673346 Missense_Mutation SNP G C3N-00217_T 430720 40673346 17944270 533 12303 CYP2S1 0 . GRCh38 19 41197807 41197807 + Nonsense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.372G>A p.Trp124Ter p.W124* ENST00000310054 3/9 298 204 94 236 235 1 strelka-varscan-mutect CYP2S1,stop_gained,p.Trp124Ter,ENST00000310054,NM_030622.7;CYP2S1,stop_gained,p.Trp124Ter,ENST00000600561,;CYP2S1,intron_variant,,ENST00000597754,;CYP2S1,upstream_gene_variant,,ENST00000593890,;CYP2S1,intron_variant,,ENST00000593545,;CYP2S1,intron_variant,,ENST00000595590,; A ENST00000310054 Transcript stop_gained 588/2782 372/1515 124/504 W/* tgG/tgA 1 1 CYP2S1 HGNC HGNC:15654 protein_coding YES CCDS12573.1 ENSP00000308032 Q96SQ9 UPI00000467C9 NM_030622.7 3/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF23,Superfamily_domains:SSF48264 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 41197807 41197807 G A 1 0 0 0 0 0 1 0 0 3977 1183 41 3 3 CYP2S1 19 41197807 Nonsense_Mutation SNP G C3N-00217_T 524461 41197807 17419809 534 12304 PSG9 0 . GRCh38 19 43268089 43268089 + Missense_Mutation SNP G G T rs374733593 C3N-00217_T C3N-00217_N G G c.125C>A p.Pro42Gln p.P42Q ENST00000270077 2/6 76 52 24 74 74 0 varscan-mutect PSG9,missense_variant,p.Pro42Gln,ENST00000244293,;PSG9,missense_variant,p.Pro42Gln,ENST00000621109,;PSG9,missense_variant,p.Pro42Gln,ENST00000596730,;PSG9,missense_variant,p.Pro42Gln,ENST00000418820,;PSG9,missense_variant,p.Pro42Gln,ENST00000270077,NM_002784.4;PSG9,missense_variant,p.Pro42Gln,ENST00000593948,NM_001301708.1;PSG9,missense_variant,p.Pro42Gln,ENST00000443718,NM_001301707.1;PSG9,missense_variant,p.Pro42Gln,ENST00000291752,NM_001301709.1; T ENST00000270077 Transcript missense_variant 222/1705 125/1281 42/426 P/Q cCa/cAa rs374733593 1 -1 PSG9 HGNC HGNC:9526 protein_coding YES CCDS12618.1 ENSP00000270077 Q00887 UPI00001327A5 NM_002784.4 deleterious(0) 2/6 Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs374733593 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 43268089 43268089 G T 1 0 0 0 0 1 0 0 0 12813 1348 47 2 2 PSG9 19 43268089 Missense_Mutation SNP G C3N-00217_T 2070282 43268089 15349527 535 12305 HIF3A 0 . GRCh38 19 46309192 46309192 + Silent SNP T T A novel C3N-00217_T C3N-00217_N T T c.603T>A p.= p.P201P ENST00000377670 6/15 164 122 42 177 177 0 strelka-varscan-mutect HIF3A,synonymous_variant,p.=,ENST00000377670,NM_152795.3;HIF3A,synonymous_variant,p.=,ENST00000300862,NM_152794.3;HIF3A,synonymous_variant,p.=,ENST00000244303,NM_022462.4;HIF3A,synonymous_variant,p.=,ENST00000600383,;HIF3A,synonymous_variant,p.=,ENST00000472815,NM_152796.2;HIF3A,downstream_gene_variant,,ENST00000533145,;RNU6-924P,upstream_gene_variant,,ENST00000362926,;HIF3A,non_coding_transcript_exon_variant,,ENST00000525854,;HIF3A,3_prime_UTR_variant,,ENST00000528563,;HIF3A,3_prime_UTR_variant,,ENST00000533789,;HIF3A,non_coding_transcript_exon_variant,,ENST00000244302,;HIF3A,non_coding_transcript_exon_variant,,ENST00000291300,;HIF3A,non_coding_transcript_exon_variant,,ENST00000475432,;HIF3A,non_coding_transcript_exon_variant,,ENST00000529205,;HIF3A,downstream_gene_variant,,ENST00000600879,;HIF3A,upstream_gene_variant,,ENST00000531043,;HIF3A,downstream_gene_variant,,ENST00000526506,; A ENST00000377670 Transcript synonymous_variant 634/5852 603/2010 201/669 P ccT/ccA 1 1 HIF3A HGNC HGNC:15825 protein_coding YES CCDS12681.2 ENSP00000366898 Q9Y2N7 UPI00002026E2 NM_152795.3 6/15 hmmpanther:PTHR23043:SF18,hmmpanther:PTHR23043 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 46309192 46309192 T A 1 0 0 0 0 0 0 0 1 6990 1567 55 4 4 HIF3A 19 46309192 Silent SNP T C3N-00217_T 3041103 46309192 12308424 536 12306 RASIP1 0 . GRCh38 19 48739471 48739471 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.312C>A p.Ser104Arg p.S104R ENST00000222145 3/12 152 104 48 111 111 0 strelka-varscan-mutect RASIP1,missense_variant,p.Ser104Arg,ENST00000222145,NM_017805.2;IZUMO1,downstream_gene_variant,,ENST00000332955,NM_182575.2;RASIP1,upstream_gene_variant,,ENST00000599291,;IZUMO1,downstream_gene_variant,,ENST00000602105,;RASIP1,upstream_gene_variant,,ENST00000594232,;IZUMO1,downstream_gene_variant,,ENST00000597553,;IZUMO1,downstream_gene_variant,,ENST00000595937,NM_001321865.1;IZUMO1,downstream_gene_variant,,ENST00000595517,;IZUMO1,downstream_gene_variant,,ENST00000599871,; T ENST00000222145 Transcript missense_variant 517/3308 312/2892 104/963 S/R agC/agA 1 -1 RASIP1 HGNC HGNC:24716 protein_coding YES CCDS12731.1 ENSP00000222145 Q5U651 UPI000020283D NM_017805.2 tolerated(0.69) 3/12 hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999986 1 1 1 0 T 3 4 43 48739471 48739471 G T 1 0 0 0 0 1 0 0 0 13239 1078 38 1 1 RASIP1 19 48739471 Missense_Mutation SNP G C3N-00217_T 2430279 48739471 9878145 537 12307 IRF3 0 . GRCh38 19 49664799 49664799 + Missense_Mutation SNP A A C rs748010879 C3N-00217_T C3N-00217_N A A c.40T>G p.Ser14Ala p.S14A ENST00000601291 2/8 127 93 34 106 105 1 strelka-varscan-mutect IRF3,missense_variant,p.Ser14Ala,ENST00000597198,;IRF3,missense_variant,p.Ser14Ala,ENST00000309877,;IRF3,missense_variant,p.Ser14Ala,ENST00000600911,;IRF3,missense_variant,p.Ser14Ala,ENST00000377139,NM_001571.5;IRF3,missense_variant,p.Ser14Ala,ENST00000601291,NM_001197122.1;IRF3,missense_variant,p.Ser14Ala,ENST00000598108,;IRF3,missense_variant,p.Ser14Ala,ENST00000599223,NM_001197124.1;IRF3,missense_variant,p.Ser14Ala,ENST00000596756,;IRF3,missense_variant,p.Ser14Ala,ENST00000601809,;IRF3,missense_variant,p.Ser14Ala,ENST00000600453,;IRF3,missense_variant,p.Ser14Ala,ENST00000593337,;IRF3,missense_variant,p.Ser14Ala,ENST00000442265,;IRF3,intron_variant,,ENST00000593922,NM_001197123.1;IRF3,intron_variant,,ENST00000598808,;IRF3,intron_variant,,ENST00000377135,NM_001197125.1;IRF3,intron_variant,,ENST00000599144,NM_001197126.1;IRF3,intron_variant,,ENST00000593818,;IRF3,intron_variant,,ENST00000600022,NM_001197127.1;IRF3,intron_variant,,ENST00000596822,;IRF3,intron_variant,,ENST00000595034,;IRF3,intron_variant,,ENST00000596765,NM_001197128.1;IRF3,intron_variant,,ENST00000601373,;BCL2L12,upstream_gene_variant,,ENST00000616144,NM_138639.1;BCL2L12,upstream_gene_variant,,ENST00000619007,NM_001282520.1,NM_001282516.1,NM_001282519.1;BCL2L12,upstream_gene_variant,,ENST00000246785,;BCL2L12,upstream_gene_variant,,ENST00000614495,NM_001282521.1;BCL2L12,upstream_gene_variant,,ENST00000441864,NM_001040668.1;BCL2L12,upstream_gene_variant,,ENST00000611631,;BCL2L12,upstream_gene_variant,,ENST00000246784,;BCL2L12,upstream_gene_variant,,ENST00000600947,;BCL2L12,upstream_gene_variant,,ENST00000594157,NM_001282517.1;BCL2L12,upstream_gene_variant,,ENST00000598306,;IRF3,intron_variant,,ENST00000597180,;IRF3,upstream_gene_variant,,ENST00000599680,;IRF3,upstream_gene_variant,,ENST00000602190,;IRF3,missense_variant,p.Ser14Ala,ENST00000597636,;IRF3,non_coding_transcript_exon_variant,,ENST00000594387,;BCL2L12,upstream_gene_variant,,ENST00000598979,;IRF3,upstream_gene_variant,,ENST00000595240,;IRF3,upstream_gene_variant,,ENST00000596644,;IRF3,upstream_gene_variant,,ENST00000597369,;IRF3,upstream_gene_variant,,ENST00000596788,;BCL2L12,upstream_gene_variant,,ENST00000601168,; C ENST00000601291 Transcript missense_variant 220/1556 40/1359 14/452 S/A Tcg/Gcg rs748010879 1 -1 IRF3 HGNC HGNC:6118 protein_coding YES CCDS59409.1 ENSP00000471896 Q14653 UPI000013CBFE NM_001197122.1 tolerated(0.18) 2/8 PROSITE_profiles:PS51507,hmmpanther:PTHR11949:SF1,hmmpanther:PTHR11949,Gene3D:1.10.10.10,Pfam_domain:PF00605,SMART_domains:SM00348,Superfamily_domains:SSF46785,Prints_domain:PR00267 MODERATE 1 SNV 1 1 PASS rs748010879 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 49664799 49664799 A C 1 0 0 0 0 1 0 0 0 7738 275 10 5 5 IRF3 19 49664799 Missense_Mutation SNP A C3N-00217_T 925328 49664799 8952817 538 12308 CD33 0 . GRCh38 19 51226033 51226033 + Missense_Mutation SNP G G C rs150408980 C3N-00217_T C3N-00217_N G G c.649G>C p.Ala217Pro p.A217P ENST00000262262 3/7 228 117 111 118 118 0 strelka-varscan-mutect CD33,missense_variant,p.Ala90Pro,ENST00000436584,;CD33,missense_variant,p.Ala217Pro,ENST00000262262,NM_001772.3;CD33,missense_variant,p.Ala217Pro,ENST00000391796,NM_001177608.1;CD33,missense_variant,p.Ala90Pro,ENST00000421133,NM_001082618.1;CD33,non_coding_transcript_exon_variant,,ENST00000598473,;CD33,non_coding_transcript_exon_variant,,ENST00000601785,; C ENST00000262262 Transcript missense_variant 670/1444 649/1095 217/364 A/P Gct/Cct rs150408980,COSM3404497 1 1 CD33 HGNC HGNC:1659 protein_coding YES CCDS33084.1 ENSP00000262262 P20138 Q546G0 UPI000013D285 NM_001772.3 tolerated(1) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF52,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF00047,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs150408980 . 0 207 0 3 0 0 0 0 -20 0.9999994 1 1 1 0 C 3 2 43 51226033 51226033 G C 1 0 0 0 0 1 0 0 0 2709 1087 38 4 4 CD33 19 51226033 Missense_Mutation SNP G C3N-00217_T 1561234 51226033 7391583 539 12309 NDUFA3 0 . GRCh38 19 54105978 54105978 + Missense_Mutation SNP A A C rs776295916 C3N-00217_T C3N-00217_N A A c.130A>C p.Met44Leu p.M44L ENST00000485876 3/4 374 294 80 203 203 0 strelka-varscan-mutect NDUFA3,start_lost,p.Met1?,ENST00000303553,;NDUFA3,missense_variant,p.Met44Leu,ENST00000485876,NM_004542.3;NDUFA3,missense_variant,p.Met44Leu,ENST00000471292,;NDUFA3,missense_variant,p.Met44Leu,ENST00000391762,;NDUFA3,missense_variant,p.Met6Leu,ENST00000420296,;NDUFA3,missense_variant,p.His47Pro,ENST00000391763,;NDUFA3,missense_variant,p.Met44Leu,ENST00000391764,;OSCAR,upstream_gene_variant,,ENST00000611261,NM_206818.2;OSCAR,upstream_gene_variant,,ENST00000284648,NM_001282349.1;OSCAR,upstream_gene_variant,,ENST00000616215,NM_001282350.1;OSCAR,upstream_gene_variant,,ENST00000617140,NM_130771.4;TFPT,downstream_gene_variant,,ENST00000391759,NM_013342.3;TFPT,downstream_gene_variant,,ENST00000391758,NM_001321792.1;TFPT,downstream_gene_variant,,ENST00000391757,;NDUFA3,upstream_gene_variant,,ENST00000480713,;NDUFA3,upstream_gene_variant,,ENST00000482960,;NDUFA3,missense_variant,p.Met41Leu,ENST00000422029,;NDUFA3,missense_variant,p.Met44Leu,ENST00000419113,;NDUFA3,3_prime_UTR_variant,,ENST00000417903,;NDUFA3,3_prime_UTR_variant,,ENST00000451517,;NDUFA3,non_coding_transcript_exon_variant,,ENST00000484103,;TFPT,downstream_gene_variant,,ENST00000420715,; C ENST00000485876 Transcript missense_variant 172/963 130/255 44/84 M/L Atg/Ctg rs776295916 1 1 NDUFA3 HGNC HGNC:7686 protein_coding YES CCDS12877.1 ENSP00000418438 O95167 UPI000013004B NM_004542.3 tolerated(0.14) 3/4 hmmpanther:PTHR15221,hmmpanther:PTHR15221:SF0,Pfam_domain:PF14987 MODERATE 1 SNV 1 1 PASS rs776295916 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 54105978 54105978 A C 1 0 0 0 0 1 0 0 0 10286 217 8 5 5 NDUFA3 19 54105978 Missense_Mutation SNP A C3N-00217_T 2879945 54105978 4511638 540 12310 LILRB4 0 . GRCh38 19 54664193 54664193 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.363C>A p.Tyr121Ter p.Y121* ENST00000391736 6/14 145 63 82 103 103 0 strelka-varscan-mutect LILRB4,stop_gained,p.Tyr121Ter,ENST00000391736,NM_001278426.3;LILRB4,stop_gained,p.Tyr121Ter,ENST00000430952,NM_001278427.3;LILRB4,stop_gained,p.Tyr121Ter,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,stop_gained,p.Tyr121Ter,ENST00000391734,;LILRB4,stop_gained,p.Tyr121Ter,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000470943,; A ENST00000391736 Transcript stop_gained 678/4002 363/1347 121/448 Y/* taC/taA 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 6/14 hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 54664193 54664193 C A 1 0 0 0 0 0 1 0 0 8701 489 17 2 2 LILRB4 19 54664193 Nonsense_Mutation SNP C C3N-00217_T 558215 54664193 3953423 541 12311 NCR1 0 . GRCh38 19 54906681 54906681 + Silent SNP C C A rs142746677 C3N-00217_T C3N-00217_N C C c.229C>A p.= p.R77R ENST00000291890 3/7 553 412 141 349 349 0 strelka-varscan-mutect NCR1,synonymous_variant,p.=,ENST00000594765,NM_001145457.2;NCR1,synonymous_variant,p.=,ENST00000291890,NM_004829.6;NCR1,synonymous_variant,p.=,ENST00000598576,;NCR1,synonymous_variant,p.=,ENST00000338835,NM_001145458.2,NM_001242357.2;NCR1,intron_variant,,ENST00000350790,NM_001242356.2;NCR1,intron_variant,,ENST00000357397,;NCR1,non_coding_transcript_exon_variant,,ENST00000601137,;NCR1,non_coding_transcript_exon_variant,,ENST00000601903,; A ENST00000291890 Transcript synonymous_variant 267/1155 229/915 77/304 R Cgg/Agg rs142746677,COSM1001282 1 1 NCR1 HGNC HGNC:6731 protein_coding YES CCDS12911.1 ENSP00000291890 A0A0A0MQZ0 UPI00034F23C0 NM_004829.6 3/7 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF14,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 LOW 1 SNV 5 0,1 1 PASS rs142746677 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 54906681 54906681 C A 1 0 0 0 0 0 0 0 1 10256 759 27 1 1 NCR1 19 54906681 Silent SNP C C3N-00217_T 242488 54906681 3710935 542 12312 NLRP7 0 . GRCh38 19 54930638 54930638 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2671G>T p.Gly891Cys p.G891C ENST00000588756 11/13 308 177 131 221 221 0 strelka-varscan-mutect NLRP7,missense_variant,p.Gly891Cys,ENST00000588756,;NLRP7,missense_variant,p.Gly863Cys,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Gly891Cys,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Gly891Cys,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Gly891Cys,ENST00000590030,;NLRP7,missense_variant,p.Gly891Cys,ENST00000586379,; A ENST00000588756 Transcript missense_variant 3158/3826 2671/3114 891/1037 G/C Ggc/Tgc 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 deleterious(0.02) 11/13 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 54930638 54930638 C A 1 0 0 0 0 1 0 0 0 10520 594 21 2 2 NLRP7 19 54930638 Missense_Mutation SNP C C3N-00217_T 23957 54930638 3686978 543 12313 ZNF628 0 . GRCh38 19 55482556 55482556 + Missense_Mutation SNP A A G rs868164487 C3N-00217_T C3N-00217_N A A c.1363A>G p.Lys455Glu p.K455E ENST00000598519 3/3 77 37 40 43 43 0 strelka-varscan-mutect ZNF628,missense_variant,p.Lys455Glu,ENST00000598519,NM_033113.2;ZNF628,missense_variant,p.Lys454Glu,ENST00000391718,;NAT14,upstream_gene_variant,,ENST00000205194,NM_020378.3;NAT14,upstream_gene_variant,,ENST00000591590,;NAT14,upstream_gene_variant,,ENST00000588985,;ZNF628,downstream_gene_variant,,ENST00000591164,;NAT14,upstream_gene_variant,,ENST00000587400,;NAT14,upstream_gene_variant,,ENST00000592719,; G ENST00000598519 Transcript missense_variant 1916/3847 1363/3180 455/1059 K/E Aaa/Gaa rs868164487 1 1 ZNF628 HGNC HGNC:28054 protein_coding YES CCDS33116.3 ENSP00000469591 Q5EBL2 UPI00026B9C6E NM_033113.2 tolerated(0.25) 3/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF19,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs868164487 . 0 195 14 0 0 0 0 0 -20 0.9999725 1 1 1 0 G 3 3 43 55482556 55482556 A G 1 0 0 0 0 1 0 0 0 18627 131 5 5 5 ZNF628 19 55482556 Missense_Mutation SNP A C3N-00217_T 551918 55482556 3135060 544 12314 ZNF549 0 . GRCh38 19 57535145 57535145 + Missense_Mutation SNP G G A rs367783563 C3N-00217_T C3N-00217_N G G c.74G>A p.Gly25Asp p.G25D ENST00000376233 3/4 85 72 13 56 56 0 strelka-mutect ZNF549,missense_variant,p.Gly25Asp,ENST00000602149,;ZNF549,missense_variant,p.Gly25Asp,ENST00000376233,NM_001199295.1;ZNF549,missense_variant,p.Gly12Asp,ENST00000240719,NM_153263.2;ZNF549,intron_variant,,ENST00000594943,;ZNF550,downstream_gene_variant,,ENST00000601415,; A ENST00000376233 Transcript missense_variant,splice_region_variant 255/4053 74/1923 25/640 G/D gGc/gAc rs367783563,COSM116988 1 1 ZNF549 HGNC HGNC:26632 protein_coding YES CCDS56106.1 ENSP00000365407 Q6P9A3 UPI0000202D31 NM_001199295.1 tolerated(0.2) 3/4 hmmpanther:PTHR24387:SF30,hmmpanther:PTHR24387,Superfamily_domains:0044637 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367783563 . 0 200 8 2 0 0 0 0 -19.99272 0.9997385 1 1 1 0 A 3 1 43 57535145 57535145 G A 1 0 0 0 0 1 0 0 0 18555 1217 42 3 3 ZNF549 19 57535145 Missense_Mutation SNP G C3N-00217_T 2052589 57535145 1082471 545 12315 ZSCAN4 0 . GRCh38 19 57678588 57678588 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.985G>T p.Ala329Ser p.A329S ENST00000318203 5/5 235 184 51 203 203 0 strelka-varscan-mutect ZSCAN4,missense_variant,p.Ala329Ser,ENST00000318203,NM_152677.2;ZSCAN4,missense_variant,p.Ala329Ser,ENST00000612521,;ZNF551,upstream_gene_variant,,ENST00000282296,NM_138347.4;ZNF551,upstream_gene_variant,,ENST00000601064,NM_001270938.1;AC003006.7,upstream_gene_variant,,ENST00000594684,;ZNF551,upstream_gene_variant,,ENST00000596085,;ZNF551,upstream_gene_variant,,ENST00000599402,;AC003006.7,upstream_gene_variant,,ENST00000599221,; T ENST00000318203 Transcript missense_variant 1682/2246 985/1302 329/433 A/S Gct/Tct 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 deleterious(0.03) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 57678588 57678588 G T 1 0 0 0 0 1 0 0 0 18836 971 34 2 2 ZSCAN4 19 57678588 Missense_Mutation SNP G C3N-00217_T 143443 57678588 939028 546 12316 ZSCAN18 0 . GRCh38 19 58088772 58088772 + Missense_Mutation SNP T T A rs748767377 C3N-00217_T C3N-00217_N T T c.637A>T p.Met213Leu p.M213L ENST00000600404 3/7 203 123 80 141 141 0 strelka-varscan-mutect ZSCAN18,missense_variant,p.Met157Leu,ENST00000240727,NM_023926.4;ZSCAN18,missense_variant,p.Met157Leu,ENST00000601144,NM_001145543.1;ZSCAN18,missense_variant,p.Met55Leu,ENST00000433686,;ZSCAN18,missense_variant,p.Met213Leu,ENST00000600404,NM_001145542.1;ZSCAN18,missense_variant,p.Met22Leu,ENST00000421612,NM_001145544.1;ZSCAN18,missense_variant,p.Met157Leu,ENST00000600897,;ZSCAN18,missense_variant,p.Met157Leu,ENST00000600845,;ZSCAN18,downstream_gene_variant,,ENST00000601063,;ZSCAN18,downstream_gene_variant,,ENST00000595721,;ZSCAN18,upstream_gene_variant,,ENST00000600522,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000598497,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000600318,;ZSCAN18,non_coding_transcript_exon_variant,,ENST00000594191,;ZNF135,downstream_gene_variant,,ENST00000515535,;ZSCAN18,upstream_gene_variant,,ENST00000596372,;ZSCAN18,upstream_gene_variant,,ENST00000595784,; A ENST00000600404 Transcript missense_variant 667/1934 637/1701 213/566 M/L Atg/Ttg rs748767377 1 -1 ZSCAN18 HGNC HGNC:21037 protein_coding YES CCDS46214.1 ENSP00000470123 Q8TBC5 UPI00017A6DAF NM_001145542.1 tolerated(0.34) 3/7 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF6,SMART_domains:SM00431 MODERATE 1 SNV 2 1 PASS rs748767377 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 58088772 58088772 T A 1 0 0 0 0 1 0 0 0 18824 1464 51 4 4 ZSCAN18 19 58088772 Missense_Mutation SNP T C3N-00217_T 410184 58088772 528844 547 12317 DEFB125 0 . GRCh38 20 87761 87762 + Frame_Shift_Del DEL AC AC - novel C3N-00217_T C3N-00217_N AC AC c.52_53delAC p.Thr18GlnfsTer3 p.T18Qfs*3 ENST00000382410 1/2 169 128 41 155 155 0 sindel-varindel DEFB125,frameshift_variant,p.Thr18GlnfsTer3,ENST00000382410,NM_153325.3;DEFB125,intron_variant,,ENST00000608838,; - ENST00000382410 Transcript frameshift_variant 52-53/587 52-53/471 18/156 T/X ACc/c 1 1 DEFB125 HGNC HGNC:18105 protein_coding YES CCDS12989.2 ENSP00000371847 Q8N687 UPI00001A36DE NM_153325.3 1/2 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF4,PD866254 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 87761 87761 AC - 1 0 1 0 1 0 0 0 0 4214 275 10 0 0 DEFB125 20 87761 Frame_Shift_Del DEL AC C3N-00217_T 87761 64356406 548 12318 PLCB4 0 . GRCh38 20 9459641 9459641 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.3043G>A p.Glu1015Lys p.E1015K ENST00000378501 31/36 60 36 24 43 43 0 strelka-varscan-mutect PLCB4,missense_variant,p.Glu1015Lys,ENST00000378501,NM_000933.3;PLCB4,missense_variant,p.Glu1015Lys,ENST00000378493,;PLCB4,missense_variant,p.Glu1027Lys,ENST00000378473,NM_001172646.1;PLCB4,missense_variant,p.Glu1015Lys,ENST00000278655,NM_182797.2;PLCB4,missense_variant,p.Glu1027Lys,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,;PLCB4,intron_variant,,ENST00000492632,; A ENST00000378501 Transcript missense_variant 3058/5833 3043/3585 1015/1194 E/K Gag/Aag 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 tolerated(0.6) 31/36 Superfamily_domains:0053448,Gene3D:1jadA00,PIRSF_domain:PIRSF000956,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 9459641 9459641 G A 1 0 0 0 0 1 0 0 0 12124 943 33 3 3 PLCB4 20 9459641 Missense_Mutation SNP G C3N-00217_T 9371880 9459641 54984526 549 12319 OTOR 0 . GRCh38 20 16748947 16748947 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.196A>T p.Ile66Phe p.I66F ENST00000246081 2/4 128 95 33 135 135 0 strelka-varscan-mutect OTOR,missense_variant,p.Ile66Phe,ENST00000246081,NM_020157.3;OTOR,upstream_gene_variant,,ENST00000486129,;OTOR,upstream_gene_variant,,ENST00000490148,; T ENST00000246081 Transcript missense_variant 240/1477 196/387 66/128 I/F Atc/Ttc 1 1 OTOR HGNC HGNC:8517 protein_coding YES CCDS13124.1 ENSP00000246081 Q9NRC9 UPI0000047809 NM_020157.3 deleterious(0) 2/4 Gene3D:2.30.30.40,Pfam_domain:PF07653,hmmpanther:PTHR23158,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 16748947 16748947 A T 1 0 0 0 0 1 0 0 0 11376 333 12 4 4 OTOR 20 16748947 Missense_Mutation SNP A C3N-00217_T 7289306 16748947 47695220 550 12320 TLDC2 0 . GRCh38 20 36889303 36889303 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.565C>A p.Pro189Thr p.P189T ENST00000217320 6/7 188 135 53 167 167 0 strelka-varscan-mutect TLDC2,missense_variant,p.Pro189Thr,ENST00000217320,NM_080628.2,NM_001304783.1;TLDC2,missense_variant,p.Pro189Thr,ENST00000602922,;TLDC2,intron_variant,,ENST00000436941,;SAMHD1,downstream_gene_variant,,ENST00000262878,NM_015474.3; A ENST00000217320 Transcript missense_variant 609/2083 565/648 189/215 P/T Cct/Act 1 1 TLDC2 HGNC HGNC:16112 protein_coding YES CCDS33465.1 ENSP00000217320 A0PJX2 UPI000049DF51 NM_080628.2,NM_001304783.1 deleterious(0.03) 6/7 hmmpanther:PTHR23354,hmmpanther:PTHR23354:SF65,Pfam_domain:PF07534,SMART_domains:SM00584 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 36889303 36889303 C A 1 0 0 0 0 1 0 0 0 16383 623 22 2 2 TLDC2 20 36889303 Missense_Mutation SNP C C3N-00217_T 20140356 36889303 27554864 551 12321 RALGAPB 0 . GRCh38 20 38532776 38532776 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.2162G>A p.Gly721Asp p.G721D ENST00000262879 15/30 213 173 40 198 198 0 strelka-varscan-mutect RALGAPB,missense_variant,p.Gly721Asp,ENST00000262879,NM_001282917.1,NM_020336.3;RALGAPB,missense_variant,p.Gly721Asp,ENST00000397042,NM_001282918.1;RALGAPB,missense_variant,p.Gly721Asp,ENST00000397040,;RALGAPB,missense_variant,p.Gly89Asp,ENST00000632792,;RALGAPB,missense_variant,p.Gly549Asp,ENST00000438490,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,;RPS3P2,upstream_gene_variant,,ENST00000421346,; A ENST00000262879 Transcript missense_variant 2446/8663 2162/4485 721/1494 G/D gGt/gAt 1 1 RALGAPB HGNC HGNC:29221 protein_coding YES CCDS13305.1 ENSP00000262879 Q86X10 UPI000000DBFD NM_001282917.1,NM_020336.3 deleterious(0.03) 15/30 hmmpanther:PTHR21344 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 38532776 38532776 G A 1 0 0 0 0 1 0 0 0 13174 1261 44 3 3 RALGAPB 20 38532776 Missense_Mutation SNP G C3N-00217_T 1643473 38532776 25911391 552 12322 HNF4A 0 . GRCh38 20 44424059 44424059 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.934C>T p.Arg312Cys p.R312C ENST00000316099 8/10 300 233 67 223 223 0 strelka-varscan-mutect HNF4A,missense_variant,p.Arg312Cys,ENST00000316099,NM_001258355.1,NM_000457.4;HNF4A,missense_variant,p.Arg287Cys,ENST00000619550,NM_001287182.1,NM_001287183.1;HNF4A,missense_variant,p.Arg312Cys,ENST00000415691,NM_178849.2;HNF4A,missense_variant,p.Arg312Cys,ENST00000443598,NM_178850.2;HNF4A,missense_variant,p.Arg290Cys,ENST00000316673,NM_175914.4;HNF4A,missense_variant,p.Arg290Cys,ENST00000457232,NM_001030003.2;HNF4A,missense_variant,p.Arg290Cys,ENST00000609795,NM_001030004.2,NM_001287184.1;HNF4A,3_prime_UTR_variant,,ENST00000372920,; T ENST00000316099 Transcript missense_variant 1023/6445 934/1425 312/474 R/C Cgt/Tgt CM1111342 1 1 HNF4A HGNC HGNC:5024 protein_coding YES CCDS13330.1 ENSP00000312987 P41235 F1D8T1 UPI000016A0BA NM_001258355.1,NM_000457.4 deleterious(0) 8/10 hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF41,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 44424059 44424059 C T 1 0 0 0 0 1 0 0 0 7144 768 27 1 1 HNF4A 20 44424059 Missense_Mutation SNP C C3N-00217_T 5891283 44424059 20020108 553 12323 CTSA 0 . GRCh38 20 45898365 45898365 + Splice_Site SNP A A T novel C3N-00217_T C3N-00217_N A A c.1414-2A>T p.X472_splice ENST00000372484 405 299 106 353 353 0 strelka-varscan-mutect CTSA,splice_acceptor_variant,,ENST00000372484,NM_000308.2;CTSA,splice_acceptor_variant,,ENST00000372459,;CTSA,splice_acceptor_variant,,ENST00000191018,NM_001127695.1;CTSA,splice_acceptor_variant,,ENST00000354880,NM_001167594.1;PLTP,downstream_gene_variant,,ENST00000477313,;PLTP,downstream_gene_variant,,ENST00000372431,NM_006227.3;PLTP,downstream_gene_variant,,ENST00000354050,NM_182676.2;PLTP,downstream_gene_variant,,ENST00000372420,NM_001242921.1;PLTP,downstream_gene_variant,,ENST00000420868,NM_001242920.1;CTSA,downstream_gene_variant,,ENST00000419493,;RP3-337O18.9,upstream_gene_variant,,ENST00000607703,;CTSA,splice_acceptor_variant,,ENST00000606788,;CTSA,splice_acceptor_variant,,ENST00000484855,;CTSA,splice_acceptor_variant,,ENST00000606000,;CTSA,downstream_gene_variant,,ENST00000493522,;CTSA,downstream_gene_variant,,ENST00000485627,;CTSA,downstream_gene_variant,,ENST00000480961,;CTSA,downstream_gene_variant,,ENST00000607187,; T ENST00000372484 Transcript splice_acceptor_variant -/2149 1414/1497 472/498 1 1 CTSA HGNC HGNC:9251 protein_coding YES CCDS13385.2 ENSP00000361562 X6R8A1 UPI000022B4F7 NM_000308.2 14/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 43 45898365 45898365 A T 1 0 0 0 0 0 0 1 0 3838 202 7 4 4 CTSA 20 45898365 Splice_Site SNP A C3N-00217_T 1474306 45898365 18545802 554 12324 CDH22 0 . GRCh38 20 46227508 46227508 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.670G>T p.Gly224Cys p.G224C ENST00000537909 4/12 179 120 59 175 175 0 strelka-varscan-mutect CDH22,missense_variant,p.Gly224Cys,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Gly224Cys,ENST00000372262,; A ENST00000537909 Transcript missense_variant,splice_region_variant 1313/3902 670/2487 224/828 G/C Ggc/Tgc 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 deleterious(0) 4/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 46227508 46227508 C A 1 0 0 0 0 1 0 0 0 2810 666 23 1 1 CDH22 20 46227508 Missense_Mutation SNP C C3N-00217_T 329143 46227508 18216659 555 12325 PREX1 0 . GRCh38 20 48708339 48708339 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.704C>A p.Ser235Tyr p.S235Y ENST00000371941 6/40 224 144 80 245 245 0 strelka-varscan-mutect PREX1,missense_variant,p.Ser235Tyr,ENST00000371941,NM_020820.3; T ENST00000371941 Transcript missense_variant 727/6636 704/4980 235/1659 S/Y tCc/tAc 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 deleterious(0) 6/40 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50010,hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS rs1484581061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 48708339 48708339 G T 1 0 0 0 0 1 0 0 0 12610 1174 41 2 2 PREX1 20 48708339 Missense_Mutation SNP G C3N-00217_T 2480831 48708339 15735828 556 12326 CYP24A1 0 . GRCh38 20 54162738 54162738 + Silent SNP G G T C3N-00217_T C3N-00217_N G G c.969C>A p.= p.L323L ENST00000216862 7/12 309 201 108 313 313 0 strelka-varscan-mutect CYP24A1,synonymous_variant,p.=,ENST00000216862,NM_000782.4;CYP24A1,synonymous_variant,p.=,ENST00000395955,NM_001128915.1;CYP24A1,synonymous_variant,p.=,ENST00000395954,;CYP24A1,non_coding_transcript_exon_variant,,ENST00000487593,; T ENST00000216862 Transcript synonymous_variant 1363/3262 969/1545 323/514 L ctC/ctA COSM1471447 1 -1 CYP24A1 HGNC HGNC:2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 7/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF5,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00463 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 54162738 54162738 G T 1 0 0 0 0 0 0 0 1 3957 1161 41 2 2 CYP24A1 20 54162738 Silent SNP G C3N-00217_T 5454399 54162738 10281429 557 12327 PHACTR3 0 . GRCh38 20 59755215 59755215 + Missense_Mutation SNP G G T rs772879716 C3N-00217_T C3N-00217_N G G c.392G>T p.Gly131Val p.G131V ENST00000371015 4/13 200 159 41 190 189 1 strelka-varscan-mutect PHACTR3,missense_variant,p.Gly131Val,ENST00000371015,NM_080672.4;PHACTR3,missense_variant,p.Gly90Val,ENST00000395636,NM_183244.1;PHACTR3,missense_variant,p.Gly90Val,ENST00000541461,NM_001281507.1;PHACTR3,missense_variant,p.Gly128Val,ENST00000359926,NM_001199505.1;PHACTR3,missense_variant,p.Gly90Val,ENST00000355648,NM_001199506.1;PHACTR3,missense_variant,p.Gly90Val,ENST00000361300,NM_183246.1; T ENST00000371015 Transcript missense_variant 859/2728 392/1680 131/559 G/V gGa/gTa rs772879716 1 1 PHACTR3 HGNC HGNC:15833 protein_coding YES CCDS13480.1 ENSP00000360054 Q96KR7 UPI000006D452 NM_080672.4 tolerated(0.05) 4/13 hmmpanther:PTHR12751:SF7,hmmpanther:PTHR12751 MODERATE 1 SNV 1 1 PASS rs772879716 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 59755215 59755215 G T 1 0 0 0 0 1 0 0 0 11900 1174 41 2 2 PHACTR3 20 59755215 Missense_Mutation SNP G C3N-00217_T 5592477 59755215 4688952 558 12328 CDH4 0 . GRCh38 20 61910436 61910436 + Frame_Shift_Del DEL C C - C3N-00217_T C3N-00217_N C C c.1206delC p.Glu403LysfsTer13 p.E403Kfs*13 ENST00000614565 9/16 69 45 24 71 71 0 sindel-varindel-pindel CDH4,frameshift_variant,p.Glu403LysfsTer13,ENST00000614565,NM_001794.4;CDH4,frameshift_variant,p.Glu309LysfsTer13,ENST00000611855,;CDH4,frameshift_variant,p.Glu329LysfsTer13,ENST00000543233,NM_001252338.2,NM_001252339.2; - ENST00000614565 Transcript frameshift_variant 1291/6513 1203/2751 401/916 V/X gtC/gt COSM4779580 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 9/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Prints_domain:PR00205 1 HIGH 1 deletion 1 3 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 61910436 61910436 C - 1 0 1 0 1 0 0 0 0 2815 842 30 0 0 CDH4 20 61910436 Frame_Shift_Del DEL C C3N-00217_T 2155221 61910436 2533731 559 12329 OGFR 0 . GRCh38 20 62813415 62813415 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1800G>T p.Glu600Asp p.E600D ENST00000290291 7/7 376 251 125 255 254 1 strelka-varscan-mutect OGFR,missense_variant,p.Glu548Asp,ENST00000370461,;OGFR,missense_variant,p.Glu600Asp,ENST00000290291,NM_007346.2;OGFR,intron_variant,,ENST00000621591,;COL9A3,upstream_gene_variant,,ENST00000343916,NM_001853.3;COL9A3,upstream_gene_variant,,ENST00000452372,;OGFR,downstream_gene_variant,,ENST00000450048,;COL9A3,upstream_gene_variant,,ENST00000489045,;COL9A3,upstream_gene_variant,,ENST00000477612,; T ENST00000290291 Transcript missense_variant 1825/2410 1800/2034 600/677 E/D gaG/gaT 1 1 OGFR HGNC HGNC:15768 protein_coding YES CCDS13504.1 ENSP00000290291 Q9NZT2 UPI000013F107 NM_007346.2 tolerated_low_confidence(0.09) 7/7 Pfam_domain:PF04680 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 62813415 62813415 G T 1 0 0 0 0 1 0 0 0 10918 933 33 2 2 OGFR 20 62813415 Missense_Mutation SNP G C3N-00217_T 902979 62813415 1630752 560 12330 ADAMTS1 0 . GRCh38 21 26837858 26837858 + Missense_Mutation SNP C C A rs776514634 C3N-00217_T C3N-00217_N C C c.2625G>T p.Gln875His p.Q875H ENST00000284984 9/9 312 256 56 355 355 0 strelka-varscan-mutect ADAMTS1,missense_variant,p.Gln875His,ENST00000284984,NM_006988.4;ADAMTS1,downstream_gene_variant,,ENST00000451462,;ADAMTS1,downstream_gene_variant,,ENST00000517777,;ADAMTS1,downstream_gene_variant,,ENST00000517452,;ADAMTS1,non_coding_transcript_exon_variant,,ENST00000464589,;ADAMTS1,downstream_gene_variant,,ENST00000492656,; A ENST00000284984 Transcript missense_variant 3080/5191 2625/2904 875/967 Q/H caG/caT rs776514634 1 -1 ADAMTS1 HGNC HGNC:217 protein_coding YES CCDS33524.1 ENSP00000284984 Q9UHI8 UPI000013DDC6 NM_006988.4 deleterious(0) 9/9 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF40,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS rs776514634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 26837858 26837858 C A 1 0 0 0 0 1 0 0 0 299 912 32 2 2 ADAMTS1 21 26837858 Missense_Mutation SNP C C3N-00217_T 26837858 19872125 561 12331 KRTAP11-1 0 . GRCh38 21 30881122 30881122 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.403G>T p.Gly135Ter p.G135* ENST00000332378 1/1 218 178 40 222 222 0 strelka-varscan-mutect KRTAP11-1,stop_gained,p.Gly135Ter,ENST00000332378,NM_175858.2; A ENST00000332378 Transcript stop_gained 434/912 403/492 135/163 G/* Gga/Tga 1 -1 KRTAP11-1 HGNC HGNC:18922 protein_coding YES CCDS13608.1 ENSP00000330720 Q8IUC1 UPI000003B46F NM_175858.2 1/1 hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF14,Pfam_domain:PF05287 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 30881122 30881122 C A 1 0 0 0 0 0 1 0 0 8400 632 22 2 2 KRTAP11-1 21 30881122 Nonsense_Mutation SNP C C3N-00217_T 4043264 30881122 15828861 562 12332 TIAM1 0 . GRCh38 21 31266178 31266178 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.795C>A p.= p.P265P ENST00000286827 5/29 332 272 60 364 364 0 strelka-varscan-mutect TIAM1,synonymous_variant,p.=,ENST00000286827,NM_003253.2;TIAM1,synonymous_variant,p.=,ENST00000541036,;TIAM1,downstream_gene_variant,,ENST00000455508,;TIAM1,intron_variant,,ENST00000469412,; T ENST00000286827 Transcript synonymous_variant 1267/7200 795/4776 265/1591 P ccC/ccA 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 5/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88 LOW 1 SNV 1 1 PASS rs1341575391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 31266178 31266178 G T 1 0 0 0 0 0 0 0 1 16324 1335 47 2 2 TIAM1 21 31266178 Silent SNP G C3N-00217_T 385056 31266178 15443805 563 12333 IL10RB 0 . GRCh38 21 33279839 33279839 + Missense_Mutation SNP A A C rs56373309 C3N-00217_T C3N-00217_N A A c.419A>C p.Tyr140Ser p.Y140S ENST00000290200 4/7 192 115 77 287 287 0 strelka-varscan-mutect IL10RB,missense_variant,p.Tyr140Ser,ENST00000290200,NM_000628.4;AP000295.9,missense_variant,p.Tyr268Ser,ENST00000433395,;IL10RB,missense_variant,p.Tyr77Ser,ENST00000451065,;IL10RB,3_prime_UTR_variant,,ENST00000422891,;AP000295.9,3_prime_UTR_variant,,ENST00000432231,;IL10RB,non_coding_transcript_exon_variant,,ENST00000493295,;IL10RB,non_coding_transcript_exon_variant,,ENST00000498371,; C ENST00000290200 Transcript missense_variant 527/1963 419/978 140/325 Y/S tAc/tCc rs56373309 1 1 IL10RB HGNC HGNC:5965 protein_coding YES CCDS13623.1 ENSP00000290200 Q08334 UPI0000072ECA NM_000628.4 tolerated(0.5) 4/7 PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF50,Pfam_domain:PF09294,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs56373309 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 33279839 33279839 A C 1 0 0 0 0 1 0 0 0 7529 391 14 5 5 IL10RB 21 33279839 Missense_Mutation SNP A C3N-00217_T 2013661 33279839 13430144 564 12334 DOPEY2 0 . GRCh38 21 36230531 36230531 + Missense_Mutation SNP C C G rs757851386 C3N-00217_T C3N-00217_N C C c.1747C>G p.Pro583Ala p.P583A ENST00000399151 14/37 156 132 24 163 163 0 strelka-mutect DOPEY2,missense_variant,p.Pro583Ala,ENST00000399151,NM_001320714.1,NM_005128.3; G ENST00000399151 Transcript missense_variant 1832/7685 1747/6897 583/2298 P/A Cct/Gct rs757851386 1 1 DOPEY2 HGNC HGNC:1291 protein_coding YES CCDS13643.1 ENSP00000382104 Q9Y3R5 UPI000013D876 NM_001320714.1,NM_005128.3 tolerated(0.11) 14/37 hmmpanther:PTHR14042,hmmpanther:PTHR14042:SF23 MODERATE 1 SNV 1 1 PASS rs757851386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 36230531 36230531 C G 1 0 0 0 0 1 0 0 0 4522 623 22 4 4 DOPEY2 21 36230531 Missense_Mutation SNP C C3N-00217_T 2950692 36230531 10479452 565 12335 COL6A2 0 . GRCh38 21 46112543 46112543 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.680A>T p.Asp227Val p.D227V ENST00000300527 3/28 154 102 52 157 157 0 strelka-varscan-mutect COL6A2,missense_variant,p.Asp227Val,ENST00000300527,NM_001849.3;COL6A2,missense_variant,p.Asp227Val,ENST00000310645,NM_058175.2;COL6A2,missense_variant,p.Asp227Val,ENST00000409416,;COL6A2,missense_variant,p.Asp227Val,ENST00000397763,NM_058174.2;COL6A2,downstream_gene_variant,,ENST00000436769,;COL6A2,non_coding_transcript_exon_variant,,ENST00000460886,;COL6A2,upstream_gene_variant,,ENST00000485591,; T ENST00000300527 Transcript missense_variant 784/3461 680/3060 227/1019 D/V gAc/gTc 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 tolerated(0.08) 3/28 PROSITE_profiles:PS50234,hmmpanther:PTHR24023:SF119,hmmpanther:PTHR24023,Gene3D:3.40.50.410,SMART_domains:SM00327 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 46112543 46112543 A T 1 0 0 0 0 1 0 0 0 3489 275 10 4 4 COL6A2 21 46112543 Missense_Mutation SNP A C3N-00217_T 9882012 46112543 597440 566 12336 PCNT 0 . GRCh38 21 46381837 46381837 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.3309G>T p.Gln1103His p.Q1103H ENST00000359568 16/47 358 293 65 345 345 0 strelka-varscan-mutect PCNT,missense_variant,p.Gln1103His,ENST00000359568,NM_006031.5;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,; T ENST00000359568 Transcript missense_variant 3416/10560 3309/10011 1103/3336 Q/H caG/caT COSM1414626 1 1 PCNT HGNC HGNC:16068 protein_coding YES CCDS33592.1 ENSP00000352572 O95613 UPI00001AEB88 NM_006031.5 deleterious(0.03) 16/47 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF204 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 46381837 46381837 G T 1 0 0 0 0 1 0 0 0 11678 985 34 2 2 PCNT 21 46381837 Missense_Mutation SNP G C3N-00217_T 269294 46381837 328146 567 12337 XKR3 0 . GRCh38 22 16783820 16783820 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1179G>T p.Met393Ile p.M393I ENST00000331428 4/4 154 123 31 229 229 0 strelka-varscan-mutect XKR3,missense_variant,p.Met393Ile,ENST00000331428,NM_001318251.1,NM_175878.3; A ENST00000331428 Transcript missense_variant 1282/1690 1179/1380 393/459 M/I atG/atT 1 -1 XKR3 HGNC HGNC:28778 protein_coding YES CCDS42975.1 ENSP00000331704 Q5GH77 UPI000013EFAE NM_001318251.1,NM_175878.3 deleterious(0) 4/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR14297:SF7,hmmpanther:PTHR14297,Pfam_domain:PF09815 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 16783820 16783820 C A 1 0 0 0 0 1 0 0 0 17991 710 25 2 2 XKR3 22 16783820 Missense_Mutation SNP C C3N-00217_T 16783820 34034648 568 12338 XKR3 0 . GRCh38 22 16807999 16807999 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.75T>C p.= p.L25L ENST00000331428 2/4 74 52 22 133 133 0 strelka-varscan-mutect XKR3,synonymous_variant,p.=,ENST00000331428,NM_001318251.1,NM_175878.3; G ENST00000331428 Transcript synonymous_variant 178/1690 75/1380 25/459 L ctT/ctC 1 -1 XKR3 HGNC HGNC:28778 protein_coding YES CCDS42975.1 ENSP00000331704 Q5GH77 UPI000013EFAE NM_001318251.1,NM_175878.3 2/4 hmmpanther:PTHR14297:SF7,hmmpanther:PTHR14297 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 16807999 16807999 A G 1 0 0 0 0 0 0 0 1 17991 117 5 5 5 XKR3 22 16807999 Silent SNP A C3N-00217_T 24179 16807999 34010469 569 12339 TBX1 0 . GRCh38 22 19766832 19766832 + Missense_Mutation SNP G G T rs774386479 C3N-00217_T C3N-00217_N G G c.1453G>T p.Ala485Ser p.A485S ENST00000332710 9/9 133 105 28 155 155 0 strelka-varscan-mutect TBX1,missense_variant,p.Ala485Ser,ENST00000332710,NM_080647.1;TBX1,intron_variant,,ENST00000359500,NM_005992.1;TBX1,intron_variant,,ENST00000329705,NM_080646.1;TBX1,intron_variant,,ENST00000621939,;TBX1,downstream_gene_variant,,ENST00000475303,;TBX1,downstream_gene_variant,,ENST00000484336,; T ENST00000332710 Transcript missense_variant 1582/2084 1453/1488 485/495 A/S Gcg/Tcg rs774386479 1 1 TBX1 HGNC HGNC:11592 protein_coding YES CCDS13767.1 ENSP00000331791 O43435 D9ZGG0 UPI0000073068 NM_080647.1 tolerated_low_confidence(0.09) 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF104 MODERATE 1 SNV 1 1 PASS rs774386479 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 19766832 19766832 G T 1 0 0 0 0 1 0 0 0 16055 1087 38 1 1 TBX1 22 19766832 Missense_Mutation SNP G C3N-00217_T 2958833 19766832 31051636 570 12340 SLC7A4 0 . GRCh38 22 21031032 21031032 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.781G>T p.Ala261Ser p.A261S ENST00000382932 2/5 112 79 33 173 173 0 strelka-varscan-mutect SLC7A4,missense_variant,p.Ala261Ser,ENST00000382932,NM_004173.2;SLC7A4,missense_variant,p.Ala261Ser,ENST00000403586,;P2RX6,downstream_gene_variant,,ENST00000413302,NM_005446.3;P2RX6,downstream_gene_variant,,ENST00000401443,NM_001159554.1;SLC7A4,downstream_gene_variant,,ENST00000426145,;MIR649,downstream_gene_variant,,ENST00000384843,;AC002472.11,upstream_gene_variant,,ENST00000450652,;P2RX6P,downstream_gene_variant,,ENST00000439119,;P2RX6,downstream_gene_variant,,ENST00000442475,;P2RX6,downstream_gene_variant,,ENST00000432930,;P2RX6,downstream_gene_variant,,ENST00000422210,;P2RX6,downstream_gene_variant,,ENST00000487342,; A ENST00000382932 Transcript missense_variant 849/2313 781/1908 261/635 A/S Gcc/Tcc 1 -1 SLC7A4 HGNC HGNC:11062 protein_coding YES CCDS33608.1 ENSP00000372390 O43246 UPI0000169EC7 NM_004173.2 deleterious(0) 2/5 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF410,Pfam_domain:PF13520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 21031032 21031032 C A 1 0 0 0 0 1 0 0 0 14982 739 26 2 2 SLC7A4 22 21031032 Missense_Mutation SNP C C3N-00217_T 1264200 21031032 29787436 571 12341 BCR 0 . GRCh38 22 23310407 23310407 + Silent SNP C C T novel C3N-00217_T C3N-00217_N C C c.3156C>T p.= p.F1052F ENST00000305877 18/23 103 97 6 133 133 0 varscan-mutect BCR,synonymous_variant,p.=,ENST00000305877,NM_004327.3;BCR,synonymous_variant,p.=,ENST00000359540,NM_021574.2;BCR,3_prime_UTR_variant,,ENST00000398512,;BCR,non_coding_transcript_exon_variant,,ENST00000436990,;BCR,non_coding_transcript_exon_variant,,ENST00000419722,;BCR,non_coding_transcript_exon_variant,,ENST00000475025,;BCR,non_coding_transcript_exon_variant,,ENST00000478978,;BCR,upstream_gene_variant,,ENST00000458056,; T ENST00000305877 Transcript synonymous_variant 3907/7082 3156/3816 1052/1271 F ttC/ttT 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 18/23 hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3,Gene3D:1.10.555.10,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.42979 1 1 1 1 0 T 2 4 43 23310407 23310407 C T 1 0 0 0 0 0 0 0 1 1535 883 31 1 1 BCR 22 23310407 Silent SNP C C3N-00217_T 2279375 23310407 27508061 572 12342 CABIN1 0 . GRCh38 22 24043051 24043051 + Missense_Mutation SNP A A C novel C3N-00217_T C3N-00217_N A A c.493A>C p.Ile165Leu p.I165L ENST00000398319 6/37 173 127 46 222 222 0 strelka-varscan-mutect CABIN1,missense_variant,p.Ile165Leu,ENST00000398319,NM_001199281.1;CABIN1,missense_variant,p.Ile165Leu,ENST00000263119,NM_012295.3;CABIN1,missense_variant,p.Ile165Leu,ENST00000617531,NM_001201429.1;CABIN1,missense_variant,p.Ile165Leu,ENST00000405822,;CABIN1,missense_variant,p.Ile120Leu,ENST00000445422,;CABIN1,missense_variant,p.Ile120Leu,ENST00000454754,; C ENST00000398319 Transcript missense_variant 878/7480 493/6663 165/2220 I/L Atc/Ctc 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 deleterious(0.03) 6/37 Gene3D:1.25.40.10,hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 24043051 24043051 A C 1 0 0 0 0 1 0 0 0 2214 101 4 5 5 CABIN1 22 24043051 Missense_Mutation SNP A C3N-00217_T 732644 24043051 26775417 573 12343 MYO18B 0 . GRCh38 22 25768248 25768248 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.332G>T p.Gly111Val p.G111V ENST00000335473 4/44 141 111 30 183 183 0 strelka-varscan-mutect MYO18B,missense_variant,p.Gly111Val,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Gly111Val,ENST00000407587,;MYO18B,missense_variant,p.Gly111Val,ENST00000536101,;MYO18B,missense_variant,p.Gly111Val,ENST00000539302,;MYO18B,upstream_gene_variant,,ENST00000418374,; T ENST00000335473 Transcript missense_variant 582/8565 332/7704 111/2567 G/V gGg/gTg 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated_low_confidence(0.07) 4/44 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 25768248 25768248 G T 1 0 0 0 0 1 0 0 0 10067 1232 43 2 2 MYO18B 22 25768248 Missense_Mutation SNP G C3N-00217_T 1725197 25768248 25050220 574 12344 MYO18B 0 . GRCh38 22 25768918 25768918 + Silent SNP G G A C3N-00217_T C3N-00217_N G G c.1002G>A p.= p.K334K ENST00000335473 4/44 233 185 48 274 274 0 strelka-varscan-mutect MYO18B,synonymous_variant,p.=,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,synonymous_variant,p.=,ENST00000407587,;MYO18B,synonymous_variant,p.=,ENST00000536101,;MYO18B,synonymous_variant,p.=,ENST00000539302,;MYO18B,upstream_gene_variant,,ENST00000418374,; A ENST00000335473 Transcript synonymous_variant 1252/8565 1002/7704 334/2567 K aaG/aaA COSM4839896 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 4/44 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 25768918 25768918 G A 1 0 0 0 0 0 0 0 1 10067 933 33 3 3 MYO18B 22 25768918 Silent SNP G C3N-00217_T 670 25768918 25049550 575 12345 PES1 0 . GRCh38 22 30584640 30584640 + Missense_Mutation SNP C C A rs768262111 C3N-00217_T C3N-00217_N C C c.446G>T p.Arg149Leu p.R149L ENST00000354694 5/15 204 173 31 277 276 1 strelka-varscan-mutect PES1,missense_variant,p.Arg10Leu,ENST00000402281,NM_001282327.1;PES1,missense_variant,p.Arg10Leu,ENST00000405677,NM_001282328.1;PES1,missense_variant,p.Arg149Leu,ENST00000354694,NM_014303.3;PES1,missense_variant,p.Arg149Leu,ENST00000402284,;PES1,missense_variant,p.Arg149Leu,ENST00000335214,NM_001243225.1;PES1,missense_variant,p.Arg10Leu,ENST00000406208,;PES1,upstream_gene_variant,,ENST00000441668,;PES1,downstream_gene_variant,,ENST00000433575,;PES1,non_coding_transcript_exon_variant,,ENST00000477762,;PES1,upstream_gene_variant,,ENST00000488719,;PES1,downstream_gene_variant,,ENST00000466614,; A ENST00000354694 Transcript missense_variant 553/2295 446/1767 149/588 R/L cGg/cTg rs768262111,COSM3731286 1 -1 PES1 HGNC HGNC:8848 protein_coding YES CCDS13880.1 ENSP00000346725 O00541 B2RDF2 UPI0000001618 NM_014303.3 deleterious(0.02) 5/15 HAMAP:MF_03028,hmmpanther:PTHR12221,Pfam_domain:PF06732 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768262111 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 30584640 30584640 C A 1 0 0 0 0 1 0 0 0 11822 652 23 1 1 PES1 22 30584640 Missense_Mutation SNP C C3N-00217_T 4815722 30584640 20233828 576 12346 CACNA1I 0 . GRCh38 22 39658978 39658978 + Missense_Mutation SNP G G A C3N-00217_T C3N-00217_N G G c.2192G>A p.Arg731Gln p.R731Q ENST00000402142 12/37 189 150 39 212 211 1 strelka-varscan-mutect CACNA1I,missense_variant,p.Arg731Gln,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Arg696Gln,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Arg731Gln,ENST00000401624,;CACNA1I,missense_variant,p.Arg696Gln,ENST00000407673,; A ENST00000402142 Transcript missense_variant 2192/10004 2192/6672 731/2223 R/Q cGg/cAg COSM1416358,COSM1416359,COSM5088223,COSM5088224 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0) 12/37 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs1400949374 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 39658978 39658978 G A 1 0 0 0 0 1 0 0 0 2234 1116 39 1 1 CACNA1I 22 39658978 Missense_Mutation SNP G C3N-00217_T 9074338 39658978 11159490 577 12347 ENTHD1 0 . GRCh38 22 39744059 39744059 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.1444G>A p.Val482Ile p.V482I ENST00000325157 7/7 170 126 44 200 200 0 strelka-varscan-mutect ENTHD1,missense_variant,p.Val482Ile,ENST00000325157,NM_152512.3; T ENST00000325157 Transcript missense_variant 1695/2710 1444/1824 482/607 V/I Gta/Ata COSM1637966 1 -1 ENTHD1 HGNC HGNC:26352 protein_coding YES CCDS13998.1 ENSP00000317431 Q8IYW4 UPI00000741D2 NM_152512.3 deleterious(0) 7/7 hmmpanther:PTHR12276:SF57,hmmpanther:PTHR12276 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 39744059 39744059 C T 1 0 0 0 0 1 0 0 0 4982 478 17 3 3 ENTHD1 22 39744059 Missense_Mutation SNP C C3N-00217_T 85081 39744059 11074409 578 12348 PACSIN2 0 . GRCh38 22 42893462 42893462 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.212A>G p.Glu71Gly p.E71G ENST00000263246 3/11 240 184 56 263 263 0 strelka-varscan-mutect PACSIN2,missense_variant,p.Glu71Gly,ENST00000263246,NM_001184970.1;PACSIN2,missense_variant,p.Glu71Gly,ENST00000337959,;PACSIN2,missense_variant,p.Glu71Gly,ENST00000407585,NM_001184971.1;PACSIN2,missense_variant,p.Glu71Gly,ENST00000403744,NM_007229.3;PACSIN2,missense_variant,p.Glu71Gly,ENST00000402229,;PACSIN2,missense_variant,p.Glu71Gly,ENST00000634914,;PACSIN2,missense_variant,p.Glu71Gly,ENST00000453643,;PACSIN2,missense_variant,p.Glu71Gly,ENST00000422336,;PACSIN2,missense_variant,p.Glu71Gly,ENST00000418133,;PACSIN2,downstream_gene_variant,,ENST00000453079,;PACSIN2,non_coding_transcript_exon_variant,,ENST00000445706,; C ENST00000263246 Transcript missense_variant 414/3249 212/1461 71/486 E/G gAg/gGg 1 -1 PACSIN2 HGNC HGNC:8571 protein_coding YES CCDS43023.1 ENSP00000263246 Q9UNF0 UPI00001311CA NM_001184970.1 deleterious(0) 3/11 Pfam_domain:PF00611,PROSITE_profiles:PS51741,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF14,SMART_domains:SM00055,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 42893462 42893462 T C 1 0 0 0 0 1 0 0 0 11453 1565 54 5 5 PACSIN2 22 42893462 Missense_Mutation SNP T C3N-00217_T 3149403 42893462 7925006 579 12349 PLXNB2 0 . GRCh38 22 50290398 50290398 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.187C>A p.Leu63Met p.L63M ENST00000449103 3/37 135 124 11 141 140 1 strelka-varscan-mutect PLXNB2,missense_variant,p.Leu63Met,ENST00000449103,;PLXNB2,missense_variant,p.Leu63Met,ENST00000359337,NM_012401.3;PLXNB2,missense_variant,p.Leu63Met,ENST00000432455,;PLXNB2,missense_variant,p.Leu63Met,ENST00000425954,;PLXNB2,upstream_gene_variant,,ENST00000411680,;PLXNB2,upstream_gene_variant,,ENST00000434732,;PLXNB2,upstream_gene_variant,,ENST00000496720,; T ENST00000449103 Transcript missense_variant 328/6383 187/5517 63/1838 L/M Ctg/Atg 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D tolerated(0.11) 3/37 PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 50290398 50290398 G T 1 0 0 0 0 1 0 0 0 12230 962 34 2 2 PLXNB2 22 50290398 Missense_Mutation SNP G C3N-00217_T 7396936 50290398 528070 580 12350 SBF1 0 . GRCh38 22 50465219 50465219 + Missense_Mutation SNP T T C novel C3N-00217_T C3N-00217_N T T c.1199A>G p.His400Arg p.H400R ENST00000380817 11/41 89 74 15 99 99 0 strelka-varscan-mutect SBF1,missense_variant,p.His400Arg,ENST00000380817,NM_002972.3;SBF1,missense_variant,p.His401Arg,ENST00000348911,;SBF1,downstream_gene_variant,,ENST00000477234,;SBF1,downstream_gene_variant,,ENST00000399627,; C ENST00000380817 Transcript missense_variant 1383/8008 1199/5682 400/1893 H/R cAt/cGt 1 -1 SBF1 HGNC HGNC:10542 protein_coding YES CCDS14091.2 ENSP00000370196 O95248 A0A024R4Z9 UPI00001D69ED NM_002972.3 deleterious(0) 11/41 PROSITE_profiles:PS50947,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF43,SMART_domains:SM00801 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 50465219 50465219 T C 1 0 0 0 0 1 0 0 0 14122 1478 51 5 5 SBF1 22 50465219 Missense_Mutation SNP T C3N-00217_T 174821 50465219 353249 581 12351 CSF2RA 0 . GRCh38 X 1282770 1282770 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.67G>A p.Glu23Lys p.E23K ENST00000417535 3/14 385 327 58 439 439 0 strelka-varscan-mutect CSF2RA,missense_variant,p.Glu23Lys,ENST00000381524,;CSF2RA,missense_variant,p.Glu23Lys,ENST00000417535,NM_001161530.1;CSF2RA,missense_variant,p.Glu23Lys,ENST00000432318,NM_001161529.1;CSF2RA,missense_variant,p.Glu23Lys,ENST00000381529,NM_006140.4,NM_172245.2;CSF2RA,missense_variant,p.Glu23Lys,ENST00000355432,NM_172246.2;CSF2RA,missense_variant,p.Glu23Lys,ENST00000381509,NM_001161531.1;CSF2RA,missense_variant,p.Glu23Lys,ENST00000355805,NM_172249.2;CSF2RA,missense_variant,p.Glu23Lys,ENST00000381500,NM_172247.2;CSF2RA,missense_variant,p.Glu23Lys,ENST00000412290,;CSF2RA,missense_variant,p.Glu23Lys,ENST00000494969,;CSF2RA,5_prime_UTR_variant,,ENST00000501036,NM_001161532.1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312,;CSF2RA,downstream_gene_variant,,ENST00000481245,;CSF2RA,upstream_gene_variant,,ENST00000477940,;CSF2RA,missense_variant,p.Glu23Lys,ENST00000486791,; A ENST00000417535 Transcript missense_variant 261/1955 67/1305 23/434 E/K Gag/Aag 1 1 CSF2RA HGNC HGNC:2435 protein_coding YES CCDS55359.1 ENSP00000394227 P15509 UPI000159C3E4 NM_001161530.1 tolerated(0.1) 3/14 hmmpanther:PTHR23036:SF94,hmmpanther:PTHR23036 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 1282770 1282770 G A 1 0 0 0 0 1 0 0 0 3735 943 33 3 3 CSF2RA 23 1282770 Missense_Mutation SNP G C3N-00217_T 1282770 154758125 582 12352 XG 0 . GRCh38 X 2782102 2782102 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.164A>T p.Gln55Leu p.Q55L ENST00000419513 4/11 313 264 49 322 322 0 strelka-varscan-mutect XG,missense_variant,p.Gln55Leu,ENST00000381174,NM_001141920.1,NM_175569.2;XG,missense_variant,p.Gln55Leu,ENST00000419513,NM_001141919.1;XG,missense_variant,p.Gln33Leu,ENST00000509484,; T ENST00000419513 Transcript missense_variant 387/979 164/588 55/195 Q/L cAg/cTg 1 1 XG HGNC HGNC:12806 protein_coding YES CCDS48073.1 ENSP00000411004 P55808 UPI0000D61D1F NM_001141919.1 deleterious(0.02) 4/11 Pfam_domain:PF12301,hmmpanther:PTHR15076,hmmpanther:PTHR15076:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 2782102 2782102 A T 1 0 0 0 0 1 0 0 0 17986 188 7 4 4 XG 23 2782102 Missense_Mutation SNP A C3N-00217_T 1499332 2782102 153258793 583 12353 ARSH 0 . GRCh38 X 3029364 3029364 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.1317G>A p.= p.K439K ENST00000381130 8/9 70 60 10 92 92 0 strelka-varscan-mutect ARSH,synonymous_variant,p.=,ENST00000381130,NM_001011719.1; A ENST00000381130 Transcript synonymous_variant 1317/1875 1317/1689 439/562 K aaG/aaA 1 1 ARSH HGNC HGNC:32488 protein_coding YES CCDS35198.1 ENSP00000370522 Q5FYA8 UPI00001D7C2E NM_001011719.1 8/9 Gene3D:3.30.1120.10,Pfam_domain:PF14707,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF240,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.9975 1 1 1 1 0 A 2 1 43 3029364 3029364 G A 1 0 0 0 0 0 0 0 1 1136 1014 35 3 3 ARSH 23 3029364 Silent SNP G C3N-00217_T 247262 3029364 153011531 584 12354 MXRA5 0 . GRCh38 X 3324598 3324598 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.1087T>A p.Leu363Met p.L363M ENST00000217939 5/7 117 95 22 127 127 0 strelka-varscan-mutect MXRA5,missense_variant,p.Leu363Met,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 1242/9793 1087/8487 363/2828 L/M Ttg/Atg 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0.03) 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 3324598 3324598 A T 1 0 0 0 0 1 0 0 0 10002 69 3 4 4 MXRA5 23 3324598 Missense_Mutation SNP A C3N-00217_T 295234 3324598 152716297 585 12355 PRKX 0 . GRCh38 X 3713136 3713136 + Nonsense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.118G>T p.Glu40Ter p.E40* ENST00000262848 1/9 187 164 23 150 150 0 strelka-varscan-mutect PRKX,stop_gained,p.Glu40Ter,ENST00000262848,NM_005044.4;RP11-558O12.1,upstream_gene_variant,,ENST00000329806,; A ENST00000262848 Transcript stop_gained 473/6031 118/1077 40/358 E/* Gag/Tag 1 -1 PRKX HGNC HGNC:9441 protein_coding YES CCDS14125.1 ENSP00000262848 P51817 A0A024RBU5 UPI000000D998 NM_005044.4 1/9 hmmpanther:PTHR24353,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS rs1169697418 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 3713136 3713136 C A 1 0 0 0 0 0 1 0 0 12659 864 30 2 2 PRKX 23 3713136 Nonsense_Mutation SNP C C3N-00217_T 388538 3713136 152327759 586 12356 MSL3 0 . GRCh38 X 11765720 11765720 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1162C>A p.Leu388Met p.L388M ENST00000312196 9/13 88 74 14 73 73 0 strelka-mutect MSL3,missense_variant,p.Leu388Met,ENST00000337339,NM_078628.1;MSL3,missense_variant,p.Leu222Met,ENST00000380693,NM_006800.3;MSL3,missense_variant,p.Leu388Met,ENST00000312196,NM_078629.3;MSL3,missense_variant,p.Leu376Met,ENST00000398527,NM_001193270.2;MSL3,missense_variant,p.Leu239Met,ENST00000361672,NM_001282174.1;MSL3,downstream_gene_variant,,ENST00000380692,;MSL3,downstream_gene_variant,,ENST00000421368,;MSL3,downstream_gene_variant,,ENST00000476743,;MSL3,non_coding_transcript_exon_variant,,ENST00000467141,;MSL3,downstream_gene_variant,,ENST00000483645,;MSL3,downstream_gene_variant,,ENST00000473806,;MSL3,3_prime_UTR_variant,,ENST00000468149,;MSL3,3_prime_UTR_variant,,ENST00000380691,;MSL3,downstream_gene_variant,,ENST00000494268,;MSL3,downstream_gene_variant,,ENST00000482871,;MSL3,downstream_gene_variant,,ENST00000478462,;MSL3,upstream_gene_variant,,ENST00000473380,; A ENST00000312196 Transcript missense_variant 1267/2345 1162/1566 388/521 L/M Ctg/Atg 1 1 MSL3 HGNC HGNC:7370 protein_coding YES CCDS14147.1 ENSP00000312244 Q8N5Y2 UPI000006E6B7 NM_078629.3 deleterious(0.01) 9/13 PROSITE_profiles:PS51640,Pfam_domain:PF05712 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 11765720 11765720 C A 1 0 0 0 0 1 0 0 0 9862 680 24 2 2 MSL3 23 11765720 Missense_Mutation SNP C C3N-00217_T 8052584 11765720 144275175 587 12357 MAGEB17 0 . GRCh38 X 16171314 16171314 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.932A>T p.Glu311Val p.E311V ENST00000400004 2/2 42 21 21 45 45 0 strelka-varscan-mutect MAGEB17,missense_variant,p.Glu311Val,ENST00000400004,NM_001277307.1;MAGEB17,missense_variant,p.Glu311Val,ENST00000400003,;RP11-431J24.2,upstream_gene_variant,,ENST00000435789,; T ENST00000400004 Transcript missense_variant 1284/1434 932/1011 311/336 E/V gAg/gTg 1 1 MAGEB17 HGNC HGNC:17418 protein_coding YES CCDS59524.1 ENSP00000382884 A8MXT2 UPI00001602F1 NM_001277307.1 deleterious(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF67 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 16171314 16171314 A T 1 0 0 0 0 1 0 0 0 9090 304 11 4 4 MAGEB17 23 16171314 Missense_Mutation SNP A C3N-00217_T 4405594 16171314 139869581 588 12358 PHKA2 0 . GRCh38 X 18900689 18900689 + Missense_Mutation SNP C C A rs753106449 C3N-00217_T C3N-00217_N C C c.3038G>T p.Arg1013Leu p.R1013L ENST00000379942 28/33 330 282 48 406 405 1 strelka-varscan-mutect PHKA2,missense_variant,p.Arg1013Leu,ENST00000379942,NM_000292.2;PHKA2,non_coding_transcript_exon_variant,,ENST00000473739,;PHKA2,non_coding_transcript_exon_variant,,ENST00000486231,;PHKA2,intron_variant,,ENST00000469645,;PHKA2,upstream_gene_variant,,ENST00000481718,;PHKA2,upstream_gene_variant,,ENST00000469485,; A ENST00000379942 Transcript missense_variant 3704/5559 3038/3708 1013/1235 R/L cGg/cTg rs753106449 1 -1 PHKA2 HGNC HGNC:8926 protein_coding YES CCDS14190.1 ENSP00000369274 P46019 UPI000012DF4B NM_000292.2 tolerated(0.1) 28/33 hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF5 MODERATE 1 SNV 1 1 PASS rs753106449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 18900689 18900689 C A 1 0 0 0 0 1 0 0 0 11932 652 23 1 1 PHKA2 23 18900689 Missense_Mutation SNP C C3N-00217_T 2729375 18900689 137140206 589 12359 PRDX4 0 . GRCh38 X 23675142 23675142 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.512G>A p.Arg171Lys p.R171K ENST00000379331 3/3 115 103 12 179 179 0 strelka-varscan-mutect PRDX4,missense_variant,p.Arg171Lys,ENST00000379331,;PRDX4,intron_variant,,ENST00000379341,NM_006406.1;PRDX4,intron_variant,,ENST00000379349,;PRDX4,intron_variant,,ENST00000439422,;PRDX4,intron_variant,,ENST00000495599,; A ENST00000379331 Transcript missense_variant 532/852 512/561 171/186 R/K aGa/aAa 1 1 PRDX4 HGNC HGNC:17169 protein_coding ENSP00000368635 A6NG45 UPI00002124AE deleterious_low_confidence(0) 3/3 PROSITE_profiles:PS51352 MODERATE SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -19.99997 1 1 1 1 0 A 3 1 43 23675142 23675142 G A 1 0 0 0 0 1 0 0 0 12599 942 33 3 3 PRDX4 23 23675142 Missense_Mutation SNP G C3N-00217_T 4774453 23675142 132365753 590 12360 PDK3 0 . GRCh38 X 24533977 24533977 + Missense_Mutation SNP G G T rs781166988 C3N-00217_T C3N-00217_N G G c.1126G>T p.Ala376Ser p.A376S ENST00000441463 11/12 104 83 21 132 132 0 strelka-varscan-mutect PDK3,missense_variant,p.Ala376Ser,ENST00000441463,NM_001142386.2;PDK3,missense_variant,p.Ala376Ser,ENST00000379162,NM_005391.4; T ENST00000441463 Transcript missense_variant 1126/1921 1126/1248 376/415 A/S Gca/Tca rs781166988 1 1 PDK3 HGNC HGNC:8811 protein_coding YES CCDS48088.1 ENSP00000387536 Q15120 UPI00002124D4 NM_001142386.2 tolerated(0.48) 11/12 hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF21 MODERATE 1 SNV 2 1 PASS rs781166988 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 24533977 24533977 G T 1 0 0 0 0 1 0 0 0 11765 1087 38 1 1 PDK3 23 24533977 Missense_Mutation SNP G C3N-00217_T 858835 24533977 131506918 591 12361 MAGEB10 0 . GRCh38 X 27821480 27821480 + Silent SNP C C T rs772388385 C3N-00217_T C3N-00217_N C C c.174C>T p.= p.S58S ENST00000356790 3/3 160 140 20 189 189 0 strelka-mutect MAGEB10,synonymous_variant,p.=,ENST00000356790,NM_182506.3;MAGEB10,synonymous_variant,p.=,ENST00000614159,; T ENST00000356790 Transcript synonymous_variant 419/1953 174/1044 58/347 S tcC/tcT rs772388385 1 1 MAGEB10 HGNC HGNC:25377 protein_coding YES CCDS35221.1 ENSP00000368304 Q96LZ2 UPI000013F050 NM_182506.3 3/3 Pfam_domain:PF12440,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF36,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS rs772388385 . 0 204 3 3 0 0 0 0 -20 0.999883 1 1 1 0 T 2 4 43 27821480 27821480 C T 1 0 0 0 0 0 0 0 1 9088 581 21 3 3 MAGEB10 23 27821480 Silent SNP C C3N-00217_T 3287503 27821480 128219415 592 12362 49 2 MAGEB10 0 . GRCh38 X 27821488 27821488 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.182C>A p.Pro61His p.P61H ENST00000356790 3/3 167 142 25 190 190 0 strelka-mutect MAGEB10,missense_variant,p.Pro61His,ENST00000356790,NM_182506.3;MAGEB10,missense_variant,p.Pro61His,ENST00000614159,; A ENST00000356790 Transcript missense_variant 427/1953 182/1044 61/347 P/H cCc/cAc 1 1 MAGEB10 HGNC HGNC:25377 protein_coding YES CCDS35221.1 ENSP00000368304 Q96LZ2 UPI000013F050 NM_182506.3 tolerated(0.05) 3/3 Pfam_domain:PF12440,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF36,SMART_domains:SM01392 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 27821488 27821488 C A 1 0 0 0 0 1 0 0 0 9088 623 22 2 2 MAGEB10 23 27821488 Missense_Mutation SNP C C3N-00217_T 8 27821488 128219407 593 12363 49 2 MAGEB10 0 . GRCh38 X 27822224 27822224 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.918G>T p.Trp306Cys p.W306C ENST00000356790 3/3 205 152 53 309 309 0 strelka-varscan-mutect MAGEB10,missense_variant,p.Trp306Cys,ENST00000356790,NM_182506.3;MAGEB10,missense_variant,p.Trp306Cys,ENST00000614159,; T ENST00000356790 Transcript missense_variant 1163/1953 918/1044 306/347 W/C tgG/tgT 1 1 MAGEB10 HGNC HGNC:25377 protein_coding YES CCDS35221.1 ENSP00000368304 Q96LZ2 UPI000013F050 NM_182506.3 tolerated(0.16) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF36 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 27822224 27822224 G T 1 0 0 0 0 1 0 0 0 9088 1270 44 2 2 MAGEB10 23 27822224 Missense_Mutation SNP G C3N-00217_T 736 27822224 128218671 594 12364 DCAF8L1 0 . GRCh38 X 27981317 27981317 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.18C>A p.= p.G6G ENST00000441525 1/1 76 59 17 69 69 0 strelka-varscan-mutect DCAF8L1,synonymous_variant,p.=,ENST00000441525,NM_001017930.1; T ENST00000441525 Transcript synonymous_variant 133/3457 18/1803 6/600 G ggC/ggA 1 -1 DCAF8L1 HGNC HGNC:31810 protein_coding YES CCDS35222.1 ENSP00000405222 A6NGE4 UPI000022DD1B NM_001017930.1 1/1 LOW 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 27981317 27981317 G T 1 0 0 0 0 0 0 0 1 4078 1306 46 2 2 DCAF8L1 23 27981317 Silent SNP G C3N-00217_T 159093 27981317 128059578 595 12365 MAGEB3 0 . GRCh38 X 30236885 30236885 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.961G>T p.Ala321Ser p.A321S ENST00000361644 5/5 146 83 63 163 163 0 strelka-varscan-mutect MAGEB3,missense_variant,p.Ala321Ser,ENST00000361644,NM_002365.4;MAGEB3,missense_variant,p.Ala321Ser,ENST00000620842,; T ENST00000361644 Transcript missense_variant 1698/2305 961/1041 321/346 A/S Gca/Tca 1 1 MAGEB3 HGNC HGNC:6810 protein_coding YES CCDS14220.1 ENSP00000355198 O15480 UPI000013E79F NM_002365.4 tolerated(0.44) 5/5 hmmpanther:PTHR11736:SF53,hmmpanther:PTHR11736 MODERATE 1 SNV 2 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999949 1 1 1 0 T 3 4 43 30236885 30236885 G T 1 0 0 0 0 1 0 0 0 9093 1319 46 2 2 MAGEB3 23 30236885 Missense_Mutation SNP G C3N-00217_T 2255568 30236885 125804010 596 12366 SYTL5 0 . GRCh38 X 38072064 38072064 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.347C>G p.Thr116Ser p.T116S ENST00000456733 3/17 101 82 19 148 148 0 strelka-varscan-mutect SYTL5,missense_variant,p.Thr116Ser,ENST00000297875,NM_138780.2,NM_001163335.1;SYTL5,missense_variant,p.Thr116Ser,ENST00000456733,NM_001163334.1;RP5-972B16.2,intron_variant,,ENST00000465127,; G ENST00000456733 Transcript missense_variant 703/4704 347/2259 116/752 T/S aCt/aGt 1 1 SYTL5 HGNC HGNC:15589 protein_coding YES CCDS55399.1 ENSP00000395220 Q8TDW5 UPI0000F0599F NM_001163334.1 tolerated(0.08) 3/17 Gene3D:3.30.40.10,Pfam_domain:PF02318,PROSITE_profiles:PS50916,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF13,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 203 4 3 0 0 0 0 -20 0.9999004 1 1 1 0 G 3 3 43 38072064 38072064 C G 1 0 0 0 0 1 0 0 0 15880 565 20 4 4 SYTL5 23 38072064 Missense_Mutation SNP C C3N-00217_T 7835179 38072064 117968831 597 12367 BCOR 0 . GRCh38 X 40073223 40073223 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.2123C>A p.Thr708Asn p.T708N ENST00000378444 4/15 140 116 24 175 174 1 strelka-varscan-mutect BCOR,missense_variant,p.Thr708Asn,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Thr708Asn,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Thr708Asn,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Thr708Asn,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Thr708Asn,ENST00000406200,;BCOR,missense_variant,p.Thr115Asn,ENST00000615339,;BCOR,downstream_gene_variant,,ENST00000412952,;BCOR,non_coding_transcript_exon_variant,,ENST00000490976,; T ENST00000378444 Transcript missense_variant 2352/6358 2123/5268 708/1755 T/N aCc/aAc 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 deleterious(0.04) 4/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117 MODERATE 1 SNV 1 1 PASS rs1353823807 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 40073223 40073223 G T 1 0 0 0 0 1 0 0 0 1533 1261 44 2 2 BCOR 23 40073223 Missense_Mutation SNP G C3N-00217_T 2001159 40073223 115967672 598 12368 SSX5 0 . GRCh38 X 48190166 48190166 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.556C>A p.Leu186Ile p.L186I ENST00000311798 7/9 160 130 30 200 200 0 strelka-varscan-mutect SSX5,missense_variant,p.Leu186Ile,ENST00000311798,NM_021015.3;SSX5,missense_variant,p.Leu145Ile,ENST00000347757,NM_175723.1;SSX5,missense_variant,p.Leu145Ile,ENST00000376923,;SSX5,missense_variant,p.Leu85Ile,ENST00000403001,; T ENST00000311798 Transcript missense_variant 609/1384 556/690 186/229 L/I Cta/Ata 1 -1 SSX5 HGNC HGNC:11339 protein_coding YES CCDS14288.1 ENSP00000312415 O60225 UPI000013F201 NM_021015.3 tolerated(0.23) 7/9 hmmpanther:PTHR14112:SF9,hmmpanther:PTHR14112 MODERATE 1 SNV 5 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 48190166 48190166 G T 1 0 0 0 0 1 0 0 0 15586 1020 36 2 2 SSX5 23 48190166 Missense_Mutation SNP G C3N-00217_T 8116943 48190166 107850729 599 12369 PIM2 0 . GRCh38 X 48914274 48914274 + Silent SNP G G T rs782498335 C3N-00217_T C3N-00217_N G G c.793C>A p.= p.R265R ENST00000376509 6/6 244 206 38 279 279 0 strelka-varscan-mutect PIM2,synonymous_variant,p.=,ENST00000376509,NM_006875.3;SLC35A2,upstream_gene_variant,,ENST00000376521,NM_001042498.2;SLC35A2,upstream_gene_variant,,ENST00000413561,;SLC35A2,upstream_gene_variant,,ENST00000445167,NM_001032289.2;SLC35A2,upstream_gene_variant,,ENST00000247138,NM_005660.2;SLC35A2,upstream_gene_variant,,ENST00000616181,NM_001282650.1;SLC35A2,upstream_gene_variant,,ENST00000452555,NM_001282651.1;SLC35A2,upstream_gene_variant,,ENST00000635589,NM_001282649.1;SLC35A2,upstream_gene_variant,,ENST00000376515,NM_001282648.1;SLC35A2,upstream_gene_variant,,ENST00000635015,;SLC35A2,upstream_gene_variant,,ENST00000376512,;PIM2,downstream_gene_variant,,ENST00000442430,;SLC35A2,upstream_gene_variant,,ENST00000446885,;SLC35A2,upstream_gene_variant,,ENST00000376529,NM_001282647.1;SLC35A2,upstream_gene_variant,,ENST00000635460,;SLC35A2,upstream_gene_variant,,ENST00000635238,;SLC35A2,upstream_gene_variant,,ENST00000634461,;SLC35A2,upstream_gene_variant,,ENST00000634665,;PIM2,non_coding_transcript_exon_variant,,ENST00000485431,;SLC35A2,upstream_gene_variant,,ENST00000635628,;SLC35A2,upstream_gene_variant,,ENST00000635285,; T ENST00000376509 Transcript synonymous_variant 983/2075 793/936 265/311 R Cgg/Agg rs782498335,COSM1293018 1 -1 PIM2 HGNC HGNC:8987 protein_coding YES CCDS14312.1 ENSP00000365692 Q9P1W9 A0A024QYW7 UPI0000049044 NM_006875.3 6/6 PROSITE_profiles:PS50011,hmmpanther:PTHR22984:SF10,hmmpanther:PTHR22984,PIRSF_domain:PIRSF037993,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 LOW 1 SNV 1 0,1 1 PASS rs782498335 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 43 48914274 48914274 G T 1 0 0 0 0 0 0 0 1 12023 1115 39 1 1 PIM2 23 48914274 Silent SNP G C3N-00217_T 724108 48914274 107126621 600 12370 SYP 0 . GRCh38 X 49191745 49191745 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.634C>A p.Leu212Met p.L212M ENST00000263233 6/7 251 208 43 240 240 0 strelka-varscan-mutect SYP,missense_variant,p.Leu212Met,ENST00000263233,NM_003179.2;SYP,missense_variant,p.Leu212Met,ENST00000479808,;SYP,missense_variant,p.Leu102Met,ENST00000472598,;SYP,3_prime_UTR_variant,,ENST00000376303,;SYP,downstream_gene_variant,,ENST00000469389,;SYP,downstream_gene_variant,,ENST00000466635,; T ENST00000263233 Transcript missense_variant 707/2498 634/942 212/313 L/M Ctg/Atg 1 -1 SYP HGNC HGNC:11506 protein_coding YES CCDS14321.1 ENSP00000263233 P08247 UPI0000117AEC NM_003179.2 deleterious(0.02) 6/7 Pfam_domain:PF01284,Prints_domain:PR00220,PROSITE_profiles:PS51225,hmmpanther:PTHR10306,hmmpanther:PTHR10306:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1278446763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 49191745 49191745 G T 1 0 0 0 0 1 0 0 0 15855 991 35 2 2 SYP 23 49191745 Missense_Mutation SNP G C3N-00217_T 277471 49191745 106849150 601 12371 PPP1R3F 0 . GRCh38 X 49270267 49270267 + Missense_Mutation SNP G G A novel C3N-00217_T C3N-00217_N G G c.398G>A p.Arg133His p.R133H ENST00000055335 1/4 35 30 5 37 37 0 strelka-varscan-mutect PPP1R3F,missense_variant,p.Arg133His,ENST00000055335,NM_033215.4;PPP1R3F,intron_variant,,ENST00000466508,;PPP1R3F,intron_variant,,ENST00000495799,NM_001184745.1;PPP1R3F,upstream_gene_variant,,ENST00000471261,;LL0XNC01-7P3.1,upstream_gene_variant,,ENST00000602455,; A ENST00000055335 Transcript missense_variant 414/3421 398/2400 133/799 R/H cGc/cAc 1 1 PPP1R3F HGNC HGNC:14944 protein_coding YES CCDS35254.1 ENSP00000055335 Q6ZSY5 UPI00001D7BA8 NM_033215.4 deleterious(0.02) 1/4 PROSITE_profiles:PS51159,hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF5 MODERATE 1 SNV 2 1 PASS rs1193283245 . 0 206 3 0 0 0 0 0 -13.56672 1 1 1 1 0 A 3 1 43 49270267 49270267 G A 1 0 0 0 0 1 0 0 0 12496 1087 38 1 1 PPP1R3F 23 49270267 Missense_Mutation SNP G C3N-00217_T 78522 49270267 106770628 602 12372 DGKK 0 . GRCh38 X 50470573 50470573 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.106C>A p.Pro36Thr p.P36T ENST00000611977 1/28 108 95 13 114 114 0 strelka-varscan-mutect DGKK,missense_variant,p.Pro36Thr,ENST00000611977,NM_001013742.3; T ENST00000611977 Transcript missense_variant 166/7407 106/3816 36/1271 P/T Cca/Aca 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 deleterious_low_confidence(0.03) 1/28 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 50470573 50470573 G T 1 0 0 0 0 1 0 0 0 4278 1261 44 2 2 DGKK 23 50470573 Missense_Mutation SNP G C3N-00217_T 1200306 50470573 105570322 603 12373 GPR173 0 . GRCh38 X 53077150 53077150 + Missense_Mutation SNP G G C novel C3N-00217_T C3N-00217_N G G c.529G>C p.Glu177Gln p.E177Q ENST00000332582 2/2 206 117 89 249 249 0 strelka-varscan-mutect GPR173,missense_variant,p.Glu177Gln,ENST00000332582,NM_018969.5;GPR173,downstream_gene_variant,,ENST00000375466,; C ENST00000332582 Transcript missense_variant 1020/4485 529/1122 177/373 E/Q Gag/Cag 1 1 GPR173 HGNC HGNC:18186 protein_coding YES CCDS14349.1 ENSP00000331600 Q9NS66 UPI0000050480 NM_018969.5 tolerated(0.37) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF4,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 53077150 53077150 G C 1 0 0 0 0 1 0 0 0 6555 1291 45 4 4 GPR173 23 53077150 Missense_Mutation SNP G C3N-00217_T 2606577 53077150 102963745 604 12374 HUWE1 0 . GRCh38 X 53591079 53591079 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.4016T>A p.Leu1339Gln p.L1339Q ENST00000342160 33/83 359 303 56 402 402 0 strelka-varscan-mutect HUWE1,missense_variant,p.Leu1339Gln,ENST00000342160,;HUWE1,missense_variant,p.Leu1339Gln,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Leu1330Gln,ENST00000612484,;HUWE1,non_coding_transcript_exon_variant,,ENST00000218328,; T ENST00000342160 Transcript missense_variant 4474/14796 4016/13125 1339/4374 L/Q cTg/cAg 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC deleterious(0) 33/83 Gene3D:1.10.8.10,Pfam_domain:PF00627,PROSITE_profiles:PS50030,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF291,SMART_domains:SM00165,Superfamily_domains:SSF46934 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 53591079 53591079 A T 1 0 0 0 0 1 0 0 0 7357 188 7 4 4 HUWE1 23 53591079 Missense_Mutation SNP A C3N-00217_T 513929 53591079 102449816 605 12375 ITIH6 0 . GRCh38 X 54758224 54758224 + Missense_Mutation SNP C C T rs751222928 C3N-00217_T C3N-00217_N C C c.1850G>A p.Ser617Asn p.S617N ENST00000218436 8/13 411 345 66 399 399 0 strelka-varscan-mutect ITIH6,missense_variant,p.Ser617Asn,ENST00000218436,NM_198510.2; T ENST00000218436 Transcript missense_variant 1880/4968 1850/3942 617/1313 S/N aGt/aAt rs751222928,COSM5616346 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 tolerated(0.36) 8/13 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751222928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 54758224 54758224 C T 1 0 0 0 0 1 0 0 0 7814 565 20 3 3 ITIH6 23 54758224 Missense_Mutation SNP C C3N-00217_T 1167145 54758224 101282671 606 12376 FOXR2 0 . GRCh38 X 55623864 55623864 + Silent SNP C C A rs377704574 C3N-00217_T C3N-00217_N C C c.153C>A p.= p.V51V ENST00000339140 1/1 249 216 33 271 270 1 strelka-varscan-mutect FOXR2,synonymous_variant,p.=,ENST00000339140,NM_198451.3; A ENST00000339140 Transcript synonymous_variant 465/1926 153/936 51/311 V gtC/gtA rs377704574 1 1 FOXR2 HGNC HGNC:30469 protein_coding YES CCDS35308.1 ENSP00000427329 Q6PJQ5 UPI00001603CE NM_198451.3 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF73 LOW 1 SNV 1 PASS rs377704574 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 55623864 55623864 C A 1 0 0 0 0 0 0 0 1 5897 871 31 1 1 FOXR2 23 55623864 Silent SNP C C3N-00217_T 865640 55623864 100417031 607 12377 UBQLN2 0 . GRCh38 X 56564769 56564769 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.896C>A p.Ser299Tyr p.S299Y ENST00000338222 1/1 232 188 44 212 212 0 strelka-varscan-mutect UBQLN2,missense_variant,p.Ser299Tyr,ENST00000338222,NM_013444.3; A ENST00000338222 Transcript missense_variant 1131/4230 896/1875 299/624 S/Y tCc/tAc 1 1 UBQLN2 HGNC HGNC:12509 protein_coding YES CCDS14374.1 ENSP00000345195 Q9UHD9 UPI000004A059 NM_013444.3 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR10677:SF5,hmmpanther:PTHR10677 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 56564769 56564769 C A 1 0 0 0 0 1 0 0 0 17421 855 30 2 2 UBQLN2 23 56564769 Missense_Mutation SNP C C3N-00217_T 940905 56564769 99476126 608 12378 ZXDB 0 . GRCh38 X 57592376 57592376 + Frame_Shift_Del DEL G G - novel C3N-00217_T C3N-00217_N G G c.329delG p.Gly110ValfsTer8 p.G110Vfs*8 ENST00000374888 1/1 158 133 25 162 162 0 sindel-varindel-pindel ZXDB,frameshift_variant,p.Gly110ValfsTer8,ENST00000374888,NM_007157.3; - ENST00000374888 Transcript frameshift_variant 725/5894 328/2412 110/803 G/X Ggt/gt 1 1 ZXDB HGNC HGNC:13199 protein_coding YES CCDS35313.1 ENSP00000364023 P98169 UPI000013C495 NM_007157.3 1/1 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF85 HIGH 1 deletion 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999943 1 1 1 0 - 7 5 43 57592376 57592376 G - 1 0 1 0 1 0 0 0 0 18854 1116 39 0 0 ZXDB 23 57592376 Frame_Shift_Del DEL G C3N-00217_T 1027607 57592376 98448519 609 12379 ZXDA 0 . GRCh38 X 57908852 57908852 + Silent SNP A A G novel C3N-00217_T C3N-00217_N A A c.1569T>C p.= p.A523A ENST00000358697 1/1 143 121 22 135 135 0 strelka-varscan-mutect ZXDA,synonymous_variant,p.=,ENST00000358697,NM_007156.4; G ENST00000358697 Transcript synonymous_variant 1969/4113 1569/2400 523/799 A gcT/gcC 1 -1 ZXDA HGNC HGNC:13198 protein_coding YES CCDS14376.1 ENSP00000351530 P98168 UPI000013C494 NM_007156.4 1/1 PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF85,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 43 57908852 57908852 A G 1 0 0 0 0 0 0 0 1 18853 291 11 5 5 ZXDA 23 57908852 Silent SNP A C3N-00217_T 316476 57908852 98132043 610 12380 HEPH 0 . GRCh38 X 66266555 66266555 + Silent SNP G G A novel C3N-00217_T C3N-00217_N G G c.3522G>A p.= p.L1174L ENST00000519389 21/21 394 342 52 404 404 0 strelka-varscan-mutect HEPH,synonymous_variant,p.=,ENST00000519389,NM_138737.4;HEPH,synonymous_variant,p.=,ENST00000343002,;HEPH,synonymous_variant,p.=,ENST00000441993,NM_001130860.3;HEPH,synonymous_variant,p.=,ENST00000336279,NM_014799.3;HEPH,synonymous_variant,p.=,ENST00000419594,NM_001282141.1; A ENST00000519389 Transcript synonymous_variant 3701/6013 3522/3639 1174/1212 L ctG/ctA 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 21/21 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 66266555 66266555 G A 1 0 0 0 0 0 0 0 1 6938 1306 46 3 3 HEPH 23 66266555 Silent SNP G C3N-00217_T 8357703 66266555 89774340 611 12381 AR 0 . GRCh38 X 67680857 67680857 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1903G>T p.Val635Phe p.V635F ENST00000612010 4/6 45 27 18 81 80 1 strelka-varscan-mutect AR,missense_variant,p.Val635Phe,ENST00000612010,;AR,intron_variant,,ENST00000612452,;AR,intron_variant,,ENST00000396044,;AR,intron_variant,,ENST00000374690,NM_000044.3;AR,intron_variant,,ENST00000504326,;AR,intron_variant,,ENST00000613054,;AR,intron_variant,,ENST00000396043,NM_001011645.2;AR,intron_variant,,ENST00000513847,;AR,3_prime_UTR_variant,,ENST00000514029,; T ENST00000612010 Transcript missense_variant 2230/3896 1903/1929 635/642 V/F Gtc/Ttc 1 1 AR HGNC HGNC:644 protein_coding ENSP00000482407 A0A087WZ66 UPI0004E4CA27 4/6 MODERATE SNV 5 1 PASS rs986094499 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 67680857 67680857 G T 1 0 0 0 0 1 0 0 0 958 1377 48 2 2 AR 23 67680857 Missense_Mutation SNP G C3N-00217_T 1414302 67680857 88360038 612 12382 ERCC6L 0 . GRCh38 X 72208212 72208212 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.555C>A p.= p.T185T ENST00000334463 2/2 202 183 19 258 258 0 strelka-varscan-mutect ERCC6L,synonymous_variant,p.=,ENST00000373657,;ERCC6L,synonymous_variant,p.=,ENST00000334463,NM_017669.2;PIN4,intron_variant,,ENST00000423432,NM_001170747.1;PIN4,intron_variant,,ENST00000496835,;PIN4,intron_variant,,ENST00000439980,; T ENST00000334463 Transcript synonymous_variant 691/4243 555/3753 185/1250 T acC/acA 1 -1 ERCC6L HGNC HGNC:20794 protein_coding YES CCDS35329.1 ENSP00000334675 Q2NKX8 UPI000021233E NM_017669.2 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00176,PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF756,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 72208212 72208212 G T 1 0 0 0 0 0 0 0 1 5067 1335 47 2 2 ERCC6L 23 72208212 Silent SNP G C3N-00217_T 4527355 72208212 83832683 613 12383 RLIM 0 . GRCh38 X 74595852 74595852 + Missense_Mutation SNP T T G novel C3N-00217_T C3N-00217_N T T c.126A>C p.Glu42Asp p.E42D ENST00000332687 2/4 86 74 12 120 120 0 strelka-varscan-mutect RLIM,missense_variant,p.Glu42Asp,ENST00000332687,NM_016120.3;RLIM,missense_variant,p.Glu42Asp,ENST00000349225,NM_183353.2; G ENST00000332687 Transcript missense_variant 345/8317 126/1875 42/624 E/D gaA/gaC 1 -1 RLIM HGNC HGNC:13429 protein_coding YES CCDS14427.1 ENSP00000328059 Q9NVW2 UPI000006FD6A NM_016120.3 tolerated(0.13) 2/4 MODERATE 1 SNV 1 1 PASS rs1464627509 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 43 74595852 74595852 T G 1 0 0 0 0 1 0 0 0 13566 1606 56 5 5 RLIM 23 74595852 Missense_Mutation SNP T C3N-00217_T 2387640 74595852 81445043 614 12384 MAGEE1 0 . GRCh38 X 76429285 76429285 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1355G>T p.Gly452Val p.G452V ENST00000361470 1/1 228 190 38 300 298 2 strelka-varscan-mutect MAGEE1,missense_variant,p.Gly452Val,ENST00000361470,NM_020932.2; T ENST00000361470 Transcript missense_variant 1562/3630 1355/2874 452/957 G/V gGt/gTt 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 deleterious(0.02) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 76429285 76429285 G T 1 0 0 0 0 1 0 0 0 9103 1261 44 2 2 MAGEE1 23 76429285 Missense_Mutation SNP G C3N-00217_T 1833433 76429285 79611610 615 12385 PGK1 0 . GRCh38 X 78124967 78124967 + Nonsense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1030G>T p.Glu344Ter p.E344* ENST00000373316 9/11 243 202 41 320 320 0 strelka-varscan-mutect PGK1,stop_gained,p.Glu344Ter,ENST00000373316,NM_000291.3;TAF9B,downstream_gene_variant,,ENST00000341864,NM_015975.4;PGK1,non_coding_transcript_exon_variant,,ENST00000476531,;PGK1,downstream_gene_variant,,ENST00000491291,;PGK1,downstream_gene_variant,,ENST00000474281,; T ENST00000373316 Transcript stop_gained 1197/4887 1030/1254 344/417 E/* Gaa/Taa 1 1 PGK1 HGNC HGNC:8896 protein_coding YES CCDS14438.1 ENSP00000362413 P00558 V9HWF4 UPI00000727EE NM_000291.3 9/11 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,Prints_domain:PR00477,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF12,Superfamily_domains:SSF53748 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 43 78124967 78124967 G T 1 0 0 0 0 0 1 0 0 11879 1291 45 2 2 PGK1 23 78124967 Nonsense_Mutation SNP G C3N-00217_T 1695682 78124967 77915928 616 12386 BRWD3 0 . GRCh38 X 80682609 80682609 + Missense_Mutation SNP C C A C3N-00217_T C3N-00217_N C C c.4253G>T p.Arg1418Leu p.R1418L ENST00000373275 38/41 151 128 23 213 213 0 strelka-varscan-mutect BRWD3,missense_variant,p.Arg1418Leu,ENST00000373275,NM_153252.4;BRWD3,non_coding_transcript_exon_variant,,ENST00000473691,; A ENST00000373275 Transcript missense_variant 4470/11381 4253/5409 1418/1802 R/L cGa/cTa COSM4666262 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 deleterious(0) 38/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370 1 MODERATE 1 SNV 1 1 1 PASS rs1401711800 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 80682609 80682609 C A 1 0 0 0 0 1 0 0 0 1700 884 31 1 1 BRWD3 23 80682609 Missense_Mutation SNP C C3N-00217_T 2557642 80682609 75358286 617 12387 CYLC1 0 . GRCh38 X 83874608 83874608 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1900C>A p.Pro634Thr p.P634T ENST00000329312 4/5 83 76 7 97 97 0 strelka-varscan-mutect CYLC1,missense_variant,p.Pro634Thr,ENST00000329312,NM_021118.2;CYLC1,intron_variant,,ENST00000621735,NM_001271680.1; A ENST00000329312 Transcript missense_variant 1937/2106 1900/1956 634/651 P/T Cca/Aca 1 1 CYLC1 HGNC HGNC:2582 protein_coding YES CCDS35341.1 ENSP00000331556 P35663 UPI0000251E1D NM_021118.2 tolerated(0.07) 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16742,hmmpanther:PTHR16742:SF1 MODERATE 1 SNV 1 1 PASS rs1007098949 . 0 206 4 0 0 0 0 0 -15.11006 1 1 1 1 0 A 3 1 43 83874608 83874608 C A 1 0 0 0 0 1 0 0 0 3944 855 30 2 2 CYLC1 23 83874608 Missense_Mutation SNP C C3N-00217_T 3191999 83874608 72166287 618 12388 POF1B 0 . GRCh38 X 85359614 85359614 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.374C>A p.Thr125Lys p.T125K ENST00000373145 4/16 80 69 11 136 136 0 strelka-varscan-mutect POF1B,missense_variant,p.Thr125Lys,ENST00000262753,NM_024921.3;POF1B,missense_variant,p.Thr125Lys,ENST00000373145,NM_001307940.1; T ENST00000373145 Transcript missense_variant 494/1972 374/1788 125/595 T/K aCa/aAa 1 -1 POF1B HGNC HGNC:13711 protein_coding YES CCDS78497.1 ENSP00000362238 Q8WVV4 UPI00001AE9F1 NM_001307940.1 deleterious_low_confidence(0) 4/16 hmmpanther:PTHR22546 MODERATE 1 SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 85359614 85359614 G T 1 0 0 0 0 1 0 0 0 12291 1377 48 2 2 POF1B 23 85359614 Missense_Mutation SNP G C3N-00217_T 1485006 85359614 70681281 619 12389 CPXCR1 0 . GRCh38 X 88753917 88753917 + Missense_Mutation SNP A A C novel C3N-00217_T C3N-00217_N A A c.503A>C p.Gln168Pro p.Q168P ENST00000276127 3/3 112 73 39 202 202 0 strelka-varscan-mutect CPXCR1,missense_variant,p.Gln168Pro,ENST00000276127,NM_033048.5;CPXCR1,missense_variant,p.Gln168Pro,ENST00000373111,NM_001184771.1;CPXCR1,missense_variant,p.Gln168Pro,ENST00000614120,; C ENST00000276127 Transcript missense_variant 762/1630 503/906 168/301 Q/P cAg/cCg 1 1 CPXCR1 HGNC HGNC:2332 protein_coding YES CCDS14458.1 ENSP00000276127 Q8N123 UPI000007369F NM_033048.5 tolerated(0.1) 3/3 hmmpanther:PTHR42213,hmmpanther:PTHR42213:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 43 88753917 88753917 A C 1 0 0 0 0 1 0 0 0 3634 188 7 5 5 CPXCR1 23 88753917 Missense_Mutation SNP A C3N-00217_T 3394303 88753917 67286978 620 12390 CPXCR1 0 . GRCh38 X 88754030 88754030 + Missense_Mutation SNP C C A rs773920980 C3N-00217_T C3N-00217_N C C c.616C>A p.Arg206Ser p.R206S ENST00000276127 3/3 145 122 23 238 237 1 strelka-varscan-mutect CPXCR1,missense_variant,p.Arg206Ser,ENST00000276127,NM_033048.5;CPXCR1,missense_variant,p.Arg206Ser,ENST00000373111,NM_001184771.1;CPXCR1,missense_variant,p.Arg206Ser,ENST00000614120,; A ENST00000276127 Transcript missense_variant 875/1630 616/906 206/301 R/S Cgt/Agt rs773920980,COSM77517 1 1 CPXCR1 HGNC HGNC:2332 protein_coding YES CCDS14458.1 ENSP00000276127 Q8N123 UPI000007369F NM_033048.5 tolerated(0.4) 3/3 hmmpanther:PTHR42213,hmmpanther:PTHR42213:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773920980 . 0 204 4 2 0 0 0 0 -20 0.9999848 1 1 1 0 A 3 1 43 88754030 88754030 C A 1 0 0 0 0 1 0 0 0 3634 652 23 1 1 CPXCR1 23 88754030 Missense_Mutation SNP C C3N-00217_T 113 88754030 67286865 621 12391 SYTL4 0 . GRCh38 X 100700974 100700974 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.462G>T p.Gln154His p.Q154H ENST00000372989 7/19 204 150 54 203 203 0 strelka-varscan-mutect SYTL4,missense_variant,p.Gln154His,ENST00000372981,;SYTL4,missense_variant,p.Gln154His,ENST00000372989,NM_080737.2;SYTL4,missense_variant,p.Gln154His,ENST00000276141,NM_001174068.1;SYTL4,missense_variant,p.Gln154His,ENST00000263033,NM_001129896.2; A ENST00000372989 Transcript missense_variant 794/3885 462/2016 154/671 Q/H caG/caT 1 -1 SYTL4 HGNC HGNC:15588 protein_coding YES CCDS14472.1 ENSP00000362080 Q96C24 A0A024RCF8 UPI00001AE9F2 NM_080737.2 tolerated(0.1) 7/19 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF9 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 100700974 100700974 C A 1 0 0 0 0 1 0 0 0 15879 564 20 2 2 SYTL4 23 100700974 Missense_Mutation SNP C C3N-00217_T 11946944 100700974 55339921 622 12392 HNRNPH2 0 . GRCh38 X 101413230 101413230 + Missense_Mutation SNP G G T C3N-00217_T C3N-00217_N G G c.1242G>T p.Gln414His p.Q414H ENST00000316594 2/2 181 124 57 152 152 0 strelka-varscan-mutect HNRNPH2,missense_variant,p.Gln414His,ENST00000316594,NM_001032393.2,NM_019597.4;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409338,;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409170,NM_001199973.1; T ENST00000316594 Transcript missense_variant 1320/2223 1242/1350 414/449 Q/H caG/caT COSM325505 1 1 HNRNPH2 HGNC HGNC:5042 protein_coding YES CCDS14485.1 ENSP00000361927 P55795 UPI0000134537 NM_001032393.2,NM_019597.4 deleterious(0) 2/2 hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF33,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 T 3 4 43 101413230 101413230 G T 1 0 0 0 0 1 0 0 0 7161 962 34 2 2 HNRNPH2 23 101413230 Missense_Mutation SNP G C3N-00217_T 712256 101413230 54627665 623 12393 ARMCX4 0 . GRCh38 X 101493229 101493229 + Frame_Shift_Del DEL G G - novel C3N-00217_T C3N-00217_N G G c.4642delG p.Asp1548IlefsTer61 p.D1548Ifs*61 ENST00000423738 2/2 207 141 66 200 200 0 sindel-varindel-pindel ARMCX4,frameshift_variant,p.Asp1548IlefsTer61,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; - ENST00000423738 Transcript frameshift_variant 4842/7424 4640/6873 1547/2290 W/X tGg/tg 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 2/2 HIGH 1 deletion 5 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 101493229 101493229 G - 1 0 1 0 1 0 0 0 0 1102 1357 47 0 0 ARMCX4 23 101493229 Frame_Shift_Del DEL G C3N-00217_T 79999 101493229 54547666 624 12394 GPRASP2 0 . GRCh38 X 102715659 102715659 + Missense_Mutation SNP A A T novel C3N-00217_T C3N-00217_N A A c.790A>T p.Thr264Ser p.T264S ENST00000543253 5/5 190 130 60 185 185 0 strelka-varscan-mutect GPRASP2,missense_variant,p.Thr264Ser,ENST00000543253,NM_001004051.3,NM_001184876.2,NM_001184874.2;GPRASP2,missense_variant,p.Thr264Ser,ENST00000535209,NM_001184875.2;GPRASP2,missense_variant,p.Thr264Ser,ENST00000332262,NM_001199818.1,NM_138437.5;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000486740,;GPRASP2,downstream_gene_variant,,ENST00000486814,;GPRASP2,downstream_gene_variant,,ENST00000483720,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602366,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602463,; T ENST00000543253 Transcript missense_variant 1862/3935 790/2517 264/838 T/S Act/Tct 1 1 GPRASP2 HGNC HGNC:25169 protein_coding YES CCDS14501.1 ENSP00000437872 Q96D09 UPI000006F01A NM_001004051.3,NM_001184876.2,NM_001184874.2 tolerated(0.44) 5/5 hmmpanther:PTHR15712:SF10,hmmpanther:PTHR15712 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 102715659 102715659 A T 1 0 0 0 0 1 0 0 0 6602 275 10 4 4 GPRASP2 23 102715659 Missense_Mutation SNP A C3N-00217_T 1222430 102715659 53325236 625 12395 GPRASP2 0 . GRCh38 X 102716615 102716615 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1746G>T p.Trp582Cys p.W582C ENST00000543253 5/5 173 118 55 173 173 0 strelka-varscan-mutect GPRASP2,missense_variant,p.Trp582Cys,ENST00000543253,NM_001004051.3,NM_001184876.2,NM_001184874.2;GPRASP2,missense_variant,p.Trp582Cys,ENST00000535209,NM_001184875.2;GPRASP2,missense_variant,p.Trp582Cys,ENST00000332262,NM_001199818.1,NM_138437.5;BHLHB9,upstream_gene_variant,,ENST00000457056,NM_001142528.1,NM_001142527.1,NM_001142525.1,NM_001142526.1,NM_001142524.1;BHLHB9,upstream_gene_variant,,ENST00000361229,NM_030639.2;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000486740,;GPRASP2,downstream_gene_variant,,ENST00000486814,;GPRASP2,downstream_gene_variant,,ENST00000483720,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602366,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602463,;BHLHB9,upstream_gene_variant,,ENST00000483294,;BHLHB9,upstream_gene_variant,,ENST00000486988,; T ENST00000543253 Transcript missense_variant 2818/3935 1746/2517 582/838 W/C tgG/tgT 1 1 GPRASP2 HGNC HGNC:25169 protein_coding YES CCDS14501.1 ENSP00000437872 Q96D09 UPI000006F01A NM_001004051.3,NM_001184876.2,NM_001184874.2 tolerated(0.05) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR15712:SF10,hmmpanther:PTHR15712 MODERATE 1 SNV 4 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 102716615 102716615 G T 1 0 0 0 0 1 0 0 0 6602 1270 44 2 2 GPRASP2 23 102716615 Missense_Mutation SNP G C3N-00217_T 956 102716615 53324280 626 12396 IL1RAPL2 0 . GRCh38 X 105755176 105755176 + Splice_Site SNP G G T C3N-00217_T C3N-00217_N G G c.1193-1G>T p.X398_splice ENST00000372582 29 22 7 67 67 0 strelka-varscan-mutect IL1RAPL2,splice_acceptor_variant,,ENST00000372582,NM_017416.1;IL1RAPL2,splice_acceptor_variant,,ENST00000344799,;IL1RAPL2,splice_acceptor_variant,,ENST00000485671,; T ENST00000372582 Transcript splice_acceptor_variant -/2985 1193/2061 398/686 COSM1464600 1 1 IL1RAPL2 HGNC HGNC:5997 protein_coding YES CCDS14517.1 ENSP00000361663 Q9NP60 UPI0000073DF7 NM_017416.1 9/10 1 HIGH 1 SNV 1 1 1 PASS . . 1 202 7 0 0 0 0 0 -18.69612 0.9999998 1 1 1 0 T 5 4 43 105755176 105755176 G T 1 0 0 0 0 0 0 1 0 7565 956 33 2 2 IL1RAPL2 23 105755176 Splice_Site SNP G C3N-00217_T 3038561 105755176 50285719 627 12397 COL4A6 0 . GRCh38 X 108188677 108188677 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1427G>T p.Gly476Val p.G476V ENST00000394872 21/46 47 33 14 42 42 0 strelka-varscan-mutect COL4A6,missense_variant,p.Gly476Val,ENST00000394872,NM_001287758.1;COL4A6,missense_variant,p.Gly476Val,ENST00000334504,NM_033641.3;COL4A6,missense_variant,p.Gly476Val,ENST00000621266,NM_001287759.1;COL4A6,missense_variant,p.Gly477Val,ENST00000372216,NM_001847.3;COL4A6,missense_variant,p.Gly476Val,ENST00000538570,NM_001287760.1;COL4A6,missense_variant,p.Gly476Val,ENST00000545689,; A ENST00000394872 Transcript missense_variant,splice_region_variant 1661/6750 1427/5124 476/1707 G/V gGa/gTa 1 -1 COL4A6 HGNC HGNC:2208 protein_coding YES CCDS76010.1 ENSP00000378340 A8MXH5 UPI000387C996 NM_001287758.1 deleterious(0) 21/46 MODERATE 1 SNV 5 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999954 1 1 1 0 A 3 1 43 108188677 108188677 C A 1 0 0 0 0 1 0 0 0 3484 869 30 2 2 COL4A6 23 108188677 Missense_Mutation SNP C C3N-00217_T 2433501 108188677 47852218 628 12398 COL4A5 0 . GRCh38 X 108621851 108621851 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.2726C>A p.Pro909His p.P909H ENST00000328300 32/53 388 269 119 413 410 3 strelka-varscan-mutect COL4A5,missense_variant,p.Pro909His,ENST00000328300,NM_033380.2;COL4A5,missense_variant,p.Pro909His,ENST00000361603,NM_000495.4;COL4A5,upstream_gene_variant,,ENST00000505728,;COL4A5,non_coding_transcript_exon_variant,,ENST00000483338,; A ENST00000328300 Transcript missense_variant 2970/6483 2726/5076 909/1691 P/H cCt/cAt 1 1 COL4A5 HGNC HGNC:2207 protein_coding YES CCDS35366.1 ENSP00000331902 P29400 UPI000002A538 NM_033380.2 tolerated(0.54) 32/53 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Pfam_domain:PF01391,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 108621851 108621851 C A 1 0 0 0 0 1 0 0 0 3483 681 24 2 2 COL4A5 23 108621851 Missense_Mutation SNP C C3N-00217_T 433174 108621851 47419044 629 12399 TMEM164 0 . GRCh38 X 110173319 110173319 + Silent SNP C C A C3N-00217_T C3N-00217_N C C c.762C>A p.= p.I254I ENST00000372073 7/7 344 242 102 290 290 0 strelka-varscan-mutect TMEM164,synonymous_variant,p.=,ENST00000372073,;TMEM164,synonymous_variant,p.=,ENST00000372068,NM_032227.3;TMEM164,synonymous_variant,p.=,ENST00000288381,;TMEM164,synonymous_variant,p.=,ENST00000372072,NM_017698.2;TMEM164,non_coding_transcript_exon_variant,,ENST00000464177,;TMEM164,downstream_gene_variant,,ENST00000461715,; A ENST00000372073 Transcript synonymous_variant 1098/5567 762/894 254/297 I atC/atA COSM1464827,COSM1464828 1 1 TMEM164 HGNC HGNC:26217 protein_coding YES CCDS14550.2 ENSP00000361143 Q5U3C3 UPI00004560FF 7/7 hmmpanther:PTHR20948,Pfam_domain:PF14808 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 110173319 110173319 C A 1 0 0 0 0 0 0 0 1 16523 903 32 2 2 TMEM164 23 110173319 Silent SNP C C3N-00217_T 1551468 110173319 45867576 630 12400 RGAG1 0 . GRCh38 X 110450692 110450692 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.75G>T p.Gln25His p.Q25H ENST00000465301 3/4 237 204 33 204 203 1 strelka-varscan-mutect RGAG1,missense_variant,p.Gln25His,ENST00000465301,NM_020769.2;RGAG1,missense_variant,p.Gln25His,ENST00000540313,;RGAG1,missense_variant,p.Gln25His,ENST00000520821,; T ENST00000465301 Transcript missense_variant 321/5426 75/4167 25/1388 Q/H caG/caT 1 1 RGAG1 HGNC HGNC:29245 protein_coding YES CCDS14552.1 ENSP00000419786 Q8NET4 UPI000006F841 NM_020769.2 deleterious_low_confidence(0.05) 3/4 hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF48 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 110450692 110450692 G T 1 0 0 0 0 1 0 0 0 13446 933 33 2 2 RGAG1 23 110450692 Missense_Mutation SNP G C3N-00217_T 277373 110450692 45590203 631 12401 TRPC5 0 . GRCh38 X 111853814 111853814 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1193C>A p.Pro398His p.P398H ENST00000262839 4/11 185 135 50 145 145 0 strelka-varscan-mutect TRPC5,missense_variant,p.Pro398His,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript missense_variant 2112/5839 1193/2922 398/973 P/H cCt/cAt 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 deleterious(0) 4/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 111853814 111853814 G T 1 0 0 0 0 1 0 0 0 17087 1000 35 2 2 TRPC5 23 111853814 Missense_Mutation SNP G C3N-00217_T 1403122 111853814 44187081 632 12402 TRPC5 0 . GRCh38 X 111952312 111952312 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.109C>A p.Leu37Ile p.L37I ENST00000262839 2/11 223 163 60 222 221 1 strelka-varscan-mutect TRPC5,missense_variant,p.Leu37Ile,ENST00000262839,NM_012471.2; T ENST00000262839 Transcript missense_variant 1028/5839 109/2922 37/973 L/I Ctc/Atc 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 deleterious(0.04) 2/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 111952312 111952312 G T 1 0 0 0 0 1 0 0 0 17087 1000 35 2 2 TRPC5 23 111952312 Missense_Mutation SNP G C3N-00217_T 98498 111952312 44088583 633 12403 SLC25A43 0 . GRCh38 X 119410335 119410335 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.663C>A p.= p.P221P ENST00000217909 3/5 182 123 59 127 127 0 strelka-varscan-mutect SLC25A43,synonymous_variant,p.=,ENST00000217909,NM_145305.2;SLC25A43,non_coding_transcript_exon_variant,,ENST00000488158,;SLC25A43,non_coding_transcript_exon_variant,,ENST00000493093,;SLC25A43,intron_variant,,ENST00000484058,; A ENST00000217909 Transcript synonymous_variant 1007/2783 663/1026 221/341 P ccC/ccA 1 1 SLC25A43 HGNC HGNC:30557 protein_coding YES CCDS14577.1 ENSP00000217909 Q8WUT9 UPI00001AE609 NM_145305.2 3/5 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,Prints_domain:PR00926,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF246,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 119410335 119410335 C A 1 0 0 0 0 0 0 0 1 14773 668 24 2 2 SLC25A43 23 119410335 Silent SNP C C3N-00217_T 7458023 119410335 36630560 634 12404 ZBTB33 0 . GRCh38 X 120254137 120254137 + Missense_Mutation SNP C C G novel C3N-00217_T C3N-00217_N C C c.722C>G p.Thr241Arg p.T241R ENST00000326624 2/2 112 99 13 130 130 0 strelka-varscan-mutect ZBTB33,missense_variant,p.Thr241Arg,ENST00000326624,NM_006777.3;ZBTB33,missense_variant,p.Thr241Arg,ENST00000557385,NM_001184742.1;TMEM255A,downstream_gene_variant,,ENST00000371369,NM_001104544.1;TMEM255A,downstream_gene_variant,,ENST00000309720,NM_017938.3;TMEM255A,downstream_gene_variant,,ENST00000440464,NM_001104545.1;TMEM255A,downstream_gene_variant,,ENST00000371352,; G ENST00000326624 Transcript missense_variant 950/5211 722/2019 241/672 T/R aCa/aGa 1 1 ZBTB33 HGNC HGNC:16682 protein_coding YES CCDS14596.1 ENSP00000314153 Q86T24 UPI0000072F87 NM_006777.3 tolerated(0.13) 2/2 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF301 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999967 1 1 1 0 G 3 3 43 120254137 120254137 C G 1 0 0 0 0 1 0 0 0 18105 478 17 4 4 ZBTB33 23 120254137 Missense_Mutation SNP C C3N-00217_T 843802 120254137 35786758 635 12405 ZBTB33 0 . GRCh38 X 120255362 120255362 + Missense_Mutation SNP T T A novel C3N-00217_T C3N-00217_N T T c.1947T>A p.Asn649Lys p.N649K ENST00000326624 2/2 128 111 17 170 170 0 strelka-varscan-mutect ZBTB33,missense_variant,p.Asn649Lys,ENST00000326624,NM_006777.3;ZBTB33,missense_variant,p.Asn649Lys,ENST00000557385,NM_001184742.1;TMEM255A,downstream_gene_variant,,ENST00000371369,NM_001104544.1;TMEM255A,downstream_gene_variant,,ENST00000309720,NM_017938.3;TMEM255A,downstream_gene_variant,,ENST00000440464,NM_001104545.1;TMEM255A,downstream_gene_variant,,ENST00000371352,; A ENST00000326624 Transcript missense_variant 2175/5211 1947/2019 649/672 N/K aaT/aaA 1 1 ZBTB33 HGNC HGNC:16682 protein_coding YES CCDS14596.1 ENSP00000314153 Q86T24 UPI0000072F87 NM_006777.3 tolerated(0.08) 2/2 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF301 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 120255362 120255362 T A 1 0 0 0 0 1 0 0 0 18105 1461 51 4 4 ZBTB33 23 120255362 Missense_Mutation SNP T C3N-00217_T 1225 120255362 35785533 636 12406 CUL4B 0 . GRCh38 X 120538754 120538754 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1812G>T p.Glu604Asp p.E604D ENST00000404115 15/22 213 194 19 292 292 0 strelka-varscan-mutect CUL4B,missense_variant,p.Glu586Asp,ENST00000371322,NM_001079872.1;CUL4B,missense_variant,p.Glu604Asp,ENST00000404115,NM_003588.3;CUL4B,missense_variant,p.Glu591Asp,ENST00000336592,;CUL4B,downstream_gene_variant,,ENST00000371323,;CUL4B,upstream_gene_variant,,ENST00000497616,; A ENST00000404115 Transcript missense_variant 2214/3264 1812/2742 604/913 E/D gaG/gaT 1 -1 CUL4B HGNC HGNC:2555 protein_coding YES CCDS35379.1 ENSP00000384109 Q13620 UPI0000246E48 NM_003588.3 deleterious(0) 15/22 Gene3D:1.20.1310.10,Pfam_domain:PF00888,PROSITE_profiles:PS50069,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF66,SMART_domains:SM00182,Superfamily_domains:SSF75632 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 120538754 120538754 C A 1 0 0 0 0 1 0 0 0 3868 680 24 2 2 CUL4B 23 120538754 Missense_Mutation SNP C C3N-00217_T 283392 120538754 35502141 637 12407 GRIA3 0 . GRCh38 X 123398780 123398780 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.1057G>T p.Asp353Tyr p.D353Y ENST00000622768 7/16 235 179 56 217 217 0 strelka-varscan-mutect GRIA3,missense_variant,p.Asp353Tyr,ENST00000622768,NM_000828.4;GRIA3,missense_variant,p.Asp353Tyr,ENST00000620443,NM_007325.4;GRIA3,missense_variant,p.Asp353Tyr,ENST00000620581,;GRIA3,missense_variant,p.Asp353Tyr,ENST00000541091,; T ENST00000622768 Transcript missense_variant 1350/5173 1057/2685 353/894 D/Y Gat/Tat 1 1 GRIA3 HGNC HGNC:4573 protein_coding YES CCDS14604.1 ENSP00000481554 P42263 UPI000013D503 NM_000828.4 deleterious(0.01) 7/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF151,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 123398780 123398780 G T 1 0 0 0 0 1 0 0 0 6649 1290 45 2 2 GRIA3 23 123398780 Missense_Mutation SNP G C3N-00217_T 2860026 123398780 32642115 638 12408 TEX13C 0 . GRCh38 X 125321760 125321760 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.1641G>T p.= p.L547L ENST00000632600 1/1 486 334 152 450 450 0 strelka-varscan-mutect TEX13C,synonymous_variant,p.=,ENST00000632600,NM_001195272.1; T ENST00000632600 Transcript synonymous_variant 1641/5095 1641/2982 547/993 L ctG/ctT 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 1/1 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 125321760 125321760 G T 1 0 0 0 0 0 0 0 1 16199 1277 45 2 2 TEX13C 23 125321760 Silent SNP G C3N-00217_T 1922980 125321760 30719135 639 12409 DCAF12L2 0 . GRCh38 X 126165656 126165656 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.269G>A p.Arg90His p.R90H ENST00000360028 1/1 226 199 27 245 244 1 strelka-varscan-mutect DCAF12L2,missense_variant,p.Arg90His,ENST00000360028,NM_001013628.2; T ENST00000360028 Transcript missense_variant 442/2599 269/1392 90/463 R/H cGc/cAc COSM5123605,COSM5123606 1 -1 DCAF12L2 HGNC HGNC:32950 protein_coding YES CCDS43991.1 ENSP00000353128 Q5VW00 UPI0000197594 NM_001013628.2 tolerated(0.09) 1/1 hmmpanther:PTHR19860:SF8,hmmpanther:PTHR19860 1,1 MODERATE 1 SNV 1,1 1 PASS . . 2 205 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 126165656 126165656 C T 1 0 0 0 0 1 0 0 0 4066 768 27 1 1 DCAF12L2 23 126165656 Missense_Mutation SNP C C3N-00217_T 843896 126165656 29875239 640 12410 IGSF1 0 . GRCh38 X 131274720 131274720 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.3645C>A p.Asp1215Glu p.D1215E ENST00000370903 18/20 320 212 108 355 353 2 strelka-varscan-mutect IGSF1,missense_variant,p.Asp1201Glu,ENST00000370904,;IGSF1,missense_variant,p.Asp1215Glu,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Asp1201Glu,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Asp1210Glu,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000467244,; T ENST00000370903 Transcript missense_variant 3928/4594 3645/4026 1215/1341 D/E gaC/gaA 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 tolerated(0.18) 18/20 Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 131274720 131274720 G T 1 0 0 0 0 1 0 0 0 7503 1020 36 2 2 IGSF1 23 131274720 Missense_Mutation SNP G C3N-00217_T 5109064 131274720 24766175 641 12411 TFDP3 0 . GRCh38 X 133217923 133217923 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.337C>A p.Arg113Ser p.R113S ENST00000310125 1/1 293 199 94 316 316 0 strelka-varscan-mutect TFDP3,missense_variant,p.Arg113Ser,ENST00000310125,NM_016521.2; T ENST00000310125 Transcript missense_variant 426/1680 337/1218 113/405 R/S Cgt/Agt 1 -1 TFDP3 HGNC HGNC:24603 protein_coding YES CCDS14636.2 ENSP00000385461 Q5H9I0 UPI0000212570 NM_016521.2 deleterious(0) 1/1 hmmpanther:PTHR12548:SF13,hmmpanther:PTHR12548,PIRSF_domain:PIRSF009404,Gene3D:1.10.10.10,Pfam_domain:PF02319,SMART_domains:SM01372,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 PASS rs1302825657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 133217923 133217923 G T 1 0 0 0 0 1 0 0 0 16232 1116 39 1 1 TFDP3 23 133217923 Missense_Mutation SNP G C3N-00217_T 1943203 133217923 22822972 642 12412 FAM127B 0 . GRCh38 X 135052047 135052047 + Missense_Mutation SNP C C T C3N-00217_T C3N-00217_N C C c.62G>A p.Arg21His p.R21H ENST00000370775 1/1 120 95 25 91 91 0 strelka-varscan-mutect FAM127B,missense_variant,p.Arg21His,ENST00000370775,NM_001078172.1;FAM127B,non_coding_transcript_exon_variant,,ENST00000520964,;FAM127B,non_coding_transcript_exon_variant,,ENST00000518153,;FAM127B,non_coding_transcript_exon_variant,,ENST00000522309,; T ENST00000370775 Transcript missense_variant 129/1244 62/342 21/113 R/H cGt/cAt COSM456784 1 -1 FAM127B HGNC HGNC:24514 protein_coding YES CCDS43998.1 ENSP00000375267 Q9BWD3 UPI0000140B18 NM_001078172.1 deleterious(0.02) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR15503:SF6,hmmpanther:PTHR15503,Pfam_domain:PF16297 1 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 135052047 135052047 C T 1 0 0 0 0 1 0 0 0 5284 536 19 1 1 FAM127B 23 135052047 Missense_Mutation SNP C C3N-00217_T 1834124 135052047 20988848 643 12413 ZNF449 0 . GRCh38 X 135360904 135360904 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1385C>A p.Pro462His p.P462H ENST00000339249 5/5 138 123 15 184 184 0 strelka-varscan-mutect ZNF449,missense_variant,p.Pro462His,ENST00000339249,NM_152695.5; A ENST00000339249 Transcript missense_variant 1525/3773 1385/1557 462/518 P/H cCt/cAt 1 1 ZNF449 HGNC HGNC:21039 protein_coding YES CCDS14649.1 ENSP00000339585 Q6P9G9 UPI000013F1DE NM_152695.5 deleterious(0.02) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR23226:SF4,hmmpanther:PTHR23226,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -19.99527 0.9999877 1 1 1 0 A 3 1 43 135360904 135360904 C A 1 0 0 0 0 1 0 0 0 18491 681 24 2 2 ZNF449 23 135360904 Missense_Mutation SNP C C3N-00217_T 308857 135360904 20679991 644 12414 ADGRG4 0 . GRCh38 X 136359438 136359438 + Missense_Mutation SNP T T A rs371045658 C3N-00217_T C3N-00217_N T T c.7127T>A p.Val2376Asp p.V2376D ENST00000394143 11/26 78 41 37 106 106 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Val2376Asp,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Val2376Asp,ENST00000370652,;ADGRG4,missense_variant,p.Val2171Asp,ENST00000394141,; A ENST00000394143 Transcript missense_variant 7418/9931 7127/9243 2376/3080 V/D gTt/gAt rs371045658 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 11/26 MODERATE 1 SNV 1 1 PASS rs371045658 . 1 203 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 136359438 136359438 T A 1 0 0 0 0 1 0 0 0 371 1725 60 4 4 ADGRG4 23 136359438 Missense_Mutation SNP T C3N-00217_T 998534 136359438 19681457 645 12415 MAGEC3 0 . GRCh38 X 141897274 141897274 + Missense_Mutation SNP G G C C3N-00217_T C3N-00217_N G G c.1516G>C p.Glu506Gln p.E506Q ENST00000298296 7/8 176 153 23 136 136 0 strelka-varscan-mutect MAGEC3,missense_variant,p.Glu506Gln,ENST00000298296,NM_138702.1;MAGEC3,missense_variant,p.Glu208Gln,ENST00000544766,NM_177456.2;MAGEC3,missense_variant,p.Glu208Gln,ENST00000409007,;MAGEC3,missense_variant,p.Glu128Gln,ENST00000443323,;MAGEC3,downstream_gene_variant,,ENST00000483584,; C ENST00000298296 Transcript missense_variant 1516/1932 1516/1932 506/643 E/Q Gag/Cag COSM1466093,COSM1466094 1 1 MAGEC3 HGNC HGNC:23798 protein_coding YES CCDS14676.1 ENSP00000298296 Q8TD91 UPI000006E09B NM_138702.1 tolerated(0.23) 7/8 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF86,SMART_domains:SM01373 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999916 1 1 1 0 C 3 2 43 141897274 141897274 G C 1 0 0 0 0 1 0 0 0 9100 943 33 4 4 MAGEC3 23 141897274 Missense_Mutation SNP G C3N-00217_T 5537836 141897274 14143621 646 12416 HSFX2 0 . GRCh38 X 149594501 149594501 + Missense_Mutation SNP G G T novel C3N-00217_T C3N-00217_N G G c.200C>A p.Ala67Asp p.A67D ENST00000598963 1/2 76 55 21 57 57 0 strelka-varscan-mutect HSFX2,missense_variant,p.Ala67Asp,ENST00000598963,NM_001164415.2;TMEM185A,downstream_gene_variant,,ENST00000600449,NM_032508.3;TMEM185A,downstream_gene_variant,,ENST00000611119,NM_001174092.2;TMEM185A,downstream_gene_variant,,ENST00000613273,;TMEM185A,downstream_gene_variant,,ENST00000502858,;TMEM185A,downstream_gene_variant,,ENST00000616857,;TMEM185A,downstream_gene_variant,,ENST00000612022,; T ENST00000598963 Transcript missense_variant 216/1365 200/1272 67/423 A/D gCt/gAt 1 -1 HSFX2 HGNC HGNC:32701 protein_coding YES CCDS48179.1 ENSP00000469223 Q9UBD0 A0A140VK21 UPI000007033B NM_001164415.2 deleterious(0) 1/2 hmmpanther:PTHR10015,hmmpanther:PTHR10015:SF163 MODERATE 1 SNV 1 1 PASS . . 25 185 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 149594501 149594501 G T 1 0 0 0 0 1 0 0 0 7295 971 34 2 2 HSFX2 23 149594501 Missense_Mutation SNP G C3N-00217_T 7697227 149594501 6446394 647 12417 PRRG3 0 . GRCh38 X 151699974 151699974 + Missense_Mutation SNP C C G C3N-00217_T C3N-00217_N C C c.10C>G p.Leu4Val p.L4V ENST00000370354 3/4 37 21 16 26 26 0 strelka-varscan-mutect PRRG3,missense_variant,p.Leu4Val,ENST00000370354,;PRRG3,intron_variant,,ENST00000370353,;PRRG3,intron_variant,,ENST00000538575,NM_024082.3;PRRG3,intron_variant,,ENST00000448726,;PRRG3,upstream_gene_variant,,ENST00000448324,; G ENST00000370354 Transcript missense_variant,splice_region_variant 107/650 10/309 4/102 L/V Ctc/Gtc COSM3964883 1 1 PRRG3 HGNC HGNC:30798 protein_coding ENSP00000359379 A6NDZ7 UPI000059DB9F deleterious_low_confidence(0.03) 3/4 1 MODERATE SNV 3 1 1 PASS . . 1 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 43 151699974 151699974 C G 1 0 0 0 0 1 0 0 0 12753 695 24 4 4 PRRG3 23 151699974 Missense_Mutation SNP C C3N-00217_T 2105473 151699974 4340921 648 12418 GABRA3 0 . GRCh38 X 152255884 152255884 + Missense_Mutation SNP G G T rs79829085 C3N-00217_T C3N-00217_N G G c.445C>A p.Pro149Thr p.P149T ENST00000370314 5/10 545 315 230 449 449 0 strelka-varscan-mutect GABRA3,missense_variant,p.Pro149Thr,ENST00000370314,NM_000808.3;GABRA3,missense_variant,p.Pro149Thr,ENST00000535043,;GABRA3,non_coding_transcript_exon_variant,,ENST00000417858,; T ENST00000370314 Transcript missense_variant 684/3712 445/1479 149/492 P/T Ccg/Acg rs79829085 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 deleterious(0) 5/10 hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS rs79829085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 43 152255884 152255884 G T 1 0 0 0 0 1 0 0 0 6033 1261 44 2 2 GABRA3 23 152255884 Missense_Mutation SNP G C3N-00217_T 555910 152255884 3785011 649 12419 GABRQ 0 . GRCh38 X 152652682 152652682 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1300C>A p.Pro434Thr p.P434T ENST00000598523 9/9 356 312 44 285 283 2 strelka-varscan-mutect GABRQ,missense_variant,p.Pro434Thr,ENST00000598523,NM_018558.3; A ENST00000598523 Transcript missense_variant 1320/6172 1300/1899 434/632 P/T Cca/Aca 1 1 GABRQ HGNC HGNC:14454 protein_coding YES CCDS14707.1 ENSP00000469332 Q9UN88 UPI000013DAC0 NM_018558.3 tolerated(0.86) 9/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1376739920 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 152652682 152652682 C A 1 0 0 0 0 1 0 0 0 6046 623 22 2 2 GABRQ 23 152652682 Missense_Mutation SNP C C3N-00217_T 396798 152652682 3388213 650 12420 ATP2B3 0 . GRCh38 X 153565046 153565046 + Silent SNP G G T novel C3N-00217_T C3N-00217_N G G c.3285G>T p.= p.R1095R ENST00000263519 19/20 269 214 55 173 172 1 strelka-varscan-mutect ATP2B3,synonymous_variant,p.=,ENST00000370186,;ATP2B3,synonymous_variant,p.=,ENST00000263519,NM_001001344.2;ATP2B3,synonymous_variant,p.=,ENST00000349466,;ATP2B3,synonymous_variant,p.=,ENST00000359149,NM_021949.3;ATP2B3,synonymous_variant,p.=,ENST00000393842,;ATP2B3,downstream_gene_variant,,ENST00000460549,;ATP2B3,upstream_gene_variant,,ENST00000496610,; T ENST00000263519 Transcript synonymous_variant 3411/6420 3285/3663 1095/1220 R cgG/cgT 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 19/20 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 43 153565046 153565046 G T 1 0 0 0 0 0 0 0 1 1294 1219 43 2 2 ATP2B3 23 153565046 Silent SNP G C3N-00217_T 912364 153565046 2475849 651 12421 L1CAM 0 . GRCh38 X 153870081 153870081 + Silent SNP C C A novel C3N-00217_T C3N-00217_N C C c.966G>T p.= p.R322R ENST00000370060 9/29 232 177 55 157 157 0 strelka-varscan-mutect L1CAM,synonymous_variant,p.=,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,synonymous_variant,p.=,ENST00000361981,NM_001143963.2;L1CAM,synonymous_variant,p.=,ENST00000370055,;L1CAM,synonymous_variant,p.=,ENST00000361699,NM_024003.3;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,downstream_gene_variant,,ENST00000458029,;L1CAM,downstream_gene_variant,,ENST00000407935,;L1CAM,upstream_gene_variant,,ENST00000455590,;L1CAM,downstream_gene_variant,,ENST00000420165,;L1CAM,downstream_gene_variant,,ENST00000464967,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,upstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000460553,;L1CAM,upstream_gene_variant,,ENST00000484652,; A ENST00000370060 Transcript synonymous_variant 1156/5113 966/3774 322/1257 R cgG/cgT 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 9/29 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 153870081 153870081 C A 1 0 0 0 0 0 0 0 1 8489 726 26 2 2 L1CAM 23 153870081 Silent SNP C C3N-00217_T 305035 153870081 2170814 652 12422 AVPR2 0 . GRCh38 X 153906700 153906700 + Missense_Mutation SNP C C A novel C3N-00217_T C3N-00217_N C C c.1088C>A p.Ser363Tyr p.S363Y ENST00000358927 4/4 201 105 96 133 132 1 strelka-varscan-mutect AVPR2,missense_variant,p.Ser363Tyr,ENST00000358927,;AVPR2,missense_variant,p.Ser363Tyr,ENST00000337474,NM_000054.4;AVPR2,missense_variant,p.Pro334Thr,ENST00000430697,;AVPR2,3_prime_UTR_variant,,ENST00000370049,NM_001146151.1;ARHGAP4,downstream_gene_variant,,ENST00000370028,NM_001164741.1;ARHGAP4,downstream_gene_variant,,ENST00000350060,NM_001666.4;ARHGAP4,downstream_gene_variant,,ENST00000370016,;ARHGAP4,downstream_gene_variant,,ENST00000393721,;ARHGAP4,downstream_gene_variant,,ENST00000442172,;ARHGAP4,downstream_gene_variant,,ENST00000454164,;ARHGAP4,downstream_gene_variant,,ENST00000467421,;AVPR2,3_prime_UTR_variant,,ENST00000434679,;L1CAM,intron_variant,,ENST00000464967,;ARHGAP4,downstream_gene_variant,,ENST00000404127,;ARHGAP4,downstream_gene_variant,,ENST00000470209,;ARHGAP4,downstream_gene_variant,,ENST00000420383,;ARHGAP4,downstream_gene_variant,,ENST00000494302,;ARHGAP4,downstream_gene_variant,,ENST00000494397,;ARHGAP4,downstream_gene_variant,,ENST00000466928,;ARHGAP4,downstream_gene_variant,,ENST00000461739,; A ENST00000358927 Transcript missense_variant 1297/1763 1088/1116 363/371 S/Y tCc/tAc 1 1 AVPR2 HGNC HGNC:897 protein_coding YES CCDS14735.1 ENSP00000351805 P30518 UPI000005043B deleterious(0.04) 4/4 hmmpanther:PTHR24241:SF20,hmmpanther:PTHR24241,Prints_domain:PR00898 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 43 153906700 153906700 C A 1 0 0 0 0 1 0 0 0 1389 855 30 2 2 AVPR2 23 153906700 Missense_Mutation SNP C C3N-00217_T 36619 153906700 2134195 653 12423 FLNA 0 . GRCh38 X 154364703 154364703 + Frame_Shift_Del DEL C C - novel C3N-00217_T C3N-00217_N C C c.1845delG p.Pro616HisfsTer60 p.P616Hfs*60 ENST00000369850 13/48 408 295 113 272 272 0 sindel-varindel-pindel FLNA,frameshift_variant,p.Pro616HisfsTer60,ENST00000422373,NM_001456.3;FLNA,frameshift_variant,p.Pro616HisfsTer60,ENST00000369850,NM_001110556.1;FLNA,frameshift_variant,p.Pro616HisfsTer60,ENST00000360319,;FLNA,frameshift_variant,p.Pro589HisfsTer60,ENST00000369856,;FLNA,frameshift_variant,p.Pro616HisfsTer60,ENST00000344736,;FLNA,frameshift_variant,p.Pro589HisfsTer60,ENST00000610817,;FLNA,frameshift_variant,p.Ala601ProfsTer2033,ENST00000420627,;FLNA,non_coding_transcript_exon_variant,,ENST00000465144,; - ENST00000369850 Transcript frameshift_variant 2082/8382 1845/7944 615/2647 G/X ggG/gg 1 -1 FLNA HGNC HGNC:3754 protein_coding YES CCDS48194.1 ENSP00000358866 P21333 UPI000013C596 NM_001110556.1 13/48 PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF173,Gene3D:2.60.40.10,Pfam_domain:PF00630,SMART_domains:SM00557,Superfamily_domains:SSF81296 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 43 154364703 154364703 C - 1 0 1 0 1 0 0 0 0 5789 726 26 0 0 FLNA 23 154364703 Frame_Shift_Del DEL C C3N-00217_T 458003 154364703 1676192 654 12424 FAM50A 0 . GRCh38 X 154449897 154449897 + Nonsense_Mutation SNP C C A rs367764750 C3N-00217_T C3N-00217_N C C c.795C>A p.Tyr265Ter p.Y265* ENST00000393600 10/13 367 285 82 294 293 1 strelka-varscan-mutect FAM50A,stop_gained,p.Tyr265Ter,ENST00000393600,NM_004699.3;FAM50A,stop_gained,p.Tyr225Ter,ENST00000158526,;MIR6858,upstream_gene_variant,,ENST00000620733,;FAM50A,non_coding_transcript_exon_variant,,ENST00000464419,;FAM50A,non_coding_transcript_exon_variant,,ENST00000494278,;FAM50A,downstream_gene_variant,,ENST00000481619,;FAM50A,downstream_gene_variant,,ENST00000478509,;FAM50A,downstream_gene_variant,,ENST00000490480,; A ENST00000393600 Transcript stop_gained 905/1352 795/1020 265/339 Y/* taC/taA rs367764750 1 1 FAM50A HGNC HGNC:18786 protein_coding YES CCDS14751.1 ENSP00000377225 Q14320 UPI0000138FCD NM_004699.3 10/13 hmmpanther:PTHR12722,hmmpanther:PTHR12722:SF2,Pfam_domain:PF04921 HIGH 1 SNV 1 1 PASS rs367764750 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 43 154449897 154449897 C A 1 0 0 0 0 0 1 0 0 5453 547 19 1 1 FAM50A 23 154449897 Nonsense_Mutation SNP C C3N-00217_T 85194 154449897 1590998 655 12425 PLXNA3 0 . GRCh38 X 154461552 154461552 + Silent SNP C C A rs150493678 C3N-00217_T C3N-00217_N C C c.1048C>A p.= p.R350R ENST00000369682 3/33 194 153 41 122 122 0 strelka-varscan-mutect PLXNA3,synonymous_variant,p.=,ENST00000369682,NM_017514.4;PLXNA3,downstream_gene_variant,,ENST00000495040,;PLXNA3,upstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000478236,;PLXNA3,upstream_gene_variant,,ENST00000482598,; A ENST00000369682 Transcript synonymous_variant 1223/10885 1048/5616 350/1871 R Cgg/Agg rs150493678 1 1 PLXNA3 HGNC HGNC:9101 protein_coding YES CCDS14752.1 ENSP00000358696 P51805 UPI0002AB801F NM_017514.4 3/33 PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF32,hmmpanther:PTHR22625,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 LOW 1 SNV 1 1 PASS rs150493678 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 43 154461552 154461552 C A 1 0 0 0 0 0 0 0 1 12227 643 23 1 1 PLXNA3 23 154461552 Silent SNP C C3N-00217_T 11655 154461552 1579343 656 12426 DPM3 0 . GRCh38 1 155140089 155140089 + Missense_Mutation SNP C C A novel C3N-00223_T C3N-00223_N C C c.242G>T p.Cys81Phe p.C81F ENST00000368399 1/1 237 203 34 181 179 2 strelka-varscan-mutect DPM3,missense_variant,p.Cys81Phe,ENST00000368399,NM_018973.3;DPM3,missense_variant,p.Cys51Phe,ENST00000341298,;DPM3,missense_variant,p.Cys51Phe,ENST00000368400,NM_153741.1;SLC50A1,downstream_gene_variant,,ENST00000368404,NM_018845.3,NM_001287587.1;SLC50A1,downstream_gene_variant,,ENST00000622581,NM_001287586.1;SLC50A1,downstream_gene_variant,,ENST00000368401,NM_001287588.1,NM_001122837.1;SLC50A1,downstream_gene_variant,,ENST00000303343,NM_001122839.1;SLC50A1,downstream_gene_variant,,ENST00000484157,NM_001287590.1;SLC50A1,downstream_gene_variant,,ENST00000368405,;SLC50A1,downstream_gene_variant,,ENST00000490770,;SLC50A1,downstream_gene_variant,,ENST00000488609,;SLC50A1,downstream_gene_variant,,ENST00000490276,;SLC50A1,downstream_gene_variant,,ENST00000475824,;SLC50A1,downstream_gene_variant,,ENST00000484027,;SLC50A1,downstream_gene_variant,,ENST00000465546,;SLC50A1,downstream_gene_variant,,ENST00000479579,;SLC50A1,downstream_gene_variant,,ENST00000506037,; A ENST00000368399 Transcript missense_variant 319/517 242/369 81/122 C/F tGc/tTc 1 -1 DPM3 HGNC HGNC:3007 protein_coding YES CCDS1094.1 ENSP00000357384 Q9P2X0 A0A140VJI4 UPI000015FDD9 NM_018973.3 tolerated(0.06) 1/1 Pfam_domain:PF08285,hmmpanther:PTHR16433,hmmpanther:PTHR16433:SF0,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 44 155140089 155140089 C A 1 0 0 0 0 1 0 0 0 4541 710 25 2 2 DPM3 1 155140089 Missense_Mutation SNP C C3N-00223_T 155140089 93816333 1 12427 ASPM 0 . GRCh38 1 197133361 197133361 + Nonsense_Mutation SNP C C T novel C3N-00223_T C3N-00223_N C C c.2408G>A p.Trp803Ter p.W803* ENST00000367409 6/28 185 170 15 80 80 0 strelka-varscan-mutect ASPM,stop_gained,p.Trp803Ter,ENST00000367409,NM_018136.4;ASPM,stop_gained,p.Trp803Ter,ENST00000294732,NM_001206846.1;ASPM,stop_gained,p.Trp53Ter,ENST00000367408,;ASPM,intron_variant,,ENST00000612785,; T ENST00000367409 Transcript stop_gained 2665/10887 2408/10434 803/3477 W/* tGg/tAg 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 6/28 Superfamily_domains:SSF47576 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999984 1 1 1 0 T 4 4 44 197133361 197133361 C T 1 0 0 0 0 0 1 0 0 1203 595 21 3 3 ASPM 1 197133361 Nonsense_Mutation SNP C C3N-00223_T 41993272 197133361 51823061 2 12428 UGT1A1 0 . GRCh38 2 233772427 233772427 + Silent SNP C C T rs114123636 C3N-00223_T C3N-00223_N C C c.1467C>T p.= p.D489D ENST00000305139 5/5 355 305 50 340 340 0 strelka-varscan-mutect UGT1A6,synonymous_variant,p.=,ENST00000305139,NM_001072.3;UGT1A9,synonymous_variant,p.=,ENST00000354728,NM_021027.2;UGT1A10,synonymous_variant,p.=,ENST00000344644,NM_019075.2;UGT1A8,synonymous_variant,p.=,ENST00000373450,NM_019076.4;UGT1A4,synonymous_variant,p.=,ENST00000373409,NM_007120.2;UGT1A1,synonymous_variant,p.=,ENST00000305208,NM_000463.2;UGT1A3,synonymous_variant,p.=,ENST00000482026,NM_019093.2;UGT1A5,synonymous_variant,p.=,ENST00000373414,NM_019078.1;UGT1A7,synonymous_variant,p.=,ENST00000373426,NM_019077.2;UGT1A6,synonymous_variant,p.=,ENST00000373424,NM_205862.1;MROH2A,upstream_gene_variant,,ENST00000610772,NM_001287395.1;UGT1A1,downstream_gene_variant,,ENST00000360418,;UGT1A10,downstream_gene_variant,,ENST00000373445,;UGT1A6,downstream_gene_variant,,ENST00000406651,;MROH2A,upstream_gene_variant,,ENST00000430892,;MROH2A,upstream_gene_variant,,ENST00000428446,;MROH2A,upstream_gene_variant,,ENST00000454283,;UGT1A4,3_prime_UTR_variant,,ENST00000450233,;UGT1A6,downstream_gene_variant,,ENST00000446481,; T ENST00000305139 Transcript synonymous_variant 1606/2479 1467/1599 489/532 D gaC/gaT rs114123636,COSM3050509,COSM3050510,COSM3050511,COSM3050512,COSM3050513,COSM3050514,COSM3050515,COSM3050516,COSM3050517 1 1 UGT1A6 HGNC HGNC:12538 protein_coding YES CCDS2507.1 ENSP00000303174 P19224 Q5DSZ8 UPI000007021F NM_001072.3 5/5 hmmpanther:PTHR11926:SF363,hmmpanther:PTHR11926,Pfam_domain:PF00201 0,1,1,1,1,1,1,1,1,1 LOW SNV 1 0,1,1,1,1,1,1,1,1,1 1 PASS rs114123636 . 0 207 0 0 0 0 0 2 -4.673957 0 0 1 0 0 T 2 4 44 233772427 233772427 C T 1 0 0 0 0 0 0 0 1 17469 535 19 1 1 UGT1A1 2 233772427 Silent SNP C C3N-00223_T 233772427 8421102 3 12429 UVSSA 0 . GRCh38 4 1383915 1383916 + Frame_Shift_Del DEL CG CG - novel C3N-00223_T C3N-00223_N CG CG c.2012_2013delGC p.Arg671HisfsTer34 p.R671Hfs*34 ENST00000389851 13/14 102 77 25 106 106 0 sindel-varindel-pindel UVSSA,frameshift_variant,p.Arg671HisfsTer34,ENST00000389851,NM_001317935.1,NM_020894.2;UVSSA,frameshift_variant,p.Arg671HisfsTer34,ENST00000511216,;UVSSA,frameshift_variant,p.Arg671HisfsTer34,ENST00000507531,;UVSSA,frameshift_variant,p.Arg222HisfsTer34,ENST00000512728,;UVSSA,frameshift_variant,p.Arg222HisfsTer34,ENST00000511563,;UVSSA,upstream_gene_variant,,ENST00000507422,;UVSSA,3_prime_UTR_variant,,ENST00000503548,; - ENST00000389851 Transcript frameshift_variant 2458-2459/4560 2011-2012/2130 671/709 R/X CGc/c 1 1 UVSSA HGNC HGNC:29304 protein_coding YES CCDS33938.1 ENSP00000374501 Q2YD98 UPI00001C1E0C NM_001317935.1,NM_020894.2 13/14 hmmpanther:PTHR28670 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 44 1383915 1383915 CG - 1 0 1 0 1 0 0 0 0 17653 884 31 0 0 UVSSA 4 1383915 Frame_Shift_Del DEL CG C3N-00223_T 1383915 188830640 4 12430 LNPEP 0 . GRCh38 5 97013733 97013733 + Silent SNP T T C novel C3N-00223_T C3N-00223_N T T c.2121T>C p.= p.D707D ENST00000231368 12/18 148 131 17 123 123 0 strelka-varscan-mutect LNPEP,synonymous_variant,p.=,ENST00000231368,NM_005575.2;LNPEP,synonymous_variant,p.=,ENST00000395770,NM_175920.3; C ENST00000231368 Transcript synonymous_variant 2813/12752 2121/3078 707/1025 D gaT/gaC 1 1 LNPEP HGNC HGNC:6656 protein_coding YES CCDS4087.1 ENSP00000231368 Q9UIQ6 UPI000013C94B NM_005575.2 12/18 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF42,Pfam_domain:PF11838 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 44 97013733 97013733 T C 1 0 0 0 0 0 0 0 1 8791 1461 51 5 5 LNPEP 5 97013733 Silent SNP T C3N-00223_T 97013733 84524526 5 12431 PCDHGA1 0 . GRCh38 5 141332620 141332620 + Missense_Mutation SNP G G A rs577475018 C3N-00223_T C3N-00223_N G G c.1936G>A p.Val646Ile p.V646I ENST00000517417 1/4 305 248 57 351 350 1 strelka-varscan-mutect PCDHGA1,missense_variant,p.Val646Ile,ENST00000517417,NM_018912.2;PCDHGA1,missense_variant,p.Val646Ile,ENST00000378105,NM_031993.1;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,; A ENST00000517417 Transcript missense_variant 1936/4604 1936/2796 646/931 V/I Gtc/Atc rs577475018,COSM4999586,COSM4999587 1 1 PCDHGA1 HGNC HGNC:8696 protein_coding YES CCDS54922.1 ENSP00000431083 Q9Y5H4 UPI0000070596 NM_018912.2 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF108,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs577475018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 44 141332620 141332620 G A 1 0 0 0 0 1 0 0 0 11637 1145 40 1 1 PCDHGA1 5 141332620 Missense_Mutation SNP G C3N-00223_T 44318887 141332620 40205639 6 12432 MDN1 0 . GRCh38 6 89787876 89787876 + Missense_Mutation SNP A A C novel C3N-00223_T C3N-00223_N A A c.1312T>G p.Phe438Val p.F438V ENST00000369393 8/102 210 186 24 195 195 0 strelka-varscan-mutect MDN1,missense_variant,p.Phe438Val,ENST00000369393,NM_014611.2;MDN1,missense_variant,p.Phe438Val,ENST00000629399,;MDN1,intron_variant,,ENST00000439638,; C ENST00000369393 Transcript missense_variant 1428/18413 1312/16791 438/5596 F/V Ttt/Gtt 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 deleterious(0) 8/102 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 44 89787876 89787876 A C 1 0 0 0 0 1 0 0 0 9353 101 4 5 5 MDN1 6 89787876 Missense_Mutation SNP A C3N-00223_T 89787876 81018103 7 12433 EGFR 0 . GRCh38 7 55174776 55174776 + Missense_Mutation SNP T T G rs397517095 C3N-00223_T C3N-00223_N T T c.2239T>G p.Leu747Val p.L747V ENST00000275493 19/28 385 324 61 277 277 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu747Val,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu702Val,ENST00000454757,;EGFR,missense_variant,p.Leu702Val,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; G ENST00000275493 Transcript missense_variant 2416/9821 2239/3633 747/1210 L/V Tta/Gta rs397517095 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0.03) 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs397517095 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 44 55174776 55174776 T G 1 0 0 0 0 1 0 0 0 4803 1490 52 5 5 EGFR 7 55174776 Missense_Mutation SNP T C3N-00223_T 55174776 104171197 8 12434 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-00223_T C3N-00223_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 445 382 63 363 363 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 44 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-00223_T 17046 55191822 104154151 9 12435 THAP5 0 . GRCh38 7 108564530 108564530 + Silent SNP G G T novel C3N-00223_T C3N-00223_N G G c.849C>A p.= p.P283P ENST00000415914 3/3 154 119 35 181 181 0 strelka-varscan-mutect THAP5,synonymous_variant,p.=,ENST00000415914,NM_001130475.2;THAP5,synonymous_variant,p.=,ENST00000313516,NM_182529.3;THAP5,downstream_gene_variant,,ENST00000438865,;THAP5,non_coding_transcript_exon_variant,,ENST00000493722,;PNPLA8,intron_variant,,ENST00000489738,;THAP5,intron_variant,,ENST00000468884,;THAP5,downstream_gene_variant,,ENST00000412935,;THAP5,downstream_gene_variant,,ENST00000446771,;THAP5,downstream_gene_variant,,ENST00000484452,; T ENST00000415914 Transcript synonymous_variant 1003/3306 849/1188 283/395 P ccC/ccA 1 -1 THAP5 HGNC HGNC:23188 protein_coding YES CCDS47687.1 ENSP00000400500 Q7Z6K1 UPI00003E4106 NM_001130475.2 3/3 hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF77 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 44 108564530 108564530 G T 1 0 0 0 0 0 0 0 1 16280 987 35 2 2 THAP5 7 108564530 Silent SNP G C3N-00223_T 53372708 108564530 50781443 10 12436 PTPRZ1 0 . GRCh38 7 122061138 122061138 + Missense_Mutation SNP A A C novel C3N-00223_T C3N-00223_N A A c.6866A>C p.Glu2289Ala p.E2289A ENST00000393386 30/30 81 72 9 95 95 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.Glu2289Ala,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.Glu1422Ala,ENST00000449182,NM_001206839.1;PTPRZ1,non_coding_transcript_exon_variant,,ENST00000474500,; C ENST00000393386 Transcript missense_variant 7277/8175 6866/6948 2289/2315 E/A gAg/gCg 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0.01) 30/30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 44 122061138 122061138 A C 1 0 0 0 0 1 0 0 0 12969 304 11 5 5 PTPRZ1 7 122061138 Missense_Mutation SNP A C3N-00223_T 13496608 122061138 37284835 11 12437 NCOA2 0 . GRCh38 8 70138301 70138302 + Frame_Shift_Ins INS - - C novel C3N-00223_T C3N-00223_N - - c.3059dupG p.Pro1021ThrfsTer4 p.P1021Tfs*4 ENST00000452400 15/23 154 115 39 117 117 0 sindel-varindel-pindel NCOA2,frameshift_variant,p.Pro1021ThrfsTer4,ENST00000452400,NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2;NCOA2,frameshift_variant,p.Pro147ThrfsTer4,ENST00000518363,;NCOA2,3_prime_UTR_variant,,ENST00000518287,;NCOA2,non_coding_transcript_exon_variant,,ENST00000522054,; C ENST00000452400 Transcript frameshift_variant 3241-3242/8447 3059-3060/4395 1020/1464 G/GX gga/ggGa 1 -1 NCOA2 HGNC HGNC:7669 protein_coding YES CCDS47872.1 ENSP00000399968 Q15596 UPI000012FE42 NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2 15/23 hmmpanther:PTHR10684:SF2,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 44 70138301 70138301 - C 1 0 1 1 0 0 0 0 0 10248 1654 58 0 0 NCOA2 8 70138301 Frame_Shift_Ins INS - C3N-00223_T 70138301 75000335 12 12438 COL14A1 0 . GRCh38 8 120197843 120197843 + Missense_Mutation SNP G G C C3N-00223_T C3N-00223_N G G c.625G>C p.Glu209Gln p.E209Q ENST00000297848 7/48 310 188 122 161 161 0 strelka-varscan-mutect COL14A1,missense_variant,p.Glu209Gln,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Glu209Gln,ENST00000309791,;COL14A1,missense_variant,p.Glu209Gln,ENST00000537875,;COL14A1,missense_variant,p.Glu22Gln,ENST00000434620,;COL14A1,intron_variant,,ENST00000523142,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,;COL14A1,missense_variant,p.Glu209Gln,ENST00000498051,; C ENST00000297848 Transcript missense_variant 895/6466 625/5391 209/1796 E/Q Gaa/Caa COSM1095602 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 deleterious(0) 7/48 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF53,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 44 120197843 120197843 G C 1 0 0 0 0 1 0 0 0 3459 943 33 4 4 COL14A1 8 120197843 Missense_Mutation SNP G C3N-00223_T 50059542 120197843 24940793 13 12439 GOLGA1 0 . GRCh38 9 124921148 124921148 + Missense_Mutation SNP A A C novel C3N-00223_T C3N-00223_N A A c.824T>G p.Leu275Arg p.L275R ENST00000373555 10/23 245 204 41 187 186 1 strelka-mutect GOLGA1,missense_variant,p.Leu275Arg,ENST00000373555,NM_002077.3;GOLGA1,missense_variant,p.Leu51Arg,ENST00000485337,;GOLGA1,intron_variant,,ENST00000475407,; C ENST00000373555 Transcript missense_variant 1158/4811 824/2304 275/767 L/R cTt/cGt 1 -1 GOLGA1 HGNC HGNC:4424 protein_coding YES CCDS6860.1 ENSP00000362656 Q92805 UPI000013D059 NM_002077.3 deleterious(0) 10/23 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 44 124921148 124921148 A C 1 0 0 0 0 1 0 0 0 6430 72 3 5 5 GOLGA1 9 124921148 Missense_Mutation SNP A C3N-00223_T 124921148 13473569 14 12440 WAC 0 . GRCh38 10 28608300 28608300 + Frame_Shift_Del DEL T T - novel C3N-00223_T C3N-00223_N T T c.1036delT p.Ser346LeufsTer41 p.S346Lfs*41 ENST00000354911 8/14 311 266 45 337 337 0 sindel-varindel-pindel WAC,frameshift_variant,p.Ser301LeufsTer41,ENST00000375664,NM_100264.2;WAC,frameshift_variant,p.Ser346LeufsTer41,ENST00000354911,NM_016628.4;WAC,frameshift_variant,p.Ser243LeufsTer41,ENST00000347934,NM_100486.3;WAC,frameshift_variant,p.Ser198LeufsTer41,ENST00000375646,;WAC,3_prime_UTR_variant,,ENST00000628285,;WAC,3_prime_UTR_variant,,ENST00000428935,;WAC,frameshift_variant,p.Ser301LeufsTer41,ENST00000439676,;WAC,3_prime_UTR_variant,,ENST00000424454,;WAC,non_coding_transcript_exon_variant,,ENST00000345541,;WAC,non_coding_transcript_exon_variant,,ENST00000476046,;WAC,upstream_gene_variant,,ENST00000495268,; - ENST00000354911 Transcript frameshift_variant 1195/3042 1034/1944 345/647 V/X gTt/gt 1 1 WAC HGNC HGNC:17327 protein_coding YES CCDS7159.1 ENSP00000346986 Q9BTA9 UPI000013D398 NM_016628.4 8/14 hmmpanther:PTHR15911,hmmpanther:PTHR15911:SF6,Low_complexity_(Seg):seg HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 44 28608300 28608300 T - 1 0 1 0 1 0 0 0 0 17807 1725 60 0 0 WAC 10 28608300 Frame_Shift_Del DEL T C3N-00223_T 28608300 105189122 15 12441 ARID5B 0 . GRCh38 10 62092988 62092988 + Silent SNP A A G novel C3N-00223_T C3N-00223_N A A c.3525A>G p.= p.P1175P ENST00000279873 10/10 98 86 12 79 79 0 strelka-varscan-mutect ARID5B,synonymous_variant,p.=,ENST00000279873,NM_032199.2;ARID5B,synonymous_variant,p.=,ENST00000309334,NM_001244638.1; G ENST00000279873 Transcript synonymous_variant 3935/7891 3525/3567 1175/1188 P ccA/ccG 1 1 ARID5B HGNC HGNC:17362 protein_coding YES CCDS31208.1 ENSP00000279873 Q14865 UPI00001606F0 NM_032199.2 10/10 hmmpanther:PTHR13964:SF29,hmmpanther:PTHR13964 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 44 62092988 62092988 A G 1 0 0 0 0 0 0 0 1 1058 204 8 5 5 ARID5B 10 62092988 Silent SNP A C3N-00223_T 33484688 62092988 71704434 16 12442 ESAM 0 . GRCh38 11 124756592 124756593 + Frame_Shift_Ins INS - - T novel C3N-00223_T C3N-00223_N - - c.399dupA p.Gln134ThrfsTer5 p.Q134Tfs*5 ENST00000278927 3/7 206 178 28 180 180 0 sindel-pindel ESAM,frameshift_variant,p.Gln134ThrfsTer5,ENST00000278927,NM_138961.2;ESAM,intron_variant,,ENST00000435477,;ESAM,intron_variant,,ENST00000444566,;VSIG2,upstream_gene_variant,,ENST00000403470,;VSIG2,upstream_gene_variant,,ENST00000326621,NM_014312.3;RP11-677M14.3,upstream_gene_variant,,ENST00000504932,;ESAM,frameshift_variant,p.Gln134ThrfsTer5,ENST00000417453,;ESAM,non_coding_transcript_exon_variant,,ENST00000464067,;ESAM,non_coding_transcript_exon_variant,,ENST00000485116,; T ENST00000278927 Transcript frameshift_variant 529-530/1826 399-400/1173 133-134/390 -/X -/A 1 -1 ESAM HGNC HGNC:17474 protein_coding YES CCDS8453.1 ENSP00000278927 Q96AP7 UPI000003721A NM_138961.2 3/7 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF126,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 44 124756592 124756592 - T 1 0 1 1 0 0 0 0 0 5109 1386 48 0 0 ESAM 11 124756592 Frame_Shift_Ins INS - C3N-00223_T 124756592 10330030 17 12443 CALCOCO1 0 . GRCh38 12 53715879 53715879 + Missense_Mutation SNP C C T C3N-00223_T C3N-00223_N C C c.1174G>A p.Gly392Ser p.G392S ENST00000550804 9/15 304 275 29 280 280 0 strelka-varscan-mutect CALCOCO1,missense_variant,p.Gly392Ser,ENST00000262059,;CALCOCO1,missense_variant,p.Gly392Ser,ENST00000548263,;CALCOCO1,missense_variant,p.Gly307Ser,ENST00000430117,NM_001143682.1;CALCOCO1,missense_variant,p.Gly392Ser,ENST00000550804,NM_020898.2;CALCOCO1,upstream_gene_variant,,ENST00000546443,;CALCOCO1,non_coding_transcript_exon_variant,,ENST00000549935,;CALCOCO1,non_coding_transcript_exon_variant,,ENST00000549613,;CALCOCO1,non_coding_transcript_exon_variant,,ENST00000552282,;CALCOCO1,downstream_gene_variant,,ENST00000547988,; T ENST00000550804 Transcript missense_variant 1235/2291 1174/2076 392/691 G/S Ggc/Agc COSM4871610,COSM941047 1 -1 CALCOCO1 HGNC HGNC:29306 protein_coding YES CCDS8864.1 ENSP00000449960 Q9P1Z2 A0A024RAZ1 UPI0000037D7A NM_020898.2 deleterious(0.03) 9/15 Pfam_domain:PF07888,hmmpanther:PTHR31915,hmmpanther:PTHR31915:SF5 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1282288769 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 44 53715879 53715879 C T 1 0 0 0 0 1 0 0 0 2267 652 23 1 1 CALCOCO1 12 53715879 Missense_Mutation SNP C C3N-00223_T 53715879 79559430 18 12444 TEX26 0 . GRCh38 13 30952821 30952821 + Missense_Mutation SNP A A T rs142207829 C3N-00223_T C3N-00223_N A A c.308A>T p.Asn103Ile p.N103I ENST00000380473 3/7 227 185 42 252 252 0 strelka-varscan-mutect TEX26,missense_variant,p.Asn103Ile,ENST00000380473,NM_152325.1;TEX26,upstream_gene_variant,,ENST00000530916,;TEX26,intron_variant,,ENST00000531960,; T ENST00000380473 Transcript missense_variant 321/1478 308/870 103/289 N/I aAt/aTt rs142207829 1 1 TEX26 HGNC HGNC:28622 protein_coding YES CCDS9339.1 ENSP00000369840 Q8N6G2 UPI0000070D41 NM_152325.1 tolerated(0.15) 3/7 hmmpanther:PTHR33769:SF1,hmmpanther:PTHR33769 MODERATE 1 SNV 1 1 PASS rs142207829 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 44 30952821 30952821 A T 1 0 0 0 0 1 0 0 0 16205 115 4 4 4 TEX26 13 30952821 Missense_Mutation SNP A C3N-00223_T 30952821 83411507 19 12445 ADAM20 0 . GRCh38 14 70522580 70522580 + Silent SNP T T A rs767490191 C3N-00223_T C3N-00223_N T T c.2328A>T p.= p.G776G ENST00000256389 2/2 78 70 8 86 86 0 strelka-varscan-mutect ADAM20,synonymous_variant,p.=,ENST00000256389,NM_003814.4;RP11-486O13.4,intron_variant,,ENST00000556646,; A ENST00000256389 Transcript synonymous_variant 2573/2795 2328/2331 776/776 G ggA/ggT rs767490191 1 -1 ADAM20 HGNC HGNC:199 protein_coding YES CCDS32111.1 ENSP00000256389 O43506 UPI0000183495 NM_003814.4 2/2 LOW 1 SNV 1 1 PASS rs767490191 . 0 206 3 0 0 0 0 0 -17.55742 1 1 1 1 0 A 2 1 44 70522580 70522580 T A 1 0 0 0 0 0 0 0 1 286 1422 50 4 4 ADAM20 14 70522580 Silent SNP T C3N-00223_T 70522580 36521138 20 12446 NPAP1 0 . GRCh38 15 24677752 24677752 + Missense_Mutation SNP C C A C3N-00223_T C3N-00223_N C C c.1885C>A p.His629Asn p.H629N ENST00000329468 1/1 236 198 38 207 206 1 strelka-varscan-mutect NPAP1,missense_variant,p.His629Asn,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1885/7526 1885/3471 629/1156 H/N Cac/Aac COSM5252146 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.52) 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 44 24677752 24677752 C A 1 0 0 0 0 1 0 0 0 10609 594 21 2 2 NPAP1 15 24677752 Missense_Mutation SNP C C3N-00223_T 24677752 77313437 21 12447 HYPK 0 . GRCh38 15 43801148 43801148 + Missense_Mutation SNP G G T novel C3N-00223_T C3N-00223_N G G c.203G>T p.Gly68Val p.G68V ENST00000406925 3/5 197 171 26 149 149 0 strelka-varscan-mutect HYPK,missense_variant,p.Gly68Val,ENST00000406925,;HYPK,missense_variant,p.Gly68Val,ENST00000442995,NM_016400.3;HYPK,intron_variant,,ENST00000458412,;SERINC4,upstream_gene_variant,,ENST00000319327,NM_001258031.1,NM_001258032.1;SERINC4,upstream_gene_variant,,ENST00000299969,;MFAP1,downstream_gene_variant,,ENST00000267812,NM_005926.2;SERF2,downstream_gene_variant,,ENST00000630046,;SERF2,downstream_gene_variant,,ENST00000409291,;SERF2,downstream_gene_variant,,ENST00000409646,;SERF2,downstream_gene_variant,,ENST00000430901,;HYPK,non_coding_transcript_exon_variant,,ENST00000498605,;HYPK,intron_variant,,ENST00000497142,;SERF2,3_prime_UTR_variant,,ENST00000448830,;SERF2,3_prime_UTR_variant,,ENST00000409617,;SERINC4,upstream_gene_variant,,ENST00000457418,;RP11-296A16.1,upstream_gene_variant,,ENST00000417761,;SERINC4,upstream_gene_variant,,ENST00000448553,;SERINC4,upstream_gene_variant,,ENST00000412697,;SERINC4,upstream_gene_variant,,ENST00000476490,;MFAP1,downstream_gene_variant,,ENST00000484386,; T ENST00000406925 Transcript missense_variant 4314/4777 203/390 68/129 G/V gGa/gTa 1 1 HYPK HGNC HGNC:18418 protein_coding YES CCDS10104.1 ENSP00000384474 Q9NX55 A0A024R5Q1 UPI000000D937 deleterious(0.02) 3/5 hmmpanther:PTHR31184:SF2,hmmpanther:PTHR31184 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 44 43801148 43801148 G T 1 0 0 0 0 1 0 0 0 7368 1174 41 2 2 HYPK 15 43801148 Missense_Mutation SNP G C3N-00223_T 19123396 43801148 58190041 22 12448 STX1B 0 . GRCh38 16 31001528 31001528 + Splice_Site SNP C C T novel C3N-00223_T C3N-00223_N C C c.105+1G>A p.X35_splice ENST00000215095 76 63 13 71 71 0 strelka-varscan-mutect STX1B,splice_donor_variant,,ENST00000215095,NM_052874.4;STX1B,splice_donor_variant,,ENST00000565419,;STX1B,upstream_gene_variant,,ENST00000569638,;STX1B,splice_donor_variant,,ENST00000561836,;STX1B,upstream_gene_variant,,ENST00000566211,; T ENST00000215095 Transcript splice_donor_variant -/4664 105/867 35/288 1 -1 STX1B HGNC HGNC:18539 protein_coding YES CCDS10699.1 ENSP00000215095 P61266 UPI0000000C13 NM_052874.4 2/9 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 44 31001528 31001528 C T 1 0 0 0 0 0 0 1 0 15728 521 18 3 3 STX1B 16 31001528 Splice_Site SNP C C3N-00223_T 31001528 59336817 23 12449 JPH3 0 . GRCh38 16 87644625 87644625 + Missense_Mutation SNP G G A novel C3N-00223_T C3N-00223_N G G c.750G>A p.Met250Ile p.M250I ENST00000284262 2/5 323 305 18 298 298 0 strelka-varscan-mutect JPH3,missense_variant,p.Met250Ile,ENST00000284262,NM_020655.3;JPH3,non_coding_transcript_exon_variant,,ENST00000537256,; A ENST00000284262 Transcript missense_variant 992/3985 750/2247 250/748 M/I atG/atA 1 1 JPH3 HGNC HGNC:14203 protein_coding YES CCDS10962.1 ENSP00000284262 Q8WXH2 UPI000012DAC4 NM_020655.3 tolerated(0.08) 2/5 PIRSF_domain:PIRSF037387,hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 44 87644625 87644625 G A 1 0 0 0 0 1 0 0 0 7874 1290 45 3 3 JPH3 16 87644625 Missense_Mutation SNP G C3N-00223_T 56643097 87644625 2693720 24 12450 MFSD11 0 . GRCh38 17 76738963 76738963 + Missense_Mutation SNP G G C novel C3N-00223_T C3N-00223_N G G c.122G>C p.Arg41Thr p.R41T ENST00000588460 2/13 173 163 10 151 151 0 strelka-varscan-mutect MFSD11,missense_variant,p.Arg41Thr,ENST00000588460,;MFSD11,missense_variant,p.Arg41Thr,ENST00000586622,;MFSD11,missense_variant,p.Arg41Thr,ENST00000621483,NM_001242534.1;MFSD11,missense_variant,p.Arg41Thr,ENST00000355954,NM_001242537.1,NM_001242536.1;MFSD11,missense_variant,p.Arg41Thr,ENST00000336509,NM_024311.3,NM_001242535.1,NM_001242532.1,NM_001242533.1;MFSD11,missense_variant,p.Arg41Thr,ENST00000593181,;MFSD11,missense_variant,p.Arg41Thr,ENST00000590514,;MFSD11,missense_variant,p.Arg41Thr,ENST00000587661,;MFSD11,missense_variant,p.Arg41Thr,ENST00000586689,;SRSF2,upstream_gene_variant,,ENST00000392485,NM_003016.4;SRSF2,upstream_gene_variant,,ENST00000359995,NM_001195427.1;SRSF2,upstream_gene_variant,,ENST00000508921,;MFSD11,downstream_gene_variant,,ENST00000590393,;SRSF2,upstream_gene_variant,,ENST00000358156,;SRSF2,upstream_gene_variant,,ENST00000583836,;RP11-318A15.7,downstream_gene_variant,,ENST00000587459,;MFSD11,downstream_gene_variant,,ENST00000591864,;SRSF2,upstream_gene_variant,,ENST00000384825,;MFSD11,missense_variant,p.Arg22Thr,ENST00000588768,;MFSD11,missense_variant,p.Arg41Thr,ENST00000588670,;MFSD11,missense_variant,p.Arg41Thr,ENST00000588031,;SRSF2,upstream_gene_variant,,ENST00000582449,;SRSF2,upstream_gene_variant,,ENST00000585202,;SRSF2,upstream_gene_variant,,ENST00000452355,;SRSF2,upstream_gene_variant,,ENST00000586778,;SRSF2,upstream_gene_variant,,ENST00000589919,;SRSF2,upstream_gene_variant,,ENST00000592676,;MFSD11,upstream_gene_variant,,ENST00000585584,; C ENST00000588460 Transcript missense_variant 2164/3612 122/1350 41/449 R/T aGg/aCg 1 1 MFSD11 HGNC HGNC:25458 protein_coding YES CCDS11750.1 ENSP00000464932 O43934 A0A024R8U7 UPI0000073F31 tolerated(0.36) 2/13 Gene3D:1.20.1250.20,Pfam_domain:PF05978,hmmpanther:PTHR23294,hmmpanther:PTHR23294:SF23,Superfamily_domains:SSF103473 MODERATE SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -13.06273 0.9999995 1 1 1 0 C 3 2 44 76738963 76738963 G C 1 0 0 0 0 1 0 0 0 9481 1000 35 4 4 MFSD11 17 76738963 Missense_Mutation SNP G C3N-00223_T 76738963 6518478 25 12451 PSMA8 0 . GRCh38 18 26192331 26192331 + Missense_Mutation SNP A A C rs773612544 C3N-00223_T C3N-00223_N A A c.691A>C p.Lys231Gln p.K231Q ENST00000308268 7/7 50 43 7 71 71 0 strelka-varscan-mutect PSMA8,missense_variant,p.Lys231Gln,ENST00000308268,NM_144662.2;PSMA8,missense_variant,p.Lys187Gln,ENST00000343848,NM_001025097.1;PSMA8,missense_variant,p.Lys199Gln,ENST00000612461,NM_001308188.1;PSMA8,missense_variant,p.Lys225Gln,ENST00000415576,NM_001025096.1;PSMA8,3_prime_UTR_variant,,ENST00000538664,; C ENST00000308268 Transcript missense_variant 780/1804 691/771 231/256 K/Q Aaa/Caa rs773612544 1 1 PSMA8 HGNC HGNC:22985 protein_coding YES CCDS32808.1 ENSP00000311121 Q8TAA3 UPI000013ECFF NM_144662.2 tolerated(0.21) 7/7 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51475,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF47,Gene3D:3.60.20.10,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS rs773612544 . 2 205 3 0 0 0 0 0 -17.05723 1 1 1 1 0 C 3 2 44 26192331 26192331 A C 1 0 0 0 0 1 0 0 0 12824 15 1 5 5 PSMA8 18 26192331 Missense_Mutation SNP A C3N-00223_T 26192331 54180954 26 12452 CNDP2 0 . GRCh38 18 74512534 74512534 + Splice_Site SNP T T G novel C3N-00223_T C3N-00223_N T T c.742+2T>G p.X248_splice ENST00000324262 73 69 4 87 87 0 varscan-mutect CNDP2,splice_donor_variant,,ENST00000324262,NM_018235.2;CNDP2,splice_donor_variant,,ENST00000579847,;CNDP2,splice_donor_variant,,ENST00000324301,NM_001168499.1;CNDP2,splice_donor_variant,,ENST00000579624,;CNDP2,splice_donor_variant,,ENST00000583785,;CNDP2,downstream_gene_variant,,ENST00000584768,;CNDP2,downstream_gene_variant,,ENST00000580672,;CNDP2,downstream_gene_variant,,ENST00000583216,;CNDP2,downstream_gene_variant,,ENST00000582666,;CNDP2,downstream_gene_variant,,ENST00000581513,;CNDP2,downstream_gene_variant,,ENST00000581272,;CNDP2,downstream_gene_variant,,ENST00000582589,;CNDP2,downstream_gene_variant,,ENST00000577355,;CNDP2,downstream_gene_variant,,ENST00000579583,;CNDP2,splice_donor_variant,,ENST00000583695,;CNDP2,splice_donor_variant,,ENST00000582620,;CNDP2,splice_donor_variant,,ENST00000577669,;CNDP2,splice_donor_variant,,ENST00000584581,;CNDP2,splice_donor_variant,,ENST00000583938,;CNDP2,downstream_gene_variant,,ENST00000585263,;CNDP2,downstream_gene_variant,,ENST00000582260,;CNDP2,upstream_gene_variant,,ENST00000581600,;CNDP2,upstream_gene_variant,,ENST00000577409,; G ENST00000324262 Transcript splice_donor_variant -/5130 742/1428 248/475 1 1 CNDP2 HGNC HGNC:24437 protein_coding YES CCDS12006.1 ENSP00000325548 Q96KP4 UPI00000463FE NM_018235.2 7/11 HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -7.503345 0.9999836 1 1 1 0 G 5 3 44 74512534 74512534 T G 1 0 0 0 0 0 0 1 0 3373 1652 57 5 5 CNDP2 18 74512534 Splice_Site SNP T C3N-00223_T 48320203 74512534 5860751 27 12453 STAP2 0 . GRCh38 19 4327152 4327152 + Silent SNP C C A C3N-00223_T C3N-00223_N C C c.735G>T p.= p.L245L ENST00000600324 8/13 283 234 49 284 284 0 strelka-varscan-mutect STAP2,synonymous_variant,p.=,ENST00000600324,NM_017720.2;STAP2,synonymous_variant,p.=,ENST00000594605,NM_001013841.1;STAP2,synonymous_variant,p.=,ENST00000601482,;STAP2,synonymous_variant,p.=,ENST00000598443,;FSD1,downstream_gene_variant,,ENST00000221856,NM_024333.2;FSD1,downstream_gene_variant,,ENST00000597590,;FSD1,downstream_gene_variant,,ENST00000597480,;STAP2,upstream_gene_variant,,ENST00000601956,;FSD1,downstream_gene_variant,,ENST00000594438,;FSD1,downstream_gene_variant,,ENST00000601006,;STAP2,non_coding_transcript_exon_variant,,ENST00000597593,;STAP2,3_prime_UTR_variant,,ENST00000599736,;STAP2,non_coding_transcript_exon_variant,,ENST00000602007,;STAP2,non_coding_transcript_exon_variant,,ENST00000596242,;STAP2,non_coding_transcript_exon_variant,,ENST00000601179,;FSD1,downstream_gene_variant,,ENST00000598179,; A ENST00000600324 Transcript synonymous_variant 803/1508 735/1350 245/449 L ctG/ctT COSM566622 1 -1 STAP2 HGNC HGNC:30430 protein_coding YES CCDS12128.1 ENSP00000468927 Q9UGK3 UPI00001AF0BC NM_017720.2 8/13 hmmpanther:PTHR16186,hmmpanther:PTHR16186:SF11 1 LOW SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 44 4327152 4327152 C A 1 0 0 0 0 0 0 0 1 15628 465 17 2 2 STAP2 19 4327152 Silent SNP C C3N-00223_T 4327152 54290464 28 12454 ZNF226 0 . GRCh38 19 44175886 44175886 + Missense_Mutation SNP G G C novel C3N-00223_T C3N-00223_N G G c.624G>C p.Trp208Cys p.W208C ENST00000590089 7/7 135 103 32 147 147 0 strelka-varscan-mutect ZNF226,missense_variant,p.Trp208Cys,ENST00000590089,NM_016444.2;ZNF226,missense_variant,p.Trp208Cys,ENST00000454662,NM_001319090.1,NM_001319089.1,NM_001319088.1,NM_001032372.1;ZNF226,missense_variant,p.Trp208Cys,ENST00000337433,NM_001032373.1;ZNF226,3_prime_UTR_variant,,ENST00000588883,;ZNF226,downstream_gene_variant,,ENST00000300823,NM_015919.3;ZNF226,downstream_gene_variant,,ENST00000413984,NM_001032374.1;ZNF226,downstream_gene_variant,,ENST00000589160,;ZNF226,downstream_gene_variant,,ENST00000588795,;ZNF226,downstream_gene_variant,,ENST00000590524,;ZNF226,downstream_gene_variant,,ENST00000585678,;ZNF226,downstream_gene_variant,,ENST00000586914,;ZNF226,downstream_gene_variant,,ENST00000588127,;ZNF226,downstream_gene_variant,,ENST00000586203,;ZNF226,downstream_gene_variant,,ENST00000590578,;ZNF226,downstream_gene_variant,,ENST00000590467,;ZNF226,downstream_gene_variant,,ENST00000586286,;ZNF226,downstream_gene_variant,,ENST00000585560,;ZNF226,downstream_gene_variant,,ENST00000588742,NM_001146220.2;ZNF226,downstream_gene_variant,,ENST00000590759,; C ENST00000590089 Transcript missense_variant 991/2788 624/2412 208/803 W/C tgG/tgC 1 1 ZNF226 HGNC HGNC:13019 protein_coding YES CCDS46102.1 ENSP00000465121 Q9NYT6 A0A024R0P4 UPI000013C32A NM_016444.2 tolerated(0.26) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 44 44175886 44175886 G C 1 0 0 0 0 1 0 0 0 18357 1183 41 4 4 ZNF226 19 44175886 Missense_Mutation SNP G C3N-00223_T 39848734 44175886 14441730 29 12455 ARHGAP35 0 . GRCh38 19 46921192 46921192 + Silent SNP A A G novel C3N-00223_T C3N-00223_N A A c.2517A>G p.= p.S839S ENST00000404338 1/6 290 240 50 287 287 0 strelka-varscan-mutect ARHGAP35,synonymous_variant,p.=,ENST00000404338,NM_004491.4;ARHGAP35,synonymous_variant,p.=,ENST00000614079,;ARHGAP35,intron_variant,,ENST00000615647,; G ENST00000404338 Transcript synonymous_variant 2517/8889 2517/4500 839/1499 S tcA/tcG 1 1 ARHGAP35 HGNC HGNC:4591 protein_coding YES CCDS46127.1 ENSP00000385720 Q9NRY4 UPI0000163F71 NM_004491.4 1/6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 44 46921192 46921192 A G 1 0 0 0 0 0 0 0 1 1008 204 8 5 5 ARHGAP35 19 46921192 Silent SNP A C3N-00223_T 2745306 46921192 11696424 30 12456 PPP2R1A 0 . GRCh38 19 52221085 52221085 + Silent SNP C C T rs187141962 C3N-00223_T C3N-00223_N C C c.1470C>T p.= p.S490S ENST00000322088 12/15 265 217 48 207 207 0 strelka-varscan-mutect PPP2R1A,synonymous_variant,p.=,ENST00000322088,NM_014225.5;PPP2R1A,synonymous_variant,p.=,ENST00000462990,;PPP2R1A,synonymous_variant,p.=,ENST00000391791,;PPP2R1A,downstream_gene_variant,,ENST00000454220,;MIR6801,upstream_gene_variant,,ENST00000614975,;CTD-2525I3.3,downstream_gene_variant,,ENST00000593857,;PPP2R1A,downstream_gene_variant,,ENST00000473820,; T ENST00000322088 Transcript synonymous_variant 1528/5380 1470/1770 490/589 S tcC/tcT rs187141962,COSM713028 1 1 PPP2R1A HGNC HGNC:9302 protein_coding YES CCDS12849.1 ENSP00000324804 P30153 A8K7B7 UPI000006EB9C NM_014225.5 12/15 hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 0,1 LOW 1 SNV 1 0,1 1 PASS rs187141962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 44 52221085 52221085 C T 1 0 0 0 0 0 0 0 1 12505 639 23 1 1 PPP2R1A 19 52221085 Silent SNP C C3N-00223_T 5299893 52221085 6396531 31 12457 APOL1 0 . GRCh38 22 36257362 36257362 + Nonsense_Mutation SNP C C T novel C3N-00223_T C3N-00223_N C C c.190C>T p.Gln64Ter p.Q64* ENST00000319136 5/7 217 186 31 188 188 0 strelka-varscan-mutect APOL1,stop_gained,p.Gln64Ter,ENST00000319136,NM_145343.2;APOL1,stop_gained,p.Gln48Ter,ENST00000397278,NM_003661.3;APOL1,stop_gained,p.Gln48Ter,ENST00000422706,NM_001136540.1;APOL1,stop_gained,p.Gln30Ter,ENST00000426053,NM_001136541.1;APOL1,stop_gained,p.Gln48Ter,ENST00000397279,;APOL1,stop_gained,p.Gln48Ter,ENST00000427990,;APOL1,stop_gained,p.Gln77Ter,ENST00000438034,;APOL1,stop_gained,p.Gln48Ter,ENST00000433768,;APOL1,stop_gained,p.Gln48Ter,ENST00000422471,;APOL1,stop_gained,p.Gln48Ter,ENST00000431184,;APOL1,stop_gained,p.Gln30Ter,ENST00000439680,;APOL1,non_coding_transcript_exon_variant,,ENST00000475519,; T ENST00000319136 Transcript stop_gained 457/3000 190/1245 64/414 Q/* Caa/Taa 1 1 APOL1 HGNC HGNC:618 protein_coding YES CCDS13925.1 ENSP00000317674 O14791 UPI0000167BCC NM_145343.2 5/7 hmmpanther:PTHR14096,hmmpanther:PTHR14096:SF38 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 44 36257362 36257362 C T 1 0 0 0 0 0 1 0 0 927 827 29 3 3 APOL1 22 36257362 Nonsense_Mutation SNP C C3N-00223_T 36257362 14561106 32 12458 UBE2J2 0 . GRCh38 1 1255215 1255215 + Silent SNP G G A rs779886665 C3N-00293_T C3N-00293_N G G c.816C>T p.= p.I272I ENST00000400930 8/8 91 84 7 56 56 0 strelka-varscan-mutect UBE2J2,synonymous_variant,p.=,ENST00000347370,NM_194458.1;UBE2J2,synonymous_variant,p.=,ENST00000349431,NM_058167.2;UBE2J2,synonymous_variant,p.=,ENST00000400929,NM_194457.1;UBE2J2,synonymous_variant,p.=,ENST00000360466,;UBE2J2,synonymous_variant,p.=,ENST00000400930,NM_194315.1;UBE2J2,downstream_gene_variant,,ENST00000435198,;UBE2J2,downstream_gene_variant,,ENST00000422076,;UBE2J2,downstream_gene_variant,,ENST00000502382,;UBE2J2,downstream_gene_variant,,ENST00000509720,;RP5-902P8.12,upstream_gene_variant,,ENST00000565563,;UBE2J2,downstream_gene_variant,,ENST00000491779,;UBE2J2,downstream_gene_variant,,ENST00000467339,;UBE2J2,3_prime_UTR_variant,,ENST00000450390,;UBE2J2,3_prime_UTR_variant,,ENST00000464036,;UBE2J2,downstream_gene_variant,,ENST00000473215,;UBE2J2,downstream_gene_variant,,ENST00000466752,;UBE2J2,downstream_gene_variant,,ENST00000503294,;UBE2J2,downstream_gene_variant,,ENST00000477894,;UBE2J2,downstream_gene_variant,,ENST00000471154,; A ENST00000400930 Transcript synonymous_variant 984/1021 816/828 272/275 I atC/atT rs779886665,COSM1333142,COSM4787262 1 -1 UBE2J2 HGNC HGNC:19268 protein_coding YES CCDS15.1 ENSP00000383719 Q8N2K1 UPI00001D69F8 NM_194315.1 8/8 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs779886665 . 0 204 6 0 0 0 0 0 -14.60763 0.9999997 1 1 1 0 A 2 1 45 1255215 1255215 G A 1 0 0 0 0 0 0 0 1 17382 1048 37 1 1 UBE2J2 1 1255215 Silent SNP G C3N-00293_T 1255215 247701207 1 12459 KAZN 0 . GRCh38 1 15114578 15114578 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.2271C>A p.Ser757Arg p.S757R ENST00000376030 15/15 260 231 29 217 217 0 strelka-varscan-mutect KAZN,missense_variant,p.Ser845Arg,ENST00000636203,;KAZN,missense_variant,p.Ser757Arg,ENST00000376030,NM_201628.2;TMEM51-AS1,non_coding_transcript_exon_variant,,ENST00000310916,;TMEM51-AS1,downstream_gene_variant,,ENST00000404665,; A ENST00000376030 Transcript missense_variant 2565/6030 2271/2328 757/775 S/R agC/agA 1 1 KAZN HGNC HGNC:29173 protein_coding YES CCDS152.2 ENSP00000365198 Q674X7 UPI0000E1E68A NM_201628.2 deleterious_low_confidence(0.04) 15/15 hmmpanther:PTHR12776,hmmpanther:PTHR12776:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 15114578 15114578 C A 1 0 0 0 0 1 0 0 0 7907 709 25 2 2 KAZN 1 15114578 Missense_Mutation SNP C C3N-00293_T 13859363 15114578 233841844 2 12460 RSC1A1 0 . GRCh38 1 15659932 15659932 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.64G>A p.Asp22Asn p.D22N ENST00000345034 1/1 130 123 7 89 88 1 strelka-mutect RSC1A1,missense_variant,p.Asp22Asn,ENST00000345034,NM_006511.1;DDI2,3_prime_UTR_variant,,ENST00000480945,NM_032341.4;DDI2,3_prime_UTR_variant,,ENST00000320153,;DDI2,downstream_gene_variant,,ENST00000548451,; A ENST00000345034 Transcript missense_variant 64/1854 64/1854 22/617 D/N Gat/Aat 1 1 RSC1A1 HGNC HGNC:10458 protein_coding YES CCDS161.1 ENSP00000341963 Q92681 UPI00000715AC NM_006511.1 deleterious(0.01) 1/1 hmmpanther:PTHR15397,hmmpanther:PTHR15397:SF2 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 15659932 15659932 G A 1 0 0 0 0 1 0 0 0 13954 1290 45 3 3 RSC1A1 1 15659932 Missense_Mutation SNP G C3N-00293_T 545354 15659932 233296490 3 12461 UBR4 0 . GRCh38 1 19198593 19198593 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.596C>T p.Ser199Leu p.S199L ENST00000375254 5/106 261 246 15 175 175 0 strelka-varscan-mutect UBR4,missense_variant,p.Ser199Leu,ENST00000375254,NM_020765.2; A ENST00000375254 Transcript missense_variant 624/15906 596/15552 199/5183 S/L tCa/tTa 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 tolerated(0.07) 5/106 hmmpanther:PTHR21725 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 19198593 19198593 G A 1 0 0 0 0 1 0 0 0 17428 1294 45 3 3 UBR4 1 19198593 Missense_Mutation SNP G C3N-00293_T 3538661 19198593 229757829 4 12462 IQCC 0 . GRCh38 1 32207497 32207497 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1056G>T p.Lys352Asn p.K352N ENST00000537469 5/5 156 137 19 90 90 0 strelka-varscan-mutect IQCC,missense_variant,p.Lys352Asn,ENST00000537469,NM_001160042.1;IQCC,missense_variant,p.Lys272Asn,ENST00000291358,NM_018134.2;CCDC28B,downstream_gene_variant,,ENST00000421922,NM_001301011.1;DCDC2B,upstream_gene_variant,,ENST00000409358,NM_001099434.1;CCDC28B,downstream_gene_variant,,ENST00000373602,NM_024296.4;RP4-622L5.7,upstream_gene_variant,,ENST00000421616,;RP4-622L5.7,upstream_gene_variant,,ENST00000373604,;CCDC28B,downstream_gene_variant,,ENST00000483009,;IQCC,non_coding_transcript_exon_variant,,ENST00000617816,;DCDC2B,upstream_gene_variant,,ENST00000487056,;CCDC28B,downstream_gene_variant,,ENST00000469003,;CCDC28B,downstream_gene_variant,,ENST00000461819,; T ENST00000537469 Transcript missense_variant 1067/2252 1056/1641 352/546 K/N aaG/aaT 1 1 IQCC HGNC HGNC:25545 protein_coding YES CCDS53293.1 ENSP00000442291 Q4KMZ1 UPI0001A42065 NM_001160042.1 deleterious(0) 5/5 hmmpanther:PTHR16049 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 32207497 32207497 G T 1 0 0 0 0 1 0 0 0 7708 1020 36 2 2 IQCC 1 32207497 Missense_Mutation SNP G C3N-00293_T 13008904 32207497 216748925 5 12463 CDC20 0 . GRCh38 1 43359798 43359798 + Missense_Mutation SNP G G A rs747181936 C3N-00293_T C3N-00293_N G G c.404G>A p.Gly135Glu p.G135E ENST00000372462 3/10 218 203 15 165 165 0 varscan-mutect CDC20,missense_variant,p.Gly135Glu,ENST00000372462,;CDC20,missense_variant,p.Gly135Glu,ENST00000310955,NM_001255.2;ELOVL1,downstream_gene_variant,,ENST00000621943,NM_001256399.1;ELOVL1,downstream_gene_variant,,ENST00000372458,NM_001256402.1,NM_022821.3;ELOVL1,downstream_gene_variant,,ENST00000413844,NM_001256401.1;ELOVL1,downstream_gene_variant,,ENST00000621166,;RP1-92O14.3,upstream_gene_variant,,ENST00000424948,;CDC20,non_coding_transcript_exon_variant,,ENST00000478882,;ELOVL1,downstream_gene_variant,,ENST00000470769,;ELOVL1,downstream_gene_variant,,ENST00000464204,;ELOVL1,downstream_gene_variant,,ENST00000482302,;ELOVL1,downstream_gene_variant,,ENST00000497050,;ELOVL1,downstream_gene_variant,,ENST00000470968,;ELOVL1,downstream_gene_variant,,ENST00000497569,;ELOVL1,downstream_gene_variant,,ENST00000487209,;ELOVL1,downstream_gene_variant,,ENST00000468865,;ELOVL1,downstream_gene_variant,,ENST00000496932,;ELOVL1,downstream_gene_variant,,ENST00000465321,;ELOVL1,downstream_gene_variant,,ENST00000479439,;ELOVL1,downstream_gene_variant,,ENST00000478481,;CDC20,upstream_gene_variant,,ENST00000482046,;ELOVL1,downstream_gene_variant,,ENST00000479686,; A ENST00000372462 Transcript missense_variant 607/1777 404/1500 135/499 G/E gGa/gAa rs747181936 1 1 CDC20 HGNC HGNC:1723 protein_coding YES CCDS484.1 ENSP00000361540 Q12834 UPI0000072C04 tolerated(0.49) 3/10 hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF3 MODERATE 1 SNV 1 1 PASS rs747181936 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 43359798 43359798 G A 1 0 0 0 0 1 0 0 0 2762 1174 41 3 3 CDC20 1 43359798 Missense_Mutation SNP G C3N-00293_T 11152301 43359798 205596624 6 12464 CCDC17 0 . GRCh38 1 45623439 45623439 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.271G>T p.Val91Leu p.V91L ENST00000528266 3/13 240 210 30 174 174 0 strelka-varscan-mutect CCDC17,missense_variant,p.Val91Leu,ENST00000528266,NM_001114938.2;CCDC17,intron_variant,,ENST00000421127,NM_001190182.1;CCDC17,intron_variant,,ENST00000445048,;GPBP1L1,downstream_gene_variant,,ENST00000355105,NM_021639.4;GPBP1L1,downstream_gene_variant,,ENST00000290795,;NASP,downstream_gene_variant,,ENST00000350030,NM_002482.3;NASP,downstream_gene_variant,,ENST00000537798,NM_001195193.1;GPBP1L1,downstream_gene_variant,,ENST00000479235,;GPBP1L1,downstream_gene_variant,,ENST00000467032,;GPBP1L1,downstream_gene_variant,,ENST00000487436,;CCDC17,upstream_gene_variant,,ENST00000464739,;CCDC17,missense_variant,p.Val59Leu,ENST00000479529,;CCDC17,non_coding_transcript_exon_variant,,ENST00000482416,;CCDC17,non_coding_transcript_exon_variant,,ENST00000491755,;CCDC17,non_coding_transcript_exon_variant,,ENST00000525599,;CCDC17,intron_variant,,ENST00000372044,; A ENST00000528266 Transcript missense_variant,splice_region_variant 419/2181 271/1869 91/622 V/L Gtg/Ttg 1 -1 CCDC17 HGNC HGNC:26574 protein_coding YES CCDS44131.2 ENSP00000432172 Q96LX7 UPI0001AE78A9 NM_001114938.2 deleterious(0.02) 3/13 hmmpanther:PTHR33820 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 45623439 45623439 C A 1 0 0 0 0 1 0 0 0 2486 521 18 2 2 CCDC17 1 45623439 Missense_Mutation SNP C C3N-00293_T 2263641 45623439 203332983 7 12465 ZFYVE9 0 . GRCh38 1 52238604 52238604 + Missense_Mutation SNP C C G C3N-00293_T C3N-00293_N C C c.1187C>G p.Ser396Cys p.S396C ENST00000287727 4/19 212 196 16 107 107 0 strelka-varscan-mutect ZFYVE9,missense_variant,p.Ser396Cys,ENST00000287727,NM_004799.3;ZFYVE9,missense_variant,p.Ser396Cys,ENST00000371591,;ZFYVE9,missense_variant,p.Ser396Cys,ENST00000357206,NM_007324.3;ZFYVE9,non_coding_transcript_exon_variant,,ENST00000361625,; G ENST00000287727 Transcript missense_variant 1639/5194 1187/4278 396/1425 S/C tCt/tGt COSM414865 1 1 ZFYVE9 HGNC HGNC:6775 protein_coding YES CCDS563.1 ENSP00000287727 O95405 UPI0000001620 NM_004799.3 deleterious_low_confidence(0.04) 4/19 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 52238604 52238604 C G 1 0 0 0 0 1 0 0 0 18248 913 32 4 4 ZFYVE9 1 52238604 Missense_Mutation SNP C C3N-00293_T 6615165 52238604 196717818 8 12466 COL11A1 0 . GRCh38 1 102946910 102946910 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.3215G>A p.Gly1072Asp p.G1072D ENST00000370096 42/67 385 351 34 289 289 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly1084Asp,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly1072Asp,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly1033Asp,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly956Asp,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; T ENST00000370096 Transcript missense_variant 3528/7286 3215/5421 1072/1806 G/D gGt/gAt 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 42/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 102946910 102946910 C T 1 0 0 0 0 1 0 0 0 3455 507 18 3 3 COL11A1 1 102946910 Missense_Mutation SNP C C3N-00293_T 50708306 102946910 146009512 9 12467 NTNG1 0 . GRCh38 1 107324736 107324736 + Missense_Mutation SNP G G T C3N-00293_T C3N-00293_N G G c.701G>T p.Gly234Val p.G234V ENST00000370068 3/8 251 209 42 159 156 3 strelka-varscan-mutect NTNG1,missense_variant,p.Gly234Val,ENST00000370067,;NTNG1,missense_variant,p.Gly234Val,ENST00000370068,;NTNG1,missense_variant,p.Gly234Val,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Gly234Val,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Gly234Val,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Gly234Val,ENST00000370065,;NTNG1,missense_variant,p.Gly234Val,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; T ENST00000370068 Transcript missense_variant 1547/4034 701/1620 234/539 G/V gGa/gTa COSM1667762,COSM1667763,COSM1667764,COSM4217157 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 199 0 7 4 0 0 0 -19.96475 0.5630604 1 1 1 0 T 3 4 45 107324736 107324736 G T 1 0 0 0 0 1 0 0 0 10769 1174 41 2 2 NTNG1 1 107324736 Missense_Mutation SNP G C3N-00293_T 4377826 107324736 141631686 10 12468 AMIGO1 0 . GRCh38 1 109508159 109508159 + Missense_Mutation SNP A A G novel C3N-00293_T C3N-00293_N A A c.754T>C p.Tyr252His p.Y252H ENST00000369864 2/2 250 214 36 171 171 0 strelka-varscan-mutect AMIGO1,missense_variant,p.Tyr252His,ENST00000369864,;AMIGO1,missense_variant,p.Tyr252His,ENST00000369862,NM_020703.2; G ENST00000369864 Transcript missense_variant 1104/5088 754/1482 252/493 Y/H Tac/Cac 1 -1 AMIGO1 HGNC HGNC:20824 protein_coding YES CCDS30795.1 ENSP00000358880 Q86WK6 UPI0000035067 tolerated(0.5) 2/2 hmmpanther:PTHR24368,hmmpanther:PTHR24368:SF1,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 109508159 109508159 A G 1 0 0 0 0 1 0 0 0 673 391 14 5 5 AMIGO1 1 109508159 Missense_Mutation SNP A C3N-00293_T 2183423 109508159 139448263 11 12469 VANGL1 0 . GRCh38 1 115659684 115659684 + Missense_Mutation SNP G G T rs529034655 C3N-00293_T C3N-00293_N G G c.115G>T p.Gly39Cys p.G39C ENST00000355485 3/8 489 433 56 409 409 0 strelka-varscan-mutect VANGL1,missense_variant,p.Gly39Cys,ENST00000355485,NM_138959.2;VANGL1,missense_variant,p.Gly39Cys,ENST00000369510,NM_001172411.1;VANGL1,missense_variant,p.Gly39Cys,ENST00000310260,NM_001172412.1;VANGL1,missense_variant,p.Gly39Cys,ENST00000369509,; T ENST00000355485 Transcript missense_variant 386/8691 115/1575 39/524 G/C Ggc/Tgc rs529034655 1 1 VANGL1 HGNC HGNC:15512 protein_coding YES CCDS883.1 ENSP00000347672 Q8TAA9 A0A024R0E3 UPI0000070B72 NM_138959.2 deleterious(0.04) 3/8 Pfam_domain:PF06638,PIRSF_domain:PIRSF007991,hmmpanther:PTHR20886,hmmpanther:PTHR20886:SF8 MODERATE 1 SNV 1 1 PASS rs529034655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 115659684 115659684 G T 1 0 0 0 0 1 0 0 0 17664 1116 39 1 1 VANGL1 1 115659684 Missense_Mutation SNP G C3N-00293_T 6151525 115659684 133296738 12 12470 WDR3 0 . GRCh38 1 117951980 117951980 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1808G>C p.Gly603Ala p.G603A ENST00000349139 17/27 119 112 7 73 73 0 strelka-mutect WDR3,missense_variant,p.Gly603Ala,ENST00000349139,NM_006784.2;SPAG17,downstream_gene_variant,,ENST00000336338,NM_206996.2;SPAG17,downstream_gene_variant,,ENST00000478697,;SPAG17,downstream_gene_variant,,ENST00000469128,;SPAG17,downstream_gene_variant,,ENST00000466857,; C ENST00000349139 Transcript missense_variant 1855/9974 1808/2832 603/943 G/A gGa/gCa 1 1 WDR3 HGNC HGNC:12755 protein_coding YES CCDS898.1 ENSP00000308179 Q9UNX4 Q5TDG3 UPI0000138EDC NM_006784.2 deleterious(0.03) 17/27 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19853:SF0,hmmpanther:PTHR19853,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF117289 MODERATE 1 SNV 1 1 PASS rs1230363396 . 0 207 2 0 0 0 0 0 -14.14 1 1 1 1 0 C 3 2 45 117951980 117951980 G C 1 0 0 0 0 1 0 0 0 17845 1188 41 4 4 WDR3 1 117951980 Missense_Mutation SNP G C3N-00293_T 2292296 117951980 131004442 13 12471 BCL9 0 . GRCh38 1 147624526 147624526 + Missense_Mutation SNP G G C C3N-00293_T C3N-00293_N G G c.3848G>C p.Arg1283Thr p.R1283T ENST00000234739 10/10 282 267 15 173 173 0 strelka-varscan-mutect BCL9,missense_variant,p.Arg1283Thr,ENST00000234739,NM_004326.3; C ENST00000234739 Transcript missense_variant 4588/6278 3848/4281 1283/1426 R/T aGa/aCa COSM1294954 1 1 BCL9 HGNC HGNC:1008 protein_coding YES CCDS30833.1 ENSP00000234739 O00512 A0A024QYY4 UPI000013C9B9 NM_004326.3 deleterious(0.04) 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 147624526 147624526 G C 1 0 0 0 0 1 0 0 0 1528 942 33 4 4 BCL9 1 147624526 Missense_Mutation SNP G C3N-00293_T 29672546 147624526 101331896 14 12472 ADAR 0 . GRCh38 1 154602190 154602190 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.452G>C p.Gly151Ala p.G151A ENST00000368474 2/15 191 181 10 96 96 0 strelka-varscan-mutect ADAR,missense_variant,p.Gly151Ala,ENST00000368474,NM_001111.4,NM_015840.3,NM_015841.3;ADAR,missense_variant,p.Gly146Ala,ENST00000529168,;ADAR,5_prime_UTR_variant,,ENST00000368471,NM_001193495.1,NM_001025107.2;ADAR,non_coding_transcript_exon_variant,,ENST00000471068,;ADAR,non_coding_transcript_exon_variant,,ENST00000494866,;ADAR,downstream_gene_variant,,ENST00000526905,;ADAR,non_coding_transcript_exon_variant,,ENST00000463920,; G ENST00000368474 Transcript missense_variant 652/6625 452/3681 151/1226 G/A gGg/gCg 1 -1 ADAR HGNC HGNC:225 protein_coding YES CCDS1071.1 ENSP00000357459 P55265 UPI000045626B NM_001111.4,NM_015840.3,NM_015841.3 tolerated(0.07) 2/15 PROSITE_profiles:PS50139,Gene3D:1.10.10.10,Pfam_domain:PF02295,SMART_domains:SM00550,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 154602190 154602190 C G 1 0 0 0 0 1 0 0 0 325 623 22 4 4 ADAR 1 154602190 Missense_Mutation SNP C C3N-00293_T 6977664 154602190 94354232 15 12473 MUC1 0 . GRCh38 1 155192305 155192305 + Missense_Mutation SNP T T C rs758495827 C3N-00293_T C3N-00293_N T T c.64A>G p.Thr22Ala p.T22A ENST00000612778 2/8 420 384 36 230 230 0 strelka-varscan-mutect MUC1,missense_variant,p.Thr22Ala,ENST00000612778,NM_001204286.1;MUC1,missense_variant,p.Thr22Ala,ENST00000462215,;MUC1,missense_variant,p.Thr22Ala,ENST00000457295,;MUC1,missense_variant,p.Thr22Ala,ENST00000338684,NM_001204289.1,NM_001204291.1;MUC1,missense_variant,p.Thr22Ala,ENST00000610359,NM_001204292.1;MUC1,missense_variant,p.Thr22Ala,ENST00000614519,;MUC1,missense_variant,p.Thr22Ala,ENST00000368392,NM_001018016.2,NM_001204288.1;MUC1,missense_variant,p.Thr22Ala,ENST00000615517,NM_001204295.1;MUC1,missense_variant,p.Thr22Ala,ENST00000342482,;MUC1,missense_variant,p.Thr22Ala,ENST00000368396,NM_001044392.2,NM_001044391.2;MUC1,intron_variant,,ENST00000611571,;MUC1,intron_variant,,ENST00000620103,NM_001204285.1;MUC1,intron_variant,,ENST00000611577,;MUC1,intron_variant,,ENST00000368393,NM_001204293.1;MUC1,intron_variant,,ENST00000438413,NM_001204290.1;MUC1,intron_variant,,ENST00000337604,NM_001204287.1,NM_002456.5;MUC1,intron_variant,,ENST00000368390,NM_001018017.2;MUC1,intron_variant,,ENST00000368398,NM_001204294.1;MUC1,intron_variant,,ENST00000343256,NM_001044390.2,NM_001204296.1;MUC1,intron_variant,,ENST00000471283,NM_001044393.2;MUC1,intron_variant,,ENST00000368389,NM_001204297.1;THBS3,downstream_gene_variant,,ENST00000541576,NM_001252607.1;THBS3,downstream_gene_variant,,ENST00000368378,NM_007112.4;THBS3,downstream_gene_variant,,ENST00000541990,;THBS3,downstream_gene_variant,,ENST00000457183,NM_001252608.1;MUC1,upstream_gene_variant,,ENST00000462317,;MUC1,upstream_gene_variant,,ENST00000485118,;AC234582.2,downstream_gene_variant,,ENST00000623940,;AC234582.1,downstream_gene_variant,,ENST00000624572,;MIR92B,upstream_gene_variant,,ENST00000607575,;MIR92B,upstream_gene_variant,,ENST00000447623,;MUC1,intron_variant,,ENST00000466913,;MUC1,missense_variant,p.Thr22Ala,ENST00000467134,;MUC1,non_coding_transcript_exon_variant,,ENST00000620770,;MUC1,intron_variant,,ENST00000610468,;MUC1,intron_variant,,ENST00000498431,;MUC1,upstream_gene_variant,,ENST00000468978,;THBS3,downstream_gene_variant,,ENST00000469769,;THBS3,downstream_gene_variant,,ENST00000498500,; C ENST00000612778 Transcript missense_variant 136/1836 64/1455 22/484 T/A Aca/Gca rs758495827 1 -1 MUC1 HGNC HGNC:7508 protein_coding YES CCDS72933.1 ENSP00000484824 A0A087X2A4 UPI000059C524 NM_001204286.1 tolerated_low_confidence(0.2) 2/8 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 5 1 PASS rs758495827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 155192305 155192305 T C 1 0 0 0 0 1 0 0 0 9968 1710 59 5 5 MUC1 1 155192305 Missense_Mutation SNP T C3N-00293_T 590115 155192305 93764117 16 12474 MNDA 0 . GRCh38 1 158845605 158845605 + Nonsense_Mutation SNP C C T C3N-00293_T C3N-00293_N C C c.589C>T p.Gln197Ter p.Q197* ENST00000368141 5/7 114 104 10 73 73 0 strelka-varscan-mutect MNDA,stop_gained,p.Gln197Ter,ENST00000368141,NM_002432.1;MNDA,upstream_gene_variant,,ENST00000438394,;MNDA,downstream_gene_variant,,ENST00000491210,; T ENST00000368141 Transcript stop_gained 850/1752 589/1224 197/407 Q/* Caa/Taa COSM312906 1 1 MNDA HGNC HGNC:7183 protein_coding YES CCDS1177.1 ENSP00000357123 P41218 Q5VUU6 UPI0000001609 NM_002432.1 5/7 Gene3D:2.40.50.140,PROSITE_profiles:PS50834,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF18 1 HIGH 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.59516 1 1 1 1 0 T 4 4 45 158845605 158845605 C T 1 0 0 0 0 0 1 0 0 9640 595 21 3 3 MNDA 1 158845605 Nonsense_Mutation SNP C C3N-00293_T 3653300 158845605 90110817 17 12475 RGS5 0 . GRCh38 1 163147465 163147465 + Silent SNP C C T rs148613695 C3N-00293_T C3N-00293_N C C c.435G>A p.= p.K145K ENST00000530507 5/5 133 126 7 90 90 0 strelka-mutect RGS5,synonymous_variant,p.=,ENST00000313961,NM_003617.3;RGS5,synonymous_variant,p.=,ENST00000618415,NM_001254748.1;RGS5,synonymous_variant,p.=,ENST00000367903,;RGS5,synonymous_variant,p.=,ENST00000530507,NM_001254749.1;RGS5,synonymous_variant,p.=,ENST00000527988,NM_001195303.2;RGS5,intron_variant,,ENST00000469495,;RGS5,downstream_gene_variant,,ENST00000531954,; T ENST00000530507 Transcript synonymous_variant 503/851 435/558 145/185 K aaG/aaA rs148613695,COSM3477502 1 -1 RGS5 HGNC HGNC:10001 protein_coding YES CCDS58041.1 ENSP00000433001 O15539 UPI0001F78466 NM_001254749.1 5/5 Gene3D:1.10.167.10,Pfam_domain:PF00615,PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF42,SMART_domains:SM00315,Superfamily_domains:SSF48097 0,1 LOW 1 SNV 3 0,1 1 PASS rs148613695 . 0 205 3 2 0 0 0 0 -10.03116 0.9999431 1 1 1 0 T 2 4 45 163147465 163147465 C T 1 0 0 0 0 0 0 0 1 13479 912 32 3 3 RGS5 1 163147465 Silent SNP C C3N-00293_T 4301860 163147465 85808957 18 12476 NME7 0 . GRCh38 1 169324431 169324431 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.73G>C p.Glu25Gln p.E25Q ENST00000367811 2/12 229 216 13 79 79 0 strelka-varscan-mutect NME7,missense_variant,p.Glu25Gln,ENST00000367811,NM_013330.4;NME7,5_prime_UTR_variant,,ENST00000472647,NM_197972.2;RP4-800F24.1,downstream_gene_variant,,ENST00000432081,;NME7,non_coding_transcript_exon_variant,,ENST00000469474,;NME7,non_coding_transcript_exon_variant,,ENST00000491225,;NME7,non_coding_transcript_exon_variant,,ENST00000485609,;NME7,intron_variant,,ENST00000480478,;NME7,missense_variant,p.Glu25Gln,ENST00000525440,;NME7,missense_variant,p.Glu25Gln,ENST00000528517,;NME7,non_coding_transcript_exon_variant,,ENST00000524967,;NME7,non_coding_transcript_exon_variant,,ENST00000527460,; G ENST00000367811 Transcript missense_variant 330/1642 73/1131 25/376 E/Q Gag/Cag 1 -1 NME7 HGNC HGNC:20461 protein_coding YES CCDS1277.1 ENSP00000356785 Q9Y5B8 UPI000012FE8C NM_013330.4 tolerated(1) 2/12 PIRSF_domain:PIRSF036503,PROSITE_profiles:PS51336,hmmpanther:PTHR11349,hmmpanther:PTHR11349:SF32,SMART_domains:SM00676 MODERATE 1 SNV 1 1 PASS rs1436937162 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 169324431 169324431 C G 1 0 0 0 0 1 0 0 0 10533 835 29 4 4 NME7 1 169324431 Missense_Mutation SNP C C3N-00293_T 6176966 169324431 79631991 19 12477 KLHL20 0 . GRCh38 1 173757138 173757138 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1130C>A p.Ser377Tyr p.S377Y ENST00000209884 7/12 148 140 8 86 86 0 strelka-varscan-mutect KLHL20,missense_variant,p.Ser377Tyr,ENST00000209884,NM_014458.3; A ENST00000209884 Transcript missense_variant 1266/3421 1130/1830 377/609 S/Y tCt/tAt 1 1 KLHL20 HGNC HGNC:25056 protein_coding YES CCDS1310.1 ENSP00000209884 Q9Y2M5 A0A024R940 UPI0000227E1A NM_014458.3 deleterious(0.03) 7/12 hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF138,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,Pfam_domain:PF01344,SMART_domains:SM00612,Superfamily_domains:0052715,Prints_domain:PR00501 MODERATE 1 SNV 1 1 PASS rs1380820717 . 0 206 4 0 0 0 0 0 -14.88294 1 1 1 1 0 A 3 1 45 173757138 173757138 C A 1 0 0 0 0 1 0 0 0 8239 913 32 2 2 KLHL20 1 173757138 Missense_Mutation SNP C C3N-00293_T 4432707 173757138 75199284 20 12478 50 2 KLHL20 0 . GRCh38 1 173757145 173757145 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.1137C>T p.= p.L379L ENST00000209884 7/12 143 135 8 81 81 0 strelka-varscan-mutect KLHL20,synonymous_variant,p.=,ENST00000209884,NM_014458.3; T ENST00000209884 Transcript synonymous_variant 1273/3421 1137/1830 379/609 L ctC/ctT 1 1 KLHL20 HGNC HGNC:25056 protein_coding YES CCDS1310.1 ENSP00000209884 Q9Y2M5 A0A024R940 UPI0000227E1A NM_014458.3 7/12 hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF138,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,Pfam_domain:PF01344,SMART_domains:SM00612,Superfamily_domains:0052715 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -14.77515 0.9999963 1 1 1 0 T 2 4 45 173757145 173757145 C T 1 0 0 0 0 0 0 0 1 8239 813 29 3 3 KLHL20 1 173757145 Silent SNP C C3N-00293_T 7 173757145 75199277 21 12479 50 2 TNN 0 . GRCh38 1 175118770 175118770 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.2596T>A p.Trp866Arg p.W866R ENST00000239462 11/19 458 435 23 323 323 0 strelka-mutect TNN,missense_variant,p.Trp866Arg,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Trp689Arg,ENST00000621086,;TNN,missense_variant,p.Trp689Arg,ENST00000622870,; A ENST00000239462 Transcript missense_variant 2709/5008 2596/3900 866/1299 W/R Tgg/Agg 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 deleterious(0.01) 11/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 175118770 175118770 T A 1 0 0 0 0 1 0 0 0 16796 1696 59 4 4 TNN 1 175118770 Missense_Mutation SNP T C3N-00293_T 1361625 175118770 73837652 22 12480 TNR 0 . GRCh38 1 175367256 175367256 + Missense_Mutation SNP C C T rs145227551 C3N-00293_T C3N-00293_N C C c.2005G>A p.Val669Ile p.V669I ENST00000367674 10/23 383 349 34 290 290 0 strelka-varscan-mutect TNR,missense_variant,p.Val669Ile,ENST00000367674,;TNR,missense_variant,p.Val669Ile,ENST00000263525,NM_003285.2; T ENST00000367674 Transcript missense_variant 2714/12949 2005/4077 669/1358 V/I Gtc/Atc rs145227551 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C tolerated(0.46) 10/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs145227551 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 175367256 175367256 C T 1 0 0 0 0 1 0 0 0 16811 536 19 1 1 TNR 1 175367256 Missense_Mutation SNP C C3N-00293_T 248486 175367256 73589166 23 12481 KIAA1614 0 . GRCh38 1 180935546 180935546 + Missense_Mutation SNP C C A rs761148715 C3N-00293_T C3N-00293_N C C c.1637C>A p.Pro546Gln p.P546Q ENST00000367588 5/9 80 46 34 58 58 0 strelka-varscan-mutect KIAA1614,missense_variant,p.Pro546Gln,ENST00000367588,NM_020950.1;KIAA1614,missense_variant,p.Pro167Gln,ENST00000367587,;KIAA1614,intron_variant,,ENST00000483705,; A ENST00000367588 Transcript missense_variant 1692/9654 1637/3573 546/1190 P/Q cCg/cAg rs761148715 1 1 KIAA1614 HGNC HGNC:29327 protein_coding YES CCDS41442.1 ENSP00000356560 Q5VZ46 UPI00001C1D75 NM_020950.1 tolerated(0.7) 5/9 hmmpanther:PTHR17130,hmmpanther:PTHR17130:SF21 MODERATE 1 SNV 1 1 PASS rs761148715 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 180935546 180935546 C A 1 0 0 0 0 1 0 0 0 8124 652 23 1 1 KIAA1614 1 180935546 Missense_Mutation SNP C C3N-00293_T 5568290 180935546 68020876 24 12482 PRG4 0 . GRCh38 1 186307711 186307711 + Silent SNP T T C rs115596185 C3N-00293_T C3N-00293_N T T c.1992T>C p.= p.P664P ENST00000445192 7/13 288 270 18 190 188 2 strelka-mutect PRG4,synonymous_variant,p.=,ENST00000445192,NM_005807.4;PRG4,synonymous_variant,p.=,ENST00000367483,NM_001127708.2;PRG4,synonymous_variant,p.=,ENST00000635041,NM_001303232.1;PRG4,synonymous_variant,p.=,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,synonymous_variant,p.=,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; C ENST00000445192 Transcript synonymous_variant 2037/5044 1992/4215 664/1404 P ccT/ccC rs115596185,COSM3849351 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 0,1 LOW SNV 5 0,1 1 PASS rs115596185 . 0 175 0 14 21 0 0 0 -3.871964 0 0 1 0 0 C 2 2 45 186307711 186307711 T C 1 0 0 0 0 0 0 0 1 12615 1567 55 5 5 PRG4 1 186307711 Silent SNP T C3N-00293_T 5372165 186307711 62648711 25 12483 ASPM 0 . GRCh38 1 197102159 197102159 + Silent SNP G G A C3N-00293_T C3N-00293_N G G c.7092C>T p.= p.I2364I ENST00000367409 18/28 326 293 33 134 134 0 strelka-varscan-mutect ASPM,synonymous_variant,p.=,ENST00000367409,NM_018136.4;ASPM,synonymous_variant,p.=,ENST00000612785,;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000367408,; A ENST00000367409 Transcript synonymous_variant 7349/10887 7092/10434 2364/3477 I atC/atT COSM5172618 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 18/28 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 197102159 197102159 G A 1 0 0 0 0 0 0 0 1 1203 1164 41 3 3 ASPM 1 197102159 Silent SNP G C3N-00293_T 10794448 197102159 51854263 26 12484 ASPM 0 . GRCh38 1 197104088 197104088 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.5163G>C p.Lys1721Asn p.K1721N ENST00000367409 18/28 424 389 35 168 168 0 strelka-varscan-mutect ASPM,missense_variant,p.Lys1721Asn,ENST00000367409,NM_018136.4;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000612785,;ASPM,intron_variant,,ENST00000367408,; G ENST00000367409 Transcript missense_variant 5420/10887 5163/10434 1721/3477 K/N aaG/aaC 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.42) 18/28 Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1410074335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 197104088 197104088 C G 1 0 0 0 0 1 0 0 0 1203 912 32 4 4 ASPM 1 197104088 Missense_Mutation SNP C C3N-00293_T 1929 197104088 51852334 27 12485 PPP2R5A 0 . GRCh38 1 212360765 212360765 + Nonsense_Mutation SNP G G T rs752977429 C3N-00293_T C3N-00293_N G G c.1456G>T p.Glu486Ter p.E486* ENST00000261461 13/13 114 108 6 48 48 0 strelka-mutect PPP2R5A,stop_gained,p.Glu486Ter,ENST00000261461,NM_006243.3;PPP2R5A,stop_gained,p.Glu429Ter,ENST00000537030,NM_001199756.1;TMEM206,downstream_gene_variant,,ENST00000261455,NM_018252.2;TMEM206,downstream_gene_variant,,ENST00000535273,NM_001198862.1;RP11-384C4.2,downstream_gene_variant,,ENST00000447949,; T ENST00000261461 Transcript stop_gained 2030/3128 1456/1461 486/486 E/* Gaa/Taa rs752977429 1 1 PPP2R5A HGNC HGNC:9309 protein_coding YES CCDS1503.1 ENSP00000261461 Q15172 UPI0000124E90 NM_006243.3 13/13 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF028043 HIGH 1 SNV 1 1 PASS rs752977429 . 0 161 47 2 0 0 0 0 -9.157371 0.2388616 0 1 0 0 T 4 4 45 212360765 212360765 G T 1 0 0 0 0 0 1 0 0 12514 1059 37 1 1 PPP2R5A 1 212360765 Nonsense_Mutation SNP G C3N-00293_T 15256677 212360765 36595657 28 12486 USH2A 0 . GRCh38 1 216073153 216073153 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.5720T>A p.Leu1907Gln p.L1907Q ENST00000307340 28/72 687 649 38 420 420 0 strelka-varscan-mutect USH2A,missense_variant,p.Leu1907Gln,ENST00000307340,NM_206933.2;RP11-22M7.2,intron_variant,,ENST00000446411,;RP11-22M7.2,intron_variant,,ENST00000430890,;RP11-22M7.2,intron_variant,,ENST00000445619,; T ENST00000307340 Transcript missense_variant 6107/18883 5720/15609 1907/5202 L/Q cTg/cAg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 28/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1473468405 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 216073153 216073153 A T 1 0 0 0 0 1 0 0 0 17570 188 7 4 4 USH2A 1 216073153 Missense_Mutation SNP A C3N-00293_T 3712388 216073153 32883269 29 12487 ESRRG 0 . GRCh38 1 216568092 216568092 + Missense_Mutation SNP C C T C3N-00293_T C3N-00293_N C C c.611G>A p.Arg204His p.R204H ENST00000366937 5/8 323 289 34 243 243 0 strelka-varscan-mutect ESRRG,missense_variant,p.Arg176His,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,missense_variant,p.Arg176His,ENST00000360012,NM_001243514.1;ESRRG,missense_variant,p.Arg204His,ENST00000366937,NM_001243518.1;ESRRG,missense_variant,p.Arg176His,ENST00000361525,NM_206594.2;ESRRG,missense_variant,p.Arg176His,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,missense_variant,p.Arg176His,ENST00000493603,NM_001243510.2;ESRRG,missense_variant,p.Arg176His,ENST00000366938,NM_001243513.1;ESRRG,missense_variant,p.Arg176His,ENST00000361395,;ESRRG,missense_variant,p.Arg199His,ENST00000408911,NM_001438.3;ESRRG,missense_variant,p.Arg176His,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,missense_variant,p.Arg176His,ENST00000616180,;ESRRG,missense_variant,p.Arg137His,ENST00000463665,NM_001243507.1;ESRRG,missense_variant,p.Arg176His,ENST00000487276,NM_001243512.1;ESRRG,missense_variant,p.Arg176His,ENST00000493748,NM_001243509.1;ESRRG,missense_variant,p.Arg176His,ENST00000475275,;ESRRG,3_prime_UTR_variant,,ENST00000586199,; T ENST00000366937 Transcript missense_variant 878/5365 611/1413 204/470 R/H cGt/cAt COSM1958540,COSM3943469 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 deleterious(0.03) 5/8 PROSITE_profiles:PS51030,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PIRSF_domain:PIRSF500939,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,Superfamily_domains:SSF57716,Superfamily_domains:SSF48508,Prints_domain:PR01292,Prints_domain:PR00398 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 216568092 216568092 C T 1 0 0 0 0 1 0 0 0 5124 536 19 1 1 ESRRG 1 216568092 Missense_Mutation SNP C C3N-00293_T 494939 216568092 32388330 30 12488 NVL 0 . GRCh38 1 224275380 224275380 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.2041G>A p.Asp681Asn p.D681N ENST00000281701 17/23 296 276 20 197 197 0 strelka-varscan-mutect NVL,missense_variant,p.Asp681Asn,ENST00000281701,NM_002533.3;NVL,missense_variant,p.Asp492Asn,ENST00000482491,;NVL,missense_variant,p.Asp575Asn,ENST00000391875,NM_206840.2;NVL,missense_variant,p.Asp590Asn,ENST00000469075,NM_001243147.1;NVL,missense_variant,p.Asp484Asn,ENST00000469968,;NVL,missense_variant,p.Asp492Asn,ENST00000340871,NM_001243146.1; T ENST00000281701 Transcript missense_variant 2301/3123 2041/2571 681/856 D/N Gat/Aat 1 -1 NVL HGNC HGNC:8070 protein_coding YES CCDS1541.1 ENSP00000281701 O15381 UPI0000073F3E NM_002533.3 deleterious(0) 17/23 hmmpanther:PTHR23077,hmmpanther:PTHR23077:SF55,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 224275380 224275380 C T 1 0 0 0 0 1 0 0 0 10853 826 29 3 3 NVL 1 224275380 Missense_Mutation SNP C C3N-00293_T 7707288 224275380 24681042 31 12489 RYR2 0 . GRCh38 1 237614590 237614590 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.5462T>A p.Leu1821His p.L1821H ENST00000366574 37/105 640 528 112 410 410 0 strelka-varscan-mutect RYR2,missense_variant,p.Leu1821His,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu1805His,ENST00000360064,; A ENST00000366574 Transcript missense_variant 5779/16562 5462/14904 1821/4967 L/H cTc/cAc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 37/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 237614590 237614590 T A 1 0 0 0 0 1 0 0 0 14029 1551 54 4 4 RYR2 1 237614590 Missense_Mutation SNP T C3N-00293_T 13339210 237614590 11341832 32 12490 ZP4 0 . GRCh38 1 237890066 237890066 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.286G>T p.Val96Phe p.V96F ENST00000611898 2/13 410 338 72 245 245 0 strelka-varscan-mutect ZP4,missense_variant,p.Val96Phe,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Val96Phe,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; A ENST00000611898 Transcript missense_variant 573/2474 286/1623 96/540 V/F Gtc/Ttc 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0.03) 2/13 hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 237890066 237890066 C A 1 0 0 0 0 1 0 0 0 18810 478 17 2 2 ZP4 1 237890066 Missense_Mutation SNP C C3N-00293_T 275476 237890066 11066356 33 12491 OR14K1 0 . GRCh38 1 247739128 247739128 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.514C>A p.Leu172Ile p.L172I ENST00000283225 1/1 609 570 39 302 302 0 strelka-varscan-mutect OR14K1,missense_variant,p.Leu172Ile,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; A ENST00000283225 Transcript missense_variant 514/945 514/945 172/314 L/I Cta/Ata 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA tolerated(0.78) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 247739128 247739128 C A 1 0 0 0 0 1 0 0 0 11026 796 28 2 2 OR14K1 1 247739128 Missense_Mutation SNP C C3N-00293_T 9849062 247739128 1217294 34 12492 OR14A16 0 . GRCh38 1 247814821 247814821 + Silent SNP C C T C3N-00293_T C3N-00293_N C C c.909G>A p.= p.K303K ENST00000357627 1/1 95 88 7 39 39 0 strelka-mutect OR14A16,synonymous_variant,p.=,ENST00000357627,NM_001001966.1; T ENST00000357627 Transcript synonymous_variant 909/930 909/930 303/309 K aaG/aaA COSM680618 1 -1 OR14A16 HGNC HGNC:15022 protein_coding YES CCDS31097.1 ENSP00000350248 Q8NHC5 UPI0000041CE2 NM_001001966.1 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF352,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS rs995142044 . 0 202 8 0 0 0 0 0 -14.33055 0.9999914 1 1 1 0 T 2 4 45 247814821 247814821 C T 1 0 0 0 0 0 0 0 1 11021 680 24 3 3 OR14A16 1 247814821 Silent SNP C C3N-00293_T 75693 247814821 1141601 35 12493 OR2T1 0 . GRCh38 1 248406535 248406535 + Nonsense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.541A>T p.Arg181Ter p.R181* ENST00000366474 1/1 295 239 56 182 181 1 strelka-varscan-mutect OR2T1,stop_gained,p.Arg181Ter,ENST00000366474,NM_030904.1; T ENST00000366474 Transcript stop_gained 541/1110 541/1110 181/369 R/* Aga/Tga 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH 1 SNV 1 PASS rs1159474130 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 45 248406535 248406535 A T 1 0 0 0 0 0 1 0 0 11094 296 11 4 4 OR2T1 1 248406535 Nonsense_Mutation SNP A C3N-00293_T 591714 248406535 549887 36 12494 OR2T27 0 . GRCh38 1 248650177 248650177 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.708G>A p.= p.K236K ENST00000344889 1/1 368 346 22 185 185 0 varscan-mutect OR2T27,synonymous_variant,p.=,ENST00000344889,NM_001001824.1; T ENST00000344889 Transcript synonymous_variant 708/954 708/954 236/317 K aaG/aaA 1 -1 OR2T27 HGNC HGNC:31252 protein_coding YES CCDS31124.1 ENSP00000342008 Q8NH04 UPI000004F239 NM_001001824.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF78,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 248650177 248650177 C T 1 0 0 0 0 0 0 0 1 11098 680 24 3 3 OR2T27 1 248650177 Silent SNP C C3N-00293_T 243642 248650177 306245 37 12495 CMPK2 0 . GRCh38 2 6865226 6865226 + Silent SNP T T A novel C3N-00293_T C3N-00293_N T T c.471A>T p.= p.P157P ENST00000256722 1/5 196 184 12 175 175 0 strelka-varscan-mutect CMPK2,synonymous_variant,p.=,ENST00000256722,NM_207315.3;CMPK2,synonymous_variant,p.=,ENST00000404168,NM_001256477.1;CMPK2,synonymous_variant,p.=,ENST00000458098,NM_001256478.1;RSAD2,upstream_gene_variant,,ENST00000442639,;CMPK2,intron_variant,,ENST00000478738,;CMPK2,intron_variant,,ENST00000465619,;CMPK2,intron_variant,,ENST00000470479,;RSAD2,upstream_gene_variant,,ENST00000474872,;CMPK2,upstream_gene_variant,,ENST00000491738,; A ENST00000256722 Transcript synonymous_variant 471/2884 471/1350 157/449 P ccA/ccT 1 -1 CMPK2 HGNC HGNC:27015 protein_coding YES CCDS42648.1 ENSP00000256722 Q5EBM0 UPI000016014D NM_207315.3 1/5 hmmpanther:PTHR10344:SF3,hmmpanther:PTHR10344,PIRSF_domain:PIRSF019736 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 6865226 6865226 T A 1 0 0 0 0 0 0 0 1 3356 1683 59 4 4 CMPK2 2 6865226 Silent SNP T C3N-00293_T 6865226 235328303 38 12496 NCOA1 0 . GRCh38 2 24710978 24710978 + Silent SNP G G A novel C3N-00293_T C3N-00293_N G G c.2466G>A p.= p.E822E ENST00000406961 14/23 315 296 19 233 233 0 strelka-varscan-mutect NCOA1,synonymous_variant,p.=,ENST00000405141,;NCOA1,synonymous_variant,p.=,ENST00000406961,;NCOA1,synonymous_variant,p.=,ENST00000288599,NM_147223.2;NCOA1,synonymous_variant,p.=,ENST00000348332,NM_003743.4;NCOA1,synonymous_variant,p.=,ENST00000395856,NM_147233.2;NCOA1,synonymous_variant,p.=,ENST00000407230,;NCOA1,non_coding_transcript_exon_variant,,ENST00000486198,; A ENST00000406961 Transcript synonymous_variant 3118/7289 2466/4326 822/1441 E gaG/gaA 1 1 NCOA1 HGNC HGNC:7668 protein_coding YES CCDS1712.1 ENSP00000385216 Q15788 UPI000006E1F7 14/23 hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 24710978 24710978 G A 1 0 0 0 0 0 0 0 1 10247 933 33 3 3 NCOA1 2 24710978 Silent SNP G C3N-00293_T 17845752 24710978 217482551 39 12497 NRXN1 0 . GRCh38 2 50346914 50346914 + Silent SNP C C A novel C3N-00293_T C3N-00293_N C C c.36G>T p.= p.L12L ENST00000342183 1/6 119 110 9 99 99 0 strelka-varscan-mutect NRXN1,synonymous_variant,p.=,ENST00000342183,NM_138735.2;NRXN1,synonymous_variant,p.=,ENST00000401710,;NRXN1,synonymous_variant,p.=,ENST00000628364,;NRXN1,intron_variant,,ENST00000406316,NM_004801.4;NRXN1,intron_variant,,ENST00000625672,;NRXN1,intron_variant,,ENST00000404971,NM_001135659.1;NRXN1,intron_variant,,ENST00000401669,;NRXN1,intron_variant,,ENST00000405472,;NRXN1,intron_variant,,ENST00000630543,;NRXN1,intron_variant,,ENST00000611589,;NRXN1,intron_variant,,ENST00000625320,;NRXN1,intron_variant,,ENST00000636298,;NRXN1,intron_variant,,ENST00000637889,;NRXN1,intron_variant,,ENST00000635264,;NRXN1,intron_variant,,ENST00000636818,;NRXN1,intron_variant,,ENST00000331040,;NRXN1,upstream_gene_variant,,ENST00000637906,; A ENST00000342183 Transcript synonymous_variant 841/3315 36/1329 12/442 L ctG/ctT 1 -1 NRXN1 HGNC HGNC:8008 protein_coding CCDS1845.1 ENSP00000341184 P58400 UPI000013D941 NM_138735.2 1/6 LOW SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -17.4546 0.999998 1 1 1 0 A 2 1 45 50346914 50346914 C A 1 0 0 0 0 0 0 0 1 10724 581 21 2 2 NRXN1 2 50346914 Silent SNP C C3N-00293_T 25635936 50346914 191846615 40 12498 TACR1 0 . GRCh38 2 75198734 75198734 + Silent SNP C C T C3N-00293_T C3N-00293_N C C c.201G>A p.= p.T67T ENST00000305249 1/5 332 310 22 245 244 1 strelka-varscan-mutect TACR1,synonymous_variant,p.=,ENST00000305249,NM_001058.3;TACR1,synonymous_variant,p.=,ENST00000409848,NM_015727.2; T ENST00000305249 Transcript synonymous_variant 967/4959 201/1224 67/407 T acG/acA COSM1023122 1 -1 TACR1 HGNC HGNC:11526 protein_coding YES CCDS1958.1 ENSP00000303522 P25103 UPI0000039D68 NM_001058.3 1/5 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF14,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 75198734 75198734 C T 1 0 0 0 0 0 0 0 1 15901 871 31 1 1 TACR1 2 75198734 Silent SNP C C3N-00293_T 24851820 75198734 166994795 41 12499 FAHD2B 0 . GRCh38 2 97090326 97090326 + Splice_Site SNP C C T novel C3N-00293_T C3N-00293_N C C c.246-1G>A p.X82_splice ENST00000414820 141 128 13 100 100 0 varscan-mutect FAHD2B,splice_acceptor_variant,,ENST00000414820,NM_001320848.1;FAHD2B,splice_acceptor_variant,,ENST00000272610,NM_199336.1;FAHD2B,splice_acceptor_variant,,ENST00000468548,;RP11-499E14.1,upstream_gene_variant,,ENST00000623986,;FAHD2B,splice_acceptor_variant,,ENST00000463096,;FAHD2B,splice_acceptor_variant,,ENST00000483657,;FAHD2B,intron_variant,,ENST00000474849,; T ENST00000414820 Transcript splice_acceptor_variant -/1388 246/945 82/314 1 -1 FAHD2B HGNC HGNC:25318 protein_coding YES CCDS2030.1 ENSP00000410470 Q6P2I3 UPI000004D29E NM_001320848.1 3/8 HIGH 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 45 97090326 97090326 C T 1 0 0 0 0 0 0 1 0 5246 927 32 3 3 FAHD2B 2 97090326 Splice_Site SNP C C3N-00293_T 21891592 97090326 145103203 42 12500 TSGA10 0 . GRCh38 2 99078662 99078662 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.879G>A p.Met293Ile p.M293I ENST00000393483 12/21 180 160 20 94 94 0 strelka-varscan-mutect TSGA10,missense_variant,p.Met293Ile,ENST00000393483,NM_025244.2;TSGA10,missense_variant,p.Met293Ile,ENST00000355053,NM_182911.3;TSGA10,missense_variant,p.Met293Ile,ENST00000410001,;TSGA10,missense_variant,p.Met293Ile,ENST00000393482,;TSGA10,missense_variant,p.Met293Ile,ENST00000409564,;TSGA10,non_coding_transcript_exon_variant,,ENST00000489546,;TSGA10,non_coding_transcript_exon_variant,,ENST00000488960,;TSGA10,intron_variant,,ENST00000478090,; T ENST00000393483 Transcript missense_variant 1724/3878 879/2097 293/698 M/I atG/atA 1 -1 TSGA10 HGNC HGNC:14927 protein_coding YES CCDS2037.1 ENSP00000377123 Q9BZW7 UPI0000072CE3 NM_025244.2 tolerated(0.87) 12/21 hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 99078662 99078662 C T 1 0 0 0 0 1 0 0 0 17123 840 29 3 3 TSGA10 2 99078662 Missense_Mutation SNP C C3N-00293_T 1988336 99078662 143114867 43 12501 RGPD4 0 . GRCh38 2 107872290 107872290 + Frame_Shift_Del DEL G G - C3N-00293_T C3N-00293_N G G c.4287delG p.Trp1429Ter p.W1429* ENST00000408999 20/23 470 426 44 266 266 0 varindel-pindel RGPD4,frameshift_variant,p.Trp1429Ter,ENST00000408999,NM_182588.2; - ENST00000408999 Transcript frameshift_variant 4363/5464 4286/5277 1429/1758 W/X tGg/tg COSM3564998,COSM3564999 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 20/23 PROSITE_profiles:PS50196,hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138,Gene3D:2.30.29.30,Pfam_domain:PF00638,SMART_domains:SM00160,Superfamily_domains:SSF50729 1,1 HIGH 1 deletion 1 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 45 107872290 107872290 G - 1 0 1 0 1 0 0 0 0 13460 1357 47 0 0 RGPD4 2 107872290 Frame_Shift_Del DEL G C3N-00293_T 8793628 107872290 134321239 44 12502 ACOXL 0 . GRCh38 2 110794138 110794138 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.309G>T p.= p.G103G ENST00000439055 5/18 329 309 20 257 257 0 strelka-varscan-mutect ACOXL,synonymous_variant,p.=,ENST00000389811,;ACOXL,synonymous_variant,p.=,ENST00000439055,NM_001142807.1;ACOXL,synonymous_variant,p.=,ENST00000340561,;ACOXL,upstream_gene_variant,,ENST00000417074,;ACOXL,downstream_gene_variant,,ENST00000448863,;ACOXL,non_coding_transcript_exon_variant,,ENST00000461340,; T ENST00000439055 Transcript synonymous_variant 533/2373 309/1743 103/580 G ggG/ggT 1 1 ACOXL HGNC HGNC:25621 protein_coding YES CCDS46389.1 ENSP00000407761 Q9NUZ1 UPI0001884BE2 NM_001142807.1 5/18 hmmpanther:PTHR10909:SF11,hmmpanther:PTHR10909,Gene3D:2.40.110.10,Pfam_domain:PF02770,Superfamily_domains:SSF56645 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 110794138 110794138 G T 1 0 0 0 0 0 0 0 1 203 1161 41 2 2 ACOXL 2 110794138 Silent SNP G C3N-00293_T 2921848 110794138 131399391 45 12503 TUBA3D 0 . GRCh38 2 131479399 131479399 + Silent SNP C C A rs561620153 C3N-00293_T C3N-00293_N C C c.318C>A p.= p.G106G ENST00000321253 3/5 319 301 18 236 236 0 varscan-mutect TUBA3D,synonymous_variant,p.=,ENST00000321253,NM_080386.3;MZT2A,downstream_gene_variant,,ENST00000309451,NM_001085365.1;TUBA3D,non_coding_transcript_exon_variant,,ENST00000409047,;MZT2A,downstream_gene_variant,,ENST00000410036,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,; A ENST00000321253 Transcript synonymous_variant 425/1546 318/1353 106/450 G ggC/ggA rs561620153 1 1 TUBA3D HGNC HGNC:24071 protein_coding YES CCDS33290.1 ENSP00000326042 Q13748 Q1ZYQ1 UPI0000027DB1 NM_080386.3 3/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.40.50.1440,Pfam_domain:PF00091,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161 LOW 1 SNV 1 1 PASS rs561620153 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 131479399 131479399 C A 1 0 0 0 0 0 0 0 1 17257 726 26 2 2 TUBA3D 2 131479399 Silent SNP C C3N-00293_T 20685261 131479399 110714130 46 12504 MAP3K19 0 . GRCh38 2 134986317 134986317 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.2555C>T p.Ser852Leu p.S852L ENST00000392915 10/13 150 141 9 63 63 0 strelka-varscan-mutect MAP3K19,missense_variant,p.Ser852Leu,ENST00000392915,;MAP3K19,missense_variant,p.Ser852Leu,ENST00000375845,NM_025052.4;MAP3K19,missense_variant,p.Ser739Leu,ENST00000358371,NM_001018044.2;MAP3K19,missense_variant,p.Ser757Leu,ENST00000637841,;MAP3K19,missense_variant,p.Ser242Leu,ENST00000437365,;MAP3K19,intron_variant,,ENST00000392917,NM_001282883.1;MAP3K19,intron_variant,,ENST00000375844,NM_001018046.2;MAP3K19,intron_variant,,ENST00000392918,NM_001018047.2;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,;MAP3K19,upstream_gene_variant,,ENST00000478805,; A ENST00000392915 Transcript missense_variant 3239/5030 2555/3987 852/1328 S/L tCa/tTa 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 tolerated(0.1) 10/13 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 134986317 134986317 G A 1 0 0 0 0 1 0 0 0 9172 1294 45 3 3 MAP3K19 2 134986317 Missense_Mutation SNP G C3N-00293_T 3506918 134986317 107207212 47 12505 SLC4A10 0 . GRCh38 2 161905831 161905831 + Silent SNP C C G novel C3N-00293_T C3N-00293_N C C c.1941C>G p.= p.L647L ENST00000446997 15/27 191 170 21 100 100 0 strelka-varscan-mutect SLC4A10,synonymous_variant,p.=,ENST00000375514,NM_001178016.1;SLC4A10,synonymous_variant,p.=,ENST00000415876,NM_022058.3;SLC4A10,synonymous_variant,p.=,ENST00000446997,NM_001178015.1;SLC4A10,synonymous_variant,p.=,ENST00000272716,;SLC4A10,synonymous_variant,p.=,ENST00000421911,;SLC4A10,downstream_gene_variant,,ENST00000493021,;SLC4A10,3_prime_UTR_variant,,ENST00000446228,; G ENST00000446997 Transcript synonymous_variant 2034/5551 1941/3357 647/1118 L ctC/ctG 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 15/27 hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834,Prints_domain:PR01231 LOW 1 SNV 1 1 PASS rs1407871071 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 45 161905831 161905831 C G 1 0 0 0 0 0 0 0 1 14928 813 29 4 4 SLC4A10 2 161905831 Silent SNP C C3N-00293_T 26919514 161905831 80287698 48 12506 SCN3A 0 . GRCh38 2 165090758 165090758 + Nonsense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.5395A>T p.Lys1799Ter p.K1799* ENST00000283254 28/28 604 572 32 350 350 0 varscan-mutect SCN3A,stop_gained,p.Lys1799Ter,ENST00000360093,;SCN3A,stop_gained,p.Lys1799Ter,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,stop_gained,p.Lys1750Ter,ENST00000409101,NM_001081677.1;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000431341,;AC013463.2,upstream_gene_variant,,ENST00000625505,;SCN3A,downstream_gene_variant,,ENST00000465043,;SCN3A,downstream_gene_variant,,ENST00000471697,; A ENST00000283254 Transcript stop_gained 5863/9091 5395/6003 1799/2000 K/* Aag/Tag 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 28/28 Prints_domain:PR00170,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 HIGH 1 SNV 1 1 PASS rs1170839078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 45 165090758 165090758 T A 1 0 0 0 0 0 1 0 0 14187 1850 64 4 4 SCN3A 2 165090758 Nonsense_Mutation SNP T C3N-00293_T 3184927 165090758 77102771 49 12507 XIRP2 0 . GRCh38 2 167249993 167249993 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.8601G>C p.Gln2867His p.Q2867H ENST00000409195 9/11 356 326 30 189 189 0 strelka-varscan-mutect XIRP2,missense_variant,p.Gln2867His,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Gln2645His,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Gln2692His,ENST00000628543,;XIRP2,missense_variant,p.Gln281His,ENST00000295237,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; C ENST00000409195 Transcript missense_variant 8690/12675 8601/10650 2867/3549 Q/H caG/caC 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.05) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 167249993 167249993 G C 1 0 0 0 0 1 0 0 0 17989 933 33 4 4 XIRP2 2 167249993 Missense_Mutation SNP G C3N-00293_T 2159235 167249993 74943536 50 12508 TTC30A 0 . GRCh38 2 177616993 177616994 + Frame_Shift_Ins INS - - T novel C3N-00293_T C3N-00293_N - - c.1708dupA p.Ser570LysfsTer6 p.S570Kfs*6 ENST00000355689 1/1 147 135 12 74 74 0 sindel-varindel TTC30A,frameshift_variant,p.Ser570LysfsTer6,ENST00000355689,NM_152275.3;AC073834.3,intron_variant,,ENST00000357045,; T ENST00000355689 Transcript frameshift_variant 1973-1974/5975 1708-1709/1998 570/665 S/KX agc/aAgc 1 -1 TTC30A HGNC HGNC:25853 protein_coding YES CCDS2276.1 ENSP00000347915 Q86WT1 UPI0000209161 NM_152275.3 1/1 hmmpanther:PTHR20931:SF3,hmmpanther:PTHR20931 HIGH insertion 1 PASS . . 0 207 0 2 0 0 0 0 -16.79823 0.9999997 1 1 1 0 T 7 5 45 177616993 177616993 - T 1 0 1 1 0 0 0 0 0 17207 797 28 0 0 TTC30A 2 177616993 Frame_Shift_Ins INS - C3N-00293_T 10367000 177616993 64576536 51 12509 TTN 0 . GRCh38 2 178620627 178620627 + Splice_Site SNP T T A rs869025548 C3N-00293_T C3N-00293_N T T c.45896-2A>T p.X15299_splice ENST00000589042 164 151 13 62 62 0 strelka-varscan-mutect TTN,splice_acceptor_variant,,ENST00000589042,NM_001267550.2;TTN,splice_acceptor_variant,,ENST00000591111,;TTN,splice_acceptor_variant,,ENST00000615779,NM_001256850.1;TTN,splice_acceptor_variant,,ENST00000342992,NM_133378.4;TTN,splice_acceptor_variant,,ENST00000460472,NM_003319.4;TTN,splice_acceptor_variant,,ENST00000342175,NM_133437.4;TTN,splice_acceptor_variant,,ENST00000359218,NM_133432.3;RP11-171I2.4,downstream_gene_variant,,ENST00000605334,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000456053,;TTN-AS1,downstream_gene_variant,,ENST00000604956,;TTN-AS1,downstream_gene_variant,,ENST00000627527,;TTN-AS1,downstream_gene_variant,,ENST00000626138,;TTN-AS1,downstream_gene_variant,,ENST00000592750,; A ENST00000589042 Transcript splice_acceptor_variant -/109224 45896/107976 15299/35991 rs869025548 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 247/362 likely_pathogenic HIGH 1 SNV 5 1 1 PASS rs869025548 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 45 178620627 178620627 T A 1 0 0 0 0 0 0 1 0 17245 1594 55 4 4 TTN 2 178620627 Splice_Site SNP T C3N-00293_T 1003634 178620627 63572902 52 12510 TTN 0 . GRCh38 2 178710826 178710826 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.28271A>T p.Gln9424Leu p.Q9424L ENST00000589042 98/363 334 315 19 243 243 0 strelka-varscan-mutect TTN,missense_variant,p.Gln9424Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gln9107Leu,ENST00000591111,;TTN,missense_variant,p.Gln9107Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gln8180Leu,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; A ENST00000589042 Transcript missense_variant 28496/109224 28271/107976 9424/35991 Q/L cAa/cTa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 98/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 178710826 178710826 T A 1 0 0 0 0 1 0 0 0 17245 1812 63 4 4 TTN 2 178710826 Missense_Mutation SNP T C3N-00293_T 90199 178710826 63482703 53 12511 SESTD1 0 . GRCh38 2 179124365 179124365 + Missense_Mutation SNP T T A rs147627596 C3N-00293_T C3N-00293_N T T c.1166A>T p.Asp389Val p.D389V ENST00000428443 11/18 139 130 9 59 59 0 strelka-varscan-mutect SESTD1,missense_variant,p.Asp389Val,ENST00000428443,NM_178123.4;SESTD1,missense_variant,p.Asp35Val,ENST00000446758,;SESTD1,missense_variant,p.Asp196Val,ENST00000426988,;SESTD1,intron_variant,,ENST00000335289,; A ENST00000428443 Transcript missense_variant,splice_region_variant 1483/10615 1166/2091 389/696 D/V gAt/gTt rs147627596 1 -1 SESTD1 HGNC HGNC:18379 protein_coding YES CCDS33338.1 ENSP00000415332 Q86VW0 UPI0000043424 NM_178123.4 deleterious(0.01) 11/18 Low_complexity_(Seg):seg,hmmpanther:PTHR22826:SF19,hmmpanther:PTHR22826 MODERATE 1 SNV 1 1 PASS rs147627596 . 0 207 3 0 0 0 0 0 -17.13717 1 1 1 1 0 A 3 1 45 179124365 179124365 T A 1 0 0 0 0 1 0 0 0 14404 1449 50 4 4 SESTD1 2 179124365 Missense_Mutation SNP T C3N-00293_T 413539 179124365 63069164 54 12512 FSIP2 0 . GRCh38 2 185796749 185796749 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.9880G>A p.Asp3294Asn p.D3294N ENST00000343098 16/23 241 226 15 97 97 0 strelka-varscan-mutect FSIP2,missense_variant,p.Asp3294Asn,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Asp3205Asn,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,missense_variant,p.Asp712Asn,ENST00000415915,; A ENST00000343098 Transcript missense_variant 9880/21054 9880/20991 3294/6996 D/N Gat/Aat 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 tolerated(1) 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 185796749 185796749 G A 1 0 0 0 0 1 0 0 0 5949 942 33 3 3 FSIP2 2 185796749 Missense_Mutation SNP G C3N-00293_T 6672384 185796749 56396780 55 12513 FSIP2 0 . GRCh38 2 185802234 185802235 + Frame_Shift_Ins INS - - G novel C3N-00293_T C3N-00293_N - - c.13198dupG p.Glu4400GlyfsTer16 p.E4400Gfs*16 ENST00000343098 17/23 210 183 27 106 106 0 sindel-varindel-pindel FSIP2,frameshift_variant,p.Glu4400GlyfsTer16,ENST00000343098,NM_173651.2;FSIP2,frameshift_variant,p.Glu4311GlyfsTer16,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; G ENST00000343098 Transcript frameshift_variant 13195-13196/21054 13195-13196/20991 4399/6996 R/RX agg/aGgg 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 HIGH insertion 5 3 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 45 185802234 185802234 - G 1 0 1 1 0 0 0 0 0 5949 63 3 0 0 FSIP2 2 185802234 Frame_Shift_Ins INS - C3N-00293_T 5485 185802234 56391295 56 12514 SF3B1 0 . GRCh38 2 197402110 197402110 + Missense_Mutation SNP T T C rs559063155 C3N-00293_T C3N-00293_N T T c.2098A>G p.Lys700Glu p.K700E ENST00000335508 15/25 161 143 18 117 117 0 strelka-varscan-mutect SF3B1,missense_variant,p.Lys700Glu,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,non_coding_transcript_exon_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; C ENST00000335508 Transcript missense_variant 2190/6526 2098/3915 700/1304 K/E Aaa/Gaa rs559063155,COSM84677 1 -1 SF3B1 HGNC HGNC:10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 UPI000013D493 NM_012433.2 deleterious(0) 15/25 hmmpanther:PTHR12097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs559063155 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 197402110 197402110 T C 1 0 0 0 0 1 0 0 0 14428 1792 62 5 5 SF3B1 2 197402110 Missense_Mutation SNP T C3N-00293_T 11599876 197402110 44791419 57 12515 PLCL1 0 . GRCh38 2 198084481 198084481 + Nonsense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.964C>T p.Gln322Ter p.Q322* ENST00000428675 2/6 263 222 41 132 132 0 strelka-varscan-mutect PLCL1,stop_gained,p.Gln245Ter,ENST00000437704,;PLCL1,stop_gained,p.Gln322Ter,ENST00000428675,NM_006226.3;PLCL1,stop_gained,p.Gln248Ter,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript stop_gained 1362/5125 964/3288 322/1095 Q/* Cag/Tag 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 2/6 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF09279,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 45 198084481 198084481 C T 1 0 0 0 0 0 1 0 0 12133 479 17 3 3 PLCL1 2 198084481 Nonsense_Mutation SNP C C3N-00293_T 682371 198084481 44109048 58 12516 AOX1 0 . GRCh38 2 200666699 200666699 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.3556G>T p.Asp1186Tyr p.D1186Y ENST00000374700 32/35 135 125 10 93 92 1 strelka-varscan-mutect AOX1,missense_variant,p.Asp1186Tyr,ENST00000374700,NM_001159.3;AOX1,missense_variant,p.Asp26Tyr,ENST00000439380,;AOX1,missense_variant,p.Asp72Tyr,ENST00000260930,;AOX1,non_coding_transcript_exon_variant,,ENST00000485106,;AOX1,non_coding_transcript_exon_variant,,ENST00000465297,; T ENST00000374700 Transcript missense_variant 3797/5074 3556/4017 1186/1338 D/Y Gac/Tac 1 1 AOX1 HGNC HGNC:553 protein_coding YES CCDS33360.1 ENSP00000363832 Q06278 UPI0000071863 NM_001159.3 deleterious(0.01) 32/35 hmmpanther:PTHR11908:SF86,hmmpanther:PTHR11908,Pfam_domain:PF02738,Gene3D:3.30.365.10,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02969,Superfamily_domains:SSF56003 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.28946 1 1 1 1 0 T 3 4 45 200666699 200666699 G T 1 0 0 0 0 1 0 0 0 839 942 33 2 2 AOX1 2 200666699 Missense_Mutation SNP G C3N-00293_T 2582218 200666699 41526830 59 12517 ATIC 0 . GRCh38 2 215338905 215338905 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.1225G>A p.Asp409Asn p.D409N ENST00000236959 12/16 350 329 21 146 146 0 strelka-varscan-mutect ATIC,missense_variant,p.Asp408Asn,ENST00000435675,;ATIC,missense_variant,p.Asp409Asn,ENST00000236959,NM_004044.6;ATIC,missense_variant,p.Asp78Asn,ENST00000426233,;ATIC,splice_region_variant,,ENST00000446622,;ATIC,splice_region_variant,,ENST00000443953,;ATIC,splice_region_variant,,ENST00000459796,;ATIC,splice_region_variant,,ENST00000479093,;ATIC,splice_region_variant,,ENST00000467388,;ATIC,downstream_gene_variant,,ENST00000427397,; A ENST00000236959 Transcript missense_variant,splice_region_variant 1551/2213 1225/1779 409/592 D/N Gat/Aat 1 1 ATIC HGNC HGNC:794 protein_coding YES CCDS2398.1 ENSP00000236959 P31939 V9HWH7 UPI000000122D NM_004044.6 tolerated(0.52) 12/16 HAMAP:MF_00139,hmmpanther:PTHR11692:SF0,hmmpanther:PTHR11692,Gene3D:3.40.140.20,Pfam_domain:PF01808,PIRSF_domain:PIRSF000414,TIGRFAM_domain:TIGR00355,SMART_domains:SM00798,Superfamily_domains:SSF53927 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 215338905 215338905 G A 1 0 0 0 0 1 0 0 0 1257 956 33 3 3 ATIC 2 215338905 Missense_Mutation SNP G C3N-00293_T 14672206 215338905 26854624 60 12518 CATIP 0 . GRCh38 2 218362760 218362760 + Missense_Mutation SNP T T G novel C3N-00293_T C3N-00293_N T T c.488T>G p.Phe163Cys p.F163C ENST00000289388 6/10 141 126 15 113 113 0 strelka-varscan-mutect CATIP,missense_variant,p.Phe163Cys,ENST00000289388,NM_198559.1;CATIP-AS2,upstream_gene_variant,,ENST00000411433,;CATIP-AS1,downstream_gene_variant,,ENST00000441749,;CATIP,intron_variant,,ENST00000481940,;CATIP,upstream_gene_variant,,ENST00000494447,;CATIP,downstream_gene_variant,,ENST00000480532,;CATIP,downstream_gene_variant,,ENST00000495773,;CATIP-AS1,downstream_gene_variant,,ENST00000425481,; G ENST00000289388 Transcript missense_variant 517/1323 488/1164 163/387 F/C tTc/tGc 1 1 CATIP HGNC HGNC:25062 protein_coding YES CCDS2414.1 ENSP00000289388 Q7Z7H3 UPI000019B2D3 NM_198559.1 deleterious(0.01) 6/10 hmmpanther:PTHR15505,hmmpanther:PTHR15505:SF3 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 218362760 218362760 T G 1 0 0 0 0 1 0 0 0 2386 1783 62 5 5 CATIP 2 218362760 Missense_Mutation SNP T C3N-00293_T 3023855 218362760 23830769 61 12519 SPEG 0 . GRCh38 2 219484393 219484393 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.6930C>T p.= p.P2310P ENST00000312358 30/41 569 526 43 465 465 0 strelka-varscan-mutect SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript synonymous_variant 7062/10782 6930/9804 2310/3267 P ccC/ccT 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 219484393 219484393 C T 1 0 0 0 0 0 0 0 1 15387 581 21 3 3 SPEG 2 219484393 Silent SNP C C3N-00293_T 1121633 219484393 22709136 62 12520 EPHA4 0 . GRCh38 2 221564113 221564113 + Silent SNP G G A novel C3N-00293_T C3N-00293_N G G c.441C>T p.= p.T147T ENST00000281821 3/18 267 253 14 205 204 1 strelka-varscan-mutect EPHA4,synonymous_variant,p.=,ENST00000281821,NM_001304536.1,NM_001304537.1,NM_004438.4;EPHA4,synonymous_variant,p.=,ENST00000409854,;EPHA4,synonymous_variant,p.=,ENST00000409938,;EPHA4,synonymous_variant,p.=,ENST00000541600,;EPHA4,synonymous_variant,p.=,ENST00000419964,;EPHA4,intron_variant,,ENST00000443796,;EPHA4,downstream_gene_variant,,ENST00000434266,;EPHA4,3_prime_UTR_variant,,ENST00000415749,; A ENST00000281821 Transcript synonymous_variant 483/6346 441/2961 147/986 T acC/acT 1 -1 EPHA4 HGNC HGNC:3388 protein_coding YES CCDS2447.1 ENSP00000281821 P54764 A0A024R452 UPI000012A077 NM_001304536.1,NM_001304537.1,NM_004438.4 3/18 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF337,hmmpanther:PTHR24416,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 221564113 221564113 G A 1 0 0 0 0 0 0 0 1 5016 1335 47 3 3 EPHA4 2 221564113 Silent SNP G C3N-00293_T 2079720 221564113 20629416 63 12521 DOCK10 0 . GRCh38 2 224795064 224795064 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.4969C>G p.Leu1657Val p.L1657V ENST00000258390 45/56 357 336 21 237 237 0 strelka-varscan-mutect DOCK10,missense_variant,p.Leu1651Val,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Leu1657Val,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492251,; C ENST00000258390 Transcript missense_variant 5037/7260 4969/6561 1657/2186 L/V Ctg/Gtg 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 deleterious(0) 45/56 Pfam_domain:PF06920,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 224795064 224795064 G C 1 0 0 0 0 1 0 0 0 4500 991 35 4 4 DOCK10 2 224795064 Missense_Mutation SNP G C3N-00293_T 3230951 224795064 17398465 64 12522 ALPPL2 0 . GRCh38 2 232407690 232407690 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.397G>C p.Ala133Pro p.A133P ENST00000295453 4/11 437 402 35 310 310 0 varscan-mutect ALPPL2,missense_variant,p.Ala133Pro,ENST00000295453,NM_031313.2; C ENST00000295453 Transcript missense_variant 449/2493 397/1599 133/532 A/P Gca/Cca 1 1 ALPPL2 HGNC HGNC:441 protein_coding YES CCDS2491.1 ENSP00000295453 P10696 UPI000013E259 NM_031313.2 deleterious(0.01) 4/11 hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF34,Pfam_domain:PF00245,Gene3D:3.40.720.10,SMART_domains:SM00098,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 232407690 232407690 G C 1 0 0 0 0 1 0 0 0 649 1319 46 4 4 ALPPL2 2 232407690 Missense_Mutation SNP G C3N-00293_T 7612626 232407690 9785839 65 12523 ITPR1 0 . GRCh38 3 4627854 4627854 + Silent SNP C C T rs367814655 C3N-00293_T C3N-00293_N C C c.255C>T p.= p.D85D ENST00000302640 5/61 107 98 9 82 82 0 strelka-varscan-mutect ITPR1,synonymous_variant,p.=,ENST00000354582,;ITPR1,synonymous_variant,p.=,ENST00000302640,NM_001168272.1;ITPR1,synonymous_variant,p.=,ENST00000357086,NM_001099952.2;ITPR1,synonymous_variant,p.=,ENST00000456211,NM_002222.5;ITPR1,synonymous_variant,p.=,ENST00000443694,;ITPR1,synonymous_variant,p.=,ENST00000544951,;ITPR1,non_coding_transcript_exon_variant,,ENST00000491868,;ITPR1,non_coding_transcript_exon_variant,,ENST00000467056,; T ENST00000302640 Transcript synonymous_variant 605/10197 255/8232 85/2743 D gaC/gaT rs367814655,COSM1423401,COSM1423402,COSM1423403 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 5/61 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52,Pfam_domain:PF08709,Gene3D:2.80.10.50 0,1,1,1 LOW 1 SNV 5 0,1,1,1 1 PASS rs367814655 . 0 206 4 0 0 0 0 0 -18.1645 1 1 1 1 0 T 2 4 45 4627854 4627854 C T 1 0 0 0 0 0 0 0 1 7826 535 19 1 1 ITPR1 3 4627854 Silent SNP C C3N-00293_T 4627854 193667705 66 12524 LRRC3B 0 . GRCh38 3 26709825 26709825 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.153C>T p.= p.S51S ENST00000396641 2/2 301 273 28 193 193 0 strelka-varscan-mutect LRRC3B,synonymous_variant,p.=,ENST00000396641,NM_052953.2;LRRC3B,synonymous_variant,p.=,ENST00000417744,NM_001317810.1;LRRC3B,synonymous_variant,p.=,ENST00000456208,NM_001317811.1;LRRC3B,synonymous_variant,p.=,ENST00000432040,;LRRC3B,synonymous_variant,p.=,ENST00000414619,;AC114877.3,upstream_gene_variant,,ENST00000446601,;LRRC3B,downstream_gene_variant,,ENST00000469437,; T ENST00000396641 Transcript synonymous_variant 745/1696 153/780 51/259 S agC/agT 1 1 LRRC3B HGNC HGNC:28105 protein_coding YES CCDS2644.1 ENSP00000379880 Q96PB8 A0A024R2R0 UPI000000D990 NM_052953.2 2/2 Gene3D:3.80.10.10,Pfam_domain:PF01462,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF346,SMART_domains:SM00013,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 26709825 26709825 C T 1 0 0 0 0 0 0 0 1 8891 709 25 3 3 LRRC3B 3 26709825 Silent SNP C C3N-00293_T 22081971 26709825 171585734 67 12525 ULK4 0 . GRCh38 3 41935875 41935875 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.304G>A p.Gly102Arg p.G102R ENST00000301831 4/37 262 247 15 135 135 0 strelka-varscan-mutect ULK4,missense_variant,p.Gly102Arg,ENST00000301831,NM_017886.2;ULK4,missense_variant,p.Gly102Arg,ENST00000420927,;ULK4,downstream_gene_variant,,ENST00000414606,;ULK4,non_coding_transcript_exon_variant,,ENST00000459802,;ULK4,3_prime_UTR_variant,,ENST00000453224,;ULK4,non_coding_transcript_exon_variant,,ENST00000497684,;ULK4,downstream_gene_variant,,ENST00000460978,;ULK4,downstream_gene_variant,,ENST00000431379,; T ENST00000301831 Transcript missense_variant 767/4613 304/3828 102/1275 G/R Gga/Aga 1 -1 ULK4 HGNC HGNC:15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 UPI0000E8267C NM_017886.2 deleterious(0) 4/37 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22983,hmmpanther:PTHR22983:SF15,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 41935875 41935875 C T 1 0 0 0 0 1 0 0 0 17501 603 21 3 3 ULK4 3 41935875 Missense_Mutation SNP C C3N-00293_T 15226050 41935875 156359684 68 12526 MUC13 0 . GRCh38 3 124908195 124908195 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1491G>T p.Met497Ile p.M497I ENST00000616727 11/12 516 457 59 452 451 1 strelka-varscan-mutect MUC13,missense_variant,p.Met497Ile,ENST00000616727,NM_033049.3;MUC13,downstream_gene_variant,,ENST00000462728,; A ENST00000616727 Transcript missense_variant 1530/2879 1491/1539 497/512 M/I atG/atT 1 -1 MUC13 HGNC HGNC:7511 protein_coding YES ENSP00000485028 Q9H3R2 UPI00000730EB NM_033049.3 tolerated(0.41) 11/12 hmmpanther:PTHR24041:SF24,hmmpanther:PTHR24041 MODERATE 1 SNV 1 1 PASS rs969504961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 124908195 124908195 C A 1 0 0 0 0 1 0 0 0 9970 710 25 2 2 MUC13 3 124908195 Missense_Mutation SNP C C3N-00293_T 82972320 124908195 73387364 69 12527 PRR23B 0 . GRCh38 3 139020251 139020251 + Silent SNP G G A rs771282672 C3N-00293_T C3N-00293_N G G c.411C>T p.= p.V137V ENST00000329447 1/1 417 372 45 335 335 0 strelka-varscan-mutect PRR23B,synonymous_variant,p.=,ENST00000329447,NM_001013650.2;MRPS22,intron_variant,,ENST00000495075,; A ENST00000329447 Transcript synonymous_variant 676/1896 411/798 137/265 V gtC/gtT rs771282672 1 -1 PRR23B HGNC HGNC:33764 protein_coding YES CCDS33868.1 ENSP00000328768 Q6ZRT6 UPI00001C0F1A NM_001013650.2 1/1 hmmpanther:PTHR31813:SF7,hmmpanther:PTHR31813,Pfam_domain:PF10630 LOW SNV 1 PASS rs771282672 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 139020251 139020251 G A 1 0 0 0 0 0 0 0 1 12730 1045 37 1 1 PRR23B 3 139020251 Silent SNP G C3N-00293_T 14112056 139020251 59275308 70 12528 RASA2 0 . GRCh38 3 141577064 141577064 + Silent SNP C C T rs765379914 C3N-00293_T C3N-00293_N C C c.1548C>T p.= p.A516A ENST00000286364 15/24 339 317 22 209 209 0 strelka-varscan-mutect RASA2,synonymous_variant,p.=,ENST00000286364,NM_001303246.1,NM_001303245.1,NM_006506.3;RASA2,synonymous_variant,p.=,ENST00000452898,;RASA2,upstream_gene_variant,,ENST00000509118,;RASA2,upstream_gene_variant,,ENST00000509032,;RASA2,upstream_gene_variant,,ENST00000505833,; T ENST00000286364 Transcript synonymous_variant 1583/5614 1548/2550 516/849 A gcC/gcT rs765379914,COSM4114064,COSM4114065,COSM729018,COSM729019 1 1 RASA2 HGNC HGNC:9872 protein_coding YES CCDS3117.1 ENSP00000286364 Q15283 UPI00001351F5 NM_001303246.1,NM_001303245.1,NM_006506.3 15/24 Low_complexity_(Seg):seg,PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF21,PROSITE_patterns:PS00509,Gene3D:1.10.506.10,Pfam_domain:PF00616,SMART_domains:SM00323,Superfamily_domains:SSF48350 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS rs765379914 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 141577064 141577064 C T 1 0 0 0 0 0 0 0 1 13220 639 23 1 1 RASA2 3 141577064 Silent SNP C C3N-00293_T 2556813 141577064 56718495 71 12529 ATR 0 . GRCh38 3 142469472 142469472 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.6417G>C p.Leu2139Phe p.L2139F ENST00000350721 38/47 294 275 19 164 164 0 strelka-varscan-mutect ATR,missense_variant,p.Leu2139Phe,ENST00000350721,NM_001184.3;ATR,upstream_gene_variant,,ENST00000513291,;RP11-383G6.3,intron_variant,,ENST00000460977,; G ENST00000350721 Transcript missense_variant 6539/8249 6417/7935 2139/2644 L/F ttG/ttC 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 tolerated(0.07) 38/47 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -5.175305 0.9848347 1 1 1 0 G 3 3 45 142469472 142469472 C G 1 0 0 0 0 1 0 0 0 1356 825 29 4 4 ATR 3 142469472 Missense_Mutation SNP C C3N-00293_T 892408 142469472 55826087 72 12530 SLC9A9 0 . GRCh38 3 143796845 143796845 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.437C>A p.Ala146Glu p.A146E ENST00000316549 3/16 119 112 7 75 75 0 strelka-varscan-mutect SLC9A9,missense_variant,p.Ala146Glu,ENST00000316549,NM_173653.3;SLC9A9,intron_variant,,ENST00000474151,;SLC9A9,3_prime_UTR_variant,,ENST00000474727,; T ENST00000316549 Transcript missense_variant 646/3627 437/1938 146/645 A/E gCa/gAa 1 -1 SLC9A9 HGNC HGNC:20653 protein_coding YES CCDS33872.1 ENSP00000320246 Q8IVB4 UPI0000074664 NM_173653.3 deleterious(0) 3/16 Pfam_domain:PF00999,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF61,TIGRFAM_domain:TIGR00840,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1200091128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 143796845 143796845 G T 1 0 0 0 0 1 0 0 0 15003 1319 46 2 2 SLC9A9 3 143796845 Missense_Mutation SNP G C3N-00293_T 1327373 143796845 54498714 73 12531 P2RY13 0 . GRCh38 3 151328140 151328140 + Frame_Shift_Del DEL C C - novel C3N-00293_T C3N-00293_N C C c.916delG p.Ala306GlnfsTer10 p.A306Qfs*10 ENST00000325602 2/2 172 155 17 80 80 0 sindel-varindel-pindel P2RY13,frameshift_variant,p.Ala306GlnfsTer10,ENST00000325602,NM_176894.2;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;MED12L,intron_variant,,ENST00000468305,; - ENST00000325602 Transcript frameshift_variant 936/2764 916/1065 306/354 A/X Gca/ca 1 -1 P2RY13 HGNC HGNC:4537 protein_coding YES CCDS3158.2 ENSP00000320376 Q9BPV8 UPI000020A470 NM_176894.2 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF10,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH 1 deletion 1 1 PASS . . 0 202 2 3 3 0 0 0 -7.102838 0.7537578 1 1 1 0 - 7 5 45 151328140 151328140 C - 1 0 1 0 1 0 0 0 0 11423 739 26 0 0 P2RY13 3 151328140 Frame_Shift_Del DEL C C3N-00293_T 7531295 151328140 46967419 74 12532 MED12L 0 . GRCh38 3 151365044 151365044 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.2918G>T p.Arg973Leu p.R973L ENST00000474524 20/43 389 344 45 279 279 0 strelka-varscan-mutect MED12L,missense_variant,p.Arg973Leu,ENST00000474524,NM_053002.5;MED12L,missense_variant,p.Arg833Leu,ENST00000273432,;P2RY12,intron_variant,,ENST00000302632,NM_176876.2,NM_022788.4; T ENST00000474524 Transcript missense_variant 2956/10744 2918/6438 973/2145 R/L cGa/cTa 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 tolerated(0.76) 20/43 hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS rs1415187136 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 151365044 151365044 G T 1 0 0 0 0 1 0 0 0 9368 1058 37 1 1 MED12L 3 151365044 Missense_Mutation SNP G C3N-00293_T 36904 151365044 46930515 75 12533 NAALADL2 0 . GRCh38 3 175463432 175463432 + Silent SNP A A T novel C3N-00293_T C3N-00293_N A A c.1266A>T p.= p.T422T ENST00000454872 7/14 225 209 16 114 114 0 strelka-varscan-mutect NAALADL2,synonymous_variant,p.=,ENST00000454872,NM_207015.2;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000489299,;NAALADL2,3_prime_UTR_variant,,ENST00000414826,; T ENST00000454872 Transcript synonymous_variant 1394/9865 1266/2388 422/795 T acA/acT 1 1 NAALADL2 HGNC HGNC:23219 protein_coding YES CCDS46960.1 ENSP00000404705 Q58DX5 UPI0000161608 NM_207015.2 7/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404,Gene3D:3.40.630.10,Superfamily_domains:SSF52025,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 175463432 175463432 A T 1 0 0 0 0 0 0 0 1 10134 175 7 4 4 NAALADL2 3 175463432 Silent SNP A C3N-00293_T 24098388 175463432 22832127 76 12534 SLC26A1 0 . GRCh38 4 989760 989760 + Silent SNP G G A rs771840183 C3N-00293_T C3N-00293_N G G c.1179C>T p.= p.F393F ENST00000361661 4/4 372 348 24 237 237 0 strelka-varscan-mutect SLC26A1,synonymous_variant,p.=,ENST00000361661,NM_213613.3;SLC26A1,synonymous_variant,p.=,ENST00000398516,NM_022042.3;IDUA,intron_variant,,ENST00000247933,NM_000203.4;SLC26A1,intron_variant,,ENST00000398520,NM_134425.2;SLC26A1,intron_variant,,ENST00000622731,;IDUA,intron_variant,,ENST00000502910,;IDUA,intron_variant,,ENST00000504568,;IDUA,upstream_gene_variant,,ENST00000509948,;IDUA,upstream_gene_variant,,ENST00000514192,;DGKQ,upstream_gene_variant,,ENST00000510286,;IDUA,downstream_gene_variant,,ENST00000509744,;SLC26A1,downstream_gene_variant,,ENST00000513138,;IDUA,intron_variant,,ENST00000514698,;IDUA,intron_variant,,ENST00000506561,;IDUA,intron_variant,,ENST00000508168,; A ENST00000361661 Transcript synonymous_variant 1557/3660 1179/2106 393/701 F ttC/ttT rs771840183,COSM4653858 1 -1 SLC26A1 HGNC HGNC:10993 protein_coding YES CCDS33934.1 ENSP00000354721 Q9H2B4 UPI000013D9D4 NM_213613.3 4/4 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF31,TIGRFAM_domain:TIGR00815,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs771840183 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 989760 989760 G A 1 0 0 0 0 0 0 0 1 14784 1049 37 1 1 SLC26A1 4 989760 Silent SNP G C3N-00293_T 989760 189224795 77 12535 CRIPAK 0 . GRCh38 4 1394857 1394857 + Missense_Mutation SNP G G T rs763178753 C3N-00293_T C3N-00293_N G G c.346G>T p.Ala116Ser p.A116S ENST00000324803 1/1 933 878 55 679 679 0 varscan-mutect CRIPAK,missense_variant,p.Ala116Ser,ENST00000324803,NM_175918.3; T ENST00000324803 Transcript missense_variant 3306/4438 346/1341 116/446 A/S Gcc/Tcc rs763178753,COSM3010975 1 1 CRIPAK HGNC HGNC:26619 protein_coding YES CCDS3349.1 ENSP00000323978 Q8N1N5 UPI0000070390 NM_175918.3 tolerated(0.46) 1/1 SMART_domains:SM00508 0,1 MODERATE 1 SNV 0,1 1 PASS rs763178753 . 0 201 0 0 9 0 0 0 -7.231774 0.0454046 1 1 0 0 T 3 4 45 1394857 1394857 G T 1 0 0 0 0 1 0 0 0 3678 1087 38 1 1 CRIPAK 4 1394857 Missense_Mutation SNP G C3N-00293_T 405097 1394857 188819698 78 12536 LCORL 0 . GRCh38 4 17886127 17886127 + Silent SNP G G C novel C3N-00293_T C3N-00293_N G G c.717C>G p.= p.T239T ENST00000382226 6/7 182 165 17 111 111 0 strelka-varscan-mutect LCORL,synonymous_variant,p.=,ENST00000635767,;LCORL,synonymous_variant,p.=,ENST00000326877,NM_153686.7;LCORL,synonymous_variant,p.=,ENST00000382226,NM_001166139.1;LCORL,synonymous_variant,p.=,ENST00000382224,;LCORL,non_coding_transcript_exon_variant,,ENST00000510121,;LCORL,3_prime_UTR_variant,,ENST00000637787,;LCORL,intron_variant,,ENST00000510451,; C ENST00000382226 Transcript synonymous_variant 826/5009 717/1809 239/602 T acC/acG 1 -1 LCORL HGNC HGNC:30776 protein_coding YES CCDS54749.1 ENSP00000371661 Q8N3X6 UPI00015E0F98 NM_001166139.1 6/7 hmmpanther:PTHR21545,hmmpanther:PTHR21545:SF10,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 45 17886127 17886127 G C 1 0 0 0 0 0 0 0 1 8596 1335 47 4 4 LCORL 4 17886127 Silent SNP G C3N-00293_T 16491270 17886127 172328428 79 12537 KCTD8 0 . GRCh38 4 44175133 44175133 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.1079G>C p.Cys360Ser p.C360S ENST00000360029 2/2 124 115 9 112 112 0 strelka-varscan-mutect KCTD8,missense_variant,p.Cys360Ser,ENST00000360029,NM_198353.2;KCTD8,missense_variant,p.Cys96Ser,ENST00000515268,; G ENST00000360029 Transcript missense_variant 1363/2587 1079/1422 360/473 C/S tGt/tCt 1 -1 KCTD8 HGNC HGNC:22394 protein_coding YES CCDS3467.1 ENSP00000353129 Q6ZWB6 UPI00001C08D6 NM_198353.2 tolerated(1) 2/2 MODERATE 1 SNV 1 1 PASS rs1173087794 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 44175133 44175133 C G 1 0 0 0 0 1 0 0 0 8032 478 17 4 4 KCTD8 4 44175133 Missense_Mutation SNP C C3N-00293_T 26289006 44175133 146039422 80 12538 GABRA4 0 . GRCh38 4 46965075 46965075 + Missense_Mutation SNP G G T rs866970927 C3N-00293_T C3N-00293_N G G c.1029C>A p.Phe343Leu p.F343L ENST00000264318 8/9 213 193 20 158 157 1 strelka-varscan-mutect GABRA4,missense_variant,p.Phe343Leu,ENST00000264318,NM_000809.3,NM_001204266.1;GABRA4,3_prime_UTR_variant,,ENST00000508560,;GABRA4,3_prime_UTR_variant,,ENST00000511523,; T ENST00000264318 Transcript missense_variant 2012/11973 1029/1665 343/554 F/L ttC/ttA rs866970927 1 -1 GABRA4 HGNC HGNC:4078 protein_coding YES CCDS3473.1 ENSP00000264318 P48169 X5D7F5 UPI0000074200 NM_000809.3,NM_001204266.1 deleterious(0.03) 8/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF393,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Gene3D:1.20.58.390,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS rs866970927 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 46965075 46965075 G T 1 0 0 0 0 1 0 0 0 6034 1281 45 2 2 GABRA4 4 46965075 Missense_Mutation SNP G C3N-00293_T 2789942 46965075 143249480 81 12539 KDR 0 . GRCh38 4 55094858 55094858 + Missense_Mutation SNP G G A C3N-00293_T C3N-00293_N G G c.2915C>T p.Ser972Leu p.S972L ENST00000263923 21/30 365 343 22 280 280 0 strelka-varscan-mutect KDR,missense_variant,p.Ser972Leu,ENST00000263923,NM_002253.2;RP11-530I17.1,downstream_gene_variant,,ENST00000511222,;KDR,non_coding_transcript_exon_variant,,ENST00000509309,; A ENST00000263923 Transcript missense_variant 3211/5831 2915/4071 972/1356 S/L tCa/tTa COSM3775894 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 tolerated(0.46) 21/30 Pfam_domain:PF07714,PROSITE_profiles:PS50011,Low_complexity_(Seg):seg,SMART_domains:SM00219 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 55094858 55094858 G A 1 0 0 0 0 1 0 0 0 8059 1294 45 3 3 KDR 4 55094858 Missense_Mutation SNP G C3N-00293_T 8129783 55094858 135119697 82 12540 UGT2B28 0 . GRCh38 4 69281030 69281030 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.530G>C p.Gly177Ala p.G177A ENST00000335568 1/6 146 124 22 92 92 0 strelka-varscan-mutect UGT2B28,missense_variant,p.Gly177Ala,ENST00000335568,NM_053039.1;UGT2B28,missense_variant,p.Gly177Ala,ENST00000511240,NM_001207004.1; C ENST00000335568 Transcript missense_variant 532/1833 530/1590 177/529 G/A gGc/gCc 1 1 UGT2B28 HGNC HGNC:13479 protein_coding YES CCDS3528.1 ENSP00000334276 Q9BY64 UPI0000137A9F NM_053039.1 tolerated(0.16) 1/6 Gene3D:3.40.50.2000,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF365,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 69281030 69281030 G C 1 0 0 0 0 1 0 0 0 17484 1203 42 4 4 UGT2B28 4 69281030 Missense_Mutation SNP G C3N-00293_T 14186172 69281030 120933525 83 12541 OPRPN 0 . GRCh38 4 70409797 70409797 + Missense_Mutation SNP C C T rs753759585 C3N-00293_T C3N-00293_N C C c.469C>T p.Pro157Ser p.P157S ENST00000399575 3/3 133 120 13 85 85 0 strelka-varscan-mutect OPRPN,missense_variant,p.Pro157Ser,ENST00000399575,NM_021225.4;OPRPN,non_coding_transcript_exon_variant,,ENST00000514338,;OPRPN,non_coding_transcript_exon_variant,,ENST00000505023,; T ENST00000399575 Transcript missense_variant 643/1040 469/747 157/248 P/S Ccc/Tcc rs753759585,COSM4496182 1 1 OPRPN HGNC HGNC:17279 protein_coding YES CCDS43235.1 ENSP00000382485 Q99935 UPI000020BE52 NM_021225.4 tolerated_low_confidence(0.36) 3/3 hmmpanther:PTHR14179,hmmpanther:PTHR14179:SF8,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753759585 . 0 203 0 6 0 0 0 0 -18.46387 0.9963377 1 1 1 0 T 3 4 45 70409797 70409797 C T 1 0 0 0 0 1 0 0 0 10963 855 30 3 3 OPRPN 4 70409797 Missense_Mutation SNP C C3N-00293_T 1128767 70409797 119804758 84 12542 SLC4A4 0 . GRCh38 4 71453534 71453534 + Silent SNP G G A rs754788772 C3N-00293_T C3N-00293_N G G c.1362G>A p.= p.A454A ENST00000425175 12/25 301 282 19 186 186 0 strelka-varscan-mutect SLC4A4,synonymous_variant,p.=,ENST00000340595,NM_003759.3;SLC4A4,synonymous_variant,p.=,ENST00000425175,NM_001134742.1;SLC4A4,synonymous_variant,p.=,ENST00000264485,NM_001098484.2;SLC4A4,synonymous_variant,p.=,ENST00000351898,;SLC4A4,synonymous_variant,p.=,ENST00000512686,;SLC4A4,non_coding_transcript_exon_variant,,ENST00000514331,; A ENST00000425175 Transcript synonymous_variant 1479/7596 1362/3285 454/1094 A gcG/gcA rs754788772,COSM1057182,COSM1057183 1 1 SLC4A4 HGNC HGNC:11030 protein_coding YES CCDS47071.1 ENSP00000393557 Q9Y6R1 A5JJ20 UPI000152897D NM_001134742.1 12/25 Gene3D:1bzkA00,Pfam_domain:PF00955,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF10,TIGRFAM_domain:TIGR00834 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs754788772 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 71453534 71453534 G A 1 0 0 0 0 0 0 0 1 14933 1074 38 1 1 SLC4A4 4 71453534 Silent SNP G C3N-00293_T 1043737 71453534 118761021 85 12543 MMRN1 0 . GRCh38 4 89895250 89895250 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.279G>T p.Glu93Asp p.E93D ENST00000394980 2/9 331 297 34 232 232 0 strelka-varscan-mutect MMRN1,missense_variant,p.Glu93Asp,ENST00000394980,;MMRN1,missense_variant,p.Glu93Asp,ENST00000264790,NM_007351.2; T ENST00000394980 Transcript missense_variant 598/5217 279/3687 93/1228 E/D gaG/gaT 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 tolerated_low_confidence(0.1) 2/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 89895250 89895250 G T 1 0 0 0 0 1 0 0 0 9633 991 35 2 2 MMRN1 4 89895250 Missense_Mutation SNP G C3N-00293_T 18441716 89895250 100319305 86 12544 RP11-766F14.2 0 . GRCh38 4 99653318 99653318 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1331C>A p.Thr444Lys p.T444K ENST00000511828 1/2 93 88 5 57 57 0 strelka-mutect RP11-766F14.2,missense_variant,p.Thr444Lys,ENST00000511828,; T ENST00000511828 Transcript missense_variant 1331/10086 1331/5382 444/1793 T/K aCg/aAg 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE deleterious_low_confidence(0.01) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -10.59913 0.999996 1 1 1 0 T 3 4 45 99653318 99653318 G T 1 0 0 0 0 1 0 0 0 13762 1145 40 1 1 RP11-766F14.2 4 99653318 Missense_Mutation SNP G C3N-00293_T 9758068 99653318 90561237 87 12545 NDST4 0 . GRCh38 4 114845871 114845871 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.2067C>G p.Ile689Met p.I689M ENST00000264363 10/14 236 207 29 173 173 0 strelka-varscan-mutect NDST4,missense_variant,p.Ile310Met,ENST00000613194,;NDST4,missense_variant,p.Ile689Met,ENST00000264363,NM_022569.1;NDST4,missense_variant,p.Ile310Met,ENST00000504854,; C ENST00000264363 Transcript missense_variant 2746/3351 2067/2619 689/872 I/M atC/atG 1 -1 NDST4 HGNC HGNC:20779 protein_coding YES CCDS3706.1 ENSP00000264363 Q9H3R1 UPI000006CED7 NM_022569.1 deleterious(0) 10/14 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF45,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 114845871 114845871 G C 1 0 0 0 0 1 0 0 0 10279 1280 45 4 4 NDST4 4 114845871 Missense_Mutation SNP G C3N-00293_T 15192553 114845871 75368684 88 12546 ANXA10 0 . GRCh38 4 168184637 168184637 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.862C>G p.Arg288Gly p.R288G ENST00000359299 11/12 203 191 12 124 124 0 strelka-varscan-mutect ANXA10,missense_variant,p.Arg288Gly,ENST00000359299,NM_007193.4;ANXA10,non_coding_transcript_exon_variant,,ENST00000507278,; G ENST00000359299 Transcript missense_variant 1048/1417 862/975 288/324 R/G Cga/Gga 1 1 ANXA10 HGNC HGNC:534 protein_coding YES CCDS34096.1 ENSP00000352248 Q9UJ72 UPI0000169E98 NM_007193.4 deleterious(0.05) 11/12 hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF100,Gene3D:1.10.220.10,Pfam_domain:PF00191,SMART_domains:SM00335,Superfamily_domains:SSF47874 MODERATE 1 SNV 1 1 PASS rs1192134579 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 168184637 168184637 C G 1 0 0 0 0 1 0 0 0 822 528 19 4 4 ANXA10 4 168184637 Missense_Mutation SNP C C3N-00293_T 53338766 168184637 22029918 89 12547 TENM3 0 . GRCh38 4 182673160 182673160 + Nonsense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.1267C>T p.Gln423Ter p.Q423* ENST00000511685 7/28 274 252 22 159 159 0 strelka-varscan-mutect TENM3,stop_gained,p.Gln423Ter,ENST00000511685,NM_001080477.2; T ENST00000511685 Transcript stop_gained 1390/10896 1267/8100 423/2699 Q/* Cag/Tag 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 7/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 45 182673160 182673160 C T 1 0 0 0 0 0 1 0 0 16173 827 29 3 3 TENM3 4 182673160 Nonsense_Mutation SNP C C3N-00293_T 14488523 182673160 7541395 90 12548 ADAMTS16 0 . GRCh38 5 5239205 5239205 + Missense_Mutation SNP G G T rs566228851 C3N-00293_T C3N-00293_N G G c.2209G>T p.Val737Leu p.V737L ENST00000274181 15/23 58 54 4 45 45 0 strelka-mutect ADAMTS16,missense_variant,p.Val737Leu,ENST00000274181,NM_139056.2;ADAMTS16,downstream_gene_variant,,ENST00000513709,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 2347/4979 2209/3675 737/1224 V/L Gtg/Ttg rs566228851 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 15/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Prints_domain:PR01857 MODERATE 1 SNV 2 1 PASS rs566228851 . 0 203 6 0 0 0 0 0 -9.864083 0.9999996 1 1 1 0 T 3 4 45 5239205 5239205 G T 1 0 0 0 0 1 0 0 0 305 1261 44 2 2 ADAMTS16 5 5239205 Missense_Mutation SNP G C3N-00293_T 5239205 176299054 91 12549 ICE1 0 . GRCh38 5 5464447 5464447 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.5113G>T p.Ala1705Ser p.A1705S ENST00000296564 13/19 367 322 45 261 261 0 strelka-varscan-mutect ICE1,missense_variant,p.Ala1705Ser,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 5335/7927 5113/6801 1705/2266 A/S Gcc/Tcc 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0.02) 13/19 Low_complexity_(Seg):seg,hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 45 5464447 5464447 G T 1 0 0 0 0 1 0 0 0 7384 971 34 2 2 ICE1 5 5464447 Missense_Mutation SNP G C3N-00293_T 225242 5464447 176073812 92 12550 ADCY2 0 . GRCh38 5 7414703 7414703 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.341G>T p.Trp114Leu p.W114L ENST00000338316 2/25 313 279 34 219 219 0 strelka-varscan-mutect ADCY2,missense_variant,p.Trp114Leu,ENST00000338316,NM_020546.2;ADCY2,non_coding_transcript_exon_variant,,ENST00000498598,;ADCY2,non_coding_transcript_exon_variant,,ENST00000484965,; T ENST00000338316 Transcript missense_variant 430/6575 341/3276 114/1091 W/L tGg/tTg 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0.02) 2/25 Pfam_domain:PF16214,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 7414703 7414703 G T 1 0 0 0 0 1 0 0 0 338 1357 47 2 2 ADCY2 5 7414703 Missense_Mutation SNP G C3N-00293_T 1950256 7414703 174123556 93 12551 BASP1 0 . GRCh38 5 17275496 17275496 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.280G>C p.Ala94Pro p.A94P ENST00000322611 2/2 63 56 7 34 34 0 strelka-mutect BASP1,missense_variant,p.Ala94Pro,ENST00000322611,NM_006317.4;BASP1,missense_variant,p.Ala94Pro,ENST00000616743,NM_001271606.1;BASP1,downstream_gene_variant,,ENST00000606445,; C ENST00000322611 Transcript missense_variant 540/1878 280/684 94/227 A/P Gca/Cca 1 1 BASP1 HGNC HGNC:957 protein_coding YES CCDS3888.1 ENSP00000319281 P80723 UPI0000140E98 NM_006317.4 tolerated(0.06) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23212,hmmpanther:PTHR23212:SF0,Pfam_domain:PF05466 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.9988 1 1 1 1 0 C 3 2 45 17275496 17275496 G C 1 0 0 0 0 1 0 0 0 1469 1203 42 4 4 BASP1 5 17275496 Missense_Mutation SNP G C3N-00293_T 9860793 17275496 164262763 94 12552 TARS 0 . GRCh38 5 33461290 33461290 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1645G>C p.Glu549Gln p.E549Q ENST00000455217 14/20 105 90 15 53 53 0 varscan-mutect TARS,missense_variant,p.Glu516Gln,ENST00000265112,NM_152295.4;TARS,missense_variant,p.Glu516Gln,ENST00000502553,NM_001258437.1;TARS,missense_variant,p.Glu549Gln,ENST00000455217,NM_001258438.1;TARS,non_coding_transcript_exon_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,downstream_gene_variant,,ENST00000504698,; C ENST00000455217 Transcript missense_variant 1767/2523 1645/2271 549/756 E/Q Gag/Cag 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 deleterious(0) 14/20 PROSITE_profiles:PS50862,HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF36,TIGRFAM_domain:TIGR00418,Gene3D:3.30.930.10,Pfam_domain:PF00587,Superfamily_domains:SSF55681 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 33461290 33461290 G C 1 0 0 0 0 1 0 0 0 15958 1304 45 4 4 TARS 5 33461290 Missense_Mutation SNP G C3N-00293_T 16185794 33461290 148076969 95 12553 IL7R 0 . GRCh38 5 35860950 35860950 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.181G>A p.Asp61Asn p.D61N ENST00000303115 2/8 464 435 29 311 311 0 strelka-varscan-mutect IL7R,missense_variant,p.Asp61Asn,ENST00000303115,NM_002185.3;IL7R,missense_variant,p.Asp61Asn,ENST00000506850,;IL7R,missense_variant,p.Asp61Asn,ENST00000511982,;IL7R,downstream_gene_variant,,ENST00000508941,;IL7R,downstream_gene_variant,,ENST00000515665,;IL7R,non_coding_transcript_exon_variant,,ENST00000511031,;IL7R,missense_variant,p.Asp61Asn,ENST00000514217,; A ENST00000303115 Transcript missense_variant 310/4626 181/1380 61/459 D/N Gac/Aac 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 tolerated(0.06) 2/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 35860950 35860950 G A 1 0 0 0 0 1 0 0 0 7609 1174 41 3 3 IL7R 5 35860950 Missense_Mutation SNP G C3N-00293_T 2399660 35860950 145677309 96 12554 BDP1 0 . GRCh38 5 71510933 71510933 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.3841G>C p.Asp1281His p.D1281H ENST00000358731 17/39 334 317 17 177 177 0 strelka-varscan-mutect BDP1,missense_variant,p.Asp1281His,ENST00000358731,NM_018429.2;BDP1,downstream_gene_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;BDP1,non_coding_transcript_exon_variant,,ENST00000508157,; C ENST00000358731 Transcript missense_variant 4104/11073 3841/7875 1281/2624 D/H Gat/Cat 1 1 BDP1 HGNC HGNC:13652 protein_coding YES CCDS43328.1 ENSP00000351575 A6H8Y1 UPI000020CA90 NM_018429.2 tolerated(0.06) 17/39 hmmpanther:PTHR22929:SF1,hmmpanther:PTHR22929 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 71510933 71510933 G C 1 0 0 0 0 1 0 0 0 1542 942 33 4 4 BDP1 5 71510933 Missense_Mutation SNP G C3N-00293_T 35649983 71510933 110027326 97 12555 PPIP5K2 0 . GRCh38 5 103186440 103186440 + Splice_Site SNP G G T novel C3N-00293_T C3N-00293_N G G c.3334+1G>T p.X1112_splice ENST00000627916 219 191 28 184 184 0 strelka-varscan-mutect PPIP5K2,splice_donor_variant,,ENST00000321521,;PPIP5K2,splice_donor_variant,,ENST00000627916,NM_001281471.1;PPIP5K2,splice_donor_variant,,ENST00000414217,NM_015216.3;PPIP5K2,splice_donor_variant,,ENST00000358359,NM_001276277.1;PPIP5K2,splice_donor_variant,,ENST00000613674,;PPIP5K2,splice_donor_variant,,ENST00000511022,;PPIP5K2,intron_variant,,ENST00000509597,;PPIP5K2,intron_variant,,ENST00000613907,;PPIP5K2,splice_donor_variant,,ENST00000511724,;PPIP5K2,intron_variant,,ENST00000510672,; T ENST00000627916 Transcript splice_donor_variant -/6010 3334/3837 1112/1278 1 1 PPIP5K2 HGNC HGNC:29035 protein_coding YES CCDS75283.1 ENSP00000486357 A0A087WZV0 UPI0002840889 NM_001281471.1 27/31 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 45 103186440 103186440 G T 1 0 0 0 0 0 0 1 0 12443 1275 44 2 2 PPIP5K2 5 103186440 Splice_Site SNP G C3N-00293_T 31675507 103186440 78351819 98 12556 TSLP 0 . GRCh38 5 111071918 111071918 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.28C>A p.Leu10Met p.L10M ENST00000344895 1/4 130 116 14 48 48 0 strelka-varscan-mutect TSLP,missense_variant,p.Leu10Met,ENST00000344895,NM_033035.4;TSLP,splice_region_variant,,ENST00000420978,;TSLP,upstream_gene_variant,,ENST00000379706,NM_138551.4; A ENST00000344895 Transcript missense_variant 227/736 28/480 10/159 L/M Ctg/Atg 1 1 TSLP HGNC HGNC:30743 protein_coding YES CCDS4101.1 ENSP00000339804 Q969D9 UPI000006DB21 NM_033035.4 tolerated(0.08) 1/4 hmmpanther:PTHR38003 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 45 111071918 111071918 C A 1 0 0 0 0 1 0 0 0 17133 912 32 2 2 TSLP 5 111071918 Missense_Mutation SNP C C3N-00293_T 7885478 111071918 70466341 99 12557 LVRN 0 . GRCh38 5 115992155 115992155 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1138G>T p.Ala380Ser p.A380S ENST00000357872 5/20 323 282 41 155 154 1 strelka-varscan-mutect LVRN,missense_variant,p.Ala380Ser,ENST00000357872,NM_173800.4;LVRN,missense_variant,p.Ala368Ser,ENST00000395528,;LVRN,missense_variant,p.Ala380Ser,ENST00000504467,;LVRN,upstream_gene_variant,,ENST00000503329,;LVRN,upstream_gene_variant,,ENST00000514509,;LVRN,upstream_gene_variant,,ENST00000512314,; T ENST00000357872 Transcript missense_variant 1262/4581 1138/2973 380/990 A/S Gca/Tca 1 1 LVRN HGNC HGNC:26904 protein_coding YES CCDS4124.1 ENSP00000350541 Q6Q4G3 A0A0A6YYA2 UPI0000457329 NM_173800.4 deleterious(0.01) 5/20 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF31,Pfam_domain:PF01433,Superfamily_domains:SSF55486,Prints_domain:PR00756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 115992155 115992155 G T 1 0 0 0 0 1 0 0 0 8998 1319 46 2 2 LVRN 5 115992155 Missense_Mutation SNP G C3N-00293_T 4920237 115992155 65546104 100 12558 SEC24A 0 . GRCh38 5 134661429 134661429 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.408G>C p.Leu136Phe p.L136F ENST00000398844 2/23 572 542 30 437 437 0 strelka-varscan-mutect SEC24A,missense_variant,p.Leu136Phe,ENST00000398844,NM_021982.2;SEC24A,missense_variant,p.Leu136Phe,ENST00000322887,NM_001252231.1; C ENST00000398844 Transcript missense_variant 696/6299 408/3282 136/1093 L/F ttG/ttC 1 1 SEC24A HGNC HGNC:10703 protein_coding YES CCDS43363.1 ENSP00000381823 O95486 UPI0000185FF9 NM_021982.2 tolerated_low_confidence(0.07) 2/23 hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 134661429 134661429 G C 1 0 0 0 0 1 0 0 0 14271 1281 45 4 4 SEC24A 5 134661429 Missense_Mutation SNP G C3N-00293_T 18669274 134661429 46876830 101 12559 PCDHA1 0 . GRCh38 5 140788509 140788509 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.2219T>A p.Val740Glu p.V740E ENST00000504120 1/4 182 149 33 184 184 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Val740Glu,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Val740Glu,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,non_coding_transcript_exon_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript missense_variant 2219/5263 2219/2853 740/950 V/E gTg/gAg 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 140788509 140788509 T A 1 0 0 0 0 1 0 0 0 11606 1696 59 4 4 PCDHA1 5 140788509 Missense_Mutation SNP T C3N-00293_T 6127080 140788509 40749750 102 12560 PCDHB10 0 . GRCh38 5 141194143 141194143 + Missense_Mutation SNP G G A C3N-00293_T C3N-00293_N G G c.1591G>A p.Val531Met p.V531M ENST00000239446 1/1 469 437 32 377 377 0 varscan-mutect PCDHB10,missense_variant,p.Val531Met,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,upstream_gene_variant,,ENST00000625144,; A ENST00000239446 Transcript missense_variant 1791/3290 1591/2403 531/800 V/M Gtg/Atg COSM5663811 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 141194143 141194143 G A 1 0 0 0 0 1 0 0 0 11622 1145 40 1 1 PCDHB10 5 141194143 Missense_Mutation SNP G C3N-00293_T 405634 141194143 40344116 103 12561 PCDHGA6 0 . GRCh38 5 141375983 141375983 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1900G>T p.Asp634Tyr p.D634Y ENST00000517434 1/4 514 450 64 384 384 0 strelka-varscan-mutect PCDHGA6,missense_variant,p.Asp634Tyr,ENST00000610583,NM_032086.1;PCDHGA6,missense_variant,p.Asp634Tyr,ENST00000517434,NM_018919.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000517434 Transcript missense_variant 2070/4775 1900/2799 634/932 D/Y Gac/Tac 1 1 PCDHGA6 HGNC HGNC:8704 protein_coding YES CCDS54926.1 ENSP00000429601 Q9Y5G7 UPI00000715C8 NM_018919.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF107,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 141375983 141375983 G T 1 0 0 0 0 1 0 0 0 11645 1174 41 2 2 PCDHGA6 5 141375983 Missense_Mutation SNP G C3N-00293_T 181840 141375983 40162276 104 12562 PCDHGA1 0 . GRCh38 5 141510977 141510977 + Missense_Mutation SNP G G T rs761149166 C3N-00293_T C3N-00293_N G G c.2693G>T p.Gly898Val p.G898V ENST00000571252 4/4 375 352 23 307 307 0 varscan-mutect PCDHGA4,missense_variant,p.Gly898Val,ENST00000571252,NM_018917.3;PCDHGA6,missense_variant,p.Gly868Val,ENST00000517434,NM_018919.2;PCDHGA3,missense_variant,p.Gly868Val,ENST00000253812,NM_018916.3;PCDHGB7,missense_variant,p.Gly865Val,ENST00000398594,NM_018927.3;PCDHGC5,missense_variant,p.Gly880Val,ENST00000252087,NM_018929.2;PCDHGA12,missense_variant,p.Gly868Val,ENST00000252085,NM_003735.2;PCDHGB3,missense_variant,p.Gly865Val,ENST00000576222,NM_018924.4;PCDHGC3,missense_variant,p.Gly870Val,ENST00000308177,NM_002588.3;PCDHGA11,missense_variant,p.Gly871Val,ENST00000398587,NM_018914.2;PCDHGC4,missense_variant,p.Gly874Val,ENST00000306593,NM_018928.2;PCDHGA10,missense_variant,p.Gly872Val,ENST00000398610,NM_018913.2;PCDHGA2,missense_variant,p.Gly868Val,ENST00000394576,NM_018915.3;PCDHGA8,missense_variant,p.Gly868Val,ENST00000398604,NM_032088.1;PCDHGA7,missense_variant,p.Gly868Val,ENST00000518325,NM_018920.3;PCDHGA9,missense_variant,p.Gly868Val,ENST00000573521,NM_018921.2;PCDHGA1,missense_variant,p.Gly867Val,ENST00000517417,NM_018912.2;PCDHGA5,missense_variant,p.Gly867Val,ENST00000518069,NM_018918.2;PCDHGB2,missense_variant,p.Gly867Val,ENST00000522605,NM_018923.2;PCDHGB6,missense_variant,p.Gly866Val,ENST00000520790,NM_018926.2;PCDHGB1,missense_variant,p.Gly863Val,ENST00000523390,NM_018922.2;PCDHGB4,missense_variant,p.Gly859Val,ENST00000519479,NM_003736.2;PCDHGB5,missense_variant,p.Gly859Val,ENST00000617380,NM_018925.2;PCDHGC3,missense_variant,p.Gly70Val,ENST00000617641,NM_032403.2;PCDHGA11,missense_variant,p.Gly686Val,ENST00000518882,NM_032092.1;PCDHGC4,missense_variant,p.Gly64Val,ENST00000618371,;PCDHGC3,missense_variant,p.Gly121Val,ENST00000617222,;DIAPH1,downstream_gene_variant,,ENST00000389054,NM_005219.4;DIAPH1,downstream_gene_variant,,ENST00000253811,;DIAPH1,downstream_gene_variant,,ENST00000398557,;DIAPH1,downstream_gene_variant,,ENST00000389057,;DIAPH1,downstream_gene_variant,,ENST00000518047,NM_001079812.2;DIAPH1,downstream_gene_variant,,ENST00000448451,;PCDHGC3,non_coding_transcript_exon_variant,,ENST00000622836,;PCDHGC3,downstream_gene_variant,,ENST00000622656,;PCDHGA3,3_prime_UTR_variant,,ENST00000612467,;DIAPH1,downstream_gene_variant,,ENST00000476339,; T ENST00000571252 Transcript missense_variant 2776/4778 2693/2889 898/962 G/V gGg/gTg rs761149166 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0) 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Pfam_domain:PF15974 MODERATE 1 SNV 1 1 PASS rs761149166 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 141510977 141510977 G T 1 0 0 0 0 1 0 0 0 11637 1232 43 2 2 PCDHGA1 5 141510977 Missense_Mutation SNP G C3N-00293_T 134994 141510977 40027282 105 12563 HTR4 0 . GRCh38 5 148509567 148509567 + Missense_Mutation SNP G G T rs761167553 C3N-00293_T C3N-00293_N G G c.965C>A p.Ala322Asp p.A322D ENST00000360693 6/8 302 262 40 197 197 0 strelka-varscan-mutect HTR4,missense_variant,p.Ala322Asp,ENST00000360693,;HTR4,missense_variant,p.Ala322Asp,ENST00000362016,NM_001040173.2;HTR4,missense_variant,p.Ala322Asp,ENST00000377888,NM_000870.6;HTR4,missense_variant,p.Ala322Asp,ENST00000521530,NM_001040169.2;HTR4,missense_variant,p.Ala322Asp,ENST00000521735,NM_199453.3;HTR4,missense_variant,p.Ala322Asp,ENST00000520514,NM_001286410.1;HTR4,missense_variant,p.Ala322Asp,ENST00000631296,;HTR4,missense_variant,p.Ala322Asp,ENST00000517929,NM_001040172.2;HTR4,missense_variant,p.Ala322Asp,ENST00000524063,;HTR4,missense_variant,p.Ala322Asp,ENST00000522588,;HTR4,non_coding_transcript_exon_variant,,ENST00000521124,; T ENST00000360693 Transcript missense_variant 1104/3082 965/1287 322/428 A/D gCc/gAc rs761167553,COSM4905218,COSM4905219,COSM4905220,COSM4905221 1 -1 HTR4 HGNC HGNC:5299 protein_coding YES CCDS34272.1 ENSP00000353915 Q13639 UPI00002323B1 deleterious(0) 6/8 hmmpanther:PTHR24249:SF33,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01059 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs761167553 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 148509567 148509567 G T 1 0 0 0 0 1 0 0 0 7345 1203 42 2 2 HTR4 5 148509567 Missense_Mutation SNP G C3N-00293_T 6998590 148509567 33028692 106 12564 SLC36A2 0 . GRCh38 5 151342905 151342905 + Silent SNP A A G novel C3N-00293_T C3N-00293_N A A c.423T>C p.= p.N141N ENST00000335244 4/10 464 436 28 395 395 0 strelka-varscan-mutect SLC36A2,synonymous_variant,p.=,ENST00000335244,NM_181776.2;SLC36A2,synonymous_variant,p.=,ENST00000521967,;SLC36A2,synonymous_variant,p.=,ENST00000518617,;SLC36A2,synonymous_variant,p.=,ENST00000518280,;SLC36A2,non_coding_transcript_exon_variant,,ENST00000522829,; G ENST00000335244 Transcript synonymous_variant 553/3421 423/1452 141/483 N aaT/aaC 1 -1 SLC36A2 HGNC HGNC:18762 protein_coding YES CCDS4315.1 ENSP00000334223 Q495M3 UPI000020D008 NM_181776.2 4/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF185 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 45 151342905 151342905 A G 1 0 0 0 0 0 0 0 1 14872 330 12 5 5 SLC36A2 5 151342905 Silent SNP A C3N-00293_T 2833338 151342905 30195354 107 12565 FAT2 0 . GRCh38 5 151531735 151531735 + Silent SNP G G C rs780126051 C3N-00293_T C3N-00293_N G G c.9663C>G p.= p.T3221T ENST00000261800 13/23 452 409 43 335 335 0 strelka-varscan-mutect FAT2,synonymous_variant,p.=,ENST00000261800,NM_001447.2;FAT2,synonymous_variant,p.=,ENST00000520200,; C ENST00000261800 Transcript synonymous_variant 9676/14534 9663/13050 3221/4349 T acC/acG rs780126051 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 13/23 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs780126051 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 45 151531735 151531735 G C 1 0 0 0 0 0 0 0 1 5550 1103 39 4 4 FAT2 5 151531735 Silent SNP G C3N-00293_T 188830 151531735 30006524 108 12566 SPARC 0 . GRCh38 5 151676167 151676167 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.22C>A p.Leu8Ile p.L8I ENST00000231061 2/10 244 223 21 216 216 0 strelka-varscan-mutect SPARC,missense_variant,p.Leu8Ile,ENST00000231061,NM_001309444.1,NM_001309443.1,NM_003118.3;SPARC,missense_variant,p.Leu8Ile,ENST00000539687,;SPARC,missense_variant,p.Leu8Ile,ENST00000522348,;SPARC,intron_variant,,ENST00000521569,;SPARC,intron_variant,,ENST00000538026,;CTB-113P19.1,upstream_gene_variant,,ENST00000510576,;CTB-113P19.1,upstream_gene_variant,,ENST00000518905,;SPARC,non_coding_transcript_exon_variant,,ENST00000521327,;SPARC,upstream_gene_variant,,ENST00000524277,; T ENST00000231061 Transcript missense_variant 336/3701 22/912 8/303 L/I Ctc/Atc 1 -1 SPARC HGNC HGNC:11219 protein_coding YES CCDS4318.1 ENSP00000231061 P09486 UPI0000040638 NM_001309444.1,NM_001309443.1,NM_003118.3 deleterious_low_confidence(0.03) 2/10 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13866,hmmpanther:PTHR13866:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 151676167 151676167 G T 1 0 0 0 0 1 0 0 0 15326 942 33 2 2 SPARC 5 151676167 Missense_Mutation SNP G C3N-00293_T 144432 151676167 29862092 109 12567 GEMIN5 0 . GRCh38 5 154913039 154913039 + Splice_Site SNP C C G novel C3N-00293_T C3N-00293_N C C c.1856-1G>C p.X619_splice ENST00000285873 139 131 8 103 103 0 strelka-varscan-mutect GEMIN5,splice_acceptor_variant,,ENST00000285873,NM_001252156.1,NM_015465.4; G ENST00000285873 Transcript splice_acceptor_variant -/5397 1856/4527 619/1508 1 -1 GEMIN5 HGNC HGNC:20043 protein_coding YES CCDS4330.1 ENSP00000285873 Q8TEQ6 UPI000020D072 NM_001252156.1,NM_015465.4 13/27 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.95388 0.9999995 1 1 1 0 G 5 3 45 154913039 154913039 C G 1 0 0 0 0 0 0 1 0 6205 927 32 4 4 GEMIN5 5 154913039 Splice_Site SNP C C3N-00293_T 3236872 154913039 26625220 110 12568 CCNG1 0 . GRCh38 5 163441141 163441141 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.328G>A p.Glu110Lys p.E110K ENST00000340828 3/7 260 240 20 132 132 0 strelka-varscan-mutect CCNG1,missense_variant,p.Glu110Lys,ENST00000340828,NM_004060.3;CCNG1,missense_variant,p.Glu110Lys,ENST00000393929,NM_199246.1;CCNG1,missense_variant,p.Glu110Lys,ENST00000510097,;CCNG1,missense_variant,p.Glu110Lys,ENST00000511490,;CCNG1,5_prime_UTR_variant,,ENST00000512163,;CCNG1,intron_variant,,ENST00000510664,;CCNG1,upstream_gene_variant,,ENST00000504553,;RP11-541P9.3,upstream_gene_variant,,ENST00000503504,;RP11-541P9.3,upstream_gene_variant,,ENST00000458002,;CCNG1,non_coding_transcript_exon_variant,,ENST00000511683,;CCNG1,upstream_gene_variant,,ENST00000509425,;CCNG1,upstream_gene_variant,,ENST00000509143,;CCNG1,non_coding_transcript_exon_variant,,ENST00000512532,;CCNG1,downstream_gene_variant,,ENST00000506186,;CCNG1,upstream_gene_variant,,ENST00000514367,; A ENST00000340828 Transcript missense_variant 552/2458 328/888 110/295 E/K Gaa/Aaa 1 1 CCNG1 HGNC HGNC:1592 protein_coding YES CCDS4360.1 ENSP00000344635 P51959 UPI00001275D2 NM_004060.3 deleterious(0.01) 3/7 Gene3D:1.10.472.10,Pfam_domain:PF00134,hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF59,SMART_domains:SM00385,Superfamily_domains:SSF47954 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 163441141 163441141 G A 1 0 0 0 0 1 0 0 0 2622 943 33 3 3 CCNG1 5 163441141 Missense_Mutation SNP G C3N-00293_T 8528102 163441141 18097118 111 12569 FAM196B 0 . GRCh38 5 169883310 169883310 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.589A>G p.Lys197Glu p.K197E ENST00000377365 2/4 183 173 10 117 117 0 strelka-varscan-mutect FAM196B,missense_variant,p.Lys197Glu,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; C ENST00000377365 Transcript missense_variant 1971/2999 589/1608 197/535 K/E Aaa/Gaa 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 deleterious(0.01) 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -17.90705 1 1 1 1 0 C 3 2 45 169883310 169883310 T C 1 0 0 0 0 1 0 0 0 5374 1792 62 5 5 FAM196B 5 169883310 Missense_Mutation SNP T C3N-00293_T 6442169 169883310 11654949 112 12570 MRS2 0 . GRCh38 6 24423690 24423690 + Missense_Mutation SNP G G A rs114959453 C3N-00293_T C3N-00293_N G G c.1337G>A p.Arg446His p.R446H ENST00000443868 12/12 133 125 8 78 78 0 strelka-varscan-mutect MRS2,missense_variant,p.Arg446His,ENST00000443868,NM_001286264.1;MRS2,missense_variant,p.Arg393His,ENST00000274747,NM_001286266.1;MRS2,missense_variant,p.Arg443His,ENST00000378386,NM_020662.3;GPLD1,downstream_gene_variant,,ENST00000230036,NM_001503.3;MRS2,downstream_gene_variant,,ENST00000378353,NM_001286265.1;MRS2,downstream_gene_variant,,ENST00000483634,;GPLD1,downstream_gene_variant,,ENST00000492917,; A ENST00000443868 Transcript missense_variant 1476/3980 1337/1341 446/446 R/H cGt/cAt rs114959453,COSM3860732,COSM3860733 1 1 MRS2 HGNC HGNC:13785 protein_coding YES CCDS69055.1 ENSP00000399585 Q9HD23 UPI00017A778D NM_001286264.1 deleterious_low_confidence(0) 12/12 0,1,1 MODERATE SNV 2 0,1,1 1 PASS rs114959453 . 0 199 2 5 0 0 0 4 -7.083414 0 0 1 0 0 A 3 1 45 24423690 24423690 G A 1 0 0 0 0 1 0 0 0 9828 1145 40 1 1 MRS2 6 24423690 Missense_Mutation SNP G C3N-00293_T 24423690 146382289 113 12571 ACOT13 0 . GRCh38 6 24701481 24701481 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.289G>A p.Gly97Arg p.G97R ENST00000230048 3/3 154 144 10 72 72 0 strelka-varscan-mutect ACOT13,missense_variant,p.Gly74Arg,ENST00000537591,NM_001160094.1;ACOT13,missense_variant,p.Gly97Arg,ENST00000230048,NM_018473.3;C6orf62,downstream_gene_variant,,ENST00000378119,NM_030939.4;C6orf62,downstream_gene_variant,,ENST00000378102,;RP1-30M3.5,non_coding_transcript_exon_variant,,ENST00000607014,;ACOT13,non_coding_transcript_exon_variant,,ENST00000476436,; A ENST00000230048 Transcript missense_variant 482/4047 289/423 97/140 G/R Gga/Aga 1 1 ACOT13 HGNC HGNC:20999 protein_coding YES CCDS4558.1 ENSP00000230048 Q9NPJ3 UPI0000131D18 NM_018473.3 deleterious(0) 3/3 Gene3D:3.10.129.10,Pfam_domain:PF03061,hmmpanther:PTHR21660,Superfamily_domains:SSF54637,TIGRFAM_domain:TIGR00369 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 24701481 24701481 G A 1 0 0 0 0 1 0 0 0 193 1001 35 3 3 ACOT13 6 24701481 Missense_Mutation SNP G C3N-00293_T 277791 24701481 146104498 114 12572 HIST1H1E 0 . GRCh38 6 26156465 26156465 + Silent SNP C C T rs374113105 C3N-00293_T C3N-00293_N C C c.75C>T p.= p.R25R ENST00000304218 1/1 181 170 11 139 139 0 strelka-varscan-mutect HIST1H1E,synonymous_variant,p.=,ENST00000304218,NM_005321.2;HIST1H2BD,upstream_gene_variant,,ENST00000289316,NM_138720.2;HIST1H2BD,upstream_gene_variant,,ENST00000377777,NM_021063.3;RP1-221C16.8,downstream_gene_variant,,ENST00000635439,; T ENST00000304218 Transcript synonymous_variant 112/754 75/660 25/219 R cgC/cgT rs374113105 1 1 HIST1H1E HGNC HGNC:4718 protein_coding YES CCDS4586.1 ENSP00000307705 P10412 A3R0T8 UPI0000000DB9 NM_005321.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11467,hmmpanther:PTHR11467:SF16,Prints_domain:PR00624 LOW SNV 1 PASS rs374113105 . 0 208 2 0 0 0 0 0 -19.5935 1 1 1 1 0 T 2 4 45 26156465 26156465 C T 1 0 0 0 0 0 0 0 1 7014 697 25 3 3 HIST1H1E 6 26156465 Silent SNP C C3N-00293_T 1454984 26156465 144649514 115 12573 BTN3A2 0 . GRCh38 6 26368698 26368698 + Missense_Mutation SNP G G T rs149839807 C3N-00293_T C3N-00293_N G G c.219G>T p.Arg73Ser p.R73S ENST00000356386 4/11 650 598 52 519 519 0 varscan-mutect BTN3A2,missense_variant,p.Arg31Ser,ENST00000508906,NM_001197249.2;BTN3A2,missense_variant,p.Arg50Ser,ENST00000396934,NM_001197248.2;BTN3A2,missense_variant,p.Arg73Ser,ENST00000356386,NM_007047.4,NM_001197247.2,NM_001197246.2;BTN3A2,missense_variant,p.Arg73Ser,ENST00000377708,;BTN3A2,missense_variant,p.Arg73Ser,ENST00000396948,;BTN3A2,missense_variant,p.Arg73Ser,ENST00000527422,;BTN3A2,missense_variant,p.Arg31Ser,ENST00000532865,;BTN3A2,missense_variant,p.Arg73Ser,ENST00000527417,;BTN3A2,missense_variant,p.Arg31Ser,ENST00000530653,;BTN3A2,upstream_gene_variant,,ENST00000527639,;BTN3A2,intron_variant,,ENST00000532994,;BTN3A2,intron_variant,,ENST00000524682,;BTN3A2,intron_variant,,ENST00000532627,;BTN3A2,non_coding_transcript_exon_variant,,ENST00000528222,;BTN3A2,non_coding_transcript_exon_variant,,ENST00000528541,;BTN3A2,intron_variant,,ENST00000524459,;BTN3A2,upstream_gene_variant,,ENST00000604202,;BTN3A2,upstream_gene_variant,,ENST00000531055,;BTN3A2,upstream_gene_variant,,ENST00000532294,; T ENST00000356386 Transcript missense_variant 407/3017 219/1005 73/334 R/S agG/agT rs149839807 1 1 BTN3A2 HGNC HGNC:1139 protein_coding YES CCDS4605.1 ENSP00000348751 P78410 UPI000006E484 NM_007047.4,NM_001197247.2,NM_001197246.2 tolerated(1) 4/11 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF70,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs149839807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 26368698 26368698 G T 1 0 0 0 0 1 0 0 0 1739 1194 42 2 2 BTN3A2 6 26368698 Missense_Mutation SNP G C3N-00293_T 212233 26368698 144437281 116 12574 IL17F 0 . GRCh38 6 52238805 52238805 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.179G>A p.Gly60Asp p.G60D ENST00000336123 2/3 536 496 40 387 387 0 strelka-varscan-mutect IL17F,missense_variant,p.Gly60Asp,ENST00000336123,NM_052872.3;IL17F,non_coding_transcript_exon_variant,,ENST00000478427,; T ENST00000336123 Transcript missense_variant 287/850 179/492 60/163 G/D gGc/gAc 1 -1 IL17F HGNC HGNC:16404 protein_coding YES CCDS4938.1 ENSP00000337432 Q96PD4 UPI0000038A0C NM_052872.3 tolerated(0.12) 2/3 hmmpanther:PTHR21295:SF8,hmmpanther:PTHR21295,Gene3D:2.10.90.10,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 52238805 52238805 C T 1 0 0 0 0 1 0 0 0 7546 739 26 3 3 IL17F 6 52238805 Missense_Mutation SNP C C3N-00293_T 25870107 52238805 118567174 117 12575 MAN1A1 0 . GRCh38 6 119348869 119348869 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.197C>T p.Ser66Phe p.S66F ENST00000368468 2/13 122 113 9 145 145 0 strelka-varscan-mutect MAN1A1,missense_variant,p.Ser66Phe,ENST00000368468,NM_005907.3; A ENST00000368468 Transcript missense_variant 639/5014 197/1962 66/653 S/F tCc/tTc 1 -1 MAN1A1 HGNC HGNC:6821 protein_coding YES CCDS5122.1 ENSP00000357453 P33908 UPI000013D632 NM_005907.3 tolerated(0.09) 2/13 hmmpanther:PTHR11742:SF31,hmmpanther:PTHR11742 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 119348869 119348869 G A 1 0 0 0 0 1 0 0 0 9131 1174 41 3 3 MAN1A1 6 119348869 Missense_Mutation SNP G C3N-00293_T 67110064 119348869 51457110 118 12576 HIVEP2 0 . GRCh38 6 142769956 142769956 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.4783G>A p.Glu1595Lys p.E1595K ENST00000367603 5/10 358 326 32 216 216 0 strelka-varscan-mutect HIVEP2,missense_variant,p.Glu1595Lys,ENST00000367603,NM_006734.3;HIVEP2,missense_variant,p.Glu1595Lys,ENST00000367604,;HIVEP2,missense_variant,p.Glu1595Lys,ENST00000012134,; T ENST00000367603 Transcript missense_variant 5526/9723 4783/7341 1595/2446 E/K Gaa/Aaa 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 tolerated(0.17) 5/10 hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 142769956 142769956 C T 1 0 0 0 0 1 0 0 0 7076 864 30 3 3 HIVEP2 6 142769956 Missense_Mutation SNP C C3N-00293_T 23421087 142769956 28036023 119 12577 MTHFD1L 0 . GRCh38 6 151034560 151034560 + Missense_Mutation SNP C C G rs753786210 C3N-00293_T C3N-00293_N C C c.2657C>G p.Ser886Cys p.S886C ENST00000611279 25/28 304 283 21 132 132 0 strelka-varscan-mutect MTHFD1L,missense_variant,p.Ser885Cys,ENST00000367321,NM_015440.4;MTHFD1L,missense_variant,p.Ser886Cys,ENST00000611279,NM_001242767.1;MTHFD1L,missense_variant,p.Ser820Cys,ENST00000618312,NM_001242768.1;MTHFD1L,missense_variant,p.Ser10Cys,ENST00000453602,;MTHFD1L,upstream_gene_variant,,ENST00000450635,; G ENST00000611279 Transcript missense_variant 2801/3475 2657/2940 886/979 S/C tCt/tGt rs753786210 1 1 MTHFD1L HGNC HGNC:21055 protein_coding YES CCDS75535.1 ENSP00000478253 B7ZM99 UPI000166C73D NM_001242767.1 deleterious(0) 25/28 HAMAP:MF_01543,hmmpanther:PTHR10025,hmmpanther:PTHR10025:SF14,Gene3D:1eg7A03,Pfam_domain:PF01268,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs753786210 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 151034560 151034560 C G 1 0 0 0 0 1 0 0 0 9917 913 32 4 4 MTHFD1L 6 151034560 Missense_Mutation SNP C C3N-00293_T 8264604 151034560 19771419 120 12578 SERAC1 0 . GRCh38 6 158128108 158128112 + Frame_Shift_Del DEL CTGAG CTGAG - novel C3N-00293_T C3N-00293_N CTGAG CTGAG c.1011_1015delCTCAG p.Ser338LeufsTer54 p.S338Lfs*54 ENST00000367104 10/17 113 106 7 67 67 0 varindel-pindel SERAC1,frameshift_variant,p.Ser338LeufsTer54,ENST00000367104,NM_032861.3;SERAC1,frameshift_variant,p.Ser338LeufsTer54,ENST00000367101,;SERAC1,frameshift_variant,p.Ser300LeufsTer54,ENST00000606965,;SERAC1,splice_region_variant,,ENST00000607742,;SERAC1,splice_region_variant,,ENST00000607071,; - ENST00000367104 Transcript frameshift_variant,splice_region_variant 1143-1147/3948 1011-1015/1965 337-339/654 RSG/RX cgCTCAGgc/cggc 1 -1 SERAC1 HGNC HGNC:21061 protein_coding YES CCDS5255.1 ENSP00000356071 Q96JX3 UPI0000070959 NM_032861.3 10/17 hmmpanther:PTHR22731,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 deletion 1 1 PASS . . 0 203 7 0 0 0 0 0 -13.7774 0.9999971 1 1 1 0 - 7 5 45 158128108 158128108 CTGAG - 1 0 1 0 1 0 0 0 0 14349 695 24 0 0 SERAC1 6 158128108 Frame_Shift_Del DEL CTGAG C3N-00293_T 7093548 158128108 12677871 121 12579 RPS6KA2 0 . GRCh38 6 166508277 166508277 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.409C>A p.Gln137Lys p.Q137K ENST00000503859 6/22 153 138 15 118 117 1 strelka-varscan-mutect RPS6KA2,missense_variant,p.Gln154Lys,ENST00000510118,NM_001318936.1;RPS6KA2,missense_variant,p.Gln129Lys,ENST00000265678,NM_001318938.1,NM_001318937.1,NM_021135.4;RPS6KA2,missense_variant,p.Gln137Lys,ENST00000503859,NM_001006932.1;RPS6KA2,missense_variant,p.Gln40Lys,ENST00000481261,;RPS6KA2,missense_variant,p.Gln40Lys,ENST00000405189,;RPS6KA2,missense_variant,p.Gln113Lys,ENST00000507371,;RPS6KA2,missense_variant,p.Gln40Lys,ENST00000507350,;RPS6KA2,missense_variant,p.Gln154Lys,ENST00000506565,;RPS6KA2,missense_variant,p.Gln40Lys,ENST00000512860,;RPS6KA2,downstream_gene_variant,,ENST00000511034,;MIR1913,downstream_gene_variant,,ENST00000411026,;RPS6KA2,non_coding_transcript_exon_variant,,ENST00000366865,; T ENST00000503859 Transcript missense_variant 790/4137 409/2226 137/741 Q/K Cag/Aag 1 -1 RPS6KA2 HGNC HGNC:10431 protein_coding YES CCDS34570.1 ENSP00000427015 Q15349 UPI000020D48C NM_001006932.1 deleterious(0) 6/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24351,hmmpanther:PTHR24351:SF25,PIRSF_domain:PIRSF000606,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 166508277 166508277 G T 1 0 0 0 0 1 0 0 0 13906 1304 45 2 2 RPS6KA2 6 166508277 Missense_Mutation SNP G C3N-00293_T 8380169 166508277 4297702 122 12580 ELFN1 0 . GRCh38 7 1745961 1745961 + Frame_Shift_Del DEL G G - rs773642663 C3N-00293_T C3N-00293_N G G c.1366delG p.Ala456GlnfsTer39 p.A456Qfs*39 ENST00000424383 3/3 119 110 9 74 74 0 varindel-pindel ELFN1,frameshift_variant,p.Ala456GlnfsTer39,ENST00000424383,;ELFN1,frameshift_variant,p.Ala456GlnfsTer39,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; - ENST00000424383 Transcript frameshift_variant 1852/3845 1365/2487 455/828 S/X tcG/tc rs773642663 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24367:SF34,hmmpanther:PTHR24367 HIGH deletion 5 1 1 PASS . . 0 203 7 0 0 0 0 0 -17.4546 0.9999981 1 1 1 0 - 7 5 45 1745961 1745961 G - 1 0 1 0 1 0 0 0 0 4891 1103 39 0 0 ELFN1 7 1745961 Frame_Shift_Del DEL G C3N-00293_T 1745961 157600012 123 12581 CCZ1 0 . GRCh38 7 5901682 5901682 + Missense_Mutation SNP G G T rs769524748 C3N-00293_T C3N-00293_N G G c.416G>T p.Arg139Leu p.R139L ENST00000325974 5/15 171 150 21 112 112 0 varscan-mutect CCZ1,missense_variant,p.Arg139Leu,ENST00000325974,NM_015622.5;CCZ1,3_prime_UTR_variant,,ENST00000628813,;CCZ1,non_coding_transcript_exon_variant,,ENST00000478672,;CCZ1,downstream_gene_variant,,ENST00000461592,;CCZ1,upstream_gene_variant,,ENST00000483394,; T ENST00000325974 Transcript missense_variant 482/1802 416/1449 139/482 R/L cGg/cTg rs769524748 1 1 CCZ1 HGNC HGNC:21691 protein_coding YES CCDS34597.1 ENSP00000325681 P86791 UPI000006CEFF NM_015622.5 tolerated(0.19) 5/15 hmmpanther:PTHR13056,Pfam_domain:PF08217 MODERATE 1 SNV 1 1 PASS rs769524748 . 9 196 2 3 0 0 0 0 -20 0.9999149 1 1 1 0 T 3 4 45 5901682 5901682 G T 1 0 0 0 0 1 0 0 0 2663 1116 39 1 1 CCZ1 7 5901682 Missense_Mutation SNP G C3N-00293_T 4155721 5901682 153444291 124 12582 YAE1D1 0 . GRCh38 7 39572315 39572315 + Nonsense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.290C>G p.Ser97Ter p.S97* ENST00000223273 3/3 174 159 15 103 103 0 strelka-varscan-mutect YAE1D1,stop_gained,p.Ser97Ter,ENST00000223273,NM_020192.4;YAE1D1,intron_variant,,ENST00000432096,NM_001282446.1;YAE1D1,intron_variant,,ENST00000448268,;YAE1D1,downstream_gene_variant,,ENST00000469737,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000485025,;YAE1D1,downstream_gene_variant,,ENST00000474392,;AC011290.5,upstream_gene_variant,,ENST00000438427,; G ENST00000223273 Transcript stop_gained 333/899 290/681 97/226 S/* tCa/tGa 1 1 YAE1D1 HGNC HGNC:24857 protein_coding YES CCDS5459.1 ENSP00000223273 Q9NRH1 UPI0000074023 NM_020192.4 3/3 hmmpanther:PTHR18829,hmmpanther:PTHR18829:SF0,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -19.83058 0.9999939 1 1 1 0 G 4 3 45 39572315 39572315 C G 1 0 0 0 0 0 1 0 0 18024 838 29 4 4 YAE1D1 7 39572315 Nonsense_Mutation SNP C C3N-00293_T 33670633 39572315 119773658 125 12583 PKD1L1 0 . GRCh38 7 47905923 47905923 + Missense_Mutation SNP T T C C3N-00293_T C3N-00293_N T T c.1442A>G p.Tyr481Cys p.Y481C ENST00000289672 10/57 240 216 24 164 164 0 strelka-varscan-mutect PKD1L1,missense_variant,p.Tyr481Cys,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; C ENST00000289672 Transcript missense_variant 1493/9092 1442/8550 481/2849 Y/C tAt/tGt COSM1644893 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.27) 10/57 hmmpanther:PTHR10877:SF145,hmmpanther:PTHR10877 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 47905923 47905923 T C 1 0 0 0 0 1 0 0 0 12060 1406 49 5 5 PKD1L1 7 47905923 Missense_Mutation SNP T C3N-00293_T 8333608 47905923 111440050 126 12584 ABCA13 0 . GRCh38 7 48288070 48288070 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.8947C>A p.His2983Asn p.H2983N ENST00000435803 20/62 145 122 23 94 94 0 strelka-varscan-mutect ABCA13,missense_variant,p.His2983Asn,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.His290Asn,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,; A ENST00000435803 Transcript missense_variant 8971/17184 8947/15177 2983/5058 H/N Cac/Aac 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0.02) 20/62 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 45 48288070 48288070 C A 1 0 0 0 0 1 0 0 0 35 594 21 2 2 ABCA13 7 48288070 Missense_Mutation SNP C C3N-00293_T 382147 48288070 111057903 127 12585 ZNF479 0 . GRCh38 7 57120259 57120259 + Missense_Mutation SNP A A G novel C3N-00293_T C3N-00293_N A A c.1156T>C p.Cys386Arg p.C386R ENST00000331162 5/5 166 156 10 93 93 0 varscan-mutect ZNF479,missense_variant,p.Cys386Arg,ENST00000331162,NM_033273.2;ZNF479,missense_variant,p.Cys386Arg,ENST00000319636,;ZNF479,missense_variant,p.Cys274Arg,ENST00000620639,; G ENST00000331162 Transcript missense_variant 1427/2072 1156/1575 386/524 C/R Tgt/Cgt 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 57120259 57120259 A G 1 0 0 0 0 1 0 0 0 18505 217 8 5 5 ZNF479 7 57120259 Missense_Mutation SNP A C3N-00293_T 8832189 57120259 102225714 128 12586 ZNF727 0 . GRCh38 7 64068894 64068894 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.7G>T p.Val3Leu p.V3L ENST00000456806 2/4 267 231 36 177 175 2 strelka-varscan-mutect ZNF727,missense_variant,p.Val3Leu,ENST00000456806,NM_001159522.1; T ENST00000456806 Transcript missense_variant 186/1679 7/1500 3/499 V/L Gtg/Ttg 1 1 ZNF727 HGNC HGNC:22785 protein_coding YES CCDS55113.1 ENSP00000485448 A8MUV8 UPI0001A23134 NM_001159522.1 tolerated(1) 2/4 hmmpanther:PTHR24384:SF98,hmmpanther:PTHR24384,Superfamily_domains:0044637 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 64068894 64068894 G T 1 0 0 0 0 1 0 0 0 18701 1043 36 2 2 ZNF727 7 64068894 Missense_Mutation SNP G C3N-00293_T 6948635 64068894 95277079 129 12587 PCLO 0 . GRCh38 7 82915547 82915547 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.12439C>T p.His4147Tyr p.H4147Y ENST00000333891 7/25 207 179 28 111 111 0 strelka-varscan-mutect PCLO,missense_variant,p.His4147Tyr,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.His4147Tyr,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.His867Tyr,ENST00000437081,; A ENST00000333891 Transcript missense_variant 12777/20329 12439/15429 4147/5142 H/Y Cat/Tat 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.11) 7/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS rs1439073582 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 45 82915547 82915547 G A 1 0 0 0 0 1 0 0 0 11671 1290 45 3 3 PCLO 7 82915547 Missense_Mutation SNP G C3N-00293_T 18846653 82915547 76430426 130 12588 C7orf62 0 . GRCh38 7 88794213 88794213 + Nonsense_Mutation SNP C C A rs763426089 C3N-00293_T C3N-00293_N C C c.730G>T p.Glu244Ter p.E244* ENST00000297203 2/2 113 102 11 55 55 0 strelka-varscan-mutect C7orf62,stop_gained,p.Glu244Ter,ENST00000297203,NM_152706.3;ZNF804B,intron_variant,,ENST00000333190,NM_181646.3; A ENST00000297203 Transcript stop_gained 916/1023 730/762 244/253 E/* Gag/Tag rs763426089,COSM124430 1 -1 C7orf62 HGNC HGNC:22402 protein_coding YES CCDS34678.1 ENSP00000297203 Q8TBZ9 UPI000005034C NM_152706.3 2/2 hmmpanther:PTHR34035,hmmpanther:PTHR34035:SF1 0,1 HIGH 1 SNV 1 0,1 1 PASS rs763426089 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 45 88794213 88794213 C A 1 0 0 0 0 0 1 0 0 2146 835 29 2 2 C7orf62 7 88794213 Nonsense_Mutation SNP C C3N-00293_T 5878666 88794213 70551760 131 12589 CFAP69 0 . GRCh38 7 90304820 90304820 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.2265A>T p.Lys755Asn p.K755N ENST00000389297 19/23 70 60 10 45 45 0 strelka-varscan-mutect CFAP69,missense_variant,p.Lys755Asn,ENST00000389297,NM_001039706.2;CFAP69,missense_variant,p.Lys737Asn,ENST00000497910,NM_001160138.1;CFAP69,missense_variant,p.Lys292Asn,ENST00000449577,;CFAP69,missense_variant,p.Lys50Asn,ENST00000412839,;CFAP69,downstream_gene_variant,,ENST00000457170,;CFAP69,upstream_gene_variant,,ENST00000445156,;CFAP69,splice_region_variant,,ENST00000475031,;CFAP69,splice_region_variant,,ENST00000427396,;CFAP69,downstream_gene_variant,,ENST00000451029,; T ENST00000389297 Transcript missense_variant,splice_region_variant 2516/3902 2265/2826 755/941 K/N aaA/aaT 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 deleterious(0) 19/23 hmmpanther:PTHR14716:SF0,hmmpanther:PTHR14716 MODERATE 1 SNV 1 1 PASS rs767754288 . 0 208 2 0 0 0 0 0 -19.999 1 1 1 1 0 T 3 4 45 90304820 90304820 A T 1 0 0 0 0 1 0 0 0 3030 86 3 4 4 CFAP69 7 90304820 Missense_Mutation SNP A C3N-00293_T 1510607 90304820 69041153 132 12590 RBM48 0 . GRCh38 7 92534882 92534882 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.929G>C p.Gly310Ala p.G310A ENST00000265732 4/5 380 356 24 195 195 0 strelka-varscan-mutect RBM48,missense_variant,p.Gly310Ala,ENST00000481551,;RBM48,missense_variant,p.Gly310Ala,ENST00000265732,NM_032120.2;RBM48,downstream_gene_variant,,ENST00000496410,; C ENST00000265732 Transcript missense_variant 970/1742 929/1104 310/367 G/A gGa/gCa 1 1 RBM48 HGNC HGNC:21785 protein_coding YES CCDS43615.1 ENSP00000265732 Q5RL73 UPI000020F54D NM_032120.2 deleterious(0) 4/5 hmmpanther:PTHR20957 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 92534882 92534882 G C 1 0 0 0 0 1 0 0 0 13308 1174 41 4 4 RBM48 7 92534882 Missense_Mutation SNP G C3N-00293_T 2230062 92534882 66811091 133 12591 COL1A2 0 . GRCh38 7 94409599 94409599 + Missense_Mutation SNP G G T rs746402161 C3N-00293_T C3N-00293_N G G c.927G>T p.Lys309Asn p.K309N ENST00000297268 18/52 749 656 93 590 589 1 strelka-varscan-mutect COL1A2,missense_variant,p.Lys309Asn,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Lys307Asn,ENST00000620463,;COL1A2,upstream_gene_variant,,ENST00000473573,;COL1A2,upstream_gene_variant,,ENST00000488298,; T ENST00000297268 Transcript missense_variant 1398/5411 927/4101 309/1366 K/N aaG/aaT rs746402161 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 deleterious(0) 18/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs746402161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 94409599 94409599 G T 1 0 0 0 0 1 0 0 0 3466 991 35 2 2 COL1A2 7 94409599 Missense_Mutation SNP G C3N-00293_T 1874717 94409599 64936374 134 12592 PON1 0 . GRCh38 7 95315325 95315325 + Missense_Mutation SNP C C T C3N-00293_T C3N-00293_N C C c.367G>A p.Glu123Lys p.E123K ENST00000222381 4/9 345 312 33 194 194 0 strelka-varscan-mutect PON1,missense_variant,p.Glu123Lys,ENST00000222381,NM_000446.5;PON1,3_prime_UTR_variant,,ENST00000433729,;PON1,non_coding_transcript_exon_variant,,ENST00000470502,; T ENST00000222381 Transcript missense_variant 599/2568 367/1068 123/355 E/K Gaa/Aaa COSM3924287 1 -1 PON1 HGNC HGNC:9204 protein_coding YES CCDS5638.1 ENSP00000222381 P27169 UPI000013C7FD NM_000446.5 tolerated(0.94) 4/9 hmmpanther:PTHR11799,hmmpanther:PTHR11799:SF16,Gene3D:2.120.10.30,Superfamily_domains:SSF63829,Prints_domain:PR01786 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 95315325 95315325 C T 1 0 0 0 0 1 0 0 0 12362 840 29 3 3 PON1 7 95315325 Missense_Mutation SNP C C3N-00293_T 905726 95315325 64030648 135 12593 LAMB1 0 . GRCh38 7 107955596 107955596 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.2725G>T p.Gly909Trp p.G909W ENST00000222399 21/34 158 141 17 121 121 0 strelka-varscan-mutect LAMB1,missense_variant,p.Gly933Trp,ENST00000393561,;LAMB1,missense_variant,p.Gly909Trp,ENST00000222399,NM_002291.2;LAMB1,downstream_gene_variant,,ENST00000393560,;LAMB1,upstream_gene_variant,,ENST00000476039,;LAMB1,upstream_gene_variant,,ENST00000479448,; A ENST00000222399 Transcript missense_variant 2956/5725 2725/5361 909/1786 G/W Ggg/Tgg COSM382505 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 deleterious(0) 21/34 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS rs1064793562 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 107955596 107955596 C A 1 0 0 0 0 1 0 0 0 8514 594 21 2 2 LAMB1 7 107955596 Missense_Mutation SNP C C3N-00293_T 12640271 107955596 51390377 136 12594 FOXP2 0 . GRCh38 7 114631529 114631529 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.674A>T p.Gln225Leu p.Q225L ENST00000408937 7/18 381 349 32 304 304 0 strelka-varscan-mutect FOXP2,splice_acceptor_variant,,ENST00000393498,;FOXP2,missense_variant,p.Gln225Leu,ENST00000408937,NM_148898.3;FOXP2,missense_variant,p.Gln217Leu,ENST00000403559,NM_148900.3;FOXP2,missense_variant,p.Gln108Leu,ENST00000393491,;FOXP2,missense_variant,p.Gln197Leu,ENST00000635534,;FOXP2,missense_variant,p.Gln183Leu,ENST00000634411,;FOXP2,missense_variant,p.Gln200Leu,ENST00000393494,;FOXP2,missense_variant,p.Gln200Leu,ENST00000350908,NM_001172766.2,NM_014491.3;FOXP2,missense_variant,p.Gln201Leu,ENST00000635638,;FOXP2,missense_variant,p.Gln108Leu,ENST00000393489,;FOXP2,missense_variant,p.Gln200Leu,ENST00000378237,;FOXP2,missense_variant,p.Gln180Leu,ENST00000634623,;FOXP2,missense_variant,p.Gln224Leu,ENST00000390668,NM_001172767.2;FOXP2,missense_variant,p.Gln200Leu,ENST00000360232,NM_148899.3;FOXP2,splice_region_variant,,ENST00000393495,;FOXP2,intron_variant,,ENST00000635563,;FOXP2,downstream_gene_variant,,ENST00000452963,;FOXP2,intron_variant,,ENST00000634372,;FOXP2,downstream_gene_variant,,ENST00000459666,;FOXP2,splice_region_variant,,ENST00000441290,;FOXP2,splice_region_variant,,ENST00000412402,;FOXP2,splice_region_variant,,ENST00000635109,;FOXP2,splice_region_variant,,ENST00000440349,; T ENST00000408937 Transcript missense_variant,splice_region_variant 1048/6443 674/2223 225/740 Q/L cAg/cTg 1 1 FOXP2 HGNC HGNC:13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 X5D2H2 UPI000007412B NM_148898.3 tolerated(0.38) 7/18 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -9.0784 0.9907932 1 1 1 0 T 3 4 45 114631529 114631529 A T 1 0 0 0 0 1 0 0 0 5892 202 7 4 4 FOXP2 7 114631529 Missense_Mutation SNP A C3N-00293_T 6675933 114631529 44714444 137 12595 LMOD2 0 . GRCh38 7 123662182 123662182 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.596T>C p.Ile199Thr p.I199T ENST00000458573 2/3 186 173 13 114 114 0 strelka-varscan-mutect LMOD2,missense_variant,p.Ile199Thr,ENST00000458573,NM_207163.1;LMOD2,intron_variant,,ENST00000456238,; C ENST00000458573 Transcript missense_variant 753/2346 596/1644 199/547 I/T aTt/aCt 1 1 LMOD2 HGNC HGNC:6648 protein_coding YES CCDS47693.1 ENSP00000411932 Q6P5Q4 UPI0001572CCA NM_207163.1 deleterious(0) 2/3 hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF12,Superfamily_domains:SSF52047 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 123662182 123662182 T C 1 0 0 0 0 1 0 0 0 8784 1493 52 5 5 LMOD2 7 123662182 Missense_Mutation SNP T C3N-00293_T 9030653 123662182 35683791 138 12596 GCC1 0 . GRCh38 7 127584197 127584197 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.986G>T p.Arg329Leu p.R329L ENST00000321407 1/2 216 192 24 153 153 0 strelka-varscan-mutect GCC1,missense_variant,p.Arg329Leu,ENST00000321407,NM_024523.5;ARF5,upstream_gene_variant,,ENST00000000233,NM_001662.3;ARF5,upstream_gene_variant,,ENST00000415666,;GCC1,intron_variant,,ENST00000497650,;ARF5,upstream_gene_variant,,ENST00000467281,;ARF5,upstream_gene_variant,,ENST00000463733,;ARF5,upstream_gene_variant,,ENST00000489673,;ARF5,upstream_gene_variant,,ENST00000459680,; A ENST00000321407 Transcript missense_variant 1411/4149 986/2328 329/775 R/L cGc/cTc COSM1085146 1 -1 GCC1 HGNC HGNC:19095 protein_coding YES CCDS5796.1 ENSP00000318821 Q96CN9 A4D0Z4 UPI0000072BA8 NM_024523.5 tolerated(0.25) 1/2 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23157,hmmpanther:PTHR23157:SF25 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 127584197 127584197 C A 1 0 0 0 0 1 0 0 0 6155 768 27 1 1 GCC1 7 127584197 Missense_Mutation SNP C C3N-00293_T 3922015 127584197 31761776 139 12597 MGAM2 0 . GRCh38 7 142154120 142154120 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.1737G>T p.= p.A579A ENST00000477922 16/48 79 69 10 73 73 0 strelka-varscan-mutect MGAM2,synonymous_variant,p.=,ENST00000477922,NM_001293626.1; T ENST00000477922 Transcript synonymous_variant 1791/7867 1737/7548 579/2515 A gcG/gcT 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 16/48 Pfam_domain:PF01055,Superfamily_domains:SSF51445 LOW 1 SNV 5 1 PASS rs947058820 . 0 204 6 0 0 0 0 0 -19.98796 0.9999999 1 1 1 0 T 2 4 45 142154120 142154120 G T 1 0 0 0 0 0 0 0 1 9500 1103 39 1 1 MGAM2 7 142154120 Silent SNP G C3N-00293_T 14569923 142154120 17191853 140 12598 EPHB6 0 . GRCh38 7 142864038 142864038 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.238G>T p.Ala80Ser p.A80S ENST00000619012 7/20 414 382 32 272 272 0 strelka-varscan-mutect EPHB6,missense_variant,p.Ala80Ser,ENST00000619012,;EPHB6,missense_variant,p.Ala80Ser,ENST00000422643,NM_004445.5;EPHB6,5_prime_UTR_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000497095,;EPHB6,missense_variant,p.Ala80Ser,ENST00000611578,;EPHB6,3_prime_UTR_variant,,ENST00000614832,;EPHB6,non_coding_transcript_exon_variant,,ENST00000616380,;EPHB6,upstream_gene_variant,,ENST00000486511,; T ENST00000619012 Transcript missense_variant 990/4011 238/3069 80/1022 A/S Gcc/Tcc 1 1 EPHB6 HGNC HGNC:3396 protein_coding YES CCDS5873.2 ENSP00000481994 F8WCM8 UPI0003EAF8C7 tolerated(0.21) 7/20 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF326,hmmpanther:PTHR24416,Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 142864038 142864038 G T 1 0 0 0 0 1 0 0 0 5025 1203 42 2 2 EPHB6 7 142864038 Missense_Mutation SNP G C3N-00293_T 709918 142864038 16481935 141 12599 OR6B1 0 . GRCh38 7 144004128 144004128 + Silent SNP C C A novel C3N-00293_T C3N-00293_N C C c.132C>A p.= p.I44I ENST00000408922 1/1 305 270 35 189 189 0 strelka-varscan-mutect OR6B1,synonymous_variant,p.=,ENST00000408922,NM_001005281.1; A ENST00000408922 Transcript synonymous_variant 200/1055 132/936 44/311 I atC/atA 1 1 OR6B1 HGNC HGNC:8354 protein_coding YES CCDS43667.1 ENSP00000386151 O95007 UPI0000041B18 NM_001005281.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF284,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 144004128 144004128 C A 1 0 0 0 0 0 0 0 1 11255 816 29 2 2 OR6B1 7 144004128 Silent SNP C C3N-00293_T 1140090 144004128 15341845 142 12600 NOM1 0 . GRCh38 7 156969645 156969645 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.2525G>A p.Arg842Lys p.R842K ENST00000275820 11/11 275 259 16 213 213 0 strelka-varscan-mutect NOM1,missense_variant,p.Arg842Lys,ENST00000275820,NM_138400.1;NOM1,non_coding_transcript_exon_variant,,ENST00000486131,;NOM1,downstream_gene_variant,,ENST00000485661,; A ENST00000275820 Transcript missense_variant 2540/6077 2525/2583 842/860 R/K aGa/aAa 1 1 NOM1 HGNC HGNC:13244 protein_coding YES CCDS34787.1 ENSP00000275820 Q5C9Z4 UPI000020E71F NM_138400.1 tolerated(0.74) 11/11 hmmpanther:PTHR18034,hmmpanther:PTHR18034:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 156969645 156969645 G A 1 0 0 0 0 1 0 0 0 10574 942 33 3 3 NOM1 7 156969645 Missense_Mutation SNP G C3N-00293_T 12965517 156969645 2376328 143 12601 CSMD1 0 . GRCh38 8 3190023 3190023 + Missense_Mutation SNP C C G rs752235970 C3N-00293_T C3N-00293_N C C c.5290G>C p.Val1764Leu p.V1764L ENST00000520002 35/71 407 342 65 349 349 0 strelka-varscan-mutect CSMD1,missense_variant,p.Val1625Leu,ENST00000537824,;CSMD1,missense_variant,p.Val1244Leu,ENST00000335551,;CSMD1,missense_variant,p.Val1764Leu,ENST00000520002,;CSMD1,missense_variant,p.Val1764Leu,ENST00000602557,;CSMD1,missense_variant,p.Val1763Leu,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Val1764Leu,ENST00000400186,;CSMD1,missense_variant,p.Val1764Leu,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; G ENST00000520002 Transcript missense_variant 5846/11740 5290/10698 1764/3565 V/L Gtc/Ctc rs752235970,COSM4168593,COSM4168594,COSM4168595 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.1) 35/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs752235970 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 3190023 3190023 C G 1 0 0 0 0 1 0 0 0 3745 536 19 4 4 CSMD1 8 3190023 Missense_Mutation SNP C C3N-00293_T 3190023 141948613 144 12602 GFRA2 0 . GRCh38 8 21750789 21750789 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.593G>A p.Arg198His p.R198H ENST00000524240 4/9 575 525 50 499 499 0 strelka-varscan-mutect GFRA2,missense_variant,p.Arg198His,ENST00000524240,NM_001495.4;GFRA2,missense_variant,p.Arg198His,ENST00000517328,;GFRA2,missense_variant,p.Arg65His,ENST00000518077,NM_001165039.1;GFRA2,missense_variant,p.Arg93His,ENST00000517892,NM_001165038.1;GFRA2,missense_variant,p.Arg198His,ENST00000522071,;GFRA2,3_prime_UTR_variant,,ENST00000306793,; T ENST00000524240 Transcript missense_variant 1244/4921 593/1395 198/464 R/H cGc/cAc 1 -1 GFRA2 HGNC HGNC:4244 protein_coding YES CCDS47816.1 ENSP00000428518 O00451 UPI000000D9B1 NM_001495.4 deleterious(0) 4/9 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF4,PIRSF_domain:PIRSF038071,Pfam_domain:PF02351,SMART_domains:SM00907,Prints_domain:PR01316 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 21750789 21750789 C T 1 0 0 0 0 1 0 0 0 6222 768 27 1 1 GFRA2 8 21750789 Missense_Mutation SNP C C3N-00293_T 18560766 21750789 123387847 145 12603 C8orf34 0 . GRCh38 8 68439631 68439631 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.460G>C p.Glu154Gln p.E154Q ENST00000518698 2/14 163 147 16 90 90 0 varscan-mutect C8orf34,missense_variant,p.Glu43Gln,ENST00000337103,;C8orf34,missense_variant,p.Glu68Gln,ENST00000348340,NM_001195639.1;C8orf34,missense_variant,p.Glu154Gln,ENST00000518698,NM_052958.2;C8orf34,missense_variant,p.Glu68Gln,ENST00000523686,;C8orf34,non_coding_transcript_exon_variant,,ENST00000349492,;C8orf34,missense_variant,p.Glu43Gln,ENST00000521406,; C ENST00000518698 Transcript missense_variant 751/2223 460/1617 154/538 E/Q Gaa/Caa 1 1 C8orf34 HGNC HGNC:30905 protein_coding YES CCDS6203.2 ENSP00000427820 Q49A92 UPI000021D12D NM_052958.2 tolerated(0.24) 2/14 hmmpanther:PTHR32000,hmmpanther:PTHR32000:SF3 MODERATE 1 SNV 2 1 PASS . . 0 191 5 9 4 0 0 0 -6.701518 0.207465 1 1 0 0 C 3 2 45 68439631 68439631 G C 1 0 0 0 0 1 0 0 0 2155 943 33 4 4 C8orf34 8 68439631 Missense_Mutation SNP G C3N-00293_T 46688842 68439631 76699005 146 12604 KCNB2 0 . GRCh38 8 72937579 72937579 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.2224G>A p.Ala742Thr p.A742T ENST00000523207 3/3 231 215 16 189 189 0 strelka-varscan-mutect KCNB2,missense_variant,p.Ala742Thr,ENST00000523207,NM_004770.2; A ENST00000523207 Transcript missense_variant 2812/3582 2224/2736 742/911 A/T Gct/Act 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 tolerated_low_confidence(0.46) 3/3 Pfam_domain:PF03521 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 72937579 72937579 G A 1 0 0 0 0 1 0 0 0 7929 971 34 3 3 KCNB2 8 72937579 Missense_Mutation SNP G C3N-00293_T 4497948 72937579 72201057 147 12605 NBN 0 . GRCh38 8 89937064 89937064 + Silent SNP T T C rs587780780 C3N-00293_T C3N-00293_N T T c.2196A>G p.= p.Q732Q ENST00000265433 15/16 308 262 46 191 191 0 strelka-varscan-mutect NBN,synonymous_variant,p.=,ENST00000265433,NM_002485.4;NBN,synonymous_variant,p.=,ENST00000409330,;NBN,synonymous_variant,p.=,ENST00000613033,;NBN,3_prime_UTR_variant,,ENST00000396252,NM_001024688.2;NBN,non_coding_transcript_exon_variant,,ENST00000474821,; C ENST00000265433 Transcript synonymous_variant 2351/4666 2196/2265 732/754 Q caA/caG rs587780780,COSM3699203 1 -1 NBN HGNC HGNC:7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 UPI0000073BF4 NM_002485.4 15/16 hmmpanther:PTHR12162,hmmpanther:PTHR12162:SF0,PIRSF_domain:PIRSF011869,Pfam_domain:PF08599,SMART_domains:SM01348 likely_benign 0,1 LOW 1 SNV 1 1,1 1 PASS rs587780780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 45 89937064 89937064 T C 1 0 0 0 0 0 0 0 1 10202 1722 60 5 5 NBN 8 89937064 Silent SNP T C3N-00293_T 16999485 89937064 55201572 148 12606 PKHD1L1 0 . GRCh38 8 109440834 109440834 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.4081G>A p.Glu1361Lys p.E1361K ENST00000378402 33/78 139 121 18 71 71 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Glu1361Lys,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 4185/13076 4081/12732 1361/4243 E/K Gag/Aag 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 tolerated(0.18) 33/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 109440834 109440834 G A 1 0 0 0 0 1 0 0 0 12068 1291 45 3 3 PKHD1L1 8 109440834 Missense_Mutation SNP G C3N-00293_T 19503770 109440834 35697802 149 12607 GLI4 0 . GRCh38 8 143276788 143276788 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.1115T>A p.Val372Glu p.V372E ENST00000340042 4/4 90 81 9 50 50 0 strelka-varscan-mutect GLI4,missense_variant,p.Val372Glu,ENST00000340042,NM_138465.3;GLI4,missense_variant,p.Val372Glu,ENST00000523522,;RP13-582O9.6,downstream_gene_variant,,ENST00000522452,;GLI4,downstream_gene_variant,,ENST00000521682,;GLI4,downstream_gene_variant,,ENST00000344692,;GLI4,downstream_gene_variant,,ENST00000517468,;GLI4,downstream_gene_variant,,ENST00000517530,;GLI4,downstream_gene_variant,,ENST00000520021,;MINCR,downstream_gene_variant,,ENST00000523031,;MINCR,downstream_gene_variant,,ENST00000517411,;MINCR,downstream_gene_variant,,ENST00000524335,;MINCR,downstream_gene_variant,,ENST00000521207,;MINCR,downstream_gene_variant,,ENST00000518073,;MINCR,downstream_gene_variant,,ENST00000519852,;GLI4,non_coding_transcript_exon_variant,,ENST00000523812,;GLI4,downstream_gene_variant,,ENST00000519876,;GLI4,downstream_gene_variant,,ENST00000522479,;GLI4,downstream_gene_variant,,ENST00000522033,; A ENST00000340042 Transcript missense_variant 1200/1341 1115/1131 372/376 V/E gTg/gAg 1 1 GLI4 HGNC HGNC:4320 protein_coding YES CCDS6398.1 ENSP00000345024 P10075 UPI0000070432 NM_138465.3 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF122,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.74331 0.9999998 1 1 1 0 A 3 1 45 143276788 143276788 T A 1 0 0 0 0 1 0 0 0 6318 1696 59 4 4 GLI4 8 143276788 Missense_Mutation SNP T C3N-00293_T 33835954 143276788 1861848 150 12608 PTPRD 0 . GRCh38 9 8500817 8500817 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.2065G>A p.Ala689Thr p.A689T ENST00000381196 21/43 252 235 17 174 174 0 strelka-varscan-mutect PTPRD,missense_variant,p.Ala689Thr,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Ala689Thr,ENST00000356435,;PTPRD,missense_variant,p.Ala689Thr,ENST00000540109,;PTPRD,intron_variant,,ENST00000355233,NM_130392.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,NM_130393.3;PTPRD,intron_variant,,ENST00000486161,NM_130391.3;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1;PTPRD,non_coding_transcript_exon_variant,,ENST00000471274,; T ENST00000381196 Transcript missense_variant 2609/9911 2065/5739 689/1912 A/T Gcc/Acc 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0.01) 21/43 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 8500817 8500817 C T 1 0 0 0 0 1 0 0 0 12953 797 28 3 3 PTPRD 9 8500817 Missense_Mutation SNP C C3N-00293_T 8500817 129893900 151 12609 OR13C4 0 . GRCh38 9 104527149 104527149 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.61C>A p.Pro21Thr p.P21T ENST00000277216 1/1 231 184 47 102 102 0 strelka-varscan-mutect OR13C4,missense_variant,p.Pro21Thr,ENST00000277216,NM_001001919.1;RP11-317C20.9,intron_variant,,ENST00000635678,; T ENST00000277216 Transcript missense_variant 61/957 61/957 21/318 P/T Ccc/Acc 1 -1 OR13C4 HGNC HGNC:14722 protein_coding YES CCDS35088.1 ENSP00000277216 Q8NGS5 A0A126GVC9 UPI0000041B46 NM_001001919.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF14,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 104527149 104527149 G T 1 0 0 0 0 1 0 0 0 11012 1232 43 2 2 OR13C4 9 104527149 Missense_Mutation SNP G C3N-00293_T 96026332 104527149 33867568 152 12610 ASTN2 0 . GRCh38 9 117414537 117414537 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.402G>T p.Gln134His p.Q134H ENST00000361209 1/22 293 276 17 268 268 0 strelka-varscan-mutect ASTN2,missense_variant,p.Gln134His,ENST00000313400,;ASTN2,missense_variant,p.Gln134His,ENST00000361209,NM_014010.4;ASTN2,5_prime_UTR_variant,,ENST00000361477,NM_198187.3; A ENST00000361209 Transcript missense_variant 534/4622 402/3867 134/1288 Q/H caG/caT 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 tolerated_low_confidence(0.13) 1/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 117414537 117414537 C A 1 0 0 0 0 1 0 0 0 1212 680 24 2 2 ASTN2 9 117414537 Missense_Mutation SNP C C3N-00293_T 12887388 117414537 20980180 153 12611 BRINP1 0 . GRCh38 9 119167464 119167464 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1906G>T p.Gly636Cys p.G636C ENST00000265922 8/8 215 192 23 141 140 1 strelka-varscan-mutect BRINP1,missense_variant,p.Gly636Cys,ENST00000265922,NM_014618.2;BRINP1,intron_variant,,ENST00000482797,; A ENST00000265922 Transcript missense_variant 2368/3202 1906/2286 636/761 G/C Ggc/Tgc 1 -1 BRINP1 HGNC HGNC:2687 protein_coding YES CCDS6822.1 ENSP00000265922 O60477 UPI000013D6A7 NM_014618.2 deleterious(0.02) 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 119167464 119167464 C A 1 0 0 0 0 1 0 0 0 1685 623 22 2 2 BRINP1 9 119167464 Missense_Mutation SNP C C3N-00293_T 1752927 119167464 19227253 154 12612 LHX6 0 . GRCh38 9 122204745 122204745 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1090C>G p.Pro364Ala p.P364A ENST00000340587 9/9 114 107 7 104 104 0 strelka-varscan-mutect LHX6,missense_variant,p.Pro364Ala,ENST00000340587,NM_199160.3;LHX6,missense_variant,p.Pro335Ala,ENST00000373754,;LHX6,missense_variant,p.Pro353Ala,ENST00000541397,NM_001242333.1;LHX6,missense_variant,p.Pro22Ala,ENST00000464484,;LHX6,3_prime_UTR_variant,,ENST00000559895,NM_001242335.1;LHX6,3_prime_UTR_variant,,ENST00000394319,NM_014368.4;LHX6,3_prime_UTR_variant,,ENST00000373755,NM_001242334.1;LHX6,3_prime_UTR_variant,,ENST00000482062,;MORN5,downstream_gene_variant,,ENST00000373764,NM_198469.3;MORN5,downstream_gene_variant,,ENST00000536616,NM_001286828.1;MORN5,downstream_gene_variant,,ENST00000486801,; C ENST00000340587 Transcript missense_variant 1291/3457 1090/1134 364/377 P/A Ccg/Gcg 1 -1 LHX6 HGNC HGNC:21735 protein_coding CCDS6837.2 ENSP00000340137 Q9UPM6 UPI0000F58F26 NM_199160.3 tolerated(0.05) 9/9 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 122204745 122204745 G C 1 0 0 0 0 1 0 0 0 8684 1174 41 4 4 LHX6 9 122204745 Missense_Mutation SNP G C3N-00293_T 3037281 122204745 16189972 155 12613 FAM208B 0 . GRCh38 10 5757584 5757584 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.6797G>A p.Gly2266Glu p.G2266E ENST00000328090 17/21 273 257 16 166 166 0 strelka-varscan-mutect FAM208B,missense_variant,p.Gly2266Glu,ENST00000328090,NM_001321784.1,NM_001321783.1,NM_017782.4;FAM208B,upstream_gene_variant,,ENST00000459693,;FAM208B,upstream_gene_variant,,ENST00000487196,; A ENST00000328090 Transcript missense_variant 7422/8626 6797/7293 2266/2430 G/E gGa/gAa 1 1 FAM208B HGNC HGNC:23484 protein_coding YES CCDS41485.1 ENSP00000328426 Q5VWN6 UPI00004589BB NM_001321784.1,NM_001321783.1,NM_017782.4 tolerated(1) 17/21 hmmpanther:PTHR16207,hmmpanther:PTHR16207:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 5757584 5757584 G A 1 0 0 0 0 1 0 0 0 5390 1174 41 3 3 FAM208B 10 5757584 Missense_Mutation SNP G C3N-00293_T 5757584 128039838 156 12614 ARHGAP21 0 . GRCh38 10 24585920 24585920 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.4369G>A p.Glu1457Lys p.E1457K ENST00000396432 26/26 309 277 32 202 201 1 varscan-mutect ARHGAP21,missense_variant,p.Glu1457Lys,ENST00000396432,NM_020824.3;ARHGAP21,missense_variant,p.Glu905Lys,ENST00000612832,;ARHGAP21,missense_variant,p.Glu906Lys,ENST00000320481,;ARHGAP21,downstream_gene_variant,,ENST00000636789,;ARHGAP21,downstream_gene_variant,,ENST00000418033,;ARHGAP21,3_prime_UTR_variant,,ENST00000638156,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000477190,; T ENST00000396432 Transcript missense_variant 4856/7167 4369/5877 1457/1958 E/K Gag/Aag 1 -1 ARHGAP21 HGNC HGNC:23725 protein_coding YES CCDS7144.2 ENSP00000379709 Q5T5U3 UPI0001639C78 NM_020824.3 deleterious(0.02) 26/26 Low_complexity_(Seg):seg,hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 24585920 24585920 C T 1 0 0 0 0 1 0 0 0 995 864 30 3 3 ARHGAP21 10 24585920 Missense_Mutation SNP C C3N-00293_T 18828336 24585920 109211502 157 12615 ALOX5 0 . GRCh38 10 45424132 45424132 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.646A>T p.Ser216Cys p.S216C ENST00000374391 5/14 162 145 17 136 136 0 strelka-varscan-mutect ALOX5,missense_variant,p.Ser216Cys,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,missense_variant,p.Ser216Cys,ENST00000542434,NM_001256154.1;ALOX5,3_prime_UTR_variant,,ENST00000612635,;ALOX5,non_coding_transcript_exon_variant,,ENST00000483623,; T ENST00000374391 Transcript missense_variant 699/2506 646/2025 216/674 S/C Agc/Tgc 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 deleterious(0) 5/14 PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Superfamily_domains:SSF48484,Prints_domain:PR00467 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 45424132 45424132 A T 1 0 0 0 0 1 0 0 0 640 188 7 4 4 ALOX5 10 45424132 Missense_Mutation SNP A C3N-00293_T 20838212 45424132 88373290 158 12616 ALOX5 0 . GRCh38 10 45441359 45441359 + Missense_Mutation SNP G G C rs755046400 C3N-00293_T C3N-00293_N G G c.1201G>C p.Val401Leu p.V401L ENST00000374391 9/14 196 174 22 146 146 0 strelka-mutect ALOX5,missense_variant,p.Val401Leu,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,missense_variant,p.Val401Leu,ENST00000542434,NM_001256154.1;ALOX5,3_prime_UTR_variant,,ENST00000612635,;RP11-67C2.2,downstream_gene_variant,,ENST00000435635,;ALOX5,non_coding_transcript_exon_variant,,ENST00000475300,;ALOX5,upstream_gene_variant,,ENST00000493336,;ALOX5,upstream_gene_variant,,ENST00000498461,;ALOX5,upstream_gene_variant,,ENST00000481117,; C ENST00000374391 Transcript missense_variant 1254/2506 1201/2025 401/674 V/L Gtg/Ctg rs755046400 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 tolerated(0.4) 9/14 PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Gene3D:1.20.245.10,Pfam_domain:PF00305,Superfamily_domains:SSF48484,Prints_domain:PR00087 MODERATE 1 SNV 1 1 PASS rs755046400 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 45441359 45441359 G C 1 0 0 0 0 1 0 0 0 640 1145 40 4 4 ALOX5 10 45441359 Missense_Mutation SNP G C3N-00293_T 17227 45441359 88356063 159 12617 MARCH8 0 . GRCh38 10 45463790 45463790 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.449G>A p.Arg150Lys p.R150K ENST00000453424 5/8 330 295 35 184 184 0 strelka-varscan-mutect MARCH8,missense_variant,p.Arg150Lys,ENST00000453424,NM_001282866.1;MARCH8,intron_variant,,ENST00000319836,NM_145021.5;MARCH8,intron_variant,,ENST00000395769,NM_001002266.2;MARCH8,intron_variant,,ENST00000453980,;MARCH8,upstream_gene_variant,,ENST00000476962,;MARCH8,intron_variant,,ENST00000602712,; T ENST00000453424 Transcript missense_variant 711/5638 449/1722 150/573 R/K aGa/aAa 1 -1 MARCH8 HGNC HGNC:23356 protein_coding YES CCDS60519.1 ENSP00000411848 Q5T0T0 UPI0000EE77CA NM_001282866.1 tolerated_low_confidence(0.19) 5/8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 45 45463790 45463790 C T 1 0 0 0 0 1 0 0 0 9232 913 32 3 3 MARCH8 10 45463790 Missense_Mutation SNP C C3N-00293_T 22431 45463790 88333632 160 12618 AGAP14P 0 . GRCh38 10 46357640 46357640 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.984A>T p.Lys328Asn p.K328N ENST00000624701 9/9 371 318 53 263 263 0 varscan-mutect AGAP14P,missense_variant,p.Lys328Asn,ENST00000624701,; T ENST00000624701 Transcript missense_variant 984/2058 984/2058 328/685 K/N aaA/aaT 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF deleterious(0) 9/9 PROSITE_profiles:PS50003,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS rs1387094633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 46357640 46357640 A T 1 0 0 0 0 1 0 0 0 444 69 3 4 4 AGAP14P 10 46357640 Missense_Mutation SNP A C3N-00293_T 893850 46357640 87439782 161 12619 OIT3 0 . GRCh38 10 72898736 72898736 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.134C>T p.Ser45Phe p.S45F ENST00000334011 2/9 194 184 10 141 141 0 strelka-varscan-mutect OIT3,missense_variant,p.Ser45Phe,ENST00000334011,NM_152635.2;OIT3,missense_variant,p.Ser45Phe,ENST00000622652,; T ENST00000334011 Transcript missense_variant 352/2365 134/1638 45/545 S/F tCt/tTt 1 1 OIT3 HGNC HGNC:29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.2 deleterious(0) 2/9 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF326 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 72898736 72898736 C T 1 0 0 0 0 1 0 0 0 10924 913 32 3 3 OIT3 10 72898736 Missense_Mutation SNP C C3N-00293_T 26541096 72898736 60898686 162 12620 ZSWIM8 0 . GRCh38 10 73799113 73799113 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.4288G>C p.Glu1430Gln p.E1430Q ENST00000398706 21/26 251 237 14 187 187 0 strelka-varscan-mutect ZSWIM8,missense_variant,p.Glu1430Gln,ENST00000604729,;ZSWIM8,missense_variant,p.Glu1430Gln,ENST00000398706,NM_015037.3;ZSWIM8,missense_variant,p.Glu1425Gln,ENST00000605216,NM_001242487.1;ZSWIM8,missense_variant,p.Glu1392Gln,ENST00000603114,NM_001242488.1;ZSWIM8,missense_variant,p.Glu765Gln,ENST00000603187,;ZSWIM8,missense_variant,p.Glu700Gln,ENST00000412198,;ZSWIM8,missense_variant,p.Glu698Gln,ENST00000604754,;ZSWIM8,intron_variant,,ENST00000604524,;NDST2,downstream_gene_variant,,ENST00000309979,NM_003635.3;NDST2,downstream_gene_variant,,ENST00000299641,;ZSWIM8,upstream_gene_variant,,ENST00000466354,;NDST2,downstream_gene_variant,,ENST00000429742,;ZSWIM8-AS1,intron_variant,,ENST00000456638,;ZSWIM8,non_coding_transcript_exon_variant,,ENST00000603409,;ZSWIM8,non_coding_transcript_exon_variant,,ENST00000604165,;ZSWIM8,downstream_gene_variant,,ENST00000431225,;ZSWIM8,upstream_gene_variant,,ENST00000603840,;ZSWIM8,upstream_gene_variant,,ENST00000603309,;ZSWIM8,downstream_gene_variant,,ENST00000489234,;ZSWIM8,upstream_gene_variant,,ENST00000603195,;ZSWIM8,downstream_gene_variant,,ENST00000425051,;ZSWIM8,downstream_gene_variant,,ENST00000487278,;ZSWIM8,upstream_gene_variant,,ENST00000466568,;ZSWIM8,3_prime_UTR_variant,,ENST00000433366,;ZSWIM8,3_prime_UTR_variant,,ENST00000492395,;RP11-574K11.31,intron_variant,,ENST00000603027,;RP11-574K11.31,intron_variant,,ENST00000603706,; C ENST00000398706 Transcript missense_variant 4543/6062 4288/5529 1430/1842 E/Q Gag/Cag 1 1 ZSWIM8 HGNC HGNC:23528 protein_coding YES CCDS44440.1 ENSP00000381693 A7E2V4 UPI0000ED938E NM_015037.3 tolerated(0.06) 21/26 hmmpanther:PTHR22619 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 73799113 73799113 G C 1 0 0 0 0 1 0 0 0 18848 1291 45 4 4 ZSWIM8 10 73799113 Missense_Mutation SNP G C3N-00293_T 900377 73799113 59998309 163 12621 LRIT1 0 . GRCh38 10 84232819 84232819 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.980T>A p.Ile327Asn p.I327N ENST00000372105 4/4 227 209 18 187 187 0 strelka-varscan-mutect LRIT1,missense_variant,p.Ile327Asn,ENST00000372105,NM_015613.2; T ENST00000372105 Transcript missense_variant 1002/2228 980/1872 327/623 I/N aTc/aAc 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 deleterious(0.03) 4/4 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 84232819 84232819 A T 1 0 0 0 0 1 0 0 0 8842 333 12 4 4 LRIT1 10 84232819 Missense_Mutation SNP A C3N-00293_T 10433706 84232819 49564603 164 12622 GRID1 0 . GRCh38 10 85869166 85869166 + Silent SNP C C G rs758170958 C3N-00293_T C3N-00293_N C C c.795G>C p.= p.P265P ENST00000327946 6/16 186 166 20 163 163 0 strelka-varscan-mutect GRID1,synonymous_variant,p.=,ENST00000327946,NM_017551.2;GRID1,synonymous_variant,p.=,ENST00000464741,; G ENST00000327946 Transcript synonymous_variant 881/5834 795/3030 265/1009 P ccG/ccC rs758170958 1 -1 GRID1 HGNC HGNC:4575 protein_coding YES CCDS31236.1 ENSP00000330148 Q9ULK0 UPI00001D8051 NM_017551.2 6/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,Superfamily_domains:SSF53822 LOW 1 SNV 2 1 PASS rs758170958 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 45 85869166 85869166 C G 1 0 0 0 0 0 0 0 1 6651 639 23 4 4 GRID1 10 85869166 Silent SNP C C3N-00293_T 1636347 85869166 47928256 165 12623 IFIT1 0 . GRCh38 10 89403335 89403335 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1060G>T p.Gly354Cys p.G354C ENST00000371804 2/2 212 193 19 85 85 0 strelka-varscan-mutect IFIT1,missense_variant,p.Gly323Cys,ENST00000546318,NM_001270927.1,NM_001270928.1,NM_001270930.1,NM_001270929.1;IFIT1,missense_variant,p.Gly354Cys,ENST00000371804,NM_001548.4;LIPA,intron_variant,,ENST00000371837,; T ENST00000371804 Transcript missense_variant 1227/1880 1060/1437 354/478 G/C Ggc/Tgc 1 1 IFIT1 HGNC HGNC:5407 protein_coding YES CCDS31243.1 ENSP00000360869 P09914 UPI0000169E8F NM_001548.4 deleterious(0) 2/2 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR10271,hmmpanther:PTHR10271:SF16,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 89403335 89403335 G T 1 0 0 0 0 1 0 0 0 7421 1000 35 2 2 IFIT1 10 89403335 Missense_Mutation SNP G C3N-00293_T 3534169 89403335 44394087 166 12624 IDE 0 . GRCh38 10 92510108 92510108 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.839A>G p.Asn280Ser p.N280S ENST00000265986 6/25 169 159 10 80 80 0 strelka-varscan-mutect IDE,missense_variant,p.Asn280Ser,ENST00000265986,NM_001322795.1,NM_001322796.1,NM_004969.3;IDE,downstream_gene_variant,,ENST00000436178,;IDE,3_prime_UTR_variant,,ENST00000478361,; C ENST00000265986 Transcript missense_variant 896/5877 839/3060 280/1019 N/S aAc/aGc 1 -1 IDE HGNC HGNC:5381 protein_coding YES CCDS7421.1 ENSP00000265986 P14735 UPI000013D6B6 NM_001322795.1,NM_001322796.1,NM_004969.3 deleterious(0.01) 6/25 hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF155,Pfam_domain:PF05193,Gene3D:3.30.830.10,Superfamily_domains:SSF63411 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 92510108 92510108 T C 1 0 0 0 0 1 0 0 0 7393 1725 60 5 5 IDE 10 92510108 Missense_Mutation SNP T C3N-00293_T 3106773 92510108 41287314 167 12625 CHRNA10 0 . GRCh38 11 3666319 3666319 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1141G>T p.Gly381Cys p.G381C ENST00000250699 5/5 162 153 9 101 101 0 strelka-varscan-mutect CHRNA10,missense_variant,p.Gly381Cys,ENST00000250699,NM_020402.3;CHRNA10,3_prime_UTR_variant,,ENST00000534359,NM_001303034.1,NM_001303035.1;ART1,downstream_gene_variant,,ENST00000250693,NM_004314.2;NUP98,downstream_gene_variant,,ENST00000533346,;Y_RNA,upstream_gene_variant,,ENST00000364409,;Y_RNA,upstream_gene_variant,,ENST00000363331,;CHRNA10,downstream_gene_variant,,ENST00000493827,;CHRNA10,3_prime_UTR_variant,,ENST00000526599,; A ENST00000250699 Transcript missense_variant 1213/1945 1141/1353 381/450 G/C Ggc/Tgc 1 -1 CHRNA10 HGNC HGNC:13800 protein_coding YES CCDS7745.1 ENSP00000250699 Q9GZZ6 UPI0000038CF1 NM_020402.3 tolerated(0.09) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR18945:SF566,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 3666319 3666319 C A 1 0 0 0 0 1 0 0 0 3142 623 22 2 2 CHRNA10 11 3666319 Missense_Mutation SNP C C3N-00293_T 3666319 131420303 168 12626 C11orf40 0 . GRCh38 11 4577773 4577773 + Silent SNP C C A novel C3N-00293_T C3N-00293_N C C c.48G>T p.= p.L16L ENST00000307616 1/4 360 320 40 271 271 0 strelka-varscan-mutect C11orf40,synonymous_variant,p.=,ENST00000307616,NM_144663.1; A ENST00000307616 Transcript synonymous_variant 48/654 48/654 16/217 L ctG/ctT 1 -1 C11orf40 HGNC HGNC:23986 protein_coding YES CCDS31354.1 ENSP00000302918 Q8WZ69 UPI0000073B2B NM_144663.1 1/4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 4577773 4577773 C A 1 0 0 0 0 0 0 0 1 1781 465 17 2 2 C11orf40 11 4577773 Silent SNP C C3N-00293_T 911454 4577773 130508849 169 12627 OR56A3 0 . GRCh38 11 5948217 5948217 + Missense_Mutation SNP C C T C3N-00293_T C3N-00293_N C C c.871C>T p.Leu291Phe p.L291F ENST00000329564 1/1 243 212 31 160 160 0 strelka-varscan-mutect OR56A3,missense_variant,p.Leu291Phe,ENST00000329564,NM_001003443.2;AC025016.1,downstream_gene_variant,,ENST00000528915,; T ENST00000329564 Transcript missense_variant 878/1022 871/948 291/315 L/F Ctt/Ttt COSM3450360 1 1 OR56A3 HGNC HGNC:14786 protein_coding YES CCDS41614.1 ENSP00000331572 Q8NH54 A0A126GWL6 UPI0000041BF7 NM_001003443.2 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF40,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999908 1 1 1 0 T 3 4 45 5948217 5948217 C T 1 0 0 0 0 1 0 0 0 11206 681 24 3 3 OR56A3 11 5948217 Missense_Mutation SNP C C3N-00293_T 1370444 5948217 129138405 170 12628 OTOG 0 . GRCh38 11 17558225 17558225 + Nonsense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.942G>A p.Trp314Ter p.W314* ENST00000399391 8/55 266 252 14 214 214 0 strelka-varscan-mutect OTOG,stop_gained,p.Trp302Ter,ENST00000399397,NM_001292063.1;OTOG,stop_gained,p.Trp314Ter,ENST00000399391,NM_001277269.1;OTOG,downstream_gene_variant,,ENST00000428619,;OTOG,non_coding_transcript_exon_variant,,ENST00000498332,;OTOG,intron_variant,,ENST00000485669,; A ENST00000399391 Transcript stop_gained 942/8778 942/8778 314/2925 W/* tgG/tgA 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 8/55 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 45 17558225 17558225 G A 1 0 0 0 0 0 1 0 0 11370 1212 42 3 3 OTOG 11 17558225 Nonsense_Mutation SNP G C3N-00293_T 11610008 17558225 117528397 171 12629 NAV2 0 . GRCh38 11 20105716 20105716 + Missense_Mutation SNP A A G novel C3N-00293_T C3N-00293_N A A c.7007A>G p.Asp2336Gly p.D2336G ENST00000396087 38/41 113 100 13 90 89 1 strelka-varscan-mutect NAV2,missense_variant,p.Asp2337Gly,ENST00000527559,;NAV2,missense_variant,p.Asp2281Gly,ENST00000540292,;NAV2,missense_variant,p.Asp2280Gly,ENST00000396085,NM_182964.5;NAV2,missense_variant,p.Asp2277Gly,ENST00000349880,NM_145117.4;NAV2,missense_variant,p.Asp2213Gly,ENST00000360655,NM_001111018.1;NAV2,missense_variant,p.Asp2336Gly,ENST00000396087,NM_001244963.1;NAV2,missense_variant,p.Asp1341Gly,ENST00000533917,NM_001111019.2;NAV2,non_coding_transcript_exon_variant,,ENST00000533746,;NAV2,upstream_gene_variant,,ENST00000525025,; G ENST00000396087 Transcript missense_variant 7106/7882 7007/7467 2336/2488 D/G gAc/gGc 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 deleterious(0.01) 38/41 hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999992 1 1 1 0 G 3 3 45 20105716 20105716 A G 1 0 0 0 0 1 0 0 0 10193 275 10 5 5 NAV2 11 20105716 Missense_Mutation SNP A C3N-00293_T 2547491 20105716 114980906 172 12630 NELL1 0 . GRCh38 11 21573185 21573185 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.2242G>A p.Glu748Lys p.E748K ENST00000298925 20/21 242 217 25 162 162 0 strelka-varscan-mutect NELL1,missense_variant,p.Glu748Lys,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Glu663Lys,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Glu720Lys,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Glu673Lys,ENST00000532434,NM_201551.2;NELL1,splice_region_variant,,ENST00000529218,; A ENST00000298925 Transcript missense_variant,splice_region_variant 2395/3329 2242/2517 748/838 E/K Gaa/Aaa 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 tolerated(0.16) 20/21 Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 21573185 21573185 G A 1 0 0 0 0 1 0 0 0 10364 1188 41 3 3 NELL1 11 21573185 Missense_Mutation SNP G C3N-00293_T 1467469 21573185 113513437 173 12631 KIF18A 0 . GRCh38 11 28091440 28091440 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.557G>T p.Gly186Val p.G186V ENST00000263181 4/17 287 270 17 175 175 0 strelka-varscan-mutect KIF18A,missense_variant,p.Gly186Val,ENST00000263181,NM_031217.3;KIF18A,non_coding_transcript_exon_variant,,ENST00000533466,;KIF18A,upstream_gene_variant,,ENST00000531047,; A ENST00000263181 Transcript missense_variant 848/3568 557/2697 186/898 G/V gGg/gTg 1 -1 KIF18A HGNC HGNC:29441 protein_coding YES CCDS7867.1 ENSP00000263181 Q8NI77 UPI0000037CCC NM_031217.3 deleterious(0) 4/17 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF399,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 28091440 28091440 C A 1 0 0 0 0 1 0 0 0 8144 623 22 2 2 KIF18A 11 28091440 Missense_Mutation SNP C C3N-00293_T 6518255 28091440 106995182 174 12632 DCDC1 0 . GRCh38 11 30931809 30931809 + Silent SNP A A T novel C3N-00293_T C3N-00293_N A A c.180T>A p.= p.T60T ENST00000406071 3/20 210 196 14 145 145 0 strelka-varscan-mutect DCDC1,synonymous_variant,p.=,ENST00000597505,;DCDC1,synonymous_variant,p.=,ENST00000406071,NM_020869.3;DCDC1,non_coding_transcript_exon_variant,,ENST00000437348,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,; T ENST00000406071 Transcript synonymous_variant 496/4758 180/2673 60/890 T acT/acA 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 3/20 PROSITE_profiles:PS50309,hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 30931809 30931809 A T 1 0 0 0 0 0 0 0 1 4086 407 15 4 4 DCDC1 11 30931809 Silent SNP A C3N-00293_T 2840369 30931809 104154813 175 12633 PAX6 0 . GRCh38 11 31790013 31790013 + Missense_Mutation SNP A A G novel C3N-00293_T C3N-00293_N A A c.1232T>C p.Ile411Thr p.I411T ENST00000419022 14/14 254 222 32 132 132 0 strelka-varscan-mutect PAX6,missense_variant,p.Ile411Thr,ENST00000419022,NM_001310158.1,NM_001310161.1,NM_001258462.1;PAX6,missense_variant,p.Ile411Thr,ENST00000606377,NM_001310161.1,NM_001258463.1;PAX6,missense_variant,p.Ile411Thr,ENST00000379129,;PAX6,missense_variant,p.Ile411Thr,ENST00000379107,;PAX6,missense_variant,p.Ile397Thr,ENST00000379132,NM_001127612.1;PAX6,missense_variant,p.Ile397Thr,ENST00000379123,NM_001258464.1,NM_000280.4;PAX6,missense_variant,p.Ile397Thr,ENST00000379109,;PAX6,missense_variant,p.Ile411Thr,ENST00000379115,NM_001604.5;PAX6,missense_variant,p.Ile397Thr,ENST00000241001,;PAX6,missense_variant,p.Ile397Thr,ENST00000379111,NM_001258465.1;PAX6,downstream_gene_variant,,ENST00000455099,;PAX6,downstream_gene_variant,,ENST00000471303,;PAX6,downstream_gene_variant,,ENST00000531910,;PAX6,downstream_gene_variant,,ENST00000530373,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000464174,;PAX6,non_coding_transcript_exon_variant,,ENST00000474783,;PAX6,downstream_gene_variant,,ENST00000532916,; G ENST00000419022 Transcript missense_variant 1701/6922 1232/1311 411/436 I/T aTt/aCt 1 -1 PAX6 HGNC HGNC:8620 protein_coding YES CCDS31452.1 ENSP00000404100 P26367 F1T0F8 UPI000002B0A0 NM_001310158.1,NM_001310161.1,NM_001258462.1 deleterious(0) 14/14 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 31790013 31790013 A G 1 0 0 0 0 1 0 0 0 11568 101 4 5 5 PAX6 11 31790013 Missense_Mutation SNP A C3N-00293_T 858204 31790013 103296609 176 12634 OR4C11 0 . GRCh38 11 55603602 55603602 + Missense_Mutation SNP G G A rs140582621 C3N-00293_T C3N-00293_N G G c.772C>T p.Arg258Cys p.R258C ENST00000302231 1/1 209 184 25 153 153 0 strelka-varscan-mutect OR4C11,missense_variant,p.Arg258Cys,ENST00000302231,NM_001004700.2; A ENST00000302231 Transcript missense_variant 797/1045 772/933 258/310 R/C Cgc/Tgc rs140582621,COSM688952 1 -1 OR4C11 HGNC HGNC:15167 protein_coding YES CCDS31503.1 ENSP00000306651 Q6IEV9 A0A126GVN6 UPI000013E7AD NM_001004700.2 tolerated(0.06) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF447,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs140582621 . 23 184 0 0 2 0 0 0 -10.87748 0.9901406 1 1 1 0 A 3 1 45 55603602 55603602 G A 1 0 0 0 0 1 0 0 0 11122 1145 40 1 1 OR4C11 11 55603602 Missense_Mutation SNP G C3N-00293_T 23813589 55603602 79483020 177 12635 OR5D14 0 . GRCh38 11 55795949 55795949 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.394C>A p.Leu132Met p.L132M ENST00000335605 1/1 194 179 15 131 131 0 strelka-varscan-mutect OR5D14,missense_variant,p.Leu132Met,ENST00000335605,NM_001004735.1; A ENST00000335605 Transcript missense_variant 394/945 394/945 132/314 L/M Ctg/Atg COSM4834518 1 1 OR5D14 HGNC HGNC:15281 protein_coding YES CCDS31508.1 ENSP00000334456 Q8NGL3 UPI000004B1F6 NM_001004735.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF67,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs949576164 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 55795949 55795949 C A 1 0 0 0 0 1 0 0 0 11225 912 32 2 2 OR5D14 11 55795949 Missense_Mutation SNP C C3N-00293_T 192347 55795949 79290673 178 12636 OR8I2 0 . GRCh38 11 56093963 56093963 + Missense_Mutation SNP T T G novel C3N-00293_T C3N-00293_N T T c.656T>G p.Ile219Ser p.I219S ENST00000302124 1/1 201 168 33 127 126 1 strelka-varscan-mutect OR8I2,missense_variant,p.Ile219Ser,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; G ENST00000302124 Transcript missense_variant 656/933 656/933 219/310 I/S aTc/aGc 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 tolerated(0.86) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 56093963 56093963 T G 1 0 0 0 0 1 0 0 0 11308 1435 50 5 5 OR8I2 11 56093963 Missense_Mutation SNP T C3N-00293_T 298014 56093963 78992659 179 12637 OR8J3 0 . GRCh38 11 56137429 56137429 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.290G>A p.Cys97Tyr p.C97Y ENST00000301529 1/1 293 273 20 189 189 0 varscan-mutect OR8J3,missense_variant,p.Cys97Tyr,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; T ENST00000301529 Transcript missense_variant 290/948 290/948 97/315 C/Y tGt/tAt 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 56137429 56137429 C T 1 0 0 0 0 1 0 0 0 11310 478 17 3 3 OR8J3 11 56137429 Missense_Mutation SNP C C3N-00293_T 43466 56137429 78949193 180 12638 OR5T1 0 . GRCh38 11 56276035 56276035 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.397G>A p.Asp133Asn p.D133N ENST00000313033 1/1 318 295 23 172 172 0 varscan-mutect OR5T1,missense_variant,p.Asp133Asn,ENST00000313033,NM_001004745.1; A ENST00000313033 Transcript missense_variant 397/981 397/981 133/326 D/N Gat/Aat 1 1 OR5T1 HGNC HGNC:14821 protein_coding YES CCDS31525.1 ENSP00000323612 Q8NG75 A0A126GVL6 UPI000004B22E NM_001004745.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF33,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 56276035 56276035 G A 1 0 0 0 0 1 0 0 0 11249 1290 45 3 3 OR5T1 11 56276035 Missense_Mutation SNP G C3N-00293_T 138606 56276035 78810587 181 12639 CTNND1 0 . GRCh38 11 57805935 57805935 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.1776G>T p.= p.R592R ENST00000399050 10/21 186 175 11 151 151 0 strelka-varscan-mutect CTNND1,synonymous_variant,p.=,ENST00000524630,;CTNND1,synonymous_variant,p.=,ENST00000399050,NM_001085458.1;CTNND1,synonymous_variant,p.=,ENST00000361332,NM_001085459.1;CTNND1,synonymous_variant,p.=,ENST00000361391,NM_001331.2;CTNND1,synonymous_variant,p.=,ENST00000361796,NM_001206885.1;CTNND1,synonymous_variant,p.=,ENST00000358694,NM_001085460.1,NM_001085461.1;CTNND1,synonymous_variant,p.=,ENST00000529526,NM_001206891.1;CTNND1,synonymous_variant,p.=,ENST00000532649,NM_001206889.1;CTNND1,synonymous_variant,p.=,ENST00000534579,;CTNND1,synonymous_variant,p.=,ENST00000428599,NM_001085462.1;CTNND1,synonymous_variant,p.=,ENST00000532844,NM_001206883.1;CTNND1,synonymous_variant,p.=,ENST00000526357,NM_001206886.1;CTNND1,synonymous_variant,p.=,ENST00000529873,NM_001206887.1;CTNND1,synonymous_variant,p.=,ENST00000530748,NM_001206884.1;CTNND1,synonymous_variant,p.=,ENST00000528621,NM_001206888.1;CTNND1,synonymous_variant,p.=,ENST00000415361,NM_001085463.1;CTNND1,synonymous_variant,p.=,ENST00000530094,NM_001085464.1;CTNND1,synonymous_variant,p.=,ENST00000426142,NM_001085467.1;CTNND1,synonymous_variant,p.=,ENST00000532787,NM_001085465.1;CTNND1,synonymous_variant,p.=,ENST00000532463,NM_001206890.1;CTNND1,synonymous_variant,p.=,ENST00000528232,NM_001085466.1;CTNND1,synonymous_variant,p.=,ENST00000529986,NM_001085468.1;CTNND1,synonymous_variant,p.=,ENST00000532245,NM_001085469.1;CTNND1,synonymous_variant,p.=,ENST00000527467,;CTNND1,synonymous_variant,p.=,ENST00000531014,;CTNND1,synonymous_variant,p.=,ENST00000533667,;CTNND1,synonymous_variant,p.=,ENST00000525902,;CTNND1,synonymous_variant,p.=,ENST00000526772,;CTNND1,synonymous_variant,p.=,ENST00000529919,;CTNND1,synonymous_variant,p.=,ENST00000526938,;CTNND1,downstream_gene_variant,,ENST00000534647,;CTNND1,upstream_gene_variant,,ENST00000531007,;CTNND1,downstream_gene_variant,,ENST00000533189,;CTNND1,upstream_gene_variant,,ENST00000530720,;CTNND1,downstream_gene_variant,,ENST00000527599,; T ENST00000399050 Transcript synonymous_variant 2312/6313 1776/2907 592/968 R cgG/cgT 1 1 CTNND1 HGNC HGNC:2515 protein_coding YES CCDS44604.1 ENSP00000382004 O60716 UPI000012860B NM_001085458.1 10/21 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF6,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -13.90485 0.9999557 1 1 1 0 T 2 4 45 57805935 57805935 G T 1 0 0 0 0 0 0 0 1 3828 1219 43 2 2 CTNND1 11 57805935 Silent SNP G C3N-00293_T 1529900 57805935 77280687 182 12640 ACY3 0 . GRCh38 11 67646833 67646833 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.211C>A p.Arg71Ser p.R71S ENST00000255082 3/8 331 283 48 247 247 0 strelka-varscan-mutect ACY3,missense_variant,p.Arg71Ser,ENST00000255082,NM_080658.1;ACY3,5_prime_UTR_variant,,ENST00000529256,;AP003385.2,downstream_gene_variant,,ENST00000426387,; T ENST00000255082 Transcript missense_variant 382/1300 211/960 71/319 R/S Cgc/Agc 1 -1 ACY3 HGNC HGNC:24104 protein_coding YES CCDS8175.1 ENSP00000255082 Q96HD9 A0A024R5L2 UPI0000073C5C NM_080658.1 deleterious(0) 3/8 HAMAP:MF_00704,hmmpanther:PTHR15162:SF5,hmmpanther:PTHR15162,Pfam_domain:PF04952,PIRSF_domain:PIRSF018001,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs928996990 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 67646833 67646833 G T 1 0 0 0 0 1 0 0 0 271 1116 39 1 1 ACY3 11 67646833 Missense_Mutation SNP G C3N-00293_T 9840898 67646833 67439789 183 12641 LRP5 0 . GRCh38 11 68448986 68448986 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.4764C>T p.= p.D1588D ENST00000294304 23/23 159 123 36 99 99 0 strelka-varscan-mutect LRP5,synonymous_variant,p.=,ENST00000294304,NM_001291902.1,NM_002335.3;LRP5,synonymous_variant,p.=,ENST00000529702,;LRP5,non_coding_transcript_exon_variant,,ENST00000529481,;LRP5,3_prime_UTR_variant,,ENST00000529993,; T ENST00000294304 Transcript synonymous_variant 4870/5159 4764/4848 1588/1615 D gaC/gaT 1 1 LRP5 HGNC HGNC:6697 protein_coding YES CCDS8181.1 ENSP00000294304 O75197 UPI0000073246 NM_001291902.1,NM_002335.3 23/23 PIRSF_domain:PIRSF036314 LOW 1 SNV 1 1 PASS rs1371150451 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 68448986 68448986 C T 1 0 0 0 0 0 0 0 1 8855 477 17 3 3 LRP5 11 68448986 Silent SNP C C3N-00293_T 802153 68448986 66637636 184 12642 TRIM64B 0 . GRCh38 11 89871017 89871017 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.954C>A p.= p.P318P ENST00000329862 6/6 615 577 38 414 414 0 varscan-mutect TRIM64B,synonymous_variant,p.=,ENST00000329862,NM_001164397.1; T ENST00000329862 Transcript synonymous_variant 954/2689 954/1350 318/449 P ccC/ccA 1 -1 TRIM64B HGNC HGNC:37147 protein_coding YES CCDS53693.1 ENSP00000332969 A6NI03 UPI0001662600 NM_001164397.1 6/6 Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF354,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 3 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 89871017 89871017 G T 1 0 0 0 0 0 0 0 1 17032 1335 47 2 2 TRIM64B 11 89871017 Silent SNP G C3N-00293_T 21422031 89871017 45215605 185 12643 FAT3 0 . GRCh38 11 92890526 92890526 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.12733G>A p.Ala4245Thr p.A4245T ENST00000525166 27/27 88 83 5 69 69 0 strelka-mutect FAT3,missense_variant,p.Ala4363Thr,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ala4245Thr,ENST00000525166,;FAT3,missense_variant,p.Ala698Thr,ENST00000533797,;FAT3,non_coding_transcript_exon_variant,,ENST00000489716,;FAT3,non_coding_transcript_exon_variant,,ENST00000469900,; A ENST00000525166 Transcript missense_variant 12755/18699 12733/13320 4245/4439 A/T Gcc/Acc 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.34) 27/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 MODERATE 1 SNV 5 1 PASS rs1292661793 . 0 196 12 2 0 0 0 0 -8.483389 0.9898568 1 1 1 0 A 3 1 45 92890526 92890526 G A 1 0 0 0 0 1 0 0 0 5551 1203 42 3 3 FAT3 11 92890526 Missense_Mutation SNP G C3N-00293_T 3019509 92890526 42196096 186 12644 JRKL 0 . GRCh38 11 96390889 96390889 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.240C>T p.= p.D80D ENST00000332349 2/2 180 170 10 118 118 0 strelka-varscan-mutect JRKL,synonymous_variant,p.=,ENST00000332349,NM_001261833.1,NM_003772.3;CCDC82,upstream_gene_variant,,ENST00000278520,NM_001318736.1,NM_024725.3;CCDC82,upstream_gene_variant,,ENST00000538597,;CCDC82,upstream_gene_variant,,ENST00000530203,;JRKL,intron_variant,,ENST00000546177,;CCDC82,upstream_gene_variant,,ENST00000525786,;CCDC82,upstream_gene_variant,,ENST00000524836,; T ENST00000332349 Transcript synonymous_variant 487/2855 240/1575 80/524 D gaC/gaT 1 1 JRKL HGNC HGNC:6200 protein_coding YES CCDS8308.1 ENSP00000333350 Q9Y4A0 UPI0000167818 NM_001261833.1,NM_003772.3 2/2 Gene3D:1.10.10.60,Pfam_domain:PF03221,PROSITE_profiles:PS51253,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF174,SMART_domains:SM00674,Superfamily_domains:SSF46689 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 96390889 96390889 C T 1 0 0 0 0 0 0 0 1 7877 477 17 3 3 JRKL 11 96390889 Silent SNP C C3N-00293_T 3500363 96390889 38695733 187 12645 CASP1 0 . GRCh38 11 105029741 105029741 + Missense_Mutation SNP A A C novel C3N-00293_T C3N-00293_N A A c.786T>G p.Phe262Leu p.F262L ENST00000533400 6/9 458 418 40 317 317 0 strelka-varscan-mutect CASP1,missense_variant,p.Phe262Leu,ENST00000533400,NM_001257118.2;CASP1,missense_variant,p.Phe225Leu,ENST00000527979,;CASP1,missense_variant,p.Phe262Leu,ENST00000436863,NM_033292.3;CASP1,missense_variant,p.Phe223Leu,ENST00000528974,;CASP1,missense_variant,p.Phe241Leu,ENST00000525825,NM_001223.4,NM_001257119.2;CASP1,missense_variant,p.Phe169Leu,ENST00000526568,NM_033293.3;CASP1,missense_variant,p.Phe169Leu,ENST00000446369,NM_033294.3;CASP1,missense_variant,p.Phe169Leu,ENST00000534497,;CASP1,missense_variant,p.Phe111Leu,ENST00000532439,;CASP1,intron_variant,,ENST00000353247,NM_033295.3;CASP1,intron_variant,,ENST00000531166,;CASP1,3_prime_UTR_variant,,ENST00000529871,;CASP1,downstream_gene_variant,,ENST00000526511,;CASP1,downstream_gene_variant,,ENST00000528424,;CASP1,downstream_gene_variant,,ENST00000532520,;CASP1,upstream_gene_variant,,ENST00000527625,; C ENST00000533400 Transcript missense_variant 822/2001 786/1215 262/404 F/L ttT/ttG 1 -1 CASP1 HGNC HGNC:1499 protein_coding YES CCDS8330.1 ENSP00000433138 P29466 UPI000003AEF8 NM_001257118.2 deleterious(0) 6/9 Gene3D:3.40.50.1460,Pfam_domain:PF00656,PIRSF_domain:PIRSF038001,PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF34,SMART_domains:SM00115,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 105029741 105029741 A C 1 0 0 0 0 1 0 0 0 2368 359 13 5 5 CASP1 11 105029741 Missense_Mutation SNP A C3N-00293_T 8638852 105029741 30056881 188 12646 IL18 0 . GRCh38 11 112148626 112148626 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.337G>C p.Glu113Gln p.E113Q ENST00000280357 5/6 225 211 14 137 137 0 strelka-varscan-mutect IL18,missense_variant,p.Glu113Gln,ENST00000280357,NM_001562.3;IL18,missense_variant,p.Glu109Gln,ENST00000524595,NM_001243211.1;IL18,missense_variant,p.Glu113Gln,ENST00000528832,;IL18,non_coding_transcript_exon_variant,,ENST00000533858,;IL18,non_coding_transcript_exon_variant,,ENST00000525547,;AP002884.2,intron_variant,,ENST00000525987,;AP002884.2,intron_variant,,ENST00000532699,;AP002884.2,intron_variant,,ENST00000531744,;IL18,downstream_gene_variant,,ENST00000534225,; G ENST00000280357 Transcript missense_variant 557/1147 337/582 113/193 E/Q Gag/Cag 1 -1 IL18 HGNC HGNC:5986 protein_coding YES CCDS44731.1 ENSP00000280357 Q14116 UPI000012D487 NM_001562.3 tolerated(0.3) 5/6 hmmpanther:PTHR11326,Pfam_domain:PF00340,Gene3D:2.80.10.50,PIRSF_domain:PIRSF015162,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 112148626 112148626 C G 1 0 0 0 0 1 0 0 0 7553 835 29 4 4 IL18 11 112148626 Missense_Mutation SNP C C3N-00293_T 7118885 112148626 22937996 189 12647 HYOU1 0 . GRCh38 11 119055002 119055002 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.478C>A p.Leu160Ile p.L160I ENST00000617285 6/26 226 212 14 164 164 0 strelka-varscan-mutect HYOU1,missense_variant,p.Leu160Ile,ENST00000617285,NM_001130991.2,NM_006389.4;HYOU1,missense_variant,p.Leu160Ile,ENST00000612687,;HYOU1,missense_variant,p.Leu160Ile,ENST00000621959,;HYOU1,missense_variant,p.Leu160Ile,ENST00000614711,;HYOU1,missense_variant,p.Leu160Ile,ENST00000532519,;HYOU1,missense_variant,p.Leu160Ile,ENST00000530473,;HYOU1,missense_variant,p.Leu160Ile,ENST00000526656,;HYOU1,missense_variant,p.Leu160Ile,ENST00000534233,;HYOU1,intron_variant,,ENST00000614668,;HYOU1,downstream_gene_variant,,ENST00000527038,;HYOU1,downstream_gene_variant,,ENST00000532421,;HYOU1,downstream_gene_variant,,ENST00000530467,;HYOU1,downstream_gene_variant,,ENST00000610597,;HYOU1,3_prime_UTR_variant,,ENST00000543287,;HYOU1,3_prime_UTR_variant,,ENST00000531968,;HYOU1,non_coding_transcript_exon_variant,,ENST00000531694,;HYOU1,downstream_gene_variant,,ENST00000533381,;HYOU1,downstream_gene_variant,,ENST00000526354,;HYOU1,downstream_gene_variant,,ENST00000529174,;HYOU1,downstream_gene_variant,,ENST00000622474,; T ENST00000617285 Transcript missense_variant 603/4529 478/3000 160/999 L/I Cta/Ata 1 -1 HYOU1 HGNC HGNC:16931 protein_coding YES CCDS8408.1 ENSP00000480150 Q9Y4L1 UPI0000130F72 NM_001130991.2,NM_006389.4 tolerated(0.2) 6/26 hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF90,Pfam_domain:PF00012,Gene3D:3.30.420.40,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 119055002 119055002 G T 1 0 0 0 0 1 0 0 0 7367 933 33 2 2 HYOU1 11 119055002 Missense_Mutation SNP G C3N-00293_T 6906376 119055002 16031620 190 12648 HMBS 0 . GRCh38 11 119092454 119092454 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.702G>T p.= p.L234L ENST00000278715 11/14 461 414 47 378 378 0 strelka-varscan-mutect HMBS,synonymous_variant,p.=,ENST00000537841,;HMBS,synonymous_variant,p.=,ENST00000442944,;HMBS,synonymous_variant,p.=,ENST00000278715,NM_000190.3;HMBS,synonymous_variant,p.=,ENST00000392841,NM_001024382.1;HMBS,synonymous_variant,p.=,ENST00000543090,;HMBS,intron_variant,,ENST00000542729,NM_001258209.1;HMBS,intron_variant,,ENST00000544387,NM_001258208.1;DPAGT1,downstream_gene_variant,,ENST00000409993,;DPAGT1,downstream_gene_variant,,ENST00000354202,NM_001382.3;H2AFX,downstream_gene_variant,,ENST00000530167,NM_002105.2;HMBS,downstream_gene_variant,,ENST00000539986,;HMBS,downstream_gene_variant,,ENST00000535253,;HMBS,downstream_gene_variant,,ENST00000546302,;DPAGT1,downstream_gene_variant,,ENST00000636404,;HMBS,downstream_gene_variant,,ENST00000536813,;HMBS,downstream_gene_variant,,ENST00000534956,;HMBS,downstream_gene_variant,,ENST00000536185,;HMBS,3_prime_UTR_variant,,ENST00000545621,;HMBS,non_coding_transcript_exon_variant,,ENST00000546226,;HMBS,non_coding_transcript_exon_variant,,ENST00000543543,;HMBS,non_coding_transcript_exon_variant,,ENST00000542044,;HMBS,non_coding_transcript_exon_variant,,ENST00000544182,;DPAGT1,downstream_gene_variant,,ENST00000481084,;DPAGT1,downstream_gene_variant,,ENST00000461999,;DPAGT1,downstream_gene_variant,,ENST00000392834,;DPAGT1,downstream_gene_variant,,ENST00000414373,;H2AFX,downstream_gene_variant,,ENST00000375167,;DPAGT1,downstream_gene_variant,,ENST00000525456,;DPAGT1,downstream_gene_variant,,ENST00000442480,;HMBS,downstream_gene_variant,,ENST00000542822,;HMBS,downstream_gene_variant,,ENST00000542345,;HMBS,upstream_gene_variant,,ENST00000539045,;HMBS,downstream_gene_variant,,ENST00000535793,;HMBS,downstream_gene_variant,,ENST00000544360,;HMBS,downstream_gene_variant,,ENST00000545901,;HMBS,downstream_gene_variant,,ENST00000543821,;DPAGT1,downstream_gene_variant,,ENST00000524658,; T ENST00000278715 Transcript synonymous_variant 853/1501 702/1086 234/361 L ctG/ctT 1 1 HMBS HGNC HGNC:4982 protein_coding YES CCDS8409.1 ENSP00000278715 P08397 UPI000012C47A NM_000190.3 11/14 HAMAP:MF_00260,hmmpanther:PTHR11557,hmmpanther:PTHR11557:SF0,PIRSF_domain:PIRSF001438,TIGRFAM_domain:TIGR00212,Superfamily_domains:SSF53850 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 119092454 119092454 G T 1 0 0 0 0 0 0 0 1 7109 1335 47 2 2 HMBS 11 119092454 Silent SNP G C3N-00293_T 37452 119092454 15994168 191 12649 OR10G7 0 . GRCh38 11 124038266 124038266 + Missense_Mutation SNP C C T rs757153234 C3N-00293_T C3N-00293_N C C c.736G>A p.Val246Met p.V246M ENST00000330487 1/1 230 218 12 147 147 0 varscan-mutect OR10G7,missense_variant,p.Val246Met,ENST00000330487,NM_001004463.1; T ENST00000330487 Transcript missense_variant 745/945 736/936 246/311 V/M Gtg/Atg rs757153234,COSM3444675 1 -1 OR10G7 HGNC HGNC:14842 protein_coding YES CCDS31705.1 ENSP00000329689 Q8NGN6 A0A126GWF3 UPI0000040A84 NM_001004463.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs757153234 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 124038266 124038266 C T 1 0 0 0 0 1 0 0 0 10979 536 19 1 1 OR10G7 11 124038266 Missense_Mutation SNP C C3N-00293_T 4945812 124038266 11048356 192 12650 FLI1 0 . GRCh38 11 128772820 128772820 + Missense_Mutation SNP C C A rs753153302 C3N-00293_T C3N-00293_N C C c.424C>A p.Leu142Met p.L142M ENST00000527786 4/9 265 220 45 220 220 0 strelka-mutect FLI1,missense_variant,p.Leu76Met,ENST00000281428,NM_001271010.1;FLI1,missense_variant,p.Leu142Met,ENST00000527786,NM_002017.4;FLI1,missense_variant,p.Leu109Met,ENST00000534087,NM_001167681.2;FLI1,intron_variant,,ENST00000344954,NM_001271012.1;FLI1,downstream_gene_variant,,ENST00000527767,;FLI1,3_prime_UTR_variant,,ENST00000429175,;FLI1,intron_variant,,ENST00000608303,;FLI1,downstream_gene_variant,,ENST00000608055,; A ENST00000527786 Transcript missense_variant 913/4127 424/1359 142/452 L/M Ctg/Atg rs753153302 1 1 FLI1 HGNC HGNC:3749 protein_coding YES CCDS44768.1 ENSP00000433488 Q01543 A0A024R3M5 UPI000012A972 NM_002017.4 deleterious(0.01) 4/9 Gene3D:1.10.150.50,Pfam_domain:PF02198,PROSITE_profiles:PS51433,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF161,SMART_domains:SM00251,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS rs753153302 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 128772820 128772820 C A 1 0 0 0 0 1 0 0 0 5786 796 28 2 2 FLI1 11 128772820 Missense_Mutation SNP C C3N-00293_T 4734554 128772820 6313802 193 12651 NCAPD3 0 . GRCh38 11 134204044 134204044 + Splice_Site SNP A A G novel C3N-00293_T C3N-00293_N A A c.1215+2T>C p.X405_splice ENST00000534548 186 150 36 100 100 0 strelka-varscan-mutect NCAPD3,splice_donor_variant,,ENST00000534548,NM_015261.2;NCAPD3,splice_donor_variant,,ENST00000534532,;NCAPD3,splice_donor_variant,,ENST00000525964,;NCAPD3,downstream_gene_variant,,ENST00000533155,;NCAPD3,downstream_gene_variant,,ENST00000528065,; G ENST00000534548 Transcript splice_donor_variant -/5061 1215/4497 405/1498 1 -1 NCAPD3 HGNC HGNC:28952 protein_coding YES CCDS31723.1 ENSP00000433681 P42695 UPI00001C1EFE NM_015261.2 10/34 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 45 134204044 134204044 A G 1 0 0 0 0 0 0 1 0 10222 405 14 5 5 NCAPD3 11 134204044 Splice_Site SNP A C3N-00293_T 5431224 134204044 882578 194 12652 TARBP2 0 . GRCh38 12 53502159 53502159 + Silent SNP C C T C3N-00293_T C3N-00293_N C C c.198C>T p.= p.V66V ENST00000266987 2/9 262 246 16 205 205 0 strelka-mutect TARBP2,synonymous_variant,p.=,ENST00000266987,NM_134323.1;TARBP2,synonymous_variant,p.=,ENST00000394357,NM_134324.2;TARBP2,synonymous_variant,p.=,ENST00000456234,NM_004178.4;TARBP2,synonymous_variant,p.=,ENST00000550407,;TARBP2,intron_variant,,ENST00000552857,;TARBP2,intron_variant,,ENST00000547064,;TARBP2,intron_variant,,ENST00000552817,;MAP3K12,upstream_gene_variant,,ENST00000267079,NM_006301.3;MAP3K12,upstream_gene_variant,,ENST00000547488,NM_001193511.1;RP11-793H13.10,downstream_gene_variant,,ENST00000591834,;NPFF,downstream_gene_variant,,ENST00000267017,NM_003717.2;MAP3K12,upstream_gene_variant,,ENST00000548565,;RP11-793H13.11,upstream_gene_variant,,ENST00000602306,;TARBP2,non_coding_transcript_exon_variant,,ENST00000549028,;MAP3K12,upstream_gene_variant,,ENST00000547151,;TARBP2,synonymous_variant,p.=,ENST00000550147,;TARBP2,synonymous_variant,p.=,ENST00000549572,;TARBP2,synonymous_variant,p.=,ENST00000548971,;TARBP2,synonymous_variant,p.=,ENST00000549679,;TARBP2,synonymous_variant,p.=,ENST00000551741,;TARBP2,non_coding_transcript_exon_variant,,ENST00000549610,;TARBP2,non_coding_transcript_exon_variant,,ENST00000546889,;TARBP2,non_coding_transcript_exon_variant,,ENST00000552650,;TARBP2,intron_variant,,ENST00000547388,;RP11-793H13.10,downstream_gene_variant,,ENST00000448979,;TARBP2,upstream_gene_variant,,ENST00000551157,;TARBP2,upstream_gene_variant,,ENST00000546763,;MAP3K12,upstream_gene_variant,,ENST00000551895,;TARBP2,upstream_gene_variant,,ENST00000547541,; T ENST00000266987 Transcript synonymous_variant 681/1867 198/1101 66/366 V gtC/gtT COSM431402 1 1 TARBP2 HGNC HGNC:11569 protein_coding YES CCDS8861.1 ENSP00000266987 Q15633 UPI0000071D96 NM_134323.1 2/9 Gene3D:3.30.160.20,HAMAP:MF_03034,Pfam_domain:PF00035,PROSITE_profiles:PS50137,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF61,SMART_domains:SM00358,Superfamily_domains:SSF54768 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 53502159 53502159 C T 1 0 0 0 0 0 0 0 1 15955 813 29 3 3 TARBP2 12 53502159 Silent SNP C C3N-00293_T 53502159 79773150 195 12653 ANKRD52 0 . GRCh38 12 56244735 56244735 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.2639A>T p.His880Leu p.H880L ENST00000267116 24/28 304 287 17 261 261 0 strelka-varscan-mutect ANKRD52,missense_variant,p.His880Leu,ENST00000267116,NM_173595.3;ANKRD52,upstream_gene_variant,,ENST00000548241,; A ENST00000267116 Transcript missense_variant 2761/8688 2639/3231 880/1076 H/L cAt/cTt 1 -1 ANKRD52 HGNC HGNC:26614 protein_coding YES CCDS44920.1 ENSP00000267116 Q8NB46 UPI0000237861 NM_173595.3 deleterious(0.01) 24/28 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24158:SF17,hmmpanther:PTHR24158,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 56244735 56244735 T A 1 0 0 0 0 1 0 0 0 782 1464 51 4 4 ANKRD52 12 56244735 Missense_Mutation SNP T C3N-00293_T 2742576 56244735 77030574 196 12654 DTX3 0 . GRCh38 12 57607094 57607094 + Silent SNP A A C novel C3N-00293_T C3N-00293_N A A c.240A>C p.= p.L80L ENST00000551632 4/6 266 238 28 198 198 0 strelka-varscan-mutect DTX3,synonymous_variant,p.=,ENST00000548198,;DTX3,synonymous_variant,p.=,ENST00000548478,;DTX3,synonymous_variant,p.=,ENST00000548804,NM_001286246.1;DTX3,synonymous_variant,p.=,ENST00000337737,NM_178502.3;DTX3,synonymous_variant,p.=,ENST00000551632,NM_001286245.1;DTX3,synonymous_variant,p.=,ENST00000549583,;PIP4K2C,downstream_gene_variant,,ENST00000354947,;PIP4K2C,downstream_gene_variant,,ENST00000540759,NM_001146258.1,NM_024779.4;ARHGEF25,upstream_gene_variant,,ENST00000286494,NM_182947.3;ARHGEF25,upstream_gene_variant,,ENST00000333972,NM_001111270.2;ARHGEF25,upstream_gene_variant,,ENST00000616622,;DTX3,upstream_gene_variant,,ENST00000550300,;DTX3,downstream_gene_variant,,ENST00000550596,;DTX3,downstream_gene_variant,,ENST00000551835,; C ENST00000551632 Transcript synonymous_variant 375/1840 240/1053 80/350 L ctA/ctC 1 1 DTX3 HGNC HGNC:24457 protein_coding YES CCDS66410.1 ENSP00000448696 Q8N9I9 UPI000006EA20 NM_001286245.1 4/6 hmmpanther:PTHR12622,hmmpanther:PTHR12622:SF24,Low_complexity_(Seg):seg LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 45 57607094 57607094 A C 1 0 0 0 0 0 0 0 1 4618 407 15 5 5 DTX3 12 57607094 Silent SNP A C3N-00293_T 1362359 57607094 75668215 197 12655 GRIP1 0 . GRCh38 12 66371729 66371729 + Missense_Mutation SNP C C G rs371211164 C3N-00293_T C3N-00293_N C C c.2821G>C p.Glu941Gln p.E941Q ENST00000398016 22/24 451 422 29 295 295 0 strelka-varscan-mutect GRIP1,missense_variant,p.Glu993Gln,ENST00000359742,;GRIP1,missense_variant,p.Glu941Gln,ENST00000398016,NM_021150.3;GRIP1,missense_variant,p.Glu926Gln,ENST00000538211,NM_001178074.1;GRIP1,missense_variant,p.Glu793Gln,ENST00000538164,;GRIP1,intron_variant,,ENST00000540854,;GRIP1,downstream_gene_variant,,ENST00000540433,;GRIP1,downstream_gene_variant,,ENST00000536215,;GRIP1,non_coding_transcript_exon_variant,,ENST00000535323,;GRIP1,downstream_gene_variant,,ENST00000541299,; G ENST00000398016 Transcript missense_variant 2890/4888 2821/3231 941/1076 E/Q Gag/Cag rs371211164 1 -1 GRIP1 HGNC HGNC:18708 protein_coding YES CCDS41807.1 ENSP00000381098 Q9Y3R0 UPI0000DD8148 NM_021150.3 deleterious(0.05) 22/24 hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF39,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs371211164 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 66371729 66371729 C G 1 0 0 0 0 1 0 0 0 6668 864 30 4 4 GRIP1 12 66371729 Missense_Mutation SNP C C3N-00293_T 8764635 66371729 66903580 198 12656 GRIP1 0 . GRCh38 12 66371754 66371754 + Silent SNP C C G novel C3N-00293_T C3N-00293_N C C c.2796G>C p.= p.L932L ENST00000398016 22/24 501 469 32 324 324 0 strelka-varscan-mutect GRIP1,synonymous_variant,p.=,ENST00000359742,;GRIP1,synonymous_variant,p.=,ENST00000398016,NM_021150.3;GRIP1,synonymous_variant,p.=,ENST00000538211,NM_001178074.1;GRIP1,synonymous_variant,p.=,ENST00000538164,;GRIP1,synonymous_variant,p.=,ENST00000540433,;GRIP1,intron_variant,,ENST00000540854,;GRIP1,downstream_gene_variant,,ENST00000536215,;GRIP1,non_coding_transcript_exon_variant,,ENST00000535323,;GRIP1,downstream_gene_variant,,ENST00000541299,; G ENST00000398016 Transcript synonymous_variant 2865/4888 2796/3231 932/1076 L ctG/ctC 1 -1 GRIP1 HGNC HGNC:18708 protein_coding YES CCDS41807.1 ENSP00000381098 Q9Y3R0 UPI0000DD8148 NM_021150.3 22/24 hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF39 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 45 66371754 66371754 C G 1 0 0 0 0 0 0 0 1 6668 813 29 4 4 GRIP1 12 66371754 Silent SNP C C3N-00293_T 25 66371754 66903555 199 12657 KCNC2 0 . GRCh38 12 75051158 75051158 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.847A>G p.Thr283Ala p.T283A ENST00000549446 3/5 263 246 17 153 153 0 strelka-varscan-mutect KCNC2,missense_variant,p.Thr283Ala,ENST00000549446,NM_139137.3;KCNC2,missense_variant,p.Thr283Ala,ENST00000298972,NM_139136.3;KCNC2,missense_variant,p.Thr283Ala,ENST00000350228,NM_153748.2;KCNC2,missense_variant,p.Thr283Ala,ENST00000548513,;KCNC2,missense_variant,p.Thr283Ala,ENST00000550433,NM_001260498.1;KCNC2,missense_variant,p.Thr283Ala,ENST00000393288,NM_001260497.1;KCNC2,missense_variant,p.Thr283Ala,ENST00000540018,NM_001260499.1;KCNC2,non_coding_transcript_exon_variant,,ENST00000546456,;KCNC2,upstream_gene_variant,,ENST00000548243,; C ENST00000549446 Transcript missense_variant 1528/5625 847/1917 283/638 T/A Acg/Gcg 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 tolerated(0.23) 3/5 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 75051158 75051158 T C 1 0 0 0 0 1 0 0 0 7931 1667 58 5 5 KCNC2 12 75051158 Missense_Mutation SNP T C3N-00293_T 8679404 75051158 58224151 200 12658 PHLDA1 0 . GRCh38 12 76031111 76031111 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.631G>A p.Glu211Lys p.E211K ENST00000266671 1/2 386 355 31 300 300 0 strelka-varscan-mutect PHLDA1,missense_variant,p.Glu211Lys,ENST00000266671,;PHLDA1,missense_variant,p.Glu211Lys,ENST00000619060,NM_007350.3;PHLDA1,missense_variant,p.Glu70Lys,ENST00000602540,;RP11-290L1.3,non_coding_transcript_exon_variant,,ENST00000552367,;RP11-290L1.2,upstream_gene_variant,,ENST00000547721,; T ENST00000266671 Transcript missense_variant 2822/8069 631/1206 211/401 E/K Gag/Aag 1 -1 PHLDA1 HGNC HGNC:8933 protein_coding YES CCDS31861.1 ENSP00000266671 Q8WV24 UPI000013D704 deleterious_low_confidence(0.01) 1/2 hmmpanther:PTHR15478:SF4,hmmpanther:PTHR15478,SMART_domains:SM00233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 76031111 76031111 C T 1 0 0 0 0 1 0 0 0 11936 893 31 1 1 PHLDA1 12 76031111 Missense_Mutation SNP C C3N-00293_T 979953 76031111 57244198 201 12659 OTOGL 0 . GRCh38 12 80320456 80320456 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.3810G>T p.Arg1270Ser p.R1270S ENST00000458043 33/58 202 180 22 141 141 0 strelka-varscan-mutect OTOGL,missense_variant,p.Arg1270Ser,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Arg1270Ser,ENST00000547103,; T ENST00000458043 Transcript missense_variant 3816/8083 3810/7035 1270/2344 R/S agG/agT 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 33/58 Pfam_domain:PF05270,Gene3D:2.80.10.50,Superfamily_domains:0050434 MODERATE 1 SNV 5 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 80320456 80320456 G T 1 0 0 0 0 1 0 0 0 11371 1194 42 2 2 OTOGL 12 80320456 Missense_Mutation SNP G C3N-00293_T 4289345 80320456 52954853 202 12660 MYF6 0 . GRCh38 12 80708930 80708930 + Frame_Shift_Del DEL C C - novel C3N-00293_T C3N-00293_N C C c.702delC p.Cys235AlafsTer10 p.C235Afs*10 ENST00000228641 3/3 461 428 33 364 364 0 sindel-varindel-pindel MYF6,frameshift_variant,p.Cys235AlafsTer10,ENST00000228641,NM_002469.2; - ENST00000228641 Transcript frameshift_variant 921/1465 699/729 233/242 L/X ctC/ct 1 1 MYF6 HGNC HGNC:7566 protein_coding YES CCDS9019.1 ENSP00000228641 P23409 UPI0000001050 NM_002469.2 3/3 hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 45 80708930 80708930 C - 1 0 1 0 1 0 0 0 0 10028 842 30 0 0 MYF6 12 80708930 Frame_Shift_Del DEL C C3N-00293_T 388474 80708930 52566379 203 12661 CCER1 0 . GRCh38 12 90954131 90954131 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.612G>A p.= p.Q204Q ENST00000358859 1/1 410 380 30 295 295 0 strelka-varscan-mutect CCER1,synonymous_variant,p.=,ENST00000358859,NM_152638.3;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,; T ENST00000358859 Transcript synonymous_variant 1046/2962 612/1221 204/406 Q caG/caA 1 -1 CCER1 HGNC HGNC:28373 protein_coding YES CCDS9036.1 ENSP00000351727 Q8TC90 UPI000006EE70 NM_152638.3 1/1 hmmpanther:PTHR37337:SF1,hmmpanther:PTHR37337,Pfam_domain:PF15482 LOW 1 SNV 1 PASS rs1190954250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 90954131 90954131 C T 1 0 0 0 0 0 0 0 1 2574 680 24 3 3 CCER1 12 90954131 Silent SNP C C3N-00293_T 10245201 90954131 42321178 204 12662 NR2C1 0 . GRCh38 12 95058339 95058339 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.515G>A p.Arg172Lys p.R172K ENST00000333003 5/14 223 204 19 106 106 0 strelka-varscan-mutect NR2C1,missense_variant,p.Arg172Lys,ENST00000333003,NM_003297.3;NR2C1,missense_variant,p.Arg172Lys,ENST00000330677,NM_001127362.1;NR2C1,missense_variant,p.Arg172Lys,ENST00000393101,NM_001032287.2;NR2C1,missense_variant,p.Arg172Lys,ENST00000622476,;NR2C1,non_coding_transcript_exon_variant,,ENST00000545833,;NR2C1,intron_variant,,ENST00000548252,;NR2C1,downstream_gene_variant,,ENST00000551386,;NR2C1,upstream_gene_variant,,ENST00000547594,;NR2C1,downstream_gene_variant,,ENST00000546367,;NR2C1,downstream_gene_variant,,ENST00000548966,;NR2C1,downstream_gene_variant,,ENST00000552417,;NR2C1,non_coding_transcript_exon_variant,,ENST00000552861,; T ENST00000333003 Transcript missense_variant 846/4143 515/1812 172/603 R/K aGa/aAa 1 -1 NR2C1 HGNC HGNC:7971 protein_coding YES CCDS9051.1 ENSP00000333275 P13056 H9NIM2 UPI00001AE7E6 NM_003297.3 tolerated(1) 5/14 Gene3D:1.10.565.10,Pfam_domain:PF00105,Prints_domain:PR00047,PROSITE_profiles:PS51030,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF49,SMART_domains:SM00399,Superfamily_domains:SSF57716 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 95058339 95058339 C T 1 0 0 0 0 1 0 0 0 10678 913 32 3 3 NR2C1 12 95058339 Missense_Mutation SNP C C3N-00293_T 4104208 95058339 38216970 205 12663 STAB2 0 . GRCh38 12 103750625 103750625 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.6485T>C p.Leu2162Pro p.L2162P ENST00000388887 60/69 197 186 11 162 162 0 strelka-varscan-mutect STAB2,missense_variant,p.Leu2162Pro,ENST00000388887,NM_017564.9;RP11-341G23.4,intron_variant,,ENST00000551299,;STAB2,upstream_gene_variant,,ENST00000548073,; C ENST00000388887 Transcript missense_variant 6689/8251 6485/7656 2162/2551 L/P cTg/cCg 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 deleterious(0.02) 60/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2.40.155.10,Pfam_domain:PF12947,SMART_domains:SM00181,SMART_domains:SM00179 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -13.7874 0.9999994 1 1 1 0 C 3 2 45 103750625 103750625 T C 1 0 0 0 0 1 0 0 0 15616 1580 55 5 5 STAB2 12 103750625 Missense_Mutation SNP T C3N-00293_T 8692286 103750625 29524684 206 12664 SLC8B1 0 . GRCh38 12 113299787 113299787 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.1745A>G p.Lys582Arg p.K582R ENST00000552014 17/17 272 258 14 211 210 1 varscan-mutect SLC8B1,missense_variant,p.Lys582Arg,ENST00000552014,;SLC8B1,missense_variant,p.Lys582Arg,ENST00000202831,NM_024959.2;SLC8B1,missense_variant,p.Lys97Arg,ENST00000550047,;SLC8B1,missense_variant,p.Lys526Arg,ENST00000546737,;SLC8B1,missense_variant,p.Lys141Arg,ENST00000549069,;TPCN1,downstream_gene_variant,,ENST00000550785,NM_001143819.2;TPCN1,downstream_gene_variant,,ENST00000335509,NM_017901.5;TPCN1,downstream_gene_variant,,ENST00000541517,;TPCN1,downstream_gene_variant,,ENST00000392569,NM_001301214.1;TPCN1,downstream_gene_variant,,ENST00000546787,;SLC8B1,3_prime_UTR_variant,,ENST00000550672,;SLC8B1,non_coding_transcript_exon_variant,,ENST00000552565,;TPCN1,downstream_gene_variant,,ENST00000552077,;TPCN1,downstream_gene_variant,,ENST00000551127,; C ENST00000552014 Transcript missense_variant 2261/3289 1745/1755 582/584 K/R aAa/aGa 1 -1 SLC8B1 HGNC HGNC:26175 protein_coding YES CCDS31909.1 ENSP00000447091 Q6J4K2 UPI000004FA44 tolerated(0.17) 17/17 MODERATE 1 SNV 1 1 PASS rs1442219898 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 113299787 113299787 T C 1 0 0 0 0 1 0 0 0 14992 1841 64 5 5 SLC8B1 12 113299787 Missense_Mutation SNP T C3N-00293_T 9549162 113299787 19975522 207 12665 SRRM4 0 . GRCh38 12 119125422 119125422 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.557A>T p.His186Leu p.H186L ENST00000267260 7/13 165 151 14 139 139 0 strelka-mutect SRRM4,missense_variant,p.His186Leu,ENST00000267260,NM_194286.3;SRRM4,non_coding_transcript_exon_variant,,ENST00000537597,;SRRM4,non_coding_transcript_exon_variant,,ENST00000545224,; T ENST00000267260 Transcript missense_variant 945/8477 557/1836 186/611 H/L cAc/cTc 1 1 SRRM4 HGNC HGNC:29389 protein_coding YES CCDS44994.1 ENSP00000267260 A7MD48 V5T9A0 UPI00001FBC3F NM_194286.3 deleterious_low_confidence(0.02) 7/13 hmmpanther:PTHR34755,hmmpanther:PTHR34755:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 119125422 119125422 A T 1 0 0 0 0 1 0 0 0 15532 159 6 4 4 SRRM4 12 119125422 Missense_Mutation SNP A C3N-00293_T 5825635 119125422 14149887 208 12666 SETD1B 0 . GRCh38 12 121809908 121809908 + Nonsense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.963C>A p.Tyr321Ter p.Y321* ENST00000542440 6/18 377 357 20 327 327 0 strelka-varscan-mutect SETD1B,stop_gained,p.Tyr321Ter,ENST00000542440,NM_015048.1;SETD1B,stop_gained,p.Tyr321Ter,ENST00000604567,;SETD1B,stop_gained,p.Tyr321Ter,ENST00000619791,;SETD1B,stop_gained,p.Tyr321Ter,ENST00000267197,; A ENST00000542440 Transcript stop_gained 1031/8185 963/5772 321/1923 Y/* taC/taA 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 6/18 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 45 121809908 121809908 C A 1 0 0 0 0 0 1 0 0 14408 489 17 2 2 SETD1B 12 121809908 Nonsense_Mutation SNP C C3N-00293_T 2684486 121809908 11465401 209 12667 NUP58 0 . GRCh38 13 25324994 25324994 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.957G>C p.Leu319Phe p.L319F ENST00000381736 10/16 157 142 15 87 87 0 varscan-mutect NUP58,missense_variant,p.Leu319Phe,ENST00000463407,;NUP58,missense_variant,p.Leu319Phe,ENST00000381736,NM_014089.3;NUP58,missense_variant,p.Leu307Phe,ENST00000381718,NM_001008564.1;NUP58,missense_variant,p.Leu319Phe,ENST00000381747,;NUP58,missense_variant,p.Leu266Phe,ENST00000394327,;NUP58,non_coding_transcript_exon_variant,,ENST00000466694,;NUP58,non_coding_transcript_exon_variant,,ENST00000476553,; C ENST00000381736 Transcript missense_variant 1207/4332 957/1800 319/599 L/F ttG/ttC 1 1 NUP58 HGNC HGNC:20261 protein_coding YES CCDS9314.1 ENSP00000371155 Q9BVL2 UPI000006D9D4 NM_014089.3 deleterious(0) 10/16 hmmpanther:PTHR13437,Pfam_domain:PF15967 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 25324994 25324994 G C 1 0 0 0 0 1 0 0 0 10833 1304 45 4 4 NUP58 13 25324994 Missense_Mutation SNP G C3N-00293_T 25324994 89039334 210 12668 RXFP2 0 . GRCh38 13 31792718 31792718 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.1416C>T p.= p.G472G ENST00000298386 16/18 335 304 31 250 250 0 strelka-varscan-mutect RXFP2,synonymous_variant,p.=,ENST00000298386,NM_130806.3;RXFP2,synonymous_variant,p.=,ENST00000380314,NM_001166058.1; T ENST00000298386 Transcript synonymous_variant 1487/3319 1416/2265 472/754 G ggC/ggT 1 1 RXFP2 HGNC HGNC:17318 protein_coding YES CCDS9342.1 ENSP00000298386 Q8WXD0 UPI0000049589 NM_130806.3 16/18 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24365:SF226,hmmpanther:PTHR24365,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01739 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 31792718 31792718 C T 1 0 0 0 0 0 0 0 1 14021 697 25 3 3 RXFP2 13 31792718 Silent SNP C C3N-00293_T 6467724 31792718 82571610 211 12669 SLC25A30 0 . GRCh38 13 45402277 45402277 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.487A>G p.Lys163Glu p.K163E ENST00000519676 6/10 191 180 11 105 105 0 strelka-mutect SLC25A30,missense_variant,p.Lys163Glu,ENST00000519676,NM_001010875.3;SLC25A30,missense_variant,p.Lys112Glu,ENST00000539591,NM_001286807.1,NM_001286806.1;SLC25A30,missense_variant,p.Lys112Glu,ENST00000519547,;SLC25A30,missense_variant,p.Lys28Glu,ENST00000618165,;SLC25A30,missense_variant,p.Lys88Glu,ENST00000522438,;SLC25A30,splice_region_variant,,ENST00000523988,;SLC25A30,splice_region_variant,,ENST00000310862,;SLC25A30,downstream_gene_variant,,ENST00000463262,; C ENST00000519676 Transcript missense_variant,splice_region_variant 623/3670 487/876 163/291 K/E Aag/Gag 1 -1 SLC25A30 HGNC HGNC:27371 protein_coding YES CCDS31967.1 ENSP00000429168 Q5SVS4 UPI00001417EE NM_001010875.3 deleterious(0.02) 6/10 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF290,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588,Prints_domain:PR00784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 45402277 45402277 T C 1 0 0 0 0 1 0 0 0 14759 1797 62 5 5 SLC25A30 13 45402277 Missense_Mutation SNP T C3N-00293_T 13609559 45402277 68962051 212 12670 CCDC168 0 . GRCh38 13 102745820 102745820 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.4877A>T p.Lys1626Met p.K1626M ENST00000322527 4/4 313 275 38 132 131 1 strelka-varscan-mutect CCDC168,missense_variant,p.Lys1626Met,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; A ENST00000322527 Transcript missense_variant 5015/21466 4877/21246 1626/7081 K/M aAg/aTg 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 102745820 102745820 T A 1 0 0 0 0 1 0 0 0 2484 1609 56 4 4 CCDC168 13 102745820 Missense_Mutation SNP T C3N-00293_T 57343543 102745820 11618508 213 12671 SLC10A2 0 . GRCh38 13 103066049 103066049 + Silent SNP G G T C3N-00293_T C3N-00293_N G G c.201C>A p.= p.G67G ENST00000245312 1/6 218 194 24 134 134 0 strelka-varscan-mutect SLC10A2,synonymous_variant,p.=,ENST00000245312,NM_000452.2; T ENST00000245312 Transcript synonymous_variant 798/3779 201/1047 67/348 G ggC/ggA COSM945216 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 1/6 hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841,Pfam_domain:PF01758 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 103066049 103066049 G T 1 0 0 0 0 0 0 0 1 14639 1306 46 2 2 SLC10A2 13 103066049 Silent SNP G C3N-00293_T 320229 103066049 11298279 214 12672 UPF3A 0 . GRCh38 13 114301753 114301753 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1030G>C p.Glu344Gln p.E344Q ENST00000375299 9/10 166 154 12 108 108 0 varscan-mutect UPF3A,missense_variant,p.Glu344Gln,ENST00000375299,NM_023011.3;UPF3A,missense_variant,p.Glu311Gln,ENST00000351487,NM_080687.2;UPF3A,non_coding_transcript_exon_variant,,ENST00000475218,;UPF3A,non_coding_transcript_exon_variant,,ENST00000480362,;UPF3A,non_coding_transcript_exon_variant,,ENST00000493727,;UPF3A,non_coding_transcript_exon_variant,,ENST00000474056,;CLCP2,upstream_gene_variant,,ENST00000392050,; C ENST00000375299 Transcript missense_variant 1086/2387 1030/1431 344/476 E/Q Gag/Cag 1 1 UPF3A HGNC HGNC:20332 protein_coding YES CCDS9543.1 ENSP00000364448 Q9H1J1 UPI0000072FCB NM_023011.3 deleterious(0.01) 9/10 hmmpanther:PTHR13112,hmmpanther:PTHR13112:SF2 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99582 1 1 1 1 0 C 3 2 45 114301753 114301753 G C 1 0 0 0 0 1 0 0 0 17531 943 33 4 4 UPF3A 13 114301753 Missense_Mutation SNP G C3N-00293_T 11235704 114301753 62575 215 12673 RNF31 0 . GRCh38 14 24157963 24157963 + Silent SNP C C G novel C3N-00293_T C3N-00293_N C C c.2793C>G p.= p.L931L ENST00000324103 17/21 272 251 21 208 208 0 strelka-varscan-mutect RNF31,synonymous_variant,p.=,ENST00000324103,NM_017999.4;RNF31,synonymous_variant,p.=,ENST00000559275,NM_001310332.1;RNF31,synonymous_variant,p.=,ENST00000560787,;RNF31,intron_variant,,ENST00000559719,;IRF9,upstream_gene_variant,,ENST00000396864,NM_006084.4;IRF9,upstream_gene_variant,,ENST00000557894,;IRF9,upstream_gene_variant,,ENST00000560275,;RNF31,downstream_gene_variant,,ENST00000560754,;IRF9,upstream_gene_variant,,ENST00000559284,;RNA5SP383,upstream_gene_variant,,ENST00000362934,;RP11-468E2.4,synonymous_variant,p.=,ENST00000558468,;RNF31,synonymous_variant,p.=,ENST00000559449,;RNF31,synonymous_variant,p.=,ENST00000483895,;RNF31,3_prime_UTR_variant,,ENST00000491351,;RNF31,non_coding_transcript_exon_variant,,ENST00000559071,;IRF9,upstream_gene_variant,,ENST00000561415,;IRF9,upstream_gene_variant,,ENST00000561342,;IRF9,upstream_gene_variant,,ENST00000560852,;IRF9,upstream_gene_variant,,ENST00000560365,;IRF9,upstream_gene_variant,,ENST00000561412,;RNF31,downstream_gene_variant,,ENST00000558452,;IRF9,upstream_gene_variant,,ENST00000561009,;RNF31,upstream_gene_variant,,ENST00000559491,;RNF31,upstream_gene_variant,,ENST00000560631,; G ENST00000324103 Transcript synonymous_variant 3113/3627 2793/3219 931/1072 L ctC/ctG 1 1 RNF31 HGNC HGNC:16031 protein_coding YES CCDS41931.1 ENSP00000315112 Q96EP0 UPI0000072F93 NM_017999.4 17/21 hmmpanther:PTHR16004,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS rs1334781055 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 45 24157963 24157963 C G 1 0 0 0 0 0 0 0 1 13667 900 32 4 4 RNF31 14 24157963 Silent SNP C C3N-00293_T 24157963 82885755 216 12674 ARHGAP5 0 . GRCh38 14 32092249 32092249 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1580G>C p.Arg527Thr p.R527T ENST00000345122 2/7 176 167 9 87 87 0 varscan-mutect ARHGAP5,missense_variant,p.Arg527Thr,ENST00000345122,NM_001030055.1;ARHGAP5,missense_variant,p.Arg527Thr,ENST00000432921,;ARHGAP5,missense_variant,p.Arg527Thr,ENST00000539826,;ARHGAP5,missense_variant,p.Arg527Thr,ENST00000556611,NM_001173.2;ARHGAP5,intron_variant,,ENST00000396582,;ARHGAP5,intron_variant,,ENST00000433497,;ARHGAP5,intron_variant,,ENST00000554090,;ARHGAP5,downstream_gene_variant,,ENST00000556191,;ARHGAP5,downstream_gene_variant,,ENST00000555814,;ARHGAP5,upstream_gene_variant,,ENST00000557643,; C ENST00000345122 Transcript missense_variant 1895/9604 1580/4509 527/1502 R/T aGa/aCa 1 1 ARHGAP5 HGNC HGNC:675 protein_coding YES CCDS32062.1 ENSP00000371897 Q13017 UPI000057B85C NM_001030055.1 deleterious(0) 2/7 Pfam_domain:PF01846,PROSITE_profiles:PS51676,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF4,SMART_domains:SM00441 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 32092249 32092249 G C 1 0 0 0 0 1 0 0 0 1016 942 33 4 4 ARHGAP5 14 32092249 Missense_Mutation SNP G C3N-00293_T 7934286 32092249 74951469 217 12675 MIS18BP1 0 . GRCh38 14 45224334 45224334 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.2253G>A p.= p.L751L ENST00000310806 11/17 327 309 18 172 172 0 strelka-varscan-mutect MIS18BP1,synonymous_variant,p.=,ENST00000310806,NM_018353.4;MIS18BP1,downstream_gene_variant,,ENST00000454990,;MIS18BP1,downstream_gene_variant,,ENST00000453142,;MIS18BP1,upstream_gene_variant,,ENST00000469020,;MIS18BP1,upstream_gene_variant,,ENST00000554093,;MIS18BP1,downstream_gene_variant,,ENST00000555653,; T ENST00000310806 Transcript synonymous_variant 2712/4777 2253/3399 751/1132 L ttG/ttA 1 -1 MIS18BP1 HGNC HGNC:20190 protein_coding YES CCDS9684.1 ENSP00000309790 Q6P0N0 UPI00001FD488 NM_018353.4 11/17 hmmpanther:PTHR16124,hmmpanther:PTHR16124:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 45224334 45224334 C T 1 0 0 0 0 0 0 0 1 9561 825 29 3 3 MIS18BP1 14 45224334 Silent SNP C C3N-00293_T 13132085 45224334 61819384 218 12676 NIN 0 . GRCh38 14 50757879 50757879 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.3151T>A p.Ser1051Thr p.S1051T ENST00000382041 18/30 198 184 14 182 182 0 strelka-varscan-mutect NIN,missense_variant,p.Ser1051Thr,ENST00000245441,NM_020921.3;NIN,missense_variant,p.Ser1051Thr,ENST00000530997,;NIN,missense_variant,p.Ser1051Thr,ENST00000453196,NM_182944.2;NIN,missense_variant,p.Ser1051Thr,ENST00000382041,NM_182946.1;NIN,missense_variant,p.Ser542Thr,ENST00000530853,;NIN,missense_variant,p.Ser542Thr,ENST00000389869,;NIN,intron_variant,,ENST00000324330,NM_016350.4;NIN,intron_variant,,ENST00000382043,;NIN,missense_variant,p.Ser1051Thr,ENST00000476352,; T ENST00000382041 Transcript missense_variant 3342/6496 3151/6273 1051/2090 S/T Tcc/Acc 1 -1 NIN HGNC HGNC:14906 protein_coding YES CCDS32079.1 ENSP00000371472 Q8N4C6 UPI0000DBEF14 NM_182946.1 tolerated(0.09) 18/30 hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 50757879 50757879 A T 1 0 0 0 0 1 0 0 0 10452 275 10 4 4 NIN 14 50757879 Missense_Mutation SNP A C3N-00293_T 5533545 50757879 56285839 219 12677 NID2 0 . GRCh38 14 52027265 52027265 + Missense_Mutation SNP A A T rs776963906 C3N-00293_T C3N-00293_N A A c.2610T>A p.His870Gln p.H870Q ENST00000216286 12/22 125 109 16 118 118 0 strelka-varscan-mutect NID2,missense_variant,p.His870Gln,ENST00000216286,NM_007361.3;NID2,missense_variant,p.His464Gln,ENST00000617139,;NID2,intron_variant,,ENST00000556572,;NID2,downstream_gene_variant,,ENST00000554284,; T ENST00000216286 Transcript missense_variant 2610/4811 2610/4128 870/1375 H/Q caT/caA rs776963906 1 -1 NID2 HGNC HGNC:13389 protein_coding YES CCDS9706.1 ENSP00000216286 Q14112 UPI000013C6E1 NM_007361.3 tolerated(0.26) 12/22 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF5,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs776963906 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 52027265 52027265 A T 1 0 0 0 0 1 0 0 0 10448 214 8 4 4 NID2 14 52027265 Missense_Mutation SNP A C3N-00293_T 1269386 52027265 55016453 220 12678 C14orf37 0 . GRCh38 14 58005158 58005158 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.2146G>T p.Val716Leu p.V716L ENST00000267485 7/8 301 280 21 217 217 0 strelka-varscan-mutect C14orf37,missense_variant,p.Val716Leu,ENST00000267485,NM_001001872.2;C14orf37,upstream_gene_variant,,ENST00000556788,; A ENST00000267485 Transcript missense_variant 2341/6495 2146/2325 716/774 V/L Gtg/Ttg 1 -1 C14orf37 HGNC HGNC:19846 protein_coding YES CCDS32089.1 ENSP00000267485 Q86TY3 UPI000000CC37 NM_001001872.2 deleterious(0.01) 7/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR21585,hmmpanther:PTHR21585:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 58005158 58005158 C A 1 0 0 0 0 1 0 0 0 1838 507 18 2 2 C14orf37 14 58005158 Missense_Mutation SNP C C3N-00293_T 5977893 58005158 49038560 221 12679 SNRPN 0 . GRCh38 15 24976998 24976998 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.389C>A p.Pro130His p.P130H ENST00000400100 10/13 113 98 15 76 76 0 strelka-varscan-mutect SNRPN,missense_variant,p.Pro134His,ENST00000554227,;SNRPN,missense_variant,p.Pro130His,ENST00000400100,NM_022807.2,NM_022808.2,NM_022806.2;SNRPN,missense_variant,p.Pro130His,ENST00000400097,NM_022805.2;SNRPN,missense_variant,p.Pro130His,ENST00000390687,;SNRPN,missense_variant,p.Pro130His,ENST00000346403,;SNRPN,missense_variant,p.Pro130His,ENST00000577565,NM_003097.3;SNRPN,missense_variant,p.Pro130His,ENST00000579070,;SNRPN,downstream_gene_variant,,ENST00000584968,;SNORD107,upstream_gene_variant,,ENST00000459433,;SNHG14,upstream_gene_variant,,ENST00000551631,;SNHG14,upstream_gene_variant,,ENST00000551361,;SNRPN,downstream_gene_variant,,ENST00000553597,;SNURF,3_prime_UTR_variant,,ENST00000580062,;RP11-701H24.9,intron_variant,,ENST00000551312,;RP11-701H24.9,intron_variant,,ENST00000557230,;SNHG14,upstream_gene_variant,,ENST00000557108,; A ENST00000400100 Transcript missense_variant 1279/1751 389/723 130/240 P/H cCt/cAt COSM470461 1 1 SNRPN HGNC HGNC:11164 protein_coding YES CCDS10017.1 ENSP00000382972 P63162 X5DP00 UPI000002948A NM_022807.2,NM_022808.2,NM_022806.2 tolerated(0.08) 10/13 PIRSF_domain:PIRSF037187,hmmpanther:PTHR10701,hmmpanther:PTHR10701:SF1,Superfamily_domains:SSF50182 1 MODERATE 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 45 24976998 24976998 C A 1 0 0 0 0 1 0 0 0 15190 681 24 2 2 SNRPN 15 24976998 Missense_Mutation SNP C C3N-00293_T 24976998 77014191 222 12680 OCA2 0 . GRCh38 15 27851404 27851404 + Silent SNP C C A novel C3N-00293_T C3N-00293_N C C c.2316G>T p.= p.L772L ENST00000354638 22/24 573 524 49 533 533 0 strelka-varscan-mutect OCA2,synonymous_variant,p.=,ENST00000354638,NM_000275.2;OCA2,synonymous_variant,p.=,ENST00000353809,NM_001300984.1; A ENST00000354638 Transcript synonymous_variant 2472/3186 2316/2517 772/838 L ctG/ctT 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 22/24 hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283,Pfam_domain:PF03600 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 27851404 27851404 C A 1 0 0 0 0 0 0 0 1 10892 581 21 2 2 OCA2 15 27851404 Silent SNP C C3N-00293_T 2874406 27851404 74139785 223 12681 GOLGA8T 0 . GRCh38 15 30143672 30143672 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1267C>A p.Pro423Thr p.P423T ENST00000569052 14/19 236 224 12 206 205 1 varscan-mutect GOLGA8T,missense_variant,p.Pro423Thr,ENST00000569052,;RN7SL469P,upstream_gene_variant,,ENST00000621501,;GOLGA8T,downstream_gene_variant,,ENST00000565649,; A ENST00000569052 Transcript missense_variant 1267/1896 1267/1896 423/631 P/T Cct/Act 1 1 GOLGA8T HGNC HGNC:44410 protein_coding YES ENSP00000455826 H3BQL2 UPI000246730F deleterious(0) 14/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 30143672 30143672 C A 1 0 0 0 0 1 0 0 0 6458 623 22 2 2 GOLGA8T 15 30143672 Missense_Mutation SNP C C3N-00293_T 2292268 30143672 71847517 224 12682 RASGRP1 0 . GRCh38 15 38490674 38490674 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.2274G>A p.= p.L758L ENST00000310803 17/17 132 114 18 80 80 0 strelka-mutect RASGRP1,missense_variant,p.Glu595Lys,ENST00000559830,NM_001306086.1;RASGRP1,missense_variant,p.Glu544Lys,ENST00000558164,;RASGRP1,synonymous_variant,p.=,ENST00000310803,NM_005739.3;RASGRP1,synonymous_variant,p.=,ENST00000539159,;RASGRP1,synonymous_variant,p.=,ENST00000558432,;RASGRP1,synonymous_variant,p.=,ENST00000561180,;RASGRP1,synonymous_variant,p.=,ENST00000450598,NM_001128602.1;FAM98B,downstream_gene_variant,,ENST00000397609,NM_173611.3;RASGRP1,3_prime_UTR_variant,,ENST00000414708,;RASGRP1,downstream_gene_variant,,ENST00000557875,; T ENST00000310803 Transcript synonymous_variant 2452/5023 2274/2394 758/797 L ctG/ctA 1 -1 RASGRP1 HGNC HGNC:9878 protein_coding YES CCDS45222.1 ENSP00000310244 O95267 UPI000006FE1C NM_005739.3 17/17 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 38490674 38490674 C T 1 0 0 0 0 0 0 0 1 13235 835 29 3 3 RASGRP1 15 38490674 Silent SNP C C3N-00293_T 8347002 38490674 63500515 225 12683 DUOX2 0 . GRCh38 15 45108063 45108063 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.1558G>A p.Glu520Lys p.E520K ENST00000603300 13/34 596 563 33 425 425 0 strelka-varscan-mutect DUOX2,missense_variant,p.Glu520Lys,ENST00000389039,;DUOX2,missense_variant,p.Glu520Lys,ENST00000603300,NM_014080.4;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,; T ENST00000603300 Transcript missense_variant 1761/6345 1558/4647 520/1548 E/K Gag/Aag 1 -1 DUOX2 HGNC HGNC:13273 protein_coding YES CCDS10117.1 ENSP00000475084 Q9NRD8 UPI000013D775 NM_014080.4 deleterious(0.05) 13/34 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 45108063 45108063 C T 1 0 0 0 0 1 0 0 0 4623 835 29 3 3 DUOX2 15 45108063 Missense_Mutation SNP C C3N-00293_T 6617389 45108063 56883126 226 12684 SEMA6D 0 . GRCh38 15 47768657 47768657 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1842G>T p.Trp614Cys p.W614C ENST00000316364 18/19 161 147 14 114 114 0 strelka-varscan-mutect SEMA6D,missense_variant,p.Trp614Cys,ENST00000316364,NM_153618.1;SEMA6D,missense_variant,p.Trp614Cys,ENST00000536845,;SEMA6D,missense_variant,p.Trp78Cys,ENST00000560006,;SEMA6D,intron_variant,,ENST00000558014,NM_001198999.1;SEMA6D,intron_variant,,ENST00000354744,NM_153617.1;SEMA6D,intron_variant,,ENST00000358066,NM_020858.1;SEMA6D,intron_variant,,ENST00000355997,NM_153619.1;SEMA6D,intron_variant,,ENST00000389428,NM_153616.1;SEMA6D,intron_variant,,ENST00000558816,;SEMA6D,downstream_gene_variant,,ENST00000389425,NM_024966.2;SEMA6D,downstream_gene_variant,,ENST00000559064,;SEMA6D,downstream_gene_variant,,ENST00000558431,; T ENST00000316364 Transcript missense_variant 2281/6099 1842/3222 614/1073 W/C tgG/tgT 1 1 SEMA6D HGNC HGNC:16770 protein_coding YES CCDS32225.1 ENSP00000324857 Q8NFY4 UPI000006E201 NM_153618.1 tolerated(0.23) 18/19 hmmpanther:PTHR11036:SF65,hmmpanther:PTHR11036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 47768657 47768657 G T 1 0 0 0 0 1 0 0 0 14318 1183 41 2 2 SEMA6D 15 47768657 Missense_Mutation SNP G C3N-00293_T 2660594 47768657 54222532 227 12685 MYO5C 0 . GRCh38 15 52208626 52208626 + Silent SNP A A G novel C3N-00293_T C3N-00293_N A A c.4314T>C p.= p.F1438F ENST00000261839 36/41 140 127 13 93 93 0 strelka-varscan-mutect MYO5C,synonymous_variant,p.=,ENST00000261839,NM_018728.3;RP11-430B1.2,downstream_gene_variant,,ENST00000560518,;RP11-430B1.2,downstream_gene_variant,,ENST00000559779,;MYO5C,3_prime_UTR_variant,,ENST00000560809,;MYO5C,non_coding_transcript_exon_variant,,ENST00000559696,; G ENST00000261839 Transcript synonymous_variant 4476/6971 4314/5229 1438/1742 F ttT/ttC 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 36/41 PROSITE_profiles:PS51126,hmmpanther:PTHR13140:SF313,hmmpanther:PTHR13140 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.61862 0.9999998 1 1 1 0 G 2 3 45 52208626 52208626 A G 1 0 0 0 0 0 0 0 1 10081 127 5 5 5 MYO5C 15 52208626 Silent SNP A C3N-00293_T 4439969 52208626 49782563 228 12686 WDR72 0 . GRCh38 15 53609531 53609531 + Missense_Mutation SNP C C A rs143816093 C3N-00293_T C3N-00293_N C C c.2934G>T p.Trp978Cys p.W978C ENST00000396328 17/20 496 468 28 271 271 0 strelka-varscan-mutect WDR72,missense_variant,p.Trp978Cys,ENST00000396328,;WDR72,missense_variant,p.Trp975Cys,ENST00000557913,;WDR72,missense_variant,p.Trp978Cys,ENST00000360509,NM_182758.3;WDR72,missense_variant,p.Trp988Cys,ENST00000559418,; A ENST00000396328 Transcript missense_variant 3174/7507 2934/3309 978/1102 W/C tgG/tgT rs143816093,CM097778 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D deleterious(0) 17/20 pathogenic MODERATE 1 SNV 1 1,1 1 PASS rs143816093 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 53609531 53609531 C A 1 0 0 0 0 1 0 0 0 17878 856 30 2 2 WDR72 15 53609531 Missense_Mutation SNP C C3N-00293_T 1400905 53609531 48381658 229 12687 ZNF280D 0 . GRCh38 15 56700982 56700982 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.332A>T p.Glu111Val p.E111V ENST00000267807 6/22 348 326 22 184 184 0 strelka-varscan-mutect ZNF280D,missense_variant,p.Glu98Val,ENST00000559237,NM_001002843.2;ZNF280D,missense_variant,p.Glu98Val,ENST00000559000,;ZNF280D,missense_variant,p.Glu111Val,ENST00000267807,NM_001288588.1,NM_017661.3;ZNF280D,missense_variant,p.Glu111Val,ENST00000558320,NM_001288589.1,NM_001002844.2;ZNF280D,downstream_gene_variant,,ENST00000559352,;ZNF280D,missense_variant,p.Glu111Val,ENST00000560002,;ZNF280D,missense_variant,p.Glu111Val,ENST00000558002,; A ENST00000267807 Transcript missense_variant 549/4328 332/2940 111/979 E/V gAg/gTg 1 -1 ZNF280D HGNC HGNC:25953 protein_coding YES CCDS32245.1 ENSP00000267807 Q6N043 UPI00003FF962 NM_001288588.1,NM_017661.3 tolerated(0.38) 6/22 Pfam_domain:PF13836 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 56700982 56700982 T A 1 0 0 0 0 1 0 0 0 18393 1551 54 4 4 ZNF280D 15 56700982 Missense_Mutation SNP T C3N-00293_T 3091451 56700982 45290207 230 12688 FAM63B 0 . GRCh38 15 58771963 58771963 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.568G>C p.Glu190Gln p.E190Q ENST00000559228 1/9 72 63 9 32 32 0 strelka-varscan-mutect FAM63B,missense_variant,p.Glu190Gln,ENST00000559228,NM_001040450.1;FAM63B,missense_variant,p.Glu190Gln,ENST00000450403,NM_001040453.1;RP11-30K9.6,upstream_gene_variant,,ENST00000500929,;FAM63B,missense_variant,p.Glu190Gln,ENST00000316848,;FAM63B,missense_variant,p.Glu190Gln,ENST00000560289,; C ENST00000559228 Transcript missense_variant 650/9238 568/1866 190/621 E/Q Gag/Cag 1 1 FAM63B HGNC HGNC:26954 protein_coding YES CCDS42046.1 ENSP00000452885 Q8NBR6 UPI0000D74C47 NM_001040450.1 tolerated_low_confidence(0.07) 1/9 hmmpanther:PTHR18063,hmmpanther:PTHR18063:SF8 MODERATE SNV 2 1 PASS rs1443009005 . 0 204 6 0 0 0 0 0 -19.57245 0.9999999 1 1 1 0 C 3 2 45 58771963 58771963 G C 1 0 0 0 0 1 0 0 0 5463 1059 37 4 4 FAM63B 15 58771963 Missense_Mutation SNP G C3N-00293_T 2070981 58771963 43219226 231 12689 HERC1 0 . GRCh38 15 63655796 63655796 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.10030G>A p.Asp3344Asn p.D3344N ENST00000443617 50/78 283 266 17 182 182 0 strelka-varscan-mutect HERC1,missense_variant,p.Asp3344Asn,ENST00000443617,NM_003922.3; T ENST00000443617 Transcript missense_variant 10118/15137 10030/14586 3344/4861 D/N Gac/Aac 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 tolerated(0.19) 50/78 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 63655796 63655796 C T 1 0 0 0 0 1 0 0 0 6941 913 32 3 3 HERC1 15 63655796 Missense_Mutation SNP C C3N-00293_T 4883833 63655796 38335393 232 12690 MAP2K1 0 . GRCh38 15 66435113 66435113 + Missense_Mutation SNP A A C C3N-00293_T C3N-00293_N A A c.167A>C p.Gln56Pro p.Q56P ENST00000307102 2/11 672 599 73 512 509 3 strelka-varscan-mutect MAP2K1,missense_variant,p.Gln56Pro,ENST00000307102,NM_002755.3;MAP2K1,non_coding_transcript_exon_variant,,ENST00000425818,; C ENST00000307102 Transcript missense_variant 698/3410 167/1182 56/393 Q/P cAg/cCg COSM1235481 1 1 MAP2K1 HGNC HGNC:6840 protein_coding YES CCDS10216.1 ENSP00000302486 Q02750 A4QPA9 UPI000013EBC9 NM_002755.3 deleterious(0.03) 2/11 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF370 1 MODERATE 1 SNV 1 1 1 PASS rs1057519729 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 66435113 66435113 A C 1 0 0 0 0 1 0 0 0 9158 188 7 5 5 MAP2K1 15 66435113 Missense_Mutation SNP A C3N-00293_T 2779317 66435113 35556076 233 12691 UACA 0 . GRCh38 15 70667996 70667996 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.2688A>T p.Glu896Asp p.E896D ENST00000322954 16/19 258 241 17 159 159 0 strelka-varscan-mutect UACA,missense_variant,p.Glu896Asp,ENST00000322954,NM_018003.2;UACA,missense_variant,p.Glu883Asp,ENST00000379983,NM_001008224.1;UACA,missense_variant,p.Glu881Asp,ENST00000560441,;UACA,missense_variant,p.Glu787Asp,ENST00000539319,;UACA,downstream_gene_variant,,ENST00000558758,;UACA,upstream_gene_variant,,ENST00000560831,;UACA,downstream_gene_variant,,ENST00000559290,;UACA,downstream_gene_variant,,ENST00000560523,;UACA,downstream_gene_variant,,ENST00000558308,; A ENST00000322954 Transcript missense_variant 2874/6939 2688/4251 896/1416 E/D gaA/gaT 1 -1 UACA HGNC HGNC:15947 protein_coding YES CCDS10235.1 ENSP00000314556 Q9BZF9 UPI000006DCF3 NM_018003.2 tolerated(0.08) 16/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 70667996 70667996 T A 1 0 0 0 0 1 0 0 0 17343 1490 52 4 4 UACA 15 70667996 Missense_Mutation SNP T C3N-00293_T 4232883 70667996 31323193 234 12692 NTRK3 0 . GRCh38 15 88126342 88126342 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.1325C>G p.Ala442Gly p.A442G ENST00000360948 13/20 270 251 19 187 187 0 strelka-varscan-mutect NTRK3,missense_variant,p.Ala442Gly,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Ala434Gly,ENST00000558676,;NTRK3,missense_variant,p.Ala442Gly,ENST00000317501,;NTRK3,missense_variant,p.Ala442Gly,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Ala434Gly,ENST00000357724,;NTRK3,missense_variant,p.Ala434Gly,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Ala442Gly,ENST00000626019,;NTRK3,missense_variant,p.Ala442Gly,ENST00000629765,;NTRK3,missense_variant,p.Ala434Gly,ENST00000557856,;NTRK3,missense_variant,p.Ala344Gly,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Ala442Gly,ENST00000540489,NM_001007156.2;NTRK3,missense_variant,p.Ala46Gly,ENST00000560017,;NTRK3,non_coding_transcript_exon_variant,,ENST00000557897,;NTRK3,intron_variant,,ENST00000558306,; C ENST00000360948 Transcript missense_variant 1631/3004 1325/2520 442/839 A/G gCc/gGc 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0.04) 13/20 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 88126342 88126342 G C 1 0 0 0 0 1 0 0 0 10774 1203 42 4 4 NTRK3 15 88126342 Missense_Mutation SNP G C3N-00293_T 17458346 88126342 13864847 235 12693 KIF7 0 . GRCh38 15 89646834 89646834 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1784G>T p.Gly595Val p.G595V ENST00000394412 7/19 482 426 56 428 426 2 strelka-varscan-mutect KIF7,missense_variant,p.Gly595Val,ENST00000394412,NM_198525.2;KIF7,downstream_gene_variant,,ENST00000445906,; A ENST00000394412 Transcript missense_variant 1861/4551 1784/4032 595/1343 G/V gGa/gTa 1 -1 KIF7 HGNC HGNC:30497 protein_coding YES CCDS32325.2 ENSP00000377934 Q2M1P5 UPI00015F81C7 NM_198525.2 tolerated(0.25) 7/19 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 89646834 89646834 C A 1 0 0 0 0 1 0 0 0 8174 869 30 2 2 KIF7 15 89646834 Missense_Mutation SNP C C3N-00293_T 1520492 89646834 12344355 236 12694 FLYWCH1 0 . GRCh38 16 2933476 2933476 + Silent SNP G G A rs554729936 C3N-00293_T C3N-00293_N G G c.1143G>A p.= p.L381L ENST00000253928 5/10 243 224 19 206 206 0 strelka-varscan-mutect FLYWCH1,synonymous_variant,p.=,ENST00000253928,NM_001308068.1;FLYWCH1,synonymous_variant,p.=,ENST00000416288,NM_032296.2,NM_020912.1;FLYWCH1,synonymous_variant,p.=,ENST00000344592,;FLYWCH1,synonymous_variant,p.=,ENST00000573564,;FLYWCH1,upstream_gene_variant,,ENST00000575679,;FLYWCH1,downstream_gene_variant,,ENST00000570425,;FLYWCH1,downstream_gene_variant,,ENST00000573525,;FLYWCH1,upstream_gene_variant,,ENST00000571580,;FLYWCH1,upstream_gene_variant,,ENST00000571983,;FLYWCH1,upstream_gene_variant,,ENST00000570752,;FLYWCH1,upstream_gene_variant,,ENST00000575604,;FLYWCH1,upstream_gene_variant,,ENST00000574985,; A ENST00000253928 Transcript synonymous_variant 1548/5037 1143/2151 381/716 L ctG/ctA rs554729936 1 1 FLYWCH1 HGNC HGNC:25404 protein_coding YES CCDS76809.1 ENSP00000253928 Q4VC44 UPI000013CE05 NM_001308068.1 5/10 Low_complexity_(Seg):seg,hmmpanther:PTHR31665,hmmpanther:PTHR31665:SF3,Pfam_domain:PF16662 LOW 1 SNV 1 1 PASS rs554729936 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 2933476 2933476 G A 1 0 0 0 0 0 0 0 1 5803 1277 45 3 3 FLYWCH1 16 2933476 Silent SNP G C3N-00293_T 2933476 87404869 237 12695 GP2 0 . GRCh38 16 20322971 20322971 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.553A>T p.Thr185Ser p.T185S ENST00000381362 5/12 158 143 15 144 144 0 strelka-varscan-mutect GP2,missense_variant,p.Thr182Ser,ENST00000302555,NM_001502.3;GP2,missense_variant,p.Thr185Ser,ENST00000381362,NM_001007240.2;GP2,missense_variant,p.Thr38Ser,ENST00000381360,NM_001007241.2;GP2,missense_variant,p.Thr35Ser,ENST00000341642,NM_001007242.2;GP2,missense_variant,p.Thr94Ser,ENST00000572347,;GP2,missense_variant,p.Thr35Ser,ENST00000575582,;GP2,missense_variant,p.Thr117Ser,ENST00000572478,;GP2,downstream_gene_variant,,ENST00000575449,;GP2,non_coding_transcript_exon_variant,,ENST00000573897,;GP2,downstream_gene_variant,,ENST00000575730,;GP2,3_prime_UTR_variant,,ENST00000574982,; A ENST00000381362 Transcript missense_variant 630/2425 553/1614 185/537 T/S Act/Tct 1 -1 GP2 HGNC HGNC:4441 protein_coding YES CCDS42128.1 ENSP00000370767 P55259 UPI000059D333 NM_001007240.2 tolerated(0.82) 5/12 hmmpanther:PTHR24044:SF284,hmmpanther:PTHR24044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 20322971 20322971 T A 1 0 0 0 0 1 0 0 0 6477 1696 59 4 4 GP2 16 20322971 Missense_Mutation SNP T C3N-00293_T 17389495 20322971 70015374 238 12696 OTOA 0 . GRCh38 16 21687508 21687508 + Missense_Mutation SNP G G C rs149356133 C3N-00293_T C3N-00293_N G G c.495G>C p.Glu165Asp p.E165D ENST00000388958 7/28 578 520 58 466 466 0 strelka-varscan-mutect OTOA,missense_variant,p.Glu165Asp,ENST00000388958,NM_144672.3;OTOA,missense_variant,p.Glu165Asp,ENST00000286149,;OTOA,missense_variant,p.Glu86Asp,ENST00000388956,NM_001161683.1; C ENST00000388958 Transcript missense_variant 496/3610 495/3420 165/1139 E/D gaG/gaC rs149356133 1 1 OTOA HGNC HGNC:16378 protein_coding YES CCDS10600.2 ENSP00000373610 Q7RTW8 UPI00005C8607 NM_144672.3 tolerated(0.18) 7/28 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF18 MODERATE 1 SNV 1 1 PASS rs149356133 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 21687508 21687508 G C 1 0 0 0 0 1 0 0 0 11368 933 33 4 4 OTOA 16 21687508 Missense_Mutation SNP G C3N-00293_T 1364537 21687508 68650837 239 12697 SLC5A11 0 . GRCh38 16 24908996 24908996 + Missense_Mutation SNP A A G novel C3N-00293_T C3N-00293_N A A c.1550A>G p.Lys517Arg p.K517R ENST00000347898 14/16 492 462 30 407 407 0 strelka-varscan-mutect SLC5A11,missense_variant,p.Lys517Arg,ENST00000347898,NM_052944.4;SLC5A11,missense_variant,p.Lys482Arg,ENST00000424767,NM_001258411.2;SLC5A11,missense_variant,p.Lys447Arg,ENST00000545376,NM_001258412.2;SLC5A11,missense_variant,p.Lys482Arg,ENST00000567758,;SLC5A11,missense_variant,p.Lys453Arg,ENST00000565769,NM_001258413.2;SLC5A11,missense_variant,p.Lys447Arg,ENST00000568579,;SLC5A11,missense_variant,p.Lys361Arg,ENST00000449109,NM_001258414.1;SLC5A11,missense_variant,p.Lys361Arg,ENST00000569071,;SLC5A11,3_prime_UTR_variant,,ENST00000488922,; G ENST00000347898 Transcript missense_variant 2172/2745 1550/2028 517/675 K/R aAg/aGg 1 1 SLC5A11 HGNC HGNC:23091 protein_coding YES CCDS10625.1 ENSP00000289932 Q8WWX8 UPI0000036161 NM_052944.4 tolerated(0.38) 14/16 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF127 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 24908996 24908996 A G 1 0 0 0 0 1 0 0 0 14946 72 3 5 5 SLC5A11 16 24908996 Missense_Mutation SNP A C3N-00293_T 3221488 24908996 65429349 240 12698 ITFG1 0 . GRCh38 16 47460856 47460856 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.190C>G p.Leu64Val p.L64V ENST00000320640 1/18 260 241 19 219 219 0 strelka-varscan-mutect ITFG1,missense_variant,p.Leu64Val,ENST00000320640,NM_030790.4;ITFG1,intron_variant,,ENST00000544001,NM_001305002.1;ITFG1,intron_variant,,ENST00000563730,;PHKB,upstream_gene_variant,,ENST00000299167,;PHKB,upstream_gene_variant,,ENST00000323584,NM_000293.2;PHKB,upstream_gene_variant,,ENST00000566044,NM_001031835.2;ITFG1,upstream_gene_variant,,ENST00000565940,;PHKB,upstream_gene_variant,,ENST00000564873,;PHKB,upstream_gene_variant,,ENST00000566037,;PHKB,upstream_gene_variant,,ENST00000563376,;PHKB,upstream_gene_variant,,ENST00000567200,;PHKB,upstream_gene_variant,,ENST00000567402,;ITFG1,upstream_gene_variant,,ENST00000563350,;PHKB,upstream_gene_variant,,ENST00000566721,;PHKB,upstream_gene_variant,,ENST00000565424,; C ENST00000320640 Transcript missense_variant 419/3400 190/1839 64/612 L/V Ctc/Gtc 1 -1 ITFG1 HGNC HGNC:30697 protein_coding YES CCDS10728.1 ENSP00000319918 Q8TB96 UPI0000039EB3 NM_030790.4 tolerated(0.42) 1/18 hmmpanther:PTHR13412:SF0,hmmpanther:PTHR13412,Gene3D:3nigC00,Pfam_domain:PF13517,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 47460856 47460856 G C 1 0 0 0 0 1 0 0 0 7777 942 33 4 4 ITFG1 16 47460856 Missense_Mutation SNP G C3N-00293_T 22551860 47460856 42877489 241 12699 PKD1L3 0 . GRCh38 16 71935374 71935374 + Missense_Mutation SNP G G T rs184152519 C3N-00293_T C3N-00293_N G G c.4597C>A p.Arg1533Ser p.R1533S ENST00000620267 26/30 110 95 15 94 94 0 strelka-varscan-mutect PKD1L3,missense_variant,p.Arg1533Ser,ENST00000620267,NM_181536.1;IST1,downstream_gene_variant,,ENST00000378799,NM_001270975.1;IST1,downstream_gene_variant,,ENST00000535424,NM_001270976.1;IST1,downstream_gene_variant,,ENST00000606369,NM_001270978.1,NM_001270979.1; T ENST00000620267 Transcript missense_variant 4597/5199 4597/5199 1533/1732 R/S Cgc/Agc rs184152519 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 tolerated(0.06) 26/30 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136,Pfam_domain:PF08016 MODERATE 1 SNV 1 1 PASS rs184152519 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 45 71935374 71935374 G T 1 0 0 0 0 1 0 0 0 12061 1116 39 1 1 PKD1L3 16 71935374 Missense_Mutation SNP G C3N-00293_T 24474518 71935374 18402971 242 12700 ZFHX3 0 . GRCh38 16 72889870 72889870 + Silent SNP G G A novel C3N-00293_T C3N-00293_N G G c.3309C>T p.= p.L1103L ENST00000268489 4/10 424 398 26 410 410 0 strelka-varscan-mutect ZFHX3,synonymous_variant,p.=,ENST00000268489,NM_006885.3;ZFHX3,synonymous_variant,p.=,ENST00000397992,NM_001164766.1;ZFHX3,upstream_gene_variant,,ENST00000563625,; A ENST00000268489 Transcript synonymous_variant 3982/16064 3309/11112 1103/3703 L ctC/ctT 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 4/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208,SMART_domains:SM00451,SMART_domains:SM00355 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 72889870 72889870 G A 1 0 0 0 0 0 0 0 1 18212 1277 45 3 3 ZFHX3 16 72889870 Silent SNP G C3N-00293_T 954496 72889870 17448475 243 12701 ZFHX3 0 . GRCh38 16 72950492 72950492 + Missense_Mutation SNP C C G rs760112688 C3N-00293_T C3N-00293_N C C c.3193G>C p.Glu1065Gln p.E1065Q ENST00000268489 3/10 194 171 23 146 146 0 strelka-varscan-mutect ZFHX3,missense_variant,p.Glu1065Gln,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Glu151Gln,ENST00000397992,NM_001164766.1; G ENST00000268489 Transcript missense_variant 3866/16064 3193/11112 1065/3703 E/Q Gag/Cag rs760112688 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 deleterious(0) 3/10 hmmpanther:PTHR24208:SF84,hmmpanther:PTHR24208 MODERATE 1 SNV 1 1 PASS rs760112688 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 72950492 72950492 C G 1 0 0 0 0 1 0 0 0 18212 893 31 4 4 ZFHX3 16 72950492 Missense_Mutation SNP C C3N-00293_T 60622 72950492 17387853 244 12702 OR1G1 0 . GRCh38 17 3127228 3127228 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.324G>A p.= p.V108V ENST00000328890 1/1 297 274 23 256 256 0 strelka-varscan-mutect OR1G1,synonymous_variant,p.=,ENST00000328890,NM_003555.1; T ENST00000328890 Transcript synonymous_variant 354/998 324/942 108/313 V gtG/gtA 1 -1 OR1G1 HGNC HGNC:8204 protein_coding YES CCDS11020.1 ENSP00000331545 P47890 A0A126GW57 UPI0000041B68 NM_003555.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 3127228 3127228 C T 1 0 0 0 0 0 0 0 1 11035 813 29 3 3 OR1G1 17 3127228 Silent SNP C C3N-00293_T 3127228 80130213 245 12703 SLC13A5 0 . GRCh38 17 6703942 6703942 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.483C>A p.= p.A161A ENST00000433363 4/12 56 52 4 64 63 1 strelka-mutect SLC13A5,synonymous_variant,p.=,ENST00000433363,NM_177550.4;SLC13A5,synonymous_variant,p.=,ENST00000293800,NM_001284509.1;SLC13A5,synonymous_variant,p.=,ENST00000381074,NM_001284510.1;SLC13A5,synonymous_variant,p.=,ENST00000573648,NM_001143838.2;SLC13A5,synonymous_variant,p.=,ENST00000572352,;SLC13A5,non_coding_transcript_exon_variant,,ENST00000576323,;SLC13A5,3_prime_UTR_variant,,ENST00000572094,;SLC13A5,non_coding_transcript_exon_variant,,ENST00000574824,;SLC13A5,downstream_gene_variant,,ENST00000575230,; T ENST00000433363 Transcript synonymous_variant 717/3435 483/1707 161/568 A gcC/gcA 1 -1 SLC13A5 HGNC HGNC:23089 protein_coding YES CCDS11079.1 ENSP00000406220 Q86YT5 UPI000000D834 NM_177550.4 4/12 hmmpanther:PTHR10283:SF82,hmmpanther:PTHR10283,Pfam_domain:PF00939 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.02015 1 1 1 1 0 T 2 4 45 6703942 6703942 G T 1 0 0 0 0 0 0 0 1 14660 1335 47 2 2 SLC13A5 17 6703942 Silent SNP G C3N-00293_T 3576714 6703942 76553499 246 12704 DNAH2 0 . GRCh38 17 7788115 7788115 + Silent SNP C C T C3N-00293_T C3N-00293_N C C c.6771C>T p.= p.F2257F ENST00000572933 44/86 119 112 7 108 108 0 strelka-mutect DNAH2,synonymous_variant,p.=,ENST00000572933,NM_020877.3;DNAH2,synonymous_variant,p.=,ENST00000389173,;DNAH2,downstream_gene_variant,,ENST00000574518,; T ENST00000572933 Transcript synonymous_variant 8231/14955 6771/13284 2257/4427 F ttC/ttT COSM3890595 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 44/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183 1 LOW 1 SNV 1 1 1 PASS rs1481450028 . 0 207 0 2 0 0 0 0 -10.40952 0.9999995 1 1 1 0 T 2 4 45 7788115 7788115 C T 1 0 0 0 0 0 0 0 1 4417 883 31 1 1 DNAH2 17 7788115 Silent SNP C C3N-00293_T 1084173 7788115 75469326 247 12705 HES7 0 . GRCh38 17 8123045 8123045 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.124C>A p.= p.R42R ENST00000541682 2/4 614 578 36 655 655 0 strelka-varscan-mutect HES7,synonymous_variant,p.=,ENST00000541682,NM_001165967.1;HES7,synonymous_variant,p.=,ENST00000317814,NM_032580.3;HES7,synonymous_variant,p.=,ENST00000577735,;ALOXE3,upstream_gene_variant,,ENST00000380149,;ALOXE3,upstream_gene_variant,,ENST00000448843,NM_021628.2;ALOXE3,upstream_gene_variant,,ENST00000318227,NM_001165960.1; T ENST00000541682 Transcript synonymous_variant 124/1674 124/693 42/230 R Cgg/Agg 1 -1 HES7 HGNC HGNC:15977 protein_coding YES CCDS54085.1 ENSP00000446205 Q9BYE0 UPI0000E59E09 NM_001165967.1 2/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50888,hmmpanther:PTHR10985:SF84,hmmpanther:PTHR10985,Gene3D:4.10.280.10,Pfam_domain:PF00010,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 8123045 8123045 G T 1 0 0 0 0 0 0 0 1 6955 1086 38 1 1 HES7 17 8123045 Silent SNP G C3N-00293_T 334930 8123045 75134396 248 12706 DNAH9 0 . GRCh38 17 11961903 11961903 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.12880C>A p.Gln4294Lys p.Q4294K ENST00000262442 68/69 72 67 5 53 53 0 strelka-mutect DNAH9,missense_variant,p.Gln4294Lys,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Gln4218Lys,ENST00000454412,;DNAH9,missense_variant,p.Gln606Lys,ENST00000608377,NM_004662.2;RP11-1096G20.5,intron_variant,,ENST00000580270,;DNAH9,non_coding_transcript_exon_variant,,ENST00000396001,; A ENST00000262442 Transcript missense_variant 12948/13750 12880/13461 4294/4486 Q/K Cag/Aag 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 tolerated(0.13) 68/69 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -11.21303 0.9999902 1 1 1 0 A 3 1 45 11961903 11961903 C A 1 0 0 0 0 1 0 0 0 4423 479 17 2 2 DNAH9 17 11961903 Missense_Mutation SNP C C3N-00293_T 3838858 11961903 71295538 249 12707 NF1 0 . GRCh38 17 31258429 31258429 + Nonsense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.4259C>G p.Ser1420Ter p.S1420* ENST00000358273 32/58 339 322 17 195 195 0 strelka-varscan-mutect NF1,stop_gained,p.Ser1420Ter,ENST00000358273,NM_001042492.2;NF1,stop_gained,p.Ser1399Ter,ENST00000356175,NM_000267.3;NF1,stop_gained,p.Ser1065Ter,ENST00000456735,;NF1,stop_gained,p.Ser1433Ter,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000466819,;NF1,3_prime_UTR_variant,,ENST00000479614,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,;NF1,downstream_gene_variant,,ENST00000495910,; G ENST00000358273 Transcript stop_gained 4642/12425 4259/8520 1420/2839 S/* tCa/tGa 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 32/58 Pfam_domain:PF00616,PROSITE_patterns:PS00509,PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,SMART_domains:SM00323,Superfamily_domains:SSF48350 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 45 31258429 31258429 C G 1 0 0 0 0 0 1 0 0 10393 838 29 4 4 NF1 17 31258429 Nonsense_Mutation SNP C C3N-00293_T 19296526 31258429 51999012 250 12708 G6PC 0 . GRCh38 17 42901089 42901089 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.213C>T p.= p.L71L ENST00000253801 1/5 613 551 62 416 416 0 strelka-varscan-mutect G6PC,synonymous_variant,p.=,ENST00000253801,NM_000151.3;G6PC,synonymous_variant,p.=,ENST00000585489,;G6PC,synonymous_variant,p.=,ENST00000592383,NM_001270397.1;LINC00671,upstream_gene_variant,,ENST00000301683,;LINC00671,upstream_gene_variant,,ENST00000436546,;LINC00671,upstream_gene_variant,,ENST00000417193,;G6PC,non_coding_transcript_exon_variant,,ENST00000588481,; T ENST00000253801 Transcript synonymous_variant 292/3096 213/1074 71/357 L ctC/ctT 1 1 G6PC HGNC HGNC:4056 protein_coding YES CCDS11446.1 ENSP00000253801 P35575 UPI000013CDF5 NM_000151.3 1/5 Gene3D:1.20.144.10,Pfam_domain:PF01569,PIRSF_domain:PIRSF000905,hmmpanther:PTHR12591,hmmpanther:PTHR12591:SF3,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 42901089 42901089 C T 1 0 0 0 0 0 0 0 1 6014 813 29 3 3 G6PC 17 42901089 Silent SNP C C3N-00293_T 11642660 42901089 40356352 251 12709 NPEPPS 0 . GRCh38 17 47531427 47531427 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.127G>C p.Ala43Pro p.A43P ENST00000322157 1/23 313 281 32 278 278 0 varscan-mutect NPEPPS,missense_variant,p.Ala43Pro,ENST00000322157,NM_006310.3;NPEPPS,missense_variant,p.Ala39Pro,ENST00000530173,;NPEPPS,missense_variant,p.Ala30Pro,ENST00000525007,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000533573,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000528751,;NPEPPS,intron_variant,,ENST00000525037,;NPEPPS,missense_variant,p.Ala43Pro,ENST00000527298,;NPEPPS,missense_variant,p.Ala39Pro,ENST00000532729,;NPEPPS,missense_variant,p.Ala39Pro,ENST00000526247,;NPEPPS,missense_variant,p.Ala14Pro,ENST00000534691,; C ENST00000322157 Transcript missense_variant 364/4353 127/2760 43/919 A/P Gcc/Ccc 1 1 NPEPPS HGNC HGNC:7900 protein_coding YES CCDS45721.1 ENSP00000320324 P55786 UPI0000140D51 NM_006310.3 tolerated(0.1) 1/23 Low_complexity_(Seg):seg,hmmpanther:PTHR11533:SF187,hmmpanther:PTHR11533 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 47531427 47531427 G C 1 0 0 0 0 1 0 0 0 10623 1087 38 4 4 NPEPPS 17 47531427 Missense_Mutation SNP G C3N-00293_T 4630338 47531427 35726014 252 12710 KIF2B 0 . GRCh38 17 53823615 53823615 + Silent SNP T T C novel C3N-00293_T C3N-00293_N T T c.582T>C p.= p.Y194Y ENST00000268919 1/1 519 479 40 386 386 0 strelka-varscan-mutect KIF2B,synonymous_variant,p.=,ENST00000268919,NM_032559.4; C ENST00000268919 Transcript synonymous_variant 715/2313 582/2022 194/673 Y taT/taC 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 1/1 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Superfamily_domains:SSF52540 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 45 53823615 53823615 T C 1 0 0 0 0 0 0 0 1 8163 1442 50 5 5 KIF2B 17 53823615 Silent SNP T C3N-00293_T 6292188 53823615 29433826 253 12711 SCN4A 0 . GRCh38 17 63941012 63941012 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.5270G>C p.Ser1757Thr p.S1757T ENST00000435607 24/24 176 162 14 150 150 0 strelka-varscan-mutect SCN4A,missense_variant,p.Ser1757Thr,ENST00000435607,NM_000334.4;SCN4A,missense_variant,p.Ser1757Thr,ENST00000578147,; G ENST00000435607 Transcript missense_variant 5347/7805 5270/5511 1757/1836 S/T aGc/aCc 1 -1 SCN4A HGNC HGNC:10591 protein_coding YES CCDS45761.1 ENSP00000396320 P35499 UPI0000201254 NM_000334.4 tolerated_low_confidence(0.35) 24/24 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF223 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 63941012 63941012 C G 1 0 0 0 0 1 0 0 0 14189 797 28 4 4 SCN4A 17 63941012 Missense_Mutation SNP C C3N-00293_T 10117397 63941012 19316429 254 12712 MAP2K6 0 . GRCh38 17 69523539 69523539 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.561C>G p.Ile187Met p.I187M ENST00000590474 8/12 300 285 15 165 165 0 strelka-varscan-mutect MAP2K6,missense_variant,p.Ile187Met,ENST00000590474,NM_002758.3;MAP2K6,missense_variant,p.Ile131Met,ENST00000589647,;MAP2K6,missense_variant,p.Ile131Met,ENST00000613873,;MAP2K6,downstream_gene_variant,,ENST00000589295,;MAP2K6,downstream_gene_variant,,ENST00000588110,;MAP2K6,3_prime_UTR_variant,,ENST00000359094,;MAP2K6,downstream_gene_variant,,ENST00000591445,;MAP2K6,downstream_gene_variant,,ENST00000586641,; G ENST00000590474 Transcript missense_variant 848/2870 561/1005 187/334 I/M atC/atG 1 1 MAP2K6 HGNC HGNC:6846 protein_coding YES CCDS11686.1 ENSP00000468348 P52564 A8K3Y2 UPI000012F492 NM_002758.3 tolerated(0.08) 8/12 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000654,PROSITE_patterns:PS00108,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF40,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 69523539 69523539 C G 1 0 0 0 0 1 0 0 0 9163 816 29 4 4 MAP2K6 17 69523539 Missense_Mutation SNP C C3N-00293_T 5582527 69523539 13733902 255 12713 SLC9A3R1 0 . GRCh38 17 74762092 74762092 + Frame_Shift_Del DEL G G - novel C3N-00293_T C3N-00293_N G G c.522delG p.Lys174AsnfsTer29 p.K174Nfs*29 ENST00000262613 2/6 450 394 56 387 387 0 sindel-varindel-pindel SLC9A3R1,frameshift_variant,p.Lys174AsnfsTer29,ENST00000262613,NM_004252.4;SLC9A3R1,frameshift_variant,p.Lys18AsnfsTer29,ENST00000413388,;SLC9A3R1,intron_variant,,ENST00000583369,;SLC9A3R1,upstream_gene_variant,,ENST00000578958,;SLC9A3R1,upstream_gene_variant,,ENST00000581356,; - ENST00000262613 Transcript frameshift_variant 717/1969 522/1077 174/358 K/X aaG/aa 1 1 SLC9A3R1 HGNC HGNC:11075 protein_coding YES CCDS11705.1 ENSP00000262613 O14745 UPI0000072521 NM_004252.4 2/6 Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF037866,PROSITE_profiles:PS50106,hmmpanther:PTHR14191,hmmpanther:PTHR14191:SF7,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 45 74762092 74762092 G - 1 0 1 0 1 0 0 0 0 14996 962 34 0 0 SLC9A3R1 17 74762092 Frame_Shift_Del DEL G C3N-00293_T 5238553 74762092 8495349 256 12714 SMCHD1 0 . GRCh38 18 2697961 2697961 + Missense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.1262G>T p.Gly421Val p.G421V ENST00000320876 10/48 423 384 39 192 192 0 strelka-varscan-mutect SMCHD1,missense_variant,p.Gly421Val,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,upstream_gene_variant,,ENST00000577880,;SMCHD1,upstream_gene_variant,,ENST00000585229,;SMCHD1,downstream_gene_variant,,ENST00000581226,; T ENST00000320876 Transcript missense_variant 1600/8821 1262/6018 421/2005 G/V gGt/gTt 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 deleterious(0) 10/48 hmmpanther:PTHR22640,hmmpanther:PTHR22640:SF2 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 2697961 2697961 G T 1 0 0 0 0 1 0 0 0 15081 1261 44 2 2 SMCHD1 18 2697961 Missense_Mutation SNP G C3N-00293_T 2697961 77675324 257 12715 PIEZO2 0 . GRCh38 18 10696470 10696470 + Silent SNP C C A novel C3N-00293_T C3N-00293_N C C c.6558G>T p.= p.V2186V ENST00000503781 42/52 291 276 15 273 273 0 strelka-mutect PIEZO2,synonymous_variant,p.=,ENST00000383408,;PIEZO2,synonymous_variant,p.=,ENST00000302079,;PIEZO2,synonymous_variant,p.=,ENST00000580640,;PIEZO2,synonymous_variant,p.=,ENST00000503781,NM_022068.3;PIEZO2,synonymous_variant,p.=,ENST00000538948,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; A ENST00000503781 Transcript synonymous_variant 6558/8259 6558/8259 2186/2752 V gtG/gtT 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 42/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 10696470 10696470 C A 1 0 0 0 0 0 0 0 1 11975 813 29 2 2 PIEZO2 18 10696470 Silent SNP C C3N-00293_T 7998509 10696470 69676815 258 12716 ANKRD30B 0 . GRCh38 18 14828302 14828302 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.2411C>T p.Thr804Ile p.T804I ENST00000358984 27/36 82 69 13 49 49 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Thr804Ile,ENST00000358984,NM_001145029.1;MIR3156-2,upstream_gene_variant,,ENST00000581101,;RP11-1157N2__B.2,upstream_gene_variant,,ENST00000581117,; T ENST00000358984 Transcript missense_variant 2591/4359 2411/4179 804/1392 T/I aCa/aTa 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.2) 27/36 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 14828302 14828302 C T 1 0 0 0 0 1 0 0 0 762 478 17 3 3 ANKRD30B 18 14828302 Missense_Mutation SNP C C3N-00293_T 4131832 14828302 65544983 259 12717 MIB1 0 . GRCh38 18 21849285 21849285 + Frame_Shift_Del DEL A A - novel C3N-00293_T C3N-00293_N A A c.2483delA p.Asp828ValfsTer66 p.D828Vfs*66 ENST00000261537 17/21 184 164 20 98 98 0 sindel-varindel-pindel MIB1,frameshift_variant,p.Asp828ValfsTer66,ENST00000261537,NM_020774.3;MIB1,non_coding_transcript_exon_variant,,ENST00000578646,; - ENST00000261537 Transcript frameshift_variant 2747/9576 2483/3021 828/1006 D/X gAt/gt 1 1 MIB1 HGNC HGNC:21086 protein_coding YES CCDS11871.1 ENSP00000261537 Q86YT6 UPI000000D833 NM_020774.3 17/21 Gene3D:3.30.40.10,Pfam_domain:PF13920,PROSITE_profiles:PS50089,hmmpanther:PTHR24202,SMART_domains:SM00184 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 45 21849285 21849285 A - 1 0 1 0 1 0 0 0 0 9523 333 12 0 0 MIB1 18 21849285 Frame_Shift_Del DEL A C3N-00293_T 7020983 21849285 58524000 260 12718 KCTD1 0 . GRCh38 18 26501183 26501183 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.53G>T p.Gly18Val p.G18V ENST00000408011 2/5 174 152 22 171 171 0 strelka-varscan-mutect KCTD1,missense_variant,p.Gly18Val,ENST00000408011,NM_001136205.2;KCTD1,missense_variant,p.Gly18Val,ENST00000579973,NM_198991.3;KCTD1,missense_variant,p.Gly18Val,ENST00000317932,;KCTD1,missense_variant,p.Gly18Val,ENST00000417602,NM_001258221.1;KCTD1,missense_variant,p.Gly18Val,ENST00000580059,;KCTD1,missense_variant,p.Gly26Val,ENST00000580191,NM_001258222.1;KCTD1,missense_variant,p.Gly18Val,ENST00000580638,;KCTD1,missense_variant,p.Gly18Val,ENST00000578973,; A ENST00000408011 Transcript missense_variant 613/2103 53/774 18/257 G/V gGc/gTc COSM1388162,COSM1388163 1 -1 KCTD1 HGNC HGNC:18249 protein_coding YES CCDS11888.1 ENSP00000384367 Q719H9 A0A024RC45 UPI00001CDFF1 NM_001136205.2 deleterious(0) 2/5 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF65 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 26501183 26501183 C A 1 0 0 0 0 1 0 0 0 8013 739 26 2 2 KCTD1 18 26501183 Missense_Mutation SNP C C3N-00293_T 4651898 26501183 53872102 261 12719 MEP1B 0 . GRCh38 18 32215212 32215212 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1710C>A p.Ser570Arg p.S570R ENST00000269202 12/15 184 163 21 104 104 0 strelka-varscan-mutect MEP1B,missense_variant,p.Ser570Arg,ENST00000269202,NM_005925.2;MEP1B,missense_variant,p.Ser570Arg,ENST00000581447,NM_001308171.1;GAREM1,intron_variant,,ENST00000583696,; A ENST00000269202 Transcript missense_variant 1757/2312 1710/2106 570/701 S/R agC/agA 1 1 MEP1B HGNC HGNC:7020 protein_coding YES CCDS45846.1 ENSP00000269202 Q16820 UPI0000201B8B NM_005925.2 tolerated(0.82) 12/15 Gene3D:2.60.210.10,PIRSF_domain:PIRSF001196,PROSITE_profiles:PS50144,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF312,Superfamily_domains:SSF49599 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 32215212 32215212 C A 1 0 0 0 0 1 0 0 0 9421 709 25 2 2 MEP1B 18 32215212 Missense_Mutation SNP C C3N-00293_T 5714029 32215212 48158073 262 12720 SERPINB11 0 . GRCh38 18 63723285 63723285 + Silent SNP T T A novel C3N-00293_T C3N-00293_N T T c.804T>A p.= p.A268A ENST00000623262 5/5 223 204 19 220 220 0 strelka-varscan-mutect SERPINB11,synonymous_variant,p.=,ENST00000382749,NM_080475.3;SERPINB11,synonymous_variant,p.=,ENST00000544088,;SERPINB11,synonymous_variant,p.=,ENST00000623262,NM_001291278.1;SERPINB11,synonymous_variant,p.=,ENST00000624518,;SERPINB11,downstream_gene_variant,,ENST00000489748,;SERPINB11,intron_variant,,ENST00000467649,;SERPINB11,3_prime_UTR_variant,,ENST00000536691,;SERPINB11,downstream_gene_variant,,ENST00000610304,; A ENST00000623262 Transcript synonymous_variant 804/918 804/918 268/305 A gcT/gcA 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 5/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 63723285 63723285 T A 1 0 0 0 0 0 0 0 1 14374 1567 55 4 4 SERPINB11 18 63723285 Silent SNP T C3N-00293_T 31508073 63723285 16650000 263 12721 NETO1 0 . GRCh38 18 72864831 72864831 + Missense_Mutation SNP C C A rs780552539 C3N-00293_T C3N-00293_N C C c.197G>T p.Arg66Leu p.R66L ENST00000327305 3/11 373 347 26 265 265 0 strelka-varscan-mutect NETO1,missense_variant,p.Arg66Leu,ENST00000327305,NM_138966.3;NETO1,missense_variant,p.Arg66Leu,ENST00000583169,NM_001201465.1;NETO1,missense_variant,p.Arg65Leu,ENST00000397929,NM_138999.1;NETO1,missense_variant,p.Arg62Leu,ENST00000579169,;RP11-676J15.1,upstream_gene_variant,,ENST00000578967,;RP11-676J15.1,upstream_gene_variant,,ENST00000580564,;NETO1,non_coding_transcript_exon_variant,,ENST00000579730,;NETO1,downstream_gene_variant,,ENST00000577184,; A ENST00000327305 Transcript missense_variant 855/3058 197/1602 66/533 R/L cGg/cTg rs780552539 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 tolerated(0.12) 3/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs780552539 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 72864831 72864831 C A 1 0 0 0 0 1 0 0 0 10374 652 23 1 1 NETO1 18 72864831 Missense_Mutation SNP C C3N-00293_T 9141546 72864831 7508454 264 12722 TBXA2R 0 . GRCh38 19 3600555 3600555 + Missense_Mutation SNP G G A C3N-00293_T C3N-00293_N G G c.80C>T p.Ser27Leu p.S27L ENST00000411851 2/4 226 200 26 124 124 0 strelka-varscan-mutect TBXA2R,missense_variant,p.Ser27Leu,ENST00000375190,NM_001060.5;TBXA2R,missense_variant,p.Ser27Leu,ENST00000589966,;TBXA2R,missense_variant,p.Ser27Leu,ENST00000411851,NM_201636.2;TBXA2R,upstream_gene_variant,,ENST00000587717,; A ENST00000411851 Transcript missense_variant 294/1494 80/1224 27/407 S/L tCg/tTg COSM5246956,COSM5246957 1 -1 TBXA2R HGNC HGNC:11608 protein_coding YES CCDS54198.1 ENSP00000393333 P21731 UPI00000711C4 NM_201636.2 deleterious(0) 2/4 Gene3D:1.20.1070.10,Prints_domain:PR00237,Prints_domain:PR00429,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF5,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1162093744 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 3600555 3600555 G A 1 0 0 0 0 1 0 0 0 16067 1059 37 1 1 TBXA2R 19 3600555 Missense_Mutation SNP G C3N-00293_T 3600555 55017061 265 12723 CACTIN 0 . GRCh38 19 3623790 3623790 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.540G>C p.Lys180Asn p.K180N ENST00000429344 2/10 457 424 33 372 372 0 strelka-varscan-mutect CACTIN,missense_variant,p.Lys180Asn,ENST00000429344,NM_001080543.1;CACTIN,missense_variant,p.Lys180Asn,ENST00000221899,;CACTIN,missense_variant,p.Lys180Asn,ENST00000248420,NM_021231.1;CACTIN,upstream_gene_variant,,ENST00000588749,;CACTIN,missense_variant,p.Lys180Asn,ENST00000585942,;CACTIN,upstream_gene_variant,,ENST00000587175,;CACTIN,upstream_gene_variant,,ENST00000589321,; G ENST00000429344 Transcript missense_variant 593/3612 540/2277 180/758 K/N aaG/aaC 1 -1 CACTIN HGNC HGNC:29938 protein_coding YES CCDS45920.1 ENSP00000415078 Q8WUQ7 UPI00006C1962 NM_001080543.1 deleterious(0) 2/10 hmmpanther:PTHR21737,hmmpanther:PTHR21737:SF6,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 3623790 3623790 C G 1 0 0 0 0 1 0 0 0 2252 912 32 4 4 CACTIN 19 3623790 Missense_Mutation SNP C C3N-00293_T 23235 3623790 54993826 266 12724 KEAP1 0 . GRCh38 19 10499684 10499684 + Missense_Mutation SNP T T A novel C3N-00293_T C3N-00293_N T T c.350A>T p.Glu117Val p.E117V ENST00000171111 2/6 332 312 20 241 241 0 strelka-varscan-mutect KEAP1,missense_variant,p.Glu117Val,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Glu117Val,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Glu117Val,ENST00000591419,;KEAP1,missense_variant,p.Glu117Val,ENST00000592055,;KEAP1,missense_variant,p.Glu117Val,ENST00000591039,;KEAP1,upstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; A ENST00000171111 Transcript missense_variant 898/2955 350/1875 117/624 E/V gAg/gTg 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 2/6 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 10499684 10499684 T A 1 0 0 0 0 1 0 0 0 8061 1551 54 4 4 KEAP1 19 10499684 Missense_Mutation SNP T C3N-00293_T 6875894 10499684 48117932 267 12725 51 2 KEAP1 0 . GRCh38 19 10499687 10499687 + Missense_Mutation SNP C C G C3N-00293_T C3N-00293_N C C c.347G>C p.Arg116Pro p.R116P ENST00000171111 2/6 331 310 21 244 244 0 strelka-varscan-mutect KEAP1,missense_variant,p.Arg116Pro,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Arg116Pro,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Arg116Pro,ENST00000591419,;KEAP1,missense_variant,p.Arg116Pro,ENST00000592055,;KEAP1,missense_variant,p.Arg116Pro,ENST00000591039,;KEAP1,upstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; G ENST00000171111 Transcript missense_variant 895/2955 347/1875 116/624 R/P cGg/cCg COSM3796565 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 2/6 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,PIRSF_domain:PIRSF037037,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 1 1 1 PASS rs1290253160 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 10499687 10499687 C G 1 0 0 0 0 1 0 0 0 8061 652 23 4 4 KEAP1 19 10499687 Missense_Mutation SNP C C3N-00293_T 3 10499687 48117929 268 12726 51 2 OCEL1 0 . GRCh38 19 17226276 17226276 + Missense_Mutation SNP C C T rs201983831 C3N-00293_T C3N-00293_N C C c.29C>T p.Pro10Leu p.P10L ENST00000215061 1/6 519 440 79 414 414 0 strelka-varscan-mutect OCEL1,missense_variant,p.Pro10Leu,ENST00000215061,NM_024578.2;OCEL1,missense_variant,p.Pro10Leu,ENST00000601529,;OCEL1,missense_variant,p.Pro9Leu,ENST00000600232,;OCEL1,upstream_gene_variant,,ENST00000598068,;OCEL1,upstream_gene_variant,,ENST00000597836,;OCEL1,upstream_gene_variant,,ENST00000595573,;OCEL1,upstream_gene_variant,,ENST00000600826,;OCEL1,non_coding_transcript_exon_variant,,ENST00000601576,;OCEL1,non_coding_transcript_exon_variant,,ENST00000602236,;OCEL1,non_coding_transcript_exon_variant,,ENST00000599588,;OCEL1,non_coding_transcript_exon_variant,,ENST00000594283,;OCEL1,upstream_gene_variant,,ENST00000596279,;OCEL1,upstream_gene_variant,,ENST00000598172,;OCEL1,upstream_gene_variant,,ENST00000595769,;OCEL1,upstream_gene_variant,,ENST00000599286,; T ENST00000215061 Transcript missense_variant 73/1133 29/795 10/264 P/L cCg/cTg rs201983831,COSM400199 1 1 OCEL1 HGNC HGNC:26221 protein_coding YES CCDS12351.1 ENSP00000215061 Q9H607 UPI000006D43F NM_024578.2 tolerated_low_confidence(0.44) 1/6 hmmpanther:PTHR23288,hmmpanther:PTHR23288:SF15 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201983831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 17226276 17226276 C T 1 0 0 0 0 1 0 0 0 10893 652 23 1 1 OCEL1 19 17226276 Missense_Mutation SNP C C3N-00293_T 6726589 17226276 41391340 269 12727 MAP1S 0 . GRCh38 19 17725965 17725965 + Missense_Mutation SNP G G T rs747950013 C3N-00293_T C3N-00293_N G G c.581G>T p.Arg194Leu p.R194L ENST00000324096 5/7 183 168 15 124 124 0 strelka-varscan-mutect MAP1S,missense_variant,p.Arg194Leu,ENST00000324096,NM_018174.4;MAP1S,missense_variant,p.Arg168Leu,ENST00000544059,NM_001308363.1;MAP1S,missense_variant,p.Arg160Leu,ENST00000600186,;MAP1S,intron_variant,,ENST00000597735,;MAP1S,downstream_gene_variant,,ENST00000594625,;MAP1S,upstream_gene_variant,,ENST00000597000,;CTD-3149D2.4,downstream_gene_variant,,ENST00000595363,;MAP1S,non_coding_transcript_exon_variant,,ENST00000599494,;MAP1S,non_coding_transcript_exon_variant,,ENST00000598916,;MAP1S,intron_variant,,ENST00000597681,;MAP1S,downstream_gene_variant,,ENST00000601544,;MAP1S,upstream_gene_variant,,ENST00000598756,;MAP1S,downstream_gene_variant,,ENST00000594340,;MAP1S,downstream_gene_variant,,ENST00000595338,;MAP1S,downstream_gene_variant,,ENST00000597067,;MAP1S,3_prime_UTR_variant,,ENST00000594212,;MAP1S,3_prime_UTR_variant,,ENST00000594365,;MAP1S,non_coding_transcript_exon_variant,,ENST00000598769,;MAP1S,downstream_gene_variant,,ENST00000596637,;MAP1S,downstream_gene_variant,,ENST00000593593,;MAP1S,downstream_gene_variant,,ENST00000600608,; T ENST00000324096 Transcript missense_variant 732/3419 581/3180 194/1059 R/L cGg/cTg rs747950013 1 1 MAP1S HGNC HGNC:15715 protein_coding YES CCDS32954.1 ENSP00000325313 Q66K74 UPI00002036F9 NM_018174.4 deleterious(0.04) 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR13843 MODERATE 1 SNV 1 1 PASS rs747950013 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 17725965 17725965 G T 1 0 0 0 0 1 0 0 0 9156 1116 39 1 1 MAP1S 19 17725965 Missense_Mutation SNP G C3N-00293_T 499689 17725965 40891651 270 12728 CILP2 0 . GRCh38 19 19543301 19543301 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.1031T>C p.Leu344Pro p.L344P ENST00000291495 7/8 252 225 27 179 179 0 strelka-varscan-mutect CILP2,missense_variant,p.Leu350Pro,ENST00000586018,;CILP2,missense_variant,p.Leu344Pro,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; C ENST00000291495 Transcript missense_variant 1116/4199 1031/3471 344/1156 L/P cTg/cCg 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 deleterious(0) 7/8 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 19543301 19543301 T C 1 0 0 0 0 1 0 0 0 3192 1580 55 5 5 CILP2 19 19543301 Missense_Mutation SNP T C3N-00293_T 1817336 19543301 39074315 271 12729 ZNF429 0 . GRCh38 19 21537319 21537319 + Silent SNP G G A C3N-00293_T C3N-00293_N G G c.1266G>A p.= p.E422E ENST00000358491 4/4 218 198 20 104 104 0 strelka-varscan-mutect ZNF429,synonymous_variant,p.=,ENST00000358491,NM_001001415.2;ZNF429,synonymous_variant,p.=,ENST00000618549,;ZNF429,intron_variant,,ENST00000597078,;ZNF429,upstream_gene_variant,,ENST00000594385,;ZNF429,downstream_gene_variant,,ENST00000594022,; A ENST00000358491 Transcript synonymous_variant 1474/2233 1266/2025 422/674 E gaG/gaA COSM4524342 1 1 ZNF429 HGNC HGNC:20817 protein_coding YES CCDS42537.1 ENSP00000351280 Q86V71 UPI000022ABC2 NM_001001415.2 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF367,Superfamily_domains:SSF57667 1 LOW 1 SNV 3 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 21537319 21537319 G A 1 0 0 0 0 0 0 0 1 18474 933 33 3 3 ZNF429 19 21537319 Silent SNP G C3N-00293_T 1994018 21537319 37080297 272 12730 ZNF100 0 . GRCh38 19 21745018 21745018 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.146G>T p.Trp49Leu p.W49L ENST00000358296 3/5 163 147 16 103 103 0 varscan-mutect ZNF100,missense_variant,p.Trp49Leu,ENST00000358296,NM_173531.3;ZNF100,missense_variant,p.Trp49Leu,ENST00000608416,;ZNF100,missense_variant,p.Trp49Leu,ENST00000598026,;ZNF100,5_prime_UTR_variant,,ENST00000305570,;ZNF100,5_prime_UTR_variant,,ENST00000594401,; A ENST00000358296 Transcript missense_variant 345/5745 146/1629 49/542 W/L tGg/tTg 1 -1 ZNF100 HGNC HGNC:12880 protein_coding YES CCDS42538.1 ENSP00000351042 Q8IYN0 UPI00001614AC NM_173531.3 deleterious(0) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF131,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 21745018 21745018 C A 1 0 0 0 0 1 0 0 0 18292 595 21 2 2 ZNF100 19 21745018 Missense_Mutation SNP C C3N-00293_T 207699 21745018 36872598 273 12731 SHANK1 0 . GRCh38 19 50702607 50702607 + Frame_Shift_Del DEL C C - rs760667018 C3N-00293_T C3N-00293_N C C c.1607delG p.Gly536AlafsTer27 p.G536Afs*27 ENST00000293441 11/23 180 168 12 154 154 0 varindel-pindel SHANK1,frameshift_variant,p.Gly536AlafsTer27,ENST00000293441,NM_016148.2;SHANK1,frameshift_variant,p.Gly536AlafsTer27,ENST00000391814,;SHANK1,frameshift_variant,p.Gly536AlafsTer27,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000461154,; - ENST00000293441 Transcript frameshift_variant 1626/6643 1607/6486 536/2161 G/X gGc/gc rs760667018 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 11/23 Low_complexity_(Seg):seg,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3 HIGH 1 deletion 1 1 PASS . . 0 201 2 7 0 0 0 0 -15.1139 0.9677701 1 1 1 0 - 7 5 45 50702607 50702607 C - 1 0 1 0 1 0 0 0 0 14523 739 26 0 0 SHANK1 19 50702607 Frame_Shift_Del DEL C C3N-00293_T 28957589 50702607 7915009 274 12732 SIGLEC14 0 . GRCh38 19 51643540 51643540 + Missense_Mutation SNP G G T C3N-00293_T C3N-00293_N G G c.1145C>A p.Thr382Asn p.T382N ENST00000360844 6/7 82 67 15 73 73 0 strelka-varscan-mutect SIGLEC14,missense_variant,p.Thr382Asn,ENST00000360844,NM_001098612.1;SIGLEC5,intron_variant,,ENST00000534261,NM_003830.3;AC018755.18,intron_variant,,ENST00000429354,;AC018755.18,intron_variant,,ENST00000599649,;LLNLR-470E3.1,upstream_gene_variant,,ENST00000619715,;SIGLEC14,non_coding_transcript_exon_variant,,ENST00000533866,; T ENST00000360844 Transcript missense_variant 1187/2035 1145/1191 382/396 T/N aCc/aAc COSM1000137 1 -1 SIGLEC14 HGNC HGNC:32926 protein_coding YES CCDS42604.1 ENSP00000354090 Q08ET2 UPI0000E44158 NM_001098612.1 deleterious(0.02) 6/7 1 MODERATE 1 SNV 1 1 1 PASS . . 64 144 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 51643540 51643540 G T 1 0 0 0 0 1 0 0 0 14573 1275 44 2 2 SIGLEC14 19 51643540 Missense_Mutation SNP G C3N-00293_T 940933 51643540 6974076 275 12733 ZNF610 0 . GRCh38 19 52365891 52365891 + Silent SNP C C T rs376963796 C3N-00293_T C3N-00293_N C C c.513C>T p.= p.F171F ENST00000403906 6/6 181 167 14 62 62 0 strelka-varscan-mutect ZNF610,synonymous_variant,p.=,ENST00000601151,NM_001161427.1;ZNF610,synonymous_variant,p.=,ENST00000403906,NM_001161425.1;ZNF610,synonymous_variant,p.=,ENST00000321287,NM_001161426.1;ZNF610,synonymous_variant,p.=,ENST00000327920,NM_173530.2;ZNF610,synonymous_variant,p.=,ENST00000616431,;ZNF610,synonymous_variant,p.=,ENST00000613461,;ZNF880,upstream_gene_variant,,ENST00000422689,NM_001145434.1;ZNF880,upstream_gene_variant,,ENST00000600321,;ZNF880,upstream_gene_variant,,ENST00000424032,;ZNF880,upstream_gene_variant,,ENST00000344085,;ZNF880,upstream_gene_variant,,ENST00000597976,;ZNF880,upstream_gene_variant,,ENST00000595099,; T ENST00000403906 Transcript synonymous_variant 969/2191 513/1389 171/462 F ttC/ttT rs376963796 1 1 ZNF610 HGNC HGNC:26687 protein_coding YES CCDS12851.1 ENSP00000383922 Q8N9Z0 UPI0000140AF2 NM_001161425.1 6/6 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF197 LOW 1 SNV 1 1 PASS rs376963796 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 52365891 52365891 C T 1 0 0 0 0 0 0 0 1 18611 825 29 3 3 ZNF610 19 52365891 Silent SNP C C3N-00293_T 722351 52365891 6251725 276 12734 ZNF534 0 . GRCh38 19 52435211 52435211 + Splice_Site SNP T T A novel C3N-00293_T C3N-00293_N T T c.310+2T>A p.X104_splice ENST00000332323 100 88 12 77 77 0 strelka-varscan-mutect ZNF534,splice_donor_variant,,ENST00000332323,NM_001143939.1;ZNF534,splice_donor_variant,,ENST00000433050,NM_001143938.1;ZNF534,splice_donor_variant,,ENST00000301085,;ZNF534,splice_donor_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; A ENST00000332323 Transcript splice_donor_variant -/2086 310/2025 104/674 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 3/3 HIGH 1 SNV 1 1 PASS rs770264627 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 45 52435211 52435211 T A 1 0 0 0 0 0 0 1 0 18546 1710 59 4 4 ZNF534 19 52435211 Splice_Site SNP T C3N-00293_T 69320 52435211 6182405 277 12735 ZNF534 0 . GRCh38 19 52438525 52438525 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.1104A>T p.Lys368Asn p.K368N ENST00000332323 4/4 161 151 10 99 99 0 strelka-varscan-mutect ZNF534,missense_variant,p.Lys368Asn,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Lys355Asn,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; T ENST00000332323 Transcript missense_variant 1165/2086 1104/2025 368/674 K/N aaA/aaT 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 deleterious(0.01) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 52438525 52438525 A T 1 0 0 0 0 1 0 0 0 18546 98 4 4 4 ZNF534 19 52438525 Missense_Mutation SNP A C3N-00293_T 3314 52438525 6179091 278 12736 PRKCG 0 . GRCh38 19 53900471 53900471 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.1426A>T p.Ile476Phe p.I476F ENST00000263431 13/18 1030 925 105 829 829 0 strelka-varscan-mutect PRKCG,missense_variant,p.Ile476Phe,ENST00000263431,NM_002739.3; T ENST00000263431 Transcript missense_variant 1708/3133 1426/2094 476/697 I/F Atc/Ttc 1 1 PRKCG HGNC HGNC:9402 protein_coding YES CCDS12867.1 ENSP00000263431 P05129 UPI000000DC69 NM_002739.3 deleterious(0) 13/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF162,hmmpanther:PTHR24356,PROSITE_patterns:PS00108,PIRSF_domain:PIRSF000550,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 53900471 53900471 A T 1 0 0 0 0 1 0 0 0 12645 217 8 4 4 PRKCG 19 53900471 Missense_Mutation SNP A C3N-00293_T 1461946 53900471 4717145 279 12737 LILRB4 0 . GRCh38 19 54666746 54666746 + Silent SNP T T A rs372559600 C3N-00293_T C3N-00293_N T T c.1038T>A p.= p.T346T ENST00000391736 12/14 219 193 26 182 182 0 strelka-varscan-mutect LILRB4,synonymous_variant,p.=,ENST00000391736,NM_001278426.3;LILRB4,synonymous_variant,p.=,ENST00000430952,NM_001278427.3;LILRB4,synonymous_variant,p.=,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,synonymous_variant,p.=,ENST00000391734,;LILRB4,synonymous_variant,p.=,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,non_coding_transcript_exon_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,non_coding_transcript_exon_variant,,ENST00000470943,;AC011515.2,upstream_gene_variant,,ENST00000441512,; A ENST00000391736 Transcript synonymous_variant 1353/4002 1038/1347 346/448 T acT/acA rs372559600 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 12/14 LOW 1 SNV 5 1 PASS rs372559600 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 54666746 54666746 T A 1 0 0 0 0 0 0 0 1 8701 1565 54 4 4 LILRB4 19 54666746 Silent SNP T C3N-00293_T 766275 54666746 3950870 280 12738 FAM71E2 0 . GRCh38 19 55362497 55362497 + Silent SNP G G T rs778545385 C3N-00293_T C3N-00293_N G G c.312C>A p.= p.I104I ENST00000424985 3/11 95 86 9 63 63 0 strelka-mutect FAM71E2,synonymous_variant,p.=,ENST00000424985,NM_001145402.1;IL11,downstream_gene_variant,,ENST00000264563,NM_000641.3;IL11,downstream_gene_variant,,ENST00000585513,;IL11,downstream_gene_variant,,ENST00000590625,NM_001267718.1;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;CTD-2105E13.6,upstream_gene_variant,,ENST00000591954,; T ENST00000424985 Transcript synonymous_variant 506/3191 312/2769 104/922 I atC/atA rs778545385,COSM4590825,COSM4590826 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 3/11 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF12,Pfam_domain:PF12480 0,1,1 LOW SNV 5 0,1,1 1 PASS rs778545385 . 0 203 7 0 0 0 0 0 -18.44646 0.9999988 1 1 1 0 T 2 4 45 55362497 55362497 G T 1 0 0 0 0 0 0 0 1 5476 1164 41 2 2 FAM71E2 19 55362497 Silent SNP G C3N-00293_T 695751 55362497 3255119 281 12739 SBK2 0 . GRCh38 19 55530128 55530128 + Missense_Mutation SNP C C A C3N-00293_T C3N-00293_N C C c.652G>T p.Gly218Trp p.G218W ENST00000413299 4/4 49 44 5 32 32 0 strelka-mutect SBK2,missense_variant,p.Gly218Trp,ENST00000413299,NM_001101401.2;SBK2,missense_variant,p.Gly218Trp,ENST00000344158,; A ENST00000413299 Transcript missense_variant 690/1085 652/1047 218/348 G/W Ggg/Tgg COSM4964458,COSM4964459 1 -1 SBK2 HGNC HGNC:34416 protein_coding YES CCDS42631.1 ENSP00000389015 P0C263 UPI00015DFA43 NM_001101401.2 deleterious(0) 4/4 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF167,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs935026083 . 0 207 3 0 0 0 0 0 -12.66033 1 1 1 1 0 A 3 1 45 55530128 55530128 C A 1 0 0 0 0 1 0 0 0 14125 652 23 1 1 SBK2 19 55530128 Missense_Mutation SNP C C3N-00293_T 167631 55530128 3087488 282 12740 NLRP5 0 . GRCh38 19 56027501 56027501 + Frame_Shift_Del DEL C C - rs374218026 C3N-00293_T C3N-00293_N C C c.1268delC p.Ser423PhefsTer6 p.S423Ffs*6 ENST00000390649 7/15 226 200 26 227 227 0 sindel-varindel-pindel NLRP5,frameshift_variant,p.Ser423PhefsTer6,ENST00000390649,NM_153447.4;NLRP5,frameshift_variant,p.Ser423PhefsTer6,ENST00000621651,; - ENST00000390649 Transcript frameshift_variant 1268/3888 1268/3603 423/1200 S/X tCt/tt rs374218026 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 7/15 hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 45 56027501 56027501 C - 1 0 1 0 1 0 0 0 0 10518 913 32 0 0 NLRP5 19 56027501 Frame_Shift_Del DEL C C3N-00293_T 497373 56027501 2590115 283 12741 ZSCAN5B 0 . GRCh38 19 56192952 56192952 + Frame_Shift_Del DEL C C - novel C3N-00293_T C3N-00293_N C C c.101delG p.Gly34GlufsTer12 p.G34Efs*12 ENST00000586855 2/5 162 148 14 129 129 0 sindel-varindel-pindel ZSCAN5B,frameshift_variant,p.Gly34GlufsTer12,ENST00000586855,;ZSCAN5B,frameshift_variant,p.Gly34GlufsTer12,ENST00000358992,NM_001080456.2;ZSCAN5B,frameshift_variant,p.Gly34GlufsTer12,ENST00000589938,;ZSCAN5B,frameshift_variant,p.Gly34GlufsTer12,ENST00000587032,; - ENST00000586855 Transcript frameshift_variant 415/2059 101/1488 34/495 G/X gGa/ga 1 -1 ZSCAN5B HGNC HGNC:34246 protein_coding YES CCDS46203.1 ENSP00000466072 A6NJL1 UPI000059D7BA 2/5 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF164 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.19363 0.9999998 1 1 1 0 - 7 5 45 56192952 56192952 C - 1 0 1 0 1 0 0 0 0 18838 855 30 0 0 ZSCAN5B 19 56192952 Frame_Shift_Del DEL C C3N-00293_T 165451 56192952 2424664 284 12742 TMEM74B 0 . GRCh38 20 1181028 1181028 + Silent SNP G G A novel C3N-00293_T C3N-00293_N G G c.591C>T p.= p.V197V ENST00000381894 2/2 162 141 21 129 129 0 strelka-varscan-mutect TMEM74B,synonymous_variant,p.=,ENST00000381894,NM_001304748.1,NM_018354.2;PSMF1,intron_variant,,ENST00000381898,;TMEM74B,downstream_gene_variant,,ENST00000429036,;TMEM74B,downstream_gene_variant,,ENST00000481747,;PSMF1,downstream_gene_variant,,ENST00000418246,; A ENST00000381894 Transcript synonymous_variant 1263/1730 591/771 197/256 V gtC/gtT 1 -1 TMEM74B HGNC HGNC:15893 protein_coding YES CCDS13011.1 ENSP00000371318 Q9NUR3 UPI0000049822 NM_001304748.1,NM_018354.2 2/2 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16125,Pfam_domain:PF14927 LOW 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 45 1181028 1181028 G A 1 0 0 0 0 0 0 0 1 16678 929 33 3 3 TMEM74B 20 1181028 Silent SNP G C3N-00293_T 1181028 63263139 285 12743 TASP1 0 . GRCh38 20 13528513 13528513 + Splice_Site SNP T T A novel C3N-00293_T C3N-00293_N T T c.796-2A>T p.X266_splice ENST00000337743 188 175 13 132 132 0 strelka-varscan-mutect TASP1,splice_acceptor_variant,,ENST00000337743,NM_017714.2;TASP1,splice_acceptor_variant,,ENST00000455532,;TASP1,splice_acceptor_variant,,ENST00000480436,;TASP1,splice_acceptor_variant,,ENST00000465381,; A ENST00000337743 Transcript splice_acceptor_variant -/2352 796/1263 266/420 1 -1 TASP1 HGNC HGNC:15859 protein_coding YES CCDS13116.1 ENSP00000338624 Q9H6P5 UPI00000382E5 NM_017714.2 9/13 HIGH 1 SNV 1 1 PASS rs772519686 . 0 196 5 7 2 0 0 0 -4.754286 0.4880462 1 1 0 0 A 5 1 45 13528513 13528513 T A 1 0 0 0 0 0 0 1 0 15988 1594 55 4 4 TASP1 20 13528513 Splice_Site SNP T C3N-00293_T 12347485 13528513 50915654 286 12744 SYNDIG1 0 . GRCh38 20 24543485 24543485 + Missense_Mutation SNP G G A C3N-00293_T C3N-00293_N G G c.388G>A p.Asp130Asn p.D130N ENST00000376862 2/4 414 356 58 350 350 0 strelka-varscan-mutect SYNDIG1,missense_variant,p.Asp130Asn,ENST00000376862,NM_024893.2; A ENST00000376862 Transcript missense_variant 1021/2522 388/777 130/258 D/N Gat/Aat COSM4399897 1 1 SYNDIG1 HGNC HGNC:15885 protein_coding YES CCDS13164.1 ENSP00000366058 Q9H7V2 UPI00001285DC NM_024893.2 tolerated(0.05) 2/4 hmmpanther:PTHR14768,hmmpanther:PTHR14768:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 24543485 24543485 G A 1 0 0 0 0 1 0 0 0 15835 1174 41 3 3 SYNDIG1 20 24543485 Missense_Mutation SNP G C3N-00293_T 11014972 24543485 39900682 287 12745 FAM182B 0 . GRCh38 20 25774950 25774950 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.370A>G p.Ser124Gly p.S124G ENST00000376403 3/3 210 197 13 147 147 0 varscan-mutect FAM182B,missense_variant,p.Ser124Gly,ENST00000376403,;FAM182B,missense_variant,p.Ser123Gly,ENST00000376404,;FAM182B,downstream_gene_variant,,ENST00000584071,;FAM182B,intron_variant,,ENST00000478164,;FAM182B,intron_variant,,ENST00000485279,;FAM182B,intron_variant,,ENST00000453481,;FAM182B,downstream_gene_variant,,ENST00000582267,;FAM182B,downstream_gene_variant,,ENST00000584356,; C ENST00000376403 Transcript missense_variant 749/1681 370/459 124/152 S/G Agt/Ggt 1 -1 FAM182B HGNC HGNC:34503 protein_coding YES ENSP00000365585 Q5T319 UPI000047001E deleterious_low_confidence(0.04) 3/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 25774950 25774950 T C 1 0 0 0 0 1 0 0 0 5356 1551 54 5 5 FAM182B 20 25774950 Missense_Mutation SNP T C3N-00293_T 1231465 25774950 38669217 288 12746 BCAS1 0 . GRCh38 20 54028558 54028558 + Missense_Mutation SNP G G C novel C3N-00293_T C3N-00293_N G G c.557C>G p.Ser186Cys p.S186C ENST00000395961 4/12 450 421 29 384 384 0 strelka-varscan-mutect BCAS1,missense_variant,p.Ser48Cys,ENST00000448484,;BCAS1,missense_variant,p.Ser186Cys,ENST00000395961,NM_003657.2;BCAS1,missense_variant,p.Ser186Cys,ENST00000371435,NM_001316361.2,NM_001323347.1; C ENST00000395961 Transcript missense_variant 724/3303 557/1755 186/584 S/C tCc/tGc 1 -1 BCAS1 HGNC HGNC:974 protein_coding YES CCDS13444.1 ENSP00000379290 O75363 UPI000013D2E2 NM_003657.2 deleterious(0) 4/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15016 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 45 54028558 54028558 G C 1 0 0 0 0 1 0 0 0 1497 1174 41 4 4 BCAS1 20 54028558 Missense_Mutation SNP G C3N-00293_T 28253608 54028558 10415609 289 12747 TMPRSS15 0 . GRCh38 21 18294396 18294396 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.2360G>A p.Gly787Glu p.G787E ENST00000284885 21/25 638 572 66 426 426 0 strelka-varscan-mutect TMPRSS15,missense_variant,p.Gly787Glu,ENST00000284885,NM_002772.2; T ENST00000284885 Transcript missense_variant 2394/3947 2360/3060 787/1019 G/E gGa/gAa 1 -1 TMPRSS15 HGNC HGNC:9490 protein_coding YES CCDS13571.1 ENSP00000284885 P98073 UPI000013DDBE NM_002772.2 deleterious(0) 21/25 PROSITE_profiles:PS50287,PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF116,hmmpanther:PTHR24256,PIRSF_domain:PIRSF001138,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 18294396 18294396 C T 1 0 0 0 0 1 0 0 0 16722 855 30 3 3 TMPRSS15 21 18294396 Missense_Mutation SNP C C3N-00293_T 18294396 28415587 290 12748 KRTAP7-1 0 . GRCh38 21 30829546 30829546 + Silent SNP G G T novel C3N-00293_T C3N-00293_N G G c.153C>A p.= p.S51S ENST00000621162 1/1 354 334 20 294 294 0 strelka-varscan KRTAP7-1,synonymous_variant,p.=,ENST00000621162,NM_181606.2; T ENST00000621162 Transcript synonymous_variant 214/721 153/264 51/87 S tcC/tcA 1 -1 KRTAP7-1 HGNC HGNC:18934 protein_coding YES CCDS74780.1 ENSP00000479656 Q8IUC3 UPI00001B3DE7 NM_181606.2 1/1 PD061258,Pfam_domain:PF15034,hmmpanther:PTHR38504,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 30829546 30829546 G T 1 0 0 0 0 0 0 0 1 8467 1219 43 2 2 KRTAP7-1 21 30829546 Silent SNP G C3N-00293_T 12535150 30829546 15880437 291 12749 SCAF4 0 . GRCh38 21 31671754 31671754 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.3089G>T p.Arg1030Met p.R1030M ENST00000286835 20/20 228 204 24 144 144 0 strelka-varscan-mutect SCAF4,missense_variant,p.Arg1030Met,ENST00000286835,NM_020706.2;SCAF4,missense_variant,p.Arg1008Met,ENST00000399804,NM_001145445.1;SCAF4,missense_variant,p.Arg1015Met,ENST00000434667,NM_001145444.1;SOD1,downstream_gene_variant,,ENST00000270142,NM_000454.4;SOD1,downstream_gene_variant,,ENST00000389995,;AP000254.8,upstream_gene_variant,,ENST00000609934,;SOD1,downstream_gene_variant,,ENST00000470944,;SOD1,downstream_gene_variant,,ENST00000476106,; A ENST00000286835 Transcript missense_variant 3472/4193 3089/3444 1030/1147 R/M aGg/aTg 1 -1 SCAF4 HGNC HGNC:19304 protein_coding YES CCDS33537.1 ENSP00000286835 O95104 UPI0000206D66 NM_020706.2 deleterious_low_confidence(0) 20/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1262982775 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 31671754 31671754 C A 1 0 0 0 0 1 0 0 0 14134 681 24 2 2 SCAF4 21 31671754 Missense_Mutation SNP C C3N-00293_T 842208 31671754 15038229 292 12750 IL10RB 0 . GRCh38 21 33283107 33283107 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.512C>T p.Pro171Leu p.P171L ENST00000290200 5/7 518 462 56 332 332 0 strelka-varscan-mutect IL10RB,missense_variant,p.Pro171Leu,ENST00000290200,NM_000628.4;AP000295.9,missense_variant,p.Pro299Leu,ENST00000433395,;IL10RB,missense_variant,p.Pro108Leu,ENST00000451065,;IL10RB,3_prime_UTR_variant,,ENST00000422891,;AP000295.9,3_prime_UTR_variant,,ENST00000432231,;IL10RB,non_coding_transcript_exon_variant,,ENST00000493295,;IL10RB,non_coding_transcript_exon_variant,,ENST00000498371,; T ENST00000290200 Transcript missense_variant 620/1963 512/978 171/325 P/L cCc/cTc 1 1 IL10RB HGNC HGNC:5965 protein_coding YES CCDS13623.1 ENSP00000290200 Q08334 UPI0000072ECA NM_000628.4 tolerated(0.07) 5/7 PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF50,Pfam_domain:PF09294,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 33283107 33283107 C T 1 0 0 0 0 1 0 0 0 7529 623 22 3 3 IL10RB 21 33283107 Missense_Mutation SNP C C3N-00293_T 1611353 33283107 13426876 293 12751 RSPH1 0 . GRCh38 21 42485734 42485734 + Nonsense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.436C>T p.Gln146Ter p.Q146* ENST00000291536 5/9 337 315 22 365 365 0 strelka-varscan-mutect RSPH1,stop_gained,p.Gln146Ter,ENST00000291536,NM_080860.3;RSPH1,stop_gained,p.Gln108Ter,ENST00000398352,NM_001286506.1;RSPH1,non_coding_transcript_exon_variant,,ENST00000493019,; A ENST00000291536 Transcript stop_gained 604/1430 436/930 146/309 Q/* Cag/Tag 1 -1 RSPH1 HGNC HGNC:12371 protein_coding YES CCDS13688.1 ENSP00000291536 Q8WYR4 UPI000004FA34 NM_080860.3 5/9 hmmpanther:PTHR23084,Pfam_domain:PF02493,Gene3D:1h3iA01,SMART_domains:SM00698,Superfamily_domains:0038399 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 45 42485734 42485734 G A 1 0 0 0 0 0 1 0 0 13959 1328 46 3 3 RSPH1 21 42485734 Nonsense_Mutation SNP G C3N-00293_T 9202627 42485734 4224249 294 12752 LRRC3 0 . GRCh38 21 44456898 44456898 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.254A>T p.Gln85Leu p.Q85L ENST00000291592 2/2 201 184 17 113 113 0 strelka-varscan-mutect LRRC3,missense_variant,p.Gln85Leu,ENST00000291592,NM_030891.4;LRRC3-AS1,upstream_gene_variant,,ENST00000426578,; T ENST00000291592 Transcript missense_variant 571/5869 254/774 85/257 Q/L cAg/cTg 1 1 LRRC3 HGNC HGNC:14965 protein_coding YES CCDS13711.1 ENSP00000291592 Q9BY71 UPI000012E946 NM_030891.4 tolerated(0.08) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 45 44456898 44456898 A T 1 0 0 0 0 1 0 0 0 8879 188 7 4 4 LRRC3 21 44456898 Missense_Mutation SNP A C3N-00293_T 1971164 44456898 2253085 295 12753 MYO18B 0 . GRCh38 22 25868329 25868329 + Nonsense_Mutation SNP G G T novel C3N-00293_T C3N-00293_N G G c.3895G>T p.Glu1299Ter p.E1299* ENST00000335473 22/44 204 183 21 191 191 0 strelka-mutect MYO18B,stop_gained,p.Glu1299Ter,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,stop_gained,p.Glu1300Ter,ENST00000407587,;MYO18B,stop_gained,p.Glu1299Ter,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript stop_gained 4145/8565 3895/7704 1299/2567 E/* Gag/Tag 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 22/44 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,Low_complexity_(Seg):seg,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 45 25868329 25868329 G T 1 0 0 0 0 0 1 0 0 10067 1175 41 2 2 MYO18B 22 25868329 Nonsense_Mutation SNP G C3N-00293_T 25868329 24950139 296 12754 TTC28 0 . GRCh38 22 27996201 27996201 + Silent SNP C C T novel C3N-00293_T C3N-00293_N C C c.5178G>A p.= p.Q1726Q ENST00000397906 17/23 202 186 16 211 211 0 strelka-varscan-mutect TTC28,synonymous_variant,p.=,ENST00000397906,NM_001145418.1;TTC28,synonymous_variant,p.=,ENST00000612946,;TTC28,synonymous_variant,p.=,ENST00000431039,;TTC28-AS1,intron_variant,,ENST00000428584,;TTC28-AS1,intron_variant,,ENST00000454741,;TTC28-AS1,intron_variant,,ENST00000433317,;TTC28-AS1,intron_variant,,ENST00000434221,;TTC28-AS1,intron_variant,,ENST00000452612,;TTC28-AS1,intron_variant,,ENST00000417497,;TTC28-AS1,intron_variant,,ENST00000435348,;TTC28-AS1,intron_variant,,ENST00000453632,;TTC28-AS1,intron_variant,,ENST00000424161,;TTC28-AS1,downstream_gene_variant,,ENST00000430853,;TTC28-AS1,downstream_gene_variant,,ENST00000430525,;TTC28-AS1,upstream_gene_variant,,ENST00000426594,;TTC28-AS1_3,downstream_gene_variant,,ENST00000615579,;TTC28-AS1,intron_variant,,ENST00000540665,;TTC28,non_coding_transcript_exon_variant,,ENST00000469670,; T ENST00000397906 Transcript synonymous_variant 5320/11795 5178/7446 1726/2481 Q caG/caA 1 -1 TTC28 HGNC HGNC:29179 protein_coding YES CCDS46678.1 ENSP00000381003 Q96AY4 UPI00003E58F8 NM_001145418.1 17/23 hmmpanther:PTHR10098,hmmpanther:PTHR10098:SF106 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 27996201 27996201 C T 1 0 0 0 0 0 0 0 1 17204 680 24 3 3 TTC28 22 27996201 Silent SNP C C3N-00293_T 2127872 27996201 22822267 297 12755 WBP2NL 0 . GRCh38 22 42022281 42022281 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.439G>A p.Asp147Asn p.D147N ENST00000328823 5/6 249 230 19 116 116 0 strelka-varscan-mutect WBP2NL,missense_variant,p.Asp147Asn,ENST00000328823,NM_152613.2;WBP2NL,missense_variant,p.Asp73Asn,ENST00000543212,;WBP2NL,non_coding_transcript_exon_variant,,ENST00000475341,;WBP2NL,upstream_gene_variant,,ENST00000487176,;WBP2NL,missense_variant,p.Asp147Asn,ENST00000329620,;WBP2NL,missense_variant,p.Asp147Asn,ENST00000436265,;WBP2NL,3_prime_UTR_variant,,ENST00000445185,;WBP2NL,intron_variant,,ENST00000412113,; A ENST00000328823 Transcript missense_variant 470/2255 439/930 147/309 D/N Gac/Aac 1 1 WBP2NL HGNC HGNC:28389 protein_coding YES CCDS14029.1 ENSP00000332983 Q6ICG8 UPI00001AF89A NM_152613.2 tolerated(0.98) 5/6 Pfam_domain:PF10349 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 42022281 42022281 G A 1 0 0 0 0 1 0 0 0 17821 1290 45 3 3 WBP2NL 22 42022281 Missense_Mutation SNP G C3N-00293_T 14026080 42022281 8796187 298 12756 NHS 0 . GRCh38 X 17732120 17732120 + Missense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.4549G>A p.Glu1517Lys p.E1517K ENST00000380060 8/8 194 148 46 135 135 0 strelka-varscan-mutect NHS,missense_variant,p.Glu1358Lys,ENST00000615422,;NHS,missense_variant,p.Glu1517Lys,ENST00000380060,NM_198270.3,NM_001291867.1;NHS,missense_variant,p.Glu1361Lys,ENST00000398097,NM_001136024.3;NHS,missense_variant,p.Glu1334Lys,ENST00000617601,NM_001291868.1; A ENST00000380060 Transcript missense_variant 4887/8761 4549/4893 1517/1630 E/K Gag/Aag 1 1 NHS HGNC HGNC:7820 protein_coding YES CCDS14181.1 ENSP00000369400 Q6T4R5 UPI00001DFBF3 NM_198270.3,NM_001291867.1 deleterious(0) 8/8 hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 17732120 17732120 G A 1 0 0 0 0 1 0 0 0 10443 1291 45 3 3 NHS 23 17732120 Missense_Mutation SNP G C3N-00293_T 17732120 138308775 299 12757 MAGEB6 0 . GRCh38 X 26194882 26194882 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1036C>A p.Gln346Lys p.Q346K ENST00000379034 2/2 139 114 25 105 105 0 strelka-varscan-mutect MAGEB6,missense_variant,p.Gln346Lys,ENST00000379034,NM_173523.2; A ENST00000379034 Transcript missense_variant 1185/1949 1036/1224 346/407 Q/K Cag/Aag 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 deleterious(0.04) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 26194882 26194882 C A 1 0 0 0 0 1 0 0 0 9096 711 25 2 2 MAGEB6 23 26194882 Missense_Mutation SNP C C3N-00293_T 8462762 26194882 129846013 300 12758 DCAF8L2 0 . GRCh38 X 27748407 27748407 + Silent SNP C C T C3N-00293_T C3N-00293_N C C c.1512C>T p.= p.I504I ENST00000451261 5/5 139 132 7 98 98 0 strelka-varscan-mutect DCAF8L2,synonymous_variant,p.=,ENST00000451261,;DCAF8L2,synonymous_variant,p.=,ENST00000545306,NM_001136533.1;DCAF8L2,downstream_gene_variant,,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,; T ENST00000451261 Transcript synonymous_variant 1911/2295 1512/1896 504/631 I atC/atT COSM4856162,COSM4856163 1 1 DCAF8L2 HGNC HGNC:31811 protein_coding YES CCDS59162.1 ENSP00000462745 P0C7V8 UPI000183CBD9 5/5 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF42,SMART_domains:SM00320,Superfamily_domains:SSF50978 1,1 LOW 1 SNV 4 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 45 27748407 27748407 C T 1 0 0 0 0 0 0 0 1 4079 816 29 3 3 DCAF8L2 23 27748407 Silent SNP C C3N-00293_T 1553525 27748407 128292488 301 12759 DMD 0 . GRCh38 X 32342194 32342194 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.5828T>A p.Met1943Lys p.M1943K ENST00000357033 41/79 102 94 8 76 76 0 strelka-varscan-mutect DMD,missense_variant,p.Met1943Lys,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Met1939Lys,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Met1943Lys,ENST00000620040,;DMD,missense_variant,p.Met1939Lys,ENST00000619831,;DMD,downstream_gene_variant,,ENST00000493412,;DMD,intron_variant,,ENST00000488902,; T ENST00000357033 Transcript missense_variant 6035/13956 5828/11058 1943/3685 M/K aTg/aAg 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 tolerated(1) 41/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,Pfam_domain:PF00435,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.35718 1 1 1 1 0 T 3 4 45 32342194 32342194 A T 1 0 0 0 0 1 0 0 0 4387 217 8 4 4 DMD 23 32342194 Missense_Mutation SNP A C3N-00293_T 4593787 32342194 123698701 302 12760 FAM47B 0 . GRCh38 X 34943134 34943134 + Silent SNP G G C rs143433018 C3N-00293_T C3N-00293_N G G c.303G>C p.= p.A101A ENST00000329357 1/1 125 105 20 109 109 0 strelka-varscan-mutect FAM47B,synonymous_variant,p.=,ENST00000329357,NM_152631.2; C ENST00000329357 Transcript synonymous_variant 339/2120 303/1938 101/645 A gcG/gcC rs143433018 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS rs143433018 . 0 205 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 45 34943134 34943134 G C 1 0 0 0 0 0 0 0 1 5448 1103 39 4 4 FAM47B 23 34943134 Silent SNP G C3N-00293_T 2600940 34943134 121097761 303 12761 ZNF630 0 . GRCh38 X 48060147 48060147 + Missense_Mutation SNP G G C rs184943023 C3N-00293_T C3N-00293_N G G c.295C>G p.Gln99Glu p.Q99E ENST00000442455 5/5 79 72 7 30 30 0 strelka-mutect ZNF630,missense_variant,p.Gln99Glu,ENST00000442455,NM_001190255.2,NM_001282201.1;ZNF630,missense_variant,p.Gln99Glu,ENST00000409324,NM_001037735.3;ZNF630,missense_variant,p.Gln85Glu,ENST00000616492,;ZNF630,missense_variant,p.Gln99Glu,ENST00000428686,;ZNF630,missense_variant,p.Gln85Glu,ENST00000627643,;ZNF630,5_prime_UTR_variant,,ENST00000276054,NM_001282202.1;ZNF630,5_prime_UTR_variant,,ENST00000421903,;ZNF630-AS1,intron_variant,,ENST00000614448,;ZNF630,intron_variant,,ENST00000428463,; C ENST00000442455 Transcript missense_variant 862/2829 295/1974 99/657 Q/E Caa/Gaa rs184943023 1 -1 ZNF630 HGNC HGNC:28855 protein_coding YES CCDS35237.2 ENSP00000393163 Q2M218 UPI0000160BE4 NM_001190255.2,NM_001282201.1 deleterious(0.01) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF216 MODERATE SNV 4 1 PASS rs184943023 . 0 206 3 0 0 0 0 0 -15.41067 1 1 1 1 0 C 3 2 45 48060147 48060147 G C 1 0 0 0 0 1 0 0 0 18629 1299 45 4 4 ZNF630 23 48060147 Missense_Mutation SNP G C3N-00293_T 13117013 48060147 107980748 304 12762 KDM5C 0 . GRCh38 X 53201883 53201883 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.1837G>A p.Glu613Lys p.E613K ENST00000375401 13/26 376 353 23 300 300 0 strelka-varscan-mutect KDM5C,missense_variant,p.Glu546Lys,ENST00000452825,NM_001146702.1;KDM5C,missense_variant,p.Glu613Lys,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Glu612Lys,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Glu613Lys,ENST00000375379,;KDM5C,missense_variant,p.Glu572Lys,ENST00000375383,;MIR6894,upstream_gene_variant,,ENST00000622662,;KDM5C,non_coding_transcript_exon_variant,,ENST00000465402,;KDM5C,upstream_gene_variant,,ENST00000477109,;KDM5C,non_coding_transcript_exon_variant,,ENST00000497100,;KDM5C,non_coding_transcript_exon_variant,,ENST00000481369,; T ENST00000375401 Transcript missense_variant 2370/6031 1837/4683 613/1560 E/K Gag/Aag 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 deleterious(0) 13/26 Pfam_domain:PF02373,PROSITE_profiles:PS51184,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43,SMART_domains:SM00558,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 53201883 53201883 C T 1 0 0 0 0 1 0 0 0 8053 893 31 1 1 KDM5C 23 53201883 Missense_Mutation SNP C C3N-00293_T 5141736 53201883 102839012 305 12763 BRWD3 0 . GRCh38 X 80676922 80676922 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.5096G>A p.Arg1699Lys p.R1699K ENST00000373275 41/41 157 139 18 125 125 0 strelka-varscan-mutect BRWD3,missense_variant,p.Arg1699Lys,ENST00000373275,NM_153252.4;BRWD3,downstream_gene_variant,,ENST00000473691,; T ENST00000373275 Transcript missense_variant 5313/11381 5096/5409 1699/1802 R/K aGa/aAa 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 tolerated_low_confidence(0.89) 41/41 Low_complexity_(Seg):seg,hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 80676922 80676922 C T 1 0 0 0 0 1 0 0 0 1700 913 32 3 3 BRWD3 23 80676922 Missense_Mutation SNP C C3N-00293_T 27475039 80676922 75363973 306 12764 HDX 0 . GRCh38 X 84344253 84344253 + Nonsense_Mutation SNP G G A novel C3N-00293_T C3N-00293_N G G c.1657C>T p.Gln553Ter p.Q553* ENST00000297977 6/10 127 117 10 91 91 0 strelka-varscan-mutect HDX,stop_gained,p.Gln553Ter,ENST00000297977,NM_001177479.1,NM_144657.4;HDX,stop_gained,p.Gln495Ter,ENST00000506585,NM_001177478.1;HDX,stop_gained,p.Gln553Ter,ENST00000373177,; A ENST00000297977 Transcript stop_gained 1769/6200 1657/2073 553/690 Q/* Caa/Taa 1 -1 HDX HGNC HGNC:26411 protein_coding YES CCDS35342.1 ENSP00000297977 Q7Z353 UPI00001A9DA4 NM_001177479.1,NM_144657.4 6/10 hmmpanther:PTHR11636:SF80,hmmpanther:PTHR11636 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.20728 1 1 1 1 0 A 4 1 45 84344253 84344253 G A 1 0 0 0 0 0 1 0 0 6909 1304 45 3 3 HDX 23 84344253 Nonsense_Mutation SNP G C3N-00293_T 3667331 84344253 71696642 307 12765 DACH2 0 . GRCh38 X 86714688 86714688 + Missense_Mutation SNP C C A novel C3N-00293_T C3N-00293_N C C c.1072C>A p.Pro358Thr p.P358T ENST00000373125 6/12 88 64 24 51 51 0 strelka-varscan-mutect DACH2,missense_variant,p.Pro13Thr,ENST00000484479,;DACH2,missense_variant,p.Pro345Thr,ENST00000373131,NM_001139514.1;DACH2,missense_variant,p.Pro358Thr,ENST00000373125,NM_053281.3;DACH2,missense_variant,p.Pro191Thr,ENST00000508860,NM_001139515.1;DACH2,missense_variant,p.Pro139Thr,ENST00000510272,;DACH2,missense_variant,p.Pro186Thr,ENST00000613770,;DACH2,missense_variant,p.Pro358Thr,ENST00000461604,;DACH2,3_prime_UTR_variant,,ENST00000506327,; A ENST00000373125 Transcript missense_variant 1072/2232 1072/1800 358/599 P/T Cca/Aca 1 1 DACH2 HGNC HGNC:16814 protein_coding YES CCDS14455.1 ENSP00000362217 Q96NX9 UPI00000717B4 NM_053281.3 tolerated(0.06) 6/12 hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 45 86714688 86714688 C A 1 0 0 0 0 1 0 0 0 4022 855 30 2 2 DACH2 23 86714688 Missense_Mutation SNP C C3N-00293_T 2370435 86714688 69326207 308 12766 RPA4 0 . GRCh38 X 96884905 96884905 + Missense_Mutation SNP A A T novel C3N-00293_T C3N-00293_N A A c.595A>T p.Asn199Tyr p.N199Y ENST00000373040 1/1 287 269 18 243 243 0 strelka-varscan-mutect RPA4,missense_variant,p.Asn199Tyr,ENST00000373040,NM_013347.4;DIAPH2,intron_variant,,ENST00000324765,NM_006729.4;DIAPH2,intron_variant,,ENST00000373061,;DIAPH2,intron_variant,,ENST00000355827,;DIAPH2,intron_variant,,ENST00000373049,NM_007309.3;DIAPH2,intron_variant,,ENST00000373054,; T ENST00000373040 Transcript missense_variant 998/1560 595/786 199/261 N/Y Aat/Tat 1 1 RPA4 HGNC HGNC:30305 protein_coding YES CCDS35345.1 ENSP00000362131 Q13156 UPI00001337A4 NM_013347.4 deleterious(0.01) 1/1 Gene3D:1.10.10.10,Pfam_domain:PF08784,PIRSF_domain:PIRSF036949,hmmpanther:PTHR13989,hmmpanther:PTHR13989:SF12,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 96884905 96884905 A T 1 0 0 0 0 1 0 0 0 13791 130 5 4 4 RPA4 23 96884905 Missense_Mutation SNP A C3N-00293_T 10170217 96884905 59155990 309 12767 NRK 0 . GRCh38 X 105895500 105895500 + Missense_Mutation SNP C C G novel C3N-00293_T C3N-00293_N C C c.557C>G p.Thr186Ser p.T186S ENST00000243300 7/29 121 110 11 95 95 0 strelka-varscan-mutect NRK,missense_variant,p.Thr186Ser,ENST00000243300,NM_198465.3;NRK,downstream_gene_variant,,ENST00000536164,;NRK,missense_variant,p.Thr186Ser,ENST00000428173,; G ENST00000243300 Transcript missense_variant 860/8062 557/4749 186/1582 T/S aCt/aGt 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0) 7/29 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF417,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 105895500 105895500 C G 1 0 0 0 0 1 0 0 0 10713 565 20 4 4 NRK 23 105895500 Missense_Mutation SNP C C3N-00293_T 9010595 105895500 50145395 310 12768 TBC1D8B 0 . GRCh38 X 106848295 106848295 + Missense_Mutation SNP G G A rs146374093 C3N-00293_T C3N-00293_N G G c.1829G>A p.Arg610Gln p.R610Q ENST00000357242 11/21 84 72 12 39 39 0 strelka-varscan-mutect TBC1D8B,missense_variant,p.Arg610Gln,ENST00000357242,NM_017752.2;TBC1D8B,missense_variant,p.Arg604Gln,ENST00000276175,;TBC1D8B,missense_variant,p.Arg610Gln,ENST00000310452,NM_198881.1;MORC4,intron_variant,,ENST00000604604,; A ENST00000357242 Transcript missense_variant 2003/5717 1829/3363 610/1120 R/Q cGa/cAa rs146374093,COSM1598612,COSM227963 1 1 TBC1D8B HGNC HGNC:24715 protein_coding YES CCDS14522.1 ENSP00000349781 Q0IIM8 UPI0000225CD5 NM_017752.2 deleterious(0) 11/21 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF320,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs146374093 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 45 106848295 106848295 G A 1 0 0 0 0 1 0 0 0 16031 1058 37 1 1 TBC1D8B 23 106848295 Missense_Mutation SNP G C3N-00293_T 952795 106848295 49192600 311 12769 TSC22D3 0 . GRCh38 X 107775284 107775284 + Missense_Mutation SNP T T G novel C3N-00293_T C3N-00293_N T T c.136A>C p.Ser46Arg p.S46R ENST00000372383 1/3 264 242 22 250 250 0 strelka-varscan-mutect TSC22D3,missense_variant,p.Ser46Arg,ENST00000372383,NM_198057.2;TSC22D3,missense_variant,p.Ser46Arg,ENST00000315660,NM_001318468.1;TSC22D3,missense_variant,p.Ser46Arg,ENST00000372384,NM_001318470.1;TSC22D3,missense_variant,p.Ser46Arg,ENST00000506081,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000514897,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000510887,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000502650,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000480691,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000506724,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000502961,;TSC22D3,missense_variant,p.Ser46Arg,ENST00000505965,;TSC22D3,5_prime_UTR_variant,,ENST00000514426,;NCBP2L,upstream_gene_variant,,ENST00000509000,; G ENST00000372383 Transcript missense_variant 504/2266 136/603 46/200 S/R Agc/Cgc 1 -1 TSC22D3 HGNC HGNC:3051 protein_coding YES CCDS14530.1 ENSP00000361458 Q99576 UPI000006DE94 NM_198057.2 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR12348 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 45 107775284 107775284 T G 1 0 0 0 0 1 0 0 0 17115 1551 54 5 5 TSC22D3 23 107775284 Missense_Mutation SNP T C3N-00293_T 926989 107775284 48265611 312 12770 TENM1 0 . GRCh38 X 124561740 124561740 + Missense_Mutation SNP C C T novel C3N-00293_T C3N-00293_N C C c.2365G>A p.Gly789Ser p.G789S ENST00000422452 14/32 199 175 24 162 162 0 strelka-varscan-mutect TENM1,missense_variant,p.Gly789Ser,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Gly789Ser,ENST00000371130,NM_014253.3; T ENST00000422452 Transcript missense_variant 2429/12891 2365/8199 789/2732 G/S Ggt/Agt 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 14/32 PROSITE_profiles:PS50026,hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 45 124561740 124561740 C T 1 0 0 0 0 1 0 0 0 16171 623 22 3 3 TENM1 23 124561740 Missense_Mutation SNP C C3N-00293_T 16786456 124561740 31479155 313 12771 MPP1 0 . GRCh38 X 154792149 154792149 + Missense_Mutation SNP T T C novel C3N-00293_T C3N-00293_N T T c.239A>G p.Glu80Gly p.E80G ENST00000369534 2/12 60 50 10 43 43 0 strelka-mutect MPP1,missense_variant,p.Glu50Gly,ENST00000413259,NM_001166462.1;MPP1,missense_variant,p.Glu80Gly,ENST00000369534,NM_001166460.1,NM_002436.3;MPP1,missense_variant,p.Glu80Gly,ENST00000393531,NM_001166461.1;MPP1,missense_variant,p.Glu34Gly,ENST00000393529,;MPP1,intron_variant,,ENST00000453245,;MPP1,intron_variant,,ENST00000428488,;MPP1,intron_variant,,ENST00000369531,;MPP1,non_coding_transcript_exon_variant,,ENST00000471821,;MPP1,non_coding_transcript_exon_variant,,ENST00000488694,;MPP1,intron_variant,,ENST00000462825,;MPP1,upstream_gene_variant,,ENST00000488754,;MPP1,3_prime_UTR_variant,,ENST00000439370,;MPP1,3_prime_UTR_variant,,ENST00000417435,;MPP1,intron_variant,,ENST00000494170,;MPP1,intron_variant,,ENST00000475943,; C ENST00000369534 Transcript missense_variant 387/2042 239/1401 80/466 E/G gAg/gGg 1 -1 MPP1 HGNC HGNC:7219 protein_coding YES CCDS14762.1 ENSP00000358547 Q00013 UPI0000129E86 NM_001166460.1,NM_002436.3 deleterious(0) 2/12 PROSITE_profiles:PS50106,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF37,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99975 1 1 1 1 0 C 3 2 45 154792149 154792149 T C 1 0 0 0 0 1 0 0 0 9699 1551 54 5 5 MPP1 23 154792149 Missense_Mutation SNP T C3N-00293_T 30230409 154792149 1248746 314 12772 SCNN1D 0 . GRCh38 1 1286959 1286959 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.1103G>C p.Arg368Thr p.R368T ENST00000379116 8/18 113 84 29 115 115 0 strelka-varscan-mutect SCNN1D,missense_variant,p.Arg204Thr,ENST00000338555,;SCNN1D,missense_variant,p.Arg368Thr,ENST00000379116,NM_001130413.3;SCNN1D,missense_variant,p.Arg369Thr,ENST00000616713,;SCNN1D,missense_variant,p.Arg204Thr,ENST00000400928,;SCNN1D,missense_variant,p.Arg270Thr,ENST00000325425,;SCNN1D,upstream_gene_variant,,ENST00000379099,;SCNN1D,downstream_gene_variant,,ENST00000470022,;SCNN1D,downstream_gene_variant,,ENST00000467651,;SCNN1D,3_prime_UTR_variant,,ENST00000379101,; C ENST00000379116 Transcript missense_variant 1329/3044 1103/2409 368/802 R/T aGa/aCa COSM3788528,COSM3788529 1 1 SCNN1D HGNC HGNC:10601 protein_coding YES CCDS44037.2 ENSP00000368411 A6NNF7 UPI0001EF94B5 NM_001130413.3 deleterious(0.04) 8/18 hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF132,TIGRFAM_domain:TIGR00859,Pfam_domain:PF00858 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1436040833 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 1286959 1286959 G C 1 0 0 0 0 1 0 0 0 14198 942 33 4 4 SCNN1D 1 1286959 Missense_Mutation SNP G C3N-00294_T 1286959 247669463 1 12773 CCNL2 0 . GRCh38 1 1390509 1390509 + Frame_Shift_Del DEL C C - novel C3N-00294_T C3N-00294_N C C c.814delG p.Glu272LysfsTer7 p.E272Kfs*7 ENST00000400809 7/11 110 90 20 155 155 0 sindel-varindel CCNL2,frameshift_variant,p.Glu272LysfsTer7,ENST00000400809,NM_030937.4;CCNL2,frameshift_variant,p.Glu50LysfsTer7,ENST00000408952,;CCNL2,downstream_gene_variant,,ENST00000408918,NM_001039577.3;CCNL2,downstream_gene_variant,,ENST00000497013,;CCNL2,non_coding_transcript_exon_variant,,ENST00000505849,;CCNL2,non_coding_transcript_exon_variant,,ENST00000469113,;CCNL2,downstream_gene_variant,,ENST00000471930,;CCNL2,3_prime_UTR_variant,,ENST00000481223,;CCNL2,3_prime_UTR_variant,,ENST00000482621,;CCNL2,3_prime_UTR_variant,,ENST00000488340,;CCNL2,non_coding_transcript_exon_variant,,ENST00000496007,;CCNL2,non_coding_transcript_exon_variant,,ENST00000418865,;CCNL2,non_coding_transcript_exon_variant,,ENST00000480479,;CCNL2,non_coding_transcript_exon_variant,,ENST00000482365,;CCNL2,non_coding_transcript_exon_variant,,ENST00000492998,;CCNL2,non_coding_transcript_exon_variant,,ENST00000480646,;CCNL2,upstream_gene_variant,,ENST00000463260,;CCNL2,downstream_gene_variant,,ENST00000425598,;CCNL2,downstream_gene_variant,,ENST00000473872,;CCNL2,downstream_gene_variant,,ENST00000463895,; - ENST00000400809 Transcript frameshift_variant 820/2305 814/1563 272/520 E/X Gaa/aa 1 -1 CCNL2 HGNC HGNC:20570 protein_coding YES CCDS30557.1 ENSP00000383611 Q96S94 UPI00000713F5 NM_030937.4 7/11 hmmpanther:PTHR10026,hmmpanther:PTHR10026:SF45,PIRSF_domain:PIRSF036580,Gene3D:1.10.472.10,Pfam_domain:PF02984,SMART_domains:SM01332,SMART_domains:SM00385,Superfamily_domains:SSF47954 HIGH 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 46 1390509 1390509 C - 1 0 1 0 1 0 0 0 0 2631 922 32 0 0 CCNL2 1 1390509 Frame_Shift_Del DEL C C3N-00294_T 103550 1390509 247565913 2 12774 MRPL20 0 . GRCh38 1 1402242 1402242 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.291C>G p.= p.L97L ENST00000344843 4/4 76 58 18 85 85 0 strelka-varscan-mutect MRPL20,synonymous_variant,p.=,ENST00000344843,NM_017971.3;MRPL20,3_prime_UTR_variant,,ENST00000492508,;CCNL2,upstream_gene_variant,,ENST00000400809,NM_030937.4;CCNL2,upstream_gene_variant,,ENST00000408918,NM_001039577.3;MRPL20,downstream_gene_variant,,ENST00000482352,;CCNL2,upstream_gene_variant,,ENST00000497013,;RP4-758J18.2,downstream_gene_variant,,ENST00000447725,;RP4-758J18.2,downstream_gene_variant,,ENST00000444362,;RP4-758J18.2,downstream_gene_variant,,ENST00000453521,;RP4-758J18.2,downstream_gene_variant,,ENST00000448629,;RP4-758J18.2,downstream_gene_variant,,ENST00000576232,;RP4-758J18.2,downstream_gene_variant,,ENST00000570344,;RN7SL657P,downstream_gene_variant,,ENST00000582431,;MRPL20,non_coding_transcript_exon_variant,,ENST00000493287,;CCNL2,upstream_gene_variant,,ENST00000471930,;MRPL20,downstream_gene_variant,,ENST00000477686,;MRPL20,non_coding_transcript_exon_variant,,ENST00000487659,;CCNL2,upstream_gene_variant,,ENST00000496007,;CCNL2,upstream_gene_variant,,ENST00000481223,;RP4-758J18.2,downstream_gene_variant,,ENST00000572242,;RP4-758J18.2,downstream_gene_variant,,ENST00000418833,;CCNL2,upstream_gene_variant,,ENST00000482621,;CCNL2,upstream_gene_variant,,ENST00000488340,;CCNL2,upstream_gene_variant,,ENST00000425598,;CCNL2,upstream_gene_variant,,ENST00000473872,;CCNL2,upstream_gene_variant,,ENST00000463895,; C ENST00000344843 Transcript synonymous_variant 387/721 291/450 97/149 L ctC/ctG 1 -1 MRPL20 HGNC HGNC:14478 protein_coding YES CCDS26.1 ENSP00000341082 Q9BYC9 UPI000006F0A8 NM_017971.3 4/4 Gene3D:2ghjB02,Pfam_domain:PF00453,Prints_domain:PR00062,hmmpanther:PTHR10986,hmmpanther:PTHR10986:SF16,Superfamily_domains:SSF74731,TIGRFAM_domain:TIGR01032 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 1402242 1402242 G C 1 0 0 0 0 0 0 0 1 9761 1277 45 4 4 MRPL20 1 1402242 Silent SNP G C3N-00294_T 11733 1402242 247554180 3 12775 ANKRD65 0 . GRCh38 1 1419270 1419270 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1030G>A p.Glu344Lys p.E344K ENST00000537107 4/4 321 259 62 348 348 0 strelka-varscan-mutect ANKRD65,missense_variant,p.Glu344Lys,ENST00000537107,NM_001145210.2;ANKRD65,missense_variant,p.Glu344Lys,ENST00000454272,;ANKRD65,synonymous_variant,p.=,ENST00000427211,NM_001243535.1;ANKRD65,synonymous_variant,p.=,ENST00000442470,;ANKRD65,3_prime_UTR_variant,,ENST00000520296,NM_001243536.1;RP4-758J18.7,upstream_gene_variant,,ENST00000428932,; T ENST00000537107 Transcript missense_variant 1342/2190 1030/1200 344/399 E/K Gag/Aag 1 -1 ANKRD65 HGNC HGNC:42950 protein_coding YES CCDS55558.1 ENSP00000445688 E5RJM6 UPI000058F1BA NM_001145210.2 deleterious(0.01) 4/4 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF25,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 1419270 1419270 C T 1 0 0 0 0 1 0 0 0 790 922 32 3 3 ANKRD65 1 1419270 Missense_Mutation SNP C C3N-00294_T 17028 1419270 247537152 4 12776 ACTRT2 0 . GRCh38 1 3021986 3021986 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.300G>A p.= p.V100V ENST00000378404 1/1 311 249 62 387 387 0 strelka-varscan-mutect ACTRT2,synonymous_variant,p.=,ENST00000378404,NM_080431.4; A ENST00000378404 Transcript synonymous_variant 504/1421 300/1134 100/377 V gtG/gtA 1 1 ACTRT2 HGNC HGNC:24026 protein_coding YES CCDS45.1 ENSP00000367658 Q8TDY3 UPI0000070494 NM_080431.4 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF38,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 3021986 3021986 G A 1 0 0 0 0 0 0 0 1 262 1277 45 3 3 ACTRT2 1 3021986 Silent SNP G C3N-00294_T 1602716 3021986 245934436 5 12777 NPHP4 0 . GRCh38 1 5986226 5986226 + Missense_Mutation SNP G G A rs773309269 C3N-00294_T C3N-00294_N G G c.64C>T p.Arg22Cys p.R22C ENST00000378156 2/30 271 209 62 279 279 0 strelka-varscan-mutect NPHP4,missense_variant,p.Arg22Cys,ENST00000378156,NM_001291594.1,NM_001291593.1,NM_015102.4;NPHP4,missense_variant,p.Arg22Cys,ENST00000622020,;NPHP4,intron_variant,,ENST00000478423,;NPHP4,missense_variant,p.Arg22Cys,ENST00000489180,;NPHP4,missense_variant,p.Arg22Cys,ENST00000378169,; A ENST00000378156 Transcript missense_variant 330/4994 64/4281 22/1426 R/C Cgc/Tgc rs773309269,COSM911210 1 -1 NPHP4 HGNC HGNC:19104 protein_coding YES CCDS44052.1 ENSP00000367398 O75161 UPI00001303E5 NM_001291594.1,NM_001291593.1,NM_015102.4 deleterious(0) 2/30 hmmpanther:PTHR31043,hmmpanther:PTHR31043:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773309269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 5986226 5986226 G A 1 0 0 0 0 1 0 0 0 10629 1087 38 1 1 NPHP4 1 5986226 Missense_Mutation SNP G C3N-00294_T 2964240 5986226 242970196 6 12778 ZBTB48 0 . GRCh38 1 6582218 6582218 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.851G>C p.Arg284Thr p.R284T ENST00000377674 3/11 230 189 41 251 251 0 strelka-varscan-mutect ZBTB48,missense_variant,p.Arg284Thr,ENST00000377674,NM_005341.3,NM_001278647.1,NM_001278648.1;ZBTB48,missense_variant,p.Arg284Thr,ENST00000319084,;ZBTB48,missense_variant,p.Arg284Thr,ENST00000435905,;ZBTB48,missense_variant,p.Arg39Thr,ENST00000488936,;TAS1R1,downstream_gene_variant,,ENST00000333172,NM_138697.3;TAS1R1,downstream_gene_variant,,ENST00000351136,NM_177540.2;TAS1R1,downstream_gene_variant,,ENST00000411823,;TAS1R1,downstream_gene_variant,,ENST00000415267,;ZBTB48,upstream_gene_variant,,ENST00000482360,;ZBTB48,upstream_gene_variant,,ENST00000498342,; C ENST00000377674 Transcript missense_variant 1009/2293 851/2067 284/688 R/T aGa/aCa 1 1 ZBTB48 HGNC HGNC:4930 protein_coding YES CCDS84.1 ENSP00000366902 P10074 UPI000012C932 NM_005341.3,NM_001278647.1,NM_001278648.1 deleterious(0.01) 3/11 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 6582218 6582218 G C 1 0 0 0 0 1 0 0 0 18119 942 33 4 4 ZBTB48 1 6582218 Missense_Mutation SNP G C3N-00294_T 595992 6582218 242374204 7 12779 KLHL21 0 . GRCh38 1 6599198 6599198 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1276G>T p.Ala426Ser p.A426S ENST00000377658 2/4 197 151 46 216 216 0 strelka-varscan-mutect KLHL21,missense_variant,p.Ala426Ser,ENST00000377663,;KLHL21,missense_variant,p.Ala426Ser,ENST00000377658,NM_014851.3;KLHL21,missense_variant,p.Ala59Ser,ENST00000467612,;KLHL21,missense_variant,p.Ala59Ser,ENST00000496707,;KLHL21,missense_variant,p.Ala59Ser,ENST00000463043,;KLHL21,intron_variant,,ENST00000610898,; A ENST00000377658 Transcript missense_variant 1328/4487 1276/1794 426/597 A/S Gcc/Tcc 1 -1 KLHL21 HGNC HGNC:29041 protein_coding YES CCDS30575.1 ENSP00000366886 Q9UJP4 UPI0000070D85 NM_014851.3 deleterious(0.04) 2/4 Superfamily_domains:0052715,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF255 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 6599198 6599198 C A 1 0 0 0 0 1 0 0 0 8240 710 25 2 2 KLHL21 1 6599198 Missense_Mutation SNP C C3N-00294_T 16980 6599198 242357224 8 12780 SLC25A33 0 . GRCh38 1 9579957 9579957 + Silent SNP G G C rs373446607 C3N-00294_T C3N-00294_N G G c.486G>C p.= p.V162V ENST00000302692 6/7 75 52 23 85 85 0 strelka-varscan-mutect SLC25A33,synonymous_variant,p.=,ENST00000302692,NM_032315.2;RP13-15M17.1,downstream_gene_variant,,ENST00000435277,; C ENST00000302692 Transcript synonymous_variant 696/3854 486/966 162/321 V gtG/gtC rs373446607 1 1 SLC25A33 HGNC HGNC:29681 protein_coding YES CCDS103.1 ENSP00000306328 Q9BSK2 UPI000004D33B NM_032315.2 6/7 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF263 LOW 1 SNV 1 1 PASS rs373446607 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 9579957 9579957 G C 1 0 0 0 0 0 0 0 1 14762 1304 45 4 4 SLC25A33 1 9579957 Silent SNP G C3N-00294_T 2980759 9579957 239376465 9 12781 UBE4B 0 . GRCh38 1 10122025 10122025 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1503C>T p.= p.F501F ENST00000343090 10/28 155 125 30 134 134 0 strelka-varscan-mutect UBE4B,synonymous_variant,p.=,ENST00000343090,NM_001105562.2;UBE4B,synonymous_variant,p.=,ENST00000253251,NM_006048.4;UBE4B,upstream_gene_variant,,ENST00000470736,;UBE4B,non_coding_transcript_exon_variant,,ENST00000475795,; T ENST00000343090 Transcript synonymous_variant 1578/5267 1503/3909 501/1302 F ttC/ttT 1 1 UBE4B HGNC HGNC:12500 protein_coding YES CCDS41245.1 ENSP00000343001 O95155 UPI0000137944 NM_001105562.2 10/28 hmmpanther:PTHR13931,hmmpanther:PTHR13931:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 10122025 10122025 C T 1 0 0 0 0 0 0 0 1 17407 825 29 3 3 UBE4B 1 10122025 Silent SNP C C3N-00294_T 542068 10122025 238834397 10 12782 VPS13D 0 . GRCh38 1 12277748 12277748 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.4160C>G p.Ser1387Cys p.S1387C ENST00000620676 19/70 160 132 28 202 202 0 strelka-varscan-mutect VPS13D,missense_variant,p.Ser1387Cys,ENST00000620676,NM_015378.3;VPS13D,missense_variant,p.Ser1387Cys,ENST00000613099,NM_018156.3;VPS13D,missense_variant,p.Ser210Cys,ENST00000011700,; G ENST00000620676 Transcript missense_variant 4290/16320 4160/13167 1387/4388 S/C tCt/tGt 1 1 VPS13D HGNC HGNC:23595 protein_coding YES CCDS30588.1 ENSP00000478104 Q5THJ4 UPI0000451CA9 NM_015378.3 tolerated(0.07) 19/70 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 12277748 12277748 C G 1 0 0 0 0 1 0 0 0 17739 913 32 4 4 VPS13D 1 12277748 Missense_Mutation SNP C C3N-00294_T 2155723 12277748 236678674 11 12783 VPS13D 0 . GRCh38 1 12506959 12506959 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.12901G>A p.Glu4301Lys p.E4301K ENST00000620676 69/70 337 264 73 352 352 0 strelka-varscan-mutect VPS13D,missense_variant,p.Glu4301Lys,ENST00000620676,NM_015378.3;VPS13D,missense_variant,p.Glu4276Lys,ENST00000613099,NM_018156.3;VPS13D,missense_variant,p.Glu3123Lys,ENST00000011700,;VPS13D,5_prime_UTR_variant,,ENST00000543766,;SNORA59A,upstream_gene_variant,,ENST00000459326,;VPS13D,non_coding_transcript_exon_variant,,ENST00000543710,;VPS13D,downstream_gene_variant,,ENST00000473099,; A ENST00000620676 Transcript missense_variant 13031/16320 12901/13167 4301/4388 E/K Gaa/Aaa COSM3769887 1 1 VPS13D HGNC HGNC:23595 protein_coding YES CCDS30588.1 ENSP00000478104 Q5THJ4 UPI0000451CA9 NM_015378.3 deleterious(0.01) 69/70 hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF104 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 12506959 12506959 G A 1 0 0 0 0 1 0 0 0 17739 943 33 3 3 VPS13D 1 12506959 Missense_Mutation SNP G C3N-00294_T 229211 12506959 236449463 12 12784 PRAMEF20 0 . GRCh38 1 13421205 13421205 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1375C>T p.Gln459Ter p.Q459* ENST00000316412 4/4 541 482 59 555 555 0 strelka-varscan-mutect PRAMEF20,stop_gained,p.Gln459Ter,ENST00000316412,NM_001099852.2;PRAMEF20,stop_gained,p.Gln459Ter,ENST00000602960,; T ENST00000316412 Transcript stop_gained 1474/1597 1375/1428 459/475 Q/* Cag/Tag 1 1 PRAMEF20 HGNC HGNC:25224 protein_coding YES CCDS41265.1 ENSP00000346275 Q5VT98 UPI0004423C14 NM_001099852.2 4/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 13421205 13421205 C T 1 0 0 0 0 0 1 0 0 12563 827 29 3 3 PRAMEF20 1 13421205 Nonsense_Mutation SNP C C3N-00294_T 914246 13421205 235535217 13 12785 SLC25A34 0 . GRCh38 1 15736575 15736575 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.90G>A p.= p.V30V ENST00000294454 1/5 51 39 12 45 45 0 strelka-varscan-mutect SLC25A34,synonymous_variant,p.=,ENST00000294454,NM_207348.2;PLEKHM2,downstream_gene_variant,,ENST00000375799,NM_015164.2;PLEKHM2,downstream_gene_variant,,ENST00000375793,;RP11-288I21.1,intron_variant,,ENST00000453804,;RP11-288I21.1,upstream_gene_variant,,ENST00000615472,;RP11-288I21.1,upstream_gene_variant,,ENST00000623689,;RP11-169K16.4,downstream_gene_variant,,ENST00000418525,;PLEKHM2,downstream_gene_variant,,ENST00000477849,;SLC25A34,upstream_gene_variant,,ENST00000489568,;SLC25A34,upstream_gene_variant,,ENST00000465495,; A ENST00000294454 Transcript synonymous_variant 171/2986 90/915 30/304 V gtG/gtA 1 1 SLC25A34 HGNC HGNC:27653 protein_coding YES CCDS162.1 ENSP00000294454 Q6PIV7 UPI00001A7D46 NM_207348.2 1/5 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF95,hmmpanther:PTHR24089,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 15736575 15736575 G A 1 0 0 0 0 0 0 0 1 14763 1277 45 3 3 SLC25A34 1 15736575 Silent SNP G C3N-00294_T 2315370 15736575 233219847 14 12786 ARHGEF19 0 . GRCh38 1 16207121 16207121 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.964G>C p.Glu322Gln p.E322Q ENST00000270747 6/16 104 81 23 93 93 0 strelka-varscan-mutect ARHGEF19,missense_variant,p.Glu322Gln,ENST00000270747,NM_153213.3;ARHGEF19,upstream_gene_variant,,ENST00000449495,;ARHGEF19,upstream_gene_variant,,ENST00000441785,;ARHGEF19,upstream_gene_variant,,ENST00000478117,;ARHGEF19,upstream_gene_variant,,ENST00000478210,;ARHGEF19,upstream_gene_variant,,ENST00000471928,; G ENST00000270747 Transcript missense_variant 1101/3029 964/2409 322/802 E/Q Gag/Cag 1 -1 ARHGEF19 HGNC HGNC:26604 protein_coding YES CCDS170.1 ENSP00000270747 Q8IW93 UPI0000074533 NM_153213.3 tolerated(0.17) 6/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 16207121 16207121 C G 1 0 0 0 0 1 0 0 0 1032 893 31 4 4 ARHGEF19 1 16207121 Missense_Mutation SNP C C3N-00294_T 470546 16207121 232749301 15 12787 PAX7 0 . GRCh38 1 18703171 18703171 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1030G>A p.Ala344Thr p.A344T ENST00000375375 7/8 328 259 69 349 349 0 strelka-varscan-mutect PAX7,missense_variant,p.Ala344Thr,ENST00000420770,NM_001135254.1;PAX7,missense_variant,p.Ala344Thr,ENST00000375375,NM_002584.2;PAX7,missense_variant,p.Ala342Thr,ENST00000400661,NM_013945.2; A ENST00000375375 Transcript missense_variant 1628/2260 1030/1563 344/520 A/T Gca/Aca 1 1 PAX7 HGNC HGNC:8621 protein_coding YES CCDS186.1 ENSP00000364524 P23759 UPI000004A132 NM_002584.2 tolerated(0.16) 7/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF248 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 18703171 18703171 G A 1 0 0 0 0 1 0 0 0 11569 1319 46 3 3 PAX7 1 18703171 Missense_Mutation SNP G C3N-00294_T 2496050 18703171 230253251 16 12788 OTUD3 0 . GRCh38 1 19906539 19906539 + Missense_Mutation SNP G G A rs763007582 C3N-00294_T C3N-00294_N G G c.943G>A p.Glu315Lys p.E315K ENST00000375120 7/8 178 140 38 210 210 0 strelka-varscan-mutect OTUD3,missense_variant,p.Glu315Lys,ENST00000375120,NM_015207.1;OTUD3,upstream_gene_variant,,ENST00000481686,; A ENST00000375120 Transcript missense_variant 944/6397 943/1197 315/398 E/K Gaa/Aaa rs763007582 1 1 OTUD3 HGNC HGNC:29038 protein_coding YES CCDS41279.1 ENSP00000364261 Q5T2D3 UPI000004DB04 NM_015207.1 tolerated(0.19) 7/8 hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF7 MODERATE 1 SNV 1 1 PASS rs763007582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 19906539 19906539 G A 1 0 0 0 0 1 0 0 0 11382 1291 45 3 3 OTUD3 1 19906539 Missense_Mutation SNP G C3N-00294_T 1203368 19906539 229049883 17 12789 PINK1 0 . GRCh38 1 20649062 20649062 + Missense_Mutation SNP G G C rs45467995 C3N-00294_T C3N-00294_N G G c.1319G>C p.Gly440Ala p.G440A ENST00000321556 7/8 354 283 71 322 322 0 strelka-varscan-mutect PINK1,missense_variant,p.Gly440Ala,ENST00000321556,NM_032409.2;DDOST,downstream_gene_variant,,ENST00000415136,NM_005216.4;DDOST,downstream_gene_variant,,ENST00000375048,;DDOST,downstream_gene_variant,,ENST00000602624,;PINK1-AS,non_coding_transcript_exon_variant,,ENST00000451424,;PINK1,non_coding_transcript_exon_variant,,ENST00000492302,;PINK1,non_coding_transcript_exon_variant,,ENST00000400490,;DDOST,downstream_gene_variant,,ENST00000475210,; C ENST00000321556 Transcript missense_variant 1413/2660 1319/1746 440/581 G/A gGa/gCa rs45467995,CM085640 1 1 PINK1 HGNC HGNC:14581 protein_coding YES CCDS211.1 ENSP00000364204 Q9BXM7 UPI0000035BA9 NM_032409.2 deleterious(0) 7/8 PROSITE_profiles:PS50011,hmmpanther:PTHR22972,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 0,1 1 PASS rs45467995 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 20649062 20649062 G C 1 0 0 0 0 1 0 0 0 12027 1174 41 4 4 PINK1 1 20649062 Missense_Mutation SNP G C3N-00294_T 742523 20649062 228307360 18 12790 NBPF3 0 . GRCh38 1 21478271 21478271 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1120G>C p.Glu374Gln p.E374Q ENST00000318249 9/15 305 241 64 290 289 1 strelka-varscan-mutect NBPF3,missense_variant,p.Glu374Gln,ENST00000318249,NM_032264.4;NBPF3,missense_variant,p.Glu304Gln,ENST00000454000,NM_001256417.2;NBPF3,missense_variant,p.Glu318Gln,ENST00000619554,;NBPF3,intron_variant,,ENST00000342104,NM_001256416.2;NBPF3,intron_variant,,ENST00000469876,;NBPF3,intron_variant,,ENST00000477050,;NBPF3,3_prime_UTR_variant,,ENST00000318220,;NBPF3,3_prime_UTR_variant,,ENST00000434838,; C ENST00000318249 Transcript missense_variant 1295/3591 1120/1902 374/633 E/Q Gag/Cag 1 1 NBPF3 HGNC HGNC:25076 protein_coding YES CCDS216.1 ENSP00000316782 Q9H094 UPI0000037D6C NM_032264.4 deleterious(0.03) 9/15 PROSITE_profiles:PS51316,hmmpanther:PTHR14199:SF18,hmmpanther:PTHR14199,Pfam_domain:PF06758,SMART_domains:SM01148 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 21478271 21478271 G C 1 0 0 0 0 1 0 0 0 10212 943 33 4 4 NBPF3 1 21478271 Missense_Mutation SNP G C3N-00294_T 829209 21478271 227478151 19 12791 ARID1A 0 . GRCh38 1 26697205 26697205 + Nonsense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.802C>T p.Gln268Ter p.Q268* ENST00000324856 1/20 25 18 7 39 39 0 strelka-varscan-mutect ARID1A,stop_gained,p.Gln268Ter,ENST00000324856,NM_006015.4;ARID1A,stop_gained,p.Gln268Ter,ENST00000457599,NM_139135.2;ARID1A,intron_variant,,ENST00000430799,;ARID1A,intron_variant,,ENST00000637465,;RP5-968P14.2,upstream_gene_variant,,ENST00000569378,; T ENST00000324856 Transcript stop_gained 1173/8577 802/6858 268/2285 Q/* Cag/Tag COSM126559 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 1/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 1 HIGH 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.60831 1 1 1 1 0 T 4 4 46 26697205 26697205 C T 1 0 0 0 0 0 1 0 0 1049 827 29 3 3 ARID1A 1 26697205 Nonsense_Mutation SNP C C3N-00294_T 5218934 26697205 222259217 20 12792 ARID1A 0 . GRCh38 1 26729830 26729830 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1317G>A p.= p.Q439Q ENST00000324856 2/20 260 199 61 265 265 0 strelka-varscan-mutect ARID1A,synonymous_variant,p.=,ENST00000324856,NM_006015.4;ARID1A,synonymous_variant,p.=,ENST00000636219,;ARID1A,synonymous_variant,p.=,ENST00000430799,;ARID1A,synonymous_variant,p.=,ENST00000374152,;ARID1A,synonymous_variant,p.=,ENST00000457599,NM_139135.2;ARID1A,synonymous_variant,p.=,ENST00000615191,;ARID1A,synonymous_variant,p.=,ENST00000637465,;ARID1A,synonymous_variant,p.=,ENST00000524572,; A ENST00000324856 Transcript synonymous_variant 1688/8577 1317/6858 439/2285 Q caG/caA 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 2/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 26729830 26729830 G A 1 0 0 0 0 0 0 0 1 1049 933 33 3 3 ARID1A 1 26729830 Silent SNP G C3N-00294_T 32625 26729830 222226592 21 12793 ARID1A 0 . GRCh38 1 26771307 26771307 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3387G>C p.Lys1129Asn p.K1129N ENST00000324856 12/20 217 171 46 192 192 0 strelka-varscan-mutect ARID1A,missense_variant,p.Lys1129Asn,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Lys748Asn,ENST00000636219,;ARID1A,missense_variant,p.Lys746Asn,ENST00000430799,;ARID1A,missense_variant,p.Lys746Asn,ENST00000374152,;ARID1A,missense_variant,p.Lys1129Asn,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Lys745Asn,ENST00000615191,;ARID1A,upstream_gene_variant,,ENST00000636794,;ARID1A,non_coding_transcript_exon_variant,,ENST00000636110,;ARID1A,upstream_gene_variant,,ENST00000466382,;ARID1A,upstream_gene_variant,,ENST00000532781,;ARID1A,upstream_gene_variant,,ENST00000636072,;ARID1A,downstream_gene_variant,,ENST00000430291,; C ENST00000324856 Transcript missense_variant 3758/8577 3387/6858 1129/2285 K/N aaG/aaC 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 deleterious(0.01) 12/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 26771307 26771307 G C 1 0 0 0 0 1 0 0 0 1049 933 33 4 4 ARID1A 1 26771307 Missense_Mutation SNP G C3N-00294_T 41477 26771307 222185115 22 12794 S100PBP 0 . GRCh38 1 32855931 32855931 + Missense_Mutation SNP G G T rs778880970 C3N-00294_T C3N-00294_N G G c.1120G>T p.Ala374Ser p.A374S ENST00000373475 7/7 150 78 72 145 145 0 strelka-varscan-mutect S100PBP,missense_variant,p.Ala374Ser,ENST00000373475,NM_022753.3;S100PBP,missense_variant,p.Ala374Ser,ENST00000373476,NM_001256121.1;S100PBP,non_coding_transcript_exon_variant,,ENST00000527692,;S100PBP,non_coding_transcript_exon_variant,,ENST00000524535,;S100PBP,non_coding_transcript_exon_variant,,ENST00000525203,;S100PBP,non_coding_transcript_exon_variant,,ENST00000475486,; T ENST00000373475 Transcript missense_variant 1374/4322 1120/1227 374/408 A/S Gcc/Tcc rs778880970 1 1 S100PBP HGNC HGNC:25768 protein_coding YES CCDS30666.1 ENSP00000362574 Q96BU1 A0A0S2Z5M0 UPI0000070449 NM_022753.3 tolerated(0.17) 7/7 hmmpanther:PTHR14455,hmmpanther:PTHR14455:SF0,Pfam_domain:PF15427 MODERATE 1 SNV 1 1 PASS rs778880970 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 32855931 32855931 G T 1 0 0 0 0 1 0 0 0 14050 1087 38 1 1 S100PBP 1 32855931 Missense_Mutation SNP G C3N-00294_T 6084624 32855931 216100491 23 12795 CLSPN 0 . GRCh38 1 35749685 35749685 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2155C>G p.Leu719Val p.L719V ENST00000318121 11/25 207 162 45 244 244 0 strelka-varscan-mutect CLSPN,missense_variant,p.Leu719Val,ENST00000251195,;CLSPN,missense_variant,p.Leu719Val,ENST00000318121,NM_022111.3;CLSPN,missense_variant,p.Leu655Val,ENST00000373220,NM_001190481.1;CLSPN,intron_variant,,ENST00000520551,;CLSPN,upstream_gene_variant,,ENST00000517467,; C ENST00000318121 Transcript missense_variant 2213/4169 2155/4020 719/1339 L/V Ctc/Gtc 1 -1 CLSPN HGNC HGNC:19715 protein_coding YES CCDS396.1 ENSP00000312995 Q9HAW4 UPI0000161087 NM_022111.3 tolerated(1) 11/25 hmmpanther:PTHR14396:SF10,hmmpanther:PTHR14396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 35749685 35749685 G C 1 0 0 0 0 1 0 0 0 3332 942 33 4 4 CLSPN 1 35749685 Missense_Mutation SNP G C3N-00294_T 2893754 35749685 213206737 24 12796 SH3D21 0 . GRCh38 1 36319707 36319707 + Silent SNP C C A rs377064888 C3N-00294_T C3N-00294_N C C c.711C>A p.= p.P237P ENST00000505871 11/13 32 13 19 39 39 0 strelka-varscan-mutect SH3D21,synonymous_variant,p.=,ENST00000453908,NM_001162530.1;SH3D21,synonymous_variant,p.=,ENST00000505871,NM_024676.4;SH3D21,synonymous_variant,p.=,ENST00000373139,;EVA1B,downstream_gene_variant,,ENST00000270824,NM_018166.2,NM_001304762.1;RP11-268J15.5,upstream_gene_variant,,ENST00000373137,;SH3D21,non_coding_transcript_exon_variant,,ENST00000508854,;SH3D21,upstream_gene_variant,,ENST00000474766,;EVA1B,downstream_gene_variant,,ENST00000490466,;SH3D21,3_prime_UTR_variant,,ENST00000480549,; A ENST00000505871 Transcript synonymous_variant 875/2206 711/1938 237/645 P ccC/ccA rs377064888 1 1 SH3D21 HGNC HGNC:26236 protein_coding YES CCDS30674.2 ENSP00000421294 A4FU49 UPI00017A7573 NM_024676.4 11/13 hmmpanther:PTHR14167,hmmpanther:PTHR14167:SF28 LOW SNV 2 1 PASS rs377064888 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 36319707 36319707 C A 1 0 0 0 0 0 0 0 1 14508 668 24 2 2 SH3D21 1 36319707 Silent SNP C C3N-00294_T 570022 36319707 212636715 25 12797 LSM10 0 . GRCh38 1 36393914 36393914 + Silent SNP G G C rs774877232 C3N-00294_T C3N-00294_N G G c.216C>G p.= p.L72L ENST00000315732 2/2 331 277 54 370 370 0 strelka-varscan-mutect LSM10,synonymous_variant,p.=,ENST00000315732,NM_032881.2;LSM10,non_coding_transcript_exon_variant,,ENST00000476041,;LSM10,downstream_gene_variant,,ENST00000489912,; C ENST00000315732 Transcript synonymous_variant 366/850 216/372 72/123 L ctC/ctG rs774877232,COSM414458 1 -1 LSM10 HGNC HGNC:17562 protein_coding YES CCDS408.1 ENSP00000319341 Q969L4 UPI000012E96D NM_032881.2 2/2 Gene3D:2.30.30.100,Pfam_domain:PF01423,hmmpanther:PTHR21196,hmmpanther:PTHR21196:SF1,SMART_domains:SM00651,Superfamily_domains:SSF50182 0,1 LOW 1 SNV 1 0,1 1 PASS rs774877232 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 36393914 36393914 G C 1 0 0 0 0 0 0 0 1 8957 929 33 4 4 LSM10 1 36393914 Silent SNP G C3N-00294_T 74207 36393914 212562508 26 12798 MTF1 0 . GRCh38 1 37823774 37823774 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1107C>G p.Ile369Met p.I369M ENST00000373036 8/11 215 180 35 218 218 0 strelka-varscan-mutect MTF1,missense_variant,p.Ile369Met,ENST00000373036,NM_005955.2; C ENST00000373036 Transcript missense_variant 1248/7972 1107/2262 369/753 I/M atC/atG 1 -1 MTF1 HGNC HGNC:7428 protein_coding YES CCDS30676.1 ENSP00000362127 Q14872 UPI000006E9B3 NM_005955.2 tolerated(0.11) 8/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 37823774 37823774 G C 1 0 0 0 0 1 0 0 0 9907 1280 45 4 4 MTF1 1 37823774 Missense_Mutation SNP G C3N-00294_T 1429860 37823774 211132648 27 12799 RLF 0 . GRCh38 1 40239668 40239668 + Nonsense_Mutation SNP G G T rs758862202 C3N-00294_T C3N-00294_N G G c.4966G>T p.Glu1656Ter p.E1656* ENST00000372771 8/8 204 171 33 227 227 0 strelka-varscan-mutect RLF,stop_gained,p.Glu1656Ter,ENST00000372771,NM_012421.3; T ENST00000372771 Transcript stop_gained 4993/6246 4966/5745 1656/1914 E/* Gaa/Taa rs758862202 1 1 RLF HGNC HGNC:10025 protein_coding YES CCDS448.1 ENSP00000361857 Q13129 UPI000013C9DA NM_012421.3 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF18 HIGH 1 SNV 1 1 PASS rs758862202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 40239668 40239668 G T 1 0 0 0 0 0 1 0 0 13565 943 33 2 2 RLF 1 40239668 Nonsense_Mutation SNP G C3N-00294_T 2415894 40239668 208716754 28 12800 ERMAP 0 . GRCh38 1 42843118 42843118 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.1314C>G p.= p.L438L ENST00000372517 12/12 171 130 41 209 209 0 strelka-varscan-mutect ERMAP,synonymous_variant,p.=,ENST00000328249,;ERMAP,synonymous_variant,p.=,ENST00000372517,NM_001017922.1;ERMAP,synonymous_variant,p.=,ENST00000372514,NM_018538.3;ZNF691,upstream_gene_variant,,ENST00000372504,;ZNF691,upstream_gene_variant,,ENST00000372502,NM_001242739.1;ZNF691,upstream_gene_variant,,ENST00000372506,;ZNF691,upstream_gene_variant,,ENST00000372507,;ZNF691,upstream_gene_variant,,ENST00000372508,NM_015911.3;RP11-342M1.3,intron_variant,,ENST00000416809,;RP11-342M1.3,intron_variant,,ENST00000444563,;RP11-342M1.3,intron_variant,,ENST00000425076,;RP11-342M1.3,intron_variant,,ENST00000414798,;ERMAP,non_coding_transcript_exon_variant,,ENST00000487556,; G ENST00000372517 Transcript synonymous_variant 1558/3423 1314/1428 438/475 L ctC/ctG 1 1 ERMAP HGNC HGNC:15743 protein_coding YES CCDS475.1 ENSP00000361595 Q96PL5 UPI000007000D NM_001017922.1 12/12 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 42843118 42843118 C G 1 0 0 0 0 0 0 0 1 5091 813 29 4 4 ERMAP 1 42843118 Silent SNP C C3N-00294_T 2603450 42843118 206113304 29 12801 SZT2 0 . GRCh38 1 43440468 43440468 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.7055G>A p.Gly2352Glu p.G2352E ENST00000562955 51/71 57 46 11 48 48 0 strelka-varscan-mutect SZT2,missense_variant,p.Gly2352Glu,ENST00000562955,NM_015284.3;SZT2,missense_variant,p.Gly2409Glu,ENST00000634258,;SZT2,downstream_gene_variant,,ENST00000471177,;SZT2,upstream_gene_variant,,ENST00000460536,;SZT2,downstream_gene_variant,,ENST00000470897,; A ENST00000562955 Transcript missense_variant 7055/12281 7055/10128 2352/3375 G/E gGa/gAa 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 tolerated(0.57) 51/71 hmmpanther:PTHR14918 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 43440468 43440468 G A 1 0 0 0 0 1 0 0 0 15883 1174 41 3 3 SZT2 1 43440468 Missense_Mutation SNP G C3N-00294_T 597350 43440468 205515954 30 12802 PTCH2 0 . GRCh38 1 44829921 44829921 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.923G>T p.Gly308Val p.G308V ENST00000372192 7/22 143 107 36 136 136 0 strelka-varscan-mutect PTCH2,missense_variant,p.Gly308Val,ENST00000447098,NM_001166292.1;PTCH2,missense_variant,p.Gly308Val,ENST00000372192,NM_003738.4; A ENST00000372192 Transcript missense_variant 1054/4225 923/3612 308/1203 G/V gGa/gTa 1 -1 PTCH2 HGNC HGNC:9586 protein_coding YES CCDS516.1 ENSP00000361266 Q9Y6C5 UPI00001328B8 NM_003738.4 deleterious(0) 7/22 hmmpanther:PTHR10796:SF62,hmmpanther:PTHR10796,TIGRFAM_domain:TIGR00918 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 44829921 44829921 C A 1 0 0 0 0 1 0 0 0 12884 855 30 2 2 PTCH2 1 44829921 Missense_Mutation SNP C C3N-00294_T 1389453 44829921 204126501 31 12803 TOE1 0 . GRCh38 1 45343670 45343670 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1501C>G p.Gln501Glu p.Q501E ENST00000372090 8/8 85 67 18 93 93 0 strelka-varscan-mutect TOE1,missense_variant,p.Gln501Glu,ENST00000372090,NM_025077.3;TESK2,downstream_gene_variant,,ENST00000372086,NM_007170.2;TESK2,downstream_gene_variant,,ENST00000372084,;MUTYH,upstream_gene_variant,,ENST00000450313,NM_001128425.1;MUTYH,upstream_gene_variant,,ENST00000372115,NM_001048171.1;MUTYH,upstream_gene_variant,,ENST00000372098,NM_012222.2;MUTYH,upstream_gene_variant,,ENST00000372104,NM_001293195.1;MUTYH,upstream_gene_variant,,ENST00000372110,NM_001293190.1;MUTYH,upstream_gene_variant,,ENST00000355498,NM_001293196.1,NM_001293192.1,NM_001048173.1;MUTYH,upstream_gene_variant,,ENST00000354383,NM_001048172.1;MUTYH,upstream_gene_variant,,ENST00000448481,NM_001293191.1;MUTYH,upstream_gene_variant,,ENST00000456914,NM_001048174.1;MUTYH,upstream_gene_variant,,ENST00000528013,;MUTYH,upstream_gene_variant,,ENST00000529984,;MUTYH,upstream_gene_variant,,ENST00000435155,;MUTYH,upstream_gene_variant,,ENST00000483127,;MUTYH,upstream_gene_variant,,ENST00000412971,;MUTYH,upstream_gene_variant,,ENST00000488731,;MUTYH,upstream_gene_variant,,ENST00000531105,;TOE1,non_coding_transcript_exon_variant,,ENST00000495703,;TESK2,downstream_gene_variant,,ENST00000486676,;TOE1,downstream_gene_variant,,ENST00000471337,;TOE1,downstream_gene_variant,,ENST00000477731,;TOE1,downstream_gene_variant,,ENST00000460057,;MUTYH,upstream_gene_variant,,ENST00000481571,;MUTYH,upstream_gene_variant,,ENST00000475516,;MUTYH,upstream_gene_variant,,ENST00000483642,;MUTYH,upstream_gene_variant,,ENST00000481139,;MUTYH,upstream_gene_variant,,ENST00000492494,;MUTYH,upstream_gene_variant,,ENST00000467940,;MUTYH,upstream_gene_variant,,ENST00000479746,;MUTYH,upstream_gene_variant,,ENST00000461495,;MUTYH,upstream_gene_variant,,ENST00000476789,;MUTYH,upstream_gene_variant,,ENST00000470256,;MUTYH,upstream_gene_variant,,ENST00000462387,;MUTYH,upstream_gene_variant,,ENST00000485484,;MUTYH,upstream_gene_variant,,ENST00000534453,;MUTYH,upstream_gene_variant,,ENST00000525160,;MUTYH,upstream_gene_variant,,ENST00000474703,; G ENST00000372090 Transcript missense_variant 2084/2389 1501/1533 501/510 Q/E Cag/Gag 1 1 TOE1 HGNC HGNC:15954 protein_coding YES CCDS521.1 ENSP00000361162 Q96GM8 UPI00000382DE NM_025077.3 tolerated(0.21) 8/8 hmmpanther:PTHR15092 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 45343670 45343670 C G 1 0 0 0 0 1 0 0 0 16823 827 29 4 4 TOE1 1 45343670 Missense_Mutation SNP C C3N-00294_T 513749 45343670 203612752 32 12804 NASP 0 . GRCh38 1 45584179 45584179 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.33C>T p.= p.V11V ENST00000350030 1/15 118 94 24 120 120 0 strelka-varscan-mutect NASP,synonymous_variant,p.=,ENST00000350030,NM_002482.3;NASP,synonymous_variant,p.=,ENST00000537798,NM_001195193.1;NASP,synonymous_variant,p.=,ENST00000351223,NM_152298.3;NASP,synonymous_variant,p.=,ENST00000372052,;NASP,synonymous_variant,p.=,ENST00000470768,;NASP,synonymous_variant,p.=,ENST00000528238,;NASP,synonymous_variant,p.=,ENST00000437901,;NASP,synonymous_variant,p.=,ENST00000525515,;NASP,synonymous_variant,p.=,ENST00000527470,;NASP,synonymous_variant,p.=,ENST00000629893,;NASP,non_coding_transcript_exon_variant,,ENST00000534101,;NASP,synonymous_variant,p.=,ENST00000453748,;NASP,synonymous_variant,p.=,ENST00000437362,;NASP,synonymous_variant,p.=,ENST00000529333,;NASP,synonymous_variant,p.=,ENST00000527359,;NASP,synonymous_variant,p.=,ENST00000531532,;NASP,synonymous_variant,p.=,ENST00000528084,;NASP,synonymous_variant,p.=,ENST00000530840,;NASP,non_coding_transcript_exon_variant,,ENST00000464190,;AL355480.1,upstream_gene_variant,,ENST00000629041,;AL355480.3,upstream_gene_variant,,ENST00000630128,; T ENST00000350030 Transcript synonymous_variant 120/3207 33/2367 11/788 V gtC/gtT 1 1 NASP HGNC HGNC:7644 protein_coding YES CCDS524.1 ENSP00000255120 P49321 UPI000012FDA0 NM_002482.3 1/15 hmmpanther:PTHR15081,hmmpanther:PTHR15081:SF1,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 45584179 45584179 C T 1 0 0 0 0 0 0 0 1 10181 871 31 1 1 NASP 1 45584179 Silent SNP C C3N-00294_T 240509 45584179 203372243 33 12805 PIK3R3 0 . GRCh38 1 46077612 46077612 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.217G>A p.Glu73Lys p.E73K ENST00000262741 3/10 137 111 26 135 135 0 strelka-varscan-mutect PIK3R3,missense_variant,p.Glu73Lys,ENST00000262741,NM_003629.3;PIK3R3,missense_variant,p.Glu73Lys,ENST00000420542,NM_001114172.1;PIK3R3,missense_variant,p.Glu73Lys,ENST00000372006,NM_001303428.1;PIK3R3,missense_variant,p.Glu73Lys,ENST00000423209,NM_001303429.1;PIK3R3,missense_variant,p.Glu119Lys,ENST00000540385,NM_001303427.1;PIK3R3,missense_variant,p.Glu73Lys,ENST00000425892,;PIK3R3,splice_region_variant,,ENST00000493202,; T ENST00000262741 Transcript missense_variant,splice_region_variant 907/5609 217/1386 73/461 E/K Gag/Aag 1 -1 PIK3R3 HGNC HGNC:8981 protein_coding YES CCDS529.1 ENSP00000262741 Q92569 UPI000013D318 NM_003629.3 deleterious(0) 3/10 Gene3D:3.30.505.10,Pfam_domain:PF00017,Prints_domain:PR00401,Prints_domain:PR00678,PROSITE_profiles:PS50001,hmmpanther:PTHR10155,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 46077612 46077612 C T 1 0 0 0 0 1 0 0 0 12015 869 30 3 3 PIK3R3 1 46077612 Missense_Mutation SNP C C3N-00294_T 493433 46077612 202878810 34 12806 CYP4X1 0 . GRCh38 1 47030126 47030126 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.314G>A p.Arg105Lys p.R105K ENST00000371901 2/12 114 85 29 123 123 0 strelka-varscan-mutect CYP4X1,missense_variant,p.Arg105Lys,ENST00000371901,NM_178033.1; A ENST00000371901 Transcript missense_variant 564/2357 314/1530 105/509 R/K aGa/aAa 1 1 CYP4X1 HGNC HGNC:20244 protein_coding YES CCDS544.1 ENSP00000360968 Q8N118 UPI000003F043 NM_178033.1 deleterious(0.05) 2/12 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF55,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs1393635084 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 47030126 47030126 G A 1 0 0 0 0 1 0 0 0 3996 956 33 3 3 CYP4X1 1 47030126 Missense_Mutation SNP G C3N-00294_T 952514 47030126 201926296 35 12807 CYP4X1 0 . GRCh38 1 47035833 47035833 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.520C>T p.Gln174Ter p.Q174* ENST00000371901 5/12 97 81 16 86 86 0 strelka-varscan-mutect CYP4X1,stop_gained,p.Gln174Ter,ENST00000371901,NM_178033.1;CYP4X1,upstream_gene_variant,,ENST00000466294,; T ENST00000371901 Transcript stop_gained 770/2357 520/1530 174/509 Q/* Cag/Tag 1 1 CYP4X1 HGNC HGNC:20244 protein_coding YES CCDS544.1 ENSP00000360968 Q8N118 UPI000003F043 NM_178033.1 5/12 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF55,Superfamily_domains:SSF48264 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 47035833 47035833 C T 1 0 0 0 0 0 1 0 0 3996 827 29 3 3 CYP4X1 1 47035833 Nonsense_Mutation SNP C C3N-00294_T 5707 47035833 201920589 36 12808 STIL 0 . GRCh38 1 47262968 47262968 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2764G>A p.Glu922Lys p.E922K ENST00000371877 15/17 247 185 62 290 290 0 strelka-varscan-mutect STIL,missense_variant,p.Glu921Lys,ENST00000360380,NM_001282936.1,NM_003035.2;STIL,missense_variant,p.Glu875Lys,ENST00000337817,NM_001282939.1,NM_001282938.1;STIL,missense_variant,p.Glu922Lys,ENST00000371877,NM_001048166.1;STIL,missense_variant,p.Glu904Lys,ENST00000396221,NM_001282937.1;STIL,missense_variant,p.Glu857Lys,ENST00000447475,;STIL,non_coding_transcript_exon_variant,,ENST00000418131,; T ENST00000371877 Transcript missense_variant 2912/5009 2764/3867 922/1288 E/K Gag/Aag 1 -1 STIL HGNC HGNC:10879 protein_coding YES CCDS41329.1 ENSP00000360944 Q15468 UPI00002042D5 NM_001048166.1 deleterious(0.02) 15/17 hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 47262968 47262968 C T 1 0 0 0 0 1 0 0 0 15659 835 29 3 3 STIL 1 47262968 Missense_Mutation SNP C C3N-00294_T 227135 47262968 201693454 37 12809 TRABD2B 0 . GRCh38 1 47794700 47794700 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.874G>A p.Asp292Asn p.D292N ENST00000606738 4/7 205 155 50 212 212 0 strelka-varscan-mutect TRABD2B,missense_variant,p.Asp292Asn,ENST00000606738,NM_001194986.1;TRABD2B,intron_variant,,ENST00000435576,; T ENST00000606738 Transcript missense_variant 980/7034 874/1554 292/517 D/N Gac/Aac 1 -1 TRABD2B HGNC HGNC:44200 protein_coding YES CCDS58000.1 ENSP00000476820 A6NFA1 UPI00017BE8EF NM_001194986.1 tolerated(0.13) 4/7 hmmpanther:PTHR31120:SF8,hmmpanther:PTHR31120,Pfam_domain:PF01963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 47794700 47794700 C T 1 0 0 0 0 1 0 0 0 16918 826 29 3 3 TRABD2B 1 47794700 Missense_Mutation SNP C C3N-00294_T 531732 47794700 201161722 38 12810 C8A 0 . GRCh38 1 56876136 56876136 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.391G>A p.Glu131Lys p.E131K ENST00000361249 4/11 476 368 108 515 515 0 strelka-varscan-mutect C8A,missense_variant,p.Glu131Lys,ENST00000361249,NM_000562.2; A ENST00000361249 Transcript missense_variant 487/2356 391/1755 131/584 E/K Gaa/Aaa 1 1 C8A HGNC HGNC:1352 protein_coding YES CCDS606.1 ENSP00000354458 P07357 UPI0000127C5A NM_000562.2 deleterious(0.03) 4/11 PROSITE_profiles:PS50068,hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 56876136 56876136 G A 1 0 0 0 0 1 0 0 0 2150 1291 45 3 3 C8A 1 56876136 Missense_Mutation SNP G C3N-00294_T 9081436 56876136 192080286 39 12811 DAB1 0 . GRCh38 1 57136619 57136619 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.230C>G p.Ser77Cys p.S77C ENST00000371236 4/15 76 68 8 112 112 0 strelka-mutect DAB1,missense_variant,p.Ser77Cys,ENST00000371236,;DAB1,missense_variant,p.Ser77Cys,ENST00000414851,NM_021080.3;DAB1,missense_variant,p.Ser77Cys,ENST00000420954,;DAB1,missense_variant,p.Ser77Cys,ENST00000371231,;DAB1,missense_variant,p.Ser77Cys,ENST00000371230,;DAB1,missense_variant,p.Ser77Cys,ENST00000371232,;DAB1,missense_variant,p.Ser77Cys,ENST00000332102,;DAB1,non_coding_transcript_exon_variant,,ENST00000485760,;DAB1,upstream_gene_variant,,ENST00000489267,; C ENST00000371236 Transcript missense_variant 494/5298 230/1668 77/555 S/C tCc/tGc 1 -1 DAB1 HGNC HGNC:2661 protein_coding YES CCDS607.1 ENSP00000360280 O75553 UPI000013EE33 deleterious(0) 4/15 PROSITE_profiles:PS01179,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF40,Gene3D:2.30.29.30,Pfam_domain:PF00640,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -17.83708 1 1 1 1 0 C 3 2 46 57136619 57136619 G C 1 0 0 0 0 1 0 0 0 4018 1174 41 4 4 DAB1 1 57136619 Missense_Mutation SNP G C3N-00294_T 260483 57136619 191819803 40 12812 MYSM1 0 . GRCh38 1 58667093 58667093 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1976C>A p.Pro659His p.P659H ENST00000472487 16/20 113 101 12 146 145 1 strelka-varscan-mutect MYSM1,missense_variant,p.Pro659His,ENST00000472487,NM_001085487.2;MYSM1,missense_variant,p.Pro65His,ENST00000622766,;MYSM1,non_coding_transcript_exon_variant,,ENST00000493821,;MYSM1,non_coding_transcript_exon_variant,,ENST00000401044,; T ENST00000472487 Transcript missense_variant 2016/7785 1976/2487 659/828 P/H cCt/cAt 1 -1 MYSM1 HGNC HGNC:29401 protein_coding YES CCDS41343.1 ENSP00000418734 Q5VVJ2 UPI0000204444 NM_001085487.2 deleterious(0) 16/20 hmmpanther:PTHR12802,hmmpanther:PTHR12802:SF20,Gene3D:3.40.140.10,Pfam_domain:PF01398,SMART_domains:SM00232,Superfamily_domains:0048572 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 58667093 58667093 G T 1 0 0 0 0 1 0 0 0 10104 1000 35 2 2 MYSM1 1 58667093 Missense_Mutation SNP G C3N-00294_T 1530474 58667093 190289329 41 12813 JUN 0 . GRCh38 1 58782737 58782737 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.334G>A p.Glu112Lys p.E112K ENST00000371222 1/1 93 71 22 85 85 0 strelka-varscan-mutect JUN,missense_variant,p.Glu112Lys,ENST00000371222,NM_002228.3;LINC01135,upstream_gene_variant,,ENST00000419531,; T ENST00000371222 Transcript missense_variant 1591/3540 334/996 112/331 E/K Gag/Aag COSM681630,COSM681631 1 -1 JUN HGNC HGNC:6204 protein_coding YES CCDS610.1 ENSP00000360266 P05412 UPI000000D908 NM_002228.3 deleterious(0.01) 1/1 Pfam_domain:PF03957,hmmpanther:PTHR11462,hmmpanther:PTHR11462:SF8 1,1 MODERATE SNV 1,1 1 PASS rs1184098204 . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 46 58782737 58782737 C T 1 0 0 0 0 1 0 0 0 7879 893 31 1 1 JUN 1 58782737 Missense_Mutation SNP C C3N-00294_T 115644 58782737 190173685 42 12814 L1TD1 0 . GRCh38 1 62209978 62209978 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1204G>A p.Gly402Arg p.G402R ENST00000498273 4/4 193 105 88 198 198 0 strelka-varscan-mutect L1TD1,missense_variant,p.Gly402Arg,ENST00000498273,NM_001164835.1,NM_019079.4;Y_RNA,upstream_gene_variant,,ENST00000363304,;RP5-1155K23.4,upstream_gene_variant,,ENST00000450606,; A ENST00000498273 Transcript missense_variant 1499/3849 1204/2598 402/865 G/R Ggg/Agg 1 1 L1TD1 HGNC HGNC:25595 protein_coding YES CCDS619.1 ENSP00000419901 Q5T7N2 UPI000013E18E NM_001164835.1,NM_019079.4 deleterious(0.04) 4/4 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 62209978 62209978 G A 1 0 0 0 0 1 0 0 0 8490 1000 35 3 3 L1TD1 1 62209978 Missense_Mutation SNP G C3N-00294_T 3427241 62209978 186746444 43 12815 IL12RB2 0 . GRCh38 1 67368018 67368018 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1452G>A p.= p.L484L ENST00000262345 10/16 405 339 66 410 410 0 strelka-varscan-mutect IL12RB2,synonymous_variant,p.=,ENST00000262345,NM_001559.2;IL12RB2,synonymous_variant,p.=,ENST00000541374,NM_001258216.1;IL12RB2,synonymous_variant,p.=,ENST00000544434,NM_001258215.1;IL12RB2,synonymous_variant,p.=,ENST00000371000,NM_001258214.1; A ENST00000262345 Transcript synonymous_variant 2092/4040 1452/2589 484/862 L ctG/ctA 1 1 IL12RB2 HGNC HGNC:5972 protein_coding YES CCDS638.1 ENSP00000262345 Q99665 UPI0000046B13 NM_001559.2 10/16 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF79,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 67368018 67368018 G A 1 0 0 0 0 0 0 0 1 7535 1277 45 3 3 IL12RB2 1 67368018 Silent SNP G C3N-00294_T 5158040 67368018 181588404 44 12816 LRRC7 0 . GRCh38 1 69931556 69931556 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.583G>A p.Glu195Lys p.E195K ENST00000035383 6/25 126 92 34 202 202 0 strelka-varscan-mutect LRRC7,missense_variant,p.Glu200Lys,ENST00000310961,;LRRC7,missense_variant,p.Glu195Lys,ENST00000035383,NM_020794.2;LRRC7,5_prime_UTR_variant,,ENST00000415775,; A ENST00000035383 Transcript missense_variant 613/5000 583/4614 195/1537 E/K Gaa/Aaa 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious(0) 6/25 PROSITE_profiles:PS51450,hmmpanther:PTHR23155:SF459,hmmpanther:PTHR23155,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00364,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 69931556 69931556 G A 1 0 0 0 0 1 0 0 0 8916 1291 45 3 3 LRRC7 1 69931556 Missense_Mutation SNP G C3N-00294_T 2563538 69931556 179024866 45 12817 NEXN 0 . GRCh38 1 77942063 77942063 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1514C>T p.Ala505Val p.A505V ENST00000334785 12/13 262 183 79 354 354 0 strelka-varscan-mutect NEXN,missense_variant,p.Ala441Val,ENST00000330010,NM_001172309.1;NEXN,missense_variant,p.Ala405Val,ENST00000342754,;NEXN,missense_variant,p.Ala505Val,ENST00000334785,NM_144573.3;NEXN,non_coding_transcript_exon_variant,,ENST00000480732,;FUBP1,downstream_gene_variant,,ENST00000489495,;FUBP1,downstream_gene_variant,,ENST00000492405,;FUBP1,downstream_gene_variant,,ENST00000474632,;FUBP1,downstream_gene_variant,,ENST00000488814,;FUBP1,downstream_gene_variant,,ENST00000483894,;FUBP1,downstream_gene_variant,,ENST00000492724,;FUBP1,downstream_gene_variant,,ENST00000480673,;NEXN,non_coding_transcript_exon_variant,,ENST00000470735,;FUBP1,downstream_gene_variant,,ENST00000294623,; T ENST00000334785 Transcript missense_variant 1698/2607 1514/2028 505/675 A/V gCt/gTt 1 1 NEXN HGNC HGNC:29557 protein_coding YES CCDS41351.1 ENSP00000333938 Q0ZGT2 UPI000022ABDC NM_144573.3 deleterious(0.05) 12/13 hmmpanther:PTHR10489:SF677,hmmpanther:PTHR10489 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 77942063 77942063 C T 1 0 0 0 0 1 0 0 0 10392 797 28 3 3 NEXN 1 77942063 Missense_Mutation SNP C C3N-00294_T 8010507 77942063 171014359 46 12818 SH3GLB1 0 . GRCh38 1 86722563 86722563 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.367G>C p.Glu123Gln p.E123Q ENST00000616170 4/10 60 40 20 116 116 0 strelka-varscan-mutect SH3GLB1,missense_variant,p.Glu123Gln,ENST00000616170,NM_001206651.1;SH3GLB1,missense_variant,p.Glu123Gln,ENST00000370558,NM_016009.4;SH3GLB1,missense_variant,p.Glu23Gln,ENST00000535010,NM_001206653.1;SH3GLB1,missense_variant,p.Glu123Gln,ENST00000482504,NM_001206652.1; C ENST00000616170 Transcript missense_variant 697/6456 367/1185 123/394 E/Q Gaa/Caa 1 1 SH3GLB1 HGNC HGNC:10833 protein_coding YES CCDS72819.1 ENSP00000479919 A0A087WW40 UPI0000E05641 NM_001206651.1 tolerated(0.61) 4/10 PROSITE_profiles:PS51021,hmmpanther:PTHR10663:SF161,hmmpanther:PTHR10663,Pfam_domain:PF03114,Gene3D:1.20.1270.60,SMART_domains:SM00721,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 86722563 86722563 G C 1 0 0 0 0 1 0 0 0 14512 943 33 4 4 SH3GLB1 1 86722563 Missense_Mutation SNP G C3N-00294_T 8780500 86722563 162233859 47 12819 BARHL2 0 . GRCh38 1 90714699 90714699 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.683G>C p.Arg228Thr p.R228T ENST00000370445 2/3 329 205 124 314 313 1 strelka-varscan-mutect BARHL2,missense_variant,p.Arg228Thr,ENST00000370445,NM_020063.1; G ENST00000370445 Transcript missense_variant 725/1979 683/1164 228/387 R/T aGa/aCa 1 -1 BARHL2 HGNC HGNC:954 protein_coding YES CCDS730.1 ENSP00000359474 Q9NY43 UPI00001B50ED NM_020063.1 deleterious(0) 2/3 hmmpanther:PTHR24330:SF4,hmmpanther:PTHR24330,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 90714699 90714699 C G 1 0 0 0 0 1 0 0 0 1466 913 32 4 4 BARHL2 1 90714699 Missense_Mutation SNP C C3N-00294_T 3992136 90714699 158241723 48 12820 BRDT 0 . GRCh38 1 91980965 91980965 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1549G>A p.Asp517Asn p.D517N ENST00000399546 10/19 88 73 15 161 161 0 strelka-varscan-mutect BRDT,missense_variant,p.Asp440Asn,ENST00000370389,NM_001242810.2;BRDT,missense_variant,p.Asp513Asn,ENST00000362005,NM_001242805.2,NM_207189.3;BRDT,missense_variant,p.Asp517Asn,ENST00000399546,NM_001242806.2;BRDT,missense_variant,p.Asp467Asn,ENST00000394530,NM_001242808.2,NM_001242807.2;BRDT,missense_variant,p.Asp513Asn,ENST00000402388,NM_001726.4;BRDT,downstream_gene_variant,,ENST00000426141,;BRDT,downstream_gene_variant,,ENST00000427104,;BRDT,downstream_gene_variant,,ENST00000440509,;BRDT,downstream_gene_variant,,ENST00000423434,;BRDT,downstream_gene_variant,,ENST00000448194,;BRDT,downstream_gene_variant,,ENST00000484781,; A ENST00000399546 Transcript missense_variant 1898/3357 1549/2856 517/951 D/N Gat/Aat 1 1 BRDT HGNC HGNC:1105 protein_coding YES CCDS72820.1 ENSP00000387822 Q58F21 UPI000292A27D NM_001242806.2 deleterious(0) 10/19 Pfam_domain:PF17035,PROSITE_profiles:PS51525,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF175 MODERATE 1 SNV 2 1 PASS rs1188709614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 91980965 91980965 G A 1 0 0 0 0 1 0 0 0 1678 1290 45 3 3 BRDT 1 91980965 Missense_Mutation SNP G C3N-00294_T 1266266 91980965 156975457 49 12821 PLPPR4 0 . GRCh38 1 99306600 99306600 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1882G>C p.Glu628Gln p.E628Q ENST00000370185 7/7 240 190 50 274 274 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Glu628Gln,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Glu570Gln,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Glu470Gln,ENST00000370184,; C ENST00000370185 Transcript missense_variant 2379/5369 1882/2292 628/763 E/Q Gag/Cag 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0.02) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 99306600 99306600 G C 1 0 0 0 0 1 0 0 0 12212 943 33 4 4 PLPPR4 1 99306600 Missense_Mutation SNP G C3N-00294_T 7325635 99306600 149649822 50 12822 WDR47 0 . GRCh38 1 108981858 108981858 + Missense_Mutation SNP A A C novel C3N-00294_T C3N-00294_N A A c.2297T>G p.Ile766Ser p.I766S ENST00000400794 13/15 96 73 23 105 105 0 strelka-varscan-mutect WDR47,missense_variant,p.Ile759Ser,ENST00000369965,NM_014969.5;WDR47,missense_variant,p.Ile758Ser,ENST00000369962,NM_001142551.1;WDR47,missense_variant,p.Ile732Ser,ENST00000357672,;WDR47,missense_variant,p.Ile766Ser,ENST00000400794,NM_001142550.1;WDR47,missense_variant,p.Ile730Ser,ENST00000361054,; C ENST00000400794 Transcript missense_variant 2431/4134 2297/2784 766/927 I/S aTt/aGt 1 -1 WDR47 HGNC HGNC:29141 protein_coding YES CCDS44186.1 ENSP00000383599 O94967 UPI0001639B05 NM_001142550.1 deleterious(0) 13/15 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19863,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 108981858 108981858 A C 1 0 0 0 0 1 0 0 0 17860 101 4 5 5 WDR47 1 108981858 Missense_Mutation SNP A C3N-00294_T 9675258 108981858 139974564 51 12823 KCNA2 0 . GRCh38 1 110603675 110603675 + Missense_Mutation SNP C C T rs756214647 C3N-00294_T C3N-00294_N C C c.1108G>A p.Val370Ile p.V370I ENST00000633222 3/3 205 178 27 221 221 0 strelka-varscan-mutect KCNA2,missense_variant,p.Val370Ile,ENST00000633222,;KCNA2,missense_variant,p.Val370Ile,ENST00000485317,;KCNA2,missense_variant,p.Val370Ile,ENST00000316361,NM_004974.3;KCNA2,intron_variant,,ENST00000369770,NM_001204269.1;KCNA2,downstream_gene_variant,,ENST00000525120,; T ENST00000633222 Transcript missense_variant 1782/11877 1108/1500 370/499 V/I Gtc/Atc rs756214647,COSM1560110 1 -1 KCNA2 HGNC HGNC:6220 protein_coding YES CCDS827.1 ENSP00000487785 P16389 UPI00001279A1 deleterious(0.03) 3/3 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF23,Superfamily_domains:SSF81324 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs756214647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 110603675 110603675 C T 1 0 0 0 0 1 0 0 0 7919 536 19 1 1 KCNA2 1 110603675 Missense_Mutation SNP C C3N-00294_T 1621817 110603675 138352747 52 12824 LRIG2 0 . GRCh38 1 113114472 113114472 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2126G>A p.Arg709Gln p.R709Q ENST00000361127 15/18 122 111 11 162 162 0 strelka-varscan-mutect LRIG2,missense_variant,p.Arg709Gln,ENST00000361127,NM_014813.2;LRIG2,non_coding_transcript_exon_variant,,ENST00000492207,;LRIG2,non_coding_transcript_exon_variant,,ENST00000466161,; A ENST00000361127 Transcript missense_variant 2324/11555 2126/3198 709/1065 R/Q cGa/cAa COSM2120114,COSM674291 1 1 LRIG2 HGNC HGNC:20889 protein_coding YES CCDS30808.1 ENSP00000355396 O94898 UPI000006F613 NM_014813.2 tolerated(0.53) 15/18 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF230,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1309314863 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 113114472 113114472 G A 1 0 0 0 0 1 0 0 0 8840 1058 37 1 1 LRIG2 1 113114472 Missense_Mutation SNP G C3N-00294_T 2510797 113114472 135841950 53 12825 DENND2C 0 . GRCh38 1 114608787 114608787 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1456C>A p.Gln486Lys p.Q486K ENST00000393274 10/21 300 186 114 301 301 0 strelka-varscan-mutect DENND2C,missense_variant,p.Gln486Lys,ENST00000393274,NM_001256404.1;DENND2C,missense_variant,p.Gln429Lys,ENST00000393276,NM_198459.3;DENND2C,missense_variant,p.Gln486Lys,ENST00000393277,;DENND2C,non_coding_transcript_exon_variant,,ENST00000481894,; T ENST00000393274 Transcript missense_variant 2082/6163 1456/2787 486/928 Q/K Cag/Aag 1 -1 DENND2C HGNC HGNC:24748 protein_coding YES CCDS58018.1 ENSP00000376955 Q68D51 UPI000048AF71 NM_001256404.1 deleterious(0.01) 10/21 Low_complexity_(Seg):seg,hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 114608787 114608787 G T 1 0 0 0 0 1 0 0 0 4234 1386 48 2 2 DENND2C 1 114608787 Missense_Mutation SNP G C3N-00294_T 1494315 114608787 134347635 54 12826 CD101 0 . GRCh38 1 117011847 117011847 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.722C>G p.Ser241Cys p.S241C ENST00000369470 3/10 302 242 60 333 333 0 strelka-varscan-mutect CD101,missense_variant,p.Ser241Cys,ENST00000369470,NM_001256109.2,NM_001256106.2,NM_004258.5,NM_001256111.2;CD101,missense_variant,p.Ser241Cys,ENST00000256652,; G ENST00000369470 Transcript missense_variant 728/3324 722/3066 241/1021 S/C tCc/tGc 1 1 CD101 HGNC HGNC:5949 protein_coding YES CCDS891.1 ENSP00000358482 Q93033 UPI000013CF1F NM_001256109.2,NM_001256106.2,NM_004258.5,NM_001256111.2 deleterious(0) 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR12207:SF25,hmmpanther:PTHR12207,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 117011847 117011847 C G 1 0 0 0 0 1 0 0 0 2665 855 30 4 4 CD101 1 117011847 Missense_Mutation SNP C C3N-00294_T 2403060 117011847 131944575 55 12827 FAM72B 0 . GRCh38 1 121181294 121181294 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.207G>A p.= p.L69L ENST00000369390 2/4 18 10 8 27 27 0 varscan-mutect FAM72B,synonymous_variant,p.=,ENST00000369390,NM_001100910.1;FAM72B,synonymous_variant,p.=,ENST00000355228,NM_001320149.1;FAM72B,synonymous_variant,p.=,ENST00000619376,;FAM72B,synonymous_variant,p.=,ENST00000452190,;FAM72B,synonymous_variant,p.=,ENST00000471903,;SRGAP2C,upstream_gene_variant,,ENST00000367123,NM_001271872.1;FAM72B,non_coding_transcript_exon_variant,,ENST00000468129,;SRGAP2C,upstream_gene_variant,,ENST00000412759,;SRGAP2C,upstream_gene_variant,,ENST00000617209,;SRGAP2C,upstream_gene_variant,,ENST00000613462,;FAM72B,downstream_gene_variant,,ENST00000616749,; T ENST00000369390 Transcript synonymous_variant 1058/2396 207/450 69/149 L ctG/ctA 1 -1 FAM72B HGNC HGNC:24805 protein_coding YES CCDS72848.1 ENSP00000358397 Q86X60 UPI000046FF4E NM_001100910.1 2/4 hmmpanther:PTHR31841,Pfam_domain:PF14976 LOW 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 2 4 46 121181294 121181294 C T 1 0 0 0 0 0 0 0 1 5480 813 29 3 3 FAM72B 1 121181294 Silent SNP C C3N-00294_T 4169447 121181294 127775128 56 12828 NBPF12 0 . GRCh38 1 146963120 146963120 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.304C>T p.Gln102Ter p.Q102* ENST00000617931 8/36 464 418 46 344 344 0 varscan-mutect NBPF12,stop_gained,p.Gln102Ter,ENST00000617931,;NBPF12,stop_gained,p.Gln102Ter,ENST00000617844,NM_001278141.1;NBPF12,stop_gained,p.Gln102Ter,ENST00000611443,;NBPF12,stop_gained,p.Gln102Ter,ENST00000579935,;NBPF12,stop_gained,p.Gln102Ter,ENST00000617614,;NBPF12,intron_variant,,ENST00000613714,;NBPF12,intron_variant,,ENST00000617864,;NBPF12,intron_variant,,ENST00000439206,; T ENST00000617931 Transcript stop_gained 1364/7061 304/4374 102/1457 Q/* Cag/Tag 1 1 NBPF12 HGNC HGNC:24297 protein_coding YES CCDS72881.1 ENSP00000478609 A0A087WUF1 UPI00032968BC 8/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14199:SF20,hmmpanther:PTHR14199 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 146963120 146963120 C T 1 0 0 0 0 0 1 0 0 10206 827 29 3 3 NBPF12 1 146963120 Nonsense_Mutation SNP C C3N-00294_T 25781826 146963120 101993302 57 12829 MCL1 0 . GRCh38 1 150578381 150578381 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.799C>T p.Leu267Phe p.L267F ENST00000369026 2/3 575 495 80 431 431 0 strelka-varscan-mutect MCL1,missense_variant,p.Leu267Phe,ENST00000369026,NM_021960.4;MCL1,missense_variant,p.Leu114Phe,ENST00000620947,NM_001197320.1;MCL1,intron_variant,,ENST00000307940,NM_182763.2;ADAMTSL4-AS1,upstream_gene_variant,,ENST00000617352,;MCL1,non_coding_transcript_exon_variant,,ENST00000464132,; A ENST00000369026 Transcript missense_variant 859/3932 799/1053 267/350 L/F Ctc/Ttc 1 -1 MCL1 HGNC HGNC:6943 protein_coding YES CCDS957.1 ENSP00000358022 Q07820 UPI000006D775 NM_021960.4 tolerated(0.06) 2/3 Gene3D:1.10.437.10,Pfam_domain:PF00452,Prints_domain:PR01862,PROSITE_patterns:PS01080,PROSITE_profiles:PS50062,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF46,SMART_domains:SM00337,Superfamily_domains:SSF56854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 150578381 150578381 G A 1 0 0 0 0 1 0 0 0 9316 942 33 3 3 MCL1 1 150578381 Missense_Mutation SNP G C3N-00294_T 3615261 150578381 98378041 58 12830 C1orf56 0 . GRCh38 1 151048841 151048841 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.994G>C p.Glu332Gln p.E332Q ENST00000368926 1/2 40 32 8 32 32 0 strelka-varscan-mutect C1orf56,missense_variant,p.Glu332Gln,ENST00000368926,NM_017860.3;CDC42SE1,downstream_gene_variant,,ENST00000439374,;CDC42SE1,downstream_gene_variant,,ENST00000540998,NM_001038707.1;CDC42SE1,downstream_gene_variant,,ENST00000357235,NM_020239.3;BNIPL,downstream_gene_variant,,ENST00000295294,NM_001159642.1;BNIPL,downstream_gene_variant,,ENST00000368931,NM_138278.3;BNIPL,downstream_gene_variant,,ENST00000361277,;C1orf56,non_coding_transcript_exon_variant,,ENST00000465135,;C1orf56,non_coding_transcript_exon_variant,,ENST00000473308,;CDC42SE1,downstream_gene_variant,,ENST00000492796,;BNIPL,downstream_gene_variant,,ENST00000491386,;CDC42SE1,downstream_gene_variant,,ENST00000483763,;BNIPL,downstream_gene_variant,,ENST00000485855,; C ENST00000368926 Transcript missense_variant 1102/2096 994/1026 332/341 E/Q Gag/Cag 1 1 C1orf56 HGNC HGNC:26045 protein_coding YES CCDS980.1 ENSP00000357922 Q9BUN1 UPI0000048EEB NM_017860.3 tolerated(0.15) 1/2 hmmpanther:PTHR16240,Pfam_domain:PF15322 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 151048841 151048841 G C 1 0 0 0 0 1 0 0 0 1994 943 33 4 4 C1orf56 1 151048841 Missense_Mutation SNP G C3N-00294_T 470460 151048841 97907581 59 12831 TMOD4 0 . GRCh38 1 151171472 151171472 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.687C>T p.= p.F229F ENST00000295314 7/10 240 214 26 139 139 0 strelka-varscan-mutect TMOD4,synonymous_variant,p.=,ENST00000295314,NM_013353.2;TMOD4,intron_variant,,ENST00000466891,;SCNM1,downstream_gene_variant,,ENST00000368905,NM_024041.3;VPS72,downstream_gene_variant,,ENST00000368892,NM_001271088.1,NM_005997.2;VPS72,downstream_gene_variant,,ENST00000354473,NM_001271087.1;SCNM1,downstream_gene_variant,,ENST00000368902,NM_001204856.1;SCNM1,downstream_gene_variant,,ENST00000602841,NM_001204848.1;TMOD4,downstream_gene_variant,,ENST00000441701,;TMOD4,non_coding_transcript_exon_variant,,ENST00000488488,;SCNM1,downstream_gene_variant,,ENST00000461862,;SCNM1,downstream_gene_variant,,ENST00000497147,;TMOD4,downstream_gene_variant,,ENST00000601585,;SCNM1,downstream_gene_variant,,ENST00000459799,;SCNM1,downstream_gene_variant,,ENST00000471039,;TMOD4,3_prime_UTR_variant,,ENST00000463543,;VPS72,non_coding_transcript_exon_variant,,ENST00000491094,; A ENST00000295314 Transcript synonymous_variant 822/1267 687/1038 229/345 F ttC/ttT 1 -1 TMOD4 HGNC HGNC:11874 protein_coding YES CCDS988.1 ENSP00000295314 Q9NZQ9 UPI00000015C0 NM_013353.2 7/10 hmmpanther:PTHR10901:SF9,hmmpanther:PTHR10901,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 151171472 151171472 G A 1 0 0 0 0 0 0 0 1 16712 1281 45 3 3 TMOD4 1 151171472 Silent SNP G C3N-00294_T 122631 151171472 97784950 60 12832 C2CD4D 0 . GRCh38 1 151838314 151838314 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.676G>C p.Glu226Gln p.E226Q ENST00000454109 2/2 85 74 11 39 39 0 strelka-varscan-mutect C2CD4D,missense_variant,p.Glu226Gln,ENST00000454109,NM_001136003.1;AL450992.2,upstream_gene_variant,,ENST00000434182,;Y_RNA,downstream_gene_variant,,ENST00000364264,; G ENST00000454109 Transcript missense_variant 1262/1757 676/1062 226/353 E/Q Gaa/Caa 1 -1 C2CD4D HGNC HGNC:37210 protein_coding YES CCDS44224.1 ENSP00000389554 B7Z1M9 UPI0001747AE2 NM_001136003.1 deleterious(0.01) 2/2 Gene3D:2.60.40.150,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF179,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS rs1346931782 . 0 202 8 0 0 0 0 0 -19.99976 0.9999974 1 1 1 0 G 3 3 46 151838314 151838314 C G 1 0 0 0 0 1 0 0 0 2029 893 31 4 4 C2CD4D 1 151838314 Missense_Mutation SNP C C3N-00294_T 666842 151838314 97118108 61 12833 THEM5 0 . GRCh38 1 151853494 151853494 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.72C>G p.Ile24Met p.I24M ENST00000368817 1/6 166 151 15 110 110 0 strelka-varscan-mutect THEM5,missense_variant,p.Ile24Met,ENST00000368817,NM_182578.3;THEM5,upstream_gene_variant,,ENST00000453881,;AL450992.2,downstream_gene_variant,,ENST00000434182,; C ENST00000368817 Transcript missense_variant 204/984 72/744 24/247 I/M atC/atG 1 -1 THEM5 HGNC HGNC:26755 protein_coding YES CCDS1005.1 ENSP00000357807 Q8N1Q8 UPI000013E246 NM_182578.3 deleterious(0.03) 1/6 hmmpanther:PTHR12418,hmmpanther:PTHR12418:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 151853494 151853494 G C 1 0 0 0 0 1 0 0 0 16292 1164 41 4 4 THEM5 1 151853494 Missense_Mutation SNP G C3N-00294_T 15180 151853494 97102928 62 12834 HRNR 0 . GRCh38 1 152218780 152218780 + Missense_Mutation SNP C C G rs755677565 C3N-00294_T C3N-00294_N C C c.2849G>C p.Gly950Ala p.G950A ENST00000368801 3/3 926 805 121 736 736 0 varscan-mutect HRNR,missense_variant,p.Gly950Ala,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENST00000368801 Transcript missense_variant 2925/9623 2849/8553 950/2850 G/A gGc/gCc rs755677565,COSM1127391 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.22) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755677565 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 152218780 152218780 C G 1 0 0 0 0 1 0 0 0 7254 739 26 4 4 HRNR 1 152218780 Missense_Mutation SNP C C3N-00294_T 365286 152218780 96737642 63 12835 IVL 0 . GRCh38 1 152911505 152911505 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1708G>C p.Glu570Gln p.E570Q ENST00000368764 2/2 161 142 19 137 137 0 strelka-varscan-mutect IVL,missense_variant,p.Glu570Gln,ENST00000368764,NM_005547.2; C ENST00000368764 Transcript missense_variant 1772/2153 1708/1758 570/585 E/Q Gag/Cag 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 tolerated_low_confidence(0.15) 2/2 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 152911505 152911505 G C 1 0 0 0 0 1 0 0 0 7835 943 33 4 4 IVL 1 152911505 Missense_Mutation SNP G C3N-00294_T 692725 152911505 96044917 64 12836 DENND4B 0 . GRCh38 1 153934173 153934173 + Missense_Mutation SNP C C T rs748707602 C3N-00294_T C3N-00294_N C C c.2903G>A p.Arg968Gln p.R968Q ENST00000361217 19/28 134 111 23 74 73 1 strelka-varscan-mutect DENND4B,missense_variant,p.Arg968Gln,ENST00000361217,NM_014856.2;DENND4B,missense_variant,p.Arg979Gln,ENST00000368646,;DENND4B,upstream_gene_variant,,ENST00000474386,;DENND4B,upstream_gene_variant,,ENST00000480340,;DENND4B,upstream_gene_variant,,ENST00000492898,;DENND4B,upstream_gene_variant,,ENST00000462423,;DENND4B,upstream_gene_variant,,ENST00000531748,;DENND4B,downstream_gene_variant,,ENST00000477746,; T ENST00000361217 Transcript missense_variant 3322/5706 2903/4491 968/1496 R/Q cGa/cAa rs748707602,COSM2208183,COSM2208184 1 -1 DENND4B HGNC HGNC:29044 protein_coding YES CCDS44228.1 ENSP00000354597 O75064 UPI000047EA3E NM_014856.2 tolerated(0.08) 19/28 hmmpanther:PTHR12296:SF18,hmmpanther:PTHR12296 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748707602 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 46 153934173 153934173 C T 1 0 0 0 0 1 0 0 0 4238 884 31 1 1 DENND4B 1 153934173 Missense_Mutation SNP C C3N-00294_T 1022668 153934173 95022249 65 12837 NUP210L 0 . GRCh38 1 154070466 154070466 + Splice_Site SNP C C T novel C3N-00294_T C3N-00294_N C C c.2362-1G>A p.X788_splice ENST00000368559 87 74 13 54 54 0 strelka-varscan-mutect NUP210L,splice_acceptor_variant,,ENST00000368559,NM_207308.2;NUP210L,splice_acceptor_variant,,ENST00000271854,NM_001159484.1; T ENST00000368559 Transcript splice_acceptor_variant -/5889 2362/5667 788/1888 1 -1 NUP210L HGNC HGNC:29915 protein_coding YES CCDS41399.1 ENSP00000357547 Q5VU65 UPI000023724F NM_207308.2 16/39 HIGH 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 46 154070466 154070466 C T 1 0 0 0 0 0 0 1 0 10826 927 32 3 3 NUP210L 1 154070466 Splice_Site SNP C C3N-00294_T 136293 154070466 94885956 66 12838 AQP10 0 . GRCh38 1 154324395 154324395 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.821C>T p.Pro274Leu p.P274L ENST00000324978 6/6 208 192 16 142 142 0 strelka-varscan-mutect AQP10,missense_variant,p.Pro274Leu,ENST00000324978,NM_080429.2;AQP10,3_prime_UTR_variant,,ENST00000484864,;ATP8B2,upstream_gene_variant,,ENST00000368489,NM_020452.3;ATP8B2,upstream_gene_variant,,ENST00000368487,NM_001005855.1;ATP8B2,upstream_gene_variant,,ENST00000426445,;AQP10,downstream_gene_variant,,ENST00000355197,;ATP8B2,upstream_gene_variant,,ENST00000368490,; T ENST00000324978 Transcript missense_variant 861/1791 821/906 274/301 P/L cCa/cTa 1 1 AQP10 HGNC HGNC:16029 protein_coding YES CCDS1065.1 ENSP00000318355 Q96PS8 UPI000007028A NM_080429.2 tolerated(0.07) 6/6 hmmpanther:PTHR19139:SF138,hmmpanther:PTHR19139 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 154324395 154324395 C T 1 0 0 0 0 1 0 0 0 945 594 21 3 3 AQP10 1 154324395 Missense_Mutation SNP C C3N-00294_T 253929 154324395 94632027 67 12839 ASH1L 0 . GRCh38 1 155349336 155349336 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.7545G>C p.= p.R2515R ENST00000392403 19/28 137 118 19 89 89 0 strelka-varscan-mutect ASH1L,synonymous_variant,p.=,ENST00000368346,;ASH1L,synonymous_variant,p.=,ENST00000392403,NM_018489.2;ASH1L,upstream_gene_variant,,ENST00000384987,;ASH1L,synonymous_variant,p.=,ENST00000492987,;ASH1L,upstream_gene_variant,,ENST00000478837,;ASH1L,upstream_gene_variant,,ENST00000548566,; G ENST00000392403 Transcript synonymous_variant 8024/10979 7545/8895 2515/2964 R cgG/cgC 1 -1 ASH1L HGNC HGNC:19088 protein_coding YES CCDS1113.2 ENSP00000376204 Q9NR48 UPI0000DACAC8 NM_018489.2 19/28 Gene3D:1.20.920.10,Pfam_domain:PF00439,PROSITE_profiles:PS50014,SMART_domains:SM00297,Superfamily_domains:SSF47370 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 155349336 155349336 C G 1 0 0 0 0 0 0 0 1 1183 842 30 4 4 ASH1L 1 155349336 Silent SNP C C3N-00294_T 1024941 155349336 93607086 68 12840 GON4L 0 . GRCh38 1 155756994 155756994 + Silent SNP C C T rs753140395 C3N-00294_T C3N-00294_N C C c.5481G>A p.= p.K1827K ENST00000368331 27/32 265 236 29 222 221 1 strelka-varscan-mutect GON4L,synonymous_variant,p.=,ENST00000368331,NM_001282860.1;GON4L,synonymous_variant,p.=,ENST00000615926,NM_001282856.1;GON4L,synonymous_variant,p.=,ENST00000437809,;GON4L,synonymous_variant,p.=,ENST00000271883,NM_001282858.1;GON4L,3_prime_UTR_variant,,ENST00000620426,;GON4L,non_coding_transcript_exon_variant,,ENST00000483032,;GON4L,non_coding_transcript_exon_variant,,ENST00000460075,;GON4L,upstream_gene_variant,,ENST00000473267,; T ENST00000368331 Transcript synonymous_variant 5656/7823 5481/6726 1827/2241 K aaG/aaA rs753140395 1 -1 GON4L HGNC HGNC:25973 protein_coding YES CCDS60296.1 ENSP00000357315 Q3T8J9 UPI0000351551 NM_001282860.1 27/32 hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF11 LOW 1 SNV 1 1 PASS rs753140395 . 0 120 0 3 87 0 0 0 -9.490975 0 0 1 0 0 T 2 4 46 155756994 155756994 C T 1 0 0 0 0 0 0 0 1 6466 912 32 3 3 GON4L 1 155756994 Silent SNP C C3N-00294_T 407658 155756994 93199428 69 12841 IQGAP3 0 . GRCh38 1 156527963 156527963 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4771C>G p.Leu1591Val p.L1591V ENST00000361170 37/38 174 153 21 119 119 0 strelka-varscan-mutect IQGAP3,missense_variant,p.Leu1591Val,ENST00000361170,NM_178229.4;IQGAP3,missense_variant,p.Leu1548Val,ENST00000491900,; C ENST00000361170 Transcript missense_variant 4782/5988 4771/4896 1591/1631 L/V Ctt/Gtt 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 tolerated(0.07) 37/38 Low_complexity_(Seg):seg,hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149,Superfamily_domains:0050767 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 46 156527963 156527963 G C 1 0 0 0 0 1 0 0 0 7722 971 34 4 4 IQGAP3 1 156527963 Missense_Mutation SNP G C3N-00294_T 770969 156527963 92428459 70 12842 NES 0 . GRCh38 1 156671778 156671778 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2410C>G p.Gln804Glu p.Q804E ENST00000368223 4/4 219 192 27 159 159 0 strelka-varscan-mutect NES,missense_variant,p.Gln804Glu,ENST00000368223,NM_006617.1; C ENST00000368223 Transcript missense_variant 2543/5558 2410/4866 804/1621 Q/E Caa/Gaa 1 -1 NES HGNC HGNC:7756 protein_coding YES CCDS1151.1 ENSP00000357206 P48681 UPI0000213DC0 NM_006617.1 tolerated(0.06) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 156671778 156671778 G C 1 0 0 0 0 1 0 0 0 10372 1299 45 4 4 NES 1 156671778 Missense_Mutation SNP G C3N-00294_T 143815 156671778 92284644 71 12843 HDGF 0 . GRCh38 1 156744228 156744228 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.472G>A p.Asp158Asn p.D158N ENST00000368206 4/6 606 518 88 527 527 0 strelka-varscan-mutect HDGF,missense_variant,p.Asp142Asn,ENST00000357325,NM_004494.2;HDGF,missense_variant,p.Asp135Asn,ENST00000368209,NM_001126051.1;HDGF,missense_variant,p.Asp142Asn,ENST00000537739,;HDGF,missense_variant,p.Asp158Asn,ENST00000368206,NM_001126050.1;MRPL24,upstream_gene_variant,,ENST00000434558,;MRPL24,upstream_gene_variant,,ENST00000361531,;MRPL24,upstream_gene_variant,,ENST00000368211,NM_145729.2,NM_024540.3;MRPL24,upstream_gene_variant,,ENST00000412846,;MRPL24,upstream_gene_variant,,ENST00000420938,;HDGF,non_coding_transcript_exon_variant,,ENST00000465180,;HDGF,non_coding_transcript_exon_variant,,ENST00000482651,;HDGF,non_coding_transcript_exon_variant,,ENST00000469145,;HDGF,non_coding_transcript_exon_variant,,ENST00000495212,;HDGF,non_coding_transcript_exon_variant,,ENST00000477306,;HDGF,non_coding_transcript_exon_variant,,ENST00000471377,; T ENST00000368206 Transcript missense_variant 557/960 472/771 158/256 D/N Gat/Aat 1 -1 HDGF HGNC HGNC:4856 protein_coding YES CCDS44247.1 ENSP00000357189 P51858 UPI00004701A4 NM_001126050.1 deleterious(0) 4/6 hmmpanther:PTHR12550 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 156744228 156744228 C T 1 0 0 0 0 1 0 0 0 6905 826 29 3 3 HDGF 1 156744228 Missense_Mutation SNP C C3N-00294_T 72450 156744228 92212194 72 12844 ETV3 0 . GRCh38 1 157125966 157125966 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.414G>C p.Gln138His p.Q138H ENST00000368192 5/5 104 86 18 60 60 0 strelka-varscan-mutect ETV3,missense_variant,p.Gln138His,ENST00000368192,NM_001145312.1;CYCSP52,upstream_gene_variant,,ENST00000422857,; G ENST00000368192 Transcript missense_variant 479/5254 414/1539 138/512 Q/H caG/caC 1 -1 ETV3 HGNC HGNC:3492 protein_coding YES CCDS44250.1 ENSP00000357175 P41162 UPI0000071047 NM_001145312.1 deleterious(0.01) 5/5 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF30,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS rs1223278264 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 157125966 157125966 C G 1 0 0 0 0 1 0 0 0 5143 912 32 4 4 ETV3 1 157125966 Missense_Mutation SNP C C3N-00294_T 381738 157125966 91830456 73 12845 FCRL4 0 . GRCh38 1 157587354 157587354 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.769G>T p.Gly257Ter p.G257* ENST00000271532 5/12 412 175 237 313 312 1 strelka-varscan-mutect FCRL4,stop_gained,p.Gly257Ter,ENST00000271532,NM_031282.2;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,; A ENST00000271532 Transcript stop_gained 905/3459 769/1548 257/515 G/* Gga/Tga 1 -1 FCRL4 HGNC HGNC:18507 protein_coding YES CCDS1166.1 ENSP00000271532 Q96PJ5 UPI000006E26B NM_031282.2 5/12 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF59,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 157587354 157587354 C A 1 0 0 0 0 0 1 0 0 5659 690 24 2 2 FCRL4 1 157587354 Nonsense_Mutation SNP C C3N-00294_T 461388 157587354 91369068 74 12846 KIRREL 0 . GRCh38 1 158094696 158094696 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1850C>A p.Ser617Tyr p.S617Y ENST00000359209 15/15 174 149 25 137 137 0 strelka-varscan-mutect KIRREL,missense_variant,p.Ser517Tyr,ENST00000368173,NM_001286349.1;KIRREL,missense_variant,p.Ser431Tyr,ENST00000368172,;KIRREL,missense_variant,p.Ser453Tyr,ENST00000360089,;KIRREL,missense_variant,p.Ser617Tyr,ENST00000359209,NM_018240.6; A ENST00000359209 Transcript missense_variant 1917/2874 1850/2274 617/757 S/Y tCc/tAc 1 1 KIRREL HGNC HGNC:15734 protein_coding YES CCDS1172.2 ENSP00000352138 Q96J84 UPI0000443FBD NM_018240.6 deleterious(0) 15/15 hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 158094696 158094696 C A 1 0 0 0 0 1 0 0 0 8188 855 30 2 2 KIRREL 1 158094696 Missense_Mutation SNP C C3N-00294_T 507342 158094696 90861726 75 12847 SPTA1 0 . GRCh38 1 158671384 158671384 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.1558G>A p.Asp520Asn p.D520N ENST00000368147 12/52 583 509 74 429 429 0 strelka-varscan-mutect SPTA1,missense_variant,p.Asp520Asn,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 1739/7999 1558/7260 520/2419 D/N Gac/Aac COSM164577 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.11) 12/52 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 158671384 158671384 C T 1 0 0 0 0 1 0 0 0 15472 913 32 3 3 SPTA1 1 158671384 Missense_Mutation SNP C C3N-00294_T 576688 158671384 90285038 76 12848 SPTA1 0 . GRCh38 1 158680681 158680681 + Missense_Mutation SNP C C T rs367689703 C3N-00294_T C3N-00294_N C C c.580G>A p.Glu194Lys p.E194K ENST00000368147 5/52 645 558 87 409 408 1 strelka-varscan-mutect SPTA1,missense_variant,p.Glu194Lys,ENST00000368147,NM_003126.2;SPTA1,intron_variant,,ENST00000467387,; T ENST00000368147 Transcript missense_variant 761/7999 580/7260 194/2419 E/K Gaa/Aaa rs367689703 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 5/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs367689703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 158680681 158680681 C T 1 0 0 0 0 1 0 0 0 15472 893 31 1 1 SPTA1 1 158680681 Missense_Mutation SNP C C3N-00294_T 9297 158680681 90275741 77 12849 FCER1A 0 . GRCh38 1 159307832 159307832 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.674C>G p.Ser225Ter p.S225* ENST00000368115 6/6 165 144 21 142 142 0 strelka-varscan-mutect FCER1A,stop_gained,p.Ser225Ter,ENST00000368115,NM_002001.3;FCER1A,stop_gained,p.Ser192Ter,ENST00000368114,; G ENST00000368115 Transcript stop_gained 773/1165 674/774 225/257 S/* tCa/tGa 1 1 FCER1A HGNC HGNC:3609 protein_coding YES CCDS1184.1 ENSP00000357097 P12319 UPI000002CFDB NM_002001.3 6/6 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF12,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999911 1 1 1 0 G 4 3 46 159307832 159307832 C G 1 0 0 0 0 0 1 0 0 5637 838 29 4 4 FCER1A 1 159307832 Nonsense_Mutation SNP C C3N-00294_T 627151 159307832 89648590 78 12850 SLAMF8 0 . GRCh38 1 159833285 159833285 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.697G>C p.Asp233His p.D233H ENST00000289707 4/5 345 293 52 241 241 0 strelka-varscan-mutect SLAMF8,missense_variant,p.Asp233His,ENST00000289707,NM_020125.2;SLAMF8,missense_variant,p.Asp124His,ENST00000368104,;C1orf204,downstream_gene_variant,,ENST00000368102,NM_001134233.1;C1orf204,downstream_gene_variant,,ENST00000621242,;SLAMF8,non_coding_transcript_exon_variant,,ENST00000471286,;SLAMF8,non_coding_transcript_exon_variant,,ENST00000497141,;C1orf204,downstream_gene_variant,,ENST00000491974,; C ENST00000289707 Transcript missense_variant 846/2996 697/858 233/285 D/H Gat/Cat 1 1 SLAMF8 HGNC HGNC:21391 protein_coding YES CCDS1188.1 ENSP00000289707 Q9P0V8 UPI000003E841 NM_020125.2 deleterious(0.02) 4/5 hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF55 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 159833285 159833285 G C 1 0 0 0 0 1 0 0 0 14635 942 33 4 4 SLAMF8 1 159833285 Missense_Mutation SNP G C3N-00294_T 525453 159833285 89123137 79 12851 SLAMF7 0 . GRCh38 1 160753105 160753105 + Splice_Site SNP G G A novel C3N-00294_T C3N-00294_N G G c.937-1G>A p.X313_splice ENST00000368043 220 183 37 143 143 0 strelka-varscan-mutect SLAMF7,splice_acceptor_variant,,ENST00000368043,NM_021181.4;SLAMF7,splice_acceptor_variant,,ENST00000621377,NM_001282594.1;SLAMF7,splice_acceptor_variant,,ENST00000359331,NM_001282592.1,NM_001282596.1;SLAMF7,splice_acceptor_variant,,ENST00000441662,NM_001282589.1;SLAMF7,splice_acceptor_variant,,ENST00000458602,NM_001282591.1;SLAMF7,splice_acceptor_variant,,ENST00000444090,NM_001282588.1;SLAMF7,splice_acceptor_variant,,ENST00000368042,NM_001282595.1,NM_001282590.1;SLAMF7,splice_acceptor_variant,,ENST00000458104,NM_001282593.1;SLAMF7,downstream_gene_variant,,ENST00000495334,;SLAMF7,downstream_gene_variant,,ENST00000488819,;SLAMF7,splice_acceptor_variant,,ENST00000484221,; A ENST00000368043 Transcript splice_acceptor_variant -/2689 937/1008 313/335 1 1 SLAMF7 HGNC HGNC:21394 protein_coding YES CCDS1209.1 ENSP00000357022 Q9NQ25 UPI00000389DC NM_021181.4 6/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 160753105 160753105 G A 1 0 0 0 0 0 0 1 0 14634 956 33 3 3 SLAMF7 1 160753105 Splice_Site SNP G C3N-00294_T 919820 160753105 88203317 80 12852 ADAMTS4 0 . GRCh38 1 161198188 161198188 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.440G>A p.Gly147Glu p.G147E ENST00000367996 1/9 257 224 33 180 180 0 strelka-varscan-mutect ADAMTS4,missense_variant,p.Gly147Glu,ENST00000367996,NM_005099.4;ADAMTS4,missense_variant,p.Gly147Glu,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000392179,NM_001166159.1;NDUFS2,upstream_gene_variant,,ENST00000367993,NM_004550.4;NDUFS2,intron_variant,,ENST00000496133,;NDUFS2,intron_variant,,ENST00000479948,;NDUFS2,upstream_gene_variant,,ENST00000478866,;NDUFS2,upstream_gene_variant,,ENST00000467295,;NDUFS2,upstream_gene_variant,,ENST00000496553,;NDUFS2,upstream_gene_variant,,ENST00000475570,;ADAMTS4,upstream_gene_variant,,ENST00000478394,; T ENST00000367996 Transcript missense_variant 869/9773 440/2514 147/837 G/E gGa/gAa 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 deleterious(0.01) 1/9 hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 161198188 161198188 C T 1 0 0 0 0 1 0 0 0 312 855 30 3 3 ADAMTS4 1 161198188 Missense_Mutation SNP C C3N-00294_T 445083 161198188 87758234 81 12853 HSPA6 0 . GRCh38 1 161526042 161526042 + Missense_Mutation SNP G G A rs779930805 C3N-00294_T C3N-00294_N G G c.1384G>A p.Glu462Lys p.E462K ENST00000309758 1/1 115 93 22 103 103 0 strelka-varscan-mutect HSPA6,missense_variant,p.Glu462Lys,ENST00000309758,NM_002155.4;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR2A,downstream_gene_variant,,ENST00000491841,;FCGR2A,downstream_gene_variant,,ENST00000467525,; A ENST00000309758 Transcript missense_variant 1503/2371 1384/1932 462/643 E/K Gaa/Aaa rs779930805 1 1 HSPA6 HGNC HGNC:5239 protein_coding YES CCDS1231.1 ENSP00000310219 P17066 UPI0000074238 NM_002155.4 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF168,Pfam_domain:PF00012,Gene3D:2.60.34.10,Superfamily_domains:SSF100920 MODERATE SNV 1 PASS rs779930805 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 161526042 161526042 G A 1 0 0 0 0 1 0 0 0 7311 1291 45 3 3 HSPA6 1 161526042 Missense_Mutation SNP G C3N-00294_T 327854 161526042 87430380 82 12854 NUF2 0 . GRCh38 1 163349036 163349036 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1216C>T p.Gln406Ter p.Q406* ENST00000271452 13/14 89 73 16 138 138 0 strelka-varscan-mutect NUF2,stop_gained,p.Gln406Ter,ENST00000271452,NM_145697.2;NUF2,stop_gained,p.Gln359Ter,ENST00000524800,;NUF2,stop_gained,p.Gln406Ter,ENST00000367900,NM_031423.3;NUF2,downstream_gene_variant,,ENST00000527439,;NUF2,downstream_gene_variant,,ENST00000497990,; T ENST00000271452 Transcript stop_gained 1495/1969 1216/1395 406/464 Q/* Caa/Taa 1 1 NUF2 HGNC HGNC:14621 protein_coding YES CCDS1245.1 ENSP00000271452 Q9BZD4 UPI000006D211 NM_145697.2 13/14 hmmpanther:PTHR21650 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 163349036 163349036 C T 1 0 0 0 0 0 1 0 0 10811 827 29 3 3 NUF2 1 163349036 Nonsense_Mutation SNP C C3N-00294_T 1822994 163349036 85607386 83 12855 RXRG 0 . GRCh38 1 165410774 165410774 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.841G>A p.Val281Ile p.V281I ENST00000359842 6/10 302 272 30 242 241 1 strelka-varscan-mutect RXRG,missense_variant,p.Val158Ile,ENST00000619224,NM_001256570.1,NM_001256571.1;RXRG,missense_variant,p.Val281Ile,ENST00000359842,NM_006917.4;RXRG,non_coding_transcript_exon_variant,,ENST00000470566,; T ENST00000359842 Transcript missense_variant 1144/2041 841/1392 281/463 V/I Gtt/Att COSM1335900 1 -1 RXRG HGNC HGNC:10479 protein_coding YES CCDS1248.1 ENSP00000352900 P48443 F1D8Q7 UPI000004989F NM_006917.4 tolerated(0.11) 6/10 hmmpanther:PTHR24083:SF95,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398 1 MODERATE 1 SNV 1 1 1 PASS rs1416940954 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 165410774 165410774 C T 1 0 0 0 0 1 0 0 0 14026 536 19 1 1 RXRG 1 165410774 Missense_Mutation SNP C C3N-00294_T 2061738 165410774 83545648 84 12856 UCK2 0 . GRCh38 1 165903270 165903270 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.588C>G p.Phe196Leu p.F196L ENST00000367879 5/7 219 184 35 164 164 0 strelka-varscan-mutect UCK2,missense_variant,p.Phe196Leu,ENST00000367879,NM_012474.4;UCK2,missense_variant,p.Phe46Leu,ENST00000470820,;UCK2,missense_variant,p.Phe46Leu,ENST00000469256,;UCK2,upstream_gene_variant,,ENST00000636291,;RP11-525G13.2,upstream_gene_variant,,ENST00000626270,;RP11-525G13.2,upstream_gene_variant,,ENST00000455257,;UCK2,non_coding_transcript_exon_variant,,ENST00000462329,;UCK2,non_coding_transcript_exon_variant,,ENST00000464197,;UCK2,non_coding_transcript_exon_variant,,ENST00000463772,;UCK2,upstream_gene_variant,,ENST00000475333,;UCK2,non_coding_transcript_exon_variant,,ENST00000479872,; G ENST00000367879 Transcript missense_variant 891/1375 588/786 196/261 F/L ttC/ttG 1 1 UCK2 HGNC HGNC:12562 protein_coding YES CCDS1252.1 ENSP00000356853 Q9BZX2 A0A024R912 UPI000003AFFE NM_012474.4 deleterious(0) 5/7 Gene3D:3.40.50.300,Pfam_domain:PF00485,Prints_domain:PR00988,hmmpanther:PTHR10285,hmmpanther:PTHR10285:SF28,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 165903270 165903270 C G 1 0 0 0 0 1 0 0 0 17448 912 32 4 4 UCK2 1 165903270 Missense_Mutation SNP C C3N-00294_T 492496 165903270 83053152 85 12857 ILDR2 0 . GRCh38 1 166921229 166921229 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1362G>A p.= p.G454G ENST00000271417 9/10 189 158 31 116 116 0 strelka-varscan-mutect ILDR2,synonymous_variant,p.=,ENST00000271417,NM_199351.2;ILDR2,synonymous_variant,p.=,ENST00000529071,;ILDR2,synonymous_variant,p.=,ENST00000528703,;ILDR2,synonymous_variant,p.=,ENST00000526687,;ILDR2,synonymous_variant,p.=,ENST00000525740,;ILDR2,intron_variant,,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; T ENST00000271417 Transcript synonymous_variant 1418/13140 1362/1920 454/639 G ggG/ggA 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 9/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 166921229 166921229 C T 1 0 0 0 0 0 0 0 1 7613 842 30 3 3 ILDR2 1 166921229 Silent SNP C C3N-00294_T 1017959 166921229 82035193 86 12858 F5 0 . GRCh38 1 169523206 169523206 + Silent SNP C C T rs767055534 C3N-00294_T C3N-00294_N C C c.6039G>A p.= p.R2013R ENST00000367797 21/25 415 364 51 335 334 1 strelka-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4; T ENST00000367797 Transcript synonymous_variant 6241/7024 6039/6675 2013/2224 R agG/agA rs767055534,COSM3771512 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 21/25 PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.120.260,PIRSF_domain:PIRSF000354,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 0,1 LOW 1 SNV 1 0,1 1 PASS rs767055534 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 169523206 169523206 C T 1 0 0 0 0 0 0 0 1 5216 854 30 3 3 F5 1 169523206 Silent SNP C C3N-00294_T 2601977 169523206 79433216 87 12859 F5 0 . GRCh38 1 169540502 169540502 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.4588G>C p.Glu1530Gln p.E1530Q ENST00000367797 13/25 528 445 83 485 485 0 strelka-varscan-mutect F5,missense_variant,p.Glu1535Gln,ENST00000367796,;F5,missense_variant,p.Glu1530Gln,ENST00000367797,NM_000130.4; G ENST00000367797 Transcript missense_variant 4790/7024 4588/6675 1530/2224 E/Q Gag/Cag 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 tolerated(0.12) 13/25 PIRSF_domain:PIRSF000354 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 169540502 169540502 C G 1 0 0 0 0 1 0 0 0 5216 922 32 4 4 F5 1 169540502 Missense_Mutation SNP C C3N-00294_T 17296 169540502 79415920 88 12860 C1orf105 0 . GRCh38 1 172468475 172468475 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.433C>G p.Leu145Val p.L145V ENST00000367727 7/7 121 100 21 87 87 0 strelka-varscan-mutect C1orf105,missense_variant,p.Leu145Val,ENST00000367727,NM_139240.3;C1orf105,missense_variant,p.Leu135Val,ENST00000367725,NM_001300760.1;C1orf105,downstream_gene_variant,,ENST00000488100,;C1orf105,non_coding_transcript_exon_variant,,ENST00000367726,; G ENST00000367727 Transcript missense_variant 631/985 433/552 145/183 L/V Ctg/Gtg 1 1 C1orf105 HGNC HGNC:29591 protein_coding YES CCDS1301.1 ENSP00000356700 O95561 UPI000006D456 NM_139240.3 tolerated(0.1) 7/7 Pfam_domain:PF15081,hmmpanther:PTHR39410,hmmpanther:PTHR39410:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 172468475 172468475 C G 1 0 0 0 0 1 0 0 0 1955 912 32 4 4 C1orf105 1 172468475 Missense_Mutation SNP C C3N-00294_T 2927973 172468475 76487947 89 12861 DARS2 0 . GRCh38 1 173857679 173857679 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1912G>C p.Asp638His p.D638H ENST00000361951 17/17 409 353 56 307 307 0 strelka-varscan-mutect DARS2,missense_variant,p.Asp638His,ENST00000361951,NM_018122.4;DARS2,non_coding_transcript_exon_variant,,ENST00000471476,; C ENST00000361951 Transcript missense_variant 2639/3506 1912/1938 638/645 D/H Gac/Cac 1 1 DARS2 HGNC HGNC:25538 protein_coding YES CCDS1311.1 ENSP00000355086 Q6PI48 A0A024R8Z9 UPI00001C1D5B NM_018122.4 deleterious_low_confidence(0.03) 17/17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 173857679 173857679 G C 1 0 0 0 0 1 0 0 0 4042 942 33 4 4 DARS2 1 173857679 Missense_Mutation SNP G C3N-00294_T 1389204 173857679 75098743 90 12862 GPR52 0 . GRCh38 1 174448990 174448990 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.879G>C p.Leu293Phe p.L293F ENST00000367685 1/1 200 168 32 136 136 0 strelka-varscan-mutect GPR52,missense_variant,p.Leu293Phe,ENST00000367685,NM_005684.4;RABGAP1L,intron_variant,,ENST00000251507,NM_014857.4;RABGAP1L,intron_variant,,ENST00000357444,;RABGAP1L,intron_variant,,ENST00000367690,;RABGAP1L,intron_variant,,ENST00000526253,; C ENST00000367685 Transcript missense_variant 880/1088 879/1086 293/361 L/F ttG/ttC 1 1 GPR52 HGNC HGNC:4508 protein_coding YES CCDS30941.1 ENSP00000356658 Q9Y2T5 F2YGU0 UPI0000153A3C NM_005684.4 tolerated(0.28) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF248,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 174448990 174448990 G C 1 0 0 0 0 1 0 0 0 6583 1339 47 4 4 GPR52 1 174448990 Missense_Mutation SNP G C3N-00294_T 591311 174448990 74507432 91 12863 TNN 0 . GRCh38 1 175077433 175077433 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.15G>C p.Glu5Asp p.E5D ENST00000239462 2/19 102 86 16 79 79 0 strelka-varscan-mutect TNN,missense_variant,p.Glu5Asp,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Glu5Asp,ENST00000621086,;TNN,missense_variant,p.Glu5Asp,ENST00000622870,; C ENST00000239462 Transcript missense_variant 128/5008 15/3900 5/1299 E/D gaG/gaC 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 tolerated_low_confidence(0.16) 2/19 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 175077433 175077433 G C 1 0 0 0 0 1 0 0 0 16796 933 33 4 4 TNN 1 175077433 Missense_Mutation SNP G C3N-00294_T 628443 175077433 73878989 92 12864 TNN 0 . GRCh38 1 175098549 175098549 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.2073G>A p.= p.Q691Q ENST00000239462 9/19 424 363 61 324 324 0 strelka-varscan-mutect TNN,synonymous_variant,p.=,ENST00000239462,NM_022093.1;TNN,intron_variant,,ENST00000621086,;TNN,intron_variant,,ENST00000622870,; A ENST00000239462 Transcript synonymous_variant 2186/5008 2073/3900 691/1299 Q caG/caA COSM122097 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 9/19 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 LOW 1 SNV 2 1 1 PASS rs989120933 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 175098549 175098549 G A 1 0 0 0 0 0 0 0 1 16796 933 33 3 3 TNN 1 175098549 Silent SNP G C3N-00294_T 21116 175098549 73857873 93 12865 PAPPA2 0 . GRCh38 1 176594952 176594952 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1348G>A p.Glu450Lys p.E450K ENST00000367662 3/23 374 314 60 283 282 1 strelka-varscan-mutect PAPPA2,missense_variant,p.Glu450Lys,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Glu450Lys,ENST00000367661,NM_021936.2; A ENST00000367662 Transcript missense_variant 2512/9691 1348/5376 450/1791 E/K Gaa/Aaa 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated(0.33) 3/23 MODERATE 1 SNV 1 1 PASS rs1267699588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 176594952 176594952 G A 1 0 0 0 0 1 0 0 0 11513 1175 41 3 3 PAPPA2 1 176594952 Missense_Mutation SNP G C3N-00294_T 1496403 176594952 72361470 94 12866 RASAL2 0 . GRCh38 1 178445585 178445585 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1550G>C p.Arg517Thr p.R517T ENST00000367649 9/18 245 210 35 171 171 0 strelka-varscan-mutect RASAL2,missense_variant,p.Arg369Thr,ENST00000462775,NM_004841.3;RASAL2,missense_variant,p.Arg517Thr,ENST00000367649,NM_170692.2; C ENST00000367649 Transcript missense_variant 1902/4378 1550/3843 517/1280 R/T aGa/aCa 1 1 RASAL2 HGNC HGNC:9874 protein_coding YES CCDS1321.2 ENSP00000356621 Q9UJF2 UPI00019B254F NM_170692.2 deleterious(0) 9/18 Gene3D:1.10.506.10,PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF52,SMART_domains:SM00323,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 178445585 178445585 G C 1 0 0 0 0 1 0 0 0 13225 942 33 4 4 RASAL2 1 178445585 Missense_Mutation SNP G C3N-00294_T 1850633 178445585 70510837 95 12867 XPR1 0 . GRCh38 1 180803397 180803397 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.233C>A p.Ala78Glu p.A78E ENST00000367590 4/15 208 172 36 134 133 1 strelka-varscan-mutect XPR1,missense_variant,p.Ala78Glu,ENST00000367590,NM_004736.3;XPR1,missense_variant,p.Ala78Glu,ENST00000367589,NM_001135669.1; A ENST00000367590 Transcript missense_variant 431/8474 233/2091 78/696 A/E gCa/gAa 1 1 XPR1 HGNC HGNC:12827 protein_coding YES CCDS1340.1 ENSP00000356562 Q9UBH6 A0A024R911 UPI0000071111 NM_004736.3 deleterious(0) 4/15 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51382,hmmpanther:PTHR10783,hmmpanther:PTHR10783:SF40,Pfam_domain:PF03105 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 180803397 180803397 C A 1 0 0 0 0 1 0 0 0 18010 710 25 2 2 XPR1 1 180803397 Missense_Mutation SNP C C3N-00294_T 2357812 180803397 68153025 96 12868 TEDDM1 0 . GRCh38 1 182400458 182400458 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.28C>G p.Pro10Ala p.P10A ENST00000367565 1/1 105 88 17 79 79 0 strelka-varscan-mutect TEDDM1,missense_variant,p.Pro10Ala,ENST00000367565,NM_172000.3; C ENST00000367565 Transcript missense_variant 159/2500 28/822 10/273 P/A Cct/Gct 1 -1 TEDDM1 HGNC HGNC:30233 protein_coding YES CCDS30953.1 ENSP00000356536 Q5T9Z0 UPI0000470B8B NM_172000.3 deleterious(0.04) 1/1 hmmpanther:PTHR16007,hmmpanther:PTHR16007:SF16 MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 182400458 182400458 G C 1 0 0 0 0 1 0 0 0 16160 1174 41 4 4 TEDDM1 1 182400458 Missense_Mutation SNP G C3N-00294_T 1597061 182400458 66555964 97 12869 LAMC1 0 . GRCh38 1 183134752 183134752 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3942G>A p.Met1314Ile p.M1314I ENST00000258341 23/28 118 104 14 117 116 1 strelka-varscan-mutect LAMC1,missense_variant,p.Met1314Ile,ENST00000258341,NM_002293.3;RP11-181K3.4,downstream_gene_variant,,ENST00000457852,;LAMC1,non_coding_transcript_exon_variant,,ENST00000495918,;LAMC1,downstream_gene_variant,,ENST00000478064,; A ENST00000258341 Transcript missense_variant 4199/7889 3942/4830 1314/1609 M/I atG/atA 1 1 LAMC1 HGNC HGNC:6492 protein_coding YES CCDS1351.1 ENSP00000258341 P11047 UPI000013CFC7 NM_002293.3 tolerated(0.28) 23/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF270,Superfamily_domains:SSF57997 MODERATE 1 SNV 1 1 PASS rs1465090734 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 183134752 183134752 G A 1 0 0 0 0 1 0 0 0 8518 1290 45 3 3 LAMC1 1 183134752 Missense_Mutation SNP G C3N-00294_T 734294 183134752 65821670 98 12870 SMG7 0 . GRCh38 1 183537204 183537204 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1223C>G p.Ser408Ter p.S408* ENST00000507469 11/23 155 133 22 128 128 0 strelka-varscan-mutect SMG7,stop_gained,p.Ser437Ter,ENST00000367537,;SMG7,stop_gained,p.Ser408Ter,ENST00000347615,NM_173156.2;SMG7,stop_gained,p.Ser408Ter,ENST00000515829,NM_201568.2;SMG7,stop_gained,p.Ser408Ter,ENST00000507469,NM_201569.2;SMG7,stop_gained,p.Ser366Ter,ENST00000508461,NM_001174061.1;SMG7,stop_gained,p.Ser366Ter,ENST00000419169,; G ENST00000507469 Transcript stop_gained 1341/4642 1223/3537 408/1178 S/* tCa/tGa 1 1 SMG7 HGNC HGNC:16792 protein_coding YES CCDS41445.2 ENSP00000425133 Q92540 UPI0000D6205B NM_201569.2 11/23 Pfam_domain:PF10373,Superfamily_domains:SSF48452 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 183537204 183537204 C G 1 0 0 0 0 0 1 0 0 15092 838 29 4 4 SMG7 1 183537204 Nonsense_Mutation SNP C C3N-00294_T 402452 183537204 65419218 99 12871 RNF2 0 . GRCh38 1 185091624 185091624 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.133C>G p.Leu45Val p.L45V ENST00000367510 3/7 175 152 23 110 110 0 strelka-varscan-mutect RNF2,missense_variant,p.Leu45Val,ENST00000367510,NM_007212.3;RNF2,missense_variant,p.Leu45Val,ENST00000367509,;RNF2,missense_variant,p.Leu45Val,ENST00000453650,;RNF2,non_coding_transcript_exon_variant,,ENST00000498201,; G ENST00000367510 Transcript missense_variant 421/3606 133/1011 45/336 L/V Cta/Gta COSM424789 1 1 RNF2 HGNC HGNC:10061 protein_coding YES CCDS1365.1 ENSP00000356480 Q99496 UPI000007131D NM_007212.3 deleterious(0) 3/7 Gene3D:3.30.40.10,hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF41,Superfamily_domains:SSF57850 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 185091624 185091624 C G 1 0 0 0 0 1 0 0 0 13650 912 32 4 4 RNF2 1 185091624 Missense_Mutation SNP C C3N-00294_T 1554420 185091624 63864798 100 12872 HMCN1 0 . GRCh38 1 185922430 185922430 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.952G>A p.Asp318Asn p.D318N ENST00000271588 7/107 522 458 64 429 429 0 strelka-varscan-mutect HMCN1,missense_variant,p.Asp318Asn,ENST00000271588,NM_031935.2; A ENST00000271588 Transcript missense_variant 1181/18208 952/16908 318/5635 D/N Gat/Aat 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.1) 7/107 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 185922430 185922430 G A 1 0 0 0 0 1 0 0 0 7111 1290 45 3 3 HMCN1 1 185922430 Missense_Mutation SNP G C3N-00294_T 830806 185922430 63033992 101 12873 HMCN1 0 . GRCh38 1 185977925 185977925 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2510G>A p.Arg837Lys p.R837K ENST00000271588 16/107 217 187 30 246 246 0 strelka-varscan-mutect HMCN1,missense_variant,p.Arg837Lys,ENST00000271588,NM_031935.2;HMCN1,non_coding_transcript_exon_variant,,ENST00000485744,;HMCN1,non_coding_transcript_exon_variant,,ENST00000493413,; A ENST00000271588 Transcript missense_variant 2739/18208 2510/16908 837/5635 R/K aGa/aAa COSM2122396 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.14) 16/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 185977925 185977925 G A 1 0 0 0 0 1 0 0 0 7111 942 33 3 3 HMCN1 1 185977925 Missense_Mutation SNP G C3N-00294_T 55495 185977925 62978497 102 12874 C1orf27 0 . GRCh38 1 186398987 186398987 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.943G>A p.Asp315Asn p.D315N ENST00000287859 11/14 122 110 12 154 154 0 strelka-mutect C1orf27,missense_variant,p.Asp315Asn,ENST00000287859,NM_017847.5;C1orf27,missense_variant,p.Asp292Asn,ENST00000367470,NM_001164245.1;C1orf27,missense_variant,p.Asp283Asn,ENST00000419367,NM_001164246.1;OCLM,upstream_gene_variant,,ENST00000574641,NM_022375.3;AL596220.1,upstream_gene_variant,,ENST00000623025,;C1orf27,non_coding_transcript_exon_variant,,ENST00000478571,; A ENST00000287859 Transcript missense_variant 1068/3792 943/1365 315/454 D/N Gat/Aat 1 1 C1orf27 HGNC HGNC:24299 protein_coding YES CCDS53448.1 ENSP00000287859 Q5SWX8 UPI00003744FF NM_017847.5 tolerated(0.1) 11/14 Pfam_domain:PF14778,hmmpanther:PTHR33966,hmmpanther:PTHR33966:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -17.68433 0.9999849 1 1 1 0 A 3 1 46 186398987 186398987 G A 1 0 0 0 0 1 0 0 0 1987 1290 45 3 3 C1orf27 1 186398987 Missense_Mutation SNP G C3N-00294_T 421062 186398987 62557435 103 12875 PTPRC 0 . GRCh38 1 198709743 198709743 + Missense_Mutation SNP G G C rs781133917 C3N-00294_T C3N-00294_N G G c.1090G>C p.Glu364Gln p.E364Q ENST00000442510 11/33 96 82 14 128 128 0 strelka-varscan-mutect PTPRC,missense_variant,p.Glu364Gln,ENST00000442510,NM_002838.4;PTPRC,missense_variant,p.Glu203Gln,ENST00000348564,NM_080921.3;PTPRC,missense_variant,p.Glu298Gln,ENST00000367367,;PTPRC,missense_variant,p.Glu250Gln,ENST00000530727,;PTPRC,downstream_gene_variant,,ENST00000367379,;PTPRC,missense_variant,p.Glu316Gln,ENST00000529828,;PTPRC,upstream_gene_variant,,ENST00000491302,; C ENST00000442510 Transcript missense_variant 1231/5164 1090/3921 364/1306 E/Q Gag/Cag rs781133917,CD012009 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 tolerated(0.38) 11/33 PIRSF_domain:PIRSF002004,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF284 MODERATE 1 SNV 1 0,1 1 PASS rs781133917 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 198709743 198709743 G C 1 0 0 0 0 1 0 0 0 12951 1291 45 4 4 PTPRC 1 198709743 Missense_Mutation SNP G C3N-00294_T 12310756 198709743 50246679 104 12876 PTPRC 0 . GRCh38 1 198712956 198712956 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1175C>T p.Pro392Leu p.P392L ENST00000442510 12/33 198 93 105 262 262 0 strelka-varscan-mutect PTPRC,missense_variant,p.Pro392Leu,ENST00000442510,NM_002838.4;PTPRC,missense_variant,p.Pro231Leu,ENST00000348564,NM_080921.3;PTPRC,missense_variant,p.Pro326Leu,ENST00000367367,;PTPRC,missense_variant,p.Pro278Leu,ENST00000530727,;PTPRC,downstream_gene_variant,,ENST00000367379,;PTPRC,missense_variant,p.Pro344Leu,ENST00000529828,;PTPRC,non_coding_transcript_exon_variant,,ENST00000491302,; T ENST00000442510 Transcript missense_variant 1316/5164 1175/3921 392/1306 P/L cCa/cTa 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 deleterious(0) 12/33 Gene3D:2.60.40.10,PIRSF_domain:PIRSF002004,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF284,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 198712956 198712956 C T 1 0 0 0 0 1 0 0 0 12951 608 21 3 3 PTPRC 1 198712956 Missense_Mutation SNP C C3N-00294_T 3213 198712956 50243466 105 12877 CAMSAP2 0 . GRCh38 1 200739857 200739857 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.30G>T p.Met10Ile p.M10I ENST00000236925 1/18 201 185 16 142 142 0 strelka-mutect CAMSAP2,missense_variant,p.Met10Ile,ENST00000358823,NM_203459.2;CAMSAP2,missense_variant,p.Met10Ile,ENST00000236925,NM_001297707.1;CAMSAP2,missense_variant,p.Met10Ile,ENST00000413307,NM_001297708.1; T ENST00000236925 Transcript missense_variant 79/7161 30/4470 10/1489 M/I atG/atT COSM3789305,COSM3789306 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 tolerated(0.29) 1/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 200739857 200739857 G T 1 0 0 0 0 1 0 0 0 2304 1290 45 2 2 CAMSAP2 1 200739857 Missense_Mutation SNP G C3N-00294_T 2026901 200739857 48216565 106 12878 CAMSAP2 0 . GRCh38 1 200850105 200850105 + Silent SNP G G C rs748971172 C3N-00294_T C3N-00294_N G G c.3369G>C p.= p.L1123L ENST00000236925 12/18 85 76 9 76 76 0 strelka-varscan-mutect CAMSAP2,synonymous_variant,p.=,ENST00000358823,NM_203459.2;CAMSAP2,synonymous_variant,p.=,ENST00000236925,NM_001297707.1;CAMSAP2,synonymous_variant,p.=,ENST00000413307,NM_001297708.1;CAMSAP2,intron_variant,,ENST00000447701,; C ENST00000236925 Transcript synonymous_variant 3418/7161 3369/4470 1123/1489 L ctG/ctC rs748971172 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 12/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 LOW 1 SNV 1 1 PASS rs748971172 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 200850105 200850105 G C 1 0 0 0 0 0 0 0 1 2304 1277 45 4 4 CAMSAP2 1 200850105 Silent SNP G C3N-00294_T 110248 200850105 48106317 107 12879 CAMSAP2 0 . GRCh38 1 200850148 200850148 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3412G>C p.Asp1138His p.D1138H ENST00000236925 12/18 55 51 4 58 58 0 strelka-varscan-mutect CAMSAP2,missense_variant,p.Asp1127His,ENST00000358823,NM_203459.2;CAMSAP2,missense_variant,p.Asp1138His,ENST00000236925,NM_001297707.1;CAMSAP2,missense_variant,p.Asp1111His,ENST00000413307,NM_001297708.1;CAMSAP2,intron_variant,,ENST00000447701,; C ENST00000236925 Transcript missense_variant 3461/7161 3412/4470 1138/1489 D/H Gat/Cat 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 deleterious(0.01) 12/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -9.913533 0.9999979 1 1 1 0 C 3 2 46 200850148 200850148 G C 1 0 0 0 0 1 0 0 0 2304 1290 45 4 4 CAMSAP2 1 200850148 Missense_Mutation SNP G C3N-00294_T 43 200850148 48106274 108 12880 C1orf106 0 . GRCh38 1 200901084 200901084 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.445G>C p.Glu149Gln p.E149Q ENST00000413687 5/10 181 162 19 136 136 0 strelka-varscan-mutect C1orf106,missense_variant,p.Glu234Gln,ENST00000367342,NM_018265.3;C1orf106,missense_variant,p.Glu149Gln,ENST00000413687,NM_001142569.2;C1orf106,downstream_gene_variant,,ENST00000451872,;C1orf106,downstream_gene_variant,,ENST00000532631,;C1orf106,upstream_gene_variant,,ENST00000531649,; C ENST00000413687 Transcript missense_variant 806/2197 445/1737 149/578 E/Q Gag/Cag 1 1 C1orf106 HGNC HGNC:25599 protein_coding YES CCDS44292.1 ENSP00000392105 Q3KP66 UPI0000204714 NM_001142569.2 tolerated(0.17) 5/10 hmmpanther:PTHR16093,hmmpanther:PTHR16093:SF4 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 200901084 200901084 G C 1 0 0 0 0 1 0 0 0 1956 1175 41 4 4 C1orf106 1 200901084 Missense_Mutation SNP G C3N-00294_T 50936 200901084 48055338 109 12881 IGFN1 0 . GRCh38 1 201212275 201212275 + Missense_Mutation SNP G G A rs143334493 C3N-00294_T C3N-00294_N G G c.7382G>A p.Arg2461Gln p.R2461Q ENST00000335211 12/24 166 139 27 135 135 0 strelka-varscan-mutect IGFN1,missense_variant,p.Arg2461Gln,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,; A ENST00000335211 Transcript missense_variant 7512/11810 7382/11127 2461/3708 R/Q cGa/cAa rs143334493 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 tolerated(1) 12/24 MODERATE 1 SNV 5 1 PASS rs143334493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 201212275 201212275 G A 1 0 0 0 0 1 0 0 0 7497 1058 37 1 1 IGFN1 1 201212275 Missense_Mutation SNP G C3N-00294_T 311191 201212275 47744147 110 12882 IGFN1 0 . GRCh38 1 201212398 201212398 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.7505C>G p.Ser2502Cys p.S2502C ENST00000335211 12/24 295 253 42 212 212 0 strelka-varscan-mutect IGFN1,missense_variant,p.Ser2502Cys,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,; G ENST00000335211 Transcript missense_variant 7635/11810 7505/11127 2502/3708 S/C tCt/tGt 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0.02) 12/24 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF630 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 201212398 201212398 C G 1 0 0 0 0 1 0 0 0 7497 913 32 4 4 IGFN1 1 201212398 Missense_Mutation SNP C C3N-00294_T 123 201212398 47744024 111 12883 NAV1 0 . GRCh38 1 201781197 201781197 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1551G>A p.= p.L517L ENST00000367296 5/30 361 315 46 300 300 0 strelka-varscan-mutect NAV1,synonymous_variant,p.=,ENST00000367296,NM_020443.4;NAV1,synonymous_variant,p.=,ENST00000367295,NM_001167738.1;NAV1,synonymous_variant,p.=,ENST00000367302,;NAV1,synonymous_variant,p.=,ENST00000430015,;IPO9-AS1,intron_variant,,ENST00000413035,;NAV1,non_coding_transcript_exon_variant,,ENST00000490213,;NAV1,upstream_gene_variant,,ENST00000469130,; A ENST00000367296 Transcript synonymous_variant 1971/13091 1551/5634 517/1877 L ctG/ctA 1 1 NAV1 HGNC HGNC:15989 protein_coding YES CCDS1414.2 ENSP00000356265 Q8NEY1 UPI00004562D4 NM_020443.4 5/30 hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF3 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 201781197 201781197 G A 1 0 0 0 0 0 0 0 1 10192 1277 45 3 3 NAV1 1 201781197 Silent SNP G C3N-00294_T 568799 201781197 47175225 112 12884 IPO9 0 . GRCh38 1 201855164 201855164 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.952G>C p.Asp318His p.D318H ENST00000361565 9/24 75 70 5 92 92 0 strelka-varscan-mutect IPO9,missense_variant,p.Asp318His,ENST00000361565,NM_018085.4;IPO9,downstream_gene_variant,,ENST00000464348,;IPO9,downstream_gene_variant,,ENST00000479374,; C ENST00000361565 Transcript missense_variant 1021/11435 952/3126 318/1041 D/H Gat/Cat 1 1 IPO9 HGNC HGNC:19425 protein_coding YES CCDS1415.1 ENSP00000354742 Q96P70 UPI000007304B NM_018085.4 deleterious(0.03) 9/24 hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF9,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -11.53146 1 1 1 1 0 C 3 2 46 201855164 201855164 G C 1 0 0 0 0 1 0 0 0 7702 942 33 4 4 IPO9 1 201855164 Missense_Mutation SNP G C3N-00294_T 73967 201855164 47101258 113 12885 LMOD1 0 . GRCh38 1 201899466 201899466 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1547C>T p.Ser516Phe p.S516F ENST00000367288 2/3 358 311 47 281 279 2 strelka-varscan-mutect LMOD1,missense_variant,p.Ser516Phe,ENST00000367288,NM_012134.2;LMOD1,intron_variant,,ENST00000616739,;RP11-307B6.3,intron_variant,,ENST00000458139,;RP11-307B6.3,intron_variant,,ENST00000414927,; A ENST00000367288 Transcript missense_variant 1794/3970 1547/1803 516/600 S/F tCt/tTt 1 -1 LMOD1 HGNC HGNC:6647 protein_coding YES CCDS53457.1 ENSP00000356257 P29536 UPI00003665F4 NM_012134.2 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 201899466 201899466 G A 1 0 0 0 0 1 0 0 0 8783 942 33 3 3 LMOD1 1 201899466 Missense_Mutation SNP G C3N-00294_T 44302 201899466 47056956 114 12886 GPR37L1 0 . GRCh38 1 202123422 202123422 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.459C>T p.= p.C153C ENST00000367282 1/2 289 243 46 233 233 0 strelka-varscan-mutect GPR37L1,synonymous_variant,p.=,ENST00000367282,NM_004767.3; T ENST00000367282 Transcript synonymous_variant 565/6588 459/1446 153/481 C tgC/tgT 1 1 GPR37L1 HGNC HGNC:14923 protein_coding YES CCDS1420.1 ENSP00000356251 O60883 UPI000013E92C NM_004767.3 1/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF33,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 202123422 202123422 C T 1 0 0 0 0 0 0 0 1 6577 718 25 3 3 GPR37L1 1 202123422 Silent SNP C C3N-00294_T 223956 202123422 46833000 115 12887 CD46 0 . GRCh38 1 207761336 207761336 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.563C>T p.Thr188Ile p.T188I ENST00000322875 5/13 308 260 48 241 241 0 strelka-varscan-mutect CD46,missense_variant,p.Thr188Ile,ENST00000358170,NM_002389.4;CD46,missense_variant,p.Thr188Ile,ENST00000367042,NM_172351.2;CD46,missense_variant,p.Thr188Ile,ENST00000367041,NM_172352.2;CD46,missense_variant,p.Thr188Ile,ENST00000322875,NM_172359.2;CD46,missense_variant,p.Thr188Ile,ENST00000354848,NM_153826.3;CD46,missense_variant,p.Thr188Ile,ENST00000357714,NM_172353.2;CD46,missense_variant,p.Thr188Ile,ENST00000322918,NM_172350.2;CD46,missense_variant,p.Thr125Ile,ENST00000367047,;CD46,missense_variant,p.Thr188Ile,ENST00000360212,NM_172361.2;CD46,missense_variant,p.Thr188Ile,ENST00000480003,;CD46,non_coding_transcript_exon_variant,,ENST00000469535,;CD46,downstream_gene_variant,,ENST00000493796,;CD46,non_coding_transcript_exon_variant,,ENST00000464082,;CDCA4P4,upstream_gene_variant,,ENST00000435216,; T ENST00000322875 Transcript missense_variant 719/3278 563/1200 188/399 T/I aCt/aTt 1 1 CD46 HGNC HGNC:6953 protein_coding YES CCDS1482.1 ENSP00000313875 P15529 UPI000015FF6E NM_172359.2 tolerated(0.22) 5/13 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF384,hmmpanther:PTHR19325,PIRSF_domain:PIRSF037971,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999941 1 1 1 0 T 3 4 46 207761336 207761336 C T 1 0 0 0 0 1 0 0 0 2722 565 20 3 3 CD46 1 207761336 Missense_Mutation SNP C C3N-00294_T 5637914 207761336 41195086 116 12888 LAMB3 0 . GRCh38 1 209627542 209627542 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1326G>T p.Met442Ile p.M442I ENST00000391911 11/22 359 139 220 292 292 0 strelka-varscan-mutect LAMB3,missense_variant,p.Met442Ile,ENST00000391911,NM_001017402.1;LAMB3,missense_variant,p.Met442Ile,ENST00000356082,NM_000228.2;LAMB3,missense_variant,p.Met442Ile,ENST00000367030,NM_001127641.1;LAMB3,upstream_gene_variant,,ENST00000583107,; A ENST00000391911 Transcript missense_variant 1716/4305 1326/3519 442/1172 M/I atG/atT 1 -1 LAMB3 HGNC HGNC:6490 protein_coding YES CCDS1487.1 ENSP00000375778 Q13751 A0A0S2Z3R6 UPI000012E76F NM_001017402.1 tolerated(0.16) 11/22 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF268,hmmpanther:PTHR10574,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 209627542 209627542 C A 1 0 0 0 0 1 0 0 0 8516 710 25 2 2 LAMB3 1 209627542 Missense_Mutation SNP C C3N-00294_T 1866206 209627542 39328880 117 12889 TATDN3 0 . GRCh38 1 212802701 212802701 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.259G>A p.Asp87Asn p.D87N ENST00000532324 5/10 128 111 17 136 136 0 strelka-varscan-mutect TATDN3,missense_variant,p.Asp87Asn,ENST00000366974,NM_001042552.2;TATDN3,missense_variant,p.Asp87Asn,ENST00000366973,NM_001042553.2;TATDN3,missense_variant,p.Asp87Asn,ENST00000532324,NM_001146171.1;TATDN3,missense_variant,p.Asp87Asn,ENST00000531963,NM_001146169.1;TATDN3,missense_variant,p.Asp87Asn,ENST00000526997,;TATDN3,missense_variant,p.Asp86Asn,ENST00000530399,;TATDN3,missense_variant,p.Asp87Asn,ENST00000488246,;TATDN3,splice_region_variant,p.=,ENST00000530441,;TATDN3,intron_variant,,ENST00000526641,NM_001146170.1;TATDN3,upstream_gene_variant,,ENST00000527693,;TATDN3,splice_region_variant,,ENST00000525569,;TATDN3,splice_region_variant,,ENST00000530392,;TATDN3,splice_region_variant,,ENST00000497768,;TATDN3,splice_region_variant,p.=,ENST00000525574,;TATDN3,intron_variant,,ENST00000533650,; A ENST00000532324 Transcript missense_variant,splice_region_variant 353/1381 259/846 87/281 D/N Gat/Aat 1 1 TATDN3 HGNC HGNC:27010 protein_coding YES CCDS53475.1 ENSP00000431376 Q17R31 UPI0000205E43 NM_001146171.1 deleterious(0) 5/10 hmmpanther:PTHR10060,hmmpanther:PTHR10060:SF25,Gene3D:3.20.20.140,Pfam_domain:PF01026,PIRSF_domain:PIRSF005902,Superfamily_domains:SSF51556 MODERATE 1 SNV 2 1 PASS . . 0 189 0 15 6 0 0 0 -8.694684 0.09579792 1 1 0 0 A 3 1 46 212802701 212802701 G A 1 0 0 0 0 1 0 0 0 15992 1188 41 3 3 TATDN3 1 212802701 Missense_Mutation SNP G C3N-00294_T 3175159 212802701 36153721 118 12890 ANGEL2 0 . GRCh38 1 212995049 212995049 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1627G>C p.Glu543Gln p.E543Q ENST00000366962 9/9 82 72 10 91 91 0 strelka-varscan-mutect ANGEL2,missense_variant,p.Glu543Gln,ENST00000366962,NM_144567.4;ANGEL2,missense_variant,p.Glu374Gln,ENST00000360506,NM_001300758.1,NM_001300755.1,NM_001300753.1,NM_001300757.1;ANGEL2,missense_variant,p.Glu374Gln,ENST00000535388,;VASH2,downstream_gene_variant,,ENST00000366968,NM_001136474.2;VASH2,downstream_gene_variant,,ENST00000366965,NM_024749.4;ANGEL2,non_coding_transcript_exon_variant,,ENST00000473303,;VASH2,downstream_gene_variant,,ENST00000519906,;ANGEL2,downstream_gene_variant,,ENST00000498650,; G ENST00000366962 Transcript missense_variant 1782/4649 1627/1635 543/544 E/Q Gag/Cag 1 -1 ANGEL2 HGNC HGNC:30534 protein_coding YES CCDS1512.1 ENSP00000355929 Q5VTE6 UPI00001D3EF4 NM_144567.4 tolerated(0.22) 9/9 hmmpanther:PTHR12121:SF27,hmmpanther:PTHR12121,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS rs1462514320 . 0 206 4 0 0 0 0 0 -19.98768 1 1 1 1 0 G 3 3 46 212995049 212995049 C G 1 0 0 0 0 1 0 0 0 707 835 29 4 4 ANGEL2 1 212995049 Missense_Mutation SNP C C3N-00294_T 192348 212995049 35961373 119 12891 PTPN14 0 . GRCh38 1 214383842 214383842 + Silent SNP G G C rs761892420 C3N-00294_T C3N-00294_N G G c.2013C>G p.= p.L671L ENST00000366956 13/19 207 184 23 146 146 0 strelka-varscan-mutect PTPN14,synonymous_variant,p.=,ENST00000366956,NM_005401.4;PTPN14,3_prime_UTR_variant,,ENST00000543945,; C ENST00000366956 Transcript synonymous_variant 2208/12985 2013/3564 671/1187 L ctC/ctG rs761892420 1 -1 PTPN14 HGNC HGNC:9647 protein_coding YES CCDS1514.1 ENSP00000355923 Q15678 UPI000013DCA6 NM_005401.4 13/19 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,PIRSF_domain:PIRSF000934 LOW 1 SNV 1 1 PASS rs761892420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 214383842 214383842 G C 1 0 0 0 0 0 0 0 1 12936 1161 41 4 4 PTPN14 1 214383842 Silent SNP G C3N-00294_T 1388793 214383842 34572580 120 12892 USH2A 0 . GRCh38 1 215625858 215625858 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.15532G>A p.Glu5178Lys p.E5178K ENST00000307340 72/72 509 456 53 390 390 0 strelka-varscan-mutect USH2A,missense_variant,p.Glu5178Lys,ENST00000307340,NM_206933.2;KCTD3,downstream_gene_variant,,ENST00000259154,NM_001319294.1,NM_016121.3;SNORD116,downstream_gene_variant,,ENST00000365628,;KCTD3,downstream_gene_variant,,ENST00000495537,; T ENST00000307340 Transcript missense_variant 15919/18883 15532/15609 5178/5202 E/K Gag/Aag 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.01) 72/72 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 215625858 215625858 C T 1 0 0 0 0 1 0 0 0 17570 922 32 3 3 USH2A 1 215625858 Missense_Mutation SNP C C3N-00294_T 1242016 215625858 33330564 121 12893 USH2A 0 . GRCh38 1 215845874 215845874 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.9005G>A p.Gly3002Glu p.G3002E ENST00000307340 45/72 576 501 75 413 413 0 strelka-varscan-mutect USH2A,missense_variant,p.Gly3002Glu,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 9392/18883 9005/15609 3002/5202 G/E gGa/gAa 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 45/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1245969744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 215845874 215845874 C T 1 0 0 0 0 1 0 0 0 17570 855 30 3 3 USH2A 1 215845874 Missense_Mutation SNP C C3N-00294_T 220016 215845874 33110548 122 12894 USH2A 0 . GRCh38 1 215878803 215878803 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.8519C>T p.Ser2840Phe p.S2840F ENST00000307340 42/72 250 208 42 197 197 0 strelka-varscan-mutect USH2A,missense_variant,p.Ser2840Phe,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 8906/18883 8519/15609 2840/5202 S/F tCt/tTt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 42/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 215878803 215878803 G A 1 0 0 0 0 1 0 0 0 17570 942 33 3 3 USH2A 1 215878803 Missense_Mutation SNP G C3N-00294_T 32929 215878803 33077619 123 12895 USH2A 0 . GRCh38 1 216089109 216089109 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.4789G>A p.Asp1597Asn p.D1597N ENST00000307340 23/72 161 141 20 178 178 0 strelka-varscan-mutect USH2A,missense_variant,p.Asp1597Asn,ENST00000307340,NM_206933.2;RP11-22M7.2,downstream_gene_variant,,ENST00000446411,;RP11-22M7.2,downstream_gene_variant,,ENST00000430890,;RP11-22M7.2,downstream_gene_variant,,ENST00000442606,;RP11-22M7.2,downstream_gene_variant,,ENST00000445619,;USH2A,non_coding_transcript_exon_variant,,ENST00000481786,;USH2A,upstream_gene_variant,,ENST00000463147,; T ENST00000307340 Transcript missense_variant 5176/18883 4789/15609 1597/5202 D/N Gat/Aat 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 23/72 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 216089109 216089109 C T 1 0 0 0 0 1 0 0 0 17570 826 29 3 3 USH2A 1 216089109 Missense_Mutation SNP C C3N-00294_T 210306 216089109 32867313 124 12896 RAB3GAP2 0 . GRCh38 1 220171978 220171978 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2488C>T p.Gln830Ter p.Q830* ENST00000358951 23/35 249 224 25 196 196 0 strelka-varscan-mutect RAB3GAP2,stop_gained,p.Gln830Ter,ENST00000358951,NM_012414.3; A ENST00000358951 Transcript stop_gained 2605/7257 2488/4182 830/1393 Q/* Cag/Tag 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 23/35 Pfam_domain:PF14656,hmmpanther:PTHR12472 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 220171978 220171978 G A 1 0 0 0 0 0 1 0 0 13095 1299 45 3 3 RAB3GAP2 1 220171978 Nonsense_Mutation SNP G C3N-00294_T 4082869 220171978 28784444 125 12897 MARK1 0 . GRCh38 1 220652018 220652018 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1604C>A p.Ser535Tyr p.S535Y ENST00000611084 15/18 170 140 30 108 108 0 strelka-varscan-mutect MARK1,missense_variant,p.Ser535Tyr,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Ser535Tyr,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Ser513Tyr,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Ser535Tyr,ENST00000366917,NM_018650.4; A ENST00000611084 Transcript missense_variant 2244/5321 1604/2391 535/796 S/Y tCt/tAt 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 tolerated(0.17) 15/18 Low_complexity_(Seg):seg,hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 220652018 220652018 C A 1 0 0 0 0 1 0 0 0 9237 913 32 2 2 MARK1 1 220652018 Missense_Mutation SNP C C3N-00294_T 480040 220652018 28304404 126 12898 NVL 0 . GRCh38 1 224305089 224305089 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.693G>C p.Lys231Asn p.K231N ENST00000281701 7/23 167 146 21 129 129 0 strelka-varscan-mutect NVL,missense_variant,p.Lys231Asn,ENST00000281701,NM_002533.3;NVL,missense_variant,p.Lys15Asn,ENST00000482491,;NVL,missense_variant,p.Lys125Asn,ENST00000391875,NM_206840.2;NVL,missense_variant,p.Lys140Asn,ENST00000469075,NM_001243147.1;NVL,missense_variant,p.Lys34Asn,ENST00000469968,;NVL,missense_variant,p.Lys15Asn,ENST00000340871,NM_001243146.1;NVL,missense_variant,p.Lys127Asn,ENST00000436927,;NVL,missense_variant,p.Lys140Asn,ENST00000488718,;NVL,missense_variant,p.Lys136Asn,ENST00000492281,;NVL,downstream_gene_variant,,ENST00000461546,;RNU6-1008P,upstream_gene_variant,,ENST00000384160,;NVL,downstream_gene_variant,,ENST00000461466,;NVL,downstream_gene_variant,,ENST00000470903,;NVL,missense_variant,p.Lys231Asn,ENST00000467882,;NVL,3_prime_UTR_variant,,ENST00000470989,;NVL,downstream_gene_variant,,ENST00000498767,; G ENST00000281701 Transcript missense_variant 953/3123 693/2571 231/856 K/N aaG/aaC 1 -1 NVL HGNC HGNC:8070 protein_coding YES CCDS1541.1 ENSP00000281701 O15381 UPI0000073F3E NM_002533.3 deleterious(0.04) 7/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23077:SF55,hmmpanther:PTHR23077 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 224305089 224305089 C G 1 0 0 0 0 1 0 0 0 10853 912 32 4 4 NVL 1 224305089 Missense_Mutation SNP C C3N-00294_T 3653071 224305089 24651333 127 12899 DNAH14 0 . GRCh38 1 225079384 225079384 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.2602G>T p.Glu868Ter p.E868* ENST00000430092 18/84 129 108 21 157 157 0 strelka-varscan-mutect DNAH14,stop_gained,p.Glu868Ter,ENST00000430092,NM_001373.1;DNAH14,stop_gained,p.Glu868Ter,ENST00000439375,;DNAH14,stop_gained,p.Glu802Ter,ENST00000445597,; T ENST00000430092 Transcript stop_gained 2817/13763 2602/13548 868/4515 E/* Gag/Tag 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 18/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 225079384 225079384 G T 1 0 0 0 0 0 1 0 0 4415 943 33 2 2 DNAH14 1 225079384 Nonsense_Mutation SNP G C3N-00294_T 774295 225079384 23877038 128 12900 SDE2 0 . GRCh38 1 225992931 225992931 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.310C>T p.Leu104Phe p.L104F ENST00000272091 3/7 337 301 36 211 211 0 strelka-varscan-mutect SDE2,missense_variant,p.Leu104Phe,ENST00000272091,NM_152608.3; A ENST00000272091 Transcript missense_variant 329/3975 310/1356 104/451 L/F Ctc/Ttc 1 -1 SDE2 HGNC HGNC:26643 protein_coding YES CCDS41473.1 ENSP00000272091 Q6IQ49 UPI0000204007 NM_152608.3 deleterious(0) 3/7 hmmpanther:PTHR12786:SF1,hmmpanther:PTHR12786,Pfam_domain:PF13019 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 225992931 225992931 G A 1 0 0 0 0 1 0 0 0 14231 942 33 3 3 SDE2 1 225992931 Missense_Mutation SNP G C3N-00294_T 913547 225992931 22963491 129 12901 JMJD4 0 . GRCh38 1 227734778 227734778 + Missense_Mutation SNP C C T rs148842395 C3N-00294_T C3N-00294_N C C c.439G>A p.Glu147Lys p.E147K ENST00000366758 2/6 236 204 32 174 174 0 strelka-varscan-mutect JMJD4,missense_variant,p.Glu147Lys,ENST00000366758,NM_023007.2;JMJD4,missense_variant,p.Glu147Lys,ENST00000615711,;JMJD4,missense_variant,p.Glu147Lys,ENST00000438896,NM_001161465.1;JMJD4,missense_variant,p.Glu101Lys,ENST00000620518,;SNAP47,intron_variant,,ENST00000366760,;SNAP47,upstream_gene_variant,,ENST00000426344,;SNAP47,upstream_gene_variant,,ENST00000315781,NM_053052.3;SNAP47,upstream_gene_variant,,ENST00000366759,;SNAP47,upstream_gene_variant,,ENST00000617596,;SNAP47,upstream_gene_variant,,ENST00000418653,;SNAP47,intron_variant,,ENST00000475930,;SNAP47,intron_variant,,ENST00000491439,;SNAP47,downstream_gene_variant,,ENST00000480897,;SNAP47,downstream_gene_variant,,ENST00000480265,;SNAP47,upstream_gene_variant,,ENST00000470038,;JMJD4,non_coding_transcript_exon_variant,,ENST00000480590,;JMJD4,upstream_gene_variant,,ENST00000485807,;JMJD4,upstream_gene_variant,,ENST00000465251,; T ENST00000366758 Transcript missense_variant 439/2595 439/1392 147/463 E/K Gaa/Aaa rs148842395 1 -1 JMJD4 HGNC HGNC:25724 protein_coding YES CCDS1561.1 ENSP00000355720 Q9H9V9 UPI000013FE0C NM_023007.2 tolerated(0.13) 2/6 hmmpanther:PTHR12480,hmmpanther:PTHR12480:SF6,Gene3D:1vrbA01,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS rs148842395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 227734778 227734778 C T 1 0 0 0 0 1 0 0 0 7865 864 30 3 3 JMJD4 1 227734778 Missense_Mutation SNP C C3N-00294_T 1741847 227734778 21221644 130 12902 OBSCN 0 . GRCh38 1 228250120 228250120 + Nonsense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.4465C>T p.Arg1489Ter p.R1489* ENST00000570156 15/116 502 469 33 404 403 1 strelka-varscan-mutect OBSCN,stop_gained,p.Arg1489Ter,ENST00000570156,NM_001271223.2;OBSCN,stop_gained,p.Arg1489Ter,ENST00000366707,;OBSCN,stop_gained,p.Arg1397Ter,ENST00000422127,NM_001098623.2;OBSCN,stop_gained,p.Arg1397Ter,ENST00000636875,;OBSCN,stop_gained,p.Arg1397Ter,ENST00000284548,NM_052843.3; T ENST00000570156 Transcript stop_gained 4539/26925 4465/26772 1489/8923 R/* Cga/Tga COSM1218205,COSM1218206,COSM1218207,COSM1218208 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 15/116 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1 HIGH 1 SNV 5 1,1,1,1 1 PASS rs1158912574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 228250120 228250120 C T 1 0 0 0 0 0 1 0 0 10889 876 31 1 1 OBSCN 1 228250120 Nonsense_Mutation SNP C C3N-00294_T 515342 228250120 20706302 131 12903 HIST3H2BB 0 . GRCh38 1 228458358 228458358 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.229G>A p.Glu77Lys p.E77K ENST00000620438 1/1 322 273 49 249 249 0 strelka-varscan-mutect HIST3H2BB,missense_variant,p.Glu77Lys,ENST00000620438,NM_175055.2;HIST3H2A,upstream_gene_variant,,ENST00000366695,NM_033445.2;MIR4666A,upstream_gene_variant,,ENST00000580160,; A ENST00000620438 Transcript missense_variant 252/2364 229/381 77/126 E/K Gag/Aag 1 1 HIST3H2BB HGNC HGNC:20514 protein_coding YES CCDS1574.1 ENSP00000479284 Q8N257 UPI00000214BE NM_175055.2 deleterious_low_confidence(0.04) 1/1 hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 228458358 228458358 G A 1 0 0 0 0 1 0 0 0 7072 1059 37 1 1 HIST3H2BB 1 228458358 Missense_Mutation SNP G C3N-00294_T 208238 228458358 20498064 132 12904 GALNT2 0 . GRCh38 1 230243411 230243411 + Missense_Mutation SNP T T G novel C3N-00294_T C3N-00294_N T T c.713T>G p.Leu238Arg p.L238R ENST00000366672 7/16 136 103 33 106 106 0 strelka-varscan-mutect GALNT2,missense_variant,p.Leu238Arg,ENST00000366672,NM_001291866.1,NM_004481.4;GALNT2,non_coding_transcript_exon_variant,,ENST00000494106,; G ENST00000366672 Transcript missense_variant 785/4454 713/1716 238/571 L/R cTg/cGg 1 1 GALNT2 HGNC HGNC:4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_001291866.1,NM_004481.4 deleterious(0) 7/16 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF49,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 230243411 230243411 T G 1 0 0 0 0 1 0 0 0 6084 1580 55 5 5 GALNT2 1 230243411 Missense_Mutation SNP T C3N-00294_T 1785053 230243411 18713011 133 12905 DISC1 0 . GRCh38 1 231818383 231818383 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1847C>G p.Ser616Ter p.S616* ENST00000366633 9/10 330 274 56 253 253 0 strelka-varscan-mutect DISC1,stop_gained,p.Ser616Ter,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,stop_gained,p.Ser616Ter,ENST00000366637,NM_001012957.1;DISC1,stop_gained,p.Ser494Ter,ENST00000620189,NM_001164540.1;DISC1,stop_gained,p.Ser616Ter,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,stop_gained,p.Ser616Ter,ENST00000366633,NM_001164539.1;DISC1,stop_gained,p.Ser616Ter,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,stop_gained,p.Ser616Ter,ENST00000366636,NM_001012959.1;DISC1,3_prime_UTR_variant,,ENST00000622252,;DISC1,3_prime_UTR_variant,,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,3_prime_UTR_variant,,ENST00000537876,;DISC1,3_prime_UTR_variant,,ENST00000602873,NM_001164556.1;DISC1,intron_variant,,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC2,downstream_gene_variant,,ENST00000612827,;DISC1,upstream_gene_variant,,ENST00000427560,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000535944,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,3_prime_UTR_variant,,ENST00000295051,;DISC1,3_prime_UTR_variant,,ENST00000602822,;DISC1,3_prime_UTR_variant,,ENST00000602713,;DISC1,3_prime_UTR_variant,,ENST00000602700,;DISC1,3_prime_UTR_variant,,ENST00000366632,; G ENST00000366633 Transcript stop_gained 1900/2676 1847/2268 616/755 S/* tCa/tGa 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 9/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs1230400140 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 231818383 231818383 C G 1 0 0 0 0 0 1 0 0 4344 838 29 4 4 DISC1 1 231818383 Nonsense_Mutation SNP C C3N-00294_T 1574972 231818383 17138039 134 12906 SIPA1L2 0 . GRCh38 1 232515096 232515096 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.244G>C p.Glu82Gln p.E82Q ENST00000366630 2/22 186 158 28 136 136 0 strelka-varscan-mutect SIPA1L2,missense_variant,p.Glu82Gln,ENST00000366630,;SIPA1L2,missense_variant,p.Glu82Gln,ENST00000262861,NM_020808.3; G ENST00000366630 Transcript missense_variant 603/6690 244/5169 82/1722 E/Q Gaa/Caa COSM4764804,COSM5209225 1 -1 SIPA1L2 HGNC HGNC:23800 protein_coding YES CCDS41474.1 ENSP00000355589 Q9P2F8 UPI00001D7D6A deleterious(0) 2/22 hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 232515096 232515096 C G 1 0 0 0 0 1 0 0 0 14593 835 29 4 4 SIPA1L2 1 232515096 Missense_Mutation SNP C C3N-00294_T 696713 232515096 16441326 135 12907 MAP10 0 . GRCh38 1 232806821 232806821 + Missense_Mutation SNP G G A rs374691511 C3N-00294_T C3N-00294_N G G c.1798G>A p.Glu600Lys p.E600K ENST00000418460 1/1 108 97 11 112 112 0 strelka-varscan-mutect MAP10,missense_variant,p.Glu600Lys,ENST00000418460,NM_019090.2; A ENST00000418460 Transcript missense_variant 1930/3516 1798/3144 600/1047 E/K Gaa/Aaa rs374691511,COSM1999154,COSM1999155 1 1 MAP10 HGNC HGNC:29265 protein_coding YES CCDS44334.1 ENSP00000403208 Q9P2G4 UPI0000418F25 NM_019090.2 tolerated(0.17) 1/1 Pfam_domain:PF14925,hmmpanther:PTHR21831,hmmpanther:PTHR21831:SF2 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs374691511 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 232806821 232806821 G A 1 0 0 0 0 1 0 0 0 9149 1291 45 3 3 MAP10 1 232806821 Missense_Mutation SNP G C3N-00294_T 291725 232806821 16149601 136 12908 LYST 0 . GRCh38 1 235808939 235808939 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1879G>T p.Glu627Ter p.E627* ENST00000389793 5/53 92 83 9 75 75 0 strelka-varscan-mutect LYST,stop_gained,p.Glu627Ter,ENST00000389793,NM_000081.3,NM_001301365.1;LYST,stop_gained,p.Glu627Ter,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000489585,;LYST,non_coding_transcript_exon_variant,,ENST00000465349,; A ENST00000389793 Transcript stop_gained 2054/13480 1879/11406 627/3801 E/* Gag/Tag 1 -1 LYST HGNC HGNC:1968 protein_coding YES CCDS31062.1 ENSP00000374443 Q99698 UPI000020509E NM_000081.3,NM_001301365.1 5/53 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF86,Superfamily_domains:SSF48371 HIGH 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -19.08962 1 1 1 1 0 A 4 1 46 235808939 235808939 C A 1 0 0 0 0 0 1 0 0 9041 922 32 2 2 LYST 1 235808939 Nonsense_Mutation SNP C C3N-00294_T 3002118 235808939 13147483 137 12909 NID1 0 . GRCh38 1 236029586 236029586 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1702G>C p.Glu568Gln p.E568Q ENST00000264187 7/20 373 313 60 301 301 0 strelka-varscan-mutect NID1,missense_variant,p.Glu568Gln,ENST00000264187,NM_002508.2;NID1,missense_variant,p.Glu568Gln,ENST00000366595,; G ENST00000264187 Transcript missense_variant 1785/5864 1702/3744 568/1247 E/Q Gag/Cag 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 tolerated(0.07) 7/20 Gene3D:2.40.155.10,Pfam_domain:PF07474,PROSITE_profiles:PS50993,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,SMART_domains:SM00682,Superfamily_domains:SSF54511 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 236029586 236029586 C G 1 0 0 0 0 1 0 0 0 10447 835 29 4 4 NID1 1 236029586 Missense_Mutation SNP C C3N-00294_T 220647 236029586 12926836 138 12910 NID1 0 . GRCh38 1 236029745 236029745 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1543G>A p.Glu515Lys p.E515K ENST00000264187 7/20 270 228 42 215 215 0 strelka-varscan-mutect NID1,missense_variant,p.Glu515Lys,ENST00000264187,NM_002508.2;NID1,missense_variant,p.Glu515Lys,ENST00000366595,; T ENST00000264187 Transcript missense_variant 1626/5864 1543/3744 515/1247 E/K Gag/Aag 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 tolerated(0.13) 7/20 Gene3D:2.40.155.10,Pfam_domain:PF07474,PROSITE_profiles:PS50993,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,SMART_domains:SM00682,Superfamily_domains:SSF54511 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 46 236029745 236029745 C T 1 0 0 0 0 1 0 0 0 10447 840 29 3 3 NID1 1 236029745 Missense_Mutation SNP C C3N-00294_T 159 236029745 12926677 139 12911 NID1 0 . GRCh38 1 236042003 236042003 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1042G>A p.Glu348Lys p.E348K ENST00000264187 4/20 211 187 24 165 165 0 strelka-varscan-mutect NID1,missense_variant,p.Glu348Lys,ENST00000264187,NM_002508.2;NID1,missense_variant,p.Glu348Lys,ENST00000366595,; T ENST00000264187 Transcript missense_variant 1125/5864 1042/3744 348/1247 E/K Gag/Aag 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 tolerated(0.51) 4/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 236042003 236042003 C T 1 0 0 0 0 1 0 0 0 10447 922 32 3 3 NID1 1 236042003 Missense_Mutation SNP C C3N-00294_T 12258 236042003 12914419 140 12912 GPR137B 0 . GRCh38 1 236178434 236178434 + Missense_Mutation SNP C C T rs764184387 C3N-00294_T C3N-00294_N C C c.485C>T p.Ser162Phe p.S162F ENST00000366592 3/7 245 215 30 151 151 0 strelka-varscan-mutect GPR137B,missense_variant,p.Ser162Phe,ENST00000366592,NM_003272.3;GPR137B,missense_variant,p.Ser26Phe,ENST00000454895,;GPR137B,synonymous_variant,p.=,ENST00000419162,;GPR137B,intron_variant,,ENST00000366591,; T ENST00000366592 Transcript missense_variant 576/2042 485/1200 162/399 S/F tCc/tTc rs764184387 1 1 GPR137B HGNC HGNC:11862 protein_coding YES CCDS1609.1 ENSP00000355551 O60478 UPI0000050441 NM_003272.3 tolerated(1) 3/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR15146:SF0,hmmpanther:PTHR15146 MODERATE 1 SNV 1 1 PASS rs764184387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 236178434 236178434 C T 1 0 0 0 0 1 0 0 0 6532 855 30 3 3 GPR137B 1 236178434 Missense_Mutation SNP C C3N-00294_T 136431 236178434 12777988 141 12913 HEATR1 0 . GRCh38 1 236590928 236590928 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.1449G>C p.Leu483Phe p.L483F ENST00000366582 12/45 93 87 6 71 71 0 strelka-mutect HEATR1,missense_variant,p.Leu483Phe,ENST00000366582,NM_018072.5;HEATR1,missense_variant,p.Leu483Phe,ENST00000366581,;HEATR1,downstream_gene_variant,,ENST00000483073,; G ENST00000366582 Transcript missense_variant 1564/8447 1449/6435 483/2144 L/F ttG/ttC COSM4793243 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 deleterious(0) 12/45 Gene3D:1.25.10.10,hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -12.64618 1 1 1 1 0 G 3 3 46 236590928 236590928 C G 1 0 0 0 0 1 0 0 0 6910 825 29 4 4 HEATR1 1 236590928 Missense_Mutation SNP C C3N-00294_T 412494 236590928 12365494 142 12914 MTR 0 . GRCh38 1 236853056 236853056 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1921G>A p.Glu641Lys p.E641K ENST00000366577 18/33 576 499 77 483 482 1 strelka-varscan-mutect MTR,missense_variant,p.Glu641Lys,ENST00000366577,NM_000254.2;MTR,missense_variant,p.Glu641Lys,ENST00000535889,NM_001291939.1;MTR,missense_variant,p.Glu195Lys,ENST00000366576,NM_001291940.1;MTR,non_coding_transcript_exon_variant,,ENST00000463959,; A ENST00000366577 Transcript missense_variant 2315/10529 1921/3798 641/1265 E/K Gag/Aag 1 1 MTR HGNC HGNC:7468 protein_coding YES CCDS1614.1 ENSP00000355536 Q99707 UPI0000036BC4 NM_000254.2 deleterious(0.05) 18/33 TIGRFAM_domain:TIGR02082,Gene3D:3.20.20.20,PIRSF_domain:PIRSF000381,Superfamily_domains:SSF51717 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 236853056 236853056 G A 1 0 0 0 0 1 0 0 0 9944 1291 45 3 3 MTR 1 236853056 Missense_Mutation SNP G C3N-00294_T 262128 236853056 12103366 143 12915 RYR2 0 . GRCh38 1 237590766 237590766 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.3934G>A p.Glu1312Lys p.E1312K ENST00000366574 31/105 141 126 15 110 110 0 strelka-varscan-mutect RYR2,missense_variant,p.Glu1312Lys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Glu1296Lys,ENST00000360064,; A ENST00000366574 Transcript missense_variant 4251/16562 3934/14904 1312/4967 E/K Gag/Aag COSM4546126,COSM4546127 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.15) 31/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 237590766 237590766 G A 1 0 0 0 0 1 0 0 0 14029 1175 41 3 3 RYR2 1 237590766 Missense_Mutation SNP G C3N-00294_T 737710 237590766 11365656 144 12916 RYR2 0 . GRCh38 1 237674184 237674184 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.8679C>T p.= p.L2893L ENST00000366574 59/105 117 105 12 113 113 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,upstream_gene_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 8996/16562 8679/14904 2893/4967 L ctC/ctT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 59/105 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 237674184 237674184 C T 1 0 0 0 0 0 0 0 1 14029 813 29 3 3 RYR2 1 237674184 Silent SNP C C3N-00294_T 83418 237674184 11282238 145 12917 RYR2 0 . GRCh38 1 237707217 237707217 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.9849C>T p.= p.I3283I ENST00000366574 68/105 91 74 17 88 88 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 10166/16562 9849/14904 3283/4967 I atC/atT COSM425711,COSM5207125 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 68/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 LOW 1 SNV 1 1,1 1 PASS rs1359021268 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 237707217 237707217 C T 1 0 0 0 0 0 0 0 1 14029 816 29 3 3 RYR2 1 237707217 Silent SNP C C3N-00294_T 33033 237707217 11249205 146 12918 FMN2 0 . GRCh38 1 240092583 240092583 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.474G>A p.= p.P158P ENST00000319653 1/18 249 205 44 195 195 0 strelka-varscan-mutect FMN2,synonymous_variant,p.=,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,intron_variant,,ENST00000447095,; A ENST00000319653 Transcript synonymous_variant 704/6434 474/5169 158/1722 P ccG/ccA COSM679805 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 1/18 1 LOW 1 SNV 5 1 1 PASS rs1198977248 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 240092583 240092583 G A 1 0 0 0 0 0 0 0 1 5806 1045 37 1 1 FMN2 1 240092583 Silent SNP G C3N-00294_T 2385366 240092583 8863839 147 12919 FMN2 0 . GRCh38 1 240207892 240207892 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3080G>A p.Gly1027Glu p.G1027E ENST00000319653 5/18 58 53 5 64 64 0 varscan-mutect FMN2,missense_variant,p.Gly1027Glu,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; A ENST00000319653 Transcript missense_variant 3310/6434 3080/5169 1027/1722 G/E gGa/gAa 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious_low_confidence(0.01) 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -12.21106 1 1 1 1 0 A 3 1 46 240207892 240207892 G A 1 0 0 0 0 1 0 0 0 5806 1174 41 3 3 FMN2 1 240207892 Missense_Mutation SNP G C3N-00294_T 115309 240207892 8748530 148 12920 FMN2 0 . GRCh38 1 240329415 240329415 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4384G>C p.Glu1462Gln p.E1462Q ENST00000319653 10/18 205 175 30 166 166 0 strelka-varscan-mutect FMN2,missense_variant,p.Glu1462Gln,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,5_prime_UTR_variant,,ENST00000545751,;FMN2,downstream_gene_variant,,ENST00000441342,;FMN2,non_coding_transcript_exon_variant,,ENST00000463398,; C ENST00000319653 Transcript missense_variant 4614/6434 4384/5169 1462/1722 E/Q Gaa/Caa 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious(0.01) 10/18 Pfam_domain:PF02181,PROSITE_profiles:PS51444,hmmpanther:PTHR13037,SMART_domains:SM00498,Superfamily_domains:SSF101447 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 240329415 240329415 G C 1 0 0 0 0 1 0 0 0 5806 943 33 4 4 FMN2 1 240329415 Missense_Mutation SNP G C3N-00294_T 121523 240329415 8627007 149 12921 RGS7 0 . GRCh38 1 240816387 240816387 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.713G>C p.Arg238Thr p.R238T ENST00000366565 11/18 331 294 37 333 333 0 strelka-varscan-mutect RGS7,missense_variant,p.Arg238Thr,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Arg238Thr,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Arg238Thr,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Arg185Thr,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Arg69Thr,ENST00000440928,; G ENST00000366565 Transcript missense_variant 1095/2494 713/1464 238/487 R/T aGa/aCa COSM363182,COSM4980445,COSM4980446,COSM4980447 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 tolerated(0.35) 11/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 240816387 240816387 C G 1 0 0 0 0 1 0 0 0 13481 913 32 4 4 RGS7 1 240816387 Missense_Mutation SNP C C3N-00294_T 486972 240816387 8140035 150 12922 CEP170 0 . GRCh38 1 243126475 243126475 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.4729G>A p.Glu1577Lys p.E1577K ENST00000366542 20/20 186 157 29 131 131 0 strelka-varscan-mutect CEP170,missense_variant,p.Glu1577Lys,ENST00000366542,NM_014812.2;CEP170,missense_variant,p.Glu1479Lys,ENST00000366544,NM_001042404.1;CEP170,missense_variant,p.Glu1453Lys,ENST00000366543,NM_001042405.1;CEP170,missense_variant,p.Glu1551Lys,ENST00000336415,;CEP170,missense_variant,p.Glu313Lys,ENST00000481987,;CEP170,missense_variant,p.Glu286Lys,ENST00000490813,;CEP170,downstream_gene_variant,,ENST00000413359,;CEP170,downstream_gene_variant,,ENST00000464936,;CEP170,non_coding_transcript_exon_variant,,ENST00000468254,;CEP170,non_coding_transcript_exon_variant,,ENST00000466495,;CEP170,intron_variant,,ENST00000476661,;CEP170,downstream_gene_variant,,ENST00000469646,;CEP170,non_coding_transcript_exon_variant,,ENST00000439296,; T ENST00000366542 Transcript missense_variant 4781/6828 4729/4755 1577/1584 E/K Gag/Aag COSM4030223,COSM679639 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 tolerated_low_confidence(0.06) 20/20 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 243126475 243126475 C T 1 0 0 0 0 1 0 0 0 2964 922 32 3 3 CEP170 1 243126475 Missense_Mutation SNP C C3N-00294_T 2310088 243126475 5829947 151 12923 AKT3 0 . GRCh38 1 243572951 243572951 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.794G>C p.Gly265Ala p.G265A ENST00000263826 8/13 158 132 26 107 107 0 strelka-varscan-mutect AKT3,missense_variant,p.Gly265Ala,ENST00000263826,NM_005465.4;AKT3,missense_variant,p.Gly265Ala,ENST00000366539,;AKT3,missense_variant,p.Gly265Ala,ENST00000336199,NM_181690.2;AKT3,missense_variant,p.Gly265Ala,ENST00000366540,NM_001206729.1; G ENST00000263826 Transcript missense_variant 906/7081 794/1440 265/479 G/A gGa/gCa 1 -1 AKT3 HGNC HGNC:393 protein_coding YES CCDS31077.1 ENSP00000263826 Q9Y243 UPI00000335E8 NM_005465.4 tolerated(0.47) 8/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF190,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 243572951 243572951 C G 1 0 0 0 0 1 0 0 0 564 855 30 4 4 AKT3 1 243572951 Missense_Mutation SNP C C3N-00294_T 446476 243572951 5383471 152 12924 HNRNPU 0 . GRCh38 1 244856042 244856042 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2029C>G p.Leu677Val p.L677V ENST00000283179 11/14 507 431 76 369 369 0 strelka-varscan-mutect HNRNPU,missense_variant,p.Leu658Val,ENST00000444376,NM_004501.3;HNRNPU,missense_variant,p.Leu677Val,ENST00000283179,NM_031844.2;HNRNPU,downstream_gene_variant,,ENST00000440865,;HNRNPU,non_coding_transcript_exon_variant,,ENST00000366525,;HNRNPU,downstream_gene_variant,,ENST00000465881,;HNRNPU,downstream_gene_variant,,ENST00000483966,;HNRNPU,downstream_gene_variant,,ENST00000468690,;HNRNPU,upstream_gene_variant,,ENST00000475997,;HNRNPU,upstream_gene_variant,,ENST00000489705,; C ENST00000283179 Transcript missense_variant 2193/3704 2029/2478 677/825 L/V Ctt/Gtt 1 -1 HNRNPU HGNC HGNC:5048 protein_coding YES CCDS41479.1 ENSP00000283179 Q00839 UPI000040E1C8 NM_031844.2 tolerated(0.16) 11/14 hmmpanther:PTHR12381,hmmpanther:PTHR12381:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 244856042 244856042 G C 1 0 0 0 0 1 0 0 0 7168 942 33 4 4 HNRNPU 1 244856042 Missense_Mutation SNP G C3N-00294_T 1283091 244856042 4100380 153 12925 ZNF670 0 . GRCh38 1 247037621 247037621 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.998G>C p.Gly333Ala p.G333A ENST00000366503 4/4 223 185 38 173 173 0 strelka-varscan-mutect ZNF670,missense_variant,p.Gly333Ala,ENST00000366503,NM_001204220.1,NM_033213.4;ZNF670-ZNF695,intron_variant,,ENST00000474541,;ZNF670-ZNF695,intron_variant,,ENST00000465049,; G ENST00000366503 Transcript missense_variant 1157/1994 998/1170 333/389 G/A gGa/gCa 1 -1 ZNF670 HGNC HGNC:28167 protein_coding YES CCDS31087.1 ENSP00000355459 Q9BS34 UPI0000070EC3 NM_001204220.1,NM_033213.4 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF168,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 247037621 247037621 C G 1 0 0 0 0 1 0 0 0 18651 855 30 4 4 ZNF670 1 247037621 Missense_Mutation SNP C C3N-00294_T 2181579 247037621 1918801 154 12926 NLRP3 0 . GRCh38 1 247423962 247423962 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.519C>T p.= p.L173L ENST00000336119 3/9 668 594 74 522 522 0 strelka-varscan-mutect NLRP3,synonymous_variant,p.=,ENST00000366497,NM_001127461.2;NLRP3,synonymous_variant,p.=,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,synonymous_variant,p.=,ENST00000366496,;NLRP3,synonymous_variant,p.=,ENST00000391828,NM_001079821.2;NLRP3,synonymous_variant,p.=,ENST00000348069,NM_183395.2;NLRP3,synonymous_variant,p.=,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; T ENST00000336119 Transcript synonymous_variant 1265/4170 519/3111 173/1036 L ctC/ctT 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 3/9 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4,Pfam_domain:PF14484,SMART_domains:SM01288 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 247423962 247423962 C T 1 0 0 0 0 0 0 0 1 10516 813 29 3 3 NLRP3 1 247423962 Silent SNP C C3N-00294_T 386341 247423962 1532460 155 12927 OR2G3 0 . GRCh38 1 247605987 247605987 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.402C>G p.= p.V134V ENST00000320002 1/1 243 212 31 176 176 0 strelka-varscan-mutect OR2G3,synonymous_variant,p.=,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; G ENST00000320002 Transcript synonymous_variant 402/930 402/930 134/309 V gtC/gtG COSM680671 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 LOW SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 247605987 247605987 C G 1 0 0 0 0 0 0 0 1 11077 813 29 4 4 OR2G3 1 247605987 Silent SNP C C3N-00294_T 182025 247605987 1350435 156 12928 OR2M7 0 . GRCh38 1 248323798 248323798 + Silent SNP G G A rs190559379 C3N-00294_T C3N-00294_N G G c.771C>T p.= p.F257F ENST00000317965 1/1 240 200 40 161 161 0 strelka-varscan-mutect OR2M7,synonymous_variant,p.=,ENST00000317965,NM_001004691.1; A ENST00000317965 Transcript synonymous_variant 771/939 771/939 257/312 F ttC/ttT rs190559379 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs190559379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 248323798 248323798 G A 1 0 0 0 0 0 0 0 1 11092 1281 45 3 3 OR2M7 1 248323798 Silent SNP G C3N-00294_T 717811 248323798 632624 157 12929 OR2T1 0 . GRCh38 1 248407075 248407075 + Missense_Mutation SNP C C G rs866541288 C3N-00294_T C3N-00294_N C C c.1081C>G p.Pro361Ala p.P361A ENST00000366474 1/1 80 73 7 58 58 0 strelka-varscan-mutect OR2T1,missense_variant,p.Pro361Ala,ENST00000366474,NM_030904.1; G ENST00000366474 Transcript missense_variant 1081/1110 1081/1110 361/369 P/A Cct/Gct rs866541288 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 tolerated(0.57) 1/1 hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs866541288 . 0 206 4 0 0 0 0 0 -15.24096 1 1 1 1 0 G 3 3 46 248407075 248407075 C G 1 0 0 0 0 1 0 0 0 11094 855 30 4 4 OR2T1 1 248407075 Missense_Mutation SNP C C3N-00294_T 83277 248407075 549347 158 12930 OR2T2 0 . GRCh38 1 248453718 248453718 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.921G>A p.= p.G307G ENST00000342927 1/1 266 238 28 263 262 1 varscan-mutect OR2T2,synonymous_variant,p.=,ENST00000342927,NM_001004136.1; A ENST00000342927 Transcript synonymous_variant 921/975 921/975 307/324 G ggG/ggA COSM5536110 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 248453718 248453718 G A 1 0 0 0 0 0 0 0 1 11097 1161 41 3 3 OR2T2 1 248453718 Silent SNP G C3N-00294_T 46643 248453718 502704 159 12931 OR2T35 0 . GRCh38 1 248638341 248638341 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.918G>A p.= p.G306G ENST00000317450 1/1 206 184 22 132 132 0 varscan-mutect OR2T35,synonymous_variant,p.=,ENST00000317450,NM_001001827.1; T ENST00000317450 Transcript synonymous_variant 918/972 918/972 306/323 G ggG/ggA 1 -1 OR2T35 HGNC HGNC:31257 protein_coding YES CCDS31123.1 ENSP00000324369 Q8NGX2 UPI0000061ED3 NM_001001827.1 1/1 hmmpanther:PTHR26453:SF18,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 248638341 248638341 C T 1 0 0 0 0 0 0 0 1 11103 842 30 3 3 OR2T35 1 248638341 Silent SNP C C3N-00294_T 184623 248638341 318081 160 12932 ASAP2 0 . GRCh38 2 9279381 9279381 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.191C>T p.Ser64Phe p.S64F ENST00000281419 2/28 250 214 36 247 247 0 strelka-varscan-mutect ASAP2,missense_variant,p.Ser64Phe,ENST00000281419,NM_003887.2;ASAP2,missense_variant,p.Ser64Phe,ENST00000315273,NM_001135191.1; T ENST00000281419 Transcript missense_variant 531/5712 191/3021 64/1006 S/F tCt/tTt 1 1 ASAP2 HGNC HGNC:2721 protein_coding YES CCDS1661.1 ENSP00000281419 O43150 UPI0000073459 NM_003887.2 deleterious(0) 2/28 Pfam_domain:PF16746,Gene3D:1.20.1270.60,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 9279381 9279381 C T 1 0 0 0 0 1 0 0 0 1153 913 32 3 3 ASAP2 2 9279381 Missense_Mutation SNP C C3N-00294_T 9279381 232914148 161 12933 CPSF3 0 . GRCh38 2 9432671 9432671 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.502G>C p.Glu168Gln p.E168Q ENST00000238112 5/18 118 102 16 87 87 0 strelka-varscan-mutect CPSF3,missense_variant,p.Glu131Gln,ENST00000460593,;CPSF3,missense_variant,p.Glu168Gln,ENST00000238112,NM_016207.3;CPSF3,missense_variant,p.Glu131Gln,ENST00000475482,; C ENST00000238112 Transcript missense_variant 708/2345 502/2055 168/684 E/Q Gag/Cag 1 1 CPSF3 HGNC HGNC:2326 protein_coding YES CCDS1664.1 ENSP00000238112 Q9UKF6 UPI00001282F5 NM_016207.3 deleterious(0.03) 5/18 hmmpanther:PTHR11203,hmmpanther:PTHR11203:SF11,Gene3D:3.60.15.10,Pfam_domain:PF00753,SMART_domains:SM00849,Superfamily_domains:SSF56281 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 9432671 9432671 G C 1 0 0 0 0 1 0 0 0 3622 1291 45 4 4 CPSF3 2 9432671 Missense_Mutation SNP G C3N-00294_T 153290 9432671 232760858 162 12934 GREB1 0 . GRCh38 2 11620950 11620950 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.4090A>T p.Arg1364Trp p.R1364W ENST00000381486 23/33 266 123 143 236 236 0 strelka-varscan-mutect GREB1,missense_variant,p.Arg1364Trp,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Arg1364Trp,ENST00000234142,;GREB1,missense_variant,p.Arg362Trp,ENST00000396123,;GREB1,downstream_gene_variant,,ENST00000472040,; T ENST00000381486 Transcript missense_variant 4390/8484 4090/5850 1364/1949 R/W Agg/Tgg 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 deleterious(0) 23/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 11620950 11620950 A T 1 0 0 0 0 1 0 0 0 6639 179 7 4 4 GREB1 2 11620950 Missense_Mutation SNP A C3N-00294_T 2188279 11620950 230572579 163 12935 DDX1 0 . GRCh38 2 15628458 15628458 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1700G>C p.Arg567Thr p.R567T ENST00000381341 22/27 105 85 20 169 169 0 strelka-varscan-mutect DDX1,missense_variant,p.Arg567Thr,ENST00000381341,;DDX1,missense_variant,p.Arg567Thr,ENST00000233084,NM_004939.2;DDX1,missense_variant,p.Arg486Thr,ENST00000617198,;DDX1,missense_variant,p.Arg486Thr,ENST00000621973,;DDX1,non_coding_transcript_exon_variant,,ENST00000470674,;DDX1,downstream_gene_variant,,ENST00000478695,; C ENST00000381341 Transcript missense_variant 2089/2817 1700/2223 567/740 R/T aGa/aCa 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 deleterious(0.01) 22/27 PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF307,hmmpanther:PTHR24031,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 15628458 15628458 G C 1 0 0 0 0 1 0 0 0 4145 942 33 4 4 DDX1 2 15628458 Missense_Mutation SNP G C3N-00294_T 4007508 15628458 226565071 164 12936 DDX1 0 . GRCh38 2 15630006 15630006 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.1988A>T p.Glu663Val p.E663V ENST00000381341 26/27 177 79 98 133 133 0 strelka-varscan-mutect DDX1,missense_variant,p.Glu663Val,ENST00000381341,;DDX1,missense_variant,p.Glu663Val,ENST00000233084,NM_004939.2;DDX1,missense_variant,p.Glu582Val,ENST00000617198,;DDX1,missense_variant,p.Glu582Val,ENST00000621973,;DDX1,downstream_gene_variant,,ENST00000470674,;DDX1,downstream_gene_variant,,ENST00000478695,; T ENST00000381341 Transcript missense_variant 2377/2817 1988/2223 663/740 E/V gAa/gTa 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 deleterious(0) 26/27 PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF307,hmmpanther:PTHR24031,Gene3D:3.40.50.300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 15630006 15630006 A T 1 0 0 0 0 1 0 0 0 4145 246 9 4 4 DDX1 2 15630006 Missense_Mutation SNP A C3N-00294_T 1548 15630006 226563523 165 12937 FAM49A 0 . GRCh38 2 16561528 16561528 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.441G>A p.= p.R147R ENST00000381323 7/12 254 221 33 196 196 0 strelka-varscan-mutect FAM49A,synonymous_variant,p.=,ENST00000381323,NM_030797.3;FAM49A,synonymous_variant,p.=,ENST00000406434,;FAM49A,downstream_gene_variant,,ENST00000451689,;FAM49A,downstream_gene_variant,,ENST00000445605,;FAM49A,upstream_gene_variant,,ENST00000469507,; T ENST00000381323 Transcript synonymous_variant 662/4670 441/972 147/323 R agG/agA 1 -1 FAM49A HGNC HGNC:25373 protein_coding YES CCDS1688.1 ENSP00000370724 Q9H0Q0 UPI0000037BBB NM_030797.3 7/12 hmmpanther:PTHR12422,hmmpanther:PTHR12422:SF4,Pfam_domain:PF07159 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 16561528 16561528 C T 1 0 0 0 0 0 0 0 1 5451 869 30 3 3 FAM49A 2 16561528 Silent SNP C C3N-00294_T 931522 16561528 225632001 166 12938 APOB 0 . GRCh38 2 21043549 21043549 + Missense_Mutation SNP C C G rs768728964 C3N-00294_T C3N-00294_N C C c.85G>C p.Glu29Gln p.E29Q ENST00000233242 2/29 399 342 57 370 370 0 strelka-varscan-mutect APOB,missense_variant,p.Glu29Gln,ENST00000233242,NM_000384.2;APOB,missense_variant,p.Glu29Gln,ENST00000399256,; G ENST00000233242 Transcript missense_variant,splice_region_variant 213/14121 85/13692 29/4563 E/Q Gag/Cag rs768728964 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.07) 2/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS rs768728964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 21043549 21043549 C G 1 0 0 0 0 1 0 0 0 907 927 32 4 4 APOB 2 21043549 Missense_Mutation SNP C C3N-00294_T 4482021 21043549 221149980 167 12939 WDCP 0 . GRCh38 2 24039064 24039064 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.431C>G p.Ser144Cys p.S144C ENST00000295148 2/4 247 200 47 203 203 0 strelka-varscan-mutect WDCP,missense_variant,p.Ser144Cys,ENST00000295148,NM_025203.2;WDCP,missense_variant,p.Ser144Cys,ENST00000406895,NM_001142319.1;WDCP,missense_variant,p.Ser144Cys,ENST00000443232,;MFSD2B,intron_variant,,ENST00000453731,; C ENST00000295148 Transcript missense_variant 489/3817 431/2166 144/721 S/C tCt/tGt COSM4883451 1 -1 WDCP HGNC HGNC:26157 protein_coding YES CCDS1705.1 ENSP00000295148 Q9H6R7 UPI0000070788 NM_025203.2 tolerated(0.68) 2/4 Superfamily_domains:0047732,Pfam_domain:PF15390,hmmpanther:PTHR14897,hmmpanther:PTHR14897:SF5 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 24039064 24039064 G C 1 0 0 0 0 1 0 0 0 17827 942 33 4 4 WDCP 2 24039064 Missense_Mutation SNP G C3N-00294_T 2995515 24039064 218154465 168 12940 GAREM2 0 . GRCh38 2 26187477 26187477 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1845C>G p.Phe615Leu p.F615L ENST00000401533 6/6 105 88 17 70 70 0 strelka-varscan-mutect GAREM2,missense_variant,p.Phe615Leu,ENST00000401533,NM_001168241.1;GAREM2,intron_variant,,ENST00000407684,NM_001191033.1;HADHA,downstream_gene_variant,,ENST00000380649,NM_000182.4;HADHA,downstream_gene_variant,,ENST00000492433,;GAREM2,downstream_gene_variant,,ENST00000496070,; G ENST00000401533 Transcript missense_variant 1975/4161 1845/2625 615/874 F/L ttC/ttG 1 1 GAREM2 HGNC HGNC:27172 protein_coding YES CCDS54336.1 ENSP00000384593 Q75VX8 UPI0000237273 NM_001168241.1 tolerated(0.45) 6/6 hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF5 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 26187477 26187477 C G 1 0 0 0 0 1 0 0 0 6110 825 29 4 4 GAREM2 2 26187477 Missense_Mutation SNP C C3N-00294_T 2148413 26187477 216006052 169 12941 OTOF 0 . GRCh38 2 26462088 26462088 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.5286G>A p.= p.V1762V ENST00000272371 42/47 327 273 54 336 336 0 strelka-varscan-mutect OTOF,synonymous_variant,p.=,ENST00000272371,NM_194248.2;OTOF,synonymous_variant,p.=,ENST00000403946,NM_001287489.1;OTOF,synonymous_variant,p.=,ENST00000402415,NM_194322.2;OTOF,synonymous_variant,p.=,ENST00000338581,NM_004802.3;OTOF,synonymous_variant,p.=,ENST00000339598,NM_194323.2;OTOF,downstream_gene_variant,,ENST00000464574,; T ENST00000272371 Transcript synonymous_variant 5413/7156 5286/5994 1762/1997 V gtG/gtA 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 42/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 26462088 26462088 C T 1 0 0 0 0 0 0 0 1 11369 840 29 3 3 OTOF 2 26462088 Silent SNP C C3N-00294_T 274611 26462088 215731441 170 12942 CENPA 0 . GRCh38 2 26792783 26792783 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.238C>T p.Arg80Cys p.R80C ENST00000335756 3/5 215 182 33 188 188 0 strelka-varscan-mutect CENPA,missense_variant,p.Arg80Cys,ENST00000335756,NM_001809.3;CENPA,intron_variant,,ENST00000233505,NM_001042426.1;CENPA,non_coding_transcript_exon_variant,,ENST00000460030,;CENPA,non_coding_transcript_exon_variant,,ENST00000472719,;CENPA,intron_variant,,ENST00000475662,;CENPA,3_prime_UTR_variant,,ENST00000419525,; T ENST00000335756 Transcript missense_variant 438/1452 238/423 80/140 R/C Cgt/Tgt COSM1200729 1 1 CENPA HGNC HGNC:1851 protein_coding YES CCDS1729.1 ENSP00000336868 P49450 UPI00001274F6 NM_001809.3 tolerated(0.05) 3/5 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113 1 MODERATE 1 SNV 1 1 1 PASS rs1392372965 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 26792783 26792783 C T 1 0 0 0 0 1 0 0 0 2934 884 31 1 1 CENPA 2 26792783 Missense_Mutation SNP C C3N-00294_T 330695 26792783 215400746 171 12943 EMILIN1 0 . GRCh38 2 27085842 27085842 + Nonsense_Mutation SNP G G T rs751281575 C3N-00294_T C3N-00294_N G G c.2878G>T p.Glu960Ter p.E960* ENST00000380320 8/8 166 138 28 108 108 0 strelka-varscan-mutect EMILIN1,stop_gained,p.Glu960Ter,ENST00000380320,NM_007046.3;EMILIN1,stop_gained,p.Glu291Ter,ENST00000433140,;KHK,upstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,upstream_gene_variant,,ENST00000260598,NM_006488.2;KHK,upstream_gene_variant,,ENST00000429697,;KHK,upstream_gene_variant,,ENST00000490823,; T ENST00000380320 Transcript stop_gained 3377/3943 2878/3051 960/1016 E/* Gag/Tag rs751281575 1 1 EMILIN1 HGNC HGNC:19880 protein_coding YES CCDS1733.1 ENSP00000369677 A0A0C4DFX3 UPI0000073B0E NM_007046.3 8/8 PROSITE_profiles:PS50871,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF1,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842 HIGH 1 SNV 1 1 PASS rs751281575 . 0 203 4 3 0 0 0 0 -20 0.9998771 1 1 1 0 T 4 4 46 27085842 27085842 G T 1 0 0 0 0 0 1 0 0 4936 1059 37 1 1 EMILIN1 2 27085842 Nonsense_Mutation SNP G C3N-00294_T 293059 27085842 215107687 172 12944 SLC5A6 0 . GRCh38 2 27204847 27204847 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.819G>A p.= p.V273V ENST00000310574 8/17 257 228 29 250 250 0 strelka-varscan-mutect SLC5A6,synonymous_variant,p.=,ENST00000310574,NM_021095.2;SLC5A6,synonymous_variant,p.=,ENST00000408041,;SLC5A6,downstream_gene_variant,,ENST00000412471,;SLC5A6,downstream_gene_variant,,ENST00000414408,;SLC5A6,downstream_gene_variant,,ENST00000401463,;SLC5A6,downstream_gene_variant,,ENST00000432106,;SLC5A6,downstream_gene_variant,,ENST00000426119,;SLC5A6,downstream_gene_variant,,ENST00000430186,;SLC5A6,downstream_gene_variant,,ENST00000428518,;SLC5A6,downstream_gene_variant,,ENST00000442731,;SLC5A6,upstream_gene_variant,,ENST00000461319,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000488743,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000476319,;SLC5A6,upstream_gene_variant,,ENST00000461757,;SLC5A6,downstream_gene_variant,,ENST00000445802,;SLC5A6,upstream_gene_variant,,ENST00000492069,;SLC5A6,downstream_gene_variant,,ENST00000464538,;SLC5A6,upstream_gene_variant,,ENST00000481751,; T ENST00000310574 Transcript synonymous_variant 1293/3231 819/1908 273/635 V gtG/gtA 1 -1 SLC5A6 HGNC HGNC:11041 protein_coding YES CCDS1740.1 ENSP00000310208 Q9Y289 UPI000006DE33 NM_021095.2 8/17 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF140,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 27204847 27204847 C T 1 0 0 0 0 0 0 0 1 14952 813 29 3 3 SLC5A6 2 27204847 Silent SNP C C3N-00294_T 119005 27204847 214988682 173 12945 SLC30A3 0 . GRCh38 2 27257176 27257176 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.755C>A p.Ala252Asp p.A252D ENST00000233535 5/8 388 217 171 385 385 0 strelka-varscan-mutect SLC30A3,missense_variant,p.Ala252Asp,ENST00000233535,NM_003459.4;SLC30A3,missense_variant,p.Pro190Thr,ENST00000445870,;SLC30A3,missense_variant,p.Ala203Asp,ENST00000432351,;SLC30A3,downstream_gene_variant,,ENST00000426924,;SLC30A3,downstream_gene_variant,,ENST00000424577,;SLC30A3,downstream_gene_variant,,ENST00000426569,;SLC30A3,downstream_gene_variant,,ENST00000450118,;SLC30A3,non_coding_transcript_exon_variant,,ENST00000497341,;SLC30A3,non_coding_transcript_exon_variant,,ENST00000482990,;SLC30A3,downstream_gene_variant,,ENST00000486309,; T ENST00000233535 Transcript missense_variant 1108/2260 755/1167 252/388 A/D gCc/gAc 1 -1 SLC30A3 HGNC HGNC:11014 protein_coding YES CCDS1743.1 ENSP00000233535 Q99726 UPI000006D0B4 NM_003459.4 deleterious(0) 5/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF30,TIGRFAM_domain:TIGR01297,Gene3D:3h90A01,Pfam_domain:PF01545,Superfamily_domains:0054606 MODERATE 1 SNV 1 1 PASS rs1363688014 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 27257176 27257176 G T 1 0 0 0 0 1 0 0 0 14826 1203 42 2 2 SLC30A3 2 27257176 Missense_Mutation SNP G C3N-00294_T 52329 27257176 214936353 174 12946 GTF3C2 0 . GRCh38 2 27336421 27336421 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.1132A>G p.Ser378Gly p.S378G ENST00000359541 8/19 153 128 25 94 94 0 strelka-varscan-mutect GTF3C2,missense_variant,p.Ser378Gly,ENST00000359541,NM_001318909.1;GTF3C2,missense_variant,p.Ser378Gly,ENST00000264720,NM_001521.3,NM_001035521.2;GTF3C2,missense_variant,p.Ser378Gly,ENST00000622534,;GTF3C2,upstream_gene_variant,,ENST00000454704,;GTF3C2-AS1,non_coding_transcript_exon_variant,,ENST00000416453,;GTF3C2-AS1,non_coding_transcript_exon_variant,,ENST00000585326,;GTF3C2-AS1,non_coding_transcript_exon_variant,,ENST00000592265,;GTF3C2-AS1,non_coding_transcript_exon_variant,,ENST00000608473,;GTF3C2-AS1,upstream_gene_variant,,ENST00000625728,;GTF3C2-AS1,upstream_gene_variant,,ENST00000626256,;GTF3C2-AS1,upstream_gene_variant,,ENST00000590383,;GTF3C2-AS1,upstream_gene_variant,,ENST00000588707,;GTF3C2-AS1,upstream_gene_variant,,ENST00000589853,;GTF3C2-AS1,upstream_gene_variant,,ENST00000587586,;GTF3C2-AS1,upstream_gene_variant,,ENST00000590754,;GTF3C2-AS1,upstream_gene_variant,,ENST00000585645,;GTF3C2-AS1,upstream_gene_variant,,ENST00000589232,;GTF3C2,non_coding_transcript_exon_variant,,ENST00000493511,;GTF3C2,non_coding_transcript_exon_variant,,ENST00000470115,;GTF3C2,non_coding_transcript_exon_variant,,ENST00000480989,; C ENST00000359541 Transcript missense_variant 1562/3992 1132/2736 378/911 S/G Agc/Ggc 1 -1 GTF3C2 HGNC HGNC:4665 protein_coding YES CCDS1749.1 ENSP00000352536 Q8WUA4 UPI0000074025 NM_001318909.1 tolerated(0.18) 8/19 hmmpanther:PTHR15052,hmmpanther:PTHR15052:SF2 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999983 1 1 1 0 C 3 2 46 27336421 27336421 T C 1 0 0 0 0 1 0 0 0 6754 1536 53 5 5 GTF3C2 2 27336421 Missense_Mutation SNP T C3N-00294_T 79245 27336421 214857108 175 12947 SLC4A1AP 0 . GRCh38 2 27663911 27663911 + Silent SNP G G A rs138567441 C3N-00294_T C3N-00294_N G G c.159G>A p.= p.L53L ENST00000613058 1/14 637 520 117 576 576 0 strelka-varscan-mutect SLC4A1AP,synonymous_variant,p.=,ENST00000613058,NM_018158.2;SLC4A1AP,synonymous_variant,p.=,ENST00000326019,;SLC4A1AP,5_prime_UTR_variant,,ENST00000618046,;SUPT7L,upstream_gene_variant,,ENST00000337768,NM_014860.2,NM_001282729.1;SUPT7L,upstream_gene_variant,,ENST00000404798,NM_001282732.1;SUPT7L,upstream_gene_variant,,ENST00000406540,;SUPT7L,upstream_gene_variant,,ENST00000464789,;SUPT7L,upstream_gene_variant,,ENST00000405491,NM_001282731.1,NM_001282730.1;SLC4A1AP,upstream_gene_variant,,ENST00000613517,;SLC4A1AP,upstream_gene_variant,,ENST00000427424,; A ENST00000613058 Transcript synonymous_variant 441/2966 159/2391 53/796 L ttG/ttA rs138567441 1 1 SLC4A1AP HGNC HGNC:13813 protein_coding YES CCDS33166.1 ENSP00000479964 Q9BWU0 UPI000006F66B NM_018158.2 1/14 hmmpanther:PTHR23308:SF2,hmmpanther:PTHR23308 LOW 1 SNV 1 1 PASS rs138567441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 27663911 27663911 G A 1 0 0 0 0 0 0 0 1 14930 1281 45 3 3 SLC4A1AP 2 27663911 Silent SNP G C3N-00294_T 327490 27663911 214529618 176 12948 MEMO1 0 . GRCh38 2 32010189 32010189 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.59C>T p.Ser20Leu p.S20L ENST00000295065 1/9 171 143 28 160 160 0 strelka-varscan-mutect MEMO1,missense_variant,p.Ser20Leu,ENST00000295065,NM_015955.3;MEMO1,missense_variant,p.Ser20Leu,ENST00000404530,NM_001301833.1;MEMO1,missense_variant,p.Ser20Leu,ENST00000426310,NM_001137602.2;MEMO1,missense_variant,p.Ser20Leu,ENST00000407893,;MEMO1,missense_variant,p.Ser20Leu,ENST00000437854,;CTC-336P14.1,upstream_gene_variant,,ENST00000605811,;MEMO1,splice_region_variant,,ENST00000413686,;DPY30,intron_variant,,ENST00000446765,;MEMO1,intron_variant,,ENST00000490459,;DPY30,downstream_gene_variant,,ENST00000452582,;DPY30,downstream_gene_variant,,ENST00000414013,; A ENST00000295065 Transcript missense_variant,splice_region_variant 369/4505 59/894 20/297 S/L tCa/tTa 1 -1 MEMO1 HGNC HGNC:14014 protein_coding YES CCDS1776.1 ENSP00000295065 Q9Y316 UPI0000001C55 NM_015955.3 tolerated(0.11) 1/9 HAMAP:MF_00055,Pfam_domain:PF01875,hmmpanther:PTHR11060,hmmpanther:PTHR11060:SF0,TIGRFAM_domain:TIGR04336 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 32010189 32010189 G A 1 0 0 0 0 1 0 0 0 9416 1304 45 3 3 MEMO1 2 32010189 Missense_Mutation SNP G C3N-00294_T 4346278 32010189 210183340 177 12949 BIRC6 0 . GRCh38 2 32499882 32499882 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.8804C>G p.Ser2935Ter p.S2935* ENST00000421745 46/74 247 206 41 246 246 0 strelka-varscan-mutect BIRC6,stop_gained,p.Ser2935Ter,ENST00000421745,NM_016252.3;BIRC6,upstream_gene_variant,,ENST00000497023,; G ENST00000421745 Transcript stop_gained 8938/15703 8804/14574 2935/4857 S/* tCa/tGa 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 46/74 hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF123 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 32499882 32499882 C G 1 0 0 0 0 0 1 0 0 1589 838 29 4 4 BIRC6 2 32499882 Nonsense_Mutation SNP C C3N-00294_T 489693 32499882 209693647 178 12950 BIRC6 0 . GRCh38 2 32529798 32529798 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.12068C>A p.Ser4023Tyr p.S4023Y ENST00000421745 60/74 90 77 13 92 92 0 strelka-varscan-mutect BIRC6,missense_variant,p.Ser4023Tyr,ENST00000421745,NM_016252.3;MIR558,upstream_gene_variant,,ENST00000384920,;AL133243.2,downstream_gene_variant,,ENST00000617415,;BIRC6,non_coding_transcript_exon_variant,,ENST00000471232,; A ENST00000421745 Transcript missense_variant 12202/15703 12068/14574 4023/4857 S/Y tCt/tAt COSM1407842,COSM1407843 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 deleterious(0) 60/74 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 2 2 0 0 0 0 -19.9833 0.9999979 1 1 1 0 A 3 1 46 32529798 32529798 C A 1 0 0 0 0 1 0 0 0 1589 913 32 2 2 BIRC6 2 32529798 Missense_Mutation SNP C C3N-00294_T 29916 32529798 209663731 179 12951 LTBP1 0 . GRCh38 2 32947801 32947801 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.477G>A p.= p.Q159Q ENST00000404816 1/34 51 42 9 53 53 0 strelka-varscan-mutect LTBP1,synonymous_variant,p.=,ENST00000404816,NM_206943.2;Y_RNA,upstream_gene_variant,,ENST00000384224,; A ENST00000404816 Transcript synonymous_variant 830/6333 477/5166 159/1721 Q caG/caA 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 1/34 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99375 1 1 1 1 0 A 2 1 46 32947801 32947801 G A 1 0 0 0 0 0 0 0 1 8979 933 33 3 3 LTBP1 2 32947801 Silent SNP G C3N-00294_T 418003 32947801 209245728 180 12952 DHX57 0 . GRCh38 2 38848396 38848396 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.2037C>T p.= p.F679F ENST00000457308 10/24 94 84 10 106 106 0 strelka-varscan-mutect DHX57,synonymous_variant,p.=,ENST00000457308,NM_198963.1;DHX57,synonymous_variant,p.=,ENST00000452978,;DHX57,3_prime_UTR_variant,,ENST00000620517,;DHX57,non_coding_transcript_exon_variant,,ENST00000622155,;DHX57,downstream_gene_variant,,ENST00000474104,; A ENST00000457308 Transcript synonymous_variant 2165/4859 2037/4161 679/1386 F ttC/ttT 1 -1 DHX57 HGNC HGNC:20086 protein_coding YES CCDS1800.1 ENSP00000405111 Q6P158 UPI0000231C8C NM_198963.1 10/24 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF145,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs779227902 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 38848396 38848396 G A 1 0 0 0 0 0 0 0 1 4317 933 33 3 3 DHX57 2 38848396 Silent SNP G C3N-00294_T 5900595 38848396 203345133 181 12953 EML4 0 . GRCh38 2 42329971 42329971 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2710C>T p.Gln904Ter p.Q904* ENST00000318522 23/23 374 298 76 278 277 1 strelka-varscan-mutect EML4,stop_gained,p.Gln904Ter,ENST00000318522,NM_019063.4;EML4,stop_gained,p.Gln915Ter,ENST00000401738,;EML4,stop_gained,p.Gln846Ter,ENST00000402711,NM_001145076.2;COX7A2L,downstream_gene_variant,,ENST00000468711,;EML4,non_coding_transcript_exon_variant,,ENST00000406175,; T ENST00000318522 Transcript stop_gained 2972/5549 2710/2946 904/981 Q/* Cag/Tag 1 1 EML4 HGNC HGNC:1316 protein_coding YES CCDS1807.1 ENSP00000320663 Q9HC35 UPI0000140350 NM_019063.4 23/23 Low_complexity_(Seg):seg,hmmpanther:PTHR13720:SF11,hmmpanther:PTHR13720 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 42329971 42329971 C T 1 0 0 0 0 0 1 0 0 4942 827 29 3 3 EML4 2 42329971 Nonsense_Mutation SNP C C3N-00294_T 3481575 42329971 199863558 182 12954 RHOQ 0 . GRCh38 2 46580978 46580978 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.513G>A p.= p.L171L ENST00000238738 5/5 39 32 7 49 49 0 strelka-varscan-mutect RHOQ,synonymous_variant,p.=,ENST00000238738,NM_012249.3;PIGF,3_prime_UTR_variant,,ENST00000281382,NM_002643.3;PIGF,downstream_gene_variant,,ENST00000306465,NM_173074.2;RHOQ,downstream_gene_variant,,ENST00000482449,;RP11-417F21.1,upstream_gene_variant,,ENST00000506009,;PIGF,downstream_gene_variant,,ENST00000482786,;RHOQ,downstream_gene_variant,,ENST00000465198,;RHOQ,3_prime_UTR_variant,,ENST00000489471,;RHOQ,3_prime_UTR_variant,,ENST00000473428,;RHOQ,non_coding_transcript_exon_variant,,ENST00000489448,;PIGF,downstream_gene_variant,,ENST00000412717,;RHOQ,downstream_gene_variant,,ENST00000432183,;RHOQ,downstream_gene_variant,,ENST00000494370,;PIGF,downstream_gene_variant,,ENST00000420164,; A ENST00000238738 Transcript synonymous_variant 832/2975 513/618 171/205 L ttG/ttA 1 1 RHOQ HGNC HGNC:17736 protein_coding YES CCDS33191.1 ENSP00000238738 P17081 V9HWD0 UPI0000073EEC NM_012249.3 5/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51420,hmmpanther:PTHR24072,hmmpanther:PTHR24072:SF13,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -17.96745 1 1 1 1 0 A 2 1 46 46580978 46580978 G A 1 0 0 0 0 0 0 0 1 13515 1281 45 3 3 RHOQ 2 46580978 Silent SNP G C3N-00294_T 4251007 46580978 195612551 183 12955 KCNK12 0 . GRCh38 2 47570139 47570139 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.193G>A p.Glu65Lys p.E65K ENST00000327876 1/2 182 142 40 147 147 0 strelka-varscan-mutect KCNK12,missense_variant,p.Glu65Lys,ENST00000327876,NM_022055.1;KCNK12,non_coding_transcript_exon_variant,,ENST00000493527,; T ENST00000327876 Transcript missense_variant 801/6227 193/1293 65/430 E/K Gag/Aag 1 -1 KCNK12 HGNC HGNC:6274 protein_coding YES CCDS1835.1 ENSP00000327611 Q9HB15 UPI000000DC4C NM_022055.1 deleterious(0) 1/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF11,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 47570139 47570139 C T 1 0 0 0 0 1 0 0 0 7977 893 31 1 1 KCNK12 2 47570139 Missense_Mutation SNP C C3N-00294_T 989161 47570139 194623390 184 12956 FBXO11 0 . GRCh38 2 47838884 47838884 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.562G>T p.Glu188Ter p.E188* ENST00000403359 4/23 179 138 41 175 175 0 strelka-varscan-mutect FBXO11,stop_gained,p.Glu188Ter,ENST00000403359,NM_001190274.1;FBXO11,stop_gained,p.Glu104Ter,ENST00000402508,NM_025133.4;FBXO11,stop_gained,p.Glu104Ter,ENST00000424163,;FBXO11,upstream_gene_variant,,ENST00000493962,;FBXO11,non_coding_transcript_exon_variant,,ENST00000480038,;FBXO11,non_coding_transcript_exon_variant,,ENST00000492225,; A ENST00000403359 Transcript stop_gained 635/4055 562/2784 188/927 E/* Gaa/Taa 1 -1 FBXO11 HGNC HGNC:13590 protein_coding YES CCDS54357.1 ENSP00000384823 Q86XK2 UPI00005793B7 NM_001190274.1 4/23 Gene3D:1.20.1280.50,Pfam_domain:PF12937,PROSITE_profiles:PS50181,hmmpanther:PTHR22990,hmmpanther:PTHR22990:SF20,SMART_domains:SM00256,Superfamily_domains:SSF81383 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 47838884 47838884 C A 1 0 0 0 0 0 1 0 0 5590 835 29 2 2 FBXO11 2 47838884 Nonsense_Mutation SNP C C3N-00294_T 268745 47838884 194354645 185 12957 NRXN1 0 . GRCh38 2 50496028 50496028 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.3067C>T p.Leu1023Phe p.L1023F ENST00000404971 16/24 157 148 9 131 131 0 strelka-varscan-mutect NRXN1,missense_variant,p.Leu983Phe,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Leu975Phe,ENST00000625672,;NRXN1,missense_variant,p.Leu1023Phe,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Leu983Phe,ENST00000401669,;NRXN1,missense_variant,p.Leu971Phe,ENST00000405472,;NRXN1,missense_variant,p.Leu975Phe,ENST00000630543,;NRXN1,missense_variant,p.Leu713Phe,ENST00000406859,;NRXN1,missense_variant,p.Leu698Phe,ENST00000402717,;NRXN1,missense_variant,p.Leu17Phe,ENST00000625320,;NRXN1,downstream_gene_variant,,ENST00000495871,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,missense_variant,p.Leu701Phe,ENST00000331040,;NRXN1,downstream_gene_variant,,ENST00000474354,;NRXN1,downstream_gene_variant,,ENST00000462791,;NRXN1,upstream_gene_variant,,ENST00000626192,; A ENST00000404971 Transcript missense_variant 4407/7578 3067/4644 1023/1547 L/F Ctc/Ttc COSM283378,COSM283379,COSM4974088,COSM4974089,COSM4974090,COSM4974091 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 16/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 50496028 50496028 G A 1 0 0 0 0 1 0 0 0 10724 942 33 3 3 NRXN1 2 50496028 Missense_Mutation SNP G C3N-00294_T 2657144 50496028 191697501 186 12958 PSME4 0 . GRCh38 2 53920242 53920242 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2371G>A p.Glu791Lys p.E791K ENST00000404125 19/47 132 110 22 122 122 0 strelka-mutect PSME4,missense_variant,p.Glu791Lys,ENST00000404125,NM_014614.2;PSME4,3_prime_UTR_variant,,ENST00000389993,; T ENST00000404125 Transcript missense_variant 2427/7099 2371/5532 791/1843 E/K Gag/Aag 1 -1 PSME4 HGNC HGNC:20635 protein_coding YES CCDS33197.2 ENSP00000384211 Q14997 UPI0000F3BE4A NM_014614.2 deleterious(0.01) 19/47 Pfam_domain:PF16507,hmmpanther:PTHR32170,hmmpanther:PTHR32170:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 53920242 53920242 C T 1 0 0 0 0 1 0 0 0 12860 835 29 3 3 PSME4 2 53920242 Missense_Mutation SNP C C3N-00294_T 3424214 53920242 188273287 187 12959 SPTBN1 0 . GRCh38 2 54629397 54629397 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2263G>A p.Asp755Asn p.D755N ENST00000356805 14/36 352 299 53 302 302 0 strelka-varscan-mutect SPTBN1,missense_variant,p.Asp755Asn,ENST00000615901,;SPTBN1,missense_variant,p.Asp742Asn,ENST00000333896,NM_178313.2;SPTBN1,missense_variant,p.Asp755Asn,ENST00000356805,NM_003128.2;SPTBN1,downstream_gene_variant,,ENST00000389980,; A ENST00000356805 Transcript missense_variant 2544/8482 2263/7095 755/2364 D/N Gac/Aac COSM1021666,COSM1021667 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 deleterious(0) 14/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 54629397 54629397 G A 1 0 0 0 0 1 0 0 0 15475 1290 45 3 3 SPTBN1 2 54629397 Missense_Mutation SNP G C3N-00294_T 709155 54629397 187564132 188 12960 SPTBN1 0 . GRCh38 2 54629411 54629411 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2277G>C p.Trp759Cys p.W759C ENST00000356805 14/36 383 324 59 306 306 0 strelka-varscan-mutect SPTBN1,missense_variant,p.Trp759Cys,ENST00000615901,;SPTBN1,missense_variant,p.Trp746Cys,ENST00000333896,NM_178313.2;SPTBN1,missense_variant,p.Trp759Cys,ENST00000356805,NM_003128.2;SPTBN1,downstream_gene_variant,,ENST00000389980,; C ENST00000356805 Transcript missense_variant 2558/8482 2277/7095 759/2364 W/C tgG/tgC 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 deleterious(0) 14/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 54629411 54629411 G C 1 0 0 0 0 1 0 0 0 15475 1183 41 4 4 SPTBN1 2 54629411 Missense_Mutation SNP G C3N-00294_T 14 54629411 187564118 189 12961 PPP4R3B 0 . GRCh38 2 55588902 55588902 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.976G>C p.Asp326His p.D326H ENST00000616407 5/17 72 59 13 130 130 0 strelka-varscan-mutect PPP4R3B,missense_variant,p.Asp326His,ENST00000611717,NM_020463.3;PPP4R3B,missense_variant,p.Asp326His,ENST00000616407,NM_001122964.2;PPP4R3B,missense_variant,p.Asp326His,ENST00000616288,NM_001282850.1; G ENST00000616407 Transcript missense_variant 1279/4385 976/2550 326/849 D/H Gat/Cat 1 -1 PPP4R3B HGNC HGNC:29267 protein_coding YES CCDS46289.1 ENSP00000483228 Q5MIZ7 UPI00001C1DBA NM_001122964.2 tolerated(0.08) 5/17 hmmpanther:PTHR23318:SF2,hmmpanther:PTHR23318,Pfam_domain:PF04802,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1268369102 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 55588902 55588902 C G 1 0 0 0 0 1 0 0 0 12528 913 32 4 4 PPP4R3B 2 55588902 Missense_Mutation SNP C C3N-00294_T 959491 55588902 186604627 190 12962 USP34 0 . GRCh38 2 61246422 61246422 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.6450G>C p.Leu2150Phe p.L2150F ENST00000398571 50/80 141 123 18 167 167 0 strelka-varscan-mutect USP34,missense_variant,p.Leu2150Phe,ENST00000398571,NM_014709.3;USP34,missense_variant,p.Leu428Phe,ENST00000453734,;USP34,upstream_gene_variant,,ENST00000411912,;USP34,intron_variant,,ENST00000472706,;USP34,non_coding_transcript_exon_variant,,ENST00000463046,;RP11-479F13.1,upstream_gene_variant,,ENST00000605372,; G ENST00000398571 Transcript missense_variant 6527/11357 6450/10641 2150/3546 L/F ttG/ttC 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 deleterious(0) 50/80 PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97,PROSITE_patterns:PS00973,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 61246422 61246422 C G 1 0 0 0 0 1 0 0 0 17607 825 29 4 4 USP34 2 61246422 Missense_Mutation SNP C C3N-00294_T 5657520 61246422 180947107 191 12963 USP34 0 . GRCh38 2 61395226 61395226 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.560C>T p.Ser187Leu p.S187L ENST00000398571 4/80 49 42 7 74 74 0 strelka-varscan-mutect USP34,missense_variant,p.Ser187Leu,ENST00000398571,NM_014709.3;USP34,intron_variant,,ENST00000453133,; A ENST00000398571 Transcript missense_variant 637/11357 560/10641 187/3546 S/L tCa/tTa COSM3799098 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 deleterious(0) 4/80 1 MODERATE 1 SNV 2 1 1 PASS . . 1 205 4 0 0 0 0 0 -17.00606 1 1 1 1 0 A 3 1 46 61395226 61395226 G A 1 0 0 0 0 1 0 0 0 17607 1294 45 3 3 USP34 2 61395226 Missense_Mutation SNP G C3N-00294_T 148804 61395226 180798303 192 12964 XPO1 0 . GRCh38 2 61492458 61492458 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1590G>C p.Gln530His p.Q530H ENST00000401558 15/25 42 35 7 69 69 0 strelka-mutect XPO1,missense_variant,p.Gln530His,ENST00000401558,NM_003400.3;XPO1,missense_variant,p.Gln530His,ENST00000404992,;XPO1,missense_variant,p.Gln530His,ENST00000406957,;XPO1,upstream_gene_variant,,ENST00000494468,;XPO1,3_prime_UTR_variant,,ENST00000428210,;XPO1,non_coding_transcript_exon_variant,,ENST00000481073,;XPO1,non_coding_transcript_exon_variant,,ENST00000469337,;XPO1,upstream_gene_variant,,ENST00000461407,;XPO1,downstream_gene_variant,,ENST00000460037,;XPO1,downstream_gene_variant,,ENST00000437159,;XPO1,downstream_gene_variant,,ENST00000475744,; G ENST00000401558 Transcript missense_variant 2318/4915 1590/3216 530/1071 Q/H caG/caC 1 -1 XPO1 HGNC HGNC:12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 UPI0000001C23 NM_003400.3 tolerated(0.16) 15/25 hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF4,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 61492458 61492458 C G 1 0 0 0 0 1 0 0 0 18004 912 32 4 4 XPO1 2 61492458 Missense_Mutation SNP C C3N-00294_T 97232 61492458 180701071 193 12965 FAM161A 0 . GRCh38 2 61854018 61854018 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.24G>A p.= p.A8A ENST00000404929 1/7 335 267 68 302 302 0 strelka-varscan-mutect FAM161A,synonymous_variant,p.=,ENST00000404929,NM_001201543.1;FAM161A,synonymous_variant,p.=,ENST00000405894,NM_032180.2;FAM161A,synonymous_variant,p.=,ENST00000418113,;FAM161A,synonymous_variant,p.=,ENST00000456262,;FAM161A,synonymous_variant,p.=,ENST00000307507,;RP11-681L4.2,upstream_gene_variant,,ENST00000612715,;RP11-681L4.1,upstream_gene_variant,,ENST00000414975,; T ENST00000404929 Transcript synonymous_variant 36/3762 24/2151 8/716 A gcG/gcA 1 -1 FAM161A HGNC HGNC:25808 protein_coding YES CCDS56120.1 ENSP00000385158 Q3B820 UPI00006C0438 NM_001201543.1 1/7 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF3 LOW 1 SNV 1 1 PASS rs1435732952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 61854018 61854018 C T 1 0 0 0 0 0 0 0 1 5321 871 31 1 1 FAM161A 2 61854018 Silent SNP C C3N-00294_T 361560 61854018 180339511 194 12966 ARHGAP25 0 . GRCh38 2 68807439 68807439 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.633G>T p.= p.L211L ENST00000409202 5/11 246 196 50 250 250 0 strelka-varscan-mutect ARHGAP25,synonymous_variant,p.=,ENST00000409202,NM_001007231.2;ARHGAP25,synonymous_variant,p.=,ENST00000409220,NM_001166276.1;ARHGAP25,synonymous_variant,p.=,ENST00000409030,NM_014882.2;ARHGAP25,synonymous_variant,p.=,ENST00000467265,NM_001166277.1;ARHGAP25,synonymous_variant,p.=,ENST00000497259,;ARHGAP25,synonymous_variant,p.=,ENST00000497079,;ARHGAP25,non_coding_transcript_exon_variant,,ENST00000456116,;ARHGAP25,non_coding_transcript_exon_variant,,ENST00000485700,;ARHGAP25,synonymous_variant,p.=,ENST00000463483,;ARHGAP25,3_prime_UTR_variant,,ENST00000473986,;ARHGAP25,3_prime_UTR_variant,,ENST00000488795,; T ENST00000409202 Transcript synonymous_variant 998/2945 633/1941 211/646 L ctG/ctT 1 1 ARHGAP25 HGNC HGNC:28951 protein_coding YES CCDS33214.2 ENSP00000386911 P42331 UPI0000251EDD NM_001007231.2 5/11 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF20,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 68807439 68807439 G T 1 0 0 0 0 0 0 0 1 999 1277 45 2 2 ARHGAP25 2 68807439 Silent SNP G C3N-00294_T 6953421 68807439 173386090 195 12967 MXD1 0 . GRCh38 2 69937303 69937303 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.387G>A p.= p.L129L ENST00000264444 5/6 187 163 24 175 175 0 strelka-varscan-mutect MXD1,synonymous_variant,p.=,ENST00000264444,NM_001202513.1,NM_002357.3;MXD1,synonymous_variant,p.=,ENST00000540449,NM_001202514.1;MXD1,synonymous_variant,p.=,ENST00000435990,;MXD1,upstream_gene_variant,,ENST00000465446,;MXD1,3_prime_UTR_variant,,ENST00000409442,; A ENST00000264444 Transcript synonymous_variant 647/5587 387/666 129/221 L ctG/ctA 1 1 MXD1 HGNC HGNC:6761 protein_coding YES CCDS1896.1 ENSP00000264444 Q05195 UPI0000035C7D NM_001202513.1,NM_002357.3 5/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11969,hmmpanther:PTHR11969:SF18,Gene3D:4.10.280.10,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 69937303 69937303 G A 1 0 0 0 0 0 0 0 1 9998 1277 45 3 3 MXD1 2 69937303 Silent SNP G C3N-00294_T 1129864 69937303 172256226 196 12968 MXD1 0 . GRCh38 2 69937331 69937331 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.415G>C p.Glu139Gln p.E139Q ENST00000264444 5/6 182 160 22 162 162 0 strelka-varscan-mutect MXD1,missense_variant,p.Glu139Gln,ENST00000264444,NM_001202513.1,NM_002357.3;MXD1,missense_variant,p.Glu129Gln,ENST00000540449,NM_001202514.1;MXD1,missense_variant,p.Glu107Gln,ENST00000435990,;MXD1,upstream_gene_variant,,ENST00000465446,;MXD1,3_prime_UTR_variant,,ENST00000409442,; C ENST00000264444 Transcript missense_variant 675/5587 415/666 139/221 E/Q Gag/Cag COSM367242 1 1 MXD1 HGNC HGNC:6761 protein_coding YES CCDS1896.1 ENSP00000264444 Q05195 UPI0000035C7D NM_001202513.1,NM_002357.3 deleterious(0.02) 5/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11969,hmmpanther:PTHR11969:SF18 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 69937331 69937331 G C 1 0 0 0 0 1 0 0 0 9998 1291 45 4 4 MXD1 2 69937331 Missense_Mutation SNP G C3N-00294_T 28 69937331 172256198 197 12969 NOTO 0 . GRCh38 2 73208414 73208414 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.397C>T p.His133Tyr p.H133Y ENST00000398468 2/3 211 162 49 157 157 0 strelka-varscan-mutect NOTO,missense_variant,p.His133Tyr,ENST00000398468,NM_001134462.1; T ENST00000398468 Transcript missense_variant 806/2749 397/756 133/251 H/Y Cac/Tac 1 1 NOTO HGNC HGNC:31839 protein_coding YES CCDS46335.1 ENSP00000381486 A8MTQ0 UPI0000198CC1 NM_001134462.1 tolerated(0.17) 2/3 hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF31 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 73208414 73208414 C T 1 0 0 0 0 1 0 0 0 10597 826 29 3 3 NOTO 2 73208414 Missense_Mutation SNP C C3N-00294_T 3271083 73208414 168985115 198 12970 CCDC142 0 . GRCh38 2 74482264 74482264 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.574G>C p.Glu192Gln p.E192Q ENST00000290418 1/9 283 238 45 281 280 1 strelka-varscan-mutect CCDC142,missense_variant,p.Glu192Gln,ENST00000393965,;CCDC142,missense_variant,p.Glu192Gln,ENST00000290418,NM_032779.3;TTC31,upstream_gene_variant,,ENST00000410003,;TTC31,upstream_gene_variant,,ENST00000233623,NM_022492.4;TTC31,upstream_gene_variant,,ENST00000442235,;CCDC142,intron_variant,,ENST00000471713,;CCDC142,intron_variant,,ENST00000474681,;TTC31,upstream_gene_variant,,ENST00000463189,;CCDC142,missense_variant,p.Glu94Gln,ENST00000454193,;TTC31,upstream_gene_variant,,ENST00000489152,;TTC31,upstream_gene_variant,,ENST00000491252,;TTC31,upstream_gene_variant,,ENST00000424122,;TTC31,upstream_gene_variant,,ENST00000449459,;TTC31,upstream_gene_variant,,ENST00000464241,;TTC31,upstream_gene_variant,,ENST00000459957,;CCDC142,upstream_gene_variant,,ENST00000497232,;CCDC142,upstream_gene_variant,,ENST00000472962,;TTC31,upstream_gene_variant,,ENST00000463704,; G ENST00000290418 Transcript missense_variant 733/2835 574/2232 192/743 E/Q Gag/Cag COSM1307005,COSM4811820 1 -1 CCDC142 HGNC HGNC:25889 protein_coding YES CCDS1945.1 ENSP00000290418 Q17RM4 UPI000013CFB5 NM_032779.3 tolerated_low_confidence(0.06) 1/9 hmmpanther:PTHR21436 1,1 MODERATE SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 74482264 74482264 C G 1 0 0 0 0 1 0 0 0 2464 864 30 4 4 CCDC142 2 74482264 Missense_Mutation SNP C C3N-00294_T 1273850 74482264 167711265 199 12971 CTNNA2 0 . GRCh38 2 80546015 80546015 + Nonsense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.1492G>T p.Glu498Ter p.E498* ENST00000402739 10/18 194 110 84 186 186 0 strelka-varscan-mutect CTNNA2,stop_gained,p.Glu498Ter,ENST00000466387,;CTNNA2,stop_gained,p.Glu498Ter,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,stop_gained,p.Glu498Ter,ENST00000402739,NM_001282597.2;CTNNA2,stop_gained,p.Glu498Ter,ENST00000629316,NM_001164883.1;CTNNA2,stop_gained,p.Glu114Ter,ENST00000361291,NM_001320810.1;CTNNA2,stop_gained,p.Glu177Ter,ENST00000343114,NM_001282599.1;CTNNA2,stop_gained,p.Glu130Ter,ENST00000541047,NM_001282600.1;CTNNA2,stop_gained,p.Glu114Ter,ENST00000540488,;CTNNA2,stop_gained,p.Glu163Ter,ENST00000409550,;CTNNA2,non_coding_transcript_exon_variant,,ENST00000465616,;CTNNA2,downstream_gene_variant,,ENST00000493024,; T ENST00000402739 Transcript stop_gained 1497/3684 1492/2862 498/953 E/* Gag/Tag COSM370819 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 10/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,Prints_domain:PR00805,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 80546015 80546015 G T 1 0 0 0 0 0 1 0 0 3822 943 33 2 2 CTNNA2 2 80546015 Nonsense_Mutation SNP G C3N-00294_T 6063751 80546015 161647514 200 12972 DNAH6 0 . GRCh38 2 84701269 84701269 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.7991C>G p.Pro2664Arg p.P2664R ENST00000389394 49/77 344 298 46 329 328 1 strelka-varscan-mutect DNAH6,missense_variant,p.Pro2664Arg,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Pro2664Arg,ENST00000237449,;DNAH6,downstream_gene_variant,,ENST00000602588,; G ENST00000389394 Transcript missense_variant 8128/12795 7991/12477 2664/4158 P/R cCc/cGc COSM3001322 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 deleterious(0) 49/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF12780,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 84701269 84701269 C G 1 0 0 0 0 1 0 0 0 4420 623 22 4 4 DNAH6 2 84701269 Missense_Mutation SNP C C3N-00294_T 4155254 84701269 157492260 201 12973 TCF7L1 0 . GRCh38 2 85309210 85309210 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1515C>T p.= p.L505L ENST00000282111 12/12 353 174 179 365 365 0 strelka-varscan-mutect TCF7L1,synonymous_variant,p.=,ENST00000282111,NM_031283.2;TCF7L1,downstream_gene_variant,,ENST00000490744,; T ENST00000282111 Transcript synonymous_variant 1790/2968 1515/1767 505/588 L ctC/ctT 1 1 TCF7L1 HGNC HGNC:11640 protein_coding YES CCDS1971.1 ENSP00000282111 Q9HCS4 UPI0000136846 NM_031283.2 12/12 hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF25 LOW 1 SNV 1 1 PASS rs1483697912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 85309210 85309210 C T 1 0 0 0 0 0 0 0 1 16104 813 29 3 3 TCF7L1 2 85309210 Silent SNP C C3N-00294_T 607941 85309210 156884319 202 12974 POLR1A 0 . GRCh38 2 86040474 86040474 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.3658G>A p.Gly1220Arg p.G1220R ENST00000263857 25/34 110 93 17 115 115 0 strelka-varscan-mutect POLR1A,missense_variant,p.Gly1220Arg,ENST00000263857,NM_015425.3;POLR1A,missense_variant,p.Gly1220Arg,ENST00000409681,;POLR1A,non_coding_transcript_exon_variant,,ENST00000462078,;POLR1A,upstream_gene_variant,,ENST00000492034,;POLR1A,upstream_gene_variant,,ENST00000496892,; T ENST00000263857 Transcript missense_variant 4037/12749 3658/5163 1220/1720 G/R Gga/Aga 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 deleterious(0) 25/34 hmmpanther:PTHR19376:SF11,hmmpanther:PTHR19376,Pfam_domain:PF04998,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS rs1461382886 . 0 204 4 2 0 0 0 0 -20 0.9999839 1 1 1 0 T 3 4 46 86040474 86040474 C T 1 0 0 0 0 1 0 0 0 12319 661 23 1 1 POLR1A 2 86040474 Missense_Mutation SNP C C3N-00294_T 731264 86040474 156153055 203 12975 KDM3A 0 . GRCh38 2 86485733 86485733 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3187G>A p.Asp1063Asn p.D1063N ENST00000409556 22/27 141 119 22 108 108 0 strelka-varscan-mutect KDM3A,missense_variant,p.Asp1063Asn,ENST00000409556,;KDM3A,missense_variant,p.Asp1063Asn,ENST00000312912,NM_018433.5;KDM3A,missense_variant,p.Asp1063Asn,ENST00000409064,NM_001146688.1;KDM3A,missense_variant,p.Asp1063Asn,ENST00000542128,;KDM3A,non_coding_transcript_exon_variant,,ENST00000462197,;KDM3A,3_prime_UTR_variant,,ENST00000441719,;KDM3A,upstream_gene_variant,,ENST00000491383,;KDM3A,upstream_gene_variant,,ENST00000470160,;KDM3A,upstream_gene_variant,,ENST00000483866,; A ENST00000409556 Transcript missense_variant 3552/4928 3187/3966 1063/1321 D/N Gat/Aat 1 1 KDM3A HGNC HGNC:20815 protein_coding YES CCDS1990.1 ENSP00000386660 Q9Y4C1 UPI0000161FAE deleterious(0.02) 22/27 PROSITE_profiles:PS51184,hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF7,SMART_domains:SM00558,Superfamily_domains:SSF51197 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 86485733 86485733 G A 1 0 0 0 0 1 0 0 0 8044 1304 45 3 3 KDM3A 2 86485733 Missense_Mutation SNP G C3N-00294_T 445259 86485733 155707796 204 12976 CHMP3 0 . GRCh38 2 86563309 86563309 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.40G>C p.Glu14Gln p.E14Q ENST00000263856 1/6 163 135 28 116 116 0 strelka-varscan-mutect CHMP3,missense_variant,p.Glu14Gln,ENST00000263856,NM_016079.3;CHMP3,missense_variant,p.Glu14Gln,ENST00000409727,NM_001193517.1;CHMP3,5_prime_UTR_variant,,ENST00000409225,NM_001005753.2;RNF103-CHMP3,intron_variant,,ENST00000604011,NM_001198954.1;RNF103-CHMP3,intron_variant,,ENST00000440757,;AC015971.2,non_coding_transcript_exon_variant,,ENST00000597638,;AC015971.2,intron_variant,,ENST00000439077,;CHMP3,non_coding_transcript_exon_variant,,ENST00000485465,;CHMP3,upstream_gene_variant,,ENST00000393773,;CHMP3,upstream_gene_variant,,ENST00000486404,; G ENST00000263856 Transcript missense_variant 169/3171 40/669 14/222 E/Q Gaa/Caa 1 -1 CHMP3 HGNC HGNC:29865 protein_coding YES CCDS33236.1 ENSP00000263856 Q9Y3E7 UPI000006E953 NM_016079.3 tolerated(0.14) 1/6 hmmpanther:PTHR10476,hmmpanther:PTHR10476:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 86563309 86563309 C G 1 0 0 0 0 1 0 0 0 3115 927 32 4 4 CHMP3 2 86563309 Missense_Mutation SNP C C3N-00294_T 77576 86563309 155630220 205 12977 RNF103 0 . GRCh38 2 86620342 86620342 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.354C>T p.= p.I118I ENST00000237455 2/4 122 105 17 90 90 0 strelka-varscan-mutect RNF103,synonymous_variant,p.=,ENST00000237455,NM_005667.3;RNF103-CHMP3,synonymous_variant,p.=,ENST00000604011,NM_001198954.1;RNF103-CHMP3,synonymous_variant,p.=,ENST00000440757,;AC015971.2,downstream_gene_variant,,ENST00000426549,;AC015971.2,downstream_gene_variant,,ENST00000424788,;AC015971.2,downstream_gene_variant,,ENST00000597638,;AC015971.2,downstream_gene_variant,,ENST00000439077,;RNF103,non_coding_transcript_exon_variant,,ENST00000477307,;RNF103,non_coding_transcript_exon_variant,,ENST00000463333,;RNF103,non_coding_transcript_exon_variant,,ENST00000472680,;RNF103,non_coding_transcript_exon_variant,,ENST00000465629,; A ENST00000237455 Transcript synonymous_variant 1323/3477 354/2058 118/685 I atC/atT 1 -1 RNF103 HGNC HGNC:12859 protein_coding YES CCDS33237.1 ENSP00000237455 O00237 UPI0000073F2A NM_005667.3 2/4 hmmpanther:PTHR15302,hmmpanther:PTHR15302:SF0 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 86620342 86620342 G A 1 0 0 0 0 0 0 0 1 13601 932 33 3 3 RNF103 2 86620342 Silent SNP G C3N-00294_T 57033 86620342 155573187 206 12978 EIF2AK3 0 . GRCh38 2 88590500 88590500 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1108G>C p.Asp370His p.D370H ENST00000303236 6/17 142 118 24 222 222 0 strelka-varscan-mutect EIF2AK3,missense_variant,p.Asp370His,ENST00000303236,NM_004836.5;EIF2AK3,missense_variant,p.Asp219His,ENST00000419748,NM_001313915.1;EIF2AK3,missense_variant,p.Asp249His,ENST00000415570,;EIF2AK3,downstream_gene_variant,,ENST00000477083,; G ENST00000303236 Transcript missense_variant 1410/4646 1108/3351 370/1116 D/H Gat/Cat 1 -1 EIF2AK3 HGNC HGNC:3255 protein_coding YES CCDS33241.1 ENSP00000307235 Q9NZJ5 UPI000013E87D NM_004836.5 tolerated(0.07) 6/17 hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF73,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 88590500 88590500 C G 1 0 0 0 0 1 0 0 0 4834 913 32 4 4 EIF2AK3 2 88590500 Missense_Mutation SNP C C3N-00294_T 1970158 88590500 153603029 207 12979 EIF2AK3 0 . GRCh38 2 88595574 88595574 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.528C>T p.= p.F176F ENST00000303236 3/17 304 251 53 324 322 2 strelka-varscan-mutect EIF2AK3,synonymous_variant,p.=,ENST00000303236,NM_004836.5;EIF2AK3,synonymous_variant,p.=,ENST00000419748,NM_001313915.1;EIF2AK3,synonymous_variant,p.=,ENST00000415570,;EIF2AK3,upstream_gene_variant,,ENST00000477083,; A ENST00000303236 Transcript synonymous_variant 830/4646 528/3351 176/1116 F ttC/ttT 1 -1 EIF2AK3 HGNC HGNC:3255 protein_coding YES CCDS33241.1 ENSP00000307235 Q9NZJ5 UPI000013E87D NM_004836.5 3/17 Gene3D:2.140.10.10,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF73,Superfamily_domains:SSF50998 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 88595574 88595574 G A 1 0 0 0 0 0 0 0 1 4834 1281 45 3 3 EIF2AK3 2 88595574 Silent SNP G C3N-00294_T 5074 88595574 153597955 208 12980 FER1L5 0 . GRCh38 2 96649668 96649668 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.385G>C p.Glu129Gln p.E129Q ENST00000624922 5/53 161 141 20 184 184 0 strelka-varscan-mutect FER1L5,missense_variant,p.Glu129Gln,ENST00000623019,;FER1L5,missense_variant,p.Glu129Gln,ENST00000624922,NM_001293083.1;FER1L5,missense_variant,p.Glu129Gln,ENST00000622983,;FER1L5,5_prime_UTR_variant,,ENST00000623246,;FER1L5,non_coding_transcript_exon_variant,,ENST00000436930,;FER1L5,non_coding_transcript_exon_variant,,ENST00000505256,; C ENST00000624922 Transcript missense_variant 385/6367 385/6174 129/2057 E/Q Gag/Cag 1 1 FER1L5 HGNC HGNC:19044 protein_coding YES CCDS77438.1 ENSP00000485238 A0A096LNV2 UPI00046B3755 NM_001293083.1 tolerated(0.19) 5/53 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF34 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 96649668 96649668 G C 1 0 0 0 0 1 0 0 0 5677 1291 45 4 4 FER1L5 2 96649668 Missense_Mutation SNP G C3N-00294_T 8054094 96649668 145543861 209 12981 CNNM4 0 . GRCh38 2 96799065 96799065 + Missense_Mutation SNP C C G rs80100937 C3N-00294_T C3N-00294_N C C c.1690C>G p.Gln564Glu p.Q564E ENST00000377075 4/7 336 290 46 304 304 0 strelka-varscan-mutect CNNM4,missense_variant,p.Gln564Glu,ENST00000377075,NM_020184.3;MIR3127,downstream_gene_variant,,ENST00000583925,;CNNM4,non_coding_transcript_exon_variant,,ENST00000496186,;CNNM4,non_coding_transcript_exon_variant,,ENST00000493384,;CNNM4,downstream_gene_variant,,ENST00000482716,; G ENST00000377075 Transcript missense_variant 1788/4800 1690/2328 564/775 Q/E Cag/Gag rs80100937,CM090742 1 1 CNNM4 HGNC HGNC:105 protein_coding YES CCDS2024.2 ENSP00000366275 Q6P4Q7 UPI0000207C95 NM_020184.3 tolerated(0.29) 4/7 hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF26 pathogenic 19200525 MODERATE 1 SNV 1 1,1 1 PASS rs80100937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 96799065 96799065 C G 1 0 0 0 0 1 0 0 0 3395 827 29 4 4 CNNM4 2 96799065 Missense_Mutation SNP C C3N-00294_T 149397 96799065 145394464 210 12982 TXNDC9 0 . GRCh38 2 99333189 99333189 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.22G>A p.Asp8Asn p.D8N ENST00000264255 2/5 210 172 38 178 178 0 strelka-varscan-mutect TXNDC9,missense_variant,p.Asp8Asn,ENST00000264255,NM_005783.3;TXNDC9,missense_variant,p.Asp8Asn,ENST00000409434,;TXNDC9,missense_variant,p.Asp8Asn,ENST00000434323,;TXNDC9,missense_variant,p.Asp8Asn,ENST00000409705,;EIF5B,upstream_gene_variant,,ENST00000289371,NM_015904.3;EIF5B,upstream_gene_variant,,ENST00000617677,;TXNDC9,downstream_gene_variant,,ENST00000477337,;TXNDC9,missense_variant,p.Asp8Asn,ENST00000422767,;TXNDC9,missense_variant,p.Asp8Asn,ENST00000438680,;TXNDC9,non_coding_transcript_exon_variant,,ENST00000463385,;TXNDC9,non_coding_transcript_exon_variant,,ENST00000465183,; T ENST00000264255 Transcript missense_variant 278/1637 22/681 8/226 D/N Gac/Aac 1 -1 TXNDC9 HGNC HGNC:24110 protein_coding YES CCDS2044.1 ENSP00000264255 O14530 UPI0000124E09 NM_005783.3 tolerated(0.33) 2/5 hmmpanther:PTHR21148 MODERATE 1 SNV 1 1 PASS rs944239035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 99333189 99333189 C T 1 0 0 0 0 1 0 0 0 17316 826 29 3 3 TXNDC9 2 99333189 Missense_Mutation SNP C C3N-00294_T 2534124 99333189 142860340 211 12983 MAP4K4 0 . GRCh38 2 101859650 101859650 + Missense_Mutation SNP G G A rs772128002 C3N-00294_T C3N-00294_N G G c.1490G>A p.Arg497Gln p.R497Q ENST00000625522 15/31 104 90 14 122 122 0 strelka-varscan-mutect MAP4K4,missense_variant,p.Arg497Gln,ENST00000625522,;MAP4K4,missense_variant,p.Arg295Gln,ENST00000302217,;MAP4K4,missense_variant,p.Arg350Gln,ENST00000456652,;MAP4K4,missense_variant,p.Arg497Gln,ENST00000347699,NM_001242559.1;MAP4K4,missense_variant,p.Arg237Gln,ENST00000421882,;MAP4K4,missense_variant,p.Arg350Gln,ENST00000627726,;MAP4K4,missense_variant,p.Arg86Gln,ENST00000418101,;MAP4K4,intron_variant,,ENST00000350878,NM_145686.3;MAP4K4,intron_variant,,ENST00000324219,NM_001242560.1;MAP4K4,intron_variant,,ENST00000350198,;MAP4K4,intron_variant,,ENST00000413150,;MAP4K4,intron_variant,,ENST00000425019,;MAP4K4,intron_variant,,ENST00000417294,;MAP4K4,intron_variant,,ENST00000634702,NM_004834.4,NM_145687.3;MAP4K4,intron_variant,,ENST00000476609,; A ENST00000625522 Transcript missense_variant 1545/7458 1490/3963 497/1320 R/Q cGa/cAa rs772128002 1 1 MAP4K4 HGNC HGNC:6866 protein_coding ENSP00000486116 A0A0D9SEY1 UPI000014130C tolerated_low_confidence(0.1) 15/31 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF225 MODERATE SNV 5 1 PASS rs772128002 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 101859650 101859650 G A 1 0 0 0 0 1 0 0 0 9186 1058 37 1 1 MAP4K4 2 101859650 Missense_Mutation SNP G C3N-00294_T 2526461 101859650 140333879 212 12984 RGPD4 0 . GRCh38 2 107838307 107838307 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.191G>A p.Arg64Lys p.R64K ENST00000408999 3/23 30 23 7 16 16 0 strelka-varscan-mutect RGPD4,missense_variant,p.Arg64Lys,ENST00000408999,NM_182588.2; A ENST00000408999 Transcript missense_variant 268/5464 191/5277 64/1758 R/K aGa/aAa 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 tolerated(0.7) 3/23 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 78 132 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 107838307 107838307 G A 1 0 0 0 0 1 0 0 0 13460 942 33 3 3 RGPD4 2 107838307 Missense_Mutation SNP G C3N-00294_T 5978657 107838307 134355222 213 12985 GCC2 0 . GRCh38 2 108471580 108471580 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2251C>G p.Gln751Glu p.Q751E ENST00000309863 6/23 83 71 12 106 106 0 strelka-varscan-mutect GCC2,missense_variant,p.Gln751Glu,ENST00000309863,NM_181453.3;GCC2,missense_variant,p.Gln714Glu,ENST00000409896,;GCC2,upstream_gene_variant,,ENST00000462897,;GCC2,downstream_gene_variant,,ENST00000409821,;GCC2,upstream_gene_variant,,ENST00000492785,;GCC2,downstream_gene_variant,,ENST00000485546,;GCC2,downstream_gene_variant,,ENST00000478207,;GCC2,3_prime_UTR_variant,,ENST00000482325,;GCC2,upstream_gene_variant,,ENST00000447558,; G ENST00000309863 Transcript missense_variant 2965/7537 2251/5055 751/1684 Q/E Cag/Gag 1 1 GCC2 HGNC HGNC:23218 protein_coding YES CCDS33268.1 ENSP00000307939 Q8IWJ2 UPI000049DF0C NM_181453.3 tolerated(0.39) 6/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF25 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 108471580 108471580 C G 1 0 0 0 0 1 0 0 0 6156 827 29 4 4 GCC2 2 108471580 Missense_Mutation SNP C C3N-00294_T 633273 108471580 133721949 214 12986 RANBP2 0 . GRCh38 2 108730844 108730844 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.211G>C p.Glu71Gln p.E71Q ENST00000283195 3/29 298 256 42 389 389 0 strelka-varscan-mutect RANBP2,missense_variant,p.Glu71Gln,ENST00000283195,NM_006267.4;RANBP2,intron_variant,,ENST00000629728,;RANBP2,non_coding_transcript_exon_variant,,ENST00000495924,;RANBP2,intron_variant,,ENST00000425282,; C ENST00000283195 Transcript missense_variant 337/11711 211/9675 71/3224 E/Q Gaa/Caa 1 1 RANBP2 HGNC HGNC:9848 protein_coding YES CCDS2079.1 ENSP00000283195 P49792 UPI0000207FB9 NM_006267.4 tolerated(0.06) 3/29 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF100,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 108730844 108730844 G C 1 0 0 0 0 1 0 0 0 13187 1291 45 4 4 RANBP2 2 108730844 Missense_Mutation SNP G C3N-00294_T 259264 108730844 133462685 215 12987 RANBP2 0 . GRCh38 2 108768327 108768327 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.7788C>T p.= p.L2596L ENST00000283195 20/29 442 362 80 564 564 0 strelka-varscan-mutect RANBP2,synonymous_variant,p.=,ENST00000283195,NM_006267.4; T ENST00000283195 Transcript synonymous_variant 7914/11711 7788/9675 2596/3224 L ctC/ctT 1 1 RANBP2 HGNC HGNC:9848 protein_coding YES CCDS2079.1 ENSP00000283195 P49792 UPI0000207FB9 NM_006267.4 20/29 hmmpanther:PTHR23138,hmmpanther:PTHR23138:SF100 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 108768327 108768327 C T 1 0 0 0 0 0 0 0 1 13187 900 32 3 3 RANBP2 2 108768327 Silent SNP C C3N-00294_T 37483 108768327 133425202 216 12988 SH3RF3 0 . GRCh38 2 109436995 109436995 + Silent SNP G G C rs765140856 C3N-00294_T C3N-00294_N G G c.1677G>C p.= p.L559L ENST00000309415 7/10 299 265 34 292 292 0 strelka-varscan-mutect SH3RF3,synonymous_variant,p.=,ENST00000309415,NM_001099289.2; C ENST00000309415 Transcript synonymous_variant 1870/5803 1677/2649 559/882 L ctG/ctC rs765140856 1 1 SH3RF3 HGNC HGNC:24699 protein_coding YES CCDS74557.1 ENSP00000309186 Q8TEJ3 UPI0000DD7AEA NM_001099289.2 7/10 LOW 1 SNV 5 1 PASS rs765140856 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 109436995 109436995 G C 1 0 0 0 0 0 0 0 1 14519 1277 45 4 4 SH3RF3 2 109436995 Silent SNP G C3N-00294_T 668668 109436995 132756534 217 12989 SOWAHC 0 . GRCh38 2 109614535 109614535 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.46G>A p.Glu16Lys p.E16K ENST00000356454 1/1 35 29 6 19 19 0 strelka-mutect SOWAHC,missense_variant,p.Glu16Lys,ENST00000356454,NM_023016.3;SEPT10,upstream_gene_variant,,ENST00000356688,NM_001321498.1;SEPT10,upstream_gene_variant,,ENST00000397712,NM_001321509.1,NM_144710.3;SEPT10,upstream_gene_variant,,ENST00000397714,NM_178584.2;SEPT10,upstream_gene_variant,,ENST00000437928,;SEPT10,upstream_gene_variant,,ENST00000415095,;SEPT10,upstream_gene_variant,,ENST00000493445,;SEPT10,upstream_gene_variant,,ENST00000442746,;SEPT10,upstream_gene_variant,,ENST00000461295,;SEPT10,upstream_gene_variant,,ENST00000423520,;SEPT10,upstream_gene_variant,,ENST00000411469,;SEPT10,upstream_gene_variant,,ENST00000486678,;SEPT10,upstream_gene_variant,,ENST00000425498,; A ENST00000356454 Transcript missense_variant 202/4657 46/1578 16/525 E/K Gag/Aag 1 1 SOWAHC HGNC HGNC:26149 protein_coding YES CCDS33270.1 ENSP00000365830 Q53LP3 UPI0000208A9B NM_023016.3 deleterious(0.01) 1/1 hmmpanther:PTHR14491,hmmpanther:PTHR14491:SF4 MODERATE SNV 1 PASS . . 2 203 5 0 0 0 0 0 -15.71268 1 1 1 1 0 A 3 1 46 109614535 109614535 G A 1 0 0 0 0 1 0 0 0 15264 1059 37 1 1 SOWAHC 2 109614535 Missense_Mutation SNP G C3N-00294_T 177540 109614535 132578994 218 12990 SOWAHC 0 . GRCh38 2 109614799 109614799 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.310G>T p.Glu104Ter p.E104* ENST00000356454 1/1 189 135 54 124 124 0 strelka-varscan-mutect SOWAHC,stop_gained,p.Glu104Ter,ENST00000356454,NM_023016.3;SEPT10,upstream_gene_variant,,ENST00000356688,NM_001321498.1;SEPT10,upstream_gene_variant,,ENST00000397712,NM_001321509.1,NM_144710.3;SEPT10,upstream_gene_variant,,ENST00000397714,NM_178584.2;SEPT10,upstream_gene_variant,,ENST00000437928,;SEPT10,upstream_gene_variant,,ENST00000415095,;SEPT10,upstream_gene_variant,,ENST00000493445,;SEPT10,upstream_gene_variant,,ENST00000442746,;SEPT10,upstream_gene_variant,,ENST00000461295,;SEPT10,upstream_gene_variant,,ENST00000423520,;SEPT10,upstream_gene_variant,,ENST00000411469,;SEPT10,upstream_gene_variant,,ENST00000486678,;SEPT10,upstream_gene_variant,,ENST00000425498,; T ENST00000356454 Transcript stop_gained 466/4657 310/1578 104/525 E/* Gag/Tag 1 1 SOWAHC HGNC HGNC:26149 protein_coding YES CCDS33270.1 ENSP00000365830 Q53LP3 UPI0000208A9B NM_023016.3 1/1 hmmpanther:PTHR14491,hmmpanther:PTHR14491:SF4,Low_complexity_(Seg):seg HIGH SNV 1 PASS rs1393591236 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 109614799 109614799 G T 1 0 0 0 0 0 1 0 0 15264 1059 37 1 1 SOWAHC 2 109614799 Nonsense_Mutation SNP G C3N-00294_T 264 109614799 132578730 219 12991 MERTK 0 . GRCh38 2 111997387 111997387 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1515C>G p.Ile505Met p.I505M ENST00000295408 10/19 724 619 105 680 680 0 strelka-varscan-mutect MERTK,missense_variant,p.Ile505Met,ENST00000295408,;MERTK,missense_variant,p.Ile505Met,ENST00000421804,NM_006343.2;MERTK,missense_variant,p.Ile329Met,ENST00000409780,;MERTK,missense_variant,p.Leu162Val,ENST00000616902,;MERTK,3_prime_UTR_variant,,ENST00000439966,;MERTK,non_coding_transcript_exon_variant,,ENST00000473065,; G ENST00000295408 Transcript missense_variant 1772/3954 1515/3000 505/999 I/M atC/atG 1 1 MERTK HGNC HGNC:7027 protein_coding YES CCDS2094.1 ENSP00000295408 Q12866 UPI000013E252 tolerated(0.06) 10/19 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 111997387 111997387 C G 1 0 0 0 0 1 0 0 0 9424 913 32 4 4 MERTK 2 111997387 Missense_Mutation SNP C C3N-00294_T 2382588 111997387 130196142 220 12992 MERTK 0 . GRCh38 2 111997414 111997414 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1542G>C p.Leu514Phe p.L514F ENST00000295408 10/19 646 548 98 567 567 0 strelka-varscan-mutect MERTK,missense_variant,p.Leu514Phe,ENST00000295408,;MERTK,missense_variant,p.Leu514Phe,ENST00000421804,NM_006343.2;MERTK,missense_variant,p.Leu338Phe,ENST00000409780,;MERTK,missense_variant,p.Leu169Phe,ENST00000616902,;MERTK,3_prime_UTR_variant,,ENST00000439966,;MERTK,non_coding_transcript_exon_variant,,ENST00000473065,; C ENST00000295408 Transcript missense_variant 1799/3954 1542/3000 514/999 L/F ttG/ttC 1 1 MERTK HGNC HGNC:7027 protein_coding YES CCDS2094.1 ENSP00000295408 Q12866 UPI000013E252 tolerated(0.11) 10/19 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 111997414 111997414 G C 1 0 0 0 0 1 0 0 0 9424 1304 45 4 4 MERTK 2 111997414 Missense_Mutation SNP G C3N-00294_T 27 111997414 130196115 221 12993 RGPD8 0 . GRCh38 2 112390187 112390187 + Missense_Mutation SNP C C G rs778910571 C3N-00294_T C3N-00294_N C C c.2758G>C p.Asp920His p.D920H ENST00000302558 20/23 223 191 32 229 229 0 strelka-varscan-mutect RGPD8,missense_variant,p.Asp920His,ENST00000302558,NM_001164463.1;RGPD8,missense_variant,p.Asp780His,ENST00000409750,;RGPD8,downstream_gene_variant,,ENST00000330575,;RGPD8,3_prime_UTR_variant,,ENST00000522286,; G ENST00000302558 Transcript missense_variant 2950/5576 2758/5298 920/1765 D/H Gat/Cat rs778910571 1 -1 RGPD8 HGNC HGNC:9849 protein_coding YES CCDS46394.1 ENSP00000306637 O14715 UPI000013E7F5 NM_001164463.1 deleterious(0.02) 20/23 hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138 MODERATE 1 SNV 1 1 PASS rs778910571 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 112390187 112390187 C G 1 0 0 0 0 1 0 0 0 13461 826 29 4 4 RGPD8 2 112390187 Missense_Mutation SNP C C3N-00294_T 392773 112390187 129803342 222 12994 RGPD8 0 . GRCh38 2 112404043 112404043 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.1199C>G p.Ser400Cys p.S400C ENST00000302558 9/23 91 76 15 105 105 0 strelka-varscan-mutect RGPD8,missense_variant,p.Ser400Cys,ENST00000302558,NM_001164463.1;RGPD8,missense_variant,p.Ser260Cys,ENST00000409750,;RGPD8,missense_variant,p.Ser400Cys,ENST00000330575,;RGPD8,intron_variant,,ENST00000522286,;RGPD8,upstream_gene_variant,,ENST00000482903,; C ENST00000302558 Transcript missense_variant 1391/5576 1199/5298 400/1765 S/C tCt/tGt COSM1590486,COSM1590487,COSM1590488 1 -1 RGPD8 HGNC HGNC:9849 protein_coding YES CCDS46394.1 ENSP00000306637 O14715 UPI000013E7F5 NM_001164463.1 deleterious(0.05) 9/23 hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 4 203 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 112404043 112404043 G C 1 0 0 0 0 1 0 0 0 13461 942 33 4 4 RGPD8 2 112404043 Missense_Mutation SNP G C3N-00294_T 13856 112404043 129789486 223 12995 TMEM185B 0 . GRCh38 2 120222332 120222332 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.645C>A p.= p.I215I ENST00000426077 1/1 434 402 32 405 405 0 strelka-varscan-mutect TMEM185B,synonymous_variant,p.=,ENST00000426077,NM_024121.2; T ENST00000426077 Transcript synonymous_variant 1077/2131 645/1053 215/350 I atC/atA 1 -1 TMEM185B HGNC HGNC:18896 protein_coding YES CCDS58722.1 ENSP00000453399 Q9H7F4 UPI0000074167 NM_024121.2 1/1 Pfam_domain:PF10269,hmmpanther:PTHR13568,hmmpanther:PTHR13568:SF5,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 120222332 120222332 G T 1 0 0 0 0 0 0 0 1 16551 1280 45 2 2 TMEM185B 2 120222332 Silent SNP G C3N-00294_T 7818289 120222332 121971197 224 12996 CLASP1 0 . GRCh38 2 121447464 121447464 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.1785C>A p.= p.L595L ENST00000263710 19/40 261 211 50 194 194 0 strelka-varscan-mutect CLASP1,synonymous_variant,p.=,ENST00000263710,NM_015282.2;CLASP1,synonymous_variant,p.=,ENST00000409078,NM_001142274.1;CLASP1,synonymous_variant,p.=,ENST00000397587,;CLASP1,synonymous_variant,p.=,ENST00000541377,NM_001207051.1;CLASP1,synonymous_variant,p.=,ENST00000455322,NM_001142273.1;CLASP1,synonymous_variant,p.=,ENST00000452274,; T ENST00000263710 Transcript synonymous_variant 2175/8092 1785/4617 595/1538 L ctC/ctA 1 -1 CLASP1 HGNC HGNC:17088 protein_coding YES ENSP00000263710 Q7Z460 UPI00001A8BFF NM_015282.2 19/40 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF28 LOW 1 SNV 5 1 PASS rs1279080270 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 121447464 121447464 G T 1 0 0 0 0 0 0 0 1 3217 1161 41 2 2 CLASP1 2 121447464 Silent SNP G C3N-00294_T 1225132 121447464 120746065 225 12997 NIFK 0 . GRCh38 2 121727792 121727792 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.814G>C p.Glu272Gln p.E272Q ENST00000285814 7/7 183 144 39 212 212 0 strelka-varscan-mutect NIFK,missense_variant,p.Glu272Gln,ENST00000285814,NM_032390.4;NIFK,missense_variant,p.Glu81Gln,ENST00000423105,;NIFK,downstream_gene_variant,,ENST00000447132,;NIFK,downstream_gene_variant,,ENST00000451734,;NIFK-AS1,intron_variant,,ENST00000419902,;NIFK,non_coding_transcript_exon_variant,,ENST00000481978,;NIFK,non_coding_transcript_exon_variant,,ENST00000498570,;NIFK,downstream_gene_variant,,ENST00000477693,; G ENST00000285814 Transcript missense_variant 887/1734 814/882 272/293 E/Q Gaa/Caa 1 -1 NIFK HGNC HGNC:17838 protein_coding YES CCDS2135.1 ENSP00000285814 Q9BYG3 UPI00000738EB NM_032390.4 deleterious(0.04) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 121727792 121727792 C G 1 0 0 0 0 1 0 0 0 10450 922 32 4 4 NIFK 2 121727792 Missense_Mutation SNP C C3N-00294_T 280328 121727792 120465737 226 12998 BIN1 0 . GRCh38 2 127057571 127057571 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1033C>T p.Pro345Ser p.P345S ENST00000316724 12/19 46 37 9 41 41 0 strelka-varscan-mutect BIN1,missense_variant,p.Pro345Ser,ENST00000316724,NM_139343.2;BIN1,missense_variant,p.Pro314Ser,ENST00000346226,NM_139347.2;BIN1,missense_variant,p.Pro329Ser,ENST00000259238,NM_139346.2;BIN1,missense_variant,p.Pro314Ser,ENST00000393040,NM_139348.2;BIN1,intron_variant,,ENST00000357970,NM_139344.2;BIN1,intron_variant,,ENST00000351659,NM_139345.2;BIN1,intron_variant,,ENST00000393041,NM_139349.2;BIN1,intron_variant,,ENST00000352848,NM_004305.3;BIN1,intron_variant,,ENST00000409400,NM_139350.2;BIN1,intron_variant,,ENST00000348750,NM_139351.2;BIN1,intron_variant,,ENST00000376113,;BIN1,non_coding_transcript_exon_variant,,ENST00000484253,;BIN1,intron_variant,,ENST00000466111,;BIN1,upstream_gene_variant,,ENST00000462958,; A ENST00000316724 Transcript missense_variant 1445/2693 1033/1782 345/593 P/S Ccc/Tcc 1 -1 BIN1 HGNC HGNC:1052 protein_coding YES CCDS2138.1 ENSP00000316779 O00499 A0A024RAF1 UPI0000001303 NM_139343.2 deleterious(0.03) 12/19 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF192,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99588 1 1 1 1 0 A 3 1 46 127057571 127057571 G A 1 0 0 0 0 1 0 0 0 1583 1174 41 3 3 BIN1 2 127057571 Missense_Mutation SNP G C3N-00294_T 5329779 127057571 115135958 227 12999 HS6ST1 0 . GRCh38 2 128268743 128268743 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.655G>C p.Glu219Gln p.E219Q ENST00000259241 2/2 803 701 102 757 757 0 varscan-mutect HS6ST1,missense_variant,p.Glu219Gln,ENST00000259241,NM_004807.2;HS6ST1,non_coding_transcript_exon_variant,,ENST00000463963,;HS6ST1,intron_variant,,ENST00000469019,; G ENST00000259241 Transcript missense_variant 669/3932 655/1236 219/411 E/Q Gag/Cag 1 -1 HS6ST1 HGNC HGNC:5201 protein_coding YES CCDS42748.1 ENSP00000259241 O60243 UPI0000D61231 NM_004807.2 deleterious(0.03) 2/2 hmmpanther:PTHR12812:SF1,hmmpanther:PTHR12812,Pfam_domain:PF03567,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1463770620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 128268743 128268743 C G 1 0 0 0 0 1 0 0 0 7264 835 29 4 4 HS6ST1 2 128268743 Missense_Mutation SNP C C3N-00294_T 1211172 128268743 113924786 228 13000 ARHGEF4 0 . GRCh38 2 131041358 131041358 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.1233G>A p.Met411Ile p.M411I ENST00000326016 9/14 372 296 76 314 314 0 strelka-varscan-mutect ARHGEF4,missense_variant,p.Met1537Ile,ENST00000409359,;ARHGEF4,missense_variant,p.Met411Ile,ENST00000525839,NM_032995.2;ARHGEF4,missense_variant,p.Met436Ile,ENST00000392953,;ARHGEF4,missense_variant,p.Met411Ile,ENST00000326016,NM_015320.3;ARHGEF4,missense_variant,p.Met351Ile,ENST00000611048,;ARHGEF4,missense_variant,p.Met288Ile,ENST00000409303,;ARHGEF4,missense_variant,p.Met340Ile,ENST00000355771,;ARHGEF4,missense_variant,p.Met28Ile,ENST00000532720,;ARHGEF4,intron_variant,,ENST00000428230,;ARHGEF4,intron_variant,,ENST00000438985,;ARHGEF4,downstream_gene_variant,,ENST00000439368,;ARHGEF4,downstream_gene_variant,,ENST00000496764,;ARHGEF4,downstream_gene_variant,,ENST00000528247,;ARHGEF4,3_prime_UTR_variant,,ENST00000636987,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000490728,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000527365,;ARHGEF4,upstream_gene_variant,,ENST00000525092,; A ENST00000326016 Transcript missense_variant 1752/3666 1233/2073 411/690 M/I atG/atA COSM3566459,COSM3566460,COSM3566461 1 1 ARHGEF4 HGNC HGNC:684 protein_coding YES CCDS2165.1 ENSP00000316845 Q9NR80 UPI00001417F6 NM_015320.3 deleterious(0) 9/14 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 131041358 131041358 G A 1 0 0 0 0 1 0 0 0 1043 1290 45 3 3 ARHGEF4 2 131041358 Missense_Mutation SNP G C3N-00294_T 2772615 131041358 111152171 229 13001 POTEE 0 . GRCh38 2 131228374 131228374 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1048C>T p.His350Tyr p.H350Y ENST00000356920 5/15 140 121 19 191 191 0 varscan-mutect POTEE,missense_variant,p.His350Tyr,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.His350Tyr,ENST00000626191,;POTEE,missense_variant,p.His350Tyr,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;RNU6-127P,upstream_gene_variant,,ENST00000390897,;POTEE,missense_variant,p.His360Tyr,ENST00000358087,;POTEE,missense_variant,p.His350Tyr,ENST00000514256,; T ENST00000356920 Transcript missense_variant 1384/4159 1048/3228 350/1075 H/Y Cat/Tat 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 deleterious_low_confidence(0) 5/15 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 131228374 131228374 C T 1 0 0 0 0 1 0 0 0 12378 826 29 3 3 POTEE 2 131228374 Missense_Mutation SNP C C3N-00294_T 187016 131228374 110965155 230 13002 MAP3K19 0 . GRCh38 2 134988075 134988075 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.797G>A p.Gly266Glu p.G266E ENST00000392915 10/13 95 83 12 76 76 0 strelka-varscan-mutect MAP3K19,missense_variant,p.Gly266Glu,ENST00000392915,;MAP3K19,missense_variant,p.Gly266Glu,ENST00000375845,NM_025052.4;MAP3K19,missense_variant,p.Gly153Glu,ENST00000358371,NM_001018044.2;MAP3K19,missense_variant,p.Gly171Glu,ENST00000637841,;MAP3K19,intron_variant,,ENST00000392917,NM_001282883.1;MAP3K19,intron_variant,,ENST00000375844,NM_001018046.2;MAP3K19,intron_variant,,ENST00000392918,NM_001018047.2;MAP3K19,upstream_gene_variant,,ENST00000437365,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,;MAP3K19,downstream_gene_variant,,ENST00000468155,;MAP3K19,upstream_gene_variant,,ENST00000478805,; T ENST00000392915 Transcript missense_variant 1481/5030 797/3987 266/1328 G/E gGa/gAa COSM5394351 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 tolerated(1) 10/13 1 MODERATE 1 SNV 2 1 1 PASS rs1023047237 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 134988075 134988075 C T 1 0 0 0 0 1 0 0 0 9172 855 30 3 3 MAP3K19 2 134988075 Missense_Mutation SNP C C3N-00294_T 3759701 134988075 107205454 231 13003 LCT 0 . GRCh38 2 135817898 135817898 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1150G>T p.Glu384Ter p.E384* ENST00000264162 6/17 484 417 67 431 431 0 strelka-varscan-mutect LCT,stop_gained,p.Glu384Ter,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; A ENST00000264162 Transcript stop_gained 1161/6279 1150/5784 384/1927 E/* Gaa/Taa 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 6/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 135817898 135817898 C A 1 0 0 0 0 0 1 0 0 8599 835 29 2 2 LCT 2 135817898 Nonsense_Mutation SNP C C3N-00294_T 829823 135817898 106375631 232 13004 THSD7B 0 . GRCh38 2 137411741 137411741 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2828G>A p.Arg943Lys p.R943K ENST00000272643 13/27 427 336 91 350 350 0 strelka-varscan-mutect THSD7B,missense_variant,p.Arg943Lys,ENST00000409968,NM_001316349.1;THSD7B,missense_variant,p.Arg943Lys,ENST00000272643,;THSD7B,missense_variant,p.Arg912Lys,ENST00000413152,NM_001080427.1; A ENST00000272643 Transcript missense_variant 2828/5939 2828/4827 943/1608 R/K aGa/aAa 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A tolerated(1) 13/27 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 137411741 137411741 G A 1 0 0 0 0 1 0 0 0 16314 942 33 3 3 THSD7B 2 137411741 Missense_Mutation SNP G C3N-00294_T 1593843 137411741 104781788 233 13005 LRP1B 0 . GRCh38 2 140841037 140841037 + Nonsense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.4995G>A p.Trp1665Ter p.W1665* ENST00000389484 30/91 152 134 18 144 144 0 strelka-varscan-mutect LRP1B,stop_gained,p.Trp1665Ter,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript stop_gained 5967/16535 4995/13800 1665/4599 W/* tgG/tgA COSM4133145 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 30/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 140841037 140841037 C T 1 0 0 0 0 0 1 0 0 8850 856 30 3 3 LRP1B 2 140841037 Nonsense_Mutation SNP C C3N-00294_T 3429296 140841037 101352492 234 13006 ACVR2A 0 . GRCh38 2 147927175 147927175 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1443G>A p.= p.Q481Q ENST00000241416 11/11 332 290 42 272 272 0 strelka-varscan-mutect ACVR2A,synonymous_variant,p.=,ENST00000241416,NM_001278579.1,NM_001616.4;ACVR2A,synonymous_variant,p.=,ENST00000535787,NM_001278580.1;ACVR2A,synonymous_variant,p.=,ENST00000404590,;ORC4,downstream_gene_variant,,ENST00000535373,NM_001190879.2;ORC4,downstream_gene_variant,,ENST00000264169,NM_181742.3;ORC4,downstream_gene_variant,,ENST00000392857,NM_181741.3,NM_002552.4;ORC4,downstream_gene_variant,,ENST00000540442,NM_001190882.2;ORC4,downstream_gene_variant,,ENST00000536575,NM_001190881.2;ACVR2A,non_coding_transcript_exon_variant,,ENST00000495775,; A ENST00000241416 Transcript synonymous_variant 2079/5728 1443/1542 481/513 Q caG/caA 1 1 ACVR2A HGNC HGNC:173 protein_coding YES CCDS33301.1 ENSP00000241416 P27037 UPI0000126673 NM_001278579.1,NM_001616.4 11/11 PROSITE_profiles:PS50011,hmmpanther:PTHR23255:SF64,hmmpanther:PTHR23255,SMART_domains:SM00220 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 147927175 147927175 G A 1 0 0 0 0 0 0 0 1 267 933 33 3 3 ACVR2A 2 147927175 Silent SNP G C3N-00294_T 7086138 147927175 94266354 235 13007 MBD5 0 . GRCh38 2 148469944 148469944 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.2001G>T p.Leu667Phe p.L667F ENST00000407073 9/15 134 117 17 124 124 0 strelka-varscan-mutect MBD5,missense_variant,p.Leu667Phe,ENST00000407073,NM_018328.4;MBD5,missense_variant,p.Leu667Phe,ENST00000404807,;MBD5,missense_variant,p.Leu667Phe,ENST00000627651,;MBD5,missense_variant,p.Leu407Phe,ENST00000416015,;MBD5,upstream_gene_variant,,ENST00000638043,;MBD5,missense_variant,p.Leu667Phe,ENST00000629878,;MBD5,missense_variant,p.Leu146Phe,ENST00000628572,; T ENST00000407073 Transcript missense_variant 2998/9512 2001/4485 667/1494 L/F ttG/ttT 1 1 MBD5 HGNC HGNC:20444 protein_coding YES CCDS33302.1 ENSP00000386049 Q9P267 UPI0000208C40 NM_018328.4 tolerated(0.29) 9/15 hmmpanther:PTHR16112:SF18,hmmpanther:PTHR16112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 148469944 148469944 G T 1 0 0 0 0 1 0 0 0 9279 1281 45 2 2 MBD5 2 148469944 Missense_Mutation SNP G C3N-00294_T 542769 148469944 93723585 236 13008 KIF5C 0 . GRCh38 2 148875686 148875686 + Missense_Mutation SNP C C G rs374455258 C3N-00294_T C3N-00294_N C C c.69C>G p.Ile23Met p.I23M ENST00000435030 1/26 265 241 24 240 240 0 strelka-varscan-mutect KIF5C,missense_variant,p.Ile23Met,ENST00000435030,NM_004522.2;AC105402.4,intron_variant,,ENST00000601658,;AC105402.4,downstream_gene_variant,,ENST00000446781,;AC105402.3,upstream_gene_variant,,ENST00000413336,; G ENST00000435030 Transcript missense_variant 437/6931 69/2874 23/957 I/M atC/atG rs374455258,COSM3296322 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 tolerated(0.07) 1/26 Gene3D:3.40.850.10,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380,SMART_domains:SM00129,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374455258 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 148875686 148875686 C G 1 0 0 0 0 1 0 0 0 8172 845 30 4 4 KIF5C 2 148875686 Missense_Mutation SNP C C3N-00294_T 405742 148875686 93317843 237 13009 NEB 0 . GRCh38 2 151662137 151662137 + Missense_Mutation SNP C C G rs146310692 C3N-00294_T C3N-00294_N C C c.5968G>C p.Glu1990Gln p.E1990Q ENST00000618972 46/183 80 69 11 82 82 0 strelka-varscan-mutect NEB,missense_variant,p.Glu1990Gln,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Glu1990Gln,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Glu1990Gln,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Glu1990Gln,ENST00000603639,;NEB,missense_variant,p.Glu1990Gln,ENST00000604864,;NEB,missense_variant,p.Glu1990Gln,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Glu1990Gln,ENST00000172853,; G ENST00000618972 Transcript missense_variant,splice_region_variant 6171/26307 5968/25683 1990/8560 E/Q Gaa/Caa rs146310692 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.08) 46/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS rs146310692 . 0 202 8 0 0 0 0 0 -19.99989 0.9999977 1 1 1 0 G 3 3 46 151662137 151662137 C G 1 0 0 0 0 1 0 0 0 10326 898 31 4 4 NEB 2 151662137 Missense_Mutation SNP C C3N-00294_T 2786451 151662137 90531392 238 13010 TBR1 0 . GRCh38 2 161423696 161423696 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.1518C>T p.= p.F506F ENST00000389554 6/6 175 135 40 164 164 0 strelka-varscan-mutect TBR1,synonymous_variant,p.=,ENST00000389554,NM_006593.2;TBR1,synonymous_variant,p.=,ENST00000410035,;TBR1,synonymous_variant,p.=,ENST00000411412,;AC009487.5,upstream_gene_variant,,ENST00000505579,;AC009487.4,upstream_gene_variant,,ENST00000444164,;AC009487.4,upstream_gene_variant,,ENST00000437683,;SLC4A10,upstream_gene_variant,,ENST00000605990,;SLC4A10,upstream_gene_variant,,ENST00000482861,;TBR1,downstream_gene_variant,,ENST00000489530,;SLC4A10,upstream_gene_variant,,ENST00000606386,;TBR1,downstream_gene_variant,,ENST00000477804,;TBR1,non_coding_transcript_exon_variant,,ENST00000463544,; T ENST00000389554 Transcript synonymous_variant 1835/4009 1518/2049 506/682 F ttC/ttT COSM3895065 1 1 TBR1 HGNC HGNC:11590 protein_coding YES CCDS33310.1 ENSP00000374205 Q16650 UPI0000136A99 NM_006593.2 6/6 hmmpanther:PTHR11267:SF88,hmmpanther:PTHR11267,Pfam_domain:PF16176 1 LOW 1 SNV 1 1 1 PASS rs1340272250 . 0 207 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 T 2 4 46 161423696 161423696 C T 1 0 0 0 0 0 0 0 1 16052 883 31 1 1 TBR1 2 161423696 Silent SNP C C3N-00294_T 9761559 161423696 80769833 239 13011 IFIH1 0 . GRCh38 2 162281345 162281345 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1507G>A p.Glu503Lys p.E503K ENST00000263642 7/16 133 110 23 94 94 0 strelka-varscan-mutect IFIH1,missense_variant,p.Glu503Lys,ENST00000263642,NM_022168.3; T ENST00000263642 Transcript missense_variant 1903/3595 1507/3078 503/1025 E/K Gaa/Aaa 1 -1 IFIH1 HGNC HGNC:18873 protein_coding YES CCDS2217.1 ENSP00000263642 Q9BYX4 UPI000013D436 NM_022168.3 tolerated(0.12) 7/16 PROSITE_profiles:PS51192,hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF14,SMART_domains:SM00487 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 162281345 162281345 C T 1 0 0 0 0 1 0 0 0 7420 835 29 3 3 IFIH1 2 162281345 Missense_Mutation SNP C C3N-00294_T 857649 162281345 79912184 240 13012 FIGN 0 . GRCh38 2 163611386 163611386 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.446G>T p.Gly149Val p.G149V ENST00000333129 3/3 220 180 40 180 180 0 strelka-varscan-mutect FIGN,missense_variant,p.Gly149Val,ENST00000333129,NM_018086.2;FIGN,intron_variant,,ENST00000409634,;FIGN,non_coding_transcript_exon_variant,,ENST00000482917,; A ENST00000333129 Transcript missense_variant 761/9536 446/2280 149/759 G/V gGa/gTa 1 -1 FIGN HGNC HGNC:13285 protein_coding YES CCDS2221.2 ENSP00000333836 Q5HY92 UPI000022BD13 NM_018086.2 tolerated(0.07) 3/3 hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 163611386 163611386 C A 1 0 0 0 0 1 0 0 0 5755 855 30 2 2 FIGN 2 163611386 Missense_Mutation SNP C C3N-00294_T 1330041 163611386 78582143 241 13013 SCN3A 0 . GRCh38 2 165130113 165130113 + Missense_Mutation SNP C C G rs200738468 C3N-00294_T C3N-00294_N C C c.2749G>C p.Asp917His p.D917H ENST00000283254 17/28 469 398 71 425 425 0 strelka-varscan-mutect SCN3A,missense_variant,p.Asp917His,ENST00000360093,;SCN3A,missense_variant,p.Asp917His,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Asp868His,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Asp868His,ENST00000440431,;AC013463.2,non_coding_transcript_exon_variant,,ENST00000629817,;AC013463.2,non_coding_transcript_exon_variant,,ENST00000628085,;AC013463.2,non_coding_transcript_exon_variant,,ENST00000625505,;SCN3A,upstream_gene_variant,,ENST00000484898,; G ENST00000283254 Transcript missense_variant 3217/9091 2749/6003 917/2000 D/H Gat/Cat rs200738468 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 tolerated(0.1) 17/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 1 PASS rs200738468 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 165130113 165130113 C G 1 0 0 0 0 1 0 0 0 14187 826 29 4 4 SCN3A 2 165130113 Missense_Mutation SNP C C3N-00294_T 1518727 165130113 77063416 242 13014 SCN2A 0 . GRCh38 2 165331329 165331329 + Splice_Site SNP G G A C3N-00294_T C3N-00294_N G G c.2150-1G>A p.X717_splice ENST00000636071 214 186 28 254 254 0 strelka-mutect SCN2A,splice_acceptor_variant,,ENST00000636071,;SCN2A,splice_acceptor_variant,,ENST00000636985,;SCN2A,splice_acceptor_variant,,ENST00000637266,;SCN2A,splice_acceptor_variant,,ENST00000375437,NM_001040142.1;SCN2A,splice_acceptor_variant,,ENST00000283256,NM_021007.2;SCN2A,splice_acceptor_variant,,ENST00000375427,NM_001040143.1;SCN2A,splice_acceptor_variant,,ENST00000631182,;SCN2A,downstream_gene_variant,,ENST00000635945,;SCN2A,downstream_gene_variant,,ENST00000638151,;SCN2A,splice_acceptor_variant,,ENST00000480032,;SCN2A,splice_acceptor_variant,,ENST00000636662,;SCN2A,splice_acceptor_variant,,ENST00000636384,;SCN2A,splice_acceptor_variant,,ENST00000636769,;SCN2A,splice_acceptor_variant,,ENST00000636135,;SCN2A,splice_acceptor_variant,,ENST00000637367,; A ENST00000636071 Transcript splice_acceptor_variant -/9303 2150/6018 717/2005 COSM1008584,COSM1008585 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 14/27 1,1 HIGH 1 SNV 1,1 1 PASS . . 0 178 0 4 27 0 0 0 -11.58801 0 0 1 0 0 A 5 1 46 165331329 165331329 G A 1 0 0 0 0 0 0 1 0 14185 956 33 3 3 SCN2A 2 165331329 Splice_Site SNP G C3N-00294_T 201216 165331329 76862200 243 13015 SCN1A 0 . GRCh38 2 166045268 166045268 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.1437C>G p.= p.L479L ENST00000303395 12/28 336 264 72 297 297 0 strelka-varscan-mutect SCN1A,synonymous_variant,p.=,ENST00000635776,;SCN1A,synonymous_variant,p.=,ENST00000637988,;SCN1A,synonymous_variant,p.=,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,synonymous_variant,p.=,ENST00000635750,;SCN1A,synonymous_variant,p.=,ENST00000423058,;SCN1A,synonymous_variant,p.=,ENST00000375405,NM_006920.4;SCN1A,synonymous_variant,p.=,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;SCN1A,synonymous_variant,p.=,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000636759,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,; C ENST00000303395 Transcript synonymous_variant 1855/8533 1437/6030 479/2009 L ctC/ctG 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 12/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 166045268 166045268 G C 1 0 0 0 0 0 0 0 1 14183 929 33 4 4 SCN1A 2 166045268 Silent SNP G C3N-00294_T 713939 166045268 76148261 244 13016 SCN1A 0 . GRCh38 2 166051938 166051938 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.745G>A p.Asp249Asn p.D249N ENST00000303395 8/28 140 109 31 115 115 0 strelka-varscan-mutect SCN1A,missense_variant,p.Asp249Asn,ENST00000635776,;SCN1A,missense_variant,p.Asp249Asn,ENST00000637988,;SCN1A,missense_variant,p.Asp249Asn,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Asp249Asn,ENST00000635750,;SCN1A,missense_variant,p.Asp249Asn,ENST00000423058,;SCN1A,missense_variant,p.Asp249Asn,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Asp249Asn,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;SCN1A,missense_variant,p.Asp249Asn,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000636759,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,; T ENST00000303395 Transcript missense_variant 1163/8533 745/6030 249/2009 D/N Gat/Aat 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 tolerated(0.11) 8/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 166051938 166051938 C T 1 0 0 0 0 1 0 0 0 14183 913 32 3 3 SCN1A 2 166051938 Missense_Mutation SNP C C3N-00294_T 6670 166051938 76141591 245 13017 SCN9A 0 . GRCh38 2 166286424 166286424 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1514C>G p.Ser505Ter p.S505* ENST00000409672 11/27 188 163 25 185 185 0 strelka-mutect SCN9A,stop_gained,p.Ser505Ter,ENST00000303354,;SCN9A,stop_gained,p.Ser505Ter,ENST00000409672,NM_002977.3;SCN9A,stop_gained,p.Ser505Ter,ENST00000409435,;SCN9A,stop_gained,p.Ser370Ter,ENST00000452182,;SCN9A,stop_gained,p.Ser370Ter,ENST00000454569,;AC010127.3,intron_variant,,ENST00000447809,; C ENST00000409672 Transcript stop_gained 1861/9768 1514/5934 505/1977 S/* tCa/tGa 1 -1 SCN9A HGNC HGNC:10597 protein_coding YES CCDS46441.1 ENSP00000386306 Q15858 UPI0000140AC7 NM_002977.3 11/27 Pfam_domain:PF11933 HIGH SNV 5 1 PASS rs1395090262 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 166286424 166286424 G C 1 0 0 0 0 0 1 0 0 14194 1294 45 4 4 SCN9A 2 166286424 Nonsense_Mutation SNP G C3N-00294_T 234486 166286424 75907105 246 13018 SCN7A 0 . GRCh38 2 166456930 166456930 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1230G>A p.= p.K410K ENST00000409855 10/25 120 106 14 175 174 1 strelka-varscan-mutect SCN7A,synonymous_variant,p.=,ENST00000619410,;SCN7A,synonymous_variant,p.=,ENST00000621965,;SCN7A,synonymous_variant,p.=,ENST00000409855,NM_002976.3;SCN7A,synonymous_variant,p.=,ENST00000419992,;SCN7A,downstream_gene_variant,,ENST00000441411,;SCN7A,synonymous_variant,p.=,ENST00000424326,;SCN7A,downstream_gene_variant,,ENST00000497562,; T ENST00000409855 Transcript synonymous_variant 1357/7183 1230/5049 410/1682 K aaG/aaA 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 10/25 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14 LOW 1 SNV 1 1 PASS rs1194200221 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 166456930 166456930 C T 1 0 0 0 0 0 0 0 1 14192 912 32 3 3 SCN7A 2 166456930 Silent SNP C C3N-00294_T 170506 166456930 75736599 247 13019 XIRP2 0 . GRCh38 2 167242606 167242606 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.1214C>T p.Ser405Leu p.S405L ENST00000409195 9/11 86 73 13 98 98 0 strelka-varscan-mutect XIRP2,missense_variant,p.Ser405Leu,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser183Leu,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser230Leu,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1; T ENST00000409195 Transcript missense_variant 1303/12675 1214/10650 405/3549 S/L tCa/tTa COSM1528900 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.03) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 46 167242606 167242606 C T 1 0 0 0 0 1 0 0 0 17989 838 29 3 3 XIRP2 2 167242606 Missense_Mutation SNP C C3N-00294_T 785676 167242606 74950923 248 13020 XIRP2 0 . GRCh38 2 167243977 167243977 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.2585T>C p.Leu862Pro p.L862P ENST00000409195 9/11 158 65 93 192 192 0 strelka-varscan-mutect XIRP2,missense_variant,p.Leu862Pro,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Leu640Pro,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Leu687Pro,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; C ENST00000409195 Transcript missense_variant 2674/12675 2585/10650 862/3549 L/P cTa/cCa 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.07) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 167243977 167243977 T C 1 0 0 0 0 1 0 0 0 17989 1522 53 5 5 XIRP2 2 167243977 Missense_Mutation SNP T C3N-00294_T 1371 167243977 74949552 249 13021 B3GALT1 0 . GRCh38 2 167869307 167869307 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.268G>A p.Glu90Lys p.E90K ENST00000392690 1/1 164 136 28 137 137 0 strelka-varscan-mutect B3GALT1,missense_variant,p.Glu90Lys,ENST00000392690,NM_020981.3;AC016723.4,intron_variant,,ENST00000436982,;AC016723.4,intron_variant,,ENST00000430546,; A ENST00000392690 Transcript missense_variant 360/5094 268/981 90/326 E/K Gaa/Aaa COSM3314428 1 1 B3GALT1 HGNC HGNC:916 protein_coding YES CCDS2227.1 ENSP00000376456 Q9Y5Z6 UPI00000255A2 NM_020981.3 deleterious(0.04) 1/1 hmmpanther:PTHR11214:SF20,hmmpanther:PTHR11214 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 167869307 167869307 G A 1 0 0 0 0 1 0 0 0 1404 1175 41 3 3 B3GALT1 2 167869307 Missense_Mutation SNP G C3N-00294_T 625330 167869307 74324222 250 13022 UBR3 0 . GRCh38 2 169927372 169927372 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2391G>A p.Met797Ile p.M797I ENST00000418381 17/39 178 162 16 168 168 0 strelka-varscan-mutect UBR3,missense_variant,p.Met797Ile,ENST00000272793,;UBR3,missense_variant,p.Met797Ile,ENST00000418381,NM_172070.3;UBR3,upstream_gene_variant,,ENST00000430321,; A ENST00000418381 Transcript missense_variant 2391/7951 2391/5667 797/1888 M/I atG/atA COSM1009384 1 1 UBR3 HGNC HGNC:30467 protein_coding YES CCDS2238.2 ENSP00000396068 Q6ZT12 UPI00015FA088 NM_172070.3 deleterious(0.01) 17/39 hmmpanther:PTHR21497 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 169927372 169927372 G A 1 0 0 0 0 1 0 0 0 17427 1290 45 3 3 UBR3 2 169927372 Missense_Mutation SNP G C3N-00294_T 2058065 169927372 72266157 251 13023 MYO3B 0 . GRCh38 2 170214456 170214456 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.399C>T p.= p.I133I ENST00000408978 4/35 319 284 35 290 290 0 strelka-varscan-mutect MYO3B,synonymous_variant,p.=,ENST00000408978,NM_138995.4;MYO3B,synonymous_variant,p.=,ENST00000409044,NM_001083615.3;MYO3B,synonymous_variant,p.=,ENST00000484338,;MYO3B,synonymous_variant,p.=,ENST00000442690,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,synonymous_variant,p.=,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; T ENST00000408978 Transcript synonymous_variant 542/5529 399/4026 133/1341 I atC/atT 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 4/35 PROSITE_profiles:PS50011,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 170214456 170214456 C T 1 0 0 0 0 0 0 0 1 10078 903 32 3 3 MYO3B 2 170214456 Silent SNP C C3N-00294_T 287084 170214456 71979073 252 13024 SCRN3 0 . GRCh38 2 174424545 174424545 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.988G>C p.Glu330Gln p.E330Q ENST00000272732 7/8 74 65 9 95 95 0 strelka-varscan-mutect SCRN3,missense_variant,p.Glu330Gln,ENST00000272732,NM_024583.4;SCRN3,missense_variant,p.Glu323Gln,ENST00000409673,NM_001193528.1;SCRN3,non_coding_transcript_exon_variant,,ENST00000548921,;SCRN3,non_coding_transcript_exon_variant,,ENST00000549848,;SCRN3,non_coding_transcript_exon_variant,,ENST00000490927,;SCRN3,non_coding_transcript_exon_variant,,ENST00000475928,;SCRN3,3_prime_UTR_variant,,ENST00000548868,;SCRN3,3_prime_UTR_variant,,ENST00000437944,; C ENST00000272732 Transcript missense_variant 1070/3037 988/1275 330/424 E/Q Gaa/Caa 1 1 SCRN3 HGNC HGNC:30382 protein_coding YES CCDS2258.1 ENSP00000272732 Q0VDG4 UPI00002090F8 NM_024583.4 deleterious(0.03) 7/8 hmmpanther:PTHR12994,hmmpanther:PTHR12994:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 174424545 174424545 G C 1 0 0 0 0 1 0 0 0 14210 1291 45 4 4 SCRN3 2 174424545 Missense_Mutation SNP G C3N-00294_T 4210089 174424545 67768984 253 13025 PLEKHA3 0 . GRCh38 2 178493976 178493976 + Missense_Mutation SNP C C G rs140472356 C3N-00294_T C3N-00294_N C C c.437C>G p.Ser146Cys p.S146C ENST00000234453 4/8 115 95 20 108 108 0 strelka-varscan-mutect PLEKHA3,missense_variant,p.Ser146Cys,ENST00000234453,NM_019091.3;PLEKHA3,upstream_gene_variant,,ENST00000421187,;PLEKHA3,non_coding_transcript_exon_variant,,ENST00000461474,;PLEKHA3,3_prime_UTR_variant,,ENST00000453653,; G ENST00000234453 Transcript missense_variant 839/13880 437/903 146/300 S/C tCt/tGt rs140472356 1 1 PLEKHA3 HGNC HGNC:14338 protein_coding YES CCDS33336.1 ENSP00000234453 Q9HB20 UPI000000DA8A NM_019091.3 deleterious(0.03) 4/8 hmmpanther:PTHR10219,hmmpanther:PTHR10219:SF25 MODERATE 1 SNV 1 1 PASS rs140472356 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 178493976 178493976 C G 1 0 0 0 0 1 0 0 0 12150 913 32 4 4 PLEKHA3 2 178493976 Missense_Mutation SNP C C3N-00294_T 4069431 178493976 63699553 254 13026 TTN 0 . GRCh38 2 178575958 178575958 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.70174G>A p.Glu23392Lys p.E23392K ENST00000589042 326/363 92 74 18 70 70 0 strelka-varscan-mutect TTN,missense_variant,p.Glu23392Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Glu21751Lys,ENST00000591111,;TTN,missense_variant,p.Glu21751Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Glu20824Lys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Glu14327Lys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Glu14519Lys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Glu14452Lys,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-171I2.2,upstream_gene_variant,,ENST00000603521,;RP11-171I2.5,upstream_gene_variant,,ENST00000604215,; T ENST00000589042 Transcript missense_variant 70399/109224 70174/107976 23392/35991 E/K Gaa/Aaa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 46 178575958 178575958 C T 1 0 0 0 0 1 0 0 0 17245 835 29 3 3 TTN 2 178575958 Missense_Mutation SNP C C3N-00294_T 81982 178575958 63617571 255 13027 TTN 0 . GRCh38 2 178672092 178672092 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.35106C>T p.= p.F11702F ENST00000589042 155/363 176 151 25 259 259 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000448510,;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN,upstream_gene_variant,,ENST00000425332,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; A ENST00000589042 Transcript synonymous_variant 35331/109224 35106/107976 11702/35991 F ttC/ttT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 155/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 178672092 178672092 G A 1 0 0 0 0 0 0 0 1 17245 1281 45 3 3 TTN 2 178672092 Silent SNP G C3N-00294_T 96134 178672092 63521437 256 13028 TTN 0 . GRCh38 2 178721015 178721015 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.23004C>T p.= p.I7668I ENST00000589042 79/363 193 163 30 185 185 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,; A ENST00000589042 Transcript synonymous_variant 23229/109224 23004/107976 7668/35991 I atC/atT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 79/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 178721015 178721015 G A 1 0 0 0 0 0 0 0 1 17245 1280 45 3 3 TTN 2 178721015 Silent SNP G C3N-00294_T 48923 178721015 63472514 257 13029 TTN 0 . GRCh38 2 178740479 178740479 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.12754C>G p.Leu4252Val p.L4252V ENST00000589042 48/363 107 91 16 106 106 0 strelka-varscan-mutect TTN,missense_variant,p.Leu4252Val,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu3935Val,ENST00000591111,;TTN,missense_variant,p.Leu3935Val,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu3889Val,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Leu4081Val,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Leu4014Val,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000342992,NM_133378.4;TTN,downstream_gene_variant,,ENST00000360870,NM_133379.4;TTN-AS1,intron_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000627661,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000631319,;TTN-AS1,upstream_gene_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000625480,; C ENST00000589042 Transcript missense_variant 12979/109224 12754/107976 4252/35991 L/V Ctt/Gtt COSM1306150,COSM4810808 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 48/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 178740479 178740479 G C 1 0 0 0 0 1 0 0 0 17245 942 33 4 4 TTN 2 178740479 Missense_Mutation SNP G C3N-00294_T 19464 178740479 63453050 258 13030 TTN 0 . GRCh38 2 178789471 178789471 + Silent SNP G G C rs760757049 C3N-00294_T C3N-00294_N G G c.1965C>G p.= p.A655A ENST00000589042 13/363 276 231 45 308 308 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN,synonymous_variant,p.=,ENST00000360870,NM_133379.4;TTN,synonymous_variant,p.=,ENST00000436599,; C ENST00000589042 Transcript synonymous_variant 2190/109224 1965/107976 655/35991 A gcC/gcG rs760757049 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 13/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF09042 LOW 1 SNV 5 1 PASS rs760757049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 178789471 178789471 G C 1 0 0 0 0 0 0 0 1 17245 987 35 4 4 TTN 2 178789471 Silent SNP G C3N-00294_T 48992 178789471 63404058 259 13031 CWC22 0 . GRCh38 2 179981998 179981998 + Splice_Site SNP C C T novel C3N-00294_T C3N-00294_N C C c.207-1G>A p.X69_splice ENST00000410053 167 134 33 153 153 0 strelka-varscan-mutect CWC22,splice_acceptor_variant,,ENST00000410053,NM_020943.2;CWC22,splice_acceptor_variant,,ENST00000404136,; T ENST00000410053 Transcript splice_acceptor_variant -/3280 207/2727 69/908 1 -1 CWC22 HGNC HGNC:29322 protein_coding YES CCDS46465.1 ENSP00000387006 Q9HCG8 UPI00001C1DAE NM_020943.2 4/19 HIGH 1 SNV 1 1 PASS rs1224611762 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 46 179981998 179981998 C T 1 0 0 0 0 0 0 1 0 3878 927 32 3 3 CWC22 2 179981998 Splice_Site SNP C C3N-00294_T 1192527 179981998 62211531 260 13032 FSIP2 0 . GRCh38 2 185804187 185804187 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.15148C>G p.Leu5050Val p.L5050V ENST00000343098 17/23 30 23 7 57 57 0 strelka-varscan-mutect FSIP2,missense_variant,p.Leu5050Val,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Leu4961Val,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; G ENST00000343098 Transcript missense_variant 15148/21054 15148/20991 5050/6996 L/V Ctt/Gtt 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS rs962101664 . 2 206 2 0 0 0 0 0 -19.07774 1 1 1 1 0 G 3 3 46 185804187 185804187 C G 1 0 0 0 0 1 0 0 0 5949 913 32 4 4 FSIP2 2 185804187 Missense_Mutation SNP C C3N-00294_T 5822189 185804187 56389342 261 13033 ANKAR 0 . GRCh38 2 189695018 189695018 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1345C>T p.Gln449Ter p.Q449* ENST00000520309 6/23 43 35 8 68 68 0 strelka-varscan-mutect ANKAR,stop_gained,p.Gln449Ter,ENST00000520309,NM_144708.3;ANKAR,stop_gained,p.Gln449Ter,ENST00000313581,;ANKAR,intron_variant,,ENST00000461516,;ANKAR,upstream_gene_variant,,ENST00000464687,;ANKAR,stop_gained,p.Gln378Ter,ENST00000433782,;ANKAR,stop_gained,p.Gln213Ter,ENST00000441800,;ANKAR,downstream_gene_variant,,ENST00000467927,; T ENST00000520309 Transcript stop_gained 1433/4410 1345/4305 449/1434 Q/* Cag/Tag 1 1 ANKAR HGNC HGNC:26350 protein_coding YES CCDS33351.2 ENSP00000427882 Q7Z5J8 UPI00001D7E11 NM_144708.3 6/23 hmmpanther:PTHR23315:SF84,hmmpanther:PTHR23315 HIGH 1 SNV 5 1 PASS rs1313078138 . 2 201 6 0 0 0 0 0 -19.52831 1 1 1 1 0 T 4 4 46 189695018 189695018 C T 1 0 0 0 0 0 1 0 0 723 827 29 3 3 ANKAR 2 189695018 Nonsense_Mutation SNP C C3N-00294_T 3890831 189695018 52498511 262 13034 ANKAR 0 . GRCh38 2 189705034 189705034 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1720C>G p.Leu574Val p.L574V ENST00000520309 8/23 185 148 37 143 143 0 strelka-varscan-mutect ANKAR,missense_variant,p.Leu574Val,ENST00000520309,NM_144708.3;ANKAR,missense_variant,p.Leu574Val,ENST00000313581,;ANKAR,intron_variant,,ENST00000464687,;ANKAR,missense_variant,p.Leu503Val,ENST00000433782,;ANKAR,missense_variant,p.Leu338Val,ENST00000441800,; G ENST00000520309 Transcript missense_variant 1808/4410 1720/4305 574/1434 L/V Cta/Gta 1 1 ANKAR HGNC HGNC:26350 protein_coding YES CCDS33351.2 ENSP00000427882 Q7Z5J8 UPI00001D7E11 NM_144708.3 deleterious(0) 8/23 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR23315:SF84,hmmpanther:PTHR23315,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 189705034 189705034 C G 1 0 0 0 0 1 0 0 0 723 912 32 4 4 ANKAR 2 189705034 Missense_Mutation SNP C C3N-00294_T 10016 189705034 52488495 263 13035 STAT1 0 . GRCh38 2 191009071 191009071 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.165C>T p.= p.I55I ENST00000361099 4/25 435 372 63 355 355 0 strelka-varscan-mutect STAT1,synonymous_variant,p.=,ENST00000361099,NM_007315.3;STAT1,synonymous_variant,p.=,ENST00000540176,;STAT1,synonymous_variant,p.=,ENST00000409465,;STAT1,synonymous_variant,p.=,ENST00000392323,;STAT1,synonymous_variant,p.=,ENST00000392322,NM_139266.2;STAT1,synonymous_variant,p.=,ENST00000424722,;STAT1,synonymous_variant,p.=,ENST00000454414,;STAT1,synonymous_variant,p.=,ENST00000432058,;STAT1,synonymous_variant,p.=,ENST00000452281,; A ENST00000361099 Transcript synonymous_variant 553/4310 165/2253 55/750 I atC/atT 1 -1 STAT1 HGNC HGNC:11362 protein_coding YES CCDS2309.1 ENSP00000354394 P42224 UPI00000473FB NM_007315.3 4/25 hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF18,Gene3D:1bgfA00,Pfam_domain:PF02865,SMART_domains:SM00964,Superfamily_domains:0035539 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 191009071 191009071 G A 1 0 0 0 0 0 0 0 1 15640 1164 41 3 3 STAT1 2 191009071 Silent SNP G C3N-00294_T 1304037 191009071 51184458 264 13036 SF3B1 0 . GRCh38 2 197402629 197402629 + Silent SNP T T A rs764419493 C3N-00294_T C3N-00294_N T T c.2004A>T p.= p.V668V ENST00000335508 14/25 321 168 153 296 296 0 strelka-varscan-mutect SF3B1,synonymous_variant,p.=,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,upstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; A ENST00000335508 Transcript synonymous_variant 2096/6526 2004/3915 668/1304 V gtA/gtT rs764419493 1 -1 SF3B1 HGNC HGNC:10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 UPI000013D493 NM_012433.2 14/25 hmmpanther:PTHR12097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs764419493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 197402629 197402629 T A 1 0 0 0 0 0 0 0 1 14428 1625 57 4 4 SF3B1 2 197402629 Silent SNP T C3N-00294_T 6393558 197402629 44790900 265 13037 52 2 SF3B1 0 . GRCh38 2 197402635 197402635 + Missense_Mutation SNP C C A rs377023736 C3N-00294_T C3N-00294_N C C c.1998G>T p.Lys666Asn p.K666N ENST00000335508 14/25 343 278 65 319 319 0 strelka-varscan-mutect SF3B1,missense_variant,p.Lys666Asn,ENST00000335508,NM_012433.2;SF3B1,upstream_gene_variant,,ENST00000424674,;SNORA4,upstream_gene_variant,,ENST00000365564,;SF3B1,upstream_gene_variant,,ENST00000462613,;SF3B1,upstream_gene_variant,,ENST00000496458,; A ENST00000335508 Transcript missense_variant 2090/6526 1998/3915 666/1304 K/N aaG/aaT rs377023736,COSM131557,COSM132937 1 -1 SF3B1 HGNC HGNC:10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 UPI000013D493 NM_012433.2 deleterious(0) 14/25 hmmpanther:PTHR12097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 pathogenic 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs377023736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 197402635 197402635 C A 1 0 0 0 0 1 0 0 0 14428 912 32 2 2 SF3B1 2 197402635 Missense_Mutation SNP C C3N-00294_T 6 197402635 44790894 266 13038 52 2 HSPD1 0 . GRCh38 2 197489205 197489205 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1012C>G p.Gln338Glu p.Q338E ENST00000388968 9/12 338 282 56 327 327 0 strelka-varscan-mutect HSPD1,missense_variant,p.Gln338Glu,ENST00000388968,NM_002156.4;HSPD1,missense_variant,p.Gln338Glu,ENST00000345042,NM_199440.1;HSPD1,downstream_gene_variant,,ENST00000452200,;HSPD1,downstream_gene_variant,,ENST00000430176,;HSPD1,non_coding_transcript_exon_variant,,ENST00000491249,;HSPD1,downstream_gene_variant,,ENST00000486181,;HSPD1,downstream_gene_variant,,ENST00000482167,; C ENST00000388968 Transcript missense_variant 1280/2455 1012/1722 338/573 Q/E Cag/Gag 1 -1 HSPD1 HGNC HGNC:5261 protein_coding YES CCDS33357.1 ENSP00000373620 P10809 A0A024R3X4 UPI0000042366 NM_002156.4 tolerated(0.41) 9/12 Gene3D:3.50.7.10,HAMAP:MF_00600,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF64,Superfamily_domains:SSF52029,TIGRFAM_domain:TIGR02348 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 197489205 197489205 G C 1 0 0 0 0 1 0 0 0 7324 1299 45 4 4 HSPD1 2 197489205 Missense_Mutation SNP G C3N-00294_T 86570 197489205 44704324 267 13039 C2orf69 0 . GRCh38 2 199925552 199925552 + Missense_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.824T>A p.Phe275Tyr p.F275Y ENST00000319974 2/2 157 138 19 164 164 0 strelka-varscan-mutect C2orf69,missense_variant,p.Phe275Tyr,ENST00000319974,NM_153689.5;TYW5,downstream_gene_variant,,ENST00000354611,NM_001039693.2;C2orf69,intron_variant,,ENST00000491721,;TYW5,downstream_gene_variant,,ENST00000483328,; A ENST00000319974 Transcript missense_variant 1007/3728 824/1158 275/385 F/Y tTt/tAt 1 1 C2orf69 HGNC HGNC:26799 protein_coding YES CCDS46482.1 ENSP00000312770 Q8N8R5 UPI0000073170 NM_153689.5 tolerated(1) 2/2 hmmpanther:PTHR31296:SF1,hmmpanther:PTHR31296,Pfam_domain:PF10561 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 46 199925552 199925552 T A 1 0 0 0 0 1 0 0 0 2043 1841 64 4 4 C2orf69 2 199925552 Missense_Mutation SNP T C3N-00294_T 2436347 199925552 42267977 268 13040 FAM126B 0 . GRCh38 2 200997519 200997519 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.552C>A p.= p.L184L ENST00000418596 8/12 120 110 10 135 135 0 strelka-varscan-mutect FAM126B,synonymous_variant,p.=,ENST00000418596,NM_001321619.1,NM_001321629.1,NM_001321618.1,NM_001321622.1,NM_001321621.1,NM_173822.3;FAM126B,synonymous_variant,p.=,ENST00000452799,;AC005037.3,intron_variant,,ENST00000413848,;FAM126B,3_prime_UTR_variant,,ENST00000286181,;FAM126B,non_coding_transcript_exon_variant,,ENST00000498780,;FAM126B,non_coding_transcript_exon_variant,,ENST00000490725,; T ENST00000418596 Transcript synonymous_variant 740/9333 552/1593 184/530 L ctC/ctA 1 -1 FAM126B HGNC HGNC:28593 protein_coding YES CCDS2335.1 ENSP00000393667 Q8IXS8 UPI0000074347 NM_001321619.1,NM_001321629.1,NM_001321618.1,NM_001321622.1,NM_001321621.1,NM_173822.3 8/12 Pfam_domain:PF09790,hmmpanther:PTHR31220,hmmpanther:PTHR31220:SF3 LOW 1 SNV 1 1 PASS rs926731753 . 0 208 0 2 0 0 0 0 -14.79816 0.9999998 1 1 1 0 T 2 4 46 200997519 200997519 G T 1 0 0 0 0 0 0 0 1 5282 1277 45 2 2 FAM126B 2 200997519 Silent SNP G C3N-00294_T 1071967 200997519 41196010 269 13041 ABI2 0 . GRCh38 2 203417000 203417000 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1285G>T p.Glu429Ter p.E429* ENST00000295851 10/11 212 182 30 164 164 0 strelka-varscan-mutect ABI2,stop_gained,p.Glu429Ter,ENST00000295851,;ABI2,stop_gained,p.Glu429Ter,ENST00000261018,NM_001282925.1;ABI2,stop_gained,p.Glu306Ter,ENST00000261016,NM_001282932.1,NM_001282927.1;ABI2,stop_gained,p.Glu391Ter,ENST00000261017,NM_005759.5;ABI2,stop_gained,p.Glu396Ter,ENST00000422511,;ABI2,stop_gained,p.Glu423Ter,ENST00000424558,NM_001282926.1;ABI2,stop_gained,p.Glu374Ter,ENST00000430418,;ABI2,stop_gained,p.Glu429Ter,ENST00000417864,;ABI2,stop_gained,p.Glu209Ter,ENST00000454023,;RAPH1,intron_variant,,ENST00000457812,;ABI2,non_coding_transcript_exon_variant,,ENST00000464761,;ABI2,non_coding_transcript_exon_variant,,ENST00000416396,;ABI2,downstream_gene_variant,,ENST00000430574,;ABI2,downstream_gene_variant,,ENST00000422719,;ABI2,3_prime_UTR_variant,,ENST00000441061,;ABI2,3_prime_UTR_variant,,ENST00000416001,; T ENST00000295851 Transcript stop_gained 1581/22209 1285/1542 429/513 E/* Gag/Tag 1 1 ABI2 HGNC HGNC:24011 protein_coding YES CCDS63093.1 ENSP00000295851 F8WAL6 UPI000013D12C 10/11 Low_complexity_(Seg):seg,hmmpanther:PTHR10460,hmmpanther:PTHR10460:SF3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 203417000 203417000 G T 1 0 0 0 0 0 1 0 0 99 1175 41 2 2 ABI2 2 203417000 Nonsense_Mutation SNP G C3N-00294_T 2419481 203417000 38776529 270 13042 NDUFS1 0 . GRCh38 2 206142774 206142774 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1087G>A p.Glu363Lys p.E363K ENST00000455934 11/19 348 304 44 297 297 0 strelka-varscan-mutect NDUFS1,missense_variant,p.Glu349Lys,ENST00000233190,NM_005006.6;NDUFS1,missense_variant,p.Glu363Lys,ENST00000455934,NM_001199984.1;NDUFS1,missense_variant,p.Glu292Lys,ENST00000423725,NM_001199983.1;NDUFS1,missense_variant,p.Glu313Lys,ENST00000440274,NM_001199981.1;NDUFS1,missense_variant,p.Glu349Lys,ENST00000449699,;NDUFS1,missense_variant,p.Glu233Lys,ENST00000457011,;NDUFS1,missense_variant,p.Glu238Lys,ENST00000432169,NM_001199982.1;NDUFS1,downstream_gene_variant,,ENST00000456284,; T ENST00000455934 Transcript missense_variant 1148/3361 1087/2226 363/741 E/K Gaa/Aaa 1 -1 NDUFS1 HGNC HGNC:7707 protein_coding YES CCDS56165.1 ENSP00000392709 P28331 UPI0000EE3600 NM_001199984.1 deleterious(0) 11/19 Gene3D:3.40.50.740,Pfam_domain:PF00384,TIGRFAM_domain:TIGR01973,Superfamily_domains:SSF53706 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 206142774 206142774 C T 1 0 0 0 0 1 0 0 0 10315 835 29 3 3 NDUFS1 2 206142774 Missense_Mutation SNP C C3N-00294_T 2725774 206142774 36050755 271 13043 CCNYL1 0 . GRCh38 2 207712016 207712016 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.120G>T p.= p.A40A ENST00000339882 1/8 36 30 6 28 28 0 strelka-varscan-mutect CCNYL1,synonymous_variant,p.=,ENST00000295414,;CCNYL1,synonymous_variant,p.=,ENST00000339882,NM_001142300.1;CCNYL1,synonymous_variant,p.=,ENST00000420822,;CCNYL1,5_prime_UTR_variant,,ENST00000392209,NM_152523.2;CCNYL1,upstream_gene_variant,,ENST00000452312,; T ENST00000339882 Transcript synonymous_variant 266/2619 120/927 40/308 A gcG/gcT 1 1 CCNYL1 HGNC HGNC:26868 protein_coding YES CCDS46503.1 ENSP00000342344 Q8N7R7 UPI000020946B NM_001142300.1 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR14248,hmmpanther:PTHR14248:SF27 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.62199 1 1 1 1 0 T 2 4 46 207712016 207712016 G T 1 0 0 0 0 0 0 0 1 2636 1103 39 1 1 CCNYL1 2 207712016 Silent SNP G C3N-00294_T 1569242 207712016 34481513 272 13044 CPS1 0 . GRCh38 2 210656574 210656574 + Missense_Mutation SNP C C T rs149518280 C3N-00294_T C3N-00294_N C C c.3626C>T p.Ser1209Leu p.S1209L ENST00000430249 31/39 366 318 48 317 317 0 strelka-varscan-mutect CPS1,missense_variant,p.Ser1203Leu,ENST00000233072,NM_001875.4;CPS1,missense_variant,p.Ser1209Leu,ENST00000430249,NM_001122633.2;CPS1,missense_variant,p.Ser752Leu,ENST00000451903,NM_001122634.3;CPS1,upstream_gene_variant,,ENST00000470791,; T ENST00000430249 Transcript missense_variant 3681/5698 3626/4521 1209/1506 S/L tCg/tTg rs149518280,CM114379,COSM1202194,COSM1202195 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 deleterious(0) 31/39 PROSITE_profiles:PS50975,hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,TIGRFAM_domain:TIGR01369,Pfam_domain:PF02786,Gene3D:3.30.470.20,Superfamily_domains:SSF56059 0,0,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs149518280 . 0 208 0 0 2 0 0 0 -19.24346 0.9960093 1 1 1 0 T 3 4 46 210656574 210656574 C T 1 0 0 0 0 1 0 0 0 3619 893 31 1 1 CPS1 2 210656574 Missense_Mutation SNP C C3N-00294_T 2944558 210656574 31536955 273 13045 IKZF2 0 . GRCh38 2 213008008 213008008 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.933G>A p.= p.L311L ENST00000434687 9/9 237 201 36 156 156 0 strelka-varscan-mutect IKZF2,synonymous_variant,p.=,ENST00000457361,;IKZF2,synonymous_variant,p.=,ENST00000451136,;IKZF2,synonymous_variant,p.=,ENST00000434687,NM_016260.2;IKZF2,synonymous_variant,p.=,ENST00000342002,;IKZF2,synonymous_variant,p.=,ENST00000374319,NM_001079526.1;AC079610.1,intron_variant,,ENST00000415387,;IKZF2,3_prime_UTR_variant,,ENST00000431520,;IKZF2,3_prime_UTR_variant,,ENST00000439848,;IKZF2,3_prime_UTR_variant,,ENST00000412444,;IKZF2,3_prime_UTR_variant,,ENST00000453575,;IKZF2,3_prime_UTR_variant,,ENST00000374326,;IKZF2,non_coding_transcript_exon_variant,,ENST00000484040,; T ENST00000434687 Transcript synonymous_variant 1243/3888 933/1581 311/526 L ctG/ctA 1 -1 IKZF2 HGNC HGNC:13177 protein_coding YES CCDS2395.1 ENSP00000412869 Q9UKS7 UPI000013D4DA NM_016260.2 9/9 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF33 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 213008008 213008008 C T 1 0 0 0 0 0 0 0 1 7523 813 29 3 3 IKZF2 2 213008008 Silent SNP C C3N-00294_T 2351434 213008008 29185521 274 13046 ABCA12 0 . GRCh38 2 215011577 215011577 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2194C>G p.Gln732Glu p.Q732E ENST00000272895 17/53 440 376 64 403 403 0 strelka-varscan-mutect ABCA12,missense_variant,p.Gln732Glu,ENST00000272895,NM_173076.2;ABCA12,missense_variant,p.Gln414Glu,ENST00000389661,NM_015657.3;AC072062.3,intron_variant,,ENST00000617699,;AC072062.3,upstream_gene_variant,,ENST00000611187,;AC072062.3,upstream_gene_variant,,ENST00000627811,; C ENST00000272895 Transcript missense_variant 2414/9100 2194/7788 732/2595 Q/E Caa/Gaa COSM5193476,COSM5193477 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 tolerated(0.35) 17/53 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF29 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 215011577 215011577 G C 1 0 0 0 0 1 0 0 0 34 1299 45 4 4 ABCA12 2 215011577 Missense_Mutation SNP G C3N-00294_T 2003569 215011577 27181952 275 13047 PLCD4 0 . GRCh38 2 218618793 218618793 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.396G>T p.Gln132His p.Q132H ENST00000450993 4/16 209 96 113 153 152 1 strelka-varscan-mutect PLCD4,missense_variant,p.Gln132His,ENST00000450993,NM_032726.3;PLCD4,missense_variant,p.Gln132His,ENST00000432688,;PLCD4,missense_variant,p.Gln132His,ENST00000417849,;PLCD4,downstream_gene_variant,,ENST00000415854,;PLCD4,3_prime_UTR_variant,,ENST00000444453,;PLCD4,3_prime_UTR_variant,,ENST00000446503,;PLCD4,non_coding_transcript_exon_variant,,ENST00000473443,;PLCD4,non_coding_transcript_exon_variant,,ENST00000483685,;PLCD4,non_coding_transcript_exon_variant,,ENST00000469493,;PLCD4,non_coding_transcript_exon_variant,,ENST00000465713,;PLCD4,upstream_gene_variant,,ENST00000459791,; T ENST00000450993 Transcript missense_variant 735/3232 396/2289 132/762 Q/H caG/caT 1 1 PLCD4 HGNC HGNC:9062 protein_coding YES CCDS46516.1 ENSP00000388631 Q9BRC7 UPI0000044279 NM_032726.3 deleterious(0.04) 4/16 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF31,Gene3D:2.30.29.30 MODERATE 1 SNV 1 1 PASS rs1353538502 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 218618793 218618793 G T 1 0 0 0 0 1 0 0 0 12127 991 35 2 2 PLCD4 2 218618793 Missense_Mutation SNP G C3N-00294_T 3607216 218618793 23574736 276 13048 NHEJ1 0 . GRCh38 2 219157511 219157511 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.351C>G p.Phe117Leu p.F117L ENST00000356853 3/8 590 550 40 492 492 0 strelka-varscan-mutect NHEJ1,missense_variant,p.Phe117Leu,ENST00000356853,NM_024782.2;NHEJ1,missense_variant,p.Phe117Leu,ENST00000409720,;NHEJ1,missense_variant,p.Phe37Leu,ENST00000426304,;NHEJ1,missense_variant,p.Phe117Leu,ENST00000457600,;SLC23A3,downstream_gene_variant,,ENST00000455516,NM_001144890.1;SLC23A3,downstream_gene_variant,,ENST00000295738,NM_144712.4;SLC23A3,downstream_gene_variant,,ENST00000409878,NM_001144889.1;NHEJ1,downstream_gene_variant,,ENST00000481764,;NHEJ1,missense_variant,p.Phe117Leu,ENST00000418099,;RP11-33O4.2,3_prime_UTR_variant,,ENST00000318673,;NHEJ1,3_prime_UTR_variant,,ENST00000450447,;RP11-33O4.2,non_coding_transcript_exon_variant,,ENST00000498327,; C ENST00000356853 Transcript missense_variant 485/2094 351/900 117/299 F/L ttC/ttG COSM1752354,COSM3933534,COSM3933535 1 -1 NHEJ1 HGNC HGNC:25737 protein_coding YES CCDS2432.1 ENSP00000349313 Q9H9Q4 UPI000006D9F7 NM_024782.2 deleterious(0) 3/8 Gene3D:2.170.210.10,Pfam_domain:PF09302,hmmpanther:PTHR32235 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1249067213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 219157511 219157511 G C 1 0 0 0 0 1 0 0 0 10435 933 33 4 4 NHEJ1 2 219157511 Missense_Mutation SNP G C3N-00294_T 538718 219157511 23036018 277 13049 SLC23A3 0 . GRCh38 2 219168773 219168773 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.577C>T p.Pro193Ser p.P193S ENST00000455516 5/12 92 77 15 84 84 0 strelka-varscan-mutect SLC23A3,missense_variant,p.Pro193Ser,ENST00000455516,NM_001144890.1;SLC23A3,missense_variant,p.Pro185Ser,ENST00000295738,NM_144712.4;SLC23A3,missense_variant,p.Pro185Ser,ENST00000409878,NM_001144889.1;SLC23A3,missense_variant,p.Pro185Ser,ENST00000409370,;SLC23A3,missense_variant,p.Pro140Ser,ENST00000430764,;CNPPD1,downstream_gene_variant,,ENST00000409789,;CNPPD1,downstream_gene_variant,,ENST00000360507,NM_001321391.1,NM_001321390.1,NM_015680.4;CNPPD1,downstream_gene_variant,,ENST00000453038,;CNPPD1,downstream_gene_variant,,ENST00000451647,;SLC23A3,downstream_gene_variant,,ENST00000421779,;RP11-33O4.2,3_prime_UTR_variant,,ENST00000318673,;SLC23A3,3_prime_UTR_variant,,ENST00000414999,;SLC23A3,non_coding_transcript_exon_variant,,ENST00000497918,;SLC23A3,non_coding_transcript_exon_variant,,ENST00000465580,;RP11-33O4.2,intron_variant,,ENST00000498327,;SLC23A3,downstream_gene_variant,,ENST00000461812,; A ENST00000455516 Transcript missense_variant 625/2048 577/1857 193/618 P/S Ccc/Tcc 1 -1 SLC23A3 HGNC HGNC:20601 protein_coding YES CCDS46517.1 ENSP00000406546 Q6PIS1 UPI0001914DC9 NM_001144890.1 tolerated(0.41) 5/12 hmmpanther:PTHR11119,hmmpanther:PTHR11119:SF3,Pfam_domain:PF00860 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 219168773 219168773 G A 1 0 0 0 0 1 0 0 0 14730 1174 41 3 3 SLC23A3 2 219168773 Missense_Mutation SNP G C3N-00294_T 11262 219168773 23024756 278 13050 ABCB6 0 . GRCh38 2 219218469 219218469 + Missense_Mutation SNP G G C rs747669898 C3N-00294_T C3N-00294_N G G c.205C>G p.Arg69Gly p.R69G ENST00000265316 1/19 165 128 37 177 176 1 strelka-varscan-mutect ABCB6,missense_variant,p.Arg69Gly,ENST00000265316,NM_005689.2;ATG9A,downstream_gene_variant,,ENST00000409618,;ATG9A,downstream_gene_variant,,ENST00000396761,NM_024085.4;ATG9A,downstream_gene_variant,,ENST00000361242,NM_001077198.2;ATG9A,downstream_gene_variant,,ENST00000409422,;ABCB6,upstream_gene_variant,,ENST00000295750,;ATG9A,downstream_gene_variant,,ENST00000429920,;ABCB6,missense_variant,p.Arg4Gly,ENST00000448398,;ATG9A,3_prime_UTR_variant,,ENST00000446716,;ATG9A,downstream_gene_variant,,ENST00000409033,;ABCB6,upstream_gene_variant,,ENST00000497882,;ATG9A,downstream_gene_variant,,ENST00000475339,;ABCB6,upstream_gene_variant,,ENST00000417678,;ABCB6,upstream_gene_variant,,ENST00000496984,;ABCB6,upstream_gene_variant,,ENST00000492953,;ABCB6,upstream_gene_variant,,ENST00000494639,;ABCB6,upstream_gene_variant,,ENST00000452545,; C ENST00000265316 Transcript missense_variant 522/3016 205/2529 69/842 R/G Cgc/Ggc rs747669898,COSM32216 1 -1 ABCB6 HGNC HGNC:47 protein_coding YES CCDS2436.1 ENSP00000265316 Q9NP58 UPI000004C4BA NM_005689.2 tolerated(0.06) 1/19 hmmpanther:PTHR24221:SF18,hmmpanther:PTHR24221,Pfam_domain:PF16185 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs747669898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 219218469 219218469 G C 1 0 0 0 0 1 0 0 0 49 1058 37 4 4 ABCB6 2 219218469 Missense_Mutation SNP G C3N-00294_T 49696 219218469 22975060 279 13051 SPEG 0 . GRCh38 2 219449173 219449173 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2015G>A p.Arg672Lys p.R672K ENST00000312358 4/41 39 33 6 24 24 0 strelka-mutect SPEG,missense_variant,p.Arg672Lys,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Arg568Lys,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; A ENST00000312358 Transcript missense_variant 2147/10782 2015/9804 672/3267 R/K aGa/aAa 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.63) 4/41 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 219449173 219449173 G A 1 0 0 0 0 1 0 0 0 15387 942 33 3 3 SPEG 2 219449173 Missense_Mutation SNP G C3N-00294_T 230704 219449173 22744356 280 13052 CUL3 0 . GRCh38 2 224505958 224505958 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1204G>A p.Gly402Arg p.G402R ENST00000264414 8/16 83 75 8 70 70 0 strelka-varscan-mutect CUL3,missense_variant,p.Gly402Arg,ENST00000264414,NM_003590.4;CUL3,missense_variant,p.Gly336Arg,ENST00000344951,NM_001257197.1;CUL3,missense_variant,p.Gly378Arg,ENST00000409777,;CUL3,missense_variant,p.Gly378Arg,ENST00000409096,NM_001257198.1;CUL3,splice_region_variant,,ENST00000617432,;CUL3,non_coding_transcript_exon_variant,,ENST00000484081,;CUL3,upstream_gene_variant,,ENST00000481135,; T ENST00000264414 Transcript missense_variant,splice_region_variant 1543/6741 1204/2307 402/768 G/R Ggg/Agg 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 deleterious(0) 8/16 PROSITE_profiles:PS50069,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.20.1310.10,Superfamily_domains:SSF75632 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -17.08603 1 1 1 1 0 T 3 4 46 224505958 224505958 C T 1 0 0 0 0 1 0 0 0 3866 695 24 3 3 CUL3 2 224505958 Missense_Mutation SNP C C3N-00294_T 5056785 224505958 17687571 281 13053 CUL3 0 . GRCh38 2 224514647 224514647 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.504G>C p.Met168Ile p.M168I ENST00000264414 4/16 92 80 12 107 107 0 strelka-mutect CUL3,missense_variant,p.Met168Ile,ENST00000264414,NM_003590.4;CUL3,missense_variant,p.Met102Ile,ENST00000344951,NM_001257197.1;CUL3,missense_variant,p.Met144Ile,ENST00000409777,;CUL3,missense_variant,p.Met144Ile,ENST00000409096,NM_001257198.1;CUL3,missense_variant,p.Met189Ile,ENST00000436172,;CUL3,non_coding_transcript_exon_variant,,ENST00000541548,;CUL3,3_prime_UTR_variant,,ENST00000432260,;CUL3,upstream_gene_variant,,ENST00000484081,; G ENST00000264414 Transcript missense_variant 843/6741 504/2307 168/768 M/I atG/atC COSM3391523 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 tolerated(0.07) 4/16 hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.20.1310.10,Superfamily_domains:SSF74788 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.38161 0.9999999 1 1 1 0 G 3 3 46 224514647 224514647 C G 1 0 0 0 0 1 0 0 0 3866 826 29 4 4 CUL3 2 224514647 Missense_Mutation SNP C C3N-00294_T 8689 224514647 17678882 282 13054 TRIP12 0 . GRCh38 2 229880001 229880001 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.79G>T p.Asp27Tyr p.D27Y ENST00000389044 2/42 328 275 53 288 287 1 strelka-varscan-mutect TRIP12,missense_variant,p.Asp27Tyr,ENST00000283943,NM_001284215.1,NM_004238.2;TRIP12,missense_variant,p.Asp27Tyr,ENST00000389044,NM_001284214.1;TRIP12,missense_variant,p.Asp27Tyr,ENST00000389045,NM_001284216.1;TRIP12,missense_variant,p.Asp27Tyr,ENST00000409677,;TRIP12,missense_variant,p.Asp27Tyr,ENST00000430954,;TRIP12,missense_variant,p.Asp27Tyr,ENST00000435716,;TRIP12,missense_variant,p.Asp27Tyr,ENST00000428959,;TRIP12,missense_variant,p.Asp27Tyr,ENST00000343290,;TRIP12,non_coding_transcript_exon_variant,,ENST00000479037,; A ENST00000389044 Transcript missense_variant 248/6405 79/6123 27/2040 D/Y Gac/Tac 1 -1 TRIP12 HGNC HGNC:12306 protein_coding YES CCDS63146.1 ENSP00000373696 Q14669 UPI0000DA6BE7 NM_001284214.1 deleterious_low_confidence(0) 2/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 229880001 229880001 C A 1 0 0 0 0 1 0 0 0 17053 913 32 2 2 TRIP12 2 229880001 Missense_Mutation SNP C C3N-00294_T 5365354 229880001 12313528 283 13055 SP140 0 . GRCh38 2 230238253 230238253 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.278G>C p.Arg93Thr p.R93T ENST00000392045 3/27 164 128 36 132 132 0 strelka-varscan-mutect SP140,missense_variant,p.Arg93Thr,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Arg93Thr,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Arg93Thr,ENST00000343805,NM_001278452.1;SP140,missense_variant,p.Arg93Thr,ENST00000417495,NM_001278453.1;SP140,missense_variant,p.Arg93Thr,ENST00000373645,NM_001005176.2;SP140,downstream_gene_variant,,ENST00000456542,;SP140,non_coding_transcript_exon_variant,,ENST00000544128,;SP140,non_coding_transcript_exon_variant,,ENST00000538494,;SP140,non_coding_transcript_exon_variant,,ENST00000543928,;SP140,downstream_gene_variant,,ENST00000473711,; C ENST00000392045 Transcript missense_variant 392/3246 278/2604 93/867 R/T aGa/aCa 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 deleterious(0) 3/27 Pfam_domain:PF03172,PROSITE_profiles:PS51414 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 230238253 230238253 G C 1 0 0 0 0 1 0 0 0 15288 942 33 4 4 SP140 2 230238253 Missense_Mutation SNP G C3N-00294_T 358252 230238253 11955276 284 13056 SP140 0 . GRCh38 2 230292761 230292761 + Silent SNP C C T rs773468716 C3N-00294_T C3N-00294_N C C c.1941C>T p.= p.G647G ENST00000392045 20/27 200 158 42 169 169 0 strelka-varscan-mutect SP140,synonymous_variant,p.=,ENST00000392045,NM_007237.4;SP140,synonymous_variant,p.=,ENST00000420434,NM_001278451.1;SP140,synonymous_variant,p.=,ENST00000343805,NM_001278452.1;SP140,synonymous_variant,p.=,ENST00000417495,NM_001278453.1;SP140,upstream_gene_variant,,ENST00000486750,;SP140,downstream_gene_variant,,ENST00000476126,; T ENST00000392045 Transcript synonymous_variant 2055/3246 1941/2604 647/867 G ggC/ggT rs773468716,COSM4310678 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 20/27 Gene3D:3.10.390.10,Pfam_domain:PF01342,PROSITE_profiles:PS50864,SMART_domains:SM00258,Superfamily_domains:SSF63763 0,1 LOW 1 SNV 2 0,1 1 PASS rs773468716 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 230292761 230292761 C T 1 0 0 0 0 0 0 0 1 15288 755 27 1 1 SP140 2 230292761 Silent SNP C C3N-00294_T 54508 230292761 11900768 285 13057 PSMD1 0 . GRCh38 2 231075572 231075572 + Splice_Site SNP G G A novel C3N-00294_T C3N-00294_N G G c.942+1G>A p.X314_splice ENST00000308696 104 93 11 85 85 0 strelka-varscan-mutect PSMD1,splice_donor_variant,,ENST00000308696,NM_002807.3;PSMD1,splice_donor_variant,,ENST00000373635,NM_001191037.1;PSMD1,splice_donor_variant,,ENST00000619128,;PSMD1,splice_donor_variant,,ENST00000409643,;PSMD1,downstream_gene_variant,,ENST00000444007,;PSMD1,splice_donor_variant,,ENST00000431051,; A ENST00000308696 Transcript splice_donor_variant -/3326 942/2862 314/953 1 1 PSMD1 HGNC HGNC:9554 protein_coding YES CCDS2482.1 ENSP00000309474 Q99460 UPI00001678A2 NM_002807.3 8/24 HIGH 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.99741 0.999999 1 1 1 0 A 5 1 46 231075572 231075572 G A 1 0 0 0 0 0 0 1 0 12843 1159 40 1 1 PSMD1 2 231075572 Splice_Site SNP G C3N-00294_T 782811 231075572 11117957 286 13058 NCL 0 . GRCh38 2 231461695 231461695 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.458G>C p.Ser153Thr p.S153T ENST00000322723 3/14 510 420 90 467 467 0 strelka-varscan-mutect NCL,missense_variant,p.Ser153Thr,ENST00000322723,NM_005381.2;NCL,missense_variant,p.Ser137Thr,ENST00000453992,;NCL,missense_variant,p.Ser137Thr,ENST00000454824,;NCL,missense_variant,p.Ser137Thr,ENST00000417652,;NCL,missense_variant,p.Ser137Thr,ENST00000436894,;NCL,upstream_gene_variant,,ENST00000356936,;SNORD82,upstream_gene_variant,,ENST00000365530,;NCL,non_coding_transcript_exon_variant,,ENST00000461347,;NCL,upstream_gene_variant,,ENST00000494618,;NCL,upstream_gene_variant,,ENST00000466274,;NCL,downstream_gene_variant,,ENST00000484328,; G ENST00000322723 Transcript missense_variant 699/4034 458/2133 153/710 S/T aGt/aCt 1 -1 NCL HGNC HGNC:7667 protein_coding YES CCDS33397.1 ENSP00000318195 P19338 A0A024R4A0 UPI0000456F25 NM_005381.2 tolerated_low_confidence(0.07) 3/14 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 231461695 231461695 C G 1 0 0 0 0 1 0 0 0 10244 565 20 4 4 NCL 2 231461695 Missense_Mutation SNP C C3N-00294_T 386123 231461695 10731834 287 13059 INPP5D 0 . GRCh38 2 233147480 233147480 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.916G>A p.Glu306Lys p.E306K ENST00000445964 9/27 161 121 40 186 186 0 strelka-varscan-mutect INPP5D,missense_variant,p.Glu305Lys,ENST00000359570,NM_005541.4;INPP5D,missense_variant,p.Glu306Lys,ENST00000445964,NM_001017915.2; A ENST00000445964 Transcript missense_variant 997/4845 916/3570 306/1189 E/K Gag/Aag 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 tolerated(0.15) 9/27 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 233147480 233147480 G A 1 0 0 0 0 1 0 0 0 7659 943 33 3 3 INPP5D 2 233147480 Missense_Mutation SNP G C3N-00294_T 1685785 233147480 9046049 288 13060 INPP5D 0 . GRCh38 2 233170077 233170077 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1704G>T p.Lys568Asn p.K568N ENST00000445964 15/27 288 258 30 264 264 0 strelka-varscan-mutect INPP5D,missense_variant,p.Lys567Asn,ENST00000359570,NM_005541.4;INPP5D,missense_variant,p.Lys568Asn,ENST00000445964,NM_001017915.2;INPP5D,missense_variant,p.Lys189Asn,ENST00000415617,;INPP5D,non_coding_transcript_exon_variant,,ENST00000472517,;INPP5D,non_coding_transcript_exon_variant,,ENST00000493632,;INPP5D,non_coding_transcript_exon_variant,,ENST00000480983,;INPP5D,upstream_gene_variant,,ENST00000465281,;INPP5D,downstream_gene_variant,,ENST00000493078,; T ENST00000445964 Transcript missense_variant 1785/4845 1704/3570 568/1189 K/N aaG/aaT 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 deleterious(0) 15/27 Gene3D:3.60.10.10,Pfam_domain:PF03372,hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69,SMART_domains:SM00128,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 233170077 233170077 G T 1 0 0 0 0 1 0 0 0 7659 933 33 2 2 INPP5D 2 233170077 Missense_Mutation SNP G C3N-00294_T 22597 233170077 9023452 289 13061 MROH2A 0 . GRCh38 2 233789873 233789873 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.430G>A p.Glu144Lys p.E144K ENST00000610772 5/42 80 68 12 62 62 0 strelka-varscan-mutect MROH2A,missense_variant,p.Glu144Lys,ENST00000389758,;MROH2A,missense_variant,p.Glu144Lys,ENST00000610772,NM_001287395.1;MROH2A,intron_variant,,ENST00000480634,; A ENST00000610772 Transcript missense_variant 523/5324 430/5067 144/1688 E/K Gag/Aag 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 deleterious(0.01) 5/42 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 233789873 233789873 G A 1 0 0 0 0 1 0 0 0 9744 943 33 3 3 MROH2A 2 233789873 Missense_Mutation SNP G C3N-00294_T 619796 233789873 8403656 290 13062 CAPN10 0 . GRCh38 2 240590902 240590902 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.361G>C p.Glu121Gln p.E121Q ENST00000391984 3/12 274 231 43 205 205 0 strelka-varscan-mutect CAPN10,missense_variant,p.Glu121Gln,ENST00000391984,NM_023083.3;CAPN10,missense_variant,p.Glu121Gln,ENST00000404753,;CAPN10,missense_variant,p.Glu121Gln,ENST00000354082,NM_023085.3;CAPN10,intron_variant,,ENST00000270364,;CAPN10,intron_variant,,ENST00000352879,;CAPN10,upstream_gene_variant,,ENST00000432084,;CAPN10-AS1,upstream_gene_variant,,ENST00000567819,;CAPN10,missense_variant,p.Glu121Gln,ENST00000416591,;CAPN10,missense_variant,p.Glu121Gln,ENST00000270361,;CAPN10,missense_variant,p.Glu121Gln,ENST00000391983,;CAPN10,missense_variant,p.Glu121Gln,ENST00000357048,;CAPN10,non_coding_transcript_exon_variant,,ENST00000494738,;CAPN10,upstream_gene_variant,,ENST00000493058,;CAPN10,downstream_gene_variant,,ENST00000463653,;CAPN10,upstream_gene_variant,,ENST00000465943,;CAPN10,upstream_gene_variant,,ENST00000483602,; C ENST00000391984 Transcript missense_variant 557/2644 361/2019 121/672 E/Q Gag/Cag 1 1 CAPN10 HGNC HGNC:1477 protein_coding YES CCDS42838.1 ENSP00000375844 Q9HC96 UPI00001AE96D NM_023083.3 deleterious(0) 3/12 Pfam_domain:PF00648,Prints_domain:PR00704,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF30,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 240590902 240590902 G C 1 0 0 0 0 1 0 0 0 2315 1175 41 4 4 CAPN10 2 240590902 Missense_Mutation SNP G C3N-00294_T 6801029 240590902 1602627 291 13063 GPR35 0 . GRCh38 2 240629979 240629979 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.120C>T p.= p.G40G ENST00000430267 2/2 66 61 5 53 53 0 strelka-varscan-mutect GPR35,synonymous_variant,p.=,ENST00000438013,;GPR35,synonymous_variant,p.=,ENST00000319838,;GPR35,synonymous_variant,p.=,ENST00000403859,;GPR35,synonymous_variant,p.=,ENST00000430267,NM_001195381.1,NM_001195382.1;GPR35,synonymous_variant,p.=,ENST00000407714,NM_005301.3; T ENST00000430267 Transcript synonymous_variant 120/1399 120/1023 40/340 G ggC/ggT 1 1 GPR35 HGNC HGNC:4492 protein_coding YES CCDS56174.1 ENSP00000411788 Q9HC97 UPI0000E6291C NM_001195381.1,NM_001195382.1 2/2 hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF54,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -11.34581 0.999931 1 1 1 0 T 2 4 46 240629979 240629979 C T 1 0 0 0 0 0 0 0 1 6575 784 28 3 3 GPR35 2 240629979 Silent SNP C C3N-00294_T 39077 240629979 1563550 292 13064 KIF1A 0 . GRCh38 2 240783087 240783087 + Missense_Mutation SNP G G A rs797045655 C3N-00294_T C3N-00294_N G G c.821C>T p.Ser274Leu p.S274L ENST00000498729 9/49 361 340 21 337 337 0 strelka-varscan-mutect KIF1A,missense_variant,p.Ser274Leu,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Ser274Leu,ENST00000320389,NM_004321.6;KIF1A,missense_variant,p.Ser274Leu,ENST00000404283,;KIF1A,missense_variant,p.Ser82Leu,ENST00000428768,; A ENST00000498729 Transcript missense_variant 1068/9223 821/5376 274/1791 S/L tCg/tTg rs797045655 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 deleterious(0) 9/49 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361,SMART_domains:SM00129,Superfamily_domains:SSF52540 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs797045655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 240783087 240783087 G A 1 0 0 0 0 1 0 0 0 8147 1059 37 1 1 KIF1A 2 240783087 Missense_Mutation SNP G C3N-00294_T 153108 240783087 1410442 293 13065 PASK 0 . GRCh38 2 241142937 241142937 + Silent SNP C C T rs763806405 C3N-00294_T C3N-00294_N C C c.96G>A p.= p.Q32Q ENST00000358649 2/18 293 243 50 290 290 0 strelka-varscan-mutect PASK,synonymous_variant,p.=,ENST00000403638,NM_001252124.1;PASK,synonymous_variant,p.=,ENST00000405260,;PASK,synonymous_variant,p.=,ENST00000544142,NM_001252120.1;PASK,synonymous_variant,p.=,ENST00000234040,NM_015148.3,NM_001252122.1;PASK,synonymous_variant,p.=,ENST00000358649,NM_001252119.1;PASK,synonymous_variant,p.=,ENST00000452907,;PASK,synonymous_variant,p.=,ENST00000629419,;PASK,intron_variant,,ENST00000415234,;PASK,upstream_gene_variant,,ENST00000433589,;PASK,synonymous_variant,p.=,ENST00000437780,;PASK,upstream_gene_variant,,ENST00000485940,; T ENST00000358649 Transcript synonymous_variant 160/4326 96/3993 32/1330 Q caG/caA rs763806405 1 -1 PASK HGNC HGNC:17270 protein_coding YES CCDS58759.1 ENSP00000351475 Q96RG2 UPI0000456F4C NM_001252119.1 2/18 hmmpanther:PTHR22971,hmmpanther:PTHR22971:SF4 LOW 1 SNV 1 1 PASS rs763806405 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 241142937 241142937 C T 1 0 0 0 0 0 0 0 1 11553 912 32 3 3 PASK 2 241142937 Silent SNP C C3N-00294_T 359850 241142937 1050592 294 13066 HDLBP 0 . GRCh38 2 241235231 241235231 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.3034G>C p.Glu1012Gln p.E1012Q ENST00000391975 23/28 229 181 48 239 239 0 strelka-varscan-mutect HDLBP,missense_variant,p.Glu1012Gln,ENST00000391975,NM_001320965.1,NM_001320966.1,NM_203346.3;HDLBP,missense_variant,p.Glu979Gln,ENST00000427183,NM_001243900.1;HDLBP,missense_variant,p.Glu1012Gln,ENST00000310931,NM_005336.4;HDLBP,missense_variant,p.Glu1012Gln,ENST00000391976,;HDLBP,missense_variant,p.Glu821Gln,ENST00000373292,;HDLBP,downstream_gene_variant,,ENST00000427487,;HDLBP,downstream_gene_variant,,ENST00000452931,;HDLBP,upstream_gene_variant,,ENST00000442730,;HDLBP,non_coding_transcript_exon_variant,,ENST00000470482,;HDLBP,non_coding_transcript_exon_variant,,ENST00000483086,;HDLBP,upstream_gene_variant,,ENST00000484412,;HDLBP,downstream_gene_variant,,ENST00000471294,;HDLBP,non_coding_transcript_exon_variant,,ENST00000487169,;HDLBP,non_coding_transcript_exon_variant,,ENST00000479894,;HDLBP,downstream_gene_variant,,ENST00000479169,;HDLBP,upstream_gene_variant,,ENST00000488013,;HDLBP,downstream_gene_variant,,ENST00000459788,; G ENST00000391975 Transcript missense_variant 3262/6372 3034/3807 1012/1268 E/Q Gag/Cag 1 -1 HDLBP HGNC HGNC:4857 protein_coding YES CCDS2547.1 ENSP00000375836 A0A024R4E5 UPI0000000C28 NM_001320965.1,NM_001320966.1,NM_203346.3 tolerated(0.13) 23/28 PROSITE_profiles:PS50084,hmmpanther:PTHR10627:SF34,hmmpanther:PTHR10627,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 241235231 241235231 C G 1 0 0 0 0 1 0 0 0 6908 835 29 4 4 HDLBP 2 241235231 Missense_Mutation SNP C C3N-00294_T 92294 241235231 958298 295 13067 CHL1 0 . GRCh38 3 328213 328213 + Missense_Mutation SNP C C T rs752032870 C3N-00294_T C3N-00294_N C C c.244C>T p.Arg82Trp p.R82W ENST00000256509 5/28 139 112 27 151 150 1 strelka-varscan-mutect CHL1,missense_variant,p.Arg82Trp,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Arg82Trp,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Arg82Trp,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Arg82Trp,ENST00000435603,;CHL1,missense_variant,p.Arg82Trp,ENST00000449294,;CHL1,missense_variant,p.Arg82Trp,ENST00000421198,;CHL1,downstream_gene_variant,,ENST00000427688,;CHL1,non_coding_transcript_exon_variant,,ENST00000461289,;CHL1,3_prime_UTR_variant,,ENST00000453040,; T ENST00000256509 Transcript missense_variant 886/8023 244/3675 82/1224 R/W Cgg/Tgg rs752032870,COSM1201060 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 deleterious(0) 5/28 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752032870 . 0 206 0 3 0 0 0 0 -20 0.9999961 1 1 1 0 T 3 4 46 328213 328213 C T 1 0 0 0 0 1 0 0 0 3108 875 31 1 1 CHL1 3 328213 Missense_Mutation SNP C C3N-00294_T 328213 197967346 296 13068 ITPR1 0 . GRCh38 3 4674322 4674322 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2532G>C p.Glu844Asp p.E844D ENST00000302640 21/61 94 73 21 150 150 0 strelka-varscan-mutect ITPR1,missense_variant,p.Glu859Asp,ENST00000354582,;ITPR1,missense_variant,p.Glu844Asp,ENST00000302640,NM_001168272.1;ITPR1,missense_variant,p.Glu859Asp,ENST00000357086,NM_001099952.2;ITPR1,missense_variant,p.Glu844Asp,ENST00000456211,NM_002222.5;ITPR1,missense_variant,p.Glu844Asp,ENST00000443694,;ITPR1,intron_variant,,ENST00000544951,;ITPR1,downstream_gene_variant,,ENST00000477577,; C ENST00000302640 Transcript missense_variant 2882/10197 2532/8232 844/2743 E/D gaG/gaC 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 tolerated(0.19) 21/61 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 4674322 4674322 G C 1 0 0 0 0 1 0 0 0 7826 933 33 4 4 ITPR1 3 4674322 Missense_Mutation SNP G C3N-00294_T 4346109 4674322 193621237 297 13069 BHLHE40 0 . GRCh38 3 4983687 4983687 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1234G>C p.Asp412His p.D412H ENST00000256495 5/5 66 54 12 83 83 0 strelka-varscan-mutect BHLHE40,missense_variant,p.Asp412His,ENST00000256495,NM_003670.2;BHLHE40-AS1,upstream_gene_variant,,ENST00000620618,;BHLHE40-AS1,upstream_gene_variant,,ENST00000615178,;BHLHE40-AS1,upstream_gene_variant,,ENST00000441386,;BHLHE40,downstream_gene_variant,,ENST00000467610,;BHLHE40,downstream_gene_variant,,ENST00000460806,; C ENST00000256495 Transcript missense_variant 1837/3473 1234/1239 412/412 D/H Gac/Cac 1 1 BHLHE40 HGNC HGNC:1046 protein_coding YES CCDS2565.1 ENSP00000256495 O14503 Q6IB83 UPI0000126923 NM_003670.2 deleterious_low_confidence(0) 5/5 hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF3 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 4983687 4983687 G C 1 0 0 0 0 1 0 0 0 1571 942 33 4 4 BHLHE40 3 4983687 Missense_Mutation SNP G C3N-00294_T 309365 4983687 193311872 298 13070 BRPF1 0 . GRCh38 3 9744259 9744259 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2671G>C p.Glu891Gln p.E891Q ENST00000383829 9/14 36 27 9 24 24 0 strelka-varscan-mutect BRPF1,missense_variant,p.Glu891Gln,ENST00000383829,NM_001003694.1;BRPF1,missense_variant,p.Glu884Gln,ENST00000424362,NM_001319050.1;BRPF1,missense_variant,p.Glu885Gln,ENST00000457855,NM_004634.2;BRPF1,intron_variant,,ENST00000433861,NM_001319049.1;BRPF1,downstream_gene_variant,,ENST00000469066,;BRPF1,upstream_gene_variant,,ENST00000497565,; C ENST00000383829 Transcript missense_variant 3075/4736 2671/3663 891/1220 E/Q Gag/Cag 1 1 BRPF1 HGNC HGNC:14255 protein_coding YES CCDS33692.1 ENSP00000373340 P55201 UPI00001A9CA3 NM_001003694.1 tolerated(0.42) 9/14 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF85 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99965 1 1 1 1 0 C 3 2 46 9744259 9744259 G C 1 0 0 0 0 1 0 0 0 1694 1291 45 4 4 BRPF1 3 9744259 Missense_Mutation SNP G C3N-00294_T 4760572 9744259 188551300 299 13071 TMEM40 0 . GRCh38 3 12742493 12742493 + Missense_Mutation SNP C C T rs764930665 C3N-00294_T C3N-00294_N C C c.316G>A p.Glu106Lys p.E106K ENST00000314124 5/12 116 91 25 108 108 0 strelka-varscan-mutect TMEM40,missense_variant,p.Glu106Lys,ENST00000314124,NM_018306.3;TMEM40,missense_variant,p.Glu30Lys,ENST00000435575,NM_001284408.1;TMEM40,missense_variant,p.Glu76Lys,ENST00000435218,NM_001284407.1;TMEM40,missense_variant,p.Glu106Lys,ENST00000264728,NM_001284406.1;TMEM40,missense_variant,p.Glu9Lys,ENST00000428020,;TMEM40,upstream_gene_variant,,ENST00000476331,;TMEM40,upstream_gene_variant,,ENST00000485124,;TMEM40,upstream_gene_variant,,ENST00000480698,; T ENST00000314124 Transcript missense_variant 673/2308 316/702 106/233 E/K Gag/Aag rs764930665,COSM4977993,COSM4977994 1 -1 TMEM40 HGNC HGNC:25620 protein_coding YES CCDS2613.1 ENSP00000322837 Q8WWA1 UPI00000732A9 NM_018306.3 tolerated_low_confidence(0.14) 5/12 hmmpanther:PTHR16108,hmmpanther:PTHR16108:SF2,Low_complexity_(Seg):seg 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs764930665 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 12742493 12742493 C T 1 0 0 0 0 1 0 0 0 16640 864 30 3 3 TMEM40 3 12742493 Missense_Mutation SNP C C3N-00294_T 2998234 12742493 185553066 300 13072 ANKRD28 0 . GRCh38 3 15724507 15724507 + Nonsense_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.568A>T p.Lys190Ter p.K190* ENST00000399451 7/28 112 53 59 117 117 0 strelka-varscan-mutect ANKRD28,stop_gained,p.Lys190Ter,ENST00000399451,NM_015199.3;ANKRD28,stop_gained,p.Lys36Ter,ENST00000624145,NM_001195098.1,NM_001195099.1;ANKRD28,non_coding_transcript_exon_variant,,ENST00000497037,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000476472,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000460278,;ANKRD28,upstream_gene_variant,,ENST00000492895,;ANKRD28,stop_gained,p.Lys190Ter,ENST00000412318,;ANKRD28,stop_gained,p.Lys134Ter,ENST00000451422,;ANKRD28,non_coding_transcript_exon_variant,,ENST00000498524,; A ENST00000399451 Transcript stop_gained 936/6564 568/3162 190/1053 K/* Aaa/Taa 1 -1 ANKRD28 HGNC HGNC:29024 protein_coding YES CCDS46769.1 ENSP00000382379 O15084 A0A024R2G8 UPI00004120FF NM_015199.3 7/28 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24158,hmmpanther:PTHR24158:SF22,Pfam_domain:PF13637,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 15724507 15724507 T A 1 0 0 0 0 0 1 0 0 759 1792 62 4 4 ANKRD28 3 15724507 Nonsense_Mutation SNP T C3N-00294_T 2982014 15724507 182571052 301 13073 PLCL2 0 . GRCh38 3 17010282 17010282 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.936C>T p.= p.F312F ENST00000615277 2/6 85 75 10 152 151 1 strelka-varscan-mutect PLCL2,synonymous_variant,p.=,ENST00000615277,NM_001144382.1;PLCL2,synonymous_variant,p.=,ENST00000432376,NM_015184.5;PLCL2,upstream_gene_variant,,ENST00000419842,;PLCL2,intron_variant,,ENST00000460467,; T ENST00000615277 Transcript synonymous_variant 1017/4147 936/3384 312/1127 F ttC/ttT 1 1 PLCL2 HGNC HGNC:9064 protein_coding YES CCDS74911.1 ENSP00000478458 Q9UPR0 UPI0000242D01 NM_001144382.1 2/6 hmmpanther:PTHR10336:SF84,hmmpanther:PTHR10336,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 17010282 17010282 C T 1 0 0 0 0 0 0 0 1 12134 825 29 3 3 PLCL2 3 17010282 Silent SNP C C3N-00294_T 1285775 17010282 181285277 302 13074 THRB 0 . GRCh38 3 24190225 24190225 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.132G>C p.Glu44Asp p.E44D ENST00000396671 5/11 320 254 66 317 317 0 strelka-varscan-mutect THRB,missense_variant,p.Glu44Asp,ENST00000396671,NM_001128176.2;THRB,missense_variant,p.Glu44Asp,ENST00000356447,NM_000461.4,NM_001128177.1;THRB,missense_variant,p.Glu44Asp,ENST00000416420,NM_001252634.1;THRB,missense_variant,p.Glu13Asp,ENST00000413780,;THRB,missense_variant,p.Glu44Asp,ENST00000447875,;THRB,missense_variant,p.Glu44Asp,ENST00000453729,;THRB,missense_variant,p.Glu44Asp,ENST00000415021,;THRB,missense_variant,p.Glu44Asp,ENST00000418247,;THRB,missense_variant,p.Glu44Asp,ENST00000447414,;THRB,missense_variant,p.Glu44Asp,ENST00000431815,;THRB,missense_variant,p.Glu44Asp,ENST00000428492,; G ENST00000396671 Transcript missense_variant 528/7506 132/1386 44/461 E/D gaG/gaC 1 -1 THRB HGNC HGNC:11799 protein_coding YES CCDS2641.1 ENSP00000379904 P10828 F1D8N7 UPI0000136D26 NM_001128176.2 deleterious_low_confidence(0.02) 5/11 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 24190225 24190225 C G 1 0 0 0 0 1 0 0 0 16309 912 32 4 4 THRB 3 24190225 Missense_Mutation SNP C C3N-00294_T 7179943 24190225 174105334 303 13075 ZNF860 0 . GRCh38 3 31989701 31989701 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.622G>A p.Glu208Lys p.E208K ENST00000360311 2/2 109 84 25 152 152 0 strelka-varscan-mutect ZNF860,missense_variant,p.Glu208Lys,ENST00000360311,NM_001137674.2;OSBPL10,intron_variant,,ENST00000479173,;ZNF860,downstream_gene_variant,,ENST00000489408,; A ENST00000360311 Transcript missense_variant 1171/3098 622/1899 208/632 E/K Gaa/Aaa 1 1 ZNF860 HGNC HGNC:34513 protein_coding YES CCDS46784.1 ENSP00000373274 A6NHJ4 UPI0000D61AE9 NM_001137674.2 deleterious(0.01) 2/2 Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 A 3 1 46 31989701 31989701 G A 1 0 0 0 0 1 0 0 0 18785 1291 45 3 3 ZNF860 3 31989701 Missense_Mutation SNP G C3N-00294_T 7799476 31989701 166305858 304 13076 DYNC1LI1 0 . GRCh38 3 32526879 32526879 + Missense_Mutation SNP C C T rs769865357 C3N-00294_T C3N-00294_N C C c.1492G>A p.Glu498Lys p.E498K ENST00000273130 13/13 104 92 12 162 162 0 strelka-mutect DYNC1LI1,missense_variant,p.Glu498Lys,ENST00000273130,NM_016141.3;DYNC1LI1,missense_variant,p.Glu382Lys,ENST00000432458,;DYNC1LI1,non_coding_transcript_exon_variant,,ENST00000481915,;DYNC1LI1,downstream_gene_variant,,ENST00000472985,; T ENST00000273130 Transcript missense_variant 1596/2504 1492/1572 498/523 E/K Gaa/Aaa rs769865357 1 -1 DYNC1LI1 HGNC HGNC:18745 protein_coding YES CCDS2654.1 ENSP00000273130 Q9Y6G9 UPI000013D99D NM_016141.3 deleterious(0) 13/13 hmmpanther:PTHR12688:SF2,hmmpanther:PTHR12688,Pfam_domain:PF05783 MODERATE 1 SNV 1 1 PASS rs769865357 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 32526879 32526879 C T 1 0 0 0 0 1 0 0 0 4668 922 32 3 3 DYNC1LI1 3 32526879 Missense_Mutation SNP C C3N-00294_T 537178 32526879 165768680 305 13077 SCN11A 0 . GRCh38 3 38897121 38897121 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.2127C>A p.= p.V709V ENST00000302328 14/26 264 208 56 285 285 0 strelka-varscan-mutect SCN11A,synonymous_variant,p.=,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,synonymous_variant,p.=,ENST00000444237,;SCN11A,synonymous_variant,p.=,ENST00000456224,; T ENST00000302328 Transcript synonymous_variant 2326/6500 2127/5376 709/1791 V gtC/gtA 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 14/26 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 38897121 38897121 G T 1 0 0 0 0 0 0 0 1 14182 1277 45 2 2 SCN11A 3 38897121 Silent SNP G C3N-00294_T 6370242 38897121 159398438 306 13078 XIRP1 0 . GRCh38 3 39185822 39185822 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.3624G>A p.= p.G1208G ENST00000340369 2/2 80 60 20 99 99 0 strelka-varscan-mutect XIRP1,synonymous_variant,p.=,ENST00000340369,NM_194293.2;XIRP1,intron_variant,,ENST00000396251,NM_001198621.2;XIRP1,intron_variant,,ENST00000421646,; T ENST00000340369 Transcript synonymous_variant 3853/6460 3624/5532 1208/1843 G ggG/ggA 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 2/2 hmmpanther:PTHR22591 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 39185822 39185822 C T 1 0 0 0 0 0 0 0 1 17988 842 30 3 3 XIRP1 3 39185822 Silent SNP C C3N-00294_T 288701 39185822 159109737 307 13079 ENTPD3 0 . GRCh38 3 40415842 40415842 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.600G>C p.Lys200Asn p.K200N ENST00000301825 7/11 126 101 25 107 107 0 strelka-varscan-mutect ENTPD3,missense_variant,p.Lys200Asn,ENST00000301825,NM_001248.3;ENTPD3,missense_variant,p.Lys200Asn,ENST00000456402,NM_001291960.1;ENTPD3,missense_variant,p.Lys200Asn,ENST00000445129,NM_001291961.1;ENTPD3-AS1,intron_variant,,ENST00000425156,;ENTPD3-AS1,intron_variant,,ENST00000452768,;ENTPD3-AS1,intron_variant,,ENST00000439293,; C ENST00000301825 Transcript missense_variant,splice_region_variant 718/2819 600/1590 200/529 K/N aaG/aaC 1 1 ENTPD3 HGNC HGNC:3365 protein_coding YES CCDS2691.1 ENSP00000301825 O75355 UPI000013E75E NM_001248.3 deleterious(0) 7/11 hmmpanther:PTHR11782:SF38,hmmpanther:PTHR11782,Pfam_domain:PF01150 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 40415842 40415842 G C 1 0 0 0 0 1 0 0 0 4985 956 33 4 4 ENTPD3 3 40415842 Missense_Mutation SNP G C3N-00294_T 1230020 40415842 157879717 308 13080 RPL14 0 . GRCh38 3 40461956 40461956 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.372G>A p.= p.K124K ENST00000338970 6/6 119 90 29 105 104 1 strelka-varscan-mutect RPL14,missense_variant,p.Glu124Lys,ENST00000416518,;RPL14,synonymous_variant,p.=,ENST00000338970,NM_003973.4;RPL14,synonymous_variant,p.=,ENST00000396203,NM_001034996.2;RPL14,downstream_gene_variant,,ENST00000461368,;RPL14,3_prime_UTR_variant,,ENST00000435633,;RPL14,non_coding_transcript_exon_variant,,ENST00000479563,;RPL14,non_coding_transcript_exon_variant,,ENST00000481798,;RPL14,downstream_gene_variant,,ENST00000465325,;RPL14,downstream_gene_variant,,ENST00000465280,; A ENST00000338970 Transcript synonymous_variant 441/7072 372/648 124/215 K aaG/aaA 1 1 RPL14 HGNC HGNC:10305 protein_coding YES CCDS33739.1 ENSP00000345156 P50914 UPI0000367134 NM_003973.4 6/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11127 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 40461956 40461956 G A 1 0 0 0 0 0 0 0 1 13813 943 33 3 3 RPL14 3 40461956 Silent SNP G C3N-00294_T 46114 40461956 157833603 309 13081 ZNF619 0 . GRCh38 3 40482308 40482308 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.257C>G p.Ser86Cys p.S86C ENST00000447116 4/6 165 140 25 194 194 0 strelka-varscan-mutect ZNF619,missense_variant,p.Ser86Cys,ENST00000447116,NM_001145082.2;ZNF619,missense_variant,p.Ser86Cys,ENST00000521353,;ZNF619,intron_variant,,ENST00000429348,;ZNF619,intron_variant,,ENST00000314686,;ZNF619,intron_variant,,ENST00000456778,NM_001145083.1;ZNF619,intron_variant,,ENST00000522736,;ZNF619,intron_variant,,ENST00000432264,NM_001145093.2;ZNF619,intron_variant,,ENST00000520737,;ZNF619,3_prime_UTR_variant,,ENST00000494154,;ZNF619,downstream_gene_variant,,ENST00000462961,; G ENST00000447116 Transcript missense_variant 564/4153 257/1851 86/616 S/C tCt/tGt 1 1 ZNF619 HGNC HGNC:26910 protein_coding YES CCDS46802.1 ENSP00000411132 Q8N2I2 UPI000192B90D NM_001145082.2 tolerated_low_confidence(0.06) 4/6 PROSITE_profiles:PS50805,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1344632506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 40482308 40482308 C G 1 0 0 0 0 1 0 0 0 18618 913 32 4 4 ZNF619 3 40482308 Missense_Mutation SNP C C3N-00294_T 20352 40482308 157813251 310 13082 NBEAL2 0 . GRCh38 3 47001767 47001767 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.4723G>A p.Glu1575Lys p.E1575K ENST00000450053 30/54 220 168 52 240 240 0 strelka-varscan-mutect NBEAL2,missense_variant,p.Glu1575Lys,ENST00000450053,NM_015175.2;NBEAL2,missense_variant,p.Glu863Lys,ENST00000416683,;NBEAL2,upstream_gene_variant,,ENST00000443829,;NBEAL2,upstream_gene_variant,,ENST00000423436,;NBEAL2,non_coding_transcript_exon_variant,,ENST00000475689,;NBEAL2,upstream_gene_variant,,ENST00000486870,;NBEAL2,upstream_gene_variant,,ENST00000441027,; A ENST00000450053 Transcript missense_variant 4902/8827 4723/8265 1575/2754 E/K Gag/Aag 1 1 NBEAL2 HGNC HGNC:31928 protein_coding YES CCDS46817.1 ENSP00000415034 Q6ZNJ1 UPI000022C020 NM_015175.2 tolerated(0.26) 30/54 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF50 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 47001767 47001767 G A 1 0 0 0 0 1 0 0 0 10200 1291 45 3 3 NBEAL2 3 47001767 Missense_Mutation SNP G C3N-00294_T 6519459 47001767 151293792 311 13083 CCDC51 0 . GRCh38 3 48432521 48432521 + Missense_Mutation SNP C C G rs776584834 C3N-00294_T C3N-00294_N C C c.1123G>C p.Glu375Gln p.E375Q ENST00000395694 4/4 342 307 35 392 392 0 strelka-varscan-mutect CCDC51,missense_variant,p.Glu375Gln,ENST00000395694,NM_024661.4,NM_001256964.1;CCDC51,missense_variant,p.Glu266Gln,ENST00000442740,NM_001256965.2;CCDC51,missense_variant,p.Glu266Gln,ENST00000447018,NM_001256966.2,NM_001256967.2;CCDC51,missense_variant,p.Glu266Gln,ENST00000412398,NM_001256969.2,NM_001256968.2;PLXNB1,upstream_gene_variant,,ENST00000358536,NM_002673.5;PLXNB1,upstream_gene_variant,,ENST00000296440,NM_001130082.2;CCDC51,downstream_gene_variant,,ENST00000446140,;CCDC51,downstream_gene_variant,,ENST00000438370,;PLXNB1,upstream_gene_variant,,ENST00000466353,; G ENST00000395694 Transcript missense_variant 1209/1560 1123/1236 375/411 E/Q Gag/Cag rs776584834 1 -1 CCDC51 HGNC HGNC:25714 protein_coding YES CCDS2766.2 ENSP00000379047 Q96ER9 UPI00005A7643 NM_024661.4,NM_001256964.1 tolerated(0.2) 4/4 hmmpanther:PTHR28624,hmmpanther:PTHR28624:SF1 MODERATE SNV 2 1 PASS rs776584834 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 48432521 48432521 C G 1 0 0 0 0 1 0 0 0 2526 864 30 4 4 CCDC51 3 48432521 Missense_Mutation SNP C C3N-00294_T 1430754 48432521 149863038 312 13084 USP19 0 . GRCh38 3 49112376 49112376 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.2667C>A p.= p.I889I ENST00000434032 19/27 248 201 47 269 269 0 strelka-varscan-mutect USP19,synonymous_variant,p.=,ENST00000453664,NM_001199162.1;USP19,synonymous_variant,p.=,ENST00000417901,NM_001199161.1;USP19,synonymous_variant,p.=,ENST00000434032,NM_001199160.1;USP19,synonymous_variant,p.=,ENST00000398892,;USP19,synonymous_variant,p.=,ENST00000398888,NM_006677.2;USP19,synonymous_variant,p.=,ENST00000398898,;USP19,synonymous_variant,p.=,ENST00000398896,;USP19,downstream_gene_variant,,ENST00000306026,;USP19,downstream_gene_variant,,ENST00000479073,;USP19,downstream_gene_variant,,ENST00000488993,;USP19,downstream_gene_variant,,ENST00000491859,;USP19,downstream_gene_variant,,ENST00000464931,;USP19,upstream_gene_variant,,ENST00000483667,;USP19,downstream_gene_variant,,ENST00000480163,; T ENST00000434032 Transcript synonymous_variant 2879/4677 2667/4260 889/1419 I atC/atA 1 -1 USP19 HGNC HGNC:12617 protein_coding YES CCDS56254.1 ENSP00000401197 O94966 UPI000198CAB3 NM_001199160.1 19/27 PROSITE_profiles:PS50235,Pfam_domain:PF00443,Superfamily_domains:SSF144232 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 49112376 49112376 G T 1 0 0 0 0 0 0 0 1 17591 932 33 2 2 USP19 3 49112376 Silent SNP G C3N-00294_T 679855 49112376 149183183 313 13085 HYAL1 0 . GRCh38 3 50300543 50300543 + Missense_Mutation SNP G G C rs782144670 C3N-00294_T C3N-00294_N G G c.1248C>G p.Phe416Leu p.F416L ENST00000266031 3/3 381 311 70 434 434 0 strelka-varscan-mutect HYAL1,missense_variant,p.Phe416Leu,ENST00000266031,;HYAL1,missense_variant,p.Phe416Leu,ENST00000320295,NM_153281.1;HYAL1,missense_variant,p.Phe416Leu,ENST00000618175,;HYAL1,missense_variant,p.Phe416Leu,ENST00000395144,NM_033159.3;HYAL1,missense_variant,p.Phe386Leu,ENST00000395143,NM_153282.2;HYAL1,missense_variant,p.Phe234Leu,ENST00000457214,NM_153283.2;HYAL1,missense_variant,p.Phe157Leu,ENST00000447605,NM_153285.2;HYAL3,upstream_gene_variant,,ENST00000336307,NM_003549.3;NAT6,upstream_gene_variant,,ENST00000443842,;HYAL3,upstream_gene_variant,,ENST00000621157,NM_001200029.1;HYAL3,upstream_gene_variant,,ENST00000359051,;NAT6,upstream_gene_variant,,ENST00000443094,NM_001200016.1;HYAL3,upstream_gene_variant,,ENST00000450982,NM_001200030.1;NAT6,upstream_gene_variant,,ENST00000354862,NM_012191.3;NAT6,upstream_gene_variant,,ENST00000417393,NM_001200018.1;HYAL3,upstream_gene_variant,,ENST00000415204,NM_001200031.1;NAT6,upstream_gene_variant,,ENST00000442620,;NAT6,upstream_gene_variant,,ENST00000450489,;HYAL3,upstream_gene_variant,,ENST00000513170,NM_001200032.1;NAT6,upstream_gene_variant,,ENST00000452674,;HYAL1,downstream_gene_variant,,ENST00000418723,;HYAL1,downstream_gene_variant,,ENST00000452672,;HYAL3,upstream_gene_variant,,ENST00000435141,; C ENST00000266031 Transcript missense_variant 1864/2517 1248/1308 416/435 F/L ttC/ttG rs782144670 1 -1 HYAL1 HGNC HGNC:5320 protein_coding YES CCDS2816.1 ENSP00000266031 Q12794 A0A024R2X3 UPI000003FD9D deleterious(0) 3/3 hmmpanther:PTHR11769:SF23,hmmpanther:PTHR11769,PIRSF_domain:PIRSF038193,Gene3D:2.10.25.10 MODERATE 1 SNV 1 1 PASS rs782144670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 50300543 50300543 G C 1 0 0 0 0 1 0 0 0 7359 1281 45 4 4 HYAL1 3 50300543 Missense_Mutation SNP G C3N-00294_T 1188167 50300543 147995016 314 13086 DCAF1 0 . GRCh38 3 51418706 51418706 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.3407C>T p.Ser1136Leu p.S1136L ENST00000423656 15/25 104 76 28 125 125 0 strelka-varscan-mutect DCAF1,missense_variant,p.Ser1135Leu,ENST00000504652,NM_001171904.1;DCAF1,missense_variant,p.Ser1136Leu,ENST00000423656,NM_014703.2;DCAF1,missense_variant,p.Ser687Leu,ENST00000335891,; A ENST00000423656 Transcript missense_variant 3537/5946 3407/4524 1136/1507 S/L tCa/tTa COSM446776 1 -1 DCAF1 HGNC HGNC:30911 protein_coding YES CCDS74943.1 ENSP00000393183 Q9Y4B6 UPI00000716AC NM_014703.2 deleterious(0) 15/25 hmmpanther:PTHR13129,hmmpanther:PTHR13129:SF4,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 1 MODERATE 1 SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 51418706 51418706 G A 1 0 0 0 0 1 0 0 0 4061 1294 45 3 3 DCAF1 3 51418706 Missense_Mutation SNP G C3N-00294_T 1118163 51418706 146876853 315 13087 ACY1 0 . GRCh38 3 51988989 51988989 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1710G>A p.Glu571Lys p.E571K ENST00000637978 17/17 535 415 120 574 574 0 strelka-varscan-mutect ABHD14A-ACY1,missense_variant,p.Glu571Lys,ENST00000637978,;ABHD14A-ACY1,missense_variant,p.Glu482Lys,ENST00000463937,;ACY1,missense_variant,p.Glu381Lys,ENST00000636358,NM_001198895.1,NM_000666.2;ACY1,missense_variant,p.Glu381Lys,ENST00000404366,;ACY1,missense_variant,p.Glu346Lys,ENST00000476351,NM_001198898.1;ACY1,missense_variant,p.Glu316Lys,ENST00000476854,NM_001198897.1;ACY1,missense_variant,p.Glu309Lys,ENST00000494103,NM_001198896.1;ACY1,missense_variant,p.Glu346Lys,ENST00000635797,;ACY1,3_prime_UTR_variant,,ENST00000637149,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637222,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000635952,;ACY1,downstream_gene_variant,,ENST00000469863,;RPL29,downstream_gene_variant,,ENST00000466397,;RPL29,downstream_gene_variant,,ENST00000294189,NM_000992.2;RPL29,downstream_gene_variant,,ENST00000495383,;RPL29,downstream_gene_variant,,ENST00000479017,;RPL29,downstream_gene_variant,,ENST00000475248,;RPL29,downstream_gene_variant,,ENST00000492277,;ACY1,downstream_gene_variant,,ENST00000636047,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637778,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637130,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000635937,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636490,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636826,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637025,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637730,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637563,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636718,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000635946,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637696,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636089,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000635951,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636646,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000463721,NM_001316331.1;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636942,;ACY1,3_prime_UTR_variant,,ENST00000635941,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000637512,;ACY1,3_prime_UTR_variant,,ENST00000636880,;ACY1,3_prime_UTR_variant,,ENST00000491318,;ABHD14A-ACY1,3_prime_UTR_variant,,ENST00000636660,;ACY1,non_coding_transcript_exon_variant,,ENST00000638136,;ACY1,non_coding_transcript_exon_variant,,ENST00000490244,;ACY1,non_coding_transcript_exon_variant,,ENST00000637199,;ACY1,non_coding_transcript_exon_variant,,ENST00000637034,;ACY1,non_coding_transcript_exon_variant,,ENST00000637746,;ACY1,non_coding_transcript_exon_variant,,ENST00000638077,;ACY1,downstream_gene_variant,,ENST00000637251,;ACY1,downstream_gene_variant,,ENST00000465121,;ACY1,downstream_gene_variant,,ENST00000637102,;ACY1,downstream_gene_variant,,ENST00000638096,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636085,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000486081,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000635785,;ACY1,downstream_gene_variant,,ENST00000636556,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000497128,;ACY1,downstream_gene_variant,,ENST00000637460,;ACY1,downstream_gene_variant,,ENST00000496679,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636029,;RPL29,downstream_gene_variant,,ENST00000480306,;ACY1,downstream_gene_variant,,ENST00000637349,;ACY1,downstream_gene_variant,,ENST00000637209,;ACY1,downstream_gene_variant,,ENST00000468068,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637461,;ACY1,downstream_gene_variant,,ENST00000464587,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636264,; A ENST00000637978 Transcript missense_variant 1710/1758 1711/1759 571/586 E/K Gag/Aag 1 1 ABHD14A-ACY1 HGNC HGNC:38856 protein_coding YES ENSP00000490744 tolerated(0.36) 17/17 hmmpanther:PTHR11014,hmmpanther:PTHR11014:SF90,TIGRFAM_domain:TIGR01880,Pfam_domain:PF01546,Superfamily_domains:SSF53187 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 51988989 51988989 G A 1 0 0 0 0 1 0 0 0 270 1291 45 3 3 ACY1 3 51988989 Missense_Mutation SNP G C3N-00294_T 570283 51988989 146306570 316 13088 GNL3 0 . GRCh38 3 52693542 52693542 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1322G>A p.Arg441Lys p.R441K ENST00000418458 12/15 134 121 13 111 111 0 strelka-mutect GNL3,missense_variant,p.Arg429Lys,ENST00000394799,NM_206826.1,NM_206825.1;GNL3,missense_variant,p.Arg441Lys,ENST00000418458,NM_014366.4;GLT8D1,downstream_gene_variant,,ENST00000266014,NM_018446.3;GLT8D1,downstream_gene_variant,,ENST00000478968,NM_001278280.1,NM_001010983.2,NM_001278281.1;GLT8D1,downstream_gene_variant,,ENST00000394783,NM_152932.2;GLT8D1,downstream_gene_variant,,ENST00000491606,;GLT8D1,downstream_gene_variant,,ENST00000497953,;GLT8D1,downstream_gene_variant,,ENST00000487642,;GLT8D1,downstream_gene_variant,,ENST00000489119,;GLT8D1,downstream_gene_variant,,ENST00000479553,;GLT8D1,downstream_gene_variant,,ENST00000497436,;GNL3,downstream_gene_variant,,ENST00000479230,;SNORD19B,downstream_gene_variant,,ENST00000459623,;SNORD19B,downstream_gene_variant,,ENST00000630615,;SNORD69,downstream_gene_variant,,ENST00000391150,;SNORD19,downstream_gene_variant,,ENST00000410413,;SNORD19,downstream_gene_variant,,ENST00000516978,;SNORD19,downstream_gene_variant,,ENST00000391191,;GLT8D1,downstream_gene_variant,,ENST00000463827,;GNL3,downstream_gene_variant,,ENST00000468146,;GNL3,splice_region_variant,,ENST00000496254,;GNL3,splice_region_variant,,ENST00000497356,;GLT8D1,downstream_gene_variant,,ENST00000484163,;GLT8D1,downstream_gene_variant,,ENST00000480080,;GLT8D1,downstream_gene_variant,,ENST00000485899,;GLT8D1,downstream_gene_variant,,ENST00000481643,;GNL3,downstream_gene_variant,,ENST00000492349,;GNL3,downstream_gene_variant,,ENST00000484022,; A ENST00000418458 Transcript missense_variant,splice_region_variant 1495/2040 1322/1650 441/549 R/K aGa/aAa 1 1 GNL3 HGNC HGNC:29931 protein_coding YES CCDS2861.1 ENSP00000395772 Q9BVP2 UPI000003C48A NM_014366.4 tolerated(0.73) 12/15 hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 52693542 52693542 G A 1 0 0 0 0 1 0 0 0 6416 956 33 3 3 GNL3 3 52693542 Missense_Mutation SNP G C3N-00294_T 704553 52693542 145602017 317 13089 FLNB 0 . GRCh38 3 58153431 58153431 + Missense_Mutation SNP G G C rs774757964 C3N-00294_T C3N-00294_N G G c.6517G>C p.Glu2173Gln p.E2173Q ENST00000490882 40/47 301 229 72 362 362 0 strelka-varscan-mutect FLNB,missense_variant,p.Glu2142Gln,ENST00000295956,NM_001457.3;FLNB,missense_variant,p.Glu2131Gln,ENST00000429972,NM_001164318.1;FLNB,missense_variant,p.Glu2118Gln,ENST00000358537,NM_001164319.1;FLNB,missense_variant,p.Glu2173Gln,ENST00000490882,NM_001164317.1;FLNB,missense_variant,p.Glu1949Gln,ENST00000493452,;FLNB,missense_variant,p.Glu66Gln,ENST00000466455,;FLNB,non_coding_transcript_exon_variant,,ENST00000481470,;FLNB,downstream_gene_variant,,ENST00000477629,;FLNB,upstream_gene_variant,,ENST00000468939,;FLNB,upstream_gene_variant,,ENST00000475487,;FLNB,downstream_gene_variant,,ENST00000470231,; C ENST00000490882 Transcript missense_variant 6682/8079 6517/7902 2173/2633 E/Q Gag/Cag rs774757964 1 1 FLNB HGNC HGNC:3755 protein_coding YES CCDS54599.1 ENSP00000420213 O75369 UPI0001765F91 NM_001164317.1 tolerated(0.23) 40/47 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF238,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs774757964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 58153431 58153431 G C 1 0 0 0 0 1 0 0 0 5790 1291 45 4 4 FLNB 3 58153431 Missense_Mutation SNP G C3N-00294_T 5459889 58153431 140142128 318 13090 PDZRN3 0 . GRCh38 3 73624655 73624655 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.171C>T p.= p.R57R ENST00000263666 1/10 112 93 19 104 104 0 strelka-varscan-mutect PDZRN3,synonymous_variant,p.=,ENST00000263666,NM_015009.2;PDZRN3,synonymous_variant,p.=,ENST00000308537,;PDZRN3-AS1,intron_variant,,ENST00000478988,;PDZRN3-AS1,intron_variant,,ENST00000608743,;PDZRN3-AS1,intron_variant,,ENST00000608304,;PDZRN3-AS1,intron_variant,,ENST00000619517,;CTD-2006M22.2,non_coding_transcript_exon_variant,,ENST00000625169,; A ENST00000263666 Transcript synonymous_variant 286/4248 171/3201 57/1066 R cgC/cgT 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 1/10 Gene3D:3.30.40.10,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 73624655 73624655 G A 1 0 0 0 0 0 0 0 1 11797 1074 38 1 1 PDZRN3 3 73624655 Silent SNP G C3N-00294_T 15471224 73624655 124670904 319 13091 EPHA6 0 . GRCh38 3 97475449 97475449 + Silent SNP G G A rs765093976 C3N-00294_T C3N-00294_N G G c.1992G>A p.= p.L664L ENST00000389672 8/18 132 102 30 115 115 0 strelka-varscan-mutect EPHA6,synonymous_variant,p.=,ENST00000389672,NM_001080448.2;EPHA6,synonymous_variant,p.=,ENST00000514100,NM_001278300.1;EPHA6,synonymous_variant,p.=,ENST00000502694,NM_173655.3;EPHA6,synonymous_variant,p.=,ENST00000477384,;EPHA6,synonymous_variant,p.=,ENST00000503760,;EPHA6,synonymous_variant,p.=,ENST00000508345,; A ENST00000389672 Transcript synonymous_variant 2030/3971 1992/3393 664/1130 L ttG/ttA rs765093976,COSM3683179,COSM3683180,COSM3683181 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 8/18 Pfam_domain:PF14575,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 0,1,1,1 LOW 1 SNV 2 0,1,1,1 1 PASS rs765093976 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 97475449 97475449 G A 1 0 0 0 0 0 0 0 1 5018 1281 45 3 3 EPHA6 3 97475449 Silent SNP G C3N-00294_T 23850794 97475449 100820110 320 13092 GABRR3 0 . GRCh38 3 98017678 98017678 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.283G>A p.Asp95Asn p.D95N ENST00000621172 4/10 135 112 23 215 215 0 strelka-varscan-mutect GABRR3,missense_variant,p.Asp95Asn,ENST00000621172,NM_001105580.2;GABRR3,missense_variant,p.Asp95Asn,ENST00000472788,;GABRR3,non_coding_transcript_exon_variant,,ENST00000470589,; T ENST00000621172 Transcript missense_variant 400/1521 283/1404 95/467 D/N Gac/Aac 1 -1 GABRR3 HGNC HGNC:17969 protein_coding YES CCDS54617.1 ENSP00000481321 A8MPY1 UPI000003F558 NM_001105580.2 deleterious(0.02) 4/10 hmmpanther:PTHR18945:SF196,hmmpanther:PTHR18945,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 98017678 98017678 C T 1 0 0 0 0 1 0 0 0 6049 826 29 3 3 GABRR3 3 98017678 Missense_Mutation SNP C C3N-00294_T 542229 98017678 100277881 321 13093 OR5H15 0 . GRCh38 3 98168730 98168730 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.31G>A p.Glu11Lys p.E11K ENST00000356526 1/1 123 105 18 121 121 0 varscan-mutect OR5H15,missense_variant,p.Glu11Lys,ENST00000356526,NM_001005515.1;OR5H15,missense_variant,p.Glu11Lys,ENST00000615035,; A ENST00000356526 Transcript missense_variant 31/942 31/942 11/313 E/K Gag/Aag COSM585111 1 1 OR5H15 HGNC HGNC:31287 protein_coding YES CCDS33799.1 ENSP00000373195 A6NDH6 UPI00001606CE NM_001005515.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF325,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs1445190708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 98168730 98168730 G A 1 0 0 0 0 1 0 0 0 11231 943 33 3 3 OR5H15 3 98168730 Missense_Mutation SNP G C3N-00294_T 151052 98168730 100126829 322 13094 IMPG2 0 . GRCh38 3 101243666 101243666 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2665G>A p.Asp889Asn p.D889N ENST00000193391 13/19 144 116 28 138 137 1 strelka-varscan-mutect IMPG2,missense_variant,p.Asp889Asn,ENST00000193391,NM_016247.3; T ENST00000193391 Transcript missense_variant 2853/8337 2665/3726 889/1241 D/N Gac/Aac 1 -1 IMPG2 HGNC HGNC:18362 protein_coding YES CCDS2940.1 ENSP00000193391 Q9BZV3 F1T0J3 UPI000013C605 NM_016247.3 tolerated(1) 13/19 hmmpanther:PTHR12199,hmmpanther:PTHR12199:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 101243666 101243666 C T 1 0 0 0 0 1 0 0 0 7631 826 29 3 3 IMPG2 3 101243666 Missense_Mutation SNP C C3N-00294_T 3074936 101243666 97051893 323 13095 DZIP3 0 . GRCh38 3 108684333 108684334 + Frame_Shift_Ins INS - - C novel C3N-00294_T C3N-00294_N - - c.3007dupC p.Leu1003ProfsTer26 p.L1003Pfs*26 ENST00000361582 27/33 130 102 28 138 138 0 sindel-varindel-pindel DZIP3,frameshift_variant,p.Leu1003ProfsTer26,ENST00000361582,NM_014648.3;DZIP3,frameshift_variant,p.Leu1003ProfsTer26,ENST00000463306,;DZIP3,3_prime_UTR_variant,,ENST00000495008,; C ENST00000361582 Transcript frameshift_variant 3231-3232/5350 3001-3002/3627 1001/1208 A/AX gcc/gCcc 1 1 DZIP3 HGNC HGNC:30938 protein_coding YES CCDS2952.1 ENSP00000355028 Q86Y13 UPI000006E7D4 NM_014648.3 27/33 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF55 HIGH 1 insertion 1 6 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999806 1 1 1 0 C 7 5 46 108684333 108684333 - C 1 0 1 1 0 0 0 0 0 4689 971 34 0 0 DZIP3 3 108684333 Frame_Shift_Ins INS - C3N-00294_T 7440667 108684333 89611226 324 13096 TAGLN3 0 . GRCh38 3 112000833 112000833 + Nonsense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.242C>G p.Ser81Ter p.S81* ENST00000393917 3/5 147 119 28 132 132 0 strelka-varscan-mutect TAGLN3,stop_gained,p.Ser81Ter,ENST00000393917,NM_013259.2;TAGLN3,stop_gained,p.Ser81Ter,ENST00000273368,;TAGLN3,stop_gained,p.Ser81Ter,ENST00000478951,NM_001008272.1;TAGLN3,stop_gained,p.Ser81Ter,ENST00000455401,NM_001008273.1;TAGLN3,stop_gained,p.Ser21Ter,ENST00000469385,;TAGLN3,5_prime_UTR_variant,,ENST00000486460,;TAGLN3,intron_variant,,ENST00000494932,; G ENST00000393917 Transcript stop_gained 794/1488 242/600 81/199 S/* tCa/tGa COSM367329,COSM367330 1 1 TAGLN3 HGNC HGNC:29868 protein_coding YES CCDS33816.1 ENSP00000377494 Q9UI15 UPI00000738C2 NM_013259.2 3/5 PROSITE_profiles:PS50021,hmmpanther:PTHR18959,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576 1,1 HIGH 1 SNV 5 1,1 1 PASS rs1218035526 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 112000833 112000833 C G 1 0 0 0 0 0 1 0 0 15936 838 29 4 4 TAGLN3 3 112000833 Nonsense_Mutation SNP C C3N-00294_T 3316500 112000833 86294726 325 13097 NEPRO 0 . GRCh38 3 113005806 113005806 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1434G>A p.= p.K478K ENST00000314400 9/9 189 171 18 237 237 0 strelka-varscan-mutect NEPRO,synonymous_variant,p.=,ENST00000314400,NM_001319115.1,NM_001319114.1,NM_015412.3;NEPRO,synonymous_variant,p.=,ENST00000383675,NM_001319110.1,NM_001319109.1;GTPBP8,downstream_gene_variant,,ENST00000383677,NM_138485.1;GTPBP8,downstream_gene_variant,,ENST00000473129,;GTPBP8,downstream_gene_variant,,ENST00000619116,;GTPBP8,downstream_gene_variant,,ENST00000383678,NM_014170.2;GTPBP8,downstream_gene_variant,,ENST00000467752,;NEPRO,downstream_gene_variant,,ENST00000472762,;NEPRO,3_prime_UTR_variant,,ENST00000472637,;NEPRO,3_prime_UTR_variant,,ENST00000473284,;NEPRO,3_prime_UTR_variant,,ENST00000469169,;NEPRO,3_prime_UTR_variant,,ENST00000489848,;NEPRO,3_prime_UTR_variant,,ENST00000469809,;NEPRO,3_prime_UTR_variant,,ENST00000462295,;NEPRO,3_prime_UTR_variant,,ENST00000472705,;NEPRO,non_coding_transcript_exon_variant,,ENST00000486271,;NEPRO,non_coding_transcript_exon_variant,,ENST00000474311,;GTPBP8,intron_variant,,ENST00000485330,;NEPRO,downstream_gene_variant,,ENST00000461381,;NEPRO,downstream_gene_variant,,ENST00000482229,;NEPRO,downstream_gene_variant,,ENST00000496206,;GTPBP8,downstream_gene_variant,,ENST00000488781,;GTPBP8,downstream_gene_variant,,ENST00000295864,;NEPRO,downstream_gene_variant,,ENST00000464816,; T ENST00000314400 Transcript synonymous_variant 1626/4992 1434/1704 478/567 K aaG/aaA 1 -1 NEPRO HGNC HGNC:24496 protein_coding YES CCDS33824.1 ENSP00000320251 Q6NW34 UPI0000367197 NM_001319115.1,NM_001319114.1,NM_015412.3 9/9 hmmpanther:PTHR34761 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 113005806 113005806 C T 1 0 0 0 0 0 0 0 1 10371 912 32 3 3 NEPRO 3 113005806 Silent SNP C C3N-00294_T 1004973 113005806 85289753 326 13098 ARHGAP31 0 . GRCh38 3 119409522 119409522 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1672G>A p.Glu558Lys p.E558K ENST00000264245 11/12 227 179 48 261 261 0 strelka-varscan-mutect ARHGAP31,missense_variant,p.Glu558Lys,ENST00000264245,NM_020754.3; A ENST00000264245 Transcript missense_variant 2204/9317 1672/4335 558/1444 E/K Gag/Aag 1 1 ARHGAP31 HGNC HGNC:29216 protein_coding YES CCDS43135.1 ENSP00000264245 Q2M1Z3 UPI00001C1DFD NM_020754.3 deleterious(0.03) 11/12 hmmpanther:PTHR15729:SF3,hmmpanther:PTHR15729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 119409522 119409522 G A 1 0 0 0 0 1 0 0 0 1005 1291 45 3 3 ARHGAP31 3 119409522 Missense_Mutation SNP G C3N-00294_T 6403716 119409522 78886037 327 13099 ARHGAP31 0 . GRCh38 3 119415852 119415852 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3923G>C p.Arg1308Thr p.R1308T ENST00000264245 12/12 185 149 36 186 186 0 strelka-varscan-mutect ARHGAP31,missense_variant,p.Arg1308Thr,ENST00000264245,NM_020754.3; C ENST00000264245 Transcript missense_variant 4455/9317 3923/4335 1308/1444 R/T aGa/aCa 1 1 ARHGAP31 HGNC HGNC:29216 protein_coding YES CCDS43135.1 ENSP00000264245 Q2M1Z3 UPI00001C1DFD NM_020754.3 deleterious(0) 12/12 hmmpanther:PTHR15729:SF3,hmmpanther:PTHR15729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 119415852 119415852 G C 1 0 0 0 0 1 0 0 0 1005 942 33 4 4 ARHGAP31 3 119415852 Missense_Mutation SNP G C3N-00294_T 6330 119415852 78879707 328 13100 LRRC58 0 . GRCh38 3 120348763 120348763 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.481G>A p.Glu161Lys p.E161K ENST00000295628 1/4 53 39 14 64 64 0 strelka-varscan-mutect LRRC58,missense_variant,p.Glu161Lys,ENST00000295628,NM_001099678.1;RP11-174O3.3,upstream_gene_variant,,ENST00000637360,;RP11-174O3.3,upstream_gene_variant,,ENST00000494869,; T ENST00000295628 Transcript missense_variant 577/7903 481/1116 161/371 E/K Gag/Aag 1 -1 LRRC58 HGNC HGNC:26968 protein_coding YES CCDS46892.1 ENSP00000295628 Q96CX6 UPI00001C1DEE NM_001099678.1 deleterious(0.04) 1/4 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 120348763 120348763 C T 1 0 0 0 0 1 0 0 0 8909 835 29 3 3 LRRC58 3 120348763 Missense_Mutation SNP C C3N-00294_T 932911 120348763 77946796 329 13101 FAM162A 0 . GRCh38 3 122407280 122407280 + Splice_Site SNP G G C novel C3N-00294_T C3N-00294_N G G c.264-1G>C p.X88_splice ENST00000477892 72 57 15 54 54 0 strelka-varscan-mutect FAM162A,splice_acceptor_variant,,ENST00000477892,NM_014367.3;FAM162A,splice_acceptor_variant,,ENST00000469967,;FAM162A,splice_acceptor_variant,,ENST00000232125,; C ENST00000477892 Transcript splice_acceptor_variant -/3052 264/465 88/154 1 1 FAM162A HGNC HGNC:17865 protein_coding YES CCDS43139.1 ENSP00000419088 Q96A26 UPI0000073F3F NM_014367.3 3/4 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 46 122407280 122407280 G C 1 0 0 0 0 0 0 1 0 5323 1014 35 4 4 FAM162A 3 122407280 Splice_Site SNP G C3N-00294_T 2058517 122407280 75888279 330 13102 KLF15 0 . GRCh38 3 126352481 126352481 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.442C>G p.Leu148Val p.L148V ENST00000296233 2/3 231 197 34 268 268 0 strelka-varscan-mutect KLF15,missense_variant,p.Leu148Val,ENST00000296233,NM_014079.3;KLF15,downstream_gene_variant,,ENST00000509675,; C ENST00000296233 Transcript missense_variant 673/2574 442/1251 148/416 L/V Ctg/Gtg COSM1484551 1 -1 KLF15 HGNC HGNC:14536 protein_coding YES CCDS3036.1 ENSP00000296233 Q9UIH9 UPI0000001659 NM_014079.3 deleterious(0) 2/3 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 126352481 126352481 G C 1 0 0 0 0 1 0 0 0 8208 933 33 4 4 KLF15 3 126352481 Missense_Mutation SNP G C3N-00294_T 3945201 126352481 71943078 331 13103 DNAJC13 0 . GRCh38 3 132453400 132453400 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.640G>C p.Glu214Gln p.E214Q ENST00000260818 7/56 214 177 37 310 310 0 strelka-varscan-mutect DNAJC13,missense_variant,p.Glu214Gln,ENST00000260818,NM_015268.3;DNAJC13,non_coding_transcript_exon_variant,,ENST00000486798,;DNAJC13,upstream_gene_variant,,ENST00000471925,; C ENST00000260818 Transcript missense_variant 888/7730 640/6732 214/2243 E/Q Gaa/Caa 1 1 DNAJC13 HGNC HGNC:30343 protein_coding YES CCDS33857.1 ENSP00000260818 O75165 UPI000022C1FD NM_015268.3 deleterious(0.04) 7/56 hmmpanther:PTHR36983 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 132453400 132453400 G C 1 0 0 0 0 1 0 0 0 4446 943 33 4 4 DNAJC13 3 132453400 Missense_Mutation SNP G C3N-00294_T 6100919 132453400 65842159 332 13104 AMOTL2 0 . GRCh38 3 134371273 134371273 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.335C>T p.Ser112Phe p.S112F ENST00000514516 2/10 216 171 45 225 225 0 strelka-varscan-mutect AMOTL2,missense_variant,p.Ser112Phe,ENST00000514516,NM_001278683.1;AMOTL2,missense_variant,p.Ser54Phe,ENST00000249883,NM_016201.3;AMOTL2,missense_variant,p.Ser54Phe,ENST00000422605,;AMOTL2,missense_variant,p.Ser54Phe,ENST00000513145,NM_001278685.1;AMOTL2,missense_variant,p.Ser54Phe,ENST00000510560,;AMOTL2,missense_variant,p.Ser54Phe,ENST00000515172,;AMOTL2,missense_variant,p.Ser54Phe,ENST00000504234,;AMOTL2,missense_variant,p.Ser54Phe,ENST00000506107,;AMOTL2,missense_variant,p.Ser54Phe,ENST00000505596,;AMOTL2,downstream_gene_variant,,ENST00000502491,;MIR6827,upstream_gene_variant,,ENST00000614799,;AMOTL2,non_coding_transcript_exon_variant,,ENST00000511759,;AMOTL2,intron_variant,,ENST00000512955,;AMOTL2,upstream_gene_variant,,ENST00000506326,; A ENST00000514516 Transcript missense_variant 514/4521 335/2514 112/837 S/F tCc/tTc 1 -1 AMOTL2 HGNC HGNC:17812 protein_coding YES CCDS63784.1 ENSP00000424765 Q9Y2J4 UPI0001D3BD1B NM_001278683.1 deleterious(0) 2/10 hmmpanther:PTHR14826,hmmpanther:PTHR14826:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 134371273 134371273 G A 1 0 0 0 0 1 0 0 0 682 1174 41 3 3 AMOTL2 3 134371273 Missense_Mutation SNP G C3N-00294_T 1917873 134371273 63924286 333 13105 PCCB 0 . GRCh38 3 136260529 136260529 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.483C>T p.= p.I161I ENST00000469217 5/16 235 194 41 241 241 0 strelka-varscan-mutect PCCB,synonymous_variant,p.=,ENST00000471595,;PCCB,synonymous_variant,p.=,ENST00000478469,;PCCB,synonymous_variant,p.=,ENST00000468777,;PCCB,synonymous_variant,p.=,ENST00000466072,;PCCB,synonymous_variant,p.=,ENST00000469217,NM_001178014.1;PCCB,synonymous_variant,p.=,ENST00000251654,NM_000532.4;PCCB,synonymous_variant,p.=,ENST00000462637,;PCCB,synonymous_variant,p.=,ENST00000465423,;PCCB,synonymous_variant,p.=,ENST00000494742,;PCCB,synonymous_variant,p.=,ENST00000459873,;PCCB,synonymous_variant,p.=,ENST00000462542,;PCCB,intron_variant,,ENST00000483687,;PCCB,intron_variant,,ENST00000490504,;PCCB,intron_variant,,ENST00000482086,;PCCB,non_coding_transcript_exon_variant,,ENST00000465176,;PCCB,intron_variant,,ENST00000474833,;PCCB,synonymous_variant,p.=,ENST00000484181,;PCCB,non_coding_transcript_exon_variant,,ENST00000473073,;PCCB,non_coding_transcript_exon_variant,,ENST00000475214,; T ENST00000469217 Transcript synonymous_variant 500/1841 483/1680 161/559 I atC/atT 1 1 PCCB HGNC HGNC:8654 protein_coding YES CCDS54643.1 ENSP00000419027 P05166 UPI000020A2DD NM_001178014.1 5/16 PROSITE_profiles:PS50980,hmmpanther:PTHR22855:SF40,hmmpanther:PTHR22855,Pfam_domain:PF01039,Gene3D:3.90.226.10,Superfamily_domains:SSF52096 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 136260529 136260529 C T 1 0 0 0 0 0 0 0 1 11592 903 32 3 3 PCCB 3 136260529 Silent SNP C C3N-00294_T 1889256 136260529 62035030 334 13106 U2SURP 0 . GRCh38 3 143036096 143036096 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2056G>C p.Glu686Gln p.E686Q ENST00000473835 20/28 49 44 5 73 73 0 strelka-varscan-mutect U2SURP,missense_variant,p.Glu686Gln,ENST00000473835,NM_001320219.1,NM_001080415.1;U2SURP,missense_variant,p.Glu685Gln,ENST00000493598,;U2SURP,missense_variant,p.Glu6Gln,ENST00000467348,;U2SURP,3_prime_UTR_variant,,ENST00000463563,;U2SURP,3_prime_UTR_variant,,ENST00000488497,;U2SURP,non_coding_transcript_exon_variant,,ENST00000480029,;U2SURP,downstream_gene_variant,,ENST00000472373,;U2SURP,upstream_gene_variant,,ENST00000461844,;U2SURP,downstream_gene_variant,,ENST00000496100,; C ENST00000473835 Transcript missense_variant 2146/7276 2056/3090 686/1029 E/Q Gaa/Caa 1 1 U2SURP HGNC HGNC:30855 protein_coding YES CCDS46928.1 ENSP00000418563 O15042 UPI0000160746 NM_001320219.1,NM_001080415.1 tolerated(0.15) 20/28 hmmpanther:PTHR23140:SF1,hmmpanther:PTHR23140 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.83643 1 1 1 1 0 C 3 2 46 143036096 143036096 G C 1 0 0 0 0 1 0 0 0 17341 1175 41 4 4 U2SURP 3 143036096 Missense_Mutation SNP G C3N-00294_T 6775567 143036096 55259463 335 13107 CHST2 0 . GRCh38 3 143122066 143122066 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.1250A>T p.Gln417Leu p.Q417L ENST00000309575 2/2 193 111 82 213 213 0 strelka-varscan-mutect CHST2,missense_variant,p.Gln417Leu,ENST00000309575,NM_004267.4;RP11-80H8.4,upstream_gene_variant,,ENST00000483262,; T ENST00000309575 Transcript missense_variant 2634/4582 1250/1593 417/530 Q/L cAg/cTg 1 1 CHST2 HGNC HGNC:1970 protein_coding YES CCDS3129.1 ENSP00000307911 Q9Y4C5 V9HVX9 UPI0000073CBC NM_004267.4 deleterious(0) 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF3,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 143122066 143122066 A T 1 0 0 0 0 1 0 0 0 3164 188 7 4 4 CHST2 3 143122066 Missense_Mutation SNP A C3N-00294_T 85970 143122066 55173493 336 13108 CPB1 0 . GRCh38 3 148845529 148845529 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.884C>A p.Ser295Tyr p.S295Y ENST00000491148 10/12 299 177 122 339 339 0 strelka-varscan-mutect CPB1,missense_variant,p.Ser295Tyr,ENST00000491148,;CPB1,missense_variant,p.Ser295Tyr,ENST00000282957,NM_001871.2;CPB1,downstream_gene_variant,,ENST00000468341,;CPB1,downstream_gene_variant,,ENST00000462345,;CPB1,downstream_gene_variant,,ENST00000484877,;CPB1,downstream_gene_variant,,ENST00000465718,; A ENST00000491148 Transcript missense_variant 1218/1773 884/1254 295/417 S/Y tCt/tAt 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD deleterious(0.01) 10/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 148845529 148845529 C A 1 0 0 0 0 1 0 0 0 3590 913 32 2 2 CPB1 3 148845529 Missense_Mutation SNP C C3N-00294_T 5723463 148845529 49450030 337 13109 GPR87 0 . GRCh38 3 151295012 151295012 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.234C>G p.Phe78Leu p.F78L ENST00000260843 3/3 106 81 25 111 111 0 strelka-varscan-mutect GPR87,missense_variant,p.Phe78Leu,ENST00000260843,NM_023915.3;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,;MED12L,intron_variant,,ENST00000491549,;GPR87,non_coding_transcript_exon_variant,,ENST00000629077,; C ENST00000260843 Transcript missense_variant 699/1608 234/1077 78/358 F/L ttC/ttG 1 -1 GPR87 HGNC HGNC:4538 protein_coding YES CCDS3157.1 ENSP00000260843 Q9BY21 UPI000003C9FF NM_023915.3 tolerated(0.19) 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF8,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 151295012 151295012 G C 1 0 0 0 0 1 0 0 0 6597 933 33 4 4 GPR87 3 151295012 Missense_Mutation SNP G C3N-00294_T 2449483 151295012 47000547 338 13110 MED12L 0 . GRCh38 3 151365076 151365076 + Missense_Mutation SNP G G A rs147847530 C3N-00294_T C3N-00294_N G G c.2950G>A p.Glu984Lys p.E984K ENST00000474524 20/43 352 285 67 335 335 0 strelka-varscan-mutect MED12L,missense_variant,p.Glu984Lys,ENST00000474524,NM_053002.5;MED12L,missense_variant,p.Glu844Lys,ENST00000273432,;P2RY12,intron_variant,,ENST00000302632,NM_176876.2,NM_022788.4; A ENST00000474524 Transcript missense_variant 2988/10744 2950/6438 984/2145 E/K Gag/Aag rs147847530 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 tolerated(0.35) 20/43 hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS rs147847530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 151365076 151365076 G A 1 0 0 0 0 1 0 0 0 9368 1291 45 3 3 MED12L 3 151365076 Missense_Mutation SNP G C3N-00294_T 70064 151365076 46930483 339 13111 VEPH1 0 . GRCh38 3 157381325 157381325 + Missense_Mutation SNP C C G rs377372657 C3N-00294_T C3N-00294_N C C c.958G>C p.Glu320Gln p.E320Q ENST00000362010 7/14 378 302 76 379 379 0 strelka-varscan-mutect VEPH1,missense_variant,p.Glu320Gln,ENST00000362010,NM_001167912.1;VEPH1,missense_variant,p.Glu320Gln,ENST00000392833,NM_001167911.1;VEPH1,missense_variant,p.Glu320Gln,ENST00000392832,NM_024621.2;RP11-550I24.2,downstream_gene_variant,,ENST00000487238,;VEPH1,non_coding_transcript_exon_variant,,ENST00000488772,;VEPH1,non_coding_transcript_exon_variant,,ENST00000482685,; G ENST00000362010 Transcript missense_variant 1266/4202 958/2502 320/833 E/Q Gag/Cag rs377372657 1 -1 VEPH1 HGNC HGNC:25735 protein_coding YES CCDS3179.1 ENSP00000354919 Q14D04 UPI000013F6EE NM_001167912.1 deleterious(0) 7/14 hmmpanther:PTHR21630,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs377372657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 157381325 157381325 C G 1 0 0 0 0 1 0 0 0 17700 864 30 4 4 VEPH1 3 157381325 Missense_Mutation SNP C C3N-00294_T 6016249 157381325 40914234 340 13112 TRIM59 0 . GRCh38 3 160438663 160438663 + Missense_Mutation SNP G G C rs375673052 C3N-00294_T C3N-00294_N G G c.521C>G p.Ser174Cys p.S174C ENST00000309784 3/3 61 56 5 81 81 0 strelka-varscan-mutect TRIM59,missense_variant,p.Ser174Cys,ENST00000543469,;TRIM59,missense_variant,p.Ser174Cys,ENST00000309784,NM_173084.2;TRIM59,missense_variant,p.Ser174Cys,ENST00000479460,;SMC4,downstream_gene_variant,,ENST00000357388,NM_001002800.2;SMC4,downstream_gene_variant,,ENST00000344722,NM_005496.3;SMC4,downstream_gene_variant,,ENST00000462787,;SMC4,downstream_gene_variant,,ENST00000469762,NM_001288753.1;TRIM59,downstream_gene_variant,,ENST00000496222,;TRIM59,downstream_gene_variant,,ENST00000468542,;TRIM59,downstream_gene_variant,,ENST00000494486,;TRIM59,downstream_gene_variant,,ENST00000471155,;TRIM59,downstream_gene_variant,,ENST00000471396,;RP11-432B6.3,missense_variant,p.Ser174Cys,ENST00000483754,;SMC4,downstream_gene_variant,,ENST00000462668,; C ENST00000309784 Transcript missense_variant 707/3867 521/1212 174/403 S/C tCt/tGt rs375673052 1 -1 TRIM59 HGNC HGNC:30834 protein_coding YES CCDS3190.1 ENSP00000311219 Q8IWR1 UPI0000074490 NM_173084.2 tolerated(1) 3/3 hmmpanther:PTHR24098,hmmpanther:PTHR24098:SF14 MODERATE 1 SNV 1 1 PASS rs375673052 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 160438663 160438663 G C 1 0 0 0 0 1 0 0 0 17025 942 33 4 4 TRIM59 3 160438663 Missense_Mutation SNP G C3N-00294_T 3057338 160438663 37856896 341 13113 SLITRK3 0 . GRCh38 3 165189845 165189845 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.986C>G p.Ser329Ter p.S329* ENST00000475390 2/2 277 233 44 334 334 0 strelka-varscan-mutect SLITRK3,stop_gained,p.Ser329Ter,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,stop_gained,p.Ser329Ter,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; C ENST00000475390 Transcript stop_gained 1430/4555 986/2934 329/977 S/* tCa/tGa 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 2/2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 165189845 165189845 G C 1 0 0 0 0 0 1 0 0 15035 1294 45 4 4 SLITRK3 3 165189845 Nonsense_Mutation SNP G C3N-00294_T 4751182 165189845 33105714 342 13114 PDCD10 0 . GRCh38 3 167684323 167684323 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.624C>T p.= p.F208F ENST00000392750 9/9 211 181 30 343 343 0 strelka-varscan-mutect PDCD10,synonymous_variant,p.=,ENST00000392750,NM_007217.3;PDCD10,synonymous_variant,p.=,ENST00000473645,NM_145859.1;PDCD10,synonymous_variant,p.=,ENST00000497056,NM_145860.1;PDCD10,synonymous_variant,p.=,ENST00000470131,;PDCD10,synonymous_variant,p.=,ENST00000461494,;PDCD10,synonymous_variant,p.=,ENST00000492396,;PDCD10,downstream_gene_variant,,ENST00000475915,;PDCD10,downstream_gene_variant,,ENST00000471885,;PDCD10,downstream_gene_variant,,ENST00000487947,;PDCD10,downstream_gene_variant,,ENST00000462725,;PDCD10,downstream_gene_variant,,ENST00000492139,;PDCD10,downstream_gene_variant,,ENST00000479121,; A ENST00000392750 Transcript synonymous_variant 1042/2067 624/639 208/212 F ttC/ttT 1 -1 PDCD10 HGNC HGNC:8761 protein_coding YES CCDS3202.1 ENSP00000376506 Q9BUL8 UPI0000071E33 NM_007217.3 9/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13250,hmmpanther:PTHR13250:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 167684323 167684323 G A 1 0 0 0 0 0 0 0 1 11704 1281 45 3 3 PDCD10 3 167684323 Silent SNP G C3N-00294_T 2494478 167684323 30611236 343 13115 TNIK 0 . GRCh38 3 171082261 171082261 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.3303G>C p.= p.V1101V ENST00000436636 27/33 128 106 22 111 111 0 strelka-varscan-mutect TNIK,synonymous_variant,p.=,ENST00000436636,NM_015028.2;TNIK,synonymous_variant,p.=,ENST00000341852,NM_001161565.1;TNIK,synonymous_variant,p.=,ENST00000284483,NM_001161560.1;TNIK,synonymous_variant,p.=,ENST00000357327,NM_001161561.1;TNIK,synonymous_variant,p.=,ENST00000470834,NM_001161562.1;TNIK,synonymous_variant,p.=,ENST00000488470,NM_001161563.1;TNIK,synonymous_variant,p.=,ENST00000460047,NM_001161564.1;TNIK,synonymous_variant,p.=,ENST00000475336,NM_001161566.1;TNIK,non_coding_transcript_exon_variant,,ENST00000496492,;TNIK,non_coding_transcript_exon_variant,,ENST00000484051,;TNIK,upstream_gene_variant,,ENST00000487846,; G ENST00000436636 Transcript synonymous_variant 3648/6970 3303/4083 1101/1360 V gtG/gtC 1 -1 TNIK HGNC HGNC:30765 protein_coding YES CCDS46956.1 ENSP00000399511 Q9UKE5 UPI000003ABDF NM_015028.2 27/33 Pfam_domain:PF00780,PROSITE_profiles:PS50219,SMART_domains:SM00036 LOW 1 SNV 1 1 PASS rs1386991811 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 171082261 171082261 C G 1 0 0 0 0 0 0 0 1 16786 813 29 4 4 TNIK 3 171082261 Silent SNP C C3N-00294_T 3397938 171082261 27213298 344 13116 FNDC3B 0 . GRCh38 3 172330539 172330539 + Splice_Site SNP A A G novel C3N-00294_T C3N-00294_N A A c.1380-2A>G p.X460_splice ENST00000336824 53 45 8 51 51 0 strelka-varscan-mutect FNDC3B,splice_acceptor_variant,,ENST00000336824,NM_001135095.1;FNDC3B,splice_acceptor_variant,,ENST00000415807,NM_022763.3;FNDC3B,splice_acceptor_variant,,ENST00000416957,;FNDC3B,splice_acceptor_variant,,ENST00000469491,;FNDC3B,non_coding_transcript_exon_variant,,ENST00000494000,; G ENST00000336824 Transcript splice_acceptor_variant -/7904 1380/3615 460/1204 1 1 FNDC3B HGNC HGNC:24670 protein_coding YES CCDS3217.1 ENSP00000338523 Q53EP0 UPI00001AE8B2 NM_001135095.1 12/25 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.96951 1 1 1 1 0 G 5 3 46 172330539 172330539 A G 1 0 0 0 0 0 0 1 0 5827 202 7 5 5 FNDC3B 3 172330539 Splice_Site SNP A C3N-00294_T 1248278 172330539 25965020 345 13117 NLGN1 0 . GRCh38 3 174280833 174280833 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2002G>A p.Asp668Asn p.D668N ENST00000457714 7/7 248 210 38 259 259 0 strelka-varscan-mutect NLGN1,missense_variant,p.Asp668Asn,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Asp668Asn,ENST00000361589,;NLGN1,missense_variant,p.Asp453Asn,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,; A ENST00000457714 Transcript missense_variant 2431/8242 2002/2472 668/823 D/N Gat/Aat 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 tolerated(0.16) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 174280833 174280833 G A 1 0 0 0 0 1 0 0 0 10498 1174 41 3 3 NLGN1 3 174280833 Missense_Mutation SNP G C3N-00294_T 1950294 174280833 24014726 346 13118 GNB4 0 . GRCh38 3 179414955 179414955 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.360C>T p.= p.I120I ENST00000232564 6/10 180 147 33 197 197 0 strelka-varscan-mutect GNB4,synonymous_variant,p.=,ENST00000232564,NM_021629.3;GNB4,synonymous_variant,p.=,ENST00000468623,;GNB4,synonymous_variant,p.=,ENST00000466899,;GNB4,downstream_gene_variant,,ENST00000497513,;GNB4,upstream_gene_variant,,ENST00000465153,; A ENST00000232564 Transcript synonymous_variant 647/6434 360/1023 120/340 I atC/atT COSM4115446 1 -1 GNB4 HGNC HGNC:20731 protein_coding YES CCDS3230.1 ENSP00000232564 Q9HAV0 UPI000012B21A NM_021629.3 6/10 Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,Prints_domain:PR00319,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,hmmpanther:PTHR19850:SF28,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 179414955 179414955 G A 1 0 0 0 0 0 0 0 1 6399 932 33 3 3 GNB4 3 179414955 Silent SNP G C3N-00294_T 5134122 179414955 18880604 347 13119 CCDC39 0 . GRCh38 3 180642193 180642193 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1674G>A p.Met558Ile p.M558I ENST00000442201 13/20 52 39 13 78 78 0 strelka-varscan-mutect CCDC39,missense_variant,p.Met558Ile,ENST00000442201,NM_181426.1;CCDC39,missense_variant,p.Met558Ile,ENST00000476379,; T ENST00000442201 Transcript missense_variant 1794/3279 1674/2826 558/941 M/I atG/atA 1 -1 CCDC39 HGNC HGNC:25244 protein_coding YES CCDS46964.1 ENSP00000405708 Q9UFE4 UPI00015D7298 NM_181426.1 deleterious(0.01) 13/20 hmmpanther:PTHR18962,hmmpanther:PTHR18962:SF0 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 180642193 180642193 C T 1 0 0 0 0 1 0 0 0 2520 826 29 3 3 CCDC39 3 180642193 Missense_Mutation SNP C C3N-00294_T 1227238 180642193 17653366 348 13120 MCCC1 0 . GRCh38 3 183086782 183086782 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.280G>A p.Glu94Lys p.E94K ENST00000265594 4/19 234 211 23 260 260 0 strelka-varscan-mutect MCCC1,missense_variant,p.Glu94Lys,ENST00000265594,NM_020166.4;MCCC1,missense_variant,p.Glu56Lys,ENST00000629669,;MCCC1,missense_variant,p.Glu47Lys,ENST00000476176,;MCCC1,5_prime_UTR_variant,,ENST00000492597,;MCCC1,5_prime_UTR_variant,,ENST00000610757,NM_001293273.1;MCCC1,missense_variant,p.Glu56Lys,ENST00000497959,;MCCC1,stop_retained_variant,p.=,ENST00000497830,;MCCC1,stop_retained_variant,p.=,ENST00000466650,;MCCC1,3_prime_UTR_variant,,ENST00000486226,;MCCC1,intron_variant,,ENST00000495767,;MCCC1,intron_variant,,ENST00000487634,;MCCC1,intron_variant,,ENST00000490284,; T ENST00000265594 Transcript missense_variant 427/2545 280/2178 94/725 E/K Gaa/Aaa COSM3774747 1 -1 MCCC1 HGNC HGNC:6936 protein_coding YES CCDS3241.1 ENSP00000265594 Q96RQ3 A0A0S2Z693 UPI000013D646 NM_020166.4 deleterious(0) 4/19 PROSITE_profiles:PS50979,hmmpanther:PTHR18866,Pfam_domain:PF00289,Gene3D:3.40.50.20,Superfamily_domains:SSF52440 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 183086782 183086782 C T 1 0 0 0 0 1 0 0 0 9304 835 29 3 3 MCCC1 3 183086782 Missense_Mutation SNP C C3N-00294_T 2444589 183086782 15208777 349 13121 YEATS2 0 . GRCh38 3 183724502 183724502 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.621G>C p.Lys207Asn p.K207N ENST00000305135 6/31 157 128 29 199 199 0 strelka-varscan-mutect YEATS2,missense_variant,p.Lys207Asn,ENST00000305135,NM_018023.4; C ENST00000305135 Transcript missense_variant 816/6506 621/4269 207/1422 K/N aaG/aaC 1 1 YEATS2 HGNC HGNC:25489 protein_coding YES CCDS43175.1 ENSP00000306983 Q9ULM3 UPI00001BB2B9 NM_018023.4 deleterious(0.01) 6/31 PROSITE_profiles:PS51037,hmmpanther:PTHR23195:SF7,hmmpanther:PTHR23195 MODERATE 1 SNV 1 1 PASS rs991662940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 183724502 183724502 G C 1 0 0 0 0 1 0 0 0 18034 933 33 4 4 YEATS2 3 183724502 Missense_Mutation SNP G C3N-00294_T 637720 183724502 14571057 350 13122 TMEM41A 0 . GRCh38 3 185495273 185495273 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.316C>T p.= p.L106L ENST00000421852 3/5 229 190 39 195 195 0 strelka-varscan-mutect TMEM41A,synonymous_variant,p.=,ENST00000421852,NM_080652.3;TMEM41A,intron_variant,,ENST00000296254,;TMEM41A,non_coding_transcript_exon_variant,,ENST00000475480,;TMEM41A,non_coding_transcript_exon_variant,,ENST00000467520,;TMEM41A,non_coding_transcript_exon_variant,,ENST00000467061,;TMEM41A,intron_variant,,ENST00000382227,; A ENST00000421852 Transcript synonymous_variant 412/2827 316/795 106/264 L Ctg/Ttg 1 -1 TMEM41A HGNC HGNC:30544 protein_coding YES CCDS3271.1 ENSP00000406885 Q96HV5 UPI0000048EAE NM_080652.3 3/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR12677,hmmpanther:PTHR12677:SF3,Pfam_domain:PF09335 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 185495273 185495273 G A 1 0 0 0 0 0 0 0 1 16641 933 33 3 3 TMEM41A 3 185495273 Silent SNP G C3N-00294_T 1770771 185495273 12800286 351 13123 MB21D2 0 . GRCh38 3 192798931 192798931 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.931C>G p.Gln311Glu p.Q311E ENST00000392452 2/2 88 69 19 106 106 0 strelka-varscan-mutect MB21D2,missense_variant,p.Gln311Glu,ENST00000392452,NM_178496.3; C ENST00000392452 Transcript missense_variant 1252/3368 931/1476 311/491 Q/E Cag/Gag COSM348040,COSM350832 1 -1 MB21D2 HGNC HGNC:30438 protein_coding YES CCDS3302.2 ENSP00000376246 Q8IYB1 UPI000013FAFE NM_178496.3 tolerated(0.19) 2/2 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF47,Pfam_domain:PF03281,SMART_domains:SM01265 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs988241015 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 192798931 192798931 G C 1 0 0 0 0 1 0 0 0 9270 1299 45 4 4 MB21D2 3 192798931 Missense_Mutation SNP G C3N-00294_T 7303658 192798931 5496628 352 13124 ATP13A4 0 . GRCh38 3 193433901 193433901 + Nonsense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2786C>G p.Ser929Ter p.S929* ENST00000342695 25/30 246 191 55 298 298 0 strelka-varscan-mutect ATP13A4,stop_gained,p.Ser929Ter,ENST00000342695,NM_032279.3;ATP13A4,stop_gained,p.Ser910Ter,ENST00000392443,;ATP13A4,missense_variant,p.Gln560Glu,ENST00000428352,;ATP13A4,3_prime_UTR_variant,,ENST00000450950,;ATP13A4,non_coding_transcript_exon_variant,,ENST00000474776,;ATP13A4,downstream_gene_variant,,ENST00000437904,; C ENST00000342695 Transcript stop_gained 3109/4208 2786/3591 929/1196 S/* tCa/tGa COSM446190 1 -1 ATP13A4 HGNC HGNC:25422 protein_coding YES CCDS3304.2 ENSP00000339182 Q4VNC1 UPI0000520D50 NM_032279.3 25/30 Superfamily_domains:0049473,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF279,TIGRFAM_domain:TIGR01657 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 193433901 193433901 G C 1 0 0 0 0 0 1 0 0 1278 1294 45 4 4 ATP13A4 3 193433901 Nonsense_Mutation SNP G C3N-00294_T 634970 193433901 4861658 353 13125 FYTTD1 0 . GRCh38 3 197756555 197756555 + Missense_Mutation SNP C C T rs758337852 C3N-00294_T C3N-00294_N C C c.233C>T p.Ser78Phe p.S78F ENST00000241502 2/9 134 110 24 111 111 0 strelka-varscan-mutect FYTTD1,missense_variant,p.Ser78Phe,ENST00000241502,NM_032288.6;FYTTD1,missense_variant,p.Ser11Phe,ENST00000424384,;FYTTD1,missense_variant,p.Ser52Phe,ENST00000415708,NM_001011537.2;FYTTD1,missense_variant,p.Ser11Phe,ENST00000428738,;FYTTD1,missense_variant,p.Ser11Phe,ENST00000426031,;FYTTD1,missense_variant,p.Ser78Phe,ENST00000412924,;FYTTD1,missense_variant,p.Ser83Phe,ENST00000494309,;FYTTD1,missense_variant,p.Ser78Phe,ENST00000418169,; T ENST00000241502 Transcript missense_variant,splice_region_variant 455/6866 233/957 78/318 S/F tCt/tTt rs758337852 1 1 FYTTD1 HGNC HGNC:25407 protein_coding YES CCDS3329.1 ENSP00000241502 Q96QD9 A0A024R9K4 UPI0000073CEC NM_032288.6 deleterious(0.05) 2/9 hmmpanther:PTHR21038:SF2,hmmpanther:PTHR21038,Pfam_domain:PF07078 MODERATE 1 SNV 1 1 PASS rs758337852 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 197756555 197756555 C T 1 0 0 0 0 1 0 0 0 5998 927 32 3 3 FYTTD1 3 197756555 Missense_Mutation SNP C C3N-00294_T 4322654 197756555 539004 354 13126 ZNF595 0 . GRCh38 4 86905 86905 + Silent SNP G G A rs188563063 C3N-00294_T C3N-00294_N G G c.1401G>A p.= p.L467L ENST00000610261 4/4 197 163 34 205 205 0 strelka-varscan-mutect ZNF595,synonymous_variant,p.=,ENST00000610261,NM_182524.3;ZNF595,synonymous_variant,p.=,ENST00000609518,NM_001286052.1;ZNF595,synonymous_variant,p.=,ENST00000608255,NM_001286053.1,NM_001286054.1; A ENST00000610261 Transcript synonymous_variant 1605/2911 1401/1947 467/648 L ctG/ctA rs188563063 1 1 ZNF595 HGNC HGNC:27196 protein_coding YES CCDS75075.1 ENSP00000477392 Q7Z3I0 UPI00001A9D0D NM_182524.3 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF303,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs188563063 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 86905 86905 G A 1 0 0 0 0 0 0 0 1 18600 1277 45 3 3 ZNF595 4 86905 Silent SNP G C3N-00294_T 86905 190127650 355 13127 HAUS3 0 . GRCh38 4 2232106 2232106 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1633C>T p.Leu545Phe p.L545F ENST00000243706 5/5 92 82 10 164 164 0 strelka-varscan-mutect HAUS3,missense_variant,p.Leu545Phe,ENST00000243706,;HAUS3,missense_variant,p.Leu545Phe,ENST00000443786,NM_024511.6,NM_001303143.1;POLN,intron_variant,,ENST00000511885,NM_181808.3;HAUS3,intron_variant,,ENST00000506763,;POLN,upstream_gene_variant,,ENST00000382865,;POLN,non_coding_transcript_exon_variant,,ENST00000506518,;POLN,intron_variant,,ENST00000515357,;COX6B1P5,upstream_gene_variant,,ENST00000509843,; A ENST00000243706 Transcript missense_variant 1863/5620 1633/1812 545/603 L/F Ctc/Ttc 1 -1 HAUS3 HGNC HGNC:28719 protein_coding YES CCDS33941.1 ENSP00000243706 Q68CZ6 UPI000020BA32 deleterious(0.02) 5/5 hmmpanther:PTHR19378,hmmpanther:PTHR19378:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 2232106 2232106 G A 1 0 0 0 0 1 0 0 0 6853 942 33 3 3 HAUS3 4 2232106 Missense_Mutation SNP G C3N-00294_T 2145201 2232106 187982449 356 13128 FAM193A 0 . GRCh38 4 2699779 2699779 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2734G>A p.Glu912Lys p.E912K ENST00000324666 17/20 238 186 52 289 289 0 strelka-varscan-mutect FAM193A,missense_variant,p.Glu1203Lys,ENST00000637812,;FAM193A,missense_variant,p.Glu912Lys,ENST00000324666,NM_001256666.1;FAM193A,missense_variant,p.Glu912Lys,ENST00000382839,NM_003704.3;FAM193A,missense_variant,p.Glu912Lys,ENST00000505311,NM_001256668.1;FAM193A,missense_variant,p.Glu934Lys,ENST00000502458,NM_001256667.1;FAM193A,missense_variant,p.Glu912Lys,ENST00000545951,;FAM193A,missense_variant,p.Glu766Lys,ENST00000513350,;FAM193A,3_prime_UTR_variant,,ENST00000512465,;FAM193A,3_prime_UTR_variant,,ENST00000513898,;FAM193A,non_coding_transcript_exon_variant,,ENST00000506120,; A ENST00000324666 Transcript missense_variant 3085/4846 2734/3798 912/1265 E/K Gaa/Aaa 1 1 FAM193A HGNC HGNC:16822 protein_coding YES CCDS58875.1 ENSP00000324587 P78312 UPI0000551BCA NM_001256666.1 tolerated(0.1) 17/20 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15109:SF2,hmmpanther:PTHR15109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 2699779 2699779 G A 1 0 0 0 0 1 0 0 0 5371 943 33 3 3 FAM193A 4 2699779 Missense_Mutation SNP G C3N-00294_T 467673 2699779 187514776 357 13129 FAM193A 0 . GRCh38 4 2699983 2699983 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2938G>C p.Glu980Gln p.E980Q ENST00000324666 17/20 245 199 46 279 278 1 strelka-varscan-mutect FAM193A,missense_variant,p.Glu1271Gln,ENST00000637812,;FAM193A,missense_variant,p.Glu980Gln,ENST00000324666,NM_001256666.1;FAM193A,missense_variant,p.Glu980Gln,ENST00000382839,NM_003704.3;FAM193A,missense_variant,p.Glu980Gln,ENST00000505311,NM_001256668.1;FAM193A,missense_variant,p.Glu1002Gln,ENST00000502458,NM_001256667.1;FAM193A,missense_variant,p.Glu980Gln,ENST00000545951,;FAM193A,missense_variant,p.Glu834Gln,ENST00000513350,;FAM193A,3_prime_UTR_variant,,ENST00000512465,;FAM193A,3_prime_UTR_variant,,ENST00000513898,;FAM193A,downstream_gene_variant,,ENST00000506120,; C ENST00000324666 Transcript missense_variant 3289/4846 2938/3798 980/1265 E/Q Gaa/Caa 1 1 FAM193A HGNC HGNC:16822 protein_coding YES CCDS58875.1 ENSP00000324587 P78312 UPI0000551BCA NM_001256666.1 deleterious_low_confidence(0.02) 17/20 Low_complexity_(Seg):seg,hmmpanther:PTHR15109:SF2,hmmpanther:PTHR15109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 2699983 2699983 G C 1 0 0 0 0 1 0 0 0 5371 943 33 4 4 FAM193A 4 2699983 Missense_Mutation SNP G C3N-00294_T 204 2699983 187514572 358 13130 ADRA2C 0 . GRCh38 4 3767149 3767149 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.543C>T p.= p.V181V ENST00000330055 1/1 302 238 64 288 288 0 strelka-varscan-mutect ADRA2C,synonymous_variant,p.=,ENST00000330055,NM_000683.3;ADRA2C,synonymous_variant,p.=,ENST00000509482,;AC141928.1,upstream_gene_variant,,ENST00000511928,; T ENST00000330055 Transcript synonymous_variant 752/2129 543/1389 181/462 V gtC/gtT 1 1 ADRA2C HGNC HGNC:283 protein_coding YES CCDS47004.1 ENSP00000386069 P18825 Q4W594 UPI000012500C NM_000683.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF25,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 3767149 3767149 C T 1 0 0 0 0 0 0 0 1 415 813 29 3 3 ADRA2C 4 3767149 Silent SNP C C3N-00294_T 1067166 3767149 186447406 359 13131 AFAP1 0 . GRCh38 4 7809739 7809739 + Nonsense_Mutation SNP G G C rs141660816 C3N-00294_T C3N-00294_N G G c.929C>G p.Ser310Ter p.S310* ENST00000420658 9/18 141 107 34 161 161 0 strelka-varscan-mutect AFAP1,stop_gained,p.Ser310Ter,ENST00000420658,NM_001134647.1;AFAP1,stop_gained,p.Ser310Ter,ENST00000358461,NM_198595.2;AFAP1,stop_gained,p.Ser310Ter,ENST00000360265,;AFAP1,stop_gained,p.Ser310Ter,ENST00000382543,;AFAP1,stop_gained,p.Ser19Ter,ENST00000614385,; C ENST00000420658 Transcript stop_gained 1202/7768 929/2445 310/814 S/* tCa/tGa rs141660816 1 -1 AFAP1 HGNC HGNC:24017 protein_coding YES CCDS47010.1 ENSP00000410689 Q8N556 UPI000048041E NM_001134647.1 9/18 hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF8 HIGH 1 SNV 2 1 PASS rs141660816 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 7809739 7809739 G C 1 0 0 0 0 0 1 0 0 430 1294 45 4 4 AFAP1 4 7809739 Nonsense_Mutation SNP G C3N-00294_T 4042590 7809739 182404816 360 13132 BOD1L1 0 . GRCh38 4 13576837 13576837 + Splice_Site SNP C C A novel C3N-00294_T C3N-00294_N C C c.9038+1G>T p.X3013_splice ENST00000040738 96 51 45 109 108 1 strelka-varscan-mutect BOD1L1,splice_donor_variant,,ENST00000040738,NM_148894.2;BOD1L1,splice_donor_variant,,ENST00000507943,;BOD1L1,splice_donor_variant,,ENST00000505343,;BOD1L1,downstream_gene_variant,,ENST00000509897,; A ENST00000040738 Transcript splice_donor_variant -/10565 9038/9156 3013/3051 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 25/25 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 13576837 13576837 C A 1 0 0 0 0 0 0 1 0 1639 521 18 2 2 BOD1L1 4 13576837 Splice_Site SNP C C3N-00294_T 5767098 13576837 176637718 361 13133 BOD1L1 0 . GRCh38 4 13600622 13600622 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.6278G>A p.Gly2093Glu p.G2093E ENST00000040738 10/26 197 159 38 183 183 0 strelka-varscan-mutect BOD1L1,missense_variant,p.Gly2093Glu,ENST00000040738,NM_148894.2; T ENST00000040738 Transcript missense_variant 6414/10565 6278/9156 2093/3051 G/E gGa/gAa 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 tolerated(1) 10/26 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 13600622 13600622 C T 1 0 0 0 0 1 0 0 0 1639 855 30 3 3 BOD1L1 4 13600622 Missense_Mutation SNP C C3N-00294_T 23785 13600622 176613933 362 13134 FAM184B 0 . GRCh38 4 17664648 17664648 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1608G>C p.Leu536Phe p.L536F ENST00000265018 8/18 136 105 31 144 144 0 strelka-varscan-mutect FAM184B,missense_variant,p.Leu536Phe,ENST00000265018,NM_015688.1; G ENST00000265018 Transcript missense_variant 1821/6622 1608/3183 536/1060 L/F ttG/ttC 1 -1 FAM184B HGNC HGNC:29235 protein_coding YES CCDS47033.1 ENSP00000265018 Q9ULE4 UPI000020BD7C NM_015688.1 tolerated(0.12) 8/18 hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 17664648 17664648 C G 1 0 0 0 0 1 0 0 0 5359 825 29 4 4 FAM184B 4 17664648 Missense_Mutation SNP C C3N-00294_T 4064026 17664648 172549907 363 13135 SEL1L3 0 . GRCh38 4 25819922 25819922 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1309G>C p.Glu437Gln p.E437Q ENST00000399878 8/24 115 96 19 160 160 0 strelka-varscan-mutect SEL1L3,missense_variant,p.Glu437Gln,ENST00000399878,NM_015187.4;SEL1L3,missense_variant,p.Glu402Gln,ENST00000264868,NM_001297592.1;SEL1L3,missense_variant,p.Glu284Gln,ENST00000502949,NM_001297594.1; G ENST00000399878 Transcript missense_variant 1432/4520 1309/3399 437/1132 E/Q Gag/Cag 1 -1 SEL1L3 HGNC HGNC:29108 protein_coding YES CCDS47037.1 ENSP00000382767 Q68CR1 UPI00001D7736 NM_015187.4 tolerated(0.21) 8/24 hmmpanther:PTHR11102,hmmpanther:PTHR11102:SF102 MODERATE 1 SNV 1 1 PASS rs1180680714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 25819922 25819922 C G 1 0 0 0 0 1 0 0 0 14289 835 29 4 4 SEL1L3 4 25819922 Missense_Mutation SNP C C3N-00294_T 8155274 25819922 164394633 364 13136 N4BP2 0 . GRCh38 4 40103106 40103106 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.1261C>G p.Gln421Glu p.Q421E ENST00000261435 4/18 182 148 34 248 248 0 strelka-mutect N4BP2,missense_variant,p.Gln421Glu,ENST00000261435,NM_018177.4;N4BP2,missense_variant,p.Gln68Glu,ENST00000513269,;N4BP2,downstream_gene_variant,,ENST00000515550,;N4BP2,3_prime_UTR_variant,,ENST00000511480,NM_001318359.1; G ENST00000261435 Transcript missense_variant 1677/9744 1261/5313 421/1770 Q/E Caa/Gaa COSM3603611 1 1 N4BP2 HGNC HGNC:29851 protein_coding YES CCDS3457.1 ENSP00000261435 Q86UW6 UPI00001A962C NM_018177.4 deleterious(0) 4/18 hmmpanther:PTHR13308,hmmpanther:PTHR13308:SF21 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 40103106 40103106 C G 1 0 0 0 0 1 0 0 0 10114 827 29 4 4 N4BP2 4 40103106 Missense_Mutation SNP C C3N-00294_T 14283184 40103106 150111449 365 13137 GRXCR1 0 . GRCh38 4 43030511 43030511 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.844C>G p.Leu282Val p.L282V ENST00000399770 4/4 323 268 55 401 401 0 strelka-varscan-mutect GRXCR1,missense_variant,p.Leu282Val,ENST00000399770,NM_001080476.2; G ENST00000399770 Transcript missense_variant 844/991 844/873 282/290 L/V Ctt/Gtt 1 1 GRXCR1 HGNC HGNC:31673 protein_coding YES CCDS43225.1 ENSP00000382670 A8MXD5 UPI00004191A5 NM_001080476.2 deleterious(0) 4/4 hmmpanther:PTHR10168:SF65,hmmpanther:PTHR10168 MODERATE 1 SNV 2 1 PASS rs1414314632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 43030511 43030511 C G 1 0 0 0 0 1 0 0 0 6694 913 32 4 4 GRXCR1 4 43030511 Missense_Mutation SNP C C3N-00294_T 2927405 43030511 147184044 366 13138 FRYL 0 . GRCh38 4 48546202 48546202 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5144C>G p.Ser1715Cys p.S1715C ENST00000358350 42/64 319 259 60 345 345 0 strelka-varscan-mutect FRYL,missense_variant,p.Ser1715Cys,ENST00000358350,NM_015030.1;FRYL,missense_variant,p.Ser1715Cys,ENST00000503238,;FRYL,missense_variant,p.Ser585Cys,ENST00000514617,;FRYL,5_prime_UTR_variant,,ENST00000507873,;FRYL,downstream_gene_variant,,ENST00000507711,;FRYL,non_coding_transcript_exon_variant,,ENST00000513401,;FRYL,downstream_gene_variant,,ENST00000502925,; C ENST00000358350 Transcript missense_variant 5749/11706 5144/9042 1715/3013 S/C tCt/tGt 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 deleterious(0) 42/64 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 48546202 48546202 G C 1 0 0 0 0 1 0 0 0 5936 942 33 4 4 FRYL 4 48546202 Missense_Mutation SNP G C3N-00294_T 5515691 48546202 141668353 367 13139 LNX1 0 . GRCh38 4 53508085 53508085 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.523G>C p.Asp175His p.D175H ENST00000263925 3/11 306 265 41 333 333 0 strelka-varscan-mutect LNX1,missense_variant,p.Asp79His,ENST00000306888,NM_032622.2;LNX1,missense_variant,p.Asp175His,ENST00000263925,NM_001126328.2;RP11-231C18.3,intron_variant,,ENST00000507166,;LNX1-AS1,intron_variant,,ENST00000510785,;LNX1-AS1,intron_variant,,ENST00000514364,;LNX1-AS1,intron_variant,,ENST00000511989,;LNX1,non_coding_transcript_exon_variant,,ENST00000511398,; G ENST00000263925 Transcript missense_variant 838/2953 523/2187 175/728 D/H Gac/Cac COSM3604477,COSM3604478 1 -1 LNX1 HGNC HGNC:6657 protein_coding YES CCDS47057.1 ENSP00000263925 Q8TBB1 UPI000012E7A6 NM_001126328.2 tolerated(0.05) 3/11 hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF14 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 53508085 53508085 C G 1 0 0 0 0 1 0 0 0 8792 913 32 4 4 LNX1 4 53508085 Missense_Mutation SNP C C3N-00294_T 4961883 53508085 136706470 368 13140 KIAA1211 0 . GRCh38 4 56315194 56315194 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1692G>A p.= p.T564T ENST00000504228 6/9 126 64 62 142 142 0 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; A ENST00000504228 Transcript synonymous_variant 1797/4628 1692/3702 564/1233 T acG/acA 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 LOW 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 56315194 56315194 G A 1 0 0 0 0 0 0 0 1 8107 1103 39 1 1 KIAA1211 4 56315194 Silent SNP G C3N-00294_T 2807109 56315194 133899361 369 13141 CENPC 0 . GRCh38 4 67519350 67519350 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.484C>G p.Leu162Val p.L162V ENST00000273853 6/19 166 137 29 270 270 0 strelka-varscan-mutect CENPC,missense_variant,p.Leu162Val,ENST00000273853,NM_001812.2;CENPC,missense_variant,p.Leu162Val,ENST00000506882,;CENPC,missense_variant,p.Leu69Val,ENST00000513216,;CENPC,non_coding_transcript_exon_variant,,ENST00000510189,; C ENST00000273853 Transcript missense_variant 735/6940 484/2832 162/943 L/V Ctt/Gtt 1 -1 CENPC HGNC HGNC:1854 protein_coding YES CCDS47063.1 ENSP00000273853 Q03188 UPI00004135A3 NM_001812.2 tolerated(0.17) 6/19 Pfam_domain:PF15622,hmmpanther:PTHR16684 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 67519350 67519350 G C 1 0 0 0 0 1 0 0 0 2937 942 33 4 4 CENPC 4 67519350 Missense_Mutation SNP G C3N-00294_T 11204156 67519350 122695205 370 13142 UBA6 0 . GRCh38 4 67626393 67626393 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2485G>C p.Glu829Gln p.E829Q ENST00000322244 28/33 117 93 24 234 234 0 strelka-varscan-mutect UBA6,missense_variant,p.Glu829Gln,ENST00000322244,NM_018227.5;UBA6,downstream_gene_variant,,ENST00000505673,;UBA6,upstream_gene_variant,,ENST00000514261,; G ENST00000322244 Transcript missense_variant 2545/9564 2485/3159 829/1052 E/Q Gaa/Caa 1 -1 UBA6 HGNC HGNC:25581 protein_coding YES CCDS3516.1 ENSP00000313454 A0AVT1 A0A024RDB0 UPI000004A4F7 NM_018227.5 tolerated(0.46) 28/33 hmmpanther:PTHR10953:SF141,hmmpanther:PTHR10953,Pfam_domain:PF10585,Gene3D:1y8qD02,TIGRFAM_domain:TIGR01408,Pfam_domain:PF00899,Superfamily_domains:SSF69572 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 67626393 67626393 C G 1 0 0 0 0 1 0 0 0 17351 922 32 4 4 UBA6 4 67626393 Missense_Mutation SNP C C3N-00294_T 107043 67626393 122588162 371 13143 UGT2A1 0 . GRCh38 4 69639412 69639412 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.832C>T p.Pro278Ser p.P278S ENST00000514019 3/7 63 50 13 105 105 0 strelka-varscan-mutect UGT2A1,missense_variant,p.Pro278Ser,ENST00000514019,NM_001252274.2;UGT2A2,missense_variant,p.Pro77Ser,ENST00000604629,NM_001105677.2;UGT2A2,missense_variant,p.Pro77Ser,ENST00000604021,NM_001301233.1;UGT2A1,intron_variant,,ENST00000503640,NM_006798.4;UGT2A1,intron_variant,,ENST00000512704,NM_001301239.1;UGT2A1,intron_variant,,ENST00000286604,NM_001252275.2; A ENST00000514019 Transcript missense_variant 948/2376 832/2082 278/693 P/S Cct/Tct 1 -1 UGT2A1 HGNC HGNC:12542 protein_coding YES CCDS58902.1 ENSP00000425497 A0A140T9Z0 UPI0004620AF5 NM_001252274.2 tolerated(0.47) 3/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF229,Superfamily_domains:SSF53756 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 69639412 69639412 G A 1 0 0 0 0 1 0 0 0 17478 1174 41 3 3 UGT2A1 4 69639412 Missense_Mutation SNP G C3N-00294_T 2013019 69639412 120575143 372 13144 RASSF6 0 . GRCh38 4 73576646 73576646 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.903C>G p.= p.L301L ENST00000342081 9/11 157 118 39 156 156 0 strelka-varscan-mutect RASSF6,synonymous_variant,p.=,ENST00000307439,NM_177532.4;RASSF6,synonymous_variant,p.=,ENST00000342081,NM_201431.2;RASSF6,synonymous_variant,p.=,ENST00000395777,NM_001270391.1;RASSF6,synonymous_variant,p.=,ENST00000335049,NM_001270392.1; C ENST00000342081 Transcript synonymous_variant 1034/4331 903/1110 301/369 L ctC/ctG 1 -1 RASSF6 HGNC HGNC:20796 protein_coding YES CCDS3558.1 ENSP00000340578 Q6ZTQ3 UPI00001C0C6F NM_201431.2 9/11 PROSITE_profiles:PS50200,hmmpanther:PTHR22738,hmmpanther:PTHR22738:SF3,Pfam_domain:PF00788,SMART_domains:SM00314,Superfamily_domains:SSF54236 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 73576646 73576646 G C 1 0 0 0 0 0 0 0 1 13251 1277 45 4 4 RASSF6 4 73576646 Silent SNP G C3N-00294_T 3937234 73576646 116637909 373 13145 USO1 0 . GRCh38 4 75790794 75790794 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1249G>C p.Asp417His p.D417H ENST00000264904 13/26 74 70 4 92 92 0 strelka-varscan-mutect USO1,missense_variant,p.Asp417His,ENST00000264904,NM_001290049.1;USO1,missense_variant,p.Asp413His,ENST00000514213,NM_003715.3; C ENST00000264904 Transcript missense_variant 1471/4135 1249/2922 417/973 D/H Gat/Cat 1 1 USO1 HGNC HGNC:30904 protein_coding YES CCDS77929.1 ENSP00000264904 O60763 UPI0001D1479E NM_001290049.1 deleterious(0) 13/26 Pfam_domain:PF04869,hmmpanther:PTHR10013 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -9.633396 1 1 1 1 0 C 3 2 46 75790794 75790794 G C 1 0 0 0 0 1 0 0 0 17573 1304 45 4 4 USO1 4 75790794 Missense_Mutation SNP G C3N-00294_T 2214148 75790794 114423761 374 13146 ANTXR2 0 . GRCh38 4 80008584 80008584 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.978G>T p.Leu326Phe p.L326F ENST00000307333 12/16 258 209 49 255 255 0 strelka-varscan-mutect ANTXR2,missense_variant,p.Leu326Phe,ENST00000403729,NM_058172.5;ANTXR2,missense_variant,p.Leu326Phe,ENST00000307333,NM_001145794.1;ANTXR2,missense_variant,p.Leu249Phe,ENST00000404191,NM_001286780.1,NM_001286781.1;ANTXR2,missense_variant,p.Leu223Phe,ENST00000346652,;ANTXR2,3_prime_UTR_variant,,ENST00000449651,; A ENST00000307333 Transcript missense_variant 981/1473 978/1470 326/489 L/F ttG/ttT 1 -1 ANTXR2 HGNC HGNC:21732 protein_coding YES CCDS47086.1 ENSP00000306185 P58335 UPI000036725D NM_001145794.1 tolerated(0.07) 12/16 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16059:SF13,hmmpanther:PTHR16059,PIRSF_domain:PIRSF038023 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 80008584 80008584 C A 1 0 0 0 0 1 0 0 0 819 593 21 2 2 ANTXR2 4 80008584 Missense_Mutation SNP C C3N-00294_T 4217790 80008584 110205971 375 13147 SEC31A 0 . GRCh38 4 82829017 82829017 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.3010G>A p.Val1004Ile p.V1004I ENST00000395310 23/27 127 120 7 138 138 0 strelka-varscan-mutect SEC31A,missense_variant,p.Val1004Ile,ENST00000395310,NM_001077207.2;SEC31A,missense_variant,p.Val1004Ile,ENST00000448323,NM_014933.3;SEC31A,missense_variant,p.Val1035Ile,ENST00000505472,;SEC31A,missense_variant,p.Val1004Ile,ENST00000355196,;SEC31A,missense_variant,p.Val984Ile,ENST00000443462,NM_001191049.1;SEC31A,missense_variant,p.Val965Ile,ENST00000348405,NM_016211.3;SEC31A,missense_variant,p.Val890Ile,ENST00000311785,NM_001077206.2;SEC31A,missense_variant,p.Val890Ile,ENST00000509142,;SEC31A,missense_variant,p.Val989Ile,ENST00000508502,NM_001077208.2;SEC31A,missense_variant,p.Val851Ile,ENST00000513858,NM_001300744.1;SEC31A,missense_variant,p.Val851Ile,ENST00000500777,;SEC31A,missense_variant,p.Val950Ile,ENST00000505984,NM_001300745.1;SEC31A,missense_variant,p.Val753Ile,ENST00000264405,;SEC31A,missense_variant,p.Val167Ile,ENST00000503937,;SEC31A,missense_variant,p.Val101Ile,ENST00000511338,;SEC31A,upstream_gene_variant,,ENST00000515062,;SEC31A,non_coding_transcript_exon_variant,,ENST00000515749,;SEC31A,non_coding_transcript_exon_variant,,ENST00000514362,;SEC31A,non_coding_transcript_exon_variant,,ENST00000509691,; T ENST00000395310 Transcript missense_variant 3193/4259 3010/3663 1004/1220 V/I Gta/Ata 1 -1 SEC31A HGNC HGNC:17052 protein_coding YES CCDS3596.1 ENSP00000378721 O94979 A0A024RDD3 UPI000003E7E1 NM_001077207.2 tolerated(0.24) 23/27 hmmpanther:PTHR13923:SF23,hmmpanther:PTHR13923 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 82829017 82829017 C T 1 0 0 0 0 1 0 0 0 14275 565 20 3 3 SEC31A 4 82829017 Missense_Mutation SNP C C3N-00294_T 2820433 82829017 107385538 376 13148 ARHGAP24 0 . GRCh38 4 85721894 85721894 + Missense_Mutation SNP T T G novel C3N-00294_T C3N-00294_N T T c.190T>G p.Phe64Val p.F64V ENST00000395184 3/10 217 188 29 330 330 0 strelka-varscan-mutect ARHGAP24,missense_variant,p.Phe64Val,ENST00000395184,NM_001025616.2;ARHGAP24,missense_variant,p.Phe64Val,ENST00000503995,;ARHGAP24,5_prime_UTR_variant,,ENST00000512201,;MIR4451,upstream_gene_variant,,ENST00000580577,;ARHGAP24,non_coding_transcript_exon_variant,,ENST00000506421,;ARHGAP24,non_coding_transcript_exon_variant,,ENST00000509709,; G ENST00000395184 Transcript missense_variant 656/4661 190/2247 64/748 F/V Ttt/Gtt 1 1 ARHGAP24 HGNC HGNC:25361 protein_coding YES CCDS34025.1 ENSP00000378611 Q8N264 UPI00001AF1D9 NM_001025616.2 tolerated(0.62) 3/10 PROSITE_profiles:PS50003,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF19,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 85721894 85721894 T G 1 0 0 0 0 1 0 0 0 998 1841 64 5 5 ARHGAP24 4 85721894 Missense_Mutation SNP T C3N-00294_T 2892877 85721894 104492661 377 13149 UNC5C 0 . GRCh38 4 95170258 95170258 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.2526C>T p.= p.F842F ENST00000453304 15/16 202 166 36 280 280 0 strelka-varscan-mutect UNC5C,synonymous_variant,p.=,ENST00000453304,NM_003728.3;UNC5C,synonymous_variant,p.=,ENST00000610318,; A ENST00000453304 Transcript synonymous_variant 2875/9875 2526/2796 842/931 F ttC/ttT 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 15/16 Gene3D:1.10.533.10,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,SMART_domains:SM00005,Superfamily_domains:SSF47986 LOW 1 SNV 1 1 PASS . . 0 204 0 6 0 0 0 0 -20 0.9988529 1 1 1 0 A 2 1 46 95170258 95170258 G A 1 0 0 0 0 0 0 0 1 17517 1281 45 3 3 UNC5C 4 95170258 Silent SNP G C3N-00294_T 9448364 95170258 95044297 378 13150 UNC5C 0 . GRCh38 4 95202875 95202875 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1992C>T p.= p.L664L ENST00000453304 12/16 406 339 67 489 489 0 strelka-varscan-mutect UNC5C,synonymous_variant,p.=,ENST00000453304,NM_003728.3;UNC5C,synonymous_variant,p.=,ENST00000610318,;UNC5C,synonymous_variant,p.=,ENST00000513796,; A ENST00000453304 Transcript synonymous_variant 2341/9875 1992/2796 664/931 L ctC/ctT 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 12/16 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 95202875 95202875 G A 1 0 0 0 0 0 0 0 1 17517 1277 45 3 3 UNC5C 4 95202875 Silent SNP G C3N-00294_T 32617 95202875 95011680 379 13151 RAP1GDS1 0 . GRCh38 4 98418720 98418720 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1106G>C p.Arg369Thr p.R369T ENST00000339360 10/15 90 79 11 117 117 0 strelka-varscan-mutect RAP1GDS1,missense_variant,p.Arg368Thr,ENST00000408927,NM_001100427.1;RAP1GDS1,missense_variant,p.Arg369Thr,ENST00000453712,NM_021159.4;RAP1GDS1,missense_variant,p.Arg369Thr,ENST00000339360,NM_001100426.1;RAP1GDS1,missense_variant,p.Arg320Thr,ENST00000380158,NM_001100428.1;RAP1GDS1,missense_variant,p.Arg319Thr,ENST00000408900,NM_001100429.1;RAP1GDS1,missense_variant,p.Arg277Thr,ENST00000264572,NM_001100430.1;RAP1GDS1,missense_variant,p.Arg178Thr,ENST00000509501,; C ENST00000339360 Transcript missense_variant 1154/2092 1106/1827 369/608 R/T aGa/aCa 1 1 RAP1GDS1 HGNC HGNC:9859 protein_coding YES CCDS47105.1 ENSP00000340454 P52306 UPI000004A01F NM_001100426.1 tolerated(0.17) 10/15 Gene3D:1.25.10.10,Pfam_domain:PF00514,PROSITE_profiles:PS50176,hmmpanther:PTHR10957,hmmpanther:PTHR10957:SF2,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -17.71347 0.9999904 1 1 1 0 C 3 2 46 98418720 98418720 G C 1 0 0 0 0 1 0 0 0 13198 942 33 4 4 RAP1GDS1 4 98418720 Missense_Mutation SNP G C3N-00294_T 3215845 98418720 91795835 380 13152 RP11-766F14.2 0 . GRCh38 4 99654434 99654434 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.215C>A p.Thr72Asn p.T72N ENST00000511828 1/2 125 66 59 128 128 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Thr72Asn,ENST00000511828,; T ENST00000511828 Transcript missense_variant 215/10086 215/5382 72/1793 T/N aCc/aAc 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE tolerated_low_confidence(0.14) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 99654434 99654434 G T 1 0 0 0 0 1 0 0 0 13762 1261 44 2 2 RP11-766F14.2 4 99654434 Missense_Mutation SNP G C3N-00294_T 1235714 99654434 90560121 381 13153 BANK1 0 . GRCh38 4 102025250 102025250 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.1335G>A p.= p.Q445Q ENST00000322953 9/17 183 140 43 185 185 0 strelka-varscan-mutect BANK1,synonymous_variant,p.=,ENST00000504592,;BANK1,synonymous_variant,p.=,ENST00000322953,NM_017935.4;BANK1,synonymous_variant,p.=,ENST00000444316,NM_001083907.2;BANK1,synonymous_variant,p.=,ENST00000428908,NM_001127507.2;BANK1,synonymous_variant,p.=,ENST00000508653,;RP11-498M5.2,intron_variant,,ENST00000505091,;BANK1,non_coding_transcript_exon_variant,,ENST00000510950,; A ENST00000322953 Transcript synonymous_variant 1609/3372 1335/2358 445/785 Q caG/caA COSM3775447 1 1 BANK1 HGNC HGNC:18233 protein_coding YES CCDS34038.1 ENSP00000320509 Q8NDB2 UPI0000D6159D NM_017935.4 9/17 hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF13 1 LOW 1 SNV 1 1 1 PASS rs1250092036 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 102025250 102025250 G A 1 0 0 0 0 0 0 0 1 1461 933 33 3 3 BANK1 4 102025250 Silent SNP G C3N-00294_T 2370816 102025250 88189305 382 13154 NFKB1 0 . GRCh38 4 102606645 102606645 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1902C>G p.Ile634Met p.I634M ENST00000226574 17/24 275 214 61 329 329 0 strelka-varscan-mutect NFKB1,missense_variant,p.Ile634Met,ENST00000226574,NM_003998.3;NFKB1,missense_variant,p.Ile453Met,ENST00000600343,;NFKB1,missense_variant,p.Ile633Met,ENST00000505458,NM_001319226.1;NFKB1,missense_variant,p.Ile633Met,ENST00000394820,NM_001165412.1; G ENST00000226574 Transcript missense_variant 2369/4085 1902/2910 634/969 I/M atC/atG 1 1 NFKB1 HGNC HGNC:7794 protein_coding YES CCDS3657.1 ENSP00000226574 P19838 UPI0000192724 NM_003998.3 tolerated(0.26) 17/24 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24169,hmmpanther:PTHR24169:SF9,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 102606645 102606645 C G 1 0 0 0 0 1 0 0 0 10412 903 32 4 4 NFKB1 4 102606645 Missense_Mutation SNP C C3N-00294_T 581395 102606645 87607910 383 13155 LEF1 0 . GRCh38 4 108070689 108070689 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1090C>T p.Pro364Ser p.P364S ENST00000265165 9/12 113 68 45 145 145 0 strelka-varscan-mutect LEF1,missense_variant,p.Pro336Ser,ENST00000379951,NM_001130714.2;LEF1,missense_variant,p.Pro364Ser,ENST00000265165,NM_016269.4;LEF1,missense_variant,p.Pro336Ser,ENST00000438313,NM_001130713.2;LEF1,missense_variant,p.Pro268Ser,ENST00000510624,NM_001166119.1;LEF1,non_coding_transcript_exon_variant,,ENST00000503879,;LEF1,non_coding_transcript_exon_variant,,ENST00000504426,;LEF1,non_coding_transcript_exon_variant,,ENST00000510135,;LEF1,non_coding_transcript_exon_variant,,ENST00000509428,;LEF1,non_coding_transcript_exon_variant,,ENST00000505379,;LEF1,non_coding_transcript_exon_variant,,ENST00000514444,;LEF1,non_coding_transcript_exon_variant,,ENST00000505297,;LEF1,non_coding_transcript_exon_variant,,ENST00000504775,;LEF1,non_coding_transcript_exon_variant,,ENST00000512407,;LEF1,3_prime_UTR_variant,,ENST00000506680,;LEF1,non_coding_transcript_exon_variant,,ENST00000507470,;LEF1,non_coding_transcript_exon_variant,,ENST00000505328,; A ENST00000265165 Transcript missense_variant 1745/3068 1090/1200 364/399 P/S Cca/Tca 1 -1 LEF1 HGNC HGNC:6551 protein_coding YES CCDS3679.1 ENSP00000265165 Q9UJU2 A0A024RDI7 UPI0000052242 NM_016269.4 deleterious(0) 9/12 PROSITE_profiles:PS50118,hmmpanther:PTHR10373,Pfam_domain:PF00505,Gene3D:1.10.30.10,SMART_domains:SM00398,Superfamily_domains:SSF47095 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 108070689 108070689 G A 1 0 0 0 0 1 0 0 0 8622 1174 41 3 3 LEF1 4 108070689 Missense_Mutation SNP G C3N-00294_T 5464044 108070689 82143866 384 13156 EGF 0 . GRCh38 4 109974794 109974794 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1816C>T p.His606Tyr p.H606Y ENST00000265171 12/24 203 166 37 277 277 0 strelka-varscan-mutect EGF,missense_variant,p.His606Tyr,ENST00000265171,NM_001963.4;EGF,missense_variant,p.His564Tyr,ENST00000509793,NM_001178131.1;EGF,missense_variant,p.His606Tyr,ENST00000503392,NM_001178130.1;EGF,upstream_gene_variant,,ENST00000541061,;EGF,non_coding_transcript_exon_variant,,ENST00000502579,; T ENST00000265171 Transcript missense_variant 2261/4880 1816/3624 606/1207 H/Y Cat/Tat 1 1 EGF HGNC HGNC:3229 protein_coding YES CCDS3689.1 ENSP00000265171 P01133 UPI000013D5C8 NM_001963.4 deleterious(0) 12/24 Gene3D:2.120.10.30,Pfam_domain:PF00058,PIRSF_domain:PIRSF001778,PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF200,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 109974794 109974794 C T 1 0 0 0 0 1 0 0 0 4798 826 29 3 3 EGF 4 109974794 Missense_Mutation SNP C C3N-00294_T 1904105 109974794 80239761 385 13157 ANK2 0 . GRCh38 4 113358864 113358864 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.10246G>C p.Glu3416Gln p.E3416Q ENST00000357077 38/46 162 110 52 144 144 0 strelka-varscan-mutect ANK2,missense_variant,p.Glu3416Gln,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Glu3383Gln,ENST00000264366,;ANK2,missense_variant,p.Glu426Gln,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,intron_variant,,ENST00000508007,; C ENST00000357077 Transcript missense_variant 10299/14196 10246/11874 3416/3957 E/Q Gag/Cag 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated(0.1) 38/46 Low_complexity_(Seg):seg,hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 113358864 113358864 G C 1 0 0 0 0 1 0 0 0 721 943 33 4 4 ANK2 4 113358864 Missense_Mutation SNP G C3N-00294_T 3384070 113358864 76855691 386 13158 TRPC3 0 . GRCh38 4 121910175 121910175 + Missense_Mutation SNP C C T rs201026202 C3N-00294_T C3N-00294_N C C c.1771G>A p.Glu591Lys p.E591K ENST00000379645 6/12 224 189 35 232 232 0 strelka-varscan-mutect TRPC3,missense_variant,p.Glu518Lys,ENST00000264811,NM_003305.2;TRPC3,missense_variant,p.Glu591Lys,ENST00000379645,NM_001130698.1;TRPC3,missense_variant,p.Glu463Lys,ENST00000513531,;TRPC3,3_prime_UTR_variant,,ENST00000506449,; T ENST00000379645 Transcript missense_variant 1845/3548 1771/2766 591/921 E/K Gag/Aag rs201026202 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 deleterious(0.04) 6/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS rs201026202 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 121910175 121910175 C T 1 0 0 0 0 1 0 0 0 17084 922 32 3 3 TRPC3 4 121910175 Missense_Mutation SNP C C3N-00294_T 8551311 121910175 68304380 387 13159 KIAA1109 0 . GRCh38 4 122336255 122336255 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.11912C>T p.Ser3971Leu p.S3971L ENST00000264501 70/86 91 71 20 151 151 0 strelka-varscan-mutect KIAA1109,missense_variant,p.Ser3971Leu,ENST00000264501,;KIAA1109,missense_variant,p.Ser3971Leu,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Ser640Leu,ENST00000438707,;KIAA1109,missense_variant,p.Ser347Leu,ENST00000306802,;KIAA1109,upstream_gene_variant,,ENST00000442707,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000483357,;KIAA1109,downstream_gene_variant,,ENST00000480651,; T ENST00000264501 Transcript missense_variant 12285/15896 11912/15018 3971/5005 S/L tCa/tTa 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 deleterious(0) 70/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 122336255 122336255 C T 1 0 0 0 0 1 0 0 0 8101 838 29 3 3 KIAA1109 4 122336255 Missense_Mutation SNP C C3N-00294_T 426080 122336255 67878300 388 13160 SPRY1 0 . GRCh38 4 123402228 123402228 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.637G>A p.Glu213Lys p.E213K ENST00000610581 3/3 259 191 68 258 258 0 strelka-varscan-mutect SPRY1,missense_variant,p.Glu213Lys,ENST00000610581,NM_001258038.1;SPRY1,missense_variant,p.Glu213Lys,ENST00000394339,NM_005841.2;SPRY1,missense_variant,p.Glu213Lys,ENST00000622283,NM_001258039.1;SPRY1,missense_variant,p.Glu213Lys,ENST00000339241,NM_199327.2;SPRY1,downstream_gene_variant,,ENST00000507703,;SPRY1,downstream_gene_variant,,ENST00000505319,;SPRY1,downstream_gene_variant,,ENST00000508849,;SPRY1,downstream_gene_variant,,ENST00000515726,; A ENST00000610581 Transcript missense_variant 1076/2608 637/960 213/319 E/K Gag/Aag 1 1 SPRY1 HGNC HGNC:11269 protein_coding YES CCDS3731.1 ENSP00000481675 O43609 UPI0000035D8F NM_001258038.1 deleterious(0.01) 3/3 Pfam_domain:PF05210,PROSITE_profiles:PS51227,hmmpanther:PTHR12365,hmmpanther:PTHR12365:SF10 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 123402228 123402228 G A 1 0 0 0 0 1 0 0 0 15461 1291 45 3 3 SPRY1 4 123402228 Missense_Mutation SNP G C3N-00294_T 1065973 123402228 66812327 389 13161 FAT4 0 . GRCh38 4 125416489 125416489 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.6885C>G p.= p.L2295L ENST00000394329 6/17 106 79 27 122 122 0 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,synonymous_variant,p.=,ENST00000335110,; G ENST00000394329 Transcript synonymous_variant 6898/16123 6885/14946 2295/4981 L ctC/ctG 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 6/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 125416489 125416489 C G 1 0 0 0 0 0 0 0 1 5552 900 32 4 4 FAT4 4 125416489 Silent SNP C C3N-00294_T 2014261 125416489 64798066 390 13162 USP38 0 . GRCh38 4 143213588 143213588 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1612G>A p.Glu538Lys p.E538K ENST00000307017 9/10 57 47 10 62 62 0 strelka-varscan-mutect USP38,missense_variant,p.Glu538Lys,ENST00000307017,NM_001290326.1,NM_032557.6;USP38,missense_variant,p.Glu538Lys,ENST00000510377,NM_001290325.1;USP38,3_prime_UTR_variant,,ENST00000511739,; A ENST00000307017 Transcript missense_variant 2118/7009 1612/3129 538/1042 E/K Gaa/Aaa 1 1 USP38 HGNC HGNC:20067 protein_coding YES CCDS3758.1 ENSP00000303434 Q8NB14 UPI0000047AF9 NM_001290326.1,NM_032557.6 deleterious(0) 9/10 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF500,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99982 1 1 1 1 0 A 3 1 46 143213588 143213588 G A 1 0 0 0 0 1 0 0 0 17611 1291 45 3 3 USP38 4 143213588 Missense_Mutation SNP G C3N-00294_T 17797099 143213588 47000967 391 13163 FREM3 0 . GRCh38 4 143611511 143611511 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.5796G>A p.= p.T1932T ENST00000329798 6/8 158 131 27 163 163 0 strelka-varscan-mutect FREM3,synonymous_variant,p.=,ENST00000329798,NM_001168235.1;FREM3,non_coding_transcript_exon_variant,,ENST00000508899,;GUSBP5,intron_variant,,ENST00000511042,; T ENST00000329798 Transcript synonymous_variant 5796/6729 5796/6420 1932/2139 T acG/acA COSM3126304 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 6/8 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31,SMART_domains:SM00237,Superfamily_domains:SSF141072 1 LOW 1 SNV 5 1 1 PASS rs1319410474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 143611511 143611511 C T 1 0 0 0 0 0 0 0 1 5913 871 31 1 1 FREM3 4 143611511 Silent SNP C C3N-00294_T 397923 143611511 46603044 392 13164 FREM3 0 . GRCh38 4 143695605 143695605 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.5071G>A p.Glu1691Lys p.E1691K ENST00000329798 1/8 281 243 38 318 318 0 strelka-varscan-mutect FREM3,missense_variant,p.Glu1691Lys,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; T ENST00000329798 Transcript missense_variant 5071/6729 5071/6420 1691/2139 E/K Gaa/Aaa 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 deleterious(0.05) 1/8 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 143695605 143695605 C T 1 0 0 0 0 1 0 0 0 5913 922 32 3 3 FREM3 4 143695605 Missense_Mutation SNP C C3N-00294_T 84094 143695605 46518950 393 13165 ZNF827 0 . GRCh38 4 145775813 145775813 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.2669G>A p.Gly890Glu p.G890E ENST00000508784 10/15 206 158 48 196 196 0 strelka-varscan-mutect ZNF827,missense_variant,p.Gly890Glu,ENST00000508784,NM_001306215.1;ZNF827,missense_variant,p.Gly890Glu,ENST00000379448,NM_178835.3;ZNF827,missense_variant,p.Gly540Glu,ENST00000513320,;ZNF827,upstream_gene_variant,,ENST00000511659,;C4orf51,downstream_gene_variant,,ENST00000510096,;ZNF827,upstream_gene_variant,,ENST00000515386,; T ENST00000508784 Transcript missense_variant 2897/7463 2669/3246 890/1081 G/E gGg/gAg COSM222949,COSM222950 1 -1 ZNF827 HGNC HGNC:27193 protein_coding YES CCDS77968.1 ENSP00000421863 Q17R98 UPI0000DA58F8 NM_001306215.1 tolerated(0.94) 10/15 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF4 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 145775813 145775813 C T 1 0 0 0 0 1 0 0 0 18766 623 22 3 3 ZNF827 4 145775813 Missense_Mutation SNP C C3N-00294_T 2080208 145775813 44438742 394 13166 TRIM2 0 . GRCh38 4 153294416 153294416 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.717G>A p.= p.Q239Q ENST00000338700 5/12 222 175 47 229 229 0 strelka-varscan-mutect TRIM2,synonymous_variant,p.=,ENST00000338700,NM_015271.4;TRIM2,synonymous_variant,p.=,ENST00000437508,NM_001130067.1;TRIM2,synonymous_variant,p.=,ENST00000494872,;TRIM2,downstream_gene_variant,,ENST00000433687,;TRIM2,downstream_gene_variant,,ENST00000441616,;TRIM2,intron_variant,,ENST00000479711,; A ENST00000338700 Transcript synonymous_variant 782/6735 717/2316 239/771 Q caG/caA COSM1052193,COSM1594344 1 1 TRIM2 HGNC HGNC:15974 protein_coding YES CCDS3781.2 ENSP00000339659 Q9C040 UPI00005A60C0 NM_015271.4 5/12 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF2,SMART_domains:SM00502 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 153294416 153294416 G A 1 0 0 0 0 0 0 0 1 16983 933 33 3 3 TRIM2 4 153294416 Silent SNP G C3N-00294_T 7518603 153294416 36920139 395 13167 GPM6A 0 . GRCh38 4 175673770 175673770 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.297G>A p.= p.L99L ENST00000280187 4/8 152 126 26 164 164 0 strelka-varscan-mutect GPM6A,synonymous_variant,p.=,ENST00000280187,NM_005277.4;GPM6A,synonymous_variant,p.=,ENST00000393658,NM_201591.2;GPM6A,synonymous_variant,p.=,ENST00000506894,NM_201592.2;GPM6A,synonymous_variant,p.=,ENST00000515090,NM_001261448.1;GPM6A,synonymous_variant,p.=,ENST00000503397,;GPM6A,synonymous_variant,p.=,ENST00000513365,;GPM6A,synonymous_variant,p.=,ENST00000505561,;GPM6A,synonymous_variant,p.=,ENST00000502754,;GPM6A,synonymous_variant,p.=,ENST00000512897,;GPM6A,synonymous_variant,p.=,ENST00000512610,;GPM6A,synonymous_variant,p.=,ENST00000513667,;GPM6A,synonymous_variant,p.=,ENST00000507540,;GPM6A,synonymous_variant,p.=,ENST00000507520,;GPM6A,synonymous_variant,p.=,ENST00000512509,;GPM6A,synonymous_variant,p.=,ENST00000505375,;GPM6A,synonymous_variant,p.=,ENST00000509865,; T ENST00000280187 Transcript synonymous_variant 343/2854 297/837 99/278 L ctG/ctA 1 -1 GPM6A HGNC HGNC:4460 protein_coding YES CCDS3824.1 ENSP00000280187 P51674 UPI000012EAE1 NM_005277.4 4/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF4,Pfam_domain:PF01275,Prints_domain:PR00214 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 175673770 175673770 C T 1 0 0 0 0 0 0 0 1 6517 813 29 3 3 GPM6A 4 175673770 Silent SNP C C3N-00294_T 22379354 175673770 14540785 396 13168 VEGFC 0 . GRCh38 4 176729581 176729581 + Missense_Mutation SNP C C T rs373436555 C3N-00294_T C3N-00294_N C C c.313G>A p.Glu105Lys p.E105K ENST00000618562 2/7 180 141 39 237 237 0 strelka-varscan-mutect VEGFC,missense_variant,p.Glu105Lys,ENST00000618562,NM_005429.4;VEGFC,non_coding_transcript_exon_variant,,ENST00000507638,; T ENST00000618562 Transcript missense_variant 729/2064 313/1260 105/419 E/K Gag/Aag rs373436555 1 -1 VEGFC HGNC HGNC:12682 protein_coding YES CCDS43285.1 ENSP00000480043 P49767 UPI0000001C2A NM_005429.4 tolerated(0.13) 2/7 hmmpanther:PTHR12025:SF3,hmmpanther:PTHR12025 MODERATE 1 SNV 1 1 PASS rs373436555 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 176729581 176729581 C T 1 0 0 0 0 1 0 0 0 17697 922 32 3 3 VEGFC 4 176729581 Missense_Mutation SNP C C3N-00294_T 1055811 176729581 13484974 397 13169 PLEKHG4B 0 . GRCh38 5 163261 163261 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.2121C>A p.= p.P707P ENST00000283426 11/18 117 108 9 98 98 0 strelka-varscan-mutect PLEKHG4B,synonymous_variant,p.=,ENST00000637938,;PLEKHG4B,synonymous_variant,p.=,ENST00000283426,NM_052909.3; A ENST00000283426 Transcript synonymous_variant 2171/11515 2121/3816 707/1271 P ccC/ccA 1 1 PLEKHG4B HGNC HGNC:29399 protein_coding YES CCDS34124.1 ENSP00000283426 Q96PX9 UPI0000D615EE NM_052909.3 11/18 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF119 LOW 1 SNV 1 1 PASS rs1445657090 . 0 206 4 0 0 0 0 0 -17.77142 1 1 1 1 0 A 2 1 46 163261 163261 C A 1 0 0 0 0 0 0 0 1 12165 581 21 2 2 PLEKHG4B 5 163261 Silent SNP C C3N-00294_T 163261 181374998 398 13170 SLC9A3 0 . GRCh38 5 524247 524247 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.76G>A p.Gly26Arg p.G26R ENST00000264938 1/17 250 200 50 161 161 0 strelka-varscan-mutect SLC9A3,missense_variant,p.Gly26Arg,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.Gly26Arg,ENST00000514375,NM_001284351.1;RP11-310P5.2,upstream_gene_variant,,ENST00000515085,; T ENST00000264938 Transcript missense_variant 86/2584 76/2505 26/834 G/R Ggg/Agg 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 tolerated(0.47) 1/17 Low_complexity_(Seg):seg,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 46 524247 524247 C T 1 0 0 0 0 1 0 0 0 14995 652 23 1 1 SLC9A3 5 524247 Missense_Mutation SNP C C3N-00294_T 360986 524247 181014012 399 13171 SLC6A3 0 . GRCh38 5 1441417 1441417 + Silent SNP G G A rs148447720 C3N-00294_T C3N-00294_N G G c.360C>T p.= p.L120L ENST00000270349 3/15 344 293 51 239 239 0 strelka-varscan-mutect SLC6A3,synonymous_variant,p.=,ENST00000270349,NM_001044.4; A ENST00000270349 Transcript synonymous_variant 488/3936 360/1863 120/620 L ctC/ctT rs148447720,COSM351164 1 -1 SLC6A3 HGNC HGNC:11049 protein_coding YES CCDS3863.1 ENSP00000270349 Q01959 UPI000013548F NM_001044.4 3/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF38,Pfam_domain:PF00209,Superfamily_domains:0053687 0,1 LOW 1 SNV 1 0,1 1 PASS rs148447720 . 0 207 0 3 0 0 0 0 -20 0.9999935 1 1 1 0 A 2 1 46 1441417 1441417 G A 1 0 0 0 0 0 0 0 1 14968 1045 37 1 1 SLC6A3 5 1441417 Silent SNP G C3N-00294_T 917170 1441417 180096842 400 13172 NDUFS6 0 . GRCh38 5 1801501 1801501 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.84C>T p.= p.F28F ENST00000274137 1/4 280 241 39 200 200 0 strelka-varscan-mutect NDUFS6,synonymous_variant,p.=,ENST00000274137,NM_004553.4;NDUFS6,synonymous_variant,p.=,ENST00000469176,;MRPL36,upstream_gene_variant,,ENST00000510999,;MRPL36,upstream_gene_variant,,ENST00000508987,;MRPL36,upstream_gene_variant,,ENST00000505059,NM_032479.3;MRPL36,upstream_gene_variant,,ENST00000505818,;MRPL36,upstream_gene_variant,,ENST00000382647,;NDUFS6,non_coding_transcript_exon_variant,,ENST00000510329,; T ENST00000274137 Transcript synonymous_variant 102/1082 84/375 28/124 F ttC/ttT 1 1 NDUFS6 HGNC HGNC:7713 protein_coding YES CCDS3866.1 ENSP00000274137 O75380 Q6IBC4 UPI000000DB49 NM_004553.4 1/4 hmmpanther:PTHR13156,PIRSF_domain:PIRSF016564 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 1801501 1801501 C T 1 0 0 0 0 0 0 0 1 10320 883 31 1 1 NDUFS6 5 1801501 Silent SNP C C3N-00294_T 360084 1801501 179736758 401 13173 ICE1 0 . GRCh38 5 5457577 5457577 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.937G>A p.Asp313Asn p.D313N ENST00000296564 12/19 189 174 15 182 182 0 strelka-varscan-mutect ICE1,missense_variant,p.Asp313Asn,ENST00000296564,NM_015325.2;ICE1,downstream_gene_variant,,ENST00000512608,; A ENST00000296564 Transcript missense_variant 1159/7927 937/6801 313/2266 D/N Gac/Aac 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 tolerated(0.08) 12/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 5457577 5457577 G A 1 0 0 0 0 1 0 0 0 7384 1290 45 3 3 ICE1 5 5457577 Missense_Mutation SNP G C3N-00294_T 3656076 5457577 176080682 402 13174 ANKRD33B 0 . GRCh38 5 10638116 10638116 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.585G>A p.Met195Ile p.M195I ENST00000296657 3/4 313 269 44 211 209 2 strelka-varscan-mutect ANKRD33B,missense_variant,p.Met195Ile,ENST00000296657,NM_001164440.1;ANKRD33B,3_prime_UTR_variant,,ENST00000504806,; A ENST00000296657 Transcript missense_variant 585/9188 585/1485 195/494 M/I atG/atA 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 tolerated(0.09) 3/4 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 10638116 10638116 G A 1 0 0 0 0 1 0 0 0 766 1290 45 3 3 ANKRD33B 5 10638116 Missense_Mutation SNP G C3N-00294_T 5180539 10638116 170900143 403 13175 CTNND2 0 . GRCh38 5 10992673 10992673 + Missense_Mutation SNP C C T rs768816374 C3N-00294_T C3N-00294_N C C c.3089G>A p.Gly1030Glu p.G1030E ENST00000304623 19/22 264 183 81 196 196 0 strelka-varscan-mutect CTNND2,missense_variant,p.Gly1030Glu,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Gly939Glu,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Gly693Glu,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Gly125Glu,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506324,;CTNND2,missense_variant,p.Gly809Glu,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 3279/5481 3089/3678 1030/1225 G/E gGa/gAa rs768816374 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0) 19/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS rs768816374 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 10992673 10992673 C T 1 0 0 0 0 1 0 0 0 3829 869 30 3 3 CTNND2 5 10992673 Missense_Mutation SNP C C3N-00294_T 354557 10992673 170545586 404 13176 CTNND2 0 . GRCh38 5 11564987 11564987 + Nonsense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.244C>T p.Arg82Ter p.R82* ENST00000304623 3/22 247 215 32 166 166 0 strelka-varscan-mutect CTNND2,stop_gained,p.Arg82Ter,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,stop_gained,p.Arg68Ter,ENST00000508761,;CTNND2,stop_gained,p.Arg68Ter,ENST00000502551,;CTNND2,5_prime_UTR_variant,,ENST00000511377,NM_001288715.1;CTNND2,5_prime_UTR_variant,,ENST00000503622,NM_001288716.1;CTNND2,5_prime_UTR_variant,,ENST00000513598,;CTNND2,non_coding_transcript_exon_variant,,ENST00000504354,;CTNND2,non_coding_transcript_exon_variant,,ENST00000511278,;CTNND2,non_coding_transcript_exon_variant,,ENST00000509868,;CTNND2,stop_gained,p.Arg82Ter,ENST00000513588,;CTNND2,stop_gained,p.Arg82Ter,ENST00000504499,; A ENST00000304623 Transcript stop_gained 434/5481 244/3678 82/1225 R/* Cga/Tga COSM1202611 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 3/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 1 HIGH 1 SNV 1 1 1 PASS rs1285911975 . 0 204 3 0 2 0 0 0 -13.91624 0.9902414 1 1 1 0 A 4 1 46 11564987 11564987 G A 1 0 0 0 0 0 1 0 0 3829 1095 38 1 1 CTNND2 5 11564987 Nonsense_Mutation SNP G C3N-00294_T 572314 11564987 169973272 405 13177 PRDM9 0 . GRCh38 5 23527342 23527342 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2254G>A p.Glu752Lys p.E752K ENST00000296682 11/11 527 462 65 542 542 0 varscan-mutect PRDM9,missense_variant,p.Glu752Lys,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; A ENST00000296682 Transcript missense_variant 2436/3691 2254/2685 752/894 E/K Gag/Aag 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 tolerated(0.09) 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR16515:SF10,hmmpanther:PTHR16515,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1295196952 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 23527342 23527342 G A 1 0 0 0 0 1 0 0 0 12595 1175 41 3 3 PRDM9 5 23527342 Missense_Mutation SNP G C3N-00294_T 11962355 23527342 158010917 406 13178 DROSHA 0 . GRCh38 5 31409091 31409091 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.3819G>C p.Arg1273Ser p.R1273S ENST00000511367 32/35 241 211 30 167 167 0 strelka-varscan-mutect DROSHA,missense_variant,p.Arg1273Ser,ENST00000511367,NM_013235.4;DROSHA,missense_variant,p.Arg1273Ser,ENST00000344624,;DROSHA,missense_variant,p.Arg1236Ser,ENST00000442743,;DROSHA,missense_variant,p.Arg1236Ser,ENST00000513349,NM_001100412.1;DROSHA,non_coding_transcript_exon_variant,,ENST00000511778,;DROSHA,non_coding_transcript_exon_variant,,ENST00000509067,;DROSHA,upstream_gene_variant,,ENST00000514927,;DROSHA,upstream_gene_variant,,ENST00000512166,; G ENST00000511367 Transcript missense_variant 4064/5305 3819/4125 1273/1374 R/S agG/agC COSM1264327 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 deleterious(0) 32/35 Gene3D:3.30.160.20,HAMAP:MF_00104,Pfam_domain:PF00035,PROSITE_profiles:PS50137,hmmpanther:PTHR11207,SMART_domains:SM00358,Superfamily_domains:SSF54768 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 31409091 31409091 C G 1 0 0 0 0 1 0 0 0 4584 854 30 4 4 DROSHA 5 31409091 Missense_Mutation SNP C C3N-00294_T 7881749 31409091 150129168 407 13179 TARS 0 . GRCh38 5 33455029 33455029 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.637G>A p.Glu213Lys p.E213K ENST00000455217 6/20 296 258 38 228 228 0 strelka-varscan-mutect TARS,missense_variant,p.Glu180Lys,ENST00000265112,NM_152295.4;TARS,missense_variant,p.Glu180Lys,ENST00000502553,NM_001258437.1;TARS,missense_variant,p.Glu213Lys,ENST00000455217,NM_001258438.1;TARS,downstream_gene_variant,,ENST00000514259,;TARS,downstream_gene_variant,,ENST00000627006,;TARS,missense_variant,p.Arg126Lys,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,downstream_gene_variant,,ENST00000513066,;TARS,upstream_gene_variant,,ENST00000504698,;TARS,downstream_gene_variant,,ENST00000505012,; A ENST00000455217 Transcript missense_variant 759/2523 637/2271 213/756 E/K Gaa/Aaa 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 deleterious(0.03) 6/20 HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF36,TIGRFAM_domain:TIGR00418,Gene3D:1tkeA02,Superfamily_domains:SSF55186 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33455029 33455029 G A 1 0 0 0 0 1 0 0 0 15958 943 33 3 3 TARS 5 33455029 Missense_Mutation SNP G C3N-00294_T 2045938 33455029 148083230 408 13180 ADAMTS12 0 . GRCh38 5 33534852 33534852 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.4587G>T p.Gln1529His p.Q1529H ENST00000504830 23/24 146 99 47 99 98 1 strelka-varscan-mutect ADAMTS12,missense_variant,p.Gln1529His,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Gln1444His,ENST00000352040,; A ENST00000504830 Transcript missense_variant 4923/8774 4587/4785 1529/1594 Q/H caG/caT COSM1567714 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 23/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33534852 33534852 C A 1 0 0 0 0 1 0 0 0 301 680 24 2 2 ADAMTS12 5 33534852 Missense_Mutation SNP C C3N-00294_T 79823 33534852 148003407 409 13181 RXFP3 0 . GRCh38 5 33937750 33937750 + Missense_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.1010T>A p.Leu337Gln p.L337Q ENST00000330120 1/1 443 311 132 355 355 0 strelka-varscan-mutect RXFP3,missense_variant,p.Leu337Gln,ENST00000330120,NM_016568.3; A ENST00000330120 Transcript missense_variant 1365/1852 1010/1410 337/469 L/Q cTg/cAg 1 1 RXFP3 HGNC HGNC:24883 protein_coding YES CCDS3900.1 ENSP00000328708 Q9NSD7 UPI0000046AEB NM_016568.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF70,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33937750 33937750 T A 1 0 0 0 0 1 0 0 0 14022 1580 55 4 4 RXFP3 5 33937750 Missense_Mutation SNP T C3N-00294_T 402898 33937750 147600509 410 13182 LMBRD2 0 . GRCh38 5 36122448 36122448 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.952C>T p.Gln318Ter p.Q318* ENST00000296603 9/18 281 246 35 225 225 0 strelka-varscan-mutect LMBRD2,stop_gained,p.Gln318Ter,ENST00000296603,NM_001007527.1; A ENST00000296603 Transcript stop_gained 1415/8185 952/2088 318/695 Q/* Cag/Tag 1 -1 LMBRD2 HGNC HGNC:25287 protein_coding YES CCDS34145.1 ENSP00000296603 Q68DH5 UPI00001602FC NM_001007527.1 9/18 Pfam_domain:PF04791,hmmpanther:PTHR21355,hmmpanther:PTHR21355:SF4 HIGH 1 SNV 1 1 PASS rs1252172317 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 36122448 36122448 G A 1 0 0 0 0 0 1 0 0 8767 1299 45 3 3 LMBRD2 5 36122448 Nonsense_Mutation SNP G C3N-00294_T 2184698 36122448 145415811 411 13183 NADK2 0 . GRCh38 5 36217817 36217817 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.712C>T p.Leu238Phe p.L238F ENST00000381937 6/12 426 386 40 366 365 1 strelka-varscan-mutect NADK2,missense_variant,p.Leu75Phe,ENST00000397338,NM_001287340.1;NADK2,missense_variant,p.Leu75Phe,ENST00000282512,NM_153013.4;NADK2,missense_variant,p.Leu238Phe,ENST00000381937,NM_001085411.2;NADK2,missense_variant,p.Leu75Phe,ENST00000506945,NM_001287341.1;NADK2,missense_variant,p.Leu238Phe,ENST00000514504,;NADK2,missense_variant,p.Leu75Phe,ENST00000617628,;NADK2,missense_variant,p.Leu75Phe,ENST00000511088,;NADK2-AS1,upstream_gene_variant,,ENST00000501794,;NADK2,upstream_gene_variant,,ENST00000511613,;NADK2,upstream_gene_variant,,ENST00000509225,;NADK2,non_coding_transcript_exon_variant,,ENST00000404560,; A ENST00000381937 Transcript missense_variant 712/2243 712/1329 238/442 L/F Ctt/Ttt 1 -1 NADK2 HGNC HGNC:26404 protein_coding YES CCDS47197.1 ENSP00000371362 Q4G0N4 UPI000150640C NM_001085411.2 deleterious(0) 6/12 hmmpanther:PTHR13158,PIRSF_domain:PIRSF017565,Pfam_domain:PF01513 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 36217817 36217817 G A 1 0 0 0 0 1 0 0 0 10144 1000 35 3 3 NADK2 5 36217817 Missense_Mutation SNP G C3N-00294_T 95369 36217817 145320442 412 13184 NIPBL 0 . GRCh38 5 36976339 36976339 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1432G>C p.Glu478Gln p.E478Q ENST00000282516 9/47 110 94 16 119 119 0 strelka-varscan-mutect NIPBL,missense_variant,p.Glu478Gln,ENST00000282516,NM_133433.3;NIPBL,missense_variant,p.Glu478Gln,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,;NIPBL,non_coding_transcript_exon_variant,,ENST00000504430,;NIPBL,downstream_gene_variant,,ENST00000505998,; C ENST00000282516 Transcript missense_variant 1931/10435 1432/8415 478/2804 E/Q Gag/Cag 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 deleterious_low_confidence(0) 9/47 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 36976339 36976339 G C 1 0 0 0 0 1 0 0 0 10463 1291 45 4 4 NIPBL 5 36976339 Missense_Mutation SNP G C3N-00294_T 758522 36976339 144561920 413 13185 C5orf42 0 . GRCh38 5 37108339 37108339 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.9371C>T p.Ser3124Leu p.S3124L ENST00000425232 51/52 319 294 25 218 218 0 strelka-varscan-mutect C5orf42,missense_variant,p.Ser3124Leu,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Ser3124Leu,ENST00000508244,;C5orf42,missense_variant,p.Ser2190Leu,ENST00000514429,;C5orf42,3_prime_UTR_variant,,ENST00000509849,; A ENST00000425232 Transcript missense_variant 9602/11199 9371/9594 3124/3197 S/L tCa/tTa 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0.03) 51/52 Pfam_domain:PF15392,hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 37108339 37108339 G A 1 0 0 0 0 1 0 0 0 2100 1294 45 3 3 C5orf42 5 37108339 Missense_Mutation SNP G C3N-00294_T 132000 37108339 144429920 414 13186 LIFR 0 . GRCh38 5 38504014 38504014 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1399G>A p.Glu467Lys p.E467K ENST00000263409 10/20 118 105 13 119 119 0 strelka-varscan-mutect LIFR,missense_variant,p.Glu467Lys,ENST00000263409,NM_002310.5;LIFR,missense_variant,p.Glu467Lys,ENST00000453190,NM_001127671.1;LIFR,non_coding_transcript_exon_variant,,ENST00000503088,;LIFR,upstream_gene_variant,,ENST00000506003,; T ENST00000263409 Transcript missense_variant 1562/10089 1399/3294 467/1097 E/K Gaa/Aaa 1 -1 LIFR HGNC HGNC:6597 protein_coding YES CCDS3927.1 ENSP00000263409 P42702 UPI000004CAC2 NM_002310.5 deleterious(0.04) 10/20 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF105,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 38504014 38504014 C T 1 0 0 0 0 1 0 0 0 8689 835 29 3 3 LIFR 5 38504014 Missense_Mutation SNP C C3N-00294_T 1395675 38504014 143034245 415 13187 RICTOR 0 . GRCh38 5 38955674 38955674 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2530G>A p.Glu844Lys p.E844K ENST00000296782 26/39 156 135 21 150 150 0 strelka-varscan-mutect RICTOR,missense_variant,p.Glu844Lys,ENST00000357387,NM_152756.4,NM_001285440.1;RICTOR,missense_variant,p.Glu844Lys,ENST00000296782,NM_001285439.1;RICTOR,non_coding_transcript_exon_variant,,ENST00000503698,;RICTOR,3_prime_UTR_variant,,ENST00000511516,; T ENST00000296782 Transcript missense_variant 2552/7505 2530/5199 844/1732 E/K Gag/Aag 1 -1 RICTOR HGNC HGNC:28611 protein_coding YES CCDS68861.1 ENSP00000296782 Q6R327 UPI0000EE67F5 NM_001285439.1 deleterious(0) 26/39 hmmpanther:PTHR13298:SF11,hmmpanther:PTHR13298,Gene3D:1.25.10.10,Pfam_domain:PF14663,SMART_domains:SM01303 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999921 1 1 1 0 T 3 4 46 38955674 38955674 C T 1 0 0 0 0 1 0 0 0 13531 835 29 3 3 RICTOR 5 38955674 Missense_Mutation SNP C C3N-00294_T 451660 38955674 142582585 416 13188 C6 0 . GRCh38 5 41186168 41186168 + Missense_Mutation SNP C C G rs779633819 C3N-00294_T C3N-00294_N C C c.628G>C p.Asp210His p.D210H ENST00000263413 6/18 555 477 78 448 448 0 strelka-varscan-mutect C6,missense_variant,p.Asp210His,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Asp210His,ENST00000337836,NM_000065.3;C6,intron_variant,,ENST00000475349,; G ENST00000263413 Transcript missense_variant 893/3661 628/2805 210/934 D/H Gat/Cat rs779633819 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 deleterious(0.01) 6/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23 MODERATE 1 SNV 1 1 PASS rs779633819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 41186168 41186168 C G 1 0 0 0 0 1 0 0 0 2111 826 29 4 4 C6 5 41186168 Missense_Mutation SNP C C3N-00294_T 2230494 41186168 140352091 417 13189 ZNF131 0 . GRCh38 5 43174942 43174942 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1681G>C p.Glu561Gln p.E561Q ENST00000509156 7/7 267 230 37 204 204 0 strelka-varscan-mutect ZNF131,missense_variant,p.Glu527Gln,ENST00000509634,;ZNF131,missense_variant,p.Glu527Gln,ENST00000505606,;ZNF131,missense_variant,p.Glu527Gln,ENST00000306938,NM_003432.2;ZNF131,missense_variant,p.Glu561Gln,ENST00000509156,NM_001297548.1;ZNF131,intron_variant,,ENST00000509931,;ZNF131,3_prime_UTR_variant,,ENST00000510026,;ZNF131,intron_variant,,ENST00000511736,;ZNF131,intron_variant,,ENST00000502623,;ZNF131,downstream_gene_variant,,ENST00000507218,;ZNF131,downstream_gene_variant,,ENST00000507231,; C ENST00000509156 Transcript missense_variant 1717/2063 1681/1872 561/623 E/Q Gaa/Caa 1 1 ZNF131 HGNC HGNC:12915 protein_coding YES CCDS78005.1 ENSP00000426504 P52739 UPI000013EBAE NM_001297548.1 tolerated_low_confidence(0.1) 7/7 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF26 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 43174942 43174942 G C 1 0 0 0 0 1 0 0 0 18302 943 33 4 4 ZNF131 5 43174942 Missense_Mutation SNP G C3N-00294_T 1988774 43174942 138363317 418 13190 MRPS30 0 . GRCh38 5 44809151 44809151 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.189C>T p.= p.I63I ENST00000507110 1/5 309 248 61 301 301 0 strelka-varscan-mutect MRPS30,synonymous_variant,p.=,ENST00000507110,NM_016640.3;RP11-53O19.1,upstream_gene_variant,,ENST00000503179,;RP11-53O19.1,upstream_gene_variant,,ENST00000503452,;RP11-53O19.1,upstream_gene_variant,,ENST00000505401,;RP11-53O19.1,upstream_gene_variant,,ENST00000514597,;RP11-53O19.1,upstream_gene_variant,,ENST00000508123,;RP11-53O19.1,upstream_gene_variant,,ENST00000505302,;RP11-53O19.1,upstream_gene_variant,,ENST00000508945,;RP11-53O19.1,upstream_gene_variant,,ENST00000505637,;MRPS30,upstream_gene_variant,,ENST00000515647,;MRPS30,upstream_gene_variant,,ENST00000508129,; T ENST00000507110 Transcript synonymous_variant 227/1678 189/1320 63/439 I atC/atT 1 1 MRPS30 HGNC HGNC:8769 protein_coding YES CCDS3951.1 ENSP00000424328 Q9NP92 UPI000013C944 NM_016640.3 1/5 hmmpanther:PTHR13014,Pfam_domain:PF07147 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 44809151 44809151 C T 1 0 0 0 0 0 0 0 1 9817 874 31 1 1 MRPS30 5 44809151 Silent SNP C C3N-00294_T 1634209 44809151 136729108 419 13191 HCN1 0 . GRCh38 5 45262634 45262634 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.1960A>G p.Thr654Ala p.T654A ENST00000303230 8/8 628 411 217 547 547 0 strelka-varscan-mutect HCN1,missense_variant,p.Thr654Ala,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; C ENST00000303230 Transcript missense_variant 2201/9885 1960/2673 654/890 T/A Acg/Gcg 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated(0.54) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 45262634 45262634 T C 1 0 0 0 0 1 0 0 0 6883 1638 57 5 5 HCN1 5 45262634 Missense_Mutation SNP T C3N-00294_T 453483 45262634 136275625 420 13192 MAP3K1 0 . GRCh38 5 56882831 56882831 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3631G>A p.Glu1211Lys p.E1211K ENST00000399503 14/20 84 75 9 86 86 0 strelka-varscan-mutect MAP3K1,missense_variant,p.Glu1211Lys,ENST00000399503,NM_005921.1;MAP3K1,upstream_gene_variant,,ENST00000469188,; A ENST00000399503 Transcript missense_variant 3631/7011 3631/4539 1211/1512 E/K Gaa/Aaa 1 1 MAP3K1 HGNC HGNC:6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 deleterious(0.04) 14/20 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF414 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -14.84342 0.9999961 1 1 1 0 A 3 1 46 56882831 56882831 G A 1 0 0 0 0 1 0 0 0 9165 1291 45 3 3 MAP3K1 5 56882831 Missense_Mutation SNP G C3N-00294_T 11620197 56882831 124655428 421 13193 MARVELD2 0 . GRCh38 5 69433076 69433076 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1486C>G p.His496Asp p.H496D ENST00000325631 5/7 403 364 39 352 352 0 strelka-varscan-mutect MARVELD2,missense_variant,p.His484Asp,ENST00000454295,NM_001244734.1;MARVELD2,missense_variant,p.His496Asp,ENST00000325631,NM_001038603.2;MARVELD2,missense_variant,p.His496Asp,ENST00000512803,;MARVELD2,missense_variant,p.His380Asp,ENST00000413223,;MARVELD2,missense_variant,p.His380Asp,ENST00000436532,; G ENST00000325631 Transcript missense_variant 1560/2153 1486/1677 496/558 H/D Cat/Gat 1 1 MARVELD2 HGNC HGNC:26401 protein_coding YES CCDS34175.1 ENSP00000323264 Q8N4S9 UPI00001416EB NM_001038603.2 tolerated(0.21) 5/7 hmmpanther:PTHR23288,hmmpanther:PTHR23288:SF3,Pfam_domain:PF07303,Superfamily_domains:0053542 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 69433076 69433076 C G 1 0 0 0 0 1 0 0 0 9244 826 29 4 4 MARVELD2 5 69433076 Missense_Mutation SNP C C3N-00294_T 12550245 69433076 112105183 422 13194 BDP1 0 . GRCh38 5 71509753 71509753 + Silent SNP G G A rs527435694 C3N-00294_T C3N-00294_N G G c.2661G>A p.= p.K887K ENST00000358731 17/39 147 128 19 183 183 0 strelka-varscan-mutect BDP1,synonymous_variant,p.=,ENST00000358731,NM_018429.2;BDP1,downstream_gene_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;BDP1,non_coding_transcript_exon_variant,,ENST00000508157,; A ENST00000358731 Transcript synonymous_variant 2924/11073 2661/7875 887/2624 K aaG/aaA rs527435694 1 1 BDP1 HGNC HGNC:13652 protein_coding YES CCDS43328.1 ENSP00000351575 A6H8Y1 UPI000020CA90 NM_018429.2 17/39 LOW 1 SNV 1 1 PASS rs527435694 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 71509753 71509753 G A 1 0 0 0 0 0 0 0 1 1542 933 33 3 3 BDP1 5 71509753 Silent SNP G C3N-00294_T 2076677 71509753 110028506 423 13195 BDP1 0 . GRCh38 5 71510144 71510144 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3052G>C p.Glu1018Gln p.E1018Q ENST00000358731 17/39 169 142 27 152 152 0 strelka-varscan-mutect BDP1,missense_variant,p.Glu1018Gln,ENST00000358731,NM_018429.2;BDP1,downstream_gene_variant,,ENST00000380675,;BDP1,non_coding_transcript_exon_variant,,ENST00000508917,;BDP1,non_coding_transcript_exon_variant,,ENST00000508157,; C ENST00000358731 Transcript missense_variant 3315/11073 3052/7875 1018/2624 E/Q Gag/Cag 1 1 BDP1 HGNC HGNC:13652 protein_coding YES CCDS43328.1 ENSP00000351575 A6H8Y1 UPI000020CA90 NM_018429.2 tolerated(0.07) 17/39 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 71510144 71510144 G C 1 0 0 0 0 1 0 0 0 1542 943 33 4 4 BDP1 5 71510144 Missense_Mutation SNP G C3N-00294_T 391 71510144 110028115 424 13196 SV2C 0 . GRCh38 5 76131961 76131961 + Missense_Mutation SNP G G A rs761310792 C3N-00294_T C3N-00294_N G G c.211G>A p.Asp71Asn p.D71N ENST00000502798 2/13 73 55 18 95 95 0 strelka-varscan-mutect SV2C,missense_variant,p.Asp71Asn,ENST00000502798,NM_014979.3;SV2C,missense_variant,p.Asp71Asn,ENST00000322285,NM_001297716.1; A ENST00000502798 Transcript missense_variant 653/11035 211/2184 71/727 D/N Gat/Aat rs761310792 1 1 SV2C HGNC HGNC:30670 protein_coding YES CCDS43331.1 ENSP00000423541 Q496J9 UPI000011DDBB NM_014979.3 tolerated(0.23) 2/13 hmmpanther:PTHR23511:SF6,hmmpanther:PTHR23511,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 1 1 PASS rs761310792 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 76131961 76131961 G A 1 0 0 0 0 1 0 0 0 15803 1058 37 1 1 SV2C 5 76131961 Missense_Mutation SNP G C3N-00294_T 4621817 76131961 105406298 425 13197 MTX3 0 . GRCh38 5 79988243 79988243 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.394G>C p.Asp132His p.D132H ENST00000512560 5/8 96 75 21 129 129 0 strelka-varscan-mutect MTX3,missense_variant,p.Asp132His,ENST00000512560,NM_001167741.1;MTX3,missense_variant,p.Asp193His,ENST00000509852,NM_001010891.4;MTX3,missense_variant,p.Asp193His,ENST00000512528,;MTX3,intron_variant,,ENST00000617335,;THBS4,upstream_gene_variant,,ENST00000513310,;THBS4,upstream_gene_variant,,ENST00000510218,; G ENST00000512560 Transcript missense_variant 514/4799 394/756 132/251 D/H Gat/Cat 1 -1 MTX3 HGNC HGNC:24812 protein_coding YES CCDS54872.1 ENSP00000423600 Q5HYI7 UPI0001BDAB0C NM_001167741.1 deleterious(0) 5/8 Gene3D:1.20.1050.10,Pfam_domain:PF17171,hmmpanther:PTHR12289,hmmpanther:PTHR12289:SF30,Superfamily_domains:SSF47616 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 79988243 79988243 C G 1 0 0 0 0 1 0 0 0 9967 927 32 4 4 MTX3 5 79988243 Missense_Mutation SNP C C3N-00294_T 3856282 79988243 101550016 426 13198 FAM81B 0 . GRCh38 5 95436850 95436850 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.837G>C p.= p.S279S ENST00000283357 7/10 245 201 44 315 315 0 strelka-varscan-mutect FAM81B,synonymous_variant,p.=,ENST00000283357,NM_152548.2;FAM81B,intron_variant,,ENST00000512365,;FAM81B,synonymous_variant,p.=,ENST00000513110,;FAM81B,3_prime_UTR_variant,,ENST00000507832,;FAM81B,3_prime_UTR_variant,,ENST00000503361,;FAM81B,downstream_gene_variant,,ENST00000513529,;CTD-2538A21.1,upstream_gene_variant,,ENST00000507713,; C ENST00000283357 Transcript synonymous_variant 883/1560 837/1359 279/452 S tcG/tcC 1 1 FAM81B HGNC HGNC:26335 protein_coding YES CCDS43341.1 ENSP00000283357 Q96LP2 UPI00005A8996 NM_152548.2 7/10 hmmpanther:PTHR22420,hmmpanther:PTHR22420:SF5 LOW 1 SNV 1 1 PASS rs996500686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 95436850 95436850 G C 1 0 0 0 0 0 0 0 1 5490 1045 37 4 4 FAM81B 5 95436850 Silent SNP G C3N-00294_T 15448607 95436850 86101409 427 13199 RHOBTB3 0 . GRCh38 5 95788840 95788840 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1702G>T p.Glu568Ter p.E568* ENST00000379982 11/12 143 87 56 202 202 0 strelka-varscan-mutect RHOBTB3,stop_gained,p.Glu568Ter,ENST00000379982,NM_014899.3;RHOBTB3,stop_gained,p.Glu150Ter,ENST00000510313,;RHOBTB3,stop_gained,p.Glu199Ter,ENST00000504179,;RHOBTB3,stop_gained,p.Glu71Ter,ENST00000503737,;RHOBTB3,stop_gained,p.Glu10Ter,ENST00000513091,;RHOBTB3,stop_gained,p.Glu8Ter,ENST00000514198,;GLRX,intron_variant,,ENST00000508780,;GLRX,intron_variant,,ENST00000507605,;RHOBTB3,non_coding_transcript_exon_variant,,ENST00000511558,;RHOBTB3,downstream_gene_variant,,ENST00000507186,; T ENST00000379982 Transcript stop_gained 2210/5537 1702/1836 568/611 E/* Gaa/Taa 1 1 RHOBTB3 HGNC HGNC:18757 protein_coding YES CCDS4077.1 ENSP00000369318 O94955 UPI0000367303 NM_014899.3 11/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 95788840 95788840 G T 1 0 0 0 0 0 1 0 0 13508 1291 45 2 2 RHOBTB3 5 95788840 Nonsense_Mutation SNP G C3N-00294_T 351990 95788840 85749419 428 13200 ERAP1 0 . GRCh38 5 96781736 96781736 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2404G>C p.Glu802Gln p.E802Q ENST00000296754 16/20 325 266 59 405 405 0 strelka-varscan-mutect ERAP1,missense_variant,p.Glu802Gln,ENST00000296754,NM_016442.3;ERAP1,missense_variant,p.Glu802Gln,ENST00000443439,NM_001198541.1,NM_001040458.1;ERAP1,upstream_gene_variant,,ENST00000512852,;CTD-2260A17.1,upstream_gene_variant,,ENST00000512856,;CTD-2260A17.1,upstream_gene_variant,,ENST00000602972,;ERAP1,non_coding_transcript_exon_variant,,ENST00000514604,;CAST,downstream_gene_variant,,ENST00000510098,;ERAP1,downstream_gene_variant,,ENST00000507859,; G ENST00000296754 Transcript missense_variant 2662/5495 2404/2847 802/948 E/Q Gaa/Caa 1 -1 ERAP1 HGNC HGNC:18173 protein_coding YES CCDS4085.1 ENSP00000296754 Q9NZ08 UPI000045731D NM_016442.3 tolerated(0.25) 16/20 hmmpanther:PTHR11533:SF156,hmmpanther:PTHR11533,Pfam_domain:PF11838 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 96781736 96781736 C G 1 0 0 0 0 1 0 0 0 5052 835 29 4 4 ERAP1 5 96781736 Missense_Mutation SNP C C3N-00294_T 992896 96781736 84756523 429 13201 CHD1 0 . GRCh38 5 98872469 98872469 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.3658G>C p.Glu1220Gln p.E1220Q ENST00000614616 27/36 184 109 75 238 238 0 strelka-varscan-mutect CHD1,missense_variant,p.Glu1220Gln,ENST00000614616,;CHD1,missense_variant,p.Glu1220Gln,ENST00000284049,NM_001270.2;CHD1,upstream_gene_variant,,ENST00000511067,;CHD1,non_coding_transcript_exon_variant,,ENST00000514344,;CHD1,upstream_gene_variant,,ENST00000512844,;CHD1,upstream_gene_variant,,ENST00000505657,;CHD1,upstream_gene_variant,,ENST00000508756,;CHD1,upstream_gene_variant,,ENST00000414220,; G ENST00000614616 Transcript missense_variant 4225/8095 3658/5133 1220/1710 E/Q Gaa/Caa COSM1071548 1 -1 CHD1 HGNC HGNC:1915 protein_coding YES CCDS34204.1 ENSP00000483667 O14646 UPI000013DD75 deleterious(0.01) 27/36 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 98872469 98872469 C G 1 0 0 0 0 1 0 0 0 3082 922 32 4 4 CHD1 5 98872469 Missense_Mutation SNP C C3N-00294_T 2090733 98872469 82665790 430 13202 KCNN2 0 . GRCh38 5 114363174 114363174 + Silent SNP G G T rs748037041 C3N-00294_T C3N-00294_N G G c.399G>T p.= p.R133R ENST00000512097 2/9 217 116 101 232 232 0 strelka-varscan-mutect KCNN2,synonymous_variant,p.=,ENST00000512097,;KCNN2,synonymous_variant,p.=,ENST00000264773,NM_021614.3;KCNN2,synonymous_variant,p.=,ENST00000631899,;KCNN2,5_prime_UTR_variant,,ENST00000610748,NM_001278204.1;KCNN2,non_coding_transcript_exon_variant,,ENST00000507750,; T ENST00000512097 Transcript synonymous_variant 1417/3076 399/1740 133/579 R cgG/cgT rs748037041 1 1 KCNN2 HGNC HGNC:6291 protein_coding YES CCDS4114.1 ENSP00000427120 Q9H2S1 UPI000013D56A 2/9 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF43,Pfam_domain:PF03530,Prints_domain:PR01451 LOW 1 SNV 5 1 PASS rs748037041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 114363174 114363174 G T 1 0 0 0 0 0 0 0 1 7995 1190 42 2 2 KCNN2 5 114363174 Silent SNP G C3N-00294_T 15490705 114363174 67175085 431 13203 DMXL1 0 . GRCh38 5 119121058 119121058 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1021C>T p.His341Tyr p.H341Y ENST00000539542 9/44 129 108 21 175 175 0 strelka-varscan-mutect DMXL1,missense_variant,p.His341Tyr,ENST00000539542,NM_001290321.2;DMXL1,missense_variant,p.His341Tyr,ENST00000311085,NM_001290322.2,NM_005509.5;DMXL1,missense_variant,p.His341Tyr,ENST00000503802,;DMXL1,non_coding_transcript_exon_variant,,ENST00000514151,; T ENST00000539542 Transcript missense_variant 1202/11236 1021/9147 341/3048 H/Y Cat/Tat 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 deleterious(0.05) 9/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 119121058 119121058 C T 1 0 0 0 0 1 0 0 0 4403 826 29 3 3 DMXL1 5 119121058 Missense_Mutation SNP C C3N-00294_T 4757884 119121058 62417201 432 13204 DMXL1 0 . GRCh38 5 119170786 119170786 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.5995G>A p.Asp1999Asn p.D1999N ENST00000539542 24/44 103 87 16 169 169 0 strelka-varscan-mutect DMXL1,missense_variant,p.Asp1999Asn,ENST00000539542,NM_001290321.2;DMXL1,missense_variant,p.Asp1999Asn,ENST00000311085,NM_001290322.2,NM_005509.5;DMXL1,non_coding_transcript_exon_variant,,ENST00000507552,;DMXL1,downstream_gene_variant,,ENST00000504497,; A ENST00000539542 Transcript missense_variant 6176/11236 5995/9147 1999/3048 D/N Gac/Aac COSM4678193,COSM4678194 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 tolerated(0.23) 24/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 119170786 119170786 G A 1 0 0 0 0 1 0 0 0 4403 1290 45 3 3 DMXL1 5 119170786 Missense_Mutation SNP G C3N-00294_T 49728 119170786 62367473 433 13205 FBN2 0 . GRCh38 5 128318203 128318203 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.4663G>A p.Glu1555Lys p.E1555K ENST00000508053 42/71 460 387 73 436 436 0 strelka-varscan-mutect FBN2,missense_variant,p.Glu1555Lys,ENST00000508053,;FBN2,missense_variant,p.Glu1555Lys,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Glu1554Lys,ENST00000619499,; T ENST00000508053 Transcript missense_variant 5638/11132 4663/8739 1555/2912 E/K Gag/Aag 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.19) 42/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 128318203 128318203 C T 1 0 0 0 0 1 0 0 0 5566 835 29 3 3 FBN2 5 128318203 Missense_Mutation SNP C C3N-00294_T 9147417 128318203 53220056 434 13206 FBN2 0 . GRCh38 5 128393212 128393212 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1388G>A p.Gly463Glu p.G463E ENST00000508053 16/71 379 343 36 396 396 0 strelka-varscan-mutect FBN2,missense_variant,p.Gly463Glu,ENST00000508053,;FBN2,missense_variant,p.Gly463Glu,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Gly462Glu,ENST00000619499,;FBN2,missense_variant,p.Gly430Glu,ENST00000508989,; T ENST00000508053 Transcript missense_variant 2363/11132 1388/8739 463/2912 G/E gGa/gAa 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.78) 16/71 PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 128393212 128393212 C T 1 0 0 0 0 1 0 0 0 5566 855 30 3 3 FBN2 5 128393212 Missense_Mutation SNP C C3N-00294_T 75009 128393212 53145047 435 13207 ADAMTS19 0 . GRCh38 5 129461151 129461151 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.123G>T p.= p.A41A ENST00000274487 2/23 60 56 4 78 78 0 strelka-mutect ADAMTS19,synonymous_variant,p.=,ENST00000274487,NM_133638.3;ADAMTS19-AS1,upstream_gene_variant,,ENST00000502827,;ADAMTS19,intron_variant,,ENST00000505791,;ADAMTS19,upstream_gene_variant,,ENST00000502709,; T ENST00000274487 Transcript synonymous_variant 268/5234 123/3624 41/1207 A gcG/gcT 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 2/23 LOW 1 SNV 1 1 PASS rs1210214890 . 0 206 4 0 0 0 0 0 -9.965967 1 1 1 1 0 T 2 4 46 129461151 129461151 G T 1 0 0 0 0 0 0 0 1 308 1074 38 1 1 ADAMTS19 5 129461151 Silent SNP G C3N-00294_T 1067939 129461151 52077108 436 13208 ADAMTS19 0 . GRCh38 5 129551886 129551886 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1333G>A p.Asp445Asn p.D445N ENST00000274487 7/23 56 50 6 120 120 0 strelka-varscan-mutect ADAMTS19,missense_variant,p.Asp445Asn,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,; A ENST00000274487 Transcript missense_variant 1478/5234 1333/3624 445/1207 D/N Gat/Aat 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 tolerated(0.42) 7/23 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs938750004 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 129551886 129551886 G A 1 0 0 0 0 1 0 0 0 308 942 33 3 3 ADAMTS19 5 129551886 Missense_Mutation SNP G C3N-00294_T 90735 129551886 51986373 437 13209 UQCRQ 0 . GRCh38 5 132867019 132867019 + Missense_Mutation SNP C C G rs14664 C3N-00294_T C3N-00294_N C C c.138C>G p.Phe46Leu p.F46L ENST00000378670 2/3 209 156 53 250 250 0 strelka-varscan-mutect UQCRQ,missense_variant,p.Phe46Leu,ENST00000378670,;UQCRQ,missense_variant,p.Phe46Leu,ENST00000378665,;UQCRQ,missense_variant,p.Phe46Leu,ENST00000378667,NM_014402.4;GDF9,upstream_gene_variant,,ENST00000378673,NM_005260.4;GDF9,upstream_gene_variant,,ENST00000621295,NM_001288825.2;GDF9,upstream_gene_variant,,ENST00000624492,NM_001288824.2;GDF9,upstream_gene_variant,,ENST00000624495,NM_001288828.2,NM_001288826.2;GDF9,upstream_gene_variant,,ENST00000296875,NM_001288827.2;UQCRQ,intron_variant,,ENST00000496429,;GDF9,upstream_gene_variant,,ENST00000464378,;GDF9,upstream_gene_variant,,ENST00000472320,;UQCRQ,non_coding_transcript_exon_variant,,ENST00000498309,;UQCRQ,non_coding_transcript_exon_variant,,ENST00000480372,; G ENST00000378670 Transcript missense_variant 279/839 138/249 46/82 F/L ttC/ttG rs14664,COSM5541415 1 1 UQCRQ HGNC HGNC:29594 protein_coding YES CCDS34237.1 ENSP00000367939 O14949 UPI000015D476 tolerated(0.08) 2/3 hmmpanther:PTHR12119,hmmpanther:PTHR12119:SF3,Pfam_domain:PF02939,Gene3D:1.20.5.210,Superfamily_domains:SSF81508,PD331499 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs14664 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 132867019 132867019 C G 1 0 0 0 0 1 0 0 0 17552 912 32 4 4 UQCRQ 5 132867019 Missense_Mutation SNP C C3N-00294_T 3315133 132867019 48671240 438 13210 JADE2 0 . GRCh38 5 134535864 134535864 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.7G>C p.Glu3Gln p.E3Q ENST00000282605 2/12 132 100 32 139 139 0 strelka-varscan-mutect JADE2,missense_variant,p.Glu3Gln,ENST00000395003,NM_015288.5;JADE2,missense_variant,p.Glu3Gln,ENST00000361895,NM_001289984.1;JADE2,missense_variant,p.Glu3Gln,ENST00000402835,;JADE2,missense_variant,p.Glu3Gln,ENST00000282605,NM_001308143.1,NM_001289985.1;JADE2,missense_variant,p.Glu3Gln,ENST00000431355,;JADE2,missense_variant,p.Glu3Gln,ENST00000512386,;JADE2,non_coding_transcript_exon_variant,,ENST00000515554,; C ENST00000282605 Transcript missense_variant 93/2748 7/2505 3/834 E/Q Gag/Cag COSM5615446,COSM5615447 1 1 JADE2 HGNC HGNC:22984 protein_coding YES CCDS78061.1 ENSP00000282605 G3XAA4 UPI00000437CA NM_001308143.1,NM_001289985.1 deleterious_low_confidence(0.03) 2/12 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF84 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1203374875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 134535864 134535864 G C 1 0 0 0 0 1 0 0 0 7845 943 33 4 4 JADE2 5 134535864 Missense_Mutation SNP G C3N-00294_T 1668845 134535864 47002395 439 13211 DDX46 0 . GRCh38 5 134795003 134795003 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1780G>A p.Glu594Lys p.E594K ENST00000452510 14/23 121 85 36 167 167 0 strelka-varscan-mutect DDX46,missense_variant,p.Glu594Lys,ENST00000452510,NM_001300860.1;DDX46,missense_variant,p.Glu594Lys,ENST00000354283,NM_014829.3;DDX46,downstream_gene_variant,,ENST00000628477,;DDX46,downstream_gene_variant,,ENST00000509178,;DDX46,3_prime_UTR_variant,,ENST00000507392,;DDX46,non_coding_transcript_exon_variant,,ENST00000503946,;DDX46,downstream_gene_variant,,ENST00000513592,; A ENST00000452510 Transcript missense_variant 1938/5689 1780/3099 594/1032 E/K Gag/Aag 1 1 DDX46 HGNC HGNC:18681 protein_coding YES CCDS75306.1 ENSP00000416534 A0A0C4DG89 UPI000006F4C9 NM_001300860.1 tolerated(0.14) 14/23 Low_complexity_(Seg):seg,PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF158,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 134795003 134795003 G A 1 0 0 0 0 1 0 0 0 4167 1175 41 3 3 DDX46 5 134795003 Missense_Mutation SNP G C3N-00294_T 259139 134795003 46743256 440 13212 APBB3 0 . GRCh38 5 140560501 140560501 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1057G>A p.Glu353Lys p.E353K ENST00000354402 12/13 77 61 16 87 87 0 strelka-varscan-mutect APBB3,missense_variant,p.Glu346Lys,ENST00000357560,NM_133173.2;APBB3,missense_variant,p.Arg307Lys,ENST00000358580,;APBB3,missense_variant,p.Glu353Lys,ENST00000354402,NM_006051.3;APBB3,missense_variant,p.Glu351Lys,ENST00000356738,NM_133172.2;APBB3,missense_variant,p.Glu344Lys,ENST00000412920,NM_133174.2;APBB3,missense_variant,p.Arg305Lys,ENST00000511201,;SLC35A4,upstream_gene_variant,,ENST00000514199,;SLC35A4,upstream_gene_variant,,ENST00000323146,NM_080670.3;SLC35A4,upstream_gene_variant,,ENST00000612662,;SRA1,upstream_gene_variant,,ENST00000336283,NM_001035235.3;SLC35A4,upstream_gene_variant,,ENST00000623481,;APBB3,downstream_gene_variant,,ENST00000617240,;SRA1,upstream_gene_variant,,ENST00000520427,;AC011380.9,downstream_gene_variant,,ENST00000507279,;APBB3,downstream_gene_variant,,ENST00000505617,;AC011380.9,downstream_gene_variant,,ENST00000513766,;APBB3,3_prime_UTR_variant,,ENST00000511896,;APBB3,3_prime_UTR_variant,,ENST00000509914,;APBB3,3_prime_UTR_variant,,ENST00000467078,;APBB3,non_coding_transcript_exon_variant,,ENST00000510241,;APBB3,non_coding_transcript_exon_variant,,ENST00000515056,;SRA1,upstream_gene_variant,,ENST00000523259,;SRA1,upstream_gene_variant,,ENST00000602775,;APBB3,downstream_gene_variant,,ENST00000506958,;APBB3,downstream_gene_variant,,ENST00000506289,;APBB3,downstream_gene_variant,,ENST00000503979,;SRA1,upstream_gene_variant,,ENST00000602875,;APBB3,downstream_gene_variant,,ENST00000513507,;APBB3,downstream_gene_variant,,ENST00000503850,;APBB3,downstream_gene_variant,,ENST00000511463,;APBB3,downstream_gene_variant,,ENST00000506165,;APBB3,downstream_gene_variant,,ENST00000511459,;APBB3,downstream_gene_variant,,ENST00000504872,; T ENST00000354402 Transcript missense_variant 1072/1810 1057/1482 353/493 E/K Gag/Aag 1 -1 APBB3 HGNC HGNC:20708 protein_coding YES CCDS4227.1 ENSP00000346378 O95704 UPI0000414594 NM_006051.3 tolerated(0.42) 12/13 Gene3D:2.30.29.30,PROSITE_profiles:PS01179,hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF10,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 140560501 140560501 C T 1 0 0 0 0 1 0 0 0 882 927 32 3 3 APBB3 5 140560501 Missense_Mutation SNP C C3N-00294_T 5765498 140560501 40977758 441 13213 CD14 0 . GRCh38 5 140631896 140631896 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1088G>C p.Gly363Ala p.G363A ENST00000302014 2/2 33 24 9 35 35 0 strelka-varscan-mutect CD14,missense_variant,p.Gly363Ala,ENST00000302014,NM_000591.3;CD14,missense_variant,p.Gly363Ala,ENST00000401743,NM_001040021.2,NM_001174105.1,NM_001174104.1;CD14,downstream_gene_variant,,ENST00000498971,;CD14,downstream_gene_variant,,ENST00000512545,;CD14,downstream_gene_variant,,ENST00000519715,; G ENST00000302014 Transcript missense_variant 1718/1886 1088/1128 363/375 G/A gGa/gCa 1 -1 CD14 HGNC HGNC:1628 protein_coding YES CCDS4232.1 ENSP00000304236 P08571 UPI000004A918 NM_000591.3 deleterious(0.05) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10630,PIRSF_domain:PIRSF002017 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -19.99976 0.9999981 1 1 1 0 G 3 3 46 140631896 140631896 C G 1 0 0 0 0 1 0 0 0 2667 855 30 4 4 CD14 5 140631896 Missense_Mutation SNP C C3N-00294_T 71395 140631896 40906363 442 13214 CD14 0 . GRCh38 5 140632085 140632085 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.899G>C p.Arg300Thr p.R300T ENST00000302014 2/2 192 165 27 220 220 0 strelka-varscan-mutect CD14,missense_variant,p.Arg300Thr,ENST00000302014,NM_000591.3;CD14,missense_variant,p.Arg300Thr,ENST00000401743,NM_001040021.2,NM_001174105.1,NM_001174104.1;CD14,downstream_gene_variant,,ENST00000498971,;CD14,downstream_gene_variant,,ENST00000512545,;CD14,downstream_gene_variant,,ENST00000519715,; G ENST00000302014 Transcript missense_variant 1529/1886 899/1128 300/375 R/T aGa/aCa 1 -1 CD14 HGNC HGNC:1628 protein_coding YES CCDS4232.1 ENSP00000304236 P08571 UPI000004A918 NM_000591.3 tolerated(0.14) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR10630,Gene3D:3.80.10.10,PIRSF_domain:PIRSF002017,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 140632085 140632085 C G 1 0 0 0 0 1 0 0 0 2667 913 32 4 4 CD14 5 140632085 Missense_Mutation SNP C C3N-00294_T 189 140632085 40906174 443 13215 PCDHA1 0 . GRCh38 5 140786803 140786803 + Silent SNP G G A rs781835560 C3N-00294_T C3N-00294_N G G c.513G>A p.= p.T171T ENST00000504120 1/4 87 56 31 101 101 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,synonymous_variant,p.=,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript synonymous_variant 513/5263 513/2853 171/950 T acG/acA rs781835560,COSM5457157,COSM5457158 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs781835560 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 140786803 140786803 G A 1 0 0 0 0 0 0 0 1 11606 1074 38 1 1 PCDHA1 5 140786803 Silent SNP G C3N-00294_T 154718 140786803 40751456 444 13216 PCDHA1 0 . GRCh38 5 140787323 140787323 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1033G>A p.Asp345Asn p.D345N ENST00000504120 1/4 106 84 22 119 119 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Asp345Asn,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Asp345Asn,ENST00000378133,NM_031410.2;PCDHA1,missense_variant,p.Asp345Asn,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript missense_variant 1033/5263 1033/2853 345/950 D/N Gat/Aat 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 140787323 140787323 G A 1 0 0 0 0 1 0 0 0 11606 1290 45 3 3 PCDHA1 5 140787323 Missense_Mutation SNP G C3N-00294_T 520 140787323 40750936 445 13217 PCDHB2 0 . GRCh38 5 141095560 141095560 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.770G>T p.Ser257Ile p.S257I ENST00000194155 1/1 126 71 55 106 106 0 strelka-varscan-mutect PCDHB2,missense_variant,p.Ser257Ile,ENST00000194155,NM_018936.3;PCDHB2,3_prime_UTR_variant,,ENST00000622947,;PCDHB2,3_prime_UTR_variant,,ENST00000624874,;PCDHB2,3_prime_UTR_variant,,ENST00000625033,;PCDHB3,upstream_gene_variant,,ENST00000231130,NM_018937.4;PCDHB2,upstream_gene_variant,,ENST00000624994,;CTC-270D5.1,intron_variant,,ENST00000623741,;AC005754.7,downstream_gene_variant,,ENST00000607216,;CTC-270D5.1,downstream_gene_variant,,ENST00000623615,;AC005754.7,downstream_gene_variant,,ENST00000625128,;AC005754.7,downstream_gene_variant,,ENST00000625066,; T ENST00000194155 Transcript missense_variant 983/4126 770/2397 257/798 S/I aGc/aTc 1 1 PCDHB2 HGNC HGNC:8687 protein_coding YES CCDS4244.1 ENSP00000194155 Q9Y5E7 UPI00001273DC NM_018936.3 deleterious_low_confidence(0.01) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 141095560 141095560 G T 1 0 0 0 0 1 0 0 0 11629 971 34 2 2 PCDHB2 5 141095560 Missense_Mutation SNP G C3N-00294_T 308237 141095560 40442699 446 13218 PCDHGB7 0 . GRCh38 5 141418070 141418070 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.211G>A p.Glu71Lys p.E71K ENST00000398594 1/4 310 234 76 297 297 0 strelka-varscan-mutect PCDHGB7,missense_variant,p.Glu71Lys,ENST00000398594,NM_018927.3;PCDHGB7,missense_variant,p.Glu71Lys,ENST00000612073,NM_032101.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,upstream_gene_variant,,ENST00000398587,NM_018914.2;PCDHGA10,downstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA11,upstream_gene_variant,,ENST00000622044,NM_032091.1;PCDHGA11,upstream_gene_variant,,ENST00000518882,NM_032092.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000398594 Transcript missense_variant 380/4765 211/2790 71/929 E/K Gag/Aag 1 1 PCDHGB7 HGNC HGNC:8714 protein_coding YES CCDS47293.1 ENSP00000381594 Q9Y5F8 UPI000007141F NM_018927.3 tolerated(0.18) 1/4 hmmpanther:PTHR24028:SF113,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 141418070 141418070 G A 1 0 0 0 0 1 0 0 0 11655 1175 41 3 3 PCDHGB7 5 141418070 Missense_Mutation SNP G C3N-00294_T 322510 141418070 40120189 447 13219 PCDHGC3 0 . GRCh38 5 141476552 141476552 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.436G>A p.Glu146Lys p.E146K ENST00000308177 1/4 304 231 73 335 335 0 strelka-varscan-mutect PCDHGC3,missense_variant,p.Glu146Lys,ENST00000308177,NM_002588.3;PCDHGC3,missense_variant,p.Glu146Lys,ENST00000611950,NM_032402.1;PCDHGC3,missense_variant,p.Glu18Lys,ENST00000621008,;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB7,intron_variant,,ENST00000398594,NM_018927.3;PCDHGA12,intron_variant,,ENST00000252085,NM_003735.2;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA11,intron_variant,,ENST00000398587,NM_018914.2;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGC3,intron_variant,,ENST00000617641,NM_032403.2;PCDHGA11,intron_variant,,ENST00000518882,NM_032092.1;PCDHGC3,intron_variant,,ENST00000617222,;RN7SL68P,upstream_gene_variant,,ENST00000488078,;PCDHGC3,intron_variant,,ENST00000616230,;PCDHGC3,intron_variant,,ENST00000622656,;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000308177 Transcript missense_variant 550/4725 436/2805 146/934 E/K Gag/Aag COSM1542497,COSM1542498 1 1 PCDHGC3 HGNC HGNC:8716 protein_coding YES CCDS4261.1 ENSP00000312070 Q9UN70 UPI000006F34F NM_002588.3 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF70,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1452697214 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 141476552 141476552 G A 1 0 0 0 0 1 0 0 0 11656 1059 37 1 1 PCDHGC3 5 141476552 Missense_Mutation SNP G C3N-00294_T 58482 141476552 40061707 448 13220 PCDH1 0 . GRCh38 5 141864382 141864382 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1949C>T p.Ser650Leu p.S650L ENST00000287008 3/5 101 81 20 119 119 0 strelka-varscan-mutect PCDH1,missense_variant,p.Ser650Leu,ENST00000287008,NM_032420.3;PCDH1,missense_variant,p.Ser650Leu,ENST00000394536,NM_001278613.1,NM_002587.4;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,downstream_gene_variant,,ENST00000514773,;PCDH1,non_coding_transcript_exon_variant,,ENST00000357517,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,downstream_gene_variant,,ENST00000505937,; A ENST00000287008 Transcript missense_variant 2097/4793 1949/3714 650/1237 S/L tCa/tTa 1 -1 PCDH1 HGNC HGNC:8655 protein_coding YES CCDS4267.1 ENSP00000287008 Q08174 UPI000016158F NM_032420.3 tolerated(0.17) 3/5 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF326,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 141864382 141864382 G A 1 0 0 0 0 1 0 0 0 11593 1294 45 3 3 PCDH1 5 141864382 Missense_Mutation SNP G C3N-00294_T 387830 141864382 39673877 449 13221 PRELID2 0 . GRCh38 5 145796459 145796459 + Nonsense_Mutation SNP G G A rs375685870 C3N-00294_T C3N-00294_N G G c.493C>T p.Arg165Ter p.R165* ENST00000334744 6/8 175 136 39 210 210 0 strelka-varscan-mutect PRELID2,stop_gained,p.Arg165Ter,ENST00000334744,NM_182960.3;PRELID2,stop_gained,p.Arg153Ter,ENST00000511435,;PRELID2,stop_gained,p.Arg124Ter,ENST00000394450,NM_138492.5;PRELID2,stop_gained,p.Arg153Ter,ENST00000505416,NM_205846.2;PRELID2,non_coding_transcript_exon_variant,,ENST00000510594,; A ENST00000334744 Transcript stop_gained 546/2140 493/570 165/189 R/* Cga/Tga rs375685870,COSM241243 1 -1 PRELID2 HGNC HGNC:28306 protein_coding YES CCDS34262.1 ENSP00000335675 Q8N945 UPI000006FB14 NM_182960.3 6/8 PROSITE_profiles:PS50904,hmmpanther:PTHR11158:SF20,hmmpanther:PTHR11158,Pfam_domain:PF04707 0,1 HIGH 1 SNV 2 0,1 1 PASS rs375685870 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 145796459 145796459 G A 1 0 0 0 0 0 1 0 0 12604 1153 40 1 1 PRELID2 5 145796459 Nonsense_Mutation SNP G C3N-00294_T 3932077 145796459 35741800 450 13222 SYNPO 0 . GRCh38 5 150649263 150649263 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.1720C>G p.Leu574Val p.L574V ENST00000394243 3/3 218 162 56 201 201 0 strelka-varscan-mutect SYNPO,missense_variant,p.Leu574Val,ENST00000394243,NM_001166208.1;SYNPO,missense_variant,p.Leu330Val,ENST00000307662,NM_007286.5;SYNPO,missense_variant,p.Leu574Val,ENST00000522122,NM_001166209.1;SYNPO,missense_variant,p.Leu330Val,ENST00000519664,NM_001109974.2;SYNPO,downstream_gene_variant,,ENST00000518872,; G ENST00000394243 Transcript missense_variant 2094/7063 1720/2790 574/929 L/V Ctg/Gtg COSM5639091,COSM5639092 1 1 SYNPO HGNC HGNC:30672 protein_coding YES CCDS54937.1 ENSP00000377789 Q8N3V7 UPI000013F943 NM_001166208.1 tolerated(0.54) 3/3 hmmpanther:PTHR24217,hmmpanther:PTHR24217:SF13 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 150649263 150649263 C G 1 0 0 0 0 1 0 0 0 15850 912 32 4 4 SYNPO 5 150649263 Missense_Mutation SNP C C3N-00294_T 4852804 150649263 30888996 451 13223 SLC36A3 0 . GRCh38 5 151296182 151296182 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.306G>C p.Gln102His p.Q102H ENST00000377713 3/11 233 201 32 334 334 0 strelka-varscan-mutect SLC36A3,missense_variant,p.Gln102His,ENST00000335230,NM_181774.3;SLC36A3,missense_variant,p.Gln102His,ENST00000377713,NM_001145017.1;SLC36A3,splice_region_variant,,ENST00000423071,; G ENST00000377713 Transcript missense_variant,splice_region_variant 448/1720 306/1536 102/511 Q/H caG/caC 1 -1 SLC36A3 HGNC HGNC:19659 protein_coding YES CCDS47316.1 ENSP00000366942 Q495N2 UPI00005764D3 NM_001145017.1 tolerated(0.5) 3/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF258 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 151296182 151296182 C G 1 0 0 0 0 1 0 0 0 14873 927 32 4 4 SLC36A3 5 151296182 Missense_Mutation SNP C C3N-00294_T 646919 151296182 30242077 452 13224 NMUR2 0 . GRCh38 5 152392241 152392241 + Nonsense_Mutation SNP C C A rs867657626 C3N-00294_T C3N-00294_N C C c.1198G>T p.Glu400Ter p.E400* ENST00000255262 4/4 130 99 31 172 172 0 strelka-varscan-mutect NMUR2,stop_gained,p.Glu400Ter,ENST00000255262,NM_020167.4;NMUR2,downstream_gene_variant,,ENST00000518933,; A ENST00000255262 Transcript stop_gained 1364/2073 1198/1248 400/415 E/* Gaa/Taa rs867657626,COSM3245179 1 -1 NMUR2 HGNC HGNC:16454 protein_coding YES CCDS4321.1 ENSP00000255262 Q9GZQ4 UPI000013CE9D NM_020167.4 4/4 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF14 0,1 HIGH 1 SNV 1 0,1 1 PASS rs867657626 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 152392241 152392241 C A 1 0 0 0 0 0 1 0 0 10548 835 29 2 2 NMUR2 5 152392241 Nonsense_Mutation SNP C C3N-00294_T 1096059 152392241 29146018 453 13225 GEMIN5 0 . GRCh38 5 154938073 154938073 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.61G>A p.Asp21Asn p.D21N ENST00000285873 1/28 42 34 8 44 44 0 strelka-varscan-mutect GEMIN5,missense_variant,p.Asp21Asn,ENST00000285873,NM_001252156.1,NM_015465.4;MRPL22,upstream_gene_variant,,ENST00000523037,NM_014180.3;MRPL22,upstream_gene_variant,,ENST00000522038,;MRPL22,upstream_gene_variant,,ENST00000265229,NM_001014990.2;MRPL22,upstream_gene_variant,,ENST00000439747,;MRPL22,upstream_gene_variant,,ENST00000519059,; T ENST00000285873 Transcript missense_variant 137/5397 61/4527 21/1508 D/N Gat/Aat COSM3381169 1 -1 GEMIN5 HGNC HGNC:20043 protein_coding YES CCDS4330.1 ENSP00000285873 Q8TEQ6 UPI000020D072 NM_001252156.1,NM_015465.4 deleterious(0.01) 1/28 hmmpanther:PTHR22850,hmmpanther:PTHR22850:SF89 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.63786 1 1 1 1 0 T 3 4 46 154938073 154938073 C T 1 0 0 0 0 1 0 0 0 6205 884 31 1 1 GEMIN5 5 154938073 Missense_Mutation SNP C C3N-00294_T 2545832 154938073 26600186 454 13226 ITK 0 . GRCh38 5 157244466 157244466 + Silent SNP C C T rs756176085 C3N-00294_T C3N-00294_N C C c.1437C>T p.= p.I479I ENST00000422843 13/17 330 262 68 353 353 0 strelka-varscan-mutect ITK,synonymous_variant,p.=,ENST00000422843,NM_005546.3;ITK,non_coding_transcript_exon_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,upstream_gene_variant,,ENST00000523926,;ITK,downstream_gene_variant,,ENST00000520173,;ITK,downstream_gene_variant,,ENST00000519759,; T ENST00000422843 Transcript synonymous_variant 1589/4528 1437/1863 479/620 I atC/atT rs756176085 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 13/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,PROSITE_patterns:PS00109,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 LOW 1 SNV 1 1 PASS rs756176085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 157244466 157244466 C T 1 0 0 0 0 0 0 0 1 7815 845 30 3 3 ITK 5 157244466 Silent SNP C C3N-00294_T 2306393 157244466 24293793 455 13227 GABRA1 0 . GRCh38 5 161897201 161897201 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1150C>A p.Pro384Thr p.P384T ENST00000393943 10/10 202 122 80 199 199 0 strelka-varscan-mutect GABRA1,missense_variant,p.Pro384Thr,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Pro384Thr,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Pro399Thr,ENST00000638159,;GABRA1,missense_variant,p.Pro384Thr,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Pro384Thr,ENST00000638112,;GABRA1,missense_variant,p.Pro384Thr,ENST00000636573,;GABRA1,missense_variant,p.Pro384Thr,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Pro384Thr,ENST00000637827,;GABRA1,missense_variant,p.Pro384Thr,ENST00000635880,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,; A ENST00000393943 Transcript missense_variant 1933/4686 1150/1371 384/456 P/T Ccg/Acg 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 tolerated(0.17) 10/10 Prints_domain:PR01614,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 161897201 161897201 C A 1 0 0 0 0 1 0 0 0 6031 623 22 2 2 GABRA1 5 161897201 Missense_Mutation SNP C C3N-00294_T 4652735 161897201 19641058 456 13228 TENM2 0 . GRCh38 5 168262325 168262325 + Missense_Mutation SNP G G A rs781581501 C3N-00294_T C3N-00294_N G G c.7840G>A p.Glu2614Lys p.E2614K ENST00000518659 29/29 170 134 36 204 204 0 strelka-varscan-mutect TENM2,missense_variant,p.Glu2493Lys,ENST00000519204,;TENM2,missense_variant,p.Glu2614Lys,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Glu2375Lys,ENST00000520394,; A ENST00000518659 Transcript missense_variant 7879/8550 7840/8325 2614/2774 E/K Gag/Aag rs781581501,COSM1065588,COSM1065589,COSM1595190 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0.04) 29/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs781581501 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 168262325 168262325 G A 1 0 0 0 0 1 0 0 0 16172 1059 37 1 1 TENM2 5 168262325 Missense_Mutation SNP G C3N-00294_T 6365124 168262325 13275934 457 13229 FGF18 0 . GRCh38 5 171436153 171436153 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.130C>T p.Arg44Trp p.R44W ENST00000274625 3/5 92 73 19 138 138 0 strelka-varscan-mutect FGF18,missense_variant,p.Arg44Trp,ENST00000274625,NM_003862.2; T ENST00000274625 Transcript missense_variant 674/1986 130/624 44/207 R/W Cgg/Tgg 1 1 FGF18 HGNC HGNC:3674 protein_coding YES CCDS4378.1 ENSP00000274625 O76093 UPI000003C116 NM_003862.2 deleterious(0.02) 3/5 Gene3D:2.80.10.50,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF4,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 171436153 171436153 C T 1 0 0 0 0 1 0 0 0 5710 875 31 1 1 FGF18 5 171436153 Missense_Mutation SNP C C3N-00294_T 3173828 171436153 10102106 458 13230 CREBRF 0 . GRCh38 5 173110711 173110711 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1607G>A p.Arg536Lys p.R536K ENST00000296953 6/9 71 34 37 61 61 0 strelka-varscan-mutect CREBRF,missense_variant,p.Arg536Lys,ENST00000296953,NM_153607.2;CREBRF,splice_region_variant,,ENST00000520464,; A ENST00000296953 Transcript missense_variant,splice_region_variant 1926/7778 1607/1920 536/639 R/K aGa/aAa 1 1 CREBRF HGNC HGNC:24050 protein_coding YES CCDS34293.1 ENSP00000296953 Q8IUR6 UPI000049E01D NM_153607.2 deleterious(0.04) 6/9 hmmpanther:PTHR21552,PROSITE_patterns:PS00036,Gene3D:1.20.5.170,Superfamily_domains:SSF57959 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 173110711 173110711 G A 1 0 0 0 0 1 0 0 0 3663 1014 35 3 3 CREBRF 5 173110711 Missense_Mutation SNP G C3N-00294_T 1674558 173110711 8427548 459 13231 DRD1 0 . GRCh38 5 175442559 175442559 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.541G>A p.Glu181Lys p.E181K ENST00000393752 2/2 153 121 32 165 165 0 strelka-varscan-mutect DRD1,missense_variant,p.Glu181Lys,ENST00000393752,NM_000794.3; T ENST00000393752 Transcript missense_variant 1534/4054 541/1341 181/446 E/K Gag/Aag 1 -1 DRD1 HGNC HGNC:3020 protein_coding YES CCDS4393.1 ENSP00000377353 P21728 UPI00000503F5 NM_000794.3 tolerated(0.85) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF221,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 175442559 175442559 C T 1 0 0 0 0 1 0 0 0 4575 835 29 3 3 DRD1 5 175442559 Missense_Mutation SNP C C3N-00294_T 2331848 175442559 6095700 460 13232 UIMC1 0 . GRCh38 5 176970840 176970840 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.259C>G p.Leu87Val p.L87V ENST00000377227 4/15 240 200 40 178 178 0 strelka-varscan-mutect UIMC1,missense_variant,p.Leu87Val,ENST00000377227,NM_016290.4;UIMC1,missense_variant,p.Leu87Val,ENST00000511320,NM_001199297.1,NM_001199298.1;UIMC1,missense_variant,p.Leu87Val,ENST00000506128,;UIMC1,missense_variant,p.Leu87Val,ENST00000509236,;UIMC1,missense_variant,p.Leu87Val,ENST00000507513,;UIMC1,upstream_gene_variant,,ENST00000510698,;UIMC1,upstream_gene_variant,,ENST00000503273,;UIMC1,downstream_gene_variant,,ENST00000505879,;UIMC1,missense_variant,p.Leu87Val,ENST00000512031,;UIMC1,non_coding_transcript_exon_variant,,ENST00000417486,;UIMC1,non_coding_transcript_exon_variant,,ENST00000515488,; C ENST00000377227 Transcript missense_variant 392/2570 259/2160 87/719 L/V Ctg/Gtg 1 -1 UIMC1 HGNC HGNC:30298 protein_coding YES CCDS4408.1 ENSP00000366434 Q96RL1 A0A024R7R0 UPI00001A9954 NM_016290.4 deleterious(0) 4/15 PROSITE_profiles:PS50330,hmmpanther:PTHR15932,hmmpanther:PTHR15932:SF2,SMART_domains:SM00726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 176970840 176970840 G C 1 0 0 0 0 1 0 0 0 17495 933 33 4 4 UIMC1 5 176970840 Missense_Mutation SNP G C3N-00294_T 1528281 176970840 4567419 461 13233 FAM193B 0 . GRCh38 5 177524614 177524614 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1867G>A p.Glu623Lys p.E623K ENST00000514747 6/9 111 94 17 81 81 0 strelka-varscan-mutect FAM193B,missense_variant,p.Glu623Lys,ENST00000514747,NM_001190946.1;FAM193B,missense_variant,p.Glu309Lys,ENST00000524677,;FAM193B,downstream_gene_variant,,ENST00000508298,;FAM193B,upstream_gene_variant,,ENST00000505241,;FAM193B,upstream_gene_variant,,ENST00000504130,;FAM193B,3_prime_UTR_variant,,ENST00000506955,;FAM193B,3_prime_UTR_variant,,ENST00000510479,;FAM193B,3_prime_UTR_variant,,ENST00000510163,;FAM193B,non_coding_transcript_exon_variant,,ENST00000505569,;FAM193B,upstream_gene_variant,,ENST00000507212,;FAM193B,downstream_gene_variant,,ENST00000513502,;FAM193B,upstream_gene_variant,,ENST00000513282,;FAM193B,upstream_gene_variant,,ENST00000506879,; T ENST00000514747 Transcript missense_variant 1916/2913 1867/2469 623/822 E/K Gag/Aag 1 -1 FAM193B HGNC HGNC:25524 protein_coding YES CCDS54954.1 ENSP00000422131 Q96PV7 UPI0001D3BB6A NM_001190946.1 deleterious(0.01) 6/9 hmmpanther:PTHR15109,hmmpanther:PTHR15109:SF3 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 177524614 177524614 C T 1 0 0 0 0 1 0 0 0 5372 864 30 3 3 FAM193B 5 177524614 Missense_Mutation SNP C C3N-00294_T 553774 177524614 4013645 462 13234 GRM6 0 . GRCh38 5 178986257 178986257 + Missense_Mutation SNP G G C rs2856347 C3N-00294_T C3N-00294_N G G c.1997C>G p.Ser666Cys p.S666C ENST00000231188 8/10 332 282 50 308 308 0 strelka-varscan-mutect GRM6,missense_variant,p.Ser666Cys,ENST00000231188,NM_000843.3;GRM6,missense_variant,p.Ser666Cys,ENST00000517717,;RP11-281O15.4,intron_variant,,ENST00000519491,;GRM6,downstream_gene_variant,,ENST00000518082,;GRM6,upstream_gene_variant,,ENST00000519003,; C ENST00000231188 Transcript missense_variant 2176/6143 1997/2634 666/877 S/C tCt/tGt rs2856347 1 -1 GRM6 HGNC HGNC:4598 protein_coding YES CCDS4442.1 ENSP00000231188 O15303 UPI000013C947 NM_000843.3 deleterious(0) 8/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF24,Pfam_domain:PF00003,Prints_domain:PR00593,Prints_domain:PR00248 MODERATE 1 SNV 2 1 PASS rs2856347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 178986257 178986257 G C 1 0 0 0 0 1 0 0 0 6683 942 33 4 4 GRM6 5 178986257 Missense_Mutation SNP G C3N-00294_T 1461643 178986257 2552002 463 13235 ZNF879 0 . GRCh38 5 179027570 179027570 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.131T>C p.Leu44Pro p.L44P ENST00000444149 3/5 270 223 47 209 209 0 strelka-varscan-mutect ZNF879,missense_variant,p.Leu44Pro,ENST00000444149,NM_001136116.1;ZNF879,missense_variant,p.Leu44Pro,ENST00000522442,;ZNF879,synonymous_variant,p.=,ENST00000519896,;ZNF879,downstream_gene_variant,,ENST00000521285,; C ENST00000444149 Transcript missense_variant 319/3304 131/1692 44/563 L/P cTg/cCg 1 1 ZNF879 HGNC HGNC:37273 protein_coding YES CCDS47352.1 ENSP00000414887 B4DU55 UPI000022C878 NM_001136116.1 deleterious(0) 3/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF33,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 179027570 179027570 T C 1 0 0 0 0 1 0 0 0 18788 1580 55 5 5 ZNF879 5 179027570 Missense_Mutation SNP T C3N-00294_T 41313 179027570 2510689 464 13236 ADAMTS2 0 . GRCh38 5 179151193 179151193 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1637C>A p.Pro546Gln p.P546Q ENST00000274609 11/11 44 33 11 32 32 0 strelka-varscan-mutect ADAMTS2,missense_variant,p.Pro546Gln,ENST00000274609,NM_021599.2;ADAMTS2,intron_variant,,ENST00000251582,NM_014244.4; T ENST00000274609 Transcript missense_variant 1739/2044 1637/1701 546/566 P/Q cCg/cAg 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding CCDS34311.1 ENSP00000274609 O95450 UPI000002A492 NM_021599.2 tolerated(0.15) 11/11 MODERATE SNV 1 1 PASS rs1021616634 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 179151193 179151193 G T 1 0 0 0 0 1 0 0 0 309 1116 39 1 1 ADAMTS2 5 179151193 Missense_Mutation SNP G C3N-00294_T 123623 179151193 2387066 465 13237 MAML1 0 . GRCh38 5 179773980 179773980 + Silent SNP G G A rs756817768 C3N-00294_T C3N-00294_N G G c.2154G>A p.= p.L718L ENST00000292599 5/5 441 377 64 278 277 1 strelka-varscan-mutect MAML1,synonymous_variant,p.=,ENST00000292599,NM_014757.4;MAML1,intron_variant,,ENST00000503050,;MAML1,non_coding_transcript_exon_variant,,ENST00000511027,;MAML1,downstream_gene_variant,,ENST00000507385,; A ENST00000292599 Transcript synonymous_variant 2417/5723 2154/3051 718/1016 L ctG/ctA rs756817768,COSM383444 1 1 MAML1 HGNC HGNC:13632 protein_coding YES CCDS34315.1 ENSP00000292599 Q92585 UPI0000071286 NM_014757.4 5/5 hmmpanther:PTHR15692:SF19,hmmpanther:PTHR15692 0,1 LOW 1 SNV 1 0,1 1 PASS rs756817768 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 179773980 179773980 G A 1 0 0 0 0 0 0 0 1 9126 1277 45 3 3 MAML1 5 179773980 Silent SNP G C3N-00294_T 622787 179773980 1764279 466 13238 SLC22A23 0 . GRCh38 6 3298098 3298098 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.1203G>C p.= p.V401V ENST00000406686 5/10 39 34 5 48 48 0 strelka-varscan-mutect SLC22A23,synonymous_variant,p.=,ENST00000436008,;SLC22A23,synonymous_variant,p.=,ENST00000406686,NM_015482.1;SLC22A23,synonymous_variant,p.=,ENST00000380302,NM_001286455.1;SLC22A23,synonymous_variant,p.=,ENST00000490273,NM_021945.6;SLC22A23,synonymous_variant,p.=,ENST00000485307,;SLC22A23,synonymous_variant,p.=,ENST00000467177,;PSMG4,intron_variant,,ENST00000451246,;SLC22A23,non_coding_transcript_exon_variant,,ENST00000496753,;SLC22A23,non_coding_transcript_exon_variant,,ENST00000467144,;SLC22A23,3_prime_UTR_variant,,ENST00000497691,; G ENST00000406686 Transcript synonymous_variant 1203/5658 1203/2061 401/686 V gtG/gtC 1 -1 SLC22A23 HGNC HGNC:21106 protein_coding YES CCDS47363.1 ENSP00000385028 A1A5C7 UPI0000EE5391 NM_015482.1 5/10 Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF192,Superfamily_domains:SSF103473 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -13.05176 1 1 1 1 0 G 2 3 46 3298098 3298098 C G 1 0 0 0 0 0 0 0 1 14717 813 29 4 4 SLC22A23 6 3298098 Silent SNP C C3N-00294_T 3298098 167507881 467 13239 RREB1 0 . GRCh38 6 7210921 7210921 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.543G>C p.Glu181Asp p.E181D ENST00000379938 7/13 118 86 32 97 97 0 strelka-varscan-mutect RREB1,missense_variant,p.Glu181Asp,ENST00000379938,NM_001003699.3;RREB1,missense_variant,p.Glu181Asp,ENST00000349384,NM_001003698.3;RREB1,missense_variant,p.Glu181Asp,ENST00000379933,NM_001168344.1;RREB1,missense_variant,p.Glu181Asp,ENST00000334984,NM_001003700.1;RREB1,missense_variant,p.Glu181Asp,ENST00000483150,;RREB1,downstream_gene_variant,,ENST00000471433,;RREB1,non_coding_transcript_exon_variant,,ENST00000475946,; C ENST00000379938 Transcript missense_variant 1080/8778 543/5229 181/1742 E/D gaG/gaC 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 tolerated(0.28) 7/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7210921 7210921 G C 1 0 0 0 0 1 0 0 0 13933 933 33 4 4 RREB1 6 7210921 Missense_Mutation SNP G C3N-00294_T 3912823 7210921 163595058 468 13240 RREB1 0 . GRCh38 6 7229303 7229303 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1204C>T p.Gln402Ter p.Q402* ENST00000379938 10/13 139 112 27 147 147 0 strelka-varscan-mutect RREB1,stop_gained,p.Gln402Ter,ENST00000379938,NM_001003699.3;RREB1,stop_gained,p.Gln402Ter,ENST00000349384,NM_001003698.3;RREB1,stop_gained,p.Gln402Ter,ENST00000379933,NM_001168344.1;RREB1,stop_gained,p.Gln402Ter,ENST00000334984,NM_001003700.1;RREB1,stop_gained,p.Gln402Ter,ENST00000483150,;RREB1,upstream_gene_variant,,ENST00000611109,; T ENST00000379938 Transcript stop_gained 1741/8778 1204/5229 402/1742 Q/* Cag/Tag 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 10/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 7229303 7229303 C T 1 0 0 0 0 0 1 0 0 13933 827 29 3 3 RREB1 6 7229303 Nonsense_Mutation SNP C C3N-00294_T 18382 7229303 163576676 469 13241 SIRT5 0 . GRCh38 6 13591792 13591792 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.373G>C p.Glu125Gln p.E125Q ENST00000606117 5/10 132 106 26 113 113 0 strelka-varscan-mutect SIRT5,missense_variant,p.Glu17Gln,ENST00000397350,NM_001242827.1;SIRT5,missense_variant,p.Glu125Gln,ENST00000606117,NM_012241.4;SIRT5,missense_variant,p.Glu125Gln,ENST00000359782,NM_001193267.2;SIRT5,missense_variant,p.Glu125Gln,ENST00000379262,NM_031244.3;SIRT5,downstream_gene_variant,,ENST00000637463,;SIRT5,stop_lost,p.Ter80SerextTer19,ENST00000379250,;SIRT5,downstream_gene_variant,,ENST00000606427,; C ENST00000606117 Transcript missense_variant 669/3922 373/933 125/310 E/Q Gag/Cag COSM5625313,COSM5625314 1 1 SIRT5 HGNC HGNC:14933 protein_coding YES CCDS4526.1 ENSP00000476228 Q9NXA8 A0A024R012 UPI0000073EB3 NM_012241.4 tolerated(0.16) 5/10 Gene3D:3.40.50.1220,HAMAP:MF_01121,Pfam_domain:PF02146,PROSITE_profiles:PS50305,hmmpanther:PTHR11085,hmmpanther:PTHR11085:SF24,Superfamily_domains:SSF52467 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 13591792 13591792 G C 1 0 0 0 0 1 0 0 0 14604 1291 45 4 4 SIRT5 6 13591792 Missense_Mutation SNP G C3N-00294_T 6362489 13591792 157214187 470 13242 SOX4 0 . GRCh38 6 21594796 21594796 + Nonsense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.262G>T p.Glu88Ter p.E88* ENST00000244745 1/1 320 247 73 311 311 0 strelka-varscan-mutect SOX4,stop_gained,p.Glu88Ter,ENST00000244745,NM_003107.2;RP11-204E9.3,intron_variant,,ENST00000637901,; T ENST00000244745 Transcript stop_gained 2029/5852 262/1425 88/474 E/* Gag/Tag COSM483731 1 1 SOX4 HGNC HGNC:11200 protein_coding YES CCDS4547.1 ENSP00000244745 Q06945 UPI0000047FA0 NM_003107.2 1/1 PROSITE_profiles:PS50118,hmmpanther:PTHR10270:SF27,hmmpanther:PTHR10270,PIRSF_domain:PIRSF038098,Gene3D:1.10.30.10,Pfam_domain:PF00505,SMART_domains:SM00398,Superfamily_domains:SSF47095 1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 21594796 21594796 G T 1 0 0 0 0 0 1 0 0 15279 1059 37 1 1 SOX4 6 21594796 Nonsense_Mutation SNP G C3N-00294_T 8003004 21594796 149211183 471 13243 HIST1H2BA 0 . GRCh38 6 25727081 25727081 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.173C>G p.Ser58Trp p.S58W ENST00000274764 1/1 149 120 29 157 157 0 strelka-varscan-mutect HIST1H2BA,missense_variant,p.Ser58Trp,ENST00000274764,NM_170610.2;HIST1H2AA,upstream_gene_variant,,ENST00000297012,NM_170745.3;HIST1H2BPS1,downstream_gene_variant,,ENST00000369177,; G ENST00000274764 Transcript missense_variant 173/384 173/384 58/127 S/W tCg/tGg COSM1696976 1 1 HIST1H2BA HGNC HGNC:18730 protein_coding YES CCDS4563.1 ENSP00000274764 Q96A08 UPI0000073C6D NM_170610.2 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 1 MODERATE 1 SNV 1 1 PASS rs968613011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 25727081 25727081 C G 1 0 0 0 0 1 0 0 0 7028 893 31 4 4 HIST1H2BA 6 25727081 Missense_Mutation SNP C C3N-00294_T 4132285 25727081 145078898 472 13244 TRIM38 0 . GRCh38 6 25983212 25983212 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.923C>T p.Ser308Phe p.S308F ENST00000357085 8/8 74 61 13 97 97 0 strelka-varscan-mutect TRIM38,missense_variant,p.Ser308Phe,ENST00000357085,NM_006355.4;U91328.21,downstream_gene_variant,,ENST00000608931,; T ENST00000357085 Transcript missense_variant 1399/9413 923/1398 308/465 S/F tCt/tTt 1 1 TRIM38 HGNC HGNC:10059 protein_coding YES CCDS4568.1 ENSP00000349596 O00635 A0A024QZY4 UPI000013431A NM_006355.4 deleterious(0.02) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF47,hmmpanther:PTHR24103,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 25983212 25983212 C T 1 0 0 0 0 1 0 0 0 17001 913 32 3 3 TRIM38 6 25983212 Missense_Mutation SNP C C3N-00294_T 256131 25983212 144822767 473 13245 HIST1H3B 0 . GRCh38 6 26031883 26031883 + Missense_Mutation SNP C C T rs753823527 C3N-00294_T C3N-00294_N C C c.178G>A p.Glu60Lys p.E60K ENST00000621411 1/1 283 220 63 320 320 0 strelka-varscan-mutect HIST1H3B,missense_variant,p.Glu60Lys,ENST00000621411,NM_003537.3;HIST1H4B,upstream_gene_variant,,ENST00000377745,NM_003544.2;HIST1H2AB,downstream_gene_variant,,ENST00000615868,NM_003513.2; T ENST00000621411 Transcript missense_variant 178/411 178/411 60/136 E/K Gag/Aag rs753823527 1 -1 HIST1H3B HGNC HGNC:4776 protein_coding YES CCDS4573.1 ENSP00000484841 P68431 UPI00000003C7 NM_003537.3 deleterious_low_confidence(0.02) 1/1 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622 MODERATE 1 SNV 1 PASS rs753823527 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 26031883 26031883 C T 1 0 0 0 0 1 0 0 0 7044 893 31 1 1 HIST1H3B 6 26031883 Missense_Mutation SNP C C3N-00294_T 48671 26031883 144774096 474 13246 ZNF184 0 . GRCh38 6 27451884 27451884 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1675C>T p.Gln559Ter p.Q559* ENST00000211936 6/6 112 85 27 142 142 0 strelka-varscan-mutect ZNF184,stop_gained,p.Gln559Ter,ENST00000211936,NM_001318892.1,NM_007149.2;ZNF184,stop_gained,p.Gln559Ter,ENST00000377419,; A ENST00000211936 Transcript stop_gained 1960/3101 1675/2256 559/751 Q/* Cag/Tag 1 -1 ZNF184 HGNC HGNC:12975 protein_coding YES CCDS4624.1 ENSP00000211936 Q99676 A0A024RCM2 UPI000013C311 NM_001318892.1,NM_007149.2 6/6 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF22,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 27451884 27451884 G A 1 0 0 0 0 0 1 0 0 18331 1299 45 3 3 ZNF184 6 27451884 Nonsense_Mutation SNP G C3N-00294_T 1420001 27451884 143354095 475 13247 ZSCAN9 0 . GRCh38 6 28227466 28227466 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.382G>C p.Glu128Gln p.E128Q ENST00000425468 2/5 84 69 15 104 104 0 strelka-varscan-mutect ZSCAN9,missense_variant,p.Glu128Gln,ENST00000527436,;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000425468,NM_001199479.1;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000252207,NM_006299.4;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000531979,NM_001199480.1;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000527844,;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000531981,;ZSCAN9,missense_variant,p.Glu128Gln,ENST00000526391,;ZSCAN9,downstream_gene_variant,,ENST00000531941,; C ENST00000425468 Transcript missense_variant 547/1791 382/1338 128/445 E/Q Gag/Cag 1 1 ZSCAN9 HGNC HGNC:12984 protein_coding YES CCDS56407.1 ENSP00000404074 O15535 UPI0000E09E19 NM_001199479.1 deleterious(0) 2/5 Low_complexity_(Seg):seg,PROSITE_profiles:PS50804,hmmpanther:PTHR23226:SF15,hmmpanther:PTHR23226,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 28227466 28227466 G C 1 0 0 0 0 1 0 0 0 18840 1175 41 4 4 ZSCAN9 6 28227466 Missense_Mutation SNP G C3N-00294_T 775582 28227466 142578513 476 13248 MDC1 0 . GRCh38 6 30704861 30704861 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.4322C>T p.Ser1441Phe p.S1441F ENST00000376406 10/15 75 62 13 59 59 0 strelka-varscan-mutect MDC1,missense_variant,p.Ser1441Phe,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; A ENST00000376406 Transcript missense_variant 4970/7576 4322/6270 1441/2089 S/F tCt/tTt 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 deleterious(0) 10/15 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 30704861 30704861 G A 1 0 0 0 0 1 0 0 0 9341 942 33 3 3 MDC1 6 30704861 Missense_Mutation SNP G C3N-00294_T 2477395 30704861 140101118 477 13249 HLA-B 0 . GRCh38 6 31355424 31355424 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.788G>A p.Arg263Lys p.R263K ENST00000412585 4/8 329 287 42 359 359 0 strelka-varscan-mutect HLA-B,missense_variant,p.Arg263Lys,ENST00000412585,NM_005514.6;HLA-B,downstream_gene_variant,,ENST00000434333,;MIR6891,upstream_gene_variant,,ENST00000618788,;HLA-B,non_coding_transcript_exon_variant,,ENST00000498007,;HLA-B,non_coding_transcript_exon_variant,,ENST00000463574,;HLA-B,downstream_gene_variant,,ENST00000474381,;HLA-B,upstream_gene_variant,,ENST00000497377,;HLA-B,upstream_gene_variant,,ENST00000481849,;XXbac-BPG248L24.12,upstream_gene_variant,,ENST00000603274,; T ENST00000412585 Transcript missense_variant 817/1547 788/1089 263/362 R/K aGa/aAa 1 -1 HLA-B HGNC HGNC:4932 protein_coding YES CCDS34394.1 ENSP00000399168 P01889,P30480,P30486,Q29836,Q31612,Q31610 E5FQ95 UPI0000000B17 NM_005514.6 deleterious_low_confidence(0) 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF181,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 31355424 31355424 C T 1 0 0 0 0 1 0 0 0 7085 913 32 3 3 HLA-B 6 31355424 Missense_Mutation SNP C C3N-00294_T 650563 31355424 139450555 478 13250 BAG6 0 . GRCh38 6 31647749 31647749 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.648G>C p.Leu216Phe p.L216F ENST00000375964 7/25 61 49 12 104 104 0 strelka-mutect BAG6,missense_variant,p.Leu216Phe,ENST00000375964,NM_004639.3;BAG6,missense_variant,p.Leu210Phe,ENST00000211379,NM_080703.2,NM_080702.2;BAG6,missense_variant,p.Leu210Phe,ENST00000375976,NM_001098534.1;BAG6,missense_variant,p.Leu210Phe,ENST00000362049,NM_001199698.1;BAG6,missense_variant,p.Leu210Phe,ENST00000439687,NM_001199697.1;BAG6,missense_variant,p.Leu210Phe,ENST00000437771,;BAG6,missense_variant,p.Leu210Phe,ENST00000435080,;BAG6,missense_variant,p.Leu210Phe,ENST00000424480,;BAG6,missense_variant,p.Leu210Phe,ENST00000428326,;BAG6,missense_variant,p.Leu192Phe,ENST00000451898,;BAG6,missense_variant,p.Leu210Phe,ENST00000433828,;BAG6,missense_variant,p.Leu210Phe,ENST00000452994,;BAG6,missense_variant,p.Leu192Phe,ENST00000456622,;BAG6,missense_variant,p.Leu192Phe,ENST00000434444,;BAG6,missense_variant,p.Leu192Phe,ENST00000424176,;BAG6,missense_variant,p.Leu192Phe,ENST00000441054,;APOM,upstream_gene_variant,,ENST00000375918,;BAG6,downstream_gene_variant,,ENST00000456286,;BAG6,upstream_gene_variant,,ENST00000438149,;APOM,upstream_gene_variant,,ENST00000375920,NM_001256169.1;BAG6,upstream_gene_variant,,ENST00000453833,;BAG6,downstream_gene_variant,,ENST00000454165,;BAG6,upstream_gene_variant,,ENST00000470875,;BAG6,upstream_gene_variant,,ENST00000469182,;BAG6,upstream_gene_variant,,ENST00000465348,;BAG6,upstream_gene_variant,,ENST00000462682,; G ENST00000375964 Transcript missense_variant 962/3815 648/3399 216/1132 L/F ttG/ttC 1 -1 BAG6 HGNC HGNC:13919 protein_coding YES CCDS47403.1 ENSP00000365131 P46379 UPI000047029D NM_004639.3 tolerated(0.09) 7/25 hmmpanther:PTHR15204:SF0,hmmpanther:PTHR15204 MODERATE 1 SNV 1 1 PASS . . 0 201 7 2 0 0 0 0 -19.99525 0.9999086 1 1 1 0 G 3 3 46 31647749 31647749 C G 1 0 0 0 0 1 0 0 0 1449 825 29 4 4 BAG6 6 31647749 Missense_Mutation SNP C C3N-00294_T 292325 31647749 139158230 479 13251 HSPA1A 0 . GRCh38 6 31815975 31815975 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.219G>A p.= p.L73L ENST00000375651 1/1 46 37 9 74 74 0 strelka-varscan-mutect HSPA1A,synonymous_variant,p.=,ENST00000375651,NM_005345.5;HSPA1A,intron_variant,,ENST00000608703,;HSPA1L,upstream_gene_variant,,ENST00000375654,NM_005527.3; A ENST00000375651 Transcript synonymous_variant 512/2483 219/1926 73/641 L ctG/ctA 1 1 HSPA1A HGNC HGNC:5232 protein_coding YES CCDS34414.1 ENSP00000364802 P0DMV8 A8K5I0 UPI0000000C40 NM_005345.5 1/1 hmmpanther:PTHR19375:SF236,hmmpanther:PTHR19375,Gene3D:3.30.30.30,Pfam_domain:PF00012,Superfamily_domains:SSF53067 LOW SNV 1 PASS . . 0 204 6 0 0 0 0 0 -19.99383 1 1 1 1 0 A 2 1 46 31815975 31815975 G A 1 0 0 0 0 0 0 0 1 7304 1277 45 3 3 HSPA1A 6 31815975 Silent SNP G C3N-00294_T 168226 31815975 138990004 480 13252 HSPA1A 0 . GRCh38 6 31817406 31817406 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1650G>A p.= p.K550K ENST00000375651 1/1 352 284 68 306 306 0 strelka-varscan-mutect HSPA1A,synonymous_variant,p.=,ENST00000375651,NM_005345.5;HSPA1A,synonymous_variant,p.=,ENST00000608703,;HSPA1L,upstream_gene_variant,,ENST00000375654,NM_005527.3; A ENST00000375651 Transcript synonymous_variant 1943/2483 1650/1926 550/641 K aaG/aaA 1 1 HSPA1A HGNC HGNC:5232 protein_coding YES CCDS34414.1 ENSP00000364802 P0DMV8 A8K5I0 UPI0000000C40 NM_005345.5 1/1 hmmpanther:PTHR19375:SF236,hmmpanther:PTHR19375,Pfam_domain:PF00012,Gene3D:1.20.1270.10,Superfamily_domains:SSF100934 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 31817406 31817406 G A 1 0 0 0 0 0 0 0 1 7304 933 33 3 3 HSPA1A 6 31817406 Silent SNP G C3N-00294_T 1431 31817406 138988573 481 13253 SKIV2L 0 . GRCh38 6 31962565 31962565 + Missense_Mutation SNP C C G rs866962006 C3N-00294_T C3N-00294_N C C c.1191C>G p.Ile397Met p.I397M ENST00000375394 11/28 101 75 26 93 93 0 strelka-varscan-mutect SKIV2L,missense_variant,p.Ile397Met,ENST00000375394,NM_006929.4;NELFE,upstream_gene_variant,,ENST00000375429,NM_002904.5;NELFE,upstream_gene_variant,,ENST00000375425,;NELFE,upstream_gene_variant,,ENST00000444811,;NELFE,upstream_gene_variant,,ENST00000441998,;NELFE,upstream_gene_variant,,ENST00000454913,;NELFE,upstream_gene_variant,,ENST00000436289,;NELFE,upstream_gene_variant,,ENST00000426722,;SKIV2L,downstream_gene_variant,,ENST00000628157,;NELFE,upstream_gene_variant,,ENST00000625905,;SKIV2L,downstream_gene_variant,,ENST00000488648,;SKIV2L,upstream_gene_variant,,ENST00000461915,;SKIV2L,3_prime_UTR_variant,,ENST00000474839,;SKIV2L,3_prime_UTR_variant,,ENST00000461073,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000465703,;SKIV2L,non_coding_transcript_exon_variant,,ENST00000466290,;NELFE,upstream_gene_variant,,ENST00000488426,;NELFE,upstream_gene_variant,,ENST00000492185,;NELFE,upstream_gene_variant,,ENST00000481121,;SKIV2L,upstream_gene_variant,,ENST00000484835,;SKIV2L,upstream_gene_variant,,ENST00000494058,;SKIV2L,downstream_gene_variant,,ENST00000492900,;NELFE,upstream_gene_variant,,ENST00000492539,;NELFE,upstream_gene_variant,,ENST00000491139,;NELFE,upstream_gene_variant,,ENST00000494956,; G ENST00000375394 Transcript missense_variant 1304/3894 1191/3741 397/1246 I/M atC/atG rs866962006,COSM3830150,COSM3830151 1 1 SKIV2L HGNC HGNC:10898 protein_coding YES CCDS4731.1 ENSP00000364543 Q15477 UPI000045740B NM_006929.4 deleterious(0) 11/28 Gene3D:3.40.50.300,Pfam_domain:PF00270,PIRSF_domain:PIRSF005198,PROSITE_profiles:PS51192,SMART_domains:SM00487,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs866962006 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 31962565 31962565 C G 1 0 0 0 0 1 0 0 0 14622 816 29 4 4 SKIV2L 6 31962565 Missense_Mutation SNP C C3N-00294_T 145159 31962565 138843414 482 13254 TAP1 0 . GRCh38 6 32853579 32853579 + Missense_Mutation SNP G G C rs773916016 C3N-00294_T C3N-00294_N G G c.238C>G p.Leu80Val p.L80V ENST00000354258 1/11 256 204 52 350 350 0 strelka-varscan-mutect TAP1,missense_variant,p.Leu80Val,ENST00000354258,NM_000593.5,NM_001292022.1;PSMB9,intron_variant,,ENST00000395330,;PSMB9,intron_variant,,ENST00000414474,;PSMB9,upstream_gene_variant,,ENST00000374859,NM_002800.4;PSMB9,upstream_gene_variant,,ENST00000464863,;TAP1,upstream_gene_variant,,ENST00000486332,;PSMB9,upstream_gene_variant,,ENST00000467593,; C ENST00000354258 Transcript missense_variant 400/2959 238/2427 80/808 L/V Ctc/Gtc rs773916016 1 -1 TAP1 HGNC HGNC:43 protein_coding YES CCDS4758.1 ENSP00000346206 Q03518 A0A0S2Z5A6 UPI000002D4E6 NM_000593.5,NM_001292022.1 tolerated_low_confidence(0.13) 1/11 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PIRSF_domain:PIRSF002773 MODERATE 1 SNV 1 1 PASS rs773916016 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 32853579 32853579 G C 1 0 0 0 0 1 0 0 0 15949 942 33 4 4 TAP1 6 32853579 Missense_Mutation SNP G C3N-00294_T 891014 32853579 137952400 483 13255 WDR46 0 . GRCh38 6 33288399 33288399 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.432C>G p.Ile144Met p.I144M ENST00000374617 4/15 208 155 53 213 213 0 strelka-varscan-mutect WDR46,missense_variant,p.Ile144Met,ENST00000374617,NM_001164267.1,NM_005452.5;WDR46,missense_variant,p.Ile79Met,ENST00000444176,;RGL2,downstream_gene_variant,,ENST00000497454,NM_004761.4,NM_001243738.1;PFDN6,upstream_gene_variant,,ENST00000463584,;PFDN6,upstream_gene_variant,,ENST00000395131,;PFDN6,upstream_gene_variant,,ENST00000374606,NM_001185181.2;PFDN6,upstream_gene_variant,,ENST00000374607,NM_014260.3,NM_001265595.1,NM_001265596.1;PFDN6,upstream_gene_variant,,ENST00000374610,;PFDN6,upstream_gene_variant,,ENST00000622807,;WDR46,upstream_gene_variant,,ENST00000622788,;WDR46,non_coding_transcript_exon_variant,,ENST00000477718,;WDR46,non_coding_transcript_exon_variant,,ENST00000468157,;RGL2,downstream_gene_variant,,ENST00000437840,;RGL2,downstream_gene_variant,,ENST00000491168,;RGL2,downstream_gene_variant,,ENST00000471319,;B3GALT4,downstream_gene_variant,,ENST00000606990,;WDR46,non_coding_transcript_exon_variant,,ENST00000481025,;RGL2,downstream_gene_variant,,ENST00000483151,;RGL2,downstream_gene_variant,,ENST00000476616,;WDR46,upstream_gene_variant,,ENST00000489905,;PFDN6,upstream_gene_variant,,ENST00000491382,;PFDN6,upstream_gene_variant,,ENST00000395134,;WDR46,upstream_gene_variant,,ENST00000488944,; C ENST00000374617 Transcript missense_variant 789/2358 432/1833 144/610 I/M atC/atG 1 -1 WDR46 HGNC HGNC:13923 protein_coding YES CCDS4772.1 ENSP00000363746 O15213 UPI000045741F NM_001164267.1,NM_005452.5 tolerated(0.1) 4/15 hmmpanther:PTHR14085:SF3,hmmpanther:PTHR14085 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 33288399 33288399 G C 1 0 0 0 0 1 0 0 0 17859 1280 45 4 4 WDR46 6 33288399 Missense_Mutation SNP G C3N-00294_T 434820 33288399 137517580 484 13256 ZBTB22 0 . GRCh38 6 33315531 33315531 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.1386G>T p.= p.G462G ENST00000431845 2/2 126 106 20 156 156 0 strelka-varscan-mutect ZBTB22,synonymous_variant,p.=,ENST00000431845,NM_005453.4;ZBTB22,synonymous_variant,p.=,ENST00000418724,NM_001145338.1;TAPBP,upstream_gene_variant,,ENST00000434618,NM_003190.4;DAXX,downstream_gene_variant,,ENST00000374542,NM_001141969.1,NM_001141970.1,NM_001350.4;DAXX,downstream_gene_variant,,ENST00000266000,;DAXX,downstream_gene_variant,,ENST00000620164,;DAXX,downstream_gene_variant,,ENST00000414083,NM_001254717.1;TAPBP,upstream_gene_variant,,ENST00000426633,NM_172208.2;TAPBP,upstream_gene_variant,,ENST00000475304,;TAPBP,upstream_gene_variant,,ENST00000489157,NM_172209.2;TAPBP,upstream_gene_variant,,ENST00000456592,;TAPBP,upstream_gene_variant,,ENST00000467025,;ZBTB22,downstream_gene_variant,,ENST00000441117,;DAXX,downstream_gene_variant,,ENST00000477162,;DAXX,downstream_gene_variant,,ENST00000468536,;TAPBP,upstream_gene_variant,,ENST00000480730,;TAPBP,upstream_gene_variant,,ENST00000437116,;TAPBP,upstream_gene_variant,,ENST00000476333,;DAXX,downstream_gene_variant,,ENST00000490173,; A ENST00000431845 Transcript synonymous_variant 1538/2651 1386/1905 462/634 G ggG/ggT 1 -1 ZBTB22 HGNC HGNC:13085 protein_coding YES CCDS4775.1 ENSP00000407545 O15209 UPI000013C34E NM_005453.4 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 33315531 33315531 C A 1 0 0 0 0 0 0 0 1 18099 842 30 2 2 ZBTB22 6 33315531 Silent SNP C C3N-00294_T 27132 33315531 137490448 485 13257 SYNGAP1 0 . GRCh38 6 33443361 33443361 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2809G>A p.Asp937Asn p.D937N ENST00000629380 15/19 296 245 51 322 322 0 strelka-varscan-mutect SYNGAP1,missense_variant,p.Asp937Asn,ENST00000629380,NM_006772.2;SYNGAP1,missense_variant,p.Asp937Asn,ENST00000418600,;SYNGAP1,missense_variant,p.Asp878Asn,ENST00000428982,;SYNGAP1,missense_variant,p.Asp937Asn,ENST00000628646,;SYNGAP1,missense_variant,p.Asp923Asn,ENST00000449372,;SYNGAP1,downstream_gene_variant,,ENST00000579078,;XXbac-BPG294E21.9,intron_variant,,ENST00000630418,;SYNGAP1,downstream_gene_variant,,ENST00000636640,;SYNGAP1,downstream_gene_variant,,ENST00000636193,;SYNGAP1,upstream_gene_variant,,ENST00000636436,;SYNGAP1,downstream_gene_variant,,ENST00000637671,;SYNGAP1,missense_variant,p.Asp922Asn,ENST00000293748,;SYNGAP1,3_prime_UTR_variant,,ENST00000638142,;SYNGAP1,downstream_gene_variant,,ENST00000479510,;SYNGAP1,upstream_gene_variant,,ENST00000470232,; A ENST00000629380 Transcript missense_variant 3004/9862 2809/4032 937/1343 D/N Gat/Aat 1 1 SYNGAP1 HGNC HGNC:11497 protein_coding YES CCDS34434.2 ENSP00000486463 Q96PV0 UPI0000470C44 NM_006772.2 tolerated(0.71) 15/19 hmmpanther:PTHR10194:SF25,hmmpanther:PTHR10194,Pfam_domain:PF12004 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33443361 33443361 G A 1 0 0 0 0 1 0 0 0 15841 1290 45 3 3 SYNGAP1 6 33443361 Missense_Mutation SNP G C3N-00294_T 127830 33443361 137362618 486 13258 SLC26A8 0 . GRCh38 6 35955318 35955318 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2066C>G p.Ser689Ter p.S689* ENST00000490799 17/20 361 303 58 441 441 0 strelka-varscan-mutect SLC26A8,stop_gained,p.Ser689Ter,ENST00000490799,NM_052961.3;SLC26A8,stop_gained,p.Ser689Ter,ENST00000355574,NM_001193476.1;SLC26A8,stop_gained,p.Ser584Ter,ENST00000394602,NM_138718.2;SLC26A8,stop_gained,p.Ser241Ter,ENST00000465492,;SLC26A8,non_coding_transcript_exon_variant,,ENST00000466805,;SLC26A8,downstream_gene_variant,,ENST00000486155,; C ENST00000490799 Transcript stop_gained 2420/3653 2066/2913 689/970 S/* tCa/tGa 1 -1 SLC26A8 HGNC HGNC:14468 protein_coding YES CCDS4813.1 ENSP00000417638 Q96RN1 A0A024RCV0 UPI00000739C0 NM_052961.3 17/20 Pfam_domain:PF01740,PROSITE_profiles:PS50801 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 35955318 35955318 G C 1 0 0 0 0 0 1 0 0 14793 1294 45 4 4 SLC26A8 6 35955318 Nonsense_Mutation SNP G C3N-00294_T 2511957 35955318 134850661 487 13259 PNPLA1 0 . GRCh38 6 36306372 36306372 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.1465G>T p.Val489Leu p.V489L ENST00000394571 7/8 95 66 29 80 80 0 strelka-varscan-mutect PNPLA1,missense_variant,p.Val394Leu,ENST00000388715,NM_173676.2;PNPLA1,missense_variant,p.Val398Leu,ENST00000636260,;PNPLA1,missense_variant,p.Val490Leu,ENST00000457797,;PNPLA1,missense_variant,p.Val489Leu,ENST00000394571,NM_001145717.1;PNPLA1,missense_variant,p.Val403Leu,ENST00000312917,NM_001145716.2; T ENST00000394571 Transcript missense_variant 1465/1599 1465/1599 489/532 V/L Gta/Tta COSM4434084,COSM4434085,COSM4434086 1 1 PNPLA1 HGNC HGNC:21246 protein_coding YES CCDS54997.1 ENSP00000378072 Q8N8W4 B8XXQ3 UPI000189560E NM_001145717.1 tolerated_low_confidence(0.41) 7/8 hmmpanther:PTHR12406,hmmpanther:PTHR12406:SF23 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1327123712 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 36306372 36306372 G T 1 0 0 0 0 1 0 0 0 12272 1391 48 2 2 PNPLA1 6 36306372 Missense_Mutation SNP G C3N-00294_T 351054 36306372 134499607 488 13260 FGD2 0 . GRCh38 6 37013703 37013703 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.622G>C p.Glu208Gln p.E208Q ENST00000274963 5/16 173 141 32 219 219 0 strelka-varscan-mutect FGD2,missense_variant,p.Glu208Gln,ENST00000274963,NM_173558.3;FGD2,3_prime_UTR_variant,,ENST00000373535,;FGD2,non_coding_transcript_exon_variant,,ENST00000493635,;FGD2,non_coding_transcript_exon_variant,,ENST00000494343,;FGD2,non_coding_transcript_exon_variant,,ENST00000464083,;FGD2,non_coding_transcript_exon_variant,,ENST00000470273,;FGD2,downstream_gene_variant,,ENST00000489356,;FGD2,downstream_gene_variant,,ENST00000487975,;FGD2,downstream_gene_variant,,ENST00000459781,;FGD2,downstream_gene_variant,,ENST00000497659,; C ENST00000274963 Transcript missense_variant 793/3046 622/1968 208/655 E/Q Gag/Cag 1 1 FGD2 HGNC HGNC:3664 protein_coding YES CCDS4829.1 ENSP00000274963 Q7Z6J4 UPI00001A9477 NM_173558.3 deleterious(0.02) 5/16 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF82,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 37013703 37013703 G C 1 0 0 0 0 1 0 0 0 5697 1291 45 4 4 FGD2 6 37013703 Missense_Mutation SNP G C3N-00294_T 707331 37013703 133792276 489 13261 DNAH8 0 . GRCh38 6 38873111 38873111 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.7443C>T p.= p.I2481I ENST00000327475 51/93 314 252 62 305 305 0 strelka-varscan-mutect DNAH8,synonymous_variant,p.=,ENST00000327475,NM_001206927.1;DNAH8,synonymous_variant,p.=,ENST00000359357,;DNAH8,synonymous_variant,p.=,ENST00000449981,;DNAH8,downstream_gene_variant,,ENST00000394393,; T ENST00000327475 Transcript synonymous_variant 7552/14360 7443/14124 2481/4707 I atC/atT 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 51/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 38873111 38873111 C T 1 0 0 0 0 0 0 0 1 4422 816 29 3 3 DNAH8 6 38873111 Silent SNP C C3N-00294_T 1859408 38873111 131932868 490 13262 KLC4 0 . GRCh38 6 43072838 43072838 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1557C>G p.Ile519Met p.I519M ENST00000259708 13/16 212 172 40 204 204 0 strelka-varscan-mutect KLC4,missense_variant,p.Ile501Met,ENST00000394056,NM_201522.2;KLC4,missense_variant,p.Ile519Met,ENST00000259708,NM_201523.2;KLC4,missense_variant,p.Ile501Met,ENST00000479388,NM_001289034.1;KLC4,missense_variant,p.Ile501Met,ENST00000347162,NM_201521.2;KLC4,missense_variant,p.Ile424Met,ENST00000453940,NM_001289035.1;PTK7,upstream_gene_variant,,ENST00000230419,NM_002821.4;PTK7,upstream_gene_variant,,ENST00000345201,NM_152880.3;PTK7,upstream_gene_variant,,ENST00000352931,NM_152882.3;PTK7,upstream_gene_variant,,ENST00000349241,NM_152881.3;PTK7,upstream_gene_variant,,ENST00000481273,NM_001270398.1;PTK7,upstream_gene_variant,,ENST00000471863,;PTK7,upstream_gene_variant,,ENST00000476760,;RP11-387M24.5,downstream_gene_variant,,ENST00000606123,;KLC4,3_prime_UTR_variant,,ENST00000467906,;KLC4,3_prime_UTR_variant,,ENST00000469987,;PTK7,upstream_gene_variant,,ENST00000487673,;PTK7,upstream_gene_variant,,ENST00000470019,;PTK7,upstream_gene_variant,,ENST00000230418,;KLC4,downstream_gene_variant,,ENST00000463063,;KLC4,upstream_gene_variant,,ENST00000486439,;KLC4,upstream_gene_variant,,ENST00000463168,; G ENST00000259708 Transcript missense_variant 1910/2688 1557/1914 519/637 I/M atC/atG 1 1 KLC4 HGNC HGNC:21624 protein_coding YES CCDS4882.1 ENSP00000259708 Q9NSK0 UPI000023C3DA NM_201523.2 tolerated(0.05) 13/16 hmmpanther:PTHR19959:SF139,hmmpanther:PTHR19959 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 43072838 43072838 C G 1 0 0 0 0 1 0 0 0 8201 816 29 4 4 KLC4 6 43072838 Missense_Mutation SNP C C3N-00294_T 4199727 43072838 127733141 491 13263 TTBK1 0 . GRCh38 6 43255838 43255838 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.843C>T p.= p.F281F ENST00000259750 9/15 153 113 40 180 180 0 strelka-varscan-mutect TTBK1,synonymous_variant,p.=,ENST00000259750,NM_032538.1;TTBK1,synonymous_variant,p.=,ENST00000304139,; T ENST00000259750 Transcript synonymous_variant 926/6932 843/3966 281/1321 F ttC/ttT 1 1 TTBK1 HGNC HGNC:19140 protein_coding YES CCDS34455.1 ENSP00000259750 Q5TCY1 UPI000041512B NM_032538.1 9/15 PROSITE_profiles:PS50011,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF130,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 43255838 43255838 C T 1 0 0 0 0 0 0 0 1 17186 825 29 3 3 TTBK1 6 43255838 Silent SNP C C3N-00294_T 183000 43255838 127550141 492 13264 VEGFA 0 . GRCh38 6 43774383 43774383 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.649C>T p.His217Tyr p.H217Y ENST00000611736 2/8 408 312 96 390 390 0 strelka-varscan-mutect VEGFA,missense_variant,p.His217Tyr,ENST00000611736,NM_001025366.2;VEGFA,missense_variant,p.His217Tyr,ENST00000621747,NM_001317010.1,NM_001025368.2;VEGFA,missense_variant,p.His217Tyr,ENST00000372067,;VEGFA,missense_variant,p.His217Tyr,ENST00000615393,NM_001025370.2;VEGFA,missense_variant,p.His217Tyr,ENST00000617771,NM_001171622.1;VEGFA,missense_variant,p.His217Tyr,ENST00000372064,;VEGFA,missense_variant,p.His37Tyr,ENST00000372077,NM_001171628.1;VEGFA,missense_variant,p.His217Tyr,ENST00000425836,NM_003376.5;VEGFA,missense_variant,p.His217Tyr,ENST00000372055,;VEGFA,missense_variant,p.His37Tyr,ENST00000520948,NM_001171624.1;VEGFA,missense_variant,p.His217Tyr,ENST00000413642,NM_001025367.2;VEGFA,missense_variant,p.His217Tyr,ENST00000482630,NM_001033756.2;VEGFA,missense_variant,p.His217Tyr,ENST00000417285,NM_001025369.2;VEGFA,missense_variant,p.His9Tyr,ENST00000230480,NM_001287044.1;VEGFA,missense_variant,p.His189Tyr,ENST00000519767,NM_001204384.1,NM_001204385.1;VEGFA,missense_variant,p.His217Tyr,ENST00000324450,;VEGFA,missense_variant,p.His37Tyr,ENST00000523950,NM_001171626.1;VEGFA,missense_variant,p.His37Tyr,ENST00000523873,NM_001171623.1;VEGFA,missense_variant,p.His37Tyr,ENST00000518689,NM_001171625.1;VEGFA,missense_variant,p.His37Tyr,ENST00000518824,NM_001171629.1;VEGFA,missense_variant,p.His37Tyr,ENST00000523125,NM_001171627.1;VEGFA,missense_variant,p.His37Tyr,ENST00000457104,NM_001171630.1;VEGFA,missense_variant,p.His11Tyr,ENST00000520265,;RP1-261G23.7,upstream_gene_variant,,ENST00000607600,;VEGFA,non_coding_transcript_exon_variant,,ENST00000480614,;VEGFA,non_coding_transcript_exon_variant,,ENST00000476772,;VEGFA,non_coding_transcript_exon_variant,,ENST00000518538,;VEGFA,non_coding_transcript_exon_variant,,ENST00000512683,;VEGFA,upstream_gene_variant,,ENST00000497139,;VEGFA,upstream_gene_variant,,ENST00000493786,; T ENST00000611736 Transcript missense_variant 1147/3659 649/1239 217/412 H/Y Cat/Tat 1 1 VEGFA HGNC HGNC:12680 protein_coding YES CCDS34457.1 ENSP00000478570 J3KPA4 UPI0000D61463 NM_001025366.2 deleterious(0.02) 2/8 hmmpanther:PTHR12025,hmmpanther:PTHR12025:SF5,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 43774383 43774383 C T 1 0 0 0 0 1 0 0 0 17695 826 29 3 3 VEGFA 6 43774383 Missense_Mutation SNP C C3N-00294_T 518545 43774383 127031596 493 13265 TDRD6 0 . GRCh38 6 46692134 46692134 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4006G>C p.Glu1336Gln p.E1336Q ENST00000316081 1/4 58 49 9 82 82 0 strelka-varscan-mutect TDRD6,missense_variant,p.Glu1336Gln,ENST00000544460,NM_001168359.1;TDRD6,missense_variant,p.Glu1336Gln,ENST00000316081,NM_001010870.2;TDRD6,upstream_gene_variant,,ENST00000450697,;RP11-446F17.3,upstream_gene_variant,,ENST00000434329,;RP11-446F17.3,upstream_gene_variant,,ENST00000422284,;RP11-446F17.3,upstream_gene_variant,,ENST00000571590,; C ENST00000316081 Transcript missense_variant 4006/6817 4006/6291 1336/2096 E/Q Gag/Cag 1 1 TDRD6 HGNC HGNC:21339 protein_coding YES CCDS34470.1 ENSP00000346065 O60522 UPI0000251E8A NM_001010870.2 deleterious(0) 1/4 hmmpanther:PTHR22948:SF15,hmmpanther:PTHR22948,Pfam_domain:PF00567,Gene3D:2.30.30.140,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 46692134 46692134 G C 1 0 0 0 0 1 0 0 0 16144 943 33 4 4 TDRD6 6 46692134 Missense_Mutation SNP G C3N-00294_T 2917751 46692134 124113845 494 13266 EFHC1 0 . GRCh38 6 52424146 52424146 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.264G>A p.= p.A88A ENST00000371068 2/11 306 243 63 344 344 0 strelka-varscan-mutect EFHC1,synonymous_variant,p.=,ENST00000371068,NM_018100.3;EFHC1,synonymous_variant,p.=,ENST00000538167,;EFHC1,synonymous_variant,p.=,ENST00000637353,;EFHC1,synonymous_variant,p.=,ENST00000636107,;EFHC1,synonymous_variant,p.=,ENST00000635996,;EFHC1,synonymous_variant,p.=,ENST00000636489,;EFHC1,synonymous_variant,p.=,ENST00000636702,;EFHC1,synonymous_variant,p.=,ENST00000637089,;EFHC1,synonymous_variant,p.=,ENST00000636954,NM_001172420.1;EFHC1,synonymous_variant,p.=,ENST00000637263,;EFHC1,synonymous_variant,p.=,ENST00000636379,;EFHC1,synonymous_variant,p.=,ENST00000637315,;EFHC1,5_prime_UTR_variant,,ENST00000635984,;EFHC1,5_prime_UTR_variant,,ENST00000635760,;EFHC1,5_prime_UTR_variant,,ENST00000636566,;EFHC1,5_prime_UTR_variant,,ENST00000638075,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637849,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637892,;EFHC1,non_coding_transcript_exon_variant,,ENST00000636311,;EFHC1,non_coding_transcript_exon_variant,,ENST00000638140,;EFHC1,non_coding_transcript_exon_variant,,ENST00000491749,;EFHC1,non_coding_transcript_exon_variant,,ENST00000635843,;EFHC1,synonymous_variant,p.=,ENST00000480623,;EFHC1,synonymous_variant,p.=,ENST00000635812,;EFHC1,synonymous_variant,p.=,ENST00000635866,;EFHC1,synonymous_variant,p.=,ENST00000637200,;EFHC1,synonymous_variant,p.=,ENST00000635963,;EFHC1,non_coding_transcript_exon_variant,,ENST00000637340,;EFHC1,non_coding_transcript_exon_variant,,ENST00000635911,;EFHC1,intron_variant,,ENST00000637602,; A ENST00000371068 Transcript synonymous_variant 479/6987 264/1923 88/640 A gcG/gcA 1 1 EFHC1 HGNC HGNC:16406 protein_coding YES CCDS4942.1 ENSP00000360107 Q5JVL4 B2CKC5 UPI0000141099 NM_018100.3 2/11 hmmpanther:PTHR12086,hmmpanther:PTHR12086:SF9 LOW 1 SNV 1 1 PASS rs1455166533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 52424146 52424146 G A 1 0 0 0 0 0 0 0 1 4781 1074 38 1 1 EFHC1 6 52424146 Silent SNP G C3N-00294_T 5732012 52424146 118381833 495 13267 KLHL31 0 . GRCh38 6 53652020 53652020 + Missense_Mutation SNP C C G rs762220452 C3N-00294_T C3N-00294_N C C c.1483G>C p.Glu495Gln p.E495Q ENST00000370905 3/3 111 95 16 127 127 0 strelka-varscan-mutect KLHL31,missense_variant,p.Glu495Gln,ENST00000370905,NM_001003760.4;KLHL31,missense_variant,p.Glu495Gln,ENST00000407079,; G ENST00000370905 Transcript missense_variant 1624/5743 1483/1905 495/634 E/Q Gag/Cag rs762220452 1 -1 KLHL31 HGNC HGNC:21353 protein_coding YES CCDS34478.1 ENSP00000359942 Q9H511 UPI000006D624 NM_001003760.4 tolerated(0.7) 3/3 hmmpanther:PTHR24412:SF247,hmmpanther:PTHR24412,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS rs762220452 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 53652020 53652020 C G 1 0 0 0 0 1 0 0 0 8250 864 30 4 4 KLHL31 6 53652020 Missense_Mutation SNP C C3N-00294_T 1227874 53652020 117153959 496 13268 COL21A1 0 . GRCh38 6 56077535 56077535 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.1851C>A p.= p.G617G ENST00000244728 18/30 180 96 84 204 203 1 strelka-varscan-mutect COL21A1,synonymous_variant,p.=,ENST00000244728,NM_001318751.1,NM_030820.3;COL21A1,synonymous_variant,p.=,ENST00000370819,NM_001318752.1;COL21A1,synonymous_variant,p.=,ENST00000535941,;COL21A1,non_coding_transcript_exon_variant,,ENST00000467045,;COL21A1,non_coding_transcript_exon_variant,,ENST00000484987,;COL21A1,3_prime_UTR_variant,,ENST00000488912,;COL21A1,non_coding_transcript_exon_variant,,ENST00000461489,; T ENST00000244728 Transcript synonymous_variant 2249/4339 1851/2874 617/957 G ggC/ggA 1 -1 COL21A1 HGNC HGNC:17025 protein_coding YES CCDS55025.1 ENSP00000244728 Q96P44 A0A158RFW1 UPI0000071DFE NM_001318751.1,NM_030820.3 18/30 hmmpanther:PTHR24023,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 56077535 56077535 G T 1 0 0 0 0 0 0 0 1 3468 1190 42 2 2 COL21A1 6 56077535 Silent SNP G C3N-00294_T 2425515 56077535 114728444 497 13269 EYS 0 . GRCh38 6 64591103 64591103 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.4764G>A p.Met1588Ile p.M1588I ENST00000370621 26/44 309 243 66 349 349 0 strelka-varscan-mutect EYS,missense_variant,p.Met1588Ile,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Met1588Ile,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; T ENST00000370621 Transcript missense_variant 5291/10485 4764/9498 1588/3165 M/I atG/atA COSM5598274 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious_low_confidence(0) 26/44 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 64591103 64591103 C T 1 0 0 0 0 1 0 0 0 5200 826 29 3 3 EYS 6 64591103 Missense_Mutation SNP C C3N-00294_T 8513568 64591103 106214876 498 13270 IRAK1BP1 0 . GRCh38 6 78885381 78885381 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.319G>C p.Glu107Gln p.E107Q ENST00000369940 2/4 78 65 13 127 127 0 strelka-varscan-mutect IRAK1BP1,missense_variant,p.Glu107Gln,ENST00000369940,NM_001010844.3;IRAK1BP1,missense_variant,p.Glu20Gln,ENST00000607739,;IRAK1BP1,missense_variant,p.Glu97Gln,ENST00000606868,; C ENST00000369940 Transcript missense_variant 424/5656 319/783 107/260 E/Q Gaa/Caa 1 1 IRAK1BP1 HGNC HGNC:17368 protein_coding YES CCDS34488.1 ENSP00000358956 Q5VVH5 UPI000016049F NM_001010844.3 tolerated(0.09) 2/4 Pfam_domain:PF04402,hmmpanther:PTHR18842 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 78885381 78885381 G C 1 0 0 0 0 1 0 0 0 7728 956 33 4 4 IRAK1BP1 6 78885381 Missense_Mutation SNP G C3N-00294_T 14294278 78885381 91920598 499 13271 PHIP 0 . GRCh38 6 78941223 78941223 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.4936G>C p.Glu1646Gln p.E1646Q ENST00000275034 40/40 232 199 33 278 278 0 strelka-varscan-mutect PHIP,missense_variant,p.Glu1646Gln,ENST00000275034,NM_017934.5;PHIP,non_coding_transcript_exon_variant,,ENST00000479165,;IRAK1BP1,intron_variant,,ENST00000606868,; G ENST00000275034 Transcript missense_variant 5104/10460 4936/5466 1646/1821 E/Q Gaa/Caa 1 -1 PHIP HGNC HGNC:15673 protein_coding YES CCDS4987.1 ENSP00000275034 Q8WWQ0 UPI000013DA40 NM_017934.5 deleterious_low_confidence(0.02) 40/40 hmmpanther:PTHR16266,hmmpanther:PTHR16266:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 78941223 78941223 C G 1 0 0 0 0 1 0 0 0 11930 922 32 4 4 PHIP 6 78941223 Missense_Mutation SNP C C3N-00294_T 55842 78941223 91864756 500 13272 CYB5R4 0 . GRCh38 6 83955449 83955449 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1498G>A p.Glu500Lys p.E500K ENST00000369681 15/16 51 42 9 51 51 0 strelka-varscan-mutect CYB5R4,missense_variant,p.Glu500Lys,ENST00000369681,NM_016230.3;CYB5R4,downstream_gene_variant,,ENST00000479164,; A ENST00000369681 Transcript missense_variant 1638/9252 1498/1566 500/521 E/K Gaa/Aaa 1 1 CYB5R4 HGNC HGNC:20147 protein_coding YES CCDS5000.2 ENSP00000358695 Q7L1T6 UPI000056D3CE NM_016230.3 tolerated(0.17) 15/16 Gene3D:3.40.50.80,Pfam_domain:PF00175,hmmpanther:PTHR19370,hmmpanther:PTHR19370:SF122,Superfamily_domains:SSF52343 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 83955449 83955449 G A 1 0 0 0 0 1 0 0 0 3933 943 33 3 3 CYB5R4 6 83955449 Missense_Mutation SNP G C3N-00294_T 5014226 83955449 86850530 501 13273 MDN1 0 . GRCh38 6 89688618 89688618 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.11214C>T p.= p.V3738V ENST00000369393 66/102 158 120 38 181 181 0 strelka-varscan-mutect MDN1,synonymous_variant,p.=,ENST00000369393,NM_014611.2;MDN1,synonymous_variant,p.=,ENST00000629399,; A ENST00000369393 Transcript synonymous_variant 11330/18413 11214/16791 3738/5596 V gtC/gtT 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 66/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 89688618 89688618 G A 1 0 0 0 0 0 0 0 1 9353 1277 45 3 3 MDN1 6 89688618 Silent SNP G C3N-00294_T 5733169 89688618 81117361 502 13274 SMPD2 0 . GRCh38 6 109441451 109441451 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.145G>A p.Glu49Lys p.E49K ENST00000258052 2/10 252 206 46 301 301 0 strelka-varscan-mutect SMPD2,missense_variant,p.Glu49Lys,ENST00000258052,NM_003080.2;PPIL6,upstream_gene_variant,,ENST00000521072,NM_173672.4;PPIL6,upstream_gene_variant,,ENST00000424445,NM_001286360.1;MICAL1,downstream_gene_variant,,ENST00000630715,NM_001286613.1;MICAL1,downstream_gene_variant,,ENST00000358807,NM_022765.3;MICAL1,downstream_gene_variant,,ENST00000358577,NM_001159291.1;PPIL6,upstream_gene_variant,,ENST00000440797,NM_001111298.2;PPIL6,upstream_gene_variant,,ENST00000417394,;SMPD2,upstream_gene_variant,,ENST00000458487,;PPIL6,upstream_gene_variant,,ENST00000520723,NM_001286361.1;PPIL6,upstream_gene_variant,,ENST00000518648,;MICAL1,downstream_gene_variant,,ENST00000465904,;MICAL1,downstream_gene_variant,,ENST00000456101,;PPIL6,upstream_gene_variant,,ENST00000447468,;SMPD2,upstream_gene_variant,,ENST00000439615,; A ENST00000258052 Transcript missense_variant,splice_region_variant 504/1645 145/1272 49/423 E/K Gag/Aag 1 1 SMPD2 HGNC HGNC:11121 protein_coding YES CCDS5075.1 ENSP00000258052 O60906 UPI000013CFAC NM_003080.2 deleterious(0) 2/10 hmmpanther:PTHR12393:SF6,hmmpanther:PTHR12393,Gene3D:3.60.10.10,Pfam_domain:PF03372,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 109441451 109441451 G A 1 0 0 0 0 1 0 0 0 15126 1188 41 3 3 SMPD2 6 109441451 Missense_Mutation SNP G C3N-00294_T 19752833 109441451 61364528 503 13275 TRAPPC3L 0 . GRCh38 6 116545496 116545496 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.19C>A p.= p.R7R ENST00000368602 1/5 107 73 34 132 132 0 strelka-varscan-mutect TRAPPC3L,synonymous_variant,p.=,ENST00000368602,NM_001139444.2;FAM26D,intron_variant,,ENST00000368597,NM_001256889.1,NM_153036.3;FAM26D,intron_variant,,ENST00000405399,NM_001256887.1;FAM26D,intron_variant,,ENST00000628083,NM_001256888.1;FAM26D,intron_variant,,ENST00000452373,;TRAPPC3L,upstream_gene_variant,,ENST00000437098,; T ENST00000368602 Transcript synonymous_variant 115/1113 19/546 7/181 R Cga/Aga 1 -1 TRAPPC3L HGNC HGNC:21090 protein_coding YES CCDS47468.1 ENSP00000357591 Q5T215 UPI000020E146 NM_001139444.2 1/5 PIRSF_domain:PIRSF018293,hmmpanther:PTHR13048,hmmpanther:PTHR13048:SF1 LOW SNV 5 1 PASS rs914356569 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 116545496 116545496 G T 1 0 0 0 0 0 0 0 1 16948 1124 39 1 1 TRAPPC3L 6 116545496 Silent SNP G C3N-00294_T 7104045 116545496 54260483 504 13276 SOGA3 0 . GRCh38 6 127516126 127516126 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.489C>T p.= p.L163L ENST00000525778 2/7 29 24 5 37 37 0 strelka-mutect SOGA3,synonymous_variant,p.=,ENST00000525778,NM_001012279.2;SOGA3,synonymous_variant,p.=,ENST00000465909,;SOGA3,downstream_gene_variant,,ENST00000467753,;C6orf58,upstream_gene_variant,,ENST00000498112,;RP3-403A15.5,synonymous_variant,p.=,ENST00000481848,; A ENST00000525778 Transcript synonymous_variant 1235/4077 489/2844 163/947 L ctC/ctT 1 -1 SOGA3 HGNC HGNC:21494 protein_coding YES CCDS43505.1 ENSP00000434570 Q5TF21 UPI0000419273 NM_001012279.2 2/7 hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF2,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1298881312 . 0 206 4 0 0 0 0 0 -13.95547 1 1 1 1 0 A 2 1 46 127516126 127516126 G A 1 0 0 0 0 0 0 0 1 15245 1045 37 1 1 SOGA3 6 127516126 Silent SNP G C3N-00294_T 10970630 127516126 43289853 505 13277 LAMA2 0 . GRCh38 6 129366277 129366277 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4776G>C p.Met1592Ile p.M1592I ENST00000421865 33/65 414 329 85 436 436 0 strelka-varscan-mutect LAMA2,missense_variant,p.Met1592Ile,ENST00000618192,;LAMA2,missense_variant,p.Met1592Ile,ENST00000617695,;LAMA2,missense_variant,p.Met1592Ile,ENST00000421865,NM_001079823.1,NM_000426.3; C ENST00000421865 Transcript missense_variant 4825/9640 4776/9369 1592/3122 M/I atG/atC 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.57) 33/65 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 129366277 129366277 G C 1 0 0 0 0 1 0 0 0 8510 1348 47 4 4 LAMA2 6 129366277 Missense_Mutation SNP G C3N-00294_T 1850151 129366277 41439702 506 13278 ENPP3 0 . GRCh38 6 131675138 131675138 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.821C>T p.Ser274Leu p.S274L ENST00000414305 10/26 294 243 51 324 324 0 strelka-varscan-mutect ENPP3,missense_variant,p.Ser274Leu,ENST00000414305,;ENPP3,missense_variant,p.Ser274Leu,ENST00000357639,NM_005021.3;ENPP3,missense_variant,p.Ser274Leu,ENST00000358229,;ENPP3,downstream_gene_variant,,ENST00000470930,;ENPP3,3_prime_UTR_variant,,ENST00000427707,;ENPP3,non_coding_transcript_exon_variant,,ENST00000494023,; T ENST00000414305 Transcript missense_variant 1149/3418 821/2628 274/875 S/L tCa/tTa 1 1 ENPP3 HGNC HGNC:3358 protein_coding YES CCDS5148.1 ENSP00000406261 O14638 UPI000013DD9F deleterious(0) 10/26 hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF64,Gene3D:3.40.720.10,Pfam_domain:PF01663,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 131675138 131675138 C T 1 0 0 0 0 1 0 0 0 4976 838 29 3 3 ENPP3 6 131675138 Missense_Mutation SNP C C3N-00294_T 2308861 131675138 39130841 507 13279 IFNGR1 0 . GRCh38 6 137204394 137204394 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.484G>A p.Asp162Asn p.D162N ENST00000367739 4/7 256 204 52 331 331 0 strelka-varscan-mutect IFNGR1,missense_variant,p.Asp162Asn,ENST00000367739,NM_000416.2;IFNGR1,missense_variant,p.Asp128Asn,ENST00000458076,;IFNGR1,missense_variant,p.Asp152Asn,ENST00000414770,;IFNGR1,downstream_gene_variant,,ENST00000478333,; T ENST00000367739 Transcript missense_variant 606/2139 484/1470 162/489 D/N Gat/Aat 1 -1 IFNGR1 HGNC HGNC:5439 protein_coding YES CCDS5185.1 ENSP00000356713 P15260 A0A0S2Z3Y2 UPI000002CE40 NM_000416.2 deleterious(0.04) 4/7 hmmpanther:PTHR20859:SF5,hmmpanther:PTHR20859,Gene3D:2.60.40.10,Pfam_domain:PF07140,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 137204394 137204394 C T 1 0 0 0 0 1 0 0 0 7449 826 29 3 3 IFNGR1 6 137204394 Missense_Mutation SNP C C3N-00294_T 5529256 137204394 33601585 508 13280 ADGRG6 0 . GRCh38 6 142420096 142420096 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.3311C>G p.Ser1104Ter p.S1104* ENST00000367609 22/25 98 77 21 131 131 0 strelka-varscan-mutect ADGRG6,stop_gained,p.Ser1104Ter,ENST00000230173,NM_020455.5;ADGRG6,stop_gained,p.Ser1104Ter,ENST00000367609,NM_198569.2;ADGRG6,stop_gained,p.Ser1076Ter,ENST00000367608,NM_001032395.2;ADGRG6,stop_gained,p.Ser1076Ter,ENST00000296932,NM_001032394.2;ADGRG6,non_coding_transcript_exon_variant,,ENST00000472054,; G ENST00000367609 Transcript stop_gained 3712/6887 3311/3753 1104/1250 S/* tCa/tGa 1 1 ADGRG6 HGNC HGNC:13841 protein_coding YES CCDS47489.1 ENSP00000356581 Q86SQ4 UPI000022CCE4 NM_198569.2 22/25 Gene3D:1.20.1070.10,Pfam_domain:PF00002,Prints_domain:PR00249,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF290,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 142420096 142420096 C G 1 0 0 0 0 0 1 0 0 373 838 29 4 4 ADGRG6 6 142420096 Nonsense_Mutation SNP C C3N-00294_T 5215702 142420096 28385883 509 13281 ADGB 0 . GRCh38 6 146635448 146635448 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.148G>A p.Glu50Lys p.E50K ENST00000397944 2/36 103 86 17 116 116 0 strelka-varscan-mutect ADGB,missense_variant,p.Glu50Lys,ENST00000397944,NM_024694.3;ADGB,missense_variant,p.Glu44Lys,ENST00000522242,;RNU6-906P,upstream_gene_variant,,ENST00000384700,;ADGB,missense_variant,p.Glu50Lys,ENST00000493950,;ADGB,3_prime_UTR_variant,,ENST00000522396,;ADGB,non_coding_transcript_exon_variant,,ENST00000326929,;RP11-715G15.2,downstream_gene_variant,,ENST00000615810,; A ENST00000397944 Transcript missense_variant 224/5325 148/5004 50/1667 E/K Gag/Aag 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 deleterious(0) 2/36 hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF304,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 146635448 146635448 G A 1 0 0 0 0 1 0 0 0 351 943 33 3 3 ADGB 6 146635448 Missense_Mutation SNP G C3N-00294_T 4215352 146635448 24170531 510 13282 STXBP5 0 . GRCh38 6 147267128 147267128 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.675C>G p.= p.L225L ENST00000321680 7/28 96 76 20 181 181 0 strelka-varscan-mutect STXBP5,synonymous_variant,p.=,ENST00000367481,NM_139244.4;STXBP5,synonymous_variant,p.=,ENST00000321680,NM_001127715.2;STXBP5,synonymous_variant,p.=,ENST00000367480,;STXBP5,synonymous_variant,p.=,ENST00000546097,; G ENST00000321680 Transcript synonymous_variant 675/3456 675/3456 225/1151 L ctC/ctG COSM121969 1 1 STXBP5 HGNC HGNC:19665 protein_coding YES CCDS47499.1 ENSP00000321826 Q5T5C0 UPI0000199FE0 NM_001127715.2 7/28 hmmpanther:PTHR10241:SF22,hmmpanther:PTHR10241,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 147267128 147267128 C G 1 0 0 0 0 0 0 0 1 15740 813 29 4 4 STXBP5 6 147267128 Silent SNP C C3N-00294_T 631680 147267128 23538851 511 13283 AKAP12 0 . GRCh38 6 151353284 151353284 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.4893C>G p.= p.S1631S ENST00000402676 4/5 168 135 33 194 194 0 strelka-varscan-mutect AKAP12,synonymous_variant,p.=,ENST00000402676,NM_005100.3;AKAP12,synonymous_variant,p.=,ENST00000253332,;AKAP12,synonymous_variant,p.=,ENST00000354675,NM_144497.2;AKAP12,synonymous_variant,p.=,ENST00000359755,;AKAP12,downstream_gene_variant,,ENST00000490177,; G ENST00000402676 Transcript synonymous_variant 5133/8432 4893/5349 1631/1782 S tcC/tcG 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 4/5 hmmpanther:PTHR23209 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 151353284 151353284 C G 1 0 0 0 0 0 0 0 1 531 581 21 4 4 AKAP12 6 151353284 Silent SNP C C3N-00294_T 4086156 151353284 19452695 512 13284 RGS17 0 . GRCh38 6 153024400 153024400 + Silent SNP G G C rs768032614 C3N-00294_T C3N-00294_N G G c.306C>G p.= p.L102L ENST00000367225 3/4 270 226 44 369 369 0 strelka-varscan-mutect RGS17,synonymous_variant,p.=,ENST00000367225,;RGS17,synonymous_variant,p.=,ENST00000206262,NM_012419.4; C ENST00000367225 Transcript synonymous_variant 331/7773 306/633 102/210 L ctC/ctG rs768032614 1 -1 RGS17 HGNC HGNC:14088 protein_coding YES CCDS5244.1 ENSP00000356194 Q9UGC6 UPI000000D76A 3/4 PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF175,hmmpanther:PTHR10845,Pfam_domain:PF00615,Gene3D:1.10.196.10,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301 LOW 1 SNV 1 1 PASS rs768032614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 153024400 153024400 G C 1 0 0 0 0 0 0 0 1 13470 1161 41 4 4 RGS17 6 153024400 Silent SNP G C3N-00294_T 1671116 153024400 17781579 513 13285 FNDC1 0 . GRCh38 6 159233716 159233716 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.3204C>T p.= p.L1068L ENST00000297267 11/23 124 101 23 141 141 0 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,synonymous_variant,p.=,ENST00000329629,; T ENST00000297267 Transcript synonymous_variant 3404/6552 3204/5685 1068/1894 L ctC/ctT 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 11/23 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 159233716 159233716 C T 1 0 0 0 0 0 0 0 1 5824 842 30 3 3 FNDC1 6 159233716 Silent SNP C C3N-00294_T 6209316 159233716 11572263 514 13286 FRMD1 0 . GRCh38 6 168078998 168078998 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.97G>A p.Glu33Lys p.E33K ENST00000283309 1/11 119 111 8 116 116 0 strelka-varscan-mutect FRMD1,missense_variant,p.Glu33Lys,ENST00000283309,NM_024919.4;FRMD1,missense_variant,p.Glu75Lys,ENST00000511714,;FRMD1,upstream_gene_variant,,ENST00000440994,NM_001122841.2;FRMD1,missense_variant,p.Glu72Lys,ENST00000468647,;FRMD1,missense_variant,p.Glu72Lys,ENST00000509157,;FRMD1,non_coding_transcript_exon_variant,,ENST00000358587,; T ENST00000283309 Transcript missense_variant 162/3067 97/1650 33/549 E/K Gag/Aag COSM4006207 1 -1 FRMD1 HGNC HGNC:21240 protein_coding YES CCDS5306.1 ENSP00000283309 Q8N878 UPI000013F36A NM_024919.4 tolerated_low_confidence(0.35) 1/11 hmmpanther:PTHR13429 1 MODERATE 1 SNV 1 1 1 PASS rs1241837386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 168078998 168078998 C T 1 0 0 0 0 1 0 0 0 5919 835 29 3 3 FRMD1 6 168078998 Missense_Mutation SNP C C3N-00294_T 8845282 168078998 2726981 515 13287 ADAP1 0 . GRCh38 7 926597 926597 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.294C>G p.= p.S98S ENST00000539900 3/11 144 108 36 87 87 0 strelka-varscan-mutect ADAP1,synonymous_variant,p.=,ENST00000265846,NM_006869.3;ADAP1,synonymous_variant,p.=,ENST00000539900,NM_001284308.1;ADAP1,synonymous_variant,p.=,ENST00000611167,NM_001284309.1;ADAP1,synonymous_variant,p.=,ENST00000449296,NM_001284310.1;ADAP1,synonymous_variant,p.=,ENST00000446141,;ADAP1,synonymous_variant,p.=,ENST00000454383,;ADAP1,synonymous_variant,p.=,ENST00000453823,;ADAP1,synonymous_variant,p.=,ENST00000435943,;ADAP1,non_coding_transcript_exon_variant,,ENST00000463358,;ADAP1,non_coding_transcript_exon_variant,,ENST00000477906,;ADAP1,upstream_gene_variant,,ENST00000488527,;COX19,3_prime_UTR_variant,,ENST00000457254,;ADAP1,non_coding_transcript_exon_variant,,ENST00000495686,; C ENST00000539900 Transcript synonymous_variant 294/2178 294/1158 98/385 S tcC/tcG 1 -1 ADAP1 HGNC HGNC:16486 protein_coding YES CCDS64577.1 ENSP00000442682 O75689 UPI0001AE701D NM_001284308.1 3/11 PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF219,Pfam_domain:PF01412,SMART_domains:SM00105,Superfamily_domains:SSF57863 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 926597 926597 G C 1 0 0 0 0 0 0 0 1 323 1335 47 4 4 ADAP1 7 926597 Silent SNP G C3N-00294_T 926597 158419376 516 13288 MICALL2 0 . GRCh38 7 1444702 1444702 + Silent SNP G G A rs141317918 C3N-00294_T C3N-00294_N G G c.1368C>T p.= p.L456L ENST00000297508 6/17 445 349 96 307 306 1 strelka-varscan-mutect MICALL2,synonymous_variant,p.=,ENST00000297508,NM_182924.3;MICALL2,synonymous_variant,p.=,ENST00000413446,;MICALL2,non_coding_transcript_exon_variant,,ENST00000472100,;MICALL2,upstream_gene_variant,,ENST00000467394,;MICALL2,upstream_gene_variant,,ENST00000479007,;MICALL2,upstream_gene_variant,,ENST00000487156,;MICALL2,downstream_gene_variant,,ENST00000482839,;MICALL2,upstream_gene_variant,,ENST00000467783,;MICALL2,downstream_gene_variant,,ENST00000490608,; A ENST00000297508 Transcript synonymous_variant 1544/3121 1368/2715 456/904 L ctC/ctT rs141317918 1 -1 MICALL2 HGNC HGNC:29672 protein_coding YES CCDS5324.1 ENSP00000297508 Q8IY33 UPI00000742E0 NM_182924.3 6/17 LOW 1 SNV 1 1 PASS rs141317918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 1444702 1444702 G A 1 0 0 0 0 0 0 0 1 9531 1277 45 3 3 MICALL2 7 1444702 Silent SNP G C3N-00294_T 518105 1444702 157901271 517 13289 MAFK 0 . GRCh38 7 1540015 1540015 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.111G>C p.= p.L37L ENST00000343242 3/3 260 230 30 154 153 1 strelka-varscan-mutect MAFK,synonymous_variant,p.=,ENST00000343242,NM_002360.3;MAFK,synonymous_variant,p.=,ENST00000406174,;TMEM184A,downstream_gene_variant,,ENST00000297477,NM_001097620.1;TMEM184A,downstream_gene_variant,,ENST00000449955,;TMEM184A,downstream_gene_variant,,ENST00000421996,;MAFK,synonymous_variant,p.=,ENST00000403150,;TMEM184A,downstream_gene_variant,,ENST00000319018,; C ENST00000343242 Transcript synonymous_variant 340/3368 111/471 37/156 L ctG/ctC 1 1 MAFK HGNC HGNC:6782 protein_coding YES CCDS5325.1 ENSP00000344903 O60675 A0A024R804 UPI000012EB23 NM_002360.3 3/3 hmmpanther:PTHR10129,Pfam_domain:PF03131,Gene3D:1.10.880.10,Superfamily_domains:SSF47454 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 1540015 1540015 G C 1 0 0 0 0 0 0 0 1 9077 1277 45 4 4 MAFK 7 1540015 Silent SNP G C3N-00294_T 95313 1540015 157805958 518 13290 TNRC18 0 . GRCh38 7 5376125 5376125 + Nonsense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2708C>G p.Ser903Ter p.S903* ENST00000430969 9/30 232 203 29 138 138 0 strelka-varscan-mutect TNRC18,stop_gained,p.Ser903Ter,ENST00000399537,;TNRC18,stop_gained,p.Ser903Ter,ENST00000430969,NM_001080495.2;TNRC18,stop_gained,p.Ser305Ter,ENST00000413081,; C ENST00000430969 Transcript stop_gained 3057/10562 2708/8907 903/2968 S/* tCa/tGa COSM3833020,COSM3833021 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 9/30 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF21,Low_complexity_(Seg):seg 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 5376125 5376125 G C 1 0 0 0 0 0 1 0 0 16812 1294 45 4 4 TNRC18 7 5376125 Nonsense_Mutation SNP G C3N-00294_T 3836110 5376125 153969848 519 13291 PHF14 0 . GRCh38 7 10982873 10982873 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.614A>T p.Asp205Val p.D205V ENST00000403050 3/17 456 360 96 340 340 0 strelka-varscan-mutect PHF14,missense_variant,p.Asp205Val,ENST00000403050,NM_014660.3;PHF14,missense_variant,p.Asp205Val,ENST00000634607,;PHF14,intron_variant,,ENST00000476009,;PHF14,non_coding_transcript_exon_variant,,ENST00000490957,;PHF14,intron_variant,,ENST00000423760,;PHF14,intron_variant,,ENST00000521747,; T ENST00000403050 Transcript missense_variant 1066/4276 614/2667 205/888 D/V gAc/gTc 1 1 PHF14 HGNC HGNC:22203 protein_coding YES CCDS47542.1 ENSP00000385795 O94880 UPI000020EB41 NM_014660.3 deleterious_low_confidence(0) 3/17 Low_complexity_(Seg):seg,hmmpanther:PTHR13793 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 10982873 10982873 A T 1 0 0 0 0 1 0 0 0 11914 275 10 4 4 PHF14 7 10982873 Missense_Mutation SNP A C3N-00294_T 5606748 10982873 148363100 520 13292 AGR3 0 . GRCh38 7 16862011 16862011 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.276G>C p.Gln92His p.Q92H ENST00000310398 5/8 101 91 10 107 107 0 strelka-varscan-mutect AGR3,missense_variant,p.Gln92His,ENST00000310398,NM_176813.4;AGR3,missense_variant,p.Gln92His,ENST00000402239,;AGR3,missense_variant,p.Gln71His,ENST00000414935,;RAD17P1,downstream_gene_variant,,ENST00000418130,; G ENST00000310398 Transcript missense_variant 347/749 276/501 92/166 Q/H caG/caC 1 -1 AGR3 HGNC HGNC:24167 protein_coding YES CCDS5365.1 ENSP00000308606 Q8TD06 UPI0000040D21 NM_176813.4 tolerated(0.76) 5/8 hmmpanther:PTHR15337:SF5,hmmpanther:PTHR15337,Pfam_domain:PF13899,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 16862011 16862011 C G 1 0 0 0 0 1 0 0 0 475 912 32 4 4 AGR3 7 16862011 Missense_Mutation SNP C C3N-00294_T 5879138 16862011 142483962 521 13293 ITGB8 0 . GRCh38 7 20367082 20367082 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.284C>G p.Ser95Ter p.S95* ENST00000222573 3/14 300 256 44 257 257 0 strelka-varscan-mutect ITGB8,stop_gained,p.Ser95Ter,ENST00000222573,NM_002214.2;ITGB8,5_prime_UTR_variant,,ENST00000537992,;ITGB8,non_coding_transcript_exon_variant,,ENST00000477859,;ITGB8,non_coding_transcript_exon_variant,,ENST00000478974,; G ENST00000222573 Transcript stop_gained 968/8751 284/2310 95/769 S/* tCa/tGa 1 1 ITGB8 HGNC HGNC:6163 protein_coding YES CCDS5370.1 ENSP00000222573 P26012 UPI000012DA14 NM_002214.2 3/14 hmmpanther:PTHR10082:SF9,hmmpanther:PTHR10082,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,SMART_domains:SM00423,SMART_domains:SM00187,Superfamily_domains:SSF103575,Prints_domain:PR01186 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 20367082 20367082 C G 1 0 0 0 0 0 1 0 0 7807 838 29 4 4 ITGB8 7 20367082 Nonsense_Mutation SNP C C3N-00294_T 3505071 20367082 138978891 522 13294 IL6 0 . GRCh38 7 22727451 22727451 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.27C>T p.= p.F9F ENST00000404625 3/6 379 331 48 320 319 1 strelka-varscan-mutect IL6,synonymous_variant,p.=,ENST00000404625,;IL6,synonymous_variant,p.=,ENST00000258743,NM_000600.3;IL6,synonymous_variant,p.=,ENST00000406575,;IL6,synonymous_variant,p.=,ENST00000426291,;IL6,intron_variant,,ENST00000407492,NM_001318095.1;IL6,intron_variant,,ENST00000401630,;IL6,intron_variant,,ENST00000401651,;AC073072.5,intron_variant,,ENST00000325042,;IL6,non_coding_transcript_exon_variant,,ENST00000485300,;IL6,upstream_gene_variant,,ENST00000464710,; T ENST00000404625 Transcript synonymous_variant 486/1527 27/639 9/212 F ttC/ttT 1 1 IL6 HGNC HGNC:6018 protein_coding YES CCDS5375.1 ENSP00000385675 P05231 Q75MH2 UPI000002C4A6 3/6 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11457:SF0,hmmpanther:PTHR11457,PIRSF_domain:PIRSF001935 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 22727451 22727451 C T 1 0 0 0 0 0 0 0 1 7605 883 31 1 1 IL6 7 22727451 Silent SNP C C3N-00294_T 2360369 22727451 136618522 523 13295 GPNMB 0 . GRCh38 7 23256996 23256996 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.472G>A p.Asp158Asn p.D158N ENST00000381990 4/11 538 461 77 383 383 0 strelka-varscan-mutect GPNMB,missense_variant,p.Asp158Asn,ENST00000258733,NM_002510.2;GPNMB,missense_variant,p.Asp158Asn,ENST00000381990,NM_001005340.1;GPNMB,missense_variant,p.Asp158Asn,ENST00000409458,;GPNMB,non_coding_transcript_exon_variant,,ENST00000465673,;GPNMB,non_coding_transcript_exon_variant,,ENST00000492858,;GPNMB,downstream_gene_variant,,ENST00000459927,;GPNMB,downstream_gene_variant,,ENST00000487890,;GPNMB,downstream_gene_variant,,ENST00000492512,; A ENST00000381990 Transcript missense_variant 633/2763 472/1719 158/572 D/N Gat/Aat COSM1312973,COSM746402 1 1 GPNMB HGNC HGNC:4462 protein_coding YES CCDS34610.1 ENSP00000371420 Q14956 UPI000007158E NM_001005340.1 deleterious(0.02) 4/11 hmmpanther:PTHR11861,hmmpanther:PTHR11861:SF11 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1236146268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 23256996 23256996 G A 1 0 0 0 0 1 0 0 0 6522 1290 45 3 3 GPNMB 7 23256996 Missense_Mutation SNP G C3N-00294_T 529545 23256996 136088977 524 13296 IGF2BP3 0 . GRCh38 7 23470064 23470064 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.47C>T p.Ser16Leu p.S16L ENST00000258729 1/15 199 171 28 101 101 0 strelka-varscan-mutect IGF2BP3,missense_variant,p.Ser16Leu,ENST00000258729,NM_006547.2;IGF2BP3,upstream_gene_variant,,ENST00000491719,;IGF2BP3,upstream_gene_variant,,ENST00000468263,;IGF2BP3,missense_variant,p.Ser16Leu,ENST00000421467,;IGF2BP3,non_coding_transcript_exon_variant,,ENST00000468005,;IGF2BP3,upstream_gene_variant,,ENST00000476938,; A ENST00000258729 Transcript missense_variant 404/4250 47/1740 16/579 S/L tCg/tTg 1 -1 IGF2BP3 HGNC HGNC:28868 protein_coding YES CCDS5382.1 ENSP00000258729 O00425 UPI0000117172 NM_006547.2 tolerated(0.2) 1/15 PROSITE_profiles:PS50102,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 46 23470064 23470064 G A 1 0 0 0 0 1 0 0 0 7481 1059 37 1 1 IGF2BP3 7 23470064 Missense_Mutation SNP G C3N-00294_T 213068 23470064 135875909 525 13297 MPP6 0 . GRCh38 7 24663699 24663699 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.761G>C p.Arg254Thr p.R254T ENST00000222644 6/12 179 156 23 258 258 0 strelka-varscan-mutect MPP6,missense_variant,p.Arg254Thr,ENST00000222644,NM_001303037.1,NM_016447.3;MPP6,missense_variant,p.Arg254Thr,ENST00000396475,;MPP6,missense_variant,p.Arg142Thr,ENST00000409761,;MPP6,missense_variant,p.Arg254Thr,ENST00000430180,;MPP6,non_coding_transcript_exon_variant,,ENST00000472674,;MPP6,upstream_gene_variant,,ENST00000464384,; C ENST00000222644 Transcript missense_variant 1011/8452 761/1623 254/540 R/T aGa/aCa 1 1 MPP6 HGNC HGNC:18167 protein_coding YES CCDS5388.1 ENSP00000222644 Q9NZW5 A0A024RA25 UPI0000001C1B NM_001303037.1,NM_016447.3 tolerated(0.23) 6/12 Gene3D:2.30.30.40,Pfam_domain:PF07653,PROSITE_profiles:PS50002,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF44,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 24663699 24663699 G C 1 0 0 0 0 1 0 0 0 9704 942 33 4 4 MPP6 7 24663699 Missense_Mutation SNP G C3N-00294_T 1193635 24663699 134682274 526 13298 HNRNPA2B1 0 . GRCh38 7 26197356 26197356 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.259G>C p.Asp87His p.D87H ENST00000354667 4/12 142 119 23 88 88 0 strelka-varscan-mutect HNRNPA2B1,missense_variant,p.Asp87His,ENST00000354667,NM_031243.2;HNRNPA2B1,missense_variant,p.Asp87His,ENST00000618183,;HNRNPA2B1,missense_variant,p.Asp75His,ENST00000356674,NM_002137.3;CBX3,upstream_gene_variant,,ENST00000337620,NM_007276.4;CBX3,upstream_gene_variant,,ENST00000396386,NM_016587.3;CBX3,upstream_gene_variant,,ENST00000409747,;CBX3,upstream_gene_variant,,ENST00000456948,;HNRNPA2B1,missense_variant,p.Asp87His,ENST00000360787,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000463181,;HNRNPA2B1,non_coding_transcript_exon_variant,,ENST00000490912,;HNRNPA2B1,upstream_gene_variant,,ENST00000495810,; G ENST00000354667 Transcript missense_variant 428/3664 259/1062 87/353 D/H Gat/Cat 1 -1 HNRNPA2B1 HGNC HGNC:5033 protein_coding YES CCDS43557.1 ENSP00000346694 P22626 UPI000002F091 NM_031243.2 deleterious(0) 4/12 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF392,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 46 26197356 26197356 C G 1 0 0 0 0 1 0 0 0 7150 826 29 4 4 HNRNPA2B1 7 26197356 Missense_Mutation SNP C C3N-00294_T 1533657 26197356 133148617 527 13299 HIBADH 0 . GRCh38 7 27662763 27662763 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.26G>T p.Gly9Val p.G9V ENST00000265395 1/8 110 67 43 69 69 0 strelka-mutect HIBADH,missense_variant,p.Gly9Val,ENST00000265395,NM_152740.3;HIBADH,missense_variant,p.Gly9Val,ENST00000428288,;HIBADH,non_coding_transcript_exon_variant,,ENST00000496814,; A ENST00000265395 Transcript missense_variant 233/1990 26/1011 9/336 G/V gGa/gTa 1 -1 HIBADH HGNC HGNC:4907 protein_coding YES CCDS5414.1 ENSP00000265395 P31937 A0A024RA75 UPI000000160A NM_152740.3 tolerated_low_confidence(0.12) 1/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 27662763 27662763 C A 1 0 0 0 0 1 0 0 0 6983 855 30 2 2 HIBADH 7 27662763 Missense_Mutation SNP C C3N-00294_T 1465407 27662763 131683210 528 13300 TRIL 0 . GRCh38 7 28955910 28955910 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.2137G>T p.Ala713Ser p.A713S ENST00000539664 1/1 374 275 99 266 266 0 strelka-varscan-mutect TRIL,missense_variant,p.Ala713Ser,ENST00000539664,NM_014817.3;AC005013.5,upstream_gene_variant,,ENST00000436594,; A ENST00000539664 Transcript missense_variant 2383/4935 2137/2436 713/811 A/S Gcc/Tcc 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 tolerated(0.28) 1/1 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 28955910 28955910 C A 1 0 0 0 0 1 0 0 0 16974 739 26 2 2 TRIL 7 28955910 Missense_Mutation SNP C C3N-00294_T 1293147 28955910 130390063 529 13301 TRIL 0 . GRCh38 7 28957744 28957744 + Missense_Mutation SNP C C G rs766065735 C3N-00294_T C3N-00294_N C C c.303G>C p.Lys101Asn p.K101N ENST00000539664 1/1 368 313 55 264 264 0 strelka-varscan-mutect TRIL,missense_variant,p.Lys101Asn,ENST00000539664,NM_014817.3;AC005013.5,non_coding_transcript_exon_variant,,ENST00000436594,; G ENST00000539664 Transcript missense_variant 549/4935 303/2436 101/811 K/N aaG/aaC rs766065735 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 deleterious(0.03) 1/1 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 1 PASS rs766065735 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 46 28957744 28957744 C G 1 0 0 0 0 1 0 0 0 16974 912 32 4 4 TRIL 7 28957744 Missense_Mutation SNP C C3N-00294_T 1834 28957744 130388229 530 13302 ELMO1 0 . GRCh38 7 37211489 37211489 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.983G>A p.Arg328Gln p.R328Q ENST00000310758 13/22 211 176 35 147 147 0 strelka-varscan-mutect ELMO1,missense_variant,p.Arg328Gln,ENST00000310758,NM_001206480.2,NM_014800.10;ELMO1,missense_variant,p.Arg328Gln,ENST00000442504,NM_001206482.1;ELMO1,missense_variant,p.Arg328Gln,ENST00000448602,;ELMO1,missense_variant,p.Arg69Gln,ENST00000424212,;ELMO1,missense_variant,p.Arg108Gln,ENST00000433246,;ELMO1,missense_variant,p.Arg66Gln,ENST00000420636,;ELMO1,non_coding_transcript_exon_variant,,ENST00000487336,; T ENST00000310758 Transcript missense_variant 1631/4022 983/2184 328/727 R/Q cGa/cAa COSM3229019 1 -1 ELMO1 HGNC HGNC:16286 protein_coding YES CCDS5449.1 ENSP00000312185 Q92556 A4D1X5 UPI000006F687 NM_001206480.2,NM_014800.10 deleterious(0) 13/22 Pfam_domain:PF04727,PROSITE_profiles:PS51335,hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF23 1 MODERATE 1 SNV 1 1 1 PASS rs1174488092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 37211489 37211489 C T 1 0 0 0 0 1 0 0 0 4899 884 31 1 1 ELMO1 7 37211489 Missense_Mutation SNP C C3N-00294_T 8253745 37211489 122134484 531 13303 SFRP4 0 . GRCh38 7 37912210 37912210 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.700C>T p.Gln234Ter p.Q234* ENST00000436072 4/6 220 191 29 187 187 0 strelka-varscan-mutect SFRP4,stop_gained,p.Gln234Ter,ENST00000436072,NM_003014.3;SFRP4,stop_gained,p.Gln100Ter,ENST00000447200,;EPDR1,intron_variant,,ENST00000476620,;SFRP4,upstream_gene_variant,,ENST00000478975,; A ENST00000436072 Transcript stop_gained 1078/2966 700/1041 234/346 Q/* Caa/Taa 1 -1 SFRP4 HGNC HGNC:10778 protein_coding YES CCDS5453.1 ENSP00000410715 Q6FHJ7 UPI000004ECBF NM_003014.3 4/6 PROSITE_profiles:PS50189,hmmpanther:PTHR11309:SF7,hmmpanther:PTHR11309,Gene3D:2.40.50.120,Pfam_domain:PF01759,SMART_domains:SM00643,Superfamily_domains:SSF50242 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 37912210 37912210 G A 1 0 0 0 0 0 1 0 0 14442 1299 45 3 3 SFRP4 7 37912210 Nonsense_Mutation SNP G C3N-00294_T 700721 37912210 121433763 532 13304 VPS41 0 . GRCh38 7 38830329 38830329 + Splice_Site SNP C C A novel C3N-00294_T C3N-00294_N C C c.247-1G>T p.X83_splice ENST00000310301 186 132 54 146 145 1 strelka-varscan-mutect VPS41,splice_acceptor_variant,,ENST00000310301,NM_014396.3;VPS41,splice_acceptor_variant,,ENST00000413141,;VPS41,splice_acceptor_variant,,ENST00000414632,;VPS41,splice_acceptor_variant,,ENST00000418457,;VPS41,splice_acceptor_variant,,ENST00000457055,;VPS41,intron_variant,,ENST00000395969,NM_080631.3;VPS41,splice_acceptor_variant,,ENST00000265745,; A ENST00000310301 Transcript splice_acceptor_variant -/5903 247/2565 83/854 1 -1 VPS41 HGNC HGNC:12713 protein_coding YES CCDS5457.1 ENSP00000309457 P49754 UPI000000DAB7 NM_014396.3 4/28 HIGH 1 SNV 1 1 PASS . . 0 193 0 11 6 0 0 0 -20 0.3665379 1 1 0 0 A 5 1 46 38830329 38830329 C A 1 0 0 0 0 0 0 1 0 17756 927 32 2 2 VPS41 7 38830329 Splice_Site SNP C C3N-00294_T 918119 38830329 120515644 533 13305 URGCP 0 . GRCh38 7 43881161 43881161 + Silent SNP T T C novel C3N-00294_T C3N-00294_N T T c.290A>G p.= p.*97* ENST00000446958 5/5 147 102 45 105 105 0 varscan-mutect URGCP,stop_retained_variant,p.=,ENST00000446958,;URGCP,intron_variant,,ENST00000336086,;URGCP,intron_variant,,ENST00000453200,NM_001077663.2;URGCP,intron_variant,,ENST00000443736,NM_001077664.2,NM_001290075.1,NM_001290076.1;URGCP,intron_variant,,ENST00000402306,NM_017920.4;URGCP,intron_variant,,ENST00000426198,;URGCP-MRPS24,intron_variant,,ENST00000603700,NM_001204871.1;URGCP,intron_variant,,ENST00000439702,;URGCP,intron_variant,,ENST00000455877,;URGCP,intron_variant,,ENST00000497914,;URGCP,intron_variant,,ENST00000467410,;URGCP,intron_variant,,ENST00000474376,; C ENST00000446958 Transcript stop_retained_variant 342/365 290/291 97/96 * tAa/tGa 1 -1 URGCP HGNC HGNC:30890 protein_coding ENSP00000409496 F8WDN0 UPI000198CD4E 5/5 LOW SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 43881161 43881161 T C 1 0 0 0 0 0 0 0 1 17556 1761 61 5 5 URGCP 7 43881161 Silent SNP T C3N-00294_T 5050832 43881161 115464812 534 13306 SPDYE1 0 . GRCh38 7 44002769 44002769 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.439G>C p.Val147Leu p.V147L ENST00000258704 2/7 254 220 34 183 183 0 varscan-mutect SPDYE1,missense_variant,p.Val147Leu,ENST00000258704,NM_175064.2;AC004951.6,downstream_gene_variant,,ENST00000447643,;POLR2J4,intron_variant,,ENST00000427076,;RP5-1165K10.2,intron_variant,,ENST00000454572,;POLR2J4,intron_variant,,ENST00000422304,; C ENST00000258704 Transcript missense_variant 576/2649 439/1011 147/336 V/L Gtg/Ctg 1 1 SPDYE1 HGNC HGNC:16408 protein_coding YES CCDS5475.1 ENSP00000258704 Q8NFV5 UPI000013CFF7 NM_175064.2 tolerated(0.32) 2/7 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 44002769 44002769 G C 1 0 0 0 0 1 0 0 0 15376 1029 36 4 4 SPDYE1 7 44002769 Missense_Mutation SNP G C3N-00294_T 121608 44002769 115343204 535 13307 PGAM2 0 . GRCh38 7 44065269 44065269 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.261C>T p.= p.L87L ENST00000297283 1/3 957 802 155 662 662 0 strelka-varscan-mutect PGAM2,synonymous_variant,p.=,ENST00000297283,NM_000290.3;DBNL,3_prime_UTR_variant,,ENST00000432854,;DBNL,downstream_gene_variant,,ENST00000494774,NM_014063.6;DBNL,downstream_gene_variant,,ENST00000468694,NM_001122956.1;DBNL,downstream_gene_variant,,ENST00000490734,NM_001284315.1;DBNL,downstream_gene_variant,,ENST00000448521,NM_001014436.2;DBNL,downstream_gene_variant,,ENST00000452943,;DBNL,downstream_gene_variant,,ENST00000440166,NM_001284313.1;DBNL,downstream_gene_variant,,ENST00000456905,;DBNL,downstream_gene_variant,,ENST00000452661,;AC017116.11,non_coding_transcript_exon_variant,,ENST00000445938,;AC017116.11,non_coding_transcript_exon_variant,,ENST00000425727,;DBNL,downstream_gene_variant,,ENST00000497184,;DBNL,downstream_gene_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000441840,;DBNL,downstream_gene_variant,,ENST00000429716,;DBNL,downstream_gene_variant,,ENST00000411855,;DBNL,downstream_gene_variant,,ENST00000498733,; A ENST00000297283 Transcript synonymous_variant 319/857 261/762 87/253 L ctC/ctT 1 -1 PGAM2 HGNC HGNC:8889 protein_coding YES CCDS34624.1 ENSP00000297283 P15259 UPI000013E3E8 NM_000290.3 1/3 Gene3D:3.40.50.1240,HAMAP:MF_01039,Pfam_domain:PF00300,hmmpanther:PTHR11931,hmmpanther:PTHR11931:SF8,SMART_domains:SM00855,Superfamily_domains:SSF53254,TIGRFAM_domain:TIGR01258 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 44065269 44065269 G A 1 0 0 0 0 0 0 0 1 11864 1277 45 3 3 PGAM2 7 44065269 Silent SNP G C3N-00294_T 62500 44065269 115280704 536 13308 AEBP1 0 . GRCh38 7 44112198 44112198 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2094C>G p.Ile698Met p.I698M ENST00000223357 17/21 92 73 19 92 92 0 strelka-varscan-mutect AEBP1,missense_variant,p.Ile698Met,ENST00000223357,NM_001129.4;AEBP1,missense_variant,p.Ile273Met,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,NM_001256879.1;POLD2,downstream_gene_variant,,ENST00000452185,NM_001127218.2;POLD2,downstream_gene_variant,,ENST00000610533,NM_006230.3;POLD2,downstream_gene_variant,,ENST00000223361,;POLD2,downstream_gene_variant,,ENST00000436844,;POLD2,downstream_gene_variant,,ENST00000433715,;AEBP1,downstream_gene_variant,,ENST00000455443,;AEBP1,downstream_gene_variant,,ENST00000449162,;POLD2,downstream_gene_variant,,ENST00000436400,;AEBP1,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,splice_region_variant,,ENST00000413907,;AEBP1,3_prime_UTR_variant,,ENST00000431035,;POLD2,downstream_gene_variant,,ENST00000463464,;POLD2,downstream_gene_variant,,ENST00000470867,;AEBP1,downstream_gene_variant,,ENST00000453052,;AEBP1,downstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000481104,;POLD2,downstream_gene_variant,,ENST00000489883,; G ENST00000223357 Transcript missense_variant 2399/4081 2094/3477 698/1158 I/M atC/atG 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 tolerated(0.07) 17/21 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF48,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 44112198 44112198 C G 1 0 0 0 0 1 0 0 0 424 903 32 4 4 AEBP1 7 44112198 Missense_Mutation SNP C C3N-00294_T 46929 44112198 115233775 537 13309 YKT6 0 . GRCh38 7 44207453 44207453 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.354C>G p.Ile118Met p.I118M ENST00000223369 4/7 332 296 36 256 256 0 strelka-varscan-mutect YKT6,missense_variant,p.Ile118Met,ENST00000223369,NM_006555.3;YKT6,missense_variant,p.Ile118Met,ENST00000496112,;YKT6,non_coding_transcript_exon_variant,,ENST00000447123,;YKT6,upstream_gene_variant,,ENST00000478411,;YKT6,non_coding_transcript_exon_variant,,ENST00000463014,;YKT6,upstream_gene_variant,,ENST00000421621,;YKT6,upstream_gene_variant,,ENST00000424864,; G ENST00000223369 Transcript missense_variant 441/2696 354/597 118/198 I/M atC/atG 1 1 YKT6 HGNC HGNC:16959 protein_coding YES CCDS5482.1 ENSP00000223369 O15498 A4D2J0 UPI000004D0E4 NM_006555.3 deleterious(0.04) 4/7 Gene3D:3.30.450.50,hmmpanther:PTHR21136,hmmpanther:PTHR21136:SF5,SMART_domains:SM01270,Superfamily_domains:SSF64356 MODERATE 1 SNV 1 1 PASS rs1337109022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 44207453 44207453 C G 1 0 0 0 0 1 0 0 0 18047 845 30 4 4 YKT6 7 44207453 Missense_Mutation SNP C C3N-00294_T 95255 44207453 115138520 538 13310 NPC1L1 0 . GRCh38 7 44516868 44516868 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.3435C>G p.= p.L1145L ENST00000289547 17/20 425 351 74 307 307 0 strelka-varscan-mutect NPC1L1,synonymous_variant,p.=,ENST00000289547,NM_013389.2;NPC1L1,synonymous_variant,p.=,ENST00000546276,;NPC1L1,synonymous_variant,p.=,ENST00000381160,NM_001101648.1; C ENST00000289547 Transcript synonymous_variant 3491/5048 3435/4080 1145/1359 L ctC/ctG 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 17/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR10796:SF89,hmmpanther:PTHR10796,Pfam_domain:PF02460,Gene3D:2j8sB01,Superfamily_domains:SSF82866 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 44516868 44516868 G C 1 0 0 0 0 0 0 0 1 10619 929 33 4 4 NPC1L1 7 44516868 Silent SNP G C3N-00294_T 309415 44516868 114829105 539 13311 ABCA13 0 . GRCh38 7 48281387 48281387 + Nonsense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.8771C>G p.Ser2924Ter p.S2924* ENST00000435803 19/62 298 255 43 251 251 0 strelka-varscan-mutect ABCA13,stop_gained,p.Ser2924Ter,ENST00000435803,NM_152701.4;ABCA13,stop_gained,p.Ser231Ter,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,; G ENST00000435803 Transcript stop_gained 8795/17184 8771/15177 2924/5058 S/* tCa/tGa COSM5046672,COSM5046673 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 19/62 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 48281387 48281387 C G 1 0 0 0 0 0 1 0 0 35 838 29 4 4 ABCA13 7 48281387 Nonsense_Mutation SNP C C3N-00294_T 3764519 48281387 111064586 540 13312 C7orf72 0 . GRCh38 7 50159118 50159118 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.1266G>C p.= p.V422V ENST00000297001 9/9 327 287 40 229 229 0 strelka-varscan-mutect C7orf72,synonymous_variant,p.=,ENST00000297001,NM_001161834.2; C ENST00000297001 Transcript synonymous_variant 1316/2028 1266/1317 422/438 V gtG/gtC 1 1 C7orf72 HGNC HGNC:22564 protein_coding YES CCDS47585.1 ENSP00000297001 A4D263 UPI00001D7424 NM_001161834.2 9/9 hmmpanther:PTHR34759,Pfam_domain:PF15073 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 50159118 50159118 G C 1 0 0 0 0 0 0 0 1 2147 1277 45 4 4 C7orf72 7 50159118 Silent SNP G C3N-00294_T 1877731 50159118 109186855 541 13313 POM121 0 . GRCh38 7 72929971 72929971 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.340C>G p.Gln114Glu p.Q114E ENST00000395270 8/16 117 98 19 71 71 0 strelka-varscan-mutect POM121,missense_variant,p.Gln114Glu,ENST00000395270,NM_001257190.2;POM121,missense_variant,p.Gln114Glu,ENST00000627934,NM_172020.4;POM121,missense_variant,p.Gln114Glu,ENST00000358357,;POM121,missense_variant,p.Gln379Glu,ENST00000434423,;POM121,missense_variant,p.Gln114Glu,ENST00000446813,;RP11-313P13.5,upstream_gene_variant,,ENST00000608799,; G ENST00000395270 Transcript missense_variant 1381/7011 340/3000 114/999 Q/E Cag/Gag 1 1 POM121 HGNC HGNC:19702 protein_coding YES CCDS59059.1 ENSP00000378687 Q96HA1 UPI000013DA6B NM_001257190.2 deleterious(0.02) 8/16 Pfam_domain:PF15229,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF5 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999984 1 1 1 0 G 3 3 46 72929971 72929971 C G 1 0 0 0 0 1 0 0 0 12350 827 29 4 4 POM121 7 72929971 Missense_Mutation SNP C C3N-00294_T 22770853 72929971 86416002 542 13314 WBSCR27 0 . GRCh38 7 73842110 73842110 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.31G>A p.Glu11Lys p.E11K ENST00000297873 2/6 254 216 38 184 184 0 strelka-varscan-mutect WBSCR27,missense_variant,p.Glu11Lys,ENST00000297873,NM_152559.2;WBSCR27,missense_variant,p.Glu11Lys,ENST00000458679,;WBSCR27,non_coding_transcript_exon_variant,,ENST00000493174,; T ENST00000297873 Transcript missense_variant 81/941 31/738 11/245 E/K Gag/Aag 1 -1 WBSCR27 HGNC HGNC:19068 protein_coding YES CCDS5561.1 ENSP00000297873 Q8N6F8 UPI000013E466 NM_152559.2 tolerated(0.09) 2/6 hmmpanther:PTHR10108,hmmpanther:PTHR10108:SF888 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 73842110 73842110 C T 1 0 0 0 0 1 0 0 0 17825 893 31 1 1 WBSCR27 7 73842110 Missense_Mutation SNP C C3N-00294_T 912139 73842110 85503863 543 13315 ELN 0 . GRCh38 7 74056680 74056680 + Missense_Mutation SNP C C G rs137854452 C3N-00294_T C3N-00294_N C C c.1324C>G p.Gln442Glu p.Q442E ENST00000358929 21/34 656 591 65 520 520 0 strelka-varscan-mutect ELN,missense_variant,p.Gln442Glu,ENST00000358929,NM_001278939.1;ELN,missense_variant,p.Gln442Glu,ENST00000252034,NM_000501.3;ELN,missense_variant,p.Gln372Glu,ENST00000621115,NM_001278918.1;ELN,missense_variant,p.Gln447Glu,ENST00000357036,NM_001081754.2;ELN,missense_variant,p.Gln447Glu,ENST00000429192,NM_001081753.2;ELN,missense_variant,p.Gln428Glu,ENST00000380584,NM_001278916.1;ELN,missense_variant,p.Gln432Glu,ENST00000458204,NM_001278917.1;ELN,missense_variant,p.Gln437Glu,ENST00000414324,NM_001278914.1;ELN,missense_variant,p.Gln442Glu,ENST00000380576,NM_001081755.2;ELN,missense_variant,p.Gln432Glu,ENST00000380575,NM_001081752.2;ELN,missense_variant,p.Gln380Glu,ENST00000320492,NM_001278913.1;ELN,missense_variant,p.Gln325Glu,ENST00000380553,;ELN,missense_variant,p.Gln442Glu,ENST00000445912,NM_001278912.1;ELN,missense_variant,p.Gln442Glu,ENST00000320399,;ELN,missense_variant,p.Gln442Glu,ENST00000380562,NM_001278915.1;ELN,downstream_gene_variant,,ENST00000438906,;ELN,downstream_gene_variant,,ENST00000438880,;CTB-51J22.1,downstream_gene_variant,,ENST00000435932,;ELN,downstream_gene_variant,,ENST00000466878,;ELN,downstream_gene_variant,,ENST00000493839,;ELN,downstream_gene_variant,,ENST00000492210,; G ENST00000358929 Transcript missense_variant 1723/3967 1324/2361 442/786 Q/E Cag/Gag rs137854452,CM970433 1 1 ELN HGNC HGNC:3327 protein_coding YES CCDS75616.1 ENSP00000351807 F8WAH6 UPI0001AE70FA NM_001278939.1 tolerated_low_confidence(0.29) 21/34 hmmpanther:PTHR24018:SF4,hmmpanther:PTHR24018 pathogenic MODERATE SNV 5 1,1 1 PASS rs137854452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 74056680 74056680 C G 1 0 0 0 0 1 0 0 0 4906 827 29 4 4 ELN 7 74056680 Missense_Mutation SNP C C3N-00294_T 214570 74056680 85289293 544 13316 CLIP2 0 . GRCh38 7 74376312 74376312 + Silent SNP G G T rs782158293 C3N-00294_T C3N-00294_N G G c.1911G>T p.= p.S637S ENST00000223398 10/17 165 112 53 126 126 0 strelka-varscan-mutect CLIP2,synonymous_variant,p.=,ENST00000223398,NM_003388.4;CLIP2,synonymous_variant,p.=,ENST00000361545,NM_032421.2;CLIP2,synonymous_variant,p.=,ENST00000395060,;CLIP2,upstream_gene_variant,,ENST00000493166,;CLIP2,non_coding_transcript_exon_variant,,ENST00000487091,;CLIP2,upstream_gene_variant,,ENST00000482424,; T ENST00000223398 Transcript synonymous_variant 2238/5563 1911/3141 637/1046 S tcG/tcT rs782158293 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 10/17 hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10 LOW 1 SNV 5 1 PASS rs782158293 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 74376312 74376312 G T 1 0 0 0 0 0 0 0 1 3302 1103 39 1 1 CLIP2 7 74376312 Silent SNP G C3N-00294_T 319632 74376312 84969661 545 13317 PCLO 0 . GRCh38 7 82955702 82955702 + Nonsense_Mutation SNP C C A rs767901868 C3N-00294_T C3N-00294_N C C c.5251G>T p.Glu1751Ter p.E1751* ENST00000333891 5/25 298 264 34 222 222 0 strelka-varscan-mutect PCLO,stop_gained,p.Glu1751Ter,ENST00000333891,NM_033026.5;PCLO,stop_gained,p.Glu1751Ter,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript stop_gained 5589/20329 5251/15429 1751/5142 E/* Gag/Tag rs767901868 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 HIGH 1 SNV 2 1 PASS rs767901868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 82955702 82955702 C A 1 0 0 0 0 0 1 0 0 11671 922 32 2 2 PCLO 7 82955702 Nonsense_Mutation SNP C C3N-00294_T 8579390 82955702 76390271 546 13318 SEMA3D 0 . GRCh38 7 85121876 85121876 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.16G>C p.Asp6His p.D6H ENST00000284136 1/17 139 93 46 110 110 0 strelka-varscan-mutect SEMA3D,missense_variant,p.Asp6His,ENST00000284136,NM_152754.2;SEMA3D,missense_variant,p.Asp6His,ENST00000444867,; G ENST00000284136 Transcript missense_variant 60/6265 16/2334 6/777 D/H Gat/Cat 1 -1 SEMA3D HGNC HGNC:10726 protein_coding YES CCDS34676.1 ENSP00000284136 O95025 UPI0000135A66 NM_152754.2 deleterious_low_confidence(0.03) 1/17 MODERATE 1 SNV 1 1 PASS rs751753248 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 85121876 85121876 C G 1 0 0 0 0 1 0 0 0 14303 913 32 4 4 SEMA3D 7 85121876 Missense_Mutation SNP C C3N-00294_T 2166174 85121876 74224097 547 13319 ABCB4 0 . GRCh38 7 87418568 87418568 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2447G>A p.Arg816Lys p.R816K ENST00000265723 20/28 575 502 73 443 443 0 strelka-varscan-mutect ABCB4,missense_variant,p.Arg816Lys,ENST00000265723,NM_018849.2;ABCB4,missense_variant,p.Arg816Lys,ENST00000359206,NM_000443.3;ABCB4,missense_variant,p.Arg816Lys,ENST00000358400,NM_018850.2;ABCB4,missense_variant,p.Arg816Lys,ENST00000453593,; T ENST00000265723 Transcript missense_variant 2559/4020 2447/3861 816/1286 R/K aGa/aAa 1 -1 ABCB4 HGNC HGNC:45 protein_coding YES CCDS5606.1 ENSP00000265723 P21439 UPI000013D66B NM_018849.2 tolerated(0.08) 20/28 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 87418568 87418568 C T 1 0 0 0 0 1 0 0 0 47 913 32 3 3 ABCB4 7 87418568 Missense_Mutation SNP C C3N-00294_T 2296692 87418568 71927405 548 13320 AKAP9 0 . GRCh38 7 92014290 92014290 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.3574C>G p.Gln1192Glu p.Q1192E ENST00000356239 10/50 287 240 47 290 290 0 strelka-varscan-mutect AKAP9,missense_variant,p.Gln1192Glu,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Gln1203Glu,ENST00000359028,;AKAP9,missense_variant,p.Gln1192Glu,ENST00000358100,;AKAP9,missense_variant,p.Gln1200Glu,ENST00000619023,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; G ENST00000356239 Transcript missense_variant 3807/12471 3574/11724 1192/3907 Q/E Caa/Gaa 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 tolerated(0.24) 10/50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 92014290 92014290 C G 1 0 0 0 0 1 0 0 0 543 827 29 4 4 AKAP9 7 92014290 Missense_Mutation SNP C C3N-00294_T 4595722 92014290 67331683 549 13321 AKAP9 0 . GRCh38 7 92076894 92076894 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.6652G>C p.Glu2218Gln p.E2218Q ENST00000356239 29/50 52 44 8 57 57 0 strelka-varscan-mutect AKAP9,missense_variant,p.Glu2218Gln,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Glu2229Gln,ENST00000359028,;AKAP9,missense_variant,p.Glu2171Gln,ENST00000358100,;AKAP9,missense_variant,p.Glu64Gln,ENST00000394534,; C ENST00000356239 Transcript missense_variant 6885/12471 6652/11724 2218/3907 E/Q Gaa/Caa 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 deleterious(0) 29/50 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF252 MODERATE 1 SNV 1 1 PASS rs1487087847 . 0 204 5 0 0 0 0 0 -18.95305 1 1 1 1 0 C 3 2 46 92076894 92076894 G C 1 0 0 0 0 1 0 0 0 543 943 33 4 4 AKAP9 7 92076894 Missense_Mutation SNP G C3N-00294_T 62604 92076894 67269079 550 13322 AKAP9 0 . GRCh38 7 92079961 92079961 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.7828G>C p.Glu2610Gln p.E2610Q ENST00000356239 31/50 52 46 6 86 86 0 strelka-varscan-mutect AKAP9,missense_variant,p.Glu2610Gln,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Glu2621Gln,ENST00000359028,;AKAP9,missense_variant,p.Glu2563Gln,ENST00000358100,;AKAP9,missense_variant,p.Glu456Gln,ENST00000394534,;AKAP9,upstream_gene_variant,,ENST00000435423,; C ENST00000356239 Transcript missense_variant 8061/12471 7828/11724 2610/3907 E/Q Gaa/Caa 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 tolerated(0.06) 31/50 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.37363 0.9999999 1 1 1 0 C 3 2 46 92079961 92079961 G C 1 0 0 0 0 1 0 0 0 543 943 33 4 4 AKAP9 7 92079961 Missense_Mutation SNP G C3N-00294_T 3067 92079961 67266012 551 13323 PPP1R9A 0 . GRCh38 7 95284083 95284083 + Missense_Mutation SNP G G A rs764328640 C3N-00294_T C3N-00294_N G G c.3362G>A p.Arg1121His p.R1121H ENST00000433360 17/20 304 215 89 205 205 0 strelka-varscan-mutect PPP1R9A,missense_variant,p.Arg1099His,ENST00000456331,NM_001166162.1;PPP1R9A,missense_variant,p.Arg1121His,ENST00000433360,NM_001166160.1;PPP1R9A,missense_variant,p.Arg1099His,ENST00000424654,;PPP1R9A,missense_variant,p.Arg1081His,ENST00000289495,NM_001166161.1;PPP1R9A,intron_variant,,ENST00000433881,;PPP1R9A,intron_variant,,ENST00000340694,NM_017650.2,NM_001166163.1; A ENST00000433360 Transcript missense_variant 3644/5369 3362/4125 1121/1374 R/H cGt/cAt rs764328640,COSM1742529,COSM1742530 1 1 PPP1R9A HGNC HGNC:14946 protein_coding YES CCDS55127.1 ENSP00000405514 Q9ULJ8 UPI000198CF27 NM_001166160.1 tolerated(0.55) 17/20 hmmpanther:PTHR16154,hmmpanther:PTHR16154:SF22 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs764328640 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 95284083 95284083 G A 1 0 0 0 0 1 0 0 0 12501 1145 40 1 1 PPP1R9A 7 95284083 Missense_Mutation SNP G C3N-00294_T 3204122 95284083 64061890 552 13324 DLX6 0 . GRCh38 7 97007802 97007802 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.601G>C p.Ala201Pro p.A201P ENST00000518156 2/3 112 94 18 76 76 0 strelka-varscan-mutect DLX6,missense_variant,p.Ala201Pro,ENST00000518156,NM_005222.3;DLX6,missense_variant,p.Ala73Pro,ENST00000555308,;DLX6-AS1,intron_variant,,ENST00000430027,;DLX6-AS1,intron_variant,,ENST00000605417,;DLX6-AS1,intron_variant,,ENST00000437331,;DLX6-AS1,intron_variant,,ENST00000452769,;DLX6-AS1,intron_variant,,ENST00000458352,;DLX6-AS1,intron_variant,,ENST00000430404,;DLX6-AS1,intron_variant,,ENST00000437541,;DLX6-AS1,upstream_gene_variant,,ENST00000431497,;DLX6,non_coding_transcript_exon_variant,,ENST00000493273,; C ENST00000518156 Transcript missense_variant 1031/2304 601/882 201/293 A/P Gca/Cca 1 1 DLX6 HGNC HGNC:2919 protein_coding YES CCDS47647.2 ENSP00000428480 P56179 UPI0000EE57E0 NM_005222.3 deleterious(0.02) 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,Prints_domain:PR00031,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF26,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 46 97007802 97007802 G C 1 0 0 0 0 1 0 0 0 4382 1203 42 4 4 DLX6 7 97007802 Missense_Mutation SNP G C3N-00294_T 1723719 97007802 62338171 553 13325 ZAN 0 . GRCh38 7 100750815 100750815 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1440C>T p.= p.L480L ENST00000613979 12/48 98 87 11 80 80 0 strelka-varscan-mutect ZAN,synonymous_variant,p.=,ENST00000613979,NM_003386.2;ZAN,synonymous_variant,p.=,ENST00000618565,;ZAN,synonymous_variant,p.=,ENST00000620596,NM_173059.2;ZAN,synonymous_variant,p.=,ENST00000546292,;ZAN,synonymous_variant,p.=,ENST00000542585,;ZAN,synonymous_variant,p.=,ENST00000538115,;ZAN,synonymous_variant,p.=,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; T ENST00000613979 Transcript synonymous_variant 1605/8669 1440/8439 480/2812 L ctC/ctT 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 12/48 Pfam_domain:PF00629,PROSITE_profiles:PS50060,SMART_domains:SM00137,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.99859 0.9999965 1 1 1 0 T 2 4 46 100750815 100750815 C T 1 0 0 0 0 0 0 0 1 18074 900 32 3 3 ZAN 7 100750815 Silent SNP C C3N-00294_T 3743013 100750815 58595158 554 13326 MUC3A 0 . GRCh38 7 100957716 100957716 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.5937C>G p.Ile1979Met p.I1979M ENST00000379458 2/12 415 384 31 291 291 0 varscan-mutect MUC3A,missense_variant,p.Ile1979Met,ENST00000379458,NM_005960.1;MUC3A,missense_variant,p.Ile1979Met,ENST00000483366,;MUC3A,upstream_gene_variant,,ENST00000414964,; G ENST00000379458 Transcript missense_variant 6007/11226 5937/9972 1979/3323 I/M atC/atG 1 1 MUC3A HGNC HGNC:7513 protein_coding YES CCDS78262.1 ENSP00000368771 Q02505 UPI000455B941 NM_005960.1 deleterious_low_confidence(0) 2/12 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 179 0 0 31 0 0 0 -6.593509 0 0 1 0 0 G 3 3 46 100957716 100957716 C G 1 0 0 0 0 1 0 0 0 9976 816 29 4 4 MUC3A 7 100957716 Missense_Mutation SNP C C3N-00294_T 206901 100957716 58388257 555 13327 MUC17 0 . GRCh38 7 101042100 101042100 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.10684C>G p.Gln3562Glu p.Q3562E ENST00000306151 3/13 212 180 32 157 157 0 strelka-varscan-mutect MUC17,missense_variant,p.Gln3562Glu,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Gln3562Glu,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; G ENST00000306151 Transcript missense_variant 10748/14247 10684/13482 3562/4493 Q/E Cag/Gag 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(1) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 101042100 101042100 C G 1 0 0 0 0 1 0 0 0 9973 827 29 4 4 MUC17 7 101042100 Missense_Mutation SNP C C3N-00294_T 84384 101042100 58303873 556 13328 SERPINE1 0 . GRCh38 7 101128507 101128507 + Silent SNP C C T rs780207027 C3N-00294_T C3N-00294_N C C c.114C>T p.= p.F38F ENST00000223095 2/9 341 291 50 243 243 0 strelka-varscan-mutect SERPINE1,synonymous_variant,p.=,ENST00000223095,NM_000602.4; T ENST00000223095 Transcript synonymous_variant 271/3190 114/1209 38/402 F ttC/ttT rs780207027,COSM1083372 1 1 SERPINE1 HGNC HGNC:8583 protein_coding YES CCDS5711.1 ENSP00000223095 P05121 A0A024QYT5 UPI0000000CAB NM_000602.4 2/9 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF49,Gene3D:3.30.497.10,Pfam_domain:PF00079,Superfamily_domains:SSF56574 0,1 LOW 1 SNV 1 0,1 1 PASS rs780207027 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 101128507 101128507 C T 1 0 0 0 0 0 0 0 1 14387 883 31 1 1 SERPINE1 7 101128507 Silent SNP C C3N-00294_T 86407 101128507 58217466 557 13329 SPDYE2 0 . GRCh38 7 102554552 102554552 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.354C>T p.= p.H118H ENST00000507918 3/9 640 601 39 489 489 0 varscan-mutect SPDYE2,synonymous_variant,p.=,ENST00000507918,NM_001031618.3;SPDYE2,synonymous_variant,p.=,ENST00000432940,;POLR2J3,intron_variant,,ENST00000513506,;RP11-514P8.7,intron_variant,,ENST00000514917,;SPDYE2,upstream_gene_variant,,ENST00000341656,;POLR2J3,intron_variant,,ENST00000503564,;POLR2J3,intron_variant,,ENST00000506060,;POLR2J3,intron_variant,,ENST00000511773,;POLR2J3,intron_variant,,ENST00000502415,;POLR2J3,intron_variant,,ENST00000504677,;POLR2J3,intron_variant,,ENST00000489144,;POLR2J3,intron_variant,,ENST00000464525,;POLR2J3,intron_variant,,ENST00000379340,;POLR2J3,intron_variant,,ENST00000486319,;POLR2J3,intron_variant,,ENST00000508848,;POLR2J3,intron_variant,,ENST00000507355,; T ENST00000507918 Transcript synonymous_variant 828/1742 354/1209 118/402 H caC/caT 1 1 SPDYE2 HGNC HGNC:33841 protein_coding YES CCDS34716.2 ENSP00000421686 Q495Y8 I6XC90 UPI0001AE70B7 NM_001031618.3 3/9 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF12 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 102554552 102554552 C T 1 0 0 0 0 0 0 0 1 15378 506 18 3 3 SPDYE2 7 102554552 Silent SNP C C3N-00294_T 1426045 102554552 56791421 558 13330 AC105052.1 0 . GRCh38 7 102672991 102672991 + Splice_Site SNP G G C C3N-00294_T C3N-00294_N G G c.373-2C>G p.X125_splice ENST00000624140 500 469 31 341 340 1 varscan-mutect AC105052.1,splice_acceptor_variant,,ENST00000624140,;POLR2J2,upstream_gene_variant,,ENST00000358438,;POLR2J2,upstream_gene_variant,,ENST00000333432,NM_032959.5;RP11-577H5.5,upstream_gene_variant,,ENST00000476151,; C ENST00000624140 Transcript splice_acceptor_variant -/483 373/483 125/160 COSM4847189 1 -1 AC105052.1 Clone_based_ensembl_gene protein_coding YES ENSP00000485271 Q86UW5 UPI0000192108 1/1 1 HIGH SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 46 102672991 102672991 G C 1 0 0 0 0 0 0 1 0 137 1043 36 4 4 AC105052.1 7 102672991 Splice_Site SNP G C3N-00294_T 118439 102672991 56672982 559 13331 ORC5 0 . GRCh38 7 104195158 104195158 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.538C>A p.Pro180Thr p.P180T ENST00000297431 5/14 109 98 11 126 126 0 strelka-varscan-mutect ORC5,missense_variant,p.Pro180Thr,ENST00000297431,NM_002553.3;ORC5,missense_variant,p.Pro180Thr,ENST00000447452,NM_181747.3;ORC5,non_coding_transcript_exon_variant,,ENST00000485726,;ORC5,non_coding_transcript_exon_variant,,ENST00000463152,;ORC5,3_prime_UTR_variant,,ENST00000422497,; T ENST00000297431 Transcript missense_variant 681/1958 538/1308 180/435 P/T Cct/Act 1 -1 ORC5 HGNC HGNC:8491 protein_coding YES CCDS5734.1 ENSP00000297431 O43913 A4D0P7 UPI0000001C1C NM_002553.3 deleterious(0) 5/14 hmmpanther:PTHR12705,Pfam_domain:PF14630,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 104195158 104195158 G T 1 0 0 0 0 1 0 0 0 11331 1232 43 2 2 ORC5 7 104195158 Missense_Mutation SNP G C3N-00294_T 1522167 104195158 55150815 560 13332 KMT2E 0 . GRCh38 7 105101924 105101924 + Silent SNP T T A novel C3N-00294_T C3N-00294_N T T c.1926T>A p.= p.P642P ENST00000311117 17/27 435 316 119 375 375 0 strelka-varscan-mutect KMT2E,synonymous_variant,p.=,ENST00000311117,NM_182931.2;KMT2E,synonymous_variant,p.=,ENST00000257745,NM_018682.3;KMT2E,synonymous_variant,p.=,ENST00000479838,;KMT2E,downstream_gene_variant,,ENST00000622386,;CTB-152G17.6,downstream_gene_variant,,ENST00000607968,;KMT2E,synonymous_variant,p.=,ENST00000334884,; A ENST00000311117 Transcript synonymous_variant 2471/6874 1926/5577 642/1858 P ccT/ccA 1 1 KMT2E HGNC HGNC:18541 protein_coding YES CCDS34723.1 ENSP00000312379 Q8IZD2 UPI0000074133 NM_182931.2 17/27 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 105101924 105101924 T A 1 0 0 0 0 0 0 0 1 8299 1567 55 4 4 KMT2E 7 105101924 Silent SNP T C3N-00294_T 906766 105101924 54244049 561 13333 CDHR3 0 . GRCh38 7 106032658 106032658 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.2619C>T p.= p.F873F ENST00000317716 19/19 194 166 28 132 132 0 strelka-varscan-mutect CDHR3,synonymous_variant,p.=,ENST00000317716,NM_152750.4;CDHR3,synonymous_variant,p.=,ENST00000478080,NM_001301161.1;CDHR3,3_prime_UTR_variant,,ENST00000466045,;CDHR3,downstream_gene_variant,,ENST00000470188,;RP4-568B10.1,upstream_gene_variant,,ENST00000623032,;CDHR3,non_coding_transcript_exon_variant,,ENST00000468143,; T ENST00000317716 Transcript synonymous_variant 2699/3813 2619/2658 873/885 F ttC/ttT 1 1 CDHR3 HGNC HGNC:26308 protein_coding YES CCDS47684.1 ENSP00000325954 Q6ZTQ4 UPI00001C0C6E NM_152750.4 19/19 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 106032658 106032658 C T 1 0 0 0 0 0 0 0 1 2823 825 29 3 3 CDHR3 7 106032658 Silent SNP C C3N-00294_T 930734 106032658 53313315 562 13334 DUS4L 0 . GRCh38 7 107577531 107577531 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.925G>C p.Asp309His p.D309H ENST00000265720 8/8 126 110 16 103 103 0 strelka-varscan-mutect DUS4L,missense_variant,p.Asp309His,ENST00000265720,NM_001270419.1,NM_181581.2;BCAP29,upstream_gene_variant,,ENST00000379119,NM_001008405.2;BCAP29,upstream_gene_variant,,ENST00000005259,NM_018844.3;BCAP29,upstream_gene_variant,,ENST00000379117,;BCAP29,upstream_gene_variant,,ENST00000445771,;BCAP29,upstream_gene_variant,,ENST00000457837,;BCAP29,upstream_gene_variant,,ENST00000465919,;BCAP29,upstream_gene_variant,,ENST00000479917,;BCAP29,upstream_gene_variant,,ENST00000473124,;BCAP29,upstream_gene_variant,,ENST00000421217,;RP4-593H12.1,downstream_gene_variant,,ENST00000610269,;BCAP29,upstream_gene_variant,,ENST00000494086,;BCAP29,upstream_gene_variant,,ENST00000466094,;DUS4L,3_prime_UTR_variant,,ENST00000436411,;DUS4L,3_prime_UTR_variant,,ENST00000443233,;DUS4L,3_prime_UTR_variant,,ENST00000422290,;DUS4L,3_prime_UTR_variant,,ENST00000431839,;DUS4L,non_coding_transcript_exon_variant,,ENST00000485825,;DUS4L,downstream_gene_variant,,ENST00000471763,;BCAP29,upstream_gene_variant,,ENST00000482371,;DUS4L,downstream_gene_variant,,ENST00000458611,;BCAP29,upstream_gene_variant,,ENST00000442065,;DUS4L,downstream_gene_variant,,ENST00000497798,;BCAP29,upstream_gene_variant,,ENST00000486326,; C ENST00000265720 Transcript missense_variant 1287/2220 925/954 309/317 D/H Gat/Cat 1 1 DUS4L HGNC HGNC:21517 protein_coding YES CCDS5745.1 ENSP00000265720 O95620 A4D0R5 UPI000006DD5D NM_001270419.1,NM_181581.2 deleterious(0.03) 8/8 hmmpanther:PTHR11082:SF31,hmmpanther:PTHR11082,PIRSF_domain:PIRSF006621,Superfamily_domains:SSF51395 MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 107577531 107577531 G C 1 0 0 0 0 1 0 0 0 4630 942 33 4 4 DUS4L 7 107577531 Missense_Mutation SNP G C3N-00294_T 1544873 107577531 51768442 563 13335 LAMB1 0 . GRCh38 7 107935618 107935618 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3985C>G p.Leu1329Val p.L1329V ENST00000222399 27/34 261 230 31 190 190 0 strelka-varscan-mutect LAMB1,missense_variant,p.Leu1353Val,ENST00000393561,;LAMB1,missense_variant,p.Leu1329Val,ENST00000222399,NM_002291.2;LAMB1,non_coding_transcript_exon_variant,,ENST00000474380,;LAMB1,non_coding_transcript_exon_variant,,ENST00000470995,;LAMB1,non_coding_transcript_exon_variant,,ENST00000491196,;LAMB1,downstream_gene_variant,,ENST00000468999,;LAMB1,upstream_gene_variant,,ENST00000468518,;DLD,downstream_gene_variant,,ENST00000417551,; C ENST00000222399 Transcript missense_variant 4216/5725 3985/5361 1329/1786 L/V Ctt/Gtt 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 tolerated(0.56) 27/34 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 107935618 107935618 G C 1 0 0 0 0 1 0 0 0 8514 942 33 4 4 LAMB1 7 107935618 Missense_Mutation SNP G C3N-00294_T 358087 107935618 51410355 564 13336 LAMB4 0 . GRCh38 7 108105876 108105876 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.811G>A p.Ala271Thr p.A271T ENST00000388781 8/34 328 238 90 255 254 1 strelka-mutect LAMB4,missense_variant,p.Ala271Thr,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Ala271Thr,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Ala271Thr,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; T ENST00000388781 Transcript missense_variant 895/5858 811/5286 271/1761 A/T Gct/Act 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0) 8/34 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 108105876 108105876 C T 1 0 0 0 0 1 0 0 0 8517 710 25 3 3 LAMB4 7 108105876 Missense_Mutation SNP C C3N-00294_T 170258 108105876 51240097 565 13337 PNPLA8 0 . GRCh38 7 108514791 108514791 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.701C>T p.Ser234Leu p.S234L ENST00000422087 4/12 139 117 22 124 124 0 strelka-varscan-mutect PNPLA8,missense_variant,p.Ser234Leu,ENST00000426128,NM_001256009.1;PNPLA8,missense_variant,p.Ser234Leu,ENST00000422087,NM_015723.3;PNPLA8,missense_variant,p.Ser234Leu,ENST00000257694,NM_001256007.1;PNPLA8,missense_variant,p.Ser234Leu,ENST00000436062,NM_001256008.1;PNPLA8,missense_variant,p.Ser134Leu,ENST00000453144,NM_001256011.1,NM_001256010.1;PNPLA8,missense_variant,p.Ser134Leu,ENST00000453085,;PNPLA8,downstream_gene_variant,,ENST00000427008,;PNPLA8,downstream_gene_variant,,ENST00000415498,;PNPLA8,intron_variant,,ENST00000483879,;PNPLA8,intron_variant,,ENST00000476592,;PNPLA8,intron_variant,,ENST00000489738,;RPL7P32,downstream_gene_variant,,ENST00000457119,; A ENST00000422087 Transcript missense_variant 1108/3530 701/2349 234/782 S/L tCa/tTa COSM4809085 1 -1 PNPLA8 HGNC HGNC:28900 protein_coding YES CCDS34733.1 ENSP00000410804 Q9NP80 A0A024R746 UPI0000073D34 NM_015723.3 tolerated(0.22) 4/12 hmmpanther:PTHR24185 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 108514791 108514791 G A 1 0 0 0 0 1 0 0 0 12279 1294 45 3 3 PNPLA8 7 108514791 Missense_Mutation SNP G C3N-00294_T 408915 108514791 50831182 566 13338 ZNF277 0 . GRCh38 7 112296277 112296277 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.431G>T p.Arg144Ile p.R144I ENST00000361822 4/12 65 55 10 83 82 1 strelka-varscan-mutect ZNF277,missense_variant,p.Arg144Ile,ENST00000361822,NM_021994.2;ZNF277,missense_variant,p.Arg144Ile,ENST00000450657,;ZNF277,intron_variant,,ENST00000425229,;ZNF277,3_prime_UTR_variant,,ENST00000361946,;ZNF277,3_prime_UTR_variant,,ENST00000457808,; T ENST00000361822 Transcript missense_variant 560/1849 431/1353 144/450 R/I aGa/aTa 1 1 ZNF277 HGNC HGNC:13070 protein_coding YES CCDS5755.2 ENSP00000354501 Q9NRM2 UPI00000437E2 NM_021994.2 deleterious(0.01) 4/12 Low_complexity_(Seg):seg,hmmpanther:PTHR13267,hmmpanther:PTHR13267:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 112296277 112296277 G T 1 0 0 0 0 1 0 0 0 18388 942 33 2 2 ZNF277 7 112296277 Missense_Mutation SNP G C3N-00294_T 3781486 112296277 47049696 567 13339 BMT2 0 . GRCh38 7 112895693 112895693 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.349G>C p.Glu117Gln p.E117Q ENST00000297145 3/5 117 94 23 142 142 0 strelka-varscan-mutect BMT2,missense_variant,p.Glu117Gln,ENST00000297145,NM_152556.2;BMT2,missense_variant,p.Glu99Gln,ENST00000432572,;BMT2,non_coding_transcript_exon_variant,,ENST00000485446,; G ENST00000297145 Transcript missense_variant 515/3981 349/1218 117/405 E/Q Gag/Cag COSM5498556 1 -1 BMT2 HGNC HGNC:26475 protein_coding YES CCDS43634.1 ENSP00000297145 Q1RMZ1 UPI000020F946 NM_152556.2 tolerated(0.16) 3/5 HAMAP:MF_03044,hmmpanther:PTHR21008,hmmpanther:PTHR21008:SF0 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 112895693 112895693 C G 1 0 0 0 0 1 0 0 0 1628 835 29 4 4 BMT2 7 112895693 Missense_Mutation SNP C C3N-00294_T 599416 112895693 46450280 568 13340 PPP1R3A 0 . GRCh38 7 113878526 113878526 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2566C>G p.Gln856Glu p.Q856E ENST00000284601 4/4 196 168 28 214 214 0 strelka-varscan-mutect PPP1R3A,missense_variant,p.Gln856Glu,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; C ENST00000284601 Transcript missense_variant 2635/4384 2566/3369 856/1122 Q/E Caa/Gaa COSM1548122,COSM4482014 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 tolerated(0.44) 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 193 0 5 12 0 0 0 -12.89562 0.04706567 1 1 0 0 C 3 2 46 113878526 113878526 G C 1 0 0 0 0 1 0 0 0 12492 1299 45 4 4 PPP1R3A 7 113878526 Missense_Mutation SNP G C3N-00294_T 982833 113878526 45467447 569 13341 ING3 0 . GRCh38 7 120966640 120966640 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.379G>A p.Asp127Asn p.D127N ENST00000315870 6/12 496 438 58 403 403 0 strelka-varscan-mutect ING3,missense_variant,p.Asp127Asn,ENST00000315870,NM_019071.2;ING3,missense_variant,p.Asp112Asn,ENST00000431467,;ING3,stop_retained_variant,p.=,ENST00000427726,;ING3,upstream_gene_variant,,ENST00000497502,; A ENST00000315870 Transcript missense_variant 527/3777 379/1257 127/418 D/N Gac/Aac 1 1 ING3 HGNC HGNC:14587 protein_coding YES CCDS5778.1 ENSP00000320566 Q9NXR8 UPI00000373B3 NM_019071.2 deleterious(0.01) 6/12 hmmpanther:PTHR10333:SF65,hmmpanther:PTHR10333 MODERATE 1 SNV 1 1 PASS rs1193501935 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 120966640 120966640 G A 1 0 0 0 0 1 0 0 0 7639 942 33 3 3 ING3 7 120966640 Missense_Mutation SNP G C3N-00294_T 7088114 120966640 38379333 570 13342 WNT16 0 . GRCh38 7 121339056 121339056 + Missense_Mutation SNP G G A rs115155201 C3N-00294_T C3N-00294_N G G c.809G>A p.Arg270Lys p.R270K ENST00000222462 4/4 351 309 42 278 278 0 strelka-varscan-mutect WNT16,missense_variant,p.Arg270Lys,ENST00000222462,NM_057168.1;WNT16,missense_variant,p.Arg260Lys,ENST00000361301,NM_016087.2; A ENST00000222462 Transcript missense_variant 1099/3147 809/1098 270/365 R/K aGa/aAa rs115155201 1 1 WNT16 HGNC HGNC:16267 protein_coding YES CCDS5781.1 ENSP00000222462 Q9UBV4 UPI000005104C NM_057168.1 tolerated(1) 4/4 Pfam_domain:PF00110,Prints_domain:PR01895,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF70,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS rs115155201 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 121339056 121339056 G A 1 0 0 0 0 1 0 0 0 17941 942 33 3 3 WNT16 7 121339056 Missense_Mutation SNP G C3N-00294_T 372416 121339056 38006917 571 13343 PTPRZ1 0 . GRCh38 7 122011573 122011573 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2527C>G p.Pro843Ala p.P843A ENST00000393386 12/30 294 244 50 230 230 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.Pro843Ala,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; G ENST00000393386 Transcript missense_variant 2938/8175 2527/6948 843/2315 P/A Cca/Gca 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious_low_confidence(0.01) 12/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 122011573 122011573 C G 1 0 0 0 0 1 0 0 0 12969 855 30 4 4 PTPRZ1 7 122011573 Missense_Mutation SNP C C3N-00294_T 672517 122011573 37334400 572 13344 TAS2R16 0 . GRCh38 7 122994957 122994957 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.678G>C p.= p.L226L ENST00000249284 1/1 165 144 21 111 111 0 strelka-varscan-mutect TAS2R16,synonymous_variant,p.=,ENST00000249284,NM_016945.2; G ENST00000249284 Transcript synonymous_variant 744/997 678/876 226/291 L ctG/ctC 1 -1 TAS2R16 HGNC HGNC:14921 protein_coding YES CCDS5785.1 ENSP00000249284 Q9NYV7 UPI0000038B18 NM_016945.2 1/1 Pfam_domain:PF05296,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF68,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 122994957 122994957 C G 1 0 0 0 0 0 0 0 1 15968 813 29 4 4 TAS2R16 7 122994957 Silent SNP C C3N-00294_T 983384 122994957 36351016 573 13345 IQUB 0 . GRCh38 7 123457513 123457513 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.2061C>T p.= p.L687L ENST00000466202 12/13 294 242 52 189 189 0 strelka-varscan-mutect IQUB,synonymous_variant,p.=,ENST00000466202,NM_001321293.1,NM_001282855.1;IQUB,synonymous_variant,p.=,ENST00000324698,NM_178827.4;RNU6-296P,downstream_gene_variant,,ENST00000384608,;RP11-332K15.1,non_coding_transcript_exon_variant,,ENST00000419832,;IQUB,3_prime_UTR_variant,,ENST00000484508,;IQUB,3_prime_UTR_variant,,ENST00000469057,; A ENST00000466202 Transcript synonymous_variant 2638/3296 2061/2376 687/791 L ctC/ctT 1 -1 IQUB HGNC HGNC:21995 protein_coding YES CCDS5787.1 ENSP00000417769 Q8NA54 A0A024R771 UPI000013E3DF NM_001321293.1,NM_001282855.1 12/13 hmmpanther:PTHR21074,hmmpanther:PTHR21074:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 123457513 123457513 G A 1 0 0 0 0 0 0 0 1 7726 1277 45 3 3 IQUB 7 123457513 Silent SNP G C3N-00294_T 462556 123457513 35888460 574 13346 ZNF800 0 . GRCh38 7 127374903 127374903 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.433C>T p.Gln145Ter p.Q145* ENST00000393313 5/6 86 75 11 90 90 0 strelka-varscan-mutect ZNF800,stop_gained,p.Gln145Ter,ENST00000393313,;ZNF800,stop_gained,p.Gln145Ter,ENST00000265827,NM_176814.4;ZNF800,stop_gained,p.Gln145Ter,ENST00000393312,;ZNF800,stop_gained,p.Gln145Ter,ENST00000619291,;ZNF800,stop_gained,p.Gln145Ter,ENST00000434602,;ZNF800,downstream_gene_variant,,ENST00000436992,;ZNF800,downstream_gene_variant,,ENST00000439506,;ZNF800,upstream_gene_variant,,ENST00000485577,; A ENST00000393313 Transcript stop_gained 1025/4358 433/1995 145/664 Q/* Caa/Taa 1 -1 ZNF800 HGNC HGNC:27267 protein_coding YES CCDS5795.1 ENSP00000376989 Q2TB10 UPI000020FA03 5/6 hmmpanther:PTHR21020 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 127374903 127374903 G A 1 0 0 0 0 0 1 0 0 18754 1299 45 3 3 ZNF800 7 127374903 Nonsense_Mutation SNP G C3N-00294_T 3917390 127374903 31971070 575 13347 SND1 0 . GRCh38 7 128074511 128074511 + Missense_Mutation SNP G G C rs764619324 C3N-00294_T C3N-00294_N G G c.1789G>C p.Glu597Gln p.E597Q ENST00000354725 17/24 93 85 8 57 57 0 strelka-varscan-mutect SND1,missense_variant,p.Glu597Gln,ENST00000354725,NM_014390.2;SND1,intron_variant,,ENST00000486037,;SND1,non_coding_transcript_exon_variant,,ENST00000470723,;SND1,non_coding_transcript_exon_variant,,ENST00000470463,;SND1,non_coding_transcript_exon_variant,,ENST00000484767,; C ENST00000354725 Transcript missense_variant 1983/3476 1789/2733 597/910 E/Q Gag/Cag rs764619324 1 1 SND1 HGNC HGNC:30646 protein_coding YES CCDS34747.1 ENSP00000346762 Q7KZF4 A0A140VK49 UPI00000727E5 NM_014390.2 tolerated(0.17) 17/24 Superfamily_domains:0047647,Gene3D:2.40.50.90,Pfam_domain:PF00565,PIRSF_domain:PIRSF017179,PROSITE_profiles:PS50830,hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF5,Low_complexity_(Seg):seg,SMART_domains:SM00318 MODERATE 1 SNV 1 1 PASS rs764619324 . 0 206 4 0 0 0 0 0 -16.72634 1 1 1 1 0 C 3 2 46 128074511 128074511 G C 1 0 0 0 0 1 0 0 0 15165 1175 41 4 4 SND1 7 128074511 Missense_Mutation SNP G C3N-00294_T 699608 128074511 31271462 576 13348 TSGA13 0 . GRCh38 7 130671706 130671706 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.613C>A p.Gln205Lys p.Q205K ENST00000456951 8/9 253 224 29 235 235 0 strelka-varscan-mutect TSGA13,missense_variant,p.Gln205Lys,ENST00000456951,NM_001304968.1;TSGA13,missense_variant,p.Gln205Lys,ENST00000356588,NM_052933.3;COPG2,upstream_gene_variant,,ENST00000425248,NM_012133.5;COPG2,upstream_gene_variant,,ENST00000330992,NM_001290033.1; T ENST00000456951 Transcript missense_variant 1465/2046 613/828 205/275 Q/K Cag/Aag COSM3703130,COSM4818915 1 -1 TSGA13 HGNC HGNC:12369 protein_coding YES CCDS5824.1 ENSP00000406047 Q96PP4 A0A024R769 UPI0000073CFB NM_001304968.1 tolerated(0.1) 8/9 Pfam_domain:PF14994,hmmpanther:PTHR37352 1,1 MODERATE SNV 2 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 130671706 130671706 G T 1 0 0 0 0 1 0 0 0 17125 1299 45 2 2 TSGA13 7 130671706 Missense_Mutation SNP G C3N-00294_T 2597195 130671706 28674267 577 13349 TSGA13 0 . GRCh38 7 130679222 130679222 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.320C>G p.Ser107Ter p.S107* ENST00000456951 6/9 230 201 29 183 183 0 strelka-varscan-mutect TSGA13,stop_gained,p.Ser107Ter,ENST00000456951,NM_001304968.1;TSGA13,stop_gained,p.Ser107Ter,ENST00000356588,NM_052933.3;TSGA13,downstream_gene_variant,,ENST00000438346,;TSGA13,downstream_gene_variant,,ENST00000443954,; C ENST00000456951 Transcript stop_gained 1172/2046 320/828 107/275 S/* tCa/tGa 1 -1 TSGA13 HGNC HGNC:12369 protein_coding YES CCDS5824.1 ENSP00000406047 Q96PP4 A0A024R769 UPI0000073CFB NM_001304968.1 6/9 Pfam_domain:PF14994,hmmpanther:PTHR37352 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 130679222 130679222 G C 1 0 0 0 0 0 1 0 0 17125 1294 45 4 4 TSGA13 7 130679222 Nonsense_Mutation SNP G C3N-00294_T 7516 130679222 28666751 578 13350 NUP205 0 . GRCh38 7 135576293 135576293 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.367C>T p.Pro123Ser p.P123S ENST00000285968 4/43 157 138 19 97 96 1 strelka-varscan-mutect NUP205,missense_variant,p.Pro123Ser,ENST00000285968,NM_015135.2;NUP205,downstream_gene_variant,,ENST00000489493,; T ENST00000285968 Transcript missense_variant 393/6266 367/6039 123/2012 P/S Cct/Tct 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 deleterious(0.01) 4/43 Pfam_domain:PF11894,hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 135576293 135576293 C T 1 0 0 0 0 1 0 0 0 10824 855 30 3 3 NUP205 7 135576293 Missense_Mutation SNP C C3N-00294_T 4897071 135576293 23769680 579 13351 NUP205 0 . GRCh38 7 135619848 135619848 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.4290G>A p.= p.Q1430Q ENST00000285968 30/43 166 148 18 121 121 0 strelka-varscan-mutect NUP205,synonymous_variant,p.=,ENST00000285968,NM_015135.2;NUP205,downstream_gene_variant,,ENST00000472132,;NUP205,synonymous_variant,p.=,ENST00000477620,;NUP205,non_coding_transcript_exon_variant,,ENST00000607647,;NUP205,downstream_gene_variant,,ENST00000463247,; A ENST00000285968 Transcript synonymous_variant 4316/6266 4290/6039 1430/2012 Q caG/caA 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 30/43 Pfam_domain:PF11894,hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 135619848 135619848 G A 1 0 0 0 0 0 0 0 1 10824 933 33 3 3 NUP205 7 135619848 Silent SNP G C3N-00294_T 43555 135619848 23726125 580 13352 ATP6V0A4 0 . GRCh38 7 138709779 138709779 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.2274C>G p.= p.L758L ENST00000310018 21/22 496 439 57 390 390 0 strelka-varscan-mutect ATP6V0A4,synonymous_variant,p.=,ENST00000310018,NM_020632.2,NM_130840.2;ATP6V0A4,synonymous_variant,p.=,ENST00000393054,NM_130841.2;ATP6V0A4,synonymous_variant,p.=,ENST00000353492,; C ENST00000310018 Transcript synonymous_variant 2557/3135 2274/2523 758/840 L ctC/ctG 1 -1 ATP6V0A4 HGNC HGNC:866 protein_coding YES CCDS5849.1 ENSP00000308122 Q9HBG4 A0A024R791 UPI000013CDFD NM_020632.2,NM_130840.2 21/22 Pfam_domain:PF01496,PIRSF_domain:PIRSF001293,hmmpanther:PTHR11629,hmmpanther:PTHR11629:SF26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 138709779 138709779 G C 1 0 0 0 0 0 0 0 1 1323 929 33 4 4 ATP6V0A4 7 138709779 Silent SNP G C3N-00294_T 3089931 138709779 20636194 581 13353 DENND2A 0 . GRCh38 7 140519710 140519710 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2920G>C p.Glu974Gln p.E974Q ENST00000275884 18/19 201 177 24 128 128 0 strelka-varscan-mutect DENND2A,missense_variant,p.Glu974Gln,ENST00000275884,NM_001318052.1;DENND2A,missense_variant,p.Glu974Gln,ENST00000496613,;DENND2A,missense_variant,p.Glu974Gln,ENST00000537639,NM_015689.3;DENND2A,3_prime_UTR_variant,,ENST00000461883,; G ENST00000275884 Transcript missense_variant 3338/3735 2920/3030 974/1009 E/Q Gag/Cag 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 deleterious(0.02) 18/19 hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF3,Pfam_domain:PF03455 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 140519710 140519710 C G 1 0 0 0 0 1 0 0 0 4233 835 29 4 4 DENND2A 7 140519710 Missense_Mutation SNP C C3N-00294_T 1809931 140519710 18826263 582 13354 DENND2A 0 . GRCh38 7 140602368 140602368 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.30C>T p.= p.I10I ENST00000275884 2/19 66 59 7 66 66 0 strelka-varscan-mutect DENND2A,synonymous_variant,p.=,ENST00000275884,NM_001318052.1;DENND2A,synonymous_variant,p.=,ENST00000492720,NM_001318053.1;DENND2A,synonymous_variant,p.=,ENST00000496613,;DENND2A,synonymous_variant,p.=,ENST00000537639,NM_015689.3;DENND2A,synonymous_variant,p.=,ENST00000491728,;DENND2A,synonymous_variant,p.=,ENST00000477488,;DENND2A,synonymous_variant,p.=,ENST00000489552,;DENND2A,intron_variant,,ENST00000475837,;DENND2A,synonymous_variant,p.=,ENST00000461883,; A ENST00000275884 Transcript synonymous_variant 448/3735 30/3030 10/1009 I atC/atT COSM5612545,COSM5612546 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 2/19 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -16.22949 1 1 1 1 0 A 2 1 46 140602368 140602368 G A 1 0 0 0 0 0 0 0 1 4233 1280 45 3 3 DENND2A 7 140602368 Silent SNP G C3N-00294_T 82658 140602368 18743605 583 13355 PRSS1 0 . GRCh38 7 142751984 142751984 + Silent SNP G G A rs369013081 C3N-00294_T C3N-00294_N G G c.411G>A p.= p.T137T ENST00000311737 3/5 401 273 128 287 287 0 strelka-varscan-mutect PRSS1,synonymous_variant,p.=,ENST00000486171,;PRSS1,synonymous_variant,p.=,ENST00000612126,;PRSS1,synonymous_variant,p.=,ENST00000311737,NM_002769.4;PRSS1,synonymous_variant,p.=,ENST00000619214,;PRSS1,synonymous_variant,p.=,ENST00000492062,;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS1,non_coding_transcript_exon_variant,,ENST00000485223,;PRSS1,non_coding_transcript_exon_variant,,ENST00000463701,;PRSS1,downstream_gene_variant,,ENST00000497041,; A ENST00000311737 Transcript synonymous_variant 417/800 411/744 137/247 T acG/acA rs369013081,COSM246810 1 1 PRSS1 HGNC HGNC:9475 protein_coding YES CCDS5872.1 ENSP00000308720 P07477 UPI0000001309 NM_002769.4 3/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24264:SF12,hmmpanther:PTHR24264,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 LOW 1 SNV 1 0,1 1 PASS rs369013081 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 142751984 142751984 G A 1 0 0 0 0 0 0 0 1 12761 1045 37 1 1 PRSS1 7 142751984 Silent SNP G C3N-00294_T 2149616 142751984 16593989 584 13356 TRPV6 0 . GRCh38 7 142873577 142873577 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1779C>T p.= p.F593F ENST00000359396 13/15 576 501 75 425 424 1 strelka-varscan-mutect TRPV6,synonymous_variant,p.=,ENST00000359396,NM_018646.5;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;TRPV6,downstream_gene_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000619250,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; A ENST00000359396 Transcript synonymous_variant 1905/2928 1779/2298 593/765 F ttC/ttT 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 13/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 142873577 142873577 G A 1 0 0 0 0 0 0 0 1 17106 1281 45 3 3 TRPV6 7 142873577 Silent SNP G C3N-00294_T 121593 142873577 16472396 585 13357 TRPV5 0 . GRCh38 7 142925546 142925546 + Nonsense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.1105C>T p.Gln369Ter p.Q369* ENST00000265310 8/15 364 328 36 291 291 0 strelka-varscan-mutect TRPV5,stop_gained,p.Gln369Ter,ENST00000265310,NM_019841.6;TRPV5,stop_gained,p.Gln369Ter,ENST00000442623,;TRPV5,stop_gained,p.Gln314Ter,ENST00000439304,; A ENST00000265310 Transcript stop_gained 1454/2952 1105/2190 369/729 Q/* Cag/Tag COSM3878891 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 8/15 Pfam_domain:PF00520,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870 1 HIGH 1 SNV 1 1 1 PASS rs1350410887 . 0 205 0 0 5 0 0 0 -11.3295 0.5535841 1 1 1 0 A 4 1 46 142925546 142925546 G A 1 0 0 0 0 0 1 0 0 17105 1357 47 3 3 TRPV5 7 142925546 Nonsense_Mutation SNP G C3N-00294_T 51969 142925546 16420427 586 13358 ZYX 0 . GRCh38 7 143382592 143382592 + Splice_Site SNP G G T novel C3N-00294_T C3N-00294_N G G c.409-1G>T p.X137_splice ENST00000322764 184 111 73 129 129 0 strelka-varscan-mutect ZYX,splice_acceptor_variant,,ENST00000322764,NM_001010972.1,NM_003461.4;ZYX,splice_acceptor_variant,,ENST00000392910,;ZYX,splice_acceptor_variant,,ENST00000457235,;ZYX,splice_acceptor_variant,,ENST00000449630,;ZYX,intron_variant,,ENST00000354434,;ZYX,upstream_gene_variant,,ENST00000446634,;MIR6892,upstream_gene_variant,,ENST00000612346,;AC093673.5,upstream_gene_variant,,ENST00000429630,;ZYX,intron_variant,,ENST00000477373,;ZYX,non_coding_transcript_exon_variant,,ENST00000468083,;ZYX,upstream_gene_variant,,ENST00000436448,; T ENST00000322764 Transcript splice_acceptor_variant -/2493 409/1719 137/572 1 1 ZYX HGNC HGNC:13200 protein_coding YES CCDS5883.1 ENSP00000324422 Q15942 UPI00000424F2 NM_001010972.1,NM_003461.4 3/9 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 46 143382592 143382592 G T 1 0 0 0 0 0 0 1 0 18858 985 34 2 2 ZYX 7 143382592 Splice_Site SNP G C3N-00294_T 457046 143382592 15963381 587 13359 TCAF2 0 . GRCh38 7 143720281 143720281 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1222G>C p.Glu408Gln p.E408Q ENST00000444908 3/7 76 70 6 84 84 0 varscan-mutect TCAF2,missense_variant,p.Glu408Gln,ENST00000441159,;TCAF2,missense_variant,p.Glu408Gln,ENST00000444908,NM_001130025.1;TCAF2,missense_variant,p.Glu408Gln,ENST00000357344,NM_173678.2;TCAF2,missense_variant,p.Glu244Gln,ENST00000411935,;TCAF2,missense_variant,p.Glu244Gln,ENST00000425618,NM_001130026.2;TCAF2,missense_variant,p.Glu223Gln,ENST00000518791,;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,; C ENST00000444908 Transcript missense_variant 1307/2976 1222/2538 408/845 E/Q Gag/Cag 1 1 TCAF2 HGNC HGNC:26878 protein_coding YES CCDS34769.1 ENSP00000412724 A6NFQ2 UPI00001AF3A8 NM_001130025.1 tolerated(0.33) 3/7 hmmpanther:PTHR15730,hmmpanther:PTHR15730:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -13.49062 1 1 1 1 0 C 3 2 46 143720281 143720281 G C 1 0 0 0 0 1 0 0 0 16071 1291 45 4 4 TCAF2 7 143720281 Missense_Mutation SNP G C3N-00294_T 337689 143720281 15625692 588 13360 OR2A5 0 . GRCh38 7 144050520 144050520 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.119G>T p.Gly40Val p.G40V ENST00000408906 1/1 90 82 8 45 45 0 strelka-varscan-mutect OR2A5,missense_variant,p.Gly40Val,ENST00000408906,NM_012365.1; T ENST00000408906 Transcript missense_variant 153/1013 119/936 40/311 G/V gGa/gTa COSM3635397 1 1 OR2A5 HGNC HGNC:8232 protein_coding YES CCDS43668.1 ENSP00000386208 Q96R48 A0A126GW49 UPI0000061F52 NM_012365.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF232,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 144050520 144050520 G T 1 0 0 0 0 1 0 0 0 11058 1174 41 2 2 OR2A5 7 144050520 Missense_Mutation SNP G C3N-00294_T 330239 144050520 15295453 589 13361 CNTNAP2 0 . GRCh38 7 148267087 148267087 + Missense_Mutation SNP T T G rs372173607 C3N-00294_T C3N-00294_N T T c.3436T>G p.Phe1146Val p.F1146V ENST00000361727 21/24 631 436 195 462 462 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Phe1146Val,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Phe205Val,ENST00000628930,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636242,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,; G ENST00000361727 Transcript missense_variant 3954/9896 3436/3996 1146/1331 F/V Ttc/Gtc rs372173607 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 21/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs372173607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 148267087 148267087 T G 1 0 0 0 0 1 0 0 0 3428 1609 56 5 5 CNTNAP2 7 148267087 Missense_Mutation SNP T C3N-00294_T 4216567 148267087 11078886 590 13362 GIMAP4 0 . GRCh38 7 150572521 150572521 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.451C>G p.Leu151Val p.L151V ENST00000255945 3/3 333 287 46 254 254 0 strelka-varscan-mutect GIMAP4,missense_variant,p.Leu151Val,ENST00000255945,NM_018326.2;GIMAP4,missense_variant,p.Leu165Val,ENST00000461940,;GIMAP4,downstream_gene_variant,,ENST00000479232,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000494750,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000478135,; G ENST00000255945 Transcript missense_variant 626/2060 451/990 151/329 L/V Ctc/Gtc 1 1 GIMAP4 HGNC HGNC:21872 protein_coding YES CCDS5904.1 ENSP00000255945 Q9NUV9 A0A090N7X0 UPI0000073CB0 NM_018326.2 tolerated(0.07) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF04548,PROSITE_profiles:PS51720,hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF57,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 150572521 150572521 C G 1 0 0 0 0 1 0 0 0 6261 913 32 4 4 GIMAP4 7 150572521 Missense_Mutation SNP C C3N-00294_T 2305434 150572521 8773452 591 13363 ATG9B 0 . GRCh38 7 151021321 151021321 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.830C>T p.Ser277Phe p.S277F ENST00000605952 5/17 116 97 19 60 60 0 strelka-varscan-mutect ATG9B,missense_variant,p.Ser277Phe,ENST00000469530,NM_173681.5;ATG9B,non_coding_transcript_exon_variant,,ENST00000617967,;ATG9B,non_coding_transcript_exon_variant,,ENST00000473409,;ATG9B,non_coding_transcript_exon_variant,,ENST00000466157,;ATG9B,upstream_gene_variant,,ENST00000611177,;ATG9B,missense_variant,p.Ser277Phe,ENST00000605952,;ATG9B,non_coding_transcript_exon_variant,,ENST00000473134,; A ENST00000605952 Transcript missense_variant,NMD_transcript_variant 906/4572 830/2775 277/924 S/F tCc/tTc 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 tolerated(0.09) 5/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 151021321 151021321 G A 1 0 0 0 0 1 0 0 0 1255 1174 41 3 3 ATG9B 7 151021321 Missense_Mutation SNP G C3N-00294_T 448800 151021321 8324652 592 13364 GALNTL5 0 . GRCh38 7 151971034 151971034 + Missense_Mutation SNP G G A rs181262306 C3N-00294_T C3N-00294_N G G c.337G>A p.Glu113Lys p.E113K ENST00000616416 4/10 213 181 32 209 209 0 strelka-varscan-mutect GALNTL5,missense_variant,p.Glu113Lys,ENST00000616416,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000392800,NM_145292.3;GALNTL5,missense_variant,p.Glu113Lys,ENST00000431418,;GALNTL5,non_coding_transcript_exon_variant,,ENST00000468278,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000416269,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000414073,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000426341,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000448366,;GALNTL5,missense_variant,p.Glu113Lys,ENST00000416062,; A ENST00000616416 Transcript missense_variant 643/1763 337/1332 113/443 E/K Gaa/Aaa rs181262306,COSM134242 1 1 GALNTL5 HGNC HGNC:21725 protein_coding YES CCDS5929.1 ENSP00000479207 Q7Z4T8 UPI000013C82E tolerated(0.09) 4/10 hmmpanther:PTHR11675:SF17,hmmpanther:PTHR11675 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs181262306 . 0 207 0 0 0 0 0 2 -3.467384 0 0 1 0 0 A 3 1 46 151971034 151971034 G A 1 0 0 0 0 1 0 0 0 6092 1059 37 1 1 GALNTL5 7 151971034 Missense_Mutation SNP G C3N-00294_T 949713 151971034 7374939 593 13365 XRCC2 0 . GRCh38 7 152649174 152649174 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.311C>T p.Ser104Phe p.S104F ENST00000359321 3/3 97 79 18 87 87 0 strelka-varscan-mutect XRCC2,missense_variant,p.Ser104Phe,ENST00000359321,NM_005431.1;XRCC2,non_coding_transcript_exon_variant,,ENST00000495707,; A ENST00000359321 Transcript missense_variant 397/3067 311/843 104/280 S/F tCt/tTt 1 -1 XRCC2 HGNC HGNC:12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 deleterious(0.01) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF08423,PROSITE_profiles:PS50162,hmmpanther:PTHR22942,hmmpanther:PTHR22942:SF44,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 152649174 152649174 G A 1 0 0 0 0 1 0 0 0 18012 942 33 3 3 XRCC2 7 152649174 Missense_Mutation SNP G C3N-00294_T 678140 152649174 6696799 594 13366 PTPRN2 0 . GRCh38 7 158167182 158167182 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.659C>G p.Thr220Ser p.T220S ENST00000389418 6/23 170 152 18 171 171 0 strelka-varscan PTPRN2,missense_variant,p.Thr220Ser,ENST00000389413,NM_130843.2;PTPRN2,missense_variant,p.Thr182Ser,ENST00000409483,NM_001308267.1;PTPRN2,missense_variant,p.Thr220Ser,ENST00000389418,NM_001308268.1,NM_002847.3;PTPRN2,missense_variant,p.Thr203Ser,ENST00000389416,NM_130842.2;PTPRN2,missense_variant,p.Thr129Ser,ENST00000404321,; C ENST00000389418 Transcript missense_variant 669/4706 659/3048 220/1015 T/S aCc/aGc 1 -1 PTPRN2 HGNC HGNC:9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 UPI000002E7C7 NM_001308268.1,NM_002847.3 tolerated(0.13) 6/23 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999864 1 1 1 0 C 3 2 46 158167182 158167182 G C 1 0 0 0 0 1 0 0 0 12962 1261 44 4 4 PTPRN2 7 158167182 Missense_Mutation SNP G C3N-00294_T 5518008 158167182 1178791 595 13367 DLGAP2 0 . GRCh38 8 1548922 1548923 + Frame_Shift_Ins INS - - G novel C3N-00294_T C3N-00294_N - - c.229_230insG p.Ser77CysfsTer199 p.S77Cfs*199 ENST00000612087 2/11 231 124 107 313 313 0 sindel-varindel DLGAP2,frameshift_variant,p.Ser77CysfsTer199,ENST00000612087,NM_001277161.1;DLGAP2,frameshift_variant,p.Ser94CysfsTer199,ENST00000520901,;DLGAP2,frameshift_variant,p.Ser157CysfsTer199,ENST00000637795,;DLGAP2,frameshift_variant,p.Ser156CysfsTer199,ENST00000421627,;DLGAP2,frameshift_variant,p.Ser77CysfsTer199,ENST00000637152,NM_004745.4; G ENST00000612087 Transcript frameshift_variant 363-364/10088 229-230/2886 77/961 S/CX tcc/tGcc 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 2/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3 HIGH 1 insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 46 1548922 1548922 - G 1 0 1 1 0 0 0 0 0 4367 1667 58 0 0 DLGAP2 8 1548922 Frame_Shift_Ins INS - C3N-00294_T 1548922 143589714 596 13368 SGK223 0 . GRCh38 8 8318175 8318175 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.4200G>A p.= p.L1400L ENST00000615670 6/6 72 62 10 108 107 1 strelka-varscan-mutect SGK223,synonymous_variant,p.=,ENST00000615670,;SGK223,synonymous_variant,p.=,ENST00000622241,NM_001080826.2; T ENST00000615670 Transcript synonymous_variant 4465/4903 4200/4221 1400/1406 L ctG/ctA 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972 LOW 1 SNV 5 1 PASS rs904964258 . 0 206 3 0 0 0 0 0 -19.99792 1 1 1 1 0 T 2 4 46 8318175 8318175 C T 1 0 0 0 0 0 0 0 1 14469 813 29 3 3 SGK223 8 8318175 Silent SNP C C3N-00294_T 6769253 8318175 136820461 597 13369 SGK223 0 . GRCh38 8 8376440 8376440 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1969G>A p.Glu657Lys p.E657K ENST00000615670 3/6 157 125 32 168 168 0 strelka-varscan-mutect SGK223,missense_variant,p.Glu657Lys,ENST00000615670,;SGK223,missense_variant,p.Glu657Lys,ENST00000622241,NM_001080826.2; T ENST00000615670 Transcript missense_variant 2234/4903 1969/4221 657/1406 E/K Gag/Aag 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F tolerated(0.29) 3/6 hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 8376440 8376440 C T 1 0 0 0 0 1 0 0 0 14469 922 32 3 3 SGK223 8 8376440 Missense_Mutation SNP C C3N-00294_T 58265 8376440 136762196 598 13370 SGK223 0 . GRCh38 8 8377223 8377223 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1186G>C p.Glu396Gln p.E396Q ENST00000615670 3/6 121 90 31 122 122 0 strelka-varscan-mutect SGK223,missense_variant,p.Glu396Gln,ENST00000615670,;SGK223,missense_variant,p.Glu396Gln,ENST00000622241,NM_001080826.2; G ENST00000615670 Transcript missense_variant 1451/4903 1186/4221 396/1406 E/Q Gag/Cag 1 -1 SGK223 Clone_based_vega_gene protein_coding YES CCDS43706.1 ENSP00000481109 Q86YV5 UPI0003EAF98F deleterious(0.05) 3/6 hmmpanther:PTHR22972:SF3,hmmpanther:PTHR22972 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 8377223 8377223 C G 1 0 0 0 0 1 0 0 0 14469 864 30 4 4 SGK223 8 8377223 Missense_Mutation SNP C C3N-00294_T 783 8377223 136761413 599 13371 NEIL2 0 . GRCh38 8 11786058 11786058 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.784G>A p.Asp262Asn p.D262N ENST00000284503 5/5 307 246 61 302 302 0 strelka-varscan-mutect NEIL2,missense_variant,p.Asp262Asn,ENST00000284503,NM_145043.2;NEIL2,missense_variant,p.Asp262Asn,ENST00000455213,;NEIL2,missense_variant,p.Asp262Asn,ENST00000436750,NM_001135746.1;NEIL2,missense_variant,p.Asp201Asn,ENST00000403422,NM_001135747.1;NEIL2,missense_variant,p.Asp146Asn,ENST00000528323,NM_001135748.1;NEIL2,3_prime_UTR_variant,,ENST00000528113,;NEIL2,non_coding_transcript_exon_variant,,ENST00000524741,;SUB1P1,upstream_gene_variant,,ENST00000524415,; A ENST00000284503 Transcript missense_variant 1383/2671 784/999 262/332 D/N Gat/Aat 1 1 NEIL2 HGNC HGNC:18956 protein_coding YES CCDS5984.1 ENSP00000284503 Q969S2 A0A024R361 UPI000006D86F NM_145043.2 deleterious(0.02) 5/5 Gene3D:1.10.8.50,Pfam_domain:PF06831,hmmpanther:PTHR22993,hmmpanther:PTHR22993:SF11,SMART_domains:SM01232,Superfamily_domains:SSF46946 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 11786058 11786058 G A 1 0 0 0 0 1 0 0 0 10347 1174 41 3 3 NEIL2 8 11786058 Missense_Mutation SNP G C3N-00294_T 3408835 11786058 133352578 600 13372 TUSC3 0 . GRCh38 8 15659556 15659556 + Missense_Mutation SNP G G T rs766923947 C3N-00294_T C3N-00294_N G G c.476G>T p.Arg159Ile p.R159I ENST00000503731 4/11 312 205 107 403 401 2 strelka-varscan-mutect TUSC3,missense_variant,p.Arg159Ile,ENST00000382020,NM_178234.2;TUSC3,missense_variant,p.Arg159Ile,ENST00000506802,;TUSC3,missense_variant,p.Arg159Ile,ENST00000503731,NM_006765.3;TUSC3,missense_variant,p.Arg159Ile,ENST00000509380,;TUSC3,missense_variant,p.Arg113Ile,ENST00000511783,;TUSC3,non_coding_transcript_exon_variant,,ENST00000503191,;TUSC3,non_coding_transcript_exon_variant,,ENST00000507400,;TUSC3,missense_variant,p.Arg159Ile,ENST00000515859,;TUSC3,missense_variant,p.Arg159Ile,ENST00000510836,; T ENST00000503731 Transcript missense_variant 624/1498 476/1047 159/348 R/I aGa/aTa rs766923947,COSM5079481,COSM5079482 1 1 TUSC3 HGNC HGNC:30242 protein_coding YES CCDS5994.1 ENSP00000424544 Q13454 UPI000012FC21 NM_006765.3 deleterious(0) 4/11 Gene3D:3.40.30.10,Pfam_domain:PF04756,hmmpanther:PTHR12692,hmmpanther:PTHR12692:SF1,Superfamily_domains:SSF52833 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766923947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 15659556 15659556 G T 1 0 0 0 0 1 0 0 0 17290 942 33 2 2 TUSC3 8 15659556 Missense_Mutation SNP G C3N-00294_T 3873498 15659556 129479080 601 13373 VPS37A 0 . GRCh38 8 17286374 17286374 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1141G>T p.Glu381Ter p.E381* ENST00000324849 11/12 128 109 19 166 166 0 strelka-varscan-mutect VPS37A,stop_gained,p.Glu381Ter,ENST00000324849,NM_152415.2;VPS37A,stop_gained,p.Glu356Ter,ENST00000521829,NM_001145152.1;VPS37A,stop_gained,p.Glu154Ter,ENST00000521976,;VPS37A,3_prime_UTR_variant,,ENST00000425020,;VPS37A,3_prime_UTR_variant,,ENST00000520140,; T ENST00000324849 Transcript stop_gained 1815/4906 1141/1194 381/397 E/* Gag/Tag 1 1 VPS37A HGNC HGNC:24928 protein_coding YES CCDS6001.1 ENSP00000318629 Q8NEZ2 UPI0000039EC3 NM_152415.2 11/12 PROSITE_profiles:PS51314,hmmpanther:PTHR13678,hmmpanther:PTHR13678:SF2,Superfamily_domains:SSF140111 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 17286374 17286374 G T 1 0 0 0 0 0 1 0 0 17751 943 33 2 2 VPS37A 8 17286374 Nonsense_Mutation SNP G C3N-00294_T 1626818 17286374 127852262 602 13374 DOCK5 0 . GRCh38 8 25408860 25408860 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.5324C>T p.Ser1775Leu p.S1775L ENST00000276440 50/52 252 209 43 302 302 0 strelka-varscan-mutect DOCK5,missense_variant,p.Ser1775Leu,ENST00000276440,NM_024940.6;DOCK5,3_prime_UTR_variant,,ENST00000467709,;DOCK5,upstream_gene_variant,,ENST00000521405,;DOCK5,upstream_gene_variant,,ENST00000479547,; T ENST00000276440 Transcript missense_variant 5368/10075 5324/5613 1775/1870 S/L tCa/tTa 1 1 DOCK5 HGNC HGNC:23476 protein_coding YES CCDS6047.1 ENSP00000276440 Q9H7D0 UPI000022D4F3 NM_024940.6 tolerated(0.11) 50/52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 25408860 25408860 C T 1 0 0 0 0 1 0 0 0 4505 838 29 3 3 DOCK5 8 25408860 Missense_Mutation SNP C C3N-00294_T 8122486 25408860 119729776 603 13375 ADRA1A 0 . GRCh38 8 26864248 26864248 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.722C>G p.Ala241Gly p.A241G ENST00000380586 1/3 229 136 93 209 209 0 strelka-varscan-mutect ADRA1A,missense_variant,p.Ala241Gly,ENST00000380573,;ADRA1A,missense_variant,p.Ala241Gly,ENST00000380586,NM_033303.3;ADRA1A,missense_variant,p.Ala241Gly,ENST00000276393,NM_000680.2;ADRA1A,missense_variant,p.Ala241Gly,ENST00000380582,NM_033302.2;ADRA1A,missense_variant,p.Ala241Gly,ENST00000519229,;ADRA1A,missense_variant,p.Ala241Gly,ENST00000354550,NM_033304.2;ADRA1A,missense_variant,p.Ala241Gly,ENST00000380572,;ADRA1A,missense_variant,p.Ala241Gly,ENST00000519096,;ADRA1A,missense_variant,p.Ala241Gly,ENST00000521711,; C ENST00000380586 Transcript missense_variant 1158/2304 722/1428 241/475 A/G gCc/gGc 1 -1 ADRA1A HGNC HGNC:277 protein_coding YES CCDS34869.1 ENSP00000369960 P35348 B0ZBD3 UPI000066DA42 NM_033303.3 tolerated(0.23) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00557,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF16,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS rs1308349036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 26864248 26864248 G C 1 0 0 0 0 1 0 0 0 410 1203 42 4 4 ADRA1A 8 26864248 Missense_Mutation SNP G C3N-00294_T 1455388 26864248 118274388 604 13376 ELP3 0 . GRCh38 8 28160227 28160227 + Splice_Site SNP A A G novel C3N-00294_T C3N-00294_N A A c.1258-2A>G p.X420_splice ENST00000256398 118 94 24 142 142 0 strelka-varscan-mutect ELP3,splice_acceptor_variant,,ENST00000256398,NM_018091.5;ELP3,splice_acceptor_variant,,ENST00000521015,NM_001284222.1;ELP3,splice_acceptor_variant,,ENST00000380353,NM_001284226.1;ELP3,splice_acceptor_variant,,ENST00000537665,NM_001284225.1,NM_001284224.1;ELP3,splice_acceptor_variant,,ENST00000524103,NM_001284220.1;ELP3,splice_acceptor_variant,,ENST00000523357,;ELP3,splice_acceptor_variant,,ENST00000517975,;ELP3,downstream_gene_variant,,ENST00000520110,;ELP3,splice_acceptor_variant,,ENST00000518112,;ELP3,splice_acceptor_variant,,ENST00000519261,;ELP3,splice_acceptor_variant,,ENST00000523687,; G ENST00000256398 Transcript splice_acceptor_variant -/3452 1258/1644 420/547 1 1 ELP3 HGNC HGNC:20696 protein_coding YES CCDS6065.1 ENSP00000256398 Q9H9T3 UPI000006F0B5 NM_018091.5 12/14 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 46 28160227 28160227 A G 1 0 0 0 0 0 0 1 0 4915 434 15 5 5 ELP3 8 28160227 Splice_Site SNP A C3N-00294_T 1295979 28160227 116978409 605 13377 KIF13B 0 . GRCh38 8 29160833 29160833 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1304C>G p.Ser435Cys p.S435C ENST00000524189 13/40 150 114 36 191 191 0 strelka-varscan-mutect KIF13B,missense_variant,p.Ser435Cys,ENST00000524189,NM_015254.3;KIF13B,missense_variant,p.Ser435Cys,ENST00000521515,;KIF13B,3_prime_UTR_variant,,ENST00000522355,;KIF13B,3_prime_UTR_variant,,ENST00000523968,; C ENST00000524189 Transcript missense_variant 1343/8745 1304/5481 435/1826 S/C tCt/tGt 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 deleterious(0) 13/40 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF338,Pfam_domain:PF16183 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 29160833 29160833 G C 1 0 0 0 0 1 0 0 0 8139 942 33 4 4 KIF13B 8 29160833 Missense_Mutation SNP G C3N-00294_T 1000606 29160833 115977803 606 13378 UNC5D 0 . GRCh38 8 35766910 35766910 + Silent SNP G G T rs772701180 C3N-00294_T C3N-00294_N G G c.2322G>T p.= p.P774P ENST00000404895 15/17 52 24 28 54 54 0 strelka-varscan-mutect UNC5D,synonymous_variant,p.=,ENST00000287272,;UNC5D,synonymous_variant,p.=,ENST00000453357,;UNC5D,synonymous_variant,p.=,ENST00000416672,;UNC5D,synonymous_variant,p.=,ENST00000404895,NM_080872.2;UNC5D,synonymous_variant,p.=,ENST00000420357,;UNC5D,synonymous_variant,p.=,ENST00000449677,; T ENST00000404895 Transcript synonymous_variant 2650/3252 2322/2862 774/953 P ccG/ccT rs772701180,COSM3899837,COSM3899838 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 15/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs772701180 . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 35766910 35766910 G T 1 0 0 0 0 0 0 0 1 17519 1132 40 1 1 UNC5D 8 35766910 Silent SNP G C3N-00294_T 6606077 35766910 109371726 607 13379 ASH2L 0 . GRCh38 8 38110743 38110743 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.495G>C p.Leu165Phe p.L165F ENST00000343823 5/16 172 139 33 173 173 0 strelka-varscan-mutect ASH2L,missense_variant,p.Leu165Phe,ENST00000343823,NM_004674.4;ASH2L,missense_variant,p.Leu26Phe,ENST00000545394,NM_001282272.1;ASH2L,missense_variant,p.Leu71Phe,ENST00000428278,NM_001105214.2;ASH2L,missense_variant,p.Leu71Phe,ENST00000521652,NM_001261832.1;ASH2L,missense_variant,p.Leu179Phe,ENST00000517719,;ASH2L,non_coding_transcript_exon_variant,,ENST00000524263,;ASH2L,missense_variant,p.Glu117Gln,ENST00000517496,;ASH2L,upstream_gene_variant,,ENST00000522675,; C ENST00000343823 Transcript missense_variant 804/3090 495/1887 165/628 L/F ttG/ttC 1 1 ASH2L HGNC HGNC:744 protein_coding YES CCDS6101.1 ENSP00000340896 Q9UBL3 UPI0000038D65 NM_004674.4 tolerated(0.8) 5/16 hmmpanther:PTHR10598 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 38110743 38110743 G C 1 0 0 0 0 1 0 0 0 1184 1304 45 4 4 ASH2L 8 38110743 Missense_Mutation SNP G C3N-00294_T 2343833 38110743 107027893 608 13380 DDHD2 0 . GRCh38 8 38252192 38252192 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1522C>G p.Pro508Ala p.P508A ENST00000397166 13/18 132 105 27 152 152 0 strelka-varscan-mutect DDHD2,missense_variant,p.Pro508Ala,ENST00000397166,NM_015214.2;DDHD2,missense_variant,p.Pro508Ala,ENST00000520272,NM_001164232.1;DDHD2,missense_variant,p.Pro127Ala,ENST00000517385,;DDHD2,missense_variant,p.Pro10Ala,ENST00000526144,;DDHD2,5_prime_UTR_variant,,ENST00000529845,;DDHD2,upstream_gene_variant,,ENST00000528613,;DDHD2,downstream_gene_variant,,ENST00000532106,;DDHD2,downstream_gene_variant,,ENST00000528888,;DDHD2,non_coding_transcript_exon_variant,,ENST00000520176,;DDHD2,non_coding_transcript_exon_variant,,ENST00000528504,;DDHD2,non_coding_transcript_exon_variant,,ENST00000528148,;DDHD2,downstream_gene_variant,,ENST00000527415,;DDHD2,upstream_gene_variant,,ENST00000524545,; G ENST00000397166 Transcript missense_variant 2047/4921 1522/2136 508/711 P/A Ccc/Gcc 1 1 DDHD2 HGNC HGNC:29106 protein_coding YES CCDS34883.1 ENSP00000380352 O94830 UPI0000160E07 NM_015214.2 deleterious(0) 13/18 PROSITE_profiles:PS51043,hmmpanther:PTHR23509,hmmpanther:PTHR23509:SF7,Pfam_domain:PF02862,SMART_domains:SM01127 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 38252192 38252192 C G 1 0 0 0 0 1 0 0 0 4130 855 30 4 4 DDHD2 8 38252192 Missense_Mutation SNP C C3N-00294_T 141449 38252192 106886444 609 13381 ADAM9 0 . GRCh38 8 39007891 39007891 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.103C>T p.Gln35Ter p.Q35* ENST00000487273 2/22 97 82 15 202 202 0 strelka-mutect ADAM9,stop_gained,p.Gln35Ter,ENST00000487273,NM_003816.2;ADAM9,stop_gained,p.Gln35Ter,ENST00000481513,;ADAM9,stop_gained,p.Gln35Ter,ENST00000466936,;ADAM9,stop_gained,p.Gln35Ter,ENST00000379917,;ADAM9,stop_gained,p.Gln35Ter,ENST00000481873,;ADAM9,stop_gained,p.Gln35Ter,ENST00000468065,; T ENST00000487273 Transcript stop_gained 181/3839 103/2460 35/819 Q/* Caa/Taa 1 1 ADAM9 HGNC HGNC:216 protein_coding YES CCDS6112.1 ENSP00000419446 Q13443 UPI0000048D87 NM_003816.2 2/22 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF136 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 39007891 39007891 C T 1 0 0 0 0 0 1 0 0 297 840 29 3 3 ADAM9 8 39007891 Nonsense_Mutation SNP C C3N-00294_T 755699 39007891 106130745 610 13382 ADAM9 0 . GRCh38 8 39013981 39013981 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.271G>A p.Asp91Asn p.D91N ENST00000487273 4/22 178 157 21 248 248 0 strelka-varscan-mutect ADAM9,missense_variant,p.Asp91Asn,ENST00000487273,NM_003816.2;ADAM9,missense_variant,p.Asp91Asn,ENST00000481513,;ADAM9,missense_variant,p.Asp91Asn,ENST00000466936,;SNORD38,downstream_gene_variant,,ENST00000384470,;ADAM9,missense_variant,p.Asp91Asn,ENST00000379917,;ADAM9,missense_variant,p.Asp91Asn,ENST00000481873,;ADAM9,missense_variant,p.Asp91Asn,ENST00000468065,;ADAM9,upstream_gene_variant,,ENST00000481058,; A ENST00000487273 Transcript missense_variant 349/3839 271/2460 91/819 D/N Gat/Aat 1 1 ADAM9 HGNC HGNC:216 protein_coding YES CCDS6112.1 ENSP00000419446 Q13443 UPI0000048D87 NM_003816.2 tolerated(0.19) 4/22 Pfam_domain:PF01562,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF136 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 39013981 39013981 G A 1 0 0 0 0 1 0 0 0 297 942 33 3 3 ADAM9 8 39013981 Missense_Mutation SNP G C3N-00294_T 6090 39013981 106124655 611 13383 ADAM9 0 . GRCh38 8 39017327 39017327 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.519G>C p.= p.L173L ENST00000487273 6/22 254 218 36 311 311 0 strelka-varscan-mutect ADAM9,synonymous_variant,p.=,ENST00000487273,NM_003816.2;ADAM9,downstream_gene_variant,,ENST00000481513,;ADAM9,downstream_gene_variant,,ENST00000466936,;SNORD38,downstream_gene_variant,,ENST00000384470,;ADAM9,synonymous_variant,p.=,ENST00000379917,;ADAM9,synonymous_variant,p.=,ENST00000481873,;ADAM9,synonymous_variant,p.=,ENST00000468065,;ADAM9,non_coding_transcript_exon_variant,,ENST00000481058,; C ENST00000487273 Transcript synonymous_variant 597/3839 519/2460 173/819 L ctG/ctC 1 1 ADAM9 HGNC HGNC:216 protein_coding YES CCDS6112.1 ENSP00000419446 Q13443 UPI0000048D87 NM_003816.2 6/22 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF136 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 39017327 39017327 G C 1 0 0 0 0 0 0 0 1 297 1277 45 4 4 ADAM9 8 39017327 Silent SNP G C3N-00294_T 3346 39017327 106121309 612 13384 SPIDR 0 . GRCh38 8 47440367 47440367 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.922G>A p.Glu308Lys p.E308K ENST00000297423 8/20 283 234 49 278 278 0 strelka-varscan-mutect SPIDR,missense_variant,p.Glu308Lys,ENST00000297423,NM_001080394.3;SPIDR,missense_variant,p.Glu238Lys,ENST00000541342,NM_001282916.1;SPIDR,missense_variant,p.Glu248Lys,ENST00000518074,NM_001282919.1;SPIDR,5_prime_UTR_variant,,ENST00000524006,;SPIDR,upstream_gene_variant,,ENST00000519401,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521214,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521550,;SPIDR,non_coding_transcript_exon_variant,,ENST00000521918,;SPIDR,3_prime_UTR_variant,,ENST00000522117,;SPIDR,3_prime_UTR_variant,,ENST00000524126,;SPIDR,3_prime_UTR_variant,,ENST00000519661,;SPIDR,3_prime_UTR_variant,,ENST00000524033,;SPIDR,3_prime_UTR_variant,,ENST00000517824,;SPIDR,non_coding_transcript_exon_variant,,ENST00000524141,; A ENST00000297423 Transcript missense_variant 1306/3988 922/2748 308/915 E/K Gag/Aag 1 1 SPIDR HGNC HGNC:28971 protein_coding YES CCDS43737.1 ENSP00000297423 Q14159 UPI0000253B92 NM_001080394.3 deleterious(0) 8/20 Pfam_domain:PF14950,hmmpanther:PTHR34347,hmmpanther:PTHR34347:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 47440367 47440367 G A 1 0 0 0 0 1 0 0 0 15404 1291 45 3 3 SPIDR 8 47440367 Missense_Mutation SNP G C3N-00294_T 8423040 47440367 97698269 613 13385 RP1 0 . GRCh38 8 54627955 54627955 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.4073C>T p.Ser1358Leu p.S1358L ENST00000220676 4/4 233 179 54 329 329 0 strelka-varscan-mutect RP1,missense_variant,p.Ser1358Leu,ENST00000220676,NM_006269.1;RP1,intron_variant,,ENST00000637698,;RP1,intron_variant,,ENST00000636932,; T ENST00000220676 Transcript missense_variant 4221/7100 4073/6471 1358/2156 S/L tCa/tTa 1 1 RP1 HGNC HGNC:10263 protein_coding YES CCDS6160.1 ENSP00000220676 P56715 UPI000013455B NM_006269.1 tolerated(1) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 54627955 54627955 C T 1 0 0 0 0 1 0 0 0 13709 838 29 3 3 RP1 8 54627955 Missense_Mutation SNP C C3N-00294_T 7187588 54627955 90510681 614 13386 RP1 0 . GRCh38 8 54649134 54649134 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.937G>A p.Glu313Lys p.E313K ENST00000637698 4/29 64 52 12 55 55 0 strelka-varscan-mutect RP1,missense_variant,p.Glu313Lys,ENST00000637698,;RP1,missense_variant,p.Glu313Lys,ENST00000636932,; A ENST00000637698 Transcript missense_variant 1085/6177 937/4251 313/1416 E/K Gaa/Aaa 1 1 RP1 HGNC HGNC:10263 protein_coding ENSP00000490104 tolerated(0.11) 4/29 PROSITE_profiles:PS50095,Gene3D:2.60.60.20,Pfam_domain:PF01477,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE 1 SNV 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999987 1 1 1 0 A 3 1 46 54649134 54649134 G A 1 0 0 0 0 1 0 0 0 13709 1291 45 3 3 RP1 8 54649134 Missense_Mutation SNP G C3N-00294_T 21179 54649134 90489502 615 13387 IMPAD1 0 . GRCh38 8 56980072 56980072 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.513C>T p.= p.V171V ENST00000262644 2/5 252 198 54 320 320 0 strelka-varscan-mutect IMPAD1,synonymous_variant,p.=,ENST00000262644,NM_017813.4;IMPAD1,intron_variant,,ENST00000517461,;IMPAD1,synonymous_variant,p.=,ENST00000520392,; A ENST00000262644 Transcript synonymous_variant 772/7199 513/1080 171/359 V gtC/gtT 1 -1 IMPAD1 HGNC HGNC:26019 protein_coding YES CCDS6169.1 ENSP00000262644 Q9NX62 A0A024R7W0 UPI000006DE7A NM_017813.4 2/5 hmmpanther:PTHR20854,hmmpanther:PTHR20854:SF23,Pfam_domain:PF00459,Gene3D:3.30.540.10,Superfamily_domains:SSF56655 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 56980072 56980072 G A 1 0 0 0 0 0 0 0 1 7627 929 33 3 3 IMPAD1 8 56980072 Silent SNP G C3N-00294_T 2330938 56980072 88158564 616 13388 COPS5 0 . GRCh38 8 67059385 67059410 + Frame_Shift_Del DEL ATGCATCACCATCTTCAGCAGAGCCA ATGCATCACCATCTTCAGCAGAGCCA - novel C3N-00294_T C3N-00294_N ATGCATCACCATCTTCAGCAGAGCCA ATGCATCACCATCTTCAGCAGAGCCA c.179_204delTGGCTCTGCTGAAGATGGTGATGCAT p.Leu60CysfsTer20 p.L60Cfs*20 ENST00000357849 2/8 269 214 55 321 321 0 sindel-pindel COPS5,frameshift_variant,p.Leu60CysfsTer20,ENST00000357849,NM_006837.2;COPS5,coding_sequence_variant,,ENST00000517736,;COPS5,coding_sequence_variant,,ENST00000518747,;CSPP1,upstream_gene_variant,,ENST00000262210,NM_024790.6;CSPP1,upstream_gene_variant,,ENST00000521919,;COPS5,non_coding_transcript_exon_variant,,ENST00000517793,;COPS5,downstream_gene_variant,,ENST00000519963,;COPS5,upstream_gene_variant,,ENST00000523086,;PPP1R42,upstream_gene_variant,,ENST00000517834,;COPS5,downstream_gene_variant,,ENST00000519057,;COPS5,downstream_gene_variant,,ENST00000518768,;COPS5,3_prime_UTR_variant,,ENST00000518374,;COPS5,3_prime_UTR_variant,,ENST00000523890,;COPS5,non_coding_transcript_exon_variant,,ENST00000521386,;COPS5,non_coding_transcript_exon_variant,,ENST00000521509,;COPS5,downstream_gene_variant,,ENST00000517406,; - ENST00000357849 Transcript frameshift_variant 500-525/1480 179-204/1005 60-68/334 LALLKMVMH/X tTGGCTCTGCTGAAGATGGTGATGCAT/t 1 -1 COPS5 HGNC HGNC:2240 protein_coding YES CCDS6198.1 ENSP00000350512 Q92905 A0A024R7W9 UPI000006D7AB NM_006837.2 2/8 Superfamily_domains:0048572,Gene3D:3.40.140.10,Pfam_domain:PF01398,hmmpanther:PTHR10410,hmmpanther:PTHR10410:SF6,SMART_domains:SM00232 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 46 67059385 67059385 ATGCATCACCATCTTCAGCAGAGCCA - 1 0 1 0 1 0 0 0 0 3529 214 8 0 0 COPS5 8 67059385 Frame_Shift_Del DEL ATGCATCACCATCTTCAGCAGAGCCA C3N-00294_T 10079313 67059385 78079251 617 13389 CSPP1 0 . GRCh38 8 67113861 67113861 + Missense_Mutation SNP C C T rs750389579 C3N-00294_T C3N-00294_N C C c.1271C>T p.Ser424Leu p.S424L ENST00000262210 10/29 134 111 23 142 142 0 strelka-varscan-mutect CSPP1,missense_variant,p.Ser424Leu,ENST00000262210,NM_024790.6;CSPP1,missense_variant,p.Ser130Leu,ENST00000519668,NM_001291339.1;CSPP1,3_prime_UTR_variant,,ENST00000519163,; T ENST00000262210 Transcript missense_variant,splice_region_variant 1302/4367 1271/3666 424/1221 S/L tCg/tTg rs750389579,COSM3942726 1 1 CSPP1 HGNC HGNC:26193 protein_coding YES CCDS43744.1 ENSP00000262210 Q1MSJ5 UPI00005A95D7 NM_024790.6 tolerated(0.22) 10/29 hmmpanther:PTHR21616 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs750389579 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67113861 67113861 C T 1 0 0 0 0 1 0 0 0 3763 898 31 1 1 CSPP1 8 67113861 Missense_Mutation SNP C C3N-00294_T 54476 67113861 78024775 618 13390 NCOA2 0 . GRCh38 8 70128887 70128887 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3418C>G p.Gln1140Glu p.Q1140E ENST00000452400 17/23 382 301 81 433 433 0 strelka-varscan-mutect NCOA2,missense_variant,p.Gln1140Glu,ENST00000452400,NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2;NCOA2,missense_variant,p.Gln266Glu,ENST00000518363,;NCOA2,3_prime_UTR_variant,,ENST00000518287,;NCOA2,upstream_gene_variant,,ENST00000521239,; C ENST00000452400 Transcript missense_variant 3600/8447 3418/4395 1140/1464 Q/E Cag/Gag 1 -1 NCOA2 HGNC HGNC:7669 protein_coding YES CCDS47872.1 ENSP00000399968 Q15596 UPI000012FE42 NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2 deleterious(0.05) 17/23 hmmpanther:PTHR10684:SF2,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 70128887 70128887 G C 1 0 0 0 0 1 0 0 0 10248 1299 45 4 4 NCOA2 8 70128887 Missense_Mutation SNP G C3N-00294_T 3015026 70128887 75009749 619 13391 TERF1 0 . GRCh38 8 73008992 73008992 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.106G>A p.Glu36Lys p.E36K ENST00000276603 1/10 127 112 15 130 130 0 strelka-varscan-mutect TERF1,missense_variant,p.Glu36Lys,ENST00000276602,NM_003218.3;TERF1,missense_variant,p.Glu36Lys,ENST00000276603,NM_017489.2;TERF1,missense_variant,p.Glu36Lys,ENST00000518874,;TERF1,upstream_gene_variant,,ENST00000517390,;TERF1,non_coding_transcript_exon_variant,,ENST00000518695,; A ENST00000276603 Transcript missense_variant 129/1677 106/1320 36/439 E/K Gag/Aag COSM3650814,COSM3650815 1 1 TERF1 HGNC HGNC:11728 protein_coding YES CCDS6211.1 ENSP00000276603 P54274 UPI000013DAD5 NM_017489.2 tolerated_low_confidence(0.07) 1/10 PIRSF_domain:PIRSF038016,hmmpanther:PTHR21717,hmmpanther:PTHR21717:SF14,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 2 0 0 0 0 -19.99879 0.9999999 1 1 1 0 A 3 1 46 73008992 73008992 G A 1 0 0 0 0 1 0 0 0 16180 1059 37 1 1 TERF1 8 73008992 Missense_Mutation SNP G C3N-00294_T 2880105 73008992 72129644 620 13392 FABP9 0 . GRCh38 8 81458434 81458434 + Splice_Site SNP C C G rs768459707 C3N-00294_T C3N-00294_N C C c.349-1G>C p.X117_splice ENST00000379071 73 50 23 95 95 0 strelka-varscan-mutect FABP9,splice_acceptor_variant,,ENST00000379071,NM_001080526.1;RP11-157I4.4,intron_variant,,ENST00000524085,; G ENST00000379071 Transcript splice_acceptor_variant -/497 349/399 117/132 rs768459707 1 -1 FABP9 HGNC HGNC:3563 protein_coding YES ENSP00000368362 Q0Z7S8 UPI000004D28E NM_001080526.1 3/3 HIGH 1 SNV 2 1 PASS rs768459707 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 46 81458434 81458434 C G 1 0 0 0 0 0 0 1 0 5235 695 24 4 4 FABP9 8 81458434 Splice_Site SNP C C3N-00294_T 8449442 81458434 63680202 621 13393 CHMP4C 0 . GRCh38 8 81755438 81755438 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.437C>G p.Ser146Ter p.S146* ENST00000297265 3/5 132 109 23 166 165 1 strelka-varscan-mutect CHMP4C,stop_gained,p.Ser146Ter,ENST00000297265,NM_152284.3; G ENST00000297265 Transcript stop_gained 630/1866 437/702 146/233 S/* tCa/tGa 1 1 CHMP4C HGNC HGNC:30599 protein_coding YES CCDS6233.1 ENSP00000297265 Q96CF2 UPI000005032A NM_152284.3 3/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22761,hmmpanther:PTHR22761:SF13,Pfam_domain:PF03357 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 81755438 81755438 C G 1 0 0 0 0 0 1 0 0 3118 838 29 4 4 CHMP4C 8 81755438 Nonsense_Mutation SNP C C3N-00294_T 297004 81755438 63383198 622 13394 LAPTM4B 0 . GRCh38 8 97776039 97776039 + Missense_Mutation SNP C C G rs758949119 C3N-00294_T C3N-00294_N C C c.303C>G p.Phe101Leu p.F101L ENST00000445593 1/7 281 218 63 284 284 0 strelka-varscan-mutect LAPTM4B,missense_variant,p.Phe101Leu,ENST00000445593,;LAPTM4B,missense_variant,p.Phe101Leu,ENST00000619747,NM_018407.4;LAPTM4B,missense_variant,p.Phe10Leu,ENST00000521545,;LAPTM4B,missense_variant,p.Phe10Leu,ENST00000517924,;Y_RNA,downstream_gene_variant,,ENST00000365529,; G ENST00000445593 Transcript missense_variant 983/3173 303/954 101/317 F/L ttC/ttG rs758949119 1 1 LAPTM4B HGNC HGNC:13646 protein_coding YES CCDS6275.1 ENSP00000402301 Q86VI4 UPI000018F5E2 tolerated(0.3) 1/7 hmmpanther:PTHR12479:SF6,hmmpanther:PTHR12479 MODERATE 1 SNV 1 1 PASS rs758949119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 97776039 97776039 C G 1 0 0 0 0 1 0 0 0 8535 912 32 4 4 LAPTM4B 8 97776039 Missense_Mutation SNP C C3N-00294_T 16020601 97776039 47362597 623 13395 KLF10 0 . GRCh38 8 102651295 102651295 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1037C>T p.Pro346Leu p.P346L ENST00000285407 3/4 39 31 8 59 59 0 strelka-varscan-mutect KLF10,missense_variant,p.Pro335Leu,ENST00000395884,NM_001032282.3;KLF10,missense_variant,p.Pro346Leu,ENST00000285407,NM_005655.3; A ENST00000285407 Transcript missense_variant 1338/3097 1037/1443 346/480 P/L cCt/cTt 1 -1 KLF10 HGNC HGNC:11810 protein_coding YES CCDS6294.1 ENSP00000285407 Q13118 UPI000012DED8 NM_005655.3 deleterious(0) 3/4 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.86016 1 1 1 1 0 A 3 1 46 102651295 102651295 G A 1 0 0 0 0 1 0 0 0 8203 1000 35 3 3 KLF10 8 102651295 Missense_Mutation SNP G C3N-00294_T 4875256 102651295 42487341 624 13396 RIMS2 0 . GRCh38 8 103975364 103975364 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2785G>A p.Gly929Ser p.G929S ENST00000504942 16/24 105 79 26 118 118 0 strelka-varscan-mutect RIMS2,missense_variant,p.Gly721Ser,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Gly707Ser,ENST00000436393,;RIMS2,missense_variant,p.Gly929Ser,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Gly871Ser,ENST00000626043,;RIMS2,missense_variant,p.Gly721Ser,ENST00000408894,;RIMS2,missense_variant,p.Gly768Ser,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Gly917Ser,ENST00000632716,;RIMS2,missense_variant,p.Gly323Ser,ENST00000507677,; A ENST00000504942 Transcript missense_variant 2924/4228 2785/4050 929/1349 G/S Ggt/Agt 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 tolerated_low_confidence(0.12) 16/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 103975364 103975364 G A 1 0 0 0 0 1 0 0 0 13543 1348 47 3 3 RIMS2 8 103975364 Missense_Mutation SNP G C3N-00294_T 1324069 103975364 41163272 625 13397 TRHR 0 . GRCh38 8 109119378 109119378 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1120G>A p.Asp374Asn p.D374N ENST00000518632 3/3 76 63 13 74 74 0 strelka-varscan-mutect TRHR,missense_variant,p.Asp374Asn,ENST00000518632,;TRHR,missense_variant,p.Asp374Asn,ENST00000311762,NM_003301.5; A ENST00000518632 Transcript missense_variant 1471/1660 1120/1197 374/398 D/N Gac/Aac 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 tolerated(0.24) 3/3 Prints_domain:PR00751,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 109119378 109119378 G A 1 0 0 0 0 1 0 0 0 16969 1290 45 3 3 TRHR 8 109119378 Missense_Mutation SNP G C3N-00294_T 5144014 109119378 36019258 626 13398 PKHD1L1 0 . GRCh38 8 109408193 109408193 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1958C>T p.Ser653Leu p.S653L ENST00000378402 18/78 83 73 10 63 63 0 strelka-mutect PKHD1L1,missense_variant,p.Ser653Leu,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript missense_variant 2062/13076 1958/12732 653/4243 S/L tCa/tTa 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0.01) 18/78 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99287 1 1 1 1 0 T 3 4 46 109408193 109408193 C T 1 0 0 0 0 1 0 0 0 12068 838 29 3 3 PKHD1L1 8 109408193 Missense_Mutation SNP C C3N-00294_T 288815 109408193 35730443 627 13399 CSMD3 0 . GRCh38 8 112292569 112292569 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.8756G>C p.Arg2919Thr p.R2919T ENST00000297405 55/71 267 210 57 248 248 0 strelka-varscan-mutect CSMD3,missense_variant,p.Arg2919Thr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Arg2879Thr,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Arg2750Thr,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Arg2189Thr,ENST00000339701,; G ENST00000297405 Transcript missense_variant 9001/13212 8756/11124 2919/3707 R/T aGa/aCa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.03) 55/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 112292569 112292569 C G 1 0 0 0 0 1 0 0 0 3747 913 32 4 4 CSMD3 8 112292569 Missense_Mutation SNP C C3N-00294_T 2884376 112292569 32846067 628 13400 RAD21 0 . GRCh38 8 116852630 116852630 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1240G>A p.Asp414Asn p.D414N ENST00000297338 10/14 130 115 15 106 106 0 strelka-varscan-mutect RAD21,missense_variant,p.Asp414Asn,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000523986,;RAD21,upstream_gene_variant,,ENST00000517749,;RAD21,upstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000517485,;RAD21,downstream_gene_variant,,ENST00000520992,;UTP23,downstream_gene_variant,,ENST00000517820,;UTP23,downstream_gene_variant,,ENST00000520733,;AC087350.1,downstream_gene_variant,,ENST00000626876,;RAD21,downstream_gene_variant,,ENST00000523547,;UTP23,downstream_gene_variant,,ENST00000521703,;UTP23,downstream_gene_variant,,ENST00000524128,; T ENST00000297338 Transcript missense_variant 1528/3749 1240/1896 414/631 D/N Gat/Aat 1 -1 RAD21 HGNC HGNC:9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 A0A024R9J0 UPI0000133018 NM_006265.2 deleterious(0.03) 10/14 hmmpanther:PTHR12585,hmmpanther:PTHR12585:SF20 MODERATE 1 SNV 1 1 PASS rs1419651477 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 116852630 116852630 C T 1 0 0 0 0 1 0 0 0 13141 855 30 3 3 RAD21 8 116852630 Missense_Mutation SNP C C3N-00294_T 4560061 116852630 28286006 629 13401 EXT1 0 . GRCh38 8 118110879 118110879 + Silent SNP G G A rs776965915 C3N-00294_T C3N-00294_N G G c.168C>T p.= p.P56P ENST00000378204 1/11 166 135 31 181 181 0 strelka-varscan-mutect EXT1,synonymous_variant,p.=,ENST00000378204,NM_000127.2;EXT1,upstream_gene_variant,,ENST00000436216,;EXT1,intron_variant,,ENST00000437196,; A ENST00000378204 Transcript synonymous_variant 975/8270 168/2241 56/746 P ccC/ccT rs776965915 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 1/11 hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF97 LOW 1 SNV 1 1 PASS rs776965915 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 2 1 46 118110879 118110879 G A 1 0 0 0 0 0 0 0 1 5191 1219 43 3 3 EXT1 8 118110879 Silent SNP G C3N-00294_T 1258249 118110879 27027757 630 13402 SAMD12 0 . GRCh38 8 118580766 118580766 + Silent SNP A A T novel C3N-00294_T C3N-00294_N A A c.141T>A p.= p.P47P ENST00000314727 2/4 135 76 59 146 146 0 strelka-varscan-mutect SAMD12,synonymous_variant,p.=,ENST00000409003,NM_001101676.1;SAMD12,synonymous_variant,p.=,ENST00000314727,NM_207506.2;SAMD12,synonymous_variant,p.=,ENST00000453675,;SAMD12,synonymous_variant,p.=,ENST00000524796,;SAMD12,synonymous_variant,p.=,ENST00000526328,;SAMD12,synonymous_variant,p.=,ENST00000526765,;SAMD12,synonymous_variant,p.=,ENST00000445741,; T ENST00000314727 Transcript synonymous_variant 278/2172 141/606 47/201 P ccT/ccA 1 -1 SAMD12 HGNC HGNC:31750 protein_coding YES CCDS6325.1 ENSP00000314173 Q8N8I0 UPI000013F8F1 NM_207506.2 2/4 hmmpanther:PTHR20843:SF2,hmmpanther:PTHR20843 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 118580766 118580766 A T 1 0 0 0 0 0 0 0 1 14076 175 7 4 4 SAMD12 8 118580766 Silent SNP A C3N-00294_T 469887 118580766 26557870 631 13403 53 2 SAMD12 0 . GRCh38 8 118580770 118580770 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.137T>A p.Val46Glu p.V46E ENST00000314727 2/4 145 79 66 155 155 0 strelka-varscan-mutect SAMD12,missense_variant,p.Val46Glu,ENST00000409003,NM_001101676.1;SAMD12,missense_variant,p.Val46Glu,ENST00000314727,NM_207506.2;SAMD12,missense_variant,p.Val43Glu,ENST00000453675,;SAMD12,missense_variant,p.Val38Glu,ENST00000524796,;SAMD12,missense_variant,p.Val46Glu,ENST00000526328,;SAMD12,missense_variant,p.Val61Glu,ENST00000526765,;SAMD12,missense_variant,p.Val46Glu,ENST00000445741,; T ENST00000314727 Transcript missense_variant 274/2172 137/606 46/201 V/E gTg/gAg 1 -1 SAMD12 HGNC HGNC:31750 protein_coding YES CCDS6325.1 ENSP00000314173 Q8N8I0 UPI000013F8F1 NM_207506.2 tolerated(0.17) 2/4 hmmpanther:PTHR20843:SF2,hmmpanther:PTHR20843 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 118580770 118580770 A T 1 0 0 0 0 1 0 0 0 14076 159 6 4 4 SAMD12 8 118580770 Missense_Mutation SNP A C3N-00294_T 4 118580770 26557866 632 13404 53 2 COL14A1 0 . GRCh38 8 120226705 120226705 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1943C>G p.Ser648Ter p.S648* ENST00000297848 16/48 178 148 30 181 181 0 strelka-varscan-mutect COL14A1,stop_gained,p.Ser648Ter,ENST00000297848,NM_021110.2;COL14A1,stop_gained,p.Ser648Ter,ENST00000309791,;COL14A1,stop_gained,p.Ser461Ter,ENST00000434620,;COL14A1,3_prime_UTR_variant,,ENST00000537875,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,;COL14A1,3_prime_UTR_variant,,ENST00000498051,; G ENST00000297848 Transcript stop_gained 2213/6466 1943/5391 648/1796 S/* tCa/tGa 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 16/48 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 120226705 120226705 C G 1 0 0 0 0 0 1 0 0 3459 838 29 4 4 COL14A1 8 120226705 Nonsense_Mutation SNP C C3N-00294_T 1645935 120226705 24911931 633 13405 MTSS1 0 . GRCh38 8 124553357 124553357 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1915G>A p.Asp639Asn p.D639N ENST00000325064 15/15 86 41 45 73 73 0 strelka-varscan-mutect MTSS1,missense_variant,p.Asp635Asn,ENST00000518547,NM_014751.5;MTSS1,missense_variant,p.Asp610Asn,ENST00000378017,NM_001282974.1;MTSS1,missense_variant,p.Asp639Asn,ENST00000325064,NM_001282971.1;MTSS1,missense_variant,p.Asp525Asn,ENST00000524090,;MTSS1,missense_variant,p.Asp423Asn,ENST00000519168,;MTSS1,missense_variant,p.Asp353Asn,ENST00000431961,;NDUFB9,intron_variant,,ENST00000522532,;MTSS1,downstream_gene_variant,,ENST00000523179,;MTSS1,downstream_gene_variant,,ENST00000522118,;NDUFB9,downstream_gene_variant,,ENST00000276689,NM_005005.2;NDUFB9,downstream_gene_variant,,ENST00000517367,NM_001311168.1,NM_001278645.1,NM_001278646.1;MTSS1,non_coding_transcript_exon_variant,,ENST00000523587,;MTSS1,downstream_gene_variant,,ENST00000520094,;MTSS1,downstream_gene_variant,,ENST00000522722,;NDUFB9,downstream_gene_variant,,ENST00000517830,;MTSS1,non_coding_transcript_exon_variant,,ENST00000520771,;NDUFB9,downstream_gene_variant,,ENST00000518657,;NDUFB9,downstream_gene_variant,,ENST00000524241,; T ENST00000325064 Transcript missense_variant 2233/2777 1915/2280 639/759 D/N Gat/Aat 1 -1 MTSS1 HGNC HGNC:20443 protein_coding YES CCDS64969.1 ENSP00000322804 O43312 UPI0001E8F264 NM_001282971.1 tolerated(0.52) 15/15 hmmpanther:PTHR15708,hmmpanther:PTHR15708:SF10 MODERATE SNV 2 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 124553357 124553357 C T 1 0 0 0 0 1 0 0 0 9959 913 32 3 3 MTSS1 8 124553357 Missense_Mutation SNP C C3N-00294_T 4326652 124553357 20585279 634 13406 FAM84B 0 . GRCh38 8 126557317 126557317 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.73G>A p.Asp25Asn p.D25N ENST00000304916 2/2 320 242 78 276 276 0 strelka-varscan-mutect FAM84B,missense_variant,p.Asp25Asn,ENST00000304916,NM_174911.4;RP11-103H7.5,non_coding_transcript_exon_variant,,ENST00000524320,;RP11-89K10.1,upstream_gene_variant,,ENST00000519880,;RP11-89K10.1,upstream_gene_variant,,ENST00000517773,;RP11-89K10.1,upstream_gene_variant,,ENST00000520512,;FAM84B,upstream_gene_variant,,ENST00000517458,; T ENST00000304916 Transcript missense_variant 529/5404 73/933 25/310 D/N Gac/Aac 1 -1 FAM84B HGNC HGNC:24166 protein_coding YES CCDS6358.1 ENSP00000302578 Q96KN1 UPI00000710F2 NM_174911.4 deleterious(0) 2/2 MODERATE 1 SNV 1 1 PASS rs1361012003 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 126557317 126557317 C T 1 0 0 0 0 1 0 0 0 5500 855 30 3 3 FAM84B 8 126557317 Missense_Mutation SNP C C3N-00294_T 2003960 126557317 18581319 635 13407 FAM135B 0 . GRCh38 8 138152436 138152436 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2039C>T p.Ser680Leu p.S680L ENST00000395297 13/20 250 201 49 257 257 0 strelka-varscan-mutect FAM135B,missense_variant,p.Ser680Leu,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Ser680Leu,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 2210/6962 2039/4221 680/1406 S/L tCa/tTa COSM3319002,COSM3319003 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 13/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 138152436 138152436 G A 1 0 0 0 0 1 0 0 0 5299 1294 45 3 3 FAM135B 8 138152436 Missense_Mutation SNP G C3N-00294_T 11595119 138152436 6986200 636 13408 ARC 0 . GRCh38 8 142613369 142613369 + Missense_Mutation SNP G G T rs778023538 C3N-00294_T C3N-00294_N G G c.903C>A p.Phe301Leu p.F301L ENST00000356613 1/3 96 84 12 127 127 0 strelka-varscan-mutect ARC,missense_variant,p.Phe301Leu,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; T ENST00000356613 Transcript missense_variant 1104/2948 903/1191 301/396 F/L ttC/ttA rs778023538 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 deleterious(0.01) 1/3 hmmpanther:PTHR15962 MODERATE 1 SNV 1 1 PASS rs778023538 . 0 208 0 2 0 0 0 0 -19.18048 0.9999999 1 1 1 0 T 3 4 46 142613369 142613369 G T 1 0 0 0 0 1 0 0 0 963 1165 41 2 2 ARC 8 142613369 Missense_Mutation SNP G C3N-00294_T 4460933 142613369 2525267 637 13409 CYP11B1 0 . GRCh38 8 142875127 142875127 + Silent SNP G G A rs200770247 C3N-00294_T C3N-00294_N G G c.1228C>T p.= p.L410L ENST00000292427 8/9 454 360 94 422 422 0 strelka-varscan-mutect CYP11B1,synonymous_variant,p.=,ENST00000292427,NM_000497.3;CYP11B1,synonymous_variant,p.=,ENST00000519285,;CYP11B1,synonymous_variant,p.=,ENST00000377675,;CYP11B1,intron_variant,,ENST00000517471,NM_001026213.1;GML,intron_variant,,ENST00000522728,;CYP11B1,intron_variant,,ENST00000314111,; A ENST00000292427 Transcript synonymous_variant 1261/2664 1228/1512 410/503 L Ctg/Ttg rs200770247 1 -1 CYP11B1 HGNC HGNC:2591 protein_coding YES CCDS6392.1 ENSP00000292427 P15538 UPI000013E0BA NM_000497.3 8/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs200770247 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 142875127 142875127 G A 1 0 0 0 0 0 0 0 1 3948 933 33 3 3 CYP11B1 8 142875127 Silent SNP G C3N-00294_T 261758 142875127 2263509 638 13410 TIGD5 0 . GRCh38 8 143598468 143598468 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.565G>A p.Glu189Lys p.E189K ENST00000504548 1/1 58 45 13 53 53 0 strelka-varscan-mutect TIGD5,missense_variant,p.Glu189Lys,ENST00000504548,NM_032862.4;EEF1D,intron_variant,,ENST00000533749,;EEF1D,upstream_gene_variant,,ENST00000423316,NM_001130053.2;EEF1D,upstream_gene_variant,,ENST00000618139,;EEF1D,upstream_gene_variant,,ENST00000442189,NM_032378.4;EEF1D,upstream_gene_variant,,ENST00000317198,NM_001130057.2;EEF1D,upstream_gene_variant,,ENST00000419152,NM_001130055.2;EEF1D,upstream_gene_variant,,ENST00000529272,;EEF1D,upstream_gene_variant,,ENST00000395119,NM_001289950.1,NM_001960.4;EEF1D,upstream_gene_variant,,ENST00000524624,;EEF1D,upstream_gene_variant,,ENST00000534380,;EEF1D,upstream_gene_variant,,ENST00000526710,;EEF1D,upstream_gene_variant,,ENST00000526838,NM_001195203.1;EEF1D,upstream_gene_variant,,ENST00000531670,;EEF1D,upstream_gene_variant,,ENST00000528610,NM_001130056.2;EEF1D,upstream_gene_variant,,ENST00000530191,;EEF1D,upstream_gene_variant,,ENST00000533204,;EEF1D,upstream_gene_variant,,ENST00000531621,;EEF1D,upstream_gene_variant,,ENST00000531281,;EEF1D,upstream_gene_variant,,ENST00000532543,;EEF1D,upstream_gene_variant,,ENST00000531218,;EEF1D,upstream_gene_variant,,ENST00000526340,;EEF1D,upstream_gene_variant,,ENST00000532596,;EEF1D,upstream_gene_variant,,ENST00000533494,;EEF1D,upstream_gene_variant,,ENST00000534377,;EEF1D,upstream_gene_variant,,ENST00000530545,;EEF1D,upstream_gene_variant,,ENST00000531931,;EEF1D,upstream_gene_variant,,ENST00000529832,;EEF1D,upstream_gene_variant,,ENST00000530306,;EEF1D,upstream_gene_variant,,ENST00000525261,;EEF1D,upstream_gene_variant,,ENST00000528303,;EEF1D,upstream_gene_variant,,ENST00000534804,;EEF1D,upstream_gene_variant,,ENST00000534475,;EEF1D,upstream_gene_variant,,ENST00000531953,;EEF1D,upstream_gene_variant,,ENST00000529516,;EEF1D,upstream_gene_variant,,ENST00000532400,;EEF1D,upstream_gene_variant,,ENST00000526133,;EEF1D,upstream_gene_variant,,ENST00000524900,;EEF1D,upstream_gene_variant,,ENST00000531770,;EEF1D,upstream_gene_variant,,ENST00000526786,;EEF1D,upstream_gene_variant,,ENST00000524397,;EEF1D,upstream_gene_variant,,ENST00000525695,;EEF1D,upstream_gene_variant,,ENST00000529007,;EEF1D,upstream_gene_variant,,ENST00000533833,;EEF1D,upstream_gene_variant,,ENST00000534232,;EEF1D,upstream_gene_variant,,ENST00000530848,; A ENST00000504548 Transcript missense_variant 634/5390 565/1929 189/642 E/K Gag/Aag 1 1 TIGD5 HGNC HGNC:18336 protein_coding YES CCDS6406.2 ENSP00000421489 Q53EQ6 UPI0001BAE24C NM_032862.4 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF283 MODERATE SNV 1 PASS rs1211583093 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 143598468 143598468 G A 1 0 0 0 0 1 0 0 0 16337 1059 37 1 1 TIGD5 8 143598468 Missense_Mutation SNP G C3N-00294_T 723341 143598468 1540168 639 13411 PLEC 0 . GRCh38 8 143917655 143917655 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.12577G>C p.Glu4193Gln p.E4193Q ENST00000322810 32/32 242 184 58 251 251 0 strelka-varscan-mutect PLEC,missense_variant,p.Glu4193Gln,ENST00000322810,NM_201380.3;PLEC,missense_variant,p.Glu4056Gln,ENST00000345136,NM_201384.2;PLEC,missense_variant,p.Glu4083Gln,ENST00000436759,NM_000445.4;PLEC,missense_variant,p.Glu4034Gln,ENST00000354958,NM_201379.2;PLEC,missense_variant,p.Glu4056Gln,ENST00000354589,NM_201382.3;PLEC,missense_variant,p.Glu4060Gln,ENST00000357649,NM_201383.2;PLEC,missense_variant,p.Glu4042Gln,ENST00000356346,NM_201378.3;PLEC,missense_variant,p.Glu4024Gln,ENST00000398774,NM_201381.2;PLEC,missense_variant,p.Glu4079Gln,ENST00000527096,;PLEC,downstream_gene_variant,,ENST00000527303,; G ENST00000322810 Transcript missense_variant 12747/15249 12577/14055 4193/4684 E/Q Gag/Cag 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 tolerated(0.12) 32/32 Gene3D:3.90.1290.10,Pfam_domain:PF00681,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,SMART_domains:SM00250,Superfamily_domains:SSF75399 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 143917655 143917655 C G 1 0 0 0 0 1 0 0 0 12145 835 29 4 4 PLEC 8 143917655 Missense_Mutation SNP C C3N-00294_T 319187 143917655 1220981 640 13412 PLEC 0 . GRCh38 8 143918451 143918451 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.11781G>A p.= p.L3927L ENST00000322810 32/32 173 140 33 183 183 0 strelka-varscan-mutect PLEC,synonymous_variant,p.=,ENST00000322810,NM_201380.3;PLEC,synonymous_variant,p.=,ENST00000345136,NM_201384.2;PLEC,synonymous_variant,p.=,ENST00000436759,NM_000445.4;PLEC,synonymous_variant,p.=,ENST00000354958,NM_201379.2;PLEC,synonymous_variant,p.=,ENST00000354589,NM_201382.3;PLEC,synonymous_variant,p.=,ENST00000357649,NM_201383.2;PLEC,synonymous_variant,p.=,ENST00000356346,NM_201378.3;PLEC,synonymous_variant,p.=,ENST00000398774,NM_201381.2;PLEC,synonymous_variant,p.=,ENST00000527096,;PLEC,downstream_gene_variant,,ENST00000527303,; T ENST00000322810 Transcript synonymous_variant 11951/15249 11781/14055 3927/4684 L ctG/ctA 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 32/32 Gene3D:3.90.1290.10,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,SMART_domains:SM00250,Superfamily_domains:SSF75399 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 143918451 143918451 C T 1 0 0 0 0 0 0 0 1 12145 813 29 3 3 PLEC 8 143918451 Silent SNP C C3N-00294_T 796 143918451 1220185 641 13413 PLEC 0 . GRCh38 8 143927332 143927332 + Silent SNP G G A rs782372916 C3N-00294_T C3N-00294_N G G c.4171C>T p.= p.L1391L ENST00000322810 28/32 603 490 113 641 641 0 strelka-varscan-mutect PLEC,synonymous_variant,p.=,ENST00000322810,NM_201380.3;PLEC,synonymous_variant,p.=,ENST00000345136,NM_201384.2;PLEC,synonymous_variant,p.=,ENST00000436759,NM_000445.4;PLEC,synonymous_variant,p.=,ENST00000354958,NM_201379.2;PLEC,synonymous_variant,p.=,ENST00000354589,NM_201382.3;PLEC,synonymous_variant,p.=,ENST00000357649,NM_201383.2;PLEC,synonymous_variant,p.=,ENST00000356346,NM_201378.3;PLEC,synonymous_variant,p.=,ENST00000398774,NM_201381.2;PLEC,synonymous_variant,p.=,ENST00000527096,;PLEC,upstream_gene_variant,,ENST00000527303,; A ENST00000322810 Transcript synonymous_variant 4341/15249 4171/14055 1391/4684 L Ctg/Ttg rs782372916 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 28/32 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,Low_complexity_(Seg):seg,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS rs782372916 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 143927332 143927332 G A 1 0 0 0 0 0 0 0 1 12145 1014 35 3 3 PLEC 8 143927332 Silent SNP G C3N-00294_T 8881 143927332 1211304 642 13414 DOCK8 0 . GRCh38 9 406929 406929 + Splice_Site SNP G G A C3N-00294_T C3N-00294_N G G c.3391-1G>A p.X1131_splice ENST00000432829 354 292 62 468 467 1 strelka-varscan-mutect DOCK8,splice_acceptor_variant,,ENST00000432829,NM_203447.3;DOCK8,splice_acceptor_variant,,ENST00000453981,NM_001193536.1;DOCK8,splice_acceptor_variant,,ENST00000469391,NM_001190458.1;DOCK8,splice_acceptor_variant,,ENST00000382329,;DOCK8,downstream_gene_variant,,ENST00000382331,;DOCK8,splice_acceptor_variant,,ENST00000495184,; A ENST00000432829 Transcript splice_acceptor_variant -/7452 3391/6300 1131/2099 COSM3926830,COSM3926831 1 1 DOCK8 HGNC HGNC:19191 protein_coding YES CCDS6440.2 ENSP00000394888 Q8NF50 UPI0000E0B9E5 NM_203447.3 27/47 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 406929 406929 G A 1 0 0 0 0 0 0 1 0 4508 956 33 3 3 DOCK8 9 406929 Splice_Site SNP G C3N-00294_T 406929 137987788 643 13415 INSL4 0 . GRCh38 9 5233724 5233724 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.267G>T p.Leu89Phe p.L89F ENST00000239316 2/2 283 177 106 313 313 0 strelka-varscan-mutect INSL4,missense_variant,p.Leu89Phe,ENST00000239316,NM_002195.1; T ENST00000239316 Transcript missense_variant 372/1952 267/420 89/139 L/F ttG/ttT COSM377998 1 1 INSL4 HGNC HGNC:6087 protein_coding YES CCDS6459.1 ENSP00000239316 Q14641 UPI0000032F5A NM_002195.1 deleterious(0.02) 2/2 Prints_domain:PR02004,hmmpanther:PTHR12004,hmmpanther:PTHR12004:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1206550366 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 5233724 5233724 G T 1 0 0 0 0 1 0 0 0 7670 1368 48 2 2 INSL4 9 5233724 Missense_Mutation SNP G C3N-00294_T 4826795 5233724 133160993 644 13416 FREM1 0 . GRCh38 9 14784533 14784533 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.4279G>C p.Glu1427Gln p.E1427Q ENST00000422223 25/38 150 117 33 153 153 0 strelka-varscan-mutect FREM1,missense_variant,p.Glu1427Gln,ENST00000422223,NM_144966.5;FREM1,missense_variant,p.Glu1427Gln,ENST00000380880,;FREM1,upstream_gene_variant,,ENST00000380894,NM_001177704.1;FREM1,non_coding_transcript_exon_variant,,ENST00000466679,;FREM1,non_coding_transcript_exon_variant,,ENST00000485068,;FREM1,non_coding_transcript_exon_variant,,ENST00000497634,;FREM1,intron_variant,,ENST00000380875,; G ENST00000422223 Transcript missense_variant 5095/10086 4279/6540 1427/2179 E/Q Gag/Cag 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 deleterious(0) 25/38 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 14784533 14784533 C G 1 0 0 0 0 1 0 0 0 5911 835 29 4 4 FREM1 9 14784533 Missense_Mutation SNP C C3N-00294_T 9550809 14784533 123610184 645 13417 CCDC171 0 . GRCh38 9 15846728 15846728 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.3294G>A p.= p.L1098L ENST00000380701 22/26 110 89 21 87 87 0 strelka-varscan-mutect CCDC171,synonymous_variant,p.=,ENST00000380701,NM_173550.2;CCDC171,synonymous_variant,p.=,ENST00000449575,;CCDC171,synonymous_variant,p.=,ENST00000432954,;CCDC171,non_coding_transcript_exon_variant,,ENST00000470191,;CCDC171,upstream_gene_variant,,ENST00000498725,; A ENST00000380701 Transcript synonymous_variant 3622/6512 3294/3981 1098/1326 L ctG/ctA 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 22/26 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 15846728 15846728 G A 1 0 0 0 0 0 0 0 1 2488 1277 45 3 3 CCDC171 9 15846728 Silent SNP G C3N-00294_T 1062195 15846728 122547989 646 13418 IFNA16 0 . GRCh38 9 21216975 21216975 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.331G>A p.Glu111Lys p.E111K ENST00000380216 1/1 223 175 48 194 194 0 strelka-varscan-mutect IFNA16,missense_variant,p.Glu111Lys,ENST00000380216,NM_002173.2; T ENST00000380216 Transcript missense_variant 337/939 331/570 111/189 E/K Gaa/Aaa COSM3656557 1 -1 IFNA16 HGNC HGNC:5421 protein_coding YES CCDS34996.1 ENSP00000369564 P05015 UPI0000047763 NM_002173.2 deleterious(0.01) 1/1 hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF39,Gene3D:1.20.1250.10,Pfam_domain:PF00143,SMART_domains:SM00076,Superfamily_domains:SSF47266 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 21216975 21216975 C T 1 0 0 0 0 1 0 0 0 7435 835 29 3 3 IFNA16 9 21216975 Missense_Mutation SNP C C3N-00294_T 5370247 21216975 117177742 647 13419 PLAA 0 . GRCh38 9 26907937 26907937 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1719G>C p.Leu573Phe p.L573F ENST00000397292 13/14 76 63 13 108 108 0 strelka-mutect PLAA,missense_variant,p.Leu573Phe,ENST00000397292,NM_001031689.2;PLAA,missense_variant,p.Leu573Phe,ENST00000520884,;PLAA,missense_variant,p.Leu100Phe,ENST00000487173,;PLAA,intron_variant,,ENST00000517642,; G ENST00000397292 Transcript missense_variant 2137/4234 1719/2388 573/795 L/F ttG/ttC 1 -1 PLAA HGNC HGNC:9043 protein_coding YES CCDS35000.1 ENSP00000380460 Q9Y263 UPI00000372D6 NM_001031689.2 deleterious(0.04) 13/14 Pfam_domain:PF08324,PROSITE_profiles:PS51396,hmmpanther:PTHR19849,hmmpanther:PTHR19849:SF0,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 26907937 26907937 C G 1 0 0 0 0 1 0 0 0 12107 825 29 4 4 PLAA 9 26907937 Missense_Mutation SNP C C3N-00294_T 5690962 26907937 111486780 648 13420 NFX1 0 . GRCh38 9 33294853 33294853 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.459G>A p.= p.E153E ENST00000379540 2/24 275 230 45 280 280 0 strelka-varscan-mutect NFX1,synonymous_variant,p.=,ENST00000379540,NM_001318758.1,NM_002504.4;NFX1,synonymous_variant,p.=,ENST00000379521,NM_147133.2;NFX1,synonymous_variant,p.=,ENST00000318524,NM_147134.2; A ENST00000379540 Transcript synonymous_variant 521/4604 459/3363 153/1120 E gaG/gaA 1 1 NFX1 HGNC HGNC:7803 protein_coding YES CCDS6538.1 ENSP00000368856 Q12986 UPI0000072140 NM_001318758.1,NM_002504.4 2/24 hmmpanther:PTHR12360,hmmpanther:PTHR12360:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 33294853 33294853 G A 1 0 0 0 0 0 0 0 1 10423 933 33 3 3 NFX1 9 33294853 Silent SNP G C3N-00294_T 6386916 33294853 105099864 649 13421 AQP7 0 . GRCh38 9 33385201 33385201 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.833C>G p.Ser278Cys p.S278C ENST00000297988 8/8 251 193 58 245 245 0 strelka-varscan-mutect AQP7,missense_variant,p.Ser277Cys,ENST00000379507,;AQP7,missense_variant,p.Ser278Cys,ENST00000297988,NM_001170.1;AQP7,synonymous_variant,p.=,ENST00000377425,;AQP7,downstream_gene_variant,,ENST00000624075,;AQP7,downstream_gene_variant,,ENST00000379506,;AQP7,downstream_gene_variant,,ENST00000447660,;AQP7,downstream_gene_variant,,ENST00000439678,;AQP7,downstream_gene_variant,,ENST00000625109,;AQP7,downstream_gene_variant,,ENST00000379503,;AQP7,downstream_gene_variant,,ENST00000623743,;AQP7,downstream_gene_variant,,ENST00000623097,;AQP7,3_prime_UTR_variant,,ENST00000537089,;AQP7,downstream_gene_variant,,ENST00000624890,;AQP7,downstream_gene_variant,,ENST00000624005,;AQP7,downstream_gene_variant,,ENST00000624420,;AQP7,downstream_gene_variant,,ENST00000624095,;AQP7,downstream_gene_variant,,ENST00000624432,; C ENST00000297988 Transcript missense_variant 1005/1256 833/1029 278/342 S/C tCc/tGc 1 -1 AQP7 HGNC HGNC:640 protein_coding YES CCDS6541.1 ENSP00000297988 O14520 UPI0000125D23 NM_001170.1 tolerated(0.2) 8/8 hmmpanther:PTHR19139:SF16,hmmpanther:PTHR19139 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 33385201 33385201 G C 1 0 0 0 0 1 0 0 0 954 1174 41 4 4 AQP7 9 33385201 Missense_Mutation SNP G C3N-00294_T 90348 33385201 105009516 650 13422 UBAP1 0 . GRCh38 9 34251508 34251508 + Silent SNP C C G rs371234489 C3N-00294_T C3N-00294_N C C c.1677C>G p.= p.L559L ENST00000625521 6/6 78 66 12 81 81 0 strelka-varscan-mutect UBAP1,synonymous_variant,p.=,ENST00000297661,NM_001171203.2,NM_016525.4,NM_001171204.2;UBAP1,synonymous_variant,p.=,ENST00000359544,;UBAP1,synonymous_variant,p.=,ENST00000379186,;UBAP1,synonymous_variant,p.=,ENST00000625521,NM_001171201.1;UBAP1,synonymous_variant,p.=,ENST00000626262,NM_001171202.1;KIF24,downstream_gene_variant,,ENST00000402558,NM_194313.2;KIF24,downstream_gene_variant,,ENST00000379174,; G ENST00000625521 Transcript synonymous_variant 1687/2029 1677/1701 559/566 L ctC/ctG rs371234489 1 1 UBAP1 HGNC HGNC:12461 protein_coding YES CCDS55303.1 ENSP00000486574 Q9NZ09 UPI0001C2BF9D NM_001171201.1 6/6 PROSITE_profiles:PS50030,hmmpanther:PTHR15960,hmmpanther:PTHR15960:SF2,Superfamily_domains:SSF46934 LOW 1 SNV 2 1 PASS rs371234489 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 34251508 34251508 C G 1 0 0 0 0 0 0 0 1 17357 813 29 4 4 UBAP1 9 34251508 Silent SNP C C3N-00294_T 866307 34251508 104143209 651 13423 ARID3C 0 . GRCh38 9 34627721 34627721 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.294G>A p.Trp98Ter p.W98* ENST00000378909 1/7 83 78 5 77 77 0 strelka-varscan-mutect ARID3C,stop_gained,p.Trp98Ter,ENST00000378909,NM_001017363.1; T ENST00000378909 Transcript stop_gained 387/1411 294/1239 98/412 W/* tgG/tgA 1 -1 ARID3C HGNC HGNC:21209 protein_coding YES CCDS35006.1 ENSP00000368189 A6NKF2 UPI0000509F06 NM_001017363.1 1/7 Gene3D:1.10.150.60,hmmpanther:PTHR15348,hmmpanther:PTHR15348:SF2,Superfamily_domains:SSF46774 HIGH 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -10.89711 0.9999969 1 1 1 0 T 4 4 46 34627721 34627721 C T 1 0 0 0 0 0 1 0 0 1054 856 30 3 3 ARID3C 9 34627721 Nonsense_Mutation SNP C C3N-00294_T 376213 34627721 103766996 652 13424 NPR2 0 . GRCh38 9 35801717 35801717 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1511C>G p.Ser504Ter p.S504* ENST00000342694 8/22 685 546 139 774 774 0 strelka-varscan-mutect NPR2,stop_gained,p.Ser504Ter,ENST00000342694,NM_003995.3;NPR2,upstream_gene_variant,,ENST00000421267,;NPR2,upstream_gene_variant,,ENST00000447210,;NPR2,non_coding_transcript_exon_variant,,ENST00000464810,;NPR2,upstream_gene_variant,,ENST00000448821,; G ENST00000342694 Transcript stop_gained 1766/3686 1511/3144 504/1047 S/* tCa/tGa 1 1 NPR2 HGNC HGNC:7944 protein_coding YES CCDS6590.1 ENSP00000341083 P20594 UPI0000125B42 NM_003995.3 8/22 hmmpanther:PTHR11920:SF305,hmmpanther:PTHR11920 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 35801717 35801717 C G 1 0 0 0 0 0 1 0 0 10651 838 29 4 4 NPR2 9 35801717 Nonsense_Mutation SNP C C3N-00294_T 1173996 35801717 102593000 653 13425 NPR2 0 . GRCh38 9 35805597 35805597 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.1974C>G p.= p.L658L ENST00000342694 13/22 378 308 70 394 394 0 strelka-varscan-mutect NPR2,synonymous_variant,p.=,ENST00000342694,NM_003995.3;NPR2,synonymous_variant,p.=,ENST00000421267,;SPAG8,downstream_gene_variant,,ENST00000340291,NM_172312.1;SPAG8,downstream_gene_variant,,ENST00000484764,;SPAG8,downstream_gene_variant,,ENST00000396638,NM_001039592.1;SPAG8,downstream_gene_variant,,ENST00000497810,;NPR2,upstream_gene_variant,,ENST00000447210,;SPAG8,downstream_gene_variant,,ENST00000479751,;SPAG8,downstream_gene_variant,,ENST00000463889,;SPAG8,downstream_gene_variant,,ENST00000489063,;NPR2,non_coding_transcript_exon_variant,,ENST00000464810,;SPAG8,downstream_gene_variant,,ENST00000475644,;SPAG8,downstream_gene_variant,,ENST00000472605,;SPAG8,downstream_gene_variant,,ENST00000495667,;SPAG8,downstream_gene_variant,,ENST00000471631,;NPR2,upstream_gene_variant,,ENST00000448821,;SPAG8,downstream_gene_variant,,ENST00000460836,;NPR2,upstream_gene_variant,,ENST00000469249,; G ENST00000342694 Transcript synonymous_variant 2229/3686 1974/3144 658/1047 L ctC/ctG 1 1 NPR2 HGNC HGNC:7944 protein_coding YES CCDS6590.1 ENSP00000341083 P20594 UPI0000125B42 NM_003995.3 13/22 PROSITE_profiles:PS50011,hmmpanther:PTHR11920:SF305,hmmpanther:PTHR11920,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 35805597 35805597 C G 1 0 0 0 0 0 0 0 1 10651 813 29 4 4 NPR2 9 35805597 Silent SNP C C3N-00294_T 3880 35805597 102589120 654 13426 CNTNAP3 0 . GRCh38 9 39133107 39133107 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1905C>T p.= p.H635H ENST00000297668 13/24 272 255 17 263 263 0 varscan-mutect CNTNAP3,synonymous_variant,p.=,ENST00000297668,NM_033655.3;CNTNAP3,synonymous_variant,p.=,ENST00000377656,;CNTNAP3,synonymous_variant,p.=,ENST00000358144,;CNTNAP3,synonymous_variant,p.=,ENST00000377659,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000448573,;CNTNAP3,synonymous_variant,p.=,ENST00000443583,; A ENST00000297668 Transcript synonymous_variant 1979/5064 1905/3867 635/1288 H caC/caT 1 -1 CNTNAP3 HGNC HGNC:13834 protein_coding YES CCDS6616.1 ENSP00000297668 Q9BZ76 UPI000013E43B NM_033655.3 13/24 Gene3D:3.90.215.10,PROSITE_profiles:PS51406,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Superfamily_domains:SSF56496 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 39133107 39133107 G A 1 0 0 0 0 0 0 0 1 3429 1136 40 1 1 CNTNAP3 9 39133107 Silent SNP G C3N-00294_T 3327510 39133107 99261610 655 13427 SPATA31A1 0 . GRCh38 9 39360857 39360857 + Missense_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.3134T>A p.Val1045Asp p.V1045D ENST00000377647 4/4 286 154 132 273 272 1 strelka-varscan-mutect SPATA31A1,missense_variant,p.Val1045Asp,ENST00000377647,NM_001085452.2;RP11-347J14.4,non_coding_transcript_exon_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 3154/4256 3134/4086 1045/1361 V/D gTt/gAt 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 tolerated(0.7) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS rs1179788436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 39360857 39360857 T A 1 0 0 0 0 1 0 0 0 15343 1725 60 4 4 SPATA31A1 9 39360857 Missense_Mutation SNP T C3N-00294_T 227750 39360857 99033860 656 13428 SPATA31A6 0 . GRCh38 9 42186624 42186624 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.922G>C p.Glu308Gln p.E308Q ENST00000332857 4/4 740 593 147 858 858 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Glu308Gln,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; C ENST00000332857 Transcript missense_variant 951/4209 922/4032 308/1343 E/Q Gag/Cag 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 deleterious(0.05) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 MODERATE 1 SNV 5 1 PASS . . 10 200 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 42186624 42186624 G C 1 0 0 0 0 1 0 0 0 15345 943 33 4 4 SPATA31A6 9 42186624 Missense_Mutation SNP G C3N-00294_T 2825767 42186624 96208093 657 13429 SPATA31A6 0 . GRCh38 9 42187614 42187614 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1912C>T p.Pro638Ser p.P638S ENST00000332857 4/4 717 557 160 729 729 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Pro638Ser,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; T ENST00000332857 Transcript missense_variant 1941/4209 1912/4032 638/1343 P/S Ccc/Tcc 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 deleterious(0.05) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS . . 37 172 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 42187614 42187614 C T 1 0 0 0 0 1 0 0 0 15345 855 30 3 3 SPATA31A6 9 42187614 Missense_Mutation SNP C C3N-00294_T 990 42187614 96207103 658 13430 FOXD4L5 0 . GRCh38 9 65283631 65283631 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.747C>A p.= p.A249A ENST00000377420 1/1 30 22 8 24 24 0 strelka-varscan-mutect FOXD4L5,synonymous_variant,p.=,ENST00000377420,NM_001126334.1;RP11-15J10.1,downstream_gene_variant,,ENST00000445695,; T ENST00000377420 Transcript synonymous_variant 1579/3109 747/1251 249/416 A gcC/gcA 1 -1 FOXD4L5 HGNC HGNC:18522 protein_coding YES CCDS47977.1 ENSP00000366637 Q5VV16 UPI0000458A33 NM_001126334.1 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 65283631 65283631 G T 1 0 0 0 0 0 0 0 1 5863 987 35 2 2 FOXD4L5 9 65283631 Silent SNP G C3N-00294_T 23096017 65283631 73111086 659 13431 FOXD4L4 0 . GRCh38 9 65737892 65737892 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.747C>A p.= p.A249A ENST00000377413 1/1 451 414 37 536 536 0 varscan-mutect FOXD4L4,synonymous_variant,p.=,ENST00000377413,NM_199244.3;CBWD5,downstream_gene_variant,,ENST00000377392,NM_001286835.1;CBWD5,downstream_gene_variant,,ENST00000382405,;CBWD5,downstream_gene_variant,,ENST00000430059,;CBWD5,downstream_gene_variant,,ENST00000429800,;CBWD5,downstream_gene_variant,,ENST00000377395,NM_001024916.3;CBWD5,downstream_gene_variant,,ENST00000489273,;CBWD5,downstream_gene_variant,,ENST00000476797,;CBWD5,downstream_gene_variant,,ENST00000468066,;CBWD5,downstream_gene_variant,,ENST00000486191,;CBWD5,downstream_gene_variant,,ENST00000485088,;CBWD5,downstream_gene_variant,,ENST00000461932,;CBWD5,downstream_gene_variant,,ENST00000480229,;CBWD5,downstream_gene_variant,,ENST00000377389,;CBWD5,downstream_gene_variant,,ENST00000486221,;CBWD5,downstream_gene_variant,,ENST00000497250,;CBWD5,downstream_gene_variant,,ENST00000463075,;CBWD5,downstream_gene_variant,,ENST00000491485,;CBWD5,downstream_gene_variant,,ENST00000480819,; A ENST00000377413 Transcript synonymous_variant 1338/2230 747/1251 249/416 A gcC/gcA 1 1 FOXD4L4 HGNC HGNC:23762 protein_coding YES CCDS75845.1 ENSP00000366630 Q8WXT5 UPI0000246F14 NM_199244.3 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149,Low_complexity_(Seg):seg LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 65737892 65737892 C A 1 0 0 0 0 0 0 0 1 5862 668 24 2 2 FOXD4L4 9 65737892 Silent SNP C C3N-00294_T 454261 65737892 72656825 660 13432 TRPM6 0 . GRCh38 9 74728249 74728249 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.5925C>T p.= p.L1975L ENST00000360774 38/39 357 296 61 408 408 0 strelka-varscan-mutect TRPM6,synonymous_variant,p.=,ENST00000360774,NM_017662.4;TRPM6,synonymous_variant,p.=,ENST00000361255,NM_001177311.1;TRPM6,synonymous_variant,p.=,ENST00000449912,NM_001177310.1; A ENST00000360774 Transcript synonymous_variant 6163/8425 5925/6069 1975/2022 L ctC/ctT 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 38/39 PROSITE_profiles:PS51158,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 74728249 74728249 G A 1 0 0 0 0 0 0 0 1 17096 1277 45 3 3 TRPM6 9 74728249 Silent SNP G C3N-00294_T 8990357 74728249 63666468 661 13433 TRPM6 0 . GRCh38 9 74762004 74762004 + Missense_Mutation SNP A A T rs763046852 C3N-00294_T C3N-00294_N A A c.4667T>A p.Ile1556Asn p.I1556N ENST00000360774 26/39 155 96 59 224 224 0 strelka-varscan-mutect TRPM6,missense_variant,p.Ile1556Asn,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Ile1551Asn,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Ile1551Asn,ENST00000449912,NM_001177310.1; T ENST00000360774 Transcript missense_variant 4905/8425 4667/6069 1556/2022 I/N aTt/aAt rs763046852 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 tolerated_low_confidence(0.37) 26/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 MODERATE 1 SNV 1 1 PASS rs763046852 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 74762004 74762004 A T 1 0 0 0 0 1 0 0 0 17096 115 4 4 4 TRPM6 9 74762004 Missense_Mutation SNP A C3N-00294_T 33755 74762004 63632713 662 13434 PRUNE2 0 . GRCh38 9 76706840 76706840 + Nonsense_Mutation SNP C C A rs546778607 C3N-00294_T C3N-00294_N C C c.5434G>T p.Glu1812Ter p.E1812* ENST00000376718 8/19 60 50 10 67 67 0 strelka-varscan-mutect PRUNE2,stop_gained,p.Glu1812Ter,ENST00000376718,NM_015225.2;PRUNE2,stop_gained,p.Glu1453Ter,ENST00000428286,;PRUNE2,stop_gained,p.Glu1812Ter,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,stop_gained,p.Glu1134Ter,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; A ENST00000376718 Transcript stop_gained 5558/12584 5434/9267 1812/3088 E/* Gaa/Taa rs546778607,COSM3433254 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 8/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112 0,1 HIGH 1 SNV 5 0,1 1 PASS rs546778607 . 0 204 5 0 0 0 0 0 -19.99959 1 1 1 1 0 A 4 1 46 76706840 76706840 C A 1 0 0 0 0 0 1 0 0 12791 893 31 1 1 PRUNE2 9 76706840 Nonsense_Mutation SNP C C3N-00294_T 1944836 76706840 61687877 663 13435 C9orf64 0 . GRCh38 9 83944831 83944831 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.756G>A p.= p.L252L ENST00000376344 3/4 226 183 43 291 291 0 strelka-varscan-mutect C9orf64,synonymous_variant,p.=,ENST00000376344,NM_032307.3;C9orf64,synonymous_variant,p.=,ENST00000314700,NM_001317997.1; T ENST00000376344 Transcript synonymous_variant 973/2443 756/1026 252/341 L ctG/ctA 1 -1 C9orf64 HGNC HGNC:28144 protein_coding YES CCDS6666.2 ENSP00000365522 Q5T6V5 UPI000013E45E NM_032307.3 3/4 Pfam_domain:PF10343,hmmpanther:PTHR21314,hmmpanther:PTHR21314:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 83944831 83944831 C T 1 0 0 0 0 0 0 0 1 2187 813 29 3 3 C9orf64 9 83944831 Silent SNP C C3N-00294_T 7237991 83944831 54449886 664 13436 NTRK2 0 . GRCh38 9 84934263 84934263 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1735G>A p.Glu579Lys p.E579K ENST00000277120 15/19 494 388 106 538 537 1 strelka-varscan-mutect NTRK2,missense_variant,p.Glu579Lys,ENST00000277120,;NTRK2,missense_variant,p.Glu579Lys,ENST00000376214,NM_006180.4;NTRK2,missense_variant,p.Glu563Lys,ENST00000376213,;NTRK2,missense_variant,p.Glu563Lys,ENST00000323115,NM_001018064.2; A ENST00000277120 Transcript missense_variant 2218/8633 1735/2517 579/838 E/K Gag/Aag 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D deleterious(0.03) 15/19 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF136,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 84934263 84934263 G A 1 0 0 0 0 1 0 0 0 10773 1291 45 3 3 NTRK2 9 84934263 Missense_Mutation SNP G C3N-00294_T 989432 84934263 53460454 665 13437 C9orf47 0 . GRCh38 9 88991469 88991469 + Splice_Site SNP G G C novel C3N-00294_T C3N-00294_N G G c.247-1G>C p.X83_splice ENST00000334490 354 267 87 345 345 0 strelka-varscan-mutect C9orf47,splice_acceptor_variant,,ENST00000375851,NM_001142413.1;C9orf47,splice_acceptor_variant,,ENST00000334490,NM_001001938.3;C9orf47,splice_acceptor_variant,,ENST00000375850,;S1PR3,5_prime_UTR_variant,,ENST00000358157,NM_005226.3; C ENST00000334490 Transcript splice_acceptor_variant -/4829 247/609 83/202 1 1 C9orf47 HGNC HGNC:23669 protein_coding YES CCDS35062.1 ENSP00000335616 Q6ZRZ4 UPI00001C0EE0 NM_001001938.3 1/2 HIGH 1 SNV 1 1 PASS rs1412408279 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 46 88991469 88991469 G C 1 0 0 0 0 0 0 1 0 2184 956 33 4 4 C9orf47 9 88991469 Splice_Site SNP G C3N-00294_T 4057206 88991469 49403248 666 13438 SECISBP2 0 . GRCh38 9 89339909 89339909 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1258G>A p.Asp420Asn p.D420N ENST00000375807 9/17 465 373 92 495 495 0 strelka-varscan-mutect SECISBP2,missense_variant,p.Asp352Asn,ENST00000534113,NM_001282690.1;SECISBP2,missense_variant,p.Asp420Asn,ENST00000375807,NM_001282688.1,NM_024077.4;SECISBP2,missense_variant,p.Asp347Asn,ENST00000339901,NM_001282689.1;SECISBP2,missense_variant,p.Asp217Asn,ENST00000425851,;SECISBP2,downstream_gene_variant,,ENST00000440898,;SECISBP2,non_coding_transcript_exon_variant,,ENST00000477484,; A ENST00000375807 Transcript missense_variant 1329/3462 1258/2565 420/854 D/N Gac/Aac 1 1 SECISBP2 HGNC HGNC:30972 protein_coding YES CCDS6683.1 ENSP00000364965 Q96T21 UPI00001AEA0A NM_001282688.1,NM_024077.4 tolerated(1) 9/17 hmmpanther:PTHR13284,hmmpanther:PTHR13284:SF9 MODERATE 1 SNV 1 1 PASS rs1226906024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 89339909 89339909 G A 1 0 0 0 0 1 0 0 0 14283 942 33 3 3 SECISBP2 9 89339909 Missense_Mutation SNP G C3N-00294_T 348440 89339909 49054808 667 13439 OGN 0 . GRCh38 9 92403290 92403290 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.118G>C p.Glu40Gln p.E40Q ENST00000262551 2/7 134 101 33 152 152 0 strelka-varscan-mutect OGN,missense_variant,p.Glu40Gln,ENST00000262551,NM_033014.2;OGN,missense_variant,p.Glu40Gln,ENST00000375561,NM_014057.3;OGN,missense_variant,p.Glu98Gln,ENST00000447356,;CENPP,intron_variant,,ENST00000375587,NM_001012267.2; G ENST00000262551 Transcript missense_variant 539/2971 118/897 40/298 E/Q Gaa/Caa 1 -1 OGN HGNC HGNC:8126 protein_coding YES CCDS6695.1 ENSP00000262551 P20774 A8K0R3 UPI00000540ED NM_033014.2 tolerated(0.1) 2/7 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 92403290 92403290 C G 1 0 0 0 0 1 0 0 0 10921 922 32 4 4 OGN 9 92403290 Missense_Mutation SNP C C3N-00294_T 3063381 92403290 45991427 668 13440 ANP32B 0 . GRCh38 9 97983591 97983591 + Missense_Mutation SNP G G T rs775002531 C3N-00294_T C3N-00294_N G G c.36G>T p.Arg12Ser p.R12S ENST00000339399 1/7 283 229 54 285 284 1 strelka-varscan-mutect ANP32B,missense_variant,p.Arg12Ser,ENST00000339399,NM_006401.2;RP11-535C21.3,downstream_gene_variant,,ENST00000411981,;ANP32B,upstream_gene_variant,,ENST00000473205,; T ENST00000339399 Transcript missense_variant 231/1463 36/756 12/251 R/S agG/agT rs775002531 1 1 ANP32B HGNC HGNC:16677 protein_coding YES CCDS6732.1 ENSP00000345848 Q92688 UPI0000125029 NM_006401.2 deleterious(0) 1/7 Gene3D:3.80.10.10,hmmpanther:PTHR11375,hmmpanther:PTHR11375:SF2,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs775002531 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 97983591 97983591 G T 1 0 0 0 0 1 0 0 0 814 1165 41 2 2 ANP32B 9 97983591 Missense_Mutation SNP G C3N-00294_T 5580301 97983591 40411126 669 13441 ANKS6 0 . GRCh38 9 98778236 98778236 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.1557C>A p.= p.T519T ENST00000353234 7/15 156 126 30 176 176 0 strelka-varscan-mutect ANKS6,synonymous_variant,p.=,ENST00000353234,NM_173551.3;ANKS6,synonymous_variant,p.=,ENST00000375019,;ANKS6,upstream_gene_variant,,ENST00000444472,;ANKS6,non_coding_transcript_exon_variant,,ENST00000634393,; T ENST00000353234 Transcript synonymous_variant 1605/7164 1557/2616 519/871 T acC/acA 1 -1 ANKS6 HGNC HGNC:26724 protein_coding YES CCDS43856.1 ENSP00000297837 Q68DC2 UPI0000530317 NM_173551.3 7/15 hmmpanther:PTHR10627:SF39,hmmpanther:PTHR10627 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 98778236 98778236 G T 1 0 0 0 0 0 0 0 1 798 1335 47 2 2 ANKS6 9 98778236 Silent SNP G C3N-00294_T 794645 98778236 39616481 670 13442 ALG2 0 . GRCh38 9 99221665 99221665 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.230G>A p.Arg77Gln p.R77Q ENST00000476832 1/2 129 99 30 118 118 0 strelka-varscan-mutect ALG2,missense_variant,p.Arg77Gln,ENST00000476832,NM_033087.3;ALG2,upstream_gene_variant,,ENST00000319033,;SEC61B,upstream_gene_variant,,ENST00000498603,;SEC61B,upstream_gene_variant,,ENST00000223641,NM_006808.2;SEC61B,upstream_gene_variant,,ENST00000481573,;ALG2,missense_variant,p.Arg77Gln,ENST00000238477,; T ENST00000476832 Transcript missense_variant 292/1880 230/1251 77/416 R/Q cGa/cAa 1 -1 ALG2 HGNC HGNC:23159 protein_coding YES CCDS6739.1 ENSP00000417764 Q9H553 A0A024R184 UPI0000073E01 NM_033087.3 deleterious(0) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR12526,hmmpanther:PTHR12526:SF401,Pfam_domain:PF13439,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs1272919288 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 99221665 99221665 C T 1 0 0 0 0 1 0 0 0 619 884 31 1 1 ALG2 9 99221665 Missense_Mutation SNP C C3N-00294_T 443429 99221665 39173052 671 13443 TEX10 0 . GRCh38 9 100320313 100320313 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.2154C>G p.= p.L718L ENST00000374902 11/15 148 117 31 128 128 0 strelka-varscan-mutect TEX10,synonymous_variant,p.=,ENST00000374902,NM_017746.3;TEX10,synonymous_variant,p.=,ENST00000535814,NM_001161584.1; C ENST00000374902 Transcript synonymous_variant 2331/3074 2154/2790 718/929 L ctC/ctG 1 -1 TEX10 HGNC HGNC:25988 protein_coding YES CCDS6748.1 ENSP00000364037 Q9NXF1 A0A024R169 UPI000013D052 NM_017746.3 11/15 hmmpanther:PTHR16056,hmmpanther:PTHR16056:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 100320313 100320313 G C 1 0 0 0 0 0 0 0 1 16193 929 33 4 4 TEX10 9 100320313 Silent SNP G C3N-00294_T 1098648 100320313 38074404 672 13444 GRIN3A 0 . GRCh38 9 101670403 101670403 + Missense_Mutation SNP A A G novel C3N-00294_T C3N-00294_N A A c.2009T>C p.Met670Thr p.M670T ENST00000361820 3/9 263 203 60 223 223 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Met670Thr,ENST00000361820,NM_133445.2; G ENST00000361820 Transcript missense_variant 2610/7770 2009/3348 670/1115 M/T aTg/aCg 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 tolerated(0.06) 3/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Gene3D:3.40.190.10,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 101670403 101670403 A G 1 0 0 0 0 1 0 0 0 6665 217 8 5 5 GRIN3A 9 101670403 Missense_Mutation SNP A C3N-00294_T 1350090 101670403 36724314 673 13445 GRIN3A 0 . GRCh38 9 101686847 101686847 + Missense_Mutation SNP T T G novel C3N-00294_T C3N-00294_N T T c.1053A>C p.Glu351Asp p.E351D ENST00000361820 2/9 196 174 22 196 196 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Glu351Asp,ENST00000361820,NM_133445.2; G ENST00000361820 Transcript missense_variant 1654/7770 1053/3348 351/1115 E/D gaA/gaC 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 tolerated(0.35) 2/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 101686847 101686847 T G 1 0 0 0 0 1 0 0 0 6665 1722 60 5 5 GRIN3A 9 101686847 Missense_Mutation SNP T C3N-00294_T 16444 101686847 36707870 674 13446 CYLC2 0 . GRCh38 9 103005349 103005349 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.718G>A p.Asp240Asn p.D240N ENST00000374798 5/8 120 97 23 173 173 0 strelka-varscan-mutect CYLC2,missense_variant,p.Asp240Asn,ENST00000374798,NM_001340.4;CYLC2,missense_variant,p.Asp240Asn,ENST00000487798,;CYLC2,missense_variant,p.Asp240Asn,ENST00000612124,; A ENST00000374798 Transcript missense_variant 788/2171 718/1047 240/348 D/N Gat/Aat 1 1 CYLC2 HGNC HGNC:2583 protein_coding YES CCDS35085.1 ENSP00000420256 Q14093 A0A024R146 UPI0000128C36 NM_001340.4 tolerated(0.18) 5/8 hmmpanther:PTHR16742,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 103005349 103005349 G A 1 0 0 0 0 1 0 0 0 3945 942 33 3 3 CYLC2 9 103005349 Missense_Mutation SNP G C3N-00294_T 1318502 103005349 35389368 675 13447 SMC2 0 . GRCh38 9 104116221 104116221 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1693G>C p.Glu565Gln p.E565Q ENST00000286398 14/25 90 68 22 153 153 0 strelka-varscan-mutect SMC2,missense_variant,p.Glu565Gln,ENST00000286398,NM_001042551.1,NM_006444.2,NM_001265602.1;SMC2,missense_variant,p.Glu565Gln,ENST00000374793,;SMC2,missense_variant,p.Glu565Gln,ENST00000374787,NM_001042550.1; C ENST00000286398 Transcript missense_variant 1997/5992 1693/3594 565/1197 E/Q Gaa/Caa 1 1 SMC2 HGNC HGNC:14011 protein_coding YES CCDS35086.1 ENSP00000286398 O95347 A0A024R158 UPI000013DE44 NM_001042551.1,NM_006444.2,NM_001265602.1 tolerated(0.7) 14/25 Superfamily_domains:0038317,Pfam_domain:PF02463,Pfam_domain:PF06470,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF9,SMART_domains:SM00968 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 104116221 104116221 G C 1 0 0 0 0 1 0 0 0 15076 943 33 4 4 SMC2 9 104116221 Missense_Mutation SNP G C3N-00294_T 1110872 104116221 34278496 676 13448 SMC2 0 . GRCh38 9 104125034 104125034 + Missense_Mutation SNP G G T C3N-00294_T C3N-00294_N G G c.2380G>T p.Ala794Ser p.A794S ENST00000286398 18/25 71 54 17 93 93 0 strelka-varscan-mutect SMC2,missense_variant,p.Ala794Ser,ENST00000286398,NM_001042551.1,NM_006444.2,NM_001265602.1;SMC2,missense_variant,p.Ala794Ser,ENST00000374793,;SMC2,missense_variant,p.Ala794Ser,ENST00000374787,NM_001042550.1;SMC2,upstream_gene_variant,,ENST00000493955,; T ENST00000286398 Transcript missense_variant 2684/5992 2380/3594 794/1197 A/S Gct/Tct COSM1103446,COSM1103447 1 1 SMC2 HGNC HGNC:14011 protein_coding YES CCDS35086.1 ENSP00000286398 O95347 A0A024R158 UPI000013DE44 NM_001042551.1,NM_006444.2,NM_001265602.1 deleterious(0) 18/25 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF9 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 104125034 104125034 G T 1 0 0 0 0 1 0 0 0 15076 1319 46 2 2 SMC2 9 104125034 Missense_Mutation SNP G C3N-00294_T 8813 104125034 34269683 677 13449 SVEP1 0 . GRCh38 9 110579172 110579172 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.372C>T p.= p.I124I ENST00000374469 1/48 272 257 15 311 310 1 strelka-varscan-mutect SVEP1,synonymous_variant,p.=,ENST00000401783,;SVEP1,synonymous_variant,p.=,ENST00000374469,NM_153366.3;SVEP1,synonymous_variant,p.=,ENST00000374461,; A ENST00000374469 Transcript synonymous_variant 567/12194 372/10716 124/3571 I atC/atT 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 1/48 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 110579172 110579172 G A 1 0 0 0 0 0 0 0 1 15805 1048 37 1 1 SVEP1 9 110579172 Silent SNP G C3N-00294_T 6454138 110579172 27815545 678 13450 SNX30 0 . GRCh38 9 112838516 112838516 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.833G>C p.Arg278Thr p.R278T ENST00000374232 6/9 113 91 22 103 103 0 strelka-varscan-mutect SNX30,missense_variant,p.Arg278Thr,ENST00000374232,NM_001012994.1;SNX30,upstream_gene_variant,,ENST00000416585,; C ENST00000374232 Transcript missense_variant 997/7622 833/1314 278/437 R/T aGa/aCa 1 1 SNX30 HGNC HGNC:23685 protein_coding YES CCDS43865.1 ENSP00000363349 Q5VWJ9 UPI0000457796 NM_001012994.1 deleterious(0.05) 6/9 hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF123,Superfamily_domains:SSF103657 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 112838516 112838516 G C 1 0 0 0 0 1 0 0 0 15221 942 33 4 4 SNX30 9 112838516 Missense_Mutation SNP G C3N-00294_T 2259344 112838516 25556201 679 13451 ZFP37 0 . GRCh38 9 113043323 113043323 + Missense_Mutation SNP G G C rs766404494 C3N-00294_T C3N-00294_N G G c.1340C>G p.Pro447Arg p.P447R ENST00000553380 4/4 136 112 24 199 199 0 strelka-varscan-mutect ZFP37,missense_variant,p.Pro432Arg,ENST00000374227,NM_003408.2;ZFP37,missense_variant,p.Pro433Arg,ENST00000555206,NM_001282518.1;ZFP37,missense_variant,p.Pro447Arg,ENST00000553380,NM_001282515.1;ZNF883,intron_variant,,ENST00000619044,NM_001101338.1; C ENST00000553380 Transcript missense_variant 1340/1969 1340/1938 447/645 P/R cCa/cGa rs766404494 1 -1 ZFP37 HGNC HGNC:12863 protein_coding YES CCDS65110.1 ENSP00000452552 Q9Y6Q3 UPI0001B04BC3 NM_001282515.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF147,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs766404494 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 113043323 113043323 G C 1 0 0 0 0 1 0 0 0 18223 1348 47 4 4 ZFP37 9 113043323 Missense_Mutation SNP G C3N-00294_T 204807 113043323 25351394 680 13452 KIF12 0 . GRCh38 9 114095217 114095217 + Silent SNP G G C rs751815395 C3N-00294_T C3N-00294_N G G c.597C>G p.= p.L199L ENST00000374118 7/16 129 122 7 147 147 0 strelka-mutect KIF12,synonymous_variant,p.=,ENST00000374118,NM_138424.1;KIF12,non_coding_transcript_exon_variant,,ENST00000473174,;KIF12,upstream_gene_variant,,ENST00000498016,;KIF12,downstream_gene_variant,,ENST00000491059,;KIF12,synonymous_variant,p.=,ENST00000468460,; C ENST00000374118 Transcript synonymous_variant 835/2003 597/1542 199/513 L ctC/ctG rs751815395 1 -1 KIF12 HGNC HGNC:21495 protein_coding YES CCDS6801.1 ENSP00000363232 B1ALC3 UPI00000729C3 NM_138424.1 7/16 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF418,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs751815395 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 114095217 114095217 G C 1 0 0 0 0 0 0 0 1 8137 1304 45 4 4 KIF12 9 114095217 Silent SNP G C3N-00294_T 1051894 114095217 24299500 681 13453 TNC 0 . GRCh38 9 115046508 115046508 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.5027A>G p.Asp1676Gly p.D1676G ENST00000350763 17/28 305 266 39 363 362 1 strelka-varscan-mutect TNC,missense_variant,p.Asp1676Gly,ENST00000350763,NM_002160.3;TNC,missense_variant,p.Asp1313Gly,ENST00000535648,;TNC,missense_variant,p.Asp1494Gly,ENST00000341037,;TNC,missense_variant,p.Asp1313Gly,ENST00000542877,;TNC,missense_variant,p.Asp239Gly,ENST00000544972,;TNC,intron_variant,,ENST00000423613,;TNC,intron_variant,,ENST00000537320,;TNC,downstream_gene_variant,,ENST00000635336,;TNC,non_coding_transcript_exon_variant,,ENST00000473855,;TNC,intron_variant,,ENST00000476680,;TNC,intron_variant,,ENST00000498724,;TNC,downstream_gene_variant,,ENST00000481475,; C ENST00000350763 Transcript missense_variant 5439/7641 5027/6606 1676/2201 D/G gAc/gGc 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 tolerated(0.32) 17/28 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 115046508 115046508 T C 1 0 0 0 0 1 0 0 0 16744 1667 58 5 5 TNC 9 115046508 Missense_Mutation SNP T C3N-00294_T 951291 115046508 23348209 682 13454 OR1J2 0 . GRCh38 9 122511479 122511479 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.678G>T p.= p.L226L ENST00000335302 1/1 114 60 54 160 160 0 strelka-varscan-mutect OR1J2,synonymous_variant,p.=,ENST00000335302,NM_054107.1; T ENST00000335302 Transcript synonymous_variant 678/942 678/942 226/313 L ctG/ctT 1 1 OR1J2 HGNC HGNC:8209 protein_coding YES CCDS35121.1 ENSP00000335575 Q8NGS2 A0A126GW18 UPI0000041CF3 NM_054107.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF324,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1417054646 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 122511479 122511479 G T 1 0 0 0 0 0 0 0 1 11038 1277 45 2 2 OR1J2 9 122511479 Silent SNP G C3N-00294_T 7464971 122511479 15883238 683 13455 DENND1A 0 . GRCh38 9 123583232 123583232 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.804G>C p.= p.L268L ENST00000373624 12/22 97 83 14 123 123 0 strelka-varscan-mutect DENND1A,synonymous_variant,p.=,ENST00000373624,NM_020946.1;DENND1A,synonymous_variant,p.=,ENST00000373620,NM_024820.2;DENND1A,synonymous_variant,p.=,ENST00000373618,;DENND1A,synonymous_variant,p.=,ENST00000394215,;DENND1A,non_coding_transcript_exon_variant,,ENST00000473039,;DENND1A,non_coding_transcript_exon_variant,,ENST00000491650,;DENND1A,non_coding_transcript_exon_variant,,ENST00000474676,;DENND1A,upstream_gene_variant,,ENST00000497135,; G ENST00000373624 Transcript synonymous_variant 1006/5010 804/3030 268/1009 L ctG/ctC COSM1105033,COSM4875657,COSM4875658,COSM4875659 1 -1 DENND1A HGNC HGNC:29324 protein_coding YES CCDS35133.1 ENSP00000362727 Q8TEH3 UPI00004589D2 NM_020946.1 12/22 Pfam_domain:PF02141,PROSITE_profiles:PS50211,hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF22,SMART_domains:SM00799 1,1,1,1 LOW 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 123583232 123583232 C G 1 0 0 0 0 0 0 0 1 4230 813 29 4 4 DENND1A 9 123583232 Silent SNP C C3N-00294_T 1071753 123583232 14811485 684 13456 NEK6 0 . GRCh38 9 124321537 124321537 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.475G>T p.Ala159Ser p.A159S ENST00000373600 6/11 138 88 50 191 191 0 strelka-varscan-mutect NEK6,missense_variant,p.Ala159Ser,ENST00000373600,NM_001145001.2;NEK6,missense_variant,p.Ala125Ser,ENST00000320246,NM_014397.5;NEK6,missense_variant,p.Ala125Ser,ENST00000373603,;NEK6,missense_variant,p.Ala150Ser,ENST00000539416,NM_001166169.1;NEK6,missense_variant,p.Ala125Ser,ENST00000546191,NM_001166170.1;NEK6,missense_variant,p.Ala143Ser,ENST00000540326,NM_001166167.1;NEK6,missense_variant,p.Ala125Ser,ENST00000545174,NM_001166168.1;NEK6,missense_variant,p.Ala159Ser,ENST00000394199,NM_001166171.1;NEK6,missense_variant,p.Ala125Ser,ENST00000425237,;NEK6,missense_variant,p.Ala125Ser,ENST00000422297,;NEK6,missense_variant,p.Ala125Ser,ENST00000444973,;NEK6,missense_variant,p.Ala125Ser,ENST00000373596,;NEK6,missense_variant,p.Ala57Ser,ENST00000454453,;NEK6,missense_variant,p.Ala159Ser,ENST00000423785,;NEK6,missense_variant,p.Ala125Ser,ENST00000447379,; T ENST00000373600 Transcript missense_variant 690/3619 475/1044 159/347 A/S Gct/Tct 1 1 NEK6 HGNC HGNC:7749 protein_coding YES CCDS48015.1 ENSP00000362702 Q9HC98 UPI000013ED34 NM_001145001.2 deleterious(0.03) 6/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24362,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 46 124321537 124321537 G T 1 0 0 0 0 1 0 0 0 10356 1203 42 2 2 NEK6 9 124321537 Missense_Mutation SNP G C3N-00294_T 738305 124321537 14073180 685 13457 PPP6C 0 . GRCh38 9 125189623 125189623 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.96C>G p.= p.L32L ENST00000451402 1/8 190 155 35 245 245 0 strelka-varscan-mutect PPP6C,synonymous_variant,p.=,ENST00000451402,NM_001123355.1;PPP6C,intron_variant,,ENST00000415905,NM_001123369.1;PPP6C,intron_variant,,ENST00000373547,NM_002721.4;PPP6C,intron_variant,,ENST00000456642,; C ENST00000451402 Transcript synonymous_variant 317/4349 96/1029 32/342 L ctC/ctG 1 -1 PPP6C HGNC HGNC:9323 protein_coding YES CCDS48018.1 ENSP00000392147 O00743 UPI000172E24D NM_001123355.1 1/8 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 125189623 125189623 G C 1 0 0 0 0 0 0 0 1 12533 1045 37 4 4 PPP6C 9 125189623 Silent SNP G C3N-00294_T 868086 125189623 13205094 686 13458 ST6GALNAC6 0 . GRCh38 9 127894635 127894635 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.174C>A p.= p.L58L ENST00000373142 4/7 229 189 40 278 276 2 strelka-varscan-mutect ST6GALNAC6,synonymous_variant,p.=,ENST00000373146,NM_013443.4;ST6GALNAC6,synonymous_variant,p.=,ENST00000373142,NM_001286999.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000373141,NM_001287001.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000373144,NM_001287000.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000622357,NM_001287002.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000291839,;ST6GALNAC6,synonymous_variant,p.=,ENST00000542456,NM_001287003.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000447681,;ST6GALNAC6,splice_region_variant,,ENST00000480417,;ST6GALNAC6,splice_region_variant,,ENST00000494541,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000485320,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000463086,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000481355,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000478319,;ST6GALNAC6,downstream_gene_variant,,ENST00000494611,; T ENST00000373142 Transcript synonymous_variant 347/2448 174/1125 58/374 L ctC/ctA 1 -1 ST6GALNAC6 HGNC HGNC:23364 protein_coding YES CCDS69669.1 ENSP00000362235 Q969X2 UPI000046FDCC NM_001286999.1 4/7 hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF45,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 127894635 127894635 G T 1 0 0 0 0 0 0 0 1 15606 929 33 2 2 ST6GALNAC6 9 127894635 Silent SNP G C3N-00294_T 2705012 127894635 10500082 687 13459 54 2 ST6GALNAC6 0 . GRCh38 9 127894641 127894641 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.168C>T p.= p.L56L ENST00000373142 4/7 218 178 40 248 248 0 strelka-varscan-mutect ST6GALNAC6,synonymous_variant,p.=,ENST00000373146,NM_013443.4;ST6GALNAC6,synonymous_variant,p.=,ENST00000373142,NM_001286999.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000373141,NM_001287001.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000373144,NM_001287000.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000622357,NM_001287002.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000291839,;ST6GALNAC6,synonymous_variant,p.=,ENST00000542456,NM_001287003.1;ST6GALNAC6,synonymous_variant,p.=,ENST00000447681,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000485320,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000463086,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000481355,;ST6GALNAC6,non_coding_transcript_exon_variant,,ENST00000478319,;ST6GALNAC6,intron_variant,,ENST00000480417,;ST6GALNAC6,intron_variant,,ENST00000494541,;ST6GALNAC6,downstream_gene_variant,,ENST00000494611,; A ENST00000373142 Transcript synonymous_variant 341/2448 168/1125 56/374 L ctC/ctT 1 -1 ST6GALNAC6 HGNC HGNC:23364 protein_coding YES CCDS69669.1 ENSP00000362235 Q969X2 UPI000046FDCC NM_001286999.1 4/7 hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF45,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 127894641 127894641 G A 1 0 0 0 0 0 0 0 1 15606 1277 45 3 3 ST6GALNAC6 9 127894641 Silent SNP G C3N-00294_T 6 127894641 10500076 688 13460 54 2 PIP5KL1 0 . GRCh38 9 127925241 127925241 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.783C>T p.= p.F261F ENST00000388747 9/10 114 88 26 127 127 0 strelka-varscan-mutect PIP5KL1,synonymous_variant,p.=,ENST00000388747,NM_001135219.1;PIP5KL1,synonymous_variant,p.=,ENST00000300432,NM_173492.1;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000490773,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000464108,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000464759,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000495448,;PIP5KL1,non_coding_transcript_exon_variant,,ENST00000497234,;PIP5KL1,intron_variant,,ENST00000498783,;PIP5KL1,downstream_gene_variant,,ENST00000492296,;PIP5KL1,upstream_gene_variant,,ENST00000485562,;PIP5KL1,upstream_gene_variant,,ENST00000477191,;PIP5KL1,downstream_gene_variant,,ENST00000476624,; A ENST00000388747 Transcript synonymous_variant 828/2198 783/1185 261/394 F ttC/ttT COSM5537085,COSM5537086 1 -1 PIP5KL1 HGNC HGNC:28711 protein_coding YES CCDS48030.1 ENSP00000373399 Q5T9C9 UPI0000EDA26F NM_001135219.1 9/10 PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF46,Gene3D:1bo1A02,Pfam_domain:PF01504,SMART_domains:SM00330,Superfamily_domains:SSF56104 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 A 2 1 46 127925241 127925241 G A 1 0 0 0 0 0 0 0 1 12037 1165 41 3 3 PIP5KL1 9 127925241 Silent SNP G C3N-00294_T 30600 127925241 10469476 689 13461 SWI5 0 . GRCh38 9 128276267 128276267 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.122C>T p.Ser41Phe p.S41F ENST00000320188 1/5 147 109 38 171 171 0 strelka-varscan-mutect SWI5,missense_variant,p.Ser41Phe,ENST00000320188,NM_001040011.1;SWI5,5_prime_UTR_variant,,ENST00000419867,;SWI5,5_prime_UTR_variant,,ENST00000608796,;SWI5,5_prime_UTR_variant,,ENST00000418976,;SWI5,intron_variant,,ENST00000372898,;SWI5,intron_variant,,ENST00000495313,;GOLGA2,upstream_gene_variant,,ENST00000421699,NM_004486.4;GOLGA2,upstream_gene_variant,,ENST00000611957,;GOLGA2,upstream_gene_variant,,ENST00000609374,;GOLGA2,upstream_gene_variant,,ENST00000610329,;GOLGA2,upstream_gene_variant,,ENST00000450617,;GOLGA2,upstream_gene_variant,,ENST00000458730,;GOLGA2,upstream_gene_variant,,ENST00000490628,; T ENST00000320188 Transcript missense_variant 122/980 122/708 41/235 S/F tCt/tTt 1 1 SWI5 HGNC HGNC:31412 protein_coding YES CCDS43883.1 ENSP00000316609 Q1ZZU3 UPI00001D76F5 NM_001040011.1 deleterious_low_confidence(0.03) 1/5 hmmpanther:PTHR28529,hmmpanther:PTHR28529:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 128276267 128276267 C T 1 0 0 0 0 1 0 0 0 15811 913 32 3 3 SWI5 9 128276267 Missense_Mutation SNP C C3N-00294_T 351026 128276267 10118450 690 13462 SPTAN1 0 . GRCh38 9 128617705 128617705 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5423G>C p.Arg1808Thr p.R1808T ENST00000372739 42/57 560 326 234 638 638 0 strelka-varscan-mutect SPTAN1,missense_variant,p.Arg1803Thr,ENST00000372731,NM_003127.3;SPTAN1,missense_variant,p.Arg1808Thr,ENST00000372739,NM_001130438.2;SPTAN1,missense_variant,p.Arg1788Thr,ENST00000630804,;SPTAN1,missense_variant,p.Arg1783Thr,ENST00000358161,NM_001195532.1;SPTAN1,missense_variant,p.Arg1808Thr,ENST00000630866,;SPTAN1,non_coding_transcript_exon_variant,,ENST00000637434,;SPTAN1,upstream_gene_variant,,ENST00000491712,;SPTAN1,downstream_gene_variant,,ENST00000476825,;SPTAN1,downstream_gene_variant,,ENST00000629378,; C ENST00000372739 Transcript missense_variant 5533/7868 5423/7434 1808/2477 R/T aGg/aCg 1 1 SPTAN1 HGNC HGNC:11273 protein_coding YES CCDS48036.1 ENSP00000361824 Q13813 UPI000045894C NM_001130438.2 tolerated(0.15) 42/57 hmmpanther:PTHR11915:SF283,hmmpanther:PTHR11915,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 128617705 128617705 G C 1 0 0 0 0 1 0 0 0 15473 1000 35 4 4 SPTAN1 9 128617705 Missense_Mutation SNP G C3N-00294_T 341438 128617705 9777012 691 13463 FAM73B 0 . GRCh38 9 129067772 129067772 + Splice_Site SNP G G A novel C3N-00294_T C3N-00294_N G G c.1171-1G>A p.X391_splice ENST00000358369 104 90 14 120 120 0 strelka-mutect FAM73B,splice_acceptor_variant,,ENST00000358369,NM_032809.2;FAM73B,splice_acceptor_variant,,ENST00000474639,;FAM73B,splice_acceptor_variant,,ENST00000495975,;FAM73B,downstream_gene_variant,,ENST00000494608,;FAM73B,splice_acceptor_variant,,ENST00000439290,;FAM73B,splice_acceptor_variant,,ENST00000445183,;FAM73B,splice_acceptor_variant,,ENST00000414342,;FAM73B,non_coding_transcript_exon_variant,,ENST00000471943,;FAM73B,upstream_gene_variant,,ENST00000483458,;FAM73B,upstream_gene_variant,,ENST00000492279,; A ENST00000358369 Transcript splice_acceptor_variant -/3637 1171/1782 391/593 1 1 FAM73B HGNC HGNC:23621 protein_coding YES CCDS6917.1 ENSP00000351138 Q7L4E1 UPI00001B4EFD NM_032809.2 11/15 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 129067772 129067772 G A 1 0 0 0 0 0 0 1 0 5484 956 33 3 3 FAM73B 9 129067772 Splice_Site SNP G C3N-00294_T 450067 129067772 9326945 692 13464 HMCN2 0 . GRCh38 9 130385631 130385631 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.9175G>T p.Val3059Phe p.V3059F ENST00000624552 60/98 307 183 124 326 326 0 strelka-varscan-mutect HMCN2,missense_variant,p.Val3059Phe,ENST00000624552,NM_001291815.1;HMCN2,missense_variant,p.Val92Phe,ENST00000487727,; T ENST00000624552 Transcript missense_variant 9175/15610 9175/15180 3059/5059 V/F Gtc/Ttc 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.01) 60/98 Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 130385631 130385631 G T 1 0 0 0 0 1 0 0 0 7112 1377 48 2 2 HMCN2 9 130385631 Missense_Mutation SNP G C3N-00294_T 1317859 130385631 8009086 693 13465 HMCN2 0 . GRCh38 9 130405988 130405988 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.12313G>C p.Glu4105Gln p.E4105Q ENST00000624552 82/98 95 75 20 90 90 0 strelka-varscan-mutect HMCN2,missense_variant,p.Glu4105Gln,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,non_coding_transcript_exon_variant,,ENST00000480829,; C ENST00000624552 Transcript missense_variant 12313/15610 12313/15180 4105/5059 E/Q Gag/Cag 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 tolerated(0.27) 82/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 130405988 130405988 G C 1 0 0 0 0 1 0 0 0 7112 1291 45 4 4 HMCN2 9 130405988 Missense_Mutation SNP G C3N-00294_T 20357 130405988 7988729 694 13466 PRRC2B 0 . GRCh38 9 131459215 131459215 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1263C>T p.= p.D421D ENST00000357304 10/31 164 126 38 161 160 1 strelka-varscan-mutect PRRC2B,synonymous_variant,p.=,ENST00000357304,NM_013318.3;PRRC2B,synonymous_variant,p.=,ENST00000405995,;PRRC2B,intron_variant,,ENST00000422467,; T ENST00000357304 Transcript synonymous_variant 1318/11042 1263/6690 421/2229 D gaC/gaT 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 10/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 131459215 131459215 C T 1 0 0 0 0 0 0 0 1 12749 477 17 3 3 PRRC2B 9 131459215 Silent SNP C C3N-00294_T 1053227 131459215 6935502 695 13467 TSC1 0 . GRCh38 9 132897538 132897538 + Nonsense_Mutation SNP G G A rs397514871 C3N-00294_T C3N-00294_N G G c.2698C>T p.Gln900Ter p.Q900* ENST00000298552 21/23 206 184 22 212 212 0 strelka-varscan-mutect TSC1,stop_gained,p.Gln900Ter,ENST00000298552,NM_000368.4,NM_001162426.1;TSC1,stop_gained,p.Gln900Ter,ENST00000440111,;TSC1,stop_gained,p.Gln849Ter,ENST00000545250,NM_001162427.1; A ENST00000298552 Transcript stop_gained 2920/8604 2698/3495 900/1164 Q/* Cag/Tag rs397514871,CM104950,COSM4954457 1 -1 TSC1 HGNC HGNC:12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 X5D9D2 UPI000013773E NM_000368.4,NM_001162426.1 21/23 hmmpanther:PTHR15154 not_provided,pathogenic 0,0,1 HIGH 1 SNV 1 1,1,1 1 PASS rs397514871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 132897538 132897538 G A 1 0 0 0 0 0 1 0 0 17111 1299 45 3 3 TSC1 9 132897538 Nonsense_Mutation SNP G C3N-00294_T 1438323 132897538 5497179 696 13468 STKLD1 0 . GRCh38 9 133405298 133405298 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.1920C>G p.= p.L640L ENST00000371957 18/18 89 76 13 88 88 0 strelka-varscan-mutect STKLD1,synonymous_variant,p.=,ENST00000371957,NM_153710.4;REXO4,downstream_gene_variant,,ENST00000371942,NM_001279350.1,NM_001279351.1,NM_020385.3;REXO4,downstream_gene_variant,,ENST00000371935,NM_001279349.1;REXO4,downstream_gene_variant,,ENST00000454825,; G ENST00000371957 Transcript synonymous_variant 2027/2825 1920/2043 640/680 L ctC/ctG 1 1 STKLD1 HGNC HGNC:28669 protein_coding YES CCDS35169.1 ENSP00000361025 Q8NE28 UPI00001D768C NM_153710.4 18/18 hmmpanther:PTHR24363,hmmpanther:PTHR24363:SF5,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 133405298 133405298 C G 1 0 0 0 0 0 0 0 1 15685 842 30 4 4 STKLD1 9 133405298 Silent SNP C C3N-00294_T 507760 133405298 4989419 697 13469 VAV2 0 . GRCh38 9 133812170 133812170 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.496G>A p.Asp166Asn p.D166N ENST00000371850 5/30 217 175 42 292 292 0 strelka-varscan-mutect VAV2,missense_variant,p.Asp166Asn,ENST00000371851,;VAV2,missense_variant,p.Asp166Asn,ENST00000371850,NM_001134398.1;VAV2,missense_variant,p.Asp166Asn,ENST00000406606,NM_003371.3; T ENST00000371850 Transcript missense_variant 528/4837 496/2637 166/878 D/N Gat/Aat 1 -1 VAV2 HGNC HGNC:12658 protein_coding YES CCDS48053.1 ENSP00000360916 P52735 UPI000013E06E NM_001134398.1 tolerated(0.05) 5/30 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF95,Low_complexity_(Seg):seg,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 133812170 133812170 C T 1 0 0 0 0 1 0 0 0 17677 855 30 3 3 VAV2 9 133812170 Missense_Mutation SNP C C3N-00294_T 406872 133812170 4582547 698 13470 CAMSAP1 0 . GRCh38 9 135822694 135822694 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1967C>G p.Ser656Ter p.S656* ENST00000389532 11/17 52 42 10 74 74 0 strelka-varscan-mutect CAMSAP1,stop_gained,p.Ser656Ter,ENST00000389532,NM_015447.3;CAMSAP1,stop_gained,p.Ser378Ter,ENST00000312405,;CAMSAP1,stop_gained,p.Ser667Ter,ENST00000409386,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,;CAMSAP1,upstream_gene_variant,,ENST00000493088,;CAMSAP1,upstream_gene_variant,,ENST00000482664,;CAMSAP1,upstream_gene_variant,,ENST00000487868,; C ENST00000389532 Transcript stop_gained 2032/7696 1967/4809 656/1602 S/* tCa/tGa 1 -1 CAMSAP1 HGNC HGNC:19946 protein_coding YES CCDS35176.2 ENSP00000374183 Q5T5Y3 UPI0000EDA283 NM_015447.3 11/17 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3 HIGH 1 SNV 5 1 PASS rs1419903826 . 0 208 2 0 0 0 0 0 -19.99997 1 1 1 1 0 C 4 2 46 135822694 135822694 G C 1 0 0 0 0 0 1 0 0 2303 1294 45 4 4 CAMSAP1 9 135822694 Nonsense_Mutation SNP G C3N-00294_T 2010524 135822694 2572023 699 13471 GRIN1 0 . GRCh38 9 137162911 137162911 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.2142C>T p.= p.F714F ENST00000371553 16/21 354 283 71 350 350 0 strelka-varscan-mutect GRIN1,synonymous_variant,p.=,ENST00000371561,NM_007327.3;GRIN1,synonymous_variant,p.=,ENST00000371546,;GRIN1,synonymous_variant,p.=,ENST00000371555,;GRIN1,synonymous_variant,p.=,ENST00000371550,NM_021569.3;GRIN1,synonymous_variant,p.=,ENST00000371553,NM_001185090.1;GRIN1,synonymous_variant,p.=,ENST00000371560,NM_001185091.1;GRIN1,synonymous_variant,p.=,ENST00000371559,NM_000832.6;GRIN1,3_prime_UTR_variant,,ENST00000350902,;GRIN1,non_coding_transcript_exon_variant,,ENST00000471122,;GRIN1,non_coding_transcript_exon_variant,,ENST00000460273,;GRIN1,downstream_gene_variant,,ENST00000485413,;GRIN1,upstream_gene_variant,,ENST00000473811,; T ENST00000371553 Transcript synonymous_variant 2148/3751 2142/2832 714/943 F ttC/ttT 1 1 GRIN1 HGNC HGNC:4584 protein_coding YES CCDS55354.1 ENSP00000360608 Q05586 UPI000014AF8E NM_001185090.1 16/21 hmmpanther:PTHR18966:SF214,hmmpanther:PTHR18966,Pfam_domain:PF00060,Gene3D:3.40.190.10,SMART_domains:SM00079,Superfamily_domains:SSF53850,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 137162911 137162911 C T 1 0 0 0 0 0 0 0 1 6660 854 30 3 3 GRIN1 9 137162911 Silent SNP C C3N-00294_T 1340217 137162911 1231806 700 13472 ZMYND19 0 . GRCh38 9 137588661 137588661 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.109G>A p.Glu37Lys p.E37K ENST00000298585 2/6 151 113 38 153 153 0 strelka-varscan-mutect ZMYND19,missense_variant,p.Glu37Lys,ENST00000298585,NM_138462.2;ZMYND19,splice_region_variant,,ENST00000471957,; T ENST00000298585 Transcript missense_variant,splice_region_variant 336/1375 109/684 37/227 E/K Gag/Aag 1 -1 ZMYND19 HGNC HGNC:21146 protein_coding YES CCDS7048.1 ENSP00000298585 Q96E35 UPI0000022A7D NM_138462.2 deleterious(0.01) 2/6 hmmpanther:PTHR13244:SF5,hmmpanther:PTHR13244 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 137588661 137588661 C T 1 0 0 0 0 1 0 0 0 18289 840 29 3 3 ZMYND19 9 137588661 Missense_Mutation SNP C C3N-00294_T 425750 137588661 806056 701 13473 PRKCQ 0 . GRCh38 10 6428329 6428329 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1999G>C p.Glu667Gln p.E667Q ENST00000263125 18/18 154 121 33 182 182 0 strelka-varscan-mutect PRKCQ,missense_variant,p.Glu667Gln,ENST00000263125,NM_001323265.1,NM_006257.4,NM_001282644.1;PRKCQ,missense_variant,p.Glu542Gln,ENST00000539722,NM_001323266.1,NM_001282645.1;PRKCQ,missense_variant,p.Glu604Gln,ENST00000397176,NM_001242413.2;PRKCQ,missense_variant,p.Glu631Gln,ENST00000610727,; G ENST00000263125 Transcript missense_variant 2099/3285 1999/2121 667/706 E/Q Gaa/Caa 1 -1 PRKCQ HGNC HGNC:9410 protein_coding YES CCDS7079.1 ENSP00000263125 Q04759 UPI000012DF74 NM_001323265.1,NM_006257.4,NM_001282644.1 deleterious(0.01) 18/18 Pfam_domain:PF00433,PIRSF_domain:PIRSF000551,PIRSF_domain:PIRSF501105,PROSITE_profiles:PS51285,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF181,SMART_domains:SM00133,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1374561756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 6428329 6428329 C G 1 0 0 0 0 1 0 0 0 12648 922 32 4 4 PRKCQ 10 6428329 Missense_Mutation SNP C C3N-00294_T 6428329 127369093 702 13474 ARHGAP21 0 . GRCh38 10 24600822 24600822 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2956G>C p.Glu986Gln p.E986Q ENST00000396432 14/26 156 134 22 207 207 0 varscan-mutect ARHGAP21,missense_variant,p.Glu986Gln,ENST00000396432,NM_020824.3;ARHGAP21,missense_variant,p.Glu773Gln,ENST00000636789,;ARHGAP21,missense_variant,p.Glu986Gln,ENST00000446003,;ARHGAP21,missense_variant,p.Glu976Gln,ENST00000376410,;ARHGAP21,intron_variant,,ENST00000612832,;ARHGAP21,intron_variant,,ENST00000320481,;ARHGAP21,upstream_gene_variant,,ENST00000418033,;ARHGAP21,upstream_gene_variant,,ENST00000418325,;ARHGAP21,intron_variant,,ENST00000493154,;ARHGAP21,missense_variant,p.Glu79Gln,ENST00000638156,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,; G ENST00000396432 Transcript missense_variant 3443/7167 2956/5877 986/1958 E/Q Gag/Cag 1 -1 ARHGAP21 HGNC HGNC:23725 protein_coding YES CCDS7144.2 ENSP00000379709 Q5T5U3 UPI0001639C78 NM_020824.3 deleterious(0.03) 14/26 PROSITE_profiles:PS50003,hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175,Pfam_domain:PF15410,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 24600822 24600822 C G 1 0 0 0 0 1 0 0 0 995 922 32 4 4 ARHGAP21 10 24600822 Missense_Mutation SNP C C3N-00294_T 18172493 24600822 109196600 703 13475 MYO3A 0 . GRCh38 10 26168791 26168791 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.3191C>T p.Ala1064Val p.A1064V ENST00000265944 28/35 170 142 28 279 279 0 strelka-varscan-mutect MYO3A,missense_variant,p.Ala1064Val,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,;MYO3A,non_coding_transcript_exon_variant,,ENST00000477691,; T ENST00000265944 Transcript missense_variant 3357/5581 3191/4851 1064/1616 A/V gCt/gTt 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0) 28/35 PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 26168791 26168791 C T 1 0 0 0 0 1 0 0 0 10077 797 28 3 3 MYO3A 10 26168791 Missense_Mutation SNP C C3N-00294_T 1567969 26168791 107628631 704 13476 WAC 0 . GRCh38 10 28611909 28611909 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.1424C>T p.Ser475Leu p.S475L ENST00000354911 10/14 125 95 30 117 117 0 strelka-mutect WAC,missense_variant,p.Ser430Leu,ENST00000375664,NM_100264.2;WAC,missense_variant,p.Ser475Leu,ENST00000354911,NM_016628.4;WAC,missense_variant,p.Ser372Leu,ENST00000347934,NM_100486.3;WAC,missense_variant,p.Ser323Leu,ENST00000375646,;WAC,3_prime_UTR_variant,,ENST00000628285,;WAC,downstream_gene_variant,,ENST00000428935,;WAC,3_prime_UTR_variant,,ENST00000439676,;WAC,non_coding_transcript_exon_variant,,ENST00000345541,;WAC,upstream_gene_variant,,ENST00000480474,;WAC,downstream_gene_variant,,ENST00000424454,;WAC,downstream_gene_variant,,ENST00000495268,;WAC,downstream_gene_variant,,ENST00000476046,; T ENST00000354911 Transcript missense_variant 1585/3042 1424/1944 475/647 S/L tCa/tTa COSM32899 1 1 WAC HGNC HGNC:17327 protein_coding YES CCDS7159.1 ENSP00000346986 Q9BTA9 UPI000013D398 NM_016628.4 deleterious(0.02) 10/14 hmmpanther:PTHR15911,hmmpanther:PTHR15911:SF6 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 28611909 28611909 C T 1 0 0 0 0 1 0 0 0 17807 838 29 3 3 WAC 10 28611909 Missense_Mutation SNP C C3N-00294_T 2443118 28611909 105185513 705 13477 ZNF239 0 . GRCh38 10 43557773 43557773 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.307G>A p.Glu103Lys p.E103K ENST00000306006 2/2 149 110 39 165 165 0 strelka-varscan-mutect ZNF239,missense_variant,p.Glu103Lys,ENST00000306006,NM_005674.2;ZNF239,missense_variant,p.Glu103Lys,ENST00000374446,NM_001324351.1,NM_001324352.1,NM_001324349.1,NM_001099282.1;ZNF239,missense_variant,p.Glu103Lys,ENST00000426961,NM_001099284.1;ZNF239,missense_variant,p.Glu103Lys,ENST00000535642,NM_001099283.1;ZNF239,non_coding_transcript_exon_variant,,ENST00000491188,; T ENST00000306006 Transcript missense_variant 960/2389 307/1377 103/458 E/K Gag/Aag 1 -1 ZNF239 HGNC HGNC:13031 protein_coding YES CCDS41502.1 ENSP00000307774 Q16600 UPI000006DD0E NM_005674.2 tolerated(0.26) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 43557773 43557773 C T 1 0 0 0 0 1 0 0 0 18367 835 29 3 3 ZNF239 10 43557773 Missense_Mutation SNP C C3N-00294_T 14945864 43557773 90239649 706 13478 AGAP9 0 . GRCh38 10 47520518 47520518 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.342G>C p.Gln114His p.Q114H ENST00000452145 3/8 197 162 35 312 312 0 strelka-varscan-mutect AGAP9,missense_variant,p.Gln114His,ENST00000452145,NM_001190810.1;RP11-144G6.12,non_coding_transcript_exon_variant,,ENST00000605970,;RP11-144G6.12,downstream_gene_variant,,ENST00000431840,; G ENST00000452145 Transcript missense_variant 454/2387 342/1977 114/658 Q/H caG/caC 1 -1 AGAP9 HGNC HGNC:23463 protein_coding YES CCDS73125.1 ENSP00000392206 Q5VTM2 UPI000019733B NM_001190810.1 tolerated_low_confidence(0.07) 3/8 MODERATE 1 SNV 1 1 PASS . . 38 171 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 47520518 47520518 C G 1 0 0 0 0 1 0 0 0 450 912 32 4 4 AGAP9 10 47520518 Missense_Mutation SNP C C3N-00294_T 3962745 47520518 86276904 707 13479 CCDC6 0 . GRCh38 10 59812776 59812776 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.706G>A p.Asp236Asn p.D236N ENST00000263102 5/9 116 83 33 85 85 0 strelka-varscan-mutect CCDC6,missense_variant,p.Asp236Asn,ENST00000263102,NM_005436.4;CCDC6,upstream_gene_variant,,ENST00000518638,; T ENST00000263102 Transcript missense_variant 938/5811 706/1425 236/474 D/N Gac/Aac 1 -1 CCDC6 HGNC HGNC:18782 protein_coding YES CCDS7257.1 ENSP00000263102 Q16204 UPI000035B25A NM_005436.4 tolerated(0.12) 5/9 hmmpanther:PTHR15276,hmmpanther:PTHR15276:SF0,Pfam_domain:PF09755 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 59812776 59812776 C T 1 0 0 0 0 1 0 0 0 2532 913 32 3 3 CCDC6 10 59812776 Missense_Mutation SNP C C3N-00294_T 12292258 59812776 73984646 708 13480 EGR2 0 . GRCh38 10 62815903 62815903 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.127G>A p.Glu43Lys p.E43K ENST00000242480 1/2 279 209 70 256 256 0 strelka-varscan-mutect EGR2,missense_variant,p.Glu43Lys,ENST00000242480,NM_001136177.1,NM_000399.3;EGR2,missense_variant,p.Glu43Lys,ENST00000439032,NM_001136178.1;EGR2,missense_variant,p.Glu43Lys,ENST00000637191,;EGR2,5_prime_UTR_variant,,ENST00000411732,NM_001136179.1;EGR2,non_coding_transcript_exon_variant,,ENST00000493899,; T ENST00000242480 Transcript missense_variant 453/2968 127/1431 43/476 E/K Gaa/Aaa COSM1297346 1 -1 EGR2 HGNC HGNC:3239 protein_coding YES CCDS7267.1 ENSP00000242480 P11161 UPI000013CB07 NM_001136177.1,NM_000399.3 deleterious(0.04) 1/2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 62815903 62815903 C T 1 0 0 0 0 1 0 0 0 4808 893 31 1 1 EGR2 10 62815903 Missense_Mutation SNP C C3N-00294_T 3003127 62815903 70981519 709 13481 ECD 0 . GRCh38 10 73163931 73163931 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.7G>C p.Glu3Gln p.E3Q ENST00000430082 2/15 125 102 23 116 116 0 varscan-mutect ECD,missense_variant,p.Glu3Gln,ENST00000372979,NM_007265.2;ECD,missense_variant,p.Glu3Gln,ENST00000430082,NM_001135752.1;ECD,missense_variant,p.Glu3Gln,ENST00000454759,NM_001135753.1;ECD,missense_variant,p.Glu3Gln,ENST00000413026,;ECD,intron_variant,,ENST00000453402,;FAM149B1,upstream_gene_variant,,ENST00000242505,NM_173348.1;ECD,non_coding_transcript_exon_variant,,ENST00000610256,;ECD,intron_variant,,ENST00000484976,; G ENST00000430082 Transcript missense_variant 219/2246 7/2034 3/677 E/Q Gaa/Caa 1 -1 ECD HGNC HGNC:17029 protein_coding YES CCDS44434.1 ENSP00000401566 O95905 UPI000181CB29 NM_001135752.1 tolerated(0.45) 2/15 hmmpanther:PTHR13060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 73163931 73163931 C G 1 0 0 0 0 1 0 0 0 4714 922 32 4 4 ECD 10 73163931 Missense_Mutation SNP C C3N-00294_T 10348028 73163931 60633491 710 13482 FUT11 0 . GRCh38 10 73773457 73773457 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.976G>A p.Asp326Asn p.D326N ENST00000372841 2/3 305 246 59 287 287 0 strelka-varscan-mutect FUT11,missense_variant,p.Asp326Asn,ENST00000394790,NM_001284194.1;FUT11,missense_variant,p.Asp326Asn,ENST00000372841,NM_173540.2;SEC24C,downstream_gene_variant,,ENST00000339365,NM_004922.3;SEC24C,downstream_gene_variant,,ENST00000345254,NM_198597.2;FUT11,non_coding_transcript_exon_variant,,ENST00000465695,;RP11-574K11.32,upstream_gene_variant,,ENST00000623453,;FUT11,upstream_gene_variant,,ENST00000489264,;SEC24C,downstream_gene_variant,,ENST00000496827,;SEC24C,downstream_gene_variant,,ENST00000465076,;SEC24C,downstream_gene_variant,,ENST00000635550,; A ENST00000372841 Transcript missense_variant 1019/2056 976/1479 326/492 D/N Gat/Aat 1 1 FUT11 HGNC HGNC:19233 protein_coding YES CCDS7333.1 ENSP00000361932 Q495W5 UPI00000474D6 NM_173540.2 deleterious(0.02) 2/3 Pfam_domain:PF00852,PIRSF_domain:PIRSF037332,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF156,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs1242167985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 73773457 73773457 G A 1 0 0 0 0 1 0 0 0 5975 1290 45 3 3 FUT11 10 73773457 Missense_Mutation SNP G C3N-00294_T 609526 73773457 60023965 711 13483 CAMK2G 0 . GRCh38 10 73847297 73847297 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.747C>T p.= p.I249I ENST00000322680 10/21 208 182 26 219 219 0 strelka-varscan-mutect CAMK2G,synonymous_variant,p.=,ENST00000423381,;CAMK2G,synonymous_variant,p.=,ENST00000322680,NM_172171.2;CAMK2G,synonymous_variant,p.=,ENST00000394762,NM_172170.4,NM_001204492.1;CAMK2G,synonymous_variant,p.=,ENST00000322635,NM_172169.2;CAMK2G,synonymous_variant,p.=,ENST00000351293,NM_001222.3,NM_172173.2;CAMK2G,synonymous_variant,p.=,ENST00000372765,;CAMK2G,synonymous_variant,p.=,ENST00000305762,;CAMK2G,synonymous_variant,p.=,ENST00000433289,;CAMK2G,synonymous_variant,p.=,ENST00000441192,;RP11-574K11.8,downstream_gene_variant,,ENST00000446730,;CAMK2G,non_coding_transcript_exon_variant,,ENST00000472912,;CAMK2G,non_coding_transcript_exon_variant,,ENST00000492020,;CAMK2G,non_coding_transcript_exon_variant,,ENST00000477652,; A ENST00000322680 Transcript synonymous_variant 877/3818 747/1671 249/556 I atC/atT 1 -1 CAMK2G HGNC HGNC:1463 protein_coding YES CCDS7338.1 ENSP00000319060 Q13555 UPI000016781F NM_172171.2 10/21 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF110,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 73847297 73847297 G A 1 0 0 0 0 0 0 0 1 2293 1280 45 3 3 CAMK2G 10 73847297 Silent SNP G C3N-00294_T 73840 73847297 59950125 712 13484 KAT6B 0 . GRCh38 10 74976166 74976166 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1829G>C p.Arg610Thr p.R610T ENST00000287239 8/18 294 224 70 270 270 0 strelka-varscan-mutect KAT6B,missense_variant,p.Arg610Thr,ENST00000287239,NM_012330.3;KAT6B,intron_variant,,ENST00000372711,NM_001256468.1;KAT6B,intron_variant,,ENST00000372724,NM_001256469.1;KAT6B,intron_variant,,ENST00000372725,;KAT6B,intron_variant,,ENST00000372714,;KAT6B,upstream_gene_variant,,ENST00000490365,; C ENST00000287239 Transcript missense_variant 2318/8287 1829/6222 610/2073 R/T aGa/aCa 1 1 KAT6B HGNC HGNC:17582 protein_coding YES CCDS7345.1 ENSP00000287239 Q8WYB5 UPI000013DEA0 NM_012330.3 tolerated_low_confidence(0.11) 8/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 74976166 74976166 G C 1 0 0 0 0 1 0 0 0 7899 942 33 4 4 KAT6B 10 74976166 Missense_Mutation SNP G C3N-00294_T 1128869 74976166 58821256 713 13485 C10orf11 0 . GRCh38 10 76036066 76036066 + Nonsense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.190C>T p.Gln64Ter p.Q64* ENST00000611255 3/7 165 145 20 217 217 0 strelka-varscan-mutect C10orf11,stop_gained,p.Gln64Ter,ENST00000611255,NM_001305581.1;C10orf11,stop_gained,p.Gln36Ter,ENST00000372499,NM_032024.3;C10orf11,stop_gained,p.Gln21Ter,ENST00000611306,;C10orf11,non_coding_transcript_exon_variant,,ENST00000593699,;C10orf11,non_coding_transcript_exon_variant,,ENST00000593817,; T ENST00000611255 Transcript stop_gained 462/1040 190/681 64/226 Q/* Cag/Tag COSM5201668 1 1 C10orf11 HGNC HGNC:23405 protein_coding YES CCDS76319.1 ENSP00000480240 A0A087WWI0 UPI00001A5016 NM_001305581.1 3/7 Gene3D:3.80.10.10,Pfam_domain:PF14580,PROSITE_profiles:PS51450,hmmpanther:PTHR10552,hmmpanther:PTHR10552:SF16,Superfamily_domains:SSF52058 1 HIGH 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 76036066 76036066 C T 1 0 0 0 0 0 1 0 0 1758 827 29 3 3 C10orf11 10 76036066 Nonsense_Mutation SNP C C3N-00294_T 1059900 76036066 57761356 714 13486 POLR3A 0 . GRCh38 10 78017580 78017580 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1426C>T p.His476Tyr p.H476Y ENST00000372371 10/31 214 176 38 220 220 0 strelka-varscan-mutect POLR3A,missense_variant,p.His476Tyr,ENST00000372371,NM_007055.3;POLR3A,non_coding_transcript_exon_variant,,ENST00000484760,;POLR3A,missense_variant,p.His77Tyr,ENST00000473588,; A ENST00000372371 Transcript missense_variant 1564/6640 1426/4173 476/1390 H/Y Cat/Tat 1 -1 POLR3A HGNC HGNC:30074 protein_coding YES CCDS7354.1 ENSP00000361446 O14802 UPI000007456A NM_007055.3 deleterious(0) 10/31 hmmpanther:PTHR19376:SF32,hmmpanther:PTHR19376,Pfam_domain:PF00623,Gene3D:2.40.40.20,SMART_domains:SM00663,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 78017580 78017580 G A 1 0 0 0 0 1 0 0 0 12339 1304 45 3 3 POLR3A 10 78017580 Missense_Mutation SNP G C3N-00294_T 1981514 78017580 55779842 715 13487 FAM35A 0 . GRCh38 10 87187114 87187114 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2222G>C p.Arg741Thr p.R741T ENST00000298784 8/9 140 115 25 176 176 0 strelka-varscan-mutect FAM35A,missense_variant,p.Arg810Thr,ENST00000298786,;FAM35A,missense_variant,p.Arg741Thr,ENST00000298784,NM_019054.2; C ENST00000298784 Transcript missense_variant 2336/3402 2222/2508 741/835 R/T aGa/aCa 1 1 FAM35A HGNC HGNC:28773 protein_coding YES CCDS7383.1 ENSP00000298784 Q86V20 UPI000013E51A NM_019054.2 tolerated(0.57) 8/9 hmmpanther:PTHR14495,hmmpanther:PTHR14495:SF2,Pfam_domain:PF15793 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 87187114 87187114 G C 1 0 0 0 0 1 0 0 0 5435 942 33 4 4 FAM35A 10 87187114 Missense_Mutation SNP G C3N-00294_T 9169534 87187114 46610308 716 13488 HECTD2 0 . GRCh38 10 91478259 91478259 + Frame_Shift_Del DEL G G - novel C3N-00294_T C3N-00294_N G G c.660delG p.Trp220Ter p.W220* ENST00000446394 6/22 59 50 9 109 109 0 sindel-varindel-pindel HECTD2,frameshift_variant,p.Trp220Ter,ENST00000446394,NM_001284274.1;HECTD2,frameshift_variant,p.Trp220Ter,ENST00000298068,NM_182765.4; - ENST00000446394 Transcript frameshift_variant 813/4939 659/2343 220/780 W/X tGg/tg 1 1 HECTD2 HGNC HGNC:26736 protein_coding YES CCDS60591.1 ENSP00000401023 E7ERR3 UPI0001AE6DAB NM_001284274.1 6/22 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF301 HIGH 1 deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 46 91478259 91478259 G - 1 0 1 0 1 0 0 0 0 6921 1357 47 0 0 HECTD2 10 91478259 Frame_Shift_Del DEL G C3N-00294_T 4291145 91478259 42319163 717 13489 CYP26C1 0 . GRCh38 10 93064432 93064432 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.757G>C p.Glu253Gln p.E253Q ENST00000285949 4/6 120 87 33 116 116 0 strelka-mutect CYP26C1,missense_variant,p.Glu253Gln,ENST00000285949,NM_183374.2;EXOC6,downstream_gene_variant,,ENST00000260762,NM_001319195.1,NM_019053.4;EXOC6,downstream_gene_variant,,ENST00000371552,NM_001319194.1,NM_001013848.2;EXOC6,downstream_gene_variant,,ENST00000443748,NM_001319200.1;RP11-348J12.2,upstream_gene_variant,,ENST00000444965,;CYP26C1,intron_variant,,ENST00000624358,; C ENST00000285949 Transcript missense_variant 757/1569 757/1569 253/522 E/Q Gag/Cag 1 1 CYP26C1 HGNC HGNC:20577 protein_coding YES CCDS7425.1 ENSP00000285949 Q6V0L0 UPI00002289F0 NM_183374.2 tolerated(0.08) 4/6 hmmpanther:PTHR24286,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 93064432 93064432 G C 1 0 0 0 0 1 0 0 0 3960 1291 45 4 4 CYP26C1 10 93064432 Missense_Mutation SNP G C3N-00294_T 1586173 93064432 40732990 718 13490 PLCE1 0 . GRCh38 10 94132285 94132285 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1318C>G p.Pro440Ala p.P440A ENST00000371380 2/32 329 251 78 349 349 0 strelka-varscan-mutect PLCE1,missense_variant,p.Pro440Ala,ENST00000371380,NM_016341.3,NM_001288989.1;PLCE1,missense_variant,p.Pro132Ala,ENST00000371375,;PLCE1,missense_variant,p.Pro132Ala,ENST00000371385,NM_001165979.2; G ENST00000371380 Transcript missense_variant 1553/12024 1318/6909 440/2302 P/A Cca/Gca 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 tolerated_low_confidence(0.23) 2/32 Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 94132285 94132285 C G 1 0 0 0 0 1 0 0 0 12128 855 30 4 4 PLCE1 10 94132285 Missense_Mutation SNP C C3N-00294_T 1067853 94132285 39665137 719 13491 HELLS 0 . GRCh38 10 94574643 94574643 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.795G>T p.Met265Ile p.M265I ENST00000394036 9/23 200 169 31 236 236 0 strelka-varscan-mutect HELLS,missense_variant,p.Met265Ile,ENST00000394036,NM_001289067.1;HELLS,missense_variant,p.Met265Ile,ENST00000348459,NM_001289069.1,NM_001289068.1,NM_001289074.1,NM_018063.4,NM_001289075.1;HELLS,missense_variant,p.Met141Ile,ENST00000239026,NM_001289071.1;HELLS,missense_variant,p.Met265Ile,ENST00000394045,NM_001289070.1,NM_001289072.1;HELLS,missense_variant,p.Met127Ile,ENST00000371332,NM_001289073.1;HELLS,downstream_gene_variant,,ENST00000419900,;RP11-119K6.6,upstream_gene_variant,,ENST00000432120,;HELLS,downstream_gene_variant,,ENST00000462057,;HELLS,downstream_gene_variant,,ENST00000466552,; T ENST00000394036 Transcript missense_variant 795/3131 795/2655 265/884 M/I atG/atT 1 1 HELLS HGNC HGNC:4861 protein_coding YES CCDS73162.1 ENSP00000377601 A0A0B4J1V9 UPI000023B7CF NM_001289067.1 deleterious(0.03) 9/23 PROSITE_profiles:PS51192,hmmpanther:PTHR10799,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 94574643 94574643 G T 1 0 0 0 0 1 0 0 0 6928 1290 45 2 2 HELLS 10 94574643 Missense_Mutation SNP G C3N-00294_T 442358 94574643 39222779 720 13492 CHUK 0 . GRCh38 10 100222913 100222913 + Missense_Mutation SNP C C A rs775967798 C3N-00294_T C3N-00294_N C C c.268G>T p.Val90Leu p.V90L ENST00000370397 3/21 230 138 92 342 342 0 strelka-varscan-mutect CHUK,missense_variant,p.Val90Leu,ENST00000370397,NM_001320928.1,NM_001278.3; A ENST00000370397 Transcript missense_variant 355/3625 268/2238 90/745 V/L Gtg/Ttg rs775967798,COSM3849485 1 -1 CHUK HGNC HGNC:1974 protein_coding YES CCDS7488.1 ENSP00000359424 O15111 UPI000013D6C7 NM_001320928.1,NM_001278.3 tolerated(1) 3/21 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF13,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775967798 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 100222913 100222913 C A 1 0 0 0 0 1 0 0 0 3177 478 17 2 2 CHUK 10 100222913 Missense_Mutation SNP C C3N-00294_T 5648270 100222913 33574509 721 13493 CWF19L1 0 . GRCh38 10 100256307 100256307 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.459C>T p.= p.L153L ENST00000354105 5/14 299 231 68 278 278 0 strelka-varscan-mutect CWF19L1,synonymous_variant,p.=,ENST00000354105,NM_018294.5,NM_001303405.1,NM_001303404.1;RNU6-422P,upstream_gene_variant,,ENST00000384632,;CWF19L1,non_coding_transcript_exon_variant,,ENST00000496796,;CWF19L1,non_coding_transcript_exon_variant,,ENST00000473842,;CWF19L1,intron_variant,,ENST00000468709,;CWF19L1,intron_variant,,ENST00000482452,;CWF19L1,intron_variant,,ENST00000466955,;CWF19L1,upstream_gene_variant,,ENST00000478047,; A ENST00000354105 Transcript synonymous_variant 546/2633 459/1617 153/538 L ctC/ctT 1 -1 CWF19L1 HGNC HGNC:25613 protein_coding YES CCDS7489.1 ENSP00000326411 Q69YN2 A0A0S2Z5E9 UPI0000070B3E NM_018294.5,NM_001303405.1,NM_001303404.1 5/14 hmmpanther:PTHR12072,hmmpanther:PTHR12072:SF4 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 100256307 100256307 G A 1 0 0 0 0 0 0 0 1 3881 1277 45 3 3 CWF19L1 10 100256307 Silent SNP G C3N-00294_T 33394 100256307 33541115 722 13494 SFXN3 0 . GRCh38 10 101034778 101034778 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.96C>T p.= p.F32F ENST00000224807 3/12 187 163 24 209 209 0 strelka-varscan-mutect SFXN3,synonymous_variant,p.=,ENST00000393459,;SFXN3,synonymous_variant,p.=,ENST00000224807,NM_030971.3;PDZD7,upstream_gene_variant,,ENST00000619208,NM_001195263.1;PDZD7,upstream_gene_variant,,ENST00000370215,NM_024895.4;PDZD7,upstream_gene_variant,,ENST00000470414,;SFXN3,upstream_gene_variant,,ENST00000466982,;SFXN3,upstream_gene_variant,,ENST00000470252,;SFXN3,upstream_gene_variant,,ENST00000487721,;SFXN3,upstream_gene_variant,,ENST00000465383,;SFXN3,synonymous_variant,p.=,ENST00000489434,;PDZD7,upstream_gene_variant,,ENST00000474125,;PDZD7,upstream_gene_variant,,ENST00000476306,; T ENST00000224807 Transcript synonymous_variant 552/3089 96/978 32/325 F ttC/ttT 1 1 SFXN3 HGNC HGNC:16087 protein_coding YES CCDS7508.2 ENSP00000224807 Q9BWM7 UPI000006EE3D NM_030971.3 3/12 Pfam_domain:PF03820,hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF20,TIGRFAM_domain:TIGR00798 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 101034778 101034778 C T 1 0 0 0 0 0 0 0 1 14456 825 29 3 3 SFXN3 10 101034778 Silent SNP C C3N-00294_T 778471 101034778 32762644 723 13495 GBF1 0 . GRCh38 10 102380588 102380588 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5072G>C p.Gly1691Ala p.G1691A ENST00000369983 38/40 123 107 16 150 150 0 strelka-varscan-mutect GBF1,missense_variant,p.Gly1691Ala,ENST00000369983,NM_001199379.1,NM_001199378.1,NM_004193.2; C ENST00000369983 Transcript missense_variant 5332/6403 5072/5580 1691/1859 G/A gGa/gCa 1 1 GBF1 HGNC HGNC:4181 protein_coding YES CCDS7533.1 ENSP00000359000 Q92538 UPI000012B228 NM_001199379.1,NM_001199378.1,NM_004193.2 tolerated(0.81) 38/40 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 102380588 102380588 G C 1 0 0 0 0 1 0 0 0 6142 1174 41 4 4 GBF1 10 102380588 Missense_Mutation SNP G C3N-00294_T 1345810 102380588 31416834 724 13496 PDCD11 0 . GRCh38 10 103445541 103445541 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5608G>C p.Glu1870Gln p.E1870Q ENST00000369797 36/36 124 101 23 107 107 0 strelka-varscan-mutect PDCD11,missense_variant,p.Glu1870Gln,ENST00000369797,NM_014976.1;CALHM2,downstream_gene_variant,,ENST00000260743,NM_015916.4;CALHM2,downstream_gene_variant,,ENST00000369788,;RP11-225H22.7,upstream_gene_variant,,ENST00000608063,;CALHM2,downstream_gene_variant,,ENST00000494180,;CALHM2,downstream_gene_variant,,ENST00000461631,;CALHM2,downstream_gene_variant,,ENST00000480642,;CALHM2,downstream_gene_variant,,ENST00000474797,;CALHM2,downstream_gene_variant,,ENST00000463878,;PDCD11,non_coding_transcript_exon_variant,,ENST00000478543,; C ENST00000369797 Transcript missense_variant 5702/6453 5608/5616 1870/1871 E/Q Gag/Cag 1 1 PDCD11 HGNC HGNC:13408 protein_coding YES CCDS31276.1 ENSP00000358812 Q14690 UPI00001C1ED1 NM_014976.1 deleterious(0.01) 36/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF10 MODERATE 1 SNV 1 1 PASS rs1415984668 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 103445541 103445541 G C 1 0 0 0 0 1 0 0 0 11705 943 33 4 4 PDCD11 10 103445541 Missense_Mutation SNP G C3N-00294_T 1064953 103445541 30351881 725 13497 NEURL1 0 . GRCh38 10 103584920 103584920 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1034C>T p.Ser345Leu p.S345L ENST00000369780 4/6 91 68 23 91 91 0 strelka-varscan-mutect NEURL1,missense_variant,p.Ser345Leu,ENST00000369780,NM_004210.4; T ENST00000369780 Transcript missense_variant 1443/4314 1034/1725 345/574 S/L tCg/tTg 1 1 NEURL1 HGNC HGNC:7761 protein_coding YES CCDS7551.1 ENSP00000358795 O76050 UPI0000073F46 NM_004210.4 tolerated(0.6) 4/6 Pfam_domain:PF07177,PROSITE_profiles:PS51065,hmmpanther:PTHR12429,hmmpanther:PTHR12429:SF13,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 103584920 103584920 C T 1 0 0 0 0 1 0 0 0 10380 893 31 1 1 NEURL1 10 103584920 Missense_Mutation SNP C C3N-00294_T 139379 103584920 30212502 726 13498 CFAP43 0 . GRCh38 10 104187458 104187458 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1722G>A p.= p.L574L ENST00000357060 14/38 106 88 18 115 115 0 strelka-mutect CFAP43,synonymous_variant,p.=,ENST00000357060,NM_025145.5;CFAP43,synonymous_variant,p.=,ENST00000278064,;CFAP43,upstream_gene_variant,,ENST00000434629,; T ENST00000357060 Transcript synonymous_variant 1838/5365 1722/4998 574/1665 L ctG/ctA 1 -1 CFAP43 HGNC HGNC:26684 protein_coding YES CCDS31281.1 ENSP00000349568 Q8NDM7 UPI0000D60FC7 NM_025145.5 14/38 hmmpanther:PTHR14885,hmmpanther:PTHR14885:SF1 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 104187458 104187458 C T 1 0 0 0 0 0 0 0 1 3018 813 29 3 3 CFAP43 10 104187458 Silent SNP C C3N-00294_T 602538 104187458 29609964 727 13499 ITPRIP 0 . GRCh38 10 104315802 104315802 + Missense_Mutation SNP C C T rs751175958 C3N-00294_T C3N-00294_N C C c.250G>A p.Val84Met p.V84M ENST00000278071 3/3 169 121 48 161 161 0 strelka-varscan-mutect ITPRIP,missense_variant,p.Val84Met,ENST00000278071,NM_033397.3;ITPRIP,missense_variant,p.Val84Met,ENST00000337478,NM_001272013.1;ITPRIP,missense_variant,p.Val84Met,ENST00000358187,NM_001272012.1;ITPRIP,missense_variant,p.Val84Met,ENST00000458723,;RP11-127L20.5,downstream_gene_variant,,ENST00000472915,; T ENST00000278071 Transcript missense_variant 703/6807 250/1644 84/547 V/M Gtg/Atg rs751175958,COSM1255118 1 -1 ITPRIP HGNC HGNC:29370 protein_coding YES CCDS7557.1 ENSP00000278071 Q8IWB1 UPI0000074521 NM_033397.3 tolerated(0.21) 3/3 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF8 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751175958 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 104315802 104315802 C T 1 0 0 0 0 1 0 0 0 7829 536 19 1 1 ITPRIP 10 104315802 Missense_Mutation SNP C C3N-00294_T 128344 104315802 29481620 728 13500 SORCS3 0 . GRCh38 10 105255726 105255726 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.3262C>T p.Leu1088Phe p.L1088F ENST00000369701 24/27 119 101 18 118 118 0 strelka-varscan-mutect SORCS3,missense_variant,p.Leu1088Phe,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Leu1088Phe,ENST00000369699,; T ENST00000369701 Transcript missense_variant 3489/5757 3262/3669 1088/1222 L/F Ctc/Ttc COSM5477082 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0.04) 24/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10 1 MODERATE 1 SNV 1 1 1 PASS rs1379690915 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 105255726 105255726 C T 1 0 0 0 0 1 0 0 0 15254 913 32 3 3 SORCS3 10 105255726 Missense_Mutation SNP C C3N-00294_T 939924 105255726 28541696 729 13501 SMC3 0 . GRCh38 10 110577436 110577436 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.214C>T p.Arg72Cys p.R72C ENST00000361804 5/29 120 101 19 246 246 0 strelka-varscan-mutect SMC3,missense_variant,p.Arg72Cys,ENST00000361804,NM_005445.3;SMC3,non_coding_transcript_exon_variant,,ENST00000462899,; T ENST00000361804 Transcript missense_variant 340/4114 214/3654 72/1217 R/C Cgt/Tgt COSM1504531 1 1 SMC3 HGNC HGNC:2468 protein_coding YES CCDS31285.1 ENSP00000354720 Q9UQE7 UPI0000135A8D NM_005445.3 deleterious(0) 5/29 Gene3D:3.40.50.300,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF8,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 110577436 110577436 C T 1 0 0 0 0 1 0 0 0 15077 884 31 1 1 SMC3 10 110577436 Missense_Mutation SNP C C3N-00294_T 5321710 110577436 23219986 730 13502 TCF7L2 0 . GRCh38 10 112951228 112951228 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.211C>T p.Arg71Cys p.R71C ENST00000627217 2/14 144 115 29 104 104 0 strelka-varscan-mutect TCF7L2,missense_variant,p.Arg71Cys,ENST00000355995,;TCF7L2,missense_variant,p.Arg71Cys,ENST00000543371,;TCF7L2,missense_variant,p.Arg71Cys,ENST00000538897,NM_001198529.1,NM_001146284.1,NM_001198531.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000536810,NM_001146285.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000369397,NM_030756.4;TCF7L2,missense_variant,p.Arg71Cys,ENST00000534894,NM_001198530.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000627217,NM_001146274.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000545257,NM_001198525.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000355717,NM_001146286.1,NM_001146283.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000629706,NM_001198526.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000352065,NM_001198528.1;TCF7L2,missense_variant,p.Arg71Cys,ENST00000369395,NM_001198527.1;TCF7L2,missense_variant,p.Arg18Cys,ENST00000346198,;TCF7L2,5_prime_UTR_variant,,ENST00000542695,;RP11-57H14.2,intron_variant,,ENST00000369391,; T ENST00000627217 Transcript missense_variant 561/3680 211/1809 71/602 R/C Cgc/Tgc 1 1 TCF7L2 HGNC HGNC:11641 protein_coding YES CCDS53577.1 ENSP00000486891 Q9NQB0 UPI000002B4A6 NM_001146274.1 deleterious(0.04) 2/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF32,Pfam_domain:PF08347 MODERATE 1 SNV 1 1 PASS rs1351120699 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 112951228 112951228 C T 1 0 0 0 0 1 0 0 0 16105 884 31 1 1 TCF7L2 10 112951228 Missense_Mutation SNP C C3N-00294_T 2373792 112951228 20846194 731 13503 NHLRC2 0 . GRCh38 10 113854996 113854996 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.124C>G p.Leu42Val p.L42V ENST00000369301 1/11 338 268 70 367 367 0 strelka-varscan-mutect NHLRC2,missense_variant,p.Leu42Val,ENST00000369301,NM_198514.3;DCLRE1A,upstream_gene_variant,,ENST00000361384,NM_014881.4;DCLRE1A,upstream_gene_variant,,ENST00000369305,NM_001271816.1;DCLRE1A,upstream_gene_variant,,ENST00000476112,;NHLRC2,non_coding_transcript_exon_variant,,ENST00000468890,; G ENST00000369301 Transcript missense_variant 336/11051 124/2181 42/726 L/V Ctg/Gtg 1 1 NHLRC2 HGNC HGNC:24731 protein_coding YES CCDS7585.1 ENSP00000358307 Q8NBF2 UPI0000071EAF NM_198514.3 tolerated(0.06) 1/11 hmmpanther:PTHR13833,hmmpanther:PTHR13833:SF49 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 113854996 113854996 C G 1 0 0 0 0 1 0 0 0 10439 912 32 4 4 NHLRC2 10 113854996 Missense_Mutation SNP C C3N-00294_T 903768 113854996 19942426 732 13504 ATRNL1 0 . GRCh38 10 115171269 115171269 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1325G>A p.Ser442Asn p.S442N ENST00000355044 8/29 124 100 24 135 135 0 strelka-varscan-mutect ATRNL1,missense_variant,p.Ser442Asn,ENST00000355044,NM_207303.4;ATRNL1,missense_variant,p.Ser442Asn,ENST00000609571,NM_001276282.3;ATRNL1,3_prime_UTR_variant,,ENST00000527407,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000524503,;ATRNL1,3_prime_UTR_variant,,ENST00000616894,; A ENST00000355044 Transcript missense_variant 1451/8479 1325/4140 442/1379 S/N aGc/aAc 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 tolerated(0.48) 8/29 hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,Gene3D:1zgkA00,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 115171269 115171269 G A 1 0 0 0 0 1 0 0 0 1360 971 34 3 3 ATRNL1 10 115171269 Missense_Mutation SNP G C3N-00294_T 1316273 115171269 18626153 733 13505 HSPA12A 0 . GRCh38 10 116707210 116707210 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.116C>T p.Ser39Phe p.S39F ENST00000369209 2/12 83 63 20 83 83 0 strelka-varscan-mutect HSPA12A,missense_variant,p.Ser56Phe,ENST00000635765,;HSPA12A,missense_variant,p.Ser39Phe,ENST00000369209,NM_025015.2;HSPA12A,missense_variant,p.Ser32Phe,ENST00000468935,; A ENST00000369209 Transcript missense_variant 221/5722 116/2028 39/675 S/F tCc/tTc 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 deleterious_low_confidence(0.02) 2/12 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 116707210 116707210 G A 1 0 0 0 0 1 0 0 0 7300 1174 41 3 3 HSPA12A 10 116707210 Missense_Mutation SNP G C3N-00294_T 1535941 116707210 17090212 734 13506 ATE1 0 . GRCh38 10 121836744 121836744 + Missense_Mutation SNP G G A rs200140033 C3N-00294_T C3N-00294_N G G c.1231C>T p.His411Tyr p.H411Y ENST00000224652 10/12 114 89 25 187 187 0 strelka-varscan-mutect ATE1,missense_variant,p.His404Tyr,ENST00000540606,NM_001288736.1;ATE1,missense_variant,p.His411Tyr,ENST00000224652,NM_001001976.2;ATE1,missense_variant,p.His411Tyr,ENST00000369043,NM_007041.3;ATE1,missense_variant,p.His296Tyr,ENST00000543447,NM_001288734.1;ATE1,missense_variant,p.His315Tyr,ENST00000369040,NM_001288735.1;ATE1,missense_variant,p.His408Tyr,ENST00000423243,;ATE1,downstream_gene_variant,,ENST00000481784,; A ENST00000224652 Transcript missense_variant 1345/4930 1231/1557 411/518 H/Y Cat/Tat rs200140033 1 -1 ATE1 HGNC HGNC:782 protein_coding YES CCDS31300.1 ENSP00000224652 O95260 UPI0000126223 NM_001001976.2 deleterious(0.01) 10/12 hmmpanther:PTHR21367,hmmpanther:PTHR21367:SF1,Pfam_domain:PF04377,PIRSF_domain:PIRSF037207,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS rs200140033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 121836744 121836744 G A 1 0 0 0 0 1 0 0 0 1227 1290 45 3 3 ATE1 10 121836744 Missense_Mutation SNP G C3N-00294_T 5129534 121836744 11960678 735 13507 TACC2 0 . GRCh38 10 122211102 122211102 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.6677C>T p.Ser2226Leu p.S2226L ENST00000369005 9/23 66 53 13 87 87 0 strelka-varscan-mutect TACC2,missense_variant,p.Ser2226Leu,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Ser2226Leu,ENST00000334433,;TACC2,missense_variant,p.Ser2230Leu,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Ser2230Leu,ENST00000453444,;TACC2,missense_variant,p.Ser2181Leu,ENST00000515603,NM_001291876.1;TACC2,missense_variant,p.Ser372Leu,ENST00000513429,NM_206861.2;TACC2,missense_variant,p.Ser304Leu,ENST00000360561,NM_206860.2;TACC2,missense_variant,p.Ser304Leu,ENST00000368999,;TACC2,missense_variant,p.Ser372Leu,ENST00000358010,;TACC2,missense_variant,p.Ser304Leu,ENST00000369004,NM_001291878.1;TACC2,missense_variant,p.Ser304Leu,ENST00000260733,NM_006997.3;TACC2,missense_variant,p.Ser321Leu,ENST00000514539,;TACC2,missense_variant,p.Ser67Leu,ENST00000505639,;TACC2,5_prime_UTR_variant,,ENST00000369000,;TACC2,5_prime_UTR_variant,,ENST00000369001,NM_001291879.1;TACC2,upstream_gene_variant,,ENST00000496913,;TACC2,upstream_gene_variant,,ENST00000508411,;TACC2,downstream_gene_variant,,ENST00000493951,;TACC2,downstream_gene_variant,,ENST00000492237,;TACC2,missense_variant,p.Ser73Leu,ENST00000440764,;TACC2,non_coding_transcript_exon_variant,,ENST00000368997,; T ENST00000369005 Transcript missense_variant 7017/9673 6677/8847 2226/2948 S/L tCa/tTa 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious(0) 9/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 122211102 122211102 C T 1 0 0 0 0 1 0 0 0 15898 838 29 3 3 TACC2 10 122211102 Missense_Mutation SNP C C3N-00294_T 374358 122211102 11586320 736 13508 IKZF5 0 . GRCh38 10 122994087 122994087 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.953C>T p.Ser318Phe p.S318F ENST00000368886 5/5 412 332 80 409 409 0 strelka-varscan-mutect IKZF5,missense_variant,p.Ser318Phe,ENST00000368886,;IKZF5,missense_variant,p.Ser318Phe,ENST00000617859,NM_001271840.1;PSTK,downstream_gene_variant,,ENST00000368887,NM_153336.2;PSTK,downstream_gene_variant,,ENST00000406217,;PSTK,intron_variant,,ENST00000497219,;PSTK,intron_variant,,ENST00000496079,;PSTK,downstream_gene_variant,,ENST00000465232,;IKZF5,downstream_gene_variant,,ENST00000479103,;PSTK,downstream_gene_variant,,ENST00000483455,;IKZF5,downstream_gene_variant,,ENST00000496605,;PSTK,downstream_gene_variant,,ENST00000483755,;IKZF5,downstream_gene_variant,,ENST00000469821,; A ENST00000368886 Transcript missense_variant 1274/4555 953/1260 318/419 S/F tCc/tTc 1 -1 IKZF5 HGNC HGNC:14283 protein_coding YES CCDS41574.1 ENSP00000357881 Q9H5V7 UPI000006DBBE tolerated(0.16) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24387:SF7,hmmpanther:PTHR24387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 122994087 122994087 G A 1 0 0 0 0 1 0 0 0 7526 1174 41 3 3 IKZF5 10 122994087 Missense_Mutation SNP G C3N-00294_T 782985 122994087 10803335 737 13509 HMX3 0 . GRCh38 10 123136284 123136284 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.234G>A p.= p.E78E ENST00000357878 1/2 125 103 22 127 127 0 strelka-varscan-mutect HMX3,synonymous_variant,p.=,ENST00000357878,NM_001105574.1; A ENST00000357878 Transcript synonymous_variant 323/1173 234/1074 78/357 E gaG/gaA 1 1 HMX3 HGNC HGNC:5019 protein_coding YES CCDS41575.1 ENSP00000350549 A6NHT5 UPI000047C635 NM_001105574.1 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF291,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 123136284 123136284 G A 1 0 0 0 0 0 0 0 1 7139 991 35 3 3 HMX3 10 123136284 Silent SNP G C3N-00294_T 142197 123136284 10661138 738 13510 GPR26 0 . GRCh38 10 123666491 123666491 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.84C>T p.= p.L28L ENST00000284674 1/3 137 95 42 109 109 0 strelka-varscan-mutect GPR26,synonymous_variant,p.=,ENST00000284674,NM_153442.3; T ENST00000284674 Transcript synonymous_variant 137/7514 84/1014 28/337 L ctC/ctT 1 1 GPR26 HGNC HGNC:4481 protein_coding YES CCDS7636.1 ENSP00000284674 Q8NDV2 UPI000006E821 NM_153442.3 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF6,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 123666491 123666491 C T 1 0 0 0 0 0 0 0 1 6568 900 32 3 3 GPR26 10 123666491 Silent SNP C C3N-00294_T 530207 123666491 10130931 739 13511 ADAM12 0 . GRCh38 10 126019801 126019801 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2563C>T p.Gln855Ter p.Q855* ENST00000368679 22/23 140 105 35 158 158 0 strelka-varscan-mutect ADAM12,stop_gained,p.Gln855Ter,ENST00000368679,NM_003474.5,NM_001288973.1; A ENST00000368679 Transcript stop_gained 2873/7938 2563/2730 855/909 Q/* Cag/Tag 1 -1 ADAM12 HGNC HGNC:190 protein_coding YES CCDS7653.1 ENSP00000357668 O43184 UPI000036672C NM_003474.5,NM_001288973.1 22/23 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF112 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 126019801 126019801 G A 1 0 0 0 0 0 1 0 0 280 1299 45 3 3 ADAM12 10 126019801 Nonsense_Mutation SNP G C3N-00294_T 2353310 126019801 7777621 740 13512 CFAP46 0 . GRCh38 10 132810982 132810982 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.7551G>A p.= p.L2517L ENST00000368586 56/58 227 189 38 322 322 0 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript synonymous_variant 7652/8278 7551/8148 2517/2715 L ttG/ttA 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 56/58 LOW 1 SNV 5 1 PASS rs1413730499 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 132810982 132810982 C T 1 0 0 0 0 0 0 0 1 3021 825 29 3 3 CFAP46 10 132810982 Silent SNP C C3N-00294_T 6791181 132810982 986440 741 13513 SIGIRR 0 . GRCh38 11 408082 408082 + Nonsense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.331C>T p.Gln111Ter p.Q111* ENST00000431843 4/10 140 119 21 154 154 0 strelka-mutect SIGIRR,stop_gained,p.Gln111Ter,ENST00000431843,NM_001135054.1;SIGIRR,stop_gained,p.Gln111Ter,ENST00000531205,;SIGIRR,stop_gained,p.Gln111Ter,ENST00000332725,NM_021805.2,NM_001135053.1;SIGIRR,stop_gained,p.Gln111Ter,ENST00000397632,;SIGIRR,synonymous_variant,p.=,ENST00000528209,;SIGIRR,intron_variant,,ENST00000530494,;PKP3,downstream_gene_variant,,ENST00000331563,NM_001303029.1,NM_007183.3;SIGIRR,upstream_gene_variant,,ENST00000526395,;SIGIRR,upstream_gene_variant,,ENST00000528845,;SIGIRR,downstream_gene_variant,,ENST00000528058,;PKP3,downstream_gene_variant,,ENST00000525642,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000529486,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000534217,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000528116,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000525299,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000530683,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000526788,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000527136,;SIGIRR,intron_variant,,ENST00000528698,;SIGIRR,non_coding_transcript_exon_variant,,ENST00000527295,;SIGIRR,upstream_gene_variant,,ENST00000527987,;SIGIRR,downstream_gene_variant,,ENST00000525070,;SIGIRR,upstream_gene_variant,,ENST00000534145,;SIGIRR,upstream_gene_variant,,ENST00000528536,; A ENST00000431843 Transcript stop_gained 638/1720 331/1233 111/410 Q/* Cag/Tag COSM1298025,COSM4811153 1 -1 SIGIRR HGNC HGNC:30575 protein_coding YES CCDS31325.1 ENSP00000403104 Q6IA17 UPI000049DD22 NM_001135054.1 4/10 hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF19 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 408082 408082 G A 1 0 0 0 0 0 1 0 0 14568 1299 45 3 3 SIGIRR 11 408082 Nonsense_Mutation SNP G C3N-00294_T 408082 134678540 742 13514 PTDSS2 0 . GRCh38 11 487028 487028 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.525C>T p.= p.L175L ENST00000308020 5/12 90 76 14 112 112 0 strelka-varscan-mutect PTDSS2,synonymous_variant,p.=,ENST00000308020,NM_030783.1;PTDSS2,non_coding_transcript_exon_variant,,ENST00000532614,;PTDSS2,3_prime_UTR_variant,,ENST00000531520,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000526878,;PTDSS2,upstream_gene_variant,,ENST00000527325,;PTDSS2,upstream_gene_variant,,ENST00000531411,;PTDSS2,upstream_gene_variant,,ENST00000530029,; T ENST00000308020 Transcript synonymous_variant 701/2445 525/1464 175/487 L ctC/ctT 1 1 PTDSS2 HGNC HGNC:15463 protein_coding YES CCDS7696.1 ENSP00000308258 Q9BVG9 A0A024RC97 UPI000004124C NM_030783.1 5/12 Pfam_domain:PF03034,hmmpanther:PTHR15362,hmmpanther:PTHR15362:SF12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 487028 487028 C T 1 0 0 0 0 0 0 0 1 12890 813 29 3 3 PTDSS2 11 487028 Silent SNP C C3N-00294_T 78946 487028 134599594 743 13515 MUC5B 0 . GRCh38 11 1241128 1241128 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.4248C>G p.= p.L1416L ENST00000529681 31/49 202 166 36 184 184 0 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;RP11-532E4.2,downstream_gene_variant,,ENST00000532061,;MUC5B,downstream_gene_variant,,ENST00000525715,; G ENST00000529681 Transcript synonymous_variant 4306/17911 4248/17289 1416/5762 L ctC/ctG 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 31/49 Pfam_domain:PF13330 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 1241128 1241128 C G 1 0 0 0 0 0 0 0 1 9979 900 32 4 4 MUC5B 11 1241128 Silent SNP C C3N-00294_T 754100 1241128 133845494 744 13516 TRIM21 0 . GRCh38 11 4385720 4385720 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.993C>T p.= p.V331V ENST00000254436 7/7 205 173 32 236 236 0 strelka-varscan-mutect TRIM21,synonymous_variant,p.=,ENST00000254436,NM_003141.3;TRIM21,synonymous_variant,p.=,ENST00000533692,; A ENST00000254436 Transcript synonymous_variant 1106/1924 993/1428 331/475 V gtC/gtT COSM3447305,COSM3447306 1 -1 TRIM21 HGNC HGNC:11312 protein_coding YES CCDS44525.1 ENSP00000254436 P19474 UPI000013450B NM_003141.3 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF46,Pfam_domain:PF13765,SMART_domains:SM00589,Superfamily_domains:SSF49899,Prints_domain:PR01407 1,1 LOW 1 SNV 1 1,1 1 PASS rs1303700804 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 4385720 4385720 G A 1 0 0 0 0 0 0 0 1 16984 1161 41 3 3 TRIM21 11 4385720 Silent SNP G C3N-00294_T 3144592 4385720 130700902 745 13517 OR52K1 0 . GRCh38 11 4489767 4489767 + Silent SNP C C G rs769252225 C3N-00294_T C3N-00294_N C C c.867C>G p.= p.V289V ENST00000307632 1/1 151 120 31 161 161 0 strelka-varscan-mutect OR52K1,synonymous_variant,p.=,ENST00000307632,NM_001005171.2; G ENST00000307632 Transcript synonymous_variant 889/1030 867/945 289/314 V gtC/gtG rs769252225 1 1 OR52K1 HGNC HGNC:15222 protein_coding YES CCDS31352.1 ENSP00000302422 Q8NGK4 A0A126GVF2 UPI00001AEE74 NM_001005171.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF144,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs769252225 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 4489767 4489767 C G 1 0 0 0 0 0 0 0 1 11196 813 29 4 4 OR52K1 11 4489767 Silent SNP C C3N-00294_T 104047 4489767 130596855 746 13518 OR51G2 0 . GRCh38 11 4914815 4914815 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.849C>T p.= p.F283F ENST00000322013 1/1 153 123 30 181 181 0 strelka-varscan-mutect OR51G2,synonymous_variant,p.=,ENST00000322013,NM_001005238.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; A ENST00000322013 Transcript synonymous_variant 849/945 849/945 283/314 F ttC/ttT COSM1719807 1 -1 OR51G2 HGNC HGNC:15198 protein_coding YES CCDS31365.1 ENSP00000322593 Q8NGK0 UPI0000041C2F NM_001005238.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF133,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 4914815 4914815 G A 1 0 0 0 0 0 0 0 1 11171 1281 45 3 3 OR51G2 11 4914815 Silent SNP G C3N-00294_T 425048 4914815 130171807 747 13519 OR10A5 0 . GRCh38 11 6846228 6846228 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.546C>A p.Ser182Arg p.S182R ENST00000299454 1/1 279 171 108 328 328 0 strelka-varscan-mutect OR10A5,missense_variant,p.Ser182Arg,ENST00000299454,NM_178168.1;RP11-413N10.3,intron_variant,,ENST00000637205,;RP11-560B16.5,upstream_gene_variant,,ENST00000530632,; A ENST00000299454 Transcript missense_variant 577/1054 546/954 182/317 S/R agC/agA 1 1 OR10A5 HGNC HGNC:15131 protein_coding YES CCDS7773.1 ENSP00000299454 Q9H207 A0A126GWR0 UPI000004C155 NM_178168.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs1247279087 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 6846228 6846228 C A 1 0 0 0 0 1 0 0 0 10969 738 26 2 2 OR10A5 11 6846228 Missense_Mutation SNP C C3N-00294_T 1931413 6846228 128240394 748 13520 PPFIBP2 0 . GRCh38 11 7651776 7651776 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2368G>A p.Glu790Lys p.E790K ENST00000299492 23/24 94 70 24 87 86 1 strelka-varscan-mutect PPFIBP2,missense_variant,p.Glu790Lys,ENST00000299492,NM_003621.3;PPFIBP2,missense_variant,p.Glu632Lys,ENST00000533792,;PPFIBP2,missense_variant,p.Glu647Lys,ENST00000530181,NM_001256569.1;PPFIBP2,missense_variant,p.Glu678Lys,ENST00000528883,NM_001256568.1;PPFIBP2,missense_variant,p.Glu22Lys,ENST00000534552,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000530582,;PPFIBP2,intron_variant,,ENST00000532926,;PPFIBP2,intron_variant,,ENST00000529021,;PPFIBP2,downstream_gene_variant,,ENST00000524495,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000529664,;PPFIBP2,downstream_gene_variant,,ENST00000532112,;PPFIBP2,downstream_gene_variant,,ENST00000528929,; A ENST00000299492 Transcript missense_variant 2756/3557 2368/2631 790/876 E/K Gaa/Aaa 1 1 PPFIBP2 HGNC HGNC:9250 protein_coding YES CCDS31419.1 ENSP00000299492 Q8ND30 UPI00001C1EF8 NM_003621.3 deleterious(0.01) 23/24 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF18 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 7651776 7651776 G A 1 0 0 0 0 1 0 0 0 12423 1291 45 3 3 PPFIBP2 11 7651776 Missense_Mutation SNP G C3N-00294_T 805548 7651776 127434846 749 13521 SWAP70 0 . GRCh38 11 9729419 9729419 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.866C>T p.Ser289Leu p.S289L ENST00000318950 6/12 147 120 27 221 221 0 strelka-varscan-mutect SWAP70,missense_variant,p.Ser289Leu,ENST00000318950,NM_015055.3;SWAP70,missense_variant,p.Ser231Leu,ENST00000447399,NM_001297714.1;SWAP70,missense_variant,p.Ser140Leu,ENST00000534662,;SWAP70,3_prime_UTR_variant,,ENST00000534562,;SWAP70,non_coding_transcript_exon_variant,,ENST00000524817,;SWAP70,downstream_gene_variant,,ENST00000526358,;SWAP70,downstream_gene_variant,,ENST00000531814,; T ENST00000318950 Transcript missense_variant 969/4882 866/1758 289/585 S/L tCa/tTa 1 1 SWAP70 HGNC HGNC:17070 protein_coding YES CCDS31426.1 ENSP00000315630 Q9UH65 UPI0000073652 NM_015055.3 deleterious(0) 6/12 PROSITE_profiles:PS50003,hmmpanther:PTHR14383,hmmpanther:PTHR14383:SF6,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 9729419 9729419 C T 1 0 0 0 0 1 0 0 0 15810 838 29 3 3 SWAP70 11 9729419 Missense_Mutation SNP C C3N-00294_T 2077643 9729419 125357203 750 13522 PARVA 0 . GRCh38 11 12517616 12517616 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.994G>C p.Asp332His p.D332H ENST00000334956 11/13 121 94 27 148 148 0 strelka-varscan-mutect PARVA,missense_variant,p.Asp332His,ENST00000334956,NM_018222.4;PARVA,downstream_gene_variant,,ENST00000533345,; C ENST00000334956 Transcript missense_variant 1337/4458 994/1239 332/412 D/H Gat/Cat 1 1 PARVA HGNC HGNC:14652 protein_coding YES CCDS44541.2 ENSP00000334008 J3KNQ4 UPI0000EE3866 NM_018222.4 deleterious(0) 11/13 Gene3D:1.10.418.10,Pfam_domain:PF00307,PIRSF_domain:PIRSF039131,PROSITE_profiles:PS50021,hmmpanther:PTHR12114,hmmpanther:PTHR12114:SF6,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs1269619011 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 12517616 12517616 G C 1 0 0 0 0 1 0 0 0 11549 942 33 4 4 PARVA 11 12517616 Missense_Mutation SNP G C3N-00294_T 2788197 12517616 122569006 751 13523 PDE3B 0 . GRCh38 11 14843892 14843892 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2386G>C p.Asp796His p.D796H ENST00000282096 12/16 235 200 35 258 258 0 strelka-varscan-mutect PDE3B,missense_variant,p.Asp796His,ENST00000282096,NM_000922.3;PDE3B,missense_variant,p.Asp745His,ENST00000455098,; C ENST00000282096 Transcript missense_variant 2739/6076 2386/3339 796/1112 D/H Gat/Cat 1 1 PDE3B HGNC HGNC:8779 protein_coding YES CCDS7817.1 ENSP00000282096 Q13370 UPI000013DCB7 NM_000922.3 deleterious(0) 12/16 Gene3D:1.10.1300.10,SMART_domains:SM00471,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 14843892 14843892 G C 1 0 0 0 0 1 0 0 0 11726 1290 45 4 4 PDE3B 11 14843892 Missense_Mutation SNP G C3N-00294_T 2326276 14843892 120242730 752 13524 MRGPRX2 0 . GRCh38 11 19055860 19055860 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.543G>C p.Gln181His p.Q181H ENST00000329773 2/2 147 114 33 134 134 0 strelka-varscan-mutect MRGPRX2,missense_variant,p.Gln181His,ENST00000329773,NM_001303615.1,NM_054030.3; G ENST00000329773 Transcript missense_variant 631/2036 543/993 181/330 Q/H caG/caC 1 -1 MRGPRX2 HGNC HGNC:17983 protein_coding YES CCDS7847.1 ENSP00000333800 Q96LB1 UPI0000038C81 NM_001303615.1,NM_054030.3 tolerated(0.11) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF35,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 19055860 19055860 C G 1 0 0 0 0 1 0 0 0 9734 912 32 4 4 MRGPRX2 11 19055860 Missense_Mutation SNP C C3N-00294_T 4211968 19055860 116030762 753 13525 METTL15 0 . GRCh38 11 28113515 28113515 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.181C>T p.Gln61Ter p.Q61* ENST00000407364 3/7 176 145 31 244 244 0 strelka-varscan-mutect METTL15,stop_gained,p.Gln61Ter,ENST00000406787,NM_001297775.1;METTL15,stop_gained,p.Gln61Ter,ENST00000407364,NM_001113528.1;METTL15,stop_gained,p.Gln61Ter,ENST00000303459,NM_152636.2;METTL15,stop_gained,p.Gln61Ter,ENST00000634721,;METTL15,stop_gained,p.Gln61Ter,ENST00000403099,;METTL15,stop_gained,p.Gln61Ter,ENST00000634762,;METTL15,stop_gained,p.Gln61Ter,ENST00000451385,;METTL15,stop_gained,p.Gln61Ter,ENST00000532947,;METTL15,stop_gained,p.Gln61Ter,ENST00000634973,;METTL15,stop_gained,p.Gln61Ter,ENST00000634627,;METTL15,stop_gained,p.Gln61Ter,ENST00000437814,; T ENST00000407364 Transcript stop_gained 533/4242 181/1224 61/407 Q/* Caa/Taa 1 1 METTL15 HGNC HGNC:26606 protein_coding YES CCDS44559.1 ENSP00000384369 A6NJ78 UPI0000DBEF34 NM_001113528.1 3/7 hmmpanther:PTHR11265,hmmpanther:PTHR11265:SF0 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 28113515 28113515 C T 1 0 0 0 0 0 1 0 0 9441 827 29 3 3 METTL15 11 28113515 Nonsense_Mutation SNP C C3N-00294_T 9057655 28113515 106973107 754 13526 IMMP1L 0 . GRCh38 11 31463225 31463225 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.52C>T p.Gln18Ter p.Q18* ENST00000278200 3/7 124 101 23 145 145 0 strelka-varscan-mutect IMMP1L,stop_gained,p.Gln18Ter,ENST00000278200,NM_144981.2;IMMP1L,stop_gained,p.Gln18Ter,ENST00000532287,NM_001304274.1;IMMP1L,stop_gained,p.Gln18Ter,ENST00000530023,;IMMP1L,stop_gained,p.Gln18Ter,ENST00000529749,;IMMP1L,stop_gained,p.Gln18Ter,ENST00000526776,;IMMP1L,intron_variant,,ENST00000534812,;IMMP1L,intron_variant,,ENST00000533642,;IMMP1L,non_coding_transcript_exon_variant,,ENST00000532624,;IMMP1L,non_coding_transcript_exon_variant,,ENST00000527184,;IMMP1L,non_coding_transcript_exon_variant,,ENST00000531693,;IMMP1L,intron_variant,,ENST00000528161,; A ENST00000278200 Transcript stop_gained 248/795 52/501 18/166 Q/* Caa/Taa 1 -1 IMMP1L HGNC HGNC:26317 protein_coding YES CCDS7874.1 ENSP00000278200 Q96LU5 UPI00000427B2 NM_144981.2 3/7 hmmpanther:PTHR12383,hmmpanther:PTHR12383:SF16 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 31463225 31463225 G A 1 0 0 0 0 0 1 0 0 7619 1299 45 3 3 IMMP1L 11 31463225 Nonsense_Mutation SNP G C3N-00294_T 3349710 31463225 103623397 755 13527 PAX6 0 . GRCh38 11 31794780 31794780 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.574C>G p.Gln192Glu p.Q192E ENST00000419022 9/14 300 240 60 285 285 0 strelka-varscan-mutect PAX6,missense_variant,p.Gln192Glu,ENST00000419022,NM_001310158.1,NM_001310161.1,NM_001258462.1;PAX6,missense_variant,p.Gln192Glu,ENST00000606377,NM_001310161.1,NM_001258463.1;PAX6,missense_variant,p.Gln192Glu,ENST00000379129,;PAX6,missense_variant,p.Gln192Glu,ENST00000379107,;PAX6,missense_variant,p.Gln178Glu,ENST00000379132,NM_001127612.1;PAX6,missense_variant,p.Gln178Glu,ENST00000379123,NM_001258464.1,NM_000280.4;PAX6,missense_variant,p.Gln178Glu,ENST00000379109,;PAX6,missense_variant,p.Gln192Glu,ENST00000379115,NM_001604.5;PAX6,missense_variant,p.Gln178Glu,ENST00000241001,;PAX6,missense_variant,p.Gln178Glu,ENST00000379111,NM_001258465.1;PAX6,incomplete_terminal_codon_variant,p.=,ENST00000455099,;PAX6,non_coding_transcript_exon_variant,,ENST00000471303,;PAX6,non_coding_transcript_exon_variant,,ENST00000531910,;PAX6,non_coding_transcript_exon_variant,,ENST00000530373,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000464174,;PAX6,upstream_gene_variant,,ENST00000474783,;PAX6,upstream_gene_variant,,ENST00000532916,; C ENST00000419022 Transcript missense_variant 1043/6922 574/1311 192/436 Q/E Cag/Gag CM1110705 1 -1 PAX6 HGNC HGNC:8620 protein_coding YES CCDS31452.1 ENSP00000404100 P26367 F1T0F8 UPI000002B0A0 NM_001310158.1,NM_001310161.1,NM_001258462.1 tolerated(0.49) 9/14 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 31794780 31794780 G C 1 0 0 0 0 1 0 0 0 11568 1357 47 4 4 PAX6 11 31794780 Missense_Mutation SNP G C3N-00294_T 331555 31794780 103291842 756 13528 DEPDC7 0 . GRCh38 11 33027738 33027738 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.517G>A p.Asp173Asn p.D173N ENST00000241051 3/9 91 71 20 96 96 0 strelka-varscan-mutect DEPDC7,missense_variant,p.Asp164Asn,ENST00000311388,NM_139160.2;DEPDC7,missense_variant,p.Asp173Asn,ENST00000241051,NM_001077242.1;DEPDC7,non_coding_transcript_exon_variant,,ENST00000532078,;DEPDC7,downstream_gene_variant,,ENST00000427755,; A ENST00000241051 Transcript missense_variant 609/1755 517/1536 173/511 D/N Gac/Aac 1 1 DEPDC7 HGNC HGNC:29899 protein_coding YES CCDS41632.1 ENSP00000241051 Q96QD5 UPI000006E96C NM_001077242.1 tolerated(0.24) 3/9 hmmpanther:PTHR16206:SF9,hmmpanther:PTHR16206,Gene3D:1.10.10.10,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33027738 33027738 G A 1 0 0 0 0 1 0 0 0 4249 1174 41 3 3 DEPDC7 11 33027738 Missense_Mutation SNP G C3N-00294_T 1232958 33027738 102058884 757 13529 FBXO3 0 . GRCh38 11 33748888 33748888 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.937G>A p.Glu313Lys p.E313K ENST00000265651 9/11 94 83 11 89 89 0 strelka-varscan-mutect FBXO3,missense_variant,p.Glu308Lys,ENST00000530401,;FBXO3,missense_variant,p.Glu200Lys,ENST00000526785,;FBXO3,missense_variant,p.Glu313Lys,ENST00000534136,;FBXO3,missense_variant,p.Glu313Lys,ENST00000265651,NM_012175.3;FBXO3,missense_variant,p.Glu313Lys,ENST00000448981,NM_033406.2;FBXO3,5_prime_UTR_variant,,ENST00000531080,;FBXO3,5_prime_UTR_variant,,ENST00000532057,;FBXO3,upstream_gene_variant,,ENST00000527772,;FBXO3,3_prime_UTR_variant,,ENST00000532927,;FBXO3,non_coding_transcript_exon_variant,,ENST00000530013,; T ENST00000265651 Transcript missense_variant 956/2397 937/1416 313/471 E/K Gaa/Aaa COSM926555 1 -1 FBXO3 HGNC HGNC:13582 protein_coding YES CCDS7887.1 ENSP00000265651 Q9UK99 UPI000000DB30 NM_012175.3 tolerated(0.06) 9/11 PROSITE_profiles:PS51087,hmmpanther:PTHR14289,hmmpanther:PTHR14289:SF16,Gene3D:1xvsA00,Pfam_domain:PF04379,Superfamily_domains:SSF110069 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 33748888 33748888 C T 1 0 0 0 0 1 0 0 0 5602 840 29 3 3 FBXO3 11 33748888 Missense_Mutation SNP C C3N-00294_T 721150 33748888 101337734 758 13530 TRAF6 0 . GRCh38 11 36490495 36490495 + Silent SNP A A G novel C3N-00294_T C3N-00294_N A A c.912T>C p.= p.G304G ENST00000526995 7/7 163 120 43 189 189 0 strelka-varscan-mutect TRAF6,synonymous_variant,p.=,ENST00000526995,NM_004620.3;TRAF6,synonymous_variant,p.=,ENST00000348124,NM_145803.2;TRAF6,non_coding_transcript_exon_variant,,ENST00000529150,; G ENST00000526995 Transcript synonymous_variant 1159/4627 912/1569 304/522 G ggT/ggC 1 -1 TRAF6 HGNC HGNC:12036 protein_coding YES CCDS7901.1 ENSP00000433623 Q9Y4K3 UPI000000D924 NM_004620.3 7/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10131:SF85,hmmpanther:PTHR10131,PIRSF_domain:PIRSF015614 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 36490495 36490495 A G 1 0 0 0 0 0 0 0 1 16928 262 10 5 5 TRAF6 11 36490495 Silent SNP A C3N-00294_T 2741607 36490495 98596127 759 13531 RAG1 0 . GRCh38 11 36573766 36573766 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.462C>T p.= p.L154L ENST00000299440 2/2 273 217 56 250 250 0 strelka-varscan-mutect RAG1,synonymous_variant,p.=,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,synonymous_variant,p.=,ENST00000534663,; T ENST00000299440 Transcript synonymous_variant 574/6564 462/3132 154/1043 L ctC/ctT 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 2/2 Pfam_domain:PF12560,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 36573766 36573766 C T 1 0 0 0 0 0 0 0 1 13164 813 29 3 3 RAG1 11 36573766 Silent SNP C C3N-00294_T 83271 36573766 98512856 760 13532 RAG2 0 . GRCh38 11 36593970 36593970 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.199T>A p.Cys67Ser p.C67S ENST00000618712 3/3 172 102 70 151 151 0 strelka-varscan-mutect RAG2,missense_variant,p.Cys67Ser,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,missense_variant,p.Cys67Ser,ENST00000311485,NM_000536.3;RAG2,missense_variant,p.Cys67Ser,ENST00000529083,;RAG2,missense_variant,p.Cys67Ser,ENST00000527033,;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,downstream_gene_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; T ENST00000618712 Transcript missense_variant 793/2818 199/1584 67/527 C/S Tgc/Agc 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 tolerated(0.06) 3/3 Superfamily_domains:0047741,Gene3D:1zgkA00,Pfam_domain:PF03089,hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 36593970 36593970 A T 1 0 0 0 0 1 0 0 0 13165 188 7 4 4 RAG2 11 36593970 Missense_Mutation SNP A C3N-00294_T 20204 36593970 98492652 761 13533 AMBRA1 0 . GRCh38 11 46542131 46542131 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1886C>G p.Ser629Cys p.S629C ENST00000534300 7/17 256 204 52 273 273 0 strelka-varscan-mutect AMBRA1,missense_variant,p.Ser629Cys,ENST00000458649,;AMBRA1,missense_variant,p.Ser629Cys,ENST00000534300,NM_001300731.1;AMBRA1,missense_variant,p.Ser539Cys,ENST00000314845,NM_017749.3,NM_001267782.1;AMBRA1,missense_variant,p.Ser539Cys,ENST00000533727,NM_001267783.1;AMBRA1,missense_variant,p.Ser629Cys,ENST00000528950,;AMBRA1,downstream_gene_variant,,ENST00000531542,;AMBRA1,downstream_gene_variant,,ENST00000524783,; C ENST00000534300 Transcript missense_variant 2200/5067 1886/3717 629/1238 S/C tCc/tGc 1 -1 AMBRA1 HGNC HGNC:25990 protein_coding YES CCDS73281.1 ENSP00000431926 Q9C0C7 UPI00005A6107 NM_001300731.1 deleterious_low_confidence(0.01) 7/17 Low_complexity_(Seg):seg,hmmpanther:PTHR22874,hmmpanther:PTHR22874:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 46542131 46542131 G C 1 0 0 0 0 1 0 0 0 661 1174 41 4 4 AMBRA1 11 46542131 Missense_Mutation SNP G C3N-00294_T 9948161 46542131 88544491 762 13534 1 10 4 4 1132 G 1.570473e-05 AMBRA1 0 . GRCh38 11 46542318 46542318 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.1699C>T p.Arg567Cys p.R567C ENST00000534300 7/17 352 277 75 383 383 0 strelka-varscan-mutect AMBRA1,missense_variant,p.Arg567Cys,ENST00000458649,;AMBRA1,missense_variant,p.Arg567Cys,ENST00000534300,NM_001300731.1;AMBRA1,missense_variant,p.Arg477Cys,ENST00000314845,NM_017749.3,NM_001267782.1;AMBRA1,missense_variant,p.Arg477Cys,ENST00000533727,NM_001267783.1;AMBRA1,missense_variant,p.Arg567Cys,ENST00000528950,;AMBRA1,downstream_gene_variant,,ENST00000531542,;AMBRA1,downstream_gene_variant,,ENST00000524783,; A ENST00000534300 Transcript missense_variant 2013/5067 1699/3717 567/1238 R/C Cgc/Tgc COSM1980570,COSM1980571 1 -1 AMBRA1 HGNC HGNC:25990 protein_coding YES CCDS73281.1 ENSP00000431926 Q9C0C7 UPI00005A6107 NM_001300731.1 deleterious_low_confidence(0) 7/17 hmmpanther:PTHR22874,hmmpanther:PTHR22874:SF1 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1214838212 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 46542318 46542318 G A 1 0 0 0 0 1 0 0 0 661 1058 37 1 1 AMBRA1 11 46542318 Missense_Mutation SNP G C3N-00294_T 187 46542318 88544304 763 13535 1 10 4 4 1132 G 1.570473e-05 AMBRA1 0 . GRCh38 11 46542783 46542783 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1234C>G p.Pro412Ala p.P412A ENST00000534300 7/17 395 323 72 462 462 0 strelka-varscan-mutect AMBRA1,missense_variant,p.Pro412Ala,ENST00000458649,;AMBRA1,missense_variant,p.Pro412Ala,ENST00000534300,NM_001300731.1;AMBRA1,missense_variant,p.Pro322Ala,ENST00000314845,NM_017749.3,NM_001267782.1;AMBRA1,missense_variant,p.Pro322Ala,ENST00000533727,NM_001267783.1;AMBRA1,missense_variant,p.Pro412Ala,ENST00000528950,;AMBRA1,downstream_gene_variant,,ENST00000531542,;AMBRA1,downstream_gene_variant,,ENST00000524783,; C ENST00000534300 Transcript missense_variant 1548/5067 1234/3717 412/1238 P/A Cct/Gct 1 -1 AMBRA1 HGNC HGNC:25990 protein_coding YES CCDS73281.1 ENSP00000431926 Q9C0C7 UPI00005A6107 NM_001300731.1 deleterious_low_confidence(0.03) 7/17 hmmpanther:PTHR22874,hmmpanther:PTHR22874:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 46542783 46542783 G C 1 0 0 0 0 1 0 0 0 661 1174 41 4 4 AMBRA1 11 46542783 Missense_Mutation SNP G C3N-00294_T 465 46542783 88543839 764 13536 1 10 4 4 1132 G 1.570473e-05 AMBRA1 0 . GRCh38 11 46543262 46543262 + Missense_Mutation SNP G G T rs73449929 C3N-00294_T C3N-00294_N G G c.755C>A p.Ser252Tyr p.S252Y ENST00000534300 7/17 138 112 26 155 155 0 strelka-varscan-mutect AMBRA1,missense_variant,p.Ser252Tyr,ENST00000458649,;AMBRA1,missense_variant,p.Ser252Tyr,ENST00000534300,NM_001300731.1;AMBRA1,missense_variant,p.Ser252Tyr,ENST00000314845,NM_017749.3,NM_001267782.1;AMBRA1,missense_variant,p.Ser252Tyr,ENST00000533727,NM_001267783.1;AMBRA1,missense_variant,p.Ser252Tyr,ENST00000528950,;AMBRA1,downstream_gene_variant,,ENST00000531542,;AMBRA1,downstream_gene_variant,,ENST00000524783,; T ENST00000534300 Transcript missense_variant 1069/5067 755/3717 252/1238 S/Y tCt/tAt rs73449929 1 -1 AMBRA1 HGNC HGNC:25990 protein_coding YES CCDS73281.1 ENSP00000431926 Q9C0C7 UPI00005A6107 NM_001300731.1 deleterious_low_confidence(0) 7/17 MODERATE 1 SNV 1 1 PASS rs73449929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 46543262 46543262 G T 1 0 0 0 0 1 0 0 0 661 942 33 2 2 AMBRA1 11 46543262 Missense_Mutation SNP G C3N-00294_T 479 46543262 88543360 765 13537 1 10 4 4 1132 G 1.570473e-05 OR4A5 0 . GRCh38 11 54707204 54707204 + Missense_Mutation SNP G G T rs368103058 C3N-00294_T C3N-00294_N G G c.320G>T p.Gly107Val p.G107V ENST00000319760 1/1 192 120 72 195 195 0 strelka-varscan-mutect OR4A5,missense_variant,p.Gly107Val,ENST00000319760,NM_001005272.3; T ENST00000319760 Transcript missense_variant 320/948 320/948 107/315 G/V gGg/gTg rs368103058 1 1 OR4A5 HGNC HGNC:15162 protein_coding YES CCDS73289.1 ENSP00000367664 Q8NH83 A0A126GWJ2 UPI0000041D58 NM_001005272.3 deleterious_low_confidence(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF306,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs368103058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 54707204 54707204 G T 1 0 0 0 0 1 0 0 0 11120 1232 43 2 2 OR4A5 11 54707204 Missense_Mutation SNP G C3N-00294_T 8163942 54707204 80379418 766 13538 OR5D18 0 . GRCh38 11 55819821 55819821 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.192C>T p.= p.L64L ENST00000333976 1/1 69 60 9 76 75 1 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; T ENST00000333976 Transcript synonymous_variant 192/942 192/942 64/313 L ctC/ctT 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 204 5 0 0 0 0 0 -19.72253 1 1 1 1 0 T 2 4 46 55819821 55819821 C T 1 0 0 0 0 0 0 0 1 11227 813 29 3 3 OR5D18 11 55819821 Silent SNP C C3N-00294_T 1112617 55819821 79266801 767 13539 OR8J1 0 . GRCh38 11 56360482 56360482 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.236C>T p.Pro79Leu p.P79L ENST00000303039 1/1 152 123 29 183 183 0 strelka-varscan-mutect OR8J1,missense_variant,p.Pro79Leu,ENST00000303039,NM_001005205.2;RPL5P29,downstream_gene_variant,,ENST00000482972,; T ENST00000303039 Transcript missense_variant 268/1074 236/951 79/316 P/L cCt/cTt COSM928342 1 1 OR8J1 HGNC HGNC:14855 protein_coding YES CCDS31529.1 ENSP00000304060 Q8NGP2 UPI000004BE58 NM_001005205.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF317,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 56360482 56360482 C T 1 0 0 0 0 1 0 0 0 11309 681 24 3 3 OR8J1 11 56360482 Missense_Mutation SNP C C3N-00294_T 540661 56360482 78726140 768 13540 DDB1 0 . GRCh38 11 61314327 61314327 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1570C>G p.Gln524Glu p.Q524E ENST00000301764 13/27 106 84 22 92 92 0 strelka-varscan-mutect DDB1,missense_variant,p.Gln524Glu,ENST00000301764,NM_001923.4;DDB1,intron_variant,,ENST00000543658,;DDB1,downstream_gene_variant,,ENST00000545930,;DDB1,downstream_gene_variant,,ENST00000538280,;DDB1,missense_variant,p.Gln524Glu,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000535147,;DDB1,non_coding_transcript_exon_variant,,ENST00000414411,;DDB1,non_coding_transcript_exon_variant,,ENST00000539739,;DDB1,non_coding_transcript_exon_variant,,ENST00000535967,;DDB1,non_coding_transcript_exon_variant,,ENST00000537877,;DDB1,non_coding_transcript_exon_variant,,ENST00000540784,;DDB1,upstream_gene_variant,,ENST00000539332,;DDB1,downstream_gene_variant,,ENST00000535174,; C ENST00000301764 Transcript missense_variant 1968/4506 1570/3423 524/1140 Q/E Cag/Gag 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 tolerated(0.15) 13/27 hmmpanther:PTHR10644,Gene3D:2.130.10.10,Pfam_domain:PF10433 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 61314327 61314327 G C 1 0 0 0 0 1 0 0 0 4126 1299 45 4 4 DDB1 11 61314327 Missense_Mutation SNP G C3N-00294_T 4953845 61314327 73772295 769 13541 FADS2 0 . GRCh38 11 61840376 61840376 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.361G>A p.Glu121Lys p.E121K ENST00000278840 3/12 345 264 81 404 403 1 strelka-varscan-mutect FADS2,missense_variant,p.Glu121Lys,ENST00000278840,NM_004265.3;FADS2,missense_variant,p.Glu99Lys,ENST00000257261,NM_001281501.1;FADS2,missense_variant,p.Glu121Lys,ENST00000521849,;FADS2,missense_variant,p.Glu90Lys,ENST00000522056,NM_001281502.1;FADS2,5_prime_UTR_variant,,ENST00000521571,;FADS2,5_prime_UTR_variant,,ENST00000517312,;FADS2,5_prime_UTR_variant,,ENST00000518606,;FADS2,upstream_gene_variant,,ENST00000520145,; A ENST00000278840 Transcript missense_variant 991/3630 361/1335 121/444 E/K Gag/Aag 1 1 FADS2 HGNC HGNC:3575 protein_coding YES CCDS8012.1 ENSP00000278840 O95864 UPI000003405E NM_004265.3 tolerated(0.09) 3/12 PIRSF_domain:PIRSF015921,hmmpanther:PTHR19353,hmmpanther:PTHR19353:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 61840376 61840376 G A 1 0 0 0 0 1 0 0 0 5238 1291 45 3 3 FADS2 11 61840376 Missense_Mutation SNP G C3N-00294_T 526049 61840376 73246246 770 13542 AHNAK 0 . GRCh38 11 62527471 62527471 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.6946G>A p.Asp2316Asn p.D2316N ENST00000378024 5/5 382 308 74 374 374 0 strelka-varscan-mutect AHNAK,missense_variant,p.Asp2316Asn,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; T ENST00000378024 Transcript missense_variant 7221/18787 6946/17673 2316/5890 D/N Gat/Aat 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0) 5/5 MODERATE 1 SNV 2 1 PASS rs948534799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 62527471 62527471 C T 1 0 0 0 0 1 0 0 0 491 826 29 3 3 AHNAK 11 62527471 Missense_Mutation SNP C C3N-00294_T 687095 62527471 72559151 771 13543 METTL12 0 . GRCh38 11 62666656 62666656 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.328C>G p.Pro110Ala p.P110A ENST00000532971 3/3 201 161 40 235 235 0 strelka-varscan-mutect METTL12,missense_variant,p.Pro110Ala,ENST00000532971,NM_001043229.1;LBHD1,intron_variant,,ENST00000431002,;LBHD1,intron_variant,,ENST00000532208,;LBHD1,intron_variant,,ENST00000354588,NM_024099.3;LBHD1,intron_variant,,ENST00000415855,;UQCC3,upstream_gene_variant,,ENST00000531323,;UQCC3,upstream_gene_variant,,ENST00000377953,NM_001085372.2;C11orf98,upstream_gene_variant,,ENST00000524958,NM_001286086.1;RP11-831H9.11,upstream_gene_variant,,ENST00000528405,;LBHD1,downstream_gene_variant,,ENST00000377954,;C11orf98,upstream_gene_variant,,ENST00000525675,;LBHD1,downstream_gene_variant,,ENST00000528862,;SNORA57,downstream_gene_variant,,ENST00000383870,;METTL12,non_coding_transcript_exon_variant,,ENST00000398922,;METTL12,downstream_gene_variant,,ENST00000594728,;LBHD1,downstream_gene_variant,,ENST00000528115,;METTL12,non_coding_transcript_exon_variant,,ENST00000529868,;LBHD1,downstream_gene_variant,,ENST00000526490,;LBHD1,downstream_gene_variant,,ENST00000527679,;C11orf98,upstream_gene_variant,,ENST00000532786,;LBHD1,downstream_gene_variant,,ENST00000524759,; G ENST00000532971 Transcript missense_variant 585/2037 328/723 110/240 P/A Cct/Gct 1 1 METTL12 HGNC HGNC:33113 protein_coding YES CCDS41657.1 ENSP00000431287 A8MUP2 UPI0000D4EAB2 NM_001043229.1 tolerated(0.15) 3/3 hmmpanther:PTHR12176,hmmpanther:PTHR12176:SF32,Gene3D:3.40.50.150,Pfam_domain:PF13847,Superfamily_domains:SSF53335 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 62666656 62666656 C G 1 0 0 0 0 1 0 0 0 9438 855 30 4 4 METTL12 11 62666656 Missense_Mutation SNP C C3N-00294_T 139185 62666656 72419966 772 13544 SLC22A24 0 . GRCh38 11 63143531 63143531 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.249G>A p.= p.L83L ENST00000612278 1/10 45 36 9 33 33 0 strelka-varscan-mutect SLC22A24,synonymous_variant,p.=,ENST00000612278,NM_001136506.2;SLC22A24,synonymous_variant,p.=,ENST00000417740,;SLC22A24,synonymous_variant,p.=,ENST00000326192,NM_173586.2;SLC22A10,intron_variant,,ENST00000525620,; T ENST00000612278 Transcript synonymous_variant 691/2101 249/1659 83/552 L ctG/ctA 1 -1 SLC22A24 HGNC HGNC:28542 protein_coding YES CCDS73308.1 ENSP00000480336 A0A087WWM3 UPI000004DAF7 NM_001136506.2 1/10 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF208 LOW 1 SNV 5 1 PASS rs1281477193 . 0 207 3 0 0 0 0 0 -19.99756 1 1 1 1 0 T 2 4 46 63143531 63143531 C T 1 0 0 0 0 0 0 0 1 14718 813 29 3 3 SLC22A24 11 63143531 Silent SNP C C3N-00294_T 476875 63143531 71943091 773 13545 SLC22A10 0 . GRCh38 11 63297564 63297564 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.667G>C p.Glu223Gln p.E223Q ENST00000332793 4/10 130 99 31 142 141 1 strelka-varscan-mutect SLC22A10,missense_variant,p.Glu223Gln,ENST00000332793,NM_001039752.3;SLC22A10,intron_variant,,ENST00000526800,;SLC22A10,non_coding_transcript_exon_variant,,ENST00000525620,;SLC22A10,missense_variant,p.Glu171Gln,ENST00000533483,;SLC22A10,intron_variant,,ENST00000532724,; C ENST00000332793 Transcript missense_variant 669/2026 667/1626 223/541 E/Q Gag/Cag 1 1 SLC22A10 HGNC HGNC:18057 protein_coding YES CCDS41661.1 ENSP00000327569 Q63ZE4 UPI0000D62620 NM_001039752.3 deleterious(0) 4/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF217,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 63297564 63297564 G C 1 0 0 0 0 1 0 0 0 14707 1304 45 4 4 SLC22A10 11 63297564 Missense_Mutation SNP G C3N-00294_T 154033 63297564 71789058 774 13546 RTN3 0 . GRCh38 11 63681690 63681690 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.54C>T p.= p.F18F ENST00000377819 1/9 94 70 24 105 105 0 strelka-varscan-mutect RTN3,synonymous_variant,p.=,ENST00000377819,NM_001265589.1;RTN3,synonymous_variant,p.=,ENST00000339997,NM_201428.2;RTN3,synonymous_variant,p.=,ENST00000540798,NM_001265590.1;RTN3,synonymous_variant,p.=,ENST00000356000,NM_201429.2;RTN3,synonymous_variant,p.=,ENST00000537981,NM_006054.3;RTN3,synonymous_variant,p.=,ENST00000341307,NM_201430.2;RTN3,synonymous_variant,p.=,ENST00000354497,NM_001265591.1;RTN3,synonymous_variant,p.=,ENST00000542238,;RTN3,synonymous_variant,p.=,ENST00000545432,;RTN3,synonymous_variant,p.=,ENST00000543552,;RTN3,non_coding_transcript_exon_variant,,ENST00000538995,;RTN3,non_coding_transcript_exon_variant,,ENST00000338850,;RTN3,synonymous_variant,p.=,ENST00000536011,;RTN3,non_coding_transcript_exon_variant,,ENST00000543123,; T ENST00000377819 Transcript synonymous_variant 208/4937 54/3099 18/1032 F ttC/ttT 1 1 RTN3 HGNC HGNC:10469 protein_coding YES CCDS58141.1 ENSP00000367050 O95197 UPI00004546A2 NM_001265589.1 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR10994,hmmpanther:PTHR10994:SF1 LOW 1 SNV 1 1 PASS rs1207733831 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 46 63681690 63681690 C T 1 0 0 0 0 0 0 0 1 13987 883 31 1 1 RTN3 11 63681690 Silent SNP C C3N-00294_T 384126 63681690 71404932 775 13547 VPS51 0 . GRCh38 11 65096455 65096455 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.205G>C p.Asp69His p.D69H ENST00000279281 1/10 48 40 8 56 56 0 strelka-varscan-mutect VPS51,missense_variant,p.Asp69His,ENST00000279281,NM_013265.3;VPS51,missense_variant,p.Asp69His,ENST00000529180,;VPS51,missense_variant,p.Asp69His,ENST00000530773,;VPS51,missense_variant,p.Asp99His,ENST00000528588,;VPS51,upstream_gene_variant,,ENST00000534557,;VPS51,upstream_gene_variant,,ENST00000526578,;VPS51,missense_variant,p.Asp69His,ENST00000534124,;VPS51,missense_variant,p.Asp69His,ENST00000533487,;VPS51,non_coding_transcript_exon_variant,,ENST00000533656,;VPS51,non_coding_transcript_exon_variant,,ENST00000528050,; C ENST00000279281 Transcript missense_variant 297/2714 205/2349 69/782 D/H Gac/Cac 1 1 VPS51 HGNC HGNC:1172 protein_coding YES CCDS8093.1 ENSP00000279281 Q9UID3 UPI000006D6D8 NM_013265.3 tolerated(0.07) 1/10 Pfam_domain:PF08700,hmmpanther:PTHR15954,hmmpanther:PTHR15954:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.53949 1 1 1 1 0 C 3 2 46 65096455 65096455 G C 1 0 0 0 0 1 0 0 0 17761 1058 37 4 4 VPS51 11 65096455 Missense_Mutation SNP G C3N-00294_T 1414765 65096455 69990167 776 13548 DPF2 0 . GRCh38 11 65346051 65346051 + Frame_Shift_Del DEL C C - novel C3N-00294_T C3N-00294_N C C c.898delC p.Arg300AlafsTer13 p.R300Afs*13 ENST00000528416 8/11 88 53 35 104 104 0 sindel-varindel DPF2,frameshift_variant,p.Arg300AlafsTer13,ENST00000528416,NM_006268.4;DPF2,frameshift_variant,p.Arg314AlafsTer13,ENST00000252268,;DPF2,frameshift_variant,p.Ala63LeufsTer41,ENST00000531989,;DPF2,intron_variant,,ENST00000415073,;DPF2,downstream_gene_variant,,ENST00000532264,;DPF2,downstream_gene_variant,,ENST00000530993,;DPF2,non_coding_transcript_exon_variant,,ENST00000524666,;DPF2,non_coding_transcript_exon_variant,,ENST00000532052,;DPF2,non_coding_transcript_exon_variant,,ENST00000530973,;DPF2,downstream_gene_variant,,ENST00000444314,;DPF2,downstream_gene_variant,,ENST00000532102,;DPF2,downstream_gene_variant,,ENST00000532492,; - ENST00000528416 Transcript frameshift_variant 1030/2799 897/1176 299/391 G/X ggC/gg 1 1 DPF2 HGNC HGNC:9964 protein_coding YES CCDS8100.1 ENSP00000436901 Q92785 A0A024R582 UPI000000D90F NM_006268.4 8/11 Gene3D:3.30.40.10,PROSITE_profiles:PS50016,hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF13,SMART_domains:SM00249,Superfamily_domains:SSF57903 HIGH 1 deletion 1 1 1 PASS . . 0 199 9 2 0 0 0 0 -20 0.9999272 1 1 1 0 - 7 5 46 65346051 65346051 C - 1 0 1 0 1 0 0 0 0 4531 726 26 0 0 DPF2 11 65346051 Frame_Shift_Del DEL C C3N-00294_T 249596 65346051 69740571 777 13549 SLC29A2 0 . GRCh38 11 66364296 66364296 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1188C>T p.= p.F396F ENST00000357440 11/12 220 172 48 231 231 0 strelka-varscan-mutect SLC29A2,missense_variant,p.His352Tyr,ENST00000619145,;SLC29A2,missense_variant,p.His352Tyr,ENST00000311161,NM_001300869.1;SLC29A2,synonymous_variant,p.=,ENST00000357440,NM_001532.2;SLC29A2,synonymous_variant,p.=,ENST00000546034,;SLC29A2,synonymous_variant,p.=,ENST00000544554,NM_001300868.1;RP11-867G23.8,intron_variant,,ENST00000580881,;RP11-867G23.8,downstream_gene_variant,,ENST00000531602,;SLC29A2,3_prime_UTR_variant,,ENST00000540386,;SLC29A2,3_prime_UTR_variant,,ENST00000541567,; A ENST00000357440 Transcript synonymous_variant 1417/2514 1188/1371 396/456 F ttC/ttT 1 -1 SLC29A2 HGNC HGNC:11004 protein_coding YES CCDS8137.1 ENSP00000350024 Q14542 UPI000013F0E7 NM_001532.2 11/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR10332:SF8,hmmpanther:PTHR10332,TIGRFAM_domain:TIGR00939,Pfam_domain:PF01733,PIRSF_domain:PIRSF016379,Superfamily_domains:SSF103473,Prints_domain:PR01130 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 66364296 66364296 G A 1 0 0 0 0 0 0 0 1 14805 1290 45 3 3 SLC29A2 11 66364296 Silent SNP G C3N-00294_T 1018245 66364296 68722326 778 13550 BBS1 0 . GRCh38 11 66514538 66514538 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.403G>A p.Glu135Lys p.E135K ENST00000419755 4/17 331 263 68 380 380 0 strelka-varscan-mutect CTD-3074O7.11,missense_variant,p.Glu135Lys,ENST00000419755,;BBS1,missense_variant,p.Glu98Lys,ENST00000318312,NM_024649.4;BBS1,missense_variant,p.Glu98Lys,ENST00000393994,;BBS1,missense_variant,p.Glu98Lys,ENST00000455748,;BBS1,missense_variant,p.Glu5Lys,ENST00000524705,;BBS1,stop_retained_variant,p.=,ENST00000630659,;BBS1,intron_variant,,ENST00000525809,;DPP3,downstream_gene_variant,,ENST00000532677,;DPP3,downstream_gene_variant,,ENST00000531863,;DPP3,downstream_gene_variant,,ENST00000541961,NM_130443.3,NM_005700.4;BBS1,downstream_gene_variant,,ENST00000526815,;BBS1,non_coding_transcript_exon_variant,,ENST00000529766,;BBS1,upstream_gene_variant,,ENST00000529953,;BBS1,missense_variant,p.Glu98Lys,ENST00000533644,;BBS1,stop_retained_variant,p.=,ENST00000526760,;BBS1,stop_retained_variant,p.=,ENST00000533557,;BBS1,stop_retained_variant,p.=,ENST00000527251,;BBS1,stop_retained_variant,p.=,ENST00000532908,;BBS1,stop_retained_variant,p.=,ENST00000524458,;BBS1,stop_retained_variant,p.=,ENST00000526035,;BBS1,non_coding_transcript_exon_variant,,ENST00000529955,;BBS1,non_coding_transcript_exon_variant,,ENST00000533430,;BBS1,non_coding_transcript_exon_variant,,ENST00000524907,;BBS1,non_coding_transcript_exon_variant,,ENST00000534730,;BBS1,upstream_gene_variant,,ENST00000528543,; A ENST00000419755 Transcript missense_variant 481/3547 403/1893 135/630 E/K Gag/Aag 1 1 CTD-3074O7.11 Clone_based_vega_gene protein_coding YES ENSP00000398526 UPI000006E494 deleterious(0.05) 4/17 hmmpanther:PTHR20870,hmmpanther:PTHR20870:SF0,Pfam_domain:PF14779 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 66514538 66514538 G A 1 0 0 0 0 1 0 0 0 1482 1294 45 3 3 BBS1 11 66514538 Missense_Mutation SNP G C3N-00294_T 150242 66514538 68572084 779 13551 SYT12 0 . GRCh38 11 67048611 67048611 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.1120G>C p.Glu374Gln p.E374Q ENST00000393946 11/11 118 94 24 108 108 0 strelka-varscan-mutect SYT12,missense_variant,p.Glu374Gln,ENST00000393946,;SYT12,missense_variant,p.Glu374Gln,ENST00000525457,NM_001177880.1;SYT12,missense_variant,p.Glu374Gln,ENST00000527043,NM_177963.3;MIR6860,downstream_gene_variant,,ENST00000635882,; C ENST00000393946 Transcript missense_variant 2282/4534 1120/1266 374/421 E/Q Gag/Cag COSM415790 1 1 SYT12 HGNC HGNC:18381 protein_coding YES CCDS8154.1 ENSP00000377520 Q8IV01 UPI00000746CD tolerated(0.08) 11/11 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF252,SMART_domains:SM00239,Superfamily_domains:SSF49562 1 MODERATE 1 SNV 2 1 1 PASS rs1026692384 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 67048611 67048611 G C 1 0 0 0 0 1 0 0 0 15862 1291 45 4 4 SYT12 11 67048611 Missense_Mutation SNP G C3N-00294_T 534073 67048611 68038011 780 13552 CLCF1 0 . GRCh38 11 67365447 67365447 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.367C>T p.Gln123Ter p.Q123* ENST00000312438 3/3 133 117 16 161 161 0 strelka-varscan-mutect CLCF1,stop_gained,p.Gln123Ter,ENST00000312438,NM_013246.2;CLCF1,stop_gained,p.Gln113Ter,ENST00000533438,NM_001166212.1;AP003419.11,intron_variant,,ENST00000543494,;RN7SKP239,downstream_gene_variant,,ENST00000364814,;RAD9A,intron_variant,,ENST00000622583,; A ENST00000312438 Transcript stop_gained 565/1844 367/678 123/225 Q/* Cag/Tag 1 -1 CLCF1 HGNC HGNC:17412 protein_coding YES CCDS31617.1 ENSP00000309338 Q9UBD9 UPI000003F7F1 NM_013246.2 3/3 Gene3D:1.20.1250.10,Pfam_domain:PF06875,hmmpanther:PTHR21353,hmmpanther:PTHR21353:SF7,Superfamily_domains:SSF47266 HIGH 1 SNV 1 1 PASS rs1363278334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 67365447 67365447 G A 1 0 0 0 0 0 1 0 0 3225 1299 45 3 3 CLCF1 11 67365447 Nonsense_Mutation SNP G C3N-00294_T 316836 67365447 67721175 781 13553 CORO1B 0 . GRCh38 11 67438865 67438865 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1150G>A p.Asp384Asn p.D384N ENST00000393893 11/12 178 146 32 207 207 0 strelka-varscan-mutect CORO1B,missense_variant,p.Asp384Asn,ENST00000393893,NM_001018070.2;CORO1B,missense_variant,p.Asp384Asn,ENST00000341356,NM_020441.2;RPS6KB2,downstream_gene_variant,,ENST00000312629,NM_003952.2;PTPRCAP,upstream_gene_variant,,ENST00000326294,NM_005608.2;CORO1B,downstream_gene_variant,,ENST00000627576,;CORO1B,downstream_gene_variant,,ENST00000545016,;AP003419.16,upstream_gene_variant,,ENST00000535922,;CORO1B,non_coding_transcript_exon_variant,,ENST00000539724,;CORO1B,3_prime_UTR_variant,,ENST00000616321,;CORO1B,3_prime_UTR_variant,,ENST00000537042,;RPS6KB2,downstream_gene_variant,,ENST00000525088,;RPS6KB2,downstream_gene_variant,,ENST00000528964,;CORO1B,downstream_gene_variant,,ENST00000453768,;CORO1B,downstream_gene_variant,,ENST00000545736,;RPS6KB2,downstream_gene_variant,,ENST00000525996,;RPS6KB2,downstream_gene_variant,,ENST00000526268,;RPS6KB2,downstream_gene_variant,,ENST00000531765,;CORO1B,downstream_gene_variant,,ENST00000539970,; T ENST00000393893 Transcript missense_variant 1283/1931 1150/1470 384/489 D/N Gat/Aat 1 -1 CORO1B HGNC HGNC:2253 protein_coding YES CCDS8164.1 ENSP00000377471 Q9BR76 A0A024R5K1 UPI0000127C42 NM_001018070.2 tolerated(0.83) 11/12 hmmpanther:PTHR10856,Pfam_domain:PF16300,SMART_domains:SM01167 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67438865 67438865 C T 1 0 0 0 0 1 0 0 0 3548 855 30 3 3 CORO1B 11 67438865 Missense_Mutation SNP C C3N-00294_T 73418 67438865 67647757 782 13554 SHANK2 0 . GRCh38 11 71113353 71113353 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.423G>A p.= p.K141K ENST00000601538 4/25 217 189 28 211 211 0 strelka-varscan-mutect SHANK2,synonymous_variant,p.=,ENST00000601538,NM_012309.4;SHANK2,missense_variant,p.Glu123Lys,ENST00000608988,; T ENST00000601538 Transcript synonymous_variant 501/9062 423/5550 141/1849 K aaG/aaA 1 -1 SHANK2 HGNC HGNC:14295 protein_coding ENSP00000469689 Q9UPX8 UPI000198F7E3 NM_012309.4 4/25 hmmpanther:PTHR24135:SF17,hmmpanther:PTHR24135 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 71113353 71113353 C T 1 0 0 0 0 0 0 0 1 14524 912 32 3 3 SHANK2 11 71113353 Silent SNP C C3N-00294_T 3674488 71113353 63973269 783 13555 NADSYN1 0 . GRCh38 11 71490849 71490849 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1567C>T p.= p.L523L ENST00000319023 17/21 115 87 28 126 126 0 strelka-varscan-mutect NADSYN1,synonymous_variant,p.=,ENST00000319023,NM_018161.4;NADSYN1,synonymous_variant,p.=,ENST00000530055,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000526039,;NADSYN1,3_prime_UTR_variant,,ENST00000525200,;NADSYN1,non_coding_transcript_exon_variant,,ENST00000531236,; T ENST00000319023 Transcript synonymous_variant 1755/2773 1567/2121 523/706 L Ctg/Ttg 1 1 NADSYN1 HGNC HGNC:29832 protein_coding YES CCDS8201.1 ENSP00000326424 Q6IA69 UPI00001404C2 NM_018161.4 17/21 hmmpanther:PTHR23090:SF9,hmmpanther:PTHR23090,PIRSF_domain:PIRSF006630,Gene3D:3.40.50.620,Pfam_domain:PF02540,TIGRFAM_domain:TIGR00552,Superfamily_domains:SSF52402 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 71490849 71490849 C T 1 0 0 0 0 0 0 0 1 10145 695 24 3 3 NADSYN1 11 71490849 Silent SNP C C3N-00294_T 377496 71490849 63595773 784 13556 OR2AT4 0 . GRCh38 11 75089321 75089321 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.393C>G p.Ile131Met p.I131M ENST00000305159 1/1 173 142 31 177 177 0 strelka-varscan-mutect OR2AT4,missense_variant,p.Ile131Met,ENST00000305159,NM_001005285.1; C ENST00000305159 Transcript missense_variant 434/1042 393/963 131/320 I/M atC/atG 1 -1 OR2AT4 HGNC HGNC:19620 protein_coding YES CCDS31639.1 ENSP00000304846 A6NND4 A0A126GWB1 UPI0000061FA5 NM_001005285.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF15,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 75089321 75089321 G C 1 0 0 0 0 1 0 0 0 11066 932 33 4 4 OR2AT4 11 75089321 Missense_Mutation SNP G C3N-00294_T 3598472 75089321 59997301 785 13557 MYO7A 0 . GRCh38 11 77182581 77182581 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.3266C>A p.Ala1089Asp p.A1089D ENST00000409709 25/49 125 59 66 140 140 0 strelka-varscan-mutect MYO7A,missense_variant,p.Ala1089Asp,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Ala1089Asp,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Ala1078Asp,ENST00000409619,;MYO7A,missense_variant,p.Ala270Asp,ENST00000458169,;MYO7A,missense_variant,p.Ala1089Asp,ENST00000409893,NM_001127179.2;MYO7A,missense_variant,p.Ala1089Asp,ENST00000620575,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,;MYO7A,upstream_gene_variant,,ENST00000467137,; A ENST00000409709 Transcript missense_variant 3538/7462 3266/6648 1089/2215 A/D gCc/gAc 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.55) 25/49 PROSITE_profiles:PS51016,hmmpanther:PTHR13140:SF369,hmmpanther:PTHR13140,SMART_domains:SM00139 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 77182581 77182581 C A 1 0 0 0 0 1 0 0 0 10083 739 26 2 2 MYO7A 11 77182581 Missense_Mutation SNP C C3N-00294_T 2093260 77182581 57904041 786 13558 PAK1 0 . GRCh38 11 77358974 77358974 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.521C>T p.Ser174Leu p.S174L ENST00000278568 6/16 223 180 43 191 191 0 strelka-varscan-mutect PAK1,missense_variant,p.Ser174Leu,ENST00000356341,NM_002576.4;PAK1,missense_variant,p.Ser174Leu,ENST00000530617,;PAK1,missense_variant,p.Ser174Leu,ENST00000278568,NM_001128620.1;PAK1,missense_variant,p.Ser76Leu,ENST00000528203,;PAK1,upstream_gene_variant,,ENST00000525542,;PAK1,missense_variant,p.Ser65Leu,ENST00000527457,;PAK1,non_coding_transcript_exon_variant,,ENST00000533568,;PAK1,non_coding_transcript_exon_variant,,ENST00000533468,;PAK1,upstream_gene_variant,,ENST00000526103,;PAK1,upstream_gene_variant,,ENST00000530358,; A ENST00000278568 Transcript missense_variant 1051/2543 521/1662 174/553 S/L tCa/tTa 1 -1 PAK1 HGNC HGNC:8590 protein_coding YES CCDS44687.1 ENSP00000278568 Q13153 UPI000013DB7F NM_001128620.1 tolerated(0.09) 6/16 Low_complexity_(Seg):seg,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF232 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 77358974 77358974 G A 1 0 0 0 0 1 0 0 0 11479 1294 45 3 3 PAK1 11 77358974 Missense_Mutation SNP G C3N-00294_T 176393 77358974 57727648 787 13559 SRSF8 0 . GRCh38 11 95067476 95067476 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.250G>A p.Glu84Lys p.E84K ENST00000587424 1/1 69 56 13 68 68 0 strelka-varscan-mutect SRSF8,missense_variant,p.Glu84Lys,ENST00000587424,NM_032102.3; A ENST00000587424 Transcript missense_variant 280/4028 250/849 84/282 E/K Gag/Aag 1 1 SRSF8 HGNC HGNC:16988 protein_coding YES CCDS73370.1 ENSP00000480140 Q9BRL6 A0A024R3A8 UPI0000071A48 NM_032102.3 tolerated(0.08) 1/1 PROSITE_profiles:PS50102,hmmpanther:PTHR23147,hmmpanther:PTHR23147:SF14,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 95067476 95067476 G A 1 0 0 0 0 1 0 0 0 15545 1059 37 1 1 SRSF8 11 95067476 Missense_Mutation SNP G C3N-00294_T 17708502 95067476 40019146 788 13560 MMP20 0 . GRCh38 11 102606599 102606599 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.889G>A p.Asp297Asn p.D297N ENST00000260228 6/10 610 539 71 663 663 0 strelka-varscan-mutect MMP20,missense_variant,p.Asp297Asn,ENST00000260228,NM_004771.3;RP11-817J15.2,upstream_gene_variant,,ENST00000542119,;RP11-817J15.2,upstream_gene_variant,,ENST00000544115,;MMP20,non_coding_transcript_exon_variant,,ENST00000544938,; T ENST00000260228 Transcript missense_variant 902/1956 889/1452 297/483 D/N Gac/Aac 1 -1 MMP20 HGNC HGNC:7167 protein_coding YES CCDS8318.1 ENSP00000260228 O60882 UPI000013D0B3 NM_004771.3 deleterious(0.03) 6/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201:SF125,hmmpanther:PTHR10201,PIRSF_domain:PIRSF001191,Gene3D:2.110.10.10,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 102606599 102606599 C T 1 0 0 0 0 1 0 0 0 9622 826 29 3 3 MMP20 11 102606599 Missense_Mutation SNP C C3N-00294_T 7539123 102606599 32480023 789 13561 ATM 0 . GRCh38 11 108250773 108250773 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1308G>A p.= p.L436L ENST00000278616 10/63 117 87 30 130 130 0 strelka-varscan-mutect ATM,synonymous_variant,p.=,ENST00000278616,NM_000051.3;ATM,synonymous_variant,p.=,ENST00000452508,;ATM,synonymous_variant,p.=,ENST00000527805,;ATM,upstream_gene_variant,,ENST00000525012,;ATM,upstream_gene_variant,,ENST00000533526,; A ENST00000278616 Transcript synonymous_variant 1693/13147 1308/9171 436/3056 L ctG/ctA 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 10/63 Low_complexity_(Seg):seg,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF72 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 108250773 108250773 G A 1 0 0 0 0 0 0 0 1 1261 1277 45 3 3 ATM 11 108250773 Silent SNP G C3N-00294_T 5644174 108250773 26835849 790 13562 ATM 0 . GRCh38 11 108317427 108317427 + Missense_Mutation SNP G G C rs730881379 C3N-00294_T C3N-00294_N G G c.6253G>C p.Asp2085His p.D2085H ENST00000278616 43/63 255 195 60 312 312 0 strelka-varscan-mutect ATM,missense_variant,p.Asp2085His,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Asp2085His,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,non_coding_transcript_exon_variant,,ENST00000532765,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; C ENST00000278616 Transcript missense_variant 6638/13147 6253/9171 2085/3056 D/H Gat/Cat rs730881379 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 deleterious(0.01) 43/63 PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF72,hmmpanther:PTHR11139 uncertain_significance MODERATE 1 SNV 5 1 1 PASS rs730881379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 108317427 108317427 G C 1 0 0 0 0 1 0 0 0 1261 1174 41 4 4 ATM 11 108317427 Missense_Mutation SNP G C3N-00294_T 66654 108317427 26769195 791 13563 PIH1D2 0 . GRCh38 11 112073171 112073171 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.4G>C p.Glu2Gln p.E2Q ENST00000280350 2/6 63 56 7 47 47 0 strelka-varscan-mutect PIH1D2,missense_variant,p.Glu2Gln,ENST00000530641,;PIH1D2,missense_variant,p.Glu2Gln,ENST00000431456,NM_001082619.1;PIH1D2,missense_variant,p.Glu2Gln,ENST00000280350,NM_138789.3;PIH1D2,missense_variant,p.Glu2Gln,ENST00000532211,;PIH1D2,missense_variant,p.Glu2Gln,ENST00000528775,;C11orf57,upstream_gene_variant,,ENST00000532163,NM_001301019.1,NM_001301021.1;C11orf57,upstream_gene_variant,,ENST00000280352,NM_001082970.1;C11orf57,upstream_gene_variant,,ENST00000393047,NM_018195.3,NM_001082969.1;C11orf57,upstream_gene_variant,,ENST00000420986,NM_001301017.1;C11orf57,upstream_gene_variant,,ENST00000525785,;PIH1D2,upstream_gene_variant,,ENST00000525072,;C11orf57,upstream_gene_variant,,ENST00000531378,;C11orf57,upstream_gene_variant,,ENST00000526879,;PIH1D2,upstream_gene_variant,,ENST00000521853,;C11orf57,upstream_gene_variant,,ENST00000530104,;C11orf57,upstream_gene_variant,,ENST00000524989,;PIH1D2,upstream_gene_variant,,ENST00000525744,; G ENST00000280350 Transcript missense_variant 227/1241 4/948 2/315 E/Q Gag/Cag COSM4968564 1 -1 PIH1D2 HGNC HGNC:25210 protein_coding YES CCDS8355.1 ENSP00000280350 Q8WWB5 UPI000007007A NM_138789.3 tolerated_low_confidence(0.05) 2/6 hmmpanther:PTHR22997,hmmpanther:PTHR22997:SF6 1 MODERATE SNV 5 1 1 PASS rs940655083 . 0 208 2 0 0 0 0 0 -16.39667 1 1 1 1 0 G 3 3 46 112073171 112073171 C G 1 0 0 0 0 1 0 0 0 12001 869 30 4 4 PIH1D2 11 112073171 Missense_Mutation SNP C C3N-00294_T 3755744 112073171 23013451 792 13564 TTC12 0 . GRCh38 11 113344294 113344294 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.1008G>C p.= p.V336V ENST00000529221 13/22 95 90 5 110 110 0 strelka-varscan-mutect TTC12,synonymous_variant,p.=,ENST00000393020,;TTC12,synonymous_variant,p.=,ENST00000314756,;TTC12,synonymous_variant,p.=,ENST00000529221,NM_001318533.1,NM_017868.3;TTC12,synonymous_variant,p.=,ENST00000483239,;TTC12,downstream_gene_variant,,ENST00000525965,;TTC12,downstream_gene_variant,,ENST00000524580,;TTC12,non_coding_transcript_exon_variant,,ENST00000478125,;TTC12,synonymous_variant,p.=,ENST00000494714,;TTC12,3_prime_UTR_variant,,ENST00000464224,;TTC12,intron_variant,,ENST00000527362,;TTC12,downstream_gene_variant,,ENST00000534793,; C ENST00000529221 Transcript synonymous_variant 1113/2315 1008/2118 336/705 V gtG/gtC 1 1 TTC12 HGNC HGNC:23700 protein_coding YES CCDS8360.2 ENSP00000433757 Q9H892 A8K8G6 UPI000013F914 NM_001318533.1,NM_017868.3 13/22 Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -10.91149 1 1 1 1 0 C 2 2 46 113344294 113344294 G C 1 0 0 0 0 0 0 0 1 17189 1277 45 4 4 TTC12 11 113344294 Silent SNP G C3N-00294_T 1271123 113344294 21742328 793 13565 KMT2A 0 . GRCh38 11 118505969 118505969 + Silent SNP G G T rs200365395 C3N-00294_T C3N-00294_N G G c.10077G>T p.= p.A3359A ENST00000534358 27/36 223 138 85 223 223 0 strelka-varscan-mutect KMT2A,synonymous_variant,p.=,ENST00000534358,NM_001197104.1;KMT2A,synonymous_variant,p.=,ENST00000389506,NM_005933.3;KMT2A,downstream_gene_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534678,;KMT2A,upstream_gene_variant,,ENST00000534085,; T ENST00000534358 Transcript synonymous_variant 10100/16602 10077/11919 3359/3972 A gcG/gcT rs200365395 1 1 KMT2A HGNC HGNC:7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 UPI0001E5E732 NM_001197104.1 27/36 Low_complexity_(Seg):seg,PIRSF_domain:PIRSF010354 LOW 1 SNV 1 1 PASS rs200365395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 118505969 118505969 G T 1 0 0 0 0 0 0 0 1 8295 1132 40 1 1 KMT2A 11 118505969 Silent SNP G C3N-00294_T 5161675 118505969 16580653 794 13566 TREH 0 . GRCh38 11 118659409 118659409 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1393C>T p.Pro465Ser p.P465S ENST00000264029 12/15 57 48 9 52 52 0 strelka-varscan-mutect TREH,missense_variant,p.Pro465Ser,ENST00000264029,NM_007180.2;TREH,missense_variant,p.Pro434Ser,ENST00000397925,NM_001301065.1;PHLDB1,downstream_gene_variant,,ENST00000361417,NM_015157.3;PHLDB1,downstream_gene_variant,,ENST00000600882,NM_001144758.2;PHLDB1,downstream_gene_variant,,ENST00000356063,NM_001144759.2;PHLDB1,downstream_gene_variant,,ENST00000534140,;PHLDB1,downstream_gene_variant,,ENST00000601898,;PHLDB1,downstream_gene_variant,,ENST00000614369,;PHLDB1,downstream_gene_variant,,ENST00000527898,;PHLDB1,downstream_gene_variant,,ENST00000524713,;TREH,3_prime_UTR_variant,,ENST00000613915,;PHLDB1,downstream_gene_variant,,ENST00000530994,;PHLDB1,downstream_gene_variant,,ENST00000620788,;PHLDB1,downstream_gene_variant,,ENST00000528594,;PHLDB1,downstream_gene_variant,,ENST00000532517,;PHLDB1,downstream_gene_variant,,ENST00000526537,;TREH,downstream_gene_variant,,ENST00000531295,;TREH,downstream_gene_variant,,ENST00000527558,; A ENST00000264029 Transcript missense_variant 1439/2771 1393/1752 465/583 P/S Ccc/Tcc 1 -1 TREH HGNC HGNC:12266 protein_coding YES CCDS73402.1 ENSP00000264029 O43280 UPI000013D4A6 NM_007180.2 deleterious(0) 12/15 Pfam_domain:PF01204,Prints_domain:PR00744,PROSITE_patterns:PS00928,hmmpanther:PTHR23403,hmmpanther:PTHR23403:SF1,Superfamily_domains:SSF48208 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.97007 1 1 1 1 0 A 3 1 46 118659409 118659409 G A 1 0 0 0 0 1 0 0 0 16958 1232 43 3 3 TREH 11 118659409 Missense_Mutation SNP G C3N-00294_T 153440 118659409 16427213 795 13567 HYOU1 0 . GRCh38 11 119048856 119048856 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2023G>C p.Glu675Gln p.E675Q ENST00000617285 18/26 65 48 17 74 74 0 strelka-varscan-mutect HYOU1,missense_variant,p.Glu675Gln,ENST00000617285,NM_001130991.2,NM_006389.4;HYOU1,missense_variant,p.Glu613Gln,ENST00000612687,;HYOU1,missense_variant,p.Glu613Gln,ENST00000621959,;HYOU1,intron_variant,,ENST00000614711,;HYOU1,intron_variant,,ENST00000532519,;HYOU1,intron_variant,,ENST00000614668,;HYOU1,downstream_gene_variant,,ENST00000530473,;RP11-110I1.6,downstream_gene_variant,,ENST00000531886,;HYOU1,3_prime_UTR_variant,,ENST00000543287,;HYOU1,downstream_gene_variant,,ENST00000531694,;HYOU1,upstream_gene_variant,,ENST00000527738,;HYOU1,upstream_gene_variant,,ENST00000531682,; G ENST00000617285 Transcript missense_variant 2148/4529 2023/3000 675/999 E/Q Gag/Cag 1 -1 HYOU1 HGNC HGNC:16931 protein_coding YES CCDS8408.1 ENSP00000480150 Q9Y4L1 UPI0000130F72 NM_001130991.2,NM_006389.4 tolerated(0.14) 18/26 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 119048856 119048856 C G 1 0 0 0 0 1 0 0 0 7367 835 29 4 4 HYOU1 11 119048856 Missense_Mutation SNP C C3N-00294_T 389447 119048856 16037766 796 13568 SORL1 0 . GRCh38 11 121589357 121589357 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4045G>C p.Asp1349His p.D1349H ENST00000260197 29/48 172 141 31 175 175 0 strelka-varscan-mutect SORL1,missense_variant,p.Asp1349His,ENST00000260197,NM_003105.5;SORL1,missense_variant,p.Asp293His,ENST00000525532,;SORL1,missense_variant,p.Asp195His,ENST00000532694,;SORL1,missense_variant,p.Asp259His,ENST00000534286,;SORL1,upstream_gene_variant,,ENST00000527934,; C ENST00000260197 Transcript missense_variant 4174/10904 4045/6645 1349/2214 D/H Gat/Cat 1 1 SORL1 HGNC HGNC:11185 protein_coding YES CCDS8436.1 ENSP00000260197 Q92673 UPI000013D0B1 NM_003105.5 deleterious(0) 29/48 Gene3D:4.10.400.10,Pfam_domain:PF00057,Prints_domain:PR00261,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 121589357 121589357 G C 1 0 0 0 0 1 0 0 0 15256 1290 45 4 4 SORL1 11 121589357 Missense_Mutation SNP G C3N-00294_T 2540501 121589357 13497265 797 13569 OR4D5 0 . GRCh38 11 123939671 123939671 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.55C>A p.Gln19Lys p.Q19K ENST00000307033 1/1 39 30 9 50 50 0 strelka-varscan-mutect OR4D5,missense_variant,p.Gln19Lys,ENST00000307033,NM_001001965.1;OR6T1,downstream_gene_variant,,ENST00000321252,NM_001005187.1; A ENST00000307033 Transcript missense_variant 129/1095 55/957 19/318 Q/K Cag/Aag 1 1 OR4D5 HGNC HGNC:14852 protein_coding YES CCDS31699.1 ENSP00000305970 Q8NGN0 A0A126GVD9 UPI000003F227 NM_001001965.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF73,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 203 5 2 0 0 0 0 -18.34754 0.9999831 1 1 1 0 A 3 1 46 123939671 123939671 C A 1 0 0 0 0 1 0 0 0 11134 827 29 2 2 OR4D5 11 123939671 Missense_Mutation SNP C C3N-00294_T 2350314 123939671 11146951 798 13570 OR10G8 0 . GRCh38 11 124030427 124030427 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.805G>A p.Gly269Arg p.G269R ENST00000431524 1/1 179 147 32 155 155 0 strelka-varscan-mutect OR10G8,missense_variant,p.Gly269Arg,ENST00000431524,NM_001004464.1; A ENST00000431524 Transcript missense_variant 838/1045 805/936 269/311 G/R Gga/Aga 1 1 OR10G8 HGNC HGNC:14845 protein_coding YES CCDS31704.1 ENSP00000389072 Q8NGN5 A0A126GVX3 UPI0000040A8F NM_001004464.1 tolerated(0.18) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF146,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 124030427 124030427 G A 1 0 0 0 0 1 0 0 0 10980 1349 47 3 3 OR10G8 11 124030427 Missense_Mutation SNP G C3N-00294_T 90756 124030427 11056195 799 13571 OR8G1 0 . GRCh38 11 124249915 124249915 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.240G>C p.Lys80Asn p.K80N ENST00000341493 1/1 305 241 64 295 295 0 strelka-varscan-mutect OR8G1,missense_variant,p.Lys80Asn,ENST00000341493,NM_001002905.1; C ENST00000341493 Transcript missense_variant 240/936 240/936 80/311 K/N aaG/aaC 1 1 OR8G1 HGNC HGNC:8484 protein_coding YES CCDS73407.1 ENSP00000476313 Q15617 A0A126GVX6 UPI0000061EA7 NM_001002905.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 124249915 124249915 G C 1 0 0 0 0 1 0 0 0 11303 933 33 4 4 OR8G1 11 124249915 Missense_Mutation SNP G C3N-00294_T 219488 124249915 10836707 800 13572 NRGN 0 . GRCh38 11 124745554 124745554 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.67G>A p.Asp23Asn p.D23N ENST00000284292 2/4 106 88 18 126 126 0 strelka-varscan-mutect NRGN,missense_variant,p.Asp23Asn,ENST00000284292,NM_006176.2,NM_001126181.1;NRGN,missense_variant,p.Asp23Asn,ENST00000412681,;VSIG2,downstream_gene_variant,,ENST00000403470,;VSIG2,downstream_gene_variant,,ENST00000326621,NM_014312.3;RP11-677M14.2,intron_variant,,ENST00000531241,; A ENST00000284292 Transcript missense_variant 306/1306 67/237 23/78 D/N Gat/Aat 1 1 NRGN HGNC HGNC:8000 protein_coding YES CCDS8451.1 ENSP00000284292 Q92686 A0A024R3M7 UPI0000054C7E NM_006176.2,NM_001126181.1 deleterious(0) 2/4 hmmpanther:PTHR10699,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 124745554 124745554 G A 1 0 0 0 0 1 0 0 0 10709 1058 37 1 1 NRGN 11 124745554 Missense_Mutation SNP G C3N-00294_T 495639 124745554 10341068 801 13573 ROBO3 0 . GRCh38 11 124879220 124879220 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.3564C>T p.= p.L1188L ENST00000397801 24/28 111 82 29 124 124 0 strelka-varscan-mutect ROBO3,synonymous_variant,p.=,ENST00000397801,NM_022370.3;ROBO3,synonymous_variant,p.=,ENST00000538940,;ROBO3,5_prime_UTR_variant,,ENST00000543966,;ROBO4,downstream_gene_variant,,ENST00000306534,NM_019055.5;RP11-664I21.5,upstream_gene_variant,,ENST00000524453,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525482,;ROBO3,non_coding_transcript_exon_variant,,ENST00000528820,;ROBO3,non_coding_transcript_exon_variant,,ENST00000528144,;ROBO3,non_coding_transcript_exon_variant,,ENST00000531075,;ROBO3,downstream_gene_variant,,ENST00000526551,;ROBO3,downstream_gene_variant,,ENST00000532472,;ROBO3,downstream_gene_variant,,ENST00000531545,;ROBO3,non_coding_transcript_exon_variant,,ENST00000527245,;ROBO3,non_coding_transcript_exon_variant,,ENST00000529658,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525448,;ROBO3,non_coding_transcript_exon_variant,,ENST00000527196,;ROBO3,non_coding_transcript_exon_variant,,ENST00000524971,;ROBO3,non_coding_transcript_exon_variant,,ENST00000525304,;ROBO4,downstream_gene_variant,,ENST00000534407,;ROBO3,downstream_gene_variant,,ENST00000534598,;ROBO3,downstream_gene_variant,,ENST00000528068,;ROBO3,downstream_gene_variant,,ENST00000531888,;ROBO3,downstream_gene_variant,,ENST00000530647,;ROBO3,downstream_gene_variant,,ENST00000531119,; T ENST00000397801 Transcript synonymous_variant 3756/4569 3564/4161 1188/1386 L ctC/ctT 1 1 ROBO3 HGNC HGNC:13433 protein_coding YES CCDS44755.1 ENSP00000380903 Q96MS0 UPI000035AA82 NM_022370.3 24/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF724,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 124879220 124879220 C T 1 0 0 0 0 0 0 0 1 13693 813 29 3 3 ROBO3 11 124879220 Silent SNP C C3N-00294_T 133666 124879220 10207402 802 13574 KCNJ5 0 . GRCh38 11 128911495 128911495 + Silent SNP G G C C3N-00294_T C3N-00294_N G G c.222G>C p.= p.L74L ENST00000529694 2/3 397 319 78 496 496 0 strelka-varscan-mutect KCNJ5,synonymous_variant,p.=,ENST00000529694,NM_000890.3;KCNJ5,synonymous_variant,p.=,ENST00000338350,;KCNJ5,synonymous_variant,p.=,ENST00000533599,; C ENST00000529694 Transcript synonymous_variant 598/5940 222/1260 74/419 L ctG/ctC COSM415273 1 1 KCNJ5 HGNC HGNC:6266 protein_coding YES CCDS8479.1 ENSP00000433295 P48544 UPI000013D428 NM_000890.3 2/3 hmmpanther:PTHR11767:SF52,hmmpanther:PTHR11767,Pfam_domain:PF01007,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81324 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 128911495 128911495 G C 1 0 0 0 0 0 0 0 1 7971 1277 45 4 4 KCNJ5 11 128911495 Silent SNP G C3N-00294_T 4032275 128911495 6175127 803 13575 ACAD8 0 . GRCh38 11 134258618 134258618 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.484G>A p.Glu162Lys p.E162K ENST00000281182 4/11 356 291 65 404 404 0 strelka-varscan-mutect ACAD8,missense_variant,p.Glu162Lys,ENST00000281182,NM_014384.2;ACAD8,intron_variant,,ENST00000374752,;ACAD8,intron_variant,,ENST00000524547,;ACAD8,upstream_gene_variant,,ENST00000524502,;ACAD8,3_prime_UTR_variant,,ENST00000526026,;ACAD8,3_prime_UTR_variant,,ENST00000524426,;ACAD8,non_coding_transcript_exon_variant,,ENST00000531338,;ACAD8,non_coding_transcript_exon_variant,,ENST00000533387,;ACAD8,non_coding_transcript_exon_variant,,ENST00000527665,;ACAD8,non_coding_transcript_exon_variant,,ENST00000530533,;ACAD8,non_coding_transcript_exon_variant,,ENST00000527082,;ACAD8,non_coding_transcript_exon_variant,,ENST00000528325,;ACAD8,non_coding_transcript_exon_variant,,ENST00000534240,;ACAD8,intron_variant,,ENST00000534433,;ACAD8,upstream_gene_variant,,ENST00000524739,;ACAD8,downstream_gene_variant,,ENST00000525961,;ACAD8,upstream_gene_variant,,ENST00000527713,; A ENST00000281182 Transcript missense_variant 590/2249 484/1248 162/415 E/K Gaa/Aaa 1 1 ACAD8 HGNC HGNC:87 protein_coding YES CCDS8498.1 ENSP00000281182 Q9UKU7 UPI00001251DD NM_014384.2 deleterious(0) 4/11 hmmpanther:PTHR10909:SF145,hmmpanther:PTHR10909,PROSITE_patterns:PS00072,Pfam_domain:PF02770,Gene3D:2.40.110.10,Superfamily_domains:SSF56645 MODERATE 1 SNV 1 1 PASS rs1331422944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 134258618 134258618 G A 1 0 0 0 0 1 0 0 0 153 1291 45 3 3 ACAD8 11 134258618 Missense_Mutation SNP G C3N-00294_T 5347123 134258618 828004 804 13576 CACNA2D4 0 . GRCh38 12 1793722 1793722 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3347C>T p.Ser1116Leu p.S1116L ENST00000382722 38/38 181 137 44 230 230 0 strelka-varscan-mutect CACNA2D4,missense_variant,p.Ser1116Leu,ENST00000382722,NM_172364.4;CACNA2D4,missense_variant,p.Ser1091Leu,ENST00000587995,;CACNA2D4,missense_variant,p.Ser1052Leu,ENST00000588077,;CACNA2D4,missense_variant,p.Ser246Leu,ENST00000538450,;CACNA2D4,missense_variant,p.Ser261Leu,ENST00000538027,;CACNA2D4,missense_variant,p.Ser263Leu,ENST00000536846,;CACNA2D4,downstream_gene_variant,,ENST00000586184,;CACNA2D4,downstream_gene_variant,,ENST00000585708,;CACNA2D4,3_prime_UTR_variant,,ENST00000444595,;CACNA2D4,3_prime_UTR_variant,,ENST00000537784,;CACNA2D4,3_prime_UTR_variant,,ENST00000545595,;CACNA2D4,3_prime_UTR_variant,,ENST00000585385,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000541444,;CACNA2D4,downstream_gene_variant,,ENST00000543405,;CACNA2D4,downstream_gene_variant,,ENST00000537923,;CACNA2D4,downstream_gene_variant,,ENST00000536818,;CACNA2D4,downstream_gene_variant,,ENST00000588896,; A ENST00000382722 Transcript missense_variant 3710/5475 3347/3414 1116/1137 S/L tCa/tTa 1 -1 CACNA2D4 HGNC HGNC:20202 protein_coding YES CCDS44785.1 ENSP00000372169 Q7Z3S7 UPI0000E593D9 NM_172364.4 tolerated(0.19) 38/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 1793722 1793722 G A 1 0 0 0 0 1 0 0 0 2239 1294 45 3 3 CACNA2D4 12 1793722 Missense_Mutation SNP G C3N-00294_T 1793722 131481587 805 13577 CACNA1C 0 . GRCh38 12 2682610 2682610 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5649G>C p.Glu1883Asp p.E1883D ENST00000347598 45/49 232 195 37 221 221 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Glu1906Asp,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Glu1906Asp,ENST00000406454,;CACNA1C,missense_variant,p.Glu1870Asp,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Glu1860Asp,ENST00000335762,;CACNA1C,missense_variant,p.Glu1883Asp,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Glu1876Asp,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Glu1870Asp,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Glu1863Asp,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Glu1855Asp,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Glu1854Asp,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Glu1854Asp,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Glu1854Asp,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Glu1852Asp,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Glu1843Asp,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Glu1843Asp,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Glu1841Asp,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Glu1835Asp,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Glu526Asp,ENST00000616390,;CACNA1C-AS1,intron_variant,,ENST00000501371,;CACNA1C,downstream_gene_variant,,ENST00000465934,; C ENST00000347598 Transcript missense_variant 5649/6655 5649/6561 1883/2186 E/D gaG/gaC 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 tolerated_low_confidence(0.32) 45/49 Pfam_domain:PF16885,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 2682610 2682610 G C 1 0 0 0 0 1 0 0 0 2228 933 33 4 4 CACNA1C 12 2682610 Missense_Mutation SNP G C3N-00294_T 888888 2682610 130592699 806 13578 CACNA1C 0 . GRCh38 12 2690947 2690947 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.6309C>T p.= p.F2103F ENST00000347598 49/49 99 76 23 109 109 0 strelka-varscan-mutect CACNA1C,synonymous_variant,p.=,ENST00000399655,NM_000719.6;CACNA1C,synonymous_variant,p.=,ENST00000399634,NM_001167625.1;CACNA1C,synonymous_variant,p.=,ENST00000406454,;CACNA1C,synonymous_variant,p.=,ENST00000399617,NM_001167624.2;CACNA1C,synonymous_variant,p.=,ENST00000399603,NM_001167623.1;CACNA1C,synonymous_variant,p.=,ENST00000335762,;CACNA1C,synonymous_variant,p.=,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,synonymous_variant,p.=,ENST00000344100,NM_001129829.1;CACNA1C,synonymous_variant,p.=,ENST00000327702,NM_001129830.2;CACNA1C,synonymous_variant,p.=,ENST00000399638,NM_001129831.1;CACNA1C,synonymous_variant,p.=,ENST00000399606,NM_001129832.1;CACNA1C,synonymous_variant,p.=,ENST00000399621,NM_001129834.1;CACNA1C,synonymous_variant,p.=,ENST00000399637,NM_001129835.1;CACNA1C,synonymous_variant,p.=,ENST00000402845,NM_001129833.1;CACNA1C,synonymous_variant,p.=,ENST00000399629,NM_001129836.1;CACNA1C,synonymous_variant,p.=,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,synonymous_variant,p.=,ENST00000399595,NM_001129837.1;CACNA1C,synonymous_variant,p.=,ENST00000399649,NM_001129839.1;CACNA1C,synonymous_variant,p.=,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,synonymous_variant,p.=,ENST00000399601,NM_001129843.1;CACNA1C,synonymous_variant,p.=,ENST00000399641,NM_001129840.1;CACNA1C,synonymous_variant,p.=,ENST00000399644,NM_001129841.1;CACNA1C,synonymous_variant,p.=,ENST00000616390,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000501371,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000544517,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000541673,;RP11-885B4.1,downstream_gene_variant,,ENST00000636122,; T ENST00000347598 Transcript synonymous_variant 6309/6655 6309/6561 2103/2186 F ttC/ttT 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 49/49 Pfam_domain:PF16885 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 2690947 2690947 C T 1 0 0 0 0 0 0 0 1 2228 825 29 3 3 CACNA1C 12 2690947 Silent SNP C C3N-00294_T 8337 2690947 130584362 807 13579 FKBP4 0 . GRCh38 12 2797165 2797165 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.133G>A p.Glu45Lys p.E45K ENST00000001008 2/10 200 174 26 199 199 0 strelka-varscan-mutect FKBP4,missense_variant,p.Glu45Lys,ENST00000001008,NM_002014.3;FKBP4,5_prime_UTR_variant,,ENST00000538622,;FKBP4,upstream_gene_variant,,ENST00000539181,;FKBP4,downstream_gene_variant,,ENST00000630279,;RP4-816N1.7,non_coding_transcript_exon_variant,,ENST00000547042,;RP4-816N1.6,intron_variant,,ENST00000547834,;FKBP4,non_coding_transcript_exon_variant,,ENST00000540260,;RP11-885B4.1,intron_variant,,ENST00000540093,;RP11-885B4.1,upstream_gene_variant,,ENST00000636122,;CBX3P4,upstream_gene_variant,,ENST00000540428,;FKBP4,3_prime_UTR_variant,,ENST00000543769,;FKBP4,upstream_gene_variant,,ENST00000543037,; A ENST00000001008 Transcript missense_variant 320/3732 133/1380 45/459 E/K Gag/Aag 1 1 FKBP4 HGNC HGNC:3720 protein_coding YES CCDS8512.1 ENSP00000001008 Q02790 UPI000013C4D0 NM_002014.3 deleterious(0.02) 2/10 hmmpanther:PTHR10516,hmmpanther:PTHR10516:SF25,Gene3D:3.10.50.40,Pfam_domain:PF00254,Superfamily_domains:SSF54534 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 46 2797165 2797165 G A 1 0 0 0 0 1 0 0 0 5774 943 33 3 3 FKBP4 12 2797165 Missense_Mutation SNP G C3N-00294_T 106218 2797165 130478144 808 13580 FOXM1 0 . GRCh38 12 2864431 2864431 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1155G>A p.= p.V385V ENST00000342628 8/10 109 90 19 121 121 0 strelka-varscan-mutect FOXM1,synonymous_variant,p.=,ENST00000627656,NM_001243088.1;FOXM1,synonymous_variant,p.=,ENST00000342628,NM_202002.2;FOXM1,synonymous_variant,p.=,ENST00000361953,NM_202003.2,NM_001243089.1;FOXM1,synonymous_variant,p.=,ENST00000359843,NM_021953.3;FOXM1,synonymous_variant,p.=,ENST00000535350,;ITFG2,downstream_gene_variant,,ENST00000545509,;ITFG2,downstream_gene_variant,,ENST00000537710,;FOXM1,downstream_gene_variant,,ENST00000537018,;FOXM1,non_coding_transcript_exon_variant,,ENST00000536066,;FOXM1,non_coding_transcript_exon_variant,,ENST00000366362,;FOXM1,downstream_gene_variant,,ENST00000545049,;FOXM1,downstream_gene_variant,,ENST00000538564,; T ENST00000342628 Transcript synonymous_variant 1269/3475 1155/2406 385/801 V gtG/gtA 1 -1 FOXM1 HGNC HGNC:3818 protein_coding YES CCDS8516.1 ENSP00000342307 Q08050 UPI000016B22B NM_202002.2 8/10 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 2864431 2864431 C T 1 0 0 0 0 0 0 0 1 5882 813 29 3 3 FOXM1 12 2864431 Silent SNP C C3N-00294_T 67266 2864431 130410878 809 13581 CCND2 0 . GRCh38 12 4274059 4274059 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.19G>A p.Glu7Lys p.E7K ENST00000261254 1/5 125 100 25 121 121 0 strelka-varscan-mutect CCND2,missense_variant,p.Glu7Lys,ENST00000261254,NM_001759.3;CCND2,upstream_gene_variant,,ENST00000536537,;CCND2-AS1,intron_variant,,ENST00000539135,;CCND2-AS2,intron_variant,,ENST00000537370,;CCND2,upstream_gene_variant,,ENST00000541542,;CCND2,upstream_gene_variant,,ENST00000536795,; A ENST00000261254 Transcript missense_variant 288/6480 19/870 7/289 E/K Gag/Aag 1 1 CCND2 HGNC HGNC:1583 protein_coding YES CCDS8524.1 ENSP00000261254 P30279 UPI00001275C5 NM_001759.3 deleterious(0) 1/5 hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF66 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 4274059 4274059 G A 1 0 0 0 0 1 0 0 0 2616 1059 37 1 1 CCND2 12 4274059 Missense_Mutation SNP G C3N-00294_T 1409628 4274059 129001250 810 13582 GALNT8 0 . GRCh38 12 4811245 4811245 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1204G>A p.Asp402Asn p.D402N ENST00000280684 1/1 335 272 63 375 375 0 strelka-varscan-mutect GALNT8,missense_variant,p.Asp402Asn,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Asp402Asn,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; A ENST00000280684 Transcript missense_variant 2070/4237 1204/1590 402/529 D/N Gac/Aac 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD tolerated(0.11) 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104,Superfamily_domains:SSF81324 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 4811245 4811245 G A 1 0 0 0 0 1 0 0 0 6090 1290 45 3 3 GALNT8 12 4811245 Missense_Mutation SNP G C3N-00294_T 537186 4811245 128464064 811 13583 VWF 0 . GRCh38 12 6057025 6057025 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1777G>A p.Glu593Lys p.E593K ENST00000261405 15/52 203 151 52 201 201 0 strelka-varscan-mutect VWF,missense_variant,p.Glu593Lys,ENST00000261405,NM_000552.3;VWF,intron_variant,,ENST00000538635,; T ENST00000261405 Transcript missense_variant 2032/8838 1777/8442 593/2813 E/K Gag/Aag 1 -1 VWF HGNC HGNC:12726 protein_coding YES CCDS8539.1 ENSP00000261405 P04275 UPI00001AE7EE NM_000552.3 tolerated(0.09) 15/52 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF259,Pfam_domain:PF08742,PIRSF_domain:PIRSF002495,SMART_domains:SM00832 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 6057025 6057025 C T 1 0 0 0 0 1 0 0 0 17806 893 31 1 1 VWF 12 6057025 Missense_Mutation SNP C C3N-00294_T 1245780 6057025 127218284 812 13584 SCNN1A 0 . GRCh38 12 6363694 6363694 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.610G>C p.Glu204Gln p.E204Q ENST00000360168 2/12 76 61 15 70 70 0 strelka-varscan-mutect SCNN1A,missense_variant,p.Glu204Gln,ENST00000360168,NM_001159576.1;SCNN1A,missense_variant,p.Glu145Gln,ENST00000228916,NM_001038.5;SCNN1A,missense_variant,p.Glu168Gln,ENST00000543768,NM_001159575.1;SCNN1A,missense_variant,p.Glu145Gln,ENST00000396966,;SCNN1A,5_prime_UTR_variant,,ENST00000540037,;SCNN1A,non_coding_transcript_exon_variant,,ENST00000544882,;SCNN1A,non_coding_transcript_exon_variant,,ENST00000536176,;SCNN1A,intron_variant,,ENST00000538979,;SCNN1A,upstream_gene_variant,,ENST00000542966,;SCNN1A,upstream_gene_variant,,ENST00000541249,;SCNN1A,missense_variant,p.Glu145Gln,ENST00000338748,; G ENST00000360168 Transcript missense_variant 874/3481 610/2187 204/728 E/Q Gag/Cag 1 -1 SCNN1A HGNC HGNC:10599 protein_coding YES CCDS53738.1 ENSP00000353292 P37088 UPI00001B07D7 NM_001159576.1 tolerated(0.2) 2/12 hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF124,Pfam_domain:PF00858,TIGRFAM_domain:TIGR00859 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 6363694 6363694 C G 1 0 0 0 0 1 0 0 0 14196 922 32 4 4 SCNN1A 12 6363694 Missense_Mutation SNP C C3N-00294_T 306669 6363694 126911615 813 13585 NOP2 0 . GRCh38 12 6563164 6563164 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.994G>C p.Glu332Gln p.E332Q ENST00000382421 10/17 117 93 24 136 135 1 strelka-varscan-mutect NOP2,missense_variant,p.Glu295Gln,ENST00000541778,NM_006170.3;NOP2,missense_variant,p.Glu332Gln,ENST00000620535,;NOP2,missense_variant,p.Glu295Gln,ENST00000545200,NM_001258310.1;NOP2,missense_variant,p.Glu332Gln,ENST00000382421,NM_001258309.1;NOP2,missense_variant,p.Glu295Gln,ENST00000399466,NM_001033714.2;NOP2,missense_variant,p.Glu299Gln,ENST00000322166,NM_001258308.1;NOP2,missense_variant,p.Glu299Gln,ENST00000537442,;NOP2,missense_variant,p.Glu295Gln,ENST00000617555,;NOP2,missense_variant,p.Glu175Gln,ENST00000542944,;NOP2,downstream_gene_variant,,ENST00000542867,;NOP2,downstream_gene_variant,,ENST00000536124,;NOP2,downstream_gene_variant,,ENST00000540228,;NOP2,downstream_gene_variant,,ENST00000545492,;NOP2,downstream_gene_variant,,ENST00000545915,;NOP2,intron_variant,,ENST00000542015,;NOP2,non_coding_transcript_exon_variant,,ENST00000542919,;NOP2,upstream_gene_variant,,ENST00000536506,;NOP2,upstream_gene_variant,,ENST00000544630,;NOP2,upstream_gene_variant,,ENST00000537708,;NOP2,downstream_gene_variant,,ENST00000538420,;NOP2,downstream_gene_variant,,ENST00000538697,;NOP2,downstream_gene_variant,,ENST00000400580,;NOP2,downstream_gene_variant,,ENST00000546053,; G ENST00000382421 Transcript missense_variant 1070/2736 994/2538 332/845 E/Q Gag/Cag COSM3812800,COSM3812801 1 -1 NOP2 HGNC HGNC:7867 protein_coding YES CCDS58204.1 ENSP00000371858 P46087 UPI00005C3039 NM_001258309.1 deleterious(0.01) 10/17 hmmpanther:PTHR22807:SF30,hmmpanther:PTHR22807,Pfam_domain:PF17125,Superfamily_domains:SSF53335,Prints_domain:PR02012 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1301911932 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 6563164 6563164 C G 1 0 0 0 0 1 0 0 0 10582 864 30 4 4 NOP2 12 6563164 Missense_Mutation SNP C C3N-00294_T 199470 6563164 126712145 814 13586 CHD4 0 . GRCh38 12 6581763 6581763 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.4567G>A p.Glu1523Lys p.E1523K ENST00000357008 31/40 31 25 6 32 32 0 strelka-varscan-mutect CHD4,missense_variant,p.Glu1548Lys,ENST00000544484,;CHD4,missense_variant,p.Glu1516Lys,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Glu1523Lys,ENST00000357008,NM_001273.3;SCARNA11,upstream_gene_variant,,ENST00000516089,;RP5-940J5.6,intron_variant,,ENST00000501075,;CHD4,intron_variant,,ENST00000536301,;CHD4,downstream_gene_variant,,ENST00000540960,;CHD4,upstream_gene_variant,,ENST00000542717,; T ENST00000357008 Transcript missense_variant 4731/6496 4567/5739 1523/1912 E/K Gag/Aag 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 tolerated(0.09) 31/40 hmmpanther:PTHR10799:SF554,hmmpanther:PTHR10799,SMART_domains:SM01146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 6581763 6581763 C T 1 0 0 0 0 1 0 0 0 3086 835 29 3 3 CHD4 12 6581763 Missense_Mutation SNP C C3N-00294_T 18599 6581763 126693546 815 13587 CHD4 0 . GRCh38 12 6593472 6593472 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.2458G>A p.Glu820Lys p.E820K ENST00000357008 16/40 169 138 31 176 176 0 strelka-varscan-mutect CHD4,missense_variant,p.Glu817Lys,ENST00000544484,;CHD4,missense_variant,p.Glu813Lys,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Glu820Lys,ENST00000357008,NM_001273.3;CHD4,downstream_gene_variant,,ENST00000536999,;CHD4,upstream_gene_variant,,ENST00000536301,;CHD4,upstream_gene_variant,,ENST00000537634,;CHD4,upstream_gene_variant,,ENST00000545083,; T ENST00000357008 Transcript missense_variant 2622/6496 2458/5739 820/1912 E/K Gag/Aag COSM3812843,COSM3812844,COSM3812845 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 deleterious(0) 16/40 PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF554,hmmpanther:PTHR10799,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 6593472 6593472 C T 1 0 0 0 0 1 0 0 0 3086 835 29 3 3 CHD4 12 6593472 Missense_Mutation SNP C C3N-00294_T 11709 6593472 126681837 816 13588 TAS2R7 0 . GRCh38 12 10801710 10801710 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.861G>C p.= p.L287L ENST00000240687 1/1 166 136 30 216 216 0 strelka-varscan-mutect TAS2R7,synonymous_variant,p.=,ENST00000240687,NM_023919.2;TAS2R8,downstream_gene_variant,,ENST00000240615,NM_023918.1; G ENST00000240687 Transcript synonymous_variant 918/1096 861/957 287/318 L ctG/ctC 1 -1 TAS2R7 HGNC HGNC:14913 protein_coding YES CCDS8631.1 ENSP00000240687 Q9NYW3 UPI0000038B0F NM_023919.2 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF58,Pfam_domain:PF05296,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 10801710 10801710 C G 1 0 0 0 0 0 0 0 1 15985 581 21 4 4 TAS2R7 12 10801710 Silent SNP C C3N-00294_T 4208238 10801710 122473599 817 13589 PTPRO 0 . GRCh38 12 15546652 15546652 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2248G>A p.Asp750Asn p.D750N ENST00000281171 13/27 327 262 65 348 348 0 strelka-varscan-mutect PTPRO,missense_variant,p.Asp750Asn,ENST00000281171,NM_030667.2;PTPRO,missense_variant,p.Asp750Asn,ENST00000348962,NM_002848.3;PTPRO,5_prime_UTR_variant,,ENST00000445537,NM_030671.2;PTPRO,5_prime_UTR_variant,,ENST00000544244,NM_030670.2;PTPRO,5_prime_UTR_variant,,ENST00000442921,NM_030669.2;PTPRO,5_prime_UTR_variant,,ENST00000542557,NM_030668.2;PTPRO,missense_variant,p.Asp13Asn,ENST00000535311,; A ENST00000281171 Transcript missense_variant 2578/5301 2248/3651 750/1216 D/N Gat/Aat 1 1 PTPRO HGNC HGNC:9678 protein_coding YES CCDS8675.1 ENSP00000281171 Q16827 UPI000013DC62 NM_030667.2 deleterious(0.01) 13/27 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF315,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 15546652 15546652 G A 1 0 0 0 0 1 0 0 0 12963 1290 45 3 3 PTPRO 12 15546652 Missense_Mutation SNP G C3N-00294_T 4744942 15546652 117728657 818 13590 STRAP 0 . GRCh38 12 15897970 15897970 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.727G>A p.Glu243Lys p.E243K ENST00000419869 7/10 97 84 13 177 177 0 strelka-varscan-mutect STRAP,missense_variant,p.Glu243Lys,ENST00000419869,NM_007178.3;STRAP,missense_variant,p.Glu256Lys,ENST00000025399,;STRAP,missense_variant,p.Glu10Lys,ENST00000538718,;STRAP,3_prime_UTR_variant,,ENST00000541731,;STRAP,non_coding_transcript_exon_variant,,ENST00000536737,;STRAP,upstream_gene_variant,,ENST00000539887,; A ENST00000419869 Transcript missense_variant 1040/1866 727/1053 243/350 E/K Gaa/Aaa 1 1 STRAP HGNC HGNC:30796 protein_coding YES CCDS8676.1 ENSP00000392270 Q9Y3F4 UPI0000137C97 NM_007178.3 deleterious(0.03) 7/10 PROSITE_profiles:PS50294,hmmpanther:PTHR19877,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 15897970 15897970 G A 1 0 0 0 0 1 0 0 0 15707 1291 45 3 3 STRAP 12 15897970 Missense_Mutation SNP G C3N-00294_T 351318 15897970 117377339 819 13591 RERGL 0 . GRCh38 12 18081424 18081424 + Missense_Mutation SNP G G C rs748778436 C3N-00294_T C3N-00294_N G G c.385C>G p.His129Asp p.H129D ENST00000229002 6/6 105 84 21 106 106 0 strelka-varscan-mutect RERGL,missense_variant,p.His129Asp,ENST00000229002,NM_024730.3;RERGL,missense_variant,p.His128Asp,ENST00000538724,NM_001286201.1;RERGL,3_prime_UTR_variant,,ENST00000536890,;RERGL,non_coding_transcript_exon_variant,,ENST00000541632,;RERGL,non_coding_transcript_exon_variant,,ENST00000540148,; C ENST00000229002 Transcript missense_variant 592/1147 385/618 129/205 H/D Cat/Gat rs748778436,COSM1746875,COSM1746876 1 -1 RERGL HGNC HGNC:26213 protein_coding YES CCDS8679.1 ENSP00000229002 Q9H628 UPI000000D9FA NM_024730.3 deleterious(0) 6/6 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF30,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748778436 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 18081424 18081424 G C 1 0 0 0 0 1 0 0 0 13403 1290 45 4 4 RERGL 12 18081424 Missense_Mutation SNP G C3N-00294_T 2183454 18081424 115193885 820 13592 PIK3C2G 0 . GRCh38 12 18282267 18282268 + Frame_Shift_Ins INS - - T novel C3N-00294_T C3N-00294_N - - c.192dupT p.Val65CysfsTer16 p.V65Cfs*16 ENST00000538779 2/33 131 111 20 182 182 0 sindel-varindel-pindel PIK3C2G,frameshift_variant,p.Val65CysfsTer16,ENST00000538779,NM_001288772.1,NM_001288774.1;PIK3C2G,frameshift_variant,p.Val65CysfsTer16,ENST00000433979,NM_004570.5;PIK3C2G,frameshift_variant,p.Val65CysfsTer16,ENST00000266497,;PIK3C2G,frameshift_variant,p.Val65CysfsTer16,ENST00000535651,;PIK3C2G,upstream_gene_variant,,ENST00000536967,;RERGL,intron_variant,,ENST00000541632,;PIK3C2G,frameshift_variant,p.Val65CysfsTer16,ENST00000546003,; T ENST00000538779 Transcript frameshift_variant 302-303/4963 186-187/4461 62-63/1486 -/X -/T 1 1 PIK3C2G HGNC HGNC:8973 protein_coding YES CCDS73452.1 ENSP00000445381 F5H369 UPI00020655D2 NM_001288772.1,NM_001288774.1 2/33 hmmpanther:PTHR10048:SF29,hmmpanther:PTHR10048 HIGH 1 insertion 5 6 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 46 18282267 18282267 - T 1 0 1 1 0 0 0 0 0 12006 668 24 0 0 PIK3C2G 12 18282267 Frame_Shift_Ins INS - C3N-00294_T 200843 18282267 114993042 821 13593 BCAT1 0 . GRCh38 12 24842130 24842130 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.805G>A p.Glu269Lys p.E269K ENST00000539282 7/11 227 186 41 207 207 0 strelka-varscan-mutect BCAT1,missense_variant,p.Glu257Lys,ENST00000261192,NM_005504.6;BCAT1,missense_variant,p.Glu256Lys,ENST00000538118,NM_001178094.1;BCAT1,missense_variant,p.Glu196Lys,ENST00000342945,NM_001178092.1;BCAT1,missense_variant,p.Glu269Lys,ENST00000539282,NM_001178093.1;BCAT1,missense_variant,p.Glu220Lys,ENST00000539780,NM_001178091.1;BCAT1,non_coding_transcript_exon_variant,,ENST00000544418,;BCAT1,missense_variant,p.Glu160Lys,ENST00000612790,; T ENST00000539282 Transcript missense_variant 892/1811 805/1197 269/398 E/K Gaa/Aaa 1 -1 BCAT1 HGNC HGNC:976 protein_coding YES CCDS53761.1 ENSP00000443459 P54687 UPI0001D27F89 NM_001178093.1 deleterious(0) 7/11 hmmpanther:PTHR11825,hmmpanther:PTHR11825:SF51,PROSITE_patterns:PS00770,TIGRFAM_domain:TIGR01123,Pfam_domain:PF01063,PIRSF_domain:PIRSF006468,Gene3D:3.20.10.10,Superfamily_domains:SSF56752 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 24842130 24842130 C T 1 0 0 0 0 1 0 0 0 1501 835 29 3 3 BCAT1 12 24842130 Missense_Mutation SNP C C3N-00294_T 6559863 24842130 108433179 822 13594 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-00294_T C3N-00294_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 293 164 129 289 289 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-00294_T 403221 25245351 108029958 823 13595 ITPR2 0 . GRCh38 12 26580030 26580030 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.4506C>T p.= p.L1502L ENST00000381340 33/57 49 42 7 93 93 0 strelka-varscan-mutect ITPR2,synonymous_variant,p.=,ENST00000381340,NM_002223.2; A ENST00000381340 Transcript synonymous_variant 4923/11405 4506/8106 1502/2701 L ctC/ctT 1 -1 ITPR2 HGNC HGNC:6181 protein_coding YES CCDS41764.1 ENSP00000370744 Q14571 UPI00001FB7D2 NM_002223.2 33/57 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF53,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 26580030 26580030 G A 1 0 0 0 0 0 0 0 1 7827 1188 41 3 3 ITPR2 12 26580030 Silent SNP G C3N-00294_T 1334679 26580030 106695279 824 13596 TM7SF3 0 . GRCh38 12 26996850 26996850 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.410G>C p.Gly137Ala p.G137A ENST00000343028 4/12 99 78 21 97 97 0 strelka-varscan-mutect TM7SF3,missense_variant,p.Gly137Ala,ENST00000343028,NM_016551.2;TM7SF3,missense_variant,p.Gly15Ala,ENST00000543088,;TM7SF3,missense_variant,p.Gly35Ala,ENST00000543803,;TM7SF3,missense_variant,p.Gly15Ala,ENST00000539741,;TM7SF3,missense_variant,p.Gly15Ala,ENST00000535423,;TM7SF3,intron_variant,,ENST00000535819,;TM7SF3,intron_variant,,ENST00000543655,;TM7SF3,downstream_gene_variant,,ENST00000512808,;TM7SF3,downstream_gene_variant,,ENST00000545600,;TM7SF3,upstream_gene_variant,,ENST00000545303,;TM7SF3,non_coding_transcript_exon_variant,,ENST00000542667,;TM7SF3,downstream_gene_variant,,ENST00000539399,;TM7SF3,3_prime_UTR_variant,,ENST00000542019,;TM7SF3,upstream_gene_variant,,ENST00000535260,;TM7SF3,upstream_gene_variant,,ENST00000543882,; G ENST00000343028 Transcript missense_variant 636/2709 410/1713 137/570 G/A gGa/gCa 1 -1 TM7SF3 HGNC HGNC:23049 protein_coding YES CCDS8710.1 ENSP00000342322 Q9NS93 UPI0000136849 NM_016551.2 deleterious(0) 4/12 hmmpanther:PTHR15937 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 26996850 26996850 C G 1 0 0 0 0 1 0 0 0 16420 855 30 4 4 TM7SF3 12 26996850 Missense_Mutation SNP C C3N-00294_T 416820 26996850 106278459 825 13597 OVOS2 0 . GRCh38 12 31150215 31150215 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.892C>T p.His298Tyr p.H298Y ENST00000632817 8/34 126 102 24 183 183 0 strelka-varscan-mutect OVOS2,missense_variant,p.His298Tyr,ENST00000398963,;OVOS2,missense_variant,p.His298Tyr,ENST00000632817,; A ENST00000632817 Transcript missense_variant 892/4299 892/4299 298/1432 H/Y Cat/Tat 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 tolerated(0.36) 8/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 31150215 31150215 G A 1 0 0 0 0 1 0 0 0 11399 1290 45 3 3 OVOS2 12 31150215 Missense_Mutation SNP G C3N-00294_T 4153365 31150215 102125094 826 13598 KIAA1551 0 . GRCh38 12 31982516 31982516 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1561G>C p.Asp521His p.D521H ENST00000312561 4/6 167 125 42 201 201 0 strelka-varscan-mutect KIAA1551,missense_variant,p.Asp521His,ENST00000312561,NM_018169.3;KIAA1551,missense_variant,p.Asp521His,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,;KIAA1551,upstream_gene_variant,,ENST00000543763,; C ENST00000312561 Transcript missense_variant 1975/6230 1561/5244 521/1747 D/H Gat/Cat 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 tolerated(0.13) 4/6 hmmpanther:PTHR21604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 31982516 31982516 G C 1 0 0 0 0 1 0 0 0 8122 1290 45 4 4 KIAA1551 12 31982516 Missense_Mutation SNP G C3N-00294_T 832301 31982516 101292793 827 13599 AMIGO2 0 . GRCh38 12 47077670 47077670 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1333C>G p.Leu445Val p.L445V ENST00000266581 2/2 187 148 39 186 186 0 strelka-varscan-mutect AMIGO2,missense_variant,p.Leu445Val,ENST00000266581,NM_181847.4;AMIGO2,missense_variant,p.Leu445Val,ENST00000429635,NM_001143668.1;AMIGO2,missense_variant,p.Leu445Val,ENST00000550413,;PCED1B,upstream_gene_variant,,ENST00000546455,NM_138371.2;PCED1B,upstream_gene_variant,,ENST00000432328,NM_001281429.1; C ENST00000266581 Transcript missense_variant 1800/3763 1333/1569 445/522 L/V Ctc/Gtc 1 -1 AMIGO2 HGNC HGNC:24073 protein_coding YES CCDS8751.1 ENSP00000266581 Q86SJ2 A0A024R127 UPI000000DC21 NM_181847.4 deleterious(0.01) 2/2 hmmpanther:PTHR24368,hmmpanther:PTHR24368:SF209 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 47077670 47077670 G C 1 0 0 0 0 1 0 0 0 674 942 33 4 4 AMIGO2 12 47077670 Missense_Mutation SNP G C3N-00294_T 15095154 47077670 86197639 828 13600 RHEBL1 0 . GRCh38 12 49065397 49065397 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.415G>C p.Glu139Gln p.E139Q ENST00000301068 7/8 220 186 34 278 278 0 strelka-varscan-mutect RHEBL1,missense_variant,p.Glu139Gln,ENST00000301068,NM_001303126.1,NM_144593.2;RHEBL1,downstream_gene_variant,,ENST00000550675,;RHEBL1,3_prime_UTR_variant,,ENST00000550797,;RHEBL1,3_prime_UTR_variant,,ENST00000420065,; G ENST00000301068 Transcript missense_variant 655/1210 415/552 139/183 E/Q Gag/Cag 1 -1 RHEBL1 HGNC HGNC:21166 protein_coding YES CCDS8778.1 ENSP00000301068 Q8TAI7 UPI00000412A8 NM_001303126.1,NM_144593.2 tolerated(0.16) 7/8 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF253,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 49065397 49065397 C G 1 0 0 0 0 1 0 0 0 13501 922 32 4 4 RHEBL1 12 49065397 Missense_Mutation SNP C C3N-00294_T 1987727 49065397 84209912 829 13601 TUBA1C 0 . GRCh38 12 49272424 49272424 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.757G>C p.Glu253Gln p.E253Q ENST00000541364 4/4 145 111 34 149 149 0 strelka-varscan-mutect TUBA1C,missense_variant,p.Glu183Gln,ENST00000301072,NM_032704.4;TUBA1C,missense_variant,p.Glu253Gln,ENST00000541364,NM_001303114.1;TUBA1C,downstream_gene_variant,,ENST00000549183,;RP11-161H23.5,intron_variant,,ENST00000550468,;TUBA1C,3_prime_UTR_variant,,ENST00000552448,NM_001303116.1;TUBA1C,non_coding_transcript_exon_variant,,ENST00000548470,;TUBA1C,downstream_gene_variant,,ENST00000552125,;TUBA1C,downstream_gene_variant,,ENST00000549818,; C ENST00000541364 Transcript missense_variant 785/1695 757/1560 253/519 E/Q Gag/Cag 1 1 TUBA1C HGNC HGNC:20768 protein_coding YES CCDS76556.1 ENSP00000443475 F5H5D3 UPI000206586E NM_001303114.1 deleterious_low_confidence(0) 4/4 Gene3D:3.40.50.1440,Pfam_domain:PF00091,Prints_domain:PR01161,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF102,SMART_domains:SM00864,Superfamily_domains:SSF52490 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 49272424 49272424 G C 1 0 0 0 0 1 0 0 0 17255 1291 45 4 4 TUBA1C 12 49272424 Missense_Mutation SNP G C3N-00294_T 207027 49272424 84002885 830 13602 AQP5 0 . GRCh38 12 49962050 49962050 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.33C>G p.= p.L11L ENST00000293599 1/4 74 60 14 90 90 0 strelka-varscan-mutect AQP5,synonymous_variant,p.=,ENST00000293599,NM_001651.3;AQP2,downstream_gene_variant,,ENST00000199280,NM_000486.5;RP11-469H8.6,intron_variant,,ENST00000550214,;RP11-469H8.6,intron_variant,,ENST00000552379,;RP11-469H8.6,intron_variant,,ENST00000550530,;AQP2,downstream_gene_variant,,ENST00000551526,;AQP5,upstream_gene_variant,,ENST00000553132,; G ENST00000293599 Transcript synonymous_variant 181/1450 33/798 11/265 L ctC/ctG 1 1 AQP5 HGNC HGNC:638 protein_coding YES CCDS8793.1 ENSP00000293599 P55064 UPI000004A0C9 NM_001651.3 1/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF38,Pfam_domain:PF00230,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338,Prints_domain:PR02017 LOW 1 SNV 1 1 PASS rs1373414214 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 49962050 49962050 C G 1 0 0 0 0 0 0 0 1 952 813 29 4 4 AQP5 12 49962050 Silent SNP C C3N-00294_T 689626 49962050 83313259 831 13603 FAM186A 0 . GRCh38 12 50352241 50352241 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4591C>G p.Leu1531Val p.L1531V ENST00000327337 4/8 102 86 16 129 129 0 strelka-varscan-mutect FAM186A,missense_variant,p.Leu1531Val,ENST00000543111,;FAM186A,missense_variant,p.Leu1531Val,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; C ENST00000327337 Transcript missense_variant 4591/7127 4591/7056 1531/2351 L/V Ctg/Gtg 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 tolerated(0.13) 4/8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 50352241 50352241 G C 1 0 0 0 0 1 0 0 0 5361 933 33 4 4 FAM186A 12 50352241 Missense_Mutation SNP G C3N-00294_T 390191 50352241 82923068 832 13604 FAM186A 0 . GRCh38 12 50353353 50353353 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.3479C>A p.Thr1160Asn p.T1160N ENST00000327337 4/8 124 100 24 114 114 0 strelka-varscan-mutect FAM186A,missense_variant,p.Thr1160Asn,ENST00000543111,;FAM186A,missense_variant,p.Thr1160Asn,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; T ENST00000327337 Transcript missense_variant 3479/7127 3479/7056 1160/2351 T/N aCc/aAc 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 deleterious(0.03) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 50353353 50353353 G T 1 0 0 0 0 1 0 0 0 5361 1261 44 2 2 FAM186A 12 50353353 Missense_Mutation SNP G C3N-00294_T 1112 50353353 82921956 833 13605 CSRNP2 0 . GRCh38 12 51064185 51064185 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1193C>G p.Ser398Ter p.S398* ENST00000228515 5/5 123 94 29 137 137 0 strelka-varscan-mutect CSRNP2,stop_gained,p.Ser398Ter,ENST00000228515,NM_030809.2;LETMD1,downstream_gene_variant,,ENST00000418425,NM_001243689.1;LETMD1,downstream_gene_variant,,ENST00000262055,NM_015416.4;LETMD1,downstream_gene_variant,,ENST00000552739,;LETMD1,downstream_gene_variant,,ENST00000547008,NM_001300765.1;LETMD1,downstream_gene_variant,,ENST00000550929,;LETMD1,downstream_gene_variant,,ENST00000553043,;LETMD1,downstream_gene_variant,,ENST00000551931,;CSRNP2,downstream_gene_variant,,ENST00000548206,;LETMD1,downstream_gene_variant,,ENST00000547256,;LETMD1,downstream_gene_variant,,ENST00000547660,;LETMD1,downstream_gene_variant,,ENST00000623495,;LETMD1,downstream_gene_variant,,ENST00000548516,;LETMD1,downstream_gene_variant,,ENST00000549395,;LETMD1,downstream_gene_variant,,ENST00000547877,;LETMD1,downstream_gene_variant,,ENST00000547318,;LETMD1,downstream_gene_variant,,ENST00000547555,;LETMD1,downstream_gene_variant,,ENST00000552645,;LETMD1,downstream_gene_variant,,ENST00000380135,;LETMD1,downstream_gene_variant,,ENST00000550100,;LETMD1,downstream_gene_variant,,ENST00000546814,;LETMD1,downstream_gene_variant,,ENST00000550274,;LETMD1,downstream_gene_variant,,ENST00000549686,; C ENST00000228515 Transcript stop_gained 1491/4471 1193/1632 398/543 S/* tCa/tGa 1 -1 CSRNP2 HGNC HGNC:16006 protein_coding YES CCDS8807.1 ENSP00000228515 Q9H175 UPI0000073111 NM_030809.2 5/5 hmmpanther:PTHR13580,hmmpanther:PTHR13580:SF6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 51064185 51064185 G C 1 0 0 0 0 0 1 0 0 3765 1294 45 4 4 CSRNP2 12 51064185 Nonsense_Mutation SNP G C3N-00294_T 710832 51064185 82211124 834 13606 KRT5 0 . GRCh38 12 52519811 52519811 + Silent SNP C C T rs762648653 C3N-00294_T C3N-00294_N C C c.486G>A p.= p.Q162Q ENST00000252242 1/9 294 234 60 274 274 0 strelka-varscan-mutect KRT5,synonymous_variant,p.=,ENST00000252242,NM_000424.3;KRT5,synonymous_variant,p.=,ENST00000549420,;KRT5,synonymous_variant,p.=,ENST00000551275,;KRT5,upstream_gene_variant,,ENST00000548409,;KRT5,upstream_gene_variant,,ENST00000551188,;KRT5,downstream_gene_variant,,ENST00000546577,;KRT5,non_coding_transcript_exon_variant,,ENST00000552629,;KRT5,upstream_gene_variant,,ENST00000549511,;KRT5,upstream_gene_variant,,ENST00000551013,;KRT5,upstream_gene_variant,,ENST00000547890,;KRT5,upstream_gene_variant,,ENST00000552952,; T ENST00000252242 Transcript synonymous_variant 877/2531 486/1773 162/590 Q caG/caA rs762648653 1 -1 KRT5 HGNC HGNC:6442 protein_coding YES CCDS8830.1 ENSP00000252242 P13647 UPI000013CD4B NM_000424.3 1/9 hmmpanther:PTHR23239:SF205,hmmpanther:PTHR23239,Pfam_domain:PF16208 LOW 1 SNV 1 1 PASS rs762648653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 52519811 52519811 C T 1 0 0 0 0 0 0 0 1 8361 912 32 3 3 KRT5 12 52519811 Silent SNP C C3N-00294_T 1455626 52519811 80755498 835 13607 HOXC13 0 . GRCh38 12 53939171 53939171 + Nonsense_Mutation SNP C C T rs751014305 C3N-00294_T C3N-00294_N C C c.265C>T p.Gln89Ter p.Q89* ENST00000243056 1/2 106 100 6 96 96 0 strelka-varscan-mutect HOXC13,stop_gained,p.Gln89Ter,ENST00000243056,NM_017410.2;HOXC13-AS,intron_variant,,ENST00000512916,; T ENST00000243056 Transcript stop_gained 407/2423 265/993 89/330 Q/* Cag/Tag rs751014305 1 1 HOXC13 HGNC HGNC:5125 protein_coding YES CCDS8865.1 ENSP00000243056 P31276 UPI000012CF7F NM_017410.2 1/2 Pfam_domain:PF12284,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF39 HIGH 1 SNV 1 1 PASS rs751014305 . 0 205 4 0 0 0 0 0 -12.34191 1 1 1 1 0 T 4 4 46 53939171 53939171 C T 1 0 0 0 0 0 1 0 0 7206 827 29 3 3 HOXC13 12 53939171 Nonsense_Mutation SNP C C3N-00294_T 1419360 53939171 79336138 836 13608 CBX5 0 . GRCh38 12 54257616 54257616 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.35C>G p.Ser12Cys p.S12C ENST00000209875 2/5 207 162 45 181 181 0 strelka-varscan-mutect CBX5,missense_variant,p.Ser12Cys,ENST00000209875,NM_012117.2;CBX5,missense_variant,p.Ser12Cys,ENST00000439541,NM_001127321.1;CBX5,missense_variant,p.Ser12Cys,ENST00000550411,NM_001127322.1;CBX5,missense_variant,p.Ser12Cys,ENST00000552562,;RP11-968A15.2,upstream_gene_variant,,ENST00000547177,;RN7SL390P,upstream_gene_variant,,ENST00000470634,; C ENST00000209875 Transcript missense_variant 172/11528 35/576 12/191 S/C tCt/tGt 1 -1 CBX5 HGNC HGNC:1555 protein_coding YES CCDS8875.1 ENSP00000209875 P45973 V9HWG0 UPI00001271FC NM_012117.2 tolerated(0.05) 2/5 Gene3D:2.40.50.40,hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF85,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 54257616 54257616 G C 1 0 0 0 0 1 0 0 0 2421 942 33 4 4 CBX5 12 54257616 Missense_Mutation SNP G C3N-00294_T 318445 54257616 79017693 837 13609 GDF11 0 . GRCh38 12 55749612 55749612 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.954C>T p.= p.L318L ENST00000257868 3/3 206 161 45 223 223 0 strelka-varscan-mutect GDF11,synonymous_variant,p.=,ENST00000257868,NM_005811.3;GDF11,synonymous_variant,p.=,ENST00000546799,;SARNP,downstream_gene_variant,,ENST00000546604,;SARNP,downstream_gene_variant,,ENST00000552884,; T ENST00000257868 Transcript synonymous_variant 991/8657 954/1224 318/407 L ctC/ctT COSM1253148 1 1 GDF11 HGNC HGNC:4216 protein_coding YES CCDS8891.1 ENSP00000257868 O95390 A0A024RB20 UPI000004C158 NM_005811.3 3/3 PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF166,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 55749612 55749612 C T 1 0 0 0 0 0 0 0 1 6185 813 29 3 3 GDF11 12 55749612 Silent SNP C C3N-00294_T 1491996 55749612 77525697 838 13610 STAT2 0 . GRCh38 12 56349508 56349508 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1259G>A p.Gly420Glu p.G420E ENST00000314128 15/24 179 137 42 214 214 0 strelka-varscan-mutect STAT2,missense_variant,p.Gly420Glu,ENST00000314128,NM_005419.3;STAT2,missense_variant,p.Gly416Glu,ENST00000557235,NM_198332.1;STAT2,missense_variant,p.Gly416Glu,ENST00000418572,;RNU7-40P,downstream_gene_variant,,ENST00000516397,;STAT2,splice_region_variant,,ENST00000556539,;STAT2,downstream_gene_variant,,ENST00000557252,;STAT2,downstream_gene_variant,,ENST00000557156,;STAT2,splice_region_variant,,ENST00000555519,;STAT2,downstream_gene_variant,,ENST00000556140,;STAT2,upstream_gene_variant,,ENST00000557199,;STAT2,upstream_gene_variant,,ENST00000555488,; T ENST00000314128 Transcript missense_variant,splice_region_variant 1283/3259 1259/2556 420/851 G/E gGg/gAg 1 -1 STAT2 HGNC HGNC:11363 protein_coding YES CCDS8917.1 ENSP00000315768 P52630 R9QE65 UPI00000473FC NM_005419.3 deleterious(0.01) 15/24 Gene3D:2.60.40.630,Pfam_domain:PF02864,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF41,Low_complexity_(Seg):seg,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 56349508 56349508 C T 1 0 0 0 0 1 0 0 0 15641 637 22 3 3 STAT2 12 56349508 Missense_Mutation SNP C C3N-00294_T 599896 56349508 76925801 839 13611 NACA 0 . GRCh38 12 56713151 56713151 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2551G>A p.Glu851Lys p.E851K ENST00000550952 9/11 217 183 34 229 229 0 strelka-varscan-mutect NACA,missense_variant,p.Glu2004Lys,ENST00000454682,;NACA,missense_variant,p.Glu851Lys,ENST00000550952,NM_001113203.2;NACA,missense_variant,p.Glu141Lys,ENST00000356769,NM_001113202.1;NACA,missense_variant,p.Glu141Lys,ENST00000552540,NM_001113201.2;NACA,missense_variant,p.Glu141Lys,ENST00000393891,NM_005594.5;NACA,missense_variant,p.Glu62Lys,ENST00000548563,;NACA,missense_variant,p.Glu141Lys,ENST00000546392,;NACA,missense_variant,p.Glu139Lys,ENST00000550920,;NACA,missense_variant,p.Glu141Lys,ENST00000549259,;NACA,missense_variant,p.Glu137Lys,ENST00000552055,;NACA,missense_variant,p.Glu62Lys,ENST00000546862,;NACA,downstream_gene_variant,,ENST00000549855,;NACA,non_coding_transcript_exon_variant,,ENST00000548386,;NACA,non_coding_transcript_exon_variant,,ENST00000551775,;NACA,downstream_gene_variant,,ENST00000551793,;NACA,downstream_gene_variant,,ENST00000550343,;NACA,3_prime_UTR_variant,,ENST00000547914,;NACA,non_coding_transcript_exon_variant,,ENST00000546410,;NACA,downstream_gene_variant,,ENST00000551520,;NACA,downstream_gene_variant,,ENST00000548084,; T ENST00000550952 Transcript missense_variant 2590/2922 2551/2778 851/925 E/K Gag/Aag 1 -1 NACA HGNC HGNC:7629 protein_coding YES CCDS44925.2 ENSP00000448035 E9PAV3 UPI000014145D NM_001113203.2 deleterious_low_confidence(0.03) 9/11 hmmpanther:PTHR21713:SF3,hmmpanther:PTHR21713 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 56713151 56713151 C T 1 0 0 0 0 1 0 0 0 10139 835 29 3 3 NACA 12 56713151 Missense_Mutation SNP C C3N-00294_T 363643 56713151 76562158 840 13612 GLI1 0 . GRCh38 12 57467386 57467386 + Silent SNP G G T rs377325662 C3N-00294_T C3N-00294_N G G c.966G>T p.= p.L322L ENST00000228682 9/12 160 120 40 137 137 0 strelka-varscan-mutect GLI1,synonymous_variant,p.=,ENST00000228682,NM_005269.2;GLI1,synonymous_variant,p.=,ENST00000546141,NM_001167609.1;GLI1,synonymous_variant,p.=,ENST00000543426,NM_001160045.1;GLI1,synonymous_variant,p.=,ENST00000528467,;ARHGAP9,downstream_gene_variant,,ENST00000393797,NM_001319850.1;ARHGAP9,downstream_gene_variant,,ENST00000550288,;ARHGAP9,downstream_gene_variant,,ENST00000393791,NM_032496.2;ARHGAP9,downstream_gene_variant,,ENST00000424809,NM_001080157.1;ARHGAP9,downstream_gene_variant,,ENST00000430041,NM_001080156.1;GLI1,downstream_gene_variant,,ENST00000532291,;ARHGAP9,downstream_gene_variant,,ENST00000550399,;GLI1,downstream_gene_variant,,ENST00000528432,;ARHGAP9,downstream_gene_variant,,ENST00000546200,;ARHGAP9,downstream_gene_variant,,ENST00000552953,;GLI1,downstream_gene_variant,,ENST00000527742,;GLI1,downstream_gene_variant,,ENST00000530789,; T ENST00000228682 Transcript synonymous_variant 1057/3613 966/3321 322/1106 L ctG/ctT rs377325662 1 1 GLI1 HGNC HGNC:4317 protein_coding YES CCDS8940.1 ENSP00000228682 P08151 UPI000012B607 NM_005269.2 9/12 PROSITE_profiles:PS50157,hmmpanther:PTHR19818:SF2,hmmpanther:PTHR19818,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs377325662 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 57467386 57467386 G T 1 0 0 0 0 0 0 0 1 6315 1306 46 2 2 GLI1 12 57467386 Silent SNP G C3N-00294_T 754235 57467386 75807923 841 13613 ARHGEF25 0 . GRCh38 12 57616787 57616787 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.1753C>A p.Leu585Ile p.L585I ENST00000333972 16/16 57 45 12 56 56 0 strelka-varscan-mutect ARHGEF25,missense_variant,p.Leu546Ile,ENST00000286494,NM_182947.3;ARHGEF25,missense_variant,p.Leu585Ile,ENST00000333972,NM_001111270.2;ARHGEF25,missense_variant,p.Leu440Ile,ENST00000616622,;SLC26A10,upstream_gene_variant,,ENST00000320442,NM_133489.2;SLC26A10,upstream_gene_variant,,ENST00000637859,;AC025165.8,intron_variant,,ENST00000356672,;AC025165.8,intron_variant,,ENST00000444467,;AC025165.8,intron_variant,,ENST00000593846,;AC025165.8,upstream_gene_variant,,ENST00000610219,;ARHGEF25,non_coding_transcript_exon_variant,,ENST00000477314,;ARHGEF25,non_coding_transcript_exon_variant,,ENST00000471370,;SLC26A10,upstream_gene_variant,,ENST00000474359,;SLC26A10,upstream_gene_variant,,ENST00000440686,;ARHGEF25,downstream_gene_variant,,ENST00000469072,;ARHGEF25,downstream_gene_variant,,ENST00000466399,;SLC26A10,upstream_gene_variant,,ENST00000497297,;SLC26A10,upstream_gene_variant,,ENST00000463802,;ARHGEF25,downstream_gene_variant,,ENST00000484357,; A ENST00000333972 Transcript missense_variant 1790/2246 1753/1860 585/619 L/I Ctt/Att COSM1147083,COSM694936 1 1 ARHGEF25 HGNC HGNC:30275 protein_coding YES CCDS44931.1 ENSP00000335560 Q86VW2 UPI000173A6BB NM_001111270.2 tolerated_low_confidence(0.1) 16/16 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF117 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999968 1 1 1 0 A 3 1 46 57616787 57616787 C A 1 0 0 0 0 1 0 0 0 1034 695 24 2 2 ARHGEF25 12 57616787 Missense_Mutation SNP C C3N-00294_T 149401 57616787 75658522 842 13614 CAND1 0 . GRCh38 12 67306036 67306036 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.2368C>T p.Leu790Phe p.L790F ENST00000545606 10/15 170 137 33 191 191 0 strelka-varscan-mutect CAND1,missense_variant,p.Leu790Phe,ENST00000545606,NM_018448.4;CAND1,missense_variant,p.Leu330Phe,ENST00000544619,;CAND1,intron_variant,,ENST00000540319,; T ENST00000545606 Transcript missense_variant 2805/11251 2368/3693 790/1230 L/F Ctt/Ttt COSM4479861 1 1 CAND1 HGNC HGNC:30688 protein_coding YES CCDS8977.1 ENSP00000442318 Q86VP6 UPI0000037CC5 NM_018448.4 tolerated(0.71) 10/15 hmmpanther:PTHR12696,hmmpanther:PTHR12696:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67306036 67306036 C T 1 0 0 0 0 1 0 0 0 2308 913 32 3 3 CAND1 12 67306036 Missense_Mutation SNP C C3N-00294_T 9689249 67306036 65969273 843 13615 LGR5 0 . GRCh38 12 71504626 71504626 + Missense_Mutation SNP G G A rs776624521 C3N-00294_T C3N-00294_N G G c.225G>A p.Met75Ile p.M75I ENST00000266674 2/18 220 190 30 264 264 0 strelka-varscan-mutect LGR5,missense_variant,p.Met75Ile,ENST00000266674,NM_003667.3;LGR5,missense_variant,p.Met75Ile,ENST00000540815,NM_001277226.1;LGR5,missense_variant,p.Met75Ile,ENST00000536515,NM_001277227.1;LGR5,non_coding_transcript_exon_variant,,ENST00000550851,; A ENST00000266674 Transcript missense_variant 536/4611 225/2724 75/907 M/I atG/atA rs776624521,COSM1705930 1 1 LGR5 HGNC HGNC:4504 protein_coding YES CCDS9000.1 ENSP00000266674 O75473 A0A0A8K8C7 UPI000004B65C NM_003667.3 deleterious(0) 2/18 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF259,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776624521 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 71504626 71504626 G A 1 0 0 0 0 1 0 0 0 8667 1290 45 3 3 LGR5 12 71504626 Missense_Mutation SNP G C3N-00294_T 4198590 71504626 61770683 844 13616 CEP290 0 . GRCh38 12 88049351 88049351 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.7273G>T p.Glu2425Ter p.E2425* ENST00000552810 54/54 89 77 12 161 161 0 strelka-mutect CEP290,stop_gained,p.Glu2425Ter,ENST00000552810,NM_025114.3;CEP290,stop_gained,p.Glu2427Ter,ENST00000309041,;CEP290,stop_gained,p.Glu1485Ter,ENST00000547691,;C12orf29,3_prime_UTR_variant,,ENST00000356891,NM_001009894.2;RNA5SP364,upstream_gene_variant,,ENST00000516938,;C12orf29,downstream_gene_variant,,ENST00000548757,;C12orf29,downstream_gene_variant,,ENST00000549345,;C12orf29,3_prime_UTR_variant,,ENST00000550333,;C12orf29,downstream_gene_variant,,ENST00000548511,;C12orf29,downstream_gene_variant,,ENST00000547468,;C12orf29,downstream_gene_variant,,ENST00000552121,;C12orf29,downstream_gene_variant,,ENST00000552847,;C12orf29,downstream_gene_variant,,ENST00000453037,; A ENST00000552810 Transcript stop_gained 7617/7948 7273/7440 2425/2479 E/* Gaa/Taa 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 54/54 hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 88049351 88049351 C A 1 0 0 0 0 0 1 0 0 2969 835 29 2 2 CEP290 12 88049351 Nonsense_Mutation SNP C C3N-00294_T 16544725 88049351 45225958 845 13617 CEP290 0 . GRCh38 12 88131212 88131212 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.448C>G p.Leu150Val p.L150V ENST00000552810 7/54 41 35 6 88 88 0 strelka-varscan-mutect CEP290,missense_variant,p.Leu150Val,ENST00000552810,NM_025114.3;CEP290,missense_variant,p.Leu150Val,ENST00000309041,;CEP290,missense_variant,p.Leu150Val,ENST00000397838,;CEP290,intron_variant,,ENST00000550962,;CEP290,upstream_gene_variant,,ENST00000604024,;CEP290,downstream_gene_variant,,ENST00000552770,;CEP290,missense_variant,p.Leu116Val,ENST00000547926,; C ENST00000552810 Transcript missense_variant 792/7948 448/7440 150/2479 L/V Ctt/Gtt 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 tolerated(0.23) 7/54 Low_complexity_(Seg):seg,hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS rs1162631374 . 0 207 3 0 0 0 0 0 -15.42737 1 1 1 1 0 C 3 2 46 88131212 88131212 G C 1 0 0 0 0 1 0 0 0 2969 942 33 4 4 CEP290 12 88131212 Missense_Mutation SNP G C3N-00294_T 81861 88131212 45144097 846 13618 LTA4H 0 . GRCh38 12 96018904 96018904 + Splice_Site SNP C C A novel C3N-00294_T C3N-00294_N C C c.712-1G>T p.X238_splice ENST00000228740 53 36 17 56 56 0 strelka-varscan-mutect LTA4H,splice_acceptor_variant,,ENST00000228740,NM_000895.2;LTA4H,splice_acceptor_variant,,ENST00000552789,NM_001256643.1;LTA4H,splice_acceptor_variant,,ENST00000413268,NM_001256644.1;LTA4H,upstream_gene_variant,,ENST00000548375,;LTA4H,splice_acceptor_variant,,ENST00000553041,;LTA4H,splice_acceptor_variant,,ENST00000548852,;LTA4H,upstream_gene_variant,,ENST00000547982,;LTA4H,upstream_gene_variant,,ENST00000552091,; A ENST00000228740 Transcript splice_acceptor_variant -/2139 712/1836 238/611 1 -1 LTA4H HGNC HGNC:6710 protein_coding YES CCDS9059.1 ENSP00000228740 P09960 A0A140VK27 UPI0000111C40 NM_000895.2 7/18 HIGH 1 SNV 1 1 PASS . . 0 186 22 2 0 0 0 0 -20 0.994133 0 1 1 0 A 5 1 46 96018904 96018904 C A 1 0 0 0 0 0 0 1 0 8975 927 32 2 2 LTA4H 12 96018904 Splice_Site SNP C C3N-00294_T 7887692 96018904 37256405 847 13619 TMPO 0 . GRCh38 12 98516140 98516140 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.273C>T p.= p.V91V ENST00000266732 1/4 43 38 5 42 42 0 strelka-varscan-mutect TMPO,synonymous_variant,p.=,ENST00000556029,NM_001032283.2;TMPO,synonymous_variant,p.=,ENST00000266732,NM_003276.2;TMPO,synonymous_variant,p.=,ENST00000343315,NM_001307975.1;TMPO,synonymous_variant,p.=,ENST00000393053,NM_001032284.2;TMPO,synonymous_variant,p.=,ENST00000261210,;TMPO-AS1,non_coding_transcript_exon_variant,,ENST00000548760,;TMPO-AS1,non_coding_transcript_exon_variant,,ENST00000546421,;TMPO,non_coding_transcript_exon_variant,,ENST00000546828,;TMPO,non_coding_transcript_exon_variant,,ENST00000548911,;TMPO,upstream_gene_variant,,ENST00000549938,; T ENST00000266732 Transcript synonymous_variant 511/3615 273/2085 91/694 V gtC/gtT 1 1 TMPO HGNC HGNC:11875 protein_coding YES CCDS9064.1 ENSP00000266732 P42166 UPI000013D709 NM_003276.2 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR12019:SF10,hmmpanther:PTHR12019 LOW 1 SNV 1 1 PASS rs1459534403 . 0 204 5 0 0 0 0 0 -12.78865 1 1 1 1 0 T 2 4 46 98516140 98516140 C T 1 0 0 0 0 0 0 0 1 16713 871 31 1 1 TMPO 12 98516140 Silent SNP C C3N-00294_T 2497236 98516140 34759169 848 13620 TMPO 0 . GRCh38 12 98533999 98533999 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.1742A>T p.Gln581Leu p.Q581L ENST00000266732 4/4 67 38 29 84 84 0 strelka-varscan-mutect TMPO,missense_variant,p.Gln581Leu,ENST00000266732,NM_003276.2;TMPO,intron_variant,,ENST00000556029,NM_001032283.2;TMPO,intron_variant,,ENST00000343315,NM_001307975.1;TMPO,intron_variant,,ENST00000393053,NM_001032284.2;TMPO,intron_variant,,ENST00000261210,;TMPO,intron_variant,,ENST00000556678,;TMPO,downstream_gene_variant,,ENST00000547214,;TMPO,downstream_gene_variant,,ENST00000549938,;TMPO,downstream_gene_variant,,ENST00000546828,;TMPO,intron_variant,,ENST00000552831,; T ENST00000266732 Transcript missense_variant 1980/3615 1742/2085 581/694 Q/L cAg/cTg 1 1 TMPO HGNC HGNC:11875 protein_coding YES CCDS9064.1 ENSP00000266732 P42166 UPI000013D709 NM_003276.2 deleterious_low_confidence(0.02) 4/4 hmmpanther:PTHR12019,hmmpanther:PTHR12019:SF10,Pfam_domain:PF11560 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 98533999 98533999 A T 1 0 0 0 0 1 0 0 0 16713 188 7 4 4 TMPO 12 98533999 Missense_Mutation SNP A C3N-00294_T 17859 98533999 34741310 849 13621 TMPO 0 . GRCh38 12 98545054 98545054 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.983G>C p.Arg328Thr p.R328T ENST00000556029 7/9 186 175 11 267 266 1 strelka-varscan-mutect TMPO,missense_variant,p.Arg328Thr,ENST00000556029,NM_001032283.2;TMPO,missense_variant,p.Arg288Thr,ENST00000343315,NM_001307975.1;TMPO,missense_variant,p.Arg163Thr,ENST00000556678,;TMPO,intron_variant,,ENST00000393053,NM_001032284.2;TMPO,non_coding_transcript_exon_variant,,ENST00000548223,;TMPO,non_coding_transcript_exon_variant,,ENST00000551987,; C ENST00000556029 Transcript missense_variant 1339/4242 983/1365 328/454 R/T aGa/aCa 1 1 TMPO HGNC HGNC:11875 protein_coding CCDS31879.1 ENSP00000450627 P42167 A0A024RBE7 UPI0000143267 NM_001032283.2 tolerated(0.66) 7/9 hmmpanther:PTHR12019,hmmpanther:PTHR12019:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 98545054 98545054 G C 1 0 0 0 0 1 0 0 0 16713 942 33 4 4 TMPO 12 98545054 Missense_Mutation SNP G C3N-00294_T 11055 98545054 34730255 850 13622 IKBIP 0 . GRCh38 12 98644633 98644633 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.69G>T p.= p.R23R ENST00000299157 1/3 126 103 23 165 165 0 strelka-varscan-mutect IKBIP,synonymous_variant,p.=,ENST00000299157,NM_153687.3;IKBIP,synonymous_variant,p.=,ENST00000342502,NM_201612.2;IKBIP,synonymous_variant,p.=,ENST00000393042,NM_201613.2;APAF1,upstream_gene_variant,,ENST00000357310,NM_181868.1;APAF1,upstream_gene_variant,,ENST00000359972,NM_001160.2;APAF1,upstream_gene_variant,,ENST00000550527,NM_013229.2;APAF1,upstream_gene_variant,,ENST00000551964,NM_181861.1;APAF1,upstream_gene_variant,,ENST00000333991,NM_181869.1;APAF1,upstream_gene_variant,,ENST00000547045,;APAF1,upstream_gene_variant,,ENST00000549007,;APAF1,upstream_gene_variant,,ENST00000552268,;APAF1,upstream_gene_variant,,ENST00000547743,; A ENST00000299157 Transcript synonymous_variant 443/3189 69/1134 23/377 R cgG/cgT 1 -1 IKBIP HGNC HGNC:26430 protein_coding YES CCDS9068.1 ENSP00000299157 Q70UQ0 UPI0000070C12 NM_153687.3 1/3 hmmpanther:PTHR21734:SF11,hmmpanther:PTHR21734 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 98644633 98644633 C A 1 0 0 0 0 0 0 0 1 7517 842 30 2 2 IKBIP 12 98644633 Silent SNP C C3N-00294_T 99579 98644633 34630676 851 13623 UHRF1BP1L 0 . GRCh38 12 100039754 100039754 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.4117G>C p.Glu1373Gln p.E1373Q ENST00000279907 20/21 152 118 34 148 148 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Glu1373Gln,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Glu1023Gln,ENST00000545232,;UHRF1BP1L,missense_variant,p.Glu134Gln,ENST00000548712,; G ENST00000279907 Transcript missense_variant 4330/5168 4117/4395 1373/1464 E/Q Gaa/Caa 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 tolerated(0.42) 20/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 100039754 100039754 C G 1 0 0 0 0 1 0 0 0 17493 922 32 4 4 UHRF1BP1L 12 100039754 Missense_Mutation SNP C C3N-00294_T 1395121 100039754 33235555 852 13624 SCYL2 0 . GRCh38 12 100314568 100314568 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1049C>T p.Ser350Leu p.S350L ENST00000360820 8/18 108 82 26 169 169 0 strelka-varscan-mutect SCYL2,missense_variant,p.Ser350Leu,ENST00000360820,NM_001317784.1,NM_017988.4;SCYL2,missense_variant,p.Ser350Leu,ENST00000635101,;SCYL2,missense_variant,p.Ser350Leu,ENST00000549687,;SCYL2,downstream_gene_variant,,ENST00000548392,;SCYL2,upstream_gene_variant,,ENST00000553148,;SCYL2,upstream_gene_variant,,ENST00000550251,; T ENST00000360820 Transcript missense_variant 1486/5779 1049/2790 350/929 S/L tCa/tTa 1 1 SCYL2 HGNC HGNC:19286 protein_coding YES CCDS9076.1 ENSP00000354061 Q6P3W7 UPI000004FD59 NM_001317784.1,NM_017988.4 deleterious(0) 8/18 hmmpanther:PTHR12984:SF6,hmmpanther:PTHR12984,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 100314568 100314568 C T 1 0 0 0 0 1 0 0 0 14220 838 29 3 3 SCYL2 12 100314568 Missense_Mutation SNP C C3N-00294_T 274814 100314568 32960741 853 13625 ACAD10 0 . GRCh38 12 111747174 111747174 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2475G>C p.Met825Ile p.M825I ENST00000455480 16/22 65 54 11 55 55 0 strelka-varscan-mutect ACAD10,missense_variant,p.Met825Ile,ENST00000455480,NM_001136538.1;ACAD10,missense_variant,p.Met794Ile,ENST00000313698,NM_025247.5;ACAD10,downstream_gene_variant,,ENST00000549590,;ACAD10,downstream_gene_variant,,ENST00000507683,;ACAD10,downstream_gene_variant,,ENST00000515283,;ACAD10,non_coding_transcript_exon_variant,,ENST00000413681,;ACAD10,non_coding_transcript_exon_variant,,ENST00000508303,;ACAD10,non_coding_transcript_exon_variant,,ENST00000550198,;ACAD10,non_coding_transcript_exon_variant,,ENST00000505487,;ACAD10,upstream_gene_variant,,ENST00000507688,;ACAD10,non_coding_transcript_exon_variant,,ENST00000504803,;ACAD10,non_coding_transcript_exon_variant,,ENST00000546647,;ACAD10,upstream_gene_variant,,ENST00000547491,;ACAD10,downstream_gene_variant,,ENST00000552177,; C ENST00000455480 Transcript missense_variant 2652/4071 2475/3273 825/1090 M/I atG/atC COSM5316218,COSM5316219,COSM5316220 1 1 ACAD10 HGNC HGNC:21597 protein_coding YES CCDS44973.1 ENSP00000389813 Q6JQN1 UPI000013F5E7 NM_001136538.1 deleterious(0.01) 16/22 hmmpanther:PTHR10909:SF221,hmmpanther:PTHR10909,Pfam_domain:PF02770,Gene3D:2.40.110.10,Superfamily_domains:SSF56645 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 111747174 111747174 G C 1 0 0 0 0 1 0 0 0 151 1290 45 4 4 ACAD10 12 111747174 Missense_Mutation SNP G C3N-00294_T 11432606 111747174 21528135 854 13626 SDS 0 . GRCh38 12 113393055 113393055 + Silent SNP G G T novel C3N-00294_T C3N-00294_N G G c.873C>A p.= p.L291L ENST00000257549 8/8 216 123 93 213 213 0 strelka-varscan-mutect SDS,synonymous_variant,p.=,ENST00000257549,NM_006843.2;PLBD2,downstream_gene_variant,,ENST00000280800,NM_173542.3;PLBD2,downstream_gene_variant,,ENST00000545182,NM_001159727.1;SDS,downstream_gene_variant,,ENST00000552280,;SDS,downstream_gene_variant,,ENST00000553112,; T ENST00000257549 Transcript synonymous_variant 996/1606 873/987 291/328 L ctC/ctA 1 -1 SDS HGNC HGNC:10691 protein_coding YES CCDS9169.1 ENSP00000257549 P20132 UPI000013CF6B NM_006843.2 8/8 hmmpanther:PTHR10314:SF103,hmmpanther:PTHR10314,Pfam_domain:PF00291,Gene3D:3.40.50.1100,Superfamily_domains:SSF53686 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 113393055 113393055 G T 1 0 0 0 0 0 0 0 1 14251 1161 41 2 2 SDS 12 113393055 Silent SNP G C3N-00294_T 1645881 113393055 19882254 855 13627 GCN1 0 . GRCh38 12 120137934 120137934 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.6360G>A p.= p.L2120L ENST00000300648 48/58 121 96 25 162 162 0 strelka-varscan-mutect GCN1,synonymous_variant,p.=,ENST00000300648,NM_006836.1;GCN1,upstream_gene_variant,,ENST00000549815,;GCN1,downstream_gene_variant,,ENST00000547263,; T ENST00000300648 Transcript synonymous_variant 6373/8675 6360/8016 2120/2671 L ctG/ctA 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 48/58 hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 120137934 120137934 C T 1 0 0 0 0 0 0 0 1 6169 813 29 3 3 GCN1 12 120137934 Silent SNP C C3N-00294_T 6744879 120137934 13137375 856 13628 MLXIP 0 . GRCh38 12 122135578 122135578 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1944C>T p.= p.L648L ENST00000319080 11/17 104 79 25 93 93 0 strelka-varscan-mutect MLXIP,synonymous_variant,p.=,ENST00000319080,NM_014938.5;MLXIP,synonymous_variant,p.=,ENST00000538698,;MLXIP,synonymous_variant,p.=,ENST00000366272,;MLXIP,downstream_gene_variant,,ENST00000535430,;MLXIP,downstream_gene_variant,,ENST00000377037,;MLXIP,upstream_gene_variant,,ENST00000542417,;MLXIP,downstream_gene_variant,,ENST00000535996,;MLXIP,non_coding_transcript_exon_variant,,ENST00000541750,;MLXIP,downstream_gene_variant,,ENST00000539861,;MLXIP,downstream_gene_variant,,ENST00000538061,; T ENST00000319080 Transcript synonymous_variant 2076/8427 1944/2760 648/919 L ctC/ctT 1 1 MLXIP HGNC HGNC:17055 protein_coding YES CCDS73540.1 ENSP00000312834 Q9HAP2 UPI0000D6226F NM_014938.5 11/17 hmmpanther:PTHR15741,hmmpanther:PTHR15741:SF23 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 122135578 122135578 C T 1 0 0 0 0 0 0 0 1 9599 900 32 3 3 MLXIP 12 122135578 Silent SNP C C3N-00294_T 1997644 122135578 11139731 857 13629 LRRC43 0 . GRCh38 12 122192788 122192788 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1133C>T p.Ser378Phe p.S378F ENST00000339777 7/12 203 165 38 253 253 0 strelka-varscan-mutect LRRC43,missense_variant,p.Ser378Phe,ENST00000339777,NM_152759.4,NM_001098519.1;LRRC43,downstream_gene_variant,,ENST00000537729,;LRRC43,intron_variant,,ENST00000541498,;LRRC43,downstream_gene_variant,,ENST00000537113,; T ENST00000339777 Transcript missense_variant 1161/2028 1133/1971 378/656 S/F tCt/tTt 1 1 LRRC43 HGNC HGNC:28562 protein_coding YES CCDS45001.1 ENSP00000344233 Q8N309 UPI00015347BE NM_152759.4,NM_001098519.1 tolerated(0.41) 7/12 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 122192788 122192788 C T 1 0 0 0 0 1 0 0 0 8897 913 32 3 3 LRRC43 12 122192788 Missense_Mutation SNP C C3N-00294_T 57210 122192788 11082521 858 13630 B3GNT4 0 . GRCh38 12 122207187 122207187 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.936G>C p.= p.L312L ENST00000324189 3/3 92 74 18 102 102 0 strelka-varscan-mutect B3GNT4,synonymous_variant,p.=,ENST00000535274,;B3GNT4,synonymous_variant,p.=,ENST00000546192,;B3GNT4,synonymous_variant,p.=,ENST00000324189,NM_030765.2;DIABLO,downstream_gene_variant,,ENST00000464942,NM_001278304.1;DIABLO,downstream_gene_variant,,ENST00000443649,NM_019887.5;LRRC43,downstream_gene_variant,,ENST00000339777,NM_152759.4,NM_001098519.1;DIABLO,downstream_gene_variant,,ENST00000413918,NM_001278303.1;DIABLO,downstream_gene_variant,,ENST00000353548,NM_001278342.1;DIABLO,downstream_gene_variant,,ENST00000267169,NM_138930.3;DIABLO,downstream_gene_variant,,ENST00000474004,;DIABLO,downstream_gene_variant,,ENST00000541656,;DIABLO,downstream_gene_variant,,ENST00000540535,;DIABLO,downstream_gene_variant,,ENST00000439489,;DIABLO,downstream_gene_variant,,ENST00000446652,;DIABLO,downstream_gene_variant,,ENST00000541273,NM_001278302.1;B3GNT4,intron_variant,,ENST00000545141,;LRRC43,downstream_gene_variant,,ENST00000537733,;B3GNT4,downstream_gene_variant,,ENST00000537991,;B3GNT4,downstream_gene_variant,,ENST00000538257,;RP11-512M8.5,downstream_gene_variant,,ENST00000535844,;DIABLO,downstream_gene_variant,,ENST00000342392,; C ENST00000324189 Transcript synonymous_variant 1292/1642 936/1137 312/378 L ctG/ctC 1 1 B3GNT4 HGNC HGNC:15683 protein_coding YES CCDS9227.1 ENSP00000319636 Q9C0J1 A0A024RBT1 UPI0000051E30 NM_030765.2 3/3 hmmpanther:PTHR11214:SF137,hmmpanther:PTHR11214,Pfam_domain:PF01762 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 122207187 122207187 G C 1 0 0 0 0 0 0 0 1 1415 1277 45 4 4 B3GNT4 12 122207187 Silent SNP G C3N-00294_T 14399 122207187 11068122 859 13631 KNTC1 0 . GRCh38 12 122568298 122568298 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.1642G>A p.Asp548Asn p.D548N ENST00000333479 21/64 97 79 18 158 158 0 strelka-varscan-mutect KNTC1,missense_variant,p.Asp548Asn,ENST00000333479,NM_014708.4;KNTC1,missense_variant,p.Asp511Asn,ENST00000450485,;RP11-324E6.8,upstream_gene_variant,,ENST00000543745,; A ENST00000333479 Transcript missense_variant 1819/6975 1642/6630 548/2209 D/N Gat/Aat COSM4816979 1 1 KNTC1 HGNC HGNC:17255 protein_coding YES CCDS45002.1 ENSP00000328236 P50748 UPI0000047FD6 NM_014708.4 tolerated(0.31) 21/64 hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 122568298 122568298 G A 1 0 0 0 0 1 0 0 0 8308 1290 45 3 3 KNTC1 12 122568298 Missense_Mutation SNP G C3N-00294_T 361111 122568298 10707011 860 13632 TCTN2 0 . GRCh38 12 123671307 123671307 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.67C>T p.= p.L23L ENST00000303372 1/18 328 296 32 372 372 0 strelka-varscan-mutect TCTN2,synonymous_variant,p.=,ENST00000303372,NM_024809.4;TCTN2,synonymous_variant,p.=,ENST00000426174,NM_001143850.2;TCTN2,synonymous_variant,p.=,ENST00000541523,; T ENST00000303372 Transcript synonymous_variant 195/2912 67/2094 23/697 L Ctg/Ttg 1 1 TCTN2 HGNC HGNC:25774 protein_coding YES CCDS9253.1 ENSP00000304941 Q96GX1 UPI0000038A56 NM_024809.4 1/18 hmmpanther:PTHR14611,hmmpanther:PTHR14611:SF2,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 123671307 123671307 C T 1 0 0 0 0 0 0 0 1 16131 912 32 3 3 TCTN2 12 123671307 Silent SNP C C3N-00294_T 1103009 123671307 9604002 861 13633 DNAH10 0 . GRCh38 12 123879314 123879314 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.8069G>A p.Arg2690Lys p.R2690K ENST00000638045 48/78 153 124 29 149 149 0 strelka-varscan-mutect DNAH10,missense_variant,p.Arg2751Lys,ENST00000409039,;DNAH10,missense_variant,p.Arg2690Lys,ENST00000638045,NM_207437.3;DNAH10,3_prime_UTR_variant,,ENST00000497783,; A ENST00000638045 Transcript missense_variant 8094/13678 8069/13416 2690/4471 R/K aGa/aAa 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0) 48/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 123879314 123879314 G A 1 0 0 0 0 1 0 0 0 4411 942 33 3 3 DNAH10 12 123879314 Missense_Mutation SNP G C3N-00294_T 208007 123879314 9395995 862 13634 TMEM132D 0 . GRCh38 12 129699977 129699977 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.801C>T p.= p.I267I ENST00000422113 2/9 302 233 69 297 297 0 strelka-varscan-mutect TMEM132D,synonymous_variant,p.=,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript synonymous_variant 1128/5776 801/3300 267/1099 I atC/atT COSM81825 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 1 LOW 1 SNV 1 1 1 PASS rs907461232 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 129699977 129699977 G A 1 0 0 0 0 0 0 0 1 16492 1048 37 1 1 TMEM132D 12 129699977 Silent SNP G C3N-00294_T 5820663 129699977 3575332 863 13635 SFSWAP 0 . GRCh38 12 131778179 131778179 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.2257G>C p.Glu753Gln p.E753Q ENST00000541286 14/19 311 257 54 330 330 0 strelka-varscan-mutect SFSWAP,missense_variant,p.Glu753Gln,ENST00000261674,NM_004592.3;SFSWAP,missense_variant,p.Glu753Gln,ENST00000541286,NM_001261411.1;SFSWAP,missense_variant,p.Glu316Gln,ENST00000537164,;SFSWAP,3_prime_UTR_variant,,ENST00000538548,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000535236,; C ENST00000541286 Transcript missense_variant 2350/3219 2257/3012 753/1003 E/Q Gag/Cag COSM5440844 1 1 SFSWAP HGNC HGNC:10790 protein_coding YES CCDS58290.1 ENSP00000437738 Q12872 UPI000204AB4C NM_001261411.1 deleterious_low_confidence(0.01) 14/19 hmmpanther:PTHR13161,hmmpanther:PTHR13161:SF15,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 131778179 131778179 G C 1 0 0 0 0 1 0 0 0 14444 943 33 4 4 SFSWAP 12 131778179 Missense_Mutation SNP G C3N-00294_T 2078202 131778179 1497130 864 13636 EP400 0 . GRCh38 12 131982170 131982170 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1621G>T p.Gly541Trp p.G541W ENST00000389562 4/52 66 38 28 57 57 0 strelka-varscan-mutect EP400,missense_variant,p.Gly541Trp,ENST00000389562,;EP400,missense_variant,p.Gly541Trp,ENST00000389561,NM_015409.4;EP400,missense_variant,p.Gly577Trp,ENST00000333577,;EP400,missense_variant,p.Gly504Trp,ENST00000332482,; T ENST00000389562 Transcript missense_variant 1656/12836 1621/9372 541/3123 G/W Ggg/Tgg 1 1 EP400 HGNC HGNC:11958 protein_coding YES CCDS31929.2 ENSP00000374213 Q96L91 UPI00004566BC deleterious_low_confidence(0) 4/52 hmmpanther:PTHR10799:SF599,hmmpanther:PTHR10799 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 131982170 131982170 G T 1 0 0 0 0 1 0 0 0 4995 1232 43 2 2 EP400 12 131982170 Missense_Mutation SNP G C3N-00294_T 203991 131982170 1293139 865 13637 POLE 0 . GRCh38 12 132672721 132672721 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1592G>A p.Gly531Glu p.G531E ENST00000320574 15/49 484 382 102 518 518 0 strelka-varscan-mutect POLE,missense_variant,p.Gly531Glu,ENST00000320574,NM_006231.3;POLE,missense_variant,p.Gly504Glu,ENST00000535270,;POLE,non_coding_transcript_exon_variant,,ENST00000539215,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,non_coding_transcript_exon_variant,,ENST00000535934,;POLE,non_coding_transcript_exon_variant,,ENST00000545015,; T ENST00000320574 Transcript missense_variant 1636/7840 1592/6861 531/2286 G/E gGa/gAa 1 -1 POLE HGNC HGNC:9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 UPI00001FBF97 NM_006231.3 deleterious(0) 15/49 hmmpanther:PTHR10670,SMART_domains:SM00486,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 132672721 132672721 C T 1 0 0 0 0 1 0 0 0 12306 855 30 3 3 POLE 12 132672721 Missense_Mutation SNP C C3N-00294_T 690551 132672721 602588 866 13638 CHFR 0 . GRCh38 12 132861474 132861474 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.780G>A p.Met260Ile p.M260I ENST00000432561 7/18 70 53 17 89 89 0 strelka-varscan-mutect CHFR,missense_variant,p.Met219Ile,ENST00000266880,NM_018223.2;CHFR,missense_variant,p.Met248Ile,ENST00000450056,NM_001161346.1;CHFR,missense_variant,p.Met168Ile,ENST00000443047,NM_001161347.1;CHFR,missense_variant,p.Met260Ile,ENST00000432561,NM_001161344.1,NM_001161345.1;CHFR,missense_variant,p.Met120Ile,ENST00000541817,;CHFR,downstream_gene_variant,,ENST00000540963,;RP11-46H11.11,downstream_gene_variant,,ENST00000623177,;CHFR,missense_variant,p.Met60Ile,ENST00000315585,;CHFR,non_coding_transcript_exon_variant,,ENST00000535897,;CHFR,upstream_gene_variant,,ENST00000535527,; T ENST00000432561 Transcript missense_variant 854/2648 780/1995 260/664 M/I atG/atA 1 -1 CHFR HGNC HGNC:20455 protein_coding YES CCDS53849.1 ENSP00000392395 Q96EP1 UPI000006FA02 NM_001161344.1,NM_001161345.1 tolerated(0.43) 7/18 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 132861474 132861474 C T 1 0 0 0 0 1 0 0 0 3096 826 29 3 3 CHFR 12 132861474 Missense_Mutation SNP C C3N-00294_T 188753 132861474 413835 867 13639 SACS 0 . GRCh38 13 23330240 23330240 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.13636C>T p.Gln4546Ter p.Q4546* ENST00000382292 9/9 153 114 39 239 239 0 strelka-varscan-mutect SACS,stop_gained,p.Gln4546Ter,ENST00000382292,NM_014363.5;SACS,stop_gained,p.Gln3796Ter,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; A ENST00000382292 Transcript stop_gained 13910/15324 13636/13740 4546/4579 Q/* Cag/Tag 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 9/9 Gene3D:1.20.120.330,Pfam_domain:PF05168,PROSITE_profiles:PS50910,hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28,SMART_domains:SM00748,Superfamily_domains:SSF81593 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 23330240 23330240 G A 1 0 0 0 0 0 1 0 0 14063 1299 45 3 3 SACS 13 23330240 Nonsense_Mutation SNP G C3N-00294_T 23330240 91034088 868 13640 FRY 0 . GRCh38 13 32131777 32131777 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.822G>T p.Met274Ile p.M274I ENST00000542859 8/61 190 141 49 264 263 1 strelka-varscan-mutect FRY,missense_variant,p.Met274Ile,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Met274Ile,ENST00000380250,; T ENST00000542859 Transcript missense_variant 1318/13200 822/9042 274/3013 M/I atG/atT 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0.01) 8/61 Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 32131777 32131777 G T 1 0 0 0 0 1 0 0 0 5935 1290 45 2 2 FRY 13 32131777 Missense_Mutation SNP G C3N-00294_T 8801537 32131777 82232551 869 13641 BRCA2 0 . GRCh38 13 32340770 32340770 + Missense_Mutation SNP G G C rs763639231 C3N-00294_T C3N-00294_N G G c.6415G>C p.Glu2139Gln p.E2139Q ENST00000380152 11/27 15 11 4 53 53 0 strelka-varscan-mutect BRCA2,missense_variant,p.Glu2139Gln,ENST00000380152,;BRCA2,missense_variant,p.Glu2139Gln,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,; C ENST00000380152 Transcript missense_variant 6648/11986 6415/10257 2139/3418 E/Q Gaa/Caa rs763639231 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC deleterious(0.03) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 MODERATE 1 SNV 5 1 PASS rs763639231 . 1 205 4 0 0 0 0 0 -13.08386 1 1 1 1 0 C 3 2 46 32340770 32340770 G C 1 0 0 0 0 1 0 0 0 1669 1291 45 4 4 BRCA2 13 32340770 Missense_Mutation SNP G C3N-00294_T 208993 32340770 82023558 870 13642 AKAP11 0 . GRCh38 13 42303298 42303298 + Missense_Mutation SNP C C G rs145560213 C3N-00294_T C3N-00294_N C C c.4552C>G p.His1518Asp p.H1518D ENST00000025301 8/13 194 148 46 186 186 0 strelka-varscan-mutect AKAP11,missense_variant,p.His1518Asp,ENST00000025301,NM_016248.3; G ENST00000025301 Transcript missense_variant 4727/9920 4552/5706 1518/1901 H/D Cac/Gac rs145560213 1 1 AKAP11 HGNC HGNC:369 protein_coding YES CCDS9383.1 ENSP00000025301 Q9UKA4 UPI0000125747 NM_016248.3 tolerated(0.06) 8/13 hmmpanther:PTHR10226:SF3,hmmpanther:PTHR10226 MODERATE 1 SNV 1 1 PASS rs145560213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 42303298 42303298 C G 1 0 0 0 0 1 0 0 0 530 826 29 4 4 AKAP11 13 42303298 Missense_Mutation SNP C C3N-00294_T 9962528 42303298 72061030 871 13643 ZC3H13 0 . GRCh38 13 45969366 45969366 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.3178G>C p.Glu1060Gln p.E1060Q ENST00000282007 14/17 126 107 19 164 164 0 strelka-varscan-mutect ZC3H13,missense_variant,p.Glu1060Gln,ENST00000242848,;ZC3H13,missense_variant,p.Glu1060Gln,ENST00000282007,NM_015070.4; G ENST00000282007 Transcript missense_variant 3249/6412 3178/4695 1060/1564 E/Q Gaa/Caa 1 -1 ZC3H13 HGNC HGNC:20368 protein_coding YES CCDS9400.1 ENSP00000282007 Q5T200 UPI0000366969 NM_015070.4 tolerated_low_confidence(0.05) 14/17 hmmpanther:PTHR13585,hmmpanther:PTHR13585:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 45969366 45969366 C G 1 0 0 0 0 1 0 0 0 18140 922 32 4 4 ZC3H13 13 45969366 Missense_Mutation SNP C C3N-00294_T 3666068 45969366 68394962 872 13644 LRCH1 0 . GRCh38 13 46681779 46681779 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.618G>A p.= p.Q206Q ENST00000389797 4/20 297 248 49 290 290 0 strelka-varscan-mutect LRCH1,synonymous_variant,p.=,ENST00000311191,NM_001164213.1;LRCH1,synonymous_variant,p.=,ENST00000389798,NM_015116.2;LRCH1,synonymous_variant,p.=,ENST00000389797,NM_001164211.1;LRCH1,5_prime_UTR_variant,,ENST00000463929,;LRCH1,5_prime_UTR_variant,,ENST00000478412,;LRCH1,non_coding_transcript_exon_variant,,ENST00000443945,; A ENST00000389797 Transcript synonymous_variant 755/3314 618/2292 206/763 Q caG/caA 1 1 LRCH1 HGNC HGNC:20309 protein_coding YES CCDS53865.1 ENSP00000374447 Q9Y2L9 UPI00015DFE06 NM_001164211.1 4/20 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF434,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 46681779 46681779 G A 1 0 0 0 0 0 0 0 1 8826 933 33 3 3 LRCH1 13 46681779 Silent SNP G C3N-00294_T 712413 46681779 67682549 873 13645 RB1 0 . GRCh38 13 48381256 48381256 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1508C>T p.Ser503Phe p.S503F ENST00000267163 17/27 87 70 17 118 118 0 strelka-mutect RB1,missense_variant,p.Ser503Phe,ENST00000267163,NM_000321.2; T ENST00000267163 Transcript missense_variant 1646/4840 1508/2787 503/928 S/F tCt/tTt 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 tolerated(0.8) 17/27 Gene3D:1.10.472.10,Pfam_domain:PF01858,hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21,SMART_domains:SM01368,Superfamily_domains:SSF47954 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 46 48381256 48381256 C T 1 0 0 0 0 1 0 0 0 13259 913 32 3 3 RB1 13 48381256 Missense_Mutation SNP C C3N-00294_T 1699477 48381256 65983072 874 13646 TRIM13 0 . GRCh38 13 50012709 50012709 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.778G>A p.Glu260Lys p.E260K ENST00000356017 4/4 158 134 24 166 166 0 strelka-varscan-mutect TRIM13,missense_variant,p.Glu257Lys,ENST00000378182,NM_213590.2,NM_052811.3;TRIM13,missense_variant,p.Glu257Lys,ENST00000420995,NM_005798.4;TRIM13,missense_variant,p.Glu260Lys,ENST00000356017,NM_001007278.2;TRIM13,missense_variant,p.Glu257Lys,ENST00000457662,;TRIM13,missense_variant,p.Glu257Lys,ENST00000378183,;KCNRG,upstream_gene_variant,,ENST00000360473,NM_199464.2;KCNRG,upstream_gene_variant,,ENST00000312942,NM_173605.1;TRIM13,downstream_gene_variant,,ENST00000442421,;DLEU2,intron_variant,,ENST00000621282,;TRIM13,intron_variant,,ENST00000478111,;TRIM13,intron_variant,,ENST00000474805,; A ENST00000356017 Transcript missense_variant 1166/1637 778/1233 260/410 E/K Gag/Aag 1 1 TRIM13 HGNC HGNC:9976 protein_coding YES CCDS41888.1 ENSP00000348299 O60858 UPI00001FCDDE NM_001007278.2 deleterious(0.01) 4/4 hmmpanther:PTHR24103:SF252,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 50012709 50012709 G A 1 0 0 0 0 1 0 0 0 16977 943 33 3 3 TRIM13 13 50012709 Missense_Mutation SNP G C3N-00294_T 1631453 50012709 64351619 875 13647 UTP14C 0 . GRCh38 13 52030239 52030239 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1435G>C p.Glu479Gln p.E479Q ENST00000521776 2/2 339 268 71 356 356 0 strelka-varscan-mutect UTP14C,missense_variant,p.Glu479Gln,ENST00000521776,NM_021645.5;ALG11,downstream_gene_variant,,ENST00000521508,NM_001004127.2;ALG11,downstream_gene_variant,,ENST00000523764,;ALG11,downstream_gene_variant,,ENST00000519151,;NEK5,downstream_gene_variant,,ENST00000529080,; C ENST00000521776 Transcript missense_variant 2168/5529 1435/2301 479/766 E/Q Gag/Cag 1 1 UTP14C HGNC HGNC:20321 protein_coding YES CCDS31978.1 ENSP00000428619 Q5TAP6 A0A024RDV0 UPI000006DB4B NM_021645.5 tolerated(0.5) 2/2 hmmpanther:PTHR14150:SF16,hmmpanther:PTHR14150,Pfam_domain:PF04615 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 52030239 52030239 G C 1 0 0 0 0 1 0 0 0 17639 943 33 4 4 UTP14C 13 52030239 Missense_Mutation SNP G C3N-00294_T 2017530 52030239 62334089 876 13648 THSD1 0 . GRCh38 13 52397560 52397560 + Silent SNP T T C novel C3N-00294_T C3N-00294_N T T c.693A>G p.= p.T231T ENST00000258613 3/5 194 112 82 186 186 0 strelka-varscan-mutect THSD1,synonymous_variant,p.=,ENST00000349258,NM_199263.2;THSD1,synonymous_variant,p.=,ENST00000258613,NM_018676.3;RNY4P24,upstream_gene_variant,,ENST00000362735,; C ENST00000258613 Transcript synonymous_variant 872/2962 693/2559 231/852 T acA/acG 1 -1 THSD1 HGNC HGNC:17754 protein_coding YES CCDS9432.1 ENSP00000258613 Q9NS62 A0A024R064 UPI000007376D NM_018676.3 3/5 hmmpanther:PTHR16311 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 52397560 52397560 T C 1 0 0 0 0 0 0 0 1 16311 1567 55 5 5 THSD1 13 52397560 Silent SNP T C3N-00294_T 367321 52397560 61966768 877 13649 DIS3 0 . GRCh38 13 72775288 72775288 + Missense_Mutation SNP C C A rs200924053 C3N-00294_T C3N-00294_N C C c.910G>T p.Ala304Ser p.A304S ENST00000377767 6/21 141 106 35 172 172 0 strelka-varscan-mutect DIS3,missense_variant,p.Ala304Ser,ENST00000377767,NM_014953.4;DIS3,missense_variant,p.Ala274Ser,ENST00000377780,NM_001128226.2;DIS3,missense_variant,p.Ala142Ser,ENST00000545453,;DIS3,missense_variant,p.Ala304Ser,ENST00000490646,; A ENST00000377767 Transcript missense_variant 1011/10604 910/2877 304/958 A/S Gca/Tca rs200924053 1 -1 DIS3 HGNC HGNC:20604 protein_coding YES CCDS9447.1 ENSP00000366997 Q9Y2L1 UPI0000141B79 NM_014953.4 tolerated(0.41) 6/21 hmmpanther:PTHR23355,hmmpanther:PTHR23355:SF35,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS rs200924053 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 72775288 72775288 C A 1 0 0 0 0 1 0 0 0 4341 797 28 2 2 DIS3 13 72775288 Missense_Mutation SNP C C3N-00294_T 20377728 72775288 41589040 878 13650 KLF5 0 . GRCh38 13 73063853 73063853 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.1165C>A p.His389Asn p.H389N ENST00000377687 3/4 56 40 16 133 133 0 strelka-varscan-mutect KLF5,missense_variant,p.His389Asn,ENST00000377687,NM_001730.4;KLF5,missense_variant,p.His298Asn,ENST00000539231,NM_001286818.1;KLF5,downstream_gene_variant,,ENST00000477333,;KLF5,downstream_gene_variant,,ENST00000476859,; A ENST00000377687 Transcript missense_variant 1701/3566 1165/1374 389/457 H/N Cat/Aat COSM84227 1 1 KLF5 HGNC HGNC:6349 protein_coding YES CCDS9448.1 ENSP00000366915 Q13887 Q5T6X2 UPI0000000C89 NM_001730.4 deleterious(0) 3/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF60,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 73063853 73063853 C A 1 0 0 0 0 1 0 0 0 8214 826 29 2 2 KLF5 13 73063853 Missense_Mutation SNP C C3N-00294_T 288565 73063853 41300475 879 13651 MYCBP2 0 . GRCh38 13 77081910 77081910 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.11006C>A p.Ser3669Ter p.S3669* ENST00000544440 64/83 127 108 19 142 142 0 strelka-varscan-mutect MYCBP2,stop_gained,p.Ser3669Ter,ENST00000357337,NM_015057.4;MYCBP2,stop_gained,p.Ser3669Ter,ENST00000544440,;MYCBP2,stop_gained,p.Ser93Ter,ENST00000429715,;RP11-226E21.4,intron_variant,,ENST00000638101,;RP11-226E21.4,downstream_gene_variant,,ENST00000638147,;MYCBP2-AS1,non_coding_transcript_exon_variant,,ENST00000631152,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2-AS1,intron_variant,,ENST00000629771,;MYCBP2-AS1,intron_variant,,ENST00000627409,;MYCBP2-AS1,intron_variant,,ENST00000630676,;MYCBP2-AS1,intron_variant,,ENST00000422231,;MYCBP2-AS1,intron_variant,,ENST00000450627,;MYCBP2-AS1,intron_variant,,ENST00000448470,;MYCBP2-AS1,downstream_gene_variant,,ENST00000596342,;MYCBP2-AS2,upstream_gene_variant,,ENST00000428716,;MYCBP2-AS1,downstream_gene_variant,,ENST00000636737,;RP11-226E21.4,intron_variant,,ENST00000637192,;RP11-226E21.4,downstream_gene_variant,,ENST00000461131,; T ENST00000544440 Transcript stop_gained 11024/14664 11006/13923 3669/4640 S/* tCa/tAa 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 64/83 Superfamily_domains:SSF49785 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 77081910 77081910 G T 1 0 0 0 0 0 1 0 0 10018 1294 45 2 2 MYCBP2 13 77081910 Nonsense_Mutation SNP G C3N-00294_T 4018057 77081910 37282418 880 13652 SLC10A2 0 . GRCh38 13 103065886 103065886 + Missense_Mutation SNP C C T rs200038147 C3N-00294_T C3N-00294_N C C c.364G>A p.Asp122Asn p.D122N ENST00000245312 1/6 197 169 28 208 207 1 strelka-varscan-mutect SLC10A2,missense_variant,p.Asp122Asn,ENST00000245312,NM_000452.2; T ENST00000245312 Transcript missense_variant 961/3779 364/1047 122/348 D/N Gac/Aac rs200038147,COSM5634136 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 deleterious(0) 1/6 hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841,Pfam_domain:PF01758 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200038147 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 103065886 103065886 C T 1 0 0 0 0 1 0 0 0 14639 884 31 1 1 SLC10A2 13 103065886 Missense_Mutation SNP C C3N-00294_T 25983976 103065886 11298442 881 13653 COL4A2 0 . GRCh38 13 110357506 110357506 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.134G>C p.Arg45Thr p.R45T ENST00000360467 4/48 236 188 48 231 231 0 strelka-varscan-mutect COL4A2,missense_variant,p.Arg45Thr,ENST00000360467,NM_001846.2;COL4A2,missense_variant,p.Arg45Thr,ENST00000400163,; C ENST00000360467 Transcript missense_variant 440/6281 134/5139 45/1712 R/T aGa/aCa 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 deleterious(0) 4/48 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 110357506 110357506 G C 1 0 0 0 0 1 0 0 0 3479 942 33 4 4 COL4A2 13 110357506 Missense_Mutation SNP G C3N-00294_T 7291620 110357506 4006822 882 13654 TUBGCP3 0 . GRCh38 13 112527447 112527447 + Missense_Mutation SNP C C A rs770762441 C3N-00294_T C3N-00294_N C C c.1373G>T p.Arg458Leu p.R458L ENST00000261965 12/22 101 48 53 117 117 0 strelka-varscan-mutect TUBGCP3,missense_variant,p.Arg458Leu,ENST00000261965,NM_006322.5,NM_001286277.1;TUBGCP3,missense_variant,p.Arg458Leu,ENST00000375669,NM_001286278.1;TUBGCP3,non_coding_transcript_exon_variant,,ENST00000462580,; A ENST00000261965 Transcript missense_variant 1560/3899 1373/2724 458/907 R/L cGa/cTa rs770762441 1 -1 TUBGCP3 HGNC HGNC:18598 protein_coding YES CCDS9525.1 ENSP00000261965 Q96CW5 UPI000000DB88 NM_006322.5,NM_001286277.1 tolerated(0.06) 12/22 Pfam_domain:PF04130,hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF14 MODERATE 1 SNV 1 1 PASS rs770762441 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 112527447 112527447 C A 1 0 0 0 0 1 0 0 0 17277 884 31 1 1 TUBGCP3 13 112527447 Missense_Mutation SNP C C3N-00294_T 2169941 112527447 1836881 883 13655 PROZ 0 . GRCh38 13 113160112 113160112 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.235G>C p.Glu79Gln p.E79Q ENST00000342783 3/9 286 244 42 319 319 0 strelka-varscan-mutect PROZ,missense_variant,p.Glu79Gln,ENST00000342783,NM_001256134.1;PROZ,missense_variant,p.Glu57Gln,ENST00000375547,NM_003891.2;RP11-98F14.11,downstream_gene_variant,,ENST00000600642,;PROZ,upstream_gene_variant,,ENST00000493630,; C ENST00000342783 Transcript missense_variant 242/1551 235/1269 79/422 E/Q Gaa/Caa 1 1 PROZ HGNC HGNC:9460 protein_coding YES CCDS58300.1 ENSP00000344458 P22891 UPI000002B1A6 NM_001256134.1 deleterious(0) 3/9 PROSITE_profiles:PS50998,hmmpanther:PTHR24278:SF20,hmmpanther:PTHR24278,PROSITE_patterns:PS00011,Pfam_domain:PF00594,PIRSF_domain:PIRSF001143,Gene3D:4.10.740.10,SMART_domains:SM00069,Superfamily_domains:SSF57630,Prints_domain:PR00001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 113160112 113160112 G C 1 0 0 0 0 1 0 0 0 12698 943 33 4 4 PROZ 13 113160112 Missense_Mutation SNP G C3N-00294_T 632665 113160112 1204216 884 13656 PROZ 0 . GRCh38 13 113160142 113160142 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.265G>A p.Glu89Lys p.E89K ENST00000342783 3/9 297 243 54 318 318 0 strelka-varscan-mutect PROZ,missense_variant,p.Glu89Lys,ENST00000342783,NM_001256134.1;PROZ,missense_variant,p.Glu67Lys,ENST00000375547,NM_003891.2;RP11-98F14.11,downstream_gene_variant,,ENST00000600642,;PROZ,upstream_gene_variant,,ENST00000493630,; A ENST00000342783 Transcript missense_variant 272/1551 265/1269 89/422 E/K Gaa/Aaa 1 1 PROZ HGNC HGNC:9460 protein_coding YES CCDS58300.1 ENSP00000344458 P22891 UPI000002B1A6 NM_001256134.1 deleterious(0) 3/9 PROSITE_profiles:PS50998,hmmpanther:PTHR24278:SF20,hmmpanther:PTHR24278,PROSITE_patterns:PS00011,Pfam_domain:PF00594,PIRSF_domain:PIRSF001143,Gene3D:4.10.740.10,SMART_domains:SM00069,Superfamily_domains:SSF57630,Prints_domain:PR00001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 113160142 113160142 G A 1 0 0 0 0 1 0 0 0 12698 943 33 3 3 PROZ 13 113160142 Missense_Mutation SNP G C3N-00294_T 30 113160142 1204186 885 13657 TMEM255B 0 . GRCh38 13 113811868 113811868 + Missense_Mutation SNP C C A rs752630188 C3N-00294_T C3N-00294_N C C c.946C>A p.Pro316Thr p.P316T ENST00000375353 9/9 242 196 46 257 257 0 strelka-varscan-mutect TMEM255B,missense_variant,p.Pro316Thr,ENST00000375353,NM_182614.2;GAS6-AS1,upstream_gene_variant,,ENST00000458001,;TMEM255B,non_coding_transcript_exon_variant,,ENST00000467169,; A ENST00000375353 Transcript missense_variant 973/6100 946/981 316/326 P/T Ccc/Acc rs752630188,COSM4046230 1 1 TMEM255B HGNC HGNC:28297 protein_coding YES CCDS45071.1 ENSP00000364502 Q8WV15 UPI0000071C2C NM_182614.2 tolerated(0.59) 9/9 hmmpanther:PTHR33721:SF3,hmmpanther:PTHR33721,Pfam_domain:PF14967 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752630188 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 113811868 113811868 C A 1 0 0 0 0 1 0 0 0 16615 855 30 2 2 TMEM255B 13 113811868 Missense_Mutation SNP C C3N-00294_T 651726 113811868 552460 886 13658 OR4K1 0 . GRCh38 14 19936183 19936183 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.517G>A p.Glu173Lys p.E173K ENST00000285600 1/1 409 369 40 346 346 0 strelka-varscan-mutect OR4K1,missense_variant,p.Glu173Lys,ENST00000285600,NM_001004063.2; A ENST00000285600 Transcript missense_variant 576/1076 517/936 173/311 E/K Gag/Aag 1 1 OR4K1 HGNC HGNC:14726 protein_coding YES CCDS32025.1 ENSP00000285600 Q8NGD4 UPI0000041B4A NM_001004063.2 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF182,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 19936183 19936183 G A 1 0 0 0 0 1 0 0 0 11144 1291 45 3 3 OR4K1 14 19936183 Missense_Mutation SNP G C3N-00294_T 19936183 87107535 887 13659 APEX1 0 . GRCh38 14 20457139 20457139 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.588G>C p.= p.L196L ENST00000216714 5/5 331 279 52 377 377 0 strelka-varscan-mutect APEX1,stop_lost,p.Ter15SerextTer74,ENST00000557054,;APEX1,synonymous_variant,p.=,ENST00000216714,NM_001244249.1,NM_001641.3;APEX1,synonymous_variant,p.=,ENST00000555414,NM_080649.2,NM_080648.2;APEX1,synonymous_variant,p.=,ENST00000398030,;APEX1,synonymous_variant,p.=,ENST00000555839,;APEX1,synonymous_variant,p.=,ENST00000553681,;APEX1,synonymous_variant,p.=,ENST00000438886,;OSGEP,upstream_gene_variant,,ENST00000206542,NM_017807.3;TMEM55B,downstream_gene_variant,,ENST00000250489,NM_144568.3;TMEM55B,downstream_gene_variant,,ENST00000398020,NM_001100814.2;TMEM55B,downstream_gene_variant,,ENST00000553460,;APEX1,downstream_gene_variant,,ENST00000556054,;APEX1,downstream_gene_variant,,ENST00000557150,;APEX1,downstream_gene_variant,,ENST00000557344,;APEX1,downstream_gene_variant,,ENST00000557592,;OSGEP,upstream_gene_variant,,ENST00000553640,;APEX1,downstream_gene_variant,,ENST00000557181,;APEX1,downstream_gene_variant,,ENST00000553368,;TMEM55B,downstream_gene_variant,,ENST00000556093,;APEX1,non_coding_transcript_exon_variant,,ENST00000557365,;APEX1,non_coding_transcript_exon_variant,,ENST00000554813,;OSGEP,upstream_gene_variant,,ENST00000556252,;OSGEP,upstream_gene_variant,,ENST00000554699,;APEX1,downstream_gene_variant,,ENST00000556296,;APEX1,non_coding_transcript_exon_variant,,ENST00000557159,;APEX1,non_coding_transcript_exon_variant,,ENST00000553555,;TMEM55B,downstream_gene_variant,,ENST00000557041,;TMEM55B,downstream_gene_variant,,ENST00000554028,;OSGEP,upstream_gene_variant,,ENST00000556439,;APEX1,downstream_gene_variant,,ENST00000555306,;OSGEP,upstream_gene_variant,,ENST00000555223,;APEX1,downstream_gene_variant,,ENST00000554325,;TMEM55B,downstream_gene_variant,,ENST00000553602,; C ENST00000216714 Transcript synonymous_variant 856/1484 588/957 196/318 L ctG/ctC 1 1 APEX1 HGNC HGNC:587 protein_coding YES CCDS9550.1 ENSP00000216714 P27695 Q5TZP7 UPI000000CBFE NM_001244249.1,NM_001641.3 5/5 PROSITE_profiles:PS51435,hmmpanther:PTHR22748,TIGRFAM_domain:TIGR00195,Gene3D:3.60.10.10,TIGRFAM_domain:TIGR00633,Pfam_domain:PF03372,Superfamily_domains:SSF56219 LOW 1 SNV 1 1 PASS rs1183830234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 20457139 20457139 G C 1 0 0 0 0 0 0 0 1 890 1285 45 4 4 APEX1 14 20457139 Silent SNP G C3N-00294_T 520956 20457139 86586579 888 13660 CHD8 0 . GRCh38 14 21427937 21427937 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1533G>A p.= p.L511L ENST00000399982 3/37 193 151 42 248 248 0 strelka-varscan-mutect CHD8,synonymous_variant,p.=,ENST00000399982,NM_001170629.1;CHD8,synonymous_variant,p.=,ENST00000557364,;CHD8,synonymous_variant,p.=,ENST00000430710,NM_020920.3;CHD8,downstream_gene_variant,,ENST00000553622,;CHD8,downstream_gene_variant,,ENST00000553283,;RN7SL650P,downstream_gene_variant,,ENST00000619902,;CHD8,intron_variant,,ENST00000555962,;CHD8,downstream_gene_variant,,ENST00000556833,;CHD8,downstream_gene_variant,,ENST00000553651,; T ENST00000399982 Transcript synonymous_variant 1598/8229 1533/7746 511/2581 L ctG/ctA 1 -1 CHD8 HGNC HGNC:20153 protein_coding YES CCDS53885.1 ENSP00000382863 Q9HCK8 UPI00002375B9 NM_001170629.1 3/37 hmmpanther:PTHR10799:SF551,hmmpanther:PTHR10799 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 21427937 21427937 C T 1 0 0 0 0 0 0 0 1 3090 813 29 3 3 CHD8 14 21427937 Silent SNP C C3N-00294_T 970798 21427937 85615781 889 13661 SALL2 0 . GRCh38 14 21523893 21523893 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1835C>T p.Ser612Leu p.S612L ENST00000614342 2/2 227 170 57 287 287 0 strelka-varscan-mutect SALL2,missense_variant,p.Ser612Leu,ENST00000614342,NM_005407.2;SALL2,missense_variant,p.Ser475Leu,ENST00000450879,NM_001291447.1;SALL2,missense_variant,p.Ser471Leu,ENST00000546363,NM_001291446.1;SALL2,intron_variant,,ENST00000613414,;SALL2,intron_variant,,ENST00000611430,;SALL2,downstream_gene_variant,,ENST00000537235,;SALL2,downstream_gene_variant,,ENST00000541965,;AE000658.22,downstream_gene_variant,,ENST00000535893,; A ENST00000614342 Transcript missense_variant 2130/4942 1835/3024 612/1007 S/L tCa/tTa 1 -1 SALL2 HGNC HGNC:10526 protein_coding YES CCDS32045.1 ENSP00000483562 Q9Y467 UPI0000135524 NM_005407.2 deleterious_low_confidence(0.01) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 21523893 21523893 G A 1 0 0 0 0 1 0 0 0 14070 1294 45 3 3 SALL2 14 21523893 Missense_Mutation SNP G C3N-00294_T 95956 21523893 85519825 890 13662 CARMIL3 0 . GRCh38 14 24058945 24058945 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.1530C>G p.= p.L510L ENST00000342740 19/40 305 262 43 289 289 0 strelka-varscan-mutect CARMIL3,synonymous_variant,p.=,ENST00000342740,NM_138360.3;CARMIL3,non_coding_transcript_exon_variant,,ENST00000559694,;CARMIL3,upstream_gene_variant,,ENST00000560349,;CARMIL3,upstream_gene_variant,,ENST00000561354,; G ENST00000342740 Transcript synonymous_variant 1684/4597 1530/4119 510/1372 L ctC/ctG 1 1 CARMIL3 HGNC HGNC:20272 protein_coding YES CCDS32054.1 ENSP00000340467 Q8ND23 UPI0000DBEF11 NM_138360.3 19/40 hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF43,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 24058945 24058945 C G 1 0 0 0 0 0 0 0 1 2353 813 29 4 4 CARMIL3 14 24058945 Silent SNP C C3N-00294_T 2535052 24058945 82984773 891 13663 DCAF11 0 . GRCh38 14 24118125 24118125 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.547G>C p.Asp183His p.D183H ENST00000446197 6/15 174 134 40 177 177 0 strelka-varscan-mutect DCAF11,missense_variant,p.Asp183His,ENST00000446197,NM_025230.4;DCAF11,missense_variant,p.Asp183His,ENST00000559115,NM_001163484.1;DCAF11,missense_variant,p.Asp83His,ENST00000396936,;DCAF11,missense_variant,p.Asp157His,ENST00000396941,NM_181357.2;DCAF11,missense_variant,p.Asp157His,ENST00000561375,;DCAF11,missense_variant,p.Asp143His,ENST00000560901,;NRL,upstream_gene_variant,,ENST00000561028,;DCAF11,upstream_gene_variant,,ENST00000559144,;DCAF11,downstream_gene_variant,,ENST00000557810,;RP11-468E2.6,upstream_gene_variant,,ENST00000558325,;DCAF11,downstream_gene_variant,,ENST00000559017,;NRL,upstream_gene_variant,,ENST00000558280,;DCAF11,downstream_gene_variant,,ENST00000558408,;DCAF11,downstream_gene_variant,,ENST00000560459,;DCAF11,downstream_gene_variant,,ENST00000558215,;DCAF11,downstream_gene_variant,,ENST00000558638,;DCAF11,downstream_gene_variant,,ENST00000559288,;DCAF11,downstream_gene_variant,,ENST00000559593,;DCAF11,downstream_gene_variant,,ENST00000561041,;DCAF11,downstream_gene_variant,,ENST00000559382,;DCAF11,downstream_gene_variant,,ENST00000559354,;DCAF11,downstream_gene_variant,,ENST00000561001,;DCAF11,downstream_gene_variant,,ENST00000560713,;DCAF11,downstream_gene_variant,,ENST00000559796,;DCAF11,downstream_gene_variant,,ENST00000559396,;DCAF11,intron_variant,,ENST00000560171,;DCAF11,downstream_gene_variant,,ENST00000561056,;DCAF11,downstream_gene_variant,,ENST00000557809,;DCAF11,downstream_gene_variant,,ENST00000561016,;DCAF11,downstream_gene_variant,,ENST00000557952,;DCAF11,3_prime_UTR_variant,,ENST00000557802,;DCAF11,3_prime_UTR_variant,,ENST00000326009,;DCAF11,3_prime_UTR_variant,,ENST00000558914,;DCAF11,non_coding_transcript_exon_variant,,ENST00000560046,;DCAF11,upstream_gene_variant,,ENST00000558624,;DCAF11,upstream_gene_variant,,ENST00000559472,;DCAF11,downstream_gene_variant,,ENST00000559451,;DCAF11,downstream_gene_variant,,ENST00000558706,;DCAF11,downstream_gene_variant,,ENST00000560457,;DCAF11,downstream_gene_variant,,ENST00000557888,;DCAF11,downstream_gene_variant,,ENST00000560614,; C ENST00000446197 Transcript missense_variant 1274/4299 547/1641 183/546 D/H Gat/Cat 1 1 DCAF11 HGNC HGNC:20258 protein_coding YES CCDS9610.1 ENSP00000415556 Q8TEB1 UPI0000073AB2 NM_025230.4 deleterious(0) 6/15 PROSITE_profiles:PS50294,hmmpanther:PTHR19847,Gene3D:2.130.10.10,PIRSF_domain:PIRSF038135,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 24118125 24118125 G C 1 0 0 0 0 1 0 0 0 4063 942 33 4 4 DCAF11 14 24118125 Missense_Mutation SNP G C3N-00294_T 59180 24118125 82925593 892 13664 AKAP6 0 . GRCh38 14 32545801 32545801 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1148C>G p.Ser383Cys p.S383C ENST00000280979 4/14 142 107 35 177 177 0 strelka-varscan-mutect AKAP6,missense_variant,p.Ser383Cys,ENST00000280979,NM_004274.4;AKAP6,missense_variant,p.Ser383Cys,ENST00000557354,;AKAP6,missense_variant,p.Ser383Cys,ENST00000557272,;AKAP6,missense_variant,p.Ser141Cys,ENST00000553547,;AKAP6,downstream_gene_variant,,ENST00000556638,;AKAP6,downstream_gene_variant,,ENST00000554410,; G ENST00000280979 Transcript missense_variant 1318/15006 1148/6960 383/2319 S/C tCt/tGt 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 deleterious(0) 4/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 32545801 32545801 C G 1 0 0 0 0 1 0 0 0 539 913 32 4 4 AKAP6 14 32545801 Missense_Mutation SNP C C3N-00294_T 8427676 32545801 74497917 893 13665 EGLN3 0 . GRCh38 14 33950430 33950430 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.323G>T p.Arg108Leu p.R108L ENST00000250457 1/5 359 295 64 421 421 0 strelka-varscan-mutect EGLN3,missense_variant,p.Arg108Leu,ENST00000547327,;EGLN3,missense_variant,p.Arg108Leu,ENST00000250457,NM_022073.3;EGLN3,intron_variant,,ENST00000553215,NM_001308103.1;EGLN3,intron_variant,,ENST00000487915,; A ENST00000250457 Transcript missense_variant 652/2709 323/720 108/239 R/L cGg/cTg 1 -1 EGLN3 HGNC HGNC:14661 protein_coding YES CCDS9646.1 ENSP00000250457 Q9H6Z9 UPI000004F8A8 NM_022073.3 deleterious(0.02) 1/5 hmmpanther:PTHR12907,hmmpanther:PTHR12907:SF5,SMART_domains:SM00702 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33950430 33950430 C A 1 0 0 0 0 1 0 0 0 4806 652 23 1 1 EGLN3 14 33950430 Missense_Mutation SNP C C3N-00294_T 1404629 33950430 73093288 894 13666 BRMS1L 0 . GRCh38 14 35831437 35831437 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.170G>A p.Arg57Lys p.R57K ENST00000216807 2/10 46 37 9 105 105 0 strelka-varscan-mutect BRMS1L,missense_variant,p.Arg57Lys,ENST00000216807,NM_032352.3;BRMS1L,upstream_gene_variant,,ENST00000551774,;RP11-317N8.5,upstream_gene_variant,,ENST00000555918,;BRMS1L,3_prime_UTR_variant,,ENST00000552677,;BRMS1L,3_prime_UTR_variant,,ENST00000547420,;BRMS1L,non_coding_transcript_exon_variant,,ENST00000548758,; A ENST00000216807 Transcript missense_variant 369/2657 170/972 57/323 R/K aGa/aAa 1 1 BRMS1L HGNC HGNC:20512 protein_coding YES CCDS32066.1 ENSP00000216807 Q5PSV4 UPI00001BBFA5 NM_032352.3 deleterious(0.03) 2/10 hmmpanther:PTHR21964:SF16,hmmpanther:PTHR21964 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 35831437 35831437 G A 1 0 0 0 0 1 0 0 0 1692 942 33 3 3 BRMS1L 14 35831437 Missense_Mutation SNP G C3N-00294_T 1881007 35831437 71212281 895 13667 CLEC14A 0 . GRCh38 14 38255453 38255453 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.570G>A p.= p.L190L ENST00000342213 1/1 199 155 44 193 193 0 strelka-varscan-mutect CLEC14A,synonymous_variant,p.=,ENST00000342213,NM_175060.2; T ENST00000342213 Transcript synonymous_variant 917/2267 570/1473 190/490 L ttG/ttA COSM5292824 1 -1 CLEC14A HGNC HGNC:19832 protein_coding YES CCDS9667.1 ENSP00000353013 Q86T13 UPI000000CBD4 NM_175060.2 1/1 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF285 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 38255453 38255453 C T 1 0 0 0 0 0 0 0 1 3265 825 29 3 3 CLEC14A 14 38255453 Silent SNP C C3N-00294_T 2424016 38255453 68788265 896 13668 SEC23A 0 . GRCh38 14 39033242 39033242 + Silent SNP A A G novel C3N-00294_T C3N-00294_N A A c.2295T>C p.= p.A765A ENST00000307712 20/20 150 79 71 257 257 0 strelka-varscan-mutect SEC23A,synonymous_variant,p.=,ENST00000537403,;SEC23A,synonymous_variant,p.=,ENST00000307712,NM_006364.2;SEC23A,synonymous_variant,p.=,ENST00000545328,;SEC23A,non_coding_transcript_exon_variant,,ENST00000554615,;SEC23A,non_coding_transcript_exon_variant,,ENST00000555363,; G ENST00000307712 Transcript synonymous_variant 2813/4135 2295/2298 765/765 A gcT/gcC 1 -1 SEC23A HGNC HGNC:10701 protein_coding YES CCDS9668.1 ENSP00000306881 Q15436 UPI000013EC46 NM_006364.2 20/20 hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF7 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 39033242 39033242 A G 1 0 0 0 0 0 0 0 1 14268 59 3 5 5 SEC23A 14 39033242 Silent SNP A C3N-00294_T 777789 39033242 68010476 897 13669 NEMF 0 . GRCh38 14 49814024 49814024 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1708C>G p.His570Asp p.H570D ENST00000298310 18/33 98 76 22 147 147 0 strelka-varscan-mutect NEMF,missense_variant,p.His570Asp,ENST00000298310,NM_001301732.1,NM_004713.4;NEMF,missense_variant,p.His528Asp,ENST00000555970,;NEMF,non_coding_transcript_exon_variant,,ENST00000556925,;NEMF,intron_variant,,ENST00000555411,; C ENST00000298310 Transcript missense_variant 2158/6234 1708/3231 570/1076 H/D Cat/Gat 1 -1 NEMF HGNC HGNC:10663 protein_coding YES CCDS9694.1 ENSP00000298310 O60524 UPI0000246D16 NM_001301732.1,NM_004713.4 deleterious(0.02) 18/33 Pfam_domain:PF05670,hmmpanther:PTHR15239,hmmpanther:PTHR15239:SF6 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 49814024 49814024 G C 1 0 0 0 0 1 0 0 0 10366 1290 45 4 4 NEMF 14 49814024 Missense_Mutation SNP G C3N-00294_T 10780782 49814024 57229694 898 13670 L2HGDH 0 . GRCh38 14 50265465 50265465 + Silent SNP C C T rs139749452 C3N-00294_T C3N-00294_N C C c.1089G>A p.= p.Q363Q ENST00000267436 9/10 154 128 26 231 231 0 strelka-varscan-mutect L2HGDH,synonymous_variant,p.=,ENST00000267436,NM_024884.2;L2HGDH,synonymous_variant,p.=,ENST00000421284,;L2HGDH,synonymous_variant,p.=,ENST00000261699,; T ENST00000267436 Transcript synonymous_variant 1487/6414 1089/1392 363/463 Q caG/caA rs139749452 1 -1 L2HGDH HGNC HGNC:20499 protein_coding YES CCDS9698.1 ENSP00000267436 Q9H9P8 UPI0000048F63 NM_024884.2 9/10 Pfam_domain:PF01266,hmmpanther:PTHR13847,hmmpanther:PTHR13847:SF191 LOW 1 SNV 1 1 PASS rs139749452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 50265465 50265465 C T 1 0 0 0 0 0 0 0 1 8491 912 32 3 3 L2HGDH 14 50265465 Silent SNP C C3N-00294_T 451441 50265465 56778253 899 13671 SAV1 0 . GRCh38 14 50645005 50645005 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.545G>A p.Arg182Lys p.R182K ENST00000324679 3/5 89 68 21 90 90 0 strelka-varscan-mutect SAV1,missense_variant,p.Arg182Lys,ENST00000324679,NM_021818.3;SAV1,missense_variant,p.Arg114Lys,ENST00000555720,;SAV1,intron_variant,,ENST00000553731,;SAV1,upstream_gene_variant,,ENST00000557458,; T ENST00000324679 Transcript missense_variant 909/3063 545/1152 182/383 R/K aGa/aAa 1 -1 SAV1 HGNC HGNC:17795 protein_coding YES CCDS9701.1 ENSP00000324729 Q9H4B6 UPI0000035DA2 NM_021818.3 tolerated(0.13) 3/5 hmmpanther:PTHR10316 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 50645005 50645005 C T 1 0 0 0 0 1 0 0 0 14117 913 32 3 3 SAV1 14 50645005 Missense_Mutation SNP C C3N-00294_T 379540 50645005 56398713 900 13672 SAMD4A 0 . GRCh38 14 54737108 54737108 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.800G>C p.Gly267Ala p.G267A ENST00000392067 3/12 364 289 75 366 366 0 strelka-varscan-mutect SAMD4A,missense_variant,p.Gly267Ala,ENST00000392067,NM_015589.5;SAMD4A,missense_variant,p.Gly267Ala,ENST00000554335,;SAMD4A,intron_variant,,ENST00000631086,;SAMD4A,intron_variant,,ENST00000251091,NM_001161576.2;SAMD4A,downstream_gene_variant,,ENST00000557013,; C ENST00000392067 Transcript missense_variant 1105/6833 800/2157 267/718 G/A gGa/gCa 1 1 SAMD4A HGNC HGNC:23023 protein_coding YES CCDS32084.2 ENSP00000375919 Q9UPU9 UPI0000229786 NM_015589.5 tolerated(0.19) 3/12 hmmpanther:PTHR12515,hmmpanther:PTHR12515:SF8 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 54737108 54737108 G C 1 0 0 0 0 1 0 0 0 14081 1174 41 4 4 SAMD4A 14 54737108 Missense_Mutation SNP G C3N-00294_T 4092103 54737108 52306610 901 13673 KTN1 0 . GRCh38 14 55616581 55616581 + Silent SNP C C T rs374315337 C3N-00294_T C3N-00294_N C C c.588C>T p.= p.L196L ENST00000395314 3/44 104 92 12 148 148 0 strelka-varscan-mutect KTN1,synonymous_variant,p.=,ENST00000395314,NM_001271014.1,NM_001079521.1;KTN1,synonymous_variant,p.=,ENST00000395311,NM_001079522.1;KTN1,synonymous_variant,p.=,ENST00000413890,;KTN1,synonymous_variant,p.=,ENST00000438792,NM_004986.3;KTN1,synonymous_variant,p.=,ENST00000395308,;KTN1,synonymous_variant,p.=,ENST00000395309,;KTN1,intron_variant,,ENST00000554567,;KTN1,downstream_gene_variant,,ENST00000555498,;KTN1,downstream_gene_variant,,ENST00000557267,;KTN1,synonymous_variant,p.=,ENST00000459737,; T ENST00000395314 Transcript synonymous_variant 656/4618 588/4074 196/1357 L ctC/ctT rs374315337 1 1 KTN1 HGNC HGNC:6467 protein_coding YES CCDS41957.1 ENSP00000378725 Q86UP2 A0A024R663 UPI0000190F88 NM_001271014.1,NM_001079521.1 3/44 hmmpanther:PTHR18864 LOW 1 SNV 1 1 PASS rs374315337 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 55616581 55616581 C T 1 0 0 0 0 0 0 0 1 8483 842 30 3 3 KTN1 14 55616581 Silent SNP C C3N-00294_T 879473 55616581 51427137 902 13674 PELI2 0 . GRCh38 14 56296760 56296760 + Missense_Mutation SNP T T C novel C3N-00294_T C3N-00294_N T T c.857T>C p.Val286Ala p.V286A ENST00000267460 6/6 155 95 60 193 193 0 strelka-varscan-mutect PELI2,missense_variant,p.Val286Ala,ENST00000267460,NM_021255.2; C ENST00000267460 Transcript missense_variant 1143/5909 857/1263 286/420 V/A gTg/gCg 1 1 PELI2 HGNC HGNC:8828 protein_coding YES CCDS9726.1 ENSP00000267460 Q9HAT8 UPI0000062262 NM_021255.2 deleterious(0.02) 6/6 hmmpanther:PTHR12098,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 56296760 56296760 T C 1 0 0 0 0 1 0 0 0 11810 1696 59 5 5 PELI2 14 56296760 Missense_Mutation SNP T C3N-00294_T 680179 56296760 50746958 903 13675 AP5M1 0 . GRCh38 14 57274430 57274430 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.261G>A p.= p.L87L ENST00000261558 2/8 163 130 33 182 182 0 strelka-varscan-mutect AP5M1,synonymous_variant,p.=,ENST00000261558,NM_018229.3;AP5M1,synonymous_variant,p.=,ENST00000431972,;AP5M1,5_prime_UTR_variant,,ENST00000556995,;AP5M1,upstream_gene_variant,,ENST00000556723,;AP5M1,downstream_gene_variant,,ENST00000554213,;AP5M1,non_coding_transcript_exon_variant,,ENST00000554931,;AP5M1,intron_variant,,ENST00000555448,; A ENST00000261558 Transcript synonymous_variant 667/11737 261/1473 87/490 L ctG/ctA 1 1 AP5M1 HGNC HGNC:20192 protein_coding YES CCDS9729.1 ENSP00000261558 Q9H0R1 A0A024R654 UPI00000719DE NM_018229.3 2/8 hmmpanther:PTHR16082,hmmpanther:PTHR16082:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 57274430 57274430 G A 1 0 0 0 0 0 0 0 1 872 1277 45 3 3 AP5M1 14 57274430 Silent SNP G C3N-00294_T 977670 57274430 49769288 904 13676 NAA30 0 . GRCh38 14 57391559 57391559 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.602C>T p.Ser201Leu p.S201L ENST00000556492 2/5 165 124 41 171 171 0 strelka-varscan-mutect NAA30,missense_variant,p.Ser201Leu,ENST00000556492,NM_001011713.2;NAA30,intron_variant,,ENST00000298406,;NAA30,intron_variant,,ENST00000555166,;NAA30,intron_variant,,ENST00000554703,; T ENST00000556492 Transcript missense_variant 756/7644 602/1089 201/362 S/L tCg/tTg COSM3814972 1 1 NAA30 HGNC HGNC:19844 protein_coding YES CCDS32088.1 ENSP00000452521 Q147X3 UPI0000161013 NM_001011713.2 tolerated(0.11) 2/5 hmmpanther:PTHR23091,hmmpanther:PTHR23091:SF227 1 MODERATE 1 SNV 1 1 1 PASS rs1224102042 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 57391559 57391559 C T 1 0 0 0 0 1 0 0 0 10125 893 31 1 1 NAA30 14 57391559 Missense_Mutation SNP C C3N-00294_T 117129 57391559 49652159 905 13677 FAM71D 0 . GRCh38 14 67204574 67204574 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.397G>A p.Asp133Asn p.D133N ENST00000612183 5/9 118 95 23 119 119 0 strelka-varscan-mutect FAM71D,missense_variant,p.Asp133Asn,ENST00000612183,NM_173526.3;FAM71D,downstream_gene_variant,,ENST00000530728,;FAM71D,downstream_gene_variant,,ENST00000524532,;FAM71D,upstream_gene_variant,,ENST00000556117,;FAM71D,upstream_gene_variant,,ENST00000557671,;FAM71D,downstream_gene_variant,,ENST00000531566,;FAM71D,missense_variant,p.Asp133Asn,ENST00000311864,;FAM71D,missense_variant,p.Asp133Asn,ENST00000534174,;FAM71D,3_prime_UTR_variant,,ENST00000556046,;FAM71D,downstream_gene_variant,,ENST00000524914,;RP11-125H8.1,downstream_gene_variant,,ENST00000553618,; A ENST00000612183 Transcript missense_variant 687/1790 397/1269 133/422 D/N Gat/Aat 1 1 FAM71D HGNC HGNC:20101 protein_coding YES CCDS9778.1 ENSP00000483154 Q8N9W8 UPI000013F210 NM_173526.3 tolerated(0.24) 5/9 hmmpanther:PTHR22574:SF6,hmmpanther:PTHR22574,Pfam_domain:PF12480 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 67204574 67204574 G A 1 0 0 0 0 1 0 0 0 5474 1290 45 3 3 FAM71D 14 67204574 Missense_Mutation SNP G C3N-00294_T 9813015 67204574 39839144 906 13678 PLEKHH1 0 . GRCh38 14 67557386 67557386 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.307A>T p.Ile103Phe p.I103F ENST00000329153 4/29 84 53 31 85 85 0 strelka-varscan-mutect PLEKHH1,missense_variant,p.Ile103Phe,ENST00000329153,NM_020715.2; T ENST00000329153 Transcript missense_variant 439/6604 307/4095 103/1364 I/F Atc/Ttc 1 1 PLEKHH1 HGNC HGNC:17733 protein_coding YES CCDS45128.1 ENSP00000330278 Q9ULM0 UPI00001C1F64 NM_020715.2 deleterious(0) 4/29 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22903:SF4,hmmpanther:PTHR22903 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67557386 67557386 A T 1 0 0 0 0 1 0 0 0 12169 217 8 4 4 PLEKHH1 14 67557386 Missense_Mutation SNP A C3N-00294_T 352812 67557386 39486332 907 13679 EXD2 0 . GRCh38 14 69235025 69235025 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1043C>T p.Ser348Phe p.S348F ENST00000312994 5/9 61 48 13 60 60 0 strelka-varscan-mutect EXD2,missense_variant,p.Ser348Phe,ENST00000312994,NM_001193362.1,NM_001193363.1;EXD2,missense_variant,p.Ser223Phe,ENST00000409014,;EXD2,missense_variant,p.Ser348Phe,ENST00000409018,NM_001193361.1,NM_001193360.1;EXD2,missense_variant,p.Ser223Phe,ENST00000409675,NM_018199.3;EXD2,missense_variant,p.Ser223Phe,ENST00000409949,;EXD2,missense_variant,p.Ser223Phe,ENST00000409242,;EXD2,downstream_gene_variant,,ENST00000413191,;RP11-363J20.2,downstream_gene_variant,,ENST00000556316,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,downstream_gene_variant,,ENST00000489133,;EXD2,downstream_gene_variant,,ENST00000494629,;EXD2,upstream_gene_variant,,ENST00000465286,; T ENST00000312994 Transcript missense_variant 1364/5107 1043/1866 348/621 S/F tCt/tTt 1 1 EXD2 HGNC HGNC:20217 protein_coding YES CCDS53902.1 ENSP00000313140 Q9NVH0 UPI0000577ED7 NM_001193362.1,NM_001193363.1 deleterious(0) 5/9 hmmpanther:PTHR13620,hmmpanther:PTHR13620:SF0 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 46 69235025 69235025 C T 1 0 0 0 0 1 0 0 0 5165 913 32 3 3 EXD2 14 69235025 Missense_Mutation SNP C C3N-00294_T 1677639 69235025 37808693 908 13680 ELMSAN1 0 . GRCh38 14 73739586 73739586 + Silent SNP G G C rs149894352 C3N-00294_T C3N-00294_N G G c.423C>G p.= p.L141L ENST00000286523 2/12 222 178 44 237 237 0 strelka-varscan-mutect ELMSAN1,synonymous_variant,p.=,ENST00000286523,NM_194278.3;ELMSAN1,synonymous_variant,p.=,ENST00000394071,NM_001043318.2;ELMSAN1,synonymous_variant,p.=,ENST00000435371,;ELMSAN1,synonymous_variant,p.=,ENST00000423556,;ELMSAN1,downstream_gene_variant,,ENST00000421708,;ELMSAN1,downstream_gene_variant,,ENST00000486739,;ELMSAN1,upstream_gene_variant,,ENST00000451078,; C ENST00000286523 Transcript synonymous_variant 1206/8091 423/3138 141/1045 L ctC/ctG rs149894352 1 -1 ELMSAN1 HGNC HGNC:19853 protein_coding YES CCDS9819.1 ENSP00000286523 Q6PJG2 A0A024R689 UPI00001FD815 NM_194278.3 2/12 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF24 LOW 1 SNV 1 1 PASS rs149894352 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 73739586 73739586 G C 1 0 0 0 0 0 0 0 1 4905 929 33 4 4 ELMSAN1 14 73739586 Silent SNP G C3N-00294_T 4504561 73739586 33304132 909 13681 LIN52 0 . GRCh38 14 74101220 74101220 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.277C>G p.Gln93Glu p.Q93E ENST00000555028 5/6 112 92 20 98 98 0 strelka-varscan-mutect LIN52,missense_variant,p.Gln93Glu,ENST00000555028,NM_001024674.2;LIN52,intron_variant,,ENST00000554938,;LIN52,non_coding_transcript_exon_variant,,ENST00000554076,;LIN52,intron_variant,,ENST00000553404,;LIN52,downstream_gene_variant,,ENST00000554289,; G ENST00000555028 Transcript missense_variant 444/2776 277/351 93/116 Q/E Cag/Gag 1 1 LIN52 HGNC HGNC:19856 protein_coding YES CCDS32120.1 ENSP00000451812 Q52LA3 UPI00000E9291 NM_001024674.2 deleterious(0) 5/6 hmmpanther:PTHR31489,Pfam_domain:PF10044 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 74101220 74101220 C G 1 0 0 0 0 1 0 0 0 8716 827 29 4 4 LIN52 14 74101220 Missense_Mutation SNP C C3N-00294_T 361634 74101220 32942498 910 13682 AREL1 0 . GRCh38 14 74675759 74675759 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1020G>A p.= p.E340E ENST00000356357 8/20 186 134 52 183 183 0 strelka-varscan-mutect AREL1,synonymous_variant,p.=,ENST00000356357,NM_001039479.1;AREL1,synonymous_variant,p.=,ENST00000556202,;AREL1,synonymous_variant,p.=,ENST00000490805,;AREL1,non_coding_transcript_exon_variant,,ENST00000557401,;AREL1,synonymous_variant,p.=,ENST00000555330,;AREL1,non_coding_transcript_exon_variant,,ENST00000469797,;AREL1,non_coding_transcript_exon_variant,,ENST00000556327,;AREL1,upstream_gene_variant,,ENST00000481010,;AREL1,downstream_gene_variant,,ENST00000553411,;AREL1,downstream_gene_variant,,ENST00000553279,; T ENST00000356357 Transcript synonymous_variant 1536/5456 1020/2472 340/823 E gaG/gaA 1 -1 AREL1 HGNC HGNC:20363 protein_coding YES CCDS41971.1 ENSP00000348714 O15033 UPI0000073D44 NM_001039479.1 8/20 hmmpanther:PTHR11254:SF340,hmmpanther:PTHR11254 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 74675759 74675759 C T 1 0 0 0 0 0 0 0 1 966 564 20 3 3 AREL1 14 74675759 Silent SNP C C3N-00294_T 574539 74675759 32367959 911 13683 NRXN3 0 . GRCh38 14 78967253 78967253 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1704C>G p.Ile568Met p.I568M ENST00000554719 10/17 161 124 37 169 169 0 strelka-varscan-mutect NRXN3,missense_variant,p.Ile930Met,ENST00000634499,;NRXN3,missense_variant,p.Ile941Met,ENST00000635466,;NRXN3,missense_variant,p.Ile568Met,ENST00000554719,NM_004796.5;NRXN3,missense_variant,p.Ile702Met,ENST00000335750,;NRXN3,non_coding_transcript_exon_variant,,ENST00000634266,;NRXN3,missense_variant,p.Ile930Met,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,; G ENST00000554719 Transcript missense_variant 2195/4156 1704/3186 568/1061 I/M atC/atG 1 1 NRXN3 HGNC HGNC:8010 protein_coding YES CCDS9870.1 ENSP00000451648 Q9Y4C0 UPI0000167BBA NM_004796.5 tolerated(1) 10/17 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 78967253 78967253 C G 1 0 0 0 0 1 0 0 0 10726 816 29 4 4 NRXN3 14 78967253 Missense_Mutation SNP C C3N-00294_T 4291494 78967253 28076465 912 13684 SEL1L 0 . GRCh38 14 81506095 81506095 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.487G>A p.Glu163Lys p.E163K ENST00000336735 4/21 91 69 22 97 97 0 strelka-varscan-mutect SEL1L,missense_variant,p.Glu163Lys,ENST00000336735,NM_005065.5;SEL1L,missense_variant,p.Glu163Lys,ENST00000555824,NM_001244984.1;SEL1L,missense_variant,p.Glu142Lys,ENST00000557372,;SEL1L,non_coding_transcript_exon_variant,,ENST00000554744,; T ENST00000336735 Transcript missense_variant 604/7925 487/2385 163/794 E/K Gaa/Aaa 1 -1 SEL1L HGNC HGNC:10717 protein_coding YES CCDS9876.1 ENSP00000337053 Q9UBV2 UPI0000135746 NM_005065.5 tolerated_low_confidence(1) 4/21 Gene3D:2.10.10.10,Pfam_domain:PF00040,Prints_domain:PR00013,PROSITE_patterns:PS00023,PROSITE_profiles:PS51092,SMART_domains:SM00059,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999993 1 1 1 0 T 3 4 46 81506095 81506095 C T 1 0 0 0 0 1 0 0 0 14287 835 29 3 3 SEL1L 14 81506095 Missense_Mutation SNP C C3N-00294_T 2538842 81506095 25537623 913 13685 CCDC88C 0 . GRCh38 14 91307203 91307203 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.3030C>G p.= p.L1010L ENST00000389857 18/30 188 150 38 214 214 0 strelka-varscan-mutect CCDC88C,synonymous_variant,p.=,ENST00000389857,NM_001080414.3; C ENST00000389857 Transcript synonymous_variant 3117/7474 3030/6087 1010/2028 L ctC/ctG 1 -1 CCDC88C HGNC HGNC:19967 protein_coding YES CCDS45151.1 ENSP00000374507 Q9P219 UPI00006C1440 NM_001080414.3 18/30 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF31 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 91307203 91307203 G C 1 0 0 0 0 0 0 0 1 2564 1277 45 4 4 CCDC88C 14 91307203 Silent SNP G C3N-00294_T 9801108 91307203 15736515 914 13686 TRIP11 0 . GRCh38 14 92006220 92006220 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1756G>C p.Glu586Gln p.E586Q ENST00000267622 11/21 82 62 20 140 140 0 strelka-varscan-mutect TRIP11,missense_variant,p.Glu586Gln,ENST00000267622,NM_001321851.1,NM_004239.3;TRIP11,missense_variant,p.Glu302Gln,ENST00000554357,; G ENST00000267622 Transcript missense_variant 2130/9996 1756/5940 586/1979 E/Q Gaa/Caa 1 -1 TRIP11 HGNC HGNC:12305 protein_coding YES CCDS9899.1 ENSP00000267622 Q15643 UPI000013D767 NM_001321851.1,NM_004239.3 tolerated(0.15) 11/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18921,hmmpanther:PTHR18921:SF5 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 92006220 92006220 C G 1 0 0 0 0 1 0 0 0 17052 922 32 4 4 TRIP11 14 92006220 Missense_Mutation SNP C C3N-00294_T 699017 92006220 15037498 915 13687 UNC79 0 . GRCh38 14 93622403 93622403 + Missense_Mutation SNP G G A rs761093792 C3N-00294_T C3N-00294_N G G c.4639G>A p.Glu1547Lys p.E1547K ENST00000256339 30/50 137 110 27 163 162 1 strelka-varscan-mutect UNC79,missense_variant,p.Glu1746Lys,ENST00000553484,;UNC79,missense_variant,p.Glu1724Lys,ENST00000555664,;UNC79,missense_variant,p.Glu1547Lys,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Glu1724Lys,ENST00000393151,;UNC79,missense_variant,p.Glu1547Lys,ENST00000621021,; A ENST00000256339 Transcript missense_variant 5294/8400 4639/7377 1547/2458 E/K Gaa/Aaa rs761093792 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated_low_confidence(0.3) 30/50 MODERATE 1 SNV 5 1 PASS rs761093792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 93622403 93622403 G A 1 0 0 0 0 1 0 0 0 17520 1059 37 1 1 UNC79 14 93622403 Missense_Mutation SNP G C3N-00294_T 1616183 93622403 13421315 916 13688 SERPINA1 0 . GRCh38 14 94382886 94382886 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.352G>A p.Glu118Lys p.E118K ENST00000448921 4/7 117 90 27 156 156 0 strelka-varscan-mutect SERPINA1,missense_variant,p.Glu118Lys,ENST00000448921,NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1;SERPINA1,missense_variant,p.Glu118Lys,ENST00000437397,NM_001127706.1,NM_001127707.1,NM_001127702.1;SERPINA1,missense_variant,p.Glu118Lys,ENST00000355814,NM_001002235.2,NM_001127700.1;SERPINA1,missense_variant,p.Glu118Lys,ENST00000440909,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000393088,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000404814,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000393087,NM_000295.4;SERPINA1,missense_variant,p.Glu118Lys,ENST00000449399,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000636712,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000402629,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000557492,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000556091,;SERPINA1,missense_variant,p.Glu32Lys,ENST00000554720,;SERPINA1,downstream_gene_variant,,ENST00000557118,;SERPINA1,downstream_gene_variant,,ENST00000553327,;SERPINA1,downstream_gene_variant,,ENST00000556955,;SERPINA1,downstream_gene_variant,,ENST00000555289,;SERPINA1,missense_variant,p.Glu118Lys,ENST00000489769,; T ENST00000448921 Transcript missense_variant 925/3532 352/1257 118/418 E/K Gaa/Aaa 1 -1 SERPINA1 HGNC HGNC:8941 protein_coding YES CCDS9925.1 ENSP00000416066 P01009 E9KL23 UPI000000CBEC NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1 tolerated(0.43) 4/7 hmmpanther:PTHR11461:SF165,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 94382886 94382886 C T 1 0 0 0 0 1 0 0 0 14362 835 29 3 3 SERPINA1 14 94382886 Missense_Mutation SNP C C3N-00294_T 760483 94382886 12660832 917 13689 DICER1 0 . GRCh38 14 95096292 95096292 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.4628C>T p.Ser1543Phe p.S1543F ENST00000526495 25/29 513 412 101 569 569 0 strelka-varscan-mutect DICER1,missense_variant,p.Ser1543Phe,ENST00000526495,NM_030621.4,NM_001291628.1;DICER1,missense_variant,p.Ser1543Phe,ENST00000343455,NM_177438.2;DICER1,missense_variant,p.Ser1543Phe,ENST00000393063,;DICER1,missense_variant,p.Ser1543Phe,ENST00000527414,NM_001271282.2;DICER1,missense_variant,p.Ser1543Phe,ENST00000541352,NM_001195573.1;DICER1,missense_variant,p.Ser441Phe,ENST00000556045,;DICER1,missense_variant,p.Ser222Phe,ENST00000532939,;DICER1,upstream_gene_variant,,ENST00000527416,;DICER1,upstream_gene_variant,,ENST00000527554,; A ENST00000526495 Transcript missense_variant 4920/10331 4628/5769 1543/1922 S/F tCc/tTc 1 -1 DICER1 HGNC HGNC:17098 protein_coding YES CCDS9931.1 ENSP00000437256 Q9UPY3 UPI0000168662 NM_030621.4,NM_001291628.1 tolerated(0.73) 25/29 Gene3D:1.10.1520.10,Pfam_domain:PF00636,hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF26,SMART_domains:SM00535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 95096292 95096292 G A 1 0 0 0 0 1 0 0 0 4325 1174 41 3 3 DICER1 14 95096292 Missense_Mutation SNP G C3N-00294_T 713406 95096292 11947426 918 13690 BDKRB1 0 . GRCh38 14 96264315 96264315 + Missense_Mutation SNP C C G rs774234943 C3N-00294_T C3N-00294_N C C c.633C>G p.Phe211Leu p.F211L ENST00000216629 3/3 290 249 41 278 278 0 strelka-varscan-mutect BDKRB1,missense_variant,p.Phe211Leu,ENST00000216629,NM_000710.3;BDKRB1,missense_variant,p.Phe211Leu,ENST00000553356,;BDKRB1,missense_variant,p.Phe211Leu,ENST00000611804,;RP11-404P21.8,downstream_gene_variant,,ENST00000553811,;RP11-404P21.3,intron_variant,,ENST00000553638,;BDKRB1,upstream_gene_variant,,ENST00000557122,;RP11-404P21.8,downstream_gene_variant,,ENST00000555847,; G ENST00000216629 Transcript missense_variant 1239/1687 633/1062 211/353 F/L ttC/ttG rs774234943,COSM3499564 1 1 BDKRB1 HGNC HGNC:1029 protein_coding YES CCDS9943.1 ENSP00000216629 P46663 UPI0000000348 NM_000710.3 deleterious(0) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF28,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774234943 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 96264315 96264315 C G 1 0 0 0 0 1 0 0 0 1539 854 30 4 4 BDKRB1 14 96264315 Missense_Mutation SNP C C3N-00294_T 1168023 96264315 10779403 919 13691 CYP46A1 0 . GRCh38 14 99716180 99716180 + Silent SNP C C T rs780395313 C3N-00294_T C3N-00294_N C C c.888C>T p.= p.F296F ENST00000261835 9/15 220 187 33 263 262 1 strelka-varscan-mutect CYP46A1,synonymous_variant,p.=,ENST00000261835,NM_006668.1;CYP46A1,synonymous_variant,p.=,ENST00000380228,;CYP46A1,synonymous_variant,p.=,ENST00000556313,;CYP46A1,3_prime_UTR_variant,,ENST00000554917,;CYP46A1,non_coding_transcript_exon_variant,,ENST00000554176,;CYP46A1,downstream_gene_variant,,ENST00000554611,;CYP46A1,upstream_gene_variant,,ENST00000556822,; T ENST00000261835 Transcript synonymous_variant 992/2181 888/1503 296/500 F ttC/ttT rs780395313,COSM3493740 1 1 CYP46A1 HGNC HGNC:2641 protein_coding YES CCDS9954.1 ENSP00000261835 Q9Y6A2 UPI00001281DC NM_006668.1 9/15 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24293,hmmpanther:PTHR24293:SF2,Superfamily_domains:SSF48264 0,1 LOW 1 SNV 1 0,1 1 PASS rs780395313 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 99716180 99716180 C T 1 0 0 0 0 0 0 0 1 3985 883 31 1 1 CYP46A1 14 99716180 Silent SNP C C3N-00294_T 3451865 99716180 7327538 920 13692 EML1 0 . GRCh38 14 99914588 99914588 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1700G>A p.Gly567Glu p.G567E ENST00000334192 16/23 104 97 7 113 113 0 strelka-varscan-mutect EML1,missense_variant,p.Gly548Glu,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Gly567Glu,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Gly536Glu,ENST00000327921,;EML1,downstream_gene_variant,,ENST00000554386,;EML1,downstream_gene_variant,,ENST00000555812,;EML1,missense_variant,p.Gly5Glu,ENST00000557313,;EML1,non_coding_transcript_exon_variant,,ENST00000554111,;EML1,downstream_gene_variant,,ENST00000554553,; A ENST00000334192 Transcript missense_variant 1834/4064 1700/2505 567/834 G/E gGa/gAa 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 deleterious(0) 16/23 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS rs1192076161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 99914588 99914588 G A 1 0 0 0 0 1 0 0 0 4939 1174 41 3 3 EML1 14 99914588 Missense_Mutation SNP G C3N-00294_T 198408 99914588 7129130 921 13693 DYNC1H1 0 . GRCh38 14 102041708 102041708 + Missense_Mutation SNP G G T rs768636289 C3N-00294_T C3N-00294_N G G c.12076G>T p.Asp4026Tyr p.D4026Y ENST00000360184 65/78 353 223 130 464 463 1 strelka-varscan-mutect DYNC1H1,missense_variant,p.Asp4026Tyr,ENST00000360184,NM_001376.4;DYNC1H1,downstream_gene_variant,,ENST00000553423,;RP11-1017G21.4,intron_variant,,ENST00000557551,;RP11-1017G21.4,intron_variant,,ENST00000557242,;RP11-1017G21.4,intron_variant,,ENST00000553701,;DYNC1H1,downstream_gene_variant,,ENST00000556791,;DYNC1H1,upstream_gene_variant,,ENST00000555102,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000556139,;DYNC1H1,downstream_gene_variant,,ENST00000556499,;DYNC1H1,downstream_gene_variant,,ENST00000555800,; T ENST00000360184 Transcript missense_variant 12240/14333 12076/13941 4026/4646 D/Y Gac/Tac rs768636289,COSM400505 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0) 65/78 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768636289 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 102041708 102041708 G T 1 0 0 0 0 1 0 0 0 4665 1058 37 1 1 DYNC1H1 14 102041708 Missense_Mutation SNP G C3N-00294_T 2127120 102041708 5002010 922 13694 DYNC1H1 0 . GRCh38 14 102042709 102042709 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.12474G>A p.= p.L4158L ENST00000360184 69/78 588 474 114 629 629 0 strelka-varscan-mutect DYNC1H1,synonymous_variant,p.=,ENST00000360184,NM_001376.4;DYNC1H1,downstream_gene_variant,,ENST00000553423,;RP11-1017G21.4,intron_variant,,ENST00000557551,;RP11-1017G21.4,intron_variant,,ENST00000557242,;RP11-1017G21.4,intron_variant,,ENST00000553701,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000555102,;DYNC1H1,downstream_gene_variant,,ENST00000556139,;DYNC1H1,upstream_gene_variant,,ENST00000556229,;DYNC1H1,downstream_gene_variant,,ENST00000556499,;DYNC1H1,downstream_gene_variant,,ENST00000555800,; A ENST00000360184 Transcript synonymous_variant 12638/14333 12474/13941 4158/4646 L ctG/ctA 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 69/78 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 102042709 102042709 G A 1 0 0 0 0 0 0 0 1 4665 1277 45 3 3 DYNC1H1 14 102042709 Silent SNP G C3N-00294_T 1001 102042709 5001009 923 13695 MOK 0 . GRCh38 14 102232587 102232587 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.814G>A p.Glu272Lys p.E272K ENST00000361847 9/12 118 95 23 106 106 0 strelka-varscan-mutect MOK,missense_variant,p.Glu272Lys,ENST00000361847,NM_014226.2;MOK,missense_variant,p.Glu271Lys,ENST00000522874,;MOK,missense_variant,p.Met4Ile,ENST00000522867,;MOK,missense_variant,p.Glu271Lys,ENST00000193029,;MOK,missense_variant,p.Glu242Lys,ENST00000524214,NM_001272011.1;MOK,missense_variant,p.Met4Ile,ENST00000517966,;MOK,missense_variant,p.Met4Ile,ENST00000524370,;MOK,missense_variant,p.Met4Ile,ENST00000523231,;MOK,missense_variant,p.Met4Ile,ENST00000519058,;MOK,missense_variant,p.Met4Ile,ENST00000522534,;MOK,missense_variant,p.Glu152Lys,ENST00000559838,;MOK,missense_variant,p.Met4Ile,ENST00000522537,;MOK,missense_variant,p.Met4Ile,ENST00000561150,;MOK,upstream_gene_variant,,ENST00000521937,;MOK,non_coding_transcript_exon_variant,,ENST00000519477,;MOK,non_coding_transcript_exon_variant,,ENST00000524120,;MOK,intron_variant,,ENST00000520266,;MOK,intron_variant,,ENST00000557823,;MOK,missense_variant,p.Met4Ile,ENST00000559138,;MOK,3_prime_UTR_variant,,ENST00000521766,;MOK,3_prime_UTR_variant,,ENST00000521388,;MOK,non_coding_transcript_exon_variant,,ENST00000521249,;MOK,non_coding_transcript_exon_variant,,ENST00000518686,;MOK,non_coding_transcript_exon_variant,,ENST00000523485,;MOK,non_coding_transcript_exon_variant,,ENST00000519569,;MOK,non_coding_transcript_exon_variant,,ENST00000520046,;MOK,non_coding_transcript_exon_variant,,ENST00000520252,;MOK,downstream_gene_variant,,ENST00000562292,; T ENST00000361847 Transcript missense_variant 1046/1940 814/1260 272/419 E/K Gag/Aag 1 -1 MOK HGNC HGNC:9833 protein_coding YES CCDS9971.1 ENSP00000355304 Q9UQ07 UPI0000035B77 NM_014226.2 tolerated(0.08) 9/12 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF72,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 102232587 102232587 C T 1 0 0 0 0 1 0 0 0 9661 835 29 3 3 MOK 14 102232587 Missense_Mutation SNP C C3N-00294_T 189878 102232587 4811131 924 13696 TRMT61A 0 . GRCh38 14 103530018 103530018 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.40G>C p.Asp14His p.D14H ENST00000389749 2/4 147 114 33 149 149 0 strelka-varscan-mutect TRMT61A,missense_variant,p.Asp14His,ENST00000389749,NM_152307.2;TRMT61A,intron_variant,,ENST00000299202,;RP11-600F24.7,upstream_gene_variant,,ENST00000568177,; C ENST00000389749 Transcript missense_variant 147/3229 40/870 14/289 D/H Gac/Cac 1 1 TRMT61A HGNC HGNC:23790 protein_coding YES CCDS41994.1 ENSP00000374399 Q96FX7 A0A024R6Q2 UPI0000072BC7 NM_152307.2 deleterious(0) 2/4 PROSITE_profiles:PS51620,hmmpanther:PTHR12133,hmmpanther:PTHR12133:SF2,Gene3D:3.10.330.20,PIRSF_domain:PIRSF017269,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 103530018 103530018 G C 1 0 0 0 0 1 0 0 0 17074 1290 45 4 4 TRMT61A 14 103530018 Missense_Mutation SNP G C3N-00294_T 1297431 103530018 3513700 925 13697 KIF26A 0 . GRCh38 14 104179715 104179715 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.5574C>T p.= p.V1858V ENST00000423312 15/15 121 104 17 138 138 0 strelka-varscan-mutect KIF26A,synonymous_variant,p.=,ENST00000315264,;KIF26A,synonymous_variant,p.=,ENST00000423312,NM_015656.1; T ENST00000423312 Transcript synonymous_variant 5574/5649 5574/5649 1858/1882 V gtC/gtT 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 15/15 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF407 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 104179715 104179715 C T 1 0 0 0 0 0 0 0 1 8159 813 29 3 3 KIF26A 14 104179715 Silent SNP C C3N-00294_T 649697 104179715 2864003 926 13698 ZBTB42 0 . GRCh38 14 104801510 104801510 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.313C>T p.= p.L105L ENST00000342537 1/1 235 198 37 282 282 0 strelka-varscan-mutect ZBTB42,synonymous_variant,p.=,ENST00000342537,;ZBTB42,synonymous_variant,p.=,ENST00000555360,NM_001137601.1; T ENST00000342537 Transcript synonymous_variant 598/3800 313/1269 105/422 L Ctg/Ttg 1 1 ZBTB42 HGNC HGNC:32550 protein_coding YES CCDS45174.1 ENSP00000409107 B2RXF5 UPI0001849D48 1/1 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF293,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 104801510 104801510 C T 1 0 0 0 0 0 0 0 1 18113 680 24 3 3 ZBTB42 14 104801510 Silent SNP C C3N-00294_T 621795 104801510 2242208 927 13699 PACS2 0 . GRCh38 14 105381061 105381061 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1230G>T p.Arg410Ser p.R410S ENST00000447393 12/25 122 67 55 130 130 0 strelka-varscan-mutect PACS2,missense_variant,p.Arg410Ser,ENST00000447393,NM_001100913.2;PACS2,missense_variant,p.Arg410Ser,ENST00000325438,NM_015197.3;PACS2,missense_variant,p.Arg335Ser,ENST00000430725,NM_001243127.2;PACS2,missense_variant,p.Arg380Ser,ENST00000547217,;PACS2,non_coding_transcript_exon_variant,,ENST00000551692,;PACS2,upstream_gene_variant,,ENST00000551743,;PACS2,upstream_gene_variant,,ENST00000547903,; T ENST00000447393 Transcript missense_variant 1405/6365 1230/2715 410/904 R/S agG/agT 1 1 PACS2 HGNC HGNC:23794 protein_coding YES CCDS45178.2 ENSP00000393559 Q86VP3 UPI0000E56F01 NM_001100913.2 tolerated(0.18) 12/25 hmmpanther:PTHR13280:SF15,hmmpanther:PTHR13280 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 105381061 105381061 G T 1 0 0 0 0 1 0 0 0 11451 1165 41 2 2 PACS2 14 105381061 Missense_Mutation SNP G C3N-00294_T 579551 105381061 1662657 928 13700 OR4N4 0 . GRCh38 15 22095172 22095172 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.651C>A p.= p.S217S ENST00000328795 1/1 98 84 14 68 68 0 varscan-mutect OR4N4,synonymous_variant,p.=,ENST00000328795,NM_001005241.3; A ENST00000328795 Transcript synonymous_variant 742/1126 651/951 217/316 S tcC/tcA 1 1 OR4N4 HGNC HGNC:15375 protein_coding YES CCDS32173.1 ENSP00000332500 Q8N0Y3 A0A126GVN2 UPI0000041C1A NM_001005241.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF97,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1185204893 . 21 185 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 22095172 22095172 C A 1 0 0 0 0 0 0 0 1 11154 668 24 2 2 OR4N4 15 22095172 Silent SNP C C3N-00294_T 22095172 79896017 929 13701 MKRN3 0 . GRCh38 15 23567096 23567096 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1314C>T p.= p.F438F ENST00000314520 1/1 202 149 53 207 207 0 strelka-varscan-mutect MKRN3,synonymous_variant,p.=,ENST00000314520,NM_005664.3;MKRN3,intron_variant,,ENST00000568252,;MKRN3,intron_variant,,ENST00000564592,;AC126407.1,upstream_gene_variant,,ENST00000626930,;MIR4508,upstream_gene_variant,,ENST00000584178,;MKRN3-AS1,downstream_gene_variant,,ENST00000563044,;MKRN3,intron_variant,,ENST00000568945,;MKRN3,intron_variant,,ENST00000570112,; T ENST00000314520 Transcript synonymous_variant 1413/2337 1314/1524 438/507 F ttC/ttT 1 1 MKRN3 HGNC HGNC:7114 protein_coding YES CCDS10013.1 ENSP00000313881 Q13064 UPI000000DAA1 NM_005664.3 1/1 hmmpanther:PTHR11224:SF38,hmmpanther:PTHR11224,Pfam_domain:PF15815 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 23567096 23567096 C T 1 0 0 0 0 0 0 0 1 9576 825 29 3 3 MKRN3 15 23567096 Silent SNP C C3N-00294_T 1471924 23567096 78424093 930 13702 MAGEL2 0 . GRCh38 15 23644149 23644149 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.3594G>A p.= p.L1198L ENST00000532292 1/1 121 99 22 148 148 0 strelka-varscan-mutect MAGEL2,synonymous_variant,p.=,ENST00000532292,NM_019066.4; T ENST00000532292 Transcript synonymous_variant 3693/4298 3594/3750 1198/1249 L ctG/ctA 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 1/1 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66 LOW 1 SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 23644149 23644149 C T 1 0 0 0 0 0 0 0 1 9107 813 29 3 3 MAGEL2 15 23644149 Silent SNP C C3N-00294_T 77053 23644149 78347040 931 13703 GOLGA8M 0 . GRCh38 15 28709537 28709537 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.220G>T p.Asp74Tyr p.D74Y ENST00000563027 3/19 63 53 10 109 109 0 varscan-mutect GOLGA8M,missense_variant,p.Asp74Tyr,ENST00000563027,NM_001282468.1;GOLGA8M,non_coding_transcript_exon_variant,,ENST00000563213,; A ENST00000563027 Transcript missense_variant 220/1899 220/1899 74/632 D/Y Gat/Tat 1 -1 GOLGA8M HGNC HGNC:44404 protein_coding YES CCDS61572.1 ENSP00000456927 H3BSY2 UPI0001A5E7A0 NM_001282468.1 deleterious(0.03) 3/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -19.99927 1 1 1 1 0 A 3 1 46 28709537 28709537 C A 1 0 0 0 0 1 0 0 0 6454 913 32 2 2 GOLGA8M 15 28709537 Missense_Mutation SNP C C3N-00294_T 5065388 28709537 73281652 932 13704 TJP1 0 . GRCh38 15 29732467 29732467 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.1983G>T p.= p.L661L ENST00000346128 15/28 104 86 18 112 112 0 strelka-varscan-mutect TJP1,synonymous_variant,p.=,ENST00000346128,NM_003257.4;TJP1,synonymous_variant,p.=,ENST00000614355,;TJP1,synonymous_variant,p.=,ENST00000400011,NM_001301026.1;TJP1,synonymous_variant,p.=,ENST00000356107,NM_001301025.1;TJP1,synonymous_variant,p.=,ENST00000545208,NM_175610.3;RP11-680F8.4,upstream_gene_variant,,ENST00000560740,;TJP1,non_coding_transcript_exon_variant,,ENST00000462916,;HMGN2P5,downstream_gene_variant,,ENST00000436882,; A ENST00000346128 Transcript synonymous_variant 2458/7950 1983/5247 661/1748 L ctG/ctT 1 -1 TJP1 HGNC HGNC:11827 protein_coding YES CCDS42007.1 ENSP00000281537 Q07157 UPI000013DC83 NM_003257.4 15/28 Gene3D:3.40.50.300,hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF25,SMART_domains:SM00072 LOW 1 SNV 1 1 PASS rs1400479695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 29732467 29732467 C A 1 0 0 0 0 0 0 0 1 16371 581 21 2 2 TJP1 15 29732467 Silent SNP C C3N-00294_T 1022930 29732467 72258722 933 13705 GOLGA8K 0 . GRCh38 15 32394175 32394175 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.1335C>G p.= p.V445V ENST00000512626 15/19 220 186 34 199 199 0 strelka-varscan-mutect GOLGA8K,synonymous_variant,p.=,ENST00000512626,NM_001282493.1;RN7SL185P,downstream_gene_variant,,ENST00000615150,;RP13-395E19.3,downstream_gene_variant,,ENST00000562108,; C ENST00000512626 Transcript synonymous_variant 1336/1894 1335/1893 445/630 V gtC/gtG 1 -1 GOLGA8K HGNC HGNC:38652 protein_coding YES CCDS61577.1 ENSP00000426691 D6RF30 UPI0001A5E7CC NM_001282493.1 15/19 Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 LOW SNV 5 1 PASS . . 4 205 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 32394175 32394175 G C 1 0 0 0 0 0 0 0 1 6453 1161 41 4 4 GOLGA8K 15 32394175 Silent SNP G C3N-00294_T 2661708 32394175 69597014 934 13706 RYR3 0 . GRCh38 15 33838332 33838332 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.12352G>A p.Glu4118Lys p.E4118K ENST00000634891 89/104 340 276 64 393 392 1 strelka-varscan-mutect RYR3,missense_variant,p.Glu4118Lys,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Glu4121Lys,ENST00000622037,;RYR3,missense_variant,p.Glu4113Lys,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Glu4117Lys,ENST00000389232,;RYR3,missense_variant,p.Glu4107Lys,ENST00000634418,;RYR3,upstream_gene_variant,,ENST00000634730,;RYR3,upstream_gene_variant,,ENST00000636568,;RYR3,downstream_gene_variant,,ENST00000635842,;RYR3,downstream_gene_variant,,ENST00000638032,;RYR3,non_coding_transcript_exon_variant,,ENST00000635749,;RYR3,upstream_gene_variant,,ENST00000638052,;RYR3,upstream_gene_variant,,ENST00000636656,;RYR3,upstream_gene_variant,,ENST00000637615,;RYR3,upstream_gene_variant,,ENST00000637984,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,upstream_gene_variant,,ENST00000637948,;RYR3,upstream_gene_variant,,ENST00000636845,; A ENST00000634891 Transcript missense_variant 12453/15591 12352/14613 4118/4870 E/K Gaa/Aaa COSM700083 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.1) 89/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 33838332 33838332 G A 1 0 0 0 0 1 0 0 0 14030 1291 45 3 3 RYR3 15 33838332 Missense_Mutation SNP G C3N-00294_T 1444157 33838332 68152857 935 13707 RYR3 0 . GRCh38 15 33864147 33864147 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.14475G>C p.= p.L4825L ENST00000634891 103/104 99 84 15 144 144 0 strelka-varscan-mutect RYR3,synonymous_variant,p.=,ENST00000634891,NM_001036.4;RYR3,synonymous_variant,p.=,ENST00000622037,;RYR3,synonymous_variant,p.=,ENST00000415757,NM_001243996.2;RYR3,synonymous_variant,p.=,ENST00000389232,;RYR3,synonymous_variant,p.=,ENST00000634418,;RYR3,synonymous_variant,p.=,ENST00000634730,;RYR3,synonymous_variant,p.=,ENST00000636568,;AVEN,downstream_gene_variant,,ENST00000306730,NM_020371.2;RP11-3D4.2,intron_variant,,ENST00000560268,;RYR3,non_coding_transcript_exon_variant,,ENST00000637072,;RYR3,non_coding_transcript_exon_variant,,ENST00000638052,;AVEN,downstream_gene_variant,,ENST00000558136,;RYR3,downstream_gene_variant,,ENST00000636878,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,3_prime_UTR_variant,,ENST00000637948,;RYR3,3_prime_UTR_variant,,ENST00000636845,;AVEN,downstream_gene_variant,,ENST00000560649,; C ENST00000634891 Transcript synonymous_variant 14576/15591 14475/14613 4825/4870 L ctG/ctC 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 103/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.99997 0.9999935 1 1 1 0 C 2 2 46 33864147 33864147 G C 1 0 0 0 0 0 0 0 1 14030 1277 45 4 4 RYR3 15 33864147 Silent SNP G C3N-00294_T 25815 33864147 68127042 936 13708 RTF1 0 . GRCh38 15 41452998 41452998 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.407C>G p.Ser136Ter p.S136* ENST00000389629 3/18 96 81 15 94 94 0 strelka-varscan-mutect RTF1,stop_gained,p.Ser136Ter,ENST00000389629,NM_015138.4;RNU6-1169P,upstream_gene_variant,,ENST00000363537,;RTF1,downstream_gene_variant,,ENST00000462276,;RTF1,downstream_gene_variant,,ENST00000558298,; G ENST00000389629 Transcript stop_gained 419/5021 407/2133 136/710 S/* tCa/tGa 1 1 RTF1 HGNC HGNC:28996 protein_coding YES CCDS32200.2 ENSP00000374280 Q92541 UPI0000E23C14 NM_015138.4 3/18 hmmpanther:PTHR13115,hmmpanther:PTHR13115:SF8,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 41452998 41452998 C G 1 0 0 0 0 0 1 0 0 13980 838 29 4 4 RTF1 15 41452998 Nonsense_Mutation SNP C C3N-00294_T 7588851 41452998 60538191 937 13709 MAP1A 0 . GRCh38 15 43523169 43523169 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1696G>A p.Glu566Lys p.E566K ENST00000300231 4/6 122 93 29 133 133 0 strelka-varscan-mutect MAP1A,missense_variant,p.Glu804Lys,ENST00000382031,;MAP1A,missense_variant,p.Glu566Lys,ENST00000300231,NM_002373.5; A ENST00000300231 Transcript missense_variant 2146/10258 1696/8412 566/2803 E/K Gag/Aag 1 1 MAP1A HGNC HGNC:6835 protein_coding YES CCDS42031.1 ENSP00000300231 P78559 UPI000013E63C NM_002373.5 tolerated(0.07) 4/6 hmmpanther:PTHR13843,hmmpanther:PTHR13843:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 43523169 43523169 G A 1 0 0 0 0 1 0 0 0 9150 1175 41 3 3 MAP1A 15 43523169 Missense_Mutation SNP G C3N-00294_T 2070171 43523169 58468020 938 13710 FRMD5 0 . GRCh38 15 43873913 43873913 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1685C>G p.Ser562Ter p.S562* ENST00000417257 14/14 97 78 19 98 98 0 strelka-varscan-mutect FRMD5,stop_gained,p.Ser328Ter,ENST00000618556,NM_001286491.1;FRMD5,stop_gained,p.Ser562Ter,ENST00000417257,NM_032892.4;FRMD5,stop_gained,p.Ser241Ter,ENST00000636859,;FRMD5,synonymous_variant,p.=,ENST00000484674,NM_001286490.1;FRMD5,synonymous_variant,p.=,ENST00000449926,;FRMD5,intron_variant,,ENST00000402883,;FRMD5,intron_variant,,ENST00000558108,;FRMD5,3_prime_UTR_variant,,ENST00000421674,;FRMD5,3_prime_UTR_variant,,ENST00000458630,;FRMD5,3_prime_UTR_variant,,ENST00000451277,;FRMD5,downstream_gene_variant,,ENST00000473965,;PIN4P1,downstream_gene_variant,,ENST00000451079,; C ENST00000417257 Transcript stop_gained 1862/5011 1685/1713 562/570 S/* tCa/tGa 1 -1 FRMD5 HGNC HGNC:28214 protein_coding YES CCDS10107.2 ENSP00000403067 Q7Z6J6 UPI00001A9475 NM_032892.4 14/14 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF5 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 43873913 43873913 G C 1 0 0 0 0 0 1 0 0 5923 1294 45 4 4 FRMD5 15 43873913 Nonsense_Mutation SNP G C3N-00294_T 350744 43873913 58117276 939 13711 SLC24A5 0 . GRCh38 15 48134281 48134281 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.325G>A p.Ala109Thr p.A109T ENST00000341459 3/9 228 175 53 186 186 0 strelka-varscan-mutect SLC24A5,missense_variant,p.Ala109Thr,ENST00000341459,NM_205850.2;SLC24A5,missense_variant,p.Ala49Thr,ENST00000449382,;MYEF2,downstream_gene_variant,,ENST00000324324,NM_016132.4;SLC24A5,non_coding_transcript_exon_variant,,ENST00000463289,; A ENST00000341459 Transcript missense_variant 398/1897 325/1503 109/500 A/T Gca/Aca 1 1 SLC24A5 HGNC HGNC:20611 protein_coding YES CCDS10128.1 ENSP00000341550 Q71RS6 UPI0000242BC9 NM_205850.2 deleterious(0) 3/9 hmmpanther:PTHR10846:SF27,hmmpanther:PTHR10846,TIGRFAM_domain:TIGR00367,Pfam_domain:PF01699 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 48134281 48134281 G A 1 0 0 0 0 1 0 0 0 14735 1319 46 3 3 SLC24A5 15 48134281 Missense_Mutation SNP G C3N-00294_T 4260368 48134281 53856908 940 13712 HDC 0 . GRCh38 15 50258465 50258465 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.257C>G p.Ser86Cys p.S86C ENST00000267845 3/12 382 295 87 365 365 0 strelka-varscan-mutect HDC,missense_variant,p.Ser86Cys,ENST00000267845,NM_002112.3;HDC,missense_variant,p.Ser86Cys,ENST00000543581,NM_001306146.1;HDC,missense_variant,p.Ser80Cys,ENST00000559683,;HDC,non_coding_transcript_exon_variant,,ENST00000558679,;HDC,non_coding_transcript_exon_variant,,ENST00000559190,;HDC,intron_variant,,ENST00000558761,; C ENST00000267845 Transcript missense_variant 660/2705 257/1989 86/662 S/C tCt/tGt 1 -1 HDC HGNC HGNC:4855 protein_coding YES CCDS10134.1 ENSP00000267845 P19113 UPI0000128FB4 NM_002112.3 deleterious(0.01) 3/12 Gene3D:3.40.640.10,Pfam_domain:PF00282,Prints_domain:PR00800,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF68,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 50258465 50258465 G C 1 0 0 0 0 1 0 0 0 6902 942 33 4 4 HDC 15 50258465 Missense_Mutation SNP G C3N-00294_T 2124184 50258465 51732724 941 13713 DMXL2 0 . GRCh38 15 51481087 51481088 + Frame_Shift_Ins INS - - T novel C3N-00294_T C3N-00294_N - - c.6018dupA p.Asp2007ArgfsTer2 p.D2007Rfs*2 ENST00000543779 24/43 51 40 11 84 84 0 sindel-varindel-pindel DMXL2,frameshift_variant,p.Asp2007ArgfsTer2,ENST00000251076,NM_015263.3;DMXL2,frameshift_variant,p.Asp2007ArgfsTer2,ENST00000543779,NM_001174116.1;DMXL2,frameshift_variant,p.Asp1371ArgfsTer2,ENST00000449909,NM_001174117.1;DMXL2,frameshift_variant,p.Asp132ArgfsTer2,ENST00000560891,;RP11-707P17.1,intron_variant,,ENST00000561007,; T ENST00000543779 Transcript frameshift_variant 6108-6109/10400 6018-6019/9114 2006-2007/3037 -/X -/A 1 -1 DMXL2 HGNC HGNC:2938 protein_coding YES CCDS53946.1 ENSP00000441858 Q8TDJ6 UPI00001FE4C2 NM_001174116.1 24/43 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF11 HIGH 1 insertion 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999914 1 1 1 0 T 7 5 46 51481087 51481087 - T 1 0 1 1 0 0 0 0 0 4404 913 32 0 0 DMXL2 15 51481087 Frame_Shift_Ins INS - C3N-00294_T 1222622 51481087 50510102 942 13714 GNB5 0 . GRCh38 15 52179856 52179856 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.150G>A p.= p.E50E ENST00000261837 3/13 303 234 69 290 290 0 strelka-varscan-mutect GNB5,synonymous_variant,p.=,ENST00000261837,NM_016194.3;GNB5,synonymous_variant,p.=,ENST00000396335,;GNB5,synonymous_variant,p.=,ENST00000358784,NM_006578.3;GNB5,synonymous_variant,p.=,ENST00000560116,;RP11-430B1.2,upstream_gene_variant,,ENST00000560518,;RP11-430B1.2,upstream_gene_variant,,ENST00000559779,;GNB5,synonymous_variant,p.=,ENST00000561313,;GNB5,non_coding_transcript_exon_variant,,ENST00000560075,; T ENST00000261837 Transcript synonymous_variant 216/8906 150/1188 50/395 E gaG/gaA 1 -1 GNB5 HGNC HGNC:4401 protein_coding YES CCDS10149.1 ENSP00000261837 O14775 A0A024R5V3 UPI000006E214 NM_016194.3 3/13 PIRSF_domain:PIRSF002394,hmmpanther:PTHR19850,hmmpanther:PTHR19850:SF36 LOW SNV 5 1 PASS rs991564773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 52179856 52179856 C T 1 0 0 0 0 0 0 0 1 6400 912 32 3 3 GNB5 15 52179856 Silent SNP C C3N-00294_T 698769 52179856 49811333 943 13715 MYO5C 0 . GRCh38 15 52242071 52242071 + Silent SNP G G A rs774686743 C3N-00294_T C3N-00294_N G G c.2533C>T p.= p.L845L ENST00000261839 20/41 60 47 13 71 71 0 strelka-varscan-mutect MYO5C,synonymous_variant,p.=,ENST00000261839,NM_018728.3;MYO5C,non_coding_transcript_exon_variant,,ENST00000559434,;MYO5C,intron_variant,,ENST00000560809,;MYO5C,intron_variant,,ENST00000558902,; A ENST00000261839 Transcript synonymous_variant 2695/6971 2533/5229 845/1742 L Ctg/Ttg rs774686743,COSM3969152 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 20/41 PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF313,Pfam_domain:PF00612,Gene3D:1wdcA00,SMART_domains:SM00015,Superfamily_domains:SSF52540 0,1 LOW 1 SNV 1 0,1 1 PASS rs774686743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 52242071 52242071 G A 1 0 0 0 0 0 0 0 1 10081 991 35 3 3 MYO5C 15 52242071 Silent SNP G C3N-00294_T 62215 52242071 49749118 944 13716 WDR72 0 . GRCh38 15 53665705 53665705 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1829C>T p.Ser610Leu p.S610L ENST00000396328 14/20 206 172 34 284 284 0 strelka-varscan-mutect WDR72,missense_variant,p.Ser610Leu,ENST00000396328,;WDR72,missense_variant,p.Ser607Leu,ENST00000557913,;WDR72,missense_variant,p.Ser610Leu,ENST00000360509,NM_182758.3;WDR72,missense_variant,p.Ser620Leu,ENST00000559418,;WDR72,missense_variant,p.Ser610Leu,ENST00000560036,;WDR72,non_coding_transcript_exon_variant,,ENST00000567575,; A ENST00000396328 Transcript missense_variant 2069/7507 1829/3309 610/1102 S/L tCa/tTa 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D deleterious(0.01) 14/20 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF408 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 53665705 53665705 G A 1 0 0 0 0 1 0 0 0 17878 1294 45 3 3 WDR72 15 53665705 Missense_Mutation SNP G C3N-00294_T 1423634 53665705 48325484 945 13717 UNC13C 0 . GRCh38 15 54235035 54235035 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.3077G>C p.Gly1026Ala p.G1026A ENST00000260323 4/32 182 127 55 217 217 0 strelka-varscan-mutect UNC13C,missense_variant,p.Gly1026Ala,ENST00000260323,NM_001080534.1; C ENST00000260323 Transcript missense_variant 3077/12946 3077/6645 1026/2214 G/A gGa/gCa COSM5193442,COSM5193443,COSM5193444 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 tolerated_low_confidence(0.35) 4/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 54235035 54235035 G C 1 0 0 0 0 1 0 0 0 17510 1188 41 4 4 UNC13C 15 54235035 Missense_Mutation SNP G C3N-00294_T 569330 54235035 47756154 946 13718 ADAM10 0 . GRCh38 15 58611984 58611984 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1519C>G p.Gln507Glu p.Q507E ENST00000260408 12/16 252 191 61 289 289 0 strelka-varscan-mutect ADAM10,missense_variant,p.Gln507Glu,ENST00000260408,NM_001110.3;ADAM10,intron_variant,,ENST00000402627,;ADAM10,intron_variant,,ENST00000561288,;ADAM10,non_coding_transcript_exon_variant,,ENST00000475898,;ADAM10,3_prime_UTR_variant,,ENST00000396136,;ADAM10,non_coding_transcript_exon_variant,,ENST00000482945,;ADAM10,non_coding_transcript_exon_variant,,ENST00000470269,;ADAM10,non_coding_transcript_exon_variant,,ENST00000481164,;ADAM10,non_coding_transcript_exon_variant,,ENST00000462061,; C ENST00000260408 Transcript missense_variant 1963/11431 1519/2247 507/748 Q/E Caa/Gaa 1 -1 ADAM10 HGNC HGNC:188 protein_coding YES CCDS10167.1 ENSP00000260408 O14672 A0A024R5U5 UPI00001254C8 NM_001110.3 tolerated(0.15) 12/16 PROSITE_profiles:PS50214,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF4,Gene3D:4.10.70.10,Pfam_domain:PF00200,SMART_domains:SM00050,Superfamily_domains:SSF57552 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 58611984 58611984 G C 1 0 0 0 0 1 0 0 0 278 1299 45 4 4 ADAM10 15 58611984 Missense_Mutation SNP G C3N-00294_T 4376949 58611984 43379205 947 13719 IGDCC4 0 . GRCh38 15 65396163 65396163 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.998C>T p.Ala333Val p.A333V ENST00000352385 7/20 81 65 16 54 54 0 strelka-mutect IGDCC4,missense_variant,p.Ala333Val,ENST00000352385,NM_020962.2;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,; A ENST00000352385 Transcript missense_variant,splice_region_variant 1208/6508 998/3753 333/1250 A/V gCg/gTg 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 tolerated(0.14) 7/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,Low_complexity_(Seg):seg,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1418145320 . 0 201 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 46 65396163 65396163 G A 1 0 0 0 0 1 0 0 0 7475 1101 38 1 1 IGDCC4 15 65396163 Missense_Mutation SNP G C3N-00294_T 6784179 65396163 36595026 948 13720 DPP8 0 . GRCh38 15 65452064 65452064 + Missense_Mutation SNP G G C rs776812617 C3N-00294_T C3N-00294_N G G c.2358C>G p.Phe786Leu p.F786L ENST00000341861 18/20 130 103 27 115 115 0 strelka-varscan-mutect DPP8,missense_variant,p.Phe786Leu,ENST00000341861,NM_197960.2;DPP8,missense_variant,p.Phe770Leu,ENST00000300141,NM_130434.3;DPP8,missense_variant,p.Phe735Leu,ENST00000321147,NM_197961.2;DPP8,missense_variant,p.Phe786Leu,ENST00000559233,;DPP8,missense_variant,p.Phe670Leu,ENST00000358939,NM_017743.4;DPP8,missense_variant,p.Phe199Leu,ENST00000558786,;DPP8,missense_variant,p.Phe355Leu,ENST00000558559,;DPP8,non_coding_transcript_exon_variant,,ENST00000560048,;DPP8,downstream_gene_variant,,ENST00000558363,;DPP8,3_prime_UTR_variant,,ENST00000395652,;DPP8,downstream_gene_variant,,ENST00000560597,; C ENST00000341861 Transcript missense_variant 3939/8699 2358/2697 786/898 F/L ttC/ttG rs776812617 1 -1 DPP8 HGNC HGNC:16490 protein_coding YES CCDS10207.1 ENSP00000339208 Q6V1X1 A0A024R5Z6 UPI00001BFAFE NM_197960.2 tolerated(0.69) 18/20 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF98,Pfam_domain:PF00326,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs776812617 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 65452064 65452064 G C 1 0 0 0 0 1 0 0 0 4547 933 33 4 4 DPP8 15 65452064 Missense_Mutation SNP G C3N-00294_T 55901 65452064 36539125 949 13721 DPP8 0 . GRCh38 15 65507254 65507254 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.409G>T p.Asp137Tyr p.D137Y ENST00000341861 3/20 72 63 9 106 105 1 strelka-varscan-mutect DPP8,missense_variant,p.Asp137Tyr,ENST00000341861,NM_197960.2;DPP8,missense_variant,p.Asp121Tyr,ENST00000300141,NM_130434.3;DPP8,missense_variant,p.Asp137Tyr,ENST00000321147,NM_197961.2;DPP8,missense_variant,p.Asp137Tyr,ENST00000559233,;DPP8,missense_variant,p.Asp121Tyr,ENST00000358939,NM_017743.4;DPP8,missense_variant,p.Asp131Tyr,ENST00000558529,;DPP8,missense_variant,p.Asp121Tyr,ENST00000559526,;DPP8,downstream_gene_variant,,ENST00000560436,;Y_RNA,downstream_gene_variant,,ENST00000516408,;DPP8,downstream_gene_variant,,ENST00000560194,;DPP8,missense_variant,p.Asp137Tyr,ENST00000395652,; A ENST00000341861 Transcript missense_variant 1990/8699 409/2697 137/898 D/Y Gat/Tat 1 -1 DPP8 HGNC HGNC:16490 protein_coding YES CCDS10207.1 ENSP00000339208 Q6V1X1 A0A024R5Z6 UPI00001BFAFE NM_197960.2 deleterious(0.01) 3/20 hmmpanther:PTHR11731:SF98,hmmpanther:PTHR11731,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 65507254 65507254 C A 1 0 0 0 0 1 0 0 0 4547 855 30 2 2 DPP8 15 65507254 Missense_Mutation SNP C C3N-00294_T 55190 65507254 36483935 950 13722 ITGA11 0 . GRCh38 15 68303060 68303060 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.3566G>A p.= p.*1189* ENST00000315757 30/30 143 116 27 160 160 0 strelka-varscan-mutect ITGA11,stop_retained_variant,p.=,ENST00000423218,;ITGA11,stop_retained_variant,p.=,ENST00000315757,NM_001004439.1; T ENST00000315757 Transcript stop_retained_variant 3662/3955 3566/3567 1189/1188 * tGa/tAa 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 30/30 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 68303060 68303060 C T 1 0 0 0 0 0 0 0 1 7781 837 29 3 3 ITGA11 15 68303060 Silent SNP C C3N-00294_T 2795806 68303060 33688129 951 13723 C15orf39 0 . GRCh38 15 75208287 75208287 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2239C>G p.Pro747Ala p.P747A ENST00000360639 2/3 309 239 70 276 276 0 strelka-varscan-mutect C15orf39,missense_variant,p.Pro747Ala,ENST00000360639,;C15orf39,missense_variant,p.Pro747Ala,ENST00000394987,NM_015492.4;C15orf39,missense_variant,p.Pro747Ala,ENST00000567617,;C15orf39,missense_variant,p.Pro616Ala,ENST00000565074,;C15orf39,downstream_gene_variant,,ENST00000563905,;C15orf39,downstream_gene_variant,,ENST00000562637,;C15orf39,downstream_gene_variant,,ENST00000564848,;RP11-69H7.3,downstream_gene_variant,,ENST00000563568,; G ENST00000360639 Transcript missense_variant 2559/4517 2239/3144 747/1047 P/A Cca/Gca 1 1 C15orf39 HGNC HGNC:24497 protein_coding YES CCDS10276.1 ENSP00000353854 Q6ZRI6 UPI000004F079 tolerated(0.22) 2/3 hmmpanther:PTHR28422,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1364949276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 75208287 75208287 C G 1 0 0 0 0 1 0 0 0 1843 855 30 4 4 C15orf39 15 75208287 Missense_Mutation SNP C C3N-00294_T 6905227 75208287 26782902 952 13724 C15orf39 0 . GRCh38 15 75208509 75208509 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2461C>G p.Gln821Glu p.Q821E ENST00000360639 2/3 206 167 39 229 229 0 strelka-varscan-mutect C15orf39,missense_variant,p.Gln821Glu,ENST00000360639,;C15orf39,missense_variant,p.Gln821Glu,ENST00000394987,NM_015492.4;C15orf39,missense_variant,p.Gln821Glu,ENST00000567617,;C15orf39,missense_variant,p.Gln690Glu,ENST00000565074,;C15orf39,downstream_gene_variant,,ENST00000563905,;C15orf39,downstream_gene_variant,,ENST00000562637,;C15orf39,downstream_gene_variant,,ENST00000564848,;RP11-69H7.3,downstream_gene_variant,,ENST00000563568,; G ENST00000360639 Transcript missense_variant 2781/4517 2461/3144 821/1047 Q/E Cag/Gag 1 1 C15orf39 HGNC HGNC:24497 protein_coding YES CCDS10276.1 ENSP00000353854 Q6ZRI6 UPI000004F079 deleterious(0) 2/3 hmmpanther:PTHR28422 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 75208509 75208509 C G 1 0 0 0 0 1 0 0 0 1843 827 29 4 4 C15orf39 15 75208509 Missense_Mutation SNP C C3N-00294_T 222 75208509 26782680 953 13725 MAN2C1 0 . GRCh38 15 75362665 75362665 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.874G>A p.Glu292Lys p.E292K ENST00000565683 7/26 162 117 45 190 190 0 strelka-varscan-mutect MAN2C1,missense_variant,p.Glu292Lys,ENST00000565683,NM_001256494.1;MAN2C1,missense_variant,p.Glu292Lys,ENST00000267978,NM_006715.3;MAN2C1,missense_variant,p.Glu292Lys,ENST00000569482,NM_001256495.1;MAN2C1,intron_variant,,ENST00000563622,NM_001256496.1;MAN2C1,upstream_gene_variant,,ENST00000618257,;MAN2C1,downstream_gene_variant,,ENST00000566256,;MAN2C1,downstream_gene_variant,,ENST00000568374,;MAN2C1,downstream_gene_variant,,ENST00000561615,;MAN2C1,downstream_gene_variant,,ENST00000563539,;MAN2C1,upstream_gene_variant,,ENST00000566253,;MAN2C1,3_prime_UTR_variant,,ENST00000566634,;MAN2C1,3_prime_UTR_variant,,ENST00000421803,;MAN2C1,3_prime_UTR_variant,,ENST00000570257,;MAN2C1,3_prime_UTR_variant,,ENST00000565784,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000564785,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563441,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000565801,;MAN2C1,upstream_gene_variant,,ENST00000567163,;MAN2C1,upstream_gene_variant,,ENST00000566099,;MAN2C1,downstream_gene_variant,,ENST00000565534,;MAN2C1,upstream_gene_variant,,ENST00000569176,;MAN2C1,downstream_gene_variant,,ENST00000569355,;MAN2C1,upstream_gene_variant,,ENST00000563013,;MAN2C1,upstream_gene_variant,,ENST00000563794,;MAN2C1,upstream_gene_variant,,ENST00000564570,;MAN2C1,upstream_gene_variant,,ENST00000566013,;MAN2C1,upstream_gene_variant,,ENST00000563368,;MAN2C1,upstream_gene_variant,,ENST00000562228,;MAN2C1,downstream_gene_variant,,ENST00000565652,;MAN2C1,upstream_gene_variant,,ENST00000563596,;MAN2C1,downstream_gene_variant,,ENST00000562071,;MAN2C1,upstream_gene_variant,,ENST00000563058,;MAN2C1,upstream_gene_variant,,ENST00000562461,;MAN2C1,upstream_gene_variant,,ENST00000568944,;MAN2C1,downstream_gene_variant,,ENST00000569069,;MAN2C1,upstream_gene_variant,,ENST00000565953,;MAN2C1,downstream_gene_variant,,ENST00000565699,;MAN2C1,upstream_gene_variant,,ENST00000567360,; T ENST00000565683 Transcript missense_variant 886/3300 874/3174 292/1057 E/K Gag/Aag 1 -1 MAN2C1 HGNC HGNC:6827 protein_coding YES CCDS58391.1 ENSP00000457788 Q9NTJ4 UPI0000229CBC NM_001256494.1 tolerated(0.07) 7/26 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF15,Pfam_domain:PF01074,Gene3D:3.20.110.10,Superfamily_domains:SSF88713 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 75362665 75362665 C T 1 0 0 0 0 1 0 0 0 9139 835 29 3 3 MAN2C1 15 75362665 Missense_Mutation SNP C C3N-00294_T 154156 75362665 26628524 954 13726 LINGO1 0 . GRCh38 15 77615667 77615667 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.240G>A p.= p.K80K ENST00000355300 2/2 71 59 12 80 80 0 strelka-varscan-mutect LINGO1,synonymous_variant,p.=,ENST00000355300,NM_032808.6;LINGO1,synonymous_variant,p.=,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,synonymous_variant,p.=,ENST00000557798,;LINGO1,synonymous_variant,p.=,ENST00000561686,;LINGO1,synonymous_variant,p.=,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000564472,; T ENST00000355300 Transcript synonymous_variant 415/3055 240/1863 80/620 K aaG/aaA 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 2/2 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.999995 1 1 1 0 T 2 4 46 77615667 77615667 C T 1 0 0 0 0 0 0 0 1 8735 912 32 3 3 LINGO1 15 77615667 Silent SNP C C3N-00294_T 2253002 77615667 24375522 955 13727 ARNT2 0 . GRCh38 15 80563177 80563177 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1254C>T p.= p.F418F ENST00000303329 12/19 296 249 47 339 339 0 strelka-varscan-mutect ARNT2,synonymous_variant,p.=,ENST00000533983,;ARNT2,synonymous_variant,p.=,ENST00000303329,NM_014862.3;ARNT2,synonymous_variant,p.=,ENST00000622346,;ARNT2,synonymous_variant,p.=,ENST00000527771,;RP11-379K22.2,upstream_gene_variant,,ENST00000558208,;ARNT2,non_coding_transcript_exon_variant,,ENST00000558849,; T ENST00000303329 Transcript synonymous_variant 1419/6558 1254/2154 418/717 F ttC/ttT 1 1 ARNT2 HGNC HGNC:16876 protein_coding YES CCDS32307.1 ENSP00000307479 Q9HBZ2 X5DQN9 UPI00001FEA05 NM_014862.3 12/19 Gene3D:3.30.450.20,Pfam_domain:PF08447,hmmpanther:PTHR23042,hmmpanther:PTHR23042:SF6,SMART_domains:SM00086,Superfamily_domains:SSF55785,TIGRFAM_domain:TIGR00229 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 80563177 80563177 C T 1 0 0 0 0 0 0 0 1 1108 825 29 3 3 ARNT2 15 80563177 Silent SNP C C3N-00294_T 2947510 80563177 21428012 956 13728 AGBL1 0 . GRCh38 15 86554379 86554379 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.2836G>A p.Asp946Asn p.D946N ENST00000441037 21/25 147 120 27 132 132 0 strelka-varscan-mutect AGBL1,missense_variant,p.Asp946Asn,ENST00000441037,;AGBL1,missense_variant,p.Asp900Asn,ENST00000635782,NM_152336.2;AGBL1,missense_variant,p.Asp900Asn,ENST00000421325,;AGBL1,intron_variant,,ENST00000614907,; A ENST00000441037 Transcript missense_variant 2836/3551 2836/3339 946/1112 D/N Gat/Aat COSM5583260,COSM5583261,COSM5583262 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 tolerated(0.11) 21/25 Pfam_domain:PF00246,hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5,Superfamily_domains:SSF53187 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 86554379 86554379 G A 1 0 0 0 0 1 0 0 0 451 1290 45 3 3 AGBL1 15 86554379 Missense_Mutation SNP G C3N-00294_T 5991202 86554379 15436810 957 13729 MRPS11 0 . GRCh38 15 88475215 88475215 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.387G>A p.= p.Q129Q ENST00000325844 4/6 206 163 43 231 231 0 strelka-varscan-mutect MRPS11,synonymous_variant,p.=,ENST00000325844,NM_001321970.1,NM_022839.3;MRPS11,synonymous_variant,p.=,ENST00000353598,NM_176805.2;MRPS11,non_coding_transcript_exon_variant,,ENST00000557974,;RP11-97O12.7,intron_variant,,ENST00000561140,;RP11-97O12.5,downstream_gene_variant,,ENST00000623274,;MRPS11,missense_variant,p.Asp109Asn,ENST00000560708,;MRPS11,non_coding_transcript_exon_variant,,ENST00000559323,;MRPS11,non_coding_transcript_exon_variant,,ENST00000558406,;MRPS11,non_coding_transcript_exon_variant,,ENST00000558548,;MRPS11,upstream_gene_variant,,ENST00000561262,;MRPS11,downstream_gene_variant,,ENST00000560850,;MRPS11,downstream_gene_variant,,ENST00000559557,; A ENST00000325844 Transcript synonymous_variant 652/3644 387/585 129/194 Q caG/caA 1 1 MRPS11 HGNC HGNC:14050 protein_coding YES CCDS10342.1 ENSP00000317376 P82912 UPI0000035FC4 NM_001321970.1,NM_022839.3 4/6 Gene3D:3.30.420.80,HAMAP:MF_01310,Pfam_domain:PF00411,hmmpanther:PTHR11759,hmmpanther:PTHR11759:SF3,Low_complexity_(Seg):seg,Superfamily_domains:SSF53137 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 88475215 88475215 G A 1 0 0 0 0 0 0 0 1 9799 933 33 3 3 MRPS11 15 88475215 Silent SNP G C3N-00294_T 1920836 88475215 13515974 958 13730 IQGAP1 0 . GRCh38 15 90449599 90449599 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1118C>G p.Ser373Cys p.S373C ENST00000268182 11/38 146 111 35 182 182 0 strelka-varscan-mutect IQGAP1,missense_variant,p.Ser373Cys,ENST00000268182,NM_003870.3;IQGAP1,intron_variant,,ENST00000560738,;IQGAP1,missense_variant,p.Ser373Cys,ENST00000633485,; G ENST00000268182 Transcript missense_variant 1242/7233 1118/4974 373/1657 S/C tCt/tGt 1 1 IQGAP1 HGNC HGNC:6110 protein_coding YES CCDS10362.1 ENSP00000268182 P46940 A0A024RC65 UPI000012D863 NM_003870.3 deleterious(0.03) 11/38 hmmpanther:PTHR14149:SF15,hmmpanther:PTHR14149,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 90449599 90449599 C G 1 0 0 0 0 1 0 0 0 7720 913 32 4 4 IQGAP1 15 90449599 Missense_Mutation SNP C C3N-00294_T 1974384 90449599 11541590 959 13731 MAN2A2 0 . GRCh38 15 90907493 90907493 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1194G>C p.Glu398Asp p.E398D ENST00000559717 8/23 83 63 20 89 89 0 strelka-varscan-mutect MAN2A2,missense_variant,p.Glu398Asp,ENST00000559717,;MAN2A2,missense_variant,p.Glu398Asp,ENST00000360468,NM_006122.2;MAN2A2,missense_variant,p.Glu83Asp,ENST00000557865,;MAN2A2,missense_variant,p.Arg36Thr,ENST00000560616,;MAN2A2,downstream_gene_variant,,ENST00000558290,;MAN2A2,upstream_gene_variant,,ENST00000558171,;MAN2A2,downstream_gene_variant,,ENST00000558853,;MAN2A2,downstream_gene_variant,,ENST00000559132,;MAN2A2,downstream_gene_variant,,ENST00000559965,;MAN2A2,downstream_gene_variant,,ENST00000559999,;MAN2A2,downstream_gene_variant,,ENST00000558640,;MAN2A2,upstream_gene_variant,,ENST00000561240,;MAN2A2,downstream_gene_variant,,ENST00000560534,;MAN2A2,missense_variant,p.Glu398Asp,ENST00000560451,;MAN2A2,missense_variant,p.Glu398Asp,ENST00000558161,;MAN2A2,splice_region_variant,,ENST00000560192,;MAN2A2,non_coding_transcript_exon_variant,,ENST00000561046,;MAN2A2,upstream_gene_variant,,ENST00000561448,;MAN2A2,upstream_gene_variant,,ENST00000561047,;MAN2A2,upstream_gene_variant,,ENST00000559374,;MAN2A2,upstream_gene_variant,,ENST00000560505,; C ENST00000559717 Transcript missense_variant,splice_region_variant 1653/6704 1194/3453 398/1150 E/D gaG/gaC 1 1 MAN2A2 HGNC HGNC:6825 protein_coding YES CCDS32332.1 ENSP00000452948 P49641 UPI0000408EF0 tolerated(0.12) 8/23 Gene3D:3.20.110.10,Pfam_domain:PF01074,hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF27,Superfamily_domains:SSF88713 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 90907493 90907493 G C 1 0 0 0 0 1 0 0 0 9136 956 33 4 4 MAN2A2 15 90907493 Missense_Mutation SNP G C3N-00294_T 457894 90907493 11083696 960 13732 LRRK1 0 . GRCh38 15 101022549 101022549 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.2019C>T p.= p.I673I ENST00000388948 15/34 126 95 31 151 151 0 strelka-mutect LRRK1,synonymous_variant,p.=,ENST00000388948,NM_024652.4;LRRK1,synonymous_variant,p.=,ENST00000525284,;LRRK1,non_coding_transcript_exon_variant,,ENST00000525617,;LRRK1,non_coding_transcript_exon_variant,,ENST00000538064,;LRRK1,intron_variant,,ENST00000531270,; T ENST00000388948 Transcript synonymous_variant 2378/7671 2019/6048 673/2015 I atC/atT 1 1 LRRK1 HGNC HGNC:18608 protein_coding YES CCDS42086.1 ENSP00000373600 Q38SD2 UPI0000D4FE63 NM_024652.4 15/34 Gene3D:2zejA01,Pfam_domain:PF08477,PROSITE_profiles:PS51424,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 101022549 101022549 C T 1 0 0 0 0 0 0 0 1 8938 816 29 3 3 LRRK1 15 101022549 Silent SNP C C3N-00294_T 10115056 101022549 968640 961 13733 CHTF18 0 . GRCh38 16 788766 788766 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.82G>C p.Glu28Gln p.E28Q ENST00000262315 1/22 206 177 29 196 196 0 strelka-varscan-mutect CHTF18,missense_variant,p.Glu225Gln,ENST00000631357,;CHTF18,missense_variant,p.Glu28Gln,ENST00000455171,;CHTF18,missense_variant,p.Glu28Gln,ENST00000262315,NM_022092.2;CHTF18,missense_variant,p.Glu28Gln,ENST00000317063,;RPUSD1,upstream_gene_variant,,ENST00000561734,;RPUSD1,upstream_gene_variant,,ENST00000007264,NM_001324415.1,NM_001324086.1,NM_058192.2;RPUSD1,upstream_gene_variant,,ENST00000565809,NM_001324411.1;RPUSD1,upstream_gene_variant,,ENST00000567114,NM_001324412.1;RPUSD1,upstream_gene_variant,,ENST00000562070,;RPUSD1,upstream_gene_variant,,ENST00000565377,;RPUSD1,upstream_gene_variant,,ENST00000569601,;CHTF18,upstream_gene_variant,,ENST00000426047,;RPUSD1,upstream_gene_variant,,ENST00000563560,;CHTF18,non_coding_transcript_exon_variant,,ENST00000570058,;CHTF18,upstream_gene_variant,,ENST00000491530,;CHTF18,upstream_gene_variant,,ENST00000461268,;CHTF18,missense_variant,p.Glu28Gln,ENST00000440239,;CHTF18,non_coding_transcript_exon_variant,,ENST00000471202,;CHTF18,non_coding_transcript_exon_variant,,ENST00000464728,;CHTF18,non_coding_transcript_exon_variant,,ENST00000479976,;CHTF18,intron_variant,,ENST00000563545,;RPUSD1,upstream_gene_variant,,ENST00000567283,;CHTF18,upstream_gene_variant,,ENST00000569270,;CHTF18,upstream_gene_variant,,ENST00000567620,;CHTF18,upstream_gene_variant,,ENST00000565787,;CHTF18,upstream_gene_variant,,ENST00000484349,;RPUSD1,upstream_gene_variant,,ENST00000565503,; C ENST00000262315 Transcript missense_variant 145/3090 82/2928 28/975 E/Q Gag/Cag 1 1 CHTF18 HGNC HGNC:18435 protein_coding YES CCDS45371.1 ENSP00000262315 Q8WVB6 UPI00000710D2 NM_022092.2 tolerated(0.08) 1/22 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1403583397 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 788766 788766 G C 1 0 0 0 0 1 0 0 0 3174 943 33 4 4 CHTF18 16 788766 Missense_Mutation SNP G C3N-00294_T 788766 89549579 962 13734 TPSG1 0 . GRCh38 16 1223534 1223534 + Missense_Mutation SNP G G T rs746784578 C3N-00294_T C3N-00294_N G G c.134C>A p.Pro45Gln p.P45Q ENST00000234798 3/6 235 123 112 177 177 0 strelka-varscan-mutect TPSG1,missense_variant,p.Pro45Gln,ENST00000234798,NM_012467.3;CACNA1H,downstream_gene_variant,,ENST00000348261,NM_021098.2;CACNA1H,downstream_gene_variant,,ENST00000358590,NM_001005407.1;CACNA1H,downstream_gene_variant,,ENST00000565831,;CACNA1H,downstream_gene_variant,,ENST00000569107,;CACNA1H,downstream_gene_variant,,ENST00000564231,;CACNA1H,downstream_gene_variant,,ENST00000562079,;TPSB2,downstream_gene_variant,,ENST00000612142,;TPSB2,downstream_gene_variant,,ENST00000606293,NM_024164.5;RP11-616M22.12,upstream_gene_variant,,ENST00000621827,;TPSG1,non_coding_transcript_exon_variant,,ENST00000564684,;TPSB2,downstream_gene_variant,,ENST00000611196,; T ENST00000234798 Transcript missense_variant 139/1108 134/966 45/321 P/Q cCg/cAg rs746784578 1 -1 TPSG1 HGNC HGNC:14134 protein_coding YES CCDS10430.1 ENSP00000234798 Q9NRR2 UPI000013C9BB NM_012467.3 tolerated(0.48) 3/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF138,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs746784578 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 1223534 1223534 G T 1 0 0 0 0 1 0 0 0 16907 1116 39 1 1 TPSG1 16 1223534 Missense_Mutation SNP G C3N-00294_T 434768 1223534 89114811 963 13735 IFT140 0 . GRCh38 16 1586229 1586229 + Missense_Mutation SNP C C A rs750247837 C3N-00294_T C3N-00294_N C C c.1056G>T p.Arg352Ser p.R352S ENST00000426508 10/31 184 148 36 191 191 0 strelka-varscan-mutect IFT140,missense_variant,p.Arg352Ser,ENST00000426508,NM_014714.3;LA16c-395F10.2,intron_variant,,ENST00000563162,;IFT140,non_coding_transcript_exon_variant,,ENST00000439987,;IFT140,intron_variant,,ENST00000397417,;IFT140,upstream_gene_variant,,ENST00000565298,; A ENST00000426508 Transcript missense_variant 1420/5270 1056/4389 352/1462 R/S agG/agT rs750247837 1 -1 IFT140 HGNC HGNC:29077 protein_coding YES CCDS10439.1 ENSP00000406012 Q96RY7 UPI0000073C64 NM_014714.3 tolerated(0.1) 10/31 Gene3D:2.130.10.10,hmmpanther:PTHR15722,SMART_domains:SM00320,Superfamily_domains:SSF50978,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS rs750247837 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 1586229 1586229 C A 1 0 0 0 0 1 0 0 0 7460 854 30 2 2 IFT140 16 1586229 Missense_Mutation SNP C C3N-00294_T 362695 1586229 88752116 964 13736 RBFOX1 0 . GRCh38 16 7518199 7518199 + Missense_Mutation SNP C C T rs527782263 C3N-00294_T C3N-00294_N C C c.209C>T p.Ser70Leu p.S70L ENST00000422070 5/16 118 102 16 123 123 0 strelka-varscan-mutect RBFOX1,missense_variant,p.Ser27Leu,ENST00000550418,NM_018723.3;RBFOX1,missense_variant,p.Ser32Leu,ENST00000340209,;RBFOX1,missense_variant,p.Ser32Leu,ENST00000620507,;RBFOX1,missense_variant,p.Ser70Leu,ENST00000547372,;RBFOX1,missense_variant,p.Ser47Leu,ENST00000355637,NM_145893.2;RBFOX1,missense_variant,p.Ser47Leu,ENST00000311745,NM_145891.2;RBFOX1,missense_variant,p.Ser27Leu,ENST00000553186,NM_001142333.1;RBFOX1,missense_variant,p.Ser27Leu,ENST00000547605,;RBFOX1,missense_variant,p.Ser70Leu,ENST00000422070,NM_001308117.1;RBFOX1,missense_variant,p.Ser63Leu,ENST00000535565,;RBFOX1,missense_variant,p.Ser47Leu,ENST00000436368,NM_145892.2;RBFOX1,missense_variant,p.Ser27Leu,ENST00000547338,NM_001142334.1;RBFOX1,missense_variant,p.Ser63Leu,ENST00000552089,;RBFOX1,missense_variant,p.Ser27Leu,ENST00000551752,;RBFOX1,missense_variant,p.Ser29Leu,ENST00000570626,;RBFOX1,non_coding_transcript_exon_variant,,ENST00000569889,; T ENST00000422070 Transcript missense_variant 405/1684 209/1278 70/425 S/L tCg/tTg rs527782263,COSM1153011,COSM3734329,COSM973771,COSM973772 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 deleterious_low_confidence(0.02) 5/16 hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932 0,1,1,1,1 MODERATE 1 SNV 2 0,1,1,1,1 1 PASS rs527782263 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 7518199 7518199 C T 1 0 0 0 0 1 0 0 0 13271 893 31 1 1 RBFOX1 16 7518199 Missense_Mutation SNP C C3N-00294_T 5931970 7518199 82820146 965 13737 CLEC16A 0 . GRCh38 16 11044040 11044040 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.1783G>C p.Glu595Gln p.E595Q ENST00000409790 16/24 103 89 14 93 93 0 strelka-varscan-mutect CLEC16A,missense_variant,p.Glu595Gln,ENST00000409790,NM_015226.2;CLEC16A,missense_variant,p.Glu577Gln,ENST00000409552,NM_001243403.1;CLEC16A,non_coding_transcript_exon_variant,,ENST00000465491,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000463459,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000476025,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000463896,;CLEC16A,non_coding_transcript_exon_variant,,ENST00000487189,; C ENST00000409790 Transcript missense_variant 2013/6891 1783/3162 595/1053 E/Q Gaa/Caa COSM1301619 1 1 CLEC16A HGNC HGNC:29013 protein_coding YES CCDS45409.1 ENSP00000387122 Q2KHT3 UPI0000253BAD NM_015226.2 tolerated(0.32) 16/24 hmmpanther:PTHR21481,hmmpanther:PTHR21481:SF0 1 MODERATE 1 SNV 5 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 11044040 11044040 G C 1 0 0 0 0 1 0 0 0 3266 943 33 4 4 CLEC16A 16 11044040 Missense_Mutation SNP G C3N-00294_T 3525841 11044040 79294305 966 13738 NTAN1 0 . GRCh38 16 15044409 15044409 + Splice_Site SNP T T A novel C3N-00294_T C3N-00294_N T T c.360-2A>T p.X120_splice ENST00000287706 196 105 91 192 192 0 strelka-varscan-mutect NTAN1,splice_acceptor_variant,,ENST00000287706,NM_173474.3;NTAN1,splice_acceptor_variant,,ENST00000624579,NM_001270766.1;NTAN1,splice_acceptor_variant,,ENST00000622833,NM_001270767.1;NTAN1,splice_acceptor_variant,,ENST00000566419,;NTAN1,splice_acceptor_variant,,ENST00000568320,;PDXDC1,intron_variant,,ENST00000535621,NM_001324020.1,NM_001285449.1;NTAN1,splice_acceptor_variant,,ENST00000565187,;NTAN1,splice_acceptor_variant,,ENST00000563940,;NTAN1,non_coding_transcript_exon_variant,,ENST00000566542,;NTAN1,intron_variant,,ENST00000568738,;NTAN1,upstream_gene_variant,,ENST00000570292,;NTAN1,downstream_gene_variant,,ENST00000567030,;NTAN1,downstream_gene_variant,,ENST00000567420,; A ENST00000287706 Transcript splice_acceptor_variant -/1204 360/933 120/310 1 -1 NTAN1 HGNC HGNC:29909 protein_coding YES CCDS10558.1 ENSP00000287706 Q96AB6 UPI0000071024 NM_173474.3 4/9 HIGH 1 SNV 1 1 PASS rs779050805 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 15044409 15044409 T A 1 0 0 0 0 0 0 1 0 10759 1594 55 4 4 NTAN1 16 15044409 Splice_Site SNP T C3N-00294_T 4000369 15044409 75293936 967 13739 C16orf45 0 . GRCh38 16 15583175 15583175 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.439G>C p.Glu147Gln p.E147Q ENST00000300006 5/6 114 90 24 154 154 0 strelka-varscan-mutect C16orf45,missense_variant,p.Glu147Gln,ENST00000300006,NM_033201.2;C16orf45,missense_variant,p.Glu130Gln,ENST00000452191,NM_001142469.1;C16orf45,missense_variant,p.Glu112Gln,ENST00000564389,;C16orf45,missense_variant,p.Glu99Gln,ENST00000561692,;C16orf45,missense_variant,p.Glu71Gln,ENST00000565857,;C16orf45,intron_variant,,ENST00000566490,;C16orf45,non_coding_transcript_exon_variant,,ENST00000565913,;C16orf45,3_prime_UTR_variant,,ENST00000561813,;C16orf45,downstream_gene_variant,,ENST00000570249,;C16orf45,downstream_gene_variant,,ENST00000567550,; C ENST00000300006 Transcript missense_variant 798/2404 439/615 147/204 E/Q Gaa/Caa 1 1 C16orf45 HGNC HGNC:19213 protein_coding YES CCDS10561.1 ENSP00000300006 Q96MC5 A0A024QZI8 UPI000006CFC7 NM_033201.2 deleterious(0.02) 5/6 hmmpanther:PTHR22704,hmmpanther:PTHR22704:SF1,Pfam_domain:PF12130,SMART_domains:SM01203 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 15583175 15583175 G C 1 0 0 0 0 1 0 0 0 1855 1175 41 4 4 C16orf45 16 15583175 Missense_Mutation SNP G C3N-00294_T 538766 15583175 74755170 968 13740 KIAA0430 0 . GRCh38 16 15630468 15630468 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1388G>C p.Arg463Thr p.R463T ENST00000396368 7/27 89 72 17 78 78 0 strelka-varscan-mutect KIAA0430,missense_variant,p.Arg463Thr,ENST00000396368,NM_014647.3;KIAA0430,missense_variant,p.Arg463Thr,ENST00000540441,;KIAA0430,missense_variant,p.Arg463Thr,ENST00000551742,NM_001184998.1;KIAA0430,missense_variant,p.Arg460Thr,ENST00000548025,NM_001184999.1;KIAA0430,missense_variant,p.Arg463Thr,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000548216,; G ENST00000396368 Transcript missense_variant 1595/7743 1388/5229 463/1742 R/T aGa/aCa 1 -1 KIAA0430 HGNC HGNC:29562 protein_coding YES CCDS10562.2 ENSP00000379654 Q9Y4F3 UPI00006881BC NM_014647.3 deleterious(0) 7/27 Gene3D:3.40.50.1010,Pfam_domain:PF01936,hmmpanther:PTHR14379,hmmpanther:PTHR14379:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 15630468 15630468 C G 1 0 0 0 0 1 0 0 0 8086 913 32 4 4 KIAA0430 16 15630468 Missense_Mutation SNP C C3N-00294_T 47293 15630468 74707877 969 13741 XYLT1 0 . GRCh38 16 17117724 17117724 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2479C>T p.His827Tyr p.H827Y ENST00000261381 11/12 178 133 45 179 179 0 strelka-varscan-mutect XYLT1,missense_variant,p.His827Tyr,ENST00000261381,NM_022166.3; A ENST00000261381 Transcript missense_variant 2564/9891 2479/2880 827/959 H/Y Cac/Tac 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 tolerated(0.33) 11/12 hmmpanther:PTHR19297:SF91,hmmpanther:PTHR19297 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 17117724 17117724 G A 1 0 0 0 0 1 0 0 0 18022 1348 47 3 3 XYLT1 16 17117724 Missense_Mutation SNP G C3N-00294_T 1487256 17117724 73220621 970 13742 C16orf62 0 . GRCh38 16 19628643 19628643 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1657C>G p.Leu553Val p.L553V ENST00000251143 17/31 142 102 40 156 156 0 strelka-varscan-mutect C16orf62,missense_variant,p.Leu553Val,ENST00000251143,NM_020314.5;C16orf62,missense_variant,p.Leu553Val,ENST00000438132,;C16orf62,missense_variant,p.Leu314Val,ENST00000448695,;C16orf62,missense_variant,p.Leu213Val,ENST00000543152,;C16orf62,missense_variant,p.Leu486Val,ENST00000542263,NM_001300743.1;C16orf62,missense_variant,p.Leu464Val,ENST00000417362,;C16orf62,downstream_gene_variant,,ENST00000538552,;C16orf62,downstream_gene_variant,,ENST00000539705,; G ENST00000251143 Transcript missense_variant 1705/3894 1657/3159 553/1052 L/V Ctt/Gtt 1 1 C16orf62 HGNC HGNC:24641 protein_coding YES CCDS32397.2 ENSP00000251143 E7EWW0 UPI0001E1129C NM_020314.5 tolerated(0.09) 17/31 hmmpanther:PTHR13673:SF0,hmmpanther:PTHR13673 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 19628643 19628643 C G 1 0 0 0 0 1 0 0 0 1861 913 32 4 4 C16orf62 16 19628643 Missense_Mutation SNP C C3N-00294_T 2510919 19628643 70709702 971 13743 DNAH3 0 . GRCh38 16 20963858 20963858 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.10026G>A p.= p.L3342L ENST00000261383 53/62 322 264 58 391 391 0 strelka-varscan-mutect DNAH3,synonymous_variant,p.=,ENST00000261383,NM_017539.2; T ENST00000261383 Transcript synonymous_variant 10026/12394 10026/12351 3342/4116 L ctG/ctA 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 53/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 20963858 20963858 C T 1 0 0 0 0 0 0 0 1 4418 813 29 3 3 DNAH3 16 20963858 Silent SNP C C3N-00294_T 1335215 20963858 69374487 972 13744 DNAH3 0 . GRCh38 16 21042179 21042179 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4486C>G p.Gln1496Glu p.Q1496E ENST00000261383 32/62 64 50 14 58 58 0 strelka-varscan-mutect DNAH3,missense_variant,p.Gln1496Glu,ENST00000261383,NM_017539.2;DNAH3,non_coding_transcript_exon_variant,,ENST00000572640,;DNAH3,upstream_gene_variant,,ENST00000572931,; C ENST00000261383 Transcript missense_variant 4486/12394 4486/12351 1496/4116 Q/E Cag/Gag 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0) 32/62 Low_complexity_(Seg):seg,hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF12774,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999971 1 1 1 0 C 3 2 46 21042179 21042179 G C 1 0 0 0 0 1 0 0 0 4418 1299 45 4 4 DNAH3 16 21042179 Missense_Mutation SNP G C3N-00294_T 78321 21042179 69296166 973 13745 PLK1 0 . GRCh38 16 23679065 23679065 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.133G>C p.Val45Leu p.V45L ENST00000300093 1/10 97 61 36 93 93 0 strelka-varscan-mutect PLK1,missense_variant,p.Val45Leu,ENST00000300093,NM_005030.4;DCTN5,downstream_gene_variant,,ENST00000300087,NM_032486.3;PLK1,upstream_gene_variant,,ENST00000567897,;PLK1,upstream_gene_variant,,ENST00000568568,;CTD-2196E14.9,downstream_gene_variant,,ENST00000565266,;PLK1,non_coding_transcript_exon_variant,,ENST00000564202,;PLK1,missense_variant,p.Val45Leu,ENST00000570220,;PLK1,non_coding_transcript_exon_variant,,ENST00000562272,;PLK1,upstream_gene_variant,,ENST00000562407,; C ENST00000300093 Transcript missense_variant 244/2227 133/1812 45/603 V/L Gtg/Ctg 1 1 PLK1 HGNC HGNC:9077 protein_coding YES CCDS10616.1 ENSP00000300093 P53350 UPI0000131BF9 NM_005030.4 tolerated(0.44) 1/10 hmmpanther:PTHR24345 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 23679065 23679065 G C 1 0 0 0 0 1 0 0 0 12190 1029 36 4 4 PLK1 16 23679065 Missense_Mutation SNP G C3N-00294_T 2636886 23679065 66659280 974 13746 PRKCB 0 . GRCh38 16 24154694 24154694 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1076C>T p.Ser359Leu p.S359L ENST00000303531 10/17 82 62 20 100 100 0 strelka-varscan-mutect PRKCB,missense_variant,p.Ser359Leu,ENST00000303531,NM_002738.6;PRKCB,missense_variant,p.Ser359Leu,ENST00000321728,NM_212535.2;PRKCB,missense_variant,p.Ser6Leu,ENST00000472066,; T ENST00000303531 Transcript missense_variant 1228/7969 1076/2022 359/673 S/L tCa/tTa 1 1 PRKCB HGNC HGNC:9395 protein_coding YES CCDS10619.1 ENSP00000305355 P05771 UPI000002ACF9 NM_002738.6 deleterious(0) 10/17 Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF000550,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF188,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 24154694 24154694 C T 1 0 0 0 0 1 0 0 0 12641 838 29 3 3 PRKCB 16 24154694 Missense_Mutation SNP C C3N-00294_T 475629 24154694 66183651 975 13747 SULT1A1 0 . GRCh38 16 28605893 28605893 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.816G>C p.Gln272His p.Q272H ENST00000395609 10/10 218 182 36 224 224 0 strelka-varscan-mutect SULT1A1,missense_variant,p.Gln272His,ENST00000395609,;SULT1A1,missense_variant,p.Gln272His,ENST00000569554,;SULT1A1,missense_variant,p.Gln272His,ENST00000395607,NM_177534.2,NM_177530.2;SULT1A1,missense_variant,p.Gln194His,ENST00000350842,NM_177536.3;SULT1A1,missense_variant,p.Gln272His,ENST00000314752,NM_001055.3,NM_177529.2;SULT1A1,missense_variant,p.Gln272His,ENST00000566189,;SULT1A1,downstream_gene_variant,,ENST00000567512,;SULT1A1,3_prime_UTR_variant,,ENST00000562058,;SULT1A1,3_prime_UTR_variant,,ENST00000564818,;SULT1A1,3_prime_UTR_variant,,ENST00000563493,;SULT1A1,non_coding_transcript_exon_variant,,ENST00000567998,;RP11-666O2.4,upstream_gene_variant,,ENST00000613051,;RP11-666O2.5,downstream_gene_variant,,ENST00000621738,; G ENST00000395609 Transcript missense_variant 1575/1871 816/888 272/295 Q/H caG/caC 1 -1 SULT1A1 HGNC HGNC:11453 protein_coding YES CCDS32420.1 ENSP00000378972 P50225 UPI000013EA41 deleterious(0) 10/10 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF87,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 28605893 28605893 C G 1 0 0 0 0 1 0 0 0 15760 912 32 4 4 SULT1A1 16 28605893 Missense_Mutation SNP C C3N-00294_T 4451199 28605893 61732452 976 13748 SEZ6L2 0 . GRCh38 16 29896972 29896972 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.361G>C p.Glu121Gln p.E121Q ENST00000617533 3/18 194 152 42 213 213 0 strelka-varscan-mutect SEZ6L2,missense_variant,p.Glu121Gln,ENST00000308713,NM_201575.3,NM_001114099.2;SEZ6L2,missense_variant,p.Glu121Gln,ENST00000617533,NM_001243332.1;SEZ6L2,missense_variant,p.Glu77Gln,ENST00000537485,NM_001243333.1;SEZ6L2,missense_variant,p.Glu121Gln,ENST00000346932,NM_001114100.2;SEZ6L2,missense_variant,p.Glu77Gln,ENST00000568380,;SEZ6L2,intron_variant,,ENST00000350527,NM_012410.3;ASPHD1,upstream_gene_variant,,ENST00000308748,NM_181718.3;ASPHD1,upstream_gene_variant,,ENST00000483405,;ASPHD1,upstream_gene_variant,,ENST00000563177,;SEZ6L2,non_coding_transcript_exon_variant,,ENST00000562159,;ASPHD1,upstream_gene_variant,,ENST00000566693,;ASPHD1,upstream_gene_variant,,ENST00000414952,; G ENST00000617533 Transcript missense_variant 606/3555 361/2772 121/923 E/Q Gaa/Caa 1 -1 SEZ6L2 HGNC HGNC:30844 protein_coding YES CCDS73865.1 ENSP00000481917 A0A087WYL5 UPI00001FFE46 NM_001243332.1 tolerated(0.37) 3/18 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 29896972 29896972 C G 1 0 0 0 0 1 0 0 0 14423 922 32 4 4 SEZ6L2 16 29896972 Missense_Mutation SNP C C3N-00294_T 1291079 29896972 60441373 977 13749 ZNF785 0 . GRCh38 16 30585200 30585200 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.256G>A p.Glu86Lys p.E86K ENST00000395216 2/3 108 91 17 124 124 0 strelka-varscan-mutect ZNF785,missense_variant,p.Glu86Lys,ENST00000395216,NM_152458.6;ZNF785,missense_variant,p.Glu86Lys,ENST00000470110,;ZNF785,missense_variant,p.Gly58Glu,ENST00000567773,;AC002310.7,downstream_gene_variant,,ENST00000492040,;AC002310.7,downstream_gene_variant,,ENST00000486926,;RP11-146F11.5,upstream_gene_variant,,ENST00000563540,;ZNF785,upstream_gene_variant,,ENST00000562128,;AC002310.17,downstream_gene_variant,,ENST00000564755,; T ENST00000395216 Transcript missense_variant 416/3282 256/1218 86/405 E/K Gag/Aag COSM4768867 1 -1 ZNF785 HGNC HGNC:26496 protein_coding YES CCDS10685.1 ENSP00000378642 A8K8V0 A0A024QZC7 UPI0000074535 NM_152458.6 deleterious(0.03) 2/3 PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF130,SMART_domains:SM00349 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 30585200 30585200 C T 1 0 0 0 0 1 0 0 0 18741 864 30 3 3 ZNF785 16 30585200 Missense_Mutation SNP C C3N-00294_T 688228 30585200 59753145 978 13750 SRCAP 0 . GRCh38 16 30700855 30700855 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.31C>G p.Gln11Glu p.Q11E ENST00000262518 3/34 145 127 18 151 151 0 strelka-varscan-mutect SRCAP,missense_variant,p.Gln11Glu,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Gln11Glu,ENST00000411466,;RNU6-1043P,downstream_gene_variant,,ENST00000410355,;RP11-146F11.1,upstream_gene_variant,,ENST00000568500,;RP11-146F11.1,upstream_gene_variant,,ENST00000564775,;RP11-2C24.9,upstream_gene_variant,,ENST00000380361,; G ENST00000262518 Transcript missense_variant 416/11754 31/9693 11/3230 Q/E Cag/Gag 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 deleterious_low_confidence(0) 3/34 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF638 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 30700855 30700855 C G 1 0 0 0 0 1 0 0 0 15493 827 29 4 4 SRCAP 16 30700855 Missense_Mutation SNP C C3N-00294_T 115655 30700855 59637490 979 13751 SRCAP 0 . GRCh38 16 30724969 30724969 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.5545G>A p.Asp1849Asn p.D1849N ENST00000262518 25/34 245 213 32 285 285 0 strelka-varscan-mutect SRCAP,missense_variant,p.Asp1849Asn,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Asp1590Asn,ENST00000395059,;SRCAP,missense_variant,p.Asp1549Asn,ENST00000483083,;RP11-2C24.9,missense_variant,p.Asp1672Asn,ENST00000380361,; A ENST00000262518 Transcript missense_variant 5930/11754 5545/9693 1849/3230 D/N Gac/Aac 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 deleterious_low_confidence(0) 25/34 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 30724969 30724969 G A 1 0 0 0 0 1 0 0 0 15493 1290 45 3 3 SRCAP 16 30724969 Missense_Mutation SNP G C3N-00294_T 24114 30724969 59613376 980 13752 SRCAP 0 . GRCh38 16 30737187 30737187 + Missense_Mutation SNP A A G novel C3N-00294_T C3N-00294_N A A c.7147A>G p.Lys2383Glu p.K2383E ENST00000262518 34/34 227 185 42 280 280 0 strelka-varscan-mutect SRCAP,missense_variant,p.Lys2383Glu,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Lys2124Glu,ENST00000395059,;TMEM265,upstream_gene_variant,,ENST00000615541,NM_001256829.1;RP11-2C24.4,upstream_gene_variant,,ENST00000483578,;RP11-2C24.9,missense_variant,p.Lys2206Glu,ENST00000380361,;SRCAP,downstream_gene_variant,,ENST00000474008,; G ENST00000262518 Transcript missense_variant 7532/11754 7147/9693 2383/3230 K/E Aaa/Gaa 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 deleterious_low_confidence(0.01) 34/34 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 30737187 30737187 A G 1 0 0 0 0 1 0 0 0 15493 363 13 5 5 SRCAP 16 30737187 Missense_Mutation SNP A C3N-00294_T 12218 30737187 59601158 981 13753 PRSS36 0 . GRCh38 16 31145812 31145812 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.697G>A p.Glu233Lys p.E233K ENST00000268281 6/15 89 71 18 108 108 0 strelka-varscan-mutect PRSS36,missense_variant,p.Glu233Lys,ENST00000268281,NM_173502.4;PRSS36,missense_variant,p.Glu233Lys,ENST00000569305,NM_001258290.1;PRSS36,missense_variant,p.Glu233Lys,ENST00000418068,NM_001258291.1;PRSS36,non_coding_transcript_exon_variant,,ENST00000562368,;PRSS36,upstream_gene_variant,,ENST00000563693,;PRSS36,downstream_gene_variant,,ENST00000569614,;PRSS36,downstream_gene_variant,,ENST00000562390,;PRSS36,downstream_gene_variant,,ENST00000561897,; T ENST00000268281 Transcript missense_variant 756/2840 697/2568 233/855 E/K Gag/Aag 1 -1 PRSS36 HGNC HGNC:26906 protein_coding YES CCDS32436.1 ENSP00000268281 Q5K4E3 UPI00001FFF6A NM_173502.4 tolerated(0.18) 6/15 PROSITE_profiles:PS50240,hmmpanther:PTHR24276,hmmpanther:PTHR24276:SF62,PIRSF_domain:PIRSF037933,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 31145812 31145812 C T 1 0 0 0 0 1 0 0 0 12772 922 32 3 3 PRSS36 16 31145812 Missense_Mutation SNP C C3N-00294_T 408625 31145812 59192533 982 13754 ITGAX 0 . GRCh38 16 31359943 31359943 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.585C>A p.Asn195Lys p.N195K ENST00000562522 7/31 207 120 87 224 224 0 strelka-varscan-mutect ITGAX,missense_variant,p.Asn195Lys,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Asn195Lys,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;ITGAX,downstream_gene_variant,,ENST00000564308,;RP11-120K18.3,downstream_gene_variant,,ENST00000561830,; A ENST00000562522 Transcript missense_variant 618/3990 585/3510 195/1169 N/K aaC/aaA 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.1) 7/31 Pfam_domain:PF00092,Prints_domain:PR00453,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 31359943 31359943 C A 1 0 0 0 0 1 0 0 0 7796 477 17 2 2 ITGAX 16 31359943 Missense_Mutation SNP C C3N-00294_T 214131 31359943 58978402 983 13755 NLRC5 0 . GRCh38 16 57039824 57039824 + Missense_Mutation SNP G G C rs777671692 C3N-00294_T C3N-00294_N G G c.2845G>C p.Glu949Gln p.E949Q ENST00000262510 16/49 146 113 33 178 178 0 strelka-varscan-mutect NLRC5,missense_variant,p.Glu949Gln,ENST00000262510,;NLRC5,missense_variant,p.Glu949Gln,ENST00000436936,NM_032206.4;NLRC5,missense_variant,p.Glu949Gln,ENST00000539144,;NLRC5,missense_variant,p.Glu702Gln,ENST00000538805,;NLRC5,missense_variant,p.Glu456Gln,ENST00000538110,;NLRC5,missense_variant,p.Glu248Gln,ENST00000543030,;NLRC5,missense_variant,p.Glu677Gln,ENST00000545081,;NLRC5,missense_variant,p.Glu100Gln,ENST00000538453,;NLRC5,3_prime_UTR_variant,,ENST00000539881,;NLRC5,upstream_gene_variant,,ENST00000540182,;NLRC5,upstream_gene_variant,,ENST00000537056,;NLRC5,upstream_gene_variant,,ENST00000538930,;NLRC5,upstream_gene_variant,,ENST00000538778,;NLRC5,upstream_gene_variant,,ENST00000541020,; C ENST00000262510 Transcript missense_variant 3070/6822 2845/5601 949/1866 E/Q Gag/Cag rs777671692 1 1 NLRC5 HGNC HGNC:29933 protein_coding YES CCDS10773.1 ENSP00000262510 Q86WI3 UPI00001AEE94 deleterious(0.05) 16/49 MODERATE 1 SNV 5 1 PASS rs777671692 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 57039824 57039824 G C 1 0 0 0 0 1 0 0 0 10507 943 33 4 4 NLRC5 16 57039824 Missense_Mutation SNP G C3N-00294_T 25679881 57039824 33298521 984 13756 RSPRY1 0 . GRCh38 16 57216106 57216106 + Splice_Site SNP G G A novel C3N-00294_T C3N-00294_N G G c.703-1G>A p.X235_splice ENST00000537866 144 115 29 175 175 0 strelka-varscan-mutect RSPRY1,splice_acceptor_variant,,ENST00000537866,;RSPRY1,splice_acceptor_variant,,ENST00000394420,NM_001305164.1,NM_133368.1;RSPRY1,splice_acceptor_variant,,ENST00000568920,;RSPRY1,intron_variant,,ENST00000562768,;RSPRY1,upstream_gene_variant,,ENST00000564530,; A ENST00000537866 Transcript splice_acceptor_variant -/3586 703/1731 235/576 1 1 RSPRY1 HGNC HGNC:29420 protein_coding YES CCDS10775.1 ENSP00000443176 Q96DX4 A0A024R6U0 UPI000006E516 6/14 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 46 57216106 57216106 G A 1 0 0 0 0 0 0 1 0 13971 956 33 3 3 RSPRY1 16 57216106 Splice_Site SNP G C3N-00294_T 176282 57216106 33122239 985 13757 PRSS54 0 . GRCh38 16 58291123 58291123 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.99G>A p.= p.Q33Q ENST00000219301 4/7 128 99 29 159 159 0 strelka-varscan-mutect PRSS54,synonymous_variant,p.=,ENST00000219301,NM_001305173.1,NM_001080492.1;PRSS54,synonymous_variant,p.=,ENST00000567164,;PRSS54,synonymous_variant,p.=,ENST00000569727,;PRSS54,intron_variant,,ENST00000543437,NM_001305174.1;PRSS54,intron_variant,,ENST00000569079,;GINS3,upstream_gene_variant,,ENST00000561952,;GINS3,upstream_gene_variant,,ENST00000564814,;GINS3,upstream_gene_variant,,ENST00000568468,;GINS3,upstream_gene_variant,,ENST00000567400,; T ENST00000219301 Transcript synonymous_variant 494/1810 99/1188 33/395 Q caG/caA 1 -1 PRSS54 HGNC HGNC:26336 protein_coding YES CCDS32463.1 ENSP00000219301 Q6PEW0 A0A140VKC3 UPI0000199F24 NM_001305173.1,NM_001080492.1 4/7 LOW 1 SNV 5 1 PASS rs1003434325 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 58291123 58291123 C T 1 0 0 0 0 0 0 0 1 12782 912 32 3 3 PRSS54 16 58291123 Silent SNP C C3N-00294_T 1075017 58291123 32047222 986 13758 NAE1 0 . GRCh38 16 66816984 66816984 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.738C>T p.= p.F246F ENST00000359087 10/20 28 23 5 73 73 0 strelka-varscan-mutect NAE1,synonymous_variant,p.=,ENST00000379463,NM_001018159.1;NAE1,synonymous_variant,p.=,ENST00000290810,NM_003905.3;NAE1,synonymous_variant,p.=,ENST00000359087,NM_001286500.1;NAE1,synonymous_variant,p.=,ENST00000394074,NM_001018160.1;NAE1,downstream_gene_variant,,ENST00000561579,;NAE1,downstream_gene_variant,,ENST00000566336,;NAE1,downstream_gene_variant,,ENST00000563185,;NAE1,downstream_gene_variant,,ENST00000564040,;NAE1,3_prime_UTR_variant,,ENST00000567743,;NAE1,3_prime_UTR_variant,,ENST00000563253,;NAE1,upstream_gene_variant,,ENST00000567521,;NAE1,downstream_gene_variant,,ENST00000569388,; A ENST00000359087 Transcript synonymous_variant 815/1825 738/1614 246/537 F ttC/ttT 1 -1 NAE1 HGNC HGNC:621 protein_coding YES CCDS67050.1 ENSP00000351990 Q13564 UPI000059D39C NM_001286500.1 10/20 Pfam_domain:PF00899,PIRSF_domain:PIRSF039099,Superfamily_domains:SSF69572 LOW 1 SNV 2 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 66816984 66816984 G A 1 0 0 0 0 0 0 0 1 10146 1281 45 3 3 NAE1 16 66816984 Silent SNP G C3N-00294_T 8525861 66816984 23521361 987 13759 TRADD 0 . GRCh38 16 67154872 67154872 + Missense_Mutation SNP C C T rs763349245 C3N-00294_T C3N-00294_N C C c.716G>A p.Arg239Gln p.R239Q ENST00000345057 5/5 135 108 27 137 137 0 strelka-varscan-mutect TRADD,missense_variant,p.Arg239Gln,ENST00000345057,NM_003789.3;TRADD,missense_variant,p.Arg179Gln,ENST00000486556,;B3GNT9,upstream_gene_variant,,ENST00000449549,NM_033309.2;TRADD,downstream_gene_variant,,ENST00000566104,;TRADD,non_coding_transcript_exon_variant,,ENST00000566247,;TRADD,downstream_gene_variant,,ENST00000563348,; T ENST00000345057 Transcript missense_variant 1185/1877 716/939 239/312 R/Q cGa/cAa rs763349245,COSM1749690 1 -1 TRADD HGNC HGNC:12030 protein_coding YES CCDS10829.1 ENSP00000341268 Q15628 UPI00001372E3 NM_003789.3 deleterious(0.02) 5/5 PROSITE_profiles:PS50017,hmmpanther:PTHR14913,Pfam_domain:PF00531,Gene3D:1.10.533.10,SMART_domains:SM00005,Superfamily_domains:SSF47986 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763349245 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67154872 67154872 C T 1 0 0 0 0 1 0 0 0 16919 884 31 1 1 TRADD 16 67154872 Missense_Mutation SNP C C3N-00294_T 337888 67154872 23183473 988 13760 ELMO3 0 . GRCh38 16 67200273 67200273 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.484C>T p.Pro162Ser p.P162S ENST00000393997 5/20 174 144 30 213 213 0 strelka-varscan-mutect ELMO3,missense_variant,p.Pro162Ser,ENST00000393997,NM_024712.3;ELMO3,missense_variant,p.Pro145Ser,ENST00000360833,;ELMO3,5_prime_UTR_variant,,ENST00000477898,;E2F4,downstream_gene_variant,,ENST00000379378,NM_001950.3;E2F4,downstream_gene_variant,,ENST00000565226,;MIR328,downstream_gene_variant,,ENST00000385213,;ELMO3,non_coding_transcript_exon_variant,,ENST00000571638,;CTC-277H1.6,downstream_gene_variant,,ENST00000623816,;ELMO3,intron_variant,,ENST00000571587,;E2F4,downstream_gene_variant,,ENST00000567007,;E2F4,downstream_gene_variant,,ENST00000568839,;E2F4,downstream_gene_variant,,ENST00000569573,;E2F4,downstream_gene_variant,,ENST00000567228,; T ENST00000393997 Transcript missense_variant 541/2531 484/2322 162/773 P/S Ccg/Tcg 1 1 ELMO3 HGNC HGNC:17289 protein_coding YES CCDS10833.2 ENSP00000377566 Q96BJ8 UPI00006976B6 NM_024712.3 tolerated(0.92) 5/20 Gene3D:1.25.10.10,hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF16,Superfamily_domains:SSF48371 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 67200273 67200273 C T 1 0 0 0 0 1 0 0 0 4901 855 30 3 3 ELMO3 16 67200273 Missense_Mutation SNP C C3N-00294_T 45401 67200273 23138072 989 13761 AC027682.1 0 . GRCh38 16 67540471 67540471 + Silent SNP C C T rs747087160 C3N-00294_T C3N-00294_N C C c.687C>T p.= p.F229F ENST00000428437 9/22 212 182 30 258 258 0 strelka-varscan-mutect FAM65A,synonymous_variant,p.=,ENST00000540839,;FAM65A,synonymous_variant,p.=,ENST00000428437,NM_001193524.1;FAM65A,synonymous_variant,p.=,ENST00000379312,NM_001193522.1;FAM65A,synonymous_variant,p.=,ENST00000042381,NM_024519.3;AC027682.1,synonymous_variant,p.=,ENST00000422602,NM_001193523.1;FAM65A,synonymous_variant,p.=,ENST00000566559,;FAM65A,synonymous_variant,p.=,ENST00000569253,;FAM65A,synonymous_variant,p.=,ENST00000569179,;FAM65A,downstream_gene_variant,,ENST00000566907,;FAM65A,downstream_gene_variant,,ENST00000566920,;FAM65A,downstream_gene_variant,,ENST00000565176,;FAM65A,downstream_gene_variant,,ENST00000562755,;FAM65A,upstream_gene_variant,,ENST00000568959,;FAM65A,downstream_gene_variant,,ENST00000562116,;CTD-2012K14.2,upstream_gene_variant,,ENST00000567122,;CTD-2012K14.3,downstream_gene_variant,,ENST00000563083,;CTD-2012K14.4,downstream_gene_variant,,ENST00000564717,;FAM65A,non_coding_transcript_exon_variant,,ENST00000566522,;FAM65A,3_prime_UTR_variant,,ENST00000566815,;FAM65A,non_coding_transcript_exon_variant,,ENST00000569474,;FAM65A,non_coding_transcript_exon_variant,,ENST00000561534,;FAM65A,non_coding_transcript_exon_variant,,ENST00000566730,;FAM65A,upstream_gene_variant,,ENST00000569733,;FAM65A,upstream_gene_variant,,ENST00000564616,;FAM65A,upstream_gene_variant,,ENST00000565190,; T ENST00000428437 Transcript synonymous_variant 812/4152 687/3702 229/1233 F ttC/ttT rs747087160,COSM5431462,COSM5431463 1 1 FAM65A HGNC HGNC:25836 protein_coding YES CCDS54027.1 ENSP00000389456 Q6ZS17 UPI00017A7136 NM_001193524.1 9/22 hmmpanther:PTHR15829:SF1,hmmpanther:PTHR15829,Pfam_domain:PF15903 0,1,1 LOW SNV 2 0,1,1 1 PASS rs747087160 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 67540471 67540471 C T 1 0 0 0 0 0 0 0 1 129 883 31 1 1 AC027682.1 16 67540471 Silent SNP C C3N-00294_T 340198 67540471 22797874 990 13762 CARMIL2 0 . GRCh38 16 67647945 67647945 + Missense_Mutation SNP C C G rs748704156 C3N-00294_T C3N-00294_N C C c.1058C>G p.Ser353Cys p.S353C ENST00000334583 13/38 64 55 9 60 60 0 strelka-varscan-mutect CARMIL2,missense_variant,p.Ser353Cys,ENST00000334583,NM_001013838.1;CARMIL2,missense_variant,p.Ser353Cys,ENST00000545661,NM_001317026.1;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602321,;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602742,;CARMIL2,downstream_gene_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602931,;CARMIL2,downstream_gene_variant,,ENST00000602467,; G ENST00000334583 Transcript missense_variant 1386/4687 1058/4308 353/1435 S/C tCc/tGc rs748704156 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 deleterious(0.03) 13/38 hmmpanther:PTHR24112:SF32,hmmpanther:PTHR24112,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs748704156 . 0 208 2 0 0 0 0 0 -19.93473 1 1 1 1 0 G 3 3 46 67647945 67647945 C G 1 0 0 0 0 1 0 0 0 2352 855 30 4 4 CARMIL2 16 67647945 Missense_Mutation SNP C C3N-00294_T 107474 67647945 22690400 991 13763 SLC12A4 0 . GRCh38 16 67945965 67945965 + Missense_Mutation SNP C C G rs778036954 C3N-00294_T C3N-00294_N C C c.2731G>C p.Glu911Gln p.E911Q ENST00000422611 19/23 100 80 20 124 124 0 strelka-varscan-mutect SLC12A4,missense_variant,p.Glu909Gln,ENST00000316341,NM_001145961.1,NM_005072.4;SLC12A4,missense_variant,p.Glu911Gln,ENST00000422611,NM_001145962.1;SLC12A4,missense_variant,p.Glu909Gln,ENST00000576616,;SLC12A4,missense_variant,p.Glu878Gln,ENST00000541864,NM_001145964.1;SLC12A4,missense_variant,p.Glu861Gln,ENST00000572037,;SLC12A4,missense_variant,p.Glu903Gln,ENST00000537830,NM_001145963.1;LCAT,upstream_gene_variant,,ENST00000264005,NM_000229.1;LCAT,upstream_gene_variant,,ENST00000570980,;LCAT,upstream_gene_variant,,ENST00000576450,;LCAT,upstream_gene_variant,,ENST00000570369,;LCAT,upstream_gene_variant,,ENST00000570396,;SLC12A4,3_prime_UTR_variant,,ENST00000575857,;SLC12A4,non_coding_transcript_exon_variant,,ENST00000570802,;SLC12A4,downstream_gene_variant,,ENST00000573023,;LCAT,upstream_gene_variant,,ENST00000573538,;SLC12A4,downstream_gene_variant,,ENST00000574665,;LCAT,upstream_gene_variant,,ENST00000575467,;SLC12A4,downstream_gene_variant,,ENST00000573702,;SLC12A4,downstream_gene_variant,,ENST00000572476,;LCAT,upstream_gene_variant,,ENST00000575277,;LCAT,upstream_gene_variant,,ENST00000573846,;SLC12A4,downstream_gene_variant,,ENST00000572766,;SLC12A4,downstream_gene_variant,,ENST00000576513,;SLC12A4,upstream_gene_variant,,ENST00000570616,; G ENST00000422611 Transcript missense_variant 2771/4670 2731/3264 911/1087 E/Q Gag/Cag rs778036954 1 -1 SLC12A4 HGNC HGNC:10913 protein_coding YES CCDS54032.1 ENSP00000395983 Q9UP95 UPI00019863A8 NM_001145962.1 deleterious(0.04) 19/23 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF46,Pfam_domain:PF03522,TIGRFAM_domain:TIGR00930 MODERATE SNV 2 1 PASS rs778036954 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 67945965 67945965 C G 1 0 0 0 0 1 0 0 0 14650 864 30 4 4 SLC12A4 16 67945965 Missense_Mutation SNP C C3N-00294_T 298020 67945965 22392380 992 13764 SLC12A4 0 . GRCh38 16 67945977 67945977 + Nonsense_Mutation SNP C C A rs200160814 C3N-00294_T C3N-00294_N C C c.2719G>T p.Glu907Ter p.E907* ENST00000422611 19/23 106 86 20 128 128 0 strelka-varscan-mutect SLC12A4,stop_gained,p.Glu905Ter,ENST00000316341,NM_001145961.1,NM_005072.4;SLC12A4,stop_gained,p.Glu907Ter,ENST00000422611,NM_001145962.1;SLC12A4,stop_gained,p.Glu905Ter,ENST00000576616,;SLC12A4,stop_gained,p.Glu874Ter,ENST00000541864,NM_001145964.1;SLC12A4,stop_gained,p.Glu857Ter,ENST00000572037,;SLC12A4,stop_gained,p.Glu899Ter,ENST00000537830,NM_001145963.1;LCAT,upstream_gene_variant,,ENST00000264005,NM_000229.1;LCAT,upstream_gene_variant,,ENST00000570980,;LCAT,upstream_gene_variant,,ENST00000576450,;LCAT,upstream_gene_variant,,ENST00000570369,;LCAT,upstream_gene_variant,,ENST00000570396,;SLC12A4,3_prime_UTR_variant,,ENST00000575857,;SLC12A4,non_coding_transcript_exon_variant,,ENST00000570802,;SLC12A4,downstream_gene_variant,,ENST00000573023,;LCAT,upstream_gene_variant,,ENST00000573538,;SLC12A4,downstream_gene_variant,,ENST00000574665,;LCAT,upstream_gene_variant,,ENST00000575467,;SLC12A4,downstream_gene_variant,,ENST00000573702,;SLC12A4,downstream_gene_variant,,ENST00000572476,;LCAT,upstream_gene_variant,,ENST00000575277,;LCAT,upstream_gene_variant,,ENST00000573846,;SLC12A4,downstream_gene_variant,,ENST00000572766,;SLC12A4,downstream_gene_variant,,ENST00000576513,;SLC12A4,upstream_gene_variant,,ENST00000570616,; A ENST00000422611 Transcript stop_gained 2759/4670 2719/3264 907/1087 E/* Gag/Tag rs200160814 1 -1 SLC12A4 HGNC HGNC:10913 protein_coding YES CCDS54032.1 ENSP00000395983 Q9UP95 UPI00019863A8 NM_001145962.1 19/23 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF46,Pfam_domain:PF03522,TIGRFAM_domain:TIGR00930 HIGH SNV 2 1 PASS rs200160814 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 67945977 67945977 C A 1 0 0 0 0 0 1 0 0 14650 835 29 2 2 SLC12A4 16 67945977 Nonsense_Mutation SNP C C3N-00294_T 12 67945977 22392368 993 13765 NFATC3 0 . GRCh38 16 68174499 68174499 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.1900C>G p.Leu634Val p.L634V ENST00000346183 6/10 39 30 9 64 64 0 strelka-varscan-mutect NFATC3,missense_variant,p.Leu634Val,ENST00000349223,NM_173163.2;NFATC3,missense_variant,p.Leu634Val,ENST00000329524,NM_004555.3;NFATC3,missense_variant,p.Leu634Val,ENST00000346183,NM_173165.2;NFATC3,missense_variant,p.Leu634Val,ENST00000575270,;NFATC3,missense_variant,p.Leu619Val,ENST00000562926,;NFATC3,missense_variant,p.Leu619Val,ENST00000570212,;NFATC3,non_coding_transcript_exon_variant,,ENST00000535127,;NFATC3,non_coding_transcript_exon_variant,,ENST00000563319,;NFATC3,non_coding_transcript_exon_variant,,ENST00000566301,;NFATC3,non_coding_transcript_exon_variant,,ENST00000563288,;NFATC3,non_coding_transcript_exon_variant,,ENST00000563796,;NFATC3,non_coding_transcript_exon_variant,,ENST00000569766,;NFATC3,non_coding_transcript_exon_variant,,ENST00000567152,;NFATC3,3_prime_UTR_variant,,ENST00000539828,;NFATC3,3_prime_UTR_variant,,ENST00000568466,;NFATC3,non_coding_transcript_exon_variant,,ENST00000553077,;NFATC3,non_coding_transcript_exon_variant,,ENST00000549350,;NFATC3,non_coding_transcript_exon_variant,,ENST00000379165,; G ENST00000346183 Transcript missense_variant 1924/6040 1900/3228 634/1075 L/V Ctt/Gtt COSM4474192,COSM4474193,COSM972682,COSM972683 1 1 NFATC3 HGNC HGNC:7777 protein_coding YES CCDS10860.1 ENSP00000300659 Q12968 B5B2S1 UPI0000000C21 NM_173165.2 tolerated(0.49) 6/10 Gene3D:2.60.40.10,Pfam_domain:PF16179,Prints_domain:PR01789,hmmpanther:PTHR12533,hmmpanther:PTHR12533:SF6,SMART_domains:SM00429,Superfamily_domains:SSF81296 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs1375594022 . 0 182 23 3 0 2 0 0 -2.592694 0.2956093 0 1 0 0 G 3 3 46 68174499 68174499 C G 1 0 0 0 0 1 0 0 0 10401 913 32 4 4 NFATC3 16 68174499 Missense_Mutation SNP C C3N-00294_T 228522 68174499 22163846 994 13766 SMPD3 0 . GRCh38 16 68372034 68372034 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.148G>C p.Asp50His p.D50H ENST00000219334 3/9 293 234 59 273 272 1 strelka-varscan-mutect SMPD3,missense_variant,p.Asp50His,ENST00000219334,NM_018667.3;SMPD3,missense_variant,p.Asp50His,ENST00000563226,;SMPD3,missense_variant,p.Asp50His,ENST00000568373,;SMPD3,missense_variant,p.Asp50His,ENST00000561749,;SMPD3,upstream_gene_variant,,ENST00000574662,;SMPD3,intron_variant,,ENST00000566723,;RP11-71L14.3,upstream_gene_variant,,ENST00000624251,;SMPD3,upstream_gene_variant,,ENST00000566009,;SMPD3,upstream_gene_variant,,ENST00000566466,;SMPD3,upstream_gene_variant,,ENST00000563455,;SMPD3,upstream_gene_variant,,ENST00000567811,;SMPD3,upstream_gene_variant,,ENST00000567223,; G ENST00000219334 Transcript missense_variant 752/5453 148/1968 50/655 D/H Gac/Cac 1 -1 SMPD3 HGNC HGNC:14240 protein_coding YES CCDS10867.1 ENSP00000219334 Q9NY59 UPI0000037769 NM_018667.3 deleterious(0.02) 3/9 hmmpanther:PTHR16320:SF8,hmmpanther:PTHR16320 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 68372034 68372034 C G 1 0 0 0 0 1 0 0 0 15127 913 32 4 4 SMPD3 16 68372034 Missense_Mutation SNP C C3N-00294_T 197535 68372034 21966311 995 13767 SNTB2 0 . GRCh38 16 69270252 69270252 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1115C>T p.Ser372Leu p.S372L ENST00000336278 4/7 246 191 55 220 220 0 strelka-varscan-mutect SNTB2,missense_variant,p.Ser372Leu,ENST00000336278,NM_006750.3;SNTB2,downstream_gene_variant,,ENST00000525632,;SNTB2,downstream_gene_variant,,ENST00000528525,;SNTB2,3_prime_UTR_variant,,ENST00000467311,; T ENST00000336278 Transcript missense_variant 1153/9789 1115/1623 372/540 S/L tCa/tTa 1 1 SNTB2 HGNC HGNC:11169 protein_coding YES CCDS10873.1 ENSP00000338191 Q13425 A0A024R732 UPI0000135B21 NM_006750.3 tolerated(0.07) 4/7 PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF8,SMART_domains:SM00233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 69270252 69270252 C T 1 0 0 0 0 1 0 0 0 15193 838 29 3 3 SNTB2 16 69270252 Missense_Mutation SNP C C3N-00294_T 898218 69270252 21068093 996 13768 TERF2 0 . GRCh38 16 69385422 69385422 + Missense_Mutation SNP A A C novel C3N-00294_T C3N-00294_N A A c.444T>G p.Cys148Trp p.C148W ENST00000254942 2/10 249 144 105 333 333 0 strelka-varscan-mutect TERF2,missense_variant,p.Cys148Trp,ENST00000254942,NM_005652.4;TERF2,missense_variant,p.Cys148Trp,ENST00000567296,;TERF2,missense_variant,p.Cys27Trp,ENST00000566750,;TERF2,missense_variant,p.Cys3Trp,ENST00000567841,;TERF2,upstream_gene_variant,,ENST00000566257,;TERF2,upstream_gene_variant,,ENST00000569542,;TERF2,non_coding_transcript_exon_variant,,ENST00000569611,;TERF2,missense_variant,p.Ser57Ala,ENST00000569280,; C ENST00000254942 Transcript missense_variant 461/2983 444/1629 148/542 C/W tgT/tgG 1 -1 TERF2 HGNC HGNC:11729 protein_coding YES CCDS10879.2 ENSP00000254942 Q15554 UPI0000EE5A05 NM_005652.4 deleterious(0.04) 2/10 hmmpanther:PTHR21717:SF13,hmmpanther:PTHR21717,Pfam_domain:PF08558,Gene3D:1.25.40.210,Superfamily_domains:SSF63600,PD014243 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 69385422 69385422 A C 1 0 0 0 0 1 0 0 0 16181 273 10 5 5 TERF2 16 69385422 Missense_Mutation SNP A C3N-00294_T 115170 69385422 20952923 997 13769 SF3B3 0 . GRCh38 16 70530784 70530784 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.437G>C p.Arg146Thr p.R146T ENST00000302516 4/26 110 78 32 128 128 0 strelka-varscan-mutect SF3B3,missense_variant,p.Arg146Thr,ENST00000302516,NM_012426.4;SF3B3,downstream_gene_variant,,ENST00000564899,;SF3B3,downstream_gene_variant,,ENST00000577085,;SF3B3,downstream_gene_variant,,ENST00000566095,;SF3B3,downstream_gene_variant,,ENST00000567654,;SF3B3,downstream_gene_variant,,ENST00000569687,;SNORD111B,downstream_gene_variant,,ENST00000408587,; C ENST00000302516 Transcript missense_variant 648/9720 437/3654 146/1217 R/T aGa/aCa 1 1 SF3B3 HGNC HGNC:10770 protein_coding YES CCDS10894.1 ENSP00000305790 Q15393 UPI0000167878 NM_012426.4 deleterious(0) 4/26 hmmpanther:PTHR10644,hmmpanther:PTHR10644:SF1,Pfam_domain:PF10433 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 70530784 70530784 G C 1 0 0 0 0 1 0 0 0 14430 942 33 4 4 SF3B3 16 70530784 Missense_Mutation SNP G C3N-00294_T 1145362 70530784 19807561 998 13770 PHLPP2 0 . GRCh38 16 71658288 71658288 + Missense_Mutation SNP C C G rs761636828 C3N-00294_T C3N-00294_N C C c.2224G>C p.Asp742His p.D742H ENST00000568954 15/19 103 80 23 141 141 0 strelka-varscan-mutect PHLPP2,missense_variant,p.Asp675His,ENST00000393524,NM_001289003.1;PHLPP2,missense_variant,p.Asp742His,ENST00000568954,NM_015020.3;PHLPP2,missense_variant,p.Asp777His,ENST00000567016,;RP11-432I5.6,intron_variant,,ENST00000567077,;PHLPP2,missense_variant,p.Asp480His,ENST00000568004,;PHLPP2,missense_variant,p.Asp105His,ENST00000564884,; G ENST00000568954 Transcript missense_variant 2603/8317 2224/3972 742/1323 D/H Gac/Cac rs761636828 1 -1 PHLPP2 HGNC HGNC:29149 protein_coding YES CCDS32479.1 ENSP00000457991 Q6ZVD8 UPI0000229F5A NM_015020.3 deleterious(0) 15/19 Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs761636828 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 71658288 71658288 C G 1 0 0 0 0 1 0 0 0 11943 826 29 4 4 PHLPP2 16 71658288 Missense_Mutation SNP C C3N-00294_T 1127504 71658288 18680057 999 13771 ZFHX3 0 . GRCh38 16 72797821 72797821 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4861C>G p.Gln1621Glu p.Q1621E ENST00000268489 9/10 181 156 25 205 204 1 strelka-varscan-mutect ZFHX3,missense_variant,p.Gln1621Glu,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Gln707Glu,ENST00000397992,NM_001164766.1; C ENST00000268489 Transcript missense_variant 5534/16064 4861/11112 1621/3703 Q/E Caa/Gaa 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 deleterious(0) 9/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF84,SMART_domains:SM00451 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 72797821 72797821 G C 1 0 0 0 0 1 0 0 0 18212 1299 45 4 4 ZFHX3 16 72797821 Missense_Mutation SNP G C3N-00294_T 1139533 72797821 17540524 1000 13772 RFWD3 0 . GRCh38 16 74651940 74651940 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.701C>G p.Ser234Cys p.S234C ENST00000361070 3/13 188 153 35 183 183 0 strelka-varscan-mutect RFWD3,missense_variant,p.Ser234Cys,ENST00000361070,NM_018124.3;RFWD3,missense_variant,p.Ser234Cys,ENST00000571750,;RFWD3,5_prime_UTR_variant,,ENST00000572337,;RFWD3,upstream_gene_variant,,ENST00000575281,; C ENST00000361070 Transcript missense_variant 799/4957 701/2325 234/774 S/C tCt/tGt 1 -1 RFWD3 HGNC HGNC:25539 protein_coding YES CCDS32486.1 ENSP00000354361 Q6PCD5 UPI0000366B66 NM_018124.3 deleterious(0.01) 3/13 hmmpanther:PTHR16047:SF7,hmmpanther:PTHR16047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 74651940 74651940 G C 1 0 0 0 0 1 0 0 0 13435 942 33 4 4 RFWD3 16 74651940 Missense_Mutation SNP G C3N-00294_T 1854119 74651940 15686405 1001 13773 RFWD3 0 . GRCh38 16 74661154 74661154 + Nonsense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.296C>G p.Ser99Ter p.S99* ENST00000361070 2/13 308 265 43 356 356 0 strelka-varscan-mutect RFWD3,stop_gained,p.Ser99Ter,ENST00000361070,NM_018124.3;RFWD3,stop_gained,p.Ser99Ter,ENST00000571750,;RFWD3,stop_gained,p.Ser99Ter,ENST00000575113,;RFWD3,stop_gained,p.Ser99Ter,ENST00000572990,;RFWD3,stop_gained,p.Ser99Ter,ENST00000576652,;RFWD3,intron_variant,,ENST00000572337,;RFWD3,non_coding_transcript_exon_variant,,ENST00000571776,;RFWD3,non_coding_transcript_exon_variant,,ENST00000575397,;RFWD3,downstream_gene_variant,,ENST00000572840,; C ENST00000361070 Transcript stop_gained 394/4957 296/2325 99/774 S/* tCa/tGa 1 -1 RFWD3 HGNC HGNC:25539 protein_coding YES CCDS32486.1 ENSP00000354361 Q6PCD5 UPI0000366B66 NM_018124.3 2/13 hmmpanther:PTHR16047:SF7,hmmpanther:PTHR16047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 46 74661154 74661154 G C 1 0 0 0 0 0 1 0 0 13435 1294 45 4 4 RFWD3 16 74661154 Nonsense_Mutation SNP G C3N-00294_T 9214 74661154 15677191 1002 13774 ADAMTS18 0 . GRCh38 16 77353884 77353884 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1463C>T p.Thr488Ile p.T488I ENST00000282849 10/23 374 217 157 388 388 0 strelka-varscan-mutect ADAMTS18,missense_variant,p.Thr488Ile,ENST00000282849,NM_001326358.1,NM_199355.2;ADAMTS18,downstream_gene_variant,,ENST00000449265,; A ENST00000282849 Transcript missense_variant,splice_region_variant 1882/5913 1463/3666 488/1221 T/I aCa/aTa 1 -1 ADAMTS18 HGNC HGNC:17110 protein_coding YES CCDS10926.1 ENSP00000282849 Q8TE60 UPI0000233610 NM_001326358.1,NM_199355.2 deleterious(0) 10/23 PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF167,hmmpanther:PTHR13723,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 77353884 77353884 G A 1 0 0 0 0 1 0 0 0 307 1391 48 3 3 ADAMTS18 16 77353884 Missense_Mutation SNP G C3N-00294_T 2692730 77353884 12984461 1003 13775 KCNG4 0 . GRCh38 16 84222261 84222261 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.1516G>C p.Asp506His p.D506H ENST00000308251 3/3 192 168 24 200 200 0 strelka-varscan-mutect KCNG4,missense_variant,p.Asp506His,ENST00000308251,NM_172347.2; G ENST00000308251 Transcript missense_variant 1585/5179 1516/1560 506/519 D/H Gac/Cac COSM4528157 1 -1 KCNG4 HGNC HGNC:19697 protein_coding YES CCDS10945.1 ENSP00000312129 Q8TDN1 Q547S7 UPI00000557D8 NM_172347.2 tolerated_low_confidence(0.06) 3/3 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF167 1 MODERATE 1 SNV 1 1 1 PASS rs1401996345 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 46 84222261 84222261 C G 1 0 0 0 0 1 0 0 0 7946 826 29 4 4 KCNG4 16 84222261 Missense_Mutation SNP C C3N-00294_T 6868377 84222261 6116084 1004 13776 FOXC2 0 . GRCh38 16 86568538 86568538 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1203G>A p.= p.P401P ENST00000320354 1/1 97 69 28 69 69 0 strelka-varscan-mutect FOXC2,synonymous_variant,p.=,ENST00000320354,NM_005251.2;FOXC2-AS1,upstream_gene_variant,,ENST00000563280,; A ENST00000320354 Transcript synonymous_variant 1288/2478 1203/1506 401/501 P ccG/ccA 1 1 FOXC2 HGNC HGNC:3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 UPI000012ADC6 NM_005251.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF189 LOW SNV 1 PASS rs1157761462 . 0 198 11 0 0 0 0 0 -20 0.9999886 1 1 1 0 A 2 1 46 86568538 86568538 G A 1 0 0 0 0 0 0 0 1 5855 1074 38 1 1 FOXC2 16 86568538 Silent SNP G C3N-00294_T 2346277 86568538 3769807 1005 13777 ZNF469 0 . GRCh38 16 88434863 88434863 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.7309G>A p.Gly2437Ser p.G2437S ENST00000437464 2/2 460 273 187 506 506 0 strelka-varscan-mutect ZNF469,missense_variant,p.Gly2465Ser,ENST00000565624,;ZNF469,missense_variant,p.Gly2437Ser,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 7309/13203 7309/11778 2437/3925 G/S Ggc/Agc 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.19) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 88434863 88434863 G A 1 0 0 0 0 1 0 0 0 18500 1232 43 3 3 ZNF469 16 88434863 Missense_Mutation SNP G C3N-00294_T 1866325 88434863 1903482 1006 13778 RPL13 0 . GRCh38 16 89561326 89561326 + Silent SNP G G A rs867542380 C3N-00294_T C3N-00294_N G G c.204G>A p.= p.T68T ENST00000311528 3/6 223 170 53 226 226 0 strelka-varscan-mutect RPL13,synonymous_variant,p.=,ENST00000311528,NM_001243130.1,NM_000977.3;RPL13,synonymous_variant,p.=,ENST00000393099,NM_033251.2;RPL13,synonymous_variant,p.=,ENST00000452368,NM_001243131.1;RPL13,synonymous_variant,p.=,ENST00000567815,;RPL13,synonymous_variant,p.=,ENST00000467736,;RPL13,5_prime_UTR_variant,,ENST00000563270,;SPG7,downstream_gene_variant,,ENST00000620811,;SPG7,downstream_gene_variant,,ENST00000268704,NM_003119.3;RPL13,upstream_gene_variant,,ENST00000472354,;SNORD68,upstream_gene_variant,,ENST00000363214,;SPG7,downstream_gene_variant,,ENST00000565891,;RPL13,non_coding_transcript_exon_variant,,ENST00000563749,;RPL13,non_coding_transcript_exon_variant,,ENST00000484610,;RPL13,non_coding_transcript_exon_variant,,ENST00000399461,;RPL13,non_coding_transcript_exon_variant,,ENST00000491523,;RPL13,non_coding_transcript_exon_variant,,ENST00000487034,;RPL13,non_coding_transcript_exon_variant,,ENST00000565571,;RPL13,intron_variant,,ENST00000562879,;SPG7,downstream_gene_variant,,ENST00000569820,;SPG7,downstream_gene_variant,,ENST00000561702,;SPG7,downstream_gene_variant,,ENST00000561911,;SPG7,downstream_gene_variant,,ENST00000569720,;RPL13,upstream_gene_variant,,ENST00000570149,; A ENST00000311528 Transcript synonymous_variant 280/4498 204/636 68/211 T acG/acA rs867542380 1 1 RPL13 HGNC HGNC:10303 protein_coding YES CCDS10979.1 ENSP00000307889 P26373 A8K4C8 UPI0000001228 NM_001243130.1,NM_000977.3 3/6 Pfam_domain:PF01294,hmmpanther:PTHR11722 LOW 1 SNV 1 1 PASS rs867542380 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 89561326 89561326 G A 1 0 0 0 0 0 0 0 1 13811 1045 37 1 1 RPL13 16 89561326 Silent SNP G C3N-00294_T 1126463 89561326 777019 1007 13779 DBNDD1 0 . GRCh38 16 90008844 90008844 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.619G>A p.Glu207Lys p.E207K ENST00000568838 3/4 100 75 25 123 123 0 strelka-varscan-mutect DBNDD1,missense_variant,p.Glu93Lys,ENST00000392973,;DBNDD1,missense_variant,p.Glu107Lys,ENST00000304733,NM_024043.3;DBNDD1,missense_variant,p.Glu87Lys,ENST00000002501,NM_001042610.2;DBNDD1,missense_variant,p.Glu207Lys,ENST00000568838,NM_001288709.1;DBNDD1,upstream_gene_variant,,ENST00000623401,;DBNDD1,3_prime_UTR_variant,,ENST00000568330,;DBNDD1,non_coding_transcript_exon_variant,,ENST00000568662,; T ENST00000568838 Transcript missense_variant 629/993 619/837 207/278 E/K Gag/Aag COSM3795246,COSM3795247 1 -1 DBNDD1 HGNC HGNC:28455 protein_coding YES CCDS73931.1 ENSP00000457625 Q9H9R9 UPI00017A7806 NM_001288709.1 deleterious_low_confidence(0) 3/4 Pfam_domain:PF04440,hmmpanther:PTHR16294,hmmpanther:PTHR16294:SF4 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1168580181 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 90008844 90008844 C T 1 0 0 0 0 1 0 0 0 4053 864 30 3 3 DBNDD1 16 90008844 Missense_Mutation SNP C C3N-00294_T 447518 90008844 329501 1008 13780 SMYD4 0 . GRCh38 17 1786823 1786823 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1871G>C p.Gly624Ala p.G624A ENST00000305513 7/11 125 96 29 152 152 0 strelka-varscan-mutect SMYD4,missense_variant,p.Gly624Ala,ENST00000305513,NM_052928.2;SMYD4,missense_variant,p.Gly428Ala,ENST00000491788,;SMYD4,upstream_gene_variant,,ENST00000476292,; G ENST00000305513 Transcript missense_variant 2039/4384 1871/2415 624/804 G/A gGa/gCa 1 -1 SMYD4 HGNC HGNC:21067 protein_coding YES CCDS11013.1 ENSP00000304360 Q8IYR2 UPI000013EA5C NM_052928.2 tolerated(0.09) 7/11 hmmpanther:PTHR12197:SF171,hmmpanther:PTHR12197 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 1786823 1786823 C G 1 0 0 0 0 1 0 0 0 15145 855 30 4 4 SMYD4 17 1786823 Missense_Mutation SNP C C3N-00294_T 1786823 81470618 1009 13781 MNT 0 . GRCh38 17 2394091 2394091 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.759G>C p.Lys253Asn p.K253N ENST00000174618 4/6 343 274 69 274 274 0 strelka-mutect MNT,missense_variant,p.Lys253Asn,ENST00000174618,NM_020310.2;MNT,intron_variant,,ENST00000575394,;MNT,upstream_gene_variant,,ENST00000575374,;MNT,downstream_gene_variant,,ENST00000574559,;MNT,upstream_gene_variant,,ENST00000572892,;MNT,downstream_gene_variant,,ENST00000571836,;MNT,upstream_gene_variant,,ENST00000571232,;MNT,upstream_gene_variant,,ENST00000575402,; G ENST00000174618 Transcript missense_variant 1165/4996 759/1749 253/582 K/N aaG/aaC 1 -1 MNT HGNC HGNC:7188 protein_coding YES CCDS11018.1 ENSP00000174618 Q99583 UPI000012F2C6 NM_020310.2 deleterious(0) 4/6 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR11969,hmmpanther:PTHR11969:SF15,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS rs1334834632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 2394091 2394091 C G 1 0 0 0 0 1 0 0 0 9642 912 32 4 4 MNT 17 2394091 Missense_Mutation SNP C C3N-00294_T 607268 2394091 80863350 1010 13782 TP53 0 . GRCh38 17 7673537 7673537 + Nonsense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.991C>T p.Gln331Ter p.Q331* ENST00000269305 9/11 282 219 63 375 375 0 strelka-varscan-mutect TP53,stop_gained,p.Gln331Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Gln331Ter,ENST00000420246,;TP53,stop_gained,p.Gln292Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Gln292Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Gln331Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Gln292Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Gln331Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Gln292Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Gln331Ter,ENST00000445888,;TP53,stop_gained,p.Gln292Ter,ENST00000619485,;TP53,stop_gained,p.Gln199Ter,ENST00000510385,NM_001126116.1;TP53,stop_gained,p.Gln172Ter,ENST00000618944,NM_001276698.1;TP53,stop_gained,p.Gln199Ter,ENST00000504290,NM_001126117.1;TP53,stop_gained,p.Gln172Ter,ENST00000610623,NM_001276699.1;TP53,stop_gained,p.Gln199Ter,ENST00000504937,NM_001126115.1;TP53,stop_gained,p.Gln172Ter,ENST00000619186,NM_001276697.1;TP53,stop_gained,p.Gln331Ter,ENST00000359597,;TP53,stop_gained,p.Gln320Ter,ENST00000615910,;TP53,stop_gained,p.Gln199Ter,ENST00000509690,;TP53,stop_gained,p.Gln18Ter,ENST00000576024,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Gln292Ter,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained,splice_region_variant 1181/2579 991/1182 331/393 Q/* Cag/Tag TP53_g.14063C>G,TP53_g.14063C>T,TP53_g.14063del,COSM11354,COSM1649348,COSM289612,COSM3522688 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 9/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:1olgA00,Pfam_domain:PF07710,Superfamily_domains:SSF47719,Prints_domain:PR00386 0,0,0,1,1,1,1 HIGH 1 SNV 1 0,0,0,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 7673537 7673537 G A 1 0 0 0 0 0 1 0 0 16859 1304 45 3 3 TP53 17 7673537 Nonsense_Mutation SNP G C3N-00294_T 5279446 7673537 75583904 1011 13783 DNAH2 0 . GRCh38 17 7719750 7719750 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.16G>C p.Glu6Gln p.E6Q ENST00000572933 2/86 160 126 34 221 221 0 strelka-varscan-mutect DNAH2,missense_variant,p.Glu6Gln,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Glu6Gln,ENST00000389173,;DNAH2,missense_variant,p.Glu6Gln,ENST00000570791,NM_001303270.1; C ENST00000572933 Transcript missense_variant 1476/14955 16/13284 6/4427 E/Q Gag/Cag 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious_low_confidence(0.04) 2/86 hmmpanther:PTHR10676:SF183,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS rs763783888 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7719750 7719750 G C 1 0 0 0 0 1 0 0 0 4417 1291 45 4 4 DNAH2 17 7719750 Missense_Mutation SNP G C3N-00294_T 46213 7719750 75537691 1012 13784 DNAH2 0 . GRCh38 17 7833469 7833469 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.13220G>T p.Gly4407Val p.G4407V ENST00000572933 86/86 148 110 38 226 226 0 strelka-varscan-mutect DNAH2,missense_variant,p.Gly4407Val,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Gly4407Val,ENST00000389173,;DNAH2,downstream_gene_variant,,ENST00000575105,; T ENST00000572933 Transcript missense_variant 14680/14955 13220/13284 4407/4427 G/V gGg/gTg 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious(0) 86/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS rs1053578905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 7833469 7833469 G T 1 0 0 0 0 1 0 0 0 4417 1232 43 2 2 DNAH2 17 7833469 Missense_Mutation SNP G C3N-00294_T 113719 7833469 75423972 1013 13785 DNAH9 0 . GRCh38 17 11690232 11690232 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.4410G>T p.Glu1470Asp p.E1470D ENST00000262442 20/69 234 218 16 279 279 0 strelka-varscan-mutect DNAH9,missense_variant,p.Glu1470Asp,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Glu1470Asp,ENST00000454412,; T ENST00000262442 Transcript missense_variant 4478/13750 4410/13461 1470/4486 E/D gaG/gaT 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0.01) 20/69 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 11690232 11690232 G T 1 0 0 0 0 1 0 0 0 4423 991 35 2 2 DNAH9 17 11690232 Missense_Mutation SNP G C3N-00294_T 3856763 11690232 71567209 1014 13786 RAI1 0 . GRCh38 17 17794101 17794101 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1153G>A p.Gly385Arg p.G385R ENST00000353383 3/6 209 193 16 281 281 0 strelka-varscan-mutect RAI1,missense_variant,p.Gly385Arg,ENST00000353383,NM_030665.3;RAI1,missense_variant,p.Gly385Arg,ENST00000395774,;RAI1,downstream_gene_variant,,ENST00000471135,;RAI1,upstream_gene_variant,,ENST00000583166,; A ENST00000353383 Transcript missense_variant 1622/7662 1153/5721 385/1906 G/R Ggg/Agg 1 1 RAI1 HGNC HGNC:9834 protein_coding YES CCDS11188.1 ENSP00000323074 Q7Z5J4 UPI0000200AAF NM_030665.3 deleterious(0) 3/6 hmmpanther:PTHR14955:SF6,hmmpanther:PTHR14955 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 17794101 17794101 G A 1 0 0 0 0 1 0 0 0 13166 1000 35 3 3 RAI1 17 17794101 Missense_Mutation SNP G C3N-00294_T 6103869 17794101 65463340 1015 13787 FAM83G 0 . GRCh38 17 19003780 19003780 + Nonsense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.262C>T p.Gln88Ter p.Q88* ENST00000388995 2/6 152 108 44 207 207 0 strelka-varscan-mutect FAM83G,stop_gained,p.Gln88Ter,ENST00000388995,NM_001039999.2;FAM83G,stop_gained,p.Gln88Ter,ENST00000345041,;SLC5A10,intron_variant,,ENST00000317977,NM_001282417.1;SLC5A10,intron_variant,,ENST00000395647,NM_152351.4;SLC5A10,intron_variant,,ENST00000395645,NM_001042450.2;SLC5A10,intron_variant,,ENST00000417251,NM_001270649.1;SLC5A10,intron_variant,,ENST00000395643,NM_001270648.1;FAM83G,non_coding_transcript_exon_variant,,ENST00000399096,; A ENST00000388995 Transcript stop_gained 486/5266 262/2472 88/823 Q/* Cag/Tag COSM1302480,COSM5327212 1 -1 FAM83G HGNC HGNC:32554 protein_coding YES CCDS42276.1 ENSP00000373647 A6ND36 UPI0000E03260 NM_001039999.2 2/6 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF5,Pfam_domain:PF07894 1,1 HIGH SNV 5 1,1 1 PASS rs969896084 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 19003780 19003780 G A 1 0 0 0 0 0 1 0 0 5497 1299 45 3 3 FAM83G 17 19003780 Nonsense_Mutation SNP G C3N-00294_T 1209679 19003780 64253661 1016 13788 KIAA0100 0 . GRCh38 17 28619969 28619969 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.5411C>G p.Ser1804Cys p.S1804C ENST00000528896 30/39 147 120 27 140 139 1 strelka-varscan-mutect KIAA0100,missense_variant,p.Ser1804Cys,ENST00000528896,NM_014680.3;KIAA0100,missense_variant,p.Ser1661Cys,ENST00000544884,;KIAA0100,missense_variant,p.Ser1661Cys,ENST00000389003,;SPAG5-AS1,downstream_gene_variant,,ENST00000414744,;SPAG5-AS1,downstream_gene_variant,,ENST00000424210,;SPAG5-AS1,downstream_gene_variant,,ENST00000554154,;KIAA0100,upstream_gene_variant,,ENST00000579924,;KIAA0100,non_coding_transcript_exon_variant,,ENST00000580395,;SPAG5-AS1,downstream_gene_variant,,ENST00000584675,;KIAA0100,upstream_gene_variant,,ENST00000583860,; C ENST00000528896 Transcript missense_variant 5486/7407 5411/6708 1804/2235 S/C tCt/tGt 1 -1 KIAA0100 HGNC HGNC:28960 protein_coding YES CCDS32595.1 ENSP00000436773 Q14667 UPI00004B4130 NM_014680.3 tolerated(0.06) 30/39 hmmpanther:PTHR15678,Pfam_domain:PF10351 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 28619969 28619969 G C 1 0 0 0 0 1 0 0 0 8074 942 33 4 4 KIAA0100 17 28619969 Missense_Mutation SNP G C3N-00294_T 9616189 28619969 54637472 1017 13789 KIAA0100 0 . GRCh38 17 28637016 28637016 + Silent SNP G G C C3N-00294_T C3N-00294_N G G c.1926C>G p.= p.L642L ENST00000528896 15/39 467 403 64 402 402 0 strelka-varscan-mutect KIAA0100,synonymous_variant,p.=,ENST00000528896,NM_014680.3;KIAA0100,synonymous_variant,p.=,ENST00000544884,;KIAA0100,synonymous_variant,p.=,ENST00000389003,;KIAA0100,upstream_gene_variant,,ENST00000577261,;RP11-192H23.7,downstream_gene_variant,,ENST00000577814,;RP11-192H23.7,downstream_gene_variant,,ENST00000583787,;KIAA0100,downstream_gene_variant,,ENST00000577417,;KIAA0100,downstream_gene_variant,,ENST00000580882,;KIAA0100,downstream_gene_variant,,ENST00000583403,;KIAA0100,downstream_gene_variant,,ENST00000577580,;KIAA0100,upstream_gene_variant,,ENST00000582417,;KIAA0100,upstream_gene_variant,,ENST00000581064,;KIAA0100,downstream_gene_variant,,ENST00000581267,;KIAA0100,downstream_gene_variant,,ENST00000579253,; C ENST00000528896 Transcript synonymous_variant 2001/7407 1926/6708 642/2235 L ctC/ctG COSM3795383,COSM3795384 1 -1 KIAA0100 HGNC HGNC:28960 protein_coding YES CCDS32595.1 ENSP00000436773 Q14667 UPI00004B4130 NM_014680.3 15/39 hmmpanther:PTHR15678,Pfam_domain:PF10344 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 28637016 28637016 G C 1 0 0 0 0 0 0 0 1 8074 1277 45 4 4 KIAA0100 17 28637016 Silent SNP G C3N-00294_T 17047 28637016 54620425 1018 13790 CORO6 0 . GRCh38 17 29617522 29617522 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.731G>C p.Arg244Pro p.R244P ENST00000345068 6/11 99 73 26 78 78 0 strelka-varscan-mutect CORO6,missense_variant,p.Arg244Pro,ENST00000345068,;CORO6,missense_variant,p.Arg244Pro,ENST00000388767,NM_032854.3;CORO6,intron_variant,,ENST00000580212,;CORO6,intron_variant,,ENST00000584969,;ANKRD13B,downstream_gene_variant,,ENST00000394859,NM_152345.4;ANKRD13B,downstream_gene_variant,,ENST00000614878,;CORO6,downstream_gene_variant,,ENST00000492276,;CORO6,downstream_gene_variant,,ENST00000584602,;ANKRD13B,downstream_gene_variant,,ENST00000579719,;ABHD15-AS1,intron_variant,,ENST00000581474,;RP11-68I3.10,downstream_gene_variant,,ENST00000582367,;CORO6,intron_variant,,ENST00000577909,;CORO6,non_coding_transcript_exon_variant,,ENST00000459686,;CORO6,non_coding_transcript_exon_variant,,ENST00000467534,;CORO6,non_coding_transcript_exon_variant,,ENST00000469090,;CORO6,intron_variant,,ENST00000480954,;ANKRD13B,downstream_gene_variant,,ENST00000487527,;ANKRD13B,downstream_gene_variant,,ENST00000488766,;ANKRD13B,downstream_gene_variant,,ENST00000493506,;CORO6,upstream_gene_variant,,ENST00000579388,; G ENST00000345068 Transcript missense_variant 945/2603 731/1419 244/472 R/P cGa/cCa 1 -1 CORO6 HGNC HGNC:21356 protein_coding YES CCDS11252.2 ENSP00000344562 Q6QEF8 UPI0000DA4C55 deleterious(0.01) 6/11 hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF23,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS rs1447995407 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 46 29617522 29617522 C G 1 0 0 0 0 1 0 0 0 3552 884 31 4 4 CORO6 17 29617522 Missense_Mutation SNP C C3N-00294_T 980506 29617522 53639919 1019 13791 SSH2 0 . GRCh38 17 29632568 29632568 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2626G>A p.Glu876Lys p.E876K ENST00000540801 16/16 201 147 54 208 208 0 strelka-varscan-mutect SSH2,missense_variant,p.Glu849Lys,ENST00000269033,NM_033389.3;SSH2,missense_variant,p.Glu876Lys,ENST00000540801,NM_001282129.1;SSH2,upstream_gene_variant,,ENST00000577991,;ABHD15-AS1,intron_variant,,ENST00000581474,; T ENST00000540801 Transcript missense_variant 2719/4538 2626/4353 876/1450 E/K Gag/Aag 1 -1 SSH2 HGNC HGNC:30580 protein_coding YES CCDS74024.1 ENSP00000444743 F5H527 UPI0002065A97 NM_001282129.1 deleterious_low_confidence(0) 16/16 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 29632568 29632568 C T 1 0 0 0 0 1 0 0 0 15561 922 32 3 3 SSH2 17 29632568 Missense_Mutation SNP C C3N-00294_T 15046 29632568 53624873 1020 13792 ATAD5 0 . GRCh38 17 30878024 30878024 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.3940G>A p.Asp1314Asn p.D1314N ENST00000321990 17/23 67 58 9 149 148 1 strelka-varscan-mutect ATAD5,missense_variant,p.Asp1314Asn,ENST00000321990,NM_024857.4;ATAD5,downstream_gene_variant,,ENST00000578295,; A ENST00000321990 Transcript missense_variant 4318/6869 3940/5535 1314/1844 D/N Gat/Aat 1 1 ATAD5 HGNC HGNC:25752 protein_coding YES CCDS11260.1 ENSP00000313171 Q96QE3 UPI0000071E9E NM_024857.4 deleterious(0) 17/23 hmmpanther:PTHR23389:SF6,hmmpanther:PTHR23389,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.85573 1 1 1 1 0 A 3 1 46 30878024 30878024 G A 1 0 0 0 0 1 0 0 0 1224 942 33 3 3 ATAD5 17 30878024 Missense_Mutation SNP G C3N-00294_T 1245456 30878024 52379417 1021 13793 NF1 0 . GRCh38 17 31159046 31159046 + Missense_Mutation SNP C C G rs587782772 C3N-00294_T C3N-00294_N C C c.241C>G p.Leu81Val p.L81V ENST00000358273 3/58 141 114 27 202 202 0 strelka-varscan-mutect NF1,missense_variant,p.Leu81Val,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Leu81Val,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Leu81Val,ENST00000431387,NM_001128147.2;NF1,missense_variant,p.Leu14Val,ENST00000489712,;NF1,missense_variant,p.Leu115Val,ENST00000579081,;NF1,missense_variant,p.Leu42Val,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,;NF1,upstream_gene_variant,,ENST00000490416,; G ENST00000358273 Transcript missense_variant 624/12425 241/8520 81/2839 L/V Ctc/Gtc rs587782772,COSM1520784,COSM1520785 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0.04) 3/58 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs587782772 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 31159046 31159046 C G 1 0 0 0 0 1 0 0 0 10393 913 32 4 4 NF1 17 31159046 Missense_Mutation SNP C C3N-00294_T 281022 31159046 52098395 1022 13794 MIEN1 0 . GRCh38 17 39730475 39730475 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.21G>C p.Gln7His p.Q7H ENST00000394231 1/4 246 206 40 166 166 0 strelka-varscan-mutect MIEN1,missense_variant,p.Gln7His,ENST00000394231,NM_032339.3;MIEN1,missense_variant,p.Gln7His,ENST00000577810,;ERBB2,downstream_gene_variant,,ENST00000584601,NM_001005862.2;ERBB2,downstream_gene_variant,,ENST00000406381,;ERBB2,downstream_gene_variant,,ENST00000269571,NM_004448.3;ERBB2,downstream_gene_variant,,ENST00000541774,NM_001289936.1;ERBB2,downstream_gene_variant,,ENST00000584450,NM_001289937.1;ERBB2,downstream_gene_variant,,ENST00000445658,;MIR4728,downstream_gene_variant,,ENST00000580969,;MIEN1,non_coding_transcript_exon_variant,,ENST00000474210,;ERBB2,downstream_gene_variant,,ENST00000584888,;MIEN1,non_coding_transcript_exon_variant,,ENST00000582963,;MIEN1,non_coding_transcript_exon_variant,,ENST00000498164,;MIEN1,non_coding_transcript_exon_variant,,ENST00000469568,;ERBB2,downstream_gene_variant,,ENST00000583038,;ERBB2,downstream_gene_variant,,ENST00000578373,; G ENST00000394231 Transcript missense_variant 313/1006 21/348 7/115 Q/H caG/caC 1 -1 MIEN1 HGNC HGNC:28230 protein_coding YES CCDS11344.1 ENSP00000377778 Q9BRT3 UPI0000043728 NM_032339.3 tolerated_low_confidence(0.11) 1/4 hmmpanther:PTHR15124,hmmpanther:PTHR15124:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 39730475 39730475 C G 1 0 0 0 0 1 0 0 0 9542 912 32 4 4 MIEN1 17 39730475 Missense_Mutation SNP C C3N-00294_T 8571429 39730475 43526966 1023 13795 IGFBP4 0 . GRCh38 17 40453945 40453945 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.525G>A p.= p.Q175Q ENST00000269593 3/4 128 99 29 136 136 0 strelka-varscan-mutect IGFBP4,synonymous_variant,p.=,ENST00000269593,NM_001552.2; A ENST00000269593 Transcript synonymous_variant 800/2200 525/777 175/258 Q caG/caA 1 1 IGFBP4 HGNC HGNC:5473 protein_coding YES CCDS11367.1 ENSP00000269593 P22692 A0A024R1U8 UPI0000035977 NM_001552.2 3/4 Gene3D:4.10.800.10,Pfam_domain:PF00086,Prints_domain:PR01976,PROSITE_profiles:PS51162,hmmpanther:PTHR11551,hmmpanther:PTHR11551:SF7,Superfamily_domains:SSF57610 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 40453945 40453945 G A 1 0 0 0 0 0 0 0 1 7487 933 33 3 3 IGFBP4 17 40453945 Silent SNP G C3N-00294_T 723470 40453945 42803496 1024 13796 KRT26 0 . GRCh38 17 40772055 40772055 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.59G>A p.Arg20Lys p.R20K ENST00000335552 1/8 257 206 51 263 262 1 strelka-varscan-mutect KRT26,missense_variant,p.Arg20Lys,ENST00000335552,NM_181539.4;KRT27,downstream_gene_variant,,ENST00000301656,NM_181537.3;KRT27,downstream_gene_variant,,ENST00000540723,; T ENST00000335552 Transcript missense_variant 108/1733 59/1407 20/468 R/K aGg/aAg 1 -1 KRT26 HGNC HGNC:30840 protein_coding YES CCDS11374.1 ENSP00000334798 Q7Z3Y9 UPI0000200C8F NM_181539.4 deleterious(0.04) 1/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF162,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 40772055 40772055 C T 1 0 0 0 0 1 0 0 0 8345 681 24 3 3 KRT26 17 40772055 Missense_Mutation SNP C C3N-00294_T 318110 40772055 42485386 1025 13797 KRTAP4-3 0 . GRCh38 17 41167631 41167631 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.542G>C p.Arg181Thr p.R181T ENST00000391356 1/1 95 78 17 81 81 0 strelka-varscan-mutect KRTAP4-3,missense_variant,p.Arg181Thr,ENST00000391356,NM_033187.1; G ENST00000391356 Transcript missense_variant 564/964 542/588 181/195 R/T aGa/aCa 1 -1 KRTAP4-3 HGNC HGNC:18908 protein_coding YES CCDS42331.1 ENSP00000375151 Q9BYR4 UPI00006C17BA NM_033187.1 tolerated(0.19) 1/1 hmmpanther:PTHR23262:SF73,hmmpanther:PTHR23262 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 41167631 41167631 C G 1 0 0 0 0 1 0 0 0 8446 913 32 4 4 KRTAP4-3 17 41167631 Missense_Mutation SNP C C3N-00294_T 395576 41167631 42089810 1026 13798 KRTAP9-4 0 . GRCh38 17 41250151 41250151 + Missense_Mutation SNP G G A rs761233657 C3N-00294_T C3N-00294_N G G c.431G>A p.Cys144Tyr p.C144Y ENST00000334109 1/1 376 310 66 363 363 0 strelka-varscan-mutect KRTAP9-4,missense_variant,p.Cys144Tyr,ENST00000334109,NM_033191.2; A ENST00000334109 Transcript missense_variant 465/967 431/465 144/154 C/Y tGt/tAt rs761233657 1 1 KRTAP9-4 HGNC HGNC:18902 protein_coding YES CCDS11386.1 ENSP00000334922 Q9BYQ2 UPI000013F6DA NM_033191.2 deleterious(0) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF65,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS rs761233657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 41250151 41250151 G A 1 0 0 0 0 1 0 0 0 8472 1377 48 3 3 KRTAP9-4 17 41250151 Missense_Mutation SNP G C3N-00294_T 82520 41250151 42007290 1027 13799 ETV4 0 . GRCh38 17 43545340 43545340 + Missense_Mutation SNP C C T rs776306922 C3N-00294_T C3N-00294_N C C c.88G>A p.Glu30Lys p.E30K ENST00000319349 3/13 84 65 19 79 79 0 strelka-varscan-mutect ETV4,missense_variant,p.Glu30Lys,ENST00000319349,NM_001079675.2;ETV4,missense_variant,p.Glu30Lys,ENST00000393664,;ETV4,missense_variant,p.Glu30Lys,ENST00000591713,NM_001986.2;ETV4,missense_variant,p.Glu30Lys,ENST00000545089,;ETV4,5_prime_UTR_variant,,ENST00000538265,NM_001261438.1;ETV4,5_prime_UTR_variant,,ENST00000545954,NM_001261437.1;ETV4,5_prime_UTR_variant,,ENST00000586764,;DHX8,downstream_gene_variant,,ENST00000589898,;RP11-392O1.4,intron_variant,,ENST00000588996,;ETV4,non_coding_transcript_exon_variant,,ENST00000585508,;ETV4,non_coding_transcript_exon_variant,,ENST00000590236,;ETV4,non_coding_transcript_exon_variant,,ENST00000587151,; T ENST00000319349 Transcript missense_variant 387/2429 88/1455 30/484 E/K Gaa/Aaa rs776306922,COSM5436797 1 -1 ETV4 HGNC HGNC:3493 protein_coding YES CCDS11465.1 ENSP00000321835 P43268 UPI0000000236 NM_001079675.2 tolerated(0.71) 3/13 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF181,Pfam_domain:PF04621 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776306922 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 43545340 43545340 C T 1 0 0 0 0 1 0 0 0 5145 893 31 1 1 ETV4 17 43545340 Missense_Mutation SNP C C3N-00294_T 2295189 43545340 39712101 1028 13800 HDAC5 0 . GRCh38 17 44093422 44093422 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.421G>C p.Glu141Gln p.E141Q ENST00000225983 5/27 145 122 23 113 113 0 strelka-varscan-mutect HDAC5,missense_variant,p.Glu141Gln,ENST00000225983,NM_001015053.1;HDAC5,missense_variant,p.Glu140Gln,ENST00000336057,;HDAC5,missense_variant,p.Glu140Gln,ENST00000586802,NM_005474.4;HDAC5,upstream_gene_variant,,ENST00000588261,;HDAC5,downstream_gene_variant,,ENST00000591714,;HDAC5,downstream_gene_variant,,ENST00000587135,;HDAC5,downstream_gene_variant,,ENST00000588703,;HDAC5,non_coding_transcript_exon_variant,,ENST00000587776,;HDAC5,upstream_gene_variant,,ENST00000592385,; G ENST00000225983 Transcript missense_variant 745/5326 421/3372 141/1123 E/Q Gag/Cag 1 -1 HDAC5 HGNC HGNC:14068 protein_coding YES CCDS32663.1 ENSP00000225983 Q9UQL6 UPI0000508BBA NM_001015053.1 tolerated(0.48) 5/27 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF12203,PIRSF_domain:PIRSF037911 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 46 44093422 44093422 C G 1 0 0 0 0 1 0 0 0 6897 864 30 4 4 HDAC5 17 44093422 Missense_Mutation SNP C C3N-00294_T 548082 44093422 39164019 1029 13801 UBTF 0 . GRCh38 17 44207307 44207307 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2230G>C p.Glu744Gln p.E744Q ENST00000302904 21/21 255 207 48 208 208 0 strelka-varscan-mutect UBTF,missense_variant,p.Glu744Gln,ENST00000302904,;UBTF,missense_variant,p.Glu707Gln,ENST00000343638,NM_001076683.1;UBTF,missense_variant,p.Glu707Gln,ENST00000533177,;UBTF,missense_variant,p.Met705Ile,ENST00000527034,;UBTF,missense_variant,p.Glu744Gln,ENST00000436088,NM_014233.3;UBTF,missense_variant,p.Glu707Gln,ENST00000393606,NM_001076684.2;UBTF,missense_variant,p.Glu744Gln,ENST00000529383,;UBTF,missense_variant,p.Glu707Gln,ENST00000526094,;UBTF,downstream_gene_variant,,ENST00000529373,;MIR6782,downstream_gene_variant,,ENST00000619539,;CTB-175E5.7,intron_variant,,ENST00000586560,;UBTF,downstream_gene_variant,,ENST00000529947,;UBTF,downstream_gene_variant,,ENST00000529042,;UBTF,downstream_gene_variant,,ENST00000531368,; G ENST00000302904 Transcript missense_variant 2723/4997 2230/2295 744/764 E/Q Gag/Cag 1 -1 UBTF HGNC HGNC:12511 protein_coding YES CCDS11480.1 ENSP00000302640 P17480 UPI000013797C 21/21 Low_complexity_(Seg):seg,hmmpanther:PTHR13711:SF216,hmmpanther:PTHR13711 MODERATE 1 SNV 2 1 PASS rs1264175938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 44207307 44207307 C G 1 0 0 0 0 1 0 0 0 17433 835 29 4 4 UBTF 17 44207307 Missense_Mutation SNP C C3N-00294_T 113885 44207307 39050134 1030 13802 GPATCH8 0 . GRCh38 17 44503356 44503356 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.15C>T p.= p.F5F ENST00000591680 1/8 696 579 117 620 620 0 strelka-varscan-mutect GPATCH8,synonymous_variant,p.=,ENST00000591680,NM_001304939.1,NM_001002909.3;GPATCH8,synonymous_variant,p.=,ENST00000585614,;GPATCH8,synonymous_variant,p.=,ENST00000587228,;GPATCH8,synonymous_variant,p.=,ENST00000590041,;GPATCH8,synonymous_variant,p.=,ENST00000592746,;GPATCH8,synonymous_variant,p.=,ENST00000586037,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000592154,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000588554,; A ENST00000591680 Transcript synonymous_variant 46/4692 15/4509 5/1502 F ttC/ttT 1 -1 GPATCH8 HGNC HGNC:29066 protein_coding YES CCDS32666.1 ENSP00000467556 Q9UKJ3 UPI0000237985 NM_001304939.1,NM_001002909.3 1/8 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 44503356 44503356 G A 1 0 0 0 0 0 0 0 1 6495 933 33 3 3 GPATCH8 17 44503356 Silent SNP G C3N-00294_T 296049 44503356 38754085 1031 13803 MAPT 0 . GRCh38 17 46018653 46018653 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2038G>C p.Asp680His p.D680H ENST00000344290 14/15 458 390 68 360 360 0 strelka-varscan-mutect MAPT,missense_variant,p.Asp680His,ENST00000344290,NM_001123066.3;MAPT,missense_variant,p.Asp662His,ENST00000262410,NM_016835.4;MAPT,missense_variant,p.Asp345His,ENST00000351559,NM_005910.5;MAPT,missense_variant,p.Asp316His,ENST00000340799,NM_001123067.3;MAPT,missense_variant,p.Asp314His,ENST00000535772,NM_001203251.1,NM_001203252.1;MAPT,missense_variant,p.Asp287His,ENST00000446361,NM_016834.4;MAPT,missense_variant,p.Asp680His,ENST00000415613,;MAPT,missense_variant,p.Asp662His,ENST00000571987,;MAPT,missense_variant,p.Asp345His,ENST00000574436,;MAPT,missense_variant,p.Asp316His,ENST00000420682,;MAPT,missense_variant,p.Asp314His,ENST00000431008,;MAPT,missense_variant,p.Asp256His,ENST00000334239,NM_016841.4;MAPT,non_coding_transcript_exon_variant,,ENST00000570299,;MAPT,non_coding_transcript_exon_variant,,ENST00000576518,; C ENST00000344290 Transcript missense_variant 2360/6816 2038/2331 680/776 D/H Gac/Cac 1 1 MAPT HGNC HGNC:6893 protein_coding YES CCDS45715.1 ENSP00000340820 P10636 UPI0001AE66E9 NM_001123066.3 deleterious(0.02) 14/15 PROSITE_profiles:PS51491,hmmpanther:PTHR11501,Pfam_domain:PF00418 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 46018653 46018653 G C 1 0 0 0 0 1 0 0 0 9220 1290 45 4 4 MAPT 17 46018653 Missense_Mutation SNP G C3N-00294_T 1515297 46018653 37238788 1032 13804 KANSL1 0 . GRCh38 17 46171309 46171309 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.835G>C p.Asp279His p.D279H ENST00000262419 2/15 162 137 25 115 115 0 strelka-varscan-mutect KANSL1,missense_variant,p.Asp279His,ENST00000262419,NM_001193466.1;KANSL1,missense_variant,p.Asp279His,ENST00000574590,;KANSL1,missense_variant,p.Asp279His,ENST00000432791,NM_001193465.1;KANSL1,missense_variant,p.Asp279His,ENST00000572904,NM_015443.3;KANSL1,missense_variant,p.Asp279His,ENST00000575318,;KANSL1,downstream_gene_variant,,ENST00000574655,;KANSL1,downstream_gene_variant,,ENST00000571698,;KANSL1,downstream_gene_variant,,ENST00000576739,;KANSL1,upstream_gene_variant,,ENST00000576248,;KANSL1,upstream_gene_variant,,ENST00000577114,; G ENST00000262419 Transcript missense_variant 1306/5309 835/3318 279/1105 D/H Gat/Cat 1 -1 KANSL1 HGNC HGNC:24565 protein_coding YES CCDS11503.2 ENSP00000262419 Q7Z3B3 A0A024R9Y2 UPI000013D2AE NM_001193466.1 deleterious(0) 2/15 hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 46171309 46171309 C G 1 0 0 0 0 1 0 0 0 7889 913 32 4 4 KANSL1 17 46171309 Missense_Mutation SNP C C3N-00294_T 152656 46171309 37086132 1033 13805 NPEPPS 0 . GRCh38 17 47613711 47613711 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2281G>C p.Asp761His p.D761H ENST00000322157 19/23 102 85 17 129 129 0 strelka-varscan-mutect NPEPPS,missense_variant,p.Asp761His,ENST00000322157,NM_006310.3;NPEPPS,missense_variant,p.Asp757His,ENST00000530173,;NPEPPS,upstream_gene_variant,,ENST00000528565,;RP11-580I16.2,intron_variant,,ENST00000582389,;RP11-580I16.2,intron_variant,,ENST00000582066,;NPEPPS,3_prime_UTR_variant,,ENST00000530514,;NPEPPS,3_prime_UTR_variant,,ENST00000525048,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000531486,; C ENST00000322157 Transcript missense_variant 2518/4353 2281/2760 761/919 D/H Gat/Cat 1 1 NPEPPS HGNC HGNC:7900 protein_coding YES CCDS45721.1 ENSP00000320324 P55786 UPI0000140D51 NM_006310.3 deleterious(0.01) 19/23 hmmpanther:PTHR11533:SF187,hmmpanther:PTHR11533,Pfam_domain:PF11838 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 47613711 47613711 G C 1 0 0 0 0 1 0 0 0 10623 942 33 4 4 NPEPPS 17 47613711 Missense_Mutation SNP G C3N-00294_T 1442402 47613711 35643730 1034 13806 KAT7 0 . GRCh38 17 49821772 49821772 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1368G>A p.= p.L456L ENST00000259021 11/15 372 310 62 289 289 0 strelka-varscan-mutect KAT7,synonymous_variant,p.=,ENST00000259021,NM_007067.4;KAT7,synonymous_variant,p.=,ENST00000435742,;KAT7,synonymous_variant,p.=,ENST00000424009,NM_001199155.1;KAT7,synonymous_variant,p.=,ENST00000454930,NM_001199156.1;KAT7,synonymous_variant,p.=,ENST00000509773,NM_001199157.1;KAT7,synonymous_variant,p.=,ENST00000510819,NM_001199158.1;KAT7,non_coding_transcript_exon_variant,,ENST00000513980,;KAT7,non_coding_transcript_exon_variant,,ENST00000512616,;KAT7,non_coding_transcript_exon_variant,,ENST00000513171,;KAT7,non_coding_transcript_exon_variant,,ENST00000514540,;KAT7,upstream_gene_variant,,ENST00000503101,;KAT7,downstream_gene_variant,,ENST00000508594,;KAT7,non_coding_transcript_exon_variant,,ENST00000509794,;KAT7,non_coding_transcript_exon_variant,,ENST00000510426,;KAT7,upstream_gene_variant,,ENST00000503635,;KAT7,upstream_gene_variant,,ENST00000513075,; A ENST00000259021 Transcript synonymous_variant 1648/9644 1368/1836 456/611 L ctG/ctA 1 1 KAT7 HGNC HGNC:17016 protein_coding YES CCDS11554.1 ENSP00000259021 O95251 UPI000006D3D5 NM_007067.4 11/15 PROSITE_profiles:PS51726,hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF111,Pfam_domain:PF01853,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 49821772 49821772 G A 1 0 0 0 0 0 0 0 1 7900 1277 45 3 3 KAT7 17 49821772 Silent SNP G C3N-00294_T 2208061 49821772 33435669 1035 13807 ACSF2 0 . GRCh38 17 50473741 50473741 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1627G>T p.Glu543Ter p.E543* ENST00000427954 14/17 292 240 52 279 279 0 strelka-varscan-mutect ACSF2,stop_gained,p.Glu543Ter,ENST00000427954,NM_001288968.1;ACSF2,stop_gained,p.Glu518Ter,ENST00000300441,NM_025149.5;ACSF2,stop_gained,p.Glu505Ter,ENST00000502667,NM_001288969.1;ACSF2,stop_gained,p.Glu475Ter,ENST00000504392,NM_001288972.1,NM_001288970.1,NM_001288971.1;CHAD,upstream_gene_variant,,ENST00000508540,NM_001267.2;CHAD,upstream_gene_variant,,ENST00000258969,;RP11-94C24.13,upstream_gene_variant,,ENST00000620769,;ACSF2,non_coding_transcript_exon_variant,,ENST00000506085,;ACSF2,non_coding_transcript_exon_variant,,ENST00000512119,;ACSF2,non_coding_transcript_exon_variant,,ENST00000513544,;ACSF2,non_coding_transcript_exon_variant,,ENST00000511147,;ACSF2,downstream_gene_variant,,ENST00000509806,;ACSF2,downstream_gene_variant,,ENST00000508734,;ACSF2,3_prime_UTR_variant,,ENST00000510410,;ACSF2,3_prime_UTR_variant,,ENST00000508245,;ACSF2,non_coding_transcript_exon_variant,,ENST00000503295,;ACSF2,non_coding_transcript_exon_variant,,ENST00000512537,;ACSF2,downstream_gene_variant,,ENST00000511288,;ACSF2,upstream_gene_variant,,ENST00000507792,;ACSF2,downstream_gene_variant,,ENST00000507769,;ACSF2,downstream_gene_variant,,ENST00000513101,;ACSF2,downstream_gene_variant,,ENST00000503387,;ACSF2,downstream_gene_variant,,ENST00000510262,; T ENST00000427954 Transcript stop_gained 1670/2251 1627/1923 543/640 E/* Gag/Tag 1 1 ACSF2 HGNC HGNC:26101 protein_coding YES CCDS74103.1 ENSP00000401831 Q96CM8 UPI00017A6F63 NM_001288968.1 14/17 Gene3D:3.30.300.30,hmmpanther:PTHR24095,Superfamily_domains:SSF56801 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 50473741 50473741 G T 1 0 0 0 0 0 1 0 0 217 1291 45 2 2 ACSF2 17 50473741 Nonsense_Mutation SNP G C3N-00294_T 651969 50473741 32783700 1036 13808 CACNA1G 0 . GRCh38 17 50572672 50572672 + Missense_Mutation SNP C C A rs761241506 C3N-00294_T C3N-00294_N C C c.865C>A p.Arg289Ser p.R289S ENST00000359106 6/38 178 83 95 144 144 0 strelka-varscan-mutect CACNA1G,missense_variant,p.Arg289Ser,ENST00000354983,NM_198396.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000352832,NM_198387.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000359106,NM_018896.4;CACNA1G,missense_variant,p.Arg289Ser,ENST00000360761,NM_198382.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000442258,NM_198388.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000429973,NM_198386.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000507336,NM_198377.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000358244,NM_198376.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000507510,NM_198385.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000515765,NM_198380.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000515411,NM_001256324.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000502264,NM_198383.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000510115,NM_198379.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000514079,NM_001256325.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000513689,NM_001256326.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000515165,NM_198384.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000507609,NM_001256327.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000512389,NM_198378.2;CACNA1G,missense_variant,p.Arg289Ser,ENST00000514181,NM_001256328.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000510366,NM_001256331.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000514717,NM_001256332.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000505165,NM_001256333.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000507896,NM_001256334.1;CACNA1G,missense_variant,p.Arg289Ser,ENST00000416767,;CACNA1G,missense_variant,p.Arg171Ser,ENST00000570567,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000506406,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000504076,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000511765,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000503436,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000511768,;CACNA1G,missense_variant,p.Arg289Ser,ENST00000503607,; A ENST00000359106 Transcript missense_variant 865/7648 865/7134 289/2377 R/S Cgc/Agc rs761241506 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 deleterious(0.05) 6/38 Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS rs761241506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 50572672 50572672 C A 1 0 0 0 0 1 0 0 0 2232 768 27 1 1 CACNA1G 17 50572672 Missense_Mutation SNP C C3N-00294_T 98931 50572672 32684769 1037 13809 CACNA1G 0 . GRCh38 17 50576262 50576262 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1860C>T p.= p.T620T ENST00000359106 8/38 548 448 100 458 458 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CACNA1G,synonymous_variant,p.=,ENST00000416767,;CACNA1G,downstream_gene_variant,,ENST00000570567,;CACNA1G,synonymous_variant,p.=,ENST00000506406,;CACNA1G,synonymous_variant,p.=,ENST00000504076,;CACNA1G,synonymous_variant,p.=,ENST00000511765,;CACNA1G,synonymous_variant,p.=,ENST00000503436,;CACNA1G,synonymous_variant,p.=,ENST00000511768,;CACNA1G,synonymous_variant,p.=,ENST00000503607,; T ENST00000359106 Transcript synonymous_variant 1860/7648 1860/7134 620/2377 T acC/acT 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 8/38 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 50576262 50576262 C T 1 0 0 0 0 0 0 0 1 2232 581 21 3 3 CACNA1G 17 50576262 Silent SNP C C3N-00294_T 3590 50576262 32681179 1038 13810 UTP18 0 . GRCh38 17 51273422 51273422 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.683C>A p.Ser228Ter p.S228* ENST00000225298 5/14 111 98 13 112 112 0 strelka-varscan-mutect UTP18,stop_gained,p.Ser228Ter,ENST00000225298,NM_016001.2;UTP18,upstream_gene_variant,,ENST00000583725,;UTP18,upstream_gene_variant,,ENST00000508506,; A ENST00000225298 Transcript stop_gained 740/1894 683/1671 228/556 S/* tCa/tAa 1 1 UTP18 HGNC HGNC:24274 protein_coding YES CCDS42362.1 ENSP00000225298 Q9Y5J1 UPI000051E38C NM_016001.2 5/14 hmmpanther:PTHR18359 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 51273422 51273422 C A 1 0 0 0 0 0 1 0 0 17641 838 29 2 2 UTP18 17 51273422 Nonsense_Mutation SNP C C3N-00294_T 697160 51273422 31984019 1039 13811 UTP18 0 . GRCh38 17 51275918 51275918 + Nonsense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.764C>G p.Ser255Ter p.S255* ENST00000225298 6/14 217 188 29 165 165 0 strelka-varscan-mutect UTP18,stop_gained,p.Ser255Ter,ENST00000225298,NM_016001.2;UTP18,upstream_gene_variant,,ENST00000583725,;UTP18,upstream_gene_variant,,ENST00000579261,;UTP18,stop_gained,p.Ser18Ter,ENST00000508506,;UTP18,upstream_gene_variant,,ENST00000583205,; G ENST00000225298 Transcript stop_gained 821/1894 764/1671 255/556 S/* tCa/tGa COSM4508059 1 1 UTP18 HGNC HGNC:24274 protein_coding YES CCDS42362.1 ENSP00000225298 Q9Y5J1 UPI000051E38C NM_016001.2 6/14 hmmpanther:PTHR18359,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 51275918 51275918 C G 1 0 0 0 0 0 1 0 0 17641 838 29 4 4 UTP18 17 51275918 Nonsense_Mutation SNP C C3N-00294_T 2496 51275918 31981523 1040 13812 TOM1L1 0 . GRCh38 17 54960579 54960579 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1384G>A p.Glu462Lys p.E462K ENST00000575882 15/16 150 140 10 170 169 1 strelka-varscan-mutect TOM1L1,missense_variant,p.Glu462Lys,ENST00000575882,NM_001321175.1,NM_001321176.1,NM_005486.2;TOM1L1,missense_variant,p.Glu451Lys,ENST00000445275,;TOM1L1,missense_variant,p.Glu385Lys,ENST00000348161,;TOM1L1,missense_variant,p.Glu385Lys,ENST00000536554,;TOM1L1,missense_variant,p.Glu455Lys,ENST00000572158,;COX11,downstream_gene_variant,,ENST00000299335,NM_004375.3;COX11,downstream_gene_variant,,ENST00000571584,NM_001321518.1;TOM1L1,downstream_gene_variant,,ENST00000574318,;RP11-257O5.4,upstream_gene_variant,,ENST00000616755,;COX11,intron_variant,,ENST00000573912,;COX11,intron_variant,,ENST00000574989,;RP11-257O5.2,upstream_gene_variant,,ENST00000623493,;TOM1L1,3_prime_UTR_variant,,ENST00000571319,;TOM1L1,non_coding_transcript_exon_variant,,ENST00000574653,;COX11,intron_variant,,ENST00000576370,;COX11,intron_variant,,ENST00000572558,NM_001162862.2;COX11,intron_variant,,ENST00000574821,; A ENST00000575882 Transcript missense_variant 1737/2507 1384/1431 462/476 E/K Gaa/Aaa 1 1 TOM1L1 HGNC HGNC:11983 protein_coding YES CCDS11582.1 ENSP00000460823 O75674 UPI000003E7E0 NM_001321175.1,NM_001321176.1,NM_005486.2 tolerated(0.07) 15/16 PIRSF_domain:PIRSF036948,hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF28 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 54960579 54960579 G A 1 0 0 0 0 1 0 0 0 16826 943 33 3 3 TOM1L1 17 54960579 Missense_Mutation SNP G C3N-00294_T 3684661 54960579 28296862 1041 13813 HLF 0 . GRCh38 17 55267960 55267960 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.325C>T p.His109Tyr p.H109Y ENST00000226067 2/4 259 210 49 264 264 0 strelka-varscan-mutect HLF,missense_variant,p.His109Tyr,ENST00000226067,NM_002126.4;HLF,missense_variant,p.His24Tyr,ENST00000575345,;HLF,missense_variant,p.His24Tyr,ENST00000573945,;HLF,missense_variant,p.His24Tyr,ENST00000430986,;HLF,missense_variant,p.His49Tyr,ENST00000572002,;RP11-515O17.2,downstream_gene_variant,,ENST00000574716,;HLF,missense_variant,p.His24Tyr,ENST00000570962,; T ENST00000226067 Transcript missense_variant 798/5547 325/888 109/295 H/Y Cac/Tac 1 1 HLF HGNC HGNC:4977 protein_coding YES CCDS11585.1 ENSP00000226067 Q16534 UPI0000001C51 NM_002126.4 tolerated(0.18) 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11988,hmmpanther:PTHR11988:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 55267960 55267960 C T 1 0 0 0 0 1 0 0 0 7104 826 29 3 3 HLF 17 55267960 Missense_Mutation SNP C C3N-00294_T 307381 55267960 27989481 1042 13814 CUEDC1 0 . GRCh38 17 57868154 57868154 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1030C>T p.Gln344Ter p.Q344* ENST00000577830 8/11 250 216 34 237 237 0 strelka-varscan-mutect CUEDC1,stop_gained,p.Gln344Ter,ENST00000577830,NM_001271875.1;CUEDC1,stop_gained,p.Gln344Ter,ENST00000360238,NM_001292025.1;CUEDC1,stop_gained,p.Gln344Ter,ENST00000407144,;CUEDC1,stop_gained,p.Gln207Ter,ENST00000577840,;CUEDC1,intron_variant,,ENST00000581898,;CUEDC1,downstream_gene_variant,,ENST00000577589,;CUEDC1,upstream_gene_variant,,ENST00000585294,;CUEDC1,non_coding_transcript_exon_variant,,ENST00000578357,;CUEDC1,upstream_gene_variant,,ENST00000577422,;CUEDC1,non_coding_transcript_exon_variant,,ENST00000584746,;CUEDC1,non_coding_transcript_exon_variant,,ENST00000581391,;CUEDC1,upstream_gene_variant,,ENST00000582951,;CUEDC1,upstream_gene_variant,,ENST00000577497,; A ENST00000577830 Transcript stop_gained 1444/3621 1030/1161 344/386 Q/* Cag/Tag 1 -1 CUEDC1 HGNC HGNC:31350 protein_coding YES CCDS11599.1 ENSP00000462717 Q9NWM3 UPI0000073340 NM_001271875.1 8/11 hmmpanther:PTHR13467 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 57868154 57868154 G A 1 0 0 0 0 0 1 0 0 3862 1304 45 3 3 CUEDC1 17 57868154 Nonsense_Mutation SNP G C3N-00294_T 2600194 57868154 25389287 1043 13815 SEPT4 0 . GRCh38 17 58521092 58521092 + Missense_Mutation SNP G G C rs371430069 C3N-00294_T C3N-00294_N G G c.1228C>G p.Leu410Val p.L410V ENST00000457347 11/13 182 163 19 204 204 0 strelka-varscan-mutect SEPT4,missense_variant,p.Leu410Val,ENST00000457347,NM_001256782.1;SEPT4,missense_variant,p.Leu395Val,ENST00000317268,NM_004574.4;SEPT4,missense_variant,p.Leu248Val,ENST00000583114,NM_001256822.1;SEPT4,missense_variant,p.Leu387Val,ENST00000412945,NM_001198713.1;SEPT4,missense_variant,p.Leu376Val,ENST00000393086,;SEPT4,missense_variant,p.Leu376Val,ENST00000317256,NM_080416.3;SEPT4,missense_variant,p.Leu296Val,ENST00000580844,;SEPT4,missense_variant,p.Leu296Val,ENST00000579371,;SEPT4,3_prime_UTR_variant,,ENST00000426861,NM_080415.3;MTMR4,upstream_gene_variant,,ENST00000323456,NM_004687.4;MTMR4,upstream_gene_variant,,ENST00000579925,;SEPT4,downstream_gene_variant,,ENST00000580809,;SEPT4,downstream_gene_variant,,ENST00000583291,;SEPT4,downstream_gene_variant,,ENST00000577729,;MTMR4,upstream_gene_variant,,ENST00000579921,;SEPT4-AS1,intron_variant,,ENST00000580589,;SEPT4-AS1,upstream_gene_variant,,ENST00000580769,;SEPT4-AS1,upstream_gene_variant,,ENST00000578022,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580796,;SEPT4,non_coding_transcript_exon_variant,,ENST00000582270,;SEPT4,non_coding_transcript_exon_variant,,ENST00000583273,;SEPT4,non_coding_transcript_exon_variant,,ENST00000577440,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584488,;SEPT4,downstream_gene_variant,,ENST00000585170,;SEPT4,downstream_gene_variant,,ENST00000584789,;SEPT4,downstream_gene_variant,,ENST00000581615,;MTMR4,upstream_gene_variant,,ENST00000582663,;SEPT4,downstream_gene_variant,,ENST00000578131,; C ENST00000457347 Transcript missense_variant 1373/1795 1228/1482 410/493 L/V Ctg/Gtg rs371430069 1 -1 SEPT4 HGNC HGNC:9165 protein_coding YES CCDS58582.1 ENSP00000402000 O43236 UPI00017A809C NM_001256782.1 deleterious(0) 11/13 Pfam_domain:PF00735,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF71 MODERATE SNV 2 1 PASS rs371430069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 58521092 58521092 G C 1 0 0 0 0 1 0 0 0 14342 991 35 4 4 SEPT4 17 58521092 Missense_Mutation SNP G C3N-00294_T 652938 58521092 24736349 1044 13816 TEX14 0 . GRCh38 17 58569231 58569231 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.3985G>A p.Glu1329Lys p.E1329K ENST00000240361 27/33 165 141 24 144 144 0 strelka-varscan-mutect TEX14,missense_variant,p.Glu1323Lys,ENST00000389934,NM_198393.3;TEX14,missense_variant,p.Glu1329Lys,ENST00000240361,NM_001201457.1;TEX14,missense_variant,p.Glu1283Lys,ENST00000349033,NM_031272.4;TEX14,upstream_gene_variant,,ENST00000584699,;TEX14,missense_variant,p.Glu137Lys,ENST00000581147,;TEX14,3_prime_UTR_variant,,ENST00000582740,; T ENST00000240361 Transcript missense_variant 4071/4911 3985/4494 1329/1497 E/K Gag/Aag 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 deleterious(0.03) 27/33 hmmpanther:PTHR23060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 58569231 58569231 C T 1 0 0 0 0 1 0 0 0 16200 835 29 3 3 TEX14 17 58569231 Missense_Mutation SNP C C3N-00294_T 48139 58569231 24688210 1045 13817 PPM1E 0 . GRCh38 17 58980751 58980751 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1988G>C p.Arg663Thr p.R663T ENST00000308249 7/7 278 249 29 232 232 0 strelka-varscan-mutect PPM1E,missense_variant,p.Arg663Thr,ENST00000308249,NM_014906.4;TRIM37,downstream_gene_variant,,ENST00000393066,NM_001005207.2;TRIM37,downstream_gene_variant,,ENST00000585287,;TRIM37,downstream_gene_variant,,ENST00000583945,; C ENST00000308249 Transcript missense_variant 2117/6542 1988/2268 663/755 R/T aGa/aCa 1 1 PPM1E HGNC HGNC:19322 protein_coding YES CCDS11613.1 ENSP00000312411 Q8WY54 UPI000013ECF6 NM_014906.4 deleterious_low_confidence(0.02) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 58980751 58980751 G C 1 0 0 0 0 1 0 0 0 12448 942 33 4 4 PPM1E 17 58980751 Missense_Mutation SNP G C3N-00294_T 411520 58980751 24276690 1046 13818 RPS6KB1 0 . GRCh38 17 59930120 59930120 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.533G>A p.Gly178Glu p.G178E ENST00000225577 6/15 132 115 17 129 129 0 strelka-varscan-mutect RPS6KB1,missense_variant,p.Gly125Glu,ENST00000393021,NM_001272044.1;RPS6KB1,missense_variant,p.Gly178Glu,ENST00000225577,NM_001272060.1,NM_003161.3;RPS6KB1,missense_variant,p.Gly178Glu,ENST00000406116,NM_001272043.1;RPS6KB1,missense_variant,p.Gly155Glu,ENST00000443572,NM_001272042.1;RPS6KB1,3_prime_UTR_variant,,ENST00000472940,;RPS6KB1,3_prime_UTR_variant,,ENST00000489824,;RPS6KB1,upstream_gene_variant,,ENST00000590928,;RPS6KB1,upstream_gene_variant,,ENST00000587622,; A ENST00000225577 Transcript missense_variant 554/5375 533/1578 178/525 G/E gGa/gAa 1 1 RPS6KB1 HGNC HGNC:10436 protein_coding YES CCDS11621.1 ENSP00000225577 P23443 UPI000013C873 NM_001272060.1,NM_003161.3 deleterious(0) 6/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24351:SF85,hmmpanther:PTHR24351,PIRSF_domain:PIRSF000605,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 59930120 59930120 G A 1 0 0 0 0 1 0 0 0 13911 1188 41 3 3 RPS6KB1 17 59930120 Missense_Mutation SNP G C3N-00294_T 949369 59930120 23327321 1047 13819 MED13 0 . GRCh38 17 62035466 62035466 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.613C>T p.Gln205Ter p.Q205* ENST00000397786 4/30 109 88 21 143 143 0 varscan-mutect MED13,stop_gained,p.Gln205Ter,ENST00000397786,NM_005121.2;Y_RNA,upstream_gene_variant,,ENST00000363972,;MED13,upstream_gene_variant,,ENST00000580896,;MED13,upstream_gene_variant,,ENST00000581994,;MED13,upstream_gene_variant,,ENST00000578132,; A ENST00000397786 Transcript stop_gained 690/10465 613/6525 205/2174 Q/* Caa/Taa 1 -1 MED13 HGNC HGNC:22474 protein_coding YES CCDS42366.1 ENSP00000380888 Q9UHV7 A0A024QZ75 UPI0000D7D6F6 NM_005121.2 4/30 hmmpanther:PTHR10791:SF51,hmmpanther:PTHR10791,Pfam_domain:PF11597 HIGH 1 SNV 1 1 PASS rs980586772 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 62035466 62035466 G A 1 0 0 0 0 0 1 0 0 9369 1304 45 3 3 MED13 17 62035466 Nonsense_Mutation SNP G C3N-00294_T 2105346 62035466 21221975 1048 13820 METTL2A 0 . GRCh38 17 62448684 62448684 + Nonsense_Mutation SNP G G A rs781133580 C3N-00294_T C3N-00294_N G G c.1092G>A p.Trp364Ter p.W364* ENST00000311506 9/9 330 270 60 242 242 0 strelka-varscan-mutect METTL2A,stop_gained,p.Trp299Ter,ENST00000616852,;METTL2A,stop_gained,p.Trp364Ter,ENST00000311506,NM_181725.3;METTL2A,non_coding_transcript_exon_variant,,ENST00000333483,; A ENST00000311506 Transcript stop_gained 1128/2537 1092/1137 364/378 W/* tgG/tgA rs781133580 1 1 METTL2A HGNC HGNC:25755 protein_coding YES CCDS45752.1 ENSP00000309610 Q96IZ6 UPI0000201189 NM_181725.3 9/9 hmmpanther:PTHR22809:SF4,hmmpanther:PTHR22809,Gene3D:3.40.50.150,PIRSF_domain:PIRSF037755,Superfamily_domains:SSF53335 HIGH 1 SNV 1 1 PASS rs781133580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 62448684 62448684 G A 1 0 0 0 0 0 1 0 0 9452 1183 41 3 3 METTL2A 17 62448684 Nonsense_Mutation SNP G C3N-00294_T 413218 62448684 20808757 1049 13821 ACE 0 . GRCh38 17 63477221 63477221 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.127G>A p.Glu43Lys p.E43K ENST00000290866 1/25 214 176 38 230 229 1 strelka-varscan-mutect ACE,missense_variant,p.Glu43Lys,ENST00000428043,;ACE,missense_variant,p.Glu43Lys,ENST00000290866,NM_000789.3;ACE,upstream_gene_variant,,ENST00000582627,;ACE,non_coding_transcript_exon_variant,,ENST00000584529,;ACE,non_coding_transcript_exon_variant,,ENST00000583336,;ACE,missense_variant,p.Glu43Lys,ENST00000582678,;ACE,non_coding_transcript_exon_variant,,ENST00000579462,;ACE,upstream_gene_variant,,ENST00000580318,; A ENST00000290866 Transcript missense_variant 151/4959 127/3921 43/1306 E/K Gag/Aag 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 deleterious(0.02) 1/25 Pfam_domain:PF01401 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 63477221 63477221 G A 1 0 0 0 0 1 0 0 0 174 1059 37 1 1 ACE 17 63477221 Missense_Mutation SNP G C3N-00294_T 1028537 63477221 19780220 1050 13822 ACE 0 . GRCh38 17 63494021 63494021 + Missense_Mutation SNP G G C rs752369560 C3N-00294_T C3N-00294_N G G c.3236G>C p.Gly1079Ala p.G1079A ENST00000290866 21/25 462 375 87 358 357 1 strelka-varscan-mutect ACE,missense_variant,p.Gly1079Ala,ENST00000428043,;ACE,missense_variant,p.Gly1079Ala,ENST00000290866,NM_000789.3;ACE,missense_variant,p.Gly505Ala,ENST00000290863,NM_152830.2;ACE,missense_variant,p.Gly505Ala,ENST00000413513,NM_001178057.1;ACE,missense_variant,p.Gly256Ala,ENST00000582761,;ACE,upstream_gene_variant,,ENST00000579409,;ACE,non_coding_transcript_exon_variant,,ENST00000577418,;CTD-2501B8.1,missense_variant,p.Gly505Ala,ENST00000577647,;ACE,3_prime_UTR_variant,,ENST00000579314,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,non_coding_transcript_exon_variant,,ENST00000578679,;ACE,downstream_gene_variant,,ENST00000584865,;ACE,downstream_gene_variant,,ENST00000582005,;ACE,downstream_gene_variant,,ENST00000583645,;ACE,downstream_gene_variant,,ENST00000579204,;ACE,upstream_gene_variant,,ENST00000582244,; C ENST00000290866 Transcript missense_variant 3260/4959 3236/3921 1079/1306 G/A gGa/gCa rs752369560 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 deleterious(0) 21/25 hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs752369560 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 63494021 63494021 G C 1 0 0 0 0 1 0 0 0 174 1174 41 4 4 ACE 17 63494021 Missense_Mutation SNP G C3N-00294_T 16800 63494021 19763420 1051 13823 KCNH6 0 . GRCh38 17 63545773 63545773 + Silent SNP G G A rs768671007 C3N-00294_T C3N-00294_N G G c.2856G>A p.= p.L952L ENST00000583023 14/14 353 170 183 322 322 0 strelka-varscan-mutect KCNH6,synonymous_variant,p.=,ENST00000583023,NM_030779.3;KCNH6,synonymous_variant,p.=,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,synonymous_variant,p.=,ENST00000581784,NM_173092.2;KCNH6,synonymous_variant,p.=,ENST00000456941,;DCAF7,upstream_gene_variant,,ENST00000614556,NM_005828.4;DCAF7,upstream_gene_variant,,ENST00000415273,;DCAF7,upstream_gene_variant,,ENST00000615512,;DCAF7,upstream_gene_variant,,ENST00000582274,;KCNH6,3_prime_UTR_variant,,ENST00000583465,;DCAF7,upstream_gene_variant,,ENST00000431926,; A ENST00000583023 Transcript synonymous_variant 2867/3821 2856/2985 952/994 L ctG/ctA rs768671007 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 14/14 LOW 1 SNV 1 1 PASS rs1489213922 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 63545773 63545773 G A 1 0 0 0 0 0 0 0 1 7952 1335 47 3 3 KCNH6 17 63545773 Silent SNP G C3N-00294_T 51752 63545773 19711668 1052 13824 CEP95 0 . GRCh38 17 64531960 64531960 + Missense_Mutation SNP C C G rs781956286 C3N-00294_T C3N-00294_N C C c.1610C>G p.Ser537Cys p.S537C ENST00000556440 14/20 110 97 13 125 125 0 strelka-varscan-mutect CEP95,missense_variant,p.Ser537Cys,ENST00000556440,NM_138363.1;CEP95,missense_variant,p.Leu473Val,ENST00000553412,;CEP95,missense_variant,p.Ser134Cys,ENST00000583457,;CEP95,upstream_gene_variant,,ENST00000583676,;CEP95,downstream_gene_variant,,ENST00000577476,;CEP95,3_prime_UTR_variant,,ENST00000553956,;CEP95,non_coding_transcript_exon_variant,,ENST00000584857,;CEP95,non_coding_transcript_exon_variant,,ENST00000579637,;CEP95,upstream_gene_variant,,ENST00000581885,;CEP95,upstream_gene_variant,,ENST00000580285,;CEP95,upstream_gene_variant,,ENST00000581980,;CEP95,downstream_gene_variant,,ENST00000579117,;CEP95,downstream_gene_variant,,ENST00000579478,;CEP95,upstream_gene_variant,,ENST00000582698,; G ENST00000556440 Transcript missense_variant 2120/3139 1610/2466 537/821 S/C tCt/tGt rs781956286 1 1 CEP95 HGNC HGNC:25141 protein_coding YES CCDS45763.1 ENSP00000450461 Q96GE4 UPI000006F4B3 NM_138363.1 deleterious(0.02) 14/20 hmmpanther:PTHR22545,hmmpanther:PTHR22545:SF0 MODERATE 1 SNV 1 1 PASS rs781956286 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 64531960 64531960 C G 1 0 0 0 0 1 0 0 0 2988 913 32 4 4 CEP95 17 64531960 Missense_Mutation SNP C C3N-00294_T 986187 64531960 18725481 1053 13825 SMURF2 0 . GRCh38 17 64555981 64555981 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1449C>G p.Phe483Leu p.F483L ENST00000262435 14/19 43 34 9 59 59 0 strelka-varscan-mutect SMURF2,missense_variant,p.Phe483Leu,ENST00000262435,NM_022739.3;SMURF2,missense_variant,p.Phe470Leu,ENST00000585301,;SMURF2,downstream_gene_variant,,ENST00000578200,;SMURF2,3_prime_UTR_variant,,ENST00000582081,;SMURF2,3_prime_UTR_variant,,ENST00000578386,;SMURF2,downstream_gene_variant,,ENST00000580072,; C ENST00000262435 Transcript missense_variant 1637/2918 1449/2247 483/748 F/L ttC/ttG 1 -1 SMURF2 HGNC HGNC:16809 protein_coding YES CCDS32707.1 ENSP00000262435 Q9HAU4 UPI00001361C5 NM_022739.3 deleterious(0) 14/19 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF300,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -19.99901 1 1 1 1 0 C 3 2 46 64555981 64555981 G C 1 0 0 0 0 1 0 0 0 15141 1165 41 4 4 SMURF2 17 64555981 Missense_Mutation SNP G C3N-00294_T 24021 64555981 18701460 1054 13826 55 2 SMURF2 0 . GRCh38 17 64555986 64555986 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.1444T>A p.Tyr482Asn p.Y482N ENST00000262435 14/19 40 32 8 55 55 0 strelka-varscan-mutect SMURF2,missense_variant,p.Tyr482Asn,ENST00000262435,NM_022739.3;SMURF2,missense_variant,p.Tyr469Asn,ENST00000585301,;SMURF2,downstream_gene_variant,,ENST00000578200,;SMURF2,3_prime_UTR_variant,,ENST00000582081,;SMURF2,3_prime_UTR_variant,,ENST00000578386,;SMURF2,downstream_gene_variant,,ENST00000580072,; T ENST00000262435 Transcript missense_variant 1632/2918 1444/2247 482/748 Y/N Tat/Aat 1 -1 SMURF2 HGNC HGNC:16809 protein_coding YES CCDS32707.1 ENSP00000262435 Q9HAU4 UPI00001361C5 NM_022739.3 deleterious(0) 14/19 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF300,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -19.8279 1 1 1 1 0 T 3 4 46 64555986 64555986 A T 1 0 0 0 0 1 0 0 0 15141 420 15 4 4 SMURF2 17 64555986 Missense_Mutation SNP A C3N-00294_T 5 64555986 18701455 1055 13827 55 2 HELZ 0 . GRCh38 17 67145870 67145870 + Missense_Mutation SNP T T C C3N-00294_T C3N-00294_N T T c.2642A>G p.Tyr881Cys p.Y881C ENST00000358691 21/33 302 152 150 274 274 0 strelka-varscan-mutect HELZ,missense_variant,p.Tyr881Cys,ENST00000358691,NM_014877.3;HELZ,missense_variant,p.Tyr882Cys,ENST00000580168,;HELZ,missense_variant,p.Tyr882Cys,ENST00000579953,; C ENST00000358691 Transcript missense_variant 2809/13810 2642/5829 881/1942 Y/C tAt/tGt COSM5499591 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 deleterious(0) 21/33 Gene3D:3.40.50.300,Pfam_domain:PF13087,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 67145870 67145870 T C 1 0 0 0 0 1 0 0 0 6931 1406 49 5 5 HELZ 17 67145870 Missense_Mutation SNP T C3N-00294_T 2589884 67145870 16111571 1056 13828 PRKAR1A 0 . GRCh38 17 68522903 68522903 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.325G>A p.Asp109Asn p.D109N ENST00000392711 3/11 231 190 41 201 201 0 strelka-varscan-mutect PRKAR1A,missense_variant,p.Asp109Asn,ENST00000392711,NM_212472.2,NM_002734.4;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000589228,NM_001278433.1;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000536854,NM_001276289.1;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000358598,NM_212471.2;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000586397,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000588188,NM_001276290.1;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000589017,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000585981,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000588702,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000588178,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000585427,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000589480,;PRKAR1A,upstream_gene_variant,,ENST00000592800,;PRKAR1A,downstream_gene_variant,,ENST00000585815,;RP11-120M18.2,non_coding_transcript_exon_variant,,ENST00000590353,;PRKAR1A,missense_variant,p.Asp109Asn,ENST00000585608,;PRKAR1A,synonymous_variant,p.=,ENST00000392710,;PRKAR1A,non_coding_transcript_exon_variant,,ENST00000585460,;PRKAR1A,upstream_gene_variant,,ENST00000586541,;PRKAR1A,upstream_gene_variant,,ENST00000585907,; A ENST00000392711 Transcript missense_variant 532/4327 325/1146 109/381 D/N Gat/Aat 1 1 PRKAR1A HGNC HGNC:9388 protein_coding YES CCDS11678.1 ENSP00000376475 P10644 B2R5T5 UPI0000001C57 NM_212472.2,NM_002734.4 deleterious(0.04) 3/11 hmmpanther:PTHR11635:SF129,hmmpanther:PTHR11635,PIRSF_domain:PIRSF000548 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 68522903 68522903 G A 1 0 0 0 0 1 0 0 0 12636 942 33 3 3 PRKAR1A 17 68522903 Missense_Mutation SNP G C3N-00294_T 1377033 68522903 14734538 1057 13829 LLGL2 0 . GRCh38 17 75569996 75569996 + Missense_Mutation SNP G G A rs541727805 C3N-00294_T C3N-00294_N G G c.1615G>A p.Glu539Lys p.E539K ENST00000392550 15/26 105 89 16 76 76 0 strelka-varscan-mutect LLGL2,missense_variant,p.Glu539Lys,ENST00000392550,NM_001031803.1;LLGL2,missense_variant,p.Glu539Lys,ENST00000167462,NM_004524.2;LLGL2,missense_variant,p.Glu539Lys,ENST00000577200,;LLGL2,3_prime_UTR_variant,,ENST00000578638,;LLGL2,3_prime_UTR_variant,,ENST00000578719,;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227,;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500,;LLGL2,upstream_gene_variant,,ENST00000579092,;LLGL2,upstream_gene_variant,,ENST00000582393,;LLGL2,upstream_gene_variant,,ENST00000577211,;LLGL2,upstream_gene_variant,,ENST00000578034,;LLGL2,upstream_gene_variant,,ENST00000583514,; A ENST00000392550 Transcript missense_variant 1732/3509 1615/3063 539/1020 E/K Gag/Aag rs541727805 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 deleterious(0.04) 15/26 Gene3D:2.130.10.10,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF20,Low_complexity_(Seg):seg,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs541727805 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 75569996 75569996 G A 1 0 0 0 0 1 0 0 0 8758 1175 41 3 3 LLGL2 17 75569996 Missense_Mutation SNP G C3N-00294_T 7047093 75569996 7687445 1058 13830 LLGL2 0 . GRCh38 17 75570176 75570176 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1795G>C p.Glu599Gln p.E599Q ENST00000392550 15/26 214 174 40 197 197 0 strelka-varscan-mutect LLGL2,missense_variant,p.Glu599Gln,ENST00000392550,NM_001031803.1;LLGL2,missense_variant,p.Glu599Gln,ENST00000167462,NM_004524.2;LLGL2,missense_variant,p.Glu599Gln,ENST00000577200,;LLGL2,3_prime_UTR_variant,,ENST00000578638,;LLGL2,3_prime_UTR_variant,,ENST00000578719,;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227,;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500,;LLGL2,upstream_gene_variant,,ENST00000579092,;LLGL2,upstream_gene_variant,,ENST00000582393,;LLGL2,upstream_gene_variant,,ENST00000577211,;LLGL2,upstream_gene_variant,,ENST00000578034,;LLGL2,upstream_gene_variant,,ENST00000583514,; C ENST00000392550 Transcript missense_variant 1912/3509 1795/3063 599/1020 E/Q Gag/Cag 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 deleterious(0.01) 15/26 Gene3D:2.130.10.10,Prints_domain:PR00962,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF20,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 75570176 75570176 G C 1 0 0 0 0 1 0 0 0 8758 1291 45 4 4 LLGL2 17 75570176 Missense_Mutation SNP G C3N-00294_T 180 75570176 7687265 1059 13831 LLGL2 0 . GRCh38 17 75571040 75571040 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2116G>C p.Glu706Gln p.E706Q ENST00000392550 17/26 178 153 25 148 148 0 strelka-varscan-mutect LLGL2,missense_variant,p.Glu706Gln,ENST00000392550,NM_001031803.1;LLGL2,missense_variant,p.Glu706Gln,ENST00000167462,NM_004524.2;LLGL2,missense_variant,p.Glu706Gln,ENST00000577200,;LLGL2,3_prime_UTR_variant,,ENST00000578638,;LLGL2,non_coding_transcript_exon_variant,,ENST00000545227,;LLGL2,non_coding_transcript_exon_variant,,ENST00000577500,;LLGL2,upstream_gene_variant,,ENST00000579092,;LLGL2,downstream_gene_variant,,ENST00000578719,;LLGL2,upstream_gene_variant,,ENST00000582393,;LLGL2,upstream_gene_variant,,ENST00000577211,;LLGL2,upstream_gene_variant,,ENST00000578034,;LLGL2,upstream_gene_variant,,ENST00000583514,; C ENST00000392550 Transcript missense_variant 2233/3509 2116/3063 706/1020 E/Q Gag/Cag 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 deleterious(0) 17/26 Prints_domain:PR00962,hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 75571040 75571040 G C 1 0 0 0 0 1 0 0 0 8758 943 33 4 4 LLGL2 17 75571040 Missense_Mutation SNP G C3N-00294_T 864 75571040 7686401 1060 13832 SPHK1 0 . GRCh38 17 76386220 76386220 + Splice_Site SNP G G C rs55664828 C3N-00294_T C3N-00294_N G G c.422-1G>C p.X141_splice ENST00000323374 80 71 9 59 59 0 strelka-varscan-mutect SPHK1,splice_acceptor_variant,,ENST00000545180,;SPHK1,splice_acceptor_variant,,ENST00000323374,NM_182965.2;SPHK1,splice_acceptor_variant,,ENST00000590959,NM_021972.3;SPHK1,splice_acceptor_variant,,ENST00000592299,NM_001142601.1;SPHK1,splice_acceptor_variant,,ENST00000392496,NM_001142602.1;SPHK1,splice_acceptor_variant,,ENST00000588682,;SPHK1,splice_acceptor_variant,,ENST00000590379,;UBE2O,downstream_gene_variant,,ENST00000319380,NM_022066.3;UBE2O,downstream_gene_variant,,ENST00000587127,;PRPSAP1,upstream_gene_variant,,ENST00000442767,;PRPSAP1,upstream_gene_variant,,ENST00000423915,;SPHK1,downstream_gene_variant,,ENST00000591651,;SPHK1,splice_acceptor_variant,,ENST00000591762,;SPHK1,splice_acceptor_variant,,ENST00000587167,; C ENST00000323374 Transcript splice_acceptor_variant -/2138 422/1413 141/470 rs55664828 1 1 SPHK1 HGNC HGNC:11240 protein_coding YES CCDS11744.1 ENSP00000313681 Q9NYA1 UPI00001AF3B5 NM_182965.2 3/5 HIGH 1 SNV 1 1 PASS rs55664828 . 0 204 6 0 0 0 0 0 -19.21959 0.9999999 1 1 1 0 C 5 2 46 76386220 76386220 G C 1 0 0 0 0 0 0 1 0 15397 956 33 4 4 SPHK1 17 76386220 Splice_Site SNP G C3N-00294_T 815180 76386220 6871221 1061 13833 TNRC6C 0 . GRCh38 17 78073052 78073052 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2866G>A p.Glu956Lys p.E956K ENST00000335749 7/21 142 123 19 139 139 0 strelka-varscan-mutect TNRC6C,missense_variant,p.Glu956Lys,ENST00000335749,NM_001142640.1;TNRC6C,missense_variant,p.Glu959Lys,ENST00000301624,NM_018996.3;TNRC6C,missense_variant,p.Glu956Lys,ENST00000588847,;TNRC6C,missense_variant,p.Glu959Lys,ENST00000588061,;TNRC6C,missense_variant,p.Glu1166Lys,ENST00000636222,;TNRC6C,non_coding_transcript_exon_variant,,ENST00000591851,;TNRC6C,non_coding_transcript_exon_variant,,ENST00000587990,; A ENST00000335749 Transcript missense_variant 3435/9740 2866/5181 956/1726 E/K Gag/Aag 1 1 TNRC6C HGNC HGNC:29318 protein_coding YES CCDS45799.1 ENSP00000336783 Q9HCJ0 UPI0000EE5F80 NM_001142640.1 deleterious(0) 7/21 Gene3D:1.10.8.10,Pfam_domain:PF00627,PROSITE_profiles:PS50030,hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF9,SMART_domains:SM00165,Superfamily_domains:SSF46934 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 78073052 78073052 G A 1 0 0 0 0 1 0 0 0 16815 1175 41 3 3 TNRC6C 17 78073052 Missense_Mutation SNP G C3N-00294_T 1686832 78073052 5184389 1062 13834 AFMID 0 . GRCh38 17 78187389 78187389 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.19G>A p.Val7Met p.V7M ENST00000327898 1/11 226 195 31 175 175 0 strelka-varscan-mutect AFMID,missense_variant,p.Val7Met,ENST00000409257,NM_001010982.4;AFMID,missense_variant,p.Val7Met,ENST00000327898,NM_001145526.2;AFMID,missense_variant,p.Val7Met,ENST00000588800,;AFMID,missense_variant,p.Val7Met,ENST00000591256,;AFMID,missense_variant,p.Val7Met,ENST00000591952,;AFMID,missense_variant,p.Val7Met,ENST00000589256,;AFMID,missense_variant,p.Val7Met,ENST00000586542,;TK1,upstream_gene_variant,,ENST00000588734,;TK1,upstream_gene_variant,,ENST00000301634,NM_003258.4;TK1,upstream_gene_variant,,ENST00000590430,;TK1,upstream_gene_variant,,ENST00000590862,;TK1,upstream_gene_variant,,ENST00000586613,;AFMID,upstream_gene_variant,,ENST00000586731,;AFMID,upstream_gene_variant,,ENST00000591538,;AFMID,missense_variant,p.Val7Met,ENST00000588199,;AFMID,missense_variant,p.Val7Met,ENST00000589107,;AFMID,non_coding_transcript_exon_variant,,ENST00000592988,;TK1,upstream_gene_variant,,ENST00000592126,; A ENST00000327898 Transcript missense_variant 28/1700 19/927 7/308 V/M Gtg/Atg 1 1 AFMID HGNC HGNC:20910 protein_coding YES CCDS45801.1 ENSP00000328938 Q63HM1 UPI000041A994 NM_001145526.2 tolerated_low_confidence(0.14) 1/11 hmmpanther:PTHR23024:SF163,hmmpanther:PTHR23024 MODERATE 1 SNV 1 1 PASS rs1295056045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 78187389 78187389 G A 1 0 0 0 0 1 0 0 0 439 1377 48 3 3 AFMID 17 78187389 Missense_Mutation SNP G C3N-00294_T 114337 78187389 5070052 1063 13835 DNAH17 0 . GRCh38 17 78572784 78572784 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.456G>A p.Met152Ile p.M152I ENST00000389840 3/81 302 252 50 223 223 0 strelka-varscan-mutect DNAH17,missense_variant,p.Met152Ile,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Met152Ile,ENST00000585328,;DNAH17,upstream_gene_variant,,ENST00000589793,; T ENST00000389840 Transcript missense_variant 581/13723 456/13389 152/4462 M/I atG/atA 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 tolerated(0.59) 3/81 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 78572784 78572784 C T 1 0 0 0 0 1 0 0 0 4416 826 29 3 3 DNAH17 17 78572784 Missense_Mutation SNP C C3N-00294_T 385395 78572784 4684657 1064 13836 CANT1 0 . GRCh38 17 78997087 78997087 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.536C>G p.Ser179Cys p.S179C ENST00000302345 2/4 575 446 129 562 562 0 strelka-varscan-mutect CANT1,missense_variant,p.Ser179Cys,ENST00000302345,NM_138793.3,NM_001159773.1;CANT1,missense_variant,p.Ser179Cys,ENST00000620915,;CANT1,missense_variant,p.Ser179Cys,ENST00000392446,;CANT1,missense_variant,p.Ser179Cys,ENST00000591773,NM_001159772.1;CANT1,downstream_gene_variant,,ENST00000588611,;CANT1,downstream_gene_variant,,ENST00000588075,;CANT1,downstream_gene_variant,,ENST00000586916,;CANT1,downstream_gene_variant,,ENST00000590370,;CANT1,downstream_gene_variant,,ENST00000591625,;CANT1,downstream_gene_variant,,ENST00000592033,;CANT1,downstream_gene_variant,,ENST00000591811,;CANT1,downstream_gene_variant,,ENST00000591732,;CANT1,downstream_gene_variant,,ENST00000592887,;CANT1,downstream_gene_variant,,ENST00000587242,;CANT1,missense_variant,p.Ser179Cys,ENST00000592228,;CANT1,upstream_gene_variant,,ENST00000588096,; C ENST00000302345 Transcript missense_variant 1031/3534 536/1206 179/401 S/C tCc/tGc COSM324918 1 -1 CANT1 HGNC HGNC:19721 protein_coding YES CCDS11760.1 ENSP00000307674 Q8WVQ1 A0A024R8U8 UPI00000734F8 NM_138793.3,NM_001159773.1 deleterious(0) 2/4 Superfamily_domains:0049295,Pfam_domain:PF06079,hmmpanther:PTHR13023 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 78997087 78997087 G C 1 0 0 0 0 1 0 0 0 2310 1174 41 4 4 CANT1 17 78997087 Missense_Mutation SNP G C3N-00294_T 424303 78997087 4260354 1065 13837 SGSH 0 . GRCh38 17 80210944 80210944 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1017G>A p.= p.K339K ENST00000326317 8/8 216 178 38 192 192 0 strelka-varscan-mutect SGSH,synonymous_variant,p.=,ENST00000326317,NM_000199.3;SGSH,3_prime_UTR_variant,,ENST00000576856,;SGSH,intron_variant,,ENST00000572257,;CARD14,downstream_gene_variant,,ENST00000573882,;CARD14,downstream_gene_variant,,ENST00000344227,NM_024110.4;SGSH,downstream_gene_variant,,ENST00000570923,;SGSH,downstream_gene_variant,,ENST00000570427,;SGSH,downstream_gene_variant,,ENST00000576707,;RP11-334C17.5,upstream_gene_variant,,ENST00000572730,;SGSH,downstream_gene_variant,,ENST00000572208,;SGSH,upstream_gene_variant,,ENST00000575484,;SGSH,upstream_gene_variant,,ENST00000571156,;SGSH,3_prime_UTR_variant,,ENST00000573150,;SGSH,non_coding_transcript_exon_variant,,ENST00000575282,;CARD14,downstream_gene_variant,,ENST00000575500,;SGSH,downstream_gene_variant,,ENST00000574505,;SGSH,downstream_gene_variant,,ENST00000576941,;SGSH,downstream_gene_variant,,ENST00000571675,;SGSH,downstream_gene_variant,,ENST00000575188,;SGSH,downstream_gene_variant,,ENST00000571051,; T ENST00000326317 Transcript synonymous_variant 1104/2784 1017/1509 339/502 K aaG/aaA 1 -1 SGSH HGNC HGNC:10818 protein_coding YES CCDS11770.1 ENSP00000314606 P51688 UPI000000DBD0 NM_000199.3 8/8 hmmpanther:PTHR10342:SF76,hmmpanther:PTHR10342,Gene3D:3.40.720.10,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 80210944 80210944 C T 1 0 0 0 0 0 0 0 1 14479 912 32 3 3 SGSH 17 80210944 Silent SNP C C3N-00294_T 1213857 80210944 3046497 1066 13838 RNF213 0 . GRCh38 17 80367810 80367810 + Silent SNP C C G novel C3N-00294_T C3N-00294_N C C c.11934C>G p.= p.L3978L ENST00000582970 43/68 480 391 89 438 438 0 strelka-varscan-mutect RNF213,synonymous_variant,p.=,ENST00000582970,NM_001256071.2;RNF213,synonymous_variant,p.=,ENST00000508628,;CTD-2047H16.4,intron_variant,,ENST00000575034,;CTD-2047H16.4,intron_variant,,ENST00000572151,;RNF213,non_coding_transcript_exon_variant,,ENST00000558116,;RNF213,upstream_gene_variant,,ENST00000411702,;RNF213,downstream_gene_variant,,ENST00000559603,;RNF213,downstream_gene_variant,,ENST00000558488,; G ENST00000582970 Transcript synonymous_variant 12077/21055 11934/15624 3978/5207 L ctC/ctG 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 43/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 80367810 80367810 C G 1 0 0 0 0 0 0 0 1 13656 900 32 4 4 RNF213 17 80367810 Silent SNP C C3N-00294_T 156866 80367810 2889631 1067 13839 AATK 0 . GRCh38 17 81120422 81120422 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.3514G>C p.Asp1172His p.D1172H ENST00000326724 11/14 64 59 5 45 45 0 strelka-mutect AATK,missense_variant,p.Asp1172His,ENST00000326724,NM_001080395.2;AATK,missense_variant,p.Asp1069His,ENST00000417379,NM_004920.2;BAIAP2,downstream_gene_variant,,ENST00000321300,NM_017451.2;BAIAP2,downstream_gene_variant,,ENST00000575245,;BAIAP2,downstream_gene_variant,,ENST00000435091,NM_006340.2;BAIAP2,downstream_gene_variant,,ENST00000428708,NM_001144888.1;BAIAP2,downstream_gene_variant,,ENST00000572498,;MIR657,downstream_gene_variant,,ENST00000385003,;AATK,downstream_gene_variant,,ENST00000572339,;AATK,downstream_gene_variant,,ENST00000573441,;AATK,3_prime_UTR_variant,,ENST00000374792,;AATK,intron_variant,,ENST00000570932,;AATK,intron_variant,,ENST00000573469,;BAIAP2,downstream_gene_variant,,ENST00000576225,; G ENST00000326724 Transcript missense_variant 3539/5257 3514/4125 1172/1374 D/H Gac/Cac 1 -1 AATK HGNC HGNC:21 protein_coding YES CCDS45807.1 ENSP00000324196 Q6ZMQ8 UPI000041EA63 NM_001080395.2 deleterious(0) 11/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24417,hmmpanther:PTHR24417:SF0 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -11.95008 1 1 1 1 0 G 3 3 46 81120422 81120422 C G 1 0 0 0 0 1 0 0 0 30 826 29 4 4 AATK 17 81120422 Missense_Mutation SNP C C3N-00294_T 752612 81120422 2137019 1068 13840 PYCR1 0 . GRCh38 17 81934385 81934385 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.819G>C p.Glu273Asp p.E273D ENST00000402252 7/8 331 269 62 294 294 0 strelka-varscan-mutect PYCR1,missense_variant,p.Glu246Asp,ENST00000619204,NM_001282280.1;PYCR1,missense_variant,p.Glu246Asp,ENST00000337943,NM_153824.2;PYCR1,missense_variant,p.Glu246Asp,ENST00000329875,NM_006907.3;PYCR1,missense_variant,p.Glu215Asp,ENST00000403172,NM_001282279.1;PYCR1,missense_variant,p.Glu273Asp,ENST00000402252,NM_001282281.1;PYCR1,missense_variant,p.Glu216Asp,ENST00000582198,;PYCR1,missense_variant,p.Glu246Asp,ENST00000405481,;PYCR1,intron_variant,,ENST00000629768,;PYCR1,intron_variant,,ENST00000577756,;PYCR1,intron_variant,,ENST00000584848,;PYCR1,downstream_gene_variant,,ENST00000585215,;PYCR1,downstream_gene_variant,,ENST00000579366,;PYCR1,downstream_gene_variant,,ENST00000585244,;PYCR1,downstream_gene_variant,,ENST00000579698,;PYCR1,downstream_gene_variant,,ENST00000581271,;PYCR1,downstream_gene_variant,,ENST00000577624,;PYCR1,downstream_gene_variant,,ENST00000583564,;MAFG-AS1,downstream_gene_variant,,ENST00000582106,;MAFG-AS1,downstream_gene_variant,,ENST00000583492,;RP11-498C9.13,downstream_gene_variant,,ENST00000583521,; G ENST00000402252 Transcript missense_variant 845/1346 819/1041 273/346 E/D gaG/gaC 1 -1 PYCR1 HGNC HGNC:9721 protein_coding YES CCDS62366.1 ENSP00000384949 P32322 UPI00017A78A7 NM_001282281.1 deleterious(0) 7/8 HAMAP:MF_01925,hmmpanther:PTHR11645,hmmpanther:PTHR11645:SF6,PROSITE_patterns:PS00521,Gene3D:2ahrA02,TIGRFAM_domain:TIGR00112,Pfam_domain:PF14748,Superfamily_domains:SSF48179 MODERATE SNV 2 1 PASS rs1285485127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 81934385 81934385 C G 1 0 0 0 0 1 0 0 0 13010 912 32 4 4 PYCR1 17 81934385 Missense_Mutation SNP C C3N-00294_T 813963 81934385 1323056 1069 13841 NOTUM 0 . GRCh38 17 81958363 81958363 + Missense_Mutation SNP C C G rs761507045 C3N-00294_T C3N-00294_N C C c.564G>C p.Trp188Cys p.W188C ENST00000409678 5/11 226 189 37 209 209 0 strelka-varscan-mutect NOTUM,missense_variant,p.Trp188Cys,ENST00000409678,NM_178493.5;NOTUM,missense_variant,p.Trp188Cys,ENST00000425009,;NOTUM,missense_variant,p.Trp46Cys,ENST00000477214,;NOTUM,downstream_gene_variant,,ENST00000489218,; G ENST00000409678 Transcript missense_variant 948/2329 564/1491 188/496 W/C tgG/tgC rs761507045 1 -1 NOTUM HGNC HGNC:27106 protein_coding YES CCDS32771.2 ENSP00000387310 Q6P988 UPI000004EE80 NM_178493.5 deleterious(0) 5/11 hmmpanther:PTHR21562,hmmpanther:PTHR21562:SF7,Pfam_domain:PF03283 MODERATE 1 SNV 1 1 PASS rs761507045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 81958363 81958363 C G 1 0 0 0 0 1 0 0 0 10598 856 30 4 4 NOTUM 17 81958363 Missense_Mutation SNP C C3N-00294_T 23978 81958363 1299078 1070 13842 SECTM1 0 . GRCh38 17 82324800 82324800 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.185C>G p.Ser62Cys p.S62C ENST00000269389 3/5 535 450 85 518 518 0 strelka-varscan-mutect SECTM1,missense_variant,p.Ser62Cys,ENST00000269389,NM_003004.2;SECTM1,missense_variant,p.Ser62Cys,ENST00000580437,;SECTM1,missense_variant,p.Ser62Cys,ENST00000581691,;SECTM1,missense_variant,p.Ser62Cys,ENST00000582563,;SECTM1,missense_variant,p.Ser62Cys,ENST00000582290,;SECTM1,missense_variant,p.Ser62Cys,ENST00000583093,;SECTM1,downstream_gene_variant,,ENST00000581954,;SECTM1,intron_variant,,ENST00000581864,; C ENST00000269389 Transcript missense_variant 536/2235 185/747 62/248 S/C tCc/tGc 1 -1 SECTM1 HGNC HGNC:10707 protein_coding YES CCDS11808.1 ENSP00000269389 Q8WVN6 UPI00000359A5 NM_003004.2 deleterious(0.02) 3/5 Gene3D:2.60.40.10,hmmpanther:PTHR15123,hmmpanther:PTHR15123:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 82324800 82324800 G C 1 0 0 0 0 1 0 0 0 14285 1174 41 4 4 SECTM1 17 82324800 Missense_Mutation SNP G C3N-00294_T 366437 82324800 932641 1071 13843 TBCD 0 . GRCh38 17 82920561 82920561 + Missense_Mutation SNP G G C rs182370230 C3N-00294_T C3N-00294_N G G c.2044G>C p.Val682Leu p.V682L ENST00000355528 24/39 196 172 24 183 183 0 strelka-varscan-mutect TBCD,missense_variant,p.Val682Leu,ENST00000355528,NM_005993.4;TBCD,missense_variant,p.Val682Leu,ENST00000539345,;TBCD,missense_variant,p.Val120Leu,ENST00000576760,;TBCD,missense_variant,p.Val120Leu,ENST00000576160,;TBCD,missense_variant,p.Val120Leu,ENST00000574422,;TBCD,missense_variant,p.Val141Leu,ENST00000574975,;TBCD,missense_variant,p.Val74Leu,ENST00000571712,;TBCD,missense_variant,p.Val120Leu,ENST00000576996,;TBCD,missense_variant,p.Val168Leu,ENST00000572953,;RP11-497H17.1,downstream_gene_variant,,ENST00000571113,;TBCD,non_coding_transcript_exon_variant,,ENST00000571618,;TBCD,non_coding_transcript_exon_variant,,ENST00000571796,;TBCD,non_coding_transcript_exon_variant,,ENST00000574818,;TBCD,upstream_gene_variant,,ENST00000574886,; C ENST00000355528 Transcript missense_variant 2174/7168 2044/3579 682/1192 V/L Gtt/Ctt rs182370230 1 1 TBCD HGNC HGNC:11581 protein_coding YES CCDS45818.1 ENSP00000347719 Q9BTW9 UPI000020053F NM_005993.4 tolerated(0.48) 24/39 hmmpanther:PTHR12658:SF0,hmmpanther:PTHR12658,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs182370230 . 0 207 0 0 3 0 0 0 -10.6137 0.9552541 1 1 1 0 C 3 2 46 82920561 82920561 G C 1 0 0 0 0 1 0 0 0 16038 1391 48 4 4 TBCD 17 82920561 Missense_Mutation SNP G C3N-00294_T 595761 82920561 336880 1072 13844 TMEM200C 0 . GRCh38 18 5890362 5890362 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1702C>T p.= p.L568L ENST00000581347 3/3 88 54 34 90 90 0 strelka-varscan-mutect TMEM200C,synonymous_variant,p.=,ENST00000581347,;TMEM200C,synonymous_variant,p.=,ENST00000383490,NM_001080209.1;RP11-945C19.4,intron_variant,,ENST00000577694,;RP11-945C19.4,downstream_gene_variant,,ENST00000582939,;RP11-945C19.4,downstream_gene_variant,,ENST00000580845,; A ENST00000581347 Transcript synonymous_variant 2348/10638 1702/1866 568/621 L Ctg/Ttg 1 -1 TMEM200C HGNC HGNC:37208 protein_coding YES CCDS45825.1 ENSP00000463375 A6NKL6 UPI000020198E 3/3 hmmpanther:PTHR31815,hmmpanther:PTHR31815:SF2 LOW SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 5890362 5890362 G A 1 0 0 0 0 0 0 0 1 16564 933 33 3 3 TMEM200C 18 5890362 Silent SNP G C3N-00294_T 5890362 74482923 1073 13845 ARHGAP28 0 . GRCh38 18 6837388 6837388 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.40G>C p.Asp14His p.D14H ENST00000419673 2/17 219 184 35 192 192 0 strelka-varscan-mutect ARHGAP28,missense_variant,p.Asp14His,ENST00000419673,NM_001010000.2;ARHGAP28,missense_variant,p.Asp14His,ENST00000314319,;ARHGAP28,missense_variant,p.Asp121His,ENST00000262227,;ARHGAP28,missense_variant,p.Asp173His,ENST00000383472,;ARHGAP28,missense_variant,p.Asp14His,ENST00000531294,;ARHGAP28,missense_variant,p.Asp14His,ENST00000581099,;ARHGAP28,missense_variant,p.Asp105His,ENST00000584387,;ARHGAP28,downstream_gene_variant,,ENST00000532723,;ARHGAP28,missense_variant,p.Asp14His,ENST00000577524,;ARHGAP28,missense_variant,p.Asp14His,ENST00000584287,; C ENST00000419673 Transcript missense_variant 257/5492 40/1713 14/570 D/H Gac/Cac 1 1 ARHGAP28 HGNC HGNC:25509 protein_coding YES CCDS32785.1 ENSP00000392660 Q9P2N2 UPI00004CEC5C NM_001010000.2 deleterious(0) 2/17 hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 46 6837388 6837388 G C 1 0 0 0 0 1 0 0 0 1002 942 33 4 4 ARHGAP28 18 6837388 Missense_Mutation SNP G C3N-00294_T 947026 6837388 73535897 1074 13846 PIEZO2 0 . GRCh38 18 10715669 10715669 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.5063T>A p.Leu1688Gln p.L1688Q ENST00000503781 35/52 57 33 24 70 70 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Leu1639Gln,ENST00000383408,;PIEZO2,missense_variant,p.Leu1688Gln,ENST00000302079,;PIEZO2,missense_variant,p.Leu1713Gln,ENST00000580640,;PIEZO2,missense_variant,p.Leu1688Gln,ENST00000503781,NM_022068.3;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; T ENST00000503781 Transcript missense_variant 5063/8259 5063/8259 1688/2752 L/Q cTg/cAg 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 35/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 10715669 10715669 A T 1 0 0 0 0 1 0 0 0 11975 188 7 4 4 PIEZO2 18 10715669 Missense_Mutation SNP A C3N-00294_T 3878281 10715669 69657616 1075 13847 RNMT 0 . GRCh38 18 13731548 13731548 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.31G>A p.Glu11Lys p.E11K ENST00000592764 3/12 30 25 5 71 71 0 strelka-varscan-mutect RNMT,missense_variant,p.Glu11Lys,ENST00000383314,NM_003799.1;RNMT,missense_variant,p.Glu11Lys,ENST00000262173,;RNMT,missense_variant,p.Glu11Lys,ENST00000592764,NM_001308263.1;RNMT,missense_variant,p.Glu11Lys,ENST00000589866,;RNMT,missense_variant,p.Glu11Lys,ENST00000543302,;RNMT,missense_variant,p.Glu11Lys,ENST00000591746,;FAM210A,upstream_gene_variant,,ENST00000322247,;FAM210A,upstream_gene_variant,,ENST00000402563,NM_001098801.1,NM_152352.3;FAM210A,upstream_gene_variant,,ENST00000592976,;FAM210A,upstream_gene_variant,,ENST00000591269,;FAM210A,upstream_gene_variant,,ENST00000585785,;RNMT,intron_variant,,ENST00000588457,; A ENST00000592764 Transcript missense_variant 228/4108 31/1515 11/504 E/K Gaa/Aaa 1 1 RNMT HGNC HGNC:10075 protein_coding YES CCDS77156.1 ENSP00000466111 O43148 UPI00000705F3 NM_001308263.1 tolerated_low_confidence(0.21) 3/12 hmmpanther:PTHR12189 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -13.98736 1 1 1 1 0 A 3 1 46 13731548 13731548 G A 1 0 0 0 0 1 0 0 0 13686 1291 45 3 3 RNMT 18 13731548 Missense_Mutation SNP G C3N-00294_T 3015879 13731548 66641737 1076 13848 RIOK3 0 . GRCh38 18 23477027 23477027 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1195G>A p.Glu399Lys p.E399K ENST00000339486 10/13 161 128 33 178 178 0 strelka-varscan-mutect RIOK3,missense_variant,p.Glu399Lys,ENST00000339486,NM_003831.3;RIOK3,missense_variant,p.Glu383Lys,ENST00000581585,;RIOK3,missense_variant,p.Glu399Lys,ENST00000577501,;RIOK3,upstream_gene_variant,,ENST00000577250,;RIOK3,3_prime_UTR_variant,,ENST00000584130,;RIOK3,non_coding_transcript_exon_variant,,ENST00000581302,;RIOK3,non_coding_transcript_exon_variant,,ENST00000581339,;RIOK3,upstream_gene_variant,,ENST00000581220,; A ENST00000339486 Transcript missense_variant 1812/4038 1195/1560 399/519 E/K Gaa/Aaa 1 1 RIOK3 HGNC HGNC:11451 protein_coding YES CCDS11877.1 ENSP00000341874 O14730 B0YJ89 UPI000013C732 NM_003831.3 tolerated(0.24) 10/13 hmmpanther:PTHR10593,hmmpanther:PTHR10593:SF22,Pfam_domain:PF01163,PIRSF_domain:PIRSF038146,Gene3D:1.10.510.10,SMART_domains:SM00090,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 23477027 23477027 G A 1 0 0 0 0 1 0 0 0 13553 1291 45 3 3 RIOK3 18 23477027 Missense_Mutation SNP G C3N-00294_T 9745479 23477027 56896258 1077 13849 PSMA8 0 . GRCh38 18 26178890 26178890 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.556G>A p.Glu186Lys p.E186K ENST00000308268 5/7 133 110 23 198 198 0 strelka-varscan-mutect PSMA8,missense_variant,p.Glu186Lys,ENST00000308268,NM_144662.2;PSMA8,missense_variant,p.Glu142Lys,ENST00000343848,NM_001025097.1;PSMA8,missense_variant,p.Glu154Lys,ENST00000612461,NM_001308188.1;PSMA8,missense_variant,p.Glu180Lys,ENST00000415576,NM_001025096.1;PSMA8,3_prime_UTR_variant,,ENST00000538664,; A ENST00000308268 Transcript missense_variant 645/1804 556/771 186/256 E/K Gaa/Aaa 1 1 PSMA8 HGNC HGNC:22985 protein_coding YES CCDS32808.1 ENSP00000311121 Q8TAA3 UPI000013ECFF NM_144662.2 tolerated(0.11) 5/7 PROSITE_profiles:PS51475,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF47,Pfam_domain:PF00227,Gene3D:3.60.20.10,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 26178890 26178890 G A 1 0 0 0 0 1 0 0 0 12824 943 33 3 3 PSMA8 18 26178890 Missense_Mutation SNP G C3N-00294_T 2701863 26178890 54194395 1078 13850 DSG4 0 . GRCh38 18 31391147 31391147 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.754G>C p.Glu252Gln p.E252Q ENST00000359747 7/15 404 327 77 445 445 0 strelka-varscan-mutect DSG4,missense_variant,p.Glu252Gln,ENST00000359747,NM_001134453.1;DSG4,missense_variant,p.Glu252Gln,ENST00000308128,NM_177986.3;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578477,;DSG1-AS1,intron_variant,,ENST00000581452,; C ENST00000359747 Transcript missense_variant 783/4526 754/3180 252/1059 E/Q Gag/Cag 1 1 DSG4 HGNC HGNC:21307 protein_coding YES CCDS45845.1 ENSP00000352785 Q86SJ6 UPI000035DB4E NM_001134453.1 tolerated(1) 7/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF10,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1213919986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 31391147 31391147 G C 1 0 0 0 0 1 0 0 0 4600 1291 45 4 4 DSG4 18 31391147 Missense_Mutation SNP G C3N-00294_T 5212257 31391147 48982138 1079 13851 MEP1B 0 . GRCh38 18 32213364 32213364 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1384C>T p.Gln462Ter p.Q462* ENST00000269202 11/15 251 213 38 320 320 0 strelka-varscan-mutect MEP1B,stop_gained,p.Gln462Ter,ENST00000269202,NM_005925.2;MEP1B,stop_gained,p.Gln462Ter,ENST00000581447,NM_001308171.1;GAREM1,intron_variant,,ENST00000583696,; T ENST00000269202 Transcript stop_gained 1431/2312 1384/2106 462/701 Q/* Cag/Tag 1 1 MEP1B HGNC HGNC:7020 protein_coding YES CCDS45846.1 ENSP00000269202 Q16820 UPI0000201B8B NM_005925.2 11/15 Gene3D:2.60.210.10,PIRSF_domain:PIRSF001196,PROSITE_profiles:PS50144,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF312,SMART_domains:SM00061,Superfamily_domains:SSF49599 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 32213364 32213364 C T 1 0 0 0 0 0 1 0 0 9421 827 29 3 3 MEP1B 18 32213364 Nonsense_Mutation SNP C C3N-00294_T 822217 32213364 48159921 1080 13852 CCDC178 0 . GRCh38 18 33333378 33333378 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.675G>C p.Leu225Phe p.L225F ENST00000583930 9/23 39 33 6 87 87 0 strelka-varscan-mutect CCDC178,missense_variant,p.Leu225Phe,ENST00000383096,;CCDC178,missense_variant,p.Leu225Phe,ENST00000403303,NM_001105528.1;CCDC178,missense_variant,p.Leu225Phe,ENST00000583930,;CCDC178,missense_variant,p.Leu225Phe,ENST00000300227,NM_198995.2;CCDC178,missense_variant,p.Leu225Phe,ENST00000406524,;CCDC178,missense_variant,p.Leu225Phe,ENST00000579947,;CCDC178,intron_variant,,ENST00000579916,;CCDC178,missense_variant,p.Leu225Phe,ENST00000399177,;CCDC178,non_coding_transcript_exon_variant,,ENST00000577268,; G ENST00000583930 Transcript missense_variant 754/3094 675/2676 225/891 L/F ttG/ttC 1 -1 CCDC178 HGNC HGNC:29588 protein_coding YES CCDS77174.1 ENSP00000463254 F8W7A7 UPI00020655A5 tolerated(0.08) 9/23 hmmpanther:PTHR35088:SF1,hmmpanther:PTHR35088 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -15.28607 0.9999999 1 1 1 0 G 3 3 46 33333378 33333378 C G 1 0 0 0 0 1 0 0 0 2493 825 29 4 4 CCDC178 18 33333378 Missense_Mutation SNP C C3N-00294_T 1120014 33333378 47039907 1081 13853 SETBP1 0 . GRCh38 18 44952694 44952694 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.3354G>A p.= p.Q1118Q ENST00000282030 4/6 325 191 134 358 358 0 strelka-varscan-mutect SETBP1,synonymous_variant,p.=,ENST00000282030,NM_015559.2; A ENST00000282030 Transcript synonymous_variant 3650/9899 3354/4791 1118/1596 Q caG/caA 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 44952694 44952694 G A 1 0 0 0 0 0 0 0 1 14406 991 35 3 3 SETBP1 18 44952694 Silent SNP G C3N-00294_T 11619316 44952694 35420591 1082 13854 ZNF532 0 . GRCh38 18 58953614 58953614 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2965C>G p.Gln989Glu p.Q989E ENST00000336078 8/11 191 162 29 193 193 0 strelka-varscan-mutect ZNF532,missense_variant,p.Gln989Glu,ENST00000336078,NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4;ZNF532,missense_variant,p.Gln989Glu,ENST00000589288,;ZNF532,missense_variant,p.Gln989Glu,ENST00000591083,;ZNF532,missense_variant,p.Gln989Glu,ENST00000591808,;ZNF532,missense_variant,p.Gln989Glu,ENST00000591230,;ZNF532,intron_variant,,ENST00000586997,;ZNF532,non_coding_transcript_exon_variant,,ENST00000592249,;ZNF532,missense_variant,p.Gln49Glu,ENST00000585662,; G ENST00000336078 Transcript missense_variant 3741/6696 2965/3906 989/1301 Q/E Cag/Gag 1 1 ZNF532 HGNC HGNC:30940 protein_coding YES CCDS11969.1 ENSP00000338217 Q9HCE3 A0A024R283 UPI000013D30C NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4 tolerated(1) 8/11 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 58953614 58953614 C G 1 0 0 0 0 1 0 0 0 18545 827 29 4 4 ZNF532 18 58953614 Missense_Mutation SNP C C3N-00294_T 14000920 58953614 21419671 1083 13855 CDH20 0 . GRCh38 18 61490658 61490658 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.105C>T p.= p.D35D ENST00000262717 2/12 342 294 48 344 344 0 strelka-varscan-mutect CDH20,synonymous_variant,p.=,ENST00000262717,;CDH20,synonymous_variant,p.=,ENST00000536675,NM_031891.2;CDH20,synonymous_variant,p.=,ENST00000538374,; T ENST00000262717 Transcript synonymous_variant 503/3882 105/2406 35/801 D gaC/gaT 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D 2/12 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 61490658 61490658 C T 1 0 0 0 0 0 0 0 1 2809 477 17 3 3 CDH20 18 61490658 Silent SNP C C3N-00294_T 2537044 61490658 18882627 1084 13856 SERPINB11 0 . GRCh38 18 63720954 63720954 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.481C>T p.= p.L161L ENST00000623262 4/5 140 116 24 170 170 0 strelka-varscan-mutect SERPINB11,synonymous_variant,p.=,ENST00000382749,NM_080475.3;SERPINB11,synonymous_variant,p.=,ENST00000544088,;SERPINB11,synonymous_variant,p.=,ENST00000623262,NM_001291278.1;SERPINB11,intron_variant,,ENST00000624518,;SERPINB11,downstream_gene_variant,,ENST00000489748,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000467649,;SERPINB11,3_prime_UTR_variant,,ENST00000536691,;SERPINB11,downstream_gene_variant,,ENST00000610304,; T ENST00000623262 Transcript synonymous_variant 481/918 481/918 161/305 L Ctg/Ttg 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 4/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 63720954 63720954 C T 1 0 0 0 0 0 0 0 1 14374 912 32 3 3 SERPINB11 18 63720954 Silent SNP C C3N-00294_T 2230296 63720954 16652331 1085 13857 DSEL 0 . GRCh38 18 67513255 67513255 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1384C>T p.Gln462Ter p.Q462* ENST00000310045 2/2 208 167 41 218 218 0 strelka-varscan-mutect DSEL,stop_gained,p.Gln462Ter,ENST00000310045,NM_032160.2;RP11-638L3.1,upstream_gene_variant,,ENST00000583687,;CTD-2541J13.2,non_coding_transcript_exon_variant,,ENST00000583493,;CTD-2541J13.2,downstream_gene_variant,,ENST00000581951,; A ENST00000310045 Transcript stop_gained 2858/9531 1384/3669 462/1222 Q/* Cag/Tag 1 -1 DSEL HGNC HGNC:18144 protein_coding YES CCDS11995.1 ENSP00000310565 Q8IZU8 UPI00000740A1 NM_032160.2 2/2 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2 HIGH SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 67513255 67513255 G A 1 0 0 0 0 0 1 0 0 4596 1299 45 3 3 DSEL 18 67513255 Nonsense_Mutation SNP G C3N-00294_T 3792301 67513255 12860030 1086 13858 SOCS6 0 . GRCh38 18 70325968 70325968 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1300G>A p.Glu434Lys p.E434K ENST00000397942 2/2 179 142 37 189 189 0 strelka-varscan-mutect SOCS6,missense_variant,p.Glu434Lys,ENST00000397942,NM_004232.3;SOCS6,missense_variant,p.Glu434Lys,ENST00000582322,;SOCS6,downstream_gene_variant,,ENST00000578377,; A ENST00000397942 Transcript missense_variant 1616/5848 1300/1608 434/535 E/K Gag/Aag 1 1 SOCS6 HGNC HGNC:16833 protein_coding YES CCDS11998.1 ENSP00000381034 O14544 A0A024R379 UPI0000072C28 NM_004232.3 deleterious(0) 2/2 PROSITE_profiles:PS50001,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF83,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 70325968 70325968 G A 1 0 0 0 0 1 0 0 0 15239 1291 45 3 3 SOCS6 18 70325968 Missense_Mutation SNP G C3N-00294_T 2812713 70325968 10047317 1087 13859 C2CD4C 0 . GRCh38 19 407097 407097 + Nonstop_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.1265A>T p.Ter422LeuextTer135 p.*422Lext*135 ENST00000332235 2/2 77 60 17 61 61 0 strelka-varscan-mutect C2CD4C,stop_lost,p.Ter422LeuextTer135,ENST00000332235,NM_001136263.1; A ENST00000332235 Transcript stop_lost 1470/3129 1265/1266 422/421 */L tAg/tTg 1 -1 C2CD4C HGNC HGNC:29417 protein_coding YES CCDS45890.1 ENSP00000328677 Q8TF44 UPI00001C2016 NM_001136263.1 2/2 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 407097 407097 T A 1 0 0 0 0 0 0 0 0 2028 1535 53 4 4 C2CD4C 19 407097 Nonstop_Mutation SNP T C3N-00294_T 407097 58210519 1088 13860 TPGS1 0 . GRCh38 19 519084 519084 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.534G>C p.= p.L178L ENST00000359315 2/2 205 168 37 173 173 0 strelka-varscan-mutect TPGS1,synonymous_variant,p.=,ENST00000359315,NM_033513.2; C ENST00000359315 Transcript synonymous_variant 544/1114 534/873 178/290 L ctG/ctC 1 1 TPGS1 HGNC HGNC:25058 protein_coding YES CCDS42454.1 ENSP00000352265 Q6ZTW0 UPI0000202E14 NM_033513.2 2/2 hmmpanther:PTHR31932 LOW 1 SNV 1 1 PASS rs900984739 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 519084 519084 G C 1 0 0 0 0 0 0 0 1 16880 1277 45 4 4 TPGS1 19 519084 Silent SNP G C3N-00294_T 111987 519084 58098532 1089 13861 ARHGAP45 0 . GRCh38 19 1083182 1083182 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.2832G>A p.= p.G944G ENST00000539243 21/23 385 317 68 375 375 0 strelka-varscan-mutect ARHGAP45,synonymous_variant,p.=,ENST00000313093,NM_012292.4;ARHGAP45,synonymous_variant,p.=,ENST00000590214,;ARHGAP45,synonymous_variant,p.=,ENST00000539243,NM_001258328.2;ARHGAP45,synonymous_variant,p.=,ENST00000586866,;ARHGAP45,synonymous_variant,p.=,ENST00000543365,NM_001282335.1;ARHGAP45,synonymous_variant,p.=,ENST00000590577,NM_001282334.1;POLR2E,downstream_gene_variant,,ENST00000615234,NM_001316324.1,NM_001316323.1,NM_002695.3;POLR2E,downstream_gene_variant,,ENST00000612655,;POLR2E,downstream_gene_variant,,ENST00000586746,;ARHGAP45,non_coding_transcript_exon_variant,,ENST00000590512,;ARHGAP45,3_prime_UTR_variant,,ENST00000587602,;ARHGAP45,non_coding_transcript_exon_variant,,ENST00000592297,;ARHGAP45,non_coding_transcript_exon_variant,,ENST00000586378,;ARHGAP45,intron_variant,,ENST00000591169,;POLR2E,downstream_gene_variant,,ENST00000586817,;POLR2E,downstream_gene_variant,,ENST00000215587,;POLR2E,downstream_gene_variant,,ENST00000591767,;POLR2E,downstream_gene_variant,,ENST00000589737,;POLR2E,downstream_gene_variant,,ENST00000590060,;ARHGAP45,downstream_gene_variant,,ENST00000591293,;ARHGAP45,downstream_gene_variant,,ENST00000586937,; A ENST00000539243 Transcript synonymous_variant 2935/4184 2832/3459 944/1152 G ggG/ggA COSM3821868,COSM3821869 1 1 ARHGAP45 HGNC HGNC:17102 protein_coding YES CCDS58637.1 ENSP00000439601 Q92619 UPI0001AE63E1 NM_001258328.2 21/23 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF18,SMART_domains:SM00324,Superfamily_domains:SSF48350 1,1 LOW SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 1083182 1083182 G A 1 0 0 0 0 0 0 0 1 1015 1161 41 3 3 ARHGAP45 19 1083182 Silent SNP G C3N-00294_T 564098 1083182 57534434 1090 13862 APC2 0 . GRCh38 19 1456387 1456387 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.799C>A p.Gln267Lys p.Q267K ENST00000535453 7/14 139 122 17 127 126 1 strelka-varscan-mutect APC2,missense_variant,p.Gln267Lys,ENST00000535453,;APC2,missense_variant,p.Gln267Lys,ENST00000233607,NM_005883.2;APC2,missense_variant,p.Gln266Lys,ENST00000238483,;APC2,missense_variant,p.Gln267Lys,ENST00000590469,;C19orf25,downstream_gene_variant,,ENST00000588427,;APC2,downstream_gene_variant,,ENST00000590877,;APC2,downstream_gene_variant,,ENST00000587869,;APC2,downstream_gene_variant,,ENST00000587149,;CTB-25B13.12,downstream_gene_variant,,ENST00000591252,;APC2,non_coding_transcript_exon_variant,,ENST00000593146,; A ENST00000535453 Transcript missense_variant 2512/11656 799/6912 267/2303 Q/K Cag/Aag COSM4848247 1 1 APC2 HGNC HGNC:24036 protein_coding YES CCDS12068.1 ENSP00000442954 O95996 UPI0000073D85 tolerated(0.08) 7/14 hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 46 1456387 1456387 C A 1 0 0 0 0 1 0 0 0 884 827 29 2 2 APC2 19 1456387 Missense_Mutation SNP C C3N-00294_T 373205 1456387 57161229 1091 13863 KLF16 0 . GRCh38 19 1863073 1863073 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.425C>T p.Ser142Leu p.S142L ENST00000250916 1/2 172 145 27 144 144 0 strelka-varscan-mutect KLF16,missense_variant,p.Ser142Leu,ENST00000250916,NM_031918.3;KLF16,missense_variant,p.Ser142Leu,ENST00000617223,;KLF16,upstream_gene_variant,,ENST00000592313,;CTB-31O20.8,downstream_gene_variant,,ENST00000586694,;KLF16,missense_variant,p.Ser142Leu,ENST00000541015,; A ENST00000250916 Transcript missense_variant 496/2890 425/759 142/252 S/L tCg/tTg 1 -1 KLF16 HGNC HGNC:16857 protein_coding YES CCDS12075.1 ENSP00000250916 Q9BXK1 UPI0000126B0D NM_031918.3 deleterious(0) 1/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs1334678718 . 0 207 0 3 0 0 0 0 -20 0.9999942 1 1 1 0 A 3 1 46 1863073 1863073 G A 1 0 0 0 0 1 0 0 0 8209 1059 37 1 1 KLF16 19 1863073 Missense_Mutation SNP G C3N-00294_T 406686 1863073 56754543 1092 13864 ZNF57 0 . GRCh38 19 2916108 2916108 + Missense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.161C>T p.Ser54Leu p.S54L ENST00000306908 3/4 89 73 16 72 72 0 strelka-varscan-mutect ZNF57,missense_variant,p.Ser54Leu,ENST00000306908,NM_001319083.1,NM_173480.2;ZNF57,missense_variant,p.Ser54Leu,ENST00000614108,;ZNF57,missense_variant,p.Ser22Leu,ENST00000523428,;ZNF57,missense_variant,p.Ser22Leu,ENST00000522294,;ZNF57,missense_variant,p.Ser22Leu,ENST00000590305,;AC006277.2,intron_variant,,ENST00000520090,; T ENST00000306908 Transcript missense_variant 309/2003 161/1668 54/555 S/L tCa/tTa COSM994326 1 1 ZNF57 HGNC HGNC:13125 protein_coding YES CCDS12098.1 ENSP00000303696 Q68EA5 A5HJR3 UPI000006FE5C NM_001319083.1,NM_173480.2 tolerated(0.18) 3/4 PROSITE_profiles:PS50805,SMART_domains:SM00349 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 2916108 2916108 C T 1 0 0 0 0 1 0 0 0 18575 838 29 3 3 ZNF57 19 2916108 Missense_Mutation SNP C C3N-00294_T 1053035 2916108 55701508 1093 13865 TJP3 0 . GRCh38 19 3733844 3733844 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.836G>C p.Arg279Thr p.R279T ENST00000589378 7/21 322 270 52 276 276 0 strelka-varscan-mutect TJP3,missense_variant,p.Arg270Thr,ENST00000541714,NM_001267560.1;TJP3,missense_variant,p.Arg279Thr,ENST00000589378,NM_001267561.1;TJP3,missense_variant,p.Arg289Thr,ENST00000587686,;TJP3,missense_variant,p.Arg234Thr,ENST00000539908,;TJP3,downstream_gene_variant,,ENST00000590545,;TJP3,downstream_gene_variant,,ENST00000587912,; C ENST00000589378 Transcript missense_variant 992/3068 836/2787 279/928 R/T aGa/aCa 1 1 TJP3 HGNC HGNC:11829 protein_coding YES CCDS59332.1 ENSP00000465419 O95049 UPI00003E3015 NM_001267561.1 deleterious(0) 7/21 Gene3D:2.30.42.10,Prints_domain:PR01597,PROSITE_profiles:PS50106,hmmpanther:PTHR13865,hmmpanther:PTHR13865:SF11,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 3733844 3733844 G C 1 0 0 0 0 1 0 0 0 16373 942 33 4 4 TJP3 19 3733844 Missense_Mutation SNP G C3N-00294_T 817736 3733844 54883772 1094 13866 PIAS4 0 . GRCh38 19 4024064 4024064 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.483G>C p.Glu161Asp p.E161D ENST00000262971 3/11 261 212 49 220 220 0 strelka-varscan-mutect PIAS4,missense_variant,p.Glu161Asp,ENST00000262971,NM_015897.3;PIAS4,non_coding_transcript_exon_variant,,ENST00000596144,;PIAS4,intron_variant,,ENST00000599999,;PIAS4,non_coding_transcript_exon_variant,,ENST00000600566,;PIAS4,upstream_gene_variant,,ENST00000601439,; C ENST00000262971 Transcript missense_variant 598/3159 483/1533 161/510 E/D gaG/gaC COSM3533836 1 1 PIAS4 HGNC HGNC:17002 protein_coding YES CCDS12118.1 ENSP00000262971 Q8N2W9 UPI0000073C15 NM_015897.3 tolerated(0.09) 3/11 Pfam_domain:PF14324,PROSITE_profiles:PS51466,hmmpanther:PTHR10782,hmmpanther:PTHR10782:SF9 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 4024064 4024064 G C 1 0 0 0 0 1 0 0 0 11968 933 33 4 4 PIAS4 19 4024064 Missense_Mutation SNP G C3N-00294_T 290220 4024064 54593552 1095 13867 CREB3L3 0 . GRCh38 19 4171097 4171097 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.897C>G p.= p.L299L ENST00000078445 8/10 556 473 83 465 465 0 strelka-varscan-mutect CREB3L3,missense_variant,p.Leu264Val,ENST00000602147,NM_001271997.1;CREB3L3,synonymous_variant,p.=,ENST00000078445,NM_032607.2;CREB3L3,synonymous_variant,p.=,ENST00000595923,NM_001271995.1;CREB3L3,synonymous_variant,p.=,ENST00000602257,NM_001271996.1;SIRT6,downstream_gene_variant,,ENST00000337491,NM_016539.2;SIRT6,downstream_gene_variant,,ENST00000594279,NM_001321064.1;SIRT6,downstream_gene_variant,,ENST00000305232,NM_001193285.1;SIRT6,downstream_gene_variant,,ENST00000601488,NM_001321063.1;SIRT6,downstream_gene_variant,,ENST00000597896,;SIRT6,downstream_gene_variant,,ENST00000601571,;CREB3L3,non_coding_transcript_exon_variant,,ENST00000598894,;SIRT6,downstream_gene_variant,,ENST00000596119,;SIRT6,downstream_gene_variant,,ENST00000600938,NM_001321058.1;SIRT6,downstream_gene_variant,,ENST00000600540,;SIRT6,downstream_gene_variant,,ENST00000599365,NM_001321061.1;SIRT6,downstream_gene_variant,,ENST00000601069,;SIRT6,downstream_gene_variant,,ENST00000595670,;SIRT6,downstream_gene_variant,,ENST00000596298,;SIRT6,downstream_gene_variant,,ENST00000599394,; G ENST00000078445 Transcript synonymous_variant 1044/2618 897/1386 299/461 L ctC/ctG COSM3971011 1 1 CREB3L3 HGNC HGNC:18855 protein_coding YES CCDS12121.1 ENSP00000078445 Q68CJ9 UPI000006FCF0 NM_032607.2 8/10 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00170,PROSITE_profiles:PS50217,hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF98,SMART_domains:SM00338,Superfamily_domains:SSF57959 1 LOW 1 SNV 1 1 1 PASS rs1041364646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 4171097 4171097 C G 1 0 0 0 0 0 0 0 1 3658 913 32 4 4 CREB3L3 19 4171097 Silent SNP C C3N-00294_T 147033 4171097 54446519 1096 13868 KDM4B 0 . GRCh38 19 5135373 5135373 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.2120C>G p.Ser707Cys p.S707C ENST00000159111 15/23 231 182 49 190 190 0 strelka-varscan-mutect KDM4B,missense_variant,p.Ser741Cys,ENST00000611640,;KDM4B,missense_variant,p.Ser707Cys,ENST00000159111,NM_015015.2;KDM4B,missense_variant,p.Ser741Cys,ENST00000536461,;KDM4B,missense_variant,p.Ser453Cys,ENST00000588361,;KDM4B,upstream_gene_variant,,ENST00000588166,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,; G ENST00000159111 Transcript missense_variant 2338/5593 2120/3291 707/1096 S/C tCc/tGc 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 deleterious(0.03) 15/23 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 5135373 5135373 C G 1 0 0 0 0 1 0 0 0 8047 855 30 4 4 KDM4B 19 5135373 Missense_Mutation SNP C C3N-00294_T 964276 5135373 53482243 1097 13869 LONP1 0 . GRCh38 19 5699087 5699087 + Missense_Mutation SNP C C T rs748047263 C3N-00294_T C3N-00294_N C C c.1625G>A p.Arg542Gln p.R542Q ENST00000360614 10/18 99 68 31 79 79 0 strelka-varscan-mutect LONP1,missense_variant,p.Arg542Gln,ENST00000360614,NM_004793.3;LONP1,missense_variant,p.Arg346Gln,ENST00000540670,NM_001276480.1;LONP1,missense_variant,p.Arg478Gln,ENST00000593119,NM_001276479.1;LONP1,missense_variant,p.Arg428Gln,ENST00000585374,;LONP1,missense_variant,p.Arg412Gln,ENST00000590729,;LONP1,missense_variant,p.Arg199Gln,ENST00000590206,;LONP1,upstream_gene_variant,,ENST00000589473,;LONP1,downstream_gene_variant,,ENST00000587365,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;LONP1,downstream_gene_variant,,ENST00000588589,; T ENST00000360614 Transcript missense_variant 1783/3236 1625/2880 542/959 R/Q cGa/cAa rs748047263,COSM1680539,COSM567900 1 -1 LONP1 HGNC HGNC:9479 protein_coding YES CCDS12148.1 ENSP00000353826 P36776 UPI000012E7EF NM_004793.3 deleterious(0) 10/18 Gene3D:3.40.50.300,HAMAP:MF_03120,Pfam_domain:PF00004,Prints_domain:PR00830,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF50,SMART_domains:SM00382,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00763 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748047263 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 5699087 5699087 C T 1 0 0 0 0 1 0 0 0 8794 884 31 1 1 LONP1 19 5699087 Missense_Mutation SNP C C3N-00294_T 563714 5699087 52918529 1098 13870 LONP1 0 . GRCh38 19 5705930 5705930 + Silent SNP G G A rs764862589 C3N-00294_T C3N-00294_N G G c.1209C>T p.= p.I403I ENST00000360614 8/18 325 265 60 255 255 0 strelka-varscan-mutect LONP1,synonymous_variant,p.=,ENST00000360614,NM_004793.3;LONP1,synonymous_variant,p.=,ENST00000540670,NM_001276480.1;LONP1,synonymous_variant,p.=,ENST00000593119,NM_001276479.1;LONP1,synonymous_variant,p.=,ENST00000585374,;LONP1,synonymous_variant,p.=,ENST00000590729,;LONP1,synonymous_variant,p.=,ENST00000590206,;LONP1,synonymous_variant,p.=,ENST00000587365,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;LONP1,non_coding_transcript_exon_variant,,ENST00000591321,;LONP1,non_coding_transcript_exon_variant,,ENST00000588589,;LONP1,downstream_gene_variant,,ENST00000586617,; A ENST00000360614 Transcript synonymous_variant 1367/3236 1209/2880 403/959 I atC/atT rs764862589,COSM567898 1 -1 LONP1 HGNC HGNC:9479 protein_coding YES CCDS12148.1 ENSP00000353826 P36776 UPI000012E7EF NM_004793.3 8/18 HAMAP:MF_03120,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF50,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00763 0,1 LOW 1 SNV 1 0,1 1 PASS rs764862589 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 5705930 5705930 G A 1 0 0 0 0 0 0 0 1 8794 1280 45 3 3 LONP1 19 5705930 Silent SNP G C3N-00294_T 6843 5705930 52911686 1099 13871 LONP1 0 . GRCh38 19 5705972 5705972 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1167G>C p.Gln389His p.Q389H ENST00000360614 8/18 187 159 28 141 141 0 strelka-varscan-mutect LONP1,missense_variant,p.Gln389His,ENST00000360614,NM_004793.3;LONP1,missense_variant,p.Gln193His,ENST00000540670,NM_001276480.1;LONP1,missense_variant,p.Gln325His,ENST00000593119,NM_001276479.1;LONP1,missense_variant,p.Gln275His,ENST00000585374,;LONP1,missense_variant,p.Gln259His,ENST00000590729,;LONP1,missense_variant,p.Gln46His,ENST00000590206,;LONP1,intron_variant,,ENST00000587365,;LONP1,3_prime_UTR_variant,,ENST00000590558,;LONP1,non_coding_transcript_exon_variant,,ENST00000587552,;LONP1,non_coding_transcript_exon_variant,,ENST00000591321,;LONP1,non_coding_transcript_exon_variant,,ENST00000588589,;LONP1,downstream_gene_variant,,ENST00000586617,; G ENST00000360614 Transcript missense_variant 1325/3236 1167/2880 389/959 Q/H caG/caC 1 -1 LONP1 HGNC HGNC:9479 protein_coding YES CCDS12148.1 ENSP00000353826 P36776 UPI000012E7EF NM_004793.3 deleterious(0) 8/18 HAMAP:MF_03120,hmmpanther:PTHR10046,hmmpanther:PTHR10046:SF50,TIGRFAM_domain:TIGR00763 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 5705972 5705972 C G 1 0 0 0 0 1 0 0 0 8794 912 32 4 4 LONP1 19 5705972 Missense_Mutation SNP C C3N-00294_T 42 5705972 52911644 1100 13872 C3 0 . GRCh38 19 6712299 6712299 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.1227C>T p.= p.L409L ENST00000245907 11/41 375 326 49 330 330 0 strelka-varscan-mutect C3,synonymous_variant,p.=,ENST00000245907,NM_000064.3;CTD-3128G10.7,downstream_gene_variant,,ENST00000614781,;C3,non_coding_transcript_exon_variant,,ENST00000594270,;C3,downstream_gene_variant,,ENST00000597442,;C3,downstream_gene_variant,,ENST00000595577,;C3,upstream_gene_variant,,ENST00000600763,; A ENST00000245907 Transcript synonymous_variant 1320/5263 1227/4992 409/1663 L ctC/ctT 1 -1 C3 HGNC HGNC:1318 protein_coding YES CCDS32883.1 ENSP00000245907 P01024 V9HWA9 UPI000013EC9B NM_000064.3 11/41 hmmpanther:PTHR11412:SF90,hmmpanther:PTHR11412 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 6712299 6712299 G A 1 0 0 0 0 0 0 0 1 2057 1277 45 3 3 C3 19 6712299 Silent SNP G C3N-00294_T 1006327 6712299 51905317 1101 13873 ARHGEF18 0 . GRCh38 19 7441666 7441666 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.556G>C p.Glu186Gln p.E186Q ENST00000359920 2/20 188 161 27 140 140 0 strelka-varscan-mutect ARHGEF18,missense_variant,p.Glu186Gln,ENST00000359920,NM_001130955.1;ARHGEF18,missense_variant,p.Glu28Gln,ENST00000319670,NM_015318.3;CTD-2207O23.3,missense_variant,p.Glu120Gln,ENST00000617428,;ARHGEF18,missense_variant,p.Glu28Gln,ENST00000599752,;ARHGEF18,upstream_gene_variant,,ENST00000595600,; C ENST00000359920 Transcript missense_variant 809/5733 556/3522 186/1173 E/Q Gag/Cag 1 1 ARHGEF18 HGNC HGNC:17090 protein_coding YES CCDS45946.1 ENSP00000352995 Q6ZSZ5 UPI0000D6170D NM_001130955.1 tolerated(0.12) 2/20 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF120 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7441666 7441666 G C 1 0 0 0 0 1 0 0 0 1031 943 33 4 4 ARHGEF18 19 7441666 Missense_Mutation SNP G C3N-00294_T 729367 7441666 51175950 1102 13874 PNPLA6 0 . GRCh38 19 7541610 7541610 + Nonsense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1121C>G p.Ser374Ter p.S374* ENST00000414982 11/34 324 282 42 293 293 0 strelka-varscan-mutect PNPLA6,stop_gained,p.Ser326Ter,ENST00000221249,NM_006702.4;PNPLA6,stop_gained,p.Ser374Ter,ENST00000414982,NM_001166111.1;PNPLA6,stop_gained,p.Ser326Ter,ENST00000545201,NM_001166112.1;PNPLA6,stop_gained,p.Ser326Ter,ENST00000450331,NM_001166113.1;PNPLA6,stop_gained,p.Ser365Ter,ENST00000600737,NM_001166114.1;PNPLA6,stop_gained,p.Ser206Ter,ENST00000595264,;PNPLA6,stop_gained,p.Ser185Ter,ENST00000594551,;PNPLA6,downstream_gene_variant,,ENST00000601001,;PNPLA6,downstream_gene_variant,,ENST00000601668,;PNPLA6,downstream_gene_variant,,ENST00000593924,;PNPLA6,downstream_gene_variant,,ENST00000600942,;PNPLA6,non_coding_transcript_exon_variant,,ENST00000599311,;PNPLA6,non_coding_transcript_exon_variant,,ENST00000595176,;CTD-2207O23.10,downstream_gene_variant,,ENST00000601870,;PNPLA6,upstream_gene_variant,,ENST00000595889,;PNPLA6,downstream_gene_variant,,ENST00000598462,;PNPLA6,downstream_gene_variant,,ENST00000602191,; G ENST00000414982 Transcript stop_gained 1316/4522 1121/4128 374/1375 S/* tCa/tGa 1 1 PNPLA6 HGNC HGNC:16268 protein_coding YES CCDS54206.1 ENSP00000407509 Q8IY17 UPI0001AE63FF NM_001166111.1 11/34 hmmpanther:PTHR14226,hmmpanther:PTHR14226:SF26 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 46 7541610 7541610 C G 1 0 0 0 0 0 1 0 0 12277 838 29 4 4 PNPLA6 19 7541610 Nonsense_Mutation SNP C C3N-00294_T 99944 7541610 51076006 1103 13875 CAMSAP3 0 . GRCh38 19 7616608 7616608 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3279G>C p.Lys1093Asn p.K1093N ENST00000446248 16/19 221 180 41 207 207 0 strelka-varscan-mutect CAMSAP3,missense_variant,p.Lys1093Asn,ENST00000446248,NM_001080429.2;CAMSAP3,missense_variant,p.Lys1066Asn,ENST00000160298,NM_020902.1;XAB2,downstream_gene_variant,,ENST00000358368,NM_020196.2;MIR6792,upstream_gene_variant,,ENST00000614460,;CAMSAP3,non_coding_transcript_exon_variant,,ENST00000595692,;CAMSAP3,non_coding_transcript_exon_variant,,ENST00000593434,;XAB2,downstream_gene_variant,,ENST00000595288,;XAB2,downstream_gene_variant,,ENST00000600230,;XAB2,downstream_gene_variant,,ENST00000596134,; C ENST00000446248 Transcript missense_variant 3380/4179 3279/3831 1093/1276 K/N aaG/aaC 1 1 CAMSAP3 HGNC HGNC:29307 protein_coding YES CCDS45947.1 ENSP00000416797 Q9P1Y5 UPI0000161861 NM_001080429.2 tolerated(0.06) 16/19 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7616608 7616608 G C 1 0 0 0 0 1 0 0 0 2305 933 33 4 4 CAMSAP3 19 7616608 Missense_Mutation SNP G C3N-00294_T 74998 7616608 51001008 1104 13876 STXBP2 0 . GRCh38 19 7639047 7639047 + Missense_Mutation SNP G G C rs200306463 C3N-00294_T C3N-00294_N G G c.116G>C p.Arg39Pro p.R39P ENST00000441779 3/19 617 312 305 646 646 0 strelka-varscan-mutect STXBP2,missense_variant,p.Arg39Pro,ENST00000441779,NM_001272034.1;STXBP2,missense_variant,p.Arg39Pro,ENST00000221283,NM_006949.3;STXBP2,missense_variant,p.Arg39Pro,ENST00000414284,NM_001127396.2;STXBP2,missense_variant,p.Arg39Pro,ENST00000595950,;STXBP2,missense_variant,p.Arg7Pro,ENST00000593535,;STXBP2,upstream_gene_variant,,ENST00000612033,;STXBP2,upstream_gene_variant,,ENST00000600702,;CTD-3214H19.6,upstream_gene_variant,,ENST00000601797,;STXBP2,missense_variant,p.Arg39Pro,ENST00000597068,;STXBP2,missense_variant,p.Arg23Pro,ENST00000599737,;CTD-3214H19.4,3_prime_UTR_variant,,ENST00000595866,;CTD-3214H19.4,3_prime_UTR_variant,,ENST00000599243,;STXBP2,non_coding_transcript_exon_variant,,ENST00000597467,;STXBP2,non_coding_transcript_exon_variant,,ENST00000595181,;STXBP2,non_coding_transcript_exon_variant,,ENST00000599905,;CTD-3214H19.4,intron_variant,,ENST00000598664,;STXBP2,upstream_gene_variant,,ENST00000599400,;STXBP2,upstream_gene_variant,,ENST00000594221,;STXBP2,upstream_gene_variant,,ENST00000599648,;STXBP2,upstream_gene_variant,,ENST00000595861,; C ENST00000441779 Transcript missense_variant 153/1914 116/1815 39/604 R/P cGc/cCc rs200306463,CM106813,COSM1003332 1 1 STXBP2 HGNC HGNC:11445 protein_coding YES CCDS62522.1 ENSP00000413606 Q15833 UPI0001AE6405 NM_001272034.1 deleterious(0) 3/19 hmmpanther:PTHR11679:SF27,hmmpanther:PTHR11679,PIRSF_domain:PIRSF005715,Gene3D:3.40.50.2060,Pfam_domain:PF00995,Superfamily_domains:SSF56815 0,0,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs200306463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7639047 7639047 G C 1 0 0 0 0 1 0 0 0 15737 1087 38 4 4 STXBP2 19 7639047 Missense_Mutation SNP G C3N-00294_T 22439 7639047 50978569 1105 13877 STXBP2 0 . GRCh38 19 7643209 7643209 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1104C>G p.Phe368Leu p.F368L ENST00000441779 13/19 414 388 26 391 391 0 strelka-varscan-mutect STXBP2,missense_variant,p.Phe368Leu,ENST00000441779,NM_001272034.1;STXBP2,missense_variant,p.Phe357Leu,ENST00000221283,NM_006949.3;STXBP2,missense_variant,p.Phe354Leu,ENST00000414284,NM_001127396.2;STXBP2,missense_variant,p.Phe52Leu,ENST00000600702,;STXBP2,downstream_gene_variant,,ENST00000612033,;STXBP2,upstream_gene_variant,,ENST00000602355,;STXBP2,downstream_gene_variant,,ENST00000595950,;STXBP2,downstream_gene_variant,,ENST00000593535,;STXBP2,3_prime_UTR_variant,,ENST00000599737,;STXBP2,non_coding_transcript_exon_variant,,ENST00000594221,;STXBP2,non_coding_transcript_exon_variant,,ENST00000595861,;STXBP2,intron_variant,,ENST00000597068,;STXBP2,upstream_gene_variant,,ENST00000595800,;STXBP2,downstream_gene_variant,,ENST00000597467,;STXBP2,upstream_gene_variant,,ENST00000599400,;CTD-3214H19.4,downstream_gene_variant,,ENST00000595866,;STXBP2,upstream_gene_variant,,ENST00000601061,;STXBP2,upstream_gene_variant,,ENST00000593854,;STXBP2,downstream_gene_variant,,ENST00000595181,;STXBP2,downstream_gene_variant,,ENST00000599905,;CTD-3214H19.4,downstream_gene_variant,,ENST00000599243,;CTD-3214H19.4,downstream_gene_variant,,ENST00000598664,;STXBP2,downstream_gene_variant,,ENST00000599648,;STXBP2,upstream_gene_variant,,ENST00000599558,;STXBP2,upstream_gene_variant,,ENST00000599278,; G ENST00000441779 Transcript missense_variant 1141/1914 1104/1815 368/604 F/L ttC/ttG 1 1 STXBP2 HGNC HGNC:11445 protein_coding YES CCDS62522.1 ENSP00000413606 Q15833 UPI0001AE6405 NM_001272034.1 deleterious(0) 13/19 hmmpanther:PTHR11679:SF27,hmmpanther:PTHR11679,PIRSF_domain:PIRSF005715,Pfam_domain:PF00995,Gene3D:3.90.830.10,Superfamily_domains:SSF56815 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 7643209 7643209 C G 1 0 0 0 0 1 0 0 0 15737 825 29 4 4 STXBP2 19 7643209 Missense_Mutation SNP C C3N-00294_T 4162 7643209 50974407 1106 13878 CLEC4G 0 . GRCh38 19 7729924 7729924 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.640C>G p.Arg214Gly p.R214G ENST00000328853 8/9 209 177 32 210 210 0 strelka-varscan-mutect CLEC4G,missense_variant,p.Arg214Gly,ENST00000328853,NM_198492.3,NM_001244856.1;CLEC4G,downstream_gene_variant,,ENST00000599020,;CLEC4G,downstream_gene_variant,,ENST00000598081,; C ENST00000328853 Transcript missense_variant 709/1360 640/882 214/293 R/G Cgg/Ggg 1 -1 CLEC4G HGNC HGNC:24591 protein_coding YES CCDS12185.1 ENSP00000327599 Q6UXB4 Q08G24 UPI000004C65D NM_198492.3,NM_001244856.1 tolerated(0.05) 8/9 PROSITE_profiles:PS50041,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF245,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs1346519848 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 46 7729924 7729924 G C 1 0 0 0 0 1 0 0 0 3285 1057 37 4 4 CLEC4G 19 7729924 Missense_Mutation SNP G C3N-00294_T 86715 7729924 50887692 1107 13879 CLEC4G 0 . GRCh38 19 7730164 7730164 + Missense_Mutation SNP G G C rs755178489 C3N-00294_T C3N-00294_N G G c.482C>G p.Ser161Cys p.S161C ENST00000328853 7/9 116 94 22 120 120 0 strelka-varscan-mutect CLEC4G,missense_variant,p.Ser161Cys,ENST00000328853,NM_198492.3,NM_001244856.1;CLEC4G,downstream_gene_variant,,ENST00000599020,;CLEC4G,downstream_gene_variant,,ENST00000598081,; C ENST00000328853 Transcript missense_variant 551/1360 482/882 161/293 S/C tCc/tGc rs755178489,COSM4496790 1 -1 CLEC4G HGNC HGNC:24591 protein_coding YES CCDS12185.1 ENSP00000327599 Q6UXB4 Q08G24 UPI000004C65D NM_198492.3,NM_001244856.1 deleterious(0) 7/9 hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF245,Gene3D:3.10.100.10,Superfamily_domains:SSF56436 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755178489 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 7730164 7730164 G C 1 0 0 0 0 1 0 0 0 3285 1188 41 4 4 CLEC4G 19 7730164 Missense_Mutation SNP G C3N-00294_T 240 7730164 50887452 1108 13880 CLEC4M 0 . GRCh38 19 7766799 7766799 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.928G>A p.Glu310Lys p.E310K ENST00000327325 5/7 169 135 34 145 145 0 strelka-varscan-mutect CLEC4M,missense_variant,p.Glu310Lys,ENST00000327325,NM_001144909.1,NM_001144905.1,NM_001144910.1,NM_014257.4;CLEC4M,missense_variant,p.Glu298Lys,ENST00000394122,;CLEC4M,missense_variant,p.Glu287Lys,ENST00000248228,;CLEC4M,missense_variant,p.Glu259Lys,ENST00000334806,NM_001144904.1;CLEC4M,missense_variant,p.Glu243Lys,ENST00000359059,NM_001144907.1;CLEC4M,missense_variant,p.Glu282Lys,ENST00000596363,NM_001144911.1;CLEC4M,missense_variant,p.Glu243Lys,ENST00000596707,;CLEC4M,missense_variant,p.Glu282Lys,ENST00000595751,;CLEC4M,missense_variant,p.Glu218Lys,ENST00000597522,NM_001144908.1;CLEC4M,missense_variant,p.Glu174Lys,ENST00000595496,NM_001144906.1;CLEC4M,non_coding_transcript_exon_variant,,ENST00000601089,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000598879,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000599333,;CLEC4M,non_coding_transcript_exon_variant,,ENST00000602143,; A ENST00000327325 Transcript missense_variant 1046/1935 928/1200 310/399 E/K Gag/Aag 1 1 CLEC4M HGNC HGNC:13523 protein_coding YES CCDS12187.1 ENSP00000316228 Q9H2X3 UPI0000073C48 NM_001144909.1,NM_001144905.1,NM_001144910.1,NM_014257.4 deleterious(0) 5/7 PROSITE_profiles:PS50041,hmmpanther:PTHR22802:SF244,hmmpanther:PTHR22802,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 7766799 7766799 G A 1 0 0 0 0 1 0 0 0 3286 1291 45 3 3 CLEC4M 19 7766799 Missense_Mutation SNP G C3N-00294_T 36635 7766799 50850817 1109 13881 MUC16 0 . GRCh38 19 8951368 8951368 + Missense_Mutation SNP T T G novel C3N-00294_T C3N-00294_N T T c.25402A>C p.Thr8468Pro p.T8468P ENST00000397910 3/84 308 208 100 286 286 0 strelka-varscan-mutect MUC16,missense_variant,p.Thr8468Pro,ENST00000397910,NM_024690.2; G ENST00000397910 Transcript missense_variant 25606/43816 25402/43524 8468/14507 T/P Acc/Ccc 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 8951368 8951368 T G 1 0 0 0 0 1 0 0 0 9972 1696 59 5 5 MUC16 19 8951368 Missense_Mutation SNP T C3N-00294_T 1184569 8951368 49666248 1110 13882 MUC16 0 . GRCh38 19 8965298 8965298 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.11472T>A p.His3824Gln p.H3824Q ENST00000397910 3/84 75 32 43 68 68 0 strelka-varscan-mutect MUC16,missense_variant,p.His3824Gln,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 11676/43816 11472/43524 3824/14507 H/Q caT/caA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 8965298 8965298 A T 1 0 0 0 0 1 0 0 0 9972 330 12 4 4 MUC16 19 8965298 Missense_Mutation SNP A C3N-00294_T 13930 8965298 49652318 1111 13883 MUC16 0 . GRCh38 19 8972219 8972219 + Nonsense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.8920G>T p.Glu2974Ter p.E2974* ENST00000397910 1/84 206 165 41 167 167 0 strelka-varscan-mutect MUC16,stop_gained,p.Glu2974Ter,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript stop_gained 9124/43816 8920/43524 2974/14507 E/* Gaa/Taa COSM5588339,COSM5588340 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 8972219 8972219 C A 1 0 0 0 0 0 1 0 0 9972 835 29 2 2 MUC16 19 8972219 Nonsense_Mutation SNP C C3N-00294_T 6921 8972219 49645397 1112 13884 OR1M1 0 . GRCh38 19 9093583 9093583 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.339C>A p.= p.V113V ENST00000429566 1/1 339 289 50 300 300 0 strelka-varscan-mutect OR1M1,synonymous_variant,p.=,ENST00000429566,NM_001004456.1; A ENST00000429566 Transcript synonymous_variant 405/1035 339/942 113/313 V gtC/gtA 1 1 OR1M1 HGNC HGNC:8220 protein_coding YES CCDS32896.1 ENSP00000401966 Q8NGA1 UPI0000041C29 NM_001004456.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF295,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs1299971830 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 9093583 9093583 C A 1 0 0 0 0 0 0 0 1 11046 813 29 2 2 OR1M1 19 9093583 Silent SNP C C3N-00294_T 121364 9093583 49524033 1113 13885 OR1M1 0 . GRCh38 19 9093835 9093835 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.591C>T p.= p.I197I ENST00000429566 1/1 450 373 77 388 388 0 strelka-varscan-mutect OR1M1,synonymous_variant,p.=,ENST00000429566,NM_001004456.1; T ENST00000429566 Transcript synonymous_variant 657/1035 591/942 197/313 I atC/atT 1 1 OR1M1 HGNC HGNC:8220 protein_coding YES CCDS32896.1 ENSP00000401966 Q8NGA1 UPI0000041C29 NM_001004456.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF295,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 9093835 9093835 C T 1 0 0 0 0 0 0 0 1 11046 903 32 3 3 OR1M1 19 9093835 Silent SNP C C3N-00294_T 252 9093835 49523781 1114 13886 COL5A3 0 . GRCh38 19 9960865 9960865 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.4877C>G p.Ser1626Cys p.S1626C ENST00000264828 66/67 195 151 44 260 260 0 strelka-varscan-mutect COL5A3,missense_variant,p.Ser1626Cys,ENST00000264828,NM_015719.3; C ENST00000264828 Transcript missense_variant 4963/6174 4877/5238 1626/1745 S/C tCc/tGc 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 deleterious(0.01) 66/67 PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516,Pfam_domain:PF01410,SMART_domains:SM00038 MODERATE 1 SNV 1 1 PASS rs1396865274 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 9960865 9960865 G C 1 0 0 0 0 1 0 0 0 3487 1174 41 4 4 COL5A3 19 9960865 Missense_Mutation SNP G C3N-00294_T 867030 9960865 48656751 1115 13887 COL5A3 0 . GRCh38 19 9996478 9996478 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.1377C>G p.= p.V459V ENST00000264828 13/67 196 150 46 186 186 0 strelka-varscan-mutect COL5A3,synonymous_variant,p.=,ENST00000264828,NM_015719.3;CTD-2553C6.1,non_coding_transcript_exon_variant,,ENST00000592332,; C ENST00000264828 Transcript synonymous_variant 1463/6174 1377/5238 459/1745 V gtC/gtG 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 13/67 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 9996478 9996478 G C 1 0 0 0 0 0 0 0 1 3487 929 33 4 4 COL5A3 19 9996478 Silent SNP G C3N-00294_T 35613 9996478 48621138 1116 13888 KRI1 0 . GRCh38 19 10559908 10559908 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.847G>C p.Val283Leu p.V283L ENST00000312962 10/19 164 127 37 169 169 0 strelka-varscan-mutect KRI1,missense_variant,p.Val283Leu,ENST00000312962,NM_023008.3;KRI1,missense_variant,p.Val165Leu,ENST00000432197,;KRI1,intron_variant,,ENST00000539027,;KRI1,downstream_gene_variant,,ENST00000543682,;KRI1,non_coding_transcript_exon_variant,,ENST00000618579,;KRI1,downstream_gene_variant,,ENST00000537964,;KRI1,non_coding_transcript_exon_variant,,ENST00000536689,;KRI1,non_coding_transcript_exon_variant,,ENST00000612875,;KRI1,non_coding_transcript_exon_variant,,ENST00000478863,;KRI1,non_coding_transcript_exon_variant,,ENST00000537363,;KRI1,upstream_gene_variant,,ENST00000536714,;KRI1,downstream_gene_variant,,ENST00000546063,;KRI1,upstream_gene_variant,,ENST00000537433,;KRI1,upstream_gene_variant,,ENST00000543842,;KRI1,downstream_gene_variant,,ENST00000544397,; G ENST00000312962 Transcript missense_variant 867/3023 847/2130 283/709 V/L Gtg/Ctg 1 -1 KRI1 HGNC HGNC:25769 protein_coding YES CCDS12242.1 ENSP00000320917 Q8N9T8 UPI0000246DCC NM_023008.3 tolerated(0.12) 10/19 hmmpanther:PTHR14490 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 10559908 10559908 C G 1 0 0 0 0 1 0 0 0 8326 478 17 4 4 KRI1 19 10559908 Missense_Mutation SNP C C3N-00294_T 563430 10559908 48057708 1117 13889 ILF3 0 . GRCh38 19 10683942 10683942 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.2043C>T p.= p.Y681Y ENST00000449870 17/20 99 74 25 96 96 0 strelka-varscan-mutect ILF3,synonymous_variant,p.=,ENST00000449870,NM_017620.2;ILF3,synonymous_variant,p.=,ENST00000592763,;ILF3,synonymous_variant,p.=,ENST00000407004,NM_001137673.1;ILF3,synonymous_variant,p.=,ENST00000590261,NM_012218.3;ILF3,synonymous_variant,p.=,ENST00000250241,NM_153464.2;ILF3,synonymous_variant,p.=,ENST00000588657,;ILF3,synonymous_variant,p.=,ENST00000589998,NM_004516.3;ILF3,synonymous_variant,p.=,ENST00000590869,;ILF3,synonymous_variant,p.=,ENST00000593061,;ILF3,downstream_gene_variant,,ENST00000590009,;ILF3,upstream_gene_variant,,ENST00000586544,;ILF3,non_coding_transcript_exon_variant,,ENST00000587928,;ILF3,upstream_gene_variant,,ENST00000591649,;ILF3,downstream_gene_variant,,ENST00000585835,;ILF3,downstream_gene_variant,,ENST00000587505,;ILF3,downstream_gene_variant,,ENST00000589416,;ILF3,downstream_gene_variant,,ENST00000587840,;ILF3,downstream_gene_variant,,ENST00000589052,;ILF3,downstream_gene_variant,,ENST00000589485,;ILF3,downstream_gene_variant,,ENST00000589173,; T ENST00000449870 Transcript synonymous_variant 2360/6119 2043/2697 681/898 Y taC/taT COSM1589644,COSM990669 1 1 ILF3 HGNC HGNC:6038 protein_coding YES CCDS45965.1 ENSP00000404121 Q12906 UPI000059D66A NM_017620.2 17/20 Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS rs1234258543 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 10683942 10683942 C T 1 0 0 0 0 0 0 0 1 7615 547 19 1 1 ILF3 19 10683942 Silent SNP C C3N-00294_T 124034 10683942 47933674 1118 13890 C19orf38 0 . GRCh38 19 10859922 10859922 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.469G>A p.Glu157Lys p.E157K ENST00000397820 5/7 143 114 29 148 148 0 strelka-varscan-mutect C19orf38,missense_variant,p.Glu157Lys,ENST00000397820,NM_001136482.1;C19orf38,missense_variant,p.Glu157Lys,ENST00000592854,;C19orf38,non_coding_transcript_exon_variant,,ENST00000587494,; A ENST00000397820 Transcript missense_variant 576/1223 469/693 157/230 E/K Gaa/Aaa 1 1 C19orf38 HGNC HGNC:34073 protein_coding YES CCDS45970.1 ENSP00000380920 A8MVS5 UPI0000160991 NM_001136482.1 deleterious(0.01) 5/7 hmmpanther:PTHR36859 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 10859922 10859922 G A 1 0 0 0 0 1 0 0 0 1909 943 33 3 3 C19orf38 19 10859922 Missense_Mutation SNP G C3N-00294_T 175980 10859922 47757694 1119 13891 SPC24 0 . GRCh38 19 11155694 11155694 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.83G>A p.Arg28Gln p.R28Q ENST00000592540 1/5 156 124 32 156 156 0 strelka-varscan-mutect SPC24,missense_variant,p.Arg28Gln,ENST00000592540,NM_182513.2;SPC24,missense_variant,p.Arg25Gln,ENST00000592967,;SPC24,missense_variant,p.Arg24Gln,ENST00000591396,;SPC24,missense_variant,p.Arg26Gln,ENST00000585486,NM_001317032.1;SPC24,missense_variant,p.Arg28Gln,ENST00000585567,;SPC24,missense_variant,p.Arg23Gln,ENST00000586708,;SPC24,missense_variant,p.Arg28Gln,ENST00000423327,; T ENST00000592540 Transcript missense_variant 115/2315 83/594 28/197 R/Q cGa/cAa 1 -1 SPC24 HGNC HGNC:26913 protein_coding YES CCDS45974.1 ENSP00000465075 Q8NBT2 UPI000007312F NM_182513.2 deleterious(0.02) 1/5 hmmpanther:PTHR22142:SF2,hmmpanther:PTHR22142 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 11155694 11155694 C T 1 0 0 0 0 1 0 0 0 15367 884 31 1 1 SPC24 19 11155694 Missense_Mutation SNP C C3N-00294_T 295772 11155694 47461922 1120 13892 ECSIT 0 . GRCh38 19 11514152 11514152 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.166C>T p.Pro56Ser p.P56S ENST00000270517 3/8 82 62 20 108 108 0 strelka-varscan-mutect ECSIT,missense_variant,p.Pro56Ser,ENST00000270517,NM_016581.4;ECSIT,missense_variant,p.Pro56Ser,ENST00000252440,NM_001142464.2;ECSIT,missense_variant,p.Pro56Ser,ENST00000591104,NM_001243204.1;ECSIT,missense_variant,p.Pro56Ser,ENST00000590480,;ECSIT,5_prime_UTR_variant,,ENST00000592312,;ECSIT,5_prime_UTR_variant,,ENST00000585318,;ECSIT,5_prime_UTR_variant,,ENST00000592665,;ECSIT,intron_variant,,ENST00000417981,NM_001142465.2;ECSIT,intron_variant,,ENST00000588998,;ECSIT,downstream_gene_variant,,ENST00000586149,;RN7SL833P,downstream_gene_variant,,ENST00000498758,;ECSIT,upstream_gene_variant,,ENST00000591352,;ECSIT,upstream_gene_variant,,ENST00000592571,;ECSIT,upstream_gene_variant,,ENST00000593231,; A ENST00000270517 Transcript missense_variant 302/1700 166/1296 56/431 P/S Ccc/Tcc 1 -1 ECSIT HGNC HGNC:29548 protein_coding YES CCDS12262.1 ENSP00000270517 Q9BQ95 UPI0000072F31 NM_016581.4 tolerated(0.14) 3/8 hmmpanther:PTHR13113,Pfam_domain:PF06239 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 11514152 11514152 G A 1 0 0 0 0 1 0 0 0 4728 1174 41 3 3 ECSIT 19 11514152 Missense_Mutation SNP G C3N-00294_T 358458 11514152 47103464 1121 13893 ZNF443 0 . GRCh38 19 12431883 12431883 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.289C>G p.Leu97Val p.L97V ENST00000301547 4/4 92 78 14 122 122 0 strelka-varscan-mutect ZNF443,missense_variant,p.Leu97Val,ENST00000301547,NM_005815.4;CTD-3105H18.16,intron_variant,,ENST00000595562,;ZNF443,3_prime_UTR_variant,,ENST00000436821,;CTD-3105H18.18,downstream_gene_variant,,ENST00000598753,; C ENST00000301547 Transcript missense_variant 487/2663 289/2016 97/671 L/V Ctt/Gtt 1 -1 ZNF443 HGNC HGNC:20878 protein_coding YES CCDS32918.1 ENSP00000301547 Q9Y2A4 UPI000020344A NM_005815.4 tolerated(0.5) 4/4 hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF16 MODERATE 1 SNV 1 1 PASS rs1191248159 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 12431883 12431883 G C 1 0 0 0 0 1 0 0 0 18487 942 33 4 4 ZNF443 19 12431883 Missense_Mutation SNP G C3N-00294_T 917731 12431883 46185733 1122 13894 IL27RA 0 . GRCh38 19 14049073 14049073 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1234G>T p.Glu412Ter p.E412* ENST00000263379 9/14 126 92 34 133 133 0 strelka-varscan-mutect IL27RA,stop_gained,p.Glu412Ter,ENST00000263379,NM_004843.3;PALM3,downstream_gene_variant,,ENST00000340790,NM_001145028.1; T ENST00000263379 Transcript stop_gained 1359/2962 1234/1911 412/636 E/* Gag/Tag 1 1 IL27RA HGNC HGNC:17290 protein_coding YES CCDS12303.1 ENSP00000263379 Q6UWB1 UPI0000039E1F NM_004843.3 9/14 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF6,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 14049073 14049073 G T 1 0 0 0 0 0 1 0 0 7584 1175 41 2 2 IL27RA 19 14049073 Nonsense_Mutation SNP G C3N-00294_T 1617190 14049073 44568543 1123 13895 PALM3 0 . GRCh38 19 14053871 14053871 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1756G>A p.Glu586Lys p.E586K ENST00000340790 6/6 175 155 20 154 154 0 strelka-mutect PALM3,missense_variant,p.Glu586Lys,ENST00000340790,NM_001145028.1;IL27RA,downstream_gene_variant,,ENST00000263379,NM_004843.3;PALM3,downstream_gene_variant,,ENST00000589048,;PALM3,downstream_gene_variant,,ENST00000586368,; T ENST00000340790 Transcript missense_variant 1756/2262 1756/2022 586/673 E/K Gag/Aag 1 -1 PALM3 HGNC HGNC:33274 protein_coding YES CCDS46001.1 ENSP00000344996 A6NDB9 UPI0001662AC1 NM_001145028.1 tolerated(0.09) 6/6 hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF13 MODERATE SNV 5 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999884 1 1 1 0 T 3 4 46 14053871 14053871 C T 1 0 0 0 0 1 0 0 0 11490 864 30 3 3 PALM3 19 14053871 Missense_Mutation SNP C C3N-00294_T 4798 14053871 44563745 1124 13896 NOTCH3 0 . GRCh38 19 15174259 15174259 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.4545C>T p.= p.L1515L ENST00000263388 25/33 247 206 41 212 212 0 strelka-varscan-mutect NOTCH3,synonymous_variant,p.=,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,upstream_gene_variant,,ENST00000595514,;NOTCH3,downstream_gene_variant,,ENST00000595045,; A ENST00000263388 Transcript synonymous_variant 4621/8666 4545/6966 1515/2321 L ctC/ctT 1 -1 NOTCH3 HGNC HGNC:7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 25/33 Pfam_domain:PF06816,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF57,Low_complexity_(Seg):seg,SMART_domains:SM01338 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 15174259 15174259 G A 1 0 0 0 0 0 0 0 1 10595 1277 45 3 3 NOTCH3 19 15174259 Silent SNP G C3N-00294_T 1120388 15174259 43443357 1125 13897 BRD4 0 . GRCh38 19 15239100 15239100 + Silent SNP G G A rs367944319 C3N-00294_T C3N-00294_N G G c.3741C>T p.= p.H1247H ENST00000263377 18/20 93 66 27 114 114 0 strelka-varscan-mutect BRD4,synonymous_variant,p.=,ENST00000263377,NM_058243.2; A ENST00000263377 Transcript synonymous_variant 3963/7169 3741/4089 1247/1362 H caC/caT rs367944319 1 -1 BRD4 HGNC HGNC:13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 UPI0000126ACE NM_058243.2 18/20 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs367944319 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 15239100 15239100 G A 1 0 0 0 0 0 0 0 1 1674 1136 40 1 1 BRD4 19 15239100 Silent SNP G C3N-00294_T 64841 15239100 43378516 1126 13898 CYP4F12 0 . GRCh38 19 15697032 15697032 + Missense_Mutation SNP G G A rs189002430 C3N-00294_T C3N-00294_N G G c.1522G>A p.Ala508Thr p.A508T ENST00000550308 13/13 175 133 42 190 189 1 strelka-varscan-mutect CYP4F12,missense_variant,p.Ala508Thr,ENST00000550308,NM_023944.3;CYP4F12,missense_variant,p.Ala508Thr,ENST00000324632,;CYP4F12,3_prime_UTR_variant,,ENST00000517734,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000546608,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000550627,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000518629,; A ENST00000550308 Transcript missense_variant 1902/2044 1522/1575 508/524 A/T Gcc/Acc rs189002430,COSM181661 1 1 CYP4F12 HGNC HGNC:18857 protein_coding YES CCDS42517.1 ENSP00000448998 A0A0A0MR49 UPI00020B9EFD NM_023944.3 tolerated(0.18) 13/13 hmmpanther:PTHR24291:SF27,hmmpanther:PTHR24291,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs189002430 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 15697032 15697032 G A 1 0 0 0 0 1 0 0 0 3990 1087 38 1 1 CYP4F12 19 15697032 Missense_Mutation SNP G C3N-00294_T 457932 15697032 42920584 1127 13899 CYP4F11 0 . GRCh38 19 15914779 15914779 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1232G>C p.Gly411Ala p.G411A ENST00000402119 9/12 157 124 33 132 132 0 strelka-varscan-mutect CYP4F11,missense_variant,p.Gly411Ala,ENST00000402119,NM_021187.3;CYP4F11,missense_variant,p.Gly411Ala,ENST00000248041,NM_001128932.1;CYP4F11,missense_variant,p.Gly411Ala,ENST00000620614,;CYP4F11,missense_variant,p.Gly411Ala,ENST00000326742,;CYP4F11,missense_variant,p.Gly86Ala,ENST00000591841,;AC005336.4,upstream_gene_variant,,ENST00000585431,; G ENST00000402119 Transcript missense_variant 1659/3161 1232/1575 411/524 G/A gGc/gCc 1 -1 CYP4F11 HGNC HGNC:13265 protein_coding YES CCDS12337.1 ENSP00000384588 Q9HBI6 UPI000013CC35 NM_021187.3 deleterious(0) 9/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF16,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 15914779 15914779 C G 1 0 0 0 0 1 0 0 0 3989 739 26 4 4 CYP4F11 19 15914779 Missense_Mutation SNP C C3N-00294_T 217747 15914779 42702837 1128 13900 MYO9B 0 . GRCh38 19 17185996 17185996 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2572G>C p.Glu858Gln p.E858Q ENST00000595618 18/40 184 137 47 216 216 0 strelka-varscan-mutect MYO9B,missense_variant,p.Glu858Gln,ENST00000595618,NM_001130065.1;MYO9B,missense_variant,p.Glu858Gln,ENST00000594824,NM_004145.3;MYO9B,missense_variant,p.Glu858Gln,ENST00000397274,;MYO9B,missense_variant,p.Glu858Gln,ENST00000595641,;MYO9B,missense_variant,p.Glu150Gln,ENST00000602177,;MYO9B,downstream_gene_variant,,ENST00000594971,;MYO9B,non_coding_transcript_exon_variant,,ENST00000601749,;MYO9B,non_coding_transcript_exon_variant,,ENST00000601490,;MYO9B,downstream_gene_variant,,ENST00000598101,;MYO9B,downstream_gene_variant,,ENST00000598464,; C ENST00000595618 Transcript missense_variant 2724/7623 2572/6069 858/2022 E/Q Gaa/Caa 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 tolerated(0.13) 18/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1232569221 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 17185996 17185996 G C 1 0 0 0 0 1 0 0 0 10086 1304 45 4 4 MYO9B 19 17185996 Missense_Mutation SNP G C3N-00294_T 1271217 17185996 41431620 1129 13901 MYO9B 0 . GRCh38 19 17202202 17202202 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.4735G>A p.Glu1579Lys p.E1579K ENST00000595618 28/40 188 157 31 215 215 0 strelka-varscan-mutect MYO9B,missense_variant,p.Glu1579Lys,ENST00000595618,NM_001130065.1;MYO9B,missense_variant,p.Glu1579Lys,ENST00000594824,NM_004145.3;MYO9B,missense_variant,p.Glu1579Lys,ENST00000397274,;MYO9B,missense_variant,p.Glu1579Lys,ENST00000595641,;MYO9B,upstream_gene_variant,,ENST00000597073,;MYO9B,upstream_gene_variant,,ENST00000596942,;CTD-3032J10.3,downstream_gene_variant,,ENST00000601929,;MYO9B,non_coding_transcript_exon_variant,,ENST00000593533,;MYO9B,non_coding_transcript_exon_variant,,ENST00000599420,;MYO9B,upstream_gene_variant,,ENST00000602158,; A ENST00000595618 Transcript missense_variant 4887/7623 4735/6069 1579/2022 E/K Gag/Aag COSM3285573,COSM3285574 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 tolerated(0.2) 28/40 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1223943947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 17202202 17202202 G A 1 0 0 0 0 1 0 0 0 10086 1291 45 3 3 MYO9B 19 17202202 Missense_Mutation SNP G C3N-00294_T 16206 17202202 41415414 1130 13902 USHBP1 0 . GRCh38 19 17260019 17260019 + Missense_Mutation SNP G G C rs200391216 C3N-00294_T C3N-00294_N G G c.646C>G p.Gln216Glu p.Q216E ENST00000252597 5/13 87 64 23 81 81 0 strelka-varscan-mutect USHBP1,missense_variant,p.Gln216Glu,ENST00000252597,NM_031941.3;USHBP1,missense_variant,p.Gln152Glu,ENST00000431146,NM_001297703.1;USHBP1,downstream_gene_variant,,ENST00000594190,;USHBP1,downstream_gene_variant,,ENST00000598309,;AC010646.3,upstream_gene_variant,,ENST00000594059,;USHBP1,downstream_gene_variant,,ENST00000598570,;USHBP1,downstream_gene_variant,,ENST00000595993,;USHBP1,missense_variant,p.Gln216Glu,ENST00000324554,;USHBP1,3_prime_UTR_variant,,ENST00000597928,;USHBP1,downstream_gene_variant,,ENST00000600286,;USHBP1,downstream_gene_variant,,ENST00000596436,; C ENST00000252597 Transcript missense_variant 820/3335 646/2112 216/703 Q/E Caa/Gaa rs200391216 1 -1 USHBP1 HGNC HGNC:24058 protein_coding YES CCDS12353.1 ENSP00000252597 Q8N6Y0 A0A024R7H3 UPI000006F7A8 NM_031941.3 deleterious(0.03) 5/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23347:SF5,hmmpanther:PTHR23347 MODERATE 1 SNV 1 1 PASS rs200391216 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 17260019 17260019 G C 1 0 0 0 0 1 0 0 0 17571 1304 45 4 4 USHBP1 19 17260019 Missense_Mutation SNP G C3N-00294_T 57817 17260019 41357597 1131 13903 PGLS 0 . GRCh38 19 17511710 17511710 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.38C>G p.Ser13Trp p.S13W ENST00000252603 1/5 134 114 20 116 116 0 strelka-varscan-mutect PGLS,missense_variant,p.Ser13Trp,ENST00000252603,NM_012088.2;PGLS,missense_variant,p.Ser13Trp,ENST00000600923,;PGLS,upstream_gene_variant,,ENST00000595782,;CTD-3131K8.2,non_coding_transcript_exon_variant,,ENST00000596643,;CTD-3131K8.2,upstream_gene_variant,,ENST00000615939,;CTD-3131K8.2,upstream_gene_variant,,ENST00000595116,;PGLS,missense_variant,p.Ser13Trp,ENST00000594761,;PGLS,non_coding_transcript_exon_variant,,ENST00000596799,;PGLS,upstream_gene_variant,,ENST00000598811,; G ENST00000252603 Transcript missense_variant 82/1028 38/777 13/258 S/W tCg/tGg 1 1 PGLS HGNC HGNC:8903 protein_coding YES CCDS12361.1 ENSP00000252603 O95336 A0A0K0K1K7 UPI0000124F8A NM_012088.2 deleterious(0) 1/5 Gene3D:3.40.50.1360,hmmpanther:PTHR11054,hmmpanther:PTHR11054:SF6,Superfamily_domains:SSF100950,TIGRFAM_domain:TIGR01198 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999936 1 1 1 0 G 3 3 46 17511710 17511710 C G 1 0 0 0 0 1 0 0 0 11881 893 31 4 4 PGLS 19 17511710 Missense_Mutation SNP C C3N-00294_T 251691 17511710 41105906 1132 13904 MAP1S 0 . GRCh38 19 17726492 17726492 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1108C>G p.Leu370Val p.L370V ENST00000324096 5/7 409 332 77 413 413 0 strelka-varscan-mutect MAP1S,missense_variant,p.Leu370Val,ENST00000324096,NM_018174.4;MAP1S,missense_variant,p.Leu344Val,ENST00000544059,NM_001308363.1;MAP1S,intron_variant,,ENST00000597735,;MAP1S,downstream_gene_variant,,ENST00000600186,;MAP1S,downstream_gene_variant,,ENST00000594625,;MAP1S,upstream_gene_variant,,ENST00000597000,;CTD-3149D2.4,downstream_gene_variant,,ENST00000595363,;MAP1S,intron_variant,,ENST00000597681,;MAP1S,downstream_gene_variant,,ENST00000601544,;MAP1S,downstream_gene_variant,,ENST00000599494,;MAP1S,upstream_gene_variant,,ENST00000598756,;MAP1S,downstream_gene_variant,,ENST00000594340,;MAP1S,downstream_gene_variant,,ENST00000595338,;MAP1S,downstream_gene_variant,,ENST00000598916,;MAP1S,downstream_gene_variant,,ENST00000597067,;MAP1S,3_prime_UTR_variant,,ENST00000594212,;MAP1S,downstream_gene_variant,,ENST00000594365,;MAP1S,downstream_gene_variant,,ENST00000598769,;MAP1S,downstream_gene_variant,,ENST00000596637,;MAP1S,downstream_gene_variant,,ENST00000593593,;MAP1S,downstream_gene_variant,,ENST00000600608,; G ENST00000324096 Transcript missense_variant 1259/3419 1108/3180 370/1059 L/V Ctg/Gtg 1 1 MAP1S HGNC HGNC:15715 protein_coding YES CCDS32954.1 ENSP00000325313 Q66K74 UPI00002036F9 NM_018174.4 tolerated(0.82) 5/7 hmmpanther:PTHR13843 MODERATE 1 SNV 1 1 PASS rs1227489354 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 17726492 17726492 C G 1 0 0 0 0 1 0 0 0 9156 912 32 4 4 MAP1S 19 17726492 Missense_Mutation SNP C C3N-00294_T 214782 17726492 40891124 1133 13905 COPE 0 . GRCh38 19 18913034 18913034 + Missense_Mutation SNP C C G rs11537885 C3N-00294_T C3N-00294_N C C c.139G>C p.Glu47Gln p.E47Q ENST00000262812 2/10 151 127 24 166 166 0 strelka-varscan-mutect COPE,missense_variant,p.Glu47Gln,ENST00000600932,;COPE,missense_variant,p.Glu47Gln,ENST00000262812,NM_007263.3;COPE,missense_variant,p.Glu47Gln,ENST00000349893,NM_199444.1;COPE,missense_variant,p.Glu47Gln,ENST00000351079,NM_199442.1;COPE,non_coding_transcript_exon_variant,,ENST00000598969,;COPE,non_coding_transcript_exon_variant,,ENST00000597646,;COPE,non_coding_transcript_exon_variant,,ENST00000599964,;COPE,missense_variant,p.Glu47Gln,ENST00000593827,;AC002985.3,3_prime_UTR_variant,,ENST00000596918,;AC002985.3,3_prime_UTR_variant,,ENST00000593484,;COPE,non_coding_transcript_exon_variant,,ENST00000597026,; G ENST00000262812 Transcript missense_variant 188/1141 139/927 47/308 E/Q Gag/Cag rs11537885 1 -1 COPE HGNC HGNC:2234 protein_coding YES CCDS12387.1 ENSP00000262812 O14579 UPI000013D334 NM_007263.3 tolerated(0.11) 2/10 Pfam_domain:PF04733,PIRSF_domain:PIRSF016478,hmmpanther:PTHR10805 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 18913034 18913034 C G 1 0 0 0 0 1 0 0 0 3522 922 32 4 4 COPE 19 18913034 Missense_Mutation SNP C C3N-00294_T 1186542 18913034 39704582 1134 13906 CILP2 0 . GRCh38 19 19538388 19538388 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.39C>A p.= p.V13V ENST00000291495 1/8 124 96 28 127 127 0 strelka-varscan-mutect CILP2,synonymous_variant,p.=,ENST00000586018,;CILP2,synonymous_variant,p.=,ENST00000291495,NM_153221.2;CTC-260F20.3,downstream_gene_variant,,ENST00000555938,;YJEFN3,downstream_gene_variant,,ENST00000514277,NM_198537.3;YJEFN3,downstream_gene_variant,,ENST00000436027,NM_001190328.1;CTC-260F20.3,downstream_gene_variant,,ENST00000586674,;CILP2,upstream_gene_variant,,ENST00000588333,;YJEFN3,downstream_gene_variant,,ENST00000458210,; A ENST00000291495 Transcript synonymous_variant 124/4199 39/3471 13/1156 V gtC/gtA 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 1/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 19538388 19538388 C A 1 0 0 0 0 0 0 0 1 3192 871 31 1 1 CILP2 19 19538388 Silent SNP C C3N-00294_T 625354 19538388 39079228 1135 13907 ZNF257 0 . GRCh38 19 22088663 22088663 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.913C>G p.Gln305Glu p.Q305E ENST00000594947 4/4 219 176 43 261 261 0 strelka-varscan-mutect ZNF257,missense_variant,p.Gln305Glu,ENST00000594947,NM_033468.2;ZNF257,downstream_gene_variant,,ENST00000600162,;ZNF257,downstream_gene_variant,,ENST00000597927,;ZNF257,3_prime_UTR_variant,,ENST00000435820,NM_001316996.1; G ENST00000594947 Transcript missense_variant 1057/3874 913/1692 305/563 Q/E Caa/Gaa COSM1304324,COSM1392121,COSM4855525 1 1 ZNF257 HGNC HGNC:13498 protein_coding YES CCDS46030.1 ENSP00000470209 Q9Y2Q1 UPI0000E045CA NM_033468.2 tolerated(0.49) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF127,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1,1 MODERATE 1 SNV 4 1,1,1 1 PASS rs1348976473 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 22088663 22088663 C G 1 0 0 0 0 1 0 0 0 18376 827 29 4 4 ZNF257 19 22088663 Missense_Mutation SNP C C3N-00294_T 2550275 22088663 36528953 1136 13908 ZNF726 0 . GRCh38 19 23932393 23932393 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.277G>C p.Asp93His p.D93H ENST00000594466 4/4 24 17 7 26 26 0 strelka-varscan-mutect ZNF726,missense_variant,p.Asp93His,ENST00000594466,NM_001244038.1;ZNF726,missense_variant,p.Asp93His,ENST00000322487,;ZNF726,intron_variant,,ENST00000575986,;ZNF726,intron_variant,,ENST00000334589,;CTB-92J24.3,intron_variant,,ENST00000596326,;CTB-92J24.2,downstream_gene_variant,,ENST00000594230,;ZNF92P3,upstream_gene_variant,,ENST00000596594,; C ENST00000594466 Transcript missense_variant 382/2473 277/1851 93/616 D/H Gat/Cat 1 1 ZNF726 HGNC HGNC:32462 protein_coding YES CCDS59372.1 ENSP00000471516 A6NNF4 UPI0002255F7F NM_001244038.1 deleterious(0.01) 4/4 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF328 MODERATE SNV 5 1 PASS rs1198045649 . 1 205 4 0 0 0 0 0 -19.51867 1 1 1 1 0 C 3 2 46 23932393 23932393 G C 1 0 0 0 0 1 0 0 0 18700 942 33 4 4 ZNF726 19 23932393 Missense_Mutation SNP G C3N-00294_T 1843730 23932393 34685223 1137 13909 ANKRD27 0 . GRCh38 19 32642049 32642049 + Silent SNP G G C rs758481090 C3N-00294_T C3N-00294_N G G c.879C>G p.= p.L293L ENST00000306065 10/29 80 65 15 64 64 0 strelka-varscan-mutect ANKRD27,synonymous_variant,p.=,ENST00000306065,NM_032139.2;ANKRD27,synonymous_variant,p.=,ENST00000587352,;ANKRD27,intron_variant,,ENST00000591100,;ANKRD27,downstream_gene_variant,,ENST00000590519,;ANKRD27,downstream_gene_variant,,ENST00000586463,;ANKRD27,downstream_gene_variant,,ENST00000586693,;ANKRD27,downstream_gene_variant,,ENST00000588700,;ANKRD27,downstream_gene_variant,,ENST00000593232,; C ENST00000306065 Transcript synonymous_variant 1038/4450 879/3153 293/1050 L ctC/ctG rs758481090,COSM710419 1 -1 ANKRD27 HGNC HGNC:25310 protein_coding YES CCDS32986.1 ENSP00000304292 Q96NW4 UPI000004FDE9 NM_032139.2 10/29 PROSITE_profiles:PS51205,hmmpanther:PTHR24170,hmmpanther:PTHR24170:SF1,Pfam_domain:PF02204,SMART_domains:SM00167,Superfamily_domains:0044157 0,1 LOW 1 SNV 1 0,1 1 PASS rs758481090 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 32642049 32642049 G C 1 0 0 0 0 0 0 0 1 758 1277 45 4 4 ANKRD27 19 32642049 Silent SNP G C3N-00294_T 8709656 32642049 25975567 1138 13910 RGS9BP 0 . GRCh38 19 32676377 32676377 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.114G>C p.Gln38His p.Q38H ENST00000334176 1/1 229 183 46 243 243 0 strelka-varscan-mutect RGS9BP,missense_variant,p.Gln38His,ENST00000334176,NM_207391.2;ANKRD27,5_prime_UTR_variant,,ENST00000590519,;ANKRD27,upstream_gene_variant,,ENST00000306065,NM_032139.2;ANKRD27,upstream_gene_variant,,ENST00000587352,;ANKRD27,upstream_gene_variant,,ENST00000586463,;ANKRD27,upstream_gene_variant,,ENST00000586693,;CTC-379B2.4,downstream_gene_variant,,ENST00000589127,;ANKRD27,upstream_gene_variant,,ENST00000588700,; C ENST00000334176 Transcript missense_variant 971/2894 114/708 38/235 Q/H caG/caC 1 1 RGS9BP HGNC HGNC:30304 protein_coding YES CCDS12424.1 ENSP00000334134 Q6ZS82 UPI0000198BA8 NM_207391.2 deleterious(0) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21029,hmmpanther:PTHR21029:SF1 MODERATE SNV 1 PASS rs1275510278 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 32676377 32676377 G C 1 0 0 0 0 1 0 0 0 13485 991 35 4 4 RGS9BP 19 32676377 Missense_Mutation SNP G C3N-00294_T 34328 32676377 25941239 1139 13911 CHST8 0 . GRCh38 19 33772993 33772993 + Missense_Mutation SNP G G A C3N-00294_T C3N-00294_N G G c.1205G>A p.Arg402His p.R402H ENST00000262622 4/4 181 141 40 184 184 0 strelka-varscan-mutect CHST8,missense_variant,p.Arg402His,ENST00000262622,NM_022467.3;CHST8,missense_variant,p.Arg402His,ENST00000434302,NM_001127895.1;CHST8,missense_variant,p.Arg402His,ENST00000438847,NM_001127896.1;CHST8,downstream_gene_variant,,ENST00000591231,; A ENST00000262622 Transcript missense_variant 1963/2479 1205/1275 402/424 R/H cGc/cAc COSM4076809 1 1 CHST8 HGNC HGNC:15993 protein_coding YES CCDS12433.1 ENSP00000262622 Q9H2A9 UPI000006F966 NM_022467.3 tolerated(0.11) 4/4 Pfam_domain:PF03567,hmmpanther:PTHR12137,hmmpanther:PTHR12137:SF7 1 MODERATE 1 SNV 1 1 1 PASS rs916046058 . 0 206 0 3 0 0 0 0 -20 0.999997 1 1 1 0 A 3 1 46 33772993 33772993 G A 1 0 0 0 0 1 0 0 0 3170 1087 38 1 1 CHST8 19 33772993 Missense_Mutation SNP G C3N-00294_T 1096616 33772993 24844623 1140 13912 ZNF345 0 . GRCh38 19 36877002 36877002 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.172G>C p.Asp58His p.D58H ENST00000529555 2/2 144 108 36 166 166 0 strelka-varscan-mutect ZNF345,missense_variant,p.Asp58His,ENST00000529555,;ZNF345,missense_variant,p.Asp58His,ENST00000589046,NM_003419.4;ZNF345,missense_variant,p.Asp58His,ENST00000614069,NM_001242474.1;ZNF345,missense_variant,p.Asp58His,ENST00000612719,NM_001242476.1,NM_001242475.1;ZNF345,missense_variant,p.Asp58His,ENST00000420450,NM_001242472.1;ZNF345,missense_variant,p.Asp58His,ENST00000585396,;ZNF345,missense_variant,p.Asp58His,ENST00000532141,;ZNF345,missense_variant,p.Asp58His,ENST00000586646,;ZNF345,missense_variant,p.Asp58His,ENST00000331800,;ZNF345,intron_variant,,ENST00000586933,;ZNF345,intron_variant,,ENST00000526123,;ZNF345,intron_variant,,ENST00000432005,;ZNF345,intron_variant,,ENST00000529989,;ZNF345,intron_variant,,ENST00000525851,;ZNF345,intron_variant,,ENST00000534729,; C ENST00000529555 Transcript missense_variant 960/3527 172/1467 58/488 D/H Gat/Cat 1 1 ZNF345 HGNC HGNC:16367 protein_coding YES CCDS12497.1 ENSP00000431202 Q14585 UPI000013C364 deleterious(0.01) 2/2 Gene3D:3.30.160.60,hmmpanther:PTHR24377,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 36877002 36877002 G C 1 0 0 0 0 1 0 0 0 18431 1290 45 4 4 ZNF345 19 36877002 Missense_Mutation SNP G C3N-00294_T 3104009 36877002 21740614 1141 13913 ZNF527 0 . GRCh38 19 37388820 37388820 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.771C>T p.= p.F257F ENST00000436120 5/5 68 62 6 110 110 0 strelka-varscan-mutect ZNF527,synonymous_variant,p.=,ENST00000436120,NM_032453.1;ZNF527,intron_variant,,ENST00000587349,;ZNF527,downstream_gene_variant,,ENST00000483919,;ZNF527,downstream_gene_variant,,ENST00000588911,;ZNF527,3_prime_UTR_variant,,ENST00000356178,;ZNF527,downstream_gene_variant,,ENST00000588512,; T ENST00000436120 Transcript synonymous_variant 878/2828 771/1830 257/609 F ttC/ttT 1 1 ZNF527 HGNC HGNC:29385 protein_coding YES CCDS42559.1 ENSP00000390179 Q8NB42 UPI00002021F5 NM_032453.1 5/5 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF71,Superfamily_domains:SSF57667 LOW 1 SNV 4 1 PASS . . 0 207 3 0 0 0 0 0 -13.83568 1 1 1 1 0 T 2 4 46 37388820 37388820 C T 1 0 0 0 0 0 0 0 1 18541 854 30 3 3 ZNF527 19 37388820 Silent SNP C C3N-00294_T 511818 37388820 21228796 1142 13914 MAP4K1 0 . GRCh38 19 38609974 38609974 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.862C>G p.Leu288Val p.L288V ENST00000591517 12/32 229 194 35 236 236 0 strelka-varscan-mutect MAP4K1,missense_variant,p.Leu288Val,ENST00000591517,NM_007181.5;MAP4K1,missense_variant,p.Leu284Val,ENST00000589130,;MAP4K1,missense_variant,p.Leu288Val,ENST00000396857,NM_001042600.2;MAP4K1,missense_variant,p.Leu288Val,ENST00000586296,;MAP4K1,upstream_gene_variant,,ENST00000591921,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000589002,;MAP4K1,3_prime_UTR_variant,,ENST00000585583,;MAP4K1,downstream_gene_variant,,ENST00000591707,;MAP4K1,downstream_gene_variant,,ENST00000592888,;MAP4K1,downstream_gene_variant,,ENST00000592225,;MAP4K1,downstream_gene_variant,,ENST00000588083,; C ENST00000591517 Transcript missense_variant 891/2700 862/2502 288/833 L/V Ctt/Gtt COSM3533540,COSM3533541 1 -1 MAP4K1 HGNC HGNC:6863 protein_coding YES CCDS59385.1 ENSP00000465039 Q92918 UPI00000747ED NM_007181.5 deleterious(0.02) 12/32 hmmpanther:PTHR24361:SF88,hmmpanther:PTHR24361,PIRSF_domain:PIRSF038172 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 38609974 38609974 G C 1 0 0 0 0 1 0 0 0 9183 942 33 4 4 MAP4K1 19 38609974 Missense_Mutation SNP G C3N-00294_T 1221154 38609974 20007642 1143 13915 HNRNPL 0 . GRCh38 19 38846044 38846044 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.433G>C p.Glu145Gln p.E145Q ENST00000221419 3/13 277 223 54 259 259 0 strelka-varscan-mutect HNRNPL,missense_variant,p.Glu145Gln,ENST00000221419,NM_001533.2;HNRNPL,missense_variant,p.Glu86Gln,ENST00000601449,;HNRNPL,missense_variant,p.Glu12Gln,ENST00000600873,NM_001005335.1;HNRNPL,missense_variant,p.Glu77Gln,ENST00000600233,;HNRNPL,missense_variant,p.Glu80Gln,ENST00000601813,;AC008982.2,upstream_gene_variant,,ENST00000600473,;HNRNPL,missense_variant,p.Glu12Gln,ENST00000388749,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000601047,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000598985,;HNRNPL,non_coding_transcript_exon_variant,,ENST00000600741,;HNRNPL,upstream_gene_variant,,ENST00000597731,;HNRNPL,upstream_gene_variant,,ENST00000595164,; G ENST00000221419 Transcript missense_variant 800/2471 433/1770 145/589 E/Q Gaa/Caa 1 -1 HNRNPL HGNC HGNC:5045 protein_coding YES CCDS33015.1 ENSP00000221419 P14866 UPI00004432FA NM_001533.2 deleterious(0) 3/13 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF472,SMART_domains:SM00360,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 38846044 38846044 C G 1 0 0 0 0 1 0 0 0 7164 835 29 4 4 HNRNPL 19 38846044 Missense_Mutation SNP C C3N-00294_T 236070 38846044 19771572 1144 13916 DYRK1B 0 . GRCh38 19 39828459 39828459 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.645G>A p.= p.R215R ENST00000593685 6/11 386 306 80 482 482 0 strelka-varscan-mutect DYRK1B,synonymous_variant,p.=,ENST00000593685,;DYRK1B,synonymous_variant,p.=,ENST00000323039,NM_004714.2;DYRK1B,synonymous_variant,p.=,ENST00000348817,NM_006484.2;DYRK1B,synonymous_variant,p.=,ENST00000430012,NM_006483.2;DYRK1B,synonymous_variant,p.=,ENST00000597639,;DYRK1B,downstream_gene_variant,,ENST00000601972,;DYRK1B,downstream_gene_variant,,ENST00000600611,;MIR6719,downstream_gene_variant,,ENST00000622428,;DYRK1B,non_coding_transcript_exon_variant,,ENST00000601696,; T ENST00000593685 Transcript synonymous_variant 1114/2724 645/1890 215/629 R cgG/cgA 1 -1 DYRK1B HGNC HGNC:3092 protein_coding YES CCDS12543.1 ENSP00000469863 Q9Y463 A0A024R0I0 UPI0000001059 6/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF27,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 39828459 39828459 C T 1 0 0 0 0 0 0 0 1 4679 842 30 3 3 DYRK1B 19 39828459 Silent SNP C C3N-00294_T 982415 39828459 18789157 1145 13917 PHLDB3 0 . GRCh38 19 43502268 43502268 + Missense_Mutation SNP G G A rs536138718 C3N-00294_T C3N-00294_N G G c.229C>T p.Pro77Ser p.P77S ENST00000292140 3/16 87 70 17 127 127 0 strelka-varscan-mutect PHLDB3,missense_variant,p.Pro77Ser,ENST00000292140,NM_198850.3;PHLDB3,missense_variant,p.Pro77Ser,ENST00000599242,;PHLDB3,missense_variant,p.Pro77Ser,ENST00000594808,;PHLDB3,missense_variant,p.Pro77Ser,ENST00000601646,;ETHE1,downstream_gene_variant,,ENST00000292147,NM_014297.3;PHLDB3,upstream_gene_variant,,ENST00000600660,;PHLDB3,non_coding_transcript_exon_variant,,ENST00000596902,;ETHE1,downstream_gene_variant,,ENST00000594342,; A ENST00000292140 Transcript missense_variant 590/2591 229/1923 77/640 P/S Ccg/Tcg rs536138718 1 -1 PHLDB3 HGNC HGNC:30499 protein_coding YES CCDS12621.2 ENSP00000292140 Q6NSJ2 UPI00015C725F NM_198850.3 tolerated(0.34) 3/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12156:SF22,hmmpanther:PTHR12156 MODERATE SNV 5 1 PASS rs536138718 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 43502268 43502268 G A 1 0 0 0 0 1 0 0 0 11941 1174 41 3 3 PHLDB3 19 43502268 Missense_Mutation SNP G C3N-00294_T 3673809 43502268 15115348 1146 13918 ZNF404 0 . GRCh38 19 43874032 43874033 + Frame_Shift_Ins INS - - T novel C3N-00294_T C3N-00294_N - - c.181dupA p.Arg61LysfsTer4 p.R61Kfs*4 ENST00000587539 3/3 28 22 6 82 82 0 sindel-varindel-pindel ZNF404,frameshift_variant,p.Arg61LysfsTer4,ENST00000587539,NM_001033719.2;ZNF404,frameshift_variant,p.Arg60LysfsTer4,ENST00000324394,; T ENST00000587539 Transcript frameshift_variant 181-182/1851 181-182/1659 61/552 R/KX aga/aAga 1 -1 ZNF404 HGNC HGNC:19417 protein_coding YES CCDS59394.1 ENSP00000466051 Q494X3 UPI00001D8172 NM_001033719.2 3/3 PROSITE_profiles:PS50805,hmmpanther:PTHR24381:SF53,hmmpanther:PTHR24381,SMART_domains:SM00349 HIGH 1 insertion 5 1 PASS . . 0 204 6 0 0 0 0 0 -16.35899 1 1 1 1 0 T 7 5 46 43874032 43874032 - T 1 0 1 1 0 0 0 0 0 18458 913 32 0 0 ZNF404 19 43874032 Frame_Shift_Ins INS - C3N-00294_T 371764 43874032 14743584 1147 13919 BLOC1S3 0 . GRCh38 19 45179630 45179630 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.334C>A p.= p.R112R ENST00000433642 2/2 135 111 24 106 106 0 strelka-varscan-mutect BLOC1S3,synonymous_variant,p.=,ENST00000433642,NM_212550.3;BLOC1S3,synonymous_variant,p.=,ENST00000587722,;MARK4,intron_variant,,ENST00000587566,;TRAPPC6A,upstream_gene_variant,,ENST00000006275,NM_024108.2;TRAPPC6A,upstream_gene_variant,,ENST00000585934,NM_001270891.1;TRAPPC6A,upstream_gene_variant,,ENST00000588062,NM_001270893.1;TRAPPC6A,upstream_gene_variant,,ENST00000592647,NM_001270892.1;BLOC1S3,upstream_gene_variant,,ENST00000592910,;BLOC1S3,upstream_gene_variant,,ENST00000588362,;AC005779.2,upstream_gene_variant,,ENST00000593083,;TRAPPC6A,upstream_gene_variant,,ENST00000587818,; A ENST00000433642 Transcript synonymous_variant 430/2601 334/609 112/202 R Cgg/Agg 1 1 BLOC1S3 HGNC HGNC:20914 protein_coding YES CCDS12656.1 ENSP00000393840 Q6QNY0 UPI0000202628 NM_212550.3 2/2 hmmpanther:PTHR31974,PIRSF_domain:PIRSF037630,Pfam_domain:PF15753 LOW SNV 2 1 PASS rs1470568928 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 45179630 45179630 C A 1 0 0 0 0 0 0 0 1 1602 875 31 1 1 BLOC1S3 19 45179630 Silent SNP C C3N-00294_T 1305598 45179630 13437986 1148 13920 MARK4 0 . GRCh38 19 45302553 45302553 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2102G>A p.Gly701Glu p.G701E ENST00000262891 17/17 237 200 37 218 218 0 strelka-varscan-mutect MARK4,missense_variant,p.Gly701Glu,ENST00000262891,NM_001199867.1;MARK4,missense_variant,p.Gly28Glu,ENST00000622871,;MARK4,3_prime_UTR_variant,,ENST00000300843,NM_031417.3;MARK4,3_prime_UTR_variant,,ENST00000620044,;CKM,downstream_gene_variant,,ENST00000221476,NM_001824.4; A ENST00000262891 Transcript missense_variant 2433/3573 2102/2259 701/752 G/E gGg/gAg 1 1 MARK4 HGNC HGNC:13538 protein_coding YES CCDS56097.1 ENSP00000262891 Q96L34 UPI0000044D47 NM_001199867.1 deleterious(0.02) 17/17 hmmpanther:PTHR24346,Gene3D:3.30.310.80,Superfamily_domains:SSF103243 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 45302553 45302553 G A 1 0 0 0 0 1 0 0 0 9240 1232 43 3 3 MARK4 19 45302553 Missense_Mutation SNP G C3N-00294_T 122923 45302553 13315063 1149 13921 MYPOP 0 . GRCh38 19 45901588 45901588 + Missense_Mutation SNP C C G rs771797600 C3N-00294_T C3N-00294_N C C c.186G>C p.Lys62Asn p.K62N ENST00000322217 2/3 231 185 46 280 280 0 strelka-varscan-mutect MYPOP,missense_variant,p.Lys62Asn,ENST00000322217,NM_001012643.3; G ENST00000322217 Transcript missense_variant 273/1890 186/1200 62/399 K/N aaG/aaC rs771797600,COSM3357161 1 -1 MYPOP HGNC HGNC:20178 protein_coding YES CCDS33055.1 ENSP00000325402 Q86VE0 UPI00001984F8 NM_001012643.3 deleterious(0) 2/3 Gene3D:1.10.10.60,Pfam_domain:PF13873,PROSITE_profiles:PS50090,hmmpanther:PTHR32345,hmmpanther:PTHR32345:SF3,SMART_domains:SM00717 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771797600 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 45901588 45901588 C G 1 0 0 0 0 1 0 0 0 10100 912 32 4 4 MYPOP 19 45901588 Missense_Mutation SNP C C3N-00294_T 599035 45901588 12716028 1150 13922 INAFM1 0 . GRCh38 19 47275263 47275263 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.344G>A p.Arg115His p.R115H ENST00000552360 1/1 307 245 62 277 276 1 strelka-varscan-mutect INAFM1,missense_variant,p.Arg115His,ENST00000552360,NM_178511.5;CCDC9,downstream_gene_variant,,ENST00000221922,NM_015603.2;CCDC9,downstream_gene_variant,,ENST00000600117,; A ENST00000552360 Transcript missense_variant 811/1255 344/429 115/142 R/H cGc/cAc 1 1 INAFM1 HGNC HGNC:27406 protein_coding YES CCDS46131.1 ENSP00000447679 C9JVW0 UPI0000070F52 NM_178511.5 tolerated_low_confidence(0.09) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR34929:SF1,hmmpanther:PTHR34929 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 47275263 47275263 G A 1 0 0 0 0 1 0 0 0 7633 1087 38 1 1 INAFM1 19 47275263 Missense_Mutation SNP G C3N-00294_T 1373675 47275263 11342353 1151 13923 SPHK2 0 . GRCh38 19 48629652 48629652 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1844C>T p.Pro615Leu p.P615L ENST00000245222 7/7 95 88 7 107 107 0 strelka-varscan-mutect SPHK2,missense_variant,p.Pro579Leu,ENST00000599029,;SPHK2,missense_variant,p.Pro615Leu,ENST00000245222,NM_020126.4;SPHK2,missense_variant,p.Pro615Leu,ENST00000598088,NM_001204159.2;SPHK2,missense_variant,p.Pro579Leu,ENST00000599748,NM_001204160.2;SPHK2,missense_variant,p.Pro409Leu,ENST00000340932,NM_001243876.1;SPHK2,missense_variant,p.Pro556Leu,ENST00000600537,NM_001204158.2;DBP,downstream_gene_variant,,ENST00000222122,NM_001352.4;DBP,downstream_gene_variant,,ENST00000601104,;SPHK2,downstream_gene_variant,,ENST00000601712,;SPHK2,downstream_gene_variant,,ENST00000593308,;DBP,downstream_gene_variant,,ENST00000593500,;DBP,downstream_gene_variant,,ENST00000599385,;SPHK2,downstream_gene_variant,,ENST00000601704,;SPHK2,downstream_gene_variant,,ENST00000599033,;SPHK2,3_prime_UTR_variant,,ENST00000426514,;SPHK2,intron_variant,,ENST00000597434,;DBP,downstream_gene_variant,,ENST00000594723,;SPHK2,downstream_gene_variant,,ENST00000598574,; T ENST00000245222 Transcript missense_variant 2210/2963 1844/1965 615/654 P/L cCa/cTa 1 1 SPHK2 HGNC HGNC:18859 protein_coding YES CCDS12727.1 ENSP00000245222 Q9NRA0 A0A024QZH5 UPI0000135E14 NM_020126.4 deleterious(0.02) 7/7 hmmpanther:PTHR12358:SF40,hmmpanther:PTHR12358,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.63158 1 1 1 1 0 T 3 4 46 48629652 48629652 C T 1 0 0 0 0 1 0 0 0 15398 594 21 3 3 SPHK2 19 48629652 Missense_Mutation SNP C C3N-00294_T 1354389 48629652 9987964 1152 13924 BAX 0 . GRCh38 19 48955789 48955789 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.189C>T p.= p.L63L ENST00000293288 3/5 68 58 10 86 86 0 strelka-varscan-mutect BAX,synonymous_variant,p.=,ENST00000293288,NM_004324.3;BAX,synonymous_variant,p.=,ENST00000345358,NM_001291428.1,NM_138761.3;BAX,synonymous_variant,p.=,ENST00000391871,;BAX,synonymous_variant,p.=,ENST00000415969,NM_138764.4;BAX,intron_variant,,ENST00000539787,NM_001291430.1;BAX,intron_variant,,ENST00000354470,NM_138763.3;BAX,intron_variant,,ENST00000506183,;BAX,synonymous_variant,p.=,ENST00000356483,;BAX,3_prime_UTR_variant,,ENST00000515540,;BAX,non_coding_transcript_exon_variant,,ENST00000502487,;BAX,non_coding_transcript_exon_variant,,ENST00000513545,;BAX,non_coding_transcript_exon_variant,,ENST00000503726,;BAX,upstream_gene_variant,,ENST00000513217,; T ENST00000293288 Transcript synonymous_variant 189/1358 189/657 63/218 L ctC/ctT COSM5203154,COSM5203155 1 1 BAX HGNC HGNC:959 protein_coding YES CCDS12744.1 ENSP00000293288 Q07812 UPI000000D900 NM_004324.3 3/5 PROSITE_profiles:PS50062,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF44,PROSITE_patterns:PS01259,Pfam_domain:PF00452,Gene3D:1.10.437.10,SMART_domains:SM00337,Superfamily_domains:SSF56854 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99929 1 1 1 1 0 T 2 4 46 48955789 48955789 C T 1 0 0 0 0 0 0 0 1 1473 813 29 3 3 BAX 19 48955789 Silent SNP C C3N-00294_T 326137 48955789 9661827 1153 13925 CGB3 0 . GRCh38 19 49023059 49023059 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.325C>G p.Gln109Glu p.Q109E ENST00000357383 3/3 37 29 8 39 39 0 varscan-mutect CGB3,missense_variant,p.Gln109Glu,ENST00000357383,NM_000737.3;CTB-60B18.6,missense_variant,p.Gln95Glu,ENST00000591656,;CTB-60B18.10,upstream_gene_variant,,ENST00000637680,;CTB-60B18.6,downstream_gene_variant,,ENST00000604577,;CTB-60B18.10,upstream_gene_variant,,ENST00000600007,;NTF6A,downstream_gene_variant,,ENST00000591175,; C ENST00000357383 Transcript missense_variant 687/877 325/498 109/165 Q/E Caa/Gaa 1 -1 CGB3 HGNC HGNC:1886 protein_coding YES CCDS12749.1 ENSP00000349954 P0DN86 A0A0F7RQP8 UPI0000035497 NM_000737.3 tolerated(0.44) 3/3 hmmpanther:PTHR11515:SF16,hmmpanther:PTHR11515,PROSITE_patterns:PS00689,Gene3D:2.10.90.10,Pfam_domain:PF00007,SMART_domains:SM00068,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -19.9112 1 1 1 1 0 C 3 2 46 49023059 49023059 G C 1 0 0 0 0 1 0 0 0 3056 1299 45 4 4 CGB3 19 49023059 Missense_Mutation SNP G C3N-00294_T 67270 49023059 9594557 1154 13926 CGB2 0 . GRCh38 19 49033048 49033048 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.319C>G p.Gln107Glu p.Q107E ENST00000359342 3/3 77 65 12 99 99 0 varscan-mutect CGB2,missense_variant,p.Gln95Glu,ENST00000474913,NM_001319065.1;CGB2,missense_variant,p.Gln107Glu,ENST00000359342,NM_033378.1;CTB-60B18.6,intron_variant,,ENST00000591656,;CTB-60B18.6,intron_variant,,ENST00000604577,;CGB1,downstream_gene_variant,,ENST00000601167,;CGB1,downstream_gene_variant,,ENST00000301407,NM_033377.1;NTF6G,downstream_gene_variant,,ENST00000591094,; G ENST00000359342 Transcript missense_variant 437/627 319/492 107/163 Q/E Caa/Gaa 1 1 CGB2 HGNC HGNC:16722 protein_coding YES CCDS12750.2 ENSP00000352295 H9KV56 UPI000059D759 NM_033378.1 tolerated(0.34) 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00007,PROSITE_patterns:PS00689,hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF16,SMART_domains:SM00068,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS rs1254010744 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 49033048 49033048 C G 1 0 0 0 0 1 0 0 0 3055 827 29 4 4 CGB2 19 49033048 Missense_Mutation SNP C C3N-00294_T 9989 49033048 9584568 1155 13927 PPFIA3 0 . GRCh38 19 49150106 49150106 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.3553G>C p.Asp1185His p.D1185H ENST00000334186 29/30 157 128 29 191 191 0 strelka-varscan-mutect PPFIA3,missense_variant,p.Asp1185His,ENST00000334186,NM_003660.3;PPFIA3,missense_variant,p.Asp1176His,ENST00000602351,;PPFIA3,missense_variant,p.Asp268His,ENST00000602848,;PPFIA3,missense_variant,p.Asp234His,ENST00000602897,;HRC,downstream_gene_variant,,ENST00000252825,NM_002152.2;HRC,downstream_gene_variant,,ENST00000595625,;HRC,downstream_gene_variant,,ENST00000598858,;PPFIA3,3_prime_UTR_variant,,ENST00000602655,;PPFIA3,non_coding_transcript_exon_variant,,ENST00000602783,;PPFIA3,non_coding_transcript_exon_variant,,ENST00000602905,;PPFIA3,downstream_gene_variant,,ENST00000602800,;HRC,downstream_gene_variant,,ENST00000595167,; C ENST00000334186 Transcript missense_variant 3902/4733 3553/3585 1185/1194 D/H Gac/Cac COSM4544353 1 1 PPFIA3 HGNC HGNC:9247 protein_coding YES CCDS12758.1 ENSP00000335614 O75145 UPI00001AE464 NM_003660.3 deleterious_low_confidence(0) 29/30 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF4 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 49150106 49150106 G C 1 0 0 0 0 1 0 0 0 12420 942 33 4 4 PPFIA3 19 49150106 Missense_Mutation SNP G C3N-00294_T 117058 49150106 9467510 1156 13928 HRC 0 . GRCh38 19 49153497 49153497 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1741G>T p.Glu581Ter p.E581* ENST00000252825 1/6 35 25 10 40 40 0 strelka-varscan-mutect HRC,stop_gained,p.Glu581Ter,ENST00000252825,NM_002152.2;HRC,stop_gained,p.Glu581Ter,ENST00000595625,;PPFIA3,downstream_gene_variant,,ENST00000334186,NM_003660.3;PPFIA3,downstream_gene_variant,,ENST00000602351,;TRPM4,upstream_gene_variant,,ENST00000252826,NM_017636.3;TRPM4,upstream_gene_variant,,ENST00000427978,NM_001195227.1;TRPM4,upstream_gene_variant,,ENST00000599628,;PPFIA3,downstream_gene_variant,,ENST00000602848,;PPFIA3,downstream_gene_variant,,ENST00000602897,;TRPM4,upstream_gene_variant,,ENST00000598691,;HRC,upstream_gene_variant,,ENST00000598858,;TRPM4,upstream_gene_variant,,ENST00000596338,;TRPM4,upstream_gene_variant,,ENST00000595519,NM_001321283.1;TRPM4,upstream_gene_variant,,ENST00000598502,NM_001321282.1;PPFIA3,downstream_gene_variant,,ENST00000602655,;TRPM4,upstream_gene_variant,,ENST00000598697,NM_001321285.1;PPFIA3,downstream_gene_variant,,ENST00000602783,;PPFIA3,downstream_gene_variant,,ENST00000602905,;HRC,upstream_gene_variant,,ENST00000595167,; A ENST00000252825 Transcript stop_gained 1928/2385 1741/2100 581/699 E/* Gag/Tag 1 -1 HRC HGNC HGNC:5178 protein_coding YES CCDS12759.1 ENSP00000252825 P23327 UPI0000135F21 NM_002152.2 1/6 hmmpanther:PTHR15054,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 49153497 49153497 C A 1 0 0 0 0 0 1 0 0 7247 835 29 2 2 HRC 19 49153497 Nonsense_Mutation SNP C C3N-00294_T 3391 49153497 9464119 1157 13929 FUZ 0 . GRCh38 19 49809181 49809181 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.768C>G p.= p.L256L ENST00000313777 7/11 405 313 92 435 435 0 strelka-varscan-mutect FUZ,synonymous_variant,p.=,ENST00000313777,NM_025129.4;FUZ,synonymous_variant,p.=,ENST00000533418,;FUZ,synonymous_variant,p.=,ENST00000528094,NM_001171937.1;AP2A1,downstream_gene_variant,,ENST00000354293,NM_130787.2;AP2A1,downstream_gene_variant,,ENST00000359032,NM_014203.2;FUZ,upstream_gene_variant,,ENST00000529634,;FUZ,downstream_gene_variant,,ENST00000529302,;FUZ,downstream_gene_variant,,ENST00000526575,;AC006942.4,intron_variant,,ENST00000600669,;FUZ,non_coding_transcript_exon_variant,,ENST00000527973,;FUZ,downstream_gene_variant,,ENST00000534008,;FUZ,3_prime_UTR_variant,,ENST00000377092,;FUZ,3_prime_UTR_variant,,ENST00000525130,;FUZ,3_prime_UTR_variant,,ENST00000525370,;AP2A1,downstream_gene_variant,,ENST00000600466,;AP2A1,downstream_gene_variant,,ENST00000601356,;AP2A1,downstream_gene_variant,,ENST00000597774,;FUZ,downstream_gene_variant,,ENST00000531017,;FUZ,downstream_gene_variant,,ENST00000528043,;FUZ,downstream_gene_variant,,ENST00000527111,;AP2A1,downstream_gene_variant,,ENST00000594838,;FUZ,downstream_gene_variant,,ENST00000525800,;FUZ,downstream_gene_variant,,ENST00000526435,;FUZ,downstream_gene_variant,,ENST00000527585,;FUZ,upstream_gene_variant,,ENST00000534138,; C ENST00000313777 Transcript synonymous_variant 932/1675 768/1257 256/418 L ctC/ctG 1 -1 FUZ HGNC HGNC:26219 protein_coding YES CCDS12781.1 ENSP00000313309 Q9BT04 A0A024QZF7 UPI00000736B0 NM_025129.4 7/11 hmmpanther:PTHR13559,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1446396688 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 49809181 49809181 G C 1 0 0 0 0 0 0 0 1 5984 1277 45 4 4 FUZ 19 49809181 Silent SNP G C3N-00294_T 655684 49809181 8808435 1158 13930 SHANK1 0 . GRCh38 19 50702506 50702506 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.1708G>T p.Glu570Ter p.E570* ENST00000293441 11/23 119 93 26 134 134 0 strelka-varscan-mutect SHANK1,stop_gained,p.Glu570Ter,ENST00000293441,NM_016148.2;SHANK1,stop_gained,p.Glu570Ter,ENST00000391814,;SHANK1,stop_gained,p.Glu570Ter,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000461154,; A ENST00000293441 Transcript stop_gained 1727/6643 1708/6486 570/2161 E/* Gag/Tag 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 11/23 PROSITE_profiles:PS50002,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 HIGH 1 SNV 1 1 PASS rs941454412 . 0 206 0 3 0 0 0 0 -20 0.9999969 1 1 1 0 A 4 1 46 50702506 50702506 C A 1 0 0 0 0 0 1 0 0 14523 893 31 1 1 SHANK1 19 50702506 Nonsense_Mutation SNP C C3N-00294_T 893325 50702506 7915110 1159 13931 C19orf48 0 . GRCh38 19 50798259 50798259 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.190G>C p.Gly64Arg p.G64R ENST00000598463 5/5 143 83 60 106 106 0 strelka-varscan-mutect C19orf48,missense_variant,p.Gly64Arg,ENST00000598463,NM_001290149.1;C19orf48,missense_variant,p.Gly64Arg,ENST00000345523,NM_001290152.1,NM_001290155.1,NM_199250.2,NM_001290151.1,NM_001290150.1;C19orf48,missense_variant,p.Gly64Arg,ENST00000391812,NM_199249.2,NM_001290154.1,NM_001290153.1;C19orf48,missense_variant,p.Gly64Arg,ENST00000596655,NM_032712.2;C19orf48,missense_variant,p.Gly64Arg,ENST00000597705,;C19orf48,missense_variant,p.Gly64Arg,ENST00000596287,;ACPT,downstream_gene_variant,,ENST00000270593,NM_033068.2;C19orf48,downstream_gene_variant,,ENST00000597493,;C19orf48,downstream_gene_variant,,ENST00000601267,;C19orf48,downstream_gene_variant,,ENST00000600373,;C19orf48,downstream_gene_variant,,ENST00000593287,;SNORD88C,downstream_gene_variant,,ENST00000408061,;SNORD88A,downstream_gene_variant,,ENST00000408314,;SNORD88B,downstream_gene_variant,,ENST00000408454,;CTD-2568A17.8,upstream_gene_variant,,ENST00000594114,;C19orf48,downstream_gene_variant,,ENST00000595794,;C19orf48,downstream_gene_variant,,ENST00000599004,;C19orf48,downstream_gene_variant,,ENST00000596554,;C19orf48,downstream_gene_variant,,ENST00000602125,; G ENST00000598463 Transcript missense_variant 1289/1844 190/354 64/117 G/R Ggg/Cgg COSM334131 1 -1 C19orf48 HGNC HGNC:29667 protein_coding YES CCDS12803.1 ENSP00000471463 Q6RUI8 A0A024R4G9 UPI000006ECB0 NM_001290149.1 deleterious_low_confidence(0) 5/5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 50798259 50798259 C G 1 0 0 0 0 1 0 0 0 1914 681 24 4 4 C19orf48 19 50798259 Missense_Mutation SNP C C3N-00294_T 95753 50798259 7819357 1160 13932 KLK1 0 . GRCh38 19 50819982 50819982 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.550G>A p.Glu184Lys p.E184K ENST00000301420 4/5 168 151 17 194 194 0 strelka-varscan-mutect KLK1,missense_variant,p.Glu184Lys,ENST00000301420,NM_002257.3;MGC45922,downstream_gene_variant,,ENST00000635639,;MGC45922,downstream_gene_variant,,ENST00000634979,;MGC45922,downstream_gene_variant,,ENST00000326989,;MGC45922,downstream_gene_variant,,ENST00000593632,;KLK1,3_prime_UTR_variant,,ENST00000593325,;KLK1,non_coding_transcript_exon_variant,,ENST00000593859,;KLK1,non_coding_transcript_exon_variant,,ENST00000596300,; T ENST00000301420 Transcript missense_variant 586/866 550/789 184/262 E/K Gag/Aag 1 -1 KLK1 HGNC HGNC:6357 protein_coding YES CCDS12804.1 ENSP00000301420 P06870 UPI000004CA0D NM_002257.3 tolerated(0.81) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF111,hmmpanther:PTHR24256,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 50819982 50819982 C T 1 0 0 0 0 1 0 0 0 8266 835 29 3 3 KLK1 19 50819982 Missense_Mutation SNP C C3N-00294_T 21723 50819982 7797634 1161 13933 SIGLEC8 0 . GRCh38 19 51455473 51455473 + Missense_Mutation SNP G G T rs771076418 C3N-00294_T C3N-00294_N G G c.996C>A p.Asn332Lys p.N332K ENST00000321424 4/7 200 132 68 261 261 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Asn332Lys,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Asn223Lys,ENST00000430817,;SIGLEC8,missense_variant,p.Asn239Lys,ENST00000340550,;SIGLEC8,downstream_gene_variant,,ENST00000597352,; T ENST00000321424 Transcript missense_variant 1063/2949 996/1500 332/499 N/K aaC/aaA rs771076418,COSM235355 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 deleterious(0.01) 4/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771076418 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 51455473 51455473 G T 1 0 0 0 0 1 0 0 0 14578 1136 40 1 1 SIGLEC8 19 51455473 Missense_Mutation SNP G C3N-00294_T 635491 51455473 7162143 1162 13934 SIGLEC12 0 . GRCh38 19 51499627 51499627 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.898G>A p.Glu300Lys p.E300K ENST00000291707 3/8 132 101 31 123 123 0 strelka-varscan-mutect SIGLEC12,missense_variant,p.Glu300Lys,ENST00000291707,NM_053003.3;SIGLEC12,missense_variant,p.Glu182Lys,ENST00000598614,NM_033329.2;SIGLEC12,3_prime_UTR_variant,,ENST00000596742,; T ENST00000291707 Transcript missense_variant 954/2121 898/1788 300/595 E/K Gaa/Aaa 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 tolerated(0.3) 3/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF53,hmmpanther:PTHR12035,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 51499627 51499627 C T 1 0 0 0 0 1 0 0 0 14572 835 29 3 3 SIGLEC12 19 51499627 Missense_Mutation SNP C C3N-00294_T 44154 51499627 7117989 1163 13935 ZNF649 0 . GRCh38 19 51891813 51891813 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.323G>A p.Gly108Glu p.G108E ENST00000354957 5/5 103 91 12 97 97 0 strelka-varscan-mutect ZNF649,missense_variant,p.Gly108Glu,ENST00000354957,NM_023074.3;ZNF649,missense_variant,p.Gly108Glu,ENST00000600738,;ZNF577,upstream_gene_variant,,ENST00000301399,NM_032679.2;ZNF649-AS1,intron_variant,,ENST00000600329,;ZNF649,downstream_gene_variant,,ENST00000599671,;ZNF649,downstream_gene_variant,,ENST00000597882,; T ENST00000354957 Transcript missense_variant 608/3197 323/1518 108/505 G/E gGa/gAa 1 -1 ZNF649 HGNC HGNC:25741 protein_coding YES CCDS12843.1 ENSP00000347043 Q9BS31 UPI000006D442 NM_023074.3 tolerated(0.28) 5/5 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF34 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 51891813 51891813 C T 1 0 0 0 0 1 0 0 0 18637 855 30 3 3 ZNF649 19 51891813 Missense_Mutation SNP C C3N-00294_T 392186 51891813 6725803 1164 13936 TSEN34 0 . GRCh38 19 54191364 54191364 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.9G>T p.Arg3Ser p.R3S ENST00000429671 2/6 243 195 48 189 189 0 strelka-varscan-mutect TSEN34,missense_variant,p.Arg3Ser,ENST00000429671,NM_001282333.1;TSEN34,missense_variant,p.Arg3Ser,ENST00000456872,;TSEN34,5_prime_UTR_variant,,ENST00000302937,NM_024075.4;TSEN34,5_prime_UTR_variant,,ENST00000396383,NM_001282332.1;TSEN34,5_prime_UTR_variant,,ENST00000396388,NM_001077446.3;TSEN34,5_prime_UTR_variant,,ENST00000455798,;MBOAT7,upstream_gene_variant,,ENST00000245615,NM_024298.4;MBOAT7,upstream_gene_variant,,ENST00000431666,NM_001146083.2;MBOAT7,upstream_gene_variant,,ENST00000338624,NM_001146056.2;MBOAT7,upstream_gene_variant,,ENST00000391754,NM_001146082.2;MBOAT7,upstream_gene_variant,,ENST00000414665,;MBOAT7,upstream_gene_variant,,ENST00000449249,;MBOAT7,upstream_gene_variant,,ENST00000453320,;MBOAT7,upstream_gene_variant,,ENST00000474910,;MBOAT7,upstream_gene_variant,,ENST00000495968,;TSEN34,non_coding_transcript_exon_variant,,ENST00000496583,;MBOAT7,upstream_gene_variant,,ENST00000437868,;MBOAT7,upstream_gene_variant,,ENST00000491216,;MBOAT7,upstream_gene_variant,,ENST00000464098,; T ENST00000429671 Transcript missense_variant 108/1912 9/948 3/315 R/S agG/agT 1 1 TSEN34 HGNC HGNC:15506 protein_coding YES CCDS74446.1 ENSP00000397402 E7EQB3 UPI000387D582 NM_001282333.1 tolerated_low_confidence(0.19) 2/6 hmmpanther:PTHR13070,PIRSF_domain:PIRSF017250 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 54191364 54191364 G T 1 0 0 0 0 1 0 0 0 17119 1188 41 2 2 TSEN34 19 54191364 Missense_Mutation SNP G C3N-00294_T 2299551 54191364 4426252 1165 13937 TSEN34 0 . GRCh38 19 54191530 54191530 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.175G>C p.Glu59Gln p.E59Q ENST00000429671 2/6 236 195 41 205 205 0 strelka-varscan-mutect TSEN34,missense_variant,p.Glu56Gln,ENST00000302937,NM_024075.4;TSEN34,missense_variant,p.Glu59Gln,ENST00000429671,NM_001282333.1;TSEN34,missense_variant,p.Glu56Gln,ENST00000396383,NM_001282332.1;TSEN34,missense_variant,p.Glu56Gln,ENST00000396388,NM_001077446.3;TSEN34,missense_variant,p.Glu56Gln,ENST00000455798,;TSEN34,missense_variant,p.Glu59Gln,ENST00000456872,;MBOAT7,upstream_gene_variant,,ENST00000245615,NM_024298.4;MBOAT7,upstream_gene_variant,,ENST00000431666,NM_001146083.2;MBOAT7,upstream_gene_variant,,ENST00000338624,NM_001146056.2;MBOAT7,upstream_gene_variant,,ENST00000391754,NM_001146082.2;MBOAT7,upstream_gene_variant,,ENST00000414665,;MBOAT7,upstream_gene_variant,,ENST00000449249,;MBOAT7,upstream_gene_variant,,ENST00000453320,;MBOAT7,upstream_gene_variant,,ENST00000474910,;MBOAT7,upstream_gene_variant,,ENST00000495968,;TSEN34,non_coding_transcript_exon_variant,,ENST00000496583,;MBOAT7,upstream_gene_variant,,ENST00000437868,;MBOAT7,upstream_gene_variant,,ENST00000491216,;MBOAT7,upstream_gene_variant,,ENST00000464098,; C ENST00000429671 Transcript missense_variant 274/1912 175/948 59/315 E/Q Gag/Cag 1 1 TSEN34 HGNC HGNC:15506 protein_coding YES CCDS74446.1 ENSP00000397402 E7EQB3 UPI000387D582 NM_001282333.1 deleterious(0) 2/6 hmmpanther:PTHR13070,PIRSF_domain:PIRSF017250 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 54191530 54191530 G C 1 0 0 0 0 1 0 0 0 17119 943 33 4 4 TSEN34 19 54191530 Missense_Mutation SNP G C3N-00294_T 166 54191530 4426086 1166 13938 LENG9 0 . GRCh38 19 54463188 54463188 + Silent SNP G G C rs201329900 C3N-00294_T C3N-00294_N G G c.339C>G p.= p.L113L ENST00000611161 1/1 103 83 20 89 89 0 strelka-varscan-mutect LENG9,synonymous_variant,p.=,ENST00000611161,NM_001301782.1;LENG8,downstream_gene_variant,,ENST00000610347,;LENG8,downstream_gene_variant,,ENST00000376514,;LENG8,downstream_gene_variant,,ENST00000326764,NM_052925.3;LENG8,downstream_gene_variant,,ENST00000616932,;CDC42EP5,downstream_gene_variant,,ENST00000301200,NM_145057.3;LENG8,downstream_gene_variant,,ENST00000421200,; C ENST00000611161 Transcript synonymous_variant 524/1916 339/1437 113/478 L ctC/ctG rs201329900 1 -1 LENG9 HGNC HGNC:16306 protein_coding YES CCDS77358.1 ENSP00000479355 A0A087WVD1 UPI000165DD07 NM_001301782.1 1/1 hmmpanther:PTHR21495,hmmpanther:PTHR21495:SF55,Pfam_domain:PF04457 LOW SNV 1 PASS rs201329900 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 54463188 54463188 G C 1 0 0 0 0 0 0 0 1 8633 1045 37 4 4 LENG9 19 54463188 Silent SNP G C3N-00294_T 271658 54463188 4154428 1167 13939 SYT5 0 . GRCh38 19 55174547 55174547 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.930C>T p.= p.F310F ENST00000354308 8/9 88 65 23 85 85 0 strelka-varscan-mutect SYT5,synonymous_variant,p.=,ENST00000354308,NM_003180.2;SYT5,synonymous_variant,p.=,ENST00000590851,NM_001297774.1;SYT5,synonymous_variant,p.=,ENST00000537500,;SYT5,synonymous_variant,p.=,ENST00000590859,;SYT5,synonymous_variant,p.=,ENST00000587067,;SYT5,downstream_gene_variant,,ENST00000592470,;SYT5,downstream_gene_variant,,ENST00000589172,;CTD-2587H24.5,intron_variant,,ENST00000591665,;SYT5,upstream_gene_variant,,ENST00000592935,;SYT5,non_coding_transcript_exon_variant,,ENST00000588305,;SYT5,non_coding_transcript_exon_variant,,ENST00000592956,;SYT5,downstream_gene_variant,,ENST00000585461,; A ENST00000354308 Transcript synonymous_variant 1300/3792 930/1161 310/386 F ttC/ttT COSM714667 1 -1 SYT5 HGNC HGNC:11513 protein_coding YES CCDS12919.1 ENSP00000346265 O00445 A0A024R4N8 UPI000013C56F NM_003180.2 8/9 PROSITE_profiles:PS50004,hmmpanther:PTHR10024:SF227,hmmpanther:PTHR10024,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 55174547 55174547 G A 1 0 0 0 0 0 0 0 1 15871 1281 45 3 3 SYT5 19 55174547 Silent SNP G C3N-00294_T 711359 55174547 3443069 1168 13940 NLRP9 0 . GRCh38 19 55711840 55711840 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2803G>A p.Glu935Lys p.E935K ENST00000332836 8/9 132 103 29 117 117 0 strelka-varscan-mutect NLRP9,missense_variant,p.Glu935Lys,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Glu935Lys,ENST00000590200,;EPN1,downstream_gene_variant,,ENST00000270460,NM_001130072.1;EPN1,downstream_gene_variant,,ENST00000589704,;CTD-2611O12.6,downstream_gene_variant,,ENST00000597650,; T ENST00000332836 Transcript missense_variant 2831/3484 2803/2976 935/991 E/K Gag/Aag 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 tolerated(0.05) 8/9 hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 55711840 55711840 C T 1 0 0 0 0 1 0 0 0 10522 835 29 3 3 NLRP9 19 55711840 Missense_Mutation SNP C C3N-00294_T 537293 55711840 2905776 1169 13941 ZNF418 0 . GRCh38 19 57927300 57927300 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.881C>G p.Ser294Cys p.S294C ENST00000396147 4/6 143 122 21 156 156 0 strelka-varscan-mutect ZNF418,missense_variant,p.Ser294Cys,ENST00000396147,NM_001317028.1,NM_133460.1;ZNF418,missense_variant,p.Ser315Cys,ENST00000425570,;ZNF418,missense_variant,p.Ser294Cys,ENST00000595830,NM_001317029.1,NM_001317030.1;ZNF418,missense_variant,p.Ser209Cys,ENST00000599852,;ZNF418,missense_variant,p.Ser294Cys,ENST00000616958,;ZNF418,intron_variant,,ENST00000600989,;ZNF418,downstream_gene_variant,,ENST00000595569,;ZNF418,downstream_gene_variant,,ENST00000593296,;ZNF418,downstream_gene_variant,,ENST00000601593,;ZNF418,intron_variant,,ENST00000598213,;ZNF418,upstream_gene_variant,,ENST00000599086,; C ENST00000396147 Transcript missense_variant 1173/3694 881/2031 294/676 S/C tCt/tGt COSM3540578 1 -1 ZNF418 HGNC HGNC:20647 protein_coding YES CCDS42642.1 ENSP00000379451 Q8TF45 UPI000013B4C8 NM_001317028.1,NM_133460.1 deleterious(0.05) 4/6 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 57927300 57927300 G C 1 0 0 0 0 1 0 0 0 18467 942 33 4 4 ZNF418 19 57927300 Missense_Mutation SNP G C3N-00294_T 2215460 57927300 690316 1170 13942 TRIM28 0 . GRCh38 19 58549982 58549982 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.2140C>T p.His714Tyr p.H714Y ENST00000253024 15/17 339 261 78 320 320 0 strelka-varscan-mutect TRIM28,missense_variant,p.His714Tyr,ENST00000253024,NM_005762.2;TRIM28,missense_variant,p.His632Tyr,ENST00000341753,;TRIM28,missense_variant,p.His339Tyr,ENST00000597136,;CHMP2A,downstream_gene_variant,,ENST00000600118,;CHMP2A,downstream_gene_variant,,ENST00000312547,NM_014453.3;CHMP2A,downstream_gene_variant,,ENST00000601220,NM_198426.2;TRIM28,downstream_gene_variant,,ENST00000594806,;CHMP2A,downstream_gene_variant,,ENST00000600006,;CHMP2A,downstream_gene_variant,,ENST00000596708,;TRIM28,downstream_gene_variant,,ENST00000593582,;CHMP2A,downstream_gene_variant,,ENST00000597848,;TRIM28,downstream_gene_variant,,ENST00000597968,;MIR6807,upstream_gene_variant,,ENST00000621968,;TRIM28,non_coding_transcript_exon_variant,,ENST00000598355,;TRIM28,non_coding_transcript_exon_variant,,ENST00000595974,;TRIM28,non_coding_transcript_exon_variant,,ENST00000600840,;TRIM28,downstream_gene_variant,,ENST00000601150,;TRIM28,downstream_gene_variant,,ENST00000597423,;TRIM28,downstream_gene_variant,,ENST00000597995,;CHMP2A,downstream_gene_variant,,ENST00000597209,;TRIM28,downstream_gene_variant,,ENST00000597618,;CHMP2A,downstream_gene_variant,,ENST00000600804,;TRIM28,downstream_gene_variant,,ENST00000597172,;TRIM28,downstream_gene_variant,,ENST00000595028,; T ENST00000253024 Transcript missense_variant 2429/2960 2140/2508 714/835 H/Y Cac/Tac 1 1 TRIM28 HGNC HGNC:16384 protein_coding YES CCDS12985.1 ENSP00000253024 Q13263 UPI0000136C15 NM_005762.2 deleterious(0.01) 15/17 Gene3D:1.20.920.10,SMART_domains:SM00297 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 58549982 58549982 C T 1 0 0 0 0 1 0 0 0 16991 826 29 3 3 TRIM28 19 58549982 Missense_Mutation SNP C C3N-00294_T 622682 58549982 67634 1171 13943 MZF1 0 . GRCh38 19 58563411 58563411 + Missense_Mutation SNP G G C rs371153551 C3N-00294_T C3N-00294_N G G c.866C>G p.Ser289Cys p.S289C ENST00000215057 6/6 155 127 28 145 145 0 strelka-varscan-mutect MZF1,missense_variant,p.Ser289Cys,ENST00000215057,NM_198055.1;MZF1,missense_variant,p.Ser289Cys,ENST00000599369,NM_003422.2;MZF1,intron_variant,,ENST00000594234,NM_001267033.1;UBE2M,upstream_gene_variant,,ENST00000253023,NM_003969.3;UBE2M,upstream_gene_variant,,ENST00000595957,;MZF1-AS1,intron_variant,,ENST00000600534,;MZF1-AS1,intron_variant,,ENST00000593642,;MZF1-AS1,intron_variant,,ENST00000600726,;MZF1,non_coding_transcript_exon_variant,,ENST00000600004,;MZF1,downstream_gene_variant,,ENST00000595245,; C ENST00000215057 Transcript missense_variant 1427/2905 866/2205 289/734 S/C tCt/tGt rs371153551 1 -1 MZF1 HGNC HGNC:13108 protein_coding YES CCDS12988.1 ENSP00000215057 P28698 A0A024R4T5 UPI0000072863 NM_198055.1 tolerated(0.14) 6/6 MODERATE 1 SNV 1 1 PASS rs371153551 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 58563411 58563411 G C 1 0 0 0 0 1 0 0 0 10109 942 33 4 4 MZF1 19 58563411 Missense_Mutation SNP G C3N-00294_T 13429 58563411 54205 1172 13944 C20orf96 0 . GRCh38 20 289622 289622 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.124C>G p.Pro42Ala p.P42A ENST00000360321 3/11 261 202 59 297 297 0 strelka-varscan-mutect C20orf96,missense_variant,p.Pro41Ala,ENST00000400269,NM_080571.1;C20orf96,missense_variant,p.Pro42Ala,ENST00000360321,NM_153269.2;C20orf96,intron_variant,,ENST00000382369,; C ENST00000360321 Transcript missense_variant 263/1575 124/1092 42/363 P/A Cca/Gca 1 -1 C20orf96 HGNC HGNC:16227 protein_coding YES CCDS12994.1 ENSP00000353470 Q9NUD7 UPI00001285F1 NM_153269.2 deleterious(0.01) 3/11 hmmpanther:PTHR28574:SF1,hmmpanther:PTHR28574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 289622 289622 G C 1 0 0 0 0 1 0 0 0 2011 1174 41 4 4 C20orf96 20 289622 Missense_Mutation SNP G C3N-00294_T 289622 64154545 1173 13945 IDH3B 0 . GRCh38 20 2663997 2663997 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.45C>G p.= p.V15V ENST00000380843 2/12 548 448 100 524 524 0 strelka-varscan-mutect IDH3B,synonymous_variant,p.=,ENST00000380843,NM_006899.3;IDH3B,synonymous_variant,p.=,ENST00000613370,NM_001258384.1;IDH3B,synonymous_variant,p.=,ENST00000474315,;IDH3B,synonymous_variant,p.=,ENST00000380851,NM_174855.2;RP4-686C3.7,upstream_gene_variant,,ENST00000418739,;IDH3B,non_coding_transcript_exon_variant,,ENST00000488299,;IDH3B,non_coding_transcript_exon_variant,,ENST00000462967,;IDH3B,non_coding_transcript_exon_variant,,ENST00000491065,;IDH3B,upstream_gene_variant,,ENST00000492240,;IDH3B,upstream_gene_variant,,ENST00000466494,;IDH3B,upstream_gene_variant,,ENST00000477689,;IDH3B,upstream_gene_variant,,ENST00000466999,;IDH3B,upstream_gene_variant,,ENST00000479376,; C ENST00000380843 Transcript synonymous_variant 76/1545 45/1158 15/385 V gtC/gtG 1 -1 IDH3B HGNC HGNC:5385 protein_coding YES CCDS13032.1 ENSP00000370223 O43837 UPI000013CBC6 NM_006899.3 2/12 hmmpanther:PTHR11835,hmmpanther:PTHR11835:SF42 LOW 1 SNV 1 1 PASS rs972207839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 2663997 2663997 G C 1 0 0 0 0 0 0 0 1 7397 929 33 4 4 IDH3B 20 2663997 Silent SNP G C3N-00294_T 2374375 2663997 61780170 1174 13946 FASTKD5 0 . GRCh38 20 3148916 3148916 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.155C>G p.Ser52Cys p.S52C ENST00000380266 2/2 240 197 43 252 252 0 strelka-varscan-mutect FASTKD5,missense_variant,p.Ser52Cys,ENST00000380266,NM_021826.4;UBOX5,intron_variant,,ENST00000217173,NM_001267584.1,NM_014948.3;UBOX5,intron_variant,,ENST00000348031,NM_199415.2;UBOX5,intron_variant,,ENST00000449731,;UBOX5-AS1,intron_variant,,ENST00000446537,; C ENST00000380266 Transcript missense_variant 477/2874 155/2295 52/764 S/C tCt/tGt 1 -1 FASTKD5 HGNC HGNC:25790 protein_coding YES CCDS13048.1 ENSP00000369618 Q7L8L6 UPI000015F514 NM_021826.4 tolerated(0.09) 2/2 hmmpanther:PTHR21228:SF30,hmmpanther:PTHR21228 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 3148916 3148916 G C 1 0 0 0 0 1 0 0 0 5548 942 33 4 4 FASTKD5 20 3148916 Missense_Mutation SNP G C3N-00294_T 484919 3148916 61295251 1175 13947 ADRA1D 0 . GRCh38 20 4248440 4248440 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.518C>A p.Ala173Asp p.A173D ENST00000379453 1/2 204 108 96 224 224 0 strelka-varscan-mutect ADRA1D,missense_variant,p.Ala173Asp,ENST00000379453,NM_000678.3; T ENST00000379453 Transcript missense_variant 635/2728 518/1719 173/572 A/D gCc/gAc 1 -1 ADRA1D HGNC HGNC:280 protein_coding YES CCDS13079.1 ENSP00000368766 P25100 B0ZBE0 UPI000003B078 NM_000678.3 deleterious(0) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF14,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 4248440 4248440 G T 1 0 0 0 0 1 0 0 0 412 1203 42 2 2 ADRA1D 20 4248440 Missense_Mutation SNP G C3N-00294_T 1099524 4248440 60195727 1176 13948 PLCB1 0 . GRCh38 20 8789524 8789524 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3285G>C p.Lys1095Asn p.K1095N ENST00000338037 30/32 89 76 13 137 137 0 strelka-varscan-mutect PLCB1,missense_variant,p.Lys1095Asn,ENST00000378641,NM_182734.2;PLCB1,missense_variant,p.Lys1095Asn,ENST00000338037,NM_015192.3;PLCB1,missense_variant,p.Lys1015Asn,ENST00000612075,;PLCB1,missense_variant,p.Lys1015Asn,ENST00000617005,;PLCB1,missense_variant,p.Lys994Asn,ENST00000637919,;PLCB1,missense_variant,p.Lys1095Asn,ENST00000378637,;PLCB1,missense_variant,p.Lys182Asn,ENST00000628239,;PLCB1,upstream_gene_variant,,ENST00000637935,;PLCB1,downstream_gene_variant,,ENST00000625874,;PLCB1,downstream_gene_variant,,ENST00000626966,;PLCB1,upstream_gene_variant,,ENST00000437439,;PLCB1,upstream_gene_variant,,ENST00000637422,;PLCB1,downstream_gene_variant,,ENST00000635830,;PLCB1,downstream_gene_variant,,ENST00000636825,;PLCB1,missense_variant,p.Lys836Asn,ENST00000487210,;PLCB1,missense_variant,p.Lys152Asn,ENST00000635929,;PLCB1,downstream_gene_variant,,ENST00000494924,; C ENST00000338037 Transcript missense_variant 3672/7092 3285/3651 1095/1216 K/N aaG/aaC 1 1 PLCB1 HGNC HGNC:15917 protein_coding YES CCDS13102.1 ENSP00000338185 Q9NQ66 UPI0000131A8F NM_015192.3 deleterious(0.03) 30/32 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,Gene3D:1jadA00,PIRSF_domain:PIRSF000956,Pfam_domain:PF08703,Superfamily_domains:0053448 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 8789524 8789524 G C 1 0 0 0 0 1 0 0 0 12121 933 33 4 4 PLCB1 20 8789524 Missense_Mutation SNP G C3N-00294_T 4541084 8789524 55654643 1177 13949 E2F1 0 . GRCh38 20 33680383 33680383 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.295C>T p.Gln99Ter p.Q99* ENST00000343380 2/7 146 123 23 160 160 0 strelka-varscan-mutect E2F1,stop_gained,p.Gln99Ter,ENST00000343380,NM_005225.2; A ENST00000343380 Transcript stop_gained 435/2503 295/1314 99/437 Q/* Cag/Tag 1 -1 E2F1 HGNC HGNC:3113 protein_coding YES CCDS13224.1 ENSP00000345571 Q01094 UPI000002EDEC NM_005225.2 2/7 hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF43 HIGH 1 SNV 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 46 33680383 33680383 G A 1 0 0 0 0 0 1 0 0 4690 1299 45 3 3 E2F1 20 33680383 Nonsense_Mutation SNP G C3N-00294_T 24890859 33680383 30763784 1178 13950 MYH7B 0 . GRCh38 20 34989792 34989792 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1766C>T p.Ser589Leu p.S589L ENST00000262873 18/43 180 142 38 186 186 0 strelka-varscan-mutect MYH7B,missense_variant,p.Ser589Leu,ENST00000262873,NM_020884.4;MYH7B,missense_variant,p.Ser588Leu,ENST00000618182,;MIR499A,upstream_gene_variant,,ENST00000384903,;MIR499B,downstream_gene_variant,,ENST00000636498,; T ENST00000262873 Transcript missense_variant 1858/6293 1766/5952 589/1983 S/L tCa/tTa 1 1 MYH7B HGNC HGNC:15906 protein_coding YES CCDS42869.1 ENSP00000262873 A7E2Y1 UPI000046D367 NM_020884.4 deleterious(0) 18/43 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF358,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 34989792 34989792 C T 1 0 0 0 0 1 0 0 0 10040 838 29 3 3 MYH7B 20 34989792 Missense_Mutation SNP C C3N-00294_T 1309409 34989792 29454375 1179 13951 TRPC4AP 0 . GRCh38 20 35044589 35044589 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.781G>A p.Asp261Asn p.D261N ENST00000252015 7/19 250 198 52 295 294 1 strelka-varscan-mutect TRPC4AP,missense_variant,p.Asp261Asn,ENST00000252015,NM_015638.2;TRPC4AP,missense_variant,p.Asp261Asn,ENST00000451813,NM_199368.1; T ENST00000252015 Transcript missense_variant 871/3226 781/2394 261/797 D/N Gat/Aat 1 -1 TRPC4AP HGNC HGNC:16181 protein_coding YES CCDS13246.1 ENSP00000252015 Q8TEL6 UPI000004FADD NM_015638.2 deleterious(0.01) 7/19 hmmpanther:PTHR31743,hmmpanther:PTHR31743:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 35044589 35044589 C T 1 0 0 0 0 1 0 0 0 17086 826 29 3 3 TRPC4AP 20 35044589 Missense_Mutation SNP C C3N-00294_T 54797 35044589 29399578 1180 13952 MMP24 0 . GRCh38 20 35254643 35254643 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.706G>C p.Asp236His p.D236H ENST00000246186 4/9 282 231 51 324 324 0 strelka-varscan-mutect MMP24,missense_variant,p.Asp236His,ENST00000246186,NM_006690.3;MMP24-AS1,intron_variant,,ENST00000635104,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000433764,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,downstream_gene_variant,,ENST00000453892,; C ENST00000246186 Transcript missense_variant 791/4414 706/1938 236/645 D/H Gat/Cat COSM3840845 1 1 MMP24 HGNC HGNC:7172 protein_coding YES CCDS46593.1 ENSP00000246186 Q9Y5R2 UPI000012F259 NM_006690.3 deleterious(0) 4/9 hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 35254643 35254643 G C 1 0 0 0 0 1 0 0 0 9624 1290 45 4 4 MMP24 20 35254643 Missense_Mutation SNP G C3N-00294_T 210054 35254643 29189524 1181 13953 FAM83C 0 . GRCh38 20 35287700 35287700 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1079C>T p.Ser360Phe p.S360F ENST00000374408 4/4 360 278 82 382 382 0 strelka-varscan-mutect FAM83C,missense_variant,p.Ser360Phe,ENST00000374408,NM_178468.5;EIF6,upstream_gene_variant,,ENST00000374450,NM_002212.3;EIF6,upstream_gene_variant,,ENST00000374436,NM_181468.2;EIF6,upstream_gene_variant,,ENST00000621148,NM_001267810.1;EIF6,upstream_gene_variant,,ENST00000374443,NM_181466.2;EIF6,upstream_gene_variant,,ENST00000456600,;FAM83C-AS1,downstream_gene_variant,,ENST00000429167,;EIF6,upstream_gene_variant,,ENST00000462894,;EIF6,upstream_gene_variant,,ENST00000447927,;EIF6,upstream_gene_variant,,ENST00000440766,;EIF6,upstream_gene_variant,,ENST00000415116,; A ENST00000374408 Transcript missense_variant 1176/3145 1079/2244 360/747 S/F tCc/tTc 1 -1 FAM83C HGNC HGNC:16121 protein_coding YES CCDS13251.1 ENSP00000363529 Q9BQN1 UPI0000072DC0 NM_178468.5 deleterious(0) 4/4 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF3 MODERATE 1 SNV 1 1 PASS rs951918774 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 35287700 35287700 G A 1 0 0 0 0 1 0 0 0 5493 1174 41 3 3 FAM83C 20 35287700 Missense_Mutation SNP G C3N-00294_T 33057 35287700 29156467 1182 13954 CEP250 0 . GRCh38 20 35494649 35494649 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.3159G>C p.Glu1053Asp p.E1053D ENST00000397527 24/35 115 90 25 123 123 0 strelka-varscan-mutect CEP250,missense_variant,p.Glu1053Asp,ENST00000397527,NM_007186.4;RP3-477O4.14,upstream_gene_variant,,ENST00000453914,;RP3-477O4.14,upstream_gene_variant,,ENST00000416260,;RP3-477O4.14,upstream_gene_variant,,ENST00000444933,;CEP250,non_coding_transcript_exon_variant,,ENST00000487467,;CEP250,upstream_gene_variant,,ENST00000425525,; C ENST00000397527 Transcript missense_variant 3879/15703 3159/7329 1053/2442 E/D gaG/gaC 1 1 CEP250 HGNC HGNC:1859 protein_coding YES CCDS13255.1 ENSP00000380661 Q9BV73 UPI000006FE8F NM_007186.4 tolerated(0.05) 24/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF1,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 35494649 35494649 G C 1 0 0 0 0 1 0 0 0 2968 933 33 4 4 CEP250 20 35494649 Missense_Mutation SNP G C3N-00294_T 206949 35494649 28949518 1183 13955 ZSWIM1 0 . GRCh38 20 45882821 45882821 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.229G>A p.Glu77Lys p.E77K ENST00000372523 2/2 255 217 38 305 305 0 strelka-varscan-mutect ZSWIM1,missense_variant,p.Glu77Lys,ENST00000372523,NM_080603.4;ZSWIM1,missense_variant,p.Glu77Lys,ENST00000372520,;ZSWIM3,downstream_gene_variant,,ENST00000255152,NM_080752.3;SPATA25,downstream_gene_variant,,ENST00000372519,NM_080608.3; A ENST00000372523 Transcript missense_variant 324/2769 229/1458 77/485 E/K Gag/Aag 1 1 ZSWIM1 HGNC HGNC:16155 protein_coding YES CCDS13382.2 ENSP00000361601 Q9BR11 UPI0000470896 NM_080603.4 tolerated(0.18) 2/2 hmmpanther:PTHR31569,hmmpanther:PTHR31569:SF0 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 45882821 45882821 G A 1 0 0 0 0 1 0 0 0 18841 1291 45 3 3 ZSWIM1 20 45882821 Missense_Mutation SNP G C3N-00294_T 10388172 45882821 18561346 1184 13956 ELMO2 0 . GRCh38 20 46374641 46374641 + Splice_Site SNP C C G novel C3N-00294_T C3N-00294_N C C c.1066-1G>C p.X356_splice ENST00000290246 107 80 27 116 116 0 strelka-varscan-mutect ELMO2,splice_acceptor_variant,,ENST00000372176,;ELMO2,splice_acceptor_variant,,ENST00000290246,NM_133171.3;ELMO2,splice_acceptor_variant,,ENST00000396391,NM_182764.1;ELMO2,splice_acceptor_variant,,ENST00000352077,;ELMO2,splice_acceptor_variant,,ENST00000425546,;ELMO2,upstream_gene_variant,,ENST00000452857,;ELMO2,downstream_gene_variant,,ENST00000450812,;RP11-394O2.3,intron_variant,,ENST00000612368,;ELMO2,splice_acceptor_variant,,ENST00000488853,;ELMO2,splice_acceptor_variant,,ENST00000462491,;ELMO2,splice_acceptor_variant,,ENST00000481852,;ELMO2,upstream_gene_variant,,ENST00000464448,;ELMO2,splice_acceptor_variant,,ENST00000467800,; G ENST00000290246 Transcript splice_acceptor_variant -/3669 1066/2163 356/720 1 -1 ELMO2 HGNC HGNC:17233 protein_coding YES CCDS13398.1 ENSP00000290246 Q96JJ3 UPI000013F6C4 NM_133171.3 13/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 46 46374641 46374641 C G 1 0 0 0 0 0 0 1 0 4900 927 32 4 4 ELMO2 20 46374641 Splice_Site SNP C C3N-00294_T 491820 46374641 18069526 1185 13957 ZMYND8 0 . GRCh38 20 47276390 47276390 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1404G>C p.Gln468His p.Q468H ENST00000471951 11/23 59 52 7 84 84 0 strelka-varscan-mutect ZMYND8,missense_variant,p.Gln448His,ENST00000355972,NM_001281773.2;ZMYND8,missense_variant,p.Gln448His,ENST00000396281,NM_001281772.2;ZMYND8,missense_variant,p.Gln448His,ENST00000446994,;ZMYND8,missense_variant,p.Gln448His,ENST00000311275,;ZMYND8,missense_variant,p.Gln475His,ENST00000536340,;ZMYND8,missense_variant,p.Gln385His,ENST00000372023,NM_001281779.2,NM_001281780.2;ZMYND8,missense_variant,p.Gln448His,ENST00000611941,;ZMYND8,missense_variant,p.Gln443His,ENST00000360911,NM_183048.3,NM_001281778.2;ZMYND8,missense_variant,p.Gln448His,ENST00000262975,NM_001281774.2;ZMYND8,missense_variant,p.Gln468His,ENST00000471951,NM_001281775.2,NM_001281776.2;ZMYND8,missense_variant,p.Gln423His,ENST00000619049,;ZMYND8,missense_variant,p.Gln468His,ENST00000352431,NM_012408.5,NM_001281783.2;ZMYND8,missense_variant,p.Gln443His,ENST00000458360,NM_001281771.2;ZMYND8,missense_variant,p.Gln375His,ENST00000467200,;ZMYND8,missense_variant,p.Gln468His,ENST00000461685,NM_001281777.2,NM_183047.3;ZMYND8,missense_variant,p.Gln443His,ENST00000617418,NM_001281782.2;ZMYND8,missense_variant,p.Gln443His,ENST00000540497,NM_001281781.2,NM_001281784.2;ZMYND8,non_coding_transcript_exon_variant,,ENST00000468376,; G ENST00000471951 Transcript missense_variant 1431/4053 1404/3705 468/1234 Q/H caG/caC 1 -1 ZMYND8 HGNC HGNC:9397 protein_coding YES CCDS63306.1 ENSP00000420095 Q9ULU4 UPI0000695D9A NM_001281775.2,NM_001281776.2 deleterious_low_confidence(0) 11/23 Pfam_domain:PF12064,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF13 MODERATE 1 SNV 1 1 PASS rs6090652 . 0 205 5 0 0 0 0 0 -16.23525 1 1 1 1 0 G 3 3 46 47276390 47276390 C G 1 0 0 0 0 1 0 0 0 18290 680 24 4 4 ZMYND8 20 47276390 Missense_Mutation SNP C C3N-00294_T 901749 47276390 17167777 1186 13958 SULF2 0 . GRCh38 20 47736751 47736751 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.367G>A p.Glu123Lys p.E123K ENST00000359930 3/21 393 301 92 393 393 0 strelka-varscan-mutect SULF2,missense_variant,p.Glu123Lys,ENST00000359930,NM_018837.3;SULF2,missense_variant,p.Glu123Lys,ENST00000484875,NM_001161841.1;SULF2,missense_variant,p.Glu123Lys,ENST00000467815,NM_198596.2;SULF2,missense_variant,p.Glu123Lys,ENST00000437955,;SULF2,non_coding_transcript_exon_variant,,ENST00000478766,;SULF2,intron_variant,,ENST00000474450,;SULF2,non_coding_transcript_exon_variant,,ENST00000463221,; T ENST00000359930 Transcript missense_variant 1219/4915 367/2613 123/870 E/K Gag/Aag 1 -1 SULF2 HGNC HGNC:20392 protein_coding YES CCDS13408.1 ENSP00000353007 Q8IWU5 UPI000003FFBA NM_018837.3 deleterious(0) 3/21 hmmpanther:PTHR10342:SF67,hmmpanther:PTHR10342,Pfam_domain:PF00884,Gene3D:3.40.720.10,PIRSF_domain:PIRSF036665,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 47736751 47736751 C T 1 0 0 0 0 1 0 0 0 15759 893 31 1 1 SULF2 20 47736751 Missense_Mutation SNP C C3N-00294_T 460361 47736751 16707416 1187 13959 DPM1 0 . GRCh38 20 50958456 50958456 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.68G>A p.Arg23Gln p.R23Q ENST00000371588 1/9 431 330 101 488 486 2 strelka-varscan-mutect DPM1,missense_variant,p.Arg23Gln,ENST00000371582,NM_001317035.1;DPM1,missense_variant,p.Arg23Gln,ENST00000371588,NM_003859.1;DPM1,missense_variant,p.Arg23Gln,ENST00000371584,;DPM1,missense_variant,p.Arg23Gln,ENST00000413082,;MOCS3,upstream_gene_variant,,ENST00000244051,NM_014484.4;DPM1,non_coding_transcript_exon_variant,,ENST00000466152,; T ENST00000371588 Transcript missense_variant 95/1075 68/783 23/260 R/Q cGa/cAa 1 -1 DPM1 HGNC HGNC:3005 protein_coding YES CCDS13434.1 ENSP00000360644 O60762 A0A0S2Z4Y5 UPI0000129751 NM_003859.1 tolerated(0.54) 1/9 hmmpanther:PTHR10859,Low_complexity_(Seg):seg,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 50958456 50958456 C T 1 0 0 0 0 1 0 0 0 4539 884 31 1 1 DPM1 20 50958456 Missense_Mutation SNP C C3N-00294_T 3221705 50958456 13485711 1188 13960 BCAS1 0 . GRCh38 20 53953590 53953590 + Missense_Mutation SNP C C T rs193016127 C3N-00294_T C3N-00294_N C C c.1522G>A p.Glu508Lys p.E508K ENST00000395961 11/12 409 330 79 474 473 1 strelka-varscan-mutect BCAS1,missense_variant,p.Glu379Lys,ENST00000448484,;BCAS1,missense_variant,p.Glu508Lys,ENST00000395961,NM_003657.2;BCAS1,missense_variant,p.Glu430Lys,ENST00000371435,NM_001316361.2,NM_001323347.1;BCAS1,missense_variant,p.Glu171Lys,ENST00000422805,; T ENST00000395961 Transcript missense_variant 1689/3303 1522/1755 508/584 E/K Gag/Aag rs193016127 1 -1 BCAS1 HGNC HGNC:974 protein_coding YES CCDS13444.1 ENSP00000379290 O75363 UPI000013D2E2 NM_003657.2 deleterious(0) 11/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15016 MODERATE 1 SNV 1 1 PASS rs193016127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 53953590 53953590 C T 1 0 0 0 0 1 0 0 0 1497 893 31 1 1 BCAS1 20 53953590 Missense_Mutation SNP C C3N-00294_T 2995134 53953590 10490577 1189 13961 SPO11 0 . GRCh38 20 57329988 57329988 + Missense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.121C>A p.Leu41Met p.L41M ENST00000371263 1/13 66 43 23 76 76 0 strelka-varscan-mutect SPO11,missense_variant,p.Leu41Met,ENST00000371263,NM_012444.2;SPO11,missense_variant,p.Leu41Met,ENST00000345868,NM_198265.1;SPO11,missense_variant,p.Leu41Met,ENST00000371260,;SPO11,missense_variant,p.Leu19Met,ENST00000418127,;SPO11,upstream_gene_variant,,ENST00000494972,;RP3-481F12.1,downstream_gene_variant,,ENST00000455840,; A ENST00000371263 Transcript missense_variant 230/1834 121/1191 41/396 L/M Ctg/Atg 1 1 SPO11 HGNC HGNC:11250 protein_coding YES CCDS13456.1 ENSP00000360310 Q9Y5K1 UPI0000135E5E NM_012444.2 tolerated_low_confidence(0.11) 1/13 hmmpanther:PTHR10848,Pfam_domain:PF03533,Prints_domain:PR01551 MODERATE 1 SNV 1 1 PASS rs1453709024 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 57329988 57329988 C A 1 0 0 0 0 1 0 0 0 15430 680 24 2 2 SPO11 20 57329988 Missense_Mutation SNP C C3N-00294_T 3376398 57329988 7114179 1190 13962 CTCFL 0 . GRCh38 20 57524177 57524177 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.29C>G p.Ser10Cys p.S10C ENST00000423479 2/12 88 74 14 104 104 0 strelka-varscan-mutect CTCFL,missense_variant,p.Ser10Cys,ENST00000608263,NM_001269041.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000429804,NM_001269046.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000609232,NM_080618.3;CTCFL,missense_variant,p.Ser10Cys,ENST00000243914,;CTCFL,missense_variant,p.Ser10Cys,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000422869,NM_001269047.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000432255,NM_001269048.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000608425,NM_001269045.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000608440,NM_001269044.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000423479,NM_001269043.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000608158,NM_001269052.1;CTCFL,missense_variant,p.Ser10Cys,ENST00000481655,NM_001269051.1;CTCFL,intron_variant,,ENST00000539382,NM_001269050.1;CTCFL,intron_variant,,ENST00000433949,NM_001269049.1;CTCFL,intron_variant,,ENST00000608903,NM_001269055.1;CTCFL,intron_variant,,ENST00000502686,NM_001269054.1;CTCFL,intron_variant,,ENST00000608858,;CTCFL,missense_variant,p.Ser10Cys,ENST00000426658,;CTCFL,missense_variant,p.Ser10Cys,ENST00000422109,;CTCFL,missense_variant,p.Ser10Cys,ENST00000608720,;CTCFL,non_coding_transcript_exon_variant,,ENST00000607923,;CTCFL,intron_variant,,ENST00000608108,; C ENST00000423479 Transcript missense_variant 120/2478 29/2103 10/700 S/C tCt/tGt 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 deleterious(0.01) 2/12 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 57524177 57524177 G C 1 0 0 0 0 1 0 0 0 3808 942 33 4 4 CTCFL 20 57524177 Missense_Mutation SNP G C3N-00294_T 194189 57524177 6919990 1191 13963 PCK1 0 . GRCh38 20 57565065 57565065 + Silent SNP C C T C3N-00294_T C3N-00294_N C C c.1344C>T p.= p.L448L ENST00000319441 9/10 152 133 19 141 140 1 strelka-varscan-mutect PCK1,synonymous_variant,p.=,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,non_coding_transcript_exon_variant,,ENST00000485958,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000470051,; T ENST00000319441 Transcript synonymous_variant 1508/4341 1344/1869 448/622 L ctC/ctT COSM3548158 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 9/10 HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,Gene3D:3.90.228.20,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 57565065 57565065 C T 1 0 0 0 0 0 0 0 1 11669 813 29 3 3 PCK1 20 57565065 Silent SNP C C3N-00294_T 40888 57565065 6879102 1192 13964 PCK1 0 . GRCh38 20 57565591 57565591 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.1656C>G p.= p.L552L ENST00000319441 10/10 278 210 68 300 300 0 strelka-varscan-mutect PCK1,synonymous_variant,p.=,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000485958,;PCK1,downstream_gene_variant,,ENST00000470051,; G ENST00000319441 Transcript synonymous_variant 1820/4341 1656/1869 552/622 L ctC/ctG COSM3379096,COSM3548164 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 10/10 HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,Gene3D:3.90.228.20,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 46 57565591 57565591 C G 1 0 0 0 0 0 0 0 1 11669 813 29 4 4 PCK1 20 57565591 Silent SNP C C3N-00294_T 526 57565591 6878576 1193 13965 HRH3 0 . GRCh38 20 62216687 62216687 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.657C>T p.= p.L219L ENST00000340177 3/3 279 234 45 292 292 0 strelka-varscan-mutect HRH3,synonymous_variant,p.=,ENST00000340177,NM_007232.2;HRH3,synonymous_variant,p.=,ENST00000317393,;HRH3,intron_variant,,ENST00000611492,; A ENST00000340177 Transcript synonymous_variant 942/2659 657/1338 219/445 L ctC/ctT 1 -1 HRH3 HGNC HGNC:5184 protein_coding YES CCDS13493.1 ENSP00000342560 Q9Y5N1 UPI000012C6ED NM_007232.2 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF292,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 62216687 62216687 G A 1 0 0 0 0 0 0 0 1 7252 1277 45 3 3 HRH3 20 62216687 Silent SNP G C3N-00294_T 4651096 62216687 2227480 1194 13966 RPS21 0 . GRCh38 20 62387624 62387624 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.64C>G p.Arg22Gly p.R22G ENST00000343986 3/6 66 45 21 71 70 1 strelka-varscan-mutect RPS21,missense_variant,p.Arg22Gly,ENST00000370562,;RPS21,missense_variant,p.Arg22Gly,ENST00000450116,;RPS21,missense_variant,p.Arg22Gly,ENST00000370592,;RPS21,missense_variant,p.Arg22Gly,ENST00000343986,NM_001024.3;CABLES2,downstream_gene_variant,,ENST00000279101,NM_031215.2;CABLES2,downstream_gene_variant,,ENST00000453274,;RP5-908M14.9,upstream_gene_variant,,ENST00000610979,;RPS21,non_coding_transcript_exon_variant,,ENST00000492356,; G ENST00000343986 Transcript missense_variant 103/344 64/252 22/83 R/G Cgc/Ggc 1 1 RPS21 HGNC HGNC:10409 protein_coding YES CCDS13497.1 ENSP00000345957 P63220 Q6FGH5 UPI0000134E79 NM_001024.3 deleterious(0) 3/6 hmmpanther:PTHR10442,hmmpanther:PTHR10442:SF1,Pfam_domain:PF01249,PIRSF_domain:PIRSF002148 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 62387624 62387624 C G 1 0 0 0 0 1 0 0 0 13888 884 31 4 4 RPS21 20 62387624 Missense_Mutation SNP C C3N-00294_T 170937 62387624 2056543 1195 13967 OGFR 0 . GRCh38 20 62813500 62813500 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1885C>T p.Pro629Ser p.P629S ENST00000290291 7/7 89 69 20 69 69 0 strelka-varscan-mutect OGFR,missense_variant,p.Pro577Ser,ENST00000370461,;OGFR,missense_variant,p.Pro629Ser,ENST00000290291,NM_007346.2;OGFR,missense_variant,p.Pro315Ser,ENST00000621591,;COL9A3,upstream_gene_variant,,ENST00000343916,NM_001853.3;COL9A3,upstream_gene_variant,,ENST00000452372,;OGFR,downstream_gene_variant,,ENST00000450048,;COL9A3,upstream_gene_variant,,ENST00000489045,;COL9A3,upstream_gene_variant,,ENST00000477612,; T ENST00000290291 Transcript missense_variant 1910/2410 1885/2034 629/677 P/S Cct/Tct 1 1 OGFR HGNC HGNC:15768 protein_coding YES CCDS13504.1 ENSP00000290291 Q9NZT2 UPI000013F107 NM_007346.2 tolerated_low_confidence(0.47) 7/7 Pfam_domain:PF04680 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 62813500 62813500 C T 1 0 0 0 0 1 0 0 0 10918 521 18 3 3 OGFR 20 62813500 Missense_Mutation SNP C C3N-00294_T 425876 62813500 1630667 1196 13968 EVA1C 0 . GRCh38 21 32412982 32412982 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.129C>T p.= p.S43S ENST00000300255 1/8 69 52 17 66 66 0 strelka-varscan-mutect EVA1C,synonymous_variant,p.=,ENST00000300255,NM_058187.4;EVA1C,synonymous_variant,p.=,ENST00000382699,NM_001286556.1;EVA1C,synonymous_variant,p.=,ENST00000401402,;EVA1C,non_coding_transcript_exon_variant,,ENST00000481638,;EVA1C,intron_variant,,ENST00000459833,;EVA1C,synonymous_variant,p.=,ENST00000437338,;EVA1C,synonymous_variant,p.=,ENST00000435323,;EVA1C,synonymous_variant,p.=,ENST00000457807,;EVA1C,non_coding_transcript_exon_variant,,ENST00000469079,; T ENST00000300255 Transcript synonymous_variant 602/1998 129/1326 43/441 S tcC/tcT 1 1 EVA1C HGNC HGNC:13239 protein_coding YES CCDS13614.1 ENSP00000300255 P58658 UPI00000373F4 NM_058187.4 1/8 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF311 LOW 1 SNV 1 1 PASS rs776985836 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 32412982 32412982 C T 1 0 0 0 0 0 0 0 1 5151 581 21 3 3 EVA1C 21 32412982 Silent SNP C C3N-00294_T 32412982 14297001 1197 13969 CBR1 0 . GRCh38 21 36072832 36072832 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.784G>T p.Glu262Ter p.E262* ENST00000290349 3/3 121 91 30 136 136 0 strelka-varscan-mutect CBR1,stop_gained,p.Glu262Ter,ENST00000290349,NM_001757.3;CBR1,3_prime_UTR_variant,,ENST00000530908,NM_001286789.1;SETD4,intron_variant,,ENST00000399201,;CBR1,downstream_gene_variant,,ENST00000439427,;CBR1,downstream_gene_variant,,ENST00000399191,;AP000688.14,intron_variant,,ENST00000535199,;AP000688.14,downstream_gene_variant,,ENST00000415147,;CBR1,downstream_gene_variant,,ENST00000466328,; T ENST00000290349 Transcript stop_gained 959/1293 784/834 262/277 E/* Gag/Tag 1 1 CBR1 HGNC HGNC:1548 protein_coding YES CCDS13641.1 ENSP00000290349 P16152 UPI000004C784 NM_001757.3 3/3 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 36072832 36072832 G T 1 0 0 0 0 0 1 0 0 2409 1291 45 2 2 CBR1 21 36072832 Nonsense_Mutation SNP G C3N-00294_T 3659850 36072832 10637151 1198 13970 MORC3 0 . GRCh38 21 36360183 36360183 + Splice_Site SNP G G C novel C3N-00294_T C3N-00294_N G G c.1332-1G>C p.X444_splice ENST00000400485 106 83 23 137 137 0 strelka-varscan-mutect MORC3,splice_acceptor_variant,,ENST00000400485,NM_001320446.1,NM_001320445.1,NM_015358.2;AP000692.9,upstream_gene_variant,,ENST00000397184,;MORC3,splice_acceptor_variant,,ENST00000487909,;MORC3,downstream_gene_variant,,ENST00000485299,;MORC3,upstream_gene_variant,,ENST00000484028,; C ENST00000400485 Transcript splice_acceptor_variant -/4246 1332/2820 444/939 1 1 MORC3 HGNC HGNC:23572 protein_coding YES CCDS42924.1 ENSP00000383333 Q14149 UPI0000167F94 NM_001320446.1,NM_001320445.1,NM_015358.2 11/16 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 46 36360183 36360183 G C 1 0 0 0 0 0 0 1 0 9667 956 33 4 4 MORC3 21 36360183 Splice_Site SNP G C3N-00294_T 287351 36360183 10349800 1199 13971 PDXK 0 . GRCh38 21 43732583 43732583 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.206G>T p.Arg69Ile p.R69I ENST00000327574 2/4 411 340 71 544 544 0 strelka-varscan-mutect PDXK,missense_variant,p.Arg69Ile,ENST00000327574,;PDXK,intron_variant,,ENST00000291565,NM_003681.4;PDXK,intron_variant,,ENST00000468090,;PDXK,intron_variant,,ENST00000398081,;PDXK,upstream_gene_variant,,ENST00000621478,;PDXK,intron_variant,,ENST00000476313,;PDXK,intron_variant,,ENST00000498040,;PDXK,intron_variant,,ENST00000398085,;PDXK,intron_variant,,ENST00000470029,;PDXK,intron_variant,,ENST00000472777,;PDXK,upstream_gene_variant,,ENST00000481512,;PDXK,downstream_gene_variant,,ENST00000438837,; T ENST00000327574 Transcript missense_variant 556/2583 206/447 69/148 R/I aGa/aTa 1 1 PDXK HGNC HGNC:8819 protein_coding ENSP00000333624 A8MT14 UPI0000E5A3F7 2/4 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 43732583 43732583 G T 1 0 0 0 0 1 0 0 0 11785 942 33 2 2 PDXK 21 43732583 Missense_Mutation SNP G C3N-00294_T 7372400 43732583 2977400 1200 13972 KRTAP10-1 0 . GRCh38 21 44539890 44539890 + Silent SNP C C T rs781835494 C3N-00294_T C3N-00294_N C C c.261G>A p.= p.P87P ENST00000400375 1/1 653 569 84 726 723 3 varscan-mutect KRTAP10-1,synonymous_variant,p.=,ENST00000400375,NM_198691.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,; T ENST00000400375 Transcript synonymous_variant 306/1215 261/849 87/282 P ccG/ccA rs781835494 1 -1 KRTAP10-1 HGNC HGNC:22966 protein_coding YES CCDS42954.1 ENSP00000383226 P60331 UPI00003D4D6C NM_198691.2 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72,Low_complexity_(Seg):seg LOW SNV 1 PASS rs781835494 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 44539890 44539890 C T 1 0 0 0 0 0 0 0 1 8388 639 23 1 1 KRTAP10-1 21 44539890 Silent SNP C C3N-00294_T 807307 44539890 2170093 1201 13973 TBX1 0 . GRCh38 22 19765053 19765053 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.780C>T p.= p.F260F ENST00000332710 6/9 517 415 102 506 505 1 strelka-varscan-mutect TBX1,synonymous_variant,p.=,ENST00000332710,NM_080647.1;TBX1,synonymous_variant,p.=,ENST00000359500,NM_005992.1;TBX1,synonymous_variant,p.=,ENST00000329705,NM_080646.1;TBX1,synonymous_variant,p.=,ENST00000621939,;TBX1,downstream_gene_variant,,ENST00000475303,;TBX1,upstream_gene_variant,,ENST00000484336,; T ENST00000332710 Transcript synonymous_variant 909/2084 780/1488 260/495 F ttC/ttT 1 1 TBX1 HGNC HGNC:11592 protein_coding YES CCDS13767.1 ENSP00000331791 O43435 D9ZGG0 UPI0000073068 NM_080647.1 6/9 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF104,Gene3D:1h6fA00,Pfam_domain:PF00907,SMART_domains:SM00425,Superfamily_domains:SSF49417 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 19765053 19765053 C T 1 0 0 0 0 0 0 0 1 16055 825 29 3 3 TBX1 22 19765053 Silent SNP C C3N-00294_T 19765053 31053415 1202 13974 TBX1 0 . GRCh38 22 19765947 19765947 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.954C>T p.= p.F318F ENST00000332710 8/9 184 153 31 140 140 0 strelka-varscan-mutect TBX1,synonymous_variant,p.=,ENST00000332710,NM_080647.1;TBX1,synonymous_variant,p.=,ENST00000359500,NM_005992.1;TBX1,synonymous_variant,p.=,ENST00000329705,NM_080646.1;TBX1,synonymous_variant,p.=,ENST00000621939,;TBX1,non_coding_transcript_exon_variant,,ENST00000484336,;TBX1,downstream_gene_variant,,ENST00000475303,; T ENST00000332710 Transcript synonymous_variant 1083/2084 954/1488 318/495 F ttC/ttT 1 1 TBX1 HGNC HGNC:11592 protein_coding YES CCDS13767.1 ENSP00000331791 O43435 D9ZGG0 UPI0000073068 NM_080647.1 8/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF104 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 19765947 19765947 C T 1 0 0 0 0 0 0 0 1 16055 883 31 1 1 TBX1 22 19765947 Silent SNP C C3N-00294_T 894 19765947 31052521 1203 13975 BCR 0 . GRCh38 22 23289523 23289523 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2609G>C p.Arg870Thr p.R870T ENST00000305877 13/23 121 99 22 118 118 0 strelka-varscan-mutect BCR,missense_variant,p.Arg870Thr,ENST00000305877,NM_004327.3;BCR,missense_variant,p.Gln435His,ENST00000398512,;BCR,missense_variant,p.Arg870Thr,ENST00000359540,NM_021574.2;BCR,downstream_gene_variant,,ENST00000427791,;BCR,upstream_gene_variant,,ENST00000419722,;BCR,non_coding_transcript_exon_variant,,ENST00000487968,;BCR,downstream_gene_variant,,ENST00000466076,; C ENST00000305877 Transcript missense_variant 3360/7082 2609/3816 870/1271 R/T aGa/aCa 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 tolerated(0.09) 13/23 PROSITE_profiles:PS50004,hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 23289523 23289523 G C 1 0 0 0 0 1 0 0 0 1535 942 33 4 4 BCR 22 23289523 Missense_Mutation SNP G C3N-00294_T 3523576 23289523 27528945 1204 13976 MYO18B 0 . GRCh38 22 25772361 25772361 + Missense_Mutation SNP G G A rs751222865 C3N-00294_T C3N-00294_N G G c.1720G>A p.Glu574Lys p.E574K ENST00000335473 7/44 103 81 22 135 135 0 strelka-varscan-mutect MYO18B,missense_variant,p.Glu574Lys,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Glu574Lys,ENST00000407587,;MYO18B,missense_variant,p.Glu574Lys,ENST00000536101,;MYO18B,missense_variant,p.Glu574Lys,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript missense_variant 1970/8565 1720/7704 574/2567 E/K Gag/Aag rs751222865,COSM1415321,COSM4530707 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0) 7/44 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs751222865 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 25772361 25772361 G A 1 0 0 0 0 1 0 0 0 10067 1059 37 1 1 MYO18B 22 25772361 Missense_Mutation SNP G C3N-00294_T 2482838 25772361 25046107 1205 13977 MYO18B 0 . GRCh38 22 25843855 25843855 + Nonsense_Mutation SNP C C A rs775172877 C3N-00294_T C3N-00294_N C C c.3329C>A p.Ser1110Ter p.S1110* ENST00000335473 18/44 106 79 27 136 136 0 strelka-varscan-mutect MYO18B,stop_gained,p.Ser1110Ter,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,stop_gained,p.Ser1111Ter,ENST00000407587,;MYO18B,stop_gained,p.Ser1110Ter,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript stop_gained 3579/8565 3329/7704 1110/2567 S/* tCg/tAg rs775172877 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 18/44 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS rs775172877 . 0 199 10 0 0 0 0 0 -20 0.9999938 1 1 1 0 A 4 1 46 25843855 25843855 C A 1 0 0 0 0 0 1 0 0 10067 893 31 1 1 MYO18B 22 25843855 Nonsense_Mutation SNP C C3N-00294_T 71494 25843855 24974613 1206 13978 NEFH 0 . GRCh38 22 29481081 29481081 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.819G>C p.Glu273Asp p.E273D ENST00000310624 1/4 423 333 90 508 508 0 strelka-varscan-mutect NEFH,missense_variant,p.Glu273Asp,ENST00000310624,NM_021076.3;AC000035.3,non_coding_transcript_exon_variant,,ENST00000634116,;RFPL1S,upstream_gene_variant,,ENST00000461286,;RFPL1S,upstream_gene_variant,,ENST00000419368,; C ENST00000310624 Transcript missense_variant 852/3783 819/3063 273/1020 E/D gaG/gaC COSM5429609 1 1 NEFH HGNC HGNC:7737 protein_coding YES CCDS13858.1 ENSP00000311997 P12036 UPI00001AEF71 NM_021076.3 tolerated(0.25) 1/4 hmmpanther:PTHR23214,hmmpanther:PTHR23214:SF1,Pfam_domain:PF00038,SMART_domains:SM01391 1 MODERATE 1 SNV 1 1 1 PASS rs917756240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 29481081 29481081 G C 1 0 0 0 0 1 0 0 0 10342 933 33 4 4 NEFH 22 29481081 Missense_Mutation SNP G C3N-00294_T 3637226 29481081 21337387 1207 13979 GATSL3 0 . GRCh38 22 30286286 30286286 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.720C>G p.= p.V240V ENST00000407689 6/9 100 84 16 100 100 0 strelka-varscan-mutect GATSL3,synonymous_variant,p.=,ENST00000407689,NM_001037666.2;RP1-130H16.18,intron_variant,,ENST00000434291,;GATSL3,intron_variant,,ENST00000404953,;GATSL3,intron_variant,,ENST00000459785,;GATSL3,downstream_gene_variant,,ENST00000498572,;GATSL3,downstream_gene_variant,,ENST00000464854,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000330168,;RP1-130H16.18,3_prime_UTR_variant,,ENST00000447976,;GATSL3,3_prime_UTR_variant,,ENST00000421236,;GATSL3,non_coding_transcript_exon_variant,,ENST00000497605,;RP1-130H16.18,intron_variant,,ENST00000434987,;RP1-130H16.18,intron_variant,,ENST00000418047,;GATSL3,intron_variant,,ENST00000440839,;GATSL3,downstream_gene_variant,,ENST00000471480,;GATSL3,downstream_gene_variant,,ENST00000463795,;GATSL3,downstream_gene_variant,,ENST00000425691,;GATSL3,downstream_gene_variant,,ENST00000415484,;GATSL3,downstream_gene_variant,,ENST00000492159,;GATSL3,downstream_gene_variant,,ENST00000440704,; C ENST00000407689 Transcript synonymous_variant 850/1623 720/990 240/329 V gtC/gtG 1 -1 GATSL3 HGNC HGNC:34423 protein_coding YES CCDS43001.1 ENSP00000384183 Q8WTX7 UPI0000071943 NM_001037666.2 6/9 hmmpanther:PTHR31131,hmmpanther:PTHR31131:SF3,Gene3D:1zvpA00 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 30286286 30286286 G C 1 0 0 0 0 0 0 0 1 6137 1277 45 4 4 GATSL3 22 30286286 Silent SNP G C3N-00294_T 805205 30286286 20532182 1208 13980 SEC14L2 0 . GRCh38 22 30399714 30399714 + Silent SNP C C G C3N-00294_T C3N-00294_N C C c.126C>G p.= p.L42L ENST00000615189 2/12 78 67 11 95 95 0 strelka-varscan-mutect SEC14L2,synonymous_variant,p.=,ENST00000615189,NM_012429.4;SEC14L2,synonymous_variant,p.=,ENST00000405717,NM_033382.2;SEC14L2,synonymous_variant,p.=,ENST00000402592,NM_001204204.2;SEC14L2,synonymous_variant,p.=,ENST00000415072,;SEC14L2,intron_variant,,ENST00000617837,NM_001291932.1;SEC14L2,intron_variant,,ENST00000428195,;SEC14L2,intron_variant,,ENST00000429917,;RNF215,intron_variant,,ENST00000431544,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000459728,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000416523,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000485482,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000484486,;SEC14L2,synonymous_variant,p.=,ENST00000437022,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000619483,;SEC14L2,non_coding_transcript_exon_variant,,ENST00000464335,;SEC14L2,intron_variant,,ENST00000452649,; G ENST00000615189 Transcript synonymous_variant 386/4382 126/1212 42/403 L ctC/ctG COSM4462980 1 1 SEC14L2 HGNC HGNC:10699 protein_coding YES CCDS13876.1 ENSP00000478755 O76054 A0A024R1I5 UPI0000135433 NM_012429.4 2/12 Gene3D:3.40.525.10,Prints_domain:PR00180,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF64,SMART_domains:SM01100,Superfamily_domains:SSF46938 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99995 1 1 1 1 0 G 2 3 46 30399714 30399714 C G 1 0 0 0 0 0 0 0 1 14258 869 30 4 4 SEC14L2 22 30399714 Silent SNP C C3N-00294_T 113428 30399714 20418754 1209 13981 INPP5J 0 . GRCh38 22 31128270 31128270 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1956C>T p.= p.L652L ENST00000331075 8/13 163 132 31 166 166 0 strelka-varscan-mutect INPP5J,synonymous_variant,p.=,ENST00000412277,NM_001284286.1;INPP5J,synonymous_variant,p.=,ENST00000331075,NM_001284285.1;INPP5J,synonymous_variant,p.=,ENST00000405300,NM_001284289.1;INPP5J,synonymous_variant,p.=,ENST00000400294,NM_001284288.1;INPP5J,synonymous_variant,p.=,ENST00000620191,NM_001284287.1;INPP5J,synonymous_variant,p.=,ENST00000404390,NM_001002837.2;INPP5J,synonymous_variant,p.=,ENST00000401755,;INPP5J,synonymous_variant,p.=,ENST00000404453,;INPP5J,synonymous_variant,p.=,ENST00000402238,;INPP5J,downstream_gene_variant,,ENST00000412985,;INPP5J,downstream_gene_variant,,ENST00000420017,;INPP5J,downstream_gene_variant,,ENST00000463528,;INPP5J,non_coding_transcript_exon_variant,,ENST00000461241,; T ENST00000331075 Transcript synonymous_variant 2005/3347 1956/3021 652/1006 L ctC/ctT 1 1 INPP5J HGNC HGNC:8956 protein_coding YES CCDS63453.1 ENSP00000333262 Q15735 UPI000004CB11 NM_001284285.1 8/13 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF127,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 31128270 31128270 C T 1 0 0 0 0 0 0 0 1 7662 813 29 3 3 INPP5J 22 31128270 Silent SNP C C3N-00294_T 728556 31128270 19690198 1210 13982 INPP5J 0 . GRCh38 22 31133457 31133457 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2383G>A p.Glu795Lys p.E795K ENST00000331075 11/13 148 113 35 152 152 0 strelka-varscan-mutect INPP5J,missense_variant,p.Glu728Lys,ENST00000412277,NM_001284286.1;INPP5J,missense_variant,p.Glu795Lys,ENST00000331075,NM_001284285.1;INPP5J,missense_variant,p.Glu428Lys,ENST00000405300,NM_001284289.1;INPP5J,missense_variant,p.Glu428Lys,ENST00000400294,NM_001284288.1;INPP5J,missense_variant,p.Glu360Lys,ENST00000620191,NM_001284287.1;INPP5J,missense_variant,p.Glu427Lys,ENST00000404390,NM_001002837.2;INPP5J,missense_variant,p.Glu160Lys,ENST00000401755,;INPP5J,missense_variant,p.Glu160Lys,ENST00000404453,;INPP5J,intron_variant,,ENST00000402238,;PLA2G3,downstream_gene_variant,,ENST00000215885,NM_015715.4;INPP5J,intron_variant,,ENST00000461241,; A ENST00000331075 Transcript missense_variant 2432/3347 2383/3021 795/1006 E/K Gaa/Aaa 1 1 INPP5J HGNC HGNC:8956 protein_coding YES CCDS63453.1 ENSP00000333262 Q15735 UPI000004CB11 NM_001284285.1 deleterious(0.03) 11/13 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF127 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 31133457 31133457 G A 1 0 0 0 0 1 0 0 0 7662 1291 45 3 3 INPP5J 22 31133457 Missense_Mutation SNP G C3N-00294_T 5187 31133457 19685011 1211 13983 C22orf42 0 . GRCh38 22 32149549 32149549 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.747C>T p.= p.L249L ENST00000382097 9/9 179 144 35 178 178 0 strelka-varscan-mutect C22orf42,synonymous_variant,p.=,ENST00000382097,NM_001010859.1;C22orf42,non_coding_transcript_exon_variant,,ENST00000490640,;C22orf42,non_coding_transcript_exon_variant,,ENST00000467813,; A ENST00000382097 Transcript synonymous_variant 820/1363 747/756 249/251 L ctC/ctT 1 -1 C22orf42 HGNC HGNC:27160 protein_coding YES CCDS33639.1 ENSP00000371529 Q6IC83 UPI00003765B0 NM_001010859.1 9/9 hmmpanther:PTHR15880,hmmpanther:PTHR15880:SF1 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 32149549 32149549 G A 1 0 0 0 0 0 0 0 1 2022 1161 41 3 3 C22orf42 22 32149549 Silent SNP G C3N-00294_T 1016092 32149549 18668919 1212 13984 HMGXB4 0 . GRCh38 22 35262403 35262403 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.13G>A p.Asp5Asn p.D5N ENST00000216106 2/11 153 127 26 202 201 1 strelka-varscan-mutect HMGXB4,missense_variant,p.Asp5Asn,ENST00000216106,NM_001003681.2;HMGXB4,intron_variant,,ENST00000455359,;HMGXB4,intron_variant,,ENST00000420166,;HMGXB4,downstream_gene_variant,,ENST00000466438,;HMGXB4,missense_variant,p.Asp5Asn,ENST00000418170,;HMGXB4,non_coding_transcript_exon_variant,,ENST00000498325,;HMGXB4,upstream_gene_variant,,ENST00000464480,; A ENST00000216106 Transcript missense_variant 141/4047 13/1806 5/601 D/N Gac/Aac 1 1 HMGXB4 HGNC HGNC:5003 protein_coding YES CCDS33641.1 ENSP00000216106 Q9UGU5 UPI00003765B4 NM_001003681.2 deleterious_low_confidence(0.01) 2/11 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 35262403 35262403 G A 1 0 0 0 0 1 0 0 0 7132 1290 45 3 3 HMGXB4 22 35262403 Missense_Mutation SNP G C3N-00294_T 3112854 35262403 15556065 1213 13985 RBFOX2 0 . GRCh38 22 35761464 35761464 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.822G>C p.Trp274Cys p.W274C ENST00000438146 8/14 177 142 35 216 216 0 strelka-varscan-mutect RBFOX2,missense_variant,p.Trp204Cys,ENST00000405409,NM_014309.2;RBFOX2,missense_variant,p.Trp203Cys,ENST00000449924,NM_001031695.2;RBFOX2,missense_variant,p.Trp203Cys,ENST00000414461,NM_001082577.1;RBFOX2,missense_variant,p.Trp185Cys,ENST00000262829,;RBFOX2,missense_variant,p.Trp183Cys,ENST00000359369,;RBFOX2,missense_variant,p.Trp274Cys,ENST00000438146,NM_001082578.1,NM_001082579.1;RBFOX2,missense_variant,p.Trp184Cys,ENST00000397303,;RBFOX2,missense_variant,p.Trp203Cys,ENST00000416721,NM_001082576.1;RBFOX2,missense_variant,p.Trp183Cys,ENST00000473487,;RBFOX2,missense_variant,p.Trp56Cys,ENST00000495377,; G ENST00000438146 Transcript missense_variant 822/1356 822/1356 274/451 W/C tgG/tgC 1 -1 RBFOX2 HGNC HGNC:9906 protein_coding YES CCDS43013.1 ENSP00000413035 O43251 UPI00015DF7D4 NM_001082578.1,NM_001082579.1 8/14 hmmpanther:PTHR15597,hmmpanther:PTHR15597:SF31,PIRSF_domain:PIRSF037932 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 35761464 35761464 C G 1 0 0 0 0 1 0 0 0 13272 869 30 4 4 RBFOX2 22 35761464 Missense_Mutation SNP C C3N-00294_T 499061 35761464 15057004 1214 13986 EIF3L 0 . GRCh38 22 37849441 37849441 + Nonsense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.121G>T p.Glu41Ter p.E41* ENST00000412331 1/13 64 47 17 74 74 0 strelka-varscan-mutect EIF3L,stop_gained,p.Glu41Ter,ENST00000412331,;EIF3L,5_prime_UTR_variant,,ENST00000624234,NM_016091.3;EIF3L,5_prime_UTR_variant,,ENST00000381683,NM_001242923.1;EIF3L,5_prime_UTR_variant,,ENST00000414316,;EIF3L,upstream_gene_variant,,ENST00000406934,;ANKRD54,upstream_gene_variant,,ENST00000609454,;EIF3L,upstream_gene_variant,,ENST00000451427,;MIR659,upstream_gene_variant,,ENST00000384963,;EIF3L,non_coding_transcript_exon_variant,,ENST00000476955,;ANKRD54,upstream_gene_variant,,ENST00000609706,;EIF3L,stop_gained,p.Glu11Ter,ENST00000439997,;EIF3L,stop_gained,p.Glu8Ter,ENST00000436452,;EIF3L,non_coding_transcript_exon_variant,,ENST00000477256,; T ENST00000412331 Transcript stop_gained 574/3220 121/1824 41/607 E/* Gag/Tag 1 1 EIF3L HGNC HGNC:18138 protein_coding ENSP00000416892 B0QY89 UPI000021D183 1/13 HIGH SNV 1 1 PASS rs1426494569 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 37849441 37849441 G T 1 0 0 0 0 0 1 0 0 4856 1059 37 1 1 EIF3L 22 37849441 Nonsense_Mutation SNP G C3N-00294_T 2087977 37849441 12969027 1215 13987 EIF3L 0 . GRCh38 22 37849465 37849465 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.16G>C p.Asp6His p.D6H ENST00000624234 1/13 53 39 14 60 60 0 strelka-varscan-mutect EIF3L,missense_variant,p.Asp49His,ENST00000412331,;EIF3L,missense_variant,p.Asp6His,ENST00000624234,NM_016091.3;EIF3L,missense_variant,p.Asp6His,ENST00000381683,NM_001242923.1;EIF3L,missense_variant,p.Asp6His,ENST00000414316,;EIF3L,upstream_gene_variant,,ENST00000406934,;ANKRD54,upstream_gene_variant,,ENST00000609454,;EIF3L,upstream_gene_variant,,ENST00000451427,;MIR659,upstream_gene_variant,,ENST00000384963,;EIF3L,non_coding_transcript_exon_variant,,ENST00000476955,;ANKRD54,upstream_gene_variant,,ENST00000609706,;EIF3L,missense_variant,p.Asp19His,ENST00000439997,;EIF3L,missense_variant,p.Asp16His,ENST00000436452,;EIF3L,non_coding_transcript_exon_variant,,ENST00000477256,; C ENST00000624234 Transcript missense_variant 94/2091 16/1695 6/564 D/H Gat/Cat 1 1 EIF3L HGNC HGNC:18138 protein_coding YES CCDS13960.1 ENSP00000485663 Q9Y262 UPI00000012D7 NM_016091.3 deleterious(0.01) 1/13 hmmpanther:PTHR13242,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 37849465 37849465 G C 1 0 0 0 0 1 0 0 0 4856 1290 45 4 4 EIF3L 22 37849465 Missense_Mutation SNP G C3N-00294_T 24 37849465 12969003 1216 13988 PLA2G6 0 . GRCh38 22 38123207 38123207 + Silent SNP G G A C3N-00294_T C3N-00294_N G G c.1479C>T p.= p.I493I ENST00000332509 11/17 488 387 101 523 523 0 strelka-varscan-mutect PLA2G6,synonymous_variant,p.=,ENST00000332509,NM_003560.2;PLA2G6,synonymous_variant,p.=,ENST00000335539,NM_001004426.1;PLA2G6,synonymous_variant,p.=,ENST00000402064,NM_001199562.1;PLA2G6,downstream_gene_variant,,ENST00000452794,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000490473,;PLA2G6,synonymous_variant,p.=,ENST00000454670,;PLA2G6,3_prime_UTR_variant,,ENST00000448094,;PLA2G6,non_coding_transcript_exon_variant,,ENST00000491986,;PLA2G6,upstream_gene_variant,,ENST00000496409,;PLA2G6,downstream_gene_variant,,ENST00000471636,;PLA2G6,downstream_gene_variant,,ENST00000480154,; A ENST00000332509 Transcript synonymous_variant 1663/3271 1479/2421 493/806 I atC/atT COSM3939651 1 -1 PLA2G6 HGNC HGNC:9039 protein_coding YES CCDS13967.1 ENSP00000333142 O60733 UPI00001310F3 NM_003560.2 11/17 hmmpanther:PTHR24139,Pfam_domain:PF01734,Gene3D:3.40.1090.10,Superfamily_domains:SSF52151 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 38123207 38123207 G A 1 0 0 0 0 0 0 0 1 12104 1280 45 3 3 PLA2G6 22 38123207 Silent SNP G C3N-00294_T 273742 38123207 12695261 1217 13989 EP300 0 . GRCh38 22 41140225 41140225 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1846G>A p.Glu616Lys p.E616K ENST00000263253 9/31 440 356 84 440 440 0 strelka-varscan-mutect EP300,missense_variant,p.Glu616Lys,ENST00000263253,NM_001429.3;EP300,missense_variant,p.Glu95Lys,ENST00000634690,;EP300,upstream_gene_variant,,ENST00000634728,; A ENST00000263253 Transcript missense_variant 3065/9587 1846/7245 616/2414 E/K Gaa/Aaa 1 1 EP300 HGNC HGNC:3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 UPI00001AE876 NM_001429.3 deleterious(0) 9/31 PROSITE_profiles:PS50952,hmmpanther:PTHR13808:SF4,hmmpanther:PTHR13808,Gene3D:1sb0A00,Pfam_domain:PF02172,Superfamily_domains:0053605 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 41140225 41140225 G A 1 0 0 0 0 1 0 0 0 4994 1291 45 3 3 EP300 22 41140225 Missense_Mutation SNP G C3N-00294_T 3017018 41140225 9678243 1218 13990 SCUBE1 0 . GRCh38 22 43218325 43218325 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.1821G>A p.= p.Q607Q ENST00000360835 15/22 337 273 64 424 424 0 strelka-varscan-mutect SCUBE1,synonymous_variant,p.=,ENST00000360835,NM_173050.3;SCUBE1,intron_variant,,ENST00000615096,;Z82214.3,downstream_gene_variant,,ENST00000420269,; T ENST00000360835 Transcript synonymous_variant 1948/9808 1821/2967 607/988 Q caG/caA 1 -1 SCUBE1 HGNC HGNC:13441 protein_coding YES CCDS14048.1 ENSP00000354080 Q8IWY4 UPI000020790F NM_173050.3 15/22 hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 43218325 43218325 C T 1 0 0 0 0 0 0 0 1 14215 912 32 3 3 SCUBE1 22 43218325 Silent SNP C C3N-00294_T 2078100 43218325 7600143 1219 13991 PHF21B 0 . GRCh38 22 44914071 44914071 + Silent SNP G G C novel C3N-00294_T C3N-00294_N G G c.582C>G p.= p.L194L ENST00000313237 5/13 41 31 10 43 43 0 strelka-varscan-mutect PHF21B,synonymous_variant,p.=,ENST00000313237,NM_138415.4;PHF21B,intron_variant,,ENST00000403565,NM_001284296.1;PHF21B,intron_variant,,ENST00000396103,NM_001242450.1;PHF21B,intron_variant,,ENST00000629843,NM_001135862.2;PHF21B,intron_variant,,ENST00000420689,;PHF21B,intron_variant,,ENST00000414269,;PHF21B,downstream_gene_variant,,ENST00000490679,;PHF21B,downstream_gene_variant,,ENST00000460507,;PHF21B,downstream_gene_variant,,ENST00000474327,; C ENST00000313237 Transcript synonymous_variant 733/3671 582/1596 194/531 L ctC/ctG 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 5/13 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 44914071 44914071 G C 1 0 0 0 0 0 0 0 1 11920 929 33 4 4 PHF21B 22 44914071 Silent SNP G C3N-00294_T 1695746 44914071 5904397 1220 13992 FBLN1 0 . GRCh38 22 45533063 45533063 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.545G>A p.Gly182Glu p.G182E ENST00000327858 6/17 271 226 45 308 308 0 strelka-varscan-mutect FBLN1,missense_variant,p.Gly182Glu,ENST00000327858,NM_006486.2;FBLN1,missense_variant,p.Gly182Glu,ENST00000442170,NM_006485.3;FBLN1,missense_variant,p.Gly220Glu,ENST00000402984,;FBLN1,missense_variant,p.Gly182Glu,ENST00000340923,NM_006487.2;FBLN1,missense_variant,p.Gly182Glu,ENST00000262722,NM_001996.3;FBLN1,missense_variant,p.Gly162Glu,ENST00000455233,;FBLN1,missense_variant,p.Gly102Glu,ENST00000451475,;FBLN1,downstream_gene_variant,,ENST00000411478,;FBLN1,downstream_gene_variant,,ENST00000454279,;FBLN1,missense_variant,p.Gly77Glu,ENST00000437711,;FBLN1,non_coding_transcript_exon_variant,,ENST00000460538,;FBLN1,upstream_gene_variant,,ENST00000465578,;FBLN1,upstream_gene_variant,,ENST00000484531,; A ENST00000327858 Transcript missense_variant,splice_region_variant 640/2896 545/2112 182/703 G/E gGa/gAa 1 1 FBLN1 HGNC HGNC:3600 protein_coding YES CCDS14067.1 ENSP00000331544 P23142 UPI00001AE84C NM_006486.2 tolerated(0.07) 6/17 Gene3D:2.10.25.10,PIRSF_domain:PIRSF036313,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF272,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 45533063 45533063 G A 1 0 0 0 0 1 0 0 0 5561 1188 41 3 3 FBLN1 22 45533063 Missense_Mutation SNP G C3N-00294_T 618992 45533063 5285405 1221 13993 PKDREJ 0 . GRCh38 22 46261632 46261632 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1691G>C p.Gly564Ala p.G564A ENST00000253255 1/1 190 136 54 152 152 0 strelka-varscan-mutect PKDREJ,missense_variant,p.Gly564Ala,ENST00000253255,NM_006071.1; G ENST00000253255 Transcript missense_variant 1724/7693 1691/6762 564/2253 G/A gGa/gCa 1 -1 PKDREJ HGNC HGNC:9015 protein_coding YES CCDS14073.1 ENSP00000253255 Q9NTG1 UPI0000031D01 NM_006071.1 deleterious(0.01) 1/1 PROSITE_profiles:PS51111,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF141,Pfam_domain:PF02010 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 46261632 46261632 C G 1 0 0 0 0 1 0 0 0 12066 855 30 4 4 PKDREJ 22 46261632 Missense_Mutation SNP C C3N-00294_T 728569 46261632 4556836 1222 13994 GPM6B 0 . GRCh38 X 13807749 13807749 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.82G>A p.Glu28Lys p.E28K ENST00000316715 2/8 47 19 28 39 39 0 strelka-varscan-mutect GPM6B,missense_variant,p.Glu28Lys,ENST00000316715,NM_001001995.1;GPM6B,missense_variant,p.Glu28Lys,ENST00000355135,NM_001001996.1;GPM6B,missense_variant,p.Glu2Lys,ENST00000493677,;GPM6B,intron_variant,,ENST00000454189,NM_001001994.1;GPM6B,intron_variant,,ENST00000356942,NM_005278.3;GPM6B,intron_variant,,ENST00000398361,;GPM6B,intron_variant,,ENST00000475307,;GPM6B,intron_variant,,ENST00000468080,;GPM6B,intron_variant,,ENST00000493085,; T ENST00000316715 Transcript missense_variant 520/3275 82/987 28/328 E/K Gaa/Aaa 1 -1 GPM6B HGNC HGNC:4461 protein_coding YES CCDS35206.1 ENSP00000316861 Q13491 UPI00000721CA NM_001001995.1 tolerated_low_confidence(0.25) 2/8 hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF10 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 13807749 13807749 C T 1 0 0 0 0 1 0 0 0 6518 864 30 3 3 GPM6B 23 13807749 Missense_Mutation SNP C C3N-00294_T 13807749 142233146 1223 13995 MAP3K15 0 . GRCh38 X 19459993 19459993 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.880G>A p.Asp294Asn p.D294N ENST00000338883 5/29 38 23 15 32 32 0 strelka-varscan-mutect MAP3K15,missense_variant,p.Asp294Asn,ENST00000338883,NM_001001671.3;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;MAP3K15,missense_variant,p.Asp46Asn,ENST00000359173,; T ENST00000338883 Transcript missense_variant 880/4012 880/3942 294/1313 D/N Gat/Aat 1 -1 MAP3K15 HGNC HGNC:31689 protein_coding YES CCDS35212.2 ENSP00000345629 Q6ZN16 UPI0000E444D0 NM_001001671.3 deleterious(0) 5/29 hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363,Pfam_domain:PF13281 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 19459993 19459993 C T 1 0 0 0 0 1 0 0 0 9171 826 29 3 3 MAP3K15 23 19459993 Missense_Mutation SNP C C3N-00294_T 5652244 19459993 136580902 1224 13996 PPP4R3CP 0 . GRCh38 X 27462527 27462527 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.770C>T p.Ser257Phe p.S257F ENST00000412172 1/1 91 55 36 157 157 0 strelka-varscan-mutect PPP4R3CP,missense_variant,p.Ser257Phe,ENST00000412172,; A ENST00000412172 Transcript missense_variant 815/3131 770/2499 257/832 S/F tCt/tTt 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 Pfam_domain:PF04802,hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 27462527 27462527 G A 1 0 0 0 0 1 0 0 0 12529 942 33 3 3 PPP4R3CP 23 27462527 Missense_Mutation SNP G C3N-00294_T 8002534 27462527 128578368 1225 13997 USP11 0 . GRCh38 X 47244702 47244702 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1993G>A p.Asp665Asn p.D665N ENST00000218348 15/21 71 38 33 81 81 0 strelka-varscan-mutect USP11,missense_variant,p.Asp622Asn,ENST00000377107,;USP11,missense_variant,p.Asp665Asn,ENST00000218348,NM_004651.3;USP11,downstream_gene_variant,,ENST00000377078,;USP11,downstream_gene_variant,,ENST00000377080,;USP11,non_coding_transcript_exon_variant,,ENST00000469080,;USP11,non_coding_transcript_exon_variant,,ENST00000488848,;USP11,non_coding_transcript_exon_variant,,ENST00000497179,;USP11,downstream_gene_variant,,ENST00000478596,;USP11,downstream_gene_variant,,ENST00000480104,;USP11,upstream_gene_variant,,ENST00000467378,;USP11,downstream_gene_variant,,ENST00000489111,;USP11,downstream_gene_variant,,ENST00000489030,; A ENST00000218348 Transcript missense_variant 2042/3338 1993/2892 665/963 D/N Gat/Aat 1 1 USP11 HGNC HGNC:12609 protein_coding YES CCDS14277.1 ENSP00000218348 P51784 UPI0000161434 NM_004651.3 tolerated(0.44) 15/21 Low_complexity_(Seg):seg,PROSITE_profiles:PS50235,Pfam_domain:PF00443 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 47244702 47244702 G A 1 0 0 0 0 1 0 0 0 17576 942 33 3 3 USP11 23 47244702 Missense_Mutation SNP G C3N-00294_T 19782175 47244702 108796193 1226 13998 EBP 0 . GRCh38 X 48528380 48528380 + Missense_Mutation SNP G G C C3N-00294_T C3N-00294_N G G c.616G>C p.Asp206His p.D206H ENST00000495186 5/5 154 96 58 174 174 0 strelka-varscan-mutect EBP,missense_variant,p.Asp206His,ENST00000495186,NM_006579.2;EBP,downstream_gene_variant,,ENST00000446158,;EBP,downstream_gene_variant,,ENST00000414061,;Metazoa_SRP,downstream_gene_variant,,ENST00000610965,;EBP,non_coding_transcript_exon_variant,,ENST00000276096,;EBP,non_coding_transcript_exon_variant,,ENST00000498425,;EBP,downstream_gene_variant,,ENST00000466461,; C ENST00000495186 Transcript missense_variant 1439/1775 616/693 206/230 D/H Gat/Cat CM086600 1 1 EBP HGNC HGNC:3133 protein_coding YES CCDS14300.1 ENSP00000417052 Q15125 A0A024QYX0 UPI000000DB82 NM_006579.2 tolerated(0.14) 5/5 Pfam_domain:PF05241,hmmpanther:PTHR14207,hmmpanther:PTHR14207:SF0 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 48528380 48528380 G C 1 0 0 0 0 1 0 0 0 4712 1290 45 4 4 EBP 23 48528380 Missense_Mutation SNP G C3N-00294_T 1283678 48528380 107512515 1227 13999 CACNA1F 0 . GRCh38 X 49205161 49205161 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.5910G>C p.Glu1970Asp p.E1970D ENST00000376265 48/48 125 88 37 98 98 0 strelka-varscan-mutect CACNA1F,missense_variant,p.Glu1970Asp,ENST00000376265,NM_005183.3;CACNA1F,missense_variant,p.Glu1959Asp,ENST00000323022,NM_001256789.2;CACNA1F,missense_variant,p.Glu1905Asp,ENST00000376251,NM_001256790.2;SYP,upstream_gene_variant,,ENST00000263233,NM_003179.2;SYP,upstream_gene_variant,,ENST00000479808,;SYP,upstream_gene_variant,,ENST00000472598,;CACNA1F,downstream_gene_variant,,ENST00000486943,;SYP-AS1,downstream_gene_variant,,ENST00000433499,;SYP,upstream_gene_variant,,ENST00000494396,;SYP,upstream_gene_variant,,ENST00000376303,;CACNA1F,downstream_gene_variant,,ENST00000481035,;SYP,upstream_gene_variant,,ENST00000469389,;SYP,upstream_gene_variant,,ENST00000472737,;SYP,upstream_gene_variant,,ENST00000466635,; G ENST00000376265 Transcript missense_variant 5972/6070 5910/5934 1970/1977 E/D gaG/gaC 1 -1 CACNA1F HGNC HGNC:1393 protein_coding YES CCDS35253.1 ENSP00000365441 O60840 UPI0000072854 NM_005183.3 tolerated_low_confidence(0.13) 48/48 Pfam_domain:PF16885 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 49205161 49205161 C G 1 0 0 0 0 1 0 0 0 2231 912 32 4 4 CACNA1F 23 49205161 Missense_Mutation SNP C C3N-00294_T 676781 49205161 106835734 1228 14000 SHROOM4 0 . GRCh38 X 50634557 50634557 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1516G>C p.Glu506Gln p.E506Q ENST00000376020 4/9 462 334 128 385 385 0 strelka-varscan-mutect SHROOM4,missense_variant,p.Glu506Gln,ENST00000376020,NM_020717.3;SHROOM4,missense_variant,p.Glu390Gln,ENST00000460112,;SHROOM4,missense_variant,p.Glu506Gln,ENST00000289292,; G ENST00000376020 Transcript missense_variant 1542/9556 1516/4482 506/1493 E/Q Gaa/Caa 1 -1 SHROOM4 HGNC HGNC:29215 protein_coding YES CCDS35277.1 ENSP00000365188 Q9ULL8 UPI00001C2068 NM_020717.3 deleterious(0.02) 4/9 hmmpanther:PTHR15012:SF35,hmmpanther:PTHR15012 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 50634557 50634557 C G 1 0 0 0 0 1 0 0 0 14559 922 32 4 4 SHROOM4 23 50634557 Missense_Mutation SNP C C3N-00294_T 1429396 50634557 105406338 1229 14001 SHROOM4 0 . GRCh38 X 50634848 50634848 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1225C>T p.Arg409Cys p.R409C ENST00000376020 4/9 386 285 101 310 310 0 strelka-varscan-mutect SHROOM4,missense_variant,p.Arg409Cys,ENST00000376020,NM_020717.3;SHROOM4,missense_variant,p.Arg293Cys,ENST00000460112,;SHROOM4,missense_variant,p.Arg409Cys,ENST00000289292,; A ENST00000376020 Transcript missense_variant 1251/9556 1225/4482 409/1493 R/C Cgc/Tgc 1 -1 SHROOM4 HGNC HGNC:29215 protein_coding YES CCDS35277.1 ENSP00000365188 Q9ULL8 UPI00001C2068 NM_020717.3 deleterious(0) 4/9 hmmpanther:PTHR15012:SF35,hmmpanther:PTHR15012 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 50634848 50634848 G A 1 0 0 0 0 1 0 0 0 14559 1058 37 1 1 SHROOM4 23 50634848 Missense_Mutation SNP G C3N-00294_T 291 50634848 105406047 1230 14002 KDM5C 0 . GRCh38 X 53224741 53224741 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.149C>T p.Ala50Val p.A50V ENST00000375401 1/26 84 75 9 77 77 0 strelka-varscan-mutect KDM5C,missense_variant,p.Ala50Val,ENST00000452825,NM_001146702.1;KDM5C,missense_variant,p.Ala50Val,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Ala50Val,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Ala50Val,ENST00000375379,;KDM5C,missense_variant,p.Ala50Val,ENST00000375383,;KDM5C,upstream_gene_variant,,ENST00000467093,;KDM5C,missense_variant,p.Ala50Val,ENST00000429877,;KDM5C,missense_variant,p.Ala50Val,ENST00000428012,;KDM5C,missense_variant,p.Ala50Val,ENST00000349663,; A ENST00000375401 Transcript missense_variant,splice_region_variant 682/6031 149/4683 50/1560 A/V gCg/gTg 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 tolerated(0.08) 1/26 PROSITE_profiles:PS51183,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43,SMART_domains:SM00545 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.18261 1 1 1 1 0 A 3 1 46 53224741 53224741 G A 1 0 0 0 0 1 0 0 0 8053 1101 38 1 1 KDM5C 23 53224741 Missense_Mutation SNP G C3N-00294_T 2589893 53224741 102816154 1231 14003 AR 0 . GRCh38 X 67546608 67546608 + Nonsense_Mutation SNP C C T C3N-00294_T C3N-00294_N C C c.1462C>T p.Gln488Ter p.Q488* ENST00000374690 1/8 263 187 76 226 226 0 strelka-varscan-mutect AR,stop_gained,p.Gln298Ter,ENST00000612452,;AR,stop_gained,p.Gln488Ter,ENST00000396044,;AR,stop_gained,p.Gln488Ter,ENST00000374690,NM_000044.3;AR,stop_gained,p.Gln488Ter,ENST00000612010,;AR,stop_gained,p.Gln488Ter,ENST00000504326,;AR,stop_gained,p.Gln488Ter,ENST00000613054,;AR,non_coding_transcript_exon_variant,,ENST00000513847,;AR,stop_gained,p.Gln488Ter,ENST00000514029,; T ENST00000374690 Transcript stop_gained 1986/10065 1462/2763 488/920 Q/* Cag/Tag CM015295,COSM4828414,COSM4828415 1 1 AR HGNC HGNC:644 protein_coding YES CCDS14387.1 ENSP00000363822 P10275 UPI0000167B08 NM_000044.3 1/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF6 0,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 67546608 67546608 C T 1 0 0 0 0 0 1 0 0 958 827 29 3 3 AR 23 67546608 Nonsense_Mutation SNP C C3N-00294_T 14321867 67546608 88494287 1232 14004 RP11-402P6.15 0 . GRCh38 X 71668843 71668843 + Missense_Mutation SNP G G T novel C3N-00294_T C3N-00294_N G G c.1040G>T p.Arg347Ile p.R347I ENST00000636096 1/5 21 4 17 10 10 0 strelka-varscan-mutect RP11-402P6.15,missense_variant,p.Arg347Ile,ENST00000636096,;RP11-402P6.15,missense_variant,p.Arg235Ile,ENST00000636797,;RP11-402P6.9,upstream_gene_variant,,ENST00000422194,;RP11-402P6.9,upstream_gene_variant,,ENST00000433410,;RP11-402P6.9,upstream_gene_variant,,ENST00000637198,; T ENST00000636096 Transcript missense_variant 1040/1732 1040/1590 347/529 R/I aGa/aTa 1 1 RP11-402P6.15 Clone_based_vega_gene protein_coding YES ENSP00000490941 deleterious(0.01) 1/5 Pfam_domain:PF15483,hmmpanther:PTHR31866,hmmpanther:PTHR31866:SF1 MODERATE 1 SNV 1 PASS . . 8 202 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 71668843 71668843 G T 1 0 0 0 0 1 0 0 0 13738 942 33 2 2 RP11-402P6.15 23 71668843 Missense_Mutation SNP G C3N-00294_T 4122235 71668843 84372052 1233 14005 BRWD3 0 . GRCh38 X 80691931 80691931 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.3373G>A p.Glu1125Lys p.E1125K ENST00000373275 30/41 332 230 102 269 269 0 strelka-varscan-mutect BRWD3,missense_variant,p.Glu1125Lys,ENST00000373275,NM_153252.4;BRWD3,non_coding_transcript_exon_variant,,ENST00000473691,; T ENST00000373275 Transcript missense_variant 3590/11381 3373/5409 1125/1802 E/K Gaa/Aaa 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 deleterious(0) 30/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 80691931 80691931 C T 1 0 0 0 0 1 0 0 0 1700 922 32 3 3 BRWD3 23 80691931 Missense_Mutation SNP C C3N-00294_T 9023088 80691931 75348964 1234 14006 DACH2 0 . GRCh38 X 86376844 86376844 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.509G>A p.Arg170Lys p.R170K ENST00000373125 2/12 39 25 14 50 50 0 strelka-varscan-mutect DACH2,missense_variant,p.Arg170Lys,ENST00000373125,NM_053281.3;DACH2,missense_variant,p.Arg3Lys,ENST00000508860,NM_001139515.1;DACH2,intron_variant,,ENST00000373131,NM_001139514.1;DACH2,intron_variant,,ENST00000510272,;DACH2,missense_variant,p.Arg170Lys,ENST00000461604,;DACH2,intron_variant,,ENST00000506327,; A ENST00000373125 Transcript missense_variant 509/2232 509/1800 170/599 R/K aGa/aAa 1 1 DACH2 HGNC HGNC:16814 protein_coding YES CCDS14455.1 ENSP00000362217 Q96NX9 UPI00000717B4 NM_053281.3 tolerated_low_confidence(0.78) 2/12 hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7 MODERATE 1 SNV 1 1 PASS . . 1 202 5 2 0 0 0 0 -20 0.9999925 1 1 1 0 A 3 1 46 86376844 86376844 G A 1 0 0 0 0 1 0 0 0 4022 942 33 3 3 DACH2 23 86376844 Missense_Mutation SNP G C3N-00294_T 5684913 86376844 69664051 1235 14007 PABPC5 0 . GRCh38 X 91436142 91436142 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.565G>A p.Glu189Lys p.E189K ENST00000312600 2/2 236 185 51 184 184 0 strelka-varscan-mutect PABPC5,missense_variant,p.Glu189Lys,ENST00000312600,NM_080832.2;PABPC5,missense_variant,p.Glu25Lys,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; A ENST00000312600 Transcript missense_variant 779/3221 565/1149 189/382 E/K Gag/Aag 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 tolerated(0.32) 2/2 Gene3D:3.30.70.330,TIGRFAM_domain:TIGR01628 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 91436142 91436142 G A 1 0 0 0 0 1 0 0 0 11445 1291 45 3 3 PABPC5 23 91436142 Missense_Mutation SNP G C3N-00294_T 5059298 91436142 64604753 1236 14008 PABPC5 0 . GRCh38 X 91436615 91436615 + Silent SNP C C A novel C3N-00294_T C3N-00294_N C C c.1038C>A p.= p.V346V ENST00000312600 2/2 235 113 122 214 214 0 strelka-varscan-mutect PABPC5,synonymous_variant,p.=,ENST00000312600,NM_080832.2;PABPC5,synonymous_variant,p.=,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; A ENST00000312600 Transcript synonymous_variant 1252/3221 1038/1149 346/382 V gtC/gtA 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01628 LOW 1 SNV 1 1 PASS rs1400539871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 91436615 91436615 C A 1 0 0 0 0 0 0 0 1 11445 900 32 2 2 PABPC5 23 91436615 Silent SNP C C3N-00294_T 473 91436615 64604280 1237 14009 NOX1 0 . GRCh38 X 100862535 100862535 + Silent SNP G G A novel C3N-00294_T C3N-00294_N G G c.528C>T p.= p.L176L ENST00000372966 6/13 73 51 22 50 50 0 strelka-mutect NOX1,synonymous_variant,p.=,ENST00000372966,NM_007052.4;NOX1,synonymous_variant,p.=,ENST00000372960,NM_001271815.1;NOX1,synonymous_variant,p.=,ENST00000217885,NM_013955.2;NOX1,intron_variant,,ENST00000372964,; A ENST00000372966 Transcript synonymous_variant 734/2529 528/1695 176/564 L ctC/ctT 1 -1 NOX1 HGNC HGNC:7889 protein_coding YES CCDS14474.1 ENSP00000362057 Q9Y5S8 UPI00001303C1 NM_007052.4 6/13 hmmpanther:PTHR11972:SF71,hmmpanther:PTHR11972,Pfam_domain:PF01794,Prints_domain:PR00466,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 46 100862535 100862535 G A 1 0 0 0 0 0 0 0 1 10602 1277 45 3 3 NOX1 23 100862535 Silent SNP G C3N-00294_T 9425920 100862535 55178360 1238 14010 CENPI 0 . GRCh38 X 101102364 101102364 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.317C>A p.Ser106Ter p.S106* ENST00000372927 3/21 59 39 20 68 68 0 strelka-varscan-mutect CENPI,stop_gained,p.Ser106Ter,ENST00000372927,;CENPI,stop_gained,p.Ser106Ter,ENST00000372926,;CENPI,stop_gained,p.Ser106Ter,ENST00000423383,NM_006733.2;CENPI,downstream_gene_variant,,ENST00000403304,;CENPI,downstream_gene_variant,,ENST00000435570,; A ENST00000372927 Transcript stop_gained 594/3262 317/2271 106/756 S/* tCa/tAa 1 1 CENPI HGNC HGNC:3968 protein_coding YES CCDS14479.1 ENSP00000362018 Q92674 A0A024RCG4 UPI000004A007 3/21 Pfam_domain:PF07778 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 101102364 101102364 C A 1 0 0 0 0 0 1 0 0 2941 838 29 2 2 CENPI 23 101102364 Nonsense_Mutation SNP C C3N-00294_T 239829 101102364 54938531 1239 14011 MORF4L2 0 . GRCh38 X 103676812 103676812 + Silent SNP C C T novel C3N-00294_T C3N-00294_N C C c.216G>A p.= p.V72V ENST00000422154 4/4 187 130 57 117 117 0 strelka-varscan-mutect MORF4L2,synonymous_variant,p.=,ENST00000422154,NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1;MORF4L2,synonymous_variant,p.=,ENST00000433176,NM_001142421.1,NM_001142428.1,NM_001142419.1,NM_001142431.1,NM_001142422.1,NM_001142420.1,NM_001142427.1,NM_001142432.1;MORF4L2,synonymous_variant,p.=,ENST00000451301,NM_001142430.1,NM_001142426.1;MORF4L2,synonymous_variant,p.=,ENST00000441076,;MORF4L2,synonymous_variant,p.=,ENST00000360458,;MORF4L2,synonymous_variant,p.=,ENST00000434230,;MORF4L2,synonymous_variant,p.=,ENST00000442614,;MORF4L2,synonymous_variant,p.=,ENST00000418819,;MORF4L2,synonymous_variant,p.=,ENST00000423833,;MORF4L2,downstream_gene_variant,,ENST00000422355,;MORF4L2,non_coding_transcript_exon_variant,,ENST00000492116,;MORF4L2,downstream_gene_variant,,ENST00000474653,;MORF4L2,downstream_gene_variant,,ENST00000498064,;MORF4L2,downstream_gene_variant,,ENST00000467755,; T ENST00000422154 Transcript synonymous_variant 671/1983 216/867 72/288 V gtG/gtA 1 -1 MORF4L2 HGNC HGNC:16849 protein_coding YES CCDS14512.1 ENSP00000394417 Q15014 UPI000012F567 NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1 4/4 hmmpanther:PTHR10880,hmmpanther:PTHR10880:SF25 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 46 103676812 103676812 C T 1 0 0 0 0 0 0 0 1 9670 813 29 3 3 MORF4L2 23 103676812 Silent SNP C C3N-00294_T 2574448 103676812 52364083 1240 14012 FAM199X 0 . GRCh38 X 104186544 104186544 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.652C>G p.Pro218Ala p.P218A ENST00000493442 4/6 91 79 12 109 109 0 strelka-varscan-mutect FAM199X,missense_variant,p.Pro218Ala,ENST00000493442,NM_207318.3;FAM199X,non_coding_transcript_exon_variant,,ENST00000299906,; G ENST00000493442 Transcript missense_variant 818/7457 652/1167 218/388 P/A Cct/Gct 1 1 FAM199X HGNC HGNC:25195 protein_coding YES CCDS35364.1 ENSP00000417581 Q6PEV8 B0QYU2 UPI00001C2069 NM_207318.3 deleterious(0) 4/6 Pfam_domain:PF15814,hmmpanther:PTHR32003,hmmpanther:PTHR32003:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 104186544 104186544 C G 1 0 0 0 0 1 0 0 0 5377 855 30 4 4 FAM199X 23 104186544 Missense_Mutation SNP C C3N-00294_T 509732 104186544 51854351 1241 14013 CAPN6 0 . GRCh38 X 111247956 111247956 + Nonsense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1521G>A p.Trp507Ter p.W507* ENST00000324068 11/13 189 172 17 129 129 0 strelka-varscan-mutect CAPN6,stop_gained,p.Trp507Ter,ENST00000324068,NM_014289.3; T ENST00000324068 Transcript stop_gained 1689/3568 1521/1926 507/641 W/* tgG/tgA 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 11/13 hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 46 111247956 111247956 C T 1 0 0 0 0 0 1 0 0 2324 856 30 3 3 CAPN6 23 111247956 Nonsense_Mutation SNP C C3N-00294_T 7061412 111247956 44792939 1242 14014 RNF113A 0 . GRCh38 X 119870767 119870767 + Nonsense_Mutation SNP C C A novel C3N-00294_T C3N-00294_N C C c.847G>T p.Glu283Ter p.E283* ENST00000371442 1/1 157 121 36 121 121 0 strelka-varscan-mutect RNF113A,stop_gained,p.Glu283Ter,ENST00000371442,NM_006978.2;NDUFA1,upstream_gene_variant,,ENST00000371437,NM_004541.3; A ENST00000371442 Transcript stop_gained 1061/1353 847/1032 283/343 E/* Gag/Tag 1 -1 RNF113A HGNC HGNC:12974 protein_coding YES CCDS14589.1 ENSP00000360497 O15541 UPI000013C310 NM_006978.2 1/1 PROSITE_profiles:PS50089,hmmpanther:PTHR12930:SF2,hmmpanther:PTHR12930,PROSITE_patterns:PS00518,Pfam_domain:PF13920,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 HIGH SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 119870767 119870767 C A 1 0 0 0 0 0 1 0 0 13605 893 31 1 1 RNF113A 23 119870767 Nonsense_Mutation SNP C C3N-00294_T 8622811 119870767 36170128 1243 14015 GRIA3 0 . GRCh38 X 123428016 123428016 + Missense_Mutation SNP T T A novel C3N-00294_T C3N-00294_N T T c.1953T>A p.Asn651Lys p.N651K ENST00000622768 12/16 266 174 92 159 159 0 strelka-varscan-mutect GRIA3,missense_variant,p.Asn651Lys,ENST00000622768,NM_000828.4;GRIA3,missense_variant,p.Asn651Lys,ENST00000620443,NM_007325.4;GRIA3,missense_variant,p.Asn651Lys,ENST00000620581,;GRIA3,missense_variant,p.Asn651Lys,ENST00000541091,; A ENST00000622768 Transcript missense_variant 2246/5173 1953/2685 651/894 N/K aaT/aaA 1 1 GRIA3 HGNC HGNC:4573 protein_coding YES CCDS14604.1 ENSP00000481554 P42263 UPI000013D503 NM_000828.4 deleterious(0.01) 12/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF151,SMART_domains:SM00079,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 123428016 123428016 T A 1 0 0 0 0 1 0 0 0 6649 1432 50 4 4 GRIA3 23 123428016 Missense_Mutation SNP T C3N-00294_T 3557249 123428016 32612879 1244 14016 TEX13C 0 . GRCh38 X 125321896 125321896 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.1777C>T p.Pro593Ser p.P593S ENST00000632600 1/1 408 286 122 276 276 0 strelka-varscan-mutect TEX13C,missense_variant,p.Pro593Ser,ENST00000632600,NM_001195272.1; T ENST00000632600 Transcript missense_variant 1777/5095 1777/2982 593/993 P/S Cca/Tca 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 tolerated(0.64) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 125321896 125321896 C T 1 0 0 0 0 1 0 0 0 16199 855 30 3 3 TEX13C 23 125321896 Missense_Mutation SNP C C3N-00294_T 1893880 125321896 30718999 1245 14017 SLC9A6 0 . GRCh38 X 136044480 136044480 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.1862C>G p.Ser621Cys p.S621C ENST00000370695 16/16 112 79 33 87 87 0 strelka-varscan-mutect SLC9A6,missense_variant,p.Ser569Cys,ENST00000637581,;SLC9A6,missense_variant,p.Ser569Cys,ENST00000636347,;SLC9A6,missense_variant,p.Ser537Cys,ENST00000637195,;SLC9A6,missense_variant,p.Ser569Cys,ENST00000370701,NM_001177651.1;SLC9A6,missense_variant,p.Ser621Cys,ENST00000370695,NM_001042537.1;SLC9A6,missense_variant,p.Ser90Cys,ENST00000636206,;SLC9A6,missense_variant,p.Ser569Cys,ENST00000636092,;SLC9A6,missense_variant,p.Ser569Cys,ENST00000637234,;SLC9A6,missense_variant,p.Ser589Cys,ENST00000370698,NM_006359.2;SLC9A6,missense_variant,p.Ser148Cys,ENST00000630721,;SLC9A6,downstream_gene_variant,,ENST00000638078,;SLC9A6,non_coding_transcript_exon_variant,,ENST00000636798,;SLC9A6,non_coding_transcript_exon_variant,,ENST00000636625,;SLC9A6,downstream_gene_variant,,ENST00000626147,; G ENST00000370695 Transcript missense_variant 1938/4725 1862/2106 621/701 S/C tCt/tGt 1 1 SLC9A6 HGNC HGNC:11079 protein_coding YES CCDS44003.1 ENSP00000359729 Q92581 UPI0000062320 NM_001042537.1 deleterious(0) 16/16 Prints_domain:PR01088,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF94,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 136044480 136044480 C G 1 0 0 0 0 1 0 0 0 15000 913 32 4 4 SLC9A6 23 136044480 Missense_Mutation SNP C C3N-00294_T 10722584 136044480 19996415 1246 14018 HTATSF1 0 . GRCh38 X 136511263 136511263 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.1518G>C p.Lys506Asn p.K506N ENST00000535601 10/10 106 87 19 80 80 0 strelka-varscan-mutect HTATSF1,missense_variant,p.Lys506Asn,ENST00000535601,NM_001163280.1;HTATSF1,missense_variant,p.Lys506Asn,ENST00000218364,NM_014500.4; C ENST00000535601 Transcript missense_variant 1940/3019 1518/2268 506/755 K/N aaG/aaC 1 1 HTATSF1 HGNC HGNC:5276 protein_coding YES CCDS14657.1 ENSP00000442699 O43719 UPI000006D876 NM_001163280.1 deleterious_low_confidence(0) 10/10 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999881 1 1 1 0 C 3 2 46 136511263 136511263 G C 1 0 0 0 0 1 0 0 0 7329 933 33 4 4 HTATSF1 23 136511263 Missense_Mutation SNP G C3N-00294_T 466783 136511263 19529632 1247 14019 SLITRK4 0 . GRCh38 X 143628877 143628877 + Missense_Mutation SNP A A T novel C3N-00294_T C3N-00294_N A A c.2232T>A p.Asp744Glu p.D744E ENST00000596188 2/2 97 44 53 96 96 0 strelka-varscan-mutect SLITRK4,missense_variant,p.Asp744Glu,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.Asp744Glu,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.Asp744Glu,ENST00000356928,NM_001184749.2; T ENST00000596188 Transcript missense_variant 2458/8545 2232/2514 744/837 D/E gaT/gaA 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 tolerated(1) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 143628877 143628877 A T 1 0 0 0 0 1 0 0 0 15036 214 8 4 4 SLITRK4 23 143628877 Missense_Mutation SNP A C3N-00294_T 7117614 143628877 12412018 1248 14020 SPANXN1 0 . GRCh38 X 145247650 145247650 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.64G>A p.Glu22Lys p.E22K ENST00000370493 1/2 177 129 48 111 111 0 strelka-varscan-mutect SPANXN1,missense_variant,p.Glu22Lys,ENST00000370493,NM_001009614.2; A ENST00000370493 Transcript missense_variant 823/1276 64/219 22/72 E/K Gaa/Aaa 1 1 SPANXN1 HGNC HGNC:33174 protein_coding YES CCDS35421.1 ENSP00000359524 Q5VSR9 UPI0000458AF7 NM_001009614.2 tolerated(1) 1/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF7 MODERATE 1 SNV 1 1 PASS . . 0 203 0 3 4 0 0 0 -20 0.8827206 1 1 1 0 A 3 1 46 145247650 145247650 G A 1 0 0 0 0 1 0 0 0 15321 1291 45 3 3 SPANXN1 23 145247650 Missense_Mutation SNP G C3N-00294_T 1618773 145247650 10793245 1249 14021 GPR50 0 . GRCh38 X 151181367 151181367 + Missense_Mutation SNP C C A C3N-00294_T C3N-00294_N C C c.1784C>A p.Thr595Asn p.T595N ENST00000218316 2/2 65 40 25 58 58 0 strelka-varscan-mutect GPR50,missense_variant,p.Thr595Asn,ENST00000218316,NM_004224.3;AF003625.3,upstream_gene_variant,,ENST00000602313,;GPR50-AS1,upstream_gene_variant,,ENST00000454196,; A ENST00000218316 Transcript missense_variant 1853/1951 1784/1854 595/617 T/N aCc/aAc COSM311585 1 1 GPR50 HGNC HGNC:4506 protein_coding YES CCDS44012.1 ENSP00000218316 Q13585 UPI000013C755 NM_004224.3 deleterious_low_confidence(0.03) 2/2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 151181367 151181367 C A 1 0 0 0 0 1 0 0 0 6582 507 18 2 2 GPR50 23 151181367 Missense_Mutation SNP C C3N-00294_T 5933717 151181367 4859528 1250 14022 MAGEA12 0 . GRCh38 X 152736561 152736561 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.400G>C p.Glu134Gln p.E134Q ENST00000393900 3/3 242 171 71 179 179 0 strelka-varscan-mutect MAGEA12,missense_variant,p.Glu134Gln,ENST00000393900,NM_001166386.3;MAGEA12,missense_variant,p.Glu134Gln,ENST00000393869,NM_001166387.3;MAGEA12,missense_variant,p.Glu134Gln,ENST00000357916,NM_005367.6;CSAG1,upstream_gene_variant,,ENST00000370291,;CSAG1,upstream_gene_variant,,ENST00000370287,NM_153478.2;CSAG1,upstream_gene_variant,,ENST00000452779,NM_001102576.2;CSAG4,intron_variant,,ENST00000361201,;CSAG1,upstream_gene_variant,,ENST00000361211,;CSAG4,upstream_gene_variant,,ENST00000583763,; C ENST00000393900 Transcript missense_variant 754/1853 400/945 134/314 E/Q Gaa/Caa 1 1 MAGEA12 HGNC HGNC:6799 protein_coding YES CCDS76048.1 ENSP00000377478 P43365 Q6FHH8 UPI0000000C51 NM_001166386.3 deleterious(0) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF74,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 152736561 152736561 G C 1 0 0 0 0 1 0 0 0 9082 943 33 4 4 MAGEA12 23 152736561 Missense_Mutation SNP G C3N-00294_T 1555194 152736561 3304334 1251 14023 PNMA5 0 . GRCh38 X 152991022 152991022 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.577G>A p.Glu193Lys p.E193K ENST00000439251 2/2 46 34 12 29 29 0 strelka-varscan-mutect PNMA5,missense_variant,p.Glu193Lys,ENST00000439251,NM_001103150.1;PNMA5,missense_variant,p.Glu193Lys,ENST00000535214,NM_001184924.1;PNMA5,missense_variant,p.Glu193Lys,ENST00000361887,NM_052926.2;PNMA5,missense_variant,p.Glu193Lys,ENST00000452693,NM_001103151.1;PNMA5,downstream_gene_variant,,ENST00000437210,; T ENST00000439251 Transcript missense_variant 1016/3213 577/1347 193/448 E/K Gag/Aag 1 -1 PNMA5 HGNC HGNC:18743 protein_coding YES CCDS14718.1 ENSP00000388850 Q96PV4 UPI0000070F7D NM_001103150.1 deleterious(0) 2/2 Pfam_domain:PF14893,hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF4 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 152991022 152991022 C T 1 0 0 0 0 1 0 0 0 12263 835 29 3 3 PNMA5 23 152991022 Missense_Mutation SNP C C3N-00294_T 254461 152991022 3049873 1252 14024 BGN 0 . GRCh38 X 153508310 153508321 + In_Frame_Del DEL CTTCGGGGTGAA CTTCGGGGTGAA - novel C3N-00294_T C3N-00294_N CTTCGGGGTGAA CTTCGGGGTGAA c.972_983delCTTCGGGGTGAA p.Phe325_Lys328del p.F325_K328del ENST00000331595 8/8 137 77 60 176 176 0 sindel-varindel-pindel BGN,inframe_deletion,p.Phe325_Lys328del,ENST00000331595,NM_001711.4;BGN,downstream_gene_variant,,ENST00000431891,;BGN,non_coding_transcript_exon_variant,,ENST00000480756,;BGN,non_coding_transcript_exon_variant,,ENST00000472615,;BGN,intron_variant,,ENST00000492658,; - ENST00000331595 Transcript inframe_deletion 1158-1169/2402 972-983/1107 324-328/368 GFGVK/G ggCTTCGGGGTGAAg/ggg 1 1 BGN HGNC HGNC:1044 protein_coding YES CCDS14721.1 ENSP00000327336 P21810 UPI000003BDBA NM_001711.4 8/8 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF6,PIRSF_domain:PIRSF002490,Superfamily_domains:SSF52058 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 46 153508310 153508310 CTTCGGGGTGAA - 1 0 1 0 1 0 0 0 0 1566 784 28 0 0 BGN 23 153508310 In_Frame_Del DEL CTTCGGGGTGAA C3N-00294_T 517288 153508310 2532585 1253 14025 SLC6A8 0 . GRCh38 X 153688739 153688739 + Nonsense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.165G>A p.Trp55Ter p.W55* ENST00000253122 1/13 161 124 37 81 81 0 strelka-varscan-mutect SLC6A8,stop_gained,p.Trp55Ter,ENST00000253122,NM_001142805.1,NM_005629.3;PNCK,intron_variant,,ENST00000458354,;SLC6A8,upstream_gene_variant,,ENST00000430077,NM_001142806.1;PNCK,upstream_gene_variant,,ENST00000425526,;PNCK,upstream_gene_variant,,ENST00000419804,;SLC6A8,upstream_gene_variant,,ENST00000442457,;SLC6A8,upstream_gene_variant,,ENST00000413787,;PNCK,upstream_gene_variant,,ENST00000423545,;SLC6A8,upstream_gene_variant,,ENST00000429147,;SLC6A8,upstream_gene_variant,,ENST00000457723,;SLC6A8,non_coding_transcript_exon_variant,,ENST00000476466,;PNCK,intron_variant,,ENST00000480693,;SLC6A8,upstream_gene_variant,,ENST00000485324,;PNCK,upstream_gene_variant,,ENST00000473831,;PNCK,upstream_gene_variant,,ENST00000460106,;SLC6A8,upstream_gene_variant,,ENST00000466243,;PNCK,upstream_gene_variant,,ENST00000484705,;SLC6A8,upstream_gene_variant,,ENST00000467402,;PNCK,upstream_gene_variant,,ENST00000488994,; A ENST00000253122 Transcript stop_gained 641/3763 165/1908 55/635 W/* tgG/tgA 1 1 SLC6A8 HGNC HGNC:11055 protein_coding YES CCDS14726.1 ENSP00000253122 P48029 X5D9C4 UPI00001354A0 NM_001142805.1,NM_005629.3 1/13 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF96,Pfam_domain:PF00209,Superfamily_domains:0053687 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 46 153688739 153688739 G A 1 0 0 0 0 0 1 0 0 14973 1183 41 3 3 SLC6A8 23 153688739 Nonsense_Mutation SNP G C3N-00294_T 180429 153688739 2352156 1254 14026 IRAK1 0 . GRCh38 X 154019251 154019251 + Missense_Mutation SNP C C T novel C3N-00294_T C3N-00294_N C C c.382G>A p.Glu128Lys p.E128K ENST00000369980 3/14 77 52 25 72 72 0 strelka-varscan-mutect IRAK1,missense_variant,p.Glu128Lys,ENST00000369980,NM_001569.3;IRAK1,missense_variant,p.Glu128Lys,ENST00000369974,NM_001025243.1;IRAK1,missense_variant,p.Glu154Lys,ENST00000429936,;IRAK1,missense_variant,p.Glu128Lys,ENST00000393687,NM_001025242.1;IRAK1,missense_variant,p.Glu124Lys,ENST00000444230,;MECP2,downstream_gene_variant,,ENST00000303391,NM_004992.3;IRAK1,upstream_gene_variant,,ENST00000443220,;IRAK1,upstream_gene_variant,,ENST00000437278,;IRAK1,upstream_gene_variant,,ENST00000455690,;IRAK1,downstream_gene_variant,,ENST00000390190,;IRAK1,upstream_gene_variant,,ENST00000477274,;IRAK1,upstream_gene_variant,,ENST00000467236,;IRAK1,missense_variant,p.Glu154Lys,ENST00000369973,;IRAK1,upstream_gene_variant,,ENST00000463031,; T ENST00000369980 Transcript missense_variant 550/3666 382/2139 128/712 E/K Gag/Aag 1 -1 IRAK1 HGNC HGNC:6112 protein_coding YES CCDS14740.1 ENSP00000358997 P51617 UPI000012D873 NM_001569.3 tolerated(0.74) 3/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF1 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 46 154019251 154019251 C T 1 0 0 0 0 1 0 0 0 7727 893 31 1 1 IRAK1 23 154019251 Missense_Mutation SNP C C3N-00294_T 330512 154019251 2021644 1255 14027 PLXNA3 0 . GRCh38 X 154465811 154465811 + Missense_Mutation SNP G G C novel C3N-00294_T C3N-00294_N G G c.2496G>C p.Gln832His p.Q832H ENST00000369682 13/33 93 65 28 67 66 1 strelka-varscan-mutect PLXNA3,missense_variant,p.Gln832His,ENST00000369682,NM_017514.4;PLXNA3,upstream_gene_variant,,ENST00000493546,;PLXNA3,downstream_gene_variant,,ENST00000495040,;PLXNA3,upstream_gene_variant,,ENST00000467463,;PLXNA3,upstream_gene_variant,,ENST00000480645,;PLXNA3,upstream_gene_variant,,ENST00000491066,;PLXNA3,upstream_gene_variant,,ENST00000478236,;PLXNA3,downstream_gene_variant,,ENST00000482598,; C ENST00000369682 Transcript missense_variant 2671/10885 2496/5616 832/1871 Q/H caG/caC 1 1 PLXNA3 HGNC HGNC:9101 protein_coding YES CCDS14752.1 ENSP00000358696 P51805 UPI0002AB801F NM_017514.4 tolerated(0.15) 13/33 hmmpanther:PTHR22625:SF32,hmmpanther:PTHR22625,Gene3D:3.30.1680.10,SMART_domains:SM00423 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 46 154465811 154465811 G C 1 0 0 0 0 1 0 0 0 12227 933 33 4 4 PLXNA3 23 154465811 Missense_Mutation SNP G C3N-00294_T 446560 154465811 1575084 1256 14028 MPP1 0 . GRCh38 X 154786234 154786234 + Missense_Mutation SNP C C G novel C3N-00294_T C3N-00294_N C C c.647G>C p.Gly216Ala p.G216A ENST00000369534 6/12 96 75 21 63 63 0 strelka-varscan-mutect MPP1,missense_variant,p.Gly186Ala,ENST00000413259,NM_001166462.1;MPP1,missense_variant,p.Gly216Ala,ENST00000369534,NM_001166460.1,NM_002436.3;MPP1,missense_variant,p.Gly196Ala,ENST00000393531,NM_001166461.1;MPP1,missense_variant,p.Gly170Ala,ENST00000393529,;MPP1,missense_variant,p.Gly90Ala,ENST00000453245,;MPP1,missense_variant,p.Gly113Ala,ENST00000428488,;MPP1,downstream_gene_variant,,ENST00000369531,;MPP1,non_coding_transcript_exon_variant,,ENST00000462825,;MPP1,non_coding_transcript_exon_variant,,ENST00000488754,;MPP1,downstream_gene_variant,,ENST00000488694,;MPP1,3_prime_UTR_variant,,ENST00000439370,;MPP1,3_prime_UTR_variant,,ENST00000417435,;MPP1,non_coding_transcript_exon_variant,,ENST00000475943,;MPP1,intron_variant,,ENST00000494170,;MPP1,upstream_gene_variant,,ENST00000491955,;MPP1,upstream_gene_variant,,ENST00000482757,;MPP1,upstream_gene_variant,,ENST00000493871,; G ENST00000369534 Transcript missense_variant 795/2042 647/1401 216/466 G/A gGa/gCa 1 -1 MPP1 HGNC HGNC:7219 protein_coding YES CCDS14762.1 ENSP00000358547 Q00013 UPI0000129E86 NM_001166460.1,NM_002436.3 deleterious(0) 6/12 PROSITE_profiles:PS50002,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF37,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 46 154786234 154786234 C G 1 0 0 0 0 1 0 0 0 9699 855 30 4 4 MPP1 23 154786234 Missense_Mutation SNP C C3N-00294_T 320423 154786234 1254661 1257 14029 F8 0 . GRCh38 X 154904932 154904932 + Missense_Mutation SNP C C G C3N-00294_T C3N-00294_N C C c.5465G>C p.Arg1822Thr p.R1822T ENST00000360256 16/26 184 137 47 152 152 0 strelka-varscan-mutect F8,missense_variant,p.Arg1822Thr,ENST00000360256,NM_000132.3;EEF1A1P31,downstream_gene_variant,,ENST00000415978,; G ENST00000360256 Transcript missense_variant 5666/9059 5465/7056 1822/2351 R/T aGa/aCa CM125452 1 -1 F8 HGNC HGNC:3546 protein_coding YES CCDS35457.1 ENSP00000353393 P00451 UPI000012A416 NM_000132.3 deleterious(0.02) 16/26 Gene3D:2.60.40.420,PIRSF_domain:PIRSF000354,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF50,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999977 1 1 1 0 G 3 3 46 154904932 154904932 C G 1 0 0 0 0 1 0 0 0 5218 913 32 4 4 F8 23 154904932 Missense_Mutation SNP C C3N-00294_T 118698 154904932 1135963 1258 14030 F8 0 . GRCh38 X 154966081 154966081 + Silent SNP T T C C3N-00294_T C3N-00294_N T T c.1332A>G p.= p.K444K ENST00000360256 9/26 139 130 9 91 91 0 strelka-varscan-mutect F8,synonymous_variant,p.=,ENST00000360256,NM_000132.3;F8,non_coding_transcript_exon_variant,,ENST00000483822,; C ENST00000360256 Transcript synonymous_variant 1533/9059 1332/7056 444/2351 K aaA/aaG CD982641,CM053241,CM0911142,CX067269,COSM4108246,COSM4108247 1 -1 F8 HGNC HGNC:3546 protein_coding YES CCDS35457.1 ENSP00000353393 P00451 UPI000012A416 NM_000132.3 9/26 Gene3D:2.60.40.420,PIRSF_domain:PIRSF000354,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF50,Superfamily_domains:SSF49503 0,0,0,0,1,1 LOW 1 SNV 1 1,1,1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 46 154966081 154966081 T C 1 0 0 0 0 0 0 0 1 5218 1606 56 5 5 F8 23 154966081 Silent SNP T C3N-00294_T 61149 154966081 1074814 1259 14031 USP9Y 0 . GRCh38 Y 12773653 12773653 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.2059G>A p.Glu687Lys p.E687K ENST00000338981 17/46 186 120 66 235 235 0 strelka-varscan-mutect USP9Y,missense_variant,p.Glu687Lys,ENST00000338981,NM_004654.3;USP9Y,non_coding_transcript_exon_variant,,ENST00000426564,; A ENST00000338981 Transcript missense_variant 3004/10036 2059/7668 687/2555 E/K Gaa/Aaa 1 1 USP9Y HGNC HGNC:12633 protein_coding YES CCDS14781.1 ENSP00000342812 O00507 UPI00001AE67D NM_004654.3 deleterious(0.05) 17/46 MODERATE 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 46 12773653 12773653 G A 1 0 0 0 0 1 0 0 0 17634 943 33 3 3 USP9Y 24 12773653 Missense_Mutation SNP G C3N-00294_T 12773653 44453762 1260 14032 USP9Y 0 . GRCh38 Y 12840272 12840272 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.5746G>A p.Glu1916Lys p.E1916K ENST00000338981 36/46 157 148 9 187 187 0 strelka-varscan-mutect USP9Y,missense_variant,p.Glu1916Lys,ENST00000338981,NM_004654.3;USP9Y,non_coding_transcript_exon_variant,,ENST00000426564,; A ENST00000338981 Transcript missense_variant 6691/10036 5746/7668 1916/2555 E/K Gaa/Aaa 1 1 USP9Y HGNC HGNC:12633 protein_coding YES CCDS14781.1 ENSP00000342812 O00507 UPI00001AE67D NM_004654.3 deleterious(0) 36/46 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF371,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 73 129 0 5 3 0 0 0 -3.512781 0.1106617 1 1 0 0 A 3 1 46 12840272 12840272 G A 1 0 0 0 0 1 0 0 0 17634 1291 45 3 3 USP9Y 24 12840272 Missense_Mutation SNP G C3N-00294_T 66619 12840272 44387143 1261 14033 RBMY1A1 0 . GRCh38 Y 21549017 21549017 + Missense_Mutation SNP G G A novel C3N-00294_T C3N-00294_N G G c.1460G>A p.Arg487Gln p.R487Q ENST00000382707 12/12 41 33 8 64 63 1 varscan-mutect RBMY1A1,missense_variant,p.Arg487Gln,ENST00000382707,NM_005058.2;RBMY1A1,missense_variant,p.Arg487Gln,ENST00000439108,;RBMY1A1,missense_variant,p.Arg450Gln,ENST00000303902,;RBMY1B,missense_variant,p.Arg450Gln,ENST00000619219,;RBMY1A1,3_prime_UTR_variant,,ENST00000361046,NM_001320945.1; A ENST00000382707 Transcript missense_variant 1612/1921 1460/1491 487/496 R/Q cGa/cAa 1 1 RBMY1A1 HGNC HGNC:9912 protein_coding YES CCDS14796.1 ENSP00000372154 P0DJD3 UPI000011D6E5 NM_005058.2 deleterious(0.01) 12/12 MODERATE 1 SNV 1 1 PASS . . 73 132 5 0 0 0 0 0 -19.69238 0.9999993 1 1 1 0 A 3 1 46 21549017 21549017 G A 1 0 0 0 0 1 0 0 0 13322 1058 37 1 1 RBMY1A1 24 21549017 Missense_Mutation SNP G C3N-00294_T 8708745 21549017 35678398 1262 14034 CPSF3L 0 . GRCh38 1 1319436 1319436 + Nonsense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.307C>T p.Gln103Ter p.Q103* ENST00000540437 6/19 195 179 16 102 102 0 varscan-mutect CPSF3L,stop_gained,p.Gln103Ter,ENST00000540437,NM_001256456.1;CPSF3L,stop_gained,p.Gln68Ter,ENST00000545578,NM_001256460.1;CPSF3L,stop_gained,p.Gln97Ter,ENST00000435064,NM_017871.5;CPSF3L,stop_gained,p.Gln97Ter,ENST00000450926,;CPSF3L,stop_gained,p.Gln97Ter,ENST00000618806,;CPSF3L,stop_gained,p.Gln97Ter,ENST00000429572,;CPSF3L,stop_gained,p.Gln97Ter,ENST00000434694,;CPSF3L,stop_gained,p.Gln144Ter,ENST00000530031,;CPSF3L,stop_gained,p.Gln103Ter,ENST00000527719,;CPSF3L,stop_gained,p.Gln157Ter,ENST00000498476,;CPSF3L,stop_gained,p.Gln98Ter,ENST00000534345,;CPSF3L,5_prime_UTR_variant,,ENST00000526332,;CPSF3L,intron_variant,,ENST00000421495,;CPSF3L,intron_variant,,ENST00000620829,NM_001256462.1;CPSF3L,intron_variant,,ENST00000411962,;CPSF3L,intron_variant,,ENST00000419704,NM_001256463.1;CPSF3L,downstream_gene_variant,,ENST00000627245,;RP5-890O3.9,upstream_gene_variant,,ENST00000444968,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000493534,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000532952,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000490853,;CPSF3L,upstream_gene_variant,,ENST00000462432,;CPSF3L,stop_gained,p.Gln97Ter,ENST00000528879,;CPSF3L,splice_region_variant,,ENST00000323275,;CPSF3L,splice_region_variant,,ENST00000526797,;CPSF3L,3_prime_UTR_variant,,ENST00000458452,;CPSF3L,3_prime_UTR_variant,,ENST00000527098,;CPSF3L,3_prime_UTR_variant,,ENST00000430786,;CPSF3L,3_prime_UTR_variant,,ENST00000531019,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000496353,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000498173,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000488042,;CPSF3L,non_coding_transcript_exon_variant,,ENST00000525603,;CPSF3L,intron_variant,,ENST00000532772,;CPSF3L,intron_variant,,ENST00000526113,;CPSF3L,intron_variant,,ENST00000526904,;CPSF3L,upstream_gene_variant,,ENST00000478641,;CPSF3L,upstream_gene_variant,,ENST00000470030,;CPSF3L,upstream_gene_variant,,ENST00000531377,;CPSF3L,upstream_gene_variant,,ENST00000531292,;CPSF3L,upstream_gene_variant,,ENST00000527383,;CPSF3L,upstream_gene_variant,,ENST00000467408,;CPSF3L,downstream_gene_variant,,ENST00000530233,;CPSF3L,downstream_gene_variant,,ENST00000470679,;CPSF3L,downstream_gene_variant,,ENST00000525285,;CPSF3L,upstream_gene_variant,,ENST00000531020,;CPSF3L,upstream_gene_variant,,ENST00000533916,; A ENST00000540437 Transcript stop_gained 841/2629 307/1821 103/606 Q/* Cag/Tag 1 -1 CPSF3L HGNC HGNC:26052 protein_coding YES CCDS57960.1 ENSP00000445001 Q5TA45 UPI0000EE7E27 NM_001256456.1 6/19 hmmpanther:PTHR11203:SF37,hmmpanther:PTHR11203,Pfam_domain:PF16661,Gene3D:3.60.15.10,SMART_domains:SM00849,Superfamily_domains:SSF56281 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 47 1319436 1319436 G A 1 0 0 0 0 0 1 0 0 3623 1357 47 3 3 CPSF3L 1 1319436 Nonsense_Mutation SNP G C3N-00433_T 1319436 247636986 1 14035 MEGF6 0 . GRCh38 1 3509197 3509197 + Missense_Mutation SNP C C G rs758378302 C3N-00433_T C3N-00433_N C C c.1406G>C p.Arg469Pro p.R469P ENST00000356575 12/37 99 94 5 48 48 0 strelka-mutect MEGF6,missense_variant,p.Arg469Pro,ENST00000356575,NM_001409.3;MEGF6,missense_variant,p.Arg364Pro,ENST00000294599,;MEGF6,missense_variant,p.Arg476Pro,ENST00000485002,; G ENST00000356575 Transcript missense_variant 1633/5455 1406/4626 469/1541 R/P cGg/cCg rs758378302 1 -1 MEGF6 HGNC HGNC:3232 protein_coding YES CCDS41237.1 ENSP00000348982 O75095 UPI0000DACACB NM_001409.3 deleterious(0.04) 12/37 hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF106 MODERATE 1 SNV 1 1 PASS rs758378302 . 0 206 3 0 0 0 0 0 -10.80378 1 1 1 1 0 G 3 3 47 3509197 3509197 C G 1 0 0 0 0 1 0 0 0 9402 652 23 4 4 MEGF6 1 3509197 Missense_Mutation SNP C C3N-00433_T 2189761 3509197 245447225 2 14036 BTBD8 0 . GRCh38 1 92102634 92102634 + Missense_Mutation SNP A A G novel C3N-00433_T C3N-00433_N A A c.509A>G p.Asp170Gly p.D170G ENST00000342818 3/9 58 53 5 90 89 1 strelka-varscan-mutect BTBD8,missense_variant,p.Asp170Gly,ENST00000636805,;BTBD8,missense_variant,p.Asp170Gly,ENST00000342818,NM_183242.3;BTBD8,missense_variant,p.Asp170Gly,ENST00000635934,;BTBD8,non_coding_transcript_exon_variant,,ENST00000370382,; G ENST00000342818 Transcript missense_variant 745/1412 509/1137 170/378 D/G gAt/gGt 1 1 BTBD8 HGNC HGNC:21019 protein_coding YES CCDS737.1 ENSP00000343686 Q5XKL5 UPI000014114A NM_183242.3 tolerated(0.16) 3/9 hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF34 MODERATE 1 SNV 1 1 PASS rs1223562373 . 0 206 4 0 0 0 0 0 -12.08612 1 1 1 1 0 G 3 3 47 92102634 92102634 A G 1 0 0 0 0 1 0 0 0 1723 333 12 5 5 BTBD8 1 92102634 Missense_Mutation SNP A C3N-00433_T 88593437 92102634 156853788 3 14037 VPS72 0 . GRCh38 1 151176729 151176729 + Nonsense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.1043C>G p.Ser348Ter p.S348* ENST00000354473 6/6 564 532 32 278 278 0 strelka-varscan-mutect VPS72,stop_gained,p.Ser337Ter,ENST00000368892,NM_001271088.1,NM_005997.2;VPS72,stop_gained,p.Ser348Ter,ENST00000354473,NM_001271087.1;TMOD4,upstream_gene_variant,,ENST00000295314,NM_013353.2;TMOD4,upstream_gene_variant,,ENST00000441701,;TMOD4,upstream_gene_variant,,ENST00000466891,;VPS72,downstream_gene_variant,,ENST00000496809,;TMOD4,upstream_gene_variant,,ENST00000601585,;TMOD4,upstream_gene_variant,,ENST00000488488,;VPS72,non_coding_transcript_exon_variant,,ENST00000491094,;TMOD4,upstream_gene_variant,,ENST00000463543,; C ENST00000354473 Transcript stop_gained 1080/1347 1043/1128 348/375 S/* tCa/tGa 1 -1 VPS72 HGNC HGNC:11644 protein_coding YES CCDS59201.1 ENSP00000346464 Q15906 UPI0000204210 NM_001271087.1 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR13275 HIGH SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 47 151176729 151176729 G C 1 0 0 0 0 0 1 0 0 17765 1294 45 4 4 VPS72 1 151176729 Nonsense_Mutation SNP G C3N-00433_T 59074095 151176729 97779693 4 14038 KCNN3 0 . GRCh38 1 154772124 154772124 + Silent SNP C C T rs2271117 C3N-00433_T C3N-00433_N C C c.1299G>A p.= p.S433S ENST00000618040 3/9 670 621 49 331 331 0 strelka-varscan-mutect KCNN3,synonymous_variant,p.=,ENST00000618040,NM_001204087.1;KCNN3,synonymous_variant,p.=,ENST00000271915,NM_002249.5;KCNN3,synonymous_variant,p.=,ENST00000361147,NM_170782.2;KCNN3,synonymous_variant,p.=,ENST00000358505,; T ENST00000618040 Transcript synonymous_variant 1613/13057 1299/2241 433/746 S tcG/tcA rs2271117,COSM1255399,COSM1255400 1 -1 KCNN3 HGNC HGNC:6292 protein_coding YES CCDS72928.1 ENSP00000481848 A0A087WYJ0 UPI0001F936D2 NM_001204087.1 3/9 Gene3D:1.10.287.70,hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF40,Superfamily_domains:SSF81324 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs2271117 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 154772124 154772124 C T 1 0 0 0 0 0 0 0 1 7996 523 19 1 1 KCNN3 1 154772124 Silent SNP C C3N-00433_T 3595395 154772124 94184298 5 14039 ARHGEF11 0 . GRCh38 1 156961758 156961758 + Silent SNP T T A rs752773914 C3N-00433_T C3N-00433_N T T c.1158A>T p.= p.A386A ENST00000368194 14/41 221 197 24 163 163 0 strelka-varscan-mutect ARHGEF11,synonymous_variant,p.=,ENST00000368194,NM_198236.2;ARHGEF11,synonymous_variant,p.=,ENST00000361409,NM_014784.3;ARHGEF11,non_coding_transcript_exon_variant,,ENST00000486670,; A ENST00000368194 Transcript synonymous_variant 2198/6889 1158/4689 386/1562 A gcA/gcT rs752773914 1 -1 ARHGEF11 HGNC HGNC:14580 protein_coding YES CCDS1163.1 ENSP00000357177 O15085 UPI00001D62A7 NM_198236.2 14/41 PROSITE_profiles:PS50132,hmmpanther:PTHR12673:SF111,hmmpanther:PTHR12673,Pfam_domain:PF09128,Gene3D:1.10.167.10,SMART_domains:SM00315,Superfamily_domains:SSF48097 LOW 1 SNV 1 1 PASS rs752773914 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 156961758 156961758 T A 1 0 0 0 0 0 0 0 1 1026 1567 55 4 4 ARHGEF11 1 156961758 Silent SNP T C3N-00433_T 2189634 156961758 91994664 6 14040 CRP 0 . GRCh38 1 159713582 159713582 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.618G>T p.= p.R206R ENST00000255030 2/2 253 236 17 148 147 1 strelka-varscan-mutect CRP,synonymous_variant,p.=,ENST00000255030,NM_000567.2;CRP,synonymous_variant,p.=,ENST00000437342,;CRP,synonymous_variant,p.=,ENST00000368112,;CRP,synonymous_variant,p.=,ENST00000368110,;CRP,synonymous_variant,p.=,ENST00000368111,;CRP,non_coding_transcript_exon_variant,,ENST00000473196,;CRP,intron_variant,,ENST00000489317,; A ENST00000255030 Transcript synonymous_variant 722/2015 618/675 206/224 R cgG/cgT 1 -1 CRP HGNC HGNC:2367 protein_coding YES CCDS30911.1 ENSP00000255030 P02741 UPI0000128478 NM_000567.2 2/2 hmmpanther:PTHR19277:SF119,hmmpanther:PTHR19277,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899,Prints_domain:PR00895 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 159713582 159713582 C A 1 0 0 0 0 0 0 0 1 3697 610 22 2 2 CRP 1 159713582 Silent SNP C C3N-00433_T 2751824 159713582 89242840 7 14041 TOMM40L 0 . GRCh38 1 161226580 161226580 + Missense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.91G>C p.Asp31His p.D31H ENST00000367988 2/10 280 265 15 123 123 0 strelka-mutect TOMM40L,missense_variant,p.Asp31His,ENST00000545897,NM_001286373.1,NM_001286374.1;TOMM40L,missense_variant,p.Asp31His,ENST00000367988,NM_032174.5;TOMM40L,missense_variant,p.Asp31His,ENST00000367987,;NR1I3,downstream_gene_variant,,ENST00000367983,NM_005122.4;NR1I3,downstream_gene_variant,,ENST00000506209,;NR1I3,downstream_gene_variant,,ENST00000367980,NM_001077482.2;NR1I3,downstream_gene_variant,,ENST00000367982,NM_001077480.2;NR1I3,downstream_gene_variant,,ENST00000628566,;NR1I3,downstream_gene_variant,,ENST00000515621,;NR1I3,downstream_gene_variant,,ENST00000428574,NM_001077469.2;NR1I3,downstream_gene_variant,,ENST00000442691,NM_001077478.2;NR1I3,downstream_gene_variant,,ENST00000515452,;NR1I3,downstream_gene_variant,,ENST00000367981,NM_001077472.2;NR1I3,downstream_gene_variant,,ENST00000367979,;NR1I3,downstream_gene_variant,,ENST00000367985,NM_001077481.2;NR1I3,downstream_gene_variant,,ENST00000511676,NM_001077479.2;NR1I3,downstream_gene_variant,,ENST00000367984,NM_001077471.2;NR1I3,downstream_gene_variant,,ENST00000412844,NM_001077473.2;NR1I3,downstream_gene_variant,,ENST00000505005,NM_001077474.2;NR1I3,downstream_gene_variant,,ENST00000508740,NM_001077476.2;NR1I3,downstream_gene_variant,,ENST00000437437,NM_001077477.2;NR1I3,downstream_gene_variant,,ENST00000504010,NM_001077470.2;NR1I3,downstream_gene_variant,,ENST00000512372,NM_001077475.2;NR1I3,downstream_gene_variant,,ENST00000502985,;NR1I3,downstream_gene_variant,,ENST00000508387,;NR1I3,downstream_gene_variant,,ENST00000511944,;APOA2,upstream_gene_variant,,ENST00000464492,;NR1I3,downstream_gene_variant,,ENST00000511748,;APOA2,upstream_gene_variant,,ENST00000367990,NM_001643.1;APOA2,upstream_gene_variant,,ENST00000463273,;APOA2,upstream_gene_variant,,ENST00000468465,;APOA2,upstream_gene_variant,,ENST00000470459,;APOA2,upstream_gene_variant,,ENST00000463812,;APOA2,upstream_gene_variant,,ENST00000469730,;APOA2,upstream_gene_variant,,ENST00000491350,;TOMM40L,upstream_gene_variant,,ENST00000583479,;TOMM40L,non_coding_transcript_exon_variant,,ENST00000474486,;TOMM40L,non_coding_transcript_exon_variant,,ENST00000492482,;TOMM40L,non_coding_transcript_exon_variant,,ENST00000470426,;TOMM40L,non_coding_transcript_exon_variant,,ENST00000465512,;NR1I3,downstream_gene_variant,,ENST00000479324,;NR1I3,downstream_gene_variant,,ENST00000488651,;NR1I3,downstream_gene_variant,,ENST00000503547,;TOMM40L,upstream_gene_variant,,ENST00000475793,;NR1I3,downstream_gene_variant,,ENST00000464422,;TOMM40L,upstream_gene_variant,,ENST00000468803,;NR1I3,downstream_gene_variant,,ENST00000506018,;APOA2,upstream_gene_variant,,ENST00000481413,;NR1I3,downstream_gene_variant,,ENST00000502848,;NR1I3,downstream_gene_variant,,ENST00000512340,;NR1I3,downstream_gene_variant,,ENST00000505944,;NR1I3,downstream_gene_variant,,ENST00000510951,;APOA2,upstream_gene_variant,,ENST00000481511,;NR1I3,downstream_gene_variant,,ENST00000507215,; C ENST00000367988 Transcript missense_variant 360/2708 91/927 31/308 D/H Gat/Cat 1 1 TOMM40L HGNC HGNC:25756 protein_coding YES CCDS1227.1 ENSP00000356967 Q969M1 UPI000006F917 NM_032174.5 deleterious(0.04) 2/10 hmmpanther:PTHR10802,hmmpanther:PTHR10802:SF0,Pfam_domain:PF01459,Gene3D:2.40.160.10 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 161226580 161226580 G C 1 0 0 0 0 1 0 0 0 16833 1058 37 4 4 TOMM40L 1 161226580 Missense_Mutation SNP G C3N-00433_T 1512998 161226580 87729842 8 14042 OLFML2B 0 . GRCh38 1 161998151 161998151 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.1151C>A p.Pro384His p.P384H ENST00000367940 6/8 221 206 15 113 113 0 strelka-varscan-mutect OLFML2B,missense_variant,p.Pro383His,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Pro384His,ENST00000367940,NM_001297713.1; T ENST00000367940 Transcript missense_variant 1361/2685 1151/2256 384/751 P/H cCc/cAc 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 deleterious(0.01) 6/8 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 161998151 161998151 G T 1 0 0 0 0 1 0 0 0 10933 1232 43 2 2 OLFML2B 1 161998151 Missense_Mutation SNP G C3N-00433_T 771571 161998151 86958271 9 14043 LMX1A 0 . GRCh38 1 165355550 165355550 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.10G>T p.Gly4Cys p.G4C ENST00000342310 2/9 362 342 20 175 175 0 strelka-varscan-mutect LMX1A,missense_variant,p.Gly4Cys,ENST00000342310,NM_177398.3;LMX1A,missense_variant,p.Gly4Cys,ENST00000294816,NM_001174069.1;LMX1A,missense_variant,p.Gly4Cys,ENST00000367893,; A ENST00000342310 Transcript missense_variant 393/3545 10/1149 4/382 G/C Ggc/Tgc 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 deleterious_low_confidence(0) 2/9 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88 MODERATE 1 SNV 2 1 PASS rs979422359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 165355550 165355550 C A 1 0 0 0 0 1 0 0 0 8788 652 23 1 1 LMX1A 1 165355550 Missense_Mutation SNP C C3N-00433_T 3357399 165355550 83600872 10 14044 ILDR2 0 . GRCh38 1 166958036 166958036 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.112A>T p.Thr38Ser p.T38S ENST00000271417 2/10 220 197 23 140 140 0 strelka-varscan-mutect ILDR2,missense_variant,p.Thr38Ser,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Thr38Ser,ENST00000529071,;ILDR2,missense_variant,p.Thr38Ser,ENST00000528703,;ILDR2,missense_variant,p.Thr38Ser,ENST00000526687,;ILDR2,missense_variant,p.Thr38Ser,ENST00000525740,;ILDR2,missense_variant,p.Thr38Ser,ENST00000469934,;ILDR2,missense_variant,p.Thr38Ser,ENST00000529387,; A ENST00000271417 Transcript missense_variant 168/13140 112/1920 38/639 T/S Act/Tct 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 deleterious(0.01) 2/10 Gene3D:2.60.40.10,hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 166958036 166958036 T A 1 0 0 0 0 1 0 0 0 7613 1696 59 4 4 ILDR2 1 166958036 Missense_Mutation SNP T C3N-00433_T 1602486 166958036 81998386 11 14045 FMO2 0 . GRCh38 1 171208998 171208998 + Silent SNP C C T rs755791366 C3N-00433_T C3N-00433_N C C c.1461C>T p.= p.A487A ENST00000209929 9/9 86 80 6 77 77 0 strelka-varscan-mutect FMO2,synonymous_variant,p.=,ENST00000209929,NM_001460.4;RP1-127D3.4,intron_variant,,ENST00000422841,;RP1-127D3.4,intron_variant,,ENST00000445909,;RP1-127D3.4,intron_variant,,ENST00000445290,;FMO2,3_prime_UTR_variant,,ENST00000529935,;FMO2,non_coding_transcript_exon_variant,,ENST00000488431,; T ENST00000209929 Transcript synonymous_variant 1619/3851 1461/1608 487/535 A gcC/gcT rs755791366 1 1 FMO2 HGNC HGNC:3770 protein_coding YES CCDS1293.2 ENSP00000209929 Q99518 UPI0000ED9123 NM_001460.4 9/9 Pfam_domain:PF00743,PIRSF_domain:PIRSF000332,hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF84 LOW 1 SNV 1 1 PASS rs755791366 . 0 206 4 0 0 0 0 0 -12.98389 1 1 1 1 0 T 2 4 47 171208998 171208998 C T 1 0 0 0 0 0 0 0 1 5811 581 21 3 3 FMO2 1 171208998 Silent SNP C C3N-00433_T 4250962 171208998 77747424 12 14046 TNN 0 . GRCh38 1 175117148 175117148 + Missense_Mutation SNP G G T rs147066934 C3N-00433_T C3N-00433_N G G c.2329G>T p.Val777Leu p.V777L ENST00000239462 10/19 607 567 40 320 320 0 varscan-mutect TNN,missense_variant,p.Val777Leu,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Val600Leu,ENST00000621086,;TNN,missense_variant,p.Val600Leu,ENST00000622870,; T ENST00000239462 Transcript missense_variant 2442/5008 2329/3900 777/1299 V/L Gtg/Ttg rs147066934,COSM318138 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 tolerated(0.21) 10/19 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs147066934 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 175117148 175117148 G T 1 0 0 0 0 1 0 0 0 16796 1145 40 1 1 TNN 1 175117148 Missense_Mutation SNP G C3N-00433_T 3908150 175117148 73839274 13 14047 ASTN1 0 . GRCh38 1 176864502 176864502 + Missense_Mutation SNP A A T novel C3N-00433_T C3N-00433_N A A c.3667T>A p.Ser1223Thr p.S1223T ENST00000361833 23/23 284 259 25 170 170 0 strelka-varscan-mutect ASTN1,missense_variant,p.Ser1223Thr,ENST00000361833,NM_004319.2;ASTN1,intron_variant,,ENST00000367657,NM_001286164.1;ASTN1,downstream_gene_variant,,ENST00000424564,NM_207108.2; T ENST00000361833 Transcript missense_variant 3681/7116 3667/3885 1223/1294 S/T Tcc/Acc 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 tolerated(0.08) 23/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 176864502 176864502 A T 1 0 0 0 0 1 0 0 0 1211 246 9 4 4 ASTN1 1 176864502 Missense_Mutation SNP A C3N-00433_T 1747354 176864502 72091920 14 14048 IGFN1 0 . GRCh38 1 201208668 201208668 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.3775C>T p.Leu1259Phe p.L1259F ENST00000335211 12/24 116 105 11 87 87 0 strelka-mutect IGFN1,missense_variant,p.Leu1259Phe,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,;IGFN1,downstream_gene_variant,,ENST00000444705,; T ENST00000335211 Transcript missense_variant 3905/11810 3775/11127 1259/3708 L/F Ctc/Ttc 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 tolerated(0.08) 12/24 hmmpanther:PTHR10489:SF630,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.99571 1 1 1 1 0 T 3 4 47 201208668 201208668 C T 1 0 0 0 0 1 0 0 0 7497 681 24 3 3 IGFN1 1 201208668 Missense_Mutation SNP C C3N-00433_T 24344166 201208668 47747754 15 14049 KCNK2 0 . GRCh38 1 215195064 215195064 + Missense_Mutation SNP G G T rs763061596 C3N-00433_T C3N-00433_N G G c.935G>T p.Arg312Leu p.R312L ENST00000444842 6/7 197 177 20 195 194 1 strelka-varscan-mutect KCNK2,missense_variant,p.Arg312Leu,ENST00000444842,NM_001017425.2;KCNK2,missense_variant,p.Arg297Leu,ENST00000391894,NM_014217.3;KCNK2,missense_variant,p.Arg308Leu,ENST00000391895,NM_001017424.2;KCNK2,3_prime_UTR_variant,,ENST00000486921,;KCNK2,3_prime_UTR_variant,,ENST00000467031,;KCNK2,3_prime_UTR_variant,,ENST00000474771,;KCNK2,downstream_gene_variant,,ENST00000470177,; T ENST00000444842 Transcript missense_variant 1085/3379 935/1281 312/426 R/L cGa/cTa rs763061596 1 1 KCNK2 HGNC HGNC:6277 protein_coding YES CCDS41467.1 ENSP00000394033 O95069 UPI000013D4B8 NM_001017425.2 deleterious(0.02) 6/7 hmmpanther:PTHR11003:SF21,hmmpanther:PTHR11003,Gene3D:1.10.287.70,Pfam_domain:PF07885,Superfamily_domains:SSF81324,Prints_domain:PR01499 MODERATE 1 SNV 1 1 PASS rs763061596 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 215195064 215195064 G T 1 0 0 0 0 1 0 0 0 7983 1058 37 1 1 KCNK2 1 215195064 Missense_Mutation SNP G C3N-00433_T 13986396 215195064 33761358 16 14050 DNAH14 0 . GRCh38 1 225374855 225374855 + Silent SNP G G A C3N-00433_T C3N-00433_N G G c.12207G>A p.= p.L4069L ENST00000430092 76/84 130 122 8 102 102 0 strelka-varscan-mutect DNAH14,synonymous_variant,p.=,ENST00000430092,NM_001373.1;DNAH14,synonymous_variant,p.=,ENST00000439375,;DNAH14,intron_variant,,ENST00000445597,;DNAH14,3_prime_UTR_variant,,ENST00000327794,; A ENST00000430092 Transcript synonymous_variant 12422/13763 12207/13548 4069/4515 L ctG/ctA COSM5681178 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 76/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254,Pfam_domain:PF03028 1 LOW SNV 5 1 1 PASS . . 0 208 2 0 0 0 0 0 -15.69519 1 1 1 1 0 A 2 1 47 225374855 225374855 G A 1 0 0 0 0 0 0 0 1 4415 1277 45 3 3 DNAH14 1 225374855 Silent SNP G C3N-00433_T 10179791 225374855 23581567 17 14051 OBSCN 0 . GRCh38 1 228212621 228212621 + Missense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.838G>A p.Glu280Lys p.E280K ENST00000570156 2/116 775 736 39 393 393 0 strelka-varscan-mutect OBSCN,missense_variant,p.Glu280Lys,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Glu280Lys,ENST00000366707,;OBSCN,missense_variant,p.Glu280Lys,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Glu280Lys,ENST00000636875,;OBSCN,missense_variant,p.Glu280Lys,ENST00000284548,NM_052843.3;C1orf145,intron_variant,,ENST00000295012,;OBSCN,upstream_gene_variant,,ENST00000493977,;C1orf145,3_prime_UTR_variant,,ENST00000337335,;C1orf145,intron_variant,,ENST00000472613,; A ENST00000570156 Transcript missense_variant 912/26925 838/26772 280/8923 E/K Gag/Aag 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.52) 2/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF708,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 228212621 228212621 G A 1 0 0 0 0 1 0 0 0 10889 1059 37 1 1 OBSCN 1 228212621 Missense_Mutation SNP G C3N-00433_T 2837766 228212621 20743801 18 14052 RYR2 0 . GRCh38 1 237388167 237388167 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.757G>T p.Gly253Cys p.G253C ENST00000366574 10/105 384 358 26 271 271 0 strelka-varscan-mutect RYR2,missense_variant,p.Gly253Cys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly237Cys,ENST00000360064,; T ENST00000366574 Transcript missense_variant 1074/16562 757/14904 253/4967 G/C Ggt/Tgt 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.01) 10/105 Gene3D:2.80.10.50,Pfam_domain:PF02815,PROSITE_profiles:PS50919,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00472,Superfamily_domains:SSF82109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 237388167 237388167 G T 1 0 0 0 0 1 0 0 0 14029 1348 47 2 2 RYR2 1 237388167 Missense_Mutation SNP G C3N-00433_T 9175546 237388167 11568255 19 14053 CEP170 0 . GRCh38 1 243172829 243172829 + Silent SNP G G A novel C3N-00433_T C3N-00433_N G G c.1584C>T p.= p.D528D ENST00000366542 11/20 53 46 7 84 84 0 strelka-varscan-mutect CEP170,synonymous_variant,p.=,ENST00000366542,NM_014812.2;CEP170,synonymous_variant,p.=,ENST00000366544,NM_001042404.1;CEP170,synonymous_variant,p.=,ENST00000366543,NM_001042405.1;CEP170,synonymous_variant,p.=,ENST00000336415,;CEP170,synonymous_variant,p.=,ENST00000522895,;RP11-261C10.4,downstream_gene_variant,,ENST00000437499,;RP11-261C10.4,downstream_gene_variant,,ENST00000422938,;CEP170,non_coding_transcript_exon_variant,,ENST00000518289,;CEP170,3_prime_UTR_variant,,ENST00000461671,;CEP170,non_coding_transcript_exon_variant,,ENST00000521911,; A ENST00000366542 Transcript synonymous_variant 1636/6828 1584/4755 528/1584 D gaC/gaT 1 -1 CEP170 HGNC HGNC:28920 protein_coding YES CCDS44339.1 ENSP00000355500 Q5SW79 UPI0000470238 NM_014812.2 11/20 hmmpanther:PTHR15715:SF17,hmmpanther:PTHR15715 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 243172829 243172829 G A 1 0 0 0 0 0 0 0 1 2964 1368 48 3 3 CEP170 1 243172829 Silent SNP G C3N-00433_T 5784662 243172829 5783593 20 14054 OR2G3 0 . GRCh38 1 247605997 247605997 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.412C>A p.Pro138Thr p.P138T ENST00000320002 1/1 274 247 27 191 190 1 strelka-varscan-mutect OR2G3,missense_variant,p.Pro138Thr,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000320002 Transcript missense_variant 412/930 412/930 138/309 P/T Cca/Aca 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 247605997 247605997 C A 1 0 0 0 0 1 0 0 0 11077 623 22 2 2 OR2G3 1 247605997 Missense_Mutation SNP C C3N-00433_T 4433168 247605997 1350425 21 14055 OR2T8 0 . GRCh38 1 247921068 247921068 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.51C>A p.Asn17Lys p.N17K ENST00000319968 1/1 109 101 8 74 74 0 varscan-mutect OR2T8,missense_variant,p.Asn17Lys,ENST00000319968,NM_001005522.1; A ENST00000319968 Transcript missense_variant 51/939 51/939 17/312 N/K aaC/aaA 1 1 OR2T8 HGNC HGNC:15020 protein_coding YES CCDS31100.1 ENSP00000326225 A6NH00 UPI00001999E3 NM_001005522.1 tolerated(0.18) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 202 8 0 0 0 0 0 -15.79175 0.9999913 1 1 1 0 A 3 1 47 247921068 247921068 C A 1 0 0 0 0 1 0 0 0 11107 506 18 2 2 OR2T8 1 247921068 Missense_Mutation SNP C C3N-00433_T 315071 247921068 1035354 22 14056 OR2T8 0 . GRCh38 1 247921375 247921375 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.358C>A p.Arg120Ser p.R120S ENST00000319968 1/1 173 159 14 98 98 0 varscan-mutect OR2T8,missense_variant,p.Arg120Ser,ENST00000319968,NM_001005522.1; A ENST00000319968 Transcript missense_variant 358/939 358/939 120/312 R/S Cgc/Agc 1 1 OR2T8 HGNC HGNC:15020 protein_coding YES CCDS31100.1 ENSP00000326225 A6NH00 UPI00001999E3 NM_001005522.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1361086206 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 247921375 247921375 C A 1 0 0 0 0 1 0 0 0 11107 652 23 1 1 OR2T8 1 247921375 Missense_Mutation SNP C C3N-00433_T 307 247921375 1035047 23 14057 KCNIP3 0 . GRCh38 2 95382458 95382458 + Nonsense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.637G>T p.Glu213Ter p.E213* ENST00000295225 7/9 111 100 11 58 58 0 strelka-varscan-mutect KCNIP3,stop_gained,p.Glu213Ter,ENST00000295225,NM_013434.4;KCNIP3,stop_gained,p.Glu213Ter,ENST00000360990,;KCNIP3,stop_gained,p.Glu187Ter,ENST00000468529,NM_001034914.1;KCNIP3,non_coding_transcript_exon_variant,,ENST00000377181,; T ENST00000295225 Transcript stop_gained 772/2940 637/771 213/256 E/* Gag/Tag 1 1 KCNIP3 HGNC HGNC:15523 protein_coding YES CCDS2013.1 ENSP00000295225 Q9Y2W7 A0A024RE22 UPI0000000CCD NM_013434.4 7/9 PROSITE_profiles:PS50222,hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF61,Gene3D:1.10.238.10,Pfam_domain:PF13499,Superfamily_domains:SSF47473 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99586 1 1 1 1 0 T 4 4 47 95382458 95382458 G T 1 0 0 0 0 0 1 0 0 7957 1175 41 2 2 KCNIP3 2 95382458 Nonsense_Mutation SNP G C3N-00433_T 95382458 146811071 24 14058 LRP1B 0 . GRCh38 2 141247261 141247261 + Missense_Mutation SNP A A G novel C3N-00433_T C3N-00433_N A A c.557T>C p.Met186Thr p.M186T ENST00000389484 5/91 304 286 18 344 344 0 strelka-varscan-mutect LRP1B,missense_variant,p.Met186Thr,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; G ENST00000389484 Transcript missense_variant 1529/16535 557/13800 186/4599 M/T aTg/aCg 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.03) 5/91 PROSITE_profiles:PS50026,PROSITE_patterns:PS01186,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 141247261 141247261 A G 1 0 0 0 0 1 0 0 0 8850 217 8 5 5 LRP1B 2 141247261 Missense_Mutation SNP A C3N-00433_T 45864803 141247261 100946268 25 14059 NEB 0 . GRCh38 2 151552740 151552740 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.19768G>A p.Asp6590Asn p.D6590N ENST00000618972 128/183 155 141 14 123 123 0 strelka-varscan-mutect NEB,missense_variant,p.Asp6590Asn,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Asp6590Asn,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Asp6590Asn,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Asp6590Asn,ENST00000603639,;NEB,missense_variant,p.Asp6590Asn,ENST00000604864,;NEB,missense_variant,p.Asp4889Asn,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Asp4889Asn,ENST00000172853,;NEB,missense_variant,p.Asp1320Asn,ENST00000413693,; T ENST00000618972 Transcript missense_variant 19971/26307 19768/25683 6590/8560 D/N Gac/Aac 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.24) 128/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039:SF37,hmmpanther:PTHR11039 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 151552740 151552740 C T 1 0 0 0 0 1 0 0 0 10326 826 29 3 3 NEB 2 151552740 Missense_Mutation SNP C C3N-00433_T 10305479 151552740 90640789 26 14060 SCN7A 0 . GRCh38 2 166405976 166405976 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.4653G>T p.Met1551Ile p.M1551I ENST00000409855 25/25 159 149 10 140 140 0 strelka-varscan-mutect SCN7A,missense_variant,p.Met1551Ile,ENST00000619410,;SCN7A,missense_variant,p.Met1551Ile,ENST00000621965,;SCN7A,missense_variant,p.Met1551Ile,ENST00000409855,NM_002976.3;SCN7A,3_prime_UTR_variant,,ENST00000424326,; A ENST00000409855 Transcript missense_variant 4780/7183 4653/5049 1551/1682 M/I atG/atT 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 tolerated(1) 25/25 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 166405976 166405976 C A 1 0 0 0 0 1 0 0 0 14192 594 21 2 2 SCN7A 2 166405976 Missense_Mutation SNP C C3N-00433_T 14853236 166405976 75787553 27 14061 GMPPA 0 . GRCh38 2 219505653 219505653 + Silent SNP G G T novel C3N-00433_T C3N-00433_N G G c.951G>T p.= p.L317L ENST00000373917 9/12 407 378 29 229 228 1 strelka-varscan-mutect GMPPA,synonymous_variant,p.=,ENST00000373917,;GMPPA,intron_variant,,ENST00000358215,NM_205847.2;GMPPA,intron_variant,,ENST00000313597,NM_013335.3;GMPPA,intron_variant,,ENST00000341142,;GMPPA,intron_variant,,ENST00000373908,;GMPPA,intron_variant,,ENST00000622191,;GMPPA,downstream_gene_variant,,ENST00000455657,;GMPPA,downstream_gene_variant,,ENST00000435316,;GMPPA,upstream_gene_variant,,ENST00000480034,;AC053503.11,intron_variant,,ENST00000429882,;GMPPA,downstream_gene_variant,,ENST00000635609,;GMPPA,non_coding_transcript_exon_variant,,ENST00000481170,;GMPPA,intron_variant,,ENST00000443704,;GMPPA,downstream_gene_variant,,ENST00000480506,;GMPPA,upstream_gene_variant,,ENST00000496536,; T ENST00000373917 Transcript synonymous_variant 1022/1630 951/1422 317/473 L ctG/ctT 1 1 GMPPA HGNC HGNC:22923 protein_coding ENSP00000363027 Q96IJ6 UPI000066D9A1 9/12 LOW SNV 5 1 PASS rs1017038834 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 219505653 219505653 G T 1 0 0 0 0 0 0 0 1 6374 1306 46 2 2 GMPPA 2 219505653 Silent SNP G C3N-00433_T 53099677 219505653 22687876 28 14062 GMPPA 0 . GRCh38 2 219506361 219506361 + Silent SNP C C T rs759296812 C3N-00433_T C3N-00433_N C C c.1101C>T p.= p.A367A ENST00000358215 12/13 253 238 15 127 127 0 strelka-varscan-mutect GMPPA,missense_variant,p.Pro367Leu,ENST00000622191,;GMPPA,synonymous_variant,p.=,ENST00000358215,NM_205847.2;GMPPA,synonymous_variant,p.=,ENST00000373917,;GMPPA,synonymous_variant,p.=,ENST00000313597,NM_013335.3;GMPPA,synonymous_variant,p.=,ENST00000341142,;GMPPA,synonymous_variant,p.=,ENST00000373908,;GMPPA,synonymous_variant,p.=,ENST00000480034,;GMPPA,downstream_gene_variant,,ENST00000455657,;GMPPA,downstream_gene_variant,,ENST00000435316,;AC053503.11,intron_variant,,ENST00000429882,;GMPPA,downstream_gene_variant,,ENST00000635609,;GMPPA,3_prime_UTR_variant,,ENST00000443704,;GMPPA,non_coding_transcript_exon_variant,,ENST00000481170,;GMPPA,non_coding_transcript_exon_variant,,ENST00000496536,;GMPPA,downstream_gene_variant,,ENST00000480506,; T ENST00000358215 Transcript synonymous_variant 1470/1823 1101/1263 367/420 A gcC/gcT rs759296812 1 1 GMPPA HGNC HGNC:22923 protein_coding YES CCDS2441.1 ENSP00000350949 Q96IJ6 A0A024R482 UPI000006D41C NM_205847.2 12/13 hmmpanther:PTHR22572,hmmpanther:PTHR22572:SF104,Gene3D:2.160.10.10 LOW 1 SNV 1 1 PASS rs759296812 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 219506361 219506361 C T 1 0 0 0 0 0 0 0 1 6374 623 22 3 3 GMPPA 2 219506361 Silent SNP C C3N-00433_T 708 219506361 22687168 29 14063 COL6A3 0 . GRCh38 2 237341092 237341092 + Missense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.7824C>G p.Asp2608Glu p.D2608E ENST00000295550 38/44 314 296 18 191 190 1 strelka-varscan-mutect COL6A3,missense_variant,p.Asp2608Glu,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Asp2402Glu,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Asp2402Glu,ENST00000409809,;COL6A3,missense_variant,p.Asp2001Glu,ENST00000472056,NM_057166.4;COL6A3,missense_variant,p.Asp2000Glu,ENST00000347401,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;COL6A3,upstream_gene_variant,,ENST00000468792,; C ENST00000295550 Transcript missense_variant 8277/10749 7824/9534 2608/3177 D/E gaC/gaG 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 tolerated(0.09) 38/44 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 237341092 237341092 G C 1 0 0 0 0 1 0 0 0 3490 1368 48 4 4 COL6A3 2 237341092 Missense_Mutation SNP G C3N-00433_T 17834731 237341092 4852437 30 14064 LRRN1 0 . GRCh38 3 3845629 3845629 + Missense_Mutation SNP C C A rs146290783 C3N-00433_T C3N-00433_N C C c.988C>A p.Arg330Ser p.R330S ENST00000319331 2/2 427 402 25 303 302 1 strelka-varscan-mutect LRRN1,missense_variant,p.Arg330Ser,ENST00000319331,NM_020873.5;LRRN1,downstream_gene_variant,,ENST00000496115,;SUMF1,intron_variant,,ENST00000448413,; A ENST00000319331 Transcript missense_variant 1749/3823 988/2151 330/716 R/S Cgc/Agc rs146290783 1 1 LRRN1 HGNC HGNC:20980 protein_coding YES CCDS33685.1 ENSP00000314901 Q6UXK5 UPI0000034CB8 NM_020873.5 deleterious(0.02) 2/2 hmmpanther:PTHR24373:SF97,hmmpanther:PTHR24373,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs146290783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 3845629 3845629 C A 1 0 0 0 0 1 0 0 0 8940 652 23 1 1 LRRN1 3 3845629 Missense_Mutation SNP C C3N-00433_T 3845629 194449930 31 14065 ULK4 0 . GRCh38 3 41918540 41918540 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.644G>A p.Gly215Glu p.G215E ENST00000301831 7/37 66 62 4 82 82 0 varscan-mutect ULK4,missense_variant,p.Gly215Glu,ENST00000301831,NM_017886.2;ULK4,missense_variant,p.Gly215Glu,ENST00000420927,;ULK4,downstream_gene_variant,,ENST00000459802,;ULK4,upstream_gene_variant,,ENST00000481226,; T ENST00000301831 Transcript missense_variant,splice_region_variant 1107/4613 644/3828 215/1275 G/E gGa/gAa 1 -1 ULK4 HGNC HGNC:15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 UPI0000E8267C NM_017886.2 deleterious(0) 7/37 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22983,hmmpanther:PTHR22983:SF15,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -9.757719 1 1 1 1 0 T 3 4 47 41918540 41918540 C T 1 0 0 0 0 1 0 0 0 17501 869 30 3 3 ULK4 3 41918540 Missense_Mutation SNP C C3N-00433_T 38072911 41918540 156377019 32 14066 MYL3 0 . GRCh38 3 46863357 46863357 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.34G>A p.Asp12Asn p.D12N ENST00000395869 1/6 321 303 18 184 184 0 strelka-varscan-mutect MYL3,missense_variant,p.Asp12Asn,ENST00000395869,;MYL3,missense_variant,p.Asp12Asn,ENST00000292327,NM_000258.2;MYL3,missense_variant,p.Asp12Asn,ENST00000431168,; T ENST00000395869 Transcript missense_variant 86/1012 34/588 12/195 D/N Gat/Aat 1 -1 MYL3 HGNC HGNC:7584 protein_coding YES CCDS2746.1 ENSP00000379210 P08590 A0A024R2Q5 UPI0000000CA2 tolerated_low_confidence(0.45) 1/6 hmmpanther:PTHR23048,hmmpanther:PTHR23048:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 46863357 46863357 C T 1 0 0 0 0 1 0 0 0 10048 826 29 3 3 MYL3 3 46863357 Missense_Mutation SNP C C3N-00433_T 4944817 46863357 151432202 33 14067 SLC25A20 0 . GRCh38 3 48862641 48862641 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.436G>A p.Glu146Lys p.E146K ENST00000319017 5/9 443 417 26 364 364 0 strelka-varscan-mutect SLC25A20,missense_variant,p.Glu146Lys,ENST00000319017,NM_000387.5;SLC25A20,missense_variant,p.Glu73Lys,ENST00000430379,;SLC25A20,3_prime_UTR_variant,,ENST00000440964,;SLC25A20,upstream_gene_variant,,ENST00000479050,; T ENST00000319017 Transcript missense_variant 635/1879 436/906 146/301 E/K Gaa/Aaa 1 -1 SLC25A20 HGNC HGNC:1421 protein_coding YES CCDS2779.1 ENSP00000326305 O43772 UPI000012ED5E NM_000387.5 tolerated(0.4) 5/9 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF323,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 48862641 48862641 C T 1 0 0 0 0 1 0 0 0 14748 922 32 3 3 SLC25A20 3 48862641 Missense_Mutation SNP C C3N-00433_T 1999284 48862641 149432918 34 14068 EEFSEC 0 . GRCh38 3 128262171 128262171 + Nonsense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.568G>T p.Gly190Ter p.G190* ENST00000254730 3/7 342 311 31 170 170 0 strelka-varscan-mutect EEFSEC,stop_gained,p.Gly190Ter,ENST00000254730,NM_021937.4;EEFSEC,stop_gained,p.Gly190Ter,ENST00000483457,;EEFSEC,intron_variant,,ENST00000484438,; T ENST00000254730 Transcript stop_gained 622/2232 568/1791 190/596 G/* Gga/Tga 1 1 EEFSEC HGNC HGNC:24614 protein_coding YES CCDS33849.1 ENSP00000254730 P57772 UPI000013CE58 NM_021937.4 3/7 Gene3D:3.40.50.300,Pfam_domain:PF00009,PROSITE_profiles:PS51722,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF91,Low_complexity_(Seg):seg,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS rs1267912892 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 47 128262171 128262171 G T 1 0 0 0 0 0 1 0 0 4762 1233 43 2 2 EEFSEC 3 128262171 Nonsense_Mutation SNP G C3N-00433_T 79399530 128262171 70033388 35 14069 COL6A5 0 . GRCh38 3 130395330 130395330 + Missense_Mutation SNP G G A rs865843996 C3N-00433_T C3N-00433_N G G c.3433G>A p.Val1145Ile p.V1145I ENST00000265379 8/43 202 191 11 242 242 0 strelka-varscan-mutect COL6A5,missense_variant,p.Val1145Ile,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Val1145Ile,ENST00000312481,; A ENST00000265379 Transcript missense_variant 3927/9214 3433/7836 1145/2611 V/I Gtt/Att rs865843996 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 tolerated(0.24) 8/43 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS rs865843996 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 130395330 130395330 G A 1 0 0 0 0 1 0 0 0 3491 1377 48 3 3 COL6A5 3 130395330 Missense_Mutation SNP G C3N-00433_T 2133159 130395330 67900229 36 14070 HTR3D 0 . GRCh38 3 184038379 184038379 + Missense_Mutation SNP T T A rs780610808 C3N-00433_T C3N-00433_N T T c.890T>A p.Leu297Gln p.L297Q ENST00000382489 7/8 336 314 22 199 199 0 strelka-varscan-mutect HTR3D,missense_variant,p.Leu297Gln,ENST00000382489,NM_001163646.1;HTR3D,intron_variant,,ENST00000334128,NM_182537.2;HTR3D,intron_variant,,ENST00000428798,NM_001145143.1;HTR3D,intron_variant,,ENST00000453435,; A ENST00000382489 Transcript missense_variant 890/1674 890/1365 297/454 L/Q cTg/cAg rs780610808,COSM3330452 1 1 HTR3D HGNC HGNC:24004 protein_coding YES CCDS54685.1 ENSP00000371929 Q70Z44 UPI000024209D NM_001163646.1 deleterious(0.03) 7/8 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF409,Pfam_domain:PF02932,Gene3D:1.20.120.370,Superfamily_domains:SSF90112 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780610808 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 184038379 184038379 T A 1 0 0 0 0 1 0 0 0 7343 1580 55 4 4 HTR3D 3 184038379 Missense_Mutation SNP T C3N-00433_T 53643049 184038379 14257180 37 14071 EIF4G1 0 . GRCh38 3 184323799 184323799 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.2315G>T p.Arg772Leu p.R772L ENST00000424196 15/32 510 479 31 299 298 1 strelka-varscan-mutect EIF4G1,missense_variant,p.Arg766Leu,ENST00000342981,NM_182917.4;EIF4G1,missense_variant,p.Arg772Leu,ENST00000424196,;EIF4G1,missense_variant,p.Arg725Leu,ENST00000414031,NM_001291157.1;EIF4G1,missense_variant,p.Arg765Leu,ENST00000346169,NM_198241.2;EIF4G1,missense_variant,p.Arg772Leu,ENST00000352767,NM_001194947.1;EIF4G1,missense_variant,p.Arg678Leu,ENST00000392537,NM_198244.2;EIF4G1,missense_variant,p.Arg772Leu,ENST00000382330,NM_001194946.1;EIF4G1,missense_variant,p.Arg679Leu,ENST00000427845,;EIF4G1,missense_variant,p.Arg570Leu,ENST00000434061,NM_004953.4;EIF4G1,missense_variant,p.Arg601Leu,ENST00000350481,NM_198242.2;EIF4G1,missense_variant,p.Arg726Leu,ENST00000411531,;EIF4G1,missense_variant,p.Arg569Leu,ENST00000435046,;EIF4G1,missense_variant,p.Arg602Leu,ENST00000441154,;EIF4G1,missense_variant,p.Arg706Leu,ENST00000426123,;EIF4G1,missense_variant,p.Arg773Leu,ENST00000421110,;EIF4G1,missense_variant,p.Arg766Leu,ENST00000450424,;EIF4G1,missense_variant,p.Arg601Leu,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000457456,;EIF4G1,downstream_gene_variant,,ENST00000427141,;EIF4G1,downstream_gene_variant,,ENST00000456033,;EIF4G1,upstream_gene_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000440448,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000428387,;SNORD66,upstream_gene_variant,,ENST00000390856,;EIF4G1,3_prime_UTR_variant,,ENST00000442406,;EIF4G1,3_prime_UTR_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,upstream_gene_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000493299,;EIF4G1,upstream_gene_variant,,ENST00000482303,; T ENST00000424196 Transcript missense_variant 2704/5653 2315/4821 772/1606 R/L cGc/cTc 1 1 EIF4G1 HGNC HGNC:3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 deleterious(0) 15/32 Gene3D:1.25.40.180,Pfam_domain:PF02854,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF10,SMART_domains:SM00543,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS rs1381509024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 184323799 184323799 G T 1 0 0 0 0 1 0 0 0 4870 1087 38 1 1 EIF4G1 3 184323799 Missense_Mutation SNP G C3N-00433_T 285420 184323799 13971760 38 14072 LSG1 0 . GRCh38 3 194672094 194672094 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.69G>T p.= p.R23R ENST00000265245 1/14 428 383 45 194 194 0 strelka-varscan-mutect LSG1,synonymous_variant,p.=,ENST00000265245,NM_018385.2;LSG1,intron_variant,,ENST00000480853,;LSG1,synonymous_variant,p.=,ENST00000427461,; A ENST00000265245 Transcript synonymous_variant 384/3572 69/1977 23/658 R cgG/cgT 1 -1 LSG1 HGNC HGNC:25652 protein_coding YES CCDS33922.1 ENSP00000265245 Q9H089 UPI0000DBEEC1 NM_018385.2 1/14 hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF7,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 194672094 194672094 C A 1 0 0 0 0 0 0 0 1 8955 842 30 2 2 LSG1 3 194672094 Silent SNP C C3N-00433_T 10348295 194672094 3623465 39 14073 PIGZ 0 . GRCh38 3 196948625 196948625 + Missense_Mutation SNP C C G rs764613440 C3N-00433_T C3N-00433_N C C c.272G>C p.Arg91Pro p.R91P ENST00000412723 3/3 59 54 5 28 28 0 strelka-mutect PIGZ,missense_variant,p.Arg91Pro,ENST00000412723,NM_025163.3;PIGZ,intron_variant,,ENST00000413127,;PIGZ,intron_variant,,ENST00000443835,;PIGZ,downstream_gene_variant,,ENST00000238138,; G ENST00000412723 Transcript missense_variant 419/2701 272/1740 91/579 R/P cGc/cCc rs764613440 1 -1 PIGZ HGNC HGNC:30596 protein_coding YES CCDS3324.1 ENSP00000413405 Q86VD9 UPI000013CA2C NM_025163.3 deleterious(0) 3/3 Pfam_domain:PF03901,hmmpanther:PTHR22760,hmmpanther:PTHR22760:SF3 MODERATE 1 SNV 1 1 PASS rs764613440 . 0 205 5 0 0 0 0 0 -11.94383 1 1 1 1 0 G 3 3 47 196948625 196948625 C G 1 0 0 0 0 1 0 0 0 11999 768 27 4 4 PIGZ 3 196948625 Missense_Mutation SNP C C3N-00433_T 2276531 196948625 1346934 40 14074 FGF5 0 . GRCh38 4 80286614 80286614 + Missense_Mutation SNP C C A rs746528773 C3N-00433_T C3N-00433_N C C c.749C>A p.Ser250Tyr p.S250Y ENST00000312465 3/3 211 198 13 193 193 0 strelka-varscan-mutect FGF5,missense_variant,p.Ser250Tyr,ENST00000312465,NM_004464.3;FGF5,3_prime_UTR_variant,,ENST00000456523,NM_033143.2;FGF5,non_coding_transcript_exon_variant,,ENST00000503413,;FGF5,intron_variant,,ENST00000507780,; A ENST00000312465 Transcript missense_variant 975/4555 749/807 250/268 S/Y tCt/tAt rs746528773 1 1 FGF5 HGNC HGNC:3683 protein_coding YES CCDS34021.1 ENSP00000311697 P12034 UPI0000039721 NM_004464.3 deleterious_low_confidence(0.01) 3/3 hmmpanther:PTHR11486:SF23,hmmpanther:PTHR11486 MODERATE 1 SNV 1 1 PASS rs746528773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 80286614 80286614 C A 1 0 0 0 0 1 0 0 0 5719 913 32 2 2 FGF5 4 80286614 Missense_Mutation SNP C C3N-00433_T 80286614 109927941 41 14075 SEC24D 0 . GRCh38 4 118744132 118744132 + Silent SNP G G C novel C3N-00433_T C3N-00433_N G G c.1851C>G p.= p.V617V ENST00000280551 15/23 190 178 12 108 108 0 strelka-varscan-mutect SEC24D,synonymous_variant,p.=,ENST00000280551,NM_001318066.1,NM_014822.2;SEC24D,synonymous_variant,p.=,ENST00000419654,;SEC24D,synonymous_variant,p.=,ENST00000511481,;SEC24D,non_coding_transcript_exon_variant,,ENST00000505134,;SEC24D,non_coding_transcript_exon_variant,,ENST00000511033,;SEC24D,3_prime_UTR_variant,,ENST00000514561,;SEC24D,upstream_gene_variant,,ENST00000502526,; C ENST00000280551 Transcript synonymous_variant 2090/4030 1851/3099 617/1032 V gtC/gtG 1 -1 SEC24D HGNC HGNC:10706 protein_coding YES CCDS3710.1 ENSP00000280551 O94855 UPI00001AEA4F NM_001318066.1,NM_014822.2 15/23 hmmpanther:PTHR13803:SF6,hmmpanther:PTHR13803,Gene3D:3.40.50.410,Pfam_domain:PF04811,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -15.35618 0.999899 1 1 1 0 C 2 2 47 118744132 118744132 G C 1 0 0 0 0 0 0 0 1 14274 929 33 4 4 SEC24D 4 118744132 Silent SNP G C3N-00433_T 38457518 118744132 71470423 42 14076 FAT4 0 . GRCh38 4 125448895 125448895 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.7879C>A p.Leu2627Met p.L2627M ENST00000394329 9/17 106 97 9 139 139 0 strelka-varscan-mutect FAT4,missense_variant,p.Leu2627Met,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Leu925Met,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; A ENST00000394329 Transcript missense_variant 7892/16123 7879/14946 2627/4981 L/M Ctg/Atg 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.01) 9/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 125448895 125448895 C A 1 0 0 0 0 1 0 0 0 5552 912 32 2 2 FAT4 4 125448895 Missense_Mutation SNP C C3N-00433_T 6704763 125448895 64765660 43 14077 VEGFC 0 . GRCh38 4 176687346 176687346 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.986G>A p.Gly329Glu p.G329E ENST00000618562 6/7 339 315 24 223 223 0 strelka-varscan-mutect VEGFC,missense_variant,p.Gly329Glu,ENST00000618562,NM_005429.4;RP11-313E19.2,intron_variant,,ENST00000509194,;RP11-313E19.2,intron_variant,,ENST00000504017,;VEGFC,downstream_gene_variant,,ENST00000507638,; T ENST00000618562 Transcript missense_variant 1402/2064 986/1260 329/419 G/E gGg/gAg 1 -1 VEGFC HGNC HGNC:12682 protein_coding YES CCDS43285.1 ENSP00000480043 P49767 UPI0000001C2A NM_005429.4 tolerated(0.06) 6/7 hmmpanther:PTHR12025:SF3,hmmpanther:PTHR12025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 176687346 176687346 C T 1 0 0 0 0 1 0 0 0 17697 623 22 3 3 VEGFC 4 176687346 Missense_Mutation SNP C C3N-00433_T 51238451 176687346 13527209 44 14078 MTMR12 0 . GRCh38 5 32248790 32248790 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.878A>T p.Gln293Leu p.Q293L ENST00000382142 9/16 154 145 9 165 165 0 strelka-varscan-mutect MTMR12,missense_variant,p.Gln293Leu,ENST00000382142,NM_001040446.2;MTMR12,missense_variant,p.Gln293Leu,ENST00000280285,NM_001294343.1;MTMR12,missense_variant,p.Gln293Leu,ENST00000264934,NM_001294344.1;MTMR12,non_coding_transcript_exon_variant,,ENST00000504049,; A ENST00000382142 Transcript missense_variant 1049/5187 878/2244 293/747 Q/L cAa/cTa 1 -1 MTMR12 HGNC HGNC:18191 protein_coding YES CCDS34138.1 ENSP00000371577 Q9C0I1 UPI00001678D2 NM_001040446.2 tolerated(0.07) 9/16 PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF37,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 32248790 32248790 T A 1 0 0 0 0 1 0 0 0 9929 1812 63 4 4 MTMR12 5 32248790 Missense_Mutation SNP T C3N-00433_T 32248790 149289469 45 14079 TSSK1B 0 . GRCh38 5 113434526 113434526 + Missense_Mutation SNP C C T rs770706524 C3N-00433_T C3N-00433_N C C c.314G>A p.Arg105Gln p.R105Q ENST00000390666 1/1 156 142 14 75 75 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Arg105Gln,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; T ENST00000390666 Transcript missense_variant 506/2478 314/1104 105/367 R/Q cGg/cAg rs770706524,COSM4851927,COSM4851928 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 tolerated(0.22) 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 MODERATE SNV 0,1,1 1 PASS rs770706524 . 0 201 8 0 0 0 0 0 -20 0.9999941 1 1 1 0 T 3 4 47 113434526 113434526 C T 1 0 0 0 0 1 0 0 0 17176 652 23 1 1 TSSK1B 5 113434526 Missense_Mutation SNP C C3N-00433_T 81185736 113434526 68103733 46 14080 ADAMTS19 0 . GRCh38 5 129596651 129596651 + Nonsense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.1447G>T p.Glu483Ter p.E483* ENST00000274487 8/23 64 58 6 104 104 0 strelka-varscan-mutect ADAMTS19,stop_gained,p.Glu483Ter,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,; T ENST00000274487 Transcript stop_gained 1592/5234 1447/3624 483/1207 E/* Gaa/Taa 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 8/23 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 47 129596651 129596651 G T 1 0 0 0 0 0 1 0 0 308 1291 45 2 2 ADAMTS19 5 129596651 Nonsense_Mutation SNP G C3N-00433_T 16162125 129596651 51941608 47 14081 SHROOM1 0 . GRCh38 5 132823095 132823095 + Missense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.2260C>T p.Arg754Trp p.R754W ENST00000378679 10/10 175 163 12 94 94 0 strelka-varscan-mutect SHROOM1,missense_variant,p.Arg754Trp,ENST00000378679,NM_001172700.1;SHROOM1,missense_variant,p.Arg754Trp,ENST00000617339,;SHROOM1,missense_variant,p.Arg749Trp,ENST00000319854,NM_133456.2;SHROOM1,missense_variant,p.Arg685Trp,ENST00000378676,;SHROOM1,downstream_gene_variant,,ENST00000440118,;SHROOM1,downstream_gene_variant,,ENST00000488072,;SHROOM1,downstream_gene_variant,,ENST00000495680,;SHROOM1,downstream_gene_variant,,ENST00000606676,; A ENST00000378679 Transcript missense_variant 3065/4019 2260/2559 754/852 R/W Cgg/Tgg 1 -1 SHROOM1 HGNC HGNC:24084 protein_coding YES CCDS54902.1 ENSP00000367950 Q2M3G4 UPI000036FD4D NM_001172700.1 deleterious(0) 10/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51307,hmmpanther:PTHR15012:SF37,hmmpanther:PTHR15012,Pfam_domain:PF08687 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.98071 0.9999977 1 1 1 0 A 3 1 47 132823095 132823095 G A 1 0 0 0 0 1 0 0 0 14556 1086 38 1 1 SHROOM1 5 132823095 Missense_Mutation SNP G C3N-00433_T 3226444 132823095 48715164 48 14082 HARS 0 . GRCh38 5 140691249 140691249 + Missense_Mutation SNP C C G C3N-00433_T C3N-00433_N C C c.56G>C p.Arg19Pro p.R19P ENST00000504156 1/13 121 113 8 51 51 0 strelka-mutect HARS,missense_variant,p.Arg19Pro,ENST00000504156,NM_001289094.1,NM_002109.5;HARS,missense_variant,p.Arg19Pro,ENST00000457527,NM_001258041.2;HARS,missense_variant,p.Arg19Pro,ENST00000438307,NM_001258040.2;HARS,missense_variant,p.Arg19Pro,ENST00000307633,NM_001258042.2;HARS,missense_variant,p.Arg19Pro,ENST00000431330,NM_001289093.1;HARS,missense_variant,p.Arg19Pro,ENST00000415192,NM_001289092.1;HARS,missense_variant,p.Arg19Pro,ENST00000507746,;HARS2,upstream_gene_variant,,ENST00000230771,NM_012208.3;HARS2,upstream_gene_variant,,ENST00000508522,NM_001278731.1;HARS2,upstream_gene_variant,,ENST00000448069,;HARS2,upstream_gene_variant,,ENST00000509299,;HARS2,upstream_gene_variant,,ENST00000503873,;HARS2,upstream_gene_variant,,ENST00000502303,;HARS,missense_variant,p.Arg19Pro,ENST00000512396,;HARS,non_coding_transcript_exon_variant,,ENST00000506579,;HARS,non_coding_transcript_exon_variant,,ENST00000518126,;HARS,non_coding_transcript_exon_variant,,ENST00000502888,;HARS2,upstream_gene_variant,,ENST00000510104,;HARS2,upstream_gene_variant,,ENST00000513688,;HARS2,upstream_gene_variant,,ENST00000511913,;HARS2,upstream_gene_variant,,ENST00000506318,;HARS2,upstream_gene_variant,,ENST00000520095,;HARS2,upstream_gene_variant,,ENST00000513912,; G ENST00000504156 Transcript missense_variant 776/3334 56/1530 19/509 R/P cGa/cCa COSM1486343,COSM1486344,COSM5297249,COSM5297250 1 -1 HARS HGNC HGNC:4816 protein_coding YES CCDS4237.1 ENSP00000425634 P12081 UPI00001364CE NM_001289094.1,NM_002109.5 deleterious(0) 1/13 PROSITE_profiles:PS51185,hmmpanther:PTHR11476,hmmpanther:PTHR11476:SF8,PROSITE_patterns:PS00762,Pfam_domain:PF00458,Gene3D:1.10.287.10,SMART_domains:SM00991,Superfamily_domains:SSF47060 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 204 6 0 0 0 0 0 -15.50198 0.9999996 1 1 1 0 G 3 3 47 140691249 140691249 C G 1 0 0 0 0 1 0 0 0 6845 884 31 4 4 HARS 5 140691249 Missense_Mutation SNP C C3N-00433_T 7868154 140691249 40847010 49 14083 PCDHA2 0 . GRCh38 5 140795944 140795944 + Missense_Mutation SNP C C G rs200424378 C3N-00433_T C3N-00433_N C C c.980C>G p.Thr327Ser p.T327S ENST00000526136 1/4 194 179 15 167 167 0 strelka-varscan-mutect PCDHA2,missense_variant,p.Thr327Ser,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Thr327Ser,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Thr327Ser,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; G ENST00000526136 Transcript missense_variant 980/5254 980/2847 327/948 T/S aCc/aGc rs200424378 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 tolerated_low_confidence(0.53) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs200424378 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 140795944 140795944 C G 1 0 0 0 0 1 0 0 0 11611 507 18 4 4 PCDHA2 5 140795944 Missense_Mutation SNP C C3N-00433_T 104695 140795944 40742315 50 14084 PCDHB5 0 . GRCh38 5 141137645 141137645 + Missense_Mutation SNP C C A rs200613472 C3N-00433_T C3N-00433_N C C c.2211C>A p.Asp737Glu p.D737E ENST00000231134 1/1 471 447 24 243 243 0 varscan-mutect PCDHB5,missense_variant,p.Asp737Glu,ENST00000231134,NM_015669.4;PCDHB5,downstream_gene_variant,,ENST00000623915,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; A ENST00000231134 Transcript missense_variant 2428/3408 2211/2388 737/795 D/E gaC/gaA rs200613472,COSM5344849 1 1 PCDHB5 HGNC HGNC:8690 protein_coding YES CCDS4247.1 ENSP00000231134 Q9Y5E4 UPI0000169DEA NM_015669.4 deleterious_low_confidence(0.02) 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90 0,1 MODERATE 1 SNV 0,1 1 PASS rs200613472 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 141137645 141137645 C A 1 0 0 0 0 1 0 0 0 11632 535 19 1 1 PCDHB5 5 141137645 Missense_Mutation SNP C C3N-00433_T 341701 141137645 40400614 51 14085 SLC26A2 0 . GRCh38 5 149981018 149981018 + Silent SNP C C T novel C3N-00433_T C3N-00433_N C C c.1425C>T p.= p.F475F ENST00000286298 3/3 178 166 12 229 229 0 strelka-varscan-mutect SLC26A2,synonymous_variant,p.=,ENST00000286298,NM_000112.3;SLC26A2,intron_variant,,ENST00000503336,;SLC26A2,downstream_gene_variant,,ENST00000433184,; T ENST00000286298 Transcript synonymous_variant 1693/8080 1425/2220 475/739 F ttC/ttT 1 1 SLC26A2 HGNC HGNC:10994 protein_coding YES CCDS4300.1 ENSP00000286298 P50443 UPI000013DE3D NM_000112.3 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF16,Pfam_domain:PF00916,TIGRFAM_domain:TIGR00815 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 149981018 149981018 C T 1 0 0 0 0 0 0 0 1 14787 912 32 3 3 SLC26A2 5 149981018 Silent SNP C C3N-00433_T 8843373 149981018 31557241 52 14086 GABRG2 0 . GRCh38 5 162153197 162153197 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.1377C>A p.= p.G459G ENST00000414552 11/11 489 460 29 417 416 1 strelka-varscan-mutect GABRG2,synonymous_variant,p.=,ENST00000356592,NM_198904.2;GABRG2,synonymous_variant,p.=,ENST00000414552,NM_198903.2;GABRG2,synonymous_variant,p.=,ENST00000361925,NM_000816.3;GABRG2,downstream_gene_variant,,ENST00000522053,;GABRG2,3_prime_UTR_variant,,ENST00000522990,;GABRG2,3_prime_UTR_variant,,ENST00000523372,; A ENST00000414552 Transcript synonymous_variant 1602/3927 1377/1548 459/515 G ggC/ggA 1 1 GABRG2 HGNC HGNC:4087 protein_coding YES CCDS47333.1 ENSP00000410732 P18507 UPI00017503BD NM_198903.2 11/11 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF498,Superfamily_domains:SSF90112,Prints_domain:PR01620 LOW 1 SNV 1 1 PASS rs1414655532 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 162153197 162153197 C A 1 0 0 0 0 0 0 0 1 6043 697 25 2 2 GABRG2 5 162153197 Silent SNP C C3N-00433_T 12172179 162153197 19385062 53 14087 SLIT3 0 . GRCh38 5 168685821 168685821 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.3442C>A p.Pro1148Thr p.P1148T ENST00000332966 31/36 224 212 12 102 102 0 strelka-varscan-mutect SLIT3,missense_variant,p.Pro1141Thr,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Pro1011Thr,ENST00000404867,;SLIT3,missense_variant,p.Pro1148Thr,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000518092,; T ENST00000332966 Transcript missense_variant 3515/4895 3442/4593 1148/1530 P/T Ccc/Acc 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 tolerated(0.05) 31/36 PROSITE_profiles:PS50026,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,Pfam_domain:PF00008,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 200 6 3 0 0 0 0 -14.26829 0.9964886 1 1 1 0 T 3 4 47 168685821 168685821 G T 1 0 0 0 0 1 0 0 0 15032 1203 42 2 2 SLIT3 5 168685821 Missense_Mutation SNP G C3N-00433_T 6532624 168685821 12852438 54 14088 CPEB4 0 . GRCh38 5 173956111 173956111 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.2164C>T p.Arg722Trp p.R722W ENST00000265085 10/10 341 323 18 168 168 0 strelka-varscan-mutect CPEB4,missense_variant,p.Arg722Trp,ENST00000265085,NM_030627.2;CPEB4,missense_variant,p.Arg705Trp,ENST00000334035,NM_001308189.1;CPEB4,missense_variant,p.Arg697Trp,ENST00000520867,NM_001308191.1;CPEB4,missense_variant,p.Arg332Trp,ENST00000522336,;CPEB4,missense_variant,p.Arg315Trp,ENST00000517880,;CPEB4,downstream_gene_variant,,ENST00000519835,;CPEB4,non_coding_transcript_exon_variant,,ENST00000519467,; T ENST00000265085 Transcript missense_variant 3618/9483 2164/2190 722/729 R/W Cgg/Tgg 1 1 CPEB4 HGNC HGNC:21747 protein_coding YES CCDS4390.1 ENSP00000265085 Q17RY0 UPI000020C179 NM_030627.2 deleterious(0) 10/10 hmmpanther:PTHR12566:SF2,hmmpanther:PTHR12566 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 173956111 173956111 C T 1 0 0 0 0 1 0 0 0 3597 875 31 1 1 CPEB4 5 173956111 Missense_Mutation SNP C C3N-00433_T 5270290 173956111 7582148 55 14089 RPP40 0 . GRCh38 6 4996022 4996022 + Silent SNP T T G novel C3N-00433_T C3N-00433_N T T c.822A>C p.= p.A274A ENST00000380051 7/8 217 204 13 224 223 1 strelka-varscan-mutect RPP40,synonymous_variant,p.=,ENST00000380051,NM_006638.3;RPP40,synonymous_variant,p.=,ENST00000319533,NM_001286132.1;RPP40,synonymous_variant,p.=,ENST00000618533,NM_001286133.1;RPP40,synonymous_variant,p.=,ENST00000464646,;RPP40,downstream_gene_variant,,ENST00000468105,;RPP40,downstream_gene_variant,,ENST00000479782,; G ENST00000380051 Transcript synonymous_variant 867/1483 822/1092 274/363 A gcA/gcC 1 -1 RPP40 HGNC HGNC:20992 protein_coding YES CCDS34333.1 ENSP00000369391 O75818 UPI000020E473 NM_006638.3 7/8 Pfam_domain:PF08584,hmmpanther:PTHR15396,hmmpanther:PTHR15396:SF1 LOW 1 SNV 5 1 PASS rs780553257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 47 4996022 4996022 T G 1 0 0 0 0 0 0 0 1 13868 1799 63 5 5 RPP40 6 4996022 Silent SNP T C3N-00433_T 4996022 165809957 56 14090 NRN1 0 . GRCh38 6 5999090 5999090 + Silent SNP G G T novel C3N-00433_T C3N-00433_N G G c.393C>A p.= p.G131G ENST00000622188 4/4 576 544 32 332 331 1 strelka-varscan-mutect NRN1,synonymous_variant,p.=,ENST00000622188,NM_001278711.1;NRN1,synonymous_variant,p.=,ENST00000244766,NM_016588.2;NRN1,synonymous_variant,p.=,ENST00000616243,NM_001278710.1;NRN1,non_coding_transcript_exon_variant,,ENST00000495850,; T ENST00000622188 Transcript synonymous_variant 707/1795 393/507 131/168 G ggC/ggA 1 -1 NRN1 HGNC HGNC:17972 protein_coding YES CCDS75393.1 ENSP00000480483 A0A087WWT2 UPI000020E485 NM_001278711.1 4/4 hmmpanther:PTHR15902,hmmpanther:PTHR15902:SF1,Pfam_domain:PF15056 LOW 1 SNV 2 1 PASS rs904570056 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 5999090 5999090 G T 1 0 0 0 0 0 0 0 1 10716 1306 46 2 2 NRN1 6 5999090 Silent SNP G C3N-00433_T 1003068 5999090 164806889 57 14091 RREB1 0 . GRCh38 6 7246988 7246988 + Missense_Mutation SNP G G A rs369802211 C3N-00433_T C3N-00433_N G G c.4538G>A p.Gly1513Asp p.G1513D ENST00000379938 12/13 222 209 13 114 114 0 strelka-varscan-mutect RREB1,missense_variant,p.Gly1513Asp,ENST00000379938,NM_001003699.3;RREB1,missense_variant,p.Gly1458Asp,ENST00000349384,NM_001003698.3;RREB1,missense_variant,p.Gly1458Asp,ENST00000379933,NM_001168344.1;RREB1,missense_variant,p.Gly526Asp,ENST00000611109,;RREB1,intron_variant,,ENST00000334984,NM_001003700.1; A ENST00000379938 Transcript missense_variant 5075/8778 4538/5229 1513/1742 G/D gGt/gAt rs369802211 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 tolerated(0.61) 12/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs369802211 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 7246988 7246988 G A 1 0 0 0 0 1 0 0 0 13933 1261 44 3 3 RREB1 6 7246988 Missense_Mutation SNP G C3N-00433_T 1247898 7246988 163558991 58 14092 OR2J3 0 . GRCh38 6 29112301 29112301 + Silent SNP C C T novel C3N-00433_T C3N-00433_N C C c.411C>T p.= p.V137V ENST00000377169 1/1 230 214 16 208 208 0 varscan-mutect OR2J3,synonymous_variant,p.=,ENST00000377169,NM_001005216.3; T ENST00000377169 Transcript synonymous_variant 411/936 411/936 137/311 V gtC/gtT 1 1 OR2J3 HGNC HGNC:8261 protein_coding YES CCDS43433.1 ENSP00000366374 O76001 A0A126GWT2 UPI000014073A NM_001005216.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF209,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 29112301 29112301 C T 1 0 0 0 0 0 0 0 1 11082 842 30 3 3 OR2J3 6 29112301 Silent SNP C C3N-00433_T 21865313 29112301 141693678 59 14093 TEAD3 0 . GRCh38 6 35475381 35475381 + Silent SNP C C T rs200643703 C3N-00433_T C3N-00433_N C C c.1149G>A p.= p.E383E ENST00000338863 12/13 257 233 24 130 130 0 strelka-varscan-mutect TEAD3,synonymous_variant,p.=,ENST00000338863,NM_003214.3;TEAD3,synonymous_variant,p.=,ENST00000402886,;RPL10A,downstream_gene_variant,,ENST00000322203,NM_007104.4;TEAD3,downstream_gene_variant,,ENST00000433586,;MIR7111,downstream_gene_variant,,ENST00000619751,;RPL10A,downstream_gene_variant,,ENST00000467020,;RPL10A,downstream_gene_variant,,ENST00000464112,;RPL10A,downstream_gene_variant,,ENST00000478340,;RPL10A,downstream_gene_variant,,ENST00000490335,; T ENST00000338863 Transcript synonymous_variant 1377/2983 1149/1308 383/435 E gaG/gaA rs200643703 1 -1 TEAD3 HGNC HGNC:11716 protein_coding YES CCDS47414.1 ENSP00000345772 Q99594 UPI000015C249 NM_003214.3 12/13 hmmpanther:PTHR11834:SF1,hmmpanther:PTHR11834,PIRSF_domain:PIRSF002603,PIRSF_domain:PIRSF500720 LOW 1 SNV 1 1 PASS rs200643703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 35475381 35475381 C T 1 0 0 0 0 0 0 0 1 16151 912 32 3 3 TEAD3 6 35475381 Silent SNP C C3N-00433_T 6363080 35475381 135330598 60 14094 KIF6 0 . GRCh38 6 39639647 39639647 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.362C>A p.Pro121Gln p.P121Q ENST00000287152 4/23 120 106 14 148 148 0 strelka-varscan-mutect KIF6,missense_variant,p.Pro121Gln,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,missense_variant,p.Pro13Gln,ENST00000458470,;KIF6,5_prime_UTR_variant,,ENST00000538893,;KIF6,downstream_gene_variant,,ENST00000482238,; T ENST00000287152 Transcript missense_variant 457/9082 362/2445 121/814 P/Q cCa/cAa 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 deleterious(0) 4/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 39639647 39639647 G T 1 0 0 0 0 1 0 0 0 8173 1348 47 2 2 KIF6 6 39639647 Missense_Mutation SNP G C3N-00433_T 4164266 39639647 131166332 61 14095 TTBK1 0 . GRCh38 6 43262925 43262925 + Nonsense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.1561G>T p.Glu521Ter p.E521* ENST00000259750 13/15 334 302 32 158 158 0 strelka-varscan-mutect TTBK1,stop_gained,p.Glu521Ter,ENST00000259750,NM_032538.1;TTBK1,stop_gained,p.Glu470Ter,ENST00000304139,; T ENST00000259750 Transcript stop_gained 1644/6932 1561/3966 521/1321 E/* Gag/Tag 1 1 TTBK1 HGNC HGNC:19140 protein_coding YES CCDS34455.1 ENSP00000259750 Q5TCY1 UPI000041512B NM_032538.1 13/15 hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF130 HIGH 1 SNV 1 1 PASS rs1452942761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 47 43262925 43262925 G T 1 0 0 0 0 0 1 0 0 17186 1175 41 2 2 TTBK1 6 43262925 Nonsense_Mutation SNP G C3N-00433_T 3623278 43262925 127543054 62 14096 CAPN11 0 . GRCh38 6 44177364 44177364 + Missense_Mutation SNP C C T rs201179894 C3N-00433_T C3N-00433_N C C c.1360C>T p.Arg454Trp p.R454W ENST00000398776 12/23 272 244 28 135 135 0 strelka-varscan-mutect CAPN11,missense_variant,p.Arg454Trp,ENST00000398776,NM_007058.3;CAPN11,non_coding_transcript_exon_variant,,ENST00000524554,;CAPN11,non_coding_transcript_exon_variant,,ENST00000533604,; T ENST00000398776 Transcript missense_variant 1398/2728 1360/2220 454/739 R/W Cgg/Tgg rs201179894 1 1 CAPN11 HGNC HGNC:1478 protein_coding YES CCDS47436.1 ENSP00000381758 Q9UMQ6 UPI00000383D5 NM_007058.3 deleterious(0.01) 12/23 Gene3D:2.60.120.380,Pfam_domain:PF01067,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF322,SMART_domains:SM00720,Superfamily_domains:SSF49758 MODERATE 1 SNV 1 1 PASS rs201179894 . 0 205 0 4 0 0 0 0 -20 0.9998211 1 1 1 0 T 3 4 47 44177364 44177364 C T 1 0 0 0 0 1 0 0 0 2316 759 27 1 1 CAPN11 6 44177364 Missense_Mutation SNP C C3N-00433_T 914439 44177364 126628615 63 14097 GJB7 0 . GRCh38 6 87284743 87284743 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.170A>T p.Gln57Leu p.Q57L ENST00000525899 3/3 196 185 11 164 164 0 strelka-varscan-mutect GJB7,missense_variant,p.Gln57Leu,ENST00000525899,NM_198568.2;GJB7,missense_variant,p.Gln57Leu,ENST00000369576,; A ENST00000525899 Transcript missense_variant 516/2281 170/672 57/223 Q/L cAg/cTg 1 -1 GJB7 HGNC HGNC:16690 protein_coding YES CCDS5008.1 ENSP00000435355 Q6PEY0 UPI000013E3A1 NM_198568.2 deleterious(0) 3/3 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF26,SMART_domains:SM00037 MODERATE 1 SNV 1 1 PASS rs1343805036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 87284743 87284743 T A 1 0 0 0 0 1 0 0 0 6290 1580 55 4 4 GJB7 6 87284743 Missense_Mutation SNP T C3N-00433_T 43107379 87284743 83521236 64 14098 METTL24 0 . GRCh38 6 110315343 110315343 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.556G>A p.Gly186Arg p.G186R ENST00000338882 3/5 143 135 8 147 147 0 strelka-varscan-mutect METTL24,missense_variant,p.Gly186Arg,ENST00000338882,NM_001123364.1; T ENST00000338882 Transcript missense_variant,splice_region_variant 556/1119 556/1101 186/366 G/R Ggg/Agg 1 -1 METTL24 HGNC HGNC:21566 protein_coding YES CCDS43489.1 ENSP00000344071 Q5JXM2 UPI0000470C21 NM_001123364.1 deleterious(0.05) 3/5 hmmpanther:PTHR32026,Pfam_domain:PF13383 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 110315343 110315343 C T 1 0 0 0 0 1 0 0 0 9450 695 24 3 3 METTL24 6 110315343 Missense_Mutation SNP C C3N-00433_T 23030600 110315343 60490636 65 14099 MEOX2 0 . GRCh38 7 15612388 15612388 + Silent SNP C C T C3N-00433_T C3N-00433_N C C c.914G>A p.= p.*305* ENST00000262041 3/3 178 166 12 159 159 0 strelka-varscan-mutect MEOX2,stop_retained_variant,p.=,ENST00000262041,NM_005924.4; T ENST00000262041 Transcript stop_retained_variant 1324/2500 914/915 305/304 * tGa/tAa COSM4562173 1 -1 MEOX2 HGNC HGNC:7014 protein_coding YES CCDS34605.1 ENSP00000262041 P50222 UPI000013D247 NM_005924.4 3/3 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 15612388 15612388 C T 1 0 0 0 0 0 0 0 1 9419 837 29 3 3 MEOX2 7 15612388 Silent SNP C C3N-00433_T 15612388 143733585 66 14100 SPDYE5 0 . GRCh38 7 75495312 75495312 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.317T>A p.Leu106Gln p.L106Q ENST00000625065 2/8 357 335 22 208 208 0 varscan-mutect SPDYE5,missense_variant,p.Leu66Gln,ENST00000624640,NM_001099435.2;SPDYE5,missense_variant,p.Leu106Gln,ENST00000625065,;SPDYE5,missense_variant,p.Leu106Gln,ENST00000455862,; A ENST00000625065 Transcript missense_variant 740/1700 317/1209 106/402 L/Q cTg/cAg 1 1 SPDYE5 HGNC HGNC:35464 protein_coding YES CCDS78241.1 ENSP00000485398 A0A096LPK5 UPI000387D8EA deleterious(0) 2/8 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF15 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 75495312 75495312 T A 1 0 0 0 0 1 0 0 0 15381 1580 55 4 4 SPDYE5 7 75495312 Missense_Mutation SNP T C3N-00433_T 59882924 75495312 83850661 67 14101 ABCB4 0 . GRCh38 7 87431566 87431566 + Splice_Site SNP C C A rs764331138 C3N-00433_T C3N-00433_N C C c.1732-1G>T p.X578_splice ENST00000265723 485 457 28 338 336 2 strelka-mutect ABCB4,splice_acceptor_variant,,ENST00000265723,NM_018849.2;ABCB4,splice_acceptor_variant,,ENST00000359206,NM_000443.3;ABCB4,splice_acceptor_variant,,ENST00000358400,NM_018850.2;ABCB4,splice_acceptor_variant,,ENST00000453593,;ABCB4,upstream_gene_variant,,ENST00000469770,; A ENST00000265723 Transcript splice_acceptor_variant -/4020 1732/3861 578/1286 rs764331138 1 -1 ABCB4 HGNC HGNC:45 protein_coding YES CCDS5606.1 ENSP00000265723 P21439 UPI000013D66B NM_018849.2 14/27 HIGH 1 SNV 1 1 PASS rs764331138 . 0 193 0 0 17 0 0 0 -4.4383 0 1 1 0 0 A 5 1 47 87431566 87431566 C A 1 0 0 0 0 0 0 1 0 47 695 24 2 2 ABCB4 7 87431566 Splice_Site SNP C C3N-00433_T 11936254 87431566 71914407 68 14102 TSPAN12 0 . GRCh38 7 120806653 120806653 + Nonsense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.508G>T p.Glu170Ter p.E170* ENST00000222747 7/8 227 211 16 236 236 0 strelka-varscan-mutect TSPAN12,stop_gained,p.Glu170Ter,ENST00000222747,NM_012338.3;TSPAN12,stop_gained,p.Glu170Ter,ENST00000415871,;TSPAN12,downstream_gene_variant,,ENST00000441017,;TSPAN12,3_prime_UTR_variant,,ENST00000450414,; A ENST00000222747 Transcript stop_gained 1116/2798 508/918 170/305 E/* Gaa/Taa 1 -1 TSPAN12 HGNC HGNC:21641 protein_coding YES CCDS5777.1 ENSP00000222747 O95859 A0A024R740 UPI00000389F8 NM_012338.3 7/8 Superfamily_domains:0037997,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF26 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 47 120806653 120806653 C A 1 0 0 0 0 0 1 0 0 17141 864 30 2 2 TSPAN12 7 120806653 Nonsense_Mutation SNP C C3N-00433_T 33375087 120806653 38539320 69 14103 WHSC1L1 0 . GRCh38 8 38288731 38288731 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.3257A>T p.Gln1086Leu p.Q1086L ENST00000317025 19/24 230 214 16 204 204 0 strelka-varscan-mutect WHSC1L1,missense_variant,p.Gln1086Leu,ENST00000317025,NM_023034.1;WHSC1L1,missense_variant,p.Gln1037Leu,ENST00000433384,;WHSC1L1,missense_variant,p.Gln1086Leu,ENST00000527502,;WHSC1L1,downstream_gene_variant,,ENST00000526050,; A ENST00000317025 Transcript missense_variant 3775/10776 3257/4314 1086/1437 Q/L cAg/cTg 1 -1 WHSC1L1 HGNC HGNC:12767 protein_coding YES CCDS43729.1 ENSP00000313983 Q9BZ95 UPI000006F297 NM_023034.1 deleterious(0.02) 19/24 hmmpanther:PTHR22884:SF371,hmmpanther:PTHR22884,Gene3D:2.170.270.10,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 38288731 38288731 T A 1 0 0 0 0 1 0 0 0 17921 1580 55 4 4 WHSC1L1 8 38288731 Missense_Mutation SNP T C3N-00433_T 38288731 106849905 70 14104 EYA1 0 . GRCh38 8 71199407 71199407 + Missense_Mutation SNP A A G novel C3N-00433_T C3N-00433_N A A c.1712T>C p.Phe571Ser p.F571S ENST00000340726 18/18 762 712 50 464 464 0 strelka-varscan-mutect EYA1,missense_variant,p.Phe571Ser,ENST00000340726,NM_000503.5;EYA1,missense_variant,p.Phe565Ser,ENST00000303824,NM_001288575.1,NM_001288574.1;EYA1,missense_variant,p.Phe571Ser,ENST00000388742,NM_172058.3;EYA1,missense_variant,p.Phe538Ser,ENST00000388740,NM_172060.3;EYA1,missense_variant,p.Phe537Ser,ENST00000388741,;EYA1,missense_variant,p.Phe570Ser,ENST00000388743,;EYA1,missense_variant,p.Phe536Ser,ENST00000419131,NM_172059.3;RP11-326E22.1,intron_variant,,ENST00000521685,;EYA1,3_prime_UTR_variant,,ENST00000465115,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,; G ENST00000340726 Transcript missense_variant 2352/4326 1712/1779 571/592 F/S tTc/tCc 1 -1 EYA1 HGNC HGNC:3519 protein_coding YES CCDS34906.1 ENSP00000342626 Q99502 A0A024R813 UPI000012A3B3 NM_000503.5 deleterious(0) 18/18 hmmpanther:PTHR10190,hmmpanther:PTHR10190:SF11,TIGRFAM_domain:TIGR01658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 71199407 71199407 A G 1 0 0 0 0 1 0 0 0 5196 246 9 5 5 EYA1 8 71199407 Missense_Mutation SNP A C3N-00433_T 32910676 71199407 73939229 71 14105 ZFHX4 0 . GRCh38 8 76854454 76854454 + Missense_Mutation SNP C C A C3N-00433_T C3N-00433_N C C c.7533C>A p.His2511Gln p.H2511Q ENST00000521891 10/11 372 349 23 275 275 0 strelka-varscan-mutect ZFHX4,missense_variant,p.His2511Gln,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.His2485Gln,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript missense_variant 7981/14019 7533/10851 2511/3616 H/Q caC/caA COSM5241300,COSM606360 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 PROSITE_patterns:PS00028,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs772117997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 76854454 76854454 C A 1 0 0 0 0 1 0 0 0 18213 506 18 2 2 ZFHX4 8 76854454 Missense_Mutation SNP C C3N-00433_T 5655047 76854454 68284182 72 14106 PUM3 0 . GRCh38 9 2811383 2811383 + Missense_Mutation SNP T T G rs776874507 C3N-00433_T C3N-00433_N T T c.1613A>C p.His538Pro p.H538P ENST00000397885 15/18 311 287 24 174 174 0 strelka-varscan-mutect PUM3,missense_variant,p.His538Pro,ENST00000397885,NM_014878.4;PUM3,upstream_gene_variant,,ENST00000382032,;PUM3,upstream_gene_variant,,ENST00000490444,; G ENST00000397885 Transcript missense_variant 1820/2321 1613/1947 538/648 H/P cAt/cCt rs776874507,COSM3906774 1 -1 PUM3 HGNC HGNC:29676 protein_coding YES CCDS6448.2 ENSP00000380982 Q15397 UPI000013D67E NM_014878.4 tolerated(0.23) 15/18 hmmpanther:PTHR13389,Pfam_domain:PF08144,Superfamily_domains:SSF48371 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776874507 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 2811383 2811383 T G 1 0 0 0 0 1 0 0 0 12984 1464 51 5 5 PUM3 9 2811383 Missense_Mutation SNP T C3N-00433_T 2811383 135583334 73 14107 CCDC171 0 . GRCh38 9 15777628 15777628 + Missense_Mutation SNP A A T novel C3N-00433_T C3N-00433_N A A c.2700A>T p.Leu900Phe p.L900F ENST00000380701 19/26 86 79 7 94 93 1 strelka-varscan-mutect CCDC171,missense_variant,p.Leu900Phe,ENST00000380701,NM_173550.2;CCDC171,missense_variant,p.Leu140Phe,ENST00000449575,;CCDC171,upstream_gene_variant,,ENST00000432954,;RNU6-14P,upstream_gene_variant,,ENST00000384630,; T ENST00000380701 Transcript missense_variant 3028/6512 2700/3981 900/1326 L/F ttA/ttT 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 tolerated(0.07) 19/26 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 15777628 15777628 A T 1 0 0 0 0 1 0 0 0 2488 388 14 4 4 CCDC171 9 15777628 Missense_Mutation SNP A C3N-00433_T 12966245 15777628 122617089 74 14108 ZCCHC6 0 . GRCh38 9 86323227 86323227 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.2523G>A p.Met841Ile p.M841I ENST00000375963 13/27 172 160 12 164 163 1 strelka-varscan-mutect ZCCHC6,missense_variant,p.Met130Ile,ENST00000277141,;ZCCHC6,missense_variant,p.Met841Ile,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,missense_variant,p.Met718Ile,ENST00000375960,NM_001185074.1;ZCCHC6,upstream_gene_variant,,ENST00000375957,;ZCCHC6,downstream_gene_variant,,ENST00000469004,; T ENST00000375963 Transcript missense_variant 2696/5379 2523/4488 841/1495 M/I atG/atA 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 tolerated(1) 13/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 86323227 86323227 C T 1 0 0 0 0 1 0 0 0 18167 826 29 3 3 ZCCHC6 9 86323227 Missense_Mutation SNP C C3N-00433_T 70545599 86323227 52071490 75 14109 INVS 0 . GRCh38 9 100284509 100284509 + Silent SNP C C T novel C3N-00433_T C3N-00433_N C C c.1974C>T p.= p.S658S ENST00000262457 13/17 793 745 48 466 466 0 strelka-varscan-mutect INVS,synonymous_variant,p.=,ENST00000262457,NM_014425.3;INVS,synonymous_variant,p.=,ENST00000262456,NM_183245.2; T ENST00000262457 Transcript synonymous_variant 2159/3709 1974/3198 658/1065 S agC/agT 1 1 INVS HGNC HGNC:17870 protein_coding YES CCDS6746.1 ENSP00000262457 Q9Y283 A0A024R153 UPI000013D2BB NM_014425.3 13/17 hmmpanther:PTHR24178 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 100284509 100284509 C T 1 0 0 0 0 0 0 0 1 7690 709 25 3 3 INVS 9 100284509 Silent SNP C C3N-00433_T 13961282 100284509 38110208 76 14110 GRIN3A 0 . GRCh38 9 101737678 101737678 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.302C>A p.Thr101Asn p.T101N ENST00000361820 1/9 272 258 14 179 178 1 strelka-mutect GRIN3A,missense_variant,p.Thr101Asn,ENST00000361820,NM_133445.2; T ENST00000361820 Transcript missense_variant 903/7770 302/3348 101/1115 T/N aCc/aAc 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 tolerated_low_confidence(0.13) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 101737678 101737678 G T 1 0 0 0 0 1 0 0 0 6665 1261 44 2 2 GRIN3A 9 101737678 Missense_Mutation SNP G C3N-00433_T 1453169 101737678 36657039 77 14111 COL5A1 0 . GRCh38 9 134835180 134835180 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.5346C>A p.= p.I1782I ENST00000371817 65/66 413 390 23 213 213 0 strelka-varscan-mutect COL5A1,synonymous_variant,p.=,ENST00000371817,NM_000093.4;COL5A1,synonymous_variant,p.=,ENST00000618395,NM_001278074.1;COL5A1,synonymous_variant,p.=,ENST00000371820,;COL5A1,downstream_gene_variant,,ENST00000460264,;COL5A1,downstream_gene_variant,,ENST00000465877,; A ENST00000371817 Transcript synonymous_variant 5760/8471 5346/5517 1782/1838 I atC/atA 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 65/66 PD002078,Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF387,SMART_domains:SM00038 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 134835180 134835180 C A 1 0 0 0 0 0 0 0 1 3485 845 30 2 2 COL5A1 9 134835180 Silent SNP C C3N-00433_T 33097502 134835180 3559537 78 14112 SEC16A 0 . GRCh38 9 136475231 136475231 + Silent SNP G G A rs764084013 C3N-00433_T C3N-00433_N G G c.2385C>T p.= p.P795P ENST00000313050 1/30 236 223 13 132 132 0 strelka-varscan-mutect SEC16A,synonymous_variant,p.=,ENST00000290037,NM_001276418.1;SEC16A,synonymous_variant,p.=,ENST00000313050,NM_014866.1;SEC16A,synonymous_variant,p.=,ENST00000371706,;SEC16A,synonymous_variant,p.=,ENST00000431893,; A ENST00000313050 Transcript synonymous_variant 2459/8806 2385/7074 795/2357 P ccC/ccT rs764084013 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 1/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 LOW 1 SNV 1 1 PASS rs764084013 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 136475231 136475231 G A 1 0 0 0 0 0 0 0 1 14263 1335 47 3 3 SEC16A 9 136475231 Silent SNP G C3N-00433_T 1640051 136475231 1919486 79 14113 LARP4B 0 . GRCh38 10 812962 812962 + Silent SNP G G A novel C3N-00433_T C3N-00433_N G G c.2181C>T p.= p.S727S ENST00000612396 18/18 94 88 6 44 44 0 strelka-mutect LARP4B,synonymous_variant,p.=,ENST00000612396,NM_015155.2;LARP4B,synonymous_variant,p.=,ENST00000316157,;LARP4B,synonymous_variant,p.=,ENST00000614908,;LARP4B,synonymous_variant,p.=,ENST00000448368,;LARP4B,downstream_gene_variant,,ENST00000440895,;LARP4B,downstream_gene_variant,,ENST00000469487,;LARP4B,non_coding_transcript_exon_variant,,ENST00000609318,;LARP4B,downstream_gene_variant,,ENST00000608970,; A ENST00000612396 Transcript synonymous_variant 2498/8546 2181/2217 727/738 S agC/agT 1 -1 LARP4B HGNC HGNC:28987 protein_coding YES CCDS31131.1 ENSP00000482767 Q92615 UPI00001F8C87 NM_015155.2 18/18 LOW 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -12.4092 0.9999883 1 1 1 0 A 2 1 47 812962 812962 G A 1 0 0 0 0 0 0 0 1 8542 1194 42 3 3 LARP4B 10 812962 Silent SNP G C3N-00433_T 812962 132984460 80 14114 KCNQ1 0 . GRCh38 11 2585253 2585253 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.1074G>T p.Lys358Asn p.K358N ENST00000155840 8/16 614 577 37 316 316 0 strelka-varscan-mutect KCNQ1,missense_variant,p.Lys358Asn,ENST00000155840,NM_000218.2;KCNQ1,missense_variant,p.Lys231Asn,ENST00000335475,NM_181798.1; T ENST00000155840 Transcript missense_variant 1182/3245 1074/2031 358/676 K/N aaG/aaT 1 1 KCNQ1 HGNC HGNC:6294 protein_coding YES CCDS7736.1 ENSP00000155840 P51787 UPI000004662D NM_000218.2 deleterious(0) 8/16 Gene3D:1.10.287.70,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF151 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 2585253 2585253 G T 1 0 0 0 0 1 0 0 0 7998 962 34 2 2 KCNQ1 11 2585253 Missense_Mutation SNP G C3N-00433_T 2585253 132501369 81 14115 MRGPRE 0 . GRCh38 11 3228151 3228151 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.649G>A p.Gly217Arg p.G217R ENST00000389832 2/2 202 185 17 96 96 0 strelka-varscan-mutect MRGPRE,missense_variant,p.Gly217Arg,ENST00000389832,NM_001039165.2;AC109309.4,intron_variant,,ENST00000418995,; T ENST00000389832 Transcript missense_variant 956/1409 649/939 217/312 G/R Ggg/Agg 1 -1 MRGPRE HGNC HGNC:30694 protein_coding YES CCDS41603.2 ENSP00000374482 Q86SM8 W4VSQ4 UPI000015F138 NM_001039165.2 tolerated(0.44) 2/2 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF26,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR02111,Prints_domain:PR02108 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 3228151 3228151 C T 1 0 0 0 0 1 0 0 0 9730 594 21 3 3 MRGPRE 11 3228151 Missense_Mutation SNP C C3N-00433_T 642898 3228151 131858471 82 14116 OR51A4 0 . GRCh38 11 4946767 4946767 + Missense_Mutation SNP G G T rs757621278 C3N-00433_T C3N-00433_N G G c.334C>A p.Leu112Met p.L112M ENST00000380373 1/1 160 150 10 173 173 0 varscan-mutect OR51A4,missense_variant,p.Leu112Met,ENST00000380373,NM_001005329.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000380373 Transcript missense_variant 334/942 334/942 112/313 L/M Ctg/Atg rs757621278 1 -1 OR51A4 HGNC HGNC:14795 protein_coding YES CCDS31367.1 ENSP00000369731 Q8NGJ6 UPI0000047195 NM_001005329.1 tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF168,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS rs757621278 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 4946767 4946767 G T 1 0 0 0 0 1 0 0 0 11162 1020 36 2 2 OR51A4 11 4946767 Missense_Mutation SNP G C3N-00433_T 1718616 4946767 130139855 83 14117 IPO7 0 . GRCh38 11 9424955 9424955 + Missense_Mutation SNP A A G novel C3N-00433_T C3N-00433_N A A c.1183A>G p.Thr395Ala p.T395A ENST00000379719 11/25 90 84 6 120 120 0 varscan-mutect IPO7,missense_variant,p.Thr395Ala,ENST00000379719,NM_006391.2;SNORA23,upstream_gene_variant,,ENST00000365128,;IPO7,non_coding_transcript_exon_variant,,ENST00000530037,;IPO7,downstream_gene_variant,,ENST00000531235,; G ENST00000379719 Transcript missense_variant 1325/6191 1183/3117 395/1038 T/A Aca/Gca 1 1 IPO7 HGNC HGNC:9852 protein_coding YES CCDS31425.1 ENSP00000369042 O95373 UPI0000072C06 NM_006391.2 tolerated(0.13) 11/25 hmmpanther:PTHR10997:SF27,hmmpanther:PTHR10997,Pfam_domain:PF08506,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 9424955 9424955 A G 1 0 0 0 0 1 0 0 0 7700 275 10 5 5 IPO7 11 9424955 Missense_Mutation SNP A C3N-00433_T 4478188 9424955 125661667 84 14118 OTOG 0 . GRCh38 11 17645833 17645833 + Nonsense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.8667C>A p.Cys2889Ter p.C2889* ENST00000399391 55/55 759 718 41 440 440 0 strelka-varscan-mutect OTOG,stop_gained,p.Cys2877Ter,ENST00000399397,NM_001292063.1;OTOG,stop_gained,p.Cys2889Ter,ENST00000399391,NM_001277269.1; A ENST00000399391 Transcript stop_gained 8667/8778 8667/8778 2889/2925 C/* tgC/tgA 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 55/55 PROSITE_profiles:PS01225,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,SMART_domains:SM00041 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 47 17645833 17645833 C A 1 0 0 0 0 0 1 0 0 11370 747 26 2 2 OTOG 11 17645833 Nonsense_Mutation SNP C C3N-00433_T 8220878 17645833 117440789 85 14119 OR8H2 0 . GRCh38 11 56105801 56105801 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.759C>A p.Ser253Arg p.S253R ENST00000313503 1/1 78 73 5 128 128 0 strelka-varscan-mutect OR8H2,missense_variant,p.Ser252Arg,ENST00000618136,;OR8H2,missense_variant,p.Ser253Arg,ENST00000313503,NM_001005200.1; A ENST00000313503 Transcript missense_variant 759/939 759/939 253/312 S/R agC/agA 1 1 OR8H2 HGNC HGNC:15308 protein_coding YES CCDS31518.1 ENSP00000323982 Q8N162 UPI0000041D0C NM_001005200.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 56105801 56105801 C A 1 0 0 0 0 1 0 0 0 11306 709 25 2 2 OR8H2 11 56105801 Missense_Mutation SNP C C3N-00433_T 38459968 56105801 78980821 86 14120 DPP3 0 . GRCh38 11 66493552 66493552 + Silent SNP C C T novel C3N-00433_T C3N-00433_N C C c.1308C>T p.= p.I436I ENST00000541961 12/18 221 203 18 109 109 0 strelka-mutect DPP3,synonymous_variant,p.=,ENST00000532677,;DPP3,synonymous_variant,p.=,ENST00000531863,;DPP3,synonymous_variant,p.=,ENST00000541961,NM_130443.3,NM_005700.4;DPP3,synonymous_variant,p.=,ENST00000530165,NM_001256670.1;DPP3,downstream_gene_variant,,ENST00000533725,;DPP3,non_coding_transcript_exon_variant,,ENST00000533799,;DPP3,downstream_gene_variant,,ENST00000525738,;DPP3,non_coding_transcript_exon_variant,,ENST00000526667,;DPP3,non_coding_transcript_exon_variant,,ENST00000526250,; T ENST00000541961 Transcript synonymous_variant 1364/2676 1308/2214 436/737 I atC/atT 1 1 DPP3 HGNC HGNC:3008 protein_coding YES CCDS8141.1 ENSP00000440502 Q9NY33 UPI000012983B NM_130443.3,NM_005700.4 12/18 Pfam_domain:PF03571,PIRSF_domain:PIRSF007828,hmmpanther:PTHR23422,hmmpanther:PTHR23422:SF11 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 66493552 66493552 C T 1 0 0 0 0 0 0 0 1 4543 845 30 3 3 DPP3 11 66493552 Silent SNP C C3N-00433_T 10387751 66493552 68593070 87 14121 FAT3 0 . GRCh38 11 92354598 92354598 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.2036C>A p.Pro679Gln p.P679Q ENST00000525166 1/27 156 145 11 190 189 1 strelka-varscan-mutect FAT3,missense_variant,p.Pro829Gln,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Pro679Gln,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; A ENST00000525166 Transcript missense_variant 2058/18699 2036/13320 679/4439 P/Q cCa/cAa 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205,Prints_domain:PR00205 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 92354598 92354598 C A 1 0 0 0 0 1 0 0 0 5551 594 21 2 2 FAT3 11 92354598 Missense_Mutation SNP C C3N-00433_T 25861046 92354598 42732024 88 14122 TRIM29 0 . GRCh38 11 120137633 120137633 + Silent SNP C C T rs772848985 C3N-00433_T C3N-00433_N C C c.399G>A p.= p.S133S ENST00000341846 1/9 559 531 28 368 368 0 strelka-varscan-mutect TRIM29,missense_variant,p.Gly83Arg,ENST00000627238,;TRIM29,synonymous_variant,p.=,ENST00000341846,NM_012101.3;TRIM29,downstream_gene_variant,,ENST00000532833,;TRIM29,downstream_gene_variant,,ENST00000529495,;TRIM29,downstream_gene_variant,,ENST00000529040,;TRIM29,downstream_gene_variant,,ENST00000529011,;TRIM29,missense_variant,p.Gly83Arg,ENST00000475051,; T ENST00000341846 Transcript synonymous_variant 821/3328 399/1767 133/588 S tcG/tcA rs772848985,COSM357945 1 -1 TRIM29 HGNC HGNC:17274 protein_coding YES CCDS8428.1 ENSP00000343129 Q14134 A0A024R3J1 UPI0000073FDE NM_012101.3 1/9 0,1 LOW 1 SNV 1 0,1 1 PASS rs772848985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 120137633 120137633 C T 1 0 0 0 0 0 0 0 1 16992 661 23 1 1 TRIM29 11 120137633 Silent SNP C C3N-00433_T 27783035 120137633 14948989 89 14123 TRIM29 0 . GRCh38 11 120138013 120138013 + Missense_Mutation SNP A A T novel C3N-00433_T C3N-00433_N A A c.19T>A p.Ser7Thr p.S7T ENST00000341846 1/9 94 88 6 59 59 0 strelka-mutect TRIM29,missense_variant,p.Ser7Thr,ENST00000341846,NM_012101.3;TRIM29,missense_variant,p.Ser7Thr,ENST00000532833,;TRIM29,missense_variant,p.Ser7Thr,ENST00000529495,;TRIM29,missense_variant,p.Ser7Thr,ENST00000529040,;TRIM29,missense_variant,p.Ser7Thr,ENST00000529011,;TRIM29,missense_variant,p.Ser7Thr,ENST00000627238,;TRIM29,missense_variant,p.Ser7Thr,ENST00000475051,; T ENST00000341846 Transcript missense_variant 441/3328 19/1767 7/588 S/T Tcc/Acc 1 -1 TRIM29 HGNC HGNC:17274 protein_coding YES CCDS8428.1 ENSP00000343129 Q14134 A0A024R3J1 UPI0000073FDE NM_012101.3 tolerated_low_confidence(0.56) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.71023 1 1 1 1 0 T 3 4 47 120138013 120138013 A T 1 0 0 0 0 1 0 0 0 16992 304 11 4 4 TRIM29 11 120138013 Missense_Mutation SNP A C3N-00433_T 380 120138013 14948609 90 14124 APOBEC1 0 . GRCh38 12 7649592 7649592 + Silent SNP G G T novel C3N-00433_T C3N-00433_N G G c.666C>A p.= p.I222I ENST00000229304 5/5 167 150 17 163 163 0 strelka-mutect APOBEC1,synonymous_variant,p.=,ENST00000229304,NM_001304566.1,NM_001644.4;APOBEC1,3_prime_UTR_variant,,ENST00000467171,NM_005889.3; T ENST00000229304 Transcript synonymous_variant 687/879 666/711 222/236 I atC/atA 1 -1 APOBEC1 HGNC HGNC:604 protein_coding YES CCDS8579.1 ENSP00000229304 P41238 UPI000013C8F4 NM_001304566.1,NM_001644.4 5/5 hmmpanther:PTHR13857:SF26,hmmpanther:PTHR13857 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 7649592 7649592 G T 1 0 0 0 0 0 0 0 1 908 1164 41 2 2 APOBEC1 12 7649592 Silent SNP G C3N-00433_T 7649592 125625717 91 14125 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-00433_T C3N-00433_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 284 253 31 246 246 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-00433_T 17595759 25245351 108029958 92 14126 OVOS2 0 . GRCh38 12 31149333 31149333 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.1026G>T p.= p.G342G ENST00000632817 9/34 53 48 5 56 56 0 varscan-mutect OVOS2,synonymous_variant,p.=,ENST00000398963,;OVOS2,synonymous_variant,p.=,ENST00000632817,; A ENST00000632817 Transcript synonymous_variant 1026/4299 1026/4299 342/1432 G ggG/ggT 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 9/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 LOW 1 SNV 5 1 PASS . . 1 204 3 2 0 0 0 0 -9.799667 0.9999827 1 1 1 0 A 2 1 47 31149333 31149333 C A 1 0 0 0 0 0 0 0 1 11399 842 30 2 2 OVOS2 12 31149333 Silent SNP C C3N-00433_T 5903982 31149333 102125976 93 14127 LARP4 0 . GRCh38 12 50429044 50429044 + Missense_Mutation SNP G G A rs747392424 C3N-00433_T C3N-00433_N G G c.276G>A p.Met92Ile p.M92I ENST00000398473 3/16 162 152 10 247 247 0 varscan-mutect LARP4,missense_variant,p.Met92Ile,ENST00000398473,NM_052879.4;LARP4,missense_variant,p.Met92Ile,ENST00000293618,NM_001170803.1,NM_001170808.1;LARP4,missense_variant,p.Met98Ile,ENST00000429001,;LARP4,missense_variant,p.Met92Ile,ENST00000347328,NM_199190.2;LARP4,missense_variant,p.Met91Ile,ENST00000518444,NM_199188.2;LARP4,missense_variant,p.Met22Ile,ENST00000614335,;LARP4,missense_variant,p.Met22Ile,ENST00000518561,;LARP4,missense_variant,p.Met92Ile,ENST00000522085,NM_001170804.1;LARP4,missense_variant,p.Met22Ile,ENST00000615080,;LARP4,missense_variant,p.Met22Ile,ENST00000548993,;LARP4,missense_variant,p.Met22Ile,ENST00000552445,;LARP4,missense_variant,p.Met22Ile,ENST00000523389,;LARP4,missense_variant,p.Met22Ile,ENST00000548697,;LARP4,missense_variant,p.Met92Ile,ENST00000551886,;LARP4,missense_variant,p.Met100Ile,ENST00000548174,;LARP4,missense_variant,p.Met91Ile,ENST00000550260,;LARP4,missense_variant,p.Met22Ile,ENST00000550522,;LARP4,missense_variant,p.Met22Ile,ENST00000517559,; A ENST00000398473 Transcript missense_variant 388/6427 276/2175 92/724 M/I atG/atA rs747392424,COSM358699 1 1 LARP4 HGNC HGNC:24320 protein_coding YES CCDS41782.1 ENSP00000381490 Q71RC2 UPI00002293C3 NM_052879.4 tolerated(0.22) 3/16 hmmpanther:PTHR22792:SF48,hmmpanther:PTHR22792 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs747392424 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 50429044 50429044 G A 1 0 0 0 0 1 0 0 0 8541 1290 45 3 3 LARP4 12 50429044 Missense_Mutation SNP G C3N-00433_T 19279711 50429044 82846265 94 14128 NEDD1 0 . GRCh38 12 96951441 96951441 + Missense_Mutation SNP C C G novel C3N-00433_T C3N-00433_N C C c.1842C>G p.Cys614Trp p.C614W ENST00000557644 14/15 77 73 4 133 133 0 strelka-varscan-mutect NEDD1,missense_variant,p.Cys607Trp,ENST00000266742,NM_152905.3;NEDD1,missense_variant,p.Cys607Trp,ENST00000429527,NM_001135176.1;NEDD1,missense_variant,p.Cys518Trp,ENST00000457368,;NEDD1,missense_variant,p.Cys518Trp,ENST00000411739,NM_001135177.1;NEDD1,missense_variant,p.Cys614Trp,ENST00000557644,NM_001135175.1; G ENST00000557644 Transcript missense_variant 1988/2367 1842/2004 614/667 C/W tgC/tgG 1 1 NEDD1 HGNC HGNC:7723 protein_coding YES CCDS44955.1 ENSP00000451211 Q8NHV4 UPI000004D249 NM_001135175.1 tolerated(0.09) 14/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 96951441 96951441 C G 1 0 0 0 0 1 0 0 0 10337 747 26 4 4 NEDD1 12 96951441 Missense_Mutation SNP C C3N-00433_T 46522397 96951441 36323868 95 14129 DNAH10 0 . GRCh38 12 123933365 123933365 + Missense_Mutation SNP C C T rs758968876 C3N-00433_T C3N-00433_N C C c.12977C>T p.Ser4326Leu p.S4326L ENST00000638045 76/78 143 133 10 81 81 0 strelka-varscan-mutect DNAH10,missense_variant,p.Ser4387Leu,ENST00000409039,;DNAH10,missense_variant,p.Ser4326Leu,ENST00000638045,NM_207437.3;DNAH10OS,intron_variant,,ENST00000514254,;CCDC92,downstream_gene_variant,,ENST00000545135,;CCDC92,downstream_gene_variant,,ENST00000238156,NM_025140.2,NM_001304960.1,NM_001304959.1,NM_001304957.1,NM_001304958.1;CCDC92,downstream_gene_variant,,ENST00000545891,NM_001304961.1;CCDC92,downstream_gene_variant,,ENST00000539551,;CCDC92,downstream_gene_variant,,ENST00000539761,;CCDC92,downstream_gene_variant,,ENST00000535556,;CCDC92,intron_variant,,ENST00000544798,;CCDC92,intron_variant,,ENST00000542348,;DNAH10,3_prime_UTR_variant,,ENST00000538983,;DNAH10,non_coding_transcript_exon_variant,,ENST00000492261,;DNAH10,downstream_gene_variant,,ENST00000545078,; T ENST00000638045 Transcript missense_variant 13002/13678 12977/13416 4326/4471 S/L tCg/tTg rs758968876,COSM4463541,COSM4463542 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0) 76/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF03028 0,1,1 MODERATE SNV 0,1,1 1 PASS rs758968876 . 0 200 8 2 0 0 0 0 -13.96093 0.9987846 1 1 1 0 T 3 4 47 123933365 123933365 C T 1 0 0 0 0 1 0 0 0 4411 893 31 1 1 DNAH10 12 123933365 Missense_Mutation SNP C C3N-00433_T 26981924 123933365 9341944 96 14130 NOC4L 0 . GRCh38 12 132152198 132152198 + Splice_Site SNP G G T novel C3N-00433_T C3N-00433_N G G c.1431+1G>T p.X477_splice ENST00000330579 222 210 12 108 108 0 strelka-varscan-mutect NOC4L,splice_donor_variant,,ENST00000330579,NM_024078.2;NOC4L,downstream_gene_variant,,ENST00000541954,;NOC4L,downstream_gene_variant,,ENST00000535343,;NOC4L,splice_donor_variant,,ENST00000538784,; T ENST00000330579 Transcript splice_donor_variant -/1632 1431/1551 477/516 1 1 NOC4L HGNC HGNC:28461 protein_coding YES CCDS9277.1 ENSP00000328854 Q9BVI4 UPI00000723C4 NM_024078.2 14/14 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 47 132152198 132152198 G T 1 0 0 0 0 0 0 1 0 10557 1275 44 2 2 NOC4L 12 132152198 Splice_Site SNP G C3N-00433_T 8218833 132152198 1123111 97 14131 KCTD12 0 . GRCh38 13 76886067 76886067 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.82G>A p.Glu28Lys p.E28K ENST00000377474 1/1 270 253 17 127 127 0 strelka-varscan-mutect KCTD12,missense_variant,p.Glu28Lys,ENST00000377474,NM_138444.3;AC000403.4,upstream_gene_variant,,ENST00000613696,; T ENST00000377474 Transcript missense_variant 324/6225 82/978 28/325 E/K Gag/Aag 1 -1 KCTD12 HGNC HGNC:14678 protein_coding YES CCDS9455.1 ENSP00000366694 Q96CX2 A0A140VJM4 UPI0000073DDF NM_138444.3 tolerated(0.32) 1/1 hmmpanther:PTHR14499:SF29,hmmpanther:PTHR14499 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 76886067 76886067 C T 1 0 0 0 0 1 0 0 0 8016 864 30 3 3 KCTD12 13 76886067 Missense_Mutation SNP C C3N-00433_T 76886067 37478261 98 14132 NALCN 0 . GRCh38 13 101258476 101258476 + Silent SNP G G A novel C3N-00433_T C3N-00433_N G G c.1233C>T p.= p.F411F ENST00000251127 11/44 284 261 23 131 131 0 strelka-varscan-mutect NALCN,synonymous_variant,p.=,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; A ENST00000251127 Transcript synonymous_variant 1315/6818 1233/5217 411/1738 F ttC/ttT 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 11/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 101258476 101258476 G A 1 0 0 0 0 0 0 0 1 10155 1281 45 3 3 NALCN 13 101258476 Silent SNP G C3N-00433_T 24372409 101258476 13105852 99 14133 CCDC168 0 . GRCh38 13 102734356 102734356 + Silent SNP T T C novel C3N-00433_T C3N-00433_N T T c.16341A>G p.= p.A5447A ENST00000322527 4/4 189 178 11 225 225 0 strelka-varscan-mutect CCDC168,synonymous_variant,p.=,ENST00000322527,NM_001146197.1; C ENST00000322527 Transcript synonymous_variant 16479/21466 16341/21246 5447/7081 A gcA/gcG 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 Pfam_domain:PF15804,hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 47 102734356 102734356 T C 1 0 0 0 0 0 0 0 1 2484 1567 55 5 5 CCDC168 13 102734356 Silent SNP T C3N-00433_T 1475880 102734356 11629972 100 14134 UPF3A 0 . GRCh38 13 114301914 114301914 + Silent SNP G G T rs749538453 C3N-00433_T C3N-00433_N G G c.1191G>T p.= p.G397G ENST00000375299 9/10 197 181 16 113 113 0 varscan-mutect UPF3A,synonymous_variant,p.=,ENST00000375299,NM_023011.3;UPF3A,synonymous_variant,p.=,ENST00000351487,NM_080687.2;UPF3A,non_coding_transcript_exon_variant,,ENST00000475218,;UPF3A,intron_variant,,ENST00000480362,;UPF3A,downstream_gene_variant,,ENST00000493727,;UPF3A,downstream_gene_variant,,ENST00000474056,;CLCP2,upstream_gene_variant,,ENST00000392050,; T ENST00000375299 Transcript synonymous_variant 1247/2387 1191/1431 397/476 G ggG/ggT rs749538453 1 1 UPF3A HGNC HGNC:20332 protein_coding YES CCDS9543.1 ENSP00000364448 Q9H1J1 UPI0000072FCB NM_023011.3 9/10 hmmpanther:PTHR13112,hmmpanther:PTHR13112:SF2 LOW 1 SNV 1 1 PASS rs749538453 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 114301914 114301914 G T 1 0 0 0 0 0 0 0 1 17531 1161 41 2 2 UPF3A 13 114301914 Silent SNP G C3N-00433_T 11567558 114301914 62414 101 14135 RALGAPA1 0 . GRCh38 14 35688607 35688607 + Silent SNP G G A novel C3N-00433_T C3N-00433_N G G c.3663C>T p.= p.S1221S ENST00000637992 17/41 100 93 7 77 77 0 strelka-varscan-mutect RALGAPA1,synonymous_variant,p.=,ENST00000637992,;RALGAPA1,intron_variant,,ENST00000307138,NM_194301.2;RALGAPA1,intron_variant,,ENST00000389698,NM_014990.1;RALGAPA1,intron_variant,,ENST00000382366,NM_001283043.1;RALGAPA1,intron_variant,,ENST00000553892,NM_001283044.1;RALGAPA1,intron_variant,,ENST00000554652,;RALGAPA1,intron_variant,,ENST00000556839,;RALGAPA1,downstream_gene_variant,,ENST00000553917,;RALGAPA1,upstream_gene_variant,,ENST00000557638,; A ENST00000637992 Transcript synonymous_variant 4042/8512 3663/7488 1221/2495 S tcC/tcT 1 -1 RALGAPA1 HGNC HGNC:17770 protein_coding ENSP00000490119 17/41 LOW SNV 1 PASS . . 0 206 3 0 0 0 0 0 -14.57544 1 1 1 1 0 A 2 1 47 35688607 35688607 G A 1 0 0 0 0 0 0 0 1 13172 1219 43 3 3 RALGAPA1 14 35688607 Silent SNP G C3N-00433_T 35688607 71355111 102 14136 NRDE2 0 . GRCh38 14 90331865 90331865 + Missense_Mutation SNP G G C rs749441372 C3N-00433_T C3N-00433_N G G c.40C>G p.Pro14Ala p.P14A ENST00000354366 1/14 355 331 24 158 156 2 strelka-varscan-mutect NRDE2,missense_variant,p.Pro14Ala,ENST00000354366,NM_017970.3;NRDE2,missense_variant,p.Pro14Ala,ENST00000628832,;NRDE2,non_coding_transcript_exon_variant,,ENST00000557106,;NRDE2,missense_variant,p.Pro14Ala,ENST00000553409,; C ENST00000354366 Transcript missense_variant 273/14208 40/3495 14/1164 P/A Ccc/Gcc rs749441372 1 -1 NRDE2 HGNC HGNC:20186 protein_coding YES CCDS9890.1 ENSP00000346335 Q9H7Z3 UPI00001FD9DB NM_017970.3 tolerated(0.27) 1/14 hmmpanther:PTHR13471 MODERATE 1 SNV 1 1 PASS rs749441372 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 90331865 90331865 G C 1 0 0 0 0 1 0 0 0 10702 1174 41 4 4 NRDE2 14 90331865 Missense_Mutation SNP G C3N-00433_T 54643258 90331865 16711853 103 14137 CYP46A1 0 . GRCh38 14 99700056 99700056 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.398G>T p.Arg133Leu p.R133L ENST00000261835 5/15 167 154 13 66 66 0 strelka-varscan-mutect CYP46A1,missense_variant,p.Arg133Leu,ENST00000261835,NM_006668.1;CYP46A1,missense_variant,p.Arg36Leu,ENST00000380228,;CYP46A1,3_prime_UTR_variant,,ENST00000554611,; T ENST00000261835 Transcript missense_variant 502/2181 398/1503 133/500 R/L cGc/cTc 1 1 CYP46A1 HGNC HGNC:2641 protein_coding YES CCDS9954.1 ENSP00000261835 Q9Y6A2 UPI00001281DC NM_006668.1 tolerated(0.42) 5/15 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24293,hmmpanther:PTHR24293:SF2,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99993 1 1 1 1 0 T 3 4 47 99700056 99700056 G T 1 0 0 0 0 1 0 0 0 3985 1087 38 1 1 CYP46A1 14 99700056 Missense_Mutation SNP G C3N-00433_T 9368191 99700056 7343662 104 14138 TECPR2 0 . GRCh38 14 102376922 102376922 + Missense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.201G>C p.Met67Ile p.M67I ENST00000359520 2/20 350 332 18 220 220 0 strelka-varscan-mutect TECPR2,missense_variant,p.Met67Ile,ENST00000359520,NM_014844.3;TECPR2,missense_variant,p.Met67Ile,ENST00000558678,NM_001172631.1;TECPR2,non_coding_transcript_exon_variant,,ENST00000561228,; C ENST00000359520 Transcript missense_variant 427/8686 201/4236 67/1411 M/I atG/atC 1 1 TECPR2 HGNC HGNC:19957 protein_coding YES CCDS32162.1 ENSP00000352510 O15040 UPI00001FDC38 NM_014844.3 tolerated(0.08) 2/20 Gene3D:2.130.10.10,hmmpanther:PTHR23287,hmmpanther:PTHR23287:SF16,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 102376922 102376922 G C 1 0 0 0 0 1 0 0 0 16155 1290 45 4 4 TECPR2 14 102376922 Missense_Mutation SNP G C3N-00433_T 2676866 102376922 4666796 105 14139 ADCY9 0 . GRCh38 16 3966189 3966189 + Missense_Mutation SNP C C G C3N-00433_T C3N-00433_N C C c.3648G>C p.Leu1216Phe p.L1216F ENST00000294016 11/11 536 505 31 340 340 0 strelka-varscan-mutect ADCY9,missense_variant,p.Leu1216Phe,ENST00000294016,NM_001116.3;ADCY9,intron_variant,,ENST00000576936,; G ENST00000294016 Transcript missense_variant 4187/7725 3648/4062 1216/1353 L/F ttG/ttC COSM417007,COSM5065602 1 -1 ADCY9 HGNC HGNC:240 protein_coding YES CCDS32382.1 ENSP00000294016 O60503 UPI000012887F NM_001116.3 deleterious(0) 11/11 Gene3D:3.30.70.1230,Pfam_domain:PF00211,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF319,SMART_domains:SM00044,Superfamily_domains:SSF55073 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1358144438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 3966189 3966189 C G 1 0 0 0 0 1 0 0 0 345 825 29 4 4 ADCY9 16 3966189 Missense_Mutation SNP C C3N-00433_T 3966189 86372156 106 14140 IGSF6 0 . GRCh38 16 21647307 21647307 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.253A>T p.Ser85Cys p.S85C ENST00000268389 2/6 340 310 30 185 185 0 strelka-varscan-mutect IGSF6,stop_gained,p.Lys85Ter,ENST00000569602,;IGSF6,missense_variant,p.Ser85Cys,ENST00000268389,NM_005849.3;METTL9,intron_variant,,ENST00000358154,NM_016025.4;METTL9,intron_variant,,ENST00000615720,;METTL9,intron_variant,,ENST00000396014,NM_001077180.2;METTL9,intron_variant,,ENST00000567404,NM_001288659.1,NM_001288660.1;METTL9,intron_variant,,ENST00000568826,;RNU6-196P,downstream_gene_variant,,ENST00000384315,;IGSF6,non_coding_transcript_exon_variant,,ENST00000565499,;METTL9,upstream_gene_variant,,ENST00000564733,; A ENST00000268389 Transcript missense_variant 315/2785 253/726 85/241 S/C Agt/Tgt 1 -1 IGSF6 HGNC HGNC:5953 protein_coding YES CCDS10599.1 ENSP00000268389 O95976 UPI000013D7B4 NM_005849.3 deleterious(0.01) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR15297,hmmpanther:PTHR15297:SF2,SMART_domains:SM00406,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 21647307 21647307 T A 1 0 0 0 0 1 0 0 0 7511 1609 56 4 4 IGSF6 16 21647307 Missense_Mutation SNP T C3N-00433_T 17681118 21647307 68691038 107 14141 USP31 0 . GRCh38 16 23068944 23068944 + Nonsense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.3161C>G p.Ser1054Ter p.S1054* ENST00000219689 16/16 186 175 11 122 122 0 strelka-varscan-mutect USP31,stop_gained,p.Ser1054Ter,ENST00000219689,NM_020718.3;USP31,stop_gained,p.Ser347Ter,ENST00000567975,;RP11-20G6.3,upstream_gene_variant,,ENST00000563129,; C ENST00000219689 Transcript stop_gained 3161/10699 3161/4059 1054/1352 S/* tCa/tGa 1 -1 USP31 HGNC HGNC:20060 protein_coding YES CCDS10607.1 ENSP00000219689 Q70CQ4 UPI0000366B06 NM_020718.3 16/16 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 47 23068944 23068944 G C 1 0 0 0 0 0 1 0 0 17604 1294 45 4 4 USP31 16 23068944 Nonsense_Mutation SNP G C3N-00433_T 1421637 23068944 67269401 108 14142 ITGAM 0 . GRCh38 16 31324729 31324729 + Missense_Mutation SNP G G T rs769503232 C3N-00433_T C3N-00433_N G G c.2239G>T p.Gly747Trp p.G747W ENST00000544665 18/30 49 45 4 41 41 0 strelka-mutect ITGAM,missense_variant,p.Gly747Trp,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Gly746Trp,ENST00000287497,NM_000632.3;ITGAM,downstream_gene_variant,,ENST00000567031,;ITGAM,non_coding_transcript_exon_variant,,ENST00000561838,;ITGAM,upstream_gene_variant,,ENST00000569746,;ITGAM,upstream_gene_variant,,ENST00000567178,; T ENST00000544665 Transcript missense_variant 2310/4718 2239/3462 747/1153 G/W Ggg/Tgg rs769503232,COSM5555979 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0.01) 18/30 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769503232 . 0 203 7 0 0 0 0 0 -10.16732 0.9999984 1 1 1 0 T 3 4 47 31324729 31324729 G T 1 0 0 0 0 1 0 0 0 7794 1116 39 1 1 ITGAM 16 31324729 Missense_Mutation SNP G C3N-00433_T 8255785 31324729 59013616 109 14143 DNAH9 0 . GRCh38 17 11705049 11705049 + Missense_Mutation SNP T T A novel C3N-00433_T C3N-00433_N T T c.5416T>A p.Trp1806Arg p.W1806R ENST00000262442 26/69 147 133 14 96 96 0 strelka-varscan-mutect DNAH9,missense_variant,p.Trp1806Arg,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Trp1806Arg,ENST00000454412,;DNAH9,non_coding_transcript_exon_variant,,ENST00000583192,; A ENST00000262442 Transcript missense_variant 5484/13750 5416/13461 1806/4486 W/R Tgg/Agg 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0) 26/69 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 11705049 11705049 T A 1 0 0 0 0 1 0 0 0 4423 1580 55 4 4 DNAH9 17 11705049 Missense_Mutation SNP T C3N-00433_T 11705049 71552392 110 14144 CRHR1 0 . GRCh38 17 45830137 45830137 + Missense_Mutation SNP T T G novel C3N-00433_T C3N-00433_N T T c.565T>G p.Ser189Ala p.S189A ENST00000398285 7/14 404 383 21 215 215 0 strelka-varscan-mutect CRHR1,missense_variant,p.Ser189Ala,ENST00000293493,;CRHR1,missense_variant,p.Ser160Ala,ENST00000314537,NM_004382.4;CRHR1,missense_variant,p.Ser59Ala,ENST00000339069,NM_001303016.1,NM_001303020.1;CRHR1,missense_variant,p.Ser189Ala,ENST00000398285,NM_001145146.1;CRHR1,missense_variant,p.Leu91Arg,ENST00000619154,;CRHR1,missense_variant,p.Ser160Ala,ENST00000577353,NM_001145148.1;CRHR1,missense_variant,p.Ser120Ala,ENST00000352855,NM_001145147.1;CRHR1,5_prime_UTR_variant,,ENST00000634540,NM_001256299.2,NM_001303018.1;CRHR1,upstream_gene_variant,,ENST00000580876,;MAPT-AS1,intron_variant,,ENST00000634876,;CRHR1,missense_variant,p.Ser88Ala,ENST00000583888,;CRHR1,non_coding_transcript_exon_variant,,ENST00000582766,;CRHR1,intron_variant,,ENST00000347197,;CRHR1,upstream_gene_variant,,ENST00000535778,;CRHR1,upstream_gene_variant,,ENST00000581479,;CRHR1,downstream_gene_variant,,ENST00000580955,; G ENST00000398285 Transcript missense_variant 565/2399 565/1335 189/444 S/A Tcc/Gcc 1 1 CRHR1 HGNC HGNC:2357 protein_coding YES CCDS45712.1 ENSP00000381333 P34998 UPI0000128429 NM_001145146.1 tolerated(0.61) 7/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF175,hmmpanther:PTHR12011,Pfam_domain:PF00002,Prints_domain:PR00249 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 45830137 45830137 T G 1 0 0 0 0 1 0 0 0 3672 1551 54 5 5 CRHR1 17 45830137 Missense_Mutation SNP T C3N-00433_T 34125088 45830137 37427304 111 14145 DLX4 0 . GRCh38 17 49973042 49973042 + Missense_Mutation SNP G G T rs749783136 C3N-00433_T C3N-00433_N G G c.37G>T p.Ala13Ser p.A13S ENST00000611342 1/1 192 180 12 127 127 0 strelka-varscan-mutect DLX4,missense_variant,p.Ala13Ser,ENST00000611342,;DLX4,missense_variant,p.Ala13Ser,ENST00000411890,NM_001934.3;DLX4,intron_variant,,ENST00000240306,NM_138281.2;DLX4,intron_variant,,ENST00000503276,;DLX4,intron_variant,,ENST00000503410,;DLX4,downstream_gene_variant,,ENST00000505318,; T ENST00000611342 Transcript missense_variant 104/1662 37/345 13/114 A/S Gcc/Tcc rs749783136,COSM3783067 1 1 DLX4 HGNC HGNC:2917 protein_coding ENSP00000480366 Q92988 UPI000035079C tolerated_low_confidence(0.1) 1/1 0,1 MODERATE SNV 0,1 1 PASS rs749783136 . 0 200 10 0 0 0 0 0 -19.91341 0.9998968 1 1 1 0 T 3 4 47 49973042 49973042 G T 1 0 0 0 0 1 0 0 0 4380 1087 38 1 1 DLX4 17 49973042 Missense_Mutation SNP G C3N-00433_T 4142905 49973042 33284399 112 14146 MTMR4 0 . GRCh38 17 58504302 58504302 + Splice_Site SNP C C A novel C3N-00433_T C3N-00433_N C C c.1485+1G>T p.X495_splice ENST00000323456 107 101 6 80 80 0 strelka-varscan-mutect MTMR4,splice_donor_variant,,ENST00000323456,NM_004687.4;MTMR4,splice_donor_variant,,ENST00000579925,;MTMR4,downstream_gene_variant,,ENST00000583656,;MTMR4,downstream_gene_variant,,ENST00000580983,;MTMR4,downstream_gene_variant,,ENST00000582663,;MTMR4,downstream_gene_variant,,ENST00000583966,; A ENST00000323456 Transcript splice_donor_variant -/5839 1485/3588 495/1195 1 -1 MTMR4 HGNC HGNC:7452 protein_coding YES CCDS11608.1 ENSP00000325285 Q9NYA4 UPI00002010DE NM_004687.4 13/18 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -12.21628 1 1 1 1 0 A 5 1 47 58504302 58504302 C A 1 0 0 0 0 0 0 1 0 9933 521 18 2 2 MTMR4 17 58504302 Splice_Site SNP C C3N-00433_T 8531260 58504302 24753139 113 14147 EFCAB3 0 . GRCh38 17 62407044 62407044 + Silent SNP A A T novel C3N-00433_T C3N-00433_N A A c.855A>T p.= p.S285S ENST00000450662 10/12 49 44 5 69 69 0 strelka-varscan-mutect EFCAB3,synonymous_variant,p.=,ENST00000450662,NM_001144933.1;EFCAB3,synonymous_variant,p.=,ENST00000305286,NM_173503.3;EFCAB3,downstream_gene_variant,,ENST00000520404,;EFCAB3,non_coding_transcript_exon_variant,,ENST00000636041,; T ENST00000450662 Transcript synonymous_variant 926/1694 855/1473 285/490 S tcA/tcT 1 1 EFCAB3 HGNC HGNC:26379 protein_coding YES CCDS45751.1 ENSP00000403932 Q8N7B9 UPI0001929531 NM_001144933.1 10/12 hmmpanther:PTHR23050:SF158,hmmpanther:PTHR23050 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -12.5354 1 1 1 1 0 T 2 4 47 62407044 62407044 A T 1 0 0 0 0 0 0 0 1 4771 175 7 4 4 EFCAB3 17 62407044 Silent SNP A C3N-00433_T 3902742 62407044 20850397 114 14148 ABCA8 0 . GRCh38 17 68924716 68924716 + Missense_Mutation SNP C C A rs147273004 C3N-00433_T C3N-00433_N C C c.1427G>T p.Gly476Val p.G476V ENST00000586539 11/40 89 82 7 83 82 1 strelka-varscan-mutect ABCA8,missense_variant,p.Gly476Val,ENST00000430352,NM_001288986.1;ABCA8,missense_variant,p.Gly476Val,ENST00000269080,NM_007168.3;ABCA8,missense_variant,p.Gly476Val,ENST00000586539,NM_001288985.1;ABCA8,missense_variant,p.Gly107Val,ENST00000615593,;ABCA8,missense_variant,p.Gly124Val,ENST00000589533,;ABCA8,non_coding_transcript_exon_variant,,ENST00000541225,;ABCA8,upstream_gene_variant,,ENST00000587206,; A ENST00000586539 Transcript missense_variant 1616/5088 1427/4866 476/1621 G/V gGg/gTg rs147273004 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 deleterious(0) 11/40 Gene3D:3.40.50.300,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148 MODERATE 1 SNV 1 1 PASS rs147273004 . 0 196 14 0 0 0 0 0 -14.31836 0.9990391 1 1 1 0 A 3 1 47 68924716 68924716 C A 1 0 0 0 0 1 0 0 0 42 623 22 2 2 ABCA8 17 68924716 Missense_Mutation SNP C C3N-00433_T 6517672 68924716 14332725 115 14149 MGAT5B 0 . GRCh38 17 76906087 76906087 + Missense_Mutation SNP G G T rs776377170 C3N-00433_T C3N-00433_N G G c.958G>T p.Gly320Trp p.G320W ENST00000428789 7/16 232 218 14 112 112 0 strelka-mutect MGAT5B,missense_variant,p.Gly309Trp,ENST00000569840,NM_001199172.1;MGAT5B,missense_variant,p.Gly309Trp,ENST00000301618,NM_144677.2;MGAT5B,missense_variant,p.Gly320Trp,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,missense_variant,p.Gly320Trp,ENST00000565043,; T ENST00000428789 Transcript missense_variant 1061/4053 958/2406 320/801 G/W Ggg/Tgg rs776377170 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 deleterious(0) 7/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 MODERATE 1 SNV 1 1 PASS rs776377170 . 0 208 2 0 0 0 0 0 -19.99995 1 1 1 1 0 T 3 4 47 76906087 76906087 G T 1 0 0 0 0 1 0 0 0 9510 1116 39 1 1 MGAT5B 17 76906087 Missense_Mutation SNP G C3N-00433_T 7981371 76906087 6351354 116 14150 TK1 0 . GRCh38 17 78174942 78174942 + Silent SNP C C G novel C3N-00433_T C3N-00433_N C C c.522G>C p.= p.V174V ENST00000301634 7/7 156 142 14 103 103 0 strelka-mutect TK1,synonymous_variant,p.=,ENST00000588734,;TK1,synonymous_variant,p.=,ENST00000301634,NM_003258.4;TK1,synonymous_variant,p.=,ENST00000586613,;TK1,3_prime_UTR_variant,,ENST00000590430,;TK1,intron_variant,,ENST00000590862,;SYNGR2,downstream_gene_variant,,ENST00000225777,NM_004710.3;SYNGR2,downstream_gene_variant,,ENST00000590201,;SYNGR2,downstream_gene_variant,,ENST00000589168,;SYNGR2,downstream_gene_variant,,ENST00000589711,;SYNGR2,downstream_gene_variant,,ENST00000588282,;SYNGR2,downstream_gene_variant,,ENST00000585591,;SYNGR2,downstream_gene_variant,,ENST00000592456,;SYNGR2,downstream_gene_variant,,ENST00000591770,;SYNGR2,downstream_gene_variant,,ENST00000589183,;TK1,downstream_gene_variant,,ENST00000592126,; G ENST00000301634 Transcript synonymous_variant 761/1628 522/705 174/234 V gtG/gtC 1 -1 TK1 HGNC HGNC:11830 protein_coding YES CCDS11754.1 ENSP00000301634 P04183 UPI000012DE94 NM_003258.4 7/7 hmmpanther:PTHR11441,hmmpanther:PTHR11441:SF0,Pfam_domain:PF00265,Gene3D:3.30.60.20,Superfamily_domains:SSF57716 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 47 78174942 78174942 C G 1 0 0 0 0 0 0 0 1 16374 813 29 4 4 TK1 17 78174942 Silent SNP C C3N-00433_T 1268855 78174942 5082499 117 14151 CCDC40 0 . GRCh38 17 80048690 80048690 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.784G>T p.Val262Leu p.V262L ENST00000397545 5/20 744 706 38 462 462 0 strelka-mutect CCDC40,missense_variant,p.Val262Leu,ENST00000397545,NM_017950.3;CCDC40,missense_variant,p.Val262Leu,ENST00000374877,NM_001243342.1;CCDC40,missense_variant,p.Val262Leu,ENST00000374876,;CCDC40,missense_variant,p.Val262Leu,ENST00000269318,;CCDC40,missense_variant,p.Ser80Ile,ENST00000573474,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;CCDC40,downstream_gene_variant,,ENST00000576241,; T ENST00000397545 Transcript missense_variant 811/4294 784/3429 262/1142 V/L Gtg/Ttg 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 tolerated(0.75) 5/20 hmmpanther:PTHR16275,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1397490311 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 80048690 80048690 G T 1 0 0 0 0 1 0 0 0 2521 1029 36 2 2 CCDC40 17 80048690 Missense_Mutation SNP G C3N-00433_T 1873748 80048690 3208751 118 14152 CDH2 0 . GRCh38 18 27952249 27952249 + Silent SNP G G A novel C3N-00433_T C3N-00433_N G G c.2625C>T p.= p.S875S ENST00000269141 16/16 481 454 27 387 387 0 strelka-varscan-mutect CDH2,synonymous_variant,p.=,ENST00000269141,NM_001792.3;CDH2,synonymous_variant,p.=,ENST00000399380,NM_001308176.1;AC015933.2,upstream_gene_variant,,ENST00000423367,; A ENST00000269141 Transcript synonymous_variant 3049/4332 2625/2721 875/906 S tcC/tcT 1 -1 CDH2 HGNC HGNC:1759 protein_coding YES CCDS11891.1 ENSP00000269141 P19022 A0A024RC42 UPI000013D7FD NM_001792.3 16/16 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF79,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1464493037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 27952249 27952249 G A 1 0 0 0 0 0 0 0 1 2808 987 35 3 3 CDH2 18 27952249 Silent SNP G C3N-00433_T 27952249 52421036 119 14153 KLHL14 0 . GRCh38 18 32680324 32680324 + Frame_Shift_Del DEL C C - novel C3N-00433_T C3N-00433_N C C c.1433delG p.Gly478ValfsTer17 p.G478Vfs*17 ENST00000359358 7/9 90 85 5 80 80 0 varindel-pindel KLHL14,frameshift_variant,p.Gly478ValfsTer17,ENST00000359358,NM_020805.1; - ENST00000359358 Transcript frameshift_variant 1872/4312 1433/1887 478/628 G/X gGt/gt 1 -1 KLHL14 HGNC HGNC:29266 protein_coding YES CCDS32813.1 ENSP00000352314 Q9P2G3 UPI00001C1FF2 NM_020805.1 7/9 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60,SMART_domains:SM00612 HIGH 1 deletion 1 1 PASS . . 0 206 2 2 0 0 0 0 -8.429449 0.9999841 1 1 1 0 - 7 5 47 32680324 32680324 C - 1 0 1 0 1 0 0 0 0 8234 521 18 0 0 KLHL14 18 32680324 Frame_Shift_Del DEL C C3N-00433_T 4728075 32680324 47692961 120 14154 MVB12A 0 . GRCh38 19 17423507 17423507 + Silent SNP C C T C3N-00433_T C3N-00433_N C C c.423C>T p.= p.G141G ENST00000317040 5/9 152 143 9 67 67 0 strelka-varscan-mutect MVB12A,missense_variant,p.Ala99Val,ENST00000528515,;MVB12A,synonymous_variant,p.=,ENST00000317040,NM_138401.3;MVB12A,synonymous_variant,p.=,ENST00000543795,;MVB12A,synonymous_variant,p.=,ENST00000529939,;MVB12A,synonymous_variant,p.=,ENST00000528911,;MVB12A,synonymous_variant,p.=,ENST00000600514,;MVB12A,synonymous_variant,p.=,ENST00000594784,;MVB12A,synonymous_variant,p.=,ENST00000528604,;BISPR,downstream_gene_variant,,ENST00000634942,;BISPR,downstream_gene_variant,,ENST00000634291,;CTD-2521M24.6,upstream_gene_variant,,ENST00000593957,;CTD-2521M24.8,upstream_gene_variant,,ENST00000597028,;MVB12A,downstream_gene_variant,,ENST00000528659,;MVB12A,downstream_gene_variant,,ENST00000529490,;MVB12A,non_coding_transcript_exon_variant,,ENST00000524382,;MVB12A,downstream_gene_variant,,ENST00000526234,;MVB12A,downstream_gene_variant,,ENST00000528997,;MVB12A,downstream_gene_variant,,ENST00000528732,; T ENST00000317040 Transcript synonymous_variant 1478/2223 423/822 141/273 G ggC/ggT COSM1391463 1 1 MVB12A HGNC HGNC:25153 protein_coding YES CCDS12359.1 ENSP00000324810 Q96EY5 A0A024R7L6 UPI0000039EC7 NM_138401.3 5/9 PROSITE_profiles:PS51498,hmmpanther:PTHR31612,hmmpanther:PTHR31612:SF2,Pfam_domain:PF10240 1 LOW 1 SNV 1 1 1 PASS rs890683307 . 0 203 5 2 0 0 0 0 -12.2626 0.9997383 1 1 1 0 T 2 4 47 17423507 17423507 C T 1 0 0 0 0 0 0 0 1 9991 768 27 1 1 MVB12A 19 17423507 Silent SNP C C3N-00433_T 17423507 41194109 121 14155 ZNF536 0 . GRCh38 19 30444279 30444279 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.717C>A p.= p.T239T ENST00000355537 2/5 246 231 15 116 116 0 strelka-varscan-mutect ZNF536,synonymous_variant,p.=,ENST00000355537,NM_014717.1;ZNF536,synonymous_variant,p.=,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; A ENST00000355537 Transcript synonymous_variant 864/4945 717/3903 239/1300 T acC/acA 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 2/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 LOW 1 SNV 1 1 PASS rs1204289475 . 0 201 9 0 0 0 0 0 -19.99999 0.9999585 1 1 1 0 A 2 1 47 30444279 30444279 C A 1 0 0 0 0 0 0 0 1 18547 610 22 2 2 ZNF536 19 30444279 Silent SNP C C3N-00433_T 13020772 30444279 28173337 122 14156 TSHZ3 0 . GRCh38 19 31277408 31277408 + Frame_Shift_Del DEL C C - novel C3N-00433_T C3N-00433_N C C c.2385delG p.Lys796ArgfsTer27 p.K796Rfs*27 ENST00000240587 2/2 139 130 9 61 61 0 sindel-varindel-pindel TSHZ3,frameshift_variant,p.Lys796ArgfsTer27,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; - ENST00000240587 Transcript frameshift_variant 2713/5176 2385/3246 795/1081 G/X ggG/gg 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -17.01238 1 1 1 1 0 - 7 5 47 31277408 31277408 C - 1 0 1 0 1 0 0 0 0 17130 842 30 0 0 TSHZ3 19 31277408 Frame_Shift_Del DEL C C3N-00433_T 833129 31277408 27340208 123 14157 SLC7A9 0 . GRCh38 19 32862188 32862188 + Nonsense_Mutation SNP C C A rs764731878 C3N-00433_T C3N-00433_N C C c.634G>T p.Glu212Ter p.E212* ENST00000023064 6/13 464 414 50 251 251 0 strelka-varscan-mutect SLC7A9,stop_gained,p.Glu212Ter,ENST00000023064,NM_001243036.1,NM_001126335.1,NM_014270.4;SLC7A9,stop_gained,p.Glu212Ter,ENST00000590341,;SLC7A9,stop_gained,p.Glu212Ter,ENST00000587772,;RN7SKP22,downstream_gene_variant,,ENST00000365097,;SLC7A9,non_coding_transcript_exon_variant,,ENST00000589659,;SLC7A9,intron_variant,,ENST00000590465,;SLC7A9,intron_variant,,ENST00000592232,; A ENST00000023064 Transcript stop_gained 826/1761 634/1464 212/487 E/* Gag/Tag rs764731878 1 -1 SLC7A9 HGNC HGNC:11067 protein_coding YES CCDS12425.1 ENSP00000023064 P82251 UPI0000037773 NM_001243036.1,NM_001126335.1,NM_014270.4 6/13 hmmpanther:PTHR11785:SF354,hmmpanther:PTHR11785,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 HIGH 1 SNV 1 1 PASS rs764731878 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 47 32862188 32862188 C A 1 0 0 0 0 0 1 0 0 14988 893 31 1 1 SLC7A9 19 32862188 Nonsense_Mutation SNP C C3N-00433_T 1584780 32862188 25755428 124 14158 LIN37 0 . GRCh38 19 35754081 35754081 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.509G>T p.Gly170Val p.G170V ENST00000301159 7/9 443 384 59 214 213 1 strelka-varscan-mutect LIN37,missense_variant,p.Gly170Val,ENST00000301159,NM_019104.2;LIN37,missense_variant,p.Gly87Val,ENST00000591163,;PROSER3,upstream_gene_variant,,ENST00000396908,NM_001039887.2;HSPB6,downstream_gene_variant,,ENST00000592984,;HSPB6,downstream_gene_variant,,ENST00000004982,NM_144617.2;PROSER3,upstream_gene_variant,,ENST00000536950,;PROSER3,upstream_gene_variant,,ENST00000301165,;PROSER3,upstream_gene_variant,,ENST00000537459,;HSPB6,downstream_gene_variant,,ENST00000587965,;PROSER3,upstream_gene_variant,,ENST00000421853,;PROSER3,upstream_gene_variant,,ENST00000444637,;LIN37,downstream_gene_variant,,ENST00000587751,;AC002398.11,upstream_gene_variant,,ENST00000591091,;AC002398.12,upstream_gene_variant,,ENST00000587767,;PROSER3,upstream_gene_variant,,ENST00000544876,;LIN37,downstream_gene_variant,,ENST00000591076,;LIN37,3_prime_UTR_variant,,ENST00000595455,;AC002398.9,3_prime_UTR_variant,,ENST00000591613,;LIN37,non_coding_transcript_exon_variant,,ENST00000587108,;LIN37,non_coding_transcript_exon_variant,,ENST00000590890,;PROSER3,upstream_gene_variant,,ENST00000620918,;PROSER3,upstream_gene_variant,,ENST00000600988,;LIN37,downstream_gene_variant,,ENST00000590706,;LIN37,downstream_gene_variant,,ENST00000592871,; T ENST00000301159 Transcript missense_variant 873/1150 509/741 170/246 G/V gGg/gTg 1 1 LIN37 HGNC HGNC:33234 protein_coding YES CCDS62642.1 ENSP00000301159 Q96GY3 UPI0000072738 NM_019104.2 tolerated(0.51) 7/9 Low_complexity_(Seg):seg,hmmpanther:PTHR31336,Pfam_domain:PF15306 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 35754081 35754081 G T 1 0 0 0 0 1 0 0 0 8715 1232 43 2 2 LIN37 19 35754081 Missense_Mutation SNP G C3N-00433_T 2891893 35754081 22863535 125 14159 ZFP30 0 . GRCh38 19 37635394 37635394 + Missense_Mutation SNP C C G novel C3N-00433_T C3N-00433_N C C c.1147G>C p.Glu383Gln p.E383Q ENST00000351218 6/6 143 111 32 188 188 0 strelka-varscan-mutect ZFP30,missense_variant,p.Glu383Gln,ENST00000351218,NM_014898.2;ZFP30,missense_variant,p.Glu383Gln,ENST00000514101,NM_001320668.1,NM_001320670.1,NM_001320671.1,NM_001320667.1,NM_001320669.1;ZFP30,missense_variant,p.Glu383Gln,ENST00000392144,;ZFP30,intron_variant,,ENST00000589018,;ZFP30,downstream_gene_variant,,ENST00000587809,; G ENST00000351218 Transcript missense_variant 1705/6090 1147/1560 383/519 E/Q Gaa/Caa 1 -1 ZFP30 HGNC HGNC:29555 protein_coding YES CCDS33005.1 ENSP00000343581 Q9Y2G7 D3Y2A0 UPI0000139E7F NM_014898.2 deleterious(0.03) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF246,hmmpanther:PTHR24377,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 37635394 37635394 C G 1 0 0 0 0 1 0 0 0 18219 835 29 4 4 ZFP30 19 37635394 Missense_Mutation SNP C C3N-00433_T 1881313 37635394 20982222 126 14160 IRGQ 0 . GRCh38 19 43592785 43592785 + Silent SNP C C T C3N-00433_T C3N-00433_N C C c.1113G>A p.= p.E371E ENST00000422989 3/3 495 465 30 320 320 0 strelka-varscan-mutect IRGQ,synonymous_variant,p.=,ENST00000422989,NM_001007561.2;IRGQ,synonymous_variant,p.=,ENST00000602269,;L34079.2,intron_variant,,ENST00000594374,;SRRM5,upstream_gene_variant,,ENST00000607544,;ZNF576,upstream_gene_variant,,ENST00000336564,NM_001145347.1;ZNF576,upstream_gene_variant,,ENST00000525771,;ZNF576,upstream_gene_variant,,ENST00000391965,NM_024327.2;ZNF576,upstream_gene_variant,,ENST00000533118,;ZNF576,upstream_gene_variant,,ENST00000528387,;ZNF576,upstream_gene_variant,,ENST00000529930,;IRGQ,downstream_gene_variant,,ENST00000598324,;IRGQ,non_coding_transcript_exon_variant,,ENST00000601520,;IRGQ,upstream_gene_variant,,ENST00000596409,;ZNF576,upstream_gene_variant,,ENST00000595041,; T ENST00000422989 Transcript synonymous_variant 1269/9685 1113/1872 371/623 E gaG/gaA COSM1210913 1 -1 IRGQ HGNC HGNC:24868 protein_coding YES CCDS33040.1 ENSP00000387535 Q8WZA9 UPI000003FDB6 NM_001007561.2 3/3 PROSITE_profiles:PS51716,hmmpanther:PTHR19364,hmmpanther:PTHR19364:SF2 1 LOW SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 47 43592785 43592785 C T 1 0 0 0 0 0 0 0 1 7747 912 32 3 3 IRGQ 19 43592785 Silent SNP C C3N-00433_T 5957391 43592785 15024831 127 14161 FTL 0 . GRCh38 19 48966368 48966374 + Frame_Shift_Del DEL GATCTTC GATCTTC - novel C3N-00433_T C3N-00433_N GATCTTC GATCTTC c.337_343delGATCTTC p.Asp113MetfsTer21 p.D113Mfs*21 ENST00000331825 3/4 735 682 53 462 462 0 sindel-varindel-pindel FTL,frameshift_variant,p.Asp113MetfsTer21,ENST00000331825,NM_000146.3;GYS1,downstream_gene_variant,,ENST00000323798,NM_002103.4;GYS1,downstream_gene_variant,,ENST00000263276,NM_001161587.1;BAX,downstream_gene_variant,,ENST00000293288,NM_004324.3;BAX,downstream_gene_variant,,ENST00000345358,NM_001291428.1,NM_138761.3;BAX,downstream_gene_variant,,ENST00000391871,;BAX,downstream_gene_variant,,ENST00000415969,NM_138764.4;BAX,downstream_gene_variant,,ENST00000354470,NM_138763.3;GYS1,downstream_gene_variant,,ENST00000594220,;BAX,downstream_gene_variant,,ENST00000506183,;CTD-2639E6.9,downstream_gene_variant,,ENST00000599784,;CTD-2639E6.9,downstream_gene_variant,,ENST00000594305,;BAX,downstream_gene_variant,,ENST00000502487,;BAX,downstream_gene_variant,,ENST00000513545,;BAX,downstream_gene_variant,,ENST00000356483,;GYS1,downstream_gene_variant,,ENST00000472004,;GYS1,downstream_gene_variant,,ENST00000496048,; - ENST00000331825 Transcript frameshift_variant 544-550/878 337-343/528 113-115/175 DLH/X GATCTTCat/at 1 1 FTL HGNC HGNC:3999 protein_coding YES CCDS33070.1 ENSP00000366525 P02792 UPI0000161F61 NM_000146.3 3/4 Gene3D:1.20.1260.10,Pfam_domain:PF00210,PROSITE_profiles:PS50905,hmmpanther:PTHR11431,Superfamily_domains:SSF47240 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 47 48966368 48966368 GATCTTC - 1 0 1 0 1 0 0 0 0 5958 1174 41 0 0 FTL 19 48966368 Frame_Shift_Del DEL GATCTTC C3N-00433_T 5373583 48966368 9651248 128 14162 PRR12 0 . GRCh38 19 49596946 49596946 + Nonsense_Mutation SNP G G T rs753477453 C3N-00433_T C3N-00433_N G G c.2611G>T p.Glu871Ter p.E871* ENST00000418929 4/14 377 354 23 206 206 0 strelka-varscan-mutect PRR12,stop_gained,p.Glu871Ter,ENST00000418929,NM_020719.1;PRR12,stop_gained,p.Glu50Ter,ENST00000615927,; T ENST00000418929 Transcript stop_gained 2623/6955 2611/6111 871/2036 E/* Gag/Tag rs753477453 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1 HIGH 1 SNV 5 1 PASS rs753477453 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 47 49596946 49596946 G T 1 0 0 0 0 0 1 0 0 12719 1059 37 1 1 PRR12 19 49596946 Nonsense_Mutation SNP G C3N-00433_T 630578 49596946 9020670 129 14163 CCDC106 0 . GRCh38 19 55652698 55652698 + Silent SNP C C G novel C3N-00433_T C3N-00433_N C C c.795C>G p.= p.L265L ENST00000586790 5/5 240 219 21 152 152 0 strelka-varscan-mutect CCDC106,synonymous_variant,p.=,ENST00000586790,;CCDC106,synonymous_variant,p.=,ENST00000591578,;CCDC106,synonymous_variant,p.=,ENST00000308964,NM_013301.2;CCDC106,synonymous_variant,p.=,ENST00000588740,;CCDC106,synonymous_variant,p.=,ENST00000591241,;U2AF2,upstream_gene_variant,,ENST00000450554,NM_001012478.1;U2AF2,upstream_gene_variant,,ENST00000308924,NM_007279.2;CCDC106,downstream_gene_variant,,ENST00000592996,;CCDC106,downstream_gene_variant,,ENST00000587213,;CCDC106,downstream_gene_variant,,ENST00000593069,;U2AF2,upstream_gene_variant,,ENST00000587196,;CCDC106,downstream_gene_variant,,ENST00000586864,;U2AF2,upstream_gene_variant,,ENST00000588850,; G ENST00000586790 Transcript synonymous_variant 1699/2162 795/843 265/280 L ctC/ctG 1 1 CCDC106 HGNC HGNC:30181 protein_coding YES CCDS33118.1 ENSP00000465757 Q9BWC9 UPI0000072074 5/5 Pfam_domain:PF15794,hmmpanther:PTHR16477,hmmpanther:PTHR16477:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 47 55652698 55652698 C G 1 0 0 0 0 0 0 0 1 2438 813 29 4 4 CCDC106 19 55652698 Silent SNP C C3N-00433_T 6055752 55652698 2964918 130 14164 NLRP5 0 . GRCh38 19 56027564 56027564 + Missense_Mutation SNP G G A rs759531334 C3N-00433_T C3N-00433_N G G c.1331G>A p.Arg444His p.R444H ENST00000390649 7/15 479 451 28 347 347 0 strelka-varscan-mutect NLRP5,missense_variant,p.Arg444His,ENST00000390649,NM_153447.4;NLRP5,missense_variant,p.Arg444His,ENST00000621651,; A ENST00000390649 Transcript missense_variant 1331/3888 1331/3603 444/1200 R/H cGc/cAc rs759531334 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 tolerated(1) 7/15 hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs759531334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 56027564 56027564 G A 1 0 0 0 0 1 0 0 0 10518 1087 38 1 1 NLRP5 19 56027564 Missense_Mutation SNP G C3N-00433_T 374866 56027564 2590052 131 14165 ZNF530 0 . GRCh38 19 57606067 57606067 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.542C>T p.Ser181Leu p.S181L ENST00000332854 3/3 151 141 10 149 149 0 strelka-varscan-mutect ZNF530,missense_variant,p.Ser181Leu,ENST00000332854,NM_020880.3;ZNF530,intron_variant,,ENST00000597864,;ZNF530,downstream_gene_variant,,ENST00000597700,;ZNF530,missense_variant,p.Ser181Leu,ENST00000600619,;ZNF530,non_coding_transcript_exon_variant,,ENST00000598297,; T ENST00000332854 Transcript missense_variant 762/2962 542/1800 181/599 S/L tCa/tTa 1 1 ZNF530 HGNC HGNC:29297 protein_coding YES CCDS12955.1 ENSP00000332861 Q6P9A1 UPI0000199017 NM_020880.3 tolerated(0.66) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 57606067 57606067 C T 1 0 0 0 0 1 0 0 0 18544 838 29 3 3 ZNF530 19 57606067 Missense_Mutation SNP C C3N-00433_T 1578503 57606067 1011549 132 14166 NKX2-2 0 . GRCh38 20 21511934 21511934 + Missense_Mutation SNP A A G novel C3N-00433_T C3N-00433_N A A c.811T>C p.Trp271Arg p.W271R ENST00000377142 2/2 86 79 7 56 56 0 strelka-varscan-mutect NKX2-2,missense_variant,p.Trp271Arg,ENST00000377142,NM_002509.3;NKX2-2-AS1,intron_variant,,ENST00000549659,; G ENST00000377142 Transcript missense_variant 1168/2092 811/822 271/273 W/R Tgg/Cgg 1 -1 NKX2-2 HGNC HGNC:7835 protein_coding YES CCDS13145.1 ENSP00000366347 O95096 UPI00001301E6 NM_002509.3 deleterious(0) 2/2 hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF24 MODERATE 1 SNV 1 1 PASS rs1402311246 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 47 21511934 21511934 A G 1 0 0 0 0 1 0 0 0 10486 159 6 5 5 NKX2-2 20 21511934 Missense_Mutation SNP A C3N-00433_T 21511934 42932233 133 14167 XKR7 0 . GRCh38 20 31995255 31995255 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.772C>A p.Pro258Thr p.P258T ENST00000562532 2/3 475 441 34 255 254 1 strelka-varscan-mutect XKR7,missense_variant,p.Pro258Thr,ENST00000562532,NM_001011718.1; A ENST00000562532 Transcript missense_variant 946/7844 772/1740 258/579 P/T Ccc/Acc 1 1 XKR7 HGNC HGNC:23062 protein_coding YES CCDS33459.1 ENSP00000477059 Q5GH72 UPI00004C7A9E NM_001011718.1 tolerated(0.58) 2/3 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 31995255 31995255 C A 1 0 0 0 0 1 0 0 0 17995 739 26 2 2 XKR7 20 31995255 Missense_Mutation SNP C C3N-00433_T 10483321 31995255 32448912 134 14168 PLAGL2 0 . GRCh38 20 32197122 32197122 + Missense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.821C>T p.Pro274Leu p.P274L ENST00000246229 3/3 637 594 43 349 349 0 varscan-mutect PLAGL2,missense_variant,p.Pro274Leu,ENST00000246229,NM_002657.3; A ENST00000246229 Transcript missense_variant 1086/5705 821/1491 274/496 P/L cCt/cTt 1 -1 PLAGL2 HGNC HGNC:9047 protein_coding YES CCDS13197.1 ENSP00000246229 Q9UPG8 UPI0000001C1D NM_002657.3 tolerated(0.22) 3/3 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF124 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 32197122 32197122 G A 1 0 0 0 0 1 0 0 0 12114 1000 35 3 3 PLAGL2 20 32197122 Missense_Mutation SNP G C3N-00433_T 201867 32197122 32247045 135 14169 DYNLRB1 0 . GRCh38 20 34534685 34534685 + Frame_Shift_Del DEL T T - novel C3N-00433_T C3N-00433_N T T c.137delT p.Met46SerfsTer6 p.M46Sfs*6 ENST00000357156 3/4 80 74 6 41 41 0 sindel-pindel DYNLRB1,frameshift_variant,p.Met98SerfsTer6,ENST00000374846,;DYNLRB1,frameshift_variant,p.Met46SerfsTer6,ENST00000357156,NM_001281727.1,NM_014183.3;DYNLRB1,downstream_gene_variant,,ENST00000300469,;DYNLRB1,non_coding_transcript_exon_variant,,ENST00000480759,; - ENST00000357156 Transcript frameshift_variant 187/675 137/291 46/96 M/X aTg/ag 1 1 DYNLRB1 HGNC HGNC:15468 protein_coding YES CCDS13235.1 ENSP00000349679 Q9NP97 UPI0000040BFB NM_001281727.1,NM_014183.3 3/4 hmmpanther:PTHR10779:SF17,hmmpanther:PTHR10779,PIRSF_domain:PIRSF009998,Gene3D:3.30.450.30,Pfam_domain:PF03259,SMART_domains:SM00960,Superfamily_domains:SSF103196 HIGH 1 deletion 1 1 PASS . . 0 202 8 0 0 0 0 0 -12.90602 0.9999917 1 1 1 0 - 7 5 47 34534685 34534685 T - 1 0 1 0 1 0 0 0 0 4674 1464 51 0 0 DYNLRB1 20 34534685 Frame_Shift_Del DEL T C3N-00433_T 2337563 34534685 29909482 136 14170 PLCG1 0 . GRCh38 20 41172879 41172879 + Splice_Site SNP T T G novel C3N-00433_T C3N-00433_N T T c.3279+2T>G p.X1093_splice ENST00000244007 123 112 11 68 68 0 strelka-varscan-mutect PLCG1,splice_donor_variant,,ENST00000373271,NM_182811.1;PLCG1,splice_donor_variant,,ENST00000244007,NM_002660.2;PLCG1,intron_variant,,ENST00000612731,;MIR6871,downstream_gene_variant,,ENST00000613433,;PLCG1,splice_donor_variant,,ENST00000608689,;PLCG1,downstream_gene_variant,,ENST00000617873,;PLCG1,upstream_gene_variant,,ENST00000609821,;PLCG1,downstream_gene_variant,,ENST00000619272,;PLCG1,splice_donor_variant,,ENST00000461641,;PLCG1,splice_donor_variant,,ENST00000599785,;PLCG1,splice_donor_variant,,ENST00000608885,;PLCG1,downstream_gene_variant,,ENST00000483175,;PLCG1,downstream_gene_variant,,ENST00000477870,;PLCG1,upstream_gene_variant,,ENST00000607954,;PLCG1,upstream_gene_variant,,ENST00000609257,; G ENST00000244007 Transcript splice_donor_variant -/5285 3279/3876 1093/1291 1 1 PLCG1 HGNC HGNC:9065 protein_coding YES CCDS13313.1 ENSP00000244007 P19174 UPI00001B94DD NM_002660.2 28/32 HIGH 1 SNV 5 1 PASS . . 0 200 9 0 0 0 0 0 -19.97406 0.9999807 1 1 1 0 G 5 3 47 41172879 41172879 T G 1 0 0 0 0 0 0 1 0 12129 1710 59 5 5 PLCG1 20 41172879 Splice_Site SNP T C3N-00433_T 6638194 41172879 23271288 137 14171 PTPRT 0 . GRCh38 20 42678018 42678018 + Missense_Mutation SNP C C A C3N-00433_T C3N-00433_N C C c.1001G>T p.Trp334Leu p.W334L ENST00000373198 7/32 667 630 37 339 338 1 strelka-varscan-mutect PTPRT,missense_variant,p.Trp334Leu,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Trp334Leu,ENST00000373193,;PTPRT,missense_variant,p.Trp334Leu,ENST00000373201,;PTPRT,missense_variant,p.Trp334Leu,ENST00000373190,;PTPRT,missense_variant,p.Trp334Leu,ENST00000373184,;PTPRT,missense_variant,p.Trp334Leu,ENST00000356100,;PTPRT,missense_variant,p.Trp334Leu,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Trp263Leu,ENST00000620410,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 1237/12746 1001/4383 334/1460 W/L tGg/tTg COSM3291985,COSM3546595 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 tolerated(0.1) 7/32 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 42678018 42678018 C A 1 0 0 0 0 1 0 0 0 12967 595 21 2 2 PTPRT 20 42678018 Missense_Mutation SNP C C3N-00433_T 1505139 42678018 21766149 138 14172 TAF4 0 . GRCh38 20 62006626 62006626 + Nonsense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.2107C>T p.Gln703Ter p.Q703* ENST00000252996 7/15 155 145 10 82 81 1 strelka-mutect TAF4,stop_gained,p.Gln703Ter,ENST00000252996,NM_003185.3;TAF4,stop_gained,p.Gln50Ter,ENST00000488539,;TAF4,downstream_gene_variant,,ENST00000609045,;TAF4,non_coding_transcript_exon_variant,,ENST00000609041,;TAF4,non_coding_transcript_exon_variant,,ENST00000436129,;TAF4,downstream_gene_variant,,ENST00000486599,; A ENST00000252996 Transcript stop_gained 2107/4628 2107/3258 703/1085 Q/* Cag/Tag 1 -1 TAF4 HGNC HGNC:11537 protein_coding YES CCDS33500.1 ENSP00000252996 O00268 UPI000020630A NM_003185.3 7/15 hmmpanther:PTHR15138:SF18,hmmpanther:PTHR15138 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -18.10475 0.9999885 1 1 1 0 A 4 1 47 62006626 62006626 G A 1 0 0 0 0 0 1 0 0 15922 1357 47 3 3 TAF4 20 62006626 Nonsense_Mutation SNP G C3N-00433_T 19328608 62006626 2437541 139 14173 COL20A1 0 . GRCh38 20 63311743 63311743 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.1658G>T p.Arg553Met p.R553M ENST00000358894 13/36 274 247 27 142 142 0 strelka-varscan-mutect COL20A1,missense_variant,p.Arg560Met,ENST00000422202,;COL20A1,missense_variant,p.Arg553Met,ENST00000358894,NM_020882.2;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,; T ENST00000358894 Transcript missense_variant 1758/4172 1658/3855 553/1284 R/M aGg/aTg 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 deleterious(0.03) 13/36 PROSITE_profiles:PS50853 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 63311743 63311743 G T 1 0 0 0 0 1 0 0 0 3467 1014 35 2 2 COL20A1 20 63311743 Missense_Mutation SNP G C3N-00433_T 1305117 63311743 1132424 140 14174 LKAAEAR1 0 . GRCh38 20 64083942 64083942 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.278C>A p.Pro93Gln p.P93Q ENST00000308906 1/2 155 145 10 67 67 0 strelka-varscan-mutect LKAAEAR1,missense_variant,p.Pro93Gln,ENST00000308906,NM_001007125.1;LKAAEAR1,missense_variant,p.Pro93Gln,ENST00000302096,;OPRL1,intron_variant,,ENST00000336866,NM_001318853.1,NM_182647.2;OPRL1,intron_variant,,ENST00000355631,NM_001318854.1,NM_000913.4;OPRL1,upstream_gene_variant,,ENST00000349451,NM_001200019.1;RGS19,upstream_gene_variant,,ENST00000395042,NM_005873.2;RGS19,upstream_gene_variant,,ENST00000332298,NM_001039467.1;RGS19,upstream_gene_variant,,ENST00000493165,;RGS19,upstream_gene_variant,,ENST00000479996,; T ENST00000308906 Transcript missense_variant 418/868 278/723 93/240 P/Q cCg/cAg 1 -1 LKAAEAR1 HGNC HGNC:33718 protein_coding YES CCDS33509.1 ENSP00000310801 Q8TD35 UPI0000070EB4 NM_001007125.1 deleterious(0.02) 1/2 hmmpanther:PTHR35665,Pfam_domain:PF15478 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.22785 0.9999996 1 1 1 0 T 3 4 47 64083942 64083942 G T 1 0 0 0 0 1 0 0 0 8756 1116 39 1 1 LKAAEAR1 20 64083942 Missense_Mutation SNP G C3N-00433_T 772199 64083942 360225 141 14175 MYT1 0 . GRCh38 20 64232217 64232217 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.2729C>A p.Ser910Tyr p.S910Y ENST00000328439 19/23 619 579 40 354 351 3 strelka-varscan-mutect MYT1,missense_variant,p.Ser937Tyr,ENST00000536311,;MYT1,missense_variant,p.Ser910Tyr,ENST00000328439,NM_004535.2;MYT1,downstream_gene_variant,,ENST00000622439,;MYT1,downstream_gene_variant,,ENST00000360149,; A ENST00000328439 Transcript missense_variant 3093/5535 2729/3366 910/1121 S/Y tCt/tAt 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 deleterious(0) 19/23 Superfamily_domains:0042508,Pfam_domain:PF01530,hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 64232217 64232217 C A 1 0 0 0 0 1 0 0 0 10105 913 32 2 2 MYT1 20 64232217 Missense_Mutation SNP C C3N-00433_T 148275 64232217 211950 142 14176 NRIP1 0 . GRCh38 21 14967806 14967806 + Missense_Mutation SNP A A T novel C3N-00433_T C3N-00433_N A A c.387T>A p.Asp129Glu p.D129E ENST00000400202 3/3 126 119 7 91 91 0 strelka-varscan-mutect NRIP1,missense_variant,p.Asp129Glu,ENST00000400202,;NRIP1,missense_variant,p.Asp129Glu,ENST00000400199,;NRIP1,missense_variant,p.Asp129Glu,ENST00000318948,NM_003489.3;NRIP1,downstream_gene_variant,,ENST00000411932,;NRIP1,downstream_gene_variant,,ENST00000638122,;AF127936.9,intron_variant,,ENST00000432230,;AF127577.11,upstream_gene_variant,,ENST00000436429,;AF127577.10,downstream_gene_variant,,ENST00000446301,; T ENST00000400202 Transcript missense_variant 1100/7671 387/3477 129/1158 D/E gaT/gaA 1 -1 NRIP1 HGNC HGNC:8001 protein_coding YES CCDS13568.1 ENSP00000383063 P48552 UPI000004A0A8 tolerated(0.48) 3/3 hmmpanther:PTHR15088,Pfam_domain:PF15687 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 14967806 14967806 A T 1 0 0 0 0 1 0 0 0 10710 446 16 4 4 NRIP1 21 14967806 Missense_Mutation SNP A C3N-00433_T 14967806 31742177 143 14177 AIRE 0 . GRCh38 21 44287048 44287048 + Silent SNP C C A novel C3N-00433_T C3N-00433_N C C c.378C>A p.= p.P126P ENST00000291582 3/14 411 389 22 212 212 0 strelka-varscan-mutect AIRE,synonymous_variant,p.=,ENST00000291582,NM_000383.3;AIRE,non_coding_transcript_exon_variant,,ENST00000530812,;AIRE,non_coding_transcript_exon_variant,,ENST00000527919,;AIRE,upstream_gene_variant,,ENST00000337909,;AIRE,upstream_gene_variant,,ENST00000397994,; A ENST00000291582 Transcript synonymous_variant 505/2257 378/1638 126/545 P ccC/ccA 1 1 AIRE HGNC HGNC:360 protein_coding YES CCDS13706.1 ENSP00000291582 O43918 UPI0000030FA6 NM_000383.3 3/14 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF15,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 47 44287048 44287048 C A 1 0 0 0 0 0 0 0 1 514 581 21 2 2 AIRE 21 44287048 Silent SNP C C3N-00433_T 29319242 44287048 2422935 144 14178 PCNT 0 . GRCh38 21 46346893 46346893 + Nonsense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.871G>T p.Glu291Ter p.E291* ENST00000359568 5/47 455 429 26 224 224 0 strelka-varscan-mutect PCNT,stop_gained,p.Glu291Ter,ENST00000359568,NM_006031.5;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,non_coding_transcript_exon_variant,,ENST00000490468,;PCNT,non_coding_transcript_exon_variant,,ENST00000466474,;PCNT,upstream_gene_variant,,ENST00000483844,; T ENST00000359568 Transcript stop_gained 978/10560 871/10011 291/3336 E/* Gag/Tag 1 1 PCNT HGNC HGNC:16068 protein_coding YES CCDS33592.1 ENSP00000352572 O95613 UPI00001AEB88 NM_006031.5 5/47 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 47 46346893 46346893 G T 1 0 0 0 0 0 1 0 0 11678 1175 41 2 2 PCNT 21 46346893 Nonsense_Mutation SNP G C3N-00433_T 2059845 46346893 363090 145 14179 MICAL3 0 . GRCh38 22 17901901 17901901 + Missense_Mutation SNP T T C novel C3N-00433_T C3N-00433_N T T c.668A>G p.Asp223Gly p.D223G ENST00000441493 5/32 119 102 17 77 77 0 strelka-varscan-mutect MICAL3,missense_variant,p.Asp223Gly,ENST00000441493,NM_015241.2;MICAL3,missense_variant,p.Asp223Gly,ENST00000414725,;MICAL3,missense_variant,p.Asp223Gly,ENST00000585038,NM_001136004.3;MICAL3,missense_variant,p.Asp223Gly,ENST00000400561,NM_001122731.2;MICAL3,missense_variant,p.Asp223Gly,ENST00000383094,;MICAL3,downstream_gene_variant,,ENST00000424046,;MICAL3,missense_variant,p.Asp223Gly,ENST00000495076,; C ENST00000441493 Transcript missense_variant 1021/9445 668/6009 223/2002 D/G gAt/gGt 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 deleterious(0.02) 5/32 hmmpanther:PTHR11915:SF239,hmmpanther:PTHR11915,Gene3D:3.50.50.60,Superfamily_domains:SSF51905,Prints_domain:PR00420 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 17901901 17901901 T C 1 0 0 0 0 1 0 0 0 9528 1435 50 5 5 MICAL3 22 17901901 Missense_Mutation SNP T C3N-00433_T 17901901 32916567 146 14180 MYH9 0 . GRCh38 22 36285275 36285275 + Missense_Mutation SNP C C T rs758825898 C3N-00433_T C3N-00433_N C C c.5329G>A p.Glu1777Lys p.E1777K ENST00000216181 38/41 602 566 36 334 334 0 strelka-varscan-mutect MYH9,missense_variant,p.Glu1777Lys,ENST00000216181,NM_002473.5;MIR6819,downstream_gene_variant,,ENST00000622122,;MYH9,non_coding_transcript_exon_variant,,ENST00000475726,;MYH9,non_coding_transcript_exon_variant,,ENST00000486218,; T ENST00000216181 Transcript missense_variant 5560/7501 5329/5883 1777/1960 E/K Gag/Aag rs758825898,COSM1258485 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 deleterious(0) 38/41 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF317,Superfamily_domains:SSF48097 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758825898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 36285275 36285275 C T 1 0 0 0 0 1 0 0 0 10042 893 31 1 1 MYH9 22 36285275 Missense_Mutation SNP C C3N-00433_T 18383374 36285275 14533193 147 14181 CBX6 0 . GRCh38 22 38866234 38866234 + Missense_Mutation SNP C C A novel C3N-00433_T C3N-00433_N C C c.1214G>T p.Gly405Val p.G405V ENST00000407418 5/5 141 133 8 81 81 0 strelka-varscan-mutect CBX6,missense_variant,p.Gly405Val,ENST00000407418,NM_014292.4;CBX6,missense_variant,p.Gly387Val,ENST00000216083,NM_001303494.1;CBX6,downstream_gene_variant,,ENST00000469420,; A ENST00000407418 Transcript missense_variant 1338/6122 1214/1239 405/412 G/V gGt/gTt 1 -1 CBX6 HGNC HGNC:1556 protein_coding YES CCDS13980.1 ENSP00000384490 O95503 UPI00001271FD NM_014292.4 tolerated_low_confidence(0.29) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF8 MODERATE 1 SNV 1 1 PASS rs1373500194 . 0 203 6 0 0 0 0 0 -14.89758 0.9999994 1 1 1 0 A 3 1 47 38866234 38866234 C A 1 0 0 0 0 1 0 0 0 2422 507 18 2 2 CBX6 22 38866234 Missense_Mutation SNP C C3N-00433_T 2580959 38866234 11952234 148 14182 PLXNB2 0 . GRCh38 22 50289828 50289828 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.757G>A p.Asp253Asn p.D253N ENST00000449103 3/37 362 341 21 217 217 0 strelka-varscan-mutect PLXNB2,missense_variant,p.Asp253Asn,ENST00000449103,;PLXNB2,missense_variant,p.Asp253Asn,ENST00000359337,NM_012401.3;PLXNB2,missense_variant,p.Asp253Asn,ENST00000432455,;PLXNB2,upstream_gene_variant,,ENST00000411680,;PLXNB2,downstream_gene_variant,,ENST00000425954,;PLXNB2,upstream_gene_variant,,ENST00000434732,;PLXNB2,upstream_gene_variant,,ENST00000496720,; T ENST00000449103 Transcript missense_variant 898/6383 757/5517 253/1838 D/N Gac/Aac 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D deleterious(0) 3/37 PROSITE_profiles:PS51004,hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 50289828 50289828 C T 1 0 0 0 0 1 0 0 0 12230 913 32 3 3 PLXNB2 22 50289828 Missense_Mutation SNP C C3N-00433_T 11423594 50289828 528640 149 14183 ARSH 0 . GRCh38 X 3024108 3024108 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.989C>T p.Pro330Leu p.P330L ENST00000381130 6/9 111 95 16 69 69 0 strelka-varscan-mutect ARSH,missense_variant,p.Pro330Leu,ENST00000381130,NM_001011719.1; T ENST00000381130 Transcript missense_variant 989/1875 989/1689 330/562 P/L cCc/cTc 1 1 ARSH HGNC HGNC:32488 protein_coding YES CCDS35198.1 ENSP00000370522 Q5FYA8 UPI00001D7C2E NM_001011719.1 tolerated(0.18) 6/9 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF240,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 3024108 3024108 C T 1 0 0 0 0 1 0 0 0 1136 623 22 3 3 ARSH 23 3024108 Missense_Mutation SNP C C3N-00433_T 3024108 153016787 150 14184 TLR7 0 . GRCh38 X 12888065 12888065 + Missense_Mutation SNP C C T novel C3N-00433_T C3N-00433_N C C c.2557C>T p.Leu853Phe p.L853F ENST00000380659 3/3 98 87 11 83 82 1 strelka-varscan-mutect TLR7,missense_variant,p.Leu853Phe,ENST00000380659,NM_016562.3; T ENST00000380659 Transcript missense_variant 2696/5011 2557/3150 853/1049 L/F Ctc/Ttc 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(0.44) 3/3 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 47 12888065 12888065 C T 1 0 0 0 0 1 0 0 0 16402 913 32 3 3 TLR7 23 12888065 Missense_Mutation SNP C C3N-00433_T 9863957 12888065 143152830 151 14185 DMD 0 . GRCh38 X 32816484 32816484 + Missense_Mutation SNP G G A rs747353479 C3N-00433_T C3N-00433_N G G c.514C>T p.Leu172Phe p.L172F ENST00000357033 6/79 115 102 13 117 117 0 strelka-varscan-mutect DMD,missense_variant,p.Leu172Phe,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Leu168Phe,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Leu172Phe,ENST00000620040,;DMD,missense_variant,p.Leu168Phe,ENST00000619831,;DMD,missense_variant,p.Leu164Phe,ENST00000288447,;DMD,intron_variant,,ENST00000447523,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,non_coding_transcript_exon_variant,,ENST00000480751,;DMD,intron_variant,,ENST00000488902,; A ENST00000357033 Transcript missense_variant 721/13956 514/11058 172/3685 L/F Ctc/Ttc rs747353479 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0.01) 6/79 PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,Pfam_domain:PF00307,Gene3D:1.10.418.10,PIRSF_domain:PIRSF002341,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs747353479 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 32816484 32816484 G A 1 0 0 0 0 1 0 0 0 4387 942 33 3 3 DMD 23 32816484 Missense_Mutation SNP G C3N-00433_T 19928419 32816484 123224411 152 14186 KDM6A 0 . GRCh38 X 45089851 45089851 + Missense_Mutation SNP G G C novel C3N-00433_T C3N-00433_N G G c.3657G>C p.Trp1219Cys p.W1219C ENST00000377967 25/29 109 103 6 121 121 0 strelka-varscan-mutect KDM6A,missense_variant,p.Trp1247Cys,ENST00000611820,NM_001291415.1;KDM6A,missense_variant,p.Trp1202Cys,ENST00000382899,NM_001291416.1;KDM6A,missense_variant,p.Trp1168Cys,ENST00000543216,;KDM6A,missense_variant,p.Trp1150Cys,ENST00000536777,NM_001291417.1,NM_001291418.1;KDM6A,missense_variant,p.Trp1219Cys,ENST00000377967,NM_021140.3;KDM6A,missense_variant,p.Trp862Cys,ENST00000433797,;KDM6A,missense_variant,p.Trp817Cys,ENST00000414389,NM_001291421.1;KDM6A,intron_variant,,ENST00000621147,;KDM6A,upstream_gene_variant,,ENST00000431196,;KDM6A,downstream_gene_variant,,ENST00000484732,; C ENST00000377967 Transcript missense_variant 3698/5438 3657/4206 1219/1401 W/C tgG/tgC 1 1 KDM6A HGNC HGNC:12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 UPI000013DA92 NM_021140.3 deleterious(0) 25/29 PROSITE_profiles:PS51184,hmmpanther:PTHR14017:SF9,hmmpanther:PTHR14017,Pfam_domain:PF02373,SMART_domains:SM00558,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 47 45089851 45089851 G C 1 0 0 0 0 1 0 0 0 8055 1183 41 4 4 KDM6A 23 45089851 Missense_Mutation SNP G C3N-00433_T 12273367 45089851 110951044 153 14187 BHLHB9 0 . GRCh38 X 102749308 102749308 + Missense_Mutation SNP G G T novel C3N-00433_T C3N-00433_N G G c.313G>T p.Ala105Ser p.A105S ENST00000372735 4/4 63 56 7 40 40 0 strelka-varscan-mutect BHLHB9,missense_variant,p.Ala105Ser,ENST00000372735,;BHLHB9,missense_variant,p.Ala105Ser,ENST00000457056,NM_001142528.1,NM_001142527.1,NM_001142525.1,NM_001142526.1,NM_001142524.1;BHLHB9,missense_variant,p.Ala105Ser,ENST00000447531,NM_001142529.1;BHLHB9,missense_variant,p.Ala105Ser,ENST00000361229,NM_030639.2;BHLHB9,missense_variant,p.Ala105Ser,ENST00000448867,NM_001142530.1;BHLHB9,downstream_gene_variant,,ENST00000483294,;BHLHB9,downstream_gene_variant,,ENST00000486988,; T ENST00000372735 Transcript missense_variant 898/5130 313/1644 105/547 A/S Gct/Tct 1 1 BHLHB9 HGNC HGNC:29353 protein_coding YES CCDS14502.1 ENSP00000361820 Q6PI77 UPI00001C1D50 tolerated(0.37) 4/4 hmmpanther:PTHR15712:SF18,hmmpanther:PTHR15712 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -15.91963 0.9999999 1 1 1 0 T 3 4 47 102749308 102749308 G T 1 0 0 0 0 1 0 0 0 1568 1203 42 2 2 BHLHB9 23 102749308 Missense_Mutation SNP G C3N-00433_T 57659457 102749308 53291587 154 14188 ESX1 0 . GRCh38 X 104250783 104250783 + Silent SNP G G C novel C3N-00433_T C3N-00433_N G G c.666C>G p.= p.A222A ENST00000372588 4/4 175 155 20 85 85 0 strelka-varscan-mutect ESX1,synonymous_variant,p.=,ENST00000372588,NM_153448.3; C ENST00000372588 Transcript synonymous_variant 750/1495 666/1221 222/406 A gcC/gcG 1 -1 ESX1 HGNC HGNC:14865 protein_coding YES CCDS14516.1 ENSP00000361669 Q8N693 UPI0000073D09 NM_153448.3 4/4 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 47 104250783 104250783 G C 1 0 0 0 0 0 0 0 1 5125 987 35 4 4 ESX1 23 104250783 Silent SNP G C3N-00433_T 1501475 104250783 51790112 155 14189 BCORL1 0 . GRCh38 X 130013841 130013841 + Missense_Mutation SNP A A T novel C3N-00433_T C3N-00433_N A A c.1069A>T p.Met357Leu p.M357L ENST00000540052 3/12 120 102 18 74 74 0 strelka-varscan-mutect BCORL1,missense_variant,p.Met357Leu,ENST00000540052,NM_021946.4;BCORL1,missense_variant,p.Met357Leu,ENST00000218147,;BCORL1,upstream_gene_variant,,ENST00000456822,;BCORL1,upstream_gene_variant,,ENST00000441294,;BCORL1,downstream_gene_variant,,ENST00000488135,; T ENST00000540052 Transcript missense_variant 1113/7127 1069/5136 357/1711 M/L Atg/Ttg 1 1 BCORL1 HGNC HGNC:25657 protein_coding YES CCDS14616.1 ENSP00000437775 Q5H9F3 UPI0001D3414A NM_021946.4 3/12 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 201 6 2 0 0 0 0 -20 0.9999151 1 1 1 0 T 3 4 47 130013841 130013841 A T 1 0 0 0 0 1 0 0 0 1534 217 8 4 4 BCORL1 23 130013841 Missense_Mutation SNP A C3N-00433_T 25763058 130013841 26027054 156 14190 NLGN4Y 0 . GRCh38 Y 14830149 14830149 + Missense_Mutation SNP G G A novel C3N-00433_T C3N-00433_N G G c.1231G>A p.Glu411Lys p.E411K ENST00000355905 5/6 191 177 14 171 171 0 varscan-mutect NLGN4Y,missense_variant,p.Glu243Lys,ENST00000382872,NM_001206850.1;NLGN4Y,missense_variant,p.Glu468Lys,ENST00000382868,;NLGN4Y,missense_variant,p.Glu411Lys,ENST00000339174,;NLGN4Y,missense_variant,p.Glu411Lys,ENST00000355905,NM_014893.4;NLGN4Y,non_coding_transcript_exon_variant,,ENST00000476359,; A ENST00000355905 Transcript missense_variant 1483/5167 1231/2451 411/816 E/K Gaa/Aaa 1 1 NLGN4Y HGNC HGNC:15529 protein_coding YES CCDS14788.1 ENSP00000348169 Q8NFZ3 A0A024R9E7 UPI000004770C NM_014893.4 deleterious(0.03) 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 73 136 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 47 14830149 14830149 G A 1 0 0 0 0 1 0 0 0 10502 1291 45 3 3 NLGN4Y 24 14830149 Missense_Mutation SNP G C3N-00433_T 14830149 42397266 157 14191 ATP13A2 0 . GRCh38 1 17000309 17000309 + Missense_Mutation SNP T T G rs538497077 C3N-00546_T C3N-00546_N T T c.844A>C p.Ser282Arg p.S282R ENST00000326735 10/29 586 481 105 413 412 1 strelka-varscan-mutect ATP13A2,missense_variant,p.Ser277Arg,ENST00000452699,NM_001141973.2;ATP13A2,missense_variant,p.Ser282Arg,ENST00000326735,NM_022089.3;ATP13A2,missense_variant,p.Ser277Arg,ENST00000341676,NM_001141974.2;ATP13A2,missense_variant,p.Ser257Arg,ENST00000510069,;ATP13A2,missense_variant,p.Ser2Arg,ENST00000506174,;ATP13A2,missense_variant,p.Ser177Arg,ENST00000511957,;ATP13A2,missense_variant,p.Ser180Arg,ENST00000508222,;ATP13A2,5_prime_UTR_variant,,ENST00000617114,;ATP13A2,upstream_gene_variant,,ENST00000503552,;ATP13A2,downstream_gene_variant,,ENST00000509619,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000463860,;ATP13A2,upstream_gene_variant,,ENST00000502860,;ATP13A2,upstream_gene_variant,,ENST00000509392,; G ENST00000326735 Transcript missense_variant 878/3840 844/3543 282/1180 S/R Agc/Cgc rs538497077,CM098008 1 -1 ATP13A2 HGNC HGNC:30213 protein_coding YES CCDS175.1 ENSP00000327214 Q9NQ11 UPI0000049724 NM_022089.3 tolerated(0.27) 10/29 Superfamily_domains:0049473,Gene3D:2.70.150.10,Pfam_domain:PF00122,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF86,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01657 MODERATE 1 SNV 1 0,1 1 PASS rs538497077 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 17000309 17000309 T G 1 0 0 0 0 1 0 0 0 1276 1623 56 5 5 ATP13A2 1 17000309 Missense_Mutation SNP T C3N-00546_T 17000309 231956113 1 14192 DNAJC6 0 . GRCh38 1 65384280 65384280 + Missense_Mutation SNP C C G novel C3N-00546_T C3N-00546_N C C c.754C>G p.Leu252Val p.L252V ENST00000371069 6/19 75 62 13 91 91 0 strelka-varscan-mutect DNAJC6,missense_variant,p.Leu182Val,ENST00000263441,NM_001256865.1;DNAJC6,missense_variant,p.Leu195Val,ENST00000395325,NM_014787.3;DNAJC6,missense_variant,p.Leu252Val,ENST00000371069,NM_001256864.1;DNAJC6,missense_variant,p.Leu226Val,ENST00000494710,;DNAJC6,non_coding_transcript_exon_variant,,ENST00000498720,;DNAJC6,downstream_gene_variant,,ENST00000472787,; G ENST00000371069 Transcript missense_variant 955/5365 754/2913 252/970 L/V Cta/Gta 1 1 DNAJC6 HGNC HGNC:15469 protein_coding YES CCDS58004.1 ENSP00000360108 O75061 UPI000022AE8A NM_001256864.1 deleterious(0) 6/19 PROSITE_profiles:PS51181,hmmpanther:PTHR23172:SF4,hmmpanther:PTHR23172,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS rs1338260319 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 65384280 65384280 C G 1 0 0 0 0 1 0 0 0 4466 796 28 4 4 DNAJC6 1 65384280 Missense_Mutation SNP C C3N-00546_T 48383971 65384280 183572142 2 14193 AK5 0 . GRCh38 1 77535905 77535905 + Missense_Mutation SNP G G A rs777102302 C3N-00546_T C3N-00546_N G G c.1487G>A p.Arg496His p.R496H ENST00000354567 13/14 204 160 44 156 156 0 strelka-varscan-mutect AK5,missense_variant,p.Arg470His,ENST00000344720,NM_012093.3;AK5,missense_variant,p.Arg496His,ENST00000354567,NM_174858.2;AK5,missense_variant,p.Arg11His,ENST00000478255,;AK5,downstream_gene_variant,,ENST00000530826,;AK5,upstream_gene_variant,,ENST00000466393,;AK5,intron_variant,,ENST00000527263,; A ENST00000354567 Transcript missense_variant 1750/3251 1487/1689 496/562 R/H cGc/cAc rs777102302 1 1 AK5 HGNC HGNC:365 protein_coding YES CCDS675.1 ENSP00000346577 Q9Y6K8 UPI0000167E20 NM_174858.2 deleterious(0) 13/14 HAMAP:MF_00235,hmmpanther:PTHR23359:SF79,hmmpanther:PTHR23359,Gene3D:3.40.50.300,Pfam_domain:PF00406,TIGRFAM_domain:TIGR01360,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs777102302 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 77535905 77535905 G A 1 0 0 0 0 1 0 0 0 522 1087 38 1 1 AK5 1 77535905 Missense_Mutation SNP G C3N-00546_T 12151625 77535905 171420517 3 14194 FUBP1 0 . GRCh38 1 77969974 77969974 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.162T>A p.Asn54Lys p.N54K ENST00000370768 2/20 196 168 28 216 216 0 strelka-varscan-mutect FUBP1,missense_variant,p.Asn54Lys,ENST00000370767,;FUBP1,missense_variant,p.Asn54Lys,ENST00000370768,NM_003902.4,NM_001303433.1;FUBP1,missense_variant,p.Asn54Lys,ENST00000421641,;FUBP1,missense_variant,p.Asn54Lys,ENST00000294623,; T ENST00000370768 Transcript missense_variant 244/2378 162/1935 54/644 N/K aaT/aaA 1 -1 FUBP1 HGNC HGNC:4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.4,NM_001303433.1 deleterious(0.02) 2/20 hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF99 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 77969974 77969974 A T 1 0 0 0 0 1 0 0 0 5963 98 4 4 4 FUBP1 1 77969974 Missense_Mutation SNP A C3N-00546_T 434069 77969974 170986448 4 14195 GBP3 0 . GRCh38 1 89013211 89013211 + Nonsense_Mutation SNP G G C C3N-00546_T C3N-00546_N G G c.842C>G p.Ser281Ter p.S281* ENST00000370481 6/11 201 179 22 185 185 0 strelka-varscan-mutect GBP3,stop_gained,p.Ser281Ter,ENST00000370481,NM_018284.2;GBP3,stop_gained,p.Ser30Ter,ENST00000445969,;GBP3,upstream_gene_variant,,ENST00000461384,;GBP3,downstream_gene_variant,,ENST00000564665,;GBP3,downstream_gene_variant,,ENST00000475853,;GBP3,stop_gained,p.Ser281Ter,ENST00000489444,;GBP3,3_prime_UTR_variant,,ENST00000493594,;GBP3,3_prime_UTR_variant,,ENST00000235878,;GBP3,non_coding_transcript_exon_variant,,ENST00000370482,;GBP3,downstream_gene_variant,,ENST00000568006,; C ENST00000370481 Transcript stop_gained 1063/3067 842/1788 281/595 S/* tCa/tGa COSM4510615 1 -1 GBP3 HGNC HGNC:4184 protein_coding YES CCDS717.2 ENSP00000359512 Q9H0R5 UPI0000204D81 NM_018284.2 6/11 hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF31 1 HIGH 1 SNV 1 1 1 PASS rs760256930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 48 89013211 89013211 G C 1 0 0 0 0 0 1 0 0 6145 1294 45 4 4 GBP3 1 89013211 Nonsense_Mutation SNP G C3N-00546_T 11043237 89013211 159943211 5 14196 HFM1 0 . GRCh38 1 91385705 91385705 + Silent SNP A A G novel C3N-00546_T C3N-00546_N A A c.624T>C p.= p.N208N ENST00000370425 5/39 248 182 66 251 251 0 strelka-varscan-mutect HFM1,synonymous_variant,p.=,ENST00000370425,NM_001017975.4;HFM1,synonymous_variant,p.=,ENST00000427444,;HFM1,synonymous_variant,p.=,ENST00000448819,;HFM1,non_coding_transcript_exon_variant,,ENST00000481900,;HFM1,non_coding_transcript_exon_variant,,ENST00000488023,; G ENST00000370425 Transcript synonymous_variant 723/4931 624/4308 208/1435 N aaT/aaC 1 -1 HFM1 HGNC HGNC:20193 protein_coding YES CCDS30769.2 ENSP00000359454 A2PYH4 UPI0000F51F79 NM_001017975.4 5/39 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 48 91385705 91385705 A G 1 0 0 0 0 0 0 0 1 6967 446 16 5 5 HFM1 1 91385705 Silent SNP A C3N-00546_T 2372494 91385705 157570717 6 14197 RWDD3 0 . GRCh38 1 95246648 95246648 + Missense_Mutation SNP A A C novel C3N-00546_T C3N-00546_N A A c.680A>C p.Glu227Ala p.E227A ENST00000370202 3/4 76 62 14 90 90 0 strelka-varscan-mutect RWDD3,missense_variant,p.Glu227Ala,ENST00000370202,NM_001199682.1,NM_015485.4;RWDD3,intron_variant,,ENST00000263893,NM_001128142.1;TMEM56-RWDD3,intron_variant,,ENST00000604203,;TMEM56-RWDD3,downstream_gene_variant,,ENST00000604534,NM_001199691.1;RP11-57H12.5,intron_variant,,ENST00000624604,;RP11-57H12.5,intron_variant,,ENST00000444665,;RP11-57H12.5,intron_variant,,ENST00000630835,;RP11-57H12.5,downstream_gene_variant,,ENST00000624135,;RP11-57H12.5,downstream_gene_variant,,ENST00000598739,;RWDD3,non_coding_transcript_exon_variant,,ENST00000495272,;RWDD3,non_coding_transcript_exon_variant,,ENST00000460571,;RWDD3,non_coding_transcript_exon_variant,,ENST00000497058,;RWDD3,intron_variant,,ENST00000473397,;RWDD3,downstream_gene_variant,,ENST00000492639,; C ENST00000370202 Transcript missense_variant 756/1235 680/804 227/267 E/A gAa/gCa 1 1 RWDD3 HGNC HGNC:21393 protein_coding YES CCDS41357.1 ENSP00000359221 Q9Y3V2 UPI000059D012 NM_001199682.1,NM_015485.4 tolerated(0.17) 3/4 hmmpanther:PTHR15628 MODERATE SNV 3 1 PASS . . 2 206 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 95246648 95246648 A C 1 0 0 0 0 1 0 0 0 14018 246 9 5 5 RWDD3 1 95246648 Missense_Mutation SNP A C3N-00546_T 3860943 95246648 153709774 7 14198 NBPF6 0 . GRCh38 1 108470612 108470612 + Missense_Mutation SNP G G A novel C3N-00546_T C3N-00546_N G G c.1891G>A p.Glu631Lys p.E631K ENST00000495380 15/15 149 126 23 149 149 0 strelka-varscan-mutect NBPF6,missense_variant,p.Glu631Lys,ENST00000495380,NM_001143988.1;NBPF6,missense_variant,p.Glu631Lys,ENST00000294652,;NBPF6,missense_variant,p.Glu660Lys,ENST00000370040,NM_001143987.1; A ENST00000495380 Transcript missense_variant 2104/2494 1891/1917 631/638 E/K Gaa/Aaa 1 1 NBPF6 HGNC HGNC:31988 protein_coding YES CCDS44184.1 ENSP00000417277 Q5VWK0 UPI0000160A67 NM_001143988.1 deleterious_low_confidence(0.02) 15/15 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 108470612 108470612 G A 1 0 0 0 0 1 0 0 0 10214 1291 45 3 3 NBPF6 1 108470612 Missense_Mutation SNP G C3N-00546_T 13223964 108470612 140485810 8 14199 DUSP27 0 . GRCh38 1 167127643 167127643 + Silent SNP C C A rs532909371 C3N-00546_T C3N-00546_N C C c.2512C>A p.= p.R838R ENST00000361200 6/6 247 211 36 221 221 0 strelka-varscan-mutect DUSP27,synonymous_variant,p.=,ENST00000361200,;DUSP27,synonymous_variant,p.=,ENST00000443333,NM_001080426.1;DUSP27,synonymous_variant,p.=,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; A ENST00000361200 Transcript synonymous_variant 2678/4164 2512/3477 838/1158 R Cgg/Agg rs532909371 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 6/6 Coiled-coils_(Ncoils):Coil LOW 1 SNV 5 1 PASS rs532909371 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 167127643 167127643 C A 1 0 0 0 0 0 0 0 1 4646 643 23 1 1 DUSP27 1 167127643 Silent SNP C C3N-00546_T 58657031 167127643 81828779 9 14200 F5 0 . GRCh38 1 169541419 169541419 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.3671C>G p.Pro1224Arg p.P1224R ENST00000367797 13/25 557 476 81 446 445 1 strelka-varscan-mutect F5,missense_variant,p.Pro1229Arg,ENST00000367796,;F5,missense_variant,p.Pro1224Arg,ENST00000367797,NM_000130.4; C ENST00000367797 Transcript missense_variant 3873/7024 3671/6675 1224/2224 P/R cCa/cGa 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 deleterious(0.02) 13/25 PIRSF_domain:PIRSF000354 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 169541419 169541419 G C 1 0 0 0 0 1 0 0 0 5216 1348 47 4 4 F5 1 169541419 Missense_Mutation SNP G C3N-00546_T 2413776 169541419 79415003 10 14201 SELP 0 . GRCh38 1 169617274 169617274 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.235C>G p.Leu79Val p.L79V ENST00000263686 3/17 367 310 57 317 317 0 strelka-varscan-mutect SELP,missense_variant,p.Leu79Val,ENST00000263686,NM_003005.3;SELP,missense_variant,p.Leu78Val,ENST00000426706,;SELP,missense_variant,p.Leu79Val,ENST00000367788,;SELP,missense_variant,p.Leu79Val,ENST00000367786,;SELP,missense_variant,p.Leu79Val,ENST00000458599,;SELP,missense_variant,p.Leu79Val,ENST00000367795,; C ENST00000263686 Transcript missense_variant 273/3142 235/2493 79/830 L/V Ctc/Gtc 1 -1 SELP HGNC HGNC:10721 protein_coding YES CCDS1282.1 ENSP00000263686 P16109 A0A024R8Y9 UPI0000204D4A NM_003005.3 deleterious(0) 3/17 PROSITE_profiles:PS50041,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF19,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 169617274 169617274 G C 1 0 0 0 0 1 0 0 0 14296 1000 35 4 4 SELP 1 169617274 Missense_Mutation SNP G C3N-00546_T 75855 169617274 79339148 11 14202 ZBTB37 0 . GRCh38 1 173885833 173885833 + Silent SNP C C A novel C3N-00546_T C3N-00546_N C C c.1221C>A p.= p.G407G ENST00000367701 4/4 300 271 29 297 296 1 strelka-varscan-mutect ZBTB37,synonymous_variant,p.=,ENST00000367701,;ZBTB37,synonymous_variant,p.=,ENST00000427304,NM_001122770.1;ZBTB37,3_prime_UTR_variant,,ENST00000367704,; A ENST00000367701 Transcript synonymous_variant 1412/19128 1221/1512 407/503 G ggC/ggA 1 1 ZBTB37 HGNC HGNC:28365 protein_coding YES CCDS44278.1 ENSP00000356674 Q5TC79 UPI0000203C09 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF2,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 173885833 173885833 C A 1 0 0 0 0 0 0 0 1 18107 697 25 2 2 ZBTB37 1 173885833 Silent SNP C C3N-00546_T 4268559 173885833 75070589 12 14203 PAPPA2 0 . GRCh38 1 176692276 176692276 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.2582C>A p.Thr861Asn p.T861N ENST00000367662 6/23 123 105 18 95 95 0 strelka-mutect PAPPA2,missense_variant,p.Thr861Asn,ENST00000367662,NM_020318.2;PAPPA2,downstream_gene_variant,,ENST00000367661,NM_021936.2; A ENST00000367662 Transcript missense_variant 3746/9691 2582/5376 861/1791 T/N aCt/aAt 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 deleterious(0) 6/23 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF1,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1329850767 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 176692276 176692276 C A 1 0 0 0 0 1 0 0 0 11513 565 20 2 2 PAPPA2 1 176692276 Missense_Mutation SNP C C3N-00546_T 2806443 176692276 72264146 13 14204 ASTN1 0 . GRCh38 1 177164491 177164491 + Silent SNP C C T novel C3N-00546_T C3N-00546_N C C c.186G>A p.= p.S62S ENST00000361833 1/23 222 204 18 155 155 0 strelka-varscan-mutect ASTN1,synonymous_variant,p.=,ENST00000361833,NM_004319.2;ASTN1,synonymous_variant,p.=,ENST00000367657,NM_001286164.1;ASTN1,synonymous_variant,p.=,ENST00000424564,NM_207108.2;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,; T ENST00000361833 Transcript synonymous_variant 200/7116 186/3885 62/1294 S tcG/tcA 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 1/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99958 0.9999998 1 1 1 0 T 2 4 48 177164491 177164491 C T 1 0 0 0 0 0 0 0 1 1211 639 23 1 1 ASTN1 1 177164491 Silent SNP C C3N-00546_T 472215 177164491 71791931 14 14205 CACNA1S 0 . GRCh38 1 201050502 201050502 + Silent SNP A A G novel C3N-00546_T C3N-00546_N A A c.4128T>C p.= p.F1376F ENST00000362061 34/44 583 490 93 460 460 0 strelka-varscan-mutect CACNA1S,synonymous_variant,p.=,ENST00000362061,NM_000069.2;CACNA1S,synonymous_variant,p.=,ENST00000367338,; G ENST00000362061 Transcript synonymous_variant 4355/6166 4128/5622 1376/1873 F ttT/ttC 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 34/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 48 201050502 201050502 A G 1 0 0 0 0 0 0 0 1 2235 127 5 5 5 CACNA1S 1 201050502 Silent SNP A C3N-00546_T 23886011 201050502 47905920 15 14206 IGFN1 0 . GRCh38 1 201211788 201211788 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.6895G>C p.Gly2299Arg p.G2299R ENST00000335211 12/24 224 180 44 195 195 0 varscan-mutect IGFN1,missense_variant,p.Gly2299Arg,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,; C ENST00000335211 Transcript missense_variant 7025/11810 6895/11127 2299/3708 G/R Ggg/Cgg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 tolerated(0.13) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 201211788 201211788 G C 1 0 0 0 0 1 0 0 0 7497 1000 35 4 4 IGFN1 1 201211788 Missense_Mutation SNP G C3N-00546_T 161286 201211788 47744634 16 14207 LGR6 0 . GRCh38 1 202319018 202319018 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.2715G>T p.Gln905His p.Q905H ENST00000367278 18/18 146 133 13 125 125 0 strelka-varscan-mutect LGR6,missense_variant,p.Gln905His,ENST00000367278,NM_001017403.1;LGR6,missense_variant,p.Gln853His,ENST00000255432,NM_021636.2;LGR6,missense_variant,p.Gln766His,ENST00000439764,NM_001017404.1;LGR6,3_prime_UTR_variant,,ENST00000487787,; T ENST00000367278 Transcript missense_variant 2804/3567 2715/2904 905/967 Q/H caG/caT 1 1 LGR6 HGNC HGNC:19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 tolerated(0.13) 18/18 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -17.97668 0.9987644 1 1 1 0 T 3 4 48 202319018 202319018 G T 1 0 0 0 0 1 0 0 0 8668 962 34 2 2 LGR6 1 202319018 Missense_Mutation SNP G C3N-00546_T 1107230 202319018 46637404 17 14208 ESRRG 0 . GRCh38 1 216568098 216568098 + Missense_Mutation SNP C C G novel C3N-00546_T C3N-00546_N C C c.605G>C p.Gly202Ala p.G202A ENST00000366937 5/8 219 196 23 198 198 0 strelka-varscan-mutect ESRRG,missense_variant,p.Gly174Ala,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000360012,NM_001243514.1;ESRRG,missense_variant,p.Gly202Ala,ENST00000366937,NM_001243518.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000361525,NM_206594.2;ESRRG,missense_variant,p.Gly174Ala,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,missense_variant,p.Gly174Ala,ENST00000493603,NM_001243510.2;ESRRG,missense_variant,p.Gly174Ala,ENST00000366938,NM_001243513.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000361395,;ESRRG,missense_variant,p.Gly197Ala,ENST00000408911,NM_001438.3;ESRRG,missense_variant,p.Gly174Ala,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000616180,;ESRRG,missense_variant,p.Gly135Ala,ENST00000463665,NM_001243507.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000487276,NM_001243512.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000493748,NM_001243509.1;ESRRG,missense_variant,p.Gly174Ala,ENST00000475275,;ESRRG,splice_region_variant,,ENST00000586199,; G ENST00000366937 Transcript missense_variant,splice_region_variant 872/5365 605/1413 202/470 G/A gGg/gCg 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 deleterious(0) 5/8 PROSITE_profiles:PS51030,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PIRSF_domain:PIRSF500939,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,Superfamily_domains:SSF57716,Superfamily_domains:SSF48508,Prints_domain:PR00398 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 216568098 216568098 C G 1 0 0 0 0 1 0 0 0 5124 637 22 4 4 ESRRG 1 216568098 Missense_Mutation SNP C C3N-00546_T 14249080 216568098 32388324 18 14209 PCNX2 0 . GRCh38 1 233054371 233054371 + Silent SNP G G A rs747167792 C3N-00546_T C3N-00546_N G G c.4248C>T p.= p.G1416G ENST00000258229 25/34 549 491 58 465 465 0 strelka-varscan-mutect PCNX2,synonymous_variant,p.=,ENST00000258229,NM_014801.3;PCNX2,synonymous_variant,p.=,ENST00000344698,;PCNX2,synonymous_variant,p.=,ENST00000462233,;PCNX2,non_coding_transcript_exon_variant,,ENST00000429988,; A ENST00000258229 Transcript synonymous_variant 4483/7518 4248/6414 1416/2137 G ggC/ggT rs747167792,COSM4866367,COSM905657 1 -1 PCNX2 HGNC HGNC:8736 protein_coding YES CCDS44335.1 ENSP00000258229 A6NKB5 UPI0000F58F23 NM_014801.3 25/34 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs747167792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 233054371 233054371 G A 1 0 0 0 0 0 0 0 1 11680 1074 38 1 1 PCNX2 1 233054371 Silent SNP G C3N-00546_T 16486273 233054371 15902051 19 14210 ZNF670 0 . GRCh38 1 247038341 247038341 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.278A>G p.Asn93Ser p.N93S ENST00000366503 4/4 295 256 39 259 259 0 strelka-varscan-mutect ZNF670,missense_variant,p.Asn93Ser,ENST00000366503,NM_001204220.1,NM_033213.4;ZNF670-ZNF695,intron_variant,,ENST00000474541,;ZNF670-ZNF695,intron_variant,,ENST00000465049,;RP11-551G24.2,upstream_gene_variant,,ENST00000439523,; C ENST00000366503 Transcript missense_variant 437/1994 278/1170 93/389 N/S aAt/aGt 1 -1 ZNF670 HGNC HGNC:28167 protein_coding YES CCDS31087.1 ENSP00000355459 Q9BS34 UPI0000070EC3 NM_001204220.1,NM_033213.4 tolerated(0.1) 4/4 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF168,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 247038341 247038341 T C 1 0 0 0 0 1 0 0 0 18651 1493 52 5 5 ZNF670 1 247038341 Missense_Mutation SNP T C3N-00546_T 13983970 247038341 1918081 20 14211 OR2G2 0 . GRCh38 1 247588874 247588874 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.515G>T p.Cys172Phe p.C172F ENST00000320065 1/1 187 161 26 196 195 1 strelka-varscan-mutect OR2G2,missense_variant,p.Cys172Phe,ENST00000320065,NM_001001915.1;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; T ENST00000320065 Transcript missense_variant 515/954 515/954 172/317 C/F tGt/tTt 1 1 OR2G2 HGNC HGNC:15007 protein_coding YES CCDS31092.1 ENSP00000326349 Q8NGZ5 UPI0000061EB9 NM_001001915.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF132,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 247588874 247588874 G T 1 0 0 0 0 1 0 0 0 11076 1377 48 2 2 OR2G2 1 247588874 Missense_Mutation SNP G C3N-00546_T 550533 247588874 1367548 21 14212 OR14A2 0 . GRCh38 1 247723212 247723212 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.832G>A p.Val278Met p.V278M ENST00000366485 1/1 318 269 49 291 291 0 strelka-varscan-mutect OR14A2,missense_variant,p.Val278Met,ENST00000366485,;RP11-634B7.5,non_coding_transcript_exon_variant,,ENST00000426444,;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; T ENST00000366485 Transcript missense_variant 832/945 832/945 278/314 V/M Gtg/Atg 1 -1 OR14A2 HGNC HGNC:15024 protein_coding YES ENSP00000355441 Q96R54 A0A126GWG8 UPI000004A5E7 tolerated(0.09) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF346,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 247723212 247723212 C T 1 0 0 0 0 1 0 0 0 11022 478 17 3 3 OR14A2 1 247723212 Missense_Mutation SNP C C3N-00546_T 134338 247723212 1233210 22 14213 TRAPPC12 0 . GRCh38 2 3388030 3388030 + Frame_Shift_Del DEL C C - novel C3N-00546_T C3N-00546_N C C c.409delC p.Arg137AlafsTer44 p.R137Afs*44 ENST00000324266 2/12 64 49 15 106 106 0 sindel-varindel-pindel TRAPPC12,frameshift_variant,p.Arg137AlafsTer44,ENST00000324266,NM_016030.5;TRAPPC12,frameshift_variant,p.Arg137AlafsTer44,ENST00000382110,NM_001321102.1;TRAPPC12,upstream_gene_variant,,ENST00000441983,;TRAPPC12,upstream_gene_variant,,ENST00000457845,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000482645,;TRAPPC12,upstream_gene_variant,,ENST00000411973,; - ENST00000324266 Transcript frameshift_variant 602/2508 407/2208 136/735 A/X gCc/gc 1 1 TRAPPC12 HGNC HGNC:24284 protein_coding YES CCDS1652.1 ENSP00000324318 Q8WVT3 UPI000014132D NM_016030.5 2/12 hmmpanther:PTHR21581,hmmpanther:PTHR21581:SF6 HIGH 1 deletion 1 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 3388030 3388030 C - 1 0 1 0 1 0 0 0 0 16942 739 26 0 0 TRAPPC12 2 3388030 Frame_Shift_Del DEL C C3N-00546_T 3388030 238805499 23 14214 C2orf16 0 . GRCh38 2 27579471 27579471 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.2899C>T p.His967Tyr p.H967Y ENST00000408964 1/1 212 196 16 225 225 0 strelka-mutect C2orf16,missense_variant,p.His967Tyr,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; T ENST00000408964 Transcript missense_variant 2950/6199 2899/5955 967/1984 H/Y Cat/Tat 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 deleterious(0.03) 1/1 hmmpanther:PTHR33888 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 27579471 27579471 C T 1 0 0 0 0 1 0 0 0 2032 826 29 3 3 C2orf16 2 27579471 Missense_Mutation SNP C C3N-00546_T 24191441 27579471 214614058 24 14215 NLRC4 0 . GRCh38 2 32252610 32252610 + Missense_Mutation SNP G G A novel C3N-00546_T C3N-00546_N G G c.71C>T p.Thr24Ile p.T24I ENST00000404025 4/10 364 299 65 320 320 0 strelka-varscan-mutect NLRC4,missense_variant,p.Thr24Ile,ENST00000404025,;NLRC4,missense_variant,p.Thr24Ile,ENST00000360906,NM_001199139.1,NM_021209.4;NLRC4,missense_variant,p.Thr24Ile,ENST00000402280,NM_001199138.1;NLRC4,missense_variant,p.Thr24Ile,ENST00000342905,NM_001302504.1; A ENST00000404025 Transcript missense_variant 560/3581 71/3075 24/1024 T/I aCa/aTa 1 -1 NLRC4 HGNC HGNC:16412 protein_coding YES CCDS33174.1 ENSP00000385090 Q9NPP4 UPI0000126FAD tolerated(0.2) 4/10 PROSITE_profiles:PS50209,hmmpanther:PTHR10044:SF104,hmmpanther:PTHR10044,Pfam_domain:PF00619,Gene3D:1.10.533.10,Superfamily_domains:SSF47986 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 32252610 32252610 G A 1 0 0 0 0 1 0 0 0 10506 1377 48 3 3 NLRC4 2 32252610 Missense_Mutation SNP G C3N-00546_T 4673139 32252610 209940919 25 14216 VIT 0 . GRCh38 2 36754977 36754977 + Missense_Mutation SNP C C A rs777757329 C3N-00546_T C3N-00546_N C C c.332C>A p.Ser111Tyr p.S111Y ENST00000379242 5/16 238 203 35 220 219 1 strelka-varscan-mutect VIT,missense_variant,p.Ser111Tyr,ENST00000379242,NM_053276.3;VIT,missense_variant,p.Ser111Tyr,ENST00000389975,NM_001177969.1;VIT,missense_variant,p.Ser111Tyr,ENST00000379241,NM_001177971.1;VIT,missense_variant,p.Ser89Tyr,ENST00000404084,;VIT,missense_variant,p.Ser111Tyr,ENST00000401530,NM_001177970.1;VIT,missense_variant,p.Ser111Tyr,ENST00000457137,NM_001177972.1;VIT,5_prime_UTR_variant,,ENST00000497382,; A ENST00000379242 Transcript missense_variant 634/2810 332/2082 111/693 S/Y tCt/tAt rs777757329 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 deleterious(0) 5/16 PROSITE_profiles:PS50820,hmmpanther:PTHR11132:SF107,hmmpanther:PTHR11132,Gene3D:1jbiA00,Pfam_domain:PF03815,SMART_domains:SM00603,Superfamily_domains:0039469 MODERATE 1 SNV 2 1 PASS rs777757329 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 36754977 36754977 C A 1 0 0 0 0 1 0 0 0 17718 913 32 2 2 VIT 2 36754977 Missense_Mutation SNP C C3N-00546_T 4502367 36754977 205438552 26 14217 BCL11A 0 . GRCh38 2 60461118 60461118 + Frame_Shift_Del DEL G G - rs200644479 C3N-00546_T C3N-00546_N G G c.1794delC p.Asp598GlufsTer32 p.D598Efs*32 ENST00000335712 4/4 72 58 14 82 82 0 sindel-varindel-pindel BCL11A,frameshift_variant,p.Asp598GlufsTer32,ENST00000335712,NM_022893.3;BCL11A,frameshift_variant,p.Asp598GlufsTer32,ENST00000356842,NM_018014.3;BCL11A,frameshift_variant,p.Asp564GlufsTer32,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,3_prime_UTR_variant,,ENST00000631857,; - ENST00000335712 Transcript frameshift_variant 2022/5942 1794/2508 598/835 D/X gaC/ga rs200644479 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 HIGH 1 deletion 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999963 1 1 1 0 - 7 5 48 60461118 60461118 G - 1 0 1 0 1 0 0 0 0 1510 1136 40 0 0 BCL11A 2 60461118 Frame_Shift_Del DEL G C3N-00546_T 23706141 60461118 181732411 27 14218 ACTR3 0 . GRCh38 2 113940069 113940069 + Silent SNP A A G novel C3N-00546_T C3N-00546_N A A c.651A>G p.= p.P217P ENST00000263238 7/12 177 156 21 280 280 0 strelka-varscan-mutect ACTR3,synonymous_variant,p.=,ENST00000263238,NM_005721.4;ACTR3,synonymous_variant,p.=,ENST00000535589,NM_001277140.1;ACTR3,3_prime_UTR_variant,,ENST00000415792,;ACTR3,3_prime_UTR_variant,,ENST00000446821,;ACTR3,non_coding_transcript_exon_variant,,ENST00000484165,; G ENST00000263238 Transcript synonymous_variant 971/6718 651/1257 217/418 P ccA/ccG 1 1 ACTR3 HGNC HGNC:170 protein_coding YES CCDS33277.1 ENSP00000263238 P61158 A0A024RAI1 UPI000000DA9A NM_005721.4 7/12 Gene3D:3.90.640.10,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF253,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 48 113940069 113940069 A G 1 0 0 0 0 0 0 0 1 255 175 7 5 5 ACTR3 2 113940069 Silent SNP A C3N-00546_T 53478951 113940069 128253460 28 14219 SAP130 0 . GRCh38 2 127955256 127955256 + Missense_Mutation SNP G G A novel C3N-00546_T C3N-00546_N G G c.2230C>T p.Pro744Ser p.P744S ENST00000357702 16/21 141 104 37 131 130 1 strelka-varscan-mutect SAP130,missense_variant,p.Pro744Ser,ENST00000357702,NM_001145928.1;SAP130,missense_variant,p.Pro717Ser,ENST00000259234,;SAP130,missense_variant,p.Pro709Ser,ENST00000259235,NM_024545.3; A ENST00000357702 Transcript missense_variant 2362/4173 2230/3252 744/1083 P/S Cct/Tct 1 -1 SAP130 HGNC HGNC:29813 protein_coding YES CCDS54397.1 ENSP00000350333 Q9H0E3 UPI00005989D6 NM_001145928.1 tolerated_low_confidence(0.25) 16/21 Pfam_domain:PF16014,hmmpanther:PTHR13497,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 127955256 127955256 G A 1 0 0 0 0 1 0 0 0 14091 1203 42 3 3 SAP130 2 127955256 Missense_Mutation SNP G C3N-00546_T 14015187 127955256 114238273 29 14220 ZEB2 0 . GRCh38 2 144399076 144399076 + Missense_Mutation SNP C C G novel C3N-00546_T C3N-00546_N C C c.2111G>C p.Arg704Thr p.R704T ENST00000637267 9/11 172 140 32 174 174 0 strelka-varscan-mutect ZEB2,missense_variant,p.Arg704Thr,ENST00000637267,;ZEB2,missense_variant,p.Arg729Thr,ENST00000636471,;ZEB2,missense_variant,p.Arg704Thr,ENST00000627532,NM_014795.3;ZEB2,missense_variant,p.Arg704Thr,ENST00000636026,;ZEB2,missense_variant,p.Arg592Thr,ENST00000638087,;ZEB2,missense_variant,p.Arg592Thr,ENST00000637304,;ZEB2,missense_variant,p.Arg592Thr,ENST00000638007,;ZEB2,missense_variant,p.Arg592Thr,ENST00000637045,;ZEB2,missense_variant,p.Arg592Thr,ENST00000636413,;ZEB2,missense_variant,p.Arg445Thr,ENST00000638128,;ZEB2,missense_variant,p.Arg704Thr,ENST00000409487,;ZEB2,missense_variant,p.Arg680Thr,ENST00000539609,NM_001171653.1;ZEB2,missense_variant,p.Arg704Thr,ENST00000558170,;ZEB2,missense_variant,p.Arg703Thr,ENST00000303660,;ZEB2,intron_variant,,ENST00000440875,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,upstream_gene_variant,,ENST00000637873,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,3_prime_UTR_variant,,ENST00000636732,;ZEB2,downstream_gene_variant,,ENST00000497268,; G ENST00000637267 Transcript missense_variant 2952/9856 2111/3645 704/1214 R/T aGg/aCg 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 tolerated(0.15) 9/11 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11,Low_complexity_(Seg):seg,SMART_domains:SM00389 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 144399076 144399076 C G 1 0 0 0 0 1 0 0 0 18200 681 24 4 4 ZEB2 2 144399076 Missense_Mutation SNP C C3N-00546_T 16443820 144399076 97794453 30 14221 SRGAP3 0 . GRCh38 3 9058386 9058386 + Silent SNP G G A rs748814269 C3N-00546_T C3N-00546_N G G c.888C>T p.= p.H296H ENST00000383836 7/22 314 259 55 275 275 0 strelka-varscan-mutect SRGAP3,synonymous_variant,p.=,ENST00000383836,NM_014850.3;SRGAP3,synonymous_variant,p.=,ENST00000360413,NM_001033117.2;SRGAP3,synonymous_variant,p.=,ENST00000618999,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000433332,;SRGAP3,downstream_gene_variant,,ENST00000480750,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000485983,;SRGAP3,downstream_gene_variant,,ENST00000470951,; A ENST00000383836 Transcript synonymous_variant 1316/8656 888/3300 296/1099 H caC/caT rs748814269 1 -1 SRGAP3 HGNC HGNC:19744 protein_coding YES CCDS2572.1 ENSP00000373347 O43295 UPI0000074099 NM_014850.3 7/22 PROSITE_profiles:PS51741,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF8,Superfamily_domains:SSF103657 LOW 1 SNV 1 1 PASS rs748814269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 9058386 9058386 G A 1 0 0 0 0 0 0 0 1 15508 1136 40 1 1 SRGAP3 3 9058386 Silent SNP G C3N-00546_T 9058386 189237173 31 14222 SEC22C 0 . GRCh38 3 42555960 42555960 + Silent SNP A A G novel C3N-00546_T C3N-00546_N A A c.681T>C p.= p.F227F ENST00000264454 6/7 161 136 25 174 174 0 strelka-varscan-mutect SEC22C,synonymous_variant,p.=,ENST00000451653,;SEC22C,synonymous_variant,p.=,ENST00000273156,NM_004206.3;SEC22C,synonymous_variant,p.=,ENST00000417572,NM_001201572.1;SEC22C,synonymous_variant,p.=,ENST00000264454,NM_032970.3;SEC22C,synonymous_variant,p.=,ENST00000456515,;SEC22C,intron_variant,,ENST00000423701,NM_001201584.1;SEC22C,3_prime_UTR_variant,,ENST00000449617,; G ENST00000264454 Transcript synonymous_variant 825/1380 681/912 227/303 F ttT/ttC 1 -1 SEC22C HGNC HGNC:16828 protein_coding YES CCDS2700.1 ENSP00000264454 Q9BRL7 A0A024R2N5 UPI000006D0A7 NM_032970.3 6/7 hmmpanther:PTHR21136,hmmpanther:PTHR21136:SF2,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 2 3 48 42555960 42555960 A G 1 0 0 0 0 0 0 0 1 14267 243 9 5 5 SEC22C 3 42555960 Silent SNP A C3N-00546_T 33497574 42555960 155739599 32 14223 NBEAL2 0 . GRCh38 3 46998144 46998144 + Missense_Mutation SNP C C G rs139218926 C3N-00546_T C3N-00546_N C C c.3036C>G p.Ser1012Arg p.S1012R ENST00000450053 21/54 278 238 40 181 181 0 strelka-varscan-mutect NBEAL2,missense_variant,p.Ser1012Arg,ENST00000450053,NM_015175.2;NBEAL2,missense_variant,p.Ser484Arg,ENST00000416683,;NBEAL2,upstream_gene_variant,,ENST00000443829,;NBEAL2,upstream_gene_variant,,ENST00000475689,; G ENST00000450053 Transcript missense_variant 3215/8827 3036/8265 1012/2754 S/R agC/agG rs139218926 1 1 NBEAL2 HGNC HGNC:31928 protein_coding YES CCDS46817.1 ENSP00000415034 Q6ZNJ1 UPI000022C020 NM_015175.2 tolerated(0.05) 21/54 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF50,Pfam_domain:PF15787 MODERATE 1 SNV 2 1 PASS rs139218926 . 0 208 0 0 2 0 0 0 -18.11643 0.9966391 1 1 1 0 G 3 3 48 46998144 46998144 C G 1 0 0 0 0 1 0 0 0 10200 767 27 4 4 NBEAL2 3 46998144 Missense_Mutation SNP C C3N-00546_T 4442184 46998144 151297415 33 14224 SETD2 0 . GRCh38 3 47120985 47120985 + Nonsense_Mutation SNP C C T rs761799105 C3N-00546_T C3N-00546_N C C c.3651G>A p.Trp1217Ter p.W1217* ENST00000409792 3/21 207 170 37 166 166 0 strelka-varscan-mutect SETD2,stop_gained,p.Trp1217Ter,ENST00000409792,NM_014159.6;SETD2,stop_gained,p.Trp1173Ter,ENST00000412450,;SETD2,stop_gained,p.Trp1089Ter,ENST00000330022,;SETD2,stop_gained,p.Trp935Ter,ENST00000431180,;SETD2,stop_gained,p.Trp851Ter,ENST00000445387,; T ENST00000409792 Transcript stop_gained 3694/8142 3651/7695 1217/2564 W/* tgG/tgA rs761799105 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 3/21 HIGH 1 SNV 5 1 PASS rs761799105 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 48 47120985 47120985 C T 1 0 0 0 0 0 1 0 0 14409 740 26 3 3 SETD2 3 47120985 Nonsense_Mutation SNP C C3N-00546_T 122841 47120985 151174574 34 14225 DNAH1 0 . GRCh38 3 52384960 52384960 + Nonsense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.8497A>T p.Lys2833Ter p.K2833* ENST00000420323 53/78 126 103 23 112 112 0 strelka-varscan-mutect DNAH1,stop_gained,p.Lys2833Ter,ENST00000420323,NM_015512.4;DNAH1,upstream_gene_variant,,ENST00000480649,;DNAH1,non_coding_transcript_exon_variant,,ENST00000486752,;DNAH1,non_coding_transcript_exon_variant,,ENST00000488988,;DNAH1,upstream_gene_variant,,ENST00000490713,; T ENST00000420323 Transcript stop_gained 8758/13104 8497/12798 2833/4265 K/* Aag/Tag 1 1 DNAH1 HGNC HGNC:2940 protein_coding YES CCDS46842.1 ENSP00000401514 Q9P2D7 A0A140VJI6 UPI00017EE9F6 NM_015512.4 53/78 Pfam_domain:PF12777,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF137 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 48 52384960 52384960 A T 1 0 0 0 0 0 1 0 0 4410 247 9 4 4 DNAH1 3 52384960 Nonsense_Mutation SNP A C3N-00546_T 5263975 52384960 145910599 35 14226 PDZRN3 0 . GRCh38 3 73404293 73404293 + Missense_Mutation SNP T T A novel C3N-00546_T C3N-00546_N T T c.1021A>T p.Arg341Trp p.R341W ENST00000263666 4/10 301 265 36 302 302 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Arg341Trp,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Arg58Trp,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Arg39Trp,ENST00000492909,NM_001303139.1;PDZRN3,5_prime_UTR_variant,,ENST00000462146,NM_001303141.1;PDZRN3,5_prime_UTR_variant,,ENST00000466780,NM_001303140.1;PDZRN3,upstream_gene_variant,,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000308537,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000498048,;PDZRN3,upstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000477434,;PDZRN3,upstream_gene_variant,,ENST00000484487,; A ENST00000263666 Transcript missense_variant 1136/4248 1021/3201 341/1066 R/W Agg/Tgg 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 tolerated(0.13) 4/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Gene3D:2.30.42.10,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 73404293 73404293 T A 1 0 0 0 0 1 0 0 0 11797 1608 56 4 4 PDZRN3 3 73404293 Missense_Mutation SNP T C3N-00546_T 21019333 73404293 124891266 36 14227 EPHA3 0 . GRCh38 3 89413173 89413173 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.1795C>A p.Pro599Thr p.P599T ENST00000336596 10/17 303 247 56 304 303 1 strelka-varscan-mutect EPHA3,missense_variant,p.Pro599Thr,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.Pro599Thr,ENST00000494014,; A ENST00000336596 Transcript missense_variant 2020/5809 1795/2952 599/983 P/T Cca/Aca 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 deleterious(0.01) 10/17 hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Gene3D:3.30.200.20,Pfam_domain:PF14575 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 89413173 89413173 C A 1 0 0 0 0 1 0 0 0 5015 623 22 2 2 EPHA3 3 89413173 Missense_Mutation SNP C C3N-00546_T 16008880 89413173 108882386 37 14228 AC026348.1 0 . GRCh38 3 113341877 113341877 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.3304G>T p.Gly1102Trp p.G1102W ENST00000393845 23/34 179 148 31 289 289 0 strelka-varscan-mutect AC026348.1,missense_variant,p.Gly1102Trp,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Gly239Trp,ENST00000465636,;CFAP44,missense_variant,p.Arg114Met,ENST00000490481,; A ENST00000393845 Transcript missense_variant 3304/5565 3304/5565 1102/1854 G/W Ggg/Tgg 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 deleterious(0.02) 23/34 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 113341877 113341877 C A 1 0 0 0 0 1 0 0 0 128 681 24 2 2 AC026348.1 3 113341877 Missense_Mutation SNP C C3N-00546_T 23928704 113341877 84953682 38 14229 XRN1 0 . GRCh38 3 142425523 142425523 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.422C>G p.Ala141Gly p.A141G ENST00000264951 4/42 155 134 21 160 160 0 strelka-varscan-mutect XRN1,missense_variant,p.Ala141Gly,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Ala141Gly,ENST00000392981,NM_001282857.1;XRN1,missense_variant,p.Ala141Gly,ENST00000463916,NM_001282859.1;XRN1,missense_variant,p.Ala2Gly,ENST00000477237,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,;XRN1,intron_variant,,ENST00000486211,;XRN1,downstream_gene_variant,,ENST00000470537,; C ENST00000264951 Transcript missense_variant 540/10143 422/5121 141/1706 A/G gCc/gGc 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 deleterious(0.03) 4/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341,Pfam_domain:PF03159 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 142425523 142425523 G C 1 0 0 0 0 1 0 0 0 18017 1203 42 4 4 XRN1 3 142425523 Missense_Mutation SNP G C3N-00546_T 29083646 142425523 55870036 39 14230 SI 0 . GRCh38 3 165037978 165037978 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.2348C>G p.Pro783Arg p.P783R ENST00000264382 21/48 364 297 67 352 352 0 strelka-varscan-mutect SI,missense_variant,p.Pro783Arg,ENST00000264382,NM_001041.3; C ENST00000264382 Transcript missense_variant 2411/6011 2348/5484 783/1827 P/R cCa/cGa 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 21/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF01055,Superfamily_domains:SSF51011 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 165037978 165037978 G C 1 0 0 0 0 1 0 0 0 14561 1348 47 4 4 SI 3 165037978 Missense_Mutation SNP G C3N-00546_T 22612455 165037978 33257581 40 14231 TBL1XR1 0 . GRCh38 3 177051686 177051686 + Missense_Mutation SNP G G A novel C3N-00546_T C3N-00546_N G G c.245C>T p.Ser82Phe p.S82F ENST00000430069 5/16 203 172 31 204 203 1 strelka-mutect TBL1XR1,missense_variant,p.Ser82Phe,ENST00000430069,NM_001321193.1,NM_001321194.1,NM_001321195.1;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000457928,NM_024665.4;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000635794,;TBL1XR1,missense_variant,p.Ser79Phe,ENST00000630796,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000352800,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000422066,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000450267,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000626672,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000630833,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000437738,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000431674,;TBL1XR1,5_prime_UTR_variant,,ENST00000424913,;TBL1XR1,5_prime_UTR_variant,,ENST00000428970,;TBL1XR1,5_prime_UTR_variant,,ENST00000431421,;TBL1XR1,downstream_gene_variant,,ENST00000413084,;TBL1XR1,downstream_gene_variant,,ENST00000443315,;TBL1XR1,downstream_gene_variant,,ENST00000422442,;TBL1XR1,downstream_gene_variant,,ENST00000427349,;TBL1XR1-AS1,downstream_gene_variant,,ENST00000617758,;TBL1XR1-AS1,downstream_gene_variant,,ENST00000454723,;TBL1XR1,downstream_gene_variant,,ENST00000627825,;TBL1XR1,missense_variant,p.Ser82Phe,ENST00000631253,;TBL1XR1,upstream_gene_variant,,ENST00000637659,; A ENST00000430069 Transcript missense_variant 505/7948 245/1545 82/514 S/F tCc/tTc 1 -1 TBL1XR1 HGNC HGNC:29529 protein_coding YES CCDS46961.1 ENSP00000405574 Q9BZK7 UPI0000136A71 NM_001321193.1,NM_001321194.1,NM_001321195.1 deleterious(0) 5/16 hmmpanther:PTHR22846,hmmpanther:PTHR22846:SF40 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 177051686 177051686 G A 1 0 0 0 0 1 0 0 0 16045 1174 41 3 3 TBL1XR1 3 177051686 Missense_Mutation SNP G C3N-00546_T 12013708 177051686 21243873 41 14232 CWH43 0 . GRCh38 4 49007303 49007303 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.1163A>T p.Lys388Met p.K388M ENST00000226432 8/16 102 85 17 163 163 0 strelka-varscan-mutect CWH43,missense_variant,p.Lys388Met,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Lys361Met,ENST00000513409,NM_001286791.1;CWH43,3_prime_UTR_variant,,ENST00000514053,;CWH43,non_coding_transcript_exon_variant,,ENST00000506221,; T ENST00000226432 Transcript missense_variant 1346/2472 1163/2100 388/699 K/M aAg/aTg 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.03) 8/16 hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 49007303 49007303 A T 1 0 0 0 0 1 0 0 0 3883 72 3 4 4 CWH43 4 49007303 Missense_Mutation SNP A C3N-00546_T 49007303 141207252 42 14233 KDR 0 . GRCh38 4 55104946 55104946 + Missense_Mutation SNP T T A novel C3N-00546_T C3N-00546_N T T c.1684A>T p.Thr562Ser p.T562S ENST00000263923 13/30 250 203 47 220 220 0 strelka-varscan-mutect KDR,missense_variant,p.Thr562Ser,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; A ENST00000263923 Transcript missense_variant 1980/5831 1684/4071 562/1356 T/S Act/Tct 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0.02) 13/30 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 55104946 55104946 T A 1 0 0 0 0 1 0 0 0 8059 1696 59 4 4 KDR 4 55104946 Missense_Mutation SNP T C3N-00546_T 6097643 55104946 135109609 43 14234 LIN54 0 . GRCh38 4 82984409 82984409 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.436G>T p.Gly146Cys p.G146C ENST00000340417 2/13 217 171 46 262 262 0 strelka-varscan-mutect LIN54,missense_variant,p.Gly146Cys,ENST00000340417,NM_194282.3;LIN54,missense_variant,p.Gly146Cys,ENST00000506560,NM_001288996.1;LIN54,missense_variant,p.Gly146Cys,ENST00000505397,;LIN54,intron_variant,,ENST00000442461,NM_001115008.2;LIN54,intron_variant,,ENST00000446851,NM_001288997.1;LIN54,intron_variant,,ENST00000510557,NM_001115007.2;LIN54,non_coding_transcript_exon_variant,,ENST00000509748,;LIN54,missense_variant,p.Gly146Cys,ENST00000508171,;LIN54,intron_variant,,ENST00000510877,; A ENST00000340417 Transcript missense_variant 814/6127 436/2250 146/749 G/C Ggc/Tgc 1 -1 LIN54 HGNC HGNC:25397 protein_coding YES CCDS3599.1 ENSP00000341947 Q6MZP7 A0A024RDD8 UPI00001D75DE NM_194282.3 deleterious(0) 2/13 hmmpanther:PTHR12446,hmmpanther:PTHR12446:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 82984409 82984409 C A 1 0 0 0 0 1 0 0 0 8717 623 22 2 2 LIN54 4 82984409 Missense_Mutation SNP C C3N-00546_T 27879463 82984409 107230146 44 14235 SYNPO2 0 . GRCh38 4 119057618 119057618 + Missense_Mutation SNP T T A rs767516054 C3N-00546_T C3N-00546_N T T c.3470T>A p.Val1157Glu p.V1157E ENST00000307142 5/5 176 143 33 197 197 0 strelka-varscan-mutect SYNPO2,missense_variant,p.Val1157Glu,ENST00000307142,NM_133477.2;SYNPO2,missense_variant,p.Val1051Glu,ENST00000504178,;SYNPO2,missense_variant,p.Val1126Glu,ENST00000610556,NM_001286754.1;SYNPO2,3_prime_UTR_variant,,ENST00000448416,NM_001286755.1; A ENST00000307142 Transcript missense_variant 3666/7295 3470/3786 1157/1261 V/E gTg/gAg rs767516054 1 1 SYNPO2 HGNC HGNC:17732 protein_coding YES CCDS34054.1 ENSP00000306015 Q9UMS6 UPI00001D75EB NM_133477.2 deleterious(0.01) 5/5 MODERATE 1 SNV 1 1 PASS rs767516054 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 119057618 119057618 T A 1 0 0 0 0 1 0 0 0 15851 1696 59 4 4 SYNPO2 4 119057618 Missense_Mutation SNP T C3N-00546_T 36073209 119057618 71156937 45 14236 DDX60 0 . GRCh38 4 168255765 168255766 + Frame_Shift_Ins INS - - CATG novel C3N-00546_T C3N-00546_N - - c.3499_3502dupCATG p.Val1168AlafsTer5 p.V1168Afs*5 ENST00000393743 26/38 124 97 27 196 196 0 sindel-varindel-pindel DDX60,frameshift_variant,p.Val1168AlafsTer5,ENST00000393743,NM_017631.5;DDX60,non_coding_transcript_exon_variant,,ENST00000505393,; CATG ENST00000393743 Transcript frameshift_variant 3794-3795/6071 3502-3503/5139 1168/1712 V/ACX gtc/gCATGtc 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 26/38 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 CATG 7 5 48 168255765 168255765 - CATG 1 0 1 1 0 0 0 0 0 4181 275 10 0 0 DDX60 4 168255765 Frame_Shift_Ins INS - C3N-00546_T 49198147 168255765 21958790 46 14237 ADAMTS16 0 . GRCh38 5 5242191 5242191 + Nonsense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.2662G>T p.Gly888Ter p.G888* ENST00000274181 17/23 196 181 15 111 111 0 strelka-varscan-mutect ADAMTS16,stop_gained,p.Gly888Ter,ENST00000274181,NM_139056.2;ADAMTS16,downstream_gene_variant,,ENST00000513709,;ADAMTS16,splice_region_variant,,ENST00000433402,; T ENST00000274181 Transcript stop_gained,splice_region_variant 2800/4979 2662/3675 888/1224 G/* Gga/Tga 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 17/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,SMART_domains:SM00209 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 48 5242191 5242191 G T 1 0 0 0 0 0 1 0 0 305 1246 43 2 2 ADAMTS16 5 5242191 Nonsense_Mutation SNP G C3N-00546_T 5242191 176296068 47 14238 FTMT 0 . GRCh38 5 121851992 121851992 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.29G>T p.Arg10Met p.R10M ENST00000321339 1/1 156 131 25 141 141 0 strelka-varscan-mutect FTMT,missense_variant,p.Arg10Met,ENST00000321339,NM_177478.1; T ENST00000321339 Transcript missense_variant 38/879 29/729 10/242 R/M aGg/aTg 1 1 FTMT HGNC HGNC:17345 protein_coding YES CCDS4128.1 ENSP00000313691 Q8N4E7 UPI000006F87E NM_177478.1 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS rs1195599491 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 121851992 121851992 G T 1 0 0 0 0 1 0 0 0 5959 1000 35 2 2 FTMT 5 121851992 Missense_Mutation SNP G C3N-00546_T 116609801 121851992 59686267 48 14239 ATP10B 0 . GRCh38 5 160607088 160607088 + Splice_Site SNP T T C novel C3N-00546_T C3N-00546_N T T c.2839-2A>G p.X947_splice ENST00000327245 124 98 26 145 145 0 strelka-varscan-mutect ATP10B,splice_acceptor_variant,,ENST00000327245,NM_025153.2;ATP10B,upstream_gene_variant,,ENST00000523758,;ATP10B,downstream_gene_variant,,ENST00000522169,;ATP10B,upstream_gene_variant,,ENST00000517815,; C ENST00000327245 Transcript splice_acceptor_variant -/7566 2839/4386 947/1461 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 18/25 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 48 160607088 160607088 T C 1 0 0 0 0 0 0 1 0 1269 1536 53 5 5 ATP10B 5 160607088 Splice_Site SNP T C3N-00546_T 38755096 160607088 20931171 49 14240 TENM2 0 . GRCh38 5 168125013 168125013 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.2172C>A p.Ser724Arg p.S724R ENST00000518659 11/29 307 258 49 272 272 0 strelka-mutect TENM2,missense_variant,p.Ser603Arg,ENST00000519204,;TENM2,missense_variant,p.Ser724Arg,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Ser492Arg,ENST00000520394,;CTB-178M22.1,intron_variant,,ENST00000517408,;CTB-105N12.2,upstream_gene_variant,,ENST00000624423,; A ENST00000518659 Transcript missense_variant 2211/8550 2172/8325 724/2774 S/R agC/agA 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 tolerated(0.4) 11/29 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,PROSITE_patterns:PS00022,Gene3D:2gy5A03,SMART_domains:SM00181 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 168125013 168125013 C A 1 0 0 0 0 1 0 0 0 16172 796 28 2 2 TENM2 5 168125013 Missense_Mutation SNP C C3N-00546_T 7517925 168125013 13413246 50 14241 SLIT3 0 . GRCh38 5 168753941 168753941 + Silent SNP C C T novel C3N-00546_T C3N-00546_N C C c.1752G>A p.= p.Q584Q ENST00000332966 17/36 218 200 18 171 171 0 strelka-varscan-mutect SLIT3,synonymous_variant,p.=,ENST00000519560,NM_003062.3;SLIT3,synonymous_variant,p.=,ENST00000404867,;SLIT3,synonymous_variant,p.=,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000519486,; T ENST00000332966 Transcript synonymous_variant 1825/4895 1752/4593 584/1530 Q caG/caA 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 17/36 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00368,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99971 0.9999998 1 1 1 0 T 2 4 48 168753941 168753941 C T 1 0 0 0 0 0 0 0 1 15032 680 24 3 3 SLIT3 5 168753941 Silent SNP C C3N-00546_T 628928 168753941 12784318 51 14242 FLT4 0 . GRCh38 5 180620660 180620660 + Silent SNP G G A novel C3N-00546_T C3N-00546_N G G c.2355C>T p.= p.I785I ENST00000261937 16/30 464 378 86 355 355 0 strelka-varscan-mutect FLT4,synonymous_variant,p.=,ENST00000261937,NM_182925.4;FLT4,synonymous_variant,p.=,ENST00000393347,NM_002020.4;FLT4,synonymous_variant,p.=,ENST00000502649,;FLT4,3_prime_UTR_variant,,ENST00000619105,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; A ENST00000261937 Transcript synonymous_variant 2434/5857 2355/4092 785/1363 I atC/atT 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 16/30 Transmembrane_helices:TMhelix,hmmpanther:PTHR24416:SF49,hmmpanther:PTHR24416 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 180620660 180620660 G A 1 0 0 0 0 0 0 0 1 5800 1048 37 1 1 FLT4 5 180620660 Silent SNP G C3N-00546_T 11866719 180620660 917599 52 14243 CUL9 0 . GRCh38 6 43187070 43187070 + Silent SNP G G A novel C3N-00546_T C3N-00546_N G G c.1362G>A p.= p.G454G ENST00000252050 5/41 133 104 29 162 162 0 strelka-varscan-mutect CUL9,synonymous_variant,p.=,ENST00000252050,NM_015089.3;CUL9,synonymous_variant,p.=,ENST00000372647,;CUL9,non_coding_transcript_exon_variant,,ENST00000515773,;CUL9,non_coding_transcript_exon_variant,,ENST00000510282,;CUL9,intron_variant,,ENST00000451399,; A ENST00000252050 Transcript synonymous_variant 1446/7780 1362/7554 454/2517 G ggG/ggA 1 1 CUL9 HGNC HGNC:15982 protein_coding YES CCDS4890.1 ENSP00000252050 Q8IWT3 UPI000006F22F NM_015089.3 5/41 hmmpanther:PTHR22771:SF2,hmmpanther:PTHR22771 LOW 1 SNV 5 1 PASS rs1200006447 . 0 206 0 3 0 0 0 0 -20 0.9999969 1 1 1 0 A 2 1 48 43187070 43187070 G A 1 0 0 0 0 0 0 0 1 3871 1219 43 3 3 CUL9 6 43187070 Silent SNP G C3N-00546_T 43187070 127618909 53 14244 DST 0 . GRCh38 6 56492337 56492338 + Frame_Shift_Ins INS - - A novel C3N-00546_T C3N-00546_N - - c.13875dupT p.Val4626CysfsTer30 p.V4626Cfs*30 ENST00000312431 77/95 221 182 39 424 424 0 sindel-varindel-pindel DST,frameshift_variant,p.Val6563CysfsTer30,ENST00000361203,;DST,frameshift_variant,p.Val4586CysfsTer30,ENST00000421834,NM_183380.3;DST,frameshift_variant,p.Val4626CysfsTer30,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,frameshift_variant,p.Val4477CysfsTer30,ENST00000370788,;DST,frameshift_variant,p.Val4260CysfsTer30,ENST00000244364,NM_015548.4;DST,downstream_gene_variant,,ENST00000340834,;DST,upstream_gene_variant,,ENST00000487754,;DST,downstream_gene_variant,,ENST00000459869,; A ENST00000312431 Transcript frameshift_variant 14001-14002/17756 13875-13876/16614 4625-4626/5537 -/X -/T 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 77/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 48 56492337 56492337 - A 1 0 1 1 0 0 0 0 0 4604 478 17 0 0 DST 6 56492337 Frame_Shift_Ins INS - C3N-00546_T 13305267 56492337 114313642 54 14245 INTS1 0 . GRCh38 7 1486637 1486637 + Silent SNP C C T novel C3N-00546_T C3N-00546_N C C c.2964G>A p.= p.V988V ENST00000404767 22/48 221 189 32 100 100 0 strelka-varscan-mutect INTS1,synonymous_variant,p.=,ENST00000404767,NM_001080453.2;INTS1,non_coding_transcript_exon_variant,,ENST00000468115,; T ENST00000404767 Transcript synonymous_variant 3050/6959 2964/6573 988/2190 V gtG/gtA 1 -1 INTS1 HGNC HGNC:24555 protein_coding YES CCDS47526.1 ENSP00000385722 Q8N201 UPI0000D7211C NM_001080453.2 22/48 hmmpanther:PTHR21224:SF1,hmmpanther:PTHR21224 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 1486637 1486637 C T 1 0 0 0 0 0 0 0 1 7677 697 25 3 3 INTS1 7 1486637 Silent SNP C C3N-00546_T 1486637 157859336 55 14246 AIMP2 0 . GRCh38 7 6017901 6017901 + Missense_Mutation SNP G G A C3N-00546_T C3N-00546_N G G c.430G>A p.Glu144Lys p.E144K ENST00000223029 3/4 463 256 207 320 319 1 strelka-varscan-mutect AIMP2,missense_variant,p.Glu144Lys,ENST00000223029,NM_006303.3;AIMP2,missense_variant,p.Glu66Lys,ENST00000400479,;AIMP2,missense_variant,p.Glu75Lys,ENST00000395236,;EIF2AK1,downstream_gene_variant,,ENST00000199389,NM_001134335.1,NM_014413.3;SNORA42,downstream_gene_variant,,ENST00000384488,;AIMP2,downstream_gene_variant,,ENST00000415999,; A ENST00000223029 Transcript missense_variant 549/1225 430/963 144/320 E/K Gag/Aag COSM5113509 1 1 AIMP2 HGNC HGNC:20609 protein_coding YES CCDS5344.1 ENSP00000223029 Q13155 A0A024QZY1 UPI000012ED59 NM_006303.3 tolerated(0.13) 3/4 hmmpanther:PTHR13438,hmmpanther:PTHR13438:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 6017901 6017901 G A 1 0 0 0 0 1 0 0 0 511 1291 45 3 3 AIMP2 7 6017901 Missense_Mutation SNP G C3N-00546_T 4531264 6017901 153328072 56 14247 YAE1D1 0 . GRCh38 7 39570609 39570609 + Missense_Mutation SNP G G A rs766403561 C3N-00546_T C3N-00546_N G G c.233G>A p.Arg78Gln p.R78Q ENST00000223273 2/3 121 114 7 116 116 0 strelka-varscan-mutect YAE1D1,missense_variant,p.Arg78Gln,ENST00000432096,NM_001282446.1;YAE1D1,missense_variant,p.Arg78Gln,ENST00000223273,NM_020192.4;YAE1D1,missense_variant,p.Arg78Gln,ENST00000448268,;AC011290.4,upstream_gene_variant,,ENST00000439751,;YAE1D1,downstream_gene_variant,,ENST00000469737,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000485025,;YAE1D1,non_coding_transcript_exon_variant,,ENST00000474392,;AC011290.5,upstream_gene_variant,,ENST00000438427,; A ENST00000223273 Transcript missense_variant 276/899 233/681 78/226 R/Q cGa/cAa rs766403561,COSM5233871,COSM601114 1 1 YAE1D1 HGNC HGNC:24857 protein_coding YES CCDS5459.1 ENSP00000223273 Q9NRH1 UPI0000074023 NM_020192.4 tolerated(1) 2/3 Pfam_domain:PF09811,hmmpanther:PTHR18829,hmmpanther:PTHR18829:SF0 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766403561 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 39570609 39570609 G A 1 0 0 0 0 1 0 0 0 18024 1058 37 1 1 YAE1D1 7 39570609 Missense_Mutation SNP G C3N-00546_T 33552708 39570609 119775364 57 14248 EGFR 0 . GRCh38 7 55174014 55174014 + Missense_Mutation SNP G G A rs28929495 C3N-00546_T C3N-00546_N G G c.2155G>A p.Gly719Ser p.G719S ENST00000275493 18/28 609 353 256 368 368 0 strelka-varscan-mutect EGFR,missense_variant,p.Gly719Ser,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Gly674Ser,ENST00000454757,;EGFR,missense_variant,p.Gly674Ser,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1; A ENST00000275493 Transcript missense_variant 2332/9821 2155/3633 719/1210 G/S Ggc/Agc rs28929495,COSM6252,COSM6253 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 18/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 likely_pathogenic,pathogenic,drug_response 0,1,1 1795663724712396 MODERATE 1 SNV 1 1,1,1 1 PASS rs28929495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 55174014 55174014 G A 1 0 0 0 0 1 0 0 0 4803 1232 43 3 3 EGFR 7 55174014 Missense_Mutation SNP G C3N-00546_T 15603405 55174014 104171959 58 14249 EGFR 0 . GRCh38 7 55181312 55181312 + Missense_Mutation SNP G G T rs121913465 C3N-00546_T C3N-00546_N G G c.2303G>T p.Ser768Ile p.S768I ENST00000275493 20/28 399 225 174 262 262 0 strelka-varscan-mutect EGFR,missense_variant,p.Ser768Ile,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Ser723Ile,ENST00000454757,;EGFR,missense_variant,p.Ser723Ile,ENST00000455089,;EGFR-AS1,non_coding_transcript_exon_variant,,ENST00000442411,; T ENST00000275493 Transcript missense_variant 2480/9821 2303/3633 768/1210 S/I aGc/aTc rs121913465,COSM12989,COSM291998,COSM6241 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 20/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs146024686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 55181312 55181312 G T 1 0 0 0 0 1 0 0 0 4803 971 34 2 2 EGFR 7 55181312 Missense_Mutation SNP G C3N-00546_T 7298 55181312 104164661 59 14250 CADPS2 0 . GRCh38 7 122491380 122491380 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.1583A>G p.Lys528Arg p.K528R ENST00000449022 10/30 190 99 91 183 183 0 strelka-varscan-mutect CADPS2,missense_variant,p.Lys528Arg,ENST00000615869,;CADPS2,missense_variant,p.Lys422Arg,ENST00000313070,NM_001167940.1;CADPS2,missense_variant,p.Lys528Arg,ENST00000334010,;CADPS2,missense_variant,p.Lys528Arg,ENST00000412584,NM_001009571.3;CADPS2,missense_variant,p.Lys528Arg,ENST00000449022,NM_017954.10;CADPS2,missense_variant,p.Lys177Arg,ENST00000397721,;CADPS2,downstream_gene_variant,,ENST00000476131,; C ENST00000449022 Transcript missense_variant 1603/4073 1583/3891 528/1296 K/R aAg/aGg 1 -1 CADPS2 HGNC HGNC:16018 protein_coding YES CCDS55158.1 ENSP00000398481 Q86UW7 UPI0000668808 NM_017954.10 tolerated(0.3) 10/30 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR12166,hmmpanther:PTHR12166:SF7,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 122491380 122491380 T C 1 0 0 0 0 1 0 0 0 2261 1609 56 5 5 CADPS2 7 122491380 Missense_Mutation SNP T C3N-00546_T 67310068 122491380 36854593 60 14251 KMT2C 0 . GRCh38 7 152224495 152224495 + Missense_Mutation SNP T T A novel C3N-00546_T C3N-00546_N T T c.3098A>T p.His1033Leu p.H1033L ENST00000262189 19/59 262 133 129 184 184 0 strelka-varscan-mutect KMT2C,missense_variant,p.His1033Leu,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.His1033Leu,ENST00000355193,;KMT2C,missense_variant,p.His189Leu,ENST00000418673,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,;KMT2C,upstream_gene_variant,,ENST00000489110,; A ENST00000262189 Transcript missense_variant 3317/16862 3098/14736 1033/4911 H/L cAc/cTc 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 deleterious(0.02) 19/59 PROSITE_profiles:PS50016,hmmpanther:PTHR22884:SF373,hmmpanther:PTHR22884,Gene3D:3.30.40.10,Pfam_domain:PF00628,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 152224495 152224495 T A 1 0 0 0 0 1 0 0 0 8297 1696 59 4 4 KMT2C 7 152224495 Missense_Mutation SNP T C3N-00546_T 29733115 152224495 7121478 61 14252 NEFM 0 . GRCh38 8 24918195 24918195 + Missense_Mutation SNP G G C C3N-00546_T C3N-00546_N G G c.2340G>C p.Glu780Asp p.E780D ENST00000221166 3/3 255 188 67 252 252 0 strelka-varscan-mutect NEFM,missense_variant,p.Glu780Asp,ENST00000221166,NM_005382.2;NEFM,missense_variant,p.Glu741Asp,ENST00000437366,;NEFM,missense_variant,p.Glu404Asp,ENST00000433454,NM_001105541.1;NEFM,intron_variant,,ENST00000518131,;GS1-72M22.1,upstream_gene_variant,,ENST00000607058,;NEFM,intron_variant,,ENST00000521540,;NEFM,downstream_gene_variant,,ENST00000523467,; C ENST00000221166 Transcript missense_variant 3122/4020 2340/2751 780/916 E/D gaG/gaC COSM4536743 1 1 NEFM HGNC HGNC:7734 protein_coding YES CCDS6046.1 ENSP00000221166 P07197 UPI000013C7A9 NM_005382.2 deleterious_low_confidence(0.02) 3/3 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 24918195 24918195 G C 1 0 0 0 0 1 0 0 0 10344 991 35 4 4 NEFM 8 24918195 Missense_Mutation SNP G C3N-00546_T 24918195 120220441 62 14253 CPNE3 0 . GRCh38 8 86540272 86540272 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.571T>C p.Trp191Arg p.W191R ENST00000517490 8/17 160 142 18 137 137 0 strelka-varscan-mutect CPNE3,missense_variant,p.Trp191Arg,ENST00000517490,NM_003909.4;CPNE3,missense_variant,p.Trp191Arg,ENST00000621783,;CPNE3,missense_variant,p.Trp80Arg,ENST00000517391,;CPNE3,upstream_gene_variant,,ENST00000517862,; C ENST00000517490 Transcript missense_variant 734/4865 571/1614 191/537 W/R Tgg/Cgg 1 1 CPNE3 HGNC HGNC:2316 protein_coding YES CCDS6243.1 ENSP00000477590 O75131 A0A024R994 UPI0000127C13 NM_003909.4 deleterious(0) 8/17 PROSITE_profiles:PS50004,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF22,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 86540272 86540272 T C 1 0 0 0 0 1 0 0 0 3608 1812 63 5 5 CPNE3 8 86540272 Missense_Mutation SNP T C3N-00546_T 61622077 86540272 58598364 63 14254 KCNV1 0 . GRCh38 8 109968408 109968408 + Missense_Mutation SNP A A G novel C3N-00546_T C3N-00546_N A A c.1183T>C p.Tyr395His p.Y395H ENST00000524391 4/4 164 103 61 138 138 0 strelka-varscan-mutect KCNV1,missense_variant,p.Tyr395His,ENST00000524391,;KCNV1,missense_variant,p.Tyr395His,ENST00000297404,NM_014379.2; G ENST00000524391 Transcript missense_variant 2216/6979 1183/1503 395/500 Y/H Tat/Cat 1 -1 KCNV1 HGNC HGNC:18861 protein_coding YES CCDS6314.1 ENSP00000435954 Q6PIU1 UPI0000073DA5 deleterious(0) 4/4 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF38,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 109968408 109968408 A G 1 0 0 0 0 1 0 0 0 8010 449 16 5 5 KCNV1 8 109968408 Missense_Mutation SNP A C3N-00546_T 23428136 109968408 35170228 64 14255 CSMD3 0 . GRCh38 8 112645123 112645123 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.3296T>A p.Val1099Glu p.V1099E ENST00000297405 20/71 452 381 71 409 409 0 strelka-varscan-mutect CSMD3,missense_variant,p.Val1099Glu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Val1059Glu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Val995Glu,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Val439Glu,ENST00000339701,;MIR2053,downstream_gene_variant,,ENST00000459295,; T ENST00000297405 Transcript missense_variant 3541/13212 3296/11124 1099/3707 V/E gTa/gAa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 20/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 112645123 112645123 A T 1 0 0 0 0 1 0 0 0 3747 391 14 4 4 CSMD3 8 112645123 Missense_Mutation SNP A C3N-00546_T 2676715 112645123 32493513 65 14256 TG 0 . GRCh38 8 132967873 132967873 + Frame_Shift_Del DEL C C - novel C3N-00546_T C3N-00546_N C C c.5768delC p.Pro1923GlnfsTer19 p.P1923Qfs*19 ENST00000220616 31/48 611 544 67 364 364 0 sindel-varindel-pindel TG,frameshift_variant,p.Pro1923GlnfsTer19,ENST00000220616,NM_003235.4;TG,frameshift_variant,p.Pro379GlnfsTer19,ENST00000519178,;TG,frameshift_variant,p.Pro77GlnfsTer19,ENST00000519543,;TG,frameshift_variant,p.Pro55GlnfsTer?,ENST00000518058,;TG,upstream_gene_variant,,ENST00000522523,;TG,upstream_gene_variant,,ENST00000524151,;TG,upstream_gene_variant,,ENST00000520197,;TG,upstream_gene_variant,,ENST00000519294,;TG,3_prime_UTR_variant,,ENST00000523756,;TG,upstream_gene_variant,,ENST00000520089,;TG,upstream_gene_variant,,ENST00000522797,; - ENST00000220616 Transcript frameshift_variant 5806/8450 5766/8307 1922/2768 Y/X taC/ta 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 31/48 PIRSF_domain:PIRSF001831 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 132967873 132967873 C - 1 0 1 0 1 0 0 0 0 16246 518 18 0 0 TG 8 132967873 Frame_Shift_Del DEL C C3N-00546_T 20322750 132967873 12170763 66 14257 WDR97 0 . GRCh38 8 144115721 144115721 + Silent SNP G G T novel C3N-00546_T C3N-00546_N G G c.4458G>T p.= p.A1486A ENST00000323662 22/24 178 130 48 135 135 0 strelka-varscan-mutect WDR97,synonymous_variant,p.=,ENST00000323662,;WDR97,downstream_gene_variant,,ENST00000533108,;WDR97,3_prime_UTR_variant,,ENST00000534167,;WDR97,non_coding_transcript_exon_variant,,ENST00000528691,;WDR97,non_coding_transcript_exon_variant,,ENST00000525150,;WDR97,non_coding_transcript_exon_variant,,ENST00000529209,; T ENST00000323662 Transcript synonymous_variant 4483/6916 4458/4869 1486/1622 A gcG/gcT 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 22/24 LOW 1 SNV 5 1 PASS rs988078017 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 144115721 144115721 G T 1 0 0 0 0 0 0 0 1 17897 1074 38 1 1 WDR97 8 144115721 Silent SNP G C3N-00546_T 11147848 144115721 1022915 67 14258 CNTNAP3B 0 . GRCh38 9 41929335 41929335 + Silent SNP G G A novel C3N-00546_T C3N-00546_N G G c.2347C>T p.= p.L783L ENST00000377561 15/24 230 157 73 168 168 0 strelka-varscan-mutect CNTNAP3B,synonymous_variant,p.=,ENST00000612828,;CNTNAP3B,synonymous_variant,p.=,ENST00000377561,NM_001201380.2;CNTNAP3B,synonymous_variant,p.=,ENST00000489789,;CNTNAP3B,synonymous_variant,p.=,ENST00000619138,;CNTNAP3B,3_prime_UTR_variant,,ENST00000479351,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,; A ENST00000377561 Transcript synonymous_variant 2740/5379 2347/3867 783/1288 L Ctg/Ttg 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1400239303 . 4 204 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 41929335 41929335 G A 1 0 0 0 0 0 0 0 1 3430 1020 36 3 3 CNTNAP3B 9 41929335 Silent SNP G C3N-00546_T 41929335 96465382 68 14259 ZNF658 0 . GRCh38 9 66918313 66918313 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.747A>T p.Arg249Ser p.R249S ENST00000612867 5/5 427 371 56 521 521 0 strelka-varscan-mutect ZNF658,missense_variant,p.Arg249Ser,ENST00000612867,NM_001317916.1;ZNF658,missense_variant,p.Arg249Ser,ENST00000621410,NM_033160.5;ZNF658,missense_variant,p.Arg249Ser,ENST00000619925,;ZNF658,downstream_gene_variant,,ENST00000616544,;ZNF658,downstream_gene_variant,,ENST00000621015,;ZNF658,missense_variant,p.Arg249Ser,ENST00000622180,; T ENST00000612867 Transcript missense_variant 1047/4160 747/3180 249/1059 R/S agA/agT 1 1 ZNF658 HGNC HGNC:25226 protein_coding YES CCDS75846.1 ENSP00000482540 Q5TYW1 UPI000046D388 NM_001317916.1 tolerated(0.47) 5/5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 66918313 66918313 A T 1 0 0 0 0 1 0 0 0 18642 243 9 4 4 ZNF658 9 66918313 Missense_Mutation SNP A C3N-00546_T 24988978 66918313 71476404 69 14260 PRUNE2 0 . GRCh38 9 76704786 76704786 + Silent SNP T T G novel C3N-00546_T C3N-00546_N T T c.7488A>C p.= p.A2496A ENST00000376718 8/19 60 51 9 57 57 0 strelka-varscan-mutect PRUNE2,synonymous_variant,p.=,ENST00000376718,NM_015225.2;PRUNE2,synonymous_variant,p.=,ENST00000428286,;PRUNE2,synonymous_variant,p.=,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,synonymous_variant,p.=,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; G ENST00000376718 Transcript synonymous_variant 7612/12584 7488/9267 2496/3088 A gcA/gcC 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 8/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.96578 1 1 1 1 0 G 2 3 48 76704786 76704786 T G 1 0 0 0 0 0 0 0 1 12791 1567 55 5 5 PRUNE2 9 76704786 Silent SNP T C3N-00546_T 9786473 76704786 61689931 70 14261 DENND1A 0 . GRCh38 9 123383804 123383804 + Missense_Mutation SNP C C T C3N-00546_T C3N-00546_N C C c.1687G>A p.Asp563Asn p.D563N ENST00000373624 21/22 349 281 68 341 341 0 strelka-varscan-mutect DENND1A,missense_variant,p.Asp563Asn,ENST00000373624,NM_020946.1;DENND1A,non_coding_transcript_exon_variant,,ENST00000473039,;CRB2,downstream_gene_variant,,ENST00000460253,; T ENST00000373624 Transcript missense_variant 1889/5010 1687/3030 563/1009 D/N Gac/Aac COSM4900301,COSM4900302 1 -1 DENND1A HGNC HGNC:29324 protein_coding YES CCDS35133.1 ENSP00000362727 Q8TEH3 UPI00004589D2 NM_020946.1 deleterious(0.01) 21/22 hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF22 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1243663517 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 123383804 123383804 C T 1 0 0 0 0 1 0 0 0 4230 826 29 3 3 DENND1A 9 123383804 Missense_Mutation SNP C C3N-00546_T 46679018 123383804 15010913 71 14262 ASS1 0 . GRCh38 9 130466797 130466797 + Missense_Mutation SNP A A G novel C3N-00546_T C3N-00546_N A A c.493A>G p.Lys165Glu p.K165E ENST00000372394 7/16 401 368 33 365 365 0 strelka-varscan-mutect ASS1,missense_variant,p.Lys165Glu,ENST00000372394,;ASS1,missense_variant,p.Lys165Glu,ENST00000352480,NM_054012.3;ASS1,missense_variant,p.Lys165Glu,ENST00000372393,NM_000050.4;ASS1,missense_variant,p.Lys165Glu,ENST00000422569,;ASS1,missense_variant,p.Lys146Glu,ENST00000443588,;ASS1,splice_region_variant,,ENST00000493984,;ASS1,splice_region_variant,,ENST00000467695,; G ENST00000372394 Transcript missense_variant,splice_region_variant 974/1973 493/1239 165/412 K/E Aag/Gag 1 1 ASS1 HGNC HGNC:758 protein_coding YES CCDS6933.1 ENSP00000361471 P00966 Q5T6L4 UPI00000015D6 tolerated(0.51) 7/16 Gene3D:3.90.1260.10,HAMAP:MF_00005,Pfam_domain:PF00764,hmmpanther:PTHR11587,Superfamily_domains:SSF52402,TIGRFAM_domain:TIGR00032 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 130466797 130466797 A G 1 0 0 0 0 1 0 0 0 1208 28 1 5 5 ASS1 9 130466797 Missense_Mutation SNP A C3N-00546_T 7082993 130466797 7927920 72 14263 MRC1 0 . GRCh38 10 17875189 17875189 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.2486A>T p.Lys829Met p.K829M ENST00000569591 17/30 503 407 96 502 501 1 strelka-varscan-mutect MRC1,missense_variant,p.Lys829Met,ENST00000569591,NM_002438.3; T ENST00000569591 Transcript missense_variant 2608/5198 2486/4371 829/1456 K/M aAg/aTg 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 deleterious(0.01) 17/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 17875189 17875189 A T 1 0 0 0 0 1 0 0 0 9722 72 3 4 4 MRC1 10 17875189 Missense_Mutation SNP A C3N-00546_T 17875189 115922233 73 14264 RPL27A 0 . GRCh38 11 8685741 8685743 + In_Frame_Del DEL TTC TTC - novel C3N-00546_T C3N-00546_N TTC TTC c.385_387delTTC p.Phe129del p.F129del ENST00000314138 5/5 271 218 53 252 252 0 sindel-varindel-pindel RPL27A,inframe_deletion,p.Phe129del,ENST00000314138,NM_000990.4;RPL27A,inframe_deletion,p.Phe72del,ENST00000530022,;RPL27A,inframe_deletion,p.Phe72del,ENST00000530913,;RPL27A,inframe_deletion,p.Phe72del,ENST00000524496,;RPL27A,inframe_deletion,p.Phe72del,ENST00000526562,;RPL27A,inframe_deletion,p.Phe94del,ENST00000532359,;RPL27A,3_prime_UTR_variant,,ENST00000525981,;RPL27A,downstream_gene_variant,,ENST00000531978,;SNORA3B,downstream_gene_variant,,ENST00000391305,;SNORA3A,downstream_gene_variant,,ENST00000364113,;RP11-152H18.4,downstream_gene_variant,,ENST00000534169,;RPL27A,upstream_gene_variant,,ENST00000531102,;RPL27A,3_prime_UTR_variant,,ENST00000534599,;RPL27A,downstream_gene_variant,,ENST00000529227,;RPL27A,downstream_gene_variant,,ENST00000530585,; - ENST00000314138 Transcript inframe_deletion 785-787/4916 382-384/447 128/148 F/- TTC/- 1 1 RPL27A HGNC HGNC:10329 protein_coding YES CCDS7790.1 ENSP00000346015 P46776 UPI0000161BF5 NM_000990.4 5/5 Gene3D:3.100.10.10,HAMAP:MF_01341,Pfam_domain:PF00828,PROSITE_patterns:PS00475,hmmpanther:PTHR11721,Superfamily_domains:SSF52080 MODERATE 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 8685741 8685741 TTC - 1 0 1 0 1 0 0 0 0 13828 1493 52 0 0 RPL27A 11 8685741 In_Frame_Del DEL TTC C3N-00546_T 8685741 126400881 74 14265 ANO3 0 . GRCh38 11 26634247 26634247 + Silent SNP G G T C3N-00546_T C3N-00546_N G G c.1917G>T p.= p.L639L ENST00000256737 19/27 241 206 35 169 169 0 strelka-varscan-mutect ANO3,synonymous_variant,p.=,ENST00000256737,NM_031418.2;ANO3,synonymous_variant,p.=,ENST00000525139,;ANO3,synonymous_variant,p.=,ENST00000531568,; T ENST00000256737 Transcript synonymous_variant 2769/6642 1917/2946 639/981 L ctG/ctT COSM5349670 1 1 ANO3 HGNC HGNC:14004 protein_coding YES CCDS31447.1 ENSP00000256737 Q9BYT9 UPI00001F9ED8 NM_031418.2 19/27 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF16 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 26634247 26634247 G T 1 0 0 0 0 0 0 0 1 805 1277 45 2 2 ANO3 11 26634247 Silent SNP G C3N-00546_T 17948506 26634247 108452375 75 14266 KIAA1549L 0 . GRCh38 11 33559895 33559895 + Silent SNP G G A C3N-00546_T C3N-00546_N G G c.3111G>A p.= p.P1037P ENST00000321505 6/20 127 117 10 108 108 0 strelka-varscan-mutect KIAA1549L,synonymous_variant,p.=,ENST00000321505,NM_012194.2;KIAA1549L,synonymous_variant,p.=,ENST00000265654,;KIAA1549L,synonymous_variant,p.=,ENST00000526400,; A ENST00000321505 Transcript synonymous_variant 3291/11678 3111/5550 1037/1849 P ccG/ccA COSM3869100,COSM3869101 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 6/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3,Pfam_domain:PF12877 1,1 LOW 1 SNV 1 1,1 1 PASS rs1243221356 . 0 200 9 0 0 0 0 0 -18.98429 0.9999748 1 1 1 0 A 2 1 48 33559895 33559895 G A 1 0 0 0 0 0 0 0 1 8121 1074 38 1 1 KIAA1549L 11 33559895 Silent SNP G C3N-00546_T 6925648 33559895 101526727 76 14267 OR1S2 0 . GRCh38 11 58203562 58203562 + Missense_Mutation SNP A A T novel C3N-00546_T C3N-00546_N A A c.620T>A p.Ile207Asn p.I207N ENST00000302592 1/1 352 303 49 327 327 0 strelka-varscan-mutect OR1S2,missense_variant,p.Ile207Asn,ENST00000302592,NM_001004459.1; T ENST00000302592 Transcript missense_variant 620/980 620/978 207/325 I/N aTc/aAc 1 -1 OR1S2 HGNC HGNC:15141 protein_coding YES CCDS31545.1 ENSP00000305469 Q8NGQ3 UPI0000041D68 NM_001004459.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF180,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 58203562 58203562 A T 1 0 0 0 0 1 0 0 0 11050 333 12 4 4 OR1S2 11 58203562 Missense_Mutation SNP A C3N-00546_T 24643667 58203562 76883060 77 14268 INCENP 0 . GRCh38 11 62146822 62146822 + Silent SNP G G C rs374721937 C3N-00546_T C3N-00546_N G G c.2124G>C p.= p.R708R ENST00000394818 15/19 336 296 40 426 426 0 strelka-varscan-mutect INCENP,synonymous_variant,p.=,ENST00000394818,NM_001040694.1;INCENP,synonymous_variant,p.=,ENST00000278849,NM_020238.2; C ENST00000394818 Transcript synonymous_variant 2326/3964 2124/2757 708/918 R cgG/cgC rs374721937,COSM4878475 1 1 INCENP HGNC HGNC:6058 protein_coding YES CCDS44624.1 ENSP00000378295 Q9NQS7 UPI0000D7D6F3 NM_001040694.1 15/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13142:SF1,hmmpanther:PTHR13142 0,1 LOW 1 SNV 1 0,1 1 PASS rs374721937 . 0 207 0 0 3 0 0 0 -15.0862 0.9530347 1 1 1 0 C 2 2 48 62146822 62146822 G C 1 0 0 0 0 0 0 0 1 7635 1219 43 4 4 INCENP 11 62146822 Silent SNP G C3N-00546_T 3943260 62146822 72939800 78 14269 GAL3ST3 0 . GRCh38 11 66042940 66042940 + Missense_Mutation SNP C C T rs745551285 C3N-00546_T C3N-00546_N C C c.863G>A p.Arg288His p.R288H ENST00000312006 3/3 29 20 9 54 54 0 strelka-varscan-mutect GAL3ST3,missense_variant,p.Arg288His,ENST00000312006,NM_033036.2;GAL3ST3,missense_variant,p.Arg288His,ENST00000527878,;GAL3ST3,downstream_gene_variant,,ENST00000527048,; T ENST00000312006 Transcript missense_variant 1145/2133 863/1296 288/431 R/H cGc/cAc rs745551285,COSM1605054,COSM5434363 1 -1 GAL3ST3 HGNC HGNC:24144 protein_coding YES CCDS8128.1 ENSP00000308591 Q96A11 UPI0000071842 NM_033036.2 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR14647:SF1,hmmpanther:PTHR14647,Pfam_domain:PF06990 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs745551285 . 0 206 3 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 48 66042940 66042940 C T 1 0 0 0 0 1 0 0 0 6067 768 27 1 1 GAL3ST3 11 66042940 Missense_Mutation SNP C C3N-00546_T 3896118 66042940 69043682 79 14270 ALDH3B1 0 . GRCh38 11 68028096 68028096 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.649C>T p.Pro217Ser p.P217S ENST00000615463 8/8 265 219 46 189 189 0 strelka-varscan-mutect ALDH3B1,missense_variant,p.Pro217Ser,ENST00000615463,;ALDH3B1,3_prime_UTR_variant,,ENST00000342456,NM_001290059.1,NM_000694.3;ALDH3B1,3_prime_UTR_variant,,ENST00000614849,NM_001161473.2;ALDH3B1,3_prime_UTR_variant,,ENST00000617288,NM_001030010.2;ALDH3B1,3_prime_UTR_variant,,ENST00000612297,NM_001290058.1;NDUFS8,upstream_gene_variant,,ENST00000313468,NM_002496.3;NDUFS8,upstream_gene_variant,,ENST00000526339,;NDUFS8,upstream_gene_variant,,ENST00000453471,;ALDH3B1,downstream_gene_variant,,ENST00000527514,;NDUFS8,upstream_gene_variant,,ENST00000525419,;NDUFS8,upstream_gene_variant,,ENST00000525628,;NDUFS8,upstream_gene_variant,,ENST00000528492,;NDUFS8,upstream_gene_variant,,ENST00000621222,;RP5-901A4.1,intron_variant,,ENST00000532296,;ALDH3B1,3_prime_UTR_variant,,ENST00000619675,;ALDH3B1,non_coding_transcript_exon_variant,,ENST00000615368,;NDUFS8,upstream_gene_variant,,ENST00000532399,;NDUFS8,upstream_gene_variant,,ENST00000432321,;NDUFS8,upstream_gene_variant,,ENST00000526446,;NDUFS8,upstream_gene_variant,,ENST00000531796,;NDUFS8,upstream_gene_variant,,ENST00000529645,;NDUFS8,upstream_gene_variant,,ENST00000531228,; T ENST00000615463 Transcript missense_variant 720/1300 649/693 217/230 P/S Cct/Tct 1 1 ALDH3B1 HGNC HGNC:410 protein_coding ENSP00000479948 Q9BUJ8 UPI0000073A88 deleterious_low_confidence(0) 8/8 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 68028096 68028096 C T 1 0 0 0 0 1 0 0 0 599 623 22 3 3 ALDH3B1 11 68028096 Missense_Mutation SNP C C3N-00546_T 1985156 68028096 67058526 80 14271 MYO7A 0 . GRCh38 11 77158331 77158331 + Missense_Mutation SNP C C T rs781922871 C3N-00546_T C3N-00546_N C C c.904C>T p.Arg302Cys p.R302C ENST00000409709 9/49 155 133 22 100 100 0 strelka-varscan-mutect MYO7A,missense_variant,p.Arg302Cys,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Arg302Cys,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Arg291Cys,ENST00000409619,;MYO7A,missense_variant,p.Arg302Cys,ENST00000409893,NM_001127179.2;MYO7A,missense_variant,p.Arg302Cys,ENST00000620575,; T ENST00000409709 Transcript missense_variant 1176/7462 904/6648 302/2215 R/C Cgc/Tgc rs781922871,COSM117062 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.09) 9/49 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF369,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781922871 . 0 196 12 0 0 0 0 0 -20 0.9999016 1 1 1 0 T 3 4 48 77158331 77158331 C T 1 0 0 0 0 1 0 0 0 10083 652 23 1 1 MYO7A 11 77158331 Missense_Mutation SNP C C3N-00546_T 9130235 77158331 57928291 81 14272 AKAP3 0 . GRCh38 12 4627839 4627839 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.1063G>T p.Val355Phe p.V355F ENST00000228850 5/6 209 168 41 248 247 1 strelka-varscan-mutect AKAP3,missense_variant,p.Val355Phe,ENST00000228850,NM_001278309.1;AKAP3,missense_variant,p.Val355Phe,ENST00000545990,NM_006422.3;AKAP3,downstream_gene_variant,,ENST00000540967,;AKAP3,downstream_gene_variant,,ENST00000536414,;RP11-500M8.7,intron_variant,,ENST00000536588,; A ENST00000228850 Transcript missense_variant 1610/3339 1063/2562 355/853 V/F Gtc/Ttc 1 -1 AKAP3 HGNC HGNC:373 protein_coding YES CCDS8531.1 ENSP00000228850 O75969 V9HWD4 UPI000013C8DF NM_001278309.1 deleterious(0.02) 5/6 Pfam_domain:PF05716,hmmpanther:PTHR10226,hmmpanther:PTHR10226:SF9,SMART_domains:SM00807 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 4627839 4627839 C A 1 0 0 0 0 1 0 0 0 536 478 17 2 2 AKAP3 12 4627839 Missense_Mutation SNP C C3N-00546_T 4627839 128647470 82 14273 NOS1 0 . GRCh38 12 117222781 117222781 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.4011G>T p.Gln1337His p.Q1337H ENST00000618760 27/30 159 140 19 195 195 0 strelka-varscan-mutect NOS1,missense_variant,p.Gln1337His,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Gln1303His,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Gln1337His,ENST00000338101,;NOS1,missense_variant,p.Gln1302His,ENST00000344089,; A ENST00000618760 Transcript missense_variant 4722/12283 4011/4407 1337/1468 Q/H caG/caT 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 tolerated(0.11) 27/30 hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Pfam_domain:PF00175,Gene3D:3.40.50.80,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF52343,Prints_domain:PR00371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 117222781 117222781 C A 1 0 0 0 0 1 0 0 0 10586 680 24 2 2 NOS1 12 117222781 Missense_Mutation SNP C C3N-00546_T 112594942 117222781 16052528 83 14274 SETD1B 0 . GRCh38 12 121827784 121827784 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.5390G>T p.Gly1797Val p.G1797V ENST00000542440 16/18 323 256 67 307 307 0 strelka-varscan-mutect SETD1B,missense_variant,p.Gly1797Val,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Gly1840Val,ENST00000604567,;SETD1B,missense_variant,p.Gly1840Val,ENST00000619791,;SETD1B,missense_variant,p.Gly1797Val,ENST00000267197,; T ENST00000542440 Transcript missense_variant 5458/8185 5390/5772 1797/1923 G/V gGc/gTc 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 deleterious(0) 16/18 Gene3D:2.170.270.10,Pfam_domain:PF00856,PROSITE_profiles:PS50280,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 121827784 121827784 G T 1 0 0 0 0 1 0 0 0 14408 1203 42 2 2 SETD1B 12 121827784 Missense_Mutation SNP G C3N-00546_T 4605003 121827784 11447525 84 14275 SFSWAP 0 . GRCh38 12 131764482 131764482 + Missense_Mutation SNP A A G novel C3N-00546_T C3N-00546_N A A c.1747A>G p.Ile583Val p.I583V ENST00000541286 12/19 192 128 64 212 212 0 strelka-varscan-mutect SFSWAP,missense_variant,p.Ile583Val,ENST00000261674,NM_004592.3;SFSWAP,missense_variant,p.Ile583Val,ENST00000541286,NM_001261411.1;SFSWAP,intron_variant,,ENST00000537164,;SFSWAP,3_prime_UTR_variant,,ENST00000538548,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000535236,; G ENST00000541286 Transcript missense_variant 1840/3219 1747/3012 583/1003 I/V Atc/Gtc 1 1 SFSWAP HGNC HGNC:10790 protein_coding YES CCDS58290.1 ENSP00000437738 Q12872 UPI000204AB4C NM_001261411.1 deleterious(0) 12/19 hmmpanther:PTHR13161,hmmpanther:PTHR13161:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 131764482 131764482 A G 1 0 0 0 0 1 0 0 0 14444 101 4 5 5 SFSWAP 12 131764482 Missense_Mutation SNP A C3N-00546_T 9936698 131764482 1510827 85 14276 ANHX 0 . GRCh38 12 133227867 133227867 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.458A>G p.Asn153Ser p.N153S ENST00000545940 3/8 190 176 14 229 228 1 strelka-varscan-mutect ANHX,missense_variant,p.Asn153Ser,ENST00000545940,;ANHX,missense_variant,p.Asn153Ser,ENST00000419717,NM_001191054.1; C ENST00000545940 Transcript missense_variant 2197/3452 458/1140 153/379 N/S aAt/aGt 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 deleterious(0.04) 3/8 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 133227867 133227867 T C 1 0 0 0 0 1 0 0 0 719 1493 52 5 5 ANHX 12 133227867 Missense_Mutation SNP T C3N-00546_T 1463385 133227867 47442 86 14277 POSTN 0 . GRCh38 13 37569320 37569320 + Missense_Mutation SNP A A G novel C3N-00546_T C3N-00546_N A A c.2411T>C p.Ile804Thr p.I804T ENST00000379747 21/23 124 105 19 148 148 0 strelka-varscan-mutect POSTN,missense_variant,p.Ile804Thr,ENST00000379747,NM_006475.2;POSTN,missense_variant,p.Ile777Thr,ENST00000379743,NM_001286665.1;POSTN,missense_variant,p.Ile717Thr,ENST00000541481,NM_001286666.1,NM_001286667.1;POSTN,missense_variant,p.Ile747Thr,ENST00000379742,NM_001135934.1;POSTN,intron_variant,,ENST00000541179,NM_001135936.1,NM_001135935.1;POSTN,intron_variant,,ENST00000379749,;POSTN,non_coding_transcript_exon_variant,,ENST00000497145,;POSTN,non_coding_transcript_exon_variant,,ENST00000474646,;POSTN,intron_variant,,ENST00000473823,;POSTN,upstream_gene_variant,,ENST00000478947,; G ENST00000379747 Transcript missense_variant 2529/3373 2411/2511 804/836 I/T aTt/aCt 1 -1 POSTN HGNC HGNC:16953 protein_coding YES CCDS9364.1 ENSP00000369071 Q15063 A0A024RDS2 UPI000013CEB8 NM_006475.2 deleterious_low_confidence(0) 21/23 PIRSF_domain:PIRSF016553,hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 37569320 37569320 A G 1 0 0 0 0 1 0 0 0 12373 101 4 5 5 POSTN 13 37569320 Missense_Mutation SNP A C3N-00546_T 37569320 76795008 87 14278 PCDH8 0 . GRCh38 13 52846224 52846224 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.2213G>T p.Gly738Val p.G738V ENST00000377942 1/3 66 52 14 87 87 0 strelka-varscan-mutect PCDH8,missense_variant,p.Gly738Val,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Gly738Val,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; A ENST00000377942 Transcript missense_variant 2417/5088 2213/3213 738/1070 G/V gGg/gTg 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 tolerated(0.08) 1/3 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 52846224 52846224 C A 1 0 0 0 0 1 0 0 0 11604 623 22 2 2 PCDH8 13 52846224 Missense_Mutation SNP C C3N-00546_T 15276904 52846224 61518104 88 14279 OR11G2 0 . GRCh38 14 20197930 20197930 + Missense_Mutation SNP G G A C3N-00546_T C3N-00546_N G G c.595G>A p.Val199Ile p.V199I ENST00000357366 1/1 297 248 49 347 347 0 strelka-varscan-mutect OR11G2,missense_variant,p.Val199Ile,ENST00000357366,NM_001005503.1; A ENST00000357366 Transcript missense_variant 595/1111 595/1038 199/345 V/I Gtc/Atc COSM117288 1 1 OR11G2 HGNC HGNC:15346 protein_coding YES CCDS32032.1 ENSP00000349930 Q8NGC1 UPI000015F241 NM_001005503.1 tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF183,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs1224442763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 20197930 20197930 G A 1 0 0 0 0 1 0 0 0 11001 1145 40 1 1 OR11G2 14 20197930 Missense_Mutation SNP G C3N-00546_T 20197930 86845788 89 14280 ARHGEF40 0 . GRCh38 14 21082323 21082323 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.3331C>T p.Pro1111Ser p.P1111S ENST00000298694 15/24 123 106 17 88 88 0 strelka-varscan-mutect ARHGEF40,missense_variant,p.Pro1111Ser,ENST00000298694,NM_001278530.1,NM_001278529.1,NM_018071.4;ARHGEF40,3_prime_UTR_variant,,ENST00000553709,;ARHGEF40,3_prime_UTR_variant,,ENST00000556399,;ARHGEF40,non_coding_transcript_exon_variant,,ENST00000555232,;ARHGEF40,non_coding_transcript_exon_variant,,ENST00000554514,; T ENST00000298694 Transcript missense_variant 3458/5919 3331/4560 1111/1519 P/S Cct/Tct 1 1 ARHGEF40 HGNC HGNC:25516 protein_coding YES CCDS32041.1 ENSP00000298694 Q8TER5 UPI00001FCFB7 NM_001278530.1,NM_001278529.1,NM_018071.4 tolerated(0.54) 15/24 Low_complexity_(Seg):seg,PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF143,hmmpanther:PTHR22826,Gene3D:1.20.900.10,Pfam_domain:PF00621,Superfamily_domains:SSF48065 MODERATE 1 SNV 2 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999977 1 1 1 0 T 3 4 48 21082323 21082323 C T 1 0 0 0 0 1 0 0 0 1044 623 22 3 3 ARHGEF40 14 21082323 Missense_Mutation SNP C C3N-00546_T 884393 21082323 85961395 90 14281 ZFHX2 0 . GRCh38 14 23529739 23529739 + Missense_Mutation SNP G G A novel C3N-00546_T C3N-00546_N G G c.2905C>T p.Pro969Ser p.P969S ENST00000419474 6/10 289 247 42 284 283 1 strelka-varscan-mutect ZFHX2,missense_variant,p.Pro969Ser,ENST00000419474,NM_033400.2;ZFHX2,3_prime_UTR_variant,,ENST00000615307,;ZFHX2,downstream_gene_variant,,ENST00000412565,;ZFHX2,downstream_gene_variant,,ENST00000555334,;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;RP11-66N24.7,upstream_gene_variant,,ENST00000622438,;RP11-66N24.4,intron_variant,,ENST00000554403,; A ENST00000419474 Transcript missense_variant 3261/9182 2905/7719 969/2572 P/S Cct/Tct 1 -1 ZFHX2 HGNC HGNC:20152 protein_coding YES CCDS55907.1 ENSP00000413418 Q9C0A1 UPI000198D01B NM_033400.2 tolerated(0.13) 6/10 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF119 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 23529739 23529739 G A 1 0 0 0 0 1 0 0 0 18211 1232 43 3 3 ZFHX2 14 23529739 Missense_Mutation SNP G C3N-00546_T 2447416 23529739 83513979 91 14282 LRFN5 0 . GRCh38 14 41891565 41891565 + Missense_Mutation SNP C C A C3N-00546_T C3N-00546_N C C c.1701C>A p.Ser567Arg p.S567R ENST00000298119 4/6 247 213 34 477 477 0 strelka-varscan-mutect LRFN5,missense_variant,p.Ser567Arg,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; A ENST00000298119 Transcript missense_variant 2890/3723 1701/2160 567/719 S/R agC/agA COSM3987646 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0.05) 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 41891565 41891565 C A 1 0 0 0 0 1 0 0 0 8835 709 25 2 2 LRFN5 14 41891565 Missense_Mutation SNP C C3N-00546_T 18361826 41891565 65152153 92 14283 FKBP3 0 . GRCh38 14 45129886 45129886 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.226G>A p.Glu76Lys p.E76K ENST00000216330 4/8 160 143 17 106 106 0 strelka-varscan-mutect FKBP3,missense_variant,p.Glu76Lys,ENST00000216330,;FKBP3,missense_variant,p.Glu76Lys,ENST00000396062,NM_002013.3;FKBP3,3_prime_UTR_variant,,ENST00000557324,;FKBP3,non_coding_transcript_exon_variant,,ENST00000556231,; T ENST00000216330 Transcript missense_variant 637/1684 226/675 76/224 E/K Gaa/Aaa 1 -1 FKBP3 HGNC HGNC:3719 protein_coding YES CCDS9683.1 ENSP00000216330 Q00688 UPI000012A815 deleterious(0.01) 4/8 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.99995 0.9999865 1 1 1 0 T 3 4 48 45129886 45129886 C T 1 0 0 0 0 1 0 0 0 5773 835 29 3 3 FKBP3 14 45129886 Missense_Mutation SNP C C3N-00546_T 3238321 45129886 61913832 93 14284 EXOC5 0 . GRCh38 14 57235778 57235779 + Frame_Shift_Ins INS - - C novel C3N-00546_T C3N-00546_N - - c.601_602insG p.Thr201SerfsTer8 p.T201Sfs*8 ENST00000621441 7/18 262 224 38 173 173 0 sindel-varindel EXOC5,frameshift_variant,p.Thr201SerfsTer8,ENST00000621441,NM_006544.3;EXOC5,frameshift_variant,p.Thr201SerfsTer8,ENST00000413566,;EXOC5,frameshift_variant,p.Thr136SerfsTer8,ENST00000340918,;EXOC5,upstream_gene_variant,,ENST00000554934,;EXOC5,3_prime_UTR_variant,,ENST00000555148,;EXOC5,non_coding_transcript_exon_variant,,ENST00000556629,;EXOC5,upstream_gene_variant,,ENST00000554011,;EXOC5,downstream_gene_variant,,ENST00000554598,; C ENST00000621441 Transcript frameshift_variant 961-962/10589 601-602/2127 201/708 T/SX acc/aGcc 1 -1 EXOC5 HGNC HGNC:10696 protein_coding YES CCDS45111.1 ENSP00000484855 O00471 UPI0000047E53 NM_006544.3 7/18 hmmpanther:PTHR12100:SF0,hmmpanther:PTHR12100,Pfam_domain:PF07393 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 7 5 48 57235778 57235778 - C 1 0 1 1 0 0 0 0 0 5175 1261 44 0 0 EXOC5 14 57235778 Frame_Shift_Ins INS - C3N-00546_T 12105892 57235778 49807940 94 14285 KCNH5 0 . GRCh38 14 62849680 62849680 + Silent SNP G G T C3N-00546_T C3N-00546_N G G c.1542C>A p.= p.S514S ENST00000322893 8/11 359 282 77 292 292 0 strelka-varscan-mutect KCNH5,synonymous_variant,p.=,ENST00000322893,NM_139318.4;KCNH5,synonymous_variant,p.=,ENST00000420622,NM_172375.2;KCNH5,synonymous_variant,p.=,ENST00000394968,; T ENST00000322893 Transcript synonymous_variant 1811/11290 1542/2967 514/988 S tcC/tcA COSM4468418,COSM4468419 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 8/11 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Gene3D:3bpzA01,Superfamily_domains:SSF51206,Prints_domain:PR01463 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 62849680 62849680 G T 1 0 0 0 0 0 0 0 1 7951 1335 47 2 2 KCNH5 14 62849680 Silent SNP G C3N-00546_T 5613902 62849680 44194038 95 14286 YLPM1 0 . GRCh38 14 74829332 74829332 + Frame_Shift_Del DEL G G - novel C3N-00546_T C3N-00546_N G G c.6285delG p.Lys2096ArgfsTer21 p.K2096Rfs*21 ENST00000325680 19/21 180 139 41 182 182 0 sindel-varindel-pindel YLPM1,frameshift_variant,p.Lys2096ArgfsTer21,ENST00000325680,NM_019589.2;YLPM1,frameshift_variant,p.Lys1390ArgfsTer21,ENST00000552421,;YLPM1,intron_variant,,ENST00000554107,;YLPM1,downstream_gene_variant,,ENST00000546901,;YLPM1,3_prime_UTR_variant,,ENST00000549293,;YLPM1,downstream_gene_variant,,ENST00000550021,; - ENST00000325680 Transcript frameshift_variant 6407/7108 6283/6441 2095/2146 G/X Ggg/gg 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 19/21 hmmpanther:PTHR13413,hmmpanther:PTHR13413:SF0 HIGH 1 deletion 5 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 74829332 74829332 G - 1 0 1 0 1 0 0 0 0 18048 1348 47 0 0 YLPM1 14 74829332 Frame_Shift_Del DEL G C3N-00546_T 11979652 74829332 32214386 96 14287 STON2 0 . GRCh38 14 81398332 81398332 + Silent SNP G G T novel C3N-00546_T C3N-00546_N G G c.51C>A p.= p.S17S ENST00000555447 3/8 169 131 38 182 182 0 strelka-varscan-mutect STON2,synonymous_variant,p.=,ENST00000555447,NM_001256430.1;STON2,synonymous_variant,p.=,ENST00000267540,NM_033104.3;STON2,synonymous_variant,p.=,ENST00000614646,;STON2,synonymous_variant,p.=,ENST00000557055,;STON2,downstream_gene_variant,,ENST00000554710,;STON2,non_coding_transcript_exon_variant,,ENST00000555226,; T ENST00000555447 Transcript synonymous_variant 464/4302 51/2763 17/920 S tcC/tcA 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 3/8 PIRSF_domain:PIRSF037099,Pfam_domain:PF12016 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 81398332 81398332 G T 1 0 0 0 0 0 0 0 1 15696 987 35 2 2 STON2 14 81398332 Silent SNP G C3N-00546_T 6569000 81398332 25645386 97 14288 DYNC1H1 0 . GRCh38 14 102020004 102020004 + Missense_Mutation SNP G G C novel C3N-00546_T C3N-00546_N G G c.8455G>C p.Glu2819Gln p.E2819Q ENST00000360184 42/78 442 355 87 352 352 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Glu2819Gln,ENST00000360184,NM_001376.4;DYNC1H1,upstream_gene_variant,,ENST00000555204,; C ENST00000360184 Transcript missense_variant 8619/14333 8455/13941 2819/4646 E/Q Gaa/Caa 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0) 42/78 Pfam_domain:PF12775,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 102020004 102020004 G C 1 0 0 0 0 1 0 0 0 4665 1291 45 4 4 DYNC1H1 14 102020004 Missense_Mutation SNP G C3N-00546_T 20621672 102020004 5023714 98 14289 LPCAT4 0 . GRCh38 15 34360177 34360177 + Silent SNP C C A novel C3N-00546_T C3N-00546_N C C c.1176G>T p.= p.V392V ENST00000314891 12/14 186 161 25 214 213 1 strelka-varscan-mutect LPCAT4,synonymous_variant,p.=,ENST00000314891,NM_153613.2;LPCAT4,synonymous_variant,p.=,ENST00000617710,;NUTM1,downstream_gene_variant,,ENST00000614490,NM_175741.2;NUTM1,downstream_gene_variant,,ENST00000537011,NM_001284292.1;NUTM1,downstream_gene_variant,,ENST00000438749,NM_001284293.1;NUTM1,downstream_gene_variant,,ENST00000333756,;LPCAT4,downstream_gene_variant,,ENST00000623384,;LPCAT4,downstream_gene_variant,,ENST00000562431,;LPCAT4,missense_variant,p.Trp81Leu,ENST00000567507,;LPCAT4,non_coding_transcript_exon_variant,,ENST00000563748,;LPCAT4,downstream_gene_variant,,ENST00000563240,;LPCAT4,downstream_gene_variant,,ENST00000566581,;LPCAT4,downstream_gene_variant,,ENST00000569804,;LPCAT4,downstream_gene_variant,,ENST00000562404,; A ENST00000314891 Transcript synonymous_variant 1354/2262 1176/1575 392/524 V gtG/gtT 1 -1 LPCAT4 HGNC HGNC:30059 protein_coding YES CCDS32191.1 ENSP00000317300 Q643R3 UPI00003D0606 NM_153613.2 12/14 Gene3D:1.10.238.10,hmmpanther:PTHR23063,hmmpanther:PTHR23063:SF7 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 34360177 34360177 C A 1 0 0 0 0 0 0 0 1 8816 581 21 2 2 LPCAT4 15 34360177 Silent SNP C C3N-00546_T 34360177 67631012 99 14290 MYO5A 0 . GRCh38 15 52425841 52425841 + Missense_Mutation SNP C C A rs754065070 C3N-00546_T C3N-00546_N C C c.444G>T p.Lys148Asn p.K148N ENST00000399231 4/41 365 300 65 400 400 0 strelka-varscan-mutect MYO5A,missense_variant,p.Lys148Asn,ENST00000399231,NM_000259.3;MYO5A,missense_variant,p.Lys148Asn,ENST00000358212,;MYO5A,missense_variant,p.Lys148Asn,ENST00000399233,;MYO5A,missense_variant,p.Lys148Asn,ENST00000613858,;MYO5A,missense_variant,p.Lys148Asn,ENST00000356338,NM_001142495.1;MYO5A,missense_variant,p.Lys148Asn,ENST00000553916,;AC018902.1,upstream_gene_variant,,ENST00000628998,;MYO5A,3_prime_UTR_variant,,ENST00000556196,;MYO5A,non_coding_transcript_exon_variant,,ENST00000561810,; A ENST00000399231 Transcript missense_variant 688/12225 444/5568 148/1855 K/N aaG/aaT rs754065070 1 -1 MYO5A HGNC HGNC:7602 protein_coding YES CCDS42037.1 ENSP00000382177 Q9Y4I1 UPI0000E445E1 NM_000259.3 deleterious(0.05) 4/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF273,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs754065070 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 52425841 52425841 C A 1 0 0 0 0 1 0 0 0 10079 796 28 2 2 MYO5A 15 52425841 Missense_Mutation SNP C C3N-00546_T 18065664 52425841 49565348 100 14291 HERC1 0 . GRCh38 15 63674849 63674849 + Missense_Mutation SNP C C G novel C3N-00546_T C3N-00546_N C C c.7339G>C p.Asp2447His p.D2447H ENST00000443617 38/78 90 74 16 104 104 0 strelka-varscan-mutect HERC1,missense_variant,p.Asp2447His,ENST00000443617,NM_003922.3;HERC1,missense_variant,p.Asp130His,ENST00000559715,;RP11-317G6.1,upstream_gene_variant,,ENST00000559303,; G ENST00000443617 Transcript missense_variant 7427/15137 7339/14586 2447/4861 D/H Gat/Cat 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 tolerated(0.07) 38/78 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999987 1 1 1 0 G 3 3 48 63674849 63674849 C G 1 0 0 0 0 1 0 0 0 6941 826 29 4 4 HERC1 15 63674849 Missense_Mutation SNP C C3N-00546_T 11249008 63674849 38316340 101 14292 PLEKHO2 0 . GRCh38 15 64865602 64865602 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.1187G>T p.Gly396Val p.G396V ENST00000323544 6/6 220 203 17 187 187 0 strelka-varscan-mutect PLEKHO2,missense_variant,p.Gly396Val,ENST00000323544,NM_025201.4;PLEKHO2,missense_variant,p.Gly346Val,ENST00000616065,NM_001195059.1;AC069368.3,intron_variant,,ENST00000437723,;AC069368.3,intron_variant,,ENST00000502574,; T ENST00000323544 Transcript missense_variant 1315/3720 1187/1473 396/490 G/V gGg/gTg 1 1 PLEKHO2 HGNC HGNC:30026 protein_coding YES CCDS10196.1 ENSP00000326706 Q8TD55 UPI000004D254 NM_025201.4 deleterious(0.03) 6/6 hmmpanther:PTHR15871,hmmpanther:PTHR15871:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 64865602 64865602 G T 1 0 0 0 0 1 0 0 0 12178 1232 43 2 2 PLEKHO2 15 64865602 Missense_Mutation SNP G C3N-00546_T 1190753 64865602 37125587 102 14293 LRRC49 0 . GRCh38 15 70919169 70919169 + Missense_Mutation SNP G G C rs759269941 C3N-00546_T C3N-00546_N G G c.702G>C p.Leu234Phe p.L234F ENST00000560369 7/16 144 126 18 117 117 0 strelka-varscan-mutect LRRC49,missense_variant,p.Leu219Phe,ENST00000544974,NM_001284357.1;LRRC49,missense_variant,p.Leu185Phe,ENST00000443425,NM_001199018.2;LRRC49,missense_variant,p.Leu229Phe,ENST00000260382,NM_017691.4;LRRC49,missense_variant,p.Leu234Phe,ENST00000560369,NM_001199017.2;LRRC49,5_prime_UTR_variant,,ENST00000560691,;LRRC49,non_coding_transcript_exon_variant,,ENST00000436542,;LRRC49,non_coding_transcript_exon_variant,,ENST00000558137,;LRRC49,non_coding_transcript_exon_variant,,ENST00000561285,;LRRC49,3_prime_UTR_variant,,ENST00000561081,;LRRC49,3_prime_UTR_variant,,ENST00000560107,;LRRC49,non_coding_transcript_exon_variant,,ENST00000560980,;LRRC49,non_coding_transcript_exon_variant,,ENST00000559469,;LRRC49,downstream_gene_variant,,ENST00000559670,; C ENST00000560369 Transcript missense_variant 971/2586 702/2076 234/691 L/F ttG/ttC rs759269941 1 1 LRRC49 HGNC HGNC:25965 protein_coding YES CCDS58376.1 ENSP00000453273 Q8IUZ0 UPI0001E92A32 NM_001199017.2 deleterious(0) 7/16 Gene3D:3.80.10.10,Pfam_domain:PF14580,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF335,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS rs759269941 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 70919169 70919169 G C 1 0 0 0 0 1 0 0 0 8901 1310 46 4 4 LRRC49 15 70919169 Missense_Mutation SNP G C3N-00546_T 6053567 70919169 31072020 103 14294 LOXL1 0 . GRCh38 15 73927708 73927708 + Missense_Mutation SNP T T A novel C3N-00546_T C3N-00546_N T T c.925T>A p.Trp309Arg p.W309R ENST00000261921 1/7 162 146 16 163 163 0 strelka-varscan-mutect LOXL1,missense_variant,p.Trp309Arg,ENST00000261921,NM_005576.2;LOXL1-AS1,non_coding_transcript_exon_variant,,ENST00000567257,;LOXL1-AS1,intron_variant,,ENST00000564194,;LOXL1-AS1,intron_variant,,ENST00000562965,;LOXL1-AS1,intron_variant,,ENST00000565756,;LOXL1-AS1,intron_variant,,ENST00000565416,;LOXL1-AS1,intron_variant,,ENST00000566675,;LOXL1-AS1,intron_variant,,ENST00000568087,;LOXL1-AS1,upstream_gene_variant,,ENST00000568229,;LOXL1-AS1,upstream_gene_variant,,ENST00000567644,;LOXL1-AS1,upstream_gene_variant,,ENST00000562739,;LOXL1-AS1,upstream_gene_variant,,ENST00000564963,;LOXL1-AS1,upstream_gene_variant,,ENST00000562130,;LOXL1,missense_variant,p.Trp309Arg,ENST00000566011,; A ENST00000261921 Transcript missense_variant 1251/2351 925/1725 309/574 W/R Tgg/Agg 1 1 LOXL1 HGNC HGNC:6665 protein_coding YES CCDS10253.1 ENSP00000261921 Q08397 UPI000013D224 NM_005576.2 tolerated(0.31) 1/7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 73927708 73927708 T A 1 0 0 0 0 1 0 0 0 8802 1580 55 4 4 LOXL1 15 73927708 Missense_Mutation SNP T C3N-00546_T 3008539 73927708 28063481 104 14295 MLST8 0 . GRCh38 16 2207205 2207205 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.433G>T p.Val145Leu p.V145L ENST00000569417 6/9 128 110 18 112 112 0 strelka-varscan-mutect MLST8,missense_variant,p.Val145Leu,ENST00000569417,NM_022372.4;MLST8,missense_variant,p.Val144Leu,ENST00000382450,NM_001199175.1;MLST8,missense_variant,p.Val145Leu,ENST00000564088,NM_001199173.1;MLST8,missense_variant,p.Val145Leu,ENST00000301724,;MLST8,missense_variant,p.Val145Leu,ENST00000397124,NM_001199174.1;MLST8,missense_variant,p.Val145Leu,ENST00000565250,;MLST8,missense_variant,p.Val151Leu,ENST00000562352,;MLST8,missense_variant,p.Val145Leu,ENST00000569457,;MLST8,missense_variant,p.Val151Leu,ENST00000562479,;PGP,downstream_gene_variant,,ENST00000333503,NM_001042371.2;BRICD5,downstream_gene_variant,,ENST00000328540,NM_182563.3;BRICD5,downstream_gene_variant,,ENST00000562360,;MLST8,downstream_gene_variant,,ENST00000563179,;BRICD5,downstream_gene_variant,,ENST00000566018,;RP11-304L19.8,upstream_gene_variant,,ENST00000561544,;MLST8,non_coding_transcript_exon_variant,,ENST00000561651,;MLST8,non_coding_transcript_exon_variant,,ENST00000562844,;MLST8,non_coding_transcript_exon_variant,,ENST00000564319,;MLST8,downstream_gene_variant,,ENST00000565926,;MLST8,downstream_gene_variant,,ENST00000562043,;MLST8,missense_variant,p.Val145Leu,ENST00000566835,;MLST8,synonymous_variant,p.=,ENST00000563107,;MLST8,3_prime_UTR_variant,,ENST00000565687,;MLST8,3_prime_UTR_variant,,ENST00000570224,;MLST8,3_prime_UTR_variant,,ENST00000565717,;MLST8,3_prime_UTR_variant,,ENST00000567623,;MLST8,3_prime_UTR_variant,,ENST00000567282,;MLST8,3_prime_UTR_variant,,ENST00000562851,;MLST8,non_coding_transcript_exon_variant,,ENST00000568194,;MLST8,non_coding_transcript_exon_variant,,ENST00000568542,;MLST8,non_coding_transcript_exon_variant,,ENST00000563067,;MLST8,non_coding_transcript_exon_variant,,ENST00000565330,;MLST8,non_coding_transcript_exon_variant,,ENST00000569848,;MLST8,upstream_gene_variant,,ENST00000562392,;MLST8,downstream_gene_variant,,ENST00000564294,;MLST8,upstream_gene_variant,,ENST00000562239,;MLST8,downstream_gene_variant,,ENST00000564679,;MLST8,downstream_gene_variant,,ENST00000566653,;MLST8,downstream_gene_variant,,ENST00000565269,;MLST8,downstream_gene_variant,,ENST00000567928,;BRICD5,downstream_gene_variant,,ENST00000566795,; T ENST00000569417 Transcript missense_variant 787/1870 433/981 145/326 V/L Gtg/Ttg 1 1 MLST8 HGNC HGNC:24825 protein_coding YES CCDS10462.2 ENSP00000456405 Q9BVC4 UPI000006D8E8 NM_022372.4 tolerated(0.14) 6/9 PROSITE_profiles:PS50294,hmmpanther:PTHR19842,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS rs1201528887 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 2207205 2207205 G T 1 0 0 0 0 1 0 0 0 9597 1145 40 1 1 MLST8 16 2207205 Missense_Mutation SNP G C3N-00546_T 2207205 88131140 105 14296 RBFOX1 0 . GRCh38 16 7587251 7587251 + Missense_Mutation SNP T T A novel C3N-00546_T C3N-00546_N T T c.548T>A p.Phe183Tyr p.F183Y ENST00000422070 7/16 59 53 6 77 77 0 strelka-mutect RBFOX1,missense_variant,p.Phe140Tyr,ENST00000550418,NM_018723.3;RBFOX1,missense_variant,p.Phe145Tyr,ENST00000340209,;RBFOX1,missense_variant,p.Phe145Tyr,ENST00000620507,;RBFOX1,missense_variant,p.Phe183Tyr,ENST00000547372,;RBFOX1,missense_variant,p.Phe160Tyr,ENST00000355637,NM_145893.2;RBFOX1,missense_variant,p.Phe160Tyr,ENST00000311745,NM_145891.2;RBFOX1,missense_variant,p.Phe140Tyr,ENST00000553186,NM_001142333.1;RBFOX1,missense_variant,p.Phe139Tyr,ENST00000547605,;RBFOX1,missense_variant,p.Phe183Tyr,ENST00000422070,NM_001308117.1;RBFOX1,missense_variant,p.Phe128Tyr,ENST00000535565,;RBFOX1,missense_variant,p.Phe160Tyr,ENST00000436368,NM_145892.2;RBFOX1,missense_variant,p.Phe140Tyr,ENST00000547338,NM_001142334.1;RBFOX1,missense_variant,p.Phe140Tyr,ENST00000551752,;RBFOX1,missense_variant,p.Phe142Tyr,ENST00000570626,;RBFOX1,intron_variant,,ENST00000552089,; A ENST00000422070 Transcript missense_variant 744/1684 548/1278 183/425 F/Y tTt/tAt 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 deleterious(0.03) 7/16 PROSITE_profiles:PS50102,hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 2 1 PASS . . 1 207 2 0 0 0 0 0 -14.45451 1 1 1 1 0 A 3 1 48 7587251 7587251 T A 1 0 0 0 0 1 0 0 0 13271 1855 64 4 4 RBFOX1 16 7587251 Missense_Mutation SNP T C3N-00546_T 5380046 7587251 82751094 106 14297 KIAA0430 0 . GRCh38 16 15602039 15602039 + Silent SNP C C T novel C3N-00546_T C3N-00546_N C C c.4578G>A p.= p.K1526K ENST00000396368 23/27 509 456 53 381 381 0 strelka-varscan-mutect KIAA0430,synonymous_variant,p.=,ENST00000396368,NM_014647.3;KIAA0430,synonymous_variant,p.=,ENST00000540441,;KIAA0430,synonymous_variant,p.=,ENST00000551742,NM_001184998.1;KIAA0430,synonymous_variant,p.=,ENST00000548025,NM_001184999.1;C16orf45,intron_variant,,ENST00000565857,;KIAA0430,downstream_gene_variant,,ENST00000547936,;KIAA0430,3_prime_UTR_variant,,ENST00000552553,;KIAA0430,upstream_gene_variant,,ENST00000552771,;KIAA0430,upstream_gene_variant,,ENST00000551878,;KIAA0430,upstream_gene_variant,,ENST00000549337,;KIAA0430,upstream_gene_variant,,ENST00000551579,; T ENST00000396368 Transcript synonymous_variant 4785/7743 4578/5229 1526/1742 K aaG/aaA 1 -1 KIAA0430 HGNC HGNC:29562 protein_coding YES CCDS10562.2 ENSP00000379654 Q9Y4F3 UPI00006881BC NM_014647.3 23/27 Pfam_domain:PF12872,PROSITE_profiles:PS51644,hmmpanther:PTHR14379,hmmpanther:PTHR14379:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 15602039 15602039 C T 1 0 0 0 0 0 0 0 1 8086 912 32 3 3 KIAA0430 16 15602039 Silent SNP C C3N-00546_T 8014788 15602039 74736306 107 14298 XYLT1 0 . GRCh38 16 17200537 17200537 + Missense_Mutation SNP C C T rs757356673 C3N-00546_T C3N-00546_N C C c.1031G>A p.Arg344His p.R344H ENST00000261381 4/12 240 189 51 216 216 0 strelka-varscan-mutect XYLT1,missense_variant,p.Arg344His,ENST00000261381,NM_022166.3;XYLT1,non_coding_transcript_exon_variant,,ENST00000575674,; T ENST00000261381 Transcript missense_variant 1116/9891 1031/2880 344/959 R/H cGc/cAc rs757356673 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 deleterious(0) 4/12 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF91,Pfam_domain:PF02485 MODERATE 1 SNV 1 1 PASS rs757356673 . 0 204 0 4 0 0 0 0 -20 0.9999552 1 1 1 0 T 3 4 48 17200537 17200537 C T 1 0 0 0 0 1 0 0 0 18022 768 27 1 1 XYLT1 16 17200537 Missense_Mutation SNP C C3N-00546_T 1598498 17200537 73137808 108 14299 TMEM219 0 . GRCh38 16 29963241 29963241 + Missense_Mutation SNP C C G C3N-00546_T C3N-00546_N C C c.98C>G p.Ser33Cys p.S33C ENST00000566848 1/5 454 431 23 332 332 0 strelka-varscan-mutect TMEM219,missense_variant,p.Ser33Cys,ENST00000566848,;TMEM219,missense_variant,p.Ser33Cys,ENST00000561899,;TMEM219,missense_variant,p.Ser33Cys,ENST00000414689,;TMEM219,missense_variant,p.Ser33Cys,ENST00000279396,NM_001083613.1,NM_194280.3;TMEM219,missense_variant,p.Ser33Cys,ENST00000575829,;TMEM219,missense_variant,p.Ser33Cys,ENST00000602948,;TMEM219,upstream_gene_variant,,ENST00000569445,;TMEM219,upstream_gene_variant,,ENST00000569481,;TMEM219,missense_variant,p.Ser24Cys,ENST00000570255,; G ENST00000566848 Transcript missense_variant 565/1292 98/723 33/240 S/C tCt/tGt COSM241937 1 1 TMEM219 HGNC HGNC:25201 protein_coding YES CCDS42145.1 ENSP00000457492 Q86XT9 A0A024R618 UPI000004F67E deleterious(0) 1/5 Pfam_domain:PF14940,hmmpanther:PTHR16002,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 29963241 29963241 C G 1 0 0 0 0 1 0 0 0 16583 913 32 4 4 TMEM219 16 29963241 Missense_Mutation SNP C C3N-00546_T 12762704 29963241 60375104 109 14300 GINS3 0 . GRCh38 16 58392725 58392725 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.124C>T p.Arg42Cys p.R42C ENST00000426538 1/4 274 233 41 238 238 0 strelka-varscan-mutect GINS3,missense_variant,p.Arg42Cys,ENST00000318129,NM_022770.3;GINS3,missense_variant,p.Arg42Cys,ENST00000328514,NM_001126130.1;GINS3,missense_variant,p.Arg42Cys,ENST00000426538,NM_001126129.1;RP11-481J2.3,non_coding_transcript_exon_variant,,ENST00000613275,;GINS3,non_coding_transcript_exon_variant,,ENST00000567909,;GINS3,downstream_gene_variant,,ENST00000564814,; T ENST00000426538 Transcript missense_variant 332/1728 124/768 42/255 R/C Cgc/Tgc 1 1 GINS3 HGNC HGNC:25851 protein_coding YES CCDS45498.1 ENSP00000401018 Q9BRX5 A0A0S2Z5P2 UPI00001FF2F1 NM_001126129.1 deleterious(0) 1/4 hmmpanther:PTHR22768,Superfamily_domains:SSF160059 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 58392725 58392725 C T 1 0 0 0 0 1 0 0 0 6271 884 31 1 1 GINS3 16 58392725 Missense_Mutation SNP C C3N-00546_T 28429484 58392725 31945620 110 14301 CDH11 0 . GRCh38 16 64982132 64982132 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.1169A>G p.His390Arg p.H390R ENST00000268603 8/13 210 176 34 234 234 0 strelka-varscan-mutect CDH11,missense_variant,p.His390Arg,ENST00000394156,NM_001308392.1;CDH11,missense_variant,p.His390Arg,ENST00000268603,NM_001797.2;CDH11,missense_variant,p.His264Arg,ENST00000566827,;CDH11,downstream_gene_variant,,ENST00000619158,;RP11-229O3.1,non_coding_transcript_exon_variant,,ENST00000624875,; C ENST00000268603 Transcript missense_variant 1785/6857 1169/2391 390/796 H/R cAc/cGc 1 -1 CDH11 HGNC HGNC:1750 protein_coding YES CCDS10803.1 ENSP00000268603 P55287 UPI000013D7C5 NM_001797.2 deleterious(0) 8/13 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF85,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 64982132 64982132 T C 1 0 0 0 0 1 0 0 0 2800 1696 59 5 5 CDH11 16 64982132 Missense_Mutation SNP T C3N-00546_T 6589407 64982132 25356213 111 14302 CNTNAP4 0 . GRCh38 16 76494996 76494996 + Frame_Shift_Del DEL A A - novel C3N-00546_T C3N-00546_N A A c.2167delA p.Thr723LeufsTer4 p.T723Lfs*4 ENST00000611870 14/24 201 167 34 239 239 0 sindel-varindel-pindel CNTNAP4,frameshift_variant,p.Thr723LeufsTer4,ENST00000307431,;CNTNAP4,frameshift_variant,p.Thr723LeufsTer4,ENST00000611870,NM_033401.3;CNTNAP4,frameshift_variant,p.Thr675LeufsTer4,ENST00000377504,;CNTNAP4,frameshift_variant,p.Thr726LeufsTer4,ENST00000476707,;CNTNAP4,frameshift_variant,p.Thr675LeufsTer4,ENST00000622250,;CNTNAP4,frameshift_variant,p.Thr650LeufsTer4,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; - ENST00000611870 Transcript frameshift_variant 2552/4867 2167/3927 723/1308 T/X Act/ct 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 14/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 76494996 76494996 A - 1 0 1 0 1 0 0 0 0 3431 391 14 0 0 CNTNAP4 16 76494996 Frame_Shift_Del DEL A C3N-00546_T 11512864 76494996 13843349 112 14303 FOXL1 0 . GRCh38 16 86579526 86579526 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.803C>T p.Ala268Val p.A268V ENST00000320241 1/1 222 197 25 187 186 1 strelka-varscan-mutect FOXL1,missense_variant,p.Ala268Val,ENST00000320241,NM_005250.2;FOXL1,downstream_gene_variant,,ENST00000593625,; T ENST00000320241 Transcript missense_variant 1021/3655 803/1038 268/345 A/V gCg/gTg 1 1 FOXL1 HGNC HGNC:3817 protein_coding YES CCDS10959.1 ENSP00000326272 Q12952 UPI000012ADE2 NM_005250.2 deleterious(0.01) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF204 MODERATE 1 SNV 1 PASS rs1315784346 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 48 86579526 86579526 C T 1 0 0 0 0 1 0 0 0 5879 768 27 1 1 FOXL1 16 86579526 Missense_Mutation SNP C C3N-00546_T 10084530 86579526 3758819 113 14304 TP53 0 . GRCh38 17 7674252 7674252 + Missense_Mutation SNP C C A rs587782664 C3N-00546_T C3N-00546_N C C c.711G>T p.Met237Ile p.M237I ENST00000269305 7/11 311 221 90 337 336 1 strelka-varscan-mutect TP53,missense_variant,p.Met237Ile,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Met237Ile,ENST00000420246,;TP53,missense_variant,p.Met198Ile,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Met198Ile,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Met237Ile,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Met198Ile,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Met237Ile,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Met198Ile,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Met237Ile,ENST00000445888,;TP53,missense_variant,p.Met198Ile,ENST00000619485,;TP53,missense_variant,p.Met105Ile,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Met78Ile,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Met105Ile,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Met78Ile,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Met105Ile,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Met78Ile,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Met237Ile,ENST00000359597,;TP53,missense_variant,p.Met226Ile,ENST00000615910,;TP53,missense_variant,p.Met237Ile,ENST00000413465,;TP53,missense_variant,p.Met105Ile,ENST00000509690,;TP53,missense_variant,p.Met144Ile,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Met198Ile,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 901/2579 711/1182 237/393 M/I atG/atT rs587782664,CM011014,TP53_g.13348G>C,TP53_g.13348G>T,TP53_g.13348G>A,TP53_g.13348del,COSM10834,COSM11063,COSM1189384,COSM1189385,COSM1189386,COSM1640834,COSM1640835,COSM301402,COSM301403,COSM301404,COSM3378348,COSM3378444,COSM44415,COSM5249615,COSM5249616,COSM99646,COSM99647,COSM99648 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs587782664 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 7674252 7674252 C A 1 0 0 0 0 1 0 0 0 16859 478 17 2 2 TP53 17 7674252 Missense_Mutation SNP C C3N-00546_T 7674252 75583189 114 14305 RAI1 0 . GRCh38 17 17798223 17798223 + Missense_Mutation SNP G G T rs777108697 C3N-00546_T C3N-00546_N G G c.5275G>T p.Gly1759Cys p.G1759C ENST00000353383 3/6 137 89 48 162 162 0 strelka-varscan-mutect RAI1,missense_variant,p.Gly1759Cys,ENST00000353383,NM_030665.3;RAI1,downstream_gene_variant,,ENST00000395774,;RAI1,upstream_gene_variant,,ENST00000583166,; T ENST00000353383 Transcript missense_variant 5744/7662 5275/5721 1759/1906 G/C Ggc/Tgc rs777108697 1 1 RAI1 HGNC HGNC:9834 protein_coding YES CCDS11188.1 ENSP00000323074 Q7Z5J4 UPI0000200AAF NM_030665.3 deleterious(0.01) 3/6 hmmpanther:PTHR14955:SF6,hmmpanther:PTHR14955 MODERATE 1 SNV 1 1 PASS rs777108697 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 17798223 17798223 G T 1 0 0 0 0 1 0 0 0 13166 1116 39 1 1 RAI1 17 17798223 Missense_Mutation SNP G C3N-00546_T 10123971 17798223 65459218 115 14306 NF1 0 . GRCh38 17 31201068 31201068 + Nonsense_Mutation SNP C C G rs864622107 C3N-00546_T C3N-00546_N C C c.1094C>G p.Ser365Ter p.S365* ENST00000358273 10/58 421 341 80 405 405 0 strelka-varscan-mutect NF1,stop_gained,p.Ser365Ter,ENST00000358273,NM_001042492.2;NF1,stop_gained,p.Ser365Ter,ENST00000356175,NM_000267.3;NF1,stop_gained,p.Ser31Ter,ENST00000456735,;NF1,stop_gained,p.Ser365Ter,ENST00000431387,NM_001128147.2;NF1,stop_gained,p.Ser399Ter,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,; G ENST00000358273 Transcript stop_gained 1477/12425 1094/8520 365/2839 S/* tCa/tGa rs864622107,CM119586 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 10/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 pathogenic HIGH 1 SNV 1 1,1 1 PASS rs864622107 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 48 31201068 31201068 C G 1 0 0 0 0 0 1 0 0 10393 838 29 4 4 NF1 17 31201068 Nonsense_Mutation SNP C C3N-00546_T 13402845 31201068 52056373 116 14307 RARA 0 . GRCh38 17 40352373 40352373 + Missense_Mutation SNP T T A rs201919660 C3N-00546_T C3N-00546_N T T c.673T>A p.Trp225Arg p.W225R ENST00000254066 6/9 106 85 21 73 73 0 strelka-mutect RARA,missense_variant,p.Trp128Arg,ENST00000425707,NM_001145302.2;RARA,missense_variant,p.Trp225Arg,ENST00000254066,NM_000964.3;RARA,missense_variant,p.Trp220Arg,ENST00000394081,NM_001024809.3;RARA,missense_variant,p.Trp225Arg,ENST00000394089,NM_001145301.2;RARA,missense_variant,p.Trp241Arg,ENST00000394086,;RARA,missense_variant,p.Trp106Arg,ENST00000475125,;RARA,downstream_gene_variant,,ENST00000577646,;RARA,non_coding_transcript_exon_variant,,ENST00000420042,;CTD-2267D19.1,upstream_gene_variant,,ENST00000623156,;RARA,downstream_gene_variant,,ENST00000579727,; A ENST00000254066 Transcript missense_variant 1128/2414 673/1389 225/462 W/R Tgg/Agg rs201919660 1 1 RARA HGNC HGNC:9864 protein_coding YES CCDS11366.1 ENSP00000254066 P10276 Q6I9R7 UPI0000134A0E NM_000964.3 deleterious(0) 6/9 Gene3D:1.10.565.10,Prints_domain:PR01292,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF115,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS rs201919660 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 40352373 40352373 T A 1 0 0 0 0 1 0 0 0 13211 1580 55 4 4 RARA 17 40352373 Missense_Mutation SNP T C3N-00546_T 9151305 40352373 42905068 117 14308 FAM187A 0 . GRCh38 17 44904501 44904501 + Silent SNP G G T novel C3N-00546_T C3N-00546_N G G c.672G>T p.= p.R224R ENST00000331733 4/4 112 87 25 74 74 0 strelka-varscan-mutect FAM187A,synonymous_variant,p.=,ENST00000331733,;CCDC103,3_prime_UTR_variant,,ENST00000417826,;EFTUD2,upstream_gene_variant,,ENST00000426333,NM_004247.3;GFAP,downstream_gene_variant,,ENST00000253408,NM_002055.4;FAM187A,downstream_gene_variant,,ENST00000412523,NM_001258399.1,NM_001258396.1,NM_213607.2,NM_001258395.1;CCDC103,downstream_gene_variant,,ENST00000410006,;CCDC103,downstream_gene_variant,,ENST00000357776,NM_001258398.1;CCDC103,downstream_gene_variant,,ENST00000577339,;CCDC103,downstream_gene_variant,,ENST00000410027,NM_001258397.1;GFAP,downstream_gene_variant,,ENST00000588735,;GFAP,downstream_gene_variant,,ENST00000591880,;GFAP,downstream_gene_variant,,ENST00000586125,;AC015936.3,non_coding_transcript_exon_variant,,ENST00000441312,;GFAP,downstream_gene_variant,,ENST00000592706,;GFAP,downstream_gene_variant,,ENST00000588640,;GFAP,downstream_gene_variant,,ENST00000592065,;GFAP,downstream_gene_variant,,ENST00000589701,;GFAP,downstream_gene_variant,,ENST00000585543,; T ENST00000331733 Transcript synonymous_variant 2508/3397 672/1242 224/413 R cgG/cgT 1 1 FAM187A HGNC HGNC:35153 protein_coding ENSP00000329499 A6NFU0 UPI000013E667 4/4 hmmpanther:PTHR32178,hmmpanther:PTHR32178:SF7 LOW SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 44904501 44904501 G T 1 0 0 0 0 0 0 0 1 5363 1161 41 2 2 FAM187A 17 44904501 Silent SNP G C3N-00546_T 4552128 44904501 38352940 118 14309 COL1A1 0 . GRCh38 17 50193037 50193037 + Missense_Mutation SNP C C G rs72651613 C3N-00546_T C3N-00546_N C C c.1778G>C p.Gly593Ala p.G593A ENST00000225964 26/51 368 314 54 284 284 0 strelka-varscan-mutect COL1A1,missense_variant,p.Gly593Ala,ENST00000225964,NM_000088.3;COL1A1,non_coding_transcript_exon_variant,,ENST00000476387,;COL1A1,downstream_gene_variant,,ENST00000471344,;COL1A1,upstream_gene_variant,,ENST00000486572,;COL1A1,upstream_gene_variant,,ENST00000511732,;COL1A1,downstream_gene_variant,,ENST00000463440,;COL1A1,downstream_gene_variant,,ENST00000495677,;COL1A1,upstream_gene_variant,,ENST00000504289,;COL1A1,downstream_gene_variant,,ENST00000485870,;COL1A1,upstream_gene_variant,,ENST00000494334,; G ENST00000225964 Transcript missense_variant 1897/6727 1778/4395 593/1464 G/A gGc/gCc rs72651613,CM070701 1 -1 COL1A1 HGNC HGNC:2197 protein_coding YES CCDS11561.1 ENSP00000225964 P02452 UPI0000DACAC3 NM_000088.3 deleterious(0) 26/51 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF569,Low_complexity_(Seg):seg MODERATE 1 SNV 1 0,1 1 PASS rs72651613 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 50193037 50193037 C G 1 0 0 0 0 1 0 0 0 3465 739 26 4 4 COL1A1 17 50193037 Missense_Mutation SNP C C3N-00546_T 5288536 50193037 33064404 119 14310 ARSG 0 . GRCh38 17 68307515 68307516 + Frame_Shift_Ins INS - - T novel C3N-00546_T C3N-00546_N - - c.26dupT p.Leu9PhefsTer37 p.L9Ffs*37 ENST00000448504 2/12 123 96 27 112 112 0 sindel-varindel-pindel ARSG,frameshift_variant,p.Leu9PhefsTer37,ENST00000448504,NM_014960.4;ARSG,frameshift_variant,p.Leu9PhefsTer37,ENST00000621439,NM_001267727.1;ARSG,frameshift_variant,p.Leu9PhefsTer?,ENST00000581639,;ARSG,intron_variant,,ENST00000452479,; T ENST00000448504 Transcript frameshift_variant 818-819/4642 22-23/1578 8/525 V/VX gtt/gTtt 1 1 ARSG HGNC HGNC:24102 protein_coding YES CCDS11676.1 ENSP00000407193 Q96EG1 A0A024R8K1 UPI000003FD81 NM_014960.4 2/12 hmmpanther:PTHR10342:SF231,hmmpanther:PTHR10342 HIGH 1 insertion 1 4 1 PASS . . 0 197 7 6 0 0 0 0 -20 0.9940224 1 1 1 0 T 7 5 48 68307515 68307515 - T 1 0 1 1 0 0 0 0 0 1135 1261 44 0 0 ARSG 17 68307515 Frame_Shift_Ins INS - C3N-00546_T 18114478 68307515 14949926 120 14311 APC2 0 . GRCh38 19 1469920 1469920 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.6619C>A p.Pro2207Thr p.P2207T ENST00000535453 14/14 142 85 57 125 125 0 strelka-varscan-mutect APC2,missense_variant,p.Pro2207Thr,ENST00000535453,;APC2,missense_variant,p.Pro2207Thr,ENST00000233607,NM_005883.2;C19orf25,intron_variant,,ENST00000588427,;C19orf25,downstream_gene_variant,,ENST00000436106,;APC2,downstream_gene_variant,,ENST00000238483,;APC2,downstream_gene_variant,,ENST00000590469,;C19orf25,downstream_gene_variant,,ENST00000588871,;C19orf25,downstream_gene_variant,,ENST00000585675,NM_152482.2;C19orf25,downstream_gene_variant,,ENST00000588849,;C19orf25,downstream_gene_variant,,ENST00000427685,;C19orf25,downstream_gene_variant,,ENST00000592872,;C19orf25,downstream_gene_variant,,ENST00000586564,;C19orf25,downstream_gene_variant,,ENST00000590621,;APC2,downstream_gene_variant,,ENST00000593146,;C19orf25,downstream_gene_variant,,ENST00000592486,; A ENST00000535453 Transcript missense_variant 8332/11656 6619/6912 2207/2303 P/T Ccg/Acg 1 1 APC2 HGNC HGNC:24036 protein_coding YES CCDS12068.1 ENSP00000442954 O95996 UPI0000073D85 deleterious(0) 14/14 hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607 MODERATE 1 SNV 1 1 PASS rs1328323543 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 1469920 1469920 C A 1 0 0 0 0 1 0 0 0 884 623 22 2 2 APC2 19 1469920 Missense_Mutation SNP C C3N-00546_T 1469920 57147696 121 14312 MYO1F 0 . GRCh38 19 8522794 8522794 + Missense_Mutation SNP C C T novel C3N-00546_T C3N-00546_N C C c.2890G>A p.Gly964Arg p.G964R ENST00000338257 26/28 173 114 59 114 114 0 strelka-varscan-mutect MYO1F,missense_variant,p.Gly964Arg,ENST00000338257,NM_012335.3;MYO1F,missense_variant,p.Gly964Arg,ENST00000613525,;MYO1F,downstream_gene_variant,,ENST00000598005,;MYO1F,downstream_gene_variant,,ENST00000600885,;MYO1F,downstream_gene_variant,,ENST00000596245,; T ENST00000338257 Transcript missense_variant 3158/4303 2890/3297 964/1098 G/R Ggg/Agg 1 -1 MYO1F HGNC HGNC:7600 protein_coding YES CCDS42494.1 ENSP00000344871 O00160 UPI00001678F0 NM_012335.3 tolerated(0.25) 26/28 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 8522794 8522794 C T 1 0 0 0 0 1 0 0 0 10074 681 24 3 3 MYO1F 19 8522794 Missense_Mutation SNP C C3N-00546_T 7052874 8522794 50094822 122 14313 MUC16 0 . GRCh38 19 8978750 8978750 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.2389C>A p.Pro797Thr p.P797T ENST00000397910 1/84 191 130 61 166 166 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro797Thr,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 2593/43816 2389/43524 797/14507 P/T Cca/Aca 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 8978750 8978750 G T 1 0 0 0 0 1 0 0 0 9972 1174 41 2 2 MUC16 19 8978750 Missense_Mutation SNP G C3N-00546_T 455956 8978750 49638866 123 14314 NPHS1 0 . GRCh38 19 35851612 35851612 + Missense_Mutation SNP T T C novel C3N-00546_T C3N-00546_N T T c.119A>G p.Asn40Ser p.N40S ENST00000378910 2/29 739 630 109 552 551 1 strelka-varscan-mutect NPHS1,missense_variant,p.Asn40Ser,ENST00000378910,NM_004646.3;NPHS1,missense_variant,p.Asn40Ser,ENST00000353632,;KIRREL2,upstream_gene_variant,,ENST00000592409,;KIRREL2,upstream_gene_variant,,ENST00000586102,;NPHS1,downstream_gene_variant,,ENST00000591817,;NPHS1,upstream_gene_variant,,ENST00000592132,; C ENST00000378910 Transcript missense_variant 119/4276 119/3726 40/1241 N/S aAc/aGc 1 -1 NPHS1 HGNC HGNC:7908 protein_coding YES CCDS32996.1 ENSP00000368190 O60500 UPI000004EF61 NM_004646.3 deleterious(0) 2/29 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF31,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs891201320 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 48 35851612 35851612 T C 1 0 0 0 0 1 0 0 0 10630 1725 60 5 5 NPHS1 19 35851612 Missense_Mutation SNP T C3N-00546_T 26872862 35851612 22766004 124 14315 ECH1 0 . GRCh38 19 38831452 38831452 + Frame_Shift_Del DEL T T - rs11549279 C3N-00546_T C3N-00546_N T T c.117delA p.Glu40ArgfsTer6 p.E40Rfs*6 ENST00000221418 2/10 203 167 36 169 169 0 sindel-varindel-pindel ECH1,frameshift_variant,p.Glu40ArgfsTer6,ENST00000221418,NM_001398.2;AC104534.3,frameshift_variant,p.Glu210ArgfsTer6,ENST00000594769,;ECH1,frameshift_variant,p.Glu37ArgfsTer6,ENST00000601778,;ECH1,frameshift_variant,p.Glu40ArgfsTer6,ENST00000595470,;ECH1,frameshift_variant,p.Gln70GlnfsTer?,ENST00000602115,;ECH1,5_prime_UTR_variant,,ENST00000601094,;ECH1,5_prime_UTR_variant,,ENST00000595567,;AC104534.3,intron_variant,,ENST00000602021,;ECH1,intron_variant,,ENST00000597205,;HNRNPL,downstream_gene_variant,,ENST00000221419,NM_001533.2;HNRNPL,downstream_gene_variant,,ENST00000601449,;ECH1,intron_variant,,ENST00000597805,;ECH1,3_prime_UTR_variant,,ENST00000594164,;ECH1,non_coding_transcript_exon_variant,,ENST00000600178,;ECH1,non_coding_transcript_exon_variant,,ENST00000598707,;ECH1,non_coding_transcript_exon_variant,,ENST00000601060,;ECH1,non_coding_transcript_exon_variant,,ENST00000598316,;HNRNPL,downstream_gene_variant,,ENST00000597731,;HNRNPL,downstream_gene_variant,,ENST00000595164,;HNRNPL,downstream_gene_variant,,ENST00000595443,;HNRNPL,downstream_gene_variant,,ENST00000388749,;HNRNPL,downstream_gene_variant,,ENST00000595804,;ECH1,upstream_gene_variant,,ENST00000596118,;ECH1,upstream_gene_variant,,ENST00000597089,; - ENST00000221418 Transcript frameshift_variant 350/1411 117/987 39/328 Q/X caA/ca rs11549279 1 -1 ECH1 HGNC HGNC:3149 protein_coding YES CCDS33014.1 ENSP00000221418 Q13011 UPI0000071141 NM_001398.2 2/10 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 38831452 38831452 T - 1 0 1 0 1 0 0 0 0 4718 1606 56 0 0 ECH1 19 38831452 Frame_Shift_Del DEL T C3N-00546_T 2979840 38831452 19786164 125 14316 HIPK4 0 . GRCh38 19 40389754 40389754 + Missense_Mutation SNP C C T rs146668696 C3N-00546_T C3N-00546_N C C c.149G>A p.Arg50His p.R50H ENST00000291823 1/4 468 428 40 370 370 0 strelka-varscan-mutect HIPK4,missense_variant,p.Arg50His,ENST00000291823,NM_144685.4;PRX,downstream_gene_variant,,ENST00000291825,NM_020956.2;PRX,downstream_gene_variant,,ENST00000324001,NM_181882.2; T ENST00000291823 Transcript missense_variant 434/2452 149/1851 50/616 R/H cGc/cAc rs146668696 1 -1 HIPK4 HGNC HGNC:19007 protein_coding YES CCDS12555.1 ENSP00000291823 Q8NE63 A0A140VJL1 UPI000006DCD3 NM_144685.4 deleterious(0.05) 1/4 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF46,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs146668696 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 40389754 40389754 C T 1 0 0 0 0 1 0 0 0 7007 768 27 1 1 HIPK4 19 40389754 Missense_Mutation SNP C C3N-00546_T 1558302 40389754 18227862 126 14317 ZNF614 0 . GRCh38 19 52017124 52017124 + Silent SNP A A G novel C3N-00546_T C3N-00546_N A A c.474T>C p.= p.F158F ENST00000270649 5/5 339 303 36 354 354 0 strelka-varscan-mutect ZNF614,synonymous_variant,p.=,ENST00000270649,NM_025040.3;ZNF614,synonymous_variant,p.=,ENST00000356322,;ZNF614,downstream_gene_variant,,ENST00000597952,;ZNF614,3_prime_UTR_variant,,ENST00000595189,; G ENST00000270649 Transcript synonymous_variant 1019/4818 474/1758 158/585 F ttT/ttC 1 -1 ZNF614 HGNC HGNC:24722 protein_coding YES CCDS12847.1 ENSP00000270649 Q8N883 UPI0000202ADA NM_025040.3 5/5 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF110 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 48 52017124 52017124 A G 1 0 0 0 0 0 0 0 1 18614 359 13 5 5 ZNF614 19 52017124 Silent SNP A C3N-00546_T 11627370 52017124 6600492 127 14318 CNOT3 0 . GRCh38 19 54148485 54148485 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.1232G>T p.Ser411Ile p.S411I ENST00000358389 10/17 51 45 6 53 53 0 strelka-mutect CNOT3,missense_variant,p.Ser411Ile,ENST00000358389,;CNOT3,missense_variant,p.Ser411Ile,ENST00000221232,NM_014516.3;CNOT3,missense_variant,p.Ser230Ile,ENST00000447684,;CNOT3,missense_variant,p.Ser333Ile,ENST00000440571,;CNOT3,upstream_gene_variant,,ENST00000457463,;CNOT3,upstream_gene_variant,,ENST00000496327,;CNOT3,3_prime_UTR_variant,,ENST00000613073,;CNOT3,non_coding_transcript_exon_variant,,ENST00000618939,;CNOT3,upstream_gene_variant,,ENST00000617930,; T ENST00000358389 Transcript missense_variant 2815/4118 1232/2262 411/753 S/I aGt/aTt 1 1 CNOT3 HGNC HGNC:7879 protein_coding YES CCDS12880.1 ENSP00000351159 O75175 A0A024R4R3 UPI00000729AD tolerated(0.18) 10/17 PIRSF_domain:PIRSF005290,hmmpanther:PTHR23326,hmmpanther:PTHR23326:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -14.36782 0.9999993 1 1 1 0 T 3 4 48 54148485 54148485 G T 1 0 0 0 0 1 0 0 0 3400 1029 36 2 2 CNOT3 19 54148485 Missense_Mutation SNP G C3N-00546_T 2131361 54148485 4469131 128 14319 ZNF787 0 . GRCh38 19 56088958 56088958 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.214G>T p.Gly72Cys p.G72C ENST00000610935 3/3 53 48 5 59 59 0 strelka-varscan-mutect ZNF787,missense_variant,p.Gly72Cys,ENST00000610935,NM_001002836.3;ZNF787,downstream_gene_variant,,ENST00000586787,; A ENST00000610935 Transcript missense_variant 333/1925 214/1149 72/382 G/C Ggc/Tgc 1 -1 ZNF787 HGNC HGNC:26998 protein_coding YES CCDS42634.1 ENSP00000478557 A0A087WUD1 UPI0001596896 NM_001002836.3 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24408:SF1,hmmpanther:PTHR24408,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.32595 1 1 1 1 0 A 3 1 48 56088958 56088958 C A 1 0 0 0 0 1 0 0 0 18743 594 21 2 2 ZNF787 19 56088958 Missense_Mutation SNP C C3N-00546_T 1940473 56088958 2528658 129 14320 ZSCAN22 0 . GRCh38 19 58339246 58339246 + Missense_Mutation SNP T T G rs754224592 C3N-00546_T C3N-00546_N T T c.1396T>G p.Cys466Gly p.C466G ENST00000329665 3/3 162 114 48 124 124 0 strelka-varscan-mutect ZSCAN22,missense_variant,p.Cys466Gly,ENST00000329665,NM_001321117.1,NM_001321116.1,NM_181846.2;MIR6806,downstream_gene_variant,,ENST00000622141,; G ENST00000329665 Transcript missense_variant 1543/4629 1396/1476 466/491 C/G Tgc/Ggc rs754224592 1 1 ZSCAN22 HGNC HGNC:4929 protein_coding YES CCDS12975.1 ENSP00000332433 P10073 UPI00001A9CCE NM_001321117.1,NM_001321116.1,NM_181846.2 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23226:SF59,hmmpanther:PTHR23226,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs754224592 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 58339246 58339246 T G 1 0 0 0 0 1 0 0 0 18828 1696 59 5 5 ZSCAN22 19 58339246 Missense_Mutation SNP T C3N-00546_T 2250288 58339246 278370 130 14321 RALGAPA2 0 . GRCh38 20 20412084 20412084 + Missense_Mutation SNP C C G C3N-00546_T C3N-00546_N C C c.5560G>C p.Glu1854Gln p.E1854Q ENST00000202677 38/40 350 304 46 307 307 0 strelka-varscan-mutect RALGAPA2,missense_variant,p.Glu1671Gln,ENST00000430436,;RALGAPA2,missense_variant,p.Glu1854Gln,ENST00000202677,NM_020343.3;RALGAPA2,3_prime_UTR_variant,,ENST00000620717,; G ENST00000202677 Transcript missense_variant 5568/6152 5560/5622 1854/1873 E/Q Gag/Cag COSM1410684,COSM1410685,COSM5175742 1 -1 RALGAPA2 HGNC HGNC:16207 protein_coding YES CCDS46584.1 ENSP00000202677 Q2PPJ7 UPI000040F987 NM_020343.3 deleterious(0) 38/40 hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF2,Superfamily_domains:0043732 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs986717961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 48 20412084 20412084 C G 1 0 0 0 0 1 0 0 0 13173 893 31 4 4 RALGAPA2 20 20412084 Missense_Mutation SNP C C3N-00546_T 20412084 44032083 131 14322 TRPC4AP 0 . GRCh38 20 35069386 35069386 + Silent SNP C C T novel C3N-00546_T C3N-00546_N C C c.324G>A p.= p.E108E ENST00000252015 3/19 201 155 46 168 168 0 strelka-varscan-mutect TRPC4AP,synonymous_variant,p.=,ENST00000252015,NM_015638.2;TRPC4AP,synonymous_variant,p.=,ENST00000451813,NM_199368.1; T ENST00000252015 Transcript synonymous_variant 414/3226 324/2394 108/797 E gaG/gaA 1 -1 TRPC4AP HGNC HGNC:16181 protein_coding YES CCDS13246.1 ENSP00000252015 Q8TEL6 UPI000004FADD NM_015638.2 3/19 hmmpanther:PTHR31743,hmmpanther:PTHR31743:SF1,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 48 35069386 35069386 C T 1 0 0 0 0 0 0 0 1 17086 680 24 3 3 TRPC4AP 20 35069386 Silent SNP C C3N-00546_T 14657302 35069386 29374781 132 14323 RBBP8NL 0 . GRCh38 20 62414075 62414084 + Frame_Shift_Del DEL GGGCGCGGCC GGGCGCGGCC - novel C3N-00546_T C3N-00546_N GGGCGCGGCC GGGCGCGGCC c.1267_1276delGGCCGCGCCC p.Gly423ArgfsTer13 p.G423Rfs*13 ENST00000252998 10/14 137 116 21 121 121 0 sindel-varindel RBBP8NL,frameshift_variant,p.Gly423ArgfsTer13,ENST00000252998,NM_080833.2; - ENST00000252998 Transcript frameshift_variant 1424-1433/2793 1267-1276/1995 423-426/664 GRAQ/X GGCCGCGCCCag/ag 1 -1 RBBP8NL HGNC HGNC:16144 protein_coding YES CCDS13498.1 ENSP00000252998 Q8NC74 UPI000013CDA2 NM_080833.2 10/14 hmmpanther:PTHR15107,hmmpanther:PTHR15107:SF3 HIGH 1 deletion 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 48 62414075 62414075 GGGCGCGGCC - 1 0 1 0 1 0 0 0 0 13267 1357 47 0 0 RBBP8NL 20 62414075 Frame_Shift_Del DEL GGGCGCGGCC C3N-00546_T 27344689 62414075 2030092 133 14324 NEFH 0 . GRCh38 22 29481081 29481081 + Silent SNP G G A C3N-00546_T C3N-00546_N G G c.819G>A p.= p.E273E ENST00000310624 1/4 307 239 68 518 517 1 strelka-varscan-mutect NEFH,synonymous_variant,p.=,ENST00000310624,NM_021076.3;AC000035.3,non_coding_transcript_exon_variant,,ENST00000634116,;RFPL1S,upstream_gene_variant,,ENST00000461286,;RFPL1S,upstream_gene_variant,,ENST00000419368,; A ENST00000310624 Transcript synonymous_variant 852/3783 819/3063 273/1020 E gaG/gaA COSM5429609 1 1 NEFH HGNC HGNC:7737 protein_coding YES CCDS13858.1 ENSP00000311997 P12036 UPI00001AEF71 NM_021076.3 1/4 hmmpanther:PTHR23214,hmmpanther:PTHR23214:SF1,Pfam_domain:PF00038,SMART_domains:SM01391 1 LOW 1 SNV 1 1 1 PASS rs917756240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 29481081 29481081 G A 1 0 0 0 0 0 0 0 1 10342 933 33 3 3 NEFH 22 29481081 Silent SNP G C3N-00546_T 29481081 21337387 134 14325 MYH9 0 . GRCh38 22 36349218 36349218 + Missense_Mutation SNP C C A rs762745890 C3N-00546_T C3N-00546_N C C c.19G>T p.Asp7Tyr p.D7Y ENST00000216181 2/41 172 145 27 146 146 0 strelka-varscan-mutect MYH9,missense_variant,p.Asp7Tyr,ENST00000216181,NM_002473.5;MYH9,missense_variant,p.Asp7Tyr,ENST00000401701,;MYH9,missense_variant,p.Asp7Tyr,ENST00000456729,; A ENST00000216181 Transcript missense_variant 250/7501 19/5883 7/1960 D/Y Gat/Tat rs762745890,COSM1033855 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 deleterious(0) 2/41 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762745890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 36349218 36349218 C A 1 0 0 0 0 1 0 0 0 10042 884 31 1 1 MYH9 22 36349218 Missense_Mutation SNP C C3N-00546_T 6868137 36349218 14469250 135 14326 ARSA 0 . GRCh38 22 50625352 50625352 + Silent SNP G G A novel C3N-00546_T C3N-00546_N G G c.1323C>T p.= p.Y441Y ENST00000216124 8/8 70 57 13 50 50 0 strelka-varscan-mutect ARSA,synonymous_variant,p.=,ENST00000216124,NM_000487.5;ARSA,synonymous_variant,p.=,ENST00000395621,NM_001085425.2;ARSA,synonymous_variant,p.=,ENST00000356098,NM_001085426.2;ARSA,synonymous_variant,p.=,ENST00000395619,NM_001085427.2;ARSA,synonymous_variant,p.=,ENST00000453344,NM_001085428.2;ARSA,upstream_gene_variant,,ENST00000610191,;ARSA,intron_variant,,ENST00000608497,;ARSA,downstream_gene_variant,,ENST00000551731,; A ENST00000216124 Transcript synonymous_variant 1716/2050 1323/1530 441/509 Y taC/taT 1 -1 ARSA HGNC HGNC:713 protein_coding YES CCDS14100.2 ENSP00000216124 A0A0C4DFZ2 UPI000013C6C4 NM_000487.5 8/8 Gene3D:3.30.1120.10,Pfam_domain:PF14707,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF229,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 48 50625352 50625352 G A 1 0 0 0 0 0 0 0 1 1130 1372 48 3 3 ARSA 22 50625352 Silent SNP G C3N-00546_T 14276134 50625352 193116 136 14327 HEPH 0 . GRCh38 X 66207272 66207272 + Missense_Mutation SNP C C A novel C3N-00546_T C3N-00546_N C C c.2531C>A p.Thr844Asn p.T844N ENST00000519389 14/21 121 83 38 123 123 0 strelka-varscan-mutect HEPH,missense_variant,p.Thr844Asn,ENST00000519389,NM_138737.4;HEPH,missense_variant,p.Thr790Asn,ENST00000343002,;HEPH,missense_variant,p.Thr793Asn,ENST00000441993,NM_001130860.3;HEPH,missense_variant,p.Thr523Asn,ENST00000336279,NM_014799.3;HEPH,missense_variant,p.Thr601Asn,ENST00000419594,NM_001282141.1;HEPH,missense_variant,p.Thr747Asn,ENST00000425114,;HEPH,non_coding_transcript_exon_variant,,ENST00000471121,; A ENST00000519389 Transcript missense_variant 2710/6013 2531/3639 844/1212 T/N aCt/aAt 1 1 HEPH HGNC HGNC:4866 protein_coding YES CCDS14384.3 ENSP00000430620 Q9BQS7 UPI0001C06560 NM_138737.4 deleterious(0.02) 14/21 hmmpanther:PTHR10127:SF622,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 66207272 66207272 C A 1 0 0 0 0 1 0 0 0 6938 565 20 2 2 HEPH 23 66207272 Missense_Mutation SNP C C3N-00546_T 66207272 89833623 137 14328 IGSF1 0 . GRCh38 X 131275612 131275612 + Missense_Mutation SNP G G T novel C3N-00546_T C3N-00546_N G G c.3065C>A p.Thr1022Asn p.T1022N ENST00000370903 16/20 332 248 84 178 178 0 strelka-varscan-mutect IGSF1,missense_variant,p.Thr1008Asn,ENST00000370904,;IGSF1,missense_variant,p.Thr1022Asn,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Thr1008Asn,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Thr1017Asn,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000467244,; T ENST00000370903 Transcript missense_variant 3348/4594 3065/4026 1022/1341 T/N aCc/aAc 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 tolerated(0.11) 16/20 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF102,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 48 131275612 131275612 G T 1 0 0 0 0 1 0 0 0 7503 1261 44 2 2 IGSF1 23 131275612 Missense_Mutation SNP G C3N-00546_T 65068340 131275612 24765283 138 14329 SRPK3 0 . GRCh38 X 153781554 153781554 + Missense_Mutation SNP C C A rs782626255 C3N-00546_T C3N-00546_N C C c.240C>A p.His80Gln p.H80Q ENST00000370101 3/15 131 115 16 46 46 0 strelka-varscan-mutect SRPK3,missense_variant,p.His147Gln,ENST00000489426,;SRPK3,missense_variant,p.His80Gln,ENST00000370101,NM_014370.3;SRPK3,missense_variant,p.His80Gln,ENST00000393786,NM_001170761.1;SRPK3,missense_variant,p.His80Gln,ENST00000370108,;SRPK3,missense_variant,p.His80Gln,ENST00000370104,NM_001170760.1;SRPK3,missense_variant,p.His38Gln,ENST00000370100,;SRPK3,missense_variant,p.His94Gln,ENST00000430541,;PLXNB3,downstream_gene_variant,,ENST00000538966,NM_001163257.1;PLXNB3,downstream_gene_variant,,ENST00000361971,NM_005393.2;IDH3G,downstream_gene_variant,,ENST00000370092,NM_174869.2;IDH3G,downstream_gene_variant,,ENST00000370093,;IDH3G,downstream_gene_variant,,ENST00000427365,;IDH3G,downstream_gene_variant,,ENST00000217901,NM_004135.3;IDH3G,downstream_gene_variant,,ENST00000619865,;PLXNB3,downstream_gene_variant,,ENST00000411613,;IDH3G,downstream_gene_variant,,ENST00000454076,;PLXNB3,downstream_gene_variant,,ENST00000448847,;PLXNB3,downstream_gene_variant,,ENST00000455214,;SRPK3,upstream_gene_variant,,ENST00000458681,;PLXNB3,downstream_gene_variant,,ENST00000485980,;PLXNB3,downstream_gene_variant,,ENST00000472415,;PLXNB3,downstream_gene_variant,,ENST00000469190,; A ENST00000370101 Transcript missense_variant 286/1958 240/1704 80/567 H/Q caC/caA rs782626255,COSM85255,COSM85256 1 1 SRPK3 HGNC HGNC:11402 protein_coding YES CCDS35441.1 ENSP00000359119 Q9UPE1 UPI000050571A NM_014370.3 tolerated(0.12) 3/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF100,hmmpanther:PTHR24055,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782626255 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 48 153781554 153781554 C A 1 0 0 0 0 1 0 0 0 15522 535 19 1 1 SRPK3 23 153781554 Missense_Mutation SNP C C3N-00546_T 22505942 153781554 2259341 139 14330 ATAD3B 0 . GRCh38 1 1485799 1485799 + Silent SNP C C G C3N-00547_T C3N-00547_N C C c.924C>G p.= p.L308L ENST00000308647 9/16 269 248 21 277 276 1 varscan-mutect ATAD3B,synonymous_variant,p.=,ENST00000308647,NM_031921.4;ATAD3B,downstream_gene_variant,,ENST00000378736,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000472194,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000474481,;ATAD3B,non_coding_transcript_exon_variant,,ENST00000485748,; G ENST00000308647 Transcript synonymous_variant 1040/2448 924/1947 308/648 L ctC/ctG COSM3930326 1 1 ATAD3B HGNC HGNC:24007 protein_coding YES CCDS30.1 ENSP00000311766 Q5T9A4 UPI000013E044 NM_031921.4 9/16 hmmpanther:PTHR23075,hmmpanther:PTHR23075:SF2 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 1485799 1485799 C G 1 0 0 0 0 0 0 0 1 1222 813 29 4 4 ATAD3B 1 1485799 Silent SNP C C3N-00547_T 1485799 247470623 1 14331 CLSTN1 0 . GRCh38 1 9736029 9736029 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1590C>T p.= p.H530H ENST00000377298 12/19 174 115 59 194 194 0 strelka-varscan-mutect CLSTN1,synonymous_variant,p.=,ENST00000377298,NM_001302883.1,NM_001009566.2;CLSTN1,synonymous_variant,p.=,ENST00000361311,NM_014944.4;CLSTN1,synonymous_variant,p.=,ENST00000435891,;CLSTN1,upstream_gene_variant,,ENST00000477264,; A ENST00000377298 Transcript synonymous_variant 2383/5221 1590/2946 530/981 H caC/caT 1 -1 CLSTN1 HGNC HGNC:17447 protein_coding YES CCDS30580.1 ENSP00000366513 O94985 UPI0000127B95 NM_001302883.1,NM_001009566.2 12/19 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4,Gene3D:2.60.120.200,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 9736029 9736029 G A 1 0 0 0 0 0 0 0 1 3333 1368 48 3 3 CLSTN1 1 9736029 Silent SNP G C3N-00547_T 8250230 9736029 239220393 2 14332 DISP3 0 . GRCh38 1 11529642 11529642 + Missense_Mutation SNP C C A rs369425675 C3N-00547_T C3N-00547_N C C c.2885C>A p.Pro962His p.P962H ENST00000294484 14/21 90 66 24 90 90 0 strelka-varscan-mutect DISP3,missense_variant,p.Pro962His,ENST00000294484,NM_020780.1;DISP3,upstream_gene_variant,,ENST00000304391,; A ENST00000294484 Transcript missense_variant 3023/5215 2885/4179 962/1392 P/H cCc/cAc rs369425675 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 deleterious_low_confidence(0) 14/21 MODERATE 1 SNV 1 1 PASS rs369425675 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 11529642 11529642 C A 1 0 0 0 0 1 0 0 0 4347 623 22 2 2 DISP3 1 11529642 Missense_Mutation SNP C C3N-00547_T 1793613 11529642 237426780 3 14333 C1orf167 0 . GRCh38 1 11785283 11785283 + Silent SNP C C A rs773185522 C3N-00547_T C3N-00547_N C C c.3633C>A p.= p.A1211A ENST00000433342 16/21 88 62 26 88 88 0 strelka-varscan-mutect C1orf167,synonymous_variant,p.=,ENST00000433342,NM_001010881.1;C1orf167,synonymous_variant,p.=,ENST00000312793,;C1orf167,synonymous_variant,p.=,ENST00000444493,;C1orf167,synonymous_variant,p.=,ENST00000449278,;MTHFR,downstream_gene_variant,,ENST00000376592,;MTHFR,downstream_gene_variant,,ENST00000376583,;MTHFR,downstream_gene_variant,,ENST00000376590,NM_005957.4;MTHFR,downstream_gene_variant,,ENST00000376585,;C1orf167,upstream_gene_variant,,ENST00000482358,;C1orf167,non_coding_transcript_exon_variant,,ENST00000475041,; A ENST00000433342 Transcript synonymous_variant 3633/4545 3633/4407 1211/1468 A gcC/gcA rs773185522 1 1 C1orf167 HGNC HGNC:25262 protein_coding YES ENSP00000414909 Q5SNV9 UPI0000DD7886 NM_001010881.1 16/21 hmmpanther:PTHR38493,hmmpanther:PTHR38493:SF1,Pfam_domain:PF15736 LOW SNV 5 1 PASS rs773185522 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 11785283 11785283 C A 1 0 0 0 0 0 0 0 1 1972 639 23 1 1 C1orf167 1 11785283 Silent SNP C C3N-00547_T 255641 11785283 237171139 4 14334 CROCC 0 . GRCh38 1 16930301 16930301 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.637C>A p.Gln213Lys p.Q213K ENST00000375541 6/37 346 305 41 360 360 0 strelka-varscan-mutect CROCC,missense_variant,p.Gln213Lys,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Gln73Lys,ENST00000445545,;CROCC,missense_variant,p.Gln107Lys,ENST00000467938,;CROCC,non_coding_transcript_exon_variant,,ENST00000466256,;CROCC,non_coding_transcript_exon_variant,,ENST00000492631,; A ENST00000375541 Transcript missense_variant 706/6656 637/6054 213/2017 Q/K Caa/Aaa 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 tolerated(0.74) 6/37 Pfam_domain:PF15035,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 MODERATE 1 SNV 5 1 PASS rs1469149650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 16930301 16930301 C A 1 0 0 0 0 1 0 0 0 3694 595 21 2 2 CROCC 1 16930301 Missense_Mutation SNP C C3N-00547_T 5145018 16930301 232026121 5 14335 ACTL8 0 . GRCh38 1 17823219 17823219 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.211C>A p.Arg71Ser p.R71S ENST00000375406 2/3 339 294 45 419 418 1 strelka-varscan-mutect ACTL8,missense_variant,p.Arg71Ser,ENST00000375406,NM_030812.2;ACTL8,missense_variant,p.Arg71Ser,ENST00000617065,; A ENST00000375406 Transcript missense_variant 427/1861 211/1101 71/366 R/S Cgc/Agc COSM5188058 1 1 ACTL8 HGNC HGNC:24018 protein_coding YES CCDS183.1 ENSP00000364555 Q9H568 UPI000007008F NM_030812.2 tolerated(0.07) 2/3 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF208,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 17823219 17823219 C A 1 0 0 0 0 1 0 0 0 246 652 23 1 1 ACTL8 1 17823219 Missense_Mutation SNP C C3N-00547_T 892918 17823219 231133203 6 14336 ARID1A 0 . GRCh38 1 26779182 26779182 + Frame_Shift_Del DEL G G - novel C3N-00547_T C3N-00547_N G G c.5287delG p.Glu1763LysfsTer7 p.E1763Kfs*7 ENST00000324856 20/20 40 31 9 42 42 0 sindel-pindel ARID1A,frameshift_variant,p.Glu1763LysfsTer7,ENST00000324856,NM_006015.4;ARID1A,frameshift_variant,p.Glu1381LysfsTer7,ENST00000636219,;ARID1A,frameshift_variant,p.Glu1379LysfsTer7,ENST00000430799,;ARID1A,frameshift_variant,p.Glu1380LysfsTer7,ENST00000374152,;ARID1A,frameshift_variant,p.Glu1546LysfsTer7,ENST00000457599,NM_139135.2;ARID1A,downstream_gene_variant,,ENST00000615191,;ARID1A,downstream_gene_variant,,ENST00000636794,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,;ARID1A,non_coding_transcript_exon_variant,,ENST00000637788,;ARID1A,downstream_gene_variant,,ENST00000636072,; - ENST00000324856 Transcript frameshift_variant 5655/8577 5284/6858 1762/2285 G/X Ggg/gg 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 20/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 HIGH 1 deletion 1 3 1 PASS . . 0 204 6 0 0 0 0 0 -19.99865 1 1 1 1 0 - 7 5 49 26779182 26779182 G - 1 0 1 0 1 0 0 0 0 1049 1348 47 0 0 ARID1A 1 26779182 Frame_Shift_Del DEL G C3N-00547_T 8955963 26779182 222177240 7 14337 SLC9A1 0 . GRCh38 1 27105942 27105942 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1428G>T p.Met476Ile p.M476I ENST00000263980 5/12 411 321 90 399 399 0 strelka-varscan-mutect SLC9A1,missense_variant,p.Met476Ile,ENST00000263980,NM_003047.4;SLC9A1,missense_variant,p.Met476Ile,ENST00000374086,;SLC9A1,upstream_gene_variant,,ENST00000374089,;SLC9A1,upstream_gene_variant,,ENST00000447808,; A ENST00000263980 Transcript missense_variant 2004/4516 1428/2448 476/815 M/I atG/atT 1 -1 SLC9A1 HGNC HGNC:11071 protein_coding YES CCDS295.1 ENSP00000263980 P19634 UPI000012FD1B NM_003047.4 deleterious(0.03) 5/12 Pfam_domain:PF00999,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF59,TIGRFAM_domain:TIGR00840 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 27105942 27105942 C A 1 0 0 0 0 1 0 0 0 14993 478 17 2 2 SLC9A1 1 27105942 Missense_Mutation SNP C C3N-00547_T 326760 27105942 221850480 8 14338 SZT2 0 . GRCh38 1 43416084 43416084 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.755C>A p.Pro252His p.P252H ENST00000562955 6/71 159 114 45 127 127 0 strelka-varscan-mutect SZT2,missense_variant,p.Pro252His,ENST00000562955,NM_015284.3;SZT2,missense_variant,p.Pro252His,ENST00000634258,;SZT2,upstream_gene_variant,,ENST00000470139,;SZT2,downstream_gene_variant,,ENST00000406439,; A ENST00000562955 Transcript missense_variant 755/12281 755/10128 252/3375 P/H cCc/cAc 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 deleterious(0) 6/71 hmmpanther:PTHR14918 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 43416084 43416084 C A 1 0 0 0 0 1 0 0 0 15883 623 22 2 2 SZT2 1 43416084 Missense_Mutation SNP C C3N-00547_T 16310142 43416084 205540338 9 14339 SZT2 0 . GRCh38 1 43426136 43426136 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.3028C>A p.Leu1010Ile p.L1010I ENST00000562955 21/71 184 101 83 133 132 1 strelka-varscan-mutect SZT2,missense_variant,p.Leu1010Ile,ENST00000562955,NM_015284.3;SZT2,missense_variant,p.Leu1010Ile,ENST00000634258,;SZT2,non_coding_transcript_exon_variant,,ENST00000470139,;SZT2,upstream_gene_variant,,ENST00000478140,; A ENST00000562955 Transcript missense_variant 3028/12281 3028/10128 1010/3375 L/I Ctc/Atc 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 tolerated(0.36) 21/71 hmmpanther:PTHR14918,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 43426136 43426136 C A 1 0 0 0 0 1 0 0 0 15883 681 24 2 2 SZT2 1 43426136 Missense_Mutation SNP C C3N-00547_T 10052 43426136 205530286 10 14340 SZT2 0 . GRCh38 1 43430355 43430355 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.4275G>T p.= p.L1425L ENST00000562955 30/71 114 89 25 112 112 0 strelka-varscan-mutect SZT2,synonymous_variant,p.=,ENST00000562955,NM_015284.3;SZT2,synonymous_variant,p.=,ENST00000634258,;SZT2,non_coding_transcript_exon_variant,,ENST00000478140,;SZT2,downstream_gene_variant,,ENST00000470139,; T ENST00000562955 Transcript synonymous_variant 4275/12281 4275/10128 1425/3375 L ctG/ctT 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 30/71 hmmpanther:PTHR14918 LOW 1 SNV 5 1 PASS rs1394793334 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 43430355 43430355 G T 1 0 0 0 0 0 0 0 1 15883 1335 47 2 2 SZT2 1 43430355 Silent SNP G C3N-00547_T 4219 43430355 205526067 11 14341 ST3GAL3 0 . GRCh38 1 43899663 43899663 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.887T>A p.Val296Asp p.V296D ENST00000262915 10/13 633 353 280 449 449 0 strelka-varscan-mutect ST3GAL3,missense_variant,p.Val296Asp,ENST00000262915,NM_174963.3;ST3GAL3,missense_variant,p.Val265Asp,ENST00000351035,NM_174971.3;ST3GAL3,missense_variant,p.Val227Asp,ENST00000361392,NM_006279.3;ST3GAL3,missense_variant,p.Val211Asp,ENST00000361400,NM_174969.2;ST3GAL3,missense_variant,p.Val196Asp,ENST00000372374,NM_001270460.1;ST3GAL3,missense_variant,p.Val227Asp,ENST00000353126,NM_174966.2;ST3GAL3,missense_variant,p.Val296Asp,ENST00000361746,;ST3GAL3,missense_variant,p.Val242Asp,ENST00000347631,NM_174964.2;ST3GAL3,missense_variant,p.Val281Asp,ENST00000372368,NM_174968.3;ST3GAL3,missense_variant,p.Val265Asp,ENST00000372372,;ST3GAL3,missense_variant,p.Val227Asp,ENST00000372369,NM_001270459.1;ST3GAL3,missense_variant,p.Val196Asp,ENST00000332628,;ST3GAL3,missense_variant,p.Val227Asp,ENST00000533933,;ST3GAL3,missense_variant,p.Val211Asp,ENST00000531993,NM_001270462.1,NM_001270461.1;ST3GAL3,missense_variant,p.Val26Asp,ENST00000490502,;ST3GAL3,intron_variant,,ENST00000335430,NM_001270465.1;ST3GAL3,intron_variant,,ENST00000545417,NM_174965.2;ST3GAL3,intron_variant,,ENST00000330208,NM_001270466.1;ST3GAL3,intron_variant,,ENST00000372365,;ST3GAL3,intron_variant,,ENST00000372366,;ST3GAL3,intron_variant,,ENST00000372367,NM_001270463.1;ST3GAL3,intron_variant,,ENST00000528371,NM_001270464.1;ST3GAL3,intron_variant,,ENST00000361812,;ST3GAL3,intron_variant,,ENST00000372362,NM_174967.2;ST3GAL3,intron_variant,,ENST00000531451,NM_174970.2;ST3GAL3,intron_variant,,ENST00000531816,;ST3GAL3,non_coding_transcript_exon_variant,,ENST00000461375,;ST3GAL3,3_prime_UTR_variant,,ENST00000530154,;ST3GAL3,3_prime_UTR_variant,,ENST00000469715,;ST3GAL3,3_prime_UTR_variant,,ENST00000533997,;ST3GAL3,3_prime_UTR_variant,,ENST00000490541,;ST3GAL3,intron_variant,,ENST00000489897,;ST3GAL3,intron_variant,,ENST00000530581,;ST3GAL3,intron_variant,,ENST00000533212,; A ENST00000262915 Transcript missense_variant 1078/2470 887/1335 296/444 V/D gTc/gAc 1 1 ST3GAL3 HGNC HGNC:10866 protein_coding YES CCDS493.1 ENSP00000262915 Q11203 UPI000007440A NM_174963.3 deleterious(0) 10/13 Pfam_domain:PF00777,PIRSF_domain:PIRSF005557,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF52 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 43899663 43899663 T A 1 0 0 0 0 1 0 0 0 15594 1667 58 4 4 ST3GAL3 1 43899663 Missense_Mutation SNP T C3N-00547_T 469308 43899663 205056759 12 14342 COL11A1 0 . GRCh38 1 102974843 102974843 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2795C>A p.Pro932Gln p.P932Q ENST00000370096 36/67 225 133 92 324 324 0 strelka-varscan-mutect COL11A1,missense_variant,p.Pro944Gln,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro932Gln,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro893Gln,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro816Gln,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; T ENST00000370096 Transcript missense_variant 3108/7286 2795/5421 932/1806 P/Q cCa/cAa 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 36/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1287107942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 102974843 102974843 G T 1 0 0 0 0 1 0 0 0 3455 1348 47 2 2 COL11A1 1 102974843 Missense_Mutation SNP G C3N-00547_T 59075180 102974843 145981579 13 14343 RBM15 0 . GRCh38 1 110339680 110339680 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.275G>T p.Gly92Val p.G92V ENST00000369784 1/3 126 90 36 142 142 0 strelka-varscan-mutect RBM15,missense_variant,p.Gly92Val,ENST00000369784,;RBM15,missense_variant,p.Gly92Val,ENST00000618772,NM_022768.4;RBM15,missense_variant,p.Gly92Val,ENST00000602849,;RBM15,missense_variant,p.Gly92Val,ENST00000487146,NM_001201545.1;RBM15,missense_variant,p.Gly48Val,ENST00000617047,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,; T ENST00000369784 Transcript missense_variant 1175/4244 275/2934 92/977 G/V gGt/gTt 1 1 RBM15 HGNC HGNC:14959 protein_coding YES CCDS822.1 ENSP00000358799 Q96T37 UPI000013E1C5 deleterious_low_confidence(0.01) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF43 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 110339680 110339680 G T 1 0 0 0 0 1 0 0 0 13282 1261 44 2 2 RBM15 1 110339680 Missense_Mutation SNP G C3N-00547_T 7364837 110339680 138616742 14 14344 CD53 0 . GRCh38 1 110892489 110892489 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.208G>T p.Gly70Cys p.G70C ENST00000271324 3/8 138 82 56 239 238 1 strelka-varscan-mutect CD53,missense_variant,p.Gly70Cys,ENST00000271324,NM_001040033.1,NM_000560.3;CD53,non_coding_transcript_exon_variant,,ENST00000476408,;CD53,non_coding_transcript_exon_variant,,ENST00000471220,;CD53,upstream_gene_variant,,ENST00000497404,; T ENST00000271324 Transcript missense_variant 320/1505 208/660 70/219 G/C Ggc/Tgc 1 1 CD53 HGNC HGNC:1686 protein_coding YES CCDS829.1 ENSP00000271324 P19397 UPI000000D991 NM_001040033.1,NM_000560.3 deleterious(0) 3/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR19282:SF39,hmmpanther:PTHR19282,PROSITE_patterns:PS00421,PIRSF_domain:PIRSF002419,Pfam_domain:PF00335,Prints_domain:PR00259 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 110892489 110892489 G T 1 0 0 0 0 1 0 0 0 2727 1232 43 2 2 CD53 1 110892489 Missense_Mutation SNP G C3N-00547_T 552809 110892489 138063933 15 14345 SLC16A1 0 . GRCh38 1 112917812 112917812 + Silent SNP G G A rs755634416 C3N-00547_T C3N-00547_N G G c.594C>T p.= p.I198I ENST00000538576 4/5 109 100 9 200 200 0 strelka-varscan-mutect SLC16A1,synonymous_variant,p.=,ENST00000538576,NM_001166496.1;SLC16A1,synonymous_variant,p.=,ENST00000369626,NM_003051.3;SLC16A1,synonymous_variant,p.=,ENST00000458229,;SLC16A1,synonymous_variant,p.=,ENST00000443580,;SLC16A1,synonymous_variant,p.=,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,; A ENST00000538576 Transcript synonymous_variant 1426/4374 594/1503 198/500 I atC/atT rs755634416,COSM1560091,COSM4946001 1 -1 SLC16A1 HGNC HGNC:10922 protein_coding YES CCDS858.1 ENSP00000441065 P53985 A0A024R0H1 UPI00000012F5 NM_001166496.1 4/5 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF24,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00892,Transmembrane_helices:TMhelix 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs755634416 . 0 207 0 2 0 0 0 0 -13.6973 0.9999998 1 1 1 0 A 2 1 49 112917812 112917812 G A 1 0 0 0 0 0 0 0 1 14668 1048 37 1 1 SLC16A1 1 112917812 Silent SNP G C3N-00547_T 2025323 112917812 136038610 16 14346 AP4B1 0 . GRCh38 1 113895282 113895282 + Missense_Mutation SNP G G C rs779808705 C3N-00547_T C3N-00547_N G G c.2003C>G p.Thr668Ser p.T668S ENST00000369569 10/10 174 104 70 230 230 0 strelka-varscan-mutect AP4B1,missense_variant,p.Thr668Ser,ENST00000369569,NM_001253852.1;AP4B1,missense_variant,p.Thr668Ser,ENST00000256658,NM_001253853.1,NM_006594.3;AP4B1,missense_variant,p.Thr500Ser,ENST00000369567,NM_001308312.1;AP4B1,downstream_gene_variant,,ENST00000369564,;AP4B1,downstream_gene_variant,,ENST00000369571,;AP4B1,downstream_gene_variant,,ENST00000432415,;AP4B1-AS1,intron_variant,,ENST00000419536,;AP4B1,non_coding_transcript_exon_variant,,ENST00000462591,;AP4B1,non_coding_transcript_exon_variant,,ENST00000479285,;AP4B1,downstream_gene_variant,,ENST00000489499,;AP4B1,downstream_gene_variant,,ENST00000484201,;AP4B1,downstream_gene_variant,,ENST00000489092,;AP4B1,downstream_gene_variant,,ENST00000479801,;AP4B1,downstream_gene_variant,,ENST00000460653,; C ENST00000369569 Transcript missense_variant 2284/2818 2003/2220 668/739 T/S aCc/aGc rs779808705 1 -1 AP4B1 HGNC HGNC:572 protein_coding YES CCDS865.1 ENSP00000358582 Q9Y6B7 A0A024R0D2 UPI0000072F63 NM_001253852.1 deleterious(0) 10/10 Gene3D:3.30.310.10,Pfam_domain:PF09066,PIRSF_domain:PIRSF002291,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF4,SMART_domains:SM01020 MODERATE 1 SNV 1 1 PASS rs779808705 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 113895282 113895282 G C 1 0 0 0 0 1 0 0 0 867 1261 44 4 4 AP4B1 1 113895282 Missense_Mutation SNP G C3N-00547_T 977470 113895282 135061140 17 14347 FLG 0 . GRCh38 1 152306759 152306759 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.8127C>A p.= p.A2709A ENST00000368799 3/3 230 209 21 195 195 0 varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript synonymous_variant 8163/12747 8127/12186 2709/4061 A gcC/gcA 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999946 1 1 1 0 T 2 4 49 152306759 152306759 G T 1 0 0 0 0 0 0 0 1 5784 1219 43 2 2 FLG 1 152306759 Silent SNP G C3N-00547_T 38411477 152306759 96649663 18 14348 FLG 0 . GRCh38 1 152313290 152313290 + Missense_Mutation SNP G G T rs765626862 C3N-00547_T C3N-00547_N G G c.1596C>A p.His532Gln p.H532Q ENST00000368799 3/3 787 458 329 563 563 0 strelka-varscan-mutect FLG,missense_variant,p.His532Gln,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 1632/12747 1596/12186 532/4061 H/Q caC/caA rs765626862,COSM2206778 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.13) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765626862 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 152313290 152313290 G T 1 0 0 0 0 1 0 0 0 5784 1136 40 1 1 FLG 1 152313290 Missense_Mutation SNP G C3N-00547_T 6531 152313290 96643132 19 14349 LOR 0 . GRCh38 1 153261137 153261137 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.188G>T p.Gly63Val p.G63V ENST00000368742 2/2 32 24 8 70 70 0 strelka-varscan-mutect LOR,missense_variant,p.Gly63Val,ENST00000368742,NM_000427.2; T ENST00000368742 Transcript missense_variant 245/1230 188/939 63/312 G/V gGc/gTc 1 1 LOR HGNC HGNC:6663 protein_coding YES CCDS30870.1 ENSP00000357731 P23490 UPI0000470BBD NM_000427.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR39228,Pfam_domain:PF15847,Prints_domain:PR01228 MODERATE 1 SNV 1 1 PASS rs895518539 . 0 204 6 0 0 0 0 0 -19.95552 1 1 1 1 0 T 3 4 49 153261137 153261137 G T 1 0 0 0 0 1 0 0 0 8799 1203 42 2 2 LOR 1 153261137 Missense_Mutation SNP G C3N-00547_T 947847 153261137 95695285 20 14350 HAPLN2 0 . GRCh38 1 156625304 156625304 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.943C>T p.Pro315Ser p.P315S ENST00000255039 7/7 176 100 76 190 190 0 strelka-varscan-mutect HAPLN2,missense_variant,p.Pro315Ser,ENST00000255039,NM_021817.2;HAPLN2,downstream_gene_variant,,ENST00000456112,;HAPLN2,non_coding_transcript_exon_variant,,ENST00000494218,;HAPLN2,downstream_gene_variant,,ENST00000487988,;HAPLN2,downstream_gene_variant,,ENST00000482204,; T ENST00000255039 Transcript missense_variant 1350/1771 943/1023 315/340 P/S Ccg/Tcg 1 1 HAPLN2 HGNC HGNC:17410 protein_coding YES CCDS1148.1 ENSP00000255039 Q9GZV7 UPI00000012E0 NM_021817.2 tolerated(0.32) 7/7 Gene3D:3.10.100.10,Pfam_domain:PF00193,PROSITE_profiles:PS50963,hmmpanther:PTHR22804,SMART_domains:SM00445,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 156625304 156625304 C T 1 0 0 0 0 1 0 0 0 6841 623 22 3 3 HAPLN2 1 156625304 Missense_Mutation SNP C C3N-00547_T 3364167 156625304 92331118 21 14351 NTRK1 0 . GRCh38 1 156871684 156871684 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.779G>T p.Arg260Met p.R260M ENST00000524377 7/17 477 388 89 325 324 1 strelka-varscan-mutect NTRK1,missense_variant,p.Arg260Met,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Arg230Met,ENST00000392302,NM_001007792.1;NTRK1,missense_variant,p.Arg260Met,ENST00000358660,;NTRK1,missense_variant,p.Arg260Met,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,upstream_gene_variant,,ENST00000534682,; T ENST00000524377 Transcript missense_variant 820/2432 779/2391 260/796 R/M aGg/aTg 1 1 NTRK1 HGNC HGNC:8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 tolerated(0.14) 7/17 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF370,Gene3D:2.60.40.10,Superfamily_domains:SSF48726,Prints_domain:PR01939 MODERATE 1 SNV 1 1 PASS rs1269456924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 156871684 156871684 G T 1 0 0 0 0 1 0 0 0 10772 1000 35 2 2 NTRK1 1 156871684 Missense_Mutation SNP G C3N-00547_T 246380 156871684 92084738 22 14352 OR10J3 0 . GRCh38 1 159314503 159314503 + Missense_Mutation SNP C C A rs754764049 C3N-00547_T C3N-00547_N C C c.157G>T p.Asp53Tyr p.D53Y ENST00000332217 1/1 378 223 155 301 300 1 strelka-varscan-mutect OR10J3,missense_variant,p.Asp53Tyr,ENST00000332217,NM_001004467.1; A ENST00000332217 Transcript missense_variant 157/990 157/990 53/329 D/Y Gac/Tac rs754764049 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs754764049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 159314503 159314503 C A 1 0 0 0 0 1 0 0 0 10988 855 30 2 2 OR10J3 1 159314503 Missense_Mutation SNP C C3N-00547_T 2442819 159314503 89641919 23 14353 FCGR2A 0 . GRCh38 1 161506342 161506342 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.115C>A p.Pro39Thr p.P39T ENST00000271450 3/7 280 219 61 188 187 1 strelka-varscan-mutect FCGR2A,missense_variant,p.Pro39Thr,ENST00000271450,NM_201563.5,NM_001136219.1;FCGR2A,missense_variant,p.Pro38Thr,ENST00000367972,NM_021642.3;FCGR2A,upstream_gene_variant,,ENST00000471026,;FCGR2A,missense_variant,p.Pro4Thr,ENST00000467525,;FCGR2A,missense_variant,p.Pro38Thr,ENST00000483665,;FCGR2A,missense_variant,p.Pro39Thr,ENST00000536731,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000467654,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000473080,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000497474,;FCGR2A,non_coding_transcript_exon_variant,,ENST00000482233,; A ENST00000271450 Transcript missense_variant 153/2412 115/954 39/317 P/T Cca/Aca 1 1 FCGR2A HGNC HGNC:3616 protein_coding YES CCDS44264.1 ENSP00000271450 P12318 UPI000013D8DE NM_201563.5,NM_001136219.1 deleterious(0.02) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF51,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 161506342 161506342 C A 1 0 0 0 0 1 0 0 0 5644 637 22 2 2 FCGR2A 1 161506342 Missense_Mutation SNP C C3N-00547_T 2191839 161506342 87450080 24 14354 LRRC52 0 . GRCh38 1 165563539 165563539 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.657G>A p.= p.E219E ENST00000294818 2/2 144 134 10 157 157 0 strelka-varscan-mutect LRRC52,synonymous_variant,p.=,ENST00000294818,NM_001005214.3;RP11-280O1.2,intron_variant,,ENST00000438275,;RP11-280O1.2,intron_variant,,ENST00000421273,;RP11-280O1.2,intron_variant,,ENST00000416424,; A ENST00000294818 Transcript synonymous_variant 947/1369 657/942 219/313 E gaG/gaA 1 1 LRRC52 HGNC HGNC:32156 protein_coding YES CCDS30930.1 ENSP00000294818 Q8N7C0 UPI000013E1BE NM_001005214.3 2/2 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF37,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.92787 0.9999997 1 1 1 0 A 2 1 49 165563539 165563539 G A 1 0 0 0 0 0 0 0 1 8904 962 34 3 3 LRRC52 1 165563539 Silent SNP G C3N-00547_T 4057197 165563539 83392883 25 14355 CREG1 0 . GRCh38 1 167553416 167553416 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.326C>T p.Pro109Leu p.P109L ENST00000370509 1/4 73 63 10 86 86 0 strelka-varscan-mutect CREG1,missense_variant,p.Pro109Leu,ENST00000370509,NM_003851.2; A ENST00000370509 Transcript missense_variant 352/1974 326/663 109/220 P/L cCg/cTg 1 -1 CREG1 HGNC HGNC:2351 protein_coding YES CCDS1262.1 ENSP00000359540 O75629 UPI0000047822 NM_003851.2 deleterious(0.03) 1/4 hmmpanther:PTHR13343:SF12,hmmpanther:PTHR13343,Gene3D:2.30.110.10,PIRSF_domain:PIRSF036911,Pfam_domain:PF13883,Superfamily_domains:SSF50475 MODERATE 1 SNV 1 1 PASS rs899922736 . 0 204 6 0 0 0 0 0 -19.99513 0.9999999 1 1 1 0 A 3 1 49 167553416 167553416 G A 1 0 0 0 0 1 0 0 0 3665 1116 39 1 1 CREG1 1 167553416 Missense_Mutation SNP G C3N-00547_T 1989877 167553416 81403006 26 14356 DPT 0 . GRCh38 1 168696616 168696616 + Splice_Site SNP C C A novel C3N-00547_T C3N-00547_N C C c.540-1G>T p.X180_splice ENST00000367817 154 91 63 131 131 0 strelka-varscan-mutect DPT,splice_acceptor_variant,,ENST00000367817,NM_001937.4; A ENST00000367817 Transcript splice_acceptor_variant -/1786 540/606 180/201 1 -1 DPT HGNC HGNC:3011 protein_coding YES CCDS1275.1 ENSP00000356791 Q07507 UPI0000032C11 NM_001937.4 3/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 49 168696616 168696616 C A 1 0 0 0 0 0 0 1 0 4554 695 24 2 2 DPT 1 168696616 Splice_Site SNP C C3N-00547_T 1143200 168696616 80259806 27 14357 METTL11B 0 . GRCh38 1 170167535 170167535 + Silent SNP T T C novel C3N-00547_T C3N-00547_N T T c.630T>C p.= p.D210D ENST00000439373 4/4 190 171 19 165 165 0 strelka-varscan-mutect METTL11B,synonymous_variant,p.=,ENST00000439373,NM_001136107.1;METTL11B,non_coding_transcript_exon_variant,,ENST00000367764,; C ENST00000439373 Transcript synonymous_variant 737/992 630/852 210/283 D gaT/gaC 1 1 METTL11B HGNC HGNC:31932 protein_coding YES CCDS44275.1 ENSP00000408058 Q5VVY1 UPI0000418EF1 NM_001136107.1 4/4 hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 170167535 170167535 T C 1 0 0 0 0 0 0 0 1 9437 1461 51 5 5 METTL11B 1 170167535 Silent SNP T C3N-00547_T 1470919 170167535 78788887 28 14358 TNR 0 . GRCh38 1 175391287 175391287 + Splice_Site SNP C C A C3N-00547_T C3N-00547_N C C c.1507+1G>T p.X503_splice ENST00000367674 113 91 22 85 85 0 strelka-varscan-mutect TNR,splice_donor_variant,,ENST00000367674,;TNR,splice_donor_variant,,ENST00000263525,NM_003285.2;TNR,downstream_gene_variant,,ENST00000422274,; A ENST00000367674 Transcript splice_donor_variant -/12949 1507/4077 503/1358 COSM1686374 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 7/22 1 HIGH 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 49 175391287 175391287 C A 1 0 0 0 0 0 0 1 0 16811 521 18 2 2 TNR 1 175391287 Splice_Site SNP C C3N-00547_T 5223752 175391287 73565135 29 14359 FAM163A 0 . GRCh38 1 179813969 179813969 + Missense_Mutation SNP G G C rs765017217 C3N-00547_T C3N-00547_N G G c.284G>C p.Cys95Ser p.C95S ENST00000341785 5/5 225 122 103 202 202 0 strelka-varscan-mutect FAM163A,missense_variant,p.Cys95Ser,ENST00000341785,NM_173509.2;RP11-12M5.3,downstream_gene_variant,,ENST00000415218,;RP11-12M5.3,downstream_gene_variant,,ENST00000453051,; C ENST00000341785 Transcript missense_variant 680/2909 284/504 95/167 C/S tGc/tCc rs765017217 1 1 FAM163A HGNC HGNC:28274 protein_coding YES CCDS1333.1 ENSP00000354891 Q96GL9 UPI000006ED82 NM_173509.2 deleterious(0.01) 5/5 Pfam_domain:PF15069,hmmpanther:PTHR31914,hmmpanther:PTHR31914:SF2 MODERATE 1 SNV 1 1 PASS rs765017217 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 179813969 179813969 G C 1 0 0 0 0 1 0 0 0 5325 1319 46 4 4 FAM163A 1 179813969 Missense_Mutation SNP G C3N-00547_T 4422682 179813969 69142453 30 14360 LAMC2 0 . GRCh38 1 183225607 183225607 + Splice_Site SNP G G T rs149195906 C3N-00547_T C3N-00547_N G G c.954-1G>T p.X318_splice ENST00000264144 411 248 163 345 345 0 strelka-varscan-mutect LAMC2,splice_acceptor_variant,,ENST00000264144,NM_005562.2;LAMC2,splice_acceptor_variant,,ENST00000493293,NM_018891.2; T ENST00000264144 Transcript splice_acceptor_variant -/5147 954/3582 318/1193 rs149195906 1 1 LAMC2 HGNC HGNC:6493 protein_coding YES CCDS1352.1 ENSP00000264144 Q13753 UPI000013D4CA NM_005562.2 7/22 HIGH 1 SNV 1 1 PASS rs149195906 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 49 183225607 183225607 G T 1 0 0 0 0 0 0 1 0 8519 1014 35 2 2 LAMC2 1 183225607 Splice_Site SNP G C3N-00547_T 3411638 183225607 65730815 31 14361 ARPC5 0 . GRCh38 1 183623473 183623473 + Splice_Site SNP T T A novel C3N-00547_T C3N-00547_N T T c.394-2A>T p.X132_splice ENST00000367534 306 238 68 215 215 0 strelka-varscan-mutect ARPC5,splice_acceptor_variant,,ENST00000367534,;ARPC5,3_prime_UTR_variant,,ENST00000359856,NM_005717.3;ARPC5,downstream_gene_variant,,ENST00000294742,NM_001270439.1;ARPC5,downstream_gene_variant,,ENST00000462965,; A ENST00000367534 Transcript splice_acceptor_variant -/622 394/408 132/135 1 -1 ARPC5 HGNC HGNC:708 protein_coding ENSP00000356504 B1ALC0 UPI0000470B43 3/3 HIGH SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 49 183623473 183623473 T A 1 0 0 0 0 0 0 1 0 1117 1594 55 4 4 ARPC5 1 183623473 Splice_Site SNP T C3N-00547_T 397866 183623473 65332949 32 14362 PRG4 0 . GRCh38 1 186306991 186306991 + Silent SNP C C A rs532352521 C3N-00547_T C3N-00547_N C C c.1272C>A p.= p.T424T ENST00000445192 7/13 729 481 248 510 510 0 strelka-varscan-mutect PRG4,synonymous_variant,p.=,ENST00000445192,NM_005807.4;PRG4,synonymous_variant,p.=,ENST00000367483,NM_001127708.2;PRG4,synonymous_variant,p.=,ENST00000635041,NM_001303232.1;PRG4,synonymous_variant,p.=,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,synonymous_variant,p.=,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; A ENST00000445192 Transcript synonymous_variant 1317/5044 1272/4215 424/1404 T acC/acA rs532352521 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 LOW SNV 5 1 PASS rs532352521 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 186306991 186306991 C A 1 0 0 0 0 0 0 0 1 12615 581 21 2 2 PRG4 1 186306991 Silent SNP C C3N-00547_T 2683518 186306991 62649431 33 14363 B3GALT2 0 . GRCh38 1 193180896 193180901 + In_Frame_Del DEL TATCTA TATCTA - novel C3N-00547_T C3N-00547_N TATCTA TATCTA c.662_667delTAGATA p.Leu221_Thr223delinsSer p.L221_T223delinsS ENST00000367434 2/2 172 139 33 193 193 0 sindel-varindel-pindel B3GALT2,inframe_deletion,p.Leu221_Thr223delinsSer,ENST00000367434,NM_003783.3;CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000635846,; - ENST00000367434 Transcript inframe_deletion 1418-1423/3274 662-667/1269 221-223/422 LDT/S tTAGATAcg/tcg 1 -1 B3GALT2 HGNC HGNC:917 protein_coding YES CCDS1383.1 ENSP00000356404 O43825 UPI0000073BFF NM_003783.3 2/2 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF19,Pfam_domain:PF01762 MODERATE 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 193180896 193180896 TATCTA - 1 0 1 0 1 0 0 0 0 1405 1638 57 0 0 B3GALT2 1 193180896 In_Frame_Del DEL TATCTA C3N-00547_T 6873905 193180896 55775526 34 14364 KCNT2 0 . GRCh38 1 196236005 196236005 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.3277A>G p.Ile1093Val p.I1093V ENST00000294725 27/28 220 191 29 206 206 0 strelka-varscan-mutect KCNT2,missense_variant,p.Ile1069Val,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Ile1093Val,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Ile1026Val,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,; C ENST00000294725 Transcript missense_variant 4193/4409 3277/3408 1093/1135 I/V Ata/Gta 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious(0.03) 27/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 196236005 196236005 T C 1 0 0 0 0 1 0 0 0 8008 1493 52 5 5 KCNT2 1 196236005 Missense_Mutation SNP T C3N-00547_T 3055109 196236005 52720417 35 14365 CFHR4 0 . GRCh38 1 196906874 196906874 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.450G>C p.Met150Ile p.M150I ENST00000367416 4/10 124 67 57 117 117 0 strelka-varscan-mutect CFHR4,missense_variant,p.Met150Ile,ENST00000367416,NM_001201551.1,NM_001201550.2;CFHR4,intron_variant,,ENST00000608469,;CFHR4,intron_variant,,ENST00000251424,NM_006684.4;CFHR4,intron_variant,,ENST00000367418,;RP4-608O15.3,intron_variant,,ENST00000367421,; C ENST00000367416 Transcript missense_variant 587/2178 450/1734 150/577 M/I atG/atC 1 1 CFHR4 HGNC HGNC:16979 protein_coding YES CCDS55671.1 ENSP00000356386 Q92496 UPI0001F6C576 NM_001201551.1,NM_001201550.2 tolerated(0.45) 4/10 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF366,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 196906874 196906874 G C 1 0 0 0 0 1 0 0 0 3045 1319 46 4 4 CFHR4 1 196906874 Missense_Mutation SNP G C3N-00547_T 670869 196906874 52049548 36 14366 56 2 CFHR4 0 . GRCh38 1 196906878 196906878 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.454G>T p.Val152Phe p.V152F ENST00000367416 4/10 130 70 60 130 130 0 strelka-varscan-mutect CFHR4,missense_variant,p.Val152Phe,ENST00000367416,NM_001201551.1,NM_001201550.2;CFHR4,intron_variant,,ENST00000608469,;CFHR4,intron_variant,,ENST00000251424,NM_006684.4;CFHR4,intron_variant,,ENST00000367418,;RP4-608O15.3,intron_variant,,ENST00000367421,; T ENST00000367416 Transcript missense_variant 591/2178 454/1734 152/577 V/F Gtt/Ttt 1 1 CFHR4 HGNC HGNC:16979 protein_coding YES CCDS55671.1 ENSP00000356386 Q92496 UPI0001F6C576 NM_001201551.1,NM_001201550.2 tolerated(0.14) 4/10 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF366,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 196906878 196906878 G T 1 0 0 0 0 1 0 0 0 3045 1377 48 2 2 CFHR4 1 196906878 Missense_Mutation SNP G C3N-00547_T 4 196906878 52049544 37 14367 56 2 LHX9 0 . GRCh38 1 197912535 197912535 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.4C>T p.= p.L2L ENST00000367390 1/6 351 304 47 285 285 0 strelka-varscan-mutect LHX9,synonymous_variant,p.=,ENST00000367390,NM_001014434.1;LHX9,synonymous_variant,p.=,ENST00000367391,;LHX9,5_prime_UTR_variant,,ENST00000606127,;LHX9,5_prime_UTR_variant,,ENST00000475727,;LHX9,upstream_gene_variant,,ENST00000367387,NM_020204.2;LHX9,upstream_gene_variant,,ENST00000561173,;LHX9,upstream_gene_variant,,ENST00000367388,;LHX9,non_coding_transcript_exon_variant,,ENST00000615520,; T ENST00000367390 Transcript synonymous_variant 31/7413 4/1167 2/388 L Ctg/Ttg 1 1 LHX9 HGNC HGNC:14222 protein_coding CCDS30962.1 ENSP00000356360 Q9NQ69 UPI000012E664 NM_001014434.1 1/6 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 197912535 197912535 C T 1 0 0 0 0 0 0 0 1 8686 796 28 3 3 LHX9 1 197912535 Silent SNP C C3N-00547_T 1005657 197912535 51043887 38 14368 PTPRC 0 . GRCh38 1 198728347 198728347 + Silent SNP T T G novel C3N-00547_T C3N-00547_N T T c.1728T>G p.= p.S576S ENST00000442510 16/33 366 314 52 239 239 0 strelka-mutect PTPRC,synonymous_variant,p.=,ENST00000442510,NM_002838.4;PTPRC,synonymous_variant,p.=,ENST00000348564,NM_080921.3;PTPRC,synonymous_variant,p.=,ENST00000367367,;PTPRC,synonymous_variant,p.=,ENST00000530727,;PTPRC,synonymous_variant,p.=,ENST00000529828,; G ENST00000442510 Transcript synonymous_variant 1869/5164 1728/3921 576/1306 S tcT/tcG 1 1 PTPRC HGNC HGNC:9666 protein_coding YES CCDS1397.2 ENSP00000411355 A0A0A0MT22 UPI000046FDB4 NM_002838.4 16/33 PIRSF_domain:PIRSF002004,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF284 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 198728347 198728347 T G 1 0 0 0 0 0 0 0 1 12951 1509 53 5 5 PTPRC 1 198728347 Silent SNP T C3N-00547_T 815812 198728347 50228075 39 14369 GPR25 0 . GRCh38 1 200873430 200873430 + Silent SNP G G C novel C3N-00547_T C3N-00547_N G G c.393G>C p.= p.A131A ENST00000304244 1/1 187 147 40 167 167 0 strelka-varscan-mutect GPR25,synonymous_variant,p.=,ENST00000304244,NM_005298.3; C ENST00000304244 Transcript synonymous_variant 476/1224 393/1086 131/361 A gcG/gcC 1 1 GPR25 HGNC HGNC:4480 protein_coding YES CCDS1405.1 ENSP00000301917 O00155 UPI000013E957 NM_005298.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF9,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs1456820974 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 200873430 200873430 G C 1 0 0 0 0 0 0 0 1 6567 1103 39 4 4 GPR25 1 200873430 Silent SNP G C3N-00547_T 2145083 200873430 48082992 40 14370 CACNA1S 0 . GRCh38 1 201089277 201089277 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.881G>T p.Trp294Leu p.W294L ENST00000362061 6/44 694 538 156 451 451 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Trp294Leu,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Trp294Leu,ENST00000367338,; A ENST00000362061 Transcript missense_variant 1108/6166 881/5622 294/1873 W/L tGg/tTg 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 deleterious(0) 6/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 201089277 201089277 C A 1 0 0 0 0 1 0 0 0 2235 595 21 2 2 CACNA1S 1 201089277 Missense_Mutation SNP C C3N-00547_T 215847 201089277 47867145 41 14371 PPP1R12B 0 . GRCh38 1 202427173 202427173 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.835C>A p.= p.R279R ENST00000608999 5/24 216 165 51 254 254 0 strelka-varscan-mutect PPP1R12B,synonymous_variant,p.=,ENST00000391959,;PPP1R12B,synonymous_variant,p.=,ENST00000608999,NM_002481.3;PPP1R12B,synonymous_variant,p.=,ENST00000480184,NM_001167857.1;PPP1R12B,synonymous_variant,p.=,ENST00000356764,NM_001167858.1;PPP1R12B,synonymous_variant,p.=,ENST00000466968,;PPP1R12B,3_prime_UTR_variant,,ENST00000476364,;PPP1R12B,upstream_gene_variant,,ENST00000488330,; A ENST00000608999 Transcript synonymous_variant 988/15248 835/2949 279/982 R Cga/Aga 1 1 PPP1R12B HGNC HGNC:7619 protein_coding YES CCDS1426.1 ENSP00000476755 O60237 UPI0000458A57 NM_002481.3 5/24 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24179:SF18,hmmpanther:PTHR24179,Gene3D:1.25.40.20,Pfam_domain:PF12796,PIRSF_domain:PIRSF038141,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS rs1025729982 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 202427173 202427173 C A 1 0 0 0 0 0 0 0 1 12465 876 31 1 1 PPP1R12B 1 202427173 Silent SNP C C3N-00547_T 1337896 202427173 46529249 42 14372 CHI3L1 0 . GRCh38 1 203180639 203180639 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.725G>T p.Gly242Val p.G242V ENST00000255409 8/10 111 63 48 215 214 1 strelka-varscan-mutect CHI3L1,missense_variant,p.Gly242Val,ENST00000255409,NM_001276.2;CHI3L1,intron_variant,,ENST00000404436,;MYBPH,upstream_gene_variant,,ENST00000255416,NM_004997.2;MYBPH,upstream_gene_variant,,ENST00000621380,;CHI3L1,non_coding_transcript_exon_variant,,ENST00000472064,;CHI3L1,intron_variant,,ENST00000473185,;CHI3L1,upstream_gene_variant,,ENST00000478742,; A ENST00000255409 Transcript missense_variant 851/1792 725/1152 242/383 G/V gGg/gTg COSM3481835 1 -1 CHI3L1 HGNC HGNC:1932 protein_coding YES CCDS1435.1 ENSP00000255409 P36222 A0A024R969 UPI0000072E4F NM_001276.2 tolerated(0.05) 8/10 Gene3D:3.20.20.80,Pfam_domain:PF00704,hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF202,SMART_domains:SM00636,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 203180639 203180639 C A 1 0 0 0 0 1 0 0 0 3099 623 22 2 2 CHI3L1 1 203180639 Missense_Mutation SNP C C3N-00547_T 753466 203180639 45775783 43 14373 PLEKHA6 0 . GRCh38 1 204261407 204261407 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.423G>T p.Glu141Asp p.E141D ENST00000272203 7/23 158 123 35 141 141 0 strelka-varscan-mutect PLEKHA6,missense_variant,p.Glu141Asp,ENST00000272203,NM_014935.4;PLEKHA6,missense_variant,p.Glu141Asp,ENST00000637508,;PLEKHA6,missense_variant,p.Glu161Asp,ENST00000414478,;PLEKHA6,non_coding_transcript_exon_variant,,ENST00000485632,; A ENST00000272203 Transcript missense_variant 740/7401 423/3147 141/1048 E/D gaG/gaT 1 -1 PLEKHA6 HGNC HGNC:17053 protein_coding YES CCDS1444.1 ENSP00000272203 Q9Y2H5 UPI000013D935 NM_014935.4 tolerated(1) 7/23 PROSITE_profiles:PS50003,hmmpanther:PTHR12752,hmmpanther:PTHR12752:SF5,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 204261407 204261407 C A 1 0 0 0 0 1 0 0 0 12153 912 32 2 2 PLEKHA6 1 204261407 Missense_Mutation SNP C C3N-00547_T 1080768 204261407 44695015 44 14374 LRRN2 0 . GRCh38 1 204619178 204619178 + Missense_Mutation SNP G G T rs774495531 C3N-00547_T C3N-00547_N G G c.815C>A p.Pro272Gln p.P272Q ENST00000367175 1/1 236 132 104 181 181 0 strelka-varscan-mutect LRRN2,missense_variant,p.Pro272Gln,ENST00000367175,;LRRN2,missense_variant,p.Pro272Gln,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Pro272Gln,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; T ENST00000367175 Transcript missense_variant 3028/5036 815/2142 272/713 P/Q cCg/cAg rs774495531 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC deleterious(0) 1/1 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF162,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 1 PASS rs774495531 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 204619178 204619178 G T 1 0 0 0 0 1 0 0 0 8941 1116 39 1 1 LRRN2 1 204619178 Missense_Mutation SNP G C3N-00547_T 357771 204619178 44337244 45 14375 SRGAP2 0 . GRCh38 1 206401560 206401560 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.971G>A p.Ser324Asn p.S324N ENST00000573034 7/22 30 23 7 45 45 0 varscan-mutect SRGAP2,missense_variant,p.Ser324Asn,ENST00000573034,NM_015326.4;SRGAP2,missense_variant,p.Ser323Asn,ENST00000624873,NM_001170637.3;SRGAP2,missense_variant,p.Ser323Asn,ENST00000605610,NM_001300952.1;SRGAP2,missense_variant,p.Ser170Asn,ENST00000419187,;SRGAP2,upstream_gene_variant,,ENST00000605476,;SRGAP2,upstream_gene_variant,,ENST00000604423,; A ENST00000573034 Transcript missense_variant 1033/6301 971/3216 324/1071 S/N aGt/aAt 1 1 SRGAP2 HGNC HGNC:19751 protein_coding YES CCDS73017.1 ENSP00000459615 A2RUF3 UPI0000DC3AA7 NM_015326.4 tolerated(0.23) 7/22 PROSITE_profiles:PS51741,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF6,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 206401560 206401560 G A 1 0 0 0 0 1 0 0 0 15505 1029 36 3 3 SRGAP2 1 206401560 Missense_Mutation SNP G C3N-00547_T 1782382 206401560 42554862 46 14376 IL19 0 . GRCh38 1 206841019 206841019 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.493T>A p.Cys165Ser p.C165S ENST00000340758 5/6 298 243 55 172 172 0 strelka-varscan-mutect IL19,missense_variant,p.Cys127Ser,ENST00000620365,;IL19,missense_variant,p.Cys127Ser,ENST00000270218,NM_013371.3;IL19,missense_variant,p.Cys165Ser,ENST00000340758,NM_153758.2;IL19,downstream_gene_variant,,ENST00000476097,; A ENST00000340758 Transcript missense_variant 518/1032 493/648 165/215 C/S Tgt/Agt 1 1 IL19 HGNC HGNC:5990 protein_coding YES CCDS1468.1 ENSP00000343000 Q9UHD0 UPI000019AB76 NM_153758.2 deleterious(0.02) 5/6 Gene3D:1.20.1250.10,Pfam_domain:PF00726,hmmpanther:PTHR11585,hmmpanther:PTHR11585:SF4,Low_complexity_(Seg):seg,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS rs1268606019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 206841019 206841019 T A 1 0 0 0 0 1 0 0 0 7557 1696 59 4 4 IL19 1 206841019 Missense_Mutation SNP T C3N-00547_T 439459 206841019 42115403 47 14377 C4BPA 0 . GRCh38 1 207143990 207143990 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1617G>A p.= p.E539E ENST00000367070 11/12 46 30 16 54 54 0 strelka-varscan-mutect C4BPA,synonymous_variant,p.=,ENST00000367070,NM_000715.3; A ENST00000367070 Transcript synonymous_variant 1811/2243 1617/1794 539/597 E gaG/gaA 1 1 C4BPA HGNC HGNC:1325 protein_coding YES CCDS1477.1 ENSP00000356037 P04003 UPI0000126C28 NM_000715.3 11/12 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF341,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 49 207143990 207143990 G A 1 0 0 0 0 0 0 0 1 2076 1043 36 3 3 C4BPA 1 207143990 Silent SNP G C3N-00547_T 302971 207143990 41812432 48 14378 HSD11B1 0 . GRCh38 1 209734351 209734351 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.709C>T p.Pro237Ser p.P237S ENST00000367028 7/7 323 265 58 256 256 0 strelka-varscan-mutect HSD11B1,missense_variant,p.Pro237Ser,ENST00000367028,NM_181755.2,NM_001206741.1;HSD11B1,missense_variant,p.Pro237Ser,ENST00000367027,NM_005525.3;HSD11B1,missense_variant,p.Pro237Ser,ENST00000261465,;HSD11B1,downstream_gene_variant,,ENST00000615289,; T ENST00000367028 Transcript missense_variant 863/1461 709/879 237/292 P/S Cca/Tca 1 1 HSD11B1 HGNC HGNC:5208 protein_coding YES CCDS1489.1 ENSP00000355995 P28845 X5D2L1 UPI000004C796 NM_181755.2,NM_001206741.1 deleterious(0.04) 7/7 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 209734351 209734351 C T 1 0 0 0 0 1 0 0 0 7270 855 30 3 3 HSD11B1 1 209734351 Missense_Mutation SNP C C3N-00547_T 2590361 209734351 39222071 49 14379 USH2A 0 . GRCh38 1 216196664 216196664 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.4140C>G p.Ile1380Met p.I1380M ENST00000307340 19/72 467 441 26 340 340 0 strelka-varscan-mutect USH2A,missense_variant,p.Ile1380Met,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Ile1380Met,ENST00000366942,NM_007123.5;RP5-1099E6.3,intron_variant,,ENST00000420867,;MRPS18BP1,downstream_gene_variant,,ENST00000414228,; C ENST00000307340 Transcript missense_variant 4527/18883 4140/15609 1380/5202 I/M atC/atG 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 19/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 216196664 216196664 G C 1 0 0 0 0 1 0 0 0 17570 932 33 4 4 USH2A 1 216196664 Missense_Mutation SNP G C3N-00547_T 6462313 216196664 32759758 50 14380 RRP15 0 . GRCh38 1 218307594 218307594 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.667G>T p.Glu223Ter p.E223* ENST00000366932 4/5 272 208 64 194 194 0 strelka-varscan-mutect RRP15,stop_gained,p.Glu223Ter,ENST00000366932,NM_016052.3;RRP15,downstream_gene_variant,,ENST00000491428,; T ENST00000366932 Transcript stop_gained 697/7771 667/849 223/282 E/* Gag/Tag 1 1 RRP15 HGNC HGNC:24255 protein_coding YES CCDS1520.2 ENSP00000355899 Q9Y3B9 UPI0000205BC1 NM_016052.3 4/5 hmmpanther:PTHR13245 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 218307594 218307594 G T 1 0 0 0 0 0 1 0 0 13942 1291 45 2 2 RRP15 1 218307594 Nonsense_Mutation SNP G C3N-00547_T 2110930 218307594 30648828 51 14381 OBSCN 0 . GRCh38 1 228219372 228219372 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.2702A>T p.Gln901Leu p.Q901L ENST00000570156 9/116 241 150 91 179 179 0 strelka-varscan-mutect OBSCN,missense_variant,p.Gln901Leu,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Gln901Leu,ENST00000366707,;OBSCN,intron_variant,,ENST00000422127,NM_001098623.2;OBSCN,intron_variant,,ENST00000636875,;OBSCN,intron_variant,,ENST00000284548,NM_052843.3;OBSCN,downstream_gene_variant,,ENST00000493977,; T ENST00000570156 Transcript missense_variant 2776/26925 2702/26772 901/8923 Q/L cAg/cTg 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.2) 9/116 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1401957305 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 228219372 228219372 A T 1 0 0 0 0 1 0 0 0 10889 188 7 4 4 OBSCN 1 228219372 Missense_Mutation SNP A C3N-00547_T 9911778 228219372 20737050 52 14382 ACTA1 0 . GRCh38 1 229432668 229432668 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.342C>T p.= p.P114P ENST00000366684 3/7 450 254 196 376 376 0 strelka-varscan-mutect ACTA1,synonymous_variant,p.=,ENST00000366684,NM_001100.3;ACTA1,synonymous_variant,p.=,ENST00000366683,; A ENST00000366684 Transcript synonymous_variant 445/1491 342/1134 114/377 P ccC/ccT 1 -1 ACTA1 HGNC HGNC:129 protein_coding YES CCDS1578.1 ENSP00000355645 P68133 UPI0000000860 NM_001100.3 3/7 Gene3D:3.30.420.40,Pfam_domain:PF00022,PROSITE_patterns:PS01132,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF193,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 229432668 229432668 G A 1 0 0 0 0 0 0 0 1 234 1335 47 3 3 ACTA1 1 229432668 Silent SNP G C3N-00547_T 1213296 229432668 19523754 53 14383 GALNT2 0 . GRCh38 1 230255244 230255244 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1036G>C p.Gly346Arg p.G346R ENST00000366672 11/16 370 208 162 264 264 0 strelka-varscan-mutect GALNT2,missense_variant,p.Gly346Arg,ENST00000366672,NM_001291866.1,NM_004481.4;RP5-956O18.2,downstream_gene_variant,,ENST00000440729,;GALNT2,upstream_gene_variant,,ENST00000485438,; C ENST00000366672 Transcript missense_variant 1108/4454 1036/1716 346/571 G/R Ggt/Cgt 1 1 GALNT2 HGNC HGNC:4124 protein_coding YES CCDS1582.1 ENSP00000355632 Q10471 UPI0000074053 NM_001291866.1,NM_004481.4 deleterious(0.02) 11/16 Gene3D:3.90.550.10,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF49,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 230255244 230255244 G C 1 0 0 0 0 1 0 0 0 6084 1348 47 4 4 GALNT2 1 230255244 Missense_Mutation SNP G C3N-00547_T 822576 230255244 18701178 54 14384 MAP10 0 . GRCh38 1 232805336 232805336 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.313C>G p.Gln105Glu p.Q105E ENST00000418460 1/1 508 417 91 418 418 0 strelka-varscan-mutect MAP10,missense_variant,p.Gln105Glu,ENST00000418460,NM_019090.2; G ENST00000418460 Transcript missense_variant 445/3516 313/3144 105/1047 Q/E Caa/Gaa 1 1 MAP10 HGNC HGNC:29265 protein_coding YES CCDS44334.1 ENSP00000403208 Q9P2G4 UPI0000418F25 NM_019090.2 tolerated_low_confidence(0.48) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 232805336 232805336 C G 1 0 0 0 0 1 0 0 0 9149 711 25 4 4 MAP10 1 232805336 Missense_Mutation SNP C C3N-00547_T 2550092 232805336 16151086 55 14385 LYST 0 . GRCh38 1 235759286 235759286 + Missense_Mutation SNP A A C novel C3N-00547_T C3N-00547_N A A c.6567T>G p.Asp2189Glu p.D2189E ENST00000389793 23/53 803 446 357 582 581 1 strelka-varscan-mutect LYST,missense_variant,p.Asp2189Glu,ENST00000389793,NM_000081.3,NM_001301365.1;LYST,3_prime_UTR_variant,,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000489585,; C ENST00000389793 Transcript missense_variant 6742/13480 6567/11406 2189/3801 D/E gaT/gaG 1 -1 LYST HGNC HGNC:1968 protein_coding YES CCDS31062.1 ENSP00000374443 Q99698 UPI000020509E NM_000081.3,NM_001301365.1 tolerated_low_confidence(0.68) 23/53 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF86 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 235759286 235759286 A C 1 0 0 0 0 1 0 0 0 9041 214 8 5 5 LYST 1 235759286 Missense_Mutation SNP A C3N-00547_T 2953950 235759286 13197136 56 14386 HEATR1 0 . GRCh38 1 236574695 236574695 + Frame_Shift_Del DEL C C - rs753548904 C3N-00547_T C3N-00547_N C C c.3293delG p.Gly1098GlufsTer31 p.G1098Efs*31 ENST00000366582 23/45 145 124 21 143 143 0 sindel-varindel-pindel HEATR1,frameshift_variant,p.Gly1098GlufsTer31,ENST00000366582,NM_018072.5;HEATR1,intron_variant,,ENST00000366581,;HEATR1,non_coding_transcript_exon_variant,,ENST00000490339,; - ENST00000366582 Transcript frameshift_variant 3408/8447 3293/6435 1098/2144 G/X gGa/ga rs753548904 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 23/45 Gene3D:1.25.10.10,hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 236574695 236574695 C - 1 0 1 0 1 0 0 0 0 6910 855 30 0 0 HEATR1 1 236574695 Frame_Shift_Del DEL C C3N-00547_T 815409 236574695 12381727 57 14387 RYR2 0 . GRCh38 1 237639139 237639139 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.7053delC p.Ile2353SerfsTer37 p.I2353Sfs*37 ENST00000366574 46/105 157 129 28 123 123 0 sindel-varindel-pindel RYR2,frameshift_variant,p.Ile2353SerfsTer37,ENST00000366574,NM_001035.2;RYR2,frameshift_variant,p.Ile2337SerfsTer37,ENST00000360064,; - ENST00000366574 Transcript frameshift_variant 7370/16562 7053/14904 2351/4967 I/X atC/at 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 46/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 237639139 237639139 C - 1 0 1 0 1 0 0 0 0 14029 816 29 0 0 RYR2 1 237639139 Frame_Shift_Del DEL C C3N-00547_T 1064444 237639139 11317283 58 14388 RYR2 0 . GRCh38 1 237674178 237674178 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.8673C>T p.= p.D2891D ENST00000366574 59/105 166 131 35 136 136 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,upstream_gene_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 8990/16562 8673/14904 2891/4967 D gaC/gaT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 59/105 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 237674178 237674178 C T 1 0 0 0 0 0 0 0 1 14029 477 17 3 3 RYR2 1 237674178 Silent SNP C C3N-00547_T 35039 237674178 11282244 59 14389 RYR2 0 . GRCh38 1 237708946 237708946 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.9990A>T p.= p.A3330A ENST00000366574 69/105 354 212 142 275 275 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 10307/16562 9990/14904 3330/4967 A gcA/gcT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 69/105 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 237708946 237708946 A T 1 0 0 0 0 0 0 0 1 14029 175 7 4 4 RYR2 1 237708946 Silent SNP A C3N-00547_T 34768 237708946 11247476 60 14390 RYR2 0 . GRCh38 1 237709505 237709505 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.10168C>G p.Pro3390Ala p.P3390A ENST00000366574 70/105 258 213 45 194 194 0 strelka-varscan-mutect RYR2,missense_variant,p.Pro3390Ala,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Pro3374Ala,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; G ENST00000366574 Transcript missense_variant 10485/16562 10168/14904 3390/4967 P/A Cca/Gca 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.46) 70/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 237709505 237709505 C G 1 0 0 0 0 1 0 0 0 14029 623 22 4 4 RYR2 1 237709505 Missense_Mutation SNP C C3N-00547_T 559 237709505 11246917 61 14391 MAP1LC3C 0 . GRCh38 1 241996209 241996209 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.398C>A p.Pro133His p.P133H ENST00000357246 4/4 222 173 49 128 127 1 strelka-varscan-mutect MAP1LC3C,missense_variant,p.Pro133His,ENST00000357246,NM_001004343.2;CFL1P4,downstream_gene_variant,,ENST00000451536,; T ENST00000357246 Transcript missense_variant 463/1182 398/444 133/147 P/H cCc/cAc 1 -1 MAP1LC3C HGNC HGNC:13353 protein_coding YES CCDS31074.1 ENSP00000349785 Q9BXW4 UPI0000070E14 NM_001004343.2 tolerated(0.08) 4/4 hmmpanther:PTHR10969,hmmpanther:PTHR10969:SF41 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 241996209 241996209 G T 1 0 0 0 0 1 0 0 0 9155 1232 43 2 2 MAP1LC3C 1 241996209 Missense_Mutation SNP G C3N-00547_T 4286704 241996209 6960213 62 14392 NLRP3 0 . GRCh38 1 247424983 247424983 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.1540T>A p.Cys514Ser p.C514S ENST00000336119 3/9 445 334 111 285 285 0 strelka-varscan-mutect NLRP3,missense_variant,p.Cys514Ser,ENST00000366497,NM_001127461.2;NLRP3,missense_variant,p.Cys514Ser,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,missense_variant,p.Cys514Ser,ENST00000366496,;NLRP3,missense_variant,p.Cys514Ser,ENST00000391828,NM_001079821.2;NLRP3,missense_variant,p.Cys514Ser,ENST00000348069,NM_183395.2;NLRP3,missense_variant,p.Cys514Ser,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript missense_variant 2286/4170 1540/3111 514/1036 C/S Tgc/Agc 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 tolerated(0.09) 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 247424983 247424983 T A 1 0 0 0 0 1 0 0 0 10516 1580 55 4 4 NLRP3 1 247424983 Missense_Mutation SNP T C3N-00547_T 5428774 247424983 1531439 63 14393 OR2T35 0 . GRCh38 1 248638759 248638759 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.500C>A p.Pro167His p.P167H ENST00000317450 1/1 282 242 40 264 264 0 varscan-mutect OR2T35,missense_variant,p.Pro167His,ENST00000317450,NM_001001827.1; T ENST00000317450 Transcript missense_variant 500/972 500/972 167/323 P/H cCc/cAc 1 -1 OR2T35 HGNC HGNC:31257 protein_coding YES CCDS31123.1 ENSP00000324369 Q8NGX2 UPI0000061ED3 NM_001001827.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF18,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 248638759 248638759 G T 1 0 0 0 0 1 0 0 0 11103 1232 43 2 2 OR2T35 1 248638759 Missense_Mutation SNP G C3N-00547_T 1213776 248638759 317663 64 14394 PXDN 0 . GRCh38 2 1649376 1649376 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2404C>A p.Leu802Met p.L802M ENST00000252804 17/23 553 291 262 722 722 0 strelka-varscan-mutect PXDN,missense_variant,p.Leu802Met,ENST00000252804,NM_012293.2;PXDN,downstream_gene_variant,,ENST00000433670,;PXDN,non_coding_transcript_exon_variant,,ENST00000465809,;PXDN,upstream_gene_variant,,ENST00000477093,;PXDN,non_coding_transcript_exon_variant,,ENST00000493779,;PXDN,intron_variant,,ENST00000478155,; T ENST00000252804 Transcript missense_variant 2455/6808 2404/4440 802/1479 L/M Ctg/Atg 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 tolerated(0.35) 17/23 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF75,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 1649376 1649376 G T 1 0 0 0 0 1 0 0 0 13001 991 35 2 2 PXDN 2 1649376 Missense_Mutation SNP G C3N-00547_T 1649376 240544153 65 14395 TRAPPC12 0 . GRCh38 2 3424630 3424630 + Missense_Mutation SNP G G C rs769005424 C3N-00547_T C3N-00547_N G G c.1384G>C p.Glu462Gln p.E462Q ENST00000324266 5/12 94 83 11 109 109 0 strelka-mutect TRAPPC12,missense_variant,p.Glu462Gln,ENST00000324266,NM_016030.5;TRAPPC12,missense_variant,p.Glu462Gln,ENST00000382110,NM_001321102.1;TRAPPC12,missense_variant,p.Glu106Gln,ENST00000441983,;TRAPPC12,missense_variant,p.Glu17Gln,ENST00000457845,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000469147,;TRAPPC12,missense_variant,p.Glu74Gln,ENST00000417243,;TRAPPC12,missense_variant,p.Glu5Gln,ENST00000441099,;TRAPPC12,downstream_gene_variant,,ENST00000411973,; C ENST00000324266 Transcript missense_variant 1579/2508 1384/2208 462/735 E/Q Gag/Cag rs769005424,COSM3743789 1 1 TRAPPC12 HGNC HGNC:24284 protein_coding YES CCDS1652.1 ENSP00000324318 Q8WVT3 UPI000014132D NM_016030.5 tolerated(0.14) 5/12 hmmpanther:PTHR21581,hmmpanther:PTHR21581:SF6 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769005424 . 0 207 0 2 0 0 0 0 -17.656 0.9999999 1 1 1 0 C 3 2 49 3424630 3424630 G C 1 0 0 0 0 1 0 0 0 16942 1059 37 4 4 TRAPPC12 2 3424630 Missense_Mutation SNP G C3N-00547_T 1775254 3424630 238768899 66 14396 DCDC2C 0 . GRCh38 2 3767871 3767871 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.844A>T p.Arg282Trp p.R282W ENST00000399143 7/11 64 27 37 74 74 0 strelka-varscan-mutect DCDC2C,missense_variant,p.Arg282Trp,ENST00000399143,NM_001287444.1;DCDC2C,missense_variant,p.Arg245Trp,ENST00000423741,;DCDC2C,non_coding_transcript_exon_variant,,ENST00000537457,; T ENST00000399143 Transcript missense_variant 1004/1480 844/1095 282/364 R/W Agg/Tgg 1 1 DCDC2C HGNC HGNC:32696 protein_coding YES CCDS74481.1 ENSP00000382097 A8MYV0 UPI0002742D44 NM_001287444.1 deleterious(0) 7/11 hmmpanther:PTHR23004:SF9,hmmpanther:PTHR23004 MODERATE 1 SNV 5 1 PASS rs543756047 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 3767871 3767871 A T 1 0 0 0 0 1 0 0 0 4089 63 3 4 4 DCDC2C 2 3767871 Missense_Mutation SNP A C3N-00547_T 343241 3767871 238425658 67 14397 RNF144A 0 . GRCh38 2 7039627 7039627 + Splice_Site SNP A A T novel C3N-00547_T C3N-00547_N A A c.748-2A>T p.X250_splice ENST00000320892 86 43 43 116 116 0 strelka-varscan-mutect RNF144A,splice_acceptor_variant,,ENST00000320892,NM_014746.4;RNF144A,intron_variant,,ENST00000432850,;RNF144A,splice_acceptor_variant,,ENST00000467276,; T ENST00000320892 Transcript splice_acceptor_variant -/5743 748/879 250/292 1 1 RNF144A HGNC HGNC:20457 protein_coding YES CCDS1657.1 ENSP00000321330 P50876 UPI00001E058A NM_014746.4 8/8 HIGH 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999994 1 1 1 0 T 5 4 49 7039627 7039627 A T 1 0 0 0 0 0 0 1 0 13623 202 7 4 4 RNF144A 2 7039627 Splice_Site SNP A C3N-00547_T 3271756 7039627 235153902 68 14398 APOB 0 . GRCh38 2 21007119 21007119 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.9749G>T p.Gly3250Val p.G3250V ENST00000233242 26/29 302 192 110 346 346 0 strelka-varscan-mutect APOB,missense_variant,p.Gly3250Val,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript missense_variant 9877/14121 9749/13692 3250/4563 G/V gGa/gTa 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 21007119 21007119 C A 1 0 0 0 0 1 0 0 0 907 855 30 2 2 APOB 2 21007119 Missense_Mutation SNP C C3N-00547_T 13967492 21007119 221186410 69 14399 SLC35F6 0 . GRCh38 2 26775049 26775049 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.156G>T p.= p.V52V ENST00000344420 3/6 96 50 46 102 102 0 strelka-varscan-mutect SLC35F6,synonymous_variant,p.=,ENST00000344420,NM_017877.3;CENPA,intron_variant,,ENST00000475662,;SLC35F6,intron_variant,,ENST00000482746,;SLC35F6,missense_variant,p.Trp28Leu,ENST00000429494,;SLC35F6,intron_variant,,ENST00000414029,; T ENST00000344420 Transcript synonymous_variant 218/3898 156/1116 52/371 V gtG/gtT 1 1 SLC35F6 HGNC HGNC:26055 protein_coding YES CCDS1728.1 ENSP00000345528 Q8N357 UPI0000071B52 NM_017877.3 3/6 PIRSF_domain:PIRSF036436,hmmpanther:PTHR13146,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1200554995 . 0 200 10 0 0 0 0 0 -20 0.9999983 1 1 1 0 T 2 4 49 26775049 26775049 G T 1 0 0 0 0 0 0 0 1 14864 1362 47 2 2 SLC35F6 2 26775049 Silent SNP G C3N-00547_T 5767930 26775049 215418480 70 14400 SLC35F6 0 . GRCh38 2 26778435 26778435 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1040G>T p.Gly347Val p.G347V ENST00000344420 6/6 111 71 40 106 106 0 strelka-varscan-mutect SLC35F6,missense_variant,p.Gly347Val,ENST00000344420,NM_017877.3;CENPA,intron_variant,,ENST00000475662,;SLC35F6,downstream_gene_variant,,ENST00000482746,;SLC35F6,3_prime_UTR_variant,,ENST00000429494,;SLC35F6,3_prime_UTR_variant,,ENST00000414029,; T ENST00000344420 Transcript missense_variant 1102/3898 1040/1116 347/371 G/V gGc/gTc 1 1 SLC35F6 HGNC HGNC:26055 protein_coding YES CCDS1728.1 ENSP00000345528 Q8N357 UPI0000071B52 NM_017877.3 tolerated(0.51) 6/6 PIRSF_domain:PIRSF036436,hmmpanther:PTHR13146,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 26778435 26778435 G T 1 0 0 0 0 1 0 0 0 14864 1203 42 2 2 SLC35F6 2 26778435 Missense_Mutation SNP G C3N-00547_T 3386 26778435 215415094 71 14401 LTBP1 0 . GRCh38 2 33020940 33020940 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.597G>A p.= p.G199G ENST00000404816 3/34 63 40 23 82 82 0 strelka-varscan-mutect LTBP1,synonymous_variant,p.=,ENST00000404816,NM_206943.2; A ENST00000404816 Transcript synonymous_variant 950/6333 597/5166 199/1721 G ggG/ggA 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 3/34 PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,SMART_domains:SM00181 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 33020940 33020940 G A 1 0 0 0 0 0 0 0 1 8979 1161 41 3 3 LTBP1 2 33020940 Silent SNP G C3N-00547_T 6242505 33020940 209172589 72 14402 FAM98A 0 . GRCh38 2 33585416 33585416 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.917G>T p.Gly306Val p.G306V ENST00000238823 8/8 174 105 69 162 162 0 strelka-varscan-mutect FAM98A,missense_variant,p.Gly306Val,ENST00000238823,NM_001304538.1,NM_015475.4;FAM98A,3_prime_UTR_variant,,ENST00000403368,;FAM98A,downstream_gene_variant,,ENST00000498340,;FAM98A,non_coding_transcript_exon_variant,,ENST00000474985,;FAM98A,non_coding_transcript_exon_variant,,ENST00000475122,;FAM98A,downstream_gene_variant,,ENST00000492649,; A ENST00000238823 Transcript missense_variant 1058/2816 917/1557 306/518 G/V gGt/gTt 1 -1 FAM98A HGNC HGNC:24520 protein_coding YES CCDS33179.1 ENSP00000238823 Q8NCA5 UPI000013F15A NM_001304538.1,NM_015475.4 deleterious(0) 8/8 Pfam_domain:PF10239,hmmpanther:PTHR31353,hmmpanther:PTHR31353:SF9 MODERATE 1 SNV 1 1 PASS rs1371255855 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 33585416 33585416 C A 1 0 0 0 0 1 0 0 0 5514 507 18 2 2 FAM98A 2 33585416 Missense_Mutation SNP C C3N-00547_T 564476 33585416 208608113 73 14403 USP34 0 . GRCh38 2 61266169 61266169 + Splice_Site SNP T T A novel C3N-00547_T C3N-00547_N T T c.5434-2A>T p.X1812_splice ENST00000398571 59 52 7 82 82 0 strelka-varscan-mutect USP34,splice_acceptor_variant,,ENST00000398571,NM_014709.3;USP34,splice_acceptor_variant,,ENST00000453734,;USP34,intron_variant,,ENST00000472706,;USP34,splice_acceptor_variant,,ENST00000484179,;USP34,upstream_gene_variant,,ENST00000492882,; A ENST00000398571 Transcript splice_acceptor_variant -/11357 5434/10641 1812/3546 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 41/79 HIGH 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -16.23525 1 1 1 1 0 A 5 1 49 61266169 61266169 T A 1 0 0 0 0 0 0 1 0 17607 1594 55 4 4 USP34 2 61266169 Splice_Site SNP T C3N-00547_T 27680753 61266169 180927360 74 14404 APLF 0 . GRCh38 2 68645872 68645872 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.51C>A p.= p.T17T ENST00000303786 2/3 249 223 26 272 272 0 strelka-varscan-mutect PROKR1,synonymous_variant,p.=,ENST00000303786,;APLF,synonymous_variant,p.=,ENST00000394342,NM_138964.2;APLF,non_coding_transcript_exon_variant,,ENST00000627740,; A ENST00000303786 Transcript synonymous_variant 471/4273 51/1182 17/393 T acC/acA 1 1 PROKR1 HGNC HGNC:4524 protein_coding YES CCDS1889.1 ENSP00000303775 Q8TCW9 UPI000003EAA7 2/3 hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF229 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 68645872 68645872 C A 1 0 0 0 0 0 0 0 1 897 581 21 2 2 APLF 2 68645872 Silent SNP C C3N-00547_T 7379703 68645872 173547657 75 14405 EXOC6B 0 . GRCh38 2 72513245 72513246 + Frame_Shift_Ins INS - - A novel C3N-00547_T C3N-00547_N - - c.1053dupT p.Val352CysfsTer3 p.V352Cfs*3 ENST00000272427 11/22 120 97 23 127 127 0 sindel-varindel-pindel EXOC6B,frameshift_variant,p.Val352CysfsTer3,ENST00000272427,NM_001321729.1,NM_001321734.1,NM_015189.1;EXOC6B,frameshift_variant,p.Val352CysfsTer3,ENST00000410104,;EXOC6B,frameshift_variant,p.Val352CysfsTer3,ENST00000634650,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000485398,;EXOC6B,3_prime_UTR_variant,,ENST00000410112,; A ENST00000272427 Transcript frameshift_variant 1184-1185/5918 1053-1054/2436 351-352/811 -/X -/T 1 -1 EXOC6B HGNC HGNC:17085 protein_coding YES CCDS46333.1 ENSP00000272427 Q9Y2D4 UPI000046995C NM_001321729.1,NM_001321734.1,NM_015189.1 11/22 hmmpanther:PTHR12702:SF3,hmmpanther:PTHR12702,PIRSF_domain:PIRSF025007 HIGH 1 insertion 2 1 PASS . . 0 181 0 21 8 0 0 0 -14.06389 0.06059829 0 1 0 0 A 7 5 49 72513245 72513245 - A 1 0 1 1 0 0 0 0 0 5177 478 17 0 0 EXOC6B 2 72513245 Frame_Shift_Ins INS - C3N-00547_T 3867373 72513245 169680284 76 14406 LRRTM4 0 . GRCh38 2 77518945 77518945 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.924G>A p.= p.L308L ENST00000409093 3/4 135 85 50 177 177 0 strelka-varscan-mutect LRRTM4,synonymous_variant,p.=,ENST00000409088,NM_024993.4;LRRTM4,synonymous_variant,p.=,ENST00000409911,;LRRTM4,synonymous_variant,p.=,ENST00000409282,NM_001282928.1;LRRTM4,synonymous_variant,p.=,ENST00000409093,NM_001282924.1;LRRTM4,synonymous_variant,p.=,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; T ENST00000409093 Transcript synonymous_variant 1261/2247 924/1773 308/590 L ttG/ttA 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 77518945 77518945 C T 1 0 0 0 0 0 0 0 1 8948 477 17 3 3 LRRTM4 2 77518945 Silent SNP C C3N-00547_T 5005700 77518945 164674584 77 14407 KCNIP3 0 . GRCh38 2 95310504 95310504 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.165A>T p.= p.T55T ENST00000295225 2/9 163 103 60 135 135 0 strelka-varscan-mutect KCNIP3,synonymous_variant,p.=,ENST00000295225,NM_013434.4;KCNIP3,synonymous_variant,p.=,ENST00000360990,;KCNIP3,intron_variant,,ENST00000377181,;KCNIP3,non_coding_transcript_exon_variant,,ENST00000475491,; T ENST00000295225 Transcript synonymous_variant 300/2940 165/771 55/256 T acA/acT 1 1 KCNIP3 HGNC HGNC:15523 protein_coding YES CCDS2013.1 ENSP00000295225 Q9Y2W7 A0A024RE22 UPI0000000CCD NM_013434.4 2/9 hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF61 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 95310504 95310504 A T 1 0 0 0 0 0 0 0 1 7957 175 7 4 4 KCNIP3 2 95310504 Silent SNP A C3N-00547_T 17791559 95310504 146883025 78 14408 DUSP2 0 . GRCh38 2 96144344 96144344 + Silent SNP C C A rs762195420 C3N-00547_T C3N-00547_N C C c.540G>T p.= p.L180L ENST00000288943 3/4 194 147 47 170 170 0 strelka-varscan-mutect DUSP2,synonymous_variant,p.=,ENST00000288943,NM_004418.3;AC012307.2,downstream_gene_variant,,ENST00000449242,;DUSP2,non_coding_transcript_exon_variant,,ENST00000488952,; A ENST00000288943 Transcript synonymous_variant 626/1688 540/945 180/314 L ctG/ctT rs762195420 1 -1 DUSP2 HGNC HGNC:3068 protein_coding YES CCDS2016.1 ENSP00000288943 Q05923 UPI000012995D NM_004418.3 3/4 Gene3D:3.90.190.10,Pfam_domain:PF00782,PIRSF_domain:PIRSF000939,PROSITE_profiles:PS50054,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF109,SMART_domains:SM00195,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS rs762195420 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 96144344 96144344 C A 1 0 0 0 0 0 0 0 1 4641 465 17 2 2 DUSP2 2 96144344 Silent SNP C C3N-00547_T 833840 96144344 146049185 79 14409 CIAO1 0 . GRCh38 2 96267670 96267670 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.334G>T p.Ala112Ser p.A112S ENST00000488633 3/7 330 224 106 287 287 0 strelka-varscan-mutect CIAO1,missense_variant,p.Ala112Ser,ENST00000488633,NM_004804.2;TMEM127,upstream_gene_variant,,ENST00000258439,NM_001193304.2,NM_017849.3;TMEM127,upstream_gene_variant,,ENST00000432959,;CIAO1,non_coding_transcript_exon_variant,,ENST00000469320,;CIAO1,non_coding_transcript_exon_variant,,ENST00000272402,;CIAO1,non_coding_transcript_exon_variant,,ENST00000491394,; T ENST00000488633 Transcript missense_variant 553/1533 334/1020 112/339 A/S Gct/Tct 1 1 CIAO1 HGNC HGNC:14280 protein_coding YES CCDS2019.1 ENSP00000418287 O76071 UPI0000127987 NM_004804.2 tolerated(0.68) 3/7 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,HAMAP:MF_03037,hmmpanther:PTHR19920,hmmpanther:PTHR19920:SF0,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 96267670 96267670 G T 1 0 0 0 0 1 0 0 0 3179 1203 42 2 2 CIAO1 2 96267670 Missense_Mutation SNP G C3N-00547_T 123326 96267670 145925859 80 14410 SLC9A4 0 . GRCh38 2 102503672 102503672 + Missense_Mutation SNP A A T rs201016853 C3N-00547_T C3N-00547_N A A c.945A>T p.Leu315Phe p.L315F ENST00000295269 3/12 192 118 74 187 187 0 strelka-varscan-mutect SLC9A4,missense_variant,p.Leu315Phe,ENST00000295269,NM_001011552.3;SLC9A4,non_coding_transcript_exon_variant,,ENST00000492154,; T ENST00000295269 Transcript missense_variant 1402/4138 945/2397 315/798 L/F ttA/ttT rs201016853 1 1 SLC9A4 HGNC HGNC:11077 protein_coding YES CCDS33264.1 ENSP00000295269 Q6AI14 UPI000047F996 NM_001011552.3 deleterious(0.03) 3/12 Pfam_domain:PF00999,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF103,TIGRFAM_domain:TIGR00840,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs201016853 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 102503672 102503672 A T 1 0 0 0 0 1 0 0 0 14998 417 15 4 4 SLC9A4 2 102503672 Missense_Mutation SNP A C3N-00547_T 6236002 102503672 139689857 81 14411 ST6GAL2 0 . GRCh38 2 106843095 106843095 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.883A>T p.Ser295Cys p.S295C ENST00000409382 2/6 36 21 15 35 35 0 strelka-varscan-mutect ST6GAL2,missense_variant,p.Ser295Cys,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Ser295Cys,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Ser295Cys,ENST00000409087,NM_001142352.1;ST6GAL2,downstream_gene_variant,,ENST00000419159,;AC016994.2,downstream_gene_variant,,ENST00000425419,; A ENST00000409382 Transcript missense_variant 1494/7275 883/1590 295/529 S/C Agc/Tgc 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 2/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713,Pfam_domain:PF00777 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 106843095 106843095 T A 1 0 0 0 0 1 0 0 0 15600 1580 55 4 4 ST6GAL2 2 106843095 Missense_Mutation SNP T C3N-00547_T 4339423 106843095 135350434 82 14412 LIMS1 0 . GRCh38 2 108655081 108655081 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.7T>G p.Phe3Val p.F3V ENST00000338045 1/10 164 135 29 169 169 0 strelka-varscan-mutect LIMS1,missense_variant,p.Phe3Val,ENST00000338045,NM_001193485.2;LIMS1,missense_variant,p.Phe3Val,ENST00000414829,;LIMS1,intron_variant,,ENST00000544547,NM_001193483.2;LIMS1,intron_variant,,ENST00000393310,NM_001193488.1;LIMS1,intron_variant,,ENST00000409441,NM_001193484.1;LIMS1,intron_variant,,ENST00000410093,NM_001193482.1;LIMS1,intron_variant,,ENST00000332345,NM_004987.5;LIMS1,intron_variant,,ENST00000428064,;LIMS1,upstream_gene_variant,,ENST00000434274,;LIMS1,non_coding_transcript_exon_variant,,ENST00000462817,;LIMS1,intron_variant,,ENST00000449684,;LIMS1,non_coding_transcript_exon_variant,,ENST00000474038,;LIMS1,non_coding_transcript_exon_variant,,ENST00000496653,;LIMS1,intron_variant,,ENST00000422797,; G ENST00000338045 Transcript missense_variant 270/1876 7/1164 3/387 F/V Ttc/Gtc 1 1 LIMS1 HGNC HGNC:6616 protein_coding YES CCDS54385.1 ENSP00000337598 P48059 UPI0000207FB5 NM_001193485.2 tolerated_low_confidence(0.07) 1/10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 108655081 108655081 T G 1 0 0 0 0 1 0 0 0 8711 1609 56 5 5 LIMS1 2 108655081 Missense_Mutation SNP T C3N-00547_T 1811986 108655081 133538448 83 14413 PTPN4 0 . GRCh38 2 119809885 119809885 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.32G>T p.Arg11Ile p.R11I ENST00000263708 2/27 172 133 39 173 173 0 strelka-varscan-mutect PTPN4,missense_variant,p.Arg11Ile,ENST00000263708,NM_002830.3;PTPN4,missense_variant,p.Arg11Ile,ENST00000488279,;PTPN4,missense_variant,p.Arg11Ile,ENST00000420482,;PTPN4,non_coding_transcript_exon_variant,,ENST00000485247,;PTPN4,non_coding_transcript_exon_variant,,ENST00000460289,;PTPN4,downstream_gene_variant,,ENST00000460162,; T ENST00000263708 Transcript missense_variant 803/10300 32/2781 11/926 R/I aGa/aTa 1 1 PTPN4 HGNC HGNC:9656 protein_coding YES CCDS2129.1 ENSP00000263708 P29074 A0A024RAE8 UPI0000000CA9 NM_002830.3 deleterious(0.01) 2/27 hmmpanther:PTHR19134:SF321,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000927 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 119809885 119809885 G T 1 0 0 0 0 1 0 0 0 12944 942 33 2 2 PTPN4 2 119809885 Missense_Mutation SNP G C3N-00547_T 11154804 119809885 122383644 84 14414 POTEF 0 . GRCh38 2 130074594 130074594 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2878G>T p.Ala960Ser p.A960S ENST00000409914 17/17 199 164 35 207 207 0 strelka-varscan-mutect POTEF,missense_variant,p.Ala960Ser,ENST00000409914,NM_001099771.2; A ENST00000409914 Transcript missense_variant 3278/3842 2878/3228 960/1075 A/S Gcg/Tcg 1 -1 POTEF HGNC HGNC:33905 protein_coding YES CCDS46409.1 ENSP00000386786 A5A3E0 UPI0000418FEA NM_001099771.2 deleterious_low_confidence(0.04) 17/17 Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs1171274753 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 130074594 130074594 C A 1 0 0 0 0 1 0 0 0 12379 739 26 2 2 POTEF 2 130074594 Missense_Mutation SNP C C3N-00547_T 10264709 130074594 112118935 85 14415 CCDC74B 0 . GRCh38 2 130140269 130140269 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.786G>T p.= p.L262L ENST00000310463 5/8 142 105 37 152 152 0 strelka-varscan-mutect CCDC74B,synonymous_variant,p.=,ENST00000310463,NM_207310.2;CCDC74B,synonymous_variant,p.=,ENST00000409943,NM_001258307.1;CCDC74B,intron_variant,,ENST00000392984,;CCDC74B,downstream_gene_variant,,ENST00000409234,;CCDC74B,downstream_gene_variant,,ENST00000409128,;CCDC74B,downstream_gene_variant,,ENST00000457413,;CCDC74B,downstream_gene_variant,,ENST00000441670,;MED15P9,downstream_gene_variant,,ENST00000427638,;CCDC74B,non_coding_transcript_exon_variant,,ENST00000496704,;CCDC74B,downstream_gene_variant,,ENST00000423263,;CCDC74B,downstream_gene_variant,,ENST00000434929,;CCDC74B,upstream_gene_variant,,ENST00000498526,;MED15P9,downstream_gene_variant,,ENST00000424716,; A ENST00000310463 Transcript synonymous_variant 924/1549 786/1143 262/380 L ctG/ctT 1 -1 CCDC74B HGNC HGNC:25267 protein_coding YES CCDS2155.1 ENSP00000308873 Q96LY2 UPI000006D822 NM_207310.2 5/8 Low_complexity_(Seg):seg,hmmpanther:PTHR14882,hmmpanther:PTHR14882:SF5 LOW SNV 2 1 PASS rs1325812982 . 0 207 0 0 2 0 0 0 -20 0.9988276 1 1 1 0 A 2 1 49 130140269 130140269 C A 1 0 0 0 0 0 0 0 1 2548 697 25 2 2 CCDC74B 2 130140269 Silent SNP C C3N-00547_T 65675 130140269 112053260 86 14416 POTEI 0 . GRCh38 2 130463166 130463166 + Missense_Mutation SNP C C A rs564436995 C3N-00547_T C3N-00547_N C C c.2878G>T p.Ala960Ser p.A960S ENST00000451531 15/15 399 285 114 462 462 0 strelka-varscan-mutect POTEI,missense_variant,p.Ala960Ser,ENST00000451531,NM_001277406.1;POTEI,downstream_gene_variant,,ENST00000631234,;POTEI,downstream_gene_variant,,ENST00000615053,; A ENST00000451531 Transcript missense_variant 3309/7020 2878/3228 960/1075 A/S Gcg/Tcg rs564436995 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0.03) 15/15 Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs564436995 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 130463166 130463166 C A 1 0 0 0 0 1 0 0 0 12382 739 26 2 2 POTEI 2 130463166 Missense_Mutation SNP C C3N-00547_T 322897 130463166 111730363 87 14417 AMER3 0 . GRCh38 2 130762171 130762171 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.99G>A p.= p.G33G ENST00000423981 2/2 135 123 12 152 152 0 strelka-mutect AMER3,synonymous_variant,p.=,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,synonymous_variant,p.=,ENST00000321420,NM_152698.2;AMER3,synonymous_variant,p.=,ENST00000458606,;AMER3,synonymous_variant,p.=,ENST00000431758,; A ENST00000423981 Transcript synonymous_variant 209/6172 99/2586 33/861 G ggG/ggA 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 LOW 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 130762171 130762171 G A 1 0 0 0 0 0 0 0 1 669 1161 41 3 3 AMER3 2 130762171 Silent SNP G C3N-00547_T 299005 130762171 111431358 88 14418 AMER3 0 . GRCh38 2 130764512 130764512 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2440G>T p.Gly814Cys p.G814C ENST00000423981 2/2 325 248 77 327 327 0 strelka-varscan-mutect AMER3,missense_variant,p.Gly814Cys,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Gly814Cys,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; T ENST00000423981 Transcript missense_variant 2550/6172 2440/2586 814/861 G/C Ggc/Tgc 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 tolerated(0.31) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 130764512 130764512 G T 1 0 0 0 0 1 0 0 0 669 1232 43 2 2 AMER3 2 130764512 Missense_Mutation SNP G C3N-00547_T 2341 130764512 111429017 89 14419 POTEE 0 . GRCh38 2 131263648 131263648 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.2195delC p.Pro732LeufsTer12 p.P732Lfs*12 ENST00000356920 15/15 67 43 24 123 123 0 sindel-varindel-pindel POTEE,frameshift_variant,p.Pro732LeufsTer12,ENST00000356920,NM_001083538.1;POTEE,3_prime_UTR_variant,,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; - ENST00000356920 Transcript frameshift_variant 2529/4159 2193/3228 731/1075 F/X ttC/tt 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 15/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 HIGH 1 deletion 1 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 131263648 131263648 C - 1 0 1 0 1 0 0 0 0 12378 854 30 0 0 POTEE 2 131263648 Frame_Shift_Del DEL C C3N-00547_T 499136 131263648 110929881 90 14420 ANKRD30BL 0 . GRCh38 2 132161688 132161688 + Frame_Shift_Del DEL G G - rs555962095 C3N-00547_T C3N-00547_N G G c.18delC p.Ala7ProfsTer27 p.A7Pfs*27 ENST00000409867 1/6 146 101 45 141 141 0 sindel-varindel-pindel ANKRD30BL,frameshift_variant,p.Ala7ProfsTer27,ENST00000409867,;ANKRD30BL,intron_variant,,ENST00000470729,;ANKRD30BL,upstream_gene_variant,,ENST00000471048,;ANKRD30BL,frameshift_variant,p.Ala7ProfsTer27,ENST00000295181,;ANKRD30BL,non_coding_transcript_exon_variant,,ENST00000481691,; - ENST00000409867 Transcript frameshift_variant 268/1251 18/777 6/258 A/X gcC/gc rs555962095 1 -1 ANKRD30BL HGNC HGNC:35167 protein_coding YES ENSP00000386398 A7E2S9 UPI0000160B5E 1/6 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF10 HIGH 1 deletion 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 132161688 132161688 G - 1 0 1 0 1 0 0 0 0 763 1103 39 0 0 ANKRD30BL 2 132161688 Frame_Shift_Del DEL G C3N-00547_T 898040 132161688 110031841 91 14421 NCKAP5 0 . GRCh38 2 132783982 132783982 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.2829C>A p.= p.P943P ENST00000409261 14/20 38 31 7 31 31 0 strelka-varscan-mutect NCKAP5,synonymous_variant,p.=,ENST00000409261,NM_207363.2;NCKAP5,synonymous_variant,p.=,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; T ENST00000409261 Transcript synonymous_variant 3203/7594 2829/5730 943/1909 P ccC/ccA 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -18.06298 1 1 1 1 0 T 2 4 49 132783982 132783982 G T 1 0 0 0 0 0 0 0 1 10241 1335 47 2 2 NCKAP5 2 132783982 Silent SNP G C3N-00547_T 622294 132783982 109409547 92 14422 LCT 0 . GRCh38 2 135817422 135817422 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1626G>T p.Glu542Asp p.E542D ENST00000264162 6/17 182 131 51 166 166 0 strelka-varscan-mutect LCT,missense_variant,p.Glu542Asp,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; A ENST00000264162 Transcript missense_variant 1637/6279 1626/5784 542/1927 E/D gaG/gaT 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 tolerated(0.05) 6/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 135817422 135817422 C A 1 0 0 0 0 1 0 0 0 8599 796 28 2 2 LCT 2 135817422 Missense_Mutation SNP C C3N-00547_T 3033440 135817422 106376107 93 14423 LRP1B 0 . GRCh38 2 141229390 141229390 + Missense_Mutation SNP C C G C3N-00547_T C3N-00547_N C C c.643G>C p.Glu215Gln p.E215Q ENST00000389484 6/91 117 87 30 230 230 0 strelka-varscan-mutect LRP1B,missense_variant,p.Glu215Gln,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; G ENST00000389484 Transcript missense_variant 1615/16535 643/13800 215/4599 E/Q Gag/Cag COSM2152527 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.66) 6/91 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 141229390 141229390 C G 1 0 0 0 0 1 0 0 0 8850 835 29 4 4 LRP1B 2 141229390 Missense_Mutation SNP C C3N-00547_T 5411968 141229390 100964139 94 14424 LRP1B 0 . GRCh38 2 141229412 141229412 + Silent SNP T T C novel C3N-00547_T C3N-00547_N T T c.621A>G p.= p.L207L ENST00000389484 6/91 97 74 23 183 183 0 strelka-varscan-mutect LRP1B,synonymous_variant,p.=,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; C ENST00000389484 Transcript synonymous_variant 1593/16535 621/13800 207/4599 L ttA/ttG 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 6/91 Gene3D:2.120.10.30,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 141229412 141229412 T C 1 0 0 0 0 0 0 0 1 8850 1751 61 5 5 LRP1B 2 141229412 Silent SNP T C3N-00547_T 22 141229412 100964117 95 14425 ZEB2 0 . GRCh38 2 144398707 144398707 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2480C>A p.Pro827His p.P827H ENST00000637267 9/11 192 144 48 189 188 1 strelka-varscan-mutect ZEB2,missense_variant,p.Pro827His,ENST00000637267,;ZEB2,missense_variant,p.Pro852His,ENST00000636471,;ZEB2,missense_variant,p.Pro827His,ENST00000627532,NM_014795.3;ZEB2,missense_variant,p.Pro827His,ENST00000636026,;ZEB2,missense_variant,p.Pro715His,ENST00000638087,;ZEB2,missense_variant,p.Pro715His,ENST00000637304,;ZEB2,missense_variant,p.Pro715His,ENST00000638007,;ZEB2,missense_variant,p.Pro715His,ENST00000637045,;ZEB2,missense_variant,p.Pro715His,ENST00000636413,;ZEB2,missense_variant,p.Pro568His,ENST00000638128,;ZEB2,missense_variant,p.Pro827His,ENST00000409487,;ZEB2,missense_variant,p.Pro803His,ENST00000539609,NM_001171653.1;ZEB2,missense_variant,p.Pro827His,ENST00000558170,;ZEB2,missense_variant,p.Pro826His,ENST00000303660,;ZEB2,intron_variant,,ENST00000440875,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,upstream_gene_variant,,ENST00000637873,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,3_prime_UTR_variant,,ENST00000636732,; T ENST00000637267 Transcript missense_variant 3321/9856 2480/3645 827/1214 P/H cCc/cAc 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 tolerated(0.12) 9/11 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 144398707 144398707 G T 1 0 0 0 0 1 0 0 0 18200 1232 43 2 2 ZEB2 2 144398707 Missense_Mutation SNP G C3N-00547_T 3169295 144398707 97794822 96 14426 KIF5C 0 . GRCh38 2 148929280 148929280 + Splice_Site SNP G G T novel C3N-00547_T C3N-00547_N G G c.218-1G>T p.X73_splice ENST00000435030 191 140 51 192 191 1 strelka-varscan-mutect KIF5C,splice_acceptor_variant,,ENST00000435030,NM_004522.2; T ENST00000435030 Transcript splice_acceptor_variant -/6931 218/2874 73/957 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 2/25 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999998 1 1 1 0 T 5 4 49 148929280 148929280 G T 1 0 0 0 0 0 0 1 0 8172 956 33 2 2 KIF5C 2 148929280 Splice_Site SNP G C3N-00547_T 4530573 148929280 93264249 97 14427 KIF5C 0 . GRCh38 2 148991164 148991164 + Frame_Shift_Del DEL G G - rs754771513 C3N-00547_T C3N-00547_N G G c.1873delG p.Glu625SerfsTer19 p.E625Sfs*19 ENST00000435030 16/26 120 79 41 153 153 0 sindel-varindel-pindel KIF5C,frameshift_variant,p.Glu625SerfsTer19,ENST00000435030,NM_004522.2;KIF5C,non_coding_transcript_exon_variant,,ENST00000464066,;KIF5C,non_coding_transcript_exon_variant,,ENST00000460377,; - ENST00000435030 Transcript frameshift_variant 2239/6931 1871/2874 624/957 R/X cGg/cg rs754771513 1 1 KIF5C HGNC HGNC:6325 protein_coding YES CCDS74586.1 ENSP00000393379 O60282 UPI000012DDB7 NM_004522.2 16/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF380 HIGH 1 deletion 1 2 1 PASS . . 0 203 4 3 0 0 0 0 -20 0.9999679 1 1 1 0 - 7 5 49 148991164 148991164 G - 1 0 1 0 1 0 0 0 0 8172 1116 39 0 0 KIF5C 2 148991164 Frame_Shift_Del DEL G C3N-00547_T 61884 148991164 93202365 98 14428 TANC1 0 . GRCh38 2 159149140 159149140 + Splice_Site SNP A A G novel C3N-00547_T C3N-00547_N A A c.365-2A>G p.X122_splice ENST00000263635 41 23 18 38 38 0 strelka-mutect TANC1,splice_acceptor_variant,,ENST00000263635,NM_033394.2,NM_001145909.1;TANC1,intron_variant,,ENST00000454300,;TANC1,splice_acceptor_variant,,ENST00000464096,;TANC1,non_coding_transcript_exon_variant,,ENST00000465963,; G ENST00000263635 Transcript splice_acceptor_variant -/7470 365/5586 122/1861 1 1 TANC1 HGNC HGNC:29364 protein_coding YES CCDS42766.1 ENSP00000263635 Q9C0D5 UPI0000421D80 NM_033394.2,NM_001145909.1 5/26 HIGH 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 49 159149140 159149140 A G 1 0 0 0 0 0 0 1 0 15941 202 7 5 5 TANC1 2 159149140 Splice_Site SNP A C3N-00547_T 10157976 159149140 83044389 99 14429 SCN3A 0 . GRCh38 2 165154652 165154652 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1180C>A p.Arg394Ser p.R394S ENST00000283254 11/28 316 220 96 303 303 0 strelka-varscan-mutect SCN3A,missense_variant,p.Arg394Ser,ENST00000360093,;SCN3A,missense_variant,p.Arg394Ser,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Arg394Ser,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Arg394Ser,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,; T ENST00000283254 Transcript missense_variant 1648/9091 1180/6003 394/2000 R/S Cgt/Agt 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 11/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs1006669315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 165154652 165154652 G T 1 0 0 0 0 1 0 0 0 14187 1145 40 1 1 SCN3A 2 165154652 Missense_Mutation SNP G C3N-00547_T 6005512 165154652 77038877 100 14430 XIRP2 0 . GRCh38 2 167239958 167239958 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.962C>G p.Thr321Arg p.T321R ENST00000409195 6/11 65 53 12 119 119 0 strelka-varscan-mutect XIRP2,missense_variant,p.Thr321Arg,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Thr99Arg,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Thr146Arg,ENST00000628543,;XIRP2,missense_variant,p.Thr354Arg,ENST00000409728,NM_001199143.1;XIRP2,missense_variant,p.Thr321Arg,ENST00000409043,NM_001079810.3;XIRP2,missense_variant,p.Thr99Arg,ENST00000409605,NM_001199145.1; G ENST00000409195 Transcript missense_variant 1051/12675 962/10650 321/3549 T/R aCa/aGa 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.15) 6/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 167239958 167239958 C G 1 0 0 0 0 1 0 0 0 17989 478 17 4 4 XIRP2 2 167239958 Missense_Mutation SNP C C3N-00547_T 2085306 167239958 74953571 101 14431 LRP2 0 . GRCh38 2 169175348 169175348 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.10613G>T p.Cys3538Phe p.C3538F ENST00000263816 55/79 234 176 58 233 233 0 strelka-varscan-mutect LRP2,missense_variant,p.Cys3538Phe,ENST00000263816,NM_004525.2;LRP2,downstream_gene_variant,,ENST00000461418,; A ENST00000263816 Transcript missense_variant 10899/15808 10613/13968 3538/4655 C/F tGc/tTc 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 deleterious(0) 55/79 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF232,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 169175348 169175348 C A 1 0 0 0 0 1 0 0 0 8851 710 25 2 2 LRP2 2 169175348 Missense_Mutation SNP C C3N-00547_T 1935390 169175348 73018181 102 14432 MYO3B 0 . GRCh38 2 170407830 170407830 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.2636C>T p.Pro879Leu p.P879L ENST00000408978 22/35 243 184 59 188 188 0 strelka-varscan-mutect MYO3B,missense_variant,p.Pro879Leu,ENST00000408978,NM_138995.4;MYO3B,missense_variant,p.Pro879Leu,ENST00000409044,NM_001083615.3;MYO3B,missense_variant,p.Pro888Leu,ENST00000484338,;AC012594.1,intron_variant,,ENST00000625968,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,non_coding_transcript_exon_variant,,ENST00000469359,;MYO3B,missense_variant,p.Pro879Leu,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; T ENST00000408978 Transcript missense_variant 2779/5529 2636/4026 879/1341 P/L cCt/cTt 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 deleterious(0) 22/35 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF476,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 170407830 170407830 C T 1 0 0 0 0 1 0 0 0 10078 681 24 3 3 MYO3B 2 170407830 Missense_Mutation SNP C C3N-00547_T 1232482 170407830 71785699 103 14433 AC013461.1 0 . GRCh38 2 173191135 173191135 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.540T>G p.Ser180Arg p.S180R ENST00000375213 7/20 217 168 49 253 252 1 strelka-varscan-mutect AC013461.1,missense_variant,p.Ser180Arg,ENST00000338983,NM_133646.2;AC013461.1,missense_variant,p.Ser180Arg,ENST00000375213,NM_016653.2;AC013461.1,missense_variant,p.Ser180Arg,ENST00000409176,;AC013461.1,missense_variant,p.Ser180Arg,ENST00000539448,;AC013461.1,downstream_gene_variant,,ENST00000422149,;MLK7-AS1,intron_variant,,ENST00000419609,;MLK7-AS1,intron_variant,,ENST00000422703,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000480606,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000468408,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000476618,; G ENST00000375213 Transcript missense_variant 618/3741 540/2403 180/800 S/R agT/agG 1 1 AC013461.1 Clone_based_vega_gene protein_coding YES CCDS42777.1 ENSP00000364361 Q9NYL2 UPI0000073F69 NM_016653.2 deleterious(0.04) 7/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF424,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 173191135 173191135 T G 1 0 0 0 0 1 0 0 0 124 1664 58 5 5 AC013461.1 2 173191135 Missense_Mutation SNP T C3N-00547_T 2783305 173191135 69002394 104 14434 HOXD10 0 . GRCh38 2 176117183 176117183 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.350C>A p.Ser117Tyr p.S117Y ENST00000249501 1/2 128 88 40 136 136 0 strelka-varscan-mutect HOXD10,missense_variant,p.Ser117Tyr,ENST00000249501,NM_002148.3;HOXD-AS2,downstream_gene_variant,,ENST00000440016,;HOXD10,intron_variant,,ENST00000490088,;HOXD10,intron_variant,,ENST00000549469,; A ENST00000249501 Transcript missense_variant 605/1989 350/1023 117/340 S/Y tCt/tAt COSM4691025 1 1 HOXD10 HGNC HGNC:5133 protein_coding YES CCDS2266.1 ENSP00000249501 P28358 UPI000013CC87 NM_002148.3 deleterious(0) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF49 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 176117183 176117183 C A 1 0 0 0 0 1 0 0 0 7213 913 32 2 2 HOXD10 2 176117183 Missense_Mutation SNP C C3N-00547_T 2926048 176117183 66076346 105 14435 TTN 0 . GRCh38 2 178552199 178552199 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.90701T>C p.Phe30234Ser p.F30234S ENST00000589042 335/363 79 70 9 78 78 0 strelka-varscan-mutect TTN,missense_variant,p.Phe30234Ser,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Phe28593Ser,ENST00000591111,;TTN,missense_variant,p.Phe28593Ser,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Phe27666Ser,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Phe21169Ser,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Phe21361Ser,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Phe21294Ser,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; G ENST00000589042 Transcript missense_variant 90926/109224 90701/107976 30234/35991 F/S tTt/tCt 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 335/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -19.49389 1 1 1 1 0 G 3 3 49 178552199 178552199 A G 1 0 0 0 0 1 0 0 0 17245 14 1 5 5 TTN 2 178552199 Missense_Mutation SNP A C3N-00547_T 2435016 178552199 63641330 106 14436 TTN 0 . GRCh38 2 178557384 178557384 + Missense_Mutation SNP C C T rs202001776 C3N-00547_T C3N-00547_N C C c.87878G>A p.Arg29293His p.R29293H ENST00000589042 329/363 398 378 20 656 656 0 strelka-varscan-mutect TTN,missense_variant,p.Arg29293His,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Arg27652His,ENST00000591111,;TTN,missense_variant,p.Arg27652His,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Arg26725His,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Arg20228His,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Arg20420His,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Arg20353His,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,non_coding_transcript_exon_variant,,ENST00000624360,; T ENST00000589042 Transcript missense_variant 88103/109224 87878/107976 29293/35991 R/H cGc/cAc rs202001776 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 329/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 uncertain_significance MODERATE SNV 5 1 1 PASS rs202001776 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 178557384 178557384 C T 1 0 0 0 0 1 0 0 0 17245 768 27 1 1 TTN 2 178557384 Missense_Mutation SNP C C3N-00547_T 5185 178557384 63636145 107 14437 TTN 0 . GRCh38 2 178718923 178718923 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.24277A>G p.Met8093Val p.M8093V ENST00000589042 84/363 96 91 5 112 112 0 strelka-varscan-mutect TTN,missense_variant,p.Met8093Val,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Met7776Val,ENST00000591111,;TTN,missense_variant,p.Met7776Val,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Met6849Val,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,;TTN-AS1,downstream_gene_variant,,ENST00000625536,;TTN-AS1,downstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000626117,; C ENST00000589042 Transcript missense_variant 24502/109224 24277/107976 8093/35991 M/V Atg/Gtg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 84/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 178718923 178718923 T C 1 0 0 0 0 1 0 0 0 17245 1493 52 5 5 TTN 2 178718923 Missense_Mutation SNP T C3N-00547_T 161539 178718923 63474606 108 14438 NEUROD1 0 . GRCh38 2 181677950 181677950 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.911C>A p.Pro304His p.P304H ENST00000295108 2/2 446 340 106 481 481 0 strelka-varscan-mutect NEUROD1,missense_variant,p.Pro304His,ENST00000295108,NM_002500.4;CERKL,intron_variant,,ENST00000479558,;CERKL,intron_variant,,ENST00000497337,;NEUROD1,intron_variant,,ENST00000496876,; T ENST00000295108 Transcript missense_variant 1369/2852 911/1071 304/356 P/H cCt/cAt COSM5660034 1 -1 NEUROD1 HGNC HGNC:7762 protein_coding YES CCDS2283.1 ENSP00000295108 Q13562 A0A0S2Z493 UPI000013E207 NM_002500.4 deleterious(0.01) 2/2 PIRSF_domain:PIRSF015618 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 181677950 181677950 G T 1 0 0 0 0 1 0 0 0 10385 1000 35 2 2 NEUROD1 2 181677950 Missense_Mutation SNP G C3N-00547_T 2959027 181677950 60515579 109 14439 COL5A2 0 . GRCh38 2 189078568 189078568 + Missense_Mutation SNP C C T rs754787960 C3N-00547_T C3N-00547_N C C c.1007G>A p.Gly336Asp p.G336D ENST00000374866 16/54 335 270 65 364 363 1 strelka-varscan-mutect COL5A2,missense_variant,p.Gly336Asp,ENST00000374866,NM_000393.3;COL5A2,intron_variant,,ENST00000618828,; T ENST00000374866 Transcript missense_variant,splice_region_variant 1282/6949 1007/4500 336/1499 G/D gGt/gAt rs754787960 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 deleterious(0) 16/54 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs754787960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 189078568 189078568 C T 1 0 0 0 0 1 0 0 0 3486 521 18 3 3 COL5A2 2 189078568 Missense_Mutation SNP C C3N-00547_T 7400618 189078568 53114961 110 14440 DNAH7 0 . GRCh38 2 195858522 195858522 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.8019G>T p.Leu2673Phe p.L2673F ENST00000312428 43/65 76 69 7 64 64 0 strelka-varscan-mutect DNAH7,missense_variant,p.Leu2673Phe,ENST00000312428,NM_018897.2; A ENST00000312428 Transcript missense_variant 8120/12394 8019/12075 2673/4024 L/F ttG/ttT 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.01) 43/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF12777 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -15.12267 0.9999947 1 1 1 0 A 3 1 49 195858522 195858522 C A 1 0 0 0 0 1 0 0 0 4421 709 25 2 2 DNAH7 2 195858522 Missense_Mutation SNP C C3N-00547_T 6779954 195858522 46335007 111 14441 PARD3B 0 . GRCh38 2 205172349 205172349 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.1759G>A p.Val587Met p.V587M ENST00000406610 12/23 170 157 13 155 155 0 strelka-varscan-mutect PARD3B,missense_variant,p.Val587Met,ENST00000406610,NM_001302769.1;PARD3B,missense_variant,p.Val451Met,ENST00000613457,;PARD3B,missense_variant,p.Val513Met,ENST00000614500,;PARD3B,missense_variant,p.Val513Met,ENST00000622699,;PARD3B,missense_variant,p.Val525Met,ENST00000358768,NM_152526.5;PARD3B,missense_variant,p.Val587Met,ENST00000351153,NM_057177.6;PARD3B,missense_variant,p.Val587Met,ENST00000349953,NM_205863.3;PARD3B,missense_variant,p.Val587Met,ENST00000462231,; A ENST00000406610 Transcript missense_variant 1966/8174 1759/3618 587/1205 V/M Gtg/Atg 1 1 PARD3B HGNC HGNC:14446 protein_coding YES CCDS77511.1 ENSP00000385848 Q8TEW8 UPI0000070178 NM_001302769.1 deleterious(0.03) 12/23 Gene3D:2.30.42.10,hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF4,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 205172349 205172349 G A 1 0 0 0 0 1 0 0 0 11524 1261 44 3 3 PARD3B 2 205172349 Missense_Mutation SNP G C3N-00547_T 9313827 205172349 37021180 112 14442 PTH2R 0 . GRCh38 2 208493287 208493287 + Missense_Mutation SNP G G T rs770797290 C3N-00547_T C3N-00547_N G G c.1281G>T p.Met427Ile p.M427I ENST00000272847 13/13 18 11 7 32 32 0 strelka-varscan-mutect PTH2R,missense_variant,p.Met427Ile,ENST00000272847,NM_005048.3;PTH2R,missense_variant,p.Met316Ile,ENST00000617735,;AC019185.4,intron_variant,,ENST00000424628,;PTH2R,intron_variant,,ENST00000419079,; T ENST00000272847 Transcript missense_variant 1494/2713 1281/1653 427/550 M/I atG/atT rs770797290 1 1 PTH2R HGNC HGNC:9609 protein_coding YES CCDS2383.1 ENSP00000272847 P49190 UPI000005041E NM_005048.3 tolerated(0.11) 13/13 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF69,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs770797290 . 3 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 208493287 208493287 G T 1 0 0 0 0 1 0 0 0 12916 1377 48 2 2 PTH2R 2 208493287 Missense_Mutation SNP G C3N-00547_T 3320938 208493287 33700242 113 14443 CPS1 0 . GRCh38 2 210612275 210612275 + Silent SNP T T A C3N-00547_T C3N-00547_N T T c.2568T>A p.= p.R856R ENST00000430249 21/39 494 425 69 485 485 0 strelka-varscan-mutect CPS1,synonymous_variant,p.=,ENST00000233072,NM_001875.4;CPS1,synonymous_variant,p.=,ENST00000430249,NM_001122633.2;CPS1,synonymous_variant,p.=,ENST00000451903,NM_001122634.3; A ENST00000430249 Transcript synonymous_variant 2623/5698 2568/4521 856/1506 R cgT/cgA COSM4154775,COSM4154776 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 21/39 hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,Pfam_domain:PF02787,TIGRFAM_domain:TIGR01369,Gene3D:1.10.1030.10,SMART_domains:SM01096,Superfamily_domains:0034967 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 210612275 210612275 T A 1 0 0 0 0 0 0 0 1 3619 1625 57 4 4 CPS1 2 210612275 Silent SNP T C3N-00547_T 2118988 210612275 31581254 114 14444 ABCA12 0 . GRCh38 2 215052512 215052512 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.482T>A p.Leu161His p.L161H ENST00000272895 5/53 397 260 137 429 429 0 strelka-varscan-mutect ABCA12,missense_variant,p.Leu161His,ENST00000272895,NM_173076.2;AC072062.3,intron_variant,,ENST00000628464,;AC072062.3,intron_variant,,ENST00000626134,;AC072062.3,intron_variant,,ENST00000626771,; T ENST00000272895 Transcript missense_variant 702/9100 482/7788 161/2595 L/H cTc/cAc 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 tolerated(0.08) 5/53 MODERATE 1 SNV 1 1 PASS rs1481610281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 215052512 215052512 A T 1 0 0 0 0 1 0 0 0 34 304 11 4 4 ABCA12 2 215052512 Missense_Mutation SNP A C3N-00547_T 4440237 215052512 27141017 115 14445 PTPRN 0 . GRCh38 2 219307532 219307532 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.192G>T p.= p.V64V ENST00000295718 3/23 76 65 11 109 109 0 strelka-varscan-mutect PTPRN,synonymous_variant,p.=,ENST00000295718,NM_002846.3;PTPRN,synonymous_variant,p.=,ENST00000409251,NM_001199763.1;PTPRN,synonymous_variant,p.=,ENST00000440552,;PTPRN,5_prime_UTR_variant,,ENST00000423636,NM_001199764.1;PTPRN,5_prime_UTR_variant,,ENST00000446182,;PTPRN,5_prime_UTR_variant,,ENST00000412847,;PTPRN,5_prime_UTR_variant,,ENST00000442029,;PTPRN,5_prime_UTR_variant,,ENST00000451506,;AC114803.3,downstream_gene_variant,,ENST00000417355,;PTPRN,non_coding_transcript_exon_variant,,ENST00000468454,;PTPRN,3_prime_UTR_variant,,ENST00000606213,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,non_coding_transcript_exon_variant,,ENST00000477819,;PTPRN,non_coding_transcript_exon_variant,,ENST00000484986,;PTPRN,upstream_gene_variant,,ENST00000476930,; A ENST00000295718 Transcript synonymous_variant 433/3784 192/2940 64/979 V gtG/gtT 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 3/23 Pfam_domain:PF14948,SMART_domains:SM01305 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99998 1 1 1 1 0 A 2 1 49 219307532 219307532 C A 1 0 0 0 0 0 0 0 1 12961 581 21 2 2 PTPRN 2 219307532 Silent SNP C C3N-00547_T 4255020 219307532 22885997 116 14446 DNPEP 0 . GRCh38 2 219382092 219382092 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.984G>T p.= p.L328L ENST00000273075 11/15 183 159 24 148 148 0 strelka-varscan-mutect DNPEP,synonymous_variant,p.=,ENST00000273075,NM_012100.2;DNPEP,synonymous_variant,p.=,ENST00000523282,;DNPEP,synonymous_variant,p.=,ENST00000373972,NM_001319121.1;DNPEP,synonymous_variant,p.=,ENST00000457935,;DNPEP,downstream_gene_variant,,ENST00000322176,;DNPEP,downstream_gene_variant,,ENST00000429013,;DNPEP,downstream_gene_variant,,ENST00000521459,;DNPEP,downstream_gene_variant,,ENST00000434339,;DNPEP,downstream_gene_variant,,ENST00000430206,;DNPEP,downstream_gene_variant,,ENST00000519905,;DNPEP,upstream_gene_variant,,ENST00000490371,;DNPEP,3_prime_UTR_variant,,ENST00000373966,;DNPEP,3_prime_UTR_variant,,ENST00000373963,;DNPEP,non_coding_transcript_exon_variant,,ENST00000488881,;DNPEP,downstream_gene_variant,,ENST00000460963,;DNPEP,downstream_gene_variant,,ENST00000520694,;DNPEP,downstream_gene_variant,,ENST00000522421,;DNPEP,downstream_gene_variant,,ENST00000523527,;DNPEP,downstream_gene_variant,,ENST00000519698,;DNPEP,upstream_gene_variant,,ENST00000488051,;DNPEP,upstream_gene_variant,,ENST00000462779,; A ENST00000273075 Transcript synonymous_variant 1205/2425 984/1458 328/485 L ctG/ctT 1 -1 DNPEP HGNC HGNC:2981 protein_coding YES CCDS42823.1 ENSP00000273075 Q9ULA0 UPI0000169DCA NM_012100.2 11/15 hmmpanther:PTHR28570,hmmpanther:PTHR28570:SF3,Gene3D:3.40.630.10,Pfam_domain:PF02127,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 219382092 219382092 C A 1 0 0 0 0 0 0 0 1 4492 581 21 2 2 DNPEP 2 219382092 Silent SNP C C3N-00547_T 74560 219382092 22811437 117 14447 SPEG 0 . GRCh38 2 219448994 219448994 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1836G>A p.= p.P612P ENST00000312358 4/41 54 47 7 54 54 0 strelka-varscan-mutect SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;SPEG,synonymous_variant,p.=,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; A ENST00000312358 Transcript synonymous_variant 1968/10782 1836/9804 612/3267 P ccG/ccA 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 4/41 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs748658115 . 0 194 13 3 0 0 0 0 -12.99686 0.9927071 1 1 1 0 A 2 1 49 219448994 219448994 G A 1 0 0 0 0 0 0 0 1 15387 1074 38 1 1 SPEG 2 219448994 Silent SNP G C3N-00547_T 66902 219448994 22744535 118 14448 EPHA4 0 . GRCh38 2 221564263 221564263 + Silent SNP C C G novel C3N-00547_T C3N-00547_N C C c.291G>C p.= p.V97V ENST00000281821 3/18 236 220 16 242 242 0 strelka-varscan-mutect EPHA4,synonymous_variant,p.=,ENST00000281821,NM_001304536.1,NM_001304537.1,NM_004438.4;EPHA4,synonymous_variant,p.=,ENST00000409854,;EPHA4,synonymous_variant,p.=,ENST00000409938,;EPHA4,synonymous_variant,p.=,ENST00000541600,;EPHA4,synonymous_variant,p.=,ENST00000419964,;EPHA4,intron_variant,,ENST00000443796,;EPHA4,downstream_gene_variant,,ENST00000434266,;EPHA4,3_prime_UTR_variant,,ENST00000415749,; G ENST00000281821 Transcript synonymous_variant 333/6346 291/2961 97/986 V gtG/gtC 1 -1 EPHA4 HGNC HGNC:3388 protein_coding YES CCDS2447.1 ENSP00000281821 P54764 A0A024R452 UPI000012A077 NM_001304536.1,NM_001304537.1,NM_004438.4 3/18 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF337,hmmpanther:PTHR24416,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 221564263 221564263 C G 1 0 0 0 0 0 0 0 1 5016 465 17 4 4 EPHA4 2 221564263 Silent SNP C C3N-00547_T 2115269 221564263 20629266 119 14449 DNER 0 . GRCh38 2 229547011 229547011 + Missense_Mutation SNP C C A rs752786455 C3N-00547_T C3N-00547_N C C c.929G>T p.Gly310Val p.G310V ENST00000341772 5/13 190 147 43 264 264 0 strelka-varscan-mutect DNER,missense_variant,p.Gly310Val,ENST00000341772,NM_139072.3; A ENST00000341772 Transcript missense_variant 1064/3260 929/2214 310/737 G/V gGg/gTg rs752786455 1 -1 DNER HGNC HGNC:24456 protein_coding YES CCDS33390.1 ENSP00000345229 Q8NFT8 UPI0000048EB8 NM_139072.3 tolerated(0.17) 5/13 PROSITE_profiles:PS50026,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs752786455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 229547011 229547011 C A 1 0 0 0 0 1 0 0 0 4480 623 22 2 2 DNER 2 229547011 Missense_Mutation SNP C C3N-00547_T 7982748 229547011 12646518 120 14450 NMUR1 0 . GRCh38 2 231525316 231525316 + Missense_Mutation SNP G G T rs773347918 C3N-00547_T C3N-00547_N G G c.1008C>A p.His336Gln p.H336Q ENST00000305141 3/3 223 200 23 286 286 0 strelka-varscan-mutect NMUR1,missense_variant,p.His336Gln,ENST00000305141,NM_006056.4; T ENST00000305141 Transcript missense_variant 1142/3298 1008/1281 336/426 H/Q caC/caA rs773347918 1 -1 NMUR1 HGNC HGNC:4518 protein_coding YES CCDS2486.1 ENSP00000305877 Q9HB89 UPI0000071CAE NM_006056.4 tolerated(0.09) 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF109,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01565,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs773347918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 231525316 231525316 G T 1 0 0 0 0 1 0 0 0 10547 1136 40 1 1 NMUR1 2 231525316 Missense_Mutation SNP G C3N-00547_T 1978305 231525316 10668213 121 14451 USP40 0 . GRCh38 2 233523180 233523180 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2224G>T p.Asp742Tyr p.D742Y ENST00000450966 15/31 77 50 27 95 95 0 strelka-varscan-mutect USP40,missense_variant,p.Asp730Tyr,ENST00000251722,;USP40,missense_variant,p.Asp742Tyr,ENST00000450966,NM_018218.2;USP40,missense_variant,p.Asp730Tyr,ENST00000427112,;USP40,missense_variant,p.Asp25Tyr,ENST00000452724,;USP40,downstream_gene_variant,,ENST00000485943,; A ENST00000450966 Transcript missense_variant 2224/5616 2224/3744 742/1247 D/Y Gat/Tat 1 -1 USP40 HGNC HGNC:20069 protein_coding YES CCDS46547.1 ENSP00000415434 Q9NVE5 UPI0000232F06 NM_018218.2 deleterious(0.01) 15/31 MODERATE 1 SNV 1 1 PASS rs970374942 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 233523180 233523180 C A 1 0 0 0 0 1 0 0 0 17614 826 29 2 2 USP40 2 233523180 Missense_Mutation SNP C C3N-00547_T 1997864 233523180 8670349 122 14452 OR6B2 0 . GRCh38 2 240030235 240030235 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.195C>A p.= p.S65S ENST00000402971 1/1 286 189 97 358 357 1 strelka-varscan-mutect OR6B2,synonymous_variant,p.=,ENST00000402971,NM_001005853.1;NDUFA10,upstream_gene_variant,,ENST00000252711,NM_004544.3;NDUFA10,upstream_gene_variant,,ENST00000404554,;NDUFA10,upstream_gene_variant,,ENST00000620965,;NDUFA10,upstream_gene_variant,,ENST00000307300,;NDUFA10,upstream_gene_variant,,ENST00000443626,;NDUFA10,upstream_gene_variant,,ENST00000407129,;NDUFA10,upstream_gene_variant,,ENST00000485344,;NDUFA10,upstream_gene_variant,,ENST00000497536,;NDUFA10,upstream_gene_variant,,ENST00000414580,; T ENST00000402971 Transcript synonymous_variant 222/1492 195/939 65/312 S tcC/tcA 1 -1 OR6B2 HGNC HGNC:15041 protein_coding YES CCDS46559.1 ENSP00000384563 Q6IFH4 UPI0000061EBF NM_001005853.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF313,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 240030235 240030235 G T 1 0 0 0 0 0 0 0 1 11256 1335 47 2 2 OR6B2 2 240030235 Silent SNP G C3N-00547_T 6507055 240030235 2163294 123 14453 AQP12B 0 . GRCh38 2 240682713 240682713 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.125T>A p.Val42Glu p.V42E ENST00000407834 1/3 878 692 186 827 827 0 strelka-varscan-mutect AQP12B,splice_donor_variant,,ENST00000621682,;AQP12B,missense_variant,p.Val42Glu,ENST00000407834,NM_001102467.1;AC011298.2,upstream_gene_variant,,ENST00000407635,;AQP12B,upstream_gene_variant,,ENST00000459806,;AQP12B,intron_variant,,ENST00000414322,;AQP12B,intron_variant,,ENST00000413999,;AQP12B,intron_variant,,ENST00000452886,; T ENST00000407834 Transcript missense_variant 188/1094 125/924 42/307 V/E gTg/gAg 1 -1 AQP12B HGNC HGNC:6096 protein_coding YES CCDS46560.1 ENSP00000384894 A6NM10 UPI0000F705B9 NM_001102467.1 deleterious(0.01) 1/3 hmmpanther:PTHR21191:SF8,hmmpanther:PTHR21191,PIRSF_domain:PIRSF017529,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 240682713 240682713 A T 1 0 0 0 0 1 0 0 0 948 159 6 4 4 AQP12B 2 240682713 Missense_Mutation SNP A C3N-00547_T 652478 240682713 1510816 124 14454 NEU4 0 . GRCh38 2 241815084 241815084 + Missense_Mutation SNP G G T rs766104247 C3N-00547_T C3N-00547_N G G c.433G>T p.Ala145Ser p.A145S ENST00000325935 3/4 89 58 31 103 103 0 strelka-varscan-mutect NEU4,missense_variant,p.Ala132Ser,ENST00000391969,NM_001167602.2;NEU4,missense_variant,p.Ala144Ser,ENST00000404257,NM_080741.3;NEU4,missense_variant,p.Ala145Ser,ENST00000325935,NM_001167599.2;NEU4,missense_variant,p.Ala132Ser,ENST00000407683,NM_001167601.2,NM_001167600.2;NEU4,missense_variant,p.Ala132Ser,ENST00000405370,;NEU4,missense_variant,p.Ala132Ser,ENST00000420288,;NEU4,missense_variant,p.Ala132Ser,ENST00000423583,;NEU4,intron_variant,,ENST00000415936,;NEU4,intron_variant,,ENST00000426032,;NEU4,downstream_gene_variant,,ENST00000428592,;NEU4,downstream_gene_variant,,ENST00000435894,;NEU4,downstream_gene_variant,,ENST00000435934,;AC114730.3,upstream_gene_variant,,ENST00000413820,;AC114730.3,upstream_gene_variant,,ENST00000420272,;AC114730.3,upstream_gene_variant,,ENST00000439270,;NEU4,missense_variant,p.Ala132Ser,ENST00000435855,;NEU4,non_coding_transcript_exon_variant,,ENST00000618597,;NEU4,downstream_gene_variant,,ENST00000488997,;NEU4,downstream_gene_variant,,ENST00000476542,;NEU4,downstream_gene_variant,,ENST00000494678,; T ENST00000325935 Transcript missense_variant 862/2288 433/1494 145/497 A/S Gcc/Tcc rs766104247 1 1 NEU4 HGNC HGNC:21328 protein_coding YES CCDS54441.1 ENSP00000320318 Q8WWR8 UPI0000EE378E NM_001167599.2 tolerated(0.21) 3/4 Gene3D:2.120.10.10,Pfam_domain:PF13088,hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF22,Superfamily_domains:SSF50939 MODERATE 1 SNV 1 1 PASS rs766104247 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 241815084 241815084 G T 1 0 0 0 0 1 0 0 0 10379 1087 38 1 1 NEU4 2 241815084 Missense_Mutation SNP G C3N-00547_T 1132371 241815084 378445 125 14455 CHL1 0 . GRCh38 3 398253 398253 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.3121G>T p.Val1041Leu p.V1041L ENST00000256509 25/28 64 49 15 102 102 0 strelka-varscan-mutect CHL1,missense_variant,p.Val1041Leu,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Val1025Leu,ENST00000397491,NM_001253387.1;CHL1,intron_variant,,ENST00000620033,NM_001253388.1;CHL1,intron_variant,,ENST00000445697,;CHL1,3_prime_UTR_variant,,ENST00000453040,; T ENST00000256509 Transcript missense_variant 3763/8023 3121/3675 1041/1224 V/L Gta/Tta 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(0.17) 25/28 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 398253 398253 G T 1 0 0 0 0 1 0 0 0 3108 1029 36 2 2 CHL1 3 398253 Missense_Mutation SNP G C3N-00547_T 398253 197897306 126 14456 CNTN6 0 . GRCh38 3 1329844 1329844 + Frame_Shift_Del DEL G G - novel C3N-00547_T C3N-00547_N G G c.1276delG p.Asp426IlefsTer55 p.D426Ifs*55 ENST00000446702 11/23 113 82 31 175 175 0 sindel-varindel-pindel CNTN6,frameshift_variant,p.Asp426IlefsTer55,ENST00000446702,;CNTN6,frameshift_variant,p.Asp426IlefsTer55,ENST00000350110,NM_014461.3,NM_001289080.1,NM_001289081.1;CNTN6,3_prime_UTR_variant,,ENST00000397479,; - ENST00000446702 Transcript frameshift_variant 1900/4513 1273/3087 425/1028 G/X Ggg/gg 1 1 CNTN6 HGNC HGNC:2176 protein_coding YES CCDS2557.1 ENSP00000407822 Q9UQ52 A0A024R2C7 UPI0000072430 11/23 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF52,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 1329844 1329844 G - 1 0 1 0 1 0 0 0 0 3426 1348 47 0 0 CNTN6 3 1329844 Frame_Shift_Del DEL G C3N-00547_T 931591 1329844 196965715 127 14457 RAD18 0 . GRCh38 3 8913715 8913715 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.895G>T p.Glu299Ter p.E299* ENST00000264926 8/13 53 43 10 84 84 0 strelka-varscan-mutect RAD18,stop_gained,p.Glu299Ter,ENST00000264926,NM_020165.3;RAD18,intron_variant,,ENST00000415439,;RAD18,upstream_gene_variant,,ENST00000473069,; A ENST00000264926 Transcript stop_gained 1012/5886 895/1488 299/495 E/* Gaa/Taa 1 -1 RAD18 HGNC HGNC:18278 protein_coding YES CCDS2571.1 ENSP00000264926 Q9NS91 UPI000013D592 NM_020165.3 8/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14134,hmmpanther:PTHR14134:SF2 HIGH 1 SNV 1 1 PASS rs1432145620 . 0 204 5 0 0 0 0 0 -19.9999 1 1 1 1 0 A 4 1 49 8913715 8913715 C A 1 0 0 0 0 0 1 0 0 13140 840 29 2 2 RAD18 3 8913715 Nonsense_Mutation SNP C C3N-00547_T 7583871 8913715 189381844 128 14458 GRIP2 0 . GRCh38 3 14505717 14505717 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2762G>T p.Ser921Ile p.S921I ENST00000619221 21/25 86 59 27 156 155 1 strelka-varscan-mutect GRIP2,missense_variant,p.Ser921Ile,ENST00000619221,;GRIP2,missense_variant,p.Ser824Ile,ENST00000621039,NM_001080423.3;GRIP2,missense_variant,p.Ser829Ile,ENST00000637182,;GRIP2,missense_variant,p.Ser283Ile,ENST00000430219,; A ENST00000619221 Transcript missense_variant 2762/7977 2762/3423 921/1140 S/I aGc/aTc 1 -1 GRIP2 HGNC HGNC:23841 protein_coding YES ENSP00000480660 A0A087WX15 UPI0001DD380B tolerated(0.05) 21/25 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 14505717 14505717 C A 1 0 0 0 0 1 0 0 0 6669 797 28 2 2 GRIP2 3 14505717 Missense_Mutation SNP C C3N-00547_T 5592002 14505717 183789842 129 14459 BTD 0 . GRCh38 3 15644768 15644768 + Silent SNP A A T rs778024234 C3N-00547_T C3N-00547_N A A c.918A>T p.= p.P306P ENST00000437172 6/6 286 223 63 315 315 0 strelka-varscan-mutect BTD,synonymous_variant,p.=,ENST00000383778,NM_001281725.1;BTD,synonymous_variant,p.=,ENST00000437172,NM_001281724.1;BTD,synonymous_variant,p.=,ENST00000303498,NM_000060.3;BTD,synonymous_variant,p.=,ENST00000449107,NM_001281723.1;BTD,downstream_gene_variant,,ENST00000436193,;BTD,downstream_gene_variant,,ENST00000482824,; T ENST00000437172 Transcript synonymous_variant 1150/2097 918/1638 306/545 P ccA/ccT rs778024234 1 1 BTD HGNC HGNC:1122 protein_coding YES CCDS63564.1 ENSP00000400995 P43251 UPI00017A7026 NM_001281724.1 6/6 Gene3D:3.60.110.10,PIRSF_domain:PIRSF011861,PROSITE_profiles:PS50263,hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF17,Superfamily_domains:SSF56317 LOW 1 SNV 2 1 PASS rs778024234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 15644768 15644768 A T 1 0 0 0 0 0 0 0 1 1726 175 7 4 4 BTD 3 15644768 Silent SNP A C3N-00547_T 1139051 15644768 182650791 130 14460 KCNH8 0 . GRCh38 3 19390523 19390523 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.854G>T p.Gly285Val p.G285V ENST00000328405 6/16 112 98 14 184 184 0 strelka-varscan-mutect KCNH8,missense_variant,p.Gly285Val,ENST00000328405,NM_144633.2;KCNH8,non_coding_transcript_exon_variant,,ENST00000475063,;KCNH8,3_prime_UTR_variant,,ENST00000452398,; T ENST00000328405 Transcript missense_variant 1120/5137 854/3324 285/1107 G/V gGc/gTc 1 1 KCNH8 HGNC HGNC:18864 protein_coding YES CCDS2632.1 ENSP00000328813 Q96L42 UPI0000167D12 NM_144633.2 deleterious(0) 6/16 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF380,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR01465 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.98794 0.9999908 1 1 1 0 T 3 4 49 19390523 19390523 G T 1 0 0 0 0 1 0 0 0 7954 1203 42 2 2 KCNH8 3 19390523 Missense_Mutation SNP G C3N-00547_T 3745755 19390523 178905036 131 14461 THRB 0 . GRCh38 3 24133434 24133434 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.767T>C p.Val256Ala p.V256A ENST00000396671 9/11 462 416 46 475 475 0 strelka-varscan-mutect THRB,missense_variant,p.Val256Ala,ENST00000396671,NM_001128176.2;THRB,missense_variant,p.Val256Ala,ENST00000356447,NM_000461.4,NM_001128177.1;THRB,missense_variant,p.Val256Ala,ENST00000416420,NM_001252634.1;THRB,missense_variant,p.Val271Ala,ENST00000280696,; G ENST00000396671 Transcript missense_variant 1163/7506 767/1386 256/461 V/A gTc/gCc 1 -1 THRB HGNC HGNC:11799 protein_coding YES CCDS2641.1 ENSP00000379904 P10828 F1D8N7 UPI0000136D26 NM_001128176.2 tolerated(0.47) 9/11 hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF210,Gene3D:1.10.565.10,Superfamily_domains:SSF48508 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 24133434 24133434 A G 1 0 0 0 0 1 0 0 0 16309 275 10 5 5 THRB 3 24133434 Missense_Mutation SNP A C3N-00547_T 4742911 24133434 174162125 132 14462 SCN5A 0 . GRCh38 3 38581041 38581041 + Missense_Mutation SNP C C A rs199473186 C3N-00547_T C3N-00547_N C C c.3118G>T p.Gly1040Trp p.G1040W ENST00000413689 17/28 145 113 32 179 179 0 strelka-varscan-mutect SCN5A,missense_variant,p.Gly1040Trp,ENST00000413689,NM_001099404.1;SCN5A,missense_variant,p.Gly1040Trp,ENST00000333535,NM_198056.2;SCN5A,missense_variant,p.Gly1040Trp,ENST00000425664,NM_001099405.1;SCN5A,missense_variant,p.Gly1040Trp,ENST00000423572,NM_000335.4;SCN5A,missense_variant,p.Gly1040Trp,ENST00000451551,NM_001160161.1;SCN5A,missense_variant,p.Gly1040Trp,ENST00000414099,;SCN5A,missense_variant,p.Gly1040Trp,ENST00000455624,NM_001160160.1;SCN5A,missense_variant,p.Gly1040Trp,ENST00000450102,;SCN5A,missense_variant,p.Gly1040Trp,ENST00000449557,; A ENST00000413689 Transcript missense_variant 3312/8504 3118/6051 1040/2016 G/W Ggg/Tgg rs199473186 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 deleterious(0.02) 17/28 Pfam_domain:PF06512,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206,Low_complexity_(Seg):seg 19841300 MODERATE 1 SNV 5 1 1 PASS rs199473186 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 38581041 38581041 C A 1 0 0 0 0 1 0 0 0 14191 652 23 1 1 SCN5A 3 38581041 Missense_Mutation SNP C C3N-00547_T 14447607 38581041 159714518 133 14463 SCN5A 0 . GRCh38 3 38597727 38597727 + Splice_Site SNP A A G novel C3N-00547_T C3N-00547_N A A c.2262+2T>C p.X754_splice ENST00000413689 49 43 6 61 61 0 strelka-varscan-mutect SCN5A,splice_donor_variant,,ENST00000413689,NM_001099404.1;SCN5A,splice_donor_variant,,ENST00000333535,NM_198056.2;SCN5A,splice_donor_variant,,ENST00000425664,NM_001099405.1;SCN5A,splice_donor_variant,,ENST00000423572,NM_000335.4;SCN5A,splice_donor_variant,,ENST00000451551,NM_001160161.1;SCN5A,splice_donor_variant,,ENST00000414099,;SCN5A,splice_donor_variant,,ENST00000455624,NM_001160160.1;SCN5A,splice_donor_variant,,ENST00000450102,;SCN5A,splice_donor_variant,,ENST00000449557,; G ENST00000413689 Transcript splice_donor_variant -/8504 2262/6051 754/2016 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 14/27 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 49 38597727 38597727 A G 1 0 0 0 0 0 0 1 0 14191 405 14 5 5 SCN5A 3 38597727 Splice_Site SNP A C3N-00547_T 16686 38597727 159697832 134 14464 SCN10A 0 . GRCh38 3 38697931 38697931 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.5289T>A p.= p.A1763A ENST00000449082 27/27 330 276 54 397 397 0 strelka-varscan-mutect SCN10A,synonymous_variant,p.=,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; T ENST00000449082 Transcript synonymous_variant 5289/6418 5289/5871 1763/1956 A gcT/gcA 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 27/27 hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037 LOW 1 SNV 1 1 PASS rs1307495200 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 38697931 38697931 A T 1 0 0 0 0 0 0 0 1 14181 291 11 4 4 SCN10A 3 38697931 Silent SNP A C3N-00547_T 100204 38697931 159597628 135 14465 XIRP1 0 . GRCh38 3 39188310 39188310 + Missense_Mutation SNP C C A rs559059786 C3N-00547_T C3N-00547_N C C c.1136G>T p.Arg379Leu p.R379L ENST00000340369 2/2 199 167 32 234 234 0 strelka-varscan-mutect XIRP1,missense_variant,p.Arg379Leu,ENST00000340369,NM_194293.2;XIRP1,missense_variant,p.Arg379Leu,ENST00000396251,NM_001198621.2;XIRP1,intron_variant,,ENST00000421646,; A ENST00000340369 Transcript missense_variant 1365/6460 1136/5532 379/1843 R/L cGc/cTc rs559059786 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 deleterious(0) 2/2 PROSITE_profiles:PS51389,hmmpanther:PTHR22591,Pfam_domain:PF08043 MODERATE 1 SNV 1 1 PASS rs559059786 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 39188310 39188310 C A 1 0 0 0 0 1 0 0 0 17988 768 27 1 1 XIRP1 3 39188310 Missense_Mutation SNP C C3N-00547_T 490379 39188310 159107249 136 14466 ZNF619 0 . GRCh38 3 40486994 40486994 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.604G>T p.Asp202Tyr p.D202Y ENST00000447116 6/6 159 126 33 176 176 0 strelka-varscan-mutect ZNF619,missense_variant,p.Asp202Tyr,ENST00000447116,NM_001145082.2;ZNF619,missense_variant,p.Asp153Tyr,ENST00000429348,;ZNF619,missense_variant,p.Asp146Tyr,ENST00000314686,;ZNF619,missense_variant,p.Asp118Tyr,ENST00000456778,NM_001145083.1;ZNF619,missense_variant,p.Asp153Tyr,ENST00000522736,;ZNF619,missense_variant,p.Asp202Tyr,ENST00000521353,;ZNF619,missense_variant,p.Asp162Tyr,ENST00000432264,NM_001145093.2;ZNF619,non_coding_transcript_exon_variant,,ENST00000520737,;ZNF619,3_prime_UTR_variant,,ENST00000494154,;ZNF619,downstream_gene_variant,,ENST00000462961,; T ENST00000447116 Transcript missense_variant 911/4153 604/1851 202/616 D/Y Gat/Tat COSM126466 1 1 ZNF619 HGNC HGNC:26910 protein_coding YES CCDS46802.1 ENSP00000411132 Q8N2I2 UPI000192B90D NM_001145082.2 deleterious(0.01) 6/6 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF138 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 40486994 40486994 G T 1 0 0 0 0 1 0 0 0 18618 942 33 2 2 ZNF619 3 40486994 Missense_Mutation SNP G C3N-00547_T 1298684 40486994 157808565 137 14467 PTPN23 0 . GRCh38 3 47409715 47409715 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.2010G>C p.Lys670Asn p.K670N ENST00000265562 19/25 178 157 21 210 210 0 strelka-varscan-mutect PTPN23,missense_variant,p.Lys670Asn,ENST00000265562,NM_001304482.1,NM_015466.3;SCAP,downstream_gene_variant,,ENST00000265565,NM_012235.2;SCAP,downstream_gene_variant,,ENST00000428413,;SCAP,downstream_gene_variant,,ENST00000545718,;PTPN23,downstream_gene_variant,,ENST00000456221,;PTPN23,3_prime_UTR_variant,,ENST00000602307,;PTPN23,non_coding_transcript_exon_variant,,ENST00000495653,;SCAP,downstream_gene_variant,,ENST00000441517,NM_001320044.1;SCAP,downstream_gene_variant,,ENST00000320017,;PTPN23,downstream_gene_variant,,ENST00000477276,; C ENST00000265562 Transcript missense_variant 2087/5244 2010/4911 670/1636 K/N aaG/aaC 1 1 PTPN23 HGNC HGNC:14406 protein_coding YES CCDS2754.1 ENSP00000265562 Q9H3S7 UPI000006EBC4 NM_001304482.1,NM_015466.3 deleterious(0.02) 19/25 Gene3D:2xs1A03,Pfam_domain:PF13949 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 47409715 47409715 G C 1 0 0 0 0 1 0 0 0 12942 933 33 4 4 PTPN23 3 47409715 Missense_Mutation SNP G C3N-00547_T 6922721 47409715 150885844 138 14468 QARS 0 . GRCh38 3 49099645 49099645 + Missense_Mutation SNP C C A rs549522450 C3N-00547_T C3N-00547_N C C c.1391G>T p.Arg464Leu p.R464L ENST00000306125 16/24 138 111 27 152 152 0 strelka-varscan-mutect QARS,missense_variant,p.Arg464Leu,ENST00000306125,NM_005051.2;QARS,missense_variant,p.Arg453Leu,ENST00000414533,NM_001272073.1;QARS,missense_variant,p.Arg319Leu,ENST00000464962,;QARS,missense_variant,p.Arg116Leu,ENST00000634432,;QARS,downstream_gene_variant,,ENST00000635443,;QARS,downstream_gene_variant,,ENST00000452739,;QARS,downstream_gene_variant,,ENST00000635541,;QARS,upstream_gene_variant,,ENST00000453392,;QARS,downstream_gene_variant,,ENST00000634527,;QARS,downstream_gene_variant,,ENST00000635622,;QARS,downstream_gene_variant,,ENST00000635194,;QARS,downstream_gene_variant,,ENST00000635231,;QARS,downstream_gene_variant,,ENST00000635292,;QARS,downstream_gene_variant,,ENST00000634602,;QARS,upstream_gene_variant,,ENST00000466179,;QARS,downstream_gene_variant,,ENST00000620931,;QARS,downstream_gene_variant,,ENST00000635501,;QARS,downstream_gene_variant,,ENST00000470619,;QARS,downstream_gene_variant,,ENST00000470225,;QARS,upstream_gene_variant,,ENST00000637908,;QARS,downstream_gene_variant,,ENST00000479495,;QARS,downstream_gene_variant,,ENST00000417025,;QARS,downstream_gene_variant,,ENST00000634425,;QARS,downstream_gene_variant,,ENST00000634359,;QARS,missense_variant,p.Arg408Leu,ENST00000636669,;QARS,missense_variant,p.Arg94Leu,ENST00000637281,;QARS,splice_region_variant,,ENST00000430182,;QARS,splice_region_variant,,ENST00000636018,;QARS,splice_region_variant,,ENST00000637543,;QARS,splice_region_variant,,ENST00000637113,;QARS,splice_region_variant,,ENST00000478561,;QARS,splice_region_variant,,ENST00000482468,;QARS,upstream_gene_variant,,ENST00000459870,;QARS,downstream_gene_variant,,ENST00000482261,;QARS,downstream_gene_variant,,ENST00000494767,;QARS,downstream_gene_variant,,ENST00000494838,;QARS,upstream_gene_variant,,ENST00000470113,;QARS,downstream_gene_variant,,ENST00000635375,;QARS,upstream_gene_variant,,ENST00000482248,;QARS,downstream_gene_variant,,ENST00000634724,;QARS,upstream_gene_variant,,ENST00000494984,;QARS,upstream_gene_variant,,ENST00000634473,;QARS,downstream_gene_variant,,ENST00000482438,;QARS,downstream_gene_variant,,ENST00000634802,;QARS,downstream_gene_variant,,ENST00000635278,;QARS,downstream_gene_variant,,ENST00000634953,;QARS,downstream_gene_variant,,ENST00000635052,;QARS,downstream_gene_variant,,ENST00000635494,;QARS,downstream_gene_variant,,ENST00000418549,;QARS,downstream_gene_variant,,ENST00000634609,;QARS,upstream_gene_variant,,ENST00000634336,;QARS,upstream_gene_variant,,ENST00000487495,;QARS,upstream_gene_variant,,ENST00000497635,; A ENST00000306125 Transcript missense_variant,splice_region_variant 1793/2827 1391/2328 464/775 R/L cGc/cTc rs549522450 1 -1 QARS HGNC HGNC:9751 protein_coding YES CCDS2788.1 ENSP00000307567 P47897 UPI000013661E NM_005051.2 deleterious(0) 16/24 hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF39,Gene3D:3.40.50.620,TIGRFAM_domain:TIGR00440,Pfam_domain:PF00749,Superfamily_domains:SSF52374 MODERATE 1 SNV 1 1 PASS rs549522450 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 49099645 49099645 C A 1 0 0 0 0 1 0 0 0 13026 782 27 1 1 QARS 3 49099645 Missense_Mutation SNP C C3N-00547_T 1689930 49099645 149195914 139 14469 DOCK3 0 . GRCh38 3 51225657 51225657 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.1261C>A p.Arg421Ser p.R421S ENST00000266037 15/53 65 49 16 81 81 0 strelka-varscan-mutect DOCK3,missense_variant,p.Arg421Ser,ENST00000266037,NM_004947.4; A ENST00000266037 Transcript missense_variant 1284/8755 1261/6093 421/2030 R/S Cgc/Agc COSM3595642,COSM3595643 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 deleterious(0) 15/53 PROSITE_profiles:PS51650,hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Pfam_domain:PF14429 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1253633877 . 0 201 9 0 0 0 0 0 -20 0.9999977 1 1 1 0 A 3 1 49 51225657 51225657 C A 1 0 0 0 0 1 0 0 0 4503 652 23 1 1 DOCK3 3 51225657 Missense_Mutation SNP C C3N-00547_T 2126012 51225657 147069902 140 14470 DCAF1 0 . GRCh38 3 51419839 51419839 + Missense_Mutation SNP C C A rs782189293 C3N-00547_T C3N-00547_N C C c.3131G>T p.Arg1044Leu p.R1044L ENST00000423656 14/25 174 133 41 199 199 0 strelka-varscan-mutect DCAF1,missense_variant,p.Arg1043Leu,ENST00000504652,NM_001171904.1;DCAF1,missense_variant,p.Arg1044Leu,ENST00000423656,NM_014703.2;DCAF1,missense_variant,p.Arg595Leu,ENST00000335891,; A ENST00000423656 Transcript missense_variant 3261/5946 3131/4524 1044/1507 R/L cGg/cTg rs782189293 1 -1 DCAF1 HGNC HGNC:30911 protein_coding YES CCDS74943.1 ENSP00000393183 Q9Y4B6 UPI00000716AC NM_014703.2 tolerated(0.09) 14/25 hmmpanther:PTHR13129,hmmpanther:PTHR13129:SF4 MODERATE 1 SNV 5 1 PASS rs782189293 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 51419839 51419839 C A 1 0 0 0 0 1 0 0 0 4061 652 23 1 1 DCAF1 3 51419839 Missense_Mutation SNP C C3N-00547_T 194182 51419839 146875720 141 14471 TLR9 0 . GRCh38 3 52222802 52222802 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.1514A>G p.His505Arg p.H505R ENST00000360658 2/2 164 135 29 240 240 0 strelka-varscan-mutect TLR9,missense_variant,p.His505Arg,ENST00000360658,NM_017442.3;RP11-330H6.5,missense_variant,p.His659Arg,ENST00000494383,;RP11-330H6.6,upstream_gene_variant,,ENST00000624096,;RP11-330H6.5,downstream_gene_variant,,ENST00000478201,; C ENST00000360658 Transcript missense_variant 2148/3870 1514/3099 505/1032 H/R cAc/cGc 1 -1 TLR9 HGNC HGNC:15633 protein_coding YES CCDS2848.1 ENSP00000353874 Q9NR96 UPI0000001625 NM_017442.3 tolerated(0.11) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF37,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 52222802 52222802 T C 1 0 0 0 0 1 0 0 0 16404 1696 59 5 5 TLR9 3 52222802 Missense_Mutation SNP T C3N-00547_T 802963 52222802 146072757 142 14472 TMF1 0 . GRCh38 3 69047440 69047440 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.1265C>T p.Thr422Ile p.T422I ENST00000398559 2/17 124 115 9 135 135 0 strelka-varscan-mutect TMF1,missense_variant,p.Thr422Ile,ENST00000398559,NM_007114.2;MIR3136,downstream_gene_variant,,ENST00000583498,;CTD-2013N24.2,intron_variant,,ENST00000482368,;CTD-2013N24.2,intron_variant,,ENST00000595925,;CTD-2013N24.2,intron_variant,,ENST00000597950,;CTD-2013N24.2,intron_variant,,ENST00000598783,;CTD-2013N24.2,intron_variant,,ENST00000596732,;CTD-2013N24.2,intron_variant,,ENST00000601735,;CTD-2013N24.2,intron_variant,,ENST00000596274,;CTD-2013N24.2,intron_variant,,ENST00000596523,;CTD-2013N24.2,upstream_gene_variant,,ENST00000610844,;TMF1,missense_variant,p.Thr422Ile,ENST00000488010,;TMF1,upstream_gene_variant,,ENST00000477872,; A ENST00000398559 Transcript missense_variant 1482/6849 1265/3282 422/1093 T/I aCt/aTt 1 -1 TMF1 HGNC HGNC:11870 protein_coding YES CCDS43105.1 ENSP00000381567 P82094 A0A024R370 UPI000013D9A7 NM_007114.2 tolerated_low_confidence(0.18) 2/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 69047440 69047440 G A 1 0 0 0 0 1 0 0 0 16703 1029 36 3 3 TMF1 3 69047440 Missense_Mutation SNP G C3N-00547_T 16824638 69047440 129248119 143 14473 PDZRN3 0 . GRCh38 3 73383591 73383591 + Missense_Mutation SNP C C G C3N-00547_T C3N-00547_N C C c.2975G>C p.Arg992Pro p.R992P ENST00000263666 10/10 259 220 39 274 274 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Arg992Pro,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Arg649Pro,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Arg709Pro,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Arg649Pro,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Arg308Pro,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000492909,NM_001303139.1;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,; G ENST00000263666 Transcript missense_variant 3090/4248 2975/3201 992/1066 R/P cGc/cCc COSM4120117,COSM4120118,COSM4120119 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 10/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 73383591 73383591 C G 1 0 0 0 0 1 0 0 0 11797 768 27 4 4 PDZRN3 3 73383591 Missense_Mutation SNP C C3N-00547_T 4336151 73383591 124911968 144 14474 CHMP2B 0 . GRCh38 3 87245785 87245785 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.198G>T p.= p.V66V ENST00000263780 3/6 277 226 51 250 250 0 strelka-varscan-mutect CHMP2B,synonymous_variant,p.=,ENST00000263780,NM_014043.3;CHMP2B,synonymous_variant,p.=,ENST00000471660,NM_001244644.1;CHMP2B,synonymous_variant,p.=,ENST00000494980,;CHMP2B,synonymous_variant,p.=,ENST00000472024,; T ENST00000263780 Transcript synonymous_variant 436/2557 198/642 66/213 V gtG/gtT 1 1 CHMP2B HGNC HGNC:24537 protein_coding YES CCDS2918.1 ENSP00000263780 Q9UQN3 B2RE76 UPI00000701F8 NM_014043.3 3/6 hmmpanther:PTHR10476:SF9,hmmpanther:PTHR10476,Pfam_domain:PF03357 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 87245785 87245785 G T 1 0 0 0 0 0 0 0 1 3114 1306 46 2 2 CHMP2B 3 87245785 Silent SNP G C3N-00547_T 13862194 87245785 111049774 145 14475 EPHA3 0 . GRCh38 3 89449304 89449304 + Missense_Mutation SNP G G A C3N-00547_T C3N-00547_N G G c.2426G>A p.Ser809Asn p.S809N ENST00000336596 14/17 185 158 27 166 166 0 strelka-varscan-mutect EPHA3,missense_variant,p.Ser809Asn,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.Ser809Asn,ENST00000494014,; A ENST00000336596 Transcript missense_variant 2651/5809 2426/2952 809/983 S/N aGt/aAt COSM3974599 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 deleterious(0.01) 14/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 89449304 89449304 G A 1 0 0 0 0 1 0 0 0 5015 1029 36 3 3 EPHA3 3 89449304 Missense_Mutation SNP G C3N-00547_T 2203519 89449304 108846255 146 14476 MTRNR2L12 0 . GRCh38 3 96617263 96617263 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.11G>T p.Arg4Leu p.R4L ENST00000600213 1/1 107 87 20 174 174 0 strelka-varscan-mutect MTRNR2L12,missense_variant,p.Arg4Leu,ENST00000600213,NM_001190470.1;RPL18AP8,upstream_gene_variant,,ENST00000486071,; A ENST00000600213 Transcript missense_variant 974/1049 11/75 4/24 R/L cGa/cTa COSM4819528 1 -1 MTRNR2L12 HGNC HGNC:37169 protein_coding YES ENSP00000468991 P0DMP1 UPI000153CE77 NM_001190470.1 1/1 hmmpanther:PTHR33895,hmmpanther:PTHR33895:SF1,Pfam_domain:PF15040 1 MODERATE 1 SNV 1 1 PASS rs1057256188 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 96617263 96617263 C A 1 0 0 0 0 1 0 0 0 9950 884 31 1 1 MTRNR2L12 3 96617263 Missense_Mutation SNP C C3N-00547_T 7167959 96617263 101678296 147 14477 FILIP1L 0 . GRCh38 3 99924361 99924361 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.474G>A p.= p.L158L ENST00000354552 4/6 232 139 93 294 294 0 strelka-varscan-mutect FILIP1L,synonymous_variant,p.=,ENST00000331335,NM_001042459.2;FILIP1L,synonymous_variant,p.=,ENST00000354552,NM_182909.3;FILIP1L,synonymous_variant,p.=,ENST00000398326,;CMSS1,intron_variant,,ENST00000421999,NM_032359.3;CMSS1,intron_variant,,ENST00000463526,;CMSS1,intron_variant,,ENST00000496116,;CMSS1,intron_variant,,ENST00000491299,; T ENST00000354552 Transcript synonymous_variant 945/3970 474/3408 158/1135 L ctG/ctA 1 -1 FILIP1L HGNC HGNC:24589 protein_coding YES CCDS43117.1 ENSP00000346560 Q4L180 UPI00001B24B2 NM_182909.3 4/6 Pfam_domain:PF09727 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 99924361 99924361 C T 1 0 0 0 0 0 0 0 1 5758 581 21 3 3 FILIP1L 3 99924361 Silent SNP C C3N-00547_T 3307098 99924361 98371198 148 14478 HCLS1 0 . GRCh38 3 121633083 121633083 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.992G>A p.Arg331Lys p.R331K ENST00000314583 11/14 88 68 20 140 139 1 strelka-varscan-mutect HCLS1,missense_variant,p.Arg331Lys,ENST00000314583,NM_005335.5;HCLS1,missense_variant,p.Arg294Lys,ENST00000428394,NM_001292041.1;FBXO40,downstream_gene_variant,,ENST00000338040,NM_016298.3;HCLS1,non_coding_transcript_exon_variant,,ENST00000473883,;HCLS1,3_prime_UTR_variant,,ENST00000495491,;HCLS1,downstream_gene_variant,,ENST00000464274,; T ENST00000314583 Transcript missense_variant 1084/2000 992/1461 331/486 R/K aGg/aAg 1 -1 HCLS1 HGNC HGNC:4844 protein_coding YES CCDS3003.1 ENSP00000320176 P14317 UPI000013F884 NM_005335.5 tolerated(0.44) 11/14 hmmpanther:PTHR10829,hmmpanther:PTHR10829:SF5 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 121633083 121633083 C T 1 0 0 0 0 1 0 0 0 6882 681 24 3 3 HCLS1 3 121633083 Missense_Mutation SNP C C3N-00547_T 21708722 121633083 76662476 149 14479 CD86 0 . GRCh38 3 122106397 122106397 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.600C>A p.= p.S200S ENST00000330540 4/7 268 240 28 218 218 0 strelka-varscan-mutect CD86,synonymous_variant,p.=,ENST00000330540,NM_175862.4;CD86,synonymous_variant,p.=,ENST00000264468,NM_176892.1;CD86,synonymous_variant,p.=,ENST00000469710,NM_001206925.1;CD86,synonymous_variant,p.=,ENST00000493101,NM_001206924.1;CD86,synonymous_variant,p.=,ENST00000393627,NM_006889.4;CD86,synonymous_variant,p.=,ENST00000478741,;CD86,downstream_gene_variant,,ENST00000482356,;CD86,downstream_gene_variant,,ENST00000483949,; A ENST00000330540 Transcript synonymous_variant 716/2708 600/990 200/329 S tcC/tcA 1 1 CD86 HGNC HGNC:1705 protein_coding YES CCDS3009.1 ENSP00000332049 P42081 UPI00001AFC7C NM_175862.4 4/7 hmmpanther:PTHR25466,hmmpanther:PTHR25466:SF2,Pfam_domain:PF13895 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 122106397 122106397 C A 1 0 0 0 0 0 0 0 1 2747 581 21 2 2 CD86 3 122106397 Silent SNP C C3N-00547_T 473314 122106397 76189162 150 14480 CASR 0 . GRCh38 3 122285179 122285179 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.3255A>T p.= p.V1085V ENST00000498619 7/7 366 172 194 429 429 0 strelka-varscan-mutect CASR,synonymous_variant,p.=,ENST00000498619,NM_001178065.1;CASR,synonymous_variant,p.=,ENST00000490131,NM_000388.3; T ENST00000498619 Transcript synonymous_variant 3693/5011 3255/3267 1085/1088 V gtA/gtT 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 7/7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 122285179 122285179 A T 1 0 0 0 0 0 0 0 1 2381 407 15 4 4 CASR 3 122285179 Silent SNP A C3N-00547_T 178782 122285179 76010380 151 14481 ITGB5 0 . GRCh38 3 124841440 124841440 + Silent SNP C C G novel C3N-00547_T C3N-00547_N C C c.723G>C p.= p.R241R ENST00000296181 5/15 126 102 24 183 183 0 strelka-mutect ITGB5,synonymous_variant,p.=,ENST00000296181,NM_002213.4;ITGB5,synonymous_variant,p.=,ENST00000488466,;ITGB5,synonymous_variant,p.=,ENST00000608657,;ITGB5,synonymous_variant,p.=,ENST00000496703,;ITGB5,3_prime_UTR_variant,,ENST00000465464,; G ENST00000296181 Transcript synonymous_variant 1020/4372 723/2400 241/799 R cgG/cgC 1 -1 ITGB5 HGNC HGNC:6160 protein_coding YES CCDS3030.1 ENSP00000296181 P18084 L7RT22 UPI000012DA10 NM_002213.4 5/15 Gene3D:3.40.50.410,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF26,SMART_domains:SM00187,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 124841440 124841440 C G 1 0 0 0 0 0 0 0 1 7804 842 30 4 4 ITGB5 3 124841440 Silent SNP C C3N-00547_T 2556261 124841440 73454119 152 14482 UROC1 0 . GRCh38 3 126504000 126504000 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.897G>T p.Arg299Ser p.R299S ENST00000383579 9/21 577 329 248 464 463 1 strelka-varscan-mutect UROC1,missense_variant,p.Arg299Ser,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.Arg299Ser,ENST00000383579,NM_001165974.1; A ENST00000383579 Transcript missense_variant 931/2735 897/2211 299/736 R/S agG/agT 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 deleterious(0.01) 9/21 HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Low_complexity_(Seg):seg,Superfamily_domains:SSF111326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 126504000 126504000 C A 1 0 0 0 0 1 0 0 0 17560 753 26 2 2 UROC1 3 126504000 Missense_Mutation SNP C C3N-00547_T 1662560 126504000 71791559 153 14483 IL20RB 0 . GRCh38 3 136991964 136991964 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.558G>T p.= p.G186G ENST00000329582 5/7 140 113 27 102 102 0 strelka-varscan-mutect IL20RB,synonymous_variant,p.=,ENST00000329582,NM_144717.3;IL20RB,downstream_gene_variant,,ENST00000484501,;IL20RB,3_prime_UTR_variant,,ENST00000475972,;IL20RB,3_prime_UTR_variant,,ENST00000491483,;IL20RB,intron_variant,,ENST00000469964,; T ENST00000329582 Transcript synonymous_variant 807/2047 558/936 186/311 G ggG/ggT 1 1 IL20RB HGNC HGNC:6004 protein_coding YES CCDS3093.1 ENSP00000328133 Q6UXL0 UPI000003E7F6 NM_144717.3 5/7 hmmpanther:PTHR20859:SF48,hmmpanther:PTHR20859,Pfam_domain:PF09294,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs1387323876 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 136991964 136991964 G T 1 0 0 0 0 0 0 0 1 7572 1219 43 2 2 IL20RB 3 136991964 Silent SNP G C3N-00547_T 10487964 136991964 61303595 154 14484 PRR23B 0 . GRCh38 3 139020024 139020024 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.638C>A p.Pro213His p.P213H ENST00000329447 1/1 155 83 72 141 141 0 strelka-varscan-mutect PRR23B,missense_variant,p.Pro213His,ENST00000329447,NM_001013650.2;MRPS22,intron_variant,,ENST00000495075,; T ENST00000329447 Transcript missense_variant 903/1896 638/798 213/265 P/H cCc/cAc 1 -1 PRR23B HGNC HGNC:33764 protein_coding YES CCDS33868.1 ENSP00000328768 Q6ZRT6 UPI00001C0F1A NM_001013650.2 tolerated(0.79) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF7,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 139020024 139020024 G T 1 0 0 0 0 1 0 0 0 12730 1232 43 2 2 PRR23B 3 139020024 Missense_Mutation SNP G C3N-00547_T 2028060 139020024 59275535 155 14485 P2RY14 0 . GRCh38 3 151214251 151214251 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.66G>T p.Gln22His p.Q22H ENST00000309170 3/3 280 111 169 223 223 0 strelka-varscan-mutect P2RY14,missense_variant,p.Gln22His,ENST00000309170,NM_014879.3;P2RY14,missense_variant,p.Gln22His,ENST00000424796,NM_001081455.1;P2RY14,missense_variant,p.Gln22His,ENST00000494668,;MED12L,intron_variant,,ENST00000474524,NM_053002.5;MED12L,intron_variant,,ENST00000273432,;MED12L,intron_variant,,ENST00000480026,; A ENST00000309170 Transcript missense_variant 379/2513 66/1017 22/338 Q/H caG/caT COSM1039936 1 -1 P2RY14 HGNC HGNC:16442 protein_coding YES CCDS3156.1 ENSP00000308361 Q15391 A5JUU3 UPI0000050418 NM_014879.3 tolerated(0.27) 3/3 hmmpanther:PTHR24233,hmmpanther:PTHR24233:SF3,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01655 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 151214251 151214251 C A 1 0 0 0 0 1 0 0 0 11424 796 28 2 2 P2RY14 3 151214251 Missense_Mutation SNP C C3N-00547_T 12194227 151214251 47081308 156 14486 SLITRK3 0 . GRCh38 3 165189159 165189159 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1672G>T p.Asp558Tyr p.D558Y ENST00000475390 2/2 347 178 169 241 240 1 strelka-varscan-mutect SLITRK3,missense_variant,p.Asp558Tyr,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Asp558Tyr,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; A ENST00000475390 Transcript missense_variant 2116/4555 1672/2934 558/977 D/Y Gac/Tac 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 deleterious(0) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 165189159 165189159 C A 1 0 0 0 0 1 0 0 0 15035 913 32 2 2 SLITRK3 3 165189159 Missense_Mutation SNP C C3N-00547_T 13974908 165189159 33106400 157 14487 NLGN1 0 . GRCh38 3 174280547 174280547 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.1716A>T p.Glu572Asp p.E572D ENST00000457714 7/7 183 75 108 113 113 0 strelka-varscan-mutect NLGN1,missense_variant,p.Glu572Asp,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Glu572Asp,ENST00000361589,;NLGN1,missense_variant,p.Glu357Asp,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,; T ENST00000457714 Transcript missense_variant 2145/8242 1716/2472 572/823 E/D gaA/gaT 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 tolerated(0.13) 7/7 hmmpanther:PTHR11559:SF52,hmmpanther:PTHR11559,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474,Prints_domain:PR01090 MODERATE 1 SNV 1 1 PASS rs1025946144 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 174280547 174280547 A T 1 0 0 0 0 1 0 0 0 10498 69 3 4 4 NLGN1 3 174280547 Missense_Mutation SNP A C3N-00547_T 9091388 174280547 24015012 158 14488 EIF2B5 0 . GRCh38 3 184143517 184143517 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1821G>C p.Gln607His p.Q607H ENST00000273783 13/16 516 481 35 628 628 0 strelka-varscan-mutect EIF2B5,missense_variant,p.Gln607His,ENST00000273783,NM_003907.2;EIF2B5,downstream_gene_variant,,ENST00000492773,;EIF2B5,downstream_gene_variant,,ENST00000479833,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000481054,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491144,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000465218,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000484154,;EIF2B5,downstream_gene_variant,,ENST00000491008,;EIF2B5,downstream_gene_variant,,ENST00000468748,;EIF2B5,downstream_gene_variant,,ENST00000432982,;EIF2B5,downstream_gene_variant,,ENST00000493740,;EIF2B5,upstream_gene_variant,,ENST00000492226,;EIF2B5,downstream_gene_variant,,ENST00000479250,; C ENST00000273783 Transcript missense_variant 1943/2655 1821/2166 607/721 Q/H caG/caC 1 1 EIF2B5 HGNC HGNC:3261 protein_coding YES CCDS3252.1 ENSP00000273783 Q13144 UPI000013D9CF NM_003907.2 deleterious(0.01) 13/16 PROSITE_profiles:PS51363,Gene3D:1.25.40.180,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 184143517 184143517 G C 1 0 0 0 0 1 0 0 0 4840 933 33 4 4 EIF2B5 3 184143517 Missense_Mutation SNP G C3N-00547_T 9862970 184143517 14152042 159 14489 MASP1 0 . GRCh38 3 187256739 187256739 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.669G>T p.Met223Ile p.M223I ENST00000296280 5/11 319 257 62 374 374 0 strelka-varscan-mutect MASP1,missense_variant,p.Met223Ile,ENST00000337774,NM_001879.5;MASP1,missense_variant,p.Met223Ile,ENST00000296280,NM_139125.3;MASP1,missense_variant,p.Met110Ile,ENST00000392472,;MASP1,missense_variant,p.Met223Ile,ENST00000169293,NM_001031849.2;MASP1,missense_variant,p.Met197Ile,ENST00000392470,;MASP1,downstream_gene_variant,,ENST00000392475,;MASP1,intron_variant,,ENST00000495249,;MASP1,downstream_gene_variant,,ENST00000490558,;MASP1,downstream_gene_variant,,ENST00000465015,;MASP1,non_coding_transcript_exon_variant,,ENST00000460839,;MASP1,upstream_gene_variant,,ENST00000483719,; A ENST00000296280 Transcript missense_variant 895/4015 669/2187 223/728 M/I atG/atT 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 tolerated(0.45) 5/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS01180,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 187256739 187256739 C A 1 0 0 0 0 1 0 0 0 9248 594 21 2 2 MASP1 3 187256739 Missense_Mutation SNP C C3N-00547_T 3113222 187256739 11038820 160 14490 UBXN7 0 . GRCh38 3 196393597 196393597 + Silent SNP T T G novel C3N-00547_T C3N-00547_N T T c.312A>C p.= p.A104A ENST00000296328 4/11 170 136 34 176 175 1 strelka-varscan-mutect UBXN7,synonymous_variant,p.=,ENST00000296328,NM_015562.1;UBXN7,synonymous_variant,p.=,ENST00000413584,;UBXN7,intron_variant,,ENST00000428095,;UBXN7,intron_variant,,ENST00000381887,;RNU6-1279P,downstream_gene_variant,,ENST00000383917,;RN7SL434P,downstream_gene_variant,,ENST00000495872,;UBXN7,missense_variant,p.His55Pro,ENST00000429160,; G ENST00000296328 Transcript synonymous_variant 387/10568 312/1470 104/489 A gcA/gcC 1 -1 UBXN7 HGNC HGNC:29119 protein_coding YES CCDS43191.1 ENSP00000296328 O94888 UPI00001C1DEF NM_015562.1 4/11 hmmpanther:PTHR23322,hmmpanther:PTHR23322:SF6,PIRSF_domain:PIRSF037991 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 196393597 196393597 T G 1 0 0 0 0 0 0 0 1 17442 1683 59 5 5 UBXN7 3 196393597 Silent SNP T C3N-00547_T 9136858 196393597 1901962 161 14491 IDUA 0 . GRCh38 4 1001720 1001720 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.631G>T p.Ala211Ser p.A211S ENST00000247933 6/14 241 182 59 222 222 0 strelka-varscan-mutect IDUA,missense_variant,p.Ala211Ser,ENST00000247933,NM_000203.4;IDUA,missense_variant,p.Ala79Ser,ENST00000514224,;IDUA,missense_variant,p.Ala142Ser,ENST00000509948,;IDUA,missense_variant,p.Ala164Ser,ENST00000502910,;IDUA,missense_variant,p.Ala150Ser,ENST00000514192,;IDUA,downstream_gene_variant,,ENST00000504568,;IDUA,non_coding_transcript_exon_variant,,ENST00000514698,;IDUA,downstream_gene_variant,,ENST00000506561,;IDUA,upstream_gene_variant,,ENST00000502829,;IDUA,downstream_gene_variant,,ENST00000508168,;IDUA,upstream_gene_variant,,ENST00000514417,; T ENST00000247933 Transcript missense_variant 719/2163 631/1962 211/653 A/S Gcc/Tcc 1 1 IDUA HGNC HGNC:5391 protein_coding YES CCDS3343.1 ENSP00000247933 P35475 UPI00004571D0 NM_000203.4 tolerated(0.38) 6/14 Gene3D:3.20.20.80,Pfam_domain:PF01229,hmmpanther:PTHR12631,hmmpanther:PTHR12631:SF8,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS rs760582777 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 1001720 1001720 G T 1 0 0 0 0 1 0 0 0 7405 1087 38 1 1 IDUA 4 1001720 Missense_Mutation SNP G C3N-00547_T 1001720 189212835 162 14492 FAM53A 0 . GRCh38 4 1641423 1641423 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1067G>T p.Arg356Met p.R356M ENST00000308132 5/5 82 58 24 146 145 1 strelka-varscan-mutect FAM53A,missense_variant,p.Arg356Met,ENST00000308132,NM_001174070.2;FAM53A,missense_variant,p.Arg356Met,ENST00000461064,;FAM53A,missense_variant,p.Arg356Met,ENST00000472884,NM_001013622.3;FAM53A,3_prime_UTR_variant,,ENST00000489363,NM_001297435.1;FAM53A,intron_variant,,ENST00000489029,;FAM53A,downstream_gene_variant,,ENST00000467215,; A ENST00000308132 Transcript missense_variant 1260/2802 1067/1197 356/398 R/M aGg/aTg 1 -1 FAM53A HGNC HGNC:31860 protein_coding YES CCDS33939.1 ENSP00000310057 Q6NSI3 UPI000023730C NM_001174070.2 deleterious(0.02) 5/5 hmmpanther:PTHR28567,hmmpanther:PTHR28567:SF2 MODERATE 1 SNV 2 1 PASS rs1312116149 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 1641423 1641423 C A 1 0 0 0 0 1 0 0 0 5455 681 24 2 2 FAM53A 4 1641423 Missense_Mutation SNP C C3N-00547_T 639703 1641423 188573132 163 14493 CRMP1 0 . GRCh38 4 5828513 5828513 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1779C>A p.Tyr593Ter p.Y593* ENST00000324989 12/14 128 89 39 130 130 0 strelka-varscan-mutect CRMP1,stop_gained,p.Tyr593Ter,ENST00000324989,NM_001288662.1,NM_001014809.2;CRMP1,stop_gained,p.Tyr479Ter,ENST00000397890,NM_001313.4;CRMP1,stop_gained,p.Tyr477Ter,ENST00000512574,NM_001288661.1;CRMP1,non_coding_transcript_exon_variant,,ENST00000511535,;CRMP1,non_coding_transcript_exon_variant,,ENST00000506216,;CRMP1,upstream_gene_variant,,ENST00000513911,; T ENST00000324989 Transcript stop_gained 1868/3146 1779/2061 593/686 Y/* taC/taA 1 -1 CRMP1 HGNC HGNC:2365 protein_coding YES CCDS33950.1 ENSP00000321606 Q14194 X5DNI1 UPI000020BA92 NM_001288662.1,NM_001014809.2 12/14 hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF54,Gene3D:2.30.40.10 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 5828513 5828513 G T 1 0 0 0 0 0 1 0 0 3691 1256 44 2 2 CRMP1 4 5828513 Nonsense_Mutation SNP G C3N-00547_T 4187090 5828513 184386042 164 14494 PSAPL1 0 . GRCh38 4 7434533 7434533 + Nonsense_Mutation SNP G G T rs753546282 C3N-00547_T C3N-00547_N G G c.347C>A p.Ser116Ter p.S116* ENST00000319098 1/1 143 105 38 151 151 0 strelka-varscan-mutect PSAPL1,stop_gained,p.Ser116Ter,ENST00000319098,NM_001085382.1;SORCS2,intron_variant,,ENST00000507866,NM_020777.2;SORCS2,intron_variant,,ENST00000329016,;SORCS2,intron_variant,,ENST00000511199,; T ENST00000319098 Transcript stop_gained 441/4680 347/1566 116/521 S/* tCg/tAg rs753546282 1 -1 PSAPL1 HGNC HGNC:33131 protein_coding YES CCDS47009.1 ENSP00000317445 Q6NUJ1 UPI000003F80E NM_001085382.1 1/1 PROSITE_profiles:PS50015,hmmpanther:PTHR11480:SF39,hmmpanther:PTHR11480,PIRSF_domain:PIRSF002431,Gene3D:1.10.225.10,SMART_domains:SM00741,Superfamily_domains:SSF47862 HIGH SNV 1 PASS rs753546282 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 7434533 7434533 G T 1 0 0 0 0 0 1 0 0 12794 1059 37 1 1 PSAPL1 4 7434533 Nonsense_Mutation SNP G C3N-00547_T 1606020 7434533 182780022 165 14495 GPR78 0 . GRCh38 4 8587071 8587071 + Missense_Mutation SNP C C A rs778580489 C3N-00547_T C3N-00547_N C C c.800C>A p.Pro267His p.P267H ENST00000382487 3/3 130 82 48 124 124 0 strelka-varscan-mutect GPR78,missense_variant,p.Pro267His,ENST00000382487,NM_080819.4;GPR78,non_coding_transcript_exon_variant,,ENST00000509216,;GPR78,non_coding_transcript_exon_variant,,ENST00000504255,;GPR78,intron_variant,,ENST00000514302,; A ENST00000382487 Transcript missense_variant 1217/1694 800/1092 267/363 P/H cCc/cAc rs778580489,COSM4625358 1 1 GPR78 HGNC HGNC:4528 protein_coding YES CCDS3403.1 ENSP00000371927 Q96P69 B2R7M4 UPI0000037A5F NM_080819.4 deleterious(0.02) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF7,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778580489 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 8587071 8587071 C A 1 0 0 0 0 1 0 0 0 6592 623 22 2 2 GPR78 4 8587071 Missense_Mutation SNP C C3N-00547_T 1152538 8587071 181627484 166 14496 FAM184B 0 . GRCh38 4 17709601 17709601 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.185G>T p.Ser62Ile p.S62I ENST00000265018 2/18 50 31 19 55 55 0 strelka-varscan-mutect FAM184B,missense_variant,p.Ser62Ile,ENST00000265018,NM_015688.1; A ENST00000265018 Transcript missense_variant 398/6622 185/3183 62/1060 S/I aGc/aTc 1 -1 FAM184B HGNC HGNC:29235 protein_coding YES CCDS47033.1 ENSP00000265018 Q9ULE4 UPI000020BD7C NM_015688.1 deleterious(0) 2/18 hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870,Pfam_domain:PF15665,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 17709601 17709601 C A 1 0 0 0 0 1 0 0 0 5359 797 28 2 2 FAM184B 4 17709601 Missense_Mutation SNP C C3N-00547_T 9122530 17709601 172504954 167 14497 STIM2 0 . GRCh38 4 27022534 27022534 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.1803A>T p.= p.T601T ENST00000465503 13/13 32 23 9 48 48 0 strelka-varscan-mutect STIM2,missense_variant,p.Gln341Leu,ENST00000473519,;STIM2,synonymous_variant,p.=,ENST00000467087,NM_020860.3;STIM2,synonymous_variant,p.=,ENST00000465503,NM_001169118.1;STIM2,3_prime_UTR_variant,,ENST00000467011,NM_001169117.1;STIM2,downstream_gene_variant,,ENST00000477474,;STIM2,non_coding_transcript_exon_variant,,ENST00000504511,; T ENST00000465503 Transcript synonymous_variant 2181/3613 1803/2265 601/754 T acA/acT 1 1 STIM2 HGNC HGNC:19205 protein_coding YES CCDS54751.1 ENSP00000417569 H0Y860 UPI0001B79443 NM_001169118.1 13/13 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF2 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 2 4 49 27022534 27022534 A T 1 0 0 0 0 0 0 0 1 15661 175 7 4 4 STIM2 4 27022534 Silent SNP A C3N-00547_T 9312933 27022534 163192021 168 14498 STIM2 0 . GRCh38 4 27022751 27022751 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2020C>A p.Pro674Thr p.P674T ENST00000465503 13/13 282 220 62 291 291 0 strelka-varscan-mutect STIM2,missense_variant,p.Pro666Thr,ENST00000467087,NM_020860.3;STIM2,missense_variant,p.Pro674Thr,ENST00000465503,NM_001169118.1;STIM2,3_prime_UTR_variant,,ENST00000467011,NM_001169117.1;STIM2,3_prime_UTR_variant,,ENST00000473519,;STIM2,downstream_gene_variant,,ENST00000477474,;STIM2,downstream_gene_variant,,ENST00000504511,; A ENST00000465503 Transcript missense_variant 2398/3613 2020/2265 674/754 P/T Cct/Act 1 1 STIM2 HGNC HGNC:19205 protein_coding YES CCDS54751.1 ENSP00000417569 H0Y860 UPI0001B79443 NM_001169118.1 deleterious_low_confidence(0.04) 13/13 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 27022751 27022751 C A 1 0 0 0 0 1 0 0 0 15661 855 30 2 2 STIM2 4 27022751 Missense_Mutation SNP C C3N-00547_T 217 27022751 163191804 169 14499 PCDH7 0 . GRCh38 4 30722688 30722688 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.1266C>A p.= p.R422R ENST00000543491 1/1 146 116 30 189 187 2 strelka-varscan-mutect PCDH7,synonymous_variant,p.=,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,synonymous_variant,p.=,ENST00000361762,NM_002589.2;PCDH7,synonymous_variant,p.=,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; A ENST00000543491 Transcript synonymous_variant 1836/4457 1266/3219 422/1072 R cgC/cgA 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 1/1 hmmpanther:PTHR24027:SF321,hmmpanther:PTHR24027,Superfamily_domains:SSF49313 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 30722688 30722688 C A 1 0 0 0 0 0 0 0 1 11603 697 25 2 2 PCDH7 4 30722688 Silent SNP C C3N-00547_T 3699937 30722688 159491867 170 14500 ARAP2 0 . GRCh38 4 36068086 36068086 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.4936G>T p.Gly1646Trp p.G1646W ENST00000303965 33/33 190 145 45 260 260 0 strelka-varscan-mutect ARAP2,missense_variant,p.Gly1646Trp,ENST00000303965,NM_015230.3;ARAP2,downstream_gene_variant,,ENST00000618163,;ARAP2,intron_variant,,ENST00000503225,;RP11-640B6.1,upstream_gene_variant,,ENST00000514630,; A ENST00000303965 Transcript missense_variant 5426/7514 4936/5115 1646/1704 G/W Ggg/Tgg 1 -1 ARAP2 HGNC HGNC:16924 protein_coding YES CCDS3441.1 ENSP00000302895 Q8WZ64 UPI000013E917 NM_015230.3 tolerated(0.07) 33/33 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 36068086 36068086 C A 1 0 0 0 0 1 0 0 0 961 594 21 2 2 ARAP2 4 36068086 Missense_Mutation SNP C C3N-00547_T 5345398 36068086 154146469 171 14501 TMEM156 0 . GRCh38 4 38998884 38998884 + Silent SNP C C A rs758892519 C3N-00547_T C3N-00547_N C C c.114G>T p.= p.L38L ENST00000381938 2/7 123 92 31 145 145 0 strelka-varscan-mutect TMEM156,synonymous_variant,p.=,ENST00000381938,NM_024943.2,NM_001303228.1;TMEM156,synonymous_variant,p.=,ENST00000344606,;TMEM156,non_coding_transcript_exon_variant,,ENST00000372489,; A ENST00000381938 Transcript synonymous_variant 222/1935 114/891 38/296 L ctG/ctT rs758892519 1 -1 TMEM156 HGNC HGNC:26260 protein_coding YES CCDS3448.1 ENSP00000371364 Q8N614 A0A024R9T9 UPI000006D7FE NM_024943.2,NM_001303228.1 2/7 hmmpanther:PTHR14788,hmmpanther:PTHR14788:SF5 LOW 1 SNV 1 1 PASS rs758892519 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 38998884 38998884 C A 1 0 0 0 0 0 0 0 1 16516 581 21 2 2 TMEM156 4 38998884 Silent SNP C C3N-00547_T 2930798 38998884 151215671 172 14502 GABRG1 0 . GRCh38 4 46064442 46064442 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.624C>A p.Ser208Arg p.S208R ENST00000295452 5/9 112 84 28 188 188 0 strelka-varscan-mutect GABRG1,missense_variant,p.Ser208Arg,ENST00000295452,NM_173536.3; T ENST00000295452 Transcript missense_variant,splice_region_variant 792/6785 624/1398 208/465 S/R agC/agA 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 deleterious(0) 5/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 46064442 46064442 G T 1 0 0 0 0 1 0 0 0 6042 985 34 2 2 GABRG1 4 46064442 Missense_Mutation SNP G C3N-00547_T 7065558 46064442 144150113 173 14503 FRYL 0 . GRCh38 4 48590659 48590659 + Nonsense_Mutation SNP C C A rs777697473 C3N-00547_T C3N-00547_N C C c.1507G>T p.Gly503Ter p.G503* ENST00000358350 17/64 45 35 10 71 71 0 strelka-varscan-mutect FRYL,stop_gained,p.Gly503Ter,ENST00000358350,NM_015030.1;FRYL,stop_gained,p.Gly503Ter,ENST00000503238,;FRYL,stop_gained,p.Gly503Ter,ENST00000507711,;FRYL,stop_gained,p.Gly209Ter,ENST00000506685,; A ENST00000358350 Transcript stop_gained,splice_region_variant 2112/11706 1507/9042 503/3013 G/* Gga/Tga rs777697473 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 17/64 Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9 HIGH 1 SNV 5 1 PASS rs777697473 . 0 203 7 0 0 0 0 0 -19.99998 0.9999998 1 1 1 0 A 4 1 49 48590659 48590659 C A 1 0 0 0 0 0 1 0 0 5936 695 24 2 2 FRYL 4 48590659 Nonsense_Mutation SNP C C3N-00547_T 2526217 48590659 141623896 174 14504 LRRC66 0 . GRCh38 4 51994565 51994565 + Silent SNP C C A rs137931708 C3N-00547_T C3N-00547_N C C c.2457G>T p.= p.P819P ENST00000343457 4/4 166 149 17 195 195 0 strelka-varscan-mutect LRRC66,synonymous_variant,p.=,ENST00000343457,NM_001024611.1; A ENST00000343457 Transcript synonymous_variant 2464/3327 2457/2643 819/880 P ccG/ccT rs137931708 1 -1 LRRC66 HGNC HGNC:34299 protein_coding YES CCDS43229.1 ENSP00000341944 Q68CR7 UPI0000425C5B NM_001024611.1 4/4 LOW 1 SNV 1 1 PASS rs137931708 . 0 208 0 2 0 0 0 0 -19.99994 0.9999999 1 1 1 0 A 2 1 49 51994565 51994565 C A 1 0 0 0 0 0 0 0 1 8914 639 23 1 1 LRRC66 4 51994565 Silent SNP C C3N-00547_T 3403906 51994565 138219990 175 14505 PDGFRA 0 . GRCh38 4 54273548 54273548 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1376A>G p.Glu459Gly p.E459G ENST00000257290 10/23 251 172 79 352 352 0 strelka-varscan-mutect PDGFRA,missense_variant,p.Glu459Gly,ENST00000257290,NM_006206.4;RP11-231C18.3,intron_variant,,ENST00000507166,;PDGFRA,missense_variant,p.Glu459Gly,ENST00000509490,;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092,;PDGFRA,upstream_gene_variant,,ENST00000507536,;PDGFRA,upstream_gene_variant,,ENST00000461294,; G ENST00000257290 Transcript missense_variant 1707/6576 1376/3270 459/1089 E/G gAa/gGa 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 tolerated(0.13) 10/23 hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 54273548 54273548 A G 1 0 0 0 0 1 0 0 0 11749 246 9 5 5 PDGFRA 4 54273548 Missense_Mutation SNP A C3N-00547_T 2278983 54273548 135941007 176 14506 ADGRL3 0 . GRCh38 4 61732775 61732775 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.416T>G p.Leu139Arg p.L139R ENST00000514591 7/25 62 52 10 86 86 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Leu139Arg,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.Leu139Arg,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Leu207Arg,ENST00000509896,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000511324,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000508693,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000507164,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000506720,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000506746,;ADGRL3,missense_variant,p.Leu207Arg,ENST00000507625,;ADGRL3,missense_variant,p.Leu139Arg,ENST00000506700,;ADGRL3,missense_variant,p.Leu139Arg,ENST00000504896,;ADGRL3,missense_variant,p.Leu139Arg,ENST00000514157,;ADGRL3,missense_variant,p.Leu139Arg,ENST00000508946,;ADGRL3,missense_variant,p.Leu139Arg,ENST00000514996,; G ENST00000514591 Transcript missense_variant 745/6297 416/4410 139/1469 L/R cTa/cGa 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0) 7/25 PROSITE_profiles:PS51132,hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,SMART_domains:SM00284 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99976 1 1 1 1 0 G 3 3 49 61732775 61732775 T G 1 0 0 0 0 1 0 0 0 377 1522 53 5 5 ADGRL3 4 61732775 Missense_Mutation SNP T C3N-00547_T 7459227 61732775 128481780 177 14507 ADGRL3 0 . GRCh38 4 61733125 61733125 + Silent SNP C C A rs371272321 C3N-00547_T C3N-00547_N C C c.766C>A p.= p.R256R ENST00000514591 7/25 185 161 24 205 205 0 strelka-varscan-mutect ADGRL3,synonymous_variant,p.=,ENST00000512091,NM_001322246.1;ADGRL3,synonymous_variant,p.=,ENST00000514591,NM_015236.4;ADGRL3,synonymous_variant,p.=,ENST00000509896,;ADGRL3,synonymous_variant,p.=,ENST00000511324,;ADGRL3,synonymous_variant,p.=,ENST00000508693,;ADGRL3,synonymous_variant,p.=,ENST00000507164,;ADGRL3,synonymous_variant,p.=,ENST00000506720,;ADGRL3,synonymous_variant,p.=,ENST00000506746,;ADGRL3,synonymous_variant,p.=,ENST00000507625,;ADGRL3,synonymous_variant,p.=,ENST00000506700,;ADGRL3,synonymous_variant,p.=,ENST00000504896,;ADGRL3,synonymous_variant,p.=,ENST00000514157,;ADGRL3,synonymous_variant,p.=,ENST00000508946,;ADGRL3,synonymous_variant,p.=,ENST00000514996,; A ENST00000514591 Transcript synonymous_variant 1095/6297 766/4410 256/1469 R Cga/Aga rs371272321 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 7/25 PROSITE_profiles:PS51132,Pfam_domain:PF02191,SMART_domains:SM00284 LOW 1 SNV 5 1 PASS rs371272321 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 61733125 61733125 C A 1 0 0 0 0 0 0 0 1 377 644 23 1 1 ADGRL3 4 61733125 Silent SNP C C3N-00547_T 350 61733125 128481430 178 14508 ADGRL3 0 . GRCh38 4 62070549 62070549 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.4051C>G p.Pro1351Ala p.P1351A ENST00000514591 25/25 216 150 66 238 238 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Pro1351Ala,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Pro1462Ala,ENST00000506720,;ADGRL3,missense_variant,p.Pro1453Ala,ENST00000506746,;ADGRL3,missense_variant,p.Pro1410Ala,ENST00000507625,;ADGRL3,missense_variant,p.Pro1394Ala,ENST00000508946,;ADGRL3,missense_variant,p.Pro1385Ala,ENST00000514996,;ADGRL3,missense_variant,p.Pro800Ala,ENST00000502815,;ADGRL3,3_prime_UTR_variant,,ENST00000512091,NM_001322246.1;ADGRL3,3_prime_UTR_variant,,ENST00000509896,;ADGRL3,3_prime_UTR_variant,,ENST00000511324,;ADGRL3,3_prime_UTR_variant,,ENST00000508693,;ADGRL3,3_prime_UTR_variant,,ENST00000507164,;ADGRL3,3_prime_UTR_variant,,ENST00000506700,;ADGRL3,3_prime_UTR_variant,,ENST00000504896,;ADGRL3,3_prime_UTR_variant,,ENST00000514157,;ADGRL3-AS1,downstream_gene_variant,,ENST00000506704,;ADGRL3-AS1,downstream_gene_variant,,ENST00000504135,;ADGRL3-AS1,downstream_gene_variant,,ENST00000509461,; G ENST00000514591 Transcript missense_variant 4380/6297 4051/4410 1351/1469 P/A Ccc/Gcc 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 tolerated_low_confidence(0.16) 25/25 Pfam_domain:PF02354 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 62070549 62070549 C G 1 0 0 0 0 1 0 0 0 377 623 22 4 4 ADGRL3 4 62070549 Missense_Mutation SNP C C3N-00547_T 337424 62070549 128144006 179 14509 TMPRSS11A 0 . GRCh38 4 67914597 67914597 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.1095T>A p.Asp365Glu p.D365E ENST00000334830 9/10 217 155 62 318 318 0 strelka-varscan-mutect TMPRSS11A,missense_variant,p.Asp362Glu,ENST00000508048,NM_001114387.1;TMPRSS11A,missense_variant,p.Asp365Glu,ENST00000334830,NM_182606.3;TMPRSS11A,missense_variant,p.Asp329Glu,ENST00000513536,;UBA6-AS1,intron_variant,,ENST00000500538,; T ENST00000334830 Transcript missense_variant 1842/3054 1095/1266 365/421 D/E gaT/gaA 1 -1 TMPRSS11A HGNC HGNC:27954 protein_coding YES CCDS3519.1 ENSP00000334611 A0A0A0MR82 UPI0000457217 NM_182606.3 deleterious(0) 9/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF37,PROSITE_patterns:PS00135,Pfam_domain:PF00089,Gene3D:2.40.10.10,PIRSF_domain:PIRSF037941,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 67914597 67914597 A T 1 0 0 0 0 1 0 0 0 16715 214 8 4 4 TMPRSS11A 4 67914597 Missense_Mutation SNP A C3N-00547_T 5844048 67914597 122299958 180 14510 TMPRSS11B 0 . GRCh38 4 68228032 68228032 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.1130A>T p.Asn377Ile p.N377I ENST00000332644 10/10 113 72 41 169 169 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Asn377Ile,ENST00000332644,NM_182502.3;TMPRSS11B,downstream_gene_variant,,ENST00000502365,;TMPRSS11B,downstream_gene_variant,,ENST00000510856,; A ENST00000332644 Transcript missense_variant 1292/2671 1130/1251 377/416 N/I aAt/aTt 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 deleterious(0) 10/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF171,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 68228032 68228032 T A 1 0 0 0 0 1 0 0 0 16716 1493 52 4 4 TMPRSS11B 4 68228032 Missense_Mutation SNP T C3N-00547_T 313435 68228032 121986523 181 14511 TMPRSS11E 0 . GRCh38 4 68466748 68466748 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.254C>A p.Ser85Ter p.S85* ENST00000305363 3/10 139 126 13 237 237 0 strelka-varscan-mutect TMPRSS11E,stop_gained,p.Ser85Ter,ENST00000305363,NM_014058.3;TMPRSS11E,stop_gained,p.Ser82Ter,ENST00000510647,; A ENST00000305363 Transcript stop_gained 318/2136 254/1272 85/423 S/* tCa/tAa 1 1 TMPRSS11E HGNC HGNC:24465 protein_coding YES CCDS33993.1 ENSP00000307519 Q9UL52 UPI00000389F7 NM_014058.3 3/10 PROSITE_profiles:PS50024,PIRSF_domain:PIRSF037941,Gene3D:1ivzA00,Pfam_domain:PF01390,Superfamily_domains:0047452 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 68466748 68466748 C A 1 0 0 0 0 0 1 0 0 16718 840 29 2 2 TMPRSS11E 4 68466748 Nonsense_Mutation SNP C C3N-00547_T 238716 68466748 121747807 182 14512 SMR3B 0 . GRCh38 4 70389766 70389766 + Missense_Mutation SNP C C A rs753598635 C3N-00547_T C3N-00547_N C C c.158C>A p.Pro53His p.P53H ENST00000304915 3/3 230 213 17 295 293 2 strelka-varscan-mutect SMR3B,missense_variant,p.Pro53His,ENST00000304915,NM_006685.3;SMR3B,missense_variant,p.Pro53His,ENST00000614072,;SMR3B,missense_variant,p.Pro53His,ENST00000504825,;SMR3B,downstream_gene_variant,,ENST00000508027,; A ENST00000304915 Transcript missense_variant 307/785 158/240 53/79 P/H cCc/cAc rs753598635 1 1 SMR3B HGNC HGNC:17326 protein_coding YES CCDS3540.1 ENSP00000302400 P02814 UPI0000132226 NM_006685.3 deleterious_low_confidence(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR14179,hmmpanther:PTHR14179:SF10,Pfam_domain:PF15621 MODERATE 1 SNV 1 1 PASS rs753598635 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 70389766 70389766 C A 1 0 0 0 0 1 0 0 0 15133 623 22 2 2 SMR3B 4 70389766 Missense_Mutation SNP C C3N-00547_T 1923018 70389766 119824789 183 14513 CNOT6L 0 . GRCh38 4 77774703 77774703 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.141C>A p.Ser47Arg p.S47R ENST00000504123 3/12 51 47 4 84 84 0 varscan-mutect CNOT6L,missense_variant,p.Ser47Arg,ENST00000504123,NM_144571.2,NM_001286790.1;CNOT6L,missense_variant,p.Ser76Arg,ENST00000515506,;CNOT6L,missense_variant,p.Ser54Arg,ENST00000512485,;CNOT6L,missense_variant,p.Ser47Arg,ENST00000515441,;CNOT6L,non_coding_transcript_exon_variant,,ENST00000506166,;CNOT6L,missense_variant,p.Ala46Asp,ENST00000504804,; T ENST00000504123 Transcript missense_variant 272/8843 141/1668 47/555 S/R agC/agA 1 -1 CNOT6L HGNC HGNC:18042 protein_coding YES CCDS68731.1 ENSP00000424896 Q96LI5 UPI0000E445DF NM_144571.2,NM_001286790.1 deleterious(0) 3/12 Low_complexity_(Seg):seg,hmmpanther:PTHR12121:SF35,hmmpanther:PTHR12121,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS rs1384585267 . 0 198 12 0 0 0 0 0 -9.845246 0.9997021 1 1 1 0 T 3 4 49 77774703 77774703 G T 1 0 0 0 0 1 0 0 0 3403 1194 42 2 2 CNOT6L 4 77774703 Missense_Mutation SNP G C3N-00547_T 7384937 77774703 112439852 184 14514 PTPN13 0 . GRCh38 4 86772947 86772947 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.5353G>C p.Asp1785His p.D1785H ENST00000436978 32/48 75 68 7 89 89 0 strelka-varscan-mutect PTPN13,missense_variant,p.Asp1785His,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Asp1761His,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Asp1780His,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Asp1785His,ENST00000511467,;PTPN13,missense_variant,p.Asp1589His,ENST00000316707,NM_080684.2; C ENST00000436978 Transcript missense_variant 5833/8573 5353/7473 1785/2490 D/H Gac/Cac 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0.01) 32/48 Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF000933,Gene3D:2.30.42.10 MODERATE 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -15.07302 0.9999552 1 1 1 0 C 3 2 49 86772947 86772947 G C 1 0 0 0 0 1 0 0 0 12935 942 33 4 4 PTPN13 4 86772947 Missense_Mutation SNP G C3N-00547_T 8998244 86772947 103441608 185 14515 UNC5C 0 . GRCh38 4 95170224 95170224 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.2560A>T p.Ser854Cys p.S854C ENST00000453304 15/16 190 171 19 240 240 0 strelka-varscan-mutect UNC5C,missense_variant,p.Ser854Cys,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Ser813Cys,ENST00000610318,; A ENST00000453304 Transcript missense_variant 2909/9875 2560/2796 854/931 S/C Agc/Tgc 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 deleterious(0.01) 15/16 Gene3D:1.10.533.10,Pfam_domain:PF00531,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,SMART_domains:SM00005,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 95170224 95170224 T A 1 0 0 0 0 1 0 0 0 17517 1522 53 4 4 UNC5C 4 95170224 Missense_Mutation SNP T C3N-00547_T 8397277 95170224 95044331 186 14516 MANBA 0 . GRCh38 4 102635899 102635899 + Missense_Mutation SNP G G A C3N-00547_T C3N-00547_N G G c.2123C>T p.Ser708Leu p.S708L ENST00000226578 15/17 279 151 128 294 294 0 strelka-varscan-mutect MANBA,missense_variant,p.Ser708Leu,ENST00000226578,NM_005908.3;MANBA,missense_variant,p.Ser651Leu,ENST00000505239,;MANBA,non_coding_transcript_exon_variant,,ENST00000514430,;MANBA,downstream_gene_variant,,ENST00000508141,; A ENST00000226578 Transcript missense_variant 2223/2904 2123/2640 708/879 S/L tCa/tTa COSM3945826 1 -1 MANBA HGNC HGNC:6831 protein_coding YES CCDS3658.1 ENSP00000226578 O00462 UPI000013C8A2 NM_005908.3 deleterious(0.04) 15/17 hmmpanther:PTHR10066,hmmpanther:PTHR10066:SF65,Superfamily_domains:SSF49303 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 102635899 102635899 G A 1 0 0 0 0 1 0 0 0 9140 1294 45 3 3 MANBA 4 102635899 Missense_Mutation SNP G C3N-00547_T 7465675 102635899 87578656 187 14517 KIAA1109 0 . GRCh38 4 122211072 122211072 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2224C>A p.Leu742Ile p.L742I ENST00000264501 20/86 147 118 29 250 249 1 strelka-varscan-mutect KIAA1109,missense_variant,p.Leu742Ile,ENST00000264501,;KIAA1109,missense_variant,p.Leu742Ile,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Leu575Ile,ENST00000424425,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000495260,;KIAA1109,non_coding_transcript_exon_variant,,ENST00000482114,; A ENST00000264501 Transcript missense_variant 2597/15896 2224/15018 742/5005 L/I Cta/Ata 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 tolerated(0.17) 20/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 122211072 122211072 C A 1 0 0 0 0 1 0 0 0 8101 564 20 2 2 KIAA1109 4 122211072 Missense_Mutation SNP C C3N-00547_T 19575173 122211072 68003483 188 14518 FREM3 0 . GRCh38 4 143698220 143698220 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2456C>A p.Thr819Lys p.T819K ENST00000329798 1/8 186 105 81 228 228 0 strelka-varscan-mutect FREM3,missense_variant,p.Thr819Lys,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; T ENST00000329798 Transcript missense_variant 2456/6729 2456/6420 819/2139 T/K aCa/aAa 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 deleterious(0) 1/8 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 143698220 143698220 G T 1 0 0 0 0 1 0 0 0 5913 1377 48 2 2 FREM3 4 143698220 Missense_Mutation SNP G C3N-00547_T 21487148 143698220 46516335 189 14519 LRBA 0 . GRCh38 4 150436744 150436744 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.6934C>G p.Leu2312Val p.L2312V ENST00000357115 46/58 88 83 5 158 158 0 strelka-varscan-mutect LRBA,missense_variant,p.Leu2301Val,ENST00000510413,NM_001199282.2;LRBA,missense_variant,p.Leu2312Val,ENST00000357115,NM_006726.4;LRBA,missense_variant,p.Leu2301Val,ENST00000507224,;LRBA,missense_variant,p.Leu954Val,ENST00000509835,;LRBA,non_coding_transcript_exon_variant,,ENST00000503716,; C ENST00000357115 Transcript missense_variant 7178/9899 6934/8592 2312/2863 L/V Ctt/Gtt 1 -1 LRBA HGNC HGNC:1742 protein_coding YES CCDS3773.1 ENSP00000349629 P50851 UPI000013E35C NM_006726.4 deleterious(0) 46/58 Gene3D:1t77A02,Pfam_domain:PF02138,PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64,SMART_domains:SM01026,Superfamily_domains:SSF81837 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 150436744 150436744 G C 1 0 0 0 0 1 0 0 0 8825 942 33 4 4 LRBA 4 150436744 Missense_Mutation SNP G C3N-00547_T 6738524 150436744 39777811 190 14520 LRBA 0 . GRCh38 4 150905847 150905847 + Silent SNP G G T rs770658064 C3N-00547_T C3N-00547_N G G c.1746C>A p.= p.T582T ENST00000357115 13/58 79 74 5 98 98 0 strelka-varscan-mutect LRBA,synonymous_variant,p.=,ENST00000510413,NM_001199282.2;LRBA,synonymous_variant,p.=,ENST00000357115,NM_006726.4;LRBA,synonymous_variant,p.=,ENST00000507224,; T ENST00000357115 Transcript synonymous_variant 1990/9899 1746/8592 582/2863 T acC/acA rs770658064 1 -1 LRBA HGNC HGNC:1742 protein_coding YES CCDS3773.1 ENSP00000349629 P50851 UPI000013E35C NM_006726.4 13/58 Pfam_domain:PF15787,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF64 LOW 1 SNV 1 1 PASS rs770658064 . 0 208 2 0 0 0 0 0 -11.57088 1 1 1 1 0 T 2 4 49 150905847 150905847 G T 1 0 0 0 0 0 0 0 1 8825 1219 43 2 2 LRBA 4 150905847 Silent SNP G C3N-00547_T 469103 150905847 39308708 191 14521 FGG 0 . GRCh38 4 154606864 154606864 + Missense_Mutation SNP C C G rs747963231 C3N-00547_T C3N-00547_N C C c.970G>C p.Asp324His p.D324H ENST00000336098 8/9 157 106 51 192 192 0 strelka-varscan-mutect FGG,missense_variant,p.Asp324His,ENST00000404648,NM_000509.4;FGG,missense_variant,p.Asp324His,ENST00000336098,NM_021870.2;FGG,missense_variant,p.Asp332His,ENST00000407946,;FGG,missense_variant,p.Asp332His,ENST00000405164,;FGG,downstream_gene_variant,,ENST00000443553,;FGG,downstream_gene_variant,,ENST00000393846,;FGG,non_coding_transcript_exon_variant,,ENST00000492082,;FGG,non_coding_transcript_exon_variant,,ENST00000465913,;FGG,downstream_gene_variant,,ENST00000473393,;FGG,downstream_gene_variant,,ENST00000465336,;FGG,downstream_gene_variant,,ENST00000464532,; G ENST00000336098 Transcript missense_variant 1009/1659 970/1362 324/453 D/H Gat/Cat rs747963231 1 -1 FGG HGNC HGNC:3694 protein_coding YES CCDS3788.1 ENSP00000336829 P02679 UPI000012A78D NM_021870.2 tolerated(0.1) 8/9 Gene3D:3.90.215.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF22,Low_complexity_(Seg):seg,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 2 1 PASS rs747963231 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 154606864 154606864 C G 1 0 0 0 0 1 0 0 0 5734 826 29 4 4 FGG 4 154606864 Missense_Mutation SNP C C3N-00547_T 3701017 154606864 35607691 192 14522 FGG 0 . GRCh38 4 154609730 154609730 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.566A>T p.Gln189Leu p.Q189L ENST00000336098 6/9 325 180 145 415 415 0 strelka-varscan-mutect FGG,missense_variant,p.Gln189Leu,ENST00000404648,NM_000509.4;FGG,missense_variant,p.Gln189Leu,ENST00000336098,NM_021870.2;FGG,missense_variant,p.Gln197Leu,ENST00000407946,;FGG,missense_variant,p.Gln197Leu,ENST00000405164,;FGG,missense_variant,p.Gln86Leu,ENST00000443553,;FGG,missense_variant,p.Gln86Leu,ENST00000393846,;FGG,non_coding_transcript_exon_variant,,ENST00000492082,;FGG,non_coding_transcript_exon_variant,,ENST00000465913,;FGG,downstream_gene_variant,,ENST00000473393,;FGG,downstream_gene_variant,,ENST00000465336,;FGG,downstream_gene_variant,,ENST00000464532,;FGG,downstream_gene_variant,,ENST00000484695,; A ENST00000336098 Transcript missense_variant 605/1659 566/1362 189/453 Q/L cAg/cTg 1 -1 FGG HGNC HGNC:3694 protein_coding YES CCDS3788.1 ENSP00000336829 P02679 UPI000012A78D NM_021870.2 tolerated(0.18) 6/9 Gene3D:3.90.215.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF22,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 154609730 154609730 T A 1 0 0 0 0 1 0 0 0 5734 1580 55 4 4 FGG 4 154609730 Missense_Mutation SNP T C3N-00547_T 2866 154609730 35604825 193 14523 NPY2R 0 . GRCh38 4 155214830 155214830 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.891C>A p.= p.V297V ENST00000329476 2/2 57 29 28 75 75 0 strelka-varscan-mutect NPY2R,synonymous_variant,p.=,ENST00000329476,NM_000910.3;NPY2R,synonymous_variant,p.=,ENST00000506608,;AC097467.2,intron_variant,,ENST00000630664,; A ENST00000329476 Transcript synonymous_variant 1380/3626 891/1146 297/381 V gtC/gtA 1 1 NPY2R HGNC HGNC:7957 protein_coding YES CCDS3791.1 ENSP00000332591 P49146 UPI000003B342 NM_000910.3 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF42,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01014 LOW 1 SNV 1 1 PASS rs1390313583 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 155214830 155214830 C A 1 0 0 0 0 0 0 0 1 10664 842 30 2 2 NPY2R 4 155214830 Silent SNP C C3N-00547_T 605100 155214830 34999725 194 14524 GUCY1A3 0 . GRCh38 4 155710934 155710934 + Missense_Mutation SNP G G T rs372152908 C3N-00547_T C3N-00547_N G G c.769G>T p.Val257Phe p.V257F ENST00000296518 6/10 111 102 9 92 92 0 strelka-varscan-mutect GUCY1A3,missense_variant,p.Val257Phe,ENST00000296518,;GUCY1A3,missense_variant,p.Val257Phe,ENST00000511108,NM_000856.5;GUCY1A3,missense_variant,p.Val257Phe,ENST00000506455,NM_001130682.2;GUCY1A3,missense_variant,p.Val257Phe,ENST00000513574,NM_001130684.2;GUCY1A3,missense_variant,p.Val257Phe,ENST00000455639,NM_001256449.1,NM_001130683.3;GUCY1A3,missense_variant,p.Val257Phe,ENST00000511507,NM_001130687.2;GUCY1A3,5_prime_UTR_variant,,ENST00000393832,NM_001130685.2;GUCY1A3,intron_variant,,ENST00000621234,;GUCY1A3,downstream_gene_variant,,ENST00000515602,;GUCY1A3,3_prime_UTR_variant,,ENST00000443668,;GUCY1A3,non_coding_transcript_exon_variant,,ENST00000512983,;GUCY1A3,intron_variant,,ENST00000515201,;GUCY1A3,intron_variant,,ENST00000509901,; T ENST00000296518 Transcript missense_variant 978/4400 769/2073 257/690 V/F Gtt/Ttt rs372152908,COSM267856 1 1 GUCY1A3 HGNC HGNC:4685 protein_coding YES CCDS34085.1 ENSP00000296518 Q02108 UPI0000033343 tolerated(0.21) 6/10 hmmpanther:PTHR11920:SF226,hmmpanther:PTHR11920 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372152908 . 0 206 4 0 0 0 0 0 -18.00326 1 1 1 1 0 T 3 4 49 155710934 155710934 G T 1 0 0 0 0 1 0 0 0 6776 1145 40 1 1 GUCY1A3 4 155710934 Missense_Mutation SNP G C3N-00547_T 496104 155710934 34503621 195 14525 RAPGEF2 0 . GRCh38 4 159330422 159330422 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.908G>T p.Arg303Met p.R303M ENST00000264431 7/24 69 47 22 123 123 0 strelka-varscan-mutect RAPGEF2,missense_variant,p.Arg303Met,ENST00000264431,NM_014247.2;RAPGEF2,upstream_gene_variant,,ENST00000512056,;RAPGEF2,non_coding_transcript_exon_variant,,ENST00000513816,; T ENST00000264431 Transcript missense_variant 1327/6949 908/4500 303/1499 R/M aGg/aTg 1 1 RAPGEF2 HGNC HGNC:16854 protein_coding YES CCDS43277.1 ENSP00000264431 Q9Y4G8 UPI0000033783 NM_014247.2 deleterious(0) 7/24 PROSITE_profiles:PS50212,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF217,Gene3D:2ii0A01,Pfam_domain:PF00618,SMART_domains:SM00229,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 159330422 159330422 G T 1 0 0 0 0 1 0 0 0 13203 1000 35 2 2 RAPGEF2 4 159330422 Missense_Mutation SNP G C3N-00547_T 3619488 159330422 30884133 196 14526 TRIM60 0 . GRCh38 4 165041256 165041256 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1184G>T p.Gly395Val p.G395V ENST00000512596 3/3 160 90 70 148 147 1 strelka-varscan-mutect TRIM60,missense_variant,p.Gly395Val,ENST00000512596,NM_152620.2;TRIM60,missense_variant,p.Gly395Val,ENST00000341062,;TRIM60,missense_variant,p.Gly395Val,ENST00000508504,NM_001258025.1;TRIM60,downstream_gene_variant,,ENST00000507119,;RP11-366M4.17,upstream_gene_variant,,ENST00000508621,; T ENST00000512596 Transcript missense_variant 1400/1888 1184/1416 395/471 G/V gGt/gTt 1 1 TRIM60 HGNC HGNC:21162 protein_coding YES CCDS3808.1 ENSP00000421142 Q495X7 UPI000006DAAD NM_152620.2 tolerated(0.22) 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF304,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS rs1432243573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 165041256 165041256 G T 1 0 0 0 0 1 0 0 0 17027 1261 44 2 2 TRIM60 4 165041256 Missense_Mutation SNP G C3N-00547_T 5710834 165041256 25173299 197 14527 CEP72 0 . GRCh38 5 639189 639189 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1307G>C p.Gly436Ala p.G436A ENST00000264935 8/12 78 68 10 89 89 0 strelka-varscan-mutect CEP72,missense_variant,p.Gly436Ala,ENST00000264935,NM_018140.3;CEP72,upstream_gene_variant,,ENST00000512038,; C ENST00000264935 Transcript missense_variant 1397/2434 1307/1944 436/647 G/A gGc/gCc 1 1 CEP72 HGNC HGNC:25547 protein_coding YES CCDS34126.1 ENSP00000264935 Q9P209 UPI0000072FB8 NM_018140.3 deleterious(0.01) 8/12 hmmpanther:PTHR23311,hmmpanther:PTHR23311:SF7 MODERATE 1 SNV 1 1 PASS rs1197507925 . 0 199 11 0 0 0 0 0 -19.9811 0.999946 1 1 1 0 C 3 2 49 639189 639189 G C 1 0 0 0 0 1 0 0 0 2981 1203 42 4 4 CEP72 5 639189 Missense_Mutation SNP G C3N-00547_T 639189 180899070 198 14528 PAPD7 0 . GRCh38 5 6751085 6751085 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1157G>T p.Ser386Ile p.S386I ENST00000631941 11/13 293 205 88 210 210 0 strelka-varscan-mutect PAPD7,missense_variant,p.Ser636Ile,ENST00000230859,;PAPD7,missense_variant,p.Ser386Ile,ENST00000631941,NM_006999.4,NM_001171805.1;PAPD7,non_coding_transcript_exon_variant,,ENST00000514697,;PAPD7,non_coding_transcript_exon_variant,,ENST00000514410,;PAPD7,downstream_gene_variant,,ENST00000511764,;PAPD7,downstream_gene_variant,,ENST00000505457,; T ENST00000631941 Transcript missense_variant 1345/1902 1157/1629 386/542 S/I aGt/aTt 1 1 PAPD7 HGNC HGNC:16705 protein_coding YES CCDS3871.1 ENSP00000488642 Q5XG87 UPI0000071E30 NM_006999.4,NM_001171805.1 tolerated_low_confidence(0.14) 11/13 hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 6751085 6751085 G T 1 0 0 0 0 1 0 0 0 11507 1029 36 2 2 PAPD7 5 6751085 Missense_Mutation SNP G C3N-00547_T 6111896 6751085 174787174 199 14529 TRIO 0 . GRCh38 5 14481597 14481597 + Silent SNP G G T rs748999267 C3N-00547_T C3N-00547_N G G c.6444G>T p.= p.V2148V ENST00000344204 45/57 229 167 62 243 242 1 strelka-varscan-mutect TRIO,synonymous_variant,p.=,ENST00000344204,NM_007118.2;TRIO,synonymous_variant,p.=,ENST00000513206,;TRIO,synonymous_variant,p.=,ENST00000620511,;TRIO,synonymous_variant,p.=,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,;TRIO,non_coding_transcript_exon_variant,,ENST00000511019,;TRIO,upstream_gene_variant,,ENST00000510281,;TRIO,downstream_gene_variant,,ENST00000506611,; T ENST00000344204 Transcript synonymous_variant 6468/11100 6444/9294 2148/3097 V gtG/gtT rs748999267 1 1 TRIO HGNC HGNC:12303 protein_coding YES CCDS3883.1 ENSP00000339299 O75962 UPI000034ECE6 NM_007118.2 45/57 hmmpanther:PTHR22826:SF104,hmmpanther:PTHR22826,Superfamily_domains:SSF48065 LOW 1 SNV 1 1 PASS rs748999267 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 14481597 14481597 G T 1 0 0 0 0 0 0 0 1 17049 1335 47 2 2 TRIO 5 14481597 Silent SNP G C3N-00547_T 7730512 14481597 167056662 200 14530 CDH10 0 . GRCh38 5 24488029 24488029 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.2001C>A p.= p.T667T ENST00000264463 12/12 475 362 113 469 469 0 strelka-varscan-mutect CDH10,synonymous_variant,p.=,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; T ENST00000264463 Transcript synonymous_variant 2509/3438 2001/2367 667/788 T acC/acA 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 12/12 hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Pfam_domain:PF01049 LOW 1 SNV 1 1 PASS rs1176079440 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 24488029 24488029 G T 1 0 0 0 0 0 0 0 1 2799 1219 43 2 2 CDH10 5 24488029 Silent SNP G C3N-00547_T 10006432 24488029 157050230 201 14531 ADAMTS12 0 . GRCh38 5 33576090 33576090 + Missense_Mutation SNP G G T rs143099189 C3N-00547_T C3N-00547_N G G c.3936C>A p.His1312Gln p.H1312Q ENST00000504830 19/24 116 79 37 127 127 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.His1312Gln,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.His1227Gln,ENST00000352040,;ADAMTS12,downstream_gene_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 4272/8774 3936/4785 1312/1594 H/Q caC/caA rs143099189 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.61) 19/24 MODERATE 1 SNV 1 1 PASS rs143099189 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 33576090 33576090 G T 1 0 0 0 0 1 0 0 0 301 1136 40 1 1 ADAMTS12 5 33576090 Missense_Mutation SNP G C3N-00547_T 9088061 33576090 147962169 202 14532 AGXT2 0 . GRCh38 5 35033519 35033519 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.616G>T p.Gly206Cys p.G206C ENST00000231420 6/14 364 267 97 340 340 0 strelka-varscan-mutect AGXT2,missense_variant,p.Gly206Cys,ENST00000231420,NM_031900.3;AGXT2,missense_variant,p.Gly206Cys,ENST00000618015,;AGXT2,missense_variant,p.Gly206Cys,ENST00000510428,;AGXT2,non_coding_transcript_exon_variant,,ENST00000505542,; A ENST00000231420 Transcript missense_variant 817/2364 616/1545 206/514 G/C Ggc/Tgc 1 -1 AGXT2 HGNC HGNC:14412 protein_coding YES CCDS3908.1 ENSP00000231420 Q9BYV1 UPI0000125709 NM_031900.3 deleterious(0) 6/14 Gene3D:3.40.640.10,Pfam_domain:PF00202,hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF58,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 35033519 35033519 C A 1 0 0 0 0 1 0 0 0 484 594 21 2 2 AGXT2 5 35033519 Missense_Mutation SNP C C3N-00547_T 1457429 35033519 146504740 203 14533 NIM1K 0 . GRCh38 5 43277071 43277071 + Missense_Mutation SNP A A C novel C3N-00547_T C3N-00547_N A A c.307A>C p.Lys103Gln p.K103Q ENST00000512796 3/4 169 115 54 178 178 0 strelka-varscan-mutect NIM1K,missense_variant,p.Lys103Gln,ENST00000512796,;NIM1K,missense_variant,p.Lys103Gln,ENST00000326035,NM_153361.3; C ENST00000512796 Transcript missense_variant 1806/2929 307/1311 103/436 K/Q Aag/Cag 1 1 NIM1K HGNC HGNC:28646 protein_coding YES CCDS3943.1 ENSP00000420849 Q8IY84 UPI0000035B5F deleterious(0) 3/4 PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF0,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 43277071 43277071 A C 1 0 0 0 0 1 0 0 0 10451 363 13 5 5 NIM1K 5 43277071 Missense_Mutation SNP A C3N-00547_T 8243552 43277071 138261188 204 14534 ITGA2 0 . GRCh38 5 53060013 53060013 + Splice_Site SNP G G T novel C3N-00547_T C3N-00547_N G G c.1312+1G>T p.X438_splice ENST00000296585 472 275 197 408 406 2 strelka-varscan-mutect ITGA2,splice_donor_variant,,ENST00000296585,NM_002203.3;ITGA2,splice_donor_variant,,ENST00000503810,;ITGA2,splice_donor_variant,,ENST00000509960,;ITGA2,splice_donor_variant,,ENST00000510722,;ITGA2,splice_donor_variant,,ENST00000513685,;ITGA2,splice_donor_variant,,ENST00000509814,; T ENST00000296585 Transcript splice_donor_variant -/7869 1312/3546 438/1181 1 1 ITGA2 HGNC HGNC:6137 protein_coding YES CCDS3957.1 ENSP00000296585 P17301 UPI0000169C36 NM_002203.3 11/29 HIGH 1 SNV 1 1 PASS rs1259129028 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 49 53060013 53060013 G T 1 0 0 0 0 0 0 1 0 7782 1275 44 2 2 ITGA2 5 53060013 Splice_Site SNP G C3N-00547_T 9782942 53060013 128478246 205 14535 RNF180 0 . GRCh38 5 64214075 64214075 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.749G>T p.Ser250Ile p.S250I ENST00000389100 4/8 222 128 94 211 211 0 strelka-varscan-mutect RNF180,missense_variant,p.Ser250Ile,ENST00000389100,NM_001113561.1;RNF180,missense_variant,p.Ser250Ile,ENST00000296615,NM_178532.3;RNF180,downstream_gene_variant,,ENST00000504296,; T ENST00000389100 Transcript missense_variant 821/4906 749/1779 250/592 S/I aGt/aTt 1 1 RNF180 HGNC HGNC:27752 protein_coding YES CCDS47219.1 ENSP00000373752 Q86T96 UPI0000141201 NM_001113561.1 deleterious(0) 4/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 64214075 64214075 G T 1 0 0 0 0 1 0 0 0 13641 1029 36 2 2 RNF180 5 64214075 Missense_Mutation SNP G C3N-00547_T 11154062 64214075 117324184 206 14536 SREK1IP1 0 . GRCh38 5 64724486 64724486 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.366G>C p.Lys122Asn p.K122N ENST00000513458 5/5 100 94 6 76 76 0 strelka-mutect SREK1IP1,missense_variant,p.Lys122Asn,ENST00000513458,NM_173829.3;SREK1IP1,downstream_gene_variant,,ENST00000495198,; G ENST00000513458 Transcript missense_variant 534/6876 366/468 122/155 K/N aaG/aaC 1 -1 SREK1IP1 HGNC HGNC:26716 protein_coding YES CCDS34171.1 ENSP00000427401 Q8N9Q2 UPI000006EDBE NM_173829.3 deleterious_low_confidence(0.01) 5/5 hmmpanther:PTHR31437,hmmpanther:PTHR31437:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs768199051 . 0 200 3 6 0 0 0 0 -9.075909 0.975995 1 1 1 0 G 3 3 49 64724486 64724486 C G 1 0 0 0 0 1 0 0 0 15501 912 32 4 4 SREK1IP1 5 64724486 Missense_Mutation SNP C C3N-00547_T 510411 64724486 116813773 207 14537 IQGAP2 0 . GRCh38 5 76671916 76671916 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.3001A>T p.Asn1001Tyr p.N1001Y ENST00000274364 24/36 200 83 117 237 237 0 strelka-varscan-mutect IQGAP2,missense_variant,p.Asn1001Tyr,ENST00000274364,NM_006633.3;IQGAP2,missense_variant,p.Asn951Tyr,ENST00000379730,NM_001285460.1;IQGAP2,missense_variant,p.Asn951Tyr,ENST00000505766,;IQGAP2,missense_variant,p.Asn497Tyr,ENST00000502745,NM_001285462.1;IQGAP2,missense_variant,p.Asn497Tyr,ENST00000396234,NM_001285461.1;IQGAP2,downstream_gene_variant,,ENST00000514001,;IQGAP2,non_coding_transcript_exon_variant,,ENST00000512383,;IQGAP2,non_coding_transcript_exon_variant,,ENST00000504558,;IQGAP2,upstream_gene_variant,,ENST00000504477,;IQGAP2,upstream_gene_variant,,ENST00000509741,; T ENST00000274364 Transcript missense_variant 3298/5844 3001/4728 1001/1575 N/Y Aac/Tac 1 1 IQGAP2 HGNC HGNC:6111 protein_coding YES CCDS34188.1 ENSP00000274364 Q13576 UPI000020CB2C NM_006633.3 deleterious(0.04) 24/36 PROSITE_profiles:PS50018,hmmpanther:PTHR14149:SF12,hmmpanther:PTHR14149,Gene3D:1.10.506.10,Pfam_domain:PF00616,SMART_domains:SM00323,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 76671916 76671916 A T 1 0 0 0 0 1 0 0 0 7721 130 5 4 4 IQGAP2 5 76671916 Missense_Mutation SNP A C3N-00547_T 11947430 76671916 104866343 208 14538 VCAN 0 . GRCh38 5 83541619 83541619 + Silent SNP T T A novel C3N-00547_T C3N-00547_N T T c.8616T>A p.= p.I2872I ENST00000265077 8/15 195 114 81 222 221 1 strelka-varscan-mutect VCAN,synonymous_variant,p.=,ENST00000265077,NM_004385.4;VCAN,synonymous_variant,p.=,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,non_coding_transcript_exon_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript synonymous_variant 9181/12625 8616/10191 2872/3396 I atT/atA 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 83541619 83541619 T A 1 0 0 0 0 0 0 0 1 17683 1800 63 4 4 VCAN 5 83541619 Silent SNP T C3N-00547_T 6869703 83541619 97996640 209 14539 TSSK1B 0 . GRCh38 5 113434225 113434225 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.615C>A p.= p.I205I ENST00000390666 1/1 173 99 74 235 235 0 strelka-varscan-mutect TSSK1B,synonymous_variant,p.=,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; T ENST00000390666 Transcript synonymous_variant 807/2478 615/1104 205/367 I atC/atA 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 113434225 113434225 G T 1 0 0 0 0 0 0 0 1 17176 1164 41 2 2 TSSK1B 5 113434225 Silent SNP G C3N-00547_T 29892606 113434225 68104034 210 14540 ISOC1 0 . GRCh38 5 129112963 129112963 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.859G>C p.Ala287Pro p.A287P ENST00000173527 5/5 115 55 60 128 128 0 strelka-mutect ISOC1,missense_variant,p.Ala287Pro,ENST00000173527,NM_016048.2; C ENST00000173527 Transcript missense_variant 875/1940 859/897 287/298 A/P Gcg/Ccg 1 1 ISOC1 HGNC HGNC:24254 protein_coding YES CCDS43357.1 ENSP00000173527 Q96CN7 UPI0000070CF3 NM_016048.2 tolerated(0.15) 5/5 hmmpanther:PTHR14119:SF3,hmmpanther:PTHR14119,Gene3D:3.40.50.850,Superfamily_domains:SSF52499 MODERATE 1 SNV 1 1 PASS rs1448118799 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 129112963 129112963 G C 1 0 0 0 0 1 0 0 0 7769 1203 42 4 4 ISOC1 5 129112963 Missense_Mutation SNP G C3N-00547_T 15678738 129112963 52425296 211 14541 HINT1 0 . GRCh38 5 131165143 131165143 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.63G>T p.Lys21Asn p.K21N ENST00000304043 1/3 193 180 13 240 240 0 strelka-varscan-mutect HINT1,missense_variant,p.Lys21Asn,ENST00000304043,NM_005340.6;HINT1,missense_variant,p.Lys21Asn,ENST00000508488,;HINT1,missense_variant,p.Lys21Asn,ENST00000506908,;HINT1,missense_variant,p.Lys21Asn,ENST00000513012,;HINT1,upstream_gene_variant,,ENST00000520028,;HINT1,intron_variant,,ENST00000506207,;HINT1,missense_variant,p.Lys21Asn,ENST00000511475,;HINT1,missense_variant,p.Lys21Asn,ENST00000508495,;HINT1,missense_variant,p.Lys21Asn,ENST00000513345,;HINT1,missense_variant,p.Lys21Asn,ENST00000504202,; A ENST00000304043 Transcript missense_variant 343/1081 63/381 21/126 K/N aaG/aaT 1 -1 HINT1 HGNC HGNC:4912 protein_coding YES CCDS4147.1 ENSP00000304229 P49773 UPI000004F5CC NM_005340.6 deleterious(0.02) 1/3 PROSITE_profiles:PS51084,hmmpanther:PTHR23089:SF3,hmmpanther:PTHR23089,Gene3D:3.30.428.10,Superfamily_domains:SSF54197,Prints_domain:PR00332 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 131165143 131165143 C A 1 0 0 0 0 1 0 0 0 6999 912 32 2 2 HINT1 5 131165143 Missense_Mutation SNP C C3N-00547_T 2052180 131165143 50373116 212 14542 VDAC1 0 . GRCh38 5 133980802 133980802 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.478G>T p.Ala160Ser p.A160S ENST00000265333 6/9 362 169 193 274 274 0 strelka-varscan-mutect VDAC1,missense_variant,p.Ala160Ser,ENST00000265333,NM_003374.2;VDAC1,missense_variant,p.Ala160Ser,ENST00000395047,;VDAC1,missense_variant,p.Ala160Ser,ENST00000395044,;VDAC1,missense_variant,p.Ala160Ser,ENST00000425992,;VDAC1,non_coding_transcript_exon_variant,,ENST00000492324,;VDAC1,upstream_gene_variant,,ENST00000489906,; A ENST00000265333 Transcript missense_variant 723/1953 478/852 160/283 A/S Gca/Tca COSM5204904 1 -1 VDAC1 HGNC HGNC:12669 protein_coding YES CCDS4168.1 ENSP00000265333 P21796 UPI000004C7D8 NM_003374.2 tolerated(0.46) 6/9 Gene3D:2.40.160.10,Pfam_domain:PF01459,hmmpanther:PTHR11743,hmmpanther:PTHR11743:SF13 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 133980802 133980802 C A 1 0 0 0 0 1 0 0 0 17691 710 25 2 2 VDAC1 5 133980802 Missense_Mutation SNP C C3N-00547_T 2815659 133980802 47557457 213 14543 PCDHA9 0 . GRCh38 5 140849923 140849923 + Silent SNP G G A rs145904051 C3N-00547_T C3N-00547_N G G c.1428G>A p.= p.T476T ENST00000532602 1/4 779 366 413 902 902 0 strelka-varscan-mutect PCDHA9,synonymous_variant,p.=,ENST00000378122,NM_014005.4;PCDHA9,synonymous_variant,p.=,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; A ENST00000532602 Transcript synonymous_variant 2461/6293 1428/2853 476/950 T acG/acA rs145904051 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs145904051 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 140849923 140849923 G A 1 0 0 0 0 0 0 0 1 11618 1103 39 1 1 PCDHA9 5 140849923 Silent SNP G C3N-00547_T 6869121 140849923 40688336 214 14544 PCDHB9 0 . GRCh38 5 141189085 141189085 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1767G>T p.= p.V589V ENST00000316105 1/1 347 179 168 472 472 0 strelka-varscan-mutect PCDHB9,synonymous_variant,p.=,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; T ENST00000316105 Transcript synonymous_variant 1959/4415 1767/2394 589/797 V gtG/gtT 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 141189085 141189085 G T 1 0 0 0 0 0 0 0 1 11636 1335 47 2 2 PCDHB9 5 141189085 Silent SNP G C3N-00547_T 339162 141189085 40349174 215 14545 PCDHB10 0 . GRCh38 5 141193021 141193021 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.469G>T p.Ala157Ser p.A157S ENST00000239446 1/1 324 158 166 330 329 1 strelka-varscan-mutect PCDHB10,missense_variant,p.Ala157Ser,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,intron_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; T ENST00000239446 Transcript missense_variant 669/3290 469/2403 157/800 A/S Gca/Tca 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 141193021 141193021 G T 1 0 0 0 0 1 0 0 0 11622 971 34 2 2 PCDHB10 5 141193021 Missense_Mutation SNP G C3N-00547_T 3936 141193021 40345238 216 14546 PCDHGC3 0 . GRCh38 5 141477934 141477934 + Silent SNP C C T C3N-00547_T C3N-00547_N C C c.1818C>T p.= p.L606L ENST00000308177 1/4 181 167 14 275 273 2 strelka-varscan-mutect PCDHGC3,synonymous_variant,p.=,ENST00000308177,NM_002588.3;PCDHGC3,synonymous_variant,p.=,ENST00000611950,NM_032402.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB7,intron_variant,,ENST00000398594,NM_018927.3;PCDHGA12,intron_variant,,ENST00000252085,NM_003735.2;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA11,intron_variant,,ENST00000398587,NM_018914.2;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGC3,intron_variant,,ENST00000617641,NM_032403.2;PCDHGA11,intron_variant,,ENST00000518882,NM_032092.1;PCDHGC3,intron_variant,,ENST00000617222,;PCDHGC3,downstream_gene_variant,,ENST00000621008,;RN7SL68P,upstream_gene_variant,,ENST00000488078,;PCDHGC3,intron_variant,,ENST00000622656,;PCDHGC3,downstream_gene_variant,,ENST00000616230,;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000308177 Transcript synonymous_variant 1932/4725 1818/2805 606/934 L ctC/ctT COSM4712655,COSM4712656 1 1 PCDHGC3 HGNC HGNC:8716 protein_coding YES CCDS4261.1 ENSP00000312070 Q9UN70 UPI000006F34F NM_002588.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF70,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 141477934 141477934 C T 1 0 0 0 0 0 0 0 1 11656 900 32 3 3 PCDHGC3 5 141477934 Silent SNP C C3N-00547_T 284913 141477934 40060325 217 14547 SLC36A2 0 . GRCh38 5 151333310 151333310 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.757C>A p.Pro253Thr p.P253T ENST00000335244 7/10 372 177 195 464 463 1 strelka-varscan-mutect SLC36A2,missense_variant,p.Pro253Thr,ENST00000335244,NM_181776.2;SLC36A2,missense_variant,p.Pro253Thr,ENST00000521967,;SLC36A2,missense_variant,p.Pro6Thr,ENST00000523044,;SLC36A2,3_prime_UTR_variant,,ENST00000518617,;SLC36A2,3_prime_UTR_variant,,ENST00000518280,; T ENST00000335244 Transcript missense_variant 887/3421 757/1452 253/483 P/T Ccc/Acc 1 -1 SLC36A2 HGNC HGNC:18762 protein_coding YES CCDS4315.1 ENSP00000334223 Q495M3 UPI000020D008 NM_181776.2 tolerated(0.16) 7/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 151333310 151333310 G T 1 0 0 0 0 1 0 0 0 14872 1232 43 2 2 SLC36A2 5 151333310 Missense_Mutation SNP G C3N-00547_T 9855376 151333310 30204949 218 14548 FAT2 0 . GRCh38 5 151554509 151554509 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.3798G>T p.= p.L1266L ENST00000261800 4/23 326 150 176 423 423 0 strelka-varscan-mutect FAT2,synonymous_variant,p.=,ENST00000261800,NM_001447.2; A ENST00000261800 Transcript synonymous_variant 3811/14534 3798/13050 1266/4349 L ctG/ctT 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 4/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 151554509 151554509 C A 1 0 0 0 0 0 0 0 1 5550 581 21 2 2 FAT2 5 151554509 Silent SNP C C3N-00547_T 221199 151554509 29983750 219 14549 GLRA1 0 . GRCh38 5 151859890 151859890 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.371C>G p.Pro124Arg p.P124R ENST00000455880 4/9 715 656 59 722 722 0 strelka-varscan-mutect GLRA1,missense_variant,p.Pro124Arg,ENST00000274576,NM_000171.3,NM_001292000.1;GLRA1,missense_variant,p.Pro124Arg,ENST00000455880,NM_001146040.1;GLRA1,non_coding_transcript_exon_variant,,ENST00000471351,;GLRA1,3_prime_UTR_variant,,ENST00000462581,; C ENST00000455880 Transcript missense_variant 658/1707 371/1374 124/457 P/R cCt/cGt 1 -1 GLRA1 HGNC HGNC:4326 protein_coding YES CCDS54942.1 ENSP00000411593 P23415 UPI0000DA6BF2 NM_001146040.1 deleterious(0) 4/9 hmmpanther:PTHR18945:SF213,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS rs1246926244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 151859890 151859890 G C 1 0 0 0 0 1 0 0 0 6333 1000 35 4 4 GLRA1 5 151859890 Missense_Mutation SNP G C3N-00547_T 305381 151859890 29678369 220 14550 HAVCR2 0 . GRCh38 5 157106843 157106843 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.178G>A p.Val60Met p.V60M ENST00000307851 2/7 216 115 101 254 254 0 strelka-varscan-mutect HAVCR2,missense_variant,p.Val60Met,ENST00000307851,NM_032782.4;HAVCR2,missense_variant,p.Val60Met,ENST00000522593,;HAVCR2,5_prime_UTR_variant,,ENST00000524219,;CTB-120L21.1,intron_variant,,ENST00000517708,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000517358,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000522902,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000521665,; T ENST00000307851 Transcript missense_variant 909/2907 178/906 60/301 V/M Gtg/Atg 1 -1 HAVCR2 HGNC HGNC:18437 protein_coding YES CCDS4333.1 ENSP00000312002 Q8TDQ0 UPI000011AAFA NM_032782.4 tolerated(0.16) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR15498:SF45,hmmpanther:PTHR15498,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 157106843 157106843 C T 1 0 0 0 0 1 0 0 0 6860 478 17 3 3 HAVCR2 5 157106843 Missense_Mutation SNP C C3N-00547_T 5246953 157106843 24431416 221 14551 GABRA1 0 . GRCh38 5 161895738 161895739 + Frame_Shift_Ins INS - - A novel C3N-00547_T C3N-00547_N - - c.931dupA p.Thr311AsnfsTer20 p.T311Nfs*20 ENST00000393943 9/10 309 136 173 355 355 0 sindel-varindel-pindel GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000428797,NM_001127643.1;GABRA1,frameshift_variant,p.Thr326AsnfsTer20,ENST00000638159,;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000437025,NM_001127645.1;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000638112,;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000636573,;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000023897,NM_000806.5;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000637827,;GABRA1,frameshift_variant,p.Thr311AsnfsTer20,ENST00000635880,;GABRA1,downstream_gene_variant,,ENST00000634335,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,;GABRA1,downstream_gene_variant,,ENST00000519542,; A ENST00000393943 Transcript frameshift_variant 1712-1713/4686 929-930/1371 310/456 A/AX gca/gcAa 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 9/10 Gene3D:1.20.58.390,Pfam_domain:PF02932,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 49 161895738 161895738 - A 1 0 1 1 0 0 0 0 0 6031 710 25 0 0 GABRA1 5 161895738 Frame_Shift_Ins INS - C3N-00547_T 4788895 161895738 19642521 222 14552 HRH2 0 . GRCh38 5 175683891 175683891 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.658A>T p.Ser220Cys p.S220C ENST00000377291 2/3 411 195 216 433 433 0 strelka-varscan-mutect HRH2,missense_variant,p.Ser220Cys,ENST00000636584,;HRH2,missense_variant,p.Ser220Cys,ENST00000377291,NM_001131055.1;HRH2,missense_variant,p.Ser220Cys,ENST00000231683,NM_022304.2;HRH2,missense_variant,p.Ser220Cys,ENST00000624694,; T ENST00000377291 Transcript missense_variant 1309/2561 658/1194 220/397 S/C Agc/Tgc 1 1 HRH2 HGNC HGNC:5183 protein_coding YES CCDS47344.1 ENSP00000366506 P25021 UPI00001B2326 NM_001131055.1 deleterious(0.01) 2/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF280,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00531 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 175683891 175683891 A T 1 0 0 0 0 1 0 0 0 7251 420 15 4 4 HRH2 5 175683891 Missense_Mutation SNP A C3N-00547_T 13788153 175683891 5854368 223 14553 SERPINB6 0 . GRCh38 6 2948678 2948678 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.808G>T p.Glu270Ter p.E270* ENST00000612421 7/7 189 119 70 195 195 0 strelka-varscan-mutect SERPINB6,stop_gained,p.Glu251Ter,ENST00000380520,;SERPINB6,stop_gained,p.Glu255Ter,ENST00000616722,NM_001195291.2;SERPINB6,stop_gained,p.Glu251Ter,ENST00000335686,NM_001297699.1,NM_001271824.1,NM_004568.5,NM_001297700.1;SERPINB6,stop_gained,p.Glu270Ter,ENST00000612421,NM_001271823.1;SERPINB6,stop_gained,p.Glu251Ter,ENST00000380524,NM_001271825.1;SERPINB6,stop_gained,p.Glu251Ter,ENST00000380546,;SERPINB6,stop_gained,p.Glu251Ter,ENST00000380529,NM_001271822.1;SERPINB6,stop_gained,p.Glu251Ter,ENST00000380539,; A ENST00000612421 Transcript stop_gained 1052/1570 808/1188 270/395 E/* Gag/Tag 1 -1 SERPINB6 HGNC HGNC:8950 protein_coding YES CCDS75387.1 ENSP00000484343 A0A087X1N8 UPI000013FEB1 NM_001271823.1 7/7 hmmpanther:PTHR11461:SF135,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574 HIGH 1 SNV 2 1 PASS rs1348902179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 2948678 2948678 C A 1 0 0 0 0 0 1 0 0 14381 893 31 1 1 SERPINB6 6 2948678 Nonsense_Mutation SNP C C3N-00547_T 2948678 167857301 224 14554 SLC17A1 0 . GRCh38 6 25819140 25819140 + Missense_Mutation SNP G G A rs149396857 C3N-00547_T C3N-00547_N G G c.544C>T p.Pro182Ser p.P182S ENST00000244527 6/13 102 70 32 116 116 0 strelka-varscan-mutect SLC17A1,missense_variant,p.Pro182Ser,ENST00000244527,NM_005074.3;SLC17A1,missense_variant,p.Pro182Ser,ENST00000476801,;SLC17A1,missense_variant,p.Pro182Ser,ENST00000468082,;SLC17A1,missense_variant,p.Pro182Ser,ENST00000377886,; A ENST00000244527 Transcript missense_variant 660/1844 544/1404 182/467 P/S Ccc/Tcc rs149396857 1 -1 SLC17A1 HGNC HGNC:10929 protein_coding YES CCDS4565.1 ENSP00000244527 Q14916 UPI00000719C0 NM_005074.3 tolerated(1) 6/13 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF26,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00894,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs149396857 . 0 197 6 6 0 0 0 0 -20 0.9974147 1 1 1 0 A 3 1 49 25819140 25819140 G A 1 0 0 0 0 1 0 0 0 14681 1261 44 3 3 SLC17A1 6 25819140 Missense_Mutation SNP G C3N-00547_T 22870462 25819140 144986839 225 14555 OR2B2 0 . GRCh38 6 27911702 27911702 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.618C>A p.Phe206Leu p.F206L ENST00000303324 1/1 74 45 29 97 97 0 strelka-varscan-mutect OR2B2,missense_variant,p.Phe206Leu,ENST00000303324,NM_033057.2; T ENST00000303324 Transcript missense_variant 695/1212 618/1074 206/357 F/L ttC/ttA 1 -1 OR2B2 HGNC HGNC:13966 protein_coding YES CCDS4641.1 ENSP00000304419 Q9GZK3 A0A126GWD0 UPI000004187A NM_033057.2 tolerated(0.14) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF254,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 27911702 27911702 G T 1 0 0 0 0 1 0 0 0 11068 1165 41 2 2 OR2B2 6 27911702 Missense_Mutation SNP G C3N-00547_T 2092562 27911702 142894277 226 14556 ZSCAN16 0 . GRCh38 6 28125685 28125685 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.242T>C p.Leu81Ser p.L81S ENST00000340487 2/4 216 201 15 259 259 0 strelka-varscan-mutect ZSCAN16,missense_variant,p.Leu81Ser,ENST00000340487,NM_025231.1;ZSCAN16-AS1,non_coding_transcript_exon_variant,,ENST00000600652,;ZSCAN16-AS1,intron_variant,,ENST00000602810,; C ENST00000340487 Transcript missense_variant 391/1328 242/1047 81/348 L/S tTa/tCa 1 1 ZSCAN16 HGNC HGNC:20813 protein_coding YES CCDS4644.1 ENSP00000366527 Q9H4T2 UPI000013A46E NM_025231.1 deleterious(0) 2/4 PROSITE_profiles:PS50804,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF52,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 28125685 28125685 T C 1 0 0 0 0 1 0 0 0 18823 1764 61 5 5 ZSCAN16 6 28125685 Missense_Mutation SNP T C3N-00547_T 213983 28125685 142680294 227 14557 TRIM27 0 . GRCh38 6 28904351 28904351 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.1261A>G p.Thr421Ala p.T421A ENST00000377199 8/8 137 119 18 131 131 0 strelka-varscan-mutect TRIM27,missense_variant,p.Thr421Ala,ENST00000377199,NM_006510.4;TRIM27,missense_variant,p.Thr156Ala,ENST00000414543,;TRIM27,intron_variant,,ENST00000377194,;TRIM27,downstream_gene_variant,,ENST00000467742,;TRIM27,non_coding_transcript_exon_variant,,ENST00000481474,; C ENST00000377199 Transcript missense_variant 1618/2967 1261/1542 421/513 T/A Acc/Gcc 1 -1 TRIM27 HGNC HGNC:9975 protein_coding YES CCDS4654.1 ENSP00000366404 P14373 UPI0000000DCE NM_006510.4 deleterious(0.01) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF362,hmmpanther:PTHR24103,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 49 28904351 28904351 T C 1 0 0 0 0 1 0 0 0 16990 1638 57 5 5 TRIM27 6 28904351 Missense_Mutation SNP T C3N-00547_T 778666 28904351 141901628 228 14558 FKBPL 0 . GRCh38 6 32129752 32129752 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.29G>C p.Gly10Ala p.G10A ENST00000375156 2/2 376 352 24 331 331 0 strelka-varscan-mutect FKBPL,missense_variant,p.Gly10Ala,ENST00000375156,NM_022110.3;ATF6B,upstream_gene_variant,,ENST00000375201,NM_001136153.1;ATF6B,upstream_gene_variant,,ENST00000375203,NM_004381.4;ATF6B,upstream_gene_variant,,ENST00000468502,;ATF6B,upstream_gene_variant,,ENST00000495579,;ATF6B,upstream_gene_variant,,ENST00000485314,; G ENST00000375156 Transcript missense_variant 300/1345 29/1050 10/349 G/A gGa/gCa 1 -1 FKBPL HGNC HGNC:13949 protein_coding YES CCDS4738.1 ENSP00000364298 Q9UIM3 A0A024RCQ6 UPI0000036B85 NM_022110.3 deleterious_low_confidence(0.02) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 32129752 32129752 C G 1 0 0 0 0 1 0 0 0 5779 855 30 4 4 FKBPL 6 32129752 Missense_Mutation SNP C C3N-00547_T 3225401 32129752 138676227 229 14559 ITPR3 0 . GRCh38 6 33664885 33664885 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1164G>T p.= p.R388R ENST00000374316 13/59 276 232 44 244 243 1 strelka-varscan-mutect ITPR3,synonymous_variant,p.=,ENST00000374316,;ITPR3,synonymous_variant,p.=,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript synonymous_variant 2224/9870 1164/8016 388/2671 R cgG/cgT 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 13/59 PROSITE_profiles:PS50919,hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715,Gene3D:2.80.10.50,Pfam_domain:PF02815,SMART_domains:SM00472,Superfamily_domains:SSF82109 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 33664885 33664885 G T 1 0 0 0 0 0 0 0 1 7828 1190 42 2 2 ITPR3 6 33664885 Silent SNP G C3N-00547_T 1535133 33664885 137141094 230 14560 PNPLA1 0 . GRCh38 6 36307673 36307673 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1556C>A p.Pro519Gln p.P519Q ENST00000394571 8/8 129 111 18 176 176 0 strelka-varscan-mutect PNPLA1,missense_variant,p.Pro424Gln,ENST00000388715,NM_173676.2;PNPLA1,missense_variant,p.Pro428Gln,ENST00000636260,;PNPLA1,missense_variant,p.Pro520Gln,ENST00000457797,;PNPLA1,missense_variant,p.Pro519Gln,ENST00000394571,NM_001145717.1;PNPLA1,missense_variant,p.Pro433Gln,ENST00000312917,NM_001145716.2; A ENST00000394571 Transcript missense_variant 1556/1599 1556/1599 519/532 P/Q cCa/cAa 1 1 PNPLA1 HGNC HGNC:21246 protein_coding YES CCDS54997.1 ENSP00000378072 Q8N8W4 B8XXQ3 UPI000189560E NM_001145717.1 tolerated_low_confidence(0.21) 8/8 hmmpanther:PTHR12406,hmmpanther:PTHR12406:SF23 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 36307673 36307673 C A 1 0 0 0 0 1 0 0 0 12272 594 21 2 2 PNPLA1 6 36307673 Missense_Mutation SNP C C3N-00547_T 2642788 36307673 134498306 231 14561 ABCC10 0 . GRCh38 6 43432908 43432908 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.928G>T p.Val310Leu p.V310L ENST00000372530 3/22 247 193 54 318 317 1 strelka-varscan-mutect ABCC10,missense_variant,p.Val267Leu,ENST00000244533,NM_033450.2;ABCC10,missense_variant,p.Val310Leu,ENST00000372530,NM_001198934.1;ABCC10,intron_variant,,ENST00000372515,;MIR6780B,upstream_gene_variant,,ENST00000610307,;ABCC10,intron_variant,,ENST00000443426,;ABCC10,downstream_gene_variant,,ENST00000502549,;ABCC10,upstream_gene_variant,,ENST00000463024,; T ENST00000372530 Transcript missense_variant 1143/5033 928/4479 310/1492 V/L Gtg/Ttg 1 1 ABCC10 HGNC HGNC:52 protein_coding YES CCDS56430.1 ENSP00000361608 Q5T3U5 A0A024RD21 UPI000004A062 NM_001198934.1 deleterious(0) 3/22 Low_complexity_(Seg):seg,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF235,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 43432908 43432908 G T 1 0 0 0 0 1 0 0 0 54 1261 44 2 2 ABCC10 6 43432908 Missense_Mutation SNP G C3N-00547_T 7125235 43432908 127373071 232 14562 POLR1C 0 . GRCh38 6 43521015 43521015 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.889G>T p.Val297Leu p.V297L ENST00000372389 8/9 469 374 95 525 525 0 strelka-varscan-mutect POLR1C,missense_variant,p.Val297Leu,ENST00000372389,NM_203290.2;POLR1C,missense_variant,p.Val297Leu,ENST00000304004,;POLR1C,missense_variant,p.Val247Leu,ENST00000372344,;XPO5,downstream_gene_variant,,ENST00000265351,NM_020750.2;YIPF3,upstream_gene_variant,,ENST00000372422,NM_015388.3;YIPF3,upstream_gene_variant,,ENST00000506469,;YIPF3,upstream_gene_variant,,ENST00000503972,;XPO5,downstream_gene_variant,,ENST00000455285,;POLR1C,downstream_gene_variant,,ENST00000428025,;YIPF3,upstream_gene_variant,,ENST00000511831,;POLR1C,downstream_gene_variant,,ENST00000423780,;RP3-337H4.9,upstream_gene_variant,,ENST00000607571,;POLR1C,non_coding_transcript_exon_variant,,ENST00000455605,;POLR1C,non_coding_transcript_exon_variant,,ENST00000481352,;XPO5,downstream_gene_variant,,ENST00000455854,;YIPF3,upstream_gene_variant,,ENST00000460547,;YIPF3,upstream_gene_variant,,ENST00000510102,;YIPF3,upstream_gene_variant,,ENST00000490447,;YIPF3,upstream_gene_variant,,ENST00000416380,;POLR1C,downstream_gene_variant,,ENST00000488601,;XPO5,downstream_gene_variant,,ENST00000488195,;YIPF3,upstream_gene_variant,,ENST00000455768,;YIPF3,upstream_gene_variant,,ENST00000502714,;YIPF3,upstream_gene_variant,,ENST00000460903,;XPO5,downstream_gene_variant,,ENST00000486936,;POLR1C,downstream_gene_variant,,ENST00000512472,; T ENST00000372389 Transcript missense_variant 977/1355 889/1041 297/346 V/L Gtg/Ttg 1 1 POLR1C HGNC HGNC:20194 protein_coding YES CCDS4901.1 ENSP00000361465 O15160 UPI00001345BC NM_203290.2 deleterious(0) 8/9 hmmpanther:PTHR11800:SF13,hmmpanther:PTHR11800,Gene3D:3.30.1360.10,Pfam_domain:PF01193,SMART_domains:SM00662,Superfamily_domains:SSF55257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 43521015 43521015 G T 1 0 0 0 0 1 0 0 0 12321 1377 48 2 2 POLR1C 6 43521015 Missense_Mutation SNP G C3N-00547_T 88107 43521015 127284964 233 14563 RCAN2 0 . GRCh38 6 46456838 46456838 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.139C>A p.Gln47Lys p.Q47K ENST00000371374 2/5 281 237 44 356 355 1 strelka-varscan-mutect RCAN2,missense_variant,p.Gln47Lys,ENST00000371374,NM_001251974.1;RCAN2,missense_variant,p.Gln47Lys,ENST00000306764,NM_001251973.1; T ENST00000371374 Transcript missense_variant 331/3327 139/732 47/243 Q/K Caa/Aaa 1 -1 RCAN2 HGNC HGNC:3041 protein_coding YES CCDS59023.1 ENSP00000360425 Q14206 UPI00001AEE48 NM_001251974.1 tolerated(0.3) 2/5 hmmpanther:PTHR10300,hmmpanther:PTHR10300:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 46456838 46456838 G T 1 0 0 0 0 1 0 0 0 13338 1299 45 2 2 RCAN2 6 46456838 Missense_Mutation SNP G C3N-00547_T 2935823 46456838 124349141 234 14564 RCAN2 0 . GRCh38 6 46456921 46456921 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.56T>A p.Val19Asp p.V19D ENST00000371374 2/5 190 141 49 288 288 0 strelka-varscan-mutect RCAN2,missense_variant,p.Val19Asp,ENST00000371374,NM_001251974.1;RCAN2,missense_variant,p.Val19Asp,ENST00000306764,NM_001251973.1; T ENST00000371374 Transcript missense_variant 248/3327 56/732 19/243 V/D gTc/gAc 1 -1 RCAN2 HGNC HGNC:3041 protein_coding YES CCDS59023.1 ENSP00000360425 Q14206 UPI00001AEE48 NM_001251974.1 deleterious_low_confidence(0.01) 2/5 hmmpanther:PTHR10300,hmmpanther:PTHR10300:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 46456921 46456921 A T 1 0 0 0 0 1 0 0 0 13338 275 10 4 4 RCAN2 6 46456921 Missense_Mutation SNP A C3N-00547_T 83 46456921 124349058 235 14565 PKHD1 0 . GRCh38 6 51659583 51659583 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.10543A>G p.Ile3515Val p.I3515V ENST00000371117 61/67 293 237 56 342 342 0 strelka-varscan-mutect PKHD1,missense_variant,p.Ile3515Val,ENST00000371117,NM_138694.3; C ENST00000371117 Transcript missense_variant 10819/16282 10543/12225 3515/4074 I/V Att/Gtt 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 tolerated(0.49) 61/67 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 51659583 51659583 T C 1 0 0 0 0 1 0 0 0 12067 1406 49 5 5 PKHD1 6 51659583 Missense_Mutation SNP T C3N-00547_T 5202662 51659583 119146396 236 14566 TINAG 0 . GRCh38 6 54351383 54351383 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.1112A>T p.Asn371Ile p.N371I ENST00000259782 8/11 98 81 17 199 199 0 strelka-varscan-mutect TINAG,missense_variant,p.Asn371Ile,ENST00000259782,NM_014464.3; T ENST00000259782 Transcript missense_variant 1208/1754 1112/1431 371/476 N/I aAt/aTt 1 1 TINAG HGNC HGNC:14599 protein_coding YES CCDS4955.1 ENSP00000259782 Q9UJW2 UPI000013D078 NM_014464.3 deleterious(0) 8/11 Gene3D:3.90.70.10,Pfam_domain:PF00112,hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF274,SMART_domains:SM00645,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 54351383 54351383 A T 1 0 0 0 0 1 0 0 0 16362 101 4 4 4 TINAG 6 54351383 Missense_Mutation SNP A C3N-00547_T 2691800 54351383 116454596 237 14567 COL21A1 0 . GRCh38 6 56069105 56069105 + Missense_Mutation SNP C C A rs757963308 C3N-00547_T C3N-00547_N C C c.2032G>T p.Ala678Ser p.A678S ENST00000244728 22/30 121 92 29 212 212 0 strelka-varscan-mutect COL21A1,missense_variant,p.Ala678Ser,ENST00000244728,NM_001318751.1,NM_030820.3;COL21A1,missense_variant,p.Ala675Ser,ENST00000370819,NM_001318752.1;COL21A1,missense_variant,p.Ala677Ser,ENST00000535941,;COL21A1,non_coding_transcript_exon_variant,,ENST00000467045,;COL21A1,upstream_gene_variant,,ENST00000467216,;COL21A1,3_prime_UTR_variant,,ENST00000488912,;COL21A1,non_coding_transcript_exon_variant,,ENST00000461489,; A ENST00000244728 Transcript missense_variant 2430/4339 2032/2874 678/957 A/S Gca/Tca rs757963308 1 -1 COL21A1 HGNC HGNC:17025 protein_coding YES CCDS55025.1 ENSP00000244728 Q96P44 A0A158RFW1 UPI0000071DFE NM_001318751.1,NM_030820.3 tolerated(0.68) 22/30 hmmpanther:PTHR24023 MODERATE 1 SNV 1 1 PASS rs757963308 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 56069105 56069105 C A 1 0 0 0 0 1 0 0 0 3468 797 28 2 2 COL21A1 6 56069105 Missense_Mutation SNP C C3N-00547_T 1717722 56069105 114736874 238 14568 EYS 0 . GRCh38 6 64591853 64591853 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.4014T>A p.Ser1338Arg p.S1338R ENST00000370621 26/44 135 108 27 134 134 0 strelka-varscan-mutect EYS,missense_variant,p.Ser1338Arg,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Ser1338Arg,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; T ENST00000370621 Transcript missense_variant 4541/10485 4014/9498 1338/3165 S/R agT/agA 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.28) 26/44 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 64591853 64591853 A T 1 0 0 0 0 1 0 0 0 5200 272 10 4 4 EYS 6 64591853 Missense_Mutation SNP A C3N-00547_T 8522748 64591853 106214126 239 14569 RIMS1 0 . GRCh38 6 72235687 72235687 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.1816A>T p.Thr606Ser p.T606S ENST00000521978 8/34 83 64 19 113 113 0 strelka-varscan-mutect RIMS1,missense_variant,p.Thr606Ser,ENST00000264839,;RIMS1,missense_variant,p.Thr606Ser,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Thr606Ser,ENST00000491071,;RIMS1,missense_variant,p.Thr606Ser,ENST00000520567,;RIMS1,missense_variant,p.Thr606Ser,ENST00000517960,;RIMS1,missense_variant,p.Thr606Ser,ENST00000518273,;RIMS1,missense_variant,p.Thr606Ser,ENST00000522291,;RIMS1,missense_variant,p.Thr80Ser,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Thr180Ser,ENST00000517433,;RIMS1,missense_variant,p.Thr80Ser,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Thr65Ser,ENST00000517827,NM_001168410.1;RIMS1,5_prime_UTR_variant,,ENST00000425662,NM_001168409.1;RIMS1,5_prime_UTR_variant,,ENST00000453976,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,;RIMS1,non_coding_transcript_exon_variant,,ENST00000524197,; T ENST00000521978 Transcript missense_variant 1816/5079 1816/5079 606/1692 T/S Aca/Tca 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 tolerated(0.75) 8/34 PROSITE_profiles:PS50106,hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157,Gene3D:2.30.42.10,Pfam_domain:PF00595,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 72235687 72235687 A T 1 0 0 0 0 1 0 0 0 13542 43 2 4 4 RIMS1 6 72235687 Missense_Mutation SNP A C3N-00547_T 7643834 72235687 98570292 240 14570 RIMS1 0 . GRCh38 6 72258279 72258279 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2925G>T p.Gln975His p.Q975H ENST00000521978 17/34 88 70 18 88 88 0 strelka-varscan-mutect RIMS1,missense_variant,p.Gln975His,ENST00000264839,;RIMS1,missense_variant,p.Gln975His,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Gln975His,ENST00000491071,;RIMS1,missense_variant,p.Gln974His,ENST00000520567,;RIMS1,missense_variant,p.Gln974His,ENST00000517960,;RIMS1,missense_variant,p.Gln975His,ENST00000518273,;RIMS1,missense_variant,p.Gln974His,ENST00000522291,;RIMS1,missense_variant,p.Gln448His,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Gln549His,ENST00000517433,;RIMS1,missense_variant,p.Gln449His,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Gln434His,ENST00000517827,NM_001168410.1;RIMS1,missense_variant,p.Gln368His,ENST00000425662,NM_001168409.1;RIMS1,missense_variant,p.Gln368His,ENST00000453976,;RIMS1,missense_variant,p.Gln66His,ENST00000522211,;RIMS1,missense_variant,p.Gln200His,ENST00000370420,;RIMS1,splice_region_variant,,ENST00000370419,;RIMS1,splice_region_variant,,ENST00000524197,;RIMS1,upstream_gene_variant,,ENST00000463023,; T ENST00000521978 Transcript missense_variant,splice_region_variant 2925/5079 2925/5079 975/1692 Q/H caG/caT 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious(0.01) 17/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 72258279 72258279 G T 1 0 0 0 0 1 0 0 0 13542 956 33 2 2 RIMS1 6 72258279 Missense_Mutation SNP G C3N-00547_T 22592 72258279 98547700 241 14571 KHDC1 0 . GRCh38 6 73241683 73241683 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.560A>T p.Asp187Val p.D187V ENST00000370384 5/5 272 211 61 336 336 0 strelka-varscan-mutect KHDC1,missense_variant,p.Asp187Val,ENST00000370384,NM_001251874.1;KHDC1,missense_variant,p.Asp114Val,ENST00000257765,NM_030568.4;KHDC1,missense_variant,p.Asp114Val,ENST00000610435,;KHDC1,missense_variant,p.Asp114Val,ENST00000610330,;KHDC1,downstream_gene_variant,,ENST00000433730,;RP11-257K9.8,intron_variant,,ENST00000423730,; A ENST00000370384 Transcript missense_variant 1061/1430 560/714 187/237 D/V gAt/gTt 1 -1 KHDC1 HGNC HGNC:21366 protein_coding YES CCDS59027.1 ENSP00000359411 Q4VXA5 UPI000020D187 NM_001251874.1 tolerated_low_confidence(0.32) 5/5 hmmpanther:PTHR31368,hmmpanther:PTHR31368:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 73241683 73241683 T A 1 0 0 0 0 1 0 0 0 8064 1435 50 4 4 KHDC1 6 73241683 Missense_Mutation SNP T C3N-00547_T 983404 73241683 97564296 242 14572 PM20D2 0 . GRCh38 6 89162144 89162144 + Missense_Mutation SNP G G T rs372156408 C3N-00547_T C3N-00547_N G G c.1192G>T p.Ala398Ser p.A398S ENST00000275072 7/7 112 82 30 132 132 0 strelka-varscan-mutect PM20D2,missense_variant,p.Ala398Ser,ENST00000275072,NM_001010853.2; T ENST00000275072 Transcript missense_variant 1287/4708 1192/1311 398/436 A/S Gcc/Tcc rs372156408 1 1 PM20D2 HGNC HGNC:21408 protein_coding YES CCDS34499.1 ENSP00000275072 Q8IYS1 UPI0000160C07 NM_001010853.2 deleterious(0.04) 7/7 Gene3D:3.40.630.10,PIRSF_domain:PIRSF037226,hmmpanther:PTHR30575,hmmpanther:PTHR30575:SF0,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs372156408 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 89162144 89162144 G T 1 0 0 0 0 1 0 0 0 12235 1203 42 2 2 PM20D2 6 89162144 Missense_Mutation SNP G C3N-00547_T 15920461 89162144 81643835 243 14573 GABRR1 0 . GRCh38 6 89178856 89178856 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.1354A>T p.Thr452Ser p.T452S ENST00000454853 10/10 427 378 49 463 463 0 strelka-varscan-mutect GABRR1,missense_variant,p.Thr365Ser,ENST00000611484,NM_001256704.1;GABRR1,missense_variant,p.Thr435Ser,ENST00000435811,NM_001256703.1;GABRR1,missense_variant,p.Thr365Ser,ENST00000621627,;GABRR1,missense_variant,p.Thr452Ser,ENST00000454853,NM_002042.4;GABRR1,missense_variant,p.Thr365Ser,ENST00000369451,NM_001267582.1;GABRR1,3_prime_UTR_variant,,ENST00000457434,; A ENST00000454853 Transcript missense_variant 1465/2820 1354/1440 452/479 T/S Acc/Tcc 1 -1 GABRR1 HGNC HGNC:4090 protein_coding YES CCDS5019.2 ENSP00000412673 P24046 UPI0000D4AF7D NM_002042.4 tolerated(0.22) 10/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF30,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 89178856 89178856 T A 1 0 0 0 0 1 0 0 0 6047 1696 59 4 4 GABRR1 6 89178856 Missense_Mutation SNP T C3N-00547_T 16712 89178856 81627123 244 14574 FHL5 0 . GRCh38 6 96610697 96610697 + Silent SNP C C T rs369256526 C3N-00547_T C3N-00547_N C C c.630C>T p.= p.C210C ENST00000326771 6/7 133 125 8 153 153 0 strelka-varscan-mutect FHL5,synonymous_variant,p.=,ENST00000326771,NM_020482.4;FHL5,synonymous_variant,p.=,ENST00000541107,NM_001170807.1;FHL5,synonymous_variant,p.=,ENST00000450218,; T ENST00000326771 Transcript synonymous_variant 1010/2031 630/855 210/284 C tgC/tgT rs369256526 1 1 FHL5 HGNC HGNC:17371 protein_coding YES CCDS5035.1 ENSP00000326022 Q5TD97 UPI000006F158 NM_020482.4 6/7 PROSITE_profiles:PS50023,hmmpanther:PTHR24205:SF7,hmmpanther:PTHR24205,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 LOW 1 SNV 1 1 PASS rs369256526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 96610697 96610697 C T 1 0 0 0 0 0 0 0 1 5746 776 27 1 1 FHL5 6 96610697 Silent SNP C C3N-00547_T 7431841 96610697 74195282 245 14575 SLC22A16 0 . GRCh38 6 110435857 110435857 + Silent SNP A A G novel C3N-00547_T C3N-00547_N A A c.1416T>C p.= p.I472I ENST00000368919 6/8 90 77 13 93 93 0 strelka-varscan-mutect SLC22A16,synonymous_variant,p.=,ENST00000330550,;SLC22A16,synonymous_variant,p.=,ENST00000368919,NM_033125.3;SLC22A16,synonymous_variant,p.=,ENST00000451557,;SLC22A16,downstream_gene_variant,,ENST00000434949,;RN7SL617P,downstream_gene_variant,,ENST00000485298,; G ENST00000368919 Transcript synonymous_variant 1483/1987 1416/1734 472/577 I atT/atC 1 -1 SLC22A16 HGNC HGNC:20302 protein_coding YES CCDS5084.1 ENSP00000357915 Q86VW1 A0A0K0K1K9 UPI000000DC13 NM_033125.3 6/8 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF186,Gene3D:1.20.1250.20,Pfam_domain:PF00083,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 110435857 110435857 A G 1 0 0 0 0 0 0 0 1 14713 144 5 5 5 SLC22A16 6 110435857 Silent SNP A C3N-00547_T 13825160 110435857 60370122 246 14576 CDK19 0 . GRCh38 6 110623313 110623313 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.910C>T p.Pro304Ser p.P304S ENST00000368911 9/13 115 83 32 91 91 0 strelka-mutect CDK19,missense_variant,p.Pro304Ser,ENST00000368911,NM_015076.4,NM_001300960.1;CDK19,missense_variant,p.Pro244Ser,ENST00000323817,NM_001300963.1,NM_001300964.1;CDK19,missense_variant,p.Pro200Ser,ENST00000413605,;CDK19,missense_variant,p.Pro244Ser,ENST00000457688,;CDK19,downstream_gene_variant,,ENST00000463016,; A ENST00000368911 Transcript missense_variant 1090/6246 910/1509 304/502 P/S Cct/Tct 1 -1 CDK19 HGNC HGNC:19338 protein_coding YES CCDS5085.1 ENSP00000357907 Q9BWU1 UPI0000070643 NM_015076.4,NM_001300960.1 tolerated(0.14) 9/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF131,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 110623313 110623313 G A 1 0 0 0 0 1 0 0 0 2839 1203 42 3 3 CDK19 6 110623313 Missense_Mutation SNP G C3N-00547_T 187456 110623313 60182666 247 14577 RFPL4B 0 . GRCh38 6 112350347 112350347 + Silent SNP T T A novel C3N-00547_T C3N-00547_N T T c.639T>A p.= p.A213A ENST00000441065 3/3 177 124 53 153 153 0 strelka-varscan-mutect RFPL4B,synonymous_variant,p.=,ENST00000441065,NM_001013734.2;RP11-506B6.7,downstream_gene_variant,,ENST00000585611,;RP11-506B6.7,downstream_gene_variant,,ENST00000587816,;RP11-506B6.7,downstream_gene_variant,,ENST00000590673,; A ENST00000441065 Transcript synonymous_variant 951/1900 639/792 213/263 A gcT/gcA 1 1 RFPL4B HGNC HGNC:33264 protein_coding YES CCDS34515.1 ENSP00000423391 Q6ZWI9 UPI00001972F0 NM_001013734.2 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF223,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 112350347 112350347 T A 1 0 0 0 0 0 0 0 1 13430 1567 55 4 4 RFPL4B 6 112350347 Silent SNP T C3N-00547_T 1727034 112350347 58455632 248 14578 RFX6 0 . GRCh38 6 116877291 116877291 + Nonsense_Mutation SNP G G T rs17853900 C3N-00547_T C3N-00547_N G G c.16G>T p.Glu6Ter p.E6* ENST00000332958 1/19 202 154 48 258 258 0 strelka-varscan-mutect RFX6,stop_gained,p.Glu6Ter,ENST00000332958,NM_173560.3;RFX6,non_coding_transcript_exon_variant,,ENST00000487683,; T ENST00000332958 Transcript stop_gained 32/3460 16/2787 6/928 E/* Gag/Tag rs17853900 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 1/19 HIGH 1 SNV 1 1 PASS rs17853900 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 116877291 116877291 G T 1 0 0 0 0 0 1 0 0 13441 1175 41 2 2 RFX6 6 116877291 Nonsense_Mutation SNP G C3N-00547_T 4526944 116877291 53928688 249 14579 EYA4 0 . GRCh38 6 133481470 133481470 + Silent SNP C C T rs773095472 C3N-00547_T C3N-00547_N C C c.996C>T p.= p.F332F ENST00000531901 12/20 292 250 42 336 335 1 strelka-varscan-mutect EYA4,synonymous_variant,p.=,ENST00000367895,NM_004100.4;EYA4,synonymous_variant,p.=,ENST00000355167,NM_172105.3;EYA4,synonymous_variant,p.=,ENST00000355286,NM_172103.3;EYA4,synonymous_variant,p.=,ENST00000525849,;EYA4,synonymous_variant,p.=,ENST00000531901,NM_001301013.1;EYA4,synonymous_variant,p.=,ENST00000452339,NM_001301012.1;EYA4,synonymous_variant,p.=,ENST00000430974,;EYA4,synonymous_variant,p.=,ENST00000431403,;EYA4,non_coding_transcript_exon_variant,,ENST00000531861,;EYA4,non_coding_transcript_exon_variant,,ENST00000532518,; T ENST00000531901 Transcript synonymous_variant 1225/2892 996/1938 332/645 F ttC/ttT rs773095472 1 1 EYA4 HGNC HGNC:3522 protein_coding YES CCDS75521.1 ENSP00000432770 F2Z2Y1 UPI0001AE72E3 NM_001301013.1 12/20 hmmpanther:PTHR10190:SF17,hmmpanther:PTHR10190 uncertain_significance LOW 1 SNV 2 1 1 PASS rs773095472 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 133481470 133481470 C T 1 0 0 0 0 0 0 0 1 5199 883 31 1 1 EYA4 6 133481470 Silent SNP C C3N-00547_T 16604179 133481470 37324509 250 14580 ECT2L 0 . GRCh38 6 138876556 138876556 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1663C>A p.Leu555Met p.L555M ENST00000541398 14/22 85 64 21 118 118 0 strelka-varscan-mutect ECT2L,missense_variant,p.Leu555Met,ENST00000541398,NM_001077706.2;ECT2L,missense_variant,p.Leu555Met,ENST00000367682,NM_001195037.2;ECT2L,missense_variant,p.Leu555Met,ENST00000423192,;RP3-509I19.6,downstream_gene_variant,,ENST00000572284,;RP3-509I19.6,downstream_gene_variant,,ENST00000404494,; A ENST00000541398 Transcript missense_variant,splice_region_variant 1988/4483 1663/2715 555/904 L/M Ctg/Atg 1 1 ECT2L HGNC HGNC:21118 protein_coding YES CCDS43508.1 ENSP00000442307 Q008S8 UPI0000E86804 NM_001077706.2 tolerated(0.08) 14/22 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF132 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 138876556 138876556 C A 1 0 0 0 0 1 0 0 0 4730 927 32 2 2 ECT2L 6 138876556 Missense_Mutation SNP C C3N-00547_T 5395086 138876556 31929423 251 14581 OPRM1 0 . GRCh38 6 154091076 154091076 + Silent SNP G G C novel C3N-00547_T C3N-00547_N G G c.1047G>C p.= p.L349L ENST00000434900 5/6 270 247 23 384 384 0 strelka-varscan-mutect OPRM1,synonymous_variant,p.=,ENST00000414028,NM_001145284.3;OPRM1,synonymous_variant,p.=,ENST00000522236,NM_001145287.2;OPRM1,synonymous_variant,p.=,ENST00000522555,NM_001285526.1;OPRM1,synonymous_variant,p.=,ENST00000435918,NM_001145283.2;OPRM1,synonymous_variant,p.=,ENST00000330432,NM_000914.4;OPRM1,synonymous_variant,p.=,ENST00000434900,NM_001145279.3,NM_001285524.1;OPRM1,synonymous_variant,p.=,ENST00000360422,NM_001285523.1;OPRM1,synonymous_variant,p.=,ENST00000520708,NM_001145280.3;OPRM1,synonymous_variant,p.=,ENST00000428397,NM_001008504.3;OPRM1,synonymous_variant,p.=,ENST00000229768,NM_001008505.2;OPRM1,synonymous_variant,p.=,ENST00000419506,NM_001145286.2;OPRM1,synonymous_variant,p.=,ENST00000337049,NM_001008503.2;OPRM1,synonymous_variant,p.=,ENST00000452687,NM_001145282.2;OPRM1,synonymous_variant,p.=,ENST00000524163,NM_001145285.2;OPRM1,synonymous_variant,p.=,ENST00000518759,NM_001145281.2;OPRM1,downstream_gene_variant,,ENST00000520282,;OPRM1,non_coding_transcript_exon_variant,,ENST00000522382,;OPRM1,non_coding_transcript_exon_variant,,ENST00000519613,;OPRM1,non_coding_transcript_exon_variant,,ENST00000521106,;OPRM1,missense_variant,p.Asp139His,ENST00000524150,;OPRM1,synonymous_variant,p.=,ENST00000519083,;OPRM1,synonymous_variant,p.=,ENST00000522739,; C ENST00000434900 Transcript synonymous_variant 1565/2033 1047/1482 349/493 L ctG/ctC 1 1 OPRM1 HGNC HGNC:8156 protein_coding YES CCDS47503.1 ENSP00000394624 P35372 UPI0001899627 NM_001145279.3,NM_001285524.1 5/6 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF7,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS rs1195911052 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 154091076 154091076 G C 1 0 0 0 0 0 0 0 1 10962 1277 45 4 4 OPRM1 6 154091076 Silent SNP G C3N-00547_T 15214520 154091076 16714903 252 14582 LPA 0 . GRCh38 6 160557568 160557568 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.4635C>A p.= p.G1545G ENST00000316300 29/39 155 126 29 174 174 0 strelka-varscan-mutect LPA,synonymous_variant,p.=,ENST00000316300,NM_005577.2; T ENST00000316300 Transcript synonymous_variant 4680/6414 4635/6123 1545/2040 G ggC/ggA 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 29/39 Gene3D:2.40.20.10,Pfam_domain:PF00051,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 LOW 1 SNV 1 1 PASS rs1370596847 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 160557568 160557568 G T 1 0 0 0 0 0 0 0 1 8806 1217 42 2 2 LPA 6 160557568 Silent SNP G C3N-00547_T 6466492 160557568 10248411 253 14583 PDE10A 0 . GRCh38 6 165396423 165396423 + Missense_Mutation SNP G G C C3N-00547_T C3N-00547_N G G c.1315C>G p.Arg439Gly p.R439G ENST00000539869 14/22 154 121 33 184 184 0 strelka-mutect PDE10A,missense_variant,p.Arg429Gly,ENST00000366882,NM_006661.3;PDE10A,missense_variant,p.Arg439Gly,ENST00000539869,NM_001130690.2; C ENST00000539869 Transcript missense_variant 1371/4401 1315/2370 439/789 R/G Cgg/Ggg COSM3024726,COSM4352899 1 -1 PDE10A HGNC HGNC:8772 protein_coding YES CCDS47513.1 ENSP00000438284 Q9Y233 UPI000006F80E NM_001130690.2 deleterious(0.01) 14/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF111,Superfamily_domains:SSF55781 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 165396423 165396423 G C 1 0 0 0 0 1 0 0 0 11718 1115 39 4 4 PDE10A 6 165396423 Missense_Mutation SNP G C3N-00547_T 4838855 165396423 5409556 254 14584 DLL1 0 . GRCh38 6 170285341 170285341 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.945T>A p.= p.S315S ENST00000366756 7/11 303 241 62 370 370 0 strelka-varscan-mutect DLL1,synonymous_variant,p.=,ENST00000366756,NM_005618.3;DLL1,downstream_gene_variant,,ENST00000630500,; T ENST00000366756 Transcript synonymous_variant 1279/3174 945/2172 315/723 S tcT/tcA 1 -1 DLL1 HGNC HGNC:2908 protein_coding YES CCDS5313.1 ENSP00000355718 O00548 UPI000004C656 NM_005618.3 7/11 Gene3D:2.10.25.10,PD936484,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF283,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 170285341 170285341 A T 1 0 0 0 0 0 0 0 1 4373 59 3 4 4 DLL1 6 170285341 Silent SNP A C3N-00547_T 4888918 170285341 520638 255 14585 UNCX 0 . GRCh38 7 1233265 1233265 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.248G>T p.Gly83Val p.G83V ENST00000316333 1/3 55 30 25 63 63 0 strelka-mutect UNCX,missense_variant,p.Gly83Val,ENST00000316333,NM_001080461.1; T ENST00000316333 Transcript missense_variant 359/2048 248/1596 83/531 G/V gGg/gTg 1 1 UNCX HGNC HGNC:33194 protein_coding YES CCDS34583.1 ENSP00000314480 A6NJT0 UPI0000D61BE6 NM_001080461.1 deleterious(0) 1/3 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF382 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 1233265 1233265 G T 1 0 0 0 0 1 0 0 0 17524 1232 43 2 2 UNCX 7 1233265 Missense_Mutation SNP G C3N-00547_T 1233265 158112708 256 14586 TNRC18 0 . GRCh38 7 5352079 5352079 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.5210A>T p.Glu1737Val p.E1737V ENST00000430969 17/30 161 102 59 146 146 0 strelka-varscan-mutect TNRC18,missense_variant,p.Glu1737Val,ENST00000399537,;TNRC18,missense_variant,p.Glu1737Val,ENST00000430969,NM_001080495.2;TNRC18,missense_variant,p.Glu227Val,ENST00000440081,; A ENST00000430969 Transcript missense_variant 5559/10562 5210/8907 1737/2968 E/V gAa/gTa 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious(0) 17/30 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF21 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 5352079 5352079 T A 1 0 0 0 0 1 0 0 0 16812 1783 62 4 4 TNRC18 7 5352079 Missense_Mutation SNP T C3N-00547_T 4118814 5352079 153993894 257 14587 DGKB 0 . GRCh38 7 14621392 14621392 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1273G>T p.Gly425Ter p.G425* ENST00000403951 15/26 308 227 81 384 384 0 strelka-varscan-mutect DGKB,stop_gained,p.Gly425Ter,ENST00000403951,;DGKB,stop_gained,p.Gly425Ter,ENST00000399322,NM_004080.2;DGKB,stop_gained,p.Gly424Ter,ENST00000402815,;DGKB,stop_gained,p.Gly417Ter,ENST00000407950,;DGKB,stop_gained,p.Gly425Ter,ENST00000406247,NM_145695.2;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,;DGKB,non_coding_transcript_exon_variant,,ENST00000471732,;DGKB,non_coding_transcript_exon_variant,,ENST00000477401,; A ENST00000403951 Transcript stop_gained 1693/6917 1273/2415 425/804 G/* Gga/Tga 1 -1 DGKB HGNC HGNC:2850 protein_coding YES CCDS47547.1 ENSP00000385780 Q9Y6T7 UPI0000033B9B 15/26 hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255 HIGH 1 SNV 5 1 PASS rs968326818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 14621392 14621392 C A 1 0 0 0 0 0 1 0 0 4272 603 21 2 2 DGKB 7 14621392 Nonsense_Mutation SNP C C3N-00547_T 9269313 14621392 144724581 258 14588 HOXA11 0 . GRCh38 7 27184712 27184712 + Nonsense_Mutation SNP C C A rs745804777 C3N-00547_T C3N-00547_N C C c.433G>T p.Glu145Ter p.E145* ENST00000006015 1/2 789 536 253 616 616 0 strelka-varscan-mutect HOXA11,stop_gained,p.Glu145Ter,ENST00000006015,NM_005523.5;HOXA11,stop_gained,p.Glu115Ter,ENST00000517402,;HOXA10,upstream_gene_variant,,ENST00000396344,;HOXA10-HOXA9,upstream_gene_variant,,ENST00000470747,;RP1-170O19.14,downstream_gene_variant,,ENST00000523331,;HOXA11-AS,non_coding_transcript_exon_variant,,ENST00000522863,;HOXA11-AS,non_coding_transcript_exon_variant,,ENST00000520360,;HOXA11-AS,upstream_gene_variant,,ENST00000522674,;HOXA11-AS,upstream_gene_variant,,ENST00000520395,;HOXA11-AS,upstream_gene_variant,,ENST00000479766,;HOXA11-AS1_4,upstream_gene_variant,,ENST00000620901,;HOXA11-AS1_5,upstream_gene_variant,,ENST00000620211,;HOXA11-AS1_2,upstream_gene_variant,,ENST00000615604,;HOXA11-AS1_6,upstream_gene_variant,,ENST00000620092,;HOXA11-AS1_3,upstream_gene_variant,,ENST00000613383,;HOXA11-AS1_1,upstream_gene_variant,,ENST00000613939,; A ENST00000006015 Transcript stop_gained 505/2295 433/942 145/313 E/* Gag/Tag rs745804777 1 -1 HOXA11 HGNC HGNC:5101 protein_coding YES CCDS5411.1 ENSP00000006015 P31270 UPI000000D992 NM_005523.5 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF50,Pfam_domain:PF12045 HIGH 1 SNV 1 1 PASS rs745804777 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 27184712 27184712 C A 1 0 0 0 0 0 1 0 0 7184 893 31 1 1 HOXA11 7 27184712 Nonsense_Mutation SNP C C3N-00547_T 12563320 27184712 132161261 259 14589 EVX1 0 . GRCh38 7 27243325 27243325 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.295C>A p.Pro99Thr p.P99T ENST00000496902 1/3 236 170 66 203 202 1 strelka-varscan-mutect EVX1,missense_variant,p.Pro99Thr,ENST00000496902,NM_001989.4,NM_001304519.1;EVX1,missense_variant,p.Pro99Thr,ENST00000222761,;EVX1,upstream_gene_variant,,ENST00000580535,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000519218,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1,upstream_gene_variant,,ENST00000518886,; A ENST00000496902 Transcript missense_variant 626/2955 295/1224 99/407 P/T Ccc/Acc 1 1 EVX1 HGNC HGNC:3506 protein_coding YES CCDS5413.1 ENSP00000419266 P49640 UPI000012A2AD NM_001989.4,NM_001304519.1 tolerated(0.1) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24329:SF246,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS rs899456755 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 27243325 27243325 C A 1 0 0 0 0 1 0 0 0 5161 623 22 2 2 EVX1 7 27243325 Missense_Mutation SNP C C3N-00547_T 58613 27243325 132102648 260 14590 HECW1 0 . GRCh38 7 43438025 43438025 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.824C>T p.Pro275Leu p.P275L ENST00000395891 9/30 217 144 73 155 155 0 strelka-varscan-mutect HECW1,missense_variant,p.Pro275Leu,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Pro275Leu,ENST00000453890,NM_001287059.1;HECW1,non_coding_transcript_exon_variant,,ENST00000471043,;HECW1,non_coding_transcript_exon_variant,,ENST00000492310,; T ENST00000395891 Transcript missense_variant 1429/9501 824/4821 275/1606 P/L cCc/cTc 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated(0.47) 9/30 PROSITE_profiles:PS50004,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 43438025 43438025 C T 1 0 0 0 0 1 0 0 0 6924 623 22 3 3 HECW1 7 43438025 Missense_Mutation SNP C C3N-00547_T 16194700 43438025 115907948 261 14591 NPC1L1 0 . GRCh38 7 44513518 44513518 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.4009A>T p.Ser1337Cys p.S1337C ENST00000289547 20/20 826 537 289 609 609 0 strelka-varscan-mutect NPC1L1,missense_variant,p.Ser1337Cys,ENST00000289547,NM_013389.2;NPC1L1,missense_variant,p.Ser1264Cys,ENST00000546276,;NPC1L1,missense_variant,p.Ser1310Cys,ENST00000381160,NM_001101648.1;AC004938.5,upstream_gene_variant,,ENST00000438468,; A ENST00000289547 Transcript missense_variant 4065/5048 4009/4080 1337/1359 S/C Agc/Tgc 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 deleterious_low_confidence(0) 20/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 44513518 44513518 T A 1 0 0 0 0 1 0 0 0 10619 1580 55 4 4 NPC1L1 7 44513518 Missense_Mutation SNP T C3N-00547_T 1075493 44513518 114832455 262 14592 TNS3 0 . GRCh38 7 47369529 47369529 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1117G>C p.Ala373Pro p.A373P ENST00000311160 17/31 183 135 48 165 165 0 strelka-varscan-mutect TNS3,missense_variant,p.Ala373Pro,ENST00000311160,NM_022748.11;TNS3,missense_variant,p.Ala476Pro,ENST00000457718,;TNS3,missense_variant,p.Ala462Pro,ENST00000450444,;TNS3,non_coding_transcript_exon_variant,,ENST00000469470,; G ENST00000311160 Transcript missense_variant 1475/7618 1117/4338 373/1445 A/P Gca/Cca 1 -1 TNS3 HGNC HGNC:21616 protein_coding YES CCDS5506.2 ENSP00000312143 Q68CZ2 UPI00001AE9DA NM_022748.11 tolerated(0.19) 17/31 hmmpanther:PTHR12305,hmmpanther:PTHR12305:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 47369529 47369529 C G 1 0 0 0 0 1 0 0 0 16818 739 26 4 4 TNS3 7 47369529 Missense_Mutation SNP C C3N-00547_T 2856011 47369529 111976444 263 14593 ZNF727 0 . GRCh38 7 64078338 64078338 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1289G>T p.Gly430Val p.G430V ENST00000456806 4/4 132 116 16 141 141 0 strelka-varscan-mutect ZNF727,missense_variant,p.Gly430Val,ENST00000456806,NM_001159522.1; T ENST00000456806 Transcript missense_variant 1468/1679 1289/1500 430/499 G/V gGc/gTc 1 1 ZNF727 HGNC HGNC:22785 protein_coding YES CCDS55113.1 ENSP00000485448 A8MUV8 UPI0001A23134 NM_001159522.1 deleterious(0.01) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF98,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 64078338 64078338 G T 1 0 0 0 0 1 0 0 0 18701 1203 42 2 2 ZNF727 7 64078338 Missense_Mutation SNP G C3N-00547_T 16708809 64078338 95267635 264 14594 WBSCR17 0 . GRCh38 7 71416027 71416027 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.728G>T p.Gly243Val p.G243V ENST00000333538 4/11 75 46 29 98 98 0 strelka-varscan-mutect WBSCR17,missense_variant,p.Gly243Val,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Gly164Val,ENST00000618959,;WBSCR17,downstream_gene_variant,,ENST00000447516,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; T ENST00000333538 Transcript missense_variant 1362/3884 728/1797 243/598 G/V gGc/gTc 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 tolerated(0.14) 4/11 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 49 71416027 71416027 G T 1 0 0 0 0 1 0 0 0 17823 1203 42 2 2 WBSCR17 7 71416027 Missense_Mutation SNP G C3N-00547_T 7337689 71416027 87929946 265 14595 CLIP2 0 . GRCh38 7 74376009 74376009 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.1610delC p.Pro537GlnfsTer35 p.P537Qfs*35 ENST00000223398 10/17 136 82 54 148 148 0 sindel-varindel-pindel CLIP2,frameshift_variant,p.Pro537GlnfsTer35,ENST00000223398,NM_003388.4;CLIP2,frameshift_variant,p.Pro502GlnfsTer35,ENST00000361545,NM_032421.2;CLIP2,frameshift_variant,p.Pro537GlnfsTer35,ENST00000395060,;CLIP2,upstream_gene_variant,,ENST00000493166,;CLIP2,upstream_gene_variant,,ENST00000487091,;CLIP2,upstream_gene_variant,,ENST00000482424,; - ENST00000223398 Transcript frameshift_variant 1935/5563 1608/3141 536/1046 H/X caC/ca 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 10/17 hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10 HIGH 1 deletion 5 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 74376009 74376009 C - 1 0 1 0 1 0 0 0 0 3302 506 18 0 0 CLIP2 7 74376009 Frame_Shift_Del DEL C C3N-00547_T 2959982 74376009 84969964 266 14596 PHTF2 0 . GRCh38 7 77929317 77929317 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1226C>G p.Pro409Arg p.P409R ENST00000422959 11/19 118 105 13 132 132 0 strelka-varscan-mutect PHTF2,missense_variant,p.Pro443Arg,ENST00000416283,;PHTF2,missense_variant,p.Pro405Arg,ENST00000307305,NM_001127358.1,NM_020432.4;PHTF2,missense_variant,p.Pro443Arg,ENST00000248550,;PHTF2,missense_variant,p.Pro405Arg,ENST00000275575,;PHTF2,missense_variant,p.Pro409Arg,ENST00000422959,NM_001127357.1;PHTF2,missense_variant,p.Pro405Arg,ENST00000424760,;PHTF2,non_coding_transcript_exon_variant,,ENST00000454592,;PHTF2,non_coding_transcript_exon_variant,,ENST00000479515,; G ENST00000422959 Transcript missense_variant 1428/3525 1226/2256 409/751 P/R cCt/cGt 1 1 PHTF2 HGNC HGNC:13411 protein_coding YES CCDS47621.1 ENSP00000403042 Q8N3S3 UPI0000E674D3 NM_001127357.1 tolerated(0.38) 11/19 hmmpanther:PTHR12680,hmmpanther:PTHR12680:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 77929317 77929317 C G 1 0 0 0 0 1 0 0 0 11951 681 24 4 4 PHTF2 7 77929317 Missense_Mutation SNP C C3N-00547_T 3553308 77929317 81416656 267 14597 SEMA3C 0 . GRCh38 7 80744961 80744961 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.2189G>A p.Gly730Asp p.G730D ENST00000265361 18/18 285 260 25 466 466 0 strelka-varscan-mutect SEMA3C,missense_variant,p.Gly730Asp,ENST00000265361,NM_006379.3;SEMA3C,missense_variant,p.Gly730Asp,ENST00000419255,; T ENST00000265361 Transcript missense_variant 2751/5174 2189/2256 730/751 G/D gGc/gAc 1 -1 SEMA3C HGNC HGNC:10725 protein_coding YES CCDS5596.1 ENSP00000265361 Q99985 UPI000011C137 NM_006379.3 tolerated(0.35) 18/18 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 80744961 80744961 C T 1 0 0 0 0 1 0 0 0 14302 739 26 3 3 SEMA3C 7 80744961 Missense_Mutation SNP C C3N-00547_T 2815644 80744961 78601012 268 14598 PCLO 0 . GRCh38 7 82950104 82950104 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.10484G>C p.Gly3495Ala p.G3495A ENST00000333891 6/25 166 91 75 185 185 0 strelka-varscan-mutect PCLO,missense_variant,p.Gly3495Ala,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Gly3495Ala,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Gly215Ala,ENST00000437081,; G ENST00000333891 Transcript missense_variant 10822/20329 10484/15429 3495/5142 G/A gGg/gCg 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.11) 6/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 82950104 82950104 C G 1 0 0 0 0 1 0 0 0 11671 623 22 4 4 PCLO 7 82950104 Missense_Mutation SNP C C3N-00547_T 2205143 82950104 76395869 269 14599 ABCB4 0 . GRCh38 7 87443436 87443436 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1239G>T p.Lys413Asn p.K413N ENST00000265723 12/28 386 246 140 495 494 1 strelka-varscan-mutect ABCB4,missense_variant,p.Lys413Asn,ENST00000265723,NM_018849.2;ABCB4,missense_variant,p.Lys413Asn,ENST00000359206,NM_000443.3;ABCB4,missense_variant,p.Lys413Asn,ENST00000358400,NM_018850.2;ABCB4,missense_variant,p.Lys413Asn,ENST00000453593,; A ENST00000265723 Transcript missense_variant 1351/4020 1239/3861 413/1286 K/N aaG/aaT 1 -1 ABCB4 HGNC HGNC:45 protein_coding YES CCDS5606.1 ENSP00000265723 P21439 UPI000013D66B NM_018849.2 tolerated(0.36) 12/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 87443436 87443436 C A 1 0 0 0 0 1 0 0 0 47 680 24 2 2 ABCB4 7 87443436 Missense_Mutation SNP C C3N-00547_T 4493332 87443436 71902537 270 14600 MTERF1 0 . GRCh38 7 91874524 91874524 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.270delG p.Lys91AsnfsTer10 p.K91Nfs*10 ENST00000351870 3/3 218 191 27 196 196 0 sindel-varindel-pindel MTERF1,frameshift_variant,p.Lys71AsnfsTer10,ENST00000419292,NM_001301134.1;MTERF1,frameshift_variant,p.Lys91AsnfsTer10,ENST00000351870,NM_006980.4;MTERF1,frameshift_variant,p.Lys71AsnfsTer10,ENST00000406735,NM_001301135.1;MTERF1,frameshift_variant,p.Lys71AsnfsTer10,ENST00000456229,;MTERF1,frameshift_variant,p.Lys91AsnfsTer10,ENST00000442961,;MTERF1,downstream_gene_variant,,ENST00000425936,;MTERF1,intron_variant,,ENST00000454222,;MTERF1,downstream_gene_variant,,ENST00000481516,; - ENST00000351870 Transcript frameshift_variant 364/1997 270/1200 90/399 R/X agG/ag 1 -1 MTERF1 HGNC HGNC:21463 protein_coding YES CCDS5621.1 ENSP00000248643 Q99551 UPI000004A0C8 NM_006980.4 3/3 Pfam_domain:PF02536,hmmpanther:PTHR15437,hmmpanther:PTHR15437:SF2 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 91874524 91874524 C - 1 0 1 0 1 0 0 0 0 9903 854 30 0 0 MTERF1 7 91874524 Frame_Shift_Del DEL C C3N-00547_T 4431088 91874524 67471449 271 14601 COL1A2 0 . GRCh38 7 94421927 94421927 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.2378G>T p.Gly793Val p.G793V ENST00000297268 39/52 221 189 32 220 219 1 strelka-varscan-mutect COL1A2,missense_variant,p.Gly793Val,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Gly791Val,ENST00000620463,;COL1A2,non_coding_transcript_exon_variant,,ENST00000497316,;COL1A2,non_coding_transcript_exon_variant,,ENST00000473573,;COL1A2,upstream_gene_variant,,ENST00000481570,;COL1A2,upstream_gene_variant,,ENST00000478215,;COL1A2,downstream_gene_variant,,ENST00000461525,;COL1A2,downstream_gene_variant,,ENST00000467931,;COL1A2,upstream_gene_variant,,ENST00000469732,;COL1A2,upstream_gene_variant,,ENST00000492110,;COL1A2,upstream_gene_variant,,ENST00000488121,; T ENST00000297268 Transcript missense_variant 2849/5411 2378/4101 793/1366 G/V gGa/gTa COSM1201824,COSM1496709 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 deleterious(0.01) 39/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 94421927 94421927 G T 1 0 0 0 0 1 0 0 0 3466 1174 41 2 2 COL1A2 7 94421927 Missense_Mutation SNP G C3N-00547_T 2547403 94421927 64924046 272 14602 PTCD1 0 . GRCh38 7 99424909 99424909 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.1623G>T p.= p.A541A ENST00000292478 6/8 616 367 249 603 603 0 strelka-varscan-mutect PTCD1,synonymous_variant,p.=,ENST00000292478,NM_015545.3;ATP5J2-PTCD1,synonymous_variant,p.=,ENST00000413834,NM_001198879.1;PTCD1,downstream_gene_variant,,ENST00000485746,; A ENST00000292478 Transcript synonymous_variant 1874/5582 1623/2103 541/700 A gcG/gcT 1 -1 PTCD1 HGNC HGNC:22198 protein_coding YES CCDS34691.1 ENSP00000292478 O75127 A4D273 UPI0000223FFA NM_015545.3 6/8 PROSITE_profiles:PS51375,hmmpanther:PTHR24014,hmmpanther:PTHR24014:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 99424909 99424909 C A 1 0 0 0 0 0 0 0 1 12880 755 27 1 1 PTCD1 7 99424909 Silent SNP C C3N-00547_T 5002982 99424909 59921064 273 14603 PTCD1 0 . GRCh38 7 99425130 99425130 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.1402A>C p.Ile468Leu p.I468L ENST00000292478 6/8 283 239 44 316 316 0 strelka-varscan-mutect PTCD1,missense_variant,p.Ile468Leu,ENST00000292478,NM_015545.3;ATP5J2-PTCD1,missense_variant,p.Ile517Leu,ENST00000413834,NM_001198879.1;PTCD1,downstream_gene_variant,,ENST00000485746,; G ENST00000292478 Transcript missense_variant 1653/5582 1402/2103 468/700 I/L Ata/Cta 1 -1 PTCD1 HGNC HGNC:22198 protein_coding YES CCDS34691.1 ENSP00000292478 O75127 A4D273 UPI0000223FFA NM_015545.3 tolerated(0.1) 6/8 hmmpanther:PTHR24014,hmmpanther:PTHR24014:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 99425130 99425130 T G 1 0 0 0 0 1 0 0 0 12880 1435 50 5 5 PTCD1 7 99425130 Missense_Mutation SNP T C3N-00547_T 221 99425130 59920843 274 14604 LHFPL3 0 . GRCh38 7 104329033 104329033 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.212C>G p.Ser71Cys p.S71C ENST00000424859 1/3 244 156 88 299 299 0 strelka-varscan-mutect LHFPL3,missense_variant,p.Ser71Cys,ENST00000424859,NM_199000.2;LHFPL3,missense_variant,p.Ser71Cys,ENST00000401970,; G ENST00000424859 Transcript missense_variant 378/1852 212/669 71/222 S/C tCc/tGc 1 1 LHFPL3 HGNC HGNC:6589 protein_coding YES ENSP00000393128 Q86UP9 UPI000020F876 NM_199000.2 deleterious(0.01) 1/3 hmmpanther:PTHR12489,hmmpanther:PTHR12489:SF13,Pfam_domain:PF10242 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 104329033 104329033 C G 1 0 0 0 0 1 0 0 0 8675 855 30 4 4 LHFPL3 7 104329033 Missense_Mutation SNP C C3N-00547_T 4903903 104329033 55016940 275 14605 PUS7 0 . GRCh38 7 105495232 105495232 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.752C>T p.Pro251Leu p.P251L ENST00000356362 6/16 138 107 31 125 125 0 strelka-varscan-mutect PUS7,missense_variant,p.Pro251Leu,ENST00000356362,NM_001318163.1,NM_001318164.1,NM_019042.3;PUS7,missense_variant,p.Pro251Leu,ENST00000469408,;PUS7,missense_variant,p.Pro92Leu,ENST00000482157,;PUS7,missense_variant,p.Pro251Leu,ENST00000481939,;PUS7,non_coding_transcript_exon_variant,,ENST00000487277,; A ENST00000356362 Transcript missense_variant 967/3480 752/1986 251/661 P/L cCa/cTa 1 -1 PUS7 HGNC HGNC:26033 protein_coding YES CCDS34725.1 ENSP00000348722 Q96PZ0 UPI00001D483E NM_001318163.1,NM_001318164.1,NM_019042.3 deleterious(0) 6/16 hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF1,Superfamily_domains:SSF55120 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 105495232 105495232 G A 1 0 0 0 0 1 0 0 0 12991 1348 47 3 3 PUS7 7 105495232 Missense_Mutation SNP G C3N-00547_T 1166199 105495232 53850741 276 14606 RINT1 0 . GRCh38 7 105542502 105542502 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.368A>G p.Gln123Arg p.Q123R ENST00000257700 4/15 340 311 29 362 362 0 strelka-varscan-mutect RINT1,missense_variant,p.Gln123Arg,ENST00000257700,NM_021930.4;RINT1,missense_variant,p.Gln92Arg,ENST00000493041,;RINT1,non_coding_transcript_exon_variant,,ENST00000477285,;RINT1,synonymous_variant,p.=,ENST00000497979,;RINT1,3_prime_UTR_variant,,ENST00000467392,;RINT1,non_coding_transcript_exon_variant,,ENST00000493258,;RINT1,downstream_gene_variant,,ENST00000482041,; G ENST00000257700 Transcript missense_variant 599/2976 368/2379 123/792 Q/R cAg/cGg 1 1 RINT1 HGNC HGNC:21876 protein_coding YES CCDS34726.1 ENSP00000257700 Q6NUQ1 UPI000020F898 NM_021930.4 tolerated(0.67) 4/15 hmmpanther:PTHR13520,hmmpanther:PTHR13520:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 105542502 105542502 A G 1 0 0 0 0 1 0 0 0 13550 188 7 5 5 RINT1 7 105542502 Missense_Mutation SNP A C3N-00547_T 47270 105542502 53803471 277 14607 LAMB1 0 . GRCh38 7 108001769 108001769 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.74delG p.Cys25LeufsTer52 p.C25Lfs*52 ENST00000393561 1/32 81 73 8 103 103 0 sindel-varindel LAMB1,frameshift_variant,p.Cys25LeufsTer52,ENST00000393561,;LAMB1,intron_variant,,ENST00000222399,NM_002291.2;LAMB1,intron_variant,,ENST00000393560,;LAMB1,intron_variant,,ENST00000439976,;LAMB1,intron_variant,,ENST00000393559,;U3,upstream_gene_variant,,ENST00000458938,; - ENST00000393561 Transcript frameshift_variant 259/5766 74/5433 25/1810 C/X tGt/tt 1 -1 LAMB1 HGNC HGNC:6486 protein_coding ENSP00000377191 G3XAI2 UPI0000EE4033 1/32 Low_complexity_(Seg):seg HIGH deletion 5 1 PASS . . 0 203 7 0 0 0 0 0 -17.03824 0.9999989 1 1 1 0 - 7 5 49 108001769 108001769 C - 1 0 1 0 1 0 0 0 0 8514 478 17 0 0 LAMB1 7 108001769 Frame_Shift_Del DEL C C3N-00547_T 2459267 108001769 51344204 278 14608 PPP1R3A 0 . GRCh38 7 113878275 113878275 + Silent SNP A A G novel C3N-00547_T C3N-00547_N A A c.2817T>C p.= p.T939T ENST00000284601 4/4 206 184 22 256 256 0 strelka-varscan-mutect PPP1R3A,synonymous_variant,p.=,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; G ENST00000284601 Transcript synonymous_variant 2886/4384 2817/3369 939/1122 T acT/acC 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 LOW 1 SNV 1 1 PASS rs1162345042 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 113878275 113878275 A G 1 0 0 0 0 0 0 0 1 12492 407 15 5 5 PPP1R3A 7 113878275 Silent SNP A C3N-00547_T 5876506 113878275 45467698 279 14609 PTPRZ1 0 . GRCh38 7 121996417 121996417 + Missense_Mutation SNP C C A rs747678780 C3N-00547_T C3N-00547_N C C c.964C>A p.Pro322Thr p.P322T ENST00000393386 9/30 110 93 17 129 129 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.Pro322Thr,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.Pro322Thr,ENST00000449182,NM_001206839.1; A ENST00000393386 Transcript missense_variant 1375/8175 964/6948 322/2315 P/T Cca/Aca rs747678780 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0) 9/30 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF214,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs747678780 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 121996417 121996417 C A 1 0 0 0 0 1 0 0 0 12969 623 22 2 2 PTPRZ1 7 121996417 Missense_Mutation SNP C C3N-00547_T 8118142 121996417 37349556 280 14610 ASB15 0 . GRCh38 7 123636879 123636879 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1665C>A p.Cys555Ter p.C555* ENST00000451558 14/14 174 124 50 210 210 0 strelka-varscan-mutect ASB15,stop_gained,p.Cys555Ter,ENST00000451558,;ASB15,stop_gained,p.Cys555Ter,ENST00000451215,NM_001290258.1;ASB15,stop_gained,p.Cys555Ter,ENST00000434204,;ASB15,stop_gained,p.Cys555Ter,ENST00000275699,NM_080928.4;ASB15,3_prime_UTR_variant,,ENST00000540573,; A ENST00000451558 Transcript stop_gained 2186/4788 1665/1767 555/588 C/* tgC/tgA 1 1 ASB15 HGNC HGNC:19767 protein_coding YES CCDS34742.1 ENSP00000397655 Q8WXK1 UPI000022D0FF 14/14 Pfam_domain:PF07525,PROSITE_profiles:PS50225,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF47,SMART_domains:SM00253,SMART_domains:SM00969,Superfamily_domains:SSF158235 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 123636879 123636879 C A 1 0 0 0 0 0 1 0 0 1161 747 26 2 2 ASB15 7 123636879 Nonsense_Mutation SNP C C3N-00547_T 1640462 123636879 35709094 281 14611 FLNC 0 . GRCh38 7 128851361 128851361 + Splice_Site SNP G G T novel C3N-00547_T C3N-00547_N G G c.5668+1G>T p.X1890_splice ENST00000325888 406 287 119 427 426 1 strelka-varscan-mutect FLNC,splice_donor_variant,,ENST00000325888,NM_001458.4;FLNC,splice_donor_variant,,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; T ENST00000325888 Transcript splice_donor_variant -/9188 5668/8178 1890/2725 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 34/47 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 49 128851361 128851361 G T 1 0 0 0 0 0 0 1 0 5791 1275 44 2 2 FLNC 7 128851361 Splice_Site SNP G C3N-00547_T 5214482 128851361 30494612 282 14612 KCP 0 . GRCh38 7 128892702 128892702 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.1513G>A p.Ala505Thr p.A505T ENST00000610776 15/40 193 167 26 267 267 0 strelka-varscan-mutect KCP,missense_variant,p.Ala505Thr,ENST00000610776,;KCP,missense_variant,p.Ala509Thr,ENST00000613019,;KCP,missense_variant,p.Ala448Thr,ENST00000620378,NM_001135914.1;KCP,non_coding_transcript_exon_variant,,ENST00000612224,;KCP,missense_variant,p.Ala509Thr,ENST00000611280,;KCP,non_coding_transcript_exon_variant,,ENST00000616669,; T ENST00000610776 Transcript missense_variant 1556/5108 1513/4887 505/1628 A/T Gcc/Acc 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 tolerated(1) 15/40 PROSITE_profiles:PS50184,PROSITE_patterns:PS01208,Pfam_domain:PF00093,Gene3D:2.10.70.10,SMART_domains:SM00215,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS rs1271036391 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 128892702 128892702 C T 1 0 0 0 0 1 0 0 0 8012 710 25 3 3 KCP 7 128892702 Missense_Mutation SNP C C3N-00547_T 41341 128892702 30453271 283 14613 LRGUK 0 . GRCh38 7 134127550 134127550 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.183G>T p.= p.L61L ENST00000285928 1/20 275 239 36 350 350 0 strelka-varscan-mutect LRGUK,synonymous_variant,p.=,ENST00000285928,NM_144648.1;LRGUK,non_coding_transcript_exon_variant,,ENST00000473068,; T ENST00000285928 Transcript synonymous_variant 252/3163 183/2478 61/825 L ctG/ctT 1 1 LRGUK HGNC HGNC:21964 protein_coding YES CCDS5830.1 ENSP00000285928 Q96M69 UPI0000072C76 NM_144648.1 1/20 LOW 1 SNV 1 1 PASS rs1363772180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 134127550 134127550 G T 1 0 0 0 0 0 0 0 1 8837 1306 46 2 2 LRGUK 7 134127550 Silent SNP G C3N-00547_T 5234848 134127550 25218423 284 14614 AKR1B1 0 . GRCh38 7 134449763 134449763 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.386G>C p.Gly129Ala p.G129A ENST00000285930 4/10 332 249 83 358 358 0 strelka-varscan-mutect AKR1B1,missense_variant,p.Gly129Ala,ENST00000285930,NM_001628.2;AKR1B1,non_coding_transcript_exon_variant,,ENST00000489022,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000487438,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000497983,;AKR1B1,missense_variant,p.Gly129Ala,ENST00000434222,;AKR1B1,3_prime_UTR_variant,,ENST00000426422,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000465351,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000491741,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000498771,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000484592,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000467829,;AKR1B1,upstream_gene_variant,,ENST00000467251,;AKR1B1,downstream_gene_variant,,ENST00000462784,;AKR1B1,upstream_gene_variant,,ENST00000498373,; G ENST00000285930 Transcript missense_variant 466/1409 386/951 129/316 G/A gGc/gCc 1 -1 AKR1B1 HGNC HGNC:381 protein_coding YES CCDS5831.1 ENSP00000285930 P15121 A0A024R7A8 UPI000000D78E NM_001628.2 deleterious(0.01) 4/10 Gene3D:3.20.20.100,PIRSF_domain:PIRSF000097,Pfam_domain:PF00248,Superfamily_domains:SSF51430 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 134449763 134449763 C G 1 0 0 0 0 1 0 0 0 550 739 26 4 4 AKR1B1 7 134449763 Missense_Mutation SNP C C3N-00547_T 322213 134449763 24896210 285 14615 RAB19 0 . GRCh38 7 140407669 140407669 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.23G>T p.Arg8Met p.R8M ENST00000537763 2/4 160 137 23 167 167 0 strelka-varscan-mutect RAB19,missense_variant,p.Arg8Met,ENST00000537763,NM_001008749.2;RAB19,missense_variant,p.Arg8Met,ENST00000356407,;RAB19,missense_variant,p.Arg8Met,ENST00000495590,;SLC37A3,upstream_gene_variant,,ENST00000491505,;SLC37A3,upstream_gene_variant,,ENST00000493423,; T ENST00000537763 Transcript missense_variant 221/952 23/654 8/217 R/M aGg/aTg 1 1 RAB19 HGNC HGNC:19982 protein_coding YES CCDS34762.2 ENSP00000440167 A4D1S5 UPI000013DA89 NM_001008749.2 tolerated(0.19) 2/4 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 49 140407669 140407669 G T 1 0 0 0 0 1 0 0 0 13062 1000 35 2 2 RAB19 7 140407669 Missense_Mutation SNP G C3N-00547_T 5957906 140407669 18938304 286 14616 MGAM2 0 . GRCh38 7 142132017 142132017 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.507C>T p.= p.S169S ENST00000477922 6/48 134 127 7 147 146 1 strelka-varscan MGAM2,synonymous_variant,p.=,ENST00000477922,NM_001293626.1;MGAM2,synonymous_variant,p.=,ENST00000550469,; T ENST00000477922 Transcript synonymous_variant 561/7867 507/7548 169/2515 S agC/agT 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 6/48 Pfam_domain:PF16863,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF74650 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 142132017 142132017 C T 1 0 0 0 0 0 0 0 1 9500 796 28 3 3 MGAM2 7 142132017 Silent SNP C C3N-00547_T 1724348 142132017 17213956 287 14617 PRSS1 0 . GRCh38 7 142752445 142752445 + Missense_Mutation SNP G G C rs200890507 C3N-00547_T C3N-00547_N G G c.469G>C p.Glu157Gln p.E157Q ENST00000311737 4/5 423 391 32 506 506 0 varscan-mutect PRSS1,missense_variant,p.Glu171Gln,ENST00000486171,;PRSS1,missense_variant,p.Glu157Gln,ENST00000612126,;PRSS1,missense_variant,p.Glu157Gln,ENST00000311737,NM_002769.4;PRSS1,missense_variant,p.Glu147Gln,ENST00000619214,;PRSS1,missense_variant,p.Glu107Gln,ENST00000492062,;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS1,non_coding_transcript_exon_variant,,ENST00000463701,;PRSS1,downstream_gene_variant,,ENST00000485223,;PRSS1,downstream_gene_variant,,ENST00000497041,; C ENST00000311737 Transcript missense_variant 475/800 469/744 157/247 E/Q Gag/Cag rs200890507,COSM3634905 1 1 PRSS1 HGNC HGNC:9475 protein_coding YES CCDS5872.1 ENSP00000308720 P07477 UPI0000001309 NM_002769.4 tolerated(0.59) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24264:SF12,hmmpanther:PTHR24264,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200890507 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 142752445 142752445 G C 1 0 0 0 0 1 0 0 0 12761 1059 37 4 4 PRSS1 7 142752445 Missense_Mutation SNP G C3N-00547_T 620428 142752445 16593528 288 14618 OR6V1 0 . GRCh38 7 143052401 143052401 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.61C>A p.Leu21Met p.L21M ENST00000418316 1/1 145 107 38 150 150 0 strelka-varscan-mutect OR6V1,missense_variant,p.Leu21Met,ENST00000418316,NM_001001667.1;OR9P1P,upstream_gene_variant,,ENST00000496431,; A ENST00000418316 Transcript missense_variant 82/1028 61/942 21/313 L/M Ctg/Atg 1 1 OR6V1 HGNC HGNC:15090 protein_coding YES CCDS47728.1 ENSP00000396085 Q8N148 A0A126GWQ4 UPI0000041C19 NM_001001667.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 143052401 143052401 C A 1 0 0 0 0 1 0 0 0 11281 796 28 2 2 OR6V1 7 143052401 Missense_Mutation SNP C C3N-00547_T 299956 143052401 16293572 289 14619 TAS2R41 0 . GRCh38 7 143478105 143478105 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.233G>T p.Gly78Val p.G78V ENST00000408916 1/1 156 112 44 214 214 0 strelka-varscan-mutect TAS2R41,missense_variant,p.Gly78Val,ENST00000408916,NM_176883.2;EPHA1-AS1,intron_variant,,ENST00000429289,; T ENST00000408916 Transcript missense_variant 233/924 233/924 78/307 G/V gGg/gTg COSM3635314 1 1 TAS2R41 HGNC HGNC:18883 protein_coding YES CCDS43663.1 ENSP00000386201 P59536 UPI000000D823 NM_176883.2 tolerated(0.46) 1/1 hmmpanther:PTHR11394:SF73,hmmpanther:PTHR11394,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 143478105 143478105 G T 1 0 0 0 0 1 0 0 0 15978 1232 43 2 2 TAS2R41 7 143478105 Missense_Mutation SNP G C3N-00547_T 425704 143478105 15867868 290 14620 CNTNAP2 0 . GRCh38 7 147486009 147486009 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1745A>G p.Glu582Gly p.E582G ENST00000361727 11/24 143 87 56 179 179 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Glu582Gly,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,; G ENST00000361727 Transcript missense_variant 2263/9896 1745/3996 582/1331 E/G gAg/gGg 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(1) 11/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 147486009 147486009 A G 1 0 0 0 0 1 0 0 0 3428 304 11 5 5 CNTNAP2 7 147486009 Missense_Mutation SNP A C3N-00547_T 4007904 147486009 11859964 291 14621 ZNF746 0 . GRCh38 7 149474740 149474740 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.1582C>T p.Arg528Cys p.R528C ENST00000458143 7/7 131 119 12 158 158 0 strelka-varscan-mutect ZNF746,missense_variant,p.Arg527Cys,ENST00000340622,NM_152557.4;ZNF746,missense_variant,p.Arg528Cys,ENST00000458143,NM_001163474.1;ZNF746,downstream_gene_variant,,ENST00000471735,; A ENST00000458143 Transcript missense_variant 1853/3797 1582/1938 528/645 R/C Cgc/Tgc 1 -1 ZNF746 HGNC HGNC:21948 protein_coding YES CCDS55180.1 ENSP00000395007 Q6NUN9 UPI00015DA840 NM_001163474.1 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF13,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 149474740 149474740 G A 1 0 0 0 0 1 0 0 0 18712 1116 39 1 1 ZNF746 7 149474740 Missense_Mutation SNP G C3N-00547_T 1988731 149474740 9871233 292 14622 SSPO 0 . GRCh38 7 149815718 149815718 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.10816G>A p.Gly3606Arg p.G3606R ENST00000378016 75/107 152 138 14 123 123 0 strelka-varscan-mutect SSPO,missense_variant,p.Gly3606Arg,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000481772,; A ENST00000378016 Transcript missense_variant 10816/15589 10816/15453 3606/5150 G/R Ggg/Agg 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 tolerated(0.07) 75/107 hmmpanther:PTHR11339:SF294,hmmpanther:PTHR11339 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 149815718 149815718 G A 1 0 0 0 0 1 0 0 0 15566 1000 35 3 3 SSPO 7 149815718 Missense_Mutation SNP G C3N-00547_T 340978 149815718 9530255 293 14623 NKX2-6 0 . GRCh38 8 23703063 23703063 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.294C>A p.= p.A98A ENST00000325017 2/2 145 86 59 292 292 0 strelka-varscan-mutect NKX2-6,synonymous_variant,p.=,ENST00000325017,NM_001136271.2;RP11-175E9.1,upstream_gene_variant,,ENST00000523874,; T ENST00000325017 Transcript synonymous_variant 294/906 294/906 98/301 A gcC/gcA 1 -1 NKX2-6 HGNC HGNC:32940 protein_coding YES ENSP00000320089 A6NCS4 UPI000016092C NM_001136271.2 2/2 hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF39 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 23703063 23703063 G T 1 0 0 0 0 0 0 0 1 10490 987 35 2 2 NKX2-6 8 23703063 Silent SNP G C3N-00547_T 23703063 121435573 294 14624 EXTL3 0 . GRCh38 8 28717295 28717295 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1236G>T p.Trp412Cys p.W412C ENST00000220562 3/7 216 145 71 174 174 0 strelka-varscan-mutect EXTL3,missense_variant,p.Trp412Cys,ENST00000220562,NM_001440.3;EXTL3,missense_variant,p.Trp28Cys,ENST00000523149,;EXTL3,intron_variant,,ENST00000521532,;EXTL3,upstream_gene_variant,,ENST00000521473,;EXTL3,intron_variant,,ENST00000519886,;EXTL3,downstream_gene_variant,,ENST00000518223,;EXTL3,downstream_gene_variant,,ENST00000522725,;EXTL3,downstream_gene_variant,,ENST00000520940,;EXTL3,downstream_gene_variant,,ENST00000454906,;EXTL3,downstream_gene_variant,,ENST00000519288,;EXTL3,intron_variant,,ENST00000522698,; T ENST00000220562 Transcript missense_variant 2138/6483 1236/2760 412/919 W/C tgG/tgT 1 1 EXTL3 HGNC HGNC:3518 protein_coding YES CCDS6070.1 ENSP00000220562 O43909 UPI000012A35D NM_001440.3 deleterious(0) 3/7 hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF73,Pfam_domain:PF03016 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 28717295 28717295 G T 1 0 0 0 0 1 0 0 0 5195 1241 43 2 2 EXTL3 8 28717295 Missense_Mutation SNP G C3N-00547_T 5014232 28717295 116421341 295 14625 KIF13B 0 . GRCh38 8 29071844 29071844 + Missense_Mutation SNP C C T rs764968047 C3N-00547_T C3N-00547_N C C c.4994G>A p.Gly1665Glu p.G1665E ENST00000524189 39/40 235 207 28 352 352 0 strelka-varscan-mutect KIF13B,missense_variant,p.Gly1665Glu,ENST00000524189,NM_015254.3;KIF13B,missense_variant,p.Gly257Glu,ENST00000523130,;CTD-2647L4.5,downstream_gene_variant,,ENST00000560714,; T ENST00000524189 Transcript missense_variant 5033/8745 4994/5481 1665/1826 G/E gGg/gAg rs764968047 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 tolerated_low_confidence(0.32) 39/40 MODERATE 1 SNV 1 1 PASS rs764968047 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 29071844 29071844 C T 1 0 0 0 0 1 0 0 0 8139 623 22 3 3 KIF13B 8 29071844 Missense_Mutation SNP C C3N-00547_T 354549 29071844 116066792 296 14626 RAB11FIP1 0 . GRCh38 8 37862939 37862939 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.3808C>T p.Leu1270Phe p.L1270F ENST00000330843 6/6 214 189 25 160 160 0 strelka-varscan-mutect RAB11FIP1,missense_variant,p.Leu1270Phe,ENST00000330843,NM_001002814.2;RAB11FIP1,missense_variant,p.Leu636Phe,ENST00000287263,NM_025151.4;RAB11FIP1,missense_variant,p.Leu488Phe,ENST00000522727,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000523182,;RP11-205M5.3,downstream_gene_variant,,ENST00000622942,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000522774,; A ENST00000330843 Transcript missense_variant 3821/7811 3808/3852 1270/1283 L/F Ctc/Ttc 1 -1 RAB11FIP1 HGNC HGNC:30265 protein_coding YES CCDS34882.1 ENSP00000331342 Q6WKZ4 UPI0000D624B1 NM_001002814.2 deleterious(0) 6/6 PROSITE_profiles:PS51511,hmmpanther:PTHR15746,hmmpanther:PTHR15746:SF22,Pfam_domain:PF09457,Superfamily_domains:SSF144270 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 37862939 37862939 G A 1 0 0 0 0 1 0 0 0 13051 1000 35 3 3 RAB11FIP1 8 37862939 Missense_Mutation SNP G C3N-00547_T 8791095 37862939 107275697 297 14627 DDHD2 0 . GRCh38 8 38252168 38252168 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1498G>T p.Glu500Ter p.E500* ENST00000397166 13/18 204 130 74 141 141 0 strelka-varscan-mutect DDHD2,stop_gained,p.Glu500Ter,ENST00000397166,NM_015214.2;DDHD2,stop_gained,p.Glu500Ter,ENST00000520272,NM_001164232.1;DDHD2,stop_gained,p.Glu119Ter,ENST00000517385,;DDHD2,stop_gained,p.Glu2Ter,ENST00000526144,;DDHD2,5_prime_UTR_variant,,ENST00000529845,;DDHD2,upstream_gene_variant,,ENST00000528613,;DDHD2,downstream_gene_variant,,ENST00000532106,;DDHD2,downstream_gene_variant,,ENST00000528888,;DDHD2,non_coding_transcript_exon_variant,,ENST00000520176,;DDHD2,non_coding_transcript_exon_variant,,ENST00000528504,;DDHD2,non_coding_transcript_exon_variant,,ENST00000528148,;DDHD2,downstream_gene_variant,,ENST00000527415,;DDHD2,upstream_gene_variant,,ENST00000524545,; T ENST00000397166 Transcript stop_gained 2023/4921 1498/2136 500/711 E/* Gag/Tag 1 1 DDHD2 HGNC HGNC:29106 protein_coding YES CCDS34883.1 ENSP00000380352 O94830 UPI0000160E07 NM_015214.2 13/18 PROSITE_profiles:PS51043,hmmpanther:PTHR23509,hmmpanther:PTHR23509:SF7,Pfam_domain:PF02862,SMART_domains:SM01127 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 38252168 38252168 G T 1 0 0 0 0 0 1 0 0 4130 943 33 2 2 DDHD2 8 38252168 Nonsense_Mutation SNP G C3N-00547_T 389229 38252168 106886468 298 14628 PLEKHA2 0 . GRCh38 8 38952222 38952222 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.543G>T p.Arg181Ser p.R181S ENST00000617275 7/12 272 213 59 146 146 0 strelka-varscan-mutect PLEKHA2,missense_variant,p.Arg181Ser,ENST00000617275,NM_021623.1;PLEKHA2,missense_variant,p.Arg132Ser,ENST00000616834,;PLEKHA2,missense_variant,p.Arg181Ser,ENST00000521746,;PLEKHA2,missense_variant,p.Arg131Ser,ENST00000616927,;PLEKHA2,upstream_gene_variant,,ENST00000521382,;PLEKHA2,non_coding_transcript_exon_variant,,ENST00000518070,; T ENST00000617275 Transcript missense_variant 721/5582 543/1278 181/425 R/S agG/agT 1 1 PLEKHA2 HGNC HGNC:14336 protein_coding YES CCDS75732.1 ENSP00000482228 A8K727 UPI0001596C50 NM_021623.1 deleterious(0.02) 7/12 hmmpanther:PTHR14336,hmmpanther:PTHR14336:SF5,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 38952222 38952222 G T 1 0 0 0 0 1 0 0 0 12149 1252 44 2 2 PLEKHA2 8 38952222 Missense_Mutation SNP G C3N-00547_T 700054 38952222 106186414 299 14629 PXDNL 0 . GRCh38 8 51408593 51408593 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.3031C>A p.His1011Asn p.H1011N ENST00000356297 17/23 265 188 77 184 184 0 strelka-varscan-mutect PXDNL,missense_variant,p.His1011Asn,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.His130Asn,ENST00000522933,;PXDNL,missense_variant,p.His277Asn,ENST00000522628,; T ENST00000356297 Transcript missense_variant 3132/4805 3031/4392 1011/1463 H/N Cac/Aac COSM2718415,COSM2718416 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 51408593 51408593 G T 1 0 0 0 0 1 0 0 0 13002 1319 46 2 2 PXDNL 8 51408593 Missense_Mutation SNP G C3N-00547_T 12456371 51408593 93730043 300 14630 PCMTD1 0 . GRCh38 8 51861115 51861115 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.37G>T p.Asp13Tyr p.D13Y ENST00000360540 3/7 208 148 60 139 139 0 strelka-varscan-mutect PCMTD1,missense_variant,p.Asp13Tyr,ENST00000360540,NM_052937.3;PCMTD1,missense_variant,p.Asp13Tyr,ENST00000521344,;PCMTD1,missense_variant,p.Asp13Tyr,ENST00000522514,;PCMTD1,intron_variant,,ENST00000544451,NM_001286782.1;PCMTD1,intron_variant,,ENST00000519559,;PCMTD1,non_coding_transcript_exon_variant,,ENST00000521046,;PCMTD1,upstream_gene_variant,,ENST00000519975,; A ENST00000360540 Transcript missense_variant 444/4252 37/1074 13/357 D/Y Gac/Tac 1 -1 PCMTD1 HGNC HGNC:30483 protein_coding YES CCDS6148.1 ENSP00000353739 Q96MG8 UPI0000047CC0 NM_052937.3 deleterious(0) 3/7 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF4 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 51861115 51861115 C A 1 0 0 0 0 1 0 0 0 11674 826 29 2 2 PCMTD1 8 51861115 Missense_Mutation SNP C C3N-00547_T 452522 51861115 93277521 301 14631 RP1 0 . GRCh38 8 54630045 54630045 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.6163A>T p.Ser2055Cys p.S2055C ENST00000220676 4/4 440 291 149 572 572 0 strelka-varscan-mutect RP1,missense_variant,p.Ser2055Cys,ENST00000220676,NM_006269.1;RP1,intron_variant,,ENST00000637698,;RP1,intron_variant,,ENST00000636932,; T ENST00000220676 Transcript missense_variant 6311/7100 6163/6471 2055/2156 S/C Agc/Tgc 1 1 RP1 HGNC HGNC:10263 protein_coding YES CCDS6160.1 ENSP00000220676 P56715 UPI000013455B NM_006269.1 tolerated(0.06) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 54630045 54630045 A T 1 0 0 0 0 1 0 0 0 13709 188 7 4 4 RP1 8 54630045 Missense_Mutation SNP A C3N-00547_T 2768930 54630045 90508591 302 14632 TRPA1 0 . GRCh38 8 72057749 72057749 + Missense_Mutation SNP G G T rs764839830 C3N-00547_T C3N-00547_N G G c.1061C>A p.Ser354Tyr p.S354Y ENST00000262209 9/27 431 408 23 355 355 0 strelka-varscan-mutect TRPA1,missense_variant,p.Ser354Tyr,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Ser206Tyr,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,downstream_gene_variant,,ENST00000457356,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;TRPA1,upstream_gene_variant,,ENST00000520788,; T ENST00000262209 Transcript missense_variant 1269/5223 1061/3360 354/1119 S/Y tCt/tAt rs764839830,COSM1101514,COSM4865571 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 9/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248,Superfamily_domains:SSF48403 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs764839830 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 72057749 72057749 G T 1 0 0 0 0 1 0 0 0 17082 942 33 2 2 TRPA1 8 72057749 Missense_Mutation SNP G C3N-00547_T 17427704 72057749 73080887 303 14633 ZFHX4 0 . GRCh38 8 76707951 76707951 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.2996T>A p.Leu999Gln p.L999Q ENST00000521891 3/11 275 235 40 241 241 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Leu999Gln,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Leu973Gln,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript missense_variant 3444/14019 2996/10851 999/3616 L/Q cTa/cAa 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 3/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 76707951 76707951 T A 1 0 0 0 0 1 0 0 0 18213 1522 53 4 4 ZFHX4 8 76707951 Missense_Mutation SNP T C3N-00547_T 4650202 76707951 68430685 304 14634 ZFHX4 0 . GRCh38 8 76855352 76855352 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.8431A>T p.Ser2811Cys p.S2811C ENST00000521891 10/11 287 146 141 239 239 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Ser2811Cys,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Ser2785Cys,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; T ENST00000521891 Transcript missense_variant 8879/14019 8431/10851 2811/3616 S/C Agt/Tgt 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 76855352 76855352 A T 1 0 0 0 0 1 0 0 0 18213 188 7 4 4 ZFHX4 8 76855352 Missense_Mutation SNP A C3N-00547_T 147401 76855352 68283284 305 14635 C8orf59 0 . GRCh38 8 85217286 85217286 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.121C>A p.His41Asn p.H41N ENST00000321777 4/4 194 182 12 126 126 0 strelka-mutect C8orf59,missense_variant,p.His41Asn,ENST00000321777,;C8orf59,intron_variant,,ENST00000619594,NM_001099673.2;C8orf59,intron_variant,,ENST00000523281,;C8orf59,intron_variant,,ENST00000614462,NM_001293320.1;C8orf59,intron_variant,,ENST00000612977,NM_001099671.2,NM_001099670.2;C8orf59,intron_variant,,ENST00000611854,;C8orf59,intron_variant,,ENST00000545322,;C8orf59,intron_variant,,ENST00000615697,;C8orf59,intron_variant,,ENST00000612809,NM_001099672.2;E2F5,downstream_gene_variant,,ENST00000418930,NM_001083588.1;E2F5,downstream_gene_variant,,ENST00000416274,NM_001951.3;E2F5,downstream_gene_variant,,ENST00000521429,;E2F5,downstream_gene_variant,,ENST00000517476,NM_001083589.1;E2F5,downstream_gene_variant,,ENST00000518234,;E2F5,downstream_gene_variant,,ENST00000520225,;CA13,upstream_gene_variant,,ENST00000517298,;CA13,upstream_gene_variant,,ENST00000517831,;CA13,upstream_gene_variant,,ENST00000522631,;C8orf59,non_coding_transcript_exon_variant,,ENST00000523245,;E2F5,downstream_gene_variant,,ENST00000256117,;C8orf59,downstream_gene_variant,,ENST00000518786,;C8orf59,downstream_gene_variant,,ENST00000521286,;C8orf59,upstream_gene_variant,,ENST00000615071,; T ENST00000321777 Transcript missense_variant 199/325 121/132 41/43 H/N Cat/Aat 1 -1 C8orf59 HGNC HGNC:32235 protein_coding ENSP00000319020 Q8N0T1 UPI000006F8D5 tolerated_low_confidence(0.29) 4/4 MODERATE SNV 1 1 PASS rs1425055245 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 85217286 85217286 G T 1 0 0 0 0 1 0 0 0 2162 1290 45 2 2 C8orf59 8 85217286 Missense_Mutation SNP G C3N-00547_T 8361934 85217286 59921350 306 14636 SLC7A13 0 . GRCh38 8 86229696 86229696 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.582G>T p.Gln194His p.Q194H ENST00000297524 1/4 290 144 146 231 231 0 strelka-varscan-mutect SLC7A13,missense_variant,p.Gln194His,ENST00000297524,NM_138817.2;SLC7A13,missense_variant,p.Gln194His,ENST00000419776,;SLC7A13,intron_variant,,ENST00000520624,; A ENST00000297524 Transcript missense_variant 686/1878 582/1413 194/470 Q/H caG/caT 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 deleterious(0.03) 1/4 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 86229696 86229696 C A 1 0 0 0 0 1 0 0 0 14978 912 32 2 2 SLC7A13 8 86229696 Missense_Mutation SNP C C3N-00547_T 1012410 86229696 58908940 307 14637 GEM 0 . GRCh38 8 94250501 94250501 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.700G>T p.Gly234Cys p.G234C ENST00000297596 5/5 351 193 158 282 282 0 strelka-varscan-mutect GEM,missense_variant,p.Gly234Cys,ENST00000297596,NM_005261.3;GEM,missense_variant,p.Gly234Cys,ENST00000396194,NM_181702.2; A ENST00000297596 Transcript missense_variant 965/2208 700/891 234/296 G/C Ggc/Tgc 1 -1 GEM HGNC HGNC:4234 protein_coding YES CCDS6261.1 ENSP00000297596 P55040 A0A024R9F5 UPI000012B3BC NM_005261.3 deleterious(0) 5/5 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF192,Pfam_domain:PF00071,Gene3D:3.40.50.300,PIRSF_domain:PIRSF038017,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 94250501 94250501 C A 1 0 0 0 0 1 0 0 0 6202 623 22 2 2 GEM 8 94250501 Missense_Mutation SNP C C3N-00547_T 8020805 94250501 50888135 308 14638 VPS13B 0 . GRCh38 8 99779024 99779024 + Frame_Shift_Del DEL G G - novel C3N-00547_T C3N-00547_N G G c.7848delG p.Trp2616CysfsTer9 p.W2616Cfs*9 ENST00000358544 42/62 321 165 156 264 264 0 sindel-varindel-pindel VPS13B,frameshift_variant,p.Trp2616CysfsTer9,ENST00000358544,NM_017890.4;VPS13B,frameshift_variant,p.Trp2591CysfsTer9,ENST00000357162,NM_152564.4;VPS13B,downstream_gene_variant,,ENST00000518569,; - ENST00000358544 Transcript frameshift_variant 7958/14094 7847/12069 2616/4022 W/X tGg/tg 1 1 VPS13B HGNC HGNC:2183 protein_coding YES CCDS6280.1 ENSP00000351346 Q7Z7G8 UPI00001D2D35 NM_017890.4 42/62 hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 99779024 99779024 G - 1 0 1 0 1 0 0 0 0 17737 1357 47 0 0 VPS13B 8 99779024 Frame_Shift_Del DEL G C3N-00547_T 5528523 99779024 45359612 309 14639 RGS22 0 . GRCh38 8 100052802 100052802 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.1689G>T p.Gln563His p.Q563H ENST00000360863 10/28 169 157 12 91 90 1 strelka-varscan-mutect RGS22,missense_variant,p.Gln563His,ENST00000360863,NM_015668.4;RGS22,missense_variant,p.Gln551His,ENST00000617334,;RGS22,missense_variant,p.Gln382His,ENST00000523287,NM_001286693.1;RGS22,missense_variant,p.Gln551His,ENST00000523437,NM_001286692.1;RGS22,intron_variant,,ENST00000517828,;RGS22,upstream_gene_variant,,ENST00000524182,;RGS22,splice_region_variant,,ENST00000519725,;RGS22,splice_region_variant,,ENST00000520923,; A ENST00000360863 Transcript missense_variant,splice_region_variant 1884/4296 1689/3795 563/1264 Q/H caG/caT COSM5234924,COSM5234925 1 -1 RGS22 HGNC HGNC:24499 protein_coding YES CCDS43758.1 ENSP00000354109 Q8NE09 UPI0000E5AF25 NM_015668.4 tolerated(0.21) 10/28 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF177 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 100052802 100052802 C A 1 0 0 0 0 1 0 0 0 13476 695 24 2 2 RGS22 8 100052802 Missense_Mutation SNP C C3N-00547_T 273778 100052802 45085834 310 14640 NCALD 0 . GRCh38 8 101692812 101692812 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.463C>A p.Gln155Lys p.Q155K ENST00000395923 5/6 303 268 35 238 238 0 strelka-varscan-mutect NCALD,missense_variant,p.Gln155Lys,ENST00000395923,NM_001040630.1;NCALD,missense_variant,p.Gln155Lys,ENST00000311028,NM_001040627.1,NM_001040629.1,NM_001040624.1,NM_001040626.1;NCALD,missense_variant,p.Gln155Lys,ENST00000220931,NM_032041.2;NCALD,missense_variant,p.Gln155Lys,ENST00000521599,NM_001040628.1,NM_001040625.1;NCALD,missense_variant,p.Gln155Lys,ENST00000519508,;NCALD,missense_variant,p.Gln155Lys,ENST00000522951,;NCALD,intron_variant,,ENST00000522448,;NCALD,downstream_gene_variant,,ENST00000520690,;KB-1107E3.1,downstream_gene_variant,,ENST00000518749,;NCALD,non_coding_transcript_exon_variant,,ENST00000522754,; T ENST00000395923 Transcript missense_variant 923/3808 463/582 155/193 Q/K Cag/Aag 1 -1 NCALD HGNC HGNC:7655 protein_coding YES CCDS6292.1 ENSP00000379256 P61601 B2RB70 UPI0000004090 NM_001040630.1 tolerated(0.73) 5/6 Gene3D:1.10.238.10,Pfam_domain:PF13499,PROSITE_profiles:PS50222,hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF87,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 101692812 101692812 G T 1 0 0 0 0 1 0 0 0 10217 1357 47 2 2 NCALD 8 101692812 Missense_Mutation SNP G C3N-00547_T 1640010 101692812 43445824 311 14641 SLC25A32 0 . GRCh38 8 103403290 103403290 + Missense_Mutation SNP C C G rs778230086 C3N-00547_T C3N-00547_N C C c.426G>C p.Trp142Cys p.W142C ENST00000297578 4/7 168 140 28 104 104 0 strelka-varscan-mutect SLC25A32,missense_variant,p.Trp142Cys,ENST00000297578,NM_030780.4;SLC25A32,upstream_gene_variant,,ENST00000523701,;SLC25A32,missense_variant,p.Gly114Arg,ENST00000523866,;SLC25A32,intron_variant,,ENST00000521645,;SLC25A32,intron_variant,,ENST00000523256,; G ENST00000297578 Transcript missense_variant 593/2891 426/948 142/315 W/C tgG/tgC rs778230086 1 -1 SLC25A32 HGNC HGNC:29683 protein_coding YES CCDS6300.1 ENSP00000297578 Q9H2D1 A0A024R9D0 UPI0000040C0F NM_030780.4 deleterious(0) 4/7 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF62 MODERATE 1 SNV 1 1 PASS rs778230086 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 103403290 103403290 C G 1 0 0 0 0 1 0 0 0 14761 624 22 4 4 SLC25A32 8 103403290 Missense_Mutation SNP C C3N-00547_T 1710478 103403290 41735346 312 14642 ZFPM2 0 . GRCh38 8 105802569 105802569 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.2487C>A p.= p.P829P ENST00000407775 8/8 641 293 348 430 430 0 strelka-varscan-mutect ZFPM2,synonymous_variant,p.=,ENST00000407775,NM_012082.3;ZFPM2,synonymous_variant,p.=,ENST00000520492,;ZFPM2,synonymous_variant,p.=,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; A ENST00000407775 Transcript synonymous_variant 2737/4700 2487/3456 829/1151 P ccC/ccA 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 105802569 105802569 C A 1 0 0 0 0 0 0 0 1 18236 581 21 2 2 ZFPM2 8 105802569 Silent SNP C C3N-00547_T 2399279 105802569 39336067 313 14643 CSMD3 0 . GRCh38 8 112301905 112301905 + Silent SNP T T A rs764146300 C3N-00547_T C3N-00547_N T T c.8328A>T p.= p.S2776S ENST00000297405 53/71 385 256 129 344 344 0 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,; A ENST00000297405 Transcript synonymous_variant 8573/13212 8328/11124 2776/3707 S tcA/tcT rs764146300 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 53/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS rs764146300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 112301905 112301905 T A 1 0 0 0 0 0 0 0 1 3747 1451 51 4 4 CSMD3 8 112301905 Silent SNP T C3N-00547_T 6499336 112301905 32836731 314 14644 CSMD3 0 . GRCh38 8 112406674 112406674 + Missense_Mutation SNP C C G rs149542393 C3N-00547_T C3N-00547_N C C c.5659G>C p.Gly1887Arg p.G1887R ENST00000297405 35/71 297 155 142 258 258 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gly1887Arg,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly1847Arg,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly1783Arg,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gly1157Arg,ENST00000339701,; G ENST00000297405 Transcript missense_variant 5904/13212 5659/11124 1887/3707 G/R Gga/Cga rs149542393 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 35/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs149542393 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 112406674 112406674 C G 1 0 0 0 0 1 0 0 0 3747 661 23 4 4 CSMD3 8 112406674 Missense_Mutation SNP C C3N-00547_T 104769 112406674 32731962 315 14645 CSMD3 0 . GRCh38 8 112975972 112975972 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.1207A>C p.Asn403His p.N403H ENST00000297405 7/71 382 342 40 345 345 0 strelka-varscan-mutect CSMD3,missense_variant,p.Asn403His,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Asn363His,ENST00000343508,NM_198124.1;CSMD3,intron_variant,,ENST00000455883,NM_052900.2; G ENST00000297405 Transcript missense_variant 1452/13212 1207/11124 403/3707 N/H Aat/Cat 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated_low_confidence(0.55) 7/71 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 112975972 112975972 T G 1 0 0 0 0 1 0 0 0 3747 1841 64 5 5 CSMD3 8 112975972 Missense_Mutation SNP T C3N-00547_T 569298 112975972 32162664 316 14646 SNTB1 0 . GRCh38 8 120538913 120538913 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.1581G>T p.= p.L527L ENST00000395601 8/8 152 143 9 128 128 0 strelka-varscan-mutect SNTB1,synonymous_variant,p.=,ENST00000395601,NM_021021.3;SNTB1,synonymous_variant,p.=,ENST00000517992,;MTBP,intron_variant,,ENST00000519841,;MTBP,intron_variant,,ENST00000519556,; A ENST00000395601 Transcript synonymous_variant 1996/5164 1581/1617 527/538 L ctG/ctT 1 -1 SNTB1 HGNC HGNC:11168 protein_coding YES CCDS6334.1 ENSP00000378965 Q13884 UPI0000135B20 NM_021021.3 8/8 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF11 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 120538913 120538913 C A 1 0 0 0 0 0 0 0 1 15192 465 17 2 2 SNTB1 8 120538913 Silent SNP C C3N-00547_T 7562941 120538913 24599723 317 14647 ZHX1 0 . GRCh38 8 123253679 123253679 + Silent SNP C C A rs149228659 C3N-00547_T C3N-00547_N C C c.2268G>T p.= p.P756P ENST00000297857 3/4 215 185 30 177 177 0 strelka-varscan-mutect ZHX1,synonymous_variant,p.=,ENST00000297857,NM_001017926.2;ZHX1,synonymous_variant,p.=,ENST00000395571,NM_007222.4;ZHX1,synonymous_variant,p.=,ENST00000522655,;ZHX1-C8orf76,intron_variant,,ENST00000357082,NM_001204180.1;ZHX1-C8orf76,intron_variant,,ENST00000622816,;ZHX1,upstream_gene_variant,,ENST00000602651,;ZHX1,intron_variant,,ENST00000517516,;ZHX1,downstream_gene_variant,,ENST00000522595,;ZHX1,downstream_gene_variant,,ENST00000524267,;ZHX1,downstream_gene_variant,,ENST00000480132,; A ENST00000297857 Transcript synonymous_variant 2973/5200 2268/2622 756/873 P ccG/ccT rs149228659 1 -1 ZHX1 HGNC HGNC:12871 protein_coding YES CCDS6342.1 ENSP00000297857 Q9UKY1 A0A024R9F1 UPI000007404F NM_001017926.2 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15467,hmmpanther:PTHR15467:SF4 LOW SNV 5 1 PASS rs149228659 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 123253679 123253679 C A 1 0 0 0 0 0 0 0 1 18254 755 27 1 1 ZHX1 8 123253679 Silent SNP C C3N-00547_T 2714766 123253679 21884957 318 14648 FER1L6 0 . GRCh38 8 124061895 124061895 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.3191G>T p.Cys1064Phe p.C1064F ENST00000522917 25/41 279 159 120 213 213 0 strelka-varscan-mutect FER1L6,missense_variant,p.Cys1064Phe,ENST00000522917,NM_001039112.2;FER1L6-AS2,intron_variant,,ENST00000520031,; T ENST00000522917 Transcript missense_variant 3397/6051 3191/5574 1064/1857 C/F tGc/tTc 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 tolerated(0.08) 25/41 hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546,Pfam_domain:PF00168,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 124061895 124061895 G T 1 0 0 0 0 1 0 0 0 5678 1319 46 2 2 FER1L6 8 124061895 Missense_Mutation SNP G C3N-00547_T 808216 124061895 21076741 319 14649 TRMT12 0 . GRCh38 8 124451293 124451293 + Nonsense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.366G>A p.Trp122Ter p.W122* ENST00000328599 1/1 309 275 34 197 197 0 strelka-varscan-mutect TRMT12,stop_gained,p.Trp122Ter,ENST00000328599,NM_017956.3;TRMT12,intron_variant,,ENST00000521443,;TRMT12,intron_variant,,ENST00000522518,; A ENST00000328599 Transcript stop_gained 474/2207 366/1347 122/448 W/* tgG/tgA 1 1 TRMT12 HGNC HGNC:26091 protein_coding YES CCDS6349.1 ENSP00000329858 Q53H54 UPI0000140A61 NM_017956.3 1/1 hmmpanther:PTHR23245:SF25,hmmpanther:PTHR23245 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 124451293 124451293 G A 1 0 0 0 0 0 1 0 0 17066 1270 44 3 3 TRMT12 8 124451293 Nonsense_Mutation SNP G C3N-00547_T 389398 124451293 20687343 320 14650 HHLA1 0 . GRCh38 8 132095584 132095584 + Missense_Mutation SNP A A G rs759144068 C3N-00547_T C3N-00547_N A A c.491T>C p.Val164Ala p.V164A ENST00000434736 8/17 221 128 93 185 185 0 strelka-varscan-mutect HHLA1,missense_variant,p.Val128Ala,ENST00000414222,NM_001145095.1;HHLA1,missense_variant,p.Val164Ala,ENST00000434736,; G ENST00000434736 Transcript missense_variant 577/2369 491/1632 164/543 V/A gTa/gCa rs759144068 1 -1 HHLA1 HGNC HGNC:4904 protein_coding YES ENSP00000407107 C9JY47 UPI00021CEF49 deleterious(0) 8/17 hmmpanther:PTHR15299,hmmpanther:PTHR15299:SF3 MODERATE 1 SNV 5 1 PASS rs759144068 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 132095584 132095584 A G 1 0 0 0 0 1 0 0 0 6980 391 14 5 5 HHLA1 8 132095584 Missense_Mutation SNP A C3N-00547_T 7644291 132095584 13043052 321 14651 FAM135B 0 . GRCh38 8 138310849 138310849 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.149G>T p.Gly50Val p.G50V ENST00000395297 3/20 168 158 10 192 192 0 strelka-mutect FAM135B,missense_variant,p.Gly50Val,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Gly50Val,ENST00000520380,;FAM135B,missense_variant,p.Gly50Val,ENST00000160713,;FAM135B,non_coding_transcript_exon_variant,,ENST00000517849,;FAM135B,missense_variant,p.Gly50Val,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; A ENST00000395297 Transcript missense_variant 320/6962 149/4221 50/1406 G/V gGg/gTg 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0.01) 3/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 138310849 138310849 C A 1 0 0 0 0 1 0 0 0 5299 623 22 2 2 FAM135B 8 138310849 Missense_Mutation SNP C C3N-00547_T 6215265 138310849 6827787 322 14652 ARC 0 . GRCh38 8 142613777 142613777 + Nonsense_Mutation SNP G G T rs769666928 C3N-00547_T C3N-00547_N G G c.495C>A p.Tyr165Ter p.Y165* ENST00000356613 1/3 232 213 19 130 130 0 strelka-varscan-mutect ARC,stop_gained,p.Tyr165Ter,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; T ENST00000356613 Transcript stop_gained 696/2948 495/1191 165/396 Y/* taC/taA rs769666928 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 1/3 Prints_domain:PR02027,hmmpanther:PTHR15962 HIGH 1 SNV 1 1 PASS rs769666928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 142613777 142613777 G T 1 0 0 0 0 0 1 0 0 963 1140 40 1 1 ARC 8 142613777 Nonsense_Mutation SNP G C3N-00547_T 4302928 142613777 2524859 323 14653 ZNF517 0 . GRCh38 8 144803646 144803646 + Silent SNP G G A rs769619930 C3N-00547_T C3N-00547_N G G c.39G>A p.= p.A13A ENST00000359971 3/5 146 135 11 148 148 0 strelka-varscan-mutect ZNF517,synonymous_variant,p.=,ENST00000359971,NM_001317936.1,NM_213605.2;ZNF517,synonymous_variant,p.=,ENST00000531720,;ZNF517,synonymous_variant,p.=,ENST00000525105,;ZNF517,synonymous_variant,p.=,ENST00000528012,;ZNF517,intron_variant,,ENST00000529429,;ZNF517,intron_variant,,ENST00000526178,;ZNF517,synonymous_variant,p.=,ENST00000533965,;ZNF517,non_coding_transcript_exon_variant,,ENST00000530879,; A ENST00000359971 Transcript synonymous_variant 146/2335 39/1479 13/492 A gcG/gcA rs769619930 1 1 ZNF517 HGNC HGNC:27984 protein_coding YES CCDS6434.1 ENSP00000353058 Q6ZMY9 UPI000045770F NM_001317936.1,NM_213605.2 3/5 Superfamily_domains:0044637,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF20 LOW 1 SNV 4 1 PASS rs769619930 . 0 206 4 0 0 0 0 0 -19.91173 1 1 1 1 0 A 2 1 49 144803646 144803646 G A 1 0 0 0 0 0 0 0 1 18533 1130 39 1 1 ZNF517 8 144803646 Silent SNP G C3N-00547_T 2189869 144803646 334990 324 14654 DMRT3 0 . GRCh38 9 990504 990504 + Silent SNP G G A C3N-00547_T C3N-00547_N G G c.918G>A p.= p.A306A ENST00000190165 2/2 221 200 21 254 254 0 strelka-varscan-mutect DMRT3,synonymous_variant,p.=,ENST00000190165,NM_021240.3;DMRT3,downstream_gene_variant,,ENST00000417254,; A ENST00000190165 Transcript synonymous_variant 956/2183 918/1419 306/472 A gcG/gcA COSM1111589 1 1 DMRT3 HGNC HGNC:13909 protein_coding YES CCDS6443.1 ENSP00000190165 Q9NQL9 UPI0000073634 NM_021240.3 2/2 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF73 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 990504 990504 G A 1 0 0 0 0 0 0 0 1 4394 1132 40 1 1 DMRT3 9 990504 Silent SNP G C3N-00547_T 990504 137404213 325 14655 PTPRD 0 . GRCh38 9 8341695 8341695 + Nonsense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.4945A>T p.Lys1649Ter p.K1649* ENST00000381196 37/43 86 71 15 83 83 0 strelka-varscan-mutect PTPRD,stop_gained,p.Lys1649Ter,ENST00000381196,NM_002839.3;PTPRD,stop_gained,p.Lys1649Ter,ENST00000356435,;PTPRD,stop_gained,p.Lys1243Ter,ENST00000355233,NM_130392.3;PTPRD,stop_gained,p.Lys1242Ter,ENST00000397617,;PTPRD,stop_gained,p.Lys1239Ter,ENST00000397611,NM_001040712.2;PTPRD,stop_gained,p.Lys1233Ter,ENST00000537002,NM_130393.3;PTPRD,stop_gained,p.Lys1649Ter,ENST00000540109,;PTPRD,stop_gained,p.Lys1242Ter,ENST00000486161,NM_130391.3;PTPRD,stop_gained,p.Lys1242Ter,ENST00000397606,NM_001171025.1; A ENST00000381196 Transcript stop_gained,splice_region_variant 5489/9911 4945/5739 1649/1912 K/* Aag/Tag 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 37/43 Gene3D:3.90.190.10,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799,Superfamily_domains:SSF52799 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 8341695 8341695 T A 1 0 0 0 0 0 1 0 0 12953 1768 61 4 4 PTPRD 9 8341695 Nonsense_Mutation SNP T C3N-00547_T 7351191 8341695 130053022 326 14656 PTPRD 0 . GRCh38 9 8518010 8518010 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1381C>A p.Gln461Lys p.Q461K ENST00000381196 18/43 264 183 81 277 277 0 strelka-varscan-mutect PTPRD,missense_variant,p.Gln461Lys,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Gln461Lys,ENST00000356435,;PTPRD,missense_variant,p.Gln461Lys,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Gln451Lys,ENST00000397617,;PTPRD,missense_variant,p.Gln458Lys,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Gln455Lys,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Gln461Lys,ENST00000540109,;PTPRD,missense_variant,p.Gln461Lys,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Gln451Lys,ENST00000397606,NM_001171025.1; T ENST00000381196 Transcript missense_variant 1925/9911 1381/5739 461/1912 Q/K Caa/Aaa 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 tolerated(0.77) 18/43 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 8518010 8518010 G T 1 0 0 0 0 1 0 0 0 12953 1299 45 2 2 PTPRD 9 8518010 Missense_Mutation SNP G C3N-00547_T 176315 8518010 129876707 327 14657 PTPRD 0 . GRCh38 9 8633395 8633395 + Missense_Mutation SNP C C T C3N-00547_T C3N-00547_N C C c.274G>A p.Asp92Asn p.D92N ENST00000381196 11/43 130 94 36 194 194 0 strelka-varscan-mutect PTPRD,missense_variant,p.Asp92Asn,ENST00000381196,NM_002839.3;PTPRD,missense_variant,p.Asp92Asn,ENST00000356435,;PTPRD,missense_variant,p.Asp92Asn,ENST00000355233,NM_130392.3;PTPRD,missense_variant,p.Asp92Asn,ENST00000397617,;PTPRD,missense_variant,p.Asp92Asn,ENST00000397611,NM_001040712.2;PTPRD,missense_variant,p.Asp92Asn,ENST00000537002,NM_130393.3;PTPRD,missense_variant,p.Asp92Asn,ENST00000540109,;PTPRD,missense_variant,p.Asp92Asn,ENST00000486161,NM_130391.3;PTPRD,missense_variant,p.Asp92Asn,ENST00000397606,NM_001171025.1;PTPRD,missense_variant,p.Asp92Asn,ENST00000463477,;PTPRD,missense_variant,p.Asp92Asn,ENST00000481079,;PTPRD,non_coding_transcript_exon_variant,,ENST00000488774,; T ENST00000381196 Transcript missense_variant 818/9911 274/5739 92/1912 D/N Gat/Aat COSM3780139,COSM3780140,COSM3780141,COSM3780142,COSM3780143,COSM3780144 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 deleterious(0) 11/43 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 8633395 8633395 C T 1 0 0 0 0 1 0 0 0 12953 855 30 3 3 PTPRD 9 8633395 Missense_Mutation SNP C C3N-00547_T 115385 8633395 129761322 328 14658 GALT 0 . GRCh38 9 34647895 34647895 + Silent SNP C C T C3N-00547_T C3N-00547_N C C c.441C>T p.= p.I147I ENST00000378842 5/11 458 372 86 542 542 0 strelka-varscan-mutect GALT,synonymous_variant,p.=,ENST00000378842,NM_000155.3;GALT,synonymous_variant,p.=,ENST00000450095,NM_001258332.1;RP11-195F19.29,intron_variant,,ENST00000556278,;IL11RA,upstream_gene_variant,,ENST00000555003,;IL11RA,upstream_gene_variant,,ENST00000441545,NM_001142784.2;IL11RA,upstream_gene_variant,,ENST00000553620,;GALT,non_coding_transcript_exon_variant,,ENST00000557541,;GALT,upstream_gene_variant,,ENST00000488412,;GALT,3_prime_UTR_variant,,ENST00000554550,;GALT,3_prime_UTR_variant,,ENST00000554085,;GALT,3_prime_UTR_variant,,ENST00000473506,;GALT,3_prime_UTR_variant,,ENST00000556244,;GALT,3_prime_UTR_variant,,ENST00000554897,;GALT,non_coding_transcript_exon_variant,,ENST00000555020,;GALT,non_coding_transcript_exon_variant,,ENST00000557706,;GALT,non_coding_transcript_exon_variant,,ENST00000554638,;GALT,non_coding_transcript_exon_variant,,ENST00000487381,;GALT,non_coding_transcript_exon_variant,,ENST00000485531,;GALT,non_coding_transcript_exon_variant,,ENST00000555086,;GALT,non_coding_transcript_exon_variant,,ENST00000472111,;GALT,non_coding_transcript_exon_variant,,ENST00000554944,;GALT,non_coding_transcript_exon_variant,,ENST00000473529,;GALT,non_coding_transcript_exon_variant,,ENST00000465543,;GALT,non_coding_transcript_exon_variant,,ENST00000556494,;GALT,non_coding_transcript_exon_variant,,ENST00000554139,;GALT,intron_variant,,ENST00000489643,;GALT,intron_variant,,ENST00000555214,;IL11RA,upstream_gene_variant,,ENST00000555247,;GALT,upstream_gene_variant,,ENST00000555754,;GALT,downstream_gene_variant,,ENST00000605275,;GALT,downstream_gene_variant,,ENST00000556403,;GALT,downstream_gene_variant,,ENST00000554330,;GALT,downstream_gene_variant,,ENST00000556157,;GALT,downstream_gene_variant,,ENST00000468099,; T ENST00000378842 Transcript synonymous_variant 483/1768 441/1140 147/379 I atC/atT COSM3657057 1 1 GALT HGNC HGNC:4135 protein_coding YES CCDS6565.1 ENSP00000368119 P07902 A0A0S2Z3Y7 UPI000012B073 NM_000155.3 5/11 Gene3D:3.30.428.10,Pfam_domain:PF01087,PIRSF_domain:PIRSF000808,hmmpanther:PTHR11943,hmmpanther:PTHR11943:SF1,Superfamily_domains:SSF54197,TIGRFAM_domain:TIGR00209 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 34647895 34647895 C T 1 0 0 0 0 0 0 0 1 6098 845 30 3 3 GALT 9 34647895 Silent SNP C C3N-00547_T 26014500 34647895 103746822 329 14659 GLIPR2 0 . GRCh38 9 36150883 36150883 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.238G>T p.Ala80Ser p.A80S ENST00000377960 4/5 86 73 13 96 96 0 strelka-varscan-mutect GLIPR2,missense_variant,p.Ala80Ser,ENST00000377960,NM_001287013.1,NM_022343.3,NM_001287011.1;GLIPR2,intron_variant,,ENST00000396613,NM_001287012.1;GLIPR2,intron_variant,,ENST00000619700,NM_001287014.1;GLIPR2,intron_variant,,ENST00000377959,NM_001287010.1;GLIPR2,non_coding_transcript_exon_variant,,ENST00000474050,; T ENST00000377960 Transcript missense_variant 272/1890 238/465 80/154 A/S Gct/Tct 1 1 GLIPR2 HGNC HGNC:18007 protein_coding YES CCDS6598.1 ENSP00000367196 Q9H4G4 UPI000006DF50 NM_001287013.1,NM_022343.3,NM_001287011.1 tolerated(0.13) 4/5 Gene3D:3.40.33.10,Pfam_domain:PF00188,Prints_domain:PR00837,hmmpanther:PTHR10334,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 49 36150883 36150883 G T 1 0 0 0 0 1 0 0 0 6322 1203 42 2 2 GLIPR2 9 36150883 Missense_Mutation SNP G C3N-00547_T 1502988 36150883 102243834 330 14660 CLTA 0 . GRCh38 9 36191188 36191188 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.132G>T p.= p.A44A ENST00000242285 1/7 149 117 32 191 191 0 strelka-varscan-mutect CLTA,synonymous_variant,p.=,ENST00000433436,;CLTA,synonymous_variant,p.=,ENST00000538225,;CLTA,synonymous_variant,p.=,ENST00000242285,NM_007096.3;CLTA,synonymous_variant,p.=,ENST00000470744,NM_001184760.1;CLTA,synonymous_variant,p.=,ENST00000396603,NM_001076677.2;CLTA,synonymous_variant,p.=,ENST00000345519,NM_001833.3,NM_001184761.1;CLTA,synonymous_variant,p.=,ENST00000540080,NM_001184762.1;CLTA,synonymous_variant,p.=,ENST00000466396,;CLTA,synonymous_variant,p.=,ENST00000464497,;CLTA,synonymous_variant,p.=,ENST00000493185,; T ENST00000242285 Transcript synonymous_variant 252/1152 132/747 44/248 A gcG/gcT 1 1 CLTA HGNC HGNC:2090 protein_coding YES CCDS6601.1 ENSP00000242285 P09496 UPI0000127A9E NM_007096.3 1/7 Pfam_domain:PF01086,hmmpanther:PTHR10639,hmmpanther:PTHR10639:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 36191188 36191188 G T 1 0 0 0 0 0 0 0 1 3336 1103 39 1 1 CLTA 9 36191188 Silent SNP G C3N-00547_T 40305 36191188 102203529 331 14661 DCAF10 0 . GRCh38 9 37801281 37801281 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.415G>C p.Asp139His p.D139H ENST00000377724 1/7 114 90 24 164 164 0 strelka-varscan-mutect DCAF10,missense_variant,p.Asp139His,ENST00000377724,NM_024345.4;DCAF10,intron_variant,,ENST00000242323,NM_001286810.1;EXOSC3,intron_variant,,ENST00000482614,;EXOSC3,upstream_gene_variant,,ENST00000489414,;RP11-613M10.9,intron_variant,,ENST00000540557,; C ENST00000377724 Transcript missense_variant 780/3862 415/1680 139/559 D/H Gac/Cac 1 1 DCAF10 HGNC HGNC:23686 protein_coding YES CCDS6613.2 ENSP00000366953 Q5QP82 UPI000046FD58 NM_024345.4 deleterious(0.04) 1/7 hmmpanther:PTHR14588:SF2,hmmpanther:PTHR14588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 37801281 37801281 G C 1 0 0 0 0 1 0 0 0 4062 1174 41 4 4 DCAF10 9 37801281 Missense_Mutation SNP G C3N-00547_T 1610093 37801281 100593436 332 14662 FOXD4L6 0 . GRCh38 9 41127475 41127475 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.909G>T p.Leu303Phe p.L303F ENST00000622588 1/1 75 59 16 110 109 1 strelka-varscan-mutect FOXD4L6,missense_variant,p.Leu303Phe,ENST00000622588,NM_001085476.1;CBWD7,downstream_gene_variant,,ENST00000613716,;CBWD7,downstream_gene_variant,,ENST00000377391,NM_001085457.1;CBWD7,downstream_gene_variant,,ENST00000456520,;CBWD7,downstream_gene_variant,,ENST00000613125,;CBWD7,downstream_gene_variant,,ENST00000617722,;CBWD7,downstream_gene_variant,,ENST00000610358,;CBWD7,downstream_gene_variant,,ENST00000622791,;CBWD7,downstream_gene_variant,,ENST00000457288,;CBWD7,downstream_gene_variant,,ENST00000617917,;CBWD7,downstream_gene_variant,,ENST00000611553,;CBWD7,downstream_gene_variant,,ENST00000486387,;CBWD7,downstream_gene_variant,,ENST00000494538,;CBWD7,downstream_gene_variant,,ENST00000382436,;FRG1HP,intron_variant,,ENST00000617940,; A ENST00000622588 Transcript missense_variant 989/2034 909/1254 303/417 L/F ttG/ttT 1 -1 FOXD4L6 HGNC HGNC:31986 protein_coding YES CCDS43826.1 ENSP00000484875 Q3SYB3 UPI0000519166 NM_001085476.1 tolerated_low_confidence(0.16) 1/1 hmmpanther:PTHR11829:SF149,hmmpanther:PTHR11829 MODERATE SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 41127475 41127475 C A 1 0 0 0 0 1 0 0 0 5864 593 21 2 2 FOXD4L6 9 41127475 Missense_Mutation SNP C C3N-00547_T 3326194 41127475 97267242 333 14663 CNTNAP3B 0 . GRCh38 9 41953244 41953244 + Silent SNP C C A rs531112058 C3N-00547_T C3N-00547_N C C c.2019G>T p.= p.A673A ENST00000377561 13/24 68 50 18 156 156 0 strelka-varscan-mutect CNTNAP3B,synonymous_variant,p.=,ENST00000612828,;CNTNAP3B,synonymous_variant,p.=,ENST00000377561,NM_001201380.2;CNTNAP3B,synonymous_variant,p.=,ENST00000341990,;CNTNAP3B,synonymous_variant,p.=,ENST00000617422,;CNTNAP3B,upstream_gene_variant,,ENST00000489789,;CNTNAP3B,synonymous_variant,p.=,ENST00000619138,;CNTNAP3B,synonymous_variant,p.=,ENST00000479351,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,; A ENST00000377561 Transcript synonymous_variant 2412/5379 2019/3867 673/1288 A gcG/gcT rs531112058 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 13/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605 LOW 1 SNV 1 1 PASS rs531112058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 41953244 41953244 C A 1 0 0 0 0 0 0 0 1 3430 639 23 1 1 CNTNAP3B 9 41953244 Silent SNP C C3N-00547_T 825769 41953244 96441473 334 14664 SPATA31A6 0 . GRCh38 9 42187773 42187773 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.2071G>A p.Gly691Arg p.G691R ENST00000332857 4/4 127 93 34 162 162 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Gly691Arg,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; A ENST00000332857 Transcript missense_variant 2100/4209 2071/4032 691/1343 G/R Ggg/Agg 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(0.3) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS . . 12 196 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 42187773 42187773 G A 1 0 0 0 0 1 0 0 0 15345 1232 43 3 3 SPATA31A6 9 42187773 Missense_Mutation SNP G C3N-00547_T 234529 42187773 96206944 335 14665 PRUNE2 0 . GRCh38 9 76711199 76711199 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1075G>T p.Glu359Ter p.E359* ENST00000376718 8/19 154 120 34 224 224 0 strelka-varscan-mutect PRUNE2,stop_gained,p.Glu359Ter,ENST00000376718,NM_015225.2;PRUNE2,stop_gained,p.Glu359Ter,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,5_prime_UTR_variant,,ENST00000428286,;PRUNE2,upstream_gene_variant,,ENST00000426088,; A ENST00000376718 Transcript stop_gained 1199/12584 1075/9267 359/3088 E/* Gag/Tag 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 8/19 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 76711199 76711199 C A 1 0 0 0 0 0 1 0 0 12791 922 32 2 2 PRUNE2 9 76711199 Nonsense_Mutation SNP C C3N-00547_T 34523426 76711199 61683518 336 14666 SPATA31D1 0 . GRCh38 9 81992578 81992578 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2108C>A p.Pro703His p.P703H ENST00000344803 4/4 498 393 105 754 753 1 strelka-varscan-mutect SPATA31D1,missense_variant,p.Pro703His,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; A ENST00000344803 Transcript missense_variant 2155/4833 2108/4731 703/1576 P/H cCc/cAc 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.06) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12,Pfam_domain:PF14650 MODERATE 1 SNV 2 1 PASS rs1460644826 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 81992578 81992578 C A 1 0 0 0 0 1 0 0 0 15347 623 22 2 2 SPATA31D1 9 81992578 Missense_Mutation SNP C C3N-00547_T 5281379 81992578 56402139 337 14667 NTRK2 0 . GRCh38 9 84745059 84745059 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.1282C>A p.= p.R428R ENST00000277120 11/19 452 370 82 530 530 0 strelka-varscan-mutect NTRK2,synonymous_variant,p.=,ENST00000277120,;NTRK2,synonymous_variant,p.=,ENST00000304053,NM_001018065.2;NTRK2,synonymous_variant,p.=,ENST00000376208,NM_001018066.2;NTRK2,synonymous_variant,p.=,ENST00000395882,NM_001291937.1,NM_001007097.2;NTRK2,synonymous_variant,p.=,ENST00000359847,;NTRK2,synonymous_variant,p.=,ENST00000376214,NM_006180.4;NTRK2,synonymous_variant,p.=,ENST00000376213,;NTRK2,synonymous_variant,p.=,ENST00000323115,NM_001018064.2; A ENST00000277120 Transcript synonymous_variant 1765/8633 1282/2517 428/838 R Cgg/Agg 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D 11/19 LOW 1 SNV 1 1 PASS rs958492686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 84745059 84745059 C A 1 0 0 0 0 0 0 0 1 10773 875 31 1 1 NTRK2 9 84745059 Silent SNP C C3N-00547_T 2752481 84745059 53649658 338 14668 ALDOB 0 . GRCh38 9 101427585 101427585 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.437G>T p.Gly146Val p.G146V ENST00000374855 5/9 460 365 95 565 565 0 strelka-varscan-mutect ALDOB,missense_variant,p.Gly146Val,ENST00000374855,NM_000035.3;ALDOB,missense_variant,p.Gly146Val,ENST00000616752,;ALDOB,intron_variant,,ENST00000468981,; A ENST00000374855 Transcript missense_variant 562/2451 437/1095 146/364 G/V gGg/gTg 1 -1 ALDOB HGNC HGNC:417 protein_coding YES CCDS6756.1 ENSP00000363988 P05062 A0A024R145 UPI000016A4A9 NM_000035.3 deleterious(0) 5/9 hmmpanther:PTHR11627,hmmpanther:PTHR11627:SF2,Gene3D:3.20.20.70,Pfam_domain:PF00274,Superfamily_domains:SSF51569 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 101427585 101427585 C A 1 0 0 0 0 1 0 0 0 608 623 22 2 2 ALDOB 9 101427585 Missense_Mutation SNP C C3N-00547_T 16682526 101427585 36967132 339 14669 GRIN3A 0 . GRCh38 9 101686803 101686803 + Missense_Mutation SNP C C A rs544327119 C3N-00547_T C3N-00547_N C C c.1097G>T p.Arg366Met p.R366M ENST00000361820 2/9 154 119 35 186 185 1 strelka-varscan-mutect GRIN3A,missense_variant,p.Arg366Met,ENST00000361820,NM_133445.2; A ENST00000361820 Transcript missense_variant 1698/7770 1097/3348 366/1115 R/M aGg/aTg rs544327119,COSM1208982 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 deleterious(0.03) 2/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF01094,Superfamily_domains:SSF53822 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs544327119 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 101686803 101686803 C A 1 0 0 0 0 1 0 0 0 6665 681 24 2 2 GRIN3A 9 101686803 Missense_Mutation SNP C C3N-00547_T 259218 101686803 36707914 340 14670 OR13C2 0 . GRCh38 9 104605082 104605082 + Silent SNP C C T rs78524552 C3N-00547_T C3N-00547_N C C c.546G>A p.= p.L182L ENST00000542196 1/1 146 120 26 187 187 0 strelka-varscan-mutect OR13C2,synonymous_variant,p.=,ENST00000542196,NM_001004481.1; T ENST00000542196 Transcript synonymous_variant 546/957 546/957 182/318 L ctG/ctA rs78524552,COSM3902720 1 -1 OR13C2 HGNC HGNC:14701 protein_coding YES CCDS35092.1 ENSP00000438815 Q8NGS9 A0A126GWR7 UPI0000041B29 NM_001004481.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF279,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 LOW 1 SNV 0,1 1 PASS rs78524552 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 104605082 104605082 C T 1 0 0 0 0 0 0 0 1 11010 581 21 3 3 OR13C2 9 104605082 Silent SNP C C3N-00547_T 2918279 104605082 33789635 341 14671 ACTL7B 0 . GRCh38 9 108855613 108855613 + Missense_Mutation SNP C C A rs780240990 C3N-00547_T C3N-00547_N C C c.318G>T p.Glu106Asp p.E106D ENST00000374667 1/1 275 224 51 344 344 0 strelka-varscan-mutect ACTL7B,missense_variant,p.Glu106Asp,ENST00000374667,NM_006686.3; A ENST00000374667 Transcript missense_variant 1355/2379 318/1248 106/415 E/D gaG/gaT rs780240990 1 -1 ACTL7B HGNC HGNC:162 protein_coding YES CCDS6771.1 ENSP00000363799 Q9Y614 A0A140VKC6 UPI0000125053 NM_006686.3 tolerated(0.06) 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF59,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 PASS rs780240990 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 108855613 108855613 C A 1 0 0 0 0 1 0 0 0 245 680 24 2 2 ACTL7B 9 108855613 Missense_Mutation SNP C C3N-00547_T 4250531 108855613 29539104 342 14672 EPB41L4B 0 . GRCh38 9 109243641 109243641 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1386G>T p.Trp462Cys p.W462C ENST00000374566 15/26 176 143 33 138 138 0 strelka-varscan-mutect EPB41L4B,missense_variant,p.Trp462Cys,ENST00000374566,NM_019114.4;EPB41L4B,missense_variant,p.Trp462Cys,ENST00000374557,NM_018424.3; A ENST00000374566 Transcript missense_variant 1904/5800 1386/2703 462/900 W/C tgG/tgT 1 -1 EPB41L4B HGNC HGNC:19818 protein_coding YES CCDS43859.1 ENSP00000363694 Q9H329 UPI0000458994 NM_019114.4 deleterious(0) 15/26 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF18 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 109243641 109243641 C A 1 0 0 0 0 1 0 0 0 5003 740 26 2 2 EPB41L4B 9 109243641 Missense_Mutation SNP C C3N-00547_T 388028 109243641 29151076 343 14673 PAPPA 0 . GRCh38 9 116187852 116187852 + Missense_Mutation SNP C C A rs144678054 C3N-00547_T C3N-00547_N C C c.1114C>A p.Arg372Ser p.R372S ENST00000328252 2/22 331 268 63 325 324 1 strelka-varscan-mutect PAPPA,missense_variant,p.Arg372Ser,ENST00000328252,NM_002581.3; A ENST00000328252 Transcript missense_variant 1483/10959 1114/4884 372/1627 R/S Cgc/Agc rs144678054,COSM3321573 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 tolerated(0.21) 2/22 Gene3D:3.40.390.10,Superfamily_domains:SSF55486 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs144678054 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 116187852 116187852 C A 1 0 0 0 0 1 0 0 0 11512 768 27 1 1 PAPPA 9 116187852 Missense_Mutation SNP C C3N-00547_T 6944211 116187852 22206865 344 14674 TLR4 0 . GRCh38 9 117713366 117713366 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.1238C>A p.Thr413Asn p.T413N ENST00000355622 3/3 238 197 41 265 264 1 strelka-varscan-mutect TLR4,missense_variant,p.Thr413Asn,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Thr373Asn,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; A ENST00000355622 Transcript missense_variant 1339/4844 1238/2520 413/839 T/N aCc/aAc COSM752872 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 tolerated(0.14) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,SMART_domains:SM00365,Superfamily_domains:SSF52047 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 117713366 117713366 C A 1 0 0 0 0 1 0 0 0 16399 507 18 2 2 TLR4 9 117713366 Missense_Mutation SNP C C3N-00547_T 1525514 117713366 20681351 345 14675 OR1Q1 0 . GRCh38 9 122614768 122614768 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.31C>A p.His11Asn p.H11N ENST00000297913 1/1 48 38 10 63 63 0 strelka-varscan-mutect OR1Q1,missense_variant,p.His11Asn,ENST00000297913,NM_012364.1;RP11-64P14.7,intron_variant,,ENST00000431442,;RP11-64P14.7,upstream_gene_variant,,ENST00000419604,; A ENST00000297913 Transcript missense_variant 31/945 31/945 11/314 H/N Cat/Aat 1 1 OR1Q1 HGNC HGNC:8223 protein_coding YES CCDS35125.1 ENSP00000297913 Q15612 UPI000003CACD NM_012364.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF92,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs920987819 . 0 201 9 0 0 0 0 0 -19.99995 0.9999967 1 1 1 0 A 3 1 49 122614768 122614768 C A 1 0 0 0 0 1 0 0 0 11049 594 21 2 2 OR1Q1 9 122614768 Missense_Mutation SNP C C3N-00547_T 4901402 122614768 15779949 346 14676 DENND1A 0 . GRCh38 9 123382450 123382450 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2012C>A p.Pro671His p.P671H ENST00000373624 22/22 77 58 19 127 127 0 strelka-varscan-mutect DENND1A,missense_variant,p.Pro671His,ENST00000373624,NM_020946.1;CRB2,downstream_gene_variant,,ENST00000373631,NM_173689.6;DENND1A,non_coding_transcript_exon_variant,,ENST00000473039,;CRB2,downstream_gene_variant,,ENST00000460253,; T ENST00000373624 Transcript missense_variant 2214/5010 2012/3030 671/1009 P/H cCt/cAt 1 -1 DENND1A HGNC HGNC:29324 protein_coding YES CCDS35133.1 ENSP00000362727 Q8TEH3 UPI00004589D2 NM_020946.1 deleterious(0.05) 22/22 hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF22 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 123382450 123382450 G T 1 0 0 0 0 1 0 0 0 4230 1000 35 2 2 DENND1A 9 123382450 Missense_Mutation SNP G C3N-00547_T 767682 123382450 15012267 347 14677 ZBTB34 0 . GRCh38 9 126879851 126879851 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.440G>T p.Ser147Ile p.S147I ENST00000373452 1/1 209 152 57 239 239 0 strelka-varscan-mutect ZBTB34,missense_variant,p.Ser151Ile,ENST00000319119,;ZBTB34,missense_variant,p.Ser147Ile,ENST00000373452,NM_001099270.1; T ENST00000373452 Transcript missense_variant 504/6528 440/1503 147/500 S/I aGt/aTt 1 1 ZBTB34 HGNC HGNC:31446 protein_coding YES CCDS48023.1 ENSP00000362551 Q8NCN2 UPI00004031FA NM_001099270.1 deleterious(0.01) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 126879851 126879851 G T 1 0 0 0 0 1 0 0 0 18106 1029 36 2 2 ZBTB34 9 126879851 Missense_Mutation SNP G C3N-00547_T 3497401 126879851 11514866 348 14678 HMCN2 0 . GRCh38 9 130405000 130405000 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.12220G>T p.Gly4074Cys p.G4074C ENST00000624552 81/98 99 69 30 104 104 0 strelka-varscan-mutect HMCN2,missense_variant,p.Gly4074Cys,ENST00000624552,NM_001291815.1;RN7SL665P,downstream_gene_variant,,ENST00000578793,;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,non_coding_transcript_exon_variant,,ENST00000480829,; T ENST00000624552 Transcript missense_variant 12220/15610 12220/15180 4074/5059 G/C Ggc/Tgc 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.02) 81/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.999979 1 1 1 0 T 3 4 49 130405000 130405000 G T 1 0 0 0 0 1 0 0 0 7112 1232 43 2 2 HMCN2 9 130405000 Missense_Mutation SNP G C3N-00547_T 3525149 130405000 7989717 349 14679 PRDM12 0 . GRCh38 9 130666647 130666647 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.263T>A p.Val88Glu p.V88E ENST00000253008 2/5 133 103 30 220 220 0 strelka-varscan-mutect PRDM12,missense_variant,p.Val88Glu,ENST00000253008,NM_021619.2; A ENST00000253008 Transcript missense_variant 323/2476 263/1104 88/367 V/E gTg/gAg 1 1 PRDM12 HGNC HGNC:13997 protein_coding YES CCDS6934.1 ENSP00000253008 Q9H4Q4 UPI0000132184 NM_021619.2 deleterious(0) 2/5 Gene3D:2.170.270.10,PIRSF_domain:PIRSF037163,PROSITE_profiles:PS50280,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 130666647 130666647 T A 1 0 0 0 0 1 0 0 0 12584 1696 59 4 4 PRDM12 9 130666647 Missense_Mutation SNP T C3N-00547_T 261647 130666647 7728070 350 14680 FCN1 0 . GRCh38 9 134914798 134914798 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.229C>A p.Leu77Ile p.L77I ENST00000371806 3/9 126 102 24 105 105 0 strelka-varscan-mutect FCN1,missense_variant,p.Leu77Ile,ENST00000616356,;FCN1,missense_variant,p.Leu77Ile,ENST00000371806,NM_002003.3; T ENST00000371806 Transcript missense_variant 321/1286 229/981 77/326 L/I Ctc/Atc 1 -1 FCN1 HGNC HGNC:3623 protein_coding YES CCDS6985.1 ENSP00000360871 O00602 UPI000012A5A7 NM_002003.3 tolerated(0.45) 3/9 Low_complexity_(Seg):seg,hmmpanther:PTHR19143:SF165,hmmpanther:PTHR19143,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 134914798 134914798 G T 1 0 0 0 0 1 0 0 0 5654 942 33 2 2 FCN1 9 134914798 Missense_Mutation SNP G C3N-00547_T 4248151 134914798 3479919 351 14681 EHMT1 0 . GRCh38 9 137834854 137834854 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.3798G>T p.= p.S1266S ENST00000460843 27/27 185 155 30 239 239 0 strelka-varscan-mutect EHMT1,synonymous_variant,p.=,ENST00000460843,NM_024757.4;EHMT1,synonymous_variant,p.=,ENST00000637161,;MIR602,upstream_gene_variant,,ENST00000384960,;EHMT1,non_coding_transcript_exon_variant,,ENST00000472849,;EHMT1,downstream_gene_variant,,ENST00000637287,;EHMT1,3_prime_UTR_variant,,ENST00000637891,;EHMT1,non_coding_transcript_exon_variant,,ENST00000475564,;EHMT1,non_coding_transcript_exon_variant,,ENST00000494249,;EHMT1,non_coding_transcript_exon_variant,,ENST00000637748,;EHMT1,non_coding_transcript_exon_variant,,ENST00000475704,;EHMT1,intron_variant,,ENST00000462942,;EHMT1,downstream_gene_variant,,ENST00000637261,; T ENST00000460843 Transcript synonymous_variant 3864/5137 3798/3897 1266/1298 S tcG/tcT 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 27/27 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs927268582 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 137834854 137834854 G T 1 0 0 0 0 0 0 0 1 4819 1045 37 1 1 EHMT1 9 137834854 Silent SNP G C3N-00547_T 2920056 137834854 559863 352 14682 TUBB8 0 . GRCh38 10 47665 47665 + Missense_Mutation SNP G G C C3N-00547_T C3N-00547_N G G c.727C>G p.Pro243Ala p.P243A ENST00000568584 4/4 236 181 55 227 227 0 strelka-varscan-mutect TUBB8,missense_variant,p.Pro209Ala,ENST00000564130,;TUBB8,missense_variant,p.Pro243Ala,ENST00000568584,NM_177987.2;TUBB8,missense_variant,p.Pro206Ala,ENST00000568866,;TUBB8,3_prime_UTR_variant,,ENST00000561967,;TUBB8,3_prime_UTR_variant,,ENST00000562809,;TUBB8,3_prime_UTR_variant,,ENST00000567466,;TUBB8,downstream_gene_variant,,ENST00000563456,;FAM166AP7,downstream_gene_variant,,ENST00000416477,; C ENST00000568584 Transcript missense_variant 1078/1790 727/1335 243/444 P/A Ccg/Gcg COSM3441492 1 -1 TUBB8 HGNC HGNC:20773 protein_coding YES CCDS7051.1 ENSP00000456206 Q3ZCM7 UPI000007238E NM_177987.2 deleterious_low_confidence(0) 4/4 Gene3D:3.40.50.1440,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF55,SMART_domains:SM00864,Superfamily_domains:SSF52490 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 47665 47665 G C 1 0 0 0 0 1 0 0 0 17271 1232 43 4 4 TUBB8 10 47665 Missense_Mutation SNP G C3N-00547_T 47665 133749757 353 14683 ITIH5 0 . GRCh38 10 7576888 7576888 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1543G>C p.Ala515Pro p.A515P ENST00000397146 10/14 197 139 58 241 241 0 strelka-varscan-mutect ITIH5,missense_variant,p.Ala515Pro,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Ala515Pro,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Ala301Pro,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,non_coding_transcript_exon_variant,,ENST00000468389,;ITIH5,downstream_gene_variant,,ENST00000461751,;ITIH5,upstream_gene_variant,,ENST00000492668,; G ENST00000397146 Transcript missense_variant 1622/6721 1543/2829 515/942 A/P Gcg/Ccg 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 deleterious(0) 10/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 7576888 7576888 C G 1 0 0 0 0 1 0 0 0 7813 710 25 4 4 ITIH5 10 7576888 Missense_Mutation SNP C C3N-00547_T 7529223 7576888 126220534 354 14684 ST8SIA6 0 . GRCh38 10 17327071 17327071 + Frame_Shift_Del DEL C C - C3N-00547_T C3N-00547_N C C c.578delG p.Gly193GlufsTer3 p.G193Efs*3 ENST00000377602 6/8 79 53 26 98 98 0 sindel-varindel-pindel ST8SIA6,frameshift_variant,p.Gly193GlufsTer3,ENST00000377602,NM_001004470.1;ST8SIA6,frameshift_variant,p.Gly14GlufsTer3,ENST00000440449,; - ENST00000377602 Transcript frameshift_variant 653/2276 578/1197 193/398 G/X gGa/ga COSM285395,COSM4176213 1 -1 ST8SIA6 HGNC HGNC:23317 protein_coding YES CCDS31158.1 ENSP00000366827 P61647 UPI0000359594 NM_001004470.1 6/8 hmmpanther:PTHR11987:SF29,hmmpanther:PTHR11987,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557 1,1 HIGH 1 deletion 1 1,1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999915 1 1 1 0 - 7 5 49 17327071 17327071 C - 1 0 1 0 1 0 0 0 0 15614 855 30 0 0 ST8SIA6 10 17327071 Frame_Shift_Del DEL C C3N-00547_T 9750183 17327071 116470351 355 14685 CACNB2 0 . GRCh38 10 18402019 18402019 + Silent SNP C C A rs112611808 C3N-00547_T C3N-00547_N C C c.309C>A p.= p.A103A ENST00000324631 3/14 535 365 170 583 583 0 strelka-varscan-mutect CACNB2,synonymous_variant,p.=,ENST00000396576,NM_000724.3;CACNB2,synonymous_variant,p.=,ENST00000617363,;CACNB2,synonymous_variant,p.=,ENST00000612134,;CACNB2,synonymous_variant,p.=,ENST00000615785,;CACNB2,synonymous_variant,p.=,ENST00000282343,NM_201571.3,NM_001167945.1;CACNB2,synonymous_variant,p.=,ENST00000377315,NM_201570.2;CACNB2,synonymous_variant,p.=,ENST00000324631,NM_201596.2,NM_201593.2;CACNB2,synonymous_variant,p.=,ENST00000377329,NM_201590.2;CACNB2,synonymous_variant,p.=,ENST00000377319,;CACNB2,synonymous_variant,p.=,ENST00000352115,NM_201597.2;CACNB2,synonymous_variant,p.=,ENST00000377331,NM_201572.3;CACNB2,synonymous_variant,p.=,ENST00000377328,;CACNB2,intron_variant,,ENST00000612743,;CACNB2,non_coding_transcript_exon_variant,,ENST00000498816,; A ENST00000324631 Transcript synonymous_variant 369/3446 309/1983 103/660 A gcC/gcA rs112611808 1 1 CACNB2 HGNC HGNC:1402 protein_coding YES CCDS7125.1 ENSP00000320025 Q08289 UPI00001AEA80 NM_201596.2,NM_201593.2 3/14 Low_complexity_(Seg):seg,hmmpanther:PTHR11824:SF9,hmmpanther:PTHR11824,Pfam_domain:PF12052,Gene3D:2.30.30.40,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS rs112611808 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 18402019 18402019 C A 1 0 0 0 0 0 0 0 1 2241 610 22 2 2 CACNB2 10 18402019 Silent SNP C C3N-00547_T 1074948 18402019 115395403 356 14686 MKX 0 . GRCh38 10 27743255 27743255 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.161A>T p.Asn54Ile p.N54I ENST00000375790 2/7 30 26 4 69 69 0 varscan-mutect MKX,missense_variant,p.Asn54Ile,ENST00000375790,;MKX,missense_variant,p.Asn54Ile,ENST00000419761,NM_173576.2,NM_001242702.1;MKX,missense_variant,p.Asn54Ile,ENST00000460919,;MKX,missense_variant,p.Asn54Ile,ENST00000561227,;MKX-AS1,upstream_gene_variant,,ENST00000419777,; A ENST00000375790 Transcript missense_variant 594/3846 161/1059 54/352 N/I aAc/aTc 1 -1 MKX HGNC HGNC:23729 protein_coding YES CCDS7156.1 ENSP00000364946 Q8IYA7 UPI0000161911 tolerated_low_confidence(0.08) 2/7 hmmpanther:PTHR11211:SF3,hmmpanther:PTHR11211 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -11.62429 1 1 1 1 0 A 3 1 49 27743255 27743255 T A 1 0 0 0 0 1 0 0 0 9578 1725 60 4 4 MKX 10 27743255 Missense_Mutation SNP T C3N-00547_T 9341236 27743255 106054167 357 14687 ANKRD30A 0 . GRCh38 10 37130217 37130217 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.181C>A p.His61Asn p.H61N ENST00000361713 3/36 139 82 57 285 284 1 strelka-varscan-mutect ANKRD30A,missense_variant,p.His61Asn,ENST00000374660,;ANKRD30A,missense_variant,p.His117Asn,ENST00000611781,;ANKRD30A,missense_variant,p.His61Asn,ENST00000602533,;ANKRD30A,missense_variant,p.His61Asn,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript missense_variant 280/4405 181/4026 61/1341 H/N Cat/Aat 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 deleterious(0.03) 3/36 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 37130217 37130217 C A 1 0 0 0 0 1 0 0 0 761 594 21 2 2 ANKRD30A 10 37130217 Missense_Mutation SNP C C3N-00547_T 9386962 37130217 96667205 358 14688 ANKRD30A 0 . GRCh38 10 37141861 37141862 + Frame_Shift_Ins INS - - A novel C3N-00547_T C3N-00547_N - - c.802dupA p.Thr268AsnfsTer3 p.T268Nfs*3 ENST00000361713 7/36 377 335 42 474 474 0 sindel-varindel ANKRD30A,frameshift_variant,p.Thr268AsnfsTer3,ENST00000374660,;ANKRD30A,frameshift_variant,p.Thr324AsnfsTer3,ENST00000611781,;ANKRD30A,frameshift_variant,p.Thr268AsnfsTer3,ENST00000602533,;ANKRD30A,frameshift_variant,p.Thr268AsnfsTer3,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript frameshift_variant 895-896/4405 796-797/4026 266/1341 E/EX gaa/gAaa 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 7/36 HIGH 1 insertion 5 6 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 49 37141861 37141861 - A 1 0 1 1 0 0 0 0 0 761 1175 41 0 0 ANKRD30A 10 37141861 Frame_Shift_Ins INS - C3N-00547_T 11644 37141861 96655561 359 14689 ANKRD30A 0 . GRCh38 10 37219320 37219320 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.3440C>T p.Ala1147Val p.A1147V ENST00000361713 34/36 130 116 14 166 166 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Ala1266Val,ENST00000374660,;ANKRD30A,missense_variant,p.Ala1203Val,ENST00000611781,;ANKRD30A,missense_variant,p.Ala1147Val,ENST00000602533,;ANKRD30A,missense_variant,p.Ala1147Val,ENST00000361713,NM_052997.2; T ENST00000361713 Transcript missense_variant 3539/4405 3440/4026 1147/1341 A/V gCt/gTt 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.14) 34/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF14915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 37219320 37219320 C T 1 0 0 0 0 1 0 0 0 761 797 28 3 3 ANKRD30A 10 37219320 Missense_Mutation SNP C C3N-00547_T 77459 37219320 96578102 360 14690 WDFY4 0 . GRCh38 10 48897458 48897458 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.7321A>T p.Ser2441Cys p.S2441C ENST00000325239 44/61 129 69 60 88 88 0 strelka-varscan-mutect WDFY4,missense_variant,p.Ser2441Cys,ENST00000325239,NM_020945.1;WDFY4,missense_variant,p.Ser528Cys,ENST00000265453,;RP11-523O18.7,intron_variant,,ENST00000430438,; T ENST00000325239 Transcript missense_variant 7321/9555 7321/9555 2441/3184 S/C Agc/Tgc 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 deleterious(0.03) 44/61 Gene3D:1t77A01,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 48897458 48897458 A T 1 0 0 0 0 1 0 0 0 17831 202 7 4 4 WDFY4 10 48897458 Missense_Mutation SNP A C3N-00547_T 11678138 48897458 84899964 361 14691 WDFY4 0 . GRCh38 10 48976817 48976817 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.9129G>T p.= p.A3043A ENST00000325239 58/61 43 37 6 32 32 0 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1;WDFY4,synonymous_variant,p.=,ENST00000265453,;RP11-523O18.5,non_coding_transcript_exon_variant,,ENST00000428825,;WDFY4,non_coding_transcript_exon_variant,,ENST00000465910,;WDFY4,non_coding_transcript_exon_variant,,ENST00000497480,;WDFY4,upstream_gene_variant,,ENST00000490507,;RP11-523O18.5,non_coding_transcript_exon_variant,,ENST00000610464,; T ENST00000325239 Transcript synonymous_variant 9129/9555 9129/9555 3043/3184 A gcG/gcT 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 58/61 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS rs1043948661 . 0 204 6 0 0 0 0 0 -14.97469 0.9999999 1 1 1 0 T 2 4 49 48976817 48976817 G T 1 0 0 0 0 0 0 0 1 17831 1103 39 1 1 WDFY4 10 48976817 Silent SNP G C3N-00547_T 79359 48976817 84820605 362 14692 ERCC6 0 . GRCh38 10 49493239 49493239 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1699G>T p.Gly567Cys p.G567C ENST00000355832 8/21 431 247 184 457 455 2 strelka-varscan-mutect ERCC6,missense_variant,p.Gly567Cys,ENST00000355832,NM_000124.3;ERCC6,non_coding_transcript_exon_variant,,ENST00000623318,;ERCC6,intron_variant,,ENST00000623115,;ERCC6,intron_variant,,ENST00000475116,;ERCC6,non_coding_transcript_exon_variant,,ENST00000623073,; A ENST00000355832 Transcript missense_variant 1778/8008 1699/4482 567/1493 G/C Ggt/Tgt 1 -1 ERCC6 HGNC HGNC:3438 protein_coding YES CCDS7229.1 ENSP00000348089 Q03468 UPI000000D8DA NM_000124.3 deleterious(0) 8/21 PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF752,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 49493239 49493239 C A 1 0 0 0 0 1 0 0 0 5066 623 22 2 2 ERCC6 10 49493239 Missense_Mutation SNP C C3N-00547_T 516422 49493239 84304183 363 14693 PALD1 0 . GRCh38 10 70534746 70534746 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1130G>C p.Arg377Thr p.R377T ENST00000263563 10/20 160 109 51 165 165 0 strelka-varscan-mutect PALD1,missense_variant,p.Arg377Thr,ENST00000263563,NM_014431.2; C ENST00000263563 Transcript missense_variant 1398/4555 1130/2571 377/856 R/T aGa/aCa 1 1 PALD1 HGNC HGNC:23530 protein_coding YES CCDS31215.1 ENSP00000263563 Q9ULE6 A0A024QZM5 UPI00001C1EDC NM_014431.2 tolerated(0.47) 10/20 hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF54,Gene3D:3.90.190.10,SMART_domains:SM00404 MODERATE 1 SNV 1 1 PASS rs1168679438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 70534746 70534746 G C 1 0 0 0 0 1 0 0 0 11486 942 33 4 4 PALD1 10 70534746 Missense_Mutation SNP G C3N-00547_T 21041507 70534746 63262676 364 14694 CDH23 0 . GRCh38 10 71778195 71778195 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.5089A>G p.Ile1697Val p.I1697V ENST00000224721 40/70 165 152 13 176 176 0 strelka-varscan-mutect CDH23,missense_variant,p.Ile1697Val,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Ile1692Val,ENST00000622827,;C10orf54,upstream_gene_variant,,ENST00000394957,NM_022153.1; G ENST00000224721 Transcript missense_variant 5479/11139 5089/10080 1697/3359 I/V Atc/Gtc 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 tolerated(0.26) 40/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 5 1 PASS . . 0 206 0 4 0 0 0 0 -17.32815 0.9997049 1 1 1 0 G 3 3 49 71778195 71778195 A G 1 0 0 0 0 1 0 0 0 2811 217 8 5 5 CDH23 10 71778195 Missense_Mutation SNP A C3N-00547_T 1243449 71778195 62019227 365 14695 CDH23 0 . GRCh38 10 71785041 71785041 + Missense_Mutation SNP C C T rs368848049 C3N-00547_T C3N-00547_N C C c.5668C>T p.Arg1890Cys p.R1890C ENST00000224721 43/70 248 230 18 202 202 0 strelka-varscan-mutect CDH23,missense_variant,p.Arg1890Cys,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Arg1885Cys,ENST00000622827,; T ENST00000224721 Transcript missense_variant 6058/11139 5668/10080 1890/3359 R/C Cgc/Tgc rs368848049,COSM3967143 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 tolerated(0.08) 43/70 PROSITE_profiles:PS50268,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs368848049 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 71785041 71785041 C T 1 0 0 0 0 1 0 0 0 2811 536 19 1 1 CDH23 10 71785041 Missense_Mutation SNP C C3N-00547_T 6846 71785041 62012381 366 14696 PLA2G12B 0 . GRCh38 10 72954514 72954514 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.172G>C p.Gly58Arg p.G58R ENST00000373032 1/4 320 291 29 338 338 0 strelka-varscan-mutect PLA2G12B,missense_variant,p.Gly58Arg,ENST00000373032,NM_032562.3; G ENST00000373032 Transcript missense_variant 265/1128 172/588 58/195 G/R Gga/Cga 1 -1 PLA2G12B HGNC HGNC:18555 protein_coding YES CCDS7319.1 ENSP00000362123 Q9BX93 UPI0000131168 NM_032562.3 deleterious(0) 1/4 Pfam_domain:PF06951,hmmpanther:PTHR12824,hmmpanther:PTHR12824:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 72954514 72954514 C G 1 0 0 0 0 1 0 0 0 12087 632 22 4 4 PLA2G12B 10 72954514 Missense_Mutation SNP C C3N-00547_T 1169473 72954514 60842908 367 14697 KAT6B 0 . GRCh38 10 75028972 75028972 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.4148A>T p.Asp1383Val p.D1383V ENST00000287239 18/18 688 427 261 644 644 0 strelka-varscan-mutect KAT6B,missense_variant,p.Asp1383Val,ENST00000287239,NM_012330.3;KAT6B,missense_variant,p.Asp1200Val,ENST00000372711,NM_001256468.1;KAT6B,missense_variant,p.Asp1091Val,ENST00000372724,NM_001256469.1;KAT6B,missense_variant,p.Asp1091Val,ENST00000372725,;KAT6B,missense_variant,p.Asp1091Val,ENST00000372714,;RP11-77G23.5,upstream_gene_variant,,ENST00000436608,;RP11-77G23.2,upstream_gene_variant,,ENST00000413431,;KAT6B,downstream_gene_variant,,ENST00000490365,; T ENST00000287239 Transcript missense_variant 4637/8287 4148/6222 1383/2073 D/V gAt/gTt 1 1 KAT6B HGNC HGNC:17582 protein_coding YES CCDS7345.1 ENSP00000287239 Q8WYB5 UPI000013DEA0 NM_012330.3 tolerated_low_confidence(0.08) 18/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 75028972 75028972 A T 1 0 0 0 0 1 0 0 0 7899 333 12 4 4 KAT6B 10 75028972 Missense_Mutation SNP A C3N-00547_T 2074458 75028972 58768450 368 14698 KCNMA1 0 . GRCh38 10 76910058 76910058 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.3055G>T p.Asp1019Tyr p.D1019Y ENST00000286628 25/28 495 455 40 664 664 0 strelka-varscan-mutect KCNMA1,missense_variant,p.Asp826Tyr,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,missense_variant,p.Asp961Tyr,ENST00000286627,NM_002247.3;KCNMA1,missense_variant,p.Asp1019Tyr,ENST00000286628,NM_001161352.1;KCNMA1,missense_variant,p.Asp854Tyr,ENST00000354353,;KCNMA1,missense_variant,p.Asp823Tyr,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,missense_variant,p.Asp988Tyr,ENST00000372443,;KCNMA1,missense_variant,p.Asp961Tyr,ENST00000372440,NM_001014797.2;KCNMA1,missense_variant,p.Asp1019Tyr,ENST00000404771,;KCNMA1,missense_variant,p.Asp993Tyr,ENST00000457953,;KCNMA1,missense_variant,p.Asp1002Tyr,ENST00000626620,NM_001161353.1;KCNMA1,missense_variant,p.Asp954Tyr,ENST00000372437,;KCNMA1,missense_variant,p.Asp935Tyr,ENST00000372421,;KCNMA1,missense_variant,p.Asp898Tyr,ENST00000372408,;KCNMA1,missense_variant,p.Asp912Tyr,ENST00000372403,;KCNMA1,missense_variant,p.Asp797Tyr,ENST00000404857,NM_001271518.1;KCNMA1,missense_variant,p.Asp669Tyr,ENST00000434208,;KCNMA1-AS1,intron_variant,,ENST00000600782,;KCNMA1-AS1,intron_variant,,ENST00000426234,;KCNMA1-AS1,intron_variant,,ENST00000458661,;KCNMA1-AS1,downstream_gene_variant,,ENST00000429850,; A ENST00000286628 Transcript missense_variant 3055/6100 3055/3711 1019/1236 D/Y Gat/Tat 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 deleterious(0) 25/28 Prints_domain:PR01449,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 76910058 76910058 C A 1 0 0 0 0 1 0 0 0 7990 826 29 2 2 KCNMA1 10 76910058 Missense_Mutation SNP C C3N-00547_T 1881086 76910058 56887364 369 14699 LRIT1 0 . GRCh38 10 84234357 84234357 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.611C>A p.Ala204Glu p.A204E ENST00000372105 3/4 21 17 4 35 35 0 strelka-varscan-mutect LRIT1,missense_variant,p.Ala204Glu,ENST00000372105,NM_015613.2; T ENST00000372105 Transcript missense_variant 633/2228 611/1872 204/623 A/E gCa/gAa COSM4016333 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 tolerated(0.09) 3/4 Gene3D:3.80.10.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,SMART_domains:SM00082,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS rs1419214268 . 0 206 4 0 0 0 0 0 -12.3058 1 1 1 1 0 T 3 4 49 84234357 84234357 G T 1 0 0 0 0 1 0 0 0 8842 1319 46 2 2 LRIT1 10 84234357 Missense_Mutation SNP G C3N-00547_T 7324299 84234357 49563065 370 14700 LIPK 0 . GRCh38 10 88740065 88740065 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.886C>A p.Gln296Lys p.Q296K ENST00000404190 7/9 113 71 42 168 168 0 strelka-varscan-mutect LIPK,missense_variant,p.Gln296Lys,ENST00000404190,NM_001080518.1; A ENST00000404190 Transcript missense_variant,splice_region_variant 886/1230 886/1200 296/399 Q/K Cag/Aag 1 1 LIPK HGNC HGNC:23444 protein_coding YES CCDS44455.1 ENSP00000383900 Q5VXJ0 UPI00000497BC NM_001080518.1 deleterious(0) 7/9 hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF45,PIRSF_domain:PIRSF000862,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 88740065 88740065 C A 1 0 0 0 0 1 0 0 0 8748 840 29 2 2 LIPK 10 88740065 Missense_Mutation SNP C C3N-00547_T 4505708 88740065 45057357 371 14701 CYP26A1 0 . GRCh38 10 93075897 93075897 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.936G>T p.= p.L312L ENST00000224356 5/7 195 137 58 207 206 1 strelka-varscan-mutect CYP26A1,synonymous_variant,p.=,ENST00000371531,NM_057157.2;CYP26A1,synonymous_variant,p.=,ENST00000224356,NM_000783.3;RP11-348J12.5,downstream_gene_variant,,ENST00000624651,;CYP26A1,missense_variant,p.Asp237Tyr,ENST00000624589,;CYP26A1,non_coding_transcript_exon_variant,,ENST00000623162,;CYP26A1,downstream_gene_variant,,ENST00000622925,;CYP26A1,upstream_gene_variant,,ENST00000625202,; T ENST00000224356 Transcript synonymous_variant 981/2125 936/1494 312/497 L ctG/ctT 1 1 CYP26A1 HGNC HGNC:2603 protein_coding YES CCDS7426.1 ENSP00000224356 O43174 UPI000013E48F NM_000783.3 5/7 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00385,hmmpanther:PTHR24286,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 93075897 93075897 G T 1 0 0 0 0 0 0 0 1 3958 1277 45 2 2 CYP26A1 10 93075897 Silent SNP G C3N-00547_T 4335832 93075897 40721525 372 14702 CYP26A1 0 . GRCh38 10 93077219 93077219 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1409G>T p.Gly470Val p.G470V ENST00000224356 7/7 68 54 14 83 83 0 strelka-varscan-mutect CYP26A1,missense_variant,p.Gly401Val,ENST00000371531,NM_057157.2;CYP26A1,missense_variant,p.Gly470Val,ENST00000224356,NM_000783.3;RP11-348J12.5,downstream_gene_variant,,ENST00000624651,;CYP26A1,3_prime_UTR_variant,,ENST00000624589,;CYP26A1,non_coding_transcript_exon_variant,,ENST00000623162,;CYP26A1,downstream_gene_variant,,ENST00000622925,;CYP26A1,downstream_gene_variant,,ENST00000625202,; T ENST00000224356 Transcript missense_variant 1454/2125 1409/1494 470/497 G/V gGa/gTa 1 1 CYP26A1 HGNC HGNC:2603 protein_coding YES CCDS7426.1 ENSP00000224356 O43174 UPI000013E48F NM_000783.3 tolerated(0.23) 7/7 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24286,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 93077219 93077219 G T 1 0 0 0 0 1 0 0 0 3958 1174 41 2 2 CYP26A1 10 93077219 Missense_Mutation SNP G C3N-00547_T 1322 93077219 40720203 373 14703 PLCE1 0 . GRCh38 10 94246064 94246064 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2539C>A p.Pro847Thr p.P847T ENST00000371380 7/32 445 399 46 496 496 0 strelka-varscan-mutect PLCE1,missense_variant,p.Pro847Thr,ENST00000371380,NM_016341.3,NM_001288989.1;PLCE1,missense_variant,p.Pro539Thr,ENST00000371375,;PLCE1,missense_variant,p.Pro539Thr,ENST00000371385,NM_001165979.2; A ENST00000371380 Transcript missense_variant 2774/12024 2539/6909 847/2302 P/T Cct/Act 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 deleterious(0) 7/32 Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 94246064 94246064 C A 1 0 0 0 0 1 0 0 0 12128 623 22 2 2 PLCE1 10 94246064 Missense_Mutation SNP C C3N-00547_T 1168845 94246064 39551358 374 14704 PLCE1 0 . GRCh38 10 94252335 94252335 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.3116G>T p.Gly1039Val p.G1039V ENST00000371380 8/32 207 145 62 215 215 0 strelka-varscan-mutect PLCE1,missense_variant,p.Gly1039Val,ENST00000371380,NM_016341.3,NM_001288989.1;PLCE1,missense_variant,p.Gly731Val,ENST00000371375,;PLCE1,missense_variant,p.Gly731Val,ENST00000371385,NM_001165979.2; T ENST00000371380 Transcript missense_variant 3351/12024 3116/6909 1039/2302 G/V gGc/gTc 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 deleterious(0) 8/32 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 94252335 94252335 G T 1 0 0 0 0 1 0 0 0 12128 1203 42 2 2 PLCE1 10 94252335 Missense_Mutation SNP G C3N-00547_T 6271 94252335 39545087 375 14705 PLCE1 0 . GRCh38 10 94270548 94270548 + Silent SNP G G T rs759614140 C3N-00547_T C3N-00547_N G G c.4452G>T p.= p.S1484S ENST00000371380 17/32 460 411 49 578 577 1 strelka-varscan-mutect PLCE1,synonymous_variant,p.=,ENST00000371380,NM_016341.3,NM_001288989.1;PLCE1,synonymous_variant,p.=,ENST00000371375,;PLCE1,synonymous_variant,p.=,ENST00000371385,NM_001165979.2; T ENST00000371380 Transcript synonymous_variant 4687/12024 4452/6909 1484/2302 S tcG/tcT rs759614140 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 17/32 Gene3D:3.20.20.190,Pfam_domain:PF00388,PROSITE_profiles:PS50007,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF6,SMART_domains:SM00148,Superfamily_domains:SSF51695 LOW 1 SNV 1 1 PASS rs759614140 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 94270548 94270548 G T 1 0 0 0 0 0 0 0 1 12128 1045 37 1 1 PLCE1 10 94270548 Silent SNP G C3N-00547_T 18213 94270548 39526874 376 14706 HOGA1 0 . GRCh38 10 97599179 97599179 + Missense_Mutation SNP G G A C3N-00547_T C3N-00547_N G G c.431G>A p.Arg144His p.R144H ENST00000370646 3/7 199 183 16 181 181 0 strelka-varscan-mutect HOGA1,missense_variant,p.Arg144His,ENST00000370646,NM_138413.3;HOGA1,intron_variant,,ENST00000370647,NM_001134670.1;RP11-548K23.11,intron_variant,,ENST00000370649,;HOGA1,upstream_gene_variant,,ENST00000370642,;HOGA1,non_coding_transcript_exon_variant,,ENST00000465608,; A ENST00000370646 Transcript missense_variant 792/2488 431/984 144/327 R/H cGc/cAc COSM922051 1 1 HOGA1 HGNC HGNC:25155 protein_coding YES CCDS7467.1 ENSP00000359680 Q86XE5 UPI000000DAE5 NM_138413.3 tolerated(0.08) 3/7 hmmpanther:PTHR12128:SF23,hmmpanther:PTHR12128,Pfam_domain:PF00701,Gene3D:3.20.20.70,PIRSF_domain:PIRSF001365,SMART_domains:SM01130,Superfamily_domains:SSF51569 1 MODERATE 1 SNV 1 1 1 PASS rs1371902226 . 0 205 0 4 0 0 0 0 -19.89686 0.9997058 1 1 1 0 A 3 1 49 97599179 97599179 G A 1 0 0 0 0 1 0 0 0 7171 1087 38 1 1 HOGA1 10 97599179 Missense_Mutation SNP G C3N-00547_T 3328631 97599179 36198243 377 14707 CHUK 0 . GRCh38 10 100207299 100207299 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.1162G>A p.Asp388Asn p.D388N ENST00000370397 11/21 182 164 18 208 208 0 strelka-varscan-mutect CHUK,missense_variant,p.Asp388Asn,ENST00000370397,NM_001320928.1,NM_001278.3; T ENST00000370397 Transcript missense_variant 1249/3625 1162/2238 388/745 D/N Gat/Aat 1 -1 CHUK HGNC HGNC:1974 protein_coding YES CCDS7488.1 ENSP00000359424 O15111 UPI000013D6C7 NM_001320928.1,NM_001278.3 tolerated(0.06) 11/21 hmmpanther:PTHR22969,hmmpanther:PTHR22969:SF13 MODERATE 1 SNV 1 1 PASS rs1454848409 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 100207299 100207299 C T 1 0 0 0 0 1 0 0 0 3177 826 29 3 3 CHUK 10 100207299 Missense_Mutation SNP C C3N-00547_T 2608120 100207299 33590123 378 14708 SEC31B 0 . GRCh38 10 100496369 100496369 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.2199G>T p.= p.G733G ENST00000370345 18/26 184 120 64 203 203 0 strelka-varscan-mutect SEC31B,synonymous_variant,p.=,ENST00000370345,NM_015490.3;SEC31B,non_coding_transcript_exon_variant,,ENST00000469824,;SEC31B,downstream_gene_variant,,ENST00000494350,;SEC31B,3_prime_UTR_variant,,ENST00000479697,;SEC31B,3_prime_UTR_variant,,ENST00000462434,;SEC31B,3_prime_UTR_variant,,ENST00000469546,;SEC31B,3_prime_UTR_variant,,ENST00000482456,;SEC31B,non_coding_transcript_exon_variant,,ENST00000484848,;SEC31B,downstream_gene_variant,,ENST00000498298,; A ENST00000370345 Transcript synonymous_variant 2297/4612 2199/3540 733/1179 G ggG/ggT 1 -1 SEC31B HGNC HGNC:23197 protein_coding YES CCDS7495.1 ENSP00000359370 Q9NQW1 UPI0000070A8E NM_015490.3 18/26 hmmpanther:PTHR13923:SF22,hmmpanther:PTHR13923 LOW 1 SNV 1 1 PASS rs964873122 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 100496369 100496369 C A 1 0 0 0 0 0 0 0 1 14276 610 22 2 2 SEC31B 10 100496369 Silent SNP C C3N-00547_T 289070 100496369 33301053 379 14709 SFXN2 0 . GRCh38 10 102726729 102726729 + Silent SNP G G C rs201760534 C3N-00547_T C3N-00547_N G G c.93G>C p.= p.T31T ENST00000369893 2/12 209 132 77 234 234 0 strelka-varscan-mutect SFXN2,synonymous_variant,p.=,ENST00000369893,NM_178858.4;SFXN2,synonymous_variant,p.=,ENST00000602831,;SFXN2,synonymous_variant,p.=,ENST00000602868,;SFXN2,synonymous_variant,p.=,ENST00000602764,;SFXN2,synonymous_variant,p.=,ENST00000602439,;SFXN2,downstream_gene_variant,,ENST00000602647,;SFXN2,non_coding_transcript_exon_variant,,ENST00000602785,;SFXN2,synonymous_variant,p.=,ENST00000459894,;SFXN2,synonymous_variant,p.=,ENST00000480358,;SFXN2,synonymous_variant,p.=,ENST00000602544,;SFXN2,synonymous_variant,p.=,ENST00000602670,;SFXN2,non_coding_transcript_exon_variant,,ENST00000602660,;SFXN2,non_coding_transcript_exon_variant,,ENST00000602287,; C ENST00000369893 Transcript synonymous_variant 260/6866 93/969 31/322 T acG/acC rs201760534 1 1 SFXN2 HGNC HGNC:16086 protein_coding YES CCDS7539.1 ENSP00000358909 Q96NB2 UPI0000001241 NM_178858.4 2/12 hmmpanther:PTHR11153,hmmpanther:PTHR11153:SF14,TIGRFAM_domain:TIGR00798,Pfam_domain:PF03820 LOW 1 SNV 1 1 PASS rs201760534 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 102726729 102726729 G C 1 0 0 0 0 0 0 0 1 14455 1103 39 4 4 SFXN2 10 102726729 Silent SNP G C3N-00547_T 2230360 102726729 31070693 380 14710 SORCS1 0 . GRCh38 10 106577459 106577459 + Silent SNP C C G C3N-00547_T C3N-00547_N C C c.3468G>C p.= p.T1156T ENST00000263054 26/26 243 219 24 253 253 0 strelka-varscan-mutect SORCS1,synonymous_variant,p.=,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,synonymous_variant,p.=,ENST00000622431,;SORCS1,3_prime_UTR_variant,,ENST00000612154,;SORCS1,3_prime_UTR_variant,,ENST00000369698,;SORCS1,intron_variant,,ENST00000452214,;SORCS1,downstream_gene_variant,,ENST00000344440,;SORCS1,non_coding_transcript_exon_variant,,ENST00000473866,; G ENST00000263054 Transcript synonymous_variant 3476/7272 3468/3507 1156/1168 T acG/acC COSM1345698 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 26/26 1 LOW 1 SNV 1 1 1 PASS rs931166469 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 106577459 106577459 C G 1 0 0 0 0 0 0 0 1 15252 755 27 4 4 SORCS1 10 106577459 Silent SNP C C3N-00547_T 3850730 106577459 27219963 381 14711 RBM20 0 . GRCh38 10 110781835 110781835 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1226A>G p.His409Arg p.H409R ENST00000369519 2/14 313 273 40 523 523 0 strelka-varscan-mutect RBM20,missense_variant,p.His409Arg,ENST00000369519,NM_001134363.2; G ENST00000369519 Transcript missense_variant 1284/7233 1226/3684 409/1227 H/R cAc/cGc 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 deleterious(0.04) 2/14 hmmpanther:PTHR15592:SF10,hmmpanther:PTHR15592,SMART_domains:SM00451 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 110781835 110781835 A G 1 0 0 0 0 1 0 0 0 13287 159 6 5 5 RBM20 10 110781835 Missense_Mutation SNP A C3N-00547_T 4204376 110781835 23015587 382 14712 ABLIM1 0 . GRCh38 10 114465786 114465786 + Silent SNP C C A rs758416758 C3N-00547_T C3N-00547_N C C c.1353G>T p.= p.T451T ENST00000277895 12/23 186 121 65 249 249 0 strelka-varscan-mutect ABLIM1,synonymous_variant,p.=,ENST00000369252,NM_001322882.1;ABLIM1,synonymous_variant,p.=,ENST00000533213,;ABLIM1,synonymous_variant,p.=,ENST00000392955,NM_001003407.1;ABLIM1,synonymous_variant,p.=,ENST00000392952,NM_001322893.1,NM_001322896.1,NM_001322890.1,NM_001322891.1,NM_001322892.1,NM_006720.3;ABLIM1,synonymous_variant,p.=,ENST00000369256,NM_001003408.1;ABLIM1,synonymous_variant,p.=,ENST00000277895,NM_002313.5;ABLIM1,synonymous_variant,p.=,ENST00000369253,;ABLIM1,synonymous_variant,p.=,ENST00000369266,;ABLIM1,synonymous_variant,p.=,ENST00000428430,;ABLIM1,synonymous_variant,p.=,ENST00000440467,;ABLIM1,non_coding_transcript_exon_variant,,ENST00000466400,; A ENST00000277895 Transcript synonymous_variant 1451/2657 1353/2337 451/778 T acG/acT rs758416758 1 -1 ABLIM1 HGNC HGNC:78 protein_coding YES CCDS7590.1 ENSP00000277895 O14639 UPI0000418D06 NM_002313.5 12/23 hmmpanther:PTHR24213,hmmpanther:PTHR24213:SF18,Pfam_domain:PF16182 LOW 1 SNV 5 1 PASS rs758416758 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 114465786 114465786 C A 1 0 0 0 0 0 0 0 1 104 871 31 1 1 ABLIM1 10 114465786 Silent SNP C C3N-00547_T 3683951 114465786 19331636 383 14713 FAM160B1 0 . GRCh38 10 114860781 114860781 + Silent SNP G G C novel C3N-00547_T C3N-00547_N G G c.1980G>C p.= p.V660V ENST00000369248 15/17 209 195 14 176 176 0 strelka-mutect FAM160B1,synonymous_variant,p.=,ENST00000369248,NM_020940.3;FAM160B1,synonymous_variant,p.=,ENST00000369250,NM_001135051.1;FAM160B1,upstream_gene_variant,,ENST00000411414,; C ENST00000369248 Transcript synonymous_variant 2315/5810 1980/2298 660/765 V gtG/gtC 1 1 FAM160B1 HGNC HGNC:29320 protein_coding YES CCDS31290.1 ENSP00000358251 Q5W0V3 UPI0000160B10 NM_020940.3 15/17 hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF10 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 114860781 114860781 G C 1 0 0 0 0 0 0 0 1 5319 1364 48 4 4 FAM160B1 10 114860781 Silent SNP G C3N-00547_T 394995 114860781 18936641 384 14714 PRLHR 0 . GRCh38 10 118594966 118594966 + Silent SNP G G A C3N-00547_T C3N-00547_N G G c.279C>T p.= p.N93N ENST00000239032 2/2 114 105 9 148 148 0 strelka-varscan-mutect PRLHR,synonymous_variant,p.=,ENST00000239032,NM_004248.2;PRLHR,synonymous_variant,p.=,ENST00000636925,; A ENST00000239032 Transcript synonymous_variant 469/5446 279/1113 93/370 N aaC/aaT COSM3716698 1 -1 PRLHR HGNC HGNC:4464 protein_coding YES CCDS7606.1 ENSP00000239032 P49683 UPI000013CA6F NM_004248.2 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 1 PASS rs1301418181 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 118594966 118594966 G A 1 0 0 0 0 0 0 0 1 12662 1136 40 1 1 PRLHR 10 118594966 Silent SNP G C3N-00547_T 3734185 118594966 15202456 385 14715 CPXM2 0 . GRCh38 10 123770967 123770967 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1051C>A p.Leu351Met p.L351M ENST00000241305 8/14 124 112 12 187 187 0 strelka-varscan-mutect CPXM2,missense_variant,p.Leu351Met,ENST00000241305,NM_198148.2;CPXM2,5_prime_UTR_variant,,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; T ENST00000241305 Transcript missense_variant 1206/3554 1051/2271 351/756 L/M Ctg/Atg 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 deleterious(0) 8/14 hmmpanther:PTHR11532:SF45,hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,Superfamily_domains:SSF53187,Prints_domain:PR00765 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 123770967 123770967 G T 1 0 0 0 0 1 0 0 0 3636 991 35 2 2 CPXM2 10 123770967 Missense_Mutation SNP G C3N-00547_T 5176001 123770967 10026455 386 14716 CFAP46 0 . GRCh38 10 132846085 132846085 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.6410T>A p.Val2137Glu p.V2137E ENST00000368586 44/58 122 108 14 172 172 0 strelka-varscan-mutect CFAP46,missense_variant,p.Val2137Glu,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript missense_variant 6511/8278 6410/8148 2137/2715 V/E gTg/gAg 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 deleterious(0) 44/58 MODERATE 1 SNV 5 1 PASS rs1049856691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 132846085 132846085 A T 1 0 0 0 0 1 0 0 0 3021 159 6 4 4 CFAP46 10 132846085 Missense_Mutation SNP A C3N-00547_T 9075118 132846085 951337 387 14717 MUC5AC 0 . GRCh38 11 1191037 1191037 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.12892A>T p.Ser4298Cys p.S4298C ENST00000621226 31/49 734 691 43 611 611 0 varscan-mutect MUC5AC,missense_variant,p.Ser4298Cys,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript missense_variant 12939/17448 12892/16965 4298/5654 S/C Agc/Tgc 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious_low_confidence(0.01) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 1191037 1191037 A T 1 0 0 0 0 1 0 0 0 9978 188 7 4 4 MUC5AC 11 1191037 Missense_Mutation SNP A C3N-00547_T 1191037 133895585 388 14718 MUC5AC 0 . GRCh38 11 1196430 1196430 + Missense_Mutation SNP C C G rs772195066 C3N-00547_T C3N-00547_N C C c.15680C>G p.Pro5227Arg p.P5227R ENST00000621226 38/49 189 121 68 238 238 0 strelka-varscan-mutect MUC5AC,missense_variant,p.Pro5227Arg,ENST00000621226,NM_001304359.1; G ENST00000621226 Transcript missense_variant 15727/17448 15680/16965 5227/5654 P/R cCg/cGg rs772195066 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0) 38/49 Gene3D:2.10.25.10,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS rs772195066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 1196430 1196430 C G 1 0 0 0 0 1 0 0 0 9978 652 23 4 4 MUC5AC 11 1196430 Missense_Mutation SNP C C3N-00547_T 5393 1196430 133890192 389 14719 MUC5B 0 . GRCh38 11 1245796 1245796 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.8916C>A p.= p.P2972P ENST00000529681 31/49 260 133 127 251 251 0 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; A ENST00000529681 Transcript synonymous_variant 8974/17911 8916/17289 2972/5762 P ccC/ccA 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 31/49 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9996279 1 1 1 0 A 2 1 49 1245796 1245796 C A 1 0 0 0 0 0 0 0 1 9979 581 21 2 2 MUC5B 11 1245796 Silent SNP C C3N-00547_T 49366 1245796 133840826 390 14720 TNNI2 0 . GRCh38 11 1840417 1840417 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.30C>T p.= p.A10A ENST00000381906 4/8 297 272 25 278 278 0 strelka-varscan-mutect TNNI2,synonymous_variant,p.=,ENST00000381906,NM_001145829.1;TNNI2,synonymous_variant,p.=,ENST00000381911,NM_003282.3;TNNI2,synonymous_variant,p.=,ENST00000381905,NM_001145841.1;TNNI2,synonymous_variant,p.=,ENST00000617947,;TNNI2,synonymous_variant,p.=,ENST00000252898,;SYT8,downstream_gene_variant,,ENST00000341958,;SYT8,downstream_gene_variant,,ENST00000381968,NM_001290334.1,NM_138567.4;SYT8,downstream_gene_variant,,ENST00000381978,NM_001290332.1,NM_001290333.1;SYT8,downstream_gene_variant,,ENST00000430303,;SYT8,downstream_gene_variant,,ENST00000417052,;SYT8,downstream_gene_variant,,ENST00000483280,;TNNI2,non_coding_transcript_exon_variant,,ENST00000468473,;SYT8,downstream_gene_variant,,ENST00000490707,;SYT8,downstream_gene_variant,,ENST00000479276,;SYT8,downstream_gene_variant,,ENST00000479089,;SYT8,downstream_gene_variant,,ENST00000464897,;SYT8,downstream_gene_variant,,ENST00000424556,;SYT8,downstream_gene_variant,,ENST00000475245,;SYT8,downstream_gene_variant,,ENST00000494431,;SYT8,downstream_gene_variant,,ENST00000482118,; T ENST00000381906 Transcript synonymous_variant 99/745 30/549 10/182 A gcC/gcT 1 1 TNNI2 HGNC HGNC:11946 protein_coding YES CCDS31333.1 ENSP00000371331 P48788 UPI0000001605 NM_001145829.1 4/8 Gene3D:1.20.5.350,hmmpanther:PTHR13738,hmmpanther:PTHR13738:SF15 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 1840417 1840417 C T 1 0 0 0 0 0 0 0 1 16800 581 21 3 3 TNNI2 11 1840417 Silent SNP C C3N-00547_T 594621 1840417 133246205 391 14721 TRPM5 0 . GRCh38 11 2415923 2415923 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1111G>T p.Gly371Trp p.G371W ENST00000155858 8/24 131 55 76 90 89 1 strelka-varscan-mutect TRPM5,missense_variant,p.Gly371Trp,ENST00000155858,NM_014555.3;TRPM5,missense_variant,p.Gly365Trp,ENST00000533881,;TRPM5,missense_variant,p.Gly371Trp,ENST00000533060,;TRPM5,missense_variant,p.Gly371Trp,ENST00000528453,; A ENST00000155858 Transcript missense_variant 1120/3929 1111/3498 371/1165 G/W Ggg/Tgg 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 deleterious(0) 8/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 2415923 2415923 C A 1 0 0 0 0 1 0 0 0 17095 594 21 2 2 TRPM5 11 2415923 Missense_Mutation SNP C C3N-00547_T 575506 2415923 132670699 392 14722 OR52E8 0 . GRCh38 11 5857683 5857683 + Missense_Mutation SNP G G C rs760316487 C3N-00547_T C3N-00547_N G G c.20C>G p.Thr7Arg p.T7R ENST00000537935 1/1 70 66 4 57 57 0 strelka-mutect OR52E8,missense_variant,p.Thr7Arg,ENST00000537935,NM_001005168.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; C ENST00000537935 Transcript missense_variant 52/1061 20/954 7/317 T/R aCg/aGg rs760316487 1 -1 OR52E8 HGNC HGNC:15217 protein_coding YES CCDS31400.1 ENSP00000444054 Q6IFG1 A0A126GVH0 UPI000004B211 NM_001005168.1 tolerated(0.35) 1/1 hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF170,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs760316487 . 0 199 11 0 0 0 0 0 -9.190096 0.9997181 1 1 1 0 C 3 2 49 5857683 5857683 G C 1 0 0 0 0 1 0 0 0 11191 1145 40 4 4 OR52E8 11 5857683 Missense_Mutation SNP G C3N-00547_T 3441760 5857683 129228939 393 14723 TRIM3 0 . GRCh38 11 6457795 6457795 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.416G>T p.Arg139Leu p.R139L ENST00000525074 4/12 146 87 59 128 128 0 strelka-varscan-mutect TRIM3,missense_variant,p.Arg139Leu,ENST00000525074,NM_001248006.1;TRIM3,missense_variant,p.Arg139Leu,ENST00000359518,NM_006458.3;TRIM3,missense_variant,p.Arg139Leu,ENST00000345851,NM_033278.3;TRIM3,missense_variant,p.Arg20Leu,ENST00000536344,NM_001248007.1;TRIM3,missense_variant,p.Arg139Leu,ENST00000528227,;TRIM3,downstream_gene_variant,,ENST00000529529,;TRIM3,non_coding_transcript_exon_variant,,ENST00000528932,;TRIM3,upstream_gene_variant,,ENST00000529058,;TRIM3,upstream_gene_variant,,ENST00000526845,;TRIM3,upstream_gene_variant,,ENST00000527237,;TRIM3,upstream_gene_variant,,ENST00000532542,; A ENST00000525074 Transcript missense_variant 811/3044 416/2235 139/744 R/L cGc/cTc COSM5126475 1 -1 TRIM3 HGNC HGNC:10064 protein_coding YES CCDS7764.1 ENSP00000433102 O75382 UPI000013C8BA NM_001248006.1 tolerated(0.15) 4/12 PROSITE_profiles:PS50119,hmmpanther:PTHR24103:SF1,hmmpanther:PTHR24103,Pfam_domain:PF00643,Gene3D:1freA00,SMART_domains:SM00336,Superfamily_domains:SSF57845 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 6457795 6457795 C A 1 0 0 0 0 1 0 0 0 16993 768 27 1 1 TRIM3 11 6457795 Missense_Mutation SNP C C3N-00547_T 600112 6457795 128628827 394 14724 DCHS1 0 . GRCh38 11 6627431 6627431 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.5608G>T p.Ala1870Ser p.A1870S ENST00000299441 14/21 319 153 166 268 268 0 strelka-varscan-mutect DCHS1,missense_variant,p.Ala1870Ser,ENST00000299441,NM_003737.3;RP11-732A19.6,upstream_gene_variant,,ENST00000526633,; A ENST00000299441 Transcript missense_variant 6020/10765 5608/9897 1870/3298 A/S Gca/Tca 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 tolerated(0.13) 14/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 6627431 6627431 C A 1 0 0 0 0 1 0 0 0 4090 710 25 2 2 DCHS1 11 6627431 Missense_Mutation SNP C C3N-00547_T 169636 6627431 128459191 395 14725 DCHS1 0 . GRCh38 11 6641406 6641406 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.208G>T p.Ala70Ser p.A70S ENST00000299441 2/21 190 97 93 151 151 0 strelka-varscan-mutect DCHS1,missense_variant,p.Ala70Ser,ENST00000299441,NM_003737.3; A ENST00000299441 Transcript missense_variant 620/10765 208/9897 70/3298 A/S Gca/Tca 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 tolerated(0.14) 2/21 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 6641406 6641406 C A 1 0 0 0 0 1 0 0 0 4090 739 26 2 2 DCHS1 11 6641406 Missense_Mutation SNP C C3N-00547_T 13975 6641406 128445216 396 14726 FAR1 0 . GRCh38 11 13710699 13710699 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.552G>T p.Met184Ile p.M184I ENST00000354817 5/12 98 49 49 129 129 0 strelka-varscan-mutect FAR1,missense_variant,p.Met184Ile,ENST00000354817,NM_032228.5;FAR1,missense_variant,p.Met184Ile,ENST00000532701,;FAR1,upstream_gene_variant,,ENST00000527202,;FAR1,non_coding_transcript_exon_variant,,ENST00000524933,; T ENST00000354817 Transcript missense_variant 696/5264 552/1548 184/515 M/I atG/atT 1 1 FAR1 HGNC HGNC:26222 protein_coding YES CCDS7813.1 ENSP00000346874 Q8WVX9 UPI00000477EF NM_032228.5 deleterious(0.03) 5/12 hmmpanther:PTHR11011:SF31,hmmpanther:PTHR11011,Pfam_domain:PF07993 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 13710699 13710699 G T 1 0 0 0 0 1 0 0 0 5534 1348 47 2 2 FAR1 11 13710699 Missense_Mutation SNP G C3N-00547_T 7069293 13710699 121375923 397 14727 SOX6 0 . GRCh38 11 16341089 16341089 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.160G>C p.Glu54Gln p.E54Q ENST00000396356 2/16 270 203 67 277 277 0 strelka-varscan-mutect SOX6,missense_variant,p.Glu54Gln,ENST00000396356,NM_033326.3;SOX6,missense_variant,p.Glu54Gln,ENST00000316399,;SOX6,missense_variant,p.Glu54Gln,ENST00000528252,NM_001145811.1;SOX6,missense_variant,p.Glu57Gln,ENST00000527619,NM_017508.2;SOX6,missense_variant,p.Glu54Gln,ENST00000528429,NM_001145819.1;SOX6,missense_variant,p.Glu54Gln,ENST00000533411,;SOX6,missense_variant,p.Glu54Gln,ENST00000529469,;SOX6,missense_variant,p.Glu54Gln,ENST00000526673,;SOX6,non_coding_transcript_exon_variant,,ENST00000533658,;SOX6,missense_variant,p.Glu54Gln,ENST00000530378,;SOX6,non_coding_transcript_exon_variant,,ENST00000533870,; G ENST00000396356 Transcript missense_variant 238/8865 160/2427 54/808 E/Q Gag/Cag 1 -1 SOX6 HGNC HGNC:16421 protein_coding YES CCDS7821.1 ENSP00000379644 P35712 UPI00001F9DE4 NM_033326.3 deleterious_low_confidence(0.01) 2/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 16341089 16341089 C G 1 0 0 0 0 1 0 0 0 15281 835 29 4 4 SOX6 11 16341089 Missense_Mutation SNP C C3N-00547_T 2630390 16341089 118745533 398 14728 OTOG 0 . GRCh38 11 17547377 17547377 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.5G>T p.Gly2Val p.G2V ENST00000399391 1/55 26 16 10 33 33 0 strelka-varscan-mutect OTOG,missense_variant,p.Gly2Val,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Gly2Val,ENST00000399391,NM_001277269.1;USH1C,upstream_gene_variant,,ENST00000005226,NM_153676.3;USH1C,upstream_gene_variant,,ENST00000318024,NM_005709.3;USH1C,upstream_gene_variant,,ENST00000527020,NM_001297764.1;OTOG,upstream_gene_variant,,ENST00000428619,;USH1C,upstream_gene_variant,,ENST00000526313,;OTOG,upstream_gene_variant,,ENST00000498332,; T ENST00000399391 Transcript missense_variant 5/8778 5/8778 2/2925 G/V gGa/gTa 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious_low_confidence(0) 1/55 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 17547377 17547377 G T 1 0 0 0 0 1 0 0 0 11370 1188 41 2 2 OTOG 11 17547377 Missense_Mutation SNP G C3N-00547_T 1206288 17547377 117539245 399 14729 OTOG 0 . GRCh38 11 17610668 17610668 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.5404C>A p.Leu1802Ile p.L1802I ENST00000399391 35/55 271 160 111 249 249 0 strelka-varscan-mutect OTOG,missense_variant,p.Leu1790Ile,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Leu1802Ile,ENST00000399391,NM_001277269.1;OTOG,missense_variant,p.Leu808Ile,ENST00000342528,; A ENST00000399391 Transcript missense_variant 5404/8778 5404/8778 1802/2925 L/I Ctt/Att 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 tolerated(0.41) 35/55 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 17610668 17610668 C A 1 0 0 0 0 1 0 0 0 11370 681 24 2 2 OTOG 11 17610668 Missense_Mutation SNP C C3N-00547_T 63291 17610668 117475954 400 14730 PTPN5 0 . GRCh38 11 18765834 18765834 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.70G>A p.Asp24Asn p.D24N ENST00000358540 3/15 403 354 49 331 331 0 strelka-varscan-mutect PTPN5,missense_variant,p.Asp24Asn,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,missense_variant,p.Asp24Asn,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,5_prime_UTR_variant,,ENST00000396168,NM_001278238.1,NM_001278239.1; T ENST00000358540 Transcript missense_variant 501/3135 70/1698 24/565 D/N Gac/Aac 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 deleterious_low_confidence(0.01) 3/15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 18765834 18765834 C T 1 0 0 0 0 1 0 0 0 12945 855 30 3 3 PTPN5 11 18765834 Missense_Mutation SNP C C3N-00547_T 1155166 18765834 116320788 401 14731 57 2 PTPN5 0 . GRCh38 11 18765836 18765836 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.68T>C p.Leu23Pro p.L23P ENST00000358540 3/15 413 365 48 332 332 0 strelka-varscan-mutect PTPN5,missense_variant,p.Leu23Pro,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,missense_variant,p.Leu23Pro,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,5_prime_UTR_variant,,ENST00000396168,NM_001278238.1,NM_001278239.1; G ENST00000358540 Transcript missense_variant 499/3135 68/1698 23/565 L/P cTg/cCg 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 tolerated_low_confidence(0.11) 3/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 18765836 18765836 A G 1 0 0 0 0 1 0 0 0 12945 188 7 5 5 PTPN5 11 18765836 Missense_Mutation SNP A C3N-00547_T 2 18765836 116320786 402 14732 57 2 MRGPRX1 0 . GRCh38 11 18934646 18934646 + Missense_Mutation SNP C C A rs371238052 C3N-00547_T C3N-00547_N C C c.139G>T p.Val47Phe p.V47F ENST00000302797 1/1 127 75 52 146 146 0 strelka-varscan-mutect MRGPRX1,missense_variant,p.Val47Phe,ENST00000302797,NM_147199.3;RP11-583F24.8,upstream_gene_variant,,ENST00000528646,;MRGPRX1,non_coding_transcript_exon_variant,,ENST00000526914,; A ENST00000302797 Transcript missense_variant 357/1190 139/969 47/322 V/F Gtt/Ttt rs371238052 1 -1 MRGPRX1 HGNC HGNC:17962 protein_coding YES CCDS7846.1 ENSP00000305766 Q96LB2 W8W3P5 UPI000003BCCF NM_147199.3 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF22,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs371238052 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 18934646 18934646 C A 1 0 0 0 0 1 0 0 0 9733 565 20 2 2 MRGPRX1 11 18934646 Missense_Mutation SNP C C3N-00547_T 168810 18934646 116151976 403 14733 PRMT3 0 . GRCh38 11 20407921 20407921 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.782A>G p.Asp261Gly p.D261G ENST00000331079 9/16 197 184 13 172 172 0 strelka-varscan-mutect PRMT3,missense_variant,p.Asp261Gly,ENST00000331079,NM_001145167.1,NM_005788.3;PRMT3,missense_variant,p.Asp199Gly,ENST00000437750,NM_001145166.1;PRMT3,3_prime_UTR_variant,,ENST00000330796,;PRMT3,non_coding_transcript_exon_variant,,ENST00000529592,; G ENST00000331079 Transcript missense_variant 999/2653 782/1596 261/531 D/G gAt/gGt 1 1 PRMT3 HGNC HGNC:30163 protein_coding YES CCDS7853.1 ENSP00000331879 O60678 UPI0000232A2C NM_001145167.1,NM_005788.3 tolerated(0.05) 9/16 PROSITE_profiles:PS51678,hmmpanther:PTHR11006:SF53,hmmpanther:PTHR11006,Pfam_domain:PF06325,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.38049 0.999965 1 1 1 0 G 3 3 49 20407921 20407921 A G 1 0 0 0 0 1 0 0 0 12669 333 12 5 5 PRMT3 11 20407921 Missense_Mutation SNP A C3N-00547_T 1473275 20407921 114678701 404 14734 SLC6A5 0 . GRCh38 11 20601219 20601219 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.94C>A p.Pro32Thr p.P32T ENST00000525748 2/16 144 110 34 158 157 1 strelka-varscan-mutect SLC6A5,missense_variant,p.Pro32Thr,ENST00000525748,NM_004211.3;SLC6A5,missense_variant,p.Pro32Thr,ENST00000298923,; A ENST00000525748 Transcript missense_variant 367/7084 94/2394 32/797 P/T Ccc/Acc 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 tolerated_low_confidence(0.61) 2/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 20601219 20601219 C A 1 0 0 0 0 1 0 0 0 14970 855 30 2 2 SLC6A5 11 20601219 Missense_Mutation SNP C C3N-00547_T 193298 20601219 114485403 405 14735 BDNF 0 . GRCh38 11 27657918 27657918 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.893G>A p.Arg298Gln p.R298Q ENST00000438929 3/3 561 488 73 443 442 1 strelka-varscan-mutect BDNF,missense_variant,p.Arg216Gln,ENST00000525528,NM_170735.5;BDNF,missense_variant,p.Arg216Gln,ENST00000439476,NM_001143816.1;BDNF,missense_variant,p.Arg224Gln,ENST00000314915,NM_170731.4;BDNF,missense_variant,p.Arg216Gln,ENST00000420794,NM_001143811.1;BDNF,missense_variant,p.Arg216Gln,ENST00000418212,NM_001143814.1;BDNF,missense_variant,p.Arg216Gln,ENST00000395981,NM_170732.4;BDNF,missense_variant,p.Arg298Gln,ENST00000438929,NM_001143810.1;BDNF,missense_variant,p.Arg216Gln,ENST00000395980,NM_170733.3;BDNF,missense_variant,p.Arg216Gln,ENST00000356660,NM_001709.4;BDNF,missense_variant,p.Arg216Gln,ENST00000533246,NM_001143813.1;BDNF,missense_variant,p.Arg216Gln,ENST00000395978,NM_001143806.1;BDNF,missense_variant,p.Arg231Gln,ENST00000395986,NM_170734.3;BDNF,missense_variant,p.Arg216Gln,ENST00000532997,NM_001143807.1;BDNF,missense_variant,p.Arg216Gln,ENST00000530861,NM_001143812.1;BDNF,missense_variant,p.Arg216Gln,ENST00000533131,;BDNF,missense_variant,p.Arg216Gln,ENST00000525950,NM_001143805.1;BDNF,missense_variant,p.Arg216Gln,ENST00000395983,NM_001143809.1,NM_001143808.1;BDNF-AS,intron_variant,,ENST00000499008,;BDNF-AS,intron_variant,,ENST00000499568,;BDNF-AS,intron_variant,,ENST00000501176,;BDNF-AS,intron_variant,,ENST00000500662,;BDNF-AS,intron_variant,,ENST00000502161,;BDNF-AS,intron_variant,,ENST00000530686,;BDNF-AS,intron_variant,,ENST00000530313,;BDNF-AS,intron_variant,,ENST00000532965,;BDNF,non_coding_transcript_exon_variant,,ENST00000584049,;BDNF,3_prime_UTR_variant,,ENST00000530786,; T ENST00000438929 Transcript missense_variant 1034/4059 893/990 298/329 R/Q cGg/cAg 1 -1 BDNF HGNC HGNC:1033 protein_coding YES CCDS44558.1 ENSP00000414303 P23560 UPI0001594492 NM_001143810.1 deleterious(0) 3/3 Gene3D:2.10.90.10,PD002052,Pfam_domain:PF00243,Prints_domain:PR00268,PROSITE_profiles:PS50270,hmmpanther:PTHR11589,hmmpanther:PTHR11589:SF3,SMART_domains:SM00140,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 27657918 27657918 C T 1 0 0 0 0 1 0 0 0 1541 652 23 1 1 BDNF 11 27657918 Missense_Mutation SNP C C3N-00547_T 7056699 27657918 107428704 406 14736 BDNF 0 . GRCh38 11 27658081 27658081 + Missense_Mutation SNP C C T C3N-00547_T C3N-00547_N C C c.730G>A p.Gly244Arg p.G244R ENST00000438929 3/3 484 391 93 413 413 0 strelka-varscan-mutect BDNF,missense_variant,p.Gly162Arg,ENST00000525528,NM_170735.5;BDNF,missense_variant,p.Gly162Arg,ENST00000439476,NM_001143816.1;BDNF,missense_variant,p.Gly170Arg,ENST00000314915,NM_170731.4;BDNF,missense_variant,p.Gly162Arg,ENST00000420794,NM_001143811.1;BDNF,missense_variant,p.Gly162Arg,ENST00000418212,NM_001143814.1;BDNF,missense_variant,p.Gly162Arg,ENST00000395981,NM_170732.4;BDNF,missense_variant,p.Gly244Arg,ENST00000438929,NM_001143810.1;BDNF,missense_variant,p.Gly162Arg,ENST00000395980,NM_170733.3;BDNF,missense_variant,p.Gly162Arg,ENST00000356660,NM_001709.4;BDNF,missense_variant,p.Gly162Arg,ENST00000533246,NM_001143813.1;BDNF,missense_variant,p.Gly162Arg,ENST00000395978,NM_001143806.1;BDNF,missense_variant,p.Gly177Arg,ENST00000395986,NM_170734.3;BDNF,missense_variant,p.Gly162Arg,ENST00000532997,NM_001143807.1;BDNF,missense_variant,p.Gly162Arg,ENST00000530861,NM_001143812.1;BDNF,missense_variant,p.Gly162Arg,ENST00000533131,;BDNF,missense_variant,p.Gly162Arg,ENST00000525950,NM_001143805.1;BDNF,missense_variant,p.Gly162Arg,ENST00000395983,NM_001143809.1,NM_001143808.1;BDNF-AS,intron_variant,,ENST00000499008,;BDNF-AS,intron_variant,,ENST00000499568,;BDNF-AS,intron_variant,,ENST00000501176,;BDNF-AS,intron_variant,,ENST00000500662,;BDNF-AS,intron_variant,,ENST00000502161,;BDNF-AS,intron_variant,,ENST00000530686,;BDNF-AS,intron_variant,,ENST00000530313,;BDNF-AS,intron_variant,,ENST00000532965,;BDNF,non_coding_transcript_exon_variant,,ENST00000584049,;BDNF,3_prime_UTR_variant,,ENST00000530786,; T ENST00000438929 Transcript missense_variant 871/4059 730/990 244/329 G/R Ggg/Agg COSM1246067,COSM1246068 1 -1 BDNF HGNC HGNC:1033 protein_coding YES CCDS44558.1 ENSP00000414303 P23560 UPI0001594492 NM_001143810.1 tolerated(0.48) 3/3 Gene3D:2.10.90.10,PD002052,Pfam_domain:PF00243,PROSITE_profiles:PS50270,hmmpanther:PTHR11589,hmmpanther:PTHR11589:SF3,SMART_domains:SM00140,Superfamily_domains:SSF57501 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 27658081 27658081 C T 1 0 0 0 0 1 0 0 0 1541 652 23 1 1 BDNF 11 27658081 Missense_Mutation SNP C C3N-00547_T 163 27658081 107428541 407 14737 DCDC1 0 . GRCh38 11 30911407 30911407 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.988G>T p.Val330Leu p.V330L ENST00000406071 9/20 256 217 39 180 180 0 strelka-varscan-mutect DCDC1,missense_variant,p.Val1223Leu,ENST00000597505,;DCDC1,missense_variant,p.Val330Leu,ENST00000406071,NM_020869.3;DCDC1,missense_variant,p.Val258Leu,ENST00000444572,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;DCDC1,upstream_gene_variant,,ENST00000303697,;DCDC1,upstream_gene_variant,,ENST00000429306,; A ENST00000406071 Transcript missense_variant 1304/4758 988/2673 330/890 V/L Gtg/Ttg 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 tolerated(0.18) 9/20 PROSITE_profiles:PS50231,hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958,Gene3D:2.80.10.50,Superfamily_domains:SSF50370 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 30911407 30911407 C A 1 0 0 0 0 1 0 0 0 4086 478 17 2 2 DCDC1 11 30911407 Missense_Mutation SNP C C3N-00547_T 3253326 30911407 104175215 408 14738 PAX6 0 . GRCh38 11 31801612 31801612 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.348C>A p.= p.I116I ENST00000419022 7/14 748 619 129 620 619 1 strelka-varscan-mutect PAX6,synonymous_variant,p.=,ENST00000419022,NM_001310158.1,NM_001310161.1,NM_001258462.1;PAX6,synonymous_variant,p.=,ENST00000606377,NM_001310161.1,NM_001258463.1;PAX6,synonymous_variant,p.=,ENST00000379129,;PAX6,synonymous_variant,p.=,ENST00000379107,;PAX6,synonymous_variant,p.=,ENST00000379132,NM_001127612.1;PAX6,synonymous_variant,p.=,ENST00000379123,NM_001258464.1,NM_000280.4;PAX6,synonymous_variant,p.=,ENST00000379109,;PAX6,synonymous_variant,p.=,ENST00000379115,NM_001604.5;PAX6,synonymous_variant,p.=,ENST00000241001,;PAX6,synonymous_variant,p.=,ENST00000379111,NM_001258465.1;PAX6,intron_variant,,ENST00000455099,;PAX6,downstream_gene_variant,,ENST00000525535,;PAX6,downstream_gene_variant,,ENST00000524853,;PAX6,downstream_gene_variant,,ENST00000423822,;PAX6,downstream_gene_variant,,ENST00000438681,;PAX6,non_coding_transcript_exon_variant,,ENST00000471303,;PAX6,non_coding_transcript_exon_variant,,ENST00000481563,;PAX6,non_coding_transcript_exon_variant,,ENST00000534353,;PAX6,downstream_gene_variant,,ENST00000533156,;PAX6,upstream_gene_variant,,ENST00000531910,;PAX6,upstream_gene_variant,,ENST00000530373,;PAX6,downstream_gene_variant,,ENST00000530714,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000534390,;PAX6,intron_variant,,ENST00000464174,;PAX6,downstream_gene_variant,,ENST00000532175,;PAX6,downstream_gene_variant,,ENST00000527769,; T ENST00000419022 Transcript synonymous_variant 817/6922 348/1311 116/436 I atC/atA 1 -1 PAX6 HGNC HGNC:8620 protein_coding YES CCDS31452.1 ENSP00000404100 P26367 F1T0F8 UPI000002B0A0 NM_001310158.1,NM_001310161.1,NM_001258462.1 7/14 Gene3D:1.10.10.10,Pfam_domain:PF00292,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294,SMART_domains:SM00351,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 31801612 31801612 G T 1 0 0 0 0 0 0 0 1 11568 1164 41 2 2 PAX6 11 31801612 Silent SNP G C3N-00547_T 890205 31801612 103285010 409 14739 LRRC4C 0 . GRCh38 11 40114701 40114701 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1592G>T p.Gly531Val p.G531V ENST00000278198 2/2 221 103 118 231 231 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Gly531Val,ENST00000278198,;LRRC4C,missense_variant,p.Gly531Val,ENST00000527150,;LRRC4C,missense_variant,p.Gly531Val,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Gly531Val,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Gly531Val,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; A ENST00000278198 Transcript missense_variant 3556/4054 1592/1923 531/640 G/V gGg/gTg 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious(0) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 40114701 40114701 C A 1 0 0 0 0 1 0 0 0 8903 623 22 2 2 LRRC4C 11 40114701 Missense_Mutation SNP C C3N-00547_T 8313089 40114701 94971921 410 14740 EXT2 0 . GRCh38 11 44206821 44206821 + Silent SNP A A C novel C3N-00547_T C3N-00547_N A A c.1623A>C p.= p.P541P ENST00000395673 10/14 337 272 65 304 304 0 strelka-varscan-mutect EXT2,synonymous_variant,p.=,ENST00000395673,NM_000401.3;EXT2,synonymous_variant,p.=,ENST00000343631,;EXT2,synonymous_variant,p.=,ENST00000533608,NM_207122.1;EXT2,synonymous_variant,p.=,ENST00000358681,NM_001178083.1;EXT2,non_coding_transcript_exon_variant,,ENST00000531161,;EXT2,upstream_gene_variant,,ENST00000528159,; C ENST00000395673 Transcript synonymous_variant 1679/3454 1623/2256 541/751 P ccA/ccC 1 1 EXT2 HGNC HGNC:3513 protein_coding YES CCDS53618.1 ENSP00000379032 Q93063 UPI0000EE3A5C NM_000401.3 10/14 Gene3D:3.90.550.10,Pfam_domain:PF09258,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS rs1170535092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 44206821 44206821 A C 1 0 0 0 0 0 0 0 1 5192 204 8 5 5 EXT2 11 44206821 Silent SNP A C3N-00547_T 4092120 44206821 90879801 411 14741 MYBPC3 0 . GRCh38 11 47332671 47332671 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.3522C>A p.= p.A1174A ENST00000545968 32/35 162 98 64 142 142 0 strelka-varscan-mutect MYBPC3,synonymous_variant,p.=,ENST00000545968,NM_000256.3;MYBPC3,synonymous_variant,p.=,ENST00000256993,;MYBPC3,synonymous_variant,p.=,ENST00000399249,;MADD,downstream_gene_variant,,ENST00000342922,NM_130470.2;MADD,downstream_gene_variant,,ENST00000311027,NM_003682.3;MADD,downstream_gene_variant,,ENST00000395336,NM_130475.2;MADD,downstream_gene_variant,,ENST00000349238,NM_130473.2;MADD,downstream_gene_variant,,ENST00000402192,NM_130476.2;MADD,downstream_gene_variant,,ENST00000407859,NM_130471.2;MADD,downstream_gene_variant,,ENST00000402799,NM_130472.2,NM_001135943.1;MADD,downstream_gene_variant,,ENST00000406482,NM_130474.2;MADD,downstream_gene_variant,,ENST00000395344,NM_001135944.1;MADD,downstream_gene_variant,,ENST00000634938,;MYBPC3,downstream_gene_variant,,ENST00000544791,;MADD,downstream_gene_variant,,ENST00000469699,; T ENST00000545968 Transcript synonymous_variant 3577/4226 3522/3825 1174/1274 A gcC/gcA 1 -1 MYBPC3 HGNC HGNC:7551 protein_coding YES CCDS53621.1 ENSP00000442795 Q14896 UPI000006EEAA NM_000256.3 32/35 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 47332671 47332671 G T 1 0 0 0 0 0 0 0 1 10013 1219 43 2 2 MYBPC3 11 47332671 Silent SNP G C3N-00547_T 3125850 47332671 87753951 412 14742 FOLH1 0 . GRCh38 11 49185783 49185783 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.712G>T p.Gly238Trp p.G238W ENST00000256999 6/19 120 98 22 139 139 0 strelka-varscan-mutect FOLH1,missense_variant,p.Gly223Trp,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Gly238Trp,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Gly238Trp,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Gly223Trp,ENST00000533034,NM_001193472.1;FOLH1,intron_variant,,ENST00000343844,NM_001193473.1;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,;FOLH1,non_coding_transcript_exon_variant,,ENST00000526226,;FOLH1,intron_variant,,ENST00000525826,; A ENST00000256999 Transcript missense_variant 973/2635 712/2253 238/750 G/W Ggg/Tgg 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 tolerated(0.06) 6/19 Gene3D:3.50.30.30,Pfam_domain:PF02225,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF52025 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 49185783 49185783 C A 1 0 0 0 0 1 0 0 0 5840 594 21 2 2 FOLH1 11 49185783 Missense_Mutation SNP C C3N-00547_T 1853112 49185783 85900839 413 14743 OR4C15 0 . GRCh38 11 55554849 55554849 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.543G>T p.Lys181Asn p.K181N ENST00000314644 1/1 108 55 53 160 160 0 strelka-varscan-mutect OR4C15,missense_variant,p.Lys181Asn,ENST00000314644,NM_001001920.1; T ENST00000314644 Transcript missense_variant 543/1113 543/1113 181/370 K/N aaG/aaT 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF14,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1239461272 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 55554849 55554849 G T 1 0 0 0 0 1 0 0 0 11125 962 34 2 2 OR4C15 11 55554849 Missense_Mutation SNP G C3N-00547_T 6369066 55554849 79531773 414 14744 TRIM51 0 . GRCh38 11 55885517 55885517 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.89G>T p.Cys30Phe p.C30F ENST00000449290 2/7 261 218 43 255 255 0 strelka-varscan-mutect TRIM51,missense_variant,p.Cys30Phe,ENST00000449290,NM_032681.3;TRIM51,upstream_gene_variant,,ENST00000244891,;RP11-738O11.9,downstream_gene_variant,,ENST00000533247,; T ENST00000449290 Transcript missense_variant 181/1629 89/1359 30/452 C/F tGt/tTt 1 1 TRIM51 HGNC HGNC:19023 protein_coding YES ENSP00000395086 Q9BSJ1 UPI0000DFFA1E NM_032681.3 deleterious(0) 2/7 PROSITE_profiles:PS50089,hmmpanther:PTHR24103:SF302,hmmpanther:PTHR24103,PROSITE_patterns:PS00518,Pfam_domain:PF15227,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 55885517 55885517 G T 1 0 0 0 0 1 0 0 0 17019 1377 48 2 2 TRIM51 11 55885517 Missense_Mutation SNP G C3N-00547_T 330668 55885517 79201105 415 14745 TRIM51 0 . GRCh38 11 55885607 55885607 + Missense_Mutation SNP G G A rs367940835 C3N-00547_T C3N-00547_N G G c.179G>A p.Arg60Gln p.R60Q ENST00000449290 2/7 221 188 33 226 226 0 strelka-varscan-mutect TRIM51,missense_variant,p.Arg60Gln,ENST00000449290,NM_032681.3;TRIM51,upstream_gene_variant,,ENST00000244891,;RP11-738O11.9,downstream_gene_variant,,ENST00000533247,; A ENST00000449290 Transcript missense_variant 271/1629 179/1359 60/452 R/Q cGg/cAg rs367940835,COSM5050881 1 1 TRIM51 HGNC HGNC:19023 protein_coding YES ENSP00000395086 Q9BSJ1 UPI0000DFFA1E NM_032681.3 tolerated(0.73) 2/7 hmmpanther:PTHR24103:SF302,hmmpanther:PTHR24103,Gene3D:3.30.40.10,Superfamily_domains:SSF57850 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs367940835 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 49 55885607 55885607 G A 1 0 0 0 0 1 0 0 0 17019 1116 39 1 1 TRIM51 11 55885607 Missense_Mutation SNP G C3N-00547_T 90 55885607 79201015 416 14746 OR8J1 0 . GRCh38 11 56360662 56360662 + Missense_Mutation SNP G G T rs759085067 C3N-00547_T C3N-00547_N G G c.416G>T p.Arg139Leu p.R139L ENST00000303039 1/1 77 42 35 84 84 0 strelka-varscan-mutect OR8J1,missense_variant,p.Arg139Leu,ENST00000303039,NM_001005205.2;RPL5P29,downstream_gene_variant,,ENST00000482972,; T ENST00000303039 Transcript missense_variant 448/1074 416/951 139/316 R/L cGg/cTg rs759085067 1 1 OR8J1 HGNC HGNC:14855 protein_coding YES CCDS31529.1 ENSP00000304060 Q8NGP2 UPI000004BE58 NM_001005205.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF317,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs759085067 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 56360662 56360662 G T 1 0 0 0 0 1 0 0 0 11309 1116 39 1 1 OR8J1 11 56360662 Missense_Mutation SNP G C3N-00547_T 475055 56360662 78725960 417 14747 OR5B12 0 . GRCh38 11 58439999 58439999 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.153C>A p.= p.S51S ENST00000302572 1/1 185 86 99 220 220 0 strelka-varscan-mutect OR5B12,synonymous_variant,p.=,ENST00000302572,NM_001004733.2; T ENST00000302572 Transcript synonymous_variant 175/1054 153/945 51/314 S tcC/tcA 1 -1 OR5B12 HGNC HGNC:15432 protein_coding YES CCDS31551.1 ENSP00000306657 Q96R08 UPI00000015B2 NM_001004733.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF15,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 58439999 58439999 G T 1 0 0 0 0 0 0 0 1 11219 987 35 2 2 OR5B12 11 58439999 Silent SNP G C3N-00547_T 2079337 58439999 76646623 418 14748 MS4A14 0 . GRCh38 11 60416600 60416600 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1731G>T p.Lys577Asn p.K577N ENST00000531783 6/6 365 200 165 404 404 0 strelka-varscan-mutect MS4A14,missense_variant,p.Lys560Asn,ENST00000395001,NM_001261827.1;MS4A14,missense_variant,p.Lys544Asn,ENST00000300187,NM_032597.4;MS4A14,missense_variant,p.Lys577Asn,ENST00000531783,NM_001261828.1;MS4A14,missense_variant,p.Lys527Asn,ENST00000395005,NM_001079692.2;MS4A14,missense_variant,p.Lys432Asn,ENST00000531787,;MS4A14,3_prime_UTR_variant,,ENST00000530662,;MS4A14,3_prime_UTR_variant,,ENST00000527841,;MS4A14,3_prime_UTR_variant,,ENST00000525397,; T ENST00000531783 Transcript missense_variant 1822/2910 1731/2139 577/712 K/N aaG/aaT 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 deleterious(0) 6/6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 60416600 60416600 G T 1 0 0 0 0 1 0 0 0 9835 933 33 2 2 MS4A14 11 60416600 Missense_Mutation SNP G C3N-00547_T 1976601 60416600 74670022 419 14749 AHNAK 0 . GRCh38 11 62526622 62526622 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.7795G>T p.Val2599Phe p.V2599F ENST00000378024 5/5 280 138 142 304 304 0 strelka-varscan-mutect AHNAK,missense_variant,p.Val2599Phe,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; A ENST00000378024 Transcript missense_variant 8070/18787 7795/17673 2599/5890 V/F Gtt/Ttt 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 62526622 62526622 C A 1 0 0 0 0 1 0 0 0 491 478 17 2 2 AHNAK 11 62526622 Missense_Mutation SNP C C3N-00547_T 2110022 62526622 72560000 420 14750 SLC22A8 0 . GRCh38 11 63014645 63014645 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.314A>G p.Lys105Arg p.K105R ENST00000336232 2/11 54 26 28 50 50 0 strelka-varscan-mutect SLC22A8,missense_variant,p.Lys105Arg,ENST00000336232,NM_001184732.1,NM_004254.3;SLC22A8,missense_variant,p.Lys105Arg,ENST00000430500,;SLC22A8,missense_variant,p.Lys105Arg,ENST00000311438,;SLC22A8,missense_variant,p.Lys14Arg,ENST00000545207,NM_001184733.1;SLC22A8,intron_variant,,ENST00000535878,NM_001184736.1;SLC22A8,non_coding_transcript_exon_variant,,ENST00000544707,; C ENST00000336232 Transcript missense_variant 450/2178 314/1629 105/542 K/R aAg/aGg 1 -1 SLC22A8 HGNC HGNC:10972 protein_coding YES CCDS8042.1 ENSP00000337335 Q8TCC7 UPI0000036DF2 NM_001184732.1,NM_004254.3 tolerated(0.55) 2/11 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF294,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 63014645 63014645 T C 1 0 0 0 0 1 0 0 0 14726 1609 56 5 5 SLC22A8 11 63014645 Missense_Mutation SNP T C3N-00547_T 488023 63014645 72071977 421 14751 VEGFB 0 . GRCh38 11 64237217 64237217 + Silent SNP A A C rs200085344 C3N-00547_T C3N-00547_N A A c.405A>C p.= p.P135P ENST00000309422 5/7 151 126 25 112 112 0 strelka-varscan-mutect VEGFB,synonymous_variant,p.=,ENST00000309422,NM_003377.4;VEGFB,synonymous_variant,p.=,ENST00000426086,NM_001243733.1;DNAJC4,downstream_gene_variant,,ENST00000321685,NM_005528.3;DNAJC4,downstream_gene_variant,,ENST00000321460,NM_001307980.1;FKBP2,upstream_gene_variant,,ENST00000394540,NM_057092.2;DNAJC4,downstream_gene_variant,,ENST00000628077,;DNAJC4,downstream_gene_variant,,ENST00000355040,;FKBP2,upstream_gene_variant,,ENST00000309366,NM_004470.3;FKBP2,upstream_gene_variant,,ENST00000535135,;FKBP2,upstream_gene_variant,,ENST00000449942,NM_001135208.1;DNAJC4,downstream_gene_variant,,ENST00000535246,;VEGFB,upstream_gene_variant,,ENST00000541681,;RP11-783K16.14,upstream_gene_variant,,ENST00000534988,;RP11-783K16.14,upstream_gene_variant,,ENST00000539963,;VEGFB,non_coding_transcript_exon_variant,,ENST00000543462,;DNAJC4,downstream_gene_variant,,ENST00000537109,;FKBP2,upstream_gene_variant,,ENST00000541388,;DNAJC4,downstream_gene_variant,,ENST00000540945,;DNAJC4,downstream_gene_variant,,ENST00000536006,;FKBP2,upstream_gene_variant,,ENST00000536642,;DNAJC4,downstream_gene_variant,,ENST00000542376,;DNAJC4,downstream_gene_variant,,ENST00000538961,;DNAJC4,downstream_gene_variant,,ENST00000543791,;DNAJC4,downstream_gene_variant,,ENST00000543685,; C ENST00000309422 Transcript synonymous_variant 701/1380 405/624 135/207 P ccA/ccC rs200085344,COSM3726590,COSM3726591 1 1 VEGFB HGNC HGNC:12681 protein_coding YES CCDS8062.1 ENSP00000311127 P49765 Q7LAP4 UPI0000001047 NM_003377.4 5/7 hmmpanther:PTHR12025,hmmpanther:PTHR12025:SF12 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs200085344 . 0 204 4 0 0 0 0 2 -2.816705 0 0 1 0 0 C 2 2 49 64237217 64237217 A C 1 0 0 0 0 0 0 0 1 17696 202 7 5 5 VEGFB 11 64237217 Silent SNP A C3N-00547_T 1222572 64237217 70849405 422 14752 GPR137 0 . GRCh38 11 64286578 64286578 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.228G>A p.= p.L76L ENST00000411458 3/9 130 113 17 105 105 0 strelka-varscan-mutect GPR137,synonymous_variant,p.=,ENST00000539851,NM_001177358.1;GPR137,synonymous_variant,p.=,ENST00000438980,NM_001170880.1;GPR137,synonymous_variant,p.=,ENST00000411458,NM_001170726.1;GPR137,synonymous_variant,p.=,ENST00000313074,NM_020155.3;GPR137,synonymous_variant,p.=,ENST00000377702,NM_001170881.1;GPR137,synonymous_variant,p.=,ENST00000546139,;GPR137,synonymous_variant,p.=,ENST00000539833,;GPR137,synonymous_variant,p.=,ENST00000543383,;GPR137,synonymous_variant,p.=,ENST00000538032,;GPR137,synonymous_variant,p.=,ENST00000535675,;GPR137,synonymous_variant,p.=,ENST00000540370,;GPR137,synonymous_variant,p.=,ENST00000541952,;GPR137,synonymous_variant,p.=,ENST00000542190,;GPR137,synonymous_variant,p.=,ENST00000538244,;GPR137,intron_variant,,ENST00000536667,;KCNK4,upstream_gene_variant,,ENST00000422670,NM_033310.2;KCNK4,upstream_gene_variant,,ENST00000538767,;BAD,upstream_gene_variant,,ENST00000394532,NM_004322.3;BAD,upstream_gene_variant,,ENST00000309032,NM_032989.2;BAD,upstream_gene_variant,,ENST00000394531,;BAD,upstream_gene_variant,,ENST00000544785,;GPR137,upstream_gene_variant,,ENST00000536282,;GPR137,synonymous_variant,p.=,ENST00000546201,;GPR137,non_coding_transcript_exon_variant,,ENST00000536017,;KCNK4,upstream_gene_variant,,ENST00000453423,;KCNK4,upstream_gene_variant,,ENST00000538846,;BAD,upstream_gene_variant,,ENST00000544271,;GPR137,upstream_gene_variant,,ENST00000545366,; A ENST00000411458 Transcript synonymous_variant 256/1495 228/1428 76/475 L ctG/ctA 1 1 GPR137 HGNC HGNC:24300 protein_coding YES CCDS53655.1 ENSP00000411827 Q96N19 UPI00017A7FAD NM_001170726.1 3/9 hmmpanther:PTHR15146,hmmpanther:PTHR15146:SF5,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 64286578 64286578 G A 1 0 0 0 0 0 0 0 1 6531 1306 46 3 3 GPR137 11 64286578 Silent SNP G C3N-00547_T 49361 64286578 70800044 423 14753 SNX32 0 . GRCh38 11 65853322 65853323 + Frame_Shift_Ins INS - - G novel C3N-00547_T C3N-00547_N - - c.1204dupG p.Glu402GlyfsTer5 p.E402Gfs*5 ENST00000308342 13/13 241 209 32 198 198 0 sindel-varindel-pindel SNX32,frameshift_variant,p.Glu402GlyfsTer5,ENST00000308342,NM_152760.2;CFL1,downstream_gene_variant,,ENST00000525451,;CFL1,downstream_gene_variant,,ENST00000308162,NM_005507.2;CFL1,downstream_gene_variant,,ENST00000531407,;CFL1,downstream_gene_variant,,ENST00000527344,;MUS81,upstream_gene_variant,,ENST00000529857,;CFL1,downstream_gene_variant,,ENST00000524553,;CFL1,downstream_gene_variant,,ENST00000532134,;CFL1,downstream_gene_variant,,ENST00000534769,;CFL1,downstream_gene_variant,,ENST00000534784,;CFL1,downstream_gene_variant,,ENST00000530413,;CFL1,downstream_gene_variant,,ENST00000531413,;CFL1,downstream_gene_variant,,ENST00000526975,;CFL1,intron_variant,,ENST00000527752,;SNX32,downstream_gene_variant,,ENST00000531795,;SNX32,intron_variant,,ENST00000530101,;CFL1,downstream_gene_variant,,ENST00000530945,;SNX32,downstream_gene_variant,,ENST00000526972,;SNX32,downstream_gene_variant,,ENST00000531503,;SNX32,downstream_gene_variant,,ENST00000533298,;SNX32,downstream_gene_variant,,ENST00000524729,;SNX32,downstream_gene_variant,,ENST00000533236,;SNX32,downstream_gene_variant,,ENST00000534387,; G ENST00000308342 Transcript frameshift_variant 1624-1625/2003 1199-1200/1212 400/403 K/KX aag/aaGg 1 1 SNX32 HGNC HGNC:26423 protein_coding YES CCDS8113.2 ENSP00000310620 Q86XE0 UPI000000DAEA NM_152760.2 13/13 hmmpanther:PTHR10555:SF137,hmmpanther:PTHR10555,PIRSF_domain:PIRSF036924 HIGH 1 insertion 1 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 49 65853322 65853322 - G 1 0 1 1 0 0 0 0 0 15223 72 3 0 0 SNX32 11 65853322 Frame_Shift_Ins INS - C3N-00547_T 1566744 65853322 69233300 424 14754 BBS1 0 . GRCh38 11 66523832 66523832 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1171G>C p.Glu391Gln p.E391Q ENST00000419755 11/17 683 648 35 687 686 1 strelka-varscan-mutect CTD-3074O7.11,missense_variant,p.Glu391Gln,ENST00000419755,;BBS1,missense_variant,p.Glu354Gln,ENST00000318312,NM_024649.4;BBS1,missense_variant,p.Glu257Gln,ENST00000455748,;BBS1,3_prime_UTR_variant,,ENST00000630659,;BBS1,intron_variant,,ENST00000393994,;ZDHHC24,intron_variant,,ENST00000526986,;BBS1,downstream_gene_variant,,ENST00000525809,;BBS1,non_coding_transcript_exon_variant,,ENST00000529766,;BBS1,downstream_gene_variant,,ENST00000529953,;BBS1,3_prime_UTR_variant,,ENST00000526760,;BBS1,3_prime_UTR_variant,,ENST00000532908,;BBS1,non_coding_transcript_exon_variant,,ENST00000529955,;BBS1,non_coding_transcript_exon_variant,,ENST00000527959,;BBS1,non_coding_transcript_exon_variant,,ENST00000529895,;ZDHHC24,intron_variant,,ENST00000534073,;BBS1,downstream_gene_variant,,ENST00000533557,;BBS1,downstream_gene_variant,,ENST00000527251,;BBS1,downstream_gene_variant,,ENST00000533644,;BBS1,downstream_gene_variant,,ENST00000524458,;BBS1,downstream_gene_variant,,ENST00000533430,;BBS1,downstream_gene_variant,,ENST00000524907,;BBS1,downstream_gene_variant,,ENST00000526035,;BBS1,downstream_gene_variant,,ENST00000532283,;BBS1,downstream_gene_variant,,ENST00000524884,;BBS1,downstream_gene_variant,,ENST00000528543,; C ENST00000419755 Transcript missense_variant 1249/3547 1171/1893 391/630 E/Q Gag/Cag 1 1 CTD-3074O7.11 Clone_based_vega_gene protein_coding YES ENSP00000398526 UPI000006E494 tolerated(0.12) 11/17 hmmpanther:PTHR20870,hmmpanther:PTHR20870:SF0,Gene3D:2.130.10.10,Superfamily_domains:SSF50998 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 66523832 66523832 G C 1 0 0 0 0 1 0 0 0 1482 943 33 4 4 BBS1 11 66523832 Missense_Mutation SNP G C3N-00547_T 670510 66523832 68562790 425 14755 FAT3 0 . GRCh38 11 92352590 92352590 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.28C>A p.Pro10Thr p.P10T ENST00000525166 1/27 153 99 54 201 200 1 strelka-varscan-mutect FAT3,missense_variant,p.Pro160Thr,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Pro10Thr,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; A ENST00000525166 Transcript missense_variant 50/18699 28/13320 10/4439 P/T Ccc/Acc COSM5254338,COSM545689,COSM545690 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.02) 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 92352590 92352590 C A 1 0 0 0 0 1 0 0 0 5551 507 18 2 2 FAT3 11 92352590 Missense_Mutation SNP C C3N-00547_T 25828758 92352590 42734032 426 14756 FAT3 0 . GRCh38 11 92882831 92882831 + Silent SNP G G C C3N-00547_T C3N-00547_N G G c.11925G>C p.= p.T3975T ENST00000525166 23/27 159 101 58 199 199 0 strelka-varscan-mutect FAT3,synonymous_variant,p.=,ENST00000409404,NM_001008781.2;FAT3,synonymous_variant,p.=,ENST00000525166,;FAT3,synonymous_variant,p.=,ENST00000533797,;FAT3,upstream_gene_variant,,ENST00000489716,;FAT3,upstream_gene_variant,,ENST00000469900,; C ENST00000525166 Transcript synonymous_variant 11947/18699 11925/13320 3975/4439 T acG/acC COSM5157553,COSM5157554,COSM5157555 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 23/27 PROSITE_profiles:PS50026,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS rs1448341536 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 92882831 92882831 G C 1 0 0 0 0 0 0 0 1 5551 1074 38 4 4 FAT3 11 92882831 Silent SNP G C3N-00547_T 530241 92882831 42203791 427 14757 PANX1 0 . GRCh38 11 94179694 94179694 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.638A>G p.Tyr213Cys p.Y213C ENST00000227638 4/5 130 76 54 163 163 0 strelka-varscan-mutect PANX1,missense_variant,p.Tyr213Cys,ENST00000227638,NM_015368.3;PANX1,missense_variant,p.Tyr213Cys,ENST00000436171,; G ENST00000227638 Transcript missense_variant 1023/2769 638/1281 213/426 Y/C tAc/tGc 1 1 PANX1 HGNC HGNC:8599 protein_coding YES CCDS8296.1 ENSP00000227638 Q96RD7 A0A024R397 UPI000004C63F NM_015368.3 deleterious(0) 4/5 Pfam_domain:PF00876,PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF5,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 94179694 94179694 A G 1 0 0 0 0 1 0 0 0 11501 391 14 5 5 PANX1 11 94179694 Missense_Mutation SNP A C3N-00547_T 1296863 94179694 40906928 428 14758 MMP8 0 . GRCh38 11 102713391 102713391 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.1361G>A p.Arg454Lys p.R454K ENST00000236826 10/10 181 121 60 210 210 0 strelka-varscan-mutect MMP8,missense_variant,p.Arg454Lys,ENST00000236826,NM_002424.2,NM_001304441.1,NM_001304442.1;MMP8,3_prime_UTR_variant,,ENST00000438475,;MMP8,3_prime_UTR_variant,,ENST00000528662,; T ENST00000236826 Transcript missense_variant 1460/3056 1361/1404 454/467 R/K aGa/aAa 1 -1 MMP8 HGNC HGNC:7175 protein_coding YES CCDS8320.1 ENSP00000236826 P22894 UPI00000422BB NM_002424.2,NM_001304441.1,NM_001304442.1 tolerated(0.07) 10/10 Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF137,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 102713391 102713391 C T 1 0 0 0 0 1 0 0 0 9631 913 32 3 3 MMP8 11 102713391 Missense_Mutation SNP C C3N-00547_T 8533697 102713391 32373231 429 14759 PKNOX2 0 . GRCh38 11 125429985 125429985 + Missense_Mutation SNP A A C novel C3N-00547_T C3N-00547_N A A c.1036A>C p.Ile346Leu p.I346L ENST00000298282 12/13 123 57 66 145 145 0 strelka-varscan-mutect PKNOX2,missense_variant,p.Ile346Leu,ENST00000298282,NM_022062.2;PKNOX2,non_coding_transcript_exon_variant,,ENST00000530517,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000531116,;PKNOX2,3_prime_UTR_variant,,ENST00000532623,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000526955,; C ENST00000298282 Transcript missense_variant 1307/3687 1036/1419 346/472 I/L Atc/Ctc 1 1 PKNOX2 HGNC HGNC:16714 protein_coding YES CCDS41730.1 ENSP00000298282 Q96KN3 UPI000023271E NM_022062.2 deleterious(0) 12/13 PROSITE_profiles:PS50071,hmmpanther:PTHR11850:SF53,hmmpanther:PTHR11850,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 125429985 125429985 A C 1 0 0 0 0 1 0 0 0 12079 217 8 5 5 PKNOX2 11 125429985 Missense_Mutation SNP A C3N-00547_T 22716594 125429985 9656637 430 14760 VPS26B 0 . GRCh38 11 134245524 134245524 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.945G>A p.= p.E315E ENST00000281187 6/6 263 208 55 211 211 0 strelka-varscan-mutect VPS26B,synonymous_variant,p.=,ENST00000281187,NM_052875.4;VPS26B,synonymous_variant,p.=,ENST00000525095,;THYN1,downstream_gene_variant,,ENST00000341541,NM_014174.2;THYN1,downstream_gene_variant,,ENST00000392594,NM_199298.1,NM_001037305.1;THYN1,downstream_gene_variant,,ENST00000392595,;THYN1,downstream_gene_variant,,ENST00000352327,NM_001037304.1,NM_199297.1;VPS26B,non_coding_transcript_exon_variant,,ENST00000531741,;THYN1,downstream_gene_variant,,ENST00000533975,;THYN1,downstream_gene_variant,,ENST00000531135,;VPS26B,downstream_gene_variant,,ENST00000527586,;THYN1,downstream_gene_variant,,ENST00000533781,;VPS26B,downstream_gene_variant,,ENST00000530402,;VPS26B,downstream_gene_variant,,ENST00000525918,; A ENST00000281187 Transcript synonymous_variant 1423/3691 945/1011 315/336 E gaG/gaA 1 1 VPS26B HGNC HGNC:28119 protein_coding YES CCDS8495.1 ENSP00000281187 Q4G0F5 A0A024R3L9 UPI000006DC43 NM_052875.4 6/6 hmmpanther:PTHR12233,hmmpanther:PTHR12233:SF5 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 134245524 134245524 G A 1 0 0 0 0 0 0 0 1 17744 991 35 3 3 VPS26B 11 134245524 Silent SNP G C3N-00547_T 8815539 134245524 841098 431 14761 IQSEC3 0 . GRCh38 12 139328 139328 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1965C>A p.Tyr655Ter p.Y655* ENST00000538872 4/14 85 59 26 74 74 0 strelka-varscan-mutect IQSEC3,stop_gained,p.Tyr655Ter,ENST00000538872,NM_001170738.1;IQSEC3,stop_gained,p.Tyr352Ter,ENST00000382841,NM_015232.1;RP11-598F7.4,intron_variant,,ENST00000505893,;RP11-598F7.4,downstream_gene_variant,,ENST00000508953,; A ENST00000538872 Transcript stop_gained 2083/7094 1965/3549 655/1182 Y/* taC/taA 1 1 IQSEC3 HGNC HGNC:29193 protein_coding YES CCDS53728.1 ENSP00000437554 Q9UPP2 UPI0000DBEEF0 NM_001170738.1 4/14 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF62,Pfam_domain:PF01369,Gene3D:1.10.220.20,SMART_domains:SM00222,Superfamily_domains:SSF48425 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 139328 139328 C A 1 0 0 0 0 0 1 0 0 7725 518 18 2 2 IQSEC3 12 139328 Nonsense_Mutation SNP C C3N-00547_T 139328 133135981 432 14762 58 2 IQSEC3 0 . GRCh38 12 139330 139330 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.1967G>A p.Arg656His p.R656H ENST00000538872 4/14 84 58 26 72 72 0 strelka-varscan-mutect IQSEC3,missense_variant,p.Arg656His,ENST00000538872,NM_001170738.1;IQSEC3,missense_variant,p.Arg353His,ENST00000382841,NM_015232.1;RP11-598F7.4,intron_variant,,ENST00000505893,;RP11-598F7.4,downstream_gene_variant,,ENST00000508953,; A ENST00000538872 Transcript missense_variant 2085/7094 1967/3549 656/1182 R/H cGc/cAc 1 1 IQSEC3 HGNC HGNC:29193 protein_coding YES CCDS53728.1 ENSP00000437554 Q9UPP2 UPI0000DBEEF0 NM_001170738.1 deleterious(0) 4/14 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF62,Pfam_domain:PF01369,Gene3D:1.10.220.20,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE SNV 5 1 PASS . . 0 195 14 0 0 0 0 0 -20 0.9999286 1 1 1 0 A 3 1 49 139330 139330 G A 1 0 0 0 0 1 0 0 0 7725 1087 38 1 1 IQSEC3 12 139330 Missense_Mutation SNP G C3N-00547_T 2 139330 133135979 433 14763 58 2 CRACR2A 0 . GRCh38 12 3638267 3638267 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1459T>C p.Phe487Leu p.F487L ENST00000440314 14/20 388 336 52 273 273 0 strelka-varscan-mutect CRACR2A,missense_variant,p.Phe487Leu,ENST00000440314,NM_001144958.1;CRACR2A,downstream_gene_variant,,ENST00000535292,;CRACR2A,3_prime_UTR_variant,,ENST00000333750,; G ENST00000440314 Transcript missense_variant 1933/2697 1459/2196 487/731 F/L Ttt/Ctt 1 -1 CRACR2A HGNC HGNC:28657 protein_coding YES CCDS44803.1 ENSP00000409382 Q9BSW2 UPI00017A8807 NM_001144958.1 tolerated(0.68) 14/20 hmmpanther:PTHR22621:SF2,hmmpanther:PTHR22621 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 3638267 3638267 A G 1 0 0 0 0 1 0 0 0 3643 72 3 5 5 CRACR2A 12 3638267 Missense_Mutation SNP A C3N-00547_T 3498937 3638267 129637042 434 14764 CRACR2A 0 . GRCh38 12 3696842 3696842 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.158G>A p.Arg53Lys p.R53K ENST00000440314 4/20 419 332 87 423 423 0 strelka-varscan-mutect CRACR2A,missense_variant,p.Arg53Lys,ENST00000440314,NM_001144958.1;CRACR2A,missense_variant,p.Arg53Lys,ENST00000252322,NM_032680.3; T ENST00000440314 Transcript missense_variant 632/2697 158/2196 53/731 R/K aGg/aAg 1 -1 CRACR2A HGNC HGNC:28657 protein_coding YES CCDS44803.1 ENSP00000409382 Q9BSW2 UPI00017A8807 NM_001144958.1 tolerated(0.39) 4/20 hmmpanther:PTHR22621:SF2,hmmpanther:PTHR22621,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 3696842 3696842 C T 1 0 0 0 0 1 0 0 0 3643 681 24 3 3 CRACR2A 12 3696842 Missense_Mutation SNP C C3N-00547_T 58575 3696842 129578467 435 14765 GALNT8 0 . GRCh38 12 4811572 4811572 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1531A>G p.Ser511Gly p.S511G ENST00000280684 1/1 168 144 24 169 169 0 strelka-varscan-mutect GALNT8,missense_variant,p.Ser511Gly,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Ser511Gly,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; G ENST00000280684 Transcript missense_variant 2397/4237 1531/1590 511/529 S/G Agc/Ggc 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD tolerated_low_confidence(0.26) 1/1 Prints_domain:PR01513,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 4811572 4811572 A G 1 0 0 0 0 1 0 0 0 6090 188 7 5 5 GALNT8 12 4811572 Missense_Mutation SNP A C3N-00547_T 1114730 4811572 128463737 436 14766 CD4 0 . GRCh38 12 6816324 6816324 + Silent SNP T T A novel C3N-00547_T C3N-00547_N T T c.876T>A p.= p.A292A ENST00000011653 6/10 248 195 53 278 278 0 strelka-varscan-mutect CD4,synonymous_variant,p.=,ENST00000011653,NM_000616.4;CD4,downstream_gene_variant,,ENST00000541982,;CD4,non_coding_transcript_exon_variant,,ENST00000538827,;CD4,downstream_gene_variant,,ENST00000536610,;CD4,downstream_gene_variant,,ENST00000536563,;CD4,downstream_gene_variant,,ENST00000536590,;CD4,non_coding_transcript_exon_variant,,ENST00000437800,;CD4,downstream_gene_variant,,ENST00000544344,;CD4,downstream_gene_variant,,ENST00000543755,; A ENST00000011653 Transcript synonymous_variant 1134/3114 876/1377 292/458 A gcT/gcA 1 1 CD4 HGNC HGNC:1678 protein_coding YES CCDS8562.1 ENSP00000011653 P01730 UPI0000001294 NM_000616.4 6/10 hmmpanther:PTHR11422:SF0,hmmpanther:PTHR11422,Gene3D:2.60.40.10,Pfam_domain:PF09191,SMART_domains:SM00409,Superfamily_domains:SSF48726,Prints_domain:PR00692 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 6816324 6816324 T A 1 0 0 0 0 0 0 0 1 2718 1567 55 4 4 CD4 12 6816324 Silent SNP T C3N-00547_T 2004752 6816324 126458985 437 14767 RP11-545J16.1 0 . GRCh38 12 20875433 20875433 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.926C>G p.Ala309Gly p.A309G ENST00000261196 7/14 76 66 10 135 135 0 strelka-varscan-mutect SLCO1B3,missense_variant,p.Ala309Gly,ENST00000261196,;SLCO1B3,missense_variant,p.Ala309Gly,ENST00000381545,NM_019844.3;RP11-545J16.1,missense_variant,p.Ala309Gly,ENST00000540229,;SLCO1B3,missense_variant,p.Ala133Gly,ENST00000544370,;RP11-545J16.1,intron_variant,,ENST00000381541,;SLCO1B3,downstream_gene_variant,,ENST00000540853,; G ENST00000261196 Transcript missense_variant 993/2840 926/2109 309/702 A/G gCt/gGt 1 1 SLCO1B3 HGNC HGNC:10961 protein_coding YES CCDS8684.1 ENSP00000261196 Q9NPD5 UPI000013544A tolerated(0.21) 7/14 PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 20875433 20875433 C G 1 0 0 0 0 1 0 0 0 13751 797 28 4 4 RP11-545J16.1 12 20875433 Missense_Mutation SNP C C3N-00547_T 14059109 20875433 112399876 438 14768 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C A rs121913529 C3N-00547_T C3N-00547_N C C c.35G>T p.Gly12Val p.G12V ENST00000256078 2/6 319 203 116 326 326 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Val,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Val,ENST00000556131,;KRAS,missense_variant,p.Gly12Val,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Val,ENST00000557334,; A ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/V gGt/gTt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 25245350 25245350 C A 1 0 0 0 0 1 0 0 0 8318 507 18 2 2 KRAS 12 25245350 Missense_Mutation SNP C C3N-00547_T 4369917 25245350 108029959 439 14769 LRRK2 0 . GRCh38 12 40235654 40235654 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.376A>T p.Asn126Tyr p.N126Y ENST00000298910 4/51 296 202 94 306 306 0 strelka-varscan-mutect LRRK2,missense_variant,p.Asn126Tyr,ENST00000298910,NM_198578.3;LRRK2,missense_variant,p.Asn126Tyr,ENST00000343742,;LRRK2,missense_variant,p.Asn55Tyr,ENST00000416796,;LRRK2,downstream_gene_variant,,ENST00000474202,; T ENST00000298910 Transcript missense_variant 434/9158 376/7584 126/2527 N/Y Aat/Tat 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 tolerated(0.16) 4/51 Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 40235654 40235654 A T 1 0 0 0 0 1 0 0 0 8939 362 13 4 4 LRRK2 12 40235654 Missense_Mutation SNP A C3N-00547_T 14990304 40235654 93039655 440 14770 NELL2 0 . GRCh38 12 44523365 44523365 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2074C>A p.His692Asn p.H692N ENST00000437801 18/21 327 270 57 350 349 1 strelka-varscan-mutect NELL2,missense_variant,p.His642Asn,ENST00000429094,NM_001145108.1;NELL2,missense_variant,p.His692Asn,ENST00000437801,NM_001145107.1;NELL2,missense_variant,p.His641Asn,ENST00000395487,NM_001145109.1;NELL2,missense_variant,p.His642Asn,ENST00000452445,NM_006159.2;NELL2,missense_variant,p.His594Asn,ENST00000551601,;NELL2,missense_variant,p.His641Asn,ENST00000549027,;NELL2,missense_variant,p.His665Asn,ENST00000333837,NM_001145110.1;NELL2,missense_variant,p.His55Asn,ENST00000550139,;NELL2,non_coding_transcript_exon_variant,,ENST00000547636,; T ENST00000437801 Transcript missense_variant 2446/3279 2074/2601 692/866 H/N Cat/Aat 1 -1 NELL2 HGNC HGNC:7751 protein_coding YES CCDS44863.1 ENSP00000416341 Q99435 UPI000191537D NM_001145107.1 tolerated(0.06) 18/21 PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF0,Gene3D:2.10.70.10,SMART_domains:SM00214 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 44523365 44523365 G T 1 0 0 0 0 1 0 0 0 10365 1348 47 2 2 NELL2 12 44523365 Missense_Mutation SNP G C3N-00547_T 4287711 44523365 88751944 441 14771 ARID2 0 . GRCh38 12 45817754 45817754 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.503G>T p.Gly168Val p.G168V ENST00000334344 5/21 263 177 86 312 312 0 strelka-varscan-mutect ARID2,missense_variant,p.Gly168Val,ENST00000334344,NM_152641.2;ARID2,missense_variant,p.Gly19Val,ENST00000422737,; T ENST00000334344 Transcript missense_variant 675/8642 503/5508 168/1835 G/V gGa/gTa 1 1 ARID2 HGNC HGNC:18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 UPI00001D7973 NM_152641.2 deleterious(0.02) 5/21 hmmpanther:PTHR22970,hmmpanther:PTHR22970:SF14,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 45817754 45817754 G T 1 0 0 0 0 1 0 0 0 1051 1174 41 2 2 ARID2 12 45817754 Missense_Mutation SNP G C3N-00547_T 1294389 45817754 87457555 442 14772 LINC00935 0 . GRCh38 12 48759300 48759300 + Missense_Mutation SNP C C A rs758541354 C3N-00547_T C3N-00547_N C C c.171C>A p.His57Gln p.H57Q ENST00000548380 2/4 186 125 61 189 189 0 strelka-varscan-mutect LINC00935,missense_variant,p.His57Gln,ENST00000548380,;LINC00935,3_prime_UTR_variant,,ENST00000548054,; A ENST00000548380 Transcript missense_variant 217/573 171/396 57/131 H/Q caC/caA rs758541354 1 1 LINC00935 HGNC HGNC:48628 protein_coding YES ENSP00000489652 UPI00001605D7 tolerated(0.58) 2/4 hmmpanther:PTHR35263 MODERATE 1 SNV 1 1 PASS rs758541354 . 0 206 0 4 0 0 0 0 -20 0.9999819 1 1 1 0 A 3 1 49 48759300 48759300 C A 1 0 0 0 0 1 0 0 0 8730 535 19 1 1 LINC00935 12 48759300 Missense_Mutation SNP C C3N-00547_T 2941546 48759300 84516009 443 14773 AQP6 0 . GRCh38 12 49975649 49975649 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.827C>G p.Ala276Gly p.A276G ENST00000615425 4/5 47 40 7 42 42 0 strelka-mutect AQP6,missense_variant,p.Ala276Gly,ENST00000615425,NM_001652.3;AQP6,missense_variant,p.Ala276Gly,ENST00000315520,;AQP6,missense_variant,p.Ala102Gly,ENST00000551733,;AQP6,downstream_gene_variant,,ENST00000618286,;RACGAP1,downstream_gene_variant,,ENST00000548961,;AQP6,non_coding_transcript_exon_variant,,ENST00000489786,; G ENST00000615425 Transcript missense_variant 827/2245 827/849 276/282 A/G gCc/gGc 1 1 AQP6 HGNC HGNC:639 protein_coding YES CCDS31798.1 ENSP00000477688 Q13520 UPI000013EBD8 NM_001652.3 tolerated(0.18) 4/5 Prints_domain:PR02018,hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF113 MODERATE 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -16.76067 0.9999827 1 1 1 0 G 3 3 49 49975649 49975649 C G 1 0 0 0 0 1 0 0 0 953 739 26 4 4 AQP6 12 49975649 Missense_Mutation SNP C C3N-00547_T 1216349 49975649 83299660 444 14774 ANKRD33 0 . GRCh38 12 51890696 51890696 + Silent SNP C C A rs779120061 C3N-00547_T C3N-00547_N C C c.750C>A p.= p.P250P ENST00000301190 5/5 217 186 31 218 218 0 strelka-varscan-mutect ANKRD33,synonymous_variant,p.=,ENST00000301190,NM_182608.3;ANKRD33,synonymous_variant,p.=,ENST00000340970,NM_001130015.1;ANKRD33,non_coding_transcript_exon_variant,,ENST00000547119,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000549316,;ANKRD33,3_prime_UTR_variant,,ENST00000549751,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548526,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548383,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000550652,; A ENST00000301190 Transcript synonymous_variant 977/1935 750/1359 250/452 P ccC/ccA rs779120061 1 1 ANKRD33 HGNC HGNC:13788 protein_coding YES CCDS8815.1 ENSP00000301190 Q7Z3H0 UPI00003668C0 NM_182608.3 5/5 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF29,SMART_domains:SM00248 LOW 1 SNV 2 1 PASS rs779120061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 51890696 51890696 C A 1 0 0 0 0 0 0 0 1 765 610 22 2 2 ANKRD33 12 51890696 Silent SNP C C3N-00547_T 1915047 51890696 81384613 445 14775 GRASP 0 . GRCh38 12 52013704 52013704 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.472G>T p.Val158Phe p.V158F ENST00000293662 5/8 273 229 44 224 224 0 strelka-varscan-mutect GRASP,missense_variant,p.Val158Phe,ENST00000293662,NM_181711.3;GRASP,missense_variant,p.Val15Phe,ENST00000552049,NM_001271856.1;GRASP,missense_variant,p.Val28Phe,ENST00000546756,;GRASP,non_coding_transcript_exon_variant,,ENST00000552963,;GRASP,non_coding_transcript_exon_variant,,ENST00000547749,;GRASP,non_coding_transcript_exon_variant,,ENST00000552508,;GRASP,non_coding_transcript_exon_variant,,ENST00000548505,;GRASP,downstream_gene_variant,,ENST00000550809,; T ENST00000293662 Transcript missense_variant 552/1933 472/1188 158/395 V/F Gtc/Ttc COSM1734782 1 1 GRASP HGNC HGNC:18707 protein_coding YES CCDS8817.1 ENSP00000293662 Q7Z6J2 UPI00001A9479 NM_181711.3 deleterious(0) 5/8 PROSITE_profiles:PS50106,hmmpanther:PTHR15963,hmmpanther:PTHR15963:SF3,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 1 MODERATE 1 SNV 1 1 1 PASS rs1258287190 . 0 208 0 0 2 0 0 0 -19.98789 0.9972737 1 1 1 0 T 3 4 49 52013704 52013704 G T 1 0 0 0 0 1 0 0 0 6634 1145 40 1 1 GRASP 12 52013704 Missense_Mutation SNP G C3N-00547_T 123008 52013704 81261605 446 14776 PPP1R1A 0 . GRCh38 12 54584263 54584263 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.142C>G p.Pro48Ala p.P48A ENST00000257905 2/7 240 162 78 315 314 1 strelka-varscan-mutect PPP1R1A,missense_variant,p.Pro48Ala,ENST00000547431,;PPP1R1A,missense_variant,p.Pro48Ala,ENST00000257905,NM_006741.3;PPP1R1A,missense_variant,p.Pro19Ala,ENST00000553113,;PPP1R1A,missense_variant,p.Pro48Ala,ENST00000547826,; C ENST00000257905 Transcript missense_variant 313/1826 142/516 48/171 P/A Cca/Gca 1 -1 PPP1R1A HGNC HGNC:9286 protein_coding YES CCDS44912.1 ENSP00000257905 Q13522 UPI000012D802 NM_006741.3 deleterious(0) 2/7 Pfam_domain:PF05395,hmmpanther:PTHR15417,hmmpanther:PTHR15417:SF4 MODERATE 1 SNV 1 1 PASS rs1183816449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 54584263 54584263 G C 1 0 0 0 0 1 0 0 0 12479 1246 43 4 4 PPP1R1A 12 54584263 Missense_Mutation SNP G C3N-00547_T 2570559 54584263 78691046 447 14777 TIMELESS 0 . GRCh38 12 56423461 56423461 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.2105C>T p.Thr702Ile p.T702I ENST00000553532 18/29 137 87 50 155 155 0 strelka-varscan-mutect TIMELESS,missense_variant,p.Thr702Ile,ENST00000553532,NM_003920.3;TIMELESS,missense_variant,p.Thr701Ile,ENST00000229201,;TIMELESS,non_coding_transcript_exon_variant,,ENST00000557589,;TIMELESS,upstream_gene_variant,,ENST00000555808,;TIMELESS,upstream_gene_variant,,ENST00000553314,; A ENST00000553532 Transcript missense_variant 2256/5121 2105/3627 702/1208 T/I aCt/aTt 1 -1 TIMELESS HGNC HGNC:11813 protein_coding YES CCDS8918.1 ENSP00000450607 Q9UNS1 UPI000013C8EA NM_003920.3 tolerated(0.18) 18/29 hmmpanther:PTHR22940,hmmpanther:PTHR22940:SF4 MODERATE 1 SNV 1 1 PASS rs1373488000 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 56423461 56423461 G A 1 0 0 0 0 1 0 0 0 16342 1029 36 3 3 TIMELESS 12 56423461 Missense_Mutation SNP G C3N-00547_T 1839198 56423461 76851848 448 14778 OS9 0 . GRCh38 12 57694872 57694872 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.285G>A p.= p.G95G ENST00000315970 2/15 373 331 42 342 342 0 strelka-varscan-mutect OS9,synonymous_variant,p.=,ENST00000315970,NM_006812.3;OS9,synonymous_variant,p.=,ENST00000257966,NM_001261420.1;OS9,synonymous_variant,p.=,ENST00000389142,NM_001017957.2;OS9,synonymous_variant,p.=,ENST00000435406,NM_001261422.1;OS9,synonymous_variant,p.=,ENST00000551035,NM_001261421.1;OS9,synonymous_variant,p.=,ENST00000552285,NM_001017956.2;OS9,synonymous_variant,p.=,ENST00000389146,NM_001017958.2;OS9,synonymous_variant,p.=,ENST00000413095,;OS9,synonymous_variant,p.=,ENST00000547079,;OS9,synonymous_variant,p.=,ENST00000550372,;OS9,intron_variant,,ENST00000439210,NM_001261423.1;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,synonymous_variant,p.=,ENST00000552787,;OS9,synonymous_variant,p.=,ENST00000552423,;OS9,3_prime_UTR_variant,,ENST00000551285,;OS9,3_prime_UTR_variant,,ENST00000550848,;OS9,non_coding_transcript_exon_variant,,ENST00000553208,;OS9,non_coding_transcript_exon_variant,,ENST00000549897,;OS9,non_coding_transcript_exon_variant,,ENST00000550793,;OS9,upstream_gene_variant,,ENST00000549307,; A ENST00000315970 Transcript synonymous_variant 326/2691 285/2004 95/667 G ggG/ggA 1 1 OS9 HGNC HGNC:16994 protein_coding YES CCDS31843.1 ENSP00000318165 Q13438 UPI0000130EAC NM_006812.3 2/15 hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 57694872 57694872 G A 1 0 0 0 0 0 0 0 1 11338 1190 42 3 3 OS9 12 57694872 Silent SNP G C3N-00547_T 1271411 57694872 75580437 449 14779 LLPH 0 . GRCh38 12 66123869 66123869 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.361G>T p.Val121Leu p.V121L ENST00000266604 3/3 129 112 17 113 113 0 strelka-varscan-mutect LLPH,missense_variant,p.Val121Leu,ENST00000266604,NM_032338.3;LLPH,missense_variant,p.Val121Leu,ENST00000446587,;RP11-745O10.4,downstream_gene_variant,,ENST00000539652,; A ENST00000266604 Transcript missense_variant 432/7746 361/390 121/129 V/L Gtg/Ttg 1 -1 LLPH HGNC HGNC:28229 protein_coding YES CCDS8974.1 ENSP00000266604 Q9BRT6 A0A024RB76 UPI000006E52D NM_032338.3 tolerated_low_confidence(0.34) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR34253:SF1,hmmpanther:PTHR34253 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 66123869 66123869 C A 1 0 0 0 0 1 0 0 0 8759 565 20 2 2 LLPH 12 66123869 Missense_Mutation SNP C C3N-00547_T 8428997 66123869 67151440 450 14780 PTPRB 0 . GRCh38 12 70592360 70592360 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1702C>A p.Pro568Thr p.P568T ENST00000334414 7/34 392 268 124 462 462 0 strelka-varscan-mutect PTPRB,missense_variant,p.Pro568Thr,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Pro568Thr,ENST00000550358,;PTPRB,missense_variant,p.Pro350Thr,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Pro350Thr,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Pro350Thr,ENST00000550857,NM_001206971.1;PTPRB,missense_variant,p.Pro567Thr,ENST00000551525,;PTPRB,missense_variant,p.Pro447Thr,ENST00000548122,;PTPRB,non_coding_transcript_exon_variant,,ENST00000538174,;PTPRB,non_coding_transcript_exon_variant,,ENST00000552253,; T ENST00000334414 Transcript missense_variant 1747/12316 1702/6648 568/2215 P/T Ccc/Acc 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious(0) 7/34 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 70592360 70592360 G T 1 0 0 0 0 1 0 0 0 12950 1232 43 2 2 PTPRB 12 70592360 Missense_Mutation SNP G C3N-00547_T 4468491 70592360 62682949 451 14781 TRHDE 0 . GRCh38 12 72618889 72618889 + Splice_Site SNP A A T novel C3N-00547_T C3N-00547_N A A c.2187-2A>T p.X729_splice ENST00000261180 58 38 20 61 61 0 varscan-mutect TRHDE,splice_acceptor_variant,,ENST00000261180,NM_013381.2;TRHDE,splice_acceptor_variant,,ENST00000549138,;TRHDE,splice_acceptor_variant,,ENST00000549922,; T ENST00000261180 Transcript splice_acceptor_variant -/10733 2187/3075 729/1024 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 12/18 HIGH 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999922 1 1 1 0 T 5 4 49 72618889 72618889 A T 1 0 0 0 0 0 0 1 0 16968 434 15 4 4 TRHDE 12 72618889 Splice_Site SNP A C3N-00547_T 2026529 72618889 60656420 452 14782 KCNC2 0 . GRCh38 12 75207624 75207624 + Silent SNP G G A rs773968350 C3N-00547_T C3N-00547_N G G c.360C>T p.= p.T120T ENST00000549446 2/5 387 324 63 379 379 0 strelka-varscan-mutect KCNC2,synonymous_variant,p.=,ENST00000549446,NM_139137.3;KCNC2,synonymous_variant,p.=,ENST00000298972,NM_139136.3;KCNC2,synonymous_variant,p.=,ENST00000350228,NM_153748.2;KCNC2,synonymous_variant,p.=,ENST00000548513,;KCNC2,synonymous_variant,p.=,ENST00000550433,NM_001260498.1;KCNC2,synonymous_variant,p.=,ENST00000393288,NM_001260497.1;KCNC2,synonymous_variant,p.=,ENST00000540018,NM_001260499.1; A ENST00000549446 Transcript synonymous_variant 1041/5625 360/1917 120/638 T acC/acT rs773968350,COSM195964,COSM195965,COSM5122854 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 2/5 Gene3D:3.30.710.10,Pfam_domain:PF02214,Prints_domain:PR00169,Prints_domain:PR01498,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,SMART_domains:SM00225,Superfamily_domains:SSF54695 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs773968350 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 75207624 75207624 G A 1 0 0 0 0 0 0 0 1 7931 1103 39 1 1 KCNC2 12 75207624 Silent SNP G C3N-00547_T 2588735 75207624 58067685 453 14783 TMTC2 0 . GRCh38 12 83061813 83061813 + Silent SNP A A C novel C3N-00547_T C3N-00547_N A A c.2313A>C p.= p.A771A ENST00000321196 11/12 122 103 19 130 130 0 strelka-varscan-mutect TMTC2,synonymous_variant,p.=,ENST00000549919,;TMTC2,synonymous_variant,p.=,ENST00000321196,NM_152588.1;TMTC2,3_prime_UTR_variant,,ENST00000546590,NM_001320321.1; C ENST00000321196 Transcript synonymous_variant 3020/5681 2313/2511 771/836 A gcA/gcC 1 1 TMTC2 HGNC HGNC:25440 protein_coding YES CCDS9025.1 ENSP00000322300 Q8N394 UPI0000073F0F NM_152588.1 11/12 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF390,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS rs904546549 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 49 83061813 83061813 A C 1 0 0 0 0 0 0 0 1 16735 175 7 5 5 TMTC2 12 83061813 Silent SNP A C3N-00547_T 7854189 83061813 50213496 454 14784 SLC6A15 0 . GRCh38 12 84861772 84861772 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.2053A>T p.Met685Leu p.M685L ENST00000266682 12/12 162 140 22 156 155 1 strelka-varscan-mutect SLC6A15,missense_variant,p.Met685Leu,ENST00000266682,NM_182767.5;SLC6A15,missense_variant,p.Met578Leu,ENST00000552192,NM_001146335.2;SLC6A15,3_prime_UTR_variant,,ENST00000309283,;SLC6A15,non_coding_transcript_exon_variant,,ENST00000548267,; A ENST00000266682 Transcript missense_variant 2595/4879 2053/2193 685/730 M/L Atg/Ttg 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 tolerated(0.59) 12/12 hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 84861772 84861772 T A 1 0 0 0 0 1 0 0 0 14961 1435 50 4 4 SLC6A15 12 84861772 Missense_Mutation SNP T C3N-00547_T 1799959 84861772 48413537 455 14785 LRRIQ1 0 . GRCh38 12 85047350 85047350 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.558A>T p.Lys186Asn p.K186N ENST00000393217 6/27 202 171 31 236 236 0 strelka-varscan-mutect LRRIQ1,missense_variant,p.Lys186Asn,ENST00000393217,NM_001079910.1;LRRIQ1,missense_variant,p.Lys84Asn,ENST00000533414,;LRRIQ1,downstream_gene_variant,,ENST00000393212,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000529408,; T ENST00000393217 Transcript missense_variant 619/5394 558/5169 186/1722 K/N aaA/aaT 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 tolerated(0.08) 6/27 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 85047350 85047350 A T 1 0 0 0 0 1 0 0 0 8935 40 2 4 4 LRRIQ1 12 85047350 Missense_Mutation SNP A C3N-00547_T 185578 85047350 48227959 456 14786 CEP290 0 . GRCh38 12 88139193 88139193 + Splice_Site SNP T T A C3N-00547_T C3N-00547_N T T c.251-2A>T p.X84_splice ENST00000552810 35 24 11 58 58 0 strelka-varscan-mutect CEP290,splice_acceptor_variant,,ENST00000552810,NM_025114.3;CEP290,splice_acceptor_variant,,ENST00000309041,;CEP290,splice_acceptor_variant,,ENST00000397838,;CEP290,splice_acceptor_variant,,ENST00000552770,;CEP290,splice_acceptor_variant,,ENST00000550962,;TMTC3,upstream_gene_variant,,ENST00000266712,NM_181783.3;TMTC3,upstream_gene_variant,,ENST00000551088,;TMTC3,upstream_gene_variant,,ENST00000549011,;CEP290,splice_acceptor_variant,,ENST00000547926,;TMTC3,upstream_gene_variant,,ENST00000547034,; A ENST00000552810 Transcript splice_acceptor_variant -/7948 251/7440 84/2479 COSM4953722,COSM5349305 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 4/53 1,1 HIGH 1 SNV 1 1,1 1 PASS rs951979448 . 6 199 5 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 49 88139193 88139193 T A 1 0 0 0 0 0 0 1 0 2969 1536 53 4 4 CEP290 12 88139193 Splice_Site SNP T C3N-00547_T 3091843 88139193 45136116 457 14787 UHRF1BP1L 0 . GRCh38 12 100058827 100058827 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.2450T>A p.Met817Lys p.M817K ENST00000279907 14/21 229 150 79 271 271 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Met817Lys,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Met467Lys,ENST00000545232,; T ENST00000279907 Transcript missense_variant 2663/5168 2450/4395 817/1464 M/K aTg/aAg 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 deleterious(0.02) 14/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 100058827 100058827 A T 1 0 0 0 0 1 0 0 0 17493 217 8 4 4 UHRF1BP1L 12 100058827 Missense_Mutation SNP A C3N-00547_T 11919634 100058827 33216482 458 14788 GAS2L3 0 . GRCh38 12 100624647 100624647 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.1842C>T p.= p.S614S ENST00000547754 10/10 309 252 57 257 257 0 strelka-varscan-mutect GAS2L3,synonymous_variant,p.=,ENST00000537247,NM_001303131.1;GAS2L3,synonymous_variant,p.=,ENST00000547754,NM_174942.2;GAS2L3,synonymous_variant,p.=,ENST00000539410,;GAS2L3,synonymous_variant,p.=,ENST00000266754,NM_001303130.1;GAS2L3,synonymous_variant,p.=,ENST00000552854,; T ENST00000547754 Transcript synonymous_variant 2068/2340 1842/2085 614/694 S tcC/tcT 1 1 GAS2L3 HGNC HGNC:27475 protein_coding YES CCDS9079.1 ENSP00000448955 Q86XJ1 A0A024RBF4 UPI000000DA3B NM_174942.2 10/10 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF256 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 100624647 100624647 C T 1 0 0 0 0 0 0 0 1 6118 581 21 3 3 GAS2L3 12 100624647 Silent SNP C C3N-00547_T 565820 100624647 32650662 459 14789 STAB2 0 . GRCh38 12 103670739 103670739 + Frame_Shift_Del DEL A A - novel C3N-00547_T C3N-00547_N A A c.2303delA p.Glu768GlyfsTer36 p.E768Gfs*36 ENST00000388887 22/69 259 177 82 271 271 0 sindel-varindel-pindel STAB2,frameshift_variant,p.Glu768GlyfsTer36,ENST00000388887,NM_017564.9;RP11-341G23.3,upstream_gene_variant,,ENST00000550175,; - ENST00000388887 Transcript frameshift_variant 2507/8251 2303/7656 768/2551 E/X gAg/gg 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 22/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 103670739 103670739 A - 1 0 1 0 1 0 0 0 0 15616 304 11 0 0 STAB2 12 103670739 Frame_Shift_Del DEL A C3N-00547_T 3046092 103670739 29604570 460 14790 ACACB 0 . GRCh38 12 109166864 109166864 + Silent SNP G G T rs145288622 C3N-00547_T C3N-00547_N G G c.657G>T p.= p.P219P ENST00000338432 3/53 310 194 116 329 329 0 strelka-varscan-mutect ACACB,synonymous_variant,p.=,ENST00000338432,;ACACB,synonymous_variant,p.=,ENST00000377848,NM_001093.3;ACACB,synonymous_variant,p.=,ENST00000544726,;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,non_coding_transcript_exon_variant,,ENST00000546328,; T ENST00000338432 Transcript synonymous_variant 776/9360 657/7377 219/2458 P ccG/ccT rs145288622 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB 3/53 hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866 LOW 1 SNV 1 1 PASS rs145288622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 109166864 109166864 G T 1 0 0 0 0 0 0 0 1 150 1072 37 1 1 ACACB 12 109166864 Silent SNP G C3N-00547_T 5496125 109166864 24108445 461 14791 RPLP0 0 . GRCh38 12 120196776 120196776 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.951C>G p.Asp317Glu p.D317E ENST00000551150 7/7 43 30 13 26 26 0 strelka-varscan-mutect RPLP0,missense_variant,p.Asp317Glu,ENST00000551150,;RPLP0,missense_variant,p.Asp317Glu,ENST00000228306,NM_053275.3;RPLP0,missense_variant,p.Asp317Glu,ENST00000392514,NM_001002.3;RPLP0,missense_variant,p.Asp281Glu,ENST00000546989,;RPLP0,missense_variant,p.Asp255Glu,ENST00000313104,;RPLP0,missense_variant,p.Asp107Glu,ENST00000552292,;GCN1,upstream_gene_variant,,ENST00000300648,NM_006836.1;RPLP0,downstream_gene_variant,,ENST00000550856,;RPLP0,downstream_gene_variant,,ENST00000547211,;RPLP0,downstream_gene_variant,,ENST00000546990,;RPLP0,downstream_gene_variant,,ENST00000547191,;RPLP0,downstream_gene_variant,,ENST00000550423,;RPLP0,downstream_gene_variant,,ENST00000551914,;PXN-AS1,upstream_gene_variant,,ENST00000535200,;PXN-AS1,upstream_gene_variant,,ENST00000542265,;PXN-AS1,upstream_gene_variant,,ENST00000539446,;PXN-AS1,upstream_gene_variant,,ENST00000542314,;PXN-AS1,upstream_gene_variant,,ENST00000538804,;RPLP0,downstream_gene_variant,,ENST00000550296,;RPLP0,downstream_gene_variant,,ENST00000551336,;RPLP0,3_prime_UTR_variant,,ENST00000549098,;RPLP0,non_coding_transcript_exon_variant,,ENST00000552461,;RPLP0,non_coding_transcript_exon_variant,,ENST00000551217,;RPLP0,downstream_gene_variant,,ENST00000548568,;RPLP0,downstream_gene_variant,,ENST00000551258,;RPLP0,downstream_gene_variant,,ENST00000552902,;RPLP0,downstream_gene_variant,,ENST00000547173,;RPLP0,downstream_gene_variant,,ENST00000546564,;RPLP0,downstream_gene_variant,,ENST00000547475,;RPLP0,downstream_gene_variant,,ENST00000551783,;RPLP0,downstream_gene_variant,,ENST00000548495,;RPLP0,downstream_gene_variant,,ENST00000548551,;RPLP0,downstream_gene_variant,,ENST00000549242,; C ENST00000551150 Transcript missense_variant 1267/1344 951/954 317/317 D/E gaC/gaG 1 -1 RPLP0 HGNC HGNC:10371 protein_coding YES CCDS9193.1 ENSP00000449328 P05388 A0A024RBS2 UPI0000134221 deleterious(0.03) 7/7 PIRSF_domain:PIRSF039087,hmmpanther:PTHR21141,hmmpanther:PTHR21141:SF49 MODERATE 1 SNV 1 1 PASS . . 0 186 24 0 0 0 0 0 -20 0.9973186 0 1 1 0 C 3 2 49 120196776 120196776 G C 1 0 0 0 0 1 0 0 0 13857 1020 36 4 4 RPLP0 12 120196776 Missense_Mutation SNP G C3N-00547_T 11029912 120196776 13078533 462 14792 PLA2G1B 0 . GRCh38 12 120325032 120325032 + Missense_Mutation SNP T T C rs774834157 C3N-00547_T C3N-00547_N T T c.224A>G p.Asp75Gly p.D75G ENST00000308366 3/4 274 258 16 210 210 0 strelka-varscan-mutect PLA2G1B,missense_variant,p.Asp75Gly,ENST00000308366,NM_000928.2;PLA2G1B,missense_variant,p.Asp46Gly,ENST00000549767,;PLA2G1B,intron_variant,,ENST00000423423,; C ENST00000308366 Transcript missense_variant 260/565 224/447 75/148 D/G gAc/gGc rs774834157 1 -1 PLA2G1B HGNC HGNC:9030 protein_coding YES CCDS9195.1 ENSP00000312286 P04054 UPI0000048FD9 NM_000928.2 tolerated(0.29) 3/4 hmmpanther:PTHR11716,Pfam_domain:PF00068,Gene3D:1.20.90.10,SMART_domains:SM00085,Superfamily_domains:SSF48619,Prints_domain:PR00389 MODERATE 1 SNV 1 1 PASS rs774834157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 120325032 120325032 T C 1 0 0 0 0 1 0 0 0 12090 1667 58 5 5 PLA2G1B 12 120325032 Missense_Mutation SNP T C3N-00547_T 128256 120325032 12950277 463 14793 TMEM132D 0 . GRCh38 12 129700195 129700195 + Nonsense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.583G>T p.Glu195Ter p.E195* ENST00000422113 2/9 218 148 70 236 236 0 strelka-varscan-mutect TMEM132D,stop_gained,p.Glu195Ter,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript stop_gained 910/5776 583/3300 195/1099 E/* Gag/Tag COSM4553206 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 1 HIGH 1 SNV 1 1 1 PASS rs994058307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 129700195 129700195 C A 1 0 0 0 0 0 1 0 0 16492 893 31 1 1 TMEM132D 12 129700195 Nonsense_Mutation SNP C C3N-00547_T 9375163 129700195 3575114 464 14794 COG3 0 . GRCh38 13 45511797 45511797 + Silent SNP A A G novel C3N-00547_T C3N-00547_N A A c.1752A>G p.= p.A584A ENST00000349995 16/23 154 120 34 156 156 0 strelka-varscan-mutect COG3,synonymous_variant,p.=,ENST00000349995,NM_031431.3;COG3,non_coding_transcript_exon_variant,,ENST00000465942,;COG3,upstream_gene_variant,,ENST00000486940,; G ENST00000349995 Transcript synonymous_variant 1864/4498 1752/2487 584/828 A gcA/gcG 1 1 COG3 HGNC HGNC:18619 protein_coding YES CCDS9398.1 ENSP00000258654 Q96JB2 UPI0000366968 NM_031431.3 16/23 hmmpanther:PTHR13302 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 45511797 45511797 A G 1 0 0 0 0 0 0 0 1 3447 204 8 5 5 COG3 13 45511797 Silent SNP A C3N-00547_T 45511797 68852531 465 14795 PCDH20 0 . GRCh38 13 61412551 61412551 + Missense_Mutation SNP A A C novel C3N-00547_T C3N-00547_N A A c.1548T>G p.His516Gln p.H516Q ENST00000409186 5/5 247 224 23 273 273 0 strelka-varscan-mutect RP11-310K10.1,missense_variant,p.His516Gln,ENST00000409186,;PCDH20,missense_variant,p.His516Gln,ENST00000409204,NM_022843.3; C ENST00000409186 Transcript missense_variant 3654/6347 1548/2856 516/951 H/Q caT/caG 1 -1 RP11-310K10.1 Clone_based_vega_gene protein_coding YES CCDS9442.2 ENSP00000386653 UPI000007371F tolerated(0.25) 5/5 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 61412551 61412551 A C 1 0 0 0 0 1 0 0 0 11602 214 8 5 5 PCDH20 13 61412551 Missense_Mutation SNP A C3N-00547_T 15900754 61412551 52951777 466 14796 FGF14 0 . GRCh38 13 101916537 101916537 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.109C>A p.Arg37Ser p.R37S ENST00000376143 1/5 211 158 53 278 278 0 strelka-varscan-mutect FGF14,missense_variant,p.Arg37Ser,ENST00000376143,NM_004115.3;FGF14,intron_variant,,ENST00000376131,NM_175929.2; T ENST00000376143 Transcript missense_variant 109/744 109/744 37/247 R/S Cgc/Agc 1 -1 FGF14 HGNC HGNC:3671 protein_coding CCDS9501.1 ENSP00000365313 Q92915 UPI000003C0F2 NM_004115.3 deleterious(0.01) 1/5 hmmpanther:PTHR11486:SF18,hmmpanther:PTHR11486 MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 101916537 101916537 G T 1 0 0 0 0 1 0 0 0 5707 1116 39 1 1 FGF14 13 101916537 Missense_Mutation SNP G C3N-00547_T 40503986 101916537 12447791 467 14797 RASA3 0 . GRCh38 13 114029811 114029811 + Missense_Mutation SNP C C G rs374146859 C3N-00547_T C3N-00547_N C C c.449G>C p.Arg150Pro p.R150P ENST00000334062 5/24 261 127 134 247 247 0 strelka-varscan-mutect RASA3,missense_variant,p.Arg150Pro,ENST00000334062,NM_001320822.1,NM_007368.2;RASA3,splice_region_variant,,ENST00000542651,; G ENST00000334062 Transcript missense_variant,splice_region_variant 571/4191 449/2505 150/834 R/P cGc/cCc rs374146859 1 -1 RASA3 HGNC HGNC:20331 protein_coding YES CCDS32016.1 ENSP00000335029 Q14644 UPI000000DBC1 NM_001320822.1,NM_007368.2 deleterious(0.01) 5/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF53,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs374146859 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 114029811 114029811 C G 1 0 0 0 0 1 0 0 0 13221 666 23 4 4 RASA3 13 114029811 Missense_Mutation SNP C C3N-00547_T 12113274 114029811 334517 468 14798 POTEG 0 . GRCh38 14 19434216 19434216 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.74G>C p.Gly25Ala p.G25A ENST00000547848 1/11 651 553 98 623 623 0 strelka-varscan-mutect POTEG,missense_variant,p.Gly25Ala,ENST00000547848,NM_001005356.2;POTEG,missense_variant,p.Gly25Ala,ENST00000547722,;POTEG,missense_variant,p.Gly25Ala,ENST00000622767,; G ENST00000547848 Transcript missense_variant 126/2204 74/1527 25/508 G/A gGc/gCc 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 deleterious_low_confidence(0.03) 1/11 MODERATE 1 SNV 1 1 PASS rs1321216290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 19434216 19434216 C G 1 0 0 0 0 1 0 0 0 12380 739 26 4 4 POTEG 14 19434216 Missense_Mutation SNP C C3N-00547_T 19434216 87609502 469 14799 POTEG 0 . GRCh38 14 19434284 19434284 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.6G>A p.= p.V2V ENST00000547848 1/11 305 258 47 315 315 0 strelka-varscan-mutect POTEG,synonymous_variant,p.=,ENST00000547848,NM_001005356.2;POTEG,synonymous_variant,p.=,ENST00000547722,;POTEG,synonymous_variant,p.=,ENST00000622767,; T ENST00000547848 Transcript synonymous_variant 58/2204 6/1527 2/508 V gtG/gtA 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 1/11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 19434284 19434284 C T 1 0 0 0 0 0 0 0 1 12380 581 21 3 3 POTEG 14 19434284 Silent SNP C C3N-00547_T 68 19434284 87609434 470 14800 OR11H2 0 . GRCh38 14 19712936 19712936 + Nonstop_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.981A>T p.Ter327TyrextTer? p.*327Yext*? ENST00000556246 1/1 120 90 30 152 152 0 strelka-varscan-mutect OR11H2,stop_lost,p.Ter327TyrextTer?,ENST00000556246,NM_001197287.1; A ENST00000556246 Transcript stop_lost 985/985 981/981 327/326 */Y taA/taT 1 -1 OR11H2 HGNC HGNC:14716 protein_coding YES CCDS76655.1 ENSP00000485150 Q8NH07 UPI0000061EAC NM_001197287.1 1/1 HIGH 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 19712936 19712936 T A 1 0 0 0 0 0 0 0 0 11004 1623 56 4 4 OR11H2 14 19712936 Nonstop_Mutation SNP T C3N-00547_T 278652 19712936 87330782 471 14801 OR11G2 0 . GRCh38 14 20197618 20197618 + Missense_Mutation SNP G G T rs562872648 C3N-00547_T C3N-00547_N G G c.283G>T p.Ala95Ser p.A95S ENST00000357366 1/1 208 186 22 211 211 0 strelka-varscan-mutect OR11G2,missense_variant,p.Ala95Ser,ENST00000357366,NM_001005503.1; T ENST00000357366 Transcript missense_variant 283/1111 283/1038 95/345 A/S Gcc/Tcc rs562872648,COSM2028735 1 1 OR11G2 HGNC HGNC:15346 protein_coding YES CCDS32032.1 ENSP00000349930 Q8NGC1 UPI000015F241 NM_001005503.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF183,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs562872648 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 20197618 20197618 G T 1 0 0 0 0 1 0 0 0 11001 1087 38 1 1 OR11G2 14 20197618 Missense_Mutation SNP G C3N-00547_T 484682 20197618 86846100 472 14802 OR11H4 0 . GRCh38 14 20243219 20243219 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.428C>A p.Pro143His p.P143H ENST00000315409 1/1 208 131 77 177 177 0 strelka-varscan-mutect OR11H4,missense_variant,p.Pro143His,ENST00000315409,NM_001004479.1; A ENST00000315409 Transcript missense_variant 481/1082 428/975 143/324 P/H cCt/cAt 1 1 OR11H4 HGNC HGNC:15347 protein_coding YES CCDS32034.1 ENSP00000318997 Q8NGC9 A0A126GW19 UPI0000041C42 NM_001004479.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247:SF99,hmmpanther:PTHR24247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs1473234021 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 20243219 20243219 C A 1 0 0 0 0 1 0 0 0 11005 681 24 2 2 OR11H4 14 20243219 Missense_Mutation SNP C C3N-00547_T 45601 20243219 86800499 473 14803 TEP1 0 . GRCh38 14 20384147 20384147 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.3425G>T p.Ser1142Ile p.S1142I ENST00000262715 24/55 182 154 28 236 236 0 strelka-varscan-mutect TEP1,missense_variant,p.Ser1142Ile,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Ser1034Ile,ENST00000556935,;TEP1,missense_variant,p.Ser1142Ile,ENST00000555727,;TEP1,missense_variant,p.Ser492Ile,ENST00000555008,;TEP1,upstream_gene_variant,,ENST00000557314,; A ENST00000262715 Transcript missense_variant 3466/10695 3425/7884 1142/2627 S/I aGt/aTt 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 tolerated(0.16) 24/55 MODERATE 1 SNV 1 1 PASS rs1214862790 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 49 20384147 20384147 C A 1 0 0 0 0 1 0 0 0 16175 565 20 2 2 TEP1 14 20384147 Missense_Mutation SNP C C3N-00547_T 140928 20384147 86659571 474 14804 TEP1 0 . GRCh38 14 20395893 20395893 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1716C>T p.= p.A572A ENST00000262715 11/55 116 105 11 108 108 0 strelka-varscan-mutect TEP1,synonymous_variant,p.=,ENST00000262715,NM_007110.4;TEP1,synonymous_variant,p.=,ENST00000556935,;TEP1,synonymous_variant,p.=,ENST00000555727,;TEP1,upstream_gene_variant,,ENST00000555008,;TEP1,downstream_gene_variant,,ENST00000557627,; A ENST00000262715 Transcript synonymous_variant 1757/10695 1716/7884 572/2627 A gcC/gcT 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 11/55 PROSITE_profiles:PS50988,Pfam_domain:PF05731,Superfamily_domains:0051422 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99713 1 1 1 1 0 A 2 1 49 20395893 20395893 G A 1 0 0 0 0 0 0 0 1 16175 1335 47 3 3 TEP1 14 20395893 Silent SNP G C3N-00547_T 11746 20395893 86647825 475 14805 IL25 0 . GRCh38 14 23375853 23375853 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.507G>A p.= p.V169V ENST00000329715 2/2 177 112 65 179 179 0 strelka-varscan-mutect IL25,synonymous_variant,p.=,ENST00000329715,NM_022789.3;IL25,synonymous_variant,p.=,ENST00000397242,NM_172314.1;CMTM5,upstream_gene_variant,,ENST00000359320,NM_138460.2;CMTM5,upstream_gene_variant,,ENST00000339180,NM_001288746.1;CMTM5,upstream_gene_variant,,ENST00000555731,;CMTM5,upstream_gene_variant,,ENST00000397227,NM_001288744.1;CMTM5,upstream_gene_variant,,ENST00000342473,NM_001288745.1;CMTM5,upstream_gene_variant,,ENST00000382809,NM_001037288.1;CMTM5,upstream_gene_variant,,ENST00000553750,;CMTM5,upstream_gene_variant,,ENST00000555487,; A ENST00000329715 Transcript synonymous_variant 765/1315 507/534 169/177 V gtG/gtA 1 1 IL25 HGNC HGNC:13765 protein_coding YES CCDS9597.1 ENSP00000328111 Q9H293 UPI0000038A0A NM_022789.3 2/2 hmmpanther:PTHR21295,hmmpanther:PTHR21295:SF7,Gene3D:2.10.90.10,Pfam_domain:PF06083,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 23375853 23375853 G A 1 0 0 0 0 0 0 0 1 7581 1364 48 3 3 IL25 14 23375853 Silent SNP G C3N-00547_T 2979960 23375853 83667865 476 14806 NYNRIN 0 . GRCh38 14 24408030 24408030 + Frame_Shift_Del DEL G G - novel C3N-00547_T C3N-00547_N G G c.362delG p.Gly121AlafsTer3 p.G121Afs*3 ENST00000382554 3/9 236 182 54 236 236 0 sindel-varindel-pindel NYNRIN,frameshift_variant,p.Gly121AlafsTer3,ENST00000382554,NM_025081.2;NYNRIN,upstream_gene_variant,,ENST00000554505,; - ENST00000382554 Transcript frameshift_variant 678/7857 360/5697 120/1898 V/X gtG/gt 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 3/9 hmmpanther:PTHR12876,hmmpanther:PTHR12876:SF2 HIGH 1 deletion 5 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 24408030 24408030 G - 1 0 1 0 1 0 0 0 0 10874 1335 47 0 0 NYNRIN 14 24408030 Frame_Shift_Del DEL G C3N-00547_T 1032177 24408030 82635688 477 14807 CTSG 0 . GRCh38 14 24573643 24573643 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.762C>A p.= p.P254P ENST00000216336 5/5 121 96 25 127 127 0 strelka-varscan-mutect CTSG,synonymous_variant,p.=,ENST00000216336,NM_001911.2;CTSG,non_coding_transcript_exon_variant,,ENST00000552252,; T ENST00000216336 Transcript synonymous_variant 799/886 762/768 254/255 P ccC/ccA 1 -1 CTSG HGNC HGNC:2532 protein_coding YES CCDS9631.1 ENSP00000216336 P08311 UPI00001270AC NM_001911.2 5/5 hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF13 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 24573643 24573643 G T 1 0 0 0 0 0 0 0 1 3844 1219 43 2 2 CTSG 14 24573643 Silent SNP G C3N-00547_T 165613 24573643 82470075 478 14808 NOVA1 0 . GRCh38 14 26448223 26448223 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1260C>A p.= p.S420S ENST00000539517 5/5 369 279 90 330 330 0 strelka-varscan-mutect NOVA1,synonymous_variant,p.=,ENST00000539517,NM_002515.2;NOVA1,synonymous_variant,p.=,ENST00000465357,NM_006489.2;NOVA1,downstream_gene_variant,,ENST00000549571,;NOVA1,downstream_gene_variant,,ENST00000449198,;NOVA1,downstream_gene_variant,,ENST00000549146,;NOVA1,downstream_gene_variant,,ENST00000347476,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,downstream_gene_variant,,ENST00000546546,; T ENST00000539517 Transcript synonymous_variant 1578/3912 1260/1524 420/507 S tcC/tcA 1 -1 NOVA1 HGNC HGNC:7886 protein_coding YES CCDS32061.1 ENSP00000438875 P51513 UPI000013D74E NM_002515.2 5/5 hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF150,SMART_domains:SM00322 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 26448223 26448223 G T 1 0 0 0 0 0 0 0 1 10600 1335 47 2 2 NOVA1 14 26448223 Silent SNP G C3N-00547_T 1874580 26448223 80595495 479 14809 NOVA1 0 . GRCh38 14 26480127 26480127 + Silent SNP C C A rs747905882 C3N-00547_T C3N-00547_N C C c.297G>T p.= p.V99V ENST00000539517 3/5 100 61 39 102 102 0 strelka-varscan-mutect NOVA1,synonymous_variant,p.=,ENST00000539517,NM_002515.2;NOVA1,synonymous_variant,p.=,ENST00000465357,NM_006489.2;NOVA1,synonymous_variant,p.=,ENST00000574031,;NOVA1,synonymous_variant,p.=,ENST00000549571,;NOVA1,synonymous_variant,p.=,ENST00000449198,;NOVA1,synonymous_variant,p.=,ENST00000547619,;NOVA1,synonymous_variant,p.=,ENST00000344429,NM_006491.2;NOVA1,5_prime_UTR_variant,,ENST00000549146,;NOVA1,5_prime_UTR_variant,,ENST00000347476,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,3_prime_UTR_variant,,ENST00000546546,; A ENST00000539517 Transcript synonymous_variant 615/3912 297/1524 99/507 V gtG/gtT rs747905882 1 -1 NOVA1 HGNC HGNC:7886 protein_coding YES CCDS32061.1 ENSP00000438875 P51513 UPI000013D74E NM_002515.2 3/5 PROSITE_profiles:PS50084,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF150,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 LOW 1 SNV 1 1 PASS rs747905882 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 26480127 26480127 C A 1 0 0 0 0 0 0 0 1 10600 465 17 2 2 NOVA1 14 26480127 Silent SNP C C3N-00547_T 31904 26480127 80563591 480 14810 MIA2 0 . GRCh38 14 39247519 39247519 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.945A>T p.= p.T315T ENST00000553728 4/28 116 101 15 151 150 1 strelka-varscan-mutect RP11-407N17.3,synonymous_variant,p.=,ENST00000553728,;MIA2,synonymous_variant,p.=,ENST00000280082,NM_054024.3;MIA2,non_coding_transcript_exon_variant,,ENST00000556784,; T ENST00000553728 Transcript synonymous_variant 1158/4392 945/4020 315/1339 T acA/acT 1 1 RP11-407N17.3 Clone_based_vega_gene protein_coding YES ENSP00000452252 G3V599 UPI00021CF1EF 4/28 hmmpanther:PTHR23158:SF38,hmmpanther:PTHR23158 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 39247519 39247519 A T 1 0 0 0 0 0 0 0 1 9521 117 5 4 4 MIA2 14 39247519 Silent SNP A C3N-00547_T 12767392 39247519 67796199 481 14811 NIN 0 . GRCh38 14 50757023 50757023 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.4007A>T p.Gln1336Leu p.Q1336L ENST00000382041 18/30 64 52 12 82 82 0 strelka-varscan-mutect NIN,missense_variant,p.Gln1336Leu,ENST00000245441,NM_020921.3;NIN,missense_variant,p.Gln1336Leu,ENST00000530997,;NIN,missense_variant,p.Gln1336Leu,ENST00000453196,NM_182944.2;NIN,missense_variant,p.Gln1336Leu,ENST00000382041,NM_182946.1;NIN,missense_variant,p.Gln827Leu,ENST00000530853,;NIN,missense_variant,p.Gln827Leu,ENST00000389869,;NIN,intron_variant,,ENST00000324330,NM_016350.4;NIN,intron_variant,,ENST00000382043,;NIN,missense_variant,p.Gln1336Leu,ENST00000476352,; A ENST00000382041 Transcript missense_variant 4198/6496 4007/6273 1336/2090 Q/L cAg/cTg 1 -1 NIN HGNC HGNC:14906 protein_coding YES CCDS32079.1 ENSP00000371472 Q8N4C6 UPI0000DBEF14 NM_182946.1 tolerated(0.1) 18/30 hmmpanther:PTHR18905,hmmpanther:PTHR18905:SF11 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -19.99073 0.9999988 1 1 1 0 A 3 1 49 50757023 50757023 T A 1 0 0 0 0 1 0 0 0 10452 1580 55 4 4 NIN 14 50757023 Missense_Mutation SNP T C3N-00547_T 11509504 50757023 56286695 482 14812 TRIM9 0 . GRCh38 14 51025321 51025321 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.862G>T p.Ala288Ser p.A288S ENST00000298355 2/10 263 182 81 240 240 0 strelka-varscan-mutect TRIM9,missense_variant,p.Ala288Ser,ENST00000298355,NM_015163.5;TRIM9,missense_variant,p.Ala288Ser,ENST00000360392,NM_052978.4;TRIM9,missense_variant,p.Ala288Ser,ENST00000338969,; A ENST00000298355 Transcript missense_variant 1984/5284 862/2133 288/710 A/S Gcc/Tcc COSM4952431,COSM4952432,COSM4952433 1 -1 TRIM9 HGNC HGNC:16288 protein_coding YES CCDS9703.1 ENSP00000298355 Q9C026 UPI000006D630 NM_015163.5 deleterious(0.01) 2/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF400,SMART_domains:SM00502 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 51025321 51025321 C A 1 0 0 0 0 1 0 0 0 17046 739 26 2 2 TRIM9 14 51025321 Missense_Mutation SNP C C3N-00547_T 268298 51025321 56018397 483 14813 C14orf166 0 . GRCh38 14 52004238 52004238 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.576A>T p.= p.T192T ENST00000261700 7/8 191 119 72 140 140 0 strelka-varscan-mutect C14orf166,splice_acceptor_variant,,ENST00000556760,;C14orf166,synonymous_variant,p.=,ENST00000261700,NM_016039.2;C14orf166,intron_variant,,ENST00000553362,;NID2,downstream_gene_variant,,ENST00000216286,NM_007361.3;NID2,downstream_gene_variant,,ENST00000617139,;NID2,downstream_gene_variant,,ENST00000556572,;C14orf166,non_coding_transcript_exon_variant,,ENST00000553479,;NID2,downstream_gene_variant,,ENST00000556686,;C14orf166,downstream_gene_variant,,ENST00000553707,;NID2,downstream_gene_variant,,ENST00000553297,;NID2,downstream_gene_variant,,ENST00000555310,;C14orf166,downstream_gene_variant,,ENST00000555319,;C14orf166,downstream_gene_variant,,ENST00000557553,; T ENST00000261700 Transcript synonymous_variant 741/7075 576/735 192/244 T acA/acT 1 1 C14orf166 HGNC HGNC:23169 protein_coding YES CCDS9705.1 ENSP00000261700 Q9Y224 Q549M8 UPI000012759D NM_016039.2 7/8 hmmpanther:PTHR15924,Pfam_domain:PF10036 LOW 1 SNV 1 1 PASS rs1426719805 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 52004238 52004238 A T 1 0 0 0 0 0 0 0 1 1831 202 7 4 4 C14orf166 14 52004238 Silent SNP A C3N-00547_T 978917 52004238 55039480 484 14814 DDHD1 0 . GRCh38 14 53152765 53152766 + In_Frame_Ins INS - - GCCGCA novel C3N-00547_T C3N-00547_N - - c.333_334insTGCGGC p.Gly111_Gly112insCysGly p.G111_G112insCG ENST00000323669 1/13 91 53 38 131 130 1 sindel-varindel-pindel DDHD1,inframe_insertion,p.Gly111_Gly112insCysGly,ENST00000395606,NM_001160147.1;DDHD1,inframe_insertion,p.Gly111_Gly112insCysGly,ENST00000612692,;DDHD1,inframe_insertion,p.Gly111_Gly112insCysGly,ENST00000357758,NM_030637.2;DDHD1,inframe_insertion,p.Gly111_Gly112insCysGly,ENST00000323669,NM_001160148.1;DDHD1,upstream_gene_variant,,ENST00000556910,;RP11-547D23.1,upstream_gene_variant,,ENST00000554235,;DDHD1,upstream_gene_variant,,ENST00000557445,; GCCGCA ENST00000323669 Transcript inframe_insertion 333-334/5503 333-334/2703 111-112/900 -/CG -/TGCGGC 1 -1 DDHD1 HGNC HGNC:19714 protein_coding YES CCDS53895.1 ENSP00000327104 Q8NEL9 UPI00001D7B55 NM_001160148.1 1/13 hmmpanther:PTHR23509,hmmpanther:PTHR23509:SF10,Low_complexity_(Seg):seg MODERATE 1 insertion 2 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999886 1 1 1 0 GCCGCA 7 5 49 53152765 53152765 - GCCGCA 1 0 1 1 0 0 0 0 0 4129 652 23 0 0 DDHD1 14 53152765 In_Frame_Ins INS - C3N-00547_T 1148527 53152765 53890953 485 14815 PELI2 0 . GRCh38 14 56178407 56178407 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.150G>T p.Lys50Asn p.K50N ENST00000267460 2/6 253 206 47 252 252 0 strelka-varscan-mutect PELI2,missense_variant,p.Lys50Asn,ENST00000267460,NM_021255.2;PELI2,5_prime_UTR_variant,,ENST00000559044,;PELI2,5_prime_UTR_variant,,ENST00000561019,; T ENST00000267460 Transcript missense_variant 436/5909 150/1263 50/420 K/N aaG/aaT 1 1 PELI2 HGNC HGNC:8828 protein_coding YES CCDS9726.1 ENSP00000267460 Q9HAT8 UPI0000062262 NM_021255.2 tolerated(0.52) 2/6 hmmpanther:PTHR12098,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 56178407 56178407 G T 1 0 0 0 0 1 0 0 0 11810 991 35 2 2 PELI2 14 56178407 Missense_Mutation SNP G C3N-00547_T 3025642 56178407 50865311 486 14816 CCDC175 0 . GRCh38 14 59568298 59568298 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.438A>G p.Ile146Met p.I146M ENST00000537690 4/20 120 103 17 131 131 0 strelka-varscan-mutect CCDC175,missense_variant,p.Ile146Met,ENST00000537690,NM_001164399.1;CCDC175,missense_variant,p.Ile146Met,ENST00000281581,;CCDC175,upstream_gene_variant,,ENST00000556996,;CCDC175,upstream_gene_variant,,ENST00000556936,; C ENST00000537690 Transcript missense_variant 494/2616 438/2382 146/793 I/M atA/atG 1 -1 CCDC175 HGNC HGNC:19847 protein_coding YES CCDS53898.1 ENSP00000453940 P0C221 UPI000059D254 NM_001164399.1 tolerated(0.05) 4/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR35347 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 59568298 59568298 T C 1 0 0 0 0 1 0 0 0 2492 1512 53 5 5 CCDC175 14 59568298 Missense_Mutation SNP T C3N-00547_T 3389891 59568298 47475420 487 14817 SMOC1 0 . GRCh38 14 70011520 70011520 + Missense_Mutation SNP C C T rs755186347 C3N-00547_T C3N-00547_N C C c.893C>T p.Ala298Val p.A298V ENST00000361956 9/12 549 488 61 501 501 0 strelka-varscan-mutect SMOC1,missense_variant,p.Ala298Val,ENST00000381280,NM_022137.5;SMOC1,missense_variant,p.Ala298Val,ENST00000361956,NM_001034852.2;SMOC1,non_coding_transcript_exon_variant,,ENST00000557483,; T ENST00000361956 Transcript missense_variant 1156/2040 893/1308 298/435 A/V gCc/gTc rs755186347 1 1 SMOC1 HGNC HGNC:20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF NM_001034852.2 deleterious(0.01) 9/12 hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF13 MODERATE 1 SNV 1 1 PASS rs755186347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 70011520 70011520 C T 1 0 0 0 0 1 0 0 0 15122 739 26 3 3 SMOC1 14 70011520 Missense_Mutation SNP C C3N-00547_T 10443222 70011520 37032198 488 14818 RPS6KL1 0 . GRCh38 14 74909797 74909797 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1016C>A p.Ala339Asp p.A339D ENST00000354625 7/11 82 71 11 67 67 0 strelka-varscan-mutect RPS6KL1,missense_variant,p.Ala339Asp,ENST00000354625,NM_031464.4;RPS6KL1,missense_variant,p.Ala339Asp,ENST00000555647,;RPS6KL1,missense_variant,p.Ala339Asp,ENST00000557413,;RPS6KL1,intron_variant,,ENST00000553789,;RPS6KL1,intron_variant,,ENST00000553971,;RPS6KL1,upstream_gene_variant,,ENST00000556848,;RPS6KL1,upstream_gene_variant,,ENST00000555910,;RPS6KL1,upstream_gene_variant,,ENST00000553315,;RPS6KL1,downstream_gene_variant,,ENST00000554900,;RPS6KL1,missense_variant,p.Ala308Asp,ENST00000555009,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000555834,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000553646,;RPS6KL1,downstream_gene_variant,,ENST00000553894,;RPS6KL1,downstream_gene_variant,,ENST00000554834,; T ENST00000354625 Transcript missense_variant 1501/5195 1016/1650 339/549 A/D gCt/gAt 1 -1 RPS6KL1 HGNC HGNC:20222 protein_coding YES CCDS9834.2 ENSP00000346644 Q9Y6S9 UPI0000035B53 NM_031464.4 tolerated(0.37) 7/11 PROSITE_profiles:PS50011,hmmpanther:PTHR15508 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 49 74909797 74909797 G T 1 0 0 0 0 1 0 0 0 13914 971 34 2 2 RPS6KL1 14 74909797 Missense_Mutation SNP G C3N-00547_T 4898277 74909797 32133921 489 14819 NRXN3 0 . GRCh38 14 79467331 79467331 + Missense_Mutation SNP A A T rs752059168 C3N-00547_T C3N-00547_N A A c.2254A>T p.Thr752Ser p.T752S ENST00000554719 13/17 147 95 52 156 156 0 strelka-varscan-mutect NRXN3,missense_variant,p.Thr120Ser,ENST00000281127,NM_138970.4;NRXN3,missense_variant,p.Thr1114Ser,ENST00000634499,;NRXN3,missense_variant,p.Thr1125Ser,ENST00000635466,;NRXN3,missense_variant,p.Thr120Ser,ENST00000428277,NM_001105250.2;NRXN3,missense_variant,p.Thr752Ser,ENST00000554719,NM_004796.5;NRXN3,missense_variant,p.Thr120Ser,ENST00000557594,NM_001272020.1;NRXN3,non_coding_transcript_exon_variant,,ENST00000556003,;NRXN3,non_coding_transcript_exon_variant,,ENST00000553803,;NRXN3,non_coding_transcript_exon_variant,,ENST00000555073,;NRXN3,missense_variant,p.Thr1114Ser,ENST00000554738,;NRXN3,missense_variant,p.Thr120Ser,ENST00000555387,; T ENST00000554719 Transcript missense_variant 2745/4156 2254/3186 752/1061 T/S Act/Tct rs752059168,COSM1217927,COSM1217928 1 1 NRXN3 HGNC HGNC:8010 protein_coding YES CCDS9870.1 ENSP00000451648 Q9Y4C0 UPI0000167BBA NM_004796.5 tolerated(0.91) 13/17 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405,SMART_domains:SM00282,Superfamily_domains:SSF49899 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs752059168 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 79467331 79467331 A T 1 0 0 0 0 1 0 0 0 10726 159 6 4 4 NRXN3 14 79467331 Missense_Mutation SNP A C3N-00547_T 4557534 79467331 27576387 490 14820 FLRT2 0 . GRCh38 14 85622686 85622686 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1172C>A p.Pro391His p.P391H ENST00000330753 2/2 139 126 13 162 162 0 strelka-varscan-mutect FLRT2,missense_variant,p.Pro391His,ENST00000330753,NM_013231.4;FLRT2,missense_variant,p.Pro391His,ENST00000554746,;FLRT2,upstream_gene_variant,,ENST00000553650,; A ENST00000330753 Transcript missense_variant 1939/33679 1172/1983 391/660 P/H cCt/cAt 1 1 FLRT2 HGNC HGNC:3761 protein_coding YES CCDS9877.1 ENSP00000332879 O43155 UPI0000049E10 NM_013231.4 tolerated(0.11) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24369:SF23,hmmpanther:PTHR24369 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 85622686 85622686 C A 1 0 0 0 0 1 0 0 0 5795 681 24 2 2 FLRT2 14 85622686 Missense_Mutation SNP C C3N-00547_T 6155355 85622686 21421032 491 14821 SLC24A4 0 . GRCh38 14 92433970 92433970 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.300C>A p.= p.V100V ENST00000532405 3/17 222 173 49 225 225 0 strelka-varscan-mutect SLC24A4,synonymous_variant,p.=,ENST00000532405,NM_153646.3;SLC24A4,synonymous_variant,p.=,ENST00000531433,NM_153647.3;SLC24A4,synonymous_variant,p.=,ENST00000393265,NM_153648.3;SLC24A4,5_prime_UTR_variant,,ENST00000554461,; A ENST00000532405 Transcript synonymous_variant 526/9950 300/1869 100/622 V gtC/gtA 1 1 SLC24A4 HGNC HGNC:10978 protein_coding YES CCDS9903.2 ENSP00000431840 Q8NFF2 UPI000044C5DE NM_153646.3 3/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR10846:SF21,hmmpanther:PTHR10846 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 92433970 92433970 C A 1 0 0 0 0 0 0 0 1 14734 842 30 2 2 SLC24A4 14 92433970 Silent SNP C C3N-00547_T 6811284 92433970 14609748 492 14822 GOLGA5 0 . GRCh38 14 92797770 92797770 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.333G>A p.= p.V111V ENST00000163416 2/13 149 87 62 165 165 0 strelka-varscan-mutect GOLGA5,synonymous_variant,p.=,ENST00000163416,NM_005113.3; A ENST00000163416 Transcript synonymous_variant 589/2969 333/2196 111/731 V gtG/gtA 1 1 GOLGA5 HGNC HGNC:4428 protein_coding YES CCDS9905.1 ENSP00000163416 Q8TBA6 UPI000013C5AA NM_005113.3 2/13 hmmpanther:PTHR13815,hmmpanther:PTHR13815:SF5 LOW 1 SNV 1 1 PASS . . 0 202 0 7 0 0 0 0 -20 0.9993044 1 1 1 0 A 2 1 49 92797770 92797770 G A 1 0 0 0 0 0 0 0 1 6434 1306 46 3 3 GOLGA5 14 92797770 Silent SNP G C3N-00547_T 363800 92797770 14245948 493 14823 DYNC1H1 0 . GRCh38 14 102027676 102027676 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.9106G>A p.Gly3036Arg p.G3036R ENST00000360184 47/78 647 418 229 620 620 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Gly3036Arg,ENST00000360184,NM_001376.4;DYNC1H1,downstream_gene_variant,,ENST00000555204,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000554854,; A ENST00000360184 Transcript missense_variant 9270/14333 9106/13941 3036/4646 G/R Ggg/Agg 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0) 47/78 Pfam_domain:PF12780,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28,SMART_domains:SM00382 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 102027676 102027676 G A 1 0 0 0 0 1 0 0 0 4665 1232 43 3 3 DYNC1H1 14 102027676 Missense_Mutation SNP G C3N-00547_T 9229906 102027676 5016042 494 14824 CKB 0 . GRCh38 14 103519997 103519997 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.1013A>G p.Asn338Ser p.N338S ENST00000348956 8/8 181 123 58 183 183 0 strelka-varscan-mutect CKB,missense_variant,p.Asn338Ser,ENST00000348956,NM_001823.4;CKB,missense_variant,p.Asn136Ser,ENST00000553610,;CKB,missense_variant,p.Asn89Ser,ENST00000555039,;CKB,downstream_gene_variant,,ENST00000553878,;CKB,downstream_gene_variant,,ENST00000557530,;CKB,3_prime_UTR_variant,,ENST00000553652,;CKB,3_prime_UTR_variant,,ENST00000554989,;CKB,non_coding_transcript_exon_variant,,ENST00000553528,;CKB,non_coding_transcript_exon_variant,,ENST00000554282,;CKB,downstream_gene_variant,,ENST00000555770,;CKB,downstream_gene_variant,,ENST00000554705,;CKB,downstream_gene_variant,,ENST00000554426,;CKB,downstream_gene_variant,,ENST00000555659,;CKB,downstream_gene_variant,,ENST00000553994,;CKB,downstream_gene_variant,,ENST00000557569,;CKB,downstream_gene_variant,,ENST00000557287,;CKB,downstream_gene_variant,,ENST00000555366,; C ENST00000348956 Transcript missense_variant 1371/1709 1013/1146 338/381 N/S aAc/aGc 1 -1 CKB HGNC HGNC:1991 protein_coding YES CCDS9981.1 ENSP00000299198 P12277 V9HWH2 UPI000012DCBA NM_001823.4 deleterious(0) 8/8 PROSITE_profiles:PS51510,hmmpanther:PTHR11547,hmmpanther:PTHR11547:SF34,Gene3D:3.30.590.10,Pfam_domain:PF00217,Superfamily_domains:SSF55931 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 103519997 103519997 T C 1 0 0 0 0 1 0 0 0 3209 1725 60 5 5 CKB 14 103519997 Missense_Mutation SNP T C3N-00547_T 1492321 103519997 3523721 495 14825 TDRD9 0 . GRCh38 14 103928650 103928650 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.141C>A p.= p.A47A ENST00000409874 1/36 20 14 6 20 20 0 strelka-varscan-mutect TDRD9,synonymous_variant,p.=,ENST00000409874,NM_153046.2;C14orf2,upstream_gene_variant,,ENST00000554880,;TDRD9,upstream_gene_variant,,ENST00000496087,; A ENST00000409874 Transcript synonymous_variant 189/4782 141/4149 47/1382 A gcC/gcA 1 1 TDRD9 HGNC HGNC:20122 protein_coding YES CCDS9987.2 ENSP00000387303 Q8NDG6 UPI0001642306 NM_153046.2 1/36 Low_complexity_(Seg):seg,hmmpanther:PTHR18934:SF113,hmmpanther:PTHR18934 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -17.95705 1 1 1 1 0 A 2 1 49 103928650 103928650 C A 1 0 0 0 0 0 0 0 1 16146 610 22 2 2 TDRD9 14 103928650 Silent SNP C C3N-00547_T 408653 103928650 3115068 496 14826 ASPG 0 . GRCh38 14 104097569 104097569 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.445C>A p.Leu149Met p.L149M ENST00000551177 5/16 189 118 71 154 154 0 strelka-varscan-mutect ASPG,missense_variant,p.Leu149Met,ENST00000551177,NM_001080464.2;ASPG,missense_variant,p.Leu149Met,ENST00000546892,;ASPG,missense_variant,p.Leu86Met,ENST00000551170,;ASPG,non_coding_transcript_exon_variant,,ENST00000548372,; A ENST00000551177 Transcript missense_variant 537/4851 445/1722 149/573 L/M Ctg/Atg 1 1 ASPG HGNC HGNC:20123 protein_coding YES CCDS45170.2 ENSP00000450040 Q86U10 UPI00001D7B76 NM_001080464.2 tolerated(0.07) 5/16 PROSITE_profiles:PS51732,hmmpanther:PTHR11707:SF28,hmmpanther:PTHR11707,TIGRFAM_domain:TIGR00519,PIRSF_domain:PIRSF001220,Gene3D:3.40.50.1170,Pfam_domain:PF00710,PIRSF_domain:PIRSF500176,SMART_domains:SM00870,Superfamily_domains:SSF53774 MODERATE 1 SNV 1 1 PASS rs1480014615 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 104097569 104097569 C A 1 0 0 0 0 1 0 0 0 1199 680 24 2 2 ASPG 14 104097569 Missense_Mutation SNP C C3N-00547_T 168919 104097569 2946149 497 14827 AHNAK2 0 . GRCh38 14 104947296 104947296 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.8155G>A p.Gly2719Ser p.G2719S ENST00000333244 7/7 392 262 130 324 323 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Gly2719Ser,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; T ENST00000333244 Transcript missense_variant 8275/18254 8155/17388 2719/5795 G/S Ggc/Agc 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.07) 7/7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 104947296 104947296 C T 1 0 0 0 0 1 0 0 0 492 623 22 3 3 AHNAK2 14 104947296 Missense_Mutation SNP C C3N-00547_T 849727 104947296 2096422 498 14828 AHNAK2 0 . GRCh38 14 104950126 104950126 + Silent SNP C C A rs375331989 C3N-00547_T C3N-00547_N C C c.5325G>T p.= p.A1775A ENST00000333244 7/7 661 522 139 654 654 0 strelka-varscan-mutect AHNAK2,synonymous_variant,p.=,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; A ENST00000333244 Transcript synonymous_variant 5445/18254 5325/17388 1775/5795 A gcG/gcT rs375331989,COSM1368630 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 7/7 hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348 0,1 LOW 1 SNV 5 0,1 1 PASS rs375331989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 104950126 104950126 C A 1 0 0 0 0 0 0 0 1 492 639 23 1 1 AHNAK2 14 104950126 Silent SNP C C3N-00547_T 2830 104950126 2093592 499 14829 NPAP1 0 . GRCh38 15 24678181 24678181 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2314C>A p.Pro772Thr p.P772T ENST00000329468 1/1 185 159 26 320 319 1 strelka-varscan-mutect NPAP1,missense_variant,p.Pro772Thr,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 2314/7526 2314/3471 772/1156 P/T Ccc/Acc 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 deleterious(0.03) 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 24678181 24678181 C A 1 0 0 0 0 1 0 0 0 10609 507 18 2 2 NPAP1 15 24678181 Missense_Mutation SNP C C3N-00547_T 24678181 77313008 500 14830 GABRG3 0 . GRCh38 15 27328871 27328871 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.557C>A p.Pro186Gln p.P186Q ENST00000615808 5/10 144 109 35 196 196 0 strelka-varscan-mutect GABRG3,missense_variant,p.Pro186Gln,ENST00000615808,NM_033223.4;GABRG3,missense_variant,p.Pro186Gln,ENST00000555083,NM_001270873.1;GABRG3,missense_variant,p.Pro7Gln,ENST00000333743,;GABRG3,missense_variant,p.Pro128Gln,ENST00000554696,;GABRG3,missense_variant,p.Pro19Gln,ENST00000557596,; A ENST00000615808 Transcript missense_variant 811/10768 557/1404 186/467 P/Q cCg/cAg 1 1 GABRG3 HGNC HGNC:4088 protein_coding YES CCDS45195.1 ENSP00000479113 Q99928 UPI000012AFCB NM_033223.4 deleterious(0) 5/10 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF195,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 27328871 27328871 C A 1 0 0 0 0 1 0 0 0 6044 652 23 1 1 GABRG3 15 27328871 Missense_Mutation SNP C C3N-00547_T 2650690 27328871 74662318 501 14831 HERC2 0 . GRCh38 15 28212574 28212574 + Missense_Mutation SNP C C G rs777318947 C3N-00547_T C3N-00547_N C C c.6796G>C p.Val2266Leu p.V2266L ENST00000261609 43/93 99 82 17 159 159 0 strelka-varscan-mutect HERC2,missense_variant,p.Val2266Leu,ENST00000261609,NM_004667.5; G ENST00000261609 Transcript missense_variant 6905/15337 6796/14505 2266/4834 V/L Gtg/Ctg rs777318947 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 tolerated(0.41) 43/93 MODERATE 1 SNV 1 1 PASS rs777318947 . 0 205 0 4 0 0 0 0 -20 0.9999348 1 1 1 0 G 3 3 49 28212574 28212574 C G 1 0 0 0 0 1 0 0 0 6942 536 19 4 4 HERC2 15 28212574 Missense_Mutation SNP C C3N-00547_T 883703 28212574 73778615 502 14832 HERC2 0 . GRCh38 15 28265618 28265618 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1870G>C p.Gly624Arg p.G624R ENST00000261609 14/93 116 72 44 200 200 0 strelka-varscan-mutect HERC2,missense_variant,p.Gly624Arg,ENST00000261609,NM_004667.5;HERC2,splice_region_variant,,ENST00000564734,; G ENST00000261609 Transcript missense_variant,splice_region_variant 1979/15337 1870/14505 624/4834 G/R Ggg/Cgg 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 deleterious(0) 14/93 Gene3D:2.130.10.30,Pfam_domain:PF00415,PROSITE_profiles:PS50012,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF325,Superfamily_domains:SSF50985 MODERATE 1 SNV 1 1 PASS rs1321031215 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 28265618 28265618 C G 1 0 0 0 0 1 0 0 0 6942 666 23 4 4 HERC2 15 28265618 Missense_Mutation SNP C C3N-00547_T 53044 28265618 73725571 503 14833 APBA2 0 . GRCh38 15 29105458 29105458 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1604C>G p.Pro535Arg p.P535R ENST00000558402 12/16 338 230 108 407 407 0 strelka-varscan-mutect APBA2,missense_variant,p.Pro535Arg,ENST00000558402,;APBA2,missense_variant,p.Pro535Arg,ENST00000558259,NM_005503.3;APBA2,missense_variant,p.Pro523Arg,ENST00000411764,NM_001130414.1;APBA2,missense_variant,p.Pro523Arg,ENST00000558330,;APBA2,missense_variant,p.Pro535Arg,ENST00000561069,;APBA2,non_coding_transcript_exon_variant,,ENST00000559814,;APBA2,downstream_gene_variant,,ENST00000382938,; G ENST00000558402 Transcript missense_variant 2203/4031 1604/2250 535/749 P/R cCc/cGc 1 1 APBA2 HGNC HGNC:579 protein_coding YES CCDS10022.1 ENSP00000453293 Q99767 UPI0000046798 deleterious(0) 12/16 PROSITE_profiles:PS01179,hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF12 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 29105458 29105458 C G 1 0 0 0 0 1 0 0 0 877 623 22 4 4 APBA2 15 29105458 Missense_Mutation SNP C C3N-00547_T 839840 29105458 72885731 504 14834 GOLGA8J 0 . GRCh38 15 30090230 30090230 + Missense_Mutation SNP G G C rs559438285 C3N-00547_T C3N-00547_N G G c.1150G>C p.Ala384Pro p.A384P ENST00000567927 13/19 94 68 26 125 125 0 strelka-varscan-mutect GOLGA8J,missense_variant,p.Ala384Pro,ENST00000567927,NM_001282472.1;RN7SL673P,upstream_gene_variant,,ENST00000616262,;GOLGA8J,downstream_gene_variant,,ENST00000568123,; C ENST00000567927 Transcript missense_variant 1150/1899 1150/1899 384/632 A/P Gca/Cca rs559438285 1 1 GOLGA8J HGNC HGNC:38650 protein_coding YES CCDS61574.1 ENSP00000456401 A6NMD2 UPI0001A5E7A2 NM_001282472.1 deleterious(0) 13/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS rs559438285 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 30090230 30090230 G C 1 0 0 0 0 1 0 0 0 6452 1087 38 4 4 GOLGA8J 15 30090230 Missense_Mutation SNP G C3N-00547_T 984772 30090230 71900959 505 14835 OTUD7A 0 . GRCh38 15 31487262 31487262 + Nonsense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1282G>T p.Glu428Ter p.E428* ENST00000307050 10/11 118 108 10 120 119 1 strelka-varscan-mutect OTUD7A,stop_gained,p.Glu428Ter,ENST00000307050,NM_130901.1; A ENST00000307050 Transcript stop_gained 1375/10770 1282/2781 428/926 E/* Gaa/Taa 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 10/11 hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 31487262 31487262 C A 1 0 0 0 0 0 1 0 0 11387 922 32 2 2 OTUD7A 15 31487262 Nonsense_Mutation SNP C C3N-00547_T 1397032 31487262 70503927 506 14836 BUB1B 0 . GRCh38 15 40210177 40210177 + Silent SNP G G A rs752774198 C3N-00547_T C3N-00547_N G G c.2352G>A p.= p.A784A ENST00000287598 18/23 292 235 57 360 359 1 strelka-varscan-mutect BUB1B,synonymous_variant,p.=,ENST00000287598,NM_001211.5;BUB1B,synonymous_variant,p.=,ENST00000412359,;BUB1B,downstream_gene_variant,,ENST00000558972,; A ENST00000287598 Transcript synonymous_variant 2547/3725 2352/3153 784/1050 A gcG/gcA rs752774198,COSM961105 1 1 BUB1B HGNC HGNC:1149 protein_coding YES CCDS10053.1 ENSP00000287598 O60566 UPI000006E699 NM_001211.5 18/23 hmmpanther:PTHR14030:SF4,hmmpanther:PTHR14030 0,1 LOW 1 SNV 1 0,1 1 PASS rs752774198 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 40210177 40210177 G A 1 0 0 0 0 0 0 0 1 1747 1074 38 1 1 BUB1B 15 40210177 Silent SNP G C3N-00547_T 8722915 40210177 61781012 507 14837 ZSCAN29 0 . GRCh38 15 43364110 43364110 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1495G>T p.Ala499Ser p.A499S ENST00000396976 4/5 133 106 27 177 177 0 strelka-varscan-mutect ZSCAN29,missense_variant,p.Ala499Ser,ENST00000396976,NM_152455.3;ZSCAN29,3_prime_UTR_variant,,ENST00000396972,;ZSCAN29,3_prime_UTR_variant,,ENST00000570181,;ZSCAN29,intron_variant,,ENST00000562072,;ZSCAN29,intron_variant,,ENST00000568898,;ZSCAN29,3_prime_UTR_variant,,ENST00000566849,; A ENST00000396976 Transcript missense_variant 1630/5595 1495/2559 499/852 A/S Gct/Tct 1 -1 ZSCAN29 HGNC HGNC:26673 protein_coding YES CCDS10095.2 ENSP00000380174 Q8IWY8 UPI0000DA5AF5 NM_152455.3 tolerated(0.5) 4/5 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF194 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 43364110 43364110 C A 1 0 0 0 0 1 0 0 0 18832 710 25 2 2 ZSCAN29 15 43364110 Missense_Mutation SNP C C3N-00547_T 3153933 43364110 58627079 508 14838 DUOX2 0 . GRCh38 15 45104253 45104253 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2447G>T p.Gly816Val p.G816V ENST00000603300 19/34 420 340 80 540 540 0 strelka-varscan-mutect DUOX2,missense_variant,p.Gly816Val,ENST00000389039,;DUOX2,missense_variant,p.Gly816Val,ENST00000603300,NM_014080.4;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,;DUOX2,upstream_gene_variant,,ENST00000558416,;DUOX2,upstream_gene_variant,,ENST00000560797,; A ENST00000603300 Transcript missense_variant 2650/6345 2447/4647 816/1548 G/V gGc/gTc 1 -1 DUOX2 HGNC HGNC:13273 protein_coding YES CCDS10117.1 ENSP00000475084 Q9NRD8 UPI000013D775 NM_014080.4 deleterious(0) 19/34 Gene3D:1.10.238.10,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF67,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 45104253 45104253 C A 1 0 0 0 0 1 0 0 0 4623 739 26 2 2 DUOX2 15 45104253 Missense_Mutation SNP C C3N-00547_T 1740143 45104253 56886936 509 14839 59 2 DUOX2 0 . GRCh38 15 45104255 45104255 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.2445G>T p.= p.L815L ENST00000603300 19/34 409 333 76 534 534 0 strelka-varscan-mutect DUOX2,synonymous_variant,p.=,ENST00000389039,;DUOX2,synonymous_variant,p.=,ENST00000603300,NM_014080.4;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,;DUOX2,upstream_gene_variant,,ENST00000558416,;DUOX2,upstream_gene_variant,,ENST00000560797,; A ENST00000603300 Transcript synonymous_variant 2648/6345 2445/4647 815/1548 L ctG/ctT 1 -1 DUOX2 HGNC HGNC:13273 protein_coding YES CCDS10117.1 ENSP00000475084 Q9NRD8 UPI000013D775 NM_014080.4 19/34 Gene3D:1.10.238.10,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF67,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 45104255 45104255 C A 1 0 0 0 0 0 0 0 1 4623 581 21 2 2 DUOX2 15 45104255 Silent SNP C C3N-00547_T 2 45104255 56886934 510 14840 59 2 SEMA6D 0 . GRCh38 15 47771586 47771586 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.3023A>T p.Lys1008Met p.K1008M ENST00000316364 19/19 120 92 28 145 145 0 strelka-varscan-mutect SEMA6D,missense_variant,p.Lys1008Met,ENST00000316364,NM_153618.1;SEMA6D,missense_variant,p.Lys946Met,ENST00000558014,NM_001198999.1;SEMA6D,missense_variant,p.Lys952Met,ENST00000354744,NM_153617.1;SEMA6D,missense_variant,p.Lys946Met,ENST00000358066,NM_020858.1;SEMA6D,missense_variant,p.Lys933Met,ENST00000389428,NM_153616.1;SEMA6D,missense_variant,p.Lys1008Met,ENST00000536845,;SEMA6D,3_prime_UTR_variant,,ENST00000355997,NM_153619.1;SEMA6D,3_prime_UTR_variant,,ENST00000558816,;SEMA6D,downstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000559064,;SEMA6D,downstream_gene_variant,,ENST00000558431,; T ENST00000316364 Transcript missense_variant 3462/6099 3023/3222 1008/1073 K/M aAg/aTg 1 1 SEMA6D HGNC HGNC:16770 protein_coding YES CCDS32225.1 ENSP00000324857 Q8NFY4 UPI000006E201 NM_153618.1 deleterious(0) 19/19 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF65 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 47771586 47771586 A T 1 0 0 0 0 1 0 0 0 14318 72 3 4 4 SEMA6D 15 47771586 Missense_Mutation SNP A C3N-00547_T 2667331 47771586 54219603 511 14841 GCNT3 0 . GRCh38 15 59618535 59618535 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.297A>T p.= p.T99T ENST00000396065 3/3 212 165 47 230 230 0 strelka-varscan-mutect GCNT3,synonymous_variant,p.=,ENST00000396065,;GCNT3,synonymous_variant,p.=,ENST00000560585,NM_004751.2;GCNT3,synonymous_variant,p.=,ENST00000559200,;GCNT3,downstream_gene_variant,,ENST00000559189,;GCNT3,downstream_gene_variant,,ENST00000559626,;GCNT3,intron_variant,,ENST00000560210,;GCNT3,downstream_gene_variant,,ENST00000560580,;GCNT3,downstream_gene_variant,,ENST00000560874,;GCNT3,downstream_gene_variant,,ENST00000558721,; T ENST00000396065 Transcript synonymous_variant 745/4933 297/1317 99/438 T acA/acT 1 1 GCNT3 HGNC HGNC:4205 protein_coding YES CCDS10172.1 ENSP00000379377 O95395 A0A024R5T9 UPI0000034962 3/3 hmmpanther:PTHR19297:SF81,hmmpanther:PTHR19297 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 59618535 59618535 A T 1 0 0 0 0 0 0 0 1 6172 175 7 4 4 GCNT3 15 59618535 Silent SNP A C3N-00547_T 11846949 59618535 42372654 512 14842 SNX1 0 . GRCh38 15 64136352 64136352 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.1388A>G p.Tyr463Cys p.Y463C ENST00000261889 13/15 204 167 37 285 285 0 strelka-varscan-mutect SNX1,missense_variant,p.Tyr463Cys,ENST00000261889,NM_001242933.1;SNX1,missense_variant,p.Tyr463Cys,ENST00000559844,NM_003099.4;SNX1,missense_variant,p.Tyr245Cys,ENST00000560829,;SNX1,missense_variant,p.Tyr398Cys,ENST00000561026,NM_148955.3;SNX1,missense_variant,p.Tyr8Cys,ENST00000560861,;SNX1,intron_variant,,ENST00000558040,;SNX1,downstream_gene_variant,,ENST00000559339,;SNX1,3_prime_UTR_variant,,ENST00000380285,;SNX1,non_coding_transcript_exon_variant,,ENST00000559961,;SNX1,downstream_gene_variant,,ENST00000560260,;SNX1,downstream_gene_variant,,ENST00000559401,; G ENST00000261889 Transcript missense_variant 1409/3373 1388/1674 463/557 Y/C tAt/tGt 1 1 SNX1 HGNC HGNC:11172 protein_coding YES CCDS58371.1 ENSP00000261889 Q13596 UPI000217BDBB NM_001242933.1 tolerated(0.18) 13/15 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF09325,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF129,Superfamily_domains:SSF103657 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 64136352 64136352 A G 1 0 0 0 0 1 0 0 0 15201 449 16 5 5 SNX1 15 64136352 Missense_Mutation SNP A C3N-00547_T 4517817 64136352 37854837 513 14843 PIF1 0 . GRCh38 15 64818293 64818293 + Silent SNP G G T rs200699011 C3N-00547_T C3N-00547_N G G c.1492C>A p.= p.R498R ENST00000333425 10/13 159 131 28 175 175 0 strelka-varscan-mutect PIF1,synonymous_variant,p.=,ENST00000268043,NM_001286499.1,NM_025049.3,NM_001286496.1;PIF1,synonymous_variant,p.=,ENST00000559239,;PIF1,synonymous_variant,p.=,ENST00000333425,NM_001286497.1;PIF1,non_coding_transcript_exon_variant,,ENST00000559522,;PIF1,non_coding_transcript_exon_variant,,ENST00000559872,;PIF1,downstream_gene_variant,,ENST00000560444,;PIF1,downstream_gene_variant,,ENST00000560504,;PIF1,downstream_gene_variant,,ENST00000558380,;PIF1,downstream_gene_variant,,ENST00000558547,; T ENST00000333425 Transcript synonymous_variant 1587/2278 1492/2124 498/707 R Cga/Aga rs200699011,COSM3754408,COSM3754409 1 -1 PIF1 HGNC HGNC:26220 protein_coding YES CCDS66797.1 ENSP00000328174 Q9H611 UPI00005DB2E0 NM_001286497.1 10/13 HAMAP:MF_03176,Pfam_domain:PF05970,hmmpanther:PTHR23274,Superfamily_domains:SSF52540 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs200699011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 64818293 64818293 G T 1 0 0 0 0 0 0 0 1 11976 1124 39 1 1 PIF1 15 64818293 Silent SNP G C3N-00547_T 681941 64818293 37172896 514 14844 KBTBD13 0 . GRCh38 15 65077051 65077051 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.236T>A p.Leu79Gln p.L79Q ENST00000432196 1/1 66 53 13 128 128 0 strelka-varscan-mutect KBTBD13,missense_variant,p.Leu79Gln,ENST00000432196,NM_001101362.2;RASL12,upstream_gene_variant,,ENST00000434605,; A ENST00000432196 Transcript missense_variant 236/1377 236/1377 79/458 L/Q cTg/cAg 1 1 KBTBD13 HGNC HGNC:37227 protein_coding YES CCDS45281.1 ENSP00000388723 C9JR72 UPI0000161560 NM_001101362.2 deleterious(0.01) 1/1 hmmpanther:PTHR24412:SF57,hmmpanther:PTHR24412,Gene3D:3.30.710.10,Pfam_domain:PF00651,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 65077051 65077051 T A 1 0 0 0 0 1 0 0 0 7909 1580 55 4 4 KBTBD13 15 65077051 Missense_Mutation SNP T C3N-00547_T 258758 65077051 36914138 515 14845 UBAP1L 0 . GRCh38 15 65102323 65102323 + Missense_Mutation SNP C C A rs763106125 C3N-00547_T C3N-00547_N C C c.482G>T p.Arg161Leu p.R161L ENST00000559089 3/6 34 27 7 73 73 0 strelka-varscan-mutect UBAP1L,missense_variant,p.Arg161Leu,ENST00000559089,;UBAP1L,missense_variant,p.Arg161Leu,ENST00000502113,NM_001163692.1;UBAP1L,intron_variant,,ENST00000558802,;UBAP1L,upstream_gene_variant,,ENST00000561387,;RP11-325L12.3,upstream_gene_variant,,ENST00000560906,; A ENST00000559089 Transcript missense_variant 703/1694 482/1146 161/381 R/L cGg/cTg rs763106125 1 -1 UBAP1L HGNC HGNC:40028 protein_coding YES CCDS53948.1 ENSP00000454012 F5GYI3 UPI00004DD5A3 deleterious(0.01) 3/6 hmmpanther:PTHR15960:SF3,hmmpanther:PTHR15960 MODERATE 1 SNV 1 1 PASS rs763106125 . 0 194 13 3 0 0 0 0 -14.68746 0.996853 1 1 1 0 A 3 1 49 65102323 65102323 C A 1 0 0 0 0 1 0 0 0 17358 652 23 1 1 UBAP1L 15 65102323 Missense_Mutation SNP C C3N-00547_T 25272 65102323 36888866 516 14846 SKOR1 0 . GRCh38 15 67833785 67833785 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.2556G>A p.= p.T852T ENST00000341418 15/15 433 386 47 464 464 0 strelka-varscan-mutect SKOR1,synonymous_variant,p.=,ENST00000380035,;SKOR1,synonymous_variant,p.=,ENST00000554054,;SKOR1,synonymous_variant,p.=,ENST00000554240,;SKOR1,synonymous_variant,p.=,ENST00000341418,NM_001258024.1;RP11-34F13.3,intron_variant,,ENST00000558889,;RP11-34F13.2,downstream_gene_variant,,ENST00000502156,;RP11-34F13.3,intron_variant,,ENST00000560577,; A ENST00000341418 Transcript synonymous_variant 2556/3332 2556/2607 852/868 T acG/acA 1 1 SKOR1 HGNC HGNC:21326 protein_coding YES CCDS58374.1 ENSP00000343200 P84550 UPI00001987EE NM_001258024.1 15/15 hmmpanther:PTHR10005,hmmpanther:PTHR10005:SF8 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 67833785 67833785 G A 1 0 0 0 0 0 0 0 1 14624 1074 38 1 1 SKOR1 15 67833785 Silent SNP G C3N-00547_T 2731462 67833785 34157404 517 14847 PKM 0 . GRCh38 15 72203082 72203082 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1247G>T p.Ser416Ile p.S416I ENST00000319622 9/11 388 344 44 462 461 1 strelka-varscan-mutect PKM,missense_variant,p.Ser416Ile,ENST00000319622,NM_001316318.1,NM_001206796.1,NM_182470.2,NM_182471.2;PKM,missense_variant,p.Ser416Ile,ENST00000565184,;PKM,missense_variant,p.Ser416Ile,ENST00000565154,;PKM,missense_variant,p.Ser251Ile,ENST00000568883,;PKM,missense_variant,p.Ser416Ile,ENST00000568459,NM_001206799.1;PKM,missense_variant,p.Ser416Ile,ENST00000561609,;PKM,intron_variant,,ENST00000449901,NM_001206798.1;PKM,intron_variant,,ENST00000335181,NM_002654.4;PKM,intron_variant,,ENST00000389093,NM_001206797.1;PKM,non_coding_transcript_exon_variant,,ENST00000564440,;PKM,non_coding_transcript_exon_variant,,ENST00000570166,;PKM,intron_variant,,ENST00000567118,;PKM,intron_variant,,ENST00000569857,;PKM,intron_variant,,ENST00000563986,;PKM,upstream_gene_variant,,ENST00000565143,;PKM,downstream_gene_variant,,ENST00000563275,;PKM,downstream_gene_variant,,ENST00000564993,; A ENST00000319622 Transcript missense_variant 1747/2717 1247/1596 416/531 S/I aGc/aTc 1 -1 PKM HGNC HGNC:9021 protein_coding YES CCDS32285.1 ENSP00000320171 P14618 A0A024R5Z9 UPI000014064D NM_001316318.1,NM_001206796.1,NM_182470.2,NM_182471.2 deleterious(0) 9/11 hmmpanther:PTHR11817,hmmpanther:PTHR11817:SF23,Gene3D:3.40.1380.20,TIGRFAM_domain:TIGR01064,Pfam_domain:PF02887,Superfamily_domains:SSF52935 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 72203082 72203082 C A 1 0 0 0 0 1 0 0 0 12073 797 28 2 2 PKM 15 72203082 Missense_Mutation SNP C C3N-00547_T 4369297 72203082 29788107 518 14848 EFL1 0 . GRCh38 15 82151844 82151844 + Silent SNP C C G novel C3N-00547_T C3N-00547_N C C c.2610G>C p.= p.V870V ENST00000268206 18/20 153 133 20 181 181 0 strelka-varscan-mutect EFL1,synonymous_variant,p.=,ENST00000268206,NM_024580.5;EFL1,synonymous_variant,p.=,ENST00000359445,NM_001040610.2;EFL1,downstream_gene_variant,,ENST00000561340,; G ENST00000268206 Transcript synonymous_variant 2779/3675 2610/3363 870/1120 V gtG/gtC 1 -1 EFL1 HGNC HGNC:25789 protein_coding YES CCDS42071.1 ENSP00000268206 Q7Z2Z2 UPI00001FEA35 NM_024580.5 18/20 hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF13,Gene3D:3.30.230.10,Superfamily_domains:SSF54211 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 82151844 82151844 C G 1 0 0 0 0 0 0 0 1 4785 813 29 4 4 EFL1 15 82151844 Silent SNP C C3N-00547_T 9948762 82151844 19839345 519 14849 NTRK3 0 . GRCh38 15 88032999 88032999 + Silent SNP C C T C3N-00547_T C3N-00547_N C C c.1443G>A p.= p.L481L ENST00000360948 14/20 163 143 20 205 205 0 strelka-varscan-mutect NTRK3,synonymous_variant,p.=,ENST00000394480,NM_002530.3;NTRK3,synonymous_variant,p.=,ENST00000558676,;NTRK3,synonymous_variant,p.=,ENST00000317501,;NTRK3,synonymous_variant,p.=,ENST00000360948,NM_001012338.2;NTRK3,synonymous_variant,p.=,ENST00000357724,;NTRK3,synonymous_variant,p.=,ENST00000355254,NM_001243101.1;NTRK3,synonymous_variant,p.=,ENST00000626019,;NTRK3,synonymous_variant,p.=,ENST00000629765,;NTRK3,synonymous_variant,p.=,ENST00000557856,;NTRK3,synonymous_variant,p.=,ENST00000542733,NM_001320135.1;NTRK3,synonymous_variant,p.=,ENST00000540489,NM_001007156.2;NTRK3,missense_variant,p.Cys26Tyr,ENST00000558306,; T ENST00000360948 Transcript synonymous_variant 1749/3004 1443/2520 481/839 L ctG/ctA COSM5454398,COSM5454399,COSM5454400 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 14/20 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 49 88032999 88032999 C T 1 0 0 0 0 0 0 0 1 10774 697 25 3 3 NTRK3 15 88032999 Silent SNP C C3N-00547_T 5881155 88032999 13958190 520 14850 ACAN 0 . GRCh38 15 88873875 88873875 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.7367C>G p.Ala2456Gly p.A2456G ENST00000439576 17/18 231 192 39 228 228 0 strelka-varscan-mutect ACAN,missense_variant,p.Ala2456Gly,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Ala2399Gly,ENST00000617301,;ACAN,missense_variant,p.Ala2418Gly,ENST00000559004,;ACAN,missense_variant,p.Ala2456Gly,ENST00000561243,;ACAN,missense_variant,p.Ala31Gly,ENST00000558704,;ACAN,intron_variant,,ENST00000352105,NM_001135.3;HAPLN3,downstream_gene_variant,,ENST00000359595,NM_178232.2;HAPLN3,downstream_gene_variant,,ENST00000562889,NM_001307952.1;ACAN,downstream_gene_variant,,ENST00000560601,;ACAN,non_coding_transcript_exon_variant,,ENST00000558604,;HAPLN3,downstream_gene_variant,,ENST00000558770,; G ENST00000439576 Transcript missense_variant 7741/8840 7367/7593 2456/2530 A/G gCc/gGc 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0) 17/18 PROSITE_profiles:PS50923,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 88873875 88873875 C G 1 0 0 0 0 1 0 0 0 160 739 26 4 4 ACAN 15 88873875 Missense_Mutation SNP C C3N-00547_T 840876 88873875 13117314 521 14851 MFGE8 0 . GRCh38 15 88905803 88905803 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.639C>T p.= p.H213H ENST00000268150 5/8 366 313 53 468 468 0 strelka-varscan-mutect MFGE8,synonymous_variant,p.=,ENST00000268150,NM_005928.2;MFGE8,synonymous_variant,p.=,ENST00000268151,NM_001114614.1;MFGE8,synonymous_variant,p.=,ENST00000566497,;MFGE8,synonymous_variant,p.=,ENST00000542878,;MFGE8,synonymous_variant,p.=,ENST00000558029,;MFGE8,intron_variant,,ENST00000559997,;MFGE8,upstream_gene_variant,,ENST00000617199,;MFGE8,upstream_gene_variant,,ENST00000560553,;MFGE8,synonymous_variant,p.=,ENST00000613965,;MFGE8,3_prime_UTR_variant,,ENST00000558018,NM_001310320.1;MFGE8,non_coding_transcript_exon_variant,,ENST00000559259,;MFGE8,downstream_gene_variant,,ENST00000558352,;MFGE8,upstream_gene_variant,,ENST00000560937,;MFGE8,downstream_gene_variant,,ENST00000559770,;MFGE8,downstream_gene_variant,,ENST00000558773,;MFGE8,downstream_gene_variant,,ENST00000557944,;MFGE8,downstream_gene_variant,,ENST00000559143,; A ENST00000268150 Transcript synonymous_variant 731/1937 639/1164 213/387 H caC/caT 1 -1 MFGE8 HGNC HGNC:7036 protein_coding YES CCDS10347.1 ENSP00000268150 Q08431 UPI000013D7A3 NM_005928.2 5/8 PROSITE_profiles:PS50022,hmmpanther:PTHR10127:SF303,hmmpanther:PTHR10127,PROSITE_patterns:PS01286,Pfam_domain:PF00754,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 88905803 88905803 G A 1 0 0 0 0 0 0 0 1 9473 1368 48 3 3 MFGE8 15 88905803 Silent SNP G C3N-00547_T 31928 88905803 13085386 522 14852 RHCG 0 . GRCh38 15 89496409 89496409 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.136C>A p.His46Asn p.H46N ENST00000268122 1/11 214 155 59 270 270 0 strelka-varscan-mutect RHCG,missense_variant,p.His46Asn,ENST00000268122,NM_001321041.1,NM_016321.2;RHCG,missense_variant,p.His46Asn,ENST00000560081,;RHCG,missense_variant,p.His46Asn,ENST00000558030,;RHCG,missense_variant,p.His46Asn,ENST00000558184,; T ENST00000268122 Transcript missense_variant 205/1982 136/1440 46/479 H/N Cac/Aac 1 -1 RHCG HGNC HGNC:18140 protein_coding YES CCDS10351.1 ENSP00000268122 Q9UBD6 UPI00000343FD NM_001321041.1,NM_016321.2 tolerated(0.59) 1/11 hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 89496409 89496409 G T 1 0 0 0 0 1 0 0 0 13498 1319 46 2 2 RHCG 15 89496409 Missense_Mutation SNP G C3N-00547_T 590606 89496409 12494780 523 14853 CLCN7 0 . GRCh38 16 1460447 1460447 + Missense_Mutation SNP C C A rs764870423 C3N-00547_T C3N-00547_N C C c.565G>T p.Val189Leu p.V189L ENST00000382745 6/25 666 470 196 527 527 0 strelka-varscan-mutect CLCN7,missense_variant,p.Val189Leu,ENST00000382745,NM_001287.5;CLCN7,missense_variant,p.Val165Leu,ENST00000448525,NM_001114331.2;CLCN7,missense_variant,p.Val165Leu,ENST00000262318,;CLCN7,missense_variant,p.Val131Leu,ENST00000569851,;CLCN7,downstream_gene_variant,,ENST00000564568,;CLCN7,upstream_gene_variant,,ENST00000563822,;CLCN7,upstream_gene_variant,,ENST00000564968,;CLCN7,downstream_gene_variant,,ENST00000567139,;CLCN7,downstream_gene_variant,,ENST00000561665,; A ENST00000382745 Transcript missense_variant 1171/4720 565/2418 189/805 V/L Gtg/Ttg rs764870423,COSM4058483 1 -1 CLCN7 HGNC HGNC:2025 protein_coding YES CCDS32361.1 ENSP00000372193 P51798 UPI000004904C NM_001287.5 tolerated(0.48) 6/25 Gene3D:1otsB00,Pfam_domain:PF00654,Prints_domain:PR01118,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF92,Superfamily_domains:SSF81340,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764870423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 1460447 1460447 C A 1 0 0 0 0 1 0 0 0 3232 536 19 1 1 CLCN7 16 1460447 Missense_Mutation SNP C C3N-00547_T 1460447 88877898 524 14854 IL32 0 . GRCh38 16 3068989 3068989 + Splice_Site SNP G G A novel C3N-00547_T C3N-00547_N G G c.340-1G>A p.X114_splice ENST00000534507 30 19 11 22 22 0 strelka-varscan-mutect IL32,splice_acceptor_variant,,ENST00000525643,;IL32,splice_acceptor_variant,,ENST00000526464,;IL32,splice_acceptor_variant,,ENST00000534507,;IL32,splice_acceptor_variant,,ENST00000325568,NM_001012718.1,NM_004221.4;IL32,splice_acceptor_variant,,ENST00000396890,;IL32,splice_acceptor_variant,,ENST00000008180,NM_001012634.1;IL32,splice_acceptor_variant,,ENST00000613483,;IL32,splice_acceptor_variant,,ENST00000548476,;IL32,splice_acceptor_variant,,ENST00000528163,NM_001012631.1;IL32,splice_acceptor_variant,,ENST00000440815,;IL32,splice_acceptor_variant,,ENST00000444393,;IL32,splice_acceptor_variant,,ENST00000382213,NM_001012636.1;IL32,splice_acceptor_variant,,ENST00000533097,;IL32,splice_acceptor_variant,,ENST00000548652,;IL32,splice_acceptor_variant,,ENST00000548807,;IL32,splice_acceptor_variant,,ENST00000551513,;IL32,splice_acceptor_variant,,ENST00000396887,NM_001012633.1;IL32,splice_acceptor_variant,,ENST00000530890,NM_001012635.1;IL32,splice_acceptor_variant,,ENST00000529550,;IL32,splice_acceptor_variant,,ENST00000531965,;IL32,splice_acceptor_variant,,ENST00000551122,;IL32,splice_acceptor_variant,,ENST00000552664,NM_001012632.1;IL32,splice_acceptor_variant,,ENST00000552936,;IL32,splice_acceptor_variant,,ENST00000530538,;IL32,splice_acceptor_variant,,ENST00000529699,;IL32,splice_acceptor_variant,,ENST00000549213,;IL32,splice_acceptor_variant,,ENST00000552356,;IL32,splice_acceptor_variant,,ENST00000525228,;IL32,splice_acceptor_variant,,ENST00000548246,;IL32,intron_variant,,ENST00000525377,;RNU1-125P,upstream_gene_variant,,ENST00000516752,;IL32,splice_acceptor_variant,,ENST00000525003,;IL32,splice_acceptor_variant,,ENST00000528652,;IL32,downstream_gene_variant,,ENST00000532247,;IL32,downstream_gene_variant,,ENST00000532086,;IL32,downstream_gene_variant,,ENST00000534748,; A ENST00000534507 Transcript splice_acceptor_variant -/1112 340/705 114/234 1 1 IL32 HGNC HGNC:16830 protein_coding YES CCDS76811.1 ENSP00000431775 P24001 UPI0000070836 5/5 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 49 3068989 3068989 G A 1 0 0 0 0 0 0 1 0 7591 1014 35 3 3 IL32 16 3068989 Splice_Site SNP G C3N-00547_T 1608542 3068989 87269356 525 14855 SEPT12 0 . GRCh38 16 4786006 4786006 + Missense_Mutation SNP G G A rs199696526 C3N-00547_T C3N-00547_N G G c.266C>T p.Thr89Met p.T89M ENST00000268231 3/10 168 156 12 107 107 0 strelka-varscan-mutect SEPT12,missense_variant,p.Thr89Met,ENST00000268231,NM_144605.4;SEPT12,missense_variant,p.Thr89Met,ENST00000396693,NM_001154458.2;SMIM22,upstream_gene_variant,,ENST00000615889,NM_001253791.1;SMIM22,upstream_gene_variant,,ENST00000615471,;SMIM22,upstream_gene_variant,,ENST00000589721,NM_001253790.1;SMIM22,upstream_gene_variant,,ENST00000589327,;SEPT12,downstream_gene_variant,,ENST00000591624,;SEPT12,non_coding_transcript_exon_variant,,ENST00000591861,;SEPT12,missense_variant,p.Thr89Met,ENST00000587603,;SEPT12,3_prime_UTR_variant,,ENST00000590741,;SEPT12,non_coding_transcript_exon_variant,,ENST00000590303,;SMIM22,upstream_gene_variant,,ENST00000591004,;SEPT12,upstream_gene_variant,,ENST00000588241,; A ENST00000268231 Transcript missense_variant 530/1469 266/1077 89/358 T/M aCg/aTg rs199696526,CM122363,COSM2149323 1 -1 SEPT12 HGNC HGNC:26348 protein_coding YES CCDS10522.1 ENSP00000268231 Q8IYM1 UPI000007422A NM_144605.4 deleterious(0.01) 3/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF66,Pfam_domain:PF00735,Gene3D:3.40.50.300,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540 risk_factor 0,0,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs199696526 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 4786006 4786006 G A 1 0 0 0 0 1 0 0 0 14338 1145 40 1 1 SEPT12 16 4786006 Missense_Mutation SNP G C3N-00547_T 1717017 4786006 85552339 526 14856 ZC3H7A 0 . GRCh38 16 11765652 11765652 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1556G>T p.Gly519Val p.G519V ENST00000396516 13/22 156 118 38 99 98 1 strelka-varscan-mutect ZC3H7A,missense_variant,p.Gly519Val,ENST00000396516,;ZC3H7A,missense_variant,p.Gly519Val,ENST00000355758,NM_014153.3;ZC3H7A,missense_variant,p.Gly429Val,ENST00000571198,;ZC3H7A,downstream_gene_variant,,ENST00000576009,;ZC3H7A,3_prime_UTR_variant,,ENST00000575041,;ZC3H7A,non_coding_transcript_exon_variant,,ENST00000571676,;ZC3H7A,non_coding_transcript_exon_variant,,ENST00000576247,;ZC3H7A,upstream_gene_variant,,ENST00000571405,;ZC3H7A,upstream_gene_variant,,ENST00000572938,;ZC3H7A,upstream_gene_variant,,ENST00000570862,; A ENST00000396516 Transcript missense_variant 1754/3845 1556/2916 519/971 G/V gGc/gTc 1 -1 ZC3H7A HGNC HGNC:30959 protein_coding YES CCDS10550.1 ENSP00000379773 Q8IWR0 UPI000000DB79 deleterious(0.01) 13/22 hmmpanther:PTHR14928,hmmpanther:PTHR14928:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 11765652 11765652 C A 1 0 0 0 0 1 0 0 0 18147 739 26 2 2 ZC3H7A 16 11765652 Missense_Mutation SNP C C3N-00547_T 6979646 11765652 78572693 527 14857 SNX29 0 . GRCh38 16 12477806 12477806 + Missense_Mutation SNP T T A C3N-00547_T C3N-00547_N T T c.2125T>A p.Tyr709Asn p.Y709N ENST00000566228 19/21 126 99 27 115 115 0 strelka-varscan-mutect SNX29,missense_variant,p.Tyr709Asn,ENST00000566228,NM_032167.4;SNX29,missense_variant,p.Tyr198Asn,ENST00000564791,; A ENST00000566228 Transcript missense_variant 2194/8171 2125/2442 709/813 Y/N Tac/Aac COSM5054628,COSM5054629,COSM5054630 1 1 SNX29 HGNC HGNC:30542 protein_coding YES CCDS10553.2 ENSP00000456480 Q8TEQ0 UPI00000382F9 NM_032167.4 tolerated(0.39) 19/21 PROSITE_profiles:PS50195,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 12477806 12477806 T A 1 0 0 0 0 1 0 0 0 15219 1638 57 4 4 SNX29 16 12477806 Missense_Mutation SNP T C3N-00547_T 712154 12477806 77860539 528 14858 NPIPA5 0 . GRCh38 16 15365233 15365233 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.895C>A p.Pro299Thr p.P299T ENST00000534094 7/7 362 268 94 470 470 0 strelka-varscan-mutect NPIPA5,missense_variant,p.Pro299Thr,ENST00000534094,;NPIPA5,intron_variant,,ENST00000360151,NM_001277325.1;NPIPA5,intron_variant,,ENST00000543801,;RP11-72I8.2,downstream_gene_variant,,ENST00000611162,; T ENST00000534094 Transcript missense_variant 895/954 895/954 299/317 P/T Ccc/Acc 1 -1 NPIPA5 HGNC HGNC:41980 protein_coding ENSP00000435611 E9PJ88 UPI0001A5E893 deleterious_low_confidence(0) 7/7 MODERATE SNV 5 1 PASS rs1416350371 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 15365233 15365233 G T 1 0 0 0 0 1 0 0 0 10634 1203 42 2 2 NPIPA5 16 15365233 Missense_Mutation SNP G C3N-00547_T 2887427 15365233 74973112 529 14859 ERN2 0 . GRCh38 16 23700677 23700677 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1531C>A p.Gln511Lys p.Q511K ENST00000634482 13/22 101 72 29 82 82 0 strelka-varscan-mutect ERN2,missense_variant,p.Gln511Lys,ENST00000634482,NM_033266.3;ERN2,missense_variant,p.Gln463Lys,ENST00000256797,;ERN2,missense_variant,p.Gln411Lys,ENST00000457008,NM_001308220.1;CTD-2196E14.8,upstream_gene_variant,,ENST00000624143,;ERN2,3_prime_UTR_variant,,ENST00000562562,; T ENST00000634482 Transcript missense_variant 1700/3616 1531/2925 511/974 Q/K Cag/Aag 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 tolerated(0.47) 13/22 Low_complexity_(Seg):seg,hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 23700677 23700677 G T 1 0 0 0 0 1 0 0 0 5096 1328 46 2 2 ERN2 16 23700677 Missense_Mutation SNP G C3N-00547_T 8335444 23700677 66637668 530 14860 C16orf82 0 . GRCh38 16 27067253 27067253 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.447C>A p.Ser149Arg p.S149R ENST00000505035 1/1 343 235 108 350 349 1 strelka-varscan-mutect C16orf82,missense_variant,p.Ser149Arg,ENST00000505035,;C16orf82,missense_variant,p.Ser86Arg,ENST00000418886,NM_001145545.1;RP11-673P17.2,intron_variant,,ENST00000565783,; A ENST00000505035 Transcript missense_variant 547/2459 447/654 149/217 S/R agC/agA 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 deleterious(0.01) 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 27067253 27067253 C A 1 0 0 0 0 1 0 0 0 1867 738 26 2 2 C16orf82 16 27067253 Missense_Mutation SNP C C3N-00547_T 3366576 27067253 63271092 531 14861 GTF3C1 0 . GRCh38 16 27470189 27470189 + Frame_Shift_Del DEL C C - novel C3N-00547_T C3N-00547_N C C c.4733delG p.Gly1578AlafsTer16 p.G1578Afs*16 ENST00000356183 31/37 285 210 75 284 284 0 sindel-pindel GTF3C1,frameshift_variant,p.Gly1578AlafsTer16,ENST00000356183,NM_001520.3;GTF3C1,frameshift_variant,p.Gly1578AlafsTer16,ENST00000561623,NM_001286242.1;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000567843,;GTF3C1,3_prime_UTR_variant,,ENST00000571886,;GTF3C1,upstream_gene_variant,,ENST00000562609,;GTF3C1,downstream_gene_variant,,ENST00000564664,;GTF3C1,downstream_gene_variant,,ENST00000569394,; - ENST00000356183 Transcript frameshift_variant 4749/7018 4733/6330 1578/2109 G/X gGc/gc 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 31/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 27470189 27470189 C - 1 0 1 0 1 0 0 0 0 6753 739 26 0 0 GTF3C1 16 27470189 Frame_Shift_Del DEL C C3N-00547_T 402936 27470189 62868156 532 14862 KIAA0556 0 . GRCh38 16 27749652 27749652 + Nonsense_Mutation SNP G G T rs376515834 C3N-00547_T C3N-00547_N G G c.2692G>T p.Glu898Ter p.E898* ENST00000261588 16/28 56 33 23 55 55 0 strelka-varscan-mutect KIAA0556,stop_gained,p.Glu898Ter,ENST00000261588,NM_015202.2;KIAA0556,non_coding_transcript_exon_variant,,ENST00000573850,; T ENST00000261588 Transcript stop_gained 2711/6616 2692/4857 898/1618 E/* Gag/Tag rs376515834 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 16/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534 HIGH 1 SNV 1 1 PASS rs376515834 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 27749652 27749652 G T 1 0 0 0 0 0 1 0 0 8088 1059 37 1 1 KIAA0556 16 27749652 Nonsense_Mutation SNP G C3N-00547_T 279463 27749652 62588693 533 14863 IL27 0 . GRCh38 16 28503903 28503903 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.179A>T p.Glu60Val p.E60V ENST00000356897 2/5 168 130 38 197 197 0 strelka-varscan-mutect IL27,missense_variant,p.Glu60Val,ENST00000356897,NM_145659.3;IL27,5_prime_UTR_variant,,ENST00000568075,;APOBR,downstream_gene_variant,,ENST00000564831,NM_018690.3;APOBR,downstream_gene_variant,,ENST00000431282,; A ENST00000356897 Transcript missense_variant 202/1044 179/732 60/243 E/V gAg/gTg 1 -1 IL27 HGNC HGNC:19157 protein_coding YES CCDS10633.1 ENSP00000349365 Q8NEV9 UPI0000141330 NM_145659.3 deleterious(0) 2/5 hmmpanther:PTHR20879,hmmpanther:PTHR20879:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 28503903 28503903 T A 1 0 0 0 0 1 0 0 0 7583 1551 54 4 4 IL27 16 28503903 Missense_Mutation SNP T C3N-00547_T 754251 28503903 61834442 534 14864 TMEM265 0 . GRCh38 16 30743843 30743843 + Missense_Mutation SNP G G T rs552279036 C3N-00547_T C3N-00547_N G G c.227G>T p.Arg76Leu p.R76L ENST00000615541 3/3 157 113 44 150 150 0 strelka-varscan-mutect TMEM265,missense_variant,p.Arg76Leu,ENST00000615541,NM_001256829.1;SRCAP,downstream_gene_variant,,ENST00000262518,NM_006662.2;SRCAP,downstream_gene_variant,,ENST00000395059,;PHKG2,upstream_gene_variant,,ENST00000563588,NM_000294.2;PHKG2,upstream_gene_variant,,ENST00000424889,NM_001172432.1;PHKG2,upstream_gene_variant,,ENST00000328273,;PHKG2,upstream_gene_variant,,ENST00000565897,;PHKG2,upstream_gene_variant,,ENST00000565924,;RP11-2C24.4,intron_variant,,ENST00000483578,;RP11-2C24.9,3_prime_UTR_variant,,ENST00000380361,;PHKG2,upstream_gene_variant,,ENST00000563913,;PHKG2,upstream_gene_variant,,ENST00000564838,;PHKG2,upstream_gene_variant,,ENST00000563607,; T ENST00000615541 Transcript missense_variant 557/995 227/327 76/108 R/L cGg/cTg rs552279036 1 1 TMEM265 HGNC HGNC:51241 protein_coding YES CCDS73870.1 ENSP00000477871 A0A087WTH1 UPI0000D4C221 NM_001256829.1 tolerated(0.07) 3/3 Pfam_domain:PF04505 MODERATE 1 SNV 1 1 PASS rs552279036 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 30743843 30743843 G T 1 0 0 0 0 1 0 0 0 16625 1116 39 1 1 TMEM265 16 30743843 Missense_Mutation SNP G C3N-00547_T 2239940 30743843 59594502 535 14865 ITGAM 0 . GRCh38 16 31297612 31297612 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1455G>T p.Gln485His p.Q485H ENST00000544665 13/30 155 107 48 208 207 1 strelka-varscan-mutect ITGAM,missense_variant,p.Gln485His,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Gln485His,ENST00000287497,NM_000632.3;ITGAM,missense_variant,p.Asp138Tyr,ENST00000567031,; T ENST00000544665 Transcript missense_variant 1526/4718 1455/3462 485/1153 Q/H caG/caT 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0.04) 13/30 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 31297612 31297612 G T 1 0 0 0 0 1 0 0 0 7794 933 33 2 2 ITGAM 16 31297612 Missense_Mutation SNP G C3N-00547_T 553769 31297612 59040733 536 14866 ITGAX 0 . GRCh38 16 31362091 31362091 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1103G>T p.Gly368Val p.G368V ENST00000562522 11/31 304 224 80 233 233 0 strelka-varscan-mutect ITGAX,missense_variant,p.Gly368Val,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Gly368Val,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,; T ENST00000562522 Transcript missense_variant 1136/3990 1103/3510 368/1169 G/V gGg/gTg 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0) 11/31 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 31362091 31362091 G T 1 0 0 0 0 1 0 0 0 7796 1232 43 2 2 ITGAX 16 31362091 Missense_Mutation SNP G C3N-00547_T 64479 31362091 58976254 537 14867 BRD7 0 . GRCh38 16 50334794 50334794 + Missense_Mutation SNP G G T rs776310283 C3N-00547_T C3N-00547_N G G c.804C>A p.Asp268Glu p.D268E ENST00000394689 7/17 286 267 19 194 194 0 varscan-mutect BRD7,missense_variant,p.Asp268Glu,ENST00000394688,NM_013263.4;BRD7,missense_variant,p.Asp268Glu,ENST00000394689,NM_001173984.2;BRD7,non_coding_transcript_exon_variant,,ENST00000475877,; T ENST00000394689 Transcript missense_variant 809/2145 804/1959 268/652 D/E gaC/gaA rs776310283 1 -1 BRD7 HGNC HGNC:14310 protein_coding YES CCDS54007.1 ENSP00000378181 Q9NPI1 UPI000013E567 NM_001173984.2 tolerated(0.34) 7/17 hmmpanther:PTHR22881,hmmpanther:PTHR22881:SF12 MODERATE 1 SNV 1 1 PASS rs776310283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 50334794 50334794 G T 1 0 0 0 0 1 0 0 0 1675 1136 40 1 1 BRD7 16 50334794 Missense_Mutation SNP G C3N-00547_T 18972703 50334794 40003551 538 14868 SALL1 0 . GRCh38 16 51139332 51139332 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.2890C>A p.Pro964Thr p.P964T ENST00000251020 2/3 762 719 43 511 509 2 strelka-varscan-mutect SALL1,missense_variant,p.Pro867Thr,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Pro964Thr,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Pro867Thr,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; T ENST00000251020 Transcript missense_variant 2924/5146 2890/3975 964/1324 P/T Cca/Aca COSM4485088 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.08) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 51139332 51139332 G T 1 0 0 0 0 1 0 0 0 14069 1232 43 2 2 SALL1 16 51139332 Missense_Mutation SNP G C3N-00547_T 804538 51139332 39199013 539 14869 CHD9 0 . GRCh38 16 53304579 53304579 + Silent SNP T T G novel C3N-00547_T C3N-00547_N T T c.6573T>G p.= p.S2191S ENST00000447540 31/39 159 143 16 134 134 0 strelka-varscan-mutect CHD9,synonymous_variant,p.=,ENST00000566029,NM_025134.4;CHD9,synonymous_variant,p.=,ENST00000447540,NM_001308319.1;CHD9,synonymous_variant,p.=,ENST00000564845,;CHD9,synonymous_variant,p.=,ENST00000398510,;CHD9,intron_variant,,ENST00000615216,;CHD9,intron_variant,,ENST00000622617,;CHD9,non_coding_transcript_exon_variant,,ENST00000219084,;RP11-454F8.2,downstream_gene_variant,,ENST00000566796,; G ENST00000447540 Transcript synonymous_variant 6782/11509 6573/8694 2191/2897 S tcT/tcG 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 31/39 Low_complexity_(Seg):seg,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF48 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 49 53304579 53304579 T G 1 0 0 0 0 0 0 0 1 3091 1596 56 5 5 CHD9 16 53304579 Silent SNP T C3N-00547_T 2165247 53304579 37033766 540 14870 EDC4 0 . GRCh38 16 67881137 67881137 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.2593C>T p.= p.L865L ENST00000358933 19/29 304 264 40 295 295 0 strelka-varscan-mutect EDC4,synonymous_variant,p.=,ENST00000358933,NM_014329.4;NRN1L,upstream_gene_variant,,ENST00000339176,NM_198443.1;NRN1L,upstream_gene_variant,,ENST00000576147,;EDC4,upstream_gene_variant,,ENST00000577105,;EDC4,upstream_gene_variant,,ENST00000575033,;EDC4,upstream_gene_variant,,ENST00000573985,;NRN1L,upstream_gene_variant,,ENST00000576758,;CTC-479C5.10,upstream_gene_variant,,ENST00000572067,;EDC4,downstream_gene_variant,,ENST00000574770,;EDC4,non_coding_transcript_exon_variant,,ENST00000572221,;EDC4,non_coding_transcript_exon_variant,,ENST00000573992,;EDC4,non_coding_transcript_exon_variant,,ENST00000575514,;EDC4,non_coding_transcript_exon_variant,,ENST00000576972,;EDC4,non_coding_transcript_exon_variant,,ENST00000577028,;EDC4,non_coding_transcript_exon_variant,,ENST00000572724,;EDC4,downstream_gene_variant,,ENST00000536072,;EDC4,downstream_gene_variant,,ENST00000572031,;EDC4,upstream_gene_variant,,ENST00000575507,; T ENST00000358933 Transcript synonymous_variant 2832/4800 2593/4206 865/1401 L Ctg/Ttg 1 1 EDC4 HGNC HGNC:17157 protein_coding YES CCDS10849.1 ENSP00000351811 Q6P2E9 UPI0000141377 NM_014329.4 19/29 hmmpanther:PTHR15598,hmmpanther:PTHR15598:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 67881137 67881137 C T 1 0 0 0 0 0 0 0 1 4736 680 24 3 3 EDC4 16 67881137 Silent SNP C C3N-00547_T 14576558 67881137 22457208 541 14871 HAS3 0 . GRCh38 16 69114391 69114391 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.787T>A p.Tyr263Asn p.Y263N ENST00000306560 4/4 117 77 40 112 112 0 strelka-varscan-mutect HAS3,missense_variant,p.Tyr263Asn,ENST00000306560,NM_005329.2;HAS3,missense_variant,p.Tyr263Asn,ENST00000569188,NM_001199280.1;HAS3,missense_variant,p.Tyr263Asn,ENST00000566118,;HAS3,intron_variant,,ENST00000219322,NM_138612.2;CHTF8,downstream_gene_variant,,ENST00000448552,NM_001039690.3;CHTF8,downstream_gene_variant,,ENST00000306585,;CHTF8,downstream_gene_variant,,ENST00000523421,;CHTF8,downstream_gene_variant,,ENST00000518041,;CHTF8,downstream_gene_variant,,ENST00000519534,; A ENST00000306560 Transcript missense_variant 943/4220 787/1662 263/553 Y/N Tac/Aac 1 1 HAS3 HGNC HGNC:4820 protein_coding YES CCDS10871.1 ENSP00000304440 O00219 UPI000013EB57 NM_005329.2 deleterious(0) 4/4 hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF6,Pfam_domain:PF13641,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 69114391 69114391 T A 1 0 0 0 0 1 0 0 0 6849 1638 57 4 4 HAS3 16 69114391 Missense_Mutation SNP T C3N-00547_T 1233254 69114391 21223954 542 14872 CNTNAP4 0 . GRCh38 16 76521258 76521258 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.2484G>T p.= p.G828G ENST00000611870 16/24 153 124 29 204 203 1 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3; T ENST00000611870 Transcript synonymous_variant 2869/4867 2484/3927 828/1308 G ggG/ggT 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 16/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs995474100 . 0 206 0 4 0 0 0 0 -20 0.9999483 1 1 1 0 T 2 4 49 76521258 76521258 G T 1 0 0 0 0 0 0 0 1 3431 1219 43 2 2 CNTNAP4 16 76521258 Silent SNP G C3N-00547_T 7406867 76521258 13817087 543 14873 ADAMTS18 0 . GRCh38 16 77367576 77367576 + Missense_Mutation SNP G G A rs760054443 C3N-00547_T C3N-00547_N G G c.643C>T p.Arg215Cys p.R215C ENST00000282849 4/23 584 501 83 500 500 0 strelka-varscan-mutect ADAMTS18,missense_variant,p.Arg215Cys,ENST00000282849,NM_001326358.1,NM_199355.2;ADAMTS18,missense_variant,p.Arg130Cys,ENST00000562345,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567121,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000564369,;ADAMTS18,missense_variant,p.Arg215Cys,ENST00000449265,;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000567914,;ADAMTS18,downstream_gene_variant,,ENST00000569309,; A ENST00000282849 Transcript missense_variant 1062/5913 643/3666 215/1221 R/C Cgt/Tgt rs760054443 1 -1 ADAMTS18 HGNC HGNC:17110 protein_coding YES CCDS10926.1 ENSP00000282849 Q8TE60 UPI0000233610 NM_001326358.1,NM_199355.2 tolerated(0.14) 4/23 hmmpanther:PTHR13723:SF167,hmmpanther:PTHR13723 MODERATE 1 SNV 1 1 PASS rs760054443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 77367576 77367576 G A 1 0 0 0 0 1 0 0 0 307 1116 39 1 1 ADAMTS18 16 77367576 Missense_Mutation SNP G C3N-00547_T 846318 77367576 12970769 544 14874 CENPN 0 . GRCh38 16 81012064 81012064 + Missense_Mutation SNP G G C rs144532651 C3N-00547_T C3N-00547_N G G c.125G>C p.Arg42Pro p.R42P ENST00000393335 2/11 156 133 23 156 156 0 strelka-varscan-mutect CENPN,missense_variant,p.Arg42Pro,ENST00000305850,NM_001100624.2;CENPN,missense_variant,p.Arg42Pro,ENST00000439957,NM_001270473.1;CENPN,missense_variant,p.Arg42Pro,ENST00000393335,NM_001100625.2;CENPN,missense_variant,p.Arg42Pro,ENST00000299572,NM_018455.5;CENPN,missense_variant,p.Arg42Pro,ENST00000428963,NM_001270474.1;CENPN,missense_variant,p.Arg42Pro,ENST00000564669,;CMC2,intron_variant,,ENST00000565914,;CMC2,upstream_gene_variant,,ENST00000219400,;RP11-303E16.3,downstream_gene_variant,,ENST00000562315,;CENPN,non_coding_transcript_exon_variant,,ENST00000569461,;CENPN,missense_variant,p.Arg42Pro,ENST00000568445,; C ENST00000393335 Transcript missense_variant 199/1556 125/1062 42/353 R/P cGa/cCa rs144532651 1 1 CENPN HGNC HGNC:30873 protein_coding YES CCDS42199.1 ENSP00000377007 Q96H22 UPI000059D3C7 NM_001100625.2 deleterious(0.04) 2/11 Pfam_domain:PF05238,hmmpanther:PTHR12309,hmmpanther:PTHR12309:SF12 MODERATE SNV 2 1 PASS rs144532651 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 81012064 81012064 G C 1 0 0 0 0 1 0 0 0 2946 1058 37 4 4 CENPN 16 81012064 Missense_Mutation SNP G C3N-00547_T 3644488 81012064 9326281 545 14875 CRISPLD2 0 . GRCh38 16 84849491 84849491 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.466G>T p.Gly156Trp p.G156W ENST00000262424 4/15 160 138 22 115 115 0 strelka-varscan-mutect CRISPLD2,missense_variant,p.Gly156Trp,ENST00000262424,NM_031476.3;CRISPLD2,missense_variant,p.Gly156Trp,ENST00000567845,;CRISPLD2,missense_variant,p.Gly156Trp,ENST00000564567,;CRISPLD2,5_prime_UTR_variant,,ENST00000563066,;CRISPLD2,5_prime_UTR_variant,,ENST00000566789,;CRISPLD2,downstream_gene_variant,,ENST00000569090,;CRISPLD2,non_coding_transcript_exon_variant,,ENST00000566431,;CRISPLD2,non_coding_transcript_exon_variant,,ENST00000569262,; T ENST00000262424 Transcript missense_variant 690/4586 466/1494 156/497 G/W Ggg/Tgg 1 1 CRISPLD2 HGNC HGNC:25248 protein_coding YES CCDS10949.1 ENSP00000262424 Q9H0B8 A0A140VK80 UPI00000411B0 NM_031476.3 deleterious(0.01) 4/15 Gene3D:3.40.33.10,Pfam_domain:PF00188,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF64,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999977 1 1 1 0 T 3 4 49 84849491 84849491 G T 1 0 0 0 0 1 0 0 0 3684 1232 43 2 2 CRISPLD2 16 84849491 Missense_Mutation SNP G C3N-00547_T 3837427 84849491 5488854 546 14876 RPA1 0 . GRCh38 17 1879356 1879356 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.901G>T p.Asp301Tyr p.D301Y ENST00000254719 10/17 118 100 18 152 152 0 strelka-varscan-mutect RPA1,missense_variant,p.Asp301Tyr,ENST00000254719,NM_002945.3;RPA1,missense_variant,p.Asp57Tyr,ENST00000574049,;RPA1,downstream_gene_variant,,ENST00000570451,;RPA1,downstream_gene_variant,,ENST00000573924,; T ENST00000254719 Transcript missense_variant 1011/4340 901/1851 301/616 D/Y Gat/Tat 1 1 RPA1 HGNC HGNC:10289 protein_coding YES CCDS11014.1 ENSP00000254719 P27694 UPI000013379A NM_002945.3 deleterious(0) 10/17 hmmpanther:PTHR23273,hmmpanther:PTHR23273:SF6,Gene3D:2.40.50.140,TIGRFAM_domain:TIGR00617,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 1879356 1879356 G T 1 0 0 0 0 1 0 0 0 13788 1290 45 2 2 RPA1 17 1879356 Missense_Mutation SNP G C3N-00547_T 1879356 81378085 547 14877 WSCD1 0 . GRCh38 17 6118021 6118021 + Missense_Mutation SNP G G C rs367620024 C3N-00547_T C3N-00547_N G G c.1208G>C p.Arg403Pro p.R403P ENST00000574946 8/9 248 184 64 315 315 0 strelka-varscan-mutect WSCD1,missense_variant,p.Arg403Pro,ENST00000574946,;WSCD1,missense_variant,p.Arg403Pro,ENST00000317744,NM_015253.1;WSCD1,missense_variant,p.Arg403Pro,ENST00000539421,;WSCD1,missense_variant,p.Arg403Pro,ENST00000574232,;WSCD1,missense_variant,p.Arg287Pro,ENST00000573634,;WSCD1,3_prime_UTR_variant,,ENST00000571494,; C ENST00000574946 Transcript missense_variant 1598/5884 1208/1728 403/575 R/P cGa/cCa rs367620024,COSM2794115 1 1 WSCD1 HGNC HGNC:29060 protein_coding YES CCDS32538.1 ENSP00000460825 Q658N2 UPI0000197208 tolerated(0.05) 8/9 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF90,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs367620024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 6118021 6118021 G C 1 0 0 0 0 1 0 0 0 17963 1058 37 4 4 WSCD1 17 6118021 Missense_Mutation SNP G C3N-00547_T 4238665 6118021 77139420 548 14878 TP53 0 . GRCh38 17 7675220 7675220 + Missense_Mutation SNP T T A C3N-00547_T C3N-00547_N T T c.392A>T p.Asn131Ile p.N131I ENST00000269305 5/11 167 127 40 290 290 0 strelka-varscan-mutect TP53,missense_variant,p.Asn131Ile,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Asn131Ile,ENST00000420246,;TP53,missense_variant,p.Asn92Ile,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Asn92Ile,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Asn131Ile,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Asn92Ile,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Asn131Ile,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Asn92Ile,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Asn131Ile,ENST00000445888,;TP53,missense_variant,p.Asn92Ile,ENST00000619485,;TP53,missense_variant,p.Asn131Ile,ENST00000359597,;TP53,missense_variant,p.Asn120Ile,ENST00000615910,;TP53,missense_variant,p.Asn131Ile,ENST00000413465,;TP53,missense_variant,p.Asn131Ile,ENST00000508793,;TP53,missense_variant,p.Asn38Ile,ENST00000514944,;TP53,splice_region_variant,,ENST00000604348,;TP53,5_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000504937,NM_001126115.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,5_prime_UTR_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Asn92Ile,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 582/2579 392/1182 131/393 N/I aAc/aTc CM087281,TP53_g.12380A>C,TP53_g.12380A>G,TP53_g.12380A>T,COSM1610869,COSM1610870,COSM1610871,COSM213373,COSM213374,COSM213375,COSM3717675,COSM3717676,COSM3717677,COSM3717678,COSM437612,COSM437613,COSM437614,COSM437615,COSM44474,COSM44794,COSM45608,COSM5221008,COSM5221009 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1131691037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 7675220 7675220 T A 1 0 0 0 0 1 0 0 0 16859 1725 60 4 4 TP53 17 7675220 Missense_Mutation SNP T C3N-00547_T 1557199 7675220 75582221 549 14879 MYH4 0 . GRCh38 17 10448663 10448663 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.4486C>A p.Leu1496Met p.L1496M ENST00000255381 32/40 121 97 24 144 144 0 strelka-varscan-mutect MYH4,missense_variant,p.Leu1496Met,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000255381 Transcript missense_variant 4597/6016 4486/5820 1496/1939 L/M Ctg/Atg 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0.01) 32/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS rs1002727252 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 10448663 10448663 G T 1 0 0 0 0 1 0 0 0 10037 991 35 2 2 MYH4 17 10448663 Missense_Mutation SNP G C3N-00547_T 2773443 10448663 72808778 550 14880 MYH2 0 . GRCh38 17 10547795 10547795 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.126G>A p.= p.E42E ENST00000245503 3/40 340 276 64 549 549 0 strelka-varscan-mutect MYH2,synonymous_variant,p.=,ENST00000245503,NM_017534.5;MYH2,synonymous_variant,p.=,ENST00000397183,NM_001100112.1;MYH2,synonymous_variant,p.=,ENST00000532183,;MYH2,synonymous_variant,p.=,ENST00000622564,;MYH2,synonymous_variant,p.=,ENST00000420805,;MYH2,upstream_gene_variant,,ENST00000578017,;MYHAS,intron_variant,,ENST00000587182,; T ENST00000245503 Transcript synonymous_variant 511/6339 126/5826 42/1941 E gaG/gaA 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 3/40 Pfam_domain:PF02736,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 10547795 10547795 C T 1 0 0 0 0 0 0 0 1 10035 796 28 3 3 MYH2 17 10547795 Silent SNP C C3N-00547_T 99132 10547795 72709646 551 14881 CCDC144A 0 . GRCh38 17 16734870 16734870 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.2599A>T p.Ile867Leu p.I867L ENST00000360524 12/18 49 30 19 62 62 0 strelka-varscan-mutect CCDC144A,missense_variant,p.Ile867Leu,ENST00000399273,;CCDC144A,missense_variant,p.Ile867Leu,ENST00000360524,NM_014695.2;CCDC144A,downstream_gene_variant,,ENST00000456009,;RP11-219A15.1,missense_variant,p.Ile867Leu,ENST00000448331,;CCDC144A,3_prime_UTR_variant,,ENST00000360495,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000470068,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000328495,; T ENST00000360524 Transcript missense_variant 2675/5830 2599/4284 867/1427 I/L Ata/Tta 1 1 CCDC144A HGNC HGNC:29072 protein_coding YES CCDS45621.1 ENSP00000353717 A2RUR9 UPI0000F095D0 NM_014695.2 tolerated(0.71) 12/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22245:SF0,hmmpanther:PTHR22245,Pfam_domain:PF14915 MODERATE 1 SNV 1 1 PASS rs1164122053 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 16734870 16734870 A T 1 0 0 0 0 1 0 0 0 2465 449 16 4 4 CCDC144A 17 16734870 Missense_Mutation SNP A C3N-00547_T 6187075 16734870 66522571 552 14882 LGALS9B 0 . GRCh38 17 20451826 20451826 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.727C>T p.= p.L243L ENST00000324290 9/11 186 125 61 287 287 0 strelka-varscan-mutect LGALS9B,synonymous_variant,p.=,ENST00000423676,;LGALS9B,synonymous_variant,p.=,ENST00000324290,NM_001042685.1;NOS2P3,downstream_gene_variant,,ENST00000458685,;LGALS9B,3_prime_UTR_variant,,ENST00000578481,;LGALS9B,non_coding_transcript_exon_variant,,ENST00000581490,;LGALS9B,non_coding_transcript_exon_variant,,ENST00000578724,;LGALS9B,downstream_gene_variant,,ENST00000584703,; A ENST00000324290 Transcript synonymous_variant 792/1243 727/1068 243/355 L Ctg/Ttg 1 -1 LGALS9B HGNC HGNC:24842 protein_coding YES CCDS42283.1 ENSP00000315564 Q3B8N2 UPI00001AF401 NM_001042685.1 9/11 Gene3D:2.60.120.200,Pfam_domain:PF00337,PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF91,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 LOW SNV 5 1 PASS rs1380283562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 20451826 20451826 G A 1 0 0 0 0 0 0 0 1 8658 991 35 3 3 LGALS9B 17 20451826 Silent SNP G C3N-00547_T 3716956 20451826 62805615 553 14883 MYO1D 0 . GRCh38 17 32494836 32494836 + Nonsense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.2944G>T p.Glu982Ter p.E982* ENST00000318217 22/22 124 97 27 153 153 0 strelka-varscan-mutect MYO1D,stop_gained,p.Glu982Ter,ENST00000318217,NM_015194.2;MYO1D,stop_gained,p.Glu894Ter,ENST00000394649,;CDK5R1,downstream_gene_variant,,ENST00000313401,NM_003885.2;RP11-466A19.1,upstream_gene_variant,,ENST00000581360,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577576,;MYO1D,non_coding_transcript_exon_variant,,ENST00000577352,; A ENST00000318217 Transcript stop_gained 3249/5563 2944/3021 982/1006 E/* Gag/Tag COSM5519473 1 -1 MYO1D HGNC HGNC:7598 protein_coding YES CCDS32615.1 ENSP00000324527 O94832 UPI0000186004 NM_015194.2 22/22 PROSITE_profiles:PS51757,Pfam_domain:PF06017 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 32494836 32494836 C A 1 0 0 0 0 0 1 0 0 10072 864 30 2 2 MYO1D 17 32494836 Nonsense_Mutation SNP C C3N-00547_T 12043010 32494836 50762605 554 14884 SLFN11 0 . GRCh38 17 35363523 35363523 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.285G>T p.Glu95Asp p.E95D ENST00000394566 4/7 137 112 25 230 229 1 strelka-varscan-mutect SLFN11,missense_variant,p.Glu95Asp,ENST00000394566,NM_001104588.1,NM_001104590.1,NM_001104587.1;SLFN11,missense_variant,p.Glu95Asp,ENST00000308377,NM_152270.3,NM_001104589.1;SLFN11,missense_variant,p.Glu95Asp,ENST00000441608,;SLFN11,missense_variant,p.Glu95Asp,ENST00000591682,;SLFN11,missense_variant,p.Glu95Asp,ENST00000589811,;SLFN11,downstream_gene_variant,,ENST00000427966,;SLFN11,downstream_gene_variant,,ENST00000430814,;SLFN11,downstream_gene_variant,,ENST00000592122,;SLFN11,downstream_gene_variant,,ENST00000588579,;SLFN11,downstream_gene_variant,,ENST00000498396,;SLFN11,upstream_gene_variant,,ENST00000586099,;SLFN11,downstream_gene_variant,,ENST00000589562,; A ENST00000394566 Transcript missense_variant 558/5030 285/2706 95/901 E/D gaG/gaT 1 -1 SLFN11 HGNC HGNC:26633 protein_coding YES CCDS11294.1 ENSP00000378067 Q7Z7L1 UPI0000140B0E NM_001104588.1,NM_001104590.1,NM_001104587.1 tolerated(0.76) 4/7 hmmpanther:PTHR12155:SF21,hmmpanther:PTHR12155 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 35363523 35363523 C A 1 0 0 0 0 1 0 0 0 15022 912 32 2 2 SLFN11 17 35363523 Missense_Mutation SNP C C3N-00547_T 2868687 35363523 47893918 555 14885 SYNRG 0 . GRCh38 17 37553447 37553447 + Missense_Mutation SNP C C G rs773084989 C3N-00547_T C3N-00547_N C C c.2276G>C p.Gly759Ala p.G759A ENST00000612223 14/22 123 104 19 301 301 0 strelka-varscan-mutect SYNRG,missense_variant,p.Gly759Ala,ENST00000612223,NM_007247.5;SYNRG,missense_variant,p.Gly681Ala,ENST00000621136,NM_080550.4;SYNRG,missense_variant,p.Gly681Ala,ENST00000616179,NM_001163546.2;SYNRG,missense_variant,p.Gly681Ala,ENST00000622045,NM_198882.2;SYNRG,missense_variant,p.Gly680Ala,ENST00000619541,NM_001163544.2,NM_001163545.2;SYNRG,missense_variant,p.Gly598Ala,ENST00000614941,NM_001163547.2;SYNRG,non_coding_transcript_exon_variant,,ENST00000611910,;SYNRG,downstream_gene_variant,,ENST00000621605,;SYNRG,non_coding_transcript_exon_variant,,ENST00000618829,; G ENST00000612223 Transcript missense_variant 2417/8229 2276/3945 759/1314 G/A gGt/gCt rs773084989 1 -1 SYNRG HGNC HGNC:557 protein_coding YES CCDS11321.1 ENSP00000483453 Q9UMZ2 UPI000013C4EA NM_007247.5 tolerated_low_confidence(0.36) 14/22 hmmpanther:PTHR15463,hmmpanther:PTHR15463:SF2 MODERATE 1 SNV 1 1 PASS rs773084989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 37553447 37553447 C G 1 0 0 0 0 1 0 0 0 15854 507 18 4 4 SYNRG 17 37553447 Missense_Mutation SNP C C3N-00547_T 2189924 37553447 45703994 556 14886 CDC6 0 . GRCh38 17 40300906 40300906 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1328G>T p.Gly443Val p.G443V ENST00000209728 10/12 336 244 92 384 384 0 strelka-varscan-mutect CDC6,missense_variant,p.Gly443Val,ENST00000209728,NM_001254.3; T ENST00000209728 Transcript missense_variant 1799/4810 1328/1683 443/560 G/V gGt/gTt 1 1 CDC6 HGNC HGNC:1744 protein_coding YES CCDS11365.1 ENSP00000209728 Q99741 A0A024R1S2 UPI0000073C6C NM_001254.3 deleterious(0) 10/12 hmmpanther:PTHR10763:SF26,hmmpanther:PTHR10763,PIRSF_domain:PIRSF001767 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 40300906 40300906 G T 1 0 0 0 0 1 0 0 0 2786 1261 44 2 2 CDC6 17 40300906 Missense_Mutation SNP G C3N-00547_T 2747459 40300906 42956535 557 14887 KRT15 0 . GRCh38 17 41518499 41518499 + Missense_Mutation SNP T T A rs777510451 C3N-00547_T C3N-00547_N T T c.329A>T p.Gln110Leu p.Q110L ENST00000254043 1/8 257 204 53 266 266 0 strelka-varscan-mutect KRT15,missense_variant,p.Gln110Leu,ENST00000254043,NM_002275.3;KRT15,missense_variant,p.Gln110Leu,ENST00000393976,;KRT15,5_prime_UTR_variant,,ENST00000393974,;KRT15,intron_variant,,ENST00000458290,;KRT15,upstream_gene_variant,,ENST00000613845,;KRT15,intron_variant,,ENST00000474031,;KRT15,intron_variant,,ENST00000497016,;KRT15,intron_variant,,ENST00000463447,;KRT15,intron_variant,,ENST00000470004,;KRT15,upstream_gene_variant,,ENST00000586794,; A ENST00000254043 Transcript missense_variant 3915/5237 329/1371 110/456 Q/L cAg/cTg rs777510451 1 -1 KRT15 HGNC HGNC:6421 protein_coding YES CCDS11398.1 ENSP00000254043 P19012 UPI000013CE0E NM_002275.3 deleterious(0) 1/8 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF164,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs777510451 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 41518499 41518499 T A 1 0 0 0 0 1 0 0 0 8334 1580 55 4 4 KRT15 17 41518499 Missense_Mutation SNP T C3N-00547_T 1217593 41518499 41738942 558 14888 KLHL11 0 . GRCh38 17 41854282 41854282 + Frame_Shift_Del DEL T T - novel C3N-00547_T C3N-00547_N T T c.1585delA p.Thr529GlnfsTer43 p.T529Qfs*43 ENST00000319121 2/2 118 99 19 167 167 0 sindel-varindel-pindel KLHL11,frameshift_variant,p.Thr529GlnfsTer43,ENST00000319121,NM_018143.2;RP11-156E6.1,upstream_gene_variant,,ENST00000560400,; - ENST00000319121 Transcript frameshift_variant 1646/2383 1585/2127 529/708 T/X Aca/ca 1 -1 KLHL11 HGNC HGNC:19008 protein_coding YES CCDS11411.1 ENSP00000314608 Q9NVR0 A0A024R1T8 UPI00000719F8 NM_018143.2 2/2 Gene3D:1zgkA00,Superfamily_domains:0052715 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 41854282 41854282 T - 1 0 1 0 1 0 0 0 0 8231 1638 57 0 0 KLHL11 17 41854282 Frame_Shift_Del DEL T C3N-00547_T 335783 41854282 41403159 559 14889 SLC4A1 0 . GRCh38 17 44259318 44259318 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.721G>T p.Val241Leu p.V241L ENST00000262418 9/20 274 213 61 261 260 1 strelka-varscan-mutect SLC4A1,missense_variant,p.Val241Leu,ENST00000262418,NM_000342.3;SLC4A1,missense_variant,p.Val241Leu,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; A ENST00000262418 Transcript missense_variant 877/4965 721/2736 241/911 V/L Gtg/Ttg 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 deleterious(0.04) 9/20 Gene3D:1hynR00,Pfam_domain:PF07565,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 44259318 44259318 C A 1 0 0 0 0 1 0 0 0 14927 507 18 2 2 SLC4A1 17 44259318 Missense_Mutation SNP C C3N-00547_T 2405036 44259318 38998123 560 14890 ITGA2B 0 . GRCh38 17 44383657 44383657 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1046C>A p.Ala349Glu p.A349E ENST00000262407 12/30 180 133 47 179 179 0 strelka-varscan-mutect ITGA2B,missense_variant,p.Ala349Glu,ENST00000262407,NM_000419.3;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592226,;ITGA2B,upstream_gene_variant,,ENST00000592462,;ITGA2B,downstream_gene_variant,,ENST00000589645,;ITGA2B,downstream_gene_variant,,ENST00000591990,;ITGA2B,downstream_gene_variant,,ENST00000592944,;ITGA2B,downstream_gene_variant,,ENST00000592253,;ITGA2B,downstream_gene_variant,,ENST00000592075,; T ENST00000262407 Transcript missense_variant 1078/3333 1046/3120 349/1039 A/E gCa/gAa 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 deleterious(0.01) 12/30 PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Gene3D:3nigC00,Pfam_domain:PF01839,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 44383657 44383657 G T 1 0 0 0 0 1 0 0 0 7783 1319 46 2 2 ITGA2B 17 44383657 Missense_Mutation SNP G C3N-00547_T 124339 44383657 38873784 561 14891 PLEKHM1 0 . GRCh38 17 45475214 45475214 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.809G>T p.Ser270Ile p.S270I ENST00000430334 4/12 343 254 89 393 392 1 strelka-varscan-mutect PLEKHM1,missense_variant,p.Ser270Ile,ENST00000430334,NM_014798.2;PLEKHM1,missense_variant,p.Ser140Ile,ENST00000584420,;PLEKHM1,downstream_gene_variant,,ENST00000589780,;PLEKHM1,downstream_gene_variant,,ENST00000636800,;PLEKHM1,intron_variant,,ENST00000582119,;PLEKHM1,downstream_gene_variant,,ENST00000586562,;PLEKHM1,missense_variant,p.Ser270Ile,ENST00000581448,;PLEKHM1,3_prime_UTR_variant,,ENST00000579197,;PLEKHM1,3_prime_UTR_variant,,ENST00000446609,;PLEKHM1,downstream_gene_variant,,ENST00000581932,;PLEKHM1,downstream_gene_variant,,ENST00000586084,; A ENST00000430334 Transcript missense_variant 943/5263 809/3171 270/1056 S/I aGc/aTc 1 -1 PLEKHM1 HGNC HGNC:29017 protein_coding YES CCDS32671.1 ENSP00000389913 Q9Y4G2 UPI00001C1FC4 NM_014798.2 deleterious(0) 4/12 Low_complexity_(Seg):seg,hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 45475214 45475214 C A 1 0 0 0 0 1 0 0 0 12173 797 28 2 2 PLEKHM1 17 45475214 Missense_Mutation SNP C C3N-00547_T 1091557 45475214 37782227 562 14892 LPO 0 . GRCh38 17 58266254 58266254 + Missense_Mutation SNP C C G rs763363576 C3N-00547_T C3N-00547_N C C c.1621C>G p.Pro541Ala p.P541A ENST00000262290 11/13 192 146 46 198 198 0 strelka-varscan-mutect LPO,missense_variant,p.Pro541Ala,ENST00000262290,NM_006151.2;LPO,missense_variant,p.Pro458Ala,ENST00000421678,NM_001160102.1;LPO,missense_variant,p.Pro458Ala,ENST00000582328,;LPO,missense_variant,p.Pro482Ala,ENST00000543544,;MPO,downstream_gene_variant,,ENST00000225275,NM_000250.1;MPO,downstream_gene_variant,,ENST00000577220,;LPO,3_prime_UTR_variant,,ENST00000580890,;LPO,3_prime_UTR_variant,,ENST00000389576,; G ENST00000262290 Transcript missense_variant 1937/2979 1621/2139 541/712 P/A Cca/Gca rs763363576 1 1 LPO HGNC HGNC:6678 protein_coding YES CCDS32689.1 ENSP00000262290 P22079 UPI0000131631 NM_006151.2 tolerated(0.22) 11/13 PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF67,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS rs763363576 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 58266254 58266254 C G 1 0 0 0 0 1 0 0 0 8821 739 26 4 4 LPO 17 58266254 Missense_Mutation SNP C C3N-00547_T 12791040 58266254 24991187 563 14893 SMARCD2 0 . GRCh38 17 63835462 63835462 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.673G>C p.Asp225His p.D225H ENST00000448276 5/13 144 94 50 214 214 0 strelka-varscan-mutect SMARCD2,missense_variant,p.Asp225His,ENST00000448276,NM_001098426.1;SMARCD2,missense_variant,p.Asp188His,ENST00000613943,;SMARCD2,missense_variant,p.Asp177His,ENST00000323347,;SMARCD2,missense_variant,p.Asp150His,ENST00000225742,;PSMC5,downstream_gene_variant,,ENST00000310144,NM_002805.5;PSMC5,downstream_gene_variant,,ENST00000580864,;PSMC5,downstream_gene_variant,,ENST00000375812,NM_001199163.1;PSMC5,downstream_gene_variant,,ENST00000581882,;SMARCD2,upstream_gene_variant,,ENST00000450364,;PSMC5,downstream_gene_variant,,ENST00000585123,;PSMC5,downstream_gene_variant,,ENST00000582130,;PSMC5,downstream_gene_variant,,ENST00000581842,;PSMC5,downstream_gene_variant,,ENST00000584320,;PSMC5,downstream_gene_variant,,ENST00000579708,;SMARCD2,3_prime_UTR_variant,,ENST00000584400,;SMARCD2,non_coding_transcript_exon_variant,,ENST00000578234,;PSMC5,downstream_gene_variant,,ENST00000579147,;PSMC5,downstream_gene_variant,,ENST00000581764,;PSMC5,downstream_gene_variant,,ENST00000578570,;PSMC5,downstream_gene_variant,,ENST00000585242,;SMARCD2,upstream_gene_variant,,ENST00000584483,;PSMC5,downstream_gene_variant,,ENST00000584536,;PSMC5,downstream_gene_variant,,ENST00000579031,;PSMC5,downstream_gene_variant,,ENST00000584880,;PSMC5,downstream_gene_variant,,ENST00000584657,;PSMC5,downstream_gene_variant,,ENST00000580063,;SMARCD2,upstream_gene_variant,,ENST00000581832,;SMARCD2,downstream_gene_variant,,ENST00000580054,;SMARCD2,downstream_gene_variant,,ENST00000577686,; G ENST00000448276 Transcript missense_variant 939/2716 673/1596 225/531 D/H Gac/Cac 1 -1 SMARCD2 HGNC HGNC:11107 protein_coding YES CCDS45756.1 ENSP00000392617 Q92925 UPI0000D695F8 NM_001098426.1 deleterious(0.02) 5/13 hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF2 MODERATE 1 SNV 1 1 PASS rs980191323 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 63835462 63835462 C G 1 0 0 0 0 1 0 0 0 15071 855 30 4 4 SMARCD2 17 63835462 Missense_Mutation SNP C C3N-00547_T 5569208 63835462 19421979 564 14894 APOH 0 . GRCh38 17 66228134 66228134 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.127C>G p.Pro43Ala p.P43A ENST00000205948 2/8 133 102 31 162 162 0 strelka-varscan-mutect APOH,missense_variant,p.Pro43Ala,ENST00000205948,NM_000042.2;APOH,missense_variant,p.Pro43Ala,ENST00000577982,;APOH,5_prime_UTR_variant,,ENST00000581797,; C ENST00000205948 Transcript missense_variant 165/1176 127/1038 43/345 P/A Cca/Gca 1 -1 APOH HGNC HGNC:616 protein_coding YES CCDS11663.1 ENSP00000205948 P02749 UPI0000125CAA NM_000042.2 tolerated(0.36) 2/8 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF323,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 66228134 66228134 G C 1 0 0 0 0 1 0 0 0 926 1203 42 4 4 APOH 17 66228134 Missense_Mutation SNP G C3N-00547_T 2392672 66228134 17029307 565 14895 DNAI2 0 . GRCh38 17 74309318 74309318 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1277C>A p.Thr426Asn p.T426N ENST00000446837 9/13 467 337 130 513 512 1 strelka-varscan-mutect DNAI2,missense_variant,p.Thr483Asn,ENST00000579490,;DNAI2,missense_variant,p.Thr426Asn,ENST00000446837,;DNAI2,missense_variant,p.Thr426Asn,ENST00000582036,NM_001172810.1;DNAI2,missense_variant,p.Thr426Asn,ENST00000311014,NM_023036.4;RP11-647F2.2,non_coding_transcript_exon_variant,,ENST00000585167,;DNAI2,3_prime_UTR_variant,,ENST00000579055,;DNAI2,upstream_gene_variant,,ENST00000579312,; A ENST00000446837 Transcript missense_variant 1583/2474 1277/1818 426/605 T/N aCc/aAc 1 1 DNAI2 HGNC HGNC:18744 protein_coding YES CCDS11697.1 ENSP00000400252 Q9GZS0 UPI000013EC1D deleterious(0.01) 9/13 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF7,hmmpanther:PTHR12442,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1191507648 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 74309318 74309318 C A 1 0 0 0 0 1 0 0 0 4425 507 18 2 2 DNAI2 17 74309318 Missense_Mutation SNP C C3N-00547_T 8081184 74309318 8948123 566 14896 TSEN54 0 . GRCh38 17 75522042 75522042 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.961G>A p.Glu321Lys p.E321K ENST00000333213 8/11 231 159 72 218 218 0 strelka-varscan-mutect TSEN54,missense_variant,p.Glu321Lys,ENST00000333213,NM_207346.2;TSEN54,missense_variant,p.Glu18Lys,ENST00000545228,;LLGL2,upstream_gene_variant,,ENST00000392550,NM_001031803.1;LLGL2,upstream_gene_variant,,ENST00000167462,NM_004524.2;LLGL2,upstream_gene_variant,,ENST00000578363,;LLGL2,upstream_gene_variant,,ENST00000375227,NM_001015002.1;TSEN54,downstream_gene_variant,,ENST00000434205,;LLGL2,upstream_gene_variant,,ENST00000580578,;LLGL2,upstream_gene_variant,,ENST00000579392,;TSEN54,downstream_gene_variant,,ENST00000580013,;TSEN54,missense_variant,p.Arg165Lys,ENST00000583173,;TSEN54,3_prime_UTR_variant,,ENST00000578415,;TSEN54,upstream_gene_variant,,ENST00000579449,;TSEN54,downstream_gene_variant,,ENST00000583818,;TSEN54,downstream_gene_variant,,ENST00000583454,;TSEN54,upstream_gene_variant,,ENST00000577197,;TSEN54,downstream_gene_variant,,ENST00000583634,; A ENST00000333213 Transcript missense_variant 997/1944 961/1581 321/526 E/K Gag/Aag 1 1 TSEN54 HGNC HGNC:27561 protein_coding YES CCDS11724.1 ENSP00000327487 Q7Z6J9 UPI00001C1FD2 NM_207346.2 tolerated(0.43) 8/11 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 75522042 75522042 G A 1 0 0 0 0 1 0 0 0 17120 943 33 3 3 TSEN54 17 75522042 Missense_Mutation SNP G C3N-00547_T 1212724 75522042 7735399 567 14897 LAMA1 0 . GRCh38 18 7080392 7080392 + Nonsense_Mutation SNP C C A rs571937115 C3N-00547_T C3N-00547_N C C c.127G>T p.Glu43Ter p.E43* ENST00000389658 2/63 384 275 109 366 366 0 strelka-varscan-mutect LAMA1,stop_gained,p.Glu43Ter,ENST00000389658,NM_005559.3;RP11-76K13.3,downstream_gene_variant,,ENST00000581502,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript stop_gained 221/9657 127/9228 43/3075 E/* Gag/Tag rs571937115 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 2/63 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00136 HIGH 1 SNV 2 1 PASS rs571937115 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 7080392 7080392 C A 1 0 0 0 0 0 1 0 0 8509 893 31 1 1 LAMA1 18 7080392 Nonsense_Mutation SNP C C3N-00547_T 7080392 73292893 568 14898 ZNF519 0 . GRCh38 18 14105464 14105464 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1076G>T p.Arg359Met p.R359M ENST00000590202 3/3 100 63 37 107 107 0 strelka-varscan-mutect ZNF519,missense_variant,p.Arg359Met,ENST00000590202,NM_145287.3;ZNF519,intron_variant,,ENST00000589498,;RP11-411B10.3,downstream_gene_variant,,ENST00000592926,;ZNF519,intron_variant,,ENST00000589203,;ZNF519,intron_variant,,ENST00000591393,;ZNF519,intron_variant,,ENST00000592345,;ZNF519,intron_variant,,ENST00000592411,;ZNF519,intron_variant,,ENST00000592049,;ZNF519,downstream_gene_variant,,ENST00000588435,;ZNF519,non_coding_transcript_exon_variant,,ENST00000624133,;ZNF519,intron_variant,,ENST00000587419,; A ENST00000590202 Transcript missense_variant 1229/2830 1076/1623 359/540 R/M aGg/aTg 1 -1 ZNF519 HGNC HGNC:30574 protein_coding YES CCDS32797.1 ENSP00000464872 Q8TB69 UPI0000201A41 NM_145287.3 tolerated(0.19) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF97,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 14105464 14105464 C A 1 0 0 0 0 1 0 0 0 18536 681 24 2 2 ZNF519 18 14105464 Missense_Mutation SNP C C3N-00547_T 7025072 14105464 66267821 569 14899 ANKRD30B 0 . GRCh38 18 14763798 14763798 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.933G>T p.Glu311Asp p.E311D ENST00000358984 7/36 343 229 114 516 516 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Glu311Asp,ENST00000358984,NM_001145029.1;RNU6-1210P,downstream_gene_variant,,ENST00000363775,;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,missense_variant,p.Glu311Asp,ENST00000580206,; T ENST00000358984 Transcript missense_variant 1113/4359 933/4179 311/1392 E/D gaG/gaT COSM4562590,COSM4562591,COSM5295218,COSM5295219 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 deleterious(0.02) 7/36 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs1040310529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 14763798 14763798 G T 1 0 0 0 0 1 0 0 0 762 991 35 2 2 ANKRD30B 18 14763798 Missense_Mutation SNP G C3N-00547_T 658334 14763798 65609487 570 14900 ANKRD30B 0 . GRCh38 18 14851956 14851956 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.3655G>T p.Val1219Leu p.V1219L ENST00000358984 36/36 78 50 28 98 98 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.Val1219Leu,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; T ENST00000358984 Transcript missense_variant 3835/4359 3655/4179 1219/1392 V/L Gtg/Ttg 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.21) 36/36 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 14851956 14851956 G T 1 0 0 0 0 1 0 0 0 762 1377 48 2 2 ANKRD30B 18 14851956 Missense_Mutation SNP G C3N-00547_T 88158 14851956 65521329 571 14901 MIB1 0 . GRCh38 18 21849360 21849360 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.2558G>C p.Cys853Ser p.C853S ENST00000261537 17/21 111 92 19 115 115 0 strelka-mutect MIB1,missense_variant,p.Cys853Ser,ENST00000261537,NM_020774.3;MIB1,non_coding_transcript_exon_variant,,ENST00000578646,; C ENST00000261537 Transcript missense_variant 2822/9576 2558/3021 853/1006 C/S tGt/tCt 1 1 MIB1 HGNC HGNC:21086 protein_coding YES CCDS11871.1 ENSP00000261537 Q86YT6 UPI000000D833 NM_020774.3 deleterious(0.02) 17/21 Gene3D:3.30.40.10,Pfam_domain:PF13920,PROSITE_profiles:PS50089,hmmpanther:PTHR24202,SMART_domains:SM00184 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 21849360 21849360 G C 1 0 0 0 0 1 0 0 0 9523 1377 48 4 4 MIB1 18 21849360 Missense_Mutation SNP G C3N-00547_T 6997404 21849360 58523925 572 14902 ZNF521 0 . GRCh38 18 25226728 25226728 + Nonsense_Mutation SNP G G T rs553401367 C3N-00547_T C3N-00547_N G G c.1190C>A p.Ser397Ter p.S397* ENST00000361524 4/8 278 189 89 283 282 1 strelka-varscan-mutect ZNF521,stop_gained,p.Ser397Ter,ENST00000361524,NM_015461.2;ZNF521,stop_gained,p.Ser177Ter,ENST00000584787,NM_001308225.1;ZNF521,stop_gained,p.Ser397Ter,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,stop_gained,p.Ser397Ter,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; T ENST00000361524 Transcript stop_gained 1339/4871 1190/3936 397/1311 S/* tCg/tAg rs553401367 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 4/8 hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402 HIGH 1 SNV 1 1 PASS rs553401367 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 25226728 25226728 G T 1 0 0 0 0 0 1 0 0 18537 1059 37 1 1 ZNF521 18 25226728 Nonsense_Mutation SNP G C3N-00547_T 3377368 25226728 55146557 573 14903 ASXL3 0 . GRCh38 18 33746254 33746254 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.6406C>A p.Gln2136Lys p.Q2136K ENST00000269197 12/12 164 121 43 228 228 0 strelka-varscan-mutect ASXL3,missense_variant,p.Gln2136Lys,ENST00000269197,NM_030632.1;ASXL3,downstream_gene_variant,,ENST00000592288,; A ENST00000269197 Transcript missense_variant 6461/11399 6406/6747 2136/2248 Q/K Caa/Aaa 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 deleterious_low_confidence(0.02) 12/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1360535131 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 33746254 33746254 C A 1 0 0 0 0 1 0 0 0 1216 595 21 2 2 ASXL3 18 33746254 Missense_Mutation SNP C C3N-00547_T 8519526 33746254 46627031 574 14904 SERPINB11 0 . GRCh38 18 63711338 63711338 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.172C>A p.Leu58Ile p.L58I ENST00000623262 2/5 127 113 14 220 220 0 strelka-varscan-mutect SERPINB11,missense_variant,p.Leu58Ile,ENST00000382749,NM_080475.3;SERPINB11,missense_variant,p.Leu58Ile,ENST00000544088,;SERPINB11,missense_variant,p.Leu58Ile,ENST00000489748,;SERPINB11,missense_variant,p.Leu58Ile,ENST00000623262,NM_001291278.1;SERPINB11,intron_variant,,ENST00000624518,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000467649,;SERPINB11,missense_variant,p.Leu58Ile,ENST00000536691,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000610304,; A ENST00000623262 Transcript missense_variant 172/918 172/918 58/305 L/I Ctt/Att COSM5388363 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 deleterious(0.03) 2/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 63711338 63711338 C A 1 0 0 0 0 1 0 0 0 14374 811 28 2 2 SERPINB11 18 63711338 Missense_Mutation SNP C C3N-00547_T 29965084 63711338 16661947 575 14905 RTTN 0 . GRCh38 18 70057801 70057801 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.4972G>T p.Val1658Phe p.V1658F ENST00000255674 37/49 172 141 31 273 273 0 strelka-varscan-mutect RTTN,missense_variant,p.Val1658Phe,ENST00000255674,NM_173630.3;RTTN,3_prime_UTR_variant,,ENST00000581161,NM_001318520.1;RTTN,3_prime_UTR_variant,,ENST00000583043,; A ENST00000255674 Transcript missense_variant 5259/7326 4972/6681 1658/2226 V/F Gtc/Ttc 1 -1 RTTN HGNC HGNC:18654 protein_coding YES CCDS42443.1 ENSP00000255674 Q86VV8 UPI0000201E92 NM_173630.3 tolerated(0.22) 37/49 hmmpanther:PTHR31691,hmmpanther:PTHR31691:SF1 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 70057801 70057801 C A 1 0 0 0 0 1 0 0 0 13998 478 17 2 2 RTTN 18 70057801 Missense_Mutation SNP C C3N-00547_T 6346463 70057801 10315484 576 14906 SALL3 0 . GRCh38 18 78994716 78994716 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.2725C>A p.Pro909Thr p.P909T ENST00000537592 2/3 93 74 19 200 200 0 strelka-varscan-mutect SALL3,missense_variant,p.Pro909Thr,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Pro776Thr,ENST00000536229,;SALL3,missense_variant,p.Pro909Thr,ENST00000575389,;SALL3,missense_variant,p.Pro641Thr,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; A ENST00000537592 Transcript missense_variant 2725/6555 2725/3903 909/1300 P/T Ccc/Acc 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 tolerated(0.25) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 78994716 78994716 C A 1 0 0 0 0 1 0 0 0 14071 623 22 2 2 SALL3 18 78994716 Missense_Mutation SNP C C3N-00547_T 8936915 78994716 1378569 577 14907 ATP9B 0 . GRCh38 18 79337352 79337352 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.2186A>G p.Glu729Gly p.E729G ENST00000426216 19/30 155 119 36 326 326 0 strelka-varscan-mutect ATP9B,missense_variant,p.Glu729Gly,ENST00000426216,NM_198531.3;ATP9B,missense_variant,p.Glu729Gly,ENST00000307671,NM_001306085.1;ATP9B,intron_variant,,ENST00000458297,;ATP9B,downstream_gene_variant,,ENST00000589326,;ATP9B,downstream_gene_variant,,ENST00000589732,;RP11-800A18.4,downstream_gene_variant,,ENST00000592906,;ATP9B,synonymous_variant,p.=,ENST00000588895,;ATP9B,non_coding_transcript_exon_variant,,ENST00000490210,; G ENST00000426216 Transcript missense_variant 2203/4361 2186/3444 729/1147 E/G gAg/gGg 1 1 ATP9B HGNC HGNC:13541 protein_coding YES CCDS12014.1 ENSP00000398076 O43861 UPI00002371AF NM_198531.3 deleterious(0) 19/30 hmmpanther:PTHR24092:SF50,hmmpanther:PTHR24092,Gene3D:3.40.1110.10,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01652,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 79337352 79337352 A G 1 0 0 0 0 1 0 0 0 1352 304 11 5 5 ATP9B 18 79337352 Missense_Mutation SNP A C3N-00547_T 342636 79337352 1035933 578 14908 ADNP2 0 . GRCh38 18 80138601 80138601 + Missense_Mutation SNP A A T rs763214529 C3N-00547_T C3N-00547_N A A c.3188A>T p.His1063Leu p.H1063L ENST00000262198 4/4 100 82 18 108 108 0 strelka-varscan-mutect ADNP2,missense_variant,p.His1063Leu,ENST00000262198,NM_014913.3;ADNP2,intron_variant,,ENST00000561195,;ADNP2,downstream_gene_variant,,ENST00000560752,;ADNP2,downstream_gene_variant,,ENST00000559951,;ADNP2,downstream_gene_variant,,ENST00000560561,; T ENST00000262198 Transcript missense_variant 3643/5393 3188/3396 1063/1131 H/L cAt/cTt rs763214529 1 1 ADNP2 HGNC HGNC:23803 protein_coding YES CCDS32853.1 ENSP00000262198 Q6IQ32 A0A024R377 UPI0000071DEA NM_014913.3 deleterious(0) 4/4 hmmpanther:PTHR15740,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs763214529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 80138601 80138601 A T 1 0 0 0 0 1 0 0 0 399 217 8 4 4 ADNP2 18 80138601 Missense_Mutation SNP A C3N-00547_T 801249 80138601 234684 579 14909 C2CD4C 0 . GRCh38 19 407449 407449 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.913C>A p.Pro305Thr p.P305T ENST00000332235 2/2 25 14 11 38 38 0 strelka-varscan-mutect C2CD4C,missense_variant,p.Pro305Thr,ENST00000332235,NM_001136263.1; T ENST00000332235 Transcript missense_variant 1118/3129 913/1266 305/421 P/T Cct/Act 1 -1 C2CD4C HGNC HGNC:29417 protein_coding YES CCDS45890.1 ENSP00000328677 Q8TF44 UPI00001C2016 NM_001136263.1 deleterious(0.03) 2/2 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF116,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 407449 407449 G T 1 0 0 0 0 1 0 0 0 2028 1232 43 2 2 C2CD4C 19 407449 Missense_Mutation SNP G C3N-00547_T 407449 58210167 580 14910 STK11 0 . GRCh38 19 1220580 1220580 + Splice_Site SNP G G T C3N-00547_T C3N-00547_N G G c.598-1G>T p.X200_splice ENST00000326873 60 36 24 52 52 0 strelka-varscan-mutect STK11,splice_acceptor_variant,,ENST00000586243,;STK11,splice_acceptor_variant,,ENST00000326873,NM_000455.4;STK11,splice_acceptor_variant,,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,splice_acceptor_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript splice_acceptor_variant -/2611 598/1302 200/433 COSM3724562,COSM51521,COSM5337504 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 4/9 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 49 1220580 1220580 G T 1 0 0 0 0 0 0 1 0 15664 1014 35 2 2 STK11 19 1220580 Splice_Site SNP G C3N-00547_T 813131 1220580 57397036 581 14911 KHSRP 0 . GRCh38 19 6416384 6416384 + Silent SNP T T A novel C3N-00547_T C3N-00547_N T T c.1512A>T p.= p.P504P ENST00000398148 15/20 114 70 44 299 299 0 strelka-varscan-mutect KHSRP,synonymous_variant,p.=,ENST00000398148,NM_003685.2;KHSRP,synonymous_variant,p.=,ENST00000619396,;KHSRP,synonymous_variant,p.=,ENST00000595223,;KHSRP,upstream_gene_variant,,ENST00000594496,;KHSRP,upstream_gene_variant,,ENST00000600480,;KHSRP,downstream_gene_variant,,ENST00000599395,;KHSRP,downstream_gene_variant,,ENST00000595548,;KHSRP,downstream_gene_variant,,ENST00000595258,;KHSRP,upstream_gene_variant,,ENST00000594745,;KHSRP,upstream_gene_variant,,ENST00000597656,;KHSRP,downstream_gene_variant,,ENST00000579148,;CTB-180A7.8,downstream_gene_variant,,ENST00000596254,;CTB-180A7.8,downstream_gene_variant,,ENST00000593563,;KHSRP,downstream_gene_variant,,ENST00000595112,;KHSRP,downstream_gene_variant,,ENST00000597704,;KHSRP,upstream_gene_variant,,ENST00000599642,;CTB-180A7.8,downstream_gene_variant,,ENST00000637688,; A ENST00000398148 Transcript synonymous_variant 1605/2993 1512/2136 504/711 P ccA/ccT 1 -1 KHSRP HGNC HGNC:6316 protein_coding YES CCDS45936.1 ENSP00000381216 Q92945 UPI000049DE96 NM_003685.2 15/20 Low_complexity_(Seg):seg,hmmpanther:PTHR10288:SF101,hmmpanther:PTHR10288 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 6416384 6416384 T A 1 0 0 0 0 0 0 0 1 8072 1567 55 4 4 KHSRP 19 6416384 Silent SNP T C3N-00547_T 5195804 6416384 52201232 582 14912 MUC16 0 . GRCh38 19 8949772 8949772 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.26998C>A p.Leu9000Met p.L9000M ENST00000397910 3/84 147 81 66 169 169 0 strelka-varscan-mutect MUC16,missense_variant,p.Leu9000Met,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 27202/43816 26998/43524 9000/14507 L/M Ctg/Atg 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 8949772 8949772 G T 1 0 0 0 0 1 0 0 0 9972 991 35 2 2 MUC16 19 8949772 Missense_Mutation SNP G C3N-00547_T 2533388 8949772 49667844 583 14913 MUC16 0 . GRCh38 19 8979940 8979940 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1199G>T p.Ser400Ile p.S400I ENST00000397910 1/84 198 125 73 257 257 0 strelka-varscan-mutect MUC16,missense_variant,p.Ser400Ile,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 1403/43816 1199/43524 400/14507 S/I aGc/aTc 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1393657491 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 8979940 8979940 C A 1 0 0 0 0 1 0 0 0 9972 797 28 2 2 MUC16 19 8979940 Missense_Mutation SNP C C3N-00547_T 30168 8979940 49637676 584 14914 OR1M1 0 . GRCh38 19 9093265 9093265 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.21C>A p.= p.T7T ENST00000429566 1/1 62 30 32 61 60 1 strelka-varscan-mutect OR1M1,synonymous_variant,p.=,ENST00000429566,NM_001004456.1; A ENST00000429566 Transcript synonymous_variant 87/1035 21/942 7/313 T acC/acA 1 1 OR1M1 HGNC HGNC:8220 protein_coding YES CCDS32896.1 ENSP00000401966 Q8NGA1 UPI0000041C29 NM_001004456.1 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF295,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 9093265 9093265 C A 1 0 0 0 0 0 0 0 1 11046 581 21 2 2 OR1M1 19 9093265 Silent SNP C C3N-00547_T 113325 9093265 49524351 585 14915 ZNF799 0 . GRCh38 19 12391769 12391769 + Missense_Mutation SNP C C A rs770188151 C3N-00547_T C3N-00547_N C C c.629G>T p.Ser210Ile p.S210I ENST00000430385 4/4 214 119 95 277 277 0 strelka-varscan-mutect ZNF799,missense_variant,p.Ser178Ile,ENST00000419318,NM_001322497.1;ZNF799,missense_variant,p.Ser210Ile,ENST00000430385,NM_001080821.2;CTD-3105H18.16,downstream_gene_variant,,ENST00000595562,;ZNF799,downstream_gene_variant,,ENST00000595766,;ZNF799,non_coding_transcript_exon_variant,,ENST00000460935,;CTD-3105H18.14,intron_variant,,ENST00000435033,; A ENST00000430385 Transcript missense_variant 830/2583 629/1932 210/643 S/I aGt/aTt rs770188151 1 -1 ZNF799 HGNC HGNC:28071 protein_coding YES CCDS45989.1 ENSP00000411084 Q96GE5 UPI000016184E NM_001080821.2 tolerated(0.06) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs770188151 . 0 199 0 0 11 0 0 0 -20 0.3722598 1 1 0 0 A 3 1 49 12391769 12391769 C A 1 0 0 0 0 1 0 0 0 18751 565 20 2 2 ZNF799 19 12391769 Missense_Mutation SNP C C3N-00547_T 3298504 12391769 46225847 586 14916 CACNA1A 0 . GRCh38 19 13335868 13335868 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1020C>T p.= p.F340F ENST00000360228 7/47 148 86 62 159 159 0 strelka-varscan-mutect CACNA1A,synonymous_variant,p.=,ENST00000638009,NM_001127221.1;CACNA1A,synonymous_variant,p.=,ENST00000635895,;CACNA1A,synonymous_variant,p.=,ENST00000637769,;CACNA1A,synonymous_variant,p.=,ENST00000360228,NM_001127222.1;CACNA1A,synonymous_variant,p.=,ENST00000614285,;CACNA1A,synonymous_variant,p.=,ENST00000637736,;CACNA1A,synonymous_variant,p.=,ENST00000636389,;CACNA1A,synonymous_variant,p.=,ENST00000638029,NM_023035.2;CACNA1A,synonymous_variant,p.=,ENST00000637432,NM_000068.3;CACNA1A,synonymous_variant,p.=,ENST00000573710,;CACNA1A,synonymous_variant,p.=,ENST00000635727,;CACNA1A,synonymous_variant,p.=,ENST00000636012,;CACNA1A,synonymous_variant,p.=,ENST00000637276,;CACNA1A,synonymous_variant,p.=,ENST00000637927,;CACNA1A,synonymous_variant,p.=,ENST00000636549,NM_001174080.1;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637966,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636974,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000593160,;CACNA1A,upstream_gene_variant,,ENST00000636022,; A ENST00000360228 Transcript synonymous_variant 1255/8627 1020/7521 340/2506 F ttC/ttT 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 7/47 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 13335868 13335868 G A 1 0 0 0 0 0 0 0 1 2226 1281 45 3 3 CACNA1A 19 13335868 Silent SNP G C3N-00547_T 944099 13335868 45281748 587 14917 SAMD1 0 . GRCh38 19 14089119 14089119 + Missense_Mutation SNP C C A rs760405675 C3N-00547_T C3N-00547_N C C c.880G>T p.Gly294Cys p.G294C ENST00000533683 2/5 136 71 65 139 139 0 strelka-varscan-mutect SAMD1,missense_variant,p.Gly294Cys,ENST00000533683,NM_138352.1;SAMD1,5_prime_UTR_variant,,ENST00000269724,;PRKACA,downstream_gene_variant,,ENST00000308677,NM_002730.3;C19orf67,upstream_gene_variant,,ENST00000548523,NM_001277378.1;PRKACA,downstream_gene_variant,,ENST00000589994,NM_207518.2;PRKACA,downstream_gene_variant,,ENST00000590853,;PRKACA,downstream_gene_variant,,ENST00000587372,;C19orf67,upstream_gene_variant,,ENST00000343945,;PRKACA,downstream_gene_variant,,ENST00000350356,;C19orf67,upstream_gene_variant,,ENST00000547589,;SAMD1,downstream_gene_variant,,ENST00000541938,;PRKACA,downstream_gene_variant,,ENST00000588209,; A ENST00000533683 Transcript missense_variant 1168/2164 880/1299 294/432 G/C Ggc/Tgc rs760405675 1 -1 SAMD1 HGNC HGNC:17958 protein_coding YES ENSP00000431971 E9PIW9 UPI0000366D4A NM_138352.1 tolerated(0.06) 2/5 hmmpanther:PTHR12247:SF82,hmmpanther:PTHR12247 MODERATE 1 SNV 1 1 PASS rs760405675 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 14089119 14089119 C A 1 0 0 0 0 1 0 0 0 14073 652 23 1 1 SAMD1 19 14089119 Missense_Mutation SNP C C3N-00547_T 753251 14089119 44528497 588 14918 CYP4F22 0 . GRCh38 19 15551367 15551367 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1492C>A p.Leu498Met p.L498M ENST00000269703 14/14 330 174 156 393 392 1 strelka-varscan-mutect CYP4F22,missense_variant,p.Leu498Met,ENST00000269703,NM_173483.3;CYP4F22,missense_variant,p.Leu498Met,ENST00000601005,; A ENST00000269703 Transcript missense_variant 1691/2641 1492/1596 498/531 L/M Ctg/Atg 1 1 CYP4F22 HGNC HGNC:26820 protein_coding YES CCDS12331.1 ENSP00000269703 Q6NT55 UPI000013D84B NM_173483.3 deleterious(0.02) 14/14 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF53,Superfamily_domains:SSF48264 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 15551367 15551367 C A 1 0 0 0 0 1 0 0 0 3992 680 24 2 2 CYP4F22 19 15551367 Missense_Mutation SNP C C3N-00547_T 1462248 15551367 43066249 589 14919 C19orf44 0 . GRCh38 19 16509716 16509716 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.1367C>G p.Ser456Cys p.S456C ENST00000221671 5/9 201 183 18 245 245 0 strelka-varscan-mutect C19orf44,missense_variant,p.Ser456Cys,ENST00000221671,NM_032207.3;C19orf44,missense_variant,p.Ser456Cys,ENST00000594035,NM_001288834.1;C19orf44,upstream_gene_variant,,ENST00000601288,;C19orf44,missense_variant,p.Ser456Cys,ENST00000593380,;CTD-3222D19.2,intron_variant,,ENST00000409035,;C19orf44,downstream_gene_variant,,ENST00000596592,;C19orf44,upstream_gene_variant,,ENST00000601109,; G ENST00000221671 Transcript missense_variant 1523/3427 1367/1974 456/657 S/C tCt/tGt 1 1 C19orf44 HGNC HGNC:26141 protein_coding YES CCDS12345.1 ENSP00000221671 Q9H6X5 UPI0000070DFC NM_032207.3 tolerated(0.08) 5/9 hmmpanther:PTHR22409,hmmpanther:PTHR22409:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 16509716 16509716 C G 1 0 0 0 0 1 0 0 0 1911 913 32 4 4 C19orf44 19 16509716 Missense_Mutation SNP C C3N-00547_T 958349 16509716 42107900 590 14920 MYO9B 0 . GRCh38 19 17145467 17145467 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.911A>G p.Tyr304Cys p.Y304C ENST00000595618 3/40 152 116 36 201 200 1 strelka-varscan-mutect MYO9B,missense_variant,p.Tyr304Cys,ENST00000595618,NM_001130065.1;MYO9B,missense_variant,p.Tyr304Cys,ENST00000594824,NM_004145.3;MYO9B,missense_variant,p.Tyr304Cys,ENST00000397274,;MYO9B,missense_variant,p.Tyr304Cys,ENST00000595641,; G ENST00000595618 Transcript missense_variant 1063/7623 911/6069 304/2022 Y/C tAc/tGc 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 deleterious(0.01) 3/40 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 17145467 17145467 A G 1 0 0 0 0 1 0 0 0 10086 391 14 5 5 MYO9B 19 17145467 Missense_Mutation SNP A C3N-00547_T 635751 17145467 41472149 591 14921 SUGP2 0 . GRCh38 19 19025473 19025473 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.875A>T p.Gln292Leu p.Q292L ENST00000452918 3/11 186 83 103 193 193 0 strelka-varscan-mutect SUGP2,missense_variant,p.Gln292Leu,ENST00000452918,NM_001321699.1,NM_001017392.3;SUGP2,missense_variant,p.Gln292Leu,ENST00000601879,;SUGP2,missense_variant,p.Gln306Leu,ENST00000600377,;SUGP2,missense_variant,p.Gln292Leu,ENST00000337018,NM_001321697.1,NM_001321698.1,NM_014884.3;SUGP2,downstream_gene_variant,,ENST00000594445,;SUGP2,downstream_gene_variant,,ENST00000598202,;SUGP2,missense_variant,p.Gln292Leu,ENST00000600239,;SUGP2,missense_variant,p.Gln292Leu,ENST00000594773,;SUGP2,missense_variant,p.Gln292Leu,ENST00000330854,;SUGP2,intron_variant,,ENST00000598240,; A ENST00000452918 Transcript missense_variant 949/6176 875/3249 292/1082 Q/L cAg/cTg 1 -1 SUGP2 HGNC HGNC:18641 protein_coding YES CCDS12392.1 ENSP00000389380 Q8IX01 UPI000019825D NM_001321699.1,NM_001017392.3 tolerated(0.1) 3/11 hmmpanther:PTHR23340,hmmpanther:PTHR23340:SF2 MODERATE 1 SNV 1 1 PASS rs1406836392 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 19025473 19025473 T A 1 0 0 0 0 1 0 0 0 15756 1580 55 4 4 SUGP2 19 19025473 Missense_Mutation SNP T C3N-00547_T 1880006 19025473 39592143 592 14922 GMIP 0 . GRCh38 19 19630525 19630525 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.2485C>G p.Gln829Glu p.Q829E ENST00000203556 20/21 154 100 54 235 235 0 strelka-varscan-mutect GMIP,missense_variant,p.Gln829Glu,ENST00000203556,NM_016573.3;GMIP,missense_variant,p.Gln803Glu,ENST00000587238,NM_001288998.1,NM_001288999.1;LPAR2,upstream_gene_variant,,ENST00000542587,;LPAR2,upstream_gene_variant,,ENST00000586703,;LPAR2,upstream_gene_variant,,ENST00000407877,NM_004720.5;GMIP,downstream_gene_variant,,ENST00000593186,;LPAR2,upstream_gene_variant,,ENST00000588461,;LPAR2,upstream_gene_variant,,ENST00000591042,;LPAR2,upstream_gene_variant,,ENST00000588233,;LPAR2,upstream_gene_variant,,ENST00000592061,;GMIP,downstream_gene_variant,,ENST00000586269,;LPAR2,upstream_gene_variant,,ENST00000589311,;GMIP,downstream_gene_variant,,ENST00000587713,;LPAR2,upstream_gene_variant,,ENST00000590629,; C ENST00000203556 Transcript missense_variant 2623/3538 2485/2913 829/970 Q/E Cag/Gag 1 -1 GMIP HGNC HGNC:24852 protein_coding YES CCDS12408.1 ENSP00000203556 Q9P107 A0A024R7N1 UPI0000203862 NM_016573.3 tolerated(0.62) 20/21 hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 19630525 19630525 G C 1 0 0 0 0 1 0 0 0 6370 1386 48 4 4 GMIP 19 19630525 Missense_Mutation SNP G C3N-00547_T 605052 19630525 38987091 593 14923 ZNF676 0 . GRCh38 19 22193103 22193103 + Missense_Mutation SNP C C A rs780562519 C3N-00547_T C3N-00547_N C C c.43G>T p.Ala15Ser p.A15S ENST00000397121 2/3 45 26 19 78 78 0 strelka-varscan-mutect ZNF676,missense_variant,p.Ala15Ser,ENST00000397121,NM_001001411.2; A ENST00000397121 Transcript missense_variant 361/2944 43/1767 15/588 A/S Gcc/Tcc rs780562519,COSM5309578 1 -1 ZNF676 HGNC HGNC:20429 protein_coding YES CCDS42539.1 ENSP00000380310 Q8N7Q3 UPI00002376EC NM_001001411.2 deleterious(0.04) 2/3 PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF112 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs780562519 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 22193103 22193103 C A 1 0 0 0 0 1 0 0 0 18656 710 25 2 2 ZNF676 19 22193103 Missense_Mutation SNP C C3N-00547_T 2562578 22193103 36424513 594 14924 ZNF729 0 . GRCh38 19 22315690 22315690 + Missense_Mutation SNP A A T rs768103519 C3N-00547_T C3N-00547_N A A c.2273A>T p.His758Leu p.H758L ENST00000601693 4/4 205 114 91 305 305 0 strelka-varscan-mutect ZNF729,missense_variant,p.His758Leu,ENST00000601693,NM_001242680.1; T ENST00000601693 Transcript missense_variant 2391/3877 2273/3759 758/1252 H/L cAt/cTt rs768103519 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs768103519 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 22315690 22315690 A T 1 0 0 0 0 1 0 0 0 18703 217 8 4 4 ZNF729 19 22315690 Missense_Mutation SNP A C3N-00547_T 122587 22315690 36301926 595 14925 ATP4A 0 . GRCh38 19 35559963 35559963 + Nonsense_Mutation SNP C C A rs140861099 C3N-00547_T C3N-00547_N C C c.898G>T p.Glu300Ter p.E300* ENST00000262623 7/22 501 412 89 503 503 0 strelka-varscan-mutect ATP4A,stop_gained,p.Glu300Ter,ENST00000262623,NM_000704.2;ATP4A,upstream_gene_variant,,ENST00000592131,;ATP4A,upstream_gene_variant,,ENST00000592767,;ATP4A,downstream_gene_variant,,ENST00000590916,; A ENST00000262623 Transcript stop_gained 927/3709 898/3108 300/1035 E/* Gag/Tag rs140861099,COSM3532607 1 -1 ATP4A HGNC HGNC:819 protein_coding YES CCDS12467.1 ENSP00000262623 P20648 UPI000016A49B NM_000704.2 7/22 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF251,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01106,TIGRFAM_domain:TIGR01494,Superfamily_domains:0049473 0,1 HIGH 1 SNV 1 0,1 1 PASS rs140861099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 35559963 35559963 C A 1 0 0 0 0 0 1 0 0 1298 893 31 1 1 ATP4A 19 35559963 Nonsense_Mutation SNP C C3N-00547_T 13244273 35559963 23057653 596 14926 CATSPERG 0 . GRCh38 19 38362759 38362759 + Missense_Mutation SNP T T C C3N-00547_T C3N-00547_N T T c.2402T>C p.Leu801Pro p.L801P ENST00000409235 20/29 238 196 42 192 192 0 strelka-varscan-mutect CATSPERG,missense_variant,p.Leu801Pro,ENST00000409235,NM_021185.4;CATSPERG,missense_variant,p.Leu761Pro,ENST00000410018,;CATSPERG,downstream_gene_variant,,ENST00000409410,;CATSPERG,downstream_gene_variant,,ENST00000489693,;AC005625.1,upstream_gene_variant,,ENST00000590304,;CATSPERG,downstream_gene_variant,,ENST00000466060,;CATSPERG,3_prime_UTR_variant,,ENST00000471517,;CATSPERG,3_prime_UTR_variant,,ENST00000312265,;CATSPERG,3_prime_UTR_variant,,ENST00000412458,;CATSPERG,upstream_gene_variant,,ENST00000492088,;CATSPERG,downstream_gene_variant,,ENST00000470292,;CATSPERG,downstream_gene_variant,,ENST00000585424,; C ENST00000409235 Transcript missense_variant 2517/3746 2402/3480 801/1159 L/P cTg/cCg COSM5150152,COSM5150153 1 1 CATSPERG HGNC HGNC:25243 protein_coding YES CCDS12514.2 ENSP00000386962 Q6ZRH7 UPI000022A813 NM_021185.4 deleterious(0) 20/29 Pfam_domain:PF15064,hmmpanther:PTHR14327 1,1 MODERATE SNV 5 1,1 1 PASS rs1338521067 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 38362759 38362759 T C 1 0 0 0 0 1 0 0 0 2393 1580 55 5 5 CATSPERG 19 38362759 Missense_Mutation SNP T C3N-00547_T 2802796 38362759 20254857 597 14927 RYR1 0 . GRCh38 19 38466381 38466381 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.3161C>A p.Pro1054His p.P1054H ENST00000359596 24/106 253 145 108 181 181 0 strelka-varscan-mutect RYR1,missense_variant,p.Pro1054His,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Pro1054His,ENST00000359596,NM_000540.2;RYR1,non_coding_transcript_exon_variant,,ENST00000594111,; A ENST00000359596 Transcript missense_variant 3161/15117 3161/15117 1054/5038 P/H cCt/cAt COSM270092 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0) 24/106 PROSITE_profiles:PS50188,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 38466381 38466381 C A 1 0 0 0 0 1 0 0 0 14028 681 24 2 2 RYR1 19 38466381 Missense_Mutation SNP C C3N-00547_T 103622 38466381 20151235 598 14928 RYR1 0 . GRCh38 19 38486064 38486064 + Silent SNP G G T rs747211958 C3N-00547_T C3N-00547_N G G c.5409G>T p.= p.P1803P ENST00000359596 34/106 157 96 61 157 157 0 strelka-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2; T ENST00000359596 Transcript synonymous_variant 5409/15117 5409/15117 1803/5038 P ccG/ccT rs747211958 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 34/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 LOW 1 SNV 5 1 PASS rs747211958 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 38486064 38486064 G T 1 0 0 0 0 0 0 0 1 14028 1074 38 1 1 RYR1 19 38486064 Silent SNP G C3N-00547_T 19683 38486064 20131552 599 14929 ECH1 0 . GRCh38 19 38815624 38815626 + In_Frame_Del DEL AGA AGA - novel C3N-00547_T C3N-00547_N AGA AGA c.974_976delTCT p.Phe325del p.F325del ENST00000221418 10/10 229 135 94 178 178 0 sindel-varindel-pindel ECH1,inframe_deletion,p.Phe325del,ENST00000221418,NM_001398.2;LGALS4,upstream_gene_variant,,ENST00000307751,NM_006149.3;AC104534.3,downstream_gene_variant,,ENST00000594769,;ECH1,downstream_gene_variant,,ENST00000601778,;LGALS4,upstream_gene_variant,,ENST00000594209,;ECH1,downstream_gene_variant,,ENST00000595470,;AC104534.3,downstream_gene_variant,,ENST00000602021,;AC104534.2,upstream_gene_variant,,ENST00000594558,;LGALS4,upstream_gene_variant,,ENST00000597803,;ECH1,non_coding_transcript_exon_variant,,ENST00000594391,;ECH1,non_coding_transcript_exon_variant,,ENST00000601333,;LGALS4,upstream_gene_variant,,ENST00000595278,;ECH1,downstream_gene_variant,,ENST00000600178,;LGALS4,upstream_gene_variant,,ENST00000597153,;ECH1,downstream_gene_variant,,ENST00000598707,;ECH1,downstream_gene_variant,,ENST00000601060,;ECH1,downstream_gene_variant,,ENST00000594164,;ECH1,downstream_gene_variant,,ENST00000598316,; - ENST00000221418 Transcript inframe_deletion 1207-1209/1411 974-976/987 325-326/328 FS/S tTCTcc/tcc 1 -1 ECH1 HGNC HGNC:3149 protein_coding YES CCDS33014.1 ENSP00000221418 Q13011 UPI0000071141 NM_001398.2 10/10 hmmpanther:PTHR11941,hmmpanther:PTHR11941:SF43 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 49 38815624 38815624 AGA - 1 0 1 0 1 0 0 0 0 4718 304 11 0 0 ECH1 19 38815624 In_Frame_Del DEL AGA C3N-00547_T 329560 38815624 19801992 600 14930 ADCK4 0 . GRCh38 19 40703613 40703613 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.727A>T p.Ile243Leu p.I243L ENST00000324464 9/15 86 72 14 98 98 0 strelka-varscan-mutect ADCK4,missense_variant,p.Ile243Leu,ENST00000324464,NM_024876.3;ADCK4,missense_variant,p.Ile202Leu,ENST00000243583,NM_001142555.2;ADCK4,missense_variant,p.Ile134Leu,ENST00000595254,;ADCK4,downstream_gene_variant,,ENST00000601967,;ADCK4,downstream_gene_variant,,ENST00000594084,;ADCK4,downstream_gene_variant,,ENST00000594720,;ADCK4,downstream_gene_variant,,ENST00000600080,;ADCK4,downstream_gene_variant,,ENST00000594490,;RNU6-195P,downstream_gene_variant,,ENST00000411352,;ADCK4,synonymous_variant,p.=,ENST00000599643,;ADCK4,non_coding_transcript_exon_variant,,ENST00000596455,;ADCK4,upstream_gene_variant,,ENST00000593724,;ADCK4,downstream_gene_variant,,ENST00000601451,;ADCK4,downstream_gene_variant,,ENST00000601304,;ADCK4,downstream_gene_variant,,ENST00000593544,; A ENST00000324464 Transcript missense_variant 1029/2443 727/1635 243/544 I/L Ata/Tta 1 -1 ADCK4 HGNC HGNC:19041 protein_coding YES CCDS12562.1 ENSP00000315118 Q96D53 UPI0000071B0F NM_024876.3 deleterious(0) 9/15 hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF22,Pfam_domain:PF03109,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 40703613 40703613 T A 1 0 0 0 0 1 0 0 0 334 1464 51 4 4 ADCK4 19 40703613 Missense_Mutation SNP T C3N-00547_T 1887989 40703613 17914003 601 14931 EGLN2 0 . GRCh38 19 40800796 40800796 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.224C>G p.Pro75Arg p.P75R ENST00000593726 1/5 155 143 12 129 129 0 strelka-varscan-mutect EGLN2,missense_variant,p.Pro75Arg,ENST00000593726,;EGLN2,missense_variant,p.Pro75Arg,ENST00000406058,NM_053046.3;EGLN2,missense_variant,p.Pro75Arg,ENST00000303961,NM_080732.3;EGLN2,missense_variant,p.Pro75Arg,ENST00000593972,;EGLN2,missense_variant,p.Pro75Arg,ENST00000593525,;EGLN2,missense_variant,p.Pro75Arg,ENST00000594380,;EGLN2,missense_variant,p.Pro75Arg,ENST00000598654,;EGLN2,missense_variant,p.Pro75Arg,ENST00000601733,;RAB4B,downstream_gene_variant,,ENST00000357052,NM_016154.4;EGLN2,upstream_gene_variant,,ENST00000594140,;EGLN2,downstream_gene_variant,,ENST00000596517,;EGLN2,downstream_gene_variant,,ENST00000593397,;EGLN2,upstream_gene_variant,,ENST00000597746,;CTC-490E21.14,upstream_gene_variant,,ENST00000595728,;RAB4B-EGLN2,downstream_gene_variant,,ENST00000601949,;RAB4B-EGLN2,3_prime_UTR_variant,,ENST00000594136,;EGLN2,upstream_gene_variant,,ENST00000599579,;EGLN2,upstream_gene_variant,,ENST00000593445,;RAB4B,downstream_gene_variant,,ENST00000597476,;RAB4B,downstream_gene_variant,,ENST00000598430,;RAB4B,downstream_gene_variant,,ENST00000378307,;RAB4B-EGLN2,downstream_gene_variant,,ENST00000596216,;CTC-490E21.12,upstream_gene_variant,,ENST00000601627,; G ENST00000593726 Transcript missense_variant 1252/2821 224/1224 75/407 P/R cCt/cGt 1 1 EGLN2 HGNC HGNC:14660 protein_coding YES CCDS12567.1 ENSP00000469686 Q96KS0 A0A024R0R2 UPI0000050C8F deleterious_low_confidence(0) 1/5 Low_complexity_(Seg):seg,hmmpanther:PTHR12907:SF6,hmmpanther:PTHR12907 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 40800796 40800796 C G 1 0 0 0 0 1 0 0 0 4805 681 24 4 4 EGLN2 19 40800796 Missense_Mutation SNP C C3N-00547_T 97183 40800796 17816820 602 14932 CIC 0 . GRCh38 19 42294688 42294688 + Missense_Mutation SNP G G T C3N-00547_T C3N-00547_N G G c.4412G>T p.Arg1471Leu p.R1471L ENST00000575354 19/20 560 318 242 454 454 0 strelka-varscan-mutect CIC,missense_variant,p.Arg2377Leu,ENST00000572681,NM_001304815.1;CIC,missense_variant,p.Arg1469Leu,ENST00000160740,;CIC,missense_variant,p.Arg1471Leu,ENST00000575354,NM_015125.4;CIC,missense_variant,p.Arg183Leu,ENST00000576505,;CIC,missense_variant,p.Arg198Leu,ENST00000573349,;PAFAH1B3,downstream_gene_variant,,ENST00000538771,NM_001145940.1,NM_001145939.1;PAFAH1B3,downstream_gene_variant,,ENST00000262890,NM_002573.3;PAFAH1B3,downstream_gene_variant,,ENST00000594989,;PAFAH1B3,downstream_gene_variant,,ENST00000595530,;PAFAH1B3,downstream_gene_variant,,ENST00000596265,;CIC,3_prime_UTR_variant,,ENST00000575287,;CIC,non_coding_transcript_exon_variant,,ENST00000571033,; T ENST00000575354 Transcript missense_variant 4452/5473 4412/4827 1471/1608 R/L cGg/cTg COSM3971029 1 1 CIC HGNC HGNC:14214 protein_coding YES CCDS12601.1 ENSP00000458663 Q96RK0 UPI000013C5A0 NM_015125.4 deleterious(0) 19/20 hmmpanther:PTHR13059 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 42294688 42294688 G T 1 0 0 0 0 1 0 0 0 3186 1116 39 1 1 CIC 19 42294688 Missense_Mutation SNP G C3N-00547_T 1493892 42294688 16322928 603 14933 PSG7 0 . GRCh38 19 42907123 42907123 + Nonsense_Mutation SNP C C A rs1065520 C3N-00547_T C3N-00547_N C C c.1039G>T p.Glu347Ter p.E347* ENST00000292125 5/6 200 171 29 214 214 0 varscan-mutect PSG6,stop_gained,p.Glu347Ter,ENST00000187910,NM_001031850.3;PSG7,stop_gained,p.Glu348Ter,ENST00000617049,;PSG6,stop_gained,p.Glu254Ter,ENST00000402603,;PSG6,stop_gained,p.Glu347Ter,ENST00000292125,NM_002782.4;PSG6,downstream_gene_variant,,ENST00000594375,;PSG6,3_prime_UTR_variant,,ENST00000599753,;PSG6,non_coding_transcript_exon_variant,,ENST00000595062,;PSG6,downstream_gene_variant,,ENST00000402456,;PSG6,downstream_gene_variant,,ENST00000484292,; A ENST00000292125 Transcript stop_gained 1084/1391 1039/1308 347/435 E/* Gaa/Taa rs1065520 1 -1 PSG6 HGNC HGNC:9523 protein_coding YES CCDS12613.1 ENSP00000292125 Q00889 UPI00001327A1 NM_002782.4 5/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS rs1065520 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 49 42907123 42907123 C A 1 0 0 0 0 0 1 0 0 12811 922 32 2 2 PSG7 19 42907123 Nonsense_Mutation SNP C C3N-00547_T 612435 42907123 15710493 604 14934 EXOC3L2 0 . GRCh38 19 45224852 45224852 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.1645T>A p.Ser549Thr p.S549T ENST00000413988 8/12 71 41 30 81 81 0 strelka-varscan-mutect EXOC3L2,missense_variant,p.Ser549Thr,ENST00000413988,;EXOC3L2,missense_variant,p.Ser156Thr,ENST00000252482,NM_138568.3;MARK4,intron_variant,,ENST00000587566,; T ENST00000413988 Transcript missense_variant 1752/2964 1645/2409 549/802 S/T Tct/Act 1 -1 EXOC3L2 Clone_based_vega_gene HGNC:30162 protein_coding YES ENSP00000400713 Q2M3D2 8/12 Pfam_domain:PF06046,hmmpanther:PTHR21292,hmmpanther:PTHR21292:SF7,Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 45224852 45224852 A T 1 0 0 0 0 1 0 0 0 5172 333 12 4 4 EXOC3L2 19 45224852 Missense_Mutation SNP A C3N-00547_T 2317729 45224852 13392764 605 14935 EML2 0 . GRCh38 19 45621244 45621244 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.1688A>C p.Gln563Pro p.Q563P ENST00000587152 14/22 108 99 9 115 114 1 strelka-mutect EML2,missense_variant,p.Gln509Pro,ENST00000536630,NM_001193269.1;EML2,missense_variant,p.Gln563Pro,ENST00000587152,NM_001193268.1;EML2,missense_variant,p.Gln362Pro,ENST00000589876,;EML2,missense_variant,p.Gln362Pro,ENST00000245925,NM_012155.2;EML2,missense_variant,p.Gln211Pro,ENST00000588496,;EML2,missense_variant,p.Gln103Pro,ENST00000590575,;EML2,missense_variant,p.Gln58Pro,ENST00000588272,;EML2,upstream_gene_variant,,ENST00000587484,;EML2,downstream_gene_variant,,ENST00000586902,;EML2,downstream_gene_variant,,ENST00000590580,;EML2,missense_variant,p.Gln520Pro,ENST00000399594,;EML2,missense_variant,p.Gln362Pro,ENST00000588308,;EML2,3_prime_UTR_variant,,ENST00000586195,;EML2,3_prime_UTR_variant,,ENST00000590819,;EML2,non_coding_transcript_exon_variant,,ENST00000588000,;EML2,non_coding_transcript_exon_variant,,ENST00000588610,;EML2,upstream_gene_variant,,ENST00000592482,;EML2,upstream_gene_variant,,ENST00000586405,;EML2,downstream_gene_variant,,ENST00000592853,; G ENST00000587152 Transcript missense_variant 1873/2763 1688/2553 563/850 Q/P cAg/cCg 1 -1 EML2 HGNC HGNC:18035 protein_coding YES CCDS59399.1 ENSP00000468312 O95834 UPI0001DD21BF NM_001193268.1 deleterious(0.01) 14/22 PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF32,Superfamily_domains:SSF50998 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 45621244 45621244 T G 1 0 0 0 0 1 0 0 0 4940 1580 55 5 5 EML2 19 45621244 Missense_Mutation SNP T C3N-00547_T 396392 45621244 12996372 606 14936 EML2 0 . GRCh38 19 45621278 45621278 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1654C>G p.Leu552Val p.L552V ENST00000587152 14/22 89 56 33 70 70 0 strelka-varscan-mutect EML2,missense_variant,p.Leu498Val,ENST00000536630,NM_001193269.1;EML2,missense_variant,p.Leu552Val,ENST00000587152,NM_001193268.1;EML2,missense_variant,p.Leu351Val,ENST00000589876,;EML2,missense_variant,p.Leu351Val,ENST00000245925,NM_012155.2;EML2,missense_variant,p.Leu200Val,ENST00000588496,;EML2,missense_variant,p.Leu92Val,ENST00000590575,;EML2,missense_variant,p.Leu47Val,ENST00000588272,;EML2,upstream_gene_variant,,ENST00000587484,;EML2,downstream_gene_variant,,ENST00000586902,;EML2,downstream_gene_variant,,ENST00000590580,;EML2,missense_variant,p.Leu509Val,ENST00000399594,;EML2,missense_variant,p.Leu351Val,ENST00000588308,;EML2,3_prime_UTR_variant,,ENST00000586195,;EML2,3_prime_UTR_variant,,ENST00000590819,;EML2,non_coding_transcript_exon_variant,,ENST00000588000,;EML2,non_coding_transcript_exon_variant,,ENST00000588610,;EML2,upstream_gene_variant,,ENST00000592482,;EML2,upstream_gene_variant,,ENST00000586405,;EML2,downstream_gene_variant,,ENST00000592853,; C ENST00000587152 Transcript missense_variant 1839/2763 1654/2553 552/850 L/V Ctg/Gtg 1 -1 EML2 HGNC HGNC:18035 protein_coding YES CCDS59399.1 ENSP00000468312 O95834 UPI0001DD21BF NM_001193268.1 tolerated(0.19) 14/22 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF32,Superfamily_domains:SSF50998 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 45621278 45621278 G C 1 0 0 0 0 1 0 0 0 4940 1020 36 4 4 EML2 19 45621278 Missense_Mutation SNP G C3N-00547_T 34 45621278 12996338 607 14937 DMWD 0 . GRCh38 19 45785703 45785703 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1793G>T p.Cys598Phe p.C598F ENST00000270223 3/5 85 52 33 99 99 0 strelka-varscan-mutect DMWD,missense_variant,p.Cys598Phe,ENST00000270223,NM_004943.1;DMWD,missense_variant,p.Cys598Phe,ENST00000377735,;DMWD,missense_variant,p.Cys70Phe,ENST00000602829,;AC011530.4,missense_variant,p.Cys4Phe,ENST00000596586,;AC011530.4,missense_variant,p.Cys4Phe,ENST00000595946,;DMPK,upstream_gene_variant,,ENST00000600757,NM_001288765.1;DMPK,upstream_gene_variant,,ENST00000291270,NM_004409.4,NM_001288764.1;DMPK,upstream_gene_variant,,ENST00000447742,NM_001081560.2;DMPK,upstream_gene_variant,,ENST00000458663,NM_001081562.2;DMPK,upstream_gene_variant,,ENST00000618091,;DMPK,upstream_gene_variant,,ENST00000354227,NM_001288766.1;DMWD,upstream_gene_variant,,ENST00000537879,;DMWD,downstream_gene_variant,,ENST00000598237,;DMWD,downstream_gene_variant,,ENST00000597053,;DMWD,downstream_gene_variant,,ENST00000601370,;AC011530.4,missense_variant,p.Cys91Phe,ENST00000593999,;AC011530.4,missense_variant,p.Cys4Phe,ENST00000597712,;DMPK,upstream_gene_variant,,ENST00000588522,;DMWD,downstream_gene_variant,,ENST00000602469,; A ENST00000270223 Transcript missense_variant 1839/3305 1793/2025 598/674 C/F tGc/tTc 1 -1 DMWD HGNC HGNC:2936 protein_coding YES CCDS33054.1 ENSP00000270223 Q09019 UPI000040C0B4 NM_004943.1 deleterious(0.01) 3/5 hmmpanther:PTHR14107:SF15,hmmpanther:PTHR14107,Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 45785703 45785703 C A 1 0 0 0 0 1 0 0 0 4402 710 25 2 2 DMWD 19 45785703 Missense_Mutation SNP C C3N-00547_T 164425 45785703 12831913 608 14938 KCNJ14 0 . GRCh38 19 48462225 48462225 + Silent SNP G G C novel C3N-00547_T C3N-00547_N G G c.501G>C p.= p.V167V ENST00000391884 1/2 137 127 10 153 153 0 strelka-varscan-mutect KCNJ14,synonymous_variant,p.=,ENST00000391884,;KCNJ14,synonymous_variant,p.=,ENST00000342291,NM_013348.3;CTC-273B12.7,upstream_gene_variant,,ENST00000595676,;CTC-273B12.5,downstream_gene_variant,,ENST00000600650,;CTC-273B12.5,downstream_gene_variant,,ENST00000600529,;CTC-273B12.5,downstream_gene_variant,,ENST00000593476,;CTC-273B12.5,downstream_gene_variant,,ENST00000596497,; C ENST00000391884 Transcript synonymous_variant 977/3990 501/1311 167/436 V gtG/gtC 1 1 KCNJ14 HGNC HGNC:6260 protein_coding YES CCDS12721.1 ENSP00000375756 Q9UNX9 UPI000003E7B4 1/2 Gene3D:1.10.287.70,Pfam_domain:PF01007,PIRSF_domain:PIRSF005465,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF40,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -18.96847 1 1 1 1 0 C 2 2 49 48462225 48462225 G C 1 0 0 0 0 0 0 0 1 7964 1306 46 4 4 KCNJ14 19 48462225 Silent SNP G C3N-00547_T 2676522 48462225 10155391 609 14939 SLC6A16 0 . GRCh38 19 49290351 49290351 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.1983C>T p.= p.L661L ENST00000335875 12/12 136 124 12 126 126 0 strelka-varscan-mutect SLC6A16,synonymous_variant,p.=,ENST00000335875,NM_014037.2;SLC6A16,3_prime_UTR_variant,,ENST00000454748,;SLC6A16,downstream_gene_variant,,ENST00000598828,;SLC6A16,downstream_gene_variant,,ENST00000598221,; A ENST00000335875 Transcript synonymous_variant 2225/2938 1983/2211 661/736 L ctC/ctT 1 -1 SLC6A16 HGNC HGNC:13622 protein_coding YES CCDS42590.1 ENSP00000338627 Q9GZN6 UPI00001305CE NM_014037.2 12/12 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF113,Pfam_domain:PF00209,Superfamily_domains:0053687 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 49290351 49290351 G A 1 0 0 0 0 0 0 0 1 14962 929 33 3 3 SLC6A16 19 49290351 Silent SNP G C3N-00547_T 828126 49290351 9327265 610 14940 SLC6A16 0 . GRCh38 19 49290377 49290377 + Missense_Mutation SNP G G C rs774455736 C3N-00547_T C3N-00547_N G G c.1957C>G p.Arg653Gly p.R653G ENST00000335875 12/12 79 72 7 98 98 0 strelka-varscan-mutect SLC6A16,missense_variant,p.Arg653Gly,ENST00000335875,NM_014037.2;SLC6A16,3_prime_UTR_variant,,ENST00000454748,;SLC6A16,downstream_gene_variant,,ENST00000598828,;SLC6A16,downstream_gene_variant,,ENST00000598221,; C ENST00000335875 Transcript missense_variant 2199/2938 1957/2211 653/736 R/G Cga/Gga rs774455736 1 -1 SLC6A16 HGNC HGNC:13622 protein_coding YES CCDS42590.1 ENSP00000338627 Q9GZN6 UPI00001305CE NM_014037.2 deleterious(0) 12/12 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF113,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 5 1 PASS rs774455736 . 0 207 3 0 0 0 0 0 -15.41067 1 1 1 1 0 C 3 2 49 49290377 49290377 G C 1 0 0 0 0 1 0 0 0 14962 1066 37 4 4 SLC6A16 19 49290377 Missense_Mutation SNP G C3N-00547_T 26 49290377 9327239 611 14941 CPT1C 0 . GRCh38 19 49692392 49692392 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.140G>C p.Trp47Ser p.W47S ENST00000392518 3/20 143 121 22 164 164 0 strelka-varscan-mutect CPT1C,missense_variant,p.Trp47Ser,ENST00000392518,NM_001199752.2;CPT1C,missense_variant,p.Trp47Ser,ENST00000405931,NM_001136052.2;CPT1C,missense_variant,p.Trp47Ser,ENST00000323446,NM_152359.2;CPT1C,missense_variant,p.Trp47Ser,ENST00000598293,NM_001199753.1;CPT1C,missense_variant,p.Trp47Ser,ENST00000598396,;CPT1C,missense_variant,p.Trp47Ser,ENST00000594587,;CPT1C,missense_variant,p.Trp47Ser,ENST00000602019,;CPT1C,missense_variant,p.Trp47Ser,ENST00000595969,;ADM5,downstream_gene_variant,,ENST00000420022,NM_001101340.1;PRMT1,downstream_gene_variant,,ENST00000532489,;PRMT1,downstream_gene_variant,,ENST00000391851,NM_198318.4;PRMT1,downstream_gene_variant,,ENST00000454376,NM_001536.5;PRMT1,downstream_gene_variant,,ENST00000610806,NM_001207042.2;CTB-33G10.6,upstream_gene_variant,,ENST00000596472,;CPT1C,splice_region_variant,,ENST00000598714,;PRMT1,downstream_gene_variant,,ENST00000527866,;PRMT1,downstream_gene_variant,,ENST00000530361,;CPT1C,missense_variant,p.Trp47Ser,ENST00000598259,;CPT1C,missense_variant,p.Trp47Ser,ENST00000595568,;CPT1C,missense_variant,p.Trp47Ser,ENST00000596922,;CPT1C,missense_variant,p.Trp47Ser,ENST00000594038,;CPT1C,splice_region_variant,,ENST00000599023,;CPT1C,splice_region_variant,,ENST00000295404,;CPT1C,splice_region_variant,,ENST00000600944,; C ENST00000392518 Transcript missense_variant,splice_region_variant 512/2910 140/2412 47/803 W/S tGg/tCg 1 1 CPT1C HGNC HGNC:18540 protein_coding YES CCDS12779.1 ENSP00000376303 Q8TCG5 A0A024QZE3 UPI0000071C78 NM_001199752.2 tolerated(0.06) 3/20 Pfam_domain:PF16484 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 49692392 49692392 G C 1 0 0 0 0 1 0 0 0 3630 1362 47 4 4 CPT1C 19 49692392 Missense_Mutation SNP G C3N-00547_T 402015 49692392 8925224 612 14942 CEACAM18 0 . GRCh38 19 51483066 51483066 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.723C>A p.= p.G241G ENST00000396477 4/6 195 154 41 159 159 0 strelka-varscan-mutect CEACAM18,synonymous_variant,p.=,ENST00000396477,NM_001278392.1; A ENST00000396477 Transcript synonymous_variant 744/1476 723/1155 241/384 G ggC/ggA 1 1 CEACAM18 HGNC HGNC:31949 protein_coding YES ENSP00000379738 A8MTB9 UPI0002C5E52C NM_001278392.1 4/6 PROSITE_profiles:PS50835,SMART_domains:SM00409 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 51483066 51483066 C A 1 0 0 0 0 0 0 0 1 2895 697 25 2 2 CEACAM18 19 51483066 Silent SNP C C3N-00547_T 1790674 51483066 7134550 613 14943 AC018755.18 0 . GRCh38 19 51629387 51629387 + Missense_Mutation SNP G G T rs756476592 C3N-00547_T C3N-00547_N G G c.671C>A p.Thr224Lys p.T224K ENST00000534261 4/10 272 171 101 348 348 0 strelka-varscan-mutect SIGLEC5,missense_variant,p.Thr224Lys,ENST00000534261,NM_003830.3;AC018755.18,missense_variant,p.Thr224Lys,ENST00000429354,;AC018755.18,missense_variant,p.Thr224Lys,ENST00000599649,; T ENST00000534261 Transcript missense_variant 1071/2360 671/1656 224/551 T/K aCg/aAg rs756476592 1 -1 SIGLEC5 HGNC HGNC:10874 protein_coding YES CCDS33088.1 ENSP00000473238 O15389 UPI000011B40C NM_003830.3 deleterious(0.01) 4/10 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF67,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs756476592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 51629387 51629387 G T 1 0 0 0 0 1 0 0 0 125 1145 40 1 1 AC018755.18 19 51629387 Missense_Mutation SNP G C3N-00547_T 146321 51629387 6988229 614 14944 ZNF578 0 . GRCh38 19 52511237 52511237 + Missense_Mutation SNP C C T C3N-00547_T C3N-00547_N C C c.856C>T p.Pro286Ser p.P286S ENST00000421239 6/6 327 205 122 350 350 0 strelka-varscan-mutect ZNF578,missense_variant,p.Pro286Ser,ENST00000421239,NM_001099694.1;ZNF578,downstream_gene_variant,,ENST00000601120,;CTD-3099C6.5,downstream_gene_variant,,ENST00000599143,; T ENST00000421239 Transcript missense_variant 1100/2017 856/1773 286/590 P/S Cct/Tct COSM4818091 1 1 ZNF578 HGNC HGNC:26449 protein_coding YES CCDS54310.1 ENSP00000459216 Q96N58 UPI000048A457 NM_001099694.1 deleterious(0.04) 6/6 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 52511237 52511237 C T 1 0 0 0 0 1 0 0 0 18584 507 18 3 3 ZNF578 19 52511237 Missense_Mutation SNP C C3N-00547_T 881850 52511237 6106379 615 14945 ERVV-2 0 . GRCh38 19 53049712 53049712 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.461C>A p.Ser154Tyr p.S154Y ENST00000601417 2/2 107 67 40 113 113 0 strelka-varscan-mutect ERVV-2,missense_variant,p.Ser154Tyr,ENST00000601417,NM_001191055.1; A ENST00000601417 Transcript missense_variant 1067/2431 461/1608 154/535 S/Y tCc/tAc 1 1 ERVV-2 HGNC HGNC:39051 protein_coding YES CCDS59420.1 ENSP00000472919 B6SEH9 M9QSX5 UPI00018258B9 NM_001191055.1 deleterious(0.01) 2/2 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424 MODERATE 1 SNV 4 1 PASS rs962478613 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 53049712 53049712 C A 1 0 0 0 0 1 0 0 0 5107 855 30 2 2 ERVV-2 19 53049712 Missense_Mutation SNP C C3N-00547_T 538475 53049712 5567904 616 14946 ZNF415 0 . GRCh38 19 53108398 53108398 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.1647G>A p.= p.E549E ENST00000500065 4/4 86 79 7 77 77 0 strelka-varscan-mutect ZNF415,synonymous_variant,p.=,ENST00000500065,NM_001136038.2;ZNF415,synonymous_variant,p.=,ENST00000421033,NM_001164309.1;ZNF415,synonymous_variant,p.=,ENST00000243643,NM_018355.3;ZNF415,synonymous_variant,p.=,ENST00000601493,;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF160,upstream_gene_variant,,ENST00000429604,NM_001322132.1,NM_001322129.1,NM_001322138.1,NM_001322134.1,NM_001322131.1,NM_001322133.1,NM_198893.2,NM_001102603.1;ZNF160,upstream_gene_variant,,ENST00000418871,NM_001322135.1,NM_001322128.1,NM_001322138.1,NM_001322136.1,NM_033288.3;ZNF160,upstream_gene_variant,,ENST00000355147,NM_001322126.1;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF160,upstream_gene_variant,,ENST00000599637,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF160,upstream_gene_variant,,ENST00000596966,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF160,upstream_gene_variant,,ENST00000596388,;ZNF160,upstream_gene_variant,,ENST00000594760,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,;ZNF160,upstream_gene_variant,,ENST00000597112,;ZNF160,upstream_gene_variant,,ENST00000600924,; T ENST00000500065 Transcript synonymous_variant 1981/2496 1647/1668 549/555 E gaG/gaA 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW SNV 4 1 PASS . . 0 207 2 0 0 0 0 0 -15.28502 1 1 1 1 0 T 2 4 49 53108398 53108398 C T 1 0 0 0 0 0 0 0 1 18464 912 32 3 3 ZNF415 19 53108398 Silent SNP C C3N-00547_T 58686 53108398 5509218 617 14947 ZNF415 0 . GRCh38 19 53116430 53116430 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.19A>T p.Thr7Ser p.T7S ENST00000500065 3/4 183 108 75 188 188 0 strelka-varscan-mutect ZNF415,missense_variant,p.Thr7Ser,ENST00000594011,;ZNF415,missense_variant,p.Thr7Ser,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Thr7Ser,ENST00000595193,;ZNF415,missense_variant,p.Thr7Ser,ENST00000597503,;ZNF415,missense_variant,p.Thr7Ser,ENST00000597748,;ZNF415,missense_variant,p.Thr7Ser,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Thr7Ser,ENST00000243643,NM_018355.3;ZNF415,missense_variant,p.Thr7Ser,ENST00000599261,;ZNF415,missense_variant,p.Thr7Ser,ENST00000601110,;ZNF415,missense_variant,p.Thr7Ser,ENST00000595813,;ZNF415,missense_variant,p.Thr7Ser,ENST00000600574,;ZNF415,missense_variant,p.Thr53Ser,ENST00000595174,;ZNF415,missense_variant,p.Thr7Ser,ENST00000596051,;ZNF415,intron_variant,,ENST00000601493,;ZNF415,intron_variant,,ENST00000601215,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596683,;ZNF415,non_coding_transcript_exon_variant,,ENST00000602110,;ZNF415,non_coding_transcript_exon_variant,,ENST00000596106,;ZNF415,non_coding_transcript_exon_variant,,ENST00000594286,;ZNF415,intron_variant,,ENST00000595359,;ZNF415,intron_variant,,ENST00000602024,;ZNF415,stop_lost,p.Ter104CysextTer17,ENST00000597877,;ZNF415,missense_variant,p.Thr7Ser,ENST00000600120,;ZNF415,missense_variant,p.Thr7Ser,ENST00000598578,;ZNF415,missense_variant,p.Thr7Ser,ENST00000598024,;ZNF415,non_coding_transcript_exon_variant,,ENST00000600098,; A ENST00000500065 Transcript missense_variant 353/2496 19/1668 7/555 T/S Aca/Tca 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 deleterious(0.03) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF145,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 53116430 53116430 T A 1 0 0 0 0 1 0 0 0 18464 1681 58 4 4 ZNF415 19 53116430 Missense_Mutation SNP T C3N-00547_T 8032 53116430 5501186 618 14948 KIR3DX1 0 . GRCh38 19 54535744 54535744 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.508G>T p.Glu170Ter p.E170* ENST00000221567 4/9 421 395 26 352 352 0 strelka-varscan-mutect KIR3DX1,stop_gained,p.Glu170Ter,ENST00000610811,;KIR3DX1,non_coding_transcript_exon_variant,,ENST00000611588,;KIR3DX1,stop_gained,p.Glu170Ter,ENST00000221567,;KIR3DX1,intron_variant,,ENST00000613375,;KIR3DX1,intron_variant,,ENST00000612759,;KIR3DX1,intron_variant,,ENST00000446586,;KIR3DX1,intron_variant,,ENST00000447145,;KIR3DX1,intron_variant,,ENST00000434659,; T ENST00000221567 Transcript stop_gained,NMD_transcript_variant 515/1378 508/1059 170/352 E/* Gag/Tag 1 1 KIR3DX1 HGNC HGNC:25043 nonsense_mediated_decay YES ENSP00000221567 Q9H7L2 UPI0000DE238B 4/9 hmmpanther:PTHR11738:SF113,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 54535744 54535744 G T 1 0 0 0 0 0 1 0 0 8187 1175 41 2 2 KIR3DX1 19 54535744 Nonsense_Mutation SNP G C3N-00547_T 1419314 54535744 4081872 619 14949 KIR3DL2 0 . GRCh38 19 54866721 54866721 + Missense_Mutation SNP G G A novel C3N-00547_T C3N-00547_N G G c.1358G>A p.Gly453Glu p.G453E ENST00000326321 9/9 152 99 53 187 187 0 strelka-varscan-mutect KIR3DL2,missense_variant,p.Gly453Glu,ENST00000326321,NM_006737.3;KIR3DL1,missense_variant,p.Gly453Glu,ENST00000402254,;KIR3DL2,missense_variant,p.Gly436Glu,ENST00000270442,NM_001242867.1;RNU6-222P,downstream_gene_variant,,ENST00000362438,; A ENST00000326321 Transcript missense_variant 1391/1877 1358/1368 453/455 G/E gGg/gAg 1 1 KIR3DL2 HGNC HGNC:6339 protein_coding YES CCDS12906.1 ENSP00000325525 P43630 A0A0U1WNF3 UPI000012DB25 NM_006737.3 deleterious_low_confidence(0) 9/9 MODERATE 1 SNV 1 1 PASS rs1446401991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 54866721 54866721 G A 1 0 0 0 0 1 0 0 0 8185 1232 43 3 3 KIR3DL2 19 54866721 Missense_Mutation SNP G C3N-00547_T 330977 54866721 3750895 620 14950 NLRP7 0 . GRCh38 19 54923775 54923775 + Missense_Mutation SNP C C G novel C3N-00547_T C3N-00547_N C C c.3079G>C p.Ala1027Pro p.A1027P ENST00000588756 13/13 580 384 196 552 552 0 strelka-varscan-mutect NLRP7,missense_variant,p.Ala1027Pro,ENST00000588756,;NLRP7,missense_variant,p.Ala999Pro,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Ala1027Pro,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Ala970Pro,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Ala970Pro,ENST00000590030,;NLRP7,3_prime_UTR_variant,,ENST00000586379,; G ENST00000588756 Transcript missense_variant 3566/3826 3079/3114 1027/1037 A/P Gca/Cca 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 tolerated(0.35) 13/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 54923775 54923775 C G 1 0 0 0 0 1 0 0 0 10520 739 26 4 4 NLRP7 19 54923775 Missense_Mutation SNP C C3N-00547_T 57054 54923775 3693841 621 14951 NLRP7 0 . GRCh38 19 54934489 54934489 + Nonsense_Mutation SNP G G T rs372546461 C3N-00547_T C3N-00547_N G G c.2471C>A p.Ser824Ter p.S824* ENST00000588756 9/13 372 308 64 318 318 0 strelka-varscan-mutect NLRP7,stop_gained,p.Ser824Ter,ENST00000588756,;NLRP7,stop_gained,p.Ser796Ter,ENST00000328092,NM_139176.3;NLRP7,stop_gained,p.Ser824Ter,ENST00000592784,NM_001127255.1;NLRP7,stop_gained,p.Ser824Ter,ENST00000340844,NM_206828.3;NLRP7,stop_gained,p.Ser824Ter,ENST00000590030,;NLRP7,stop_gained,p.Ser824Ter,ENST00000586379,; T ENST00000588756 Transcript stop_gained,splice_region_variant 2958/3826 2471/3114 824/1037 S/* tCg/tAg rs372546461 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 9/13 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS rs372546461 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 54934489 54934489 G T 1 0 0 0 0 0 1 0 0 10520 1072 37 1 1 NLRP7 19 54934489 Nonsense_Mutation SNP G C3N-00547_T 10714 54934489 3683127 622 14952 NLRP2 0 . GRCh38 19 54970138 54970138 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.123G>C p.Lys41Asn p.K41N ENST00000543010 2/13 658 415 243 651 651 0 strelka-varscan-mutect NLRP2,missense_variant,p.Lys41Asn,ENST00000543010,NM_001174081.1;NLRP2,missense_variant,p.Lys41Asn,ENST00000448584,NM_017852.3;NLRP2,missense_variant,p.Lys41Asn,ENST00000537859,NM_001174082.1;NLRP2,missense_variant,p.Lys41Asn,ENST00000263437,;NLRP2,missense_variant,p.Lys41Asn,ENST00000339757,;NLRP2,missense_variant,p.Lys41Asn,ENST00000391721,;NLRP2,missense_variant,p.Lys41Asn,ENST00000427260,NM_001174083.1;NLRP2,missense_variant,p.Lys41Asn,ENST00000588619,;NLRP2,missense_variant,p.Lys41Asn,ENST00000588107,;NLRP2,missense_variant,p.Lys41Asn,ENST00000433772,;NLRP2,intron_variant,,ENST00000585500,;NLRP7,upstream_gene_variant,,ENST00000588756,;NLRP7,upstream_gene_variant,,ENST00000590659,;NLRP7,upstream_gene_variant,,ENST00000587103,;NLRP2,upstream_gene_variant,,ENST00000397169,;NLRP7,upstream_gene_variant,,ENST00000587844,;NLRP2,missense_variant,p.Lys41Asn,ENST00000539848,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;CTC-550B14.1,upstream_gene_variant,,ENST00000466725,; C ENST00000543010 Transcript missense_variant 266/3576 123/3189 41/1062 K/N aaG/aaC 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 deleterious(0.05) 2/13 PROSITE_profiles:PS50824,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF129,Gene3D:1.10.533.10,Pfam_domain:PF02758,SMART_domains:SM01289,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 54970138 54970138 G C 1 0 0 0 0 1 0 0 0 10514 933 33 4 4 NLRP2 19 54970138 Missense_Mutation SNP G C3N-00547_T 35649 54970138 3647478 623 14953 NLRP8 0 . GRCh38 19 55948115 55948115 + Silent SNP C C T rs761430783 C3N-00547_T C3N-00547_N C C c.213C>T p.= p.I71I ENST00000291971 1/10 318 290 28 345 345 0 strelka-varscan-mutect NLRP8,synonymous_variant,p.=,ENST00000291971,NM_176811.2;NLRP8,synonymous_variant,p.=,ENST00000590542,; T ENST00000291971 Transcript synonymous_variant 284/3934 213/3147 71/1048 I atC/atT rs761430783 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 1/10 PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF54,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Pfam_domain:PF02758,SMART_domains:SM01289,Superfamily_domains:SSF47986 LOW 1 SNV 2 1 PASS rs761430783 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 55948115 55948115 C T 1 0 0 0 0 0 0 0 1 10521 816 29 3 3 NLRP8 19 55948115 Silent SNP C C3N-00547_T 977977 55948115 2669501 624 14954 ZNF470 0 . GRCh38 19 56576892 56576892 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.463C>A p.His155Asn p.H155N ENST00000330619 6/6 32 18 14 36 36 0 strelka-varscan-mutect ZNF470,missense_variant,p.His155Asn,ENST00000330619,NM_001001668.3;ZNF470,missense_variant,p.His155Asn,ENST00000391709,;ZNF470,intron_variant,,ENST00000601902,;ZNF470,intron_variant,,ENST00000594953,;ZNF470,intron_variant,,ENST00000601059,; A ENST00000330619 Transcript missense_variant 1149/7151 463/2154 155/717 H/N Cat/Aat 1 1 ZNF470 HGNC HGNC:22220 protein_coding YES CCDS33122.1 ENSP00000333223 Q6ECI4 UPI0000D61826 NM_001001668.3 tolerated(0.33) 6/6 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF282 MODERATE 1 SNV 1 1 PASS . . 3 202 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 56576892 56576892 C A 1 0 0 0 0 1 0 0 0 18501 478 17 2 2 ZNF470 19 56576892 Missense_Mutation SNP C C3N-00547_T 628777 56576892 2040724 625 14955 SMIM17 0 . GRCh38 19 56645748 56645748 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.81G>T p.= p.R27R ENST00000598409 2/4 179 104 75 173 173 0 strelka-varscan-mutect SMIM17,synonymous_variant,p.=,ENST00000598409,NM_001193628.1;SMIM17,synonymous_variant,p.=,ENST00000600547,; T ENST00000598409 Transcript synonymous_variant 247/1076 81/357 27/118 R cgG/cgT 1 1 SMIM17 HGNC HGNC:27114 protein_coding YES CCDS58683.1 ENSP00000471126 P0DL12 UPI000016107D NM_001193628.1 2/4 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 56645748 56645748 G T 1 0 0 0 0 0 0 0 1 15104 1219 43 2 2 SMIM17 19 56645748 Silent SNP G C3N-00547_T 68856 56645748 1971868 626 14956 ZNF543 0 . GRCh38 19 57328707 57328707 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1245G>T p.= p.R415R ENST00000321545 4/4 243 149 94 265 265 0 strelka-varscan-mutect ZNF543,synonymous_variant,p.=,ENST00000321545,NM_213598.3; T ENST00000321545 Transcript synonymous_variant 1590/3659 1245/1803 415/600 R cgG/cgT 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 57328707 57328707 G T 1 0 0 0 0 0 0 0 1 18550 1161 41 2 2 ZNF543 19 57328707 Silent SNP G C3N-00547_T 682959 57328707 1288909 627 14957 ZNF17 0 . GRCh38 19 57420932 57420932 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1440G>T p.= p.V480V ENST00000601808 3/3 146 117 29 150 150 0 strelka-varscan-mutect ZNF17,synonymous_variant,p.=,ENST00000307658,;ZNF17,synonymous_variant,p.=,ENST00000601808,NM_006959.2;AC004076.7,intron_variant,,ENST00000597410,;AC003002.6,downstream_gene_variant,,ENST00000596400,;AC003002.6,downstream_gene_variant,,ENST00000596617,;ZNF17,downstream_gene_variant,,ENST00000597350,;ZNF17,downstream_gene_variant,,ENST00000595206,;ZNF17,downstream_gene_variant,,ENST00000599867,;ZNF17,non_coding_transcript_exon_variant,,ENST00000602050,;ZNF17,downstream_gene_variant,,ENST00000595162,; T ENST00000601808 Transcript synonymous_variant 1653/2524 1440/1989 480/662 V gtG/gtT 1 1 ZNF17 HGNC HGNC:12958 protein_coding YES CCDS42636.1 ENSP00000471905 P17021 UPI00001D8198 NM_006959.2 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF166,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 57420932 57420932 G T 1 0 0 0 0 0 0 0 1 18323 1335 47 2 2 ZNF17 19 57420932 Silent SNP G C3N-00547_T 92225 57420932 1196684 628 14958 ZNF419 0 . GRCh38 19 57491559 57491559 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.164A>T p.Asn55Ile p.N55I ENST00000424930 3/5 177 156 21 167 167 0 varscan-mutect ZNF419,missense_variant,p.Asn55Ile,ENST00000347466,NM_001098494.1,NM_001291743.1;ZNF419,missense_variant,p.Asn55Ile,ENST00000424930,NM_001098491.1;ZNF419,missense_variant,p.Asn42Ile,ENST00000426954,NM_001098492.1;ZNF419,missense_variant,p.Asn54Ile,ENST00000221735,NM_024691.3;ZNF419,missense_variant,p.Asn41Ile,ENST00000415379,NM_001098496.1,NM_001098495.1;ZNF419,missense_variant,p.Asn41Ile,ENST00000442920,NM_001098493.1;ZNF419,missense_variant,p.Asn42Ile,ENST00000354197,;ZNF419,missense_variant,p.Asn31Ile,ENST00000618093,;ZNF419,missense_variant,p.Asn55Ile,ENST00000518999,;ZNF419,missense_variant,p.Asn54Ile,ENST00000521137,;ZNF419,missense_variant,p.Asn55Ile,ENST00000523882,;ZNF419,missense_variant,p.Asn41Ile,ENST00000523312,;ZNF419,missense_variant,p.Asn42Ile,ENST00000520540,;ZNF419,missense_variant,p.Asn42Ile,ENST00000521754,;ZNF419,missense_variant,p.Asn54Ile,ENST00000523138,;ZNF419,5_prime_UTR_variant,,ENST00000519310,;AC003005.4,missense_variant,p.Asn41Ile,ENST00000601674,;AC003005.4,missense_variant,p.Asn41Ile,ENST00000599674,;ZNF419,non_coding_transcript_exon_variant,,ENST00000522346,;ZNF419,non_coding_transcript_exon_variant,,ENST00000523439,; T ENST00000424930 Transcript missense_variant 393/2323 164/1536 55/511 N/I aAt/aTt 1 1 ZNF419 HGNC HGNC:20648 protein_coding YES CCDS54325.1 ENSP00000388864 Q96HQ0 UPI0000E04CBA NM_001098491.1 deleterious(0) 3/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24387:SF195,hmmpanther:PTHR24387,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 57491559 57491559 A T 1 0 0 0 0 1 0 0 0 18468 101 4 4 4 ZNF419 19 57491559 Missense_Mutation SNP A C3N-00547_T 70627 57491559 1126057 629 14959 ZSCAN1 0 . GRCh38 19 58040469 58040469 + Silent SNP G G T rs143428215 C3N-00547_T C3N-00547_N G G c.390G>T p.= p.S130S ENST00000282326 4/6 178 156 22 173 173 0 strelka-varscan-mutect ZSCAN1,synonymous_variant,p.=,ENST00000282326,NM_182572.3;ZSCAN1,downstream_gene_variant,,ENST00000391700,;ZSCAN1,downstream_gene_variant,,ENST00000601162,;LETM1P2,upstream_gene_variant,,ENST00000597330,; T ENST00000282326 Transcript synonymous_variant 637/2054 390/1227 130/408 S tcG/tcT rs143428215 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 4/6 hmmpanther:PTHR10032:SF187,hmmpanther:PTHR10032,SMART_domains:SM00431 LOW 1 SNV 2 1 PASS rs143428215 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 49 58040469 58040469 G T 1 0 0 0 0 0 0 0 1 18820 1103 39 1 1 ZSCAN1 19 58040469 Silent SNP G C3N-00547_T 548910 58040469 577147 630 14960 TGM3 0 . GRCh38 20 2339967 2339967 + Silent SNP G G T rs144898218 C3N-00547_T C3N-00547_N G G c.1914G>T p.= p.L638L ENST00000381458 12/13 240 204 36 182 182 0 strelka-mutect TGM3,synonymous_variant,p.=,ENST00000381458,NM_003245.3; T ENST00000381458 Transcript synonymous_variant 1977/2642 1914/2082 638/693 L ctG/ctT rs144898218 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 12/13 Gene3D:2.60.40.10,Pfam_domain:PF00927,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS rs144898218 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 2339967 2339967 G T 1 0 0 0 0 0 0 0 1 16264 1364 48 2 2 TGM3 20 2339967 Silent SNP G C3N-00547_T 2339967 62104200 631 14961 TGM6 0 . GRCh38 20 2403721 2403721 + Missense_Mutation SNP C C A rs200536588 C3N-00547_T C3N-00547_N C C c.1234C>A p.Arg412Ser p.R412S ENST00000202625 9/13 731 629 102 600 600 0 strelka-varscan-mutect TGM6,missense_variant,p.Arg412Ser,ENST00000202625,NM_198994.2;TGM6,missense_variant,p.Arg412Ser,ENST00000381423,NM_001254734.1;TGM6,downstream_gene_variant,,ENST00000477505,; A ENST00000202625 Transcript missense_variant 1295/2292 1234/2121 412/706 R/S Cgt/Agt rs200536588,COSM4136783 1 1 TGM6 HGNC HGNC:16255 protein_coding YES CCDS13025.1 ENSP00000202625 O95932 UPI0000367011 NM_198994.2 deleterious(0) 9/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF50,PIRSF_domain:PIRSF000459,Gene3D:1ex0A02,Superfamily_domains:SSF54001 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200536588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 2403721 2403721 C A 1 0 0 0 0 1 0 0 0 16267 768 27 1 1 TGM6 20 2403721 Missense_Mutation SNP C C3N-00547_T 63754 2403721 62040446 632 14962 AL031664.1 0 . GRCh38 20 17494634 17494634 + Missense_Mutation SNP C C T rs767136257 C3N-00547_T C3N-00547_N C C c.1438G>A p.Val480Met p.V480M ENST00000377873 8/8 216 192 24 181 181 0 strelka-varscan-mutect BFSP1,missense_variant,p.Val480Met,ENST00000377873,NM_001195.4;BFSP1,missense_variant,p.Val355Met,ENST00000377868,NM_001161705.1,NM_001278607.1;AL031664.1,missense_variant,p.Val341Met,ENST00000536626,NM_001278606.1,NM_001278608.1; T ENST00000377873 Transcript missense_variant 1478/2207 1438/1998 480/665 V/M Gtg/Atg rs767136257,COSM1740669,COSM1740670 1 -1 BFSP1 HGNC HGNC:1040 protein_coding YES CCDS13126.1 ENSP00000367104 Q12934 UPI00001268C7 NM_001195.4 tolerated(0.11) 8/8 hmmpanther:PTHR14069,hmmpanther:PTHR14069:SF0 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs767136257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 17494634 17494634 C T 1 0 0 0 0 1 0 0 0 568 536 19 1 1 AL031664.1 20 17494634 Missense_Mutation SNP C C3N-00547_T 15090913 17494634 46949533 633 14963 SNX5 0 . GRCh38 20 17956940 17956940 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.149A>C p.His50Pro p.H50P ENST00000377768 3/14 169 99 70 107 107 0 strelka-varscan-mutect SNX5,missense_variant,p.His50Pro,ENST00000377768,NM_152227.2,NM_001282454.1;SNX5,missense_variant,p.His50Pro,ENST00000377759,NM_014426.3;SNX5,missense_variant,p.His50Pro,ENST00000431277,;SNX5,intron_variant,,ENST00000419004,;SNX5,non_coding_transcript_exon_variant,,ENST00000483485,;SNX5,non_coding_transcript_exon_variant,,ENST00000490175,;SNX5,non_coding_transcript_exon_variant,,ENST00000475716,;SNX5,non_coding_transcript_exon_variant,,ENST00000469704,;SNX5,non_coding_transcript_exon_variant,,ENST00000474883,;SNX5,non_coding_transcript_exon_variant,,ENST00000494401,;SNX5,upstream_gene_variant,,ENST00000476648,;OVOL2,downstream_gene_variant,,ENST00000486776,; G ENST00000377768 Transcript missense_variant 462/2288 149/1215 50/404 H/P cAc/cCc 1 -1 SNX5 HGNC HGNC:14969 protein_coding YES CCDS13130.1 ENSP00000366998 Q9Y5X3 UPI0000135B43 NM_152227.2,NM_001282454.1 deleterious(0) 3/14 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PIRSF_domain:PIRSF036924,PROSITE_profiles:PS50195,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF6,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 17956940 17956940 T G 1 0 0 0 0 1 0 0 0 15226 1696 59 5 5 SNX5 20 17956940 Missense_Mutation SNP T C3N-00547_T 462306 17956940 46487227 634 14964 CFAP61 0 . GRCh38 20 20263049 20263049 + Missense_Mutation SNP T T G novel C3N-00547_T C3N-00547_N T T c.2422T>G p.Cys808Gly p.C808G ENST00000245957 21/27 180 165 15 178 178 0 strelka-varscan-mutect CFAP61,missense_variant,p.Cys808Gly,ENST00000245957,NM_015585.3;CFAP61,missense_variant,p.Cys164Gly,ENST00000377293,;CFAP61,missense_variant,p.Cys164Gly,ENST00000389656,;RP5-1096J16.1,intron_variant,,ENST00000460400,;CFAP61,non_coding_transcript_exon_variant,,ENST00000488640,;CFAP61,missense_variant,p.Cys164Gly,ENST00000377308,; G ENST00000245957 Transcript missense_variant 2498/4082 2422/3714 808/1237 C/G Tgc/Ggc 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 tolerated(0.11) 21/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 20263049 20263049 T G 1 0 0 0 0 1 0 0 0 3028 1812 63 5 5 CFAP61 20 20263049 Missense_Mutation SNP T C3N-00547_T 2306109 20263049 44181118 635 14965 XRN2 0 . GRCh38 20 21330536 21330536 + Silent SNP A A T novel C3N-00547_T C3N-00547_N A A c.483A>T p.= p.T161T ENST00000377191 5/30 208 187 21 203 203 0 strelka-varscan-mutect XRN2,synonymous_variant,p.=,ENST00000377191,NM_001317960.1,NM_012255.3; T ENST00000377191 Transcript synonymous_variant 578/3437 483/2853 161/950 T acA/acT 1 1 XRN2 HGNC HGNC:12836 protein_coding YES CCDS13144.1 ENSP00000366396 Q9H0D6 UPI0000037D02 NM_001317960.1,NM_012255.3 5/30 Pfam_domain:PF03159,PIRSF_domain:PIRSF037239,hmmpanther:PTHR12341,hmmpanther:PTHR12341:SF35 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 21330536 21330536 A T 1 0 0 0 0 0 0 0 1 18018 173 6 4 4 XRN2 20 21330536 Silent SNP A C3N-00547_T 1067487 21330536 43113631 636 14966 DEFB123 0 . GRCh38 20 31450033 31450033 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.63C>A p.= p.G21G ENST00000376309 2/2 73 58 15 95 95 0 strelka-varscan-mutect DEFB123,synonymous_variant,p.=,ENST00000376309,NM_153324.3; A ENST00000376309 Transcript synonymous_variant 243/467 63/204 21/67 G ggC/ggA 1 1 DEFB123 HGNC HGNC:18103 protein_coding YES CCDS13180.1 ENSP00000365486 Q8N688 UPI0000128D96 NM_153324.3 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF3,PD866254 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 49 31450033 31450033 C A 1 0 0 0 0 0 0 0 1 4212 724 25 2 2 DEFB123 20 31450033 Silent SNP C C3N-00547_T 10119497 31450033 32994134 637 14967 TLDC2 0 . GRCh38 20 36879189 36879189 + Missense_Mutation SNP G G T rs779293943 C3N-00547_T C3N-00547_N G G c.338G>T p.Gly113Val p.G113V ENST00000217320 3/7 112 100 12 141 141 0 strelka-varscan-mutect TLDC2,missense_variant,p.Gly113Val,ENST00000217320,NM_080628.2,NM_001304783.1;TLDC2,missense_variant,p.Gly113Val,ENST00000602922,; T ENST00000217320 Transcript missense_variant 382/2083 338/648 113/215 G/V gGg/gTg rs779293943 1 1 TLDC2 HGNC HGNC:16112 protein_coding YES CCDS33465.1 ENSP00000217320 A0PJX2 UPI000049DF51 NM_080628.2,NM_001304783.1 deleterious(0) 3/7 hmmpanther:PTHR23354,hmmpanther:PTHR23354:SF65,Pfam_domain:PF07534,SMART_domains:SM00584 MODERATE 1 SNV 1 1 PASS rs779293943 . 0 205 5 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 49 36879189 36879189 G T 1 0 0 0 0 1 0 0 0 16383 1246 43 2 2 TLDC2 20 36879189 Missense_Mutation SNP G C3N-00547_T 5429156 36879189 27564978 638 14968 RALGAPB 0 . GRCh38 20 38525966 38525966 + Silent SNP G G T novel C3N-00547_T C3N-00547_N G G c.1974G>T p.= p.L658L ENST00000262879 13/30 148 99 49 228 228 0 strelka-varscan-mutect RALGAPB,synonymous_variant,p.=,ENST00000262879,NM_001282917.1,NM_020336.3;RALGAPB,synonymous_variant,p.=,ENST00000397042,NM_001282918.1;RALGAPB,synonymous_variant,p.=,ENST00000397040,;RALGAPB,synonymous_variant,p.=,ENST00000632792,;RALGAPB,synonymous_variant,p.=,ENST00000438490,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,; T ENST00000262879 Transcript synonymous_variant 2258/8663 1974/4485 658/1494 L ctG/ctT 1 1 RALGAPB HGNC HGNC:29221 protein_coding YES CCDS13305.1 ENSP00000262879 Q86X10 UPI000000DBFD NM_001282917.1,NM_020336.3 13/30 hmmpanther:PTHR21344 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 38525966 38525966 G T 1 0 0 0 0 0 0 0 1 13174 1277 45 2 2 RALGAPB 20 38525966 Silent SNP G C3N-00547_T 1646777 38525966 25918201 639 14969 CHD6 0 . GRCh38 20 41415332 41415332 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.6793A>G p.Ile2265Val p.I2265V ENST00000373233 34/37 369 322 47 442 442 0 strelka-varscan-mutect CHD6,missense_variant,p.Ile2265Val,ENST00000373233,NM_032221.4;CHD6,upstream_gene_variant,,ENST00000480022,; C ENST00000373233 Transcript missense_variant 6971/10818 6793/8148 2265/2715 I/V Atc/Gtc 1 -1 CHD6 HGNC HGNC:19057 protein_coding YES CCDS13317.1 ENSP00000362330 Q8TD26 UPI0000168656 NM_032221.4 deleterious(0.04) 34/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 41415332 41415332 T C 1 0 0 0 0 1 0 0 0 3088 1435 50 5 5 CHD6 20 41415332 Missense_Mutation SNP T C3N-00547_T 2889366 41415332 23028835 640 14970 SGK2 0 . GRCh38 20 43566333 43566333 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.18C>T p.= p.T6T ENST00000341458 1/12 76 48 28 70 70 0 strelka-varscan-mutect SGK2,synonymous_variant,p.=,ENST00000341458,NM_016276.3;SGK2,synonymous_variant,p.=,ENST00000426287,;SGK2,intron_variant,,ENST00000373100,;SGK2,intron_variant,,ENST00000423407,NM_001199264.1;SGK2,intron_variant,,ENST00000373092,NM_170693.2;SGK2,intron_variant,,ENST00000412111,;SGK2,intron_variant,,ENST00000617268,;SGK2,upstream_gene_variant,,ENST00000485914,;SGK2,intron_variant,,ENST00000496343,;SGK2,intron_variant,,ENST00000373077,;SGK2,intron_variant,,ENST00000617358,;RP1-138B7.6,intron_variant,,ENST00000621802,; T ENST00000341458 Transcript synonymous_variant 571/2498 18/1284 6/427 T acC/acT 1 1 SGK2 HGNC HGNC:13900 protein_coding YES CCDS13320.1 ENSP00000340608 Q9HBY8 UPI0000033528 NM_016276.3 1/12 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 49 43566333 43566333 C T 1 0 0 0 0 0 0 0 1 14468 668 24 3 3 SGK2 20 43566333 Silent SNP C C3N-00547_T 2151001 43566333 20877834 641 14971 HNF4A 0 . GRCh38 20 44406163 44406163 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.221C>T p.Ala74Val p.A74V ENST00000316099 2/10 262 245 17 288 288 0 strelka-varscan-mutect HNF4A,missense_variant,p.Ala74Val,ENST00000316099,NM_001258355.1,NM_000457.4;HNF4A,missense_variant,p.Ala49Val,ENST00000619550,NM_001287182.1,NM_001287183.1;HNF4A,missense_variant,p.Ala74Val,ENST00000415691,NM_178849.2;HNF4A,missense_variant,p.Ala74Val,ENST00000443598,NM_178850.2;HNF4A,missense_variant,p.Ala52Val,ENST00000316673,NM_175914.4;HNF4A,missense_variant,p.Ala52Val,ENST00000457232,NM_001030003.2;HNF4A,missense_variant,p.Ala52Val,ENST00000609795,NM_001030004.2,NM_001287184.1;HNF4A,missense_variant,p.Ala49Val,ENST00000609262,;MIR3646,upstream_gene_variant,,ENST00000578301,;HNF4A,synonymous_variant,p.=,ENST00000372920,; T ENST00000316099 Transcript missense_variant 310/6445 221/1425 74/474 A/V gCc/gTc 1 1 HNF4A HGNC HGNC:5024 protein_coding YES CCDS13330.1 ENSP00000312987 P41235 F1D8T1 UPI000016A0BA NM_001258355.1,NM_000457.4 deleterious(0) 2/10 PROSITE_profiles:PS51030,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF41,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 44406163 44406163 C T 1 0 0 0 0 1 0 0 0 7144 739 26 3 3 HNF4A 20 44406163 Missense_Mutation SNP C C3N-00547_T 839830 44406163 20038004 642 14972 SLC12A5 0 . GRCh38 20 46043895 46043896 + Frame_Shift_Ins INS - - T novel C3N-00547_T C3N-00547_N - - c.1428dupT p.Gly477TrpfsTer5 p.G477Wfs*5 ENST00000454036 11/26 67 46 21 90 90 0 sindel-varindel-pindel SLC12A5,frameshift_variant,p.Gly454TrpfsTer5,ENST00000243964,NM_020708.4;SLC12A5,frameshift_variant,p.Gly477TrpfsTer5,ENST00000454036,NM_001134771.1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616201,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,intron_variant,,ENST00000539566,;SLC12A5,downstream_gene_variant,,ENST00000629054,;SLC12A5,downstream_gene_variant,,ENST00000625683,;SLC12A5,downstream_gene_variant,,ENST00000372315,;SLC12A5,downstream_gene_variant,,ENST00000622711,;SLC12A5,upstream_gene_variant,,ENST00000626144,;SLC12A5,downstream_gene_variant,,ENST00000608594,; T ENST00000454036 Transcript frameshift_variant 1501-1502/3593 1425-1426/3420 475-476/1139 -/X -/T 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 11/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930,Transmembrane_helices:TMhelix HIGH 1 insertion 5 3 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 49 46043895 46043895 - T 1 0 1 1 0 0 0 0 0 14651 1364 48 0 0 SLC12A5 20 46043895 Frame_Shift_Ins INS - C3N-00547_T 1637732 46043895 18400272 643 14973 SLC12A5 0 . GRCh38 20 46053690 46053690 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.2729A>T p.Glu910Val p.E910V ENST00000454036 20/26 61 38 23 70 70 0 strelka-varscan-mutect SLC12A5,missense_variant,p.Glu887Val,ENST00000243964,NM_020708.4;SLC12A5,missense_variant,p.Glu910Val,ENST00000454036,NM_001134771.1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616201,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,upstream_gene_variant,,ENST00000637437,;SLC12A5,downstream_gene_variant,,ENST00000539566,;SLC12A5,upstream_gene_variant,,ENST00000628413,; T ENST00000454036 Transcript missense_variant 2805/3593 2729/3420 910/1139 E/V gAg/gTg 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 deleterious(0.05) 20/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF03522,TIGRFAM_domain:TIGR00930 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 46053690 46053690 A T 1 0 0 0 0 1 0 0 0 14651 304 11 4 4 SLC12A5 20 46053690 Missense_Mutation SNP A C3N-00547_T 9795 46053690 18390477 644 14974 ARFGEF2 0 . GRCh38 20 48991166 48991166 + Missense_Mutation SNP G G A rs765305868 C3N-00547_T C3N-00547_N G G c.2941G>A p.Asp981Asn p.D981N ENST00000371917 21/39 465 413 52 555 554 1 strelka-varscan-mutect ARFGEF2,missense_variant,p.Asp981Asn,ENST00000371917,NM_006420.2; A ENST00000371917 Transcript missense_variant 2941/8852 2941/5358 981/1785 D/N Gat/Aat rs765305868 1 1 ARFGEF2 HGNC HGNC:15853 protein_coding YES CCDS13411.1 ENSP00000360985 Q9Y6D5 UPI000013D378 NM_006420.2 deleterious(0) 21/39 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124 MODERATE 1 SNV 1 1 PASS rs765305868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 48991166 48991166 G A 1 0 0 0 0 1 0 0 0 976 1058 37 1 1 ARFGEF2 20 48991166 Missense_Mutation SNP G C3N-00547_T 2937476 48991166 15453001 645 14975 MC3R 0 . GRCh38 20 56249765 56249765 + Missense_Mutation SNP A A G novel C3N-00547_T C3N-00547_N A A c.922A>G p.Asn308Asp p.N308D ENST00000243911 1/1 526 486 40 718 718 0 strelka-varscan-mutect MC3R,missense_variant,p.Asn308Asp,ENST00000243911,NM_019888.3; G ENST00000243911 Transcript missense_variant 1034/1084 922/972 308/323 N/D Aac/Gac 1 1 MC3R HGNC HGNC:6931 protein_coding YES CCDS13449.2 ENSP00000243911 P41968 UPI0000E5A34B NM_019888.3 tolerated(0.11) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00534,Prints_domain:PR00535,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF4,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 49 56249765 56249765 A G 1 0 0 0 0 1 0 0 0 9298 130 5 5 5 MC3R 20 56249765 Missense_Mutation SNP A C3N-00547_T 7258599 56249765 8194402 646 14976 CASS4 0 . GRCh38 20 56452906 56452906 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1730C>A p.Ala577Asp p.A577D ENST00000360314 6/7 164 94 70 208 208 0 strelka-varscan-mutect CASS4,missense_variant,p.Ala577Asp,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,intron_variant,,ENST00000434344,NM_001164115.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; A ENST00000360314 Transcript missense_variant 1955/2619 1730/2361 577/786 A/D gCc/gAc 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0.01) 6/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654,Pfam_domain:PF08824 MODERATE 1 SNV 1 1 PASS rs1284248278 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 56452906 56452906 C A 1 0 0 0 0 1 0 0 0 2382 739 26 2 2 CASS4 20 56452906 Missense_Mutation SNP C C3N-00547_T 203141 56452906 7991261 647 14977 RTFDC1 0 . GRCh38 20 56517166 56517166 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.797G>T p.Arg266Ile p.R266I ENST00000023939 9/10 291 250 41 297 297 0 strelka-varscan-mutect RTFDC1,stop_gained,p.Glu218Ter,ENST00000395881,NM_001283037.1;RTFDC1,missense_variant,p.Arg236Ile,ENST00000357348,NM_016407.4,NM_001283036.1;RTFDC1,missense_variant,p.Arg266Ile,ENST00000023939,NM_001283035.1;RTFDC1,missense_variant,p.Arg266Ile,ENST00000449062,;GCNT7,intron_variant,,ENST00000243913,;FAM209A,upstream_gene_variant,,ENST00000481560,;RTFDC1,non_coding_transcript_exon_variant,,ENST00000477573,;RTFDC1,non_coding_transcript_exon_variant,,ENST00000477485,; T ENST00000023939 Transcript missense_variant 910/1745 797/1011 266/336 R/I aGa/aTa 1 1 RTFDC1 HGNC HGNC:15890 protein_coding YES CCDS63316.1 ENSP00000023939 A0A0A0MQR2 UPI0001AE65A5 NM_001283035.1 tolerated(0.19) 9/10 hmmpanther:PTHR12775,Pfam_domain:PF04641 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 56517166 56517166 G T 1 0 0 0 0 1 0 0 0 13981 943 33 2 2 RTFDC1 20 56517166 Missense_Mutation SNP G C3N-00547_T 64260 56517166 7927001 648 14978 OSBPL2 0 . GRCh38 20 62284071 62284071 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.898G>T p.Gly300Cys p.G300C ENST00000313733 10/14 123 82 41 110 110 0 varscan-mutect OSBPL2,missense_variant,p.Gly300Cys,ENST00000313733,NM_144498.2;OSBPL2,missense_variant,p.Gly288Cys,ENST00000358053,NM_014835.3;OSBPL2,missense_variant,p.Gly208Cys,ENST00000439951,NM_001278649.1;OSBPL2,downstream_gene_variant,,ENST00000622332,;OSBPL2,downstream_gene_variant,,ENST00000448156,;OSBPL2,downstream_gene_variant,,ENST00000618198,;OSBPL2,non_coding_transcript_exon_variant,,ENST00000621075,;OSBPL2,downstream_gene_variant,,ENST00000620616,; T ENST00000313733 Transcript missense_variant 1139/4009 898/1443 300/480 G/C Ggc/Tgc 1 1 OSBPL2 HGNC HGNC:15761 protein_coding YES CCDS13495.1 ENSP00000316649 Q9H1P3 UPI0000130E96 NM_144498.2 deleterious(0) 10/14 Superfamily_domains:0051579,Pfam_domain:PF01237,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF54 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 62284071 62284071 G T 1 0 0 0 0 1 0 0 0 11344 1348 47 2 2 OSBPL2 20 62284071 Missense_Mutation SNP G C3N-00547_T 5766905 62284071 2160096 649 14979 COL20A1 0 . GRCh38 20 63305521 63305521 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.298G>T p.Gly100Cys p.G100C ENST00000358894 4/36 70 45 25 92 92 0 strelka-varscan-mutect COL20A1,missense_variant,p.Gly100Cys,ENST00000422202,;COL20A1,missense_variant,p.Gly100Cys,ENST00000358894,NM_020882.2;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,; T ENST00000358894 Transcript missense_variant 398/4172 298/3855 100/1284 G/C Ggc/Tgc 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 deleterious(0) 4/36 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 63305521 63305521 G T 1 0 0 0 0 1 0 0 0 3467 1348 47 2 2 COL20A1 20 63305521 Missense_Mutation SNP G C3N-00547_T 1021450 63305521 1138646 650 14980 KCNQ2 0 . GRCh38 20 63406845 63406845 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2418C>A p.Ser806Arg p.S806R ENST00000359125 17/17 516 454 62 492 492 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Ser788Arg,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Ser806Arg,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Ser605Arg,ENST00000637193,;KCNQ2,missense_variant,p.Ser778Arg,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Ser775Arg,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Ser662Arg,ENST00000357249,;KCNQ2,intron_variant,,ENST00000370224,;KCNQ2,intron_variant,,ENST00000625514,;KCNQ2,intron_variant,,ENST00000629241,;KCNQ2,intron_variant,,ENST00000629676,;KCNQ2,downstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000637063,;KCNQ2,downstream_gene_variant,,ENST00000637338,;KCNQ2,downstream_gene_variant,,ENST00000637656,; T ENST00000359125 Transcript missense_variant 2545/3253 2418/2619 806/872 S/R agC/agA 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious(0) 17/17 Pfam_domain:PF11956 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 63406845 63406845 G T 1 0 0 0 0 1 0 0 0 7999 1310 46 2 2 KCNQ2 20 63406845 Missense_Mutation SNP G C3N-00547_T 101324 63406845 1037322 651 14981 KCNQ2 0 . GRCh38 20 63414959 63414959 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.1469G>T p.Ser490Ile p.S490I ENST00000359125 13/17 335 290 45 263 263 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Ser472Ile,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Ser490Ile,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Ser462Ile,ENST00000370224,;KCNQ2,missense_variant,p.Ser289Ile,ENST00000637193,;KCNQ2,missense_variant,p.Ser450Ile,ENST00000625514,;KCNQ2,missense_variant,p.Ser462Ile,ENST00000629241,;KCNQ2,missense_variant,p.Ser462Ile,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Ser460Ile,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Ser346Ile,ENST00000357249,;KCNQ2,missense_variant,p.Ser462Ile,ENST00000629676,;KCNQ2,missense_variant,p.Ser177Ile,ENST00000627221,;KCNQ2,missense_variant,p.Ser26Ile,ENST00000629318,;KCNQ2,upstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000635867,;KCNQ2,upstream_gene_variant,,ENST00000636499,;KCNQ2,downstream_gene_variant,,ENST00000637584,; A ENST00000359125 Transcript missense_variant 1596/3253 1469/2619 490/872 S/I aGc/aTc 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious(0.01) 13/17 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF6,Pfam_domain:PF03520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 63414959 63414959 C A 1 0 0 0 0 1 0 0 0 7999 797 28 2 2 KCNQ2 20 63414959 Missense_Mutation SNP C C3N-00547_T 8114 63414959 1029208 652 14982 GMEB2 0 . GRCh38 20 63592649 63592649 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.713G>T p.Arg238Leu p.R238L ENST00000266068 7/9 113 71 42 236 236 0 strelka-varscan-mutect GMEB2,missense_variant,p.Arg238Leu,ENST00000266068,;GMEB2,missense_variant,p.Arg238Leu,ENST00000370077,NM_012384.3;GMEB2,missense_variant,p.Arg187Leu,ENST00000370069,; A ENST00000266068 Transcript missense_variant 1192/4559 713/1593 238/530 R/L cGg/cTg 1 -1 GMEB2 HGNC HGNC:4371 protein_coding YES CCDS13528.1 ENSP00000266068 Q9UKD1 UPI000012B8AD deleterious(0.01) 7/9 hmmpanther:PTHR10417:SF2,hmmpanther:PTHR10417 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 63592649 63592649 C A 1 0 0 0 0 1 0 0 0 6367 652 23 1 1 GMEB2 20 63592649 Missense_Mutation SNP C C3N-00547_T 177690 63592649 851518 653 14983 KCNE1B 0 . GRCh38 21 7819402 7819402 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.230C>A p.Ser77Ter p.S77* ENST00000623803 3/3 15 8 7 19 19 0 strelka-varscan-mutect KCNE1B,stop_gained,p.Ser77Ter,ENST00000618699,;KCNE1B,stop_gained,p.Ser74Ter,ENST00000622690,;KCNE1B,stop_gained,p.Ser77Ter,ENST00000623803,;KCNE1B,stop_gained,p.Ser77Ter,ENST00000617668,; T ENST00000623803 Transcript stop_gained 453/811 230/399 77/132 S/* tCg/tAg 1 -1 KCNE1B HGNC HGNC:52280 protein_coding YES ENSP00000485125 A0A087WTH5 UPI0003EAFC6E 3/3 Pfam_domain:PF02060,hmmpanther:PTHR15282,hmmpanther:PTHR15282:SF10 HIGH 1 SNV 1 1 PASS . . 18 190 2 0 0 0 0 0 -19.99475 1 1 1 1 0 T 4 4 49 7819402 7819402 G T 1 0 0 0 0 0 1 0 0 7938 1059 37 1 1 KCNE1B 21 7819402 Nonsense_Mutation SNP G C3N-00547_T 7819402 38890581 654 14984 ADAMTS5 0 . GRCh38 21 26954802 26954802 + Missense_Mutation SNP G G C rs202109841 C3N-00547_T C3N-00547_N G G c.1174C>G p.Arg392Gly p.R392G ENST00000284987 2/8 224 181 43 290 290 0 strelka-varscan-mutect ADAMTS5,missense_variant,p.Arg392Gly,ENST00000284987,NM_007038.3;MIR4759,downstream_gene_variant,,ENST00000584048,; C ENST00000284987 Transcript missense_variant 1296/9056 1174/2793 392/930 R/G Cgc/Ggc rs202109841,COSM1029708 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 deleterious(0) 2/8 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37,Superfamily_domains:SSF55486 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs202109841 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 26954802 26954802 G C 1 0 0 0 0 1 0 0 0 313 1087 38 4 4 ADAMTS5 21 26954802 Missense_Mutation SNP G C3N-00547_T 19135400 26954802 19755181 655 14985 GRIK1 0 . GRCh38 21 29587435 29587435 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.1724C>A p.Ser575Tyr p.S575Y ENST00000399907 12/17 279 213 66 351 351 0 strelka-varscan-mutect GRIK1,missense_variant,p.Ser560Tyr,ENST00000399914,;GRIK1,missense_variant,p.Ser575Tyr,ENST00000399907,NM_000830.3;GRIK1,missense_variant,p.Ser560Tyr,ENST00000399909,;GRIK1,missense_variant,p.Ser575Tyr,ENST00000399913,;GRIK1,missense_variant,p.Ser575Tyr,ENST00000327783,;GRIK1,missense_variant,p.Ser560Tyr,ENST00000389125,NM_175611.2;GRIK1,missense_variant,p.Ser575Tyr,ENST00000389124,;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; T ENST00000399907 Transcript missense_variant 2136/3472 1724/2757 575/918 S/Y tCt/tAt 1 -1 GRIK1 HGNC HGNC:4579 protein_coding YES CCDS42913.1 ENSP00000382791 P39086 UPI000012B612 NM_000830.3 deleterious(0) 12/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF36,Gene3D:1.10.287.70,SMART_domains:SM00079 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 29587435 29587435 G T 1 0 0 0 0 1 0 0 0 6655 942 33 2 2 GRIK1 21 29587435 Missense_Mutation SNP G C3N-00547_T 2632633 29587435 17122548 656 14986 CLDN17 0 . GRCh38 21 30166061 30166061 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.557G>T p.Cys186Phe p.C186F ENST00000286808 1/1 348 280 68 427 426 1 strelka-varscan-mutect CLDN17,missense_variant,p.Cys186Phe,ENST00000286808,NM_012131.2; A ENST00000286808 Transcript missense_variant 696/1193 557/675 186/224 C/F tGc/tTc 1 -1 CLDN17 HGNC HGNC:2038 protein_coding YES CCDS13586.1 ENSP00000286808 P56750 UPI000004E655 NM_012131.2 tolerated(0.51) 1/1 hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF75,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 30166061 30166061 C A 1 0 0 0 0 1 0 0 0 3242 710 25 2 2 CLDN17 21 30166061 Missense_Mutation SNP C C3N-00547_T 578626 30166061 16543922 657 14987 KRTAP21-2 0 . GRCh38 21 30747048 30747048 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.155G>T p.Gly52Val p.G52V ENST00000333892 1/1 244 175 69 280 279 1 strelka-mutect KRTAP21-2,missense_variant,p.Gly52Val,ENST00000333892,NM_181617.1;KRTAP21-4P,upstream_gene_variant,,ENST00000454921,; A ENST00000333892 Transcript missense_variant 186/440 155/252 52/83 G/V gGa/gTa COSM3550190 1 -1 KRTAP21-2 HGNC HGNC:18946 protein_coding YES CCDS13605.1 ENSP00000334287 Q3LI59 UPI00001A9E4D NM_181617.1 deleterious_low_confidence(0) 1/1 Pfam_domain:PF11759,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 30747048 30747048 C A 1 0 0 0 0 1 0 0 0 8428 855 30 2 2 KRTAP21-2 21 30747048 Missense_Mutation SNP C C3N-00547_T 580987 30747048 15962935 658 14988 KRTAP8-1 0 . GRCh38 21 30813199 30813199 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.22G>T p.Gly8Trp p.G8W ENST00000329621 1/1 103 76 27 150 150 0 strelka-varscan-mutect KRTAP8-1,missense_variant,p.Gly8Trp,ENST00000329621,NM_175857.3; A ENST00000329621 Transcript missense_variant 54/556 22/192 8/63 G/W Ggg/Tgg 1 -1 KRTAP8-1 HGNC HGNC:18935 protein_coding YES CCDS13607.1 ENSP00000332805 Q8IUC2 UPI00000747A5 NM_175857.3 deleterious_low_confidence(0.01) 1/1 hmmpanther:PTHR36131,Pfam_domain:PF11759,PD027172 MODERATE 1 SNV 1 PASS rs1157284010 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 30813199 30813199 C A 1 0 0 0 0 1 0 0 0 8468 652 23 1 1 KRTAP8-1 21 30813199 Missense_Mutation SNP C C3N-00547_T 66151 30813199 15896784 659 14989 IFNAR1 0 . GRCh38 21 33353689 33353689 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.1346C>T p.Ala449Val p.A449V ENST00000270139 10/11 92 74 18 125 125 0 strelka-varscan-mutect IFNAR1,missense_variant,p.Ala449Val,ENST00000270139,NM_000629.2; T ENST00000270139 Transcript missense_variant 1498/6139 1346/1674 449/557 A/V gCt/gTt 1 1 IFNAR1 HGNC HGNC:5432 protein_coding YES CCDS13624.1 ENSP00000270139 P17181 UPI000006FE3C NM_000629.2 tolerated(0.6) 10/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF54,PIRSF_domain:PIRSF016567 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 33353689 33353689 C T 1 0 0 0 0 1 0 0 0 7444 797 28 3 3 IFNAR1 21 33353689 Missense_Mutation SNP C C3N-00547_T 2540490 33353689 13356294 660 14990 KCNE1 0 . GRCh38 21 34449414 34449414 + Nonsense_Mutation SNP G G T rs74315446 C3N-00547_T C3N-00547_N G G c.221C>A p.Ser74Ter p.S74* ENST00000337385 3/3 189 138 51 250 249 1 strelka-varscan-mutect KCNE1,stop_gained,p.Ser74Ter,ENST00000337385,NM_001270402.2,NM_001270403.2;KCNE1,stop_gained,p.Ser74Ter,ENST00000611936,NM_001270404.2;KCNE1,stop_gained,p.Ser74Ter,ENST00000432085,NM_001127668.3;KCNE1,stop_gained,p.Ser74Ter,ENST00000399289,NM_001127669.3;KCNE1,stop_gained,p.Ser74Ter,ENST00000621601,NM_001270405.2;KCNE1,stop_gained,p.Ser74Ter,ENST00000399286,NM_000219.5;KCNE1,stop_gained,p.Ser74Ter,ENST00000416357,NM_001127670.3;KCNE1,stop_gained,p.Ser74Ter,ENST00000399284,; T ENST00000337385 Transcript stop_gained 621/3347 221/390 74/129 S/* tCg/tAg rs74315446,CM970799,LQTS_4557686:c.221C>T 1 -1 KCNE1 HGNC HGNC:6240 protein_coding YES CCDS13636.1 ENSP00000337255 P15382 C7S316 UPI000012F141 NM_001270402.2,NM_001270403.2 3/3 Pfam_domain:PF02060,hmmpanther:PTHR15282,hmmpanther:PTHR15282:SF10 pathogenic 1.50516369354802e+22 HIGH 1 SNV 3 1,1,0 1 PASS rs74315446 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 34449414 34449414 G T 1 0 0 0 0 0 1 0 0 7937 1059 37 1 1 KCNE1 21 34449414 Nonsense_Mutation SNP G C3N-00547_T 1095725 34449414 12260569 661 14991 DIP2A 0 . GRCh38 21 46549914 46549914 + Missense_Mutation SNP G G T rs201345375 C3N-00547_T C3N-00547_N G G c.2666G>T p.Arg889Leu p.R889L ENST00000457905 22/22 82 49 33 124 124 0 strelka-varscan-mutect DIP2A,missense_variant,p.Arg889Leu,ENST00000457905,NM_206889.2;DIP2A,intron_variant,,ENST00000400274,NM_001146116.1;DIP2A,intron_variant,,ENST00000417564,NM_015151.3;DIP2A,downstream_gene_variant,,ENST00000435722,NM_206891.2,NM_206890.2;DIP2A,downstream_gene_variant,,ENST00000466639,NM_001146115.1;DIP2A,downstream_gene_variant,,ENST00000473752,;DIP2A,upstream_gene_variant,,ENST00000472364,;DIP2A,downstream_gene_variant,,ENST00000494435,;DIP2A,downstream_gene_variant,,ENST00000480553,; T ENST00000457905 Transcript missense_variant 2848/3044 2666/2670 889/889 R/L cGg/cTg rs201345375 1 1 DIP2A HGNC HGNC:17217 protein_coding CCDS46656.1 ENSP00000393434 Q14689 UPI000007466D NM_206889.2 deleterious_low_confidence(0) 22/22 MODERATE SNV 1 1 PASS rs201345375 . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 49 46549914 46549914 G T 1 0 0 0 0 1 0 0 0 4332 1116 39 1 1 DIP2A 21 46549914 Missense_Mutation SNP G C3N-00547_T 12100500 46549914 160069 662 14992 CECR6 0 . GRCh38 22 17119439 17119439 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.1689G>T p.= p.G563G ENST00000331437 1/1 240 208 32 554 554 0 strelka-varscan-mutect CECR6,synonymous_variant,p.=,ENST00000331437,NM_031890.3;CECR6,synonymous_variant,p.=,ENST00000399875,NM_001163079.1;IL17RA,downstream_gene_variant,,ENST00000319363,NM_014339.6;IL17RA,downstream_gene_variant,,ENST00000612619,NM_001289905.1;AC006946.15,upstream_gene_variant,,ENST00000441544,;AC006946.15,upstream_gene_variant,,ENST00000428078,; A ENST00000331437 Transcript synonymous_variant 1815/4954 1689/1737 563/578 G ggG/ggT 1 -1 CECR6 HGNC HGNC:1844 protein_coding YES CCDS13740.1 ENSP00000329318 Q9BXQ6 UPI0000127513 NM_031890.3 1/1 hmmpanther:PTHR22146,hmmpanther:PTHR22146:SF1 LOW SNV 1 PASS rs1162430765 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 17119439 17119439 C A 1 0 0 0 0 0 0 0 1 2915 610 22 2 2 CECR6 22 17119439 Silent SNP C C3N-00547_T 17119439 33699029 663 14993 CECR1 0 . GRCh38 22 17181491 17181491 + Missense_Mutation SNP T T C novel C3N-00547_T C3N-00547_N T T c.1528A>G p.Thr510Ala p.T510A ENST00000399837 10/10 131 117 14 155 155 0 strelka-varscan-mutect CECR1,missense_variant,p.Thr510Ala,ENST00000399837,NM_001282226.1,NM_001282225.1;CECR1,missense_variant,p.Thr468Ala,ENST00000449907,NM_001282228.1,NM_001282227.1;CECR1,missense_variant,p.Thr390Ala,ENST00000610390,NM_001282229.1;CECR1,missense_variant,p.Thr510Ala,ENST00000399839,;CECR1,missense_variant,p.Thr510Ala,ENST00000262607,;CECR1,missense_variant,p.Thr269Ala,ENST00000330232,NM_177405.2;CECR1,downstream_gene_variant,,ENST00000469063,; C ENST00000399837 Transcript missense_variant 1804/4505 1528/1536 510/511 T/A Aca/Gca 1 -1 CECR1 HGNC HGNC:1839 protein_coding YES CCDS13742.1 ENSP00000382731 Q9NZK5 UPI000013D2E8 NM_001282226.1,NM_001282225.1 tolerated(0.48) 10/10 hmmpanther:PTHR11409,hmmpanther:PTHR11409:SF39 MODERATE 1 SNV 1 1 PASS rs1259827703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 17181491 17181491 T C 1 0 0 0 0 1 0 0 0 2912 1638 57 5 5 CECR1 22 17181491 Missense_Mutation SNP T C3N-00547_T 62052 17181491 33636977 664 14994 DGCR2 0 . GRCh38 22 19041218 19041218 + Silent SNP C C G rs780473059 C3N-00547_T C3N-00547_N C C c.1236G>C p.= p.P412P ENST00000263196 9/10 212 160 52 260 260 0 strelka-varscan-mutect DGCR2,synonymous_variant,p.=,ENST00000545799,;DGCR2,synonymous_variant,p.=,ENST00000263196,NM_005137.2,NM_001184781.1;DGCR2,synonymous_variant,p.=,ENST00000537045,NM_001173534.1,NM_001173533.1;DGCR11,downstream_gene_variant,,ENST00000609958,;Y_RNA,upstream_gene_variant,,ENST00000384012,;DGCR2,synonymous_variant,p.=,ENST00000389262,;DGCR2,non_coding_transcript_exon_variant,,ENST00000467659,; G ENST00000263196 Transcript synonymous_variant 1484/4480 1236/1653 412/550 P ccG/ccC rs780473059 1 -1 DGCR2 HGNC HGNC:2845 protein_coding YES CCDS33598.1 ENSP00000263196 P98153 UPI0000001613 NM_005137.2,NM_001184781.1 9/10 hmmpanther:PTHR15256 LOW 1 SNV 1 1 PASS rs780473059 . 0 207 0 0 2 0 0 0 -20 0.9986927 1 1 1 0 G 2 3 49 19041218 19041218 C G 1 0 0 0 0 0 0 0 1 4268 755 27 4 4 DGCR2 22 19041218 Silent SNP C C3N-00547_T 1859727 19041218 31777250 665 14995 MYO18B 0 . GRCh38 22 25847514 25847514 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.3637G>C p.Gly1213Arg p.G1213R ENST00000335473 20/44 279 217 62 378 378 0 strelka-varscan-mutect MYO18B,missense_variant,p.Gly1213Arg,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Gly1214Arg,ENST00000407587,;MYO18B,missense_variant,p.Gly1213Arg,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; C ENST00000335473 Transcript missense_variant 3887/8565 3637/7704 1213/2567 G/R Ggg/Cgg 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated(0.07) 20/44 PROSITE_profiles:PS51456,Low_complexity_(Seg):seg,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 25847514 25847514 G C 1 0 0 0 0 1 0 0 0 10067 1348 47 4 4 MYO18B 22 25847514 Missense_Mutation SNP G C3N-00547_T 6806296 25847514 24970954 666 14996 MYO18B 0 . GRCh38 22 25946221 25946221 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.5602C>A p.Leu1868Met p.L1868M ENST00000335473 35/44 106 90 16 148 147 1 strelka-varscan-mutect MYO18B,missense_variant,p.Leu1868Met,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Leu1869Met,ENST00000407587,;MYO18B,missense_variant,p.Leu1868Met,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript missense_variant 5852/8565 5602/7704 1868/2567 L/M Ctg/Atg 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated(0.17) 35/44 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 25946221 25946221 C A 1 0 0 0 0 1 0 0 0 10067 796 28 2 2 MYO18B 22 25946221 Missense_Mutation SNP C C3N-00547_T 98707 25946221 24872247 667 14997 MN1 0 . GRCh38 22 27799761 27799761 + Silent SNP C C T rs376859079 C3N-00547_T C3N-00547_N C C c.783G>A p.= p.A261A ENST00000302326 1/2 82 66 16 102 101 1 strelka-varscan-mutect MN1,synonymous_variant,p.=,ENST00000302326,NM_002430.2;MN1,upstream_gene_variant,,ENST00000424656,; T ENST00000302326 Transcript synonymous_variant 1738/7556 783/3963 261/1320 A gcG/gcA rs376859079 1 -1 MN1 HGNC HGNC:7180 protein_coding YES CCDS42998.1 ENSP00000304956 Q10571 A0A024R1C3 UPI0000207445 NM_002430.2 1/2 hmmpanther:PTHR15821 LOW 1 SNV 1 1 PASS rs376859079 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 27799761 27799761 C T 1 0 0 0 0 0 0 0 1 9637 639 23 1 1 MN1 22 27799761 Silent SNP C C3N-00547_T 1853540 27799761 23018707 668 14998 APOL4 0 . GRCh38 22 36191452 36191452 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.679C>A p.Pro227Thr p.P227T ENST00000352371 5/5 322 246 76 355 355 0 strelka-varscan-mutect APOL4,missense_variant,p.Pro224Thr,ENST00000616056,NM_030643.4;APOL4,missense_variant,p.Pro227Thr,ENST00000352371,NM_145660.2;APOL4,missense_variant,p.Pro224Thr,ENST00000332987,;APOL4,downstream_gene_variant,,ENST00000419360,;APOL4,downstream_gene_variant,,ENST00000457630,;APOL4,non_coding_transcript_exon_variant,,ENST00000613247,;APOL4,non_coding_transcript_exon_variant,,ENST00000449084,;APOL4,downstream_gene_variant,,ENST00000493203,; T ENST00000352371 Transcript missense_variant 904/3227 679/1056 227/351 P/T Ccc/Acc 1 -1 APOL4 HGNC HGNC:14867 protein_coding YES CCDS74852.1 ENSP00000338260 Q9BPW4 UPI0000125C98 NM_145660.2 deleterious(0.02) 5/5 Pfam_domain:PF05461,hmmpanther:PTHR14096,hmmpanther:PTHR14096:SF39 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 36191452 36191452 G T 1 0 0 0 0 1 0 0 0 930 1261 44 2 2 APOL4 22 36191452 Missense_Mutation SNP G C3N-00547_T 8391691 36191452 14627016 669 14999 RAC2 0 . GRCh38 22 37232858 37232858 + Missense_Mutation SNP C C A C3N-00547_T C3N-00547_N C C c.168G>T p.Trp56Cys p.W56C ENST00000249071 3/7 402 316 86 481 480 1 strelka-varscan-mutect RAC2,missense_variant,p.Trp56Cys,ENST00000249071,NM_002872.4;RAC2,missense_variant,p.Trp12Cys,ENST00000406508,;RAC2,missense_variant,p.Trp49Cys,ENST00000405484,;RAC2,missense_variant,p.Trp56Cys,ENST00000441619,;RAC2,non_coding_transcript_exon_variant,,ENST00000469532,;RAC2,upstream_gene_variant,,ENST00000481215,; A ENST00000249071 Transcript missense_variant 290/1482 168/579 56/192 W/C tgG/tgT RAC2base_D0070:g.12413G>A,COSM5449669 1 -1 RAC2 HGNC HGNC:9802 protein_coding YES CCDS13945.1 ENSP00000249071 P15153 A0A024R1P2 UPI00001110AB NM_002872.4 deleterious_low_confidence(0) 3/7 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51420,hmmpanther:PTHR24072,hmmpanther:PTHR24072:SF169,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 37232858 37232858 C A 1 0 0 0 0 1 0 0 0 13134 624 22 2 2 RAC2 22 37232858 Missense_Mutation SNP C C3N-00547_T 1041406 37232858 13585610 670 15000 CYTH4 0 . GRCh38 22 37299298 37299298 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.426G>T p.Gln142His p.Q142H ENST00000248901 6/13 228 182 46 265 264 1 strelka-varscan-mutect CYTH4,missense_variant,p.Gln142His,ENST00000248901,NM_001318024.1,NM_013385.3;CYTH4,missense_variant,p.Gln142His,ENST00000405206,;CYTH4,missense_variant,p.Gln142His,ENST00000402997,;CYTH4,downstream_gene_variant,,ENST00000457992,;CYTH4,non_coding_transcript_exon_variant,,ENST00000439667,;CYTH4,upstream_gene_variant,,ENST00000447919,;CYTH4,non_coding_transcript_exon_variant,,ENST00000462927,;CYTH4,downstream_gene_variant,,ENST00000469886,;CYTH4,downstream_gene_variant,,ENST00000480510,;CYTH4,downstream_gene_variant,,ENST00000467664,; T ENST00000248901 Transcript missense_variant 613/3206 426/1185 142/394 Q/H caG/caT 1 1 CYTH4 HGNC HGNC:9505 protein_coding YES CCDS13946.1 ENSP00000248901 Q9UIA0 UPI000000D99D NM_001318024.1,NM_013385.3 deleterious(0) 6/13 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,Gene3D:1.10.1000.11,Pfam_domain:PF01369,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 37299298 37299298 G T 1 0 0 0 0 1 0 0 0 4011 991 35 2 2 CYTH4 22 37299298 Missense_Mutation SNP G C3N-00547_T 66440 37299298 13519170 671 15001 CACNA1I 0 . GRCh38 22 39662250 39662250 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.3187G>T p.Asp1063Tyr p.D1063Y ENST00000402142 17/37 145 110 35 233 233 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Asp1063Tyr,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Asp1028Tyr,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Asp1063Tyr,ENST00000401624,;CACNA1I,missense_variant,p.Asp1028Tyr,ENST00000407673,; T ENST00000402142 Transcript missense_variant 3187/10004 3187/6672 1063/2223 D/Y Gac/Tac 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 tolerated(0.08) 17/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 39662250 39662250 G T 1 0 0 0 0 1 0 0 0 2234 1174 41 2 2 CACNA1I 22 39662250 Missense_Mutation SNP G C3N-00547_T 2362952 39662250 11156218 672 15002 MEI1 0 . GRCh38 22 41718071 41718071 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.530G>T p.Gly177Val p.G177V ENST00000401548 6/31 60 50 10 49 49 0 strelka-varscan-mutect MEI1,missense_variant,p.Gly177Val,ENST00000401548,NM_152513.3;MEI1,splice_region_variant,,ENST00000540833,;RNU6ATAC22P,downstream_gene_variant,,ENST00000516794,; T ENST00000401548 Transcript missense_variant,splice_region_variant 570/4020 530/3825 177/1274 G/V gGc/gTc 1 1 MEI1 HGNC HGNC:28613 protein_coding YES CCDS46718.1 ENSP00000384115 Q5TIA1 UPI00006E232C NM_152513.3 tolerated(0.59) 6/31 hmmpanther:PTHR12044,hmmpanther:PTHR12044:SF10,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -19.9995 1 1 1 1 0 T 3 4 49 41718071 41718071 G T 1 0 0 0 0 1 0 0 0 9405 1217 42 2 2 MEI1 22 41718071 Missense_Mutation SNP G C3N-00547_T 2055821 41718071 9100397 673 15003 SAMM50 0 . GRCh38 22 43989233 43989233 + Missense_Mutation SNP G G C novel C3N-00547_T C3N-00547_N G G c.1198G>C p.Gly400Arg p.G400R ENST00000350028 13/15 139 110 29 150 150 0 strelka-varscan-mutect SAMM50,missense_variant,p.Gly400Arg,ENST00000350028,NM_015380.4;SAMM50,upstream_gene_variant,,ENST00000465768,;SAMM50,non_coding_transcript_exon_variant,,ENST00000494795,;SAMM50,non_coding_transcript_exon_variant,,ENST00000474323,; C ENST00000350028 Transcript missense_variant 1355/1717 1198/1410 400/469 G/R Gga/Cga 1 1 SAMM50 HGNC HGNC:24276 protein_coding YES CCDS14055.1 ENSP00000345445 Q9Y512 UPI000016A33D NM_015380.4 deleterious(0) 13/15 Gene3D:2qdzA01,Pfam_domain:PF01103,hmmpanther:PTHR12815,hmmpanther:PTHR12815:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 43989233 43989233 G C 1 0 0 0 0 1 0 0 0 14089 1001 35 4 4 SAMM50 22 43989233 Missense_Mutation SNP G C3N-00547_T 2271162 43989233 6829235 674 15004 PHF21B 0 . GRCh38 22 44893510 44893510 + Missense_Mutation SNP G G A C3N-00547_T C3N-00547_N G G c.907C>T p.Arg303Trp p.R303W ENST00000313237 7/13 151 143 8 164 164 0 strelka-varscan-mutect PHF21B,missense_variant,p.Arg303Trp,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Arg99Trp,ENST00000403565,NM_001284296.1;PHF21B,missense_variant,p.Arg249Trp,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Arg261Trp,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Arg99Trp,ENST00000414269,; A ENST00000313237 Transcript missense_variant 1058/3671 907/1596 303/531 R/W Cgg/Tgg COSM1220376 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious(0) 7/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 1 MODERATE 1 SNV 1 1 1 PASS rs1448839516 . 0 205 0 4 0 0 0 0 -10.62167 0.9993077 1 1 1 0 A 3 1 49 44893510 44893510 G A 1 0 0 0 0 1 0 0 0 11920 1086 38 1 1 PHF21B 22 44893510 Missense_Mutation SNP G C3N-00547_T 904277 44893510 5924958 675 15005 PKDREJ 0 . GRCh38 22 46259714 46259714 + Nonsense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.3609G>A p.Trp1203Ter p.W1203* ENST00000253255 1/1 207 148 59 281 280 1 strelka-varscan-mutect PKDREJ,stop_gained,p.Trp1203Ter,ENST00000253255,NM_006071.1; T ENST00000253255 Transcript stop_gained 3642/7693 3609/6762 1203/2253 W/* tgG/tgA 1 -1 PKDREJ HGNC HGNC:9015 protein_coding YES CCDS14073.1 ENSP00000253255 Q9NTG1 UPI0000031D01 NM_006071.1 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF141 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 46259714 46259714 C T 1 0 0 0 0 0 1 0 0 12066 624 22 3 3 PKDREJ 22 46259714 Nonsense_Mutation SNP C C3N-00547_T 1366204 46259714 4558754 676 15006 MAP3K15 0 . GRCh38 X 19431584 19431584 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.1020G>A p.= p.E340E ENST00000338883 7/29 69 26 43 65 65 0 strelka-varscan-mutect MAP3K15,synonymous_variant,p.=,ENST00000338883,NM_001001671.3;MAP3K15,non_coding_transcript_exon_variant,,ENST00000518578,;MAP3K15,synonymous_variant,p.=,ENST00000359173,; T ENST00000338883 Transcript synonymous_variant 1020/4012 1020/3942 340/1313 E gaG/gaA 1 -1 MAP3K15 HGNC HGNC:31689 protein_coding YES CCDS35212.2 ENSP00000345629 Q6ZN16 UPI0000E444D0 NM_001001671.3 7/29 hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363,Pfam_domain:PF13281 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 19431584 19431584 C T 1 0 0 0 0 0 0 0 1 9171 912 32 3 3 MAP3K15 23 19431584 Silent SNP C C3N-00547_T 19431584 136609311 677 15007 MAGEB6 0 . GRCh38 X 26194538 26194538 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.692C>T p.Pro231Leu p.P231L ENST00000379034 2/2 71 52 19 46 46 0 strelka-varscan-mutect MAGEB6,missense_variant,p.Pro231Leu,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript missense_variant 841/1949 692/1224 231/407 P/L cCc/cTc 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 tolerated(0.19) 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 26194538 26194538 C T 1 0 0 0 0 1 0 0 0 9096 623 22 3 3 MAGEB6 23 26194538 Missense_Mutation SNP C C3N-00547_T 6762954 26194538 129846357 678 15008 HUWE1 0 . GRCh38 X 53559497 53559497 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.7772A>T p.Gln2591Leu p.Q2591L ENST00000342160 56/83 166 73 93 132 132 0 strelka-varscan-mutect HUWE1,missense_variant,p.Gln2591Leu,ENST00000342160,;HUWE1,missense_variant,p.Gln2591Leu,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Gln2582Leu,ENST00000612484,;MIR98,upstream_gene_variant,,ENST00000606724,;MIRLET7F2,upstream_gene_variant,,ENST00000385277,; A ENST00000342160 Transcript missense_variant 8230/14796 7772/13125 2591/4374 Q/L cAg/cTg 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC deleterious(0) 56/83 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 53559497 53559497 T A 1 0 0 0 0 1 0 0 0 7357 1580 55 4 4 HUWE1 23 53559497 Missense_Mutation SNP T C3N-00547_T 27364959 53559497 102481398 679 15009 AMER1 0 . GRCh38 X 64190247 64190247 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.3040G>T p.Gly1014Trp p.G1014W ENST00000330258 2/2 54 17 37 57 57 0 strelka-varscan-mutect AMER1,missense_variant,p.Gly1014Trp,ENST00000330258,NM_152424.3;AMER1,intron_variant,,ENST00000374869,; A ENST00000330258 Transcript missense_variant 3313/8443 3040/3408 1014/1135 G/W Ggg/Tgg 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 deleterious(0.01) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999979 1 1 1 0 A 3 1 49 64190247 64190247 C A 1 0 0 0 0 1 0 0 0 667 594 21 2 2 AMER1 23 64190247 Missense_Mutation SNP C C3N-00547_T 10630750 64190247 91850648 680 15010 OTUD6A 0 . GRCh38 X 70062975 70062975 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.451C>A p.His151Asn p.H151N ENST00000338352 1/1 193 71 122 122 122 0 strelka-varscan-mutect OTUD6A,missense_variant,p.His151Asn,ENST00000338352,NM_207320.2; A ENST00000338352 Transcript missense_variant 485/1689 451/867 151/288 H/N Cac/Aac 1 1 OTUD6A HGNC HGNC:32312 protein_coding YES CCDS14395.1 ENSP00000339389 Q7L8S5 UPI00000712B7 NM_207320.2 tolerated(0.07) 1/1 PROSITE_profiles:PS50802,hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF13,Pfam_domain:PF02338,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 70062975 70062975 C A 1 0 0 0 0 1 0 0 0 11385 594 21 2 2 OTUD6A 23 70062975 Missense_Mutation SNP C C3N-00547_T 5872728 70062975 85977920 681 15011 DGAT2L6 0 . GRCh38 X 70200385 70200385 + Missense_Mutation SNP C C T novel C3N-00547_T C3N-00547_N C C c.398C>T p.Ser133Phe p.S133F ENST00000333026 4/7 202 80 122 227 227 0 strelka-varscan-mutect DGAT2L6,missense_variant,p.Ser133Phe,ENST00000333026,NM_198512.2; T ENST00000333026 Transcript missense_variant 498/1553 398/1014 133/337 S/F tCc/tTc 1 1 DGAT2L6 HGNC HGNC:23250 protein_coding YES CCDS14397.1 ENSP00000328036 Q6ZPD8 UPI00001C10BF NM_198512.2 deleterious(0) 4/7 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF19 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 70200385 70200385 C T 1 0 0 0 0 1 0 0 0 4266 855 30 3 3 DGAT2L6 23 70200385 Missense_Mutation SNP C C3N-00547_T 137410 70200385 85840510 682 15012 PHKA1 0 . GRCh38 X 72667423 72667423 + Silent SNP C C T novel C3N-00547_T C3N-00547_N C C c.669G>A p.= p.G223G ENST00000373542 7/32 238 84 154 175 175 0 strelka-varscan-mutect PHKA1,synonymous_variant,p.=,ENST00000373545,;PHKA1,synonymous_variant,p.=,ENST00000339490,NM_001122670.1;PHKA1,synonymous_variant,p.=,ENST00000373542,NM_002637.3;PHKA1,synonymous_variant,p.=,ENST00000541944,NM_001172436.1;PHKA1,synonymous_variant,p.=,ENST00000373539,; T ENST00000373542 Transcript synonymous_variant 829/6020 669/3672 223/1223 G ggG/ggA 1 -1 PHKA1 HGNC HGNC:8925 protein_coding YES CCDS14421.1 ENSP00000362643 P46020 UPI000013D340 NM_002637.3 7/32 hmmpanther:PTHR10749:SF4,hmmpanther:PTHR10749,Pfam_domain:PF00723,Gene3D:1.50.10.10,Superfamily_domains:SSF48208 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 49 72667423 72667423 C T 1 0 0 0 0 0 0 0 1 11931 726 26 3 3 PHKA1 23 72667423 Silent SNP C C3N-00547_T 2467038 72667423 83373472 683 15013 BRWD3 0 . GRCh38 X 80692940 80692940 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.3263A>T p.His1088Leu p.H1088L ENST00000373275 28/41 140 55 85 144 144 0 strelka-varscan-mutect BRWD3,missense_variant,p.His1088Leu,ENST00000373275,NM_153252.4;BRWD3,splice_region_variant,,ENST00000473691,; A ENST00000373275 Transcript missense_variant,splice_region_variant 3480/11381 3263/5409 1088/1802 H/L cAc/cTc 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 tolerated(0.16) 28/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 80692940 80692940 T A 1 0 0 0 0 1 0 0 0 1700 1594 55 4 4 BRWD3 23 80692940 Missense_Mutation SNP T C3N-00547_T 8025517 80692940 75347955 684 15014 BRWD3 0 . GRCh38 X 80809032 80809032 + Missense_Mutation SNP T T A novel C3N-00547_T C3N-00547_N T T c.101A>T p.Gln34Leu p.Q34L ENST00000373275 3/41 267 111 156 224 224 0 strelka-varscan-mutect BRWD3,missense_variant,p.Gln34Leu,ENST00000373275,NM_153252.4;BRWD3,non_coding_transcript_exon_variant,,ENST00000478415,; A ENST00000373275 Transcript missense_variant 318/11381 101/5409 34/1802 Q/L cAg/cTg 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 tolerated(0.12) 3/41 hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 80809032 80809032 T A 1 0 0 0 0 1 0 0 0 1700 1580 55 4 4 BRWD3 23 80809032 Missense_Mutation SNP T C3N-00547_T 116092 80809032 75231863 685 15015 DACH2 0 . GRCh38 X 86514287 86514287 + Missense_Mutation SNP C C A novel C3N-00547_T C3N-00547_N C C c.536C>A p.Pro179His p.P179H ENST00000373125 3/12 128 42 86 107 107 0 strelka-varscan-mutect DACH2,missense_variant,p.Pro166His,ENST00000373131,NM_001139514.1;DACH2,missense_variant,p.Pro179His,ENST00000373125,NM_053281.3;DACH2,missense_variant,p.Pro12His,ENST00000508860,NM_001139515.1;DACH2,missense_variant,p.Pro7His,ENST00000613770,;DACH2,5_prime_UTR_variant,,ENST00000510272,;DACH2,missense_variant,p.Pro179His,ENST00000461604,;DACH2,3_prime_UTR_variant,,ENST00000506327,; A ENST00000373125 Transcript missense_variant 536/2232 536/1800 179/599 P/H cCc/cAc 1 1 DACH2 HGNC HGNC:16814 protein_coding YES CCDS14455.1 ENSP00000362217 Q96NX9 UPI00000717B4 NM_053281.3 deleterious(0) 3/12 hmmpanther:PTHR12577,hmmpanther:PTHR12577:SF7 MODERATE 1 SNV 1 1 PASS . . 0 203 3 4 0 0 0 0 -20 0.9999718 1 1 1 0 A 3 1 49 86514287 86514287 C A 1 0 0 0 0 1 0 0 0 4022 623 22 2 2 DACH2 23 86514287 Missense_Mutation SNP C C3N-00547_T 5705255 86514287 69526608 686 15016 DIAPH2 0 . GRCh38 X 97141764 97141764 + Nonsense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.2689G>T p.Glu897Ter p.E897* ENST00000324765 22/27 61 30 31 129 129 0 strelka-varscan-mutect DIAPH2,stop_gained,p.Glu897Ter,ENST00000324765,NM_006729.4;DIAPH2,stop_gained,p.Glu897Ter,ENST00000373061,;DIAPH2,stop_gained,p.Glu897Ter,ENST00000355827,;DIAPH2,stop_gained,p.Glu897Ter,ENST00000373049,NM_007309.3;DIAPH2,stop_gained,p.Glu904Ter,ENST00000373054,; T ENST00000324765 Transcript stop_gained 3036/9333 2689/3306 897/1101 E/* Gaa/Taa 1 1 DIAPH2 HGNC HGNC:2877 protein_coding YES CCDS14467.1 ENSP00000321348 O60879 UPI00001293C8 NM_006729.4 22/27 PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF174,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 49 97141764 97141764 G T 1 0 0 0 0 0 1 0 0 4323 943 33 2 2 DIAPH2 23 97141764 Nonsense_Mutation SNP G C3N-00547_T 10627477 97141764 58899131 687 15017 GPRASP2 0 . GRCh38 X 102715726 102715726 + Missense_Mutation SNP A A T novel C3N-00547_T C3N-00547_N A A c.857A>T p.Asp286Val p.D286V ENST00000543253 5/5 115 67 48 139 139 0 strelka-varscan-mutect GPRASP2,missense_variant,p.Asp286Val,ENST00000543253,NM_001004051.3,NM_001184876.2,NM_001184874.2;GPRASP2,missense_variant,p.Asp286Val,ENST00000535209,NM_001184875.2;GPRASP2,missense_variant,p.Asp286Val,ENST00000332262,NM_001199818.1,NM_138437.5;BHLHB9,upstream_gene_variant,,ENST00000457056,NM_001142528.1,NM_001142527.1,NM_001142525.1,NM_001142526.1,NM_001142524.1;BHLHB9,upstream_gene_variant,,ENST00000361229,NM_030639.2;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000486740,;GPRASP2,downstream_gene_variant,,ENST00000486814,;GPRASP2,downstream_gene_variant,,ENST00000483720,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602366,;ARMCX5-GPRASP2,downstream_gene_variant,,ENST00000602463,;BHLHB9,upstream_gene_variant,,ENST00000483294,; T ENST00000543253 Transcript missense_variant 1929/3935 857/2517 286/838 D/V gAt/gTt 1 1 GPRASP2 HGNC HGNC:25169 protein_coding YES CCDS14501.1 ENSP00000437872 Q96D09 UPI000006F01A NM_001004051.3,NM_001184876.2,NM_001184874.2 deleterious(0) 5/5 hmmpanther:PTHR15712:SF10,hmmpanther:PTHR15712 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 102715726 102715726 A T 1 0 0 0 0 1 0 0 0 6602 333 12 4 4 GPRASP2 23 102715726 Missense_Mutation SNP A C3N-00547_T 5573962 102715726 53325169 688 15018 ACSL4 0 . GRCh38 X 109681119 109681119 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.657C>T p.= p.I219I ENST00000340800 7/17 95 80 15 105 105 0 strelka-varscan-mutect ACSL4,synonymous_variant,p.=,ENST00000340800,NM_001318509.1,NM_022977.2;ACSL4,synonymous_variant,p.=,ENST00000469796,;ACSL4,synonymous_variant,p.=,ENST00000348502,NM_001318510.1,NM_004458.2;ACSL4,downstream_gene_variant,,ENST00000502391,;ACSL4,downstream_gene_variant,,ENST00000508092,;ACSL4,downstream_gene_variant,,ENST00000505855,;ACSL4,downstream_gene_variant,,ENST00000504980,;ACSL4,downstream_gene_variant,,ENST00000469857,; A ENST00000340800 Transcript synonymous_variant 1162/5333 657/2136 219/711 I atC/atT 1 -1 ACSL4 HGNC HGNC:3571 protein_coding YES CCDS14548.1 ENSP00000339787 O60488 UPI000012E293 NM_001318509.1,NM_022977.2 7/17 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF241,Superfamily_domains:SSF56801 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 109681119 109681119 G A 1 0 0 0 0 0 0 0 1 221 1280 45 3 3 ACSL4 23 109681119 Silent SNP G C3N-00547_T 6965393 109681119 46359776 689 15019 DOCK11 0 . GRCh38 X 118681138 118681138 + Missense_Mutation SNP G G T novel C3N-00547_T C3N-00547_N G G c.5752G>T p.Ala1918Ser p.A1918S ENST00000276202 50/53 43 29 14 57 57 0 strelka-varscan-mutect DOCK11,missense_variant,p.Ala1918Ser,ENST00000276204,;DOCK11,missense_variant,p.Ala1918Ser,ENST00000276202,NM_144658.3;DOCK11,missense_variant,p.Ala1747Ser,ENST00000633080,;DOCK11,upstream_gene_variant,,ENST00000632573,; T ENST00000276202 Transcript missense_variant 5815/6625 5752/6222 1918/2073 A/S Gcc/Tcc 1 1 DOCK11 HGNC HGNC:23483 protein_coding YES CCDS35373.1 ENSP00000276202 Q5JSL3 UPI000022DB8F NM_144658.3 deleterious(0) 50/53 Pfam_domain:PF06920,PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF81 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 49 118681138 118681138 G T 1 0 0 0 0 1 0 0 0 4501 1319 46 2 2 DOCK11 23 118681138 Missense_Mutation SNP G C3N-00547_T 9000019 118681138 37359757 690 15020 SEPT6 0 . GRCh38 X 119652908 119652908 + Silent SNP C C A novel C3N-00547_T C3N-00547_N C C c.474G>T p.= p.T158T ENST00000343984 4/10 80 45 35 82 82 0 strelka-mutect SEPT6,synonymous_variant,p.=,ENST00000394610,NM_145799.3;SEPT6,synonymous_variant,p.=,ENST00000354416,;SEPT6,synonymous_variant,p.=,ENST00000343984,NM_015129.5;SEPT6,synonymous_variant,p.=,ENST00000360156,NM_145800.3;SEPT6,synonymous_variant,p.=,ENST00000489216,;SEPT6,synonymous_variant,p.=,ENST00000354228,NM_145802.3;SEPT6,synonymous_variant,p.=,ENST00000460411,; A ENST00000343984 Transcript synonymous_variant 739/2693 474/1305 158/434 T acG/acT 1 -1 SEPT6 HGNC HGNC:15848 protein_coding YES CCDS14584.1 ENSP00000341524 Q14141 UPI0000001C54 NM_015129.5 4/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF55,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 119652908 119652908 C A 1 0 0 0 0 0 0 0 1 14344 639 23 1 1 SEPT6 23 119652908 Silent SNP C C3N-00547_T 971770 119652908 36387987 691 15021 RHOXF1 0 . GRCh38 X 120115767 120115767 + Missense_Mutation SNP G G C C3N-00547_T C3N-00547_N G G c.96C>G p.Ser32Arg p.S32R ENST00000217999 1/3 75 36 39 111 111 0 strelka-varscan-mutect RHOXF1,missense_variant,p.Ser32Arg,ENST00000217999,NM_139282.2;LINC01402,downstream_gene_variant,,ENST00000422226,;RHOXF1-AS1,intron_variant,,ENST00000553843,;RHOXF1-AS1,upstream_gene_variant,,ENST00000555831,;RHOXF1-AS1,upstream_gene_variant,,ENST00000557073,; C ENST00000217999 Transcript missense_variant 171/769 96/555 32/184 S/R agC/agG COSM5366920 1 -1 RHOXF1 HGNC HGNC:29993 protein_coding YES CCDS14593.1 ENSP00000217999 Q8NHV9 UPI0000046608 NM_139282.2 tolerated(0.53) 1/3 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF317 1 MODERATE 1 SNV 1 1 1 PASS rs1377162159 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 49 120115767 120115767 G C 1 0 0 0 0 1 0 0 0 13520 1078 38 4 4 RHOXF1 23 120115767 Missense_Mutation SNP G C3N-00547_T 462859 120115767 35925128 692 15022 RAB33A 0 . GRCh38 X 130184575 130184575 + Silent SNP G G A novel C3N-00547_T C3N-00547_N G G c.549G>A p.= p.K183K ENST00000257017 2/2 281 162 119 317 316 1 strelka-varscan-mutect RAB33A,synonymous_variant,p.=,ENST00000257017,NM_004794.2; A ENST00000257017 Transcript synonymous_variant 963/1258 549/714 183/237 K aaG/aaA 1 1 RAB33A HGNC HGNC:9773 protein_coding YES CCDS14621.1 ENSP00000257017 Q14088 UPI000000126B NM_004794.2 2/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF326,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 49 130184575 130184575 G A 1 0 0 0 0 0 0 0 1 13081 991 35 3 3 RAB33A 23 130184575 Silent SNP G C3N-00547_T 10068808 130184575 25856320 693 15023 PLAC1 0 . GRCh38 X 134566199 134566199 + Missense_Mutation SNP C C A rs200146015 C3N-00547_T C3N-00547_N C C c.484G>T p.Asp162Tyr p.D162Y ENST00000359237 3/3 304 107 197 179 178 1 strelka-varscan-mutect PLAC1,missense_variant,p.Asp162Tyr,ENST00000359237,NM_021796.3;PLAC1,non_coding_transcript_exon_variant,,ENST00000476971,;PLAC1,downstream_gene_variant,,ENST00000473897,; A ENST00000359237 Transcript missense_variant 770/1131 484/639 162/212 D/Y Gat/Tat rs200146015,COSM4589198 1 -1 PLAC1 HGNC HGNC:9044 protein_coding YES CCDS14642.1 ENSP00000352173 Q9HBJ0 UPI0000070F9F NM_021796.3 deleterious(0.03) 3/3 hmmpanther:PTHR14380,hmmpanther:PTHR14380:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200146015 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 49 134566199 134566199 C A 1 0 0 0 0 1 0 0 0 12108 884 31 1 1 PLAC1 23 134566199 Missense_Mutation SNP C C3N-00547_T 4381624 134566199 21474696 694 15024 CFAP74 0 . GRCh38 1 1966451 1966451 + Missense_Mutation SNP G G T rs754420662 C3N-00549_T C3N-00549_N G G c.1321C>A p.Pro441Thr p.P441T ENST00000493964 12/38 61 21 40 65 65 0 strelka-varscan-mutect CFAP74,missense_variant,p.Pro441Thr,ENST00000493964,NM_001304360.1;CFAP74,non_coding_transcript_exon_variant,,ENST00000270720,;CFAP74,non_coding_transcript_exon_variant,,ENST00000468610,; T ENST00000493964 Transcript missense_variant 1477/5247 1321/4755 441/1584 P/T Ccc/Acc rs754420662 1 -1 CFAP74 HGNC HGNC:29368 protein_coding YES ENSP00000417061 Q9C0B2 UPI0004620AE2 NM_001304360.1 tolerated(0.56) 12/38 hmmpanther:PTHR22538 MODERATE 1 SNV 5 1 PASS rs754420662 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 1966451 1966451 G T 1 0 0 0 0 1 0 0 0 3033 1232 43 2 2 CFAP74 1 1966451 Missense_Mutation SNP G C3N-00549_T 1966451 246989971 1 15025 SPEN 0 . GRCh38 1 15931584 15931584 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.5344G>T p.Asp1782Tyr p.D1782Y ENST00000375759 11/15 87 35 52 103 103 0 strelka-varscan-mutect SPEN,missense_variant,p.Asp1782Tyr,ENST00000375759,NM_015001.2; T ENST00000375759 Transcript missense_variant 5548/12232 5344/10995 1782/3664 D/Y Gat/Tat 1 1 SPEN HGNC HGNC:17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 deleterious(0.02) 11/15 hmmpanther:PTHR23189:SF48,hmmpanther:PTHR23189 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 15931584 15931584 G T 1 0 0 0 0 1 0 0 0 15389 942 33 2 2 SPEN 1 15931584 Missense_Mutation SNP G C3N-00549_T 13965133 15931584 233024838 2 15026 SPATA21 0 . GRCh38 1 16409912 16409912 + Silent SNP C C A rs145844310 C3N-00549_T C3N-00549_N C C c.276G>T p.= p.V92V ENST00000335496 6/13 67 28 39 123 123 0 strelka-varscan-mutect SPATA21,synonymous_variant,p.=,ENST00000335496,NM_198546.1;SPATA21,synonymous_variant,p.=,ENST00000540400,;SPATA21,non_coding_transcript_exon_variant,,ENST00000466212,; A ENST00000335496 Transcript synonymous_variant 759/2015 276/1410 92/469 V gtG/gtT rs145844310 1 -1 SPATA21 HGNC HGNC:28026 protein_coding YES CCDS172.1 ENSP00000335612 Q7Z572 UPI00001B4B16 NM_198546.1 6/13 hmmpanther:PTHR10891:SF596,hmmpanther:PTHR10891 LOW 1 SNV 1 1 PASS rs145844310 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 16409912 16409912 C A 1 0 0 0 0 0 0 0 1 15337 581 21 2 2 SPATA21 1 16409912 Silent SNP C C3N-00549_T 478328 16409912 232546510 3 15027 PAX7 0 . GRCh38 1 18700689 18700689 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.823C>A p.Gln275Lys p.Q275K ENST00000375375 6/8 50 13 37 62 62 0 strelka-varscan-mutect PAX7,missense_variant,p.Gln275Lys,ENST00000420770,NM_001135254.1;PAX7,missense_variant,p.Gln275Lys,ENST00000375375,NM_002584.2;PAX7,missense_variant,p.Gln273Lys,ENST00000400661,NM_013945.2; A ENST00000375375 Transcript missense_variant 1421/2260 823/1563 275/520 Q/K Cag/Aag 1 1 PAX7 HGNC HGNC:8621 protein_coding YES CCDS186.1 ENSP00000364524 P23759 UPI000004A132 NM_002584.2 deleterious(0.01) 6/8 PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF248,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 199 9 2 0 0 0 0 -20 0.9999763 1 1 1 0 A 3 1 50 18700689 18700689 C A 1 0 0 0 0 1 0 0 0 11569 711 25 2 2 PAX7 1 18700689 Missense_Mutation SNP C C3N-00549_T 2290777 18700689 230255733 4 15028 FGR 0 . GRCh38 1 27614481 27614481 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1198G>T p.Asp400Tyr p.D400Y ENST00000374005 11/13 137 46 91 155 155 0 strelka-varscan-mutect FGR,missense_variant,p.Asp400Tyr,ENST00000374005,NM_005248.2;FGR,missense_variant,p.Asp400Tyr,ENST00000399173,NM_001042747.1;FGR,missense_variant,p.Asp400Tyr,ENST00000374004,;FGR,missense_variant,p.Asp400Tyr,ENST00000374003,NM_001042729.1;FGR,downstream_gene_variant,,ENST00000457296,; A ENST00000374005 Transcript missense_variant 1487/2729 1198/1590 400/529 D/Y Gac/Tac 1 -1 FGR HGNC HGNC:3697 protein_coding YES CCDS305.1 ENSP00000363117 P09769 UPI000012A72F NM_005248.2 deleterious(0) 11/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF224,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 27614481 27614481 C A 1 0 0 0 0 1 0 0 0 5738 913 32 2 2 FGR 1 27614481 Missense_Mutation SNP C C3N-00549_T 8913792 27614481 221341941 5 15029 COL16A1 0 . GRCh38 1 31681044 31681044 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.2562G>C p.Gln854His p.Q854H ENST00000373672 38/71 43 19 24 97 97 0 strelka-varscan-mutect COL16A1,missense_variant,p.Gln854His,ENST00000373672,NM_001856.3;COL16A1,missense_variant,p.Gln854His,ENST00000373668,;COL16A1,missense_variant,p.Gln75His,ENST00000458715,;COL16A1,downstream_gene_variant,,ENST00000482478,;COL16A1,downstream_gene_variant,,ENST00000474000,;COL16A1,downstream_gene_variant,,ENST00000529928,; G ENST00000373672 Transcript missense_variant 3079/5736 2562/4815 854/1604 Q/H caG/caC 1 -1 COL16A1 HGNC HGNC:2193 protein_coding YES CCDS41297.1 ENSP00000362776 Q07092 UPI0000203DD1 NM_001856.3 tolerated(0.19) 38/71 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 31681044 31681044 C G 1 0 0 0 0 1 0 0 0 3461 912 32 4 4 COL16A1 1 31681044 Missense_Mutation SNP C C3N-00549_T 4066563 31681044 217275378 6 15030 CSMD2 0 . GRCh38 1 33546083 33546083 + Silent SNP G G C novel C3N-00549_T C3N-00549_N G G c.9054C>G p.= p.T3018T ENST00000373381 57/71 116 32 84 166 166 0 strelka-varscan-mutect CSMD2,synonymous_variant,p.=,ENST00000373381,NM_001281956.1;CSMD2,synonymous_variant,p.=,ENST00000619121,;CSMD2,synonymous_variant,p.=,ENST00000373388,NM_052896.4;CSMD2,synonymous_variant,p.=,ENST00000241312,; C ENST00000373381 Transcript synonymous_variant 9231/13698 9054/10896 3018/3631 T acC/acG 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 57/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF371,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 33546083 33546083 G C 1 0 0 0 0 0 0 0 1 3746 987 35 4 4 CSMD2 1 33546083 Silent SNP G C3N-00549_T 1865039 33546083 215410339 7 15031 PATJ 0 . GRCh38 1 61990350 61990350 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.3853G>T p.Asp1285Tyr p.D1285Y ENST00000371158 28/43 91 21 70 86 86 0 strelka-varscan-mutect PATJ,missense_variant,p.Asp1285Tyr,ENST00000371158,NM_176877.2;PATJ,missense_variant,p.Asp69Tyr,ENST00000635137,;PATJ,missense_variant,p.Asp69Tyr,ENST00000307297,;PATJ,missense_variant,p.Asp131Tyr,ENST00000494842,;PATJ,missense_variant,p.Asp101Tyr,ENST00000490547,;PATJ,intron_variant,,ENST00000613764,;PATJ,missense_variant,p.Asp744Tyr,ENST00000484937,;PATJ,3_prime_UTR_variant,,ENST00000635023,;PATJ,non_coding_transcript_exon_variant,,ENST00000484562,;PATJ,non_coding_transcript_exon_variant,,ENST00000459752,;PATJ,non_coding_transcript_exon_variant,,ENST00000635214,; T ENST00000371158 Transcript missense_variant 3967/8505 3853/5406 1285/1801 D/Y Gat/Tat 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 deleterious(0) 28/43 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 61990350 61990350 G T 1 0 0 0 0 1 0 0 0 11558 942 33 2 2 PATJ 1 61990350 Missense_Mutation SNP G C3N-00549_T 28444267 61990350 186966072 8 15032 MIER1 0 . GRCh38 1 66984855 66984855 + Silent SNP A A T novel C3N-00549_T C3N-00549_N A A c.1653A>T p.= p.A551A ENST00000401041 14/14 77 24 53 100 100 0 strelka-varscan-mutect MIER1,synonymous_variant,p.=,ENST00000357692,NM_001146112.1,NM_020948.3,NM_001146110.1;MIER1,synonymous_variant,p.=,ENST00000355356,NM_001077701.2;MIER1,synonymous_variant,p.=,ENST00000401041,NM_001077700.2;MIER1,intron_variant,,ENST00000371018,NM_001146111.1;MIER1,intron_variant,,ENST00000355977,NM_001146113.1;MIER1,intron_variant,,ENST00000371016,NM_001077702.2;MIER1,intron_variant,,ENST00000371014,NM_001077703.2;MIER1,intron_variant,,ENST00000401042,NM_001077704.2; T ENST00000401041 Transcript synonymous_variant 1723/2552 1653/1698 551/565 A gcA/gcT 1 1 MIER1 HGNC HGNC:29657 protein_coding YES CCDS53326.1 ENSP00000383820 Q8N108 UPI0000204526 NM_001077700.2 14/14 hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF24 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 66984855 66984855 A T 1 0 0 0 0 0 0 0 1 9543 175 7 4 4 MIER1 1 66984855 Silent SNP A C3N-00549_T 4994505 66984855 181971567 9 15033 ERICH3 0 . GRCh38 1 74589692 74589692 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.2115G>C p.Trp705Cys p.W705C ENST00000326665 12/15 203 125 78 186 186 0 strelka-varscan-mutect ERICH3,missense_variant,p.Trp705Cys,ENST00000326665,NM_001002912.4;ERICH3,missense_variant,p.Trp508Cys,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,upstream_gene_variant,,ENST00000416017,;ERICH3-AS1,upstream_gene_variant,,ENST00000620678,; G ENST00000326665 Transcript missense_variant 2334/7159 2115/4593 705/1530 W/C tgG/tgC 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0.02) 12/15 hmmpanther:PTHR23034 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 74589692 74589692 C G 1 0 0 0 0 1 0 0 0 5083 624 22 4 4 ERICH3 1 74589692 Missense_Mutation SNP C C3N-00549_T 7604837 74589692 174366730 10 15034 ZZZ3 0 . GRCh38 1 77632397 77632397 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.958G>A p.Val320Met p.V320M ENST00000370801 5/15 254 159 95 235 235 0 strelka-varscan-mutect ZZZ3,missense_variant,p.Val320Met,ENST00000370801,NM_015534.4;ZZZ3,intron_variant,,ENST00000370798,NM_001308237.1;ZZZ3,downstream_gene_variant,,ENST00000433749,;ZZZ3,downstream_gene_variant,,ENST00000414381,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000476275,;ZZZ3,upstream_gene_variant,,ENST00000481346,;ZZZ3,downstream_gene_variant,,ENST00000463166,; T ENST00000370801 Transcript missense_variant 1434/4328 958/2712 320/903 V/M Gtg/Atg 1 -1 ZZZ3 HGNC HGNC:24523 protein_coding YES CCDS677.1 ENSP00000359837 Q8IYH5 UPI0000074256 NM_015534.4 deleterious(0.02) 5/15 hmmpanther:PTHR22705 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 77632397 77632397 C T 1 0 0 0 0 1 0 0 0 18860 478 17 3 3 ZZZ3 1 77632397 Missense_Mutation SNP C C3N-00549_T 3042705 77632397 171324025 11 15035 VAV3 0 . GRCh38 1 107779448 107779448 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.366G>T p.Leu122Phe p.L122F ENST00000370056 3/27 90 67 23 101 101 0 strelka-varscan-mutect VAV3,missense_variant,p.Leu122Phe,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Leu122Phe,ENST00000527011,;VAV3,missense_variant,p.Leu117Phe,ENST00000490388,;VAV3,non_coding_transcript_exon_variant,,ENST00000343258,;VAV3,non_coding_transcript_exon_variant,,ENST00000469325,;VAV3,non_coding_transcript_exon_variant,,ENST00000530671,;VAV3,non_coding_transcript_exon_variant,,ENST00000524574,; A ENST00000370056 Transcript missense_variant 641/4990 366/2544 122/847 L/F ttG/ttT 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 deleterious(0.02) 3/27 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 107779448 107779448 C A 1 0 0 0 0 1 0 0 0 17678 593 21 2 2 VAV3 1 107779448 Missense_Mutation SNP C C3N-00549_T 30147051 107779448 141176974 12 15036 AHCYL1 0 . GRCh38 1 110017945 110017945 + Splice_Site SNP G G T novel C3N-00549_T C3N-00549_N G G c.1053-1G>T p.X351_splice ENST00000369799 223 145 78 210 210 0 strelka-varscan-mutect AHCYL1,splice_acceptor_variant,,ENST00000393614,NM_001242673.1,NM_001242674.1;AHCYL1,splice_acceptor_variant,,ENST00000369799,NM_006621.5;AHCYL1,splice_acceptor_variant,,ENST00000359172,NM_001242675.1,NM_001242676.1;AHCYL1,splice_acceptor_variant,,ENST00000481423,;AHCYL1,downstream_gene_variant,,ENST00000475081,;AHCYL1,upstream_gene_variant,,ENST00000469401,; T ENST00000369799 Transcript splice_acceptor_variant -/4015 1053/1593 351/530 1 1 AHCYL1 HGNC HGNC:344 protein_coding YES CCDS818.1 ENSP00000358814 O43865 A0A024R0A8 UPI00000022AC NM_006621.5 10/16 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 50 110017945 110017945 G T 1 0 0 0 0 0 0 1 0 487 985 34 2 2 AHCYL1 1 110017945 Splice_Site SNP G C3N-00549_T 2238497 110017945 138938477 13 15037 HIST2H2BE 0 . GRCh38 1 149886414 149886414 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.227G>T p.Gly76Val p.G76V ENST00000369155 1/1 563 358 205 482 481 1 strelka-varscan-mutect HIST2H2BE,missense_variant,p.Gly76Val,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2;HIST2H2AC,upstream_gene_variant,,ENST00000331380,NM_003517.2; A ENST00000369155 Transcript missense_variant 239/2194 227/381 76/126 G/V gGa/gTa 1 -1 HIST2H2BE HGNC HGNC:4760 protein_coding YES CCDS936.1 ENSP00000358151 Q16778 UPI0000000C6F NM_003528.2 deleterious_low_confidence(0.03) 1/1 hmmpanther:PTHR23428,Pfam_domain:PF00125,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 149886414 149886414 C A 1 0 0 0 0 1 0 0 0 7067 855 30 2 2 HIST2H2BE 1 149886414 Missense_Mutation SNP C C3N-00549_T 39868469 149886414 99070008 14 15038 OTUD7B 0 . GRCh38 1 149949002 149949002 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1205G>T p.Gly402Val p.G402V ENST00000581312 10/12 187 122 65 113 112 1 strelka-varscan-mutect OTUD7B,missense_variant,p.Gly402Val,ENST00000581312,NM_020205.3;OTUD7B,missense_variant,p.Gly402Val,ENST00000417191,; A ENST00000581312 Transcript missense_variant 1500/8872 1205/2532 402/843 G/V gGc/gTc 1 -1 OTUD7B HGNC HGNC:16683 protein_coding YES CCDS72903.1 ENSP00000462729 Q6GQQ9 UPI000020415D NM_020205.3 deleterious(0.02) 10/12 hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF9 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 50 149949002 149949002 C A 1 0 0 0 0 1 0 0 0 11388 739 26 2 2 OTUD7B 1 149949002 Missense_Mutation SNP C C3N-00549_T 62588 149949002 99007420 15 15039 HRNR 0 . GRCh38 1 152220906 152220906 + Silent SNP G G A rs775099464 C3N-00549_T C3N-00549_N G G c.723C>T p.= p.S241S ENST00000368801 3/3 576 336 240 623 623 0 strelka-varscan-mutect HRNR,synonymous_variant,p.=,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368801 Transcript synonymous_variant 799/9623 723/8553 241/2850 S tcC/tcT rs775099464 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 LOW 1 SNV 1 1 PASS rs775099464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 152220906 152220906 G A 1 0 0 0 0 0 0 0 1 7254 987 35 3 3 HRNR 1 152220906 Silent SNP G C3N-00549_T 2271904 152220906 96735516 16 15040 FLG 0 . GRCh38 1 152306980 152306980 + Missense_Mutation SNP C C A rs138880214 C3N-00549_T C3N-00549_N C C c.7906G>T p.Gly2636Cys p.G2636C ENST00000368799 3/3 126 76 50 107 107 0 strelka-varscan-mutect FLG,missense_variant,p.Gly2636Cys,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript missense_variant 7942/12747 7906/12186 2636/4061 G/C Ggt/Tgt rs138880214 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.12) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS rs138880214 . 0 204 2 3 0 0 0 0 -20 0.9999938 1 1 1 0 A 3 1 50 152306980 152306980 C A 1 0 0 0 0 1 0 0 0 5784 594 21 2 2 FLG 1 152306980 Missense_Mutation SNP C C3N-00549_T 86074 152306980 96649442 17 15041 FLG 0 . GRCh38 1 152310591 152310591 + Missense_Mutation SNP C C T C3N-00549_T C3N-00549_N C C c.4295G>A p.Gly1432Glu p.G1432E ENST00000368799 3/3 713 423 290 504 504 0 strelka-varscan-mutect FLG,missense_variant,p.Gly1432Glu,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 4331/12747 4295/12186 1432/4061 G/E gGg/gAg COSM3474039 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) 3/3 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 152310591 152310591 C T 1 0 0 0 0 1 0 0 0 5784 623 22 3 3 FLG 1 152310591 Missense_Mutation SNP C C3N-00549_T 3611 152310591 96645831 18 15042 FLG 0 . GRCh38 1 152313721 152313721 + Missense_Mutation SNP G G T rs780239211 C3N-00549_T C3N-00549_N G G c.1165C>A p.Gln389Lys p.Q389K ENST00000368799 3/3 617 375 242 543 543 0 strelka-varscan-mutect FLG,missense_variant,p.Gln389Lys,ENST00000368799,NM_002016.1;FLG-AS1,non_coding_transcript_exon_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 1201/12747 1165/12186 389/4061 Q/K Cag/Aag rs780239211 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.02) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 PASS rs780239211 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 152313721 152313721 G T 1 0 0 0 0 1 0 0 0 5784 1357 47 2 2 FLG 1 152313721 Missense_Mutation SNP G C3N-00549_T 3130 152313721 96642701 19 15043 FLG2 0 . GRCh38 1 152351246 152351246 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.6540C>T p.= p.H2180H ENST00000388718 3/3 219 136 83 199 199 0 strelka-varscan-mutect FLG2,synonymous_variant,p.=,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; A ENST00000388718 Transcript synonymous_variant 6613/9124 6540/7176 2180/2391 H caC/caT 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 152351246 152351246 G A 1 0 0 0 0 0 0 0 1 5785 1368 48 3 3 FLG2 1 152351246 Silent SNP G C3N-00549_T 37525 152351246 96605176 20 15044 KPRP 0 . GRCh38 1 152760795 152760795 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1207G>T p.Ala403Ser p.A403S ENST00000606109 1/1 293 165 128 237 237 0 strelka-varscan-mutect KPRP,missense_variant,p.Ala403Ser,ENST00000606109,NM_001025231.1; T ENST00000606109 Transcript missense_variant 1235/2492 1207/1740 403/579 A/S Gct/Tct 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 tolerated(0.13) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF98 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 152760795 152760795 G T 1 0 0 0 0 1 0 0 0 8316 1319 46 2 2 KPRP 1 152760795 Missense_Mutation SNP G C3N-00549_T 409549 152760795 96195627 21 15045 LCE1C 0 . GRCh38 1 152805374 152805374 + Silent SNP A A T C3N-00549_T C3N-00549_N A A c.105T>A p.= p.P35P ENST00000607093 1/1 421 262 159 387 387 0 strelka-varscan-mutect LCE1C,synonymous_variant,p.=,ENST00000607093,NM_001276331.1,NM_178351.3;LCE1C,intron_variant,,ENST00000606576,; T ENST00000607093 Transcript synonymous_variant 105/644 105/357 35/118 P ccT/ccA COSM4022558 1 -1 LCE1C HGNC HGNC:29464 protein_coding YES CCDS1026.1 ENSP00000475270 Q5T751 UPI0000140B0A NM_001276331.1,NM_178351.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23263,Pfam_domain:PF14672,Prints_domain:PR00021 1 LOW 1 SNV 1 1 PASS rs757242686 . 0 208 0 0 2 0 0 0 -20 0.9994141 1 1 1 0 T 2 4 50 152805374 152805374 A T 1 0 0 0 0 0 0 0 1 8566 407 15 4 4 LCE1C 1 152805374 Silent SNP A C3N-00549_T 44579 152805374 96151048 22 15046 ADAR 0 . GRCh38 1 154586239 154586239 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.3144G>T p.= p.L1048L ENST00000368474 12/15 388 209 179 290 290 0 strelka-varscan-mutect ADAR,synonymous_variant,p.=,ENST00000368474,NM_001111.4,NM_015840.3,NM_015841.3;ADAR,synonymous_variant,p.=,ENST00000368471,NM_001193495.1,NM_001025107.2;ADAR,synonymous_variant,p.=,ENST00000529168,;ADAR,non_coding_transcript_exon_variant,,ENST00000534279,;ADAR,non_coding_transcript_exon_variant,,ENST00000530954,;ADAR,upstream_gene_variant,,ENST00000492630,; A ENST00000368474 Transcript synonymous_variant 3344/6625 3144/3681 1048/1226 L ctG/ctT 1 -1 ADAR HGNC HGNC:225 protein_coding YES CCDS1071.1 ENSP00000357459 P55265 UPI000045626B NM_001111.4,NM_015840.3,NM_015841.3 12/15 PROSITE_profiles:PS50141,hmmpanther:PTHR10910:SF107,hmmpanther:PTHR10910,Pfam_domain:PF02137,SMART_domains:SM00552 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 154586239 154586239 C A 1 0 0 0 0 0 0 0 1 325 697 25 2 2 ADAR 1 154586239 Silent SNP C C3N-00549_T 1780865 154586239 94370183 23 15047 BCAN 0 . GRCh38 1 156647093 156647093 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.384C>A p.= p.R128R ENST00000329117 3/14 129 76 53 78 78 0 strelka-varscan-mutect BCAN,synonymous_variant,p.=,ENST00000329117,NM_021948.4;BCAN,synonymous_variant,p.=,ENST00000361588,NM_198427.1;BCAN,synonymous_variant,p.=,ENST00000457777,;BCAN,synonymous_variant,p.=,ENST00000441358,;BCAN,intron_variant,,ENST00000424639,;RP11-284F21.7,non_coding_transcript_exon_variant,,ENST00000448869,;RP11-284F21.10,upstream_gene_variant,,ENST00000605886,;BCAN,synonymous_variant,p.=,ENST00000479949,;BCAN,upstream_gene_variant,,ENST00000491823,; A ENST00000329117 Transcript synonymous_variant 720/3466 384/2736 128/911 R cgC/cgA 1 1 BCAN HGNC HGNC:23059 protein_coding YES CCDS1149.1 ENSP00000331210 Q96GW7 UPI000006F0E9 NM_021948.4 3/14 PROSITE_profiles:PS50835,hmmpanther:PTHR22804,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 156647093 156647093 C A 1 0 0 0 0 0 0 0 1 1492 726 26 2 2 BCAN 1 156647093 Silent SNP C C3N-00549_T 2060854 156647093 92309329 24 15048 NES 0 . GRCh38 1 156670553 156670553 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.3635A>G p.Glu1212Gly p.E1212G ENST00000368223 4/4 94 52 42 67 67 0 strelka-varscan-mutect NES,missense_variant,p.Glu1212Gly,ENST00000368223,NM_006617.1; C ENST00000368223 Transcript missense_variant 3768/5558 3635/4866 1212/1621 E/G gAg/gGg 1 -1 NES HGNC HGNC:7756 protein_coding YES CCDS1151.1 ENSP00000357206 P48681 UPI0000213DC0 NM_006617.1 tolerated(0.06) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 156670553 156670553 T C 1 0 0 0 0 1 0 0 0 10372 1551 54 5 5 NES 1 156670553 Missense_Mutation SNP T C3N-00549_T 23460 156670553 92285869 25 15049 OR10J3 0 . GRCh38 1 159313929 159313929 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.731C>A p.Ser244Tyr p.S244Y ENST00000332217 1/1 410 237 173 330 330 0 strelka-varscan-mutect OR10J3,missense_variant,p.Ser244Tyr,ENST00000332217,NM_001004467.1; T ENST00000332217 Transcript missense_variant 731/990 731/990 244/329 S/Y tCc/tAc COSM5378101 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 159313929 159313929 G T 1 0 0 0 0 1 0 0 0 10988 1174 41 2 2 OR10J3 1 159313929 Missense_Mutation SNP G C3N-00549_T 2643376 159313929 89642493 26 15050 OR10J3 0 . GRCh38 1 159314120 159314120 + Nonsense_Mutation SNP A A T C3N-00549_T C3N-00549_N A A c.540T>A p.Cys180Ter p.C180* ENST00000332217 1/1 281 165 116 204 204 0 strelka-varscan-mutect OR10J3,stop_gained,p.Cys180Ter,ENST00000332217,NM_001004467.1; T ENST00000332217 Transcript stop_gained 540/990 540/990 180/329 C/* tgT/tgA COSM675970 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 159314120 159314120 A T 1 0 0 0 0 0 1 0 0 10988 157 6 4 4 OR10J3 1 159314120 Nonsense_Mutation SNP A C3N-00549_T 191 159314120 89642302 27 15051 TEX35 0 . GRCh38 1 178522419 178522419 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.681G>T p.Lys227Asn p.K227N ENST00000319416 9/9 163 108 55 98 98 0 strelka-varscan-mutect TEX35,missense_variant,p.Lys227Asn,ENST00000319416,NM_032126.4;TEX35,3_prime_UTR_variant,,ENST00000367642,;TEX35,3_prime_UTR_variant,,ENST00000367641,;TEX35,intron_variant,,ENST00000367639,NM_001170722.1,NM_001170724.1;TEX35,downstream_gene_variant,,ENST00000367643,NM_001170723.1;TEX35,downstream_gene_variant,,ENST00000442872,;TEX35,intron_variant,,ENST00000419909,; T ENST00000319416 Transcript missense_variant 793/1023 681/702 227/233 K/N aaG/aaT 1 1 TEX35 HGNC HGNC:25366 protein_coding YES CCDS1323.1 ENSP00000323795 Q5T0J7 UPI00001405CF NM_032126.4 tolerated_low_confidence(0.22) 9/9 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 178522419 178522419 G T 1 0 0 0 0 1 0 0 0 16211 1020 36 2 2 TEX35 1 178522419 Missense_Mutation SNP G C3N-00549_T 19208299 178522419 70434003 28 15052 CACNA1E 0 . GRCh38 1 181739253 181739253 + Missense_Mutation SNP C C T C3N-00549_T C3N-00549_N C C c.3719C>T p.Ala1240Val p.A1240V ENST00000367573 25/48 157 104 53 130 130 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Ala1221Val,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Ala1240Val,ENST00000621551,;CACNA1E,missense_variant,p.Ala1240Val,ENST00000367567,;CACNA1E,missense_variant,p.Ala1221Val,ENST00000358338,;CACNA1E,missense_variant,p.Ala1240Val,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Ala1240Val,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Ala1239Val,ENST00000357570,;CACNA1E,missense_variant,p.Ala1221Val,ENST00000360108,; T ENST00000367573 Transcript missense_variant,splice_region_variant 3719/7067 3719/6942 1240/2313 A/V gCg/gTg COSM3934304,COSM3934305,COSM3934306,COSM5081247,COSM5081248 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0) 25/48 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 181739253 181739253 C T 1 0 0 0 0 1 0 0 0 2230 782 27 1 1 CACNA1E 1 181739253 Missense_Mutation SNP C C3N-00549_T 3216834 181739253 67217169 29 15053 DHX9 0 . GRCh38 1 182879333 182879333 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.2435G>A p.Gly812Glu p.G812E ENST00000367549 21/28 88 54 34 112 112 0 strelka-varscan-mutect DHX9,missense_variant,p.Gly812Glu,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000474446,;DHX9,upstream_gene_variant,,ENST00000473076,;DHX9,downstream_gene_variant,,ENST00000490519,; A ENST00000367549 Transcript missense_variant 2545/4240 2435/3813 812/1270 G/E gGa/gAa 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 tolerated(0.29) 21/28 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 182879333 182879333 G A 1 0 0 0 0 1 0 0 0 4320 1174 41 3 3 DHX9 1 182879333 Missense_Mutation SNP G C3N-00549_T 1140080 182879333 66077089 30 15054 NMNAT2 0 . GRCh38 1 183290163 183290163 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.286T>A p.Cys96Ser p.C96S ENST00000287713 4/11 154 105 49 155 154 1 strelka-varscan-mutect NMNAT2,missense_variant,p.Cys96Ser,ENST00000287713,NM_015039.3;NMNAT2,missense_variant,p.Cys91Ser,ENST00000294868,NM_170706.3;NMNAT2,non_coding_transcript_exon_variant,,ENST00000473046,; T ENST00000287713 Transcript missense_variant 621/5663 286/924 96/307 C/S Tgc/Agc 1 -1 NMNAT2 HGNC HGNC:16789 protein_coding YES CCDS1353.1 ENSP00000287713 Q9BZQ4 UPI00000706AB NM_015039.3 deleterious(0.01) 4/11 Gene3D:3.40.50.620,Pfam_domain:PF01467,hmmpanther:PTHR12039,hmmpanther:PTHR12039:SF2,Superfamily_domains:SSF52374 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 183290163 183290163 A T 1 0 0 0 0 1 0 0 0 10538 188 7 4 4 NMNAT2 1 183290163 Missense_Mutation SNP A C3N-00549_T 410830 183290163 65666259 31 15055 BRINP3 0 . GRCh38 1 190098874 190098874 + Missense_Mutation SNP G G T rs760035565 C3N-00549_T C3N-00549_N G G c.1445C>A p.Thr482Asn p.T482N ENST00000367462 8/8 313 184 129 304 304 0 strelka-varscan-mutect BRINP3,missense_variant,p.Thr482Asn,ENST00000367462,NM_199051.1; T ENST00000367462 Transcript missense_variant 1930/3142 1445/2301 482/766 T/N aCc/aAc rs760035565,COSM5678014 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 tolerated(0.13) 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760035565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 190098874 190098874 G T 1 0 0 0 0 1 0 0 0 1687 1261 44 2 2 BRINP3 1 190098874 Missense_Mutation SNP G C3N-00549_T 6808711 190098874 58857548 32 15056 FAM71A 0 . GRCh38 1 212625555 212625555 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.678G>T p.Met226Ile p.M226I ENST00000294829 1/1 203 108 95 176 176 0 strelka-varscan-mutect FAM71A,missense_variant,p.Met226Ile,ENST00000294829,NM_153606.3;ATF3,downstream_gene_variant,,ENST00000341491,NM_001674.3;ATF3,downstream_gene_variant,,ENST00000613954,NM_001206488.2,NM_001206484.2;ATF3,downstream_gene_variant,,ENST00000366987,NM_001030287.3;RP11-338C15.5,non_coding_transcript_exon_variant,,ENST00000427949,;ATF3,downstream_gene_variant,,ENST00000492118,; T ENST00000294829 Transcript missense_variant 1082/2305 678/1785 226/594 M/I atG/atT 1 1 FAM71A HGNC HGNC:26541 protein_coding YES CCDS1507.1 ENSP00000294829 Q8IYT1 UPI000013E1C2 NM_153606.3 tolerated(0.19) 1/1 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF9 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 212625555 212625555 G T 1 0 0 0 0 1 0 0 0 5471 1348 47 2 2 FAM71A 1 212625555 Missense_Mutation SNP G C3N-00549_T 22526681 212625555 36330867 33 15057 RAB3GAP2 0 . GRCh38 1 220210826 220210826 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.485C>A p.Ser162Ter p.S162* ENST00000358951 6/35 661 411 250 556 556 0 strelka-varscan-mutect RAB3GAP2,stop_gained,p.Ser162Ter,ENST00000358951,NM_012414.3;RAB3GAP2,stop_gained,p.Ser64Ter,ENST00000484658,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,3_prime_UTR_variant,,ENST00000474178,;RAB3GAP2,intron_variant,,ENST00000237724,;RP11-568G11.4,downstream_gene_variant,,ENST00000604232,; T ENST00000358951 Transcript stop_gained 602/7257 485/4182 162/1393 S/* tCa/tAa 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 6/35 Pfam_domain:PF14655,hmmpanther:PTHR12472 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 220210826 220210826 G T 1 0 0 0 0 0 1 0 0 13095 1294 45 2 2 RAB3GAP2 1 220210826 Nonsense_Mutation SNP G C3N-00549_T 7585271 220210826 28745596 34 15058 DEGS1 0 . GRCh38 1 224189762 224189762 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.268G>T p.Glu90Ter p.E90* ENST00000323699 2/3 231 137 94 157 157 0 strelka-varscan-mutect DEGS1,stop_gained,p.Glu90Ter,ENST00000323699,NM_003676.3;DEGS1,stop_gained,p.Glu90Ter,ENST00000391877,;DEGS1,stop_gained,p.Glu69Ter,ENST00000415210,;DEGS1,non_coding_transcript_exon_variant,,ENST00000465848,;DEGS1,upstream_gene_variant,,ENST00000498813,; T ENST00000323699 Transcript stop_gained 434/2101 268/972 90/323 E/* Gag/Tag 1 1 DEGS1 HGNC HGNC:13709 protein_coding YES CCDS1540.1 ENSP00000316476 O15121 A0A024R3P1 UPI000007137B NM_003676.3 2/3 hmmpanther:PTHR12879:SF2,hmmpanther:PTHR12879,Pfam_domain:PF00487,PIRSF_domain:PIRSF017228 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 224189762 224189762 G T 1 0 0 0 0 0 1 0 0 4227 1291 45 2 2 DEGS1 1 224189762 Nonsense_Mutation SNP G C3N-00549_T 3978936 224189762 24766660 35 15059 RYR2 0 . GRCh38 1 237503434 237503434 + Missense_Mutation SNP C C A rs765102386 C3N-00549_T C3N-00549_N C C c.2542C>A p.Arg848Ser p.R848S ENST00000366574 22/105 296 181 115 223 223 0 strelka-varscan-mutect RYR2,missense_variant,p.Arg848Ser,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Arg832Ser,ENST00000360064,; A ENST00000366574 Transcript missense_variant 2859/16562 2542/14904 848/4967 R/S Cgc/Agc rs765102386,COSM403302 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.07) 22/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765102386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 237503434 237503434 C A 1 0 0 0 0 1 0 0 0 14029 536 19 1 1 RYR2 1 237503434 Missense_Mutation SNP C C3N-00549_T 13313672 237503434 11452988 36 15060 RYR2 0 . GRCh38 1 237589835 237589835 + Missense_Mutation SNP G G T rs775350665 C3N-00549_T C3N-00549_N G G c.3641G>T p.Arg1214Met p.R1214M ENST00000366574 30/105 330 194 136 259 259 0 strelka-varscan-mutect RYR2,missense_variant,p.Arg1214Met,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Arg1198Met,ENST00000360064,; T ENST00000366574 Transcript missense_variant 3958/16562 3641/14904 1214/4967 R/M aGg/aTg rs775350665 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 30/105 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449 MODERATE 1 SNV 1 1 PASS rs775350665 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 237589835 237589835 G T 1 0 0 0 0 1 0 0 0 14029 1000 35 2 2 RYR2 1 237589835 Missense_Mutation SNP G C3N-00549_T 86401 237589835 11366587 37 15061 RYR2 0 . GRCh38 1 237614745 237614745 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.5617G>A p.Ala1873Thr p.A1873T ENST00000366574 37/105 165 103 62 91 91 0 strelka-varscan-mutect RYR2,missense_variant,p.Ala1873Thr,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ala1857Thr,ENST00000360064,; A ENST00000366574 Transcript missense_variant 5934/16562 5617/14904 1873/4967 A/T Gca/Aca 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.25) 37/105 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1312516879 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 237614745 237614745 G A 1 0 0 0 0 1 0 0 0 14029 1319 46 3 3 RYR2 1 237614745 Missense_Mutation SNP G C3N-00549_T 24910 237614745 11341677 38 15062 NLRP3 0 . GRCh38 1 247423289 247423289 + Nonsense_Mutation SNP G G T rs763971331 C3N-00549_T C3N-00549_N G G c.343G>T p.Glu115Ter p.E115* ENST00000336119 2/9 625 392 233 532 532 0 strelka-varscan-mutect NLRP3,stop_gained,p.Glu115Ter,ENST00000366497,NM_001127461.2;NLRP3,stop_gained,p.Glu115Ter,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,stop_gained,p.Glu115Ter,ENST00000366496,;NLRP3,stop_gained,p.Glu115Ter,ENST00000391828,NM_001079821.2;NLRP3,stop_gained,p.Glu115Ter,ENST00000348069,NM_183395.2;NLRP3,stop_gained,p.Glu115Ter,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; T ENST00000336119 Transcript stop_gained 1089/4170 343/3111 115/1036 E/* Gag/Tag rs763971331 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 2/9 HIGH 1 SNV 1 1 PASS rs763971331 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 247423289 247423289 G T 1 0 0 0 0 0 1 0 0 10516 943 33 2 2 NLRP3 1 247423289 Nonsense_Mutation SNP G C3N-00549_T 9808544 247423289 1533133 39 15063 OR2B11 0 . GRCh38 1 247451797 247451797 + Silent SNP G G T C3N-00549_T C3N-00549_N G G c.186C>A p.= p.P62P ENST00000318749 1/1 254 133 121 175 175 0 strelka-varscan-mutect OR2B11,synonymous_variant,p.=,ENST00000318749,NM_001004492.1;NLRP3,downstream_gene_variant,,ENST00000366497,NM_001127461.2;NLRP3,downstream_gene_variant,,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,downstream_gene_variant,,ENST00000366496,;NLRP3,downstream_gene_variant,,ENST00000391828,NM_001079821.2;NLRP3,downstream_gene_variant,,ENST00000348069,NM_183395.2;NLRP3,downstream_gene_variant,,ENST00000391827,NM_001127462.2;NLRP3,downstream_gene_variant,,ENST00000532083,; T ENST00000318749 Transcript synonymous_variant 186/954 186/954 62/317 P ccC/ccA COSM5600110,COSM680716 1 -1 OR2B11 HGNC HGNC:31249 protein_coding YES CCDS31090.1 ENSP00000325682 Q5JQS5 A0A126GVY5 UPI0000418F50 NM_001004492.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF112,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1,1 LOW SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 247451797 247451797 G T 1 0 0 0 0 0 0 0 1 11067 1335 47 2 2 OR2B11 1 247451797 Silent SNP G C3N-00549_T 28508 247451797 1504625 40 15064 OR2AK2 0 . GRCh38 1 247965976 247965976 + Silent SNP C C A C3N-00549_T C3N-00549_N C C c.645C>A p.= p.L215L ENST00000366480 1/1 74 50 24 70 70 0 strelka-varscan-mutect OR2AK2,synonymous_variant,p.=,ENST00000366480,NM_001004491.1; A ENST00000366480 Transcript synonymous_variant 744/1107 645/1008 215/335 L ctC/ctA COSM4503655 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS rs1316936520 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 247965976 247965976 C A 1 0 0 0 0 0 0 0 1 11064 842 30 2 2 OR2AK2 1 247965976 Silent SNP C C3N-00549_T 514179 247965976 990446 41 15065 OR2L2 0 . GRCh38 1 248038315 248038315 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.48G>T p.= p.L16L ENST00000366479 1/1 101 61 40 93 93 0 strelka-varscan-mutect OR2L2,synonymous_variant,p.=,ENST00000366479,NM_001004686.2; T ENST00000366479 Transcript synonymous_variant 48/939 48/939 16/312 L ctG/ctT 1 1 OR2L2 HGNC HGNC:8266 protein_coding YES CCDS31103.1 ENSP00000355435 Q8NH16 A0A126GW34 UPI0000061EAA NM_001004686.2 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF189,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs963247224 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 248038315 248038315 G T 1 0 0 0 0 0 0 0 1 11085 1364 48 2 2 OR2L2 1 248038315 Silent SNP G C3N-00549_T 72339 248038315 918107 42 15066 OR14C36 0 . GRCh38 1 248348917 248348917 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.143C>A p.Thr48Asn p.T48N ENST00000317861 1/1 162 109 53 138 138 0 strelka-varscan-mutect OR14C36,missense_variant,p.Thr48Asn,ENST00000317861,NM_001001918.1; A ENST00000317861 Transcript missense_variant 143/939 143/939 48/312 T/N aCc/aAc 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 248348917 248348917 C A 1 0 0 0 0 1 0 0 0 11023 507 18 2 2 OR14C36 1 248348917 Missense_Mutation SNP C C3N-00549_T 310602 248348917 607505 43 15067 OR2T35 0 . GRCh38 1 248638570 248638570 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.689C>A p.Ser230Tyr p.S230Y ENST00000317450 1/1 633 502 131 630 629 1 strelka-varscan-mutect OR2T35,missense_variant,p.Ser230Tyr,ENST00000317450,NM_001001827.1; T ENST00000317450 Transcript missense_variant 689/972 689/972 230/323 S/Y tCt/tAt 1 -1 OR2T35 HGNC HGNC:31257 protein_coding YES CCDS31123.1 ENSP00000324369 Q8NGX2 UPI0000061ED3 NM_001001827.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF18,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 248638570 248638570 G T 1 0 0 0 0 1 0 0 0 11103 942 33 2 2 OR2T35 1 248638570 Missense_Mutation SNP G C3N-00549_T 289653 248638570 317852 44 15068 OR2T35 0 . GRCh38 1 248638607 248638607 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.652T>A p.Tyr218Asn p.Y218N ENST00000317450 1/1 981 747 234 969 969 0 strelka-varscan-mutect OR2T35,missense_variant,p.Tyr218Asn,ENST00000317450,NM_001001827.1; T ENST00000317450 Transcript missense_variant 652/972 652/972 218/323 Y/N Tac/Aac 1 -1 OR2T35 HGNC HGNC:31257 protein_coding YES CCDS31123.1 ENSP00000324369 Q8NGX2 UPI0000061ED3 NM_001001827.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF18,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 248638607 248638607 A T 1 0 0 0 0 1 0 0 0 11103 420 15 4 4 OR2T35 1 248638607 Missense_Mutation SNP A C3N-00549_T 37 248638607 317815 45 15069 PXDN 0 . GRCh38 2 1649510 1649510 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2270G>T p.Gly757Val p.G757V ENST00000252804 17/23 454 261 193 428 428 0 strelka-varscan-mutect PXDN,missense_variant,p.Gly757Val,ENST00000252804,NM_012293.2;PXDN,downstream_gene_variant,,ENST00000433670,;PXDN,non_coding_transcript_exon_variant,,ENST00000465809,;PXDN,upstream_gene_variant,,ENST00000477093,;PXDN,non_coding_transcript_exon_variant,,ENST00000493779,;PXDN,intron_variant,,ENST00000478155,; A ENST00000252804 Transcript missense_variant 2321/6808 2270/4440 757/1479 G/V gGc/gTc 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 deleterious(0) 17/23 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF75,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 1649510 1649510 C A 1 0 0 0 0 1 0 0 0 13001 739 26 2 2 PXDN 2 1649510 Missense_Mutation SNP C C3N-00549_T 1649510 240544019 46 15070 NOL10 0 . GRCh38 2 10689824 10689824 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.38G>T p.Ser13Ile p.S13I ENST00000381685 1/21 198 141 57 190 190 0 strelka-varscan-mutect NOL10,missense_variant,p.Ser13Ile,ENST00000538384,NM_001261392.1;NOL10,missense_variant,p.Ser13Ile,ENST00000345985,NM_001261394.1;NOL10,missense_variant,p.Ser13Ile,ENST00000381685,NM_024894.3;RN7SL832P,upstream_gene_variant,,ENST00000607781,;Metazoa_SRP,upstream_gene_variant,,ENST00000487171,;NOL10,non_coding_transcript_exon_variant,,ENST00000473087,; A ENST00000381685 Transcript missense_variant 144/2589 38/2067 13/688 S/I aGc/aTc 1 -1 NOL10 HGNC HGNC:25862 protein_coding YES CCDS1673.2 ENSP00000371101 Q9BSC4 UPI000006F6E2 NM_024894.3 deleterious(0) 1/21 hmmpanther:PTHR14927,hmmpanther:PTHR14927:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 10689824 10689824 C A 1 0 0 0 0 1 0 0 0 10563 797 28 2 2 NOL10 2 10689824 Missense_Mutation SNP C C3N-00549_T 9040314 10689824 231503705 47 15071 VSNL1 0 . GRCh38 2 17649427 17649427 + Missense_Mutation SNP C C A rs148418595 C3N-00549_T C3N-00549_N C C c.180C>A p.Asp60Glu p.D60E ENST00000406397 3/4 290 164 126 226 226 0 strelka-varscan-mutect VSNL1,missense_variant,p.Asp60Glu,ENST00000406397,;VSNL1,missense_variant,p.Asp60Glu,ENST00000295156,NM_003385.4;VSNL1,missense_variant,p.Asp60Glu,ENST00000404666,;VSNL1,missense_variant,p.Asp60Glu,ENST00000457525,;VSNL1,missense_variant,p.Asp60Glu,ENST00000451533,; A ENST00000406397 Transcript missense_variant 705/2725 180/576 60/191 D/E gaC/gaA rs148418595,COSM5552382 1 1 VSNL1 HGNC HGNC:12722 protein_coding YES CCDS1689.1 ENSP00000384719 P62760 UPI0000001467 deleterious(0.04) 3/4 PROSITE_profiles:PS50222,hmmpanther:PTHR23055,hmmpanther:PTHR23055:SF101,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs148418595 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 17649427 17649427 C A 1 0 0 0 0 1 0 0 0 17778 535 19 1 1 VSNL1 2 17649427 Missense_Mutation SNP C C3N-00549_T 6959603 17649427 224544102 48 15072 ASXL2 0 . GRCh38 2 25743405 25743405 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.2932A>G p.Lys978Glu p.K978E ENST00000435504 13/13 280 165 115 233 233 0 strelka-varscan-mutect ASXL2,missense_variant,p.Lys978Glu,ENST00000435504,NM_018263.4;ASXL2,missense_variant,p.Lys950Glu,ENST00000336112,;ASXL2,intron_variant,,ENST00000404843,; C ENST00000435504 Transcript missense_variant 3226/12878 2932/4308 978/1435 K/E Aaa/Gaa 1 -1 ASXL2 HGNC HGNC:23805 protein_coding ENSP00000391447 Q76L83 UPI00001DFBE8 NM_018263.4 deleterious(0) 13/13 hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 25743405 25743405 T C 1 0 0 0 0 1 0 0 0 1215 1792 62 5 5 ASXL2 2 25743405 Missense_Mutation SNP T C3N-00549_T 8093978 25743405 216450124 49 15073 ASXL2 0 . GRCh38 2 25744300 25744300 + Silent SNP T T G novel C3N-00549_T C3N-00549_N T T c.1257A>C p.= p.A419A ENST00000404843 9/10 258 145 113 214 214 0 strelka-varscan-mutect ASXL2,synonymous_variant,p.=,ENST00000435504,NM_018263.4;ASXL2,synonymous_variant,p.=,ENST00000336112,;ASXL2,synonymous_variant,p.=,ENST00000404843,; G ENST00000404843 Transcript synonymous_variant 1695/3299 1257/2757 419/918 A gcA/gcC 1 -1 ASXL2 HGNC HGNC:23805 protein_coding YES ENSP00000383920 Q76L83 UPI0000246C78 9/10 Low_complexity_(Seg):seg,hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578 LOW 1 SNV 1 1 PASS rs764128572 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 50 25744300 25744300 T G 1 0 0 0 0 0 0 0 1 1215 1567 55 5 5 ASXL2 2 25744300 Silent SNP T C3N-00549_T 895 25744300 216449229 50 15074 EMILIN1 0 . GRCh38 2 27079112 27079112 + Missense_Mutation SNP C C T rs777527430 C3N-00549_T C3N-00549_N C C c.47C>T p.Thr16Met p.T16M ENST00000380320 1/8 129 82 47 155 155 0 strelka-varscan-mutect EMILIN1,missense_variant,p.Thr16Met,ENST00000380320,NM_007046.3;EMILIN1,upstream_gene_variant,,ENST00000433140,; T ENST00000380320 Transcript missense_variant 546/3943 47/3051 16/1016 T/M aCg/aTg rs777527430 1 1 EMILIN1 HGNC HGNC:19880 protein_coding YES CCDS1733.1 ENSP00000369677 A0A0C4DFX3 UPI0000073B0E NM_007046.3 deleterious(0.01) 1/8 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF1 MODERATE 1 SNV 1 1 PASS rs777527430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 27079112 27079112 C T 1 0 0 0 0 1 0 0 0 4936 536 19 1 1 EMILIN1 2 27079112 Missense_Mutation SNP C C3N-00549_T 1334812 27079112 215114417 51 15075 C2orf71 0 . GRCh38 2 29072034 29072034 + Missense_Mutation SNP C C A rs369823170 C3N-00549_T C3N-00549_N C C c.2228G>T p.Ser743Ile p.S743I ENST00000331664 1/2 240 142 98 178 178 0 strelka-varscan-mutect C2orf71,missense_variant,p.Ser743Ile,ENST00000331664,NM_001029883.2; A ENST00000331664 Transcript missense_variant 2228/7044 2228/3867 743/1288 S/I aGt/aTt rs369823170 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 deleterious(0.03) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 MODERATE 1 SNV 2 1 PASS rs369823170 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 29072034 29072034 C A 1 0 0 0 0 1 0 0 0 2045 565 20 2 2 C2orf71 2 29072034 Missense_Mutation SNP C C3N-00549_T 1992922 29072034 213121495 52 15076 VIT 0 . GRCh38 2 36775069 36775069 + Splice_Site SNP T T A novel C3N-00549_T C3N-00549_N T T c.802+2T>A p.X268_splice ENST00000379242 164 102 62 152 152 0 strelka-varscan VIT,splice_donor_variant,,ENST00000379242,NM_053276.3;VIT,splice_donor_variant,,ENST00000389975,NM_001177969.1;VIT,splice_donor_variant,,ENST00000497382,;VIT,splice_donor_variant,,ENST00000401530,NM_001177970.1;VIT,splice_donor_variant,,ENST00000464309,;VIT,intron_variant,,ENST00000379241,NM_001177971.1;VIT,intron_variant,,ENST00000404084,; A ENST00000379242 Transcript splice_donor_variant -/2810 802/2082 268/693 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 9/15 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 36775069 36775069 T A 1 0 0 0 0 0 0 1 0 17718 1652 57 4 4 VIT 2 36775069 Splice_Site SNP T C3N-00549_T 7703035 36775069 205418460 53 15077 SLC3A1 0 . GRCh38 2 44304338 44304338 + Frame_Shift_Del DEL G G - novel C3N-00549_T C3N-00549_N G G c.1332+1delG ENST00000260649 7/10 324 196 128 266 266 0 sindel-varindel-pindel SLC3A1,frameshift_variant,,ENST00000260649,NM_000341.3;SLC3A1,frameshift_variant,,ENST00000409229,;SLC3A1,frameshift_variant,,ENST00000409380,;SLC3A1,frameshift_variant,,ENST00000409387,;SLC3A1,frameshift_variant,,ENST00000611973,;SLC3A1,frameshift_variant,,ENST00000409741,;SLC3A1,frameshift_variant,,ENST00000409740,;SLC3A1,frameshift_variant,,ENST00000409294,;SLC3A1,downstream_gene_variant,,ENST00000410056,;SLC3A1,downstream_gene_variant,,ENST00000427285,; - ENST00000260649 Transcript frameshift_variant,splice_region_variant 1408/2989 1332/2058 444/685 M/X atG/at 1 1 SLC3A1 HGNC HGNC:11025 protein_coding YES CCDS1819.1 ENSP00000260649 Q07837 A0A0S2Z4E1 UPI000013D0F2 NM_000341.3 7/10 Gene3D:3.20.20.80,Pfam_domain:PF00128,hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73,SMART_domains:SM00642,Superfamily_domains:SSF51445 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 44304338 44304338 G - 1 0 1 0 1 0 0 0 0 14904 1362 47 0 0 SLC3A1 2 44304338 Frame_Shift_Del DEL G C3N-00549_T 7529269 44304338 197889191 54 15078 NRXN1 0 . GRCh38 2 51028084 51028084 + Missense_Mutation SNP G G A rs201566733 C3N-00549_T C3N-00549_N G G c.190C>T p.Arg64Cys p.R64C ENST00000404971 2/24 94 55 39 56 56 0 strelka-varscan NRXN1,missense_variant,p.Arg64Cys,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Arg64Cys,ENST00000625672,;NRXN1,missense_variant,p.Arg64Cys,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Arg64Cys,ENST00000401669,;NRXN1,missense_variant,p.Arg64Cys,ENST00000405472,;NRXN1,missense_variant,p.Arg64Cys,ENST00000405581,;NRXN1,missense_variant,p.Arg64Cys,ENST00000630543,;NRXN1,missense_variant,p.Arg64Cys,ENST00000637511,;NRXN1,missense_variant,p.Arg64Cys,ENST00000628515,;NRXN1,missense_variant,p.Arg64Cys,ENST00000626899,;NRXN1,upstream_gene_variant,,ENST00000636066,;NRXN1,upstream_gene_variant,,ENST00000627198,;NRXN1,upstream_gene_variant,,ENST00000496792,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000635126,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,upstream_gene_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; A ENST00000404971 Transcript missense_variant 1530/7578 190/4644 64/1547 R/C Cgc/Tgc rs201566733 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.02) 2/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 51028084 51028084 G A 1 0 0 0 0 1 0 0 0 10724 1116 39 1 1 NRXN1 2 51028084 Missense_Mutation SNP G C3N-00549_T 6723746 51028084 191165445 55 15079 OTX1 0 . GRCh38 2 63055951 63055951 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.700G>T p.Gly234Cys p.G234C ENST00000282549 5/5 410 234 176 335 335 0 strelka-varscan OTX1,missense_variant,p.Gly234Cys,ENST00000282549,NM_014562.3;OTX1,missense_variant,p.Gly234Cys,ENST00000366671,NM_001199770.1;OTX1,3_prime_UTR_variant,,ENST00000405984,;OTX1,downstream_gene_variant,,ENST00000484066,;OTX1,downstream_gene_variant,,ENST00000477348,;OTX1,downstream_gene_variant,,ENST00000476383,; T ENST00000282549 Transcript missense_variant 976/2861 700/1065 234/354 G/C Ggc/Tgc 1 1 OTX1 HGNC HGNC:8521 protein_coding YES CCDS1873.1 ENSP00000282549 P32242 UPI0000130F36 NM_014562.3 deleterious(0) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24329:SF310,hmmpanther:PTHR24329,Pfam_domain:PF03529 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 63055951 63055951 G T 1 0 0 0 0 1 0 0 0 11390 1000 35 2 2 OTX1 2 63055951 Missense_Mutation SNP G C3N-00549_T 12027867 63055951 179137578 56 15080 FAM136A 0 . GRCh38 2 70297464 70297464 + Missense_Mutation SNP C C A rs368899781 C3N-00549_T C3N-00549_N C C c.242G>T p.Arg81Leu p.R81L ENST00000037869 3/3 142 76 66 95 95 0 strelka-varscan FAM136A,missense_variant,p.Arg81Leu,ENST00000037869,NM_032822.2;FAM136A,missense_variant,p.Arg188Leu,ENST00000430566,;FAM136A,missense_variant,p.Arg151Leu,ENST00000438759,;FAM136A,3_prime_UTR_variant,,ENST00000450256,;SNRPG,upstream_gene_variant,,ENST00000482975,;SNRPG,upstream_gene_variant,,ENST00000272348,NM_001317166.1,NM_001317171.1,NM_003096.2;SNRPG,upstream_gene_variant,,ENST00000454893,;SNRPG,upstream_gene_variant,,ENST00000438261,;SNRPG,upstream_gene_variant,,ENST00000449935,;SNRPG,upstream_gene_variant,,ENST00000413456,;AC022201.5,upstream_gene_variant,,ENST00000445084,;SNRPG,upstream_gene_variant,,ENST00000429728,;FAM136A,non_coding_transcript_exon_variant,,ENST00000460307,;FAM136A,downstream_gene_variant,,ENST00000498665,;SNRPG,upstream_gene_variant,,ENST00000480370,;SNRPG,upstream_gene_variant,,ENST00000488400,; A ENST00000037869 Transcript missense_variant 321/1810 242/417 81/138 R/L cGg/cTg rs368899781 1 -1 FAM136A HGNC HGNC:25911 protein_coding YES CCDS1904.1 ENSP00000037869 Q96C01 UPI000006D92A NM_032822.2 deleterious(0) 3/3 hmmpanther:PTHR21096,Pfam_domain:PF05811 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 50 70297464 70297464 C A 1 0 0 0 0 1 0 0 0 5300 652 23 1 1 FAM136A 2 70297464 Missense_Mutation SNP C C3N-00549_T 7241513 70297464 171896065 57 15081 SUCLG1 0 . GRCh38 2 84441281 84441281 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.497G>T p.Arg166Met p.R166M ENST00000393868 4/9 594 369 225 447 445 2 strelka-varscan SUCLG1,missense_variant,p.Arg166Met,ENST00000393868,NM_003849.3;SUCLG1,non_coding_transcript_exon_variant,,ENST00000491642,;SUCLG1,non_coding_transcript_exon_variant,,ENST00000483605,;SUCLG1,non_coding_transcript_exon_variant,,ENST00000430989,;SUCLG1,upstream_gene_variant,,ENST00000488234,;SUCLG1,3_prime_UTR_variant,,ENST00000442240,; A ENST00000393868 Transcript missense_variant 708/1475 497/1041 166/346 R/M aGg/aTg 1 -1 SUCLG1 HGNC HGNC:11449 protein_coding YES CCDS1967.2 ENSP00000377446 P53597 UPI000014BF59 NM_003849.3 deleterious(0) 4/9 hmmpanther:PTHR11117,TIGRFAM_domain:TIGR01019,PIRSF_domain:PIRSF001553,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 84441281 84441281 C A 1 0 0 0 0 1 0 0 0 15748 681 24 2 2 SUCLG1 2 84441281 Missense_Mutation SNP C C3N-00549_T 14143817 84441281 157752248 58 15082 TRABD2A 0 . GRCh38 2 84870284 84870284 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.610G>T p.Gly204Trp p.G204W ENST00000409520 2/7 158 104 54 147 147 0 strelka-varscan TRABD2A,missense_variant,p.Gly204Trp,ENST00000409520,NM_001277053.1;TRABD2A,missense_variant,p.Gly204Trp,ENST00000335459,NM_001080824.2;TRABD2A,missense_variant,p.Gly204Trp,ENST00000409133,NM_001307978.1;TRABD2A,downstream_gene_variant,,ENST00000436322,;TRABD2A,downstream_gene_variant,,ENST00000474298,;RPL12P18,upstream_gene_variant,,ENST00000437175,; A ENST00000409520 Transcript missense_variant 816/1975 610/1518 204/505 G/W Ggg/Tgg 1 -1 TRABD2A HGNC HGNC:27013 protein_coding YES CCDS62946.1 ENSP00000387075 Q86V40 UPI000016012F NM_001277053.1 deleterious(0) 2/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31120,hmmpanther:PTHR31120:SF7,Pfam_domain:PF01963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 84870284 84870284 C A 1 0 0 0 0 1 0 0 0 16917 594 21 2 2 TRABD2A 2 84870284 Missense_Mutation SNP C C3N-00549_T 429003 84870284 157323245 59 15083 SLC5A7 0 . GRCh38 2 108008651 108008651 + Missense_Mutation SNP G G T rs147656110 C3N-00549_T C3N-00549_N G G c.1082G>T p.Arg361Leu p.R361L ENST00000264047 8/9 213 142 71 169 169 0 strelka-varscan SLC5A7,missense_variant,p.Arg361Leu,ENST00000264047,NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3;SLC5A7,missense_variant,p.Arg361Leu,ENST00000409059,; T ENST00000264047 Transcript missense_variant 1358/5152 1082/1743 361/580 R/L cGg/cTg rs147656110,COSM3565027 1 1 SLC5A7 HGNC HGNC:14025 protein_coding YES CCDS2074.1 ENSP00000264047 Q9GZV3 UPI0000070792 NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3 deleterious(0.01) 8/9 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF129 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 108008651 108008651 G T 1 0 0 0 0 1 0 0 0 14953 1116 39 1 1 SLC5A7 2 108008651 Missense_Mutation SNP G C3N-00549_T 23138367 108008651 134184878 60 15084 NT5DC4 0 . GRCh38 2 112724803 112724803 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.734G>C p.Trp245Ser p.W245S ENST00000327581 11/17 116 25 91 180 180 0 strelka-varscan NT5DC4,missense_variant,p.Trp245Ser,ENST00000327581,;NT5DC4,non_coding_transcript_exon_variant,,ENST00000497526,;NT5DC4,upstream_gene_variant,,ENST00000491170,;NT5DC4,upstream_gene_variant,,ENST00000462854,;NT5DC4,downstream_gene_variant,,ENST00000470675,;NT5DC4,downstream_gene_variant,,ENST00000484666,; C ENST00000327581 Transcript missense_variant 785/1767 734/1287 245/428 W/S tGg/tCg 1 1 NT5DC4 HGNC HGNC:27678 protein_coding YES ENSP00000330247 Q86YG4 UPI0000197313 deleterious(0) 11/17 hmmpanther:PTHR12103,hmmpanther:PTHR12103:SF18,Gene3D:3.40.50.1000,Pfam_domain:PF05761,PIRSF_domain:PIRSF017434,TIGRFAM_domain:TIGR02244,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 112724803 112724803 G C 1 0 0 0 0 1 0 0 0 10756 1357 47 4 4 NT5DC4 2 112724803 Missense_Mutation SNP G C3N-00549_T 4716152 112724803 129468726 61 15085 MYO7B 0 . GRCh38 2 127620403 127620403 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.3384C>A p.= p.A1128A ENST00000428314 26/47 58 29 29 81 81 0 strelka-varscan MYO7B,synonymous_variant,p.=,ENST00000428314,NM_001080527.1;MYO7B,synonymous_variant,p.=,ENST00000409816,;MYO7B,5_prime_UTR_variant,,ENST00000409090,;MYO7B,5_prime_UTR_variant,,ENST00000437387,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,; A ENST00000428314 Transcript synonymous_variant 3437/6715 3384/6351 1128/2116 A gcC/gcA 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 26/47 Pfam_domain:PF00784,PROSITE_profiles:PS51016,SMART_domains:SM00139 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 127620403 127620403 C A 1 0 0 0 0 0 0 0 1 10084 610 22 2 2 MYO7B 2 127620403 Silent SNP C C3N-00549_T 14895600 127620403 114573126 62 15086 ARHGEF4 0 . GRCh38 2 130946513 130946513 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.305G>T p.Trp102Leu p.W102L ENST00000326016 4/14 51 19 32 77 77 0 strelka-varscan ARHGEF4,missense_variant,p.Trp1288Leu,ENST00000409359,;ARHGEF4,missense_variant,p.Trp102Leu,ENST00000525839,NM_032995.2;ARHGEF4,missense_variant,p.Trp127Leu,ENST00000392953,;ARHGEF4,missense_variant,p.Trp102Leu,ENST00000326016,NM_015320.3;ARHGEF4,missense_variant,p.Trp102Leu,ENST00000611048,;ARHGEF4,missense_variant,p.Trp102Leu,ENST00000428230,;ARHGEF4,missense_variant,p.Trp282Leu,ENST00000438985,;ARHGEF4,3_prime_UTR_variant,,ENST00000636987,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000526381,; T ENST00000326016 Transcript missense_variant 824/3666 305/2073 102/690 W/L tGg/tTg 1 1 ARHGEF4 HGNC HGNC:684 protein_coding YES CCDS2165.1 ENSP00000316845 Q9NR80 UPI00001417F6 NM_015320.3 tolerated_low_confidence(0.54) 4/14 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 130946513 130946513 G T 1 0 0 0 0 1 0 0 0 1043 1362 47 2 2 ARHGEF4 2 130946513 Missense_Mutation SNP G C3N-00549_T 3326110 130946513 111247016 63 15087 NCKAP5 0 . GRCh38 2 132783050 132783050 + Missense_Mutation SNP G G T rs200887045 C3N-00549_T C3N-00549_N G G c.3761C>A p.Ser1254Tyr p.S1254Y ENST00000409261 14/20 66 26 40 100 100 0 strelka-varscan NCKAP5,missense_variant,p.Ser1254Tyr,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Ser1254Tyr,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; T ENST00000409261 Transcript missense_variant 4135/7594 3761/5730 1254/1909 S/Y tCc/tAc rs200887045,COSM569969 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 deleterious(0) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 0,1 MODERATE 1 SNV 5 0,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 132783050 132783050 G T 1 0 0 0 0 1 0 0 0 10241 1174 41 2 2 NCKAP5 2 132783050 Missense_Mutation SNP G C3N-00549_T 1836537 132783050 109410479 64 15088 NCKAP5 0 . GRCh38 2 132784175 132784175 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2636C>A p.Pro879His p.P879H ENST00000409261 14/20 15 5 10 18 18 0 strelka-varscan NCKAP5,missense_variant,p.Pro879His,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Pro879His,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; T ENST00000409261 Transcript missense_variant 3010/7594 2636/5730 879/1909 P/H cCc/cAc 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 deleterious(0) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 132784175 132784175 G T 1 0 0 0 0 1 0 0 0 10241 1232 43 2 2 NCKAP5 2 132784175 Missense_Mutation SNP G C3N-00549_T 1125 132784175 109409354 65 15089 PLA2R1 0 . GRCh38 2 160033041 160033041 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.759G>T p.Trp253Cys p.W253C ENST00000283243 4/30 85 23 62 235 234 1 strelka-varscan PLA2R1,missense_variant,p.Trp253Cys,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.Trp253Cys,ENST00000392771,NM_001007267.2; A ENST00000283243 Transcript missense_variant 966/14371 759/4392 253/1463 W/C tgG/tgT 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 deleterious(0) 4/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,Low_complexity_(Seg):seg,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 160033041 160033041 C A 1 0 0 0 0 1 0 0 0 12106 856 30 2 2 PLA2R1 2 160033041 Missense_Mutation SNP C C3N-00549_T 27248866 160033041 82160488 66 15090 SLC4A10 0 . GRCh38 2 161904059 161904059 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1498G>T p.Asp500Tyr p.D500Y ENST00000446997 13/27 112 34 78 116 116 0 strelka-varscan SLC4A10,missense_variant,p.Asp481Tyr,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Asp470Tyr,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Asp500Tyr,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Asp470Tyr,ENST00000272716,;SLC4A10,missense_variant,p.Asp500Tyr,ENST00000421911,;SLC4A10,downstream_gene_variant,,ENST00000493021,;SLC4A10,3_prime_UTR_variant,,ENST00000446228,; T ENST00000446997 Transcript missense_variant 1591/5551 1498/3357 500/1118 D/Y Gac/Tac 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 deleterious(0) 13/27 hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Pfam_domain:PF00955,Gene3D:1bzkA00,TIGRFAM_domain:TIGR00834,Prints_domain:PR01231 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 161904059 161904059 G T 1 0 0 0 0 1 0 0 0 14928 1290 45 2 2 SLC4A10 2 161904059 Missense_Mutation SNP G C3N-00549_T 1871018 161904059 80289470 67 15091 ITGA4 0 . GRCh38 2 181535436 181535436 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.3008G>A p.Gly1003Asp p.G1003D ENST00000397033 28/28 29 9 20 19 19 0 strelka-varscan ITGA4,missense_variant,p.Gly1003Asp,ENST00000397033,NM_000885.4;CERKL,downstream_gene_variant,,ENST00000410087,NM_201548.4;CERKL,downstream_gene_variant,,ENST00000409440,NM_001160277.1;CERKL,downstream_gene_variant,,ENST00000339098,NM_001030311.2;CERKL,downstream_gene_variant,,ENST00000374970,NM_001030313.2;CERKL,downstream_gene_variant,,ENST00000374969,NM_001030312.2;CERKL,downstream_gene_variant,,ENST00000494398,;CERKL,downstream_gene_variant,,ENST00000374967,;CERKL,downstream_gene_variant,,ENST00000452174,;CERKL,downstream_gene_variant,,ENST00000421817,; A ENST00000397033 Transcript missense_variant 3438/4189 3008/3099 1003/1032 G/D gGc/gAc 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 deleterious(0) 28/28 hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,PROSITE_patterns:PS00242,Gene3D:2k1aA00,Prints_domain:PR01185 MODERATE 1 SNV 1 1 PASS . . 3 204 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 181535436 181535436 G A 1 0 0 0 0 1 0 0 0 7785 1217 42 3 3 ITGA4 2 181535436 Missense_Mutation SNP G C3N-00549_T 19631377 181535436 60658093 68 15092 DNAJC10 0 . GRCh38 2 182736348 182736348 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.949G>T p.Gly317Ter p.G317* ENST00000264065 11/24 63 29 34 106 105 1 strelka-varscan DNAJC10,stop_gained,p.Gly317Ter,ENST00000264065,NM_018981.2;DNAJC10,stop_gained,p.Gly317Ter,ENST00000537515,;DNAJC10,intron_variant,,ENST00000616986,NM_001271581.1;DNAJC10,intron_variant,,ENST00000613960,;DNAJC10,stop_gained,p.Gly106Ter,ENST00000444005,;DNAJC10,non_coding_transcript_exon_variant,,ENST00000491074,;DNAJC10,intron_variant,,ENST00000418559,;DNAJC10,downstream_gene_variant,,ENST00000459930,; T ENST00000264065 Transcript stop_gained 1364/20129 949/2382 317/793 G/* Gga/Tga 1 1 DNAJC10 HGNC HGNC:24637 protein_coding YES CCDS33345.1 ENSP00000264065 Q8IXB1 UPI000007376C NM_018981.2 11/24 PIRSF_domain:PIRSF037293,Superfamily_domains:SSF52833 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 182736348 182736348 G T 1 0 0 0 0 0 1 0 0 4443 1349 47 2 2 DNAJC10 2 182736348 Nonsense_Mutation SNP G C3N-00549_T 1200912 182736348 59457181 69 15093 PMS1 0 . GRCh38 2 189853968 189853968 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.852C>G p.Cys284Trp p.C284W ENST00000441310 8/13 95 31 64 84 84 0 strelka-varscan PMS1,missense_variant,p.Cys108Trp,ENST00000624204,NM_001289408.1;PMS1,missense_variant,p.Cys108Trp,ENST00000432292,NM_001289409.1;PMS1,missense_variant,p.Cys284Trp,ENST00000441310,NM_000534.4;PMS1,missense_variant,p.Cys245Trp,ENST00000418224,;PMS1,missense_variant,p.Cys245Trp,ENST00000409823,NM_001128143.1;PMS1,missense_variant,p.Cys284Trp,ENST00000447232,NM_001128144.1;PMS1,missense_variant,p.Cys223Trp,ENST00000424307,;PMS1,missense_variant,p.Cys69Trp,ENST00000409593,;PMS1,intron_variant,,ENST00000618056,;PMS1,upstream_gene_variant,,ENST00000452382,;PMS1,non_coding_transcript_exon_variant,,ENST00000421722,;PMS1,non_coding_transcript_exon_variant,,ENST00000424059,;PMS1,upstream_gene_variant,,ENST00000483293,;PMS1,missense_variant,p.Cys245Trp,ENST00000450931,;PMS1,3_prime_UTR_variant,,ENST00000342075,;PMS1,downstream_gene_variant,,ENST00000447734,; G ENST00000441310 Transcript missense_variant 1085/3225 852/2799 284/932 C/W tgC/tgG 1 1 PMS1 HGNC HGNC:9121 protein_coding YES CCDS2302.1 ENSP00000406490 P54277 UPI00000405F5 NM_000534.4 tolerated(0.11) 8/13 Gene3D:3.30.230.10,Pfam_domain:PF01119,hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF43,SMART_domains:SM01340,Superfamily_domains:SSF54211,TIGRFAM_domain:TIGR00585 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 189853968 189853968 C G 1 0 0 0 0 1 0 0 0 12249 747 26 4 4 PMS1 2 189853968 Missense_Mutation SNP C C3N-00549_T 7117620 189853968 52339561 70 15094 KIAA2012 0 . GRCh38 2 202154799 202154799 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2035C>A p.Pro679Thr p.P679T ENST00000498697 14/24 51 17 34 84 84 0 strelka-varscan KIAA2012,missense_variant,p.Pro679Thr,ENST00000498697,;KIAA2012,missense_variant,p.Pro714Thr,ENST00000541917,NM_001277372.1;KIAA2012,downstream_gene_variant,,ENST00000409515,;KIAA2012,non_coding_transcript_exon_variant,,ENST00000469462,; A ENST00000498697 Transcript missense_variant 2035/3772 2035/3546 679/1181 P/T Ccg/Acg 1 1 KIAA2012 HGNC HGNC:51250 protein_coding YES ENSP00000419834 H7C5G6 UPI0005D0279F 14/24 Pfam_domain:PF15709,hmmpanther:PTHR21937,hmmpanther:PTHR21937:SF3 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 202154799 202154799 C A 1 0 0 0 0 1 0 0 0 8131 739 26 2 2 KIAA2012 2 202154799 Missense_Mutation SNP C C3N-00549_T 12300831 202154799 40038730 71 15095 MAP2 0 . GRCh38 2 209693011 209693011 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.841G>T p.Val281Phe p.V281F ENST00000360351 7/15 53 20 33 88 88 0 strelka-varscan MAP2,missense_variant,p.Val281Phe,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Val277Phe,ENST00000447185,;MAP2,missense_variant,p.Val363Phe,ENST00000445941,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,non_coding_transcript_exon_variant,,ENST00000461253,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000481649,; T ENST00000360351 Transcript missense_variant 1347/9711 841/5484 281/1827 V/F Gtt/Ttt 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0.04) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 209693011 209693011 G T 1 0 0 0 0 1 0 0 0 9157 1029 36 2 2 MAP2 2 209693011 Missense_Mutation SNP G C3N-00549_T 7538212 209693011 32500518 72 15096 VWC2L 0 . GRCh38 2 214436725 214436726 + Frame_Shift_Ins INS - - A novel C3N-00549_T C3N-00549_N - - c.489dupA p.Pro164ThrfsTer26 p.P164Tfs*26 ENST00000312504 3/4 100 40 60 167 167 0 sindel-varindel-pindel VWC2L,frameshift_variant,p.Pro164ThrfsTer26,ENST00000312504,NM_001080500.2;VWC2L,intron_variant,,ENST00000427124,;AC107218.3,intron_variant,,ENST00000437883,;AC107218.3,intron_variant,,ENST00000412896,; A ENST00000312504 Transcript frameshift_variant 1289-1290/4610 487-488/669 163/222 E/EX gaa/gAaa 1 1 VWC2L HGNC HGNC:37203 protein_coding YES CCDS46509.1 ENSP00000308976 B2RUY7 UPI00004912C1 NM_001080500.2 3/4 PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,SMART_domains:SM00214,Superfamily_domains:SSF57603 HIGH 1 insertion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 50 214436725 214436725 - A 1 0 1 1 0 0 0 0 0 17803 1291 45 0 0 VWC2L 2 214436725 Frame_Shift_Ins INS - C3N-00549_T 4743714 214436725 27756804 73 15097 VWC2L 0 . GRCh38 2 214436750 214436750 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.512G>T p.Cys171Phe p.C171F ENST00000312504 3/4 81 31 50 131 131 0 strelka-varscan VWC2L,missense_variant,p.Cys171Phe,ENST00000312504,NM_001080500.2;VWC2L,intron_variant,,ENST00000427124,;AC107218.3,intron_variant,,ENST00000437883,;AC107218.3,intron_variant,,ENST00000412896,; T ENST00000312504 Transcript missense_variant 1314/4610 512/669 171/222 C/F tGc/tTc 1 1 VWC2L HGNC HGNC:37203 protein_coding YES CCDS46509.1 ENSP00000308976 B2RUY7 UPI00004912C1 NM_001080500.2 deleterious(0) 3/4 PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS . . 0 195 7 6 2 0 0 0 -20 0.9772349 1 1 1 0 T 3 4 50 214436750 214436750 G T 1 0 0 0 0 1 0 0 0 17803 1319 46 2 2 VWC2L 2 214436750 Missense_Mutation SNP G C3N-00549_T 25 214436750 27756779 74 15098 ZNF142 0 . GRCh38 2 218642433 218642433 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.4083G>T p.Glu1361Asp p.E1361D ENST00000411696 7/9 66 22 44 56 56 0 strelka-varscan ZNF142,missense_variant,p.Glu1361Asp,ENST00000411696,;ZNF142,missense_variant,p.Glu1361Asp,ENST00000449707,NM_001105537.2;ZNF142,3_prime_UTR_variant,,ENST00000450765,;ZNF142,3_prime_UTR_variant,,ENST00000433921,; A ENST00000411696 Transcript missense_variant 4527/5926 4083/5064 1361/1687 E/D gaG/gaT 1 -1 ZNF142 HGNC HGNC:12927 protein_coding YES CCDS42817.1 ENSP00000398798 P52746 UPI000013D5FC deleterious(0.04) 7/9 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF43,PROSITE_patterns:PS00028,SMART_domains:SM00355 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 218642433 218642433 C A 1 0 0 0 0 1 0 0 0 18312 680 24 2 2 ZNF142 2 218642433 Missense_Mutation SNP C C3N-00549_T 4205683 218642433 23551096 75 15099 CFAP65 0 . GRCh38 2 219029622 219029622 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.1431C>A p.= p.V477V ENST00000341552 11/35 121 27 94 149 149 0 strelka-varscan CFAP65,synonymous_variant,p.=,ENST00000341552,NM_194302.3;CFAP65,synonymous_variant,p.=,ENST00000453220,;CFAP65,synonymous_variant,p.=,ENST00000409865,NM_001278295.1;CFAP65,synonymous_variant,p.=,ENST00000410037,NM_001278296.1;CFAP65,5_prime_UTR_variant,,ENST00000441968,;CFAP65,downstream_gene_variant,,ENST00000295729,NM_152389.3;CFAP65,downstream_gene_variant,,ENST00000457968,;CFAP65,downstream_gene_variant,,ENST00000436631,;CFAP65,non_coding_transcript_exon_variant,,ENST00000462848,;CFAP65,non_coding_transcript_exon_variant,,ENST00000463683,;CFAP65,non_coding_transcript_exon_variant,,ENST00000474601,; T ENST00000341552 Transcript synonymous_variant 1515/5953 1431/5778 477/1925 V gtC/gtA 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 11/35 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF223 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 219029622 219029622 G T 1 0 0 0 0 0 0 0 1 3029 1277 45 2 2 CFAP65 2 219029622 Silent SNP G C3N-00549_T 387189 219029622 23163907 76 15100 SPEG 0 . GRCh38 2 219448458 219448458 + Missense_Mutation SNP C C A rs748467065 C3N-00549_T C3N-00549_N C C c.1300C>A p.Arg434Ser p.R434S ENST00000312358 4/41 55 13 42 92 92 0 strelka-varscan SPEG,missense_variant,p.Arg434Ser,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Arg330Ser,ENST00000396698,;SPEG,missense_variant,p.Arg281Ser,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; A ENST00000312358 Transcript missense_variant 1432/10782 1300/9804 434/3267 R/S Cgc/Agc rs748467065 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.28) 4/41 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 219448458 219448458 C A 1 0 0 0 0 1 0 0 0 15387 652 23 1 1 SPEG 2 219448458 Missense_Mutation SNP C C3N-00549_T 418836 219448458 22745071 77 15101 SP140 0 . GRCh38 2 230225858 230225858 + Missense_Mutation SNP G G T rs753172617 C3N-00549_T C3N-00549_N G G c.14G>T p.Gly5Val p.G5V ENST00000392045 1/27 142 47 95 303 303 0 strelka-varscan SP140,missense_variant,p.Gly5Val,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Gly5Val,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Gly5Val,ENST00000343805,NM_001278452.1;SP140,missense_variant,p.Gly5Val,ENST00000417495,NM_001278453.1;SP140,missense_variant,p.Gly5Val,ENST00000373645,NM_001005176.2;SP140,missense_variant,p.Gly5Val,ENST00000456542,;AC009950.1,upstream_gene_variant,,ENST00000540870,NM_001185015.1;SP110,upstream_gene_variant,,ENST00000416610,;SP140,upstream_gene_variant,,ENST00000544128,;SP140,upstream_gene_variant,,ENST00000538494,;SP140,non_coding_transcript_exon_variant,,ENST00000473711,;SP140,non_coding_transcript_exon_variant,,ENST00000543928,; T ENST00000392045 Transcript missense_variant 128/3246 14/2604 5/867 G/V gGc/gTc rs753172617 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 deleterious_low_confidence(0.01) 1/27 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 230225858 230225858 G T 1 0 0 0 0 1 0 0 0 15288 1203 42 2 2 SP140 2 230225858 Missense_Mutation SNP G C3N-00549_T 10777400 230225858 11967671 78 15102 SUMF1 0 . GRCh38 3 4452967 4452967 + Missense_Mutation SNP C C T rs770788735 C3N-00549_T C3N-00549_N C C c.353G>A p.Arg118Lys p.R118K ENST00000272902 2/9 212 80 132 280 280 0 strelka-varscan-mutect SUMF1,missense_variant,p.Arg118Lys,ENST00000272902,NM_182760.3;SUMF1,missense_variant,p.Arg118Lys,ENST00000383843,NM_001164674.1;SUMF1,missense_variant,p.Arg118Lys,ENST00000405420,NM_001164675.1;SUMF1,missense_variant,p.Arg118Lys,ENST00000458465,;SUMF1,missense_variant,p.Arg118Lys,ENST00000448413,; T ENST00000272902 Transcript missense_variant 389/2159 353/1125 118/374 R/K aGa/aAa rs770788735,COSM3067464,COSM3067465 1 -1 SUMF1 HGNC HGNC:20376 protein_coding YES CCDS2564.1 ENSP00000272902 Q8NBK3 UPI0000040734 NM_182760.3 tolerated(0.65) 2/9 Gene3D:1z70X00,Pfam_domain:PF03781,hmmpanther:PTHR23150,hmmpanther:PTHR23150:SF23,Superfamily_domains:SSF56436 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770788735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 4452967 4452967 C T 1 0 0 0 0 1 0 0 0 15771 913 32 3 3 SUMF1 3 4452967 Missense_Mutation SNP C C3N-00549_T 4452967 193842592 79 15103 ATG7 0 . GRCh38 3 11554837 11554837 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.2106C>A p.= p.T702T ENST00000354449 19/19 89 38 51 146 146 0 strelka-varscan-mutect ATG7,synonymous_variant,p.=,ENST00000354449,NM_006395.2;ATG7,synonymous_variant,p.=,ENST00000354956,NM_001136031.2;ATG7,synonymous_variant,p.=,ENST00000446450,NM_001144912.1;VGLL4,downstream_gene_variant,,ENST00000273038,NM_014667.3;VGLL4,downstream_gene_variant,,ENST00000413604,NM_001284391.1;VGLL4,downstream_gene_variant,,ENST00000426568,NM_001284390.1;VGLL4,downstream_gene_variant,,ENST00000430365,NM_001128219.2;VGLL4,downstream_gene_variant,,ENST00000424529,NM_001128221.2;VGLL4,downstream_gene_variant,,ENST00000451674,NM_001128220.2;VGLL4,downstream_gene_variant,,ENST00000418000,;VGLL4,downstream_gene_variant,,ENST00000458499,;VGLL4,downstream_gene_variant,,ENST00000445411,; A ENST00000354449 Transcript synonymous_variant 2131/4959 2106/2112 702/703 T acC/acA 1 1 ATG7 HGNC HGNC:16935 protein_coding YES CCDS2605.1 ENSP00000346437 O95352 UPI00000705C7 NM_006395.2 19/19 hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF3 LOW 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999937 1 1 1 0 A 2 1 50 11554837 11554837 C A 1 0 0 0 0 0 0 0 1 1253 581 21 2 2 ATG7 3 11554837 Silent SNP C C3N-00549_T 7101870 11554837 186740722 80 15104 SMARCC1 0 . GRCh38 3 47590744 47590744 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3137G>T p.Ser1046Ile p.S1046I ENST00000254480 27/28 39 10 29 78 78 0 strelka-varscan-mutect SMARCC1,missense_variant,p.Ser1046Ile,ENST00000254480,NM_003074.3;SMARCC1,non_coding_transcript_exon_variant,,ENST00000425518,;SMARCC1,downstream_gene_variant,,ENST00000492896,; A ENST00000254480 Transcript missense_variant 3257/6375 3137/3318 1046/1105 S/I aGt/aTt 1 -1 SMARCC1 HGNC HGNC:11104 protein_coding YES CCDS2758.1 ENSP00000254480 Q92922 UPI000013CE3B NM_003074.3 tolerated_low_confidence(0.05) 27/28 Low_complexity_(Seg):seg,hmmpanther:PTHR12802,hmmpanther:PTHR12802:SF9 MODERATE 1 SNV 1 1 PASS rs1384230695 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 47590744 47590744 C A 1 0 0 0 0 1 0 0 0 15068 565 20 2 2 SMARCC1 3 47590744 Missense_Mutation SNP C C3N-00549_T 36035907 47590744 150704815 81 15105 FRMD4B 0 . GRCh38 3 69180949 69180949 + Missense_Mutation SNP C C A rs779137900 C3N-00549_T C3N-00549_N C C c.2801G>T p.Gly934Val p.G934V ENST00000398540 21/23 89 26 63 70 70 0 strelka-varscan FRMD4B,missense_variant,p.Gly934Val,ENST00000398540,NM_015123.2;FRMD4B,missense_variant,p.Gly586Val,ENST00000478263,; A ENST00000398540 Transcript missense_variant 2885/5060 2801/3105 934/1034 G/V gGg/gTg rs779137900,COSM398241 1 -1 FRMD4B HGNC HGNC:24886 protein_coding YES CCDS46863.1 ENSP00000381549 Q9Y2L6 UPI00001C1DF1 NM_015123.2 tolerated(0.17) 21/23 hmmpanther:PTHR23281:SF16,hmmpanther:PTHR23281 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999979 1 1 1 0 A 3 1 50 69180949 69180949 C A 1 0 0 0 0 1 0 0 0 5922 623 22 2 2 FRMD4B 3 69180949 Missense_Mutation SNP C C3N-00549_T 21590205 69180949 129114610 82 15106 OR5H15 0 . GRCh38 3 98169507 98169507 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.808C>A p.Gln270Lys p.Q270K ENST00000356526 1/1 185 73 112 291 291 0 strelka-varscan OR5H15,missense_variant,p.Gln270Lys,ENST00000356526,NM_001005515.1;OR5H15,intron_variant,,ENST00000615035,; A ENST00000356526 Transcript missense_variant 808/942 808/942 270/313 Q/K Caa/Aaa 1 1 OR5H15 HGNC HGNC:31287 protein_coding YES CCDS33799.1 ENSP00000373195 A6NDH6 UPI00001606CE NM_001005515.1 tolerated(0.46) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF325,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 98169507 98169507 C A 1 0 0 0 0 1 0 0 0 11231 827 29 2 2 OR5H15 3 98169507 Missense_Mutation SNP C C3N-00549_T 28988558 98169507 100126052 83 15107 AC026348.1 0 . GRCh38 3 113407012 113407012 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.920G>A p.Gly307Asp p.G307D ENST00000393845 7/34 193 79 114 277 276 1 strelka-varscan-mutect AC026348.1,missense_variant,p.Gly307Asp,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Gly307Asp,ENST00000295868,NM_018338.3;CFAP44-AS1,intron_variant,,ENST00000498480,;CFAP44-AS1,intron_variant,,ENST00000473329,;CFAP44,3_prime_UTR_variant,,ENST00000488854,;CFAP44,3_prime_UTR_variant,,ENST00000489938,;CFAP44,upstream_gene_variant,,ENST00000465186,; T ENST00000393845 Transcript missense_variant 920/5565 920/5565 307/1854 G/D gGt/gAt 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 deleterious(0) 7/34 PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 113407012 113407012 C T 1 0 0 0 0 1 0 0 0 128 507 18 3 3 AC026348.1 3 113407012 Missense_Mutation SNP C C3N-00549_T 15237505 113407012 84888547 84 15108 STAG1 0 . GRCh38 3 136500240 136500240 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.885A>G p.Ile295Met p.I295M ENST00000383202 9/34 48 16 32 49 49 0 strelka-varscan-mutect STAG1,missense_variant,p.Ile295Met,ENST00000383202,NM_005862.2;STAG1,missense_variant,p.Ile295Met,ENST00000236698,;STAG1,missense_variant,p.Ile69Met,ENST00000434713,;STAG1,3_prime_UTR_variant,,ENST00000629124,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,;STAG1,non_coding_transcript_exon_variant,,ENST00000462818,; C ENST00000383202 Transcript missense_variant 1142/6055 885/3777 295/1258 I/M atA/atG 1 -1 STAG1 HGNC HGNC:11354 protein_coding YES CCDS3090.1 ENSP00000372689 Q8WVM7 UPI000020A2DE NM_005862.2 deleterious(0.01) 9/34 hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 136500240 136500240 T C 1 0 0 0 0 1 0 0 0 15620 1396 49 5 5 STAG1 3 136500240 Missense_Mutation SNP T C3N-00549_T 23093228 136500240 61795319 85 15109 ECT2 0 . GRCh38 3 172757112 172757112 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.433G>C p.Asp145His p.D145H ENST00000392692 5/25 80 48 32 94 94 0 strelka-varscan-mutect ECT2,missense_variant,p.Asp114His,ENST00000540509,NM_001258316.1;ECT2,missense_variant,p.Asp113His,ENST00000417960,;ECT2,missense_variant,p.Asp145His,ENST00000392692,NM_001258315.1;ECT2,missense_variant,p.Asp114His,ENST00000232458,NM_018098.5;ECT2,missense_variant,p.Asp114His,ENST00000441497,;ECT2,missense_variant,p.Asp113His,ENST00000428567,;ECT2,missense_variant,p.Asp114His,ENST00000415665,;ECT2,missense_variant,p.Asp145His,ENST00000438041,;ECT2,downstream_gene_variant,,ENST00000366090,;ECT2,downstream_gene_variant,,ENST00000426894,;ECT2,downstream_gene_variant,,ENST00000366254,; C ENST00000392692 Transcript missense_variant 609/4158 433/2745 145/914 D/H Gat/Cat 1 1 ECT2 HGNC HGNC:3155 protein_coding YES CCDS58860.1 ENSP00000376457 Q9H8V3 UPI00003DFD0A NM_001258315.1 deleterious(0.01) 5/25 hmmpanther:PTHR16777,hmmpanther:PTHR16777:SF2,Superfamily_domains:SSF52113 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 172757112 172757112 G C 1 0 0 0 0 1 0 0 0 4729 1290 45 4 4 ECT2 3 172757112 Missense_Mutation SNP G C3N-00549_T 36256872 172757112 25538447 86 15110 MASP1 0 . GRCh38 3 187223194 187223194 + Frame_Shift_Del DEL C C - rs757257707 C3N-00549_T C3N-00549_N C C c.1742delG p.Gly581GlufsTer21 p.G581Efs*21 ENST00000337774 14/16 265 71 194 439 439 0 sindel-varindel-pindel MASP1,frameshift_variant,p.Gly581GlufsTer21,ENST00000337774,NM_001879.5;MASP1,downstream_gene_variant,,ENST00000468121,; - ENST00000337774 Transcript frameshift_variant,splice_region_variant 2132/5276 1742/2100 581/699 G/X gGa/ga rs757257707 1 -1 MASP1 HGNC HGNC:6901 protein_coding CCDS33907.1 ENSP00000336792 P48740 UPI0000161FB8 NM_001879.5 14/16 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS50240,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00020,Superfamily_domains:SSF50494 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 187223194 187223194 C - 1 0 1 0 1 0 0 0 0 9248 869 30 0 0 MASP1 3 187223194 Frame_Shift_Del DEL C C3N-00549_T 14466082 187223194 11072365 87 15111 FAM43A 0 . GRCh38 3 194687698 194687715 + In_Frame_Del DEL CAGCAGAGGAGGAGGCCG CAGCAGAGGAGGAGGCCG - novel C3N-00549_T C3N-00549_N CAGCAGAGGAGGAGGCCG CAGCAGAGGAGGAGGCCG c.872_889delCAGCAGAGGAGGAGGCCG p.Pro291_Glu297delinsGln p.P291_E297delinsQ ENST00000329759 1/1 53 21 32 85 85 0 sindel-varindel-pindel FAM43A,inframe_deletion,p.Pro291_Glu297delinsGln,ENST00000329759,NM_153690.4; - ENST00000329759 Transcript inframe_deletion 1155-1172/2494 872-889/1272 291-297/423 PAEEEAE/Q cCAGCAGAGGAGGAGGCCGag/cag 1 1 FAM43A HGNC HGNC:26888 protein_coding YES CCDS33923.1 ENSP00000371397 Q8N2R8 UPI0000074368 NM_153690.4 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11232:SF36,hmmpanther:PTHR11232 MODERATE 1 deletion 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 194687698 194687698 CAGCAGAGGAGGAGGCCG - 1 0 1 0 1 0 0 0 0 5440 594 21 0 0 FAM43A 3 194687698 In_Frame_Del DEL CAGCAGAGGAGGAGGCCG C3N-00549_T 7464504 194687698 3607861 88 15112 JAKMIP1 0 . GRCh38 4 6105691 6105691 + Missense_Mutation SNP C C A rs768570614 C3N-00549_T C3N-00549_N C C c.406G>T p.Ala136Ser p.A136S ENST00000409021 3/21 170 60 110 171 171 0 strelka-varscan-mutect JAKMIP1,missense_variant,p.Ala136Ser,ENST00000409021,NM_001099433.1;JAKMIP1,missense_variant,p.Ala136Ser,ENST00000282924,NM_144720.3;JAKMIP1,missense_variant,p.Ala136Ser,ENST00000409831,NM_001306133.1;JAKMIP1,intron_variant,,ENST00000409371,;JAKMIP1,intron_variant,,ENST00000410077,NM_001306134.1;JAKMIP1,intron_variant,,ENST00000457227,;JAKMIP1,missense_variant,p.Ala136Ser,ENST00000473053,; A ENST00000409021 Transcript missense_variant 856/2975 406/2496 136/831 A/S Gcg/Tcg rs768570614 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 deleterious(0) 3/21 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 MODERATE 1 SNV 1 1 PASS rs768570614 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 6105691 6105691 C A 1 0 0 0 0 1 0 0 0 7853 739 26 2 2 JAKMIP1 4 6105691 Missense_Mutation SNP C C3N-00549_T 6105691 184108864 89 15113 GPR78 0 . GRCh38 4 8581401 8581401 + Missense_Mutation SNP C C A rs372133797 C3N-00549_T C3N-00549_N C C c.419C>A p.Ala140Asp p.A140D ENST00000382487 1/3 69 19 50 88 88 0 strelka-varscan-mutect GPR78,missense_variant,p.Ala140Asp,ENST00000382487,NM_080819.4;GPR78,intron_variant,,ENST00000509216,;GPR78,upstream_gene_variant,,ENST00000504255,;GPR78,downstream_gene_variant,,ENST00000503448,;GPR78,downstream_gene_variant,,ENST00000503981,;GPR78,missense_variant,p.Ala140Asp,ENST00000514302,; A ENST00000382487 Transcript missense_variant 836/1694 419/1092 140/363 A/D gCt/gAt rs372133797 1 1 GPR78 HGNC HGNC:4528 protein_coding YES CCDS3403.1 ENSP00000371927 Q96P69 B2R7M4 UPI0000037A5F NM_080819.4 deleterious(0.02) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs372133797 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 8581401 8581401 C A 1 0 0 0 0 1 0 0 0 6592 797 28 2 2 GPR78 4 8581401 Missense_Mutation SNP C C3N-00549_T 2475710 8581401 181633154 90 15114 CC2D2A 0 . GRCh38 4 15537980 15537980 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.1846C>G p.Leu616Val p.L616V ENST00000424120 16/37 157 41 116 264 264 0 strelka-varscan-mutect CC2D2A,missense_variant,p.Leu616Val,ENST00000424120,;CC2D2A,missense_variant,p.Leu616Val,ENST00000503292,NM_001080522.2;CC2D2A,missense_variant,p.Leu437Val,ENST00000389652,;CC2D2A,downstream_gene_variant,,ENST00000512702,;CC2D2A,non_coding_transcript_exon_variant,,ENST00000513811,;CC2D2A,missense_variant,p.Leu59Val,ENST00000506643,;CC2D2A,3_prime_UTR_variant,,ENST00000634028,;CC2D2A,downstream_gene_variant,,ENST00000510220,; G ENST00000424120 Transcript missense_variant 2100/5249 1846/4863 616/1620 L/V Ctt/Gtt 1 1 CC2D2A HGNC HGNC:29253 protein_coding YES CCDS47026.1 ENSP00000403465 Q9P2K1 UPI000023731A tolerated(0.52) 16/37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 15537980 15537980 C G 1 0 0 0 0 1 0 0 0 2429 681 24 4 4 CC2D2A 4 15537980 Missense_Mutation SNP C C3N-00549_T 6956579 15537980 174676575 91 15115 KDR 0 . GRCh38 4 55104912 55104912 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1718C>A p.Ala573Glu p.A573E ENST00000263923 13/30 165 84 81 148 148 0 strelka-varscan-mutect KDR,missense_variant,p.Ala573Glu,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; T ENST00000263923 Transcript missense_variant 2014/5831 1718/4071 573/1356 A/E gCa/gAa 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0) 13/30 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 55104912 55104912 G T 1 0 0 0 0 1 0 0 0 8059 1319 46 2 2 KDR 4 55104912 Missense_Mutation SNP G C3N-00549_T 39566932 55104912 135109643 92 15116 KDR 0 . GRCh38 4 55113436 55113436 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.844G>A p.Gly282Arg p.G282R ENST00000263923 7/30 182 136 46 202 202 0 strelka-varscan-mutect KDR,missense_variant,p.Gly282Arg,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; T ENST00000263923 Transcript missense_variant 1140/5831 844/4071 282/1356 G/R Ggg/Agg 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 tolerated(0.55) 7/30 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 55113436 55113436 C T 1 0 0 0 0 1 0 0 0 8059 594 21 3 3 KDR 4 55113436 Missense_Mutation SNP C C3N-00549_T 8524 55113436 135101119 93 15117 EPHA5 0 . GRCh38 4 65669625 65669625 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.118C>A p.Leu40Ile p.L40I ENST00000622150 1/18 29 20 9 40 40 0 strelka-varscan-mutect EPHA5,missense_variant,p.Leu40Ile,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Leu40Ile,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Leu40Ile,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Leu40Ile,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Leu40Ile,ENST00000432638,;EPHA5,missense_variant,p.Leu40Ile,ENST00000354839,NM_182472.3;EPHA5-AS1,upstream_gene_variant,,ENST00000509473,;EPHA5-AS1,upstream_gene_variant,,ENST00000514260,;EPHA5-AS1,upstream_gene_variant,,ENST00000507117,; T ENST00000622150 Transcript missense_variant 871/8421 118/3117 40/1038 L/I Ctc/Atc 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.15) 1/18 PIRSF_domain:PIRSF000666,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1015973614 . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 50 65669625 65669625 G T 1 0 0 0 0 1 0 0 0 5017 1000 35 2 2 EPHA5 4 65669625 Missense_Mutation SNP G C3N-00549_T 10556189 65669625 124544930 94 15118 TMPRSS11B 0 . GRCh38 4 68231292 68231292 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.597G>C p.Gln199His p.Q199H ENST00000332644 7/10 135 97 38 204 204 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Gln199His,ENST00000332644,NM_182502.3;TMPRSS11B,downstream_gene_variant,,ENST00000502365,;TMPRSS11B,upstream_gene_variant,,ENST00000510856,; G ENST00000332644 Transcript missense_variant 759/2671 597/1251 199/416 Q/H caG/caC 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 deleterious(0) 7/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF171,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 68231292 68231292 C G 1 0 0 0 0 1 0 0 0 16716 680 24 4 4 TMPRSS11B 4 68231292 Missense_Mutation SNP C C3N-00549_T 2561667 68231292 121983263 95 15119 GC 0 . GRCh38 4 71756791 71756791 + Frame_Shift_Del DEL G G - rs747885267 C3N-00549_T C3N-00549_N G G c.1012delC p.Gln338AsnfsTer8 p.Q338Nfs*8 ENST00000504199 9/14 342 165 177 438 438 0 sindel-varindel-pindel GC,frameshift_variant,p.Gln319AsnfsTer8,ENST00000273951,NM_000583.3,NM_001204306.1;GC,frameshift_variant,p.Gln338AsnfsTer8,ENST00000504199,NM_001204307.1;GC,frameshift_variant,p.Gln319AsnfsTer8,ENST00000513476,;RNA5SP163,downstream_gene_variant,,ENST00000410304,;GC,non_coding_transcript_exon_variant,,ENST00000503472,;GC,upstream_gene_variant,,ENST00000503364,;GC,frameshift_variant,p.Gln319AsnfsTer8,ENST00000509740,; - ENST00000504199 Transcript frameshift_variant 1107/1777 1012/1482 338/493 Q/X Caa/aa rs747885267 1 -1 GC HGNC HGNC:4187 protein_coding YES CCDS56332.1 ENSP00000421725 P02774 UPI0001D3B4EE NM_001204307.1 9/14 Pfam_domain:PF00273,PROSITE_profiles:PS51438,hmmpanther:PTHR11385,hmmpanther:PTHR11385:SF11,SMART_domains:SM00103,Superfamily_domains:SSF48552 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 71756791 71756791 G - 1 0 1 0 1 0 0 0 0 6152 1357 47 0 0 GC 4 71756791 Frame_Shift_Del DEL G C3N-00549_T 3525499 71756791 118457764 96 15120 RASGEF1B 0 . GRCh38 4 81432342 81432342 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.1354G>A p.Gly452Arg p.G452R ENST00000264400 13/14 145 107 38 91 91 0 strelka-varscan-mutect RASGEF1B,missense_variant,p.Gly451Arg,ENST00000509081,NM_001300735.1;RASGEF1B,missense_variant,p.Gly539Arg,ENST00000638048,;RASGEF1B,missense_variant,p.Gly452Arg,ENST00000264400,NM_152545.2;RASGEF1B,missense_variant,p.Gly410Arg,ENST00000335927,NM_001300736.1;RASGEF1B,downstream_gene_variant,,ENST00000504863,; T ENST00000264400 Transcript missense_variant 1506/2277 1354/1422 452/473 G/R Gga/Aga 1 -1 RASGEF1B HGNC HGNC:24881 protein_coding YES CCDS34022.1 ENSP00000264400 Q0VAM2 UPI0000044685 NM_152545.2 deleterious(0.03) 13/14 PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF197,hmmpanther:PTHR23113,SMART_domains:SM00147,Superfamily_domains:0041591 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 81432342 81432342 C T 1 0 0 0 0 1 0 0 0 13231 690 24 3 3 RASGEF1B 4 81432342 Missense_Mutation SNP C C3N-00549_T 9675551 81432342 108782213 97 15121 RP11-766F14.2 0 . GRCh38 4 99651893 99651893 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2756C>A p.Thr919Lys p.T919K ENST00000511828 1/2 122 43 79 168 168 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Thr919Lys,ENST00000511828,; T ENST00000511828 Transcript missense_variant 2756/10086 2756/5382 919/1793 T/K aCa/aAa 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE tolerated(0.83) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 99651893 99651893 G T 1 0 0 0 0 1 0 0 0 13762 1377 48 2 2 RP11-766F14.2 4 99651893 Missense_Mutation SNP G C3N-00549_T 18219551 99651893 90562662 98 15122 ANK2 0 . GRCh38 4 113336635 113336636 + Frame_Shift_Ins INS - - A novel C3N-00549_T C3N-00549_N - - c.3650_3651insA p.Ser1217ArgfsTer9 p.S1217Rfs*9 ENST00000357077 31/46 233 85 148 464 464 0 sindel-varindel ANK2,frameshift_variant,p.Ser1217ArgfsTer9,ENST00000357077,NM_001148.4;ANK2,frameshift_variant,p.Ser1184ArgfsTer9,ENST00000264366,;ANK2,frameshift_variant,p.Ser1208ArgfsTer9,ENST00000506722,NM_001127493.1;ANK2,frameshift_variant,p.Ser1217ArgfsTer9,ENST00000394537,NM_020977.3;ANK2,frameshift_variant,p.Ser1232ArgfsTer9,ENST00000504454,;ANK2,frameshift_variant,p.Ser230ArgfsTer9,ENST00000514960,;ANK2,frameshift_variant,p.Ser1130ArgfsTer9,ENST00000503423,;ANK2,frameshift_variant,p.Ser393ArgfsTer9,ENST00000509550,;ANK2,frameshift_variant,p.Ser1188ArgfsTer?,ENST00000634436,;ANK2,downstream_gene_variant,,ENST00000503271,;ANK2,non_coding_transcript_exon_variant,,ENST00000504887,;ANK2,downstream_gene_variant,,ENST00000514160,; A ENST00000357077 Transcript frameshift_variant 3703-3704/14196 3650-3651/11874 1217/3957 S/RX agc/agAc 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 31/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Pfam_domain:PF00791 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 50 113336635 113336635 - A 1 0 1 1 0 0 0 0 0 721 971 34 0 0 ANK2 4 113336635 Frame_Shift_Ins INS - C3N-00549_T 13684742 113336635 76877920 99 15123 ANK2 0 . GRCh38 4 113353671 113353671 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.5053G>T p.Asp1685Tyr p.D1685Y ENST00000357077 38/46 130 41 89 169 169 0 strelka-varscan-mutect ANK2,missense_variant,p.Asp1685Tyr,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Asp1652Tyr,ENST00000264366,;ANK2,missense_variant,p.Asp1700Tyr,ENST00000504454,;ANK2,missense_variant,p.Asp1598Tyr,ENST00000503423,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; T ENST00000357077 Transcript missense_variant 5106/14196 5053/11874 1685/3957 D/Y Gat/Tat 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0.01) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 113353671 113353671 G T 1 0 0 0 0 1 0 0 0 721 942 33 2 2 ANK2 4 113353671 Missense_Mutation SNP G C3N-00549_T 17036 113353671 76860884 100 15124 ANK2 0 . GRCh38 4 113358695 113358695 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.10077G>T p.Gln3359His p.Q3359H ENST00000357077 38/46 122 33 89 153 153 0 strelka-varscan-mutect ANK2,missense_variant,p.Gln3359His,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Gln3326His,ENST00000264366,;ANK2,missense_variant,p.Gln369His,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; T ENST00000357077 Transcript missense_variant 10130/14196 10077/11874 3359/3957 Q/H caG/caT 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(0.1) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 113358695 113358695 G T 1 0 0 0 0 1 0 0 0 721 962 34 2 2 ANK2 4 113358695 Missense_Mutation SNP G C3N-00549_T 5024 113358695 76855860 101 15125 GYPB 0 . GRCh38 4 144001268 144001268 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.53C>A p.Ser18Ter p.S18* ENST00000502664 2/5 278 106 172 463 462 1 strelka-varscan-mutect GYPB,stop_gained,p.Ser18Ter,ENST00000502664,NM_002100.5,NM_001304382.1;GYPB,stop_gained,p.Ser18Ter,ENST00000429670,;GYPB,intron_variant,,ENST00000513128,;RP11-673E1.4,intron_variant,,ENST00000506982,;GYPB,non_coding_transcript_exon_variant,,ENST00000510196,;GYPB,non_coding_transcript_exon_variant,,ENST00000507009,;GYPB,intron_variant,,ENST00000513557,;GYPB,intron_variant,,ENST00000513677,;GYPB,3_prime_UTR_variant,,ENST00000504951,;GYPB,3_prime_UTR_variant,,ENST00000506679,;GYPB,3_prime_UTR_variant,,ENST00000505583,;GYPB,3_prime_UTR_variant,,ENST00000506516,;GYPB,3_prime_UTR_variant,,ENST00000511198,;GYPB,non_coding_transcript_exon_variant,,ENST00000508841,;GYPB,non_coding_transcript_exon_variant,,ENST00000503255,;GYPB,non_coding_transcript_exon_variant,,ENST00000508618,; T ENST00000502664 Transcript stop_gained 105/521 53/276 18/91 S/* tCa/tAa 1 -1 GYPB HGNC HGNC:4703 protein_coding YES CCDS54809.1 ENSP00000427690 P06028 UPI000016A9BA NM_002100.5,NM_001304382.1 2/5 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR13813,hmmpanther:PTHR13813:SF2 HIGH 1 SNV 1 1 PASS rs757056176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 144001268 144001268 G T 1 0 0 0 0 0 1 0 0 6791 1294 45 2 2 GYPB 4 144001268 Nonsense_Mutation SNP G C3N-00549_T 30642573 144001268 46213287 102 15126 DCHS2 0 . GRCh38 4 154235774 154235774 + Missense_Mutation SNP C C G rs749501585 C3N-00549_T C3N-00549_N C C c.7513G>C p.Ala2505Pro p.A2505P ENST00000623607 25/25 97 32 65 138 138 0 strelka-varscan-mutect DCHS2,missense_variant,p.Ala2505Pro,ENST00000357232,;DCHS2,missense_variant,p.Ala2505Pro,ENST00000623607,NM_017639.3;RP11-290O12.2,intron_variant,,ENST00000624941,;RP11-290O12.2,intron_variant,,ENST00000623325,;RP11-9N12.2,upstream_gene_variant,,ENST00000625026,; G ENST00000623607 Transcript missense_variant 7513/8912 7513/8751 2505/2916 A/P Gct/Cct rs749501585 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 deleterious(0) 25/25 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs749501585 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 154235774 154235774 C G 1 0 0 0 0 1 0 0 0 4091 768 27 4 4 DCHS2 4 154235774 Missense_Mutation SNP C C3N-00549_T 10234506 154235774 35978781 103 15127 CYP4V2 0 . GRCh38 4 186210561 186210561 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1498G>T p.Gly500Cys p.G500C ENST00000378802 11/11 201 50 151 244 243 1 strelka-varscan-mutect CYP4V2,missense_variant,p.Gly500Cys,ENST00000378802,NM_207352.3;KLKB1,intron_variant,,ENST00000511608,;CYP4V2,non_coding_transcript_exon_variant,,ENST00000502665,;CYP4V2,non_coding_transcript_exon_variant,,ENST00000513354,;CYP4V2,non_coding_transcript_exon_variant,,ENST00000507209,; T ENST00000378802 Transcript missense_variant 1802/2042 1498/1578 500/525 G/C Ggt/Tgt 1 1 CYP4V2 HGNC HGNC:23198 protein_coding YES CCDS34119.1 ENSP00000368079 Q6ZWL3 UPI00002372FE NM_207352.3 tolerated(0.07) 11/11 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF56,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 186210561 186210561 G T 1 0 0 0 0 1 0 0 0 3995 1348 47 2 2 CYP4V2 4 186210561 Missense_Mutation SNP G C3N-00549_T 31974787 186210561 4003994 104 15128 TERT 0 . GRCh38 5 1294469 1294469 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.417G>T p.= p.L139L ENST00000310581 2/16 335 201 134 428 427 1 strelka-varscan-mutect TERT,synonymous_variant,p.=,ENST00000310581,NM_198253.2;TERT,synonymous_variant,p.=,ENST00000334602,NM_001193376.1;TERT,synonymous_variant,p.=,ENST00000508104,;TERT,downstream_gene_variant,,ENST00000522877,;TERT,synonymous_variant,p.=,ENST00000460137,; A ENST00000310581 Transcript synonymous_variant 475/4018 417/3399 139/1132 L ctG/ctT 1 -1 TERT HGNC HGNC:11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 UPI0000031309 NM_198253.2 2/16 hmmpanther:PTHR12066,hmmpanther:PTHR12066:SF0,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1027515033 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 1294469 1294469 C A 1 0 0 0 0 0 0 0 1 16183 697 25 2 2 TERT 5 1294469 Silent SNP C C3N-00549_T 1294469 180243790 105 15129 SEMA5A 0 . GRCh38 5 9154509 9154509 + Missense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.1460G>T p.Cys487Phe p.C487F ENST00000382496 12/23 256 168 88 238 237 1 strelka-varscan-mutect SEMA5A,missense_variant,p.Cys487Phe,ENST00000382496,NM_003966.2; A ENST00000382496 Transcript missense_variant 2126/11762 1460/3225 487/1074 C/F tGc/tTc COSM213421 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0) 12/23 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78,Gene3D:3.30.1680.10,SMART_domains:SM00423,Superfamily_domains:SSF101912,Superfamily_domains:SSF103575 1 MODERATE 1 SNV 1 1 1 PASS rs1221069422 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 9154509 9154509 C A 1 0 0 0 0 1 0 0 0 14313 710 25 2 2 SEMA5A 5 9154509 Missense_Mutation SNP C C3N-00549_T 7860040 9154509 172383750 106 15130 SEMA5A 0 . GRCh38 5 9379880 9379880 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.67G>A p.Glu23Lys p.E23K ENST00000382496 3/23 161 111 50 165 164 1 strelka-varscan-mutect SEMA5A,missense_variant,p.Glu23Lys,ENST00000382496,NM_003966.2;SEMA5A,missense_variant,p.Glu23Lys,ENST00000513968,;CTD-2201E9.4,intron_variant,,ENST00000511310,;SEMA5A,non_coding_transcript_exon_variant,,ENST00000509486,; T ENST00000382496 Transcript missense_variant 733/11762 67/3225 23/1074 E/K Gag/Aag 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 tolerated_low_confidence(0.18) 3/23 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 9379880 9379880 C T 1 0 0 0 0 1 0 0 0 14313 922 32 3 3 SEMA5A 5 9379880 Missense_Mutation SNP C C3N-00549_T 225371 9379880 172158379 107 15131 ADAMTS12 0 . GRCh38 5 33588664 33588664 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.2800A>G p.Thr934Ala p.T934A ENST00000504830 18/24 238 150 88 304 304 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Thr934Ala,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Thr849Ala,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; C ENST00000504830 Transcript missense_variant 3136/8774 2800/4785 934/1594 T/A Acc/Gcc 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.93) 18/24 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 33588664 33588664 T C 1 0 0 0 0 1 0 0 0 301 1667 58 5 5 ADAMTS12 5 33588664 Missense_Mutation SNP T C3N-00549_T 24208784 33588664 147949595 108 15132 AGXT2 0 . GRCh38 5 35039438 35039438 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.248A>T p.Gln83Leu p.Q83L ENST00000231420 3/14 283 172 111 192 192 0 strelka-varscan-mutect AGXT2,missense_variant,p.Gln83Leu,ENST00000231420,NM_031900.3;AGXT2,missense_variant,p.Gln83Leu,ENST00000618015,;AGXT2,missense_variant,p.Gln83Leu,ENST00000510428,;AGXT2,non_coding_transcript_exon_variant,,ENST00000505542,; A ENST00000231420 Transcript missense_variant 449/2364 248/1545 83/514 Q/L cAg/cTg 1 -1 AGXT2 HGNC HGNC:14412 protein_coding YES CCDS3908.1 ENSP00000231420 Q9BYV1 UPI0000125709 NM_031900.3 deleterious(0.01) 3/14 hmmpanther:PTHR11986,hmmpanther:PTHR11986:SF58,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 35039438 35039438 T A 1 0 0 0 0 1 0 0 0 484 1580 55 4 4 AGXT2 5 35039438 Missense_Mutation SNP T C3N-00549_T 1450774 35039438 146498821 109 15133 DAB2 0 . GRCh38 5 39376966 39376966 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1821G>T p.Gln607His p.Q607H ENST00000320816 12/15 351 211 140 281 281 0 strelka-varscan-mutect DAB2,missense_variant,p.Gln586His,ENST00000545653,NM_001244871.1;DAB2,missense_variant,p.Gln607His,ENST00000320816,NM_001343.3;DAB2,missense_variant,p.Gln389His,ENST00000339788,;DAB2,missense_variant,p.Gln586His,ENST00000509337,;C9,intron_variant,,ENST00000483232,;DAB2,upstream_gene_variant,,ENST00000502879,; A ENST00000320816 Transcript missense_variant 2289/4534 1821/2313 607/770 Q/H caG/caT 1 -1 DAB2 HGNC HGNC:2662 protein_coding YES CCDS34149.1 ENSP00000313391 P98082 A0A024R036 UPI0000169E27 NM_001343.3 tolerated(0.13) 12/15 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF30 MODERATE 1 SNV 1 1 PASS rs1297766147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 39376966 39376966 C A 1 0 0 0 0 1 0 0 0 4019 796 28 2 2 DAB2 5 39376966 Missense_Mutation SNP C C3N-00549_T 4337528 39376966 142161293 110 15134 CARD6 0 . GRCh38 5 40853864 40853864 + Silent SNP A A G novel C3N-00549_T C3N-00549_N A A c.2532A>G p.= p.A844A ENST00000254691 3/3 312 201 111 205 205 0 strelka-varscan-mutect CARD6,synonymous_variant,p.=,ENST00000254691,NM_032587.3;CARD6,intron_variant,,ENST00000381677,; G ENST00000254691 Transcript synonymous_variant 2731/4221 2532/3114 844/1037 A gcA/gcG 1 1 CARD6 HGNC HGNC:16394 protein_coding YES CCDS3935.1 ENSP00000254691 Q9BX69 UPI000013CE50 NM_032587.3 3/3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 50 40853864 40853864 A G 1 0 0 0 0 0 0 0 1 2346 175 7 5 5 CARD6 5 40853864 Silent SNP A C3N-00549_T 1476898 40853864 140684395 111 15135 C6 0 . GRCh38 5 41158677 41158677 + Silent SNP G G T C3N-00549_T C3N-00549_N G G c.1965C>A p.= p.I655I ENST00000263413 13/18 378 250 128 314 313 1 strelka-varscan-mutect C6,synonymous_variant,p.=,ENST00000263413,NM_001115131.2;C6,synonymous_variant,p.=,ENST00000337836,NM_000065.3;C6,downstream_gene_variant,,ENST00000475349,;C6,upstream_gene_variant,,ENST00000461473,;C6,downstream_gene_variant,,ENST00000473450,;C6,non_coding_transcript_exon_variant,,ENST00000511470,; T ENST00000263413 Transcript synonymous_variant 2230/3661 1965/2805 655/934 I atC/atA COSM3616604,COSM5351199 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 13/18 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 41158677 41158677 G T 1 0 0 0 0 0 0 0 1 2111 1188 41 2 2 C6 5 41158677 Silent SNP G C3N-00549_T 304813 41158677 140379582 112 15136 PAIP1 0 . GRCh38 5 43555986 43555986 + Silent SNP G G A rs757134803 C3N-00549_T C3N-00549_N G G c.279C>T p.= p.P93P ENST00000306846 2/11 117 72 45 112 112 0 strelka-varscan-mutect PAIP1,synonymous_variant,p.=,ENST00000306846,NM_006451.4;PAIP1,synonymous_variant,p.=,ENST00000436644,NM_182789.3;PAIP1,synonymous_variant,p.=,ENST00000514514,;PAIP1,5_prime_UTR_variant,,ENST00000338972,NM_183323.2;PAIP1,5_prime_UTR_variant,,ENST00000508537,;PAIP1,5_prime_UTR_variant,,ENST00000511321,;PAIP1,intron_variant,,ENST00000515338,;PAIP1,intron_variant,,ENST00000504075,;PAIP1,synonymous_variant,p.=,ENST00000504639,; A ENST00000306846 Transcript synonymous_variant 512/2782 279/1440 93/479 P ccC/ccT rs757134803,COSM3855376 1 -1 PAIP1 HGNC HGNC:16945 protein_coding YES CCDS3947.1 ENSP00000302768 Q9H074 UPI00000728C0 NM_006451.4 2/11 hmmpanther:PTHR23254,hmmpanther:PTHR23254:SF15 0,1 LOW 1 SNV 1 0,1 1 PASS rs757134803 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 43555986 43555986 G A 1 0 0 0 0 0 0 0 1 11476 1219 43 3 3 PAIP1 5 43555986 Silent SNP G C3N-00549_T 2397309 43555986 137982273 113 15137 HCN1 0 . GRCh38 5 45645426 45645426 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.608G>T p.Ser203Ile p.S203I ENST00000303230 2/8 205 124 81 158 158 0 strelka-varscan-mutect HCN1,missense_variant,p.Ser203Ile,ENST00000303230,NM_021072.3;HCN1,missense_variant,p.Ser203Ile,ENST00000634658,;HCN1,upstream_gene_variant,,ENST00000637256,; A ENST00000303230 Transcript missense_variant 849/9885 608/2673 203/890 S/I aGt/aTt 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 deleterious(0) 2/8 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 45645426 45645426 C A 1 0 0 0 0 1 0 0 0 6883 565 20 2 2 HCN1 5 45645426 Missense_Mutation SNP C C3N-00549_T 2089440 45645426 135892833 114 15138 VCAN 0 . GRCh38 5 83521248 83521248 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.2942C>G p.Thr981Arg p.T981R ENST00000265077 7/15 77 26 51 103 103 0 strelka-varscan-mutect VCAN,missense_variant,p.Thr981Arg,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Thr981Arg,ENST00000342785,NM_001164098.1;VCAN,missense_variant,p.Thr933Arg,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; G ENST00000265077 Transcript missense_variant 3507/12625 2942/10191 981/3396 T/R aCa/aGa 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.19) 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 83521248 83521248 C G 1 0 0 0 0 1 0 0 0 17683 478 17 4 4 VCAN 5 83521248 Missense_Mutation SNP C C3N-00549_T 37875822 83521248 98017011 115 15139 APC 0 . GRCh38 5 112839111 112839111 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.3517G>T p.Val1173Leu p.V1173L ENST00000257430 16/16 238 94 144 232 232 0 strelka-varscan-mutect APC,missense_variant,p.Val1173Leu,ENST00000257430,NM_000038.5;APC,missense_variant,p.Val1173Leu,ENST00000508376,NM_001127510.2;APC,missense_variant,p.Val1173Leu,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,3_prime_UTR_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,; T ENST00000257430 Transcript missense_variant 3573/10701 3517/8532 1173/2843 V/L Gtg/Ttg 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 tolerated_low_confidence(0.35) 16/16 Pfam_domain:PF05972,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 112839111 112839111 G T 1 0 0 0 0 1 0 0 0 883 1377 48 2 2 APC 5 112839111 Missense_Mutation SNP G C3N-00549_T 29317863 112839111 68699148 116 15140 APC 0 . GRCh38 5 112839558 112839558 + Frame_Shift_Del DEL G G - rs752926571 C3N-00549_T C3N-00549_N G G c.3964delG p.Glu1322LysfsTer93 p.E1322Kfs*93 ENST00000257430 16/16 355 116 239 503 502 1 sindel-varindel-pindel APC,frameshift_variant,p.Glu1322LysfsTer93,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu1322LysfsTer93,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,3_prime_UTR_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,; - ENST00000257430 Transcript frameshift_variant 4020/10701 3964/8532 1322/2843 E/X Gaa/aa rs752926571,COSM18702,COSM4169380 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 16/16 Pfam_domain:PF16633,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 0,1,1 HIGH deletion 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 112839558 112839558 G - 1 0 1 0 1 0 0 0 0 883 1059 37 0 0 APC 5 112839558 Frame_Shift_Del DEL G C3N-00549_T 447 112839558 68698701 117 15141 FAM170A 0 . GRCh38 5 119634420 119634420 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.672G>T p.Met224Ile p.M224I ENST00000613773 3/5 167 58 109 201 201 0 strelka-varscan-mutect FAM170A,missense_variant,p.Met224Ile,ENST00000613773,NM_182761.3;FAM170A,missense_variant,p.Met177Ile,ENST00000620555,NM_001163991.1;FAM170A,missense_variant,p.Met224Ile,ENST00000515256,;FAM170A,intron_variant,,ENST00000509264,;FAM170A,missense_variant,p.Met224Ile,ENST00000335286,;FAM170A,missense_variant,p.Met177Ile,ENST00000504819,;FAM170A,missense_variant,p.Met177Ile,ENST00000379555,;HSD17B4,intron_variant,,ENST00000515235,; T ENST00000613773 Transcript missense_variant 882/1374 672/990 224/329 M/I atG/atT 1 1 FAM170A HGNC HGNC:27963 protein_coding YES CCDS43353.1 ENSP00000482552 A1A519 UPI00001C1E37 NM_182761.3 tolerated(0.18) 3/5 hmmpanther:PTHR33517:SF3,hmmpanther:PTHR33517 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 119634420 119634420 G T 1 0 0 0 0 1 0 0 0 5335 1348 47 2 2 FAM170A 5 119634420 Missense_Mutation SNP G C3N-00549_T 6794862 119634420 61903839 118 15142 PCDHGA4 0 . GRCh38 5 141355987 141355987 + Missense_Mutation SNP A A T rs775400390 C3N-00549_T C3N-00549_N A A c.880A>T p.Thr294Ser p.T294S ENST00000571252 1/4 146 53 93 178 178 0 strelka-varscan PCDHGA4,missense_variant,p.Thr294Ser,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Thr294Ser,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 963/4778 880/2889 294/962 T/S Acc/Tcc rs775400390 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 tolerated_low_confidence(0.12) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 141355987 141355987 A T 1 0 0 0 0 1 0 0 0 11643 159 6 4 4 PCDHGA4 5 141355987 Missense_Mutation SNP A C3N-00549_T 21721567 141355987 40182272 119 15143 DPYSL3 0 . GRCh38 5 147418591 147418591 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.511A>G p.Thr171Ala p.T171A ENST00000343218 3/14 115 17 98 139 139 0 strelka-varscan DPYSL3,missense_variant,p.Thr171Ala,ENST00000343218,NM_001197294.1;DPYSL3,missense_variant,p.Thr57Ala,ENST00000398514,NM_001387.2;DPYSL3,missense_variant,p.Thr57Ala,ENST00000512722,;DPYSL3,non_coding_transcript_exon_variant,,ENST00000519672,;DPYSL3,intron_variant,,ENST00000507309,; C ENST00000343218 Transcript missense_variant 709/5476 511/2055 171/684 T/A Acc/Gcc 1 -1 DPYSL3 HGNC HGNC:3015 protein_coding YES CCDS56387.1 ENSP00000343690 Q14195 A0A140VK07 UPI000020CF0E NM_001197294.1 deleterious(0.03) 3/14 Gene3D:2.30.40.10,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF57,Superfamily_domains:SSF51338,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 147418591 147418591 T C 1 0 0 0 0 1 0 0 0 4563 1667 58 5 5 DPYSL3 5 147418591 Missense_Mutation SNP T C3N-00549_T 6062604 147418591 34119668 120 15144 HAVCR1 0 . GRCh38 5 157055200 157055200 + Splice_Site SNP C C A rs760073263 C3N-00549_T C3N-00549_N C C c.379+1G>T p.X127_splice ENST00000625904 34 6 28 29 29 0 strelka-varscan HAVCR1,splice_donor_variant,,ENST00000339252,NM_001099414.1,NM_012206.2;HAVCR1,splice_donor_variant,,ENST00000625904,;HAVCR1,splice_donor_variant,,ENST00000522693,NM_001308156.1;HAVCR1,splice_donor_variant,,ENST00000523175,NM_001173393.1;HAVCR1,splice_donor_variant,,ENST00000518745,; A ENST00000625904 Transcript splice_donor_variant -/1807 379/1206 127/401 rs760073263 1 -1 HAVCR1 HGNC HGNC:17866 protein_coding YES CCDS78076.1 ENSP00000487363 E9PFX0 UPI000020C020 2/6 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 157055200 157055200 C A 1 0 0 0 0 0 0 1 0 6859 550 19 1 1 HAVCR1 5 157055200 Splice_Site SNP C C3N-00549_T 9636609 157055200 24483059 121 15145 DUSP22 0 . GRCh38 6 348127 348127 + Silent SNP G G T rs756999142 C3N-00549_T C3N-00549_N G G c.288G>T p.= p.V96V ENST00000419235 6/7 264 208 56 242 242 0 strelka-varscan-mutect DUSP22,synonymous_variant,p.=,ENST00000419235,NM_001286555.1;DUSP22,synonymous_variant,p.=,ENST00000344450,NM_020185.4;DUSP22,synonymous_variant,p.=,ENST00000603296,;DUSP22,5_prime_UTR_variant,,ENST00000604971,;DUSP22,5_prime_UTR_variant,,ENST00000605035,;DUSP22,5_prime_UTR_variant,,ENST00000605315,;DUSP22,5_prime_UTR_variant,,ENST00000603453,;DUSP22,5_prime_UTR_variant,,ENST00000605863,;DUSP22,5_prime_UTR_variant,,ENST00000603881,;DUSP22,non_coding_transcript_exon_variant,,ENST00000605391,;DUSP22,non_coding_transcript_exon_variant,,ENST00000604914,;DUSP22,non_coding_transcript_exon_variant,,ENST00000604988,;DUSP22,non_coding_transcript_exon_variant,,ENST00000603005,;DUSP22,downstream_gene_variant,,ENST00000603290,;DUSP22,3_prime_UTR_variant,,ENST00000603795,;DUSP22,3_prime_UTR_variant,,ENST00000603726,; T ENST00000419235 Transcript synonymous_variant 366/3098 288/618 96/205 V gtG/gtT rs756999142 1 1 DUSP22 HGNC HGNC:16077 protein_coding YES CCDS69035.1 ENSP00000397459 Q9NRW4 UPI000020E3B7 NM_001286555.1 6/7 Gene3D:3.90.190.10,Pfam_domain:PF00782,PROSITE_profiles:PS50054,PROSITE_profiles:PS50056,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF29,SMART_domains:SM00195,Superfamily_domains:SSF52799 LOW 1 SNV 2 1 PASS rs756999142 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 348127 348127 G T 1 0 0 0 0 0 0 0 1 4643 1277 45 2 2 DUSP22 6 348127 Silent SNP G C3N-00549_T 348127 170457852 122 15146 MYLK4 0 . GRCh38 6 2679300 2679300 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.867G>T p.= p.V289V ENST00000274643 9/13 222 120 102 269 269 0 strelka-varscan-mutect MYLK4,synonymous_variant,p.=,ENST00000274643,NM_001012418.3; A ENST00000274643 Transcript synonymous_variant 1210/5806 867/1167 289/388 V gtG/gtT 1 -1 MYLK4 HGNC HGNC:27972 protein_coding YES CCDS34330.1 ENSP00000274643 Q86YV6 UPI00000498AE NM_001012418.3 9/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF119,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 2679300 2679300 C A 1 0 0 0 0 0 0 0 1 10059 581 21 2 2 MYLK4 6 2679300 Silent SNP C C3N-00549_T 2331173 2679300 168126679 123 15147 NRN1 0 . GRCh38 6 5999028 5999028 + Missense_Mutation SNP G G A rs768743224 C3N-00549_T C3N-00549_N G G c.455C>T p.Pro152Leu p.P152L ENST00000622188 4/4 258 142 116 192 192 0 strelka-varscan-mutect NRN1,missense_variant,p.Pro152Leu,ENST00000622188,NM_001278711.1;NRN1,missense_variant,p.Pro126Leu,ENST00000244766,NM_016588.2;NRN1,missense_variant,p.Pro126Leu,ENST00000616243,NM_001278710.1;NRN1,non_coding_transcript_exon_variant,,ENST00000495850,; A ENST00000622188 Transcript missense_variant 769/1795 455/507 152/168 P/L cCg/cTg rs768743224 1 -1 NRN1 HGNC HGNC:17972 protein_coding YES CCDS75393.1 ENSP00000480483 A0A087WWT2 UPI000020E485 NM_001278711.1 tolerated(0.25) 4/4 hmmpanther:PTHR15902,hmmpanther:PTHR15902:SF1 MODERATE 1 SNV 2 1 PASS rs768743224 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 5999028 5999028 G A 1 0 0 0 0 1 0 0 0 10716 1116 39 1 1 NRN1 6 5999028 Missense_Mutation SNP G C3N-00549_T 3319728 5999028 164806951 124 15148 F13A1 0 . GRCh38 6 6174842 6174842 + Silent SNP T T A novel C3N-00549_T C3N-00549_N T T c.1485A>T p.= p.L495L ENST00000264870 12/15 375 212 163 287 287 0 strelka-varscan-mutect F13A1,synonymous_variant,p.=,ENST00000264870,NM_000129.3; A ENST00000264870 Transcript synonymous_variant 1751/3999 1485/2199 495/732 L ctA/ctT 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 12/15 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF42,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 6174842 6174842 T A 1 0 0 0 0 0 0 0 1 5208 1509 53 4 4 F13A1 6 6174842 Silent SNP T C3N-00549_T 175814 6174842 164631137 125 15149 TFAP2A 0 . GRCh38 6 10402593 10402593 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.782G>T p.Gly261Val p.G261V ENST00000482890 6/8 361 213 148 339 339 0 strelka-varscan-mutect TFAP2A,missense_variant,p.Gly263Val,ENST00000379613,;TFAP2A,missense_variant,p.Gly255Val,ENST00000379608,NM_001032280.2;TFAP2A,missense_variant,p.Gly261Val,ENST00000482890,NM_003220.2;TFAP2A,missense_variant,p.Gly257Val,ENST00000319516,NM_001042425.1;TFAP2A,missense_variant,p.Gly261Val,ENST00000466073,;TFAP2A,missense_variant,p.Gly166Val,ENST00000475264,;TFAP2A,missense_variant,p.Gly36Val,ENST00000461628,;TFAP2A,missense_variant,p.Gly118Val,ENST00000498450,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000497266,;TFAP2A,downstream_gene_variant,,ENST00000490875,;TFAP2A,downstream_gene_variant,,ENST00000473652,;TFAP2A,downstream_gene_variant,,ENST00000462727,;TFAP2A,3_prime_UTR_variant,,ENST00000489805,;TFAP2A,3_prime_UTR_variant,,ENST00000488193,;TFAP2A,non_coding_transcript_exon_variant,,ENST00000478375,;TFAP2A,downstream_gene_variant,,ENST00000474952,; A ENST00000482890 Transcript missense_variant 1135/2071 782/1314 261/437 G/V gGa/gTa 1 -1 TFAP2A HGNC HGNC:11742 protein_coding YES CCDS4510.1 ENSP00000418541 P05549 UPI0000125BC5 NM_003220.2 deleterious(0) 6/8 Pfam_domain:PF03299,Prints_domain:PR01748,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 10402593 10402593 C A 1 0 0 0 0 1 0 0 0 16220 855 30 2 2 TFAP2A 6 10402593 Missense_Mutation SNP C C3N-00549_T 4227751 10402593 160403386 126 15150 RANBP9 0 . GRCh38 6 13711099 13711099 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.407G>T p.Gly136Val p.G136V ENST00000011619 1/14 201 120 81 209 209 0 strelka-varscan-mutect RANBP9,missense_variant,p.Gly136Val,ENST00000011619,NM_005493.2; A ENST00000011619 Transcript missense_variant 466/3113 407/2190 136/729 G/V gGg/gTg 1 -1 RANBP9 HGNC HGNC:13727 protein_coding YES CCDS4529.1 ENSP00000011619 Q96S59 A0A024QZW3 UPI000006ED83 NM_005493.2 tolerated_low_confidence(0.19) 1/14 hmmpanther:PTHR12864:SF18,hmmpanther:PTHR12864 MODERATE 1 SNV 1 1 PASS rs1484400119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 13711099 13711099 C A 1 0 0 0 0 1 0 0 0 13191 623 22 2 2 RANBP9 6 13711099 Missense_Mutation SNP C C3N-00549_T 3308506 13711099 157094880 127 15151 CD83 0 . GRCh38 6 14118034 14118034 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.122C>T p.Pro41Leu p.P41L ENST00000379153 2/5 171 110 61 197 197 0 strelka-varscan-mutect CD83,missense_variant,p.Pro41Leu,ENST00000379153,NM_004233.3,NM_001040280.1;CD83,5_prime_UTR_variant,,ENST00000612003,NM_001251901.1; T ENST00000379153 Transcript missense_variant 293/2471 122/618 41/205 P/L cCg/cTg 1 1 CD83 HGNC HGNC:1703 protein_coding YES CCDS4532.1 ENSP00000368450 Q01151 UPI000004C561 NM_004233.3,NM_001040280.1 tolerated(0.05) 2/5 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR15193,hmmpanther:PTHR15193:SF1,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 14118034 14118034 C T 1 0 0 0 0 1 0 0 0 2745 652 23 1 1 CD83 6 14118034 Missense_Mutation SNP C C3N-00549_T 406935 14118034 156687945 128 15152 ATXN1 0 . GRCh38 6 16327702 16327702 + Missense_Mutation SNP C C A rs199744696 C3N-00549_T C3N-00549_N C C c.609G>T p.Gln203His p.Q203H ENST00000244769 8/9 396 270 126 402 402 0 strelka-varscan-mutect ATXN1,missense_variant,p.Gln203His,ENST00000244769,NM_000332.3;ATXN1,missense_variant,p.Gln203His,ENST00000436367,NM_001128164.1; A ENST00000244769 Transcript missense_variant 1546/10602 609/2448 203/815 Q/H caG/caT rs199744696,COSM222477 1 -1 ATXN1 HGNC HGNC:10548 protein_coding YES CCDS34342.1 ENSP00000244769 P54253 UPI000013CB8B NM_000332.3 tolerated_low_confidence(0.15) 8/9 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199744696 . 0 208 0 0 0 2 0 0 -9.935446 0.7986908 1 1 1 0 A 3 1 50 16327702 16327702 C A 1 0 0 0 0 1 0 0 0 1362 796 28 2 2 ATXN1 6 16327702 Missense_Mutation SNP C C3N-00549_T 2209668 16327702 154478277 129 15153 KIF13A 0 . GRCh38 6 17781204 17781204 + Silent SNP C C T novel C3N-00549_T C3N-00549_N C C c.3642G>A p.= p.L1214L ENST00000259711 30/39 160 103 57 177 177 0 strelka-varscan-mutect KIF13A,synonymous_variant,p.=,ENST00000378814,NM_001105568.2;KIF13A,synonymous_variant,p.=,ENST00000259711,NM_022113.5;KIF13A,synonymous_variant,p.=,ENST00000378826,NM_001105566.2;KIF13A,synonymous_variant,p.=,ENST00000378843,NM_001105567.2;KIF13A,synonymous_variant,p.=,ENST00000636847,;KIF13A,synonymous_variant,p.=,ENST00000358380,;KIF13A,synonymous_variant,p.=,ENST00000502297,;KIF13A,synonymous_variant,p.=,ENST00000506044,;KIF13A,downstream_gene_variant,,ENST00000514714,; T ENST00000259711 Transcript synonymous_variant 3748/5941 3642/5418 1214/1805 L ctG/ctA 1 -1 KIF13A HGNC HGNC:14566 protein_coding YES CCDS47381.1 ENSP00000259711 Q9H1H9 UPI0000E20DA3 NM_022113.5 30/39 Pfam_domain:PF12473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 17781204 17781204 C T 1 0 0 0 0 0 0 0 1 8138 697 25 3 3 KIF13A 6 17781204 Silent SNP C C3N-00549_T 1453502 17781204 153024775 130 15154 HIST1H2BL 0 . GRCh38 6 27807609 27807609 + Missense_Mutation SNP G G T rs779644008 C3N-00549_T C3N-00549_N G G c.298C>A p.Arg100Ser p.R100S ENST00000377401 1/1 345 213 132 273 273 0 strelka-varscan-mutect HIST1H2BL,missense_variant,p.Arg100Ser,ENST00000377401,NM_003519.3;HIST1H3H,upstream_gene_variant,,ENST00000369163,NM_003536.2;HIST1H2AI,upstream_gene_variant,,ENST00000358739,NM_003509.2;HIST1H4PS1,downstream_gene_variant,,ENST00000406085,; T ENST00000377401 Transcript missense_variant 323/488 298/381 100/126 R/S Cgc/Agc rs779644008,COSM1442755 1 -1 HIST1H2BL HGNC HGNC:4748 protein_coding YES CCDS4625.1 ENSP00000366618 Q99880 UPI0000001BD6 NM_003519.3 deleterious_low_confidence(0.04) 1/1 hmmpanther:PTHR23428,PROSITE_patterns:PS00357,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 0,1 MODERATE 1 SNV 0,1 1 PASS rs779644008 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 27807609 27807609 G T 1 0 0 0 0 1 0 0 0 7039 1087 38 1 1 HIST1H2BL 6 27807609 Missense_Mutation SNP G C3N-00549_T 10026405 27807609 142998370 131 15155 ZBED9 0 . GRCh38 6 28573319 28573319 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2570G>T p.Gly857Val p.G857V ENST00000452236 4/4 262 162 100 495 495 0 strelka-varscan-mutect ZBED9,missense_variant,p.Gly857Val,ENST00000452236,NM_052923.1;ZBED9,downstream_gene_variant,,ENST00000530247,; A ENST00000452236 Transcript missense_variant 3188/4877 2570/3978 857/1325 G/V gGt/gTt 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 deleterious(0.01) 4/4 hmmpanther:PTHR11697:SF108,hmmpanther:PTHR11697 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 28573319 28573319 C A 1 0 0 0 0 1 0 0 0 18086 507 18 2 2 ZBED9 6 28573319 Missense_Mutation SNP C C3N-00549_T 765710 28573319 142232660 132 15156 OR2H1 0 . GRCh38 6 29462668 29462668 + Missense_Mutation SNP G G T rs530184651 C3N-00549_T C3N-00549_N G G c.899G>T p.Arg300Met p.R300M ENST00000377136 4/4 231 153 78 205 204 1 strelka-varscan-mutect OR2H1,missense_variant,p.Arg300Met,ENST00000377136,;OR2H1,missense_variant,p.Arg300Met,ENST00000377133,NM_001318022.1,NM_030883.3;OR2H1,missense_variant,p.Arg300Met,ENST00000377132,;OR2H1,missense_variant,p.Arg300Met,ENST00000396792,;OR2H1,non_coding_transcript_exon_variant,,ENST00000473369,;OR2H1,non_coding_transcript_exon_variant,,ENST00000484554,;OR2H1,downstream_gene_variant,,ENST00000484371,;UBDP1,downstream_gene_variant,,ENST00000457888,; T ENST00000377136 Transcript missense_variant 1364/3024 899/951 300/316 R/M aGg/aTg rs530184651 1 1 OR2H1 HGNC HGNC:8252 protein_coding YES CCDS4660.1 ENSP00000366340 Q9GZK4 A0A024RCM6 UPI000000DCA7 tolerated(0.08) 4/4 hmmpanther:PTHR26453:SF190,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs530184651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 29462668 29462668 G T 1 0 0 0 0 1 0 0 0 11079 1000 35 2 2 OR2H1 6 29462668 Missense_Mutation SNP G C3N-00549_T 889349 29462668 141343311 133 15157 DDX39B 0 . GRCh38 6 31540460 31540460 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.73G>C p.Asp25His p.D25H ENST00000396172 2/11 350 234 116 289 289 0 strelka-varscan-mutect DDX39B,missense_variant,p.Asp25His,ENST00000396172,NM_004640.6;DDX39B,missense_variant,p.Asp25His,ENST00000458640,NM_080598.5;DDX39B,missense_variant,p.Asp25His,ENST00000376177,;DDX39B,missense_variant,p.Asp25His,ENST00000427214,;DDX39B,missense_variant,p.Asp25His,ENST00000456662,;DDX39B,missense_variant,p.Asp25His,ENST00000419338,;DDX39B,missense_variant,p.Glu20Asp,ENST00000431908,;DDX39B,missense_variant,p.Asp25His,ENST00000428098,;DDX39B,missense_variant,p.Asp25His,ENST00000456976,;DDX39B,missense_variant,p.Asp25His,ENST00000428450,;DDX39B,missense_variant,p.Asp48His,ENST00000449757,;DDX39B,missense_variant,p.Asp40His,ENST00000418897,;DDX39B,missense_variant,p.Asp25His,ENST00000419020,;ATP6V1G2,downstream_gene_variant,,ENST00000303892,NM_130463.3;ATP6V1G2,downstream_gene_variant,,ENST00000376151,NM_001204078.1;ATP6V1G2,downstream_gene_variant,,ENST00000483251,NM_138282.2;ATP6V1G2,downstream_gene_variant,,ENST00000415099,;SNORD84,downstream_gene_variant,,ENST00000584275,;SNORD117,upstream_gene_variant,,ENST00000364915,;DDX39B-AS1,upstream_gene_variant,,ENST00000420520,;DDX39B-AS1,upstream_gene_variant,,ENST00000416684,;ATP6V1G2,downstream_gene_variant,,ENST00000483170,;ATP6V1G2-DDX39B,downstream_gene_variant,,ENST00000475917,;ATP6V1G2-DDX39B,3_prime_UTR_variant,,ENST00000376185,;ATP6V1G2-DDX39B,3_prime_UTR_variant,,ENST00000480131,;DDX39B,non_coding_transcript_exon_variant,,ENST00000481456,;DDX39B,non_coding_transcript_exon_variant,,ENST00000462256,;DDX39B,non_coding_transcript_exon_variant,,ENST00000482195,;DDX39B,upstream_gene_variant,,ENST00000484566,; G ENST00000396172 Transcript missense_variant 704/2133 73/1287 25/428 D/H Gat/Cat 1 -1 DDX39B HGNC HGNC:13917 protein_coding YES CCDS4697.1 ENSP00000379475 Q13838 A0A024RCM3 UPI0000001D0B NM_004640.6 deleterious(0.03) 2/11 hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 31540460 31540460 C G 1 0 0 0 0 1 0 0 0 4160 913 32 4 4 DDX39B 6 31540460 Missense_Mutation SNP C C3N-00549_T 2077792 31540460 139265519 134 15158 BRD2 0 . GRCh38 6 32976648 32976649 + In_Frame_Ins INS - - AGTCTT novel C3N-00549_T C3N-00549_N - - c.913_918dupAGTCTT p.Ser305_Leu306dup p.S305_L306dup ENST00000395287 6/13 190 115 75 129 129 0 sindel-varindel-pindel BRD2,inframe_insertion,p.Ser305_Leu306dup,ENST00000374825,NM_005104.3;BRD2,inframe_insertion,p.Ser305_Leu306dup,ENST00000374831,NM_001113182.2;BRD2,inframe_insertion,p.Ser305_Leu306dup,ENST00000395287,NM_001199455.1;BRD2,inframe_insertion,p.Ser311_Leu312dup,ENST00000449025,;BRD2,inframe_insertion,p.Ser258_Leu259dup,ENST00000449085,NM_001291986.1,NM_001199456.1;BRD2,inframe_insertion,p.Ser305_Leu306dup,ENST00000607833,;BRD2,inframe_insertion,p.Ser48_Leu49dup,ENST00000606059,;BRD2,downstream_gene_variant,,ENST00000456339,;BRD2,downstream_gene_variant,,ENST00000496118,;XXbac-BPG181M17.6,upstream_gene_variant,,ENST00000580587,;BRD2,downstream_gene_variant,,ENST00000580234,;BRD2,downstream_gene_variant,,ENST00000581002,;BRD2,downstream_gene_variant,,ENST00000584808,;BRD2,inframe_insertion,p.Ser305_Leu306dup,ENST00000495733,;BRD2,inframe_insertion,p.Ser28_Leu29dup,ENST00000481259,;BRD2,3_prime_UTR_variant,,ENST00000482914,;BRD2,non_coding_transcript_exon_variant,,ENST00000464592,;BRD2,upstream_gene_variant,,ENST00000469132,;BRD2,upstream_gene_variant,,ENST00000463639,;BRD2,upstream_gene_variant,,ENST00000482838,; AGTCTT ENST00000395287 Transcript inframe_insertion 1081-1082/3467 912-913/2511 304-305/836 -/SL -/AGTCTT 1 1 BRD2 HGNC HGNC:1103 protein_coding YES CCDS56420.1 ENSP00000378702 P25440 UPI0000227E6A NM_001199455.1 6/13 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF126,Low_complexity_(Seg):seg MODERATE 1 insertion 1 6 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 AGTCTT 7 5 50 32976648 32976648 - AGTCTT 1 0 1 1 0 0 0 0 0 1672 1161 41 0 0 BRD2 6 32976648 In_Frame_Ins INS - C3N-00549_T 1436188 32976648 137829331 135 15159 BRPF3 0 . GRCh38 6 36201327 36201327 + Silent SNP A A T novel C3N-00549_T C3N-00549_N A A c.1005A>T p.= p.A335A ENST00000357641 2/13 326 202 124 266 266 0 strelka-varscan-mutect BRPF3,synonymous_variant,p.=,ENST00000357641,NM_015695.2;BRPF3,synonymous_variant,p.=,ENST00000339717,;BRPF3,synonymous_variant,p.=,ENST00000534694,;BRPF3,synonymous_variant,p.=,ENST00000534400,;BRPF3,downstream_gene_variant,,ENST00000454960,;BRPF3,upstream_gene_variant,,ENST00000527657,;BRPF3,downstream_gene_variant,,ENST00000446974,;RP1-179N16.6,upstream_gene_variant,,ENST00000499560,;RP1-179N16.6,upstream_gene_variant,,ENST00000526611,;BRPF3,synonymous_variant,p.=,ENST00000441123,;BRPF3,synonymous_variant,p.=,ENST00000449261,;BRPF3,synonymous_variant,p.=,ENST00000532330,; T ENST00000357641 Transcript synonymous_variant 1258/6052 1005/3618 335/1205 A gcA/gcT 1 1 BRPF3 HGNC HGNC:14256 protein_coding YES CCDS34437.1 ENSP00000350267 Q9ULD4 UPI00001C1E4C NM_015695.2 2/13 hmmpanther:PTHR13793:SF19,hmmpanther:PTHR13793,Pfam_domain:PF13832,SMART_domains:SM00249 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 36201327 36201327 A T 1 0 0 0 0 0 0 0 1 1695 175 7 4 4 BRPF3 6 36201327 Silent SNP A C3N-00549_T 3224679 36201327 134604652 136 15160 FGD2 0 . GRCh38 6 37028114 37028114 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1919C>A p.Ala640Asp p.A640D ENST00000274963 16/16 100 45 55 72 72 0 strelka-varscan-mutect FGD2,missense_variant,p.Ala640Asp,ENST00000274963,NM_173558.3;FGD2,3_prime_UTR_variant,,ENST00000373535,;FGD2,non_coding_transcript_exon_variant,,ENST00000493635,;FGD2,non_coding_transcript_exon_variant,,ENST00000494343,;FGD2,non_coding_transcript_exon_variant,,ENST00000464083,;FGD2,non_coding_transcript_exon_variant,,ENST00000487920,; A ENST00000274963 Transcript missense_variant 2090/3046 1919/1968 640/655 A/D gCc/gAc 1 1 FGD2 HGNC HGNC:3664 protein_coding YES CCDS4829.1 ENSP00000274963 Q7Z6J4 UPI00001A9477 NM_173558.3 deleterious(0) 16/16 PROSITE_profiles:PS50003,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF82,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999987 1 1 1 0 A 3 1 50 37028114 37028114 C A 1 0 0 0 0 1 0 0 0 5697 739 26 2 2 FGD2 6 37028114 Missense_Mutation SNP C C3N-00549_T 826787 37028114 133777865 137 15161 HMGCLL1 0 . GRCh38 6 55514130 55514130 + Missense_Mutation SNP T T A rs773175695 C3N-00549_T C3N-00549_N T T c.550A>T p.Ile184Phe p.I184F ENST00000398661 6/10 189 117 72 188 188 0 strelka-varscan-mutect HMGCLL1,missense_variant,p.Ile184Phe,ENST00000398661,NM_019036.2;HMGCLL1,missense_variant,p.Ile154Phe,ENST00000274901,NM_001287746.1,NM_001042406.1;HMGCLL1,missense_variant,p.Ile122Phe,ENST00000428842,;HMGCLL1,missense_variant,p.Ile122Phe,ENST00000308161,NM_001287741.1;HMGCLL1,intron_variant,,ENST00000370850,NM_001287753.1;HMGCLL1,intron_variant,,ENST00000508459,;HMGCLL1,3_prime_UTR_variant,,ENST00000370852,;HMGCLL1,downstream_gene_variant,,ENST00000515546,; A ENST00000398661 Transcript missense_variant 682/2532 550/1113 184/370 I/F Att/Ttt rs773175695 1 -1 HMGCLL1 HGNC HGNC:21359 protein_coding YES CCDS43475.1 ENSP00000381654 Q8TB92 UPI000023780E NM_019036.2 deleterious(0) 6/10 Gene3D:3.20.20.70,Pfam_domain:PF00682,PROSITE_profiles:PS50991,hmmpanther:PTHR10277,hmmpanther:PTHR10277:SF33,Superfamily_domains:SSF51569 MODERATE 1 SNV 2 1 PASS rs773175695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 55514130 55514130 T A 1 0 0 0 0 1 0 0 0 7122 1406 49 4 4 HMGCLL1 6 55514130 Missense_Mutation SNP T C3N-00549_T 18486016 55514130 115291849 138 15162 KCNQ5 0 . GRCh38 6 73194937 73194937 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.2379G>A p.= p.Q793Q ENST00000342056 15/15 248 89 159 272 272 0 strelka-varscan-mutect KCNQ5,synonymous_variant,p.=,ENST00000342056,NM_001160132.1,NM_001160133.1;KCNQ5,synonymous_variant,p.=,ENST00000355635,;KCNQ5,synonymous_variant,p.=,ENST00000402622,;KCNQ5,synonymous_variant,p.=,ENST00000355194,;KCNQ5,synonymous_variant,p.=,ENST00000403813,;KCNQ5,synonymous_variant,p.=,ENST00000370398,NM_019842.3;KCNQ5,synonymous_variant,p.=,ENST00000414165,;KCNQ5,synonymous_variant,p.=,ENST00000628967,NM_001160134.1;KCNQ5,synonymous_variant,p.=,ENST00000629977,NM_001160130.1; A ENST00000342056 Transcript synonymous_variant 2777/6688 2379/2856 793/951 Q caG/caA 1 1 KCNQ5 HGNC HGNC:6299 protein_coding YES CCDS55034.1 ENSP00000345055 Q9NR82 UPI000155D644 NM_001160132.1,NM_001160133.1 15/15 hmmpanther:PTHR11537:SF128,hmmpanther:PTHR11537 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 73194937 73194937 G A 1 0 0 0 0 0 0 0 1 8002 991 35 3 3 KCNQ5 6 73194937 Silent SNP G C3N-00549_T 17680807 73194937 97611042 139 15163 SNAP91 0 . GRCh38 6 83582277 83582277 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2094G>T p.Glu698Asp p.E698D ENST00000439399 23/30 167 62 105 243 243 0 strelka-varscan-mutect SNAP91,missense_variant,p.Glu698Asp,ENST00000521485,;SNAP91,missense_variant,p.Glu698Asp,ENST00000439399,NM_014841.2;SNAP91,missense_variant,p.Glu698Asp,ENST00000369694,NM_001242792.1;SNAP91,missense_variant,p.Glu698Asp,ENST00000195649,NM_001256718.1;SNAP91,missense_variant,p.Glu698Asp,ENST00000521743,;SNAP91,missense_variant,p.Glu668Asp,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,missense_variant,p.Glu391Asp,ENST00000520213,NM_001242794.1;SNAP91,missense_variant,p.Glu511Asp,ENST00000521931,;SNAP91,missense_variant,p.Glu39Asp,ENST00000523448,;SNAP91,upstream_gene_variant,,ENST00000519133,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,; A ENST00000439399 Transcript missense_variant 2411/4452 2094/2724 698/907 E/D gaG/gaT 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 tolerated(1) 23/30 hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 83582277 83582277 C A 1 0 0 0 0 1 0 0 0 15154 680 24 2 2 SNAP91 6 83582277 Missense_Mutation SNP C C3N-00549_T 10387340 83582277 87223702 140 15164 GABRR2 0 . GRCh38 6 89271705 89271705 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.238G>T p.Gly80Cys p.G80C ENST00000402938 3/9 173 71 102 197 197 0 strelka-varscan-mutect GABRR2,missense_variant,p.Gly80Cys,ENST00000402938,NM_002043.3;GABRR2,non_coding_transcript_exon_variant,,ENST00000602808,;GABRR2,upstream_gene_variant,,ENST00000602432,; A ENST00000402938 Transcript missense_variant 372/1682 238/1398 80/465 G/C Ggc/Tgc 1 -1 GABRR2 HGNC HGNC:4091 protein_coding YES CCDS5020.3 ENSP00000386029 P28476 UPI000012B0DB NM_002043.3 deleterious(0) 3/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF197,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs1487812503 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 89271705 89271705 C A 1 0 0 0 0 1 0 0 0 6048 623 22 2 2 GABRR2 6 89271705 Missense_Mutation SNP C C3N-00549_T 5689428 89271705 81534274 141 15165 MARCKS 0 . GRCh38 6 113860015 113860015 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.435G>A p.= p.S145S ENST00000612661 2/2 79 49 30 114 113 1 strelka-varscan-mutect MARCKS,synonymous_variant,p.=,ENST00000612661,NM_002356.6; A ENST00000612661 Transcript synonymous_variant 819/4275 435/999 145/332 S tcG/tcA 1 1 MARCKS HGNC HGNC:6759 protein_coding YES CCDS5101.1 ENSP00000478061 P29966 UPI000013DDF0 NM_002356.6 2/2 hmmpanther:PTHR14353,hmmpanther:PTHR14353:SF9,Pfam_domain:PF02063 LOW 1 SNV 1 1 PASS rs1417954840 . 0 197 11 2 0 0 0 0 -20 0.9998051 1 1 1 0 A 2 1 50 113860015 113860015 G A 1 0 0 0 0 0 0 0 1 9234 1074 38 1 1 MARCKS 6 113860015 Silent SNP G C3N-00549_T 24588310 113860015 56945964 142 15166 MARCKS 0 . GRCh38 6 113860416 113860417 + Frame_Shift_Del DEL GC GC - novel C3N-00549_T C3N-00549_N GC GC c.837_838delCG p.Cys279Ter p.C279* ENST00000612661 2/2 42 25 17 79 78 1 sindel-varindel-pindel MARCKS,frameshift_variant,p.Cys279Ter,ENST00000612661,NM_002356.6; - ENST00000612661 Transcript frameshift_variant 1220-1221/4275 836-837/999 279/332 C/X tGC/t 1 1 MARCKS HGNC HGNC:6759 protein_coding YES CCDS5101.1 ENSP00000478061 P29966 UPI000013DDF0 NM_002356.6 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR14353,hmmpanther:PTHR14353:SF9,Pfam_domain:PF02063 HIGH 1 deletion 1 1 1 PASS . . 0 196 13 0 0 0 0 0 -20 0.9999757 1 1 1 0 - 7 5 50 113860416 113860416 GC - 1 0 1 0 1 0 0 0 0 9234 1319 46 0 0 MARCKS 6 113860416 Frame_Shift_Del DEL GC C3N-00549_T 401 113860416 56945563 143 15167 SLC35F1 0 . GRCh38 6 118267023 118267023 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.506T>C p.Val169Ala p.V169A ENST00000360388 4/8 188 104 84 139 138 1 strelka-varscan-mutect SLC35F1,missense_variant,p.Val169Ala,ENST00000360388,NM_001029858.3;SLC35F1,missense_variant,p.Val110Ala,ENST00000621341,; C ENST00000360388 Transcript missense_variant 707/4852 506/1227 169/408 V/A gTg/gCg 1 1 SLC35F1 HGNC HGNC:21483 protein_coding YES CCDS34524.1 ENSP00000353557 Q5T1Q4 UPI00001609C1 NM_001029858.3 deleterious(0) 4/8 Superfamily_domains:0043518,Pfam_domain:PF06027,hmmpanther:PTHR14233,hmmpanther:PTHR14233:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 118267023 118267023 T C 1 0 0 0 0 1 0 0 0 14859 1696 59 5 5 SLC35F1 6 118267023 Missense_Mutation SNP T C3N-00549_T 4406607 118267023 52538956 144 15168 SAMD3 0 . GRCh38 6 130144641 130144641 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.1514C>T p.Pro505Leu p.P505L ENST00000457563 11/11 426 268 158 441 440 1 strelka-varscan-mutect SAMD3,missense_variant,p.Pro481Leu,ENST00000368134,NM_001258275.2;SAMD3,missense_variant,p.Pro481Leu,ENST00000439090,NM_001017373.3;SAMD3,missense_variant,p.Pro481Leu,ENST00000437477,;SAMD3,missense_variant,p.Pro505Leu,ENST00000457563,NM_001277185.1;L3MBTL3,downstream_gene_variant,,ENST00000529410,;L3MBTL3,downstream_gene_variant,,ENST00000368136,;L3MBTL3,downstream_gene_variant,,ENST00000361794,NM_032438.2;L3MBTL3,downstream_gene_variant,,ENST00000368139,;L3MBTL3,downstream_gene_variant,,ENST00000526019,;L3MBTL3,downstream_gene_variant,,ENST00000533560,NM_001007102.2;SAMD3,downstream_gene_variant,,ENST00000463253,;RP11-73O6.3,non_coding_transcript_exon_variant,,ENST00000614735,;RP11-73O6.3,non_coding_transcript_exon_variant,,ENST00000622734,;RP11-73O6.3,upstream_gene_variant,,ENST00000609978,;RP11-73O6.3,upstream_gene_variant,,ENST00000415964,; A ENST00000457563 Transcript missense_variant 1554/1877 1514/1635 505/544 P/L cCa/cTa 1 -1 SAMD3 HGNC HGNC:21574 protein_coding YES CCDS64525.1 ENSP00000402092 Q8N6K7 UPI0000E0A4FD NM_001277185.1 deleterious(0) 11/11 hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF18 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 130144641 130144641 G A 1 0 0 0 0 1 0 0 0 14080 1348 47 3 3 SAMD3 6 130144641 Missense_Mutation SNP G C3N-00549_T 11877618 130144641 40661338 145 15169 TMEM200A 0 . GRCh38 6 130441706 130441706 + Missense_Mutation SNP G G T rs145230140 C3N-00549_T C3N-00549_N G G c.1284G>T p.Lys428Asn p.K428N ENST00000392429 2/2 191 119 72 189 189 0 strelka-varscan-mutect TMEM200A,missense_variant,p.Lys428Asn,ENST00000392429,NM_052913.2;TMEM200A,missense_variant,p.Lys428Asn,ENST00000296978,NM_001258277.1;TMEM200A,missense_variant,p.Lys428Asn,ENST00000545622,NM_001258278.1;TMEM200A,missense_variant,p.Lys428Asn,ENST00000617887,NM_001258276.1; T ENST00000392429 Transcript missense_variant 3662/5017 1284/1476 428/491 K/N aaG/aaT rs145230140,COSM1440457,COSM1440458 1 1 TMEM200A HGNC HGNC:21075 protein_coding YES CCDS5140.1 ENSP00000376224 Q86VY9 A8K2A1 UPI000000DA85 NM_052913.2 deleterious(0.02) 2/2 hmmpanther:PTHR31815:SF0,hmmpanther:PTHR31815 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs145230140 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 130441706 130441706 G T 1 0 0 0 0 1 0 0 0 16562 991 35 2 2 TMEM200A 6 130441706 Missense_Mutation SNP G C3N-00549_T 297065 130441706 40364273 146 15170 IL20RA 0 . GRCh38 6 137008713 137008713 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.610G>T p.Val204Leu p.V204L ENST00000316649 5/7 97 56 41 54 54 0 strelka-varscan-mutect IL20RA,missense_variant,p.Val93Leu,ENST00000367748,NM_001278724.1,NM_001278723.1;IL20RA,missense_variant,p.Val204Leu,ENST00000316649,NM_014432.3;IL20RA,missense_variant,p.Val155Leu,ENST00000541547,NM_001278722.1;IL20RA,missense_variant,p.Val93Leu,ENST00000468393,;IL20RA,missense_variant,p.Val71Leu,ENST00000635289,;IL20RA,downstream_gene_variant,,ENST00000367746,; A ENST00000316649 Transcript missense_variant 846/3485 610/1662 204/553 V/L Gtg/Ttg 1 -1 IL20RA HGNC HGNC:6003 protein_coding YES CCDS5181.1 ENSP00000314976 Q9UHF4 UPI000006FA41 NM_014432.3 tolerated(0.08) 5/7 PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF21,Gene3D:2.60.40.10,Pfam_domain:PF09294,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 137008713 137008713 C A 1 0 0 0 0 1 0 0 0 7571 507 18 2 2 IL20RA 6 137008713 Missense_Mutation SNP C C3N-00549_T 6567007 137008713 33797266 147 15171 UTRN 0 . GRCh38 6 144482380 144482380 + Missense_Mutation SNP A A G novel C3N-00549_T C3N-00549_N A A c.3679A>G p.Thr1227Ala p.T1227A ENST00000367545 26/74 112 72 40 171 171 0 strelka-varscan-mutect UTRN,missense_variant,p.Thr1227Ala,ENST00000367545,NM_007124.2; G ENST00000367545 Transcript missense_variant 3679/12339 3679/10302 1227/3433 T/A Acg/Gcg 1 1 UTRN HGNC HGNC:12635 protein_coding YES CCDS34547.1 ENSP00000356515 P46939 UPI00003673F1 NM_007124.2 deleterious(0) 26/74 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF225,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 144482380 144482380 A G 1 0 0 0 0 1 0 0 0 17647 159 6 5 5 UTRN 6 144482380 Missense_Mutation SNP A C3N-00549_T 7473667 144482380 26323599 148 15172 OPRM1 0 . GRCh38 6 154039727 154039727 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.462G>T p.= p.P154P ENST00000434900 3/6 150 85 65 128 127 1 strelka-varscan-mutect OPRM1,synonymous_variant,p.=,ENST00000414028,NM_001145284.3;OPRM1,synonymous_variant,p.=,ENST00000435918,NM_001145283.2;OPRM1,synonymous_variant,p.=,ENST00000330432,NM_000914.4;OPRM1,synonymous_variant,p.=,ENST00000434900,NM_001145279.3,NM_001285524.1;OPRM1,synonymous_variant,p.=,ENST00000360422,NM_001285523.1;OPRM1,synonymous_variant,p.=,ENST00000428397,NM_001008504.3;OPRM1,synonymous_variant,p.=,ENST00000229768,NM_001008505.2;OPRM1,synonymous_variant,p.=,ENST00000419506,NM_001145286.2;OPRM1,synonymous_variant,p.=,ENST00000337049,NM_001008503.2;OPRM1,synonymous_variant,p.=,ENST00000452687,NM_001145282.2;OPRM1,synonymous_variant,p.=,ENST00000524163,NM_001145285.2;OPRM1,synonymous_variant,p.=,ENST00000520282,;OPRM1,intron_variant,,ENST00000520708,NM_001145280.3;OPRM1,intron_variant,,ENST00000518759,NM_001145281.2;OPRM1,non_coding_transcript_exon_variant,,ENST00000523520,;OPRM1,synonymous_variant,p.=,ENST00000519083,;OPRM1,synonymous_variant,p.=,ENST00000522739,;OPRM1,synonymous_variant,p.=,ENST00000524150,; T ENST00000434900 Transcript synonymous_variant 980/2033 462/1482 154/493 P ccG/ccT 1 1 OPRM1 HGNC HGNC:8156 protein_coding YES CCDS47503.1 ENSP00000394624 P35372 UPI0001899627 NM_001145279.3,NM_001285524.1 3/6 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF7,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs1168832508 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 154039727 154039727 G T 1 0 0 0 0 0 0 0 1 10962 1045 37 1 1 OPRM1 6 154039727 Silent SNP G C3N-00549_T 9557347 154039727 16766252 149 15173 ARID1B 0 . GRCh38 6 156901457 156901457 + Frame_Shift_Del DEL C C - rs751317747 C3N-00549_T C3N-00549_N C C c.1862delC p.Pro621ArgfsTer47 p.P621Rfs*47 ENST00000346085 4/20 347 223 124 412 412 0 sindel-varindel-pindel ARID1B,frameshift_variant,p.Pro621ArgfsTer47,ENST00000346085,NM_020732.3;ARID1B,frameshift_variant,p.Pro118ArgfsTer47,ENST00000636748,;ARID1B,frameshift_variant,p.Pro608ArgfsTer47,ENST00000636930,;ARID1B,frameshift_variant,p.Pro608ArgfsTer47,ENST00000350026,NM_017519.2;ARID1B,frameshift_variant,p.Pro107ArgfsTer47,ENST00000414678,;ARID1B,frameshift_variant,p.Pro29ArgfsTer47,ENST00000319584,;ARID1B,frameshift_variant,p.Pro97ArgfsTer47,ENST00000638000,;ARID1B,frameshift_variant,p.Pro33ArgfsTer47,ENST00000637532,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636205,; - ENST00000346085 Transcript frameshift_variant 2414/10194 1858/6750 620/2249 P/X Ccc/cc rs751317747 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 4/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 HIGH 1 deletion 1 4 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9993537 1 1 1 0 - 7 5 50 156901457 156901457 C - 1 0 1 0 1 0 0 0 0 1050 739 26 0 0 ARID1B 6 156901457 Frame_Shift_Del DEL C C3N-00549_T 2861730 156901457 13904522 150 15174 LPA 0 . GRCh38 6 160585053 160585053 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.4282C>A p.Pro1428Thr p.P1428T ENST00000316300 26/39 380 235 145 275 274 1 strelka-varscan-mutect LPA,missense_variant,p.Pro1428Thr,ENST00000316300,NM_005577.2;LPA,downstream_gene_variant,,ENST00000447678,; T ENST00000316300 Transcript missense_variant 4327/6414 4282/6123 1428/2040 P/T Cca/Aca 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 deleterious(0.01) 26/39 Gene3D:2.40.20.10,Pfam_domain:PF00051,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS rs1016345351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 160585053 160585053 G T 1 0 0 0 0 1 0 0 0 8806 1174 41 2 2 LPA 6 160585053 Missense_Mutation SNP G C3N-00549_T 3683596 160585053 10220926 151 15175 TCP10L2 0 . GRCh38 6 167177130 167177130 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.494C>T p.Pro165Leu p.P165L ENST00000366832 4/8 57 28 29 85 85 0 strelka-varscan-mutect TCP10L2,missense_variant,p.Pro165Leu,ENST00000366832,NM_001145121.1;TCP10L2,downstream_gene_variant,,ENST00000486697,;TCP10L2,missense_variant,p.Pro165Leu,ENST00000283507,;TCP10L2,non_coding_transcript_exon_variant,,ENST00000464222,;TCP10L2,downstream_gene_variant,,ENST00000382669,; T ENST00000366832 Transcript missense_variant 625/2185 494/1062 165/353 P/L cCa/cTa 1 1 TCP10L2 HGNC HGNC:21254 protein_coding YES CCDS47514.1 ENSP00000355797 B9ZVM9 UPI0000253B82 NM_001145121.1 tolerated(0.19) 4/8 hmmpanther:PTHR10331 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 167177130 167177130 C T 1 0 0 0 0 1 0 0 0 16119 608 21 3 3 TCP10L2 6 167177130 Missense_Mutation SNP C C3N-00549_T 6592077 167177130 3628849 152 15176 TCP10 0 . GRCh38 6 167377959 167377959 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.413C>T p.Pro138Leu p.P138L ENST00000397829 4/8 121 93 28 161 161 0 strelka-varscan-mutect TCP10,missense_variant,p.Pro134Leu,ENST00000460930,;TCP10,missense_variant,p.Pro138Leu,ENST00000366827,;TCP10,missense_variant,p.Pro164Leu,ENST00000617120,;TCP10,missense_variant,p.Pro138Leu,ENST00000397829,NM_004610.3;TCP10,downstream_gene_variant,,ENST00000476779,;TCP10,downstream_gene_variant,,ENST00000485157,;TCP10,non_coding_transcript_exon_variant,,ENST00000508373,;TCP10,non_coding_transcript_exon_variant,,ENST00000463894,;TCP10,non_coding_transcript_exon_variant,,ENST00000491085,;TCP10,upstream_gene_variant,,ENST00000514083,; A ENST00000397829 Transcript missense_variant 581/2141 413/981 138/326 P/L cCa/cTa 1 -1 TCP10 HGNC HGNC:11656 protein_coding YES CCDS43527.1 ENSP00000380929 D1MPS5 UPI0000D820CE NM_004610.3 tolerated(0.16) 4/8 hmmpanther:PTHR10331 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 167377959 167377959 G A 1 0 0 0 0 1 0 0 0 16117 1362 47 3 3 TCP10 6 167377959 Missense_Mutation SNP G C3N-00549_T 200829 167377959 3428020 153 15177 GPER1 0 . GRCh38 7 1092402 1092402 + Missense_Mutation SNP T T G novel C3N-00549_T C3N-00549_N T T c.674T>G p.Val225Gly p.V225G ENST00000397092 3/3 194 132 62 95 94 1 strelka-varscan-mutect GPER1,missense_variant,p.Val225Gly,ENST00000397092,NM_001039966.1;GPER1,missense_variant,p.Val225Gly,ENST00000297469,NM_001505.2;GPER1,missense_variant,p.Val225Gly,ENST00000397088,NM_001098201.1;GPER1,missense_variant,p.Val225Gly,ENST00000617001,;GPER1,missense_variant,p.Val225Gly,ENST00000401670,;C7orf50,intron_variant,,ENST00000397098,NM_001318252.1;C7orf50,intron_variant,,ENST00000357429,NM_001134395.1,NM_032350.5;C7orf50,intron_variant,,ENST00000397100,NM_001134396.1;C7orf50,intron_variant,,ENST00000491163,;GPER1,downstream_gene_variant,,ENST00000413368,;GPER1,upstream_gene_variant,,ENST00000619052,;C7orf50,intron_variant,,ENST00000488073,; G ENST00000397092 Transcript missense_variant 1558/2971 674/1128 225/375 V/G gTg/gGg 1 1 GPER1 HGNC HGNC:4485 protein_coding YES CCDS5322.1 ENSP00000380281 Q99527 A0A024R849 UPI00000503F2 NM_001039966.1 deleterious(0) 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24226:SF2,hmmpanther:PTHR24226,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 1092402 1092402 T G 1 0 0 0 0 1 0 0 0 6509 1696 59 5 5 GPER1 7 1092402 Missense_Mutation SNP T C3N-00549_T 1092402 158253571 154 15178 MIOS 0 . GRCh38 7 7583150 7583150 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1426G>T p.Gly476Trp p.G476W ENST00000340080 6/13 176 79 97 75 75 0 strelka-varscan-mutect MIOS,missense_variant,p.Gly476Trp,ENST00000340080,NM_019005.3;MIOS,missense_variant,p.Gly476Trp,ENST00000405785,;MIOS,non_coding_transcript_exon_variant,,ENST00000461907,;MIOS,non_coding_transcript_exon_variant,,ENST00000493227,; T ENST00000340080 Transcript missense_variant 1847/3453 1426/2628 476/875 G/W Ggg/Tgg 1 1 MIOS HGNC HGNC:21905 protein_coding YES CCDS43554.1 ENSP00000339881 Q9NXC5 A0A024RA24 UPI000020EB0B NM_019005.3 deleterious(0.04) 6/13 hmmpanther:PTHR16453,hmmpanther:PTHR16453:SF9 MODERATE 1 SNV 1 1 PASS rs1392480213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 7583150 7583150 G T 1 0 0 0 0 1 0 0 0 9554 1348 47 2 2 MIOS 7 7583150 Missense_Mutation SNP G C3N-00549_T 6490748 7583150 151762823 155 15179 GLCCI1 0 . GRCh38 7 8055434 8055434 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.698A>T p.Gln233Leu p.Q233L ENST00000223145 4/8 236 164 72 145 145 0 strelka-varscan-mutect GLCCI1,splice_acceptor_variant,,ENST00000414914,;GLCCI1,missense_variant,p.Gln233Leu,ENST00000223145,NM_138426.3;GLCCI1,missense_variant,p.Gln121Leu,ENST00000430798,;GLCCI1,splice_acceptor_variant,,ENST00000470583,;GLCCI1,splice_region_variant,,ENST00000474269,;GLCCI1,upstream_gene_variant,,ENST00000496617,;GLCCI1,splice_acceptor_variant,,ENST00000489405,;GLCCI1,upstream_gene_variant,,ENST00000438949,; T ENST00000223145 Transcript missense_variant,splice_region_variant 1255/4743 698/1644 233/547 Q/L cAg/cTg 1 1 GLCCI1 HGNC HGNC:18713 protein_coding YES CCDS34601.1 ENSP00000223145 Q86VQ1 UPI00001907F7 NM_138426.3 deleterious_low_confidence(0) 4/8 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15388,hmmpanther:PTHR14972,hmmpanther:PTHR14972:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 8055434 8055434 A T 1 0 0 0 0 1 0 0 0 6309 202 7 4 4 GLCCI1 7 8055434 Missense_Mutation SNP A C3N-00549_T 472284 8055434 151290539 156 15180 HDAC9 0 . GRCh38 7 18585372 18585372 + Silent SNP C C T C3N-00549_T C3N-00549_N C C c.114C>T p.= p.D38D ENST00000441542 2/25 643 483 160 457 457 0 strelka-varscan-mutect HDAC9,synonymous_variant,p.=,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,synonymous_variant,p.=,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,synonymous_variant,p.=,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,synonymous_variant,p.=,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,synonymous_variant,p.=,ENST00000401921,;HDAC9,synonymous_variant,p.=,ENST00000441542,NM_178425.2;HDAC9,synonymous_variant,p.=,ENST00000432645,NM_058176.2;HDAC9,synonymous_variant,p.=,ENST00000417496,NM_001204144.1;HDAC9,synonymous_variant,p.=,ENST00000428307,NM_001204145.1;HDAC9,synonymous_variant,p.=,ENST00000456174,NM_001204148.1;HDAC9,synonymous_variant,p.=,ENST00000524023,NM_001204147.1;HDAC9,synonymous_variant,p.=,ENST00000413380,;HDAC9,synonymous_variant,p.=,ENST00000441986,;HDAC9,synonymous_variant,p.=,ENST00000413509,;HDAC9,synonymous_variant,p.=,ENST00000430454,;HDAC9,downstream_gene_variant,,ENST00000433709,;HDAC9,non_coding_transcript_exon_variant,,ENST00000476135,;HDAC9,missense_variant,p.Pro35Ser,ENST00000446646,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; T ENST00000441542 Transcript synonymous_variant 114/3210 114/3210 38/1069 D gaC/gaT COSM1549505,COSM1549506,COSM1549507,COSM1549508 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 2/25 Low_complexity_(Seg):seg,Pfam_domain:PF12203,PIRSF_domain:PIRSF037911 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 18585372 18585372 C T 1 0 0 0 0 0 0 0 1 6901 506 18 3 3 HDAC9 7 18585372 Silent SNP C C3N-00549_T 10529938 18585372 140760601 157 15181 FERD3L 0 . GRCh38 7 19145294 19145294 + Silent SNP G G T C3N-00549_T C3N-00549_N G G c.69C>A p.= p.A23A ENST00000275461 1/1 231 164 67 109 109 0 strelka-varscan-mutect FERD3L,synonymous_variant,p.=,ENST00000275461,NM_152898.2;AC003986.5,non_coding_transcript_exon_variant,,ENST00000452700,; T ENST00000275461 Transcript synonymous_variant 128/640 69/501 23/166 A gcC/gcA COSM4505696 1 -1 FERD3L HGNC HGNC:16660 protein_coding YES CCDS5368.1 ENSP00000275461 Q96RJ6 UPI0000073BBA NM_152898.2 1/1 hmmpanther:PTHR23349:SF63,hmmpanther:PTHR23349 1 LOW SNV 1 1 PASS rs1159435662 . 0 202 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 19145294 19145294 G T 1 0 0 0 0 0 0 0 1 5679 987 35 2 2 FERD3L 7 19145294 Silent SNP G C3N-00549_T 559922 19145294 140200679 158 15182 NEUROD6 0 . GRCh38 7 31338954 31338954 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.315C>A p.Asn105Lys p.N105K ENST00000297142 2/2 436 293 143 224 222 2 strelka-varscan-mutect NEUROD6,missense_variant,p.Asn105Lys,ENST00000297142,NM_022728.3; T ENST00000297142 Transcript missense_variant 638/2131 315/1014 105/337 N/K aaC/aaA 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 deleterious(0.01) 2/2 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50888,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 31338954 31338954 G T 1 0 0 0 0 1 0 0 0 10388 1368 48 2 2 NEUROD6 7 31338954 Missense_Mutation SNP G C3N-00549_T 12193660 31338954 128007019 159 15183 PDE1C 0 . GRCh38 7 31850673 31850673 + Silent SNP G G T rs758775742 C3N-00549_T C3N-00549_N G G c.999C>A p.= p.T333T ENST00000396193 9/19 476 373 103 247 247 0 strelka-varscan-mutect PDE1C,synonymous_variant,p.=,ENST00000396184,NM_001322057.1,NM_001322056.1,NM_001322059.1,NM_005020.3;PDE1C,synonymous_variant,p.=,ENST00000396193,NM_001191058.2;PDE1C,synonymous_variant,p.=,ENST00000396191,NM_001191057.2;PDE1C,synonymous_variant,p.=,ENST00000321453,NM_001191059.2;PDE1C,synonymous_variant,p.=,ENST00000396182,NM_001191056.2;PDE1C,non_coding_transcript_exon_variant,,ENST00000478736,; T ENST00000396193 Transcript synonymous_variant 1593/5109 999/2310 333/769 T acC/acA rs758775742,COSM1144545,COSM600936,COSM600937 1 -1 PDE1C HGNC HGNC:8776 protein_coding YES CCDS55100.1 ENSP00000379496 A0A0A0MS69 UPI00043788D1 NM_001191058.2 9/19 Gene3D:1.10.1300.10,Pfam_domain:PF00233,Prints_domain:PR00387,PROSITE_patterns:PS00126,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,SMART_domains:SM00471,Superfamily_domains:SSF109604 0,1,1,1 LOW 1 SNV 2 0,1,1,1 1 PASS rs758775742 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 31850673 31850673 G T 1 0 0 0 0 0 0 0 1 11723 1103 39 1 1 PDE1C 7 31850673 Silent SNP G C3N-00549_T 511719 31850673 127495300 160 15184 DPY19L1 0 . GRCh38 7 34938121 34938121 + Splice_Site SNP T T A novel C3N-00549_T C3N-00549_N T T c.1746-2A>T p.X582_splice ENST00000310974 110 89 21 48 48 0 strelka-varscan-mutect DPY19L1,splice_acceptor_variant,,ENST00000638088,;DPY19L1,splice_acceptor_variant,,ENST00000310974,NM_015283.1;DPY19L1,splice_acceptor_variant,,ENST00000612226,;DPY19L1,intron_variant,,ENST00000428054,;MIR548N,downstream_gene_variant,,ENST00000408742,; A ENST00000310974 Transcript splice_acceptor_variant -/4870 1746/2028 582/675 1 -1 DPY19L1 HGNC HGNC:22205 protein_coding YES CCDS43567.1 ENSP00000308695 Q2PZI1 UPI000067CB92 NM_015283.1 20/21 HIGH 1 SNV 1 1 PASS . . 0 196 11 3 0 0 0 0 -20 0.9980011 1 1 1 0 A 5 1 50 34938121 34938121 T A 1 0 0 0 0 0 0 1 0 4555 1623 56 4 4 DPY19L1 7 34938121 Splice_Site SNP T C3N-00549_T 3087448 34938121 124407852 161 15185 POU6F2 0 . GRCh38 7 39207465 39207465 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.356A>T p.Gln119Leu p.Q119L ENST00000403058 5/11 496 197 299 254 254 0 strelka-varscan-mutect POU6F2,missense_variant,p.Gln119Leu,ENST00000518318,NM_001166018.1;POU6F2,missense_variant,p.Gln111Leu,ENST00000559001,;POU6F2,missense_variant,p.Gln119Leu,ENST00000403058,NM_007252.3;POU6F2,missense_variant,p.Gln111Leu,ENST00000524147,;POU6F2,missense_variant,p.Gln111Leu,ENST00000520104,;POU6F2,missense_variant,p.Gln120Leu,ENST00000451021,;POU6F2,non_coding_transcript_exon_variant,,ENST00000517348,; T ENST00000403058 Transcript missense_variant 510/2335 356/2076 119/691 Q/L cAg/cTg 1 1 POU6F2 HGNC HGNC:21694 protein_coding YES CCDS34620.2 ENSP00000384004 P78424 UPI0000480E81 NM_007252.3 deleterious(0) 5/11 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF68 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 39207465 39207465 A T 1 0 0 0 0 1 0 0 0 12401 188 7 4 4 POU6F2 7 39207465 Missense_Mutation SNP A C3N-00549_T 4269344 39207465 120138508 162 15186 POU6F2 0 . GRCh38 7 39433133 39433133 + Missense_Mutation SNP C C G rs368929654 C3N-00549_T C3N-00549_N C C c.1083C>G p.Ser361Arg p.S361R ENST00000403058 8/11 483 334 149 240 240 0 strelka-varscan-mutect POU6F2,missense_variant,p.Ser361Arg,ENST00000518318,NM_001166018.1;POU6F2,missense_variant,p.Ser306Arg,ENST00000559001,;POU6F2,missense_variant,p.Ser361Arg,ENST00000403058,NM_007252.3;POU6F2,missense_variant,p.Ser306Arg,ENST00000524147,;POU6F2,missense_variant,p.Ser353Arg,ENST00000520104,;POU6F2,missense_variant,p.Ser60Arg,ENST00000416452,; G ENST00000403058 Transcript missense_variant 1237/2335 1083/2076 361/691 S/R agC/agG rs368929654 1 1 POU6F2 HGNC HGNC:21694 protein_coding YES CCDS34620.2 ENSP00000384004 P78424 UPI0000480E81 NM_007252.3 deleterious(0.02) 8/11 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF68 MODERATE 1 SNV 5 1 PASS rs368929654 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 39433133 39433133 C G 1 0 0 0 0 1 0 0 0 12401 767 27 4 4 POU6F2 7 39433133 Missense_Mutation SNP C C3N-00549_T 225668 39433133 119912840 163 15187 NPC1L1 0 . GRCh38 7 44539592 44539592 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.805C>G p.Pro269Ala p.P269A ENST00000289547 2/20 234 149 85 176 176 0 strelka-varscan-mutect NPC1L1,missense_variant,p.Pro269Ala,ENST00000289547,NM_013389.2;NPC1L1,missense_variant,p.Pro269Ala,ENST00000546276,;NPC1L1,missense_variant,p.Pro269Ala,ENST00000381160,NM_001101648.1;NPC1L1,missense_variant,p.Pro269Ala,ENST00000423141,NM_001300967.1; C ENST00000289547 Transcript missense_variant 861/5048 805/4080 269/1359 P/A Ccc/Gcc 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 tolerated(0.07) 2/20 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89,Pfam_domain:PF16414 MODERATE 1 SNV 1 1 PASS rs1267125217 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 44539592 44539592 G C 1 0 0 0 0 1 0 0 0 10619 1232 43 4 4 NPC1L1 7 44539592 Missense_Mutation SNP G C3N-00549_T 5106459 44539592 114806381 164 15188 NACAD 0 . GRCh38 7 45085706 45085706 + Silent SNP C C T novel C3N-00549_T C3N-00549_N C C c.474G>A p.= p.Q158Q ENST00000490531 2/8 144 89 55 119 119 0 strelka-varscan-mutect NACAD,synonymous_variant,p.=,ENST00000490531,NM_001146334.1;NACAD,upstream_gene_variant,,ENST00000460409,; T ENST00000490531 Transcript synonymous_variant 494/4780 474/4689 158/1562 Q caG/caA 1 -1 NACAD HGNC HGNC:22196 protein_coding YES CCDS47582.1 ENSP00000420477 O15069 UPI00001D747D NM_001146334.1 2/8 hmmpanther:PTHR21713:SF1,hmmpanther:PTHR21713 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 45085706 45085706 C T 1 0 0 0 0 0 0 0 1 10141 680 24 3 3 NACAD 7 45085706 Silent SNP C C3N-00549_T 546114 45085706 114260267 165 15189 ADCY1 0 . GRCh38 7 45592783 45592783 + Missense_Mutation SNP G G A rs369079165 C3N-00549_T C3N-00549_N G G c.664G>A p.Val222Ile p.V222I ENST00000297323 2/20 225 142 83 175 175 0 strelka-varscan-mutect ADCY1,missense_variant,p.Val222Ile,ENST00000297323,NM_021116.2;ADCY1,5_prime_UTR_variant,,ENST00000432715,NM_001281768.1;ADCY1,5_prime_UTR_variant,,ENST00000621543,; A ENST00000297323 Transcript missense_variant 686/12503 664/3360 222/1119 V/I Gtc/Atc rs369079165,COSM453130 1 1 ADCY1 HGNC HGNC:232 protein_coding YES CCDS34631.1 ENSP00000297323 Q08828 UPI0000199C4A NM_021116.2 tolerated(0.69) 2/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR11920:SF336,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,Pfam_domain:PF16214 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369079165 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 45592783 45592783 G A 1 0 0 0 0 1 0 0 0 336 1145 40 1 1 ADCY1 7 45592783 Missense_Mutation SNP G C3N-00549_T 507077 45592783 113753190 166 15190 ABCA13 0 . GRCh38 7 48374365 48374365 + Missense_Mutation SNP G G T rs777083484 C3N-00549_T C3N-00549_N G G c.11152G>T p.Ala3718Ser p.A3718S ENST00000435803 34/62 180 100 80 276 276 0 strelka-varscan-mutect ABCA13,missense_variant,p.Ala3718Ser,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Ala1025Ser,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,non_coding_transcript_exon_variant,,ENST00000484268,;ABCA13,upstream_gene_variant,,ENST00000453246,; T ENST00000435803 Transcript missense_variant 11176/17184 11152/15177 3718/5058 A/S Gcc/Tcc rs777083484,COSM3264800,COSM3264801 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0.02) 34/62 Transmembrane_helices:TMhelix,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Pfam_domain:PF12698 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs777083484 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 48374365 48374365 G T 1 0 0 0 0 1 0 0 0 35 1087 38 1 1 ABCA13 7 48374365 Missense_Mutation SNP G C3N-00549_T 2781582 48374365 110971608 167 15191 SEPT14 0 . GRCh38 7 55834486 55834486 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.659T>A p.Ile220Asn p.I220N ENST00000388975 6/10 152 108 44 116 116 0 strelka-varscan-mutect SEPT14,missense_variant,p.Ile220Asn,ENST00000388975,NM_207366.2; T ENST00000388975 Transcript missense_variant 776/3785 659/1299 220/432 I/N aTc/aAc 1 -1 SEPT14 HGNC HGNC:33280 protein_coding YES CCDS5519.2 ENSP00000373627 Q6ZU15 UPI0000E0AB69 NM_207366.2 deleterious(0) 6/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884:SF51,hmmpanther:PTHR18884,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 55834486 55834486 A T 1 0 0 0 0 1 0 0 0 14339 333 12 4 4 SEPT14 7 55834486 Missense_Mutation SNP A C3N-00549_T 7460121 55834486 103511487 168 15192 RUNDC3B 0 . GRCh38 7 87693907 87693907 + Splice_Site SNP G G A novel C3N-00549_T C3N-00549_N G G c.239-1G>A p.X80_splice ENST00000338056 111 79 32 146 146 0 strelka-varscan-mutect RUNDC3B,splice_acceptor_variant,,ENST00000338056,NM_138290.2;ABCB1,intron_variant,,ENST00000265724,NM_000927.4;ABCB1,intron_variant,,ENST00000543898,;RUNDC3B,intron_variant,,ENST00000394654,NM_001134405.1;RUNDC3B,intron_variant,,ENST00000493037,NM_001134406.1;ABCB1,intron_variant,,ENST00000416177,;RUNDC3B,splice_acceptor_variant,,ENST00000466676,;RUNDC3B,intron_variant,,ENST00000489461,;ABCB1,intron_variant,,ENST00000476862,;RUNDC3B,intron_variant,,ENST00000497788,;RUNDC3B,intron_variant,,ENST00000476114,; A ENST00000338056 Transcript splice_acceptor_variant -/4099 239/1422 80/473 1 1 RUNDC3B HGNC HGNC:30286 protein_coding YES CCDS5609.1 ENSP00000337732 Q96NL0 UPI0000071425 NM_138290.2 2/11 HIGH 1 SNV 2 1 PASS . . 0 169 0 25 14 0 0 0 -19.99996 0.02999897 0 1 0 0 A 5 1 50 87693907 87693907 G A 1 0 0 0 0 0 0 1 0 14006 956 33 3 3 RUNDC3B 7 87693907 Splice_Site SNP G C3N-00549_T 31859421 87693907 71652066 169 15193 CFAP69 0 . GRCh38 7 90299938 90299938 + Silent SNP A A T novel C3N-00549_T C3N-00549_N A A c.1929A>T p.= p.A643A ENST00000389297 17/23 175 95 80 198 198 0 strelka-varscan-mutect CFAP69,synonymous_variant,p.=,ENST00000389297,NM_001039706.2;CFAP69,synonymous_variant,p.=,ENST00000497910,NM_001160138.1;CFAP69,synonymous_variant,p.=,ENST00000449577,;CFAP69,intron_variant,,ENST00000457170,;CFAP69,upstream_gene_variant,,ENST00000412839,;CFAP69,3_prime_UTR_variant,,ENST00000451029,;CFAP69,3_prime_UTR_variant,,ENST00000427396,;CFAP69,non_coding_transcript_exon_variant,,ENST00000475031,; T ENST00000389297 Transcript synonymous_variant 2180/3902 1929/2826 643/941 A gcA/gcT 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 17/23 hmmpanther:PTHR14716:SF0,hmmpanther:PTHR14716,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 90299938 90299938 A T 1 0 0 0 0 0 0 0 1 3030 175 7 4 4 CFAP69 7 90299938 Silent SNP A C3N-00549_T 2606031 90299938 69046035 170 15194 CUX1 0 . GRCh38 7 102197187 102197187 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.1809G>T p.= p.R603R ENST00000360264 15/24 379 189 190 355 355 0 strelka-varscan-mutect CUX1,synonymous_variant,p.=,ENST00000360264,NM_001202543.1;CUX1,synonymous_variant,p.=,ENST00000292535,NM_181552.3;CUX1,synonymous_variant,p.=,ENST00000549414,;CUX1,synonymous_variant,p.=,ENST00000550008,;CUX1,synonymous_variant,p.=,ENST00000546411,;CUX1,synonymous_variant,p.=,ENST00000556210,;CUX1,intron_variant,,ENST00000437600,NM_001913.4;CUX1,intron_variant,,ENST00000622516,NM_181500.3;CUX1,intron_variant,,ENST00000292538,;CUX1,intron_variant,,ENST00000547394,NM_001202544.2;CUX1,intron_variant,,ENST00000425244,NM_001202545.2;CUX1,intron_variant,,ENST00000393824,NM_001202546.2;SNORA48,upstream_gene_variant,,ENST00000517015,;CUX1,intron_variant,,ENST00000560541,;CUX1,intron_variant,,ENST00000558836,; T ENST00000360264 Transcript synonymous_variant 1829/13762 1809/4551 603/1516 R cgG/cgT 1 1 CUX1 HGNC HGNC:2557 protein_coding YES CCDS56498.1 ENSP00000353401 P39880 UPI00001AEB98 NM_001202543.1 15/24 PROSITE_profiles:PS51042,hmmpanther:PTHR14043:SF4,hmmpanther:PTHR14043,Gene3D:1.10.260.40,Pfam_domain:PF02376,SMART_domains:SM01109,Superfamily_domains:SSF47413 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9996445 1 1 1 0 T 2 4 50 102197187 102197187 G T 1 0 0 0 0 0 0 0 1 3874 1190 42 2 2 CUX1 7 102197187 Silent SNP G C3N-00549_T 11897249 102197187 57148786 171 15195 RELN 0 . GRCh38 7 103503135 103503135 + Silent SNP G G C novel C3N-00549_T C3N-00549_N G G c.8370C>G p.= p.V2790V ENST00000428762 52/65 603 323 280 652 651 1 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2;CTB-107G13.1,intron_variant,,ENST00000422488,; C ENST00000428762 Transcript synonymous_variant 8530/11571 8370/10383 2790/3460 V gtC/gtG 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 52/65 hmmpanther:PTHR11841,Gene3D:2.130.10.140,Superfamily_domains:SSF50939,Superfamily_domains:SSF50939 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 103503135 103503135 G C 1 0 0 0 0 0 0 0 1 13390 1161 41 4 4 RELN 7 103503135 Silent SNP G C3N-00549_T 1305948 103503135 55842838 172 15196 RELN 0 . GRCh38 7 103636385 103636385 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.2153C>G p.Ser718Cys p.S718C ENST00000428762 18/65 487 364 123 551 551 0 strelka-varscan-mutect RELN,missense_variant,p.Ser718Cys,ENST00000424685,;RELN,missense_variant,p.Ser718Cys,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Ser718Cys,ENST00000343529,NM_173054.2; C ENST00000428762 Transcript missense_variant 2313/11571 2153/10383 718/3460 S/C tCc/tGc 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0.01) 18/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 103636385 103636385 G C 1 0 0 0 0 1 0 0 0 13390 1174 41 4 4 RELN 7 103636385 Missense_Mutation SNP G C3N-00549_T 133250 103636385 55709588 173 15197 KCP 0 . GRCh38 7 128884826 128884826 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3078G>T p.Glu1026Asp p.E1026D ENST00000610776 28/40 228 134 94 260 260 0 strelka-varscan-mutect KCP,missense_variant,p.Glu1026Asp,ENST00000610776,;KCP,missense_variant,p.Glu1030Asp,ENST00000613019,;KCP,missense_variant,p.Glu966Asp,ENST00000620378,NM_001135914.1;KCP,missense_variant,p.Glu1030Asp,ENST00000611280,;KCP,upstream_gene_variant,,ENST00000492679,; A ENST00000610776 Transcript missense_variant 3121/5108 3078/4887 1026/1628 E/D gaG/gaT 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 tolerated(0.55) 28/40 PROSITE_profiles:PS50184,hmmpanther:PTHR11339:SF280,hmmpanther:PTHR11339,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS rs1378052717 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 128884826 128884826 C A 1 0 0 0 0 1 0 0 0 8012 912 32 2 2 KCP 7 128884826 Missense_Mutation SNP C C3N-00549_T 25248441 128884826 30461147 174 15198 CPA4 0 . GRCh38 7 130312055 130312055 + Silent SNP T T A rs779579199 C3N-00549_T C3N-00549_N T T c.1011T>A p.= p.L337L ENST00000222482 10/11 195 97 98 205 205 0 strelka-varscan-mutect CPA4,synonymous_variant,p.=,ENST00000222482,NM_016352.3;CPA4,synonymous_variant,p.=,ENST00000445470,NM_001163446.1;CPA4,synonymous_variant,p.=,ENST00000493259,;CPA4,non_coding_transcript_exon_variant,,ENST00000488025,; A ENST00000222482 Transcript synonymous_variant 1039/2797 1011/1266 337/421 L ctT/ctA rs779579199 1 1 CPA4 HGNC HGNC:15740 protein_coding YES CCDS5818.1 ENSP00000222482 Q9UI42 A4D1M3 UPI0000048F00 NM_016352.3 10/11 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF50,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS rs779579199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 130312055 130312055 T A 1 0 0 0 0 0 0 0 1 3586 1799 63 4 4 CPA4 7 130312055 Silent SNP T C3N-00549_T 1427229 130312055 29033918 175 15199 CPA1 0 . GRCh38 7 130382189 130382189 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.463C>A p.Arg155Ser p.R155S ENST00000011292 4/10 127 74 53 142 142 0 strelka-varscan-mutect CPA1,missense_variant,p.Arg155Ser,ENST00000011292,NM_001868.3;CPA1,missense_variant,p.Arg67Ser,ENST00000484324,;CPA1,missense_variant,p.Arg67Ser,ENST00000476062,;CPA1,missense_variant,p.Arg67Ser,ENST00000481342,;CPA1,intron_variant,,ENST00000604896,;CPA1,non_coding_transcript_exon_variant,,ENST00000491460,;CPA1,upstream_gene_variant,,ENST00000479106,;CPA1,upstream_gene_variant,,ENST00000478096,;CPA1,upstream_gene_variant,,ENST00000470838,; A ENST00000011292 Transcript missense_variant 613/1487 463/1260 155/419 R/S Cgt/Agt 1 1 CPA1 HGNC HGNC:2296 protein_coding YES CCDS5820.1 ENSP00000011292 P15085 UPI000004D332 NM_001868.3 deleterious(0) 4/10 hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF74,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187,Prints_domain:PR00765 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 130382189 130382189 C A 1 0 0 0 0 1 0 0 0 3583 768 27 1 1 CPA1 7 130382189 Missense_Mutation SNP C C3N-00549_T 70134 130382189 28963784 176 15200 AKR1B15 0 . GRCh38 7 134564639 134564639 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.20C>A p.Pro7His p.P7H ENST00000457545 3/12 109 56 53 110 110 0 strelka-varscan-mutect AKR1B15,missense_variant,p.Pro7His,ENST00000457545,NM_001080538.2;AKR1B15,missense_variant,p.Pro7His,ENST00000423958,;AKR1B15,upstream_gene_variant,,ENST00000467156,; A ENST00000457545 Transcript missense_variant 280/1621 20/1035 7/344 P/H cCc/cAc 1 1 AKR1B15 HGNC HGNC:37281 protein_coding YES CCDS47715.2 ENSP00000389289 C9JRZ8 UPI00004193E1 NM_001080538.2 3/12 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 134564639 134564639 C A 1 0 0 0 0 1 0 0 0 552 623 22 2 2 AKR1B15 7 134564639 Missense_Mutation SNP C C3N-00549_T 4182450 134564639 24781334 177 15201 DENND2A 0 . GRCh38 7 140601880 140601880 + Missense_Mutation SNP C C T rs764964047 C3N-00549_T C3N-00549_N C C c.518G>A p.Gly173Glu p.G173E ENST00000275884 2/19 228 162 66 252 252 0 strelka-varscan-mutect DENND2A,missense_variant,p.Gly173Glu,ENST00000275884,NM_001318052.1;DENND2A,missense_variant,p.Gly173Glu,ENST00000492720,NM_001318053.1;DENND2A,missense_variant,p.Gly173Glu,ENST00000496613,;DENND2A,missense_variant,p.Gly173Glu,ENST00000537639,NM_015689.3;DENND2A,intron_variant,,ENST00000475837,;DENND2A,downstream_gene_variant,,ENST00000491728,;DENND2A,downstream_gene_variant,,ENST00000477488,;DENND2A,downstream_gene_variant,,ENST00000489552,;DENND2A,missense_variant,p.Gly173Glu,ENST00000461883,; T ENST00000275884 Transcript missense_variant 936/3735 518/3030 173/1009 G/E gGg/gAg rs764964047 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 tolerated(0.26) 2/19 hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF3 MODERATE 1 SNV 1 1 PASS rs764964047 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 140601880 140601880 C T 1 0 0 0 0 1 0 0 0 4233 623 22 3 3 DENND2A 7 140601880 Missense_Mutation SNP C C3N-00549_T 6037241 140601880 18744093 178 15202 CNTNAP2 0 . GRCh38 7 147300239 147300239 + Silent SNP C C A rs752550849 C3N-00549_T C3N-00549_N C C c.1447C>A p.= p.R483R ENST00000361727 9/24 328 252 76 339 339 0 strelka-varscan-mutect CNTNAP2,synonymous_variant,p.=,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,; A ENST00000361727 Transcript synonymous_variant 1965/9896 1447/3996 483/1331 R Cga/Aga rs752550849,COSM1699530,COSM3879063 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 pathogenic 0,1,1 LOW 1 SNV 1 1,1,1 1 PASS rs752550849 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 147300239 147300239 C A 1 0 0 0 0 0 0 0 1 3428 876 31 1 1 CNTNAP2 7 147300239 Silent SNP C C3N-00549_T 6698359 147300239 12045734 179 15203 CNTNAP2 0 . GRCh38 7 148172281 148172281 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2813G>T p.Arg938Leu p.R938L ENST00000361727 18/24 375 176 199 386 386 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Arg938Leu,ENST00000361727,NM_014141.5;CNTNAP2,5_prime_UTR_variant,,ENST00000628930,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000631199,;CNTNAP2,upstream_gene_variant,,ENST00000636988,; T ENST00000361727 Transcript missense_variant 3331/9896 2813/3996 938/1331 R/L cGc/cTc 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 18/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1048353998 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 148172281 148172281 G T 1 0 0 0 0 1 0 0 0 3428 1087 38 1 1 CNTNAP2 7 148172281 Missense_Mutation SNP G C3N-00549_T 872042 148172281 11173692 180 15204 GIMAP8 0 . GRCh38 7 150467238 150467238 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.540C>A p.= p.T180T ENST00000307271 2/5 252 181 71 275 275 0 strelka-varscan-mutect GIMAP8,synonymous_variant,p.=,ENST00000307271,NM_175571.3; A ENST00000307271 Transcript synonymous_variant 1114/4184 540/1998 180/665 T acC/acA 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 2/5 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF73,hmmpanther:PTHR10903,Gene3D:3.40.50.300,Pfam_domain:PF04548,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 150467238 150467238 C A 1 0 0 0 0 0 0 0 1 6265 610 22 2 2 GIMAP8 7 150467238 Silent SNP C C3N-00549_T 2294957 150467238 8878735 181 15205 ABCB8 0 . GRCh38 7 151035880 151035880 + Splice_Site SNP A A T novel C3N-00549_T C3N-00549_N A A c.979-2A>T p.X327_splice ENST00000297504 244 123 121 166 166 0 strelka-varscan-mutect ABCB8,splice_acceptor_variant,,ENST00000358849,NM_007188.4;ABCB8,splice_acceptor_variant,,ENST00000542328,NM_001282293.1;ABCB8,splice_acceptor_variant,,ENST00000297504,NM_001282291.1;ABCB8,splice_acceptor_variant,,ENST00000498578,NM_001282292.1;ABCB8,splice_acceptor_variant,,ENST00000477719,;ABCB8,splice_acceptor_variant,,ENST00000477092,;ABCB8,splice_acceptor_variant,,ENST00000491920,;ABCB8,downstream_gene_variant,,ENST00000461373,;ABCB8,downstream_gene_variant,,ENST00000493338,;ABCB8,downstream_gene_variant,,ENST00000488370,;ABCB8,downstream_gene_variant,,ENST00000466956,;ABCB8,downstream_gene_variant,,ENST00000488826,;ABCB8,downstream_gene_variant,,ENST00000471796,;ABCB8,downstream_gene_variant,,ENST00000472698,;ABCB8,downstream_gene_variant,,ENST00000469410,;ABCB8,splice_acceptor_variant,,ENST00000466514,;ABCB8,splice_acceptor_variant,,ENST00000482309,;ABCB8,3_prime_UTR_variant,,ENST00000470645,;ABCB8,upstream_gene_variant,,ENST00000482899,;ABCB8,downstream_gene_variant,,ENST00000489192,;ABCB8,downstream_gene_variant,,ENST00000462605,;ABCB8,downstream_gene_variant,,ENST00000488551,; T ENST00000297504 Transcript splice_acceptor_variant -/2487 979/2208 327/735 1 1 ABCB8 HGNC HGNC:49 protein_coding YES CCDS64799.1 ENSP00000297504 Q9NUT2 UPI000013E41A NM_001282291.1 7/16 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 50 151035880 151035880 A T 1 0 0 0 0 0 0 1 0 51 202 7 4 4 ABCB8 7 151035880 Splice_Site SNP A C3N-00549_T 568642 151035880 8310093 182 15206 SLC4A2 0 . GRCh38 7 151071538 151071538 + Nonsense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2124C>A p.Cys708Ter p.C708* ENST00000485713 14/23 294 156 138 304 304 0 strelka-varscan-mutect SLC4A2,stop_gained,p.Cys708Ter,ENST00000485713,NM_001199692.1;SLC4A2,stop_gained,p.Cys694Ter,ENST00000461735,NM_001199694.1;SLC4A2,stop_gained,p.Cys708Ter,ENST00000413384,NM_003040.3;SLC4A2,stop_gained,p.Cys699Ter,ENST00000392826,NM_001199693.1;RP11-148K1.12,downstream_gene_variant,,ENST00000485974,;SLC4A2,upstream_gene_variant,,ENST00000482697,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000480107,;SLC4A2,non_coding_transcript_exon_variant,,ENST00000493040,;SLC4A2,upstream_gene_variant,,ENST00000472204,;SLC4A2,upstream_gene_variant,,ENST00000460010,;SLC4A2,downstream_gene_variant,,ENST00000494298,;SLC4A2,downstream_gene_variant,,ENST00000469355,;SLC4A2,upstream_gene_variant,,ENST00000469467,; A ENST00000485713 Transcript stop_gained 3164/4925 2124/3726 708/1241 C/* tgC/tgA 1 1 SLC4A2 HGNC HGNC:11028 protein_coding YES CCDS5917.1 ENSP00000419412 P04920 UPI000013EFE9 NM_001199692.1 14/23 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF14,TIGRFAM_domain:TIGR00834,Gene3D:1bzkA00,Pfam_domain:PF00955,Prints_domain:PR00165 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 151071538 151071538 C A 1 0 0 0 0 0 1 0 0 14931 747 26 2 2 SLC4A2 7 151071538 Nonsense_Mutation SNP C C3N-00549_T 35658 151071538 8274435 183 15207 PRKAG2 0 . GRCh38 7 151675463 151675463 + Missense_Mutation SNP C C A rs781267213 C3N-00549_T C3N-00549_N C C c.641G>T p.Arg214Met p.R214M ENST00000287878 4/16 309 151 158 344 344 0 strelka-varscan-mutect PRKAG2,missense_variant,p.Arg214Met,ENST00000287878,NM_016203.3;PRKAG2,missense_variant,p.Arg90Met,ENST00000492843,NM_001304527.1;PRKAG2,missense_variant,p.Arg170Met,ENST00000392801,NM_001040633.1;PRKAG2,non_coding_transcript_exon_variant,,ENST00000487375,;PRKAG2,downstream_gene_variant,,ENST00000461529,;PRKAG2,missense_variant,p.Arg214Met,ENST00000488258,;PRKAG2,non_coding_transcript_exon_variant,,ENST00000481434,; A ENST00000287878 Transcript missense_variant 1146/3305 641/1710 214/569 R/M aGg/aTg rs781267213 1 -1 PRKAG2 HGNC HGNC:9386 protein_coding YES CCDS5928.1 ENSP00000287878 Q9UGJ0 A0A090N8Q6 UPI00001250B5 NM_016203.3 tolerated_low_confidence(0.06) 4/16 hmmpanther:PTHR13780,hmmpanther:PTHR13780:SF26 MODERATE 1 SNV 1 1 PASS rs781267213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 151675463 151675463 C A 1 0 0 0 0 1 0 0 0 12634 681 24 2 2 PRKAG2 7 151675463 Missense_Mutation SNP C C3N-00549_T 603925 151675463 7670510 184 15208 HTR5A 0 . GRCh38 7 155071028 155071028 + Silent SNP T T A novel C3N-00549_T C3N-00549_N T T c.129T>A p.= p.I43I ENST00000287907 1/2 265 133 132 257 257 0 strelka-varscan-mutect HTR5A,synonymous_variant,p.=,ENST00000287907,NM_024012.3;HTR5A-AS1,splice_region_variant,,ENST00000395731,;HTR5A-AS1,splice_region_variant,,ENST00000493904,;RP11-5C23.4,upstream_gene_variant,,ENST00000637588,; A ENST00000287907 Transcript synonymous_variant 705/2912 129/1074 43/357 I atT/atA 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 1/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 155071028 155071028 T A 1 0 0 0 0 0 0 0 1 7346 1771 62 4 4 HTR5A 7 155071028 Silent SNP T C3N-00549_T 3395565 155071028 4274945 185 15209 DLGAP2 0 . GRCh38 8 1549565 1549565 + Missense_Mutation SNP G G C C3N-00549_T C3N-00549_N G G c.872G>C p.Trp291Ser p.W291S ENST00000612087 2/11 289 183 106 193 193 0 strelka-varscan-mutect DLGAP2,missense_variant,p.Trp291Ser,ENST00000612087,NM_001277161.1;DLGAP2,missense_variant,p.Trp308Ser,ENST00000520901,;DLGAP2,missense_variant,p.Trp371Ser,ENST00000637795,;DLGAP2,missense_variant,p.Trp370Ser,ENST00000421627,;DLGAP2,missense_variant,p.Trp291Ser,ENST00000637152,NM_004745.4; C ENST00000612087 Transcript missense_variant 1006/10088 872/2886 291/961 W/S tGg/tCg COSM3663666,COSM3663667 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 deleterious(0.02) 2/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 1549565 1549565 G C 1 0 0 0 0 1 0 0 0 4367 1357 47 4 4 DLGAP2 8 1549565 Missense_Mutation SNP G C3N-00549_T 1549565 143589071 186 15210 CSGALNACT1 0 . GRCh38 8 19505228 19505228 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.607C>A p.Pro203Thr p.P203T ENST00000454498 4/10 244 152 92 217 217 0 strelka-varscan-mutect CSGALNACT1,missense_variant,p.Pro203Thr,ENST00000454498,NM_001130518.1;CSGALNACT1,missense_variant,p.Pro203Thr,ENST00000332246,NM_018371.4;CSGALNACT1,missense_variant,p.Pro203Thr,ENST00000522854,;CSGALNACT1,downstream_gene_variant,,ENST00000523262,;CSGALNACT1,downstream_gene_variant,,ENST00000517494,;CSGALNACT1,downstream_gene_variant,,ENST00000520003,;CSGALNACT1,downstream_gene_variant,,ENST00000524213,;CSGALNACT1,downstream_gene_variant,,ENST00000523227,;CSGALNACT1,downstream_gene_variant,,ENST00000517651,;CSGALNACT1,downstream_gene_variant,,ENST00000522573,;CSGALNACT1,downstream_gene_variant,,ENST00000522732,;CSGALNACT1,missense_variant,p.Pro203Thr,ENST00000397998,;CSGALNACT1,missense_variant,p.Pro203Thr,ENST00000519222,; T ENST00000454498 Transcript missense_variant 1621/4232 607/1599 203/532 P/T Cct/Act 1 -1 CSGALNACT1 HGNC HGNC:24290 protein_coding YES CCDS6010.1 ENSP00000411816 Q8TDX6 UPI000013F19F NM_001130518.1 tolerated(0.64) 4/10 hmmpanther:PTHR12369:SF19,hmmpanther:PTHR12369,Pfam_domain:PF05679 MODERATE 1 SNV 1 1 PASS rs1025904631 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 19505228 19505228 G T 1 0 0 0 0 1 0 0 0 3739 1174 41 2 2 CSGALNACT1 8 19505228 Missense_Mutation SNP G C3N-00549_T 17955663 19505228 125633408 187 15211 EGR3 0 . GRCh38 8 22690639 22690639 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.998T>A p.Phe333Tyr p.F333Y ENST00000317216 2/2 210 124 86 139 139 0 strelka-varscan-mutect EGR3,missense_variant,p.Phe333Tyr,ENST00000317216,NM_004430.2;EGR3,missense_variant,p.Phe295Tyr,ENST00000522910,NM_001199880.1;EGR3,3_prime_UTR_variant,,ENST00000519492,;RP11-459E5.1,intron_variant,,ENST00000523627,;EGR3,non_coding_transcript_exon_variant,,ENST00000524088,;EGR3,downstream_gene_variant,,ENST00000518773,; T ENST00000317216 Transcript missense_variant 1356/4336 998/1164 333/387 F/Y tTt/tAt 1 -1 EGR3 HGNC HGNC:3240 protein_coding YES CCDS6033.1 ENSP00000318057 Q06889 UPI0000129E0F NM_004430.2 deleterious(0) 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 22690639 22690639 A T 1 0 0 0 0 1 0 0 0 4809 14 1 4 4 EGR3 8 22690639 Missense_Mutation SNP A C3N-00549_T 3185411 22690639 122447997 188 15212 ADGRA2 0 . GRCh38 8 37797319 37797319 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.51G>T p.= p.L17L ENST00000412232 1/19 29 11 18 28 28 0 strelka-varscan ADGRA2,synonymous_variant,p.=,ENST00000315215,;ADGRA2,synonymous_variant,p.=,ENST00000412232,NM_032777.9;ADGRA2,intron_variant,,ENST00000428068,; T ENST00000412232 Transcript synonymous_variant 64/5651 51/4017 17/1338 L ctG/ctT 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 1/19 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 37797319 37797319 G T 1 0 0 0 0 0 0 0 1 353 1306 46 2 2 ADGRA2 8 37797319 Silent SNP G C3N-00549_T 15106680 37797319 107341317 189 15213 ANK1 0 . GRCh38 8 41723144 41723144 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.989C>A p.Pro330Gln p.P330Q ENST00000265709 9/43 631 362 269 438 438 0 strelka-varscan ANK1,missense_variant,p.Pro297Gln,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Pro297Gln,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Pro330Gln,ENST00000265709,NM_001142446.1; T ENST00000265709 Transcript missense_variant 1271/6379 989/5694 330/1897 P/Q cCa/cAa COSM5433785,COSM5433786 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 deleterious(0.03) 9/43 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 41723144 41723144 G T 1 0 0 0 0 1 0 0 0 720 1348 47 2 2 ANK1 8 41723144 Missense_Mutation SNP G C3N-00549_T 3925825 41723144 103415492 190 15214 PRKDC 0 . GRCh38 8 47957182 47957182 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.313G>A p.Val105Ile p.V105I ENST00000314191 3/86 79 34 45 55 55 0 strelka-varscan PRKDC,missense_variant,p.Val105Ile,ENST00000314191,NM_006904.6;PRKDC,missense_variant,p.Val105Ile,ENST00000338368,NM_001081640.1;PRKDC,missense_variant,p.Val10Ile,ENST00000540819,;MCM4,upstream_gene_variant,,ENST00000262105,NM_005914.3;MCM4,upstream_gene_variant,,ENST00000523944,NM_182746.2;MCM4,upstream_gene_variant,,ENST00000519170,;MCM4,upstream_gene_variant,,ENST00000518221,;MCM4,upstream_gene_variant,,ENST00000519138,;MCM4,upstream_gene_variant,,ENST00000520934,;MCM4,upstream_gene_variant,,ENST00000524086,;MCM4,upstream_gene_variant,,ENST00000520994,; T ENST00000314191 Transcript missense_variant 370/13509 313/12387 105/4128 V/I Gtt/Att 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 tolerated(0.11) 3/86 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF68,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 203 2 5 0 0 0 0 -20 0.9999057 1 1 1 0 T 3 4 50 47957182 47957182 C T 1 0 0 0 0 1 0 0 0 12654 478 17 3 3 PRKDC 8 47957182 Missense_Mutation SNP C C3N-00549_T 6234038 47957182 97181454 191 15215 ATP6V1H 0 . GRCh38 8 53772143 53772143 + Silent SNP T T G novel C3N-00549_T C3N-00549_N T T c.895A>C p.= p.R299R ENST00000359530 10/14 165 101 64 151 151 0 strelka-varscan ATP6V1H,synonymous_variant,p.=,ENST00000355221,NM_213619.2;ATP6V1H,synonymous_variant,p.=,ENST00000359530,NM_015941.3;ATP6V1H,synonymous_variant,p.=,ENST00000520188,;ATP6V1H,synonymous_variant,p.=,ENST00000396774,NM_213620.2;ATP6V1H,intron_variant,,ENST00000523426,;ATP6V1H,intron_variant,,ENST00000523343,;ATP6V1H,intron_variant,,ENST00000521900,;ATP6V1H,upstream_gene_variant,,ENST00000523899,;ATP6V1H,3_prime_UTR_variant,,ENST00000524164,;ATP6V1H,upstream_gene_variant,,ENST00000521707,; G ENST00000359530 Transcript synonymous_variant 1159/2007 895/1452 299/483 R Aga/Cga 1 -1 ATP6V1H HGNC HGNC:18303 protein_coding YES CCDS6153.1 ENSP00000352522 Q9UI12 A0A024R7U9 UPI0000000966 NM_015941.3 10/14 hmmpanther:PTHR10698,PIRSF_domain:PIRSF032184,Gene3D:1.25.10.10,Pfam_domain:PF03224,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 50 53772143 53772143 T G 1 0 0 0 0 0 0 0 1 1342 1617 56 5 5 ATP6V1H 8 53772143 Silent SNP T C3N-00549_T 5814961 53772143 91366493 192 15216 XKR4 0 . GRCh38 8 55524032 55524032 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.1758C>A p.= p.R586R ENST00000327381 3/3 206 116 90 219 219 0 strelka-varscan XKR4,synonymous_variant,p.=,ENST00000327381,NM_052898.1;XKR4,synonymous_variant,p.=,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; A ENST00000327381 Transcript synonymous_variant 1858/19880 1758/1953 586/650 R cgC/cgA 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 55524032 55524032 C A 1 0 0 0 0 0 0 0 1 17992 726 26 2 2 XKR4 8 55524032 Silent SNP C C3N-00549_T 1751889 55524032 89614604 193 15217 CHD7 0 . GRCh38 8 60741469 60741469 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.37G>T p.Asp13Tyr p.D13Y ENST00000423902 2/38 153 85 68 91 91 0 strelka-varscan CHD7,missense_variant,p.Asp13Tyr,ENST00000423902,NM_017780.3;CHD7,missense_variant,p.Asp13Tyr,ENST00000525508,;CHD7,missense_variant,p.Asp13Tyr,ENST00000524602,;CHD7,missense_variant,p.Asp13Tyr,ENST00000526846,;CHD7,upstream_gene_variant,,ENST00000527825,;CHD7,upstream_gene_variant,,ENST00000527900,; T ENST00000423902 Transcript missense_variant 516/11568 37/8994 13/2997 D/Y Gat/Tat 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 deleterious_low_confidence(0) 2/38 MODERATE 1 SNV 5 1 PASS . . 0 192 6 10 2 0 0 0 -20 0.901878 1 1 1 0 T 3 4 50 60741469 60741469 G T 1 0 0 0 0 1 0 0 0 3089 1174 41 2 2 CHD7 8 60741469 Missense_Mutation SNP G C3N-00549_T 5217437 60741469 84397167 194 15218 ZFHX4 0 . GRCh38 8 76855531 76855531 + Missense_Mutation SNP C C G C3N-00549_T C3N-00549_N C C c.8610C>G p.Ser2870Arg p.S2870R ENST00000521891 10/11 166 118 48 163 163 0 strelka-varscan ZFHX4,missense_variant,p.Ser2870Arg,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Ser2844Arg,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; G ENST00000521891 Transcript missense_variant 9058/14019 8610/10851 2870/3616 S/R agC/agG COSM3651146,COSM3651147 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 76855531 76855531 C G 1 0 0 0 0 1 0 0 0 18213 738 26 4 4 ZFHX4 8 76855531 Missense_Mutation SNP C C3N-00549_T 16114062 76855531 68283105 195 15219 ZFHX4 0 . GRCh38 8 76864513 76864513 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.10799C>T p.Ser3600Phe p.S3600F ENST00000521891 11/11 90 49 41 77 77 0 strelka-varscan ZFHX4,missense_variant,p.Ser3600Phe,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Ser3574Phe,ENST00000518282,; T ENST00000521891 Transcript missense_variant 11247/14019 10799/10851 3600/3616 S/F tCt/tTt 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious_low_confidence(0.02) 11/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 76864513 76864513 C T 1 0 0 0 0 1 0 0 0 18213 913 32 3 3 ZFHX4 8 76864513 Missense_Mutation SNP C C3N-00549_T 8982 76864513 68274123 196 15220 DCAF4L2 0 . GRCh38 8 87873015 87873015 + Silent SNP G G T rs143361209 C3N-00549_T C3N-00549_N G G c.957C>A p.= p.P319P ENST00000319675 1/1 222 130 92 180 180 0 strelka-varscan DCAF4L2,synonymous_variant,p.=,ENST00000319675,NM_152418.3;CTB-118P15.3,downstream_gene_variant,,ENST00000613582,; T ENST00000319675 Transcript synonymous_variant 1054/3326 957/1188 319/395 P ccC/ccA rs143361209 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 1/1 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF457,hmmpanther:PTHR22847,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 87873015 87873015 G T 1 0 0 0 0 0 0 0 1 4073 1103 39 1 1 DCAF4L2 8 87873015 Silent SNP G C3N-00549_T 11008502 87873015 57265621 197 15221 CSMD3 0 . GRCh38 8 112517167 112517167 + Silent SNP C C A C3N-00549_T C3N-00549_N C C c.4623G>T p.= p.G1541G ENST00000297405 28/71 264 154 110 229 229 0 strelka-varscan CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,; A ENST00000297405 Transcript synonymous_variant 4868/13212 4623/11124 1541/3707 G ggG/ggT COSM5514212,COSM5514213 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 28/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 112517167 112517167 C A 1 0 0 0 0 0 0 0 1 3747 610 22 2 2 CSMD3 8 112517167 Silent SNP C C3N-00549_T 24644152 112517167 32621469 198 15222 CSMD3 0 . GRCh38 8 113019128 113019128 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.969C>A p.= p.L323L ENST00000297405 6/71 274 159 115 260 259 1 strelka-varscan CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,; T ENST00000297405 Transcript synonymous_variant 1214/13212 969/11124 323/3707 L ctC/ctA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 6/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 113019128 113019128 G T 1 0 0 0 0 0 0 0 1 3747 1277 45 2 2 CSMD3 8 113019128 Silent SNP G C3N-00549_T 501961 113019128 32119508 199 15223 COL22A1 0 . GRCh38 8 138690875 138690875 + Splice_Site SNP C C A C3N-00549_T C3N-00549_N C C c.2755-1G>T p.X919_splice ENST00000303045 61 38 23 59 59 0 strelka-varscan COL22A1,splice_acceptor_variant,,ENST00000303045,NM_152888.2;COL22A1,splice_acceptor_variant,,ENST00000435777,;COL22A1,splice_acceptor_variant,,ENST00000341807,; A ENST00000303045 Transcript splice_acceptor_variant -/6346 2755/4881 919/1626 COSM3645638 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 35/64 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 138690875 138690875 C A 1 0 0 0 0 0 0 1 0 3469 695 24 2 2 COL22A1 8 138690875 Splice_Site SNP C C3N-00549_T 25671747 138690875 6447761 200 15224 CCDC166 0 . GRCh38 8 143707106 143707106 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.908C>T p.Pro303Leu p.P303L ENST00000542437 2/2 89 51 38 75 75 0 strelka-varscan CCDC166,missense_variant,p.Pro303Leu,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; A ENST00000542437 Transcript missense_variant 908/1320 908/1320 303/439 P/L cCg/cTg 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 tolerated(0.15) 2/2 hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4 MODERATE 1 SNV 2 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 3 1 50 143707106 143707106 G A 1 0 0 0 0 1 0 0 0 2482 1116 39 1 1 CCDC166 8 143707106 Missense_Mutation SNP G C3N-00549_T 5016231 143707106 1431530 201 15225 CCDC171 0 . GRCh38 9 15594093 15594093 + Missense_Mutation SNP G G T rs752038797 C3N-00549_T C3N-00549_N G G c.596G>T p.Arg199Met p.R199M ENST00000380701 6/26 82 30 52 187 185 2 strelka-varscan-mutect CCDC171,missense_variant,p.Arg199Met,ENST00000380701,NM_173550.2;CCDC171,missense_variant,p.Arg199Met,ENST00000535968,; T ENST00000380701 Transcript missense_variant 924/6512 596/3981 199/1326 R/M aGg/aTg rs752038797 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 tolerated_low_confidence(0.06) 6/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 MODERATE 1 SNV 1 1 PASS rs752038797 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 15594093 15594093 G T 1 0 0 0 0 1 0 0 0 2488 1000 35 2 2 CCDC171 9 15594093 Missense_Mutation SNP G C3N-00549_T 15594093 122800624 202 15226 FRMPD1 0 . GRCh38 9 37740240 37740240 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.1712G>A p.Arg571Lys p.R571K ENST00000539465 15/16 148 47 101 196 196 0 strelka-varscan-mutect FRMPD1,missense_variant,p.Arg571Lys,ENST00000539465,;FRMPD1,missense_variant,p.Arg571Lys,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; A ENST00000539465 Transcript missense_variant 2305/5465 1712/4737 571/1578 R/K aGg/aAg 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC tolerated(0.57) 15/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 37740240 37740240 G A 1 0 0 0 0 1 0 0 0 5927 1000 35 3 3 FRMPD1 9 37740240 Missense_Mutation SNP G C3N-00549_T 22146147 37740240 100654477 203 15227 PSAT1 0 . GRCh38 9 78317701 78317701 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.766G>T p.Glu256Ter p.E256* ENST00000376588 7/9 315 98 217 422 422 0 strelka-varscan-mutect PSAT1,stop_gained,p.Glu256Ter,ENST00000376588,NM_058179.3;PSAT1,stop_gained,p.Glu256Ter,ENST00000347159,NM_021154.4; T ENST00000376588 Transcript stop_gained 834/2188 766/1113 256/370 E/* Gag/Tag 1 1 PSAT1 HGNC HGNC:19129 protein_coding YES CCDS6660.1 ENSP00000365773 Q9Y617 A0A024R222 UPI0000001C03 NM_058179.3 7/9 HAMAP:MF_00160,hmmpanther:PTHR21152:SF17,hmmpanther:PTHR21152,Pfam_domain:PF00266,PIRSF_domain:PIRSF000525,Gene3D:3.40.640.10,TIGRFAM_domain:TIGR01364,Superfamily_domains:SSF53383 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 78317701 78317701 G T 1 0 0 0 0 0 1 0 0 12795 1175 41 2 2 PSAT1 9 78317701 Nonsense_Mutation SNP G C3N-00549_T 40577461 78317701 60077016 204 15228 SEMA4D 0 . GRCh38 9 89363777 89363777 + Nonsense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.2056A>T p.Lys686Ter p.K686* ENST00000420987 18/20 208 58 150 242 242 0 strelka-varscan-mutect SEMA4D,stop_gained,p.Lys686Ter,ENST00000420987,NM_001142287.1;SEMA4D,stop_gained,p.Lys686Ter,ENST00000339861,;SEMA4D,stop_gained,p.Lys686Ter,ENST00000455551,;SEMA4D,stop_gained,p.Lys71Ter,ENST00000420101,;SECISBP2,downstream_gene_variant,,ENST00000534113,NM_001282690.1;SECISBP2,downstream_gene_variant,,ENST00000375807,NM_001282688.1,NM_024077.4;SECISBP2,downstream_gene_variant,,ENST00000339901,NM_001282689.1;SEMA4D,non_coding_transcript_exon_variant,,ENST00000469653,;SEMA4D,non_coding_transcript_exon_variant,,ENST00000475255,;SEMA4D,synonymous_variant,p.=,ENST00000429836,;SEMA4D,synonymous_variant,p.=,ENST00000537934,;SEMA4D,non_coding_transcript_exon_variant,,ENST00000492386,; A ENST00000420987 Transcript stop_gained 2503/4275 2056/2217 686/738 K/* Aag/Tag 1 -1 SEMA4D HGNC HGNC:10732 protein_coding CCDS47991.1 ENSP00000391733 Q92854 UPI000185BDB1 NM_001142287.1 18/20 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 HIGH SNV 5 1 PASS rs1331625192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 89363777 89363777 T A 1 0 0 0 0 0 1 0 0 14310 1821 63 4 4 SEMA4D 9 89363777 Nonsense_Mutation SNP T C3N-00549_T 11046076 89363777 49030940 205 15229 OR13C8 0 . GRCh38 9 104569532 104569532 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.365G>T p.Arg122Leu p.R122L ENST00000335040 1/1 128 35 93 180 180 0 strelka-varscan-mutect OR13C8,missense_variant,p.Arg122Leu,ENST00000335040,NM_001004483.1; T ENST00000335040 Transcript missense_variant 365/963 365/963 122/320 R/L cGc/cTc COSM4709657 1 1 OR13C8 HGNC HGNC:15103 protein_coding YES CCDS35090.1 ENSP00000334068 Q8NGS7 A0A126GVC7 UPI000004B203 NM_001004483.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF87,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS rs1323175968 . 0 206 0 2 2 0 0 0 -20 0.9990439 1 1 1 0 T 3 4 50 104569532 104569532 G T 1 0 0 0 0 1 0 0 0 11014 1087 38 1 1 OR13C8 9 104569532 Missense_Mutation SNP G C3N-00549_T 15205755 104569532 33825185 206 15230 TLR4 0 . GRCh38 9 117714175 117714175 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2047C>A p.Gln683Lys p.Q683K ENST00000355622 3/3 98 35 63 126 126 0 strelka-varscan-mutect TLR4,missense_variant,p.Gln683Lys,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Gln643Lys,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,; A ENST00000355622 Transcript missense_variant 2148/4844 2047/2520 683/839 Q/K Cag/Aag 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 tolerated(0.8) 3/3 PROSITE_profiles:PS50104,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.40.50.10140,Pfam_domain:PF01582,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 117714175 117714175 C A 1 0 0 0 0 1 0 0 0 16399 595 21 2 2 TLR4 9 117714175 Missense_Mutation SNP C C3N-00549_T 13144643 117714175 20680542 207 15231 CDK5RAP2 0 . GRCh38 9 120439927 120439927 + Missense_Mutation SNP C C A rs777420257 C3N-00549_T C3N-00549_N C C c.3194G>T p.Cys1065Phe p.C1065F ENST00000349780 24/38 170 63 107 195 195 0 strelka-varscan-mutect CDK5RAP2,missense_variant,p.Cys1065Phe,ENST00000349780,NM_018249.5;CDK5RAP2,missense_variant,p.Cys1065Phe,ENST00000360190,NM_001011649.2;CDK5RAP2,missense_variant,p.Cys835Phe,ENST00000360822,NM_001272039.1;CDK5RAP2,missense_variant,p.Cys459Phe,ENST00000416449,;CDK5RAP2,missense_variant,p.Cys75Phe,ENST00000425647,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000479584,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000468989,;CDK5RAP2,3_prime_UTR_variant,,ENST00000473282,;CDK5RAP2,3_prime_UTR_variant,,ENST00000480112,;CDK5RAP2,non_coding_transcript_exon_variant,,ENST00000483412,; A ENST00000349780 Transcript missense_variant 3374/6228 3194/5682 1065/1893 C/F tGc/tTc rs777420257 1 -1 CDK5RAP2 HGNC HGNC:18672 protein_coding YES CCDS6823.1 ENSP00000343818 Q96SN8 UPI0000367673 NM_018249.5 tolerated(0.25) 24/38 MODERATE 1 SNV 1 1 PASS rs777420257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 120439927 120439927 C A 1 0 0 0 0 1 0 0 0 2850 710 25 2 2 CDK5RAP2 9 120439927 Missense_Mutation SNP C C3N-00549_T 2725752 120439927 17954790 208 15232 OR1Q1 0 . GRCh38 9 122614917 122614917 + Nonsense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.180C>A p.Tyr60Ter p.Y60* ENST00000297913 1/1 104 42 62 154 154 0 strelka-varscan-mutect OR1Q1,stop_gained,p.Tyr60Ter,ENST00000297913,NM_012364.1;RP11-64P14.7,intron_variant,,ENST00000431442,;RP11-64P14.7,upstream_gene_variant,,ENST00000419604,; A ENST00000297913 Transcript stop_gained 180/945 180/945 60/314 Y/* taC/taA 1 1 OR1Q1 HGNC HGNC:8223 protein_coding YES CCDS35125.1 ENSP00000297913 Q15612 UPI000003CACD NM_012364.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH SNV 1 PASS rs1161745970 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 122614917 122614917 C A 1 0 0 0 0 0 1 0 0 11049 489 17 2 2 OR1Q1 9 122614917 Nonsense_Mutation SNP C C3N-00549_T 2174990 122614917 15779800 209 15233 GOLGA2 0 . GRCh38 9 128260598 128260598 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1544G>T p.Gly515Val p.G515V ENST00000421699 17/26 339 215 124 231 230 1 strelka-varscan-mutect GOLGA2,missense_variant,p.Gly515Val,ENST00000421699,NM_004486.4;GOLGA2,missense_variant,p.Gly515Val,ENST00000611957,;GOLGA2,missense_variant,p.Gly503Val,ENST00000609374,;GOLGA2,intron_variant,,ENST00000610329,;GOLGA2,downstream_gene_variant,,ENST00000450617,;GOLGA2,downstream_gene_variant,,ENST00000458730,;GOLGA2,non_coding_transcript_exon_variant,,ENST00000486411,;GOLGA2,downstream_gene_variant,,ENST00000490257,;GOLGA2,upstream_gene_variant,,ENST00000462089,;GOLGA2,downstream_gene_variant,,ENST00000470630,;GOLGA2,downstream_gene_variant,,ENST00000468488,;GOLGA2,downstream_gene_variant,,ENST00000461031,;GOLGA2,upstream_gene_variant,,ENST00000496221,; A ENST00000421699 Transcript missense_variant 1557/4260 1544/3009 515/1002 G/V gGg/gTg 1 -1 GOLGA2 HGNC HGNC:4425 protein_coding YES CCDS6896.2 ENSP00000416097 Q08379 UPI0000D4C11A NM_004486.4 tolerated(0.26) 17/26 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF45 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 128260598 128260598 C A 1 0 0 0 0 1 0 0 0 6431 623 22 2 2 GOLGA2 9 128260598 Missense_Mutation SNP C C3N-00549_T 5645681 128260598 10134119 210 15234 ZER1 0 . GRCh38 9 128755518 128755518 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.48C>T p.= p.F16F ENST00000291900 2/16 301 188 113 242 242 0 strelka-varscan-mutect ZER1,synonymous_variant,p.=,ENST00000291900,NM_006336.3;ZER1,synonymous_variant,p.=,ENST00000414921,;ZER1,synonymous_variant,p.=,ENST00000427848,;ZER1,intron_variant,,ENST00000494461,; A ENST00000291900 Transcript synonymous_variant 455/4259 48/2301 16/766 F ttC/ttT 1 -1 ZER1 HGNC HGNC:30960 protein_coding YES CCDS6910.1 ENSP00000291900 Q7Z7L7 A0A024R8B0 UPI000013E085 NM_006336.3 2/16 hmmpanther:PTHR12904,hmmpanther:PTHR12904:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 128755518 128755518 G A 1 0 0 0 0 0 0 0 1 18201 933 33 3 3 ZER1 9 128755518 Silent SNP G C3N-00549_T 494920 128755518 9639199 211 15235 COL5A1 0 . GRCh38 9 134690947 134690947 + Missense_Mutation SNP C C A rs372168541 C3N-00549_T C3N-00549_N C C c.145C>A p.His49Asn p.H49N ENST00000371817 2/66 375 116 259 499 498 1 strelka-varscan-mutect COL5A1,missense_variant,p.His49Asn,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.His49Asn,ENST00000618395,NM_001278074.1;COL5A1,non_coding_transcript_exon_variant,,ENST00000464187,; A ENST00000371817 Transcript missense_variant 559/8471 145/5517 49/1838 H/N Cac/Aac rs372168541 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 tolerated(0.7) 2/66 SMART_domains:SM00210,Superfamily_domains:SSF49899 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs372168541 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 134690947 134690947 C A 1 0 0 0 0 1 0 0 0 3485 826 29 2 2 COL5A1 9 134690947 Missense_Mutation SNP C C3N-00549_T 5935429 134690947 3703770 212 15236 GLT6D1 0 . GRCh38 9 135624231 135624231 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.697G>C p.Gly233Arg p.G233R ENST00000371763 5/5 62 17 45 54 54 0 strelka-varscan-mutect GLT6D1,missense_variant,p.Gly233Arg,ENST00000371763,NM_182974.2;GLT6D1,missense_variant,p.Gly233Arg,ENST00000613244,; G ENST00000371763 Transcript missense_variant 951/1526 697/831 233/276 G/R Ggt/Cgt 1 -1 GLT6D1 HGNC HGNC:23671 protein_coding YES CCDS43900.1 ENSP00000360829 Q7Z4J2 UPI0000246F68 NM_182974.2 deleterious(0) 5/5 hmmpanther:PTHR10462:SF27,hmmpanther:PTHR10462,Gene3D:3.90.550.10,Pfam_domain:PF03414,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999997 1 1 1 0 G 3 3 50 135624231 135624231 C G 1 0 0 0 0 1 0 0 0 6345 594 21 4 4 GLT6D1 9 135624231 Missense_Mutation SNP C C3N-00549_T 933284 135624231 2770486 213 15237 GRIN1 0 . GRCh38 9 137142064 137142064 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.310C>A p.Pro104Thr p.P104T ENST00000371553 2/21 383 119 264 445 444 1 strelka-varscan-mutect GRIN1,missense_variant,p.Pro104Thr,ENST00000371561,NM_007327.3;GRIN1,missense_variant,p.Pro104Thr,ENST00000371546,;GRIN1,missense_variant,p.Pro104Thr,ENST00000371555,;GRIN1,missense_variant,p.Pro104Thr,ENST00000371550,NM_021569.3;GRIN1,missense_variant,p.Pro104Thr,ENST00000371553,NM_001185090.1;GRIN1,missense_variant,p.Pro104Thr,ENST00000371560,NM_001185091.1;GRIN1,missense_variant,p.Pro104Thr,ENST00000371559,NM_000832.6;GRIN1,missense_variant,p.Pro104Thr,ENST00000350902,;GRIN1,non_coding_transcript_exon_variant,,ENST00000471122,; A ENST00000371553 Transcript missense_variant 316/3751 310/2832 104/943 P/T Ccc/Acc 1 1 GRIN1 HGNC HGNC:4584 protein_coding YES CCDS55354.1 ENSP00000360608 Q05586 UPI000014AF8E NM_001185090.1 deleterious(0.03) 2/21 hmmpanther:PTHR18966:SF214,hmmpanther:PTHR18966,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 137142064 137142064 C A 1 0 0 0 0 1 0 0 0 6660 855 30 2 2 GRIN1 9 137142064 Missense_Mutation SNP C C3N-00549_T 1517833 137142064 1252653 214 15238 NSMF 0 . GRCh38 9 137450009 137450009 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.1333A>T p.Ser445Cys p.S445C ENST00000371475 14/16 205 54 151 267 267 0 strelka-varscan-mutect NSMF,missense_variant,p.Ser445Cys,ENST00000371475,NM_001130969.1;NSMF,missense_variant,p.Ser443Cys,ENST00000265663,NM_015537.4;NSMF,missense_variant,p.Ser422Cys,ENST00000437259,NM_001130970.1;NSMF,missense_variant,p.Ser420Cys,ENST00000371474,NM_001130971.1;NSMF,missense_variant,p.Ser415Cys,ENST00000371473,NM_001178064.1;NSMF,missense_variant,p.Ser278Cys,ENST00000339554,;NSMF,missense_variant,p.Ser443Cys,ENST00000371472,;NSMF,missense_variant,p.Ser160Cys,ENST00000482448,;NSMF,downstream_gene_variant,,ENST00000611474,;NSMF,non_coding_transcript_exon_variant,,ENST00000371482,;NSMF,non_coding_transcript_exon_variant,,ENST00000484316,;NSMF,downstream_gene_variant,,ENST00000371468,; A ENST00000371475 Transcript missense_variant 1565/3646 1333/1593 445/530 S/C Agc/Tgc 1 -1 NSMF HGNC HGNC:29843 protein_coding YES CCDS48069.1 ENSP00000360530 Q6X4W1 UPI000035198D NM_001130969.1 deleterious(0.01) 14/16 hmmpanther:PTHR32061 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 137450009 137450009 T A 1 0 0 0 0 1 0 0 0 10739 1551 54 4 4 NSMF 9 137450009 Missense_Mutation SNP T C3N-00549_T 307945 137450009 944708 215 15239 ITGA8 0 . GRCh38 10 15605792 15605792 + Splice_Site SNP C C A novel C3N-00549_T C3N-00549_N C C c.1903-1G>T p.X635_splice ENST00000378076 146 109 37 159 159 0 strelka-varscan-mutect ITGA8,splice_acceptor_variant,,ENST00000378076,NM_003638.2,NM_001291494.1;ITGA8,upstream_gene_variant,,ENST00000477064,; A ENST00000378076 Transcript splice_acceptor_variant -/6755 1903/3192 635/1063 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 18/29 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 15605792 15605792 C A 1 0 0 0 0 0 0 1 0 7789 695 24 2 2 ITGA8 10 15605792 Splice_Site SNP C C3N-00549_T 15605792 118191630 216 15240 ITGA8 0 . GRCh38 10 15678738 15678738 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.614G>T p.Ser205Ile p.S205I ENST00000378076 5/30 143 114 29 172 172 0 strelka-varscan-mutect ITGA8,missense_variant,p.Ser205Ile,ENST00000378076,NM_003638.2,NM_001291494.1; A ENST00000378076 Transcript missense_variant 968/6755 614/3192 205/1063 S/I aGt/aTt 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 deleterious(0) 5/30 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999966 1 1 1 0 A 3 1 50 15678738 15678738 C A 1 0 0 0 0 1 0 0 0 7789 565 20 2 2 ITGA8 10 15678738 Missense_Mutation SNP C C3N-00549_T 72946 15678738 118118684 217 15241 NSUN6 0 . GRCh38 10 18548229 18548229 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1080G>T p.Gln360His p.Q360H ENST00000377304 10/11 108 78 30 127 127 0 strelka-varscan-mutect NSUN6,missense_variant,p.Gln360His,ENST00000377304,NM_182543.3;RP11-499P20.2,upstream_gene_variant,,ENST00000425669,;RP11-499P20.2,upstream_gene_variant,,ENST00000436485,;NSUN6,non_coding_transcript_exon_variant,,ENST00000493816,; A ENST00000377304 Transcript missense_variant 1499/2201 1080/1410 360/469 Q/H caG/caT 1 -1 NSUN6 HGNC HGNC:23529 protein_coding YES CCDS7130.1 ENSP00000366519 Q8TEA1 UPI0000073CED NM_182543.3 tolerated(0.09) 10/11 PROSITE_profiles:PS51686,hmmpanther:PTHR22807,hmmpanther:PTHR22807:SF34,Pfam_domain:PF01189,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 18548229 18548229 C A 1 0 0 0 0 1 0 0 0 10745 796 28 2 2 NSUN6 10 18548229 Missense_Mutation SNP C C3N-00549_T 2869491 18548229 115249193 218 15242 ANKRD30A 0 . GRCh38 10 37217816 37217816 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3037C>A p.Leu1013Ile p.L1013I ENST00000361713 33/36 68 55 13 51 51 0 strelka-varscan ANKRD30A,missense_variant,p.Leu1132Ile,ENST00000374660,;ANKRD30A,missense_variant,p.Leu1069Ile,ENST00000611781,;ANKRD30A,missense_variant,p.Leu1013Ile,ENST00000602533,;ANKRD30A,missense_variant,p.Leu1013Ile,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript missense_variant 3136/4405 3037/4026 1013/1341 L/I Ctt/Att 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.76) 33/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 37217816 37217816 C A 1 0 0 0 0 1 0 0 0 761 565 20 2 2 ANKRD30A 10 37217816 Missense_Mutation SNP C C3N-00549_T 18669587 37217816 96579606 219 15243 FAM21C 0 . GRCh38 10 45789034 45789034 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.3188G>T p.Arg1063Ile p.R1063I ENST00000374362 28/30 725 334 391 776 776 0 strelka-varscan FAM21C,missense_variant,p.Arg1084Ile,ENST00000336378,;FAM21C,missense_variant,p.Arg1063Ile,ENST00000374362,NM_015262.2;FAM21C,missense_variant,p.Arg1084Ile,ENST00000623400,;FAM21C,missense_variant,p.Arg1022Ile,ENST00000540872,NM_001169106.1;FAM21C,missense_variant,p.Arg1005Ile,ENST00000359860,;FAM21C,missense_variant,p.Arg988Ile,ENST00000537517,NM_001169107.1;FAM21C,non_coding_transcript_exon_variant,,ENST00000471102,;FAM21C,downstream_gene_variant,,ENST00000374359,; T ENST00000374362 Transcript missense_variant 3287/4623 3188/3963 1063/1320 R/I aGa/aTa 1 1 FAM21C HGNC HGNC:23414 protein_coding YES CCDS44374.2 ENSP00000363482 Q9Y4E1 UPI0000551BE9 NM_015262.2 tolerated(0.08) 28/30 hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 45789034 45789034 G T 1 0 0 0 0 1 0 0 0 5412 942 33 2 2 FAM21C 10 45789034 Missense_Mutation SNP G C3N-00549_T 8571218 45789034 88008388 220 15244 CHAT 0 . GRCh38 10 49619767 49619767 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.430G>T p.Ala144Ser p.A144S ENST00000337653 3/15 493 243 250 416 416 0 strelka-varscan CHAT,missense_variant,p.Ala62Ser,ENST00000395562,NM_001142933.1;CHAT,missense_variant,p.Ala144Ser,ENST00000337653,NM_020549.4;CHAT,missense_variant,p.Ala26Ser,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,missense_variant,p.Ala26Ser,ENST00000339797,NM_020984.3;CHAT,missense_variant,p.Ala26Ser,ENST00000395559,NM_020986.3;CHAT,non_coding_transcript_exon_variant,,ENST00000460699,;CHAT,non_coding_transcript_exon_variant,,ENST00000490270,;CHAT,non_coding_transcript_exon_variant,,ENST00000481336,;CHAT,3_prime_UTR_variant,,ENST00000466590,; T ENST00000337653 Transcript missense_variant 583/2458 430/2247 144/748 A/S Gcc/Tcc 1 1 CHAT HGNC HGNC:1912 protein_coding YES CCDS7232.1 ENSP00000337103 P28329 UPI000013F1B9 NM_020549.4 tolerated(0.71) 3/15 Pfam_domain:PF00755,PROSITE_patterns:PS00439,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF14,Superfamily_domains:SSF52777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 49619767 49619767 G T 1 0 0 0 0 1 0 0 0 3073 1203 42 2 2 CHAT 10 49619767 Missense_Mutation SNP G C3N-00549_T 3830733 49619767 84177655 221 15245 PCDH15 0 . GRCh38 10 54023133 54023133 + Missense_Mutation SNP A A C novel C3N-00549_T C3N-00549_N A A c.2300T>G p.Leu767Arg p.L767R ENST00000373957 20/35 240 175 65 280 280 0 strelka-varscan-mutect PCDH15,missense_variant,p.Leu767Arg,ENST00000614895,;PCDH15,missense_variant,p.Leu762Arg,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Leu762Arg,ENST00000414778,;PCDH15,missense_variant,p.Leu767Arg,ENST00000617051,;PCDH15,missense_variant,p.Leu767Arg,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Leu762Arg,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Leu762Arg,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Leu740Arg,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Leu725Arg,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Leu762Arg,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Leu691Arg,ENST00000622048,;PCDH15,missense_variant,p.Leu691Arg,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Leu762Arg,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Leu774Arg,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Leu769Arg,ENST00000395445,;PCDH15,missense_variant,p.Leu762Arg,ENST00000616114,;PCDH15,missense_variant,p.Leu762Arg,ENST00000395438,;PCDH15,missense_variant,p.Leu774Arg,ENST00000612394,;PCDH15,missense_variant,p.Leu767Arg,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Leu373Arg,ENST00000409834,;PCDH15,missense_variant,p.Leu762Arg,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; C ENST00000373957 Transcript missense_variant 2695/7032 2300/5889 767/1962 L/R cTt/cGt 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 deleterious(0.02) 20/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 54023133 54023133 A C 1 0 0 0 0 1 0 0 0 11598 72 3 5 5 PCDH15 10 54023133 Missense_Mutation SNP A C3N-00549_T 4403366 54023133 79774289 222 15246 OIT3 0 . GRCh38 10 72924237 72924237 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.960T>A p.Asn320Lys p.N320K ENST00000334011 7/9 33 19 14 22 22 0 strelka-varscan-mutect OIT3,missense_variant,p.Asn320Lys,ENST00000334011,NM_152635.2;OIT3,intron_variant,,ENST00000622652,; A ENST00000334011 Transcript missense_variant 1178/2365 960/1638 320/545 N/K aaT/aaA 1 1 OIT3 HGNC HGNC:29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.2 tolerated(0.67) 7/9 PROSITE_profiles:PS51034,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF326,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 72924237 72924237 T A 1 0 0 0 0 1 0 0 0 10924 1461 51 4 4 OIT3 10 72924237 Missense_Mutation SNP T C3N-00549_T 18901104 72924237 60873185 223 15247 SAMD8 0 . GRCh38 10 75164679 75164679 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.613G>T p.Glu205Ter p.E205* ENST00000542569 3/6 260 187 73 294 294 0 strelka-varscan-mutect SAMD8,stop_gained,p.Glu205Ter,ENST00000372687,NM_144660.2;SAMD8,stop_gained,p.Glu205Ter,ENST00000542569,NM_001174156.1;SAMD8,stop_gained,p.Glu268Ter,ENST00000372690,;SAMD8,stop_gained,p.Glu205Ter,ENST00000447533,; T ENST00000542569 Transcript stop_gained 716/6782 613/1248 205/415 E/* Gaa/Taa 1 1 SAMD8 HGNC HGNC:26320 protein_coding YES CCDS53543.1 ENSP00000438042 Q96LT4 UPI000023FEEB NM_001174156.1 3/6 hmmpanther:PTHR21290,hmmpanther:PTHR21290:SF25,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 75164679 75164679 G T 1 0 0 0 0 0 1 0 0 14085 1175 41 2 2 SAMD8 10 75164679 Nonsense_Mutation SNP G C3N-00549_T 2240442 75164679 58632743 224 15248 COL17A1 0 . GRCh38 10 104063770 104063770 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.815C>A p.Pro272His p.P272H ENST00000353479 11/56 807 427 380 616 613 3 strelka-varscan-mutect COL17A1,missense_variant,p.Pro272His,ENST00000353479,NM_000494.3;COL17A1,missense_variant,p.Pro272His,ENST00000369733,;COL17A1,missense_variant,p.Pro272His,ENST00000393211,;COL17A1,non_coding_transcript_exon_variant,,ENST00000488320,; T ENST00000353479 Transcript missense_variant 1106/5734 815/4494 272/1497 P/H cCt/cAt 1 -1 COL17A1 HGNC HGNC:2194 protein_coding YES CCDS7554.1 ENSP00000340937 Q9UMD9 UPI000006DB58 NM_000494.3 deleterious(0.02) 11/56 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 104063770 104063770 G T 1 0 0 0 0 1 0 0 0 3462 1000 35 2 2 COL17A1 10 104063770 Missense_Mutation SNP G C3N-00549_T 28899091 104063770 29733652 225 15249 MKI67 0 . GRCh38 10 128103711 128103711 + Frame_Shift_Del DEL G G - rs540401023 C3N-00549_T C3N-00549_N G G c.8129delC p.Pro2710HisfsTer2 p.P2710Hfs*2 ENST00000368654 13/15 345 189 156 239 239 0 sindel-varindel-pindel MKI67,frameshift_variant,p.Pro2710HisfsTer2,ENST00000368654,NM_002417.4;MKI67,frameshift_variant,p.Pro2350HisfsTer2,ENST00000368653,NM_001145966.1;MKI67,upstream_gene_variant,,ENST00000464771,; - ENST00000368654 Transcript frameshift_variant 8505/12678 8129/9771 2710/3256 P/X cCa/ca rs540401023 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 13/15 Pfam_domain:PF08065,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM01295 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 128103711 128103711 G - 1 0 1 0 1 0 0 0 0 9566 1348 47 0 0 MKI67 10 128103711 Frame_Shift_Del DEL G C3N-00549_T 24039941 128103711 5693711 226 15250 MKI67 0 . GRCh38 10 128105066 128105083 + In_Frame_Del DEL TCGTTTCCTGAGTGCTAA TCGTTTCCTGAGTGCTAA - novel C3N-00549_T C3N-00549_N TCGTTTCCTGAGTGCTAA TCGTTTCCTGAGTGCTAA c.6757_6774delTTAGCACTCAGGAAACGA p.Leu2253_Arg2258del p.L2253_R2258del ENST00000368654 13/15 528 331 197 342 342 0 sindel-varindel-pindel MKI67,inframe_deletion,p.Leu2253_Arg2258del,ENST00000368654,NM_002417.4;MKI67,inframe_deletion,p.Leu1893_Arg1898del,ENST00000368653,NM_001145966.1;MKI67,upstream_gene_variant,,ENST00000464771,; - ENST00000368654 Transcript inframe_deletion 7133-7150/12678 6757-6774/9771 2253-2258/3256 LALRKR/- TTAGCACTCAGGAAACGA/- 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 13/15 Pfam_domain:PF08065,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM01295 MODERATE 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 128105066 128105066 TCGTTTCCTGAGTGCTAA - 1 0 1 0 1 0 0 0 0 9566 1770 62 0 0 MKI67 10 128105066 In_Frame_Del DEL TCGTTTCCTGAGTGCTAA C3N-00549_T 1355 128105066 5692356 227 15251 PHRF1 0 . GRCh38 11 607734 607734 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2278G>T p.Ala760Ser p.A760S ENST00000264555 14/18 100 26 74 101 101 0 strelka-varscan-mutect PHRF1,missense_variant,p.Ala760Ser,ENST00000264555,NM_001286581.1;PHRF1,missense_variant,p.Ala759Ser,ENST00000416188,NM_020901.3;PHRF1,missense_variant,p.Ala758Ser,ENST00000413872,NM_001286582.1;PHRF1,missense_variant,p.Ala756Ser,ENST00000533464,NM_001286583.1;IRF7,downstream_gene_variant,,ENST00000397566,NM_004031.2;IRF7,downstream_gene_variant,,ENST00000330243,;IRF7,downstream_gene_variant,,ENST00000397574,NM_001572.3;IRF7,downstream_gene_variant,,ENST00000397570,;IRF7,downstream_gene_variant,,ENST00000348655,NM_004029.2;IRF7,downstream_gene_variant,,ENST00000525445,;PHRF1,missense_variant,p.Ala760Ser,ENST00000534320,;IRF7,downstream_gene_variant,,ENST00000533182,;IRF7,downstream_gene_variant,,ENST00000469048,;IRF7,downstream_gene_variant,,ENST00000532326,;IRF7,downstream_gene_variant,,ENST00000531912,;PHRF1,downstream_gene_variant,,ENST00000532550,;IRF7,downstream_gene_variant,,ENST00000528413,; T ENST00000264555 Transcript missense_variant 2406/5523 2278/4950 760/1649 A/S Gcc/Tcc 1 1 PHRF1 HGNC HGNC:24351 protein_coding YES CCDS65988.1 ENSP00000264555 Q9P1Y6 A0A024RCA1 UPI000041A715 NM_001286581.1 tolerated(0.75) 14/18 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 607734 607734 G T 1 0 0 0 0 1 0 0 0 11949 1203 42 2 2 PHRF1 11 607734 Missense_Mutation SNP G C3N-00549_T 607734 134478888 228 15252 OR52E8 0 . GRCh38 11 5856761 5856761 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.942G>T p.Lys314Asn p.K314N ENST00000537935 1/1 14 2 12 18 18 0 strelka-varscan-mutect OR52E8,missense_variant,p.Lys314Asn,ENST00000537935,NM_001005168.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000537935 Transcript missense_variant 974/1061 942/954 314/317 K/N aaG/aaT 1 -1 OR52E8 HGNC HGNC:15217 protein_coding YES CCDS31400.1 ENSP00000444054 Q6IFG1 A0A126GVH0 UPI000004B211 NM_001005168.1 tolerated(0.08) 1/1 hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF170,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 5856761 5856761 C A 1 0 0 0 0 1 0 0 0 11191 912 32 2 2 OR52E8 11 5856761 Missense_Mutation SNP C C3N-00549_T 5249027 5856761 129229861 229 15253 C11orf42 0 . GRCh38 11 6210934 6210934 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.894C>A p.= p.R298R ENST00000316375 3/3 46 18 28 76 76 0 strelka-varscan-mutect C11orf42,synonymous_variant,p.=,ENST00000316375,NM_173525.2;FAM160A2,downstream_gene_variant,,ENST00000265978,NM_032127.3;FAM160A2,downstream_gene_variant,,ENST00000449352,NM_001098794.1;FAM160A2,downstream_gene_variant,,ENST00000529360,; A ENST00000316375 Transcript synonymous_variant 944/1142 894/1002 298/333 R cgC/cgA 1 1 C11orf42 HGNC HGNC:28541 protein_coding YES CCDS7759.1 ENSP00000321021 Q8N5U0 UPI000013FD81 NM_173525.2 3/3 Pfam_domain:PF15668,hmmpanther:PTHR36872,hmmpanther:PTHR36872:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 6210934 6210934 C A 1 0 0 0 0 0 0 0 1 1782 697 25 2 2 C11orf42 11 6210934 Silent SNP C C3N-00549_T 354173 6210934 128875688 230 15254 PIK3C2A 0 . GRCh38 11 17101428 17101428 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.3858G>T p.= p.R1286R ENST00000265970 24/32 51 18 33 61 61 0 strelka-varscan-mutect PIK3C2A,synonymous_variant,p.=,ENST00000265970,NM_001321378.1,NM_002645.2;PIK3C2A,intron_variant,,ENST00000531428,; A ENST00000265970 Transcript synonymous_variant 3858/8227 3858/5061 1286/1686 R cgG/cgT 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 24/32 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF28,SMART_domains:SM00146,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 17101428 17101428 C A 1 0 0 0 0 0 0 0 1 12004 610 22 2 2 PIK3C2A 11 17101428 Silent SNP C C3N-00549_T 10890494 17101428 117985194 231 15255 MRGPRX2 0 . GRCh38 11 19055893 19055893 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.510C>A p.Phe170Leu p.F170L ENST00000329773 2/2 109 32 77 138 138 0 strelka-varscan-mutect MRGPRX2,missense_variant,p.Phe170Leu,ENST00000329773,NM_001303615.1,NM_054030.3; T ENST00000329773 Transcript missense_variant 598/2036 510/993 170/330 F/L ttC/ttA 1 -1 MRGPRX2 HGNC HGNC:17983 protein_coding YES CCDS7847.1 ENSP00000333800 Q96LB1 UPI0000038C81 NM_001303615.1,NM_054030.3 tolerated(0.22) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF35,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 19055893 19055893 G T 1 0 0 0 0 1 0 0 0 9734 933 33 2 2 MRGPRX2 11 19055893 Missense_Mutation SNP G C3N-00549_T 1954465 19055893 116030729 232 15256 SLC6A5 0 . GRCh38 11 20652442 20652442 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.2224G>A p.Gly742Arg p.G742R ENST00000525748 15/16 329 122 207 426 426 0 strelka-varscan-mutect SLC6A5,missense_variant,p.Gly742Arg,ENST00000525748,NM_004211.3;SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; A ENST00000525748 Transcript missense_variant 2497/7084 2224/2394 742/797 G/R Gga/Aga 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 deleterious(0) 15/16 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 20652442 20652442 G A 1 0 0 0 0 1 0 0 0 14970 1349 47 3 3 SLC6A5 11 20652442 Missense_Mutation SNP G C3N-00549_T 1596549 20652442 114434180 233 15257 RAPSN 0 . GRCh38 11 47448091 47448091 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.252G>C p.Glu84Asp p.E84D ENST00000298854 2/8 224 78 146 249 249 0 strelka-varscan-mutect RAPSN,missense_variant,p.Glu84Asp,ENST00000298854,NM_005055.4;RAPSN,missense_variant,p.Glu84Asp,ENST00000524487,;RAPSN,missense_variant,p.Glu84Asp,ENST00000352508,NM_032645.4;RAPSN,missense_variant,p.Glu84Asp,ENST00000529341,; G ENST00000298854 Transcript missense_variant 466/1671 252/1239 84/412 E/D gaG/gaC 1 -1 RAPSN HGNC HGNC:9863 protein_coding YES CCDS7936.1 ENSP00000298854 Q13702 A0A0S2Z4F8 UPI0000071D46 NM_005055.4 tolerated(0.12) 2/8 hmmpanther:PTHR10098,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 47448091 47448091 C G 1 0 0 0 0 1 0 0 0 13210 912 32 4 4 RAPSN 11 47448091 Missense_Mutation SNP C C3N-00549_T 26795649 47448091 87638531 234 15258 OR4A15 0 . GRCh38 11 55368388 55368388 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.505T>A p.Cys169Ser p.C169S ENST00000314706 1/1 267 161 106 168 168 0 strelka-varscan-mutect OR4A15,missense_variant,p.Cys169Ser,ENST00000314706,NM_001005275.1; A ENST00000314706 Transcript missense_variant 505/1035 505/1035 169/344 C/S Tgt/Agt 1 1 OR4A15 HGNC HGNC:15152 protein_coding YES CCDS31500.1 ENSP00000325065 Q8NGL6 UPI000004618F NM_001005275.1 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF63,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 55368388 55368388 T A 1 0 0 0 0 1 0 0 0 11117 1580 55 4 4 OR4A15 11 55368388 Missense_Mutation SNP T C3N-00549_T 7920297 55368388 79718234 235 15259 OR8I2 0 . GRCh38 11 56094039 56094039 + Silent SNP C C A rs759448888 C3N-00549_T C3N-00549_N C C c.732C>A p.= p.L244L ENST00000302124 1/1 119 63 56 104 104 0 strelka-varscan-mutect OR8I2,synonymous_variant,p.=,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; A ENST00000302124 Transcript synonymous_variant 732/933 732/933 244/310 L ctC/ctA rs759448888 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS rs759448888 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 56094039 56094039 C A 1 0 0 0 0 0 0 0 1 11308 813 29 2 2 OR8I2 11 56094039 Silent SNP C C3N-00549_T 725651 56094039 78992583 236 15260 OR8J3 0 . GRCh38 11 56137484 56137484 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.235C>A p.Pro79Thr p.P79T ENST00000301529 1/1 200 117 83 223 223 0 strelka-varscan-mutect OR8J3,missense_variant,p.Pro79Thr,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; T ENST00000301529 Transcript missense_variant 235/948 235/948 79/315 P/T Cct/Act COSM3449241,COSM5235815 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 50 56137484 56137484 G T 1 0 0 0 0 1 0 0 0 11310 1232 43 2 2 OR8J3 11 56137484 Missense_Mutation SNP G C3N-00549_T 43445 56137484 78949138 237 15261 OR5AP2 0 . GRCh38 11 56641953 56641953 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.487G>T p.Ala163Ser p.A163S ENST00000302981 1/1 223 150 73 203 202 1 strelka-varscan-mutect OR5AP2,missense_variant,p.Ala164Ser,ENST00000544374,;OR5AP2,missense_variant,p.Ala163Ser,ENST00000302981,NM_001002925.1; A ENST00000302981 Transcript missense_variant 487/951 487/951 163/316 A/S Gcc/Tcc 1 -1 OR5AP2 HGNC HGNC:15258 protein_coding YES CCDS31534.1 ENSP00000303111 Q8NGF4 UPI0000061EE6 NM_001002925.1 tolerated(0.34) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF151,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1344453420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 56641953 56641953 C A 1 0 0 0 0 1 0 0 0 11216 797 28 2 2 OR5AP2 11 56641953 Missense_Mutation SNP C C3N-00549_T 504469 56641953 78444669 238 15262 OR10W1 0 . GRCh38 11 58267185 58267185 + Missense_Mutation SNP C C A rs200070425 C3N-00549_T C3N-00549_N C C c.674G>T p.Arg225Leu p.R225L ENST00000395079 1/1 147 85 62 128 128 0 strelka-varscan-mutect OR10W1,missense_variant,p.Arg225Leu,ENST00000395079,NM_207374.3; A ENST00000395079 Transcript missense_variant 1076/1469 674/918 225/305 R/L cGc/cTc rs200070425,COSM290329 1 -1 OR10W1 HGNC HGNC:15139 protein_coding YES CCDS7968.1 ENSP00000378516 Q8NGF6 UPI000004B229 NM_207374.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF165,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs200070425 . 0 203 0 6 0 0 0 0 -20 0.9997528 1 1 1 0 A 3 1 50 58267185 58267185 C A 1 0 0 0 0 1 0 0 0 10998 768 27 1 1 OR10W1 11 58267185 Missense_Mutation SNP C C3N-00549_T 1625232 58267185 76819437 239 15263 OR5B21 0 . GRCh38 11 58508034 58508034 + Silent SNP G G A C3N-00549_T C3N-00549_N G G c.72C>T p.= p.P24P ENST00000360374 1/1 200 114 86 151 151 0 strelka-varscan-mutect OR5B21,synonymous_variant,p.=,ENST00000360374,NM_001005218.1;RP11-655C2.3,upstream_gene_variant,,ENST00000531715,;RP11-655C2.3,upstream_gene_variant,,ENST00000528978,;RP11-655C2.3,upstream_gene_variant,,ENST00000527054,; A ENST00000360374 Transcript synonymous_variant 72/931 72/930 24/309 P ccC/ccT COSM3953472 1 -1 OR5B21 HGNC HGNC:19616 protein_coding YES CCDS31552.1 ENSP00000353537 A6NL26 UPI000015FCAA NM_001005218.1 1/1 hmmpanther:PTHR26452:SF329,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 58508034 58508034 G A 1 0 0 0 0 0 0 0 1 11222 1219 43 3 3 OR5B21 11 58508034 Silent SNP G C3N-00549_T 240849 58508034 76578588 240 15264 TCN1 0 . GRCh38 11 59852978 59852978 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1299C>A p.Tyr433Ter p.Y433* ENST00000257264 9/9 564 355 209 448 448 0 strelka-varscan-mutect TCN1,stop_gained,p.Tyr433Ter,ENST00000257264,NM_001062.3;TCN1,downstream_gene_variant,,ENST00000532419,;TCN1,downstream_gene_variant,,ENST00000534531,;TCN1,non_coding_transcript_exon_variant,,ENST00000529251,; T ENST00000257264 Transcript stop_gained 1404/1582 1299/1302 433/433 Y/* taC/taA 1 -1 TCN1 HGNC HGNC:11652 protein_coding YES CCDS7978.1 ENSP00000257264 P20061 UPI000013CF55 NM_001062.3 9/9 hmmpanther:PTHR10559,hmmpanther:PTHR10559:SF13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 59852978 59852978 G T 1 0 0 0 0 0 1 0 0 16113 1024 36 2 2 TCN1 11 59852978 Nonsense_Mutation SNP G C3N-00549_T 1344944 59852978 75233644 241 15265 SLC22A12 0 . GRCh38 11 64599748 64599748 + Silent SNP C C T novel C3N-00549_T C3N-00549_N C C c.1143C>T p.= p.L381L ENST00000377574 7/10 460 274 186 363 363 0 strelka-varscan-mutect SLC22A12,synonymous_variant,p.=,ENST00000377574,NM_144585.3;SLC22A12,synonymous_variant,p.=,ENST00000377572,NM_001276327.1;SLC22A12,synonymous_variant,p.=,ENST00000377567,;SLC22A12,synonymous_variant,p.=,ENST00000473690,NM_153378.2;SLC22A12,synonymous_variant,p.=,ENST00000336464,NM_001276326.1; T ENST00000377574 Transcript synonymous_variant 1890/3206 1143/1662 381/553 L ctC/ctT 1 1 SLC22A12 HGNC HGNC:17989 protein_coding YES CCDS8075.1 ENSP00000366797 Q96S37 UPI0000040C17 NM_144585.3 7/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF205,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 64599748 64599748 C T 1 0 0 0 0 0 0 0 1 14709 842 30 3 3 SLC22A12 11 64599748 Silent SNP C C3N-00549_T 4746770 64599748 70486874 242 15266 NRXN2 0 . GRCh38 11 64690405 64690405 + Missense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.850G>T p.Gly284Cys p.G284C ENST00000265459 5/23 320 206 114 194 194 0 strelka-varscan-mutect NRXN2,missense_variant,p.Gly284Cys,ENST00000265459,NM_015080.3;NRXN2,missense_variant,p.Gly284Cys,ENST00000409571,;NRXN2,missense_variant,p.Gly284Cys,ENST00000377551,;NRXN2,missense_variant,p.Gly55Cys,ENST00000442300,;NRXN2,missense_variant,p.Gly74Cys,ENST00000437746,;NRXN2,missense_variant,p.Gly45Cys,ENST00000417749,;NRXN2,intron_variant,,ENST00000377559,NM_138732.2;NRXN2,intron_variant,,ENST00000466324,; A ENST00000265459 Transcript missense_variant,splice_region_variant 1312/6621 850/5139 284/1712 G/C Ggc/Tgc COSM4977317 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 deleterious(0) 5/23 1 MODERATE 1 SNV 5 1 1 PASS rs1159935878 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 64690405 64690405 C A 1 0 0 0 0 1 0 0 0 10725 695 24 2 2 NRXN2 11 64690405 Missense_Mutation SNP C C3N-00549_T 90657 64690405 70396217 243 15267 EIF1AD 0 . GRCh38 11 65999574 65999574 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.298G>T p.Gly100Trp p.G100W ENST00000312234 4/6 157 95 62 149 149 0 strelka-varscan-mutect EIF1AD,missense_variant,p.Gly100Trp,ENST00000312234,NM_001242482.1,NM_032325.3,NM_001242481.1,NM_001242483.1;EIF1AD,missense_variant,p.Gly100Trp,ENST00000526451,NM_001242486.1,NM_001242484.1,NM_001242485.1;EIF1AD,missense_variant,p.Gly100Trp,ENST00000533544,;EIF1AD,missense_variant,p.Gly100Trp,ENST00000527249,;EIF1AD,missense_variant,p.Gly100Trp,ENST00000529964,;EIF1AD,missense_variant,p.Gly48Trp,ENST00000525767,;EIF1AD,missense_variant,p.Gly100Trp,ENST00000532707,;EIF1AD,missense_variant,p.Gly100Trp,ENST00000530462,;BANF1,upstream_gene_variant,,ENST00000312175,NM_001143985.1,NM_003860.3;BANF1,upstream_gene_variant,,ENST00000533166,;BANF1,upstream_gene_variant,,ENST00000445560,;BANF1,upstream_gene_variant,,ENST00000527348,;EIF1AD,downstream_gene_variant,,ENST00000527051,;BANF1,upstream_gene_variant,,ENST00000530204,;BANF1,upstream_gene_variant,,ENST00000524628,;BANF1,upstream_gene_variant,,ENST00000528648,;BANF1,upstream_gene_variant,,ENST00000524663,;EIF1AD,3_prime_UTR_variant,,ENST00000529973,;EIF1AD,downstream_gene_variant,,ENST00000526449,; A ENST00000312234 Transcript missense_variant 633/2887 298/498 100/165 G/W Ggg/Tgg 1 -1 EIF1AD HGNC HGNC:28147 protein_coding YES CCDS8124.1 ENSP00000309175 Q8N9N8 A0A024R5B9 UPI0000070E9C NM_001242482.1,NM_032325.3,NM_001242481.1,NM_001242483.1 deleterious(0) 4/6 hmmpanther:PTHR21641,Gene3D:2.40.50.140,SMART_domains:SM00652,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS rs960732747 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 65999574 65999574 C A 1 0 0 0 0 1 0 0 0 4827 623 22 2 2 EIF1AD 11 65999574 Missense_Mutation SNP C C3N-00549_T 1309169 65999574 69087048 244 15268 SLC29A2 0 . GRCh38 11 66367527 66367527 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.670G>T p.Ala224Ser p.A224S ENST00000357440 7/12 388 272 116 285 285 0 strelka-varscan-mutect SLC29A2,missense_variant,p.Ala224Ser,ENST00000357440,NM_001532.2;SLC29A2,missense_variant,p.Ala224Ser,ENST00000546034,;SLC29A2,missense_variant,p.Ala224Ser,ENST00000544554,NM_001300868.1;SLC29A2,missense_variant,p.Ala224Ser,ENST00000619145,;SLC29A2,missense_variant,p.Ala224Ser,ENST00000311161,NM_001300869.1;RP11-867G23.8,downstream_gene_variant,,ENST00000580881,;RP11-867G23.8,downstream_gene_variant,,ENST00000531602,;SLC29A2,missense_variant,p.Ala224Ser,ENST00000540386,;SLC29A2,missense_variant,p.Gly201Val,ENST00000541567,; A ENST00000357440 Transcript missense_variant 899/2514 670/1371 224/456 A/S Gcc/Tcc 1 -1 SLC29A2 HGNC HGNC:11004 protein_coding YES CCDS8137.1 ENSP00000350024 Q14542 UPI000013F0E7 NM_001532.2 tolerated(0.7) 7/12 hmmpanther:PTHR10332:SF8,hmmpanther:PTHR10332,TIGRFAM_domain:TIGR00939,Pfam_domain:PF01733,PIRSF_domain:PIRSF016379,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs1348381815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 66367527 66367527 C A 1 0 0 0 0 1 0 0 0 14805 739 26 2 2 SLC29A2 11 66367527 Missense_Mutation SNP C C3N-00549_T 367953 66367527 68719095 245 15269 GPR152 0 . GRCh38 11 67452231 67452231 + Missense_Mutation SNP G G A rs374063857 C3N-00549_T C3N-00549_N G G c.494C>T p.Pro165Leu p.P165L ENST00000312457 1/1 369 209 160 260 260 0 strelka-varscan-mutect GPR152,missense_variant,p.Pro165Leu,ENST00000312457,NM_206997.1;CABP4,upstream_gene_variant,,ENST00000325656,NM_145200.3;CABP4,upstream_gene_variant,,ENST00000438189,NM_001300896.1,NM_001300895.1;CABP4,upstream_gene_variant,,ENST00000542025,;CABP4,upstream_gene_variant,,ENST00000538060,;CABP4,upstream_gene_variant,,ENST00000542233,;CABP4,upstream_gene_variant,,ENST00000545040,;CABP4,upstream_gene_variant,,ENST00000545777,; A ENST00000312457 Transcript missense_variant 499/1429 494/1413 165/470 P/L cCc/cTc rs374063857 1 -1 GPR152 HGNC HGNC:23622 protein_coding YES CCDS8165.1 ENSP00000310255 Q8TDT2 A0A0I9RJ67 UPI000003B364 NM_206997.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF1,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS rs374063857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 67452231 67452231 G A 1 0 0 0 0 1 0 0 0 6544 1232 43 3 3 GPR152 11 67452231 Missense_Mutation SNP G C3N-00549_T 1084704 67452231 67634391 246 15270 MYEOV 0 . GRCh38 11 69296193 69296193 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.743C>A p.Ser248Tyr p.S248Y ENST00000308946 3/3 140 84 56 87 86 1 strelka-varscan-mutect MYEOV,missense_variant,p.Ser190Tyr,ENST00000535407,NM_001300923.1,NM_001300924.1,NM_001293294.1,NM_001293296.1;MYEOV,missense_variant,p.Ser248Tyr,ENST00000308946,NM_138768.3;MYEOV,missense_variant,p.Ser248Tyr,ENST00000441339,NM_001293291.1;MYEOV,intron_variant,,ENST00000544008,;MYEOV,downstream_gene_variant,,ENST00000539691,;MYEOV,downstream_gene_variant,,ENST00000540760,;MYEOV,downstream_gene_variant,,ENST00000535597,;MYEOV,non_coding_transcript_exon_variant,,ENST00000535653,;MYEOV,upstream_gene_variant,,ENST00000544781,; A ENST00000308946 Transcript missense_variant 1193/2287 743/942 248/313 S/Y tCc/tAc 1 1 MYEOV HGNC HGNC:7563 protein_coding YES CCDS8190.1 ENSP00000308330 Q96EZ4 A0A024R5F1 UPI0000039DE8 NM_138768.3 deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 1 1 PASS rs1246868067 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 69296193 69296193 C A 1 0 0 0 0 1 0 0 0 10026 855 30 2 2 MYEOV 11 69296193 Missense_Mutation SNP C C3N-00549_T 1843962 69296193 65790429 247 15271 FGF3 0 . GRCh38 11 69818836 69818836 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.98G>A p.Gly33Asp p.G33D ENST00000334134 1/3 278 161 117 332 332 0 strelka-varscan-mutect FGF3,missense_variant,p.Gly33Asp,ENST00000334134,NM_005247.2; T ENST00000334134 Transcript missense_variant 189/892 98/720 33/239 G/D gGc/gAc 1 -1 FGF3 HGNC HGNC:3681 protein_coding YES CCDS8195.1 ENSP00000334122 P11487 UPI0000040661 NM_005247.2 deleterious(0.04) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11486:SF26,hmmpanther:PTHR11486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 69818836 69818836 C T 1 0 0 0 0 1 0 0 0 5717 739 26 3 3 FGF3 11 69818836 Missense_Mutation SNP C C3N-00549_T 522643 69818836 65267786 248 15272 ANO1 0 . GRCh38 11 70131999 70131999 + Nonsense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.1178C>G p.Ser393Ter p.S393* ENST00000355303 11/26 268 166 102 182 182 0 strelka-varscan-mutect ANO1,stop_gained,p.Ser393Ter,ENST00000355303,NM_018043.5;ANO1,stop_gained,p.Ser128Ter,ENST00000531349,;ANO1,stop_gained,p.Ser277Ter,ENST00000530676,;ANO1,stop_gained,p.Ser365Ter,ENST00000316296,;ANO1,stop_gained,p.Ser258Ter,ENST00000530480,;RP11-805J14.3,intron_variant,,ENST00000530525,; G ENST00000355303 Transcript stop_gained 1483/4790 1178/2961 393/986 S/* tCa/tGa 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 11/26 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 50 70131999 70131999 C G 1 0 0 0 0 0 1 0 0 802 838 29 4 4 ANO1 11 70131999 Nonsense_Mutation SNP C C3N-00549_T 313163 70131999 64954623 249 15273 GRM5 0 . GRCh38 11 88590716 88590716 + Missense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.1575G>T p.Lys525Asn p.K525N ENST00000305447 6/9 169 102 67 134 134 0 strelka-varscan-mutect GRM5,missense_variant,p.Lys525Asn,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Lys525Asn,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Lys525Asn,ENST00000305432,; A ENST00000305447 Transcript missense_variant 1725/4571 1575/3639 525/1212 K/N aaG/aaT COSM1357621,COSM1357622 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0.01) 6/9 Pfam_domain:PF07562,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 88590716 88590716 C A 1 0 0 0 0 1 0 0 0 6682 680 24 2 2 GRM5 11 88590716 Missense_Mutation SNP C C3N-00549_T 18458717 88590716 46495906 250 15274 TRIM77 0 . GRCh38 11 89715908 89715908 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.780G>T p.= p.L260L ENST00000398290 5/6 121 71 50 88 88 0 strelka-varscan-mutect TRIM77,synonymous_variant,p.=,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,synonymous_variant,p.=,ENST00000534392,; T ENST00000398290 Transcript synonymous_variant 780/1353 780/1353 260/450 L ctG/ctT 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 5/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 89715908 89715908 G T 1 0 0 0 0 0 0 0 1 17044 1335 47 2 2 TRIM77 11 89715908 Silent SNP G C3N-00549_T 1125192 89715908 45370714 251 15275 TRIM64 0 . GRCh38 11 89971255 89971255 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.758G>A p.Arg253Lys p.R253K ENST00000533122 4/6 83 55 28 52 52 0 strelka-varscan-mutect TRIM64,missense_variant,p.Arg253Lys,ENST00000533122,NM_001136486.1; A ENST00000533122 Transcript missense_variant,splice_region_variant 760/2691 758/1350 253/449 R/K aGg/aAg 1 1 TRIM64 HGNC HGNC:14663 protein_coding YES CCDS73363.1 ENSP00000483764 A6NGJ6 UPI0001662601 NM_001136486.1 tolerated(0.15) 4/6 hmmpanther:PTHR24103:SF354,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS . . 173 35 0 0 0 0 0 0 -20 1 0 1 1 0 A 3 1 50 89971255 89971255 G A 1 0 0 0 0 1 0 0 0 17031 1014 35 3 3 TRIM64 11 89971255 Missense_Mutation SNP G C3N-00549_T 255347 89971255 45115367 252 15276 CNTN5 0 . GRCh38 11 99916116 99916116 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.640G>T p.Val214Phe p.V214F ENST00000524871 7/25 187 123 64 178 178 0 strelka-varscan-mutect CNTN5,missense_variant,p.Val214Phe,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Val198Phe,ENST00000279463,;CNTN5,missense_variant,p.Val136Phe,ENST00000619298,;CNTN5,missense_variant,p.Val214Phe,ENST00000527185,NM_001243271.1;CNTN5,missense_variant,p.Val214Phe,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Val140Phe,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; T ENST00000524871 Transcript missense_variant 930/6258 640/3303 214/1100 V/F Gtt/Ttt 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 deleterious(0) 7/25 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs953993946 . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 T 3 4 50 99916116 99916116 G T 1 0 0 0 0 1 0 0 0 3425 1145 40 1 1 CNTN5 11 99916116 Missense_Mutation SNP G C3N-00549_T 9944861 99916116 35170506 253 15277 CNTN5 0 . GRCh38 11 100350808 100350808 + Missense_Mutation SNP G G C rs781672395 C3N-00549_T C3N-00549_N G G c.3137G>C p.Arg1046Pro p.R1046P ENST00000524871 24/25 109 74 35 106 106 0 strelka-varscan-mutect CNTN5,missense_variant,p.Arg1046Pro,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Arg1030Pro,ENST00000279463,;CNTN5,missense_variant,p.Arg968Pro,ENST00000619298,;CNTN5,missense_variant,p.Arg1046Pro,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Arg972Pro,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,; C ENST00000524871 Transcript missense_variant 3427/6258 3137/3303 1046/1100 R/P cGa/cCa rs781672395 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 deleterious(0) 24/25 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs781672395 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 100350808 100350808 G C 1 0 0 0 0 1 0 0 0 3425 1058 37 4 4 CNTN5 11 100350808 Missense_Mutation SNP G C3N-00549_T 434692 100350808 34735814 254 15278 DYNC2H1 0 . GRCh38 11 103158977 103158977 + Missense_Mutation SNP A A T rs766791709 C3N-00549_T C3N-00549_N A A c.4328A>T p.Gln1443Leu p.Q1443L ENST00000398093 28/90 198 131 67 219 218 1 strelka-varscan-mutect DYNC2H1,missense_variant,p.Gln1443Leu,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Gln1443Leu,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,; T ENST00000398093 Transcript missense_variant 4328/12945 4328/12945 1443/4314 Q/L cAg/cTg rs766791709 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0) 28/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF08393 MODERATE 1 SNV 5 1 PASS rs766791709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 103158977 103158977 A T 1 0 0 0 0 1 0 0 0 4670 188 7 4 4 DYNC2H1 11 103158977 Missense_Mutation SNP A C3N-00549_T 2808169 103158977 31927645 255 15279 ALKBH8 0 . GRCh38 11 107532390 107532390 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.797A>G p.Lys266Arg p.K266R ENST00000417449 8/12 192 130 62 143 143 0 strelka-varscan-mutect ALKBH8,missense_variant,p.Lys263Arg,ENST00000428149,NM_138775.2;ALKBH8,missense_variant,p.Lys263Arg,ENST00000389568,;ALKBH8,missense_variant,p.Lys266Arg,ENST00000417449,NM_001301010.1;ALKBH8,intron_variant,,ENST00000429370,;ALKBH8,stop_retained_variant,p.=,ENST00000260318,;ALKBH8,3_prime_UTR_variant,,ENST00000393100,; C ENST00000417449 Transcript missense_variant 907/2114 797/2004 266/667 K/R aAg/aGg 1 -1 ALKBH8 HGNC HGNC:25189 protein_coding YES CCDS73376.1 ENSP00000397673 Q96BT7 UPI00017A6D55 NM_001301010.1 tolerated(0.48) 8/12 PROSITE_profiles:PS51471,hmmpanther:PTHR13069,hmmpanther:PTHR13069:SF28,Gene3D:3i3qA00,Pfam_domain:PF13532,Superfamily_domains:SSF51197 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 107532390 107532390 T C 1 0 0 0 0 1 0 0 0 633 1609 56 5 5 ALKBH8 11 107532390 Missense_Mutation SNP T C3N-00549_T 4373413 107532390 27554232 256 15280 UBE4A 0 . GRCh38 11 118372534 118372534 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.589C>T p.Pro197Ser p.P197S ENST00000431736 6/20 96 53 43 128 127 1 strelka-varscan-mutect UBE4A,missense_variant,p.Pro197Ser,ENST00000252108,NM_001204077.1;UBE4A,missense_variant,p.Pro197Ser,ENST00000431736,NM_004788.3; T ENST00000431736 Transcript missense_variant 661/6061 589/3222 197/1073 P/S Ccc/Tcc 1 1 UBE4A HGNC HGNC:12499 protein_coding YES CCDS8396.1 ENSP00000387362 Q14139 UPI000013CD3F NM_004788.3 tolerated(0.94) 6/20 hmmpanther:PTHR13931:SF2,hmmpanther:PTHR13931 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 118372534 118372534 C T 1 0 0 0 0 1 0 0 0 17406 507 18 3 3 UBE4A 11 118372534 Missense_Mutation SNP C C3N-00549_T 10840144 118372534 16714088 257 15281 TECTA 0 . GRCh38 11 121125570 121125570 + Missense_Mutation SNP G G A rs760011660 C3N-00549_T C3N-00549_N G G c.1472G>A p.Arg491His p.R491H ENST00000392793 8/24 238 133 105 163 163 0 strelka-varscan-mutect TECTA,missense_variant,p.Arg491His,ENST00000392793,;TECTA,missense_variant,p.Arg491His,ENST00000264037,NM_005422.2; A ENST00000392793 Transcript missense_variant 1743/7426 1472/6468 491/2155 R/H cGt/cAt rs760011660,COSM273725 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D deleterious(0.01) 8/24 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF235,hmmpanther:PTHR11339 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs760011660 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 121125570 121125570 G A 1 0 0 0 0 1 0 0 0 16158 1145 40 1 1 TECTA 11 121125570 Missense_Mutation SNP G C3N-00549_T 2753036 121125570 13961052 258 15282 SPATA19 0 . GRCh38 11 133842523 133842523 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.399G>T p.Glu133Asp p.E133D ENST00000299140 5/7 187 131 56 152 152 0 strelka-varscan-mutect SPATA19,missense_variant,p.Glu133Asp,ENST00000299140,NM_001291992.1,NM_174927.2;SPATA19,missense_variant,p.Glu133Asp,ENST00000532889,; A ENST00000299140 Transcript missense_variant 454/861 399/504 133/167 E/D gaG/gaT 1 -1 SPATA19 HGNC HGNC:30614 protein_coding YES CCDS8493.1 ENSP00000299140 Q7Z5L4 A0A140VKB6 UPI000007021D NM_001291992.1,NM_174927.2 tolerated(1) 5/7 hmmpanther:PTHR36468,Pfam_domain:PF15212 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 133842523 133842523 C A 1 0 0 0 0 1 0 0 0 15334 680 24 2 2 SPATA19 11 133842523 Missense_Mutation SNP C C3N-00549_T 12716953 133842523 1244099 259 15283 TSPAN9 0 . GRCh38 12 3281905 3281905 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.736G>T p.Val246Leu p.V246L ENST00000407263 6/6 539 360 179 323 322 1 strelka-varscan-mutect TSPAN9,missense_variant,p.Val246Leu,ENST00000407263,;TSPAN9,intron_variant,,ENST00000011898,NM_006675.4;TSPAN9,intron_variant,,ENST00000537971,NM_001168320.1;TSPAN9,downstream_gene_variant,,ENST00000492305,;TSPAN9,downstream_gene_variant,,ENST00000431374,;TSPAN9,downstream_gene_variant,,ENST00000444315,; T ENST00000407263 Transcript missense_variant 755/958 736/816 246/271 V/L Gta/Tta 1 1 TSPAN9 HGNC HGNC:21640 protein_coding ENSP00000384488 B5MD23 UPI0001611390 6/6 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 3281905 3281905 G T 1 0 0 0 0 1 0 0 0 17159 1261 44 2 2 TSPAN9 12 3281905 Missense_Mutation SNP G C3N-00549_T 3281905 129993404 260 15284 RAD51AP1 0 . GRCh38 12 4541927 4541927 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.61A>T p.Ser21Cys p.S21C ENST00000228843 2/10 83 63 20 60 60 0 strelka-varscan-mutect RAD51AP1,missense_variant,p.Ser21Cys,ENST00000228843,NM_001130862.1;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000352618,NM_006479.4;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000544927,;RAD51AP1,missense_variant,p.Ser16Cys,ENST00000536117,;C12orf4,upstream_gene_variant,,ENST00000261250,NM_020374.3,NM_001304811.1;C12orf4,upstream_gene_variant,,ENST00000545746,;C12orf4,upstream_gene_variant,,ENST00000541014,;C12orf4,upstream_gene_variant,,ENST00000542080,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000442992,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000535558,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000398012,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000536886,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000536346,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000538817,;RAD51AP1,missense_variant,p.Ser21Cys,ENST00000544110,;RAD51AP1,missense_variant,p.Ser15Cys,ENST00000544173,;RAD51AP1,upstream_gene_variant,,ENST00000544029,;C12orf4,upstream_gene_variant,,ENST00000544697,;C12orf4,upstream_gene_variant,,ENST00000535030,; T ENST00000228843 Transcript missense_variant 111/2163 61/1059 21/352 S/C Agt/Tgt 1 1 RAD51AP1 HGNC HGNC:16956 protein_coding YES CCDS44805.1 ENSP00000228843 Q96B01 UPI000006DAE6 NM_001130862.1 deleterious(0.01) 2/10 hmmpanther:PTHR15361,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 4541927 4541927 A T 1 0 0 0 0 1 0 0 0 13147 188 7 4 4 RAD51AP1 12 4541927 Missense_Mutation SNP A C3N-00549_T 1260022 4541927 128733382 261 15285 CD163L1 0 . GRCh38 12 7379278 7379278 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.2101A>T p.Arg701Trp p.R701W ENST00000416109 9/20 161 70 91 119 119 0 strelka-varscan-mutect CD163L1,missense_variant,p.Arg691Trp,ENST00000313599,NM_174941.5;CD163L1,missense_variant,p.Arg701Trp,ENST00000416109,NM_001297650.1;CD163L1,upstream_gene_variant,,ENST00000544331,; A ENST00000416109 Transcript missense_variant 2120/4603 2101/4392 701/1463 R/W Agg/Tgg 1 -1 CD163L1 HGNC HGNC:30375 protein_coding YES CCDS73434.1 ENSP00000393474 Q9NR16 UPI0001AE6A76 NM_001297650.1 deleterious(0) 9/20 PROSITE_profiles:PS50287,Gene3D:3.10.250.10,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 7379278 7379278 T A 1 0 0 0 0 1 0 0 0 2671 1550 54 4 4 CD163L1 12 7379278 Missense_Mutation SNP T C3N-00549_T 2837351 7379278 125896031 262 15286 PZP 0 . GRCh38 12 9165365 9165365 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2261C>A p.Ser754Ter p.S754* ENST00000261336 19/36 219 146 73 141 141 0 strelka-varscan-mutect PZP,stop_gained,p.Ser754Ter,ENST00000261336,NM_002864.2;PZP,splice_region_variant,,ENST00000539983,;PZP,splice_region_variant,,ENST00000546197,;PZP,splice_region_variant,,ENST00000543108,;PZP,splice_region_variant,,ENST00000540995,;PZP,downstream_gene_variant,,ENST00000546116,;PZP,splice_region_variant,,ENST00000535230,; T ENST00000261336 Transcript stop_gained,splice_region_variant 2290/4610 2261/4449 754/1482 S/* tCa/tAa 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 19/36 Pfam_domain:PF00207,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92,SMART_domains:SM01360 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 9165365 9165365 G T 1 0 0 0 0 0 1 0 0 13025 1304 45 2 2 PZP 12 9165365 Nonsense_Mutation SNP G C3N-00549_T 1786087 9165365 124109944 263 15287 CASC1 0 . GRCh38 12 25149755 25149755 + Missense_Mutation SNP A A C novel C3N-00549_T C3N-00549_N A A c.458T>G p.Phe153Cys p.F153C ENST00000395987 7/16 118 62 56 83 83 0 strelka-varscan-mutect CASC1,missense_variant,p.Phe211Cys,ENST00000354189,NM_001082972.1;CASC1,missense_variant,p.Phe107Cys,ENST00000395990,NM_001204102.1;CASC1,missense_variant,p.Phe153Cys,ENST00000395987,NM_018272.3;CASC1,missense_variant,p.Phe147Cys,ENST00000320267,NM_001082973.1;CASC1,missense_variant,p.Phe88Cys,ENST00000545133,NM_001204101.1;CASC1,missense_variant,p.Phe118Cys,ENST00000556006,;CASC1,downstream_gene_variant,,ENST00000554347,;CASC1,non_coding_transcript_exon_variant,,ENST00000557684,;CASC1,upstream_gene_variant,,ENST00000555554,;CASC1,3_prime_UTR_variant,,ENST00000554533,NM_001319977.1;CASC1,non_coding_transcript_exon_variant,,ENST00000556547,;CASC1,downstream_gene_variant,,ENST00000556467,;CASC1,downstream_gene_variant,,ENST00000555240,; C ENST00000395987 Transcript missense_variant 524/2363 458/2169 153/722 F/C tTt/tGt 1 -1 CASC1 HGNC HGNC:29599 protein_coding YES CCDS31759.2 ENSP00000379310 F8W8F9 UPI00001FB7A4 NM_018272.3 deleterious(0.02) 7/16 Pfam_domain:PF15927,hmmpanther:PTHR20929 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 25149755 25149755 A C 1 0 0 0 0 1 0 0 0 2359 14 1 5 5 CASC1 12 25149755 Missense_Mutation SNP A C3N-00549_T 15984390 25149755 108125554 264 15288 BHLHE41 0 . GRCh38 12 26124141 26124141 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.165A>T p.Lys55Asn p.K55N ENST00000242728 3/5 218 144 74 123 123 0 strelka-varscan-mutect BHLHE41,missense_variant,p.Lys55Asn,ENST00000242728,NM_030762.2;SSPN,intron_variant,,ENST00000538142,;RP11-283G6.3,downstream_gene_variant,,ENST00000545819,;RP11-283G6.3,downstream_gene_variant,,ENST00000535914,;SSPN,intron_variant,,ENST00000534829,;BHLHE41,non_coding_transcript_exon_variant,,ENST00000541271,;BHLHE41,upstream_gene_variant,,ENST00000394326,; A ENST00000242728 Transcript missense_variant 513/3837 165/1449 55/482 K/N aaA/aaT 1 -1 BHLHE41 HGNC HGNC:16617 protein_coding YES CCDS8706.1 ENSP00000242728 Q9C0J9 A0A024RAV8 UPI0000052B52 NM_030762.2 deleterious(0) 3/5 PROSITE_profiles:PS50888,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF76,Gene3D:4.10.280.10,Pfam_domain:PF00010,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 26124141 26124141 T A 1 0 0 0 0 1 0 0 0 1572 1838 64 4 4 BHLHE41 12 26124141 Missense_Mutation SNP T C3N-00549_T 974386 26124141 107151168 265 15289 PKP2 0 . GRCh38 12 32896681 32896681 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.51G>T p.= p.L17L ENST00000070846 1/14 129 73 56 86 86 0 strelka-varscan-mutect PKP2,synonymous_variant,p.=,ENST00000340811,NM_001005242.2;PKP2,synonymous_variant,p.=,ENST00000070846,NM_004572.3;PKP2,upstream_gene_variant,,ENST00000546741,; A ENST00000070846 Transcript synonymous_variant 76/4241 51/2646 17/881 L ctG/ctT 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 1/14 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25 LOW 1 SNV 1 1 PASS rs1251253044 . 0 205 3 2 0 0 0 0 -20 0.9999992 1 1 1 0 A 2 1 50 32896681 32896681 C A 1 0 0 0 0 0 0 0 1 12081 581 21 2 2 PKP2 12 32896681 Silent SNP C C3N-00549_T 6772540 32896681 100378628 266 15290 PDZRN4 0 . GRCh38 12 41188767 41188767 + Missense_Mutation SNP C C G C3N-00549_T C3N-00549_N C C c.312C>G p.Cys104Trp p.C104W ENST00000402685 1/10 45 25 20 50 50 0 strelka-varscan-mutect PDZRN4,missense_variant,p.Cys104Trp,ENST00000402685,NM_001164595.1; G ENST00000402685 Transcript missense_variant 320/3347 312/3111 104/1036 C/W tgC/tgG COSM4652238 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 deleterious_low_confidence(0) 1/10 Gene3D:1k2fA02,Superfamily_domains:SSF49599 1 MODERATE 1 SNV 2 1 1 PASS rs954361223 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 41188767 41188767 C G 1 0 0 0 0 1 0 0 0 11798 776 27 4 4 PDZRN4 12 41188767 Missense_Mutation SNP C C3N-00549_T 8292086 41188767 92086542 267 15291 ADAMTS20 0 . GRCh38 12 43551255 43551255 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.107C>G p.Thr36Arg p.T36R ENST00000389420 2/39 96 49 47 81 81 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Thr36Arg,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Thr36Arg,ENST00000395541,;ADAMTS20,missense_variant,p.Thr36Arg,ENST00000553158,; C ENST00000389420 Transcript missense_variant 107/6076 107/5733 36/1910 T/R aCa/aGa 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(0.07) 2/39 MODERATE 1 SNV 1 1 PASS rs1295649822 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 43551255 43551255 G C 1 0 0 0 0 1 0 0 0 310 1377 48 4 4 ADAMTS20 12 43551255 Missense_Mutation SNP G C3N-00549_T 2362488 43551255 89724054 268 15292 KRT1 0 . GRCh38 12 52675279 52675279 + Nonsense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1849G>T p.Gly617Ter p.G617* ENST00000252244 9/9 706 364 342 543 543 0 strelka-varscan-mutect KRT1,stop_gained,p.Gly617Ter,ENST00000252244,NM_006121.3;KRT1,downstream_gene_variant,,ENST00000548765,; A ENST00000252244 Transcript stop_gained 1908/2451 1849/1935 617/644 G/* Gga/Tga 1 -1 KRT1 HGNC HGNC:6412 protein_coding YES CCDS8836.1 ENSP00000252244 P04264 UPI000013CD4D NM_006121.3 9/9 Low_complexity_(Seg):seg,Pfam_domain:PF16210 HIGH 1 SNV 1 1 PASS rs1336433142 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 52675279 52675279 C A 1 0 0 0 0 0 1 0 0 8329 632 22 2 2 KRT1 12 52675279 Nonsense_Mutation SNP C C3N-00549_T 9124024 52675279 80600030 269 15293 RARG 0 . GRCh38 12 53215387 53215387 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.381C>T p.= p.H127H ENST00000425354 5/10 321 213 108 302 302 0 strelka-varscan-mutect RARG,synonymous_variant,p.=,ENST00000425354,NM_000966.5;RARG,synonymous_variant,p.=,ENST00000394426,NM_001243730.1,NM_001243731.1;RARG,synonymous_variant,p.=,ENST00000338561,NM_001042728.2;RARG,synonymous_variant,p.=,ENST00000543726,NM_001243732.1;RARG,non_coding_transcript_exon_variant,,ENST00000543762,;RARG,non_coding_transcript_exon_variant,,ENST00000550265,;RARG,non_coding_transcript_exon_variant,,ENST00000548284,;RARG,upstream_gene_variant,,ENST00000551580,;RARG,upstream_gene_variant,,ENST00000548317,; A ENST00000425354 Transcript synonymous_variant 869/2959 381/1365 127/454 H caC/caT 1 -1 RARG HGNC HGNC:9866 protein_coding YES CCDS8850.1 ENSP00000388510 P13631 A8K3H3 UPI000000105D NM_000966.5 5/10 PROSITE_profiles:PS51030,hmmpanther:PTHR24082:SF116,hmmpanther:PTHR24082,Gene3D:3.30.50.10,Pfam_domain:PF00105,SMART_domains:SM00399,Superfamily_domains:SSF57716 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 53215387 53215387 G A 1 0 0 0 0 0 0 0 1 13213 1252 44 3 3 RARG 12 53215387 Silent SNP G C3N-00549_T 540108 53215387 80059922 270 15294 HOXC4 0 . GRCh38 12 54054155 54054155 + Missense_Mutation SNP C C G rs751434557 C3N-00549_T C3N-00549_N C C c.233C>G p.Ser78Trp p.S78W ENST00000430889 1/2 491 243 248 360 360 0 strelka-varscan-mutect HOXC4,missense_variant,p.Ser78Trp,ENST00000430889,NM_153633.2;HOXC4,missense_variant,p.Ser78Trp,ENST00000303406,NM_014620.5;FLJ12825,upstream_gene_variant,,ENST00000515617,;HOXC4,downstream_gene_variant,,ENST00000507650,; G ENST00000430889 Transcript missense_variant 279/1666 233/795 78/264 S/W tCg/tGg rs751434557 1 1 HOXC4 HGNC HGNC:5126 protein_coding YES CCDS8873.1 ENSP00000399808 P09017 A0A024RB51 UPI000013E89C NM_153633.2 tolerated(0.1) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF161 MODERATE 1 SNV 1 1 PASS rs751434557 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 54054155 54054155 C G 1 0 0 0 0 1 0 0 0 7207 893 31 4 4 HOXC4 12 54054155 Missense_Mutation SNP C C3N-00549_T 838768 54054155 79221154 271 15295 OR6C4 0 . GRCh38 12 55551412 55551412 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.186G>T p.= p.R62R ENST00000394256 1/1 156 88 68 183 183 0 strelka-varscan-mutect OR6C4,synonymous_variant,p.=,ENST00000394256,NM_001005494.1;RP11-110A12.2,intron_variant,,ENST00000556750,;RP11-110A12.2,intron_variant,,ENST00000555138,; T ENST00000394256 Transcript synonymous_variant 214/1046 186/930 62/309 R cgG/cgT 1 1 OR6C4 HGNC HGNC:19632 protein_coding YES CCDS31827.1 ENSP00000377799 Q8NGE1 UPI000004A282 NM_001005494.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF9,hmmpanther:PTHR26454,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 55551412 55551412 G T 1 0 0 0 0 0 0 0 1 11261 1161 41 2 2 OR6C4 12 55551412 Silent SNP G C3N-00549_T 1497257 55551412 77723897 272 15296 SLC26A10 0 . GRCh38 12 57624038 57624038 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.1167C>A p.= p.R389R ENST00000320442 9/14 69 47 22 92 92 0 strelka-varscan-mutect SLC26A10,synonymous_variant,p.=,ENST00000320442,NM_133489.2;B4GALNT1,downstream_gene_variant,,ENST00000341156,NM_001478.4;B4GALNT1,downstream_gene_variant,,ENST00000418555,NM_001276468.1;B4GALNT1,downstream_gene_variant,,ENST00000449184,;B4GALNT1,downstream_gene_variant,,ENST00000547741,;SLC26A10,downstream_gene_variant,,ENST00000637859,;AC025165.8,upstream_gene_variant,,ENST00000593846,;ARHGEF25,downstream_gene_variant,,ENST00000477314,;SLC26A10,upstream_gene_variant,,ENST00000490243,;SLC26A10,upstream_gene_variant,,ENST00000483647,;SLC26A10,synonymous_variant,p.=,ENST00000474359,;SLC26A10,synonymous_variant,p.=,ENST00000440686,;B4GALNT1,non_coding_transcript_exon_variant,,ENST00000553142,;SLC26A10,non_coding_transcript_exon_variant,,ENST00000487816,;B4GALNT1,downstream_gene_variant,,ENST00000552468,;B4GALNT1,downstream_gene_variant,,ENST00000552798,;B4GALNT1,downstream_gene_variant,,ENST00000549391,;SLC26A10,upstream_gene_variant,,ENST00000474791,;SLC26A10,downstream_gene_variant,,ENST00000497297,;SLC26A10,downstream_gene_variant,,ENST00000463802,; A ENST00000320442 Transcript synonymous_variant 1478/2389 1167/1692 389/563 R cgC/cgA 1 1 SLC26A10 HGNC HGNC:14470 protein_coding YES CCDS8949.2 ENSP00000320217 Q8NG04 UPI000007059E NM_133489.2 9/14 hmmpanther:PTHR11814:SF99,hmmpanther:PTHR11814,Pfam_domain:PF00916 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 57624038 57624038 C A 1 0 0 0 0 0 0 0 1 14785 726 26 2 2 SLC26A10 12 57624038 Silent SNP C C3N-00549_T 2072626 57624038 75651271 273 15297 MSRB3 0 . GRCh38 12 65369020 65369020 + Missense_Mutation SNP G G T rs542501613 C3N-00549_T C3N-00549_N G G c.307G>T p.Gly103Cys p.G103C ENST00000355192 4/6 155 86 69 108 108 0 strelka-varscan-mutect MSRB3,missense_variant,p.Gly96Cys,ENST00000308259,NM_001031679.2,NM_001193460.1;MSRB3,missense_variant,p.Gly103Cys,ENST00000355192,NM_198080.3;MSRB3,missense_variant,p.Gly96Cys,ENST00000614640,NM_001193461.1;MSRB3,missense_variant,p.Gly96Cys,ENST00000535664,;MSRB3,missense_variant,p.Gly103Cys,ENST00000540804,;MSRB3,missense_variant,p.Gly96Cys,ENST00000535239,;MSRB3,missense_variant,p.Gly112Cys,ENST00000541189,;MSRB3,missense_variant,p.Gly96Cys,ENST00000538045,;MSRB3,missense_variant,p.Gly55Cys,ENST00000446731,;MSRB3,non_coding_transcript_exon_variant,,ENST00000535143,;MSRB3,3_prime_UTR_variant,,ENST00000541897,; T ENST00000355192 Transcript missense_variant 433/4289 307/579 103/192 G/C Ggt/Tgt rs542501613,COSM4044187,COSM4044188 1 1 MSRB3 HGNC HGNC:27375 protein_coding YES CCDS8973.1 ENSP00000347324 Q8IXL7 UPI0000051E32 NM_198080.3 deleterious(0) 4/6 HAMAP:MF_01400,hmmpanther:PTHR10173,hmmpanther:PTHR10173:SF18,Pfam_domain:PF01641,Gene3D:2.170.150.20,TIGRFAM_domain:TIGR00357,Superfamily_domains:SSF51316 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs542501613 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 65369020 65369020 G T 1 0 0 0 0 1 0 0 0 9873 1116 39 1 1 MSRB3 12 65369020 Missense_Mutation SNP G C3N-00549_T 7744982 65369020 67906289 274 15298 KCNMB4 0 . GRCh38 12 70400228 70400228 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.356G>T p.Cys119Phe p.C119F ENST00000258111 2/3 82 40 42 71 71 0 strelka-varscan-mutect KCNMB4,missense_variant,p.Cys119Phe,ENST00000258111,NM_014505.5;KCNMB4,missense_variant,p.Cys7Phe,ENST00000531884,; T ENST00000258111 Transcript missense_variant 815/4731 356/633 119/210 C/F tGt/tTt 1 1 KCNMB4 HGNC HGNC:6289 protein_coding YES CCDS8997.1 ENSP00000258111 Q86W47 UPI0000073E0E NM_014505.5 deleterious(0.02) 2/3 hmmpanther:PTHR10258,hmmpanther:PTHR10258:SF3,Pfam_domain:PF03185 MODERATE 1 SNV 1 1 PASS . . 0 202 4 3 0 0 0 0 -20 0.9999843 1 1 1 0 T 3 4 50 70400228 70400228 G T 1 0 0 0 0 1 0 0 0 7993 1377 48 2 2 KCNMB4 12 70400228 Missense_Mutation SNP G C3N-00549_T 5031208 70400228 62875081 275 15299 TRHDE 0 . GRCh38 12 72272781 72272781 + Frame_Shift_Del DEL G G - novel C3N-00549_T C3N-00549_N G G c.7delG p.Glu3LysfsTer143 p.E3Kfs*143 ENST00000261180 1/19 53 29 24 36 36 0 sindel-varindel-pindel TRHDE,frameshift_variant,p.Glu3LysfsTer143,ENST00000261180,NM_013381.2;TRHDE,upstream_gene_variant,,ENST00000547300,;TRHDE-AS1,non_coding_transcript_exon_variant,,ENST00000426250,;TRHDE-AS1,upstream_gene_variant,,ENST00000435350,;TRHDE-AS1,upstream_gene_variant,,ENST00000550334,;TRHDE,intron_variant,,ENST00000548156,;TRHDE,upstream_gene_variant,,ENST00000552503,; - ENST00000261180 Transcript frameshift_variant,start_lost 99/10733 3/3075 1/1024 M/X atG/at 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 1/19 HIGH 1 deletion 1 4 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999981 1 1 1 0 - 7 5 50 72272781 72272781 G - 1 0 1 0 1 0 0 0 0 16968 1348 47 0 0 TRHDE 12 72272781 Frame_Shift_Del DEL G C3N-00549_T 1872553 72272781 61002528 276 15300 E2F7 0 . GRCh38 12 77064557 77064557 + Frame_Shift_Del DEL C C - C3N-00549_T C3N-00549_N C C c.79delG p.Glu27LysfsTer21 p.E27Kfs*21 ENST00000322886 2/13 228 156 72 196 196 0 sindel-varindel-pindel E2F7,frameshift_variant,p.Glu27LysfsTer21,ENST00000322886,NM_203394.2;E2F7,frameshift_variant,p.Glu27LysfsTer21,ENST00000416496,;E2F7,frameshift_variant,p.Glu27LysfsTer21,ENST00000550669,;E2F7,frameshift_variant,p.Glu27LysfsTer21,ENST00000547316,;E2F7,non_coding_transcript_exon_variant,,ENST00000551558,; - ENST00000322886 Transcript frameshift_variant 315/5740 79/2736 27/911 E/X Gaa/aa COSM1299876,COSM1299877 1 -1 E2F7 HGNC HGNC:23820 protein_coding YES CCDS9016.1 ENSP00000323246 Q96AV8 UPI00001B64A1 NM_203394.2 2/13 hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF25 1,1 HIGH 1 deletion 1 1,1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999986 1 1 1 0 - 7 5 50 77064557 77064557 C - 1 0 1 0 1 0 0 0 0 4696 864 30 0 0 E2F7 12 77064557 Frame_Shift_Del DEL C C3N-00549_T 4791776 77064557 56210752 277 15301 OTOGL 0 . GRCh38 12 80253475 80253475 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.1268T>C p.Met423Thr p.M423T ENST00000458043 13/58 177 112 65 134 134 0 strelka-varscan-mutect OTOGL,missense_variant,p.Met423Thr,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Met423Thr,ENST00000547103,; C ENST00000458043 Transcript missense_variant 1274/8083 1268/7035 423/2344 M/T aTg/aCg 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0.03) 13/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 80253475 80253475 T C 1 0 0 0 0 1 0 0 0 11371 1464 51 5 5 OTOGL 12 80253475 Missense_Mutation SNP T C3N-00549_T 3188918 80253475 53021834 278 15302 MYF5 0 . GRCh38 12 80719010 80719010 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.727C>A p.Pro243Thr p.P243T ENST00000228644 3/3 245 163 82 190 190 0 strelka-varscan-mutect MYF5,missense_variant,p.Pro243Thr,ENST00000228644,NM_005593.2; A ENST00000228644 Transcript missense_variant 879/1542 727/768 243/255 P/T Cca/Aca 1 1 MYF5 HGNC HGNC:7565 protein_coding YES CCDS9020.1 ENSP00000228644 P13349 UPI000013C8D9 NM_005593.2 tolerated(0.09) 3/3 hmmpanther:PTHR11534:SF3,hmmpanther:PTHR11534 MODERATE 1 SNV 1 1 PASS rs1187358892 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 80719010 80719010 C A 1 0 0 0 0 1 0 0 0 10027 855 30 2 2 MYF5 12 80719010 Missense_Mutation SNP C C3N-00549_T 465535 80719010 52556299 279 15303 PPFIA2 0 . GRCh38 12 81597973 81597973 + Silent SNP C C A novel C3N-00549_T C3N-00549_N C C c.60G>T p.= p.G20G ENST00000333447 1/29 215 112 103 237 235 2 strelka-varscan-mutect PPFIA2,synonymous_variant,p.=,ENST00000333447,NM_001220478.2;PPFIA2,synonymous_variant,p.=,ENST00000407050,NM_001220477.2;PPFIA2,synonymous_variant,p.=,ENST00000443686,;PPFIA2,intron_variant,,ENST00000550584,NM_001220473.2;PPFIA2,intron_variant,,ENST00000549396,NM_003625.4;PPFIA2,intron_variant,,ENST00000549325,NM_001220474.2;PPFIA2,intron_variant,,ENST00000548586,NM_001220476.2;PPFIA2,intron_variant,,ENST00000552948,NM_001220475.2;PPFIA2,intron_variant,,ENST00000551442,;PPFIA2,intron_variant,,ENST00000547623,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000545296,;PPFIA2,intron_variant,,ENST00000552020,; A ENST00000333447 Transcript synonymous_variant 399/5517 60/3459 20/1152 G ggG/ggT 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding CCDS55852.1 ENSP00000327416 O75334 UPI0002065590 NM_001220478.2 1/29 LOW SNV 5 1 PASS rs891593191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 81597973 81597973 C A 1 0 0 0 0 0 0 0 1 12419 842 30 2 2 PPFIA2 12 81597973 Silent SNP C C3N-00549_T 878963 81597973 51677336 280 15304 CEP290 0 . GRCh38 12 88117074 88117074 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1783G>T p.Asp595Tyr p.D595Y ENST00000552810 18/54 112 77 35 62 62 0 strelka-varscan-mutect CEP290,missense_variant,p.Asp595Tyr,ENST00000552810,NM_025114.3;CEP290,missense_variant,p.Asp597Tyr,ENST00000309041,;CEP290,missense_variant,p.Asp317Tyr,ENST00000604024,;CEP290,missense_variant,p.Asp597Tyr,ENST00000397838,;CEP290,missense_variant,p.Asp561Tyr,ENST00000547926,; A ENST00000552810 Transcript missense_variant 2127/7948 1783/7440 595/2479 D/Y Gat/Tat 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 deleterious(0) 18/54 hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 88117074 88117074 C A 1 0 0 0 0 1 0 0 0 2969 855 30 2 2 CEP290 12 88117074 Missense_Mutation SNP C C3N-00549_T 6519101 88117074 45158235 281 15305 SNRPF 0 . GRCh38 12 95861167 95861167 + Splice_Site SNP G G T novel C3N-00549_T C3N-00549_N G G c.4-1G>T p.X2_splice ENST00000266735 149 98 51 156 156 0 strelka-varscan-mutect SNRPF,splice_acceptor_variant,,ENST00000266735,NM_003095.2;SNRPF,splice_acceptor_variant,,ENST00000552085,;SNRPF,splice_acceptor_variant,,ENST00000553192,;RP11-536G4.2,upstream_gene_variant,,ENST00000553194,;RP11-536G4.2,upstream_gene_variant,,ENST00000551893,;SNRPF,splice_acceptor_variant,,ENST00000551316,;SNRPF,upstream_gene_variant,,ENST00000549580,;RP11-536G4.2,upstream_gene_variant,,ENST00000553163,; T ENST00000266735 Transcript splice_acceptor_variant -/1389 4/261 2/86 1 1 SNRPF HGNC HGNC:11162 protein_coding YES CCDS9055.1 ENSP00000266735 P62306 UPI0000027DBC NM_003095.2 1/3 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 50 95861167 95861167 G T 1 0 0 0 0 0 0 1 0 15188 956 33 2 2 SNRPF 12 95861167 Splice_Site SNP G C3N-00549_T 7744093 95861167 37414142 282 15306 HAL 0 . GRCh38 12 95983940 95983940 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.1258A>T p.Thr420Ser p.T420S ENST00000261208 15/21 401 272 129 211 211 0 strelka-varscan-mutect HAL,missense_variant,p.Thr420Ser,ENST00000261208,NM_002108.3;HAL,missense_variant,p.Thr212Ser,ENST00000541929,NM_001258333.1;HAL,missense_variant,p.Thr420Ser,ENST00000538703,NM_001258334.1;HAL,downstream_gene_variant,,ENST00000552509,;HAL,upstream_gene_variant,,ENST00000548808,;HAL,3_prime_UTR_variant,,ENST00000544080,;HAL,3_prime_UTR_variant,,ENST00000546999,;HAL,non_coding_transcript_exon_variant,,ENST00000548636,; A ENST00000261208 Transcript missense_variant 1627/3913 1258/1974 420/657 T/S Aca/Tca 1 -1 HAL HGNC HGNC:4806 protein_coding YES CCDS9058.1 ENSP00000261208 P42357 UPI000012CE8E NM_002108.3 tolerated(0.08) 15/21 hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7,Pfam_domain:PF00221,TIGRFAM_domain:TIGR01225,Gene3D:1.20.200.10,Superfamily_domains:SSF48557 MODERATE 1 SNV 1 1 PASS rs769324608 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 95983940 95983940 T A 1 0 0 0 0 1 0 0 0 6833 1696 59 4 4 HAL 12 95983940 Missense_Mutation SNP T C3N-00549_T 122773 95983940 37291369 283 15307 SLC5A8 0 . GRCh38 12 101193710 101193710 + Missense_Mutation SNP C C A rs746207517 C3N-00549_T C3N-00549_N C C c.607G>T p.Val203Leu p.V203L ENST00000536262 5/15 222 166 56 215 215 0 strelka-varscan-mutect SLC5A8,missense_variant,p.Val203Leu,ENST00000536262,NM_145913.3; A ENST00000536262 Transcript missense_variant 1166/4178 607/1833 203/610 V/L Gtg/Ttg rs746207517 1 -1 SLC5A8 HGNC HGNC:19119 protein_coding YES CCDS9080.1 ENSP00000445340 Q8N695 UPI000004DAF6 NM_145913.3 deleterious(0.01) 5/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF121,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs746207517 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 101193710 101193710 C A 1 0 0 0 0 1 0 0 0 14954 536 19 1 1 SLC5A8 12 101193710 Missense_Mutation SNP C C3N-00549_T 5209770 101193710 32081599 284 15308 SSH1 0 . GRCh38 12 108805088 108805088 + Nonsense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.922A>T p.Lys308Ter p.K308* ENST00000326495 10/15 272 196 76 155 155 0 strelka-varscan-mutect SSH1,stop_gained,p.Lys308Ter,ENST00000326495,NM_018984.3;SSH1,stop_gained,p.Lys319Ter,ENST00000326470,NM_001161331.1;SSH1,stop_gained,p.Lys308Ter,ENST00000551165,NM_001161330.1;SSH1,downstream_gene_variant,,ENST00000546697,;SSH1,stop_gained,p.Lys84Ter,ENST00000546433,;SSH1,downstream_gene_variant,,ENST00000547862,;SSH1,downstream_gene_variant,,ENST00000548522,;SSH1,downstream_gene_variant,,ENST00000547381,; A ENST00000326495 Transcript stop_gained 1016/13040 922/3150 308/1049 K/* Aag/Tag 1 -1 SSH1 HGNC HGNC:30579 protein_coding YES CCDS9121.1 ENSP00000315713 Q8WYL5 UPI000003E894 NM_018984.3 10/15 PROSITE_profiles:PS50054,hmmpanther:PTHR10159:SF138,hmmpanther:PTHR10159,SMART_domains:SM00195,Superfamily_domains:SSF52799 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 108805088 108805088 T A 1 0 0 0 0 0 1 0 0 15560 1821 63 4 4 SSH1 12 108805088 Nonsense_Mutation SNP T C3N-00549_T 7611378 108805088 24470221 285 15309 TPCN1 0 . GRCh38 12 113226756 113226756 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.120G>T p.Glu40Asp p.E40D ENST00000550785 3/29 206 151 55 159 159 0 strelka-varscan-mutect TPCN1,missense_variant,p.Glu40Asp,ENST00000550785,NM_001143819.2;TPCN1,missense_variant,p.Glu40Asp,ENST00000541517,;TPCN1,missense_variant,p.Glu54Asp,ENST00000552985,;TPCN1,missense_variant,p.Glu23Asp,ENST00000547275,;TPCN1,missense_variant,p.Glu40Asp,ENST00000551096,;TPCN1,5_prime_UTR_variant,,ENST00000335509,NM_017901.5;TPCN1,5_prime_UTR_variant,,ENST00000551099,;TPCN1,5_prime_UTR_variant,,ENST00000549279,;TPCN1,5_prime_UTR_variant,,ENST00000550873,;TPCN1,intron_variant,,ENST00000552897,;TPCN1,intron_variant,,ENST00000552642,;TPCN1,non_coding_transcript_exon_variant,,ENST00000552077,; T ENST00000550785 Transcript missense_variant 289/5345 120/2667 40/888 E/D gaG/gaT 1 1 TPCN1 HGNC HGNC:18182 protein_coding YES CCDS44985.1 ENSP00000448083 Q9ULQ1 UPI00004066FB NM_001143819.2 deleterious_low_confidence(0.05) 3/29 hmmpanther:PTHR10037 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 113226756 113226756 G T 1 0 0 0 0 1 0 0 0 16874 962 34 2 2 TPCN1 12 113226756 Missense_Mutation SNP G C3N-00549_T 4421668 113226756 20048553 286 15310 SETD1B 0 . GRCh38 12 121827644 121827644 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.5334G>T p.Gln1778His p.Q1778H ENST00000542440 15/18 196 116 80 125 125 0 strelka-varscan-mutect SETD1B,missense_variant,p.Gln1778His,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Gln1821His,ENST00000604567,;SETD1B,missense_variant,p.Gln1821His,ENST00000619791,;SETD1B,missense_variant,p.Gln1778His,ENST00000267197,; T ENST00000542440 Transcript missense_variant 5402/8185 5334/5772 1778/1923 Q/H caG/caT 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 deleterious(0) 15/18 Pfam_domain:PF11764,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 121827644 121827644 G T 1 0 0 0 0 1 0 0 0 14408 962 34 2 2 SETD1B 12 121827644 Missense_Mutation SNP G C3N-00549_T 8600888 121827644 11447665 287 15311 ITGBL1 0 . GRCh38 13 101583264 101583264 + Missense_Mutation SNP G G T rs112482922 C3N-00549_T C3N-00549_N G G c.776G>T p.Gly259Val p.G259V ENST00000376180 6/11 197 115 82 180 180 0 strelka-varscan-mutect ITGBL1,missense_variant,p.Gly118Val,ENST00000545560,NM_001271754.1;ITGBL1,missense_variant,p.Gly259Val,ENST00000376180,NM_004791.2;ITGBL1,missense_variant,p.Gly166Val,ENST00000622834,;ITGBL1,missense_variant,p.Gly210Val,ENST00000618057,NM_001271755.1;ITGBL1,missense_variant,p.Gly166Val,ENST00000376162,NM_001271756.1; T ENST00000376180 Transcript missense_variant 995/2494 776/1485 259/494 G/V gGg/gTg rs112482922 1 1 ITGBL1 HGNC HGNC:6164 protein_coding YES CCDS9499.1 ENSP00000365351 O95965 A0A024RDW7 UPI0000073C95 NM_004791.2 deleterious(0) 6/11 hmmpanther:PTHR10082:SF3,hmmpanther:PTHR10082,Gene3D:2.10.25.10,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs112482922 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 101583264 101583264 G T 1 0 0 0 0 1 0 0 0 7808 1232 43 2 2 ITGBL1 13 101583264 Missense_Mutation SNP G C3N-00549_T 101583264 12781064 288 15312 CCDC168 0 . GRCh38 13 102744860 102744860 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.5837A>T p.Gln1946Leu p.Q1946L ENST00000322527 4/4 216 144 72 172 172 0 strelka-varscan-mutect CCDC168,missense_variant,p.Gln1946Leu,ENST00000322527,NM_001146197.1;LINC00283,non_coding_transcript_exon_variant,,ENST00000430111,; A ENST00000322527 Transcript missense_variant 5975/21466 5837/21246 1946/7081 Q/L cAa/cTa 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.01) 4/4 MODERATE 1 SNV 3 1 PASS rs1406154105 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 102744860 102744860 T A 1 0 0 0 0 1 0 0 0 2484 1812 63 4 4 CCDC168 13 102744860 Missense_Mutation SNP T C3N-00549_T 1161596 102744860 11619468 289 15313 SLC10A2 0 . GRCh38 13 103051346 103051346 + Silent SNP G G A novel C3N-00549_T C3N-00549_N G G c.672C>T p.= p.P224P ENST00000245312 4/6 549 324 225 434 434 0 strelka-varscan-mutect SLC10A2,synonymous_variant,p.=,ENST00000245312,NM_000452.2; A ENST00000245312 Transcript synonymous_variant 1269/3779 672/1047 224/348 P ccC/ccT 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 4/6 hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 103051346 103051346 G A 1 0 0 0 0 0 0 0 1 14639 1335 47 3 3 SLC10A2 13 103051346 Silent SNP G C3N-00549_T 306486 103051346 11312982 290 15314 GRK1 0 . GRCh38 13 113731289 113731289 + Silent SNP C C G novel C3N-00549_T C3N-00549_N C C c.1140C>G p.= p.V380V ENST00000335678 5/7 168 63 105 203 203 0 strelka-varscan-mutect GRK1,synonymous_variant,p.=,ENST00000335678,;GRK1,non_coding_transcript_exon_variant,,ENST00000545304,;GRK1,upstream_gene_variant,,ENST00000606140,; G ENST00000335678 Transcript synonymous_variant 1372/4296 1140/1692 380/563 V gtC/gtG 1 1 GRK1 HGNC HGNC:10013 protein_coding YES ENSP00000334876 Q15835 UPI0000133B08 5/7 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF11,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 50 113731289 113731289 C G 1 0 0 0 0 0 0 0 1 6671 813 29 4 4 GRK1 13 113731289 Silent SNP C C3N-00549_T 10679943 113731289 633039 291 15315 CARMIL3 0 . GRCh38 14 24058039 24058039 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.1297A>T p.Thr433Ser p.T433S ENST00000342740 16/40 287 147 140 359 358 1 strelka-varscan-mutect CARMIL3,missense_variant,p.Thr433Ser,ENST00000342740,NM_138360.3;CARMIL3,non_coding_transcript_exon_variant,,ENST00000559694,;CARMIL3,upstream_gene_variant,,ENST00000560349,;CARMIL3,upstream_gene_variant,,ENST00000561354,; T ENST00000342740 Transcript missense_variant 1451/4597 1297/4119 433/1372 T/S Aca/Tca 1 1 CARMIL3 HGNC HGNC:20272 protein_coding YES CCDS32054.1 ENSP00000340467 Q8ND23 UPI0000DBEF11 NM_138360.3 deleterious(0) 16/40 hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF43,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 24058039 24058039 A T 1 0 0 0 0 1 0 0 0 2353 159 6 4 4 CARMIL3 14 24058039 Missense_Mutation SNP A C3N-00549_T 24058039 82985679 292 15316 PRKD1 0 . GRCh38 14 29597510 29597510 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.2415G>T p.Trp805Cys p.W805C ENST00000331968 16/18 139 73 66 119 119 0 strelka-varscan-mutect PRKD1,missense_variant,p.Trp805Cys,ENST00000331968,NM_002742.2;PRKD1,missense_variant,p.Trp805Cys,ENST00000616995,;PRKD1,missense_variant,p.Trp813Cys,ENST00000415220,;PRKD1,missense_variant,p.Trp53Cys,ENST00000490795,; A ENST00000331968 Transcript missense_variant 2645/3726 2415/2739 805/912 W/C tgG/tgT 1 -1 PRKD1 HGNC HGNC:9407 protein_coding YES CCDS9637.1 ENSP00000333568 Q15139 UPI0000456761 NM_002742.2 deleterious(0) 16/18 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000552,PROSITE_profiles:PS50011,hmmpanther:PTHR22968,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 29597510 29597510 C A 1 0 0 0 0 1 0 0 0 12651 856 30 2 2 PRKD1 14 29597510 Missense_Mutation SNP C C3N-00549_T 5539471 29597510 77446208 293 15317 FANCM 0 . GRCh38 14 45159233 45159233 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1534G>T p.Ala512Ser p.A512S ENST00000267430 9/23 224 120 104 232 232 0 strelka-varscan-mutect FANCM,missense_variant,p.Ala512Ser,ENST00000267430,NM_020937.2;FANCM,missense_variant,p.Ala486Ser,ENST00000542564,NM_001308133.1;FANCM,missense_variant,p.Ala97Ser,ENST00000556250,;FANCM,missense_variant,p.Ala512Ser,ENST00000556036,NM_001308134.1; T ENST00000267430 Transcript missense_variant 1619/7111 1534/6147 512/2048 A/S Gcc/Tcc 1 1 FANCM HGNC HGNC:23168 protein_coding YES CCDS32070.1 ENSP00000267430 Q8IYD8 UPI000059F032 NM_020937.2 tolerated(0.61) 9/23 PROSITE_profiles:PS51194,hmmpanther:PTHR14025:SF20,hmmpanther:PTHR14025,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1176304267 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 45159233 45159233 G T 1 0 0 0 0 1 0 0 0 5531 1319 46 2 2 FANCM 14 45159233 Missense_Mutation SNP G C3N-00549_T 15561723 45159233 61884485 294 15318 TRIM9 0 . GRCh38 14 50979515 50979515 + Missense_Mutation SNP C C A rs768449747 C3N-00549_T C3N-00549_N C C c.1942G>T p.Gly648Trp p.G648W ENST00000298355 9/10 137 101 36 135 135 0 strelka-varscan-mutect TRIM9,missense_variant,p.Gly648Trp,ENST00000298355,NM_015163.5;TRIM9,missense_variant,p.Gly729Trp,ENST00000338969,;TRIM9,downstream_gene_variant,,ENST00000557456,;TRIM9,non_coding_transcript_exon_variant,,ENST00000555170,;TRIM9,downstream_gene_variant,,ENST00000555933,; A ENST00000298355 Transcript missense_variant 3064/5284 1942/2133 648/710 G/W Ggg/Tgg rs768449747 1 -1 TRIM9 HGNC HGNC:16288 protein_coding YES CCDS9703.1 ENSP00000298355 Q9C026 UPI000006D630 NM_015163.5 deleterious(0) 9/10 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF400,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs768449747 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 50979515 50979515 C A 1 0 0 0 0 1 0 0 0 17046 594 21 2 2 TRIM9 14 50979515 Missense_Mutation SNP C C3N-00549_T 5820282 50979515 56064203 295 15319 GMFB 0 . GRCh38 14 54480949 54480949 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.208G>T p.Val70Leu p.V70L ENST00000358056 5/7 53 33 20 45 45 0 strelka-varscan-mutect GMFB,missense_variant,p.Val70Leu,ENST00000358056,NM_004124.2;GMFB,missense_variant,p.Val70Leu,ENST00000616146,;GMFB,missense_variant,p.Val83Leu,ENST00000553333,;GMFB,3_prime_UTR_variant,,ENST00000554908,;GMFB,3_prime_UTR_variant,,ENST00000628554,;GMFB,downstream_gene_variant,,ENST00000553566,;GMFB,splice_region_variant,,ENST00000554247,;GMFB,non_coding_transcript_exon_variant,,ENST00000554163,;GMFB,downstream_gene_variant,,ENST00000553952,;GMFB,downstream_gene_variant,,ENST00000554682,; A ENST00000358056 Transcript missense_variant 477/4301 208/429 70/142 V/L Gtg/Ttg 1 -1 GMFB HGNC HGNC:4373 protein_coding YES CCDS9718.1 ENSP00000350757 P60983 UPI0000161C06 NM_004124.2 tolerated(0.58) 5/7 PROSITE_profiles:PS51263,hmmpanther:PTHR11249,hmmpanther:PTHR11249:SF3,Gene3D:3.40.20.10,Pfam_domain:PF00241,PIRSF_domain:PIRSF001788,SMART_domains:SM00102,Superfamily_domains:SSF55753 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 54480949 54480949 C A 1 0 0 0 0 1 0 0 0 6368 478 17 2 2 GMFB 14 54480949 Missense_Mutation SNP C C3N-00549_T 3501434 54480949 52562769 296 15320 SAMD4A 0 . GRCh38 14 54760307 54760307 + Missense_Mutation SNP G G T rs754157629 C3N-00549_T C3N-00549_N G G c.1323G>T p.Met441Ile p.M441I ENST00000392067 6/12 147 111 36 238 238 0 strelka-varscan-mutect SAMD4A,missense_variant,p.Met441Ile,ENST00000392067,NM_015589.5;SAMD4A,missense_variant,p.Met32Ile,ENST00000631086,;SAMD4A,missense_variant,p.Met353Ile,ENST00000251091,NM_001161576.2;SAMD4A,missense_variant,p.Met441Ile,ENST00000554335,;SAMD4A,missense_variant,p.Met32Ile,ENST00000555192,NM_001161577.1; T ENST00000392067 Transcript missense_variant 1628/6833 1323/2157 441/718 M/I atG/atT rs754157629 1 1 SAMD4A HGNC HGNC:23023 protein_coding YES CCDS32084.2 ENSP00000375919 Q9UPU9 UPI0000229786 NM_015589.5 tolerated(0.58) 6/12 hmmpanther:PTHR12515,hmmpanther:PTHR12515:SF8 MODERATE 1 SNV 2 1 PASS rs754157629 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 54760307 54760307 G T 1 0 0 0 0 1 0 0 0 14081 1348 47 2 2 SAMD4A 14 54760307 Missense_Mutation SNP G C3N-00549_T 279358 54760307 52283411 297 15321 MNAT1 0 . GRCh38 14 60879761 60879761 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.735G>T p.= p.L245L ENST00000261245 7/8 199 115 84 191 191 0 strelka-varscan-mutect MNAT1,synonymous_variant,p.=,ENST00000261245,NM_002431.3;MNAT1,synonymous_variant,p.=,ENST00000539616,NM_001177963.1;MNAT1,synonymous_variant,p.=,ENST00000557134,;MNAT1,synonymous_variant,p.=,ENST00000554002,;RP11-193F5.1,non_coding_transcript_exon_variant,,ENST00000553946,;MNAT1,non_coding_transcript_exon_variant,,ENST00000554641,; T ENST00000261245 Transcript synonymous_variant 836/2635 735/930 245/309 L ctG/ctT 1 1 MNAT1 HGNC HGNC:7181 protein_coding YES CCDS9750.1 ENSP00000261245 P51948 A0A024R688 UPI000002FC14 NM_002431.3 7/8 hmmpanther:PTHR12683,TIGRFAM_domain:TIGR00570,PIRSF_domain:PIRSF003338,Pfam_domain:PF06391 LOW 1 SNV 1 1 PASS rs1427238944 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 60879761 60879761 G T 1 0 0 0 0 0 0 0 1 9638 1364 48 2 2 MNAT1 14 60879761 Silent SNP G C3N-00549_T 6119454 60879761 46163957 298 15322 MLH3 0 . GRCh38 14 75042405 75042405 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3353G>T p.Arg1118Met p.R1118M ENST00000355774 3/13 292 216 76 354 354 0 strelka-varscan-mutect MLH3,missense_variant,p.Arg1118Met,ENST00000355774,NM_001040108.1;MLH3,missense_variant,p.Arg1118Met,ENST00000380968,NM_014381.2;MLH3,missense_variant,p.Arg1118Met,ENST00000556740,;MLH3,intron_variant,,ENST00000556257,;MLH3,intron_variant,,ENST00000553713,;MLH3,non_coding_transcript_exon_variant,,ENST00000555499,;MLH3,intron_variant,,ENST00000555671,;MLH3,missense_variant,p.Arg114Met,ENST00000555144,;MLH3,intron_variant,,ENST00000556453,; A ENST00000355774 Transcript missense_variant 3569/7896 3353/4362 1118/1453 R/M aGg/aTg 1 -1 MLH3 HGNC HGNC:7128 protein_coding YES CCDS32123.1 ENSP00000348020 Q9UHC1 UPI00001AEEE0 NM_001040108.1 deleterious(0.02) 3/13 hmmpanther:PTHR10073:SF7,hmmpanther:PTHR10073 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 75042405 75042405 C A 1 0 0 0 0 1 0 0 0 9585 681 24 2 2 MLH3 14 75042405 Missense_Mutation SNP C C3N-00549_T 14162644 75042405 32001313 299 15323 ITPK1 0 . GRCh38 14 92941782 92941782 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.1024C>G p.Leu342Val p.L342V ENST00000267615 11/11 271 211 60 359 359 0 strelka-varscan-mutect ITPK1,missense_variant,p.Leu342Val,ENST00000267615,;ITPK1,missense_variant,p.Leu342Val,ENST00000556603,NM_001142593.1,NM_014216.4;ITPK1,missense_variant,p.Leu223Val,ENST00000555495,;ITPK1,intron_variant,,ENST00000354313,NM_001142594.1;ITPK1,downstream_gene_variant,,ENST00000556954,;ITPK1,downstream_gene_variant,,ENST00000553695,; C ENST00000267615 Transcript missense_variant 1198/6066 1024/1245 342/414 L/V Ctg/Gtg 1 -1 ITPK1 HGNC HGNC:6177 protein_coding YES CCDS9907.1 ENSP00000267615 Q13572 A0A024R6H3 UPI000006F88A tolerated_low_confidence(0.11) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 92941782 92941782 G C 1 0 0 0 0 1 0 0 0 7822 933 33 4 4 ITPK1 14 92941782 Missense_Mutation SNP G C3N-00549_T 17899377 92941782 14101936 300 15324 DYNC1H1 0 . GRCh38 14 101979365 101979365 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.391G>A p.Val131Met p.V131M ENST00000360184 3/78 280 139 141 262 262 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Val131Met,ENST00000360184,NM_001376.4; A ENST00000360184 Transcript missense_variant 555/14333 391/13941 131/4646 V/M Gtg/Atg 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0.03) 3/78 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 MODERATE 1 SNV 1 1 PASS rs1488184652 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 101979365 101979365 G A 1 0 0 0 0 1 0 0 0 4665 1145 40 1 1 DYNC1H1 14 101979365 Missense_Mutation SNP G C3N-00549_T 9037583 101979365 5064353 301 15325 C14orf180 0 . GRCh38 14 104586446 104586446 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.16G>A p.Gly6Arg p.G6R ENST00000331952 2/5 63 45 18 65 65 0 strelka-varscan-mutect C14orf180,missense_variant,p.Gly6Arg,ENST00000557649,NM_001008404.2;C14orf180,missense_variant,p.Gly6Arg,ENST00000410013,NM_001286400.1;C14orf180,missense_variant,p.Gly6Arg,ENST00000331952,NM_001286399.1;TMEM179,intron_variant,,ENST00000415614,;TMEM179,downstream_gene_variant,,ENST00000616017,;TMEM179,downstream_gene_variant,,ENST00000556320,;RP11-614O9.1,downstream_gene_variant,,ENST00000556073,; A ENST00000331952 Transcript missense_variant 272/1455 16/534 6/177 G/R Gga/Aga 1 1 C14orf180 HGNC HGNC:33795 protein_coding YES CCDS66722.1 ENSP00000333041 J3KNP8 UPI00021CF38C NM_001286399.1 tolerated_low_confidence(0.93) 2/5 hmmpanther:PTHR36868:SF1,hmmpanther:PTHR36868 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 104586446 104586446 G A 1 0 0 0 0 1 0 0 0 1835 1001 35 3 3 C14orf180 14 104586446 Missense_Mutation SNP G C3N-00549_T 2607081 104586446 2457272 302 15326 AHNAK2 0 . GRCh38 14 104943804 104943804 + Nonsense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.11647A>T p.Lys3883Ter p.K3883* ENST00000333244 7/7 430 208 222 365 365 0 strelka-varscan-mutect AHNAK2,stop_gained,p.Lys3883Ter,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript stop_gained 11767/18254 11647/17388 3883/5795 K/* Aaa/Taa 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 104943804 104943804 T A 1 0 0 0 0 0 1 0 0 492 1821 63 4 4 AHNAK2 14 104943804 Nonsense_Mutation SNP T C3N-00549_T 357358 104943804 2099914 303 15327 NPAP1 0 . GRCh38 15 24678653 24678653 + Missense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.2786C>A p.Thr929Lys p.T929K ENST00000329468 1/1 415 198 217 290 290 0 strelka-varscan-mutect NPAP1,missense_variant,p.Thr929Lys,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 2786/7526 2786/3471 929/1156 T/K aCa/aAa COSM4933053 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.21) 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 24678653 24678653 C A 1 0 0 0 0 1 0 0 0 10609 478 17 2 2 NPAP1 15 24678653 Missense_Mutation SNP C C3N-00549_T 24678653 77312536 304 15328 NPAP1 0 . GRCh38 15 24678858 24678858 + Silent SNP G G C novel C3N-00549_T C3N-00549_N G G c.2991G>C p.= p.L997L ENST00000329468 1/1 352 266 86 248 248 0 strelka-varscan-mutect NPAP1,synonymous_variant,p.=,ENST00000329468,NM_018958.2; C ENST00000329468 Transcript synonymous_variant 2991/7526 2991/3471 997/1156 L ctG/ctC 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 LOW 1 SNV 1 PASS rs919442957 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 24678858 24678858 G C 1 0 0 0 0 0 0 0 1 10609 1335 47 4 4 NPAP1 15 24678858 Silent SNP G C3N-00549_T 205 24678858 77312331 305 15329 GOLGA8J 0 . GRCh38 15 30092710 30092710 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1371C>A p.Ser457Arg p.S457R ENST00000567927 16/19 71 48 23 37 37 0 strelka-varscan-mutect GOLGA8J,missense_variant,p.Ser457Arg,ENST00000567927,NM_001282472.1;RN7SL673P,downstream_gene_variant,,ENST00000616262,;GOLGA8J,downstream_gene_variant,,ENST00000568123,; A ENST00000567927 Transcript missense_variant,splice_region_variant 1371/1899 1371/1899 457/632 S/R agC/agA 1 1 GOLGA8J HGNC HGNC:38650 protein_coding YES CCDS61574.1 ENSP00000456401 A6NMD2 UPI0001A5E7A2 NM_001282472.1 deleterious(0.02) 16/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS rs904887147 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 30092710 30092710 C A 1 0 0 0 0 1 0 0 0 6452 724 25 2 2 GOLGA8J 15 30092710 Missense_Mutation SNP C C3N-00549_T 5413852 30092710 71898479 306 15330 GOLGA8J 0 . GRCh38 15 30093334 30093334 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1734G>T p.Glu578Asp p.E578D ENST00000567927 19/19 244 111 133 214 214 0 strelka-varscan-mutect GOLGA8J,missense_variant,p.Glu578Asp,ENST00000567927,NM_001282472.1;RN7SL673P,downstream_gene_variant,,ENST00000616262,;GOLGA8J,downstream_gene_variant,,ENST00000568123,; T ENST00000567927 Transcript missense_variant 1734/1899 1734/1899 578/632 E/D gaG/gaT 1 1 GOLGA8J HGNC HGNC:38650 protein_coding YES CCDS61574.1 ENSP00000456401 A6NMD2 UPI0001A5E7A2 NM_001282472.1 tolerated(0.1) 19/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 30093334 30093334 G T 1 0 0 0 0 1 0 0 0 6452 991 35 2 2 GOLGA8J 15 30093334 Missense_Mutation SNP G C3N-00549_T 624 30093334 71897855 307 15331 GOLGA8H 0 . GRCh38 15 30614540 30614540 + Nonsense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.1878G>A p.Trp626Ter p.W626* ENST00000566740 19/19 619 283 336 471 471 0 strelka-varscan-mutect GOLGA8H,stop_gained,p.Trp626Ter,ENST00000566740,NM_001282490.1;RP11-932O9.9,upstream_gene_variant,,ENST00000602594,;RP11-932O9.7,downstream_gene_variant,,ENST00000501830,;RN7SL628P,downstream_gene_variant,,ENST00000619139,; A ENST00000566740 Transcript stop_gained 1878/1899 1878/1899 626/632 W/* tgG/tgA 1 1 GOLGA8H HGNC HGNC:37443 protein_coding YES CCDS61576.1 ENSP00000456894 P0CJ92 UPI0001A5E7A5 NM_001282490.1 19/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 30614540 30614540 G A 1 0 0 0 0 0 1 0 0 6451 1212 42 3 3 GOLGA8H 15 30614540 Nonsense_Mutation SNP G C3N-00549_T 521206 30614540 71376649 308 15332 UBR1 0 . GRCh38 15 43003842 43003842 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3504G>T p.Trp1168Cys p.W1168C ENST00000290650 31/47 687 520 167 489 487 2 strelka-varscan-mutect UBR1,missense_variant,p.Trp1168Cys,ENST00000290650,NM_174916.2;UBR1,non_coding_transcript_exon_variant,,ENST00000568782,; A ENST00000290650 Transcript missense_variant 3583/7761 3504/5250 1168/1749 W/C tgG/tgT 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 deleterious(0) 31/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27,Gene3D:3.30.40.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 43003842 43003842 C A 1 0 0 0 0 1 0 0 0 17425 753 26 2 2 UBR1 15 43003842 Missense_Mutation SNP C C3N-00549_T 12389302 43003842 58987347 309 15333 TLN2 0 . GRCh38 15 62805726 62805726 + Missense_Mutation SNP G G T rs778720944 C3N-00549_T C3N-00549_N G G c.6604G>T p.Val2202Leu p.V2202L ENST00000561311 50/58 250 114 136 157 157 0 strelka-varscan-mutect TLN2,missense_variant,p.Val2202Leu,ENST00000561311,NM_015059.2;TLN2,missense_variant,p.Val1200Leu,ENST00000306829,;TLN2,missense_variant,p.Val1227Leu,ENST00000636159,;TLN2,missense_variant,p.Val1116Leu,ENST00000494733,;TLN2,non_coding_transcript_exon_variant,,ENST00000489129,; T ENST00000561311 Transcript missense_variant 6834/11880 6604/7629 2202/2542 V/L Gtg/Ttg rs778720944 1 1 TLN2 HGNC HGNC:15447 protein_coding YES CCDS32261.1 ENSP00000453508 Q9Y4G6 UPI00001FE5FC NM_015059.2 deleterious(0.02) 50/58 hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15 MODERATE 1 SNV 5 1 PASS rs778720944 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 62805726 62805726 G T 1 0 0 0 0 1 0 0 0 16394 1145 40 1 1 TLN2 15 62805726 Missense_Mutation SNP G C3N-00549_T 19801884 62805726 39185463 310 15334 APH1B 0 . GRCh38 15 63302405 63302405 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.539G>C p.Gly180Ala p.G180A ENST00000261879 5/6 186 147 39 121 121 0 strelka-varscan-mutect APH1B,missense_variant,p.Gly180Ala,ENST00000261879,NM_031301.3;APH1B,missense_variant,p.Gly126Ala,ENST00000560890,;APH1B,missense_variant,p.Gly139Ala,ENST00000380343,NM_001145646.1;APH1B,intron_variant,,ENST00000560353,;APH1B,non_coding_transcript_exon_variant,,ENST00000560716,;APH1B,intron_variant,,ENST00000559823,;APH1B,3_prime_UTR_variant,,ENST00000559971,;APH1B,3_prime_UTR_variant,,ENST00000380340,;APH1B,non_coding_transcript_exon_variant,,ENST00000558631,; C ENST00000261879 Transcript missense_variant 609/4189 539/774 180/257 G/A gGc/gCc 1 1 APH1B HGNC HGNC:24080 protein_coding YES CCDS10184.1 ENSP00000261879 Q8WW43 UPI000004222D NM_031301.3 tolerated(1) 5/6 hmmpanther:PTHR12889,hmmpanther:PTHR12889:SF1,Pfam_domain:PF06105 MODERATE 1 SNV 1 1 PASS . . 0 197 0 11 2 0 0 0 -19.99993 0.7751721 1 1 1 0 C 3 2 50 63302405 63302405 G C 1 0 0 0 0 1 0 0 0 893 1203 42 4 4 APH1B 15 63302405 Missense_Mutation SNP G C3N-00549_T 496679 63302405 38688784 311 15335 HERC1 0 . GRCh38 15 63666382 63666382 + Missense_Mutation SNP T T G C3N-00549_T C3N-00549_N T T c.8297A>C p.Gln2766Pro p.Q2766P ENST00000443617 41/78 207 90 117 183 183 0 strelka-varscan-mutect HERC1,missense_variant,p.Gln2766Pro,ENST00000443617,NM_003922.3; G ENST00000443617 Transcript missense_variant 8385/15137 8297/14586 2766/4861 Q/P cAg/cCg COSM331791,COSM331792 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 deleterious(0.01) 41/78 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 63666382 63666382 T G 1 0 0 0 0 1 0 0 0 6941 1580 55 5 5 HERC1 15 63666382 Missense_Mutation SNP T C3N-00549_T 363977 63666382 38324807 312 15336 LCTL 0 . GRCh38 15 66565356 66565356 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.10G>T p.Val4Leu p.V4L ENST00000341509 1/13 149 52 97 140 140 0 strelka-varscan-mutect LCTL,missense_variant,p.Val4Leu,ENST00000341509,NM_207338.3;LCTL,intron_variant,,ENST00000537670,NM_001278562.1;LCTL,intron_variant,,ENST00000563438,;LCTL,intron_variant,,ENST00000562179,;LCTL,intron_variant,,ENST00000565875,; A ENST00000341509 Transcript missense_variant 142/3147 10/1704 4/567 V/L Gtg/Ttg 1 -1 LCTL HGNC HGNC:15583 protein_coding YES CCDS10220.1 ENSP00000343490 Q6UWM7 UPI00002520EC NM_207338.3 tolerated_low_confidence(0.28) 1/13 hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF24,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1201827745 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 66565356 66565356 C A 1 0 0 0 0 1 0 0 0 8600 565 20 2 2 LCTL 15 66565356 Missense_Mutation SNP C C3N-00549_T 2898974 66565356 35425833 313 15337 PML 0 . GRCh38 15 74044745 74044745 + Missense_Mutation SNP C C T rs754836240 C3N-00549_T C3N-00549_N C C c.2386C>T p.Arg796Cys p.R796C ENST00000268058 9/9 409 118 291 204 201 3 strelka-varscan-mutect PML,missense_variant,p.Arg748Cys,ENST00000565898,;PML,missense_variant,p.Arg796Cys,ENST00000268058,NM_033238.2;PML,downstream_gene_variant,,ENST00000395135,NM_002675.3;PML,downstream_gene_variant,,ENST00000569965,;PML,downstream_gene_variant,,ENST00000564428,NM_033249.2;PML,downstream_gene_variant,,ENST00000359928,NM_033246.2;PML,downstream_gene_variant,,ENST00000565317,; T ENST00000268058 Transcript missense_variant 2482/4508 2386/2649 796/882 R/C Cgc/Tgc rs754836240,COSM3771884 1 1 PML HGNC HGNC:9113 protein_coding YES CCDS10255.1 ENSP00000268058 P29590 UPI000013D78F NM_033238.2 deleterious(0) 9/9 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754836240 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 74044745 74044745 C T 1 0 0 0 0 1 0 0 0 12242 652 23 1 1 PML 15 74044745 Missense_Mutation SNP C C3N-00549_T 7479389 74044745 27946444 314 15338 MESDC1 0 . GRCh38 15 81002744 81002744 + Missense_Mutation SNP A A G novel C3N-00549_T C3N-00549_N A A c.473A>G p.His158Arg p.H158R ENST00000267984 1/1 164 59 105 93 93 0 strelka-varscan-mutect MESDC1,missense_variant,p.His158Arg,ENST00000267984,NM_022566.2;CFAP161,upstream_gene_variant,,ENST00000560091,;RP11-775C24.5,upstream_gene_variant,,ENST00000620635,; G ENST00000267984 Transcript missense_variant 1801/4845 473/1089 158/362 H/R cAc/cGc 1 1 MESDC1 HGNC HGNC:13519 protein_coding YES CCDS10316.1 ENSP00000267984 Q9H1K6 UPI000012EE04 NM_022566.2 tolerated(0.05) 1/1 hmmpanther:PTHR19981 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 81002744 81002744 A G 1 0 0 0 0 1 0 0 0 9425 159 6 5 5 MESDC1 15 81002744 Missense_Mutation SNP A C3N-00549_T 6957999 81002744 20988445 315 15339 ACAN 0 . GRCh38 15 88843536 88843536 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.939G>T p.Lys313Asn p.K313N ENST00000439576 6/18 206 85 121 157 157 0 strelka-varscan-mutect ACAN,missense_variant,p.Lys313Asn,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Lys313Asn,ENST00000617301,;ACAN,missense_variant,p.Lys313Asn,ENST00000559004,;ACAN,missense_variant,p.Lys313Asn,ENST00000561243,;ACAN,missense_variant,p.Lys313Asn,ENST00000352105,NM_001135.3;ACAN,missense_variant,p.Lys313Asn,ENST00000558207,; T ENST00000439576 Transcript missense_variant 1313/8840 939/7593 313/2530 K/N aaG/aaT 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0.03) 6/18 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,PROSITE_patterns:PS01241,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 88843536 88843536 G T 1 0 0 0 0 1 0 0 0 160 991 35 2 2 ACAN 15 88843536 Missense_Mutation SNP G C3N-00549_T 7840792 88843536 13147653 316 15340 ANPEP 0 . GRCh38 15 89803242 89803242 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1566G>T p.Gln522His p.Q522H ENST00000300060 10/21 294 238 56 158 158 0 strelka-varscan-mutect ANPEP,missense_variant,p.Gln522His,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,3_prime_UTR_variant,,ENST00000560030,;ANPEP,downstream_gene_variant,,ENST00000560028,;ANPEP,downstream_gene_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000559761,; A ENST00000300060 Transcript missense_variant 1880/3678 1566/2904 522/967 Q/H caG/caT 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 deleterious(0) 10/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 89803242 89803242 C A 1 0 0 0 0 1 0 0 0 817 695 24 2 2 ANPEP 15 89803242 Missense_Mutation SNP C C3N-00549_T 959706 89803242 12187947 317 15341 UNC45A 0 . GRCh38 15 90946815 90946815 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1401G>T p.Lys467Asn p.K467N ENST00000418476 10/20 323 112 211 195 195 0 strelka-varscan-mutect UNC45A,missense_variant,p.Lys452Asn,ENST00000394275,NM_001039675.1;UNC45A,missense_variant,p.Lys467Asn,ENST00000418476,NM_001323619.1,NM_018671.3;UNC45A,downstream_gene_variant,,ENST00000553671,;UNC45A,non_coding_transcript_exon_variant,,ENST00000556704,;UNC45A,non_coding_transcript_exon_variant,,ENST00000554481,;UNC45A,upstream_gene_variant,,ENST00000487875,;UNC45A,upstream_gene_variant,,ENST00000471780,;UNC45A,downstream_gene_variant,,ENST00000557212,; T ENST00000418476 Transcript missense_variant 1441/3252 1401/2835 467/944 K/N aaG/aaT 1 1 UNC45A HGNC HGNC:30594 protein_coding YES CCDS10367.1 ENSP00000407487 Q9H3U1 UPI000000D953 NM_001323619.1,NM_018671.3 deleterious(0) 10/20 Pfam_domain:PF11701,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF275,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 90946815 90946815 G T 1 0 0 0 0 1 0 0 0 17512 991 35 2 2 UNC45A 15 90946815 Missense_Mutation SNP G C3N-00549_T 1143573 90946815 11044374 318 15342 LRRC28 0 . GRCh38 15 99361346 99361346 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.706C>G p.Pro236Ala p.P236A ENST00000301981 8/10 99 25 74 108 108 0 strelka-varscan-mutect LRRC28,missense_variant,p.Pro236Ala,ENST00000301981,NM_001321680.1,NM_001321675.1,NM_001321679.1,NM_144598.3;LRRC28,missense_variant,p.Pro236Ala,ENST00000447360,NM_001284400.1;LRRC28,missense_variant,p.Pro191Ala,ENST00000561276,;LRRC28,missense_variant,p.Pro132Ala,ENST00000558172,;LRRC28,intron_variant,,ENST00000331450,;LRRC28,intron_variant,,ENST00000558879,;LRRC28,3_prime_UTR_variant,,ENST00000559433,;LRRC28,3_prime_UTR_variant,,ENST00000558471,;LRRC28,non_coding_transcript_exon_variant,,ENST00000559819,;LRRC28,non_coding_transcript_exon_variant,,ENST00000558890,;LRRC28,non_coding_transcript_exon_variant,,ENST00000560483,;LRRC28,upstream_gene_variant,,ENST00000560236,; G ENST00000301981 Transcript missense_variant 946/5971 706/1104 236/367 P/A Ccc/Gcc 1 1 LRRC28 HGNC HGNC:28355 protein_coding YES CCDS10380.1 ENSP00000304923 Q86X40 UPI000000DBCB NM_001321680.1,NM_001321675.1,NM_001321679.1,NM_144598.3 tolerated(0.62) 8/10 Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs1445669194 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 99361346 99361346 C G 1 0 0 0 0 1 0 0 0 8877 855 30 4 4 LRRC28 15 99361346 Missense_Mutation SNP C C3N-00549_T 8414531 99361346 2629843 319 15343 MMP25 0 . GRCh38 16 3057375 3057375 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.904C>A p.Pro302Thr p.P302T ENST00000336577 6/10 115 70 45 132 132 0 strelka-mutect MMP25,missense_variant,p.Pro302Thr,ENST00000336577,NM_022468.4;MMP25,downstream_gene_variant,,ENST00000612971,;MMP25-AS1,intron_variant,,ENST00000573953,;MMP25-AS1,intron_variant,,ENST00000572574,;MMP25-AS1,intron_variant,,ENST00000576250,;MMP25-AS1,upstream_gene_variant,,ENST00000573130,;MMP25-AS1,downstream_gene_variant,,ENST00000572427,;MMP25-AS1,upstream_gene_variant,,ENST00000570949,;MMP25-AS1,upstream_gene_variant,,ENST00000573878,;MMP25-AS1,upstream_gene_variant,,ENST00000572930,;MMP25-AS1,downstream_gene_variant,,ENST00000572222,;MMP25,downstream_gene_variant,,ENST00000570755,;MMP25,non_coding_transcript_exon_variant,,ENST00000575441,; A ENST00000336577 Transcript missense_variant 1141/3554 904/1689 302/562 P/T Ccg/Acg 1 1 MMP25 HGNC HGNC:14246 protein_coding YES CCDS10492.1 ENSP00000337816 Q9NPA2 UPI000003DC71 NM_022468.4 tolerated(0.07) 6/10 PIRSF_domain:PIRSF001191,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF142,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 3057375 3057375 C A 1 0 0 0 0 1 0 0 0 9625 623 22 2 2 MMP25 16 3057375 Missense_Mutation SNP C C3N-00549_T 3057375 87280970 320 15344 GRIN2A 0 . GRCh38 16 9764850 9764850 + Silent SNP G G T rs569998469 C3N-00549_T C3N-00549_N G G c.2694C>A p.= p.L898L ENST00000396573 14/14 536 351 185 453 452 1 strelka-varscan-mutect GRIN2A,synonymous_variant,p.=,ENST00000396573,NM_000833.4;GRIN2A,synonymous_variant,p.=,ENST00000396575,;GRIN2A,synonymous_variant,p.=,ENST00000330684,NM_001134407.2;GRIN2A,synonymous_variant,p.=,ENST00000562109,NM_001134408.2;GRIN2A,synonymous_variant,p.=,ENST00000535259,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000463531,; T ENST00000396573 Transcript synonymous_variant 3004/14450 2694/4395 898/1464 L ctC/ctA rs569998469 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 14/14 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF16,Pfam_domain:PF10565 benign LOW 1 SNV 1 1 1 PASS rs569998469 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 9764850 9764850 G T 1 0 0 0 0 0 0 0 1 6661 1161 41 2 2 GRIN2A 16 9764850 Silent SNP G C3N-00549_T 6707475 9764850 80573495 321 15345 SMG1 0 . GRCh38 16 18849948 18849948 + Splice_Site SNP C C A novel C3N-00549_T C3N-00549_N C C c.5461+1G>T p.X1821_splice ENST00000446231 136 77 59 112 112 0 strelka-varscan-mutect SMG1,splice_donor_variant,,ENST00000446231,NM_015092.4;SMG1,splice_donor_variant,,ENST00000565324,;SMG1,splice_donor_variant,,ENST00000563448,;SMG1,upstream_gene_variant,,ENST00000562668,; A ENST00000446231 Transcript splice_donor_variant -/16115 5461/10986 1821/3661 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 35/62 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 18849948 18849948 C A 1 0 0 0 0 0 0 1 0 15089 521 18 2 2 SMG1 16 18849948 Splice_Site SNP C C3N-00549_T 9085098 18849948 71488397 322 15346 ACSM2A 0 . GRCh38 16 20460217 20460217 + Missense_Mutation SNP T T A novel C3N-00549_T C3N-00549_N T T c.103T>A p.Trp35Arg p.W35R ENST00000573854 2/14 138 82 56 179 179 0 strelka-varscan-mutect ACSM2A,missense_variant,p.Trp35Arg,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,missense_variant,p.Trp35Arg,ENST00000396104,;ACSM2A,missense_variant,p.Trp35Arg,ENST00000575690,;ACSM2A,missense_variant,p.Trp35Arg,ENST00000219054,;ACSM2A,missense_variant,p.Trp35Arg,ENST00000571894,;ACSM2A,missense_variant,p.Trp35Arg,ENST00000576361,;ACSM2A,intron_variant,,ENST00000417235,NM_001308169.1;ACSM2A,intron_variant,,ENST00000574251,;ACSM2A,intron_variant,,ENST00000575558,;ACSM2A,missense_variant,p.Trp35Arg,ENST00000574692,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,; A ENST00000573854 Transcript missense_variant 217/2837 103/1734 35/577 W/R Tgg/Agg 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 tolerated(0.23) 2/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS rs1181528729 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 20460217 20460217 T A 1 0 0 0 0 1 0 0 0 225 1696 59 4 4 ACSM2A 16 20460217 Missense_Mutation SNP T C3N-00549_T 1610269 20460217 69878128 323 15347 ARHGAP17 0 . GRCh38 16 24942052 24942052 + Silent SNP C C A C3N-00549_T C3N-00549_N C C c.1425G>T p.= p.G475G ENST00000289968 16/20 228 149 79 217 217 0 strelka-varscan-mutect ARHGAP17,synonymous_variant,p.=,ENST00000289968,NM_001006634.2;ARHGAP17,synonymous_variant,p.=,ENST00000303665,NM_018054.5;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000572314,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000575412,;ARHGAP17,upstream_gene_variant,,ENST00000575283,;ARHGAP17,downstream_gene_variant,,ENST00000570841,; A ENST00000289968 Transcript synonymous_variant 1495/3461 1425/2646 475/881 G ggG/ggT COSM4662728,COSM4662729 1 -1 ARHGAP17 HGNC HGNC:18239 protein_coding YES CCDS32409.1 ENSP00000289968 Q68EM7 UPI00000433FD NM_001006634.2 16/20 hmmpanther:PTHR14130,hmmpanther:PTHR14130:SF3 1,1 LOW 1 SNV 1 1,1 1 PASS rs1384358253 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 24942052 24942052 C A 1 0 0 0 0 0 0 0 1 991 842 30 2 2 ARHGAP17 16 24942052 Silent SNP C C3N-00549_T 4481835 24942052 65396293 324 15348 ITGAM 0 . GRCh38 16 31325286 31325286 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2390G>T p.Gly797Val p.G797V ENST00000544665 20/30 78 45 33 62 62 0 strelka-varscan-mutect ITGAM,missense_variant,p.Gly797Val,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Gly796Val,ENST00000287497,NM_000632.3;ITGAM,downstream_gene_variant,,ENST00000567031,;ITGAM,non_coding_transcript_exon_variant,,ENST00000561838,;ITGAM,upstream_gene_variant,,ENST00000569746,;ITGAM,upstream_gene_variant,,ENST00000567178,; T ENST00000544665 Transcript missense_variant 2461/4718 2390/3462 797/1153 G/V gGg/gTg 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 tolerated(0.57) 20/30 Gene3D:2.60.40.1510,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs1198454343 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 31325286 31325286 G T 1 0 0 0 0 1 0 0 0 7794 1232 43 2 2 ITGAM 16 31325286 Missense_Mutation SNP G C3N-00549_T 6383234 31325286 59013059 325 15349 CDH8 0 . GRCh38 16 61817636 61817636 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1120G>T p.Asp374Tyr p.D374Y ENST00000577390 7/12 192 99 93 160 160 0 strelka-varscan-mutect CDH8,missense_variant,p.Asp374Tyr,ENST00000577390,NM_001796.4;CDH8,missense_variant,p.Asp374Tyr,ENST00000577730,;CDH8,missense_variant,p.Asp374Tyr,ENST00000584337,;CDH8,missense_variant,p.Asp374Tyr,ENST00000299345,;CDH8,missense_variant,p.Asp374Tyr,ENST00000583382,;CDH8,missense_variant,p.Asp374Tyr,ENST00000585315,;CDH8,non_coding_transcript_exon_variant,,ENST00000582242,; A ENST00000577390 Transcript missense_variant 2075/9721 1120/2400 374/799 D/Y Gac/Tac 1 -1 CDH8 HGNC HGNC:1767 protein_coding YES CCDS10802.1 ENSP00000462701 P55286 UPI0000126D9F NM_001796.4 deleterious(0) 7/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF273,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 61817636 61817636 C A 1 0 0 0 0 1 0 0 0 2819 913 32 2 2 CDH8 16 61817636 Missense_Mutation SNP C C3N-00549_T 30492350 61817636 28520709 326 15350 RANBP10 0 . GRCh38 16 67729455 67729455 + Missense_Mutation SNP C C G rs758630219 C3N-00549_T C3N-00549_N C C c.1177G>C p.Val393Leu p.V393L ENST00000317506 10/14 190 103 87 142 142 0 strelka-varscan-mutect RANBP10,missense_variant,p.Val393Leu,ENST00000317506,NM_020850.1;RANBP10,missense_variant,p.Val393Leu,ENST00000630626,;RANBP10,missense_variant,p.Val393Leu,ENST00000602677,;RANBP10,missense_variant,p.Val337Leu,ENST00000448631,;RANBP10,3_prime_UTR_variant,,ENST00000602506,;RANBP10,downstream_gene_variant,,ENST00000602525,;RANBP10,downstream_gene_variant,,ENST00000602638,; G ENST00000317506 Transcript missense_variant 1293/5341 1177/1863 393/620 V/L Gtc/Ctc rs758630219,COSM271959,COSM5113570,COSM972567 1 -1 RANBP10 HGNC HGNC:29285 protein_coding YES CCDS32469.1 ENSP00000316589 Q6VN20 UPI00001C1FA6 NM_020850.1 tolerated(0.16) 10/14 Pfam_domain:PF10607 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs758630219 . 0 201 3 5 0 0 0 0 -20 0.9997865 1 1 1 0 G 3 3 50 67729455 67729455 C G 1 0 0 0 0 1 0 0 0 13185 536 19 4 4 RANBP10 16 67729455 Missense_Mutation SNP C C3N-00549_T 5911819 67729455 22608890 327 15351 ZFP90 0 . GRCh38 16 68564353 68564353 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1566G>T p.Glu522Asp p.E522D ENST00000570495 5/5 184 104 80 130 130 0 strelka-varscan-mutect ZFP90,missense_variant,p.Glu522Asp,ENST00000570495,NM_001305203.1;ZFP90,missense_variant,p.Glu522Asp,ENST00000398253,NM_133458.2;ZFP90,missense_variant,p.Glu522Asp,ENST00000563169,;ZFP90,intron_variant,,ENST00000611381,NM_001305204.1;ZFP90,intron_variant,,ENST00000573113,;ZFP90,downstream_gene_variant,,ENST00000564323,;ZFP90,downstream_gene_variant,,ENST00000573685,;ZFP90,downstream_gene_variant,,ENST00000562156,;ZFP90,3_prime_UTR_variant,,ENST00000564558,;ZFP90,non_coding_transcript_exon_variant,,ENST00000571720,;ZFP90,downstream_gene_variant,,ENST00000571809,;ZFP90,downstream_gene_variant,,ENST00000576805,;ZFP90,downstream_gene_variant,,ENST00000569323,; T ENST00000570495 Transcript missense_variant 1858/4636 1566/1911 522/636 E/D gaG/gaT 1 1 ZFP90 HGNC HGNC:23329 protein_coding YES CCDS42183.1 ENSP00000460547 Q8TF47 UPI000004C096 NM_001305203.1 deleterious(0.01) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF143,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 68564353 68564353 G T 1 0 0 0 0 1 0 0 0 18231 933 33 2 2 ZFP90 16 68564353 Missense_Mutation SNP G C3N-00549_T 834898 68564353 21773992 328 15352 ZNF469 0 . GRCh38 16 88439198 88439198 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.11644G>T p.Ala3882Ser p.A3882S ENST00000437464 2/2 419 210 209 364 364 0 strelka-varscan-mutect ZNF469,missense_variant,p.Ala3910Ser,ENST00000565624,;ZNF469,missense_variant,p.Ala3882Ser,ENST00000437464,NM_001127464.2; T ENST00000437464 Transcript missense_variant 11644/13203 11644/11778 3882/3925 A/S Gct/Tct 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.09) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 88439198 88439198 G T 1 0 0 0 0 1 0 0 0 18500 971 34 2 2 ZNF469 16 88439198 Missense_Mutation SNP G C3N-00549_T 19874845 88439198 1899147 329 15353 RAP1GAP2 0 . GRCh38 17 2905303 2905303 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.100A>T p.Ser34Cys p.S34C ENST00000254695 3/25 177 123 54 155 155 0 strelka-varscan-mutect RAP1GAP2,missense_variant,p.Ser34Cys,ENST00000254695,NM_015085.4;RAP1GAP2,missense_variant,p.Ser34Cys,ENST00000366401,NM_001100398.1;RAP1GAP2,missense_variant,p.Ser15Cys,ENST00000540393,;RAP1GAP2,missense_variant,p.Ser75Cys,ENST00000637138,;RAP1GAP2,missense_variant,p.Ser34Cys,ENST00000542807,; T ENST00000254695 Transcript missense_variant 190/6661 100/2193 34/730 S/C Agc/Tgc 1 1 RAP1GAP2 HGNC HGNC:29176 protein_coding YES CCDS45573.1 ENSP00000254695 Q684P5 UPI0000D622A3 NM_015085.4 tolerated(0.08) 3/25 hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 2905303 2905303 A T 1 0 0 0 0 1 0 0 0 13197 188 7 4 4 RAP1GAP2 17 2905303 Missense_Mutation SNP A C3N-00549_T 2905303 80352138 330 15354 ENO3 0 . GRCh38 17 4953089 4953089 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.220G>T p.Gly74Cys p.G74C ENST00000323997 4/12 698 442 256 481 480 1 strelka-varscan-mutect ENO3,missense_variant,p.Gly74Cys,ENST00000323997,NM_001976.4,NM_053013.3;ENO3,missense_variant,p.Gly74Cys,ENST00000518175,;ENO3,missense_variant,p.Gly74Cys,ENST00000522301,;ENO3,missense_variant,p.Gly74Cys,ENST00000519602,;ENO3,missense_variant,p.Gly74Cys,ENST00000520221,;ENO3,missense_variant,p.Gly74Cys,ENST00000521811,;ENO3,missense_variant,p.Gly74Cys,ENST00000522798,;ENO3,missense_variant,p.Gly74Cys,ENST00000522249,;ENO3,intron_variant,,ENST00000519584,NM_001193503.1;PFN1,upstream_gene_variant,,ENST00000225655,NM_005022.3;PFN1,upstream_gene_variant,,ENST00000572383,;ENO3,downstream_gene_variant,,ENST00000519266,;ENO3,3_prime_UTR_variant,,ENST00000521659,;ENO3,non_coding_transcript_exon_variant,,ENST00000519834,;ENO3,non_coding_transcript_exon_variant,,ENST00000571235,;ENO3,upstream_gene_variant,,ENST00000522954,;ENO3,upstream_gene_variant,,ENST00000522425,;ENO3,downstream_gene_variant,,ENST00000518972,;ENO3,downstream_gene_variant,,ENST00000519300,; T ENST00000323997 Transcript missense_variant 352/1521 220/1305 74/434 G/C Ggc/Tgc 1 1 ENO3 HGNC HGNC:3354 protein_coding YES CCDS11062.1 ENSP00000324105 P13929 UPI000016A894 NM_001976.4,NM_053013.3 deleterious_low_confidence(0) 4/12 Gene3D:3.30.390.10,HAMAP:MF_00318,Pfam_domain:PF03952,PIRSF_domain:PIRSF001400,hmmpanther:PTHR11902,hmmpanther:PTHR11902:SF5,SMART_domains:SM01193,Superfamily_domains:SSF54826,TIGRFAM_domain:TIGR01060 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 4953089 4953089 G T 1 0 0 0 0 1 0 0 0 4967 1232 43 2 2 ENO3 17 4953089 Missense_Mutation SNP G C3N-00549_T 2047786 4953089 78304352 331 15355 ZNF232 0 . GRCh38 17 5105990 5105990 + Missense_Mutation SNP T T C novel C3N-00549_T C3N-00549_N T T c.1169A>G p.Asn390Ser p.N390S ENST00000250076 5/5 186 105 81 185 185 0 strelka-varscan-mutect ZNF232,missense_variant,p.Asn390Ser,ENST00000250076,NM_014519.2;ZNF232,missense_variant,p.Asn381Ser,ENST00000575898,;ZNF232,downstream_gene_variant,,ENST00000575538,;ZNF232,3_prime_UTR_variant,,ENST00000570486,;ZNF232,3_prime_UTR_variant,,ENST00000573015,;ZNF232,non_coding_transcript_exon_variant,,ENST00000574735,;ZNF232,downstream_gene_variant,,ENST00000572468,;ZNF232,downstream_gene_variant,,ENST00000571076,; C ENST00000250076 Transcript missense_variant 1824/2179 1169/1335 390/444 N/S aAt/aGt 1 -1 ZNF232 HGNC HGNC:13026 protein_coding YES CCDS11068.1 ENSP00000250076 Q9UNY5 UPI00001D69EB NM_014519.2 tolerated(0.23) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF54,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 5105990 5105990 T C 1 0 0 0 0 1 0 0 0 18362 1493 52 5 5 ZNF232 17 5105990 Missense_Mutation SNP T C3N-00549_T 152901 5105990 78151451 332 15356 SLC13A5 0 . GRCh38 17 6706683 6706683 + Silent SNP G G T rs761010502 C3N-00549_T C3N-00549_N G G c.327C>A p.= p.I109I ENST00000433363 3/12 243 144 99 222 222 0 strelka-varscan-mutect SLC13A5,synonymous_variant,p.=,ENST00000433363,NM_177550.4;SLC13A5,synonymous_variant,p.=,ENST00000293800,NM_001284509.1;SLC13A5,synonymous_variant,p.=,ENST00000381074,NM_001284510.1;SLC13A5,synonymous_variant,p.=,ENST00000573648,NM_001143838.2;SLC13A5,synonymous_variant,p.=,ENST00000572352,;SLC13A5,non_coding_transcript_exon_variant,,ENST00000576323,;SLC13A5,3_prime_UTR_variant,,ENST00000572094,;SLC13A5,3_prime_UTR_variant,,ENST00000575230,;SLC13A5,upstream_gene_variant,,ENST00000574824,; T ENST00000433363 Transcript synonymous_variant 561/3435 327/1707 109/568 I atC/atA rs761010502 1 -1 SLC13A5 HGNC HGNC:23089 protein_coding YES CCDS11079.1 ENSP00000406220 Q86YT5 UPI000000D834 NM_177550.4 3/12 hmmpanther:PTHR10283:SF82,hmmpanther:PTHR10283,Pfam_domain:PF00939 LOW 1 SNV 1 1 PASS rs761010502 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 6706683 6706683 G T 1 0 0 0 0 0 0 0 1 14660 1048 37 1 1 SLC13A5 17 6706683 Silent SNP G C3N-00549_T 1600693 6706683 76550758 333 15357 EIF5A 0 . GRCh38 17 7309685 7309685 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.140C>G p.Thr47Ser p.T47S ENST00000336452 2/6 546 337 209 539 539 0 strelka-varscan-mutect EIF5A,missense_variant,p.Thr17Ser,ENST00000336458,NM_001970.4;EIF5A,missense_variant,p.Thr17Ser,ENST00000576930,;EIF5A,missense_variant,p.Thr17Ser,ENST00000571955,;EIF5A,missense_variant,p.Thr17Ser,ENST00000416016,NM_001143762.1;EIF5A,missense_variant,p.Thr17Ser,ENST00000419711,NM_001143761.1;EIF5A,missense_variant,p.Thr47Ser,ENST00000336452,NM_001143760.1;EIF5A,missense_variant,p.Thr17Ser,ENST00000573542,;EIF5A,missense_variant,p.Thr17Ser,ENST00000572815,;EIF5A,missense_variant,p.Thr17Ser,ENST00000573714,;GPS2,downstream_gene_variant,,ENST00000380728,;GPS2,downstream_gene_variant,,ENST00000389167,NM_004489.4;GPS2,downstream_gene_variant,,ENST00000570780,;GPS2,downstream_gene_variant,,ENST00000577040,;GPS2,downstream_gene_variant,,ENST00000573684,;GPS2,downstream_gene_variant,,ENST00000574458,;EIF5A,non_coding_transcript_exon_variant,,ENST00000355068,;EIF5A,non_coding_transcript_exon_variant,,ENST00000575001,;RP11-542C16.2,downstream_gene_variant,,ENST00000575474,;RP11-542C16.2,downstream_gene_variant,,ENST00000315601,;GPS2,downstream_gene_variant,,ENST00000571697,;GPS2,downstream_gene_variant,,ENST00000571569,;GPS2,downstream_gene_variant,,ENST00000572172,;GPS2,downstream_gene_variant,,ENST00000572363,;GPS2,downstream_gene_variant,,ENST00000571098,;GPS2,downstream_gene_variant,,ENST00000572707,;GPS2,downstream_gene_variant,,ENST00000573059,;GPS2,downstream_gene_variant,,ENST00000573807,;GPS2,downstream_gene_variant,,ENST00000571695,;GPS2,downstream_gene_variant,,ENST00000574201,; G ENST00000336452 Transcript missense_variant 188/1256 140/555 47/184 T/S aCc/aGc 1 1 EIF5A HGNC HGNC:3300 protein_coding YES CCDS45601.1 ENSP00000336702 P63241 UPI00001B5C0C NM_001143760.1 deleterious(0.03) 2/6 Gene3D:2.30.30.30,PIRSF_domain:PIRSF003025,hmmpanther:PTHR11673,hmmpanther:PTHR11673:SF11,Superfamily_domains:SSF50104,TIGRFAM_domain:TIGR00037 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 7309685 7309685 C G 1 0 0 0 0 1 0 0 0 4874 507 18 4 4 EIF5A 17 7309685 Missense_Mutation SNP C C3N-00549_T 603002 7309685 75947756 334 15358 TP53 0 . GRCh38 17 7674229 7674229 + Missense_Mutation SNP C C A rs121912656 C3N-00549_T C3N-00549_N C C c.734G>T p.Gly245Val p.G245V ENST00000269305 7/11 362 248 114 292 291 1 strelka-varscan-mutect TP53,missense_variant,p.Gly245Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly245Val,ENST00000420246,;TP53,missense_variant,p.Gly206Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly206Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly245Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly206Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly245Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly206Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly245Val,ENST00000445888,;TP53,missense_variant,p.Gly206Val,ENST00000619485,;TP53,missense_variant,p.Gly113Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly86Val,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly113Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly86Val,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly113Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly86Val,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly245Val,ENST00000359597,;TP53,missense_variant,p.Gly234Val,ENST00000615910,;TP53,missense_variant,p.Gly245Val,ENST00000413465,;TP53,missense_variant,p.Gly113Val,ENST00000509690,;TP53,missense_variant,p.Gly152Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly206Val,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 924/2579 734/1182 245/393 G/V gGc/gTc rs121912656,CM010464,CM900209,TP53_g.13371G>C,TP53_g.13371del,TP53_g.13371G>A,TP53_g.13371G>T,COSM11196,COSM131475,COSM131476,COSM131477,COSM1640832,COSM1646856,COSM179805,COSM179806,COSM179807,COSM3388184,COSM3388185,COSM3388186,COSM3388187,COSM3388188,COSM3388189,COSM3717638,COSM43606,COSM43965,COSM45770 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912656 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 7674229 7674229 C A 1 0 0 0 0 1 0 0 0 16859 739 26 2 2 TP53 17 7674229 Missense_Mutation SNP C C3N-00549_T 364544 7674229 75583212 335 15359 TP53 0 . GRCh38 17 7676185 7676185 + Nonsense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.184G>T p.Glu62Ter p.E62* ENST00000269305 4/11 304 183 121 259 259 0 strelka-varscan-mutect TP53,stop_gained,p.Glu62Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Glu62Ter,ENST00000420246,;TP53,stop_gained,p.Glu23Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Glu23Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Glu62Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Glu23Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Glu62Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Glu23Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Glu62Ter,ENST00000445888,;TP53,stop_gained,p.Glu23Ter,ENST00000619485,;TP53,stop_gained,p.Glu62Ter,ENST00000359597,;TP53,stop_gained,p.Glu62Ter,ENST00000615910,;TP53,stop_gained,p.Glu62Ter,ENST00000413465,;TP53,stop_gained,p.Glu62Ter,ENST00000508793,;TP53,stop_gained,p.Glu62Ter,ENST00000604348,;TP53,stop_gained,p.Glu62Ter,ENST00000503591,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000510385,NM_001126116.1;TP53,upstream_gene_variant,,ENST00000618944,NM_001276698.1;TP53,upstream_gene_variant,,ENST00000504290,NM_001126117.1;TP53,upstream_gene_variant,,ENST00000610623,NM_001276699.1;TP53,upstream_gene_variant,,ENST00000504937,NM_001126115.1;TP53,upstream_gene_variant,,ENST00000619186,NM_001276697.1;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Glu23Ter,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained 374/2579 184/1182 62/393 E/* Gaa/Taa CM120852,TP53_g.11415G>T,COSM10827,COSM116688,COSM116689,COSM116690,COSM1664640,COSM1664641,COSM1664642,COSM4995784,COSM4995785 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 4/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6 0,0,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,0,1,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 7676185 7676185 C A 1 0 0 0 0 0 1 0 0 16859 835 29 2 2 TP53 17 7676185 Nonsense_Mutation SNP C C3N-00549_T 1956 7676185 75581256 336 15360 ALOXE3 0 . GRCh38 17 8110440 8110440 + Frame_Shift_Del DEL G G - novel C3N-00549_T C3N-00549_N G G c.1442delC p.Pro481HisfsTer99 p.P481Hfs*99 ENST00000318227 9/16 107 63 44 67 67 0 sindel-varindel-pindel ALOXE3,frameshift_variant,p.Pro505HisfsTer99,ENST00000380149,;ALOXE3,frameshift_variant,p.Pro349HisfsTer99,ENST00000448843,NM_021628.2;ALOXE3,frameshift_variant,p.Pro481HisfsTer99,ENST00000318227,NM_001165960.1; - ENST00000318227 Transcript frameshift_variant 1711/3053 1442/2532 481/843 P/X cCa/ca 1 -1 ALOXE3 HGNC HGNC:13743 protein_coding YES CCDS54084.1 ENSP00000314879 Q9BYJ1 UPI0000EE63AA NM_001165960.1 9/16 Gene3D:3.10.450.60,Pfam_domain:PF00305,PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF62,Superfamily_domains:SSF48484 HIGH 1 deletion 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 50 8110440 8110440 G - 1 0 1 0 1 0 0 0 0 642 1348 47 0 0 ALOXE3 17 8110440 Frame_Shift_Del DEL G C3N-00549_T 434255 8110440 75147001 337 15361 SPDYE4 0 . GRCh38 17 8753340 8753340 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.635C>A p.Ser212Tyr p.S212Y ENST00000328794 5/6 130 78 52 105 105 0 strelka-varscan-mutect SPDYE4,missense_variant,p.Ser212Tyr,ENST00000328794,NM_001128076.1;SPDYE4,downstream_gene_variant,,ENST00000580999,;SPDYE4,3_prime_UTR_variant,,ENST00000582989,; T ENST00000328794 Transcript missense_variant 812/923 635/714 212/237 S/Y tCc/tAc COSM5539614 1 -1 SPDYE4 HGNC HGNC:35463 protein_coding YES CCDS45609.1 ENSP00000329522 A6NLX3 UPI0000DD83CC NM_001128076.1 deleterious(0.01) 5/6 hmmpanther:PTHR31156,Pfam_domain:PF11357 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 8753340 8753340 G T 1 0 0 0 0 1 0 0 0 15380 1174 41 2 2 SPDYE4 17 8753340 Missense_Mutation SNP G C3N-00549_T 642900 8753340 74504101 338 15362 MYH1 0 . GRCh38 17 10498786 10498786 + Missense_Mutation SNP G G A rs3744564 C3N-00549_T C3N-00549_N G G c.4021C>T p.Arg1341Cys p.R1341C ENST00000226207 30/40 202 122 80 167 167 0 strelka-varscan-mutect MYH1,missense_variant,p.Arg1341Cys,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 4116/6024 4021/5820 1341/1939 R/C Cgc/Tgc rs3744564,COSM361171 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 30/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 0,1 MODERATE SNV 5 0,1 1 PASS rs3744564 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 10498786 10498786 G A 1 0 0 0 0 1 0 0 0 10029 1116 39 1 1 MYH1 17 10498786 Missense_Mutation SNP G C3N-00549_T 1745446 10498786 72758655 339 15363 MYH1 0 . GRCh38 17 10512780 10512780 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.909G>T p.Met303Ile p.M303I ENST00000226207 11/40 314 225 89 245 244 1 strelka-varscan-mutect MYH1,missense_variant,p.Met303Ile,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 1004/6024 909/5820 303/1939 M/I atG/atT 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0.02) 11/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 10512780 10512780 C A 1 0 0 0 0 1 0 0 0 10029 724 25 2 2 MYH1 17 10512780 Missense_Mutation SNP C C3N-00549_T 13994 10512780 72744661 340 15364 EFCAB5 0 . GRCh38 17 30059683 30059683 + Nonsense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.2719A>T p.Lys907Ter p.K907* ENST00000394835 14/23 96 52 44 74 74 0 strelka-varscan-mutect EFCAB5,stop_gained,p.Lys907Ter,ENST00000394835,NM_198529.3;EFCAB5,stop_gained,p.Lys706Ter,ENST00000588978,;EFCAB5,intron_variant,,ENST00000419434,;EFCAB5,intron_variant,,ENST00000536908,NM_001145053.1;AC104984.4,non_coding_transcript_exon_variant,,ENST00000583250,;RNY4P13,upstream_gene_variant,,ENST00000384284,;EFCAB5,stop_gained,p.Lys907Ter,ENST00000440741,;EFCAB5,non_coding_transcript_exon_variant,,ENST00000581617,;EFCAB5,intron_variant,,ENST00000423598,;RNY4P13,upstream_gene_variant,,ENST00000590718,; T ENST00000394835 Transcript stop_gained 2911/5132 2719/4512 907/1503 K/* Aaa/Taa 1 1 EFCAB5 HGNC HGNC:24801 protein_coding YES CCDS11254.2 ENSP00000378312 A4FU69 UPI0000E59EF5 NM_198529.3 14/23 Gene3D:1.10.238.10,hmmpanther:PTHR31938,hmmpanther:PTHR31938:SF6 HIGH 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 30059683 30059683 A T 1 0 0 0 0 0 1 0 0 4772 15 1 4 4 EFCAB5 17 30059683 Nonsense_Mutation SNP A C3N-00549_T 19546903 30059683 53197758 341 15365 NF1 0 . GRCh38 17 31230879 31230879 + Nonsense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.3151G>T p.Gly1051Ter p.G1051* ENST00000358273 24/58 303 182 121 206 206 0 strelka-varscan-mutect NF1,stop_gained,p.Gly1051Ter,ENST00000358273,NM_001042492.2;NF1,stop_gained,p.Gly1051Ter,ENST00000356175,NM_000267.3;NF1,stop_gained,p.Gly717Ter,ENST00000456735,;NF1,stop_gained,p.Gly1085Ter,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000466819,;NF1,upstream_gene_variant,,ENST00000479614,; T ENST00000358273 Transcript stop_gained 3534/12425 3151/8520 1051/2839 G/* Gga/Tga CD982826 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 24/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 31230879 31230879 G T 1 0 0 0 0 0 1 0 0 10393 1233 43 2 2 NF1 17 31230879 Nonsense_Mutation SNP G C3N-00549_T 1171196 31230879 52026562 342 15366 KRT17 0 . GRCh38 17 41624137 41624137 + Missense_Mutation SNP G G T rs747955715 C3N-00549_T C3N-00549_N G G c.373C>A p.Pro125Thr p.P125T ENST00000311208 1/8 759 451 308 713 712 1 strelka-varscan-mutect KRT17,missense_variant,p.Pro125Thr,ENST00000311208,NM_000422.2;KRT17,missense_variant,p.Pro42Thr,ENST00000540235,;KRT17,missense_variant,p.Pro110Thr,ENST00000577817,;KRT17,5_prime_UTR_variant,,ENST00000463128,;KRT17,upstream_gene_variant,,ENST00000590038,;KRT42P,downstream_gene_variant,,ENST00000438131,;KRT42P,downstream_gene_variant,,ENST00000398469,;KRT17,non_coding_transcript_exon_variant,,ENST00000493253,;KRT17,non_coding_transcript_exon_variant,,ENST00000491673,;KRT42P,downstream_gene_variant,,ENST00000587335,;KRT42P,downstream_gene_variant,,ENST00000458343,; T ENST00000311208 Transcript missense_variant 441/1524 373/1299 125/432 P/T Ccg/Acg rs747955715 1 -1 KRT17 HGNC HGNC:6427 protein_coding YES CCDS11402.1 ENSP00000308452 Q04695 UPI0000148FD6 NM_000422.2 deleterious(0.05) 1/8 hmmpanther:PTHR23239:SF180,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs747955715 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 41624137 41624137 G T 1 0 0 0 0 1 0 0 0 8336 1232 43 2 2 KRT17 17 41624137 Missense_Mutation SNP G C3N-00549_T 10393258 41624137 41633304 343 15367 SKAP1 0 . GRCh38 17 48187868 48187868 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.417C>A p.= p.L139L ENST00000336915 6/13 151 89 62 139 139 0 strelka-varscan-mutect SKAP1,synonymous_variant,p.=,ENST00000336915,NM_003726.3,NM_001075099.1;SKAP1,synonymous_variant,p.=,ENST00000584924,;SKAP1,upstream_gene_variant,,ENST00000579336,;RP11-456D7.1,intron_variant,,ENST00000582246,;SKAP1,synonymous_variant,p.=,ENST00000581400,;SKAP1,3_prime_UTR_variant,,ENST00000584709,;SKAP1,3_prime_UTR_variant,,ENST00000581419,; T ENST00000336915 Transcript synonymous_variant 487/1534 417/1080 139/359 L ctC/ctA 1 -1 SKAP1 HGNC HGNC:15605 protein_coding YES CCDS32674.1 ENSP00000338171 Q86WV1 UPI0000200EFD NM_003726.3,NM_001075099.1 6/13 PROSITE_profiles:PS50003,hmmpanther:PTHR15129:SF1,hmmpanther:PTHR15129,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 48187868 48187868 G T 1 0 0 0 0 0 0 0 1 14617 929 33 2 2 SKAP1 17 48187868 Silent SNP G C3N-00549_T 6563731 48187868 35069573 344 15368 ABCC3 0 . GRCh38 17 50691107 50691107 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.4491C>A p.Asp1497Glu p.D1497E ENST00000285238 31/31 272 144 128 181 181 0 strelka-varscan-mutect ABCC3,missense_variant,p.Asp1497Glu,ENST00000285238,NM_003786.3;ANKRD40,downstream_gene_variant,,ENST00000285243,NM_052855.3;RP11-294J22.6,upstream_gene_variant,,ENST00000574246,;ABCC3,3_prime_UTR_variant,,ENST00000502426,;ABCC3,3_prime_UTR_variant,,ENST00000505699,;ABCC3,non_coding_transcript_exon_variant,,ENST00000503337,;ABCC3,non_coding_transcript_exon_variant,,ENST00000508929,;ABCC3,downstream_gene_variant,,ENST00000504586,; A ENST00000285238 Transcript missense_variant 4571/5716 4491/4584 1497/1527 D/E gaC/gaA 1 1 ABCC3 HGNC HGNC:54 protein_coding YES CCDS32681.1 ENSP00000285238 O15438 UPI000004B145 NM_003786.3 tolerated(0.18) 31/31 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF221,SMART_domains:SM00382,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00957 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 50691107 50691107 C A 1 0 0 0 0 1 0 0 0 58 477 17 2 2 ABCC3 17 50691107 Missense_Mutation SNP C C3N-00549_T 2503239 50691107 32566334 345 15369 PCTP 0 . GRCh38 17 55774817 55774817 + Silent SNP G G T rs79806530 C3N-00549_T C3N-00549_N G G c.537G>T p.= p.P179P ENST00000268896 5/6 217 132 85 243 243 0 strelka-varscan-mutect PCTP,synonymous_variant,p.=,ENST00000576183,;PCTP,synonymous_variant,p.=,ENST00000268896,NM_021213.3;PCTP,synonymous_variant,p.=,ENST00000325214,NM_001102402.2;PCTP,synonymous_variant,p.=,ENST00000573500,;PCTP,synonymous_variant,p.=,ENST00000572536,;PCTP,non_coding_transcript_exon_variant,,ENST00000576221,;PCTP,3_prime_UTR_variant,,ENST00000417982,;PCTP,non_coding_transcript_exon_variant,,ENST00000571489,; T ENST00000268896 Transcript synonymous_variant 662/2044 537/645 179/214 P ccG/ccT rs79806530,COSM5321276 1 1 PCTP HGNC HGNC:8752 protein_coding YES CCDS11588.1 ENSP00000268896 Q9UKL6 Q549N3 UPI0000112490 NM_021213.3 5/6 Gene3D:3.30.530.20,Pfam_domain:PF01852,PROSITE_profiles:PS50848,hmmpanther:PTHR19308,hmmpanther:PTHR19308:SF15,SMART_domains:SM00234,Superfamily_domains:SSF55961 0,1 LOW 1 SNV 1 0,1 1 PASS rs79806530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 55774817 55774817 G T 1 0 0 0 0 0 0 0 1 11695 1103 39 1 1 PCTP 17 55774817 Silent SNP G C3N-00549_T 5083710 55774817 27482624 346 15370 TUBD1 0 . GRCh38 17 59878285 59878285 + Missense_Mutation SNP C C A rs760435470 C3N-00549_T C3N-00549_N C C c.587G>T p.Arg196Leu p.R196L ENST00000325752 5/9 254 160 94 235 234 1 strelka-varscan-mutect TUBD1,missense_variant,p.Arg196Leu,ENST00000325752,NM_016261.3;TUBD1,missense_variant,p.Arg196Leu,ENST00000613721,NM_001193611.1;TUBD1,missense_variant,p.Arg196Leu,ENST00000340993,NM_001193609.1,NM_001193612.1;TUBD1,missense_variant,p.Arg196Leu,ENST00000394239,NM_001193610.1;TUBD1,missense_variant,p.Arg196Leu,ENST00000592426,;TUBD1,missense_variant,p.Arg196Leu,ENST00000376094,;TUBD1,5_prime_UTR_variant,,ENST00000539018,NM_001193613.1;TUBD1,intron_variant,,ENST00000346141,;TUBD1,downstream_gene_variant,,ENST00000590498,;TUBD1,downstream_gene_variant,,ENST00000591611,;TUBD1,3_prime_UTR_variant,,ENST00000591548,;TUBD1,non_coding_transcript_exon_variant,,ENST00000587476,;TUBD1,non_coding_transcript_exon_variant,,ENST00000588009,;TUBD1,intron_variant,,ENST00000593110,; A ENST00000325752 Transcript missense_variant 875/2490 587/1362 196/453 R/L cGa/cTa rs760435470,COSM3196510 1 -1 TUBD1 HGNC HGNC:16811 protein_coding YES CCDS11620.1 ENSP00000320797 Q9UJT1 UPI000013D7FA NM_016261.3 tolerated(0.05) 5/9 hmmpanther:PTHR11588:SF4,hmmpanther:PTHR11588,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161,Prints_domain:PR01224 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs760435470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 59878285 59878285 C A 1 0 0 0 0 1 0 0 0 17272 884 31 1 1 TUBD1 17 59878285 Missense_Mutation SNP C C3N-00549_T 4103468 59878285 23379156 347 15371 KCNH6 0 . GRCh38 17 63542306 63542306 + Missense_Mutation SNP G G T rs201547916 C3N-00549_T C3N-00549_N G G c.2020G>T p.Val674Leu p.V674L ENST00000583023 9/14 291 188 103 229 229 0 strelka-varscan-mutect KCNH6,missense_variant,p.Val674Leu,ENST00000583023,NM_030779.3;KCNH6,missense_variant,p.Val674Leu,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,missense_variant,p.Val621Leu,ENST00000581784,NM_173092.2;KCNH6,missense_variant,p.Val621Leu,ENST00000456941,;KCNH6,3_prime_UTR_variant,,ENST00000583465,; T ENST00000583023 Transcript missense_variant 2031/3821 2020/2985 674/994 V/L Gtg/Ttg rs201547916 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 deleterious(0.01) 9/14 Gene3D:2.60.120.10,Pfam_domain:PF00027,Prints_domain:PR01463,PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS rs201547916 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 63542306 63542306 G T 1 0 0 0 0 1 0 0 0 7952 1145 40 1 1 KCNH6 17 63542306 Missense_Mutation SNP G C3N-00549_T 3664021 63542306 19715135 348 15372 SCN4A 0 . GRCh38 17 63941494 63941494 + Silent SNP G G A C3N-00549_T C3N-00549_N G G c.4788C>T p.= p.I1596I ENST00000435607 24/24 726 444 282 541 541 0 strelka-varscan-mutect SCN4A,synonymous_variant,p.=,ENST00000435607,NM_000334.4;SCN4A,synonymous_variant,p.=,ENST00000578147,; A ENST00000435607 Transcript synonymous_variant 4865/7805 4788/5511 1596/1836 I atC/atT COSM4496590 1 -1 SCN4A HGNC HGNC:10591 protein_coding YES CCDS45761.1 ENSP00000396320 P35499 UPI0000201254 NM_000334.4 24/24 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF223,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00170 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 63941494 63941494 G A 1 0 0 0 0 0 0 0 1 14189 1280 45 3 3 SCN4A 17 63941494 Silent SNP G C3N-00549_T 399188 63941494 19315947 349 15373 CACNG1 0 . GRCh38 17 67056084 67056084 + Nonsense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.482C>A p.Ser161Ter p.S161* ENST00000226021 4/4 247 115 132 217 217 0 strelka-varscan-mutect CACNG1,stop_gained,p.Ser161Ter,ENST00000226021,NM_000727.3; A ENST00000226021 Transcript stop_gained 553/1266 482/669 161/222 S/* tCg/tAg 1 1 CACNG1 HGNC HGNC:1405 protein_coding YES CCDS11668.1 ENSP00000226021 Q06432 UPI00001272A9 NM_000727.3 4/4 Pfam_domain:PF13903,Prints_domain:PR01792,hmmpanther:PTHR15025,hmmpanther:PTHR15025:SF1 HIGH 1 SNV 1 1 PASS rs1324628915 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 50 67056084 67056084 C A 1 0 0 0 0 0 1 0 0 2244 893 31 1 1 CACNG1 17 67056084 Nonsense_Mutation SNP C C3N-00549_T 3114590 67056084 16201357 350 15374 MGAT5B 0 . GRCh38 17 76925071 76925071 + Silent SNP C C T novel C3N-00549_T C3N-00549_N C C c.1164C>T p.= p.H388H ENST00000428789 8/16 207 112 95 177 177 0 strelka-varscan-mutect MGAT5B,synonymous_variant,p.=,ENST00000569840,NM_001199172.1;MGAT5B,synonymous_variant,p.=,ENST00000301618,NM_144677.2;MGAT5B,synonymous_variant,p.=,ENST00000428789,NM_198955.1;MGAT5B,downstream_gene_variant,,ENST00000563627,;MGAT5B,synonymous_variant,p.=,ENST00000565043,; T ENST00000428789 Transcript synonymous_variant 1267/4053 1164/2406 388/801 H caC/caT 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 8/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 76925071 76925071 C T 1 0 0 0 0 0 0 0 1 9510 477 17 3 3 MGAT5B 17 76925071 Silent SNP C C3N-00549_T 9868987 76925071 6332370 351 15375 CBX2 0 . GRCh38 17 79779369 79779369 + Missense_Mutation SNP A A G novel C3N-00549_T C3N-00549_N A A c.124A>G p.Ser42Gly p.S42G ENST00000310942 3/5 598 391 207 480 480 0 strelka-varscan-mutect CBX2,missense_variant,p.Ser42Gly,ENST00000310942,NM_005189.2;CBX2,missense_variant,p.Ser42Gly,ENST00000269399,NM_032647.3;CBX2,non_coding_transcript_exon_variant,,ENST00000571484,; G ENST00000310942 Transcript missense_variant 228/4644 124/1599 42/532 S/G Agc/Ggc 1 1 CBX2 HGNC HGNC:1552 protein_coding YES CCDS32757.1 ENSP00000308750 Q14781 UPI000004C4E1 NM_005189.2 deleterious(0.01) 3/5 PROSITE_profiles:PS50013,hmmpanther:PTHR22812,hmmpanther:PTHR22812:SF98,PROSITE_patterns:PS00598,Pfam_domain:PF00385,Gene3D:2.40.50.40,SMART_domains:SM00298,Superfamily_domains:SSF54160 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 79779369 79779369 A G 1 0 0 0 0 1 0 0 0 2418 188 7 5 5 CBX2 17 79779369 Missense_Mutation SNP A C3N-00549_T 2854298 79779369 3478072 352 15376 BAHCC1 0 . GRCh38 17 81443178 81443178 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1829G>T p.Gly610Val p.G610V ENST00000584436 5/29 161 90 71 99 99 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Gly610Val,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Gly610Val,ENST00000307745,;BAHCC1,upstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 2196/10801 1829/7920 610/2639 G/V gGc/gTc 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0) 5/29 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 81443178 81443178 G T 1 0 0 0 0 1 0 0 0 1451 1203 42 2 2 BAHCC1 17 81443178 Missense_Mutation SNP G C3N-00549_T 1663809 81443178 1814263 353 15377 CEP192 0 . GRCh38 18 13099526 13099526 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.6608A>T p.Gln2203Leu p.Q2203L ENST00000506447 37/45 67 21 46 122 122 0 strelka-varscan-mutect CEP192,missense_variant,p.Gln2203Leu,ENST00000506447,NM_032142.3;CEP192,missense_variant,p.Gln1728Leu,ENST00000325971,;CEP192,missense_variant,p.Gln1742Leu,ENST00000511820,;CEP192,3_prime_UTR_variant,,ENST00000430049,;CEP192,non_coding_transcript_exon_variant,,ENST00000540847,;CEP192,upstream_gene_variant,,ENST00000508539,;CEP192,missense_variant,p.Gln1803Leu,ENST00000510237,;CEP192,missense_variant,p.Gln751Leu,ENST00000589993,;CEP192,3_prime_UTR_variant,,ENST00000513432,;CEP192,downstream_gene_variant,,ENST00000508150,; T ENST00000506447 Transcript missense_variant 6688/7960 6608/7614 2203/2537 Q/L cAg/cTg 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 tolerated(0.19) 37/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 13099526 13099526 A T 1 0 0 0 0 1 0 0 0 2967 188 7 4 4 CEP192 18 13099526 Missense_Mutation SNP A C3N-00549_T 13099526 67273759 354 15378 DSC1 0 . GRCh38 18 31156092 31156092 + Missense_Mutation SNP G G T rs773770610 C3N-00549_T C3N-00549_N G G c.422C>A p.Ala141Asp p.A141D ENST00000257198 4/16 124 41 83 238 237 1 strelka-varscan-mutect DSC1,missense_variant,p.Ala141Asp,ENST00000257197,NM_004948.3;DSC1,missense_variant,p.Ala141Asp,ENST00000257198,NM_024421.2;DSCAS,intron_variant,,ENST00000581836,; T ENST00000257198 Transcript missense_variant 684/4225 422/2685 141/894 A/D gCt/gAt rs773770610,COSM1303658,COSM1303659 1 -1 DSC1 HGNC HGNC:3035 protein_coding YES CCDS11894.1 ENSP00000257198 Q08554 UPI000006DF10 NM_024421.2 deleterious(0) 4/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF8,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs773770610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 31156092 31156092 G T 1 0 0 0 0 1 0 0 0 4586 971 34 2 2 DSC1 18 31156092 Missense_Mutation SNP G C3N-00549_T 18056566 31156092 49217193 355 15379 LOXHD1 0 . GRCh38 18 46563077 46563077 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.2586G>C p.Lys862Asn p.K862N ENST00000536736 18/40 68 18 50 74 74 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Lys862Asn,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Lys862Asn,ENST00000441551,;LOXHD1,upstream_gene_variant,,ENST00000300591,NM_001145472.2;LOXHD1,upstream_gene_variant,,ENST00000582408,;LOXHD1,upstream_gene_variant,,ENST00000419859,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; G ENST00000536736 Transcript missense_variant 2586/6848 2586/6636 862/2211 K/N aaG/aaC 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 deleterious(0.04) 18/40 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,Superfamily_domains:SSF49723 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 46563077 46563077 C G 1 0 0 0 0 1 0 0 0 8801 680 24 4 4 LOXHD1 18 46563077 Missense_Mutation SNP C C3N-00549_T 15406985 46563077 33810208 356 15380 NEDD4L 0 . GRCh38 18 58367853 58367853 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.2171G>T p.Gly724Val p.G724V ENST00000400345 22/31 118 30 88 140 140 0 strelka-varscan-mutect NEDD4L,missense_variant,p.Gly603Val,ENST00000456986,NM_001144964.1,NM_001144965.1;NEDD4L,missense_variant,p.Gly704Val,ENST00000382850,NM_015277.5;NEDD4L,missense_variant,p.Gly583Val,ENST00000456173,NM_001144970.2;NEDD4L,missense_variant,p.Gly1003Val,ENST00000635997,;NEDD4L,missense_variant,p.Gly724Val,ENST00000400345,NM_001144967.2;NEDD4L,missense_variant,p.Gly716Val,ENST00000357895,NM_001144968.1;NEDD4L,missense_variant,p.Gly583Val,ENST00000435432,NM_001144971.1;NEDD4L,missense_variant,p.Gly696Val,ENST00000586263,NM_001144969.1;NEDD4L,missense_variant,p.Gly603Val,ENST00000431212,NM_001144966.2;NEDD4L,missense_variant,p.Gly660Val,ENST00000356462,NM_001243960.1;NEDD4L,missense_variant,p.Gly620Val,ENST00000256830,;NEDD4L,missense_variant,p.Gly388Val,ENST00000587881,;NEDD4L,intron_variant,,ENST00000589054,;RP11-845C23.2,upstream_gene_variant,,ENST00000587933,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000587246,;NEDD4L,downstream_gene_variant,,ENST00000585970,;NEDD4L,downstream_gene_variant,,ENST00000590638,; T ENST00000400345 Transcript missense_variant 2454/3647 2171/2928 724/975 G/V gGg/gTg 1 1 NEDD4L HGNC HGNC:7728 protein_coding YES CCDS45872.1 ENSP00000383199 Q96PU5 UPI000058E3AE NM_001144967.2 deleterious(0) 22/31 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF310,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 58367853 58367853 G T 1 0 0 0 0 1 0 0 0 10339 1232 43 2 2 NEDD4L 18 58367853 Missense_Mutation SNP G C3N-00549_T 11804776 58367853 22005432 357 15381 SERPINB2 0 . GRCh38 18 63901792 63901792 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.588G>T p.Met196Ile p.M196I ENST00000457692 7/9 70 20 50 116 116 0 strelka-mutect SERPINB2,missense_variant,p.Met196Ile,ENST00000457692,NM_001143818.1;SERPINB2,missense_variant,p.Met196Ile,ENST00000299502,NM_002575.2;SERPINB10,missense_variant,p.Met73Ile,ENST00000397996,;SERPINB10,missense_variant,p.Met73Ile,ENST00000418725,;SERPINB2,downstream_gene_variant,,ENST00000413956,;SERPINB2,downstream_gene_variant,,ENST00000443281,;SERPINB2,downstream_gene_variant,,ENST00000404622,;SERPINB2,non_coding_transcript_exon_variant,,ENST00000482254,; T ENST00000457692 Transcript missense_variant 921/2155 588/1248 196/415 M/I atG/atT 1 1 SERPINB2 HGNC HGNC:8584 protein_coding YES CCDS11989.1 ENSP00000401645 P05120 UPI000002BB06 NM_001143818.1 deleterious(0.01) 7/9 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF61,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 63901792 63901792 G T 1 0 0 0 0 1 0 0 0 14377 1348 47 2 2 SERPINB2 18 63901792 Missense_Mutation SNP G C3N-00549_T 5533939 63901792 16471493 358 15382 CDH19 0 . GRCh38 18 66504985 66504985 + Missense_Mutation SNP C C T novel C3N-00549_T C3N-00549_N C C c.2146G>A p.Asp716Asn p.D716N ENST00000262150 12/12 158 49 109 254 254 0 strelka-varscan-mutect CDH19,missense_variant,p.Asp716Asn,ENST00000262150,NM_021153.3;CDH19,downstream_gene_variant,,ENST00000540086,NM_001271028.1;CDH19,3_prime_UTR_variant,,ENST00000579658,; T ENST00000262150 Transcript missense_variant 2439/6341 2146/2319 716/772 D/N Gat/Aat 1 -1 CDH19 HGNC HGNC:1758 protein_coding YES CCDS11994.1 ENSP00000262150 Q9H159 UPI0000048ECF NM_021153.3 deleterious(0) 12/12 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF323 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 66504985 66504985 C T 1 0 0 0 0 1 0 0 0 2807 826 29 3 3 CDH19 18 66504985 Missense_Mutation SNP C C3N-00549_T 2603193 66504985 13868300 359 15383 STK11 0 . GRCh38 19 1219382 1219382 + Nonsense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.433G>T p.Glu145Ter p.E145* ENST00000326873 3/10 188 46 142 207 207 0 strelka-varscan-mutect STK11,stop_gained,p.Glu145Ter,ENST00000586243,;STK11,stop_gained,p.Glu145Ter,ENST00000326873,NM_000455.4;STK11,stop_gained,p.Glu21Ter,ENST00000585748,;STK11,intron_variant,,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,upstream_gene_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript stop_gained 883/2611 433/1302 145/433 E/* Gag/Tag 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 3/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS rs1241537285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 1219382 1219382 G T 1 0 0 0 0 0 1 0 0 15664 1175 41 2 2 STK11 19 1219382 Nonsense_Mutation SNP G C3N-00549_T 1219382 57398234 360 15384 MUC16 0 . GRCh38 19 8949744 8949744 + Missense_Mutation SNP G G T rs200826565 C3N-00549_T C3N-00549_N G G c.27026C>A p.Thr9009Asn p.T9009N ENST00000397910 3/84 102 33 69 161 161 0 strelka-varscan-mutect MUC16,missense_variant,p.Thr9009Asn,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 27230/43816 27026/43524 9009/14507 T/N aCc/aAc rs200826565,COSM4620390,COSM4620391 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs200826565 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 8949744 8949744 G T 1 0 0 0 0 1 0 0 0 9972 1261 44 2 2 MUC16 19 8949744 Missense_Mutation SNP G C3N-00549_T 7730362 8949744 49667872 361 15385 S1PR5 0 . GRCh38 19 10514069 10514069 + Missense_Mutation SNP G G T rs866372730 C3N-00549_T C3N-00549_N G G c.943C>A p.His315Asn p.H315N ENST00000333430 2/2 138 35 103 181 180 1 strelka-varscan-mutect S1PR5,missense_variant,p.His315Asn,ENST00000333430,NM_030760.4;S1PR5,missense_variant,p.His315Asn,ENST00000439028,NM_001166215.1;S1PR5,missense_variant,p.His171Asn,ENST00000617721,;S1PR5,downstream_gene_variant,,ENST00000590601,; T ENST00000333430 Transcript missense_variant 1014/2341 943/1197 315/398 H/N Cac/Aac rs866372730 1 -1 S1PR5 HGNC HGNC:14299 protein_coding YES CCDS12240.1 ENSP00000328472 Q9H228 UPI000003BC79 NM_030760.4 deleterious(0.03) 2/2 hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF20,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01523 MODERATE 1 SNV 1 1 PASS rs866372730 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 10514069 10514069 G T 1 0 0 0 0 1 0 0 0 14056 1348 47 2 2 S1PR5 19 10514069 Missense_Mutation SNP G C3N-00549_T 1564325 10514069 48103547 362 15386 SIN3B 0 . GRCh38 19 16841937 16841937 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.551G>T p.Arg184Met p.R184M ENST00000379803 4/20 177 53 124 230 230 0 strelka-varscan-mutect SIN3B,missense_variant,p.Arg184Met,ENST00000379803,NM_015260.3;SIN3B,missense_variant,p.Arg184Met,ENST00000248054,NM_001297595.1;SIN3B,missense_variant,p.Arg184Met,ENST00000596802,;SIN3B,upstream_gene_variant,,ENST00000596638,;CTD-2538G9.5,upstream_gene_variant,,ENST00000600987,; T ENST00000379803 Transcript missense_variant 565/5129 551/3489 184/1162 R/M aGg/aTg 1 1 SIN3B HGNC HGNC:19354 protein_coding YES CCDS32946.1 ENSP00000369131 O75182 UPI0000425EFA NM_015260.3 deleterious(0) 4/20 PROSITE_profiles:PS51477,hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF1,Gene3D:1g1eB00,Pfam_domain:PF02671,Superfamily_domains:SSF47762 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 16841937 16841937 G T 1 0 0 0 0 1 0 0 0 14590 1000 35 2 2 SIN3B 19 16841937 Missense_Mutation SNP G C3N-00549_T 6327868 16841937 41775679 363 15387 ZNF536 0 . GRCh38 19 30444476 30444476 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.914G>A p.Cys305Tyr p.C305Y ENST00000355537 2/5 114 79 35 119 119 0 strelka-varscan-mutect ZNF536,missense_variant,p.Cys305Tyr,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Cys305Tyr,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; A ENST00000355537 Transcript missense_variant 1061/4945 914/3903 305/1300 C/Y tGc/tAc 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 2/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 30444476 30444476 G A 1 0 0 0 0 1 0 0 0 18547 1319 46 3 3 ZNF536 19 30444476 Missense_Mutation SNP G C3N-00549_T 13602539 30444476 28173140 364 15388 SUPT5H 0 . GRCh38 19 39457725 39457725 + Missense_Mutation SNP G G T rs758081369 C3N-00549_T C3N-00549_N G G c.292G>T p.Asp98Tyr p.D98Y ENST00000599117 5/31 204 99 105 160 160 0 strelka-varscan-mutect SUPT5H,missense_variant,p.Asp98Tyr,ENST00000599117,NM_001319990.1;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000359191,NM_001319991.1;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000598725,NM_001319990.1,NM_003169.3;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000432763,NM_001111020.2,NM_001130824.1;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000402194,NM_001130825.1;SUPT5H,missense_variant,p.Asp9Tyr,ENST00000593727,;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000601515,;SUPT5H,missense_variant,p.Asp98Tyr,ENST00000594729,;SUPT5H,downstream_gene_variant,,ENST00000594990,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000595368,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000598459,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000601978,;SUPT5H,upstream_gene_variant,,ENST00000599907,;SUPT5H,upstream_gene_variant,,ENST00000598786,; T ENST00000599117 Transcript missense_variant 659/3902 292/3264 98/1087 D/Y Gac/Tac rs758081369 1 1 SUPT5H HGNC HGNC:11469 protein_coding YES CCDS12536.1 ENSP00000470252 O00267 UPI000006D81A NM_001319990.1 deleterious(0) 5/31 hmmpanther:PTHR11125,PIRSF_domain:PIRSF036945,Pfam_domain:PF11942 MODERATE 1 SNV 5 1 PASS rs758081369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 39457725 39457725 G T 1 0 0 0 0 1 0 0 0 15786 1174 41 2 2 SUPT5H 19 39457725 Missense_Mutation SNP G C3N-00549_T 9013249 39457725 19159891 365 15389 SHKBP1 0 . GRCh38 19 40580882 40580882 + Missense_Mutation SNP G G T rs753952010 C3N-00549_T C3N-00549_N G G c.790G>T p.Gly264Cys p.G264C ENST00000291842 9/18 65 29 36 58 58 0 strelka-varscan-mutect SHKBP1,missense_variant,p.Gly264Cys,ENST00000291842,NM_138392.3;SHKBP1,missense_variant,p.Gly264Cys,ENST00000600733,;SHKBP1,missense_variant,p.Gly259Cys,ENST00000600718,;SPTBN4,downstream_gene_variant,,ENST00000338932,;SPTBN4,downstream_gene_variant,,ENST00000352632,;SPTBN4,downstream_gene_variant,,ENST00000392025,;SHKBP1,upstream_gene_variant,,ENST00000600320,;SHKBP1,upstream_gene_variant,,ENST00000602011,;SHKBP1,upstream_gene_variant,,ENST00000593764,;SHKBP1,downstream_gene_variant,,ENST00000595631,;SHKBP1,upstream_gene_variant,,ENST00000597649,;SHKBP1,downstream_gene_variant,,ENST00000600552,;SHKBP1,non_coding_transcript_exon_variant,,ENST00000594973,;SHKBP1,non_coding_transcript_exon_variant,,ENST00000598201,;SHKBP1,non_coding_transcript_exon_variant,,ENST00000598907,;SPTBN4,downstream_gene_variant,,ENST00000596411,;SHKBP1,downstream_gene_variant,,ENST00000595945,;SHKBP1,downstream_gene_variant,,ENST00000599575,;SHKBP1,downstream_gene_variant,,ENST00000595803,;SHKBP1,downstream_gene_variant,,ENST00000598558,;SHKBP1,downstream_gene_variant,,ENST00000595523,;SHKBP1,downstream_gene_variant,,ENST00000599716,;SHKBP1,upstream_gene_variant,,ENST00000600791,;SHKBP1,downstream_gene_variant,,ENST00000597325,;SHKBP1,upstream_gene_variant,,ENST00000595874,; T ENST00000291842 Transcript missense_variant 839/2363 790/2124 264/707 G/C Ggc/Tgc rs753952010,COSM712855 1 1 SHKBP1 HGNC HGNC:19214 protein_coding YES CCDS12560.1 ENSP00000291842 Q8TBC3 UPI0000036171 NM_138392.3 tolerated(0.22) 9/18 Gene3D:2.130.10.10,hmmpanther:PTHR15859,hmmpanther:PTHR15859:SF5,Superfamily_domains:SSF50978 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753952010 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 40580882 40580882 G T 1 0 0 0 0 1 0 0 0 14547 1116 39 1 1 SHKBP1 19 40580882 Missense_Mutation SNP G C3N-00549_T 1123157 40580882 18036734 366 15390 CLPTM1 0 . GRCh38 19 44986479 44986479 + Nonsense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.697G>T p.Glu233Ter p.E233* ENST00000337392 7/14 154 69 85 177 177 0 strelka-varscan-mutect CLPTM1,stop_gained,p.Glu219Ter,ENST00000541297,NM_001282175.1;CLPTM1,stop_gained,p.Glu233Ter,ENST00000337392,NM_001294.3;CLPTM1,stop_gained,p.Glu131Ter,ENST00000546079,NM_001282176.1;CLPTM1,downstream_gene_variant,,ENST00000591304,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000589158,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000588855,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000587537,;CLPTM1,upstream_gene_variant,,ENST00000588274,;CLPTM1,upstream_gene_variant,,ENST00000586975,;CLPTM1,upstream_gene_variant,,ENST00000589347,; T ENST00000337392 Transcript stop_gained 847/2604 697/2010 233/669 E/* Gag/Tag COSM712378,COSM712379 1 1 CLPTM1 HGNC HGNC:2087 protein_coding YES CCDS12651.1 ENSP00000336994 O96005 A0A0S2Z3H2 UPI0000072CBA NM_001294.3 7/14 Pfam_domain:PF05602,hmmpanther:PTHR21347,hmmpanther:PTHR21347:SF0 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 44986479 44986479 G T 1 0 0 0 0 0 1 0 0 3326 1175 41 2 2 CLPTM1 19 44986479 Nonsense_Mutation SNP G C3N-00549_T 4405597 44986479 13631137 367 15391 CCDC61 0 . GRCh38 19 46003099 46003099 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.81G>T p.Gln27His p.Q27H ENST00000595358 2/14 143 64 79 196 195 1 strelka-varscan-mutect CCDC61,missense_variant,p.Gln27His,ENST00000595358,NM_001267723.1;CCDC61,missense_variant,p.Gln27His,ENST00000536603,;CCDC61,missense_variant,p.Gln27His,ENST00000594087,;CCDC61,missense_variant,p.Gln27His,ENST00000594672,;CCDC61,missense_variant,p.Gln27His,ENST00000596687,;CCDC61,non_coding_transcript_exon_variant,,ENST00000599044,;CCDC61,non_coding_transcript_exon_variant,,ENST00000596161,; T ENST00000595358 Transcript missense_variant 130/1817 81/1539 27/512 Q/H caG/caT 1 1 CCDC61 HGNC HGNC:33629 protein_coding YES CCDS46120.2 ENSP00000471454 Q9Y6R9 UPI000040C0FF NM_001267723.1 tolerated(0.17) 2/14 hmmpanther:PTHR22691,hmmpanther:PTHR22691:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 46003099 46003099 G T 1 0 0 0 0 1 0 0 0 2534 991 35 2 2 CCDC61 19 46003099 Missense_Mutation SNP G C3N-00549_T 1016620 46003099 12614517 368 15392 ZC3H4 0 . GRCh38 19 47086383 47086383 + Splice_Site SNP C C A novel C3N-00549_T C3N-00549_N C C c.870+1G>T p.X290_splice ENST00000253048 115 89 26 254 253 1 strelka-varscan-mutect ZC3H4,splice_donor_variant,,ENST00000253048,NM_015168.1;ZC3H4,upstream_gene_variant,,ENST00000601973,;ZC3H4,intron_variant,,ENST00000594019,;ZC3H4,downstream_gene_variant,,ENST00000597069,; A ENST00000253048 Transcript splice_donor_variant -/6119 870/3912 290/1303 1 -1 ZC3H4 HGNC HGNC:17808 protein_coding YES CCDS42582.1 ENSP00000253048 Q9UPT8 UPI00001C2000 NM_015168.1 6/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 47086383 47086383 C A 1 0 0 0 0 0 0 1 0 18145 550 19 1 1 ZC3H4 19 47086383 Splice_Site SNP C C3N-00549_T 1083284 47086383 11531233 369 15393 SULT2B1 0 . GRCh38 19 48591731 48591731 + Silent SNP C C T rs746998782 C3N-00549_T C3N-00549_N C C c.546C>T p.= p.G182G ENST00000201586 4/7 69 53 16 75 75 0 strelka-varscan-mutect SULT2B1,synonymous_variant,p.=,ENST00000323090,NM_004605.2;SULT2B1,synonymous_variant,p.=,ENST00000201586,NM_177973.1;SULT2B1,non_coding_transcript_exon_variant,,ENST00000594274,;SULT2B1,upstream_gene_variant,,ENST00000597923,; T ENST00000201586 Transcript synonymous_variant 724/1295 546/1098 182/365 G ggC/ggT rs746998782,COSM999018,COSM999019 1 1 SULT2B1 HGNC HGNC:11459 protein_coding YES CCDS12723.1 ENSP00000201586 O00204 UPI0000073F98 NM_177973.1 4/7 hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF9,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs746998782 . 0 202 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 2 4 50 48591731 48591731 C T 1 0 0 0 0 0 0 0 1 15768 782 27 1 1 SULT2B1 19 48591731 Silent SNP C C3N-00549_T 1505348 48591731 10025885 370 15394 TRPM4 0 . GRCh38 19 49200329 49200329 + Missense_Mutation SNP G G C rs866510018 C3N-00549_T C3N-00549_N G G c.2675G>C p.Arg892Pro p.R892P ENST00000252826 18/25 347 281 66 329 329 0 strelka-varscan-mutect TRPM4,missense_variant,p.Arg892Pro,ENST00000252826,NM_017636.3;TRPM4,missense_variant,p.Arg747Pro,ENST00000427978,NM_001195227.1;TRPM4,3_prime_UTR_variant,,ENST00000595519,NM_001321283.1;TRPM4,3_prime_UTR_variant,,ENST00000598502,NM_001321282.1;TRPM4,3_prime_UTR_variant,,ENST00000598697,NM_001321285.1;TRPM4,non_coding_transcript_exon_variant,,ENST00000596338,;TRPM4,non_coding_transcript_exon_variant,,ENST00000595071,;TRPM4,downstream_gene_variant,,ENST00000595882,; C ENST00000252826 Transcript missense_variant 2801/4109 2675/3645 892/1214 R/P cGc/cCc rs866510018 1 1 TRPM4 HGNC HGNC:17993 protein_coding YES CCDS33073.1 ENSP00000252826 Q8TD43 UPI0000070598 NM_017636.3 deleterious(0) 18/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS rs866510018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 49200329 49200329 G C 1 0 0 0 0 1 0 0 0 17094 1087 38 4 4 TRPM4 19 49200329 Missense_Mutation SNP G C3N-00549_T 608598 49200329 9417287 371 15395 ATF5 0 . GRCh38 19 49930998 49930998 + Missense_Mutation SNP G G T rs778518946 C3N-00549_T C3N-00549_N G G c.148G>T p.Gly50Trp p.G50W ENST00000423777 2/3 62 42 20 57 57 0 strelka-varscan-mutect ATF5,missense_variant,p.Gly50Trp,ENST00000423777,NM_001193646.1,NM_001290746.1;ATF5,missense_variant,p.Gly50Trp,ENST00000595125,NM_012068.5;ATF5,missense_variant,p.Gly50Trp,ENST00000597227,;ATF5,missense_variant,p.Gly50Trp,ENST00000596658,;ATF5,missense_variant,p.Gly50Trp,ENST00000600336,;NUP62,upstream_gene_variant,,ENST00000596217,;NUP62,upstream_gene_variant,,ENST00000422090,NM_012346.4,NM_153718.3,NM_001193357.1;NUP62,upstream_gene_variant,,ENST00000352066,NM_016553.4;IL4I1,upstream_gene_variant,,ENST00000595948,NM_001258018.1;IL4I1,upstream_gene_variant,,ENST00000341114,NM_172374.2,NM_001258017.1;NUP62,upstream_gene_variant,,ENST00000597029,NM_153719.3;NUP62,upstream_gene_variant,,ENST00000597723,;NUP62,upstream_gene_variant,,ENST00000593652,;NUP62,upstream_gene_variant,,ENST00000596437,;IL4I1,upstream_gene_variant,,ENST00000596022,;IL4I1,upstream_gene_variant,,ENST00000596011,;IL4I1,upstream_gene_variant,,ENST00000597295,;NUP62,upstream_gene_variant,,ENST00000600935,;NUP62,upstream_gene_variant,,ENST00000599567,;NUP62,upstream_gene_variant,,ENST00000594673,;NUP62,upstream_gene_variant,,ENST00000599788,;NUP62,upstream_gene_variant,,ENST00000596680,;ATF5,upstream_gene_variant,,ENST00000578027,;NUP62,upstream_gene_variant,,ENST00000600583,;NUP62,upstream_gene_variant,,ENST00000599830,;NUP62,upstream_gene_variant,,ENST00000598301,;NUP62,upstream_gene_variant,,ENST00000595463,;NUP62,upstream_gene_variant,,ENST00000599560,;NUP62,upstream_gene_variant,,ENST00000601665,;NUP62,upstream_gene_variant,,ENST00000597814,;NUP62,upstream_gene_variant,,ENST00000599186,;CTC-326K19.6,intron_variant,,ENST00000451973,;IL4I1,upstream_gene_variant,,ENST00000601717,; T ENST00000423777 Transcript missense_variant 525/2069 148/849 50/282 G/W Ggg/Tgg rs778518946 1 1 ATF5 HGNC HGNC:790 protein_coding YES CCDS12789.1 ENSP00000396954 Q9Y2D1 A0A024QZG3 UPI000003842F NM_001193646.1,NM_001290746.1 deleterious(0.02) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR13044,hmmpanther:PTHR13044:SF3 MODERATE 1 SNV 1 1 PASS rs778518946 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 50 49930998 49930998 G T 1 0 0 0 0 1 0 0 0 1232 1116 39 1 1 ATF5 19 49930998 Missense_Mutation SNP G C3N-00549_T 730669 49930998 8686618 372 15396 SIGLEC11 0 . GRCh38 19 49959529 49959529 + Silent SNP C C A rs775285253 C3N-00549_T C3N-00549_N C C c.888G>T p.= p.T296T ENST00000447370 5/11 62 13 49 31 31 0 strelka-varscan-mutect SIGLEC11,synonymous_variant,p.=,ENST00000447370,NM_052884.2;SIGLEC11,synonymous_variant,p.=,ENST00000426971,NM_001135163.1;SIGLEC11,upstream_gene_variant,,ENST00000426296,;CTC-326K19.6,upstream_gene_variant,,ENST00000451973,; A ENST00000447370 Transcript synonymous_variant 979/3173 888/2097 296/698 T acG/acT rs775285253 1 -1 SIGLEC11 HGNC HGNC:15622 protein_coding YES CCDS12790.2 ENSP00000412361 Q96RL6 UPI00018131F5 NM_052884.2 5/11 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF44,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs775285253 . 0 202 7 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 50 49959529 49959529 C A 1 0 0 0 0 0 0 0 1 14571 755 27 1 1 SIGLEC11 19 49959529 Silent SNP C C3N-00549_T 28531 49959529 8658087 373 15397 SIGLEC14 0 . GRCh38 19 51645992 51645992 + Missense_Mutation SNP A A G novel C3N-00549_T C3N-00549_N A A c.490T>C p.Cys164Arg p.C164R ENST00000360844 3/7 43 20 23 60 60 0 strelka-mutect SIGLEC14,missense_variant,p.Cys164Arg,ENST00000360844,NM_001098612.1;AC018755.18,intron_variant,,ENST00000429354,;AC018755.18,intron_variant,,ENST00000599649,;SIGLEC5,upstream_gene_variant,,ENST00000534261,NM_003830.3;SIGLEC14,upstream_gene_variant,,ENST00000533866,;RPL7P51,upstream_gene_variant,,ENST00000490532,; G ENST00000360844 Transcript missense_variant 532/2035 490/1191 164/396 C/R Tgc/Cgc 1 -1 SIGLEC14 HGNC HGNC:32926 protein_coding YES CCDS42604.1 ENSP00000354090 Q08ET2 UPI0000E44158 NM_001098612.1 deleterious(0) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF67,hmmpanther:PTHR12035,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 61 147 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 51645992 51645992 A G 1 0 0 0 0 1 0 0 0 14573 188 7 5 5 SIGLEC14 19 51645992 Missense_Mutation SNP A C3N-00549_T 1686463 51645992 6971624 374 15398 ZNF616 0 . GRCh38 19 52116191 52116191 + Missense_Mutation SNP A A C novel C3N-00549_T C3N-00549_N A A c.973T>G p.Phe325Val p.F325V ENST00000600228 4/4 316 164 152 342 342 0 strelka-varscan-mutect ZNF616,missense_variant,p.Phe325Val,ENST00000600228,NM_178523.3;ZNF616,3_prime_UTR_variant,,ENST00000330123,;ZNF616,downstream_gene_variant,,ENST00000596290,; C ENST00000600228 Transcript missense_variant 1235/4335 973/2346 325/781 F/V Ttc/Gtc 1 -1 ZNF616 HGNC HGNC:28062 protein_coding YES CCDS33090.1 ENSP00000471000 Q08AN1 UPI0000140D49 NM_178523.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF275,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 52116191 52116191 A C 1 0 0 0 0 1 0 0 0 18616 72 3 5 5 ZNF616 19 52116191 Missense_Mutation SNP A C3N-00549_T 470199 52116191 6501425 375 15399 60 2 ZNF616 0 . GRCh38 19 52116193 52116193 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.971C>A p.Pro324His p.P324H ENST00000600228 4/4 314 159 155 337 337 0 strelka-varscan-mutect ZNF616,missense_variant,p.Pro324His,ENST00000600228,NM_178523.3;ZNF616,3_prime_UTR_variant,,ENST00000330123,;ZNF616,downstream_gene_variant,,ENST00000596290,; T ENST00000600228 Transcript missense_variant 1233/4335 971/2346 324/781 P/H cCc/cAc 1 -1 ZNF616 HGNC HGNC:28062 protein_coding YES CCDS33090.1 ENSP00000471000 Q08AN1 UPI0000140D49 NM_178523.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF275,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 52116193 52116193 G T 1 0 0 0 0 1 0 0 0 18616 1232 43 2 2 ZNF616 19 52116193 Missense_Mutation SNP G C3N-00549_T 2 52116193 6501423 376 15400 60 2 ZNF528 0 . GRCh38 19 52415828 52415828 + Missense_Mutation SNP A A T novel C3N-00549_T C3N-00549_N A A c.976A>T p.Ser326Cys p.S326C ENST00000360465 7/7 118 89 29 142 142 0 strelka-varscan-mutect ZNF528,missense_variant,p.Ser326Cys,ENST00000360465,NM_032423.2;ZNF528,3_prime_UTR_variant,,ENST00000391788,;ZNF528,downstream_gene_variant,,ENST00000448954,;ZNF528,non_coding_transcript_exon_variant,,ENST00000598479,;ZNF528,downstream_gene_variant,,ENST00000479718,; T ENST00000360465 Transcript missense_variant 1402/3978 976/1887 326/628 S/C Agt/Tgt 1 1 ZNF528 HGNC HGNC:29384 protein_coding YES CCDS33091.1 ENSP00000353652 Q3MIS6 UPI00001B6535 NM_032423.2 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF143,hmmpanther:PTHR24377,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 52415828 52415828 A T 1 0 0 0 0 1 0 0 0 18542 188 7 4 4 ZNF528 19 52415828 Missense_Mutation SNP A C3N-00549_T 299635 52415828 6201788 377 15401 ZNF677 0 . GRCh38 19 53238263 53238263 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.464C>A p.Ala155Glu p.A155E ENST00000598513 5/5 126 88 38 95 95 0 strelka-varscan-mutect ZNF677,missense_variant,p.Ala155Glu,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,missense_variant,p.Ala155Glu,ENST00000333952,;ZNF677,downstream_gene_variant,,ENST00000594681,;ZNF677,downstream_gene_variant,,ENST00000599012,;ZNF677,downstream_gene_variant,,ENST00000598806,;ZNF677,downstream_gene_variant,,ENST00000594517,;CTD-2245F17.6,upstream_gene_variant,,ENST00000596041,;ZNF677,downstream_gene_variant,,ENST00000599328,;ZNF677,downstream_gene_variant,,ENST00000593539,; T ENST00000598513 Transcript missense_variant 615/3497 464/1755 155/584 A/E gCa/gAa 1 -1 ZNF677 HGNC HGNC:28730 protein_coding YES CCDS12861.1 ENSP00000469391 Q86XU0 UPI000017DF85 NM_001317998.1,NM_182609.2 tolerated(0.12) 5/5 MODERATE 1 SNV 1 1 PASS rs1267713089 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 53238263 53238263 G T 1 0 0 0 0 1 0 0 0 18657 1319 46 2 2 ZNF677 19 53238263 Missense_Mutation SNP G C3N-00549_T 822435 53238263 5379353 378 15402 VN1R2 0 . GRCh38 19 53258640 53258640 + Missense_Mutation SNP G G T C3N-00549_T C3N-00549_N G G c.265G>T p.Gly89Trp p.G89W ENST00000341702 1/1 122 89 33 114 113 1 strelka-varscan-mutect VN1R2,missense_variant,p.Gly89Trp,ENST00000341702,NM_173856.2;ZNF677,upstream_gene_variant,,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,upstream_gene_variant,,ENST00000594681,;ZNF677,upstream_gene_variant,,ENST00000599012,;ZNF677,upstream_gene_variant,,ENST00000601828,;ZNF677,upstream_gene_variant,,ENST00000601413,;ZNF677,upstream_gene_variant,,ENST00000598806,;ZNF677,upstream_gene_variant,,ENST00000594517,;ZNF677,upstream_gene_variant,,ENST00000595293,;VN1R2,upstream_gene_variant,,ENST00000598458,; T ENST00000341702 Transcript missense_variant 349/1311 265/1188 89/395 G/W Ggg/Tgg COSM5249405 1 1 VN1R2 HGNC HGNC:19872 protein_coding YES CCDS12862.1 ENSP00000351244 Q8NFZ6 UPI0000062046 NM_173856.2 deleterious(0) 1/1 1 MODERATE SNV 1 1 PASS rs1430771919 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 53258640 53258640 G T 1 0 0 0 0 1 0 0 0 17727 1232 43 2 2 VN1R2 19 53258640 Missense_Mutation SNP G C3N-00549_T 20377 53258640 5358976 379 15403 ZNF813 0 . GRCh38 19 53491533 53491533 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.1301G>T p.Ser434Ile p.S434I ENST00000396403 4/4 247 185 62 170 170 0 strelka-varscan-mutect ZNF813,missense_variant,p.Ser434Ile,ENST00000396403,NM_001004301.3;ZNF813,downstream_gene_variant,,ENST00000490956,;ZNF813,downstream_gene_variant,,ENST00000468450,;CTD-2224J9.4,upstream_gene_variant,,ENST00000483735,; T ENST00000396403 Transcript missense_variant 1429/6151 1301/1854 434/617 S/I aGt/aTt 1 1 ZNF813 HGNC HGNC:33257 protein_coding YES CCDS46172.1 ENSP00000379684 Q6ZN06 UPI000040C511 NM_001004301.3 deleterious(0.01) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS rs1306575204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 53491533 53491533 G T 1 0 0 0 0 1 0 0 0 18761 1029 36 2 2 ZNF813 19 53491533 Missense_Mutation SNP G C3N-00549_T 232893 53491533 5126083 380 15404 TARM1 0 . GRCh38 19 54081334 54081334 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.7C>A p.Pro3Thr p.P3T ENST00000432826 1/5 72 54 18 174 174 0 strelka-varscan-mutect TARM1,missense_variant,p.Pro3Thr,ENST00000432826,NM_001135686.2;TARM1,upstream_gene_variant,,ENST00000616041,; T ENST00000432826 Transcript missense_variant 32/897 7/816 3/271 P/T Cct/Act 1 -1 TARM1 HGNC HGNC:37250 protein_coding YES CCDS46173.1 ENSP00000439454 B6A8C7 UPI00034F23B2 NM_001135686.2 tolerated(0.05) 1/5 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF84,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1235224152 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 54081334 54081334 G T 1 0 0 0 0 1 0 0 0 15957 1232 43 2 2 TARM1 19 54081334 Missense_Mutation SNP G C3N-00549_T 589801 54081334 4536282 381 15405 LILRB2 0 . GRCh38 19 54279577 54279577 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.426C>A p.= p.L142L ENST00000391749 5/14 230 117 113 219 219 0 strelka-varscan-mutect LILRB2,synonymous_variant,p.=,ENST00000391748,NM_001278403.2;LILRB2,synonymous_variant,p.=,ENST00000434421,NM_001278404.2;LILRB2,synonymous_variant,p.=,ENST00000314446,NM_001080978.3;LILRB2,synonymous_variant,p.=,ENST00000391749,NM_005874.4;LILRB2,synonymous_variant,p.=,ENST00000391746,NM_001278405.2;MIR4752,upstream_gene_variant,,ENST00000579672,;LILRB2,downstream_gene_variant,,ENST00000471216,;LILRB2,non_coding_transcript_exon_variant,,ENST00000493242,;LILRB2,upstream_gene_variant,,ENST00000455108,; T ENST00000391749 Transcript synonymous_variant 698/2286 426/1797 142/598 L ctC/ctA 1 -1 LILRB2 HGNC HGNC:6606 protein_coding YES CCDS12886.1 ENSP00000375629 Q8N423 UPI00034F23A2 NM_005874.4 5/14 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 54279577 54279577 G T 1 0 0 0 0 0 0 0 1 8699 1161 41 2 2 LILRB2 19 54279577 Silent SNP G C3N-00549_T 198243 54279577 4338039 382 15406 LILRA5 0 . GRCh38 19 54312355 54312355 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.104C>T p.Pro35Leu p.P35L ENST00000432233 3/7 308 234 74 310 310 0 strelka-varscan-mutect LILRA5,missense_variant,p.Pro35Leu,ENST00000432233,NM_021250.3;LILRA5,intron_variant,,ENST00000486742,NM_181985.3;AC008984.2,intron_variant,,ENST00000616950,;LILRA5,non_coding_transcript_exon_variant,,ENST00000446712,;LILRA5,intron_variant,,ENST00000489504,;LILRA5,upstream_gene_variant,,ENST00000477720,; A ENST00000432233 Transcript missense_variant 224/1363 104/900 35/299 P/L cCc/cTc 1 -1 LILRA5 HGNC HGNC:16309 protein_coding YES CCDS12888.1 ENSP00000404236 A6NI73 UPI0000034C06 NM_021250.3 tolerated(0.83) 3/7 hmmpanther:PTHR11738 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 54312355 54312355 G A 1 0 0 0 0 1 0 0 0 8696 1232 43 3 3 LILRA5 19 54312355 Missense_Mutation SNP G C3N-00549_T 32778 54312355 4305261 383 15407 NLRP2 0 . GRCh38 19 54986184 54986184 + Silent SNP G G C novel C3N-00549_T C3N-00549_N G G c.2235G>C p.= p.R745R ENST00000543010 8/13 454 247 207 438 438 0 strelka-varscan-mutect NLRP2,synonymous_variant,p.=,ENST00000543010,NM_001174081.1;NLRP2,synonymous_variant,p.=,ENST00000448584,NM_017852.3;NLRP2,synonymous_variant,p.=,ENST00000537859,NM_001174082.1;NLRP2,synonymous_variant,p.=,ENST00000263437,;NLRP2,synonymous_variant,p.=,ENST00000339757,;NLRP2,synonymous_variant,p.=,ENST00000391721,;NLRP2,synonymous_variant,p.=,ENST00000427260,NM_001174083.1;NLRP2,synonymous_variant,p.=,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,upstream_gene_variant,,ENST00000586512,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; C ENST00000543010 Transcript synonymous_variant 2378/3576 2235/3189 745/1062 R cgG/cgC 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 8/13 hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS rs1190657804 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 54986184 54986184 G C 1 0 0 0 0 0 0 0 1 10514 1161 41 4 4 NLRP2 19 54986184 Silent SNP G C3N-00549_T 673829 54986184 3631432 384 15408 TNNI3 0 . GRCh38 19 55154036 55154036 + Silent SNP G G T novel C3N-00549_T C3N-00549_N G G c.543C>A p.= p.T181T ENST00000344887 7/8 337 177 160 314 313 1 strelka-varscan-mutect TNNI3,synonymous_variant,p.=,ENST00000344887,NM_000363.4;TNNI3,synonymous_variant,p.=,ENST00000588882,;DNAAF3,downstream_gene_variant,,ENST00000455045,NM_001256716.1;DNAAF3,downstream_gene_variant,,ENST00000527223,NM_001256714.1;DNAAF3,downstream_gene_variant,,ENST00000391720,NM_178837.4;DNAAF3,downstream_gene_variant,,ENST00000524407,NM_001256715.1;TNNT1,upstream_gene_variant,,ENST00000588981,NM_003283.5;TNNT1,upstream_gene_variant,,ENST00000587758,NM_001291774.1;TNNT1,upstream_gene_variant,,ENST00000291901,NM_001126132.2;TNNT1,upstream_gene_variant,,ENST00000356783,NM_001126133.2;TNNT1,upstream_gene_variant,,ENST00000536926,;DNAAF3,downstream_gene_variant,,ENST00000588076,;TNNT1,upstream_gene_variant,,ENST00000588426,;TNNT1,upstream_gene_variant,,ENST00000588147,;TNNI3,downstream_gene_variant,,ENST00000586858,;CTD-2587H24.5,upstream_gene_variant,,ENST00000591665,;DNAAF3,downstream_gene_variant,,ENST00000587789,;TNNT1,upstream_gene_variant,,ENST00000592920,;TNNI3,downstream_gene_variant,,ENST00000590463,;TNNI3,downstream_gene_variant,,ENST00000586669,;TNNI3,non_coding_transcript_exon_variant,,ENST00000585806,;TNNI3,non_coding_transcript_exon_variant,,ENST00000589864,;DNAAF3,downstream_gene_variant,,ENST00000528412,;DNAAF3,downstream_gene_variant,,ENST00000533527,;TNNI3,downstream_gene_variant,,ENST00000587176,;CTD-2587H24.4,downstream_gene_variant,,ENST00000587871,;TNNI3,downstream_gene_variant,,ENST00000586446,;TNNT1,upstream_gene_variant,,ENST00000586282,; T ENST00000344887 Transcript synonymous_variant 686/840 543/633 181/210 T acC/acA 1 -1 TNNI3 HGNC HGNC:11947 protein_coding YES CCDS42628.1 ENSP00000341838 P19429 Q6FGX2 UPI0000155A10 NM_000363.4 7/8 hmmpanther:PTHR13738:SF2,hmmpanther:PTHR13738,Gene3D:1.20.5.350,Superfamily_domains:SSF90250 LOW 1 SNV 1 1 PASS rs926550445 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 55154036 55154036 G T 1 0 0 0 0 0 0 0 1 16801 1103 39 1 1 TNNI3 19 55154036 Silent SNP G C3N-00549_T 167852 55154036 3463580 385 15409 HSPBP1 0 . GRCh38 19 55274492 55274492 + Silent SNP C C T novel C3N-00549_T C3N-00549_N C C c.546G>A p.= p.Q182Q ENST00000255631 5/9 332 236 96 288 288 0 strelka-varscan-mutect HSPBP1,synonymous_variant,p.=,ENST00000255631,NM_001130106.1,NM_012267.4;HSPBP1,synonymous_variant,p.=,ENST00000433386,;HSPBP1,synonymous_variant,p.=,ENST00000587922,NM_001297600.1;HSPBP1,synonymous_variant,p.=,ENST00000593263,;HSPBP1,synonymous_variant,p.=,ENST00000585927,;HSPBP1,synonymous_variant,p.=,ENST00000587959,;HSPBP1,downstream_gene_variant,,ENST00000588971,;HSPBP1,downstream_gene_variant,,ENST00000585698,; T ENST00000255631 Transcript synonymous_variant 857/1768 546/1080 182/359 Q caG/caA 1 -1 HSPBP1 HGNC HGNC:24989 protein_coding YES CCDS33111.1 ENSP00000255631 Q9NZL4 UPI0000074015 NM_001130106.1,NM_012267.4 5/9 hmmpanther:PTHR19316:SF18,hmmpanther:PTHR19316,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 55274492 55274492 C T 1 0 0 0 0 0 0 0 1 7323 680 24 3 3 HSPBP1 19 55274492 Silent SNP C C3N-00549_T 120456 55274492 3343124 386 15410 FAM71E2 0 . GRCh38 19 55361409 55361409 + Splice_Site SNP C C A novel C3N-00549_T C3N-00549_N C C c.589+1G>T p.X197_splice ENST00000424985 25 20 5 43 43 0 strelka-varscan-mutect FAM71E2,splice_donor_variant,,ENST00000424985,NM_001145402.1;IL11,downstream_gene_variant,,ENST00000264563,NM_000641.3;IL11,downstream_gene_variant,,ENST00000585513,;IL11,downstream_gene_variant,,ENST00000590625,NM_001267718.1;FAM71E2,intron_variant,,ENST00000585734,;CTD-2105E13.6,upstream_gene_variant,,ENST00000591954,; A ENST00000424985 Transcript splice_donor_variant -/3191 589/2769 197/922 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 4/10 HIGH SNV 5 1 PASS rs1434809172 . 0 203 7 0 0 0 0 0 -14.12241 0.9999998 1 1 1 0 A 5 1 50 55361409 55361409 C A 1 0 0 0 0 0 0 1 0 5476 521 18 2 2 FAM71E2 19 55361409 Splice_Site SNP C C3N-00549_T 86917 55361409 3256207 387 15411 NLRP4 0 . GRCh38 19 55858563 55858563 + Silent SNP G G T rs147261455 C3N-00549_T C3N-00549_N G G c.1170G>T p.= p.P390P ENST00000301295 3/10 170 95 75 178 178 0 strelka-varscan-mutect NLRP4,synonymous_variant,p.=,ENST00000301295,NM_134444.4;NLRP4,synonymous_variant,p.=,ENST00000587891,;NLRP4,upstream_gene_variant,,ENST00000589437,;NLRP4,downstream_gene_variant,,ENST00000587464,; T ENST00000301295 Transcript synonymous_variant 1592/3670 1170/2985 390/994 P ccG/ccT rs147261455 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 3/10 hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106 LOW 1 SNV 1 1 PASS rs147261455 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 55858563 55858563 G T 1 0 0 0 0 0 0 0 1 10517 1074 38 1 1 NLRP4 19 55858563 Silent SNP G C3N-00549_T 497154 55858563 2759053 388 15412 ZNF71 0 . GRCh38 19 56621878 56621878 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.591G>T p.Gln197His p.Q197H ENST00000328070 3/3 128 78 50 148 148 0 strelka-varscan-mutect ZNF71,missense_variant,p.Gln197His,ENST00000328070,NM_021216.4;ZNF71,downstream_gene_variant,,ENST00000599599,; T ENST00000328070 Transcript missense_variant 825/5428 591/1470 197/489 Q/H caG/caT 1 1 ZNF71 HGNC HGNC:13141 protein_coding YES CCDS12947.1 ENSP00000328245 Q9NQZ8 UPI00000437FA NM_021216.4 deleterious(0.04) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF115,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs923968108 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 56621878 56621878 G T 1 0 0 0 0 1 0 0 0 18689 962 34 2 2 ZNF71 19 56621878 Missense_Mutation SNP G C3N-00549_T 763315 56621878 1995738 389 15413 SIRPA 0 . GRCh38 20 1915286 1915286 + Silent SNP G G T rs761970927 C3N-00549_T C3N-00549_N G G c.267G>T p.= p.R89R ENST00000400068 3/9 496 305 191 412 410 2 strelka-varscan-mutect SIRPA,synonymous_variant,p.=,ENST00000622179,;SIRPA,synonymous_variant,p.=,ENST00000400068,NM_001040022.1;SIRPA,synonymous_variant,p.=,ENST00000358771,NM_001040023.1;SIRPA,synonymous_variant,p.=,ENST00000356025,NM_080792.2; T ENST00000400068 Transcript synonymous_variant 627/4201 267/1515 89/504 R cgG/cgT rs761970927 1 1 SIRPA HGNC HGNC:9662 protein_coding YES CCDS13022.1 ENSP00000382941 P78324 UPI0000073ADE NM_001040022.1 3/9 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs761970927 . 5 205 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 50 1915286 1915286 G T 1 0 0 0 0 0 0 0 1 14595 1219 43 2 2 SIRPA 20 1915286 Silent SNP G C3N-00549_T 1915286 62528881 390 15414 ASXL1 0 . GRCh38 20 32434922 32434922 + Missense_Mutation SNP T T G rs761847705 C3N-00549_T C3N-00549_N T T c.2210T>G p.Val737Gly p.V737G ENST00000375687 13/13 577 420 157 272 272 0 strelka-varscan-mutect ASXL1,missense_variant,p.Val737Gly,ENST00000613218,;ASXL1,missense_variant,p.Val737Gly,ENST00000375687,NM_015338.5;ASXL1,missense_variant,p.Val732Gly,ENST00000306058,;ASXL1,missense_variant,p.Val737Gly,ENST00000620121,;ASXL1,downstream_gene_variant,,ENST00000553345,;ASXL1,downstream_gene_variant,,ENST00000619344,;ASXL1,downstream_gene_variant,,ENST00000555564,; G ENST00000375687 Transcript missense_variant 2634/7031 2210/4626 737/1541 V/G gTt/gGt rs761847705,COSM4770116,COSM4770117 1 1 ASXL1 HGNC HGNC:18318 protein_coding YES CCDS13201.1 ENSP00000364839 Q8IXJ9 UPI000018691A NM_015338.5 tolerated_low_confidence(0.76) 13/13 hmmpanther:PTHR13578:SF19,hmmpanther:PTHR13578 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs761847705 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 32434922 32434922 T G 1 0 0 0 0 1 0 0 0 1214 1725 60 5 5 ASXL1 20 32434922 Missense_Mutation SNP T C3N-00549_T 30519636 32434922 32009245 391 15415 LPIN3 0 . GRCh38 20 41349094 41349094 + Missense_Mutation SNP T T G novel C3N-00549_T C3N-00549_N T T c.560T>G p.Val187Gly p.V187G ENST00000373257 5/20 196 139 57 98 98 0 strelka-varscan-mutect LPIN3,missense_variant,p.Val187Gly,ENST00000373257,;LPIN3,missense_variant,p.Val188Gly,ENST00000632009,NM_001301860.1;LPIN3,upstream_gene_variant,,ENST00000445975,; G ENST00000373257 Transcript missense_variant,splice_region_variant 651/4363 560/2556 187/851 V/G gTc/gGc 1 1 LPIN3 HGNC HGNC:14451 protein_coding YES ENSP00000362354 Q9BQK8 UPI0000470AE3 tolerated(0.36) 5/20 hmmpanther:PTHR12181,hmmpanther:PTHR12181:SF32 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 41349094 41349094 T G 1 0 0 0 0 1 0 0 0 8820 1681 58 5 5 LPIN3 20 41349094 Missense_Mutation SNP T C3N-00549_T 8914172 41349094 23095073 392 15416 PTPRT 0 . GRCh38 20 42119970 42119970 + Missense_Mutation SNP C C G C3N-00549_T C3N-00549_N C C c.2906G>C p.Gly969Ala p.G969A ENST00000373198 21/32 144 115 29 85 85 0 strelka-varscan-mutect PTPRT,missense_variant,p.Gly969Ala,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Gly972Ala,ENST00000373193,;PTPRT,missense_variant,p.Gly940Ala,ENST00000373201,;PTPRT,missense_variant,p.Gly949Ala,ENST00000373190,;PTPRT,missense_variant,p.Gly940Ala,ENST00000373184,;PTPRT,missense_variant,p.Gly959Ala,ENST00000356100,;PTPRT,missense_variant,p.Gly950Ala,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Gly568Ala,ENST00000612229,;PTPRT,missense_variant,p.Gly585Ala,ENST00000618610,;PTPRT,splice_region_variant,,ENST00000617474,; G ENST00000373198 Transcript missense_variant,splice_region_variant 3142/12746 2906/4383 969/1460 G/A gGa/gCa COSM5586358,COSM5586359 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 21/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,Superfamily_domains:SSF52799 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 42119970 42119970 C G 1 0 0 0 0 1 0 0 0 12967 869 30 4 4 PTPRT 20 42119970 Missense_Mutation SNP C C3N-00549_T 770876 42119970 22324197 393 15417 CEBPB 0 . GRCh38 20 50191420 50191420 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.387G>T p.Lys129Asn p.K129N ENST00000303004 1/1 257 110 147 202 202 0 strelka-varscan-mutect CEBPB,missense_variant,p.Lys129Asn,ENST00000303004,NM_001285879.1,NM_005194.3,NM_001285878.1;CEBPB-AS1,non_coding_transcript_exon_variant,,ENST00000613921,; T ENST00000303004 Transcript missense_variant 687/1956 387/1038 129/345 K/N aaG/aaT 1 1 CEBPB HGNC HGNC:1834 protein_coding YES CCDS13429.1 ENSP00000305422 P17676 UPI000000D8BA NM_001285879.1,NM_005194.3,NM_001285878.1 tolerated(0.39) 1/1 hmmpanther:PTHR23334:SF21,hmmpanther:PTHR23334,PIRSF_domain:PIRSF005879 MODERATE SNV 1 PASS rs1400337208 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 50191420 50191420 G T 1 0 0 0 0 1 0 0 0 2906 933 33 2 2 CEBPB 20 50191420 Missense_Mutation SNP G C3N-00549_T 8071450 50191420 14252747 394 15418 TSHZ2 0 . GRCh38 20 53255397 53255397 + Nonsense_Mutation SNP G G T rs149845942 C3N-00549_T C3N-00549_N G G c.1939G>T p.Glu647Ter p.E647* ENST00000371497 2/3 178 83 95 97 97 0 strelka-varscan-mutect TSHZ2,stop_gained,p.Glu647Ter,ENST00000371497,NM_173485.5;TSHZ2,stop_gained,p.Glu644Ter,ENST00000603338,NM_001193421.1;TSHZ2,stop_gained,p.Glu644Ter,ENST00000329613,;RP4-678D15.1,downstream_gene_variant,,ENST00000606932,;TSHZ2,upstream_gene_variant,,ENST00000605656,; T ENST00000371497 Transcript stop_gained 2826/12187 1939/3105 647/1034 E/* Gag/Tag rs149845942 1 1 TSHZ2 HGNC HGNC:13010 protein_coding YES CCDS33490.1 ENSP00000360552 Q9NRE2 UPI0000206747 NM_173485.5 2/3 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF3 HIGH 1 SNV 1 1 PASS rs149845942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 50 53255397 53255397 G T 1 0 0 0 0 0 1 0 0 17129 1059 37 1 1 TSHZ2 20 53255397 Nonsense_Mutation SNP G C3N-00549_T 3063977 53255397 11188770 395 15419 BCAS1 0 . GRCh38 20 54028887 54028888 + Frame_Shift_Ins INS - - T novel C3N-00549_T C3N-00549_N - - c.227dupA p.Asn76LysfsTer17 p.N76Kfs*17 ENST00000395961 4/12 272 117 155 146 146 0 sindel-varindel-pindel BCAS1,frameshift_variant,p.Asn76LysfsTer17,ENST00000395961,NM_003657.2;BCAS1,frameshift_variant,p.Asn76LysfsTer17,ENST00000371435,NM_001316361.2,NM_001323347.1;BCAS1,upstream_gene_variant,,ENST00000448484,; T ENST00000395961 Transcript frameshift_variant 394-395/3303 227-228/1755 76/584 N/KX aac/aaAc 1 -1 BCAS1 HGNC HGNC:974 protein_coding YES CCDS13444.1 ENSP00000379290 O75363 UPI000013D2E2 NM_003657.2 4/12 hmmpanther:PTHR15016 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 50 54028887 54028887 - T 1 0 1 1 0 0 0 0 0 1497 1136 40 0 0 BCAS1 20 54028887 Frame_Shift_Ins INS - C3N-00549_T 773490 54028887 10415280 396 15420 EEF1A2 0 . GRCh38 20 63490648 63490648 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.860C>A p.Thr287Asn p.T287N ENST00000217182 6/8 642 287 355 290 289 1 strelka-varscan-mutect EEF1A2,missense_variant,p.Thr287Asn,ENST00000217182,NM_001958.3;EEF1A2,missense_variant,p.Thr287Asn,ENST00000298049,; T ENST00000217182 Transcript missense_variant 1189/2006 860/1392 287/463 T/N aCt/aAt 1 -1 EEF1A2 HGNC HGNC:3192 protein_coding YES CCDS13522.1 ENSP00000217182 Q05639 UPI0000000136 NM_001958.3 deleterious_low_confidence(0) 6/8 HAMAP:MF_00118_A,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF104,Pfam_domain:PF03144,Gene3D:2.40.30.10,TIGRFAM_domain:TIGR00483,Superfamily_domains:SSF50447 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 63490648 63490648 G T 1 0 0 0 0 1 0 0 0 4753 1029 36 2 2 EEF1A2 20 63490648 Missense_Mutation SNP G C3N-00549_T 9461761 63490648 953519 397 15421 CXADR 0 . GRCh38 21 17561469 17561469 + Missense_Mutation SNP G G T rs372788152 C3N-00549_T C3N-00549_N G G c.826G>T p.Asp276Tyr p.D276Y ENST00000284878 6/7 84 53 31 72 72 0 strelka-varscan-mutect CXADR,missense_variant,p.Asp276Tyr,ENST00000284878,NM_001338.4;CXADR,missense_variant,p.Asp276Tyr,ENST00000400169,NM_001207066.1;CXADR,intron_variant,,ENST00000400166,NM_001207063.1;CXADR,intron_variant,,ENST00000400165,NM_001207064.1;CXADR,intron_variant,,ENST00000356275,NM_001207065.1; T ENST00000284878 Transcript missense_variant 1574/6254 826/1098 276/365 D/Y Gat/Tat rs372788152,COSM5577386,COSM5577387 1 1 CXADR HGNC HGNC:2559 protein_coding YES CCDS33519.1 ENSP00000284878 P78310 UPI000004F892 NM_001338.4 deleterious(0) 6/7 hmmpanther:PTHR12231:SF146,hmmpanther:PTHR12231 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs372788152 . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 50 17561469 17561469 G T 1 0 0 0 0 1 0 0 0 3886 1058 37 1 1 CXADR 21 17561469 Missense_Mutation SNP G C3N-00549_T 17561469 29148514 398 15422 N6AMT1 0 . GRCh38 21 28878258 28878258 + Missense_Mutation SNP G G C novel C3N-00549_T C3N-00549_N G G c.472C>G p.Leu158Val p.L158V ENST00000303775 5/6 96 77 19 132 132 0 strelka-varscan-mutect N6AMT1,missense_variant,p.Leu158Val,ENST00000303775,NM_013240.5;N6AMT1,missense_variant,p.Leu130Val,ENST00000351429,NM_182749.4;N6AMT1,missense_variant,p.Leu158Val,ENST00000460212,; C ENST00000303775 Transcript missense_variant 498/4865 472/645 158/214 L/V Ctg/Gtg 1 -1 N6AMT1 HGNC HGNC:16021 protein_coding YES CCDS33526.1 ENSP00000303584 B2RA97 UPI000003B020 NM_013240.5 tolerated(0.33) 5/6 Gene3D:3.40.50.150,hmmpanther:PTHR18895,hmmpanther:PTHR18895:SF71,Superfamily_domains:SSF53335,TIGRFAM_domain:TIGR00537 MODERATE 1 SNV 1 1 PASS rs1235274550 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 50 28878258 28878258 G C 1 0 0 0 0 1 0 0 0 10118 991 35 4 4 N6AMT1 21 28878258 Missense_Mutation SNP G C3N-00549_T 11316789 28878258 17831725 399 15423 KRTAP6-3 0 . GRCh38 21 30592659 30592659 + Missense_Mutation SNP G G A novel C3N-00549_T C3N-00549_N G G c.214G>A p.Gly72Ser p.G72S ENST00000391624 1/1 226 175 51 362 362 0 strelka-varscan-mutect KRTAP6-3,missense_variant,p.Gly72Ser,ENST00000391624,NM_181605.3;KRTAP22-2,upstream_gene_variant,,ENST00000382830,NM_001164434.1; A ENST00000391624 Transcript missense_variant 220/636 214/333 72/110 G/S Ggc/Agc 1 1 KRTAP6-3 HGNC HGNC:18933 protein_coding YES CCDS77622.1 ENSP00000375482 Q3LI67 UPI00003D4D73 NM_181605.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31678,hmmpanther:PTHR31678:SF4 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 30592659 30592659 G A 1 0 0 0 0 1 0 0 0 8466 1348 47 3 3 KRTAP6-3 21 30592659 Missense_Mutation SNP G C3N-00549_T 1714401 30592659 16117324 400 15424 URB1 0 . GRCh38 21 32334335 32334335 + Splice_Site SNP C C A novel C3N-00549_T C3N-00549_N C C c.4686-1G>T p.X1562_splice ENST00000382751 64 23 41 87 87 0 strelka-varscan-mutect URB1,splice_acceptor_variant,,ENST00000382751,NM_014825.2;URB1,splice_acceptor_variant,,ENST00000492603,;URB1,upstream_gene_variant,,ENST00000480196,; A ENST00000382751 Transcript splice_acceptor_variant -/10832 4686/6816 1562/2271 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 28/38 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 50 32334335 32334335 C A 1 0 0 0 0 0 0 1 0 17554 695 24 2 2 URB1 21 32334335 Splice_Site SNP C C3N-00549_T 1741676 32334335 14375648 401 15425 SON 0 . GRCh38 21 33573361 33573361 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.6939G>T p.Met2313Ile p.M2313I ENST00000356577 9/12 155 131 24 179 179 0 strelka-varscan-mutect SON,missense_variant,p.Met2313Ile,ENST00000356577,NM_138927.2;SON,missense_variant,p.Met1308Ile,ENST00000436227,;SON,missense_variant,p.Met341Ile,ENST00000381692,NM_001291412.1;DONSON,downstream_gene_variant,,ENST00000453626,;DONSON,downstream_gene_variant,,ENST00000303071,NM_017613.3;DONSON,downstream_gene_variant,,ENST00000303113,;DONSON,downstream_gene_variant,,ENST00000437395,;DONSON,downstream_gene_variant,,ENST00000432378,;SON,non_coding_transcript_exon_variant,,ENST00000470533,;SON,non_coding_transcript_exon_variant,,ENST00000467616,;SON,non_coding_transcript_exon_variant,,ENST00000473102,;SON,non_coding_transcript_exon_variant,,ENST00000484294,;SON,3_prime_UTR_variant,,ENST00000455528,;SON,3_prime_UTR_variant,,ENST00000457208,;DONSON,3_prime_UTR_variant,,ENST00000439593,;SON,non_coding_transcript_exon_variant,,ENST00000478183,;SON,non_coding_transcript_exon_variant,,ENST00000491794,;SON,non_coding_transcript_exon_variant,,ENST00000465834,;SON,non_coding_transcript_exon_variant,,ENST00000477419,;DONSON,downstream_gene_variant,,ENST00000457359,;DONSON,downstream_gene_variant,,ENST00000417871,;DONSON,downstream_gene_variant,,ENST00000442660,;DONSON,downstream_gene_variant,,ENST00000444517,;DONSON,downstream_gene_variant,,ENST00000460557,;SON,downstream_gene_variant,,ENST00000429093,;SON,downstream_gene_variant,,ENST00000474355,; T ENST00000356577 Transcript missense_variant 7414/8813 6939/7281 2313/2426 M/I atG/atT 1 1 SON HGNC HGNC:11183 protein_coding YES CCDS13629.1 ENSP00000348984 P18583 UPI0000140BFD NM_138927.2 deleterious_low_confidence(0.02) 9/12 Pfam_domain:PF01585,PROSITE_profiles:PS50174,hmmpanther:PTHR23106,hmmpanther:PTHR23106:SF13,SMART_domains:SM00443 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 50 33573361 33573361 G T 1 0 0 0 0 1 0 0 0 15248 1290 45 2 2 SON 21 33573361 Missense_Mutation SNP G C3N-00549_T 1239026 33573361 13136622 402 15426 PPIL2 0 . GRCh38 22 21675074 21675074 + Missense_Mutation SNP G G T novel C3N-00549_T C3N-00549_N G G c.254G>T p.Gly85Val p.G85V ENST00000626352 6/21 94 23 71 156 156 0 strelka-varscan-mutect PPIL2,missense_variant,p.Gly85Val,ENST00000335025,NM_148175.2;PPIL2,missense_variant,p.Gly85Val,ENST00000406385,NM_014337.3;PPIL2,missense_variant,p.Gly85Val,ENST00000626352,NM_148176.2;PPIL2,missense_variant,p.Gly85Val,ENST00000398831,;PPIL2,missense_variant,p.Gly116Val,ENST00000458567,;PPIL2,non_coding_transcript_exon_variant,,ENST00000484439,;MIR130B,downstream_gene_variant,,ENST00000498589,;PPIL2,downstream_gene_variant,,ENST00000485930,;PPIL2,3_prime_UTR_variant,,ENST00000417788,;PPIL2,downstream_gene_variant,,ENST00000498109,;PPIL2,downstream_gene_variant,,ENST00000496819,; T ENST00000626352 Transcript missense_variant 332/2625 254/1584 85/527 G/V gGg/gTg 1 1 PPIL2 HGNC HGNC:9261 protein_coding YES CCDS46670.1 ENSP00000486725 Q13356 UPI000002A7A2 NM_148176.2 tolerated(0.41) 6/21 Gene3D:3.30.40.10,PROSITE_profiles:PS51698,SMART_domains:SM00504,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs1033128986 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 50 21675074 21675074 G T 1 0 0 0 0 1 0 0 0 12438 1232 43 2 2 PPIL2 22 21675074 Missense_Mutation SNP G C3N-00549_T 21675074 29143394 403 15427 MXRA5 0 . GRCh38 X 3310769 3310769 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.7434G>T p.Trp2478Cys p.W2478C ENST00000217939 7/7 114 23 91 120 120 0 strelka-varscan-mutect MXRA5,missense_variant,p.Trp2478Cys,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 7589/9793 7434/8487 2478/2828 W/C tgG/tgT 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 3310769 3310769 C A 1 0 0 0 0 1 0 0 0 10002 624 22 2 2 MXRA5 23 3310769 Missense_Mutation SNP C C3N-00549_T 3310769 152730126 404 15428 MAGEB6 0 . GRCh38 X 26193939 26193939 + Silent SNP T T C novel C3N-00549_T C3N-00549_N T T c.93T>C p.= p.T31T ENST00000379034 2/2 30 9 21 39 39 0 strelka-varscan-mutect MAGEB6,synonymous_variant,p.=,ENST00000379034,NM_173523.2; C ENST00000379034 Transcript synonymous_variant 242/1949 93/1224 31/407 T acT/acC 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 2/2 hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 26193939 26193939 T C 1 0 0 0 0 0 0 0 1 9096 1567 55 5 5 MAGEB6 23 26193939 Silent SNP T C3N-00549_T 22883170 26193939 129846956 405 15429 CFAP47 0 . GRCh38 X 35967754 35967754 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.1736C>A p.Pro579Gln p.P579Q ENST00000297866 10/16 184 49 135 215 214 1 strelka-varscan-mutect CFAP47,missense_variant,p.Pro579Gln,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Pro579Gln,ENST00000297866,NM_152632.3;CFAP47,missense_variant,p.Pro579Gln,ENST00000493930,; A ENST00000297866 Transcript missense_variant 1802/3608 1736/2931 579/976 P/Q cCa/cAa 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 tolerated(0.29) 10/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 35967754 35967754 C A 1 0 0 0 0 1 0 0 0 3022 594 21 2 2 CFAP47 23 35967754 Missense_Mutation SNP C C3N-00549_T 9773815 35967754 120073141 406 15430 TRO 0 . GRCh38 X 54930398 54930398 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.3674C>A p.Thr1225Asn p.T1225N ENST00000173898 12/13 140 28 112 155 155 0 strelka-varscan-mutect TRO,missense_variant,p.Thr1225Asn,ENST00000173898,NM_001039705.2;TRO,missense_variant,p.Thr756Asn,ENST00000420798,NM_001271183.1;TRO,missense_variant,p.Thr828Asn,ENST00000375041,NM_001271184.1;TRO,intron_variant,,ENST00000319167,NM_016157.3;TRO,intron_variant,,ENST00000375022,NM_177556.2;TRO,intron_variant,,ENST00000622017,;TRO,intron_variant,,ENST00000399736,NM_177557.2;PFKFB1,downstream_gene_variant,,ENST00000375006,NM_001271804.1,NM_002625.3;PFKFB1,downstream_gene_variant,,ENST00000545676,NM_001271805.1;PFKFB1,downstream_gene_variant,,ENST00000614686,;PFKFB1,downstream_gene_variant,,ENST00000374992,;TRO,downstream_gene_variant,,ENST00000431115,;SNORA11,downstream_gene_variant,,ENST00000408823,;TRO,intron_variant,,ENST00000475183,;TRO,downstream_gene_variant,,ENST00000484031,;TRO,downstream_gene_variant,,ENST00000492142,;TRO,non_coding_transcript_exon_variant,,ENST00000492706,;TRO,intron_variant,,ENST00000445561,;TRO,downstream_gene_variant,,ENST00000469211,; A ENST00000173898 Transcript missense_variant 3786/4647 3674/4296 1225/1431 T/N aCc/aAc 1 1 TRO HGNC HGNC:12326 protein_coding YES CCDS43959.1 ENSP00000173898 Q12816 UPI000021208F NM_001039705.2 tolerated_low_confidence(0.14) 12/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 54930398 54930398 C A 1 0 0 0 0 1 0 0 0 17079 507 18 2 2 TRO 23 54930398 Missense_Mutation SNP C C3N-00549_T 18962644 54930398 101110497 407 15431 GLRA4 0 . GRCh38 X 103724220 103724220 + Missense_Mutation SNP C C A novel C3N-00549_T C3N-00549_N C C c.352G>T p.Asp118Tyr p.D118Y ENST00000372617 4/9 167 32 135 170 170 0 strelka-varscan-mutect GLRA4,missense_variant,p.Asp118Tyr,ENST00000372617,NM_001024452.2;GLRA4,upstream_gene_variant,,ENST00000469567,;GLRA4,3_prime_UTR_variant,,ENST00000436213,;GLRA4,non_coding_transcript_exon_variant,,ENST00000480725,; A ENST00000372617 Transcript missense_variant 773/1795 352/1254 118/417 D/Y Gac/Tac 1 -1 GLRA4 HGNC HGNC:31715 protein_coding YES CCDS43980.2 ENSP00000361700 Q5JXX5 UPI000188140C NM_001024452.2 deleterious(0) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR18945:SF211,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932,Prints_domain:PR01673 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 103724220 103724220 C A 1 0 0 0 0 1 0 0 0 6336 855 30 2 2 GLRA4 23 103724220 Missense_Mutation SNP C C3N-00549_T 48793822 103724220 52316675 408 15432 SLC25A53 0 . GRCh38 X 104105022 104105022 + Missense_Mutation SNP C C A C3N-00549_T C3N-00549_N C C c.236G>T p.Arg79Leu p.R79L ENST00000594199 2/2 96 19 77 90 90 0 strelka-varscan-mutect SLC25A53,missense_variant,p.Arg79Leu,ENST00000594199,NM_001012755.4; A ENST00000594199 Transcript missense_variant 417/6225 236/924 79/307 R/L cGg/cTg COSM4759620 1 -1 SLC25A53 HGNC HGNC:31894 protein_coding YES CCDS35363.1 ENSP00000468980 Q5H9E4 UPI0000140AFF NM_001012755.4 deleterious(0) 2/2 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF235 1 MODERATE 1 SNV 1 1 1 PASS rs1300891685 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 104105022 104105022 C A 1 0 0 0 0 1 0 0 0 14782 652 23 1 1 SLC25A53 23 104105022 Missense_Mutation SNP C C3N-00549_T 380802 104105022 51935873 409 15433 RBMX2 0 . GRCh38 X 130412391 130412391 + Frame_Shift_Del DEL A A - novel C3N-00549_T C3N-00549_N A A c.516delA p.Glu173ArgfsTer22 p.E173Rfs*22 ENST00000305536 6/6 56 13 43 40 40 0 sindel-varindel-pindel RBMX2,frameshift_variant,p.Glu173ArgfsTer22,ENST00000305536,NM_016024.2;RBMX2,non_coding_transcript_exon_variant,,ENST00000487274,;RBMX2,downstream_gene_variant,,ENST00000469953,; - ENST00000305536 Transcript frameshift_variant 576/1528 512/969 171/322 E/X gAa/ga 1 1 RBMX2 HGNC HGNC:24282 protein_coding YES CCDS43993.1 ENSP00000339090 Q9Y388 UPI00000704DB NM_016024.2 6/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23139,hmmpanther:PTHR23139:SF67,Low_complexity_(Seg):seg HIGH 1 deletion 1 4 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999997 1 1 1 0 - 7 5 50 130412391 130412391 A - 1 0 1 0 1 0 0 0 0 13318 246 9 0 0 RBMX2 23 130412391 Frame_Shift_Del DEL A C3N-00549_T 26307369 130412391 25628504 410 15434 IGSF1 0 . GRCh38 X 131283004 131283004 + Missense_Mutation SNP C C A rs144062892 C3N-00549_T C3N-00549_N C C c.928G>T p.Asp310Tyr p.D310Y ENST00000370903 6/20 65 16 49 50 50 0 strelka-varscan-mutect IGSF1,missense_variant,p.Asp301Tyr,ENST00000370904,;IGSF1,missense_variant,p.Asp310Tyr,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Asp301Tyr,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Asp310Tyr,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000370901,NM_205833.3;IGSF1,downstream_gene_variant,,ENST00000370900,NM_001170963.1;IGSF1,upstream_gene_variant,,ENST00000469836,; A ENST00000370903 Transcript missense_variant 1211/4594 928/4026 310/1341 D/Y Gat/Tat rs144062892 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 deleterious(0) 6/20 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs144062892 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 131283004 131283004 C A 1 0 0 0 0 1 0 0 0 7503 826 29 2 2 IGSF1 23 131283004 Missense_Mutation SNP C C3N-00549_T 870613 131283004 24757891 411 15435 SLITRK2 0 . GRCh38 X 145823333 145823333 + Missense_Mutation SNP G G A rs373498501 C3N-00549_T C3N-00549_N G G c.908G>A p.Arg303Gln p.R303Q ENST00000370490 1/1 133 20 113 120 119 1 strelka-varscan-mutect SLITRK2,missense_variant,p.Arg303Gln,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,missense_variant,p.Arg303Gln,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; A ENST00000370490 Transcript missense_variant 5163/7672 908/2538 303/845 R/Q cGg/cAg rs373498501,COSM4107245 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 deleterious(0.02) 1/1 0,1 MODERATE 1 SNV 0,1 1 PASS rs373498501 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 50 145823333 145823333 G A 1 0 0 0 0 1 0 0 0 15034 1116 39 1 1 SLITRK2 23 145823333 Missense_Mutation SNP G C3N-00549_T 14540329 145823333 10217562 412 15436 PNMA5 0 . GRCh38 X 152991230 152991230 + Silent SNP G G C novel C3N-00549_T C3N-00549_N G G c.369C>G p.= p.A123A ENST00000439251 2/2 32 4 28 35 35 0 strelka-varscan-mutect PNMA5,synonymous_variant,p.=,ENST00000439251,NM_001103150.1;PNMA5,synonymous_variant,p.=,ENST00000535214,NM_001184924.1;PNMA5,synonymous_variant,p.=,ENST00000361887,NM_052926.2;PNMA5,synonymous_variant,p.=,ENST00000452693,NM_001103151.1;PNMA5,synonymous_variant,p.=,ENST00000437210,; C ENST00000439251 Transcript synonymous_variant 808/3213 369/1347 123/448 A gcC/gcG 1 -1 PNMA5 HGNC HGNC:18743 protein_coding YES CCDS14718.1 ENSP00000388850 Q96PV4 UPI0000070F7D NM_001103150.1 2/2 Pfam_domain:PF14893,hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF4 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 50 152991230 152991230 G C 1 0 0 0 0 0 0 0 1 12263 1219 43 4 4 PNMA5 23 152991230 Silent SNP G C3N-00549_T 7167897 152991230 3049665 413 15437 ATP2B3 0 . GRCh38 X 153541901 153541901 + Frame_Shift_Del DEL G G - novel C3N-00549_T C3N-00549_N G G c.643delG p.Asp215ThrfsTer30 p.D215Tfs*30 ENST00000263519 3/20 95 12 83 60 60 0 sindel-varindel-pindel ATP2B3,frameshift_variant,p.Asp215ThrfsTer30,ENST00000370186,;ATP2B3,frameshift_variant,p.Asp215ThrfsTer30,ENST00000263519,NM_001001344.2;ATP2B3,frameshift_variant,p.Asp215ThrfsTer30,ENST00000349466,;ATP2B3,frameshift_variant,p.Asp215ThrfsTer30,ENST00000359149,NM_021949.3;ATP2B3,frameshift_variant,p.Asp215ThrfsTer30,ENST00000393842,; - ENST00000263519 Transcript frameshift_variant 765/6420 639/3663 213/1220 V/X gtG/gt 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 3/20 Low_complexity_(Seg):seg,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,Superfamily_domains:0049471 HIGH 1 deletion 1 4 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999994 1 1 1 0 - 7 5 50 153541901 153541901 G - 1 0 1 0 1 0 0 0 0 1294 1335 47 0 0 ATP2B3 23 153541901 Frame_Shift_Del DEL G C3N-00549_T 550671 153541901 2498994 414 15438 AVPR2 0 . GRCh38 X 153905681 153905681 + Missense_Mutation SNP C C G novel C3N-00549_T C3N-00549_N C C c.175C>G p.Leu59Val p.L59V ENST00000358927 3/4 164 29 135 120 120 0 strelka-varscan-mutect AVPR2,missense_variant,p.Leu59Val,ENST00000358927,;AVPR2,missense_variant,p.Leu59Val,ENST00000337474,NM_000054.4;AVPR2,missense_variant,p.Leu59Val,ENST00000370049,NM_001146151.1;AVPR2,missense_variant,p.Leu59Val,ENST00000430697,;ARHGAP4,downstream_gene_variant,,ENST00000370028,NM_001164741.1;ARHGAP4,downstream_gene_variant,,ENST00000350060,NM_001666.4;ARHGAP4,downstream_gene_variant,,ENST00000370016,;ARHGAP4,downstream_gene_variant,,ENST00000393721,;ARHGAP4,downstream_gene_variant,,ENST00000442172,;ARHGAP4,downstream_gene_variant,,ENST00000454164,;ARHGAP4,downstream_gene_variant,,ENST00000467421,;AVPR2,intron_variant,,ENST00000434679,;L1CAM,intron_variant,,ENST00000464967,;ARHGAP4,downstream_gene_variant,,ENST00000404127,;ARHGAP4,downstream_gene_variant,,ENST00000470209,;ARHGAP4,downstream_gene_variant,,ENST00000420383,;ARHGAP4,downstream_gene_variant,,ENST00000494302,;ARHGAP4,downstream_gene_variant,,ENST00000494397,;ARHGAP4,downstream_gene_variant,,ENST00000466928,;ARHGAP4,downstream_gene_variant,,ENST00000461739,; G ENST00000358927 Transcript missense_variant 384/1763 175/1116 59/371 L/V Ctg/Gtg 1 1 AVPR2 HGNC HGNC:897 protein_coding YES CCDS14735.1 ENSP00000351805 P30518 UPI000005043B deleterious(0.02) 3/4 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF20,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 50 153905681 153905681 C G 1 0 0 0 0 1 0 0 0 1389 796 28 4 4 AVPR2 23 153905681 Missense_Mutation SNP C C3N-00549_T 363780 153905681 2135214 415 15439 RGL1 0 . GRCh38 1 183884796 183884796 + Missense_Mutation SNP A A C novel C3N-00550_T C3N-00550_N A A c.914A>C p.Lys305Thr p.K305T ENST00000304685 8/19 328 295 33 394 394 0 strelka-varscan-mutect RGL1,missense_variant,p.Lys305Thr,ENST00000304685,NM_001297669.1,NM_015149.4,NM_001297670.1;RGL1,missense_variant,p.Lys270Thr,ENST00000360851,NM_001297671.1,NM_001297672.1; C ENST00000304685 Transcript missense_variant 1363/5100 914/2412 305/803 K/T aAa/aCa 1 1 RGL1 HGNC HGNC:30281 protein_coding YES CCDS1359.1 ENSP00000303192 Q9NZL6 UPI000002B24C NM_001297669.1,NM_015149.4,NM_001297670.1 deleterious(0.01) 8/19 PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF199,hmmpanther:PTHR23113,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 183884796 183884796 A C 1 0 0 0 0 1 0 0 0 13449 14 1 5 5 RGL1 1 183884796 Missense_Mutation SNP A C3N-00550_T 183884796 65071626 1 15440 CYP1B1 0 . GRCh38 2 38074349 38074349 + Missense_Mutation SNP G G T C3N-00550_T C3N-00550_N G G c.1040C>A p.Thr347Asn p.T347N ENST00000610745 2/3 182 133 49 266 265 1 strelka-varscan CYP1B1,missense_variant,p.Thr347Asn,ENST00000610745,NM_000104.3;CYP1B1,missense_variant,p.Thr347Asn,ENST00000614273,;CYP1B1,intron_variant,,ENST00000494864,;CYP1B1,downstream_gene_variant,,ENST00000490576,;CYP1B1-AS1,non_coding_transcript_exon_variant,,ENST00000628232,;CYP1B1-AS1,non_coding_transcript_exon_variant,,ENST00000629719,;CYP1B1-AS1,upstream_gene_variant,,ENST00000626582,;CYP1B1-AS1,upstream_gene_variant,,ENST00000629547,;CYP1B1-AS1,upstream_gene_variant,,ENST00000630542,;CYP1B1-AS1,upstream_gene_variant,,ENST00000627992,;CYP1B1-AS1,upstream_gene_variant,,ENST00000628580,;CYP1B1-AS1,upstream_gene_variant,,ENST00000629439,;CYP1B1-AS1,upstream_gene_variant,,ENST00000628135,;CYP1B1-AS1,upstream_gene_variant,,ENST00000589303,;CYP1B1-AS1,upstream_gene_variant,,ENST00000629773,;CYP1B1-AS1,upstream_gene_variant,,ENST00000620177,;CYP1B1,non_coding_transcript_exon_variant,,ENST00000613082,;CYP1B1,upstream_gene_variant,,ENST00000492443,;CYP1B1,upstream_gene_variant,,ENST00000491456,; T ENST00000610745 Transcript missense_variant 1443/5250 1040/1632 347/543 T/N aCc/aAc COSM5569795 1 -1 CYP1B1 HGNC HGNC:2597 protein_coding YES CCDS1793.1 ENSP00000478561 Q16678 UPI0000169C18 NM_000104.3 deleterious(0) 2/3 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00385,Prints_domain:PR00463,hmmpanther:PTHR24299,hmmpanther:PTHR24299:SF0,Low_complexity_(Seg):seg,Superfamily_domains:SSF48264 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 38074349 38074349 G T 1 0 0 0 0 1 0 0 0 3954 1275 44 2 2 CYP1B1 2 38074349 Missense_Mutation SNP G C3N-00550_T 38074349 204119180 2 15441 NRXN1 0 . GRCh38 2 51027530 51027530 + Silent SNP G G A rs202043138 C3N-00550_T C3N-00550_N G G c.744C>T p.= p.T248T ENST00000404971 2/24 26 22 4 31 31 0 strelka-varscan NRXN1,synonymous_variant,p.=,ENST00000406316,NM_004801.4;NRXN1,synonymous_variant,p.=,ENST00000625672,;NRXN1,synonymous_variant,p.=,ENST00000404971,NM_001135659.1;NRXN1,synonymous_variant,p.=,ENST00000401669,;NRXN1,synonymous_variant,p.=,ENST00000405472,;NRXN1,synonymous_variant,p.=,ENST00000405581,;NRXN1,synonymous_variant,p.=,ENST00000630543,;NRXN1,synonymous_variant,p.=,ENST00000637511,;NRXN1,synonymous_variant,p.=,ENST00000628515,;NRXN1,synonymous_variant,p.=,ENST00000636066,;NRXN1,synonymous_variant,p.=,ENST00000626899,;NRXN1,synonymous_variant,p.=,ENST00000627198,;NRXN1,synonymous_variant,p.=,ENST00000496792,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; A ENST00000404971 Transcript synonymous_variant 2084/7578 744/4644 248/1547 T acC/acT rs202043138,COSM4507392,COSM4507393,COSM4507394,COSM4507395 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 2/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,SMART_domains:SM00181 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -11.72418 1 1 1 1 0 A 2 1 51 51027530 51027530 G A 1 0 0 0 0 0 0 0 1 10724 1103 39 1 1 NRXN1 2 51027530 Silent SNP G C3N-00550_T 12953181 51027530 191165999 3 15442 CTNNA2 0 . GRCh38 2 80619092 80619092 + Missense_Mutation SNP T T C novel C3N-00550_T C3N-00550_N T T c.2438T>C p.Val813Ala p.V813A ENST00000402739 17/18 42 31 11 40 40 0 strelka-varscan CTNNA2,missense_variant,p.Val813Ala,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Val429Ala,ENST00000361291,NM_001320810.1;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,intron_variant,,ENST00000343114,NM_001282599.1;CTNNA2,intron_variant,,ENST00000541047,NM_001282600.1;CTNNA2,intron_variant,,ENST00000540488,;AC008067.2,upstream_gene_variant,,ENST00000430876,;AC008067.2,upstream_gene_variant,,ENST00000609950,; C ENST00000402739 Transcript missense_variant 2443/3684 2438/2862 813/953 V/A gTt/gCt 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 tolerated_low_confidence(0.8) 17/18 Pfam_domain:PF01044 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 80619092 80619092 T C 1 0 0 0 0 1 0 0 0 3822 1725 60 5 5 CTNNA2 2 80619092 Missense_Mutation SNP T C3N-00550_T 29591562 80619092 161574437 4 15443 TUBA3E 0 . GRCh38 2 130191836 130191836 + Missense_Mutation SNP A A G novel C3N-00550_T C3N-00550_N A A c.1348T>C p.Tyr450His p.Y450H ENST00000312988 5/5 54 44 10 85 84 1 strelka-varscan TUBA3E,missense_variant,p.Tyr450His,ENST00000312988,NM_207312.2;MZT2B,downstream_gene_variant,,ENST00000281871,NM_025029.3;MZT2B,downstream_gene_variant,,ENST00000409255,;MZT2B,downstream_gene_variant,,ENST00000425361,;MZT2B,downstream_gene_variant,,ENST00000457492,;MZT2B,downstream_gene_variant,,ENST00000455239,;MZT2B,downstream_gene_variant,,ENST00000491178,;MZT2B,downstream_gene_variant,,ENST00000480182,; G ENST00000312988 Transcript missense_variant 1449/1542 1348/1353 450/450 Y/H Tac/Cac 1 -1 TUBA3E HGNC HGNC:20765 protein_coding YES CCDS2158.1 ENSP00000318197 Q6PEY2 UPI00001BE8EB NM_207312.2 deleterious_low_confidence(0) 5/5 hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF94 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 51 130191836 130191836 A G 1 0 0 0 0 1 0 0 0 17258 449 16 5 5 TUBA3E 2 130191836 Missense_Mutation SNP A C3N-00550_T 49572744 130191836 112001693 5 15444 CCDC150 0 . GRCh38 2 196729302 196729302 + Missense_Mutation SNP A A G novel C3N-00550_T C3N-00550_N A A c.2666A>G p.Lys889Arg p.K889R ENST00000389175 23/28 288 267 21 331 331 0 strelka-varscan-mutect CCDC150,missense_variant,p.Lys889Arg,ENST00000389175,NM_001080539.1;CCDC150,missense_variant,p.Lys376Arg,ENST00000409270,;CCDC150,non_coding_transcript_exon_variant,,ENST00000487663,;CCDC150,non_coding_transcript_exon_variant,,ENST00000494389,;CCDC150,upstream_gene_variant,,ENST00000461243,;CCDC150,upstream_gene_variant,,ENST00000483877,;CCDC150,missense_variant,p.Lys376Arg,ENST00000448409,;CCDC150,3_prime_UTR_variant,,ENST00000431807,;CCDC150,3_prime_UTR_variant,,ENST00000424427,;CCDC150,downstream_gene_variant,,ENST00000463826,; G ENST00000389175 Transcript missense_variant 2801/3685 2666/3306 889/1101 K/R aAg/aGg 1 1 CCDC150 HGNC HGNC:26834 protein_coding YES CCDS46478.1 ENSP00000373827 Q8NCX0 UPI0000DD7A7C NM_001080539.1 tolerated(0.06) 23/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR35352 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 51 196729302 196729302 A G 1 0 0 0 0 1 0 0 0 2471 72 3 5 5 CCDC150 2 196729302 Missense_Mutation SNP A C3N-00550_T 66537466 196729302 45464227 6 15445 SF3B1 0 . GRCh38 2 197410004 197410004 + Missense_Mutation SNP G G C novel C3N-00550_T C3N-00550_N G G c.670C>G p.Pro224Ala p.P224A ENST00000335508 7/25 123 114 9 158 157 1 strelka-varscan-mutect SF3B1,missense_variant,p.Pro224Ala,ENST00000335508,NM_012433.2;SF3B1,non_coding_transcript_exon_variant,,ENST00000470268,;SF3B1,upstream_gene_variant,,ENST00000468925,; C ENST00000335508 Transcript missense_variant 762/6526 670/3915 224/1304 P/A Cct/Gct 1 -1 SF3B1 HGNC HGNC:10768 protein_coding YES CCDS33356.1 ENSP00000335321 O75533 UPI000013D493 NM_012433.2 tolerated(0.18) 7/25 hmmpanther:PTHR12097 MODERATE 1 SNV 1 1 PASS . . 0 203 0 7 0 0 0 0 -12.62829 0.983966 1 1 1 0 C 3 2 51 197410004 197410004 G C 1 0 0 0 0 1 0 0 0 14428 1246 43 4 4 SF3B1 2 197410004 Missense_Mutation SNP G C3N-00550_T 680702 197410004 44783525 7 15446 ULK4 0 . GRCh38 3 41800140 41800140 + Missense_Mutation SNP C C A novel C3N-00550_T C3N-00550_N C C c.2002G>T p.Ala668Ser p.A668S ENST00000301831 20/37 77 63 14 128 127 1 strelka-varscan-mutect ULK4,missense_variant,p.Ala668Ser,ENST00000301831,NM_017886.2;ULK4,non_coding_transcript_exon_variant,,ENST00000460406,; A ENST00000301831 Transcript missense_variant 2465/4613 2002/3828 668/1275 A/S Gca/Tca 1 -1 ULK4 HGNC HGNC:15784 protein_coding YES CCDS43071.1 ENSP00000301831 Q96C45 UPI0000E8267C NM_017886.2 deleterious(0.03) 20/37 Gene3D:1.25.10.10,hmmpanther:PTHR22983,hmmpanther:PTHR22983:SF15,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 41800140 41800140 C A 1 0 0 0 0 1 0 0 0 17501 797 28 2 2 ULK4 3 41800140 Missense_Mutation SNP C C3N-00550_T 41800140 156495419 8 15447 DNAJC13 0 . GRCh38 3 132453495 132453495 + Silent SNP T T G novel C3N-00550_T C3N-00550_N T T c.735T>G p.= p.P245P ENST00000260818 7/56 179 143 36 227 227 0 strelka-varscan-mutect DNAJC13,synonymous_variant,p.=,ENST00000260818,NM_015268.3;DNAJC13,non_coding_transcript_exon_variant,,ENST00000486798,;DNAJC13,upstream_gene_variant,,ENST00000471925,; G ENST00000260818 Transcript synonymous_variant 983/7730 735/6732 245/2243 P ccT/ccG 1 1 DNAJC13 HGNC HGNC:30343 protein_coding YES CCDS33857.1 ENSP00000260818 O75165 UPI000022C1FD NM_015268.3 7/56 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 51 132453495 132453495 T G 1 0 0 0 0 0 0 0 1 4446 1509 53 5 5 DNAJC13 3 132453495 Silent SNP T C3N-00550_T 90653355 132453495 65842064 9 15448 GAK 0 . GRCh38 4 877761 877761 + Silent SNP G G A novel C3N-00550_T C3N-00550_N G G c.1710C>T p.= p.P570P ENST00000314167 16/28 102 75 27 114 114 0 strelka-varscan-mutect GAK,synonymous_variant,p.=,ENST00000314167,NM_005255.2;GAK,synonymous_variant,p.=,ENST00000511163,NM_001318134.1,NM_001286833.1;GAK,intron_variant,,ENST00000618573,;GAK,upstream_gene_variant,,ENST00000509566,; A ENST00000314167 Transcript synonymous_variant 1821/4442 1710/3936 570/1311 P ccC/ccT 1 -1 GAK HGNC HGNC:4113 protein_coding YES CCDS3340.1 ENSP00000314499 O14976 UPI000012B04A NM_005255.2 16/28 hmmpanther:PTHR23172:SF34,hmmpanther:PTHR23172,Gene3D:3.90.190.10,SMART_domains:SM01326 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 51 877761 877761 G A 1 0 0 0 0 0 0 0 1 6063 1219 43 3 3 GAK 4 877761 Silent SNP G C3N-00550_T 877761 189336794 10 15449 VEGFC 0 . GRCh38 4 176727779 176727786 + Frame_Shift_Del DEL GTCTTGCT GTCTTGCT - novel C3N-00550_T C3N-00550_N GTCTTGCT GTCTTGCT c.544_551delAGCAAGAC p.Ser182ValfsTer3 p.S182Vfs*3 ENST00000618562 3/7 69 48 21 99 99 0 sindel-varindel-pindel VEGFC,frameshift_variant,p.Ser182ValfsTer3,ENST00000618562,NM_005429.4;VEGFC,splice_region_variant,,ENST00000507638,; - ENST00000618562 Transcript frameshift_variant,splice_region_variant 960-967/2064 544-551/1260 182-184/419 SKT/X AGCAAGACg/g 1 -1 VEGFC HGNC HGNC:12682 protein_coding YES CCDS43285.1 ENSP00000480043 P49767 UPI0000001C2A NM_005429.4 3/7 PROSITE_profiles:PS50278,hmmpanther:PTHR12025:SF3,hmmpanther:PTHR12025,Pfam_domain:PF00341,Gene3D:2.10.90.10,SMART_domains:SM00141,Superfamily_domains:SSF57501 HIGH 1 deletion 1 1 PASS . . 0 198 10 2 0 0 0 0 -20 0.9998098 1 1 1 0 - 7 5 51 176727779 176727779 GTCTTGCT - 1 0 1 0 1 0 0 0 0 17697 1159 40 0 0 VEGFC 4 176727779 Frame_Shift_Del DEL GTCTTGCT C3N-00550_T 175850018 176727779 13486776 11 15450 ADGRV1 0 . GRCh38 5 90675332 90675332 + Missense_Mutation SNP G G C C3N-00550_T C3N-00550_N G G c.5200G>C p.Glu1734Gln p.E1734Q ENST00000405460 24/90 277 254 23 316 316 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Glu1734Gln,ENST00000405460,NM_032119.3;ADGRV1,non_coding_transcript_exon_variant,,ENST00000450321,; C ENST00000405460 Transcript missense_variant 5296/19338 5200/18921 1734/6306 E/Q Gag/Cag COSM3618589 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 deleterious(0) 24/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,SMART_domains:SM00237,Superfamily_domains:SSF141072 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 90675332 90675332 G C 1 0 0 0 0 1 0 0 0 379 1175 41 4 4 ADGRV1 5 90675332 Missense_Mutation SNP G C3N-00550_T 90675332 90862927 12 15451 FABP6 0 . GRCh38 5 160213812 160213812 + Missense_Mutation SNP A A C novel C3N-00550_T C3N-00550_N A A c.128A>C p.Lys43Thr p.K43T ENST00000393980 3/7 299 228 71 346 346 0 strelka-varscan-mutect FABP6,missense_variant,p.Lys43Thr,ENST00000393980,NM_001130958.1,NM_001040442.1;FABP6,missense_variant,p.Lys29Thr,ENST00000523955,; C ENST00000393980 Transcript missense_variant 274/756 128/534 43/177 K/T aAa/aCa 1 1 FABP6 HGNC HGNC:3561 protein_coding YES CCDS43393.1 ENSP00000377549 P51161 UPI000020C072 NM_001130958.1,NM_001040442.1 deleterious_low_confidence(0.01) 3/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 160213812 160213812 A C 1 0 0 0 0 1 0 0 0 5233 14 1 5 5 FABP6 5 160213812 Missense_Mutation SNP A C3N-00550_T 69538480 160213812 21324447 13 15452 RUNX2 0 . GRCh38 6 45512303 45512303 + Missense_Mutation SNP A A G novel C3N-00550_T C3N-00550_N A A c.917A>G p.Tyr306Cys p.Y306C ENST00000371438 6/8 253 215 38 311 311 0 strelka-varscan-mutect RUNX2,missense_variant,p.Tyr306Cys,ENST00000371438,NM_001024630.3;RUNX2,missense_variant,p.Tyr306Cys,ENST00000371432,NM_001015051.3;RUNX2,missense_variant,p.Tyr292Cys,ENST00000359524,;RUNX2,missense_variant,p.Tyr306Cys,ENST00000576263,;RUNX2,missense_variant,p.Tyr306Cys,ENST00000465038,;RUNX2,missense_variant,p.Tyr306Cys,ENST00000371436,;RUNX2,missense_variant,p.Tyr292Cys,ENST00000625924,NM_001278478.1;RUNX2,missense_variant,p.Tyr234Cys,ENST00000478660,;RUNX2,3_prime_UTR_variant,,ENST00000483377,; G ENST00000371438 Transcript missense_variant 1275/5698 917/1566 306/521 Y/C tAc/tGc 1 1 RUNX2 HGNC HGNC:10472 protein_coding YES CCDS43467.2 ENSP00000360493 Q13950 UPI000013532F NM_001024630.3 deleterious(0) 6/8 hmmpanther:PTHR11950:SF7,hmmpanther:PTHR11950,PIRSF_domain:PIRSF009374 MODERATE 1 SNV 5 1 PASS rs1199475592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 51 45512303 45512303 A G 1 0 0 0 0 1 0 0 0 14009 391 14 5 5 RUNX2 6 45512303 Missense_Mutation SNP A C3N-00550_T 45512303 125293676 14 15453 CARD11 0 . GRCh38 7 2937950 2937950 + Missense_Mutation SNP G G T rs746318779 C3N-00550_T C3N-00550_N G G c.1100C>A p.Thr367Lys p.T367K ENST00000396946 8/25 210 175 35 217 216 1 strelka-varscan-mutect CARD11,missense_variant,p.Thr367Lys,ENST00000396946,NM_001324281.1,NM_032415.5; T ENST00000396946 Transcript missense_variant 1504/4366 1100/3465 367/1154 T/K aCg/aAg rs746318779 1 -1 CARD11 HGNC HGNC:16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 A0A024R854 UPI00003FED38 NM_001324281.1,NM_032415.5 deleterious(0.03) 8/25 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14559:SF4,hmmpanther:PTHR14559 MODERATE 1 SNV 1 1 PASS rs746318779 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 2937950 2937950 G T 1 0 0 0 0 1 0 0 0 2340 1145 40 1 1 CARD11 7 2937950 Missense_Mutation SNP G C3N-00550_T 2937950 156408023 15 15454 EGFR 0 . GRCh38 7 55156599 55156599 + Missense_Mutation SNP A A G novel C3N-00550_T C3N-00550_N A A c.1073A>G p.His358Arg p.H358R ENST00000275493 9/28 657 564 93 485 485 0 strelka-varscan-mutect EGFR,missense_variant,p.His358Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.His313Arg,ENST00000454757,;EGFR,missense_variant,p.His313Arg,ENST00000455089,;EGFR,missense_variant,p.His358Arg,ENST00000344576,NM_201284.1;EGFR,missense_variant,p.His358Arg,ENST00000342916,NM_201282.1;EGFR,missense_variant,p.His358Arg,ENST00000420316,NM_201283.1; G ENST00000275493 Transcript missense_variant 1250/9821 1073/3633 358/1210 H/R cAc/cGc 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 tolerated(0.37) 9/28 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 51 55156599 55156599 A G 1 0 0 0 0 1 0 0 0 4803 159 6 5 5 EGFR 7 55156599 Missense_Mutation SNP A C3N-00550_T 52218649 55156599 104189374 16 15455 KCND2 0 . GRCh38 7 120745798 120745798 + Missense_Mutation SNP G G A C3N-00550_T C3N-00550_N G G c.1486G>A p.Glu496Lys p.E496K ENST00000331113 5/6 253 200 53 311 311 0 strelka-varscan-mutect KCND2,missense_variant,p.Glu496Lys,ENST00000331113,NM_012281.2;KCND2,missense_variant,p.Glu82Lys,ENST00000425288,;RP4-797C5.2,downstream_gene_variant,,ENST00000450480,;KCND2,non_coding_transcript_exon_variant,,ENST00000473190,; A ENST00000331113 Transcript missense_variant 2451/5331 1486/1893 496/630 E/K Gaa/Aaa COSM3632373 1 1 KCND2 HGNC HGNC:6238 protein_coding YES CCDS5776.1 ENSP00000333496 Q9NZV8 A4D0V9 UPI0000073D37 NM_012281.2 tolerated_low_confidence(0.08) 5/6 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF159,Pfam_domain:PF11879 1 MODERATE 1 SNV 1 1 1 PASS rs1044289793 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 120745798 120745798 G A 1 0 0 0 0 1 0 0 0 7935 1059 37 1 1 KCND2 7 120745798 Missense_Mutation SNP G C3N-00550_T 65589199 120745798 38600175 17 15456 PIP 0 . GRCh38 7 143139541 143139541 + Missense_Mutation SNP G G T rs149269022 C3N-00550_T C3N-00550_N G G c.340G>T p.Val114Phe p.V114F ENST00000291009 4/4 221 179 42 208 208 0 strelka-varscan-mutect PIP,missense_variant,p.Val114Phe,ENST00000291009,NM_002652.2; T ENST00000291009 Transcript missense_variant 380/585 340/441 114/146 V/F Gtt/Ttt rs149269022 1 1 PIP HGNC HGNC:8993 protein_coding YES CCDS34768.1 ENSP00000291009 P12273 UPI0000131B05 NM_002652.2 deleterious(0) 4/4 hmmpanther:PTHR15096:SF5,hmmpanther:PTHR15096,Pfam_domain:PF05326,PIRSF_domain:PIRSF002572,Superfamily_domains:SSF81296,PD021604 MODERATE 1 SNV 1 1 PASS rs149269022 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 143139541 143139541 G T 1 0 0 0 0 1 0 0 0 12030 1145 40 1 1 PIP 7 143139541 Missense_Mutation SNP G C3N-00550_T 22393743 143139541 16206432 18 15457 TNC 0 . GRCh38 9 115090950 115090950 + Silent SNP C C T rs779652011 C3N-00550_T C3N-00550_N C C c.69G>A p.= p.G23G ENST00000350763 2/28 329 230 99 352 352 0 strelka-varscan-mutect TNC,synonymous_variant,p.=,ENST00000350763,NM_002160.3;TNC,synonymous_variant,p.=,ENST00000535648,;TNC,synonymous_variant,p.=,ENST00000341037,;TNC,synonymous_variant,p.=,ENST00000423613,;TNC,synonymous_variant,p.=,ENST00000542877,;TNC,synonymous_variant,p.=,ENST00000537320,;TNC,synonymous_variant,p.=,ENST00000534839,; T ENST00000350763 Transcript synonymous_variant 481/7641 69/6606 23/2201 G ggG/ggA rs779652011 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 2/28 Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs779652011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 51 115090950 115090950 C T 1 0 0 0 0 0 0 0 1 16744 610 22 3 3 TNC 9 115090950 Silent SNP C C3N-00550_T 115090950 23303767 19 15458 CCSER2 0 . GRCh38 10 84373714 84373714 + Missense_Mutation SNP G G T novel C3N-00550_T C3N-00550_N G G c.1513G>T p.Asp505Tyr p.D505Y ENST00000372088 3/10 274 249 25 355 355 0 strelka-varscan-mutect CCSER2,missense_variant,p.Asp505Tyr,ENST00000224756,NM_018999.3;CCSER2,missense_variant,p.Asp505Tyr,ENST00000372088,NM_001284240.1;CCSER2,missense_variant,p.Asp505Tyr,ENST00000359979,NM_001284241.1; T ENST00000372088 Transcript missense_variant 1772/7657 1513/3144 505/1047 D/Y Gat/Tat 1 1 CCSER2 HGNC HGNC:29197 protein_coding YES CCDS60582.1 ENSP00000361160 Q9H7U1 UPI00001F92C7 NM_001284240.1 deleterious(0) 3/10 Low_complexity_(Seg):seg,hmmpanther:PTHR22461,hmmpanther:PTHR22461:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 84373714 84373714 G T 1 0 0 0 0 1 0 0 0 2653 1290 45 2 2 CCSER2 10 84373714 Missense_Mutation SNP G C3N-00550_T 84373714 49423708 20 15459 NLRP14 0 . GRCh38 11 7071178 7071178 + Missense_Mutation SNP G G A novel C3N-00550_T C3N-00550_N G G c.3152G>A p.Cys1051Tyr p.C1051Y ENST00000299481 12/12 445 390 55 427 426 1 strelka-varscan-mutect NLRP14,missense_variant,p.Cys1051Tyr,ENST00000299481,NM_176822.3; A ENST00000299481 Transcript missense_variant 3498/3628 3152/3282 1051/1093 C/Y tGc/tAc 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 tolerated(0.13) 12/12 Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 7071178 7071178 G A 1 0 0 0 0 1 0 0 0 10513 1333 46 3 3 NLRP14 11 7071178 Missense_Mutation SNP G C3N-00550_T 7071178 128015444 21 15460 AMBRA1 0 . GRCh38 11 46543291 46543291 + Missense_Mutation SNP A A C novel C3N-00550_T C3N-00550_N A A c.726T>G p.Asn242Lys p.N242K ENST00000534300 7/17 158 144 14 191 191 0 strelka-varscan-mutect AMBRA1,missense_variant,p.Asn242Lys,ENST00000458649,;AMBRA1,missense_variant,p.Asn242Lys,ENST00000534300,NM_001300731.1;AMBRA1,missense_variant,p.Asn242Lys,ENST00000314845,NM_017749.3,NM_001267782.1;AMBRA1,missense_variant,p.Asn242Lys,ENST00000533727,NM_001267783.1;AMBRA1,missense_variant,p.Asn242Lys,ENST00000528950,;AMBRA1,downstream_gene_variant,,ENST00000531542,;AMBRA1,downstream_gene_variant,,ENST00000524783,; C ENST00000534300 Transcript missense_variant 1040/5067 726/3717 242/1238 N/K aaT/aaG 1 -1 AMBRA1 HGNC HGNC:25990 protein_coding YES CCDS73281.1 ENSP00000431926 Q9C0C7 UPI00005A6107 NM_001300731.1 deleterious_low_confidence(0) 7/17 hmmpanther:PTHR22874,hmmpanther:PTHR22874:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 46543291 46543291 A C 1 0 0 0 0 1 0 0 0 661 98 4 5 5 AMBRA1 11 46543291 Missense_Mutation SNP A C3N-00550_T 39472113 46543291 88543331 22 15461 FADS2 0 . GRCh38 11 61840355 61840355 + Missense_Mutation SNP C C T rs199630600 C3N-00550_T C3N-00550_N C C c.340C>T p.Arg114Trp p.R114W ENST00000278840 3/12 328 271 57 305 304 1 strelka-varscan-mutect FADS2,missense_variant,p.Arg114Trp,ENST00000278840,NM_004265.3;FADS2,missense_variant,p.Arg92Trp,ENST00000257261,NM_001281501.1;FADS2,missense_variant,p.Arg114Trp,ENST00000521849,;FADS2,missense_variant,p.Arg83Trp,ENST00000522056,NM_001281502.1;FADS2,5_prime_UTR_variant,,ENST00000521571,;FADS2,5_prime_UTR_variant,,ENST00000517312,;FADS2,5_prime_UTR_variant,,ENST00000518606,;FADS2,upstream_gene_variant,,ENST00000520145,; T ENST00000278840 Transcript missense_variant 970/3630 340/1335 114/444 R/W Cgg/Tgg rs199630600 1 1 FADS2 HGNC HGNC:3575 protein_coding YES CCDS8012.1 ENSP00000278840 O95864 UPI000003405E NM_004265.3 deleterious(0) 3/12 PIRSF_domain:PIRSF015921,hmmpanther:PTHR19353,hmmpanther:PTHR19353:SF12 MODERATE 1 SNV 1 1 PASS rs199630600 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 61840355 61840355 C T 1 0 0 0 0 1 0 0 0 5238 643 23 1 1 FADS2 11 61840355 Missense_Mutation SNP C C3N-00550_T 15297064 61840355 73246267 23 15462 JRKL 0 . GRCh38 11 96391760 96391760 + Missense_Mutation SNP A A C novel C3N-00550_T C3N-00550_N A A c.1111A>C p.Met371Leu p.M371L ENST00000332349 2/2 258 206 52 232 232 0 strelka-varscan-mutect JRKL,missense_variant,p.Met371Leu,ENST00000332349,NM_001261833.1,NM_003772.3;CCDC82,upstream_gene_variant,,ENST00000278520,NM_001318736.1,NM_024725.3;CCDC82,upstream_gene_variant,,ENST00000538597,;JRKL,intron_variant,,ENST00000546177,;CCDC82,upstream_gene_variant,,ENST00000525786,;CCDC82,upstream_gene_variant,,ENST00000524836,; C ENST00000332349 Transcript missense_variant 1358/2855 1111/1575 371/524 M/L Atg/Ctg 1 1 JRKL HGNC HGNC:6200 protein_coding YES CCDS8308.1 ENSP00000333350 Q9Y4A0 UPI0000167818 NM_001261833.1,NM_003772.3 tolerated(0.33) 2/2 Pfam_domain:PF03184,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF174 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 96391760 96391760 A C 1 0 0 0 0 1 0 0 0 7877 101 4 5 5 JRKL 11 96391760 Missense_Mutation SNP A C3N-00550_T 34551405 96391760 38694862 24 15463 CACNA1C 0 . GRCh38 12 2668933 2668933 + Missense_Mutation SNP C C T C3N-00550_T C3N-00550_N C C c.4768C>T p.Arg1590Cys p.R1590C ENST00000347598 40/49 119 89 30 111 111 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000406454,;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Arg1567Cys,ENST00000335762,;CACNA1C,missense_variant,p.Arg1590Cys,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Arg1564Cys,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Arg1570Cys,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Arg1562Cys,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Arg1559Cys,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Arg1531Cys,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Arg1531Cys,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Arg1529Cys,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Arg1542Cys,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Arg233Cys,ENST00000616390,;CACNA1C-AS2,non_coding_transcript_exon_variant,,ENST00000545526,;CACNA1C,splice_region_variant,,ENST00000465934,; T ENST00000347598 Transcript missense_variant,splice_region_variant 4768/6655 4768/6561 1590/2186 R/C Cgc/Tgc COSM4041181,COSM468212,COSM468213,COSM468214,COSM468215,COSM468216 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0) 40/49 Pfam_domain:PF16905,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 2668933 2668933 C T 1 0 0 0 0 1 0 0 0 2228 782 27 1 1 CACNA1C 12 2668933 Missense_Mutation SNP C C3N-00550_T 2668933 130606376 25 15464 CLEC2B 0 . GRCh38 12 9857594 9857594 + Missense_Mutation SNP C C A C3N-00550_T C3N-00550_N C C c.117G>T p.Trp39Cys p.W39C ENST00000228438 3/5 167 151 16 194 193 1 strelka-varscan-mutect CLEC2B,missense_variant,p.Trp39Cys,ENST00000228438,NM_005127.2;CLEC2B,upstream_gene_variant,,ENST00000538152,;CLEC2B,non_coding_transcript_exon_variant,,ENST00000540743,;CLEC2B,non_coding_transcript_exon_variant,,ENST00000539028,; A ENST00000228438 Transcript missense_variant 1051/1700 117/450 39/149 W/C tgG/tgT COSM1365139 1 -1 CLEC2B HGNC HGNC:2053 protein_coding YES CCDS8605.1 ENSP00000228438 Q92478 UPI000013C8D4 NM_005127.2 deleterious(0) 3/5 Gene3D:3.10.100.10,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF172,SMART_domains:SM00034,Superfamily_domains:SSF56436 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 9857594 9857594 C A 1 0 0 0 0 1 0 0 0 3275 856 30 2 2 CLEC2B 12 9857594 Missense_Mutation SNP C C3N-00550_T 7188661 9857594 123417715 26 15465 ETV6 0 . GRCh38 12 11839283 11839283 + Missense_Mutation SNP C C T C3N-00550_T C3N-00550_N C C c.307C>T p.Arg103Cys p.R103C ENST00000396373 3/8 72 52 20 79 79 0 strelka-varscan-mutect ETV6,missense_variant,p.Arg103Cys,ENST00000396373,NM_001987.4;ETV6,missense_variant,p.Arg75Cys,ENST00000545027,; T ENST00000396373 Transcript missense_variant 581/5989 307/1359 103/452 R/C Cgc/Tgc COSM4973065 1 1 ETV6 HGNC HGNC:3495 protein_coding YES CCDS8643.1 ENSP00000379658 P41212 A0A0S2Z3C9 UPI000000DA45 NM_001987.4 deleterious(0) 3/8 PROSITE_profiles:PS51433,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF19,Gene3D:1.10.150.50,Pfam_domain:PF02198,SMART_domains:SM00251,Superfamily_domains:SSF47769 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 11839283 11839283 C T 1 0 0 0 0 1 0 0 0 5147 884 31 1 1 ETV6 12 11839283 Missense_Mutation SNP C C3N-00550_T 1981689 11839283 121436026 27 15466 KCNC2 0 . GRCh38 12 75207941 75207941 + Missense_Mutation SNP C C T C3N-00550_T C3N-00550_N C C c.43G>A p.Gly15Arg p.G15R ENST00000549446 2/5 217 179 38 541 541 0 strelka-varscan-mutect KCNC2,missense_variant,p.Gly15Arg,ENST00000549446,NM_139137.3;KCNC2,missense_variant,p.Gly15Arg,ENST00000298972,NM_139136.3;KCNC2,missense_variant,p.Gly15Arg,ENST00000350228,NM_153748.2;KCNC2,missense_variant,p.Gly15Arg,ENST00000548513,;KCNC2,missense_variant,p.Gly15Arg,ENST00000550433,NM_001260498.1;KCNC2,missense_variant,p.Gly15Arg,ENST00000393288,NM_001260497.1;KCNC2,missense_variant,p.Gly15Arg,ENST00000540018,NM_001260499.1; T ENST00000549446 Transcript missense_variant 724/5625 43/1917 15/638 G/R Ggg/Agg COSM3671199,COSM3671200,COSM3671201 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 deleterious(0) 2/5 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,SMART_domains:SM00225,Superfamily_domains:SSF54695 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 75207941 75207941 C T 1 0 0 0 0 1 0 0 0 7931 652 23 1 1 KCNC2 12 75207941 Missense_Mutation SNP C C3N-00550_T 63368658 75207941 58067368 28 15467 DUOX1 0 . GRCh38 15 45135657 45135657 + Frame_Shift_Del DEL G G - novel C3N-00550_T C3N-00550_N G G c.681delG p.Arg229GlyfsTer112 p.R229Gfs*112 ENST00000321429 7/35 32 26 6 60 60 0 sindel-varindel DUOX1,frameshift_variant,p.Arg229GlyfsTer112,ENST00000321429,NM_017434.4;DUOX1,frameshift_variant,p.Arg229GlyfsTer112,ENST00000389037,NM_175940.2;DUOX1,upstream_gene_variant,,ENST00000561166,;DUOX1,downstream_gene_variant,,ENST00000558322,;DUOX1,frameshift_variant,p.Arg229GlyfsTer112,ENST00000561220,;DUOX1,upstream_gene_variant,,ENST00000558991,; - ENST00000321429 Transcript frameshift_variant 1086/5738 679/4656 227/1551 G/X Ggg/gg 1 1 DUOX1 HGNC HGNC:3062 protein_coding YES CCDS32221.1 ENSP00000317997 Q9NRD9 UPI000006E50E NM_017434.4 7/35 PROSITE_profiles:PS50292,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 HIGH 1 deletion 1 2 1 PASS . . 0 201 9 0 0 0 0 0 -15.7472 0.999996 1 1 1 0 - 7 5 51 45135657 45135657 G - 1 0 1 0 1 0 0 0 0 4622 1116 39 0 0 DUOX1 15 45135657 Frame_Shift_Del DEL G C3N-00550_T 45135657 56855532 29 15468 BNIP2 0 . GRCh38 15 59672660 59672660 + Missense_Mutation SNP T T G rs374057170 C3N-00550_T C3N-00550_N T T c.915A>C p.Arg305Ser p.R305S ENST00000267859 6/10 142 111 31 163 163 0 strelka-varscan-mutect BNIP2,missense_variant,p.Arg305Ser,ENST00000267859,NM_001320675.1;BNIP2,missense_variant,p.Arg305Ser,ENST00000612191,NM_004330.2;BNIP2,missense_variant,p.Arg184Ser,ENST00000607373,;BNIP2,missense_variant,p.Arg246Ser,ENST00000415213,;BNIP2,missense_variant,p.Arg62Ser,ENST00000439052,;AC092755.4,upstream_gene_variant,,ENST00000441746,;BNIP2,upstream_gene_variant,,ENST00000478981,;BNIP2,3_prime_UTR_variant,,ENST00000448414,;BNIP2,non_coding_transcript_exon_variant,,ENST00000464390,;BNIP2,upstream_gene_variant,,ENST00000560776,;PIGHP1,upstream_gene_variant,,ENST00000558833,; G ENST00000267859 Transcript missense_variant 1009/6325 915/1308 305/435 R/S agA/agC rs374057170 1 -1 BNIP2 HGNC HGNC:1083 protein_coding YES CCDS10174.2 ENSP00000267859 J3KN59 UPI0000E59C57 NM_001320675.1 tolerated(0.18) 6/10 Pfam_domain:PF13716,PROSITE_profiles:PS50191,hmmpanther:PTHR12112,hmmpanther:PTHR12112:SF12,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS rs374057170 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 51 59672660 59672660 T G 1 0 0 0 0 1 0 0 0 1633 1432 50 5 5 BNIP2 15 59672660 Missense_Mutation SNP T C3N-00550_T 14537003 59672660 42318529 30 15469 MRPL28 0 . GRCh38 16 368352 368356 + Frame_Shift_Del DEL CTCAA CTCAA - novel C3N-00550_T C3N-00550_N CTCAA CTCAA c.635_639delTTGAG p.Ile212LysfsTer52 p.I212Kfs*52 ENST00000199706 5/6 254 236 18 213 213 0 sindel-varindel-pindel MRPL28,frameshift_variant,p.Ile212LysfsTer52,ENST00000199706,NM_006428.4;MRPL28,frameshift_variant,p.Ile212LysfsTer52,ENST00000389675,;MRPL28,frameshift_variant,p.Ile212LysfsTer?,ENST00000441883,;MRPL28,frameshift_variant,p.Ile212LysfsTer?,ENST00000447696,;MRPL28,intron_variant,,ENST00000429738,;TMEM8A,downstream_gene_variant,,ENST00000431232,NM_021259.2;TMEM8A,downstream_gene_variant,,ENST00000250930,;TMEM8A,downstream_gene_variant,,ENST00000448854,;TMEM8A,downstream_gene_variant,,ENST00000424078,;MRPL28,downstream_gene_variant,,ENST00000450882,;MRPL28,non_coding_transcript_exon_variant,,ENST00000481453,;MRPL28,non_coding_transcript_exon_variant,,ENST00000483764,;MRPL28,non_coding_transcript_exon_variant,,ENST00000461550,;MRPL28,non_coding_transcript_exon_variant,,ENST00000469744,; - ENST00000199706 Transcript frameshift_variant 671-675/1098 635-639/771 212-213/256 IE/X aTTGAG/a 1 -1 MRPL28 HGNC HGNC:14484 protein_coding YES CCDS32349.1 ENSP00000199706 Q13084 UPI00001678A4 NM_006428.4 5/6 hmmpanther:PTHR13528,hmmpanther:PTHR13528:SF2 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 51 368352 368352 CTCAA - 1 0 1 0 1 0 0 0 0 9767 912 32 0 0 MRPL28 16 368352 Frame_Shift_Del DEL CTCAA C3N-00550_T 368352 89969993 31 15470 NOB1 0 . GRCh38 16 69748250 69748250 + Missense_Mutation SNP C C T rs199699618 C3N-00550_T C3N-00550_N C C c.806G>A p.Arg269His p.R269H ENST00000268802 7/9 152 132 20 182 182 0 strelka-varscan-mutect NOB1,missense_variant,p.Arg269His,ENST00000268802,NM_014062.2;NOB1,3_prime_UTR_variant,,ENST00000569871,;NOB1,3_prime_UTR_variant,,ENST00000564620,;NOB1,downstream_gene_variant,,ENST00000561677,;NOB1,downstream_gene_variant,,ENST00000562416,;NOB1,downstream_gene_variant,,ENST00000563055,; T ENST00000268802 Transcript missense_variant 836/1734 806/1239 269/412 R/H cGc/cAc rs199699618,COSM1217537 1 -1 NOB1 HGNC HGNC:29540 protein_coding YES CCDS10884.1 ENSP00000268802 Q9ULX3 UPI0000034E10 NM_014062.2 deleterious(0) 7/9 hmmpanther:PTHR12814:SF2,hmmpanther:PTHR12814,Pfam_domain:PF08772,Superfamily_domains:0052201 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199699618 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 69748250 69748250 C T 1 0 0 0 0 1 0 0 0 10553 768 27 1 1 NOB1 16 69748250 Missense_Mutation SNP C C3N-00550_T 69379898 69748250 20590095 32 15471 NECAB2 0 . GRCh38 16 83998306 83998306 + Missense_Mutation SNP G G T novel C3N-00550_T C3N-00550_N G G c.951G>T p.Arg317Ser p.R317S ENST00000305202 10/13 135 120 15 136 135 1 strelka-varscan-mutect NECAB2,missense_variant,p.Arg234Ser,ENST00000565691,;NECAB2,missense_variant,p.Arg317Ser,ENST00000305202,NM_019065.2;NECAB2,missense_variant,p.Arg19Ser,ENST00000564166,;NECAB2,downstream_gene_variant,,ENST00000566836,;NECAB2,downstream_gene_variant,,ENST00000567703,; T ENST00000305202 Transcript missense_variant 968/1608 951/1161 317/386 R/S agG/agT 1 1 NECAB2 HGNC HGNC:23746 protein_coding YES CCDS10940.1 ENSP00000307449 Q7Z6G3 UPI00001A9944 NM_019065.2 tolerated(0.75) 10/13 PROSITE_profiles:PS51725,hmmpanther:PTHR12178:SF2,hmmpanther:PTHR12178,Pfam_domain:PF03992,Gene3D:3.30.70.900,Superfamily_domains:SSF54909 MODERATE 1 SNV 1 1 PASS rs1410011644 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 83998306 83998306 G T 1 0 0 0 0 1 0 0 0 10329 1165 41 2 2 NECAB2 16 83998306 Missense_Mutation SNP G C3N-00550_T 14250056 83998306 6340039 33 15472 TP53 0 . GRCh38 17 7675238 7675238 + Splice_Site SNP T T C rs786202799 C3N-00550_T C3N-00550_N T T c.376-2A>G p.X126_splice ENST00000269305 188 142 46 302 302 0 strelka-varscan-mutect TP53,splice_acceptor_variant,,ENST00000617185,NM_001126114.2;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000622645,NM_001276696.1;TP53,splice_acceptor_variant,,ENST00000610292,NM_001126118.1;TP53,splice_acceptor_variant,,ENST00000455263,NM_001126113.2;TP53,splice_acceptor_variant,,ENST00000610538,NM_001276695.1;TP53,splice_acceptor_variant,,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,splice_acceptor_variant,,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000619485,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000508793,;TP53,splice_acceptor_variant,,ENST00000503591,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,missense_variant,p.Lys114Arg,ENST00000615910,;TP53,5_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000504937,NM_001126115.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000635293,;TP53,splice_acceptor_variant,,ENST00000505014,; C ENST00000269305 Transcript splice_acceptor_variant -/2579 376/1182 126/393 rs786202799,CS114003,TP53_g.12362A>G,TP53_g.12362A>T,TP53_g.12362del,TP53_g.12362A>C,COSM1646843,COSM1649367,COSM21585,COSM318166,COSM318167,COSM318168,COSM3388230,COSM3675526,COSM3675527,COSM3675528,COSM3675529,COSM3675530,COSM3717681,COSM45658,COSM45672,COSM46049,COSM562615,COSM562616,COSM562617 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 4/10 likely_pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs786202799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 51 7675238 7675238 T C 1 0 0 0 0 0 0 1 0 16859 1594 55 5 5 TP53 17 7675238 Splice_Site SNP T C3N-00550_T 7675238 75582203 34 15473 ZNF385C 0 . GRCh38 17 42028188 42028188 + Silent SNP G G T novel C3N-00550_T C3N-00550_N G G c.789C>A p.= p.G263G ENST00000618554 6/8 63 58 5 96 95 1 strelka-varscan-mutect ZNF385C,synonymous_variant,p.=,ENST00000618554,NM_001242704.1;ZNF385C,synonymous_variant,p.=,ENST00000436535,;NKIRAS2,downstream_gene_variant,,ENST00000307641,NM_001001349.2;NKIRAS2,downstream_gene_variant,,ENST00000393885,NM_001144927.1,NM_017595.5;NKIRAS2,downstream_gene_variant,,ENST00000393880,;NKIRAS2,downstream_gene_variant,,ENST00000393881,;NKIRAS2,downstream_gene_variant,,ENST00000449471,NM_001144928.1;NKIRAS2,downstream_gene_variant,,ENST00000479407,NM_001144929.1;NKIRAS2,downstream_gene_variant,,ENST00000316082,;NKIRAS2,downstream_gene_variant,,ENST00000462043,;NKIRAS2,downstream_gene_variant,,ENST00000587337,;ZNF385C,non_coding_transcript_exon_variant,,ENST00000461831,;NKIRAS2,downstream_gene_variant,,ENST00000393879,;ZNF385C,upstream_gene_variant,,ENST00000496039,;NKIRAS2,downstream_gene_variant,,ENST00000491638,;NKIRAS2,downstream_gene_variant,,ENST00000485789,; T ENST00000618554 Transcript synonymous_variant 789/2596 789/1275 263/424 G ggC/ggA 1 -1 ZNF385C HGNC HGNC:33722 protein_coding YES CCDS74065.1 ENSP00000480744 A0A087WX54 UPI0001E6F8A9 NM_001242704.1 6/8 hmmpanther:PTHR23067,hmmpanther:PTHR23067:SF6,Low_complexity_(Seg):seg LOW SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -11.56581 0.9999927 1 1 1 0 T 2 4 51 42028188 42028188 G T 1 0 0 0 0 0 0 0 1 18450 1190 42 2 2 ZNF385C 17 42028188 Silent SNP G C3N-00550_T 34352950 42028188 41229253 35 15474 POLRMT 0 . GRCh38 19 619669 619669 + Missense_Mutation SNP T T A novel C3N-00550_T C3N-00550_N T T c.2983A>T p.Met995Leu p.M995L ENST00000588649 13/21 111 80 31 150 150 0 strelka-varscan-mutect POLRMT,missense_variant,p.Met995Leu,ENST00000588649,NM_005035.3;HCN2,downstream_gene_variant,,ENST00000251287,NM_001194.3;POLRMT,downstream_gene_variant,,ENST00000590573,;POLRMT,upstream_gene_variant,,ENST00000590336,;POLRMT,upstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000590709,;POLRMT,upstream_gene_variant,,ENST00000589961,;POLRMT,upstream_gene_variant,,ENST00000592633,; A ENST00000588649 Transcript missense_variant 3075/3835 2983/3693 995/1230 M/L Atg/Ttg 1 -1 POLRMT HGNC HGNC:9200 protein_coding YES CCDS12036.1 ENSP00000465759 O00411 UPI000013C68E NM_005035.3 deleterious(0) 13/21 hmmpanther:PTHR10102:SF0,hmmpanther:PTHR10102,PROSITE_patterns:PS00489,Gene3D:1.10.150.20,Pfam_domain:PF00940,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS rs1290937780 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 619669 619669 T A 1 0 0 0 0 1 0 0 0 12349 1435 50 4 4 POLRMT 19 619669 Missense_Mutation SNP T C3N-00550_T 619669 57997947 36 15475 GRIN3B 0 . GRCh38 19 1009526 1009526 + Missense_Mutation SNP C C A novel C3N-00550_T C3N-00550_N C C c.3056C>A p.Pro1019His p.P1019H ENST00000234389 9/9 81 65 16 157 157 0 strelka-varscan-mutect GRIN3B,missense_variant,p.Pro1019His,ENST00000234389,NM_138690.1;TMEM259,downstream_gene_variant,,ENST00000356663,NM_001033026.1;TMEM259,downstream_gene_variant,,ENST00000333175,NM_033420.3;TMEM259,downstream_gene_variant,,ENST00000592590,;TMEM259,downstream_gene_variant,,ENST00000586285,;TMEM259,downstream_gene_variant,,ENST00000586250,;LLNLR-284B4.1,upstream_gene_variant,,ENST00000610701,;GRIN3B,downstream_gene_variant,,ENST00000588335,;TMEM259,downstream_gene_variant,,ENST00000586704,;TMEM259,downstream_gene_variant,,ENST00000593068,;TMEM259,downstream_gene_variant,,ENST00000592618,;TMEM259,downstream_gene_variant,,ENST00000592052,;TMEM259,downstream_gene_variant,,ENST00000589055,;TMEM259,downstream_gene_variant,,ENST00000607316,;TMEM259,downstream_gene_variant,,ENST00000589831,; A ENST00000234389 Transcript missense_variant 3075/3281 3056/3132 1019/1043 P/H cCt/cAt 1 1 GRIN3B HGNC HGNC:16768 protein_coding YES CCDS32861.1 ENSP00000234389 O60391 UPI000004064B NM_138690.1 deleterious_low_confidence(0) 9/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 1009526 1009526 C A 1 0 0 0 0 1 0 0 0 6666 681 24 2 2 GRIN3B 19 1009526 Missense_Mutation SNP C C3N-00550_T 389857 1009526 57608090 37 15476 ZNF114 0 . GRCh38 19 48286383 48286383 + Silent SNP C C T rs764325220 C3N-00550_T C3N-00550_N C C c.759C>T p.= p.C253C ENST00000595607 6/6 243 188 55 329 329 0 strelka-varscan-mutect ZNF114,synonymous_variant,p.=,ENST00000595607,NM_153608.2;ZNF114,synonymous_variant,p.=,ENST00000315849,;ZNF114,synonymous_variant,p.=,ENST00000597695,NM_001301062.1;ZNF114,synonymous_variant,p.=,ENST00000600687,;ZNF114,downstream_gene_variant,,ENST00000595408,;ZNF114,downstream_gene_variant,,ENST00000594024,;ZNF114,downstream_gene_variant,,ENST00000601320,;ZNF114,downstream_gene_variant,,ENST00000598898,; T ENST00000595607 Transcript synonymous_variant 1253/2478 759/1254 253/417 C tgC/tgT rs764325220,COSM316714 1 1 ZNF114 HGNC HGNC:12894 protein_coding YES CCDS12713.1 ENSP00000469998 Q8NC26 UPI000007282E NM_153608.2 6/6 0,1 LOW 1 SNV 1 0,1 1 PASS rs764325220 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 51 48286383 48286383 C T 1 0 0 0 0 0 0 0 1 18297 776 27 1 1 ZNF114 19 48286383 Silent SNP C C3N-00550_T 47276857 48286383 10331233 38 15477 AC018755.18 0 . GRCh38 19 51629899 51629899 + Missense_Mutation SNP G G A rs773993688 C3N-00550_T C3N-00550_N G G c.355C>T p.Arg119Cys p.R119C ENST00000534261 3/10 61 44 17 67 67 0 strelka-varscan-mutect SIGLEC5,missense_variant,p.Arg119Cys,ENST00000534261,NM_003830.3;AC018755.18,missense_variant,p.Arg119Cys,ENST00000429354,;AC018755.18,intron_variant,,ENST00000599649,; A ENST00000534261 Transcript missense_variant 755/2360 355/1656 119/551 R/C Cgc/Tgc rs773993688 1 -1 SIGLEC5 HGNC HGNC:10874 protein_coding YES CCDS33088.1 ENSP00000473238 O15389 UPI000011B40C NM_003830.3 deleterious(0) 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF67,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs773993688 . 11 192 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 51 51629899 51629899 G A 1 0 0 0 0 1 0 0 0 125 1116 39 1 1 AC018755.18 19 51629899 Missense_Mutation SNP G C3N-00550_T 3343516 51629899 6987717 39 15478 BRSK1 0 . GRCh38 19 55308695 55308695 + Missense_Mutation SNP A A T novel C3N-00550_T C3N-00550_N A A c.2146A>T p.Thr716Ser p.T716S ENST00000309383 18/19 255 186 69 352 352 0 strelka-varscan-mutect BRSK1,missense_variant,p.Thr716Ser,ENST00000309383,NM_032430.1;BRSK1,missense_variant,p.Thr732Ser,ENST00000590333,;BRSK1,missense_variant,p.Thr411Ser,ENST00000326848,;TMEM150B,downstream_gene_variant,,ENST00000326652,NM_001085488.2,NM_001282011.1;BRSK1,downstream_gene_variant,,ENST00000591774,;TMEM150B,downstream_gene_variant,,ENST00000585918,;CTD-2105E13.14,downstream_gene_variant,,ENST00000596786,;BRSK1,downstream_gene_variant,,ENST00000588584,;TMEM150B,downstream_gene_variant,,ENST00000586609,;TMEM150B,downstream_gene_variant,,ENST00000592603,;BRSK1,downstream_gene_variant,,ENST00000586626,;TMEM150B,downstream_gene_variant,,ENST00000592731,; T ENST00000309383 Transcript missense_variant 2423/3079 2146/2337 716/778 T/S Act/Tct 1 1 BRSK1 HGNC HGNC:18994 protein_coding YES CCDS12921.1 ENSP00000310649 Q8TDC3 UPI0000070495 NM_032430.1 tolerated(0.33) 18/19 MODERATE 1 SNV 1 1 PASS rs1254458750 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 51 55308695 55308695 A T 1 0 0 0 0 1 0 0 0 1697 159 6 4 4 BRSK1 19 55308695 Missense_Mutation SNP A C3N-00550_T 3678796 55308695 3308921 40 15479 NLRP4 0 . GRCh38 19 55870830 55870830 + Silent SNP G G A novel C3N-00550_T C3N-00550_N G G c.2358G>A p.= p.L786L ENST00000301295 7/10 69 65 4 83 83 0 varscan-mutect NLRP4,synonymous_variant,p.=,ENST00000301295,NM_134444.4;NLRP4,synonymous_variant,p.=,ENST00000587891,;NLRP4,synonymous_variant,p.=,ENST00000589437,; A ENST00000301295 Transcript synonymous_variant 2780/3670 2358/2985 786/994 L ttG/ttA 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 7/10 hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -9.484691 0.9999995 1 1 1 0 A 2 1 51 55870830 55870830 G A 1 0 0 0 0 0 0 0 1 10517 1362 47 3 3 NLRP4 19 55870830 Silent SNP G C3N-00550_T 562135 55870830 2746786 41 15480 NPEPL1 0 . GRCh38 20 58713947 58713947 + Missense_Mutation SNP G G A C3N-00550_T C3N-00550_N G G c.1156G>A p.Val386Met p.V386M ENST00000356091 10/12 37 33 4 65 65 0 strelka-mutect NPEPL1,missense_variant,p.Val386Met,ENST00000356091,NM_024663.3;NPEPL1,missense_variant,p.Val358Met,ENST00000525967,NM_001204872.1;NPEPL1,missense_variant,p.Val338Met,ENST00000525817,NM_001204873.1;RP11-261P9.4,downstream_gene_variant,,ENST00000530479,;STX16-NPEPL1,3_prime_UTR_variant,,ENST00000530122,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000529976,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000527587,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000527081,;NPEPL1,non_coding_transcript_exon_variant,,ENST00000525068,;NPEPL1,upstream_gene_variant,,ENST00000532531,;NPEPL1,downstream_gene_variant,,ENST00000533788,; A ENST00000356091 Transcript missense_variant 1444/2378 1156/1572 386/523 V/M Gtg/Atg COSM4656338 1 1 NPEPL1 HGNC HGNC:16244 protein_coding YES CCDS46621.1 ENSP00000348395 Q8NDH3 UPI000036789E NM_024663.3 tolerated(0.07) 10/12 hmmpanther:PTHR11963:SF4,hmmpanther:PTHR11963,Pfam_domain:PF00883,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 1 MODERATE 1 SNV 1 1 1 PASS rs1433511548 . 0 206 4 0 0 0 0 0 -11.03145 1 1 1 1 0 A 3 1 51 58713947 58713947 G A 1 0 0 0 0 1 0 0 0 10622 1261 44 3 3 NPEPL1 20 58713947 Missense_Mutation SNP G C3N-00550_T 58713947 5730220 42 15481 PATZ1 0 . GRCh38 22 31327310 31327310 + Splice_Site SNP C C A novel C3N-00550_T C3N-00550_N C C c.1646-1G>T p.X549_splice ENST00000266269 107 101 6 131 130 1 varscan-mutect PATZ1,splice_acceptor_variant,,ENST00000266269,NM_014323.2;PATZ1,splice_acceptor_variant,,ENST00000405309,NM_032052.1;PATZ1,splice_acceptor_variant,,ENST00000351933,NM_032050.1;PIK3IP1-AS1,intron_variant,,ENST00000440456,; A ENST00000266269 Transcript splice_acceptor_variant -/3781 1646/2064 549/687 1 -1 PATZ1 HGNC HGNC:13071 protein_coding YES CCDS13894.1 ENSP00000266269 Q9HBE1 A0A024R1M5 UPI000006D7C4 NM_014323.2 4/4 HIGH 1 SNV 1 1 PASS . . 0 176 20 10 3 0 0 0 -3.197113 0.06223107 0 1 0 0 A 5 1 51 31327310 31327310 C A 1 0 0 0 0 0 0 1 0 11561 927 32 2 2 PATZ1 22 31327310 Splice_Site SNP C C3N-00550_T 31327310 19491158 43 15482 TENM1 0 . GRCh38 X 124653762 124653762 + Missense_Mutation SNP A A C novel C3N-00550_T C3N-00550_N A A c.1190T>G p.Ile397Arg p.I397R ENST00000422452 7/32 212 184 28 225 225 0 strelka-varscan-mutect TENM1,missense_variant,p.Ile397Arg,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Ile397Arg,ENST00000371130,NM_014253.3; C ENST00000422452 Transcript missense_variant 1254/12891 1190/8199 397/2732 I/R aTa/aGa 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious_low_confidence(0) 7/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 51 124653762 124653762 A C 1 0 0 0 0 1 0 0 0 16171 449 16 5 5 TENM1 23 124653762 Missense_Mutation SNP A C3N-00550_T 124653762 31387133 44 15483 AGRN 0 . GRCh38 1 1043333 1043333 + Silent SNP G G T rs756019159 C3N-00551_T C3N-00551_N G G c.1479G>T p.= p.A493A ENST00000379370 8/36 444 327 117 395 395 0 strelka-varscan-mutect AGRN,synonymous_variant,p.=,ENST00000620552,NM_001305275.1;AGRN,synonymous_variant,p.=,ENST00000379370,NM_198576.3;AGRN,downstream_gene_variant,,ENST00000477585,;AGRN,downstream_gene_variant,,ENST00000469403,;AGRN,upstream_gene_variant,,ENST00000479707,;AGRN,upstream_gene_variant,,ENST00000466223,;AGRN,upstream_gene_variant,,ENST00000478677,; T ENST00000379370 Transcript synonymous_variant 1529/7323 1479/6138 493/2045 A gcG/gcT rs756019159 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 8/36 Gene3D:3.30.60.30,PROSITE_profiles:PS51465,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288,SMART_domains:SM00280,Superfamily_domains:SSF100895 LOW 1 SNV 1 1 PASS rs756019159 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 1043333 1043333 G T 1 0 0 0 0 0 0 0 1 476 1132 40 1 1 AGRN 1 1043333 Silent SNP G C3N-00551_T 1043333 247913089 1 15484 TNFRSF4 0 . GRCh38 1 1212698 1212698 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.377C>T p.Ala126Val p.A126V ENST00000379236 4/7 45 39 6 45 45 0 strelka-varscan-mutect TNFRSF4,missense_variant,p.Ala126Val,ENST00000379236,NM_003327.3;SDF4,downstream_gene_variant,,ENST00000263741,NM_016547.2;SDF4,downstream_gene_variant,,ENST00000360001,NM_016176.3;TNFRSF4,non_coding_transcript_exon_variant,,ENST00000453580,;TNFRSF4,non_coding_transcript_exon_variant,,ENST00000497869,;SDF4,downstream_gene_variant,,ENST00000494748,;SDF4,downstream_gene_variant,,ENST00000478938,;SDF4,downstream_gene_variant,,ENST00000465727,; A ENST00000379236 Transcript missense_variant 382/1068 377/834 126/277 A/V gCc/gTc 1 -1 TNFRSF4 HGNC HGNC:11918 protein_coding YES CCDS11.1 ENSP00000368538 P43489 UPI00001370E5 NM_003327.3 tolerated(0.45) 4/7 Gene3D:2.10.50.10,hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF132,SMART_domains:SM01411,Superfamily_domains:SSF57586 MODERATE 1 SNV 1 1 PASS . . 0 198 10 2 0 0 0 0 -11.99642 0.9991099 1 1 1 0 A 3 1 52 1212698 1212698 G A 1 0 0 0 0 1 0 0 0 16771 1203 42 3 3 TNFRSF4 1 1212698 Missense_Mutation SNP G C3N-00551_T 169365 1212698 247743724 2 15485 MIB2 0 . GRCh38 1 1625121 1625121 + Silent SNP G G T rs202053540 C3N-00551_T C3N-00551_N G G c.1002G>T p.= p.V334V ENST00000505820 6/20 153 96 57 187 186 1 strelka-varscan-mutect MIB2,synonymous_variant,p.=,ENST00000520777,NM_001170686.1;MIB2,synonymous_variant,p.=,ENST00000504599,;MIB2,synonymous_variant,p.=,ENST00000505820,NM_080875.2;MIB2,synonymous_variant,p.=,ENST00000355826,NM_001170687.1;MIB2,synonymous_variant,p.=,ENST00000378708,;MIB2,synonymous_variant,p.=,ENST00000514234,;MIB2,intron_variant,,ENST00000518681,NM_001170688.1;MIB2,intron_variant,,ENST00000378712,NM_001170689.1;MIB2,upstream_gene_variant,,ENST00000483015,;MIB2,downstream_gene_variant,,ENST00000510793,;MIB2,downstream_gene_variant,,ENST00000503789,;MIB2,downstream_gene_variant,,ENST00000512004,;MIB2,synonymous_variant,p.=,ENST00000487053,;MIB2,synonymous_variant,p.=,ENST00000506488,;MIB2,3_prime_UTR_variant,,ENST00000489635,;MIB2,non_coding_transcript_exon_variant,,ENST00000479659,;MIB2,non_coding_transcript_exon_variant,,ENST00000511502,;MIB2,non_coding_transcript_exon_variant,,ENST00000507229,;MIB2,non_coding_transcript_exon_variant,,ENST00000467597,;MIB2,non_coding_transcript_exon_variant,,ENST00000508148,;MIB2,upstream_gene_variant,,ENST00000473511,;MIB2,upstream_gene_variant,,ENST00000464570,;MIB2,upstream_gene_variant,,ENST00000505370,;MIB2,downstream_gene_variant,,ENST00000502470,;MIB2,downstream_gene_variant,,ENST00000514363,;MIB2,upstream_gene_variant,,ENST00000511910,;MIB2,upstream_gene_variant,,ENST00000486072,;MIB2,downstream_gene_variant,,ENST00000508455,;MIB2,upstream_gene_variant,,ENST00000470373,; T ENST00000505820 Transcript synonymous_variant 1019/3305 1002/3213 334/1070 V gtG/gtT rs202053540 1 1 MIB2 HGNC HGNC:30577 protein_coding YES CCDS41224.2 ENSP00000426103 Q96AX9 UPI0001C0B37A NM_080875.2 6/20 PROSITE_profiles:PS51416,hmmpanther:PTHR24202:SF4,hmmpanther:PTHR24202,Pfam_domain:PF06701,Superfamily_domains:0053823 LOW 1 SNV 1 1 PASS rs202053540 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 1625121 1625121 G T 1 0 0 0 0 0 0 0 1 9524 1335 47 2 2 MIB2 1 1625121 Silent SNP G C3N-00551_T 412423 1625121 247331301 3 15486 CAMTA1 0 . GRCh38 1 7677692 7677692 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2873C>A p.Pro958His p.P958H ENST00000303635 11/23 136 93 43 170 170 0 strelka-varscan-mutect CAMTA1,missense_variant,p.Pro958His,ENST00000303635,NM_015215.3; A ENST00000303635 Transcript missense_variant 3080/8444 2873/5022 958/1673 P/H cCc/cAc 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 deleterious(0.01) 11/23 hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 7677692 7677692 C A 1 0 0 0 0 1 0 0 0 2306 623 22 2 2 CAMTA1 1 7677692 Missense_Mutation SNP C C3N-00551_T 6052571 7677692 241278730 4 15487 RSC1A1 0 . GRCh38 1 15660124 15660124 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.256C>T p.His86Tyr p.H86Y ENST00000345034 1/1 147 113 34 242 242 0 strelka-varscan-mutect RSC1A1,missense_variant,p.His86Tyr,ENST00000345034,NM_006511.1;DDI2,3_prime_UTR_variant,,ENST00000480945,NM_032341.4;DDI2,3_prime_UTR_variant,,ENST00000320153,;DDI2,downstream_gene_variant,,ENST00000548451,; T ENST00000345034 Transcript missense_variant 256/1854 256/1854 86/617 H/Y Cat/Tat 1 1 RSC1A1 HGNC HGNC:10458 protein_coding YES CCDS161.1 ENSP00000341963 Q92681 UPI00000715AC NM_006511.1 tolerated(0.19) 1/1 hmmpanther:PTHR15397,hmmpanther:PTHR15397:SF2 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 15660124 15660124 C T 1 0 0 0 0 1 0 0 0 13954 594 21 3 3 RSC1A1 1 15660124 Missense_Mutation SNP C C3N-00551_T 7982432 15660124 233296298 5 15488 CROCC 0 . GRCh38 1 16930559 16930559 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.814G>T p.Glu272Ter p.E272* ENST00000375541 7/37 256 233 23 252 252 0 strelka-varscan-mutect CROCC,stop_gained,p.Glu272Ter,ENST00000375541,NM_014675.4;CROCC,stop_gained,p.Glu132Ter,ENST00000445545,;CROCC,stop_gained,p.Glu166Ter,ENST00000467938,;CROCC,non_coding_transcript_exon_variant,,ENST00000466256,;CROCC,non_coding_transcript_exon_variant,,ENST00000492631,; T ENST00000375541 Transcript stop_gained 883/6656 814/6054 272/2017 E/* Gag/Tag 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 7/37 Pfam_domain:PF15035,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17,Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 16930559 16930559 G T 1 0 0 0 0 0 1 0 0 3694 1175 41 2 2 CROCC 1 16930559 Nonsense_Mutation SNP G C3N-00551_T 1270435 16930559 232025863 6 15489 PADI2 0 . GRCh38 1 17086616 17086616 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.739G>A p.Glu247Lys p.E247K ENST00000375486 7/16 206 170 36 287 287 0 strelka-varscan-mutect PADI2,missense_variant,p.Glu247Lys,ENST00000375486,NM_007365.2;PADI2,missense_variant,p.Glu247Lys,ENST00000375481,;PADI2,upstream_gene_variant,,ENST00000466151,; T ENST00000375486 Transcript missense_variant 803/4345 739/1998 247/665 E/K Gag/Aag 1 -1 PADI2 HGNC HGNC:18341 protein_coding YES CCDS177.1 ENSP00000364635 Q9Y2J8 A0A024RA98 UPI00001314AF NM_007365.2 tolerated(0.28) 7/16 Superfamily_domains:0044952,PD936484,Pfam_domain:PF08527,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 17086616 17086616 C T 1 0 0 0 0 1 0 0 0 11456 864 30 3 3 PADI2 1 17086616 Missense_Mutation SNP C C3N-00551_T 156057 17086616 231869806 7 15490 TCEA3 0 . GRCh38 1 23419091 23419091 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.118A>G p.Ile40Val p.I40V ENST00000450454 2/11 55 43 12 42 42 0 strelka-varscan-mutect TCEA3,missense_variant,p.Ile40Val,ENST00000450454,NM_003196.2;TCEA3,missense_variant,p.Ile40Val,ENST00000374601,;TCEA3,missense_variant,p.Ile3Val,ENST00000461794,;TCEA3,non_coding_transcript_exon_variant,,ENST00000374602,;TCEA3,upstream_gene_variant,,ENST00000492271,; C ENST00000450454 Transcript missense_variant 225/1559 118/1047 40/348 I/V Atc/Gtc 1 -1 TCEA3 HGNC HGNC:11615 protein_coding YES CCDS44086.1 ENSP00000406293 O75764 UPI0000136AC2 NM_003196.2 tolerated(0.09) 2/11 Gene3D:1.20.930.10,Pfam_domain:PF08711,PIRSF_domain:PIRSF006704,PROSITE_profiles:PS51319,hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF4,SMART_domains:SM00509,Superfamily_domains:SSF47676,TIGRFAM_domain:TIGR01385 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 23419091 23419091 T C 1 0 0 0 0 1 0 0 0 16076 1464 51 5 5 TCEA3 1 23419091 Missense_Mutation SNP T C3N-00551_T 6332475 23419091 225537331 8 15491 UBXN11 0 . GRCh38 1 26284452 26284452 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.883G>A p.Glu295Lys p.E295K ENST00000374222 12/16 91 67 24 125 125 0 strelka-varscan-mutect UBXN11,missense_variant,p.Glu175Lys,ENST00000314675,NM_001077262.1;UBXN11,missense_variant,p.Glu295Lys,ENST00000374222,;UBXN11,missense_variant,p.Glu262Lys,ENST00000374217,NM_145345.2;UBXN11,missense_variant,p.Glu295Lys,ENST00000374221,NM_183008.2;UBXN11,missense_variant,p.Glu262Lys,ENST00000357089,;UBXN11,missense_variant,p.Glu52Lys,ENST00000374223,;SH3BGRL3,downstream_gene_variant,,ENST00000270792,NM_031286.3;UBXN11,downstream_gene_variant,,ENST00000374215,;UBXN11,downstream_gene_variant,,ENST00000452980,;SH3BGRL3,downstream_gene_variant,,ENST00000319041,;UBXN11,downstream_gene_variant,,ENST00000442942,;UBXN11,non_coding_transcript_exon_variant,,ENST00000472155,;UBXN11,non_coding_transcript_exon_variant,,ENST00000475591,;UBXN11,non_coding_transcript_exon_variant,,ENST00000496466,;UBXN11,non_coding_transcript_exon_variant,,ENST00000494942,; T ENST00000374222 Transcript missense_variant 1348/2043 883/1563 295/520 E/K Gag/Aag 1 -1 UBXN11 HGNC HGNC:30600 protein_coding YES CCDS41288.1 ENSP00000363339 Q5T124 UPI00004700E1 tolerated(0.07) 12/16 hmmpanther:PTHR23333:SF4,hmmpanther:PTHR23333,Pfam_domain:PF08059,Superfamily_domains:SSF102848 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 26284452 26284452 C T 1 0 0 0 0 1 0 0 0 17437 864 30 3 3 UBXN11 1 26284452 Missense_Mutation SNP C C3N-00551_T 2865361 26284452 222671970 9 15492 GPN2 0 . GRCh38 1 26889857 26889857 + Silent SNP G G A rs542731126 C3N-00551_T C3N-00551_N G G c.240C>T p.= p.G80G ENST00000374135 1/5 106 75 31 117 117 0 strelka-varscan-mutect GPN2,synonymous_variant,p.=,ENST00000374135,NM_018066.3;GPN2,intron_variant,,ENST00000431781,;GPATCH3,downstream_gene_variant,,ENST00000361720,NM_022078.2;GPN2,upstream_gene_variant,,ENST00000374133,;GPATCH3,downstream_gene_variant,,ENST00000445019,;GPATCH3,downstream_gene_variant,,ENST00000450844,;GPN2,upstream_gene_variant,,ENST00000461282,;GPN2,upstream_gene_variant,,ENST00000477418,; A ENST00000374135 Transcript synonymous_variant 441/4678 240/933 80/310 G ggC/ggT rs542731126 1 -1 GPN2 HGNC HGNC:25513 protein_coding YES CCDS289.1 ENSP00000363250 Q9H9Y4 UPI0000071F43 NM_018066.3 1/5 hmmpanther:PTHR21231:SF3,hmmpanther:PTHR21231,Gene3D:3.40.50.300,Pfam_domain:PF03029,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs542731126 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 26889857 26889857 G A 1 0 0 0 0 0 0 0 1 6520 1190 42 3 3 GPN2 1 26889857 Silent SNP G C3N-00551_T 605405 26889857 222066565 10 15493 SYTL1 0 . GRCh38 1 27351283 27351283 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1190C>G p.Pro397Arg p.P397R ENST00000543823 11/14 123 97 26 141 141 0 strelka-varscan-mutect SYTL1,missense_variant,p.Pro397Arg,ENST00000543823,;SYTL1,missense_variant,p.Pro385Arg,ENST00000318074,NM_032872.2;SYTL1,missense_variant,p.Pro397Arg,ENST00000616558,NM_001193308.1;SYTL1,missense_variant,p.Pro332Arg,ENST00000618673,;MAP3K6,downstream_gene_variant,,ENST00000374040,NM_001297609.1;MAP3K6,downstream_gene_variant,,ENST00000493901,NM_004672.4;MAP3K6,downstream_gene_variant,,ENST00000357582,;MAP3K6,downstream_gene_variant,,ENST00000472410,;MAP3K6,downstream_gene_variant,,ENST00000486046,;SYTL1,downstream_gene_variant,,ENST00000473280,;SYTL1,non_coding_transcript_exon_variant,,ENST00000490170,;SYTL1,non_coding_transcript_exon_variant,,ENST00000483926,;SYTL1,non_coding_transcript_exon_variant,,ENST00000485269,;SYTL1,non_coding_transcript_exon_variant,,ENST00000496001,;SYTL1,non_coding_transcript_exon_variant,,ENST00000615284,;SYTL1,upstream_gene_variant,,ENST00000475199,;MAP3K6,downstream_gene_variant,,ENST00000470890,; G ENST00000543823 Transcript missense_variant 1652/2229 1190/1689 397/562 P/R cCg/cGg 1 1 SYTL1 HGNC HGNC:15584 protein_coding YES CCDS53286.1 ENSP00000440704 Q8IYJ3 UPI0000074245 tolerated(0.1) 11/14 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF11,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 27351283 27351283 C G 1 0 0 0 0 1 0 0 0 15876 652 23 4 4 SYTL1 1 27351283 Missense_Mutation SNP C C3N-00551_T 461426 27351283 221605139 11 15494 P3H1 0 . GRCh38 1 42766686 42766686 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.286G>T p.Ala96Ser p.A96S ENST00000236040 1/14 82 62 20 191 191 0 strelka-varscan-mutect P3H1,missense_variant,p.Ala96Ser,ENST00000236040,NM_001243246.1;P3H1,missense_variant,p.Ala96Ser,ENST00000397054,NM_001146289.1;P3H1,missense_variant,p.Ala96Ser,ENST00000296388,NM_022356.3;P3H1,missense_variant,p.Ala96Ser,ENST00000372526,;C1orf50,upstream_gene_variant,,ENST00000372525,NM_024097.3;C1orf50,upstream_gene_variant,,ENST00000468913,;P3H1,non_coding_transcript_exon_variant,,ENST00000492956,;P3H1,non_coding_transcript_exon_variant,,ENST00000495874,;P3H1,non_coding_transcript_exon_variant,,ENST00000460031,;RP5-994D16.12,upstream_gene_variant,,ENST00000603943,;P3H1,upstream_gene_variant,,ENST00000463465,;RP5-994D16.12,upstream_gene_variant,,ENST00000464081,; A ENST00000236040 Transcript missense_variant 327/2993 286/2415 96/804 A/S Gcc/Tcc 1 -1 P3H1 HGNC HGNC:19316 protein_coding YES CCDS57986.1 ENSP00000236040 Q32P28 UPI000013E32E NM_001243246.1 tolerated(0.74) 1/14 hmmpanther:PTHR14049,hmmpanther:PTHR14049:SF5,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS rs1236695594 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 42766686 42766686 C A 1 0 0 0 0 1 0 0 0 11429 739 26 2 2 P3H1 1 42766686 Missense_Mutation SNP C C3N-00551_T 15415403 42766686 206189736 12 15495 PATJ 0 . GRCh38 1 62084631 62084631 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.4360G>A p.Gly1454Arg p.G1454R ENST00000371158 33/43 129 120 9 290 289 1 strelka-varscan-mutect PATJ,missense_variant,p.Gly1454Arg,ENST00000371158,NM_176877.2;PATJ,missense_variant,p.Gly238Arg,ENST00000635137,;PATJ,missense_variant,p.Gly238Arg,ENST00000307297,;PATJ,intron_variant,,ENST00000613764,;PATJ,missense_variant,p.Gly913Arg,ENST00000484937,;PATJ,3_prime_UTR_variant,,ENST00000635023,;PATJ,non_coding_transcript_exon_variant,,ENST00000484562,;PATJ,non_coding_transcript_exon_variant,,ENST00000459752,;PATJ,non_coding_transcript_exon_variant,,ENST00000635214,; A ENST00000371158 Transcript missense_variant 4474/8505 4360/5406 1454/1801 G/R Gga/Aga 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 tolerated(0.07) 33/43 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 62084631 62084631 G A 1 0 0 0 0 1 0 0 0 11558 1001 35 3 3 PATJ 1 62084631 Missense_Mutation SNP G C3N-00551_T 19317945 62084631 186871791 13 15496 L1TD1 0 . GRCh38 1 62206865 62206865 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.237A>T p.= p.A79A ENST00000498273 3/4 136 102 34 144 144 0 strelka-varscan-mutect L1TD1,synonymous_variant,p.=,ENST00000498273,NM_001164835.1,NM_019079.4;Y_RNA,upstream_gene_variant,,ENST00000363304,;RP5-1155K23.4,downstream_gene_variant,,ENST00000450606,; T ENST00000498273 Transcript synonymous_variant 532/3849 237/2598 79/865 A gcA/gcT 1 1 L1TD1 HGNC HGNC:25595 protein_coding YES CCDS619.1 ENSP00000419901 Q5T7N2 UPI000013E18E NM_001164835.1,NM_019079.4 3/4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 62206865 62206865 A T 1 0 0 0 0 0 0 0 1 8490 175 7 4 4 L1TD1 1 62206865 Silent SNP A C3N-00551_T 122234 62206865 186749557 14 15497 DOCK7 0 . GRCh38 1 62474078 62474078 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.6083A>T p.Glu2028Val p.E2028V ENST00000454575 47/49 168 125 43 198 198 0 strelka-varscan-mutect DOCK7,missense_variant,p.Glu2030Val,ENST00000251157,;DOCK7,missense_variant,p.Glu2028Val,ENST00000454575,NM_001271999.1;DOCK7,missense_variant,p.Glu2008Val,ENST00000340370,NM_033407.3;DOCK7,missense_variant,p.Glu2039Val,ENST00000635253,;DOCK7,missense_variant,p.Glu1999Val,ENST00000634264,NM_001272000.1;DOCK7,missense_variant,p.Glu1997Val,ENST00000635123,NM_001272001.1;DOCK7,missense_variant,p.Glu1128Val,ENST00000637255,;DOCK7,non_coding_transcript_exon_variant,,ENST00000634495,;DOCK7,downstream_gene_variant,,ENST00000637839,;DOCK7,downstream_gene_variant,,ENST00000637487,;DOCK7,downstream_gene_variant,,ENST00000636370,;DOCK7,upstream_gene_variant,,ENST00000637306,;DOCK7,downstream_gene_variant,,ENST00000638042,;DOCK7,non_coding_transcript_exon_variant,,ENST00000635983,;DOCK7,non_coding_transcript_exon_variant,,ENST00000489185,;DOCK7,downstream_gene_variant,,ENST00000467758,;DOCK7,downstream_gene_variant,,ENST00000635088,; A ENST00000454575 Transcript missense_variant 6094/6985 6083/6390 2028/2129 E/V gAa/gTa 1 -1 DOCK7 HGNC HGNC:19190 protein_coding YES CCDS60156.1 ENSP00000413583 Q96N67 H0Y7L2 UPI0000E45660 NM_001271999.1 deleterious(0) 47/49 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF78,hmmpanther:PTHR23317,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 62474078 62474078 T A 1 0 0 0 0 1 0 0 0 4507 1783 62 4 4 DOCK7 1 62474078 Missense_Mutation SNP T C3N-00551_T 267213 62474078 186482344 15 15498 ROR1 0 . GRCh38 1 64049745 64049745 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.218A>T p.Gln73Leu p.Q73L ENST00000371079 3/9 215 158 57 242 242 0 strelka-varscan-mutect ROR1,missense_variant,p.Gln73Leu,ENST00000371079,NM_005012.3;ROR1,missense_variant,p.Gln18Leu,ENST00000545203,;ROR1,missense_variant,p.Gln73Leu,ENST00000371080,NM_001083592.1;ROR1,non_coding_transcript_exon_variant,,ENST00000482426,; T ENST00000371079 Transcript missense_variant 593/5832 218/2814 73/937 Q/L cAg/cTg 1 1 ROR1 HGNC HGNC:10256 protein_coding YES CCDS626.1 ENSP00000360120 Q01973 UPI00001AF82C NM_005012.3 deleterious(0) 3/9 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF134,Pfam_domain:PF07679,PIRSF_domain:PIRSF000624,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 64049745 64049745 A T 1 0 0 0 0 1 0 0 0 13703 188 7 4 4 ROR1 1 64049745 Missense_Mutation SNP A C3N-00551_T 1575667 64049745 184906677 16 15499 C1orf141 0 . GRCh38 1 67093282 67093282 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.926G>C p.Arg309Thr p.R309T ENST00000371007 8/8 212 167 45 223 223 0 strelka-varscan-mutect C1orf141,missense_variant,p.Arg309Thr,ENST00000371007,NM_001276351.1;C1orf141,missense_variant,p.Arg309Thr,ENST00000371006,;C1orf141,3_prime_UTR_variant,,ENST00000621590,;C1orf141,3_prime_UTR_variant,,ENST00000475209,NM_001276352.1;C1orf141,downstream_gene_variant,,ENST00000448166,;C1orf141,downstream_gene_variant,,ENST00000603691,;C1orf141,3_prime_UTR_variant,,ENST00000544837,;C1orf141,non_coding_transcript_exon_variant,,ENST00000371004,; G ENST00000371007 Transcript missense_variant 1036/2153 926/1203 309/400 R/T aGa/aCa 1 -1 C1orf141 HGNC HGNC:32044 protein_coding YES CCDS30745.1 ENSP00000360046 Q5JVX7 UPI0000470AFA NM_001276351.1 tolerated(0.17) 8/8 hmmpanther:PTHR36873,Pfam_domain:PF15078 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 67093282 67093282 C G 1 0 0 0 0 1 0 0 0 1966 913 32 4 4 C1orf141 1 67093282 Missense_Mutation SNP C C3N-00551_T 3043537 67093282 181863140 17 15500 CTH 0 . GRCh38 1 70411552 70411552 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.137C>A p.Thr46Lys p.T46K ENST00000370938 1/12 154 121 33 194 194 0 strelka-varscan-mutect CTH,missense_variant,p.Thr46Lys,ENST00000411986,NM_001190463.1;CTH,missense_variant,p.Thr46Lys,ENST00000370938,NM_001902.5;CTH,missense_variant,p.Thr46Lys,ENST00000346806,NM_153742.4;CTH,non_coding_transcript_exon_variant,,ENST00000464926,; A ENST00000370938 Transcript missense_variant 281/1805 137/1218 46/405 T/K aCg/aAg 1 1 CTH HGNC HGNC:2501 protein_coding YES CCDS650.1 ENSP00000359976 P32929 UPI00001275DE NM_001902.5 deleterious(0) 1/12 Gene3D:3.40.640.10,Pfam_domain:PF01053,PIRSF_domain:PIRSF001434,hmmpanther:PTHR11808,hmmpanther:PTHR11808:SF15,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 70411552 70411552 C A 1 0 0 0 0 1 0 0 0 3817 536 19 1 1 CTH 1 70411552 Missense_Mutation SNP C C3N-00551_T 3318270 70411552 178544870 18 15501 TMED5 0 . GRCh38 1 93156041 93156041 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.515A>G p.His172Arg p.H172R ENST00000479918 4/5 41 37 4 26 26 0 strelka-mutect TMED5,missense_variant,p.His172Arg,ENST00000479918,NM_001167830.1;TMED5,3_prime_UTR_variant,,ENST00000370280,;TMED5,intron_variant,,ENST00000370282,NM_016040.4;TMED5,intron_variant,,ENST00000483033,;TMED5,intron_variant,,ENST00000370290,; C ENST00000479918 Transcript missense_variant 634/1296 515/582 172/193 H/R cAt/cGt 1 -1 TMED5 HGNC HGNC:24251 protein_coding CCDS53342.1 ENSP00000418992 Q9Y3A6 UPI0000470A98 NM_001167830.1 tolerated(0.09) 4/5 SMART_domains:SM01190 MODERATE SNV 3 1 PASS . . 1 206 3 0 0 0 0 0 -10.92873 1 1 1 1 0 C 3 2 52 93156041 93156041 T C 1 0 0 0 0 1 0 0 0 16452 1478 51 5 5 TMED5 1 93156041 Missense_Mutation SNP T C3N-00551_T 22744489 93156041 155800381 19 15502 COL11A1 0 . GRCh38 1 102978914 102978914 + Splice_Site SNP C C A novel C3N-00551_T C3N-00551_N C C c.2656-1G>T p.X886_splice ENST00000370096 486 455 31 536 536 0 strelka-varscan-mutect COL11A1,splice_acceptor_variant,,ENST00000358392,NM_080629.2;COL11A1,splice_acceptor_variant,,ENST00000370096,NM_001854.3;COL11A1,splice_acceptor_variant,,ENST00000353414,NM_001190709.1;COL11A1,splice_acceptor_variant,,ENST00000512756,NM_080630.3;COL11A1,splice_acceptor_variant,,ENST00000635193,; A ENST00000370096 Transcript splice_acceptor_variant -/7286 2656/5421 886/1806 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 33/66 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 52 102978914 102978914 C A 1 0 0 0 0 0 0 1 0 3455 695 24 2 2 COL11A1 1 102978914 Splice_Site SNP C C3N-00551_T 9822873 102978914 145977508 20 15503 SORT1 0 . GRCh38 1 109340792 109340792 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.1196G>A p.Gly399Asp p.G399D ENST00000256637 10/20 185 170 15 265 265 0 strelka-varscan-mutect SORT1,missense_variant,p.Gly399Asp,ENST00000256637,NM_002959.5;SORT1,missense_variant,p.Gly262Asp,ENST00000538502,NM_001205228.1;SORT1,upstream_gene_variant,,ENST00000466471,; T ENST00000256637 Transcript missense_variant 1255/7028 1196/2496 399/831 G/D gGc/gAc 1 -1 SORT1 HGNC HGNC:11186 protein_coding YES CCDS798.1 ENSP00000256637 Q99523 UPI0000074182 NM_002959.5 tolerated(0.13) 10/20 Gene3D:2.130.10.140,Pfam_domain:PF15902,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF23,SMART_domains:SM00602 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 109340792 109340792 C T 1 0 0 0 0 1 0 0 0 15257 739 26 3 3 SORT1 1 109340792 Missense_Mutation SNP C C3N-00551_T 6361878 109340792 139615630 21 15504 SPAG17 0 . GRCh38 1 118023380 118023380 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3993C>A p.His1331Gln p.H1331Q ENST00000336338 28/49 252 229 23 235 235 0 strelka-varscan-mutect SPAG17,missense_variant,p.His1331Gln,ENST00000336338,NM_206996.2;SPAG17,downstream_gene_variant,,ENST00000470550,; T ENST00000336338 Transcript missense_variant 4059/6924 3993/6672 1331/2223 H/Q caC/caA 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 tolerated(0.19) 28/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 118023380 118023380 G T 1 0 0 0 0 1 0 0 0 15310 1368 48 2 2 SPAG17 1 118023380 Missense_Mutation SNP G C3N-00551_T 8682588 118023380 130933042 22 15505 PI4KB 0 . GRCh38 1 151292933 151292933 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.2406G>A p.= p.E802E ENST00000368875 13/13 229 199 30 266 266 0 strelka-varscan-mutect PI4KB,synonymous_variant,p.=,ENST00000368875,NM_002651.2;PI4KB,synonymous_variant,p.=,ENST00000368874,NM_001198774.1;PI4KB,synonymous_variant,p.=,ENST00000368873,;PI4KB,synonymous_variant,p.=,ENST00000368872,NM_001198773.1;PI4KB,synonymous_variant,p.=,ENST00000529142,NM_001198775.1;PI4KB,synonymous_variant,p.=,ENST00000455060,;PI4KB,3_prime_UTR_variant,,ENST00000446339,;ZNF687,downstream_gene_variant,,ENST00000324048,NM_001304763.1;ZNF687,downstream_gene_variant,,ENST00000336715,NM_001304764.1,NM_020832.2;ZNF687,downstream_gene_variant,,ENST00000426871,;PI4KB,downstream_gene_variant,,ENST00000489889,;ZNF687,downstream_gene_variant,,ENST00000436614,;ZNF687,downstream_gene_variant,,ENST00000449313,;ZNF687,downstream_gene_variant,,ENST00000459919,; T ENST00000368875 Transcript synonymous_variant 2987/3983 2406/2487 802/828 E gaG/gaA 1 -1 PI4KB HGNC HGNC:8984 protein_coding YES CCDS993.1 ENSP00000357869 A0A0B4J1S8 UPI000007161F NM_002651.2 13/13 PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF22,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 151292933 151292933 C T 1 0 0 0 0 0 0 0 1 11963 796 28 3 3 PI4KB 1 151292933 Silent SNP C C3N-00551_T 33269553 151292933 97663489 23 15506 SPRR2A 0 . GRCh38 1 153056624 153056624 + Missense_Mutation SNP G G T rs759301202 C3N-00551_T C3N-00551_N G G c.112C>A p.Pro38Thr p.P38T ENST00000392653 2/2 83 62 21 131 131 0 strelka-varscan-mutect SPRR2A,missense_variant,p.Pro38Thr,ENST00000392653,NM_005988.2; T ENST00000392653 Transcript missense_variant 198/709 112/219 38/72 P/T Cca/Aca rs759301202 1 -1 SPRR2A HGNC HGNC:11261 protein_coding YES CCDS1034.1 ENSP00000376423 P35326 UPI0000135D6D NM_005988.2 deleterious_low_confidence(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263,Pfam_domain:PF14820,Prints_domain:PR01217 MODERATE 1 SNV 1 1 PASS rs759301202 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 153056624 153056624 G T 1 0 0 0 0 1 0 0 0 15452 1261 44 2 2 SPRR2A 1 153056624 Missense_Mutation SNP G C3N-00551_T 1763691 153056624 95899798 24 15507 PRR9 0 . GRCh38 1 153218328 153218328 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.184C>A p.Gln62Lys p.Q62K ENST00000368744 2/2 295 274 21 434 433 1 strelka-varscan-mutect PRR9,missense_variant,p.Gln62Lys,ENST00000368744,NM_001195571.1; A ENST00000368744 Transcript missense_variant 240/1229 184/351 62/116 Q/K Caa/Aaa 1 1 PRR9 HGNC HGNC:32057 protein_coding YES CCDS55639.1 ENSP00000357733 Q5T870 UPI0000038D61 NM_001195571.1 tolerated(0.17) 2/2 hmmpanther:PTHR23263:SF26,hmmpanther:PTHR23263 MODERATE 1 SNV 5 1 PASS rs1204270245 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 153218328 153218328 C A 1 0 0 0 0 1 0 0 0 12746 827 29 2 2 PRR9 1 153218328 Missense_Mutation SNP C C3N-00551_T 161704 153218328 95738094 25 15508 PBXIP1 0 . GRCh38 1 154946286 154946286 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.1388A>T p.Lys463Met p.K463M ENST00000368463 10/11 312 248 64 320 320 0 strelka-varscan-mutect PBXIP1,missense_variant,p.Lys463Met,ENST00000368463,NM_020524.2;PBXIP1,missense_variant,p.Lys434Met,ENST00000368465,NM_001317734.1;PBXIP1,downstream_gene_variant,,ENST00000368460,;Metazoa_SRP,downstream_gene_variant,,ENST00000600454,;PBXIP1,downstream_gene_variant,,ENST00000498553,;PBXIP1,downstream_gene_variant,,ENST00000493133,;PBXIP1,downstream_gene_variant,,ENST00000490230,; A ENST00000368463 Transcript missense_variant 1460/3212 1388/2196 463/731 K/M aAg/aTg 1 -1 PBXIP1 HGNC HGNC:21199 protein_coding YES CCDS1074.1 ENSP00000357448 Q96AQ6 UPI000006FE01 NM_020524.2 deleterious(0.01) 10/11 hmmpanther:PTHR28638,hmmpanther:PTHR28638:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 154946286 154946286 T A 1 0 0 0 0 1 0 0 0 11583 1609 56 4 4 PBXIP1 1 154946286 Missense_Mutation SNP T C3N-00551_T 1727958 154946286 94010136 26 15509 MEF2D 0 . GRCh38 1 156477160 156477160 + Missense_Mutation SNP G G A rs781562967 C3N-00551_T C3N-00551_N G G c.707C>T p.Pro236Leu p.P236L ENST00000348159 7/12 117 94 23 117 117 0 strelka-varscan-mutect MEF2D,missense_variant,p.Pro236Leu,ENST00000348159,NM_005920.3;MEF2D,missense_variant,p.Pro235Leu,ENST00000464356,;MEF2D,missense_variant,p.Pro236Leu,ENST00000360595,NM_001271629.1;MEF2D,3_prime_UTR_variant,,ENST00000368240,;MEF2D,3_prime_UTR_variant,,ENST00000475587,;MEF2D,non_coding_transcript_exon_variant,,ENST00000493077,; A ENST00000348159 Transcript missense_variant 1188/5965 707/1566 236/521 P/L cCt/cTt rs781562967,COSM1214872 1 -1 MEF2D HGNC HGNC:6997 protein_coding YES CCDS1143.1 ENSP00000271555 Q14814 UPI000012EEB6 NM_005920.3 tolerated(0.08) 7/12 hmmpanther:PTHR11945:SF23,hmmpanther:PTHR11945 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781562967 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 156477160 156477160 G A 1 0 0 0 0 1 0 0 0 9398 1000 35 3 3 MEF2D 1 156477160 Missense_Mutation SNP G C3N-00551_T 1530874 156477160 92479262 27 15510 INSRR 0 . GRCh38 1 156851290 156851290 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1229G>C p.Gly410Ala p.G410A ENST00000368195 5/22 536 430 106 560 560 0 strelka-varscan-mutect INSRR,missense_variant,p.Gly410Ala,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; G ENST00000368195 Transcript missense_variant,splice_region_variant 1626/5101 1229/3894 410/1297 G/A gGg/gCg 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 deleterious(0.03) 5/22 Pfam_domain:PF01030,PIRSF_domain:PIRSF000620,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 156851290 156851290 C G 1 0 0 0 0 1 0 0 0 7676 637 22 4 4 INSRR 1 156851290 Missense_Mutation SNP C C3N-00551_T 374130 156851290 92105132 28 15511 CD1B 0 . GRCh38 1 158330988 158330988 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.136G>T p.Gly46Cys p.G46C ENST00000368168 2/6 198 161 37 171 171 0 strelka-varscan-mutect CD1B,missense_variant,p.Gly46Cys,ENST00000368168,NM_001764.2;CD1B,missense_variant,p.Gly14Cys,ENST00000451207,; A ENST00000368168 Transcript missense_variant 244/1395 136/1002 46/333 G/C Ggc/Tgc 1 -1 CD1B HGNC HGNC:1635 protein_coding YES CCDS1176.1 ENSP00000357150 P29016 UPI0000127333 NM_001764.2 deleterious(0.04) 2/6 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF130,Pfam_domain:PF16497,Gene3D:3.30.500.10,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 158330988 158330988 C A 1 0 0 0 0 1 0 0 0 2678 681 24 2 2 CD1B 1 158330988 Missense_Mutation SNP C C3N-00551_T 1479698 158330988 90625434 29 15512 CADM3 0 . GRCh38 1 159199761 159199761 + Silent SNP G G T rs753580284 C3N-00551_T C3N-00551_N G G c.1065G>T p.= p.P355P ENST00000368124 9/10 299 235 64 244 244 0 strelka-varscan-mutect CADM3,synonymous_variant,p.=,ENST00000368125,NM_001127173.1;CADM3,synonymous_variant,p.=,ENST00000368124,NM_021189.3;ACKR1,upstream_gene_variant,,ENST00000537147,;ACKR1,upstream_gene_variant,,ENST00000368122,NM_002036.3;CADM3,downstream_gene_variant,,ENST00000416746,;CADM3-AS1,intron_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; T ENST00000368124 Transcript synonymous_variant 1222/2546 1065/1299 355/432 P ccG/ccT rs753580284 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 9/10 Gene3D:2.60.40.10,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,Low_complexity_(Seg):seg,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs753580284 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 159199761 159199761 G T 1 0 0 0 0 0 0 0 1 2258 1103 39 1 1 CADM3 1 159199761 Silent SNP G C3N-00551_T 868773 159199761 89756661 30 15513 ITLN2 0 . GRCh38 1 160945219 160945219 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.899G>T p.Trp300Leu p.W300L ENST00000368029 8/8 74 65 9 129 129 0 strelka-varscan-mutect ITLN2,missense_variant,p.Trp300Leu,ENST00000368029,NM_080878.2;RP11-544M22.1,intron_variant,,ENST00000356006,;ITLN2,non_coding_transcript_exon_variant,,ENST00000494442,; A ENST00000368029 Transcript missense_variant 957/1151 899/978 300/325 W/L tGg/tTg 1 -1 ITLN2 HGNC HGNC:20599 protein_coding YES CCDS1212.1 ENSP00000357008 Q8WWU7 UPI0000048F3E NM_080878.2 deleterious(0.02) 8/8 hmmpanther:PTHR16146:SF21,hmmpanther:PTHR16146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 160945219 160945219 C A 1 0 0 0 0 1 0 0 0 7817 595 21 2 2 ITLN2 1 160945219 Missense_Mutation SNP C C3N-00551_T 1745458 160945219 88011203 31 15514 ADCY10 0 . GRCh38 1 167860995 167860995 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1685C>A p.Ala562Asp p.A562D ENST00000367851 15/33 363 329 34 310 310 0 strelka-varscan-mutect ADCY10,missense_variant,p.Ala470Asp,ENST00000367848,NM_001297772.1;ADCY10,missense_variant,p.Ala562Asp,ENST00000367851,NM_018417.5;ADCY10,missense_variant,p.Ala409Asp,ENST00000545172,NM_001167749.2; T ENST00000367851 Transcript missense_variant 1870/5051 1685/4833 562/1610 A/D gCc/gAc 1 -1 ADCY10 HGNC HGNC:21285 protein_coding YES CCDS1265.1 ENSP00000356825 Q96PN6 A0A0K0K1J8 UPI0000204D00 NM_018417.5 deleterious(0) 15/33 hmmpanther:PTHR16305,hmmpanther:PTHR16305:SF32,PIRSF_domain:PIRSF011131,Gene3D:3.40.50.300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 167860995 167860995 G T 1 0 0 0 0 1 0 0 0 337 1203 42 2 2 ADCY10 1 167860995 Missense_Mutation SNP G C3N-00551_T 6915776 167860995 81095427 32 15515 C1orf112 0 . GRCh38 1 169843680 169843680 + Missense_Mutation SNP G G C rs543462948 C3N-00551_T C3N-00551_N G G c.1855G>C p.Asp619His p.D619H ENST00000286031 19/24 113 105 8 121 121 0 strelka-mutect C1orf112,missense_variant,p.Asp619His,ENST00000286031,NM_018186.2;C1orf112,missense_variant,p.Asp619His,ENST00000359326,;C1orf112,missense_variant,p.Asp296His,ENST00000413811,;C1orf112,non_coding_transcript_exon_variant,,ENST00000498289,;C1orf112,3_prime_UTR_variant,,ENST00000459772,; C ENST00000286031 Transcript missense_variant 2555/4355 1855/2562 619/853 D/H Gat/Cat rs543462948,COSM5643093 1 1 C1orf112 HGNC HGNC:25565 protein_coding YES CCDS1285.1 ENSP00000286031 Q9NSG2 A0A024R922 UPI000006E467 NM_018186.2 deleterious(0.02) 19/24 hmmpanther:PTHR16071,Pfam_domain:PF14868 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs543462948 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 169843680 169843680 G C 1 0 0 0 0 1 0 0 0 1959 942 33 4 4 C1orf112 1 169843680 Missense_Mutation SNP G C3N-00551_T 1982685 169843680 79112742 33 15516 C1orf112 0 . GRCh38 1 169843693 169843693 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.1868T>G p.Val623Gly p.V623G ENST00000286031 19/24 136 126 10 148 148 0 strelka-varscan-mutect C1orf112,missense_variant,p.Val623Gly,ENST00000286031,NM_018186.2;C1orf112,missense_variant,p.Val623Gly,ENST00000359326,;C1orf112,missense_variant,p.Val300Gly,ENST00000413811,;C1orf112,non_coding_transcript_exon_variant,,ENST00000498289,;C1orf112,3_prime_UTR_variant,,ENST00000459772,; G ENST00000286031 Transcript missense_variant 2568/4355 1868/2562 623/853 V/G gTt/gGt 1 1 C1orf112 HGNC HGNC:25565 protein_coding YES CCDS1285.1 ENSP00000286031 Q9NSG2 A0A024R922 UPI000006E467 NM_018186.2 deleterious(0) 19/24 hmmpanther:PTHR16071,Pfam_domain:PF14868 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 169843693 169843693 T G 1 0 0 0 0 1 0 0 0 1959 1725 60 5 5 C1orf112 1 169843693 Missense_Mutation SNP T C3N-00551_T 13 169843693 79112729 34 15517 CACNA1E 0 . GRCh38 1 181784720 181784720 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.5530C>A p.Pro1844Thr p.P1844T ENST00000367573 41/48 203 174 29 254 254 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Pro1825Thr,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Pro1844Thr,ENST00000621551,;CACNA1E,missense_variant,p.Pro1844Thr,ENST00000367567,;CACNA1E,missense_variant,p.Pro1825Thr,ENST00000358338,;CACNA1E,missense_variant,p.Pro1844Thr,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Pro1844Thr,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Pro1843Thr,ENST00000357570,;CACNA1E,missense_variant,p.Pro1825Thr,ENST00000360108,; A ENST00000367573 Transcript missense_variant 5530/7067 5530/6942 1844/2313 P/T Cct/Act 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0) 41/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF08763 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 181784720 181784720 C A 1 0 0 0 0 1 0 0 0 2230 739 26 2 2 CACNA1E 1 181784720 Missense_Mutation SNP C C3N-00551_T 11941027 181784720 67171702 35 15518 LAMC1 0 . GRCh38 1 183142664 183142664 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.4704G>T p.Gln1568His p.Q1568H ENST00000258341 28/28 224 169 55 239 239 0 strelka-varscan-mutect LAMC1,missense_variant,p.Gln1568His,ENST00000258341,NM_002293.3;RP11-181K3.4,upstream_gene_variant,,ENST00000457852,;LAMC1,downstream_gene_variant,,ENST00000495918,; T ENST00000258341 Transcript missense_variant 4961/7889 4704/4830 1568/1609 Q/H caG/caT 1 1 LAMC1 HGNC HGNC:6492 protein_coding YES CCDS1351.1 ENSP00000258341 P11047 UPI000013CFC7 NM_002293.3 deleterious(0) 28/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF270 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 183142664 183142664 G T 1 0 0 0 0 1 0 0 0 8518 991 35 2 2 LAMC1 1 183142664 Missense_Mutation SNP G C3N-00551_T 1357944 183142664 65813758 36 15519 F13B 0 . GRCh38 1 197055840 197055840 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1229G>T p.Gly410Val p.G410V ENST00000367412 8/12 280 235 45 358 358 0 strelka-varscan-mutect F13B,missense_variant,p.Gly410Val,ENST00000367412,NM_001994.2;F13B,upstream_gene_variant,,ENST00000490002,; A ENST00000367412 Transcript missense_variant 1273/2217 1229/1986 410/661 G/V gGg/gTg 1 -1 F13B HGNC HGNC:3534 protein_coding YES CCDS1388.1 ENSP00000356382 P05160 UPI000013D8E0 NM_001994.2 tolerated(0.28) 8/12 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF314,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 197055840 197055840 C A 1 0 0 0 0 1 0 0 0 5209 623 22 2 2 F13B 1 197055840 Missense_Mutation SNP C C3N-00551_T 13913176 197055840 51900582 37 15520 KIF14 0 . GRCh38 1 200565137 200565137 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.4003G>C p.Ala1335Pro p.A1335P ENST00000367350 25/30 155 141 14 176 176 0 strelka-varscan-mutect KIF14,missense_variant,p.Ala1335Pro,ENST00000367350,NM_014875.2;KIF14,missense_variant,p.Ala1335Pro,ENST00000614960,; G ENST00000367350 Transcript missense_variant 4442/7274 4003/4947 1335/1648 A/P Gca/Cca 1 -1 KIF14 HGNC HGNC:19181 protein_coding YES CCDS30963.1 ENSP00000356319 Q15058 UPI000012DDA3 NM_014875.2 tolerated(0.13) 25/30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 200565137 200565137 C G 1 0 0 0 0 1 0 0 0 8140 797 28 4 4 KIF14 1 200565137 Missense_Mutation SNP C C3N-00551_T 3509297 200565137 48391285 38 15521 IGFN1 0 . GRCh38 1 201210198 201210198 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.5305G>T p.Gly1769Trp p.G1769W ENST00000335211 12/24 79 62 17 87 87 0 strelka-varscan-mutect IGFN1,missense_variant,p.Gly1769Trp,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,;IGFN1,downstream_gene_variant,,ENST00000444705,; T ENST00000335211 Transcript missense_variant 5435/11810 5305/11127 1769/3708 G/W Ggg/Tgg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious_low_confidence(0) 12/24 MODERATE 1 SNV 5 1 PASS rs1179016260 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 201210198 201210198 G T 1 0 0 0 0 1 0 0 0 7497 1000 35 2 2 IGFN1 1 201210198 Missense_Mutation SNP G C3N-00551_T 645061 201210198 47746224 39 15522 NFASC 0 . GRCh38 1 204987418 204987418 + Nonsense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.2471T>A p.Leu824Ter p.L824* ENST00000339876 22/30 193 168 25 171 171 0 strelka-varscan-mutect NFASC,stop_gained,p.Leu824Ter,ENST00000339876,NM_001005388.2;NFASC,stop_gained,p.Leu824Ter,ENST00000401399,;NFASC,stop_gained,p.Leu794Ter,ENST00000367173,;NFASC,stop_gained,p.Leu56Ter,ENST00000425360,;NFASC,missense_variant,p.Val927Glu,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Val927Glu,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Val910Glu,ENST00000404076,;NFASC,missense_variant,p.Val927Glu,ENST00000404907,;NFASC,missense_variant,p.Val918Glu,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Val927Glu,ENST00000513543,;NFASC,upstream_gene_variant,,ENST00000413225,;NFASC,splice_region_variant,,ENST00000404977,;NFASC,splice_region_variant,,ENST00000468328,;NFASC,non_coding_transcript_exon_variant,,ENST00000495396,;NFASC,upstream_gene_variant,,ENST00000492085,;NFASC,downstream_gene_variant,,ENST00000471392,;NFASC,splice_region_variant,,ENST00000512826,;NFASC,splice_region_variant,,ENST00000504476,; A ENST00000339876 Transcript stop_gained,splice_region_variant 2799/10333 2471/3723 824/1240 L/* tTa/tAa 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 22/30 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Superfamily_domains:SSF49265 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 204987418 204987418 T A 1 0 0 0 0 0 1 0 0 10396 1652 57 4 4 NFASC 1 204987418 Nonsense_Mutation SNP T C3N-00551_T 3777220 204987418 43969004 40 15523 TMCC2 0 . GRCh38 1 205269646 205269646 + Missense_Mutation SNP G G A rs531333872 C3N-00551_T C3N-00551_N G G c.1444G>A p.Ala482Thr p.A482T ENST00000358024 3/5 322 294 28 248 248 0 strelka-varscan-mutect TMCC2,missense_variant,p.Ala482Thr,ENST00000358024,NM_014858.3;TMCC2,missense_variant,p.Ala404Thr,ENST00000545499,NM_001242925.1;TMCC2,missense_variant,p.Ala242Thr,ENST00000329800,NM_001297613.1;TMCC2,missense_variant,p.Ala287Thr,ENST00000330675,;TMCC2,missense_variant,p.Ala257Thr,ENST00000637895,NM_001297611.1;TMCC2,non_coding_transcript_exon_variant,,ENST00000495538,;TMCC2,non_coding_transcript_exon_variant,,ENST00000481950,;TMCC2,intron_variant,,ENST00000468846,;TMCC2,downstream_gene_variant,,ENST00000367159,; A ENST00000358024 Transcript missense_variant 1833/3738 1444/2130 482/709 A/T Gcc/Acc rs531333872 1 1 TMCC2 HGNC HGNC:24239 protein_coding YES CCDS30984.1 ENSP00000350718 O75069 UPI00002056FC NM_014858.3 tolerated(0.08) 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR17613,hmmpanther:PTHR17613:SF9,Pfam_domain:PF10267 MODERATE 1 SNV 1 1 PASS rs531333872 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 205269646 205269646 G A 1 0 0 0 0 1 0 0 0 16439 1087 38 1 1 TMCC2 1 205269646 Missense_Mutation SNP G C3N-00551_T 282228 205269646 43686776 41 15524 CR1 0 . GRCh38 1 207496304 207496304 + Frame_Shift_Del DEL G G - C3N-00551_T C3N-00551_N G G c.39delG p.Pro14ArgfsTer44 p.P14Rfs*44 ENST00000367049 1/47 257 219 38 410 410 0 sindel-varindel-pindel CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000367049,NM_000651.4;CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000367051,;CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000367052,;CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000367053,;CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000400960,NM_000573.3;CR1,upstream_gene_variant,,ENST00000529814,;CR1,non_coding_transcript_exon_variant,,ENST00000367050,;CR1,frameshift_variant,p.Pro14ArgfsTer44,ENST00000534202,;CR1,non_coding_transcript_exon_variant,,ENST00000530487,;CR1,upstream_gene_variant,,ENST00000434033,;CR1,upstream_gene_variant,,ENST00000436595,;CR1,upstream_gene_variant,,ENST00000450439,; - ENST00000367049 Transcript frameshift_variant 37/7470 37/7470 13/2489 G/X Ggg/gg COSM5053033,COSM5053034 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 1/47 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-TM 1,1 HIGH 1 deletion 5 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 207496304 207496304 G - 1 0 1 0 1 0 0 0 0 3638 1116 39 0 0 CR1 1 207496304 Frame_Shift_Del DEL G C3N-00551_T 2226658 207496304 41460118 42 15525 CENPF 0 . GRCh38 1 214645558 214645558 + Frame_Shift_Del DEL T T - novel C3N-00551_T C3N-00551_N T T c.5988delT p.Ser1996ArgfsTer14 p.S1996Rfs*14 ENST00000366955 13/20 255 241 14 230 230 0 varindel-pindel CENPF,frameshift_variant,p.Ser1996ArgfsTer14,ENST00000366955,NM_016343.3;CENPF,upstream_gene_variant,,ENST00000614578,;CENPF,upstream_gene_variant,,ENST00000467765,; - ENST00000366955 Transcript frameshift_variant 6156/10307 5988/9345 1996/3114 S/X agT/ag 1 1 CENPF HGNC HGNC:1857 protein_coding YES CCDS31023.1 ENSP00000355922 P49454 UPI00001AE985 NM_016343.3 13/20 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10473,hmmpanther:PTHR18874 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 214645558 214645558 T - 1 0 1 0 1 0 0 0 0 2939 1693 59 0 0 CENPF 1 214645558 Frame_Shift_Del DEL T C3N-00551_T 7149254 214645558 34310864 43 15526 USH2A 0 . GRCh38 1 215798916 215798916 + Missense_Mutation SNP G G A rs200696560 C3N-00551_T C3N-00551_N G G c.9949C>T p.Arg3317Cys p.R3317C ENST00000307340 50/72 479 450 29 539 539 0 strelka-varscan USH2A,missense_variant,p.Arg3317Cys,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 10336/18883 9949/15609 3317/5202 R/C Cgc/Tgc rs200696560,COSM1931267,COSM4231346 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.17) 50/72 SMART_domains:SM00060 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 215798916 215798916 G A 1 0 0 0 0 1 0 0 0 17570 1058 37 1 1 USH2A 1 215798916 Missense_Mutation SNP G C3N-00551_T 1153358 215798916 33157506 44 15527 TMEM63A 0 . GRCh38 1 225862229 225862229 + Silent SNP G G T rs191286059 C3N-00551_T C3N-00551_N G G c.1074C>A p.= p.S358S ENST00000366835 13/25 147 132 15 112 112 0 strelka-varscan TMEM63A,synonymous_variant,p.=,ENST00000366835,NM_014698.2;TMEM63A,synonymous_variant,p.=,ENST00000537914,;TMEM63A,non_coding_transcript_exon_variant,,ENST00000474478,;TMEM63A,upstream_gene_variant,,ENST00000487971,;TMEM63A,downstream_gene_variant,,ENST00000483779,; T ENST00000366835 Transcript synonymous_variant 1345/4098 1074/2424 358/807 S tcC/tcA rs191286059 1 -1 TMEM63A HGNC HGNC:29118 protein_coding YES CCDS31042.1 ENSP00000355800 O94886 A0A024R3T3 UPI000006DE50 NM_014698.2 13/25 Gene3D:3.30.70.330,Pfam_domain:PF14703,hmmpanther:PTHR13018,hmmpanther:PTHR13018:SF24,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 225862229 225862229 G T 1 0 0 0 0 0 0 0 1 16666 1335 47 2 2 TMEM63A 1 225862229 Silent SNP G C3N-00551_T 10063313 225862229 23094193 45 15528 SIPA1L2 0 . GRCh38 1 232439493 232439493 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3646G>T p.Gly1216Trp p.G1216W ENST00000366630 14/22 71 53 18 96 95 1 strelka-varscan SIPA1L2,missense_variant,p.Gly1216Trp,ENST00000366630,;SIPA1L2,missense_variant,p.Gly1216Trp,ENST00000262861,NM_020808.3;SIPA1L2,missense_variant,p.Gly290Trp,ENST00000308942,; A ENST00000366630 Transcript missense_variant 4005/6690 3646/5169 1216/1722 G/W Ggg/Tgg 1 -1 SIPA1L2 HGNC HGNC:23800 protein_coding YES CCDS41474.1 ENSP00000355589 Q9P2F8 UPI00001D7D6A deleterious(0.01) 14/22 hmmpanther:PTHR15711:SF7,hmmpanther:PTHR15711 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 232439493 232439493 C A 1 0 0 0 0 1 0 0 0 14593 608 21 2 2 SIPA1L2 1 232439493 Missense_Mutation SNP C C3N-00551_T 6577264 232439493 16516929 46 15529 RGS7 0 . GRCh38 1 240813653 240813653 + Silent SNP C C A rs775061802 C3N-00551_T C3N-00551_N C C c.921G>T p.= p.L307L ENST00000366565 13/18 499 448 51 443 442 1 strelka-varscan-mutect RGS7,synonymous_variant,p.=,ENST00000366565,NM_002924.5;RGS7,synonymous_variant,p.=,ENST00000366564,NM_001282778.1;RGS7,synonymous_variant,p.=,ENST00000366563,NM_001282775.1;RGS7,synonymous_variant,p.=,ENST00000348120,NM_001282773.1;RGS7,synonymous_variant,p.=,ENST00000440928,; A ENST00000366565 Transcript synonymous_variant 1303/2494 921/1464 307/487 L ctG/ctT rs775061802 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 13/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26,Pfam_domain:PF00631,Gene3D:4.10.260.10,SMART_domains:SM00224,SMART_domains:SM01224,Superfamily_domains:SSF48670 LOW 1 SNV 1 1 PASS rs775061802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 240813653 240813653 C A 1 0 0 0 0 0 0 0 1 13481 465 17 2 2 RGS7 1 240813653 Silent SNP C C3N-00551_T 8374160 240813653 8142769 47 15530 KMO 0 . GRCh38 1 241568532 241568532 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.842C>T p.Pro281Leu p.P281L ENST00000366559 10/15 236 185 51 404 404 0 strelka-varscan-mutect KMO,missense_variant,p.Pro281Leu,ENST00000366559,NM_003679.4;KMO,missense_variant,p.Pro281Leu,ENST00000366557,;KMO,missense_variant,p.Pro281Leu,ENST00000366558,;KMO,upstream_gene_variant,,ENST00000366555,;KMO,non_coding_transcript_exon_variant,,ENST00000431245,;KMO,downstream_gene_variant,,ENST00000477907,; T ENST00000366559 Transcript missense_variant 1153/5261 842/1461 281/486 P/L cCt/cTt 1 1 KMO HGNC HGNC:6381 protein_coding YES CCDS1618.1 ENSP00000355517 O15229 UPI000045632A NM_003679.4 deleterious(0.01) 10/15 HAMAP:MF_01971,Pfam_domain:PF01494,hmmpanther:PTHR13789,hmmpanther:PTHR13789:SF205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 241568532 241568532 C T 1 0 0 0 0 1 0 0 0 8294 681 24 3 3 KMO 1 241568532 Missense_Mutation SNP C C3N-00551_T 754879 241568532 7387890 48 15531 AKT3 0 . GRCh38 1 243695636 243695636 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.127C>A p.Gln43Lys p.Q43K ENST00000263826 2/13 206 170 36 180 180 0 strelka-varscan-mutect AKT3,missense_variant,p.Gln43Lys,ENST00000263826,NM_005465.4;AKT3,missense_variant,p.Gln43Lys,ENST00000366539,;AKT3,missense_variant,p.Gln43Lys,ENST00000336199,NM_181690.2;AKT3,missense_variant,p.Gln43Lys,ENST00000366540,NM_001206729.1;AKT3,missense_variant,p.Gln43Lys,ENST00000552631,;AKT3,non_coding_transcript_exon_variant,,ENST00000490018,;AKT3,non_coding_transcript_exon_variant,,ENST00000491219,;AKT3,non_coding_transcript_exon_variant,,ENST00000463991,; T ENST00000263826 Transcript missense_variant 239/7081 127/1440 43/479 Q/K Caa/Aaa 1 -1 AKT3 HGNC HGNC:393 protein_coding YES CCDS31077.1 ENSP00000263826 Q9Y243 UPI00000335E8 NM_005465.4 tolerated(0.6) 2/13 PROSITE_profiles:PS50003,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF190,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 243695636 243695636 G T 1 0 0 0 0 1 0 0 0 564 1299 45 2 2 AKT3 1 243695636 Missense_Mutation SNP G C3N-00551_T 2127104 243695636 5260786 49 15532 ZNF124 0 . GRCh38 1 247156576 247156576 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.1046A>T p.Lys349Ile p.K349I ENST00000543802 4/4 23 17 6 31 31 0 strelka-varscan-mutect ZNF124,missense_variant,p.Lys287Ile,ENST00000340684,NM_003431.3,NM_001297569.1;ZNF124,missense_variant,p.Lys349Ile,ENST00000543802,NM_001297568.1;ZNF124,intron_variant,,ENST00000472531,NM_001243740.2;ZNF124,intron_variant,,ENST00000491356,NM_001297567.1;ZNF124,downstream_gene_variant,,ENST00000491848,; A ENST00000543802 Transcript missense_variant 1136/1292 1046/1056 349/351 K/I aAa/aTa 1 -1 ZNF124 HGNC HGNC:12907 protein_coding YES CCDS73057.1 ENSP00000440365 Q15973 UPI000050ED7E NM_001297568.1 deleterious(0) 4/4 Gene3D:3.30.160.60,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF136,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -17.31146 1 1 1 1 0 A 3 1 52 247156576 247156576 T A 1 0 0 0 0 1 0 0 0 18301 1841 64 4 4 ZNF124 1 247156576 Missense_Mutation SNP T C3N-00551_T 3460940 247156576 1799846 50 15533 NLRP3 0 . GRCh38 1 247424898 247424898 + Silent SNP G G A rs749604905 C3N-00551_T C3N-00551_N G G c.1455G>A p.= p.E485E ENST00000336119 3/9 339 267 72 293 293 0 strelka-varscan-mutect NLRP3,synonymous_variant,p.=,ENST00000366497,NM_001127461.2;NLRP3,synonymous_variant,p.=,ENST00000336119,NM_004895.4,NM_001243133.1;NLRP3,synonymous_variant,p.=,ENST00000366496,;NLRP3,synonymous_variant,p.=,ENST00000391828,NM_001079821.2;NLRP3,synonymous_variant,p.=,ENST00000348069,NM_183395.2;NLRP3,synonymous_variant,p.=,ENST00000391827,NM_001127462.2;NLRP3,non_coding_transcript_exon_variant,,ENST00000474792,; A ENST00000336119 Transcript synonymous_variant 2201/4170 1455/3111 485/1036 E gaG/gaA rs749604905,COSM3865046 1 1 NLRP3 HGNC HGNC:16400 protein_coding YES CCDS1632.1 ENSP00000337383 Q96P20 UPI00001CE3AD NM_004895.4,NM_001243133.1 3/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF4 0,1 LOW 1 SNV 1 0,1 1 PASS rs749604905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 247424898 247424898 G A 1 0 0 0 0 0 0 0 1 10516 991 35 3 3 NLRP3 1 247424898 Silent SNP G C3N-00551_T 268322 247424898 1531524 51 15534 OR6F1 0 . GRCh38 1 247712710 247712710 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.46G>T p.Gly16Cys p.G16C ENST00000302084 1/1 115 89 26 84 84 0 strelka-varscan-mutect OR6F1,missense_variant,p.Gly16Cys,ENST00000302084,NM_001005286.1;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; A ENST00000302084 Transcript missense_variant 46/927 46/927 16/308 G/C Ggc/Tgc 1 -1 OR6F1 HGNC HGNC:15027 protein_coding YES CCDS31095.1 ENSP00000305640 Q8NGZ6 A0A126GV68 UPI0000041CD7 NM_001005286.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF12,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs1228479932 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 247712710 247712710 C A 1 0 0 0 0 1 0 0 0 11269 623 22 2 2 OR6F1 1 247712710 Missense_Mutation SNP C C3N-00551_T 287812 247712710 1243712 52 15535 OR1C1 0 . GRCh38 1 247758237 247758237 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.170C>A p.Ser57Tyr p.S57Y ENST00000408896 1/1 277 241 36 258 258 0 strelka-varscan-mutect OR1C1,missense_variant,p.Ser57Tyr,ENST00000408896,NM_012353.2; T ENST00000408896 Transcript missense_variant 170/945 170/945 57/314 S/Y tCc/tAc COSM403934 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 247758237 247758237 G T 1 0 0 0 0 1 0 0 0 11029 1174 41 2 2 OR1C1 1 247758237 Missense_Mutation SNP G C3N-00551_T 45527 247758237 1198185 53 15536 OR14A16 0 . GRCh38 1 247815565 247815565 + Silent SNP G G T rs372061599 C3N-00551_T C3N-00551_N G G c.165C>A p.= p.T55T ENST00000357627 1/1 185 163 22 210 210 0 strelka-varscan-mutect OR14A16,synonymous_variant,p.=,ENST00000357627,NM_001001966.1; T ENST00000357627 Transcript synonymous_variant 165/930 165/930 55/309 T acC/acA rs372061599 1 -1 OR14A16 HGNC HGNC:15022 protein_coding YES CCDS31097.1 ENSP00000350248 Q8NHC5 UPI0000041CE2 NM_001001966.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF352,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs372061599 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 52 247815565 247815565 G T 1 0 0 0 0 0 0 0 1 11021 1219 43 2 2 OR14A16 1 247815565 Silent SNP G C3N-00551_T 57328 247815565 1140857 54 15537 OR2L3 0 . GRCh38 1 248060883 248060883 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.202A>G p.Ile68Val p.I68V ENST00000359959 1/1 302 233 69 334 334 0 strelka-varscan-mutect OR2L3,missense_variant,p.Ile68Val,ENST00000359959,NM_001004687.1; G ENST00000359959 Transcript missense_variant 202/939 202/939 68/312 I/V Att/Gtt 1 1 OR2L3 HGNC HGNC:15009 protein_coding YES CCDS31104.1 ENSP00000353044 Q8NG85 UPI0000061EB8 NM_001004687.1 deleterious(0.05) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF166,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 248060883 248060883 A G 1 0 0 0 0 1 0 0 0 11086 217 8 5 5 OR2L3 1 248060883 Missense_Mutation SNP A C3N-00551_T 245318 248060883 895539 55 15538 OR2M5 0 . GRCh38 1 248145778 248145778 + Missense_Mutation SNP G G T rs770451149 C3N-00551_T C3N-00551_N G G c.631G>T p.Val211Phe p.V211F ENST00000366476 1/1 448 402 46 544 544 0 strelka-varscan-mutect OR2M5,missense_variant,p.Val211Phe,ENST00000366476,NM_001004690.1; T ENST00000366476 Transcript missense_variant 631/939 631/939 211/312 V/F Gtt/Ttt rs770451149 1 1 OR2M5 HGNC HGNC:19576 protein_coding YES CCDS31105.1 ENSP00000355432 A3KFT3 UPI00001612E2 NM_001004690.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs770451149 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 248145778 248145778 G T 1 0 0 0 0 1 0 0 0 11091 1377 48 2 2 OR2M5 1 248145778 Missense_Mutation SNP G C3N-00551_T 84895 248145778 810644 56 15539 OR2T6 0 . GRCh38 1 248388215 248388215 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.607T>A p.Cys203Ser p.C203S ENST00000355728 1/1 260 227 33 240 240 0 strelka-varscan-mutect OR2T6,missense_variant,p.Cys203Ser,ENST00000355728,NM_001005471.1; A ENST00000355728 Transcript missense_variant 607/927 607/927 203/308 C/S Tgc/Agc 1 1 OR2T6 HGNC HGNC:15018 protein_coding YES CCDS31114.1 ENSP00000347965 Q8NHC8 UPI0000199147 NM_001005471.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF57,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 248388215 248388215 T A 1 0 0 0 0 1 0 0 0 11106 1580 55 4 4 OR2T6 1 248388215 Missense_Mutation SNP T C3N-00551_T 242437 248388215 568207 57 15540 OR14I1 0 . GRCh38 1 248681946 248681946 + Missense_Mutation SNP C C A rs767063023 C3N-00551_T C3N-00551_N C C c.359G>T p.Arg120Leu p.R120L ENST00000342623 1/1 183 156 27 212 211 1 strelka-varscan-mutect OR14I1,missense_variant,p.Arg120Leu,ENST00000342623,NM_001004734.1; A ENST00000342623 Transcript missense_variant 359/936 359/936 120/311 R/L cGc/cTc rs767063023,COSM322236,COSM534048 1 -1 OR14I1 HGNC HGNC:19575 protein_coding YES CCDS31125.1 ENSP00000339726 A6ND48 UPI0000199BC9 NM_001004734.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF316,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs767063023 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 52 248681946 248681946 C A 1 0 0 0 0 1 0 0 0 11024 768 27 1 1 OR14I1 1 248681946 Missense_Mutation SNP C C3N-00551_T 293731 248681946 274476 58 15541 MYT1L 0 . GRCh38 2 1887487 1887487 + Splice_Site SNP C C G rs869320675 C3N-00551_T C3N-00551_N C C c.2642+1G>C p.X881_splice ENST00000399161 164 147 17 208 208 0 strelka-varscan-mutect MYT1L,splice_donor_variant,,ENST00000399161,NM_001303052.1;MYT1L,splice_donor_variant,,ENST00000428368,NM_015025.3;MYT1L,splice_donor_variant,,ENST00000602387,;MYT1L,splice_donor_variant,,ENST00000490585,;MYT1L,splice_donor_variant,,ENST00000470954,; G ENST00000399161 Transcript splice_donor_variant -/7063 2642/3561 881/1186 rs869320675 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 17/24 pathogenic HIGH 1 SNV 1 1 1 PASS rs869320675 . 0 206 0 4 0 0 0 0 -19.9999 0.9998302 1 1 1 0 G 5 3 52 1887487 1887487 C G 1 0 0 0 0 0 0 1 0 10106 550 19 4 4 MYT1L 2 1887487 Splice_Site SNP C C3N-00551_T 1887487 240306042 59 15542 RNF144A 0 . GRCh38 2 7030156 7030156 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.688G>T p.Gly230Ter p.G230* ENST00000320892 8/9 137 111 26 152 151 1 strelka-varscan-mutect RNF144A,stop_gained,p.Gly230Ter,ENST00000320892,NM_014746.4;RNF144A,stop_gained,p.Gly226Ter,ENST00000432850,;RNF144A,non_coding_transcript_exon_variant,,ENST00000467276,; T ENST00000320892 Transcript stop_gained 1130/5743 688/879 230/292 G/* Gga/Tga 1 1 RNF144A HGNC HGNC:20457 protein_coding YES CCDS1657.1 ENSP00000321330 P50876 UPI00001E058A NM_014746.4 8/9 hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF99,SMART_domains:SM00647 HIGH 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -20 0.999712 1 1 1 0 T 4 4 52 7030156 7030156 G T 1 0 0 0 0 0 1 0 0 13623 1233 43 2 2 RNF144A 2 7030156 Nonsense_Mutation SNP G C3N-00551_T 5142669 7030156 235163373 60 15543 TRIB2 0 . GRCh38 2 12723463 12723463 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.474G>T p.Gln158His p.Q158H ENST00000155926 2/3 363 314 49 410 410 0 strelka-varscan-mutect TRIB2,missense_variant,p.Gln158His,ENST00000155926,NM_021643.3;TRIB2,missense_variant,p.Gln22His,ENST00000381465,;TRIB2,missense_variant,p.Gln158His,ENST00000405331,; T ENST00000155926 Transcript missense_variant 1893/4391 474/1032 158/343 Q/H caG/caT 1 1 TRIB2 HGNC HGNC:30809 protein_coding YES CCDS1683.1 ENSP00000155926 Q92519 UPI0000051C55 NM_021643.3 deleterious(0) 2/3 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF15,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 12723463 12723463 G T 1 0 0 0 0 1 0 0 0 16972 933 33 2 2 TRIB2 2 12723463 Missense_Mutation SNP G C3N-00551_T 5693307 12723463 229470066 61 15544 APOB 0 . GRCh38 2 21011634 21011634 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.5234C>A p.Ser1745Ter p.S1745* ENST00000233242 26/29 240 189 51 245 245 0 strelka-varscan-mutect APOB,stop_gained,p.Ser1745Ter,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript stop_gained 5362/14121 5234/13692 1745/4563 S/* tCa/tAa 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 21011634 21011634 G T 1 0 0 0 0 0 1 0 0 907 1294 45 2 2 APOB 2 21011634 Nonsense_Mutation SNP G C3N-00551_T 8288171 21011634 221181895 62 15545 ASXL2 0 . GRCh38 2 25878178 25878178 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.45G>C p.Glu15Asp p.E15D ENST00000435504 1/13 286 259 27 346 346 0 strelka-varscan-mutect ASXL2,missense_variant,p.Glu15Asp,ENST00000435504,NM_018263.4;ASXL2,5_prime_UTR_variant,,ENST00000336112,; G ENST00000435504 Transcript missense_variant 339/12878 45/4308 15/1435 E/D gaG/gaC 1 -1 ASXL2 HGNC HGNC:23805 protein_coding ENSP00000391447 Q76L83 UPI00001DFBE8 NM_018263.4 deleterious(0) 1/13 hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578,Pfam_domain:PF05066 MODERATE SNV 5 1 PASS rs1179292295 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 25878178 25878178 C G 1 0 0 0 0 1 0 0 0 1215 680 24 4 4 ASXL2 2 25878178 Missense_Mutation SNP C C3N-00551_T 4866544 25878178 216315351 63 15546 OTOF 0 . GRCh38 2 26476024 26476024 + Missense_Mutation SNP G G T rs745435855 C3N-00551_T C3N-00551_N G G c.2881C>A p.Gln961Lys p.Q961K ENST00000272371 24/47 277 247 30 212 212 0 strelka-varscan-mutect OTOF,missense_variant,p.Gln961Lys,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Gln961Lys,ENST00000403946,NM_001287489.1;OTOF,missense_variant,p.Gln271Lys,ENST00000402415,NM_194322.2;OTOF,missense_variant,p.Gln214Lys,ENST00000338581,NM_004802.3;OTOF,missense_variant,p.Gln214Lys,ENST00000339598,NM_194323.2;OTOF,upstream_gene_variant,,ENST00000426958,; T ENST00000272371 Transcript missense_variant 3008/7156 2881/5994 961/1997 Q/K Cag/Aag rs745435855 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 deleterious(0.01) 24/47 PROSITE_profiles:PS50004,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs745435855 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 26476024 26476024 G T 1 0 0 0 0 1 0 0 0 11369 1357 47 2 2 OTOF 2 26476024 Missense_Mutation SNP G C3N-00551_T 597846 26476024 215717505 64 15547 PRR30 0 . GRCh38 2 27137673 27137673 + Silent SNP C C A C3N-00551_T C3N-00551_N C C c.657G>T p.= p.L219L ENST00000335524 3/3 152 139 13 148 148 0 strelka-varscan-mutect PRR30,missense_variant,p.Gly55Trp,ENST00000432962,;PRR30,synonymous_variant,p.=,ENST00000335524,NM_178553.3;PREB,upstream_gene_variant,,ENST00000260643,NM_013388.4;PREB,upstream_gene_variant,,ENST00000406567,;PREB,upstream_gene_variant,,ENST00000416802,;PREB,upstream_gene_variant,,ENST00000468045,;PREB,upstream_gene_variant,,ENST00000444452,;PREB,upstream_gene_variant,,ENST00000474802,; A ENST00000335524 Transcript synonymous_variant 1183/2008 657/1239 219/412 L ctG/ctT COSM1306660 1 -1 PRR30 HGNC HGNC:28677 protein_coding YES CCDS1739.1 ENSP00000335017 Q53SZ7 UPI00001995FD NM_178553.3 3/3 hmmpanther:PTHR22235:SF2,hmmpanther:PTHR22235,Pfam_domain:PF15728 1 LOW 1 SNV 1 1 1 PASS rs1217925043 . 0 208 0 2 0 0 0 0 -18.12575 0.9999998 1 1 1 0 A 2 1 52 27137673 27137673 C A 1 0 0 0 0 0 0 0 1 12737 581 21 2 2 PRR30 2 27137673 Silent SNP C C3N-00551_T 661649 27137673 215055856 65 15548 C2orf16 0 . GRCh38 2 27579928 27579928 + Missense_Mutation SNP C C A rs772106641 C3N-00551_T C3N-00551_N C C c.3356C>A p.Pro1119His p.P1119H ENST00000408964 1/1 239 215 24 245 244 1 strelka-varscan-mutect C2orf16,missense_variant,p.Pro1119His,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; A ENST00000408964 Transcript missense_variant 3407/6199 3356/5955 1119/1984 P/H cCt/cAt rs772106641 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 deleterious(0) 1/1 hmmpanther:PTHR33888 MODERATE SNV 1 PASS rs772106641 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 27579928 27579928 C A 1 0 0 0 0 1 0 0 0 2032 681 24 2 2 C2orf16 2 27579928 Missense_Mutation SNP C C3N-00551_T 442255 27579928 214613601 66 15549 ALK 0 . GRCh38 2 29233605 29233605 + Missense_Mutation SNP C C A rs771130459 C3N-00551_T C3N-00551_N C C c.2447G>T p.Gly816Val p.G816V ENST00000389048 14/29 450 411 39 494 493 1 strelka-varscan-mutect ALK,missense_variant,p.Gly816Val,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Gly439Val,ENST00000618119,; A ENST00000389048 Transcript missense_variant 3354/6220 2447/4863 816/1620 G/V gGa/gTa rs771130459 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 deleterious(0) 14/29 Low_complexity_(Seg):seg,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF276,Pfam_domain:PF12810 MODERATE 1 SNV 1 1 PASS rs771130459 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 29233605 29233605 C A 1 0 0 0 0 1 0 0 0 625 855 30 2 2 ALK 2 29233605 Missense_Mutation SNP C C3N-00551_T 1653677 29233605 212959924 67 15550 GALNT14 0 . GRCh38 2 30958437 30958437 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.441G>T p.= p.L147L ENST00000324589 5/16 183 162 21 213 213 0 strelka-varscan-mutect GALNT14,synonymous_variant,p.=,ENST00000349752,NM_024572.3;GALNT14,synonymous_variant,p.=,ENST00000406653,NM_001253827.1;GALNT14,synonymous_variant,p.=,ENST00000324589,NM_001253826.1;GALNT14,synonymous_variant,p.=,ENST00000430167,;GALNT14,non_coding_transcript_exon_variant,,ENST00000464038,;GALNT14,non_coding_transcript_exon_variant,,ENST00000481023,;GALNT14,non_coding_transcript_exon_variant,,ENST00000496397,;GALNT14,non_coding_transcript_exon_variant,,ENST00000461193,;GALNT14,upstream_gene_variant,,ENST00000486564,;GALNT14,3_prime_UTR_variant,,ENST00000455477,;GALNT14,3_prime_UTR_variant,,ENST00000424136,; A ENST00000324589 Transcript synonymous_variant 502/2169 441/1674 147/557 L ctG/ctT 1 -1 GALNT14 HGNC HGNC:22946 protein_coding YES CCDS58706.1 ENSP00000314500 Q96FL9 UPI0000073A6F NM_001253826.1 5/16 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF8,Pfam_domain:PF00535,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 30958437 30958437 C A 1 0 0 0 0 0 0 0 1 6080 813 29 2 2 GALNT14 2 30958437 Silent SNP C C3N-00551_T 1724832 30958437 211235092 68 15551 LTBP1 0 . GRCh38 2 33273700 33273700 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2662C>A p.His888Asn p.H888N ENST00000404816 16/34 181 146 35 232 231 1 strelka-varscan-mutect LTBP1,missense_variant,p.His888Asn,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.His562Asn,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.His509Asn,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.His562Asn,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.His509Asn,ENST00000402934,;LTBP1,missense_variant,p.His216Asn,ENST00000413303,;LTBP1,missense_variant,p.His206Asn,ENST00000468091,;LTBP1,upstream_gene_variant,,ENST00000415140,; A ENST00000404816 Transcript missense_variant 3015/6333 2662/5166 888/1721 H/N Cac/Aac 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 tolerated(0.17) 16/34 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS rs1228768716 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 33273700 33273700 C A 1 0 0 0 0 1 0 0 0 8979 478 17 2 2 LTBP1 2 33273700 Missense_Mutation SNP C C3N-00551_T 2315263 33273700 208919829 69 15552 LTBP1 0 . GRCh38 2 33398462 33398462 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.5083G>T p.Gly1695Cys p.G1695C ENST00000404816 34/34 197 177 20 267 266 1 strelka-varscan-mutect LTBP1,missense_variant,p.Gly1695Cys,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Gly1327Cys,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Gly1316Cys,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Gly1369Cys,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Gly1314Cys,ENST00000402934,; T ENST00000404816 Transcript missense_variant 5436/6333 5083/5166 1695/1721 G/C Ggc/Tgc 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0) 34/34 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 33398462 33398462 G T 1 0 0 0 0 1 0 0 0 8979 1000 35 2 2 LTBP1 2 33398462 Missense_Mutation SNP G C3N-00551_T 124762 33398462 208795067 70 15553 THADA 0 . GRCh38 2 43581804 43581804 + Missense_Mutation SNP C C A rs771706208 C3N-00551_T C3N-00551_N C C c.658G>T p.Asp220Tyr p.D220Y ENST00000405006 8/38 131 118 13 296 296 0 strelka-varscan-mutect THADA,missense_variant,p.Asp220Tyr,ENST00000403856,;THADA,missense_variant,p.Asp220Tyr,ENST00000405006,NM_001083953.1;THADA,missense_variant,p.Asp220Tyr,ENST00000405975,NM_022065.4;THADA,missense_variant,p.Asp220Tyr,ENST00000404790,NM_001271644.1;THADA,missense_variant,p.Asp220Tyr,ENST00000402360,NM_001271643.1;THADA,missense_variant,p.Asp220Tyr,ENST00000398653,;THADA,missense_variant,p.Asp220Tyr,ENST00000408045,;THADA,missense_variant,p.Asp220Tyr,ENST00000474159,; A ENST00000405006 Transcript missense_variant 1010/6310 658/5862 220/1953 D/Y Gat/Tat rs771706208 1 -1 THADA HGNC HGNC:19217 protein_coding YES CCDS46268.1 ENSP00000385995 Q6YHU6 UPI00001C0473 NM_001083953.1 deleterious(0.02) 8/38 hmmpanther:PTHR14387,hmmpanther:PTHR14387:SF2 MODERATE 1 SNV 1 1 PASS rs771706208 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 43581804 43581804 C A 1 0 0 0 0 1 0 0 0 16272 884 31 1 1 THADA 2 43581804 Missense_Mutation SNP C C3N-00551_T 10183342 43581804 198611725 71 15554 EML6 0 . GRCh38 2 54869252 54869252 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2123C>A p.Ala708Glu p.A708E ENST00000356458 14/41 168 131 37 168 168 0 strelka-varscan-mutect EML6,missense_variant,p.Ala708Glu,ENST00000356458,NM_001039753.2;EML6,non_coding_transcript_exon_variant,,ENST00000493997,; A ENST00000356458 Transcript missense_variant 2643/8320 2123/5877 708/1958 A/E gCa/gAa 1 1 EML6 HGNC HGNC:35412 protein_coding YES CCDS46286.1 ENSP00000348842 Q6ZMW3 UPI00006C0432 NM_001039753.2 deleterious(0) 14/41 Low_complexity_(Seg):seg,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF8,Pfam_domain:PF03451,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS rs906853387 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 54869252 54869252 C A 1 0 0 0 0 1 0 0 0 4944 710 25 2 2 EML6 2 54869252 Missense_Mutation SNP C C3N-00551_T 11287448 54869252 187324277 72 15555 OTX1 0 . GRCh38 2 63056202 63056202 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.951G>T p.Leu317Phe p.L317F ENST00000282549 5/5 249 218 31 303 303 0 strelka-varscan-mutect OTX1,missense_variant,p.Leu317Phe,ENST00000282549,NM_014562.3;OTX1,missense_variant,p.Leu317Phe,ENST00000366671,NM_001199770.1;OTX1,3_prime_UTR_variant,,ENST00000405984,;OTX1,downstream_gene_variant,,ENST00000484066,;OTX1,downstream_gene_variant,,ENST00000477348,;OTX1,downstream_gene_variant,,ENST00000476383,; T ENST00000282549 Transcript missense_variant 1227/2861 951/1065 317/354 L/F ttG/ttT 1 1 OTX1 HGNC HGNC:8521 protein_coding YES CCDS1873.1 ENSP00000282549 P32242 UPI0000130F36 NM_014562.3 deleterious(0.01) 5/5 hmmpanther:PTHR24329:SF310,hmmpanther:PTHR24329,Prints_domain:PR01255 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 63056202 63056202 G T 1 0 0 0 0 1 0 0 0 11390 1339 47 2 2 OTX1 2 63056202 Missense_Mutation SNP G C3N-00551_T 8186950 63056202 179137327 73 15556 CLEC4F 0 . GRCh38 2 70816125 70816125 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1256C>A p.Ala419Asp p.A419D ENST00000272367 4/7 300 258 42 340 340 0 strelka-varscan-mutect CLEC4F,missense_variant,p.Ala419Asp,ENST00000272367,NM_001258027.1,NM_173535.2;CLEC4F,missense_variant,p.Ala419Asp,ENST00000426626,;AC007395.4,upstream_gene_variant,,ENST00000451333,; T ENST00000272367 Transcript missense_variant 1333/2475 1256/1770 419/589 A/D gCc/gAc 1 -1 CLEC4F HGNC HGNC:25357 protein_coding YES CCDS1910.1 ENSP00000272367 Q8N1N0 UPI0000376BCC NM_001258027.1,NM_173535.2 tolerated(0.11) 4/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF238 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 70816125 70816125 G T 1 0 0 0 0 1 0 0 0 3284 1203 42 2 2 CLEC4F 2 70816125 Missense_Mutation SNP G C3N-00551_T 7759923 70816125 171377404 74 15557 EMX1 0 . GRCh38 2 72918046 72918046 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.194G>T p.Gly65Val p.G65V ENST00000258106 1/3 59 40 19 83 83 0 strelka-varscan-mutect EMX1,missense_variant,p.Gly65Val,ENST00000258106,NM_004097.2;EMX1,intron_variant,,ENST00000394111,;EMX1,upstream_gene_variant,,ENST00000473732,; T ENST00000258106 Transcript missense_variant 572/2188 194/873 65/290 G/V gGc/gTc 1 1 EMX1 HGNC HGNC:3340 protein_coding YES CCDS1921.2 ENSP00000258106 Q04741 UPI0000D47CF7 NM_004097.2 tolerated(0.24) 1/3 hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF26,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 72918046 72918046 G T 1 0 0 0 0 1 0 0 0 4949 1203 42 2 2 EMX1 2 72918046 Missense_Mutation SNP G C3N-00551_T 2101921 72918046 169275483 75 15558 ALMS1 0 . GRCh38 2 73489988 73489988 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.8029G>T p.Asp2677Tyr p.D2677Y ENST00000613296 10/23 375 282 93 369 369 0 strelka-varscan-mutect ALMS1,missense_variant,p.Asp2677Tyr,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Asp2635Tyr,ENST00000484298,;ALMS1,missense_variant,p.Asp2677Tyr,ENST00000614410,;ALMS1,missense_variant,p.Asp954Tyr,ENST00000423048,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,; T ENST00000613296 Transcript missense_variant 8140/12925 8029/12507 2677/4168 D/Y Gac/Tac 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 deleterious(0) 10/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 73489988 73489988 G T 1 0 0 0 0 1 0 0 0 635 1174 41 2 2 ALMS1 2 73489988 Missense_Mutation SNP G C3N-00551_T 571942 73489988 168703541 76 15559 ALMS1 0 . GRCh38 2 73490522 73490522 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.8563G>T p.Gly2855Ter p.G2855* ENST00000613296 10/23 355 323 32 397 396 1 strelka-varscan-mutect ALMS1,stop_gained,p.Gly2855Ter,ENST00000613296,NM_015120.4;ALMS1,stop_gained,p.Gly2813Ter,ENST00000484298,;ALMS1,stop_gained,p.Gly2855Ter,ENST00000614410,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,;ALMS1,intron_variant,,ENST00000423048,; T ENST00000613296 Transcript stop_gained 8674/12925 8563/12507 2855/4168 G/* Gga/Tga 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 10/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 73490522 73490522 G T 1 0 0 0 0 0 1 0 0 635 1001 35 2 2 ALMS1 2 73490522 Nonsense_Mutation SNP G C3N-00551_T 534 73490522 168703007 77 15560 ALMS1 0 . GRCh38 2 73491345 73491345 + Missense_Mutation SNP A A T rs372015288 C3N-00551_T C3N-00551_N A A c.9386A>T p.Gln3129Leu p.Q3129L ENST00000613296 10/23 211 195 16 181 181 0 strelka-varscan-mutect ALMS1,missense_variant,p.Gln3129Leu,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Gln3087Leu,ENST00000484298,;ALMS1,missense_variant,p.Gln3129Leu,ENST00000614410,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,;ALMS1,intron_variant,,ENST00000423048,; T ENST00000613296 Transcript missense_variant 9497/12925 9386/12507 3129/4168 Q/L cAg/cTg rs372015288 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 tolerated(0.08) 10/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS rs372015288 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 73491345 73491345 A T 1 0 0 0 0 1 0 0 0 635 188 7 4 4 ALMS1 2 73491345 Missense_Mutation SNP A C3N-00551_T 823 73491345 168702184 78 15561 LOXL3 0 . GRCh38 2 74535743 74535743 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1261G>T p.Gly421Trp p.G421W ENST00000264094 8/14 35 31 4 44 44 0 strelka-varscan-mutect LOXL3,missense_variant,p.Gly421Trp,ENST00000264094,NM_032603.3;LOXL3,missense_variant,p.Gly276Trp,ENST00000393937,NM_001289164.1;LOXL3,missense_variant,p.Gly276Trp,ENST00000409986,;LOXL3,missense_variant,p.Gly148Trp,ENST00000420535,;LOXL3,intron_variant,,ENST00000409549,;LOXL3,intron_variant,,ENST00000409249,;HTRA2,downstream_gene_variant,,ENST00000258080,NM_013247.4;HTRA2,downstream_gene_variant,,ENST00000437202,;HTRA2,downstream_gene_variant,,ENST00000352222,NM_145074.2;LOXL3,downstream_gene_variant,,ENST00000413469,;LOXL3,intron_variant,,ENST00000481835,;HTRA2,downstream_gene_variant,,ENST00000467961,;HTRA2,downstream_gene_variant,,ENST00000462909,;LOXL3,downstream_gene_variant,,ENST00000484369,;HTRA2,downstream_gene_variant,,ENST00000484881,;LOXL3,non_coding_transcript_exon_variant,,ENST00000470907,;HTRA2,downstream_gene_variant,,ENST00000484352,;HTRA2,downstream_gene_variant,,ENST00000482331,;HTRA2,downstream_gene_variant,,ENST00000465521,;HTRA2,downstream_gene_variant,,ENST00000482205,; A ENST00000264094 Transcript missense_variant 1333/3502 1261/2262 421/753 G/W Ggg/Tgg 1 -1 LOXL3 HGNC HGNC:13869 protein_coding YES CCDS1953.1 ENSP00000264094 P58215 UPI0000044959 NM_032603.3 deleterious(0) 8/14 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF305,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.05814 1 1 1 1 0 A 3 1 52 74535743 74535743 C A 1 0 0 0 0 1 0 0 0 8804 594 21 2 2 LOXL3 2 74535743 Missense_Mutation SNP C C3N-00551_T 1044398 74535743 167657786 79 15562 LRRTM4 0 . GRCh38 2 77519429 77519429 + Missense_Mutation SNP G G T rs781578647 C3N-00551_T C3N-00551_N G G c.440C>A p.Thr147Lys p.T147K ENST00000409093 3/4 227 202 25 262 261 1 strelka-varscan-mutect LRRTM4,missense_variant,p.Thr147Lys,ENST00000409088,NM_024993.4;LRRTM4,missense_variant,p.Thr148Lys,ENST00000409911,;LRRTM4,missense_variant,p.Thr148Lys,ENST00000409282,NM_001282928.1;LRRTM4,missense_variant,p.Thr147Lys,ENST00000409093,NM_001282924.1;LRRTM4,missense_variant,p.Thr147Lys,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; T ENST00000409093 Transcript missense_variant 777/2247 440/1773 147/590 T/K aCa/aAa rs781578647 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 tolerated(0.05) 3/4 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1,Gene3D:3.80.10.10,Pfam_domain:PF00560,SMART_domains:SM00369,Superfamily_domains:SSF52058,Prints_domain:PR00019 MODERATE 1 SNV 2 1 PASS rs781578647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 77519429 77519429 G T 1 0 0 0 0 1 0 0 0 8948 1377 48 2 2 LRRTM4 2 77519429 Missense_Mutation SNP G C3N-00551_T 2983686 77519429 164674100 80 15563 CTNNA2 0 . GRCh38 2 79869834 79869834 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.484G>A p.Ala162Thr p.A162T ENST00000402739 4/18 133 123 10 183 183 0 strelka-varscan-mutect CTNNA2,missense_variant,p.Ala162Thr,ENST00000466387,;CTNNA2,missense_variant,p.Ala162Thr,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Ala162Thr,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Ala162Thr,ENST00000629316,NM_001164883.1;MIR8080,upstream_gene_variant,,ENST00000622224,; A ENST00000402739 Transcript missense_variant 489/3684 484/2862 162/953 A/T Gct/Act 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 tolerated(0.2) 4/18 Gene3D:1.20.120.230,Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 79869834 79869834 G A 1 0 0 0 0 1 0 0 0 3822 971 34 3 3 CTNNA2 2 79869834 Missense_Mutation SNP G C3N-00551_T 2350405 79869834 162323695 81 15564 POLR1A 0 . GRCh38 2 86030390 86030390 + Missense_Mutation SNP C C A rs752242589 C3N-00551_T C3N-00551_N C C c.4585G>T p.Val1529Leu p.V1529L ENST00000263857 31/34 199 179 20 213 213 0 strelka-varscan-mutect POLR1A,missense_variant,p.Val1529Leu,ENST00000263857,NM_015425.3;POLR1A,missense_variant,p.Val1468Leu,ENST00000409681,;POLR1A,downstream_gene_variant,,ENST00000492034,;POLR1A,downstream_gene_variant,,ENST00000496892,;POLR1A,upstream_gene_variant,,ENST00000471427,; A ENST00000263857 Transcript missense_variant 4964/12749 4585/5163 1529/1720 V/L Gtg/Ttg rs752242589 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 tolerated(1) 31/34 hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF11,Pfam_domain:PF04998 MODERATE 1 SNV 1 1 PASS rs752242589 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 86030390 86030390 C A 1 0 0 0 0 1 0 0 0 12319 565 20 2 2 POLR1A 2 86030390 Missense_Mutation SNP C C3N-00551_T 6160556 86030390 156163139 82 15565 ZAP70 0 . GRCh38 2 97739433 97739433 + Missense_Mutation SNP A A T rs754998342 C3N-00551_T C3N-00551_N A A c.1795A>T p.Ser599Cys p.S599C ENST00000264972 14/14 241 224 17 168 168 0 strelka-varscan-mutect ZAP70,missense_variant,p.Ser599Cys,ENST00000264972,NM_001079.3;ZAP70,missense_variant,p.Ser292Cys,ENST00000451498,NM_207519.1;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000487283,;ZAP70,downstream_gene_variant,,ENST00000495754,;ZAP70,downstream_gene_variant,,ENST00000489250,; T ENST00000264972 Transcript missense_variant 2010/2437 1795/1860 599/619 S/C Agc/Tgc rs754998342 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 deleterious(0.01) 14/14 PIRSF_domain:PIRSF000604,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs754998342 . 0 208 0 2 0 0 0 0 -19.94723 0.9999997 1 1 1 0 T 3 4 52 97739433 97739433 A T 1 0 0 0 0 1 0 0 0 18075 188 7 4 4 ZAP70 2 97739433 Missense_Mutation SNP A C3N-00551_T 11709043 97739433 144454096 83 15566 KIAA1211L 0 . GRCh38 2 98832486 98832486 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.402G>C p.Met134Ile p.M134I ENST00000397899 5/10 109 87 22 97 97 0 strelka-varscan-mutect KIAA1211L,missense_variant,p.Met134Ile,ENST00000397899,NM_207362.2;KIAA1211L,missense_variant,p.Met162Ile,ENST00000423771,;KIAA1211L,missense_variant,p.Met148Ile,ENST00000428096,;KIAA1211L,missense_variant,p.Met148Ile,ENST00000415261,;KIAA1211L,non_coding_transcript_exon_variant,,ENST00000462314,; G ENST00000397899 Transcript missense_variant 734/3907 402/2889 134/962 M/I atG/atC 1 -1 KIAA1211L HGNC HGNC:33454 protein_coding YES CCDS42720.1 ENSP00000380996 Q6NV74 UPI0000E59245 NM_207362.2 deleterious(0.04) 5/10 Pfam_domain:PF15262,hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF16 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 98832486 98832486 C G 1 0 0 0 0 1 0 0 0 8108 594 21 4 4 KIAA1211L 2 98832486 Missense_Mutation SNP C C3N-00551_T 1093053 98832486 143361043 84 15567 MAP4K4 0 . GRCh38 2 101891204 101891204 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.3777G>C p.Gln1259His p.Q1259H ENST00000350878 31/31 282 262 20 315 315 0 strelka-varscan-mutect MAP4K4,missense_variant,p.Gln1259His,ENST00000350878,NM_145686.3;MAP4K4,missense_variant,p.Gln1221His,ENST00000324219,NM_001242560.1;MAP4K4,missense_variant,p.Gln1306His,ENST00000625522,;MAP4K4,missense_variant,p.Gln1151His,ENST00000350198,;MAP4K4,missense_variant,p.Gln1140His,ENST00000413150,;MAP4K4,missense_variant,p.Gln973His,ENST00000302217,;MAP4K4,missense_variant,p.Gln1258His,ENST00000425019,;MAP4K4,missense_variant,p.Gln1156His,ENST00000417294,;MAP4K4,missense_variant,p.Gln1024His,ENST00000456652,;MAP4K4,missense_variant,p.Gln1151His,ENST00000634702,NM_004834.4,NM_145687.3;MAP4K4,missense_variant,p.Gln1225His,ENST00000347699,NM_001242559.1;MAP4K4,missense_variant,p.Gln1042His,ENST00000421882,;MAP4K4,missense_variant,p.Gln1030His,ENST00000627726,; C ENST00000350878 Transcript missense_variant 4155/7640 3777/3822 1259/1273 Q/H caG/caC 1 1 MAP4K4 HGNC HGNC:6866 protein_coding YES CCDS74546.1 ENSP00000343658 E7ESS2 UPI0000EE6D9F NM_145686.3 deleterious_low_confidence(0) 31/31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 101891204 101891204 G C 1 0 0 0 0 1 0 0 0 9186 991 35 4 4 MAP4K4 2 101891204 Missense_Mutation SNP G C3N-00551_T 3058718 101891204 140302325 85 15568 IL1R2 0 . GRCh38 2 102008621 102008621 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.46C>A p.Leu16Ile p.L16I ENST00000332549 2/9 244 228 16 307 306 1 strelka-varscan-mutect IL1R2,missense_variant,p.Leu16Ile,ENST00000332549,NM_004633.3;IL1R2,missense_variant,p.Leu16Ile,ENST00000393414,;IL1R2,missense_variant,p.Leu16Ile,ENST00000441002,NM_001261419.1;IL1R2,missense_variant,p.Leu16Ile,ENST00000457817,;IL1R2,non_coding_transcript_exon_variant,,ENST00000464994,;IL1R2,non_coding_transcript_exon_variant,,ENST00000493749,;IL1R2,upstream_gene_variant,,ENST00000482658,; A ENST00000332549 Transcript missense_variant 275/1578 46/1197 16/398 L/I Ctt/Att COSM1690821 1 1 IL1R2 HGNC HGNC:5994 protein_coding YES CCDS2054.1 ENSP00000330959 P27930 UPI0000001C78 NM_004633.3 tolerated(1) 2/9 hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 102008621 102008621 C A 1 0 0 0 0 1 0 0 0 7562 681 24 2 2 IL1R2 2 102008621 Missense_Mutation SNP C C3N-00551_T 117417 102008621 140184908 86 15569 IL1R2 0 . GRCh38 2 102015998 102015998 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.460G>T p.Asp154Tyr p.D154Y ENST00000332549 4/9 259 228 31 233 233 0 strelka-varscan-mutect IL1R2,missense_variant,p.Asp154Tyr,ENST00000332549,NM_004633.3;IL1R2,missense_variant,p.Asp154Tyr,ENST00000393414,;IL1R2,missense_variant,p.Asp154Tyr,ENST00000441002,NM_001261419.1;IL1R2,missense_variant,p.Asp154Tyr,ENST00000457817,;IL1R2,non_coding_transcript_exon_variant,,ENST00000482658,; T ENST00000332549 Transcript missense_variant 689/1578 460/1197 154/398 D/Y Gac/Tac 1 1 IL1R2 HGNC HGNC:5994 protein_coding YES CCDS2054.1 ENSP00000330959 P27930 UPI0000001C78 NM_004633.3 deleterious(0) 4/9 PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF3,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726,Prints_domain:PR01536,Prints_domain:PR01539 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 102015998 102015998 G T 1 0 0 0 0 1 0 0 0 7562 1290 45 2 2 IL1R2 2 102015998 Missense_Mutation SNP G C3N-00551_T 7377 102015998 140177531 87 15570 CHCHD5 0 . GRCh38 2 112586235 112586235 + Missense_Mutation SNP A A C novel C3N-00551_T C3N-00551_N A A c.179A>C p.Gln60Pro p.Q60P ENST00000324913 3/4 127 113 14 96 96 0 strelka-varscan-mutect CHCHD5,missense_variant,p.Gln60Pro,ENST00000409719,;CHCHD5,missense_variant,p.Gln60Pro,ENST00000324913,NM_032309.3;AC012442.6,upstream_gene_variant,,ENST00000436885,;AC012442.5,upstream_gene_variant,,ENST00000414784,;CHCHD5,non_coding_transcript_exon_variant,,ENST00000489052,;CHCHD5,non_coding_transcript_exon_variant,,ENST00000469030,;CHCHD5,3_prime_UTR_variant,,ENST00000454841,; C ENST00000324913 Transcript missense_variant 386/691 179/333 60/110 Q/P cAg/cCg 1 1 CHCHD5 HGNC HGNC:17840 protein_coding YES CCDS2098.1 ENSP00000325655 Q9BSY4 UPI0000034E2C NM_032309.3 deleterious(0.03) 3/4 hmmpanther:PTHR21107,hmmpanther:PTHR21107:SF0,Pfam_domain:PF06747 MODERATE 1 SNV 1 1 PASS rs1054016534 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 112586235 112586235 A C 1 0 0 0 0 1 0 0 0 3079 188 7 5 5 CHCHD5 2 112586235 Missense_Mutation SNP A C3N-00551_T 10570237 112586235 129607294 88 15571 FOXD4L1 0 . GRCh38 2 113499436 113499436 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.180G>T p.Gln60His p.Q60H ENST00000306507 1/1 368 256 112 485 485 0 strelka-varscan-mutect FOXD4L1,missense_variant,p.Gln60His,ENST00000306507,NM_012184.4;CBWD2,downstream_gene_variant,,ENST00000259199,NM_172003.3;CBWD2,downstream_gene_variant,,ENST00000416503,;CBWD2,downstream_gene_variant,,ENST00000433343,;CBWD2,downstream_gene_variant,,ENST00000479583,;CBWD2,downstream_gene_variant,,ENST00000468417,;CBWD2,downstream_gene_variant,,ENST00000358604,;CBWD2,downstream_gene_variant,,ENST00000456188,; T ENST00000306507 Transcript missense_variant 772/2491 180/1227 60/408 Q/H caG/caT 1 1 FOXD4L1 HGNC HGNC:18521 protein_coding YES CCDS2117.1 ENSP00000302756 Q9NU39 UPI000012ADD0 NM_012184.4 tolerated(0.21) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF219 MODERATE SNV 1 PASS rs958979465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 113499436 113499436 G T 1 0 0 0 0 1 0 0 0 5860 991 35 2 2 FOXD4L1 2 113499436 Missense_Mutation SNP G C3N-00551_T 913201 113499436 128694093 89 15572 CFAP221 0 . GRCh38 2 119656438 119656438 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.2491A>G p.Lys831Glu p.K831E ENST00000413369 24/24 236 200 36 279 279 0 strelka-varscan-mutect CFAP221,missense_variant,p.Lys390Glu,ENST00000443972,;CFAP221,missense_variant,p.Lys831Glu,ENST00000413369,NM_001271049.1;CFAP221,non_coding_transcript_exon_variant,,ENST00000464578,;CFAP221,3_prime_UTR_variant,,ENST00000295220,; G ENST00000413369 Transcript missense_variant 2578/2801 2491/2523 831/840 K/E Aaa/Gaa 1 1 CFAP221 HGNC HGNC:33720 protein_coding YES CCDS33282.2 ENSP00000393222 Q4G0U5 UPI0001D322F9 NM_001271049.1 deleterious(0) 24/24 hmmpanther:PTHR23053 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 119656438 119656438 A G 1 0 0 0 0 1 0 0 0 3016 131 5 5 5 CFAP221 2 119656438 Missense_Mutation SNP A C3N-00551_T 6157002 119656438 122537091 90 15573 CLASP1 0 . GRCh38 2 121527838 121527838 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.431G>T p.Arg144Leu p.R144L ENST00000263710 5/40 190 170 20 179 179 0 strelka-varscan-mutect CLASP1,missense_variant,p.Arg144Leu,ENST00000263710,NM_015282.2;CLASP1,missense_variant,p.Arg144Leu,ENST00000409078,NM_001142274.1;CLASP1,missense_variant,p.Arg144Leu,ENST00000397587,;CLASP1,missense_variant,p.Arg144Leu,ENST00000541377,NM_001207051.1;CLASP1,missense_variant,p.Arg144Leu,ENST00000455322,NM_001142273.1;RNU4ATAC,upstream_gene_variant,,ENST00000580972,;RP11-204L24.2,upstream_gene_variant,,ENST00000577914,;CLASP1,non_coding_transcript_exon_variant,,ENST00000485112,;CLASP1,upstream_gene_variant,,ENST00000474065,; A ENST00000263710 Transcript missense_variant 821/8092 431/4617 144/1538 R/L cGa/cTa 1 -1 CLASP1 HGNC HGNC:17088 protein_coding YES ENSP00000263710 Q7Z460 UPI00001A8BFF NM_015282.2 deleterious(0) 5/40 Gene3D:1.25.10.10,Pfam_domain:PF12348,hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF28,SMART_domains:SM01349,Superfamily_domains:SSF48371 MODERATE SNV 5 1 PASS rs1470907638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 121527838 121527838 C A 1 0 0 0 0 1 0 0 0 3217 884 31 1 1 CLASP1 2 121527838 Missense_Mutation SNP C C3N-00551_T 1871400 121527838 120665691 91 15574 MYO7B 0 . GRCh38 2 127608852 127608852 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2788G>T p.Glu930Ter p.E930* ENST00000428314 22/47 185 172 13 151 151 0 strelka-varscan-mutect MYO7B,stop_gained,p.Glu930Ter,ENST00000428314,NM_001080527.1;MYO7B,stop_gained,p.Glu930Ter,ENST00000409816,;MYO7B,upstream_gene_variant,,ENST00000563538,; T ENST00000428314 Transcript stop_gained 2841/6715 2788/6351 930/2116 E/* Gag/Tag 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 22/47 HIGH 1 SNV 5 1 PASS rs1254826226 . 0 208 2 0 0 0 0 0 -19.99985 1 1 1 1 0 T 4 4 52 127608852 127608852 G T 1 0 0 0 0 0 1 0 0 10084 1175 41 2 2 MYO7B 2 127608852 Nonsense_Mutation SNP G C3N-00551_T 6081014 127608852 114584677 92 15575 POTEE 0 . GRCh38 2 131218849 131218849 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.447G>T p.Trp149Cys p.W149C ENST00000356920 1/15 354 320 34 439 438 1 varscan-mutect POTEE,missense_variant,p.Trp149Cys,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.Trp149Cys,ENST00000626191,;POTEE,missense_variant,p.Trp149Cys,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,missense_variant,p.Trp149Cys,ENST00000358087,;POTEE,missense_variant,p.Trp149Cys,ENST00000514256,; T ENST00000356920 Transcript missense_variant 783/4159 447/3228 149/1075 W/C tgG/tgT 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 deleterious_low_confidence(0) 1/15 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 131218849 131218849 G T 1 0 0 0 0 1 0 0 0 12378 1241 43 2 2 POTEE 2 131218849 Missense_Mutation SNP G C3N-00551_T 3609997 131218849 110974680 93 15576 NCKAP5 0 . GRCh38 2 132784197 132784197 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2614C>A p.Leu872Ile p.L872I ENST00000409261 14/20 29 25 4 32 32 0 strelka-varscan-mutect NCKAP5,missense_variant,p.Leu872Ile,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Leu872Ile,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; T ENST00000409261 Transcript missense_variant 2988/7594 2614/5730 872/1909 L/I Ctt/Att 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 tolerated(0.17) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 132784197 132784197 G T 1 0 0 0 0 1 0 0 0 10241 1029 36 2 2 NCKAP5 2 132784197 Missense_Mutation SNP G C3N-00551_T 1565348 132784197 109409332 94 15577 NCKAP5 0 . GRCh38 2 132784797 132784797 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.2014G>T p.Asp672Tyr p.D672Y ENST00000409261 14/20 68 60 8 71 71 0 strelka-varscan-mutect NCKAP5,missense_variant,p.Asp672Tyr,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Asp672Tyr,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; A ENST00000409261 Transcript missense_variant 2388/7594 2014/5730 672/1909 D/Y Gat/Tat COSM715718 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 deleterious(0) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 1 MODERATE 1 SNV 5 1 1 PASS . . 0 204 6 0 0 0 0 0 -17.81133 0.9999999 1 1 1 0 A 3 1 52 132784797 132784797 C A 1 0 0 0 0 1 0 0 0 10241 826 29 2 2 NCKAP5 2 132784797 Missense_Mutation SNP C C3N-00551_T 600 132784797 109408732 95 15578 SCN3A 0 . GRCh38 2 165095610 165095610 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.4332G>T p.Met1444Ile p.M1444I ENST00000283254 25/28 101 91 10 83 83 0 strelka-varscan-mutect SCN3A,missense_variant,p.Met1444Ile,ENST00000360093,;SCN3A,missense_variant,p.Met1444Ile,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Met1395Ile,ENST00000409101,NM_001081677.1;SCN3A,downstream_gene_variant,,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000431341,;SCN3A,upstream_gene_variant,,ENST00000465043,;SCN3A,non_coding_transcript_exon_variant,,ENST00000471697,; A ENST00000283254 Transcript missense_variant 4800/9091 4332/6003 1444/2000 M/I atG/atT 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0.01) 25/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 165095610 165095610 C A 1 0 0 0 0 1 0 0 0 14187 478 17 2 2 SCN3A 2 165095610 Missense_Mutation SNP C C3N-00551_T 32310813 165095610 77097919 96 15579 61 2 SCN3A 0 . GRCh38 2 165095617 165095617 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.4325T>A p.Leu1442Gln p.L1442Q ENST00000283254 25/28 98 89 9 78 78 0 strelka-varscan-mutect SCN3A,missense_variant,p.Leu1442Gln,ENST00000360093,;SCN3A,missense_variant,p.Leu1442Gln,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Leu1393Gln,ENST00000409101,NM_001081677.1;SCN3A,downstream_gene_variant,,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000431341,;SCN3A,upstream_gene_variant,,ENST00000465043,;SCN3A,non_coding_transcript_exon_variant,,ENST00000471697,; T ENST00000283254 Transcript missense_variant 4793/9091 4325/6003 1442/2000 L/Q cTg/cAg 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0.01) 25/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 165095617 165095617 A T 1 0 0 0 0 1 0 0 0 14187 188 7 4 4 SCN3A 2 165095617 Missense_Mutation SNP A C3N-00551_T 7 165095617 77097912 97 15580 61 2 SCN3A 0 . GRCh38 2 165130251 165130251 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2611C>A p.Leu871Ile p.L871I ENST00000283254 17/28 292 261 31 357 357 0 strelka-varscan-mutect SCN3A,missense_variant,p.Leu871Ile,ENST00000360093,;SCN3A,missense_variant,p.Leu871Ile,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Leu822Ile,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Leu822Ile,ENST00000440431,;AC013463.2,non_coding_transcript_exon_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,;SCN3A,upstream_gene_variant,,ENST00000484898,; T ENST00000283254 Transcript missense_variant 3079/9091 2611/6003 871/2000 L/I Cta/Ata 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0.01) 17/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 165130251 165130251 G T 1 0 0 0 0 1 0 0 0 14187 962 34 2 2 SCN3A 2 165130251 Missense_Mutation SNP G C3N-00551_T 34634 165130251 77063278 98 15581 CDCA7 0 . GRCh38 2 173363231 173363231 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.390G>T p.= p.L130L ENST00000306721 4/10 174 158 16 201 201 0 strelka-varscan-mutect CDCA7,synonymous_variant,p.=,ENST00000306721,NM_031942.4;CDCA7,synonymous_variant,p.=,ENST00000347703,NM_145810.2;CDCA7,synonymous_variant,p.=,ENST00000410019,;CDCA7,synonymous_variant,p.=,ENST00000410101,;CDCA7,3_prime_UTR_variant,,ENST00000435616,;CDCA7,non_coding_transcript_exon_variant,,ENST00000467411,;CDCA7,non_coding_transcript_exon_variant,,ENST00000496441,;CDCA7,non_coding_transcript_exon_variant,,ENST00000468359,; T ENST00000306721 Transcript synonymous_variant 493/2789 390/1353 130/450 L ctG/ctT 1 1 CDCA7 HGNC HGNC:14628 protein_coding YES CCDS2252.1 ENSP00000306968 Q9BWT1 UPI0000456EA4 NM_031942.4 4/10 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 173363231 173363231 G T 1 0 0 0 0 0 0 0 1 2793 1333 46 2 2 CDCA7 2 173363231 Silent SNP G C3N-00551_T 8232980 173363231 68830298 99 15582 TTN 0 . GRCh38 2 178722907 178722928 + Frame_Shift_Del DEL GGTTCCAGTTCCGTAACAAAAT GGTTCCAGTTCCGTAACAAAAT - novel C3N-00551_T C3N-00551_N GGTTCCAGTTCCGTAACAAAAT GGTTCCAGTTCCGTAACAAAAT c.21971_21992delATTTTGTTACGGAACTGGAACC p.Tyr7324PhefsTer55 p.Y7324Ffs*55 ENST00000589042 76/363 123 109 14 123 123 0 sindel-varindel-pindel TTN,frameshift_variant,p.Tyr7324PhefsTer55,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Tyr7007PhefsTer55,ENST00000591111,;TTN,frameshift_variant,p.Tyr7007PhefsTer55,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Tyr6080PhefsTer55,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,; - ENST00000589042 Transcript frameshift_variant 22196-22217/109224 21971-21992/107976 7324-7331/35991 YFVTELEP/X tATTTTGTTACGGAACTGGAACCt/tt 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 76/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726,Superfamily_domains:SSF48726 HIGH 1 deletion 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 178722907 178722907 GGTTCCAGTTCCGTAACAAAAT - 1 0 1 0 1 0 0 0 0 17245 1000 35 0 0 TTN 2 178722907 Frame_Shift_Del DEL GGTTCCAGTTCCGTAACAAAAT C3N-00551_T 5359676 178722907 63470622 100 15583 TTN 0 . GRCh38 2 178773146 178773147 + Frame_Shift_Ins INS - - G novel C3N-00551_T C3N-00551_N - - c.7817dupC p.Glu2608ArgfsTer26 p.E2608Rfs*26 ENST00000589042 33/363 120 107 13 151 151 0 sindel-varindel-pindel TTN,frameshift_variant,p.Glu2608ArgfsTer26,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Glu2608ArgfsTer26,ENST00000591111,;TTN,frameshift_variant,p.Glu2608ArgfsTer26,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Glu2608ArgfsTer26,ENST00000342992,NM_133378.4;TTN,frameshift_variant,p.Glu2562ArgfsTer26,ENST00000460472,NM_003319.4;TTN,frameshift_variant,p.Glu2562ArgfsTer26,ENST00000342175,NM_133437.4;TTN,frameshift_variant,p.Glu2562ArgfsTer26,ENST00000359218,NM_133432.3;TTN,frameshift_variant,p.Glu2608ArgfsTer26,ENST00000360870,NM_133379.4;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000584485,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000610005,;TTN-AS1,upstream_gene_variant,,ENST00000582038,;TTN-AS1,upstream_gene_variant,,ENST00000629094,; G ENST00000589042 Transcript frameshift_variant 8042-8043/109224 7817-7818/107976 2606/35991 A/AX gcg/gcCg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 33/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 insertion 5 1 PASS . . 0 207 0 2 0 0 0 0 -19.44916 0.9999999 1 1 1 0 G 7 5 52 178773146 178773146 - G 1 0 1 1 0 0 0 0 0 17245 639 23 0 0 TTN 2 178773146 Frame_Shift_Ins INS - C3N-00551_T 50239 178773146 63420383 101 15584 CWC22 0 . GRCh38 2 179945269 179945269 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2587G>T p.Gly863Cys p.G863C ENST00000410053 20/20 210 192 18 280 280 0 strelka-varscan-mutect CWC22,missense_variant,p.Gly863Cys,ENST00000410053,NM_020943.2;CWC22,downstream_gene_variant,,ENST00000404136,; A ENST00000410053 Transcript missense_variant 2887/3280 2587/2727 863/908 G/C Ggc/Tgc 1 -1 CWC22 HGNC HGNC:29322 protein_coding YES CCDS46465.1 ENSP00000387006 Q9HCG8 UPI00001C1DAE NM_020943.2 deleterious_low_confidence(0.03) 20/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 179945269 179945269 C A 1 0 0 0 0 1 0 0 0 3878 681 24 2 2 CWC22 2 179945269 Missense_Mutation SNP C C3N-00551_T 1172123 179945269 62248260 102 15585 FSIP2 0 . GRCh38 2 185739380 185739380 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.401C>G p.Pro134Arg p.P134R ENST00000343098 2/23 73 65 8 96 96 0 strelka-mutect FSIP2,missense_variant,p.Pro134Arg,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Pro45Arg,ENST00000424728,;AC007966.1,intron_variant,,ENST00000427269,;AC007966.1,upstream_gene_variant,,ENST00000421998,;AC007966.1,upstream_gene_variant,,ENST00000437717,;FSIP2,non_coding_transcript_exon_variant,,ENST00000465275,;FSIP2,upstream_gene_variant,,ENST00000469367,; G ENST00000343098 Transcript missense_variant 401/21054 401/20991 134/6996 P/R cCg/cGg 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 2/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS rs1404049977 . 0 204 6 0 0 0 0 0 -17.52457 0.9999999 1 1 1 0 G 3 3 52 185739380 185739380 C G 1 0 0 0 0 1 0 0 0 5949 652 23 4 4 FSIP2 2 185739380 Missense_Mutation SNP C C3N-00551_T 5794111 185739380 56454149 103 15586 WDR75 0 . GRCh38 2 189474215 189474215 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.2079C>T p.= p.T693T ENST00000314761 19/21 83 74 9 137 137 0 strelka-mutect WDR75,synonymous_variant,p.=,ENST00000314761,NM_032168.2,NM_001303096.1;WDR75,3_prime_UTR_variant,,ENST00000427960,;WDR75,3_prime_UTR_variant,,ENST00000436347,; T ENST00000314761 Transcript synonymous_variant 2139/2701 2079/2493 693/830 T acC/acT 1 1 WDR75 HGNC HGNC:25725 protein_coding YES CCDS2298.1 ENSP00000314193 Q8IWA0 UPI000007452C NM_032168.2,NM_001303096.1 19/21 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -14.72052 0.9999871 1 1 1 0 T 2 4 52 189474215 189474215 C T 1 0 0 0 0 0 0 0 1 17881 610 22 3 3 WDR75 2 189474215 Silent SNP C C3N-00551_T 3734835 189474215 52719314 104 15587 SLC40A1 0 . GRCh38 2 189562003 189562003 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1591G>T p.Val531Leu p.V531L ENST00000261024 8/8 411 363 48 472 472 0 strelka-varscan-mutect SLC40A1,missense_variant,p.Val531Leu,ENST00000261024,NM_014585.5;SLC40A1,downstream_gene_variant,,ENST00000427241,; A ENST00000261024 Transcript missense_variant 2018/3442 1591/1716 531/571 V/L Gtg/Ttg 1 -1 SLC40A1 HGNC HGNC:10909 protein_coding YES CCDS2299.1 ENSP00000261024 Q9NP59 UPI0000034CC2 NM_014585.5 deleterious(0.01) 8/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11660,hmmpanther:PTHR11660:SF47,Gene3D:1.20.1250.20,Pfam_domain:PF06963,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 189562003 189562003 C A 1 0 0 0 0 1 0 0 0 14906 478 17 2 2 SLC40A1 2 189562003 Missense_Mutation SNP C C3N-00551_T 87788 189562003 52631526 105 15588 SATB2 0 . GRCh38 2 199328815 199328815 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.1269T>A p.Asn423Lys p.N423K ENST00000417098 8/11 512 480 32 558 558 0 strelka-varscan-mutect SATB2,missense_variant,p.Asn364Lys,ENST00000443023,;SATB2,missense_variant,p.Asn423Lys,ENST00000417098,NM_001172509.1;SATB2,missense_variant,p.Asn423Lys,ENST00000260926,NM_001172517.1;SATB2,missense_variant,p.Asn305Lys,ENST00000614512,;SATB2,missense_variant,p.Asn423Lys,ENST00000457245,NM_015265.3;SATB2,missense_variant,p.Asn305Lys,ENST00000428695,;RP11-486F17.1,non_coding_transcript_exon_variant,,ENST00000489557,;SATB2,non_coding_transcript_exon_variant,,ENST00000473517,; T ENST00000417098 Transcript missense_variant 2086/5730 1269/2202 423/733 N/K aaT/aaA 1 -1 SATB2 HGNC HGNC:21637 protein_coding YES CCDS2327.1 ENSP00000401112 Q9UPW6 A0A024R3U6 UPI00000336B1 NM_001172509.1 deleterious(0.02) 8/11 PROSITE_profiles:PS51042,hmmpanther:PTHR15116:SF15,hmmpanther:PTHR15116,Gene3D:1.10.260.40,Pfam_domain:PF02376,SMART_domains:SM01109,Superfamily_domains:SSF47413 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 199328815 199328815 A T 1 0 0 0 0 1 0 0 0 14115 330 12 4 4 SATB2 2 199328815 Missense_Mutation SNP A C3N-00551_T 9766812 199328815 42864714 106 15589 DYTN 0 . GRCh38 2 206663347 206663347 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1189G>T p.Gly397Trp p.G397W ENST00000452335 11/12 99 82 17 113 113 0 strelka-varscan-mutect DYTN,missense_variant,p.Gly397Trp,ENST00000452335,NM_001093730.1; A ENST00000452335 Transcript missense_variant 1306/2051 1189/1737 397/578 G/W Ggg/Tgg 1 -1 DYTN HGNC HGNC:23279 protein_coding YES CCDS46502.1 ENSP00000396593 A2CJ06 UPI0000EE0AB9 NM_001093730.1 deleterious(0) 11/12 hmmpanther:PTHR11915:SF282,hmmpanther:PTHR11915 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 206663347 206663347 C A 1 0 0 0 0 1 0 0 0 4684 623 22 2 2 DYTN 2 206663347 Missense_Mutation SNP C C3N-00551_T 7334532 206663347 35530182 107 15590 MAP2 0 . GRCh38 2 209694246 209694246 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2076G>T p.Arg692Ser p.R692S ENST00000360351 7/15 123 112 11 144 144 0 strelka-varscan-mutect MAP2,missense_variant,p.Arg692Ser,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Arg688Ser,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; T ENST00000360351 Transcript missense_variant 2582/9711 2076/5484 692/1827 R/S agG/agT 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious(0.04) 7/15 Low_complexity_(Seg):seg,hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 209694246 209694246 G T 1 0 0 0 0 1 0 0 0 9157 1252 44 2 2 MAP2 2 209694246 Missense_Mutation SNP G C3N-00551_T 3030899 209694246 32499283 108 15591 MAP2 0 . GRCh38 2 209725747 209725747 + Silent SNP G G C rs770619493 C3N-00551_T C3N-00551_N G G c.5112G>C p.= p.V1704V ENST00000360351 13/15 101 92 9 171 171 0 strelka-varscan-mutect MAP2,synonymous_variant,p.=,ENST00000360351,NM_002374.3;MAP2,synonymous_variant,p.=,ENST00000447185,;MAP2,synonymous_variant,p.=,ENST00000392194,NM_031845.2;MAP2,synonymous_variant,p.=,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,synonymous_variant,p.=,ENST00000361559,;RNA5SP118,upstream_gene_variant,,ENST00000410385,;MAP2,non_coding_transcript_exon_variant,,ENST00000475600,; C ENST00000360351 Transcript synonymous_variant 5618/9711 5112/5484 1704/1827 V gtG/gtC rs770619493 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 13/15 PROSITE_profiles:PS51491,hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF00418 LOW 1 SNV 5 1 PASS rs770619493 . 0 208 0 2 0 0 0 0 -14.03059 0.9999998 1 1 1 0 C 2 2 52 209725747 209725747 G C 1 0 0 0 0 0 0 0 1 9157 1277 45 4 4 MAP2 2 209725747 Silent SNP G C3N-00551_T 31501 209725747 32467782 109 15592 SPAG16 0 . GRCh38 2 214149138 214149138 + Splice_Site SNP A A T novel C3N-00551_T C3N-00551_N A A c.1594-2A>T p.X532_splice ENST00000331683 102 85 17 137 137 0 varscan-mutect SPAG16,splice_acceptor_variant,,ENST00000331683,NM_024532.4;SPAG16,splice_acceptor_variant,,ENST00000451561,;SPAG16,splice_acceptor_variant,,ENST00000480494,;SPAG16,splice_acceptor_variant,,ENST00000452556,;SPAG16,splice_acceptor_variant,,ENST00000406979,; T ENST00000331683 Transcript splice_acceptor_variant -/2177 1594/1896 532/631 1 1 SPAG16 HGNC HGNC:23225 protein_coding YES CCDS2396.1 ENSP00000332592 Q8N0X2 UPI00001AFF12 NM_024532.4 14/15 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 52 214149138 214149138 A T 1 0 0 0 0 0 0 1 0 15309 86 3 4 4 SPAG16 2 214149138 Splice_Site SNP A C3N-00551_T 4423391 214149138 28044391 110 15593 ABCA12 0 . GRCh38 2 215049736 215049736 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.583G>A p.Asp195Asn p.D195N ENST00000272895 6/53 271 250 21 312 312 0 strelka-varscan-mutect ABCA12,missense_variant,p.Asp195Asn,ENST00000272895,NM_173076.2;AC072062.3,intron_variant,,ENST00000628464,;AC072062.3,intron_variant,,ENST00000626134,;AC072062.3,intron_variant,,ENST00000626771,; T ENST00000272895 Transcript missense_variant 803/9100 583/7788 195/2595 D/N Gat/Aat 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 tolerated(0.58) 6/53 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 215049736 215049736 C T 1 0 0 0 0 1 0 0 0 34 826 29 3 3 ABCA12 2 215049736 Missense_Mutation SNP C C3N-00551_T 900598 215049736 27143793 111 15594 RUFY4 0 . GRCh38 2 218089274 218089274 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.1585A>G p.Arg529Gly p.R529G ENST00000374155 11/12 134 114 20 203 203 0 strelka-varscan-mutect RUFY4,missense_variant,p.Arg529Gly,ENST00000374155,;RUFY4,missense_variant,p.Arg509Gly,ENST00000344321,NM_198483.3;RUFY4,3_prime_UTR_variant,,ENST00000457754,; G ENST00000374155 Transcript missense_variant 1995/2977 1585/1824 529/607 R/G Agg/Ggg 1 1 RUFY4 HGNC HGNC:24804 protein_coding YES ENSP00000363270 C9J235 UPI000035E73D deleterious(0) 11/12 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 52 218089274 218089274 A G 1 0 0 0 0 1 0 0 0 14003 295 11 5 5 RUFY4 2 218089274 Missense_Mutation SNP A C3N-00551_T 3039538 218089274 24104255 112 15595 WNT10A 0 . GRCh38 2 218889984 218889984 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.377G>T p.Gly126Val p.G126V ENST00000258411 3/4 306 274 32 253 252 1 strelka-varscan-mutect WNT10A,missense_variant,p.Gly126Val,ENST00000258411,NM_025216.2;WNT10A,intron_variant,,ENST00000458582,;WNT10A,splice_region_variant,,ENST00000483911,;WNT10A,upstream_gene_variant,,ENST00000489887,; T ENST00000258411 Transcript missense_variant,splice_region_variant 1010/2547 377/1254 126/417 G/V gGt/gTt 1 1 WNT10A HGNC HGNC:13829 protein_coding YES CCDS2426.1 ENSP00000258411 Q9GZT5 UPI0000032F2A NM_025216.2 deleterious(0) 3/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF89,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 218889984 218889984 G T 1 0 0 0 0 1 0 0 0 17938 1275 44 2 2 WNT10A 2 218889984 Missense_Mutation SNP G C3N-00551_T 800710 218889984 23303545 113 15596 ATG9A 0 . GRCh38 2 219222645 219222645 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1848G>T p.Glu616Asp p.E616D ENST00000409618 11/16 126 117 9 142 142 0 strelka-varscan-mutect ATG9A,missense_variant,p.Glu616Asp,ENST00000409618,;ATG9A,missense_variant,p.Glu616Asp,ENST00000396761,NM_024085.4;ATG9A,missense_variant,p.Glu616Asp,ENST00000361242,NM_001077198.2;ATG9A,missense_variant,p.Glu555Asp,ENST00000409422,;ATG9A,missense_variant,p.Glu175Asp,ENST00000429920,;ABCB6,upstream_gene_variant,,ENST00000265316,NM_005689.2;ABCB6,upstream_gene_variant,,ENST00000295750,;ATG9A,downstream_gene_variant,,ENST00000436856,;ATG9A,downstream_gene_variant,,ENST00000432520,;ATG9A,downstream_gene_variant,,ENST00000428226,;ATG9A,downstream_gene_variant,,ENST00000457841,;ATG9A,downstream_gene_variant,,ENST00000443140,;ATG9A,downstream_gene_variant,,ENST00000439812,;ATG9A,downstream_gene_variant,,ENST00000431715,;ATG9A,downstream_gene_variant,,ENST00000434939,;ATG9A,downstream_gene_variant,,ENST00000455079,;ATG9A,downstream_gene_variant,,ENST00000488833,;ATG9A,missense_variant,p.Glu32Asp,ENST00000446716,;ATG9A,splice_region_variant,,ENST00000409033,;ABCB6,upstream_gene_variant,,ENST00000448398,;ATG9A,upstream_gene_variant,,ENST00000475339,;ABCB6,upstream_gene_variant,,ENST00000417678,;ATG9A,downstream_gene_variant,,ENST00000466217,;ATG9A,downstream_gene_variant,,ENST00000486766,;ATG9A,downstream_gene_variant,,ENST00000456708,;ATG9A,downstream_gene_variant,,ENST00000412355,;ABCB6,upstream_gene_variant,,ENST00000452545,; A ENST00000409618 Transcript missense_variant,splice_region_variant 2288/4025 1848/2520 616/839 E/D gaG/gaT 1 -1 ATG9A HGNC HGNC:22408 protein_coding YES CCDS42820.1 ENSP00000386710 Q7Z3C6 A0A024R438 UPI0000209615 tolerated(0.36) 11/16 Low_complexity_(Seg):seg,hmmpanther:PTHR13038,hmmpanther:PTHR13038:SF13 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 219222645 219222645 C A 1 0 0 0 0 1 0 0 0 1254 695 24 2 2 ATG9A 2 219222645 Missense_Mutation SNP C C3N-00551_T 332661 219222645 22970884 114 15597 PTPRN 0 . GRCh38 2 219309222 219309222 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.111C>A p.= p.A37A ENST00000295718 1/23 101 88 13 163 161 2 strelka-varscan-mutect PTPRN,synonymous_variant,p.=,ENST00000295718,NM_002846.3;PTPRN,synonymous_variant,p.=,ENST00000409251,NM_001199763.1;PTPRN,intron_variant,,ENST00000446182,;PTPRN,intron_variant,,ENST00000451506,;PTPRN,upstream_gene_variant,,ENST00000423636,NM_001199764.1;PTPRN,upstream_gene_variant,,ENST00000440552,;PTPRN,upstream_gene_variant,,ENST00000412847,;PTPRN,upstream_gene_variant,,ENST00000442029,;PTPRN,upstream_gene_variant,,ENST00000468454,;PTPRN,synonymous_variant,p.=,ENST00000606213,;PTPRN,non_coding_transcript_exon_variant,,ENST00000484986,;PTPRN,upstream_gene_variant,,ENST00000462351,;PTPRN,upstream_gene_variant,,ENST00000477819,; T ENST00000295718 Transcript synonymous_variant 352/3784 111/2940 37/979 A gcC/gcA 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 1/23 LOW 1 SNV 1 1 PASS rs1024048106 . 0 208 0 2 0 0 0 0 -19.91662 0.9999999 1 1 1 0 T 2 4 52 219309222 219309222 G T 1 0 0 0 0 0 0 0 1 12961 1246 43 2 2 PTPRN 2 219309222 Silent SNP G C3N-00551_T 86577 219309222 22884307 115 15598 SPEG 0 . GRCh38 2 219451802 219451802 + Missense_Mutation SNP G G T rs754947125 C3N-00551_T C3N-00551_N G G c.2435G>T p.Arg812Ile p.R812I ENST00000312358 6/41 53 47 6 48 48 0 strelka-varscan-mutect SPEG,missense_variant,p.Arg812Ile,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Arg708Ile,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,non_coding_transcript_exon_variant,,ENST00000462545,;SPEG,non_coding_transcript_exon_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000409595,; T ENST00000312358 Transcript missense_variant 2567/10782 2435/9804 812/3267 R/I aGa/aTa rs754947125 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 6/41 Gene3D:2.60.40.10,Pfam_domain:PF16650,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs754947125 . 0 208 2 0 0 0 0 0 -14.79083 1 1 1 1 0 T 3 4 52 219451802 219451802 G T 1 0 0 0 0 1 0 0 0 15387 956 33 2 2 SPEG 2 219451802 Missense_Mutation SNP G C3N-00551_T 142580 219451802 22741727 116 15599 SPEG 0 . GRCh38 2 219489447 219489447 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.8429C>A p.Ala2810Asp p.A2810D ENST00000312358 36/41 157 146 11 168 168 0 strelka-varscan-mutect SPEG,missense_variant,p.Ala2810Asp,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000412982,;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; A ENST00000312358 Transcript missense_variant 8561/10782 8429/9804 2810/3267 A/D gCt/gAt 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.18) 36/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 219489447 219489447 C A 1 0 0 0 0 1 0 0 0 15387 797 28 2 2 SPEG 2 219489447 Missense_Mutation SNP C C3N-00551_T 37645 219489447 22704082 117 15600 CHPF 0 . GRCh38 2 219539669 219539669 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.2042A>T p.Asn681Ile p.N681I ENST00000243776 4/4 210 181 29 165 165 0 strelka-varscan-mutect CHPF,missense_variant,p.Asn681Ile,ENST00000243776,NM_024536.5;CHPF,missense_variant,p.Asn519Ile,ENST00000535926,NM_001195731.1;ASIC4,downstream_gene_variant,,ENST00000358078,;ASIC4,downstream_gene_variant,,ENST00000347842,NM_182847.2;TMEM198,upstream_gene_variant,,ENST00000344458,NM_001303098.1;TMEM198,upstream_gene_variant,,ENST00000373883,NM_001005209.2;CHPF,downstream_gene_variant,,ENST00000373891,;TMEM198,upstream_gene_variant,,ENST00000421791,;TMEM198,upstream_gene_variant,,ENST00000451952,;ASIC4,downstream_gene_variant,,ENST00000474489,; A ENST00000243776 Transcript missense_variant 2291/3013 2042/2328 681/775 N/I aAc/aTc 1 -1 CHPF HGNC HGNC:24291 protein_coding YES CCDS2443.1 ENSP00000243776 Q8IZ52 UPI00001AE6D6 NM_024536.5 deleterious(0) 4/4 Pfam_domain:PF05679,hmmpanther:PTHR12369,hmmpanther:PTHR12369:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 219539669 219539669 T A 1 0 0 0 0 1 0 0 0 3128 1725 60 4 4 CHPF 2 219539669 Missense_Mutation SNP T C3N-00551_T 50222 219539669 22653860 118 15601 CUL3 0 . GRCh38 2 224482039 224482039 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1882G>C p.Val628Leu p.V628L ENST00000264414 14/16 147 136 11 322 322 0 strelka-mutect CUL3,missense_variant,p.Val628Leu,ENST00000264414,NM_003590.4;CUL3,missense_variant,p.Val562Leu,ENST00000344951,NM_001257197.1;CUL3,missense_variant,p.Val604Leu,ENST00000409777,;CUL3,missense_variant,p.Val604Leu,ENST00000409096,NM_001257198.1;CUL3,missense_variant,p.Val202Leu,ENST00000617432,;CUL3,intron_variant,,ENST00000451538,;CUL3,non_coding_transcript_exon_variant,,ENST00000536702,;CUL3,intron_variant,,ENST00000454323,;CUL3,upstream_gene_variant,,ENST00000497715,; G ENST00000264414 Transcript missense_variant 2221/6741 1882/2307 628/768 V/L Gtt/Ctt 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 tolerated(0.16) 14/16 PROSITE_profiles:PS50069,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.10.10.10,Superfamily_domains:SSF75632 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 224482039 224482039 C G 1 0 0 0 0 1 0 0 0 3866 478 17 4 4 CUL3 2 224482039 Missense_Mutation SNP C C3N-00551_T 4942370 224482039 17711490 119 15602 NYAP2 0 . GRCh38 2 225627037 225627037 + Nonsense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1739G>A p.Trp580Ter p.W580* ENST00000636099 6/7 402 355 47 502 502 0 strelka-varscan-mutect NYAP2,stop_gained,p.Trp580Ter,ENST00000636099,;NYAP2,stop_gained,p.Trp580Ter,ENST00000272907,NM_020864.1; A ENST00000636099 Transcript stop_gained 2785/5461 1739/1962 580/653 W/* tGg/tAg 1 1 NYAP2 HGNC HGNC:29291 protein_coding YES CCDS46529.1 ENSP00000490942 UPI00001C1DB6 6/7 hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF1,Pfam_domain:PF15452 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 225627037 225627037 G A 1 0 0 0 0 0 1 0 0 10873 1357 47 3 3 NYAP2 2 225627037 Nonsense_Mutation SNP G C3N-00551_T 1144998 225627037 16566492 120 15603 SLC16A14 0 . GRCh38 2 230046224 230046224 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.902A>T p.Tyr301Phe p.Y301F ENST00000295190 4/5 141 123 18 193 193 0 strelka-varscan-mutect SLC16A14,missense_variant,p.Tyr301Phe,ENST00000295190,NM_152527.4;SLC16A14,missense_variant,p.Tyr301Phe,ENST00000457406,;SLC16A14,missense_variant,p.Tyr301Phe,ENST00000412034,; A ENST00000295190 Transcript missense_variant 1361/4398 902/1533 301/510 Y/F tAt/tTt 1 -1 SLC16A14 HGNC HGNC:26417 protein_coding YES CCDS2473.1 ENSP00000295190 Q7RTX9 UPI000004EE99 NM_152527.4 deleterious(0.04) 4/5 Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF121,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 230046224 230046224 T A 1 0 0 0 0 1 0 0 0 14673 1406 49 4 4 SLC16A14 2 230046224 Missense_Mutation SNP T C3N-00551_T 4419187 230046224 12147305 121 15604 CAB39 0 . GRCh38 2 230790996 230790996 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.239T>A p.Leu80His p.L80H ENST00000258418 3/9 125 114 11 167 167 0 strelka-varscan-mutect CAB39,missense_variant,p.Leu80His,ENST00000258418,NM_016289.3;CAB39,missense_variant,p.Leu80His,ENST00000409788,NM_001130849.1;CAB39,missense_variant,p.Leu80His,ENST00000614925,;CAB39,missense_variant,p.Leu80His,ENST00000410084,NM_001130850.1;CAB39,downstream_gene_variant,,ENST00000484398,;CAB39,non_coding_transcript_exon_variant,,ENST00000478152,; A ENST00000258418 Transcript missense_variant 668/3826 239/1026 80/341 L/H cTt/cAt 1 1 CAB39 HGNC HGNC:20292 protein_coding YES CCDS2478.1 ENSP00000258418 Q9Y376 A0A024R496 UPI000003622D NM_016289.3 deleterious(0) 3/9 Gene3D:1.25.10.10,Pfam_domain:PF08569,hmmpanther:PTHR10182,hmmpanther:PTHR10182:SF11,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 230790996 230790996 T A 1 0 0 0 0 1 0 0 0 2212 1609 56 4 4 CAB39 2 230790996 Missense_Mutation SNP T C3N-00551_T 744772 230790996 11402533 122 15605 ALPPL2 0 . GRCh38 2 232409341 232409341 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1193C>A p.Pro398His p.P398H ENST00000295453 10/11 215 203 12 226 226 0 varscan-mutect ALPPL2,missense_variant,p.Pro398His,ENST00000295453,NM_031313.2; A ENST00000295453 Transcript missense_variant 1245/2493 1193/1599 398/532 P/H cCt/cAt 1 1 ALPPL2 HGNC HGNC:441 protein_coding YES CCDS2491.1 ENSP00000295453 P10696 UPI000013E259 NM_031313.2 deleterious(0.01) 10/11 hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF34,Pfam_domain:PF00245,Gene3D:3.40.720.10,SMART_domains:SM00098,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 232409341 232409341 C A 1 0 0 0 0 1 0 0 0 649 681 24 2 2 ALPPL2 2 232409341 Missense_Mutation SNP C C3N-00551_T 1618345 232409341 9784188 123 15606 NEU2 0 . GRCh38 2 233034668 233034668 + Missense_Mutation SNP G G T rs774136106 C3N-00551_T C3N-00551_N G G c.754G>T p.Gly252Trp p.G252W ENST00000233840 2/2 40 35 5 49 49 0 strelka-varscan-mutect NEU2,missense_variant,p.Gly252Trp,ENST00000233840,NM_005383.2; T ENST00000233840 Transcript missense_variant 754/1143 754/1143 252/380 G/W Ggg/Tgg rs774136106,COSM4706511 1 1 NEU2 HGNC HGNC:7759 protein_coding YES CCDS2501.1 ENSP00000233840 Q9Y3R4 UPI000013C98F NM_005383.2 deleterious(0) 2/2 hmmpanther:PTHR10628:SF6,hmmpanther:PTHR10628,Gene3D:2.120.10.10,Pfam_domain:PF13088,Superfamily_domains:SSF50939 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774136106 . 0 202 8 0 0 0 0 0 -12.7793 0.9999972 1 1 1 0 T 3 4 52 233034668 233034668 G T 1 0 0 0 0 1 0 0 0 10377 1116 39 1 1 NEU2 2 233034668 Missense_Mutation SNP G C3N-00551_T 625327 233034668 9158861 124 15607 INPP5D 0 . GRCh38 2 233204256 233204256 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3106G>T p.Asp1036Tyr p.D1036Y ENST00000445964 26/27 163 132 31 190 190 0 strelka-varscan-mutect INPP5D,missense_variant,p.Asp1035Tyr,ENST00000359570,NM_005541.4;INPP5D,missense_variant,p.Asp1036Tyr,ENST00000445964,NM_001017915.2;INPP5D,missense_variant,p.Asp657Tyr,ENST00000415617,;INPP5D,intron_variant,,ENST00000417661,;RN7SL32P,upstream_gene_variant,,ENST00000580514,;INPP5D,upstream_gene_variant,,ENST00000491070,; T ENST00000445964 Transcript missense_variant 3187/4845 3106/3570 1036/1189 D/Y Gac/Tac 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 deleterious(0) 26/27 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 233204256 233204256 G T 1 0 0 0 0 1 0 0 0 7659 1174 41 2 2 INPP5D 2 233204256 Missense_Mutation SNP G C3N-00551_T 169588 233204256 8989273 125 15608 ESPNL 0 . GRCh38 2 238128807 238128807 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1316G>T p.Arg439Leu p.R439L ENST00000343063 8/9 199 183 16 202 202 0 strelka-varscan-mutect ESPNL,missense_variant,p.Arg439Leu,ENST00000343063,NM_194312.2;ESPNL,missense_variant,p.Arg395Leu,ENST00000409169,;ESPNL,missense_variant,p.Arg71Leu,ENST00000409506,NM_001308370.1;ESPNL,missense_variant,p.Arg71Leu,ENST00000423032,;ESPNL,5_prime_UTR_variant,,ENST00000612395,;ESPNL,upstream_gene_variant,,ENST00000477241,; T ENST00000343063 Transcript missense_variant 1579/4836 1316/3018 439/1005 R/L cGg/cTg COSM720968 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 deleterious(0.04) 8/9 hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153 1 MODERATE 1 SNV 2 1 1 PASS rs1044194444 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 238128807 238128807 G T 1 0 0 0 0 1 0 0 0 5117 1116 39 1 1 ESPNL 2 238128807 Missense_Mutation SNP G C3N-00551_T 4924551 238128807 4064722 126 15609 ESPNL 0 . GRCh38 2 238131189 238131189 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.2475G>T p.= p.R825R ENST00000343063 9/9 201 171 30 199 199 0 strelka-varscan-mutect ESPNL,synonymous_variant,p.=,ENST00000343063,NM_194312.2;ESPNL,synonymous_variant,p.=,ENST00000409169,;ESPNL,synonymous_variant,p.=,ENST00000409506,NM_001308370.1;ESPNL,5_prime_UTR_variant,,ENST00000612395,;ESPNL,downstream_gene_variant,,ENST00000423032,;ESPNL,non_coding_transcript_exon_variant,,ENST00000477241,; T ENST00000343063 Transcript synonymous_variant 2738/4836 2475/3018 825/1005 R cgG/cgT 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 9/9 hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153 LOW 1 SNV 2 1 PASS rs1356154197 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 238131189 238131189 G T 1 0 0 0 0 0 0 0 1 5117 1190 42 2 2 ESPNL 2 238131189 Silent SNP G C3N-00551_T 2382 238131189 4062340 127 15610 AGXT 0 . GRCh38 2 240875984 240875984 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.826C>T p.= p.L276L ENST00000307503 8/11 361 315 46 414 414 0 strelka-varscan-mutect AGXT,synonymous_variant,p.=,ENST00000307503,NM_000030.2;AGXT,non_coding_transcript_exon_variant,,ENST00000476698,;AGXT,upstream_gene_variant,,ENST00000470255,;AGXT,downstream_gene_variant,,ENST00000472436,; T ENST00000307503 Transcript synonymous_variant 1213/1865 826/1179 276/392 L Ctg/Ttg 1 1 AGXT HGNC HGNC:341 protein_coding YES CCDS2543.1 ENSP00000302620 P21549 UPI0000135E9B NM_000030.2 8/11 Gene3D:3.40.640.10,Pfam_domain:PF00266,PIRSF_domain:PIRSF000524,hmmpanther:PTHR21152,hmmpanther:PTHR21152:SF22,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 240875984 240875984 C T 1 0 0 0 0 0 0 0 1 483 680 24 3 3 AGXT 2 240875984 Silent SNP C C3N-00551_T 2744795 240875984 1317545 128 15611 CHL1 0 . GRCh38 3 401678 401678 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.3438T>A p.Asp1146Glu p.D1146E ENST00000256509 27/28 53 47 6 91 91 0 strelka-mutect CHL1,missense_variant,p.Asp1146Glu,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Asp1093Glu,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Asp1130Glu,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Asp280Glu,ENST00000445697,;CHL1,downstream_gene_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant 4080/8023 3438/3675 1146/1224 D/E gaT/gaA 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(0.07) 27/28 Pfam_domain:PF13882,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 401678 401678 T A 1 0 0 0 0 1 0 0 0 3108 1461 51 4 4 CHL1 3 401678 Missense_Mutation SNP T C3N-00551_T 401678 197893881 129 15612 GPD1L 0 . GRCh38 3 32158920 32158920 + Nonsense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.663T>A p.Cys221Ter p.C221* ENST00000282541 6/8 372 345 27 417 417 0 strelka-varscan-mutect GPD1L,stop_gained,p.Cys221Ter,ENST00000282541,NM_015141.3;GPD1L,downstream_gene_variant,,ENST00000425459,;GPD1L,3_prime_UTR_variant,,ENST00000428684,;GPD1L,non_coding_transcript_exon_variant,,ENST00000474846,;GPD1L,non_coding_transcript_exon_variant,,ENST00000496151,; A ENST00000282541 Transcript stop_gained 864/4060 663/1056 221/351 C/* tgT/tgA 1 1 GPD1L HGNC HGNC:28956 protein_coding YES CCDS33729.1 ENSP00000282541 Q8N335 UPI000006E26D NM_015141.3 6/8 Gene3D:1.10.1040.10,Pfam_domain:PF07479,PIRSF_domain:PIRSF000114,Prints_domain:PR00077,hmmpanther:PTHR11728,hmmpanther:PTHR11728:SF7,Superfamily_domains:SSF48179,TIGRFAM_domain:TIGR03376 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 32158920 32158920 T A 1 0 0 0 0 0 1 0 0 6507 1702 59 4 4 GPD1L 3 32158920 Nonsense_Mutation SNP T C3N-00551_T 31757242 32158920 166136639 130 15613 ACVR2B 0 . GRCh38 3 38481407 38481407 + Missense_Mutation SNP A A T C3N-00551_T C3N-00551_N A A c.1016A>T p.Asp339Val p.D339V ENST00000352511 8/11 370 296 74 459 459 0 strelka-varscan-mutect ACVR2B,missense_variant,p.Asp339Val,ENST00000352511,NM_001106.3;ACVR2B,non_coding_transcript_exon_variant,,ENST00000461232,;ACVR2B,non_coding_transcript_exon_variant,,ENST00000465020,; T ENST00000352511 Transcript missense_variant 1488/11821 1016/1539 339/512 D/V gAc/gTc COSM1738817,COSM1738818 1 1 ACVR2B HGNC HGNC:174 protein_coding YES CCDS2679.1 ENSP00000340361 Q13705 UPI00001AF0AE NM_001106.3 deleterious(0) 8/11 Gene3D:1.10.510.10,Pfam_domain:PF00069,Prints_domain:PR00653,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF57,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 38481407 38481407 A T 1 0 0 0 0 1 0 0 0 268 275 10 4 4 ACVR2B 3 38481407 Missense_Mutation SNP A C3N-00551_T 6322487 38481407 159814152 131 15614 SCN5A 0 . GRCh38 3 38560286 38560286 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.4106G>T p.Gly1369Val p.G1369V ENST00000413689 23/28 352 299 53 400 400 0 strelka-varscan-mutect SCN5A,missense_variant,p.Gly1369Val,ENST00000413689,NM_001099404.1;SCN5A,missense_variant,p.Gly1369Val,ENST00000333535,NM_198056.2;SCN5A,missense_variant,p.Gly1369Val,ENST00000425664,NM_001099405.1;SCN5A,missense_variant,p.Gly1368Val,ENST00000423572,NM_000335.4;SCN5A,missense_variant,p.Gly1315Val,ENST00000451551,NM_001160161.1;SCN5A,missense_variant,p.Gly1369Val,ENST00000414099,;SCN5A,missense_variant,p.Gly1368Val,ENST00000455624,NM_001160160.1;SCN5A,missense_variant,p.Gly1315Val,ENST00000450102,;SCN5A,missense_variant,p.Gly1315Val,ENST00000449557,; A ENST00000413689 Transcript missense_variant 4300/8504 4106/6051 1369/2016 G/V gGa/gTa 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 deleterious(0.04) 23/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 38560286 38560286 C A 1 0 0 0 0 1 0 0 0 14191 855 30 2 2 SCN5A 3 38560286 Missense_Mutation SNP C C3N-00551_T 78879 38560286 159735273 132 15615 LTF 0 . GRCh38 3 46439324 46439324 + Missense_Mutation SNP C C A rs145382222 C3N-00551_T C3N-00551_N C C c.1880G>T p.Arg627Leu p.R627L ENST00000231751 15/17 79 74 5 119 119 0 strelka-mutect LTF,missense_variant,p.Arg627Leu,ENST00000231751,NM_002343.4;LTF,missense_variant,p.Arg614Leu,ENST00000443496,NM_001321122.1;LTF,missense_variant,p.Arg583Leu,ENST00000426532,NM_001199149.1;LTF,missense_variant,p.Arg625Leu,ENST00000417439,;LTF,non_coding_transcript_exon_variant,,ENST00000493056,;LTF,non_coding_transcript_exon_variant,,ENST00000478874,; A ENST00000231751 Transcript missense_variant 2176/2979 1880/2133 627/710 R/L cGc/cTc rs145382222 1 -1 LTF HGNC HGNC:6720 protein_coding YES CCDS33747.1 ENSP00000231751 P02788 V9HWI4 UPI000016ABE3 NM_002343.4 tolerated(0.7) 15/17 PROSITE_profiles:PS51408,hmmpanther:PTHR11485:SF33,hmmpanther:PTHR11485,PIRSF_domain:PIRSF500683,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,Gene3D:3.40.190.10,SMART_domains:SM00094,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS rs145382222 . 0 201 5 4 0 0 0 0 -8.462 0.9943239 1 1 1 0 A 3 1 52 46439324 46439324 C A 1 0 0 0 0 1 0 0 0 8985 768 27 1 1 LTF 3 46439324 Missense_Mutation SNP C C3N-00551_T 7879038 46439324 151856235 133 15616 USP4 0 . GRCh38 3 49298587 49298587 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1561G>T p.Ala521Ser p.A521S ENST00000265560 12/22 251 210 41 275 275 0 strelka-varscan-mutect USP4,missense_variant,p.Ala474Ser,ENST00000351842,NM_199443.2;USP4,missense_variant,p.Ala521Ser,ENST00000265560,NM_003363.3;USP4,missense_variant,p.Ala260Ser,ENST00000431357,;USP4,non_coding_transcript_exon_variant,,ENST00000486549,;USP4,downstream_gene_variant,,ENST00000488520,;USP4,upstream_gene_variant,,ENST00000475873,;USP4,non_coding_transcript_exon_variant,,ENST00000485450,; A ENST00000265560 Transcript missense_variant 1608/3126 1561/2892 521/963 A/S Gct/Tct 1 -1 USP4 HGNC HGNC:12627 protein_coding YES CCDS2793.1 ENSP00000265560 Q13107 A0A024R2T0 UPI000013D63C NM_003363.3 tolerated(0.19) 12/22 Pfam_domain:PF00443,PROSITE_profiles:PS50235 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -19.89236 0.9972591 1 1 1 0 A 3 1 52 49298587 49298587 C A 1 0 0 0 0 1 0 0 0 17613 739 26 2 2 USP4 3 49298587 Missense_Mutation SNP C C3N-00551_T 2859263 49298587 148996972 134 15617 GRM2 0 . GRCh38 3 51709127 51709127 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.144G>T p.Glu48Asp p.E48D ENST00000395052 2/6 177 155 22 171 170 1 strelka-varscan-mutect GRM2,missense_variant,p.Glu48Asp,ENST00000395052,NM_000839.3;GRM2,missense_variant,p.Glu48Asp,ENST00000442933,;GRM2,missense_variant,p.Glu48Asp,ENST00000419928,;TEX264,downstream_gene_variant,,ENST00000415259,;TEX264,downstream_gene_variant,,ENST00000395057,NM_001243725.1;TEX264,downstream_gene_variant,,ENST00000611400,NM_001278195.1;TEX264,downstream_gene_variant,,ENST00000457573,NM_001129884.2;TEX264,downstream_gene_variant,,ENST00000341333,NM_015926.5;TEX264,downstream_gene_variant,,ENST00000416589,NM_001243726.1;TEX264,downstream_gene_variant,,ENST00000614067,NM_001243727.2;GRM2,intron_variant,,ENST00000475478,;TEX264,downstream_gene_variant,,ENST00000463857,;GRM2,upstream_gene_variant,,ENST00000496661,;GRM2,upstream_gene_variant,,ENST00000477330,;GRM2,missense_variant,p.Glu48Asp,ENST00000296479,;GRM2,non_coding_transcript_exon_variant,,ENST00000464585,; T ENST00000395052 Transcript missense_variant 378/3151 144/2619 48/872 E/D gaG/gaT COSM5522804 1 1 GRM2 HGNC HGNC:4594 protein_coding YES CCDS2834.1 ENSP00000378492 Q14416 UPI000013E346 NM_000839.3 tolerated(0.51) 2/6 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF111,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 52 51709127 51709127 G T 1 0 0 0 0 1 0 0 0 6679 991 35 2 2 GRM2 3 51709127 Missense_Mutation SNP G C3N-00551_T 2410540 51709127 146586432 135 15618 ITIH3 0 . GRCh38 3 52803862 52803862 + Missense_Mutation SNP G G A rs548417682 C3N-00551_T C3N-00551_N G G c.1717G>A p.Ala573Thr p.A573T ENST00000449956 14/22 141 130 11 163 163 0 strelka-varscan-mutect ITIH3,missense_variant,p.Ala573Thr,ENST00000621946,;ITIH3,missense_variant,p.Ala573Thr,ENST00000449956,NM_002217.3;ITIH3,intron_variant,,ENST00000416872,;ITIH3,downstream_gene_variant,,ENST00000465243,;ITIH3,downstream_gene_variant,,ENST00000463893,;ITIH3,non_coding_transcript_exon_variant,,ENST00000475931,;ITIH3,upstream_gene_variant,,ENST00000493136,;ITIH3,upstream_gene_variant,,ENST00000495622,;ITIH3,downstream_gene_variant,,ENST00000464804,;ITIH3,downstream_gene_variant,,ENST00000465314,; A ENST00000449956 Transcript missense_variant 1723/3007 1717/2673 573/890 A/T Gcc/Acc rs548417682,COSM4119216,COSM4119217 1 1 ITIH3 HGNC HGNC:6168 protein_coding YES CCDS46845.1 ENSP00000415769 Q06033 UPI00005CE290 NM_002217.3 tolerated(0.07) 14/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10338:SF115,hmmpanther:PTHR10338 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs548417682 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 52803862 52803862 G A 1 0 0 0 0 1 0 0 0 7811 1087 38 1 1 ITIH3 3 52803862 Missense_Mutation SNP G C3N-00551_T 1094735 52803862 145491697 136 15619 C3orf67 0 . GRCh38 3 58884674 58884674 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.211A>T p.Thr71Ser p.T71S ENST00000295966 7/16 146 119 27 142 142 0 strelka-varscan-mutect C3orf67,missense_variant,p.Thr71Ser,ENST00000295966,NM_198463.2;C3orf67,missense_variant,p.Thr71Ser,ENST00000482387,;C3orf67,5_prime_UTR_variant,,ENST00000472469,;C3orf67-AS1,intron_variant,,ENST00000482372,;C3orf67-AS1,intron_variant,,ENST00000493123,;C3orf67-AS1,intron_variant,,ENST00000492031,;C3orf67-AS1,intron_variant,,ENST00000463703,;C3orf67,3_prime_UTR_variant,,ENST00000468415,;C3orf67,downstream_gene_variant,,ENST00000479931,; A ENST00000295966 Transcript missense_variant 715/2650 211/1692 71/563 T/S Aca/Tca 1 -1 C3orf67 HGNC HGNC:24763 protein_coding YES CCDS33776.1 ENSP00000295966 Q6ZVT6 UPI00001C098C NM_198463.2 tolerated(0.1) 7/16 hmmpanther:PTHR12458 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 58884674 58884674 T A 1 0 0 0 0 1 0 0 0 2071 1638 57 4 4 C3orf67 3 58884674 Missense_Mutation SNP T C3N-00551_T 6080812 58884674 139410885 137 15620 PDZRN3 0 . GRCh38 3 73383385 73383385 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.3181C>T p.= p.L1061L ENST00000263666 10/10 56 41 15 76 76 0 strelka-varscan-mutect PDZRN3,synonymous_variant,p.=,ENST00000263666,NM_015009.2;PDZRN3,synonymous_variant,p.=,ENST00000462146,NM_001303141.1;PDZRN3,synonymous_variant,p.=,ENST00000479530,NM_001303142.1;PDZRN3,synonymous_variant,p.=,ENST00000466780,NM_001303140.1;PDZRN3,synonymous_variant,p.=,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000492909,NM_001303139.1;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,; A ENST00000263666 Transcript synonymous_variant 3296/4248 3181/3201 1061/1066 L Cta/Tta 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 10/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 73383385 73383385 G A 1 0 0 0 0 0 0 0 1 11797 991 35 3 3 PDZRN3 3 73383385 Silent SNP G C3N-00551_T 14498711 73383385 124912174 138 15621 PDZRN3 0 . GRCh38 3 73388045 73388045 + Missense_Mutation SNP G G T rs775690269 C3N-00551_T C3N-00551_N G G c.1441C>A p.Arg481Ser p.R481S ENST00000263666 8/10 74 61 13 93 92 1 strelka-varscan-mutect PDZRN3,missense_variant,p.Arg481Ser,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Arg138Ser,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Arg198Ser,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Arg138Ser,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Arg78Ser,ENST00000494559,;PDZRN3,missense_variant,p.Arg179Ser,ENST00000492909,NM_001303139.1;PDZRN3,non_coding_transcript_exon_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000498048,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000478209,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000484487,;PDZRN3,downstream_gene_variant,,ENST00000477434,; T ENST00000263666 Transcript missense_variant 1556/4248 1441/3201 481/1066 R/S Cgt/Agt rs775690269,COSM4442164,COSM4442165,COSM4442166 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 8/10 PROSITE_profiles:PS50106,hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs775690269 . 0 195 13 2 0 0 0 0 -19.99907 0.9983223 1 1 1 0 T 3 4 52 73388045 73388045 G T 1 0 0 0 0 1 0 0 0 11797 1116 39 1 1 PDZRN3 3 73388045 Missense_Mutation SNP G C3N-00551_T 4660 73388045 124907514 139 15622 PDZRN3 0 . GRCh38 3 73404271 73404271 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1043C>T p.Pro348Leu p.P348L ENST00000263666 4/10 257 212 45 336 336 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Pro348Leu,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Pro5Leu,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Pro65Leu,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Pro5Leu,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Pro46Leu,ENST00000492909,NM_001303139.1;PDZRN3,upstream_gene_variant,,ENST00000494559,;PDZRN3,downstream_gene_variant,,ENST00000308537,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000498048,;PDZRN3,upstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000477434,;PDZRN3,upstream_gene_variant,,ENST00000484487,; A ENST00000263666 Transcript missense_variant 1158/4248 1043/3201 348/1066 P/L cCa/cTa 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 tolerated(0.63) 4/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 73404271 73404271 G A 1 0 0 0 0 1 0 0 0 11797 1348 47 3 3 PDZRN3 3 73404271 Missense_Mutation SNP G C3N-00551_T 16226 73404271 124891288 140 15623 OR5AC2 0 . GRCh38 3 98087508 98087508 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.336A>T p.= p.T112T ENST00000358642 1/1 218 187 31 239 239 0 strelka-varscan-mutect OR5AC2,synonymous_variant,p.=,ENST00000358642,NM_054106.1; T ENST00000358642 Transcript synonymous_variant 336/930 336/930 112/309 T acA/acT 1 1 OR5AC2 HGNC HGNC:15431 protein_coding YES CCDS33796.1 ENSP00000351466 Q9NZP5 UPI0000441EFD NM_054106.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF96,hmmpanther:PTHR26452,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs1233740137 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 98087508 98087508 A T 1 0 0 0 0 0 0 0 1 11213 175 7 4 4 OR5AC2 3 98087508 Silent SNP A C3N-00551_T 24683237 98087508 100208051 141 15624 OR5AC2 0 . GRCh38 3 98087940 98087940 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.768T>A p.= p.T256T ENST00000358642 1/1 132 110 22 126 126 0 strelka-varscan-mutect OR5AC2,synonymous_variant,p.=,ENST00000358642,NM_054106.1; A ENST00000358642 Transcript synonymous_variant 768/930 768/930 256/309 T acT/acA 1 1 OR5AC2 HGNC HGNC:15431 protein_coding YES CCDS33796.1 ENSP00000351466 Q9NZP5 UPI0000441EFD NM_054106.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF96,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 98087940 98087940 T A 1 0 0 0 0 0 0 0 1 11213 1538 54 4 4 OR5AC2 3 98087940 Silent SNP T C3N-00551_T 432 98087940 100207619 142 15625 CPOX 0 . GRCh38 3 98585615 98585615 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.998G>T p.Gly333Val p.G333V ENST00000264193 5/7 309 273 36 284 284 0 strelka-varscan-mutect CPOX,missense_variant,p.Gly333Val,ENST00000264193,NM_000097.5;CPOX,non_coding_transcript_exon_variant,,ENST00000510489,;CPOX,downstream_gene_variant,,ENST00000515041,;CPOX,downstream_gene_variant,,ENST00000513674,;CPOX,upstream_gene_variant,,ENST00000512905,; A ENST00000264193 Transcript missense_variant 1217/2825 998/1365 333/454 G/V gGc/gTc COSM3945791 1 -1 CPOX HGNC HGNC:2321 protein_coding YES CCDS2932.1 ENSP00000264193 P36551 UPI0000073C93 NM_000097.5 deleterious(0) 5/7 Gene3D:3.40.1500.10,Pfam_domain:PF01218,Prints_domain:PR00073,PROSITE_patterns:PS01021,hmmpanther:PTHR10755,hmmpanther:PTHR10755:SF0,Low_complexity_(Seg):seg,Superfamily_domains:SSF102886 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 98585615 98585615 C A 1 0 0 0 0 1 0 0 0 3616 739 26 2 2 CPOX 3 98585615 Missense_Mutation SNP C C3N-00551_T 497675 98585615 99709944 143 15626 COL8A1 0 . GRCh38 3 99795626 99795626 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.1725C>T p.= p.P575P ENST00000261037 5/5 108 95 13 77 77 0 strelka-varscan-mutect COL8A1,synonymous_variant,p.=,ENST00000261037,;COL8A1,synonymous_variant,p.=,ENST00000273342,NM_020351.3,NM_001850.4;COL8A1,downstream_gene_variant,,ENST00000621757,;COL8A1,downstream_gene_variant,,ENST00000452013,; T ENST00000261037 Transcript synonymous_variant 2105/5705 1725/2235 575/744 P ccC/ccT 1 1 COL8A1 HGNC HGNC:2215 protein_coding YES CCDS2934.1 ENSP00000261037 P27658 UPI0000126D21 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF565 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 99795626 99795626 C T 1 0 0 0 0 0 0 0 1 3494 610 22 3 3 COL8A1 3 99795626 Silent SNP C C3N-00551_T 1210011 99795626 98499933 144 15627 PHLDB2 0 . GRCh38 3 111974535 111974535 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3734C>A p.Ala1245Glu p.A1245E ENST00000431670 18/18 104 88 16 129 128 1 strelka-varscan-mutect PHLDB2,missense_variant,p.Ala1245Glu,ENST00000431670,NM_001134438.1;PHLDB2,missense_variant,p.Ala1202Glu,ENST00000412622,NM_145753.2;PHLDB2,missense_variant,p.Ala1229Glu,ENST00000393923,NM_001134437.1;PHLDB2,missense_variant,p.Ala1245Glu,ENST00000393925,NM_001134439.1;PHLDB2,missense_variant,p.Ala1202Glu,ENST00000481953,;PHLDB2,missense_variant,p.Ala736Glu,ENST00000495180,;PHLDB2,downstream_gene_variant,,ENST00000498699,;ABHD10,upstream_gene_variant,,ENST00000273359,NM_018394.3;ABHD10,upstream_gene_variant,,ENST00000494817,NM_001272069.1;PHLDB2,non_coding_transcript_exon_variant,,ENST00000486886,;ABHD10,upstream_gene_variant,,ENST00000491580,;ABHD10,upstream_gene_variant,,ENST00000493784,;ABHD10,upstream_gene_variant,,ENST00000497293,; A ENST00000431670 Transcript missense_variant 4145/6127 3734/3762 1245/1253 A/E gCa/gAa 1 1 PHLDB2 HGNC HGNC:29573 protein_coding YES CCDS46886.1 ENSP00000405405 Q86SQ0 UPI0000457152 NM_001134438.1 deleterious(0) 18/18 PROSITE_profiles:PS50003,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF21,SMART_domains:SM00233 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 52 111974535 111974535 C A 1 0 0 0 0 1 0 0 0 11940 710 25 2 2 PHLDB2 3 111974535 Missense_Mutation SNP C C3N-00551_T 12178909 111974535 86321024 145 15628 SIDT1 0 . GRCh38 3 113567572 113567572 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.377G>T p.Ser126Ile p.S126I ENST00000393830 3/26 96 82 14 121 121 0 strelka-varscan-mutect SIDT1,missense_variant,p.Ser126Ile,ENST00000264852,NM_001322294.1,NM_001322299.1,NM_017699.2;SIDT1,missense_variant,p.Ser126Ile,ENST00000393830,NM_001308350.1;SIDT1,non_coding_transcript_exon_variant,,ENST00000491730,;SIDT1,non_coding_transcript_exon_variant,,ENST00000483946,; T ENST00000393830 Transcript missense_variant 416/2572 377/2499 126/832 S/I aGc/aTc 1 1 SIDT1 HGNC HGNC:25967 protein_coding YES CCDS77790.1 ENSP00000377416 Q9NXL6 UPI0000DA58D9 NM_001308350.1 deleterious(0) 3/26 hmmpanther:PTHR12185,hmmpanther:PTHR12185:SF15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 113567572 113567572 G T 1 0 0 0 0 1 0 0 0 14566 971 34 2 2 SIDT1 3 113567572 Missense_Mutation SNP G C3N-00551_T 1593037 113567572 84727987 146 15629 SEMA5B 0 . GRCh38 3 122927904 122927904 + Frame_Shift_Del DEL C C - novel C3N-00551_T C3N-00551_N C C c.898delG p.Glu300SerfsTer95 p.E300Sfs*95 ENST00000451055 8/23 76 58 18 61 61 0 sindel-varindel-pindel SEMA5B,frameshift_variant,p.Glu246SerfsTer95,ENST00000616742,NM_001256346.1;SEMA5B,frameshift_variant,p.Glu246SerfsTer95,ENST00000357599,NM_001031702.3;SEMA5B,frameshift_variant,p.Glu300SerfsTer95,ENST00000451055,NM_001256347.1;SEMA5B,frameshift_variant,p.Glu188SerfsTer95,ENST00000195173,NM_001256348.1;SEMA5B,frameshift_variant,p.Glu246SerfsTer95,ENST00000393583,;SEMA5B,frameshift_variant,p.Glu246SerfsTer95,ENST00000475244,; - ENST00000451055 Transcript frameshift_variant 909/4579 898/3618 300/1205 E/X Gag/ag 1 -1 SEMA5B HGNC HGNC:10737 protein_coding YES CCDS58848.1 ENSP00000389588 Q9P283 UPI0002065011 NM_001256347.1 8/23 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF39,SMART_domains:SM00630,Superfamily_domains:SSF101912 HIGH 1 deletion 2 1 PASS . . 0 193 14 3 0 0 0 0 -20 0.9967977 1 1 1 0 - 7 5 52 122927904 122927904 C - 1 0 1 0 1 0 0 0 0 14314 864 30 0 0 SEMA5B 3 122927904 Frame_Shift_Del DEL C C3N-00551_T 9360332 122927904 75367655 147 15630 COL6A6 0 . GRCh38 3 130568161 130568161 + Missense_Mutation SNP A A T rs774012639 C3N-00551_T C3N-00551_N A A c.1958A>T p.Gln653Leu p.Q653L ENST00000358511 5/36 291 249 42 375 375 0 strelka-varscan-mutect COL6A6,missense_variant,p.Gln653Leu,ENST00000358511,NM_001102608.1; T ENST00000358511 Transcript missense_variant 1989/9581 1958/6792 653/2263 Q/L cAg/cTg rs774012639 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 deleterious(0.01) 5/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS rs774012639 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 130568161 130568161 A T 1 0 0 0 0 1 0 0 0 3492 188 7 4 4 COL6A6 3 130568161 Missense_Mutation SNP A C3N-00551_T 7640257 130568161 67727398 148 15631 COPB2 0 . GRCh38 3 139369288 139369288 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.1374A>T p.= p.I458I ENST00000333188 12/22 119 106 13 133 133 0 strelka-varscan-mutect COPB2,synonymous_variant,p.=,ENST00000333188,NM_004766.2;COPB2,synonymous_variant,p.=,ENST00000507777,;COPB2,synonymous_variant,p.=,ENST00000512309,;COPB2,downstream_gene_variant,,ENST00000510181,; A ENST00000333188 Transcript synonymous_variant 1556/3360 1374/2721 458/906 I atA/atT 1 -1 COPB2 HGNC HGNC:2232 protein_coding YES CCDS3108.1 ENSP00000329419 P35606 UPI0000161FB4 NM_004766.2 12/22 hmmpanther:PTHR19876,Pfam_domain:PF04053,PIRSF_domain:PIRSF005567,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs1247149216 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 139369288 139369288 T A 1 0 0 0 0 0 0 0 1 3521 1628 57 4 4 COPB2 3 139369288 Silent SNP T C3N-00551_T 8801127 139369288 58926271 149 15632 PLOD2 0 . GRCh38 3 146110423 146110423 + Missense_Mutation SNP G G T rs766067972 C3N-00551_T C3N-00551_N G G c.364C>A p.Pro122Thr p.P122T ENST00000282903 4/20 117 104 13 185 184 1 strelka-varscan-mutect PLOD2,missense_variant,p.Pro122Thr,ENST00000282903,NM_182943.2;PLOD2,missense_variant,p.Pro122Thr,ENST00000360060,NM_000935.2;PLOD2,missense_variant,p.Pro67Thr,ENST00000494950,;PLOD2,missense_variant,p.Pro94Thr,ENST00000469350,;PLOD2,3_prime_UTR_variant,,ENST00000480704,; T ENST00000282903 Transcript missense_variant 542/3732 364/2277 122/758 P/T Cca/Aca rs766067972,COSM5033154 1 -1 PLOD2 HGNC HGNC:9082 protein_coding YES CCDS3132.1 ENSP00000282903 O00469 UPI0000049C44 NM_182943.2 tolerated(0.08) 4/20 hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF6 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs766067972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 146110423 146110423 G T 1 0 0 0 0 1 0 0 0 12198 1174 41 2 2 PLOD2 3 146110423 Missense_Mutation SNP G C3N-00551_T 6741135 146110423 52185136 150 15633 PLSCR2 0 . GRCh38 3 146459858 146459858 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.266A>G p.Tyr89Cys p.Y89C ENST00000497985 4/10 124 108 16 203 203 0 strelka-varscan-mutect PLSCR2,missense_variant,p.Tyr89Cys,ENST00000497985,NM_001199978.1;PLSCR2,missense_variant,p.Tyr16Cys,ENST00000336685,NM_020359.2;PLSCR2,missense_variant,p.Tyr85Cys,ENST00000613069,NM_001199979.1;PLSCR2,missense_variant,p.Tyr16Cys,ENST00000610787,;PLSCR2,missense_variant,p.Tyr16Cys,ENST00000489015,;PLSCR2,missense_variant,p.Tyr16Cys,ENST00000463633,; C ENST00000497985 Transcript missense_variant 706/1441 266/894 89/297 Y/C tAc/tGc 1 -1 PLSCR2 HGNC HGNC:16494 protein_coding YES CCDS56284.1 ENSP00000420132 Q9NRY7 UPI0001B79690 NM_001199978.1 deleterious(0.04) 4/10 hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF29,Pfam_domain:PF03803 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 146459858 146459858 T C 1 0 0 0 0 1 0 0 0 12218 1638 57 5 5 PLSCR2 3 146459858 Missense_Mutation SNP T C3N-00551_T 349435 146459858 51835701 151 15634 CPB1 0 . GRCh38 3 148827893 148827893 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.70G>T p.Gly24Cys p.G24C ENST00000491148 2/12 130 116 14 214 214 0 strelka-varscan-mutect CPB1,missense_variant,p.Gly24Cys,ENST00000491148,;CPB1,missense_variant,p.Gly24Cys,ENST00000282957,NM_001871.2;CPB1,missense_variant,p.Gly24Cys,ENST00000468341,;CPB1,missense_variant,p.Gly24Cys,ENST00000494888,;CPB1,missense_variant,p.Gly24Cys,ENST00000462345,;CPB1,upstream_gene_variant,,ENST00000465718,;HMGB1P30,upstream_gene_variant,,ENST00000492455,; T ENST00000491148 Transcript missense_variant,splice_region_variant 404/1773 70/1254 24/417 G/C Ggc/Tgc COSM1039655 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD deleterious(0.03) 2/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.30.70.340,Superfamily_domains:SSF54897 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 148827893 148827893 G T 1 0 0 0 0 1 0 0 0 3590 1014 35 2 2 CPB1 3 148827893 Missense_Mutation SNP G C3N-00551_T 2368035 148827893 49467666 152 15635 MED12L 0 . GRCh38 3 151159939 151159939 + Silent SNP C C G novel C3N-00551_T C3N-00551_N C C c.945C>G p.= p.A315A ENST00000474524 7/43 237 192 45 247 247 0 strelka-varscan-mutect MED12L,synonymous_variant,p.=,ENST00000474524,NM_053002.5;MED12L,synonymous_variant,p.=,ENST00000309237,;MED12L,synonymous_variant,p.=,ENST00000422248,;MED12L,intron_variant,,ENST00000273432,; G ENST00000474524 Transcript synonymous_variant 983/10744 945/6438 315/2145 A gcC/gcG 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 7/43 hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992,Pfam_domain:PF12145 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 151159939 151159939 C G 1 0 0 0 0 0 0 0 1 9368 610 22 4 4 MED12L 3 151159939 Silent SNP C C3N-00551_T 2332046 151159939 47135620 153 15636 C3orf70 0 . GRCh38 3 185083297 185083297 + Missense_Mutation SNP G G T rs767517434 C3N-00551_T C3N-00551_N G G c.463C>A p.His155Asn p.H155N ENST00000335012 2/2 216 166 50 262 261 1 strelka-varscan-mutect C3orf70,missense_variant,p.His155Asn,ENST00000335012,NM_001025266.1; T ENST00000335012 Transcript missense_variant 654/5901 463/753 155/250 H/N Cac/Aac rs767517434 1 -1 C3orf70 HGNC HGNC:33731 protein_coding YES CCDS33900.1 ENSP00000334974 A6NLC5 UPI000016128B NM_001025266.1 tolerated_low_confidence(0.23) 2/2 hmmpanther:PTHR31785,hmmpanther:PTHR31785:SF2,Pfam_domain:PF15823 MODERATE 1 SNV 1 1 PASS rs767517434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 185083297 185083297 G T 1 0 0 0 0 1 0 0 0 2072 1348 47 2 2 C3orf70 3 185083297 Missense_Mutation SNP G C3N-00551_T 33923358 185083297 13212262 154 15637 HRG 0 . GRCh38 3 186677244 186677244 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.939A>T p.= p.P313P ENST00000232003 7/7 459 395 64 423 423 0 strelka-varscan-mutect HRG,synonymous_variant,p.=,ENST00000232003,NM_000412.3;RP11-573D15.8,intron_variant,,ENST00000630864,;RP11-573D15.8,intron_variant,,ENST00000625303,;RP11-573D15.8,intron_variant,,ENST00000629106,;RP11-573D15.8,intron_variant,,ENST00000630315,;RP11-573D15.8,intron_variant,,ENST00000627830,;RP11-573D15.8,intron_variant,,ENST00000628253,;RP11-573D15.8,intron_variant,,ENST00000630178,;RP11-573D15.8,intron_variant,,ENST00000628505,;RP11-573D15.8,intron_variant,,ENST00000626649,;RP11-573D15.8,intron_variant,,ENST00000625741,;RP11-573D15.8,intron_variant,,ENST00000626845,;RP11-573D15.8,intron_variant,,ENST00000629451,;RP11-573D15.8,intron_variant,,ENST00000627469,;RP11-573D15.8,intron_variant,,ENST00000628190,;RP11-573D15.8,intron_variant,,ENST00000625386,;RP11-573D15.8,intron_variant,,ENST00000630331,;RP11-573D15.8,intron_variant,,ENST00000625877,;RP11-573D15.8,intron_variant,,ENST00000628728,;RP11-573D15.8,intron_variant,,ENST00000626633,;RP11-573D15.8,intron_variant,,ENST00000625839,;RP11-573D15.8,intron_variant,,ENST00000630726,;RP11-573D15.8,upstream_gene_variant,,ENST00000626006,;HRG,non_coding_transcript_exon_variant,,ENST00000495413,; T ENST00000232003 Transcript synonymous_variant 1019/2015 939/1578 313/525 P ccA/ccT 1 1 HRG HGNC HGNC:5181 protein_coding YES CCDS3280.1 ENSP00000232003 P04196 UPI000012CBC3 NM_000412.3 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR13814,hmmpanther:PTHR13814:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 186677244 186677244 A T 1 0 0 0 0 0 0 0 1 7249 146 6 4 4 HRG 3 186677244 Silent SNP A C3N-00551_T 1593947 186677244 11618315 155 15638 FGF12 0 . GRCh38 3 192408114 192408114 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.110G>T p.Gly37Val p.G37V ENST00000454309 1/5 205 174 31 237 236 1 strelka-varscan-mutect FGF12,missense_variant,p.Gly37Val,ENST00000454309,NM_021032.4;FGF12,intron_variant,,ENST00000445105,NM_004113.5;FGF12,intron_variant,,ENST00000450716,;FGF12,intron_variant,,ENST00000418610,;FGF12,intron_variant,,ENST00000430714,;FGF12,intron_variant,,ENST00000448795,; A ENST00000454309 Transcript missense_variant 936/3058 110/732 37/243 G/V gGg/gTg 1 -1 FGF12 HGNC HGNC:3668 protein_coding YES CCDS3301.1 ENSP00000413496 P61328 UPI0000003FDD NM_021032.4 tolerated(0.09) 1/5 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF17 MODERATE 1 SNV 1 1 PASS rs1403732685 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 192408114 192408114 C A 1 0 0 0 0 1 0 0 0 5705 623 22 2 2 FGF12 3 192408114 Missense_Mutation SNP C C3N-00551_T 5730870 192408114 5887445 156 15639 CPN2 0 . GRCh38 3 194341152 194341152 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.1551C>T p.= p.Y517Y ENST00000323830 2/2 148 130 18 122 122 0 strelka-mutect CPN2,synonymous_variant,p.=,ENST00000323830,NM_001291988.1,NM_001080513.3;CPN2,synonymous_variant,p.=,ENST00000429275,; A ENST00000323830 Transcript synonymous_variant 1641/3028 1551/1638 517/545 Y taC/taT 1 -1 CPN2 HGNC HGNC:2313 protein_coding YES CCDS33920.1 ENSP00000319464 P22792 UPI0001AE76B7 NM_001291988.1,NM_001080513.3 2/2 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF278 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 194341152 194341152 G A 1 0 0 0 0 0 0 0 1 3605 1372 48 3 3 CPN2 3 194341152 Silent SNP G C3N-00551_T 1933038 194341152 3954407 157 15640 CLNK 0 . GRCh38 4 10513477 10513477 + Missense_Mutation SNP C C A rs761640065 C3N-00551_T C3N-00551_N C C c.893G>T p.Arg298Met p.R298M ENST00000226951 16/19 130 122 8 276 276 0 strelka-varscan-mutect CLNK,missense_variant,p.Arg298Met,ENST00000226951,NM_052964.2;CLNK,missense_variant,p.Arg36Met,ENST00000515667,;CLNK,missense_variant,p.Arg298Met,ENST00000442825,; A ENST00000226951 Transcript missense_variant 1133/5599 893/1287 298/428 R/M aGg/aTg rs761640065 1 -1 CLNK HGNC HGNC:17438 protein_coding YES CCDS47024.1 ENSP00000226951 Q7Z7G1 UPI000004A23A NM_052964.2 deleterious(0) 16/19 hmmpanther:PTHR14098:SF2,hmmpanther:PTHR14098,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs761640065 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 10513477 10513477 C A 1 0 0 0 0 1 0 0 0 3317 681 24 2 2 CLNK 4 10513477 Missense_Mutation SNP C C3N-00551_T 10513477 179701078 158 15641 CLRN2 0 . GRCh38 4 17522928 17522928 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.318C>G p.Phe106Leu p.F106L ENST00000511148 2/3 153 145 8 153 153 0 strelka-mutect CLRN2,missense_variant,p.Phe106Leu,ENST00000511148,NM_001079827.2; G ENST00000511148 Transcript missense_variant 420/823 318/699 106/232 F/L ttC/ttG 1 1 CLRN2 HGNC HGNC:33939 protein_coding YES CCDS47032.1 ENSP00000424711 A0PK11 UPI0000D6154A NM_001079827.2 tolerated(0.74) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR31548,hmmpanther:PTHR31548:SF5,PD525711,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 17522928 17522928 C G 1 0 0 0 0 1 0 0 0 3330 854 30 4 4 CLRN2 4 17522928 Missense_Mutation SNP C C3N-00551_T 7009451 17522928 172691627 159 15642 PCDH7 0 . GRCh38 4 30724531 30724531 + Missense_Mutation SNP A A T rs780554695 C3N-00551_T C3N-00551_N A A c.3109A>T p.Ile1037Phe p.I1037F ENST00000543491 1/1 149 138 11 228 228 0 strelka-varscan-mutect PCDH7,missense_variant,p.Ile727Phe,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,missense_variant,p.Ile1037Phe,ENST00000361762,NM_002589.2;PCDH7,missense_variant,p.Ile1037Phe,ENST00000543491,NM_032456.2;PCDH7,missense_variant,p.Ile352Phe,ENST00000621961,;PCDH7,missense_variant,p.Ile3Phe,ENST00000509759,;PCDH7,non_coding_transcript_exon_variant,,ENST00000507864,; T ENST00000543491 Transcript missense_variant 3679/4457 3109/3219 1037/1072 I/F Att/Ttt rs780554695 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 tolerated(0.27) 1/1 hmmpanther:PTHR24027:SF321,hmmpanther:PTHR24027,Pfam_domain:PF08374 MODERATE 1 SNV 1 PASS rs780554695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 30724531 30724531 A T 1 0 0 0 0 1 0 0 0 11603 217 8 4 4 PCDH7 4 30724531 Missense_Mutation SNP A C3N-00551_T 13201603 30724531 159490024 160 15643 TBC1D1 0 . GRCh38 4 38044373 38044373 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1425G>A p.Met475Ile p.M475I ENST00000261439 9/20 82 76 6 111 111 0 strelka-varscan-mutect TBC1D1,missense_variant,p.Met475Ile,ENST00000261439,NM_015173.3;TBC1D1,missense_variant,p.Met475Ile,ENST00000508802,NM_001253912.1;TBC1D1,missense_variant,p.Met123Ile,ENST00000510573,;TBC1D1,missense_variant,p.Met346Ile,ENST00000446803,;TBC1D1,intron_variant,,ENST00000615497,;TBC1D1,intron_variant,,ENST00000513936,;TBC1D1,upstream_gene_variant,,ENST00000443855,;TBC1D1,upstream_gene_variant,,ENST00000421339,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000509761,; A ENST00000261439 Transcript missense_variant 1780/5700 1425/3507 475/1168 M/I atG/atA 1 1 TBC1D1 HGNC HGNC:11578 protein_coding YES CCDS33972.1 ENSP00000261439 Q86TI0 B9A6J6 UPI0000367235 NM_015173.3 tolerated(0.2) 9/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 38044373 38044373 G A 1 0 0 0 0 1 0 0 0 15997 1348 47 3 3 TBC1D1 4 38044373 Missense_Mutation SNP G C3N-00551_T 7319842 38044373 152170182 161 15644 PDS5A 0 . GRCh38 4 39928003 39928003 + Silent SNP G G T C3N-00551_T C3N-00551_N G G c.300C>A p.= p.I100I ENST00000303538 3/33 281 236 45 315 315 0 strelka-varscan-mutect PDS5A,synonymous_variant,p.=,ENST00000303538,NM_001100399.1;PDS5A,synonymous_variant,p.=,ENST00000503396,NM_001100400.1;PDS5A,synonymous_variant,p.=,ENST00000513798,;TCEB1P33,upstream_gene_variant,,ENST00000603716,; T ENST00000303538 Transcript synonymous_variant 840/7176 300/4014 100/1337 I atC/atA COSM1055289,COSM1594546 1 -1 PDS5A HGNC HGNC:29088 protein_coding YES CCDS47045.1 ENSP00000303427 Q29RF7 G1UI16 UPI00006C6A7E NM_001100399.1 3/33 hmmpanther:PTHR12663:SF2,hmmpanther:PTHR12663,Superfamily_domains:SSF48371 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 39928003 39928003 G T 1 0 0 0 0 0 0 0 1 11779 932 33 2 2 PDS5A 4 39928003 Silent SNP G C3N-00551_T 1883630 39928003 150286552 162 15645 KCTD8 0 . GRCh38 4 44448183 44448183 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.341G>T p.Arg114Leu p.R114L ENST00000360029 1/2 189 146 43 176 176 0 strelka-varscan-mutect KCTD8,missense_variant,p.Arg114Leu,ENST00000360029,NM_198353.2;KCTD8,upstream_gene_variant,,ENST00000515268,; A ENST00000360029 Transcript missense_variant 625/2587 341/1422 114/473 R/L cGg/cTg 1 -1 KCTD8 HGNC HGNC:22394 protein_coding YES CCDS3467.1 ENSP00000353129 Q6ZWB6 UPI00001C08D6 NM_198353.2 deleterious(0) 1/2 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF68,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS rs1363571367 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 44448183 44448183 C A 1 0 0 0 0 1 0 0 0 8032 652 23 1 1 KCTD8 4 44448183 Missense_Mutation SNP C C3N-00551_T 4520180 44448183 145766372 163 15646 SCFD2 0 . GRCh38 4 53352657 53352657 + Silent SNP T T G novel C3N-00551_T C3N-00551_N T T c.948A>C p.= p.A316A ENST00000401642 2/9 225 200 25 237 237 0 strelka-varscan-mutect SCFD2,synonymous_variant,p.=,ENST00000401642,NM_152540.3;SCFD2,synonymous_variant,p.=,ENST00000388940,;SCFD2,synonymous_variant,p.=,ENST00000611795,;SCFD2,synonymous_variant,p.=,ENST00000503450,; G ENST00000401642 Transcript synonymous_variant 1082/3176 948/2055 316/684 A gcA/gcC 1 -1 SCFD2 HGNC HGNC:30676 protein_coding YES CCDS33984.1 ENSP00000384182 Q8WU76 UPI000006FB05 NM_152540.3 2/9 Gene3D:3.40.50.1910,Pfam_domain:PF00995,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF29,Superfamily_domains:SSF56815 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 53352657 53352657 T G 1 0 0 0 0 0 0 0 1 14156 1683 59 5 5 SCFD2 4 53352657 Silent SNP T C3N-00551_T 8904474 53352657 136861898 164 15647 SCFD2 0 . GRCh38 4 53365155 53365155 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.787G>C p.Ala263Pro p.A263P ENST00000401642 1/9 128 112 16 168 168 0 strelka-varscan-mutect SCFD2,missense_variant,p.Ala263Pro,ENST00000401642,NM_152540.3;SCFD2,missense_variant,p.Ala263Pro,ENST00000388940,;SCFD2,missense_variant,p.Ala263Pro,ENST00000611795,;SCFD2,5_prime_UTR_variant,,ENST00000503450,; G ENST00000401642 Transcript missense_variant 921/3176 787/2055 263/684 A/P Gct/Cct 1 -1 SCFD2 HGNC HGNC:30676 protein_coding YES CCDS33984.1 ENSP00000384182 Q8WU76 UPI000006FB05 NM_152540.3 deleterious(0.01) 1/9 Gene3D:3.40.50.1910,Pfam_domain:PF00995,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF29,Superfamily_domains:SSF56815 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 53365155 53365155 C G 1 0 0 0 0 1 0 0 0 14156 710 25 4 4 SCFD2 4 53365155 Missense_Mutation SNP C C3N-00551_T 12498 53365155 136849400 165 15648 KDR 0 . GRCh38 4 55105838 55105838 + Missense_Mutation SNP C C T rs761405036 C3N-00551_T C3N-00551_N C C c.1639G>A p.Val547Met p.V547M ENST00000263923 12/30 406 342 64 527 527 0 strelka-mutect KDR,missense_variant,p.Val547Met,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; T ENST00000263923 Transcript missense_variant 1935/5831 1639/4071 547/1356 V/M Gtg/Atg rs761405036 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0) 12/30 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS rs761405036 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 55105838 55105838 C T 1 0 0 0 0 1 0 0 0 8059 536 19 1 1 KDR 4 55105838 Missense_Mutation SNP C C3N-00551_T 1740683 55105838 135108717 166 15649 YTHDC1 0 . GRCh38 4 68316419 68316419 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.1854A>T p.= p.P618P ENST00000344157 16/17 115 106 9 126 126 0 strelka-varscan-mutect YTHDC1,synonymous_variant,p.=,ENST00000344157,NM_001031732.2;YTHDC1,synonymous_variant,p.=,ENST00000355665,NM_133370.2;YTHDC1,synonymous_variant,p.=,ENST00000579690,;YTHDC1,synonymous_variant,p.=,ENST00000507529,; A ENST00000344157 Transcript synonymous_variant 2190/6232 1854/2184 618/727 P ccA/ccT 1 -1 YTHDC1 HGNC HGNC:30626 protein_coding YES CCDS33992.1 ENSP00000339245 Q96MU7 UPI000020B86D NM_001031732.2 16/17 hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF33,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.14539 1 1 1 1 0 A 2 1 52 68316419 68316419 T A 1 0 0 0 0 0 0 0 1 18057 1683 59 4 4 YTHDC1 4 68316419 Silent SNP T C3N-00551_T 13210581 68316419 121898136 167 15650 YTHDC1 0 . GRCh38 4 68337063 68337063 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.847G>T p.Gly283Trp p.G283W ENST00000344157 4/17 77 72 5 66 66 0 strelka-varscan-mutect YTHDC1,missense_variant,p.Gly283Trp,ENST00000344157,NM_001031732.2;YTHDC1,missense_variant,p.Gly283Trp,ENST00000355665,NM_133370.2;YTHDC1,missense_variant,p.Gly283Trp,ENST00000579690,;YTHDC1,downstream_gene_variant,,ENST00000510746,;YTHDC1,downstream_gene_variant,,ENST00000505251,; A ENST00000344157 Transcript missense_variant 1183/6232 847/2184 283/727 G/W Ggg/Tgg 1 -1 YTHDC1 HGNC HGNC:30626 protein_coding YES CCDS33992.1 ENSP00000339245 Q96MU7 UPI000020B86D NM_001031732.2 deleterious(0) 4/17 hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF33 MODERATE 1 SNV 1 1 PASS rs1218769585 . 0 208 2 0 0 0 0 0 -11.6383 1 1 1 1 0 A 3 1 52 68337063 68337063 C A 1 0 0 0 0 1 0 0 0 18057 594 21 2 2 YTHDC1 4 68337063 Missense_Mutation SNP C C3N-00551_T 20644 68337063 121877492 168 15651 UGT2B11 0 . GRCh38 4 69200655 69200655 + Silent SNP G G T rs764600893 C3N-00551_T C3N-00551_N G G c.1375C>A p.= p.R459R ENST00000446444 6/6 221 199 22 275 275 0 varscan-mutect UGT2B11,synonymous_variant,p.=,ENST00000446444,NM_001073.1;RP11-704M14.1,intron_variant,,ENST00000505646,;RP11-704M14.1,intron_variant,,ENST00000504301,;UGT2B11,downstream_gene_variant,,ENST00000513315,; T ENST00000446444 Transcript synonymous_variant 1384/2088 1375/1590 459/529 R Cga/Aga rs764600893,COSM396563,COSM4465294 1 -1 UGT2B11 HGNC HGNC:12545 protein_coding YES CCDS3527.1 ENSP00000387683 O75310 UPI0000137A97 NM_001073.1 6/6 Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF365,Superfamily_domains:SSF53756 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs764600893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 69200655 69200655 G T 1 0 0 0 0 0 0 0 1 17481 1066 37 1 1 UGT2B11 4 69200655 Silent SNP G C3N-00551_T 863592 69200655 121013900 169 15652 UGT2B28 0 . GRCh38 4 69286833 69286833 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.952G>T p.Ala318Ser p.A318S ENST00000335568 3/6 115 76 39 160 160 0 strelka-varscan-mutect UGT2B28,missense_variant,p.Ala318Ser,ENST00000335568,NM_053039.1;UGT2B28,missense_variant,p.Ala318Ser,ENST00000511240,NM_001207004.1; T ENST00000335568 Transcript missense_variant 954/1833 952/1590 318/529 A/S Gca/Tca 1 1 UGT2B28 HGNC HGNC:13479 protein_coding YES CCDS3528.1 ENSP00000334276 Q9BY64 UPI0000137A9F NM_053039.1 deleterious(0.03) 3/6 Gene3D:3.40.50.2000,Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF365,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 69286833 69286833 G T 1 0 0 0 0 1 0 0 0 17484 971 34 2 2 UGT2B28 4 69286833 Missense_Mutation SNP G C3N-00551_T 86178 69286833 120927722 170 15653 SHROOM3 0 . GRCh38 4 76436216 76436216 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.164C>A p.Ser55Tyr p.S55Y ENST00000296043 1/11 182 154 28 187 187 0 strelka-varscan-mutect SHROOM3,missense_variant,p.Ser55Tyr,ENST00000296043,NM_020859.3;SHROOM3,non_coding_transcript_exon_variant,,ENST00000466541,;SHROOM3,non_coding_transcript_exon_variant,,ENST00000497440,; A ENST00000296043 Transcript missense_variant 1117/11020 164/5991 55/1996 S/Y tCt/tAt 1 1 SHROOM3 HGNC HGNC:30422 protein_coding YES CCDS3579.2 ENSP00000296043 Q8TF72 UPI0000E5AC1C NM_020859.3 deleterious(0) 1/11 PROSITE_profiles:PS50106,hmmpanther:PTHR15012:SF33,hmmpanther:PTHR15012,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 76436216 76436216 C A 1 0 0 0 0 1 0 0 0 14558 927 32 2 2 SHROOM3 4 76436216 Missense_Mutation SNP C C3N-00551_T 7149383 76436216 113778339 171 15654 BMP2K 0 . GRCh38 4 78872616 78872616 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1611G>T p.Met537Ile p.M537I ENST00000335016 13/16 71 59 12 80 80 0 strelka-varscan-mutect BMP2K,missense_variant,p.Met230Ile,ENST00000502613,;BMP2K,missense_variant,p.Met537Ile,ENST00000335016,NM_198892.1;BMP2K,missense_variant,p.Met537Ile,ENST00000502871,NM_017593.3;BMP2K,splice_region_variant,,ENST00000628286,;BMP2K,splice_region_variant,,ENST00000389010,;BMP2K,non_coding_transcript_exon_variant,,ENST00000507670,; T ENST00000335016 Transcript missense_variant,splice_region_variant 1777/3804 1611/3486 537/1161 M/I atG/atT 1 1 BMP2K HGNC HGNC:18041 protein_coding YES CCDS47083.1 ENSP00000334836 Q9NSY1 UPI00001BDC7C NM_198892.1 tolerated_low_confidence(0.05) 13/16 hmmpanther:PTHR22967,hmmpanther:PTHR22967:SF10,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 169 32 9 0 0 0 0 -19.85047 0.60151 0 1 1 0 T 3 4 52 78872616 78872616 G T 1 0 0 0 0 1 0 0 0 1615 1333 46 2 2 BMP2K 4 78872616 Missense_Mutation SNP G C3N-00551_T 2436400 78872616 111341939 172 15655 PRDM8 0 . GRCh38 4 80200247 80200247 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.167C>A p.Ala56Asp p.A56D ENST00000339711 8/10 303 261 42 295 294 1 strelka-varscan-mutect PRDM8,missense_variant,p.Ala56Asp,ENST00000339711,NM_020226.3;PRDM8,missense_variant,p.Ala56Asp,ENST00000504452,;PRDM8,missense_variant,p.Ala56Asp,ENST00000415738,NM_001099403.1;PRDM8,missense_variant,p.Ala56Asp,ENST00000515013,;PRDM8,downstream_gene_variant,,ENST00000508061,;PRDM8,downstream_gene_variant,,ENST00000511825,;PRDM8,downstream_gene_variant,,ENST00000508965,;PRDM8,downstream_gene_variant,,ENST00000507025,;PRDM8,downstream_gene_variant,,ENST00000509375,;PRDM8,downstream_gene_variant,,ENST00000506547,; A ENST00000339711 Transcript missense_variant 1398/4095 167/2070 56/689 A/D gCt/gAt 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 deleterious(0) 8/10 Gene3D:2.170.270.10,PROSITE_profiles:PS50280,hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 80200247 80200247 C A 1 0 0 0 0 1 0 0 0 12594 797 28 2 2 PRDM8 4 80200247 Missense_Mutation SNP C C3N-00551_T 1327631 80200247 110014308 173 15656 MAPK10 0 . GRCh38 4 86029245 86029245 + Nonsense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1204G>T p.Glu402Ter p.E402* ENST00000359221 13/14 133 117 16 177 177 0 strelka-varscan-mutect MAPK10,stop_gained,p.Glu257Ter,ENST00000395161,;MAPK10,stop_gained,p.Glu364Ter,ENST00000395169,NM_138980.2;MAPK10,stop_gained,p.Glu364Ter,ENST00000395166,;MAPK10,stop_gained,p.Glu402Ter,ENST00000359221,NM_138982.2;MAPK10,stop_gained,p.Glu257Ter,ENST00000449047,;MAPK10,stop_gained,p.Glu402Ter,ENST00000361569,NM_002753.3;MAPK10,stop_gained,p.Glu257Ter,ENST00000395160,NM_138981.2;MAPK10,stop_gained,p.Glu257Ter,ENST00000395157,;MAPK10,stop_gained,p.Glu315Ter,ENST00000515400,;MAPK10,3_prime_UTR_variant,,ENST00000310816,;MAPK10,non_coding_transcript_exon_variant,,ENST00000508262,; A ENST00000359221 Transcript stop_gained 1731/2672 1204/1395 402/464 E/* Gaa/Taa 1 -1 MAPK10 HGNC HGNC:6872 protein_coding YES CCDS34026.1 ENSP00000352157 P53779 UPI0000049042 NM_138982.2 13/14 hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF162 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99995 0.9999999 1 1 1 0 A 4 1 52 86029245 86029245 C A 1 0 0 0 0 0 1 0 0 9196 922 32 2 2 MAPK10 4 86029245 Nonsense_Mutation SNP C C3N-00551_T 5828998 86029245 104185310 174 15657 HERC5 0 . GRCh38 4 88504304 88504304 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.2655G>T p.= p.R885R ENST00000264350 21/23 162 141 21 183 183 0 strelka-varscan-mutect HERC5,synonymous_variant,p.=,ENST00000264350,NM_016323.3;HERC5,synonymous_variant,p.=,ENST00000508159,;HERC5,non_coding_transcript_exon_variant,,ENST00000510223,;HERC5,non_coding_transcript_exon_variant,,ENST00000502913,;RP11-466G12.3,downstream_gene_variant,,ENST00000340589,; T ENST00000264350 Transcript synonymous_variant 2808/3513 2655/3075 885/1024 R cgG/cgT 1 1 HERC5 HGNC HGNC:24368 protein_coding YES CCDS3630.1 ENSP00000264350 Q9UII4 UPI000013D500 NM_016323.3 21/23 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF344,SMART_domains:SM00119,Superfamily_domains:SSF56204 LOW 1 SNV 1 1 PASS rs1252829120 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 52 88504304 88504304 G T 1 0 0 0 0 0 0 0 1 6945 1161 41 2 2 HERC5 4 88504304 Silent SNP G C3N-00551_T 2475059 88504304 101710251 175 15658 GRID2 0 . GRCh38 4 93772105 93772105 + Silent SNP C C A C3N-00551_T C3N-00551_N C C c.2631C>A p.= p.L877L ENST00000282020 16/16 92 81 11 151 151 0 strelka-varscan-mutect GRID2,synonymous_variant,p.=,ENST00000282020,NM_001510.3;GRID2,synonymous_variant,p.=,ENST00000611049,;GRID2,synonymous_variant,p.=,ENST00000510992,NM_001286838.1;GRID2,intron_variant,,ENST00000637838,; A ENST00000282020 Transcript synonymous_variant 3666/6117 2631/3024 877/1007 L ctC/ctA COSM5254868 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 16/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 93772105 93772105 C A 1 0 0 0 0 0 0 0 1 6652 842 30 2 2 GRID2 4 93772105 Silent SNP C C3N-00551_T 5267801 93772105 96442450 176 15659 SLC9B2 0 . GRCh38 4 103048933 103048933 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.673T>C p.Tyr225His p.Y225H ENST00000394785 6/12 185 157 28 179 179 0 strelka-varscan-mutect SLC9B2,missense_variant,p.Tyr225His,ENST00000394785,NM_178833.5;SLC9B2,missense_variant,p.Tyr225His,ENST00000362026,;SLC9B2,missense_variant,p.Tyr168His,ENST00000503103,NM_001300756.1;SLC9B2,missense_variant,p.Tyr168His,ENST00000503230,NM_001300754.1;SLC9B2,missense_variant,p.Tyr125His,ENST00000506288,;SLC9B2,non_coding_transcript_exon_variant,,ENST00000515424,;SLC9B2,upstream_gene_variant,,ENST00000510976,; G ENST00000394785 Transcript missense_variant 1305/3126 673/1614 225/537 Y/H Tac/Cac 1 -1 SLC9B2 HGNC HGNC:25143 protein_coding YES CCDS3662.1 ENSP00000378265 Q86UD5 A0A024RDJ7 UPI000020B27F NM_178833.5 deleterious(0) 6/12 Pfam_domain:PF00999,hmmpanther:PTHR31102,hmmpanther:PTHR31102:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 103048933 103048933 A G 1 0 0 0 0 1 0 0 0 15005 362 13 5 5 SLC9B2 4 103048933 Missense_Mutation SNP A C3N-00551_T 9276828 103048933 87165622 177 15660 BDH2 0 . GRCh38 4 103086531 103086531 + Nonsense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.367C>T p.Gln123Ter p.Q123* ENST00000296424 6/10 135 121 14 156 155 1 strelka-varscan-mutect BDH2,stop_gained,p.Gln123Ter,ENST00000296424,NM_020139.3;BDH2,stop_gained,p.Gln123Ter,ENST00000504285,;BDH2,downstream_gene_variant,,ENST00000509245,;BDH2,3_prime_UTR_variant,,ENST00000511354,;BDH2,3_prime_UTR_variant,,ENST00000506521,;BDH2,non_coding_transcript_exon_variant,,ENST00000464039,;BDH2,non_coding_transcript_exon_variant,,ENST00000492366,;BDH2,non_coding_transcript_exon_variant,,ENST00000475058,;SLC9B2,upstream_gene_variant,,ENST00000508136,; A ENST00000296424 Transcript stop_gained 488/1126 367/738 123/245 Q/* Cag/Tag 1 -1 BDH2 HGNC HGNC:32389 protein_coding YES CCDS3663.1 ENSP00000296424 Q9BUT1 A0A024RDG9 UPI000003E73A NM_020139.3 6/10 hmmpanther:PTHR24321,Gene3D:3.40.50.720,Pfam_domain:PF13561,Superfamily_domains:SSF51735,Prints_domain:PR00081 HIGH 1 SNV 1 1 PASS rs1398294809 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 103086531 103086531 G A 1 0 0 0 0 0 1 0 0 1538 1299 45 3 3 BDH2 4 103086531 Nonsense_Mutation SNP G C3N-00551_T 37598 103086531 87128024 178 15661 ETNPPL 0 . GRCh38 4 108760216 108760216 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.147C>A p.Tyr49Ter p.Y49* ENST00000296486 2/13 104 82 22 107 107 0 strelka-mutect ETNPPL,stop_gained,p.Tyr49Ter,ENST00000296486,NM_031279.3;ETNPPL,stop_gained,p.Tyr49Ter,ENST00000411864,NM_001146590.1;ETNPPL,stop_gained,p.Tyr9Ter,ENST00000510706,;ETNPPL,intron_variant,,ENST00000512646,NM_001146627.1;ETNPPL,intron_variant,,ENST00000512320,;ETNPPL,intron_variant,,ENST00000510723,;ETNPPL,stop_gained,p.Tyr49Ter,ENST00000505233,;ETNPPL,intron_variant,,ENST00000509402,; T ENST00000296486 Transcript stop_gained 302/2099 147/1500 49/499 Y/* taC/taA 1 -1 ETNPPL HGNC HGNC:14404 protein_coding YES CCDS3682.1 ENSP00000296486 Q8TBG4 UPI000004B638 NM_031279.3 2/13 hmmpanther:PTHR11986:SF63,hmmpanther:PTHR11986,Gene3D:3.90.1150.10,Pfam_domain:PF00202,Superfamily_domains:SSF53383 HIGH 1 SNV 1 1 PASS rs764832748 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 108760216 108760216 G T 1 0 0 0 0 0 1 0 0 5138 1024 36 2 2 ETNPPL 4 108760216 Nonsense_Mutation SNP G C3N-00551_T 5673685 108760216 81454339 179 15662 SEC24B 0 . GRCh38 4 109520403 109520403 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.2254A>G p.Thr752Ala p.T752A ENST00000504968 13/25 103 97 6 201 201 0 strelka-mutect SEC24B,missense_variant,p.Thr722Ala,ENST00000265175,NM_001318085.1,NM_006323.3;SEC24B,missense_variant,p.Thr752Ala,ENST00000504968,NM_001300813.1;SEC24B,missense_variant,p.Thr687Ala,ENST00000399100,NM_001042734.2; G ENST00000504968 Transcript missense_variant 2352/4066 2254/3897 752/1298 T/A Acc/Gcc 1 1 SEC24B HGNC HGNC:10704 protein_coding YES CCDS75179.1 ENSP00000428564 O95487 UPI000189A7A7 NM_001300813.1 tolerated(0.2) 13/25 hmmpanther:PTHR13803:SF7,hmmpanther:PTHR13803,Pfam_domain:PF04811,Gene3D:3.40.50.410,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 109520403 109520403 A G 1 0 0 0 0 1 0 0 0 14272 275 10 5 5 SEC24B 4 109520403 Missense_Mutation SNP A C3N-00551_T 760187 109520403 80694152 180 15663 RRH 0 . GRCh38 4 109844092 109844092 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.909G>C p.Arg303Ser p.R303S ENST00000317735 7/7 336 294 42 480 480 0 strelka-varscan-mutect RRH,missense_variant,p.Arg303Ser,ENST00000317735,NM_006583.2;LRIT3,upstream_gene_variant,,ENST00000594814,NM_198506.4; C ENST00000317735 Transcript missense_variant 943/1455 909/1014 303/337 R/S agG/agC 1 1 RRH HGNC HGNC:10450 protein_coding YES CCDS3687.1 ENSP00000314992 O14718 UPI000005043C NM_006583.2 tolerated(0.09) 7/7 hmmpanther:PTHR24240,hmmpanther:PTHR24240:SF77,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 109844092 109844092 G C 1 0 0 0 0 1 0 0 0 13934 1223 43 4 4 RRH 4 109844092 Missense_Mutation SNP G C3N-00551_T 323689 109844092 80370463 181 15664 LRIT3 0 . GRCh38 4 109870446 109870446 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1697G>A p.Cys566Tyr p.C566Y ENST00000594814 4/4 136 116 20 142 142 0 strelka-varscan-mutect LRIT3,missense_variant,p.Cys383Tyr,ENST00000327908,;LRIT3,missense_variant,p.Cys566Tyr,ENST00000594814,NM_198506.4; A ENST00000594814 Transcript missense_variant 1697/3566 1697/2040 566/679 C/Y tGc/tAc 1 1 LRIT3 HGNC HGNC:24783 protein_coding YES CCDS3688.3 ENSP00000469759 Q3SXY7 UPI0000F07E94 NM_198506.4 deleterious(0) 4/4 PROSITE_profiles:PS50853,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF236 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 109870446 109870446 G A 1 0 0 0 0 1 0 0 0 8844 1319 46 3 3 LRIT3 4 109870446 Missense_Mutation SNP G C3N-00551_T 26354 109870446 80344109 182 15665 ANK2 0 . GRCh38 4 113358035 113358035 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.9417G>A p.= p.R3139R ENST00000357077 38/46 468 411 57 580 580 0 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript synonymous_variant 9470/14196 9417/11874 3139/3957 R agG/agA 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 113358035 113358035 G A 1 0 0 0 0 0 0 0 1 721 1223 43 3 3 ANK2 4 113358035 Silent SNP G C3N-00551_T 3487589 113358035 76856520 183 15666 DCHS2 0 . GRCh38 4 154333056 154333056 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.1655T>A p.Leu552Gln p.L552Q ENST00000623607 9/25 168 143 25 159 159 0 strelka-varscan-mutect DCHS2,missense_variant,p.Leu552Gln,ENST00000357232,;DCHS2,missense_variant,p.Leu552Gln,ENST00000623607,NM_017639.3;DCHS2,missense_variant,p.Leu1051Gln,ENST00000339452,NM_001142552.1;DCHS2,non_coding_transcript_exon_variant,,ENST00000507542,;DCHS2,downstream_gene_variant,,ENST00000504580,;DCHS2,non_coding_transcript_exon_variant,,ENST00000624983,; T ENST00000623607 Transcript missense_variant 1655/8912 1655/8751 552/2916 L/Q cTg/cAg 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 deleterious(0) 9/25 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 154333056 154333056 A T 1 0 0 0 0 1 0 0 0 4091 188 7 4 4 DCHS2 4 154333056 Missense_Mutation SNP A C3N-00551_T 40975021 154333056 35881499 184 15667 GRIA2 0 . GRCh38 4 157341321 157341321 + Silent SNP C C A C3N-00551_T C3N-00551_N C C c.1902C>A p.= p.I634I ENST00000296526 12/16 243 218 25 275 275 0 strelka-varscan-mutect GRIA2,synonymous_variant,p.=,ENST00000296526,NM_000826.3;GRIA2,synonymous_variant,p.=,ENST00000393815,NM_001083620.1;GRIA2,synonymous_variant,p.=,ENST00000264426,NM_001083619.1;GRIA2,synonymous_variant,p.=,ENST00000507898,;GRIA2,upstream_gene_variant,,ENST00000510854,;GRIA2,synonymous_variant,p.=,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; A ENST00000296526 Transcript synonymous_variant 2227/5621 1902/2652 634/883 I atC/atA COSM281518,COSM281519 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 12/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,SMART_domains:SM00079,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 157341321 157341321 C A 1 0 0 0 0 0 0 0 1 6648 903 32 2 2 GRIA2 4 157341321 Silent SNP C C3N-00551_T 3008265 157341321 32873234 185 15668 TKTL2 0 . GRCh38 4 163472685 163472685 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.1050C>A p.= p.T350T ENST00000280605 1/1 116 100 16 219 219 0 strelka-varscan-mutect TKTL2,synonymous_variant,p.=,ENST00000280605,NM_032136.4; T ENST00000280605 Transcript synonymous_variant 1062/2654 1050/1881 350/626 T acC/acA 1 -1 TKTL2 HGNC HGNC:25313 protein_coding YES CCDS3805.1 ENSP00000280605 Q9H0I9 A0A140VKC2 UPI0000037C67 NM_032136.4 1/1 hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF49,Gene3D:3.40.50.970,Pfam_domain:PF02779,SMART_domains:SM00861,Superfamily_domains:SSF52518 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 163472685 163472685 G T 1 0 0 0 0 0 0 0 1 16379 987 35 2 2 TKTL2 4 163472685 Silent SNP G C3N-00551_T 6131364 163472685 26741870 186 15669 DDX60 0 . GRCh38 4 168267983 168267983 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2787G>T p.Glu929Asp p.E929D ENST00000393743 21/38 70 61 9 93 93 0 strelka-varscan-mutect DDX60,missense_variant,p.Glu929Asp,ENST00000393743,NM_017631.5;DDX60,upstream_gene_variant,,ENST00000505393,;DDX60,missense_variant,p.Glu20Asp,ENST00000513997,; A ENST00000393743 Transcript missense_variant,splice_region_variant 3079/6071 2787/5139 929/1712 E/D gaG/gaT 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 deleterious(0.03) 21/38 PROSITE_profiles:PS51192,Gene3D:3.40.50.300,SMART_domains:SM00487 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.60976 0.9999994 1 1 1 0 A 3 1 52 168267983 168267983 C A 1 0 0 0 0 1 0 0 0 4181 521 18 2 2 DDX60 4 168267983 Missense_Mutation SNP C C3N-00551_T 4795298 168267983 21946572 187 15670 ING2 0 . GRCh38 4 183510917 183510917 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.808A>T p.Thr270Ser p.T270S ENST00000302327 2/2 64 56 8 85 85 0 strelka-varscan-mutect ING2,missense_variant,p.Thr270Ser,ENST00000302327,NM_001564.3;ING2,downstream_gene_variant,,ENST00000412117,; T ENST00000302327 Transcript missense_variant 1010/1189 808/843 270/280 T/S Act/Tct 1 1 ING2 HGNC HGNC:6063 protein_coding YES CCDS3833.1 ENSP00000307183 Q9H160 UPI000003BC86 NM_001564.3 tolerated_low_confidence(0.18) 2/2 hmmpanther:PTHR10333,hmmpanther:PTHR10333:SF37 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.52363 1 1 1 1 0 T 3 4 52 183510917 183510917 A T 1 0 0 0 0 1 0 0 0 7638 391 14 4 4 ING2 4 183510917 Missense_Mutation SNP A C3N-00551_T 15242934 183510917 6703638 188 15671 CASP3 0 . GRCh38 4 184635340 184635340 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.132G>T p.Met44Ile p.M44I ENST00000308394 4/8 97 91 6 157 157 0 strelka-mutect CASP3,missense_variant,p.Met44Ile,ENST00000308394,NM_004346.3;CASP3,missense_variant,p.Met44Ile,ENST00000393585,;CASP3,missense_variant,p.Met44Ile,ENST00000523916,NM_032991.2;CASP3,missense_variant,p.Met44Ile,ENST00000517513,;CASP3,missense_variant,p.Met44Ile,ENST00000393588,;CASP3,missense_variant,p.Met44Ile,ENST00000447121,; A ENST00000308394 Transcript missense_variant 395/2673 132/834 44/277 M/I atG/atT 1 -1 CASP3 HGNC HGNC:1504 protein_coding YES CCDS3836.1 ENSP00000311032 P42574 UPI000000D90B NM_004346.3 tolerated(0.7) 4/8 PROSITE_profiles:PS50208,hmmpanther:PTHR10454:SF30,hmmpanther:PTHR10454,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129,Prints_domain:PR00376 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 184635340 184635340 C A 1 0 0 0 0 1 0 0 0 2372 594 21 2 2 CASP3 4 184635340 Missense_Mutation SNP C C3N-00551_T 1124423 184635340 5579215 189 15672 SLC6A19 0 . GRCh38 5 1216931 1216931 + Missense_Mutation SNP G G T rs550686902 C3N-00551_T C3N-00551_N G G c.1159G>T p.Ala387Ser p.A387S ENST00000304460 8/12 779 711 68 404 404 0 strelka-varscan-mutect SLC6A19,missense_variant,p.Ala387Ser,ENST00000304460,NM_001003841.2;SLC6A19,3_prime_UTR_variant,,ENST00000515652,; T ENST00000304460 Transcript missense_variant 1215/5174 1159/1905 387/634 A/S Gcc/Tcc rs550686902,COSM5484735 1 1 SLC6A19 HGNC HGNC:27960 protein_coding YES CCDS34130.1 ENSP00000305302 Q695T7 UPI0000401AF8 NM_001003841.2 tolerated(1) 8/12 Pfam_domain:PF00209,PROSITE_profiles:PS50267 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs550686902 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 1216931 1216931 G T 1 0 0 0 0 1 0 0 0 14965 1087 38 1 1 SLC6A19 5 1216931 Missense_Mutation SNP G C3N-00551_T 1216931 180321328 190 15673 IRX4 0 . GRCh38 5 1878041 1878041 + Silent SNP G G A C3N-00551_T C3N-00551_N G G c.1566C>T p.= p.D522D ENST00000613726 7/7 127 120 7 151 151 0 strelka-varscan-mutect IRX4,synonymous_variant,p.=,ENST00000505790,NM_001278634.1;IRX4,synonymous_variant,p.=,ENST00000613726,NM_001278635.1;IRX4,synonymous_variant,p.=,ENST00000622814,NM_001278633.1;IRX4,synonymous_variant,p.=,ENST00000513692,NM_001278632.1;IRX4,synonymous_variant,p.=,ENST00000231357,NM_016358.2;IRX4,downstream_gene_variant,,ENST00000511126,;IRX4,downstream_gene_variant,,ENST00000505938,;IRX4,3_prime_UTR_variant,,ENST00000508261,; A ENST00000613726 Transcript synonymous_variant 1789/2403 1566/1638 522/545 D gaC/gaT COSM5081483,COSM5081484 1 -1 IRX4 HGNC HGNC:6129 protein_coding YES CCDS75225.1 ENSP00000482393 P78413 UPI000020BF08 NM_001278635.1 7/7 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF16,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS rs1333692482 . 0 200 9 0 0 0 0 0 -13.25905 0.9999461 1 1 1 0 A 2 1 52 1878041 1878041 G A 1 0 0 0 0 0 0 0 1 7754 1136 40 1 1 IRX4 5 1878041 Silent SNP G C3N-00551_T 661110 1878041 179660218 191 15674 ICE1 0 . GRCh38 5 5461016 5461016 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.1682C>T p.Ser561Leu p.S561L ENST00000296564 13/19 348 328 20 202 202 0 strelka-varscan-mutect ICE1,missense_variant,p.Ser561Leu,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 1904/7927 1682/6801 561/2266 S/L tCa/tTa 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 tolerated(0.19) 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 5461016 5461016 C T 1 0 0 0 0 1 0 0 0 7384 838 29 3 3 ICE1 5 5461016 Missense_Mutation SNP C C3N-00551_T 3582975 5461016 176077243 192 15675 ICE1 0 . GRCh38 5 5473737 5473737 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.6402T>G p.Asp2134Glu p.D2134E ENST00000296564 16/19 159 147 12 166 166 0 strelka-varscan-mutect ICE1,missense_variant,p.Asp2134Glu,ENST00000296564,NM_015325.2; G ENST00000296564 Transcript missense_variant 6624/7927 6402/6801 2134/2266 D/E gaT/gaG 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0) 16/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS rs1425870309 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 5473737 5473737 T G 1 0 0 0 0 1 0 0 0 7384 1403 49 5 5 ICE1 5 5473737 Missense_Mutation SNP T C3N-00551_T 12721 5473737 176064522 193 15676 NSUN2 0 . GRCh38 5 6632679 6632679 + Silent SNP C C A rs745966593 C3N-00551_T C3N-00551_N C C c.174G>T p.= p.V58V ENST00000264670 2/19 336 315 21 224 224 0 strelka-varscan-mutect NSUN2,synonymous_variant,p.=,ENST00000264670,NM_017755.5;NSUN2,synonymous_variant,p.=,ENST00000506139,NM_001193455.1;SRD5A1,upstream_gene_variant,,ENST00000274192,NM_001047.2;SRD5A1,upstream_gene_variant,,ENST00000504286,;NSUN2,synonymous_variant,p.=,ENST00000504374,;SRD5A1,upstream_gene_variant,,ENST00000510531,;SRD5A1,upstream_gene_variant,,ENST00000513117,; A ENST00000264670 Transcript synonymous_variant 486/3303 174/2304 58/767 V gtG/gtT rs745966593 1 -1 NSUN2 HGNC HGNC:25994 protein_coding YES CCDS3869.1 ENSP00000264670 Q08J23 UPI000020BF2B NM_017755.5 2/19 hmmpanther:PTHR22808,hmmpanther:PTHR22808:SF11,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS rs745966593 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 6632679 6632679 C A 1 0 0 0 0 0 0 0 1 10741 697 25 2 2 NSUN2 5 6632679 Silent SNP C C3N-00551_T 1158942 6632679 174905580 194 15677 CMBL 0 . GRCh38 5 10282226 10282226 + Nonsense_Mutation SNP C C A rs769323134 C3N-00551_T C3N-00551_N C C c.529G>T p.Glu177Ter p.E177* ENST00000296658 5/6 242 165 77 244 243 1 strelka-varscan-mutect CMBL,stop_gained,p.Glu177Ter,ENST00000296658,NM_138809.3;CMBL,non_coding_transcript_exon_variant,,ENST00000503834,;CMBL,intron_variant,,ENST00000510532,;CMBL,downstream_gene_variant,,ENST00000506821,;CMBL,downstream_gene_variant,,ENST00000511963,; A ENST00000296658 Transcript stop_gained 950/2335 529/738 177/245 E/* Gaa/Taa rs769323134 1 -1 CMBL HGNC HGNC:25090 protein_coding YES CCDS3878.1 ENSP00000296658 Q96DG6 UPI00000411DF NM_138809.3 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF01738,hmmpanther:PTHR17630,hmmpanther:PTHR17630:SF44,Superfamily_domains:SSF53474 HIGH 1 SNV 1 1 PASS rs769323134 . 0 207 0 0 2 0 0 0 -20 0.9991804 1 1 1 0 A 4 1 52 10282226 10282226 C A 1 0 0 0 0 0 1 0 0 3349 835 29 2 2 CMBL 5 10282226 Nonsense_Mutation SNP C C3N-00551_T 3649547 10282226 171256033 195 15678 DNAH5 0 . GRCh38 5 13871624 13871624 + Nonsense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3538G>T p.Glu1180Ter p.E1180* ENST00000265104 23/79 376 210 166 285 285 0 strelka-varscan-mutect DNAH5,stop_gained,p.Glu1180Ter,ENST00000265104,NM_001369.2;CTB-51A17.1,intron_variant,,ENST00000637153,;CTB-51A17.1,intron_variant,,ENST00000503244,; A ENST00000265104 Transcript stop_gained 3643/15633 3538/13875 1180/4624 E/* Gag/Tag 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 23/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 13871624 13871624 C A 1 0 0 0 0 0 1 0 0 4419 922 32 2 2 DNAH5 5 13871624 Nonsense_Mutation SNP C C3N-00551_T 3589398 13871624 167666635 196 15679 TRIO 0 . GRCh38 5 14508384 14508384 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.9256A>G p.Lys3086Glu p.K3086E ENST00000344204 57/57 123 111 12 110 110 0 strelka-varscan-mutect TRIO,missense_variant,p.Lys3086Glu,ENST00000344204,NM_007118.2;TRIO,missense_variant,p.Lys585Glu,ENST00000344135,;TRIO,intron_variant,,ENST00000513206,;TRIO,intron_variant,,ENST00000620511,;TRIO,3_prime_UTR_variant,,ENST00000512070,;TRIO,downstream_gene_variant,,ENST00000508717,;TRIO,downstream_gene_variant,,ENST00000508283,; G ENST00000344204 Transcript missense_variant 9280/11100 9256/9294 3086/3097 K/E Aaa/Gaa 1 1 TRIO HGNC HGNC:12303 protein_coding YES CCDS3883.1 ENSP00000339299 O75962 UPI000034ECE6 NM_007118.2 deleterious_low_confidence(0.01) 57/57 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99992 1 1 1 1 0 G 3 3 52 14508384 14508384 A G 1 0 0 0 0 1 0 0 0 17049 363 13 5 5 TRIO 5 14508384 Missense_Mutation SNP A C3N-00551_T 636760 14508384 167029875 197 15680 FAM105A 0 . GRCh38 5 14608950 14608950 + Missense_Mutation SNP C C A rs142414423 C3N-00551_T C3N-00551_N C C c.830C>A p.Ser277Tyr p.S277Y ENST00000274217 7/8 213 192 21 209 209 0 strelka-varscan-mutect FAM105A,missense_variant,p.Ser277Tyr,ENST00000274217,NM_019018.2;FAM105A,upstream_gene_variant,,ENST00000506258,;FAM105A,downstream_gene_variant,,ENST00000513825,; A ENST00000274217 Transcript missense_variant 950/3597 830/1071 277/356 S/Y tCc/tAc rs142414423 1 1 FAM105A HGNC HGNC:25629 protein_coding YES CCDS3884.1 ENSP00000274217 Q9NUU6 UPI000004A036 NM_019018.2 deleterious(0) 7/8 Pfam_domain:PF16218,Prints_domain:PR02055,hmmpanther:PTHR33662,hmmpanther:PTHR33662:SF1 MODERATE 1 SNV 1 1 PASS rs142414423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 14608950 14608950 C A 1 0 0 0 0 1 0 0 0 5255 855 30 2 2 FAM105A 5 14608950 Missense_Mutation SNP C C3N-00551_T 100566 14608950 166929309 198 15681 PRDM9 0 . GRCh38 5 23522668 23522668 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.665C>A p.Pro222His p.P222H ENST00000296682 8/11 389 307 82 489 489 0 strelka-varscan-mutect PRDM9,missense_variant,p.Pro222His,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Pro163His,ENST00000635252,; A ENST00000296682 Transcript missense_variant 847/3691 665/2685 222/894 P/H cCt/cAt 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 8/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Pfam_domain:PF00856 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 23522668 23522668 C A 1 0 0 0 0 1 0 0 0 12595 681 24 2 2 PRDM9 5 23522668 Missense_Mutation SNP C C3N-00551_T 8913718 23522668 158015591 199 15682 ADAMTS12 0 . GRCh38 5 33576759 33576759 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3267G>T p.Gln1089His p.Q1089H ENST00000504830 19/24 321 208 113 372 370 2 strelka-varscan-mutect ADAMTS12,missense_variant,p.Gln1089His,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Gln1004His,ENST00000352040,;ADAMTS12,downstream_gene_variant,,ENST00000504582,; A ENST00000504830 Transcript missense_variant 3603/8774 3267/4785 1089/1594 Q/H caG/caT 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.17) 19/24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 33576759 33576759 C A 1 0 0 0 0 1 0 0 0 301 796 28 2 2 ADAMTS12 5 33576759 Missense_Mutation SNP C C3N-00551_T 10054091 33576759 147961500 200 15683 BRIX1 0 . GRCh38 5 34925385 34925385 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.952A>G p.Ile318Val p.I318V ENST00000336767 10/10 335 309 26 365 364 1 strelka-varscan-mutect BRIX1,missense_variant,p.Ile318Val,ENST00000336767,NM_018321.3;DNAJC21,upstream_gene_variant,,ENST00000382021,NM_194283.3;DNAJC21,upstream_gene_variant,,ENST00000342382,NM_001012339.2;BRIX1,downstream_gene_variant,,ENST00000506023,;BRIX1,non_coding_transcript_exon_variant,,ENST00000515798,;BRIX1,downstream_gene_variant,,ENST00000510834,;BRIX1,downstream_gene_variant,,ENST00000510960,; G ENST00000336767 Transcript missense_variant 1315/1926 952/1062 318/353 I/V Ata/Gta 1 1 BRIX1 HGNC HGNC:24170 protein_coding YES CCDS34143.1 ENSP00000338862 Q8TDN6 UPI000007186B NM_018321.3 tolerated(0.28) 10/10 hmmpanther:PTHR13634:SF0,hmmpanther:PTHR13634 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 34925385 34925385 A G 1 0 0 0 0 1 0 0 0 1689 101 4 5 5 BRIX1 5 34925385 Missense_Mutation SNP A C3N-00551_T 1348626 34925385 146612874 201 15684 UGT3A1 0 . GRCh38 5 35957290 35957290 + Missense_Mutation SNP G G T rs753596965 C3N-00551_T C3N-00551_N G G c.973C>A p.Gln325Lys p.Q325K ENST00000274278 5/7 389 365 24 419 419 0 strelka-varscan-mutect UGT3A1,missense_variant,p.Gln325Lys,ENST00000274278,NM_152404.3;UGT3A1,missense_variant,p.Gln325Lys,ENST00000503189,;UGT3A1,missense_variant,p.Gln291Lys,ENST00000507113,;UGT3A1,downstream_gene_variant,,ENST00000625798,NM_001171873.1;UGT3A1,non_coding_transcript_exon_variant,,ENST00000513233,;UGT3A1,3_prime_UTR_variant,,ENST00000515801,; T ENST00000274278 Transcript missense_variant 1331/5122 973/1572 325/523 Q/K Caa/Aaa rs753596965 1 -1 UGT3A1 HGNC HGNC:26625 protein_coding YES CCDS3913.1 ENSP00000274278 Q6NUS8 A8K444 UPI000003C38B NM_152404.3 deleterious(0.01) 5/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF208,Gene3D:3.40.50.2000,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs753596965 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 35957290 35957290 G T 1 0 0 0 0 1 0 0 0 17487 1299 45 2 2 UGT3A1 5 35957290 Missense_Mutation SNP G C3N-00551_T 1031905 35957290 145580969 202 15685 EGFLAM 0 . GRCh38 5 38435235 38435235 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2265C>A p.Phe755Leu p.F755L ENST00000354891 16/23 161 151 10 155 155 0 strelka-varscan-mutect EGFLAM,missense_variant,p.Phe755Leu,ENST00000322350,NM_152403.3;EGFLAM,missense_variant,p.Phe755Leu,ENST00000354891,NM_001205301.1;EGFLAM,missense_variant,p.Phe521Leu,ENST00000336740,NM_182798.2;EGFLAM,missense_variant,p.Phe121Leu,ENST00000397202,; A ENST00000354891 Transcript missense_variant 2611/3963 2265/3054 755/1017 F/L ttC/ttA 1 1 EGFLAM HGNC HGNC:26810 protein_coding YES CCDS56363.1 ENSP00000346964 Q63HQ2 UPI000022C806 NM_001205301.1 deleterious(0.02) 16/23 PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 38435235 38435235 C A 1 0 0 0 0 1 0 0 0 4802 825 29 2 2 EGFLAM 5 38435235 Missense_Mutation SNP C C3N-00551_T 2477945 38435235 143103024 203 15686 MROH2B 0 . GRCh38 5 41018913 41018913 + Silent SNP G G T C3N-00551_T C3N-00551_N G G c.2547C>A p.= p.G849G ENST00000399564 25/42 189 146 43 188 188 0 strelka-mutect MROH2B,synonymous_variant,p.=,ENST00000399564,NM_173489.4;MROH2B,synonymous_variant,p.=,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,; T ENST00000399564 Transcript synonymous_variant 2998/5239 2547/4758 849/1585 G ggC/ggA COSM5518582 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 25/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 1 LOW 1 SNV 1 1 1 PASS rs1268829035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 41018913 41018913 G T 1 0 0 0 0 0 0 0 1 9745 1190 42 2 2 MROH2B 5 41018913 Silent SNP G C3N-00551_T 2583678 41018913 140519346 204 15687 ZSWIM6 0 . GRCh38 5 61332446 61332446 + Silent SNP G G T rs571004627 C3N-00551_T C3N-00551_N G G c.174G>T p.= p.G58G ENST00000252744 1/14 20 14 6 21 21 0 strelka-varscan-mutect ZSWIM6,synonymous_variant,p.=,ENST00000252744,NM_020928.1; T ENST00000252744 Transcript synonymous_variant 174/5501 174/3648 58/1215 G ggG/ggT rs571004627 1 1 ZSWIM6 HGNC HGNC:29316 protein_coding YES CCDS47215.1 ENSP00000252744 Q9HCJ5 UPI0001837EA2 NM_020928.1 1/14 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs571004627 . 0 206 3 0 0 0 0 0 -17.78228 1 1 1 1 0 T 2 4 52 61332446 61332446 G T 1 0 0 0 0 0 0 0 1 18846 1219 43 2 2 ZSWIM6 5 61332446 Silent SNP G C3N-00551_T 20313533 61332446 120205813 205 15688 CCNB1 0 . GRCh38 5 69175062 69175062 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.891G>T p.= p.L297L ENST00000256442 6/9 230 163 67 282 281 1 strelka-varscan-mutect CCNB1,synonymous_variant,p.=,ENST00000256442,NM_031966.3;CCNB1,synonymous_variant,p.=,ENST00000506572,;CCNB1,synonymous_variant,p.=,ENST00000505500,;CCNB1,synonymous_variant,p.=,ENST00000508407,;CCNB1,synonymous_variant,p.=,ENST00000507798,;CCNB1,downstream_gene_variant,,ENST00000503507,;CCNB1,upstream_gene_variant,,ENST00000513102,; T ENST00000256442 Transcript synonymous_variant 1144/2169 891/1302 297/433 L ctG/ctT 1 1 CCNB1 HGNC HGNC:1579 protein_coding YES CCDS3997.1 ENSP00000256442 P14635 UPI00001275A9 NM_031966.3 6/9 hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF193,Pfam_domain:PF00134,Gene3D:1.10.472.10,PIRSF_domain:PIRSF001771,Superfamily_domains:SSF47954 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 69175062 69175062 G T 1 0 0 0 0 0 0 0 1 2610 1335 47 2 2 CCNB1 5 69175062 Silent SNP G C3N-00551_T 7842616 69175062 112363197 206 15689 OCLN 0 . GRCh38 5 69514022 69514025 + Frame_Shift_Del DEL AAGA AAGA - novel C3N-00551_T C3N-00551_N AAGA AAGA c.808_811delAAGA p.Lys270TrpfsTer61 p.K270Wfs*61 ENST00000355237 4/9 355 306 49 410 410 0 sindel-varindel-pindel OCLN,frameshift_variant,p.Lys270TrpfsTer61,ENST00000355237,NM_002538.3;OCLN,frameshift_variant,p.Lys19TrpfsTer61,ENST00000538151,NM_001205255.1;OCLN,frameshift_variant,p.Lys270TrpfsTer61,ENST00000396442,NM_001205254.1; - ENST00000355237 Transcript frameshift_variant 1240-1243/6438 804-807/1569 268-269/522 RR/X cgAAGA/cg 1 1 OCLN HGNC HGNC:8104 protein_coding YES CCDS4006.1 ENSP00000347379 Q16625 UPI00000341F0 NM_002538.3 4/9 PROSITE_profiles:PS51225,hmmpanther:PTHR23288:SF4,hmmpanther:PTHR23288,PIRSF_domain:PIRSF005993,Superfamily_domains:SSF103473 HIGH 1 deletion 1 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 69514022 69514022 AAGA - 1 0 1 0 1 0 0 0 0 10897 233 9 0 0 OCLN 5 69514022 Frame_Shift_Del DEL AAGA C3N-00551_T 338960 69514022 112024237 207 15690 UTP15 0 . GRCh38 5 73579096 73579096 + Missense_Mutation SNP C C T rs761103496 C3N-00551_T C3N-00551_N C C c.1226C>T p.Ala409Val p.A409V ENST00000296792 11/13 212 192 20 296 296 0 strelka-varscan-mutect UTP15,missense_variant,p.Ala219Val,ENST00000543251,NM_001284431.1;UTP15,missense_variant,p.Ala409Val,ENST00000296792,NM_032175.3;UTP15,missense_variant,p.Ala436Val,ENST00000509005,;UTP15,missense_variant,p.Ala390Val,ENST00000508491,NM_001284430.1;UTP15,downstream_gene_variant,,ENST00000512550,; T ENST00000296792 Transcript missense_variant 1481/3687 1226/1557 409/518 A/V gCg/gTg rs761103496,COSM1069948 1 1 UTP15 HGNC HGNC:25758 protein_coding YES CCDS34186.1 ENSP00000296792 Q8TED0 UPI000020CADC NM_032175.3 deleterious(0) 11/13 hmmpanther:PTHR19924:SF26,hmmpanther:PTHR19924,Pfam_domain:PF09384 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761103496 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 73579096 73579096 C T 1 0 0 0 0 1 0 0 0 17640 768 27 1 1 UTP15 5 73579096 Missense_Mutation SNP C C3N-00551_T 4065074 73579096 107959163 208 15691 PDE8B 0 . GRCh38 5 77409051 77409051 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.1524G>A p.= p.L508L ENST00000264917 14/22 368 280 88 517 517 0 strelka-varscan-mutect PDE8B,synonymous_variant,p.=,ENST00000264917,NM_003719.3;PDE8B,synonymous_variant,p.=,ENST00000340978,NM_001029854.2;PDE8B,synonymous_variant,p.=,ENST00000346042,NM_001029851.2;PDE8B,synonymous_variant,p.=,ENST00000342343,NM_001029853.2;PDE8B,intron_variant,,ENST00000333194,NM_001029852.2;PDE8B,upstream_gene_variant,,ENST00000505283,; A ENST00000264917 Transcript synonymous_variant 1569/5956 1524/2658 508/885 L ctG/ctA 1 1 PDE8B HGNC HGNC:8794 protein_coding YES CCDS4037.1 ENSP00000264917 O95263 UPI0000001BBE NM_003719.3 14/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF98 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 77409051 77409051 G A 1 0 0 0 0 0 0 0 1 11742 1277 45 3 3 PDE8B 5 77409051 Silent SNP G C3N-00551_T 3829955 77409051 104129208 209 15692 MEF2C 0 . GRCh38 5 88722718 88722718 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.1338A>T p.= p.R446R ENST00000340208 12/12 309 266 43 402 402 0 strelka-varscan-mutect MEF2C,synonymous_variant,p.=,ENST00000504921,NM_001193350.1,NM_002397.4;MEF2C,synonymous_variant,p.=,ENST00000424173,NM_001131005.2;MEF2C,synonymous_variant,p.=,ENST00000340208,NM_001193347.1;MEF2C,synonymous_variant,p.=,ENST00000637481,NM_001308002.1;MEF2C,synonymous_variant,p.=,ENST00000636998,;MEF2C,synonymous_variant,p.=,ENST00000625674,;MEF2C,synonymous_variant,p.=,ENST00000437473,;MEF2C,synonymous_variant,p.=,ENST00000625585,;MEF2C,synonymous_variant,p.=,ENST00000510942,;MEF2C,synonymous_variant,p.=,ENST00000514028,;MEF2C,synonymous_variant,p.=,ENST00000637732,;MEF2C,synonymous_variant,p.=,ENST00000629612,;MEF2C,synonymous_variant,p.=,ENST00000514015,;MEF2C,synonymous_variant,p.=,ENST00000636294,;MEF2C,synonymous_variant,p.=,ENST00000627659,;MEF2C,synonymous_variant,p.=,ENST00000508569,;MEF2C,synonymous_variant,p.=,ENST00000503554,;MEF2C,synonymous_variant,p.=,ENST00000628656,NM_001193348.1;MEF2C,synonymous_variant,p.=,ENST00000626391,NM_001193349.1;MEF2C,3_prime_UTR_variant,,ENST00000506554,;MEF2C,3_prime_UTR_variant,,ENST00000627717,;MEF2C,3_prime_UTR_variant,,ENST00000627170,;CTC-467M3.1,non_coding_transcript_exon_variant,,ENST00000510274,;MEF2C,non_coding_transcript_exon_variant,,ENST00000636143,;MEF2C,downstream_gene_variant,,ENST00000510980,; A ENST00000340208 Transcript synonymous_variant 1715/6192 1338/1452 446/483 R cgA/cgT 1 -1 MEF2C HGNC HGNC:6996 protein_coding YES CCDS54878.1 ENSP00000340874 Q06413 UPI0000D9B539 NM_001193347.1 12/12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 88722718 88722718 T A 1 0 0 0 0 0 0 0 1 9397 1538 54 4 4 MEF2C 5 88722718 Silent SNP T C3N-00551_T 11313667 88722718 92815541 210 15693 ADGRV1 0 . GRCh38 5 90802835 90802835 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.14614G>T p.Ala4872Ser p.A4872S ENST00000405460 71/90 138 115 23 158 158 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Ala4872Ser,ENST00000405460,NM_032119.3;ADGRV1,missense_variant,p.Ala533Ser,ENST00000425867,;ADGRV1,upstream_gene_variant,,ENST00000513828,; T ENST00000405460 Transcript missense_variant 14710/19338 14614/18921 4872/6306 A/S Gca/Tca 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 deleterious(0.05) 71/90 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 90802835 90802835 G T 1 0 0 0 0 1 0 0 0 379 971 34 2 2 ADGRV1 5 90802835 Missense_Mutation SNP G C3N-00551_T 2080117 90802835 90735424 211 15694 MEGF10 0 . GRCh38 5 127420151 127420151 + Missense_Mutation SNP G G C rs758236594 C3N-00551_T C3N-00551_N G G c.1534G>C p.Gly512Arg p.G512R ENST00000274473 13/26 178 146 32 225 225 0 strelka-varscan-mutect MEGF10,missense_variant,p.Gly512Arg,ENST00000274473,NM_032446.2;MEGF10,missense_variant,p.Gly512Arg,ENST00000503335,NM_001256545.1;MEGF10,missense_variant,p.Gly512Arg,ENST00000508365,NM_001308121.1;MEGF10,missense_variant,p.Gly512Arg,ENST00000418761,;MEGF10,upstream_gene_variant,,ENST00000506709,;MEGF10,downstream_gene_variant,,ENST00000515002,; C ENST00000274473 Transcript missense_variant 1801/7594 1534/3423 512/1140 G/R Ggg/Cgg rs758236594 1 1 MEGF10 HGNC HGNC:29634 protein_coding YES CCDS4142.1 ENSP00000274473 Q96KG7 UPI000006F868 NM_032446.2 deleterious(0) 13/26 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,SMART_domains:SM00180,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs758236594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 127420151 127420151 G C 1 0 0 0 0 1 0 0 0 9400 1116 39 4 4 MEGF10 5 127420151 Missense_Mutation SNP G C3N-00551_T 36617316 127420151 54118108 212 15695 SOWAHA 0 . GRCh38 5 132814841 132814841 + Missense_Mutation SNP G G A rs763068818 C3N-00551_T C3N-00551_N G G c.1220G>A p.Arg407His p.R407H ENST00000378693 1/1 45 36 9 48 48 0 strelka-varscan-mutect SOWAHA,missense_variant,p.Arg407His,ENST00000378693,NM_175873.5;AC004775.5,downstream_gene_variant,,ENST00000607389,; A ENST00000378693 Transcript missense_variant 1255/3211 1220/1650 407/549 R/H cGt/cAt rs763068818,COSM1433082 1 1 SOWAHA HGNC HGNC:27033 protein_coding YES CCDS43361.1 ENSP00000367965 Q2M3V2 UPI000156802F NM_175873.5 tolerated(0.11) 1/1 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR14491,hmmpanther:PTHR14491:SF2,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 0,1 MODERATE 1 SNV 0,1 1 PASS rs763068818 . 0 207 3 0 0 0 0 0 -19.99756 1 1 1 1 0 A 3 1 52 132814841 132814841 G A 1 0 0 0 0 1 0 0 0 15262 1145 40 1 1 SOWAHA 5 132814841 Missense_Mutation SNP G C3N-00551_T 5394690 132814841 48723418 213 15696 PCDHA10 0 . GRCh38 5 140857383 140857383 + Silent SNP C C A rs781834606 C3N-00551_T C3N-00551_N C C c.1335C>A p.= p.A445A ENST00000307360 1/4 490 405 85 704 704 0 strelka-varscan-mutect PCDHA10,synonymous_variant,p.=,ENST00000562220,NM_031859.2;PCDHA10,synonymous_variant,p.=,ENST00000307360,NM_018901.3;PCDHA10,synonymous_variant,p.=,ENST00000506939,NM_031860.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; A ENST00000307360 Transcript synonymous_variant 1335/5254 1335/2847 445/948 A gcC/gcA rs781834606,COSM3851113,COSM3851114,COSM3851115 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 1/4 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs781834606 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 140857383 140857383 C A 1 0 0 0 0 0 0 0 1 11607 639 23 1 1 PCDHA10 5 140857383 Silent SNP C C3N-00551_T 8042542 140857383 40680876 214 15697 JAKMIP2 0 . GRCh38 5 147628818 147628818 + Splice_Site SNP T T C novel C3N-00551_T C3N-00551_N T T c.1930-2A>G p.X644_splice ENST00000616793 107 90 17 128 128 0 strelka-varscan-mutect JAKMIP2,splice_acceptor_variant,,ENST00000616793,NM_001270941.1;JAKMIP2,splice_acceptor_variant,,ENST00000265272,NM_014790.4;JAKMIP2,splice_acceptor_variant,,ENST00000507386,NM_001270934.1;JAKMIP2,splice_acceptor_variant,,ENST00000333010,NM_001282282.1;JAKMIP2-AS1,intron_variant,,ENST00000626945,;JAKMIP2-AS1,intron_variant,,ENST00000627433,;JAKMIP2-AS1,intron_variant,,ENST00000630514,;JAKMIP2-AS1,upstream_gene_variant,,ENST00000630801,;JAKMIP2,downstream_gene_variant,,ENST00000504845,; C ENST00000616793 Transcript splice_acceptor_variant -/9272 1930/2463 644/820 1 -1 JAKMIP2 HGNC HGNC:29067 protein_coding YES CCDS75352.1 ENSP00000479248 Q96AA8 UPI0000E5AC9B NM_001270941.1 15/21 HIGH SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 5 2 52 147628818 147628818 T C 1 0 0 0 0 0 0 1 0 7854 1594 55 5 5 JAKMIP2 5 147628818 Splice_Site SNP T C3N-00551_T 6771435 147628818 33909441 215 15698 ATP10B 0 . GRCh38 5 160632352 160632352 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1397C>A p.Thr466Asn p.T466N ENST00000327245 13/26 134 113 21 161 160 1 strelka-varscan-mutect ATP10B,missense_variant,p.Thr466Asn,ENST00000327245,NM_025153.2;ATP10B,missense_variant,p.Thr74Asn,ENST00000520108,;CTC-348L5.1,intron_variant,,ENST00000523598,;ATP10B,downstream_gene_variant,,ENST00000326831,;ATP10B,downstream_gene_variant,,ENST00000517802,;ATP10B,downstream_gene_variant,,ENST00000521033,; T ENST00000327245 Transcript missense_variant 2244/7566 1397/4386 466/1461 T/N aCc/aAc COSM5615495 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0.03) 13/26 hmmpanther:PTHR24092:SF79,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Gene3D:3.40.1110.10 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 52 160632352 160632352 G T 1 0 0 0 0 1 0 0 0 1269 1261 44 2 2 ATP10B 5 160632352 Missense_Mutation SNP G C3N-00551_T 13003534 160632352 20905907 216 15699 GABRA6 0 . GRCh38 5 161689041 161689041 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.318G>T p.Leu106Phe p.L106F ENST00000274545 4/9 318 270 48 487 486 1 strelka-varscan-mutect GABRA6,missense_variant,p.Leu96Phe,ENST00000523217,;GABRA6,missense_variant,p.Leu106Phe,ENST00000274545,NM_000811.2;GABRA6,missense_variant,p.Leu46Phe,ENST00000520000,;GABRA6,missense_variant,p.Leu1Phe,ENST00000523691,;GABRA6,missense_variant,p.Leu53Phe,ENST00000517823,;RP11-348M17.2,intron_variant,,ENST00000521984,;GABRA6,downstream_gene_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,non_coding_transcript_exon_variant,,ENST00000524220,;GABRA6,upstream_gene_variant,,ENST00000521520,; T ENST00000274545 Transcript missense_variant 751/2128 318/1362 106/453 L/F ttG/ttT COSM3613553 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 tolerated(0.38) 4/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR01079 1 MODERATE 1 SNV 1 1 1 PASS rs1208616228 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 161689041 161689041 G T 1 0 0 0 0 1 0 0 0 6036 1281 45 2 2 GABRA6 5 161689041 Missense_Mutation SNP G C3N-00551_T 1056689 161689041 19849218 217 15700 C5orf58 0 . GRCh38 5 170246034 170246034 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.230A>G p.Glu77Gly p.E77G ENST00000593851 4/4 175 162 13 194 194 0 strelka-varscan-mutect C5orf58,missense_variant,p.Glu56Gly,ENST00000521850,;C5orf58,missense_variant,p.Glu77Gly,ENST00000593851,NM_001102609.1;C5orf58,missense_variant,p.Glu56Gly,ENST00000421269,;C5orf58,intron_variant,,ENST00000524171,;C5orf58,intron_variant,,ENST00000517575,;LCP2,downstream_gene_variant,,ENST00000046794,NM_005565.3;LCP2,downstream_gene_variant,,ENST00000628092,;LCP2,downstream_gene_variant,,ENST00000521416,;C5orf58,non_coding_transcript_exon_variant,,ENST00000518395,;LCP2,downstream_gene_variant,,ENST00000520322,; G ENST00000593851 Transcript missense_variant 313/509 230/309 77/102 E/G gAa/gGa 1 1 C5orf58 HGNC HGNC:37272 protein_coding YES ENSP00000490013 C9J3I9 UPI0000160413 NM_001102609.1 deleterious(0) 4/4 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 170246034 170246034 A G 1 0 0 0 0 1 0 0 0 2108 246 9 5 5 C5orf58 5 170246034 Missense_Mutation SNP A C3N-00551_T 8556993 170246034 11292225 218 15701 KCNMB1 0 . GRCh38 5 170378934 170378934 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.346G>T p.Ala116Ser p.A116S ENST00000274629 4/4 139 114 25 194 194 0 varscan-mutect KCNMB1,missense_variant,p.Ala116Ser,ENST00000274629,NM_004137.3;KCNIP1,intron_variant,,ENST00000377360,NM_001034838.2;KCNMB1,downstream_gene_variant,,ENST00000521859,;KCNIP1,intron_variant,,ENST00000518527,;KCNIP1,intron_variant,,ENST00000517344,; A ENST00000274629 Transcript missense_variant 789/5052 346/576 116/191 A/S Gcc/Tcc 1 -1 KCNMB1 HGNC HGNC:6285 protein_coding YES CCDS4373.1 ENSP00000274629 Q16558 UPI0000000DBA NM_004137.3 tolerated(0.17) 4/4 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10258:SF1,hmmpanther:PTHR10258,Pfam_domain:PF03185 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 170378934 170378934 C A 1 0 0 0 0 1 0 0 0 7991 739 26 2 2 KCNMB1 5 170378934 Missense_Mutation SNP C C3N-00551_T 132900 170378934 11159325 219 15702 NEURL1B 0 . GRCh38 5 172683827 172683827 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.986G>T p.Arg329Leu p.R329L ENST00000369800 3/5 22 14 8 39 39 0 strelka-varscan-mutect NEURL1B,missense_variant,p.Arg329Leu,ENST00000369800,NM_001142651.1;NEURL1B,missense_variant,p.Arg147Leu,ENST00000522853,;NEURL1B,intron_variant,,ENST00000520919,NM_001308178.1; T ENST00000369800 Transcript missense_variant 1127/6424 986/1668 329/555 R/L cGt/cTt 1 1 NEURL1B HGNC HGNC:35422 protein_coding YES CCDS47342.1 ENSP00000358815 A8MQ27 UPI0000D6E5EA NM_001142651.1 tolerated(0.05) 3/5 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,Pfam_domain:PF07177,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS rs1372646676 . 0 201 9 0 0 0 0 0 -19.9985 0.9999989 1 1 1 0 T 3 4 52 172683827 172683827 G T 1 0 0 0 0 1 0 0 0 10381 1145 40 1 1 NEURL1B 5 172683827 Missense_Mutation SNP G C3N-00551_T 2304893 172683827 8854432 220 15703 LRRC16A 0 . GRCh38 6 25500206 25500206 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1366G>T p.Gly456Trp p.G456W ENST00000329474 17/37 239 215 24 305 305 0 strelka-varscan-mutect LRRC16A,missense_variant,p.Gly456Trp,ENST00000329474,NM_001173977.1,NM_017640.5;LRRC16A,missense_variant,p.Gly46Trp,ENST00000635618,; T ENST00000329474 Transcript missense_variant 1734/5431 1366/4116 456/1371 G/W Ggg/Tgg 1 1 LRRC16A HGNC HGNC:21581 protein_coding YES CCDS54973.1 ENSP00000331983 Q5VZK9 UPI00004588AB NM_001173977.1,NM_017640.5 deleterious(0) 17/37 Gene3D:3.80.10.10,hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF39,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 25500206 25500206 G T 1 0 0 0 0 1 0 0 0 8867 1000 35 2 2 LRRC16A 6 25500206 Missense_Mutation SNP G C3N-00551_T 25500206 145305773 221 15704 SLC17A2 0 . GRCh38 6 25918543 25918543 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.593G>T p.Cys198Phe p.C198F ENST00000377850 6/12 259 238 21 288 288 0 strelka-varscan-mutect SLC17A2,missense_variant,p.Cys198Phe,ENST00000377850,NM_001286123.1;SLC17A2,missense_variant,p.Cys198Phe,ENST00000360488,NM_005835.3,NM_001286125.1;SLC17A2,missense_variant,p.Cys198Phe,ENST00000265425,; A ENST00000377850 Transcript missense_variant 1126/2524 593/1437 198/478 C/F tGt/tTt 1 -1 SLC17A2 HGNC HGNC:10930 protein_coding YES CCDS69060.1 ENSP00000367081 O00624 UPI000052BFEE NM_001286123.1 deleterious(0.03) 6/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF193,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 25918543 25918543 C A 1 0 0 0 0 1 0 0 0 14682 478 17 2 2 SLC17A2 6 25918543 Missense_Mutation SNP C C3N-00551_T 418337 25918543 144887436 222 15705 SLC17A2 0 . GRCh38 6 25921066 25921066 + Missense_Mutation SNP T T C rs776445761 C3N-00551_T C3N-00551_N T T c.502A>G p.Ile168Val p.I168V ENST00000377850 5/12 238 213 25 345 345 0 strelka-varscan-mutect SLC17A2,missense_variant,p.Ile168Val,ENST00000377850,NM_001286123.1;SLC17A2,missense_variant,p.Ile168Val,ENST00000360488,NM_005835.3,NM_001286125.1;SLC17A2,missense_variant,p.Ile168Val,ENST00000265425,; C ENST00000377850 Transcript missense_variant 1035/2524 502/1437 168/478 I/V Att/Gtt rs776445761 1 -1 SLC17A2 HGNC HGNC:10930 protein_coding YES CCDS69060.1 ENSP00000367081 O00624 UPI000052BFEE NM_001286123.1 tolerated(0.07) 5/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF193,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS rs776445761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 25921066 25921066 T C 1 0 0 0 0 1 0 0 0 14682 1406 49 5 5 SLC17A2 6 25921066 Missense_Mutation SNP T C3N-00551_T 2523 25921066 144884913 223 15706 BTN1A1 0 . GRCh38 6 26508840 26508840 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.1247C>A p.Ala416Glu p.A416E ENST00000244513 7/7 188 158 30 179 179 0 strelka-varscan-mutect BTN1A1,missense_variant,p.Ala416Glu,ENST00000244513,NM_001732.2;BTN1A1,missense_variant,p.Ala416Glu,ENST00000613186,; A ENST00000244513 Transcript missense_variant 1313/2895 1247/1581 416/526 A/E gCa/gAa COSM5258622 1 1 BTN1A1 HGNC HGNC:1135 protein_coding YES CCDS4614.1 ENSP00000244513 Q13410 UPI000006E521 NM_001732.2 tolerated(0.45) 7/7 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF47,Low_complexity_(Seg):seg,SMART_domains:SM00449,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 26508840 26508840 C A 1 0 0 0 0 1 0 0 0 1735 710 25 2 2 BTN1A1 6 26508840 Missense_Mutation SNP C C3N-00551_T 587774 26508840 144297139 224 15707 HIST1H2AK 0 . GRCh38 6 27838161 27838161 + Missense_Mutation SNP G G A rs781034322 C3N-00551_T C3N-00551_N G G c.179C>T p.Thr60Ile p.T60I ENST00000618958 1/1 207 191 16 232 232 0 strelka-varscan-mutect HIST1H2AK,missense_variant,p.Thr60Ile,ENST00000618958,NM_003510.2;HIST1H2BN,5_prime_UTR_variant,,ENST00000612898,NM_003520.3;HIST1H2BN,upstream_gene_variant,,ENST00000606613,;HIST1H2BN,upstream_gene_variant,,ENST00000396980,;HIST1H2BN,upstream_gene_variant,,ENST00000449538,; A ENST00000618958 Transcript missense_variant 179/393 179/393 60/130 T/I aCc/aTc rs781034322 1 -1 HIST1H2AK HGNC HGNC:4726 protein_coding YES CCDS4632.1 ENSP00000482431 P0C0S8 A4FTV9 UPI0000000E01 NM_003510.2 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00620,hmmpanther:PTHR23430,SMART_domains:SM00414,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS rs781034322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 27838161 27838161 G A 1 0 0 0 0 1 0 0 0 7025 1261 44 3 3 HIST1H2AK 6 27838161 Missense_Mutation SNP G C3N-00551_T 1329321 27838161 142967818 225 15708 HIST1H1B 0 . GRCh38 6 27867274 27867274 + Missense_Mutation SNP C C T rs760223590 C3N-00551_T C3N-00551_N C C c.256G>A p.Gly86Ser p.G86S ENST00000331442 1/1 420 359 61 445 445 0 strelka-varscan-mutect HIST1H1B,missense_variant,p.Gly86Ser,ENST00000331442,NM_005322.2;HIST1H2BN,downstream_gene_variant,,ENST00000396980,;HIST1H3I,downstream_gene_variant,,ENST00000616365,NM_003533.2;HIST1H2AL,downstream_gene_variant,,ENST00000613174,NM_003511.2;HIST1H2BPS2,upstream_gene_variant,,ENST00000402707,; T ENST00000331442 Transcript missense_variant 256/681 256/681 86/226 G/S Ggc/Agc rs760223590 1 -1 HIST1H1B HGNC HGNC:4719 protein_coding YES CCDS4635.1 ENSP00000330074 P16401 UPI0000001BDA NM_005322.2 tolerated(0.06) 1/1 PROSITE_profiles:PS51504,hmmpanther:PTHR11467:SF24,hmmpanther:PTHR11467,Pfam_domain:PF00538,Gene3D:1.10.10.10,SMART_domains:SM00526,Superfamily_domains:SSF46785,Prints_domain:PR00624 MODERATE 1 SNV 1 PASS rs760223590 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 27867274 27867274 C T 1 0 0 0 0 1 0 0 0 7011 623 22 3 3 HIST1H1B 6 27867274 Missense_Mutation SNP C C3N-00551_T 29113 27867274 142938705 226 15709 BAG6 0 . GRCh38 6 31643933 31643933 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.1623G>T p.= p.V541V ENST00000375964 13/25 161 144 17 234 234 0 strelka-varscan-mutect BAG6,synonymous_variant,p.=,ENST00000375964,NM_004639.3;BAG6,synonymous_variant,p.=,ENST00000211379,NM_080703.2,NM_080702.2;BAG6,synonymous_variant,p.=,ENST00000375976,NM_001098534.1;BAG6,synonymous_variant,p.=,ENST00000362049,NM_001199698.1;BAG6,synonymous_variant,p.=,ENST00000439687,NM_001199697.1;BAG6,synonymous_variant,p.=,ENST00000437771,;BAG6,synonymous_variant,p.=,ENST00000438149,;BAG6,synonymous_variant,p.=,ENST00000453833,;BAG6,downstream_gene_variant,,ENST00000435080,;BAG6,downstream_gene_variant,,ENST00000424480,;BAG6,downstream_gene_variant,,ENST00000428326,;BAG6,downstream_gene_variant,,ENST00000451898,;BAG6,downstream_gene_variant,,ENST00000433828,;BAG6,downstream_gene_variant,,ENST00000452994,;BAG6,downstream_gene_variant,,ENST00000456622,;BAG6,downstream_gene_variant,,ENST00000456286,;BAG6,upstream_gene_variant,,ENST00000441793,;BAG6,downstream_gene_variant,,ENST00000434444,;BAG6,downstream_gene_variant,,ENST00000424176,;BAG6,downstream_gene_variant,,ENST00000441054,;BAG6,downstream_gene_variant,,ENST00000454165,;BAG6,upstream_gene_variant,,ENST00000422948,;BAG6,non_coding_transcript_exon_variant,,ENST00000470875,;BAG6,non_coding_transcript_exon_variant,,ENST00000469182,;BAG6,non_coding_transcript_exon_variant,,ENST00000465348,;BAG6,upstream_gene_variant,,ENST00000464126,;BAG6,upstream_gene_variant,,ENST00000464869,;BAG6,downstream_gene_variant,,ENST00000462682,;BAG6,upstream_gene_variant,,ENST00000462875,; A ENST00000375964 Transcript synonymous_variant 1937/3815 1623/3399 541/1132 V gtG/gtT 1 -1 BAG6 HGNC HGNC:13919 protein_coding YES CCDS47403.1 ENSP00000365131 P46379 UPI000047029D NM_004639.3 13/25 hmmpanther:PTHR15204:SF0,hmmpanther:PTHR15204 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 31643933 31643933 C A 1 0 0 0 0 0 0 0 1 1449 813 29 2 2 BAG6 6 31643933 Silent SNP C C3N-00551_T 3776659 31643933 139162046 227 15710 C6orf10 0 . GRCh38 6 32293484 32293484 + Frame_Shift_Del DEL G G - novel C3N-00551_T C3N-00551_N G G c.1189delC p.Gln397ArgfsTer2 p.Q397Rfs*2 ENST00000447241 23/23 240 200 40 299 299 0 sindel-varindel-pindel C6orf10,frameshift_variant,p.Gln397ArgfsTer2,ENST00000612031,;C6orf10,frameshift_variant,p.Gln396ArgfsTer2,ENST00000375015,;C6orf10,frameshift_variant,p.Gln395ArgfsTer2,ENST00000533191,NM_001286474.1;C6orf10,frameshift_variant,p.Gln397ArgfsTer2,ENST00000447241,NM_006781.4;C6orf10,frameshift_variant,p.Gln395ArgfsTer2,ENST00000375007,;C6orf10,frameshift_variant,p.Gln381ArgfsTer2,ENST00000527965,NM_001286475.1;C6orf10,frameshift_variant,p.Gln392ArgfsTer2,ENST00000617061,;C6orf10,frameshift_variant,p.Gln388ArgfsTer2,ENST00000442822,;XXbac-BPG154L12.5,intron_variant,,ENST00000611838,; - ENST00000447241 Transcript frameshift_variant 1362/2148 1189/1692 397/563 Q/X Cag/ag 1 -1 C6orf10 HGNC HGNC:13922 protein_coding YES CCDS34422.1 ENSP00000415517 Q5SRN2 UPI0000470279 NM_006781.4 23/23 hmmpanther:PTHR14368 HIGH deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 32293484 32293484 G - 1 0 1 0 1 0 0 0 0 2113 1357 47 0 0 C6orf10 6 32293484 Frame_Shift_Del DEL G C3N-00551_T 649551 32293484 138512495 228 15711 FGD2 0 . GRCh38 6 37027576 37027576 + Splice_Site SNP G G T novel C3N-00551_T C3N-00551_N G G c.1752+1G>T p.X584_splice ENST00000274963 123 113 10 115 115 0 strelka-mutect FGD2,splice_donor_variant,,ENST00000274963,NM_173558.3;FGD2,splice_donor_variant,,ENST00000493635,;FGD2,splice_donor_variant,,ENST00000494343,;FGD2,splice_donor_variant,,ENST00000464083,;FGD2,splice_donor_variant,,ENST00000373535,;FGD2,non_coding_transcript_exon_variant,,ENST00000487920,; T ENST00000274963 Transcript splice_donor_variant -/3046 1752/1968 584/655 1 1 FGD2 HGNC HGNC:3664 protein_coding YES CCDS4829.1 ENSP00000274963 Q7Z6J4 UPI00001A9477 NM_173558.3 15/15 HIGH 1 SNV 1 1 PASS . . 0 205 3 0 0 0 0 0 -19.49783 1 1 1 1 0 T 5 4 52 37027576 37027576 G T 1 0 0 0 0 0 0 1 0 5697 1275 44 2 2 FGD2 6 37027576 Splice_Site SNP G C3N-00551_T 4734092 37027576 133778403 229 15712 LRFN2 0 . GRCh38 6 40392092 40392092 + Missense_Mutation SNP C C A rs755101920 C3N-00551_T C3N-00551_N C C c.2221G>T p.Gly741Cys p.G741C ENST00000338305 3/3 100 93 7 144 144 0 strelka-varscan-mutect LRFN2,missense_variant,p.Gly741Cys,ENST00000338305,NM_020737.2; A ENST00000338305 Transcript missense_variant 2764/3270 2221/2370 741/789 G/C Ggc/Tgc rs755101920,COSM5615686 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 tolerated(0.12) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755101920 . 0 208 2 0 0 0 0 0 -14.75153 1 1 1 1 0 A 3 1 52 40392092 40392092 C A 1 0 0 0 0 1 0 0 0 8832 652 23 1 1 LRFN2 6 40392092 Missense_Mutation SNP C C3N-00551_T 3364516 40392092 130413887 230 15713 PGK2 0 . GRCh38 6 49786176 49786176 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1012G>T p.Gly338Trp p.G338W ENST00000304801 1/1 372 353 19 373 373 0 strelka-varscan-mutect PGK2,missense_variant,p.Gly338Trp,ENST00000304801,NM_138733.4; A ENST00000304801 Transcript missense_variant 1132/1657 1012/1254 338/417 G/W Ggg/Tgg 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 deleterious(0) 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,Prints_domain:PR00477,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 49786176 49786176 C A 1 0 0 0 0 1 0 0 0 11880 594 21 2 2 PGK2 6 49786176 Missense_Mutation SNP C C3N-00551_T 9394084 49786176 121019803 231 15714 PKHD1 0 . GRCh38 6 52050262 52050262 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.2174G>T p.Gly725Val p.G725V ENST00000371117 22/67 590 500 90 615 614 1 strelka-varscan-mutect PKHD1,missense_variant,p.Gly725Val,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Gly725Val,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 2450/16282 2174/12225 725/4074 G/V gGg/gTg COSM1144239,COSM597158 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0) 22/67 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1410841686 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 52050262 52050262 C A 1 0 0 0 0 1 0 0 0 12067 623 22 2 2 PKHD1 6 52050262 Missense_Mutation SNP C C3N-00551_T 2264086 52050262 118755717 232 15715 DST 0 . GRCh38 6 56611590 56611590 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.4552A>T p.Ser1518Cys p.S1518C ENST00000312431 35/95 141 119 22 245 245 0 strelka-mutect DST,missense_variant,p.Ser1478Cys,ENST00000361203,;DST,missense_variant,p.Ser1478Cys,ENST00000421834,NM_183380.3;DST,missense_variant,p.Ser1518Cys,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Ser1478Cys,ENST00000370788,;DST,missense_variant,p.Ser1152Cys,ENST00000244364,NM_015548.4;DST,missense_variant,p.Ser1152Cys,ENST00000439203,;DST,downstream_gene_variant,,ENST00000370765,NM_001723.5;DST,downstream_gene_variant,,ENST00000520645,; A ENST00000312431 Transcript missense_variant 4678/17756 4552/16614 1518/5537 S/C Agt/Tgt 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.05) 35/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 56611590 56611590 T A 1 0 0 0 0 1 0 0 0 4604 1580 55 4 4 DST 6 56611590 Missense_Mutation SNP T C3N-00551_T 4561328 56611590 114194389 233 15716 OOEP 0 . GRCh38 6 73369305 73369305 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.271C>A p.Leu91Ile p.L91I ENST00000370359 2/3 155 141 14 176 176 0 strelka-varscan-mutect OOEP,missense_variant,p.Leu36Ile,ENST00000370363,;OOEP,missense_variant,p.Leu36Ile,ENST00000441145,;OOEP,missense_variant,p.Leu91Ile,ENST00000370359,NM_001080507.2;OOEP-AS1,upstream_gene_variant,,ENST00000445350,;RPL39P3,downstream_gene_variant,,ENST00000424573,; T ENST00000370359 Transcript missense_variant 271/478 271/450 91/149 L/I Cta/Ata 1 -1 OOEP HGNC HGNC:21382 protein_coding YES CCDS47451.1 ENSP00000359384 A6NGQ2 UPI00001D8132 NM_001080507.2 deleterious(0.02) 2/3 hmmpanther:PTHR19447:SF14,hmmpanther:PTHR19447,Pfam_domain:PF16005 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 73369305 73369305 G T 1 0 0 0 0 1 0 0 0 10946 991 35 2 2 OOEP 6 73369305 Missense_Mutation SNP G C3N-00551_T 16757715 73369305 97436674 234 15717 CD109 0 . GRCh38 6 73787299 73787299 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.2403C>A p.= p.A801A ENST00000287097 21/33 241 208 33 358 357 1 strelka-varscan-mutect CD109,synonymous_variant,p.=,ENST00000437994,NM_001159587.2;CD109,synonymous_variant,p.=,ENST00000422508,NM_001159588.2;CD109,synonymous_variant,p.=,ENST00000287097,NM_133493.4; A ENST00000287097 Transcript synonymous_variant 2515/9130 2403/4338 801/1445 A gcC/gcA 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 21/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 73787299 73787299 C A 1 0 0 0 0 0 0 0 1 2666 581 21 2 2 CD109 6 73787299 Silent SNP C C3N-00551_T 417994 73787299 97018680 235 15718 CGA 0 . GRCh38 6 87085795 87085795 + Silent SNP C C G rs145923049 C3N-00551_T C3N-00551_N C C c.405G>C p.= p.T135T ENST00000610310 5/5 235 211 24 362 362 0 strelka-varscan-mutect CGA,synonymous_variant,p.=,ENST00000627148,NM_000735.3;CGA,synonymous_variant,p.=,ENST00000369582,;CGA,synonymous_variant,p.=,ENST00000610310,NM_001252383.1;CGA,3_prime_UTR_variant,,ENST00000630630,;CGA,downstream_gene_variant,,ENST00000625577,;RN7SKP209,downstream_gene_variant,,ENST00000516888,;CGA,downstream_gene_variant,,ENST00000627552,; G ENST00000610310 Transcript synonymous_variant 504/615 405/444 135/147 T acG/acC rs145923049 1 -1 CGA HGNC HGNC:1885 protein_coding YES CCDS75492.1 ENSP00000482232 A0A087WYZ4 UPI00005AF4BC NM_001252383.1 5/5 PROSITE_profiles:PS50277,hmmpanther:PTHR11509:SF0,hmmpanther:PTHR11509,PROSITE_patterns:PS00780,Gene3D:2.10.90.10,Pfam_domain:PF00236,SMART_domains:SM00067,Superfamily_domains:SSF57501,Prints_domain:PR00274 LOW 1 SNV 3 1 PASS rs145923049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 87085795 87085795 C G 1 0 0 0 0 0 0 0 1 3053 666 23 4 4 CGA 6 87085795 Silent SNP C C3N-00551_T 13298496 87085795 83720184 236 15719 BACH2 0 . GRCh38 6 89950925 89950925 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.1181A>G p.Gln394Arg p.Q394R ENST00000257749 7/9 27 21 6 34 34 0 strelka-varscan-mutect BACH2,missense_variant,p.Gln394Arg,ENST00000257749,NM_021813.3;BACH2,missense_variant,p.Gln394Arg,ENST00000537989,NM_001170794.1;BACH2,missense_variant,p.Gln394Arg,ENST00000343122,;RP3-512E2.2,intron_variant,,ENST00000445838,;RP3-512E2.2,intron_variant,,ENST00000413986,; C ENST00000257749 Transcript missense_variant 1889/9113 1181/2526 394/841 Q/R cAg/cGg 1 -1 BACH2 HGNC HGNC:14078 protein_coding YES CCDS5026.1 ENSP00000257749 Q9BYV9 UPI000004F8AD NM_021813.3 tolerated(0.54) 7/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 89950925 89950925 T C 1 0 0 0 0 1 0 0 0 1442 1580 55 5 5 BACH2 6 89950925 Missense_Mutation SNP T C3N-00551_T 2865130 89950925 80855054 237 15720 LAMA4 0 . GRCh38 6 112133427 112133427 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3618G>T p.Gln1206His p.Q1206H ENST00000230538 27/39 437 395 42 463 463 0 strelka-varscan-mutect LAMA4,missense_variant,p.Gln1206His,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Gln1199His,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Gln1199His,ENST00000389463,;LAMA4,missense_variant,p.Gln1199His,ENST00000424408,;LAMA4,upstream_gene_variant,,ENST00000604740,;LAMA4,downstream_gene_variant,,ENST00000519245,;LAMA4,upstream_gene_variant,,ENST00000521693,; A ENST00000230538 Transcript missense_variant 4016/6547 3618/5472 1206/1823 Q/H caG/caT 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0) 27/39 PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 112133427 112133427 C A 1 0 0 0 0 1 0 0 0 8512 564 20 2 2 LAMA4 6 112133427 Missense_Mutation SNP C C3N-00551_T 22182502 112133427 58672552 238 15721 TRDN 0 . GRCh38 6 123571071 123571071 + Silent SNP G G T rs145992727 C3N-00551_T C3N-00551_N G G c.84C>A p.= p.P28P ENST00000334268 2/41 266 251 15 277 277 0 strelka-varscan-mutect TRDN,synonymous_variant,p.=,ENST00000334268,NM_006073.3;TRDN,synonymous_variant,p.=,ENST00000628709,NM_001256020.1;TRDN,synonymous_variant,p.=,ENST00000542443,NM_001256022.1;TRDN,synonymous_variant,p.=,ENST00000546248,NM_001256021.1; T ENST00000334268 Transcript synonymous_variant 402/4770 84/2190 28/729 P ccC/ccA rs145992727 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 2/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 LOW 1 SNV 1 1 PASS rs145992727 . 0 208 0 0 2 0 0 0 -4.152755 0.9803041 1 1 1 0 T 2 4 52 123571071 123571071 G T 1 0 0 0 0 0 0 0 1 16957 1103 39 1 1 TRDN 6 123571071 Silent SNP G C3N-00551_T 11437644 123571071 47234908 239 15722 HEY2 0 . GRCh38 6 125759333 125759333 + Missense_Mutation SNP C C T rs541948433 C3N-00551_T C3N-00551_N C C c.545C>T p.Pro182Leu p.P182L ENST00000368364 5/5 72 62 10 118 118 0 strelka-varscan-mutect HEY2,missense_variant,p.Pro182Leu,ENST00000368364,NM_012259.2;HEY2,missense_variant,p.Pro136Leu,ENST00000368365,; T ENST00000368364 Transcript missense_variant 742/2678 545/1014 182/337 P/L cCg/cTg rs541948433 1 1 HEY2 HGNC HGNC:4881 protein_coding YES CCDS5131.1 ENSP00000357348 Q9UBP5 UPI0000037AFE NM_012259.2 tolerated(0.24) 5/5 hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF88,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs541948433 . 0 202 7 0 0 0 0 0 -19.99516 0.9999995 1 1 1 0 T 3 4 52 125759333 125759333 C T 1 0 0 0 0 1 0 0 0 6963 652 23 1 1 HEY2 6 125759333 Missense_Mutation SNP C C3N-00551_T 2188262 125759333 45046646 240 15723 VNN1 0 . GRCh38 6 132692356 132692356 + Missense_Mutation SNP C C T C3N-00551_T C3N-00551_N C C c.1055G>A p.Gly352Glu p.G352E ENST00000367928 5/7 166 156 10 205 205 0 strelka-varscan-mutect VNN1,missense_variant,p.Gly352Glu,ENST00000367928,NM_004666.2; T ENST00000367928 Transcript missense_variant 1069/3106 1055/1542 352/513 G/E gGa/gAa COSM3620747 1 -1 VNN1 HGNC HGNC:12705 protein_coding YES CCDS5159.1 ENSP00000356905 O95497 UPI000013C91E NM_004666.2 deleterious(0.02) 5/7 hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF16,PIRSF_domain:PIRSF011861 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 132692356 132692356 C T 1 0 0 0 0 1 0 0 0 17729 855 30 3 3 VNN1 6 132692356 Missense_Mutation SNP C C3N-00551_T 6933023 132692356 38113623 241 15724 SF3B5 0 . GRCh38 6 144095427 144095427 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.71C>G p.Ala24Gly p.A24G ENST00000367569 1/1 409 356 53 429 429 0 strelka-mutect SF3B5,missense_variant,p.Ala24Gly,ENST00000367569,NM_031287.2; C ENST00000367569 Transcript missense_variant 147/693 71/261 24/86 A/G gCc/gGc 1 -1 SF3B5 HGNC HGNC:21083 protein_coding YES CCDS5204.1 ENSP00000356541 Q9BWJ5 UPI0000135473 NM_031287.2 deleterious(0.03) 1/1 hmmpanther:PTHR20978:SF0,hmmpanther:PTHR20978,PIRSF_domain:PIRSF037010,Pfam_domain:PF07189 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 144095427 144095427 G C 1 0 0 0 0 1 0 0 0 14432 1203 42 4 4 SF3B5 6 144095427 Missense_Mutation SNP G C3N-00551_T 11403071 144095427 26710552 242 15725 SYNE1 0 . GRCh38 6 152458821 152458821 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.2504A>T p.Asn835Ile p.N835I ENST00000367255 22/146 253 226 27 377 377 0 strelka-varscan-mutect SYNE1,missense_variant,p.Asn835Ile,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Asn842Ile,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Asn825Ile,ENST00000341594,;SYNE1,missense_variant,p.Asn825Ile,ENST00000367248,;SYNE1,missense_variant,p.Asn835Ile,ENST00000367253,;SYNE1,missense_variant,p.Asn835Ile,ENST00000413186,;SYNE1,missense_variant,p.Asn402Ile,ENST00000495090,;SYNE1,downstream_gene_variant,,ENST00000466159,;SYNE1,non_coding_transcript_exon_variant,,ENST00000535896,;SYNE1,downstream_gene_variant,,ENST00000481502,;SYNE1,downstream_gene_variant,,ENST00000498751,;SYNE1,3_prime_UTR_variant,,ENST00000474655,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; A ENST00000367255 Transcript missense_variant 3106/27748 2504/26394 835/8797 N/I aAt/aTt 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 22/146 MODERATE 1 SNV 1 1 PASS rs1412442790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 152458821 152458821 T A 1 0 0 0 0 1 0 0 0 15837 1493 52 4 4 SYNE1 6 152458821 Missense_Mutation SNP T C3N-00551_T 8363394 152458821 18347158 243 15726 TULP4 0 . GRCh38 6 158502557 158502557 + Missense_Mutation SNP C C G rs776454064 C3N-00551_T C3N-00551_N C C c.2894C>G p.Ala965Gly p.A965G ENST00000367097 13/14 131 123 8 149 149 0 strelka-varscan-mutect TULP4,missense_variant,p.Ala965Gly,ENST00000367097,NM_020245.4;TULP4,intron_variant,,ENST00000367094,NM_001007466.2;TULP4,downstream_gene_variant,,ENST00000613390,; G ENST00000367097 Transcript missense_variant 4423/11295 2894/4632 965/1543 A/G gCc/gGc rs776454064 1 1 TULP4 HGNC HGNC:15530 protein_coding YES CCDS34561.1 ENSP00000356064 Q9NRJ4 UPI000013CD76 NM_020245.4 deleterious_low_confidence(0.03) 13/14 MODERATE 1 SNV 1 1 PASS rs776454064 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 158502557 158502557 C G 1 0 0 0 0 1 0 0 0 17286 739 26 4 4 TULP4 6 158502557 Missense_Mutation SNP C C3N-00551_T 6043736 158502557 12303422 244 15727 FNDC1 0 . GRCh38 6 159233632 159233632 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.3120G>T p.= p.R1040R ENST00000297267 11/23 143 120 23 154 154 0 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,synonymous_variant,p.=,ENST00000329629,; T ENST00000297267 Transcript synonymous_variant 3320/6552 3120/5685 1040/1894 R cgG/cgT 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 11/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999945 1 1 1 0 T 2 4 52 159233632 159233632 G T 1 0 0 0 0 0 0 0 1 5824 1190 42 2 2 FNDC1 6 159233632 Silent SNP G C3N-00551_T 731075 159233632 11572347 245 15728 LPA 0 . GRCh38 6 160548512 160548512 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.5121C>G p.Ile1707Met p.I1707M ENST00000316300 31/39 306 255 51 336 336 0 strelka-varscan-mutect LPA,missense_variant,p.Ile1707Met,ENST00000316300,NM_005577.2; C ENST00000316300 Transcript missense_variant 5166/6414 5121/6123 1707/2040 I/M atC/atG 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 tolerated(0.11) 31/39 hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,Superfamily_domains:SSF57440,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 160548512 160548512 G C 1 0 0 0 0 1 0 0 0 8806 1164 41 4 4 LPA 6 160548512 Missense_Mutation SNP G C3N-00551_T 1314880 160548512 10257467 246 15729 RPS6KA2 0 . GRCh38 6 166538688 166538688 + Nonsense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.220G>T p.Gly74Ter p.G74* ENST00000503859 3/22 115 89 26 125 125 0 strelka-varscan-mutect RPS6KA2,stop_gained,p.Gly91Ter,ENST00000510118,NM_001318936.1;RPS6KA2,stop_gained,p.Gly66Ter,ENST00000265678,NM_001318938.1,NM_001318937.1,NM_021135.4;RPS6KA2,stop_gained,p.Gly74Ter,ENST00000503859,NM_001006932.1;RPS6KA2,stop_gained,p.Gly50Ter,ENST00000507371,;RPS6KA2,stop_gained,p.Gly91Ter,ENST00000506565,;RPS6KA2,5_prime_UTR_variant,,ENST00000481261,;RPS6KA2,5_prime_UTR_variant,,ENST00000405189,;RPS6KA2,5_prime_UTR_variant,,ENST00000511034,;RPS6KA2,5_prime_UTR_variant,,ENST00000507350,;RPS6KA2,5_prime_UTR_variant,,ENST00000512860,; A ENST00000503859 Transcript stop_gained 601/4137 220/2226 74/741 G/* Gga/Tga 1 -1 RPS6KA2 HGNC HGNC:10431 protein_coding YES CCDS34570.1 ENSP00000427015 Q15349 UPI000020D48C NM_001006932.1 3/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24351,hmmpanther:PTHR24351:SF25,PROSITE_patterns:PS00107,PIRSF_domain:PIRSF000606,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 166538688 166538688 C A 1 0 0 0 0 0 1 0 0 13906 690 24 2 2 RPS6KA2 6 166538688 Nonsense_Mutation SNP C C3N-00551_T 5990176 166538688 4267291 247 15730 FAM120B 0 . GRCh38 6 170330472 170330472 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2008G>T p.Val670Phe p.V670F ENST00000537664 4/11 158 141 17 224 223 1 strelka-varscan-mutect FAM120B,missense_variant,p.Val647Phe,ENST00000476287,NM_032448.2;FAM120B,missense_variant,p.Val659Phe,ENST00000630384,NM_001286379.1;FAM120B,missense_variant,p.Val670Phe,ENST00000537664,NM_001286380.1;FAM120B,5_prime_UTR_variant,,ENST00000625626,NM_001286381.1;MIR4644,upstream_gene_variant,,ENST00000579929,; T ENST00000537664 Transcript missense_variant 2093/3212 2008/2802 670/933 V/F Gtc/Ttc 1 1 FAM120B HGNC HGNC:21109 protein_coding YES CCDS75555.1 ENSP00000440125 F5GY05 UPI00020654A4 NM_001286380.1 deleterious(0) 4/11 hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF17 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 170330472 170330472 G T 1 0 0 0 0 1 0 0 0 5274 1377 48 2 2 FAM120B 6 170330472 Missense_Mutation SNP G C3N-00551_T 3791784 170330472 475507 248 15731 MAD1L1 0 . GRCh38 7 2014505 2014505 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1356G>T p.Met452Ile p.M452I ENST00000406869 13/19 56 46 10 46 46 0 strelka-varscan-mutect MAD1L1,missense_variant,p.Met452Ile,ENST00000406869,;MAD1L1,missense_variant,p.Met452Ile,ENST00000399654,NM_001013836.1,NM_003550.2,NM_001013837.1,NM_001304523.1;MAD1L1,missense_variant,p.Met452Ile,ENST00000265854,;MAD1L1,missense_variant,p.Met360Ile,ENST00000402746,NM_001304524.1;MAD1L1,missense_variant,p.Met119Ile,ENST00000438959,;MAD1L1,missense_variant,p.Met42Ile,ENST00000444373,;MAD1L1,downstream_gene_variant,,ENST00000421113,; A ENST00000406869 Transcript missense_variant 1914/2991 1356/2157 452/718 M/I atG/atT 1 -1 MAD1L1 HGNC HGNC:6762 protein_coding YES CCDS43539.1 ENSP00000385334 Q9Y6D9 UPI0000072C4D tolerated(0.14) 13/19 hmmpanther:PTHR23168:SF0,hmmpanther:PTHR23168,Pfam_domain:PF05557,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 2014505 2014505 C A 1 0 0 0 0 1 0 0 0 9063 608 21 2 2 MAD1L1 7 2014505 Missense_Mutation SNP C C3N-00551_T 2014505 157331468 249 15732 CARD11 0 . GRCh38 7 2934537 2934537 + Silent SNP G G T C3N-00551_T C3N-00551_N G G c.1434C>A p.= p.S478S ENST00000396946 10/25 202 190 12 206 206 0 strelka-mutect CARD11,synonymous_variant,p.=,ENST00000396946,NM_001324281.1,NM_032415.5;CARD11,upstream_gene_variant,,ENST00000355508,; T ENST00000396946 Transcript synonymous_variant 1838/4366 1434/3465 478/1154 S tcC/tcA COSM5607998 1 -1 CARD11 HGNC HGNC:16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 A0A024R854 UPI00003FED38 NM_001324281.1,NM_032415.5 10/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14559:SF4,hmmpanther:PTHR14559 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 2934537 2934537 G T 1 0 0 0 0 0 0 0 1 2340 1335 47 2 2 CARD11 7 2934537 Silent SNP G C3N-00551_T 920032 2934537 156411436 250 15733 CARD11 0 . GRCh38 7 2947699 2947699 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.96G>T p.Met32Ile p.M32I ENST00000396946 3/25 328 291 37 574 574 0 strelka-varscan-mutect CARD11,missense_variant,p.Met32Ile,ENST00000396946,NM_001324281.1,NM_032415.5;CARD11,missense_variant,p.Met32Ile,ENST00000356408,;AC004906.3,downstream_gene_variant,,ENST00000423194,; A ENST00000396946 Transcript missense_variant 500/4366 96/3465 32/1154 M/I atG/atT 1 -1 CARD11 HGNC HGNC:16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 A0A024R854 UPI00003FED38 NM_001324281.1,NM_032415.5 tolerated(0.21) 3/25 PROSITE_profiles:PS50209,hmmpanther:PTHR14559:SF4,hmmpanther:PTHR14559,Pfam_domain:PF00619,Gene3D:1.10.533.10,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 2947699 2947699 C A 1 0 0 0 0 1 0 0 0 2340 710 25 2 2 CARD11 7 2947699 Missense_Mutation SNP C C3N-00551_T 13162 2947699 156398274 251 15734 VWDE 0 . GRCh38 7 12389282 12389282 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.320T>A p.Ile107Asn p.I107N ENST00000275358 3/29 205 183 22 209 209 0 strelka-varscan-mutect VWDE,missense_variant,p.Ile107Asn,ENST00000275358,NM_001135924.1;VWDE,5_prime_UTR_variant,,ENST00000614403,;VWDE,missense_variant,p.Ile107Asn,ENST00000452576,;VWDE,missense_variant,p.Ile107Asn,ENST00000521169,;VWDE,missense_variant,p.Ile107Asn,ENST00000326715,; T ENST00000275358 Transcript missense_variant 509/5260 320/4773 107/1590 I/N aTc/aAc 1 -1 VWDE HGNC HGNC:21897 protein_coding YES CCDS47544.1 ENSP00000275358 Q8N2E2 UPI00006C0B98 NM_001135924.1 deleterious(0) 3/29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 12389282 12389282 A T 1 0 0 0 0 1 0 0 0 17805 333 12 4 4 VWDE 7 12389282 Missense_Mutation SNP A C3N-00551_T 9441583 12389282 146956691 252 15735 AGMO 0 . GRCh38 7 15431023 15431023 + Silent SNP G G C novel C3N-00551_T C3N-00551_N G G c.495C>G p.= p.L165L ENST00000342526 4/13 110 94 16 160 160 0 strelka-varscan-mutect AGMO,synonymous_variant,p.=,ENST00000342526,NM_001004320.1; C ENST00000342526 Transcript synonymous_variant 665/2475 495/1338 165/445 L ctC/ctG 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 4/13 Pfam_domain:PF04116,hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 LOW 1 SNV 1 1 PASS rs1278779091 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 52 15431023 15431023 G C 1 0 0 0 0 0 0 0 1 463 1161 41 4 4 AGMO 7 15431023 Silent SNP G C3N-00551_T 3041741 15431023 143914950 253 15736 SP8 0 . GRCh38 7 20785258 20785258 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.559G>T p.Val187Leu p.V187L ENST00000418710 2/2 152 124 28 208 207 1 strelka-varscan-mutect SP8,missense_variant,p.Val145Leu,ENST00000617581,;SP8,missense_variant,p.Val169Leu,ENST00000361443,NM_198956.3;SP8,missense_variant,p.Val187Leu,ENST00000418710,NM_182700.5; A ENST00000418710 Transcript missense_variant 647/1618 559/1527 187/508 V/L Gtg/Ttg 1 -1 SP8 HGNC HGNC:19196 protein_coding YES CCDS43555.1 ENSP00000408792 Q8IXZ3 UPI00001AADF2 NM_182700.5 tolerated(0.1) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 20785258 20785258 C A 1 0 0 0 0 1 0 0 0 15296 478 17 2 2 SP8 7 20785258 Missense_Mutation SNP C C3N-00551_T 5354235 20785258 138560715 254 15737 SKAP2 0 . GRCh38 7 26738844 26738844 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.420G>T p.= p.R140R ENST00000345317 6/13 203 188 15 229 229 0 strelka-varscan-mutect SKAP2,synonymous_variant,p.=,ENST00000345317,NM_003930.4,NM_001303468.1;SKAP2,synonymous_variant,p.=,ENST00000432747,;SKAP2,non_coding_transcript_exon_variant,,ENST00000489977,;SKAP2,non_coding_transcript_exon_variant,,ENST00000495802,;SKAP2,downstream_gene_variant,,ENST00000490456,;SKAP2,non_coding_transcript_exon_variant,,ENST00000468712,; A ENST00000345317 Transcript synonymous_variant 734/3998 420/1080 140/359 R cgG/cgT 1 -1 SKAP2 HGNC HGNC:15687 protein_coding YES CCDS5400.1 ENSP00000005587 O75563 UPI0000073C8C NM_003930.4,NM_001303468.1 6/13 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR15129,hmmpanther:PTHR15129:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 26738844 26738844 C A 1 0 0 0 0 0 0 0 1 14618 494 18 2 2 SKAP2 7 26738844 Silent SNP C C3N-00551_T 5953586 26738844 132607129 255 15738 TRIL 0 . GRCh38 7 28955773 28955773 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.2274C>G p.Asp758Glu p.D758E ENST00000539664 1/1 197 179 18 214 214 0 strelka-varscan-mutect TRIL,missense_variant,p.Asp758Glu,ENST00000539664,NM_014817.3;AC005013.5,upstream_gene_variant,,ENST00000436594,; C ENST00000539664 Transcript missense_variant 2520/4935 2274/2436 758/811 D/E gaC/gaG 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 tolerated(0.09) 1/1 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 28955773 28955773 G C 1 0 0 0 0 1 0 0 0 16974 1020 36 4 4 TRIL 7 28955773 Missense_Mutation SNP G C3N-00551_T 2216929 28955773 130390200 256 15739 CCDC129 0 . GRCh38 7 31577945 31577945 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.759C>A p.Asn253Lys p.N253K ENST00000451887 8/15 100 90 10 113 113 0 strelka-varscan-mutect CCDC129,missense_variant,p.Asn227Lys,ENST00000319386,;CCDC129,missense_variant,p.Asn237Lys,ENST00000615280,NM_001257967.1;CCDC129,missense_variant,p.Asn135Lys,ENST00000409210,;CCDC129,missense_variant,p.Asn253Lys,ENST00000451887,NM_001257968.1;CCDC129,missense_variant,p.Asn227Lys,ENST00000407970,NM_194300.3;CCDC129,downstream_gene_variant,,ENST00000454513,;CCDC129,downstream_gene_variant,,ENST00000409717,;CCDC129,downstream_gene_variant,,ENST00000456011,;CCDC129,downstream_gene_variant,,ENST00000482748,; A ENST00000451887 Transcript missense_variant 853/3611 759/3189 253/1062 N/K aaC/aaA 1 1 CCDC129 HGNC HGNC:27363 protein_coding YES CCDS59050.1 ENSP00000395835 Q6ZRS4 UPI00020655D9 NM_001257968.1 tolerated(0.06) 8/15 hmmpanther:PTHR17469,hmmpanther:PTHR17469:SF14,Pfam_domain:PF14722,SMART_domains:SM01257 MODERATE 1 SNV 2 1 PASS rs750949457 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 31577945 31577945 C A 1 0 0 0 0 1 0 0 0 2456 477 17 2 2 CCDC129 7 31577945 Missense_Mutation SNP C C3N-00551_T 2622172 31577945 127768028 257 15740 SUGCT 0 . GRCh38 7 40860378 40860378 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1315C>G p.Gln439Glu p.Q439E ENST00000628514 15/15 227 205 22 252 252 0 strelka-varscan SUGCT,missense_variant,p.Gln413Glu,ENST00000335693,NM_001193313.1;SUGCT,missense_variant,p.Gln439Glu,ENST00000628514,NM_024728.2,NM_001193311.1;SUGCT,missense_variant,p.Gln365Glu,ENST00000401647,NM_001193312.1;SUGCT,non_coding_transcript_exon_variant,,ENST00000464028,;SUGCT,non_coding_transcript_exon_variant,,ENST00000460466,; G ENST00000628514 Transcript missense_variant 1338/1591 1315/1416 439/471 Q/E Cag/Gag 1 1 SUGCT HGNC HGNC:16001 protein_coding YES CCDS55104.1 ENSP00000486291 Q9HAC7 UPI000013EF6B NM_024728.2,NM_001193311.1 tolerated(0.29) 15/15 Gene3D:3.40.50.10540,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF593,Superfamily_domains:SSF89796 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 40860378 40860378 C G 1 0 0 0 0 1 0 0 0 15754 711 25 4 4 SUGCT 7 40860378 Missense_Mutation SNP C C3N-00551_T 9282433 40860378 118485595 258 15741 INHBA 0 . GRCh38 7 41690208 41690208 + Silent SNP C C A rs750879883 C3N-00551_T C3N-00551_N C C c.723G>T p.= p.R241R ENST00000242208 3/3 124 99 25 163 163 0 strelka-varscan INHBA,synonymous_variant,p.=,ENST00000242208,NM_002192.2;INHBA,synonymous_variant,p.=,ENST00000638023,;INHBA,synonymous_variant,p.=,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript synonymous_variant 970/6064 723/1281 241/426 R cgG/cgT rs750879883 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 3/3 hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00688 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 41690208 41690208 C A 1 0 0 0 0 0 0 0 1 7643 842 30 2 2 INHBA 7 41690208 Silent SNP C C3N-00551_T 829830 41690208 117655765 259 15742 GLI3 0 . GRCh38 7 41964935 41964935 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.4138G>T p.Val1380Phe p.V1380F ENST00000395925 15/15 849 728 121 937 937 0 strelka-varscan GLI3,missense_variant,p.Val1380Phe,ENST00000395925,NM_000168.5;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,; A ENST00000395925 Transcript missense_variant 4223/8208 4138/4743 1380/1580 V/F Gtc/Ttc 1 -1 GLI3 HGNC HGNC:4319 protein_coding YES CCDS5465.1 ENSP00000379258 P10071 UPI000020EE4C NM_000168.5 tolerated_low_confidence(0.26) 15/15 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 41964935 41964935 C A 1 0 0 0 0 1 0 0 0 6317 478 17 2 2 GLI3 7 41964935 Missense_Mutation SNP C C3N-00551_T 274727 41964935 117381038 260 15743 TNS3 0 . GRCh38 7 47415163 47415163 + Frame_Shift_Del DEL T T - novel C3N-00551_T C3N-00551_N T T c.517delA p.Met173Ter p.M173* ENST00000311160 11/31 59 52 7 135 135 0 sindel-varindel-pindel TNS3,frameshift_variant,p.Met173Ter,ENST00000311160,NM_022748.11;TNS3,frameshift_variant,p.Met276Ter,ENST00000457718,;TNS3,frameshift_variant,p.Met262Ter,ENST00000450444,;TNS3,frameshift_variant,p.Met173Ter,ENST00000442536,;TNS3,frameshift_variant,p.Met173Ter,ENST00000458317,; - ENST00000311160 Transcript frameshift_variant 875/7618 517/4338 173/1445 M/X Atg/tg 1 -1 TNS3 HGNC HGNC:21616 protein_coding YES CCDS5506.2 ENSP00000312143 Q68CZ2 UPI00001AE9DA NM_022748.11 11/31 hmmpanther:PTHR12305,hmmpanther:PTHR12305:SF42,SMART_domains:SM00404,SMART_domains:SM01326,Superfamily_domains:SSF49562 HIGH 1 deletion 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.63307 1 1 1 1 0 - 7 5 52 47415163 47415163 T - 1 0 1 0 1 0 0 0 0 16818 1493 52 0 0 TNS3 7 47415163 Frame_Shift_Del DEL T C3N-00551_T 5450228 47415163 111930810 261 15744 ABCA13 0 . GRCh38 7 48271787 48271787 + Missense_Mutation SNP G G T rs765525995 C3N-00551_T C3N-00551_N G G c.2121G>T p.Arg707Ser p.R707S ENST00000435803 17/62 51 46 5 44 44 0 strelka-varscan ABCA13,missense_variant,p.Arg707Ser,ENST00000435803,NM_152701.4;ABCA13,splice_region_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant,splice_region_variant 2145/17184 2121/15177 707/5058 R/S agG/agT rs765525995 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0) 17/62 MODERATE 1 SNV 1 1 PASS . . 1 196 12 0 0 0 0 0 -11.95142 0.999795 1 1 1 0 T 3 4 52 48271787 48271787 G T 1 0 0 0 0 1 0 0 0 35 1246 43 2 2 ABCA13 7 48271787 Missense_Mutation SNP G C3N-00551_T 856624 48271787 111074186 262 15745 RP11-15K19.2 0 . GRCh38 7 55923654 55923654 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.262G>C p.Glu88Gln p.E88Q ENST00000429591 6/7 184 165 19 224 224 0 strelka-varscan ZNF713,missense_variant,p.Glu88Gln,ENST00000429591,NM_182633.2;ZNF713,missense_variant,p.Glu75Gln,ENST00000633730,;RP11-15K19.2,missense_variant,p.Glu75Gln,ENST00000426595,;ZNF713,non_coding_transcript_exon_variant,,ENST00000482436,;ZNF713,non_coding_transcript_exon_variant,,ENST00000466630,;ZNF713,downstream_gene_variant,,ENST00000411863,; C ENST00000429591 Transcript missense_variant 1050/4339 262/1332 88/443 E/Q Gaa/Caa 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 deleterious(0.02) 6/7 PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80,SMART_domains:SM00349 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 55923654 55923654 G C 1 0 0 0 0 1 0 0 0 13715 1175 41 4 4 RP11-15K19.2 7 55923654 Missense_Mutation SNP G C3N-00551_T 7651867 55923654 103422319 263 15746 ZNF107 0 . GRCh38 7 64707806 64707806 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1709G>T p.Cys570Phe p.C570F ENST00000620827 4/4 107 80 27 121 121 0 strelka-varscan ZNF107,missense_variant,p.Cys501Phe,ENST00000395391,;ZNF107,missense_variant,p.Cys501Phe,ENST00000423627,NM_016220.4;ZNF107,missense_variant,p.Cys570Phe,ENST00000620827,NM_001282359.1;ZNF107,missense_variant,p.Cys538Phe,ENST00000613690,NM_001282360.1;ZNF107,missense_variant,p.Cys501Phe,ENST00000344930,NM_001013746.2;ZNF107,downstream_gene_variant,,ENST00000360117,; T ENST00000620827 Transcript missense_variant 1909/5685 1709/2559 570/852 C/F tGt/tTt 1 1 ZNF107 HGNC HGNC:12887 protein_coding YES CCDS75605.1 ENSP00000483720 A0A0B4J2G0 UPI0000049C52 NM_001282359.1 deleterious(0.01) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF121,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 64707806 64707806 G T 1 0 0 0 0 1 0 0 0 18295 1377 48 2 2 ZNF107 7 64707806 Missense_Mutation SNP G C3N-00551_T 8784152 64707806 94638167 264 15747 HGF 0 . GRCh38 7 81729777 81729777 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.868G>C p.Asp290His p.D290H ENST00000222390 8/18 172 140 32 193 193 0 strelka-varscan HGF,missense_variant,p.Asp290His,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Asp285His,ENST00000457544,NM_001010932.1; G ENST00000222390 Transcript missense_variant,splice_region_variant 1095/5989 868/2187 290/728 D/H Gac/Cac 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 tolerated(0.18) 8/18 hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 81729777 81729777 C G 1 0 0 0 0 1 0 0 0 6969 840 29 4 4 HGF 7 81729777 Missense_Mutation SNP C C3N-00551_T 17021971 81729777 77616196 265 15748 SEMA3D 0 . GRCh38 7 85065433 85065433 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.709T>C p.Trp237Arg p.W237R ENST00000284136 6/17 207 150 57 204 203 1 strelka-varscan SEMA3D,missense_variant,p.Trp237Arg,ENST00000284136,NM_152754.2;SEMA3D,missense_variant,p.Trp237Arg,ENST00000444867,; G ENST00000284136 Transcript missense_variant 753/6265 709/2334 237/777 W/R Tgg/Cgg 1 -1 SEMA3D HGNC HGNC:10726 protein_coding YES CCDS34676.1 ENSP00000284136 O95025 UPI0000135A66 NM_152754.2 deleterious(0) 6/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF36,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 85065433 85065433 A G 1 0 0 0 0 1 0 0 0 14303 188 7 5 5 SEMA3D 7 85065433 Missense_Mutation SNP A C3N-00551_T 3335656 85065433 74280540 266 15749 RUNDC3B 0 . GRCh38 7 87710573 87710573 + Nonsense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.427A>T p.Arg143Ter p.R143* ENST00000338056 5/12 149 102 47 180 180 0 strelka-varscan RUNDC3B,stop_gained,p.Arg143Ter,ENST00000338056,NM_138290.2;RUNDC3B,stop_gained,p.Arg126Ter,ENST00000394654,NM_001134405.1;RUNDC3B,stop_gained,p.Arg126Ter,ENST00000493037,NM_001134406.1;ABCB1,intron_variant,,ENST00000265724,NM_000927.4;ABCB1,intron_variant,,ENST00000543898,;ABCB1,intron_variant,,ENST00000416177,;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000496000,;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000489461,;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000466676,;ABCB1,intron_variant,,ENST00000476862,;RUNDC3B,non_coding_transcript_exon_variant,,ENST00000312373,; T ENST00000338056 Transcript stop_gained 838/4099 427/1422 143/473 R/* Aga/Tga 1 1 RUNDC3B HGNC HGNC:30286 protein_coding YES CCDS5609.1 ENSP00000337732 Q96NL0 UPI0000071425 NM_138290.2 5/12 PROSITE_profiles:PS50826,hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835,Pfam_domain:PF02759,SMART_domains:SM00593,Superfamily_domains:0052343 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 87710573 87710573 A T 1 0 0 0 0 0 1 0 0 14006 434 15 4 4 RUNDC3B 7 87710573 Nonsense_Mutation SNP A C3N-00551_T 2645140 87710573 71635400 267 15750 RUNDC3B 0 . GRCh38 7 87807395 87807395 + Silent SNP T T C novel C3N-00551_T C3N-00551_N T T c.1030T>C p.= p.L344L ENST00000338056 10/12 182 172 10 197 197 0 strelka-varscan RUNDC3B,synonymous_variant,p.=,ENST00000338056,NM_138290.2;RUNDC3B,synonymous_variant,p.=,ENST00000394654,NM_001134405.1;RUNDC3B,intron_variant,,ENST00000493037,NM_001134406.1;RUNDC3B,intron_variant,,ENST00000312373,; C ENST00000338056 Transcript synonymous_variant 1441/4099 1030/1422 344/473 L Tta/Cta 1 1 RUNDC3B HGNC HGNC:30286 protein_coding YES CCDS5609.1 ENSP00000337732 Q96NL0 UPI0000071425 NM_138290.2 10/12 hmmpanther:PTHR22835:SF124,hmmpanther:PTHR22835 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 52 87807395 87807395 T C 1 0 0 0 0 0 0 0 1 14006 1838 64 5 5 RUNDC3B 7 87807395 Silent SNP T C3N-00551_T 96822 87807395 71538578 268 15751 PEX1 0 . GRCh38 7 92509399 92509399 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1600C>T p.Pro534Ser p.P534S ENST00000248633 9/24 290 237 53 294 294 0 strelka-varscan PEX1,missense_variant,p.Pro534Ser,ENST00000248633,NM_000466.2;PEX1,missense_variant,p.Pro534Ser,ENST00000428214,NM_001282677.1;PEX1,missense_variant,p.Pro212Ser,ENST00000438045,NM_001282678.1;PEX1,non_coding_transcript_exon_variant,,ENST00000484913,;PEX1,intron_variant,,ENST00000422866,;PEX1,upstream_gene_variant,,ENST00000496420,;PEX1,downstream_gene_variant,,ENST00000476923,; A ENST00000248633 Transcript missense_variant 1696/4385 1600/3852 534/1283 P/S Cct/Tct 1 -1 PEX1 HGNC HGNC:8850 protein_coding YES CCDS5627.1 ENSP00000248633 O43933 UPI0000001C39 NM_000466.2 tolerated(0.07) 9/24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 92509399 92509399 G A 1 0 0 0 0 1 0 0 0 11825 1174 41 3 3 PEX1 7 92509399 Missense_Mutation SNP G C3N-00551_T 4702004 92509399 66836574 269 15752 SAMD9 0 . GRCh38 7 93102692 93102692 + Missense_Mutation SNP C C G rs759775100 C3N-00551_T C3N-00551_N C C c.3406G>C p.Glu1136Gln p.E1136Q ENST00000379958 3/3 404 359 45 400 400 0 strelka-varscan SAMD9,missense_variant,p.Glu1136Gln,ENST00000379958,NM_017654.3;SAMD9,missense_variant,p.Glu1136Gln,ENST00000620985,NM_001193307.1;SAMD9,missense_variant,p.Glu1136Gln,ENST00000446617,; G ENST00000379958 Transcript missense_variant 3676/6852 3406/4770 1136/1589 E/Q Gag/Cag rs759775100 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 tolerated(0.06) 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 93102692 93102692 C G 1 0 0 0 0 1 0 0 0 14086 922 32 4 4 SAMD9 7 93102692 Missense_Mutation SNP C C3N-00551_T 593293 93102692 66243281 270 15753 CALCR 0 . GRCh38 7 93426493 93426493 + Missense_Mutation SNP C C A rs143204333 C3N-00551_T C3N-00551_N C C c.1390G>T p.Ala464Ser p.A464S ENST00000359558 16/16 142 111 31 119 119 0 strelka-varscan CALCR,missense_variant,p.Ala464Ser,ENST00000359558,NM_001164737.1;CALCR,missense_variant,p.Ala446Ser,ENST00000421592,;CALCR,missense_variant,p.Ala430Ser,ENST00000394441,NM_001164738.1;CALCR,missense_variant,p.Ala430Ser,ENST00000426151,NM_001742.3;CALCR,3_prime_UTR_variant,,ENST00000360249,;CALCR,3_prime_UTR_variant,,ENST00000423724,;CALCR,3_prime_UTR_variant,,ENST00000415529,; A ENST00000359558 Transcript missense_variant 1690/3696 1390/1527 464/508 A/S Gcc/Tcc rs143204333 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 tolerated(0.29) 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Prints_domain:PR00361 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 93426493 93426493 C A 1 0 0 0 0 1 0 0 0 2269 797 28 2 2 CALCR 7 93426493 Missense_Mutation SNP C C3N-00551_T 323801 93426493 65919480 271 15754 COL1A2 0 . GRCh38 7 94429393 94429393 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3917G>T p.Ser1306Ile p.S1306I ENST00000297268 51/52 329 228 101 376 376 0 strelka-varscan COL1A2,missense_variant,p.Ser1306Ile,ENST00000297268,NM_000089.3;COL1A2,missense_variant,p.Ser1304Ile,ENST00000620463,;COL1A2,non_coding_transcript_exon_variant,,ENST00000481570,;COL1A2,non_coding_transcript_exon_variant,,ENST00000464916,;COL1A2,downstream_gene_variant,,ENST00000478215,;COL1A2,downstream_gene_variant,,ENST00000469732,;COL1A2,downstream_gene_variant,,ENST00000492110,;COL1A2,downstream_gene_variant,,ENST00000488121,; T ENST00000297268 Transcript missense_variant 4388/5411 3917/4101 1306/1366 S/I aGc/aTc 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 tolerated(0.09) 51/52 PD002078,Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,SMART_domains:SM00038 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 94429393 94429393 G T 1 0 0 0 0 1 0 0 0 3466 971 34 2 2 COL1A2 7 94429393 Missense_Mutation SNP G C3N-00551_T 1002900 94429393 64916580 272 15755 TMEM130 0 . GRCh38 7 98851534 98851534 + Missense_Mutation SNP G G C rs148698491 C3N-00551_T C3N-00551_N G G c.893C>G p.Ala298Gly p.A298G ENST00000416379 6/8 200 147 53 172 172 0 strelka-varscan TMEM130,missense_variant,p.Ala214Gly,ENST00000450876,;TMEM130,missense_variant,p.Ala298Gly,ENST00000339375,NM_152913.2;TMEM130,missense_variant,p.Ala298Gly,ENST00000416379,NM_001134450.1;TMEM130,missense_variant,p.Ala196Gly,ENST00000345589,NM_001134451.1;TMEM130,non_coding_transcript_exon_variant,,ENST00000461092,;TMEM130,upstream_gene_variant,,ENST00000474857,; C ENST00000416379 Transcript missense_variant 898/2881 893/1308 298/435 A/G gCg/gGg rs148698491 1 -1 TMEM130 HGNC HGNC:25429 protein_coding YES CCDS47650.1 ENSP00000413163 Q8N3G9 UPI000006EF2E NM_001134450.1 tolerated(0.18) 6/8 hmmpanther:PTHR11861:SF10,hmmpanther:PTHR11861,Superfamily_domains:SSF49299 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999998 1 1 1 0 C 3 2 52 98851534 98851534 G C 1 0 0 0 0 1 0 0 0 16487 1087 38 4 4 TMEM130 7 98851534 Missense_Mutation SNP G C3N-00551_T 4422141 98851534 60494439 273 15756 RELN 0 . GRCh38 7 103635538 103635538 + Silent SNP C C A rs148510862 C3N-00551_T C3N-00551_N C C c.2352G>T p.= p.T784T ENST00000428762 19/65 202 173 29 252 252 0 strelka-varscan RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript synonymous_variant 2512/11571 2352/10383 784/3460 T acG/acT rs148510862,COSM598293 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 19/65 hmmpanther:PTHR11841,Superfamily_domains:SSF50939 0,1 LOW 1 SNV 5 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 103635538 103635538 C A 1 0 0 0 0 0 0 0 1 13390 523 19 1 1 RELN 7 103635538 Silent SNP C C3N-00551_T 4784004 103635538 55710435 274 15757 PRKAR2B 0 . GRCh38 7 107045151 107045151 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.244C>A p.Gln82Lys p.Q82K ENST00000265717 1/11 55 46 9 42 42 0 strelka-varscan PRKAR2B,missense_variant,p.Gln82Lys,ENST00000265717,NM_002736.2; A ENST00000265717 Transcript missense_variant 503/3745 244/1257 82/418 Q/K Cag/Aag 1 1 PRKAR2B HGNC HGNC:9392 protein_coding YES CCDS5740.1 ENSP00000265717 P31323 A0A024R712 UPI000013D669 NM_002736.2 tolerated(0.83) 1/11 PIRSF_domain:PIRSF000548,hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF121 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.96605 1 1 1 1 0 A 3 1 52 107045151 107045151 C A 1 0 0 0 0 1 0 0 0 12639 711 25 2 2 PRKAR2B 7 107045151 Missense_Mutation SNP C C3N-00551_T 3409613 107045151 52300822 275 15758 LAMB1 0 . GRCh38 7 107959307 107959307 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2632C>A p.Pro878Thr p.P878T ENST00000222399 20/34 223 165 58 250 250 0 strelka-varscan LAMB1,missense_variant,p.Pro902Thr,ENST00000393561,;LAMB1,missense_variant,p.Pro878Thr,ENST00000222399,NM_002291.2;LAMB1,downstream_gene_variant,,ENST00000393560,; T ENST00000222399 Transcript missense_variant 2863/5725 2632/5361 878/1786 P/T Cca/Aca 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 tolerated(0.3) 20/34 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_profiles:PS50027,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 107959307 107959307 G T 1 0 0 0 0 1 0 0 0 8514 1232 43 2 2 LAMB1 7 107959307 Missense_Mutation SNP G C3N-00551_T 914156 107959307 51386666 276 15759 LAMB4 0 . GRCh38 7 108103062 108103062 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1162G>T p.Asp388Tyr p.D388Y ENST00000388781 10/34 71 57 14 57 57 0 strelka-varscan LAMB4,missense_variant,p.Asp388Tyr,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Asp388Tyr,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Asp388Tyr,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; A ENST00000388781 Transcript missense_variant 1246/5858 1162/5286 388/1761 D/Y Gat/Tat 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0) 10/34 PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00180 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 108103062 108103062 C A 1 0 0 0 0 1 0 0 0 8517 913 32 2 2 LAMB4 7 108103062 Missense_Mutation SNP C C3N-00551_T 143755 108103062 51242911 277 15760 IMMP2L 0 . GRCh38 7 110963551 110963552 + Frame_Shift_Ins INS - - GGTTT novel C3N-00551_T C3N-00551_N - - c.249_253dupAAACC p.Pro85GlnfsTer11 p.P85Qfs*11 ENST00000405709 4/6 78 66 12 56 56 0 sindel-pindel IMMP2L,frameshift_variant,p.Pro85GlnfsTer11,ENST00000405709,NM_032549.3;IMMP2L,frameshift_variant,p.Pro85GlnfsTer11,ENST00000331762,NM_001244606.1;IMMP2L,frameshift_variant,p.Pro85GlnfsTer11,ENST00000447215,;IMMP2L,frameshift_variant,p.Pro85GlnfsTer11,ENST00000452895,;IMMP2L,frameshift_variant,p.Pro67GlnfsTer11,ENST00000450877,;IMMP2L,non_coding_transcript_exon_variant,,ENST00000489381,;IMMP2L,non_coding_transcript_exon_variant,,ENST00000487733,; GGTTT ENST00000405709 Transcript frameshift_variant 696-697/1522 253-254/528 85/175 P/QTX cca/cAAACCca 1 -1 IMMP2L HGNC HGNC:14598 protein_coding YES CCDS5753.1 ENSP00000384966 Q96T52 A4D0S9 UPI000006D162 NM_032549.3 4/6 Gene3D:2.10.109.10,Pfam_domain:PF00717,hmmpanther:PTHR12383,hmmpanther:PTHR12383:SF3,Superfamily_domains:SSF51306,TIGRFAM_domain:TIGR02227 HIGH 1 insertion 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 GGTTT 7 5 52 110963551 110963551 - GGTTT 1 0 1 1 0 0 0 0 0 7620 1348 47 0 0 IMMP2L 7 110963551 Frame_Shift_Ins INS - C3N-00551_T 2860489 110963551 48382422 278 15761 CFTR 0 . GRCh38 7 117614613 117614613 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3368G>T p.Gly1123Val p.G1123V ENST00000003084 21/27 300 227 73 380 380 0 strelka-varscan CFTR,missense_variant,p.Gly1123Val,ENST00000003084,NM_000492.3;CFTR,missense_variant,p.Gly1093Val,ENST00000426809,;CFTR,missense_variant,p.Gly65Val,ENST00000468795,;AC000111.6,intron_variant,,ENST00000456270,; T ENST00000003084 Transcript missense_variant,splice_region_variant 3500/6132 3368/4443 1123/1480 G/V gGa/gTa 1 1 CFTR HGNC HGNC:1884 protein_coding YES CCDS5773.1 ENSP00000003084 P13569 A0A024R730 UPI000013C4D4 NM_000492.3 deleterious(0.01) 21/27 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF19,Superfamily_domains:SSF90123,TIGRFAM_domain:TIGR01271 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 117614613 117614613 G T 1 0 0 0 0 1 0 0 0 3052 1188 41 2 2 CFTR 7 117614613 Missense_Mutation SNP G C3N-00551_T 6651062 117614613 41731360 279 15762 CPED1 0 . GRCh38 7 121100023 121100023 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.847C>T p.Pro283Ser p.P283S ENST00000310396 7/23 242 224 18 236 236 0 strelka-varscan CPED1,missense_variant,p.Pro283Ser,ENST00000310396,NM_024913.4;CPED1,missense_variant,p.Pro283Ser,ENST00000450913,NM_001105533.1;CPED1,missense_variant,p.Pro283Ser,ENST00000428526,;CPED1,missense_variant,p.Pro63Ser,ENST00000423795,;CPED1,missense_variant,p.Pro63Ser,ENST00000443817,;CPED1,downstream_gene_variant,,ENST00000520801,; T ENST00000310396 Transcript missense_variant 1314/5340 847/3081 283/1026 P/S Cct/Tct 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 deleterious(0) 7/23 hmmpanther:PTHR14776 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 121100023 121100023 C T 1 0 0 0 0 1 0 0 0 3598 623 22 3 3 CPED1 7 121100023 Missense_Mutation SNP C C3N-00551_T 3485410 121100023 38245950 280 15763 TAS2R16 0 . GRCh38 7 122995106 122995106 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.529C>A p.Gln177Lys p.Q177K ENST00000249284 1/1 165 118 47 202 201 1 strelka-varscan TAS2R16,missense_variant,p.Gln177Lys,ENST00000249284,NM_016945.2; T ENST00000249284 Transcript missense_variant 595/997 529/876 177/291 Q/K Cag/Aag COSM4498879 1 -1 TAS2R16 HGNC HGNC:14921 protein_coding YES CCDS5785.1 ENSP00000249284 Q9NYV7 UPI0000038B18 NM_016945.2 tolerated(0.17) 1/1 Pfam_domain:PF05296,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF68,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 122995106 122995106 G T 1 0 0 0 0 1 0 0 0 15968 1299 45 2 2 TAS2R16 7 122995106 Missense_Mutation SNP G C3N-00551_T 1895083 122995106 36350867 281 15764 HYAL4 0 . GRCh38 7 123868732 123868732 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.459G>T p.Trp153Cys p.W153C ENST00000223026 3/5 149 102 47 167 167 0 strelka-varscan HYAL4,missense_variant,p.Trp153Cys,ENST00000223026,NM_012269.2;HYAL4,missense_variant,p.Trp153Cys,ENST00000476325,;HYAL4,downstream_gene_variant,,ENST00000489978,;HYAL4,downstream_gene_variant,,ENST00000488323,;HYAL4,missense_variant,p.Trp153Cys,ENST00000483878,; T ENST00000223026 Transcript missense_variant 1097/2407 459/1446 153/481 W/C tgG/tgT 1 1 HYAL4 HGNC HGNC:5323 protein_coding YES CCDS5789.1 ENSP00000223026 Q2M3T9 UPI000006F62B NM_012269.2 deleterious(0.02) 3/5 Gene3D:3.20.20.70,Pfam_domain:PF01630,PIRSF_domain:PIRSF038193,Prints_domain:PR00846,hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF7,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 123868732 123868732 G T 1 0 0 0 0 1 0 0 0 7362 1241 43 2 2 HYAL4 7 123868732 Missense_Mutation SNP G C3N-00551_T 873626 123868732 35477241 282 15765 GRM8 0 . GRCh38 7 126446207 126446207 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2596C>A p.Gln866Lys p.Q866K ENST00000339582 10/11 464 408 56 489 489 0 strelka-varscan GRM8,missense_variant,p.Gln866Lys,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Gln866Lys,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Gln374Lys,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000489939,;GRM8,non_coding_transcript_exon_variant,,ENST00000495315,;GRM8,missense_variant,p.Gln866Lys,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; T ENST00000339582 Transcript missense_variant 3405/4057 2596/2727 866/908 Q/K Caa/Aaa 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious(0.01) 10/11 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 126446207 126446207 G T 1 0 0 0 0 1 0 0 0 6685 1328 46 2 2 GRM8 7 126446207 Missense_Mutation SNP G C3N-00551_T 2577475 126446207 32899766 283 15766 FLNC 0 . GRCh38 7 128843870 128843870 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.2886C>A p.= p.P962P ENST00000325888 19/48 598 448 150 593 593 0 strelka-varscan FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;FLNC,downstream_gene_variant,,ENST00000388853,; A ENST00000325888 Transcript synonymous_variant 3147/9188 2886/8178 962/2725 P ccC/ccA 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 19/48 PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 128843870 128843870 C A 1 0 0 0 0 0 0 0 1 5791 610 22 2 2 FLNC 7 128843870 Silent SNP C C3N-00551_T 2397663 128843870 30502103 284 15767 CHRM2 0 . GRCh38 7 137014982 137014982 + Silent SNP C C A rs755854009 C3N-00551_T C3N-00551_N C C c.117C>A p.= p.I39I ENST00000445907 3/3 285 248 37 307 307 0 strelka-varscan CHRM2,synonymous_variant,p.=,ENST00000445907,NM_001006630.1,NM_001006627.1;CHRM2,synonymous_variant,p.=,ENST00000401861,NM_000739.2,NM_001006626.1,NM_001006628.1;CHRM2,synonymous_variant,p.=,ENST00000453373,NM_001006631.1,NM_001006629.1;CHRM2,synonymous_variant,p.=,ENST00000320658,NM_001006632.1;AC009264.1,intron_variant,,ENST00000439694,;AC009264.1,intron_variant,,ENST00000425981,;AC009264.1,intron_variant,,ENST00000586239,;AC009264.1,intron_variant,,ENST00000597642,;AC009264.1,intron_variant,,ENST00000598184,;AC009264.1,intron_variant,,ENST00000593789,;AC009264.1,intron_variant,,ENST00000592183,; A ENST00000445907 Transcript synonymous_variant 645/5918 117/1401 39/466 I atC/atA rs755854009,COSM328223 1 1 CHRM2 HGNC HGNC:1951 protein_coding YES CCDS5843.1 ENSP00000399745 P08172 A4D1Q0 UPI0000050410 NM_001006630.1,NM_001006627.1 3/3 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 137014982 137014982 C A 1 0 0 0 0 0 0 0 1 3137 874 31 1 1 CHRM2 7 137014982 Silent SNP C C3N-00551_T 8171112 137014982 22330991 285 15768 DGKI 0 . GRCh38 7 137391295 137391295 + Silent SNP T T C novel C3N-00551_T C3N-00551_N T T c.3123A>G p.= p.P1041P ENST00000288490 34/34 120 111 9 152 152 0 strelka-varscan DGKI,synonymous_variant,p.=,ENST00000453654,;DGKI,synonymous_variant,p.=,ENST00000424189,;DGKI,synonymous_variant,p.=,ENST00000446122,;DGKI,synonymous_variant,p.=,ENST00000288490,NM_004717.2;DGKI,synonymous_variant,p.=,ENST00000614521,;DGKI,non_coding_transcript_exon_variant,,ENST00000494390,;DGKI,non_coding_transcript_exon_variant,,ENST00000497321,;DGKI,non_coding_transcript_exon_variant,,ENST00000477835,;DGKI,non_coding_transcript_exon_variant,,ENST00000486153,; C ENST00000288490 Transcript synonymous_variant 3124/3895 3123/3198 1041/1065 P ccA/ccG 1 -1 DGKI HGNC HGNC:2855 protein_coding YES CCDS5845.1 ENSP00000288490 O75912 UPI000012DD23 NM_004717.2 34/34 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF41,Superfamily_domains:SSF48403 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 52 137391295 137391295 T C 1 0 0 0 0 0 0 0 1 4277 1567 55 5 5 DGKI 7 137391295 Silent SNP T C3N-00551_T 376313 137391295 21954678 286 15769 UBN2 0 . GRCh38 7 139276120 139276120 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1997G>T p.Ser666Ile p.S666I ENST00000473989 12/18 207 166 41 296 295 1 strelka-varscan UBN2,missense_variant,p.Ser666Ile,ENST00000473989,NM_173569.3;UBN2,missense_variant,p.Ser435Ile,ENST00000483726,; T ENST00000473989 Transcript missense_variant 1997/14444 1997/4044 666/1347 S/I aGt/aTt COSM4887328,COSM4887329 1 1 UBN2 HGNC HGNC:21931 protein_coding YES CCDS43655.2 ENSP00000418648 Q6ZU65 UPI00001D74DF NM_173569.3 tolerated(0.07) 12/18 hmmpanther:PTHR21669:SF10,hmmpanther:PTHR21669 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 139276120 139276120 G T 1 0 0 0 0 1 0 0 0 17417 1029 36 2 2 UBN2 7 139276120 Missense_Mutation SNP G C3N-00551_T 1884825 139276120 20069853 287 15770 CLCN1 0 . GRCh38 7 143331232 143331232 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.980T>C p.Val327Ala p.V327A ENST00000343257 9/23 506 477 29 630 630 0 strelka-varscan CLCN1,missense_variant,p.Val327Ala,ENST00000343257,NM_000083.2;CLCN1,downstream_gene_variant,,ENST00000495612,;CLCN1,downstream_gene_variant,,ENST00000455478,;CLCN1,downstream_gene_variant,,ENST00000432192,; C ENST00000343257 Transcript missense_variant,splice_region_variant 1067/3172 980/2967 327/988 V/A gTc/gCc 1 1 CLCN1 HGNC HGNC:2019 protein_coding YES CCDS5881.1 ENSP00000339867 P35523 UPI000020F1EC NM_000083.2 tolerated(0.25) 9/23 hmmpanther:PTHR11689:SF29,hmmpanther:PTHR11689,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 143331232 143331232 T C 1 0 0 0 0 1 0 0 0 3226 1681 58 5 5 CLCN1 7 143331232 Missense_Mutation SNP T C3N-00551_T 4055112 143331232 16014741 288 15771 CNTNAP2 0 . GRCh38 7 148118282 148118282 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2548C>A p.Leu850Met p.L850M ENST00000361727 16/24 390 354 36 385 385 0 strelka-varscan CNTNAP2,missense_variant,p.Leu850Met,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000631199,; A ENST00000361727 Transcript missense_variant 3066/9896 2548/3996 850/1331 L/M Ctg/Atg 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(0.07) 16/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 148118282 148118282 C A 1 0 0 0 0 1 0 0 0 3428 796 28 2 2 CNTNAP2 7 148118282 Missense_Mutation SNP C C3N-00551_T 4787050 148118282 11227691 289 15772 KMT2C 0 . GRCh38 7 152144784 152144784 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.14272A>C p.Lys4758Gln p.K4758Q ENST00000262189 55/59 145 137 8 152 152 0 strelka-varscan KMT2C,missense_variant,p.Lys4758Gln,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Lys4758Gln,ENST00000355193,;KMT2C,missense_variant,p.Lys2315Gln,ENST00000360104,;KMT2C,missense_variant,p.Lys1371Gln,ENST00000424877,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; G ENST00000262189 Transcript missense_variant 14491/16862 14272/14736 4758/4911 K/Q Aag/Cag 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 deleterious(0) 55/59 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF373,Gene3D:2.170.270.10,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 152144784 152144784 T G 1 0 0 0 0 1 0 0 0 8297 1821 63 5 5 KMT2C 7 152144784 Missense_Mutation SNP T C3N-00551_T 4026502 152144784 7201189 290 15773 HTR5A 0 . GRCh38 7 155084301 155084301 + Silent SNP C C G novel C3N-00551_T C3N-00551_N C C c.888C>G p.= p.L296L ENST00000287907 2/2 320 292 28 353 353 0 strelka-varscan HTR5A,synonymous_variant,p.=,ENST00000287907,NM_024012.3;HTR5A,non_coding_transcript_exon_variant,,ENST00000486819,; G ENST00000287907 Transcript synonymous_variant 1464/2912 888/1074 296/357 L ctC/ctG 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 155084301 155084301 C G 1 0 0 0 0 0 0 0 1 7346 900 32 4 4 HTR5A 7 155084301 Silent SNP C C3N-00551_T 2939517 155084301 4261672 291 15774 GATA4 0 . GRCh38 8 11750136 11750136 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.812C>A p.Ser271Tyr p.S271Y ENST00000532059 3/6 581 534 47 681 680 1 strelka-varscan-mutect GATA4,missense_variant,p.Ser270Tyr,ENST00000335135,NM_002052.3;GATA4,missense_variant,p.Ser64Tyr,ENST00000528712,NM_001308094.1;GATA4,missense_variant,p.Ser269Tyr,ENST00000622443,;GATA4,missense_variant,p.Ser271Tyr,ENST00000532059,NM_001308093.1;GATA4,missense_variant,p.Ser64Tyr,ENST00000526716,; A ENST00000532059 Transcript missense_variant 892/1459 812/1332 271/443 S/Y tCc/tAc 1 1 GATA4 HGNC HGNC:4173 protein_coding YES CCDS78303.1 ENSP00000435712 P43694 UPI0000210221 NM_001308093.1 deleterious(0.01) 3/6 Gene3D:3.30.50.10,PIRSF_domain:PIRSF003028,PROSITE_profiles:PS50114,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF154,SMART_domains:SM00401,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 11750136 11750136 C A 1 0 0 0 0 1 0 0 0 6126 855 30 2 2 GATA4 8 11750136 Missense_Mutation SNP C C3N-00551_T 11750136 133388500 292 15775 ATP6V1B2 0 . GRCh38 8 20210344 20210344 + Splice_Site SNP A A G novel C3N-00551_T C3N-00551_N A A c.292-2A>G p.X98_splice ENST00000276390 109 99 10 150 150 0 strelka-varscan-mutect ATP6V1B2,splice_acceptor_variant,,ENST00000276390,NM_001693.3;ATP6V1B2,splice_acceptor_variant,,ENST00000519667,;ATP6V1B2,splice_acceptor_variant,,ENST00000523482,;ATP6V1B2,splice_acceptor_variant,,ENST00000520830,;ATP6V1B2,splice_acceptor_variant,,ENST00000523478,; G ENST00000276390 Transcript splice_acceptor_variant -/2875 292/1536 98/511 1 1 ATP6V1B2 HGNC HGNC:854 protein_coding YES CCDS6014.1 ENSP00000276390 P21281 A0A140VK65 UPI00001380AD NM_001693.3 3/13 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 52 20210344 20210344 A G 1 0 0 0 0 0 0 1 0 1332 434 15 5 5 ATP6V1B2 8 20210344 Splice_Site SNP A C3N-00551_T 8460208 20210344 124928292 293 15776 PPP3CC 0 . GRCh38 8 22522731 22522731 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.925G>A p.Asp309Asn p.D309N ENST00000397775 8/15 129 121 8 170 170 0 strelka-varscan-mutect PPP3CC,missense_variant,p.Asp309Asn,ENST00000240139,NM_005605.4;PPP3CC,missense_variant,p.Asp309Asn,ENST00000289963,NM_001243975.1;PPP3CC,missense_variant,p.Asp309Asn,ENST00000397775,NM_001243974.1;PPP3CC,missense_variant,p.Asp309Asn,ENST00000518852,;PPP3CC,missense_variant,p.Asp186Asn,ENST00000521651,;PPP3CC,missense_variant,p.Asp159Asn,ENST00000522034,;PPP3CC,incomplete_terminal_codon_variant,p.=,ENST00000523620,; A ENST00000397775 Transcript missense_variant 1199/2094 925/1566 309/521 D/N Gat/Aat 1 1 PPP3CC HGNC HGNC:9316 protein_coding YES CCDS59093.1 ENSP00000380878 P48454 UPI00017A7ABA NM_001243974.1 deleterious(0) 8/15 Gene3D:3.60.21.10,Prints_domain:PR00114,hmmpanther:PTHR11668,hmmpanther:PTHR11668:SF186,SMART_domains:SM00156,Superfamily_domains:SSF56300 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 22522731 22522731 G A 1 0 0 0 0 1 0 0 0 12521 942 33 3 3 PPP3CC 8 22522731 Missense_Mutation SNP G C3N-00551_T 2312387 22522731 122615905 294 15777 EPHX2 0 . GRCh38 8 27511839 27511839 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.664C>T p.Leu222Phe p.L222F ENST00000521400 6/19 180 144 36 248 248 0 strelka-varscan-mutect EPHX2,missense_variant,p.Leu222Phe,ENST00000521400,NM_001979.5;EPHX2,missense_variant,p.Leu169Phe,ENST00000380476,NM_001256482.1,NM_001256484.1;EPHX2,missense_variant,p.Leu156Phe,ENST00000521780,NM_001256483.1;EPHX2,missense_variant,p.Leu222Phe,ENST00000518379,;EPHX2,missense_variant,p.Leu181Phe,ENST00000521684,;EPHX2,intron_variant,,ENST00000517536,;EPHX2,downstream_gene_variant,,ENST00000520666,;EPHX2,non_coding_transcript_exon_variant,,ENST00000520623,;EPHX2,non_coding_transcript_exon_variant,,ENST00000521924,;EPHX2,upstream_gene_variant,,ENST00000523326,; T ENST00000521400 Transcript missense_variant 1094/3140 664/1668 222/555 L/F Ctc/Ttc 1 1 EPHX2 HGNC HGNC:3402 protein_coding YES CCDS6060.1 ENSP00000430269 P34913 UPI0000073FE5 NM_001979.5 tolerated(0.11) 6/19 hmmpanther:PTHR10992:SF855,hmmpanther:PTHR10992 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 27511839 27511839 C T 1 0 0 0 0 1 0 0 0 5027 927 32 3 3 EPHX2 8 27511839 Missense_Mutation SNP C C3N-00551_T 4989108 27511839 117626797 295 15778 KIF13B 0 . GRCh38 8 29140519 29140519 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.2433C>T p.= p.F811F ENST00000524189 20/40 99 91 8 119 119 0 strelka-varscan-mutect KIF13B,synonymous_variant,p.=,ENST00000524189,NM_015254.3;CTD-2647L4.1,non_coding_transcript_exon_variant,,ENST00000517632,;CTD-2647L4.1,non_coding_transcript_exon_variant,,ENST00000523661,; A ENST00000524189 Transcript synonymous_variant 2472/8745 2433/5481 811/1826 F ttC/ttT 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 20/40 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF338 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.55458 0.9999998 1 1 1 0 A 2 1 52 29140519 29140519 G A 1 0 0 0 0 0 0 0 1 8139 933 33 3 3 KIF13B 8 29140519 Silent SNP G C3N-00551_T 1628680 29140519 115998117 296 15779 UNC5D 0 . GRCh38 8 35748659 35748659 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.1899C>A p.= p.I633I ENST00000404895 12/17 127 120 7 208 208 0 strelka-varscan UNC5D,synonymous_variant,p.=,ENST00000287272,;UNC5D,synonymous_variant,p.=,ENST00000453357,;UNC5D,synonymous_variant,p.=,ENST00000416672,;UNC5D,synonymous_variant,p.=,ENST00000404895,NM_080872.2;UNC5D,synonymous_variant,p.=,ENST00000420357,;UNC5D,synonymous_variant,p.=,ENST00000449677,; A ENST00000404895 Transcript synonymous_variant 2227/3252 1899/2862 633/953 I atC/atA 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 12/17 Pfam_domain:PF00791,PROSITE_profiles:PS51145,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5,SMART_domains:SM00218 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 35748659 35748659 C A 1 0 0 0 0 0 0 0 1 17519 845 30 2 2 UNC5D 8 35748659 Silent SNP C C3N-00551_T 6608140 35748659 109389977 297 15780 UNC5D 0 . GRCh38 8 35759374 35759374 + Frame_Shift_Del DEL T T - novel C3N-00551_T C3N-00551_N T T c.2219delT p.Leu740CysfsTer86 p.L740Cfs*86 ENST00000404895 14/17 98 91 7 250 250 0 sindel-varindel-pindel UNC5D,frameshift_variant,p.Leu671CysfsTer86,ENST00000287272,;UNC5D,frameshift_variant,p.Leu735CysfsTer86,ENST00000453357,;UNC5D,frameshift_variant,p.Leu745CysfsTer86,ENST00000416672,;UNC5D,frameshift_variant,p.Leu740CysfsTer86,ENST00000404895,NM_080872.2;UNC5D,frameshift_variant,p.Leu673CysfsTer86,ENST00000420357,;UNC5D,frameshift_variant,p.Leu316CysfsTer86,ENST00000449677,; - ENST00000404895 Transcript frameshift_variant 2546/3252 2218/2862 740/953 L/X Ttg/tg 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 14/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 35759374 35759374 T - 1 0 1 0 1 0 0 0 0 17519 1490 52 0 0 UNC5D 8 35759374 Frame_Shift_Del DEL T C3N-00551_T 10715 35759374 109379262 298 15781 ADAM18 0 . GRCh38 8 39680100 39680100 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.1695T>A p.= p.A565A ENST00000265707 16/20 165 143 22 316 316 0 strelka-varscan ADAM18,synonymous_variant,p.=,ENST00000265707,NM_014237.2;ADAM18,synonymous_variant,p.=,ENST00000379866,NM_001320313.1;ADAM18,3_prime_UTR_variant,,ENST00000520087,; A ENST00000265707 Transcript synonymous_variant 1740/2388 1695/2220 565/739 A gcT/gcA 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 16/20 Pfam_domain:PF08516,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,SMART_domains:SM00608 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 39680100 39680100 T A 1 0 0 0 0 0 0 0 1 283 1538 54 4 4 ADAM18 8 39680100 Silent SNP T C3N-00551_T 3920726 39680100 105458536 299 15782 SNTG1 0 . GRCh38 8 50704654 50704654 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1093G>T p.Gly365Trp p.G365W ENST00000522124 16/19 278 239 39 361 361 0 strelka-varscan SNTG1,missense_variant,p.Gly365Trp,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Gly365Trp,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Gly365Trp,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,;SNTG1,3_prime_UTR_variant,,ENST00000524004,; T ENST00000522124 Transcript missense_variant 1754/3504 1093/1554 365/517 G/W Ggg/Tgg 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 16/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 50704654 50704654 G T 1 0 0 0 0 1 0 0 0 15194 1348 47 2 2 SNTG1 8 50704654 Missense_Mutation SNP G C3N-00551_T 11024554 50704654 94433982 300 15783 TRPA1 0 . GRCh38 8 72034275 72034275 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.2658C>A p.= p.L886L ENST00000262209 22/27 260 212 48 257 257 0 strelka-varscan TRPA1,synonymous_variant,p.=,ENST00000262209,NM_007332.2;TRPA1,synonymous_variant,p.=,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000512290,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;TRPA1,downstream_gene_variant,,ENST00000519720,;TRPA1,downstream_gene_variant,,ENST00000522271,; T ENST00000262209 Transcript synonymous_variant 2866/5223 2658/3360 886/1119 L ctC/ctA 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 22/27 Pfam_domain:PF00520,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 72034275 72034275 G T 1 0 0 0 0 0 0 0 1 17082 1277 45 2 2 TRPA1 8 72034275 Silent SNP G C3N-00551_T 21329621 72034275 73104361 301 15784 GDAP1 0 . GRCh38 8 74361951 74361951 + Silent SNP A A T rs746438323 C3N-00551_T C3N-00551_N A A c.552A>T p.= p.A184A ENST00000220822 4/6 487 439 48 494 494 0 strelka-varscan GDAP1,synonymous_variant,p.=,ENST00000220822,NM_018972.2;GDAP1,synonymous_variant,p.=,ENST00000434412,NM_001040875.2;GDAP1,non_coding_transcript_exon_variant,,ENST00000521096,;GDAP1,non_coding_transcript_exon_variant,,ENST00000520797,;GDAP1,non_coding_transcript_exon_variant,,ENST00000524366,;GDAP1,upstream_gene_variant,,ENST00000524195,;GDAP1,downstream_gene_variant,,ENST00000523640,;GDAP1,3_prime_UTR_variant,,ENST00000522568,; T ENST00000220822 Transcript synonymous_variant 632/3666 552/1077 184/358 A gcA/gcT rs746438323 1 1 GDAP1 HGNC HGNC:15968 protein_coding YES CCDS34911.1 ENSP00000220822 Q8TB36 UPI00001AE62B NM_018972.2 4/6 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50405 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 74361951 74361951 A T 1 0 0 0 0 0 0 0 1 6179 204 8 4 4 GDAP1 8 74361951 Silent SNP A C3N-00551_T 2327676 74361951 70776685 302 15785 KCNS2 0 . GRCh38 8 98429188 98429188 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.1209C>A p.= p.V403V ENST00000287042 2/2 119 77 42 97 97 0 strelka-varscan KCNS2,synonymous_variant,p.=,ENST00000287042,NM_020697.2;KCNS2,synonymous_variant,p.=,ENST00000521839,;STK3,intron_variant,,ENST00000517832,; A ENST00000287042 Transcript synonymous_variant 1559/5219 1209/1434 403/477 V gtC/gtA 1 1 KCNS2 HGNC HGNC:6301 protein_coding YES CCDS6279.1 ENSP00000287042 Q9ULS6 UPI0000001653 NM_020697.2 2/2 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,Prints_domain:PR01491,Prints_domain:PR01494,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF60,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 98429188 98429188 C A 1 0 0 0 0 0 0 0 1 8005 842 30 2 2 KCNS2 8 98429188 Silent SNP C C3N-00551_T 24067237 98429188 46709448 303 15786 FZD6 0 . GRCh38 8 103325465 103325465 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.1359T>G p.His453Gln p.H453Q ENST00000358755 4/7 268 234 34 200 200 0 strelka-varscan FZD6,missense_variant,p.His453Gln,ENST00000358755,NM_003506.3;FZD6,missense_variant,p.His453Gln,ENST00000522566,NM_001164615.1;FZD6,missense_variant,p.His421Gln,ENST00000523739,NM_001164616.1;FZD6,missense_variant,p.His453Gln,ENST00000522484,;FZD6,3_prime_UTR_variant,,ENST00000521195,;FZD6,3_prime_UTR_variant,,ENST00000519011,;FZD6,3_prime_UTR_variant,,ENST00000523933,; G ENST00000358755 Transcript missense_variant 1676/3788 1359/2121 453/706 H/Q caT/caG 1 1 FZD6 HGNC HGNC:4044 protein_coding YES CCDS6298.1 ENSP00000351605 O60353 A0A024R9E9 UPI0000061EB0 NM_003506.3 tolerated(0.33) 4/7 PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF75,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 103325465 103325465 T G 1 0 0 0 0 1 0 0 0 6005 1490 52 5 5 FZD6 8 103325465 Missense_Mutation SNP T C3N-00551_T 4896277 103325465 41813171 304 15787 RIMS2 0 . GRCh38 8 103961095 103961095 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.2732C>G p.Ser911Cys p.S911C ENST00000504942 15/24 151 135 16 125 125 0 strelka-varscan RIMS2,missense_variant,p.Ser703Cys,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Ser689Cys,ENST00000436393,;RIMS2,missense_variant,p.Ser911Cys,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Ser853Cys,ENST00000626043,;RIMS2,missense_variant,p.Ser703Cys,ENST00000408894,;RIMS2,missense_variant,p.Ser750Cys,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Ser899Cys,ENST00000632716,;RIMS2,missense_variant,p.Ser305Cys,ENST00000507677,; G ENST00000504942 Transcript missense_variant 2871/4228 2732/4050 911/1349 S/C tCt/tGt 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 15/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 103961095 103961095 C G 1 0 0 0 0 1 0 0 0 13543 913 32 4 4 RIMS2 8 103961095 Missense_Mutation SNP C C3N-00551_T 635630 103961095 41177541 305 15788 PKHD1L1 0 . GRCh38 8 109427136 109427136 + Missense_Mutation SNP G G A rs199692519 C3N-00551_T C3N-00551_N G G c.2980G>A p.Gly994Arg p.G994R ENST00000378402 25/78 187 169 18 302 302 0 strelka-varscan PKHD1L1,missense_variant,p.Gly994Arg,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 3084/13076 2980/12732 994/4243 G/R Gga/Aga rs199692519,COSM748795 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 25/78 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 109427136 109427136 G A 1 0 0 0 0 1 0 0 0 12068 1117 39 1 1 PKHD1L1 8 109427136 Missense_Mutation SNP G C3N-00551_T 5466041 109427136 35711500 306 15789 PKHD1L1 0 . GRCh38 8 109445020 109445020 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.5151T>A p.= p.A1717A ENST00000378402 38/78 260 236 24 200 200 0 strelka-varscan PKHD1L1,synonymous_variant,p.=,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript synonymous_variant 5255/13076 5151/12732 1717/4243 A gcT/gcA 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 38/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 109445020 109445020 T A 1 0 0 0 0 0 0 0 1 12068 1567 55 4 4 PKHD1L1 8 109445020 Silent SNP T C3N-00551_T 17884 109445020 35693616 307 15790 PKHD1L1 0 . GRCh38 8 109481452 109481452 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.9347G>T p.Gly3116Val p.G3116V ENST00000378402 56/78 108 95 13 139 139 0 strelka-varscan PKHD1L1,missense_variant,p.Gly3116Val,ENST00000378402,NM_177531.4;PKHD1L1,missense_variant,p.Gly44Val,ENST00000526472,; T ENST00000378402 Transcript missense_variant 9451/13076 9347/12732 3116/4243 G/V gGc/gTc 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 56/78 Pfam_domain:PF10162,PROSITE_profiles:PS51484,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF330,SMART_domains:SM01225 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 109481452 109481452 G T 1 0 0 0 0 1 0 0 0 12068 1203 42 2 2 PKHD1L1 8 109481452 Missense_Mutation SNP G C3N-00551_T 36432 109481452 35657184 308 15791 EXT1 0 . GRCh38 8 118110431 118110431 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.616G>T p.Asp206Tyr p.D206Y ENST00000378204 1/11 733 515 218 620 619 1 strelka-varscan EXT1,missense_variant,p.Asp206Tyr,ENST00000378204,NM_000127.2;EXT1,upstream_gene_variant,,ENST00000436216,;EXT1,intron_variant,,ENST00000437196,; A ENST00000378204 Transcript missense_variant 1423/8270 616/2241 206/746 D/Y Gac/Tac 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 deleterious(0) 1/11 Pfam_domain:PF03016,hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF97 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 118110431 118110431 C A 1 0 0 0 0 1 0 0 0 5191 855 30 2 2 EXT1 8 118110431 Missense_Mutation SNP C C3N-00551_T 8628979 118110431 27028205 309 15792 TAF2 0 . GRCh38 8 119795590 119795590 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.1133A>G p.Tyr378Cys p.Y378C ENST00000378164 9/26 498 470 28 490 489 1 strelka-varscan TAF2,missense_variant,p.Tyr378Cys,ENST00000378164,NM_003184.3;TAF2,missense_variant,p.Tyr71Cys,ENST00000523904,;TAF2,upstream_gene_variant,,ENST00000523734,; C ENST00000378164 Transcript missense_variant 1432/5048 1133/3600 378/1199 Y/C tAt/tGt 1 -1 TAF2 HGNC HGNC:11536 protein_coding YES CCDS34937.1 ENSP00000367406 Q6P1X5 UPI0000210507 NM_003184.3 tolerated(0.2) 9/26 hmmpanther:PTHR15137,Pfam_domain:PF01433,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 119795590 119795590 T C 1 0 0 0 0 1 0 0 0 15920 1406 49 5 5 TAF2 8 119795590 Missense_Mutation SNP T C3N-00551_T 1685159 119795590 25343046 310 15793 SNTB1 0 . GRCh38 8 120548907 120548907 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.1188G>T p.= p.L396L ENST00000395601 6/8 94 87 7 102 102 0 strelka-varscan SNTB1,synonymous_variant,p.=,ENST00000395601,NM_021021.3;SNTB1,synonymous_variant,p.=,ENST00000517992,; A ENST00000395601 Transcript synonymous_variant 1603/5164 1188/1617 396/538 L ctG/ctT 1 -1 SNTB1 HGNC HGNC:11168 protein_coding YES CCDS6334.1 ENSP00000378965 Q13884 UPI0000135B20 NM_021021.3 6/8 PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF11,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -14.79392 1 1 1 1 0 A 2 1 52 120548907 120548907 C A 1 0 0 0 0 0 0 0 1 15192 465 17 2 2 SNTB1 8 120548907 Silent SNP C C3N-00551_T 753317 120548907 24589729 311 15794 FER1L6 0 . GRCh38 8 123956025 123956025 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.27G>A p.= p.K9K ENST00000522917 2/41 249 184 65 216 216 0 strelka-varscan FER1L6,synonymous_variant,p.=,ENST00000522917,NM_001039112.2; A ENST00000522917 Transcript synonymous_variant 233/6051 27/5574 9/1857 K aaG/aaA 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 2/41 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF37 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 123956025 123956025 G A 1 0 0 0 0 0 0 0 1 5678 933 33 3 3 FER1L6 8 123956025 Silent SNP G C3N-00551_T 3407118 123956025 21182611 312 15795 KCNQ3 0 . GRCh38 8 132184300 132184301 + Frame_Shift_Ins INS - - A novel C3N-00551_T C3N-00551_N - - c.544dupT p.Cys182LeufsTer102 p.C182Lfs*102 ENST00000388996 3/15 716 500 216 699 699 0 sindel-varindel-pindel KCNQ3,frameshift_variant,p.Cys182LeufsTer102,ENST00000388996,NM_004519.3;KCNQ3,frameshift_variant,p.Cys61LeufsTer102,ENST00000621976,;KCNQ3,frameshift_variant,p.Cys182LeufsTer102,ENST00000519445,;KCNQ3,frameshift_variant,p.Cys62LeufsTer102,ENST00000521134,NM_001204824.1;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,; A ENST00000388996 Transcript frameshift_variant 965-966/11441 544-545/2619 182/872 C/LX tgc/tTgc 1 -1 KCNQ3 HGNC HGNC:6297 protein_coding YES CCDS34943.1 ENSP00000373648 O43525 UPI00001279F0 NM_004519.3 3/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR01459,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF5,Superfamily_domains:SSF81324 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 52 132184300 132184300 - A 1 0 1 1 0 0 0 0 0 8000 710 25 0 0 KCNQ3 8 132184300 Frame_Shift_Ins INS - C3N-00551_T 8228275 132184300 12954336 313 15796 ZFAT 0 . GRCh38 8 134601841 134601841 + Silent SNP C C A rs777603767 C3N-00551_T C3N-00551_N C C c.1878G>T p.= p.T626T ENST00000377838 6/16 88 77 11 122 122 0 strelka-varscan ZFAT,synonymous_variant,p.=,ENST00000520727,NM_001029939.3,NM_001289394.1;ZFAT,synonymous_variant,p.=,ENST00000377838,NM_020863.3;ZFAT,synonymous_variant,p.=,ENST00000429442,;ZFAT,synonymous_variant,p.=,ENST00000520214,NM_001167583.2;ZFAT,synonymous_variant,p.=,ENST00000520356,NM_001174158.1;ZFAT,synonymous_variant,p.=,ENST00000523399,NM_001174157.1;ZFAT-AS1,downstream_gene_variant,,ENST00000505776,;ZFAT-AS1_2,downstream_gene_variant,,ENST00000613742,;ZFAT-AS1_3,downstream_gene_variant,,ENST00000611506,;ZFAT-AS1_1,downstream_gene_variant,,ENST00000620907,;ZFAT,downstream_gene_variant,,ENST00000523040,;ZFAT,synonymous_variant,p.=,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000522974,;ZFAT,upstream_gene_variant,,ENST00000519827,; A ENST00000377838 Transcript synonymous_variant 2053/4597 1878/3732 626/1243 T acG/acT rs777603767,COSM604396,COSM604397 1 -1 ZFAT HGNC HGNC:19899 protein_coding YES CCDS47924.1 ENSP00000367069 Q9P243 UPI0000210061 NM_020863.3 6/16 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 198 11 0 0 0 0 0 -19.9995 0.9999408 1 1 1 0 A 2 1 52 134601841 134601841 C A 1 0 0 0 0 0 0 0 1 18209 755 27 1 1 ZFAT 8 134601841 Silent SNP C C3N-00551_T 2417541 134601841 10536795 314 15797 FAM135B 0 . GRCh38 8 138152157 138152157 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.2318C>A p.Ala773Asp p.A773D ENST00000395297 13/20 114 96 18 120 120 0 strelka-varscan FAM135B,missense_variant,p.Ala773Asp,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Ala773Asp,ENST00000276737,;FAM135B,missense_variant,p.Ala83Asp,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,; T ENST00000395297 Transcript missense_variant 2489/6962 2318/4221 773/1406 A/D gCt/gAt COSM1096482,COSM1096483 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 13/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 138152157 138152157 G T 1 0 0 0 0 1 0 0 0 5299 971 34 2 2 FAM135B 8 138152157 Missense_Mutation SNP G C3N-00551_T 3550316 138152157 6986479 315 15798 FAM135B 0 . GRCh38 8 138242983 138242983 + Missense_Mutation SNP A A C C3N-00551_T C3N-00551_N A A c.628T>G p.Leu210Val p.L210V ENST00000395297 7/20 186 175 11 166 166 0 strelka-varscan FAM135B,missense_variant,p.Leu210Val,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Leu210Val,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; C ENST00000395297 Transcript missense_variant 799/6962 628/4221 210/1406 L/V Ttg/Gtg COSM3319132,COSM3319133,COSM604319,COSM604320 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.57) 7/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 138242983 138242983 A C 1 0 0 0 0 1 0 0 0 5299 69 3 5 5 FAM135B 8 138242983 Missense_Mutation SNP A C3N-00551_T 90826 138242983 6895653 316 15799 PTK2 0 . GRCh38 8 140735290 140735290 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1991G>T p.Ser664Ile p.S664I ENST00000340930 22/33 422 288 134 343 343 0 strelka-varscan PTK2,missense_variant,p.Ser664Ile,ENST00000522684,NM_153831.3;PTK2,missense_variant,p.Ser708Ile,ENST00000517887,;PTK2,missense_variant,p.Ser708Ile,ENST00000519419,;PTK2,missense_variant,p.Ser664Ile,ENST00000395218,;PTK2,missense_variant,p.Ser664Ile,ENST00000340930,NM_001199649.1;PTK2,missense_variant,p.Ser664Ile,ENST00000521059,NM_005607.4;PTK2,missense_variant,p.Ser675Ile,ENST00000519654,;PTK2,missense_variant,p.Ser292Ile,ENST00000519465,;PTK2,missense_variant,p.Ser336Ile,ENST00000523539,;PTK2,missense_variant,p.Ser362Ile,ENST00000521986,;MIR151A,upstream_gene_variant,,ENST00000521276,;PTK2,non_coding_transcript_exon_variant,,ENST00000518509,;PTK2,splice_region_variant,,ENST00000521981,;PTK2,3_prime_UTR_variant,,ENST00000519993,NM_001316342.1;PTK2,3_prime_UTR_variant,,ENST00000524202,;PTK2,3_prime_UTR_variant,,ENST00000521029,;PTK2,non_coding_transcript_exon_variant,,ENST00000520917,;PTK2,intron_variant,,ENST00000521250,; A ENST00000340930 Transcript missense_variant 2146/4414 1991/3198 664/1065 S/I aGc/aTc 1 -1 PTK2 HGNC HGNC:9611 protein_coding YES CCDS56557.1 ENSP00000341189 Q05397 UPI0001E8F57E NM_001199649.1 deleterious(0.04) 22/33 Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF78,Prints_domain:PR00109 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 140735290 140735290 C A 1 0 0 0 0 1 0 0 0 12918 797 28 2 2 PTK2 8 140735290 Missense_Mutation SNP C C3N-00551_T 2492307 140735290 4403346 317 15800 RHPN1 0 . GRCh38 8 143378796 143378796 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.560G>T p.Arg187Met p.R187M ENST00000289013 6/15 255 230 25 231 230 1 strelka-varscan RHPN1,missense_variant,p.Arg187Met,ENST00000289013,NM_052924.2;RHPN1,non_coding_transcript_exon_variant,,ENST00000522335,;RHPN1,upstream_gene_variant,,ENST00000522899,; T ENST00000289013 Transcript missense_variant 661/3683 560/2013 187/670 R/M aGg/aTg 1 1 RHPN1 HGNC HGNC:19973 protein_coding YES CCDS47927.1 ENSP00000289013 Q8TCX5 UPI0000071870 NM_052924.2 deleterious(0) 6/15 PROSITE_profiles:PS51180,hmmpanther:PTHR23031:SF6,hmmpanther:PTHR23031,Pfam_domain:PF03097,Gene3D:2xs1A01,SMART_domains:SM01041 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 143378796 143378796 G T 1 0 0 0 0 1 0 0 0 13523 1000 35 2 2 RHPN1 8 143378796 Missense_Mutation SNP G C3N-00551_T 2643506 143378796 1759840 318 15801 PLEC 0 . GRCh38 8 143922364 143922364 + Missense_Mutation SNP T T A rs782783768 C3N-00551_T C3N-00551_N T T c.7868A>T p.Gln2623Leu p.Q2623L ENST00000322810 32/32 568 401 167 654 654 0 strelka-varscan PLEC,missense_variant,p.Gln2623Leu,ENST00000322810,NM_201380.3;PLEC,missense_variant,p.Gln2486Leu,ENST00000345136,NM_201384.2;PLEC,missense_variant,p.Gln2513Leu,ENST00000436759,NM_000445.4;PLEC,missense_variant,p.Gln2464Leu,ENST00000354958,NM_201379.2;PLEC,missense_variant,p.Gln2486Leu,ENST00000354589,NM_201382.3;PLEC,missense_variant,p.Gln2490Leu,ENST00000357649,NM_201383.2;PLEC,missense_variant,p.Gln2472Leu,ENST00000356346,NM_201378.3;PLEC,missense_variant,p.Gln2454Leu,ENST00000398774,NM_201381.2;PLEC,missense_variant,p.Gln2509Leu,ENST00000527096,;PLEC,missense_variant,p.Gln56Leu,ENST00000527303,; A ENST00000322810 Transcript missense_variant 8038/15249 7868/14055 2623/4684 Q/L cAg/cTg rs782783768 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 deleterious_low_confidence(0.02) 32/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 143922364 143922364 T A 1 0 0 0 0 1 0 0 0 12145 1580 55 4 4 PLEC 8 143922364 Missense_Mutation SNP T C3N-00551_T 543568 143922364 1216272 319 15802 MROH1 0 . GRCh38 8 144261123 144261123 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.4681T>G p.Phe1561Val p.F1561V ENST00000528919 41/43 302 251 51 239 239 0 strelka-varscan MROH1,missense_variant,p.Phe1561Val,ENST00000528919,NM_032450.2;MROH1,missense_variant,p.Phe1561Val,ENST00000326134,;MROH1,missense_variant,p.Phe1552Val,ENST00000534366,NM_001288814.1;MROH1,missense_variant,p.Phe523Val,ENST00000544576,;BOP1,downstream_gene_variant,,ENST00000569669,NM_015201.4;BOP1,downstream_gene_variant,,ENST00000569403,;BOP1,downstream_gene_variant,,ENST00000616126,;BOP1,downstream_gene_variant,,ENST00000563210,;BOP1,downstream_gene_variant,,ENST00000568812,;BOP1,downstream_gene_variant,,ENST00000569160,; G ENST00000528919 Transcript missense_variant 4802/5234 4681/4926 1561/1641 F/V Ttc/Gtc 1 1 MROH1 HGNC HGNC:26958 protein_coding YES CCDS47938.1 ENSP00000435565 Q8NDA8 UPI0001AE6FA6 NM_032450.2 deleterious(0) 41/43 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 144261123 144261123 T G 1 0 0 0 0 1 0 0 0 9743 1841 64 5 5 MROH1 8 144261123 Missense_Mutation SNP T C3N-00551_T 338759 144261123 877513 320 15803 IL33 0 . GRCh38 9 6241769 6241769 + Missense_Mutation SNP G G T rs750079169 C3N-00551_T C3N-00551_N G G c.75G>T p.Leu25Phe p.L25F ENST00000381434 1/7 79 72 7 145 145 0 strelka-varscan-mutect IL33,missense_variant,p.Leu25Phe,ENST00000381434,NM_001314046.1,NM_001314047.1,NM_001314044.1,NM_001314045.1,NM_033439.3;IL33,missense_variant,p.Leu25Phe,ENST00000456383,NM_001199640.1;IL33,missense_variant,p.Leu25Phe,ENST00000417746,NM_001199641.1;IL33,missense_variant,p.Leu25Phe,ENST00000611532,;IL33,non_coding_transcript_exon_variant,,ENST00000463336,; T ENST00000381434 Transcript missense_variant 88/2641 75/813 25/270 L/F ttG/ttT rs750079169 1 1 IL33 HGNC HGNC:16028 protein_coding YES CCDS6468.1 ENSP00000370842 O95760 UPI000000DBB2 NM_001314046.1,NM_001314047.1,NM_001314044.1,NM_001314045.1,NM_033439.3 deleterious(0.02) 1/7 Pfam_domain:PF15095,hmmpanther:PTHR21114,hmmpanther:PTHR21114:SF0 MODERATE 1 SNV 1 1 PASS rs750079169 . 0 204 4 2 0 0 0 0 -11.82533 0.9999502 1 1 1 0 T 3 4 52 6241769 6241769 G T 1 0 0 0 0 1 0 0 0 7592 1368 48 2 2 IL33 9 6241769 Missense_Mutation SNP G C3N-00551_T 6241769 132152948 321 15804 FREM1 0 . GRCh38 9 14812999 14812999 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.2706A>T p.= p.S902S ENST00000422223 17/38 121 105 16 176 176 0 strelka-varscan-mutect FREM1,synonymous_variant,p.=,ENST00000422223,NM_144966.5;FREM1,synonymous_variant,p.=,ENST00000380880,;FREM1,synonymous_variant,p.=,ENST00000380875,; A ENST00000422223 Transcript synonymous_variant 3522/10086 2706/6540 902/2179 S tcA/tcT 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 17/38 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 14812999 14812999 T A 1 0 0 0 0 0 0 0 1 5911 1567 55 4 4 FREM1 9 14812999 Silent SNP T C3N-00551_T 8571230 14812999 123581718 322 15805 SAXO1 0 . GRCh38 9 18928879 18928879 + Missense_Mutation SNP G G T rs757111310 C3N-00551_T C3N-00551_N G G c.598C>A p.Pro200Thr p.P200T ENST00000380534 4/4 213 184 29 287 286 1 strelka-varscan-mutect SAXO1,missense_variant,p.Pro200Thr,ENST00000380534,NM_153707.3;SAXO1,missense_variant,p.Pro135Thr,ENST00000542071,NM_001287049.1;SAXO1,3_prime_UTR_variant,,ENST00000380530,NM_001287050.1; T ENST00000380534 Transcript missense_variant 878/2099 598/1425 200/474 P/T Ccc/Acc rs757111310 1 -1 SAXO1 HGNC HGNC:28566 protein_coding YES CCDS6487.1 ENSP00000369907 Q8IYX7 UPI0000367609 NM_153707.3 deleterious(0) 4/4 hmmpanther:PTHR31516,hmmpanther:PTHR31516:SF9 MODERATE 1 SNV 1 1 PASS rs757111310 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 18928879 18928879 G T 1 0 0 0 0 1 0 0 0 14118 1232 43 2 2 SAXO1 9 18928879 Missense_Mutation SNP G C3N-00551_T 4115880 18928879 119465838 323 15806 ARID3C 0 . GRCh38 9 34622467 34622467 + Silent SNP G G T rs146137441 C3N-00551_T C3N-00551_N G G c.928C>A p.= p.R310R ENST00000378909 5/7 80 62 18 100 100 0 strelka-varscan-mutect ARID3C,synonymous_variant,p.=,ENST00000378909,NM_001017363.1;DCTN3,upstream_gene_variant,,ENST00000378913,;DCTN3,upstream_gene_variant,,ENST00000341694,NM_024348.3,NM_001281426.1;DCTN3,upstream_gene_variant,,ENST00000259632,NM_007234.4;DCTN3,upstream_gene_variant,,ENST00000378916,NM_001281425.1;DCTN3,upstream_gene_variant,,ENST00000477738,NM_001281427.1;DCTN3,upstream_gene_variant,,ENST00000421919,;DCTN3,upstream_gene_variant,,ENST00000378911,; T ENST00000378909 Transcript synonymous_variant 1021/1411 928/1239 310/412 R Cgg/Agg rs146137441 1 -1 ARID3C HGNC HGNC:21209 protein_coding YES CCDS35006.1 ENSP00000368189 A6NKF2 UPI0000509F06 NM_001017363.1 5/7 PROSITE_profiles:PS51486,hmmpanther:PTHR15348,hmmpanther:PTHR15348:SF2 LOW SNV 2 1 PASS rs146137441 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 34622467 34622467 G T 1 0 0 0 0 0 0 0 1 1054 1144 40 1 1 ARID3C 9 34622467 Silent SNP G C3N-00551_T 15693588 34622467 103772250 324 15807 SPATA31A1 0 . GRCh38 9 39359356 39359356 + Missense_Mutation SNP A A C novel C3N-00551_T C3N-00551_N A A c.1633A>C p.Lys545Gln p.K545Q ENST00000377647 4/4 337 304 33 470 470 0 varscan-mutect SPATA31A1,missense_variant,p.Lys545Gln,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; C ENST00000377647 Transcript missense_variant 1653/4256 1633/4086 545/1361 K/Q Aaa/Caa 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 deleterious(0.01) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF14650 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 39359356 39359356 A C 1 0 0 0 0 1 0 0 0 15343 363 13 5 5 SPATA31A1 9 39359356 Missense_Mutation SNP A C3N-00551_T 4736889 39359356 99035361 325 15808 APBA1 0 . GRCh38 9 69432654 69432654 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2324G>T p.Gly775Val p.G775V ENST00000265381 12/13 44 31 13 33 33 0 strelka-mutect APBA1,missense_variant,p.Gly775Val,ENST00000265381,NM_001163.3;RP11-548B3.3,upstream_gene_variant,,ENST00000457328,; A ENST00000265381 Transcript missense_variant 2547/6534 2324/2514 775/837 G/V gGa/gTa 1 -1 APBA1 HGNC HGNC:578 protein_coding YES CCDS6630.1 ENSP00000265381 Q02410 UPI000013D611 NM_001163.3 deleterious(0) 12/13 PROSITE_profiles:PS50106,hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF14,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs1445102276 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 69432654 69432654 C A 1 0 0 0 0 1 0 0 0 876 855 30 2 2 APBA1 9 69432654 Missense_Mutation SNP C C3N-00551_T 30073298 69432654 68962063 326 15809 KIAA0368 0 . GRCh38 9 111383304 111383304 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.4244A>T p.Lys1415Ile p.K1415I ENST00000259335 36/51 134 92 42 138 138 0 strelka-varscan-mutect KIAA0368,missense_variant,p.Lys1415Ile,ENST00000259335,NM_001080398.1;KIAA0368,missense_variant,p.Lys1237Ile,ENST00000338205,; A ENST00000259335 Transcript missense_variant 4244/7391 4244/6054 1415/2017 K/I aAa/aTa 1 -1 KIAA0368 HGNC HGNC:29020 protein_coding YES CCDS48006.1 ENSP00000259335 J3KN16 UPI0000DD7F7A NM_001080398.1 tolerated(0.29) 36/51 hmmpanther:PTHR23346,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS rs1423090125 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 111383304 111383304 T A 1 0 0 0 0 1 0 0 0 8083 1841 64 4 4 KIAA0368 9 111383304 Missense_Mutation SNP T C3N-00551_T 41950650 111383304 27011413 327 15810 DNM1 0 . GRCh38 9 128219159 128219159 + Nonsense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.496A>T p.Lys166Ter p.K166* ENST00000372923 4/22 343 241 102 364 364 0 strelka-varscan-mutect DNM1,stop_gained,p.Lys166Ter,ENST00000627543,;DNM1,stop_gained,p.Lys166Ter,ENST00000628346,;DNM1,stop_gained,p.Lys166Ter,ENST00000341179,NM_001005336.2;DNM1,stop_gained,p.Lys166Ter,ENST00000393594,NM_001288737.1,NM_001288738.1;DNM1,stop_gained,p.Lys166Ter,ENST00000372923,NM_004408.3;DNM1,stop_gained,p.Lys166Ter,ENST00000486160,NM_001288739.1;DNM1,stop_gained,p.Lys166Ter,ENST00000634267,;DNM1,stop_gained,p.Lys166Ter,ENST00000627061,;DNM1,stop_gained,p.Lys166Ter,ENST00000475805,;DNM1,downstream_gene_variant,,ENST00000637094,;DNM1,downstream_gene_variant,,ENST00000636103,;DNM1,downstream_gene_variant,,ENST00000636874,;DNM1,downstream_gene_variant,,ENST00000635766,;DNM1,stop_gained,p.Lys166Ter,ENST00000636280,;DNM1,stop_gained,p.Lys109Ter,ENST00000637999,;DNM1,non_coding_transcript_exon_variant,,ENST00000441149,;DNM1,upstream_gene_variant,,ENST00000482638,; T ENST00000372923 Transcript stop_gained 615/3244 496/2595 166/864 K/* Aag/Tag 1 1 DNM1 HGNC HGNC:2972 protein_coding YES CCDS6895.1 ENSP00000362014 Q05193 UPI000013CA31 NM_004408.3 4/22 Gene3D:3.40.50.300,Pfam_domain:PF00350,PROSITE_profiles:PS51718,hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF32,SMART_domains:SM00053,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 128219159 128219159 A T 1 0 0 0 0 0 1 0 0 4483 131 5 4 4 DNM1 9 128219159 Nonsense_Mutation SNP A C3N-00551_T 16835855 128219159 10175558 328 15811 HMCN2 0 . GRCh38 9 130393906 130393906 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.10396C>A p.Leu3466Met p.L3466M ENST00000624552 68/98 165 135 30 198 198 0 strelka-varscan-mutect HMCN2,missense_variant,p.Leu3466Met,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,; A ENST00000624552 Transcript missense_variant 10396/15610 10396/15180 3466/5059 L/M Ctg/Atg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.03) 68/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 130393906 130393906 C A 1 0 0 0 0 1 0 0 0 7112 680 24 2 2 HMCN2 9 130393906 Missense_Mutation SNP C C3N-00551_T 2174747 130393906 8000811 329 15812 FAM78A 0 . GRCh38 9 131260985 131260985 + Missense_Mutation SNP C C A rs143378086 C3N-00551_T C3N-00551_N C C c.689G>T p.Arg230Leu p.R230L ENST00000372271 2/2 83 63 20 86 86 0 strelka-varscan-mutect FAM78A,missense_variant,p.Arg230Leu,ENST00000372271,NM_033387.3;FAM78A,missense_variant,p.Arg227Leu,ENST00000372269,;FAM78A,missense_variant,p.Arg199Leu,ENST00000464831,;FAM78A,non_coding_transcript_exon_variant,,ENST00000247295,; A ENST00000372271 Transcript missense_variant 1057/3966 689/852 230/283 R/L cGg/cTg rs143378086 1 -1 FAM78A HGNC HGNC:25465 protein_coding YES CCDS6941.2 ENSP00000361345 Q5JUQ0 UPI000013F430 NM_033387.3 deleterious(0.04) 2/2 hmmpanther:PTHR31655,hmmpanther:PTHR31655:SF3 MODERATE 1 SNV 1 1 PASS rs143378086 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 131260985 131260985 C A 1 0 0 0 0 1 0 0 0 5487 652 23 1 1 FAM78A 9 131260985 Missense_Mutation SNP C C3N-00551_T 867079 131260985 7133732 330 15813 TSC1 0 . GRCh38 9 132927305 132927305 + Splice_Site SNP C C A novel C3N-00551_T C3N-00551_N C C c.107-1G>T p.X36_splice ENST00000298552 387 306 81 535 535 0 strelka-varscan-mutect TSC1,splice_acceptor_variant,,ENST00000298552,NM_000368.4,NM_001162426.1;TSC1,splice_acceptor_variant,,ENST00000440111,;TSC1,splice_acceptor_variant,,ENST00000545250,NM_001162427.1;TSC1,splice_acceptor_variant,,ENST00000403810,;TSC1,splice_acceptor_variant,,ENST00000475903,;TSC1,splice_acceptor_variant,,ENST00000490179,;TSC1,upstream_gene_variant,,ENST00000461879,;TSC1,splice_acceptor_variant,,ENST00000493467,; A ENST00000298552 Transcript splice_acceptor_variant -/8604 107/3495 36/1164 1 -1 TSC1 HGNC HGNC:12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 X5D9D2 UPI000013773E NM_000368.4,NM_001162426.1 3/22 HIGH 1 SNV 1 1 PASS rs1064793494 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 52 132927305 132927305 C A 1 0 0 0 0 0 0 1 0 17111 927 32 2 2 TSC1 9 132927305 Splice_Site SNP C C3N-00551_T 1666320 132927305 5467412 331 15814 GBGT1 0 . GRCh38 9 133154113 133154113 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.508A>G p.Ile170Val p.I170V ENST00000372040 7/7 123 112 11 167 167 0 strelka-varscan-mutect GBGT1,missense_variant,p.Ile170Val,ENST00000372040,NM_021996.5,NM_001288572.1;GBGT1,missense_variant,p.Ile153Val,ENST00000540636,NM_001288573.1,NM_001282632.1;GBGT1,synonymous_variant,p.=,ENST00000372043,NM_001282629.1;GBGT1,3_prime_UTR_variant,,ENST00000372038,;RALGDS,upstream_gene_variant,,ENST00000393160,NM_001042368.2;GBGT1,non_coding_transcript_exon_variant,,ENST00000472281,;GBGT1,non_coding_transcript_exon_variant,,ENST00000470431,; C ENST00000372040 Transcript missense_variant 820/1980 508/1044 170/347 I/V Atc/Gtc 1 -1 GBGT1 HGNC HGNC:20460 protein_coding YES CCDS6960.1 ENSP00000361110 Q8N5D6 J7Q0Z1 UPI000013DB02 NM_021996.5,NM_001288572.1 tolerated(1) 7/7 Gene3D:3.90.550.10,Pfam_domain:PF03414,hmmpanther:PTHR10462,hmmpanther:PTHR10462:SF29,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.98254 0.9999998 1 1 1 0 C 3 2 52 133154113 133154113 T C 1 0 0 0 0 1 0 0 0 6143 1464 51 5 5 GBGT1 9 133154113 Missense_Mutation SNP T C3N-00551_T 226808 133154113 5240604 332 15815 OBP2B 0 . GRCh38 9 133208137 133208137 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.273C>G p.Ser91Arg p.S91R ENST00000618116 3/7 197 165 32 277 277 0 strelka-varscan-mutect OBP2B,missense_variant,p.Ser91Arg,ENST00000618116,NM_001288987.1;OBP2B,missense_variant,p.Ser91Arg,ENST00000372032,;OBP2B,missense_variant,p.Ser91Arg,ENST00000372034,NM_014581.3;OBP2B,non_coding_transcript_exon_variant,,ENST00000461961,;OBP2B,missense_variant,p.Ser91Arg,ENST00000473737,; C ENST00000618116 Transcript missense_variant 324/961 273/513 91/170 S/R agC/agG 1 -1 OBP2B HGNC HGNC:23381 protein_coding YES CCDS6961.1 ENSP00000484615 Q9NPH6 UPI00000377BC NM_001288987.1 tolerated(0.08) 3/7 hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF6,Pfam_domain:PF00061,Gene3D:2.40.128.20,Superfamily_domains:SSF50814,Prints_domain:PR01175 MODERATE 1 SNV 1 1 PASS rs1299648620 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 133208137 133208137 G C 1 0 0 0 0 1 0 0 0 10888 1101 38 4 4 OBP2B 9 133208137 Missense_Mutation SNP G C3N-00551_T 54024 133208137 5186580 333 15816 BRD3 0 . GRCh38 9 134053312 134053312 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.166G>T p.Ala56Ser p.A56S ENST00000303407 2/12 245 178 67 291 291 0 strelka-varscan-mutect BRD3,missense_variant,p.Ala56Ser,ENST00000303407,NM_007371.3;BRD3,missense_variant,p.Ala56Ser,ENST00000371834,;BRD3,missense_variant,p.Ala56Ser,ENST00000371842,;BRD3,downstream_gene_variant,,ENST00000433041,;RP11-374P20.4,upstream_gene_variant,,ENST00000412181,;BRD3,upstream_gene_variant,,ENST00000494743,; A ENST00000303407 Transcript missense_variant 352/5652 166/2181 56/726 A/S Gcc/Tcc 1 -1 BRD3 HGNC HGNC:1104 protein_coding YES CCDS6980.1 ENSP00000305918 Q15059 A0A024R8H6 UPI0000126ACD NM_007371.3 tolerated(0.7) 2/12 Gene3D:1.20.920.10,Pfam_domain:PF00439,Prints_domain:PR00503,PROSITE_patterns:PS00633,PROSITE_profiles:PS50014,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF20,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 1 1 PASS rs988329845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 134053312 134053312 C A 1 0 0 0 0 1 0 0 0 1673 768 27 1 1 BRD3 9 134053312 Missense_Mutation SNP C C3N-00551_T 845175 134053312 4341405 334 15817 CAMSAP1 0 . GRCh38 9 135818457 135818457 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.4119G>T p.= p.V1373V ENST00000389532 13/17 193 136 57 232 232 0 strelka-varscan-mutect CAMSAP1,synonymous_variant,p.=,ENST00000389532,NM_015447.3;CAMSAP1,synonymous_variant,p.=,ENST00000312405,;CAMSAP1,synonymous_variant,p.=,ENST00000409386,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000483991,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000493088,;CAMSAP1,non_coding_transcript_exon_variant,,ENST00000482664,;CAMSAP1,upstream_gene_variant,,ENST00000487868,; A ENST00000389532 Transcript synonymous_variant 4184/7696 4119/4809 1373/1602 V gtG/gtT 1 -1 CAMSAP1 HGNC HGNC:19946 protein_coding YES CCDS35176.2 ENSP00000374183 Q5T5Y3 UPI0000EDA283 NM_015447.3 13/17 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 135818457 135818457 C A 1 0 0 0 0 0 0 0 1 2303 697 25 2 2 CAMSAP1 9 135818457 Silent SNP C C3N-00551_T 1765145 135818457 2576260 335 15818 SNAPC4 0 . GRCh38 9 136387793 136387793 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1179G>T p.Lys393Asn p.K393N ENST00000298532 11/23 309 251 58 385 385 0 strelka-varscan-mutect SNAPC4,missense_variant,p.Lys393Asn,ENST00000298532,NM_003086.2;SNAPC4,missense_variant,p.Lys393Asn,ENST00000637388,; A ENST00000298532 Transcript missense_variant 1548/5010 1179/4410 393/1469 K/N aaG/aaT 1 -1 SNAPC4 HGNC HGNC:11137 protein_coding YES CCDS6998.1 ENSP00000298532 Q5SXM2 A0A024R8F4 UPI000013E4EC NM_003086.2 deleterious(0) 11/23 Gene3D:1.10.10.60,PROSITE_profiles:PS50090,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF486,SMART_domains:SM00717,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1322259710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 136387793 136387793 C A 1 0 0 0 0 1 0 0 0 15158 912 32 2 2 SNAPC4 9 136387793 Missense_Mutation SNP C C3N-00551_T 569336 136387793 2006924 336 15819 CLIC3 0 . GRCh38 9 136995490 136995490 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.221A>T p.Asp74Val p.D74V ENST00000494426 3/6 152 123 29 138 138 0 strelka-varscan-mutect CLIC3,missense_variant,p.Asp74Val,ENST00000494426,NM_004669.2;C9orf142,downstream_gene_variant,,ENST00000371620,NM_183241.1;CLIC3,non_coding_transcript_exon_variant,,ENST00000480181,;CLIC3,non_coding_transcript_exon_variant,,ENST00000473911,;C9orf142,downstream_gene_variant,,ENST00000498095,;C9orf142,downstream_gene_variant,,ENST00000493968,;C9orf142,downstream_gene_variant,,ENST00000481187,;C9orf142,downstream_gene_variant,,ENST00000467845,;C9orf142,downstream_gene_variant,,ENST00000483807,;C9orf142,downstream_gene_variant,,ENST00000492564,;C9orf142,downstream_gene_variant,,ENST00000463765,; A ENST00000494426 Transcript missense_variant 481/1017 221/711 74/236 D/V gAc/gTc 1 -1 CLIC3 HGNC HGNC:2064 protein_coding YES CCDS7021.1 ENSP00000419378 O95833 UPI00001AE551 NM_004669.2 deleterious(0) 3/6 PROSITE_profiles:PS50405,hmmpanther:PTHR11260:SF266,hmmpanther:PTHR11260,Gene3D:3.40.30.10,Pfam_domain:PF13417,Superfamily_domains:SSF52833,Prints_domain:PR01263 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999961 1 1 1 0 A 3 1 52 136995490 136995490 T A 1 0 0 0 0 1 0 0 0 3296 1667 58 4 4 CLIC3 9 136995490 Missense_Mutation SNP T C3N-00551_T 607697 136995490 1399227 337 15820 AKR1C4 0 . GRCh38 10 5213006 5213006 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.693C>T p.= p.N231N ENST00000380448 9/11 158 137 21 125 125 0 strelka-varscan-mutect AKR1C4,synonymous_variant,p.=,ENST00000380448,;AKR1C4,synonymous_variant,p.=,ENST00000263126,NM_001818.3; T ENST00000380448 Transcript synonymous_variant 946/1414 693/972 231/323 N aaC/aaT 1 1 AKR1C4 HGNC HGNC:387 protein_coding YES CCDS7064.1 ENSP00000369814 P17516 UPI000013D3B2 9/11 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF134,Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 5213006 5213006 C T 1 0 0 0 0 0 0 0 1 556 564 20 3 3 AKR1C4 10 5213006 Silent SNP C C3N-00551_T 5213006 128584416 338 15821 TAF3 0 . GRCh38 10 8009315 8009315 + Silent SNP G G T rs774790162 C3N-00551_T C3N-00551_N G G c.2553G>T p.= p.T851T ENST00000344293 5/7 190 162 28 276 276 0 strelka-varscan-mutect TAF3,synonymous_variant,p.=,ENST00000344293,NM_031923.3; T ENST00000344293 Transcript synonymous_variant 2759/4872 2553/2790 851/929 T acG/acT rs774790162,COSM4732003 1 1 TAF3 HGNC HGNC:17303 protein_coding YES CCDS41487.1 ENSP00000340271 Q5VWG9 UPI00004588FA NM_031923.3 5/7 hmmpanther:PTHR12321,hmmpanther:PTHR12321:SF34,Superfamily_domains:SSF57903 0,1 LOW 1 SNV 2 0,1 1 PASS rs774790162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 8009315 8009315 G T 1 0 0 0 0 0 0 0 1 15921 1103 39 1 1 TAF3 10 8009315 Silent SNP G C3N-00551_T 2796309 8009315 125788107 339 15822 MYO3A 0 . GRCh38 10 26128479 26128479 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.2203A>T p.Asn735Tyr p.N735Y ENST00000265944 20/35 300 271 29 312 312 0 strelka-varscan-mutect MYO3A,missense_variant,p.Asn735Tyr,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; T ENST00000265944 Transcript missense_variant 2369/5581 2203/4851 735/1616 N/Y Aac/Tac 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0) 20/35 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 26128479 26128479 A T 1 0 0 0 0 1 0 0 0 10077 362 13 4 4 MYO3A 10 26128479 Missense_Mutation SNP A C3N-00551_T 18119164 26128479 107668943 340 15823 ZNF438 0 . GRCh38 10 30848632 30848632 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1773G>T p.Arg591Ser p.R591S ENST00000442986 7/8 281 221 60 303 303 0 strelka-varscan-mutect ZNF438,missense_variant,p.Arg581Ser,ENST00000452305,NM_001143770.1,NM_001143771.1;ZNF438,missense_variant,p.Arg542Ser,ENST00000538351,NM_001143769.1;ZNF438,missense_variant,p.Arg591Ser,ENST00000442986,NM_182755.2;ZNF438,missense_variant,p.Arg581Ser,ENST00000331737,;ZNF438,missense_variant,p.Arg591Ser,ENST00000436087,NM_001143766.1,NM_001143768.1;ZNF438,missense_variant,p.Arg591Ser,ENST00000361310,;ZNF438,missense_variant,p.Arg591Ser,ENST00000413025,NM_001143767.1;ZNF438,missense_variant,p.Arg155Ser,ENST00000375311,;ZNF438,intron_variant,,ENST00000609683,; A ENST00000442986 Transcript missense_variant 2208/3245 1773/2487 591/828 R/S agG/agT 1 -1 ZNF438 HGNC HGNC:21029 protein_coding YES CCDS7168.1 ENSP00000412363 Q7Z4V0 UPI00001B3D8F NM_182755.2 deleterious(0) 7/8 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF291 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 30848632 30848632 C A 1 0 0 0 0 1 0 0 0 18481 622 22 2 2 ZNF438 10 30848632 Missense_Mutation SNP C C3N-00551_T 4720153 30848632 102948790 341 15824 GJD4 0 . GRCh38 10 35607860 35607860 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.347A>T p.Glu116Val p.E116V ENST00000321660 2/2 197 160 37 202 202 0 strelka-varscan-mutect GJD4,missense_variant,p.Glu116Val,ENST00000321660,NM_153368.2;RP11-425A6.5,non_coding_transcript_exon_variant,,ENST00000609313,;RP11-425A6.5,non_coding_transcript_exon_variant,,ENST00000635993,; T ENST00000321660 Transcript missense_variant 505/1580 347/1113 116/370 E/V gAg/gTg 1 1 GJD4 HGNC HGNC:23296 protein_coding YES CCDS7191.1 ENSP00000315070 Q96KN9 UPI000007118B NM_153368.2 tolerated(0.19) 2/2 hmmpanther:PTHR11984:SF3,hmmpanther:PTHR11984,Pfam_domain:PF00029,Gene3D:2zw3A00 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 35607860 35607860 A T 1 0 0 0 0 1 0 0 0 6296 304 11 4 4 GJD4 10 35607860 Missense_Mutation SNP A C3N-00551_T 4759228 35607860 98189562 342 15825 ANKRD30A 0 . GRCh38 10 37197413 37197413 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.2481C>T p.= p.A827A ENST00000361713 29/36 356 251 105 407 407 0 strelka-varscan-mutect ANKRD30A,synonymous_variant,p.=,ENST00000374660,;ANKRD30A,synonymous_variant,p.=,ENST00000611781,;ANKRD30A,synonymous_variant,p.=,ENST00000602533,;ANKRD30A,synonymous_variant,p.=,ENST00000361713,NM_052997.2;ANKRD30A,downstream_gene_variant,,ENST00000475522,; T ENST00000361713 Transcript synonymous_variant 2580/4405 2481/4026 827/1341 A gcC/gcT 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 29/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 37197413 37197413 C T 1 0 0 0 0 0 0 0 1 761 608 21 3 3 ANKRD30A 10 37197413 Silent SNP C C3N-00551_T 1589553 37197413 96600009 343 15826 RET 0 . GRCh38 10 43119709 43119709 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.2571G>C p.Gln857His p.Q857H ENST00000355710 14/20 570 536 34 636 636 0 strelka-varscan-mutect RET,missense_variant,p.Gln857His,ENST00000355710,NM_020975.4;RET,missense_variant,p.Asp433His,ENST00000615310,;RET,missense_variant,p.Gln857His,ENST00000340058,NM_020630.4; C ENST00000355710 Transcript missense_variant 2803/5659 2571/3345 857/1114 Q/H caG/caC 1 1 RET HGNC HGNC:9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 A0A024R7T2 UPI00001336E1 NM_020975.4 deleterious(0) 14/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000631,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF345,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 43119709 43119709 G C 1 0 0 0 0 1 0 0 0 13406 942 33 4 4 RET 10 43119709 Missense_Mutation SNP G C3N-00551_T 5922296 43119709 90677713 344 15827 C10orf71 0 . GRCh38 10 49325243 49325243 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.2698G>T p.Gly900Cys p.G900C ENST00000374144 3/3 234 219 15 266 265 1 strelka-varscan-mutect C10orf71,missense_variant,p.Gly900Cys,ENST00000374144,NM_001135196.1; T ENST00000374144 Transcript missense_variant 2986/5230 2698/4308 900/1435 G/C Ggt/Tgt 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS rs1333463581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 49325243 49325243 G T 1 0 0 0 0 1 0 0 0 1769 1232 43 2 2 C10orf71 10 49325243 Missense_Mutation SNP G C3N-00551_T 6205534 49325243 84472179 345 15828 PCDH15 0 . GRCh38 10 54023098 54023098 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.2335G>T p.Ala779Ser p.A779S ENST00000373957 20/35 366 343 23 466 466 0 strelka-varscan-mutect PCDH15,missense_variant,p.Ala779Ser,ENST00000614895,;PCDH15,missense_variant,p.Ala774Ser,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Ala774Ser,ENST00000414778,;PCDH15,missense_variant,p.Ala779Ser,ENST00000617051,;PCDH15,missense_variant,p.Ala779Ser,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Ala774Ser,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Ala774Ser,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Ala752Ser,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Ala737Ser,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Ala774Ser,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Ala703Ser,ENST00000622048,;PCDH15,missense_variant,p.Ala703Ser,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Ala774Ser,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Ala786Ser,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Ala781Ser,ENST00000395445,;PCDH15,missense_variant,p.Ala774Ser,ENST00000616114,;PCDH15,missense_variant,p.Ala774Ser,ENST00000395438,;PCDH15,missense_variant,p.Ala786Ser,ENST00000612394,;PCDH15,missense_variant,p.Ala779Ser,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Ala385Ser,ENST00000409834,;PCDH15,missense_variant,p.Ala774Ser,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript missense_variant 2730/7032 2335/5889 779/1962 A/S Gca/Tca COSM2147353,COSM2147354,COSM2147355,COSM2147356 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.24) 20/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 54023098 54023098 C A 1 0 0 0 0 1 0 0 0 11598 797 28 2 2 PCDH15 10 54023098 Missense_Mutation SNP C C3N-00551_T 4697855 54023098 79774324 346 15829 BICC1 0 . GRCh38 10 58813863 58813863 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2410C>A p.Arg804Ser p.R804S ENST00000373886 18/21 179 144 35 239 239 0 strelka-varscan-mutect BICC1,missense_variant,p.Arg804Ser,ENST00000373886,NM_001080512.2;BICC1,missense_variant,p.Arg430Ser,ENST00000263103,; A ENST00000373886 Transcript missense_variant 2414/5475 2410/2925 804/974 R/S Cgt/Agt 1 1 BICC1 HGNC HGNC:19351 protein_coding YES CCDS31206.1 ENSP00000362993 Q9H694 UPI000059D156 NM_001080512.2 deleterious(0.04) 18/21 hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF38 MODERATE 1 SNV 2 1 PASS rs1201651719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 58813863 58813863 C A 1 0 0 0 0 1 0 0 0 1576 884 31 1 1 BICC1 10 58813863 Missense_Mutation SNP C C3N-00551_T 4790765 58813863 74983559 347 15830 LRIT1 0 . GRCh38 10 84232658 84232658 + Silent SNP T T G rs753198750 C3N-00551_T C3N-00551_N T T c.1141A>C p.= p.R381R ENST00000372105 4/4 105 96 9 98 98 0 strelka-varscan-mutect LRIT1,synonymous_variant,p.=,ENST00000372105,NM_015613.2; G ENST00000372105 Transcript synonymous_variant 1163/2228 1141/1872 381/623 R Agg/Cgg rs753198750 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 4/4 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9 LOW 1 SNV 1 1 PASS rs753198750 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 84232658 84232658 T G 1 0 0 0 0 0 0 0 1 8842 1579 55 5 5 LRIT1 10 84232658 Silent SNP T C3N-00551_T 25418795 84232658 49564764 348 15831 LDB3 0 . GRCh38 10 86716357 86716357 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1277G>T p.Gly426Val p.G426V ENST00000429277 10/14 215 153 62 219 218 1 strelka-varscan-mutect LDB3,missense_variant,p.Gly426Val,ENST00000429277,NM_001171610.1;LDB3,missense_variant,p.Gly421Val,ENST00000361373,NM_007078.2;LDB3,missense_variant,p.Gly311Val,ENST00000263066,NM_001080114.1;LDB3,missense_variant,p.Gly426Val,ENST00000623056,;LDB3,upstream_gene_variant,,ENST00000477489,; T ENST00000429277 Transcript missense_variant 1422/5436 1277/2199 426/732 G/V gGg/gTg 1 1 LDB3 HGNC HGNC:15710 protein_coding YES CCDS53550.1 ENSP00000401437 O75112 UPI00017A876A NM_001171610.1 deleterious(0.05) 10/14 hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF9 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 86716357 86716357 G T 1 0 0 0 0 1 0 0 0 8604 1232 43 2 2 LDB3 10 86716357 Missense_Mutation SNP G C3N-00551_T 2483699 86716357 47081065 349 15832 LDB3 0 . GRCh38 10 86716400 86716400 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.1320T>A p.= p.P440P ENST00000429277 10/14 129 89 40 107 107 0 strelka-varscan-mutect LDB3,synonymous_variant,p.=,ENST00000429277,NM_001171610.1;LDB3,synonymous_variant,p.=,ENST00000361373,NM_007078.2;LDB3,synonymous_variant,p.=,ENST00000263066,NM_001080114.1;LDB3,synonymous_variant,p.=,ENST00000623056,;LDB3,upstream_gene_variant,,ENST00000477489,; A ENST00000429277 Transcript synonymous_variant 1465/5436 1320/2199 440/732 P ccT/ccA 1 1 LDB3 HGNC HGNC:15710 protein_coding YES CCDS53550.1 ENSP00000401437 O75112 UPI00017A876A NM_001171610.1 10/14 Low_complexity_(Seg):seg,hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF9 LOW 1 SNV 2 1 PASS rs1009984915 . 0 186 16 7 0 0 0 0 -20 0.9725883 0 1 1 0 A 2 1 52 86716400 86716400 T A 1 0 0 0 0 0 0 0 1 8604 1567 55 4 4 LDB3 10 86716400 Silent SNP T C3N-00551_T 43 86716400 47081022 350 15833 DNTT 0 . GRCh38 10 96304586 96304586 + Missense_Mutation SNP T T A rs142422958 C3N-00551_T C3N-00551_N T T c.89T>A p.Ile30Asn p.I30N ENST00000371174 1/11 359 316 43 381 381 0 strelka-varscan-mutect DNTT,missense_variant,p.Ile30Asn,ENST00000371174,NM_004088.3;DNTT,missense_variant,p.Ile30Asn,ENST00000630152,NM_001017520.1;RP11-35J23.1,intron_variant,,ENST00000454484,; A ENST00000371174 Transcript missense_variant 191/1972 89/1530 30/509 I/N aTc/aAc rs142422958 1 1 DNTT HGNC HGNC:2983 protein_coding YES CCDS7447.1 ENSP00000360216 P04053 UPI000013C84B NM_004088.3 deleterious(0.05) 1/11 PIRSF_domain:PIRSF000817,PIRSF_domain:PIRSF501175,PROSITE_profiles:PS50172,hmmpanther:PTHR11276,hmmpanther:PTHR11276:SF21,SMART_domains:SM00292 MODERATE 1 SNV 1 1 PASS rs142422958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 96304586 96304586 T A 1 0 0 0 0 1 0 0 0 4494 1435 50 4 4 DNTT 10 96304586 Missense_Mutation SNP T C3N-00551_T 9588186 96304586 37492836 351 15834 HPSE2 0 . GRCh38 10 99232449 99232449 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.347G>A p.Gly116Glu p.G116E ENST00000370552 2/12 333 309 24 342 342 0 strelka-varscan-mutect HPSE2,missense_variant,p.Gly116Glu,ENST00000370552,NM_021828.4;HPSE2,missense_variant,p.Gly116Glu,ENST00000370549,NM_001166244.1;HPSE2,missense_variant,p.Gly116Glu,ENST00000370546,NM_001166246.1;HPSE2,missense_variant,p.Gly116Glu,ENST00000628193,NM_001166245.1;HPSE2,missense_variant,p.Gly116Glu,ENST00000614306,; T ENST00000370552 Transcript missense_variant 407/2295 347/1779 116/592 G/E gGg/gAg 1 -1 HPSE2 HGNC HGNC:18374 protein_coding YES CCDS7477.1 ENSP00000359583 Q8WWQ2 UPI00001AEEC0 NM_021828.4 deleterious(0.02) 2/12 hmmpanther:PTHR14363,hmmpanther:PTHR14363:SF15,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 99232449 99232449 C T 1 0 0 0 0 1 0 0 0 7240 623 22 3 3 HPSE2 10 99232449 Missense_Mutation SNP C C3N-00551_T 2927863 99232449 34564973 352 15835 NFKB2 0 . GRCh38 10 102399395 102399396 + Frame_Shift_Ins INS - - C novel C3N-00551_T C3N-00551_N - - c.1227dupC p.Thr410HisfsTer96 p.T410Hfs*96 ENST00000369966 13/23 79 70 9 110 110 0 sindel-varindel NFKB2,frameshift_variant,p.Thr410HisfsTer96,ENST00000428099,NM_001288724.1;NFKB2,frameshift_variant,p.Thr410HisfsTer96,ENST00000369966,NM_001077494.3;NFKB2,frameshift_variant,p.Thr410HisfsTer96,ENST00000189444,NM_001322934.1,NM_001261403.2,NM_002502.5;PSD,downstream_gene_variant,,ENST00000020673,NM_002779.4;PSD,downstream_gene_variant,,ENST00000406432,NM_001270965.1;PSD,downstream_gene_variant,,ENST00000611678,NM_001270966.1;NFKB2,downstream_gene_variant,,ENST00000601386,;NFKB2,downstream_gene_variant,,ENST00000471698,;NFKB2,non_coding_transcript_exon_variant,,ENST00000336486,;NFKB2,downstream_gene_variant,,ENST00000593908,;NFKB2,downstream_gene_variant,,ENST00000467116,;NFKB2,upstream_gene_variant,,ENST00000473400,; C ENST00000369966 Transcript frameshift_variant 1475-1476/3101 1225-1226/2703 409/900 A/AX gcc/gCcc 1 1 NFKB2 HGNC HGNC:7795 protein_coding YES CCDS41564.1 ENSP00000358983 Q00653 UPI000016A5CD NM_001077494.3 13/23 Low_complexity_(Seg):seg HIGH 1 insertion 1 2 1 PASS . . 0 204 6 0 0 0 0 0 -19.26647 0.9999999 1 1 1 0 C 7 5 52 102399395 102399395 - C 1 0 1 1 0 0 0 0 0 10413 1087 38 0 0 NFKB2 10 102399395 Frame_Shift_Ins INS - C3N-00551_T 3166946 102399395 31398027 353 15836 CUEDC2 0 . GRCh38 10 102423432 102423432 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.858C>A p.Phe286Leu p.F286L ENST00000369937 9/9 159 143 16 176 176 0 strelka-varscan-mutect CUEDC2,missense_variant,p.Phe286Leu,ENST00000369937,NM_024040.2;PSD,upstream_gene_variant,,ENST00000020673,NM_002779.4;PSD,upstream_gene_variant,,ENST00000406432,NM_001270965.1;PSD,upstream_gene_variant,,ENST00000611678,NM_001270966.1;FBXL15,downstream_gene_variant,,ENST00000224862,NM_024326.3;FBXL15,downstream_gene_variant,,ENST00000369956,;FBXL15,downstream_gene_variant,,ENST00000432590,;FBXL15,downstream_gene_variant,,ENST00000440407,;FBXL15,downstream_gene_variant,,ENST00000425536,;FBXL15,downstream_gene_variant,,ENST00000457067,;CUEDC2,non_coding_transcript_exon_variant,,ENST00000465409,;PSD,upstream_gene_variant,,ENST00000492902,;FBXL15,downstream_gene_variant,,ENST00000481808,;CUEDC2,downstream_gene_variant,,ENST00000477994,;PSD,upstream_gene_variant,,ENST00000472685,;CUEDC2,downstream_gene_variant,,ENST00000486762,; T ENST00000369937 Transcript missense_variant 1004/1191 858/864 286/287 F/L ttC/ttA 1 -1 CUEDC2 HGNC HGNC:28352 protein_coding YES CCDS41566.1 ENSP00000358953 Q9H467 UPI000006EFB6 NM_024040.2 tolerated(0.07) 9/9 hmmpanther:PTHR12493 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99878 0.9999999 1 1 1 0 T 3 4 52 102423432 102423432 G T 1 0 0 0 0 1 0 0 0 3863 1165 41 2 2 CUEDC2 10 102423432 Missense_Mutation SNP G C3N-00551_T 24037 102423432 31373990 354 15837 NEURL1 0 . GRCh38 10 103571644 103571644 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.471G>T p.= p.L157L ENST00000369780 3/6 352 290 62 415 415 0 strelka-varscan-mutect NEURL1,synonymous_variant,p.=,ENST00000369780,NM_004210.4;NEURL1,synonymous_variant,p.=,ENST00000437579,;NEURL1,synonymous_variant,p.=,ENST00000455386,;NEURL1,upstream_gene_variant,,ENST00000465048,; T ENST00000369780 Transcript synonymous_variant 880/4314 471/1725 157/574 L ctG/ctT 1 1 NEURL1 HGNC HGNC:7761 protein_coding YES CCDS7551.1 ENSP00000358795 O76050 UPI0000073F46 NM_004210.4 3/6 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,hmmpanther:PTHR12429:SF13,SMART_domains:SM00588 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 103571644 103571644 G T 1 0 0 0 0 0 0 0 1 10380 1306 46 2 2 NEURL1 10 103571644 Silent SNP G C3N-00551_T 1148212 103571644 30225778 355 15838 SORCS3 0 . GRCh38 10 105216978 105216978 + Frame_Shift_Del DEL G G - novel C3N-00551_T C3N-00551_N G G c.2592delG p.Ile865LeufsTer27 p.I865Lfs*27 ENST00000369701 19/27 179 169 10 244 244 0 varindel-pindel SORCS3,frameshift_variant,p.Ile865LeufsTer27,ENST00000369701,NM_014978.2;SORCS3,frameshift_variant,p.Ile865LeufsTer27,ENST00000369699,; - ENST00000369701 Transcript frameshift_variant 2817/5757 2590/3669 864/1222 G/X Ggg/gg 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 19/27 Gene3D:2.60.40.670,Pfam_domain:PF00801,PROSITE_profiles:PS50093,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Superfamily_domains:SSF49299 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 105216978 105216978 G - 1 0 1 0 1 0 0 0 0 15254 1348 47 0 0 SORCS3 10 105216978 Frame_Shift_Del DEL G C3N-00551_T 1645334 105216978 28580444 356 15839 SORCS1 0 . GRCh38 10 106675048 106675048 + Splice_Site SNP C C T C3N-00551_T C3N-00551_N C C c.1940+1G>A p.X647_splice ENST00000263054 125 114 11 134 134 0 strelka-varscan-mutect SORCS1,splice_donor_variant,,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,splice_donor_variant,,ENST00000612154,;SORCS1,splice_donor_variant,,ENST00000622431,;SORCS1,splice_donor_variant,,ENST00000344440,;SORCS1,splice_donor_variant,,ENST00000369698,;SORCS1,splice_donor_variant,,ENST00000472196,; T ENST00000263054 Transcript splice_donor_variant -/7272 1940/3507 647/1168 COSM4729042,COSM4729043 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 14/25 1,1 HIGH 1 SNV 1 1,1 1 PASS rs1447669165 . 0 206 2 0 0 0 0 0 -19.99281 1 1 1 1 0 T 5 4 52 106675048 106675048 C T 1 0 0 0 0 0 0 1 0 15252 550 19 1 1 SORCS1 10 106675048 Splice_Site SNP C C3N-00551_T 1458070 106675048 27122374 357 15840 PLEKHS1 0 . GRCh38 10 113768864 113768864 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.391A>G p.Ile131Val p.I131V ENST00000369310 5/12 125 102 23 154 154 0 strelka-varscan-mutect PLEKHS1,missense_variant,p.Ile49Val,ENST00000369312,NM_001193434.1;PLEKHS1,missense_variant,p.Ile137Val,ENST00000361048,NM_024889.4;PLEKHS1,missense_variant,p.Ile49Val,ENST00000619563,NM_001193435.1;PLEKHS1,missense_variant,p.Ile131Val,ENST00000369310,NM_182601.1;PLEKHS1,upstream_gene_variant,,ENST00000354462,;PLEKHS1,upstream_gene_variant,,ENST00000369309,; G ENST00000369310 Transcript missense_variant 953/2046 391/1398 131/465 I/V Ata/Gta 1 1 PLEKHS1 HGNC HGNC:26285 protein_coding YES CCDS53580.1 ENSP00000358316 Q5SXH7 UPI000047020C NM_182601.1 tolerated(0.39) 5/12 hmmpanther:PTHR12156:SF19,hmmpanther:PTHR12156,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 113768864 113768864 A G 1 0 0 0 0 1 0 0 0 12179 449 16 5 5 PLEKHS1 10 113768864 Missense_Mutation SNP A C3N-00551_T 7093816 113768864 20028558 358 15841 VWA2 0 . GRCh38 10 114286190 114286190 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1249G>T p.Gly417Cys p.G417C ENST00000392982 11/14 171 157 14 170 170 0 strelka-varscan-mutect VWA2,missense_variant,p.Gly417Cys,ENST00000392982,NM_001272046.1;VWA2,missense_variant,p.Gly113Cys,ENST00000603594,;CTB-1144G6.6,upstream_gene_variant,,ENST00000622689,;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,; T ENST00000392982 Transcript missense_variant 1499/2794 1249/2268 417/755 G/C Ggt/Tgt 1 1 VWA2 HGNC HGNC:24709 protein_coding YES CCDS7589.2 ENSP00000376708 Q5GFL6 UPI00004C7AA3 NM_001272046.1 deleterious(0) 11/14 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF117,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 114286190 114286190 G T 1 0 0 0 0 1 0 0 0 17793 1348 47 2 2 VWA2 10 114286190 Missense_Mutation SNP G C3N-00551_T 517326 114286190 19511232 359 15842 HSPA12A 0 . GRCh38 10 116674856 116674856 + Silent SNP G G T rs782209908 C3N-00551_T C3N-00551_N G G c.1953C>A p.= p.T651T ENST00000369209 12/12 295 272 23 257 257 0 strelka-varscan-mutect HSPA12A,synonymous_variant,p.=,ENST00000635765,;HSPA12A,synonymous_variant,p.=,ENST00000369209,NM_025015.2;C10orf82,upstream_gene_variant,,ENST00000369210,NM_144661.2;C10orf82,upstream_gene_variant,,ENST00000588184,;RP11-498B4.5,downstream_gene_variant,,ENST00000433600,;C10orf82,upstream_gene_variant,,ENST00000588224,;C10orf82,upstream_gene_variant,,ENST00000467153,; T ENST00000369209 Transcript synonymous_variant 2058/5722 1953/2028 651/675 T acC/acA rs782209908,COSM5497988 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 12/12 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46 0,1 LOW 1 SNV 1 0,1 1 PASS rs782209908 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 116674856 116674856 G T 1 0 0 0 0 0 0 0 1 7300 1103 39 1 1 HSPA12A 10 116674856 Silent SNP G C3N-00551_T 2388666 116674856 17122566 360 15843 UROS 0 . GRCh38 10 125815100 125815100 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.178A>G p.Ile60Val p.I60V ENST00000368797 4/10 638 592 46 759 759 0 strelka-varscan-mutect UROS,missense_variant,p.Ile60Val,ENST00000368778,NM_001324039.1;UROS,missense_variant,p.Ile60Val,ENST00000368797,NM_000375.2;UROS,missense_variant,p.Ile60Val,ENST00000368786,;UROS,missense_variant,p.Ile32Val,ENST00000420761,;UROS,missense_variant,p.Ile60Val,ENST00000368774,;MIR4484,upstream_gene_variant,,ENST00000582855,; C ENST00000368797 Transcript missense_variant 403/1313 178/798 60/265 I/V Att/Gtt 1 -1 UROS HGNC HGNC:12592 protein_coding YES CCDS7648.1 ENSP00000357787 P10746 A0A0S2Z4T8 UPI000012C4A4 NM_000375.2 tolerated(0.34) 4/10 Gene3D:3.40.50.10090,Pfam_domain:PF02602,hmmpanther:PTHR12390,Superfamily_domains:SSF69618 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 125815100 125815100 T C 1 0 0 0 0 1 0 0 0 17562 1464 51 5 5 UROS 10 125815100 Missense_Mutation SNP T C3N-00551_T 9140244 125815100 7982322 361 15844 C10orf90 0 . GRCh38 10 126504937 126504937 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.263T>A p.Leu88Gln p.L88Q ENST00000284694 3/9 156 144 12 252 252 0 strelka-varscan-mutect C10orf90,missense_variant,p.Leu88Gln,ENST00000284694,NM_001004298.2;C10orf90,missense_variant,p.Leu41Gln,ENST00000356858,;C10orf90,missense_variant,p.Leu88Gln,ENST00000432642,;C10orf90,missense_variant,p.Leu41Gln,ENST00000488181,;C10orf90,upstream_gene_variant,,ENST00000424927,;C10orf90,non_coding_transcript_exon_variant,,ENST00000368674,;C10orf90,3_prime_UTR_variant,,ENST00000463082,; T ENST00000284694 Transcript missense_variant 384/3076 263/2100 88/699 L/Q cTg/cAg 1 -1 C10orf90 HGNC HGNC:26563 protein_coding YES CCDS31310.1 ENSP00000284694 Q96M02 UPI00001D808F NM_001004298.2 deleterious(0.02) 3/9 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 126504937 126504937 A T 1 0 0 0 0 1 0 0 0 1773 188 7 4 4 C10orf90 10 126504937 Missense_Mutation SNP A C3N-00551_T 689837 126504937 7292485 362 15845 KNDC1 0 . GRCh38 10 133186598 133186598 + Missense_Mutation SNP G G T rs556311295 C3N-00551_T C3N-00551_N G G c.1250G>T p.Gly417Val p.G417V ENST00000304613 6/30 110 86 24 177 177 0 strelka-varscan-mutect KNDC1,missense_variant,p.Gly417Val,ENST00000304613,NM_152643.6;KNDC1,missense_variant,p.Gly352Val,ENST00000368571,; T ENST00000304613 Transcript missense_variant 1271/6793 1250/5250 417/1749 G/V gGt/gTt rs556311295 1 1 KNDC1 HGNC HGNC:29374 protein_coding YES CCDS7674.1 ENSP00000304437 Q76NI1 UPI00003529F7 NM_152643.6 tolerated(0.29) 6/30 hmmpanther:PTHR21560,hmmpanther:PTHR21560:SF0 MODERATE 1 SNV 2 1 PASS rs556311295 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 133186598 133186598 G T 1 0 0 0 0 1 0 0 0 8304 1261 44 2 2 KNDC1 10 133186598 Missense_Mutation SNP G C3N-00551_T 6681661 133186598 610824 363 15846 OR51H1 0 . GRCh38 11 4860291 4860291 + Missense_Mutation SNP G G T rs542973543 C3N-00551_T C3N-00551_N G G c.274C>A p.Pro92Thr p.P92T ENST00000322059 1/1 105 82 23 198 198 0 strelka-varscan-mutect OR51H1,missense_variant,p.Pro92Thr,ENST00000322059,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322059 Transcript missense_variant 274/909 274/909 92/302 P/T Cct/Act rs542973543 1 -1 OR51H1 HGNC HGNC:14833 protein_coding YES ENSP00000322724 Q8NH63 A0A126GVH7 UPI0000061F03 tolerated(0.21) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF53,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs542973543 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 4860291 4860291 G T 1 0 0 0 0 1 0 0 0 11172 1232 43 2 2 OR51H1 11 4860291 Missense_Mutation SNP G C3N-00551_T 4860291 130226331 364 15847 OR51V1 0 . GRCh38 11 5200606 5200606 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.95A>G p.Gln32Arg p.Q32R ENST00000321255 1/1 96 83 13 120 120 0 strelka-varscan-mutect OR51V1,missense_variant,p.Gln32Arg,ENST00000321255,NM_001004760.2;AC104389.16,upstream_gene_variant,,ENST00000418080,; C ENST00000321255 Transcript missense_variant 95/966 95/966 32/321 Q/R cAa/cGa 1 -1 OR51V1 HGNC HGNC:19597 protein_coding YES CCDS31375.1 ENSP00000321729 Q9H2C8 UPI0000140ADA NM_001004760.2 tolerated(0.34) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF67,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -19.95823 0.9999999 1 1 1 0 C 3 2 52 5200606 5200606 T C 1 0 0 0 0 1 0 0 0 11181 1812 63 5 5 OR51V1 11 5200606 Missense_Mutation SNP T C3N-00551_T 340315 5200606 129886016 365 15848 PPFIBP2 0 . GRCh38 11 7639853 7639853 + Missense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.1358G>A p.Ser453Asn p.S453N ENST00000299492 15/24 70 63 7 100 100 0 strelka-varscan-mutect PPFIBP2,missense_variant,p.Ser453Asn,ENST00000299492,NM_003621.3;PPFIBP2,missense_variant,p.Ser295Asn,ENST00000533792,;PPFIBP2,missense_variant,p.Ser310Asn,ENST00000530181,NM_001256569.1;PPFIBP2,missense_variant,p.Ser341Asn,ENST00000528883,NM_001256568.1;PPFIBP2,missense_variant,p.Ser133Asn,ENST00000534409,;PPFIBP2,missense_variant,p.Ser97Asn,ENST00000530081,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000530582,;PPFIBP2,intron_variant,,ENST00000532926,;PPFIBP2,intron_variant,,ENST00000529021,;PPFIBP2,upstream_gene_variant,,ENST00000524495,;PPFIBP2,non_coding_transcript_exon_variant,,ENST00000532172,;PPFIBP2,downstream_gene_variant,,ENST00000532381,; A ENST00000299492 Transcript missense_variant 1746/3557 1358/2631 453/876 S/N aGc/aAc 1 1 PPFIBP2 HGNC HGNC:9250 protein_coding YES CCDS31419.1 ENSP00000299492 Q8ND30 UPI00001C1EF8 NM_003621.3 tolerated(0.53) 15/24 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF18 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.25037 0.9999998 1 1 1 0 A 3 1 52 7639853 7639853 G A 1 0 0 0 0 1 0 0 0 12423 971 34 3 3 PPFIBP2 11 7639853 Missense_Mutation SNP G C3N-00551_T 2439247 7639853 127446769 366 15849 STK33 0 . GRCh38 11 8454743 8454743 + Splice_Site SNP C C A novel C3N-00551_T C3N-00551_N C C c.786+1G>T p.X262_splice ENST00000447869 51 43 8 97 97 0 strelka-varscan-mutect STK33,splice_donor_variant,,ENST00000447869,;STK33,splice_donor_variant,,ENST00000315204,NM_030906.3;STK33,splice_donor_variant,,ENST00000396672,NM_001289061.1;STK33,splice_donor_variant,,ENST00000358872,NM_001289059.1;STK33,splice_donor_variant,,ENST00000534493,NM_001289058.1;STK33,splice_donor_variant,,ENST00000444064,;STK33,splice_donor_variant,,ENST00000524760,;STK33,downstream_gene_variant,,ENST00000418597,;STK33,downstream_gene_variant,,ENST00000422559,;STK33,intron_variant,,ENST00000526517,;STK33,upstream_gene_variant,,ENST00000473980,;STK33,splice_donor_variant,,ENST00000486305,; A ENST00000447869 Transcript splice_donor_variant -/3103 786/1545 262/514 1 -1 STK33 HGNC HGNC:14568 protein_coding YES CCDS7789.1 ENSP00000416750 Q9BYT3 UPI000004496E 6/11 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.2178 1 1 1 1 0 A 5 1 52 8454743 8454743 C A 1 0 0 0 0 0 0 1 0 15677 521 18 2 2 STK33 11 8454743 Splice_Site SNP C C3N-00551_T 814890 8454743 126631879 367 15850 MYOD1 0 . GRCh38 11 17720323 17720323 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.541C>G p.Pro181Ala p.P181A ENST00000250003 1/3 117 110 7 188 188 0 strelka-mutect MYOD1,missense_variant,p.Pro181Ala,ENST00000250003,NM_002478.4; G ENST00000250003 Transcript missense_variant 756/1801 541/963 181/320 P/A Ccg/Gcg 1 1 MYOD1 HGNC HGNC:7611 protein_coding YES CCDS7826.1 ENSP00000250003 P15172 UPI000007280C NM_002478.4 deleterious(0.02) 1/3 hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 17720323 17720323 C G 1 0 0 0 0 1 0 0 0 10089 739 26 4 4 MYOD1 11 17720323 Missense_Mutation SNP C C3N-00551_T 9265580 17720323 117366299 368 15851 TPH1 0 . GRCh38 11 18022803 18022803 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1155G>T p.Lys385Asn p.K385N ENST00000250018 9/10 356 323 33 457 457 0 strelka-varscan-mutect TPH1,missense_variant,p.Lys385Asn,ENST00000250018,NM_004179.2;RP1-59M18.2,non_coding_transcript_exon_variant,,ENST00000525523,;TPH1,non_coding_transcript_exon_variant,,ENST00000525406,;TPH1,3_prime_UTR_variant,,ENST00000417164,; A ENST00000250018 Transcript missense_variant 1718/5325 1155/1335 385/444 K/N aaG/aaT 1 -1 TPH1 HGNC HGNC:12008 protein_coding YES CCDS7829.1 ENSP00000250018 P17752 UPI000013CC9C NM_004179.2 deleterious(0) 9/10 PROSITE_profiles:PS51410,hmmpanther:PTHR11473:SF23,hmmpanther:PTHR11473,Pfam_domain:PF00351,Gene3D:1.10.800.10,TIGRFAM_domain:TIGR01270,PIRSF_domain:PIRSF000336,Superfamily_domains:SSF56534 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 18022803 18022803 C A 1 0 0 0 0 1 0 0 0 16882 927 32 2 2 TPH1 11 18022803 Missense_Mutation SNP C C3N-00551_T 302480 18022803 117063819 369 15852 SLC6A5 0 . GRCh38 11 20654760 20654760 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.2286A>T p.Leu762Phe p.L762F ENST00000525748 16/16 445 408 37 509 509 0 strelka-varscan-mutect SLC6A5,missense_variant,p.Leu762Phe,ENST00000525748,NM_004211.3;SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; T ENST00000525748 Transcript missense_variant 2559/7084 2286/2394 762/797 L/F ttA/ttT 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 deleterious(0) 16/16 hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 20654760 20654760 A T 1 0 0 0 0 1 0 0 0 14970 417 15 4 4 SLC6A5 11 20654760 Missense_Mutation SNP A C3N-00551_T 2631957 20654760 114431862 370 15853 KIAA1549L 0 . GRCh38 11 33606816 33606816 + Silent SNP C C T rs375293606 C3N-00551_T C3N-00551_N C C c.4164C>T p.= p.N1388N ENST00000321505 13/20 80 73 7 95 95 0 strelka-varscan-mutect KIAA1549L,synonymous_variant,p.=,ENST00000321505,NM_012194.2;KIAA1549L,synonymous_variant,p.=,ENST00000526400,; T ENST00000321505 Transcript synonymous_variant 4344/11678 4164/5550 1388/1849 N aaC/aaT rs375293606,COSM256431 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 13/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3,Pfam_domain:PF12877 0,1 LOW 1 SNV 1 0,1 1 PASS rs375293606 . 0 205 5 0 0 0 0 0 -15.14405 1 1 1 1 0 T 2 4 52 33606816 33606816 C T 1 0 0 0 0 0 0 0 1 8121 535 19 1 1 KIAA1549L 11 33606816 Silent SNP C C3N-00551_T 12952056 33606816 101479806 371 15854 OR4C13 0 . GRCh38 11 49953129 49953129 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.707C>A p.Ser236Tyr p.S236Y ENST00000555099 1/1 164 154 10 198 197 1 strelka-varscan-mutect OR4C13,missense_variant,p.Ser236Tyr,ENST00000555099,NM_001001955.2; A ENST00000555099 Transcript missense_variant 739/1029 707/930 236/309 S/Y tCt/tAt 1 1 OR4C13 HGNC HGNC:15169 protein_coding YES CCDS31495.1 ENSP00000452277 Q8NGP0 UPI000013F7D1 NM_001001955.2 deleterious_low_confidence(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF60,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 49953129 49953129 C A 1 0 0 0 0 1 0 0 0 11124 913 32 2 2 OR4C13 11 49953129 Missense_Mutation SNP C C3N-00551_T 16346313 49953129 85133493 372 15855 OR5D18 0 . GRCh38 11 55820381 55820381 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.752T>A p.Ile251Asn p.I251N ENST00000333976 1/1 194 173 21 187 187 0 strelka-varscan-mutect OR5D18,missense_variant,p.Ile251Asn,ENST00000333976,NM_001001952.1; A ENST00000333976 Transcript missense_variant 752/942 752/942 251/313 I/N aTc/aAc 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 55820381 55820381 T A 1 0 0 0 0 1 0 0 0 11227 1435 50 4 4 OR5D18 11 55820381 Missense_Mutation SNP T C3N-00551_T 5867252 55820381 79266241 373 15856 OR5M3 0 . GRCh38 11 56469957 56469957 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.541C>A p.Pro181Thr p.P181T ENST00000312240 1/1 124 101 23 118 118 0 strelka-varscan-mutect OR5M3,missense_variant,p.Pro181Thr,ENST00000312240,NM_001004742.2; T ENST00000312240 Transcript missense_variant 541/924 541/924 181/307 P/T Cct/Act 1 -1 OR5M3 HGNC HGNC:14806 protein_coding YES CCDS31532.1 ENSP00000312208 Q8NGP4 UPI0000041BAA NM_001004742.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF17,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 56469957 56469957 G T 1 0 0 0 0 1 0 0 0 11244 1261 44 2 2 OR5M3 11 56469957 Missense_Mutation SNP G C3N-00551_T 649576 56469957 78616665 374 15857 LRRC55 0 . GRCh38 11 57182247 57182247 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.354C>A p.Asn118Lys p.N118K ENST00000497933 1/2 176 159 17 168 168 0 strelka-varscan-mutect LRRC55,missense_variant,p.Asn118Lys,ENST00000497933,NM_001005210.2; A ENST00000497933 Transcript missense_variant 501/5410 354/1026 118/341 N/K aaC/aaA 1 1 LRRC55 HGNC HGNC:32324 protein_coding YES CCDS31539.1 ENSP00000419542 Q6ZSA7 UPI00001C0E6F NM_001005210.2 deleterious(0) 1/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 57182247 57182247 C A 1 0 0 0 0 1 0 0 0 8906 506 18 2 2 LRRC55 11 57182247 Missense_Mutation SNP C C3N-00551_T 712290 57182247 77904375 375 15858 VWCE 0 . GRCh38 11 61286410 61286410 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.445T>C p.Ser149Pro p.S149P ENST00000335613 5/20 248 234 14 203 203 0 strelka-varscan-mutect VWCE,missense_variant,p.Ser149Pro,ENST00000335613,NM_152718.2;VWCE,5_prime_UTR_variant,,ENST00000613271,;VWCE,missense_variant,p.Ser149Pro,ENST00000301770,;VWCE,3_prime_UTR_variant,,ENST00000535599,;VWCE,non_coding_transcript_exon_variant,,ENST00000538579,; G ENST00000335613 Transcript missense_variant 832/3640 445/2868 149/955 S/P Tcc/Ccc 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 deleterious(0.03) 5/20 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -16.51038 0.9999995 1 1 1 0 G 3 3 52 61286410 61286410 A G 1 0 0 0 0 1 0 0 0 17804 304 11 5 5 VWCE 11 61286410 Missense_Mutation SNP A C3N-00551_T 4104163 61286410 73800212 376 15859 AHNAK 0 . GRCh38 11 62522723 62522723 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.11694G>A p.= p.V3898V ENST00000378024 5/5 313 292 21 331 331 0 strelka-varscan-mutect AHNAK,synonymous_variant,p.=,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; T ENST00000378024 Transcript synonymous_variant 11969/18787 11694/17673 3898/5890 V gtG/gtA 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 62522723 62522723 C T 1 0 0 0 0 0 0 0 1 491 581 21 3 3 AHNAK 11 62522723 Silent SNP C C3N-00551_T 1236313 62522723 72563899 377 15860 HNRNPUL2 0 . GRCh38 11 62726838 62726838 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.319G>T p.Ala107Ser p.A107S ENST00000301785 1/14 81 59 22 88 88 0 strelka-varscan-mutect HNRNPUL2,missense_variant,p.Ala107Ser,ENST00000301785,NM_001079559.2;TTC9C,upstream_gene_variant,,ENST00000316461,NM_173810.3;TTC9C,upstream_gene_variant,,ENST00000532583,;TTC9C,upstream_gene_variant,,ENST00000530625,;HNRNPUL2-BSCL2,missense_variant,p.Ala107Ser,ENST00000403734,;TTC9C,upstream_gene_variant,,ENST00000294161,;HNRNPUL2,upstream_gene_variant,,ENST00000540127,; A ENST00000301785 Transcript missense_variant 512/5106 319/2244 107/747 A/S Gcg/Tcg 1 -1 HNRNPUL2 HGNC HGNC:25451 protein_coding YES CCDS41659.1 ENSP00000301785 Q1KMD3 UPI0000161949 NM_001079559.2 tolerated(0.3) 1/14 Low_complexity_(Seg):seg,hmmpanther:PTHR12381,hmmpanther:PTHR12381:SF43 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 52 62726838 62726838 C A 1 0 0 0 0 1 0 0 0 7170 768 27 1 1 HNRNPUL2 11 62726838 Missense_Mutation SNP C C3N-00551_T 204115 62726838 72359784 378 15861 LTBP3 0 . GRCh38 11 65551429 65551429 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.1594A>G p.Thr532Ala p.T532A ENST00000301873 10/28 553 451 102 447 447 0 strelka-varscan-mutect LTBP3,missense_variant,p.Thr532Ala,ENST00000301873,NM_001130144.2;LTBP3,missense_variant,p.Thr532Ala,ENST00000322147,NM_001164266.1,NM_021070.4;LTBP3,missense_variant,p.Thr443Ala,ENST00000530866,;LTBP3,missense_variant,p.Thr183Ala,ENST00000526927,;LTBP3,upstream_gene_variant,,ENST00000532932,;LTBP3,upstream_gene_variant,,ENST00000529189,;LTBP3,upstream_gene_variant,,ENST00000527339,;LTBP3,downstream_gene_variant,,ENST00000530426,;LTBP3,3_prime_UTR_variant,,ENST00000528516,;LTBP3,non_coding_transcript_exon_variant,,ENST00000528966,;LTBP3,non_coding_transcript_exon_variant,,ENST00000529764,;LTBP3,downstream_gene_variant,,ENST00000526825,;LTBP3,downstream_gene_variant,,ENST00000527792,;LTBP3,downstream_gene_variant,,ENST00000524798,; C ENST00000301873 Transcript missense_variant 1863/4443 1594/3912 532/1303 T/A Acc/Gcc 1 -1 LTBP3 HGNC HGNC:6716 protein_coding YES CCDS44647.1 ENSP00000301873 Q9NS15 UPI00003667EB NM_001130144.2 tolerated(0.06) 10/28 Low_complexity_(Seg):seg,hmmpanther:PTHR24034:SF46,hmmpanther:PTHR24034 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 65551429 65551429 T C 1 0 0 0 0 1 0 0 0 8981 1696 59 5 5 LTBP3 11 65551429 Missense_Mutation SNP T C3N-00551_T 2824591 65551429 69535193 379 15862 TSGA10IP 0 . GRCh38 11 65953599 65953599 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.1184A>T p.Gln395Leu p.Q395L ENST00000532620 5/8 67 46 21 76 76 0 strelka-varscan-mutect TSGA10IP,missense_variant,p.Gln395Leu,ENST00000532620,NM_152762.2;TSGA10IP,synonymous_variant,p.=,ENST00000608857,;TSGA10IP,synonymous_variant,p.=,ENST00000534740,; T ENST00000532620 Transcript missense_variant 1415/1925 1184/1671 395/556 Q/L cAg/cTg 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 tolerated(0.28) 5/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 52 65953599 65953599 A T 1 0 0 0 0 1 0 0 0 17124 188 7 4 4 TSGA10IP 11 65953599 Missense_Mutation SNP A C3N-00551_T 402170 65953599 69133023 380 15863 TENM4 0 . GRCh38 11 78708360 78708360 + Splice_Site SNP C C A novel C3N-00551_T C3N-00551_N C C c.4209+1G>T p.X1403_splice ENST00000278550 85 67 18 96 95 1 strelka-varscan-mutect TENM4,splice_donor_variant,,ENST00000278550,NM_001098816.2; A ENST00000278550 Transcript splice_donor_variant -/14000 4209/8310 1403/2769 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 27/33 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 52 78708360 78708360 C A 1 0 0 0 0 0 0 1 0 16174 521 18 2 2 TENM4 11 78708360 Splice_Site SNP C C3N-00551_T 12754761 78708360 56378262 381 15864 CCDC81 0 . GRCh38 11 86375215 86375215 + Missense_Mutation SNP C C G rs751443342 C3N-00551_T C3N-00551_N C C c.52C>G p.Pro18Ala p.P18A ENST00000445632 1/15 166 155 11 222 222 0 strelka-varscan-mutect CCDC81,missense_variant,p.Pro18Ala,ENST00000445632,NM_001156474.1;CCDC81,missense_variant,p.Pro18Ala,ENST00000354755,NM_021827.4;CCDC81,missense_variant,p.Pro18Ala,ENST00000531271,; G ENST00000445632 Transcript missense_variant 324/2528 52/1959 18/652 P/A Ccc/Gcc rs751443342 1 1 CCDC81 HGNC HGNC:26281 protein_coding YES CCDS53691.1 ENSP00000415528 Q6ZN84 UPI0000E5BE97 NM_001156474.1 deleterious(0.04) 1/15 hmmpanther:PTHR14362,hmmpanther:PTHR14362:SF2 MODERATE 1 SNV 1 1 PASS rs751443342 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 86375215 86375215 C G 1 0 0 0 0 1 0 0 0 2553 739 26 4 4 CCDC81 11 86375215 Missense_Mutation SNP C C3N-00551_T 7666855 86375215 48711407 382 15865 GRM5 0 . GRCh38 11 88604733 88604733 + Frame_Shift_Del DEL C C - novel C3N-00551_T C3N-00551_N C C c.1379delG p.Gly460GlufsTer9 p.G460Efs*9 ENST00000305447 4/9 131 102 29 207 207 0 sindel-varindel-pindel GRM5,frameshift_variant,p.Gly460GlufsTer9,ENST00000455756,NM_000842.4;GRM5,frameshift_variant,p.Gly460GlufsTer9,ENST00000305447,NM_001143831.2;GRM5,frameshift_variant,p.Gly460GlufsTer9,ENST00000305432,; - ENST00000305447 Transcript frameshift_variant 1529/4571 1379/3639 460/1212 G/X gGa/ga 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 4/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 88604733 88604733 C - 1 0 1 0 1 0 0 0 0 6682 855 30 0 0 GRM5 11 88604733 Frame_Shift_Del DEL C C3N-00551_T 2229518 88604733 46481889 383 15866 FAT3 0 . GRCh38 11 92799307 92799307 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.5844A>T p.Glu1948Asp p.E1948D ENST00000525166 9/27 219 194 25 225 225 0 strelka-varscan-mutect FAT3,missense_variant,p.Glu2098Asp,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Glu1948Asp,ENST00000525166,; T ENST00000525166 Transcript missense_variant 5866/18699 5844/13320 1948/4439 E/D gaA/gaT 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.08) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 92799307 92799307 A T 1 0 0 0 0 1 0 0 0 5551 40 2 4 4 FAT3 11 92799307 Missense_Mutation SNP A C3N-00551_T 4194574 92799307 42287315 384 15867 CEP295 0 . GRCh38 11 93698284 93698284 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3372G>T p.Gln1124His p.Q1124H ENST00000325212 15/30 222 172 50 262 261 1 strelka-varscan-mutect CEP295,missense_variant,p.Gln1124His,ENST00000325212,NM_033395.1;CEP295,intron_variant,,ENST00000531700,;CEP295,upstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000531877,;CEP295,downstream_gene_variant,,ENST00000531622,; T ENST00000325212 Transcript missense_variant 3534/8057 3372/7806 1124/2601 Q/H caG/caT 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 tolerated(0.07) 15/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 93698284 93698284 G T 1 0 0 0 0 1 0 0 0 2970 991 35 2 2 CEP295 11 93698284 Missense_Mutation SNP G C3N-00551_T 898977 93698284 41388338 385 15868 KDM4D 0 . GRCh38 11 94997758 94997758 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.386G>T p.Arg129Leu p.R129L ENST00000335080 3/3 409 344 65 335 335 0 strelka-varscan-mutect KDM4D,missense_variant,p.Arg129Leu,ENST00000335080,NM_018039.2;KDM4D,missense_variant,p.Arg129Leu,ENST00000536741,;KDM4D,missense_variant,p.Arg129Leu,ENST00000610872,; T ENST00000335080 Transcript missense_variant 1218/2978 386/1572 129/523 R/L cGc/cTc COSM1211750 1 1 KDM4D HGNC HGNC:25498 protein_coding YES CCDS8302.1 ENSP00000334181 Q6B0I6 UPI00001A82EC NM_018039.2 tolerated(1) 3/3 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF21,Superfamily_domains:SSF51197 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 94997758 94997758 G T 1 0 0 0 0 1 0 0 0 8049 1087 38 1 1 KDM4D 11 94997758 Missense_Mutation SNP G C3N-00551_T 1299474 94997758 40088864 386 15869 MTMR2 0 . GRCh38 11 95850648 95850648 + Missense_Mutation SNP A A C novel C3N-00551_T C3N-00551_N A A c.756T>G p.Asp252Glu p.D252E ENST00000346299 8/15 380 303 77 388 387 1 strelka-varscan-mutect MTMR2,missense_variant,p.Asp252Glu,ENST00000346299,NM_016156.5;MTMR2,missense_variant,p.Asp180Glu,ENST00000393223,;MTMR2,missense_variant,p.Asp180Glu,ENST00000409459,NM_001243571.1;MTMR2,missense_variant,p.Asp180Glu,ENST00000352297,NM_201281.2,NM_201278.2;MTMR2,missense_variant,p.Asp180Glu,ENST00000444541,;MTMR2,non_coding_transcript_exon_variant,,ENST00000484818,; C ENST00000346299 Transcript missense_variant 1097/4681 756/1932 252/643 D/E gaT/gaG 1 -1 MTMR2 HGNC HGNC:7450 protein_coding YES CCDS8305.1 ENSP00000345752 Q13614 UPI00001AF36F NM_016156.5 tolerated(0.22) 8/15 Pfam_domain:PF06602,PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF42,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 95850648 95850648 A C 1 0 0 0 0 1 0 0 0 9931 214 8 5 5 MTMR2 11 95850648 Missense_Mutation SNP A C3N-00551_T 852890 95850648 39235974 387 15870 PGR 0 . GRCh38 11 101050001 101050001 + Missense_Mutation SNP G G T rs773336784 C3N-00551_T C3N-00551_N G G c.2416C>A p.Gln806Lys p.Q806K ENST00000325455 6/8 342 300 42 422 422 0 strelka-varscan-mutect PGR,missense_variant,p.Gln806Lys,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,missense_variant,p.His749Gln,ENST00000619228,;PGR,missense_variant,p.Gln704Lys,ENST00000263463,NM_001271161.2;PGR,missense_variant,p.Gln212Lys,ENST00000534013,NM_001271162.1;PGR,intron_variant,,ENST00000617858,;PGR,missense_variant,p.His788Gln,ENST00000534780,;PGR,missense_variant,p.His749Gln,ENST00000528960,;PGR,non_coding_transcript_exon_variant,,ENST00000533207,;PGR,non_coding_transcript_exon_variant,,ENST00000530764,;PGR,intron_variant,,ENST00000526300,; T ENST00000325455 Transcript missense_variant 3870/13748 2416/2802 806/933 Q/K Cag/Aag rs773336784 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 deleterious(0.01) 6/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS rs773336784 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 101050001 101050001 G T 1 0 0 0 0 1 0 0 0 11894 1386 48 2 2 PGR 11 101050001 Missense_Mutation SNP G C3N-00551_T 5199353 101050001 34036621 388 15871 DYNC2H1 0 . GRCh38 11 103128917 103128917 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.1865A>G p.His622Arg p.H622R ENST00000398093 13/90 149 123 26 158 158 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.His622Arg,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.His622Arg,ENST00000398093,NM_001080463.1;DYNC2H1,missense_variant,p.His622Arg,ENST00000334267,; G ENST00000398093 Transcript missense_variant 1865/12945 1865/12945 622/4314 H/R cAt/cGt 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0.01) 13/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF08385 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 103128917 103128917 A G 1 0 0 0 0 1 0 0 0 4670 217 8 5 5 DYNC2H1 11 103128917 Missense_Mutation SNP A C3N-00551_T 2078916 103128917 31957705 389 15872 DYNC2H1 0 . GRCh38 11 103358267 103358267 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.12085G>T p.Gly4029Cys p.G4029C ENST00000398093 84/90 116 95 21 138 138 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Gly4022Cys,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Gly4029Cys,ENST00000398093,NM_001080463.1;DYNC2H1,missense_variant,p.Gly9Cys,ENST00000533197,;DYNC2H1,intron_variant,,ENST00000334267,;DYNC2H1,3_prime_UTR_variant,,ENST00000528670,; T ENST00000398093 Transcript missense_variant 12085/12945 12085/12945 4029/4314 G/C Ggc/Tgc 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0.05) 84/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF03028 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999987 1 1 1 0 T 3 4 52 103358267 103358267 G T 1 0 0 0 0 1 0 0 0 4670 1232 43 2 2 DYNC2H1 11 103358267 Missense_Mutation SNP G C3N-00551_T 229350 103358267 31728355 390 15873 ACAT1 0 . GRCh38 11 108143991 108143991 + Missense_Mutation SNP G G C rs780486838 C3N-00551_T C3N-00551_N G G c.949G>C p.Asp317His p.D317H ENST00000265838 10/12 275 255 20 350 350 0 varscan-mutect ACAT1,missense_variant,p.Asp317His,ENST00000265838,NM_000019.3;ACAT1,downstream_gene_variant,,ENST00000528370,;ACAT1,non_coding_transcript_exon_variant,,ENST00000532792,;ACAT1,non_coding_transcript_exon_variant,,ENST00000533610,;ACAT1,downstream_gene_variant,,ENST00000531813,;ACAT1,upstream_gene_variant,,ENST00000533597,;ACAT1,downstream_gene_variant,,ENST00000534773,; C ENST00000265838 Transcript missense_variant 1040/1761 949/1284 317/427 D/H Gac/Cac rs780486838 1 1 ACAT1 HGNC HGNC:93 protein_coding YES CCDS8339.1 ENSP00000265838 P24752 A0A140VJX1 UPI0000136E41 NM_000019.3 deleterious(0) 10/12 Gene3D:3.40.47.10,Pfam_domain:PF02803,PIRSF_domain:PIRSF000429,hmmpanther:PTHR18919,hmmpanther:PTHR18919:SF81,Superfamily_domains:SSF53901,TIGRFAM_domain:TIGR01930 MODERATE 1 SNV 1 1 PASS rs780486838 . 0 204 0 2 4 0 0 0 -5.674928 0.5106852 1 1 1 0 C 3 2 52 108143991 108143991 G C 1 0 0 0 0 1 0 0 0 164 1290 45 4 4 ACAT1 11 108143991 Missense_Mutation SNP G C3N-00551_T 4785724 108143991 26942631 391 15874 RDX 0 . GRCh38 11 110253967 110253967 + Missense_Mutation SNP T T G C3N-00551_T C3N-00551_N T T c.938A>C p.Lys313Thr p.K313T ENST00000405097 9/16 438 391 47 473 473 0 strelka-varscan-mutect RDX,missense_variant,p.Lys313Thr,ENST00000343115,NM_002906.3;RDX,missense_variant,p.Lys177Thr,ENST00000544551,NM_001260494.1;RDX,missense_variant,p.Lys313Thr,ENST00000405097,NM_001260492.1;RDX,missense_variant,p.Lys313Thr,ENST00000528498,NM_001260493.1;RDX,intron_variant,,ENST00000528900,NM_001260495.1;RDX,intron_variant,,ENST00000530301,NM_001260496.1;RDX,downstream_gene_variant,,ENST00000534683,;RDX,downstream_gene_variant,,ENST00000532118,;RDX,missense_variant,p.Lys313Thr,ENST00000530749,;RDX,3_prime_UTR_variant,,ENST00000530131,;RDX,non_coding_transcript_exon_variant,,ENST00000529774,; G ENST00000405097 Transcript missense_variant 1248/2761 938/1815 313/604 K/T aAa/aCa COSM4841302 1 -1 RDX HGNC HGNC:9944 protein_coding YES CCDS58174.1 ENSP00000384136 P35241 UPI0000EE3914 NM_001260492.1 deleterious(0) 9/16 Gene3D:1e5wA04,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF002305,hmmpanther:PTHR23281,hmmpanther:PTHR23281:SF14,Superfamily_domains:SSF50729 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 110253967 110253967 T G 1 0 0 0 0 1 0 0 0 13367 1841 64 5 5 RDX 11 110253967 Missense_Mutation SNP T C3N-00551_T 2109976 110253967 24832655 392 15875 RDX 0 . GRCh38 11 110253989 110253989 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.916A>C p.Lys306Gln p.K306Q ENST00000405097 9/16 445 404 41 488 488 0 strelka-varscan-mutect RDX,missense_variant,p.Lys306Gln,ENST00000343115,NM_002906.3;RDX,missense_variant,p.Lys170Gln,ENST00000544551,NM_001260494.1;RDX,missense_variant,p.Lys306Gln,ENST00000405097,NM_001260492.1;RDX,missense_variant,p.Lys306Gln,ENST00000528498,NM_001260493.1;RDX,intron_variant,,ENST00000528900,NM_001260495.1;RDX,intron_variant,,ENST00000530301,NM_001260496.1;RDX,downstream_gene_variant,,ENST00000534683,;RDX,downstream_gene_variant,,ENST00000532118,;RDX,missense_variant,p.Lys306Gln,ENST00000530749,;RDX,3_prime_UTR_variant,,ENST00000530131,;RDX,non_coding_transcript_exon_variant,,ENST00000529774,; G ENST00000405097 Transcript missense_variant 1226/2761 916/1815 306/604 K/Q Aag/Cag 1 -1 RDX HGNC HGNC:9944 protein_coding YES CCDS58174.1 ENSP00000384136 P35241 UPI0000EE3914 NM_001260492.1 deleterious(0) 9/16 Gene3D:1e5wA04,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF002305,hmmpanther:PTHR23281,hmmpanther:PTHR23281:SF14,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 110253989 110253989 T G 1 0 0 0 0 1 0 0 0 13367 1792 62 5 5 RDX 11 110253989 Missense_Mutation SNP T C3N-00551_T 22 110253989 24832633 393 15876 ZBTB16 0 . GRCh38 11 114064256 114064256 + Missense_Mutation SNP G G T rs772815592 C3N-00551_T C3N-00551_N G G c.956G>T p.Arg319Leu p.R319L ENST00000335953 2/7 438 372 66 514 514 0 strelka-varscan-mutect ZBTB16,missense_variant,p.Arg319Leu,ENST00000335953,NM_006006.4;ZBTB16,missense_variant,p.Arg319Leu,ENST00000392996,NM_001018011.1;ZBTB16,downstream_gene_variant,,ENST00000544220,;ZBTB16,downstream_gene_variant,,ENST00000535700,;ZBTB16,non_coding_transcript_exon_variant,,ENST00000541602,;ZBTB16,upstream_gene_variant,,ENST00000539918,; T ENST00000335953 Transcript missense_variant 1336/2523 956/2022 319/673 R/L cGa/cTa rs772815592,COSM3443625 1 1 ZBTB16 HGNC HGNC:12930 protein_coding YES CCDS8367.1 ENSP00000338157 Q05516 A0A024R3C6 UPI000000018E NM_006006.4 tolerated(0.31) 2/7 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772815592 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 114064256 114064256 G T 1 0 0 0 0 1 0 0 0 18093 1058 37 1 1 ZBTB16 11 114064256 Missense_Mutation SNP G C3N-00551_T 3810267 114064256 21022366 394 15877 GRIK4 0 . GRCh38 11 120960980 120960980 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.1946T>C p.Met649Thr p.M649T ENST00000527524 17/21 189 161 28 281 281 0 strelka-mutect GRIK4,missense_variant,p.Met649Thr,ENST00000527524,NM_014619.4;GRIK4,missense_variant,p.Met649Thr,ENST00000438375,NM_001282473.2,NM_001282470.2;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,; C ENST00000527524 Transcript missense_variant 2233/5802 1946/2871 649/956 M/T aTg/aCg 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 deleterious(0) 17/21 hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 120960980 120960980 T C 1 0 0 0 0 1 0 0 0 6658 1464 51 5 5 GRIK4 11 120960980 Missense_Mutation SNP T C3N-00551_T 6896724 120960980 14125642 395 15878 SORL1 0 . GRCh38 11 121514216 121514216 + Missense_Mutation SNP G G C rs772660461 C3N-00551_T C3N-00551_N G G c.1106G>C p.Arg369Pro p.R369P ENST00000260197 8/48 206 188 18 227 227 0 strelka-varscan-mutect SORL1,missense_variant,p.Arg369Pro,ENST00000260197,NM_003105.5;SORL1,non_coding_transcript_exon_variant,,ENST00000532451,; C ENST00000260197 Transcript missense_variant 1235/10904 1106/6645 369/2214 R/P cGc/cCc rs772660461,COSM924043 1 1 SORL1 HGNC HGNC:11185 protein_coding YES CCDS8436.1 ENSP00000260197 Q92673 UPI000013D0B1 NM_003105.5 tolerated(0.22) 8/48 Pfam_domain:PF15902,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF20,SMART_domains:SM00602,Superfamily_domains:SSF110296 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772660461 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 121514216 121514216 G C 1 0 0 0 0 1 0 0 0 15256 1087 38 4 4 SORL1 11 121514216 Missense_Mutation SNP G C3N-00551_T 553236 121514216 13572406 396 15879 OR8B2 0 . GRCh38 11 124382488 124382488 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.856C>A p.Pro286Thr p.P286T ENST00000375013 1/1 289 232 57 300 300 0 strelka-varscan-mutect OR8B2,missense_variant,p.Pro286Thr,ENST00000375013,NM_001005468.1;OR8C1P,upstream_gene_variant,,ENST00000427511,; T ENST00000375013 Transcript missense_variant 875/968 856/942 286/313 P/T Ccc/Acc COSM348374 1 -1 OR8B2 HGNC HGNC:8471 protein_coding YES CCDS31708.1 ENSP00000364152 Q96RD0 A0A126GVQ4 UPI000004B1E5 NM_001005468.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF258,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 124382488 124382488 G T 1 0 0 0 0 1 0 0 0 11297 1174 41 2 2 OR8B2 11 124382488 Missense_Mutation SNP G C3N-00551_T 2868272 124382488 10704134 397 15880 SNX19 0 . GRCh38 11 130906011 130906011 + Silent SNP C C A rs553468459 C3N-00551_T C3N-00551_N C C c.2385G>T p.= p.V795V ENST00000265909 7/11 195 153 42 294 294 0 strelka-varscan-mutect SNX19,synonymous_variant,p.=,ENST00000265909,NM_014758.2;SNX19,synonymous_variant,p.=,ENST00000533214,;SNX19,synonymous_variant,p.=,ENST00000534726,;SNX19,synonymous_variant,p.=,ENST00000530356,;SNX19,synonymous_variant,p.=,ENST00000528555,NM_001301089.1;SNX19,non_coding_transcript_exon_variant,,ENST00000533318,;SNX19,non_coding_transcript_exon_variant,,ENST00000524460,;SNX19,upstream_gene_variant,,ENST00000526579,;SNX19,non_coding_transcript_exon_variant,,ENST00000527451,;SNX19,downstream_gene_variant,,ENST00000531608,; A ENST00000265909 Transcript synonymous_variant 2955/6535 2385/2979 795/992 V gtG/gtT rs553468459 1 -1 SNX19 HGNC HGNC:21532 protein_coding YES CCDS31721.1 ENSP00000265909 Q92543 UPI000013D6A5 NM_014758.2 7/11 hmmpanther:PTHR22775,hmmpanther:PTHR22775:SF31 LOW 1 SNV 1 1 PASS rs553468459 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 130906011 130906011 C A 1 0 0 0 0 0 0 0 1 15211 581 21 2 2 SNX19 11 130906011 Silent SNP C C3N-00551_T 6523523 130906011 4180611 398 15881 NTM 0 . GRCh38 11 132146354 132146354 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.240C>A p.Asp80Glu p.D80E ENST00000425719 2/8 344 305 39 445 445 0 strelka-varscan-mutect NTM,missense_variant,p.Asp80Glu,ENST00000374786,NM_016522.2;NTM,missense_variant,p.Asp80Glu,ENST00000374791,NM_001048209.1;NTM,missense_variant,p.Asp80Glu,ENST00000425719,NM_001144058.1;NTM,missense_variant,p.Asp80Glu,ENST00000374784,NM_001144059.1;NTM,missense_variant,p.Asp71Glu,ENST00000550167,;NTM,5_prime_UTR_variant,,ENST00000427481,;NTM,5_prime_UTR_variant,,ENST00000539799,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,intron_variant,,ENST00000498764,;NTM,non_coding_transcript_exon_variant,,ENST00000479431,; A ENST00000425719 Transcript missense_variant 260/1607 240/1068 80/355 D/E gaC/gaA 1 1 NTM HGNC HGNC:17941 protein_coding YES CCDS44777.1 ENSP00000396722 Q9P121 UPI00001A58B9 NM_001144058.1 tolerated(0.12) 2/8 PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF116,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1436314297 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 132146354 132146354 C A 1 0 0 0 0 1 0 0 0 10763 477 17 2 2 NTM 11 132146354 Missense_Mutation SNP C C3N-00551_T 1240343 132146354 2940268 399 15882 SLC6A13 0 . GRCh38 12 243729 243729 + Missense_Mutation SNP G G T rs773882024 C3N-00551_T C3N-00551_N G G c.287C>A p.Thr96Asn p.T96N ENST00000343164 3/15 160 120 40 220 219 1 strelka-varscan-mutect SLC6A13,missense_variant,p.Thr96Asn,ENST00000343164,NM_016615.4;SLC6A13,intron_variant,,ENST00000445055,NM_001190997.2;SLC6A13,intron_variant,,ENST00000546319,;SLC6A13,missense_variant,p.Thr96Asn,ENST00000539260,;SLC6A13,5_prime_UTR_variant,,ENST00000542272,;SLC6A13,non_coding_transcript_exon_variant,,ENST00000536842,; T ENST00000343164 Transcript missense_variant 340/2185 287/1809 96/602 T/N aCt/aAt rs773882024 1 -1 SLC6A13 HGNC HGNC:11046 protein_coding YES CCDS8502.1 ENSP00000339260 Q9NSD5 UPI0000046060 NM_016615.4 deleterious(0) 3/15 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF111,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS rs773882024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 243729 243729 G T 1 0 0 0 0 1 0 0 0 14959 1029 36 2 2 SLC6A13 12 243729 Missense_Mutation SNP G C3N-00551_T 243729 133031580 400 15883 NANOGNB 0 . GRCh38 12 7770288 7770288 + Silent SNP A A G novel C3N-00551_T C3N-00551_N A A c.408A>G p.= p.S136S ENST00000382119 2/4 87 54 33 99 99 0 strelka-varscan-mutect NANOGNB,synonymous_variant,p.=,ENST00000382119,NM_001145465.1; G ENST00000382119 Transcript synonymous_variant 478/907 408/567 136/188 S tcA/tcG 1 1 NANOGNB HGNC HGNC:24958 protein_coding YES CCDS44826.1 ENSP00000371553 Q7Z5D8 UPI00001B3DAD NM_001145465.1 2/4 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR12157,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS rs1021121764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 7770288 7770288 A G 1 0 0 0 0 0 0 0 1 10158 204 8 5 5 NANOGNB 12 7770288 Silent SNP A C3N-00551_T 7526559 7770288 125505021 401 15884 CMAS 0 . GRCh38 12 22065128 22065128 + Missense_Mutation SNP A A C novel C3N-00551_T C3N-00551_N A A c.1122A>C p.Glu374Asp p.E374D ENST00000229329 8/8 75 67 8 69 69 0 strelka-varscan-mutect CMAS,missense_variant,p.Glu374Asp,ENST00000229329,NM_018686.4;CMAS,downstream_gene_variant,,ENST00000538498,;ST8SIA1,intron_variant,,ENST00000536535,;ST8SIA1,downstream_gene_variant,,ENST00000544732,;CMAS,3_prime_UTR_variant,,ENST00000534981,;CMAS,downstream_gene_variant,,ENST00000535610,;CMAS,downstream_gene_variant,,ENST00000537658,; C ENST00000229329 Transcript missense_variant 1252/1787 1122/1305 374/434 E/D gaA/gaC 1 1 CMAS HGNC HGNC:18290 protein_coding YES CCDS8696.1 ENSP00000229329 Q8NFW8 UPI0000034274 NM_018686.4 tolerated(1) 8/8 hmmpanther:PTHR21485,hmmpanther:PTHR21485:SF3,Gene3D:3.40.50.1000,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -17.2397 0.9999872 1 1 1 0 C 3 2 52 22065128 22065128 A C 1 0 0 0 0 1 0 0 0 3348 69 3 5 5 CMAS 12 22065128 Missense_Mutation SNP A C3N-00551_T 14294840 22065128 111210181 402 15885 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C A rs121913529 C3N-00551_T C3N-00551_N C C c.35G>T p.Gly12Val p.G12V ENST00000256078 2/6 308 209 99 360 360 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Val,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Val,ENST00000556131,;KRAS,missense_variant,p.Gly12Val,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Val,ENST00000557334,; A ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/V gGt/gTt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 25245350 25245350 C A 1 0 0 0 0 1 0 0 0 8318 507 18 2 2 KRAS 12 25245350 Missense_Mutation SNP C C3N-00551_T 3180222 25245350 108029959 403 15886 KIAA1551 0 . GRCh38 12 31981418 31981418 + Nonsense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.463C>T p.Gln155Ter p.Q155* ENST00000312561 4/6 210 170 40 255 255 0 strelka-varscan-mutect KIAA1551,stop_gained,p.Gln155Ter,ENST00000312561,NM_018169.3;KIAA1551,stop_gained,p.Gln155Ter,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,; T ENST00000312561 Transcript stop_gained 877/6230 463/5244 155/1747 Q/* Caa/Taa 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 4/6 hmmpanther:PTHR21604 HIGH 1 SNV 1 1 PASS rs1414074670 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 31981418 31981418 C T 1 0 0 0 0 0 1 0 0 8122 827 29 3 3 KIAA1551 12 31981418 Nonsense_Mutation SNP C C3N-00551_T 6736068 31981418 101293891 404 15887 KMT2D 0 . GRCh38 12 49032705 49032705 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.12000C>A p.= p.G4000G ENST00000301067 39/54 685 479 206 669 669 0 strelka-varscan-mutect KMT2D,synonymous_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,; T ENST00000301067 Transcript synonymous_variant 12000/19419 12000/16614 4000/5537 G ggC/ggA 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 39/54 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 49032705 49032705 G T 1 0 0 0 0 0 0 0 1 8298 1306 46 2 2 KMT2D 12 49032705 Silent SNP G C3N-00551_T 17051287 49032705 84242604 405 15888 HOXC12 0 . GRCh38 12 53955029 53955029 + Missense_Mutation SNP G G T rs766902318 C3N-00551_T C3N-00551_N G G c.100G>T p.Ala34Ser p.A34S ENST00000243103 1/2 350 252 98 286 286 0 strelka-varscan-mutect HOXC12,missense_variant,p.Ala34Ser,ENST00000243103,NM_173860.1; T ENST00000243103 Transcript missense_variant 196/3335 100/849 34/282 A/S Gcg/Tcg rs766902318 1 1 HOXC12 HGNC HGNC:5124 protein_coding YES CCDS8866.1 ENSP00000243103 P31275 UPI000012CF7E NM_173860.1 tolerated(0.23) 1/2 hmmpanther:PTHR24326:SF164,hmmpanther:PTHR24326 MODERATE 1 SNV 2 1 PASS rs766902318 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 53955029 53955029 G T 1 0 0 0 0 1 0 0 0 7205 1203 42 2 2 HOXC12 12 53955029 Missense_Mutation SNP G C3N-00551_T 4922324 53955029 79320280 406 15889 HOXC12 0 . GRCh38 12 53956375 53956375 + Missense_Mutation SNP C C A rs745865686 C3N-00551_T C3N-00551_N C C c.658C>A p.Pro220Thr p.P220T ENST00000243103 2/2 83 57 26 77 77 0 strelka-varscan-mutect HOXC12,missense_variant,p.Pro220Thr,ENST00000243103,NM_173860.1; A ENST00000243103 Transcript missense_variant 754/3335 658/849 220/282 P/T Ccc/Acc rs745865686 1 1 HOXC12 HGNC HGNC:5124 protein_coding YES CCDS8866.1 ENSP00000243103 P31275 UPI000012CF7E NM_173860.1 deleterious(0) 2/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS50071,hmmpanther:PTHR24326:SF164,hmmpanther:PTHR24326,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 2 1 PASS rs745865686 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 52 53956375 53956375 C A 1 0 0 0 0 1 0 0 0 7205 739 26 2 2 HOXC12 12 53956375 Missense_Mutation SNP C C3N-00551_T 1346 53956375 79318934 407 15890 HOXC6 0 . GRCh38 12 54028599 54028599 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.78C>T p.= p.L26L ENST00000243108 1/2 228 154 74 261 261 0 strelka-varscan-mutect HOXC6,synonymous_variant,p.=,ENST00000243108,NM_004503.3;HOXC6,5_prime_UTR_variant,,ENST00000394331,NM_153693.4;HOXC6,5_prime_UTR_variant,,ENST00000504315,;HOXC4,intron_variant,,ENST00000303406,NM_014620.5;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,intron_variant,,ENST00000509328,;HOXC5,upstream_gene_variant,,ENST00000312492,NM_018953.3;RP11-834C11.14,intron_variant,,ENST00000512206,; T ENST00000243108 Transcript synonymous_variant 242/1733 78/708 26/235 L ctC/ctT 1 1 HOXC6 HGNC HGNC:5128 protein_coding YES CCDS8871.1 ENSP00000243108 P09630 UPI0000020BA4 NM_004503.3 1/2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 54028599 54028599 C T 1 0 0 0 0 0 0 0 1 7209 813 29 3 3 HOXC6 12 54028599 Silent SNP C C3N-00551_T 72224 54028599 79246710 408 15891 ZBTB39 0 . GRCh38 12 57003844 57003844 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.1074G>T p.= p.L358L ENST00000300101 2/2 255 162 93 283 283 0 strelka-varscan-mutect ZBTB39,synonymous_variant,p.=,ENST00000300101,NM_014830.2; A ENST00000300101 Transcript synonymous_variant 1160/6170 1074/2139 358/712 L ctG/ctT 1 -1 ZBTB39 HGNC HGNC:29014 protein_coding YES CCDS31839.1 ENSP00000300101 O15060 UPI0000139682 NM_014830.2 2/2 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF218 LOW 1 SNV 1 1 PASS rs983338125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 57003844 57003844 C A 1 0 0 0 0 0 0 0 1 18109 813 29 2 2 ZBTB39 12 57003844 Silent SNP C C3N-00551_T 2975245 57003844 76271465 409 15892 SRGAP1 0 . GRCh38 12 64111910 64111910 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2068C>A p.His690Asn p.H690N ENST00000355086 17/22 242 183 59 277 276 1 strelka-varscan-mutect SRGAP1,missense_variant,p.His690Asn,ENST00000355086,NM_020762.2;SRGAP1,missense_variant,p.His627Asn,ENST00000631006,;SRGAP1,missense_variant,p.His627Asn,ENST00000543397,;RP11-196H14.4,intron_variant,,ENST00000535806,;SRGAP1,non_coding_transcript_exon_variant,,ENST00000537585,; A ENST00000355086 Transcript missense_variant 2592/23331 2068/3258 690/1085 H/N Cat/Aat 1 1 SRGAP1 HGNC HGNC:17382 protein_coding YES CCDS8967.1 ENSP00000347198 Q7Z6B7 UPI00001A9CB9 NM_020762.2 tolerated(0.16) 17/22 Low_complexity_(Seg):seg,PROSITE_profiles:PS50238,hmmpanther:PTHR14166:SF15,hmmpanther:PTHR14166,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 64111910 64111910 C A 1 0 0 0 0 1 0 0 0 15504 594 21 2 2 SRGAP1 12 64111910 Missense_Mutation SNP C C3N-00551_T 7108066 64111910 69163399 410 15893 RAP1B 0 . GRCh38 12 68654156 68654156 + Silent SNP A A G novel C3N-00551_T C3N-00551_N A A c.228A>G p.= p.Q76Q ENST00000250559 5/8 184 168 16 205 205 0 varscan-mutect RAP1B,synonymous_variant,p.=,ENST00000250559,;RAP1B,synonymous_variant,p.=,ENST00000393436,NM_015646.5,NM_001010942.2;RAP1B,synonymous_variant,p.=,ENST00000450214,NM_001251917.1,NM_001251918.1;RAP1B,synonymous_variant,p.=,ENST00000540209,NM_001251921.1;RAP1B,synonymous_variant,p.=,ENST00000537460,;RAP1B,synonymous_variant,p.=,ENST00000378985,;RAP1B,synonymous_variant,p.=,ENST00000539091,;RAP1B,synonymous_variant,p.=,ENST00000543393,;RAP1B,synonymous_variant,p.=,ENST00000425247,;RAP1B,synonymous_variant,p.=,ENST00000543697,;RAP1B,synonymous_variant,p.=,ENST00000341355,;RAP1B,synonymous_variant,p.=,ENST00000541216,;RAP1B,synonymous_variant,p.=,ENST00000545270,;RAP1B,synonymous_variant,p.=,ENST00000542018,;RAP1B,synonymous_variant,p.=,ENST00000534899,;RAP1B,synonymous_variant,p.=,ENST00000538283,;RAP1B,synonymous_variant,p.=,ENST00000538980,;RAP1B,synonymous_variant,p.=,ENST00000540781,;RAP1B,synonymous_variant,p.=,ENST00000541167,;RAP1B,synonymous_variant,p.=,ENST00000545720,;RAP1B,synonymous_variant,p.=,ENST00000453560,;RAP1B,synonymous_variant,p.=,ENST00000535492,;RAP1B,intron_variant,,ENST00000542145,NM_001251922.1;RAP1B,downstream_gene_variant,,ENST00000538877,;RAP1B,downstream_gene_variant,,ENST00000422358,;RAP1B,downstream_gene_variant,,ENST00000485252,;RAP1B,non_coding_transcript_exon_variant,,ENST00000463493,;RAP1B,downstream_gene_variant,,ENST00000460800,;RAP1B,non_coding_transcript_exon_variant,,ENST00000544639,;RAP1B,non_coding_transcript_exon_variant,,ENST00000541968,;RAP1B,downstream_gene_variant,,ENST00000501412,; G ENST00000250559 Transcript synonymous_variant 459/13438 228/555 76/184 Q caA/caG 1 1 RAP1B HGNC HGNC:9857 protein_coding YES CCDS8984.1 ENSP00000250559 P61224 A0A024RB87 UPI0000001221 5/8 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 68654156 68654156 A G 1 0 0 0 0 0 0 0 1 13195 69 3 5 5 RAP1B 12 68654156 Silent SNP A C3N-00551_T 4542246 68654156 64621153 411 15894 NAV3 0 . GRCh38 12 78197265 78197265 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.6310G>C p.Ala2104Pro p.A2104P ENST00000397909 35/40 99 68 31 93 93 0 strelka-varscan-mutect NAV3,missense_variant,p.Ala2104Pro,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Ala2082Pro,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Ala977Pro,ENST00000552895,;NAV3,missense_variant,p.Ala704Pro,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000551162,;NAV3,upstream_gene_variant,,ENST00000547884,; C ENST00000397909 Transcript missense_variant 6483/9821 6310/7158 2104/2385 A/P Gct/Cct 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 35/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 78197265 78197265 G C 1 0 0 0 0 1 0 0 0 10194 971 34 4 4 NAV3 12 78197265 Missense_Mutation SNP G C3N-00551_T 9543109 78197265 55078044 412 15895 KERA 0 . GRCh38 12 91056007 91056007 + Missense_Mutation SNP T T G novel C3N-00551_T C3N-00551_N T T c.275A>C p.Glu92Ala p.E92A ENST00000266719 2/3 120 85 35 138 138 0 strelka-varscan-mutect KERA,missense_variant,p.Glu92Ala,ENST00000266719,NM_007035.3; G ENST00000266719 Transcript missense_variant 523/2162 275/1059 92/352 E/A gAg/gCg 1 -1 KERA HGNC HGNC:6309 protein_coding YES CCDS9037.1 ENSP00000266719 O60938 UPI000000161F NM_007035.3 tolerated(0.63) 2/3 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF133,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 91056007 91056007 T G 1 0 0 0 0 1 0 0 0 8063 1551 54 5 5 KERA 12 91056007 Missense_Mutation SNP T C3N-00551_T 12858742 91056007 42219302 413 15896 STAB2 0 . GRCh38 12 103712441 103712441 + Missense_Mutation SNP C C A rs138119925 C3N-00551_T C3N-00551_N C C c.4409C>A p.Thr1470Lys p.T1470K ENST00000388887 41/69 215 147 68 217 217 0 strelka-varscan-mutect STAB2,missense_variant,p.Thr1470Lys,ENST00000388887,NM_017564.9;STAB2,non_coding_transcript_exon_variant,,ENST00000549798,; A ENST00000388887 Transcript missense_variant,splice_region_variant 4613/8251 4409/7656 1470/2551 T/K aCa/aAa rs138119925 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 tolerated(0.18) 41/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2.40.155.10,SMART_domains:SM00181,SMART_domains:SM00179 MODERATE 1 SNV 1 1 PASS rs138119925 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 103712441 103712441 C A 1 0 0 0 0 1 0 0 0 15616 492 17 2 2 STAB2 12 103712441 Missense_Mutation SNP C C3N-00551_T 12656434 103712441 29562868 414 15897 BTBD11 0 . GRCh38 12 107617432 107617432 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2227C>A p.His743Asn p.H743N ENST00000280758 9/17 114 80 34 146 146 0 strelka-varscan-mutect BTBD11,missense_variant,p.His743Asn,ENST00000280758,NM_001018072.1;BTBD11,missense_variant,p.His743Asn,ENST00000490090,;BTBD11,missense_variant,p.His280Asn,ENST00000357167,NM_001017523.1;BTBD11,intron_variant,,ENST00000420571,;RP11-128P10.1,intron_variant,,ENST00000548473,; A ENST00000280758 Transcript missense_variant 2755/5767 2227/3315 743/1104 H/N Cac/Aac 1 1 BTBD11 HGNC HGNC:23844 protein_coding YES CCDS31893.1 ENSP00000280758 A6QL63 UPI000051901E NM_001018072.1 deleterious(0) 9/17 hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF76,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 107617432 107617432 C A 1 0 0 0 0 1 0 0 0 1714 492 17 2 2 BTBD11 12 107617432 Missense_Mutation SNP C C3N-00551_T 3904991 107617432 25657877 415 15898 ATP2A2 0 . GRCh38 12 110339719 110339719 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1759G>T p.Glu587Ter p.E587* ENST00000539276 13/20 295 253 42 365 364 1 strelka-varscan-mutect ATP2A2,stop_gained,p.Glu587Ter,ENST00000308664,NM_001681.3;ATP2A2,stop_gained,p.Glu587Ter,ENST00000539276,NM_170665.3;ATP2A2,stop_gained,p.Glu478Ter,ENST00000548169,;ATP2A2,splice_region_variant,,ENST00000377685,;ATP2A2,upstream_gene_variant,,ENST00000547792,; T ENST00000539276 Transcript stop_gained,splice_region_variant 1868/4094 1759/3129 587/1042 E/* Gag/Tag 1 1 ATP2A2 HGNC HGNC:812 protein_coding YES CCDS9144.1 ENSP00000440045 P16615 A0A0S2Z3L2 UPI0000001C3A NM_170665.3 13/20 Gene3D:3.40.1110.10,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF234,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660,TIGRFAM_domain:TIGR01116 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 110339719 110339719 G T 1 0 0 0 0 0 1 0 0 1290 1304 45 2 2 ATP2A2 12 110339719 Nonsense_Mutation SNP G C3N-00551_T 2722287 110339719 22935590 416 15899 SETD1B 0 . GRCh38 12 121810633 121810633 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1688G>T p.Arg563Leu p.R563L ENST00000542440 6/18 104 75 29 109 108 1 strelka-varscan-mutect SETD1B,missense_variant,p.Arg563Leu,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Arg563Leu,ENST00000604567,;SETD1B,missense_variant,p.Arg563Leu,ENST00000619791,;SETD1B,missense_variant,p.Arg563Leu,ENST00000267197,; T ENST00000542440 Transcript missense_variant 1756/8185 1688/5772 563/1923 R/L cGc/cTc COSM4638143 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 deleterious(0) 6/18 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS rs942845427 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 121810633 121810633 G T 1 0 0 0 0 1 0 0 0 14408 1087 38 1 1 SETD1B 12 121810633 Missense_Mutation SNP G C3N-00551_T 11470914 121810633 11464676 417 15900 LRRC43 0 . GRCh38 12 122186195 122186195 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.417C>T p.= p.T139T ENST00000339777 3/12 125 87 38 130 130 0 strelka-varscan-mutect LRRC43,synonymous_variant,p.=,ENST00000339777,NM_152759.4,NM_001098519.1;LRRC43,5_prime_UTR_variant,,ENST00000537729,;LRRC43,non_coding_transcript_exon_variant,,ENST00000538800,;LRRC43,intron_variant,,ENST00000541498,;LRRC43,non_coding_transcript_exon_variant,,ENST00000537113,; T ENST00000339777 Transcript synonymous_variant 445/2028 417/1971 139/656 T acC/acT 1 1 LRRC43 HGNC HGNC:28562 protein_coding YES CCDS45001.1 ENSP00000344233 Q8N309 UPI00015347BE NM_152759.4,NM_001098519.1 3/12 Low_complexity_(Seg):seg,hmmpanther:PTHR24365:SF373,hmmpanther:PTHR24365,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 122186195 122186195 C T 1 0 0 0 0 0 0 0 1 8897 637 22 3 3 LRRC43 12 122186195 Silent SNP C C3N-00551_T 375562 122186195 11089114 418 15901 TMEM132C 0 . GRCh38 12 128544000 128544000 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.1018C>A p.Arg340Ser p.R340S ENST00000435159 3/9 77 45 32 113 113 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Arg340Ser,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript missense_variant 1018/4947 1018/3327 340/1108 R/S Cgt/Agt COSM5162262 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 tolerated(1) 3/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 1 MODERATE 1 SNV 5 1 1 PASS rs1002960609 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 128544000 128544000 C A 1 0 0 0 0 1 0 0 0 16491 652 23 1 1 TMEM132C 12 128544000 Missense_Mutation SNP C C3N-00551_T 6357805 128544000 4731309 419 15902 TMEM132C 0 . GRCh38 12 128705909 128705909 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.2941C>A p.Leu981Met p.L981M ENST00000435159 9/9 137 110 27 170 170 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Leu981Met,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript missense_variant 2941/4947 2941/3327 981/1108 L/M Ctg/Atg COSM4485509,COSM4485510 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 128705909 128705909 C A 1 0 0 0 0 1 0 0 0 16491 680 24 2 2 TMEM132C 12 128705909 Missense_Mutation SNP C C3N-00551_T 161909 128705909 4569400 420 15903 TUBA3C 0 . GRCh38 13 19177181 19177181 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.802C>A p.Pro268Thr p.P268T ENST00000400113 4/5 203 174 29 250 250 0 strelka-varscan-mutect TUBA3C,missense_variant,p.Pro268Thr,ENST00000400113,NM_006001.2;TUBA3C,missense_variant,p.Pro268Thr,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; T ENST00000400113 Transcript missense_variant 907/1551 802/1353 268/450 P/T Ccc/Acc COSM3467501 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 deleterious_low_confidence(0) 4/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.40.50.1440,Pfam_domain:PF03953,SMART_domains:SM00865,Superfamily_domains:SSF55307 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 19177181 19177181 G T 1 0 0 0 0 1 0 0 0 17256 1232 43 2 2 TUBA3C 13 19177181 Missense_Mutation SNP G C3N-00551_T 19177181 95187147 421 15904 POSTN 0 . GRCh38 13 37584019 37584019 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.1193G>A p.Arg398Lys p.R398K ENST00000379747 9/23 154 134 20 228 228 0 strelka-varscan-mutect POSTN,missense_variant,p.Arg398Lys,ENST00000379747,NM_006475.2;POSTN,missense_variant,p.Arg398Lys,ENST00000541179,NM_001135936.1,NM_001135935.1;POSTN,missense_variant,p.Arg398Lys,ENST00000379749,;POSTN,missense_variant,p.Arg398Lys,ENST00000379743,NM_001286665.1;POSTN,missense_variant,p.Arg398Lys,ENST00000541481,NM_001286666.1,NM_001286667.1;POSTN,missense_variant,p.Arg398Lys,ENST00000379742,NM_001135934.1; T ENST00000379747 Transcript missense_variant 1311/3373 1193/2511 398/836 R/K aGg/aAg 1 -1 POSTN HGNC HGNC:16953 protein_coding YES CCDS9364.1 ENSP00000369071 Q15063 A0A024RDS2 UPI000013CEB8 NM_006475.2 tolerated(0.67) 9/23 Gene3D:2.30.180.10,Pfam_domain:PF02469,PIRSF_domain:PIRSF016553,PROSITE_profiles:PS50213,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 37584019 37584019 C T 1 0 0 0 0 1 0 0 0 12373 681 24 3 3 POSTN 13 37584019 Missense_Mutation SNP C C3N-00551_T 18406838 37584019 76780309 422 15905 DZIP1 0 . GRCh38 13 95586047 95586047 + Missense_Mutation SNP G G T rs767706909 C3N-00551_T C3N-00551_N G G c.2308C>A p.Pro770Thr p.P770T ENST00000347108 19/21 121 101 20 200 200 0 strelka-varscan-mutect DZIP1,missense_variant,p.Pro751Thr,ENST00000361396,NM_014934.4;DZIP1,missense_variant,p.Pro770Thr,ENST00000347108,;DZIP1,missense_variant,p.Pro751Thr,ENST00000361156,;DZIP1,missense_variant,p.Pro770Thr,ENST00000376829,NM_198968.3;DZIP1,non_coding_transcript_exon_variant,,ENST00000485031,;DZIP1,non_coding_transcript_exon_variant,,ENST00000479518,; T ENST00000347108 Transcript missense_variant 2741/7068 2308/2604 770/867 P/T Cct/Act rs767706909 1 -1 DZIP1 HGNC HGNC:20908 protein_coding YES CCDS9478.1 ENSP00000257312 Q86YF9 UPI000000D9B8 tolerated(0.2) 19/21 hmmpanther:PTHR21502,hmmpanther:PTHR21502:SF5 MODERATE 1 SNV 5 1 PASS rs767706909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 95586047 95586047 G T 1 0 0 0 0 1 0 0 0 4687 1232 43 2 2 DZIP1 13 95586047 Missense_Mutation SNP G C3N-00551_T 58002028 95586047 18778281 423 15906 OR4K5 0 . GRCh38 14 19920649 19920649 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.43T>A p.Leu15Met p.L15M ENST00000315915 1/1 88 80 8 123 122 1 strelka-varscan-mutect OR4K5,missense_variant,p.Leu15Met,ENST00000315915,NM_001005483.1; A ENST00000315915 Transcript missense_variant 68/1078 43/972 15/323 L/M Ttg/Atg 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 deleterious(0.01) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF46,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1412627946 . 0 208 2 0 0 0 0 0 -17.24849 1 1 1 1 0 A 3 1 52 19920649 19920649 T A 1 0 0 0 0 1 0 0 0 11150 1722 60 4 4 OR4K5 14 19920649 Missense_Mutation SNP T C3N-00551_T 19920649 87123069 424 15907 OR4K5 0 . GRCh38 14 19921551 19921551 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.945A>T p.= p.S315S ENST00000315915 1/1 127 106 21 172 171 1 strelka-varscan-mutect OR4K5,synonymous_variant,p.=,ENST00000315915,NM_001005483.1; T ENST00000315915 Transcript synonymous_variant 970/1078 945/972 315/323 S tcA/tcT 1 1 OR4K5 HGNC HGNC:14745 protein_coding YES CCDS32024.1 ENSP00000319511 Q8NGD3 A0A126GVN5 UPI0000061E9E NM_001005483.1 1/1 Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 19921551 19921551 A T 1 0 0 0 0 0 0 0 1 11150 146 6 4 4 OR4K5 14 19921551 Silent SNP A C3N-00551_T 902 19921551 87122167 425 15908 RNASE11 0 . GRCh38 14 20584028 20584028 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.447G>T p.Glu149Asp p.E149D ENST00000553849 2/2 239 203 36 287 286 1 strelka-varscan-mutect RNASE11,missense_variant,p.Glu149Asp,ENST00000553849,NM_145250.3;RNASE11,missense_variant,p.Glu149Asp,ENST00000398009,;RNASE11,missense_variant,p.Glu149Asp,ENST00000432835,;RNASE11,missense_variant,p.Glu149Asp,ENST00000555841,;RNASE11,missense_variant,p.Glu149Asp,ENST00000620912,;RNASE11,missense_variant,p.Glu149Asp,ENST00000398008,;RNASE11,missense_variant,p.Glu149Asp,ENST00000443456,;RNASE11,missense_variant,p.Glu149Asp,ENST00000557105,;RNASE11,missense_variant,p.Glu149Asp,ENST00000557503,;RNASE11,downstream_gene_variant,,ENST00000413502,;RP11-14J7.7,downstream_gene_variant,,ENST00000555283,;RNASE11,downstream_gene_variant,,ENST00000554842,;RP11-14J7.6,upstream_gene_variant,,ENST00000554006,;RP11-14J7.6,upstream_gene_variant,,ENST00000553604,;RP11-14J7.6,upstream_gene_variant,,ENST00000554529,;RP11-14J7.6,upstream_gene_variant,,ENST00000556487,;RP11-14J7.7,3_prime_UTR_variant,,ENST00000335950,; A ENST00000553849 Transcript missense_variant 632/1101 447/600 149/199 E/D gaG/gaT 1 -1 RNASE11 HGNC HGNC:19269 protein_coding YES CCDS9553.1 ENSP00000451318 Q8TAA1 Q5GAN5 UPI000000CC00 NM_145250.3 tolerated(0.16) 2/2 hmmpanther:PTHR11437:SF22,hmmpanther:PTHR11437,Pfam_domain:PF00074,Gene3D:3.10.130.10,Superfamily_domains:SSF54076,PD000535 MODERATE 1 SNV 1 1 PASS rs1344618736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 20584028 20584028 C A 1 0 0 0 0 1 0 0 0 13580 912 32 2 2 RNASE11 14 20584028 Missense_Mutation SNP C C3N-00551_T 662477 20584028 86459690 426 15909 OR4E2 0 . GRCh38 14 21665780 21665780 + Missense_Mutation SNP G G C rs200419591 C3N-00551_T C3N-00551_N G G c.698G>C p.Arg233Pro p.R233P ENST00000408935 1/1 97 85 12 126 126 0 strelka-varscan-mutect OR4E2,missense_variant,p.Arg233Pro,ENST00000408935,NM_001001912.2;OR4E1,downstream_gene_variant,,ENST00000610316,; C ENST00000408935 Transcript missense_variant 698/942 698/942 233/313 R/P cGc/cCc rs200419591,COSM1315950 1 1 OR4E2 HGNC HGNC:8297 protein_coding YES CCDS41916.1 ENSP00000386195 Q8NGC2 A0A126GVR8 UPI0000EE498D NM_001001912.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF160,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs200419591 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 21665780 21665780 G C 1 0 0 0 0 1 0 0 0 11137 1087 38 4 4 OR4E2 14 21665780 Missense_Mutation SNP G C3N-00551_T 1081752 21665780 85377938 427 15910 OR6J1 0 . GRCh38 14 22634695 22634695 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.117G>T p.= p.L39L ENST00000540461 1/1 196 172 24 204 204 0 strelka-varscan-mutect OR6J1,synonymous_variant,p.=,ENST00000540461,;AC243945.1,downstream_gene_variant,,ENST00000623775,; A ENST00000540461 Transcript synonymous_variant 117/1044 117/1044 39/347 L ctG/ctT 1 -1 OR6J1 HGNC HGNC:14707 protein_coding YES ENSP00000437629 Q8NGC5 UPI000462094B 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26454:SF53,hmmpanther:PTHR26454,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 22634695 22634695 C A 1 0 0 0 0 0 0 0 1 11270 581 21 2 2 OR6J1 14 22634695 Silent SNP C C3N-00551_T 968915 22634695 84409023 428 15911 CDH24 0 . GRCh38 14 23054274 23054274 + Missense_Mutation SNP C C A rs757586503 C3N-00551_T C3N-00551_N C C c.839G>T p.Arg280Leu p.R280L ENST00000397359 6/14 99 81 18 114 114 0 strelka-varscan-mutect CDH24,missense_variant,p.Arg280Leu,ENST00000397359,NM_022478.3;CDH24,missense_variant,p.Arg280Leu,ENST00000487137,NM_144985.3;CDH24,missense_variant,p.Arg280Leu,ENST00000267383,;CDH24,missense_variant,p.Arg280Leu,ENST00000554034,;CDH24,intron_variant,,ENST00000610348,;ACIN1,downstream_gene_variant,,ENST00000262710,NM_014977.3;ACIN1,downstream_gene_variant,,ENST00000457657,NM_001164815.1;ACIN1,downstream_gene_variant,,ENST00000605057,;ACIN1,downstream_gene_variant,,ENST00000555053,NM_001164814.1;ACIN1,downstream_gene_variant,,ENST00000557515,;ACIN1,downstream_gene_variant,,ENST00000397341,;ACIN1,downstream_gene_variant,,ENST00000357481,NM_001164817.1;ACIN1,downstream_gene_variant,,ENST00000338631,NM_001164816.1;CDH24,upstream_gene_variant,,ENST00000485922,;ACIN1,downstream_gene_variant,,ENST00000473758,; A ENST00000397359 Transcript missense_variant 1099/3552 839/2460 280/819 R/L cGg/cTg rs757586503 1 -1 CDH24 HGNC HGNC:14265 protein_coding YES CCDS9585.1 ENSP00000380517 Q86UP0 UPI0000190F86 NM_022478.3 deleterious(0) 6/14 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF272,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 MODERATE SNV 5 1 PASS rs757586503 . 0 202 6 2 0 0 0 0 -20 0.9999439 1 1 1 0 A 3 1 52 23054274 23054274 C A 1 0 0 0 0 1 0 0 0 2812 652 23 1 1 CDH24 14 23054274 Missense_Mutation SNP C C3N-00551_T 419579 23054274 83989444 429 15912 MYH7 0 . GRCh38 14 23415260 23415260 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.5294T>A p.Met1765Lys p.M1765K ENST00000355349 37/40 662 574 88 643 642 1 strelka-varscan-mutect MYH7,missense_variant,p.Met1765Lys,ENST00000355349,NM_000257.3;MIR208B,downstream_gene_variant,,ENST00000401172,;CTD-2201G16.1,upstream_gene_variant,,ENST00000557368,; T ENST00000355349 Transcript missense_variant 5457/6087 5294/5808 1765/1935 M/K aTg/aAg 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 deleterious(0) 37/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 23415260 23415260 A T 1 0 0 0 0 1 0 0 0 10039 217 8 4 4 MYH7 14 23415260 Missense_Mutation SNP A C3N-00551_T 360986 23415260 83628458 430 15913 MYH7 0 . GRCh38 14 23425358 23425358 + Missense_Mutation SNP G G T rs727503258 C3N-00551_T C3N-00551_N G G c.2347C>A p.Arg783Ser p.R783S ENST00000355349 21/40 452 379 73 518 518 0 strelka-varscan-mutect MYH7,missense_variant,p.Arg783Ser,ENST00000355349,NM_000257.3; T ENST00000355349 Transcript missense_variant 2510/6087 2347/5808 783/1935 R/S Cgc/Agc rs727503258 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 tolerated(0.23) 21/40 Gene3D:1wdcA00,PROSITE_profiles:PS50096,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00015,Superfamily_domains:SSF52540 uncertain_significance,pathogenic MODERATE 1 SNV 1 1 1 PASS rs727503258 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 23425358 23425358 G T 1 0 0 0 0 1 0 0 0 10039 1116 39 1 1 MYH7 14 23425358 Missense_Mutation SNP G C3N-00551_T 10098 23425358 83618360 431 15914 TGM1 0 . GRCh38 14 24262051 24262051 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.302G>T p.Gly101Val p.G101V ENST00000206765 2/15 331 291 40 289 289 0 strelka-varscan-mutect TGM1,missense_variant,p.Gly101Val,ENST00000206765,NM_000359.2;TGM1,missense_variant,p.Gly101Val,ENST00000558074,;TGM1,intron_variant,,ENST00000544573,;RABGGTA,downstream_gene_variant,,ENST00000399409,NM_004581.5;RABGGTA,downstream_gene_variant,,ENST00000216840,NM_182836.2;RABGGTA,downstream_gene_variant,,ENST00000560777,;TGM1,upstream_gene_variant,,ENST00000559136,;RABGGTA,downstream_gene_variant,,ENST00000560521,;TGM1,downstream_gene_variant,,ENST00000560226,;TGM1,downstream_gene_variant,,ENST00000560478,;TGM1,downstream_gene_variant,,ENST00000560443,;TGM1,downstream_gene_variant,,ENST00000561067,;RABGGTA,downstream_gene_variant,,ENST00000560871,;RABGGTA,downstream_gene_variant,,ENST00000559551,;RABGGTA,downstream_gene_variant,,ENST00000560998,;RABGGTA,downstream_gene_variant,,ENST00000559974,;RABGGTA,downstream_gene_variant,,ENST00000558376,;RABGGTA,downstream_gene_variant,,ENST00000558649,;RABGGTA,downstream_gene_variant,,ENST00000561055,;RABGGTA,downstream_gene_variant,,ENST00000560243,;RABGGTA,downstream_gene_variant,,ENST00000559850,; A ENST00000206765 Transcript missense_variant 426/2777 302/2454 101/817 G/V gGa/gTa 1 -1 TGM1 HGNC HGNC:11777 protein_coding YES CCDS9622.1 ENSP00000206765 P22735 UPI000000164D NM_000359.2 tolerated(0.14) 2/15 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF49,Gene3D:2.60.40.10,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 24262051 24262051 C A 1 0 0 0 0 1 0 0 0 16262 855 30 2 2 TGM1 14 24262051 Missense_Mutation SNP C C3N-00551_T 836693 24262051 82781667 432 15915 FRMD6 0 . GRCh38 14 51708207 51708207 + Missense_Mutation SNP G G T rs374236968 C3N-00551_T C3N-00551_N G G c.688G>T p.Ala230Ser p.A230S ENST00000344768 7/14 184 146 38 195 195 0 strelka-varscan-mutect FRMD6,missense_variant,p.Ala222Ser,ENST00000395718,NM_152330.3;FRMD6,missense_variant,p.Ala222Ser,ENST00000356218,NM_001042481.2;FRMD6,missense_variant,p.Ala153Ser,ENST00000554167,;FRMD6,missense_variant,p.Ala230Ser,ENST00000344768,NM_001267046.1;FRMD6,missense_variant,p.Ala120Ser,ENST00000557405,;FRMD6,upstream_gene_variant,,ENST00000555197,;FRMD6,downstream_gene_variant,,ENST00000555936,;FRMD6,non_coding_transcript_exon_variant,,ENST00000557183,;FRMD6,non_coding_transcript_exon_variant,,ENST00000554495,; T ENST00000344768 Transcript missense_variant 884/2972 688/1869 230/622 A/S Gct/Tct rs374236968,COSM4051229,COSM956158 1 1 FRMD6 HGNC HGNC:19839 protein_coding YES CCDS58318.1 ENSP00000343899 Q96NE9 UPI00000473F6 NM_001267046.1 deleterious(0.02) 7/14 Pfam_domain:PF00373,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF9,SMART_domains:SM00295,Superfamily_domains:SSF50729 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs374236968 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 51708207 51708207 G T 1 0 0 0 0 1 0 0 0 5924 1087 38 1 1 FRMD6 14 51708207 Missense_Mutation SNP G C3N-00551_T 27446156 51708207 55335511 433 15916 RTN1 0 . GRCh38 14 59605475 59605475 + Nonsense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.2005C>T p.Gln669Ter p.Q669* ENST00000267484 5/9 156 137 19 196 196 0 strelka-varscan-mutect RTN1,stop_gained,p.Gln669Ter,ENST00000267484,NM_021136.2;RTN1,stop_gained,p.Gln595Ter,ENST00000611068,;RTN1,stop_gained,p.Gln101Ter,ENST00000342503,NM_206852.2;RTN1,stop_gained,p.Gln86Ter,ENST00000395090,;RTN1,intron_variant,,ENST00000557422,;RTN1,non_coding_transcript_exon_variant,,ENST00000481205,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;RTN1,non_coding_transcript_exon_variant,,ENST00000474911,;RTN1,non_coding_transcript_exon_variant,,ENST00000490111,; A ENST00000267484 Transcript stop_gained 2341/3435 2005/2331 669/776 Q/* Cag/Tag 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 5/9 PROSITE_profiles:PS50845,hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994,Pfam_domain:PF02453 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 59605475 59605475 G A 1 0 0 0 0 0 1 0 0 13985 1299 45 3 3 RTN1 14 59605475 Nonsense_Mutation SNP G C3N-00551_T 7897268 59605475 47438243 434 15917 TRMT5 0 . GRCh38 14 60975526 60975526 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.1393A>T p.Thr465Ser p.T465S ENST00000261249 4/5 131 102 29 129 129 0 strelka-varscan-mutect TRMT5,missense_variant,p.Thr465Ser,ENST00000261249,NM_020810.3;TRMT5,downstream_gene_variant,,ENST00000555420,;TRMT5,downstream_gene_variant,,ENST00000553903,;RNU6-398P,downstream_gene_variant,,ENST00000384143,;RP11-193F5.1,intron_variant,,ENST00000553946,;RP11-193F5.4,upstream_gene_variant,,ENST00000556317,; A ENST00000261249 Transcript missense_variant 1778/5573 1393/1530 465/509 T/S Acg/Tcg 1 -1 TRMT5 HGNC HGNC:23141 protein_coding YES CCDS32092.1 ENSP00000261249 Q32P41 UPI0000049FE8 NM_020810.3 tolerated(1) 4/5 Gene3D:3.40.50.150,HAMAP:MF_03152,PROSITE_profiles:PS51684,hmmpanther:PTHR23245,hmmpanther:PTHR23245:SF36,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 60975526 60975526 T A 1 0 0 0 0 1 0 0 0 17072 1696 59 4 4 TRMT5 14 60975526 Missense_Mutation SNP T C3N-00551_T 1370051 60975526 46068192 435 15918 PLEKHH1 0 . GRCh38 14 67575469 67575469 + Missense_Mutation SNP C C A rs768872305 C3N-00551_T C3N-00551_N C C c.2166C>A p.Asp722Glu p.D722E ENST00000329153 15/29 136 117 19 150 150 0 strelka-varscan-mutect PLEKHH1,missense_variant,p.Asp722Glu,ENST00000329153,NM_020715.2;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000557971,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558386,;PLEKHH1,non_coding_transcript_exon_variant,,ENST00000558981,;PLEKHH1,upstream_gene_variant,,ENST00000561370,;PLEKHH1,upstream_gene_variant,,ENST00000560100,;PLEKHH1,upstream_gene_variant,,ENST00000558296,;PLEKHH1,downstream_gene_variant,,ENST00000561456,;PLEKHH1,downstream_gene_variant,,ENST00000561135,; A ENST00000329153 Transcript missense_variant 2298/6604 2166/4095 722/1364 D/E gaC/gaA rs768872305 1 1 PLEKHH1 HGNC HGNC:17733 protein_coding YES CCDS45128.1 ENSP00000330278 Q9ULM0 UPI00001C1F64 NM_020715.2 tolerated(0.06) 15/29 PROSITE_profiles:PS50003,hmmpanther:PTHR22903:SF4,hmmpanther:PTHR22903,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs768872305 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 52 67575469 67575469 C A 1 0 0 0 0 1 0 0 0 12169 492 17 2 2 PLEKHH1 14 67575469 Missense_Mutation SNP C C3N-00551_T 6599943 67575469 39468249 436 15919 RGS6 0 . GRCh38 14 72510218 72510218 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1030C>A p.Gln344Lys p.Q344K ENST00000553525 14/18 149 118 31 207 206 1 strelka-varscan-mutect RGS6,missense_variant,p.Gln344Lys,ENST00000553530,NM_001204418.1,NM_004296.5,NM_001204420.1,NM_001204422.1;RGS6,missense_variant,p.Gln309Lys,ENST00000622468,;RGS6,missense_variant,p.Gln309Lys,ENST00000402788,NM_001204423.1;RGS6,missense_variant,p.Gln272Lys,ENST00000343854,;RGS6,missense_variant,p.Gln344Lys,ENST00000553525,NM_001204424.1;RGS6,missense_variant,p.Gln275Lys,ENST00000434263,;RGS6,missense_variant,p.Gln344Lys,ENST00000555571,;RGS6,missense_variant,p.Gln344Lys,ENST00000556437,NM_001204417.1,NM_001204421.1,NM_001204419.1,NM_001204416.1;RGS6,missense_variant,p.Gln344Lys,ENST00000355512,;RGS6,missense_variant,p.Gln344Lys,ENST00000404301,;RGS6,missense_variant,p.Gln344Lys,ENST00000407322,;RGS6,missense_variant,p.Gln344Lys,ENST00000406236,;RGS6,missense_variant,p.Gln205Lys,ENST00000554782,;RGS6,upstream_gene_variant,,ENST00000553519,;RGS6,missense_variant,p.Gln344Lys,ENST00000554474,; A ENST00000553525 Transcript missense_variant 1553/2005 1030/1473 344/490 Q/K Cag/Aag 1 1 RGS6 HGNC HGNC:10002 protein_coding YES CCDS55924.1 ENSP00000451030 P49758 UPI00001698D0 NM_001204424.1 deleterious(0.01) 14/18 PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF27,hmmpanther:PTHR10845,Gene3D:1.10.196.10,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 72510218 72510218 C A 1 0 0 0 0 1 0 0 0 13480 595 21 2 2 RGS6 14 72510218 Missense_Mutation SNP C C3N-00551_T 4934749 72510218 34533500 437 15920 ENTPD5 0 . GRCh38 14 73983065 73983065 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.394G>A p.Gly132Arg p.G132R ENST00000334696 6/16 131 110 21 131 131 0 strelka-varscan-mutect ENTPD5,missense_variant,p.Gly132Arg,ENST00000334696,NM_001249.2;ENTPD5,missense_variant,p.Gly132Arg,ENST00000557325,;ENTPD5,missense_variant,p.Gly132Arg,ENST00000553284,;ENTPD5,downstream_gene_variant,,ENST00000556242,; T ENST00000334696 Transcript missense_variant 714/5842 394/1287 132/428 G/R Gga/Aga 1 -1 ENTPD5 HGNC HGNC:3367 protein_coding YES CCDS9825.1 ENSP00000335246 O75356 A0A024R6D3 UPI0000052B69 NM_001249.2 deleterious(0) 6/16 hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF35,Pfam_domain:PF01150 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 73983065 73983065 C T 1 0 0 0 0 1 0 0 0 4987 690 24 3 3 ENTPD5 14 73983065 Missense_Mutation SNP C C3N-00551_T 1472847 73983065 33060653 438 15921 ISM2 0 . GRCh38 14 77484553 77484553 + Missense_Mutation SNP G G A rs11850175 C3N-00551_T C3N-00551_N G G c.397C>T p.Pro133Ser p.P133S ENST00000342219 3/7 53 43 10 60 60 0 strelka-varscan-mutect ISM2,missense_variant,p.Pro133Ser,ENST00000342219,NM_199296.2;ISM2,missense_variant,p.Pro133Ser,ENST00000493585,NM_182509.3;ISM2,intron_variant,,ENST00000554801,;ISM2,3_prime_UTR_variant,,ENST00000216481,;ISM2,3_prime_UTR_variant,,ENST00000480979,;ISM2,3_prime_UTR_variant,,ENST00000471734,;ISM2,non_coding_transcript_exon_variant,,ENST00000472744,;ISM2,upstream_gene_variant,,ENST00000487738,; A ENST00000342219 Transcript missense_variant 454/2971 397/1716 133/571 P/S Cca/Tca rs11850175 1 -1 ISM2 HGNC HGNC:23176 protein_coding YES CCDS9864.1 ENSP00000341490 Q6H9L7 UPI000019950C NM_199296.2 tolerated(0.22) 3/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs11850175 . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 A 3 1 52 77484553 77484553 G A 1 0 0 0 0 1 0 0 0 7768 1232 43 3 3 ISM2 14 77484553 Missense_Mutation SNP G C3N-00551_T 3501488 77484553 29559165 439 15922 CCDC88C 0 . GRCh38 14 91305825 91305825 + Silent SNP T T C novel C3N-00551_T C3N-00551_N T T c.3297A>G p.= p.K1099K ENST00000389857 19/30 153 143 10 168 168 0 strelka-varscan-mutect CCDC88C,synonymous_variant,p.=,ENST00000389857,NM_001080414.3; C ENST00000389857 Transcript synonymous_variant 3384/7474 3297/6087 1099/2028 K aaA/aaG 1 -1 CCDC88C HGNC HGNC:19967 protein_coding YES CCDS45151.1 ENSP00000374507 Q9P219 UPI00006C1440 NM_001080414.3 19/30 hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF31 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 52 91305825 91305825 T C 1 0 0 0 0 0 0 0 1 2564 1722 60 5 5 CCDC88C 14 91305825 Silent SNP T C3N-00551_T 13821272 91305825 15737893 440 15923 UNC79 0 . GRCh38 14 93538219 93538219 + Splice_Site SNP G G T novel C3N-00551_T C3N-00551_N G G c.821+1G>T p.X274_splice ENST00000256339 39 25 14 57 57 0 strelka-varscan-mutect UNC79,splice_donor_variant,,ENST00000553484,;UNC79,splice_donor_variant,,ENST00000555664,;UNC79,splice_donor_variant,,ENST00000256339,NM_020818.3;UNC79,splice_donor_variant,,ENST00000393151,;UNC79,splice_donor_variant,,ENST00000621021,; T ENST00000256339 Transcript splice_donor_variant -/8400 821/7377 274/2458 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 12/49 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 52 93538219 93538219 G T 1 0 0 0 0 0 0 1 0 17520 1275 44 2 2 UNC79 14 93538219 Splice_Site SNP G C3N-00551_T 2232394 93538219 13505499 441 15924 FAM181A 0 . GRCh38 14 93929098 93929098 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.999G>T p.= p.V333V ENST00000267594 3/3 40 27 13 22 22 0 strelka-varscan-mutect FAM181A,synonymous_variant,p.=,ENST00000267594,NM_138344.4;FAM181A,synonymous_variant,p.=,ENST00000557000,NM_001207072.1;FAM181A,synonymous_variant,p.=,ENST00000556222,NM_001207074.1,NM_001207073.1;FAM181A,synonymous_variant,p.=,ENST00000557719,NM_001207071.1;FAM181A,downstream_gene_variant,,ENST00000554404,;FAM181A-AS1,upstream_gene_variant,,ENST00000554742,;FAM181A-AS1,upstream_gene_variant,,ENST00000554538,;FAM181A-AS1,upstream_gene_variant,,ENST00000556290,;FAM181A-AS1,upstream_gene_variant,,ENST00000555732,; T ENST00000267594 Transcript synonymous_variant 1306/1816 999/1065 333/354 V gtG/gtT 1 1 FAM181A HGNC HGNC:20491 protein_coding YES CCDS9914.1 ENSP00000267594 Q8N9Y4 UPI00004567C0 NM_138344.4 3/3 Pfam_domain:PF15238,hmmpanther:PTHR33766,hmmpanther:PTHR33766:SF1 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 93929098 93929098 G T 1 0 0 0 0 0 0 0 1 5354 1306 46 2 2 FAM181A 14 93929098 Silent SNP G C3N-00551_T 390879 93929098 13114620 442 15925 SERPINA1 0 . GRCh38 14 94381007 94381007 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.781A>T p.Ser261Cys p.S261C ENST00000448921 5/7 414 342 72 529 528 1 strelka-varscan-mutect SERPINA1,missense_variant,p.Ser261Cys,ENST00000448921,NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1;SERPINA1,missense_variant,p.Ser261Cys,ENST00000437397,NM_001127706.1,NM_001127707.1,NM_001127702.1;SERPINA1,missense_variant,p.Ser261Cys,ENST00000355814,NM_001002235.2,NM_001127700.1;SERPINA1,missense_variant,p.Ser261Cys,ENST00000440909,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000393088,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000404814,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000393087,NM_000295.4;SERPINA1,missense_variant,p.Ser261Cys,ENST00000449399,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000636712,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000402629,;SERPINA1,downstream_gene_variant,,ENST00000557492,;SERPINA1,downstream_gene_variant,,ENST00000556091,;SERPINA1,downstream_gene_variant,,ENST00000557118,;SERPINA1,downstream_gene_variant,,ENST00000553327,;SERPINA1,downstream_gene_variant,,ENST00000556955,;SERPINA1,downstream_gene_variant,,ENST00000554720,;SERPINA1,downstream_gene_variant,,ENST00000555289,;SERPINA1,missense_variant,p.Ser261Cys,ENST00000489769,; A ENST00000448921 Transcript missense_variant 1354/3532 781/1257 261/418 S/C Agc/Tgc 1 -1 SERPINA1 HGNC HGNC:8941 protein_coding YES CCDS9925.1 ENSP00000416066 P01009 E9KL23 UPI000000CBEC NM_001002236.2,NM_001127703.1,NM_001127701.1,NM_001127704.1,NM_001127705.1 tolerated(0.4) 5/7 hmmpanther:PTHR11461:SF165,hmmpanther:PTHR11461,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 94381007 94381007 T A 1 0 0 0 0 1 0 0 0 14362 1580 55 4 4 SERPINA1 14 94381007 Missense_Mutation SNP T C3N-00551_T 451909 94381007 12662711 443 15926 PPP2R5C 0 . GRCh38 14 101925210 101925210 + Missense_Mutation SNP A A T novel C3N-00551_T C3N-00551_N A A c.1606A>T p.Thr536Ser p.T536S ENST00000422945 16/16 202 181 21 284 284 0 strelka-varscan-mutect PPP2R5C,missense_variant,p.Thr536Ser,ENST00000422945,NM_001161725.1;PPP2R5C,missense_variant,p.Thr505Ser,ENST00000334743,NM_002719.3;PPP2R5C,missense_variant,p.Thr521Ser,ENST00000328724,NM_001161726.1;PPP2R5C,missense_variant,p.Thr466Ser,ENST00000350249,NM_178586.2;PPP2R5C,missense_variant,p.Thr534Ser,ENST00000557268,;PPP2R5C,downstream_gene_variant,,ENST00000555237,;PPP2R5C,3_prime_UTR_variant,,ENST00000557071,;PPP2R5C,non_coding_transcript_exon_variant,,ENST00000554147,; T ENST00000422945 Transcript missense_variant 1702/4481 1606/1668 536/555 T/S Acc/Tcc 1 1 PPP2R5C HGNC HGNC:9311 protein_coding YES CCDS53912.1 ENSP00000412324 Q13362 UPI0001A7AE62 NM_001161725.1 deleterious_low_confidence(0.03) 16/16 hmmpanther:PTHR10257,hmmpanther:PTHR10257:SF22,PIRSF_domain:PIRSF028043 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 101925210 101925210 A T 1 0 0 0 0 1 0 0 0 12516 159 6 4 4 PPP2R5C 14 101925210 Missense_Mutation SNP A C3N-00551_T 7544203 101925210 5118508 444 15927 PPP1R13B 0 . GRCh38 14 103797392 103797392 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.136G>A p.Ala46Thr p.A46T ENST00000202556 2/17 144 132 12 165 165 0 strelka-varscan-mutect PPP1R13B,missense_variant,p.Ala46Thr,ENST00000202556,NM_015316.2;PPP1R13B,missense_variant,p.Ala46Thr,ENST00000553739,;PPP1R13B,missense_variant,p.Ala43Thr,ENST00000555734,;SNORD51,upstream_gene_variant,,ENST00000365405,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000554106,;PPP1R13B,intron_variant,,ENST00000556325,;PPP1R13B,missense_variant,p.Ala45Thr,ENST00000557082,;PPP1R13B,non_coding_transcript_exon_variant,,ENST00000554136,; T ENST00000202556 Transcript missense_variant 419/4958 136/3273 46/1090 A/T Gct/Act 1 -1 PPP1R13B HGNC HGNC:14950 protein_coding YES CCDS41997.1 ENSP00000202556 Q96KQ4 UPI000049DDC7 NM_015316.2 deleterious(0) 2/17 hmmpanther:PTHR24131,hmmpanther:PTHR24131:SF5,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.73919 0.9999786 1 1 1 0 T 3 4 52 103797392 103797392 C T 1 0 0 0 0 1 0 0 0 12467 797 28 3 3 PPP1R13B 14 103797392 Missense_Mutation SNP C C3N-00551_T 1872182 103797392 3246326 445 15928 C14orf180 0 . GRCh38 14 104588703 104588703 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.359C>A p.Pro120His p.P120H ENST00000331952 5/5 144 114 30 194 194 0 strelka-varscan-mutect C14orf180,missense_variant,p.Leu135Met,ENST00000557649,NM_001008404.2;C14orf180,missense_variant,p.Leu135Met,ENST00000410013,NM_001286400.1;C14orf180,missense_variant,p.Pro120His,ENST00000331952,NM_001286399.1;TMEM179,intron_variant,,ENST00000415614,;TMEM179,downstream_gene_variant,,ENST00000616017,;TMEM179,downstream_gene_variant,,ENST00000556573,NM_001286389.1;TMEM179,downstream_gene_variant,,ENST00000556320,;RP11-614O9.1,downstream_gene_variant,,ENST00000556073,; A ENST00000331952 Transcript missense_variant 615/1455 359/534 120/177 P/H cCt/cAt 1 1 C14orf180 HGNC HGNC:33795 protein_coding YES CCDS66722.1 ENSP00000333041 J3KNP8 UPI00021CF38C NM_001286399.1 tolerated_low_confidence(0.14) 5/5 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1158255628 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 104588703 104588703 C A 1 0 0 0 0 1 0 0 0 1835 680 24 2 2 C14orf180 14 104588703 Missense_Mutation SNP C C3N-00551_T 791311 104588703 2455015 446 15929 CRIP2 0 . GRCh38 14 105479186 105479186 + Nonsense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.690C>A p.Cys230Ter p.C230* ENST00000483017 6/8 183 166 17 211 211 0 strelka-varscan-mutect CRIP2,stop_gained,p.Cys156Ter,ENST00000329146,NM_001312.3;CRIP2,stop_gained,p.Cys230Ter,ENST00000483017,NM_001270837.1;CRIP2,stop_gained,p.Cys140Ter,ENST00000538259,;CRIP2,stop_gained,p.Cys52Ter,ENST00000550577,NM_001270841.1;CRIP2,non_coding_transcript_exon_variant,,ENST00000548989,;CRIP2,non_coding_transcript_exon_variant,,ENST00000548309,;CRIP2,downstream_gene_variant,,ENST00000548923,;CRIP2,non_coding_transcript_exon_variant,,ENST00000552643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000547643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000551836,;CRIP2,non_coding_transcript_exon_variant,,ENST00000551738,; A ENST00000483017 Transcript stop_gained 976/1176 690/849 230/282 C/* tgC/tgA 1 1 CRIP2 HGNC HGNC:2361 protein_coding YES CCDS59246.1 ENSP00000426119 P52943 UPI0001914E41 NM_001270837.1 6/8 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 HIGH 1 SNV 2 1 PASS rs992542614 . 0 207 0 0 2 0 0 0 -6.907917 0.9921639 1 1 1 0 A 4 1 52 105479186 105479186 C A 1 0 0 0 0 0 1 0 0 3676 776 27 1 1 CRIP2 14 105479186 Nonsense_Mutation SNP C C3N-00551_T 890483 105479186 1564532 447 15930 NPAP1 0 . GRCh38 15 24678123 24678123 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.2256A>T p.= p.S752S ENST00000329468 1/1 207 166 41 304 304 0 strelka-varscan-mutect NPAP1,synonymous_variant,p.=,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript synonymous_variant 2256/7526 2256/3471 752/1156 S tcA/tcT 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 24678123 24678123 A T 1 0 0 0 0 0 0 0 1 10609 175 7 4 4 NPAP1 15 24678123 Silent SNP A C3N-00551_T 24678123 77313066 448 15931 GABRA5 0 . GRCh38 15 26943323 26943323 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.986C>A p.Ala329Asp p.A329D ENST00000335625 10/11 295 240 55 377 377 0 strelka-varscan-mutect GABRA5,missense_variant,p.Ala329Asp,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Ala329Asp,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Ala329Asp,ENST00000355395,;GABRB3,upstream_gene_variant,,ENST00000541819,; A ENST00000335625 Transcript missense_variant 1874/3251 986/1389 329/462 A/D gCc/gAc 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 deleterious(0) 10/11 Gene3D:1.20.58.390,Pfam_domain:PF02932,Prints_domain:PR00253,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1376608583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 26943323 26943323 C A 1 0 0 0 0 1 0 0 0 6035 739 26 2 2 GABRA5 15 26943323 Missense_Mutation SNP C C3N-00551_T 2265200 26943323 75047866 449 15932 GOLGA8T 0 . GRCh38 15 30145461 30145461 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1790C>G p.Pro597Arg p.P597R ENST00000569052 19/19 246 216 30 346 346 0 varscan-mutect GOLGA8T,missense_variant,p.Pro597Arg,ENST00000569052,;RN7SL469P,downstream_gene_variant,,ENST00000621501,; G ENST00000569052 Transcript missense_variant 1790/1896 1790/1896 597/631 P/R cCt/cGt 1 1 GOLGA8T HGNC HGNC:44410 protein_coding YES ENSP00000455826 H3BQL2 UPI000246730F deleterious(0.03) 19/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48,Pfam_domain:PF15070 MODERATE 1 SNV 5 1 PASS rs1488266874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 30145461 30145461 C G 1 0 0 0 0 1 0 0 0 6458 681 24 4 4 GOLGA8T 15 30145461 Missense_Mutation SNP C C3N-00551_T 3202138 30145461 71845728 450 15933 IVD 0 . GRCh38 15 40414888 40414888 + Splice_Site SNP G G C C3N-00551_T C3N-00551_N G G c.794-1G>C p.X265_splice ENST00000487418 431 306 125 466 466 0 strelka-varscan-mutect IVD,splice_acceptor_variant,,ENST00000479013,NM_001159508.1;IVD,splice_acceptor_variant,,ENST00000487418,NM_002225.3;IVD,splice_acceptor_variant,,ENST00000491554,;IVD,splice_acceptor_variant,,ENST00000473112,;IVD,downstream_gene_variant,,ENST00000558610,;IVD,downstream_gene_variant,,ENST00000610693,;IVD,upstream_gene_variant,,ENST00000466756,;IVD,upstream_gene_variant,,ENST00000559575,;IVD,splice_acceptor_variant,,ENST00000497252,;IVD,non_coding_transcript_exon_variant,,ENST00000560660,;IVD,intron_variant,,ENST00000481262,;IVD,upstream_gene_variant,,ENST00000497816,;IVD,downstream_gene_variant,,ENST00000484250,; C ENST00000487418 Transcript splice_acceptor_variant -/1809 794/1281 265/426 CS001433 1 1 IVD HGNC HGNC:6186 protein_coding YES CCDS10057.2 ENSP00000418397 A0A0A0MT83 UPI0000D4AF3D NM_002225.3 7/11 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 52 40414888 40414888 G C 1 0 0 0 0 0 0 1 0 7834 985 34 4 4 IVD 15 40414888 Splice_Site SNP G C3N-00551_T 10269427 40414888 61576301 451 15934 TP53BP1 0 . GRCh38 15 43456640 43456640 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.1968A>T p.Lys656Asn p.K656N ENST00000382044 12/28 244 176 68 271 270 1 strelka-varscan-mutect TP53BP1,missense_variant,p.Lys656Asn,ENST00000382044,NM_001141980.1;TP53BP1,missense_variant,p.Lys651Asn,ENST00000263801,NM_005657.2;TP53BP1,missense_variant,p.Lys656Asn,ENST00000450115,NM_001141979.1;TP53BP1,missense_variant,p.Lys656Asn,ENST00000382039,;TP53BP1,missense_variant,p.Lys656Asn,ENST00000413546,;TP53BP1,upstream_gene_variant,,ENST00000605155,;TP53BP1,upstream_gene_variant,,ENST00000414758,;TP53BP1,non_coding_transcript_exon_variant,,ENST00000572085,;TP53BP1,upstream_gene_variant,,ENST00000411772,;TP53BP1,upstream_gene_variant,,ENST00000480860,; A ENST00000382044 Transcript missense_variant 2096/10384 1968/5934 656/1977 K/N aaA/aaT 1 -1 TP53BP1 HGNC HGNC:11999 protein_coding YES CCDS45250.1 ENSP00000371475 Q12888 UPI0000D720ED NM_001141980.1 deleterious(0.02) 12/28 hmmpanther:PTHR15321,hmmpanther:PTHR15321:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 43456640 43456640 T A 1 0 0 0 0 1 0 0 0 16861 1606 56 4 4 TP53BP1 15 43456640 Missense_Mutation SNP T C3N-00551_T 3041752 43456640 58534549 452 15935 CA12 0 . GRCh38 15 63346707 63346707 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.109C>A p.Pro37Thr p.P37T ENST00000178638 3/11 364 249 115 431 430 1 strelka-varscan-mutect CA12,missense_variant,p.Pro37Thr,ENST00000178638,NM_001218.4;CA12,missense_variant,p.Pro37Thr,ENST00000344366,NM_206925.2;CA12,intron_variant,,ENST00000422263,NM_001293642.1;CA12,upstream_gene_variant,,ENST00000558287,; T ENST00000178638 Transcript missense_variant,splice_region_variant 550/6413 109/1065 37/354 P/T Cct/Act 1 -1 CA12 HGNC HGNC:1371 protein_coding YES CCDS10185.1 ENSP00000178638 O43570 UPI0000035CDD NM_001218.4 deleterious(0.03) 3/11 Gene3D:3.10.200.10,Pfam_domain:PF00194,PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF19,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS rs1180179299 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 63346707 63346707 G T 1 0 0 0 0 1 0 0 0 2199 1188 41 2 2 CA12 15 63346707 Missense_Mutation SNP G C3N-00551_T 19890067 63346707 38644482 453 15936 CLN6 0 . GRCh38 15 68218613 68218613 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.121G>T p.Ala41Ser p.A41S ENST00000249806 2/7 504 371 133 435 435 0 strelka-varscan-mutect CLN6,missense_variant,p.Ala41Ser,ENST00000249806,NM_017882.2;CLN6,missense_variant,p.Ala73Ser,ENST00000538696,;CLN6,missense_variant,p.Ala41Ser,ENST00000566347,;CLN6,missense_variant,p.Ala41Ser,ENST00000564752,;CLN6,missense_variant,p.Ala41Ser,ENST00000637667,;CLN6,missense_variant,p.Ala41Ser,ENST00000637494,;RP11-315D16.2,intron_variant,,ENST00000562767,;CLN6,intron_variant,,ENST00000565471,;CLN6,intron_variant,,ENST00000636314,;CLN6,intron_variant,,ENST00000638144,;CLN6,intron_variant,,ENST00000563917,;RP11-315D16.2,missense_variant,p.Ala41Ser,ENST00000637054,;RP11-315D16.2,missense_variant,p.Ala41Ser,ENST00000637888,;CLN6,missense_variant,p.Ala41Ser,ENST00000638076,;CLN6,missense_variant,p.Ala12Ser,ENST00000637329,;CLN6,missense_variant,p.Ala41Ser,ENST00000636212,;CLN6,missense_variant,p.Ala41Ser,ENST00000567060,;CLN6,missense_variant,p.Ala17Ser,ENST00000637823,;CLN6,3_prime_UTR_variant,,ENST00000635747,;CLN6,3_prime_UTR_variant,,ENST00000636876,;CLN6,3_prime_UTR_variant,,ENST00000637223,;CLN6,non_coding_transcript_exon_variant,,ENST00000564846,;CLN6,non_coding_transcript_exon_variant,,ENST00000636020,;CLN6,non_coding_transcript_exon_variant,,ENST00000569336,;CLN6,intron_variant,,ENST00000637450,;CLN6,upstream_gene_variant,,ENST00000635754,; A ENST00000249806 Transcript missense_variant 280/2243 121/936 41/311 A/S Gct/Tct COSM4793328 1 -1 CLN6 HGNC HGNC:2077 protein_coding YES CCDS10227.1 ENSP00000249806 Q9NWW5 A0A024R601 UPI000006D91F NM_017882.2 tolerated_low_confidence(0.47) 2/7 hmmpanther:PTHR16244,Pfam_domain:PF15156 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 68218613 68218613 C A 1 0 0 0 0 1 0 0 0 3315 739 26 2 2 CLN6 15 68218613 Missense_Mutation SNP C C3N-00551_T 4871906 68218613 33772576 454 15937 HCN4 0 . GRCh38 15 73322821 73322821 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3272C>A p.Pro1091Gln p.P1091Q ENST00000261917 8/8 27 20 7 31 31 0 strelka-varscan-mutect HCN4,missense_variant,p.Pro1091Gln,ENST00000261917,NM_005477.2; T ENST00000261917 Transcript missense_variant 4266/7228 3272/3612 1091/1203 P/Q cCa/cAa 1 -1 HCN4 HGNC HGNC:16882 protein_coding YES CCDS10248.1 ENSP00000261917 Q9Y3Q4 UPI000003FFB5 NM_005477.2 deleterious_low_confidence(0) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.27068 1 1 1 1 0 T 3 4 52 73322821 73322821 G T 1 0 0 0 0 1 0 0 0 6886 1348 47 2 2 HCN4 15 73322821 Missense_Mutation SNP G C3N-00551_T 5104208 73322821 28668368 455 15938 CSPG4 0 . GRCh38 15 75689092 75689092 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1973C>A p.Ala658Asp p.A658D ENST00000308508 3/10 70 47 23 59 59 0 strelka-mutect CSPG4,missense_variant,p.Ala658Asp,ENST00000308508,NM_001897.4; T ENST00000308508 Transcript missense_variant 2066/8290 1973/6969 658/2322 A/D gCc/gAc 1 -1 CSPG4 HGNC HGNC:2466 protein_coding YES CCDS10284.1 ENSP00000312506 Q6UVK1 UPI00001AEEB6 NM_001897.4 deleterious(0) 3/10 hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF16 MODERATE 1 SNV 1 1 PASS rs1191683465 . 0 198 11 0 0 0 0 0 -20 0.9999911 1 1 1 0 T 3 4 52 75689092 75689092 G T 1 0 0 0 0 1 0 0 0 3761 1203 42 2 2 CSPG4 15 75689092 Missense_Mutation SNP G C3N-00551_T 2366271 75689092 26302097 456 15939 CSPG4 0 . GRCh38 15 75693154 75693154 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.168C>A p.= p.S56S ENST00000308508 2/10 102 70 32 119 119 0 strelka-varscan-mutect CSPG4,synonymous_variant,p.=,ENST00000308508,NM_001897.4; T ENST00000308508 Transcript synonymous_variant 261/8290 168/6969 56/2322 S tcC/tcA 1 -1 CSPG4 HGNC HGNC:2466 protein_coding YES CCDS10284.1 ENSP00000312506 Q6UVK1 UPI00001AEEB6 NM_001897.4 2/10 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF16,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 75693154 75693154 G T 1 0 0 0 0 0 0 0 1 3761 1335 47 2 2 CSPG4 15 75693154 Silent SNP G C3N-00551_T 4062 75693154 26298035 457 15940 SV2B 0 . GRCh38 15 91252431 91252431 + Missense_Mutation SNP G G A rs779548438 C3N-00551_T C3N-00551_N G G c.695G>A p.Arg232Gln p.R232Q ENST00000394232 4/13 125 118 7 108 108 0 strelka-varscan-mutect SV2B,missense_variant,p.Arg232Gln,ENST00000394232,NM_001323038.1,NM_001323031.1,NM_001323040.1,NM_001323039.1,NM_001323032.1,NM_001323036.1,NM_001323037.1,NM_014848.4;SV2B,missense_variant,p.Arg232Gln,ENST00000330276,;SV2B,missense_variant,p.Arg81Gln,ENST00000545111,NM_001167580.1;SV2B,downstream_gene_variant,,ENST00000557291,;SV2B,missense_variant,p.Arg232Gln,ENST00000557410,; A ENST00000394232 Transcript missense_variant 1165/11279 695/2052 232/683 R/Q cGa/cAa rs779548438 1 1 SV2B HGNC HGNC:16874 protein_coding YES CCDS10370.1 ENSP00000377779 Q7L1I2 UPI000006FCF1 NM_001323038.1,NM_001323031.1,NM_001323040.1,NM_001323039.1,NM_001323032.1,NM_001323036.1,NM_001323037.1,NM_014848.4 deleterious(0) 4/13 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_patterns:PS00217,PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF2,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 5 1 PASS rs779548438 . 0 206 3 0 0 0 0 0 -13.79168 1 1 1 1 0 A 3 1 52 91252431 91252431 G A 1 0 0 0 0 1 0 0 0 15802 1058 37 1 1 SV2B 15 91252431 Missense_Mutation SNP G C3N-00551_T 15559277 91252431 10738758 458 15941 ADAMTS17 0 . GRCh38 15 100096464 100096464 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2029G>T p.Asp677Tyr p.D677Y ENST00000268070 15/22 281 197 84 388 388 0 strelka-varscan-mutect ADAMTS17,missense_variant,p.Asp677Tyr,ENST00000268070,NM_139057.2;ADAMTS17,missense_variant,p.Asp45Tyr,ENST00000568565,;ADAMTS17,non_coding_transcript_exon_variant,,ENST00000378898,; A ENST00000268070 Transcript missense_variant 2135/6207 2029/3288 677/1095 D/Y Gac/Tac 1 -1 ADAMTS17 HGNC HGNC:17109 protein_coding YES CCDS10383.1 ENSP00000268070 Q8TE56 UPI00001AE929 NM_139057.2 deleterious(0) 15/22 hmmpanther:PTHR13723:SF151,hmmpanther:PTHR13723,Prints_domain:PR01857 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 100096464 100096464 C A 1 0 0 0 0 1 0 0 0 306 826 29 2 2 ADAMTS17 15 100096464 Missense_Mutation SNP C C3N-00551_T 8844033 100096464 1894725 459 15942 PRR35 0 . GRCh38 16 564057 564057 + Missense_Mutation SNP C C A rs767822670 C3N-00551_T C3N-00551_N C C c.763C>A p.Pro255Thr p.P255T ENST00000409413 2/3 80 61 19 84 84 0 strelka-varscan-mutect PRR35,missense_variant,p.Pro255Thr,ENST00000409413,NM_145270.2;NHLRC4,upstream_gene_variant,,ENST00000424439,NM_176677.2,NM_001301159.1;NHLRC4,upstream_gene_variant,,ENST00000540585,;PIGQ,upstream_gene_variant,,ENST00000409527,;PIGQ,upstream_gene_variant,,ENST00000293874,;LA16c-407A10.3,upstream_gene_variant,,ENST00000409439,; A ENST00000409413 Transcript missense_variant 1042/2216 763/1716 255/571 P/T Cct/Act rs767822670 1 1 PRR35 HGNC HGNC:14139 protein_coding YES CCDS45365.1 ENSP00000386499 P0CG20 UPI000006F4B0 NM_145270.2 tolerated(0.08) 2/3 hmmpanther:PTHR14678:SF2,hmmpanther:PTHR14678 MODERATE 1 SNV 1 1 PASS rs767822670 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 564057 564057 C A 1 0 0 0 0 1 0 0 0 12740 623 22 2 2 PRR35 16 564057 Missense_Mutation SNP C C3N-00551_T 564057 89774288 460 15943 SSTR5 0 . GRCh38 16 1079937 1079937 + Missense_Mutation SNP G G T rs34947461 C3N-00551_T C3N-00551_N G G c.1069G>T p.Gly357Trp p.G357W ENST00000293897 1/1 71 59 12 68 68 0 strelka-varscan-mutect SSTR5,missense_variant,p.Gly357Trp,ENST00000293897,NM_001172560.1,NM_001053.3;SSTR5-AS1,upstream_gene_variant,,ENST00000569832,;SSTR5-AS1,upstream_gene_variant,,ENST00000566499,;SSTR5-AS1,upstream_gene_variant,,ENST00000624643,; T ENST00000293897 Transcript missense_variant 1157/1362 1069/1095 357/364 G/W Ggg/Tgg rs34947461 1 1 SSTR5 HGNC HGNC:11334 protein_coding YES CCDS10429.1 ENSP00000293897 P35346 UPI00000015DC NM_001172560.1,NM_001053.3 deleterious(0) 1/1 hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF20 21810856 MODERATE SNV 1 PASS rs34947461 . 0 200 9 0 0 0 0 0 -20 0.9999948 1 1 1 0 T 3 4 52 1079937 1079937 G T 1 0 0 0 0 1 0 0 0 15578 1116 39 1 1 SSTR5 16 1079937 Missense_Mutation SNP G C3N-00551_T 515880 1079937 89258408 461 15944 GNPTG 0 . GRCh38 16 1362265 1362265 + Frame_Shift_Del DEL C C - rs564859061 C3N-00551_T C3N-00551_N C C c.471delC p.Cys157TrpfsTer5 p.C157Wfs*5 ENST00000204679 7/11 334 302 32 361 361 0 sindel-varindel-pindel GNPTG,frameshift_variant,p.Cys157TrpfsTer5,ENST00000204679,NM_032520.4;GNPTG,frameshift_variant,p.Cys180TrpfsTer5,ENST00000529110,;UNKL,downstream_gene_variant,,ENST00000389221,NM_001193388.3;UNKL,downstream_gene_variant,,ENST00000248104,NM_001276414.1;UNKL,downstream_gene_variant,,ENST00000508903,;UNKL,downstream_gene_variant,,ENST00000397464,NM_001193389.1;LA16c-316G12.2,upstream_gene_variant,,ENST00000569831,;UNKL,downstream_gene_variant,,ENST00000562537,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527076,;GNPTG,non_coding_transcript_exon_variant,,ENST00000527168,;GNPTG,non_coding_transcript_exon_variant,,ENST00000529957,;UNKL,downstream_gene_variant,,ENST00000403703,;UNKL,downstream_gene_variant,,ENST00000511095,;GNPTG,downstream_gene_variant,,ENST00000526820,;GNPTG,downstream_gene_variant,,ENST00000527876,;GNPTG,downstream_gene_variant,,ENST00000534197,; - ENST00000204679 Transcript frameshift_variant 514/1983 471/918 157/305 C/X tgC/tg rs564859061,CD110269 1 1 GNPTG HGNC HGNC:23026 protein_coding YES CCDS10436.1 ENSP00000204679 Q9UJJ9 UPI0000073F3C NM_032520.4 7/11 hmmpanther:PTHR12630,hmmpanther:PTHR12630:SF6,Gene3D:2.70.130.10,Pfam_domain:PF13015,Superfamily_domains:SSF50911 HIGH 1 deletion 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 1362265 1362265 C - 1 0 1 0 1 0 0 0 0 6425 776 27 0 0 GNPTG 16 1362265 Frame_Shift_Del DEL C C3N-00551_T 282328 1362265 88976080 462 15945 MAPK8IP3 0 . GRCh38 16 1729534 1729534 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.558G>T p.Gln186His p.Q186H ENST00000250894 4/32 220 197 23 210 210 0 strelka-varscan-mutect MAPK8IP3,missense_variant,p.Gln186His,ENST00000250894,NM_001318852.1,NM_015133.3;MAPK8IP3,missense_variant,p.Gln186His,ENST00000610761,;MAPK8IP3,missense_variant,p.Gln186His,ENST00000356010,NM_001040439.1;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000564098,;MAPK8IP3,non_coding_transcript_exon_variant,,ENST00000561765,; T ENST00000250894 Transcript missense_variant 715/5661 558/4011 186/1336 Q/H caG/caT 1 1 MAPK8IP3 HGNC HGNC:6884 protein_coding YES CCDS10442.2 ENSP00000250894 Q9UPT6 UPI000034ECA7 NM_001318852.1,NM_015133.3 tolerated(0.15) 4/32 hmmpanther:PTHR13886,hmmpanther:PTHR13886:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 1729534 1729534 G T 1 0 0 0 0 1 0 0 0 9210 991 35 2 2 MAPK8IP3 16 1729534 Missense_Mutation SNP G C3N-00551_T 367269 1729534 88608811 463 15946 SPSB3 0 . GRCh38 16 1778528 1778530 + In_Frame_Del DEL AGA AGA - novel C3N-00551_T C3N-00551_N AGA AGA c.209_211delTCT p.Phe70del p.F70del ENST00000566339 3/7 105 96 9 110 110 0 sindel-varindel-pindel SPSB3,inframe_deletion,p.Phe70del,ENST00000566339,NM_080861.3;SPSB3,inframe_deletion,p.Phe70del,ENST00000301717,;SPSB3,inframe_deletion,p.Phe70del,ENST00000569769,;NUBP2,upstream_gene_variant,,ENST00000262302,NM_012225.3;EME2,downstream_gene_variant,,ENST00000568449,NM_001257370.1;NUBP2,upstream_gene_variant,,ENST00000565987,NM_001284501.1;NUBP2,upstream_gene_variant,,ENST00000568287,;NUBP2,upstream_gene_variant,,ENST00000565134,;NUBP2,upstream_gene_variant,,ENST00000563136,;EME2,3_prime_UTR_variant,,ENST00000561903,;EME2,non_coding_transcript_exon_variant,,ENST00000570069,;SPSB3,non_coding_transcript_exon_variant,,ENST00000564709,;SPSB3,non_coding_transcript_exon_variant,,ENST00000569380,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563741,;SPSB3,non_coding_transcript_exon_variant,,ENST00000567868,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563668,;SPSB3,non_coding_transcript_exon_variant,,ENST00000565550,;SPSB3,non_coding_transcript_exon_variant,,ENST00000563705,;SPSB3,non_coding_transcript_exon_variant,,ENST00000564070,;NUBP2,upstream_gene_variant,,ENST00000567700,;NUBP2,upstream_gene_variant,,ENST00000568834,NM_001284502.1;NUBP2,upstream_gene_variant,,ENST00000565603,;NUBP2,upstream_gene_variant,,ENST00000564227,;NUBP2,upstream_gene_variant,,ENST00000566090,;NUBP2,upstream_gene_variant,,ENST00000569898,;EME2,downstream_gene_variant,,ENST00000564182,;SPSB3,downstream_gene_variant,,ENST00000568416,;NUBP2,upstream_gene_variant,,ENST00000566447,;EME2,downstream_gene_variant,,ENST00000561564,;EME2,downstream_gene_variant,,ENST00000565326,; - ENST00000566339 Transcript inframe_deletion 540-542/1784 209-211/1068 70-71/355 FC/C tTCTgt/tgt 1 -1 SPSB3 HGNC HGNC:30629 protein_coding YES CCDS32365.1 ENSP00000457206 Q6PJ21 UPI000006FA20 NM_080861.3 3/7 hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF5 MODERATE 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.24717 1 1 1 1 0 - 7 5 52 1778528 1778528 AGA - 1 0 1 0 1 0 0 0 0 15470 188 7 0 0 SPSB3 16 1778528 In_Frame_Del DEL AGA C3N-00551_T 48994 1778528 88559817 464 15947 CASKIN1 0 . GRCh38 16 2180445 2180445 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.2923G>A p.Gly975Ser p.G975S ENST00000343516 18/20 182 171 11 214 214 0 strelka-varscan-mutect CASKIN1,missense_variant,p.Gly975Ser,ENST00000343516,NM_020764.3;TRAF7,downstream_gene_variant,,ENST00000326181,NM_032271.2;CASKIN1,downstream_gene_variant,,ENST00000564289,; T ENST00000343516 Transcript missense_variant 3016/5759 2923/4296 975/1431 G/S Ggc/Agc 1 -1 CASKIN1 HGNC HGNC:20879 protein_coding YES CCDS42103.1 ENSP00000345436 Q8WXD9 UPI0000073A3B NM_020764.3 tolerated(0.25) 18/20 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 2180445 2180445 C T 1 0 0 0 0 1 0 0 0 2366 594 21 3 3 CASKIN1 16 2180445 Missense_Mutation SNP C C3N-00551_T 401917 2180445 88157900 465 15948 PRSS22 0 . GRCh38 16 2853254 2853254 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.793G>T p.Gly265Cys p.G265C ENST00000161006 6/6 301 246 55 343 343 0 strelka-varscan-mutect PRSS22,missense_variant,p.Gly265Cys,ENST00000161006,NM_022119.3;PRSS22,missense_variant,p.Gly155Cys,ENST00000571228,;LA16c-325D7.1,upstream_gene_variant,,ENST00000577140,;PRSS22,downstream_gene_variant,,ENST00000574768,;PRSS22,downstream_gene_variant,,ENST00000577177,;PRSS22,non_coding_transcript_exon_variant,,ENST00000575164,;PRSS22,downstream_gene_variant,,ENST00000576381,;PRSS22,downstream_gene_variant,,ENST00000570950,;PRSS22,downstream_gene_variant,,ENST00000572061,; A ENST00000161006 Transcript missense_variant 859/1386 793/954 265/317 G/C Ggc/Tgc 1 -1 PRSS22 HGNC HGNC:14368 protein_coding YES CCDS10481.1 ENSP00000161006 Q9GZN4 UPI0000126AFA NM_022119.3 deleterious(0) 6/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24253:SF6,hmmpanther:PTHR24253,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 2853254 2853254 C A 1 0 0 0 0 1 0 0 0 12766 623 22 2 2 PRSS22 16 2853254 Missense_Mutation SNP C C3N-00551_T 672809 2853254 87485091 466 15949 UBALD1 0 . GRCh38 16 4610212 4610212 + Silent SNP C C T novel C3N-00551_T C3N-00551_N C C c.60G>A p.= p.L20L ENST00000590891 1/1 199 187 12 182 182 0 strelka-varscan-mutect UBALD1,synonymous_variant,p.=,ENST00000590891,;UBALD1,intron_variant,,ENST00000590965,;UBALD1,intron_variant,,ENST00000283474,NM_145253.2;UBALD1,intron_variant,,ENST00000591401,;UBALD1,intron_variant,,ENST00000591897,;UBALD1,intron_variant,,ENST00000587615,;UBALD1,intron_variant,,ENST00000587649,;UBALD1,intron_variant,,ENST00000591113,;UBALD1,intron_variant,,ENST00000588691,; T ENST00000590891 Transcript synonymous_variant 1312/2641 60/639 20/212 L ctG/ctA 1 -1 UBALD1 HGNC HGNC:29576 protein_coding ENSP00000465706 Q8TB05 UPI000022EEB5 1/1 Low_complexity_(Seg):seg LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 4610212 4610212 C T 1 0 0 0 0 0 0 0 1 17355 581 21 3 3 UBALD1 16 4610212 Silent SNP C C3N-00551_T 1756958 4610212 85728133 467 15950 MKL2 0 . GRCh38 16 14245556 14245556 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1108G>T p.Gly370Trp p.G370W ENST00000571589 11/17 183 142 41 229 229 0 strelka-varscan-mutect MKL2,missense_variant,p.Gly370Trp,ENST00000571589,NM_001308142.1;MKL2,missense_variant,p.Gly370Trp,ENST00000318282,;MKL2,missense_variant,p.Gly370Trp,ENST00000574045,NM_014048.3;MKL2,downstream_gene_variant,,ENST00000572567,;MKL2,downstream_gene_variant,,ENST00000573051,;MKL2,upstream_gene_variant,,ENST00000572588,; T ENST00000571589 Transcript missense_variant 1280/8799 1108/3300 370/1099 G/W Ggg/Tgg COSM5148783,COSM5148784 1 1 MKL2 HGNC HGNC:29819 protein_coding YES CCDS76823.1 ENSP00000459626 Q9ULH7 UPI00001FEE5A NM_001308142.1 deleterious(0.01) 11/17 Low_complexity_(Seg):seg,hmmpanther:PTHR22793:SF5,hmmpanther:PTHR22793 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 14245556 14245556 G T 1 0 0 0 0 1 0 0 0 9569 1348 47 2 2 MKL2 16 14245556 Missense_Mutation SNP G C3N-00551_T 9635344 14245556 76092789 468 15951 ACSM1 0 . GRCh38 16 20624195 20624195 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.1548C>A p.= p.V516V ENST00000307493 12/13 114 108 6 94 94 0 strelka-mutect ACSM1,synonymous_variant,p.=,ENST00000307493,NM_001318890.1,NM_052956.2;ACSM1,synonymous_variant,p.=,ENST00000520010,;ACSM1,synonymous_variant,p.=,ENST00000524149,;ACSM3,intron_variant,,ENST00000568235,;ACSM1,3_prime_UTR_variant,,ENST00000519745,;ACSM1,intron_variant,,ENST00000519031,;RP11-143N13.3,upstream_gene_variant,,ENST00000618989,; T ENST00000307493 Transcript synonymous_variant 1616/2051 1548/1734 516/577 V gtC/gtA 1 -1 ACSM1 HGNC HGNC:18049 protein_coding YES CCDS10587.1 ENSP00000301956 Q08AH1 UPI00000558D0 NM_001318890.1,NM_052956.2 12/13 hmmpanther:PTHR24095:SF150,hmmpanther:PTHR24095,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.24452 1 1 1 1 0 T 2 4 52 20624195 20624195 G T 1 0 0 0 0 0 0 0 1 224 1161 41 2 2 ACSM1 16 20624195 Silent SNP G C3N-00551_T 6378639 20624195 69714150 469 15952 SCNN1B 0 . GRCh38 16 23348783 23348783 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.184C>G p.Leu62Val p.L62V ENST00000343070 2/13 422 327 95 445 445 0 strelka-varscan-mutect SCNN1B,missense_variant,p.Leu62Val,ENST00000343070,NM_000336.2;SCNN1B,missense_variant,p.Leu107Val,ENST00000307331,;SCNN1B,missense_variant,p.Leu62Val,ENST00000568923,;SCNN1B,missense_variant,p.Leu62Val,ENST00000568085,;SCNN1B,non_coding_transcript_exon_variant,,ENST00000569789,;SCNN1B,missense_variant,p.Leu62Val,ENST00000564275,;SCNN1B,upstream_gene_variant,,ENST00000566870,; G ENST00000343070 Transcript missense_variant 360/2597 184/1923 62/640 L/V Ctc/Gtc 1 1 SCNN1B HGNC HGNC:10600 protein_coding YES CCDS10609.1 ENSP00000345751 P51168 B2R812 UPI0000135616 NM_000336.2 tolerated(0.09) 2/13 Pfam_domain:PF00858,Prints_domain:PR01078,hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF18,TIGRFAM_domain:TIGR00859,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 23348783 23348783 C G 1 0 0 0 0 1 0 0 0 14197 681 24 4 4 SCNN1B 16 23348783 Missense_Mutation SNP C C3N-00551_T 2724588 23348783 66989562 470 15953 PLK1 0 . GRCh38 16 23689947 23689947 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1696C>G p.Leu566Val p.L566V ENST00000300093 10/10 287 271 16 283 283 0 strelka-varscan-mutect PLK1,missense_variant,p.Leu566Val,ENST00000300093,NM_005030.4;ERN2,downstream_gene_variant,,ENST00000634482,NM_033266.3;ERN2,downstream_gene_variant,,ENST00000256797,;ERN2,downstream_gene_variant,,ENST00000457008,NM_001308220.1;CTD-2196E14.5,upstream_gene_variant,,ENST00000566143,;PLK1,non_coding_transcript_exon_variant,,ENST00000562272,;PLK1,non_coding_transcript_exon_variant,,ENST00000564794,;ERN2,downstream_gene_variant,,ENST00000562562,;ERN2,downstream_gene_variant,,ENST00000562458,;PLK1,downstream_gene_variant,,ENST00000564947,;PLK1,downstream_gene_variant,,ENST00000562407,; G ENST00000300093 Transcript missense_variant 1807/2227 1696/1812 566/603 L/V Ctc/Gtc 1 1 PLK1 HGNC HGNC:9077 protein_coding YES CCDS10616.1 ENSP00000300093 P53350 UPI0000131BF9 NM_005030.4 tolerated(0.3) 10/10 PROSITE_profiles:PS50078,hmmpanther:PTHR24345,Pfam_domain:PF00659,Gene3D:3.30.1120.30,Superfamily_domains:SSF82615 MODERATE 1 SNV 1 1 PASS rs1048434068 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 23689947 23689947 C G 1 0 0 0 0 1 0 0 0 12190 913 32 4 4 PLK1 16 23689947 Missense_Mutation SNP C C3N-00551_T 341164 23689947 66648398 471 15954 TNRC6A 0 . GRCh38 16 24789402 24789402 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.760A>G p.Met254Val p.M254V ENST00000395799 6/25 135 111 24 207 207 0 strelka-varscan-mutect TNRC6A,missense_variant,p.Met254Val,ENST00000395799,NM_014494.2;TNRC6A,missense_variant,p.Met254Val,ENST00000315183,;TNRC6A,upstream_gene_variant,,ENST00000450465,;TNRC6A,3_prime_UTR_variant,,ENST00000491718,;TNRC6A,upstream_gene_variant,,ENST00000568903,;TNRC6A,upstream_gene_variant,,ENST00000567232,; G ENST00000395799 Transcript missense_variant 889/8438 760/5889 254/1962 M/V Atg/Gtg 1 1 TNRC6A HGNC HGNC:11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 UPI000059D33E NM_014494.2 tolerated(0.31) 6/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 24789402 24789402 A G 1 0 0 0 0 1 0 0 0 16813 449 16 5 5 TNRC6A 16 24789402 Missense_Mutation SNP A C3N-00551_T 1099455 24789402 65548943 472 15955 C16orf82 0 . GRCh38 16 27067060 27067060 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.254A>G p.Gln85Arg p.Q85R ENST00000505035 1/1 384 242 142 451 451 0 strelka-varscan-mutect C16orf82,missense_variant,p.Gln85Arg,ENST00000505035,;C16orf82,missense_variant,p.Gln22Arg,ENST00000418886,NM_001145545.1;RP11-673P17.2,intron_variant,,ENST00000565783,; G ENST00000505035 Transcript missense_variant 354/2459 254/654 85/217 Q/R cAg/cGg 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 tolerated(0.25) 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 27067060 27067060 A G 1 0 0 0 0 1 0 0 0 1867 188 7 5 5 C16orf82 16 27067060 Missense_Mutation SNP A C3N-00551_T 2277658 27067060 63271285 473 15956 C16orf82 0 . GRCh38 16 27067440 27067440 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.634C>A p.Gln212Lys p.Q212K ENST00000505035 1/1 101 72 29 99 99 0 strelka-varscan-mutect C16orf82,missense_variant,p.Gln212Lys,ENST00000505035,;C16orf82,missense_variant,p.Gln149Lys,ENST00000418886,NM_001145545.1;RP11-673P17.2,non_coding_transcript_exon_variant,,ENST00000565783,; A ENST00000505035 Transcript missense_variant 734/2459 634/654 212/217 Q/K Cag/Aag 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 tolerated(0.06) 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 MODERATE SNV 1 PASS rs896806060 . 0 198 11 0 0 0 0 0 -20 0.9999884 1 1 1 0 A 3 1 52 27067440 27067440 C A 1 0 0 0 0 1 0 0 0 1867 711 25 2 2 C16orf82 16 27067440 Missense_Mutation SNP C C3N-00551_T 380 27067440 63270905 474 15957 KDM8 0 . GRCh38 16 27215010 27215010 + Splice_Site SNP T T C novel C3N-00551_T C3N-00551_N T T c.912+2T>C p.X304_splice ENST00000441782 150 126 24 145 145 0 strelka-varscan-mutect KDM8,splice_donor_variant,,ENST00000286096,NM_024773.2;KDM8,splice_donor_variant,,ENST00000441782,NM_001145348.1;KDM8,splice_donor_variant,,ENST00000567735,;KDM8,intron_variant,,ENST00000568965,;KDM8,downstream_gene_variant,,ENST00000569329,;KDM8,downstream_gene_variant,,ENST00000562733,;CTD-3203P2.1,upstream_gene_variant,,ENST00000567108,;KDM8,splice_donor_variant,,ENST00000567785,;KDM8,splice_donor_variant,,ENST00000567366,;KDM8,downstream_gene_variant,,ENST00000562269,;KDM8,splice_donor_variant,,ENST00000563571,;KDM8,splice_donor_variant,,ENST00000568792,;KDM8,downstream_gene_variant,,ENST00000564961,; C ENST00000441782 Transcript splice_donor_variant -/1612 912/1365 304/454 1 1 KDM8 HGNC HGNC:25840 protein_coding YES CCDS45448.1 ENSP00000398410 Q8N371 UPI00017A73AE NM_001145348.1 4/7 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 52 27215010 27215010 T C 1 0 0 0 0 0 0 1 0 8058 1652 57 5 5 KDM8 16 27215010 Splice_Site SNP T C3N-00551_T 147570 27215010 63123335 475 15958 NUDT21 0 . GRCh38 16 56447911 56447911 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.195G>T p.Gln65His p.Q65H ENST00000300291 2/7 291 250 41 386 386 0 strelka-varscan-mutect NUDT21,missense_variant,p.Gln65His,ENST00000300291,NM_007006.2;NUDT21,5_prime_UTR_variant,,ENST00000566340,;NUDT21,5_prime_UTR_variant,,ENST00000568822,;OGFOD1,upstream_gene_variant,,ENST00000566157,NM_018233.3;OGFOD1,upstream_gene_variant,,ENST00000568397,;OGFOD1,upstream_gene_variant,,ENST00000562150,;OGFOD1,upstream_gene_variant,,ENST00000561646,;OGFOD1,upstream_gene_variant,,ENST00000568172,;NUDT21,non_coding_transcript_exon_variant,,ENST00000567110,;OGFOD1,upstream_gene_variant,,ENST00000336111,;OGFOD1,upstream_gene_variant,,ENST00000563733,;OGFOD1,upstream_gene_variant,,ENST00000569645,;OGFOD1,upstream_gene_variant,,ENST00000565682,;NUDT21,upstream_gene_variant,,ENST00000612596,;OGFOD1,upstream_gene_variant,,ENST00000569802,; A ENST00000300291 Transcript missense_variant 368/4436 195/684 65/227 Q/H caG/caT 1 -1 NUDT21 HGNC HGNC:13870 protein_coding YES CCDS10760.1 ENSP00000300291 O43809 A0A024R6W2 UPI0000073E79 NM_007006.2 deleterious(0.01) 2/7 Gene3D:3.90.79.10,Pfam_domain:PF13869,PIRSF_domain:PIRSF017888,hmmpanther:PTHR13047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 56447911 56447911 C A 1 0 0 0 0 1 0 0 0 10802 796 28 2 2 NUDT21 16 56447911 Missense_Mutation SNP C C3N-00551_T 29232901 56447911 33890434 476 15959 CNOT1 0 . GRCh38 16 58547644 58547644 + Silent SNP T T C novel C3N-00551_T C3N-00551_N T T c.3561A>G p.= p.S1187S ENST00000317147 26/49 143 135 8 173 173 0 strelka-varscan-mutect CNOT1,synonymous_variant,p.=,ENST00000317147,NM_016284.4;CNOT1,synonymous_variant,p.=,ENST00000569240,NM_001265612.1;CNOT1,synonymous_variant,p.=,ENST00000441024,NM_206999.2;CNOT1,intron_variant,,ENST00000567285,;CNOT1,downstream_gene_variant,,ENST00000562046,;CNOT1,upstream_gene_variant,,ENST00000567133,;SNORA46,downstream_gene_variant,,ENST00000384762,;CNOT1,downstream_gene_variant,,ENST00000569732,;CNOT1,synonymous_variant,p.=,ENST00000567188,;CNOT1,upstream_gene_variant,,ENST00000566240,; C ENST00000317147 Transcript synonymous_variant 3894/8471 3561/7131 1187/2376 S tcA/tcG 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 26/49 hmmpanther:PTHR13162,Pfam_domain:PF16415 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 52 58547644 58547644 T C 1 0 0 0 0 0 0 0 1 3396 1567 55 5 5 CNOT1 16 58547644 Silent SNP T C3N-00551_T 2099733 58547644 31790701 477 15960 CDH11 0 . GRCh38 16 64950767 64950767 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.1894G>T p.Val632Phe p.V632F ENST00000268603 12/13 100 90 10 99 99 0 strelka-varscan-mutect CDH11,missense_variant,p.Gly632Cys,ENST00000394156,NM_001308392.1;CDH11,missense_variant,p.Val632Phe,ENST00000268603,NM_001797.2;CDH11,missense_variant,p.Val506Phe,ENST00000566827,; A ENST00000268603 Transcript missense_variant,splice_region_variant 2510/6857 1894/2391 632/796 V/F Gtc/Ttc COSM4871464,COSM972128 1 -1 CDH11 HGNC HGNC:1750 protein_coding YES CCDS10803.1 ENSP00000268603 P55287 UPI000013D7C5 NM_001797.2 deleterious(0.01) 12/13 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF85,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1454976552 . 0 206 3 0 0 0 0 0 -19.91755 1 1 1 1 0 A 3 1 52 64950767 64950767 C A 1 0 0 0 0 1 0 0 0 2800 637 22 2 2 CDH11 16 64950767 Missense_Mutation SNP C C3N-00551_T 6403123 64950767 25387578 478 15961 CDH11 0 . GRCh38 16 64982230 64982230 + Missense_Mutation SNP C C A rs539135992 C3N-00551_T C3N-00551_N C C c.1071G>T p.Lys357Asn p.K357N ENST00000268603 8/13 273 256 17 362 362 0 strelka-varscan-mutect CDH11,missense_variant,p.Lys357Asn,ENST00000394156,NM_001308392.1;CDH11,missense_variant,p.Lys357Asn,ENST00000268603,NM_001797.2;CDH11,missense_variant,p.Lys231Asn,ENST00000566827,;CDH11,downstream_gene_variant,,ENST00000619158,;RP11-229O3.1,non_coding_transcript_exon_variant,,ENST00000624875,; A ENST00000268603 Transcript missense_variant 1687/6857 1071/2391 357/796 K/N aaG/aaT rs539135992 1 -1 CDH11 HGNC HGNC:1750 protein_coding YES CCDS10803.1 ENSP00000268603 P55287 UPI000013D7C5 NM_001797.2 tolerated(0.07) 8/13 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF85,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs539135992 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 64982230 64982230 C A 1 0 0 0 0 1 0 0 0 2800 564 20 2 2 CDH11 16 64982230 Missense_Mutation SNP C C3N-00551_T 31463 64982230 25356115 479 15962 ESRP2 0 . GRCh38 16 68235896 68235896 + Silent SNP G G T rs571597168 C3N-00551_T C3N-00551_N G G c.150C>A p.= p.T50T ENST00000473183 1/15 219 171 48 293 293 0 strelka-varscan-mutect ESRP2,synonymous_variant,p.=,ENST00000473183,NM_024939.2;ESRP2,synonymous_variant,p.=,ENST00000565858,;ESRP2,intron_variant,,ENST00000564382,;ESRP2,intron_variant,,ENST00000562724,;ESRP2,upstream_gene_variant,,ENST00000612812,;RP11-96D1.6,downstream_gene_variant,,ENST00000564147,;ESRP2,non_coding_transcript_exon_variant,,ENST00000251366,;ESRP2,upstream_gene_variant,,ENST00000566774,;ESRP2,upstream_gene_variant,,ENST00000562567,;ESRP2,upstream_gene_variant,,ENST00000564465,;ESRP2,upstream_gene_variant,,ENST00000563159,;ESRP2,upstream_gene_variant,,ENST00000562738,;ESRP2,upstream_gene_variant,,ENST00000569964,;ESRP2,upstream_gene_variant,,ENST00000565213,; T ENST00000473183 Transcript synonymous_variant 689/3793 150/2154 50/717 T acC/acA rs571597168 1 -1 ESRP2 HGNC HGNC:26152 protein_coding YES CCDS10863.1 ENSP00000418748 Q9H6T0 UPI000006FB08 NM_024939.2 1/15 Gene3D:3.30.420.10,hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF30 LOW 1 SNV 1 1 PASS rs571597168 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 68235896 68235896 G T 1 0 0 0 0 0 0 0 1 5121 1103 39 1 1 ESRP2 16 68235896 Silent SNP G C3N-00551_T 3253666 68235896 22102449 480 15963 CNTNAP4 0 . GRCh38 16 76538268 76538268 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.3148C>A p.= p.R1050R ENST00000611870 19/24 175 162 13 349 348 1 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3; A ENST00000611870 Transcript synonymous_variant 3533/4867 3148/3927 1050/1308 R Cga/Aga 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 19/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1220482671 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 76538268 76538268 C A 1 0 0 0 0 0 0 0 1 3431 528 19 1 1 CNTNAP4 16 76538268 Silent SNP C C3N-00551_T 8302372 76538268 13800077 481 15964 VAT1L 0 . GRCh38 16 77825296 77825296 + Silent SNP G G T rs768480632 C3N-00551_T C3N-00551_N G G c.414G>T p.= p.V138V ENST00000302536 3/9 383 332 51 437 437 0 strelka-varscan-mutect VAT1L,synonymous_variant,p.=,ENST00000302536,NM_020927.2; T ENST00000302536 Transcript synonymous_variant 567/3825 414/1260 138/419 V gtG/gtT rs768480632 1 1 VAT1L HGNC HGNC:29315 protein_coding YES CCDS32492.1 ENSP00000303129 Q9HCJ6 UPI00000741CE NM_020927.2 3/9 Gene3D:3.90.180.10,hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF600,SMART_domains:SM00829,Superfamily_domains:SSF50129 LOW 1 SNV 1 1 PASS rs768480632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 77825296 77825296 G T 1 0 0 0 0 0 0 0 1 17675 1335 47 2 2 VAT1L 16 77825296 Silent SNP G C3N-00551_T 1287028 77825296 12513049 482 15965 ATMIN 0 . GRCh38 16 81044147 81044147 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.1649A>G p.Asn550Ser p.N550S ENST00000299575 4/4 136 115 21 193 193 0 strelka-varscan-mutect ATMIN,missense_variant,p.Asn394Ser,ENST00000566488,;ATMIN,missense_variant,p.Asn550Ser,ENST00000299575,NM_015251.2;ATMIN,missense_variant,p.Asn394Ser,ENST00000564241,NM_001300728.1;ATMIN,downstream_gene_variant,,ENST00000565237,;ATMIN,non_coding_transcript_exon_variant,,ENST00000539819,;ATMIN,downstream_gene_variant,,ENST00000562969,; G ENST00000299575 Transcript missense_variant 1673/4884 1649/2472 550/823 N/S aAt/aGt 1 1 ATMIN HGNC HGNC:29034 protein_coding YES CCDS32494.1 ENSP00000299575 O43313 UPI00001B2485 NM_015251.2 tolerated(0.4) 4/4 hmmpanther:PTHR10593:SF10,hmmpanther:PTHR10593 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 81044147 81044147 A G 1 0 0 0 0 1 0 0 0 1262 101 4 5 5 ATMIN 16 81044147 Missense_Mutation SNP A C3N-00551_T 3218851 81044147 9294198 483 15966 DNAAF1 0 . GRCh38 16 84170176 84170176 + Missense_Mutation SNP C C G rs777616161 C3N-00551_T C3N-00551_N C C c.1348C>G p.Pro450Ala p.P450A ENST00000378553 8/12 332 280 52 542 541 1 strelka-varscan-mutect DNAAF1,missense_variant,p.Pro450Ala,ENST00000378553,NM_178452.4;DNAAF1,non_coding_transcript_exon_variant,,ENST00000563818,;DNAAF1,downstream_gene_variant,,ENST00000567666,;DNAAF1,non_coding_transcript_exon_variant,,ENST00000570298,;DNAAF1,intron_variant,,ENST00000563093,; G ENST00000378553 Transcript missense_variant 1472/2379 1348/2178 450/725 P/A Ccg/Gcg rs777616161 1 1 DNAAF1 HGNC HGNC:30539 protein_coding YES CCDS10943.2 ENSP00000367815 Q8NEP3 A0A140VJN4 UPI000059D3C9 NM_178452.4 tolerated(0.63) 8/12 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs777616161 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 84170176 84170176 C G 1 0 0 0 0 1 0 0 0 4406 623 22 4 4 DNAAF1 16 84170176 Missense_Mutation SNP C C3N-00551_T 3126029 84170176 6168169 484 15967 COX4I1 0 . GRCh38 16 85805778 85805778 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.287G>T p.Gly96Val p.G96V ENST00000562336 4/5 169 153 16 219 219 0 strelka-varscan-mutect COX4I1,missense_variant,p.Gly96Val,ENST00000564903,;COX4I1,missense_variant,p.Gly96Val,ENST00000562336,;COX4I1,missense_variant,p.Gly96Val,ENST00000568794,;COX4I1,missense_variant,p.Gly96Val,ENST00000561569,;COX4I1,missense_variant,p.Gly96Val,ENST00000253452,NM_001318797.1,NM_001861.3;COX4I1,missense_variant,p.Gly58Val,ENST00000566405,;COX4I1,downstream_gene_variant,,ENST00000565078,;COX4I1,non_coding_transcript_exon_variant,,ENST00000562929,;COX4I1,downstream_gene_variant,,ENST00000570123,;COX4I1,3_prime_UTR_variant,,ENST00000564544,;COX4I1,non_coding_transcript_exon_variant,,ENST00000569997,;COX4I1,non_coding_transcript_exon_variant,,ENST00000568339,;COX4I1,non_coding_transcript_exon_variant,,ENST00000564648,;COX4I1,downstream_gene_variant,,ENST00000566617,;COX4I1,downstream_gene_variant,,ENST00000563774,;COX4I1,downstream_gene_variant,,ENST00000567241,;COX4I1,downstream_gene_variant,,ENST00000567266,;COX4I1,downstream_gene_variant,,ENST00000566115,; T ENST00000562336 Transcript missense_variant 480/873 287/510 96/169 G/V gGc/gTc 1 1 COX4I1 HGNC HGNC:2265 protein_coding YES CCDS10955.1 ENSP00000457513 P13073 UPI0000128787 tolerated(0.23) 4/5 hmmpanther:PTHR10707:SF12,hmmpanther:PTHR10707,Gene3D:1v54D00,Pfam_domain:PF02936,Superfamily_domains:0041782,Prints_domain:PR01873 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -19.99649 0.9999998 1 1 1 0 T 3 4 52 85805778 85805778 G T 1 0 0 0 0 1 0 0 0 3565 1203 42 2 2 COX4I1 16 85805778 Missense_Mutation SNP G C3N-00551_T 1635602 85805778 4532567 485 15968 ZNF469 0 . GRCh38 16 88438281 88438281 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.10727C>A p.Pro3576Gln p.P3576Q ENST00000437464 2/2 88 81 7 99 99 0 strelka-varscan-mutect ZNF469,missense_variant,p.Pro3604Gln,ENST00000565624,;ZNF469,missense_variant,p.Pro3576Gln,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 10727/13203 10727/11778 3576/3925 P/Q cCg/cAg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 deleterious(0.02) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS rs957402222 . 0 199 11 0 0 0 0 0 -14.46313 0.9998579 1 1 1 0 A 3 1 52 88438281 88438281 C A 1 0 0 0 0 1 0 0 0 18500 652 23 1 1 ZNF469 16 88438281 Missense_Mutation SNP C C3N-00551_T 2632503 88438281 1900064 486 15969 TCF25 0 . GRCh38 16 89904131 89904131 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.1395G>T p.= p.L465L ENST00000263346 13/18 160 128 32 163 163 0 strelka-varscan-mutect TCF25,synonymous_variant,p.=,ENST00000263347,;TCF25,synonymous_variant,p.=,ENST00000263346,NM_014972.2;TCF25,synonymous_variant,p.=,ENST00000562256,;TCF25,synonymous_variant,p.=,ENST00000568409,;TCF25,synonymous_variant,p.=,ENST00000562193,;TCF25,upstream_gene_variant,,ENST00000566283,;TCF25,non_coding_transcript_exon_variant,,ENST00000570116,;TCF25,downstream_gene_variant,,ENST00000563636,;TCF25,downstream_gene_variant,,ENST00000562184,;RP11-566K11.7,upstream_gene_variant,,ENST00000570217,;TCF25,upstream_gene_variant,,ENST00000563484,; T ENST00000263346 Transcript synonymous_variant 1451/2233 1395/2031 465/676 L ctG/ctT 1 1 TCF25 HGNC HGNC:29181 protein_coding YES CCDS10987.1 ENSP00000263346 Q9BQ70 UPI000012A80B NM_014972.2 13/18 hmmpanther:PTHR22684,hmmpanther:PTHR22684:SF0,Pfam_domain:PF04910 LOW 1 SNV 1 1 PASS rs1222140728 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 89904131 89904131 G T 1 0 0 0 0 0 0 0 1 16100 1306 46 2 2 TCF25 16 89904131 Silent SNP G C3N-00551_T 1465850 89904131 434214 487 15970 HIC1 0 . GRCh38 17 2056704 2056704 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.71T>C p.Met24Thr p.M24T ENST00000322941 2/2 86 73 13 78 78 0 strelka-varscan-mutect HIC1,missense_variant,p.Met5Thr,ENST00000619757,;HIC1,missense_variant,p.Met5Thr,ENST00000399849,NM_006497.3;HIC1,missense_variant,p.Met24Thr,ENST00000322941,NM_001098202.1;HIC1,missense_variant,p.Met5Thr,ENST00000574370,;HIC1,missense_variant,p.Met5Thr,ENST00000571875,;HIC1,missense_variant,p.Met5Thr,ENST00000576444,;HIC1,missense_variant,p.Met5Thr,ENST00000571990,;SMG6,downstream_gene_variant,,ENST00000263073,NM_017575.4;SMG6,downstream_gene_variant,,ENST00000354901,NM_001256827.1;SMG6,downstream_gene_variant,,ENST00000536871,NM_001256828.1;SMG6,downstream_gene_variant,,ENST00000573166,;SMG6,downstream_gene_variant,,ENST00000570756,;SMG6,downstream_gene_variant,,ENST00000576218,;SMG6,downstream_gene_variant,,ENST00000573827,;SMG6,downstream_gene_variant,,ENST00000573153,;SMG6,downstream_gene_variant,,ENST00000574501,; C ENST00000322941 Transcript missense_variant 71/3053 71/2202 24/733 M/T aTg/aCg 1 1 HIC1 HGNC HGNC:4909 protein_coding YES CCDS42229.1 ENSP00000314080 Q14526 UPI0000140F7F NM_001098202.1 deleterious(0) 2/2 Gene3D:3.30.710.10,Superfamily_domains:SSF54695 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 2056704 2056704 T C 1 0 0 0 0 1 0 0 0 6985 1464 51 5 5 HIC1 17 2056704 Missense_Mutation SNP T C3N-00551_T 2056704 81200737 488 15971 ASPA 0 . GRCh38 17 3483565 3483565 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.499A>G p.Thr167Ala p.T167A ENST00000263080 3/6 312 241 71 452 452 0 strelka-varscan-mutect ASPA,missense_variant,p.Thr167Ala,ENST00000263080,NM_000049.2;ASPA,missense_variant,p.Thr167Ala,ENST00000456349,NM_001128085.1;SPATA22,intron_variant,,ENST00000541913,NM_001321336.1;SPATA22,intron_variant,,ENST00000570318,;ASPA,3_prime_UTR_variant,,ENST00000571278,; G ENST00000263080 Transcript missense_variant 657/5431 499/942 167/313 T/A Act/Gct 1 1 ASPA HGNC HGNC:756 protein_coding YES CCDS11028.1 ENSP00000263080 P45381 Q6FH48 UPI00000012D1 NM_000049.2 tolerated(0.41) 3/6 HAMAP:MF_00704,hmmpanther:PTHR15162,hmmpanther:PTHR15162:SF9,PIRSF_domain:PIRSF018001,Pfam_domain:PF04952,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 3483565 3483565 A G 1 0 0 0 0 1 0 0 0 1197 159 6 5 5 ASPA 17 3483565 Missense_Mutation SNP A C3N-00551_T 1426861 3483565 79773876 489 15972 SPNS3 0 . GRCh38 17 4439706 4439706 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.248C>A p.Ala83Asp p.A83D ENST00000355530 2/12 159 126 33 183 183 0 strelka-varscan-mutect SPNS3,missense_variant,p.Ala83Asp,ENST00000355530,NM_182538.4;SPNS3,non_coding_transcript_exon_variant,,ENST00000576069,;SPNS3,missense_variant,p.Ala83Asp,ENST00000575194,NM_001320449.1; A ENST00000355530 Transcript missense_variant 528/2133 248/1539 83/512 A/D gCt/gAt 1 1 SPNS3 HGNC HGNC:28433 protein_coding YES CCDS11045.1 ENSP00000347721 Q6ZMD2 UPI00001971EC NM_182538.4 deleterious(0) 2/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF3,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 4439706 4439706 C A 1 0 0 0 0 1 0 0 0 15429 797 28 2 2 SPNS3 17 4439706 Missense_Mutation SNP C C3N-00551_T 956141 4439706 78817735 490 15973 ZMYND15 0 . GRCh38 17 4743836 4743836 + Missense_Mutation SNP G G T rs750129765 C3N-00551_T C3N-00551_N G G c.1367G>T p.Arg456Leu p.R456L ENST00000269289 7/14 103 82 21 129 129 0 strelka-varscan-mutect ZMYND15,missense_variant,p.Arg456Leu,ENST00000269289,NM_001267822.1;ZMYND15,missense_variant,p.Arg456Leu,ENST00000433935,NM_001136046.2;ZMYND15,missense_variant,p.Arg456Leu,ENST00000573751,;ZMYND15,missense_variant,p.Arg456Leu,ENST00000592813,NM_032265.2;CXCL16,upstream_gene_variant,,ENST00000293778,NM_022059.3;CXCL16,upstream_gene_variant,,ENST00000574412,NM_001100812.1;CXCL16,upstream_gene_variant,,ENST00000573123,;ZMYND15,non_coding_transcript_exon_variant,,ENST00000574829,;ZMYND15,non_coding_transcript_exon_variant,,ENST00000571782,; T ENST00000269289 Transcript missense_variant 1433/2448 1367/2253 456/750 R/L cGg/cTg rs750129765 1 1 ZMYND15 HGNC HGNC:20997 protein_coding YES CCDS58506.1 ENSP00000269289 Q9H091 UPI0000D4C064 NM_001267822.1 tolerated(0.33) 7/14 hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF161 MODERATE SNV 5 1 PASS rs750129765 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 4743836 4743836 G T 1 0 0 0 0 1 0 0 0 18288 1116 39 1 1 ZMYND15 17 4743836 Missense_Mutation SNP G C3N-00551_T 304130 4743836 78513605 491 15974 PITPNM3 0 . GRCh38 17 6538016 6538016 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.89G>T p.Ser30Ile p.S30I ENST00000262483 2/20 399 326 73 468 468 0 strelka-varscan-mutect PITPNM3,missense_variant,p.Ser30Ile,ENST00000262483,NM_031220.3;PITPNM3,missense_variant,p.Ser30Ile,ENST00000421306,NM_001165966.1; A ENST00000262483 Transcript missense_variant 177/7086 89/2925 30/974 S/I aGc/aTc 1 -1 PITPNM3 HGNC HGNC:21043 protein_coding YES CCDS11076.1 ENSP00000262483 Q9BZ71 UPI000022A281 NM_031220.3 deleterious(0) 2/20 hmmpanther:PTHR10658,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 6538016 6538016 C A 1 0 0 0 0 1 0 0 0 12048 797 28 2 2 PITPNM3 17 6538016 Missense_Mutation SNP C C3N-00551_T 1794180 6538016 76719425 492 15975 TP53 0 . GRCh38 17 7673783 7673783 + Frame_Shift_Del DEL C C - rs786201322 C3N-00551_T C3N-00551_N C C c.837delG p.Arg280GlufsTer65 p.R280Efs*65 ENST00000269305 8/11 637 503 134 650 650 0 sindel-varindel-pindel TP53,frameshift_variant,p.Arg280GlufsTer71,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.Arg280GlufsTer71,ENST00000420246,;TP53,frameshift_variant,p.Arg241GlufsTer71,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.Arg241GlufsTer65,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.Arg280GlufsTer63,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.Arg241GlufsTer63,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.Arg280GlufsTer65,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.Arg241GlufsTer65,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.Arg280GlufsTer65,ENST00000445888,;TP53,frameshift_variant,p.Arg241GlufsTer65,ENST00000619485,;TP53,frameshift_variant,p.Arg148GlufsTer71,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.Arg121GlufsTer71,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.Arg148GlufsTer63,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.Arg121GlufsTer63,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.Arg148GlufsTer65,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.Arg121GlufsTer65,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.Arg280GlufsTer72,ENST00000359597,;TP53,frameshift_variant,p.Arg269GlufsTer65,ENST00000615910,;TP53,frameshift_variant,p.Arg148GlufsTer?,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,frameshift_variant,p.Arg241GlufsTer65,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; - ENST00000269305 Transcript frameshift_variant 1027/2579 837/1182 279/393 G/X ggG/gg rs786201322,CD963012,TP53_g.13817G>T,TP53_g.13817G>A,COSM45624,COSM46284 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_benign 0,0,0,0,1,1 HIGH 1 deletion 1 1,1,0,0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 7673783 7673783 C - 1 0 1 0 1 0 0 0 0 16859 842 30 0 0 TP53 17 7673783 Frame_Shift_Del DEL C C3N-00551_T 1135767 7673783 75583658 493 15976 DNAH2 0 . GRCh38 17 7763922 7763922 + Missense_Mutation SNP C C A rs377307607 C3N-00551_T C3N-00551_N C C c.3070C>A p.Leu1024Met p.L1024M ENST00000572933 19/86 339 257 82 406 406 0 strelka-varscan-mutect DNAH2,missense_variant,p.Leu1024Met,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Leu1024Met,ENST00000389173,;DNAH2,missense_variant,p.Leu95Met,ENST00000574518,; A ENST00000572933 Transcript missense_variant 4530/14955 3070/13284 1024/4427 L/M Ctg/Atg rs377307607 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious(0.01) 19/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183 MODERATE 1 SNV 1 1 PASS rs377307607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 7763922 7763922 C A 1 0 0 0 0 1 0 0 0 4417 680 24 2 2 DNAH2 17 7763922 Missense_Mutation SNP C C3N-00551_T 90139 7763922 75493519 494 15977 MYH8 0 . GRCh38 17 10401428 10401428 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2955G>T p.Met985Ile p.M985I ENST00000403437 24/40 341 279 62 380 380 0 strelka-varscan-mutect MYH8,missense_variant,p.Met985Ile,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript missense_variant 3050/6041 2955/5814 985/1937 M/I atG/atT 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 tolerated(0.07) 24/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 10401428 10401428 C A 1 0 0 0 0 1 0 0 0 10041 594 21 2 2 MYH8 17 10401428 Missense_Mutation SNP C C3N-00551_T 2637506 10401428 72856013 495 15978 MYH4 0 . GRCh38 17 10455697 10455697 + Silent SNP C C A novel C3N-00551_T C3N-00551_N C C c.2091G>T p.= p.L697L ENST00000255381 19/40 229 190 39 354 353 1 strelka-varscan-mutect MYH4,synonymous_variant,p.=,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000255381 Transcript synonymous_variant 2202/6016 2091/5820 697/1939 L ctG/ctT 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 19/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 10455697 10455697 C A 1 0 0 0 0 0 0 0 1 10037 813 29 2 2 MYH4 17 10455697 Silent SNP C C3N-00551_T 54269 10455697 72801744 496 15979 SREBF1 0 . GRCh38 17 17814675 17814675 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.2765A>T p.Glu922Val p.E922V ENST00000355815 16/20 604 557 47 564 564 0 strelka-varscan-mutect SREBF1,missense_variant,p.Glu922Val,ENST00000355815,NM_001321096.2,NM_001005291.2;SREBF1,missense_variant,p.Glu892Val,ENST00000261646,NM_004176.4;SREBF1,missense_variant,p.Glu638Val,ENST00000395757,;RAI1,downstream_gene_variant,,ENST00000353383,NM_030665.3;SREBF1,downstream_gene_variant,,ENST00000423161,;SREBF1,upstream_gene_variant,,ENST00000478616,;SREBF1,downstream_gene_variant,,ENST00000577897,;SREBF1,upstream_gene_variant,,ENST00000486311,;MIR33B,upstream_gene_variant,,ENST00000385104,;MIR6777,upstream_gene_variant,,ENST00000613934,;RAI1,downstream_gene_variant,,ENST00000582514,;SREBF1,downstream_gene_variant,,ENST00000583732,;SREBF1,3_prime_UTR_variant,,ENST00000395751,;SREBF1,3_prime_UTR_variant,,ENST00000395756,;SREBF1,non_coding_transcript_exon_variant,,ENST00000490796,;SREBF1,non_coding_transcript_exon_variant,,ENST00000581707,;SREBF1,intron_variant,,ENST00000447641,;SREBF1,downstream_gene_variant,,ENST00000469356,;SREBF1,upstream_gene_variant,,ENST00000485080,;SREBF1,downstream_gene_variant,,ENST00000471445,;SREBF1,upstream_gene_variant,,ENST00000578469,;SREBF1,downstream_gene_variant,,ENST00000584760,;SREBF1,downstream_gene_variant,,ENST00000580540,;SREBF1,downstream_gene_variant,,ENST00000583080,;SREBF1,downstream_gene_variant,,ENST00000487401,;SREBF1,downstream_gene_variant,,ENST00000470247,; A ENST00000355815 Transcript missense_variant 2935/4253 2765/3534 922/1177 E/V gAg/gTg 1 -1 SREBF1 HGNC HGNC:11289 protein_coding YES CCDS32583.1 ENSP00000348069 P36956 UPI00004432F6 NM_001321096.2,NM_001005291.2 tolerated(0.15) 16/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 17814675 17814675 T A 1 0 0 0 0 1 0 0 0 15498 1551 54 4 4 SREBF1 17 17814675 Missense_Mutation SNP T C3N-00551_T 7358978 17814675 65442766 497 15980 TOP3A 0 . GRCh38 17 18306912 18306912 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.369A>T p.= p.P123P ENST00000542570 4/19 147 106 41 200 199 1 strelka-varscan-mutect TOP3A,synonymous_variant,p.=,ENST00000542570,NM_004618.3;TOP3A,synonymous_variant,p.=,ENST00000321105,;TOP3A,synonymous_variant,p.=,ENST00000580095,;TOP3A,non_coding_transcript_exon_variant,,ENST00000584669,;TOP3A,downstream_gene_variant,,ENST00000582230,;TOP3A,downstream_gene_variant,,ENST00000584887,;TOP3A,missense_variant,p.Gln136Leu,ENST00000461127,;TOP3A,3_prime_UTR_variant,,ENST00000584582,;TOP3A,3_prime_UTR_variant,,ENST00000582981,;TOP3A,non_coding_transcript_exon_variant,,ENST00000469739,;TOP3A,non_coding_transcript_exon_variant,,ENST00000472959,;TOP3A,non_coding_transcript_exon_variant,,ENST00000583328,;TOP3A,upstream_gene_variant,,ENST00000583804,;TOP3A,upstream_gene_variant,,ENST00000581536,;TOP3A,downstream_gene_variant,,ENST00000585031,;TOP3A,downstream_gene_variant,,ENST00000580713,;RPL7AP65,upstream_gene_variant,,ENST00000418183,; A ENST00000542570 Transcript synonymous_variant 598/4116 369/3006 123/1001 P ccA/ccT 1 -1 TOP3A HGNC HGNC:11992 protein_coding YES CCDS11194.1 ENSP00000442336 Q13472 UPI00001371A0 NM_004618.3 4/19 PROSITE_profiles:PS50880,hmmpanther:PTHR11390:SF21,hmmpanther:PTHR11390,Pfam_domain:PF01751,Gene3D:3.40.50.140,SMART_domains:SM00493,Superfamily_domains:SSF56712 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 18306912 18306912 T A 1 0 0 0 0 0 0 0 1 16843 1567 55 4 4 TOP3A 17 18306912 Silent SNP T C3N-00551_T 492237 18306912 64950529 498 15981 CCDC144NL 0 . GRCh38 17 20895749 20895749 + Frame_Shift_Del DEL C C - novel C3N-00551_T C3N-00551_N C C c.272delG p.Gly91AlafsTer29 p.G91Afs*29 ENST00000327925 1/4 153 117 36 225 225 0 sindel-varindel-pindel CCDC144NL,frameshift_variant,p.Gly91AlafsTer29,ENST00000327925,NM_001004306.2;RNU6-1178P,upstream_gene_variant,,ENST00000516674,;CCDC144NL-AS1,intron_variant,,ENST00000577537,;CCDC144NL-AS1,intron_variant,,ENST00000583962,;CCDC144NL-AS1,intron_variant,,ENST00000577860,;CCDC144NL-AS1,intron_variant,,ENST00000582324,;CCDC144NL-AS1,intron_variant,,ENST00000417232,;CCDC144NL-AS1,intron_variant,,ENST00000439794,; - ENST00000327925 Transcript frameshift_variant 392/2806 272/666 91/221 G/X gGc/gc 1 -1 CCDC144NL HGNC HGNC:33735 protein_coding YES CCDS32591.1 ENSP00000328054 Q6NUI1 UPI00001D7A84 NM_001004306.2 1/4 hmmpanther:PTHR22245,hmmpanther:PTHR22245:SF1 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 20895749 20895749 C - 1 0 1 0 1 0 0 0 0 2466 739 26 0 0 CCDC144NL 17 20895749 Frame_Shift_Del DEL C C3N-00551_T 2588837 20895749 62361692 499 15982 TMEM199 0 . GRCh38 17 28359359 28359359 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.330G>T p.= p.L110L ENST00000292114 3/6 243 218 25 213 213 0 strelka-varscan-mutect TMEM199,synonymous_variant,p.=,ENST00000292114,NM_152464.2;TMEM199,5_prime_UTR_variant,,ENST00000395404,;POLDIP2,upstream_gene_variant,,ENST00000540200,NM_015584.4;POLDIP2,upstream_gene_variant,,ENST00000618887,NM_001290145.1;CTB-96E2.2,downstream_gene_variant,,ENST00000555059,;SEBOX,downstream_gene_variant,,ENST00000536498,NM_001080837.3;TMEM199,upstream_gene_variant,,ENST00000585070,;CTB-96E2.7,downstream_gene_variant,,ENST00000577850,;CTB-96E2.3,non_coding_transcript_exon_variant,,ENST00000591482,;TMEM199,non_coding_transcript_exon_variant,,ENST00000581386,;SARM1,upstream_gene_variant,,ENST00000379061,;TMEM199,downstream_gene_variant,,ENST00000579762,;TMEM199,synonymous_variant,p.=,ENST00000555264,;TMEM199,3_prime_UTR_variant,,ENST00000580868,;TMEM199,non_coding_transcript_exon_variant,,ENST00000483505,;TMEM199,non_coding_transcript_exon_variant,,ENST00000509083,;TMEM199,upstream_gene_variant,,ENST00000585027,; T ENST00000292114 Transcript synonymous_variant 420/3148 330/627 110/208 L ctG/ctT 1 1 TMEM199 HGNC HGNC:18085 protein_coding YES CCDS11228.1 ENSP00000292114 Q8N511 UPI0000039EBA NM_152464.2 3/6 hmmpanther:PTHR31394,hmmpanther:PTHR31394:SF1,Pfam_domain:PF11712 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 28359359 28359359 G T 1 0 0 0 0 0 0 0 1 16560 1335 47 2 2 TMEM199 17 28359359 Silent SNP G C3N-00551_T 7463610 28359359 54898082 500 15983 ASIC2 0 . GRCh38 17 33291705 33291705 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.411C>A p.Asn137Lys p.N137K ENST00000225823 1/10 172 124 48 197 197 0 strelka-varscan-mutect ASIC2,missense_variant,p.Asn137Lys,ENST00000225823,NM_183377.1;ASIC2,intron_variant,,ENST00000359872,NM_001094.4;ASIC2,upstream_gene_variant,,ENST00000448983,;ASIC2,upstream_gene_variant,,ENST00000579816,; T ENST00000225823 Transcript missense_variant 1284/3443 411/1692 137/563 N/K aaC/aaA 1 -1 ASIC2 HGNC HGNC:99 protein_coding YES CCDS11276.1 ENSP00000225823 Q16515 UPI000013C881 NM_183377.1 deleterious(0) 1/10 hmmpanther:PTHR11690:SF128,hmmpanther:PTHR11690,Gene3D:2qtsA02,Pfam_domain:PF00858,Prints_domain:PR01078 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 33291705 33291705 G T 1 0 0 0 0 1 0 0 0 1186 1368 48 2 2 ASIC2 17 33291705 Missense_Mutation SNP G C3N-00551_T 4932346 33291705 49965736 501 15984 KRT10 0 . GRCh38 17 40820535 40820535 + Silent SNP G G T rs201038946 C3N-00551_T C3N-00551_N G G c.843C>A p.= p.A281A ENST00000269576 3/8 472 368 104 481 481 0 strelka-varscan-mutect KRT10,synonymous_variant,p.=,ENST00000269576,NM_000421.3;TMEM99,intron_variant,,ENST00000622451,NM_001195386.1;TMEM99,intron_variant,,ENST00000301665,NM_001195387.1,NM_145274.3;TMEM99,intron_variant,,ENST00000436612,;KRT10,upstream_gene_variant,,ENST00000635956,;TMEM99,intron_variant,,ENST00000496847,; T ENST00000269576 Transcript synonymous_variant 853/2124 843/1755 281/584 A gcC/gcA rs201038946 1 -1 KRT10 HGNC HGNC:6413 protein_coding YES CCDS11377.1 ENSP00000269576 P13645 UPI000013D842 NM_000421.3 3/8 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF137,SMART_domains:SM01391,Superfamily_domains:SSF46579 LOW 1 SNV 1 1 PASS rs201038946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 40820535 40820535 G T 1 0 0 0 0 0 0 0 1 8330 987 35 2 2 KRT10 17 40820535 Silent SNP G C3N-00551_T 7528830 40820535 42436906 502 15985 EFTUD2 0 . GRCh38 17 44862900 44862900 + Frame_Shift_Del DEL G G - novel C3N-00551_T C3N-00551_N G G c.1420delC p.Leu474Ter p.L474* ENST00000426333 16/28 77 59 18 65 65 0 sindel-varindel-pindel EFTUD2,frameshift_variant,p.Leu474Ter,ENST00000426333,NM_004247.3;EFTUD2,frameshift_variant,p.Leu474Ter,ENST00000591382,NM_001258353.1;EFTUD2,frameshift_variant,p.Leu464Ter,ENST00000592576,NM_001258354.1;EFTUD2,frameshift_variant,p.Leu439Ter,ENST00000402521,NM_001142605.1;EFTUD2,non_coding_transcript_exon_variant,,ENST00000585616,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586276,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590367,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586654,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000585794,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000587914,;EFTUD2,upstream_gene_variant,,ENST00000590977,;EFTUD2,downstream_gene_variant,,ENST00000591856,; - ENST00000426333 Transcript frameshift_variant 1718/4548 1420/2919 474/972 L/X Ctg/tg 1 -1 EFTUD2 HGNC HGNC:30858 protein_coding YES CCDS11489.1 ENSP00000392094 Q15029 UPI0000137931 NM_004247.3 16/28 hmmpanther:PTHR23115:SF5,hmmpanther:PTHR23115,Gene3D:2.40.30.10,Superfamily_domains:SSF50447 HIGH 1 deletion 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 - 7 5 52 44862900 44862900 G - 1 0 1 0 1 0 0 0 0 4797 991 35 0 0 EFTUD2 17 44862900 Frame_Shift_Del DEL G C3N-00551_T 4042365 44862900 38394541 503 15986 KANSL1 0 . GRCh38 17 46172111 46172111 + Silent SNP T T A rs769676607 C3N-00551_T C3N-00551_N T T c.33A>T p.= p.A11A ENST00000262419 2/15 197 181 16 161 161 0 strelka-varscan-mutect KANSL1,synonymous_variant,p.=,ENST00000262419,NM_001193466.1;KANSL1,synonymous_variant,p.=,ENST00000574590,;KANSL1,synonymous_variant,p.=,ENST00000432791,NM_001193465.1;KANSL1,synonymous_variant,p.=,ENST00000572904,NM_015443.3;KANSL1,synonymous_variant,p.=,ENST00000575318,;KANSL1,synonymous_variant,p.=,ENST00000574655,;KANSL1,synonymous_variant,p.=,ENST00000571698,;KANSL1,downstream_gene_variant,,ENST00000576739,;KANSL1,upstream_gene_variant,,ENST00000576248,;KANSL1,upstream_gene_variant,,ENST00000577114,; A ENST00000262419 Transcript synonymous_variant 504/5309 33/3318 11/1105 A gcA/gcT rs769676607 1 -1 KANSL1 HGNC HGNC:24565 protein_coding YES CCDS11503.2 ENSP00000262419 Q7Z3B3 A0A024R9Y2 UPI000013D2AE NM_001193466.1 2/15 Low_complexity_(Seg):seg,hmmpanther:PTHR22443:SF14,hmmpanther:PTHR22443 LOW 1 SNV 1 1 PASS rs769676607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 46172111 46172111 T A 1 0 0 0 0 0 0 0 1 7889 1567 55 4 4 KANSL1 17 46172111 Silent SNP T C3N-00551_T 1309211 46172111 37085330 504 15987 HOXB5 0 . GRCh38 17 48593585 48593585 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.98C>A p.Ser33Tyr p.S33Y ENST00000239151 1/2 243 209 34 220 220 0 strelka-varscan-mutect HOXB5,missense_variant,p.Ser33Tyr,ENST00000239151,NM_002147.3;HOXB3,upstream_gene_variant,,ENST00000498678,;HOXB6,downstream_gene_variant,,ENST00000484302,;HOXB3,upstream_gene_variant,,ENST00000472863,;HOXB6,downstream_gene_variant,,ENST00000225648,NM_018952.4;HOXB3,upstream_gene_variant,,ENST00000460160,;HOXB3,upstream_gene_variant,,ENST00000476342,;HOXB-AS3,intron_variant,,ENST00000474040,;HOXB-AS3,intron_variant,,ENST00000476204,;HOXB-AS3,intron_variant,,ENST00000467155,;HOXB-AS3,intron_variant,,ENST00000480872,;HOXB-AS3,intron_variant,,ENST00000429755,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS3,intron_variant,,ENST00000487849,;HOXB-AS3,intron_variant,,ENST00000492897,;HOXB-AS3,upstream_gene_variant,,ENST00000477144,;HOXB-AS3,upstream_gene_variant,,ENST00000460041,;HOXB-AS3,upstream_gene_variant,,ENST00000481995,;HOXB-AS3,upstream_gene_variant,,ENST00000466037,;HOXB-AS3,upstream_gene_variant,,ENST00000474324,;HOXB3,intron_variant,,ENST00000552000,;HOXB6,downstream_gene_variant,,ENST00000490419,;HOXB6,downstream_gene_variant,,ENST00000470193,; T ENST00000239151 Transcript missense_variant 377/2041 98/810 33/269 S/Y tCt/tAt 1 -1 HOXB5 HGNC HGNC:5116 protein_coding YES CCDS11530.1 ENSP00000239151 P09067 UPI000012CF58 NM_002147.3 deleterious(0.04) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF165,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 48593585 48593585 G T 1 0 0 0 0 1 0 0 0 7198 942 33 2 2 HOXB5 17 48593585 Missense_Mutation SNP G C3N-00551_T 2421474 48593585 34663856 505 15988 DLX4 0 . GRCh38 17 49973098 49973098 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.309G>A p.= p.P103P ENST00000240306 2/3 292 270 22 258 258 0 strelka-varscan-mutect DLX4,synonymous_variant,p.=,ENST00000240306,NM_138281.2;DLX4,synonymous_variant,p.=,ENST00000611342,;DLX4,synonymous_variant,p.=,ENST00000411890,NM_001934.3;DLX4,non_coding_transcript_exon_variant,,ENST00000503276,;DLX4,non_coding_transcript_exon_variant,,ENST00000503410,;DLX4,downstream_gene_variant,,ENST00000505318,; A ENST00000240306 Transcript synonymous_variant 604/2034 309/723 103/240 P ccG/ccA 1 1 DLX4 HGNC HGNC:2917 protein_coding YES CCDS11555.1 ENSP00000240306 Q92988 UPI0000070F94 NM_138281.2 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24327:SF21,hmmpanther:PTHR24327,Gene3D:1.10.10.60 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 49973098 49973098 G A 1 0 0 0 0 0 0 0 1 4380 1103 39 1 1 DLX4 17 49973098 Silent SNP G C3N-00551_T 1379513 49973098 33284343 506 15989 KIF2B 0 . GRCh38 17 53823911 53823911 + Missense_Mutation SNP G G T rs370500459 C3N-00551_T C3N-00551_N G G c.878G>T p.Arg293Leu p.R293L ENST00000268919 1/1 247 209 38 268 267 1 strelka-varscan-mutect KIF2B,missense_variant,p.Arg293Leu,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 1011/2313 878/2022 293/673 R/L cGc/cTc rs370500459,COSM1212455 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 deleterious(0) 1/1 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 0,1 1 PASS rs370500459 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 53823911 53823911 G T 1 0 0 0 0 1 0 0 0 8163 1087 38 1 1 KIF2B 17 53823911 Missense_Mutation SNP G C3N-00551_T 3850813 53823911 29433530 507 15990 RNF43 0 . GRCh38 17 58363284 58363284 + Silent SNP G G A C3N-00551_T C3N-00551_N G G c.573C>T p.= p.P191P ENST00000584437 4/9 161 130 31 154 154 0 strelka-varscan-mutect RNF43,synonymous_variant,p.=,ENST00000584437,;RNF43,synonymous_variant,p.=,ENST00000407977,;RNF43,synonymous_variant,p.=,ENST00000577716,NM_017763.4;RNF43,synonymous_variant,p.=,ENST00000583753,;RNF43,synonymous_variant,p.=,ENST00000581868,;RNF43,synonymous_variant,p.=,ENST00000577625,;TSPOAP1-AS1,intron_variant,,ENST00000583841,;RNF43,non_coding_transcript_exon_variant,,ENST00000582293,; A ENST00000584437 Transcript synonymous_variant 2529/5575 573/2352 191/783 P ccC/ccT COSM981866 1 -1 RNF43 HGNC HGNC:18505 protein_coding YES CCDS11607.1 ENSP00000463069 Q68DV7 UPI000022A469 4/9 hmmpanther:PTHR16200,hmmpanther:PTHR16200:SF2 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 58363284 58363284 G A 1 0 0 0 0 0 0 0 1 13675 1219 43 3 3 RNF43 17 58363284 Silent SNP G C3N-00551_T 4539373 58363284 24894157 508 15991 TANC2 0 . GRCh38 17 63415566 63415566 + Silent SNP C C T rs191181540 C3N-00551_T C3N-00551_N C C c.3807C>T p.= p.Y1269Y ENST00000424789 23/25 255 228 27 263 263 0 strelka-varscan-mutect TANC2,synonymous_variant,p.=,ENST00000424789,NM_025185.3;TANC2,synonymous_variant,p.=,ENST00000583356,;TANC2,synonymous_variant,p.=,ENST00000389520,;TANC2,synonymous_variant,p.=,ENST00000613171,;RP11-269G24.3,intron_variant,,ENST00000583552,;AC015923.1,upstream_gene_variant,,ENST00000431604,;TANC2,non_coding_transcript_exon_variant,,ENST00000579541,; T ENST00000424789 Transcript synonymous_variant 3811/11721 3807/5973 1269/1990 Y taC/taT rs191181540,COSM706511,COSM706512 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 23/25 Gene3D:1.25.40.10,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21,SMART_domains:SM00028,Superfamily_domains:SSF48452 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs191181540 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 63415566 63415566 C T 1 0 0 0 0 0 0 0 1 15942 547 19 1 1 TANC2 17 63415566 Silent SNP C C3N-00551_T 5052282 63415566 19841875 509 15992 ABCA5 0 . GRCh38 17 69286025 69286025 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.2145C>G p.Asp715Glu p.D715E ENST00000392676 17/39 97 84 13 110 110 0 strelka-varscan-mutect ABCA5,missense_variant,p.Asp715Glu,ENST00000392676,NM_172232.3;ABCA5,missense_variant,p.Asp715Glu,ENST00000588877,NM_018672.4;ABCA5,missense_variant,p.Asp715Glu,ENST00000593153,;ABCA5,missense_variant,p.Asp386Glu,ENST00000586995,;ABCA5,missense_variant,p.Asp18Glu,ENST00000591234,; C ENST00000392676 Transcript missense_variant 2210/8220 2145/4929 715/1642 D/E gaC/gaG 1 -1 ABCA5 HGNC HGNC:35 protein_coding YES CCDS11685.1 ENSP00000376443 Q8WWZ7 UPI000013DD9E NM_172232.3 tolerated(0.12) 17/39 hmmpanther:PTHR19229:SF100,hmmpanther:PTHR19229 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 69286025 69286025 G C 1 0 0 0 0 1 0 0 0 39 1368 48 4 4 ABCA5 17 69286025 Missense_Mutation SNP G C3N-00551_T 5870459 69286025 13971416 510 15993 DNAI2 0 . GRCh38 17 74289728 74289728 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.602G>T p.Trp201Leu p.W201L ENST00000446837 4/13 274 238 36 256 256 0 strelka-varscan-mutect DNAI2,missense_variant,p.Trp258Leu,ENST00000579490,;DNAI2,missense_variant,p.Trp201Leu,ENST00000446837,;DNAI2,missense_variant,p.Trp201Leu,ENST00000582036,NM_001172810.1;DNAI2,missense_variant,p.Trp201Leu,ENST00000311014,NM_023036.4;DNAI2,synonymous_variant,p.=,ENST00000579055,; T ENST00000446837 Transcript missense_variant 908/2474 602/1818 201/605 W/L tGg/tTg 1 1 DNAI2 HGNC HGNC:18744 protein_coding YES CCDS11697.1 ENSP00000400252 Q9GZS0 UPI000013EC1D deleterious(0) 4/13 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF7,hmmpanther:PTHR12442,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 74289728 74289728 G T 1 0 0 0 0 1 0 0 0 4425 1357 47 2 2 DNAI2 17 74289728 Missense_Mutation SNP G C3N-00551_T 5003703 74289728 8967713 511 15994 BTBD17 0 . GRCh38 17 74357250 74357250 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.844G>A p.Val282Met p.V282M ENST00000375366 3/3 164 108 56 208 208 0 strelka-varscan-mutect BTBD17,missense_variant,p.Val282Met,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000389916,NM_153209.3;KIF19,downstream_gene_variant,,ENST00000551294,; T ENST00000375366 Transcript missense_variant 971/1805 844/1437 282/478 V/M Gtg/Atg 1 -1 BTBD17 HGNC HGNC:33758 protein_coding YES CCDS32719.1 ENSP00000364515 A6NE02 UPI00001D7961 NM_001080466.1 deleterious(0.02) 3/3 hmmpanther:PTHR24410:SF12,hmmpanther:PTHR24410 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 74357250 74357250 C T 1 0 0 0 0 1 0 0 0 1716 507 18 3 3 BTBD17 17 74357250 Missense_Mutation SNP C C3N-00551_T 67522 74357250 8900191 512 15995 GPR142 0 . GRCh38 17 74371865 74371865 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.654G>T p.Gln218His p.Q218H ENST00000335666 4/4 250 223 27 188 188 0 strelka-varscan-mutect GPR142,missense_variant,p.Gln218His,ENST00000335666,NM_181790.1;GPR142,3_prime_UTR_variant,,ENST00000582579,;GPR142,downstream_gene_variant,,ENST00000585308,; T ENST00000335666 Transcript missense_variant 702/1437 654/1389 218/462 Q/H caG/caT 1 1 GPR142 HGNC HGNC:20088 protein_coding YES CCDS11698.1 ENSP00000335158 Q7Z601 UPI00001AA7F1 NM_181790.1 deleterious(0.03) 4/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF48,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 74371865 74371865 G T 1 0 0 0 0 1 0 0 0 6536 991 35 2 2 GPR142 17 74371865 Missense_Mutation SNP G C3N-00551_T 14615 74371865 8885576 513 15996 UBE2O 0 . GRCh38 17 76402075 76402075 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.739G>T p.Val247Phe p.V247F ENST00000319380 5/18 151 133 18 182 182 0 strelka-varscan-mutect UBE2O,missense_variant,p.Val247Phe,ENST00000319380,NM_022066.3;UBE2O,missense_variant,p.Val32Phe,ENST00000590658,;UBE2O,upstream_gene_variant,,ENST00000587127,;UBE2O,upstream_gene_variant,,ENST00000587581,;UBE2O,non_coding_transcript_exon_variant,,ENST00000586409,;UBE2O,non_coding_transcript_exon_variant,,ENST00000586505,; A ENST00000319380 Transcript missense_variant 804/5436 739/3879 247/1292 V/F Gtc/Ttc 1 -1 UBE2O HGNC HGNC:29554 protein_coding YES CCDS32742.1 ENSP00000323687 Q9C0C9 UPI000020032F NM_022066.3 deleterious(0.01) 5/18 MODERATE 1 SNV 1 1 PASS rs1257815392 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 76402075 76402075 C A 1 0 0 0 0 1 0 0 0 17389 536 19 1 1 UBE2O 17 76402075 Missense_Mutation SNP C C3N-00551_T 2030210 76402075 6855366 514 15997 TNRC6C 0 . GRCh38 17 78051078 78051078 + Silent SNP A A G novel C3N-00551_T C3N-00551_N A A c.2016A>G p.= p.Q672Q ENST00000335749 3/21 55 50 5 55 55 0 strelka-varscan-mutect TNRC6C,synonymous_variant,p.=,ENST00000335749,NM_001142640.1;TNRC6C,synonymous_variant,p.=,ENST00000301624,NM_018996.3;TNRC6C,synonymous_variant,p.=,ENST00000588847,;TNRC6C,synonymous_variant,p.=,ENST00000588061,;TNRC6C,synonymous_variant,p.=,ENST00000636222,;TNRC6C,intron_variant,,ENST00000585438,;TNRC6C,downstream_gene_variant,,ENST00000588549,;TNRC6C,non_coding_transcript_exon_variant,,ENST00000591851,; G ENST00000335749 Transcript synonymous_variant 2585/9740 2016/5181 672/1726 Q caA/caG 1 1 TNRC6C HGNC HGNC:29318 protein_coding YES CCDS45799.1 ENSP00000336783 Q9HCJ0 UPI0000EE5F80 NM_001142640.1 3/21 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF9 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -12.52834 1 1 1 1 0 G 2 3 52 78051078 78051078 A G 1 0 0 0 0 0 0 0 1 16815 69 3 5 5 TNRC6C 17 78051078 Silent SNP A C3N-00551_T 1649003 78051078 5206363 515 15998 CEP131 0 . GRCh38 17 81199428 81199428 + Missense_Mutation SNP G G T rs573986931 C3N-00551_T C3N-00551_N G G c.1145C>A p.Pro382His p.P382H ENST00000450824 10/26 214 188 26 218 218 0 strelka-varscan-mutect CEP131,missense_variant,p.Pro382His,ENST00000269392,NM_001319228.1;CEP131,missense_variant,p.Pro382His,ENST00000450824,NM_014984.2;CEP131,missense_variant,p.Pro382His,ENST00000374782,NM_001319229.1,NM_001009811.2;CEP131,missense_variant,p.Pro382His,ENST00000575907,;CEP131,upstream_gene_variant,,ENST00000573053,;RP11-455O6.2,intron_variant,,ENST00000571085,;CEP131,downstream_gene_variant,,ENST00000570482,; T ENST00000450824 Transcript missense_variant 1324/3543 1145/3243 382/1080 P/H cCc/cAc rs573986931 1 -1 CEP131 HGNC HGNC:29511 protein_coding YES CCDS45808.1 ENSP00000393583 Q9UPN4 UPI00002017B6 NM_014984.2 tolerated(0.12) 10/26 hmmpanther:PTHR31540,hmmpanther:PTHR31540:SF1 MODERATE 1 SNV 1 1 PASS rs573986931 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 81199428 81199428 G T 1 0 0 0 0 1 0 0 0 2959 1232 43 2 2 CEP131 17 81199428 Missense_Mutation SNP G C3N-00551_T 3148350 81199428 2058013 516 15999 FAAP100 0 . GRCh38 17 81547972 81547972 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.57G>T p.Trp19Cys p.W19C ENST00000425898 1/5 180 150 30 155 155 0 strelka-varscan-mutect FAAP100,missense_variant,p.Trp19Cys,ENST00000425898,;FAAP100,intron_variant,,ENST00000327787,NM_025161.5;FAAP100,downstream_gene_variant,,ENST00000541246,;FAAP100,downstream_gene_variant,,ENST00000544302,;FAAP100,downstream_gene_variant,,ENST00000536161,;FAAP100,intron_variant,,ENST00000443656,;FAAP100,upstream_gene_variant,,ENST00000545865,; A ENST00000425898 Transcript missense_variant 527/2996 57/1593 19/530 W/C tgG/tgT 1 -1 FAAP100 HGNC HGNC:26171 protein_coding ENSP00000399674 E7EVV8 UPI0001AE66C4 1/5 MODERATE SNV 1 1 PASS rs1159837642 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 52 81547972 81547972 C A 1 0 0 0 0 1 0 0 0 5224 740 26 2 2 FAAP100 17 81547972 Missense_Mutation SNP C C3N-00551_T 348544 81547972 1709469 517 16000 FASN 0 . GRCh38 17 82091577 82091577 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1137G>T p.Gln379His p.Q379H ENST00000306749 9/43 374 282 92 319 319 0 strelka-varscan-mutect FASN,missense_variant,p.Gln379His,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Gln379His,ENST00000634990,;FASN,downstream_gene_variant,,ENST00000635197,;FASN,downstream_gene_variant,,ENST00000636968,;FASN,downstream_gene_variant,,ENST00000637026,;FASN,downstream_gene_variant,,ENST00000637525,;FASN,downstream_gene_variant,,ENST00000635733,; A ENST00000306749 Transcript missense_variant 1356/8565 1137/7536 379/2511 Q/H caG/caT 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 deleterious(0.01) 9/43 Gene3D:3.40.47.10,Pfam_domain:PF16197,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,SMART_domains:SM00825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 82091577 82091577 C A 1 0 0 0 0 1 0 0 0 5543 796 28 2 2 FASN 17 82091577 Missense_Mutation SNP C C3N-00551_T 543605 82091577 1165864 518 16001 PIEZO2 0 . GRCh38 18 10773552 10773552 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2570G>T p.Arg857Met p.R857M ENST00000503781 18/52 414 363 51 495 495 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Arg806Met,ENST00000383408,;PIEZO2,missense_variant,p.Arg857Met,ENST00000302079,;PIEZO2,missense_variant,p.Arg882Met,ENST00000580640,;PIEZO2,missense_variant,p.Arg857Met,ENST00000503781,NM_022068.3;PIEZO2,missense_variant,p.Arg186Met,ENST00000583325,;PIEZO2,missense_variant,p.Arg871Met,ENST00000582913,;PIEZO2,non_coding_transcript_exon_variant,,ENST00000578145,; A ENST00000503781 Transcript missense_variant 2570/8259 2570/8259 857/2752 R/M aGg/aTg 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0.02) 18/52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 10773552 10773552 C A 1 0 0 0 0 1 0 0 0 11975 681 24 2 2 PIEZO2 18 10773552 Missense_Mutation SNP C C3N-00551_T 10773552 69599733 519 16002 SEH1L 0 . GRCh38 18 12963259 12963259 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.409G>T p.Gly137Cys p.G137C ENST00000399892 4/9 313 273 40 370 370 0 strelka-varscan-mutect SEH1L,missense_variant,p.Gly137Cys,ENST00000262124,NM_031216.3;SEH1L,missense_variant,p.Gly137Cys,ENST00000399892,NM_001013437.1;SEH1L,missense_variant,p.Gly137Cys,ENST00000587761,;SEH1L,missense_variant,p.Gly120Cys,ENST00000589446,;SEH1L,missense_variant,p.Gly88Cys,ENST00000585730,;SEH1L,non_coding_transcript_exon_variant,,ENST00000588251,; T ENST00000399892 Transcript missense_variant 510/1846 409/1266 137/421 G/C Ggt/Tgt 1 1 SEH1L HGNC HGNC:30379 protein_coding YES CCDS32791.1 ENSP00000382779 Q96EE3 UPI0000070285 NM_001013437.1 deleterious(0.02) 4/9 PROSITE_profiles:PS50294,hmmpanther:PTHR11024,hmmpanther:PTHR11024:SF3,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1380810925 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 12963259 12963259 G T 1 0 0 0 0 1 0 0 0 14286 1348 47 2 2 SEH1L 18 12963259 Missense_Mutation SNP G C3N-00551_T 2189707 12963259 67410026 520 16003 DSG1 0 . GRCh38 18 31343965 31343965 + Missense_Mutation SNP G G A rs398122400 C3N-00551_T C3N-00551_N G G c.1861G>A p.Ala621Thr p.A621T ENST00000257192 13/15 251 234 17 304 304 0 strelka-varscan-mutect DSG1,missense_variant,p.Ala621Thr,ENST00000257192,NM_001942.3;DSG1,5_prime_UTR_variant,,ENST00000462981,;RNU6-167P,downstream_gene_variant,,ENST00000384292,;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578119,;DSG1-AS1,downstream_gene_variant,,ENST00000578477,; A ENST00000257192 Transcript missense_variant 2073/5045 1861/3150 621/1049 A/T Gca/Aca rs398122400,COSM4751823 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 tolerated(0.16) 13/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9 pathogenic 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs1361944257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 31343965 31343965 G A 1 0 0 0 0 1 0 0 0 4597 1087 38 1 1 DSG1 18 31343965 Missense_Mutation SNP G C3N-00551_T 18380706 31343965 49029320 521 16004 DSG4 0 . GRCh38 18 31399290 31399290 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1024G>T p.Ala342Ser p.A342S ENST00000359747 9/15 199 168 31 260 260 0 strelka-varscan-mutect DSG4,missense_variant,p.Ala342Ser,ENST00000359747,NM_001134453.1;DSG4,missense_variant,p.Ala342Ser,ENST00000308128,NM_177986.3;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578477,;DSG1-AS1,intron_variant,,ENST00000581452,; T ENST00000359747 Transcript missense_variant 1053/4526 1024/3180 342/1059 A/S Gca/Tca COSM708113,COSM708114 1 1 DSG4 HGNC HGNC:21307 protein_coding YES CCDS45845.1 ENSP00000352785 Q86SJ6 UPI000035DB4E NM_001134453.1 deleterious(0.02) 9/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF10,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 31399290 31399290 G T 1 0 0 0 0 1 0 0 0 4600 971 34 2 2 DSG4 18 31399290 Missense_Mutation SNP G C3N-00551_T 55325 31399290 48973995 522 16005 RIT2 0 . GRCh38 18 43115431 43115431 + Frame_Shift_Del DEL C C - novel C3N-00551_T C3N-00551_N C C c.89delG p.Gly30GlufsTer7 p.G30Efs*7 ENST00000326695 1/5 93 75 18 216 216 0 sindel-varindel RIT2,frameshift_variant,p.Gly30GlufsTer7,ENST00000589109,NM_001272077.1;RIT2,frameshift_variant,p.Gly30GlufsTer7,ENST00000326695,NM_002930.3;RIT2,frameshift_variant,p.Gly30GlufsTer7,ENST00000590910,; - ENST00000326695 Transcript frameshift_variant 261/1092 89/654 30/217 G/X gGa/ga 1 -1 RIT2 HGNC HGNC:10017 protein_coding YES CCDS11921.1 ENSP00000321805 Q99578 UPI0000073E97 NM_002930.3 1/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF203,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 52 43115431 43115431 C - 1 0 1 0 1 0 0 0 0 13562 855 30 0 0 RIT2 18 43115431 Frame_Shift_Del DEL C C3N-00551_T 11716141 43115431 37257854 523 16006 ST8SIA5 0 . GRCh38 18 46756449 46756449 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.60C>A p.Phe20Leu p.F20L ENST00000538168 1/8 313 270 43 364 363 1 strelka-varscan-mutect ST8SIA5,missense_variant,p.Phe20Leu,ENST00000538168,NM_001307986.1;ST8SIA5,missense_variant,p.Phe20Leu,ENST00000315087,NM_013305.4;ST8SIA5,missense_variant,p.Phe20Leu,ENST00000536490,NM_001307987.1;RP11-742D12.2,upstream_gene_variant,,ENST00000602333,;RP11-742D12.2,upstream_gene_variant,,ENST00000602329,;RP11-742D12.2,upstream_gene_variant,,ENST00000624895,;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000588155,;ST8SIA5,intron_variant,,ENST00000590488,;ST8SIA5,intron_variant,,ENST00000591375,; T ENST00000538168 Transcript missense_variant 361/13761 60/1239 20/412 F/L ttC/ttA 1 -1 ST8SIA5 HGNC HGNC:17827 protein_coding YES CCDS77184.1 ENSP00000445492 O15466 UPI0000E03E3B NM_001307986.1 1/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11987:SF4,hmmpanther:PTHR11987,PIRSF_domain:PIRSF005557 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 46756449 46756449 G T 1 0 0 0 0 1 0 0 0 15613 1281 45 2 2 ST8SIA5 18 46756449 Missense_Mutation SNP G C3N-00551_T 3641018 46756449 33616836 524 16007 DYM 0 . GRCh38 18 49272247 49272247 + Silent SNP C C A rs866648614 C3N-00551_T C3N-00551_N C C c.1182G>T p.= p.V394V ENST00000269445 11/17 168 149 19 196 196 0 strelka-varscan-mutect DYM,synonymous_variant,p.=,ENST00000269445,NM_017653.3;DYM,synonymous_variant,p.=,ENST00000442713,; A ENST00000269445 Transcript synonymous_variant 1640/5049 1182/2010 394/669 V gtG/gtT rs866648614 1 -1 DYM HGNC HGNC:21317 protein_coding YES CCDS11937.1 ENSP00000269445 Q7RTS9 UPI00001AE953 NM_017653.3 11/17 hmmpanther:PTHR12895:SF9,hmmpanther:PTHR12895,Pfam_domain:PF09742 LOW 1 SNV 1 1 PASS rs866648614 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 49272247 49272247 C A 1 0 0 0 0 0 0 0 1 4663 465 17 2 2 DYM 18 49272247 Silent SNP C C3N-00551_T 2515798 49272247 31101038 525 16008 MYO5B 0 . GRCh38 18 49974584 49974584 + Missense_Mutation SNP C C A rs369568383 C3N-00551_T C3N-00551_N C C c.1088G>T p.Arg363Leu p.R363L ENST00000285039 10/40 158 136 22 166 166 0 strelka-varscan-mutect MYO5B,missense_variant,p.Arg363Leu,ENST00000285039,NM_001080467.2;RP11-813F20.4,upstream_gene_variant,,ENST00000591362,; A ENST00000285039 Transcript missense_variant 1388/9505 1088/5547 363/1848 R/L cGa/cTa rs369568383 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 deleterious(0.02) 10/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs369568383 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 49974584 49974584 C A 1 0 0 0 0 1 0 0 0 10080 884 31 1 1 MYO5B 18 49974584 Missense_Mutation SNP C C3N-00551_T 702337 49974584 30398701 526 16009 SERPINB13 0 . GRCh38 18 63597256 63597256 + Missense_Mutation SNP T T A rs771813572 C3N-00551_T C3N-00551_N T T c.1096T>A p.Ser366Thr p.S366T ENST00000269489 8/8 185 159 26 257 257 0 strelka-varscan-mutect SERPINB13,missense_variant,p.Ser366Thr,ENST00000269489,NM_001307923.1;SERPINB13,missense_variant,p.Ser357Thr,ENST00000344731,NM_012397.3;SERPINB13,intron_variant,,ENST00000415733,;SERPINB13,downstream_gene_variant,,ENST00000431153,;SERPINB13,3_prime_UTR_variant,,ENST00000438844,; A ENST00000269489 Transcript missense_variant 1264/3206 1096/1203 366/400 S/T Tcc/Acc rs771813572 1 1 SERPINB13 HGNC HGNC:8944 protein_coding YES CCDS77195.1 ENSP00000269489 A0A0A0MQW3 UPI000004EE0A NM_001307923.1 tolerated(0.1) 8/8 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF161,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs771813572 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 63597256 63597256 T A 1 0 0 0 0 1 0 0 0 14376 1435 50 4 4 SERPINB13 18 63597256 Missense_Mutation SNP T C3N-00551_T 13622672 63597256 16776029 527 16010 CCDC102B 0 . GRCh38 18 68837088 68837088 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.325G>T p.Val109Phe p.V109F ENST00000360242 2/8 310 264 46 361 361 0 strelka-varscan-mutect CCDC102B,missense_variant,p.Val109Phe,ENST00000360242,NM_001093729.1,NM_024781.2;CCDC102B,missense_variant,p.Val109Phe,ENST00000584156,;CCDC102B,missense_variant,p.Val109Phe,ENST00000584775,;CCDC102B,missense_variant,p.Val109Phe,ENST00000582371,;CCDC102B,missense_variant,p.Val109Phe,ENST00000581520,;CCDC102B,upstream_gene_variant,,ENST00000358653,;CCDC102B,downstream_gene_variant,,ENST00000578970,;CCDC102B,non_coding_transcript_exon_variant,,ENST00000577772,; T ENST00000360242 Transcript missense_variant 442/2711 325/1542 109/513 V/F Gtt/Ttt 1 1 CCDC102B HGNC HGNC:26295 protein_coding YES CCDS11996.2 ENSP00000353377 Q68D86 UPI0000201E87 NM_001093729.1,NM_024781.2 deleterious(0) 2/8 hmmpanther:PTHR13140:SF479,hmmpanther:PTHR13140 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 68837088 68837088 G T 1 0 0 0 0 1 0 0 0 2435 1029 36 2 2 CCDC102B 18 68837088 Missense_Mutation SNP G C3N-00551_T 5239832 68837088 11536197 528 16011 SALL3 0 . GRCh38 18 78993822 78993822 + Missense_Mutation SNP G G T C3N-00551_T C3N-00551_N G G c.1831G>T p.Ala611Ser p.A611S ENST00000537592 2/3 61 56 5 82 82 0 strelka-varscan-mutect SALL3,missense_variant,p.Ala611Ser,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Ala478Ser,ENST00000536229,;SALL3,missense_variant,p.Ala611Ser,ENST00000575389,;SALL3,missense_variant,p.Ala343Ser,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript missense_variant 1831/6555 1831/3903 611/1300 A/S Gct/Tct COSM1611428 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 tolerated(0.94) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 1 MODERATE 1 SNV 5 1 1 PASS rs1184749893 . 0 197 12 0 0 0 0 0 -11.47519 0.9997171 1 1 1 0 T 3 4 52 78993822 78993822 G T 1 0 0 0 0 1 0 0 0 14071 1087 38 1 1 SALL3 18 78993822 Missense_Mutation SNP G C3N-00551_T 10156734 78993822 1379463 529 16012 ZNRF4 0 . GRCh38 19 5455727 5455727 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.236C>A p.Ala79Asp p.A79D ENST00000222033 1/1 133 99 34 107 107 0 strelka-varscan-mutect ZNRF4,missense_variant,p.Ala79Asp,ENST00000222033,NM_181710.3; A ENST00000222033 Transcript missense_variant 297/1426 236/1290 79/429 A/D gCc/gAc 1 1 ZNRF4 HGNC HGNC:17726 protein_coding YES CCDS42475.1 ENSP00000222033 Q8WWF5 UPI0000366CF5 NM_181710.3 deleterious(0) 1/1 hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF49,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 5455727 5455727 C A 1 0 0 0 0 1 0 0 0 18806 739 26 2 2 ZNRF4 19 5455727 Missense_Mutation SNP C C3N-00551_T 5455727 53161889 530 16013 MUC16 0 . GRCh38 19 8948272 8948272 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.28498C>A p.Leu9500Met p.L9500M ENST00000397910 3/84 138 102 36 124 124 0 strelka-mutect MUC16,missense_variant,p.Leu9500Met,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 28702/43816 28498/43524 9500/14507 L/M Ctg/Atg 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 8948272 8948272 G T 1 0 0 0 0 1 0 0 0 9972 933 33 2 2 MUC16 19 8948272 Missense_Mutation SNP G C3N-00551_T 3492545 8948272 49669344 531 16014 MUC16 0 . GRCh38 19 8951081 8951081 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.25689C>A p.= p.S8563S ENST00000397910 3/84 129 94 35 128 128 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 25893/43816 25689/43524 8563/14507 S tcC/tcA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 8951081 8951081 G T 1 0 0 0 0 0 0 0 1 9972 987 35 2 2 MUC16 19 8951081 Silent SNP G C3N-00551_T 2809 8951081 49666535 532 16015 ZNF627 0 . GRCh38 19 11616987 11616987 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.484C>G p.Pro162Ala p.P162A ENST00000361113 4/4 159 149 10 206 206 0 strelka-varscan-mutect ZNF627,missense_variant,p.Pro162Ala,ENST00000361113,NM_001290084.1,NM_145295.3,NM_001290085.1;ZNF627,3_prime_UTR_variant,,ENST00000588174,;ZNF627,downstream_gene_variant,,ENST00000587939,;ZNF627,downstream_gene_variant,,ENST00000585493,; G ENST00000361113 Transcript missense_variant 692/2840 484/1386 162/461 P/A Cct/Gct 1 1 ZNF627 HGNC HGNC:30570 protein_coding YES CCDS42502.1 ENSP00000354414 Q7L945 UPI0000071491 NM_001290084.1,NM_145295.3,NM_001290085.1 deleterious(0.04) 4/4 hmmpanther:PTHR24379:SF30,hmmpanther:PTHR24379,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 11616987 11616987 C G 1 0 0 0 0 1 0 0 0 18626 855 30 4 4 ZNF627 19 11616987 Missense_Mutation SNP C C3N-00551_T 2665906 11616987 47000629 533 16016 KCNN1 0 . GRCh38 19 17982114 17982114 + Missense_Mutation SNP C C A rs774227733 C3N-00551_T C3N-00551_N C C c.904C>A p.Arg302Ser p.R302S ENST00000222249 5/11 46 40 6 61 61 0 strelka-varscan-mutect KCNN1,missense_variant,p.Arg302Ser,ENST00000222249,NM_002248.4;KCNN1,missense_variant,p.Arg302Ser,ENST00000615435,; A ENST00000222249 Transcript missense_variant 1223/3625 904/1632 302/543 R/S Cgc/Agc rs774227733,COSM5066699,COSM5066700 1 1 KCNN1 HGNC HGNC:6290 protein_coding YES CCDS67611.1 ENSP00000476519 Q92952 UPI00001649F9 NM_002248.4 tolerated(0.07) 5/11 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF38,Gene3D:1.10.287.70,Pfam_domain:PF07885,Superfamily_domains:SSF81324 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs774227733 . 0 197 12 0 0 0 0 0 -14.45965 0.9998882 1 1 1 0 A 3 1 52 17982114 17982114 C A 1 0 0 0 0 1 0 0 0 7994 768 27 1 1 KCNN1 19 17982114 Missense_Mutation SNP C C3N-00551_T 6365127 17982114 40635502 534 16017 ZNF99 0 . GRCh38 19 22769301 22769301 + Silent SNP C C G novel C3N-00551_T C3N-00551_N C C c.27G>C p.= p.V9V ENST00000596209 2/4 129 96 33 196 196 0 strelka-varscan-mutect ZNF99,synonymous_variant,p.=,ENST00000596209,NM_001080409.2;ZNF99,synonymous_variant,p.=,ENST00000397104,;BNIP3P34,upstream_gene_variant,,ENST00000600724,;CTB-159G17.3,upstream_gene_variant,,ENST00000604384,;CTB-159G17.4,upstream_gene_variant,,ENST00000624425,; G ENST00000596209 Transcript synonymous_variant 118/7817 27/2595 9/864 V gtG/gtC 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24375:SF187,hmmpanther:PTHR24375,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 52 22769301 22769301 C G 1 0 0 0 0 0 0 0 1 18797 813 29 4 4 ZNF99 19 22769301 Silent SNP C C3N-00551_T 4787187 22769301 35848315 535 16018 ZNF91 0 . GRCh38 19 23359758 23359758 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.3221G>T p.Arg1074Ile p.R1074I ENST00000300619 4/4 149 115 34 207 206 1 strelka-varscan-mutect ZNF91,missense_variant,p.Arg1074Ile,ENST00000300619,NM_003430.3;ZNF91,missense_variant,p.Arg1042Ile,ENST00000397082,NM_001300951.1;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000596528,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000593341,; A ENST00000300619 Transcript missense_variant 3427/5489 3221/3576 1074/1191 R/I aGa/aTa 1 -1 ZNF91 HGNC HGNC:13166 protein_coding YES CCDS42541.1 ENSP00000300619 Q05481 UPI00002038F9 NM_003430.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF195,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 23359758 23359758 C A 1 0 0 0 0 1 0 0 0 18793 913 32 2 2 ZNF91 19 23359758 Missense_Mutation SNP C C3N-00551_T 590457 23359758 35257858 536 16019 KIRREL2 0 . GRCh38 19 35866374 35866374 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.2009T>C p.Phe670Ser p.F670S ENST00000360202 15/15 160 119 41 307 307 0 strelka-varscan-mutect KIRREL2,missense_variant,p.Phe670Ser,ENST00000360202,NM_199180.3;KIRREL2,missense_variant,p.Phe635Ser,ENST00000592409,;KIRREL2,intron_variant,,ENST00000347900,NM_199179.3;KIRREL2,intron_variant,,ENST00000262625,NM_032123.6;APLP1,upstream_gene_variant,,ENST00000221891,NM_005166.3,NM_001024807.1;APLP1,upstream_gene_variant,,ENST00000537454,;APLP1,upstream_gene_variant,,ENST00000586861,;APLP1,upstream_gene_variant,,ENST00000592316,;APLP1,upstream_gene_variant,,ENST00000589743,;NPHS1,intron_variant,,ENST00000591817,;APLP1,upstream_gene_variant,,ENST00000590561,; C ENST00000360202 Transcript missense_variant 2207/2942 2009/2127 670/708 F/S tTc/tCc 1 1 KIRREL2 HGNC HGNC:18816 protein_coding YES CCDS12481.1 ENSP00000353331 Q6UWL6 UPI0000048F5B NM_199180.3 deleterious(0) 15/15 hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF51 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 35866374 35866374 T C 1 0 0 0 0 1 0 0 0 8189 1783 62 5 5 KIRREL2 19 35866374 Missense_Mutation SNP T C3N-00551_T 12506616 35866374 22751242 537 16020 RYR1 0 . GRCh38 19 38561382 38561382 + Silent SNP C C T rs775632796 C3N-00551_T C3N-00551_N C C c.12552C>T p.= p.G4184G ENST00000359596 90/106 209 154 55 202 201 1 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2;RYR1,3_prime_UTR_variant,,ENST00000594335,; T ENST00000359596 Transcript synonymous_variant 12552/15117 12552/15117 4184/5038 G ggC/ggT rs775632796,COSM4077812 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 90/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 0,1 LOW 1 SNV 5 0,1 1 PASS rs775632796 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 38561382 38561382 C T 1 0 0 0 0 0 0 0 1 14028 755 27 1 1 RYR1 19 38561382 Silent SNP C C3N-00551_T 2695008 38561382 20056234 538 16021 SPTBN4 0 . GRCh38 19 40513221 40513221 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.2432T>C p.Leu811Pro p.L811P ENST00000352632 14/36 115 86 29 151 151 0 strelka-varscan-mutect SPTBN4,missense_variant,p.Leu811Pro,ENST00000338932,;SPTBN4,missense_variant,p.Leu811Pro,ENST00000352632,;SPTBN4,missense_variant,p.Leu811Pro,ENST00000392025,;SPTBN4,missense_variant,p.Leu811Pro,ENST00000598249,NM_020971.2;SPTBN4,missense_variant,p.Leu811Pro,ENST00000595535,;SPTBN4,missense_variant,p.Leu203Pro,ENST00000597389,; C ENST00000352632 Transcript missense_variant 2518/8676 2432/7695 811/2564 L/P cTg/cCg 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB deleterious(0) 14/36 Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS rs939879148 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 40513221 40513221 T C 1 0 0 0 0 1 0 0 0 15477 1580 55 5 5 SPTBN4 19 40513221 Missense_Mutation SNP T C3N-00551_T 1951839 40513221 18104395 539 16022 ZNF541 0 . GRCh38 19 47544126 47544126 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.2403G>C p.Gln801His p.Q801H ENST00000391901 3/15 67 49 18 78 78 0 strelka-varscan-mutect ZNF541,missense_variant,p.Gln801His,ENST00000314121,;ZNF541,missense_variant,p.Gln801His,ENST00000391901,NM_001277075.1;ZNF541,missense_variant,p.Gln379His,ENST00000595558,;ZNF541,missense_variant,p.Gln392His,ENST00000263351,;ZNF541,upstream_gene_variant,,ENST00000487275,; G ENST00000391901 Transcript missense_variant,splice_region_variant 2403/4580 2403/4041 801/1346 Q/H caG/caC 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 deleterious(0) 3/15 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 47544126 47544126 C G 1 0 0 0 0 1 0 0 0 18549 695 24 4 4 ZNF541 19 47544126 Missense_Mutation SNP C C3N-00551_T 7030905 47544126 11073490 540 16023 LIG1 0 . GRCh38 19 48136121 48136121 + Frame_Shift_Del DEL G G - novel C3N-00551_T C3N-00551_N G G c.1336delC p.Leu446Ter p.L446* ENST00000263274 15/28 113 94 19 168 168 0 sindel-varindel LIG1,frameshift_variant,p.Leu446Ter,ENST00000613670,;LIG1,frameshift_variant,p.Leu446Ter,ENST00000263274,NM_001320970.1,NM_000234.2;LIG1,frameshift_variant,p.Leu378Ter,ENST00000536218,NM_001289064.1;LIG1,frameshift_variant,p.Leu415Ter,ENST00000427526,NM_001320971.1,NM_001289063.1;LIG1,frameshift_variant,p.Leu445Ter,ENST00000594759,;LIG1,frameshift_variant,p.Leu446Ter,ENST00000601091,;LIG1,3_prime_UTR_variant,,ENST00000542460,;LIG1,non_coding_transcript_exon_variant,,ENST00000594067,;LIG1,non_coding_transcript_exon_variant,,ENST00000597901,;LIG1,upstream_gene_variant,,ENST00000596457,;LIG1,upstream_gene_variant,,ENST00000596672,; - ENST00000263274 Transcript frameshift_variant 1756/3384 1336/2760 446/919 L/X Ctg/tg 1 -1 LIG1 HGNC HGNC:6598 protein_coding YES CCDS12711.1 ENSP00000263274 P18858 UPI0000129656 NM_001320970.1,NM_000234.2 15/28 Low_complexity_(Seg):seg,hmmpanther:PTHR10459,Pfam_domain:PF04675,TIGRFAM_domain:TIGR00574,Gene3D:1x9nA01,Superfamily_domains:0050884 HIGH 1 deletion 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 52 48136121 48136121 G - 1 0 1 0 1 0 0 0 0 8690 1014 35 0 0 LIG1 19 48136121 Frame_Shift_Del DEL G C3N-00551_T 591995 48136121 10481495 541 16024 RASIP1 0 . GRCh38 19 48727008 48727008 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2022G>T p.Glu674Asp p.E674D ENST00000222145 7/12 134 111 23 133 132 1 strelka-varscan-mutect RASIP1,missense_variant,p.Glu674Asp,ENST00000222145,NM_017805.2;RASIP1,intron_variant,,ENST00000599291,;RASIP1,downstream_gene_variant,,ENST00000594232,;RASIP1,upstream_gene_variant,,ENST00000601530,; A ENST00000222145 Transcript missense_variant,splice_region_variant 2227/3308 2022/2892 674/963 E/D gaG/gaT 1 -1 RASIP1 HGNC HGNC:24716 protein_coding YES CCDS12731.1 ENSP00000222145 Q5U651 UPI000020283D NM_017805.2 deleterious(0.05) 7/12 PROSITE_profiles:PS51126,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 48727008 48727008 C A 1 0 0 0 0 1 0 0 0 13239 695 24 2 2 RASIP1 19 48727008 Missense_Mutation SNP C C3N-00551_T 590887 48727008 9890608 542 16025 SCAF1 0 . GRCh38 19 49653107 49653107 + Silent SNP A A T novel C3N-00551_T C3N-00551_N A A c.2718A>T p.= p.A906A ENST00000360565 7/11 71 64 7 74 74 0 strelka-varscan-mutect SCAF1,synonymous_variant,p.=,ENST00000360565,NM_021228.2;SCAF1,downstream_gene_variant,,ENST00000598359,; T ENST00000360565 Transcript synonymous_variant 2842/4306 2718/3939 906/1312 A gcA/gcT 1 1 SCAF1 HGNC HGNC:30403 protein_coding YES CCDS33074.1 ENSP00000353769 Q9H7N4 UPI0000071891 NM_021228.2 7/11 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 49653107 49653107 A T 1 0 0 0 0 0 0 0 1 14132 175 7 4 4 SCAF1 19 49653107 Silent SNP A C3N-00551_T 926099 49653107 8964509 543 16026 IL4I1 0 . GRCh38 19 49894285 49894285 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.616C>A p.Gln206Lys p.Q206K ENST00000595948 7/10 269 226 43 254 254 0 strelka-varscan-mutect IL4I1,missense_variant,p.Gln206Lys,ENST00000595948,NM_001258018.1;IL4I1,missense_variant,p.Gln206Lys,ENST00000341114,NM_172374.2,NM_001258017.1;IL4I1,missense_variant,p.Gln184Lys,ENST00000391826,NM_152899.1;IL4I1,missense_variant,p.Gln147Lys,ENST00000593956,;IL4I1,downstream_gene_variant,,ENST00000596022,;IL4I1,downstream_gene_variant,,ENST00000596011,;IL4I1,downstream_gene_variant,,ENST00000597295,;IL4I1,3_prime_UTR_variant,,ENST00000601717,; T ENST00000595948 Transcript missense_variant 1237/2407 616/1770 206/589 Q/K Cag/Aag 1 -1 IL4I1 HGNC HGNC:19094 protein_coding YES CCDS12786.1 ENSP00000472474 Q96RQ9 UPI00001678CE NM_001258018.1 tolerated(0.08) 7/10 hmmpanther:PTHR10742,hmmpanther:PTHR10742:SF21,Gene3D:1.10.405.10,Pfam_domain:PF01593,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 49894285 49894285 G T 1 0 0 0 0 1 0 0 0 7601 1357 47 2 2 IL4I1 19 49894285 Missense_Mutation SNP G C3N-00551_T 241178 49894285 8723331 544 16027 SIGLEC11 0 . GRCh38 19 49960888 49960888 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.124G>T p.Val42Leu p.V42L ENST00000447370 2/11 93 67 26 85 85 0 strelka-varscan-mutect SIGLEC11,missense_variant,p.Val42Leu,ENST00000447370,NM_052884.2;SIGLEC11,missense_variant,p.Val42Leu,ENST00000426971,NM_001135163.1;SIGLEC11,upstream_gene_variant,,ENST00000426296,;CTC-326K19.6,upstream_gene_variant,,ENST00000451973,; A ENST00000447370 Transcript missense_variant 215/3173 124/2097 42/698 V/L Gtg/Ttg 1 -1 SIGLEC11 HGNC HGNC:15622 protein_coding YES CCDS12790.2 ENSP00000412361 Q96RL6 UPI00018131F5 NM_052884.2 deleterious(0) 2/11 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF44,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 49960888 49960888 C A 1 0 0 0 0 1 0 0 0 14571 507 18 2 2 SIGLEC11 19 49960888 Missense_Mutation SNP C C3N-00551_T 66603 49960888 8656728 545 16028 CD33 0 . GRCh38 19 51225972 51225972 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.588G>T p.= p.V196V ENST00000262262 3/7 249 202 47 312 312 0 strelka-varscan-mutect CD33,synonymous_variant,p.=,ENST00000436584,;CD33,synonymous_variant,p.=,ENST00000262262,NM_001772.3;CD33,synonymous_variant,p.=,ENST00000391796,NM_001177608.1;CD33,synonymous_variant,p.=,ENST00000421133,NM_001082618.1;CD33,non_coding_transcript_exon_variant,,ENST00000598473,;CD33,non_coding_transcript_exon_variant,,ENST00000601785,; T ENST00000262262 Transcript synonymous_variant 609/1444 588/1095 196/364 V gtG/gtT 1 1 CD33 HGNC HGNC:1659 protein_coding YES CCDS33084.1 ENSP00000262262 P20138 Q546G0 UPI000013D285 NM_001772.3 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF52,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF00047,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 51225972 51225972 G T 1 0 0 0 0 0 0 0 1 2709 1306 46 2 2 CD33 19 51225972 Silent SNP G C3N-00551_T 1265084 51225972 7391644 546 16029 FCAR 0 . GRCh38 19 54885416 54885416 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.252G>T p.Glu84Asp p.E84D ENST00000355524 3/5 359 281 78 421 420 1 strelka-varscan-mutect FCAR,missense_variant,p.Glu84Asp,ENST00000355524,NM_002000.3;FCAR,missense_variant,p.Glu84Asp,ENST00000469767,;FCAR,missense_variant,p.Glu84Asp,ENST00000391725,NM_133269.3;FCAR,missense_variant,p.Glu72Asp,ENST00000359272,NM_133272.3;FCAR,missense_variant,p.Glu72Asp,ENST00000391724,NM_133278.3;FCAR,missense_variant,p.Glu72Asp,ENST00000391723,NM_133274.3;FCAR,missense_variant,p.Glu72Asp,ENST00000391726,NM_133273.3;FCAR,missense_variant,p.Glu84Asp,ENST00000345937,NM_133271.3;FCAR,intron_variant,,ENST00000353758,NM_133277.3;FCAR,non_coding_transcript_exon_variant,,ENST00000482092,;FCAR,non_coding_transcript_exon_variant,,ENST00000471750,;FCAR,non_coding_transcript_exon_variant,,ENST00000472634,;FCAR,missense_variant,p.Glu72Asp,ENST00000488066,; T ENST00000355524 Transcript missense_variant 262/1483 252/864 84/287 E/D gaG/gaT 1 1 FCAR HGNC HGNC:3608 protein_coding YES CCDS12907.1 ENSP00000347714 P24071 UPI000011B429 NM_002000.3 tolerated(0.09) 3/5 Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF4,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 54885416 54885416 G T 1 0 0 0 0 1 0 0 0 5636 1020 36 2 2 FCAR 19 54885416 Missense_Mutation SNP G C3N-00551_T 3659444 54885416 3732200 547 16030 NLRP5 0 . GRCh38 19 56015758 56015758 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.525G>T p.= p.V175V ENST00000390649 4/15 55 37 18 57 57 0 strelka-varscan-mutect NLRP5,synonymous_variant,p.=,ENST00000390649,NM_153447.4;NLRP5,intron_variant,,ENST00000621651,;NLRP5,synonymous_variant,p.=,ENST00000597673,; T ENST00000390649 Transcript synonymous_variant 525/3888 525/3603 175/1200 V gtG/gtT 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 4/15 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 56015758 56015758 G T 1 0 0 0 0 0 0 0 1 10518 1306 46 2 2 NLRP5 19 56015758 Silent SNP G C3N-00551_T 1130342 56015758 2601858 548 16031 ZNF787 0 . GRCh38 19 56088607 56088607 + Nonsense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.565C>T p.Gln189Ter p.Q189* ENST00000610935 3/3 67 45 22 133 133 0 strelka-varscan-mutect ZNF787,stop_gained,p.Gln189Ter,ENST00000610935,NM_001002836.3;ZNF787,downstream_gene_variant,,ENST00000586787,; A ENST00000610935 Transcript stop_gained 684/1925 565/1149 189/382 Q/* Cag/Tag 1 -1 ZNF787 HGNC HGNC:26998 protein_coding YES CCDS42634.1 ENSP00000478557 A0A087WUD1 UPI0001596896 NM_001002836.3 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24408:SF1,hmmpanther:PTHR24408,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 A 4 1 52 56088607 56088607 G A 1 0 0 0 0 0 1 0 0 18743 1357 47 3 3 ZNF787 19 56088607 Nonsense_Mutation SNP G C3N-00551_T 72849 56088607 2529009 549 16032 ZNF419 0 . GRCh38 19 57493936 57493936 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.1382G>C p.Cys461Ser p.C461S ENST00000424930 5/5 203 156 47 288 288 0 strelka-varscan-mutect ZNF419,missense_variant,p.Cys428Ser,ENST00000347466,NM_001098494.1,NM_001291743.1;ZNF419,missense_variant,p.Cys461Ser,ENST00000424930,NM_001098491.1;ZNF419,missense_variant,p.Cys448Ser,ENST00000426954,NM_001098492.1;ZNF419,missense_variant,p.Cys460Ser,ENST00000221735,NM_024691.3;ZNF419,missense_variant,p.Cys414Ser,ENST00000415379,NM_001098496.1,NM_001098495.1;ZNF419,missense_variant,p.Cys447Ser,ENST00000442920,NM_001098493.1;ZNF419,intron_variant,,ENST00000354197,;ZNF419,downstream_gene_variant,,ENST00000618093,;ZNF419,downstream_gene_variant,,ENST00000518999,;ZNF419,downstream_gene_variant,,ENST00000521137,;ZNF419,downstream_gene_variant,,ENST00000523882,;ZNF419,downstream_gene_variant,,ENST00000523312,;ZNF419,downstream_gene_variant,,ENST00000520540,;ZNF419,downstream_gene_variant,,ENST00000519310,;ZNF419,downstream_gene_variant,,ENST00000521754,;ZNF419,downstream_gene_variant,,ENST00000523138,;ZNF419,non_coding_transcript_exon_variant,,ENST00000522346,;ZNF419,non_coding_transcript_exon_variant,,ENST00000523439,;AC003005.4,intron_variant,,ENST00000601674,;AC003005.4,intron_variant,,ENST00000599674,; C ENST00000424930 Transcript missense_variant 1611/2323 1382/1536 461/511 C/S tGt/tCt 1 1 ZNF419 HGNC HGNC:20648 protein_coding YES CCDS54325.1 ENSP00000388864 Q96HQ0 UPI0000E04CBA NM_001098491.1 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF195,hmmpanther:PTHR24387,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1382664695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 57493936 57493936 G C 1 0 0 0 0 1 0 0 0 18468 1377 48 4 4 ZNF419 19 57493936 Missense_Mutation SNP G C3N-00551_T 1405329 57493936 1123680 550 16033 ZNF329 0 . GRCh38 19 58129481 58129481 + Missense_Mutation SNP C C A rs371224762 C3N-00551_T C3N-00551_N C C c.23G>T p.Arg8Leu p.R8L ENST00000597186 5/5 51 38 13 48 48 0 strelka-varscan-mutect ZNF329,missense_variant,p.Arg8Leu,ENST00000597186,;ZNF329,missense_variant,p.Arg8Leu,ENST00000598312,NM_024620.3;ZNF329,missense_variant,p.Arg8Leu,ENST00000358067,;ZNF329,missense_variant,p.Arg8Leu,ENST00000601887,;ZNF329,missense_variant,p.Arg8Leu,ENST00000500161,; A ENST00000597186 Transcript missense_variant 701/3930 23/1626 8/541 R/L cGg/cTg rs371224762 1 -1 ZNF329 HGNC HGNC:14209 protein_coding YES CCDS12972.1 ENSP00000470323 Q86UD4 A0A024R4Q4 UPI0000246E79 deleterious(0.01) 5/5 hmmpanther:PTHR24381:SF118,hmmpanther:PTHR24381 MODERATE 1 SNV 5 1 PASS rs371224762 . 0 201 9 0 0 0 0 0 -20 0.9999978 1 1 1 0 A 3 1 52 58129481 58129481 C A 1 0 0 0 0 1 0 0 0 18419 652 23 1 1 ZNF329 19 58129481 Missense_Mutation SNP C C3N-00551_T 635545 58129481 488135 551 16034 SNPH 0 . GRCh38 20 1305911 1305911 + Missense_Mutation SNP C C T rs749027780 C3N-00551_T C3N-00551_N C C c.1342C>T p.Arg448Trp p.R448W ENST00000381873 6/6 87 81 6 110 109 1 strelka-varscan-mutect SNPH,missense_variant,p.Arg492Trp,ENST00000381867,NM_001318234.1;SNPH,missense_variant,p.Arg492Trp,ENST00000614659,;SNPH,missense_variant,p.Arg448Trp,ENST00000381873,NM_014723.2;SDCBP2,downstream_gene_variant,,ENST00000381812,;SDCBP2,downstream_gene_variant,,ENST00000360779,NM_080489.4;SDCBP2,downstream_gene_variant,,ENST00000339987,NM_001199784.1;SDCBP2,downstream_gene_variant,,ENST00000381808,NM_015685.5;SDCBP2,downstream_gene_variant,,ENST00000467129,; T ENST00000381873 Transcript missense_variant 1578/4995 1342/1485 448/494 R/W Cgg/Tgg rs749027780,COSM3991548,COSM3991549 1 1 SNPH HGNC HGNC:15931 protein_coding YES CCDS13012.1 ENSP00000371297 O15079 UPI000007424E NM_014723.2 deleterious(0) 6/6 hmmpanther:PTHR16208:SF1,hmmpanther:PTHR16208 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs749027780 . 0 195 11 3 0 0 0 0 -9.794286 0.9862139 1 1 1 0 T 3 4 52 1305911 1305911 C T 1 0 0 0 0 1 0 0 0 15170 759 27 1 1 SNPH 20 1305911 Missense_Mutation SNP C C3N-00551_T 1305911 63138256 552 16035 SIRPB1 0 . GRCh38 20 1571990 1571990 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.481C>A p.Pro161Thr p.P161T ENST00000381605 3/6 426 334 92 432 432 0 strelka-varscan-mutect SIRPB1,missense_variant,p.Pro161Thr,ENST00000381605,NM_006065.3;SIRPB1,intron_variant,,ENST00000381603,NM_001083910.2;SIRPB1,intron_variant,,ENST00000262929,;RP4-576H24.4,intron_variant,,ENST00000564763,;SIRPB1,intron_variant,,ENST00000563840,;RP4-576H24.4,intron_variant,,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPB1,intron_variant,,ENST00000569629,;SIRPB1,upstream_gene_variant,,ENST00000565076,; T ENST00000381605 Transcript missense_variant 546/3241 481/1197 161/398 P/T Cct/Act 1 -1 SIRPB1 HGNC HGNC:15928 protein_coding YES CCDS13019.1 ENSP00000371018 O00241 UPI000036700F NM_006065.3 deleterious(0.05) 3/6 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 1571990 1571990 G T 1 0 0 0 0 1 0 0 0 14596 1261 44 2 2 SIRPB1 20 1571990 Missense_Mutation SNP G C3N-00551_T 266079 1571990 62872177 553 16036 SIGLEC1 0 . GRCh38 20 3693052 3693052 + Missense_Mutation SNP G G C novel C3N-00551_T C3N-00551_N G G c.3588C>G p.Asp1196Glu p.D1196E ENST00000344754 14/21 93 78 15 105 105 0 strelka-varscan-mutect SIGLEC1,missense_variant,p.Asp1196Glu,ENST00000344754,NM_023068.3;SIGLEC1,missense_variant,p.Asp10Glu,ENST00000419548,; C ENST00000344754 Transcript missense_variant 3588/6720 3588/5130 1196/1709 D/E gaC/gaG 1 -1 SIGLEC1 HGNC HGNC:11127 protein_coding YES CCDS13060.1 ENSP00000341141 Q9BZZ2 UPI0000049BA6 NM_023068.3 tolerated(0.12) 14/21 Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF70,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 3693052 3693052 G C 1 0 0 0 0 1 0 0 0 14569 1368 48 4 4 SIGLEC1 20 3693052 Missense_Mutation SNP G C3N-00551_T 2121062 3693052 60751115 554 16037 GPCPD1 0 . GRCh38 20 5575539 5575539 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.875A>G p.Tyr292Cys p.Y292C ENST00000379019 10/20 97 84 13 86 86 0 varscan-mutect GPCPD1,missense_variant,p.Tyr292Cys,ENST00000379019,NM_019593.3;GPCPD1,upstream_gene_variant,,ENST00000418646,;GPCPD1,non_coding_transcript_exon_variant,,ENST00000481038,;GPCPD1,downstream_gene_variant,,ENST00000481690,;GPCPD1,upstream_gene_variant,,ENST00000633552,;GPCPD1,upstream_gene_variant,,ENST00000473797,; C ENST00000379019 Transcript missense_variant 1088/5489 875/2019 292/672 Y/C tAt/tGt 1 -1 GPCPD1 HGNC HGNC:26957 protein_coding YES CCDS13090.1 ENSP00000368305 Q9NPB8 UPI0000062241 NM_019593.3 deleterious(0) 10/20 hmmpanther:PTHR22958 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.92953 0.999992 1 1 1 0 C 3 2 52 5575539 5575539 T C 1 0 0 0 0 1 0 0 0 6505 1406 49 5 5 GPCPD1 20 5575539 Missense_Mutation SNP T C3N-00551_T 1882487 5575539 58868628 555 16038 AL031664.1 0 . GRCh38 20 17494624 17494624 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.1448G>A p.Arg483Lys p.R483K ENST00000377873 8/8 238 184 54 208 208 0 strelka-varscan-mutect BFSP1,missense_variant,p.Arg483Lys,ENST00000377873,NM_001195.4;BFSP1,missense_variant,p.Arg358Lys,ENST00000377868,NM_001161705.1,NM_001278607.1;AL031664.1,missense_variant,p.Arg344Lys,ENST00000536626,NM_001278606.1,NM_001278608.1; T ENST00000377873 Transcript missense_variant 1488/2207 1448/1998 483/665 R/K aGa/aAa 1 -1 BFSP1 HGNC HGNC:1040 protein_coding YES CCDS13126.1 ENSP00000367104 Q12934 UPI00001268C7 NM_001195.4 tolerated(0.27) 8/8 hmmpanther:PTHR14069,hmmpanther:PTHR14069:SF0 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 17494624 17494624 C T 1 0 0 0 0 1 0 0 0 568 913 32 3 3 AL031664.1 20 17494624 Missense_Mutation SNP C C3N-00551_T 11919085 17494624 46949543 556 16039 CD93 0 . GRCh38 20 23085057 23085057 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1136G>T p.Gly379Val p.G379V ENST00000246006 1/2 74 67 7 91 91 0 strelka-varscan-mutect CD93,missense_variant,p.Gly379Val,ENST00000246006,NM_012072.3; A ENST00000246006 Transcript missense_variant 1284/6708 1136/1959 379/652 G/V gGa/gTa 1 -1 CD93 HGNC HGNC:15855 protein_coding YES CCDS13149.1 ENSP00000246006 Q9NPY3 UPI00001273BC NM_012072.3 tolerated(0.08) 1/2 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF285,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -15.6438 1 1 1 1 0 A 3 1 52 23085057 23085057 C A 1 0 0 0 0 1 0 0 0 2751 855 30 2 2 CD93 20 23085057 Missense_Mutation SNP C C3N-00551_T 5590433 23085057 41359110 557 16040 DNMT3B 0 . GRCh38 20 32793559 32793559 + Missense_Mutation SNP C C T rs752673059 C3N-00551_T C3N-00551_N C C c.1090C>T p.Arg364Cys p.R364C ENST00000328111 10/23 495 470 25 511 511 0 strelka-varscan-mutect DNMT3B,missense_variant,p.Arg364Cys,ENST00000328111,NM_006892.3;DNMT3B,intron_variant,,ENST00000201963,NM_175850.2;DNMT3B,intron_variant,,ENST00000353855,NM_175848.1;DNMT3B,intron_variant,,ENST00000348286,NM_175849.1;DNMT3B,intron_variant,,ENST00000443239,NM_001207055.1;DNMT3B,intron_variant,,ENST00000456297,NM_001207056.1; T ENST00000328111 Transcript missense_variant 1411/4336 1090/2562 364/853 R/C Cgt/Tgt rs752673059 1 1 DNMT3B HGNC HGNC:2979 protein_coding YES CCDS13205.1 ENSP00000328547 Q9UBC3 UPI0000001046 NM_006892.3 tolerated(0.13) 10/23 MODERATE 1 SNV 1 1 PASS rs752673059 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 32793559 32793559 C T 1 0 0 0 0 1 0 0 0 4490 884 31 1 1 DNMT3B 20 32793559 Missense_Mutation SNP C C3N-00551_T 9708502 32793559 31650608 558 16041 EIF2S2 0 . GRCh38 20 34089749 34089750 + In_Frame_Ins INS - - GCT novel C3N-00551_T C3N-00551_N - - c.980_982dupAGC p.Gln327dup p.Q327dup ENST00000374980 9/9 82 67 15 134 134 0 sindel-varindel-pindel EIF2S2,inframe_insertion,p.Gln327dup,ENST00000374980,NM_001316363.1,NM_003908.3;RALY,downstream_gene_variant,,ENST00000375114,NM_007367.3;RALY,intron_variant,,ENST00000489384,; GCT ENST00000374980 Transcript inframe_insertion 1204-1205/2656 982-983/1002 328/333 L/QL ctc/cAGCtc 1 -1 EIF2S2 HGNC HGNC:3266 protein_coding YES CCDS13231.1 ENSP00000364119 P20042 Q6IBR8 UPI000012D28F NM_001316363.1,NM_003908.3 9/9 hmmpanther:PTHR23001 MODERATE 1 insertion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 GCT 7 5 52 34089749 34089749 - GCT 1 0 1 1 0 0 0 0 0 4843 304 11 0 0 EIF2S2 20 34089749 In_Frame_Ins INS - C3N-00551_T 1296190 34089749 30354418 559 16042 NCOA6 0 . GRCh38 20 34757301 34757301 + Nonsense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1447G>T p.Gly483Ter p.G483* ENST00000374796 8/16 78 63 15 90 90 0 strelka-varscan-mutect NCOA6,stop_gained,p.Gly483Ter,ENST00000374796,NM_001318240.1;NCOA6,stop_gained,p.Gly483Ter,ENST00000359003,NM_014071.3;NCOA6,stop_gained,p.Gly483Ter,ENST00000612493,NM_001242539.1;NCOA6,stop_gained,p.Gly483Ter,ENST00000616167,; A ENST00000374796 Transcript stop_gained 4018/9311 1447/6192 483/2063 G/* Gga/Tga 1 -1 NCOA6 HGNC HGNC:15936 protein_coding YES CCDS13241.1 ENSP00000363929 Q14686 UPI000013C634 NM_001318240.1 8/16 hmmpanther:PTHR15690,hmmpanther:PTHR15690:SF0 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 34757301 34757301 C A 1 0 0 0 0 0 1 0 0 10252 632 22 2 2 NCOA6 20 34757301 Nonsense_Mutation SNP C C3N-00551_T 667552 34757301 29686866 560 16043 SLC12A5 0 . GRCh38 20 46048066 46048066 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2062C>A p.Pro688Thr p.P688T ENST00000454036 16/26 164 114 50 167 167 0 strelka-varscan-mutect SLC12A5,missense_variant,p.Pro665Thr,ENST00000243964,NM_020708.4;SLC12A5,missense_variant,p.Pro688Thr,ENST00000454036,NM_001134771.1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616201,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,3_prime_UTR_variant,,ENST00000539566,;SLC12A5,downstream_gene_variant,,ENST00000626144,;SLC12A5,downstream_gene_variant,,ENST00000608594,; A ENST00000454036 Transcript missense_variant 2138/3593 2062/3420 688/1139 P/T Cca/Aca 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 deleterious(0.05) 16/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930 MODERATE 1 SNV 5 1 PASS rs1357044095 . 0 201 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 52 46048066 46048066 C A 1 0 0 0 0 1 0 0 0 14651 623 22 2 2 SLC12A5 20 46048066 Missense_Mutation SNP C C3N-00551_T 11290765 46048066 18396101 561 16044 CDH22 0 . GRCh38 20 46241106 46241106 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.407G>T p.Arg136Leu p.R136L ENST00000537909 3/12 328 286 42 306 306 0 strelka-varscan-mutect CDH22,missense_variant,p.Arg136Leu,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Arg136Leu,ENST00000372262,; A ENST00000537909 Transcript missense_variant 1050/3902 407/2487 136/828 R/L cGg/cTg 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 deleterious(0.02) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS rs1185236454 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 46241106 46241106 C A 1 0 0 0 0 1 0 0 0 2810 652 23 1 1 CDH22 20 46241106 Missense_Mutation SNP C C3N-00551_T 193040 46241106 18203061 562 16045 BCAS1 0 . GRCh38 20 54028813 54028813 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.302G>T p.Arg101Leu p.R101L ENST00000395961 4/12 343 220 123 254 254 0 strelka-varscan-mutect BCAS1,missense_variant,p.Arg101Leu,ENST00000395961,NM_003657.2;BCAS1,missense_variant,p.Arg101Leu,ENST00000371435,NM_001316361.2,NM_001323347.1;BCAS1,upstream_gene_variant,,ENST00000448484,; A ENST00000395961 Transcript missense_variant 469/3303 302/1755 101/584 R/L cGg/cTg COSM4164763,COSM4164764,COSM578135 1 -1 BCAS1 HGNC HGNC:974 protein_coding YES CCDS13444.1 ENSP00000379290 O75363 UPI000013D2E2 NM_003657.2 tolerated(0.1) 4/12 hmmpanther:PTHR15016 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs770667715 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 54028813 54028813 C A 1 0 0 0 0 1 0 0 0 1497 652 23 1 1 BCAS1 20 54028813 Missense_Mutation SNP C C3N-00551_T 7787707 54028813 10415354 563 16046 BMP7 0 . GRCh38 20 57183875 57183875 + Missense_Mutation SNP C C A rs757024706 C3N-00551_T C3N-00551_N C C c.805G>T p.Gly269Trp p.G269W ENST00000395863 4/7 569 378 191 438 438 0 strelka-varscan-mutect BMP7,missense_variant,p.Gly269Trp,ENST00000395863,NM_001719.2;BMP7,missense_variant,p.Gly269Trp,ENST00000450594,;BMP7,missense_variant,p.Gly191Trp,ENST00000433911,;BMP7,intron_variant,,ENST00000395864,;BMP7,non_coding_transcript_exon_variant,,ENST00000460817,;BMP7,non_coding_transcript_exon_variant,,ENST00000463939,; A ENST00000395863 Transcript missense_variant 1311/4013 805/1296 269/431 G/W Ggg/Tgg rs757024706 1 -1 BMP7 HGNC HGNC:1074 protein_coding YES CCDS13455.1 ENSP00000379204 P18075 A8K571 UPI00000349AD NM_001719.2 deleterious(0) 4/7 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF135 MODERATE 1 SNV 1 1 PASS rs757024706 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 57183875 57183875 C A 1 0 0 0 0 1 0 0 0 1620 652 23 1 1 BMP7 20 57183875 Missense_Mutation SNP C C3N-00551_T 3155062 57183875 7260292 564 16047 ZNF831 0 . GRCh38 20 59191915 59191915 + Missense_Mutation SNP G G T rs779936120 C3N-00551_T C3N-00551_N G G c.896G>T p.Arg299Leu p.R299L ENST00000637017 4/8 173 105 68 183 183 0 strelka-varscan-mutect ZNF831,missense_variant,p.Arg299Leu,ENST00000637017,;ZNF831,missense_variant,p.Arg299Leu,ENST00000371030,NM_178457.2; T ENST00000637017 Transcript missense_variant 2445/10953 896/5034 299/1677 R/L cGt/cTt rs779936120 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 tolerated(0.25) 4/8 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52 MODERATE 1 SNV 1 PASS rs779936120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 59191915 59191915 G T 1 0 0 0 0 1 0 0 0 18770 1145 40 1 1 ZNF831 20 59191915 Missense_Mutation SNP G C3N-00551_T 2008040 59191915 5252252 565 16048 CDH4 0 . GRCh38 20 61910470 61910470 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.1237C>A p.Leu413Ile p.L413I ENST00000614565 9/16 287 196 91 231 231 0 strelka-varscan-mutect CDH4,missense_variant,p.Leu413Ile,ENST00000614565,NM_001794.4;CDH4,missense_variant,p.Leu319Ile,ENST00000611855,;CDH4,missense_variant,p.Leu339Ile,ENST00000543233,NM_001252338.2,NM_001252339.2; A ENST00000614565 Transcript missense_variant 1325/6513 1237/2751 413/916 L/I Ctc/Atc COSM4905239 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 deleterious(0) 9/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999986 1 1 1 0 A 3 1 52 61910470 61910470 C A 1 0 0 0 0 1 0 0 0 2815 681 24 2 2 CDH4 20 61910470 Missense_Mutation SNP C C3N-00551_T 2718555 61910470 2533697 566 16049 LAMA5 0 . GRCh38 20 62336421 62336421 + Missense_Mutation SNP C C A C3N-00551_T C3N-00551_N C C c.2242G>T p.Ala748Ser p.A748S ENST00000252999 18/80 103 81 22 105 105 0 strelka-varscan-mutect LAMA5,missense_variant,p.Ala748Ser,ENST00000252999,NM_005560.4;LAMA5,upstream_gene_variant,,ENST00000577688,;LAMA5,3_prime_UTR_variant,,ENST00000474128,; A ENST00000252999 Transcript missense_variant 2309/11426 2242/11088 748/3695 A/S Gct/Tct COSM3405255 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 tolerated(0.38) 18/80 PROSITE_profiles:PS50027,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS rs1178002208 . 0 202 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 62336421 62336421 C A 1 0 0 0 0 1 0 0 0 8513 739 26 2 2 LAMA5 20 62336421 Missense_Mutation SNP C C3N-00551_T 425951 62336421 2107746 567 16050 COL9A3 0 . GRCh38 20 62821197 62821197 + Missense_Mutation SNP C C A rs367778234 C3N-00551_T C3N-00551_N C C c.326C>A p.Pro109Gln p.P109Q ENST00000343916 6/32 240 213 27 181 181 0 strelka-varscan-mutect COL9A3,missense_variant,p.Pro109Gln,ENST00000343916,NM_001853.3;COL9A3,missense_variant,p.Pro72Gln,ENST00000452372,;COL9A3,non_coding_transcript_exon_variant,,ENST00000489045,;COL9A3,non_coding_transcript_exon_variant,,ENST00000477612,;COL9A3,upstream_gene_variant,,ENST00000463487,; A ENST00000343916 Transcript missense_variant 329/2485 326/2055 109/684 P/Q cCg/cAg rs367778234 1 1 COL9A3 HGNC HGNC:2219 protein_coding YES CCDS13505.1 ENSP00000341640 Q14050 UPI0000126D51 NM_001853.3 deleterious(0.04) 6/32 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF529,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs367778234 . 0 207 0 3 0 0 0 0 -20 0.9999886 1 1 1 0 A 3 1 52 62821197 62821197 C A 1 0 0 0 0 1 0 0 0 3498 652 23 1 1 COL9A3 20 62821197 Missense_Mutation SNP C C3N-00551_T 484776 62821197 1622970 568 16051 EEF1A2 0 . GRCh38 20 63490684 63490684 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.824G>T p.Gly275Val p.G275V ENST00000217182 6/8 335 238 97 245 245 0 strelka-varscan-mutect EEF1A2,missense_variant,p.Gly275Val,ENST00000217182,NM_001958.3;EEF1A2,missense_variant,p.Gly275Val,ENST00000298049,; A ENST00000217182 Transcript missense_variant 1153/2006 824/1392 275/463 G/V gGc/gTc 1 -1 EEF1A2 HGNC HGNC:3192 protein_coding YES CCDS13522.1 ENSP00000217182 Q05639 UPI0000000136 NM_001958.3 deleterious_low_confidence(0) 6/8 HAMAP:MF_00118_A,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF104,Pfam_domain:PF03144,Gene3D:2.40.30.10,TIGRFAM_domain:TIGR00483,Superfamily_domains:SSF50447 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 63490684 63490684 C A 1 0 0 0 0 1 0 0 0 4753 739 26 2 2 EEF1A2 20 63490684 Missense_Mutation SNP C C3N-00551_T 669487 63490684 953483 569 16052 SRMS 0 . GRCh38 20 63540899 63540899 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1386C>A p.Cys462Ter p.C462* ENST00000217188 8/8 160 123 37 166 166 0 strelka-varscan-mutect SRMS,stop_gained,p.Cys462Ter,ENST00000217188,NM_080823.3;PTK6,upstream_gene_variant,,ENST00000542869,NM_005975.3;PTK6,upstream_gene_variant,,ENST00000217185,NM_001256358.1;RP4-697K14.15,upstream_gene_variant,,ENST00000620908,; T ENST00000217188 Transcript stop_gained 1427/1516 1386/1467 462/488 C/* tgC/tgA 1 -1 SRMS HGNC HGNC:11298 protein_coding YES CCDS13525.1 ENSP00000217188 Q9H3Y6 UPI000004F1F3 NM_080823.3 8/8 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF23,SMART_domains:SM00219,Superfamily_domains:SSF56112 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 63540899 63540899 G T 1 0 0 0 0 0 1 0 0 15513 963 34 2 2 SRMS 20 63540899 Nonsense_Mutation SNP G C3N-00551_T 50215 63540899 903268 570 16053 HSPA13 0 . GRCh38 21 14375691 14375691 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.709A>G p.Asn237Asp p.N237D ENST00000285667 4/5 147 134 13 192 192 0 strelka-varscan-mutect HSPA13,missense_variant,p.Asn237Asp,ENST00000285667,NM_006948.4;HSPA13,downstream_gene_variant,,ENST00000478035,; C ENST00000285667 Transcript missense_variant 777/3986 709/1416 237/471 N/D Aat/Gat 1 -1 HSPA13 HGNC HGNC:11375 protein_coding YES CCDS13567.1 ENSP00000285667 P48723 A0A140VK72 UPI00001360C2 NM_006948.4 tolerated(0.13) 4/5 hmmpanther:PTHR19375:SF169,hmmpanther:PTHR19375,Pfam_domain:PF00012,Gene3D:3.30.420.40,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 14375691 14375691 T C 1 0 0 0 0 1 0 0 0 7302 1783 62 5 5 HSPA13 21 14375691 Missense_Mutation SNP T C3N-00551_T 14375691 32334292 571 16054 GRIK1 0 . GRCh38 21 29561787 29561787 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.2193C>A p.= p.A731A ENST00000399907 15/17 339 290 49 375 375 0 strelka-varscan-mutect GRIK1,synonymous_variant,p.=,ENST00000399914,;GRIK1,synonymous_variant,p.=,ENST00000399907,NM_000830.3;GRIK1,synonymous_variant,p.=,ENST00000399909,;GRIK1,synonymous_variant,p.=,ENST00000399913,;GRIK1,synonymous_variant,p.=,ENST00000327783,;GRIK1,synonymous_variant,p.=,ENST00000389125,NM_175611.2;GRIK1,synonymous_variant,p.=,ENST00000389124,;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; T ENST00000399907 Transcript synonymous_variant 2605/3472 2193/2757 731/918 A gcC/gcA 1 -1 GRIK1 HGNC HGNC:4579 protein_coding YES CCDS42913.1 ENSP00000382791 P39086 UPI000012B612 NM_000830.3 15/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF36,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 29561787 29561787 G T 1 0 0 0 0 0 0 0 1 6655 1219 43 2 2 GRIK1 21 29561787 Silent SNP G C3N-00551_T 15186096 29561787 17148196 572 16055 ITSN1 0 . GRCh38 21 33811010 33811010 + Silent SNP T T A novel C3N-00551_T C3N-00551_N T T c.2355T>A p.= p.L785L ENST00000381318 21/40 166 146 20 197 197 0 strelka-varscan-mutect ITSN1,synonymous_variant,p.=,ENST00000381318,NM_003024.2;ITSN1,synonymous_variant,p.=,ENST00000381285,;ITSN1,synonymous_variant,p.=,ENST00000399367,;ITSN1,synonymous_variant,p.=,ENST00000381291,NM_001001132.1;ITSN1,synonymous_variant,p.=,ENST00000399352,;ITSN1,synonymous_variant,p.=,ENST00000399349,;ITSN1,synonymous_variant,p.=,ENST00000399355,;ITSN1,synonymous_variant,p.=,ENST00000399353,;ITSN1,synonymous_variant,p.=,ENST00000399338,;ITSN1,synonymous_variant,p.=,ENST00000440794,;ITSN1,3_prime_UTR_variant,,ENST00000379960,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,stop_gained,p.Leu74Ter,ENST00000419241,;ITSN1,upstream_gene_variant,,ENST00000465143,; A ENST00000381318 Transcript synonymous_variant 2643/17015 2355/5166 785/1721 L ctT/ctA 1 1 ITSN1 HGNC HGNC:6183 protein_coding YES CCDS33545.1 ENSP00000370719 Q15811 UPI00001403C6 NM_003024.2 21/40 PROSITE_profiles:PS50002,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF68,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 33811010 33811010 T A 1 0 0 0 0 0 0 0 1 7832 1799 63 4 4 ITSN1 21 33811010 Silent SNP T C3N-00551_T 4249223 33811010 12898973 573 16056 CHAF1B 0 . GRCh38 21 36413262 36413262 + Silent SNP A A T rs374268527 C3N-00551_T C3N-00551_N A A c.1440A>T p.= p.P480P ENST00000314103 12/14 93 79 14 107 107 0 strelka-varscan-mutect CHAF1B,synonymous_variant,p.=,ENST00000314103,NM_005441.2;CHAF1B,downstream_gene_variant,,ENST00000481458,; T ENST00000314103 Transcript synonymous_variant 1591/4480 1440/1680 480/559 P ccA/ccT rs374268527 1 1 CHAF1B HGNC HGNC:1911 protein_coding YES CCDS13644.1 ENSP00000315700 Q13112 UPI0000126DD1 NM_005441.2 12/14 hmmpanther:PTHR15271,Pfam_domain:PF15512 LOW 1 SNV 1 1 PASS rs374268527 . 0 204 4 2 0 0 0 0 -19.99956 0.9999831 1 1 1 0 T 2 4 52 36413262 36413262 A T 1 0 0 0 0 0 0 0 1 3071 204 8 4 4 CHAF1B 21 36413262 Silent SNP A C3N-00551_T 2602252 36413262 10296721 574 16057 HLCS 0 . GRCh38 21 36937356 36937356 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.89A>T p.Lys30Met p.K30M ENST00000399120 5/12 180 151 29 211 211 0 strelka-varscan-mutect HLCS,missense_variant,p.Lys30Met,ENST00000399120,NM_001242784.1;HLCS,missense_variant,p.Lys30Met,ENST00000612277,NM_001242785.1;HLCS,missense_variant,p.Lys30Met,ENST00000336648,NM_000411.6;HLCS,missense_variant,p.Lys30Met,ENST00000448340,;HLCS,missense_variant,p.Lys177Met,ENST00000419461,;HLCS,missense_variant,p.Lys30Met,ENST00000427746,; A ENST00000399120 Transcript missense_variant 1320/6466 89/2181 30/726 K/M aAg/aTg 1 -1 HLCS HGNC HGNC:4976 protein_coding YES CCDS13647.1 ENSP00000382071 P50747 UPI0000126A8C NM_001242784.1 deleterious(0.03) 5/12 hmmpanther:PTHR12835,hmmpanther:PTHR12835:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 36937356 36937356 T A 1 0 0 0 0 1 0 0 0 7103 1609 56 4 4 HLCS 21 36937356 Missense_Mutation SNP T C3N-00551_T 524094 36937356 9772627 575 16058 ADARB1 0 . GRCh38 21 45175752 45175752 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.51G>A p.= p.K17K ENST00000360697 2/10 134 122 12 216 215 1 strelka-varscan-mutect ADARB1,synonymous_variant,p.=,ENST00000348831,NM_001112.3;ADARB1,synonymous_variant,p.=,ENST00000360697,;ADARB1,synonymous_variant,p.=,ENST00000437626,NM_015833.3;ADARB1,synonymous_variant,p.=,ENST00000629643,;ADARB1,synonymous_variant,p.=,ENST00000389863,NM_001160230.1,NM_015834.3;ADARB1,synonymous_variant,p.=,ENST00000449478,;ADARB1,non_coding_transcript_exon_variant,,ENST00000389861,;ADARB1,upstream_gene_variant,,ENST00000481022,;ADARB1,downstream_gene_variant,,ENST00000464215,;ADARB1,upstream_gene_variant,,ENST00000631642,;ADARB1,synonymous_variant,p.=,ENST00000496664,;ADARB1,synonymous_variant,p.=,ENST00000492414,; A ENST00000360697 Transcript synonymous_variant 66/6604 51/2226 17/741 K aaG/aaA 1 1 ADARB1 HGNC HGNC:226 protein_coding YES CCDS33589.1 ENSP00000353920 P78563 UPI0000133622 2/10 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF58 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 45175752 45175752 G A 1 0 0 0 0 0 0 0 1 326 991 35 3 3 ADARB1 21 45175752 Silent SNP G C3N-00551_T 8238396 45175752 1534231 576 16059 COL18A1 0 . GRCh38 21 45493172 45493172 + Nonsense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3469G>T p.Gly1157Ter p.G1157* ENST00000359759 24/41 328 294 34 386 386 0 strelka-varscan-mutect COL18A1,stop_gained,p.Gly1157Ter,ENST00000359759,NM_130444.2;COL18A1,stop_gained,p.Gly922Ter,ENST00000355480,NM_030582.3;COL18A1,stop_gained,p.Gly742Ter,ENST00000400337,NM_130445.3;COL18A1,stop_gained,p.Gly89Ter,ENST00000342220,;SLC19A1,downstream_gene_variant,,ENST00000417954,;COL18A1,upstream_gene_variant,,ENST00000459895,; T ENST00000359759 Transcript stop_gained 3469/6586 3469/5265 1157/1754 G/* Gga/Tga 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 24/41 hmmpanther:PTHR24023,Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 52 45493172 45493172 G T 1 0 0 0 0 0 1 0 0 3463 1001 35 2 2 COL18A1 21 45493172 Nonsense_Mutation SNP G C3N-00551_T 317420 45493172 1216811 577 16060 COL18A1 0 . GRCh38 21 45504431 45504431 + Silent SNP C C A rs753824908 C3N-00551_T C3N-00551_N C C c.3988C>A p.= p.R1330R ENST00000359759 33/41 79 68 11 107 107 0 strelka-mutect COL18A1,synonymous_variant,p.=,ENST00000359759,NM_130444.2;COL18A1,synonymous_variant,p.=,ENST00000355480,NM_030582.3;COL18A1,synonymous_variant,p.=,ENST00000400337,NM_130445.3;COL18A1,synonymous_variant,p.=,ENST00000342220,;SLC19A1,intron_variant,,ENST00000417954,;SLC19A1,intron_variant,,ENST00000567670,;COL18A1,upstream_gene_variant,,ENST00000423214,;SLC19A1,upstream_gene_variant,,ENST00000461785,;COL18A1,upstream_gene_variant,,ENST00000473212,; A ENST00000359759 Transcript synonymous_variant 3988/6586 3988/5265 1330/1754 R Cga/Aga rs753824908 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 33/41 hmmpanther:PTHR24023 likely_pathogenic LOW 1 SNV 5 1 1 PASS rs753824908 . 0 204 5 0 0 0 0 0 -19.99994 1 1 1 1 0 A 2 1 52 45504431 45504431 C A 1 0 0 0 0 0 0 0 1 3463 644 23 1 1 COL18A1 21 45504431 Silent SNP C C3N-00551_T 11259 45504431 1205552 578 16061 CLTCL1 0 . GRCh38 22 19191416 19191416 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.4211G>C p.Cys1404Ser p.C1404S ENST00000427926 27/33 191 154 37 203 203 0 strelka-varscan-mutect CLTCL1,missense_variant,p.Cys1404Ser,ENST00000427926,NM_007098.3;CLTCL1,missense_variant,p.Cys1404Ser,ENST00000621271,NM_001835.3;CLTCL1,missense_variant,p.Cys227Ser,ENST00000622493,;CLTCL1,missense_variant,p.Cys227Ser,ENST00000617926,;CLTCL1,3_prime_UTR_variant,,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,downstream_gene_variant,,ENST00000611723,;CLTCL1,upstream_gene_variant,,ENST00000538828,; G ENST00000427926 Transcript missense_variant 4284/5513 4211/4923 1404/1640 C/S tGt/tCt 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 deleterious(0.01) 27/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:1.25.40.10,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 19191416 19191416 C G 1 0 0 0 0 1 0 0 0 3339 478 17 4 4 CLTCL1 22 19191416 Missense_Mutation SNP C C3N-00551_T 19191416 31627052 579 16062 BCR 0 . GRCh38 22 23289560 23289560 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.2646G>T p.= p.L882L ENST00000305877 13/23 187 174 13 209 209 0 strelka-varscan-mutect BCR,missense_variant,p.Asp448Tyr,ENST00000398512,;BCR,synonymous_variant,p.=,ENST00000305877,NM_004327.3;BCR,synonymous_variant,p.=,ENST00000359540,NM_021574.2;BCR,downstream_gene_variant,,ENST00000427791,;BCR,upstream_gene_variant,,ENST00000419722,;BCR,non_coding_transcript_exon_variant,,ENST00000487968,;BCR,downstream_gene_variant,,ENST00000466076,; T ENST00000305877 Transcript synonymous_variant 3397/7082 2646/3816 882/1271 L ctG/ctT 1 1 BCR HGNC HGNC:1014 protein_coding YES CCDS13806.1 ENSP00000303507 P11274 UPI000016A088 NM_004327.3 13/23 PROSITE_profiles:PS50004,hmmpanther:PTHR23182,hmmpanther:PTHR23182:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 23289560 23289560 G T 1 0 0 0 0 0 0 0 1 1535 1290 45 2 2 BCR 22 23289560 Silent SNP G C3N-00551_T 4098144 23289560 27528908 580 16063 PES1 0 . GRCh38 22 30578975 30578975 + Silent SNP G G A novel C3N-00551_T C3N-00551_N G G c.1545C>T p.= p.T515T ENST00000354694 14/15 132 110 22 105 105 0 strelka-mutect PES1,synonymous_variant,p.=,ENST00000402281,NM_001282327.1;PES1,synonymous_variant,p.=,ENST00000405677,NM_001282328.1;PES1,synonymous_variant,p.=,ENST00000354694,NM_014303.3;PES1,synonymous_variant,p.=,ENST00000402284,;PES1,synonymous_variant,p.=,ENST00000335214,NM_001243225.1;PES1,synonymous_variant,p.=,ENST00000441668,;GAL3ST1,upstream_gene_variant,,ENST00000406361,NM_001318104.1,NM_001318113.1;GAL3ST1,upstream_gene_variant,,ENST00000402369,NM_001318103.1,NM_001318109.1;PES1,downstream_gene_variant,,ENST00000406208,;GAL3ST1,upstream_gene_variant,,ENST00000431313,;PES1,non_coding_transcript_exon_variant,,ENST00000488719,; A ENST00000354694 Transcript synonymous_variant 1652/2295 1545/1767 515/588 T acC/acT 1 -1 PES1 HGNC HGNC:8848 protein_coding YES CCDS13880.1 ENSP00000346725 O00541 B2RDF2 UPI0000001618 NM_014303.3 14/15 HAMAP:MF_03028,hmmpanther:PTHR12221 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 52 30578975 30578975 G A 1 0 0 0 0 0 0 0 1 11822 987 35 3 3 PES1 22 30578975 Silent SNP G C3N-00551_T 7289415 30578975 20239493 581 16064 CELSR1 0 . GRCh38 22 46464000 46464000 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.3890A>T p.Gln1297Leu p.Q1297L ENST00000262738 2/35 347 236 111 314 314 0 strelka-varscan-mutect CELSR1,missense_variant,p.Gln1297Leu,ENST00000262738,NM_014246.1;CELSR1,missense_variant,p.Gln672Leu,ENST00000454637,; A ENST00000262738 Transcript missense_variant 3890/11389 3890/9045 1297/3014 Q/L cAg/cTg 1 -1 CELSR1 HGNC HGNC:1850 protein_coding YES CCDS14076.1 ENSP00000262738 Q9NYQ6 UPI0000040648 NM_014246.1 tolerated(1) 2/35 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF36 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 46464000 46464000 T A 1 0 0 0 0 1 0 0 0 2928 1580 55 4 4 CELSR1 22 46464000 Missense_Mutation SNP T C3N-00551_T 15885025 46464000 4354468 582 16065 TBC1D22A 0 . GRCh38 22 46891292 46891292 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.735G>T p.= p.R245R ENST00000337137 6/13 126 92 34 158 156 2 strelka-varscan-mutect TBC1D22A,synonymous_variant,p.=,ENST00000380995,NM_001284304.1;TBC1D22A,synonymous_variant,p.=,ENST00000337137,NM_014346.3;TBC1D22A,synonymous_variant,p.=,ENST00000406733,NM_001284305.1;TBC1D22A,synonymous_variant,p.=,ENST00000407381,;TBC1D22A,synonymous_variant,p.=,ENST00000355704,NM_001284303.1;TBC1D22A,stop_gained,p.Glu222Ter,ENST00000394449,;TBC1D22A,synonymous_variant,p.=,ENST00000441162,; T ENST00000337137 Transcript synonymous_variant 901/3787 735/1554 245/517 R cgG/cgT 1 1 TBC1D22A HGNC HGNC:1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 UPI0000128722 NM_014346.3 6/13 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF255,Gene3D:2qq8A02,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 46891292 46891292 G T 1 0 0 0 0 0 0 0 1 16011 1161 41 2 2 TBC1D22A 22 46891292 Silent SNP G C3N-00551_T 427292 46891292 3927176 583 16066 ARSF 0 . GRCh38 X 3112316 3112316 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.1533G>T p.Arg511Ser p.R511S ENST00000381127 11/11 102 76 26 118 118 0 strelka-varscan-mutect ARSF,missense_variant,p.Arg511Ser,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,missense_variant,p.Arg511Ser,ENST00000359361,NM_004042.4;RP13-824C8.2,downstream_gene_variant,,ENST00000443851,; T ENST00000381127 Transcript missense_variant 1754/2164 1533/1773 511/590 R/S agG/agT 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 tolerated(0.17) 11/11 hmmpanther:PTHR10342:SF220,hmmpanther:PTHR10342,Pfam_domain:PF14707,Gene3D:3.30.1120.10,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 3112316 3112316 G T 1 0 0 0 0 1 0 0 0 1134 1223 43 2 2 ARSF 23 3112316 Missense_Mutation SNP G C3N-00551_T 3112316 152928579 584 16067 MXRA5 0 . GRCh38 X 3323748 3323748 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1937G>T p.Ser646Ile p.S646I ENST00000217939 5/7 61 46 15 61 61 0 strelka-varscan-mutect MXRA5,missense_variant,p.Ser646Ile,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 2092/9793 1937/8487 646/2828 S/I aGt/aTt 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0.01) 5/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 3323748 3323748 C A 1 0 0 0 0 1 0 0 0 10002 565 20 2 2 MXRA5 23 3323748 Missense_Mutation SNP C C3N-00551_T 211432 3323748 152717147 585 16068 EGFL6 0 . GRCh38 X 13617825 13617825 + Missense_Mutation SNP A A G novel C3N-00551_T C3N-00551_N A A c.874A>G p.Lys292Glu p.K292E ENST00000380602 8/12 172 130 42 141 141 0 strelka-varscan-mutect EGFL6,missense_variant,p.Lys292Glu,ENST00000361306,NM_015507.3;EGFL6,missense_variant,p.Lys292Glu,ENST00000380602,NM_001167890.1; G ENST00000380602 Transcript missense_variant 1114/2385 874/1665 292/554 K/E Aag/Gag 1 1 EGFL6 HGNC HGNC:3235 protein_coding YES CCDS55370.1 ENSP00000369976 Q8IUX8 UPI0000034CAE NM_001167890.1 tolerated(0.09) 8/12 hmmpanther:PTHR24050,hmmpanther:PTHR24050:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 13617825 13617825 A G 1 0 0 0 0 1 0 0 0 4799 15 1 5 5 EGFL6 23 13617825 Missense_Mutation SNP A C3N-00551_T 10294077 13617825 142423070 586 16069 GRPR 0 . GRCh38 X 16150538 16150538 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.647T>A p.Leu216Gln p.L216Q ENST00000380289 2/3 174 123 51 224 224 0 strelka-varscan-mutect GRPR,missense_variant,p.Leu216Gln,ENST00000380289,NM_005314.2;RP11-431J24.2,downstream_gene_variant,,ENST00000435789,;RP11-431J24.2,downstream_gene_variant,,ENST00000454712,;RP11-431J24.2,downstream_gene_variant,,ENST00000422438,; A ENST00000380289 Transcript missense_variant 1045/1929 647/1155 216/384 L/Q cTg/cAg 1 1 GRPR HGNC HGNC:4609 protein_coding YES CCDS14174.1 ENSP00000369643 P30550 X5D7H2 UPI00000503FE NM_005314.2 deleterious(0) 2/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF116,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 16150538 16150538 T A 1 0 0 0 0 1 0 0 0 6690 1580 55 4 4 GRPR 23 16150538 Missense_Mutation SNP T C3N-00551_T 2532713 16150538 139890357 587 16070 NHS 0 . GRCh38 X 17726789 17726789 + Missense_Mutation SNP G G A rs770236873 C3N-00551_T C3N-00551_N G G c.2620G>A p.Ala874Thr p.A874T ENST00000380060 6/8 123 109 14 103 103 0 strelka-varscan-mutect NHS,missense_variant,p.Ala715Thr,ENST00000615422,;NHS,missense_variant,p.Ala874Thr,ENST00000380060,NM_198270.3,NM_001291867.1;NHS,missense_variant,p.Ala718Thr,ENST00000398097,NM_001136024.3;NHS,missense_variant,p.Ala691Thr,ENST00000617601,NM_001291868.1;NHS,downstream_gene_variant,,ENST00000485305,; A ENST00000380060 Transcript missense_variant 2958/8761 2620/4893 874/1630 A/T Gcc/Acc rs770236873,COSM302749,COSM302750 1 1 NHS HGNC HGNC:7820 protein_coding YES CCDS14181.1 ENSP00000369400 Q6T4R5 UPI00001DFBF3 NM_198270.3,NM_001291867.1 deleterious(0.02) 6/8 Pfam_domain:PF15273,hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF5 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770236873 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 17726789 17726789 G A 1 0 0 0 0 1 0 0 0 10443 1087 38 1 1 NHS 23 17726789 Missense_Mutation SNP G C3N-00551_T 1576251 17726789 138314106 588 16071 CXorf23 0 . GRCh38 X 19965277 19965277 + Missense_Mutation SNP T T A novel C3N-00551_T C3N-00551_N T T c.1041A>T p.Lys347Asn p.K347N ENST00000379687 3/11 104 67 37 115 115 0 strelka-varscan-mutect CXorf23,missense_variant,p.Lys347Asn,ENST00000379687,NM_198279.3;CXorf23,missense_variant,p.Lys347Asn,ENST00000379682,;CXorf23,upstream_gene_variant,,ENST00000340625,;CXorf23,5_prime_UTR_variant,,ENST00000472158,; A ENST00000379687 Transcript missense_variant 1075/6528 1041/2049 347/682 K/N aaA/aaT 1 -1 CXorf23 HGNC HGNC:27413 protein_coding YES CCDS14194.2 ENSP00000369009 A2AJT9 UPI0000458B03 NM_198279.3 deleterious(0) 3/11 Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF17 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 19965277 19965277 T A 1 0 0 0 0 1 0 0 0 3911 1606 56 4 4 CXorf23 23 19965277 Missense_Mutation SNP T C3N-00551_T 2238488 19965277 136075618 589 16072 PCYT1B 0 . GRCh38 X 24590142 24590142 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.367G>T p.Gly123Cys p.G123C ENST00000379144 4/8 90 62 28 101 101 0 strelka-varscan-mutect PCYT1B,missense_variant,p.Gly105Cys,ENST00000379145,NM_001163264.1;PCYT1B,missense_variant,p.Gly123Cys,ENST00000379144,NM_004845.4;PCYT1B,missense_variant,p.Gly123Cys,ENST00000356768,NM_001163265.1;PCYT1B,missense_variant,p.Gly97Cys,ENST00000496020,; A ENST00000379144 Transcript missense_variant 498/1692 367/1110 123/369 G/C Ggt/Tgt 1 -1 PCYT1B HGNC HGNC:8755 protein_coding YES CCDS14213.1 ENSP00000368439 Q9Y5K3 UPI000012864E NM_004845.4 deleterious(0) 4/8 Gene3D:3.40.50.620,Pfam_domain:PF01467,hmmpanther:PTHR10739,hmmpanther:PTHR10739:SF20,Superfamily_domains:SSF52374,TIGRFAM_domain:TIGR00125 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 24590142 24590142 C A 1 0 0 0 0 1 0 0 0 11699 681 24 2 2 PCYT1B 23 24590142 Missense_Mutation SNP C C3N-00551_T 4624865 24590142 131450753 590 16073 POLA1 0 . GRCh38 X 24726054 24726054 + Missense_Mutation SNP C C T novel C3N-00551_T C3N-00551_N C C c.1373C>T p.Ser458Leu p.S458L ENST00000379059 13/37 62 44 18 77 77 0 strelka-mutect POLA1,missense_variant,p.Ser464Leu,ENST00000379068,;POLA1,missense_variant,p.Ser458Leu,ENST00000379059,NM_016937.3;POLA1,missense_variant,p.Ser458Leu,ENST00000611764,;POLA1,upstream_gene_variant,,ENST00000493342,; T ENST00000379059 Transcript missense_variant,splice_region_variant 1388/5440 1373/4389 458/1462 S/L tCg/tTg 1 1 POLA1 HGNC HGNC:9173 protein_coding YES CCDS14214.1 ENSP00000368349 P09884 UPI000014D383 NM_016937.3 tolerated(0.08) 13/37 hmmpanther:PTHR10322:SF21,hmmpanther:PTHR10322,TIGRFAM_domain:TIGR00592,Pfam_domain:PF03104,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 24726054 24726054 C T 1 0 0 0 0 1 0 0 0 12297 898 31 1 1 POLA1 23 24726054 Missense_Mutation SNP C C3N-00551_T 135912 24726054 131314841 591 16074 FAM47B 0 . GRCh38 X 34943994 34943994 + Missense_Mutation SNP G G T rs202142258 C3N-00551_T C3N-00551_N G G c.1163G>T p.Arg388Leu p.R388L ENST00000329357 1/1 160 118 42 229 229 0 strelka-varscan-mutect FAM47B,missense_variant,p.Arg388Leu,ENST00000329357,NM_152631.2; T ENST00000329357 Transcript missense_variant 1199/2120 1163/1938 388/645 R/L cGg/cTg rs202142258,COSM1557692 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 tolerated(0.06) 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192 0,1 MODERATE 1 SNV 0,1 1 PASS rs202142258 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 34943994 34943994 G T 1 0 0 0 0 1 0 0 0 5448 1116 39 1 1 FAM47B 23 34943994 Missense_Mutation SNP G C3N-00551_T 10217940 34943994 121096901 592 16075 KDM5C 0 . GRCh38 X 53196816 53196816 + Nonsense_Mutation SNP G G A novel C3N-00551_T C3N-00551_N G G c.2851C>T p.Arg951Ter p.R951* ENST00000375401 19/26 184 146 38 212 212 0 strelka-varscan-mutect KDM5C,stop_gained,p.Arg884Ter,ENST00000452825,NM_001146702.1;KDM5C,stop_gained,p.Arg951Ter,ENST00000375401,NM_004187.3;KDM5C,stop_gained,p.Arg950Ter,ENST00000404049,NM_001282622.1;KDM5C,stop_gained,p.Arg951Ter,ENST00000375379,;KDM5C,stop_gained,p.Arg910Ter,ENST00000375383,;MIR6895,upstream_gene_variant,,ENST00000613497,;MIR6894,downstream_gene_variant,,ENST00000622662,;KDM5C,downstream_gene_variant,,ENST00000465402,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000481369,; A ENST00000375401 Transcript stop_gained 3384/6031 2851/4683 951/1560 R/* Cga/Tga 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 19/26 Pfam_domain:PF08429,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 52 53196816 53196816 G A 1 0 0 0 0 0 1 0 0 8053 1095 38 1 1 KDM5C 23 53196816 Nonsense_Mutation SNP G C3N-00551_T 18252822 53196816 102844079 593 16076 HUWE1 0 . GRCh38 X 53603411 53603411 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.2833G>T p.Val945Leu p.V945L ENST00000342160 26/83 138 99 39 201 201 0 strelka-varscan-mutect HUWE1,missense_variant,p.Val945Leu,ENST00000342160,;HUWE1,missense_variant,p.Val945Leu,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Val945Leu,ENST00000612484,;HUWE1,non_coding_transcript_exon_variant,,ENST00000218328,; A ENST00000342160 Transcript missense_variant 3291/14796 2833/13125 945/4374 V/L Gtg/Ttg 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC deleterious(0) 26/83 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF291 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 53603411 53603411 C A 1 0 0 0 0 1 0 0 0 7357 507 18 2 2 HUWE1 23 53603411 Missense_Mutation SNP C C3N-00551_T 406595 53603411 102437484 594 16077 ZXDB 0 . GRCh38 X 57593058 57593058 + Missense_Mutation SNP C C A rs769580805 C3N-00551_T C3N-00551_N C C c.1010C>A p.Pro337Gln p.P337Q ENST00000374888 1/1 148 120 28 174 174 0 strelka-varscan-mutect ZXDB,missense_variant,p.Pro337Gln,ENST00000374888,NM_007157.3; A ENST00000374888 Transcript missense_variant 1407/5894 1010/2412 337/803 P/Q cCg/cAg rs769580805 1 1 ZXDB HGNC HGNC:13199 protein_coding YES CCDS35313.1 ENSP00000364023 P98169 UPI000013C495 NM_007157.3 tolerated(0.21) 1/1 PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF85,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS rs769580805 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 57593058 57593058 C A 1 0 0 0 0 1 0 0 0 18854 652 23 1 1 ZXDB 23 57593058 Missense_Mutation SNP C C3N-00551_T 3989647 57593058 98447837 595 16078 ZC4H2 0 . GRCh38 X 64917826 64917826 + Missense_Mutation SNP C C T C3N-00551_T C3N-00551_N C C c.632G>A p.Arg211Gln p.R211Q ENST00000374839 5/5 150 139 11 165 165 0 strelka-varscan-mutect ZC4H2,missense_variant,p.Gly157Ser,ENST00000447788,NM_001178033.2;ZC4H2,missense_variant,p.Arg188Gln,ENST00000337990,NM_001178032.2,NM_001243804.1;ZC4H2,missense_variant,p.Arg211Gln,ENST00000374839,NM_018684.3;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488608,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000492653,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488406,;ZC4H2,downstream_gene_variant,,ENST00000476032,;ZC4H2,downstream_gene_variant,,ENST00000488831,; T ENST00000374839 Transcript missense_variant 739/2184 632/675 211/224 R/Q cGg/cAg COSM1151685,COSM757874 1 -1 ZC4H2 HGNC HGNC:24931 protein_coding YES CCDS14380.1 ENSP00000363972 Q9NQZ6 UPI0000025CAA NM_018684.3 deleterious(0) 5/5 Pfam_domain:PF10146,hmmpanther:PTHR31058,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 64917826 64917826 C T 1 0 0 0 0 1 0 0 0 18153 652 23 1 1 ZC4H2 23 64917826 Missense_Mutation SNP C C3N-00551_T 7324768 64917826 91123069 596 16079 RP11-69A21.2 0 . GRCh38 X 72807565 72807565 + Silent SNP G G T rs5938971 C3N-00551_T C3N-00551_N G G c.223C>A p.= p.R75R ENST00000419795 3/3 99 73 26 130 130 0 strelka-varscan-mutect RP11-69A21.2,synonymous_variant,p.=,ENST00000458170,;RP11-69A21.2,synonymous_variant,p.=,ENST00000419795,;DMRTC1B,intron_variant,,ENST00000334036,;DMRTC1B,intron_variant,,ENST00000472595,; T ENST00000419795 Transcript synonymous_variant 293/433 223/240 75/79 R Cgg/Agg rs5938971 1 -1 RP11-69A21.2 Clone_based_vega_gene protein_coding YES ENSP00000489739 3/3 LOW 1 SNV 5 1 PASS rs5938971 . 117 83 10 0 0 0 0 0 -20 0.9976145 0 1 1 0 T 2 4 52 72807565 72807565 G T 1 0 0 0 0 0 0 0 1 13757 1115 39 1 1 RP11-69A21.2 23 72807565 Silent SNP G C3N-00551_T 7889739 72807565 83233330 597 16080 GPR174 0 . GRCh38 X 79171704 79171704 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.697C>G p.Leu233Val p.L233V ENST00000276077 1/1 96 73 23 139 139 0 strelka-varscan-mutect GPR174,missense_variant,p.Leu233Val,ENST00000276077,NM_032553.1; G ENST00000276077 Transcript missense_variant 733/1258 697/1002 233/333 L/V Cta/Gta 1 1 GPR174 HGNC HGNC:30245 protein_coding YES CCDS14443.1 ENSP00000276077 Q9BXC1 UPI0000050477 NM_032553.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF4,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 79171704 79171704 C G 1 0 0 0 0 1 0 0 0 6556 912 32 4 4 GPR174 23 79171704 Missense_Mutation SNP C C3N-00551_T 6364139 79171704 76869191 598 16081 TMEM31 0 . GRCh38 X 103713850 103713850 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.359G>T p.Gly120Val p.G120V ENST00000319560 3/3 176 129 47 184 184 0 strelka-varscan-mutect TMEM31,missense_variant,p.Gly120Val,ENST00000319560,NM_182541.2;GLRA4,intron_variant,,ENST00000372617,NM_001024452.2;GLRA4,intron_variant,,ENST00000436213,;GLRA4,downstream_gene_variant,,ENST00000480725,; T ENST00000319560 Transcript missense_variant 550/728 359/507 120/168 G/V gGa/gTa 1 1 TMEM31 HGNC HGNC:28601 protein_coding YES CCDS35359.1 ENSP00000316940 Q5JXX7 A0A140VK58 UPI0000140633 NM_182541.2 tolerated_low_confidence(0.07) 3/3 Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 103713850 103713850 G T 1 0 0 0 0 1 0 0 0 16631 1174 41 2 2 TMEM31 23 103713850 Missense_Mutation SNP G C3N-00551_T 24542146 103713850 52327045 599 16082 RGAG1 0 . GRCh38 X 110454310 110454310 + Missense_Mutation SNP G G T novel C3N-00551_T C3N-00551_N G G c.3693G>T p.Glu1231Asp p.E1231D ENST00000465301 3/4 100 68 32 113 113 0 strelka-varscan-mutect RGAG1,missense_variant,p.Glu1231Asp,ENST00000465301,NM_020769.2;RGAG1,missense_variant,p.Glu1231Asp,ENST00000540313,;RGAG1,downstream_gene_variant,,ENST00000520821,; T ENST00000465301 Transcript missense_variant 3939/5426 3693/4167 1231/1388 E/D gaG/gaT 1 1 RGAG1 HGNC HGNC:29245 protein_coding YES CCDS14552.1 ENSP00000419786 Q8NET4 UPI000006F841 NM_020769.2 tolerated_low_confidence(0.12) 3/4 hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF48 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 110454310 110454310 G T 1 0 0 0 0 1 0 0 0 13446 933 33 2 2 RGAG1 23 110454310 Missense_Mutation SNP G C3N-00551_T 6740460 110454310 45586585 600 16083 ADGRG4 0 . GRCh38 X 136350303 136350303 + Silent SNP G G T novel C3N-00551_T C3N-00551_N G G c.6597G>T p.= p.G2199G ENST00000394143 6/26 124 93 31 170 170 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; T ENST00000394143 Transcript synonymous_variant 6888/9931 6597/9243 2199/3080 G ggG/ggT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 52 136350303 136350303 G T 1 0 0 0 0 0 0 0 1 371 1219 43 2 2 ADGRG4 23 136350303 Silent SNP G C3N-00551_T 25895993 136350303 19690592 601 16084 SOX3 0 . GRCh38 X 140503878 140503878 + Missense_Mutation SNP C C G novel C3N-00551_T C3N-00551_N C C c.1183G>C p.Gly395Arg p.G395R ENST00000370536 1/1 85 68 17 84 84 0 strelka-varscan-mutect SOX3,missense_variant,p.Gly395Arg,ENST00000370536,NM_005634.2; G ENST00000370536 Transcript missense_variant 1239/2132 1183/1341 395/446 G/R Ggc/Cgc 1 -1 SOX3 HGNC HGNC:11199 protein_coding YES CCDS14669.1 ENSP00000359567 P41225 UPI000006F00F NM_005634.2 deleterious(0) 1/1 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF111 MODERATE 1 SNV 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 52 140503878 140503878 C G 1 0 0 0 0 1 0 0 0 15277 652 23 4 4 SOX3 23 140503878 Missense_Mutation SNP C C3N-00551_T 4153575 140503878 15537017 602 16085 MAGEC1 0 . GRCh38 X 141908324 141908324 + Missense_Mutation SNP T T C novel C3N-00551_T C3N-00551_N T T c.2920T>C p.Tyr974His p.Y974H ENST00000285879 4/4 113 86 27 119 119 0 strelka-varscan-mutect MAGEC1,missense_variant,p.Tyr974His,ENST00000285879,NM_005462.4;MAGEC1,missense_variant,p.Tyr41His,ENST00000406005,; C ENST00000285879 Transcript missense_variant 3206/4270 2920/3429 974/1142 Y/H Tat/Cat 1 1 MAGEC1 HGNC HGNC:6812 protein_coding YES CCDS35417.1 ENSP00000285879 O60732 UPI000006F2FD NM_005462.4 deleterious(0) 4/4 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF17,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 52 141908324 141908324 T C 1 0 0 0 0 1 0 0 0 9098 1522 53 5 5 MAGEC1 23 141908324 Missense_Mutation SNP T C3N-00551_T 1404446 141908324 14132571 603 16086 AFF2 0 . GRCh38 X 148953579 148953579 + Splice_Site SNP G G T C3N-00551_T C3N-00551_N G G c.1398-1G>T p.X466_splice ENST00000370460 41 27 14 53 53 0 strelka-varscan-mutect AFF2,splice_acceptor_variant,,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,splice_acceptor_variant,,ENST00000286437,NM_001170628.1;AFF2,splice_acceptor_variant,,ENST00000342251,NM_001169122.1;AFF2,splice_acceptor_variant,,ENST00000370457,NM_001169124.1,NM_001169125.1; T ENST00000370460 Transcript splice_acceptor_variant -/13746 1398/3936 466/1311 COSM5153673,COSM5153674,COSM5153675 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 9/20 1,1,1 HIGH 1 SNV 5 1,1,1 1 PASS . . 0 179 27 4 0 0 0 0 -20 0.9704271 0 1 1 0 T 5 4 52 148953579 148953579 G T 1 0 0 0 0 0 0 1 0 434 985 34 2 2 AFF2 23 148953579 Splice_Site SNP G C3N-00551_T 7045255 148953579 7087316 604 16087 CXorf40B 0 . GRCh38 X 149933794 149933794 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.81G>T p.Trp27Cys p.W27C ENST00000370406 4/5 179 115 64 188 188 0 strelka-varscan-mutect CXorf40B,missense_variant,p.Trp27Cys,ENST00000370406,;CXorf40B,missense_variant,p.Trp27Cys,ENST00000462691,;CXorf40B,missense_variant,p.Trp27Cys,ENST00000370404,NM_001013845.1;CXorf40B,missense_variant,p.Trp27Cys,ENST00000370409,;CXorf40B,missense_variant,p.Trp27Cys,ENST00000355203,;CXorf40B,missense_variant,p.Trp27Cys,ENST00000483447,;XX-FW81066F1.2,downstream_gene_variant,,ENST00000457775,;LINC00894,upstream_gene_variant,,ENST00000449111,;CXorf40B,downstream_gene_variant,,ENST00000497550,; A ENST00000370406 Transcript missense_variant 910/1653 81/477 27/158 W/C tgG/tgT 1 -1 CXorf40B HGNC HGNC:17402 protein_coding YES CCDS35426.1 ENSP00000359434 Q96DE9 UPI0000072E4A deleterious(0.03) 4/5 Gene3D:2.30.130.30,hmmpanther:PTHR31666,hmmpanther:PTHR31666:SF0,SMART_domains:SM01022,Superfamily_domains:SSF88697 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 149933794 149933794 C A 1 0 0 0 0 1 0 0 0 3915 740 26 2 2 CXorf40B 23 149933794 Missense_Mutation SNP C C3N-00551_T 980215 149933794 6107101 605 16088 GABRQ 0 . GRCh38 X 152652829 152652829 + Missense_Mutation SNP C C A rs782062554 C3N-00551_T C3N-00551_N C C c.1447C>A p.Arg483Ser p.R483S ENST00000598523 9/9 161 125 36 187 187 0 strelka-varscan-mutect GABRQ,missense_variant,p.Arg483Ser,ENST00000598523,NM_018558.3; A ENST00000598523 Transcript missense_variant 1467/6172 1447/1899 483/632 R/S Cgc/Agc rs782062554,COSM4762628 1 1 GABRQ HGNC HGNC:14454 protein_coding YES CCDS14707.1 ENSP00000469332 Q9UN88 UPI000013DAC0 NM_018558.3 tolerated(0.39) 9/9 Prints_domain:PR01725 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs782062554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 152652829 152652829 C A 1 0 0 0 0 1 0 0 0 6046 652 23 1 1 GABRQ 23 152652829 Missense_Mutation SNP C C3N-00551_T 2719035 152652829 3388066 606 16089 GABRQ 0 . GRCh38 X 152653164 152653164 + Missense_Mutation SNP C C A novel C3N-00551_T C3N-00551_N C C c.1782C>A p.Phe594Leu p.F594L ENST00000598523 9/9 158 113 45 229 229 0 strelka-varscan-mutect GABRQ,missense_variant,p.Phe594Leu,ENST00000598523,NM_018558.3; A ENST00000598523 Transcript missense_variant 1802/6172 1782/1899 594/632 F/L ttC/ttA 1 1 GABRQ HGNC HGNC:14454 protein_coding YES CCDS14707.1 ENSP00000469332 Q9UN88 UPI000013DAC0 NM_018558.3 tolerated(0.32) 9/9 hmmpanther:PTHR18945:SF199,hmmpanther:PTHR18945,Superfamily_domains:SSF90112,Prints_domain:PR01725 MODERATE 1 SNV 1 1 PASS rs1235662467 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 52 152653164 152653164 C A 1 0 0 0 0 1 0 0 0 6046 912 32 2 2 GABRQ 23 152653164 Missense_Mutation SNP C C3N-00551_T 335 152653164 3387731 607 16090 ABCD1 0 . GRCh38 X 153736487 153736487 + Missense_Mutation SNP G G T rs782159028 C3N-00551_T C3N-00551_N G G c.1367G>T p.Arg456Leu p.R456L ENST00000218104 4/10 199 153 46 207 207 0 strelka-varscan-mutect ABCD1,missense_variant,p.Arg456Leu,ENST00000218104,NM_000033.3;U52111.14,intron_variant,,ENST00000434284,;ABCD1,non_coding_transcript_exon_variant,,ENST00000443684,; T ENST00000218104 Transcript missense_variant 1766/3664 1367/2238 456/745 R/L cGt/cTt rs782159028,COSM755757 1 1 ABCD1 HGNC HGNC:61 protein_coding YES CCDS14728.1 ENSP00000218104 P33897 UPI0000000DF5 NM_000033.3 tolerated(0.35) 4/10 hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF21,TIGRFAM_domain:TIGR00954 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs782159028 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 52 153736487 153736487 G T 1 0 0 0 0 1 0 0 0 64 1145 40 1 1 ABCD1 23 153736487 Missense_Mutation SNP G C3N-00551_T 1083323 153736487 2304408 608 16091 GPATCH3 0 . GRCh38 1 26900036 26900036 + Missense_Mutation SNP C C A novel C3N-00552_T C3N-00552_N C C c.407G>T p.Gly136Val p.G136V ENST00000361720 1/7 255 206 49 199 199 0 strelka-varscan-mutect GPATCH3,missense_variant,p.Gly136Val,ENST00000361720,NM_022078.2;NUDC,upstream_gene_variant,,ENST00000435827,; A ENST00000361720 Transcript missense_variant 431/2123 407/1578 136/525 G/V gGt/gTt 1 -1 GPATCH3 HGNC HGNC:25720 protein_coding YES CCDS290.1 ENSP00000354645 Q96I76 UPI000003E830 NM_022078.2 tolerated(0.06) 1/7 hmmpanther:PTHR14390,hmmpanther:PTHR14390:SF2 MODERATE 1 SNV 1 1 PASS rs1465844078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 26900036 26900036 C A 1 0 0 0 0 1 0 0 0 6493 507 18 2 2 GPATCH3 1 26900036 Missense_Mutation SNP C C3N-00552_T 26900036 222056386 1 16092 LRRC8B 0 . GRCh38 1 89583281 89583281 + Missense_Mutation SNP C C G novel C3N-00552_T C3N-00552_N C C c.631C>G p.Pro211Ala p.P211A ENST00000330947 5/6 238 193 45 223 223 0 strelka-varscan-mutect LRRC8B,missense_variant,p.Pro211Ala,ENST00000330947,NM_001134476.1;LRRC8B,missense_variant,p.Pro211Ala,ENST00000439853,NM_015350.2;LRRC8B,missense_variant,p.Pro211Ala,ENST00000358200,;LRRC8B,downstream_gene_variant,,ENST00000449440,;FLJ27354,non_coding_transcript_exon_variant,,ENST00000443562,; G ENST00000330947 Transcript missense_variant 991/7593 631/2412 211/803 P/A Cca/Gca 1 1 LRRC8B HGNC HGNC:30692 protein_coding YES CCDS724.1 ENSP00000332674 Q6P9F7 UPI00000739FF NM_001134476.1 tolerated(0.55) 5/6 Pfam_domain:PF12534 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 53 89583281 89583281 C G 1 0 0 0 0 1 0 0 0 8926 739 26 4 4 LRRC8B 1 89583281 Missense_Mutation SNP C C3N-00552_T 62683245 89583281 159373141 2 16093 MTR 0 . GRCh38 1 236835585 236835585 + Silent SNP A A T novel C3N-00552_T C3N-00552_N A A c.1227A>T p.= p.G409G ENST00000366577 14/33 495 399 96 377 377 0 strelka-varscan MTR,synonymous_variant,p.=,ENST00000366577,NM_000254.2;MTR,synonymous_variant,p.=,ENST00000535889,NM_001291939.1;MTR,upstream_gene_variant,,ENST00000366576,NM_001291940.1;MTR,non_coding_transcript_exon_variant,,ENST00000463959,; T ENST00000366577 Transcript synonymous_variant 1621/10529 1227/3798 409/1265 G ggA/ggT 1 1 MTR HGNC HGNC:7468 protein_coding YES CCDS1614.1 ENSP00000355536 Q99707 UPI0000036BC4 NM_000254.2 14/33 PROSITE_profiles:PS50972,TIGRFAM_domain:TIGR02082,Gene3D:3.20.20.20,Pfam_domain:PF00809,PIRSF_domain:PIRSF000381,Superfamily_domains:SSF51717,Superfamily_domains:SSF82282 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 53 236835585 236835585 A T 1 0 0 0 0 0 0 0 1 9944 291 11 4 4 MTR 1 236835585 Silent SNP A C3N-00552_T 147252304 236835585 12120837 3 16094 ROCK2 0 . GRCh38 2 11221238 11221238 + Nonsense_Mutation SNP G G A novel C3N-00552_T C3N-00552_N G G c.1219C>T p.Gln407Ter p.Q407* ENST00000315872 9/33 140 119 21 133 133 0 strelka-varscan-mutect ROCK2,stop_gained,p.Gln407Ter,ENST00000315872,NM_001321643.1,NM_004850.3;ROCK2,stop_gained,p.Gln164Ter,ENST00000401753,;ROCK2,5_prime_UTR_variant,,ENST00000616279,;ROCK2,downstream_gene_variant,,ENST00000431087,;ROCK2,stop_gained,p.Gln407Ter,ENST00000261535,;ROCK2,non_coding_transcript_exon_variant,,ENST00000484951,; A ENST00000315872 Transcript stop_gained 1668/8292 1219/4167 407/1388 Q/* Cag/Tag 1 -1 ROCK2 HGNC HGNC:10252 protein_coding YES CCDS42654.1 ENSP00000317985 O75116 UPI000034ECB0 NM_001321643.1,NM_004850.3 9/33 PROSITE_profiles:PS51285,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,PIRSF_domain:PIRSF037568,SMART_domains:SM00133,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 53 11221238 11221238 G A 1 0 0 0 0 0 1 0 0 13696 1299 45 3 3 ROCK2 2 11221238 Nonsense_Mutation SNP G C3N-00552_T 11221238 230972291 4 16095 PPIG 0 . GRCh38 2 169630975 169630975 + Missense_Mutation SNP A A G C3N-00552_T C3N-00552_N A A c.749A>G p.Lys250Arg p.K250R ENST00000260970 10/14 111 93 18 180 180 0 varscan-mutect PPIG,missense_variant,p.Lys250Arg,ENST00000260970,NM_004792.2;PPIG,missense_variant,p.Lys235Arg,ENST00000409714,;PPIG,missense_variant,p.Lys250Arg,ENST00000448752,;PPIG,missense_variant,p.Lys250Arg,ENST00000462903,;PPIG,missense_variant,p.Lys246Arg,ENST00000433207,;PPIG,downstream_gene_variant,,ENST00000414307,;PPIG,non_coding_transcript_exon_variant,,ENST00000482772,;PPIG,downstream_gene_variant,,ENST00000530152,;PPIG,upstream_gene_variant,,ENST00000466142,;PPIG,downstream_gene_variant,,ENST00000417938,; G ENST00000260970 Transcript missense_variant 969/6368 749/2265 250/754 K/R aAa/aGa COSM5368551 1 1 PPIG HGNC HGNC:14650 protein_coding YES CCDS2235.1 ENSP00000260970 Q13427 UPI000013D124 NM_004792.2 tolerated(0.17) 10/14 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11071:SF292,hmmpanther:PTHR11071 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 53 169630975 169630975 A G 1 0 0 0 0 1 0 0 0 12435 14 1 5 5 PPIG 2 169630975 Missense_Mutation SNP A C3N-00552_T 158409737 169630975 72562554 5 16096 SETD2 0 . GRCh38 3 47121201 47121201 + Frame_Shift_Del DEL A A - novel C3N-00552_T C3N-00552_N A A c.3435delT p.Phe1145LeufsTer9 p.F1145Lfs*9 ENST00000409792 3/21 183 155 28 144 144 0 sindel-varindel-pindel SETD2,frameshift_variant,p.Phe1145LeufsTer9,ENST00000409792,NM_014159.6;SETD2,frameshift_variant,p.Phe1101LeufsTer9,ENST00000412450,;SETD2,frameshift_variant,p.Phe1017LeufsTer9,ENST00000330022,;SETD2,frameshift_variant,p.Phe863LeufsTer9,ENST00000431180,;SETD2,frameshift_variant,p.Phe779LeufsTer9,ENST00000445387,; - ENST00000409792 Transcript frameshift_variant 3478/8142 3435/7695 1145/2564 F/X ttT/tt 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 3/21 hmmpanther:PTHR22884:SF344,hmmpanther:PTHR22884 HIGH 1 deletion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 53 47121201 47121201 A - 1 0 1 0 1 0 0 0 0 14409 359 13 0 0 SETD2 3 47121201 Frame_Shift_Del DEL A C3N-00552_T 47121201 151174358 6 16097 SETD2 0 . GRCh38 3 47123130 47123133 + Frame_Shift_Del DEL TAAG TAAG - novel C3N-00552_T C3N-00552_N TAAG TAAG c.1503_1506delCTTA p.Tyr501Ter p.Y501* ENST00000409792 3/21 139 111 28 115 115 0 sindel-varindel-pindel SETD2,frameshift_variant,p.Tyr501Ter,ENST00000409792,NM_014159.6;SETD2,frameshift_variant,p.Tyr457Ter,ENST00000412450,;SETD2,frameshift_variant,p.Tyr373Ter,ENST00000330022,;SETD2,frameshift_variant,p.Tyr219Ter,ENST00000431180,;SETD2,frameshift_variant,p.Tyr135Ter,ENST00000445387,; - ENST00000409792 Transcript frameshift_variant 1546-1549/8142 1503-1506/7695 501-502/2564 YL/X taCTTA/ta 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 3/21 hmmpanther:PTHR22884:SF344,hmmpanther:PTHR22884 HIGH 1 deletion 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 53 47123130 47123130 TAAG - 1 0 1 0 1 0 0 0 0 14409 1519 53 0 0 SETD2 3 47123130 Frame_Shift_Del DEL TAAG C3N-00552_T 1929 47123130 151172429 7 16098 PARP9 0 . GRCh38 3 122550669 122550671 + In_Frame_Del DEL TCA TCA - novel C3N-00552_T C3N-00552_N TCA TCA c.1344_1346delTGA p.Asp448del p.D448del ENST00000360356 6/11 241 225 16 181 181 0 varindel-pindel PARP9,inframe_deletion,p.Asp413del,ENST00000462315,NM_001146106.1;PARP9,inframe_deletion,p.Asp448del,ENST00000360356,NM_001146102.1,NM_031458.2;PARP9,inframe_deletion,p.Asp413del,ENST00000477522,NM_001146103.1,NM_001146105.1;PARP9,inframe_deletion,p.Asp413del,ENST00000471785,NM_001146104.1;PARP9,intron_variant,,ENST00000492382,;PARP9,upstream_gene_variant,,ENST00000489652,; - ENST00000360356 Transcript inframe_deletion 1572-1574/3198 1344-1346/2565 448-449/854 DE/E gaTGAa/gaa 1 -1 PARP9 HGNC HGNC:24118 protein_coding YES CCDS3014.1 ENSP00000353512 Q8IXQ6 UPI000013D133 NM_001146102.1,NM_031458.2 6/11 PROSITE_profiles:PS51154,hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF61,Gene3D:3.40.220.10,Superfamily_domains:SSF52949 MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 53 122550669 122550669 TCA - 1 0 1 0 1 0 0 0 0 11546 1783 62 0 0 PARP9 3 122550669 In_Frame_Del DEL TCA C3N-00552_T 75427539 122550669 75744890 8 16099 PDCD10 0 . GRCh38 3 167697033 167697033 + Missense_Mutation SNP G G A rs868732450 C3N-00552_T C3N-00552_N G G c.244C>T p.Arg82Cys p.R82C ENST00000392750 5/9 431 349 82 333 333 0 strelka-varscan PDCD10,missense_variant,p.Arg82Cys,ENST00000392750,NM_007217.3;PDCD10,missense_variant,p.Arg82Cys,ENST00000473645,NM_145859.1;PDCD10,missense_variant,p.Arg82Cys,ENST00000497056,NM_145860.1;PDCD10,missense_variant,p.Arg82Cys,ENST00000470131,;PDCD10,missense_variant,p.Arg82Cys,ENST00000461494,;PDCD10,missense_variant,p.Arg82Cys,ENST00000475915,;PDCD10,missense_variant,p.Arg19Cys,ENST00000492396,;PDCD10,missense_variant,p.Arg82Cys,ENST00000471885,;PDCD10,missense_variant,p.Arg82Cys,ENST00000487947,;PDCD10,missense_variant,p.Arg82Cys,ENST00000462725,;PDCD10,missense_variant,p.Arg82Cys,ENST00000492139,;PDCD10,missense_variant,p.Arg63Cys,ENST00000479121,;PDCD10,downstream_gene_variant,,ENST00000464360,;PDCD10,non_coding_transcript_exon_variant,,ENST00000462830,;PDCD10,3_prime_UTR_variant,,ENST00000494502,;PDCD10,non_coding_transcript_exon_variant,,ENST00000483451,;HMGN1P8,upstream_gene_variant,,ENST00000463578,; A ENST00000392750 Transcript missense_variant 662/2067 244/639 82/212 R/C Cgt/Tgt rs868732450,COSM1693757 1 -1 PDCD10 HGNC HGNC:8761 protein_coding YES CCDS3202.1 ENSP00000376506 Q9BUL8 UPI0000071E33 NM_007217.3 deleterious(0) 5/9 Pfam_domain:PF06840,hmmpanther:PTHR13250,hmmpanther:PTHR13250:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 167697033 167697033 G A 1 0 0 0 0 1 0 0 0 11704 1058 37 1 1 PDCD10 3 167697033 Missense_Mutation SNP G C3N-00552_T 45146364 167697033 30598526 9 16100 MAN2B2 0 . GRCh38 4 6594714 6594714 + Missense_Mutation SNP T T A rs111767216 C3N-00552_T C3N-00552_N T T c.1039T>A p.Phe347Ile p.F347I ENST00000285599 7/19 409 325 84 306 306 0 strelka-varscan-mutect MAN2B2,missense_variant,p.Phe346Ile,ENST00000505907,;MAN2B2,missense_variant,p.Phe347Ile,ENST00000285599,NM_015274.2;MAN2B2,missense_variant,p.Phe296Ile,ENST00000504248,NM_001292038.1; A ENST00000285599 Transcript missense_variant 1075/5143 1039/3030 347/1009 F/I Ttc/Atc rs111767216 1 1 MAN2B2 HGNC HGNC:29623 protein_coding YES CCDS33951.1 ENSP00000285599 Q9Y2E5 UPI000004BF05 NM_015274.2 deleterious(0) 7/19 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF28,Pfam_domain:PF01074,Gene3D:3.20.110.10,Superfamily_domains:SSF88713 1 MODERATE 1 SNV 1 1 PASS rs111767216 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 6594714 6594714 T A 1 0 0 0 0 1 0 0 0 9138 1609 56 4 4 MAN2B2 4 6594714 Missense_Mutation SNP T C3N-00552_T 6594714 183619841 10 16101 CSN3 0 . GRCh38 4 70249064 70249064 + Missense_Mutation SNP C C T rs770368585 C3N-00552_T C3N-00552_N C C c.154C>T p.Pro52Ser p.P52S ENST00000304954 4/5 93 78 15 73 73 0 strelka-varscan-mutect CSN3,missense_variant,p.Pro52Ser,ENST00000304954,NM_005212.2; T ENST00000304954 Transcript missense_variant 240/836 154/549 52/182 P/S Cca/Tca rs770368585,COSM4125730,COSM70321 1 1 CSN3 HGNC HGNC:2446 protein_coding YES CCDS3538.1 ENSP00000304822 P07498 UPI000004F262 NM_005212.2 deleterious(0) 4/5 hmmpanther:PTHR11470:SF2,hmmpanther:PTHR11470,Pfam_domain:PF00997,PIRSF_domain:PIRSF002374 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770368585 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 70249064 70249064 C T 1 0 0 0 0 1 0 0 0 3749 739 26 3 3 CSN3 4 70249064 Missense_Mutation SNP C C3N-00552_T 63654350 70249064 119965491 11 16102 MTTP 0 . GRCh38 4 99608943 99608943 + Missense_Mutation SNP G G A novel C3N-00552_T C3N-00552_N G G c.1816G>A p.Val606Ile p.V606I ENST00000511045 12/18 356 297 59 283 283 0 strelka-varscan-mutect MTTP,missense_variant,p.Val579Ile,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Val579Ile,ENST00000265517,;MTTP,missense_variant,p.Val606Ile,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; A ENST00000511045 Transcript missense_variant 1829/3154 1816/2766 606/921 V/I Gtt/Att 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 tolerated(1) 12/18 Superfamily_domains:0040642,Gene3D:1lshA02,Pfam_domain:PF01347,PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1,SMART_domains:SM00638 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 99608943 99608943 G A 1 0 0 0 0 1 0 0 0 9961 1377 48 3 3 MTTP 4 99608943 Missense_Mutation SNP G C3N-00552_T 29359879 99608943 90605612 12 16103 SYNJ2 0 . GRCh38 6 158064858 158064858 + Missense_Mutation SNP G G T novel C3N-00552_T C3N-00552_N G G c.1392G>T p.Met464Ile p.M464I ENST00000355585 11/27 58 49 9 61 61 0 strelka-varscan-mutect SYNJ2,missense_variant,p.Met464Ile,ENST00000355585,NM_003898.3,NM_001178088.1;SYNJ2,downstream_gene_variant,,ENST00000485863,; T ENST00000355585 Transcript missense_variant 1467/7378 1392/4491 464/1496 M/I atG/atT 1 1 SYNJ2 HGNC HGNC:11504 protein_coding YES CCDS5254.1 ENSP00000347792 O15056 UPI000006E2F8 NM_003898.3,NM_001178088.1 deleterious(0.05) 11/27 hmmpanther:PTHR11200:SF148,hmmpanther:PTHR11200 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.93119 0.9999999 1 1 1 0 T 3 4 53 158064858 158064858 G T 1 0 0 0 0 1 0 0 0 15847 1377 48 2 2 SYNJ2 6 158064858 Missense_Mutation SNP G C3N-00552_T 158064858 12741121 13 16104 HDAC9 0 . GRCh38 7 18829486 18829486 + Missense_Mutation SNP G G A C3N-00552_T C3N-00552_N G G c.2404G>A p.Ala802Thr p.A802T ENST00000441542 18/25 115 97 18 119 119 0 strelka-mutect HDAC9,missense_variant,p.Ala799Thr,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Ala758Thr,ENST00000401921,;HDAC9,missense_variant,p.Ala802Thr,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Ala799Thr,ENST00000432645,NM_058176.2;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000490851,;HDAC9,downstream_gene_variant,,ENST00000461159,; A ENST00000441542 Transcript missense_variant 2404/3210 2404/3210 802/1069 A/T Gca/Aca COSM371174,COSM371175 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0) 18/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,Gene3D:3.40.800.20,Pfam_domain:PF00850,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768,Prints_domain:PR01270 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999249 1 1 1 0 A 3 1 53 18829486 18829486 G A 1 0 0 0 0 1 0 0 0 6901 1319 46 3 3 HDAC9 7 18829486 Missense_Mutation SNP G C3N-00552_T 18829486 140516487 14 16105 SLC35G5 0 . GRCh38 8 11331954 11331954 + Missense_Mutation SNP G G A novel C3N-00552_T C3N-00552_N G G c.848G>A p.Cys283Tyr p.C283Y ENST00000382435 1/1 429 375 54 384 384 0 varscan-mutect SLC35G5,missense_variant,p.Cys283Tyr,ENST00000382435,NM_054028.1;MTMR9,downstream_gene_variant,,ENST00000221086,NM_015458.3; A ENST00000382435 Transcript missense_variant 1067/1321 848/1017 283/338 C/Y tGc/tAc 1 1 SLC35G5 HGNC HGNC:15546 protein_coding YES CCDS5980.1 ENSP00000371872 Q96KT7 UPI0000071B8F NM_054028.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR22911:SF32,hmmpanther:PTHR22911,Superfamily_domains:0043518 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 11331954 11331954 G A 1 0 0 0 0 1 0 0 0 14869 1319 46 3 3 SLC35G5 8 11331954 Missense_Mutation SNP G C3N-00552_T 11331954 133806682 15 16106 INTS9 0 . GRCh38 8 28846764 28846764 + Missense_Mutation SNP C C T novel C3N-00552_T C3N-00552_N C C c.244G>A p.Glu82Lys p.E82K ENST00000521022 4/17 221 191 30 171 171 0 strelka-varscan-mutect INTS9,missense_variant,p.Glu82Lys,ENST00000521022,NM_018250.3;INTS9,missense_variant,p.Glu58Lys,ENST00000521777,NM_001172562.1;INTS9,missense_variant,p.Glu82Lys,ENST00000523436,;INTS9,missense_variant,p.Glu74Lys,ENST00000524081,;INTS9,missense_variant,p.Glu58Lys,ENST00000520184,;INTS9,intron_variant,,ENST00000416984,NM_001145159.2;INTS9,missense_variant,p.Glu82Lys,ENST00000523303,;INTS9,missense_variant,p.Glu82Lys,ENST00000518510,;INTS9,non_coding_transcript_exon_variant,,ENST00000520983,;INTS9,intron_variant,,ENST00000522363,;INTS9,intron_variant,,ENST00000520437,;INTS9,downstream_gene_variant,,ENST00000520831,; T ENST00000521022 Transcript missense_variant 326/2544 244/1977 82/658 E/K Gaa/Aaa 1 -1 INTS9 HGNC HGNC:25592 protein_coding YES CCDS34873.1 ENSP00000429065 Q9NV88 UPI0000071C2E NM_018250.3 deleterious(0.01) 4/17 hmmpanther:PTHR11203:SF2,hmmpanther:PTHR11203,Superfamily_domains:SSF56281 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 28846764 28846764 C T 1 0 0 0 0 1 0 0 0 7688 864 30 3 3 INTS9 8 28846764 Missense_Mutation SNP C C3N-00552_T 17514810 28846764 116291872 16 16107 SPATA31D1 0 . GRCh38 9 81988950 81988950 + Silent SNP C C T novel C3N-00552_T C3N-00552_N C C c.132C>T p.= p.Y44Y ENST00000344803 1/4 312 254 58 249 249 0 strelka-varscan-mutect SPATA31D1,synonymous_variant,p.=,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,non_coding_transcript_exon_variant,,ENST00000603921,; T ENST00000344803 Transcript synonymous_variant 179/4833 132/4731 44/1576 Y taC/taT 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 1/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12 LOW 1 SNV 2 1 PASS rs1397482654 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 53 81988950 81988950 C T 1 0 0 0 0 0 0 0 1 15347 547 19 1 1 SPATA31D1 9 81988950 Silent SNP C C3N-00552_T 81988950 56405767 17 16108 HSD17B3 0 . GRCh38 9 96240879 96240879 + Missense_Mutation SNP G G A novel C3N-00552_T C3N-00552_N G G c.701C>T p.Ala234Val p.A234V ENST00000375263 10/11 310 247 63 199 199 0 strelka-varscan-mutect HSD17B3,missense_variant,p.Ala234Val,ENST00000375263,NM_000197.1;HSD17B3,intron_variant,,ENST00000375262,;HSD17B3,non_coding_transcript_exon_variant,,ENST00000464104,;HSD17B3,non_coding_transcript_exon_variant,,ENST00000494814,;HSD17B3,non_coding_transcript_exon_variant,,ENST00000484816,;HSD17B3,upstream_gene_variant,,ENST00000467499,; A ENST00000375263 Transcript missense_variant 749/1135 701/933 234/310 A/V gCa/gTa 1 -1 HSD17B3 HGNC HGNC:5212 protein_coding YES CCDS6716.1 ENSP00000364412 P37058 Q6FH62 UPI0000001643 NM_000197.1 deleterious(0.04) 10/11 Gene3D:3.40.50.720,Pfam_domain:PF00106,PIRSF_domain:PIRSF000126,Prints_domain:PR00081,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 53 96240879 96240879 G A 1 0 0 0 0 1 0 0 0 7280 1319 46 3 3 HSD17B3 9 96240879 Missense_Mutation SNP G C3N-00552_T 14251929 96240879 42153838 18 16109 SNX30 0 . GRCh38 9 112836390 112836390 + Silent SNP G G T novel C3N-00552_T C3N-00552_N G G c.795G>T p.= p.R265R ENST00000374232 5/9 94 77 17 74 74 0 strelka-varscan-mutect SNX30,synonymous_variant,p.=,ENST00000374232,NM_001012994.1;SNX30,upstream_gene_variant,,ENST00000416585,; T ENST00000374232 Transcript synonymous_variant 959/7622 795/1314 265/437 R cgG/cgT 1 1 SNX30 HGNC HGNC:23685 protein_coding YES CCDS43865.1 ENSP00000363349 Q5VWJ9 UPI0000457796 NM_001012994.1 5/9 hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF123,Superfamily_domains:SSF103657 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 53 112836390 112836390 G T 1 0 0 0 0 0 0 0 1 15221 1161 41 2 2 SNX30 9 112836390 Silent SNP G C3N-00552_T 16595511 112836390 25558327 19 16110 OR1Q1 0 . GRCh38 9 122615483 122615483 + Missense_Mutation SNP C C T novel C3N-00552_T C3N-00552_N C C c.746C>T p.Ala249Val p.A249V ENST00000297913 1/1 119 98 21 72 72 0 strelka-varscan-mutect OR1Q1,missense_variant,p.Ala249Val,ENST00000297913,NM_012364.1;RP11-64P14.7,intron_variant,,ENST00000431442,;RP11-64P14.7,upstream_gene_variant,,ENST00000419604,; T ENST00000297913 Transcript missense_variant 746/945 746/945 249/314 A/V gCc/gTc 1 1 OR1Q1 HGNC HGNC:8223 protein_coding YES CCDS35125.1 ENSP00000297913 Q15612 UPI000003CACD NM_012364.1 tolerated(0.21) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs1457572702 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 122615483 122615483 C T 1 0 0 0 0 1 0 0 0 11049 739 26 3 3 OR1Q1 9 122615483 Missense_Mutation SNP C C3N-00552_T 9779093 122615483 15779234 20 16111 NT5C2 0 . GRCh38 10 103093182 103093182 + Silent SNP A A T novel C3N-00552_T C3N-00552_N A A c.1116T>A p.= p.I372I ENST00000343289 14/18 77 64 13 69 69 0 strelka-varscan-mutect NT5C2,synonymous_variant,p.=,ENST00000343289,NM_001134373.2,NM_012229.4;NT5C2,synonymous_variant,p.=,ENST00000404739,;NT5C2,synonymous_variant,p.=,ENST00000421281,;CNNM2,downstream_gene_variant,,ENST00000369878,NM_017649.4;NT5C2,downstream_gene_variant,,ENST00000458345,;NT5C2,non_coding_transcript_exon_variant,,ENST00000369857,;NT5C2,downstream_gene_variant,,ENST00000461461,;NT5C2,downstream_gene_variant,,ENST00000452156,;NT5C2,downstream_gene_variant,,ENST00000469228,; T ENST00000343289 Transcript synonymous_variant 1211/3435 1116/1686 372/561 I atT/atA 1 -1 NT5C2 HGNC HGNC:8022 protein_coding YES CCDS7544.1 ENSP00000339479 P49902 UPI0000124F44 NM_001134373.2,NM_012229.4 14/18 Gene3D:3.40.50.1000,Pfam_domain:PF05761,PIRSF_domain:PIRSF017434,hmmpanther:PTHR12103,hmmpanther:PTHR12103:SF17,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR02244 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 53 103093182 103093182 A T 1 0 0 0 0 0 0 0 1 10750 242 9 4 4 NT5C2 10 103093182 Silent SNP A C3N-00552_T 103093182 30704240 21 16112 FNBP4 0 . GRCh38 11 47723063 47723064 + Frame_Shift_Ins INS - - A novel C3N-00552_T C3N-00552_N - - c.2717_2718insT p.Pro907ThrfsTer20 p.P907Tfs*20 ENST00000263773 15/17 172 139 33 202 202 0 sindel-varindel-pindel FNBP4,frameshift_variant,p.Pro907ThrfsTer20,ENST00000263773,NM_001318339.1,NM_015308.2;Y_RNA,downstream_gene_variant,,ENST00000363220,;FNBP4,non_coding_transcript_exon_variant,,ENST00000532646,;FNBP4,intron_variant,,ENST00000526109,;FNBP4,downstream_gene_variant,,ENST00000525792,;FNBP4,downstream_gene_variant,,ENST00000531394,;FNBP4,non_coding_transcript_exon_variant,,ENST00000530207,; A ENST00000263773 Transcript frameshift_variant 2730-2731/3972 2717-2718/3054 906/1017 P/PX cca/ccTa 1 -1 FNBP4 HGNC HGNC:19752 protein_coding YES CCDS41644.1 ENSP00000263773 Q8N3X1 UPI0000DBEF37 NM_001318339.1,NM_015308.2 15/17 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF175,Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 7 5 53 47723063 47723063 - A 1 0 1 1 0 0 0 0 0 5823 1683 59 0 0 FNBP4 11 47723063 Frame_Shift_Ins INS - C3N-00552_T 47723063 87363559 22 16113 UBE4A 0 . GRCh38 11 118384683 118384683 + Missense_Mutation SNP A A T novel C3N-00552_T C3N-00552_N A A c.2267A>T p.Tyr756Phe p.Y756F ENST00000431736 14/20 195 158 37 134 134 0 strelka-varscan-mutect UBE4A,missense_variant,p.Tyr749Phe,ENST00000252108,NM_001204077.1;UBE4A,missense_variant,p.Tyr756Phe,ENST00000431736,NM_004788.3;UBE4A,missense_variant,p.Tyr221Phe,ENST00000545354,; T ENST00000431736 Transcript missense_variant 2339/6061 2267/3222 756/1073 Y/F tAt/tTt 1 1 UBE4A HGNC HGNC:12499 protein_coding YES CCDS8396.1 ENSP00000387362 Q14139 UPI000013CD3F NM_004788.3 tolerated(0.06) 14/20 hmmpanther:PTHR13931:SF2,hmmpanther:PTHR13931,Pfam_domain:PF10408 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 118384683 118384683 A T 1 0 0 0 0 1 0 0 0 17406 449 16 4 4 UBE4A 11 118384683 Missense_Mutation SNP A C3N-00552_T 70661620 118384683 16701939 23 16114 MRPS35 0 . GRCh38 12 27710852 27710852 + Silent SNP C C T novel C3N-00552_T C3N-00552_N C C c.9C>T p.= p.A3A ENST00000081029 1/8 197 186 11 128 128 0 strelka-varscan-mutect MRPS35,synonymous_variant,p.=,ENST00000081029,NM_021821.3;MRPS35,synonymous_variant,p.=,ENST00000538315,NM_001190864.1;MRPS35,synonymous_variant,p.=,ENST00000542791,;RP11-1060J15.7,downstream_gene_variant,,ENST00000538640,;RP11-1060J15.4,upstream_gene_variant,,ENST00000536317,;RP11-1060J15.4,upstream_gene_variant,,ENST00000542660,;MRPS35,synonymous_variant,p.=,ENST00000536569,;MRPS35,upstream_gene_variant,,ENST00000542199,; T ENST00000081029 Transcript synonymous_variant 80/1888 9/972 3/323 A gcC/gcT 1 1 MRPS35 HGNC HGNC:16635 protein_coding YES CCDS8714.1 ENSP00000081029 P82673 UPI000003B0E7 NM_021821.3 1/8 LOW 1 SNV 1 1 PASS rs1033768892 . 0 207 0 2 0 0 0 0 -13.7874 0.9999994 1 1 1 0 T 2 4 53 27710852 27710852 C T 1 0 0 0 0 0 0 0 1 9821 639 23 1 1 MRPS35 12 27710852 Silent SNP C C3N-00552_T 27710852 105564457 24 16115 FAM179B 0 . GRCh38 14 45027407 45027407 + Missense_Mutation SNP C C T novel C3N-00552_T C3N-00552_N C C c.3437C>T p.Ser1146Leu p.S1146L ENST00000361462 9/20 153 139 14 161 161 0 strelka-varscan-mutect FAM179B,missense_variant,p.Ser1146Leu,ENST00000361462,NM_001308120.1;FAM179B,missense_variant,p.Ser1146Leu,ENST00000361577,NM_015091.2;KLHL28,intron_variant,,ENST00000556239,;KLHL28,intron_variant,,ENST00000553817,;FAM179B,3_prime_UTR_variant,,ENST00000557423,;FAM179B,non_coding_transcript_exon_variant,,ENST00000556105,;FAM179B,downstream_gene_variant,,ENST00000555586,; T ENST00000361462 Transcript missense_variant 3620/6375 3437/5322 1146/1773 S/L tCa/tTa 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 deleterious(0.04) 9/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 45027407 45027407 C T 1 0 0 0 0 1 0 0 0 5351 838 29 3 3 FAM179B 14 45027407 Missense_Mutation SNP C C3N-00552_T 45027407 62016311 25 16116 NGB 0 . GRCh38 14 77270855 77270857 + In_Frame_Del DEL AAC AAC - novel C3N-00552_T C3N-00552_N AAC AAC c.81_83delGTT p.Phe28del p.F28del ENST00000298352 1/4 230 208 22 242 242 0 sindel-varindel NGB,inframe_deletion,p.Phe28del,ENST00000298352,NM_021257.3;POMT2,downstream_gene_variant,,ENST00000261534,NM_013382.5;MIR1260A,downstream_gene_variant,,ENST00000408827,;POMT2,downstream_gene_variant,,ENST00000452340,;POMT2,downstream_gene_variant,,ENST00000554767,; - ENST00000298352 Transcript inframe_deletion 456-458/1884 81-83/456 27-28/151 LF/L ctGTTt/ctt 1 -1 NGB HGNC HGNC:14077 protein_coding YES CCDS9856.1 ENSP00000298352 Q9NPG2 A0M8W9 UPI0000073D72 NM_021257.3 1/4 PROSITE_profiles:PS01033,hmmpanther:PTHR22924,Gene3D:1.10.490.10,Pfam_domain:PF00042,Superfamily_domains:SSF46458 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 53 77270855 77270855 AAC - 1 0 1 0 1 0 0 0 0 10428 14 1 0 0 NGB 14 77270855 In_Frame_Del DEL AAC C3N-00552_T 32243448 77270855 29772863 26 16117 KCNK13 0 . GRCh38 14 90184787 90184787 + Silent SNP G G A rs764305711 C3N-00552_T C3N-00552_N G G c.1011G>A p.= p.T337T ENST00000282146 2/2 173 145 28 146 146 0 strelka-varscan-mutect KCNK13,synonymous_variant,p.=,ENST00000282146,NM_022054.3; A ENST00000282146 Transcript synonymous_variant 1452/2522 1011/1227 337/408 T acG/acA rs764305711 1 1 KCNK13 HGNC HGNC:6275 protein_coding YES CCDS9889.1 ENSP00000282146 Q9HB14 UPI0000127A55 NM_022054.3 2/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF57 LOW 1 SNV 1 1 PASS rs764305711 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 53 90184787 90184787 G A 1 0 0 0 0 0 0 0 1 7978 1103 39 1 1 KCNK13 14 90184787 Silent SNP G C3N-00552_T 12913932 90184787 16858931 27 16118 CDT1 0 . GRCh38 16 88806601 88806601 + Missense_Mutation SNP A A G novel C3N-00552_T C3N-00552_N A A c.1049A>G p.Gln350Arg p.Q350R ENST00000301019 7/10 473 399 74 302 302 0 strelka-varscan-mutect CDT1,missense_variant,p.Gln350Arg,ENST00000301019,NM_030928.3;CDT1,missense_variant,p.Gln107Arg,ENST00000569140,;APRT,downstream_gene_variant,,ENST00000378364,NM_000485.2;APRT,downstream_gene_variant,,ENST00000569616,;APRT,downstream_gene_variant,,ENST00000563655,;APRT,downstream_gene_variant,,ENST00000426324,NM_001030018.1;APRT,downstream_gene_variant,,ENST00000567713,;CDT1,downstream_gene_variant,,ENST00000562747,;APRT,downstream_gene_variant,,ENST00000567391,;APRT,downstream_gene_variant,,ENST00000564858,;APRT,downstream_gene_variant,,ENST00000568319,;APRT,downstream_gene_variant,,ENST00000562464,;APRT,downstream_gene_variant,,ENST00000568575,;APRT,downstream_gene_variant,,ENST00000567057,; G ENST00000301019 Transcript missense_variant 1668/3240 1049/1641 350/546 Q/R cAg/cGg 1 1 CDT1 HGNC HGNC:24576 protein_coding YES CCDS32510.1 ENSP00000301019 Q9H211 UPI00001FF6B1 NM_030928.3 tolerated(0.21) 7/10 hmmpanther:PTHR28637:SF1,hmmpanther:PTHR28637,SMART_domains:SM01075,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 53 88806601 88806601 A G 1 0 0 0 0 1 0 0 0 2886 188 7 5 5 CDT1 16 88806601 Missense_Mutation SNP A C3N-00552_T 88806601 1531744 28 16119 TP53 0 . GRCh38 17 7674230 7674230 + Missense_Mutation SNP C C T rs28934575 C3N-00552_T C3N-00552_N C C c.733G>A p.Gly245Ser p.G245S ENST00000269305 7/11 325 253 72 252 252 0 strelka-varscan-mutect TP53,missense_variant,p.Gly245Ser,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly245Ser,ENST00000420246,;TP53,missense_variant,p.Gly206Ser,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly206Ser,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly245Ser,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly206Ser,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly245Ser,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly206Ser,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly245Ser,ENST00000445888,;TP53,missense_variant,p.Gly206Ser,ENST00000619485,;TP53,missense_variant,p.Gly113Ser,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly86Ser,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly113Ser,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly86Ser,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly113Ser,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly86Ser,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly245Ser,ENST00000359597,;TP53,missense_variant,p.Gly234Ser,ENST00000615910,;TP53,missense_variant,p.Gly245Ser,ENST00000413465,;TP53,missense_variant,p.Gly113Ser,ENST00000509690,;TP53,missense_variant,p.Gly152Ser,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly206Ser,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 923/2579 733/1182 245/393 G/S Ggc/Agc rs28934575,CM010463,CM900210,CM920674,TP53_g.13370G>T,TP53_g.13370G>C,TP53_g.13370del,TP53_g.13370G>A,COSM10957,COSM11081,COSM121035,COSM121036,COSM121037,COSM1610835,COSM1610836,COSM1610837,COSM1640833,COSM1646855,COSM3356965,COSM3388190,COSM3717639,COSM3717640,COSM3726870,COSM3726871,COSM3726872,COSM3726873,COSM3726874,COSM44642,COSM562651,COSM562652,COSM562653,COSM6932 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic,pathogenic 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 2.50327002510566e+23 MODERATE 1 SNV 1 1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs28934575 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 7674230 7674230 C T 1 0 0 0 0 1 0 0 0 16859 652 23 1 1 TP53 17 7674230 Missense_Mutation SNP C C3N-00552_T 7674230 75583211 29 16120 SP6 0 . GRCh38 17 47847532 47847532 + Missense_Mutation SNP C C T novel C3N-00552_T C3N-00552_N C C c.898G>A p.Glu300Lys p.E300K ENST00000536300 2/2 452 429 23 383 383 0 strelka-varscan-mutect SP6,missense_variant,p.Glu300Lys,ENST00000536300,NM_001258248.1;SP6,missense_variant,p.Glu300Lys,ENST00000342234,NM_199262.2; T ENST00000536300 Transcript missense_variant 1230/3848 898/1131 300/376 E/K Gag/Aag 1 -1 SP6 HGNC HGNC:14530 protein_coding YES CCDS11520.1 ENSP00000438209 Q3SY56 UPI000022A416 NM_001258248.1 deleterious(0) 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR23235,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 53 47847532 47847532 C T 1 0 0 0 0 1 0 0 0 15294 893 31 1 1 SP6 17 47847532 Missense_Mutation SNP C C3N-00552_T 40173302 47847532 35409909 30 16121 NOL11 0 . GRCh38 17 67724114 67724114 + Frame_Shift_Del DEL A A - rs144436026 C3N-00552_T C3N-00552_N A A c.585delA p.Leu195PhefsTer10 p.L195Ffs*10 ENST00000253247 6/18 49 45 4 80 80 0 sindel-pindel NOL11,frameshift_variant,p.Leu195PhefsTer10,ENST00000253247,NM_015462.4,NM_001303272.1;NOL11,frameshift_variant,p.Leu67PhefsTer10,ENST00000580833,;NOL11,downstream_gene_variant,,ENST00000581106,;NOL11,downstream_gene_variant,,ENST00000581966,;NOL11,3_prime_UTR_variant,,ENST00000581375,;NOL11,non_coding_transcript_exon_variant,,ENST00000580914,;NOL11,downstream_gene_variant,,ENST00000584942,; - ENST00000253247 Transcript frameshift_variant 700/2947 585/2160 195/719 L/X ttA/tt rs144436026 1 1 NOL11 HGNC HGNC:24557 protein_coding YES CCDS11671.1 ENSP00000253247 Q9H8H0 UPI0000072B83 NM_015462.4,NM_001303272.1 6/18 hmmpanther:PTHR15633,hmmpanther:PTHR15633:SF2,Superfamily_domains:SSF50978 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.41036 1 1 1 1 0 - 7 5 53 67724114 67724114 A - 1 0 1 0 1 0 0 0 0 10564 388 14 0 0 NOL11 17 67724114 Frame_Shift_Del DEL A C3N-00552_T 19876582 67724114 15533327 31 16122 SMAD4 0 . GRCh38 18 51078399 51078409 + Frame_Shift_Del DEL CGGGCCCTCCA CGGGCCCTCCA - novel C3N-00552_T C3N-00552_N CGGGCCCTCCA CGGGCCCTCCA c.1591_1601delCGGGCCCTCCA p.Arg531AlafsTer42 p.R531Afs*42 ENST00000342988 12/12 262 219 43 268 268 0 sindel-pindel SMAD4,frameshift_variant,p.Arg531AlafsTer42,ENST00000342988,NM_005359.5;SMAD4,frameshift_variant,p.Arg531AlafsTer42,ENST00000398417,;SMAD4,frameshift_variant,p.Arg435AlafsTer?,ENST00000588745,;SMAD4,downstream_gene_variant,,ENST00000593223,;SMAD4,non_coding_transcript_exon_variant,,ENST00000586253,;SMAD4,3_prime_UTR_variant,,ENST00000611848,;SMAD4,3_prime_UTR_variant,,ENST00000592186,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,downstream_gene_variant,,ENST00000590499,; - ENST00000342988 Transcript frameshift_variant 2129-2139/8769 1591-1601/1659 531-534/552 RALQ/X CGGGCCCTCCAg/g 1 1 SMAD4 HGNC HGNC:6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 A0A024R274 UPI0000053431 NM_005359.5 12/12 Gene3D:2.60.200.10,PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF39,Superfamily_domains:SSF49879 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 53 51078399 51078399 CGGGCCCTCCA - 1 0 1 0 1 0 0 0 0 15053 643 23 0 0 SMAD4 18 51078399 Frame_Shift_Del DEL CGGGCCCTCCA C3N-00552_T 51078399 29294886 32 16123 TDRD12 0 . GRCh38 19 32815617 32815617 + Missense_Mutation SNP C C A novel C3N-00552_T C3N-00552_N C C c.3311C>A p.Thr1104Asn p.T1104N ENST00000444215 26/28 119 104 15 96 96 0 strelka-varscan-mutect TDRD12,missense_variant,p.Thr1104Asn,ENST00000444215,;TDRD12,missense_variant,p.Thr180Asn,ENST00000637289,;TDRD12,missense_variant,p.Thr19Asn,ENST00000564769,; A ENST00000444215 Transcript missense_variant 3631/3934 3311/3534 1104/1177 T/N aCc/aAc 1 1 TDRD12 HGNC HGNC:25044 protein_coding ENSP00000416248 Q587J7 UPI0000251D93 tolerated(0.06) 26/28 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 53 32815617 32815617 C A 1 0 0 0 0 1 0 0 0 16140 521 18 2 2 TDRD12 19 32815617 Missense_Mutation SNP C C3N-00552_T 32815617 25801999 33 16124 CACNG7 0 . GRCh38 19 53942037 53942037 + Missense_Mutation SNP G G A novel C3N-00552_T C3N-00552_N G G c.572G>A p.Gly191Glu p.G191E ENST00000391767 6/6 54 48 6 24 24 0 strelka-mutect CACNG7,missense_variant,p.Gly191Glu,ENST00000391767,;CACNG7,missense_variant,p.Gly191Glu,ENST00000222212,NM_031896.4;CACNG7,downstream_gene_variant,,ENST00000391766,;CACNG7,downstream_gene_variant,,ENST00000468076,; A ENST00000391767 Transcript missense_variant,splice_region_variant 784/2688 572/828 191/275 G/E gGg/gAg 1 1 CACNG7 HGNC HGNC:13626 protein_coding YES CCDS12868.1 ENSP00000375647 P62955 UPI00000010F1 tolerated(0.1) 6/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR12107:SF3,hmmpanther:PTHR12107,Pfam_domain:PF13903,Prints_domain:PR01792 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -14.43106 1 1 1 1 0 A 3 1 53 53942037 53942037 G A 1 0 0 0 0 1 0 0 0 2250 1246 43 3 3 CACNG7 19 53942037 Missense_Mutation SNP G C3N-00552_T 21126420 53942037 4675579 34 16125 RALGAPB 0 . GRCh38 20 38524841 38524841 + Silent SNP C C T novel C3N-00552_T C3N-00552_N C C c.1683C>T p.= p.A561A ENST00000262879 11/30 254 221 33 296 296 0 strelka-varscan-mutect RALGAPB,synonymous_variant,p.=,ENST00000262879,NM_001282917.1,NM_020336.3;RALGAPB,synonymous_variant,p.=,ENST00000397042,NM_001282918.1;RALGAPB,synonymous_variant,p.=,ENST00000397040,;RALGAPB,synonymous_variant,p.=,ENST00000438490,;RALGAPB,upstream_gene_variant,,ENST00000632792,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,; T ENST00000262879 Transcript synonymous_variant 1967/8663 1683/4485 561/1494 A gcC/gcT 1 1 RALGAPB HGNC HGNC:29221 protein_coding YES CCDS13305.1 ENSP00000262879 Q86X10 UPI000000DBFD NM_001282917.1,NM_020336.3 11/30 hmmpanther:PTHR21344 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 53 38524841 38524841 C T 1 0 0 0 0 0 0 0 1 13174 581 21 3 3 RALGAPB 20 38524841 Silent SNP C C3N-00552_T 38524841 25919326 35 16126 MYH9 0 . GRCh38 22 36312212 36312212 + Missense_Mutation SNP G G C C3N-00552_T C3N-00552_N G G c.1565C>G p.Pro522Arg p.P522R ENST00000216181 14/41 217 193 24 169 169 0 strelka-varscan-mutect MYH9,missense_variant,p.Pro522Arg,ENST00000216181,NM_002473.5;MYH9,downstream_gene_variant,,ENST00000477189,; C ENST00000216181 Transcript missense_variant 1796/7501 1565/5883 522/1960 P/R cCg/cGg COSM3149655 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 deleterious(0) 14/41 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF317,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 0 9 0 0 0 0 -20 0.9682868 1 1 1 0 C 3 2 53 36312212 36312212 G C 1 0 0 0 0 1 0 0 0 10042 1116 39 4 4 MYH9 22 36312212 Missense_Mutation SNP G C3N-00552_T 36312212 14506256 36 16127 XAGE3 0 . GRCh38 X 52866496 52866497 + Frame_Shift_Ins INS - - AGTT novel C3N-00552_T C3N-00552_N - - c.120_123dupAACT p.Glu42AsnfsTer2 p.E42Nfs*2 ENST00000346279 3/5 143 121 22 166 166 0 sindel-pindel XAGE3,frameshift_variant,p.Glu42AsnfsTer2,ENST00000346279,NM_133179.2;XAGE3,frameshift_variant,p.Glu42AsnfsTer2,ENST00000375491,NM_130776.1; AGTT ENST00000346279 Transcript frameshift_variant 194-195/497 123-124/336 41-42/111 -/NX -/AACT 1 -1 XAGE3 HGNC HGNC:14618 protein_coding YES CCDS14347.1 ENSP00000303061 Q8WTP9 UPI0000131BD0 NM_133179.2 3/5 Pfam_domain:PF05831,hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF4,Low_complexity_(Seg):seg,SMART_domains:SM01379 HIGH 1 insertion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 AGTT 7 5 53 52866496 52866496 - AGTT 1 0 1 1 0 0 0 0 0 17979 835 29 0 0 XAGE3 23 52866496 Frame_Shift_Ins INS - C3N-00552_T 52866496 103174399 37 16128 P2RY4 0 . GRCh38 X 70259329 70259329 + Missense_Mutation SNP T T C novel C3N-00552_T C3N-00552_N T T c.296A>G p.Asn99Ser p.N99S ENST00000374519 1/1 268 213 55 320 320 0 strelka-varscan-mutect P2RY4,missense_variant,p.Asn99Ser,ENST00000374519,NM_002565.3; C ENST00000374519 Transcript missense_variant 436/1595 296/1098 99/365 N/S aAc/aGc 1 -1 P2RY4 HGNC HGNC:8542 protein_coding YES CCDS14398.1 ENSP00000363643 P51582 UPI000002E776 NM_002565.3 tolerated(0.2) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF21,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 53 70259329 70259329 T C 1 0 0 0 0 1 0 0 0 11426 1725 60 5 5 P2RY4 23 70259329 Missense_Mutation SNP T C3N-00552_T 17392833 70259329 85781566 38 16129 AGRN 0 . GRCh38 1 1045510 1045510 + Silent SNP G G C novel C3N-00556_T C3N-00556_N G G c.2523G>C p.= p.R841R ENST00000379370 14/36 134 120 14 144 144 0 strelka-varscan-mutect AGRN,synonymous_variant,p.=,ENST00000620552,NM_001305275.1;AGRN,synonymous_variant,p.=,ENST00000379370,NM_198576.3;AGRN,downstream_gene_variant,,ENST00000477585,;AGRN,non_coding_transcript_exon_variant,,ENST00000479707,;AGRN,downstream_gene_variant,,ENST00000469403,;AGRN,upstream_gene_variant,,ENST00000492947,;AGRN,upstream_gene_variant,,ENST00000466223,;AGRN,upstream_gene_variant,,ENST00000478677,; C ENST00000379370 Transcript synonymous_variant 2573/7323 2523/6138 841/2045 R cgG/cgC 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 14/36 PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288,SMART_domains:SM00180 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 1045510 1045510 G C 1 0 0 0 0 0 0 0 1 476 1161 41 4 4 AGRN 1 1045510 Silent SNP G C3N-00556_T 1045510 247910912 1 16130 MEGF6 0 . GRCh38 1 3501090 3501090 + Nonsense_Mutation SNP G G T rs776401705 C3N-00556_T C3N-00556_N G G c.2451C>A p.Cys817Ter p.C817* ENST00000356575 20/37 191 173 18 212 212 0 strelka-varscan-mutect MEGF6,stop_gained,p.Cys817Ter,ENST00000356575,NM_001409.3;MEGF6,stop_gained,p.Cys712Ter,ENST00000294599,;MEGF6,upstream_gene_variant,,ENST00000491842,;MEGF6,stop_gained,p.Cys824Ter,ENST00000485002,; T ENST00000356575 Transcript stop_gained 2678/5455 2451/4626 817/1541 C/* tgC/tgA rs776401705 1 -1 MEGF6 HGNC HGNC:3232 protein_coding YES CCDS41237.1 ENSP00000348982 O75095 UPI0000DACACB NM_001409.3 20/37 PROSITE_patterns:PS01186,Gene3D:2gy5A03,SMART_domains:SM00180 HIGH 1 SNV 1 1 PASS rs776401705 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 3501090 3501090 G T 1 0 0 0 0 0 1 0 0 9402 1217 42 2 2 MEGF6 1 3501090 Nonsense_Mutation SNP G C3N-00556_T 2455580 3501090 245455332 2 16131 TP73 0 . GRCh38 1 3730119 3730119 + Missense_Mutation SNP C C T rs760067757 C3N-00556_T C3N-00556_N C C c.1316C>T p.Ser439Leu p.S439L ENST00000378295 11/14 59 51 8 56 56 0 strelka-varscan-mutect TP73,missense_variant,p.Ser439Leu,ENST00000378295,NM_005427.3,NM_001204185.1;TP73,missense_variant,p.Ser390Leu,ENST00000378288,NM_001204191.1,NM_001126240.2,NM_001204190.1;TP73,missense_variant,p.Ser439Leu,ENST00000354437,NM_001204184.1;TP73,missense_variant,p.Ser390Leu,ENST00000378285,NM_001126241.2;TP73,missense_variant,p.Ser368Leu,ENST00000378290,NM_001204192.1;TP73,intron_variant,,ENST00000357733,NM_001204187.1;TP73,intron_variant,,ENST00000346387,NM_001204188.1;TP73,intron_variant,,ENST00000604074,NM_001204189.1,NM_001204186.1;TP73,intron_variant,,ENST00000378280,NM_001126242.2;TP73,intron_variant,,ENST00000603362,;TP73,intron_variant,,ENST00000604479,;TP73,intron_variant,,ENST00000604566,;TP73,downstream_gene_variant,,ENST00000603364,; T ENST00000378295 Transcript missense_variant 1471/5188 1316/1911 439/636 S/L tCg/tTg rs760067757,COSM3688827,COSM3688828 1 1 TP73 HGNC HGNC:12003 protein_coding YES CCDS49.1 ENSP00000367545 O15350 A0A024R4C3 UPI000002E988 NM_005427.3,NM_001204185.1 deleterious(0.05) 11/14 hmmpanther:PTHR11447:SF21,hmmpanther:PTHR11447 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs760067757 . 0 201 8 0 0 0 0 0 -18.2613 0.9999975 1 1 1 0 T 3 4 54 3730119 3730119 C T 1 0 0 0 0 1 0 0 0 16872 893 31 1 1 TP73 1 3730119 Missense_Mutation SNP C C3N-00556_T 229029 3730119 245226303 3 16132 CHD5 0 . GRCh38 1 6106496 6106496 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.5756C>G p.Ser1919Cys p.S1919C ENST00000262450 40/42 201 189 12 215 215 0 strelka-varscan-mutect CHD5,missense_variant,p.Ser1919Cys,ENST00000262450,NM_015557.2;CHD5,intron_variant,,ENST00000475121,;CHD5,3_prime_UTR_variant,,ENST00000496404,;CHD5,intron_variant,,ENST00000462991,;CHD5,intron_variant,,ENST00000377999,; C ENST00000262450 Transcript missense_variant 5856/9646 5756/5865 1919/1954 S/C tCc/tGc 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 tolerated_low_confidence(0.21) 40/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 6106496 6106496 G C 1 0 0 0 0 1 0 0 0 3087 1174 41 4 4 CHD5 1 6106496 Missense_Mutation SNP G C3N-00556_T 2376377 6106496 242849926 4 16133 TAS1R1 0 . GRCh38 1 6575228 6575228 + Nonsense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1096G>T p.Glu366Ter p.E366* ENST00000333172 3/6 112 101 11 131 131 0 strelka-varscan-mutect TAS1R1,stop_gained,p.Glu366Ter,ENST00000333172,NM_138697.3;TAS1R1,stop_gained,p.Glu292Ter,ENST00000411823,;TAS1R1,intron_variant,,ENST00000351136,NM_177540.2;TAS1R1,intron_variant,,ENST00000415267,;ZBTB48,upstream_gene_variant,,ENST00000377674,NM_005341.3,NM_001278647.1,NM_001278648.1;ZBTB48,upstream_gene_variant,,ENST00000319084,;ZBTB48,upstream_gene_variant,,ENST00000435905,;ZBTB48,upstream_gene_variant,,ENST00000488936,; T ENST00000333172 Transcript stop_gained 1289/2892 1096/2526 366/841 E/* Gaa/Taa 1 1 TAS1R1 HGNC HGNC:14448 protein_coding YES CCDS81.1 ENSP00000331867 Q7RTX1 UPI000004737B NM_138697.3 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF3,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99629 1 1 1 1 0 T 4 4 54 6575228 6575228 G T 1 0 0 0 0 0 1 0 0 15961 943 33 2 2 TAS1R1 1 6575228 Nonsense_Mutation SNP G C3N-00556_T 468732 6575228 242381194 5 16134 SLC2A7 0 . GRCh38 1 9010228 9010228 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1031G>T p.Arg344Leu p.R344L ENST00000400906 9/12 139 126 13 133 132 1 strelka-varscan-mutect SLC2A7,missense_variant,p.Arg344Leu,ENST00000400906,NM_207420.2; A ENST00000400906 Transcript missense_variant 1031/1539 1031/1539 344/512 R/L cGg/cTg 1 -1 SLC2A7 HGNC HGNC:13445 protein_coding YES CCDS98.2 ENSP00000383698 Q6PXP3 UPI00001A73A8 NM_207420.2 tolerated(0.44) 9/12 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_patterns:PS00216,PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF30,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879 MODERATE 1 SNV 1 1 PASS rs1265865058 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 9010228 9010228 C A 1 0 0 0 0 1 0 0 0 14820 652 23 1 1 SLC2A7 1 9010228 Missense_Mutation SNP C C3N-00556_T 2435000 9010228 239946194 6 16135 AADACL3 0 . GRCh38 1 12725322 12725322 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.550C>A p.Pro184Thr p.P184T ENST00000359318 4/4 174 153 21 231 231 0 strelka-varscan-mutect AADACL3,missense_variant,p.Pro184Thr,ENST00000359318,NM_001103170.2;AADACL3,non_coding_transcript_exon_variant,,ENST00000620146,; A ENST00000359318 Transcript missense_variant 584/3662 550/1224 184/407 P/T Cca/Aca COSM4021446,COSM4021447 1 1 AADACL3 HGNC HGNC:32037 protein_coding YES CCDS41253.2 ENSP00000352268 Q5VUY0 UPI0003EAEC70 NM_001103170.2 deleterious(0) 4/4 Gene3D:3.40.50.1820,Pfam_domain:PF07859,PIRSF_domain:PIRSF037251,hmmpanther:PTHR23024,hmmpanther:PTHR23024:SF115,Superfamily_domains:SSF53474 1,1 MODERATE 1 SNV 3 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 12725322 12725322 C A 1 0 0 0 0 1 0 0 0 12 855 30 2 2 AADACL3 1 12725322 Missense_Mutation SNP C C3N-00556_T 3715094 12725322 236231100 7 16136 ACTL8 0 . GRCh38 1 17823084 17823084 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.76C>T p.Gln26Ter p.Q26* ENST00000375406 2/3 250 224 26 298 298 0 strelka-varscan-mutect ACTL8,stop_gained,p.Gln26Ter,ENST00000375406,NM_030812.2;ACTL8,stop_gained,p.Gln26Ter,ENST00000617065,; T ENST00000375406 Transcript stop_gained 292/1861 76/1101 26/366 Q/* Cag/Tag 1 1 ACTL8 HGNC HGNC:24018 protein_coding YES CCDS183.1 ENSP00000364555 Q9H568 UPI000007008F NM_030812.2 2/3 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF208,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 17823084 17823084 C T 1 0 0 0 0 0 1 0 0 246 827 29 3 3 ACTL8 1 17823084 Nonsense_Mutation SNP C C3N-00556_T 5097762 17823084 231133338 8 16137 ACTL8 0 . GRCh38 1 17823227 17823227 + Silent SNP C C G novel C3N-00556_T C3N-00556_N C C c.219C>G p.= p.L73L ENST00000375406 2/3 337 301 36 314 314 0 strelka-varscan-mutect ACTL8,synonymous_variant,p.=,ENST00000375406,NM_030812.2;ACTL8,synonymous_variant,p.=,ENST00000617065,; G ENST00000375406 Transcript synonymous_variant 435/1861 219/1101 73/366 L ctC/ctG 1 1 ACTL8 HGNC HGNC:24018 protein_coding YES CCDS183.1 ENSP00000364555 Q9H568 UPI000007008F NM_030812.2 2/3 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF208,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067,Prints_domain:PR00190 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 17823227 17823227 C G 1 0 0 0 0 0 0 0 1 246 813 29 4 4 ACTL8 1 17823227 Silent SNP C C3N-00556_T 143 17823227 231133195 9 16138 UBR4 0 . GRCh38 1 19113764 19113764 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.11392C>T p.Gln3798Ter p.Q3798* ENST00000375254 77/106 186 159 27 241 241 0 strelka-varscan-mutect UBR4,stop_gained,p.Gln3798Ter,ENST00000375254,NM_020765.2;UBR4,3_prime_UTR_variant,,ENST00000375218,;UBR4,upstream_gene_variant,,ENST00000494503,;UBR4,upstream_gene_variant,,ENST00000466969,; A ENST00000375254 Transcript stop_gained 11420/15906 11392/15552 3798/5183 Q/* Cag/Tag 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 77/106 hmmpanther:PTHR21725 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 19113764 19113764 G A 1 0 0 0 0 0 1 0 0 17428 1328 46 3 3 UBR4 1 19113764 Nonsense_Mutation SNP G C3N-00556_T 1290537 19113764 229842658 10 16139 HSPG2 0 . GRCh38 1 21847798 21847798 + Missense_Mutation SNP G G A rs747900019 C3N-00556_T C3N-00556_N G G c.7916C>T p.Pro2639Leu p.P2639L ENST00000374695 61/97 320 303 17 354 354 0 strelka-varscan-mutect HSPG2,missense_variant,p.Pro2639Leu,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,non_coding_transcript_exon_variant,,ENST00000453796,;HSPG2,downstream_gene_variant,,ENST00000493940,; A ENST00000374695 Transcript missense_variant 7996/14327 7916/13176 2639/4391 P/L cCc/cTc rs747900019 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 deleterious(0.03) 61/97 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs747900019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 21847798 21847798 G A 1 0 0 0 0 1 0 0 0 7326 1232 43 3 3 HSPG2 1 21847798 Missense_Mutation SNP G C3N-00556_T 2734034 21847798 227108624 11 16140 PNRC2 0 . GRCh38 1 23961591 23961591 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.134G>C p.Arg45Thr p.R45T ENST00000334351 3/3 175 150 25 222 222 0 strelka-varscan-mutect PNRC2,missense_variant,p.Arg45Thr,ENST00000334351,NM_017761.3;PNRC2,missense_variant,p.Arg45Thr,ENST00000374468,;SRSF10,downstream_gene_variant,,ENST00000344989,NM_006625.5,NM_001300937.1;SRSF10,downstream_gene_variant,,ENST00000453840,NM_001191007.2;PNRC2,downstream_gene_variant,,ENST00000471915,;PNRC2,downstream_gene_variant,,ENST00000579103,;SRSF10,downstream_gene_variant,,ENST00000341154,; C ENST00000334351 Transcript missense_variant 545/2416 134/420 45/139 R/T aGa/aCa 1 1 PNRC2 HGNC HGNC:23158 protein_coding YES CCDS246.1 ENSP00000334840 Q9NPJ4 A0A024RAC2 UPI0000052C60 NM_017761.3 deleterious(0.04) 3/3 hmmpanther:PTHR15405,hmmpanther:PTHR15405:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 23961591 23961591 G C 1 0 0 0 0 1 0 0 0 12283 942 33 4 4 PNRC2 1 23961591 Missense_Mutation SNP G C3N-00556_T 2113793 23961591 224994831 12 16141 CNKSR1 0 . GRCh38 1 26184489 26184489 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.1110C>A p.= p.L370L ENST00000374253 12/21 275 261 14 317 317 0 strelka-varscan-mutect CNKSR1,synonymous_variant,p.=,ENST00000531191,NM_001297648.1;CNKSR1,synonymous_variant,p.=,ENST00000361530,NM_006314.2;CNKSR1,synonymous_variant,p.=,ENST00000374253,NM_001297647.1;CNKSR1,downstream_gene_variant,,ENST00000480348,;CNKSR1,downstream_gene_variant,,ENST00000528001,;CNKSR1,3_prime_UTR_variant,,ENST00000482227,;CNKSR1,3_prime_UTR_variant,,ENST00000525687,;CNKSR1,3_prime_UTR_variant,,ENST00000528281,;CNKSR1,downstream_gene_variant,,ENST00000481077,;CNKSR1,upstream_gene_variant,,ENST00000484874,;CNKSR1,downstream_gene_variant,,ENST00000465415,;CNKSR1,downstream_gene_variant,,ENST00000531150,;CNKSR1,downstream_gene_variant,,ENST00000524529,;CNKSR1,upstream_gene_variant,,ENST00000480617,; A ENST00000374253 Transcript synonymous_variant 1149/2538 1110/2163 370/720 L ctC/ctA 1 1 CNKSR1 HGNC HGNC:19700 protein_coding YES CCDS72732.1 ENSP00000363371 Q969H4 UPI0000070054 NM_001297647.1 12/21 hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF10,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 26184489 26184489 C A 1 0 0 0 0 0 0 0 1 3386 842 30 2 2 CNKSR1 1 26184489 Silent SNP C C3N-00556_T 2222898 26184489 222771933 13 16142 RPS6KA1 0 . GRCh38 1 26554227 26554227 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.616G>A p.Glu206Lys p.E206K ENST00000531382 7/21 118 109 9 131 131 0 strelka-varscan-mutect RPS6KA1,missense_variant,p.Glu197Lys,ENST00000374168,NM_002953.3;RPS6KA1,missense_variant,p.Glu197Lys,ENST00000374166,;RPS6KA1,missense_variant,p.Glu181Lys,ENST00000530003,;RPS6KA1,missense_variant,p.Glu105Lys,ENST00000526792,;RPS6KA1,missense_variant,p.Glu206Lys,ENST00000531382,NM_001006665.1;RPS6KA1,missense_variant,p.Glu105Lys,ENST00000529454,;RPS6KA1,upstream_gene_variant,,ENST00000403732,;MIR1976,upstream_gene_variant,,ENST00000459548,;RPS6KA1,upstream_gene_variant,,ENST00000488985,;RPS6KA1,3_prime_UTR_variant,,ENST00000374163,;RPS6KA1,non_coding_transcript_exon_variant,,ENST00000531113,;RPS6KA1,non_coding_transcript_exon_variant,,ENST00000527264,;RPS6KA1,downstream_gene_variant,,ENST00000474934,;RPS6KA1,downstream_gene_variant,,ENST00000366866,;RPS6KA1,downstream_gene_variant,,ENST00000530607,;RPS6KA1,downstream_gene_variant,,ENST00000524436,;RPS6KA1,downstream_gene_variant,,ENST00000526040,; A ENST00000531382 Transcript missense_variant 665/2359 616/2235 206/744 E/K Gag/Aag 1 1 RPS6KA1 HGNC HGNC:10430 protein_coding YES CCDS30649.1 ENSP00000435412 Q15418 UPI000046D37A NM_001006665.1 tolerated(0.14) 7/21 PROSITE_profiles:PS50011,hmmpanther:PTHR24351:SF43,hmmpanther:PTHR24351,PIRSF_domain:PIRSF000606,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 26554227 26554227 G A 1 0 0 0 0 1 0 0 0 13905 1291 45 3 3 RPS6KA1 1 26554227 Missense_Mutation SNP G C3N-00556_T 369738 26554227 222402195 14 16143 SYTL1 0 . GRCh38 1 27347553 27347553 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.324G>A p.= p.R108R ENST00000543823 2/14 177 163 14 195 195 0 strelka-varscan-mutect SYTL1,synonymous_variant,p.=,ENST00000543823,;SYTL1,synonymous_variant,p.=,ENST00000318074,NM_032872.2;SYTL1,synonymous_variant,p.=,ENST00000616558,NM_001193308.1;SYTL1,synonymous_variant,p.=,ENST00000618673,;SYTL1,downstream_gene_variant,,ENST00000473280,;SYTL1,non_coding_transcript_exon_variant,,ENST00000490170,;SYTL1,non_coding_transcript_exon_variant,,ENST00000483926,;SYTL1,upstream_gene_variant,,ENST00000475199,;SYTL1,upstream_gene_variant,,ENST00000485269,;SYTL1,upstream_gene_variant,,ENST00000496001,;SYTL1,upstream_gene_variant,,ENST00000615284,; A ENST00000543823 Transcript synonymous_variant 786/2229 324/1689 108/562 R agG/agA 1 1 SYTL1 HGNC HGNC:15584 protein_coding YES CCDS53286.1 ENSP00000440704 Q8IYJ3 UPI0000074245 2/14 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 27347553 27347553 G A 1 0 0 0 0 0 0 0 1 15876 1165 41 3 3 SYTL1 1 27347553 Silent SNP G C3N-00556_T 793326 27347553 221608869 15 16144 RCC1 0 . GRCh38 1 28536773 28536773 + Missense_Mutation SNP G G C C3N-00556_T C3N-00556_N G G c.1057G>C p.Glu353Gln p.E353Q ENST00000373831 10/11 115 109 6 133 133 0 strelka-mutect RCC1,missense_variant,p.Glu322Gln,ENST00000373833,;RCC1,missense_variant,p.Glu322Gln,ENST00000398958,NM_001048199.2;RCC1,missense_variant,p.Glu322Gln,ENST00000373832,NM_001269.4;RCC1,missense_variant,p.Glu353Gln,ENST00000373831,NM_001048195.2,NM_001048194.2;RCC1,missense_variant,p.Glu339Gln,ENST00000411533,;RCC1,downstream_gene_variant,,ENST00000430407,;RCC1,downstream_gene_variant,,ENST00000434290,;RCC1,downstream_gene_variant,,ENST00000419074,;RCC1,downstream_gene_variant,,ENST00000427469,;RCC1,downstream_gene_variant,,ENST00000486790,;RCC1,downstream_gene_variant,,ENST00000429051,;RCC1,non_coding_transcript_exon_variant,,ENST00000478232,; C ENST00000373831 Transcript missense_variant 1118/1577 1057/1359 353/452 E/Q Gag/Cag COSM3369676,COSM3369677 1 1 RCC1 HGNC HGNC:1913 protein_coding YES CCDS41295.1 ENSP00000362937 P18754 A0A0S2Z404 UPI0000204066 NM_001048195.2,NM_001048194.2 tolerated(0.06) 10/11 Gene3D:2.130.10.30,Pfam_domain:PF00415,PROSITE_profiles:PS50012,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF179,Superfamily_domains:SSF50985 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 28536773 28536773 G C 1 0 0 0 0 1 0 0 0 13342 1291 45 4 4 RCC1 1 28536773 Missense_Mutation SNP G C3N-00556_T 1189220 28536773 220419649 16 16145 ZCCHC17 0 . GRCh38 1 31348865 31348865 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.521G>A p.Gly174Glu p.G174E ENST00000615916 6/7 181 171 10 199 199 0 varscan-mutect ZCCHC17,missense_variant,p.Gly152Glu,ENST00000373714,NM_001282568.1;ZCCHC17,missense_variant,p.Gly144Glu,ENST00000546109,NM_001282569.1;ZCCHC17,missense_variant,p.Gly174Glu,ENST00000615916,NM_001282566.1;ZCCHC17,missense_variant,p.Gly152Glu,ENST00000344147,NM_016505.3;ZCCHC17,missense_variant,p.Gly90Glu,ENST00000616393,NM_001282571.1;ZCCHC17,missense_variant,p.Gly154Glu,ENST00000627541,NM_001282570.1,NM_001282567.1;ZCCHC17,intron_variant,,ENST00000618216,NM_001282572.1,NM_001282574.1;ZCCHC17,intron_variant,,ENST00000616859,NM_001282573.1;RP11-266K22.2,upstream_gene_variant,,ENST00000430143,;ZCCHC17,non_coding_transcript_exon_variant,,ENST00000479629,; A ENST00000615916 Transcript missense_variant 621/1652 521/792 174/263 G/E gGg/gAg 1 1 ZCCHC17 HGNC HGNC:30246 protein_coding YES CCDS72741.1 ENSP00000480986 A0A087WXF8 UPI0003940499 NM_001282566.1 deleterious(0.01) 6/7 hmmpanther:PTHR15838 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 31348865 31348865 G A 1 0 0 0 0 1 0 0 0 18160 1232 43 3 3 ZCCHC17 1 31348865 Missense_Mutation SNP G C3N-00556_T 2812092 31348865 217607557 17 16146 CSMD2 0 . GRCh38 1 33600919 33600919 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.6802C>T p.Leu2268Phe p.L2268F ENST00000373381 44/71 250 237 13 259 259 0 strelka-varscan-mutect CSMD2,missense_variant,p.Leu2268Phe,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Leu2228Phe,ENST00000619121,;CSMD2,missense_variant,p.Leu2270Phe,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Leu1141Phe,ENST00000373380,;CSMD2,missense_variant,p.Leu367Phe,ENST00000373377,;CSMD2,non_coding_transcript_exon_variant,,ENST00000489419,;CSMD2,missense_variant,p.Leu2270Phe,ENST00000241312,; A ENST00000373381 Transcript missense_variant 6979/13698 6802/10896 2268/3631 L/F Ctc/Ttc 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 tolerated(0.05) 44/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 33600919 33600919 G A 1 0 0 0 0 1 0 0 0 3746 971 34 3 3 CSMD2 1 33600919 Missense_Mutation SNP G C3N-00556_T 2252054 33600919 215355503 18 16147 MYCL 0 . GRCh38 1 39897418 39897418 + Missense_Mutation SNP C C A rs561113951 C3N-00556_T C3N-00556_N C C c.1139G>T p.Arg380Leu p.R380L ENST00000397332 3/3 54 49 5 85 84 1 strelka-varscan-mutect MYCL,missense_variant,p.Arg380Leu,ENST00000397332,NM_001033082.2;MYCL,missense_variant,p.Arg350Leu,ENST00000372816,NM_001033081.2;MYCL,downstream_gene_variant,,ENST00000372815,NM_005376.4;MYCL,downstream_gene_variant,,ENST00000450953,;RP1-118J21.5,upstream_gene_variant,,ENST00000418255,; A ENST00000397332 Transcript missense_variant 1264/3256 1139/1185 380/394 R/L cGg/cTg rs561113951 1 -1 MYCL HGNC HGNC:7555 protein_coding YES CCDS53300.1 ENSP00000380494 P12524 UPI000047097E NM_001033082.2 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11514,hmmpanther:PTHR11514:SF1,Gene3D:4.10.280.10,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS rs561113951 . 0 196 12 2 0 0 0 0 -9.747711 0.996062 1 1 1 0 A 3 1 54 39897418 39897418 C A 1 0 0 0 0 1 0 0 0 10020 652 23 1 1 MYCL 1 39897418 Missense_Mutation SNP C C3N-00556_T 6296499 39897418 209059004 19 16148 MFSD2A 0 . GRCh38 1 39967669 39967669 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1092G>C p.Leu364Phe p.L364F ENST00000372809 10/14 273 258 15 323 323 0 strelka-varscan-mutect MFSD2A,missense_variant,p.Leu364Phe,ENST00000372809,NM_001136493.2;MFSD2A,missense_variant,p.Leu351Phe,ENST00000372811,NM_032793.4,NM_001287809.1;MFSD2A,missense_variant,p.Leu195Phe,ENST00000420632,NM_001287808.1;MFSD2A,downstream_gene_variant,,ENST00000434861,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000480630,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000481612,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000491515,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000459917,;MFSD2A,intron_variant,,ENST00000483824,;MFSD2A,downstream_gene_variant,,ENST00000469745,;RP3-342P20.2,downstream_gene_variant,,ENST00000438210,; C ENST00000372809 Transcript missense_variant 1235/2173 1092/1632 364/543 L/F ttG/ttC 1 1 MFSD2A HGNC HGNC:25897 protein_coding YES CCDS44118.1 ENSP00000361895 Q8NA29 UPI0000072562 NM_001136493.2 deleterious(0) 10/14 hmmpanther:PTHR11328:SF29,hmmpanther:PTHR11328,Pfam_domain:PF13347,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 39967669 39967669 G C 1 0 0 0 0 1 0 0 0 9487 1281 45 4 4 MFSD2A 1 39967669 Missense_Mutation SNP G C3N-00556_T 70251 39967669 208988753 20 16149 KIF2C 0 . GRCh38 1 44759319 44759319 + Missense_Mutation SNP C C G rs867051345 C3N-00556_T C3N-00556_N C C c.1338C>G p.Ile446Met p.I446M ENST00000372224 14/21 177 150 27 163 163 0 strelka-varscan-mutect KIF2C,missense_variant,p.Ile392Met,ENST00000372217,NM_001297657.1,NM_001297656.1;KIF2C,missense_variant,p.Ile446Met,ENST00000372224,NM_006845.3,NM_001297655.1;KIF2C,downstream_gene_variant,,ENST00000452259,;KIF2C,downstream_gene_variant,,ENST00000455186,;KIF2C,upstream_gene_variant,,ENST00000423289,;RP11-269F19.2,non_coding_transcript_exon_variant,,ENST00000428791,;RP11-269F19.2,non_coding_transcript_exon_variant,,ENST00000440985,;KIF2C,downstream_gene_variant,,ENST00000493027,;KIF2C,upstream_gene_variant,,ENST00000472235,; G ENST00000372224 Transcript missense_variant 1451/2879 1338/2178 446/725 I/M atC/atG rs867051345 1 1 KIF2C HGNC HGNC:6393 protein_coding YES CCDS512.1 ENSP00000361298 Q99661 A0A140VKF1 UPI000012DDAD NM_006845.3,NM_001297655.1 deleterious(0.03) 14/21 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF454,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs867051345 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 54 44759319 44759319 C G 1 0 0 0 0 1 0 0 0 8164 816 29 4 4 KIF2C 1 44759319 Missense_Mutation SNP C C3N-00556_T 4791650 44759319 204197103 21 16150 LURAP1 0 . GRCh38 1 46220112 46220112 + Silent SNP G G A rs189814441 C3N-00556_T C3N-00556_N G G c.612G>A p.= p.E204E ENST00000371980 2/2 195 178 17 248 248 0 strelka-varscan-mutect LURAP1,synonymous_variant,p.=,ENST00000371980,NM_001013615.2;POMGNT1,5_prime_UTR_variant,,ENST00000396420,;POMGNT1,5_prime_UTR_variant,,ENST00000371992,NM_001243766.1; A ENST00000371980 Transcript synonymous_variant 705/1854 612/720 204/239 E gaG/gaA rs189814441,COSM51134 1 1 LURAP1 HGNC HGNC:32327 protein_coding YES CCDS30703.1 ENSP00000361048 Q96LR2 UPI0000072C34 NM_001013615.2 2/2 hmmpanther:PTHR33767 0,1 LOW 1 SNV 1 0,1 1 PASS rs189814441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 46220112 46220112 G A 1 0 0 0 0 0 0 0 1 8993 933 33 3 3 LURAP1 1 46220112 Silent SNP G C3N-00556_T 1460793 46220112 202736310 22 16151 OSBPL9 0 . GRCh38 1 51772687 51772687 + Silent SNP C C G C3N-00556_T C3N-00556_N C C c.1164C>G p.= p.L388L ENST00000447887 14/24 153 139 14 184 184 0 strelka-varscan-mutect OSBPL9,synonymous_variant,p.=,ENST00000371714,NM_148908.3;OSBPL9,synonymous_variant,p.=,ENST00000447887,NM_148909.3;OSBPL9,synonymous_variant,p.=,ENST00000428468,NM_024586.5;OSBPL9,synonymous_variant,p.=,ENST00000453295,NM_148906.2;OSBPL9,synonymous_variant,p.=,ENST00000462759,NM_148904.3;OSBPL9,synonymous_variant,p.=,ENST00000361556,NM_148907.2;OSBPL9,synonymous_variant,p.=,ENST00000486942,NM_148905.3;OSBPL9,synonymous_variant,p.=,ENST00000531828,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000533825,;OSBPL9,3_prime_UTR_variant,,ENST00000495776,;OSBPL9,3_prime_UTR_variant,,ENST00000435274,;OSBPL9,3_prime_UTR_variant,,ENST00000489990,;OSBPL9,3_prime_UTR_variant,,ENST00000528603,;OSBPL9,3_prime_UTR_variant,,ENST00000531061,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000531819,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000475697,; G ENST00000447887 Transcript synonymous_variant 1183/2940 1164/2241 388/746 L ctC/ctG COSM5201283,COSM5201284,COSM5201285,COSM5201286,COSM5201287,COSM5201288 1 1 OSBPL9 HGNC HGNC:16386 protein_coding YES CCDS44145.1 ENSP00000412733 Q96SU4 UPI0000167BAD NM_148909.3 14/24 hmmpanther:PTHR10972:SF27,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579 1,1,1,1,1,1 LOW 1 SNV 2 1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 51772687 51772687 C G 1 0 0 0 0 0 0 0 1 11350 900 32 4 4 OSBPL9 1 51772687 Silent SNP C C3N-00556_T 5552575 51772687 197183735 23 16152 C8B 0 . GRCh38 1 56952090 56952090 + Silent SNP C C T rs148088012 C3N-00556_T C3N-00556_N C C c.624G>A p.= p.T208T ENST00000371237 5/12 411 384 27 494 493 1 strelka-varscan-mutect C8B,synonymous_variant,p.=,ENST00000543257,NM_001278543.1;C8B,synonymous_variant,p.=,ENST00000535057,NM_001278544.1;C8B,synonymous_variant,p.=,ENST00000371237,NM_000066.3;C8B,downstream_gene_variant,,ENST00000468990,; T ENST00000371237 Transcript synonymous_variant 691/2037 624/1776 208/591 T acG/acA rs148088012,COSM3491217 1 -1 C8B HGNC HGNC:1353 protein_coding YES CCDS30730.1 ENSP00000360281 P07358 UPI000013C9B2 NM_000066.3 5/12 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF385,hmmpanther:PTHR19325 0,1 LOW 1 SNV 1 0,1 1 PASS rs148088012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 56952090 56952090 C T 1 0 0 0 0 0 0 0 1 2151 871 31 1 1 C8B 1 56952090 Silent SNP C C3N-00556_T 5179403 56952090 192004332 24 16153 LRRC53 0 . GRCh38 1 74472202 74472202 + Splice_Site SNP C C G novel C3N-00556_T C3N-00556_N C C c.1421-1G>C p.X474_splice ENST00000294635 123 114 9 126 126 0 strelka-varscan-mutect LRRC53,splice_acceptor_variant,,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2;RP4-650F12.2,downstream_gene_variant,,ENST00000442876,;RP4-650F12.2,downstream_gene_variant,,ENST00000411417,; G ENST00000294635 Transcript splice_acceptor_variant -/3859 1421/3744 474/1247 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE 4/4 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 54 74472202 74472202 C G 1 0 0 0 0 0 0 1 0 8905 927 32 4 4 LRRC53 1 74472202 Splice_Site SNP C C3N-00556_T 17520112 74472202 174484220 25 16154 ERICH3 0 . GRCh38 1 74606732 74606732 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1358C>T p.Ser453Leu p.S453L ENST00000326665 10/15 279 252 27 320 320 0 strelka-varscan-mutect ERICH3,missense_variant,p.Ser453Leu,ENST00000326665,NM_001002912.4;ERICH3,missense_variant,p.Ser256Leu,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,; A ENST00000326665 Transcript missense_variant 1577/7159 1358/4593 453/1530 S/L tCa/tTa 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 tolerated(0.11) 10/15 hmmpanther:PTHR23034 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 74606732 74606732 G A 1 0 0 0 0 1 0 0 0 5083 1294 45 3 3 ERICH3 1 74606732 Missense_Mutation SNP G C3N-00556_T 134530 74606732 174349690 26 16155 COL11A1 0 . GRCh38 1 103031127 103031127 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.769C>T p.Gln257Ter p.Q257* ENST00000370096 5/67 235 215 20 288 287 1 strelka-varscan-mutect COL11A1,stop_gained,p.Gln257Ter,ENST00000358392,NM_080629.2;COL11A1,stop_gained,p.Gln257Ter,ENST00000370096,NM_001854.3;COL11A1,stop_gained,p.Gln257Ter,ENST00000353414,NM_001190709.1;COL11A1,stop_gained,p.Gln257Ter,ENST00000512756,NM_080630.3;COL11A1,stop_gained,p.Gln257Ter,ENST00000427239,;COL11A1,stop_gained,p.Gln184Ter,ENST00000447608,;COL11A1,stop_gained,p.Gln30Ter,ENST00000635193,; A ENST00000370096 Transcript stop_gained 1082/7286 769/5421 257/1806 Q/* Cag/Tag 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 5/67 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 103031127 103031127 G A 1 0 0 0 0 0 1 0 0 3455 1299 45 3 3 COL11A1 1 103031127 Nonsense_Mutation SNP G C3N-00556_T 28424395 103031127 145925295 27 16156 MYBPHL 0 . GRCh38 1 109297127 109297127 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.493G>C p.Glu165Gln p.E165Q ENST00000357155 4/9 257 242 15 264 264 0 strelka-varscan-mutect MYBPHL,missense_variant,p.Glu165Gln,ENST00000357155,NM_001010985.2,NM_001265613.1;MYBPHL,intron_variant,,ENST00000477962,;MYBPHL,upstream_gene_variant,,ENST00000489706,; G ENST00000357155 Transcript missense_variant 543/1372 493/1065 165/354 E/Q Gaa/Caa 1 -1 MYBPHL HGNC HGNC:30434 protein_coding YES CCDS30793.1 ENSP00000349678 A2RUH7 UPI000022B031 NM_001010985.2,NM_001265613.1 deleterious(0.04) 4/9 Gene3D:2.60.40.10,Pfam_domain:PF00041,Prints_domain:PR00014,PROSITE_profiles:PS50853,hmmpanther:PTHR13817,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 109297127 109297127 C G 1 0 0 0 0 1 0 0 0 10015 864 30 4 4 MYBPHL 1 109297127 Missense_Mutation SNP C C3N-00556_T 6266000 109297127 139659295 28 16157 MOV10 0 . GRCh38 1 112698362 112698362 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.2392G>C p.Glu798Gln p.E798Q ENST00000413052 16/21 186 155 31 196 196 0 strelka-varscan-mutect MOV10,missense_variant,p.Glu742Gln,ENST00000369644,NM_001286072.1;MOV10,missense_variant,p.Glu798Gln,ENST00000413052,NM_020963.4;MOV10,missense_variant,p.Glu798Gln,ENST00000369645,NM_001321324.1,NM_001130079.2;MOV10,missense_variant,p.Glu798Gln,ENST00000357443,;RHOC,downstream_gene_variant,,ENST00000285735,;RHOC,downstream_gene_variant,,ENST00000339083,NM_175744.4;RHOC,downstream_gene_variant,,ENST00000369642,NM_001042678.1;RHOC,downstream_gene_variant,,ENST00000369633,NM_001042679.1;RHOC,downstream_gene_variant,,ENST00000369638,;RHOC,downstream_gene_variant,,ENST00000369632,;RHOC,downstream_gene_variant,,ENST00000369637,;RHOC,downstream_gene_variant,,ENST00000425265,;RP11-426L16.10,downstream_gene_variant,,ENST00000606505,;RHOC,downstream_gene_variant,,ENST00000369636,;RP11-426L16.10,downstream_gene_variant,,ENST00000605933,;RHOC,downstream_gene_variant,,ENST00000534717,;RHOC,downstream_gene_variant,,ENST00000484054,;RHOC,downstream_gene_variant,,ENST00000436685,;RHOC,downstream_gene_variant,,ENST00000414971,;RP11-426L16.3,upstream_gene_variant,,ENST00000421943,;MOV10,non_coding_transcript_exon_variant,,ENST00000468624,;MOV10,non_coding_transcript_exon_variant,,ENST00000496577,;MOV10,non_coding_transcript_exon_variant,,ENST00000490413,;MOV10,non_coding_transcript_exon_variant,,ENST00000488160,;MOV10,non_coding_transcript_exon_variant,,ENST00000471160,;MOV10,non_coding_transcript_exon_variant,,ENST00000482545,;MOV10,non_coding_transcript_exon_variant,,ENST00000481711,;RP11-426L16.10,downstream_gene_variant,,ENST00000471038,;MOV10,upstream_gene_variant,,ENST00000494319,;MOV10,upstream_gene_variant,,ENST00000495374,;MOV10,downstream_gene_variant,,ENST00000479858,;RHOC,downstream_gene_variant,,ENST00000468093,;RHOC,downstream_gene_variant,,ENST00000473074,;RHOC,downstream_gene_variant,,ENST00000484280,;RP11-426L16.10,downstream_gene_variant,,ENST00000607158,;RP11-426L16.10,downstream_gene_variant,,ENST00000606954,;RHOC,downstream_gene_variant,,ENST00000528831,; C ENST00000413052 Transcript missense_variant 2782/3641 2392/3012 798/1003 E/Q Gaa/Caa 1 1 MOV10 HGNC HGNC:7200 protein_coding YES CCDS853.1 ENSP00000399797 Q9HCE1 UPI000012FA84 NM_020963.4 tolerated(0.54) 16/21 Gene3D:3.40.50.300,Pfam_domain:PF13087,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF322,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 112698362 112698362 G C 1 0 0 0 0 1 0 0 0 9680 1291 45 4 4 MOV10 1 112698362 Missense_Mutation SNP G C3N-00556_T 3401235 112698362 136258060 29 16158 HIST2H2AC 0 . GRCh38 1 149887143 149887143 + Missense_Mutation SNP G G C C3N-00556_T C3N-00556_N G G c.169G>C p.Glu57Gln p.E57Q ENST00000331380 1/1 521 487 34 451 450 1 varscan-mutect HIST2H2AC,missense_variant,p.Glu57Gln,ENST00000331380,NM_003517.2;HIST2H2BE,upstream_gene_variant,,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2; C ENST00000331380 Transcript missense_variant 169/390 169/390 57/129 E/Q Gag/Cag COSM383719 1 1 HIST2H2AC HGNC HGNC:4738 protein_coding YES CCDS937.1 ENSP00000332194 Q16777 UPI000007478F NM_003517.2 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00620,hmmpanther:PTHR23430,SMART_domains:SM00414,Superfamily_domains:SSF47113 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 149887143 149887143 G C 1 0 0 0 0 1 0 0 0 7066 1059 37 4 4 HIST2H2AC 1 149887143 Missense_Mutation SNP G C3N-00556_T 37188781 149887143 99069279 30 16159 SV2A 0 . GRCh38 1 149906784 149906784 + Missense_Mutation SNP G G T rs149927876 C3N-00556_T C3N-00556_N G G c.1751C>A p.Pro584Gln p.P584Q ENST00000369146 11/13 465 366 99 373 373 0 strelka-varscan-mutect SV2A,missense_variant,p.Pro584Gln,ENST00000369146,NM_014849.4;SV2A,missense_variant,p.Pro584Gln,ENST00000369145,; T ENST00000369146 Transcript missense_variant 2242/4416 1751/2229 584/742 P/Q cCg/cAg rs149927876 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 tolerated(1) 11/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF11,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 1 1 PASS rs149927876 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 149906784 149906784 G T 1 0 0 0 0 1 0 0 0 15801 1116 39 1 1 SV2A 1 149906784 Missense_Mutation SNP G C3N-00556_T 19641 149906784 99049638 31 16160 ZNF687 0 . GRCh38 1 151287794 151287794 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1503C>G p.Phe501Leu p.F501L ENST00000324048 3/10 300 273 27 231 231 0 strelka-mutect ZNF687,missense_variant,p.Phe501Leu,ENST00000324048,NM_001304763.1;ZNF687,missense_variant,p.Phe501Leu,ENST00000336715,NM_001304764.1,NM_020832.2;ZNF687,missense_variant,p.Phe104Leu,ENST00000426871,;PI4KB,downstream_gene_variant,,ENST00000368875,NM_002651.2;PI4KB,downstream_gene_variant,,ENST00000368874,NM_001198774.1;PI4KB,downstream_gene_variant,,ENST00000368873,;PI4KB,downstream_gene_variant,,ENST00000368872,NM_001198773.1;PI4KB,downstream_gene_variant,,ENST00000529142,NM_001198775.1;PI4KB,downstream_gene_variant,,ENST00000455060,;ZNF687,downstream_gene_variant,,ENST00000443959,;ZNF687,upstream_gene_variant,,ENST00000436614,;PI4KB,downstream_gene_variant,,ENST00000446339,;ZNF687,missense_variant,p.Phe501Leu,ENST00000449313,;ZNF687,upstream_gene_variant,,ENST00000459919,; G ENST00000324048 Transcript missense_variant 2473/5378 1503/3714 501/1237 F/L ttC/ttG 1 1 ZNF687 HGNC HGNC:29277 protein_coding YES CCDS992.1 ENSP00000319829 Q8N1G0 UPI00000721F7 NM_001304763.1 deleterious(0) 3/10 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF108 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 151287794 151287794 C G 1 0 0 0 0 1 0 0 0 18665 825 29 4 4 ZNF687 1 151287794 Missense_Mutation SNP C C3N-00556_T 1381010 151287794 97668628 32 16161 MEF2D 0 . GRCh38 1 156468931 156468931 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1096C>T p.Gln366Ter p.Q366* ENST00000348159 10/12 231 218 13 169 169 0 strelka-varscan-mutect MEF2D,stop_gained,p.Gln366Ter,ENST00000348159,NM_005920.3;MEF2D,stop_gained,p.Gln358Ter,ENST00000464356,;MEF2D,stop_gained,p.Gln359Ter,ENST00000360595,NM_001271629.1;MEF2D,3_prime_UTR_variant,,ENST00000368240,;MEF2D,3_prime_UTR_variant,,ENST00000475587,; A ENST00000348159 Transcript stop_gained 1577/5965 1096/1566 366/521 Q/* Cag/Tag 1 -1 MEF2D HGNC HGNC:6997 protein_coding YES CCDS1143.1 ENSP00000271555 Q14814 UPI000012EEB6 NM_005920.3 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR11945:SF23,hmmpanther:PTHR11945 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 156468931 156468931 G A 1 0 0 0 0 0 1 0 0 9398 1386 48 3 3 MEF2D 1 156468931 Nonsense_Mutation SNP G C3N-00556_T 5181137 156468931 92487491 33 16162 CD1A 0 . GRCh38 1 158257016 158257016 + Missense_Mutation SNP C C T rs141426527 C3N-00556_T C3N-00556_N C C c.835C>T p.Arg279Trp p.R279W ENST00000289429 4/6 125 88 37 107 107 0 strelka-varscan-mutect CD1A,missense_variant,p.Arg279Trp,ENST00000289429,NM_001763.2; T ENST00000289429 Transcript missense_variant 1368/2096 835/984 279/327 R/W Cgg/Tgg rs141426527,COSM1742953 1 1 CD1A HGNC HGNC:1634 protein_coding YES CCDS1174.1 ENSP00000289429 P06126 UPI0000161A54 NM_001763.2 deleterious(0.04) 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF160,SMART_domains:SM00407,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs141426527 . 0 201 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 54 158257016 158257016 C T 1 0 0 0 0 1 0 0 0 2677 875 31 1 1 CD1A 1 158257016 Missense_Mutation SNP C C3N-00556_T 1788085 158257016 90699406 34 16163 F5 0 . GRCh38 1 169546485 169546485 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.1719G>T p.= p.V573V ENST00000367797 11/25 424 397 27 415 414 1 strelka-varscan-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4; A ENST00000367797 Transcript synonymous_variant 1921/7024 1719/6675 573/2224 V gtG/gtT 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 11/25 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.40.420,PIRSF_domain:PIRSF000354,Superfamily_domains:SSF49503 LOW 1 SNV 1 1 PASS rs1199153980 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 169546485 169546485 C A 1 0 0 0 0 0 0 0 1 5216 813 29 2 2 F5 1 169546485 Silent SNP C C3N-00556_T 11289469 169546485 79409937 35 16164 RGSL1 0 . GRCh38 1 182527628 182527628 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1981G>A p.Glu661Lys p.E661K ENST00000294854 11/22 173 163 10 148 148 0 strelka-varscan RGSL1,missense_variant,p.Glu661Lys,ENST00000294854,NM_001137669.1;RGSL1,non_coding_transcript_exon_variant,,ENST00000456971,;RGSL1,missense_variant,p.Glu696Lys,ENST00000443996,;RGSL1,3_prime_UTR_variant,,ENST00000415960,;RGSL1,non_coding_transcript_exon_variant,,ENST00000436031,; A ENST00000294854 Transcript missense_variant 2001/3696 1981/3231 661/1076 E/K Gag/Aag 1 1 RGSL1 HGNC HGNC:18636 protein_coding YES CCDS58049.1 ENSP00000457748 A5PLK6 UPI000156571A NM_001137669.1 deleterious(0.01) 11/22 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF173,Pfam_domain:PF00615,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 182527628 182527628 G A 1 0 0 0 0 1 0 0 0 13486 1175 41 3 3 RGSL1 1 182527628 Missense_Mutation SNP G C3N-00556_T 12981143 182527628 66428794 36 16165 DHX9 0 . GRCh38 1 182878122 182878122 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2300G>A p.Arg767Gln p.R767Q ENST00000367549 20/28 245 211 34 213 213 0 strelka-varscan DHX9,missense_variant,p.Arg767Gln,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000474446,;DHX9,upstream_gene_variant,,ENST00000473076,;DHX9,downstream_gene_variant,,ENST00000490519,; A ENST00000367549 Transcript missense_variant 2410/4240 2300/3813 767/1270 R/Q cGa/cAa 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 deleterious(0) 20/28 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 182878122 182878122 G A 1 0 0 0 0 1 0 0 0 4320 1058 37 1 1 DHX9 1 182878122 Missense_Mutation SNP G C3N-00556_T 350494 182878122 66078300 37 16166 LAMC1 0 . GRCh38 1 183126250 183126250 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2932G>A p.Glu978Lys p.E978K ENST00000258341 16/28 145 112 33 132 132 0 strelka-varscan LAMC1,missense_variant,p.Glu978Lys,ENST00000258341,NM_002293.3;LAMC1,non_coding_transcript_exon_variant,,ENST00000466964,;LAMC1,upstream_gene_variant,,ENST00000478064,; A ENST00000258341 Transcript missense_variant 3189/7889 2932/4830 978/1609 E/K Gaa/Aaa 1 1 LAMC1 HGNC HGNC:6492 protein_coding YES CCDS1351.1 ENSP00000258341 P11047 UPI000013CFC7 NM_002293.3 tolerated(0.56) 16/28 PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF270,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196,Prints_domain:PR00011 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 183126250 183126250 G A 1 0 0 0 0 1 0 0 0 8518 1291 45 3 3 LAMC1 1 183126250 Missense_Mutation SNP G C3N-00556_T 248128 183126250 65830172 38 16167 PRG4 0 . GRCh38 1 186312363 186312363 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3982C>T p.Gln1328Ter p.Q1328* ENST00000445192 11/13 74 68 6 114 114 0 strelka-varscan PRG4,stop_gained,p.Gln1328Ter,ENST00000445192,NM_005807.4;PRG4,stop_gained,p.Gln1287Ter,ENST00000367483,NM_001127708.2;PRG4,stop_gained,p.Gln1285Ter,ENST00000635041,NM_001303232.1;PRG4,stop_gained,p.Gln1235Ter,ENST00000367485,NM_001127709.2,NM_001127710.2;TPR,3_prime_UTR_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000367482,;RNU6-1240P,upstream_gene_variant,,ENST00000365155,; T ENST00000445192 Transcript stop_gained 4027/5044 3982/4215 1328/1404 Q/* Caa/Taa 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 11/13 hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 HIGH SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -13.27218 0.9999997 1 1 1 0 T 4 4 54 186312363 186312363 C T 1 0 0 0 0 0 1 0 0 12615 827 29 3 3 PRG4 1 186312363 Nonsense_Mutation SNP C C3N-00556_T 3186113 186312363 62644059 39 16168 TPR 0 . GRCh38 1 186359978 186359978 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1210G>T p.Glu404Ter p.E404* ENST00000367478 12/51 219 192 27 260 260 0 strelka-varscan TPR,stop_gained,p.Glu404Ter,ENST00000367478,NM_003292.2;TPR,stop_gained,p.Glu404Ter,ENST00000613151,;TPR,non_coding_transcript_exon_variant,,ENST00000474852,;TPR,upstream_gene_variant,,ENST00000491783,; A ENST00000367478 Transcript stop_gained 1507/9708 1210/7092 404/2363 E/* Gaa/Taa 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 12/51 hmmpanther:PTHR18898 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 186359978 186359978 C A 1 0 0 0 0 0 1 0 0 16897 864 30 2 2 TPR 1 186359978 Nonsense_Mutation SNP C C3N-00556_T 47615 186359978 62596444 40 16169 F13B 0 . GRCh38 1 197067170 197067170 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.54C>A p.= p.L18L ENST00000367412 1/12 186 155 31 194 194 0 strelka-varscan F13B,synonymous_variant,p.=,ENST00000367412,NM_001994.2; T ENST00000367412 Transcript synonymous_variant 98/2217 54/1986 18/661 L ctC/ctA 1 -1 F13B HGNC HGNC:3534 protein_coding YES CCDS1388.1 ENSP00000356382 P05160 UPI000013D8E0 NM_001994.2 1/12 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 197067170 197067170 G T 1 0 0 0 0 0 0 0 1 5209 929 33 2 2 F13B 1 197067170 Silent SNP G C3N-00556_T 10707192 197067170 51889252 41 16170 ZNF281 0 . GRCh38 1 200407946 200407946 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1760C>T p.Ser587Leu p.S587L ENST00000294740 2/2 223 207 16 249 249 0 strelka-varscan ZNF281,missense_variant,p.Ser587Leu,ENST00000294740,NM_012482.4,NM_001281293.1;ZNF281,missense_variant,p.Ser587Leu,ENST00000367353,;ZNF281,missense_variant,p.Ser551Leu,ENST00000367352,NM_001281294.1;RP11-469A15.2,intron_variant,,ENST00000637430,;RP11-469A15.2,upstream_gene_variant,,ENST00000634596,;RP11-469A15.2,upstream_gene_variant,,ENST00000635220,; A ENST00000294740 Transcript missense_variant 1885/4891 1760/2688 587/895 S/L tCa/tTa 1 -1 ZNF281 HGNC HGNC:13075 protein_coding YES CCDS1402.1 ENSP00000294740 Q9Y2X9 UPI000013C345 NM_012482.4,NM_001281293.1 deleterious(0.05) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 200407946 200407946 G A 1 0 0 0 0 1 0 0 0 18394 1294 45 3 3 ZNF281 1 200407946 Missense_Mutation SNP G C3N-00556_T 3340776 200407946 48548476 42 16171 ARL8A 0 . GRCh38 1 202138433 202138433 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.139G>A p.Glu47Lys p.E47K ENST00000272217 2/7 213 181 32 214 214 0 strelka-varscan ARL8A,missense_variant,p.Glu47Lys,ENST00000272217,NM_138795.3;ARL8A,missense_variant,p.Glu47Lys,ENST00000614750,NM_001256129.1;GPR37L1,downstream_gene_variant,,ENST00000367282,NM_004767.3;ARL8A,upstream_gene_variant,,ENST00000486225,;ARL8A,upstream_gene_variant,,ENST00000491358,; T ENST00000272217 Transcript missense_variant 308/1793 139/561 47/186 E/K Gag/Aag 1 -1 ARL8A HGNC HGNC:25192 protein_coding YES CCDS1421.1 ENSP00000272217 Q96BM9 A0A024R977 UPI00000372D3 NM_138795.3 deleterious(0.02) 2/7 Gene3D:3.40.50.300,Pfam_domain:PF00025,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF122,SMART_domains:SM00175,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 202138433 202138433 C T 1 0 0 0 0 1 0 0 0 1086 893 31 1 1 ARL8A 1 202138433 Missense_Mutation SNP C C3N-00556_T 1730487 202138433 46817989 43 16172 LAX1 0 . GRCh38 1 203774385 203774385 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.901G>A p.Asp301Asn p.D301N ENST00000442561 5/5 268 253 15 337 336 1 strelka-varscan-mutect LAX1,missense_variant,p.Asp301Asn,ENST00000442561,NM_017773.3;LAX1,missense_variant,p.Asp285Asn,ENST00000367217,NM_001136190.1;LAX1,non_coding_transcript_exon_variant,,ENST00000367215,; A ENST00000442561 Transcript missense_variant 1291/3023 901/1197 301/398 D/N Gat/Aat 1 1 LAX1 HGNC HGNC:26005 protein_coding YES CCDS1441.2 ENSP00000406970 Q8IWV1 UPI000007446D NM_017773.3 tolerated(0.13) 5/5 PD319679,Pfam_domain:PF15681,hmmpanther:PTHR24091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 203774385 203774385 G A 1 0 0 0 0 1 0 0 0 8553 942 33 3 3 LAX1 1 203774385 Missense_Mutation SNP G C3N-00556_T 1635952 203774385 45182037 44 16173 DIEXF 0 . GRCh38 1 209830822 209830822 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.167C>T p.Ser56Leu p.S56L ENST00000491415 3/12 142 127 15 188 188 0 strelka-varscan-mutect DIEXF,missense_variant,p.Ser56Leu,ENST00000491415,NM_014388.6; T ENST00000491415 Transcript missense_variant 224/8446 167/2271 56/756 S/L tCa/tTa 1 1 DIEXF HGNC HGNC:28440 protein_coding YES CCDS1493.1 ENSP00000419005 Q68CQ4 UPI000006D987 NM_014388.6 tolerated(0.05) 3/12 hmmpanther:PTHR12933,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 209830822 209830822 C T 1 0 0 0 0 1 0 0 0 4327 838 29 3 3 DIEXF 1 209830822 Missense_Mutation SNP C C3N-00556_T 6056437 209830822 39125600 45 16174 DNAH14 0 . GRCh38 1 225240708 225240708 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.6568G>A p.Glu2190Lys p.E2190K ENST00000430092 42/84 262 245 17 365 365 0 strelka-varscan-mutect DNAH14,missense_variant,p.Glu2190Lys,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Glu2190Lys,ENST00000439375,;DNAH14,missense_variant,p.Glu1785Lys,ENST00000445597,;DNAH14,upstream_gene_variant,,ENST00000327794,; A ENST00000430092 Transcript missense_variant 6783/13763 6568/13548 2190/4515 E/K Gaa/Aaa 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 deleterious(0.01) 42/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 225240708 225240708 G A 1 0 0 0 0 1 0 0 0 4415 1291 45 3 3 DNAH14 1 225240708 Missense_Mutation SNP G C3N-00556_T 15409886 225240708 23715714 46 16175 H3F3A 0 . GRCh38 1 226064408 226064408 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.57G>A p.= p.K19K ENST00000366813 1/3 163 130 33 183 183 0 strelka-varscan-mutect H3F3A,synonymous_variant,p.=,ENST00000366814,;H3F3A,synonymous_variant,p.=,ENST00000366813,;H3F3A,synonymous_variant,p.=,ENST00000366815,NM_002107.4;H3F3A,synonymous_variant,p.=,ENST00000366816,;RP11-396C23.4,upstream_gene_variant,,ENST00000609423,; A ENST00000366813 Transcript synonymous_variant 432/1308 57/411 19/136 K aaG/aaA 1 1 H3F3A HGNC HGNC:4764 protein_coding YES CCDS1550.1 ENSP00000355778 P84243 B2R4P9 UPI00000007B0 1/3 hmmpanther:PTHR11426,PROSITE_patterns:PS00322,Pfam_domain:PF00125,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00622 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 226064408 226064408 G A 1 0 0 0 0 0 0 0 1 6815 962 34 3 3 H3F3A 1 226064408 Silent SNP G C3N-00556_T 823700 226064408 22892014 47 16176 NID1 0 . GRCh38 1 236011935 236011935 + Missense_Mutation SNP C C T rs760250427 C3N-00556_T C3N-00556_N C C c.2513G>A p.Arg838His p.R838H ENST00000264187 12/20 112 100 12 119 119 0 strelka-varscan NID1,missense_variant,p.Arg838His,ENST00000264187,NM_002508.2;NID1,intron_variant,,ENST00000366595,; T ENST00000264187 Transcript missense_variant 2596/5864 2513/3744 838/1247 R/H cGt/cAt rs760250427,COSM4706876 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 tolerated(0.2) 12/20 Gene3D:2.40.155.10,Pfam_domain:PF12947,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57610 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 207 0 2 0 0 0 0 -18.34569 0.9999999 1 1 1 0 T 3 4 54 236011935 236011935 C T 1 0 0 0 0 1 0 0 0 10447 536 19 1 1 NID1 1 236011935 Missense_Mutation SNP C C3N-00556_T 9947527 236011935 12944487 48 16177 RYR2 0 . GRCh38 1 237496557 237496557 + Missense_Mutation SNP T T G C3N-00556_T C3N-00556_N T T c.2008T>G p.Tyr670Asp p.Y670D ENST00000366574 20/105 162 148 14 257 256 1 strelka-varscan RYR2,missense_variant,p.Tyr670Asp,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Tyr654Asp,ENST00000360064,; G ENST00000366574 Transcript missense_variant 2325/16562 2008/14904 670/4967 Y/D Tat/Gat COSM4627068,COSM4627069 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 20/105 PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 237496557 237496557 T G 1 0 0 0 0 1 0 0 0 14029 1638 57 5 5 RYR2 1 237496557 Missense_Mutation SNP T C3N-00556_T 1484622 237496557 11459865 49 16178 FH 0 . GRCh38 1 241504212 241504212 + Missense_Mutation SNP T T A novel C3N-00556_T C3N-00556_N T T c.938A>T p.Glu313Val p.E313V ENST00000366560 7/10 291 254 37 402 401 1 strelka-varscan FH,missense_variant,p.Glu313Val,ENST00000366560,NM_000143.3; A ENST00000366560 Transcript missense_variant 977/1797 938/1533 313/510 E/V gAa/gTa 1 -1 FH HGNC HGNC:3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 A0A0S2Z4C3 UPI000012AD6A NM_000143.3 deleterious(0) 7/10 HAMAP:MF_00743,hmmpanther:PTHR11444:SF1,hmmpanther:PTHR11444,TIGRFAM_domain:TIGR00979,Gene3D:1.20.200.10,Pfam_domain:PF00206,Superfamily_domains:SSF48557 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 241504212 241504212 T A 1 0 0 0 0 1 0 0 0 5739 1783 62 4 4 FH 1 241504212 Missense_Mutation SNP T C3N-00556_T 4007655 241504212 7452210 50 16179 ZNF692 0 . GRCh38 1 248850332 248850332 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1453G>C p.Glu485Gln p.E485Q ENST00000451251 12/12 114 105 9 114 114 0 strelka-varscan ZNF692,missense_variant,p.Glu485Gln,ENST00000451251,NM_001136036.2;ZNF692,missense_variant,p.Glu480Gln,ENST00000306601,NM_017865.3;ZNF692,missense_variant,p.Glu435Gln,ENST00000366471,NM_001193328.1;ZNF692,missense_variant,p.Glu234Gln,ENST00000476503,;ZNF672,downstream_gene_variant,,ENST00000306562,NM_024836.2;ZNF672,downstream_gene_variant,,ENST00000428515,;ZNF672,downstream_gene_variant,,ENST00000423362,;ZNF672,downstream_gene_variant,,ENST00000505503,;ZNF672,downstream_gene_variant,,ENST00000502697,;ZNF672,downstream_gene_variant,,ENST00000510904,;ZNF672,downstream_gene_variant,,ENST00000515369,;ZNF692,3_prime_UTR_variant,,ENST00000463519,;ZNF692,3_prime_UTR_variant,,ENST00000412341,;ZNF692,3_prime_UTR_variant,,ENST00000477070,;ZNF692,3_prime_UTR_variant,,ENST00000482023,;ZNF692,non_coding_transcript_exon_variant,,ENST00000533927,;ZNF692,non_coding_transcript_exon_variant,,ENST00000470787,;ZNF692,downstream_gene_variant,,ENST00000474351,;ZNF692,downstream_gene_variant,,ENST00000462037,; G ENST00000451251 Transcript missense_variant 1799/2065 1453/1575 485/524 E/Q Gag/Cag 1 -1 ZNF692 HGNC HGNC:26049 protein_coding YES CCDS44348.1 ENSP00000391200 Q9BU19 UPI00017A804A NM_001136036.2 tolerated(0.29) 12/12 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -18.18358 1 1 1 1 0 G 3 3 54 248850332 248850332 C G 1 0 0 0 0 1 0 0 0 18670 922 32 4 4 ZNF692 1 248850332 Missense_Mutation SNP C C3N-00556_T 7346120 248850332 106090 51 16180 GREB1 0 . GRCh38 2 11576446 11576446 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.548C>A p.Pro183His p.P183H ENST00000381486 5/33 218 183 35 251 251 0 strelka-varscan-mutect GREB1,missense_variant,p.Pro183His,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Pro183His,ENST00000234142,;GREB1,missense_variant,p.Pro183His,ENST00000263834,NM_148903.2;GREB1,missense_variant,p.Pro183His,ENST00000381483,NM_033090.2;GREB1,missense_variant,p.Pro73His,ENST00000389825,; A ENST00000381486 Transcript missense_variant 848/8484 548/5850 183/1949 P/H cCc/cAc 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 deleterious(0) 5/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 11576446 11576446 C A 1 0 0 0 0 1 0 0 0 6639 623 22 2 2 GREB1 2 11576446 Missense_Mutation SNP C C3N-00556_T 11576446 230617083 52 16181 SMC6 0 . GRCh38 2 17715045 17715045 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1546G>T p.Asp516Tyr p.D516Y ENST00000448223 16/28 261 234 27 262 262 0 strelka-varscan-mutect SMC6,missense_variant,p.Asp516Tyr,ENST00000448223,NM_001142286.1;SMC6,missense_variant,p.Asp516Tyr,ENST00000351948,NM_024624.5;SMC6,missense_variant,p.Asp516Tyr,ENST00000402989,;SMC6,missense_variant,p.Asp542Tyr,ENST00000446852,;SMC6,downstream_gene_variant,,ENST00000381272,;SMC6,upstream_gene_variant,,ENST00000430591,; A ENST00000448223 Transcript missense_variant 1816/5233 1546/3276 516/1091 D/Y Gac/Tac 1 -1 SMC6 HGNC HGNC:20466 protein_coding YES CCDS1690.1 ENSP00000404092 Q96SB8 UPI0000073C3B NM_001142286.1 tolerated(0.08) 16/28 hmmpanther:PTHR19306,hmmpanther:PTHR19306:SF5,Pfam_domain:PF02463 MODERATE 1 SNV 1 1 PASS rs1244163133 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 17715045 17715045 C A 1 0 0 0 0 1 0 0 0 15080 855 30 2 2 SMC6 2 17715045 Missense_Mutation SNP C C3N-00556_T 6138599 17715045 224478484 53 16182 APOB 0 . GRCh38 2 21007072 21007072 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.9796G>A p.Glu3266Lys p.E3266K ENST00000233242 26/29 327 309 18 397 396 1 strelka-varscan APOB,missense_variant,p.Glu3266Lys,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 9924/14121 9796/13692 3266/4563 E/K Gag/Aag 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.07) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 21007072 21007072 C T 1 0 0 0 0 1 0 0 0 907 922 32 3 3 APOB 2 21007072 Missense_Mutation SNP C C3N-00556_T 3292027 21007072 221186457 54 16183 TDRD15 0 . GRCh38 2 21141650 21141650 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.4183C>T p.Gln1395Ter p.Q1395* ENST00000405799 4/4 144 130 14 192 192 0 strelka-varscan-mutect TDRD15,stop_gained,p.Gln1395Ter,ENST00000405799,;TDRD15,stop_gained,p.Gln1395Ter,ENST00000622654,; T ENST00000405799 Transcript stop_gained 4513/6135 4183/5805 1395/1934 Q/* Cag/Tag 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 Gene3D:2.30.30.140,Pfam_domain:PF00567,PROSITE_profiles:PS50304,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,SMART_domains:SM00333,Superfamily_domains:SSF63748 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 21141650 21141650 C T 1 0 0 0 0 0 1 0 0 16141 827 29 3 3 TDRD15 2 21141650 Nonsense_Mutation SNP C C3N-00556_T 134578 21141650 221051879 55 16184 GAREM2 0 . GRCh38 2 26184711 26184711 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.863G>C p.Cys288Ser p.C288S ENST00000401533 4/6 148 138 10 137 137 0 strelka-varscan-mutect GAREM2,missense_variant,p.Cys211Ser,ENST00000407684,NM_001191033.1;GAREM2,missense_variant,p.Cys288Ser,ENST00000401533,NM_001168241.1;GAREM2,upstream_gene_variant,,ENST00000496070,; C ENST00000401533 Transcript missense_variant 993/4161 863/2625 288/874 C/S tGc/tCc 1 1 GAREM2 HGNC HGNC:27172 protein_coding YES CCDS54336.1 ENSP00000384593 Q75VX8 UPI0000237273 NM_001168241.1 tolerated(0.45) 4/6 Pfam_domain:PF12736,hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 26184711 26184711 G C 1 0 0 0 0 1 0 0 0 6110 1319 46 4 4 GAREM2 2 26184711 Missense_Mutation SNP G C3N-00556_T 5043061 26184711 216008818 56 16185 CGREF1 0 . GRCh38 2 27101750 27101750 + Missense_Mutation SNP G G C rs754790317 C3N-00556_T C3N-00556_N G G c.481C>G p.Gln161Glu p.Q161E ENST00000402394 6/6 454 368 86 473 473 0 strelka-varscan-mutect CGREF1,missense_variant,p.Gln161Glu,ENST00000402394,NM_006569.5;CGREF1,missense_variant,p.Gln161Glu,ENST00000312734,;CGREF1,missense_variant,p.Gln283Glu,ENST00000404694,;CGREF1,missense_variant,p.Gln161Glu,ENST00000405600,NM_001166239.1;CGREF1,missense_variant,p.Gln161Glu,ENST00000260595,;CGREF1,intron_variant,,ENST00000402550,NM_001166240.1;KHK,downstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,downstream_gene_variant,,ENST00000260598,NM_006488.2;KHK,downstream_gene_variant,,ENST00000429697,;KHK,downstream_gene_variant,,ENST00000490823,;CGREF1,intron_variant,,ENST00000440612,;KHK,downstream_gene_variant,,ENST00000464371,;KHK,downstream_gene_variant,,ENST00000469936,;CGREF1,downstream_gene_variant,,ENST00000467539,; C ENST00000402394 Transcript missense_variant 750/1906 481/957 161/318 Q/E Cag/Gag rs754790317 1 -1 CGREF1 HGNC HGNC:16962 protein_coding YES CCDS33162.2 ENSP00000385452 Q99674 UPI000013D0EB NM_006569.5 tolerated(0.35) 6/6 hmmpanther:PTHR23104,hmmpanther:PTHR23104:SF11 MODERATE SNV 2 1 PASS rs754790317 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 27101750 27101750 G C 1 0 0 0 0 1 0 0 0 3063 1299 45 4 4 CGREF1 2 27101750 Missense_Mutation SNP G C3N-00556_T 917039 27101750 215091779 57 16186 ATRAID 0 . GRCh38 2 27212349 27212349 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.146G>A p.Gly49Glu p.G49E ENST00000611786 1/7 346 317 29 342 342 0 strelka-varscan-mutect ATRAID,missense_variant,p.Gly49Glu,ENST00000611786,NM_080592.3;ATRAID,missense_variant,p.Gly49Glu,ENST00000380171,;ATRAID,5_prime_UTR_variant,,ENST00000606999,NM_001170795.1;SLC5A6,intron_variant,,ENST00000432106,;SLC5A6,intron_variant,,ENST00000430186,;SLC5A6,intron_variant,,ENST00000428518,;SLC5A6,intron_variant,,ENST00000442731,;SLC5A6,upstream_gene_variant,,ENST00000310574,NM_021095.2;SLC5A6,upstream_gene_variant,,ENST00000408041,;ATRAID,upstream_gene_variant,,ENST00000405489,NM_016085.4;SLC5A6,upstream_gene_variant,,ENST00000412471,;SLC5A6,upstream_gene_variant,,ENST00000414408,;SLC5A6,upstream_gene_variant,,ENST00000401463,;SLC5A6,upstream_gene_variant,,ENST00000426119,;ATRAID,upstream_gene_variant,,ENST00000419744,;ATRAID,non_coding_transcript_exon_variant,,ENST00000484646,;SLC5A6,upstream_gene_variant,,ENST00000488743,;SLC5A6,upstream_gene_variant,,ENST00000445802,;ATRAID,upstream_gene_variant,,ENST00000472515,;ATRAID,upstream_gene_variant,,ENST00000491220,; A ENST00000611786 Transcript missense_variant 319/1256 146/855 49/284 G/E gGa/gAa 1 1 ATRAID HGNC HGNC:24090 protein_coding YES CCDS1741.1 ENSP00000484228 Q6UW56 UPI0000456D96 NM_080592.3 tolerated_low_confidence(0.2) 1/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 27212349 27212349 G A 1 0 0 0 0 1 0 0 0 1357 1174 41 3 3 ATRAID 2 27212349 Missense_Mutation SNP G C3N-00556_T 110599 27212349 214981180 58 16187 GTF3C2 0 . GRCh38 2 27343120 27343120 + Nonsense_Mutation SNP G G C rs774560559 C3N-00556_T C3N-00556_N G G c.275C>G p.Ser92Ter p.S92* ENST00000359541 3/19 64 59 5 111 111 0 strelka-mutect GTF3C2,stop_gained,p.Ser92Ter,ENST00000359541,NM_001318909.1;GTF3C2,stop_gained,p.Ser92Ter,ENST00000264720,NM_001521.3,NM_001035521.2;GTF3C2,stop_gained,p.Ser92Ter,ENST00000622534,;GTF3C2,stop_gained,p.Ser92Ter,ENST00000457748,;GTF3C2,downstream_gene_variant,,ENST00000423998,;GTF3C2-AS1,downstream_gene_variant,,ENST00000625728,;GTF3C2-AS1,downstream_gene_variant,,ENST00000626256,;GTF3C2-AS1,downstream_gene_variant,,ENST00000590383,;GTF3C2-AS1,downstream_gene_variant,,ENST00000588707,;GTF3C2-AS1,downstream_gene_variant,,ENST00000589853,;GTF3C2-AS1,downstream_gene_variant,,ENST00000587586,;GTF3C2-AS1,downstream_gene_variant,,ENST00000589232,;GTF3C2,upstream_gene_variant,,ENST00000480989,; C ENST00000359541 Transcript stop_gained 705/3992 275/2736 92/911 S/* tCa/tGa rs774560559 1 -1 GTF3C2 HGNC HGNC:4665 protein_coding YES CCDS1749.1 ENSP00000352536 Q8WUA4 UPI0000074025 NM_001318909.1 3/19 hmmpanther:PTHR15052,hmmpanther:PTHR15052:SF2 HIGH 1 SNV 1 1 PASS rs774560559 . 0 208 2 0 0 0 0 0 -12.12618 1 1 1 1 0 C 4 2 54 27343120 27343120 G C 1 0 0 0 0 0 1 0 0 6754 1294 45 4 4 GTF3C2 2 27343120 Nonsense_Mutation SNP G C3N-00556_T 130771 27343120 214850409 59 16188 PLB1 0 . GRCh38 2 28538338 28538338 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.575G>T p.Gly192Val p.G192V ENST00000327757 10/58 232 202 30 205 205 0 strelka-varscan PLB1,missense_variant,p.Gly203Val,ENST00000422425,NM_001170585.1;PLB1,missense_variant,p.Gly192Val,ENST00000327757,NM_153021.4;PLB1,missense_variant,p.Gly202Val,ENST00000404858,;PLB1,missense_variant,p.Gly147Val,ENST00000416713,; T ENST00000327757 Transcript missense_variant 619/5107 575/4377 192/1458 G/V gGc/gTc 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 tolerated(0.5) 10/58 hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 28538338 28538338 G T 1 0 0 0 0 1 0 0 0 12118 1203 42 2 2 PLB1 2 28538338 Missense_Mutation SNP G C3N-00556_T 1195218 28538338 213655191 60 16189 ALK 0 . GRCh38 2 29226943 29226943 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3046G>A p.Glu1016Lys p.E1016K ENST00000389048 18/29 414 340 74 373 373 0 strelka-varscan ALK,missense_variant,p.Glu1016Lys,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Glu639Lys,ENST00000618119,;ALK,upstream_gene_variant,,ENST00000431873,;ALK,upstream_gene_variant,,ENST00000453137,; T ENST00000389048 Transcript missense_variant 3953/6220 3046/4863 1016/1620 E/K Gag/Aag 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 tolerated(0.53) 18/29 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF276 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 29226943 29226943 C T 1 0 0 0 0 1 0 0 0 625 835 29 3 3 ALK 2 29226943 Missense_Mutation SNP C C3N-00556_T 688605 29226943 212966586 61 16190 XDH 0 . GRCh38 2 31381691 31381691 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.1074C>A p.= p.I358I ENST00000379416 12/36 469 418 51 431 431 0 strelka-varscan XDH,synonymous_variant,p.=,ENST00000379416,NM_000379.3;XDH,downstream_gene_variant,,ENST00000491727,;XDH,downstream_gene_variant,,ENST00000476043,; T ENST00000379416 Transcript synonymous_variant 1123/5688 1074/4002 358/1333 I atC/atA 1 -1 XDH HGNC HGNC:12805 protein_coding YES CCDS1775.1 ENSP00000368727 P47989 UPI0000036BC9 NM_000379.3 12/36 PROSITE_profiles:PS51387,hmmpanther:PTHR11908,hmmpanther:PTHR11908:SF78,Gene3D:3.30.465.10,TIGRFAM_domain:TIGR02963,Pfam_domain:PF00941,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF56176 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 31381691 31381691 G T 1 0 0 0 0 0 0 0 1 17985 932 33 2 2 XDH 2 31381691 Silent SNP G C3N-00556_T 2154748 31381691 210811838 62 16191 GTF2A1L 0 . GRCh38 2 48671612 48671612 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.3373G>A p.Asp1125Asn p.D1125N ENST00000394754 10/11 130 113 17 108 108 0 strelka-varscan STON1-GTF2A1L,missense_variant,p.Asp1125Asn,ENST00000394754,NM_172311.2;STON1-GTF2A1L,missense_variant,p.Asp1125Asn,ENST00000405008,;STON1-GTF2A1L,missense_variant,p.Asp1125Asn,ENST00000402114,NM_001198593.1;STON1-GTF2A1L,missense_variant,p.Asp1078Asn,ENST00000394751,NM_001198594.1;GTF2A1L,missense_variant,p.Asp421Asn,ENST00000403751,NM_006872.4;GTF2A1L,missense_variant,p.Asp387Asn,ENST00000430487,NM_001193487.2;GTF2A1L,missense_variant,p.Asp70Asn,ENST00000508440,;RP11-310N16.1,intron_variant,,ENST00000602369,; A ENST00000394754 Transcript missense_variant 3487/3824 3373/3549 1125/1182 D/N Gat/Aat 1 1 STON1-GTF2A1L HGNC HGNC:30651 protein_coding YES CCDS1840.1 ENSP00000378236 Q53S48 UPI000013C976 NM_172311.2 deleterious(0) 10/11 hmmpanther:PTHR12694,hmmpanther:PTHR12694:SF9,Pfam_domain:PF03153,Gene3D:2.30.18.10,SMART_domains:SM01371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 54 48671612 48671612 G A 1 0 0 0 0 1 0 0 0 6735 1290 45 3 3 GTF2A1L 2 48671612 Missense_Mutation SNP G C3N-00556_T 17289921 48671612 193521917 63 16192 NRXN1 0 . GRCh38 2 50623516 50623516 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1031C>T p.Ser344Leu p.S344L ENST00000404971 7/24 274 258 16 322 321 1 strelka-varscan NRXN1,missense_variant,p.Ser311Leu,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Ser311Leu,ENST00000625672,;NRXN1,missense_variant,p.Ser344Leu,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Ser311Leu,ENST00000401669,;NRXN1,missense_variant,p.Ser307Leu,ENST00000405472,;NRXN1,missense_variant,p.Ser311Leu,ENST00000630543,;NRXN1,missense_variant,p.Ser291Leu,ENST00000628515,;NRXN1,missense_variant,p.Ser34Leu,ENST00000406859,;NRXN1,missense_variant,p.Ser34Leu,ENST00000402717,;NRXN1,missense_variant,p.Ser46Leu,ENST00000625891,;NRXN1,upstream_gene_variant,,ENST00000495871,;RP11-358H12.1,intron_variant,,ENST00000634985,;NRXN1,non_coding_transcript_exon_variant,,ENST00000628761,;NRXN1,non_coding_transcript_exon_variant,,ENST00000630431,;NRXN1,upstream_gene_variant,,ENST00000636298,;NRXN1,upstream_gene_variant,,ENST00000637605,;NRXN1,missense_variant,p.Ser46Leu,ENST00000331040,;NRXN1,3_prime_UTR_variant,,ENST00000626249,; A ENST00000404971 Transcript missense_variant 2371/7578 1031/4644 344/1547 S/L tCa/tTa 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 tolerated(0.07) 7/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 50623516 50623516 G A 1 0 0 0 0 1 0 0 0 10724 1294 45 3 3 NRXN1 2 50623516 Missense_Mutation SNP G C3N-00556_T 1951904 50623516 191570013 64 16193 SPTBN1 0 . GRCh38 2 54664655 54664655 + Frame_Shift_Del DEL A A - novel C3N-00556_T C3N-00556_N A A c.6623delA p.His2208ProfsTer22 p.H2208Pfs*22 ENST00000356805 33/36 136 115 21 150 150 0 sindel-varindel-pindel SPTBN1,frameshift_variant,p.His2210ProfsTer22,ENST00000615901,;SPTBN1,frameshift_variant,p.His2208ProfsTer22,ENST00000356805,NM_003128.2;SPTBN1,downstream_gene_variant,,ENST00000333896,NM_178313.2;AC093110.3,non_coding_transcript_exon_variant,,ENST00000626206,;AC093110.3,upstream_gene_variant,,ENST00000456363,;SPTBN1,non_coding_transcript_exon_variant,,ENST00000467371,;SPTBN1,downstream_gene_variant,,ENST00000496323,; - ENST00000356805 Transcript frameshift_variant 6904/8482 6623/7095 2208/2364 H/X cAc/cc 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 33/36 PROSITE_profiles:PS50003,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,PIRSF_domain:PIRSF002297,Gene3D:2.30.29.30,Pfam_domain:PF15410,SMART_domains:SM00233,Superfamily_domains:SSF50729,Prints_domain:PR00683 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 54 54664655 54664655 A - 1 0 1 0 1 0 0 0 0 15475 159 6 0 0 SPTBN1 2 54664655 Frame_Shift_Del DEL A C3N-00556_T 4041139 54664655 187528874 65 16194 USP34 0 . GRCh38 2 61236194 61236194 + Silent SNP T T C novel C3N-00556_T C3N-00556_N T T c.6885A>G p.= p.P2295P ENST00000398571 55/80 180 129 51 208 208 0 strelka-varscan USP34,synonymous_variant,p.=,ENST00000398571,NM_014709.3;USP34,synonymous_variant,p.=,ENST00000411912,;USP34,synonymous_variant,p.=,ENST00000453734,;USP34,intron_variant,,ENST00000472706,;USP34,non_coding_transcript_exon_variant,,ENST00000463046,; C ENST00000398571 Transcript synonymous_variant 6962/11357 6885/10641 2295/3546 P ccA/ccG 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 55/80 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 61236194 61236194 T C 1 0 0 0 0 0 0 0 1 17607 1567 55 5 5 USP34 2 61236194 Silent SNP T C3N-00556_T 6571539 61236194 180957335 66 16195 LGALSL 0 . GRCh38 2 64454570 64454570 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.25G>A p.Asp9Asn p.D9N ENST00000238875 1/5 68 59 9 41 41 0 strelka-varscan LGALSL,missense_variant,p.Asp9Asn,ENST00000238875,NM_014181.2;LGALSL,missense_variant,p.Asp9Asn,ENST00000409537,;LGALSL,missense_variant,p.Asp9Asn,ENST00000464281,;AC008074.3,upstream_gene_variant,,ENST00000441630,;LGALSL,missense_variant,p.Asp9Asn,ENST00000420552,;LGALSL,missense_variant,p.Asp9Asn,ENST00000462737,;AC008074.5,downstream_gene_variant,,ENST00000425381,; A ENST00000238875 Transcript missense_variant 479/3926 25/519 9/172 D/N Gat/Aat 1 1 LGALSL HGNC HGNC:25012 protein_coding YES CCDS1877.1 ENSP00000238875 Q3ZCW2 UPI000013CA5E NM_014181.2 tolerated_low_confidence(0.06) 1/5 hmmpanther:PTHR11346:SF98,hmmpanther:PTHR11346 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.88375 1 1 1 1 0 A 3 1 54 64454570 64454570 G A 1 0 0 0 0 1 0 0 0 8660 1058 37 1 1 LGALSL 2 64454570 Missense_Mutation SNP G C3N-00556_T 3218376 64454570 177738959 67 16196 ZNF638 0 . GRCh38 2 71423670 71423670 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.4156G>A p.Asp1386Asn p.D1386N ENST00000409544 22/28 155 119 36 246 246 0 strelka-varscan ZNF638,missense_variant,p.Asp1386Asn,ENST00000409544,NM_001252612.1;ZNF638,missense_variant,p.Asp1386Asn,ENST00000264447,NM_014497.4,NM_001014972.2,NM_001252613.1;ZNF638,upstream_gene_variant,,ENST00000493576,;ZNF638,upstream_gene_variant,,ENST00000461991,;ZNF638,non_coding_transcript_exon_variant,,ENST00000409407,;ZNF638,non_coding_transcript_exon_variant,,ENST00000487638,;ZNF638,intron_variant,,ENST00000483421,;ZNF638,intron_variant,,ENST00000494241,;ZNF638,upstream_gene_variant,,ENST00000492262,;ZNF638,upstream_gene_variant,,ENST00000472758,; A ENST00000409544 Transcript missense_variant 4786/6821 4156/5937 1386/1978 D/N Gat/Aat 1 1 ZNF638 HGNC HGNC:17894 protein_coding YES CCDS1917.1 ENSP00000386433 Q14966 UPI000013D51B NM_001252612.1 tolerated(1) 22/28 hmmpanther:PTHR15592,hmmpanther:PTHR15592:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 71423670 71423670 G A 1 0 0 0 0 1 0 0 0 18630 942 33 3 3 ZNF638 2 71423670 Missense_Mutation SNP G C3N-00556_T 6969100 71423670 170769859 68 16197 DCTN1 0 . GRCh38 2 74368761 74368761 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.1821G>T p.= p.L607L ENST00000361874 16/32 396 303 93 398 398 0 strelka-varscan DCTN1,synonymous_variant,p.=,ENST00000361874,NM_004082.4;DCTN1,synonymous_variant,p.=,ENST00000628224,;DCTN1,synonymous_variant,p.=,ENST00000394003,NM_001190837.1;DCTN1,synonymous_variant,p.=,ENST00000409240,NM_001190836.1;DCTN1,synonymous_variant,p.=,ENST00000409868,;DCTN1,synonymous_variant,p.=,ENST00000633691,NM_023019.3;DCTN1,synonymous_variant,p.=,ENST00000409438,NM_001135041.2;DCTN1,synonymous_variant,p.=,ENST00000409567,NM_001135040.2;DCTN1,downstream_gene_variant,,ENST00000458655,;DCTN1,intron_variant,,ENST00000497666,;DCTN1,upstream_gene_variant,,ENST00000495643,;DCTN1,downstream_gene_variant,,ENST00000463583,;DCTN1,synonymous_variant,p.=,ENST00000434055,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,;DCTN1,upstream_gene_variant,,ENST00000491465,;DCTN1,downstream_gene_variant,,ENST00000477966,;DCTN1,downstream_gene_variant,,ENST00000470351,;DCTN1,upstream_gene_variant,,ENST00000495895,;DCTN1,downstream_gene_variant,,ENST00000462813,; A ENST00000361874 Transcript synonymous_variant 2139/4500 1821/3837 607/1278 L ctG/ctT 1 -1 DCTN1 HGNC HGNC:2711 protein_coding YES CCDS1939.1 ENSP00000354791 Q14203 UPI0000129A25 NM_004082.4 16/32 Pfam_domain:PF12455,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF40 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 74368761 74368761 C A 1 0 0 0 0 0 0 0 1 4109 581 21 2 2 DCTN1 2 74368761 Silent SNP C C3N-00556_T 2945091 74368761 167824768 69 16198 C2orf68 0 . GRCh38 2 85611896 85611896 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.89G>A p.Arg30Gln p.R30Q ENST00000306336 1/4 119 107 12 100 100 0 strelka-varscan C2orf68,missense_variant,p.Arg30Gln,ENST00000306336,NM_001013649.3;C2orf68,missense_variant,p.Arg30Gln,ENST00000409734,;USP39,upstream_gene_variant,,ENST00000323701,NM_006590.3;USP39,upstream_gene_variant,,ENST00000613444,NM_001256727.1;USP39,upstream_gene_variant,,ENST00000450066,NM_001256728.1;USP39,upstream_gene_variant,,ENST00000409470,NM_001256725.1;USP39,upstream_gene_variant,,ENST00000409766,NM_001256726.1;USP39,upstream_gene_variant,,ENST00000409025,;USP39,upstream_gene_variant,,ENST00000448971,;USP39,upstream_gene_variant,,ENST00000442708,;USP39,intron_variant,,ENST00000459775,;USP39,intron_variant,,ENST00000491659,;USP39,intron_variant,,ENST00000474572,;USP39,upstream_gene_variant,,ENST00000455732,;USP39,upstream_gene_variant,,ENST00000465282,;C2orf68,upstream_gene_variant,,ENST00000478626,;C2orf68,missense_variant,p.Arg14Gln,ENST00000420686,;C2orf68,missense_variant,p.Arg30Gln,ENST00000423181,;USP39,upstream_gene_variant,,ENST00000493829,;USP39,upstream_gene_variant,,ENST00000458268,; T ENST00000306336 Transcript missense_variant 134/2837 89/501 30/166 R/Q cGa/cAa 1 -1 C2orf68 HGNC HGNC:34353 protein_coding YES CCDS42704.1 ENSP00000304410 Q2NKX9 L7T9J5 UPI00002377B0 NM_001013649.3 tolerated(0.07) 1/4 Pfam_domain:PF10573,hmmpanther:PTHR34256 MODERATE 1 SNV 1 1 PASS . . 0 202 4 4 0 0 0 0 -17.70248 0.9984781 1 1 1 0 T 3 4 54 85611896 85611896 C T 1 0 0 0 0 1 0 0 0 2042 884 31 1 1 C2orf68 2 85611896 Missense_Mutation SNP C C3N-00556_T 11243135 85611896 156581633 70 16199 SFTPB 0 . GRCh38 2 85667713 85667713 + Missense_Mutation SNP T T C novel C3N-00556_T C3N-00556_N T T c.197A>G p.His66Arg p.H66R ENST00000409383 3/12 350 310 40 299 299 0 strelka-varscan SFTPB,missense_variant,p.His54Arg,ENST00000393822,;SFTPB,missense_variant,p.His54Arg,ENST00000519937,;SFTPB,missense_variant,p.His66Arg,ENST00000409383,NM_198843.2,NM_000542.3;SFTPB,missense_variant,p.His51Arg,ENST00000428225,;SFTPB,upstream_gene_variant,,ENST00000494165,;SFTPB,non_coding_transcript_exon_variant,,ENST00000473692,;SFTPB,upstream_gene_variant,,ENST00000491167,; C ENST00000409383 Transcript missense_variant 297/1867 197/1182 66/393 H/R cAt/cGt 1 -1 SFTPB HGNC HGNC:10801 protein_coding YES CCDS1983.2 ENSP00000386346 D6W5L6 UPI0000421A06 NM_198843.2,NM_000542.3 deleterious(0.05) 3/12 Pfam_domain:PF02199,PROSITE_profiles:PS51110,hmmpanther:PTHR11480,hmmpanther:PTHR11480:SF33,SMART_domains:SM00162 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 85667713 85667713 T C 1 0 0 0 0 1 0 0 0 14451 1464 51 5 5 SFTPB 2 85667713 Missense_Mutation SNP T C3N-00556_T 55817 85667713 156525816 71 16200 ZC3H8 0 . GRCh38 2 112254972 112254972 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.10G>A p.Glu4Lys p.E4K ENST00000409573 1/9 90 83 7 77 77 0 strelka-varscan ZC3H8,missense_variant,p.Glu4Lys,ENST00000409573,NM_032494.2;ZC3H8,missense_variant,p.Glu4Lys,ENST00000272570,;ZC3H8,missense_variant,p.Glu4Lys,ENST00000615791,;ZC3H8,non_coding_transcript_exon_variant,,ENST00000474234,;ZC3H8,intron_variant,,ENST00000464305,;ZC3H8,non_coding_transcript_exon_variant,,ENST00000495264,; T ENST00000409573 Transcript missense_variant 140/5965 10/876 4/291 E/K Gag/Aag 1 -1 ZC3H8 HGNC HGNC:30941 protein_coding YES CCDS46392.1 ENSP00000386488 Q8N5P1 UPI00000467EA NM_032494.2 deleterious_low_confidence(0) 1/9 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF21 MODERATE 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -11.37095 0.9999753 1 1 1 0 T 3 4 54 112254972 112254972 C T 1 0 0 0 0 1 0 0 0 18149 835 29 3 3 ZC3H8 2 112254972 Missense_Mutation SNP C C3N-00556_T 26587259 112254972 129938557 72 16201 CLASP1 0 . GRCh38 2 121418694 121418694 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.2248C>G p.Gln750Glu p.Q750E ENST00000263710 23/40 179 166 13 190 190 0 strelka-varscan CLASP1,missense_variant,p.Gln750Glu,ENST00000263710,NM_015282.2;CLASP1,intron_variant,,ENST00000409078,NM_001142274.1;CLASP1,intron_variant,,ENST00000397587,;CLASP1,intron_variant,,ENST00000541377,NM_001207051.1;CLASP1,intron_variant,,ENST00000455322,NM_001142273.1;CLASP1,intron_variant,,ENST00000452274,;CLASP1,intron_variant,,ENST00000463621,; C ENST00000263710 Transcript missense_variant 2638/8092 2248/4617 750/1538 Q/E Cag/Gag 1 -1 CLASP1 HGNC HGNC:17088 protein_coding YES ENSP00000263710 Q7Z460 UPI00001A8BFF NM_015282.2 tolerated(0.1) 23/40 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 121418694 121418694 G C 1 0 0 0 0 1 0 0 0 3217 1299 45 4 4 CLASP1 2 121418694 Missense_Mutation SNP G C3N-00556_T 9163722 121418694 120774835 73 16202 LRP1B 0 . GRCh38 2 140883862 140883862 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.4124G>T p.Gly1375Val p.G1375V ENST00000389484 25/91 231 187 44 277 277 0 strelka-varscan LRP1B,missense_variant,p.Gly1375Val,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Gly520Val,ENST00000434794,; A ENST00000389484 Transcript missense_variant 5096/16535 4124/13800 1375/4599 G/V gGa/gTa 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 25/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 140883862 140883862 C A 1 0 0 0 0 1 0 0 0 8850 855 30 2 2 LRP1B 2 140883862 Missense_Mutation SNP C C3N-00556_T 19465168 140883862 101309667 74 16203 GTDC1 0 . GRCh38 2 144145658 144145658 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.261G>T p.= p.L87L ENST00000392869 4/11 155 138 17 178 178 0 strelka-varscan GTDC1,synonymous_variant,p.=,ENST00000392869,;GTDC1,synonymous_variant,p.=,ENST00000409214,NM_001006636.3;GTDC1,synonymous_variant,p.=,ENST00000542155,NM_001164629.3;GTDC1,synonymous_variant,p.=,ENST00000344850,;GTDC1,synonymous_variant,p.=,ENST00000392867,NM_024659.4;GTDC1,synonymous_variant,p.=,ENST00000241391,NM_001284233.1;GTDC1,synonymous_variant,p.=,ENST00000618778,NM_001284238.1;GTDC1,synonymous_variant,p.=,ENST00000409298,;GTDC1,synonymous_variant,p.=,ENST00000437114,;GTDC1,synonymous_variant,p.=,ENST00000417450,;GTDC1,5_prime_UTR_variant,,ENST00000463875,NM_001284234.1;GTDC1,non_coding_transcript_exon_variant,,ENST00000482601,;GTDC1,non_coding_transcript_exon_variant,,ENST00000476958,;GTDC1,synonymous_variant,p.=,ENST00000392871,;GTDC1,3_prime_UTR_variant,,ENST00000415569,;GTDC1,non_coding_transcript_exon_variant,,ENST00000491448,; A ENST00000392869 Transcript synonymous_variant 414/10514 261/1377 87/458 L ctG/ctT 1 -1 GTDC1 HGNC HGNC:20887 protein_coding YES CCDS33300.1 ENSP00000376608 Q4AE62 UPI000022BC3B 4/11 hmmpanther:PTHR13615,hmmpanther:PTHR13615:SF3,Pfam_domain:PF12038 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 144145658 144145658 C A 1 0 0 0 0 0 0 0 1 6733 465 17 2 2 GTDC1 2 144145658 Silent SNP C C3N-00556_T 3261796 144145658 98047871 75 16204 LRP2 0 . GRCh38 2 169128678 169128678 + Silent SNP T T C novel C3N-00556_T C3N-00556_N T T c.13953A>G p.= p.E4651E ENST00000263816 79/79 315 272 43 382 382 0 strelka-varscan LRP2,synonymous_variant,p.=,ENST00000263816,NM_004525.2;LRP2,downstream_gene_variant,,ENST00000491228,; C ENST00000263816 Transcript synonymous_variant 14239/15808 13953/13968 4651/4655 E gaA/gaG 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 79/79 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 169128678 169128678 T C 1 0 0 0 0 0 0 0 1 8851 1606 56 5 5 LRP2 2 169128678 Silent SNP T C3N-00556_T 24983020 169128678 73064851 76 16205 KLHL41 0 . GRCh38 2 169525592 169525592 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1717G>C p.Asp573His p.D573H ENST00000284669 6/6 131 123 8 129 129 0 strelka-varscan KLHL41,missense_variant,p.Asp573His,ENST00000284669,NM_006063.2;RP11-724O16.1,missense_variant,p.Asp511His,ENST00000513963,;FASTKD1,downstream_gene_variant,,ENST00000453153,NM_024622.4;FASTKD1,downstream_gene_variant,,ENST00000453929,NM_001281476.1;KLHL41,downstream_gene_variant,,ENST00000463400,;FASTKD1,downstream_gene_variant,,ENST00000495505,;FASTKD1,downstream_gene_variant,,ENST00000490590,;FASTKD1,downstream_gene_variant,,ENST00000488951,; C ENST00000284669 Transcript missense_variant 1794/2464 1717/1821 573/606 D/H Gat/Cat 1 1 KLHL41 HGNC HGNC:16905 protein_coding YES CCDS2234.1 ENSP00000284669 O60662 UPI0000000DC5 NM_006063.2 deleterious(0) 6/6 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 169525592 169525592 G C 1 0 0 0 0 1 0 0 0 8259 942 33 4 4 KLHL41 2 169525592 Missense_Mutation SNP G C3N-00556_T 396914 169525592 72667937 77 16206 MYO3B 0 . GRCh38 2 170382047 170382047 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1003C>T p.His335Tyr p.H335Y ENST00000408978 10/35 96 80 16 124 124 0 strelka-varscan MYO3B,missense_variant,p.His335Tyr,ENST00000408978,NM_138995.4;MYO3B,missense_variant,p.His335Tyr,ENST00000409044,NM_001083615.3;MYO3B,missense_variant,p.His344Tyr,ENST00000484338,;MYO3B,missense_variant,p.His335Tyr,ENST00000442690,;AC012594.1,intron_variant,,ENST00000625968,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,missense_variant,p.His335Tyr,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; T ENST00000408978 Transcript missense_variant 1146/5529 1003/4026 335/1341 H/Y Cat/Tat 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 tolerated(1) 10/35 Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 170382047 170382047 C T 1 0 0 0 0 1 0 0 0 10078 826 29 3 3 MYO3B 2 170382047 Missense_Mutation SNP C C3N-00556_T 856455 170382047 71811482 78 16207 TTN 0 . GRCh38 2 178589762 178589762 + Missense_Mutation SNP C C T rs776314797 C3N-00556_T C3N-00556_N C C c.61963G>A p.Glu20655Lys p.E20655K ENST00000589042 304/363 312 286 26 359 358 1 strelka-varscan TTN,missense_variant,p.Glu20655Lys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Glu19014Lys,ENST00000591111,;TTN,missense_variant,p.Glu19014Lys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Glu18087Lys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Glu11590Lys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Glu11782Lys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Glu11715Lys,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000590743,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000629117,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000626517,;TTN-AS1,downstream_gene_variant,,ENST00000586707,;TTN-AS1,downstream_gene_variant,,ENST00000592600,;TTN-AS1,upstream_gene_variant,,ENST00000589234,;TTN-AS1,downstream_gene_variant,,ENST00000586831,;TTN-AS1,upstream_gene_variant,,ENST00000610290,; T ENST00000589042 Transcript missense_variant 62188/109224 61963/107976 20655/35991 E/K Gaa/Aaa rs776314797,COSM2900970,COSM2900971,COSM2900972,COSM2900973 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 304/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 0,1,1,1,1 MODERATE SNV 5 0,1,1,1,1 1 PASS . . 0 204 0 0 6 0 0 0 -7.442104 0.2965284 1 1 0 0 T 3 4 54 178589762 178589762 C T 1 0 0 0 0 1 0 0 0 17245 893 31 1 1 TTN 2 178589762 Missense_Mutation SNP C C3N-00556_T 8207715 178589762 63603767 79 16208 TTN 0 . GRCh38 2 178607918 178607918 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.52869G>A p.Met17623Ile p.M17623I ENST00000589042 276/363 450 400 50 472 472 0 strelka-varscan TTN,missense_variant,p.Met17623Ile,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Met15982Ile,ENST00000591111,;TTN,missense_variant,p.Met15982Ile,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Met15055Ile,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Met8558Ile,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Met8750Ile,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Met8683Ile,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000419746,;TTN-AS1,downstream_gene_variant,,ENST00000586452,;TTN-AS1,upstream_gene_variant,,ENST00000627527,; T ENST00000589042 Transcript missense_variant 53094/109224 52869/107976 17623/35991 M/I atG/atA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 276/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 178607918 178607918 C T 1 0 0 0 0 1 0 0 0 17245 826 29 3 3 TTN 2 178607918 Missense_Mutation SNP C C3N-00556_T 18156 178607918 63585611 80 16209 ZNF804A 0 . GRCh38 2 184936379 184936379 + Nonsense_Mutation SNP C C A rs866933954 C3N-00556_T C3N-00556_N C C c.983C>A p.Ser328Ter p.S328* ENST00000302277 4/4 137 116 21 208 208 0 strelka-varscan-mutect ZNF804A,stop_gained,p.Ser328Ter,ENST00000302277,NM_194250.1;ZNF804A,stop_gained,p.Ser243Ter,ENST00000613975,; A ENST00000302277 Transcript stop_gained 1577/4690 983/3630 328/1209 S/* tCa/tAa rs866933954,COSM3896167 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 0,1 HIGH 1 SNV 1 0,1 1 PASS rs866933954 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 184936379 184936379 C A 1 0 0 0 0 0 1 0 0 18755 838 29 2 2 ZNF804A 2 184936379 Nonsense_Mutation SNP C C3N-00556_T 6328461 184936379 57257150 81 16210 ITGAV 0 . GRCh38 2 186590366 186590366 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.28C>T p.Arg10Cys p.R10C ENST00000261023 1/30 167 157 10 151 151 0 strelka-varscan-mutect ITGAV,missense_variant,p.Arg10Cys,ENST00000261023,NM_002210.4;ITGAV,missense_variant,p.Arg10Cys,ENST00000374907,NM_001145000.2; T ENST00000261023 Transcript missense_variant 302/7030 28/3147 10/1048 R/C Cgc/Tgc COSM418963 1 1 ITGAV HGNC HGNC:6150 protein_coding YES CCDS2292.1 ENSP00000261023 P06756 L7RXH0 UPI000013D12E NM_002210.4 tolerated(0.13) 1/30 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23220:SF4,hmmpanther:PTHR23220 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 186590366 186590366 C T 1 0 0 0 0 1 0 0 0 7795 768 27 1 1 ITGAV 2 186590366 Missense_Mutation SNP C C3N-00556_T 1653987 186590366 55603163 82 16211 BMPR2 0 . GRCh38 2 202555433 202555433 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.1768G>A p.Glu590Lys p.E590K ENST00000374580 12/13 169 159 10 223 222 1 strelka-varscan-mutect BMPR2,missense_variant,p.Glu590Lys,ENST00000374580,NM_001204.6;BMPR2,intron_variant,,ENST00000374574,; A ENST00000374580 Transcript missense_variant 2307/11461 1768/3117 590/1038 E/K Gaa/Aaa COSM3798523 1 1 BMPR2 HGNC HGNC:1078 protein_coding YES CCDS33361.1 ENSP00000363708 Q13873 UPI0000126A3B NM_001204.6 deleterious(0.01) 12/13 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.17243 0.9999995 1 1 1 0 A 3 1 54 202555433 202555433 G A 1 0 0 0 0 1 0 0 0 1626 1291 45 3 3 BMPR2 2 202555433 Missense_Mutation SNP G C3N-00556_T 15965067 202555433 39638096 83 16212 ALPP 0 . GRCh38 2 232379625 232379625 + Missense_Mutation SNP A A G novel C3N-00556_T C3N-00556_N A A c.422A>G p.Asn141Ser p.N141S ENST00000392027 4/11 221 192 29 286 286 0 varscan-mutect ALPP,missense_variant,p.Asn141Ser,ENST00000392027,NM_001632.4;AC068134.8,downstream_gene_variant,,ENST00000441266,;AC068134.8,downstream_gene_variant,,ENST00000439072,;ALPP,non_coding_transcript_exon_variant,,ENST00000474529,;ALPP,upstream_gene_variant,,ENST00000485563,; G ENST00000392027 Transcript missense_variant 691/2971 422/1608 141/535 N/S aAc/aGc 1 1 ALPP HGNC HGNC:439 protein_coding YES CCDS2490.1 ENSP00000375881 P05187 UPI0000131FF9 NM_001632.4 tolerated(0.67) 4/11 Gene3D:3.40.720.10,Pfam_domain:PF00245,hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF31,SMART_domains:SM00098,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS rs1435270301 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 232379625 232379625 A G 1 0 0 0 0 1 0 0 0 648 43 2 5 5 ALPP 2 232379625 Missense_Mutation SNP A C3N-00556_T 29824192 232379625 9813904 84 16213 ATG16L1 0 . GRCh38 2 233292153 233292153 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1456G>C p.Glu486Gln p.E486Q ENST00000392017 15/18 174 159 15 161 161 0 strelka-varscan-mutect ATG16L1,missense_variant,p.Glu486Gln,ENST00000392017,NM_001190266.1,NM_001190267.1,NM_030803.6;ATG16L1,missense_variant,p.Glu503Gln,ENST00000392018,;ATG16L1,missense_variant,p.Glu467Gln,ENST00000392020,NM_017974.3;ATG16L1,missense_variant,p.Glu323Gln,ENST00000347464,NM_198890.2;ATG16L1,missense_variant,p.Glu307Gln,ENST00000373525,;SCARNA6,downstream_gene_variant,,ENST00000515982,;ATG16L1,downstream_gene_variant,,ENST00000498620,;ATG16L1,downstream_gene_variant,,ENST00000464645,;ATG16L1,3_prime_UTR_variant,,ENST00000392021,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000474148,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000479942,;ATG16L1,non_coding_transcript_exon_variant,,ENST00000473865,; C ENST00000392017 Transcript missense_variant 1713/3405 1456/1824 486/607 E/Q Gag/Cag 1 1 ATG16L1 HGNC HGNC:21498 protein_coding YES CCDS2503.2 ENSP00000375872 Q676U5 UPI0000208D0D NM_001190266.1,NM_001190267.1,NM_030803.6 tolerated(0.5) 15/18 PROSITE_profiles:PS50294,hmmpanther:PTHR19878:SF6,hmmpanther:PTHR19878,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 233292153 233292153 G C 1 0 0 0 0 1 0 0 0 1243 1175 41 4 4 ATG16L1 2 233292153 Missense_Mutation SNP G C3N-00556_T 912528 233292153 8901376 85 16214 USP40 0 . GRCh38 2 233524527 233524527 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1879G>A p.Asp627Asn p.D627N ENST00000450966 14/31 139 126 13 134 134 0 strelka-varscan-mutect USP40,missense_variant,p.Asp615Asn,ENST00000251722,;USP40,missense_variant,p.Asp627Asn,ENST00000450966,NM_018218.2;USP40,missense_variant,p.Asp615Asn,ENST00000427112,;USP40,upstream_gene_variant,,ENST00000452724,;USP40,downstream_gene_variant,,ENST00000485943,; T ENST00000450966 Transcript missense_variant 1879/5616 1879/3744 627/1247 D/N Gat/Aat 1 -1 USP40 HGNC HGNC:20069 protein_coding YES CCDS46547.1 ENSP00000415434 Q9NVE5 UPI0000232F06 NM_018218.2 tolerated(0.07) 14/31 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -18.49148 0.9999832 1 1 1 0 T 3 4 54 233524527 233524527 C T 1 0 0 0 0 1 0 0 0 17614 826 29 3 3 USP40 2 233524527 Missense_Mutation SNP C C3N-00556_T 232374 233524527 8669002 86 16215 UGT1A5 0 . GRCh38 2 233713510 233713510 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.519G>C p.Leu173Phe p.L173F ENST00000373414 1/5 183 171 12 282 282 0 varscan-mutect UGT1A5,missense_variant,p.Leu173Phe,ENST00000373414,NM_019078.1;UGT1A6,intron_variant,,ENST00000305139,NM_001072.3;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A7,intron_variant,,ENST00000373426,NM_019077.2;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,NM_205862.1;UGT1A6,intron_variant,,ENST00000406651,;AC114812.8,upstream_gene_variant,,ENST00000439336,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,intron_variant,,ENST00000478062,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,; C ENST00000373414 Transcript missense_variant 519/2345 519/1605 173/534 L/F ttG/ttC 1 1 UGT1A5 HGNC HGNC:12537 protein_coding YES CCDS33404.1 ENSP00000362513 P35504 Q5DSZ9 UPI0000001043 NM_019078.1 tolerated(0.1) 1/5 Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF173,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs956773418 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 233713510 233713510 G C 1 0 0 0 0 1 0 0 0 17473 1281 45 4 4 UGT1A5 2 233713510 Missense_Mutation SNP G C3N-00556_T 188983 233713510 8480019 87 16216 RNPEPL1 0 . GRCh38 2 240575034 240575034 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.600G>A p.= p.V200V ENST00000270357 7/11 137 115 22 131 131 0 strelka-varscan-mutect RNPEPL1,synonymous_variant,p.=,ENST00000270357,NM_018226.4;RNPEPL1,intron_variant,,ENST00000451363,;RNPEPL1,upstream_gene_variant,,ENST00000437406,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000464550,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000481757,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000486058,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000493398,;RNPEPL1,non_coding_transcript_exon_variant,,ENST00000460884,;RNPEPL1,upstream_gene_variant,,ENST00000471657,;RNPEPL1,upstream_gene_variant,,ENST00000498042,; A ENST00000270357 Transcript synonymous_variant 1193/5558 600/1485 200/494 V gtG/gtA 1 1 RNPEPL1 HGNC HGNC:10079 protein_coding YES ENSP00000270357 Q9HAU8 UPI000013D885 NM_018226.4 7/11 hmmpanther:PTHR11533:SF6,hmmpanther:PTHR11533,Pfam_domain:PF01433,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 240575034 240575034 G A 1 0 0 0 0 0 0 0 1 13689 1304 45 3 3 RNPEPL1 2 240575034 Silent SNP G C3N-00556_T 6861524 240575034 1618495 88 16217 C3orf20 0 . GRCh38 3 14704595 14704595 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1137C>G p.Phe379Leu p.F379L ENST00000253697 7/17 182 159 23 270 270 0 strelka-varscan-mutect C3orf20,missense_variant,p.Phe379Leu,ENST00000253697,NM_032137.4;C3orf20,missense_variant,p.Phe257Leu,ENST00000435614,NM_001184958.1;C3orf20,missense_variant,p.Phe257Leu,ENST00000412910,NM_001184957.1;C3orf20,non_coding_transcript_exon_variant,,ENST00000495387,; G ENST00000253697 Transcript missense_variant 1589/3326 1137/2715 379/904 F/L ttC/ttG 1 1 C3orf20 HGNC HGNC:25320 protein_coding YES CCDS33706.1 ENSP00000253697 Q8ND61 UPI000013CDE9 NM_032137.4 tolerated(0.16) 7/17 hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF16,Pfam_domain:PF14977 MODERATE 1 SNV 1 1 PASS rs1368286770 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 14704595 14704595 C G 1 0 0 0 0 1 0 0 0 2061 912 32 4 4 C3orf20 3 14704595 Missense_Mutation SNP C C3N-00556_T 14704595 183590964 89 16218 TGFBR2 0 . GRCh38 3 30691570 30691570 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1750G>A p.Glu584Lys p.E584K ENST00000359013 8/8 295 275 20 310 309 1 strelka-varscan-mutect TGFBR2,missense_variant,p.Glu559Lys,ENST00000295754,NM_003242.5;TGFBR2,missense_variant,p.Glu584Lys,ENST00000359013,NM_001024847.2; A ENST00000359013 Transcript missense_variant 2033/4605 1750/1779 584/592 E/K Gaa/Aaa 1 1 TGFBR2 HGNC HGNC:11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 deleterious_low_confidence(0.01) 8/8 hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PIRSF_domain:PIRSF037393 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 30691570 30691570 G A 1 0 0 0 0 1 0 0 0 16255 1291 45 3 3 TGFBR2 3 30691570 Missense_Mutation SNP G C3N-00556_T 15986975 30691570 167603989 90 16219 TTC21A 0 . GRCh38 3 39138578 39138578 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.3840C>A p.Tyr1280Ter p.Y1280* ENST00000431162 28/29 253 227 26 338 336 2 strelka-varscan-mutect TTC21A,stop_gained,p.Tyr1280Ter,ENST00000431162,NM_145755.2;TTC21A,stop_gained,p.Tyr1232Ter,ENST00000440121,NM_001105513.2;CSRNP1,downstream_gene_variant,,ENST00000273153,NM_001320560.1,NM_001320559.1,NM_033027.3;CSRNP1,downstream_gene_variant,,ENST00000514182,;TTC21A,downstream_gene_variant,,ENST00000621888,;TTC21A,non_coding_transcript_exon_variant,,ENST00000493856,;TTC21A,non_coding_transcript_exon_variant,,ENST00000472866,;TTC21A,downstream_gene_variant,,ENST00000481734,;TTC21A,downstream_gene_variant,,ENST00000490245,;TTC21A,downstream_gene_variant,,ENST00000465962,;TTC21A,3_prime_UTR_variant,,ENST00000430597,;TTC21A,non_coding_transcript_exon_variant,,ENST00000460460,;TTC21A,downstream_gene_variant,,ENST00000473587,; A ENST00000431162 Transcript stop_gained 3974/4209 3840/3963 1280/1320 Y/* taC/taA 1 1 TTC21A HGNC HGNC:30761 protein_coding YES CCDS46800.1 ENSP00000398211 Q8NDW8 UPI00015D46B9 NM_145755.2 28/29 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF2,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 39138578 39138578 C A 1 0 0 0 0 0 1 0 0 17195 518 18 2 2 TTC21A 3 39138578 Nonsense_Mutation SNP C C3N-00556_T 8447008 39138578 159156981 91 16220 TOPAZ1 0 . GRCh38 3 44243601 44243601 + Missense_Mutation SNP G G C rs762485741 C3N-00556_T C3N-00556_N G G c.1095G>C p.Met365Ile p.M365I ENST00000309765 2/20 188 171 17 236 236 0 strelka-varscan-mutect TOPAZ1,missense_variant,p.Met365Ile,ENST00000309765,NM_001145030.1; C ENST00000309765 Transcript missense_variant 1263/5334 1095/5079 365/1692 M/I atG/atC rs762485741 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 tolerated(0.61) 2/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1 MODERATE 1 SNV 5 1 PASS rs762485741 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 44243601 44243601 G C 1 0 0 0 0 1 0 0 0 16845 1290 45 4 4 TOPAZ1 3 44243601 Missense_Mutation SNP G C3N-00556_T 5105023 44243601 154051958 92 16221 TOPAZ1 0 . GRCh38 3 44243713 44243713 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1207G>C p.Glu403Gln p.E403Q ENST00000309765 2/20 115 109 6 195 195 0 strelka-varscan-mutect TOPAZ1,missense_variant,p.Glu403Gln,ENST00000309765,NM_001145030.1; C ENST00000309765 Transcript missense_variant 1375/5334 1207/5079 403/1692 E/Q Gaa/Caa 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 tolerated(0.36) 2/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -12.09292 1 1 1 1 0 C 3 2 54 44243713 44243713 G C 1 0 0 0 0 1 0 0 0 16845 943 33 4 4 TOPAZ1 3 44243713 Missense_Mutation SNP G C3N-00556_T 112 44243713 154051846 93 16222 ZKSCAN7 0 . GRCh38 3 44570059 44570059 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.949G>A p.Asp317Asn p.D317N ENST00000273320 6/6 98 87 11 154 154 0 strelka-varscan-mutect ZKSCAN7,missense_variant,p.Asp317Asn,ENST00000273320,NM_018651.3,NM_001288590.1;ZKSCAN7,missense_variant,p.Asp317Asn,ENST00000426540,;ZKSCAN7,missense_variant,p.Asp166Asn,ENST00000447279,NM_001288592.1;ZKSCAN7,intron_variant,,ENST00000341840,NM_025169.2;ZKSCAN7,intron_variant,,ENST00000431636,NM_001288591.1;ZKSCAN7,intron_variant,,ENST00000419137,;RP11-944L7.4,intron_variant,,ENST00000457331,;ZKSCAN7,3_prime_UTR_variant,,ENST00000418719,;ZKSCAN7,downstream_gene_variant,,ENST00000496563,; A ENST00000273320 Transcript missense_variant 1378/3477 949/2265 317/754 D/N Gat/Aat 1 1 ZKSCAN7 HGNC HGNC:12955 protein_coding YES CCDS2715.1 ENSP00000273320 Q9P0L1 UPI000013D9A9 NM_018651.3,NM_001288590.1 tolerated(0.06) 6/6 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF205 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 44570059 44570059 G A 1 0 0 0 0 1 0 0 0 18269 942 33 3 3 ZKSCAN7 3 44570059 Missense_Mutation SNP G C3N-00556_T 326346 44570059 153725500 94 16223 TMIE 0 . GRCh38 3 46709650 46709650 + Missense_Mutation SNP G G C rs780884910 C3N-00556_T C3N-00556_N G G c.433G>C p.Glu145Gln p.E145Q ENST00000326431 4/4 384 358 26 483 482 1 strelka-varscan-mutect TMIE,missense_variant,p.Glu145Gln,ENST00000326431,NM_147196.2;PRSS50,downstream_gene_variant,,ENST00000460241,;PRSS50,downstream_gene_variant,,ENST00000315170,NM_013270.4; C ENST00000326431 Transcript missense_variant 588/1824 433/471 145/156 E/Q Gag/Cag rs780884910 1 1 TMIE HGNC HGNC:30800 protein_coding YES CCDS43081.1 ENSP00000324775 Q8NEW7 UPI0000141917 NM_147196.2 tolerated(0.2) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR28635 MODERATE 1 SNV 1 1 PASS rs780884910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 46709650 46709650 G C 1 0 0 0 0 1 0 0 0 16704 1291 45 4 4 TMIE 3 46709650 Missense_Mutation SNP G C3N-00556_T 2139591 46709650 151585909 95 16224 HYAL2 0 . GRCh38 3 50319952 50319952 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.538G>C p.Glu180Gln p.E180Q ENST00000447092 1/3 177 164 13 230 230 0 strelka-varscan-mutect HYAL2,missense_variant,p.Glu180Gln,ENST00000447092,;HYAL2,missense_variant,p.Glu180Gln,ENST00000442581,NM_033158.4;HYAL2,missense_variant,p.Glu180Gln,ENST00000395139,;HYAL2,missense_variant,p.Glu180Gln,ENST00000357750,NM_003773.4;TUSC2,downstream_gene_variant,,ENST00000232496,NM_007275.2;HYAL2,downstream_gene_variant,,ENST00000458018,;HYAL2,downstream_gene_variant,,ENST00000428028,;HYAL2,downstream_gene_variant,,ENST00000424190,;HYAL2,downstream_gene_variant,,ENST00000426286,;HYAL2,downstream_gene_variant,,ENST00000415028,;TUSC2,downstream_gene_variant,,ENST00000462137,;HYAL2,non_coding_transcript_exon_variant,,ENST00000481597,; G ENST00000447092 Transcript missense_variant 2831/4054 538/1422 180/473 E/Q Gag/Cag 1 -1 HYAL2 HGNC HGNC:5321 protein_coding YES CCDS2818.1 ENSP00000401853 Q12891 UPI000013C4E6 deleterious(0.01) 1/3 Gene3D:3.20.20.70,Pfam_domain:PF01630,PIRSF_domain:PIRSF038193,hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF6,Low_complexity_(Seg):seg,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 50319952 50319952 C G 1 0 0 0 0 1 0 0 0 7360 835 29 4 4 HYAL2 3 50319952 Missense_Mutation SNP C C3N-00556_T 3610302 50319952 147975607 96 16225 STAB1 0 . GRCh38 3 52505121 52505121 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1496C>T p.Ser499Phe p.S499F ENST00000321725 13/69 130 120 10 151 151 0 strelka-varscan-mutect STAB1,missense_variant,p.Ser499Phe,ENST00000321725,NM_015136.2;STAB1,non_coding_transcript_exon_variant,,ENST00000481607,;STAB1,downstream_gene_variant,,ENST00000479355,;STAB1,upstream_gene_variant,,ENST00000484850,; T ENST00000321725 Transcript missense_variant 1572/7928 1496/7713 499/2570 S/F tCt/tTt 1 1 STAB1 HGNC HGNC:18628 protein_coding YES CCDS33768.1 ENSP00000312946 Q9NY15 UPI0000140C12 NM_015136.2 tolerated(0.17) 13/69 hmmpanther:PTHR24038,hmmpanther:PTHR24038:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 52505121 52505121 C T 1 0 0 0 0 1 0 0 0 15615 913 32 3 3 STAB1 3 52505121 Missense_Mutation SNP C C3N-00556_T 2185169 52505121 145790438 97 16226 SMIM4 0 . GRCh38 3 52540512 52540512 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.107C>A p.Ser36Ter p.S36* ENST00000307106 2/2 96 87 9 85 85 0 strelka-varscan-mutect SMIM4,stop_gained,p.Ser36Ter,ENST00000307106,;SMIM4,3_prime_UTR_variant,,ENST00000477703,NM_001124767.1;SMIM4,intron_variant,,ENST00000476842,;PBRM1,downstream_gene_variant,,ENST00000356770,;SMIM4,non_coding_transcript_exon_variant,,ENST00000482728,;SMIM4,non_coding_transcript_exon_variant,,ENST00000491607,; A ENST00000307106 Transcript stop_gained 261/274 107/114 36/37 S/* tCa/tAa 1 1 SMIM4 HGNC HGNC:37257 protein_coding ENSP00000305661 F8W7Q2 UPI000020AD34 2/2 HIGH SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -18.91841 1 1 1 1 0 A 4 1 54 52540512 52540512 C A 1 0 0 0 0 0 1 0 0 15112 838 29 2 2 SMIM4 3 52540512 Nonsense_Mutation SNP C C3N-00556_T 35391 52540512 145755047 98 16227 ITIH1 0 . GRCh38 3 52789778 52789778 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2245C>G p.Gln749Glu p.Q749E ENST00000273283 19/22 302 279 23 306 305 1 strelka-varscan-mutect ITIH1,missense_variant,p.Gln749Glu,ENST00000273283,NM_002215.3,NM_001166434.2;ITIH1,missense_variant,p.Gln461Glu,ENST00000537050,NM_001166435.2,NM_001166436.2;ITIH1,missense_variant,p.Gln302Glu,ENST00000428133,;ITIH1,missense_variant,p.Gln115Glu,ENST00000405128,;ITIH3,upstream_gene_variant,,ENST00000621946,;ITIH1,non_coding_transcript_exon_variant,,ENST00000628722,;ITIH1,non_coding_transcript_exon_variant,,ENST00000482836,;ITIH1,upstream_gene_variant,,ENST00000494705,;ITIH3,upstream_gene_variant,,ENST00000467268,;ITIH1,downstream_gene_variant,,ENST00000484844,; G ENST00000273283 Transcript missense_variant 2269/2911 2245/2736 749/911 Q/E Cag/Gag 1 1 ITIH1 HGNC HGNC:6166 protein_coding YES CCDS2864.1 ENSP00000273283 P19827 UPI000012DA1C NM_002215.3,NM_001166434.2 tolerated(1) 19/22 hmmpanther:PTHR10338:SF106,hmmpanther:PTHR10338,Pfam_domain:PF06668 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 52789778 52789778 C G 1 0 0 0 0 1 0 0 0 7809 827 29 4 4 ITIH1 3 52789778 Missense_Mutation SNP C C3N-00556_T 249266 52789778 145505781 99 16228 MORC1 0 . GRCh38 3 109114403 109114403 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.100G>A p.Glu34Lys p.E34K ENST00000232603 2/28 269 237 32 250 250 0 strelka-varscan-mutect MORC1,missense_variant,p.Glu34Lys,ENST00000232603,NM_014429.3;MORC1,missense_variant,p.Glu34Lys,ENST00000483760,;MORC1-AS1,downstream_gene_variant,,ENST00000480826,;FLJ22763,upstream_gene_variant,,ENST00000479039,; T ENST00000232603 Transcript missense_variant 183/3764 100/2955 34/984 E/K Gaa/Aaa 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 deleterious(0) 2/28 hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337,Gene3D:3.30.565.10,Pfam_domain:PF13589,Superfamily_domains:SSF55874 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 109114403 109114403 C T 1 0 0 0 0 1 0 0 0 9665 835 29 3 3 MORC1 3 109114403 Missense_Mutation SNP C C3N-00556_T 56324625 109114403 89181156 100 16229 CCDC191 0 . GRCh38 3 113980784 113980784 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2173G>C p.Glu725Gln p.E725Q ENST00000295878 14/17 323 267 56 335 335 0 strelka-varscan-mutect CCDC191,missense_variant,p.Glu725Gln,ENST00000295878,NM_020817.1;CCDC191,3_prime_UTR_variant,,ENST00000460813,;CCDC191,non_coding_transcript_exon_variant,,ENST00000527855,;RP11-255E6.5,upstream_gene_variant,,ENST00000605304,; G ENST00000295878 Transcript missense_variant 2320/3976 2173/2811 725/936 E/Q Gag/Cag 1 -1 CCDC191 HGNC HGNC:29272 protein_coding YES CCDS2977.1 ENSP00000295878 Q8NCU4 UPI00000732E9 NM_020817.1 deleterious(0) 14/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22028,hmmpanther:PTHR22028:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 113980784 113980784 C G 1 0 0 0 0 1 0 0 0 2506 835 29 4 4 CCDC191 3 113980784 Missense_Mutation SNP C C3N-00556_T 4866381 113980784 84314775 101 16230 CCDC14 0 . GRCh38 3 123931515 123931515 + Missense_Mutation SNP G G C rs868462664 C3N-00556_T C3N-00556_N G G c.1459C>G p.Gln487Glu p.Q487E ENST00000488653 10/12 88 80 8 115 115 0 strelka-varscan-mutect CCDC14,missense_variant,p.Gln328Glu,ENST00000485727,;CCDC14,missense_variant,p.Gln328Glu,ENST00000489746,;CCDC14,missense_variant,p.Gln487Glu,ENST00000488653,NM_022757.4;CCDC14,missense_variant,p.Gln487Glu,ENST00000433542,;CCDC14,missense_variant,p.Gln439Glu,ENST00000310351,;CCDC14,missense_variant,p.Gln480Glu,ENST00000409697,;CCDC14,missense_variant,p.Gln169Glu,ENST00000419247,;CCDC14,missense_variant,p.Gln110Glu,ENST00000479903,;CCDC14,intron_variant,,ENST00000483247,;CCDC14,intron_variant,,ENST00000463996,;CCDC14,3_prime_UTR_variant,,ENST00000409657,;CCDC14,non_coding_transcript_exon_variant,,ENST00000495381,;CCDC14,upstream_gene_variant,,ENST00000487498,;CCDC14,downstream_gene_variant,,ENST00000471054,;CCDC14,downstream_gene_variant,,ENST00000485949,; C ENST00000488653 Transcript missense_variant 1550/4156 1459/2739 487/912 Q/E Cag/Gag rs868462664 1 -1 CCDC14 HGNC HGNC:25766 protein_coding YES CCDS3025.2 ENSP00000420180 Q49A88 UPI00016632FB NM_022757.4 deleterious(0) 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR22367:SF2,hmmpanther:PTHR22367,Pfam_domain:PF15254 MODERATE 1 SNV 1 1 PASS rs868462664 . 0 202 8 0 0 0 0 0 -16.64701 0.9999945 1 1 1 0 C 3 2 54 123931515 123931515 G C 1 0 0 0 0 1 0 0 0 2462 1299 45 4 4 CCDC14 3 123931515 Missense_Mutation SNP G C3N-00556_T 9950731 123931515 74364044 102 16231 DNAJC13 0 . GRCh38 3 132465998 132465998 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1896G>C p.Gln632His p.Q632H ENST00000260818 18/56 175 153 22 179 179 0 strelka-varscan-mutect DNAJC13,missense_variant,p.Gln632His,ENST00000260818,NM_015268.3;DNAJC13,non_coding_transcript_exon_variant,,ENST00000486798,; C ENST00000260818 Transcript missense_variant 2144/7730 1896/6732 632/2243 Q/H caG/caC 1 1 DNAJC13 HGNC HGNC:30343 protein_coding YES CCDS33857.1 ENSP00000260818 O75165 UPI000022C1FD NM_015268.3 deleterious(0.03) 18/56 hmmpanther:PTHR36983 MODERATE 1 SNV 1 1 PASS . . 0 201 0 9 0 0 0 0 -20 0.9753566 1 1 1 0 C 3 2 54 132465998 132465998 G C 1 0 0 0 0 1 0 0 0 4446 985 34 4 4 DNAJC13 3 132465998 Missense_Mutation SNP G C3N-00556_T 8534483 132465998 65829561 103 16232 NPHP3 0 . GRCh38 3 132715098 132715098 + Missense_Mutation SNP T T C rs149565564 C3N-00556_T C3N-00556_N T T c.944A>G p.Asp315Gly p.D315G ENST00000337331 5/27 229 217 12 279 279 0 strelka-varscan-mutect NPHP3,missense_variant,p.Asp315Gly,ENST00000337331,NM_153240.4;NPHP3,non_coding_transcript_exon_variant,,ENST00000476742,;NPHP3,downstream_gene_variant,,ENST00000471145,;NPHP3-ACAD11,missense_variant,p.Asp315Gly,ENST00000471702,;NPHP3,missense_variant,p.Asp217Gly,ENST00000465756,;NPHP3,3_prime_UTR_variant,,ENST00000469232,;NPHP3,non_coding_transcript_exon_variant,,ENST00000490993,; C ENST00000337331 Transcript missense_variant 1031/4362 944/3993 315/1330 D/G gAt/gGt rs149565564 1 -1 NPHP3 HGNC HGNC:7907 protein_coding YES CCDS3078.1 ENSP00000338766 Q7Z494 UPI00001B6B30 NM_153240.4 deleterious(0.03) 5/27 hmmpanther:PTHR19959:SF153,hmmpanther:PTHR19959 MODERATE 1 SNV 1 1 PASS rs149565564 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 132715098 132715098 T C 1 0 0 0 0 1 0 0 0 10628 1435 50 5 5 NPHP3 3 132715098 Missense_Mutation SNP T C3N-00556_T 249100 132715098 65580461 104 16233 TRIM42 0 . GRCh38 3 140688355 140688355 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1673G>C p.Arg558Thr p.R558T ENST00000286349 3/5 214 198 16 200 200 0 strelka-varscan-mutect TRIM42,missense_variant,p.Arg558Thr,ENST00000286349,NM_152616.4; C ENST00000286349 Transcript missense_variant 1864/2539 1673/2172 558/723 R/T aGa/aCa 1 1 TRIM42 HGNC HGNC:19014 protein_coding YES CCDS3113.1 ENSP00000286349 Q8IWZ5 UPI00001AEAE0 NM_152616.4 deleterious(0.01) 3/5 MODERATE 1 SNV 1 1 PASS rs1215907736 . 0 207 0 3 0 0 0 0 -19.77142 0.9999731 1 1 1 0 C 3 2 54 140688355 140688355 G C 1 0 0 0 0 1 0 0 0 17007 942 33 4 4 TRIM42 3 140688355 Missense_Mutation SNP G C3N-00556_T 7973257 140688355 57607204 105 16234 PXYLP1 0 . GRCh38 3 141292438 141292438 + Missense_Mutation SNP G G C rs375469010 C3N-00556_T C3N-00556_N G G c.676G>C p.Asp226His p.D226H ENST00000286353 6/6 216 200 16 219 219 0 strelka-varscan-mutect PXYLP1,missense_variant,p.Asp217His,ENST00000508812,;PXYLP1,missense_variant,p.Asp226His,ENST00000286353,NM_001037172.2;PXYLP1,missense_variant,p.Asp226His,ENST00000393010,NM_152282.4;PXYLP1,missense_variant,p.Asp188His,ENST00000502783,NM_001282728.1;PXYLP1,missense_variant,p.Asp209His,ENST00000504264,;PXYLP1,downstream_gene_variant,,ENST00000512457,;RP11-438D8.2,intron_variant,,ENST00000507698,;PXYLP1,downstream_gene_variant,,ENST00000514263,;PXYLP1,3_prime_UTR_variant,,ENST00000514880,;PXYLP1,intron_variant,,ENST00000637751,;PXYLP1,intron_variant,,ENST00000636601,;PXYLP1,intron_variant,,ENST00000637579,; C ENST00000286353 Transcript missense_variant 813/3281 676/1443 226/480 D/H Gac/Cac rs375469010 1 1 PXYLP1 HGNC HGNC:26303 protein_coding YES CCDS3116.1 ENSP00000286353 Q8TE99 UPI0000048EC7 NM_001037172.2 deleterious(0) 6/6 hmmpanther:PTHR11567:SF125,hmmpanther:PTHR11567,Gene3D:3.40.50.1240,Pfam_domain:PF00328,Superfamily_domains:SSF53254 MODERATE 1 SNV 1 1 PASS rs375469010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 141292438 141292438 G C 1 0 0 0 0 1 0 0 0 13008 1290 45 4 4 PXYLP1 3 141292438 Missense_Mutation SNP G C3N-00556_T 604083 141292438 57003121 106 16235 IGSF10 0 . GRCh38 3 151444944 151444944 + Silent SNP G G T rs146833534 C3N-00556_T C3N-00556_N G G c.5037C>A p.= p.T1679T ENST00000282466 4/6 79 63 16 107 107 0 strelka-varscan-mutect IGSF10,synonymous_variant,p.=,ENST00000282466,NM_178822.4;IGSF10,upstream_gene_variant,,ENST00000489791,;IGSF10,upstream_gene_variant,,ENST00000495443,;IGSF10,upstream_gene_variant,,ENST00000493841,; T ENST00000282466 Transcript synonymous_variant 5037/11067 5037/7872 1679/2623 T acC/acA rs146833534 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs146833534 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 151444944 151444944 G T 1 0 0 0 0 0 0 0 1 7504 1335 47 2 2 IGSF10 3 151444944 Silent SNP G C3N-00556_T 10152506 151444944 46850615 107 16236 MBNL1 0 . GRCh38 3 152300213 152300213 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.20C>G p.Pro7Arg p.P7R ENST00000282486 2/10 101 95 6 87 87 0 strelka-varscan-mutect MBNL1,missense_variant,p.Pro7Arg,ENST00000282488,;MBNL1,missense_variant,p.Pro7Arg,ENST00000282486,;MBNL1,missense_variant,p.Pro7Arg,ENST00000355460,NM_207292.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000324210,NM_021038.3;MBNL1,missense_variant,p.Pro7Arg,ENST00000498502,;MBNL1,missense_variant,p.Pro7Arg,ENST00000357472,NM_207297.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000324196,NM_207296.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000545754,NM_207295.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000463374,NM_207293.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000485910,NM_207294.1;MBNL1,missense_variant,p.Pro7Arg,ENST00000492948,;MBNL1,missense_variant,p.Pro7Arg,ENST00000485509,;MBNL1,missense_variant,p.Pro6Arg,ENST00000464596,;MBNL1,missense_variant,p.Pro7Arg,ENST00000465907,;MBNL1,intron_variant,,ENST00000493459,;MBNL1,intron_variant,,ENST00000460591,;MBNL1,intron_variant,,ENST00000459747,;MBNL1,intron_variant,,ENST00000495875,;MBNL1,non_coding_transcript_exon_variant,,ENST00000461436,;MBNL1,non_coding_transcript_exon_variant,,ENST00000466565,;MBNL1,downstream_gene_variant,,ENST00000477171,; G ENST00000282486 Transcript missense_variant 1862/6422 20/1167 7/388 P/R cCa/cGa 1 1 MBNL1 HGNC HGNC:6923 protein_coding YES CCDS3165.1 ENSP00000282486 Q9NR56 UPI000003B440 tolerated(0.38) 2/10 hmmpanther:PTHR12675:SF7,hmmpanther:PTHR12675 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -12.18883 0.9999863 1 1 1 0 G 3 3 54 152300213 152300213 C G 1 0 0 0 0 1 0 0 0 9285 594 21 4 4 MBNL1 3 152300213 Missense_Mutation SNP C C3N-00556_T 855269 152300213 45995346 108 16237 RAP2B 0 . GRCh38 3 153162698 153162698 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.5G>C p.Arg2Thr p.R2T ENST00000323534 1/1 69 63 6 77 77 0 strelka-varscan-mutect RAP2B,missense_variant,p.Arg2Thr,ENST00000323534,NM_002886.3;RP11-529G21.2,upstream_gene_variant,,ENST00000487827,; C ENST00000323534 Transcript missense_variant 429/8351 5/552 2/183 R/T aGa/aCa 1 1 RAP2B HGNC HGNC:9862 protein_coding YES CCDS3170.1 ENSP00000319096 P61225 UPI0000004042 NM_002886.3 tolerated(0.06) 1/1 PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF194,hmmpanther:PTHR24070,TIGRFAM_domain:TIGR00231,SMART_domains:SM00173,Superfamily_domains:SSF52540 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -13.7903 1 1 1 1 0 C 3 2 54 153162698 153162698 G C 1 0 0 0 0 1 0 0 0 13200 942 33 4 4 RAP2B 3 153162698 Missense_Mutation SNP G C3N-00556_T 862485 153162698 45132861 109 16238 VEPH1 0 . GRCh38 3 157317073 157317073 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1864C>G p.Leu622Val p.L622V ENST00000362010 10/14 164 152 12 167 167 0 strelka-varscan-mutect VEPH1,missense_variant,p.Leu622Val,ENST00000362010,NM_001167912.1;VEPH1,missense_variant,p.Leu622Val,ENST00000392833,NM_001167911.1;VEPH1,missense_variant,p.Leu622Val,ENST00000392832,NM_024621.2;RP11-550I24.2,intron_variant,,ENST00000487238,;RP11-550I24.2,downstream_gene_variant,,ENST00000494885,;RP11-550I24.2,downstream_gene_variant,,ENST00000475102,; C ENST00000362010 Transcript missense_variant 2172/4202 1864/2502 622/833 L/V Cta/Gta 1 -1 VEPH1 HGNC HGNC:25735 protein_coding YES CCDS3179.1 ENSP00000354919 Q14D04 UPI000013F6EE NM_001167912.1 deleterious(0) 10/14 hmmpanther:PTHR21630 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 157317073 157317073 G C 1 0 0 0 0 1 0 0 0 17700 933 33 4 4 VEPH1 3 157317073 Missense_Mutation SNP G C3N-00556_T 4154375 157317073 40978486 110 16239 IQCJ 0 . GRCh38 3 159262589 159262589 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.116C>A p.Pro39His p.P39H ENST00000476809 3/10 148 107 41 128 128 0 strelka-varscan-mutect IQCJ-SCHIP1,missense_variant,p.Pro66His,ENST00000485419,NM_001197113.1;IQCJ-SCHIP1,missense_variant,p.Pro39His,ENST00000476809,NM_001197114.1;IQCJ,missense_variant,p.Pro66His,ENST00000397832,NM_001042706.2;IQCJ,missense_variant,p.Pro39His,ENST00000482126,NM_001197100.1;IQCJ,missense_variant,p.Pro66His,ENST00000451172,NM_001042705.2;IQCJ,non_coding_transcript_exon_variant,,ENST00000481796,; A ENST00000476809 Transcript missense_variant 116/1611 116/1611 39/536 P/H cCc/cAc COSM4475308,COSM4475309,COSM4475310 1 1 IQCJ-SCHIP1 HGNC HGNC:38842 protein_coding YES CCDS56291.1 ENSP00000418692 UPI00016277EB NM_001197114.1 tolerated_low_confidence(0.45) 3/10 Pfam_domain:PF15157 1,1,1 MODERATE SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 159262589 159262589 C A 1 0 0 0 0 1 0 0 0 7718 623 22 2 2 IQCJ 3 159262589 Missense_Mutation SNP C C3N-00556_T 1945516 159262589 39032970 111 16240 SI 0 . GRCh38 3 165006951 165006951 + Missense_Mutation SNP A A G novel C3N-00556_T C3N-00556_N A A c.4271T>C p.Leu1424Pro p.L1424P ENST00000264382 37/48 208 174 34 244 244 0 strelka-varscan-mutect SI,missense_variant,p.Leu1424Pro,ENST00000264382,NM_001041.3; G ENST00000264382 Transcript missense_variant 4334/6011 4271/5484 1424/1827 L/P cTc/cCc 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 37/48 Pfam_domain:PF01055 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 165006951 165006951 A G 1 0 0 0 0 1 0 0 0 14561 318 11 5 5 SI 3 165006951 Missense_Mutation SNP A C3N-00556_T 5744362 165006951 33288608 112 16241 MB21D2 0 . GRCh38 3 192798721 192798721 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1141C>T p.Gln381Ter p.Q381* ENST00000392452 2/2 229 216 13 241 241 0 strelka-varscan-mutect MB21D2,stop_gained,p.Gln381Ter,ENST00000392452,NM_178496.3; A ENST00000392452 Transcript stop_gained 1462/3368 1141/1476 381/491 Q/* Cag/Tag 1 -1 MB21D2 HGNC HGNC:30438 protein_coding YES CCDS3302.2 ENSP00000376246 Q8IYB1 UPI000013FAFE NM_178496.3 2/2 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF47,Pfam_domain:PF03281,SMART_domains:SM01265 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 192798721 192798721 G A 1 0 0 0 0 0 1 0 0 9270 1299 45 3 3 MB21D2 3 192798721 Nonsense_Mutation SNP G C3N-00556_T 27791770 192798721 5496838 113 16242 MB21D2 0 . GRCh38 3 192798931 192798931 + Nonsense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.931C>T p.Gln311Ter p.Q311* ENST00000392452 2/2 130 109 21 155 155 0 strelka-varscan-mutect MB21D2,stop_gained,p.Gln311Ter,ENST00000392452,NM_178496.3; A ENST00000392452 Transcript stop_gained 1252/3368 931/1476 311/491 Q/* Cag/Tag COSM348040,COSM350832 1 -1 MB21D2 HGNC HGNC:30438 protein_coding YES CCDS3302.2 ENSP00000376246 Q8IYB1 UPI000013FAFE NM_178496.3 2/2 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF47,Pfam_domain:PF03281,SMART_domains:SM01265 1,1 HIGH 1 SNV 1 1,1 1 PASS rs988241015 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 192798931 192798931 G A 1 0 0 0 0 0 1 0 0 9270 1299 45 3 3 MB21D2 3 192798931 Nonsense_Mutation SNP G C3N-00556_T 210 192798931 5496628 114 16243 OTOP1 0 . GRCh38 4 4197635 4197635 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1199G>A p.Gly400Asp p.G400D ENST00000296358 5/6 206 195 11 232 231 1 varscan-mutect OTOP1,missense_variant,p.Gly400Asp,ENST00000296358,NM_177998.1; T ENST00000296358 Transcript missense_variant 1224/1864 1199/1839 400/612 G/D gGc/gAc 1 -1 OTOP1 HGNC HGNC:19656 protein_coding YES CCDS3372.1 ENSP00000296358 Q7RTM1 UPI0000186945 NM_177998.1 deleterious(0) 5/6 Pfam_domain:PF03189,hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 4197635 4197635 C T 1 0 0 0 0 1 0 0 0 11373 739 26 3 3 OTOP1 4 4197635 Missense_Mutation SNP C C3N-00556_T 4197635 186016920 115 16244 EVC2 0 . GRCh38 4 5640615 5640615 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1369G>A p.Glu457Lys p.E457K ENST00000344408 10/22 279 262 17 314 314 0 strelka-varscan-mutect EVC2,missense_variant,p.Glu377Lys,ENST00000310917,NM_001166136.1;EVC2,missense_variant,p.Glu457Lys,ENST00000344408,NM_147127.4;EVC2,missense_variant,p.Glu377Lys,ENST00000475313,;EVC2,missense_variant,p.Glu377Lys,ENST00000509670,; T ENST00000344408 Transcript missense_variant 1423/4390 1369/3927 457/1308 E/K Gaa/Aaa 1 -1 EVC2 HGNC HGNC:19747 protein_coding YES CCDS3382.2 ENSP00000342144 Q86UK5 UPI00001910B5 NM_147127.4 deleterious(0) 10/22 Pfam_domain:PF12297,hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 5640615 5640615 C T 1 0 0 0 0 1 0 0 0 5153 835 29 3 3 EVC2 4 5640615 Missense_Mutation SNP C C3N-00556_T 1442980 5640615 184573940 116 16245 LIMCH1 0 . GRCh38 4 41360901 41360901 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.61G>A p.Glu21Lys p.E21K ENST00000313860 1/27 212 186 26 144 144 0 strelka-varscan LIMCH1,missense_variant,p.Glu21Lys,ENST00000313860,NM_014988.3;LIMCH1,missense_variant,p.Glu21Lys,ENST00000512820,NM_001289122.1;LIMCH1,missense_variant,p.Glu21Lys,ENST00000512946,NM_001112717.2;LIMCH1,missense_variant,p.Glu21Lys,ENST00000508501,NM_001112718.2;LIMCH1,missense_variant,p.Glu21Lys,ENST00000512632,;LIMCH1,5_prime_UTR_variant,,ENST00000509638,;LIMCH1,intron_variant,,ENST00000513024,NM_001289124.1;LIMCH1,non_coding_transcript_exon_variant,,ENST00000514190,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000512228,; A ENST00000313860 Transcript missense_variant 115/6165 61/3252 21/1083 E/K Gag/Aag 1 1 LIMCH1 HGNC HGNC:29191 protein_coding YES CCDS33977.1 ENSP00000316891 Q9UPQ0 UPI0000D61554 NM_014988.3 deleterious(0) 1/27 Low_complexity_(Seg):seg,PROSITE_profiles:PS50021,hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 41360901 41360901 G A 1 0 0 0 0 1 0 0 0 8705 1059 37 1 1 LIMCH1 4 41360901 Missense_Mutation SNP G C3N-00556_T 35720286 41360901 148853654 117 16246 TXK 0 . GRCh38 4 48095146 48095146 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.578G>A p.Arg193Lys p.R193K ENST00000264316 7/15 279 262 17 293 293 0 strelka-varscan TXK,missense_variant,p.Arg193Lys,ENST00000264316,NM_003328.2;TXK,non_coding_transcript_exon_variant,,ENST00000510457,; T ENST00000264316 Transcript missense_variant 664/2914 578/1584 193/527 R/K aGa/aAa 1 -1 TXK HGNC HGNC:12434 protein_coding YES CCDS3480.1 ENSP00000264316 P42681 UPI000013D4F9 NM_003328.2 tolerated(0.94) 7/15 Gene3D:3.30.505.10,Pfam_domain:PF00017,PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF247,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 48095146 48095146 C T 1 0 0 0 0 1 0 0 0 17302 927 32 3 3 TXK 4 48095146 Missense_Mutation SNP C C3N-00556_T 6734245 48095146 142119409 118 16247 TMPRSS11A 0 . GRCh38 4 67929987 67929987 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.383C>A p.Ser128Tyr p.S128Y ENST00000334830 5/10 111 83 28 143 143 0 strelka-varscan TMPRSS11A,missense_variant,p.Ser125Tyr,ENST00000508048,NM_001114387.1;TMPRSS11A,missense_variant,p.Ser128Tyr,ENST00000334830,NM_182606.3;TMPRSS11A,missense_variant,p.Ser105Tyr,ENST00000513536,;UBA6-AS1,intron_variant,,ENST00000500538,; T ENST00000334830 Transcript missense_variant 1130/3054 383/1266 128/421 S/Y tCt/tAt 1 -1 TMPRSS11A HGNC HGNC:27954 protein_coding YES CCDS3519.1 ENSP00000334611 A0A0A0MR82 UPI0000457217 NM_182606.3 deleterious(0.04) 5/10 PROSITE_profiles:PS50024,Pfam_domain:PF01390,PIRSF_domain:PIRSF037941,Gene3D:1ivzA00,Superfamily_domains:0047452 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 67929987 67929987 G T 1 0 0 0 0 1 0 0 0 16715 942 33 2 2 TMPRSS11A 4 67929987 Missense_Mutation SNP G C3N-00556_T 19834841 67929987 122284568 119 16248 ANKRD17 0 . GRCh38 4 73118823 73118823 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.4053G>A p.= p.K1351K ENST00000358602 22/34 139 127 12 164 163 1 strelka-varscan ANKRD17,synonymous_variant,p.=,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,synonymous_variant,p.=,ENST00000558247,;ANKRD17,synonymous_variant,p.=,ENST00000509867,NM_001286771.1;ANKRD17,synonymous_variant,p.=,ENST00000330838,NM_198889.1;ANKRD17,synonymous_variant,p.=,ENST00000561029,;ANKRD17,non_coding_transcript_exon_variant,,ENST00000514252,; T ENST00000358602 Transcript synonymous_variant 4170/10784 4053/7812 1351/2603 K aaG/aaA 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 22/34 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 73118823 73118823 C T 1 0 0 0 0 0 0 0 1 747 912 32 3 3 ANKRD17 4 73118823 Silent SNP C C3N-00556_T 5188836 73118823 117095732 120 16249 SHROOM3 0 . GRCh38 4 76740756 76740756 + Missense_Mutation SNP G G T rs747838287 C3N-00556_T C3N-00556_N G G c.2583G>T p.Gln861His p.Q861H ENST00000296043 5/11 124 108 16 123 122 1 strelka-varscan SHROOM3,missense_variant,p.Gln861His,ENST00000296043,NM_020859.3;SHROOM3,intron_variant,,ENST00000469923,;SHROOM3,downstream_gene_variant,,ENST00000473602,;SHROOM3,downstream_gene_variant,,ENST00000481002,;SHROOM3,non_coding_transcript_exon_variant,,ENST00000486758,; T ENST00000296043 Transcript missense_variant 3536/11020 2583/5991 861/1996 Q/H caG/caT rs747838287 1 1 SHROOM3 HGNC HGNC:30422 protein_coding YES CCDS3579.2 ENSP00000296043 Q8TF72 UPI0000E5AC1C NM_020859.3 tolerated(0.25) 5/11 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -19.99998 0.9999974 1 1 1 0 T 3 4 54 76740756 76740756 G T 1 0 0 0 0 1 0 0 0 14558 962 34 2 2 SHROOM3 4 76740756 Missense_Mutation SNP G C3N-00556_T 3621933 76740756 113473799 121 16250 SEPT11 0 . GRCh38 4 77011772 77011772 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.406G>A p.Glu136Lys p.E136K ENST00000510515 6/12 146 134 12 181 181 0 strelka-varscan SEPT11,missense_variant,p.Glu126Lys,ENST00000264893,NM_018243.2;SEPT11,missense_variant,p.Glu126Lys,ENST00000502584,;SEPT11,missense_variant,p.Glu126Lys,ENST00000505788,;SEPT11,missense_variant,p.Glu136Lys,ENST00000510515,NM_001306147.1;SEPT11,missense_variant,p.Glu118Lys,ENST00000510641,;SEPT11,missense_variant,p.Glu136Lys,ENST00000512778,;SEPT11,downstream_gene_variant,,ENST00000504637,;SEPT11,non_coding_transcript_exon_variant,,ENST00000512333,;SEPT11,non_coding_transcript_exon_variant,,ENST00000504460,;SEPT11,intron_variant,,ENST00000512575,;SEPT11,upstream_gene_variant,,ENST00000506047,; A ENST00000510515 Transcript missense_variant 663/1886 406/1320 136/439 E/K Gag/Aag 1 1 SEPT11 HGNC HGNC:25589 protein_coding YES CCDS77931.1 ENSP00000422896 Q9NVA2 UPI000191506E NM_001306147.1 deleterious(0.01) 6/12 PROSITE_profiles:PS51719,hmmpanther:PTHR18884:SF48,hmmpanther:PTHR18884,PIRSF_domain:PIRSF006698,Pfam_domain:PF00735,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 77011772 77011772 G A 1 0 0 0 0 1 0 0 0 14337 1059 37 1 1 SEPT11 4 77011772 Missense_Mutation SNP G C3N-00556_T 271016 77011772 113202783 122 16251 PRDM8 0 . GRCh38 4 80203151 80203151 + Silent SNP G G T rs766188088 C3N-00556_T C3N-00556_N G G c.1689G>T p.= p.P563P ENST00000339711 10/10 421 398 23 373 373 0 strelka-varscan PRDM8,synonymous_variant,p.=,ENST00000339711,NM_020226.3;PRDM8,synonymous_variant,p.=,ENST00000504452,;PRDM8,synonymous_variant,p.=,ENST00000415738,NM_001099403.1;PRDM8,downstream_gene_variant,,ENST00000515013,; T ENST00000339711 Transcript synonymous_variant 2920/4095 1689/2070 563/689 P ccG/ccT rs766188088 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 10/10 hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF7,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 80203151 80203151 G T 1 0 0 0 0 0 0 0 1 12594 1045 37 1 1 PRDM8 4 80203151 Silent SNP G C3N-00556_T 3191379 80203151 110011404 123 16252 AFF1 0 . GRCh38 4 87046273 87046273 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.146G>C p.Gly49Ala p.G49A ENST00000395146 3/21 122 110 12 97 97 0 strelka-varscan AFF1,missense_variant,p.Gly42Ala,ENST00000307808,NM_001313959.1,NM_005935.2;AFF1,missense_variant,p.Gly49Ala,ENST00000395146,NM_001166693.1;AFF1,missense_variant,p.Gly42Ala,ENST00000544085,;AFF1,missense_variant,p.Gly49Ala,ENST00000507468,;AFF1,missense_variant,p.Gly49Ala,ENST00000503477,;AFF1,5_prime_UTR_variant,,ENST00000511442,;AFF1,intron_variant,,ENST00000511722,;AFF1,upstream_gene_variant,,ENST00000514970,;AFF1,intron_variant,,ENST00000504956,; C ENST00000395146 Transcript missense_variant 421/9285 146/3657 49/1218 G/A gGa/gCa 1 1 AFF1 HGNC HGNC:7135 protein_coding YES CCDS54775.1 ENSP00000378578 P51825 UPI000013EC52 NM_001166693.1 tolerated(0.76) 3/21 Pfam_domain:PF05110,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF6 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -17.85937 0.9999998 1 1 1 0 C 3 2 54 87046273 87046273 G C 1 0 0 0 0 1 0 0 0 433 1174 41 4 4 AFF1 4 87046273 Missense_Mutation SNP G C3N-00556_T 6843122 87046273 103168282 124 16253 SPP1 0 . GRCh38 4 87981538 87981538 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.280G>C p.Asp94His p.D94H ENST00000395080 6/7 228 203 25 277 277 0 strelka-varscan SPP1,missense_variant,p.Asp80His,ENST00000237623,NM_000582.2;SPP1,missense_variant,p.Asp94His,ENST00000395080,NM_001040058.1;SPP1,missense_variant,p.Asp67His,ENST00000360804,NM_001040060.1;SPP1,missense_variant,p.Asp53His,ENST00000508233,NM_001251829.1;SPP1,splice_region_variant,,ENST00000614857,NM_001251830.1;SPP1,non_coding_transcript_exon_variant,,ENST00000509659,;SPP1,non_coding_transcript_exon_variant,,ENST00000509334,;SPP1,non_coding_transcript_exon_variant,,ENST00000513981,;SPP1,downstream_gene_variant,,ENST00000508002,;SPP1,downstream_gene_variant,,ENST00000504310,;SPP1,downstream_gene_variant,,ENST00000505146,; C ENST00000395080 Transcript missense_variant 407/1473 280/945 94/314 D/H Gat/Cat 1 1 SPP1 HGNC HGNC:11255 protein_coding YES CCDS43250.1 ENSP00000378517 P10451 A0A024RDE2 UPI0000000E0B NM_001040058.1 deleterious(0.04) 6/7 Low_complexity_(Seg):seg,hmmpanther:PTHR10607:SF1,hmmpanther:PTHR10607,Pfam_domain:PF00865,SMART_domains:SM00017 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 87981538 87981538 G C 1 0 0 0 0 1 0 0 0 15439 1304 45 4 4 SPP1 4 87981538 Missense_Mutation SNP G C3N-00556_T 935265 87981538 102233017 125 16254 SPP1 0 . GRCh38 4 87981785 87981785 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.527G>C p.Arg176Thr p.R176T ENST00000395080 6/7 111 98 13 137 137 0 strelka-varscan SPP1,missense_variant,p.Arg162Thr,ENST00000237623,NM_000582.2;SPP1,missense_variant,p.Arg154Thr,ENST00000614857,NM_001251830.1;SPP1,missense_variant,p.Arg176Thr,ENST00000395080,NM_001040058.1;SPP1,missense_variant,p.Arg149Thr,ENST00000360804,NM_001040060.1;SPP1,missense_variant,p.Arg135Thr,ENST00000508233,NM_001251829.1;SPP1,non_coding_transcript_exon_variant,,ENST00000509659,;SPP1,downstream_gene_variant,,ENST00000509334,;SPP1,downstream_gene_variant,,ENST00000513981,;SPP1,downstream_gene_variant,,ENST00000508002,;SPP1,downstream_gene_variant,,ENST00000504310,;SPP1,downstream_gene_variant,,ENST00000505146,; C ENST00000395080 Transcript missense_variant 654/1473 527/945 176/314 R/T aGa/aCa 1 1 SPP1 HGNC HGNC:11255 protein_coding YES CCDS43250.1 ENSP00000378517 P10451 A0A024RDE2 UPI0000000E0B NM_001040058.1 tolerated(0.69) 6/7 hmmpanther:PTHR10607:SF1,hmmpanther:PTHR10607,Pfam_domain:PF00865,SMART_domains:SM00017 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 87981785 87981785 G C 1 0 0 0 0 1 0 0 0 15439 942 33 4 4 SPP1 4 87981785 Missense_Mutation SNP G C3N-00556_T 247 87981785 102232770 126 16255 GRID2 0 . GRCh38 4 93769451 93769451 + Splice_Site SNP G G C novel C3N-00556_T C3N-00556_N G G c.2601+1G>C p.X867_splice ENST00000282020 137 123 14 159 159 0 strelka-varscan GRID2,splice_donor_variant,,ENST00000282020,NM_001510.3;GRID2,splice_donor_variant,,ENST00000611049,;GRID2,splice_donor_variant,,ENST00000637838,;GRID2,splice_donor_variant,,ENST00000510992,NM_001286838.1; C ENST00000282020 Transcript splice_donor_variant -/6117 2601/3024 867/1007 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 15/15 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.8474 0.9999999 1 1 1 0 C 5 2 54 93769451 93769451 G C 1 0 0 0 0 0 0 1 0 6652 1275 44 4 4 GRID2 4 93769451 Splice_Site SNP G C3N-00556_T 5787666 93769451 96445104 127 16256 DNAJB14 0 . GRCh38 4 99946461 99946461 + Silent SNP G G C novel C3N-00556_T C3N-00556_N G G c.111C>G p.= p.L37L ENST00000442697 1/8 489 464 25 402 402 0 strelka-varscan DNAJB14,synonymous_variant,p.=,ENST00000442697,NM_001031723.3,NM_001278310.1;DNAJB14,synonymous_variant,p.=,ENST00000610281,NM_001278311.1;H2AFZ,downstream_gene_variant,,ENST00000296417,NM_002106.3;RP11-15B17.1,upstream_gene_variant,,ENST00000507494,;RP11-15B17.1,upstream_gene_variant,,ENST00000514624,;RP11-15B17.1,upstream_gene_variant,,ENST00000501976,;DNAJB14,non_coding_transcript_exon_variant,,ENST00000471738,;H2AFZ,downstream_gene_variant,,ENST00000529158,;RP11-15B17.4,upstream_gene_variant,,ENST00000623099,;DNAJB14,synonymous_variant,p.=,ENST00000334223,;DNAJB14,synonymous_variant,p.=,ENST00000398991,;DNAJB14,synonymous_variant,p.=,ENST00000426476,;DNAJB14,non_coding_transcript_exon_variant,,ENST00000469942,;DNAJB14,non_coding_transcript_exon_variant,,ENST00000474664,;H2AFZ,downstream_gene_variant,,ENST00000511203,;H2AFZ,downstream_gene_variant,,ENST00000511348,;H2AFZ,downstream_gene_variant,,ENST00000511319,;H2AFZ,downstream_gene_variant,,ENST00000527366,; C ENST00000442697 Transcript synonymous_variant 266/6075 111/1140 37/379 L ctC/ctG 1 -1 DNAJB14 HGNC HGNC:25881 protein_coding YES CCDS34035.1 ENSP00000404381 Q8TBM8 UPI0000072A32 NM_001031723.3,NM_001278310.1 1/8 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 99946461 99946461 G C 1 0 0 0 0 0 0 0 1 4434 929 33 4 4 DNAJB14 4 99946461 Silent SNP G C3N-00556_T 6177010 99946461 90268094 128 16257 DDIT4L 0 . GRCh38 4 100187774 100187774 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.485C>G p.Ser162Cys p.S162C ENST00000273990 3/3 228 206 22 227 227 0 strelka-varscan DDIT4L,missense_variant,p.Ser162Cys,ENST00000273990,NM_145244.3;DDIT4L,missense_variant,p.Ser162Cys,ENST00000502763,;DDIT4L,downstream_gene_variant,,ENST00000513992,;RP11-15B17.1,intron_variant,,ENST00000515026,;RP11-588P8.1,upstream_gene_variant,,ENST00000515782,; C ENST00000273990 Transcript missense_variant 700/2604 485/582 162/193 S/C tCt/tGt 1 -1 DDIT4L HGNC HGNC:30555 protein_coding YES CCDS34036.1 ENSP00000354830 Q96D03 UPI000004919B NM_145244.3 deleterious(0) 3/3 Pfam_domain:PF07809,hmmpanther:PTHR12478,hmmpanther:PTHR12478:SF17,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 100187774 100187774 G C 1 0 0 0 0 1 0 0 0 4136 942 33 4 4 DDIT4L 4 100187774 Missense_Mutation SNP G C3N-00556_T 241313 100187774 90026781 129 16258 CXXC4 0 . GRCh38 4 104490974 104490974 + Missense_Mutation SNP G G T rs778098431 C3N-00556_T C3N-00556_N G G c.829C>A p.Leu277Met p.L277M ENST00000394767 2/3 259 243 16 261 261 0 strelka-varscan CXXC4,missense_variant,p.Leu277Met,ENST00000394767,NM_025212.2;AC004053.1,non_coding_transcript_exon_variant,,ENST00000500179,;CXXC4,intron_variant,,ENST00000466963,; T ENST00000394767 Transcript missense_variant 1280/5565 829/1104 277/367 L/M Ctg/Atg rs778098431 1 -1 CXXC4 HGNC HGNC:24593 protein_coding YES CCDS3665.2 ENSP00000378248 J9JIF5 UPI0000E5AC2D NM_025212.2 deleterious(0.02) 2/3 hmmpanther:PTHR13419,hmmpanther:PTHR13419:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 104490974 104490974 G T 1 0 0 0 0 1 0 0 0 3908 933 33 2 2 CXXC4 4 104490974 Missense_Mutation SNP G C3N-00556_T 4303200 104490974 85723581 130 16259 EGF 0 . GRCh38 4 109943335 109943335 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.409G>A p.Glu137Lys p.E137K ENST00000265171 3/24 76 68 8 120 120 0 strelka-varscan EGF,missense_variant,p.Glu137Lys,ENST00000265171,NM_001963.4;EGF,missense_variant,p.Glu137Lys,ENST00000509793,NM_001178131.1;EGF,missense_variant,p.Glu137Lys,ENST00000503392,NM_001178130.1;EGF,non_coding_transcript_exon_variant,,ENST00000502723,; A ENST00000265171 Transcript missense_variant 854/4880 409/3624 137/1207 E/K Gaa/Aaa 1 1 EGF HGNC HGNC:3229 protein_coding YES CCDS3689.1 ENSP00000265171 P01133 UPI000013D5C8 NM_001963.4 tolerated(0.9) 3/24 Gene3D:2.120.10.30,PIRSF_domain:PIRSF001778,PROSITE_profiles:PS51120,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.44094 1 1 1 1 0 A 3 1 54 109943335 109943335 G A 1 0 0 0 0 1 0 0 0 4798 1175 41 3 3 EGF 4 109943335 Missense_Mutation SNP G C3N-00556_T 5452361 109943335 80271220 131 16260 ANK2 0 . GRCh38 4 113355669 113355669 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.7051G>A p.Glu2351Lys p.E2351K ENST00000357077 38/46 217 170 47 281 281 0 strelka-varscan ANK2,missense_variant,p.Glu2351Lys,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Glu2318Lys,ENST00000264366,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; A ENST00000357077 Transcript missense_variant 7104/14196 7051/11874 2351/3957 E/K Gaa/Aaa 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(0.38) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 113355669 113355669 G A 1 0 0 0 0 1 0 0 0 721 1291 45 3 3 ANK2 4 113355669 Missense_Mutation SNP G C3N-00556_T 3412334 113355669 76858886 132 16261 FSTL5 0 . GRCh38 4 161455081 161455081 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.1764C>A p.= p.T588T ENST00000306100 15/16 134 108 26 125 124 1 strelka-varscan FSTL5,synonymous_variant,p.=,ENST00000306100,NM_020116.4;FSTL5,synonymous_variant,p.=,ENST00000379164,NM_001128427.2;FSTL5,synonymous_variant,p.=,ENST00000427802,NM_001128428.2; T ENST00000306100 Transcript synonymous_variant 2201/4831 1764/2544 588/847 T acC/acA 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 15/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Gene3D:2.130.10.10,Superfamily_domains:0047643 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 161455081 161455081 G T 1 0 0 0 0 0 0 0 1 5954 1219 43 2 2 FSTL5 4 161455081 Silent SNP G C3N-00556_T 48099412 161455081 28759474 133 16262 CPE 0 . GRCh38 4 165482328 165482328 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.759G>T p.= p.V253V ENST00000402744 4/9 191 169 22 189 188 1 strelka-varscan CPE,synonymous_variant,p.=,ENST00000402744,NM_001873.2;CPE,synonymous_variant,p.=,ENST00000431967,;CPE,synonymous_variant,p.=,ENST00000511992,;CPE,downstream_gene_variant,,ENST00000513982,; T ENST00000402744 Transcript synonymous_variant 1039/2421 759/1431 253/476 V gtG/gtT 1 1 CPE HGNC HGNC:2303 protein_coding YES CCDS3810.1 ENSP00000386104 P16870 UPI000000163E NM_001873.2 4/9 hmmpanther:PTHR11532,PROSITE_patterns:PS00133,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187,Prints_domain:PR00765 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 165482328 165482328 G T 1 0 0 0 0 0 0 0 1 3593 1335 47 2 2 CPE 4 165482328 Silent SNP G C3N-00556_T 4027247 165482328 24732227 134 16263 PLEKHG4B 0 . GRCh38 5 143079 143079 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.442G>A p.Asp148Asn p.D148N ENST00000283426 2/18 249 234 15 245 245 0 strelka-varscan-mutect PLEKHG4B,missense_variant,p.Asp504Asn,ENST00000637938,;PLEKHG4B,missense_variant,p.Asp148Asn,ENST00000283426,NM_052909.3;PLEKHG4B,missense_variant,p.Asp62Asn,ENST00000502646,;Y_RNA,downstream_gene_variant,,ENST00000362670,; A ENST00000283426 Transcript missense_variant 492/11515 442/3816 148/1271 D/N Gac/Aac 1 1 PLEKHG4B HGNC HGNC:29399 protein_coding YES CCDS34124.1 ENSP00000283426 Q96PX9 UPI0000D615EE NM_052909.3 tolerated(0.41) 2/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 143079 143079 G A 1 0 0 0 0 1 0 0 0 12165 942 33 3 3 PLEKHG4B 5 143079 Missense_Mutation SNP G C3N-00556_T 143079 181395180 135 16264 SEMA5A 0 . GRCh38 5 9051908 9051908 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.2810G>T p.Ser937Ile p.S937I ENST00000382496 20/23 221 152 69 197 197 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Ser937Ile,ENST00000382496,NM_003966.2;MIR4636,downstream_gene_variant,,ENST00000582271,; A ENST00000382496 Transcript missense_variant 3476/11762 2810/3225 937/1074 S/I aGc/aTc 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 tolerated(0.11) 20/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,Prints_domain:PR01705 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 9051908 9051908 C A 1 0 0 0 0 1 0 0 0 14313 797 28 2 2 SEMA5A 5 9051908 Missense_Mutation SNP C C3N-00556_T 8908829 9051908 172486351 136 16265 RXFP3 0 . GRCh38 5 33938064 33938064 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1324G>A p.Glu442Lys p.E442K ENST00000330120 1/1 160 139 21 168 168 0 strelka-varscan-mutect RXFP3,missense_variant,p.Glu442Lys,ENST00000330120,NM_016568.3; A ENST00000330120 Transcript missense_variant 1679/1852 1324/1410 442/469 E/K Gag/Aag 1 1 RXFP3 HGNC HGNC:24883 protein_coding YES CCDS3900.1 ENSP00000328708 Q9NSD7 UPI0000046AEB NM_016568.3 deleterious(0.04) 1/1 hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF70,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 33938064 33938064 G A 1 0 0 0 0 1 0 0 0 14022 1175 41 3 3 RXFP3 5 33938064 Missense_Mutation SNP G C3N-00556_T 24886156 33938064 147600195 137 16266 PTGER4 0 . GRCh38 5 40692254 40692254 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.1343C>T p.Ser448Leu p.S448L ENST00000302472 3/3 151 141 10 153 153 0 strelka-varscan-mutect PTGER4,missense_variant,p.Ser448Leu,ENST00000302472,NM_000958.2;TTC33,intron_variant,,ENST00000636106,;TTC33,intron_variant,,ENST00000637375,;TTC33,intron_variant,,ENST00000636863,;PTGER4,downstream_gene_variant,,ENST00000512578,;PTGER4,downstream_gene_variant,,ENST00000513635,; T ENST00000302472 Transcript missense_variant 2367/3848 1343/1467 448/488 S/L tCa/tTa COSM5208706 1 1 PTGER4 HGNC HGNC:9596 protein_coding YES CCDS3930.1 ENSP00000302846 P35408 UPI000005042F NM_000958.2 tolerated_low_confidence(0.24) 3/3 hmmpanther:PTHR11866:SF6,hmmpanther:PTHR11866 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 40692254 40692254 C T 1 0 0 0 0 1 0 0 0 12900 838 29 3 3 PTGER4 5 40692254 Missense_Mutation SNP C C3N-00556_T 6754190 40692254 140846005 138 16267 MROH2B 0 . GRCh38 5 41004523 41004523 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.4017G>A p.= p.K1339K ENST00000399564 37/42 85 80 5 99 99 0 strelka-varscan-mutect MROH2B,synonymous_variant,p.=,ENST00000399564,NM_173489.4;MROH2B,synonymous_variant,p.=,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,;MROH2B,upstream_gene_variant,,ENST00000511934,; T ENST00000399564 Transcript synonymous_variant 4468/5239 4017/4758 1339/1585 K aaG/aaA 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 37/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -11.37872 1 1 1 1 0 T 2 4 54 41004523 41004523 C T 1 0 0 0 0 0 0 0 1 9745 927 32 3 3 MROH2B 5 41004523 Silent SNP C C3N-00556_T 312269 41004523 140533736 139 16268 CCDC152 0 . GRCh38 5 42762442 42762443 + Frame_Shift_Ins INS - - A novel C3N-00556_T C3N-00556_N - - c.91dupA p.Met31AsnfsTer19 p.M31Nfs*19 ENST00000361970 83 51 32 110 110 0 sindel-varindel-pindel CCDC152,frameshift_variant,p.Met31AsnfsTer19,ENST00000361970,NM_001134848.1;CCDC152,frameshift_variant,p.Met31AsnfsTer19,ENST00000388827,; A ENST00000361970 Transcript frameshift_variant,splice_region_variant 174-175/3431 87-88/765 29-30/254 -/X -/A 1 1 CCDC152 HGNC HGNC:34438 protein_coding YES CCDS47203.1 ENSP00000354888 Q4G0S7 A0A024R043 UPI0000160C50 NM_001134848.1 hmmpanther:PTHR35253,hmmpanther:PTHR35253:SF1 HIGH 1 insertion 1 4 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 54 42762442 42762442 - A 1 0 1 1 0 0 0 0 0 2473 956 33 0 0 CCDC152 5 42762442 Frame_Shift_Ins INS - C3N-00556_T 1757919 42762442 138775817 140 16269 HTR1A 0 . GRCh38 5 63961188 63961188 + Missense_Mutation SNP G G T C3N-00556_T C3N-00556_N G G c.532C>A p.Pro178Thr p.P178T ENST00000323865 1/1 407 318 89 453 453 0 strelka-varscan-mutect HTR1A,missense_variant,p.Pro178Thr,ENST00000323865,NM_000524.3;HTR1A,downstream_gene_variant,,ENST00000506598,;RP11-158J3.2,intron_variant,,ENST00000502882,; T ENST00000323865 Transcript missense_variant 946/1778 532/1269 178/422 P/T Ccg/Acg COSM5455415 1 -1 HTR1A HGNC HGNC:5286 protein_coding YES CCDS34168.1 ENSP00000316244 P08908 Q5ZGX3 UPI0000124F1A NM_000524.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF20,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00512 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 63961188 63961188 G T 1 0 0 0 0 1 0 0 0 7332 1232 43 2 2 HTR1A 5 63961188 Missense_Mutation SNP G C3N-00556_T 21198746 63961188 117577071 141 16270 SLCO4C1 0 . GRCh38 5 102291508 102291508 + Missense_Mutation SNP C C T rs763016704 C3N-00556_T C3N-00556_N C C c.454G>A p.Asp152Asn p.D152N ENST00000310954 2/13 249 236 13 273 273 0 strelka-varscan SLCO4C1,missense_variant,p.Asp152Asn,ENST00000310954,NM_180991.4; T ENST00000310954 Transcript missense_variant 741/5334 454/2175 152/724 D/N Gat/Aat rs763016704,COSM1695996 1 -1 SLCO4C1 HGNC HGNC:23612 protein_coding YES CCDS34205.1 ENSP00000309741 Q6ZQN7 UPI00001C10B6 NM_180991.4 deleterious(0) 2/13 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF103,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 102291508 102291508 C T 1 0 0 0 0 1 0 0 0 15017 884 31 1 1 SLCO4C1 5 102291508 Missense_Mutation SNP C C3N-00556_T 38330320 102291508 79246751 142 16271 APC 0 . GRCh38 5 112819284 112819284 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.1252G>A p.Glu418Lys p.E418K ENST00000257430 10/16 114 106 8 179 179 0 strelka-varscan-mutect APC,missense_variant,p.Glu418Lys,ENST00000257430,NM_000038.5;APC,missense_variant,p.Glu418Lys,ENST00000508376,NM_001127510.2;APC,missense_variant,p.Glu418Lys,ENST00000512211,;APC,missense_variant,p.Glu400Lys,ENST00000507379,NM_001127511.2;APC,upstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,upstream_gene_variant,,ENST00000502371,; A ENST00000257430 Transcript missense_variant 1308/10701 1252/8532 418/2843 E/K Gaa/Aaa COSM1541294,COSM1541295 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 deleterious(0) 10/16 Gene3D:1.25.10.10,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11,Superfamily_domains:SSF48371 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 112819284 112819284 G A 1 0 0 0 0 1 0 0 0 883 1291 45 3 3 APC 5 112819284 Missense_Mutation SNP G C3N-00556_T 10527776 112819284 68718975 143 16272 DDX46 0 . GRCh38 5 134781951 134781951 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.910C>T p.Gln304Ter p.Q304* ENST00000452510 8/23 209 182 27 302 302 0 strelka-varscan-mutect DDX46,stop_gained,p.Gln304Ter,ENST00000452510,NM_001300860.1;DDX46,stop_gained,p.Gln304Ter,ENST00000354283,NM_014829.3;DDX46,stop_gained,p.Gln256Ter,ENST00000628477,;DDX46,upstream_gene_variant,,ENST00000509178,;DDX46,stop_gained,p.Gln256Ter,ENST00000507392,;DDX46,non_coding_transcript_exon_variant,,ENST00000513987,;DDX46,intron_variant,,ENST00000505592,;DDX46,upstream_gene_variant,,ENST00000513592,;DDX46,downstream_gene_variant,,ENST00000509255,; T ENST00000452510 Transcript stop_gained 1068/5689 910/3099 304/1032 Q/* Cag/Tag 1 1 DDX46 HGNC HGNC:18681 protein_coding YES CCDS75306.1 ENSP00000416534 A0A0C4DG89 UPI000006F4C9 NM_001300860.1 8/23 Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 134781951 134781951 C T 1 0 0 0 0 0 1 0 0 4167 827 29 3 3 DDX46 5 134781951 Nonsense_Mutation SNP C C3N-00556_T 21962667 134781951 46756308 144 16273 KIF20A 0 . GRCh38 5 138181624 138181624 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.271G>C p.Glu91Gln p.E91Q ENST00000394894 4/19 197 177 20 225 224 1 strelka-varscan-mutect KIF20A,missense_variant,p.Glu91Gln,ENST00000394894,NM_005733.2;KIF20A,missense_variant,p.Glu73Gln,ENST00000508792,;KIF20A,missense_variant,p.Glu91Gln,ENST00000504621,;KIF20A,missense_variant,p.Glu91Gln,ENST00000513276,;BRD8,upstream_gene_variant,,ENST00000254900,NM_139199.1;BRD8,upstream_gene_variant,,ENST00000230901,NM_006696.3;BRD8,upstream_gene_variant,,ENST00000454473,NM_001300966.1;BRD8,upstream_gene_variant,,ENST00000402931,NM_001300961.1,NM_001300962.1;BRD8,upstream_gene_variant,,ENST00000411594,NM_001164326.1;BRD8,upstream_gene_variant,,ENST00000418329,;BRD8,upstream_gene_variant,,ENST00000441656,;BRD8,upstream_gene_variant,,ENST00000430331,;BRD8,upstream_gene_variant,,ENST00000425764,;KIF20A,non_coding_transcript_exon_variant,,ENST00000511638,;KIF20A,non_coding_transcript_exon_variant,,ENST00000503417,;BRD8,upstream_gene_variant,,ENST00000512140,;BRD8,upstream_gene_variant,,ENST00000432618,;BRD8,upstream_gene_variant,,ENST00000428808,;KIF20A,upstream_gene_variant,,ENST00000502338,;BRD8,upstream_gene_variant,,ENST00000450756,;BRD8,upstream_gene_variant,,ENST00000515254,;BRD8,upstream_gene_variant,,ENST00000471437,; C ENST00000394894 Transcript missense_variant 497/3201 271/2673 91/890 E/Q Gag/Cag 1 1 KIF20A HGNC HGNC:9787 protein_coding YES CCDS4199.1 ENSP00000378356 O95235 UPI0000000CCE NM_005733.2 tolerated(0.35) 4/19 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF352,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 54 138181624 138181624 G C 1 0 0 0 0 1 0 0 0 8151 1291 45 4 4 KIF20A 5 138181624 Missense_Mutation SNP G C3N-00556_T 3399673 138181624 43356635 145 16274 LRRTM2 0 . GRCh38 5 138874429 138874429 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.132C>T p.= p.L44L ENST00000274711 2/2 221 208 13 245 245 0 strelka-mutect LRRTM2,synonymous_variant,p.=,ENST00000274711,NM_015564.2;CTNNA1,intron_variant,,ENST00000627109,NM_001290307.1;CTNNA1,intron_variant,,ENST00000302763,NM_001323984.1,NM_001323983.1,NM_001903.3,NM_001290310.1,NM_001290309.1;CTNNA1,intron_variant,,ENST00000518825,;LRRTM2,intron_variant,,ENST00000518785,;LRRTM2,intron_variant,,ENST00000521094,;CTNNA1,intron_variant,,ENST00000518381,;CTNNA1,upstream_gene_variant,,ENST00000540387,NM_001290312.1;CTNNA1,upstream_gene_variant,,ENST00000522013,;CTNNA1,upstream_gene_variant,,ENST00000520260,;CTNNA1,upstream_gene_variant,,ENST00000523685,;CTNNA1,upstream_gene_variant,,ENST00000519634,;CTNNA1,upstream_gene_variant,,ENST00000517533,;CTNNA1,upstream_gene_variant,,ENST00000523298,;CTNNA1,upstream_gene_variant,,ENST00000521640,;CTNNA1,upstream_gene_variant,,ENST00000521683,;CTNNA1,upstream_gene_variant,,ENST00000519116,;CTNNA1,upstream_gene_variant,,ENST00000519768,;CTNNA1,upstream_gene_variant,,ENST00000520865,;CTNNA1,upstream_gene_variant,,ENST00000517656,;CTNNA1,intron_variant,,ENST00000520400,;LRRTM2,intron_variant,,ENST00000523537,;CTNNA1,upstream_gene_variant,,ENST00000524292,;CTNNA1,upstream_gene_variant,,ENST00000518263,;CTNNA1,intron_variant,,ENST00000521724,;CTNNA1,intron_variant,,ENST00000523275,;CTNNA1,intron_variant,,ENST00000517534,;CTNNA1,upstream_gene_variant,,ENST00000522052,; A ENST00000274711 Transcript synonymous_variant 511/6017 132/1551 44/516 L ctC/ctT 1 -1 LRRTM2 HGNC HGNC:19409 protein_coding YES CCDS47272.1 ENSP00000274711 O43300 UPI0000070039 NM_015564.2 2/2 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF262,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 138874429 138874429 G A 1 0 0 0 0 0 0 0 1 8946 929 33 3 3 LRRTM2 5 138874429 Silent SNP G C3N-00556_T 692805 138874429 42663830 146 16275 PCDHB12 0 . GRCh38 5 141211036 141211036 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.2129C>A p.Ala710Glu p.A710E ENST00000239450 1/1 304 237 67 351 350 1 strelka-varscan-mutect PCDHB12,missense_variant,p.Ala710Glu,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Ala373Glu,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239450 Transcript missense_variant 2318/3853 2129/2388 710/795 A/E gCg/gAg COSM5229689 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Pfam_domain:PF16492,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 141211036 141211036 C A 1 0 0 0 0 1 0 0 0 11624 768 27 1 1 PCDHB12 5 141211036 Missense_Mutation SNP C C3N-00556_T 2336607 141211036 40327223 147 16276 PCDHGA2 0 . GRCh38 5 141340672 141340672 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1701C>T p.= p.F567F ENST00000394576 1/4 345 327 18 387 387 0 varscan-mutect PCDHGA2,synonymous_variant,p.=,ENST00000394576,NM_018915.3;PCDHGA2,synonymous_variant,p.=,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; T ENST00000394576 Transcript synonymous_variant 1701/4605 1701/2799 567/932 F ttC/ttT 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 1/4 hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 141340672 141340672 C T 1 0 0 0 0 0 0 0 1 11641 854 30 3 3 PCDHGA2 5 141340672 Silent SNP C C3N-00556_T 129636 141340672 40197587 148 16277 PCDHGB7 0 . GRCh38 5 141419405 141419405 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.1546G>A p.Ala516Thr p.A516T ENST00000398594 1/4 325 244 81 338 338 0 strelka-varscan-mutect PCDHGB7,missense_variant,p.Ala516Thr,ENST00000398594,NM_018927.3;PCDHGB7,missense_variant,p.Ala516Thr,ENST00000612073,NM_032101.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,upstream_gene_variant,,ENST00000398587,NM_018914.2;PCDHGA10,downstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA11,upstream_gene_variant,,ENST00000622044,NM_032091.1;PCDHGA11,upstream_gene_variant,,ENST00000518882,NM_032092.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000398594 Transcript missense_variant 1715/4765 1546/2790 516/929 A/T Gcg/Acg COSM1434529 1 1 PCDHGB7 HGNC HGNC:8714 protein_coding YES CCDS47293.1 ENSP00000381594 Q9Y5F8 UPI000007141F NM_018927.3 deleterious(0.02) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF113,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 1 MODERATE 1 SNV 1 1 1 PASS rs1219399978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 141419405 141419405 G A 1 0 0 0 0 1 0 0 0 11655 1087 38 1 1 PCDHGB7 5 141419405 Missense_Mutation SNP G C3N-00556_T 78733 141419405 40118854 149 16278 GABRB2 0 . GRCh38 5 161331033 161331033 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.927G>A p.= p.L309L ENST00000274547 9/11 97 89 8 104 103 1 strelka-varscan-mutect GABRB2,synonymous_variant,p.=,ENST00000274547,NM_021911.2;GABRB2,synonymous_variant,p.=,ENST00000393959,;GABRB2,synonymous_variant,p.=,ENST00000612710,;GABRB2,synonymous_variant,p.=,ENST00000520240,;GABRB2,synonymous_variant,p.=,ENST00000353437,NM_000813.2;GABRB2,synonymous_variant,p.=,ENST00000517901,;GABRB2,synonymous_variant,p.=,ENST00000517547,; T ENST00000274547 Transcript synonymous_variant 1145/7409 927/1539 309/512 L ctG/ctA 1 -1 GABRB2 HGNC HGNC:4082 protein_coding YES CCDS4355.1 ENSP00000274547 P47870 UPI000002AA29 NM_021911.2 9/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF221,hmmpanther:PTHR18945,Gene3D:1.20.58.390,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112,Prints_domain:PR00253,Prints_domain:PR01160 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -16.461 1 1 1 1 0 T 2 4 54 161331033 161331033 C T 1 0 0 0 0 0 0 0 1 6038 813 29 3 3 GABRB2 5 161331033 Silent SNP C C3N-00556_T 19911628 161331033 20207226 150 16279 TUBB2B 0 . GRCh38 6 3226590 3226590 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.137G>A p.Arg46Lys p.R46K ENST00000259818 2/4 309 292 17 319 318 1 strelka-varscan-mutect TUBB2B,missense_variant,p.Arg46Lys,ENST00000259818,NM_178012.4;TUBB2B,non_coding_transcript_exon_variant,,ENST00000473006,;PSMG4,upstream_gene_variant,,ENST00000509933,; T ENST00000259818 Transcript missense_variant 329/2020 137/1338 46/445 R/K aGa/aAa 1 -1 TUBB2B HGNC HGNC:30829 protein_coding YES CCDS4485.1 ENSP00000259818 Q9BVA1 UPI0000024E6E NM_178012.4 deleterious_low_confidence(0.04) 2/4 Gene3D:3.40.50.1440,Pfam_domain:PF00091,Prints_domain:PR01163,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF138,Superfamily_domains:SSF52490 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 3226590 3226590 C T 1 0 0 0 0 1 0 0 0 17266 913 32 3 3 TUBB2B 6 3226590 Missense_Mutation SNP C C3N-00556_T 3226590 167579389 151 16280 DCDC2 0 . GRCh38 6 24302030 24302030 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.363C>T p.= p.I121I ENST00000378454 3/10 90 84 6 118 118 0 strelka-varscan-mutect DCDC2,synonymous_variant,p.=,ENST00000378454,NM_016356.4,NM_001195610.1; A ENST00000378454 Transcript synonymous_variant 665/4707 363/1431 121/476 I atC/atT COSM4903828 1 -1 DCDC2 HGNC HGNC:18141 protein_coding YES CCDS4550.1 ENSP00000367715 Q9UHG0 UPI000013DA24 NM_016356.4,NM_001195610.1 3/10 hmmpanther:PTHR23004,hmmpanther:PTHR23004:SF5 1 LOW 1 SNV 1 1 1 PASS rs1286510688 . 0 208 2 0 0 0 0 0 -13.14494 1 1 1 1 0 A 2 1 54 24302030 24302030 G A 1 0 0 0 0 0 0 0 1 4087 1164 41 3 3 DCDC2 6 24302030 Silent SNP G C3N-00556_T 21075440 24302030 146503949 152 16281 HIST1H2BL 0 . GRCh38 6 27807685 27807685 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.222C>T p.= p.I74I ENST00000377401 1/1 339 299 40 360 360 0 strelka-varscan HIST1H2BL,synonymous_variant,p.=,ENST00000377401,NM_003519.3;HIST1H3H,upstream_gene_variant,,ENST00000369163,NM_003536.2;HIST1H2AI,upstream_gene_variant,,ENST00000358739,NM_003509.2;HIST1H4PS1,downstream_gene_variant,,ENST00000406085,; A ENST00000377401 Transcript synonymous_variant 247/488 222/381 74/126 I atC/atT COSM373212,COSM461831 1 -1 HIST1H2BL HGNC HGNC:4748 protein_coding YES CCDS4625.1 ENSP00000366618 Q99880 UPI0000001BD6 NM_003519.3 1/1 hmmpanther:PTHR23428,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00427,Superfamily_domains:SSF47113,Prints_domain:PR00621 1,1 LOW 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 27807685 27807685 G A 1 0 0 0 0 0 0 0 1 7039 1048 37 1 1 HIST1H2BL 6 27807685 Silent SNP G C3N-00556_T 3505655 27807685 142998294 153 16282 MDC1 0 . GRCh38 6 30703233 30703233 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.5736G>A p.= p.L1912L ENST00000376406 12/15 123 116 7 94 94 0 strelka-varscan MDC1,synonymous_variant,p.=,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,non_coding_transcript_exon_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,; T ENST00000376406 Transcript synonymous_variant 6384/7576 5736/6270 1912/2089 L ctG/ctA 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 12/15 Low_complexity_(Seg):seg,PROSITE_profiles:PS50172,hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1,Gene3D:3.40.50.10190,Pfam_domain:PF16770,Superfamily_domains:SSF52113 LOW SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -14.02421 1 1 1 1 0 T 2 4 54 30703233 30703233 C T 1 0 0 0 0 0 0 0 1 9341 581 21 3 3 MDC1 6 30703233 Silent SNP C C3N-00556_T 2895548 30703233 140102746 154 16283 NOTCH4 0 . GRCh38 6 32220245 32220245 + Missense_Mutation SNP G G T rs755786715 C3N-00556_T C3N-00556_N G G c.1199C>A p.Pro400Gln p.P400Q ENST00000375023 7/30 150 113 37 159 159 0 strelka-varscan NOTCH4,missense_variant,p.Pro400Gln,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; T ENST00000375023 Transcript missense_variant 1338/6745 1199/6012 400/2003 P/Q cCg/cAg rs755786715 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0.01) 7/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF64,hmmpanther:PTHR24033,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 32220245 32220245 G T 1 0 0 0 0 1 0 0 0 10596 1116 39 1 1 NOTCH4 6 32220245 Missense_Mutation SNP G C3N-00556_T 1517012 32220245 138585734 155 16284 DNAH8 0 . GRCh38 6 38842815 38842815 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.4757C>T p.Thr1586Ile p.T1586I ENST00000327475 35/93 308 230 78 343 343 0 strelka-varscan DNAH8,missense_variant,p.Thr1586Ile,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Thr1369Ile,ENST00000359357,;DNAH8,missense_variant,p.Thr1586Ile,ENST00000449981,; T ENST00000327475 Transcript missense_variant 4866/14360 4757/14124 1586/4707 T/I aCt/aTt 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0.03) 35/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF08393 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 38842815 38842815 C T 1 0 0 0 0 1 0 0 0 4422 565 20 3 3 DNAH8 6 38842815 Missense_Mutation SNP C C3N-00556_T 6622570 38842815 131963164 156 16285 TMEM63B 0 . GRCh38 6 44136352 44136352 + Silent SNP G G T rs199751940 C3N-00556_T C3N-00556_N G G c.282G>T p.= p.V94V ENST00000259746 5/24 140 115 25 114 114 0 strelka-varscan TMEM63B,synonymous_variant,p.=,ENST00000259746,NM_001318792.1;TMEM63B,synonymous_variant,p.=,ENST00000323267,NM_018426.1;TMEM63B,synonymous_variant,p.=,ENST00000371893,;TMEM63B,synonymous_variant,p.=,ENST00000532634,;TMEM63B,upstream_gene_variant,,ENST00000527188,;TMEM63B,non_coding_transcript_exon_variant,,ENST00000534326,;TMEM63B,non_coding_transcript_exon_variant,,ENST00000525294,;TMEM63B,upstream_gene_variant,,ENST00000533121,;TMEM63B,upstream_gene_variant,,ENST00000525873,;TMEM63B,upstream_gene_variant,,ENST00000497371,; T ENST00000259746 Transcript synonymous_variant 465/3318 282/2499 94/832 V gtG/gtT rs199751940 1 1 TMEM63B HGNC HGNC:17735 protein_coding YES CCDS34461.1 ENSP00000259746 Q5T3F8 UPI000020DDEE NM_001318792.1 5/24 hmmpanther:PTHR13018:SF38,hmmpanther:PTHR13018 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 44136352 44136352 G T 1 0 0 0 0 0 0 0 1 16667 1362 47 2 2 TMEM63B 6 44136352 Silent SNP G C3N-00556_T 5293537 44136352 126669627 157 16286 TTK 0 . GRCh38 6 80039746 80039746 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.2181G>T p.Met727Ile p.M727I ENST00000369798 19/22 139 124 15 141 141 0 strelka-varscan-mutect TTK,missense_variant,p.Met726Ile,ENST00000509894,;TTK,missense_variant,p.Met726Ile,ENST00000230510,NM_001166691.1;TTK,missense_variant,p.Met727Ile,ENST00000369798,NM_003318.4;TTK,non_coding_transcript_exon_variant,,ENST00000504590,; T ENST00000369798 Transcript missense_variant 2292/3010 2181/2574 727/857 M/I atG/atT 1 1 TTK HGNC HGNC:12401 protein_coding YES CCDS4993.1 ENSP00000358813 P33981 UPI0000073C7B NM_003318.4 deleterious(0.02) 19/22 PROSITE_profiles:PS50011,hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF21,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 80039746 80039746 G T 1 0 0 0 0 1 0 0 0 17232 1290 45 2 2 TTK 6 80039746 Missense_Mutation SNP G C3N-00556_T 35903394 80039746 90766233 158 16287 BCKDHB 0 . GRCh38 6 80203164 80203164 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.903C>A p.= p.V301V ENST00000320393 8/10 272 242 30 338 336 2 strelka-varscan-mutect BCKDHB,synonymous_variant,p.=,ENST00000320393,NM_001318975.1,NM_183050.2;BCKDHB,synonymous_variant,p.=,ENST00000356489,NM_000056.3;BCKDHB,non_coding_transcript_exon_variant,,ENST00000468520,; A ENST00000320393 Transcript synonymous_variant 950/3692 903/1179 301/392 V gtC/gtA 1 1 BCKDHB HGNC HGNC:987 protein_coding YES CCDS4994.1 ENSP00000318351 P21953 A0A140VKB3 UPI0000001C97 NM_001318975.1,NM_183050.2 8/10 Gene3D:3.40.50.920,Pfam_domain:PF02780,hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF21,Superfamily_domains:SSF52922 LOW 1 SNV 1 1 PASS rs1163904802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 80203164 80203164 C A 1 0 0 0 0 0 0 0 1 1507 813 29 2 2 BCKDHB 6 80203164 Silent SNP C C3N-00556_T 163418 80203164 90602815 159 16288 AIM1 0 . GRCh38 6 106558516 106558516 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.4522G>C p.Glu1508Gln p.E1508Q ENST00000369066 16/20 71 65 6 119 119 0 strelka-varscan-mutect AIM1,missense_variant,p.Glu1916Gln,ENST00000633556,;AIM1,missense_variant,p.Glu1508Gln,ENST00000369066,NM_001624.3;AIM1,downstream_gene_variant,,ENST00000457437,; C ENST00000369066 Transcript missense_variant 5009/7553 4522/5172 1508/1723 E/Q Gaa/Caa 1 1 AIM1 HGNC HGNC:356 protein_coding YES CCDS34506.1 ENSP00000358062 Q9Y4K1 UPI000013C91D NM_001624.3 deleterious(0.01) 16/20 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF2,Pfam_domain:PF00030,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -10.58709 0.9999792 1 1 1 0 C 3 2 54 106558516 106558516 G C 1 0 0 0 0 1 0 0 0 507 1291 45 4 4 AIM1 6 106558516 Missense_Mutation SNP G C3N-00556_T 26355352 106558516 64247463 160 16289 TRDN 0 . GRCh38 6 123331909 123331909 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1441G>C p.Glu481Gln p.E481Q ENST00000334268 23/41 70 65 5 96 96 0 strelka-varscan TRDN,missense_variant,p.Glu481Gln,ENST00000334268,NM_006073.3; G ENST00000334268 Transcript missense_variant 1759/4770 1441/2190 481/729 E/Q Gag/Cag 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 deleterious_low_confidence(0) 23/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 123331909 123331909 C G 1 0 0 0 0 1 0 0 0 16957 922 32 4 4 TRDN 6 123331909 Missense_Mutation SNP C C3N-00556_T 16773393 123331909 47474070 161 16290 LAMA2 0 . GRCh38 6 129250125 129250125 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1796G>C p.Gly599Ala p.G599A ENST00000421865 13/65 310 292 18 403 403 0 strelka-varscan LAMA2,missense_variant,p.Gly599Ala,ENST00000618192,;LAMA2,missense_variant,p.Gly599Ala,ENST00000617695,;LAMA2,missense_variant,p.Gly599Ala,ENST00000421865,NM_001079823.1,NM_000426.3; C ENST00000421865 Transcript missense_variant 1845/9640 1796/9369 599/3122 G/A gGa/gCa 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 deleterious(0) 13/65 Pfam_domain:PF00052,PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,SMART_domains:SM00281 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 129250125 129250125 G C 1 0 0 0 0 1 0 0 0 8510 1174 41 4 4 LAMA2 6 129250125 Missense_Mutation SNP G C3N-00556_T 5918216 129250125 41555854 162 16291 SHPRH 0 . GRCh38 6 145924795 145924795 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3346G>A p.Glu1116Lys p.E1116K ENST00000367505 17/30 157 149 8 171 171 0 strelka-varscan SHPRH,missense_variant,p.Glu1125Lys,ENST00000629427,;SHPRH,missense_variant,p.Glu1116Lys,ENST00000367505,;SHPRH,missense_variant,p.Glu1125Lys,ENST00000438092,NM_173082.3;SHPRH,missense_variant,p.Glu1116Lys,ENST00000275233,NM_001042683.2;SHPRH,3_prime_UTR_variant,,ENST00000367503,;SHPRH,3_prime_UTR_variant,,ENST00000433355,;SHPRH,3_prime_UTR_variant,,ENST00000519632,;SHPRH,non_coding_transcript_exon_variant,,ENST00000523276,; T ENST00000367505 Transcript missense_variant 3611/7201 3346/5052 1116/1683 E/K Gaa/Aaa 1 -1 SHPRH HGNC HGNC:19336 protein_coding YES CCDS43513.2 ENSP00000356475 Q149N8 UPI0000458A24 tolerated(0.06) 17/30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 145924795 145924795 C T 1 0 0 0 0 1 0 0 0 14554 835 29 3 3 SHPRH 6 145924795 Missense_Mutation SNP C C3N-00556_T 16674670 145924795 24881184 163 16292 SCAF8 0 . GRCh38 6 154808079 154808079 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1225C>G p.Gln409Glu p.Q409E ENST00000417268 11/21 127 120 7 142 142 0 strelka-varscan SCAF8,missense_variant,p.Gln331Glu,ENST00000367178,NM_001286199.1,NM_014892.4;SCAF8,missense_variant,p.Gln409Glu,ENST00000417268,NM_001286188.1,NM_001286194.1;SCAF8,missense_variant,p.Gln397Glu,ENST00000367186,NM_001286189.1; G ENST00000417268 Transcript missense_variant 1270/4944 1225/4050 409/1349 Q/E Cag/Gag 1 1 SCAF8 HGNC HGNC:20959 protein_coding YES CCDS75541.1 ENSP00000413098 A0A0A0MT33 UPI0003BD245C NM_001286188.1,NM_001286194.1 tolerated(1) 11/21 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -10.18793 0.9999994 1 1 1 0 G 3 3 54 154808079 154808079 C G 1 0 0 0 0 1 0 0 0 14135 827 29 4 4 SCAF8 6 154808079 Missense_Mutation SNP C C3N-00556_T 8883284 154808079 15997900 164 16293 C6orf118 0 . GRCh38 6 165298052 165298052 + Missense_Mutation SNP G G A rs768763065 C3N-00556_T C3N-00556_N G G c.986C>T p.Ala329Val p.A329V ENST00000230301 5/9 96 88 8 99 99 0 strelka-varscan C6orf118,missense_variant,p.Ala329Val,ENST00000230301,NM_144980.3;C6orf118,upstream_gene_variant,,ENST00000494696,; A ENST00000230301 Transcript missense_variant 1007/1812 986/1410 329/469 A/V gCg/gTg rs768763065,COSM1487450,COSM4812784 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 tolerated(0.07) 5/9 hmmpanther:PTHR34916,Pfam_domain:PF15739 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 201 8 0 0 0 0 0 -16.29836 0.9999931 1 1 1 0 A 3 1 54 165298052 165298052 G A 1 0 0 0 0 1 0 0 0 2115 1087 38 1 1 C6orf118 6 165298052 Missense_Mutation SNP G C3N-00556_T 10489973 165298052 5507927 165 16294 C6orf118 0 . GRCh38 6 165301788 165301788 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.534G>T p.= p.R178R ENST00000230301 2/9 113 101 12 134 134 0 strelka-varscan C6orf118,synonymous_variant,p.=,ENST00000230301,NM_144980.3; A ENST00000230301 Transcript synonymous_variant 555/1812 534/1410 178/469 R cgG/cgT 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 2/9 Low_complexity_(Seg):seg,hmmpanther:PTHR34916 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99998 1 1 1 1 0 A 2 1 54 165301788 165301788 C A 1 0 0 0 0 0 0 0 1 2115 726 26 2 2 C6orf118 6 165301788 Silent SNP C C3N-00556_T 3736 165301788 5504191 166 16295 TTLL2 0 . GRCh38 6 167340156 167340156 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.256C>A p.Pro86Thr p.P86T ENST00000239587 3/3 60 51 9 81 81 0 strelka-varscan TTLL2,missense_variant,p.Pro86Thr,ENST00000239587,NM_031949.4;TTLL2,missense_variant,p.Pro86Thr,ENST00000515138,;TTLL2,downstream_gene_variant,,ENST00000512917,; A ENST00000239587 Transcript missense_variant 344/2075 256/1779 86/592 P/T Ccg/Acg COSM741147 1 1 TTLL2 HGNC HGNC:21211 protein_coding YES CCDS5301.1 ENSP00000239587 Q9BWV7 UPI00001A3A8B NM_031949.4 deleterious(0.02) 3/3 PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF11 1 MODERATE 1 SNV 1 1 1 PASS . . 0 199 11 0 0 0 0 0 -19.83835 0.9999605 1 1 1 0 A 3 1 54 167340156 167340156 C A 1 0 0 0 0 1 0 0 0 17238 739 26 2 2 TTLL2 6 167340156 Missense_Mutation SNP C C3N-00556_T 2038368 167340156 3465823 167 16296 TCTE3 0 . GRCh38 6 169751448 169751448 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.11G>A p.Arg4Gln p.R4Q ENST00000366774 1/4 124 109 15 174 174 0 strelka-varscan TCTE3,missense_variant,p.Arg4Gln,ENST00000366774,NM_174910.1;ERMARD,upstream_gene_variant,,ENST00000588451,;ERMARD,upstream_gene_variant,,ENST00000366773,NM_018341.2;ERMARD,upstream_gene_variant,,ENST00000366772,NM_001278531.1;ERMARD,upstream_gene_variant,,ENST00000392095,NM_001278532.1;ERMARD,upstream_gene_variant,,ENST00000418781,NM_001278533.1;ERMARD,upstream_gene_variant,,ENST00000590711,;ERMARD,upstream_gene_variant,,ENST00000592745,;ERMARD,upstream_gene_variant,,ENST00000592367,;ERMARD,upstream_gene_variant,,ENST00000588437,;ERMARD,upstream_gene_variant,,ENST00000586341,;TCTE3,non_coding_transcript_exon_variant,,ENST00000628156,;ERMARD,upstream_gene_variant,,ENST00000592580,;ERMARD,upstream_gene_variant,,ENST00000592315,;ERMARD,upstream_gene_variant,,ENST00000590017,; T ENST00000366774 Transcript missense_variant 112/769 11/597 4/198 R/Q cGa/cAa 1 -1 TCTE3 HGNC HGNC:11695 protein_coding YES CCDS5310.1 ENSP00000355736 Q8IZS6 UPI0000061E54 NM_174910.1 deleterious_low_confidence(0.01) 1/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 169751448 169751448 C T 1 0 0 0 0 1 0 0 0 16126 884 31 1 1 TCTE3 6 169751448 Missense_Mutation SNP C C3N-00556_T 2411292 169751448 1054531 168 16297 DNAAF5 0 . GRCh38 7 763928 763928 + Silent SNP A A C novel C3N-00556_T C3N-00556_N A A c.1737A>C p.= p.A579A ENST00000297440 8/13 315 257 58 276 274 2 strelka-varscan-mutect DNAAF5,synonymous_variant,p.=,ENST00000297440,NM_017802.3;DNAAF5,synonymous_variant,p.=,ENST00000440747,;DNAAF5,upstream_gene_variant,,ENST00000403952,;DNAAF5,non_coding_transcript_exon_variant,,ENST00000491496,; C ENST00000297440 Transcript synonymous_variant 1757/3410 1737/2568 579/855 A gcA/gcC 1 1 DNAAF5 HGNC HGNC:26013 protein_coding YES CCDS34580.1 ENSP00000297440 Q86Y56 UPI0000D61BE2 NM_017802.3 8/13 Gene3D:1.25.10.10,hmmpanther:PTHR16216,hmmpanther:PTHR16216:SF2,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 763928 763928 A C 1 0 0 0 0 0 0 0 1 4409 146 6 5 5 DNAAF5 7 763928 Silent SNP A C3N-00556_T 763928 158582045 169 16298 ZFAND2A 0 . GRCh38 7 1153205 1153205 + Nonsense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.302C>G p.Ser101Ter p.S101* ENST00000316495 5/5 135 126 9 140 140 0 strelka-varscan-mutect ZFAND2A,stop_gained,p.Ser101Ter,ENST00000401903,;ZFAND2A,stop_gained,p.Ser101Ter,ENST00000316495,NM_182491.2;ZFAND2A,missense_variant,p.Gln107Glu,ENST00000397083,;ZFAND2A,intron_variant,,ENST00000574135,;ZFAND2A,non_coding_transcript_exon_variant,,ENST00000471448,;ZFAND2A,downstream_gene_variant,,ENST00000484977,; C ENST00000316495 Transcript stop_gained 562/860 302/438 101/145 S/* tCa/tGa 1 -1 ZFAND2A HGNC HGNC:28073 protein_coding YES CCDS5323.1 ENSP00000314619 Q8N6M9 UPI000013FDD5 NM_182491.2 5/5 PROSITE_profiles:PS51039,hmmpanther:PTHR14677:SF11,hmmpanther:PTHR14677,Pfam_domain:PF01428,Gene3D:4.10.1110.10,SMART_domains:SM00154,Superfamily_domains:SSF118310 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 54 1153205 1153205 G C 1 0 0 0 0 0 1 0 0 18203 1294 45 4 4 ZFAND2A 7 1153205 Nonsense_Mutation SNP G C3N-00556_T 389277 1153205 158192768 170 16299 CARD11 0 . GRCh38 7 2928687 2928687 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1665G>A p.= p.R555R ENST00000396946 13/25 168 145 23 135 135 0 strelka-varscan-mutect CARD11,synonymous_variant,p.=,ENST00000396946,NM_001324281.1,NM_032415.5;CARD11,synonymous_variant,p.=,ENST00000355508,; T ENST00000396946 Transcript synonymous_variant 2069/4366 1665/3465 555/1154 R cgG/cgA 1 -1 CARD11 HGNC HGNC:16393 protein_coding YES CCDS5336.2 ENSP00000380150 Q9BXL7 A0A024R854 UPI00003FED38 NM_001324281.1,NM_032415.5 13/25 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 2928687 2928687 C T 1 0 0 0 0 0 0 0 1 2340 842 30 3 3 CARD11 7 2928687 Silent SNP C C3N-00556_T 1775482 2928687 156417286 171 16300 ISPD 0 . GRCh38 7 16091696 16091696 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1355G>A p.= p.*452* ENST00000407010 10/10 185 175 10 253 253 0 strelka-varscan-mutect ISPD,stop_retained_variant,p.=,ENST00000407010,NM_001101426.3;ISPD,stop_retained_variant,p.=,ENST00000399310,NM_001101417.3; T ENST00000407010 Transcript stop_retained_variant 1355/5524 1355/1356 452/451 * tGa/tAa 1 -1 ISPD HGNC HGNC:37276 protein_coding YES ENSP00000385478 A4D126 UPI00015CFC06 NM_001101426.3 10/10 LOW 1 SNV 5 1 PASS . . 0 202 0 6 0 0 0 0 -12.27209 0.9881184 1 1 1 0 T 2 4 54 16091696 16091696 C T 1 0 0 0 0 0 0 0 1 7771 837 29 3 3 ISPD 7 16091696 Silent SNP C C3N-00556_T 13163009 16091696 143254277 172 16301 SP4 0 . GRCh38 7 21429901 21429901 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.736C>T p.Leu246Phe p.L246F ENST00000222584 3/6 265 249 16 307 306 1 strelka-varscan-mutect SP4,missense_variant,p.Leu246Phe,ENST00000222584,NM_001326542.1,NM_001326543.1,NM_003112.3;SP4,intron_variant,,ENST00000432066,;SP4,intron_variant,,ENST00000448246,;SP4,downstream_gene_variant,,ENST00000440636,; T ENST00000222584 Transcript missense_variant 954/6126 736/2355 246/784 L/F Ctt/Ttt 1 1 SP4 HGNC HGNC:11209 protein_coding YES CCDS5373.1 ENSP00000222584 Q02446 UPI000013C807 NM_001326542.1,NM_001326543.1,NM_003112.3 tolerated(0.69) 3/6 hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 21429901 21429901 C T 1 0 0 0 0 1 0 0 0 15292 913 32 3 3 SP4 7 21429901 Missense_Mutation SNP C C3N-00556_T 5338205 21429901 137916072 173 16302 NEUROD6 0 . GRCh38 7 31339115 31339115 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.154C>T p.Pro52Ser p.P52S ENST00000297142 2/2 428 351 77 419 419 0 strelka-varscan NEUROD6,missense_variant,p.Pro52Ser,ENST00000297142,NM_022728.3; A ENST00000297142 Transcript missense_variant 477/2131 154/1014 52/337 P/S Cct/Tct 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 tolerated(0.74) 2/2 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,PIRSF_domain:PIRSF015618 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 31339115 31339115 G A 1 0 0 0 0 1 0 0 0 10388 1232 43 3 3 NEUROD6 7 31339115 Missense_Mutation SNP G C3N-00556_T 9909214 31339115 128006858 174 16303 KIAA0895 0 . GRCh38 7 36335079 36335079 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.967C>T p.His323Tyr p.H323Y ENST00000297063 4/7 184 153 31 188 187 1 strelka-varscan KIAA0895,missense_variant,p.His272Tyr,ENST00000317020,NM_015314.2;KIAA0895,missense_variant,p.His323Tyr,ENST00000297063,NM_001100425.1;KIAA0895,missense_variant,p.His310Tyr,ENST00000338533,NM_001199707.1;KIAA0895,missense_variant,p.His320Tyr,ENST00000440378,NM_001199706.1;KIAA0895,missense_variant,p.His220Tyr,ENST00000436884,NM_001199708.1;KIAA0895,missense_variant,p.His78Tyr,ENST00000453212,NM_001300956.1;KIAA0895,missense_variant,p.His78Tyr,ENST00000431396,;Y_RNA,downstream_gene_variant,,ENST00000364562,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000480192,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000483526,;KIAA0895,non_coding_transcript_exon_variant,,ENST00000483360,; A ENST00000297063 Transcript missense_variant 1018/4153 967/1563 323/520 H/Y Cat/Tat 1 -1 KIAA0895 HGNC HGNC:22206 protein_coding YES CCDS43570.1 ENSP00000297063 Q8NCT3 UPI000013E3C0 NM_001100425.1 tolerated(0.23) 4/7 Pfam_domain:PF08014,hmmpanther:PTHR31817,hmmpanther:PTHR31817:SF3,SMART_domains:SM01154 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 36335079 36335079 G A 1 0 0 0 0 1 0 0 0 8092 1319 46 3 3 KIAA0895 7 36335079 Missense_Mutation SNP G C3N-00556_T 4995964 36335079 123010894 175 16304 AOAH 0 . GRCh38 7 36532192 36532192 + Silent SNP G G A rs768364625 C3N-00556_T C3N-00556_N G G c.1380C>T p.= p.H460H ENST00000617267 18/22 310 254 56 343 343 0 strelka-varscan AOAH,synonymous_variant,p.=,ENST00000617267,NM_001177506.1;AOAH,synonymous_variant,p.=,ENST00000617537,NM_001637.3;AOAH,synonymous_variant,p.=,ENST00000612871,NM_001177507.1;AOAH,non_coding_transcript_exon_variant,,ENST00000491444,;AOAH,downstream_gene_variant,,ENST00000487014,;AOAH,upstream_gene_variant,,ENST00000614254,;AOAH,downstream_gene_variant,,ENST00000495942,; A ENST00000617267 Transcript synonymous_variant 1681/2398 1380/2067 460/688 H caC/caT rs768364625,COSM236992 1 -1 AOAH HGNC HGNC:548 protein_coding YES CCDS75584.1 ENSP00000479664 A0A087WVT3 UPI0001D043BB NM_001177506.1 18/22 Pfam_domain:PF00657,hmmpanther:PTHR15010 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 36532192 36532192 G A 1 0 0 0 0 0 0 0 1 835 1136 40 1 1 AOAH 7 36532192 Silent SNP G C3N-00556_T 197113 36532192 122813781 176 16305 AMPH 0 . GRCh38 7 38534943 38534943 + Silent SNP G G A rs140832560 C3N-00556_T C3N-00556_N G G c.138C>T p.= p.F46F ENST00000356264 2/21 203 192 11 230 230 0 strelka-varscan AMPH,synonymous_variant,p.=,ENST00000356264,NM_001635.3;AMPH,synonymous_variant,p.=,ENST00000325590,NM_139316.2;RN7SL83P,upstream_gene_variant,,ENST00000468131,; A ENST00000356264 Transcript synonymous_variant 354/3418 138/2088 46/695 F ttC/ttT rs140832560,COSM3229284,COSM3638575 1 -1 AMPH HGNC HGNC:471 protein_coding YES CCDS5456.1 ENSP00000348602 P49418 UPI00001259EA NM_001635.3 2/21 Gene3D:1.20.1270.60,Pfam_domain:PF03114,PROSITE_profiles:PS51021,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF211,SMART_domains:SM00721,Superfamily_domains:SSF103657 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 38534943 38534943 G A 1 0 0 0 0 0 0 0 1 686 1281 45 3 3 AMPH 7 38534943 Silent SNP G C3N-00556_T 2002751 38534943 120811030 177 16306 COA1 0 . GRCh38 7 43640633 43640633 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.281C>G p.Ser94Cys p.S94C ENST00000395879 4/5 152 143 9 180 180 0 strelka-varscan COA1,missense_variant,p.Ser94Cys,ENST00000395879,;COA1,missense_variant,p.Ser94Cys,ENST00000310564,NM_001321197.1;COA1,missense_variant,p.Ser94Cys,ENST00000223336,NM_001321201.1,NM_018224.3;COA1,missense_variant,p.Ser94Cys,ENST00000415798,;COA1,downstream_gene_variant,,ENST00000431651,;COA1,non_coding_transcript_exon_variant,,ENST00000488813,;COA1,missense_variant,p.Ser94Cys,ENST00000438444,;COA1,missense_variant,p.Ser94Cys,ENST00000415076,;COA1,missense_variant,p.Ser94Cys,ENST00000446330,;COA1,missense_variant,p.Ser94Cys,ENST00000446564,;COA1,non_coding_transcript_exon_variant,,ENST00000490251,; C ENST00000395879 Transcript missense_variant 1963/2448 281/441 94/146 S/C tCt/tGt 1 -1 COA1 HGNC HGNC:21868 protein_coding YES CCDS5471.1 ENSP00000379218 Q9GZY4 A0A024RA60 UPI000006E8D7 deleterious(0.04) 4/5 hmmpanther:PTHR10768,Pfam_domain:PF08695 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 43640633 43640633 G C 1 0 0 0 0 1 0 0 0 3435 942 33 4 4 COA1 7 43640633 Missense_Mutation SNP G C3N-00556_T 5105690 43640633 115705340 178 16307 TBRG4 0 . GRCh38 7 45109072 45109072 + Missense_Mutation SNP C C G rs771152697 C3N-00556_T C3N-00556_N C C c.166G>C p.Glu56Gln p.E56Q ENST00000258770 2/11 163 134 29 135 135 0 strelka-varscan TBRG4,missense_variant,p.Glu56Gln,ENST00000258770,NM_004749.3;TBRG4,missense_variant,p.Glu56Gln,ENST00000395655,;TBRG4,missense_variant,p.Glu56Gln,ENST00000494076,NM_001261834.1;TBRG4,missense_variant,p.Glu56Gln,ENST00000361278,NM_030900.3,NM_199122.2;TBRG4,missense_variant,p.Glu56Gln,ENST00000478532,;TBRG4,missense_variant,p.Glu2Gln,ENST00000461363,;TBRG4,missense_variant,p.Glu56Gln,ENST00000475893,;TBRG4,missense_variant,p.Glu56Gln,ENST00000495078,;TBRG4,missense_variant,p.Glu56Gln,ENST00000482285,;TBRG4,upstream_gene_variant,,ENST00000483615,;SNORA5C,upstream_gene_variant,,ENST00000364902,;SNORA5A,upstream_gene_variant,,ENST00000384111,;SNORA5B,upstream_gene_variant,,ENST00000363786,;TBRG4,non_coding_transcript_exon_variant,,ENST00000471142,;TBRG4,upstream_gene_variant,,ENST00000495973,;TBRG4,upstream_gene_variant,,ENST00000488222,;TBRG4,upstream_gene_variant,,ENST00000484326,;TBRG4,upstream_gene_variant,,ENST00000477328,; G ENST00000258770 Transcript missense_variant 288/2243 166/1896 56/631 E/Q Gag/Cag rs771152697 1 -1 TBRG4 HGNC HGNC:17443 protein_coding YES CCDS5501.1 ENSP00000258770 Q969Z0 UPI0000071F89 NM_004749.3 tolerated(0.21) 2/11 hmmpanther:PTHR21228,hmmpanther:PTHR21228:SF26 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 45109072 45109072 C G 1 0 0 0 0 1 0 0 0 16054 864 30 4 4 TBRG4 7 45109072 Missense_Mutation SNP C C3N-00556_T 1468439 45109072 114236901 179 16308 TYW1B 0 . GRCh38 7 72694687 72694687 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1506G>T p.Lys502Asn p.K502N ENST00000620995 11/14 92 77 15 78 78 0 strelka-varscan TYW1B,missense_variant,p.Lys502Asn,ENST00000620995,NM_001145440.2;TYW1B,missense_variant,p.Lys340Asn,ENST00000612372,;MIR4650-2,upstream_gene_variant,,ENST00000581927,; A ENST00000620995 Transcript missense_variant,splice_region_variant 1629/3113 1506/2007 502/668 K/N aaG/aaT 1 -1 TYW1B HGNC HGNC:33908 protein_coding YES CCDS69309.1 ENSP00000482502 A0A087WZB2 UPI000178DF1B NM_001145440.2 deleterious(0) 11/14 Gene3D:3.20.20.70,Pfam_domain:PF04055,hmmpanther:PTHR13930,Superfamily_domains:SSF102114 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 54 72694687 72694687 C A 1 0 0 0 0 1 0 0 0 17334 695 24 2 2 TYW1B 7 72694687 Missense_Mutation SNP C C3N-00556_T 27585615 72694687 86651286 180 16309 GATSL2 0 . GRCh38 7 75020092 75020092 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.689C>G p.Ser230Cys p.S230C ENST00000616305 6/9 343 299 44 255 255 0 strelka-varscan GATSL2,missense_variant,p.Ser230Cys,ENST00000616305,NM_001145064.2;GATSL2,non_coding_transcript_exon_variant,,ENST00000622472,; G ENST00000616305 Transcript missense_variant 857/1257 689/990 230/329 S/C tCc/tGc 1 1 GATSL2 HGNC HGNC:37073 protein_coding YES CCDS75620.1 ENSP00000484732 A6NHX0 UPI000013F134 NM_001145064.2 deleterious(0.01) 6/9 hmmpanther:PTHR31131,hmmpanther:PTHR31131:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 75020092 75020092 C G 1 0 0 0 0 1 0 0 0 6136 855 30 4 4 GATSL2 7 75020092 Missense_Mutation SNP C C3N-00556_T 2325405 75020092 84325881 181 16310 CACNA2D1 0 . GRCh38 7 81967608 81967608 + Silent SNP T T C novel C3N-00556_T C3N-00556_N T T c.2451A>G p.= p.S817S ENST00000356860 30/39 83 72 11 110 110 0 strelka-varscan CACNA2D1,synonymous_variant,p.=,ENST00000356860,NM_000722.3;CACNA2D1,synonymous_variant,p.=,ENST00000356253,;CACNA2D1,downstream_gene_variant,,ENST00000443883,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000486539,;CACNA2D1,upstream_gene_variant,,ENST00000469297,; C ENST00000356860 Transcript synonymous_variant 2790/7563 2451/3276 817/1091 S tcA/tcG 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 30/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99993 1 1 1 1 0 C 2 2 54 81967608 81967608 T C 1 0 0 0 0 0 0 0 1 2236 1799 63 5 5 CACNA2D1 7 81967608 Silent SNP T C3N-00556_T 6947516 81967608 77378365 182 16311 CACNA2D1 0 . GRCh38 7 82117091 82117091 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.479C>G p.Ser160Cys p.S160C ENST00000356860 6/39 335 284 51 339 339 0 strelka-varscan CACNA2D1,missense_variant,p.Ser160Cys,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Ser160Cys,ENST00000356253,;CACNA2D1,missense_variant,p.Ser160Cys,ENST00000423588,NM_001302890.1;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000484706,; C ENST00000356860 Transcript missense_variant 818/7563 479/3276 160/1091 S/C tCt/tGt 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 deleterious(0) 6/39 Pfam_domain:PF08399,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 82117091 82117091 G C 1 0 0 0 0 1 0 0 0 2236 942 33 4 4 CACNA2D1 7 82117091 Missense_Mutation SNP G C3N-00556_T 149483 82117091 77228882 183 16312 AKAP9 0 . GRCh38 7 91973738 91973738 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.76C>G p.Gln26Glu p.Q26E ENST00000356239 2/50 293 277 16 334 334 0 strelka-varscan AKAP9,missense_variant,p.Gln26Glu,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Gln37Glu,ENST00000359028,;AKAP9,missense_variant,p.Gln26Glu,ENST00000358100,;AKAP9,missense_variant,p.Gln34Glu,ENST00000619023,;AKAP9,missense_variant,p.Gln26Glu,ENST00000394564,;AKAP9,upstream_gene_variant,,ENST00000438114,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; G ENST00000356239 Transcript missense_variant 309/12471 76/11724 26/3907 Q/E Cag/Gag 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 deleterious(0.01) 2/50 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 91973738 91973738 C G 1 0 0 0 0 1 0 0 0 543 827 29 4 4 AKAP9 7 91973738 Missense_Mutation SNP C C3N-00556_T 9856647 91973738 67372235 184 16313 ANKIB1 0 . GRCh38 7 92352598 92352598 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.1353G>A p.= p.L451L ENST00000265742 9/20 156 132 24 159 159 0 strelka-varscan ANKIB1,synonymous_variant,p.=,ENST00000265742,NM_019004.1;ANKIB1,3_prime_UTR_variant,,ENST00000413588,; A ENST00000265742 Transcript synonymous_variant 1729/6081 1353/3270 451/1089 L ctG/ctA 1 1 ANKIB1 HGNC HGNC:22215 protein_coding YES CCDS47639.1 ENSP00000265742 Q9P2G1 UPI00001C1E7C NM_019004.1 9/20 Pfam_domain:PF01485,SMART_domains:SM00647,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999982 1 1 1 0 A 2 1 54 92352598 92352598 G A 1 0 0 0 0 0 0 0 1 731 1277 45 3 3 ANKIB1 7 92352598 Silent SNP G C3N-00556_T 378860 92352598 66993375 185 16314 SAMD9 0 . GRCh38 7 93102822 93102822 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.3276C>T p.= p.F1092F ENST00000379958 3/3 307 281 26 406 406 0 strelka-varscan SAMD9,synonymous_variant,p.=,ENST00000379958,NM_017654.3;SAMD9,synonymous_variant,p.=,ENST00000620985,NM_001193307.1;SAMD9,synonymous_variant,p.=,ENST00000446617,; A ENST00000379958 Transcript synonymous_variant 3546/6852 3276/4770 1092/1589 F ttC/ttT 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 93102822 93102822 G A 1 0 0 0 0 0 0 0 1 14086 933 33 3 3 SAMD9 7 93102822 Silent SNP G C3N-00556_T 750224 93102822 66243151 186 16315 COPS6 0 . GRCh38 7 100091518 100091518 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.841G>C p.Asp281His p.D281H ENST00000303904 9/10 136 126 10 213 213 0 strelka-varscan COPS6,missense_variant,p.Asp281His,ENST00000303904,NM_006833.4;COPS6,missense_variant,p.Asp280His,ENST00000418625,;MCM7,downstream_gene_variant,,ENST00000621318,NM_001278595.1;MCM7,downstream_gene_variant,,ENST00000354230,NM_182776.2;MCM7,downstream_gene_variant,,ENST00000303887,NM_005916.4;MCM7,downstream_gene_variant,,ENST00000343023,;COPS6,downstream_gene_variant,,ENST00000419210,;MIR25,downstream_gene_variant,,ENST00000384816,;MIR106B,downstream_gene_variant,,ENST00000385301,;MIR93,downstream_gene_variant,,ENST00000385024,;COPS6,splice_region_variant,,ENST00000474823,;COPS6,splice_region_variant,,ENST00000426712,;MCM7,downstream_gene_variant,,ENST00000485286,;MCM7,downstream_gene_variant,,ENST00000489841,;COPS6,downstream_gene_variant,,ENST00000465027,;COPS6,downstream_gene_variant,,ENST00000472107,;COPS6,downstream_gene_variant,,ENST00000468499,;COPS6,downstream_gene_variant,,ENST00000483891,;MCM7,downstream_gene_variant,,ENST00000491245,;COPS6,downstream_gene_variant,,ENST00000496358,;MCM7,downstream_gene_variant,,ENST00000493352,; C ENST00000303904 Transcript missense_variant,splice_region_variant 878/1432 841/984 281/327 D/H Gat/Cat 1 1 COPS6 HGNC HGNC:21749 protein_coding YES CCDS5682.1 ENSP00000304102 Q7L5N1 UPI000014F97E NM_006833.4 tolerated(0.07) 9/10 hmmpanther:PTHR10540,hmmpanther:PTHR10540:SF8,Pfam_domain:PF13012 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -14.02349 0.9999721 1 1 1 0 C 3 2 54 100091518 100091518 G C 1 0 0 0 0 1 0 0 0 3530 1304 45 4 4 COPS6 7 100091518 Missense_Mutation SNP G C3N-00556_T 6988696 100091518 59254455 187 16316 EPO 0 . GRCh38 7 100721988 100721988 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.186G>T p.Leu62Phe p.L62F ENST00000252723 3/5 183 153 30 212 211 1 strelka-varscan EPO,missense_variant,p.Leu62Phe,ENST00000252723,NM_000799.2; T ENST00000252723 Transcript missense_variant 367/1330 186/582 62/193 L/F ttG/ttT 1 1 EPO HGNC HGNC:3415 protein_coding YES CCDS5705.1 ENSP00000252723 P01588 G9JKG7 UPI0000033477 NM_000799.2 tolerated(0.41) 3/5 hmmpanther:PTHR10370,Pfam_domain:PF00758,PIRSF_domain:PIRSF001951,Gene3D:1.20.1250.10,Superfamily_domains:SSF47266,Prints_domain:PR00272 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 100721988 100721988 G T 1 0 0 0 0 1 0 0 0 5035 1281 45 2 2 EPO 7 100721988 Missense_Mutation SNP G C3N-00556_T 630470 100721988 58623985 188 16317 MYL10 0 . GRCh38 7 101623061 101623061 + Missense_Mutation SNP G G C rs779412213 C3N-00556_T C3N-00556_N G G c.285C>G p.Ile95Met p.I95M ENST00000223167 4/8 176 160 16 135 135 0 strelka-varscan MYL10,missense_variant,p.Ile95Met,ENST00000223167,NM_138403.4; C ENST00000223167 Transcript missense_variant 463/1009 285/681 95/226 I/M atC/atG rs779412213 1 -1 MYL10 HGNC HGNC:29825 protein_coding YES CCDS34713.1 ENSP00000223167 Q9BUA6 UPI00001BBFAD NM_138403.4 tolerated(0.55) 4/8 Gene3D:1.10.238.10,Pfam_domain:PF13405,PROSITE_profiles:PS50222,hmmpanther:PTHR23049,hmmpanther:PTHR23049:SF36,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 101623061 101623061 G C 1 0 0 0 0 1 0 0 0 10044 1280 45 4 4 MYL10 7 101623061 Missense_Mutation SNP G C3N-00556_T 901073 101623061 57722912 189 16318 ALKBH4 0 . GRCh38 7 102464804 102464804 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.33C>T p.= p.V11V ENST00000292566 1/3 97 90 7 82 82 0 strelka-varscan ALKBH4,synonymous_variant,p.=,ENST00000292566,NM_017621.3;LRWD1,upstream_gene_variant,,ENST00000292616,NM_001317721.1,NM_152892.1;LRWD1,upstream_gene_variant,,ENST00000463739,;LRWD1,upstream_gene_variant,,ENST00000468175,;LRWD1,upstream_gene_variant,,ENST00000626402,;LRWD1,upstream_gene_variant,,ENST00000582533,;ALKBH4,synonymous_variant,p.=,ENST00000490528,;ALKBH4,non_coding_transcript_exon_variant,,ENST00000498283,;LRWD1,upstream_gene_variant,,ENST00000473880,;LRWD1,upstream_gene_variant,,ENST00000485808,;LRWD1,upstream_gene_variant,,ENST00000476270,;LRWD1,upstream_gene_variant,,ENST00000464107,;LRWD1,upstream_gene_variant,,ENST00000485417,; A ENST00000292566 Transcript synonymous_variant 73/2105 33/909 11/302 V gtC/gtT 1 -1 ALKBH4 HGNC HGNC:21900 protein_coding YES CCDS5723.1 ENSP00000292566 Q9NXW9 UPI0000073F0C NM_017621.3 1/3 hmmpanther:PTHR12463 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -11.1114 0.9998264 1 1 1 0 A 2 1 54 102464804 102464804 G A 1 0 0 0 0 0 0 0 1 629 1161 41 3 3 ALKBH4 7 102464804 Silent SNP G C3N-00556_T 841743 102464804 56881169 190 16319 SLC26A5 0 . GRCh38 7 103376837 103376837 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.2012G>A p.Gly671Asp p.G671D ENST00000306312 19/20 236 191 45 254 254 0 strelka-varscan SLC26A5,missense_variant,p.Gly671Asp,ENST00000306312,NM_198999.2;SLC26A5,missense_variant,p.Gly673Asp,ENST00000354356,;SLC26A5,missense_variant,p.Gly639Asp,ENST00000432958,NM_001167962.1;SLC26A5,missense_variant,p.Gly639Asp,ENST00000393730,;SLC26A5,missense_variant,p.Gly671Asp,ENST00000339444,NM_206883.2;SLC26A5,missense_variant,p.Gly634Asp,ENST00000393729,;SLC26A5,missense_variant,p.Gly673Asp,ENST00000393727,;SLC26A5,missense_variant,p.Gly641Asp,ENST00000393723,;SLC26A5,intron_variant,,ENST00000393735,NM_206884.2;SLC26A5,intron_variant,,ENST00000356767,NM_206885.2;SLC26A5,3_prime_UTR_variant,,ENST00000423416,;SLC26A5,3_prime_UTR_variant,,ENST00000456463,;SLC26A5,3_prime_UTR_variant,,ENST00000445809,;SLC26A5,3_prime_UTR_variant,,ENST00000454864,; T ENST00000306312 Transcript missense_variant 2274/2689 2012/2235 671/744 G/D gGt/gAt 1 -1 SLC26A5 HGNC HGNC:9359 protein_coding YES CCDS5733.1 ENSP00000304783 P58743 UPI0000132195 NM_198999.2 tolerated(1) 19/20 PROSITE_profiles:PS50801,hmmpanther:PTHR11814:SF32,hmmpanther:PTHR11814,TIGRFAM_domain:TIGR00815,Pfam_domain:PF01740,Gene3D:3.30.750.24,Superfamily_domains:SSF52091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 103376837 103376837 C T 1 0 0 0 0 1 0 0 0 14790 507 18 3 3 SLC26A5 7 103376837 Missense_Mutation SNP C C3N-00556_T 912033 103376837 55969136 191 16320 RELN 0 . GRCh38 7 103651762 103651763 + Frame_Shift_Ins INS - - T novel C3N-00556_T C3N-00556_N - - c.1790dupA p.His597GlnfsTer11 p.H597Qfs*11 ENST00000428762 15/65 260 220 40 253 253 0 sindel-varindel-pindel RELN,frameshift_variant,p.His597GlnfsTer11,ENST00000424685,;RELN,frameshift_variant,p.His597GlnfsTer11,ENST00000428762,NM_005045.3;RELN,frameshift_variant,p.His597GlnfsTer11,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript frameshift_variant 1950-1951/11571 1790-1791/10383 597/3460 H/QX cat/caAt 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 15/65 hmmpanther:PTHR11841,Superfamily_domains:SSF50939 HIGH 1 insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 54 103651762 103651762 - T 1 0 1 1 0 0 0 0 0 13390 214 8 0 0 RELN 7 103651762 Frame_Shift_Ins INS - C3N-00556_T 274925 103651762 55694211 192 16321 RINT1 0 . GRCh38 7 105542515 105542515 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.381C>T p.= p.L127L ENST00000257700 4/15 337 318 19 326 326 0 strelka-varscan-mutect RINT1,synonymous_variant,p.=,ENST00000257700,NM_021930.4;RINT1,synonymous_variant,p.=,ENST00000493041,;RINT1,non_coding_transcript_exon_variant,,ENST00000477285,;RINT1,missense_variant,p.Leu54Phe,ENST00000497979,;RINT1,3_prime_UTR_variant,,ENST00000467392,;RINT1,non_coding_transcript_exon_variant,,ENST00000493258,;RINT1,downstream_gene_variant,,ENST00000482041,; T ENST00000257700 Transcript synonymous_variant 612/2976 381/2379 127/792 L ctC/ctT 1 1 RINT1 HGNC HGNC:21876 protein_coding YES CCDS34726.1 ENSP00000257700 Q6NUQ1 UPI000020F898 NM_021930.4 4/15 hmmpanther:PTHR13520,hmmpanther:PTHR13520:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 105542515 105542515 C T 1 0 0 0 0 0 0 0 1 13550 900 32 3 3 RINT1 7 105542515 Silent SNP C C3N-00556_T 1890753 105542515 53803458 193 16322 GRM8 0 . GRCh38 7 126770015 126770015 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1207C>T p.Gln403Ter p.Q403* ENST00000339582 7/11 196 182 14 195 195 0 strelka-varscan-mutect GRM8,stop_gained,p.Gln403Ter,ENST00000339582,NM_000845.2;GRM8,stop_gained,p.Gln403Ter,ENST00000358373,NM_001127323.1;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,non_coding_transcript_exon_variant,,ENST00000448250,;GRM8,stop_gained,p.Gln403Ter,ENST00000472701,;GRM8,stop_gained,p.Gln403Ter,ENST00000341617,; A ENST00000339582 Transcript stop_gained 2016/4057 1207/2727 403/908 Q/* Caa/Taa 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 7/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00593,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 126770015 126770015 G A 1 0 0 0 0 0 1 0 0 6685 1357 47 3 3 GRM8 7 126770015 Nonsense_Mutation SNP G C3N-00556_T 21227500 126770015 32575958 194 16323 CCDC136 0 . GRCh38 7 128794521 128794521 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.190C>T p.Gln64Ter p.Q64* ENST00000297788 2/18 152 142 10 164 164 0 strelka-varscan-mutect CCDC136,stop_gained,p.Gln64Ter,ENST00000297788,NM_022742.4;CCDC136,stop_gained,p.Gln64Ter,ENST00000487361,;CCDC136,stop_gained,p.Gln114Ter,ENST00000464832,;CCDC136,stop_gained,p.Gln114Ter,ENST00000378685,NM_001201372.1;CCDC136,stop_gained,p.Gln64Ter,ENST00000485998,;CCDC136,stop_gained,p.Gln64Ter,ENST00000459946,;CCDC136,incomplete_terminal_codon_variant,p.=,ENST00000488925,;CCDC136,downstream_gene_variant,,ENST00000472049,; T ENST00000297788 Transcript stop_gained 557/4169 190/3465 64/1154 Q/* Cag/Tag 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 2/18 hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26,Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 128794521 128794521 C T 1 0 0 0 0 0 1 0 0 2459 827 29 3 3 CCDC136 7 128794521 Nonsense_Mutation SNP C C3N-00556_T 2024506 128794521 30551452 195 16324 LUC7L2 0 . GRCh38 7 139409630 139409630 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.755G>C p.Arg252Thr p.R252T ENST00000354926 7/10 110 104 6 130 129 1 varscan-mutect LUC7L2,missense_variant,p.Arg251Thr,ENST00000619796,NM_001270643.1;LUC7L2,missense_variant,p.Arg252Thr,ENST00000354926,NM_016019.4;LUC7L2,missense_variant,p.Arg249Thr,ENST00000263545,;C7orf55-LUC7L2,missense_variant,p.Arg318Thr,ENST00000541515,NM_001244584.2;LUC7L2,missense_variant,p.Arg249Thr,ENST00000541170,NM_001244585.1;LUC7L2,3_prime_UTR_variant,,ENST00000456182,;LUC7L2,non_coding_transcript_exon_variant,,ENST00000498518,;LUC7L2,non_coding_transcript_exon_variant,,ENST00000463912,; C ENST00000354926 Transcript missense_variant 1109/2645 755/1179 252/392 R/T aGa/aCa 1 1 LUC7L2 HGNC HGNC:21608 protein_coding YES CCDS43656.1 ENSP00000347005 Q9Y383 UPI000003F000 NM_016019.4 tolerated(0.14) 7/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12375,hmmpanther:PTHR12375:SF28,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 0 4 0 0 0 0 -8.967993 0.9993233 1 1 1 0 C 3 2 54 139409630 139409630 G C 1 0 0 0 0 1 0 0 0 8990 942 33 4 4 LUC7L2 7 139409630 Missense_Mutation SNP G C3N-00556_T 10615109 139409630 19936343 196 16325 HIPK2 0 . GRCh38 7 139573143 139573143 + Silent SNP C C A rs776716441 C3N-00556_T C3N-00556_N C C c.3381G>T p.= p.A1127A ENST00000406875 15/15 267 235 32 260 257 3 strelka-varscan-mutect HIPK2,synonymous_variant,p.=,ENST00000406875,NM_022740.4;HIPK2,synonymous_variant,p.=,ENST00000428878,NM_001113239.2; A ENST00000406875 Transcript synonymous_variant 3476/15049 3381/3597 1127/1198 A gcG/gcT rs776716441 1 -1 HIPK2 HGNC HGNC:14402 protein_coding YES CCDS75667.1 ENSP00000385571 Q9H2X6 UPI000012C71E NM_022740.4 15/15 LOW 1 SNV 1 1 PASS rs776716441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 139573143 139573143 C A 1 0 0 0 0 0 0 0 1 7005 755 27 1 1 HIPK2 7 139573143 Silent SNP C C3N-00556_T 163513 139573143 19772830 197 16326 MGAM 0 . GRCh38 7 142038571 142038571 + Missense_Mutation SNP T T C novel C3N-00556_T C3N-00556_N T T c.2272T>C p.Phe758Leu p.F758L ENST00000549489 19/48 78 66 12 95 95 0 strelka-varscan-mutect MGAM,missense_variant,p.Phe758Leu,ENST00000475668,;MGAM,missense_variant,p.Phe758Leu,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Phe758Leu,ENST00000620571,;MGAM,non_coding_transcript_exon_variant,,ENST00000490593,; C ENST00000549489 Transcript missense_variant 2367/6525 2272/5574 758/1857 F/L Ttc/Ctc 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0.05) 19/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055,Superfamily_domains:SSF51011 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 142038571 142038571 T C 1 0 0 0 0 1 0 0 0 9499 1725 60 5 5 MGAM 7 142038571 Missense_Mutation SNP T C3N-00556_T 2465428 142038571 17307402 198 16327 CASP2 0 . GRCh38 7 143300002 143300002 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.827C>T p.Ser276Leu p.S276L ENST00000310447 7/11 340 291 49 383 383 0 strelka-varscan-mutect CASP2,missense_variant,p.Ser276Leu,ENST00000310447,NM_032982.3;CASP2,3_prime_UTR_variant,,ENST00000619992,NM_032983.3;RN7SL481P,downstream_gene_variant,,ENST00000477764,;CASP2,non_coding_transcript_exon_variant,,ENST00000493642,;CASP2,3_prime_UTR_variant,,ENST00000350623,;CASP2,non_coding_transcript_exon_variant,,ENST00000472067,; T ENST00000310447 Transcript missense_variant 1068/4225 827/1359 276/452 S/L tCg/tTg 1 1 CASP2 HGNC HGNC:1503 protein_coding YES CCDS5879.1 ENSP00000312664 P42575 A0A0S2Z3H1 UPI000020F1E8 NM_032982.3 deleterious(0) 7/11 PROSITE_profiles:PS50208,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF151,PROSITE_patterns:PS01121,Pfam_domain:PF00656,PIRSF_domain:PIRSF038001,Gene3D:3.40.50.1460,SMART_domains:SM00115,Superfamily_domains:SSF52129,Prints_domain:PR00376 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 143300002 143300002 C T 1 0 0 0 0 1 0 0 0 2371 893 31 1 1 CASP2 7 143300002 Missense_Mutation SNP C C3N-00556_T 1261431 143300002 16045971 199 16328 ZNF282 0 . GRCh38 7 149198576 149198576 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.409G>A p.Glu137Lys p.E137K ENST00000610704 2/8 306 288 18 285 285 0 strelka-varscan-mutect ZNF282,missense_variant,p.Glu137Lys,ENST00000610704,NM_003575.3;ZNF282,missense_variant,p.Glu137Lys,ENST00000479907,NM_001303481.1; A ENST00000610704 Transcript missense_variant 514/3722 409/2016 137/671 E/K Gaa/Aaa 1 1 ZNF282 HGNC HGNC:13076 protein_coding YES CCDS5895.1 ENSP00000477841 Q9UDV7 A0A090N8Y3 UPI000013D255 NM_003575.3 deleterious(0) 2/8 Pfam_domain:PF12417 MODERATE 1 SNV 1 1 PASS rs750103234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 149198576 149198576 G A 1 0 0 0 0 1 0 0 0 18395 1291 45 3 3 ZNF282 7 149198576 Missense_Mutation SNP G C3N-00556_T 5898574 149198576 10147397 200 16329 MCPH1 0 . GRCh38 8 6621670 6621670 + Silent SNP C C T rs752120382 C3N-00556_T C3N-00556_N C C c.2431C>T p.= p.L811L ENST00000344683 13/14 244 231 13 395 395 0 strelka-varscan-mutect MCPH1,synonymous_variant,p.=,ENST00000344683,NM_024596.3;CTD-2541M15.3,upstream_gene_variant,,ENST00000607368,;MIR8055,downstream_gene_variant,,ENST00000610739,;MCPH1-AS1,intron_variant,,ENST00000515608,;MCPH1-AS1,intron_variant,,ENST00000522897,;MCPH1,non_coding_transcript_exon_variant,,ENST00000521175,;MCPH1,non_coding_transcript_exon_variant,,ENST00000519221,;MCPH1,downstream_gene_variant,,ENST00000521129,; T ENST00000344683 Transcript synonymous_variant 2507/8039 2431/2508 811/835 L Ctg/Ttg rs752120382,COSM1101001 1 1 MCPH1 HGNC HGNC:6954 protein_coding YES CCDS43689.1 ENSP00000342924 A0A075B6F8 UPI000020FF7E NM_024596.3 13/14 Gene3D:3.40.50.10190,Pfam_domain:PF16589,PROSITE_profiles:PS50172,hmmpanther:PTHR14625,hmmpanther:PTHR14625:SF3,SMART_domains:SM00292,Superfamily_domains:SSF52113 0,1 LOW 1 SNV 1 0,1 1 PASS rs752120382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 6621670 6621670 C T 1 0 0 0 0 0 0 0 1 9332 912 32 3 3 MCPH1 8 6621670 Silent SNP C C3N-00556_T 6621670 138516966 201 16330 RP1L1 0 . GRCh38 8 10609406 10609406 + Silent SNP C C A rs140493813 C3N-00556_T C3N-00556_N C C c.4692G>T p.= p.V1564V ENST00000382483 4/4 232 197 35 226 226 0 strelka-varscan-mutect RP1L1,synonymous_variant,p.=,ENST00000382483,NM_178857.5; A ENST00000382483 Transcript synonymous_variant 4916/7973 4692/7203 1564/2400 V gtG/gtT rs140493813 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 LOW 1 SNV 1 1 PASS rs140493813 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 10609406 10609406 C A 1 0 0 0 0 0 0 0 1 13773 581 21 2 2 RP1L1 8 10609406 Silent SNP C C3N-00556_T 3987736 10609406 134529230 202 16331 SLC18A1 0 . GRCh38 8 20174394 20174394 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.598C>T p.Gln200Ter p.Q200* ENST00000440926 6/17 228 211 17 274 274 0 strelka-varscan-mutect SLC18A1,stop_gained,p.Gln200Ter,ENST00000440926,NM_001135691.2;SLC18A1,stop_gained,p.Gln200Ter,ENST00000437980,NM_001142325.1;SLC18A1,stop_gained,p.Gln200Ter,ENST00000265808,NM_001142324.1;SLC18A1,stop_gained,p.Gln200Ter,ENST00000276373,NM_003053.3;SLC18A1,stop_gained,p.Gln200Ter,ENST00000519026,;SLC18A1,stop_gained,p.Gln200Ter,ENST00000381608,;SLC18A1,intron_variant,,ENST00000522513,;SLC18A1,non_coding_transcript_exon_variant,,ENST00000524272,;SLC18A1,stop_gained,p.Gln200Ter,ENST00000517776,; A ENST00000440926 Transcript stop_gained 1069/2956 598/1578 200/525 Q/* Caa/Taa 1 -1 SLC18A1 HGNC HGNC:10934 protein_coding YES CCDS6013.1 ENSP00000387549 P54219 UPI00001389CE NM_001135691.2 6/17 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23506:SF15,hmmpanther:PTHR23506,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00880,Pfam_domain:PF07690,Superfamily_domains:SSF103473 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 20174394 20174394 G A 1 0 0 0 0 0 1 0 0 14690 1299 45 3 3 SLC18A1 8 20174394 Nonsense_Mutation SNP G C3N-00556_T 9564988 20174394 124964242 203 16332 PNMA2 0 . GRCh38 8 26508455 26508455 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.301G>C p.Glu101Gln p.E101Q ENST00000522362 3/3 228 197 31 282 282 0 strelka-varscan-mutect PNMA2,missense_variant,p.Glu101Gln,ENST00000522362,NM_007257.5;BNIP3L,downstream_gene_variant,,ENST00000523949,;PNMA2,downstream_gene_variant,,ENST00000522764,;PNMA2,downstream_gene_variant,,ENST00000523244,;PNMA2,downstream_gene_variant,,ENST00000518212,;PNMA2,downstream_gene_variant,,ENST00000521875,;PNMA2,downstream_gene_variant,,ENST00000522450,;PNMA2,downstream_gene_variant,,ENST00000521740,;PNMA2,downstream_gene_variant,,ENST00000523616,; G ENST00000522362 Transcript missense_variant 1196/4965 301/1095 101/364 E/Q Gag/Cag 1 -1 PNMA2 HGNC HGNC:9159 protein_coding YES CCDS34868.1 ENSP00000429344 Q9UL42 UPI0000073D3F NM_007257.5 deleterious(0.02) 3/3 Pfam_domain:PF14893,hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 26508455 26508455 C G 1 0 0 0 0 1 0 0 0 12261 835 29 4 4 PNMA2 8 26508455 Missense_Mutation SNP C C3N-00556_T 6334061 26508455 118630181 204 16333 PLPP5 0 . GRCh38 8 38267910 38267910 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.325C>G p.Leu109Val p.L109V ENST00000424479 4/7 125 109 16 154 154 0 strelka-mutect PLPP5,missense_variant,p.Leu68Val,ENST00000529359,;PLPP5,missense_variant,p.Leu109Val,ENST00000424479,NM_001102559.1;PLPP5,missense_variant,p.Leu109Val,ENST00000422581,NM_032483.3;PLPP5,missense_variant,p.Leu90Val,ENST00000524616,;PLPP5,missense_variant,p.Leu109Val,ENST00000419686,NM_001102560.1;PLPP5,missense_variant,p.Leu103Val,ENST00000534339,;PLPP5,5_prime_UTR_variant,,ENST00000531823,;WHSC1L1,downstream_gene_variant,,ENST00000317025,NM_023034.1;PLPP5,non_coding_transcript_exon_variant,,ENST00000527793,;DDHD2,intron_variant,,ENST00000529872,;DDHD2,intron_variant,,ENST00000526071,;PLPP5,upstream_gene_variant,,ENST00000531483,;PLPP5,upstream_gene_variant,,ENST00000530193,;PLPP5,upstream_gene_variant,,ENST00000527758,;PLPP5,3_prime_UTR_variant,,ENST00000531109,;PLPP5,non_coding_transcript_exon_variant,,ENST00000528814,;PLPP5,upstream_gene_variant,,ENST00000530432,;PLPP5,downstream_gene_variant,,ENST00000524409,; C ENST00000424479 Transcript missense_variant 346/2130 325/795 109/264 L/V Ctg/Gtg 1 -1 PLPP5 HGNC HGNC:25026 protein_coding YES CCDS47841.1 ENSP00000392553 Q8NEB5 A0A140VK38 UPI000044C28E NM_001102559.1 tolerated(0.13) 4/7 Gene3D:1.20.144.10,Pfam_domain:PF01569,hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF87,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 38267910 38267910 G C 1 0 0 0 0 1 0 0 0 12206 1020 36 4 4 PLPP5 8 38267910 Missense_Mutation SNP G C3N-00556_T 11759455 38267910 106870726 205 16334 NSMAF 0 . GRCh38 8 58599750 58599750 + Missense_Mutation SNP T T G novel C3N-00556_T C3N-00556_N T T c.1546A>C p.Ser516Arg p.S516R ENST00000427130 18/31 150 142 8 139 139 0 varscan-mutect NSMAF,missense_variant,p.Ser485Arg,ENST00000038176,NM_003580.3;NSMAF,missense_variant,p.Ser516Arg,ENST00000427130,NM_001144772.1;NSMAF,splice_region_variant,,ENST00000523982,;NSMAF,downstream_gene_variant,,ENST00000519858,;NSMAF,upstream_gene_variant,,ENST00000523177,;NSMAF,splice_region_variant,,ENST00000519227,;NSMAF,upstream_gene_variant,,ENST00000523106,;NSMAF,upstream_gene_variant,,ENST00000524148,; G ENST00000427130 Transcript missense_variant,splice_region_variant 1734/3371 1546/2847 516/948 S/R Agt/Cgt 1 -1 NSMAF HGNC HGNC:8017 protein_coding YES CCDS47864.1 ENSP00000411012 Q92636 UPI000192950C NM_001144772.1 tolerated(0.07) 18/31 PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF53,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 58599750 58599750 T G 1 0 0 0 0 1 0 0 0 10734 1594 55 5 5 NSMAF 8 58599750 Missense_Mutation SNP T C3N-00556_T 20331840 58599750 86538886 206 16335 PREX2 0 . GRCh38 8 68224585 68224585 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.4734G>A p.= p.K1578K ENST00000288368 39/40 242 222 20 257 256 1 strelka-varscan-mutect PREX2,synonymous_variant,p.=,ENST00000288368,NM_024870.2;Y_RNA,upstream_gene_variant,,ENST00000516401,;PREX2,downstream_gene_variant,,ENST00000520235,; A ENST00000288368 Transcript synonymous_variant 5011/10750 4734/4821 1578/1606 K aaG/aaA COSM1221965,COSM231667 1 1 PREX2 HGNC HGNC:22950 protein_coding YES CCDS6201.1 ENSP00000288368 Q70Z35 UPI0000375435 NM_024870.2 39/40 hmmpanther:PTHR22829:SF1,hmmpanther:PTHR22829 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 68224585 68224585 G A 1 0 0 0 0 0 0 0 1 12611 933 33 3 3 PREX2 8 68224585 Silent SNP G C3N-00556_T 9624835 68224585 76914051 207 16336 TRPA1 0 . GRCh38 8 72055563 72055563 + Missense_Mutation SNP C C T rs756082155 C3N-00556_T C3N-00556_N C C c.1402G>A p.Asp468Asn p.D468N ENST00000262209 12/27 272 233 39 312 312 0 strelka-varscan-mutect TRPA1,missense_variant,p.Asp468Asn,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Asp320Asn,ENST00000523582,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000457356,;MSC-AS1,non_coding_transcript_exon_variant,,ENST00000519068,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;MSC-AS1,downstream_gene_variant,,ENST00000519751,;MSC-AS1,downstream_gene_variant,,ENST00000524152,;TRPA1,upstream_gene_variant,,ENST00000520788,; T ENST00000262209 Transcript missense_variant 1610/5223 1402/3360 468/1119 D/N Gac/Aac rs756082155 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 tolerated(0.19) 12/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs756082155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 72055563 72055563 C T 1 0 0 0 0 1 0 0 0 17082 913 32 3 3 TRPA1 8 72055563 Missense_Mutation SNP C C3N-00556_T 3830978 72055563 73083073 208 16337 RDH10 0 . GRCh38 8 73297238 73297238 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.334G>A p.Val112Ile p.V112I ENST00000240285 2/6 351 330 21 328 328 0 strelka-varscan-mutect RDH10,missense_variant,p.Val112Ile,ENST00000240285,NM_172037.4;RDH10,5_prime_UTR_variant,,ENST00000519380,;RDH10,5_prime_UTR_variant,,ENST00000521928,;RPL7,upstream_gene_variant,,ENST00000396467,;RPL7,upstream_gene_variant,,ENST00000396465,;RPL7,upstream_gene_variant,,ENST00000352983,NM_000971.3;RPL7,upstream_gene_variant,,ENST00000396466,;RPL7,upstream_gene_variant,,ENST00000431653,;RPL7,upstream_gene_variant,,ENST00000435330,;RDH10-AS1,downstream_gene_variant,,ENST00000520894,;RDH10,non_coding_transcript_exon_variant,,ENST00000518870,; A ENST00000240285 Transcript missense_variant 1012/3949 334/1026 112/341 V/I Gtt/Att 1 1 RDH10 HGNC HGNC:19975 protein_coding YES CCDS6213.1 ENSP00000240285 Q8IZV5 A0A024R7X6 UPI0000054C83 NM_172037.4 deleterious(0.03) 2/6 hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF466,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 73297238 73297238 G A 1 0 0 0 0 1 0 0 0 13358 1261 44 3 3 RDH10 8 73297238 Missense_Mutation SNP G C3N-00556_T 1241675 73297238 71841398 209 16338 ZFHX4 0 . GRCh38 8 76855426 76855426 + Silent SNP G G T C3N-00556_T C3N-00556_N G G c.8505G>T p.= p.P2835P ENST00000521891 10/11 150 105 45 138 138 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; T ENST00000521891 Transcript synonymous_variant 8953/14019 8505/10851 2835/3616 P ccG/ccT COSM1101807,COSM751701 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 76855426 76855426 G T 1 0 0 0 0 0 0 0 1 18213 1103 39 1 1 ZFHX4 8 76855426 Silent SNP G C3N-00556_T 3558188 76855426 68283210 210 16339 OSGIN2 0 . GRCh38 8 89914155 89914155 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.278C>G p.Pro93Arg p.P93R ENST00000451899 3/6 209 192 17 162 162 0 strelka-varscan-mutect OSGIN2,missense_variant,p.Pro93Arg,ENST00000451899,NM_001126111.1;OSGIN2,missense_variant,p.Pro49Arg,ENST00000297438,NM_004337.2;OSGIN2,missense_variant,p.Pro93Arg,ENST00000520659,; G ENST00000451899 Transcript missense_variant 538/4266 278/1650 93/549 P/R cCa/cGa 1 1 OSGIN2 HGNC HGNC:1355 protein_coding YES CCDS47888.1 ENSP00000396445 Q9Y236 UPI0000E5AF0B NM_001126111.1 deleterious(0) 3/6 Gene3D:3.50.50.60,hmmpanther:PTHR15192,hmmpanther:PTHR15192:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 89914155 89914155 C G 1 0 0 0 0 1 0 0 0 11357 594 21 4 4 OSGIN2 8 89914155 Missense_Mutation SNP C C3N-00556_T 13058729 89914155 55224481 211 16340 SLC25A32 0 . GRCh38 8 103401989 103401989 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.618G>A p.= p.L206L ENST00000297578 5/7 205 194 11 193 193 0 strelka-varscan SLC25A32,synonymous_variant,p.=,ENST00000297578,NM_030780.4;SLC25A32,non_coding_transcript_exon_variant,,ENST00000523701,;SLC25A32,stop_retained_variant,p.=,ENST00000523256,;SLC25A32,3_prime_UTR_variant,,ENST00000521645,;SLC25A32,3_prime_UTR_variant,,ENST00000523866,; T ENST00000297578 Transcript synonymous_variant 785/2891 618/948 206/315 L ctG/ctA 1 -1 SLC25A32 HGNC HGNC:29683 protein_coding YES CCDS6300.1 ENSP00000297578 Q9H2D1 A0A024R9D0 UPI0000040C0F NM_030780.4 5/7 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF62 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 103401989 103401989 C T 1 0 0 0 0 0 0 0 1 14761 813 29 3 3 SLC25A32 8 103401989 Silent SNP C C3N-00556_T 13487834 103401989 41736647 212 16341 DCAF13 0 . GRCh38 8 103415514 103415514 + Missense_Mutation SNP G G C rs149094412 C3N-00556_T C3N-00556_N G G c.524G>C p.Arg175Thr p.R175T ENST00000297579 1/11 61 57 4 69 69 0 strelka-varscan-mutect DCAF13,missense_variant,p.Arg175Thr,ENST00000297579,NM_015420.6;DCAF13,missense_variant,p.Arg175Thr,ENST00000616836,;DCAF13,missense_variant,p.Arg23Thr,ENST00000521971,;DCAF13,missense_variant,p.Arg23Thr,ENST00000618975,;DCAF13,missense_variant,p.Arg23Thr,ENST00000612750,;DCAF13,missense_variant,p.Arg23Thr,ENST00000519682,;DCAF13,splice_region_variant,,ENST00000521999,;SLC25A32,upstream_gene_variant,,ENST00000297578,NM_030780.4;DCAF13,splice_region_variant,,ENST00000518554,;DCAF13,splice_region_variant,,ENST00000521716,;SLC25A32,upstream_gene_variant,,ENST00000521645,;SLC25A32,upstream_gene_variant,,ENST00000523256,;SLC25A32,upstream_gene_variant,,ENST00000523866,; C ENST00000297579 Transcript missense_variant,splice_region_variant 801/2642 524/1794 175/597 R/T aGa/aCa rs149094412 1 1 DCAF13 HGNC HGNC:24535 protein_coding YES CCDS34934.1 ENSP00000297579 A0A087WT20 UPI0000DBEF2A NM_015420.6 deleterious(0.01) 1/11 hmmpanther:PTHR22851,hmmpanther:PTHR22851:SF0,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs149094412 . 0 208 2 0 0 0 0 0 -10.23084 1 1 1 1 0 C 3 2 54 103415514 103415514 G C 1 0 0 0 0 1 0 0 0 4067 956 33 4 4 DCAF13 8 103415514 Missense_Mutation SNP G C3N-00556_T 13525 103415514 41723122 213 16342 PKHD1L1 0 . GRCh38 8 109475133 109475133 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.8621C>A p.Pro2874Gln p.P2874Q ENST00000378402 51/78 107 96 11 100 99 1 strelka-varscan-mutect PKHD1L1,missense_variant,p.Pro2874Gln,ENST00000378402,NM_177531.4;RP11-419L20.2,downstream_gene_variant,,ENST00000518703,; A ENST00000378402 Transcript missense_variant 8725/13076 8621/12732 2874/4243 P/Q cCa/cAa 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0.01) 51/78 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF330 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99789 1 1 1 1 0 A 3 1 54 109475133 109475133 C A 1 0 0 0 0 1 0 0 0 12068 594 21 2 2 PKHD1L1 8 109475133 Missense_Mutation SNP C C3N-00556_T 6059619 109475133 35663503 214 16343 PKHD1L1 0 . GRCh38 8 109504446 109504446 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.10948G>A p.Asp3650Asn p.D3650N ENST00000378402 68/78 65 53 12 83 83 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Asp3650Asn,ENST00000378402,NM_177531.4;PKHD1L1,missense_variant,p.Asp578Asn,ENST00000526472,; A ENST00000378402 Transcript missense_variant 11052/13076 10948/12732 3650/4243 D/N Gat/Aat 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 tolerated(0.35) 68/78 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF330 MODERATE 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 109504446 109504446 G A 1 0 0 0 0 1 0 0 0 12068 1290 45 3 3 PKHD1L1 8 109504446 Missense_Mutation SNP G C3N-00556_T 29313 109504446 35634190 215 16344 CSMD3 0 . GRCh38 8 112517144 112517144 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.4646C>G p.Thr1549Ser p.T1549S ENST00000297405 28/71 270 240 30 291 291 0 strelka-varscan-mutect CSMD3,missense_variant,p.Thr1549Ser,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Thr1509Ser,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Thr1445Ser,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Thr889Ser,ENST00000339701,; C ENST00000297405 Transcript missense_variant 4891/13212 4646/11124 1549/3707 T/S aCt/aGt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.89) 28/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs1354758891 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 112517144 112517144 G C 1 0 0 0 0 1 0 0 0 3747 1029 36 4 4 CSMD3 8 112517144 Missense_Mutation SNP G C3N-00556_T 3012698 112517144 32621492 216 16345 CSMD3 0 . GRCh38 8 113019132 113019132 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.965G>T p.Trp322Leu p.W322L ENST00000297405 6/71 309 213 96 313 311 2 strelka-varscan-mutect CSMD3,missense_variant,p.Trp322Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Trp282Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Trp322Leu,ENST00000455883,NM_052900.2;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,; A ENST00000297405 Transcript missense_variant 1210/13212 965/11124 322/3707 W/L tGg/tTg 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.38) 6/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 113019132 113019132 C A 1 0 0 0 0 1 0 0 0 3747 595 21 2 2 CSMD3 8 113019132 Missense_Mutation SNP C C3N-00556_T 501988 113019132 32119504 217 16346 TRPS1 0 . GRCh38 8 115414465 115414465 + Missense_Mutation SNP G G A rs376813799 C3N-00556_T C3N-00556_N G G c.3443C>T p.Pro1148Leu p.P1148L ENST00000395715 7/7 245 169 76 313 312 1 strelka-varscan-mutect TRPS1,missense_variant,p.Pro1148Leu,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Pro1135Leu,ENST00000220888,;TRPS1,missense_variant,p.Pro1139Leu,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Pro889Leu,ENST00000519076,;TRPS1,missense_variant,p.Pro260Leu,ENST00000518018,; A ENST00000395715 Transcript missense_variant 4021/9990 3443/3885 1148/1294 P/L cCa/cTa rs376813799 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 deleterious_low_confidence(0.01) 7/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176 MODERATE 1 SNV 1 1 PASS rs376813799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 115414465 115414465 G A 1 0 0 0 0 1 0 0 0 17099 1348 47 3 3 TRPS1 8 115414465 Missense_Mutation SNP G C3N-00556_T 2395333 115414465 29724171 218 16347 TBC1D31 0 . GRCh38 8 123129115 123129115 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.2167G>C p.Asp723His p.D723H ENST00000287380 15/22 129 111 18 106 106 0 strelka-varscan-mutect TBC1D31,missense_variant,p.Asp723His,ENST00000287380,NM_145647.3;TBC1D31,missense_variant,p.Asp600His,ENST00000521676,;TBC1D31,missense_variant,p.Asp618His,ENST00000522420,;TBC1D31,missense_variant,p.Asp723His,ENST00000327098,NM_001145088.1;TBC1D31,missense_variant,p.Asp277His,ENST00000518805,;TBC1D31,3_prime_UTR_variant,,ENST00000524307,;TBC1D31,3_prime_UTR_variant,,ENST00000518577,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000518866,; C ENST00000287380 Transcript missense_variant 2257/3502 2167/3201 723/1066 D/H Gat/Cat 1 1 TBC1D31 HGNC HGNC:30888 protein_coding YES CCDS6338.1 ENSP00000287380 Q96DN5 UPI000013DEAB NM_145647.3 deleterious(0) 15/22 hmmpanther:PTHR19853:SF1,hmmpanther:PTHR19853 MODERATE 1 SNV 1 1 PASS rs1202482451 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 123129115 123129115 G C 1 0 0 0 0 1 0 0 0 16021 942 33 4 4 TBC1D31 8 123129115 Missense_Mutation SNP G C3N-00556_T 7714650 123129115 22009521 219 16348 MFSD3 0 . GRCh38 8 144510634 144510634 + Missense_Mutation SNP C C G rs766400259 C3N-00556_T C3N-00556_N C C c.867C>G p.Phe289Leu p.F289L ENST00000301327 3/5 49 44 5 56 56 0 strelka-mutect MFSD3,missense_variant,p.Phe289Leu,ENST00000301327,NM_138431.2;RECQL4,downstream_gene_variant,,ENST00000621189,;RECQL4,downstream_gene_variant,,ENST00000617875,NM_004260.3;GPT,downstream_gene_variant,,ENST00000394955,NM_005309.2;GPT,downstream_gene_variant,,ENST00000528431,;RECQL4,downstream_gene_variant,,ENST00000534626,;RECQL4,downstream_gene_variant,,ENST00000532846,;RECQL4,downstream_gene_variant,,ENST00000531875,;CTD-2517M22.17,upstream_gene_variant,,ENST00000580385,;RECQL4,downstream_gene_variant,,ENST00000529424,;MFSD3,non_coding_transcript_exon_variant,,ENST00000528047,;MFSD3,non_coding_transcript_exon_variant,,ENST00000526749,;MFSD3,non_coding_transcript_exon_variant,,ENST00000534427,;GPT,downstream_gene_variant,,ENST00000527165,;GPT,downstream_gene_variant,,ENST00000534702,;RECQL4,downstream_gene_variant,,ENST00000301323,; G ENST00000301327 Transcript missense_variant 1127/1548 867/1239 289/412 F/L ttC/ttG rs766400259,COSM5299337 1 1 MFSD3 HGNC HGNC:25157 protein_coding YES CCDS6431.1 ENSP00000301327 Q96ES6 UPI0000072E5F NM_138431.2 tolerated(1) 3/5 hmmpanther:PTHR12778,hmmpanther:PTHR12778:SF10,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs766400259 . 0 205 5 0 0 0 0 0 -12.43849 1 1 1 1 0 G 3 3 54 144510634 144510634 C G 1 0 0 0 0 1 0 0 0 9489 854 30 4 4 MFSD3 8 144510634 Missense_Mutation SNP C C3N-00556_T 21381519 144510634 628002 220 16349 MPDZ 0 . GRCh38 9 13196186 13196186 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1591C>A p.Gln531Lys p.Q531K ENST00000541718 13/46 167 157 10 187 187 0 strelka-varscan-mutect MPDZ,missense_variant,p.Gln531Lys,ENST00000319217,;MPDZ,missense_variant,p.Gln531Lys,ENST00000541718,NM_003829.4;MPDZ,missense_variant,p.Gln531Lys,ENST00000381022,NM_001261406.1;MPDZ,missense_variant,p.Gln531Lys,ENST00000546205,;MPDZ,missense_variant,p.Gln531Lys,ENST00000447879,;MPDZ,missense_variant,p.Gln531Lys,ENST00000536827,NM_001261407.1; T ENST00000541718 Transcript missense_variant 1813/7603 1591/6126 531/2041 Q/K Caa/Aaa 1 -1 MPDZ HGNC HGNC:7208 protein_coding YES CCDS47951.1 ENSP00000439807 O75970 UPI00015367D3 NM_003829.4 tolerated(0.8) 13/46 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF10 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -12.83039 0.9972851 1 1 1 0 T 3 4 54 13196186 13196186 G T 1 0 0 0 0 1 0 0 0 9687 1386 48 2 2 MPDZ 9 13196186 Missense_Mutation SNP G C3N-00556_T 13196186 125198531 221 16350 TEK 0 . GRCh38 9 27229218 27229218 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.3361G>A p.Glu1121Lys p.E1121K ENST00000380036 23/23 466 437 29 449 449 0 strelka-varscan-mutect TEK,missense_variant,p.Glu1121Lys,ENST00000380036,NM_000459.4;TEK,missense_variant,p.Glu1078Lys,ENST00000406359,NM_001290077.1;TEK,missense_variant,p.Glu973Lys,ENST00000519097,NM_001290078.1;TEK,3_prime_UTR_variant,,ENST00000615002,; A ENST00000380036 Transcript missense_variant 3803/4760 3361/3375 1121/1124 E/K Gaa/Aaa 1 1 TEK HGNC HGNC:11724 protein_coding YES CCDS6519.1 ENSP00000369375 Q02763 UPI000021121E NM_000459.4 deleterious(0) 23/23 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF125 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 27229218 27229218 G A 1 0 0 0 0 1 0 0 0 16163 1291 45 3 3 TEK 9 27229218 Missense_Mutation SNP G C3N-00556_T 14033032 27229218 111165499 222 16351 LINGO2 0 . GRCh38 9 27950618 27950618 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.54G>T p.= p.V18V ENST00000379992 6/6 14 6 8 22 22 0 strelka-mutect LINGO2,synonymous_variant,p.=,ENST00000379992,NM_152570.2,NM_001258282.1;LINGO2,synonymous_variant,p.=,ENST00000308675,;LINGO2,synonymous_variant,p.=,ENST00000613945,; A ENST00000379992 Transcript synonymous_variant 504/3044 54/1821 18/606 V gtG/gtT 1 -1 LINGO2 HGNC HGNC:21207 protein_coding YES CCDS6524.1 ENSP00000369328 Q7L985 UPI000004C7CD NM_152570.2,NM_001258282.1 6/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF38,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 43 165 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 27950618 27950618 C A 1 0 0 0 0 0 0 0 1 8736 465 17 2 2 LINGO2 9 27950618 Silent SNP C C3N-00556_T 721400 27950618 110444099 223 16352 ANKRD18A 0 . GRCh38 9 38595708 38595708 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1632G>C p.Glu544Asp p.E544D ENST00000399703 9/16 174 157 17 191 191 0 strelka-varscan-mutect ANKRD18A,missense_variant,p.Glu544Asp,ENST00000399703,NM_147195.2;ANKRD18A,upstream_gene_variant,,ENST00000602295,; G ENST00000399703 Transcript missense_variant 2007/4041 1632/2979 544/992 E/D gaG/gaC 1 -1 ANKRD18A HGNC HGNC:23643 protein_coding YES CCDS55311.1 ENSP00000382610 Q8IVF6 UPI00001AF4AF NM_147195.2 deleterious(0.01) 9/16 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF27,hmmpanther:PTHR24147,Pfam_domain:PF14915 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 38595708 38595708 C G 1 0 0 0 0 1 0 0 0 748 912 32 4 4 ANKRD18A 9 38595708 Missense_Mutation SNP C C3N-00556_T 10645090 38595708 99799009 224 16353 FOXD4L4 0 . GRCh38 9 65738091 65738091 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.946C>T p.Arg316Cys p.R316C ENST00000377413 1/1 607 570 37 652 651 1 varscan-mutect FOXD4L4,missense_variant,p.Arg316Cys,ENST00000377413,NM_199244.3;CBWD5,downstream_gene_variant,,ENST00000377392,NM_001286835.1;CBWD5,downstream_gene_variant,,ENST00000382405,;CBWD5,downstream_gene_variant,,ENST00000430059,;CBWD5,downstream_gene_variant,,ENST00000429800,;CBWD5,downstream_gene_variant,,ENST00000377395,NM_001024916.3;CBWD5,downstream_gene_variant,,ENST00000489273,;CBWD5,downstream_gene_variant,,ENST00000476797,;CBWD5,downstream_gene_variant,,ENST00000468066,;CBWD5,downstream_gene_variant,,ENST00000486191,;CBWD5,downstream_gene_variant,,ENST00000485088,;CBWD5,downstream_gene_variant,,ENST00000461932,;CBWD5,downstream_gene_variant,,ENST00000480229,;CBWD5,downstream_gene_variant,,ENST00000377389,;CBWD5,downstream_gene_variant,,ENST00000486221,;CBWD5,downstream_gene_variant,,ENST00000497250,;CBWD5,downstream_gene_variant,,ENST00000463075,;CBWD5,downstream_gene_variant,,ENST00000491485,;CBWD5,downstream_gene_variant,,ENST00000480819,; T ENST00000377413 Transcript missense_variant 1537/2230 946/1251 316/416 R/C Cgc/Tgc 1 1 FOXD4L4 HGNC HGNC:23762 protein_coding YES CCDS75845.1 ENSP00000366630 Q8WXT5 UPI0000246F14 NM_199244.3 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 65738091 65738091 C T 1 0 0 0 0 1 0 0 0 5862 884 31 1 1 FOXD4L4 9 65738091 Missense_Mutation SNP C C3N-00556_T 27142383 65738091 72656626 225 16354 TRPM6 0 . GRCh38 9 74786048 74786048 + Silent SNP A A G novel C3N-00556_T C3N-00556_N A A c.2745T>C p.= p.T915T ENST00000360774 21/39 257 241 16 313 312 1 strelka-varscan-mutect TRPM6,synonymous_variant,p.=,ENST00000360774,NM_017662.4;TRPM6,synonymous_variant,p.=,ENST00000361255,NM_001177311.1;TRPM6,synonymous_variant,p.=,ENST00000449912,NM_001177310.1; G ENST00000360774 Transcript synonymous_variant 2983/8425 2745/6069 915/2022 T acT/acC 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 21/39 Pfam_domain:PF00520,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 74786048 74786048 A G 1 0 0 0 0 0 0 0 1 17096 175 7 5 5 TRPM6 9 74786048 Silent SNP A C3N-00556_T 9047957 74786048 63608669 226 16355 GCNT1 0 . GRCh38 9 76503404 76503404 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1023G>T p.Lys341Asn p.K341N ENST00000442371 3/3 232 179 53 316 315 1 strelka-varscan-mutect GCNT1,missense_variant,p.Lys341Asn,ENST00000442371,NM_001097634.1;GCNT1,missense_variant,p.Lys341Asn,ENST00000376730,NM_001490.4;GCNT1,missense_variant,p.Lys341Asn,ENST00000444201,NM_001097633.1,NM_001097635.1,NM_001097636.1;GCNT1,downstream_gene_variant,,ENST00000488136,;GCNT1,downstream_gene_variant,,ENST00000480311,; T ENST00000442371 Transcript missense_variant 1962/5972 1023/1287 341/428 K/N aaG/aaT 1 1 GCNT1 HGNC HGNC:4203 protein_coding YES CCDS6653.1 ENSP00000415454 Q02742 UPI000013CF63 NM_001097634.1 deleterious(0) 3/3 Pfam_domain:PF02485,hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF81 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 76503404 76503404 G T 1 0 0 0 0 1 0 0 0 6170 1020 36 2 2 GCNT1 9 76503404 Missense_Mutation SNP G C3N-00556_T 1717356 76503404 61891313 227 16356 NTRK2 0 . GRCh38 9 84707854 84707854 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.370C>T p.Arg124Ter p.R124* ENST00000277120 5/19 125 103 22 198 198 0 strelka-varscan-mutect NTRK2,stop_gained,p.Arg124Ter,ENST00000277120,;NTRK2,stop_gained,p.Arg124Ter,ENST00000304053,NM_001018065.2;NTRK2,stop_gained,p.Arg124Ter,ENST00000376208,NM_001018066.2;NTRK2,stop_gained,p.Arg124Ter,ENST00000395882,NM_001291937.1,NM_001007097.2;NTRK2,stop_gained,p.Arg124Ter,ENST00000359847,;NTRK2,stop_gained,p.Arg124Ter,ENST00000376214,NM_006180.4;NTRK2,stop_gained,p.Arg124Ter,ENST00000376213,;NTRK2,stop_gained,p.Arg124Ter,ENST00000323115,NM_001018064.2; T ENST00000277120 Transcript stop_gained 853/8633 370/2517 124/838 R/* Cga/Tga 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D 5/19 Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF136,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS rs1229434307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 84707854 84707854 C T 1 0 0 0 0 0 1 0 0 10773 644 23 1 1 NTRK2 9 84707854 Nonsense_Mutation SNP C C3N-00556_T 8204450 84707854 53686863 228 16357 SPTLC1 0 . GRCh38 9 92080070 92080070 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.373C>G p.Leu125Val p.L125V ENST00000262554 5/15 295 226 69 369 369 0 strelka-varscan-mutect SPTLC1,missense_variant,p.Leu125Val,ENST00000262554,NM_006415.3,NM_001281303.1;SPTLC1,missense_variant,p.Leu125Val,ENST00000337841,NM_178324.2;SPTLC1,non_coding_transcript_exon_variant,,ENST00000482632,;SPTLC1,non_coding_transcript_exon_variant,,ENST00000477888,; C ENST00000262554 Transcript missense_variant 379/1894 373/1422 125/473 L/V Cta/Gta 1 -1 SPTLC1 HGNC HGNC:11277 protein_coding YES CCDS6692.1 ENSP00000262554 O15269 A0A024R277 UPI000012E27B NM_006415.3,NM_001281303.1 tolerated(0.23) 5/15 hmmpanther:PTHR13693:SF2,hmmpanther:PTHR13693,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 92080070 92080070 G C 1 0 0 0 0 1 0 0 0 15479 933 33 4 4 SPTLC1 9 92080070 Missense_Mutation SNP G C3N-00556_T 7372216 92080070 46314647 229 16358 GABBR2 0 . GRCh38 9 98388944 98388944 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1439C>A p.Pro480His p.P480H ENST00000259455 10/19 137 112 25 139 139 0 strelka-varscan-mutect GABBR2,missense_variant,p.Pro480His,ENST00000259455,NM_005458.7;GABBR2,non_coding_transcript_exon_variant,,ENST00000637410,;GABBR2,upstream_gene_variant,,ENST00000634314,; T ENST00000259455 Transcript missense_variant 1899/5788 1439/2826 480/941 P/H cCt/cAt 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 tolerated(0.08) 10/19 hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF40 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 98388944 98388944 G T 1 0 0 0 0 1 0 0 0 6027 1000 35 2 2 GABBR2 9 98388944 Missense_Mutation SNP G C3N-00556_T 6308874 98388944 40005773 230 16359 FRRS1L 0 . GRCh38 9 109137604 109137604 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.886G>C p.Asp296His p.D296H ENST00000561981 5/5 64 59 5 77 77 0 strelka-varscan-mutect FRRS1L,missense_variant,p.Asp296His,ENST00000561981,NM_014334.2; G ENST00000561981 Transcript missense_variant 886/8197 886/1035 296/344 D/H Gac/Cac 1 -1 FRRS1L HGNC HGNC:1362 protein_coding YES CCDS35098.1 ENSP00000477141 Q9P0K9 UPI000013D040 NM_014334.2 deleterious(0.01) 5/5 hmmpanther:PTHR23130,hmmpanther:PTHR23130:SF65 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.12618 1 1 1 1 0 G 3 3 54 109137604 109137604 C G 1 0 0 0 0 1 0 0 0 5932 913 32 4 4 FRRS1L 9 109137604 Missense_Mutation SNP C C3N-00556_T 10748660 109137604 29257113 231 16360 PALM2 0 . GRCh38 9 109923739 109923739 + Missense_Mutation SNP G G C C3N-00556_T C3N-00556_N G G c.262G>C p.Glu88Gln p.E88Q ENST00000374530 4/11 148 140 8 163 163 0 strelka-varscan-mutect PALM2-AKAP2,missense_variant,p.Glu88Gln,ENST00000374530,NM_007203.4;PALM2-AKAP2,missense_variant,p.Glu88Gln,ENST00000302798,NM_147150.2;PALM2,missense_variant,p.Glu90Gln,ENST00000374531,NM_001037293.2;PALM2,missense_variant,p.Glu88Gln,ENST00000483909,;PALM2-AKAP2,missense_variant,p.Glu88Gln,ENST00000413420,;PALM2,missense_variant,p.Glu88Gln,ENST00000314527,NM_053016.5;PALM2,missense_variant,p.Glu74Gln,ENST00000497711,;PALM2,non_coding_transcript_exon_variant,,ENST00000465091,; C ENST00000374530 Transcript missense_variant 442/7507 262/3312 88/1103 E/Q Gag/Cag COSM3652761,COSM3652762 1 1 PALM2-AKAP2 HGNC HGNC:33529 protein_coding YES CCDS35100.1 ENSP00000363654 UPI0000125755 NM_007203.4 deleterious_low_confidence(0.01) 4/11 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF03285,hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF10 1,1 MODERATE SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 109923739 109923739 G C 1 0 0 0 0 1 0 0 0 11489 1188 41 4 4 PALM2 9 109923739 Missense_Mutation SNP G C3N-00556_T 786135 109923739 28470978 232 16361 PALM2 0 . GRCh38 9 109943379 109943379 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1190C>A p.Pro397Gln p.P397Q ENST00000314527 7/7 120 94 26 149 149 0 strelka-varscan-mutect PALM2,missense_variant,p.Pro365Gln,ENST00000374531,NM_001037293.2;PALM2,missense_variant,p.Pro363Gln,ENST00000483909,;PALM2-AKAP2,missense_variant,p.Pro397Gln,ENST00000413420,;PALM2,missense_variant,p.Pro397Gln,ENST00000314527,NM_053016.5;PALM2-AKAP2,intron_variant,,ENST00000374530,NM_007203.4;PALM2-AKAP2,intron_variant,,ENST00000302798,NM_147150.2;PALM2,downstream_gene_variant,,ENST00000497711,; A ENST00000314527 Transcript missense_variant 1240/1332 1190/1236 397/411 P/Q cCa/cAa 1 1 PALM2 HGNC HGNC:15845 protein_coding YES CCDS48002.2 ENSP00000323805 Q8IXS6 UPI0000071924 NM_053016.5 tolerated(0.18) 7/7 Pfam_domain:PF03285,hmmpanther:PTHR10498 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 109943379 109943379 C A 1 0 0 0 0 1 0 0 0 11489 594 21 2 2 PALM2 9 109943379 Missense_Mutation SNP C C3N-00556_T 19640 109943379 28451338 233 16362 MUSK 0 . GRCh38 9 110800824 110800824 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.2446C>A p.= p.R816R ENST00000374448 15/15 72 47 25 154 153 1 strelka-varscan-mutect MUSK,synonymous_variant,p.=,ENST00000416899,;MUSK,synonymous_variant,p.=,ENST00000374448,NM_005592.3;MUSK,synonymous_variant,p.=,ENST00000189978,NM_001166281.1,NM_001166280.1;MUSK,synonymous_variant,p.=,ENST00000374440,; A ENST00000374448 Transcript synonymous_variant 2580/2754 2446/2610 816/869 R Cga/Aga 1 1 MUSK HGNC HGNC:7525 protein_coding YES CCDS48005.1 ENSP00000363571 O15146 UPI000006D2F7 NM_005592.3 15/15 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF317,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 5 1 PASS rs1487680236 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 110800824 110800824 C A 1 0 0 0 0 0 0 0 1 9987 760 27 1 1 MUSK 9 110800824 Silent SNP C C3N-00556_T 857445 110800824 27593893 234 16363 CDC26 0 . GRCh38 9 113272433 113272433 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.75C>A p.Asp25Glu p.D25E ENST00000374206 3/4 129 95 34 223 222 1 strelka-varscan-mutect CDC26,missense_variant,p.Asp25Glu,ENST00000374206,NM_139286.3;PRPF4,upstream_gene_variant,,ENST00000374199,NM_001244926.1;PRPF4,upstream_gene_variant,,ENST00000374198,NM_004697.4;CDC26,non_coding_transcript_exon_variant,,ENST00000490408,; T ENST00000374206 Transcript missense_variant 434/872 75/258 25/85 D/E gaC/gaA 1 -1 CDC26 HGNC HGNC:17839 protein_coding YES CCDS6790.1 ENSP00000363322 Q8NHZ8 A0A024R832 UPI0000073C4F NM_139286.3 tolerated(1) 3/4 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR28579:SF1,hmmpanther:PTHR28579,Pfam_domain:PF10471 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 113272433 113272433 G T 1 0 0 0 0 1 0 0 0 2768 1252 44 2 2 CDC26 9 113272433 Missense_Mutation SNP G C3N-00556_T 2471609 113272433 25122284 235 16364 LMX1B 0 . GRCh38 9 126693228 126693228 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.646C>A p.Pro216Thr p.P216T ENST00000355497 4/8 65 45 20 38 38 0 strelka-varscan-mutect LMX1B,missense_variant,p.Pro216Thr,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Pro216Thr,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Pro193Thr,ENST00000561065,;LMX1B,missense_variant,p.Pro216Thr,ENST00000526117,NM_002316.3; A ENST00000355497 Transcript missense_variant 653/5809 646/1221 216/406 P/T Ccg/Acg 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 tolerated(0.54) 4/8 Gene3D:1.10.10.60,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96,Low_complexity_(Seg):seg,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1458074441 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 126693228 126693228 C A 1 0 0 0 0 1 0 0 0 8789 623 22 2 2 LMX1B 9 126693228 Missense_Mutation SNP C C3N-00556_T 13420795 126693228 11701489 236 16365 PTGES2 0 . GRCh38 9 128127604 128127604 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.114C>T p.= p.F38F ENST00000338961 1/7 24 19 5 18 18 0 strelka-mutect PTGES2,synonymous_variant,p.=,ENST00000338961,NM_025072.6;PTGES2,synonymous_variant,p.=,ENST00000449878,;PTGES2,intron_variant,,ENST00000277462,NM_198938.2;PTGES2,intron_variant,,ENST00000617202,NM_001256335.1;PTGES2-AS1,upstream_gene_variant,,ENST00000443493,;PTGES2,non_coding_transcript_exon_variant,,ENST00000483625,;PTGES2,non_coding_transcript_exon_variant,,ENST00000474124,;PTGES2,intron_variant,,ENST00000476748,;PTGES2,intron_variant,,ENST00000497109,;PTGES2,intron_variant,,ENST00000487063,;PTGES2,intron_variant,,ENST00000485237,;PTGES2,non_coding_transcript_exon_variant,,ENST00000496594,;PTGES2,non_coding_transcript_exon_variant,,ENST00000485510,;PTGES2,upstream_gene_variant,,ENST00000493205,;PTGES2,upstream_gene_variant,,ENST00000476655,; A ENST00000338961 Transcript synonymous_variant 859/2331 114/1134 38/377 F ttC/ttT 1 -1 PTGES2 HGNC HGNC:17822 protein_coding YES CCDS6891.1 ENSP00000345341 Q9H7Z7 UPI000003F04A NM_025072.6 1/7 hmmpanther:PTHR12782,hmmpanther:PTHR12782:SF5,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1463229922 . 1 207 2 0 0 0 0 0 -14.78004 1 1 1 1 0 A 2 1 54 128127604 128127604 G A 1 0 0 0 0 0 0 0 1 12902 1049 37 1 1 PTGES2 9 128127604 Silent SNP G C3N-00556_T 1434376 128127604 10267113 237 16366 LAMC3 0 . GRCh38 9 131009284 131009284 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.70G>A p.Ala24Thr p.A24T ENST00000361069 1/28 62 57 5 73 73 0 varscan-mutect LAMC3,missense_variant,p.Ala24Thr,ENST00000361069,NM_006059.3;LAMC3,non_coding_transcript_exon_variant,,ENST00000480883,; A ENST00000361069 Transcript missense_variant 203/6133 70/4728 24/1575 A/T Gcg/Acg 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 tolerated(0.13) 1/28 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 202 7 0 0 0 0 0 -11.66618 0.9999983 1 1 1 0 A 3 1 54 131009284 131009284 G A 1 0 0 0 0 1 0 0 0 8520 1087 38 1 1 LAMC3 9 131009284 Missense_Mutation SNP G C3N-00556_T 2881680 131009284 7385433 238 16367 LAMC3 0 . GRCh38 9 131073319 131073319 + Missense_Mutation SNP G G T C3N-00556_T C3N-00556_N G G c.3492G>T p.Arg1164Ser p.R1164S ENST00000361069 20/28 363 342 21 349 349 0 strelka-varscan-mutect LAMC3,missense_variant,p.Arg1164Ser,ENST00000361069,NM_006059.3;LAMC3,intron_variant,,ENST00000480883,; T ENST00000361069 Transcript missense_variant,splice_region_variant 3625/6133 3492/4728 1164/1575 R/S agG/agT COSM3654945 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 tolerated(0.07) 20/28 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240 1 MODERATE 1 SNV 2 1 1 PASS rs1365220452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 131073319 131073319 G T 1 0 0 0 0 1 0 0 0 8520 1188 41 2 2 LAMC3 9 131073319 Missense_Mutation SNP G C3N-00556_T 64035 131073319 7321398 239 16368 C9orf172 0 . GRCh38 9 136846622 136846622 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2208C>G p.Phe736Leu p.F736L ENST00000436881 1/1 124 89 35 117 117 0 strelka-varscan-mutect C9orf172,missense_variant,p.Phe736Leu,ENST00000436881,NM_001080482.2;PHPT1,upstream_gene_variant,,ENST00000371661,NM_001287343.1,NM_001135861.2;PHPT1,upstream_gene_variant,,ENST00000247665,NM_014172.5,NM_001287342.1;MAMDC4,upstream_gene_variant,,ENST00000485732,;PHPT1,upstream_gene_variant,,ENST00000492540,;PHPT1,upstream_gene_variant,,ENST00000463215,;PHPT1,upstream_gene_variant,,ENST00000462205,;PHPT1,upstream_gene_variant,,ENST00000497413,; G ENST00000436881 Transcript missense_variant 2208/4387 2208/2931 736/976 F/L ttC/ttG 1 1 C9orf172 HGNC HGNC:37284 protein_coding YES CCDS48059.1 ENSP00000412388 C9J069 UPI00015386B2 NM_001080482.2 tolerated(0.14) 1/1 hmmpanther:PTHR21517 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 136846622 136846622 C G 1 0 0 0 0 1 0 0 0 2179 912 32 4 4 C9orf172 9 136846622 Missense_Mutation SNP C C3N-00556_T 5773303 136846622 1548095 240 16369 PTGDS 0 . GRCh38 9 136980242 136980242 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.508C>A p.Gln170Lys p.Q170K ENST00000371625 5/7 253 179 74 269 269 0 strelka-varscan-mutect PTGDS,missense_variant,p.Gln170Lys,ENST00000371625,NM_000954.5;PTGDS,missense_variant,p.Gln103Lys,ENST00000446677,;LCNL1,upstream_gene_variant,,ENST00000408973,NM_207510.3;PTGDS,downstream_gene_variant,,ENST00000457950,;PTGDS,upstream_gene_variant,,ENST00000444903,;RP11-229P13.19,downstream_gene_variant,,ENST00000413913,;PTGDS,missense_variant,p.Gln170Lys,ENST00000471521,;PTGDS,non_coding_transcript_exon_variant,,ENST00000492068,;PTGDS,non_coding_transcript_exon_variant,,ENST00000462514,;LCNL1,upstream_gene_variant,,ENST00000482657,;LCNL1,upstream_gene_variant,,ENST00000460177,;LCNL1,upstream_gene_variant,,ENST00000432827,;PTGDS,downstream_gene_variant,,ENST00000371623,;PTGDS,downstream_gene_variant,,ENST00000460340,; A ENST00000371625 Transcript missense_variant 582/807 508/573 170/190 Q/K Cag/Aag 1 1 PTGDS HGNC HGNC:9592 protein_coding YES CCDS7019.1 ENSP00000360687 P41222 A0A024R8G3 UPI00001317A4 NM_000954.5 tolerated(0.17) 5/7 Gene3D:2.40.128.20,Pfam_domain:PF00061,Prints_domain:PR01254,hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF86,Superfamily_domains:SSF50814 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 136980242 136980242 C A 1 0 0 0 0 1 0 0 0 12896 595 21 2 2 PTGDS 9 136980242 Missense_Mutation SNP C C3N-00556_T 133620 136980242 1414475 241 16370 ANAPC2 0 . GRCh38 9 137175280 137175280 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2213C>T p.Ser738Phe p.S738F ENST00000323927 12/13 198 185 13 223 222 1 strelka-varscan-mutect ANAPC2,missense_variant,p.Ser738Phe,ENST00000323927,NM_013366.3;TMEM210,upstream_gene_variant,,ENST00000413619,NM_001282477.1;RP11-350O14.18,upstream_gene_variant,,ENST00000568665,;ANAPC2,non_coding_transcript_exon_variant,,ENST00000483432,;TMEM210,upstream_gene_variant,,ENST00000430332,;ANAPC2,downstream_gene_variant,,ENST00000485970,;ANAPC2,non_coding_transcript_exon_variant,,ENST00000487917,;ANAPC2,non_coding_transcript_exon_variant,,ENST00000493730,;TMEM210,upstream_gene_variant,,ENST00000535352,;TMEM210,upstream_gene_variant,,ENST00000427366,; A ENST00000323927 Transcript missense_variant 2218/2632 2213/2469 738/822 S/F tCc/tTc 1 -1 ANAPC2 HGNC HGNC:19989 protein_coding YES CCDS7033.1 ENSP00000314004 Q9UJX6 UPI0000043E1B NM_013366.3 deleterious(0) 12/13 hmmpanther:PTHR11932:SF73,hmmpanther:PTHR11932 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 137175280 137175280 G A 1 0 0 0 0 1 0 0 0 701 1174 41 3 3 ANAPC2 9 137175280 Missense_Mutation SNP G C3N-00556_T 195038 137175280 1219437 242 16371 SFMBT2 0 . GRCh38 10 7220498 7220498 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1243G>A p.Glu415Lys p.E415K ENST00000397167 11/21 187 140 47 219 219 0 strelka-varscan-mutect SFMBT2,missense_variant,p.Glu415Lys,ENST00000397167,NM_001029880.2;SFMBT2,missense_variant,p.Glu415Lys,ENST00000361972,NM_001018039.1; T ENST00000397167 Transcript missense_variant 1436/8024 1243/2685 415/894 E/K Gaa/Aaa 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 deleterious(0.01) 11/21 PROSITE_profiles:PS51079,hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF02820,Gene3D:2.30.30.160,SMART_domains:SM00561,Superfamily_domains:SSF63748 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 7220498 7220498 C T 1 0 0 0 0 1 0 0 0 14436 835 29 3 3 SFMBT2 10 7220498 Missense_Mutation SNP C C3N-00556_T 7220498 126576924 243 16372 ITIH5 0 . GRCh38 10 7577002 7577002 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1429G>A p.Glu477Lys p.E477K ENST00000397146 10/14 59 55 4 73 73 0 strelka-varscan ITIH5,missense_variant,p.Glu477Lys,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Glu477Lys,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Glu263Lys,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,3_prime_UTR_variant,,ENST00000461751,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,non_coding_transcript_exon_variant,,ENST00000468389,;ITIH5,upstream_gene_variant,,ENST00000492668,; T ENST00000397146 Transcript missense_variant 1508/6721 1429/2829 477/942 E/K Gaa/Aaa 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 deleterious(0) 10/14 PROSITE_profiles:PS50234,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 7577002 7577002 C T 1 0 0 0 0 1 0 0 0 7813 835 29 3 3 ITIH5 10 7577002 Missense_Mutation SNP C C3N-00556_T 356504 7577002 126220420 244 16373 FRMD4A 0 . GRCh38 10 13858875 13858875 + Missense_Mutation SNP T T A novel C3N-00556_T C3N-00556_N T T c.83A>T p.Asp28Val p.D28V ENST00000357447 3/25 219 208 11 238 238 0 strelka-varscan-mutect FRMD4A,missense_variant,p.Asp28Val,ENST00000357447,NM_001318336.1,NM_018027.3;FRMD4A,missense_variant,p.Asp61Val,ENST00000264546,;FRMD4A,non_coding_transcript_exon_variant,,ENST00000342409,; A ENST00000357447 Transcript missense_variant 452/6821 83/3120 28/1039 D/V gAt/gTt 1 -1 FRMD4A HGNC HGNC:25491 protein_coding YES CCDS7101.1 ENSP00000350032 Q9P2Q2 UPI0000366665 NM_001318336.1,NM_018027.3 deleterious(0) 3/25 PROSITE_profiles:PS50057,hmmpanther:PTHR23281:SF12,hmmpanther:PTHR23281,Gene3D:3.10.20.90,Pfam_domain:PF09379,SMART_domains:SM00295,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 13858875 13858875 T A 1 0 0 0 0 1 0 0 0 5921 1435 50 4 4 FRMD4A 10 13858875 Missense_Mutation SNP T C3N-00556_T 6281873 13858875 119938547 245 16374 SLC18A3 0 . GRCh38 10 49612018 49612018 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1278C>G p.Ile426Met p.I426M ENST00000374115 1/1 167 154 13 175 175 0 strelka-varscan-mutect SLC18A3,missense_variant,p.Ile426Met,ENST00000374115,NM_003055.2;CHAT,intron_variant,,ENST00000339797,NM_020984.3;CHAT,upstream_gene_variant,,ENST00000395562,NM_001142933.1;CHAT,upstream_gene_variant,,ENST00000337653,NM_020549.4;CHAT,upstream_gene_variant,,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,upstream_gene_variant,,ENST00000395559,NM_020986.3;CHAT,upstream_gene_variant,,ENST00000460699,;CHAT,upstream_gene_variant,,ENST00000490270,;CHAT,upstream_gene_variant,,ENST00000481336,;CHAT,upstream_gene_variant,,ENST00000466590,; G ENST00000374115 Transcript missense_variant 1718/2420 1278/1599 426/532 I/M atC/atG 1 1 SLC18A3 HGNC HGNC:10936 protein_coding YES CCDS7231.1 ENSP00000363229 Q16572 UPI00001F98C1 NM_003055.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF13,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 49612018 49612018 C G 1 0 0 0 0 1 0 0 0 14692 903 32 4 4 SLC18A3 10 49612018 Missense_Mutation SNP C C3N-00556_T 35753143 49612018 84185404 246 16375 TIMM23B 0 . GRCh38 10 49952175 49952175 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.215G>C p.Arg72Thr p.R72T ENST00000374098 3/7 200 187 13 245 245 0 varscan-mutect TIMM23B,missense_variant,p.Arg72Thr,ENST00000451577,NM_001290118.1;TIMM23B,missense_variant,p.Arg72Thr,ENST00000374098,NM_001290117.1;PARG,intron_variant,,ENST00000402038,NM_001324381.1;SNORA74,upstream_gene_variant,,ENST00000411179,;TIMM23B,3_prime_UTR_variant,,ENST00000478381,;TIMM23B,3_prime_UTR_variant,,ENST00000483296,; C ENST00000374098 Transcript missense_variant 377/1142 215/567 72/188 R/T aGa/aCa 1 1 TIMM23B HGNC HGNC:23581 protein_coding YES CCDS73131.1 ENSP00000363211 Q5SRD1 UPI000387CD3B NM_001290117.1 deleterious(0) 3/7 hmmpanther:PTHR15371,hmmpanther:PTHR15371:SF4,TIGRFAM_domain:TIGR00983 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 49952175 49952175 G C 1 0 0 0 0 1 0 0 0 16351 942 33 4 4 TIMM23B 10 49952175 Missense_Mutation SNP G C3N-00556_T 340157 49952175 83845247 247 16376 FAM13C 0 . GRCh38 10 59252986 59252986 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.1345G>T p.Asp449Tyr p.D449Y ENST00000618804 12/14 196 168 28 298 297 1 strelka-varscan-mutect FAM13C,missense_variant,p.Asp365Tyr,ENST00000618427,NM_001166698.1;FAM13C,missense_variant,p.Asp469Tyr,ENST00000621119,;FAM13C,missense_variant,p.Asp470Tyr,ENST00000614220,;FAM13C,missense_variant,p.Asp449Tyr,ENST00000618804,NM_198215.3;FAM13C,missense_variant,p.Asp351Tyr,ENST00000611933,NM_001001971.2;FAM13C,missense_variant,p.Asp366Tyr,ENST00000468840,NM_001143773.1;FAM13C,missense_variant,p.Asp449Tyr,ENST00000435852,;FAM13C,downstream_gene_variant,,ENST00000422313,;FAM13C,3_prime_UTR_variant,,ENST00000622363,;FAM13C,3_prime_UTR_variant,,ENST00000489341,; A ENST00000618804 Transcript missense_variant 1435/3333 1345/1758 449/585 D/Y Gac/Tac COSM3439126 1 -1 FAM13C HGNC HGNC:19371 protein_coding YES CCDS7255.1 ENSP00000481854 Q8NE31 UPI00001AEA18 NM_198215.3 deleterious(0) 12/14 hmmpanther:PTHR15904:SF19,hmmpanther:PTHR15904 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 59252986 59252986 C A 1 0 0 0 0 1 0 0 0 5303 855 30 2 2 FAM13C 10 59252986 Missense_Mutation SNP C C3N-00556_T 9300811 59252986 74544436 248 16377 ANK3 0 . GRCh38 10 60068865 60068865 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.12016G>C p.Glu4006Gln p.E4006Q ENST00000280772 37/44 172 163 9 217 217 0 strelka-varscan-mutect ANK3,missense_variant,p.Glu4006Gln,ENST00000280772,NM_020987.3;ANK3,intron_variant,,ENST00000373827,NM_001204403.1;ANK3,intron_variant,,ENST00000503366,NM_001204404.1;ANK3,intron_variant,,ENST00000610321,;ANK3,intron_variant,,ENST00000355288,NM_001149.3;ANK3,intron_variant,,ENST00000616444,;ANK3,intron_variant,,ENST00000373820,;ANK3,intron_variant,,ENST00000610901,;ANK3,intron_variant,,ENST00000613207,;ANK3,intron_variant,,ENST00000511043,;ANK3,upstream_gene_variant,,ENST00000459732,;ANK3,upstream_gene_variant,,ENST00000514197,;ANK3,synonymous_variant,p.=,ENST00000621739,; G ENST00000280772 Transcript missense_variant 12208/16874 12016/13134 4006/4377 E/Q Gag/Cag 1 -1 ANK3 HGNC HGNC:494 protein_coding YES CCDS7258.1 ENSP00000280772 Q12955 UPI0000141BA9 NM_020987.3 deleterious_low_confidence(0.03) 37/44 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 60068865 60068865 C G 1 0 0 0 0 1 0 0 0 722 835 29 4 4 ANK3 10 60068865 Missense_Mutation SNP C C3N-00556_T 815879 60068865 73728557 249 16378 SIRT1 0 . GRCh38 10 67891431 67891431 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.819C>A p.Phe273Leu p.F273L ENST00000212015 4/9 171 156 15 220 220 0 strelka-varscan-mutect SIRT1,missense_variant,p.Phe273Leu,ENST00000212015,NM_012238.4;SIRT1,5_prime_UTR_variant,,ENST00000432464,NM_001142498.1;SIRT1,upstream_gene_variant,,ENST00000406900,NM_001314049.1;SIRT1,non_coding_transcript_exon_variant,,ENST00000497639,;SIRT1,non_coding_transcript_exon_variant,,ENST00000473922,; A ENST00000212015 Transcript missense_variant 872/4094 819/2244 273/747 F/L ttC/ttA 1 1 SIRT1 HGNC HGNC:14929 protein_coding YES CCDS7273.1 ENSP00000212015 Q96EB6 A0A024QZQ1 UPI0000073E1A NM_012238.4 deleterious(0) 4/9 PROSITE_profiles:PS50305,hmmpanther:PTHR11085,hmmpanther:PTHR11085:SF15,Gene3D:3.30.1600.10,Pfam_domain:PF02146,Superfamily_domains:SSF52467 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 67891431 67891431 C A 1 0 0 0 0 1 0 0 0 14600 825 29 2 2 SIRT1 10 67891431 Missense_Mutation SNP C C3N-00556_T 7822566 67891431 65905991 250 16379 HNRNPH3 0 . GRCh38 10 68341210 68341210 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.676G>C p.Asp226His p.D226H ENST00000265866 7/10 130 116 14 136 136 0 varscan-mutect HNRNPH3,missense_variant,p.Asp226His,ENST00000265866,NM_001322442.1,NM_001322436.1,NM_001322443.1,NM_001322434.1,NM_012207.2;HNRNPH3,missense_variant,p.Asp211His,ENST00000354695,NM_021644.3;RUFY2,missense_variant,p.Gln117Glu,ENST00000463210,;RUFY2,downstream_gene_variant,,ENST00000388768,NM_017987.4;RUFY2,downstream_gene_variant,,ENST00000602465,;RUFY2,downstream_gene_variant,,ENST00000265865,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000469172,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000481819,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000491200,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000490442,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000478698,;HNRNPH3,non_coding_transcript_exon_variant,,ENST00000480987,;RUFY2,non_coding_transcript_exon_variant,,ENST00000484083,;HNRNPH3,downstream_gene_variant,,ENST00000461310,;HNRNPH3,downstream_gene_variant,,ENST00000486854,;RUFY2,downstream_gene_variant,,ENST00000473398,;HNRNPH3,downstream_gene_variant,,ENST00000467249,;RUFY2,3_prime_UTR_variant,,ENST00000466493,;RUFY2,downstream_gene_variant,,ENST00000466187,; C ENST00000265866 Transcript missense_variant 841/2339 676/1041 226/346 D/H Gat/Cat 1 1 HNRNPH3 HGNC HGNC:5043 protein_coding YES CCDS7278.1 ENSP00000265866 P31942 A0A024QZK8 UPI0000134539 NM_001322442.1,NM_001322436.1,NM_001322443.1,NM_001322434.1,NM_012207.2 tolerated(0.05) 7/10 PROSITE_profiles:PS50102,hmmpanther:PTHR13976:SF36,hmmpanther:PTHR13976,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs995618284 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 68341210 68341210 G C 1 0 0 0 0 1 0 0 0 7162 1290 45 4 4 HNRNPH3 10 68341210 Missense_Mutation SNP G C3N-00556_T 449779 68341210 65456212 251 16380 DNA2 0 . GRCh38 10 68445084 68445084 + Splice_Site SNP C C T rs771783178 C3N-00556_T C3N-00556_N C C c.1058-1G>A p.X353_splice ENST00000358410 68 48 20 83 83 0 strelka-varscan-mutect DNA2,splice_acceptor_variant,,ENST00000358410,NM_001080449.2;DNA2,splice_acceptor_variant,,ENST00000551118,;DNA2,splice_acceptor_variant,,ENST00000399180,;DNA2,splice_acceptor_variant,,ENST00000399179,;DNA2,upstream_gene_variant,,ENST00000478029,; T ENST00000358410 Transcript splice_acceptor_variant -/4208 1058/3183 353/1060 rs771783178,COSM3931103,COSM3931104 1 -1 DNA2 HGNC HGNC:2939 protein_coding YES CCDS44415.2 ENSP00000351185 P51530 UPI00001C1EDB NM_001080449.2 7/20 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs771783178 . 0 117 51 27 3 12 0 0 -2.828369 0 0 1 0 0 T 5 4 54 68445084 68445084 C T 1 0 0 0 0 0 0 1 0 4405 927 32 3 3 DNA2 10 68445084 Splice_Site SNP C C3N-00556_T 103874 68445084 65352338 252 16381 DDX21 0 . GRCh38 10 68970204 68970204 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1240C>T p.= p.L414L ENST00000354185 8/15 94 80 14 84 84 0 strelka-varscan-mutect DDX21,synonymous_variant,p.=,ENST00000620315,NM_001256910.1;DDX21,synonymous_variant,p.=,ENST00000354185,NM_004728.3; T ENST00000354185 Transcript synonymous_variant 1338/4711 1240/2352 414/783 L Ctg/Ttg 1 1 DDX21 HGNC HGNC:2744 protein_coding YES CCDS31211.1 ENSP00000346120 Q9NR30 UPI00001A92E8 NM_004728.3 8/15 Gene3D:3.40.50.300,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF237,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 54 68970204 68970204 C T 1 0 0 0 0 0 0 0 1 4152 927 32 3 3 DDX21 10 68970204 Silent SNP C C3N-00556_T 525120 68970204 64827218 253 16382 SEC24C 0 . GRCh38 10 73760122 73760122 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.586C>T p.His196Tyr p.H196Y ENST00000339365 6/24 153 142 11 146 146 0 strelka-varscan-mutect SEC24C,missense_variant,p.His196Tyr,ENST00000339365,NM_004922.3;SEC24C,missense_variant,p.His196Tyr,ENST00000345254,NM_198597.2;SEC24C,missense_variant,p.His5Tyr,ENST00000634508,;SEC24C,missense_variant,p.His196Tyr,ENST00000465076,;SEC24C,synonymous_variant,p.=,ENST00000635550,; T ENST00000339365 Transcript missense_variant 748/4513 586/3285 196/1094 H/Y Cat/Tat COSM5147184 1 1 SEC24C HGNC HGNC:10705 protein_coding YES CCDS7332.1 ENSP00000343405 P53992 A0A024QZM6 UPI000013F621 NM_004922.3 tolerated(1) 6/24 hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF5 1 MODERATE 1 SNV 5 1 1 PASS rs1406595070 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 73760122 73760122 C T 1 0 0 0 0 1 0 0 0 14273 826 29 3 3 SEC24C 10 73760122 Missense_Mutation SNP C C3N-00556_T 4789918 73760122 60037300 254 16383 C10orf55 0 . GRCh38 10 73911768 73911768 + Nonsense_Mutation SNP T T A novel C3N-00556_T C3N-00556_N T T c.373A>T p.Lys125Ter p.K125* ENST00000412307 4/4 201 161 40 237 237 0 strelka-varscan-mutect C10orf55,stop_gained,p.Lys125Ter,ENST00000412307,NM_001001791.2;PLAU,5_prime_UTR_variant,,ENST00000446342,NM_001145031.1;PLAU,intron_variant,,ENST00000372764,NM_001319191.1,NM_002658.3;PLAU,intron_variant,,ENST00000481390,;C10orf55,non_coding_transcript_exon_variant,,ENST00000409178,;PLAU,intron_variant,,ENST00000494287,;PLAU,downstream_gene_variant,,ENST00000496926,; A ENST00000412307 Transcript stop_gained 570/2360 373/456 125/151 K/* Aag/Tag 1 -1 C10orf55 HGNC HGNC:31008 protein_coding YES CCDS53541.1 ENSP00000409225 Q5SWW7 UPI0000470217 NM_001001791.2 4/4 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 73911768 73911768 T A 1 0 0 0 0 0 1 0 0 1766 1821 63 4 4 C10orf55 10 73911768 Nonsense_Mutation SNP T C3N-00556_T 151646 73911768 59885654 255 16384 CYP2C18 0 . GRCh38 10 94688217 94688217 + Missense_Mutation SNP G G C rs767161951 C3N-00556_T C3N-00556_N G G c.424G>C p.Glu142Gln p.E142Q ENST00000285979 3/9 217 203 14 239 239 0 varscan-mutect CYP2C18,missense_variant,p.Glu142Gln,ENST00000285979,NM_000772.2;CYP2C18,missense_variant,p.Glu142Gln,ENST00000339022,NM_001128925.1;RP11-400G3.5,missense_variant,p.Glu22Gln,ENST00000464755,; C ENST00000285979 Transcript missense_variant 623/2418 424/1473 142/490 E/Q Gag/Cag rs767161951 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 deleterious(0) 3/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs767161951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 94688217 94688217 G C 1 0 0 0 0 1 0 0 0 3968 1059 37 4 4 CYP2C18 10 94688217 Missense_Mutation SNP G C3N-00556_T 20776449 94688217 39109205 256 16385 CCNJ 0 . GRCh38 10 96056870 96056870 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.450C>T p.= p.F150F ENST00000465148 4/6 296 280 16 321 321 0 varscan-mutect CCNJ,synonymous_variant,p.=,ENST00000265992,NM_019084.4;CCNJ,synonymous_variant,p.=,ENST00000403870,NM_001134376.1;CCNJ,synonymous_variant,p.=,ENST00000465148,NM_001134375.1;ENTPD1-AS1,intron_variant,,ENST00000416301,;ENTPD1-AS1,intron_variant,,ENST00000458228,;ENTPD1-AS1,intron_variant,,ENST00000454638,;ENTPD1-AS1,intron_variant,,ENST00000452728,;ENTPD1-AS1,intron_variant,,ENST00000427846,;ENTPD1-AS1,intron_variant,,ENST00000451364,; T ENST00000465148 Transcript synonymous_variant 628/2677 450/1152 150/383 F ttC/ttT 1 1 CCNJ HGNC HGNC:23434 protein_coding YES CCDS44462.1 ENSP00000435373 Q5T5M9 UPI00001F9448 NM_001134375.1 4/6 hmmpanther:PTHR10177:SF62,hmmpanther:PTHR10177,Pfam_domain:PF02984,Gene3D:1.10.472.10,SMART_domains:SM01332,Superfamily_domains:SSF47954 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 96056870 96056870 C T 1 0 0 0 0 0 0 0 1 2627 825 29 3 3 CCNJ 10 96056870 Silent SNP C C3N-00556_T 1368653 96056870 37740552 257 16386 MMS19 0 . GRCh38 10 97465948 97465948 + Nonsense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1613C>G p.Ser538Ter p.S538* ENST00000438925 18/31 105 94 11 131 131 0 strelka-varscan-mutect MMS19,stop_gained,p.Ser538Ter,ENST00000438925,NM_022362.4,NM_001289404.1;MMS19,stop_gained,p.Ser495Ter,ENST00000355839,NM_001289403.1;MMS19,stop_gained,p.Ser538Ter,ENST00000370782,NM_001289405.1;MMS19,stop_gained,p.Ser440Ter,ENST00000327238,;MMS19,stop_gained,p.Ser113Ter,ENST00000434538,;MMS19,downstream_gene_variant,,ENST00000437002,;MMS19,downstream_gene_variant,,ENST00000422685,;MMS19,downstream_gene_variant,,ENST00000483626,;MMS19,3_prime_UTR_variant,,ENST00000415383,;MMS19,3_prime_UTR_variant,,ENST00000434392,;MMS19,upstream_gene_variant,,ENST00000495415,;MMS19,downstream_gene_variant,,ENST00000441194,;MMS19,upstream_gene_variant,,ENST00000478452,;MMS19,upstream_gene_variant,,ENST00000480108,; C ENST00000438925 Transcript stop_gained 1949/3797 1613/3093 538/1030 S/* tCa/tGa 1 -1 MMS19 HGNC HGNC:13824 protein_coding YES CCDS7464.1 ENSP00000412698 Q96T76 UPI000013DDF7 NM_022362.4,NM_001289404.1 18/31 hmmpanther:PTHR12891,Gene3D:1.25.10.10 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 54 97465948 97465948 G C 1 0 0 0 0 0 1 0 0 9635 1294 45 4 4 MMS19 10 97465948 Nonsense_Mutation SNP G C3N-00556_T 1409078 97465948 36331474 258 16387 R3HCC1L 0 . GRCh38 10 98208128 98208128 + Nonsense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.14C>G p.Ser5Ter p.S5* ENST00000612478 3/9 111 105 6 152 152 0 strelka-varscan-mutect R3HCC1L,stop_gained,p.Ser5Ter,ENST00000298999,NM_014472.4;R3HCC1L,stop_gained,p.Ser5Ter,ENST00000370584,NM_138469.2,NM_001256620.1;R3HCC1L,stop_gained,p.Ser5Ter,ENST00000612478,NM_001256619.1;R3HCC1L,stop_gained,p.Ser5Ter,ENST00000314594,;R3HCC1L,intron_variant,,ENST00000613938,;R3HCC1L,intron_variant,,ENST00000370586,NM_001256621.1; G ENST00000612478 Transcript stop_gained 236/3337 14/2379 5/792 S/* tCa/tGa 1 1 R3HCC1L HGNC HGNC:23512 protein_coding YES CCDS73178.1 ENSP00000483494 A0A087X0M0 UPI00001F94F3 NM_001256619.1 3/9 HIGH 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -9.242131 0.9999994 1 1 1 0 G 4 3 54 98208128 98208128 C G 1 0 0 0 0 0 1 0 0 13043 838 29 4 4 R3HCC1L 10 98208128 Nonsense_Mutation SNP C C3N-00556_T 742180 98208128 35589294 259 16388 COX15 0 . GRCh38 10 99729685 99729685 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.140C>T p.Ser47Phe p.S47F ENST00000016171 2/9 290 267 23 283 283 0 strelka-varscan-mutect COX15,missense_variant,p.Ser47Phe,ENST00000370483,NM_004376.5;COX15,missense_variant,p.Ser47Phe,ENST00000016171,NM_078470.4;CUTC,upstream_gene_variant,,ENST00000370476,NM_015960.2;CUTC,upstream_gene_variant,,ENST00000370472,;CUTC,intron_variant,,ENST00000493385,;CUTC,upstream_gene_variant,,ENST00000471520,; A ENST00000016171 Transcript missense_variant 191/2356 140/1233 47/410 S/F tCt/tTt 1 -1 COX15 HGNC HGNC:2263 protein_coding YES CCDS7482.1 ENSP00000016171 Q7KZN9 UPI000006E691 NM_078470.4 deleterious(0.01) 2/9 hmmpanther:PTHR23289 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 99729685 99729685 G A 1 0 0 0 0 1 0 0 0 3559 942 33 3 3 COX15 10 99729685 Missense_Mutation SNP G C3N-00556_T 1521557 99729685 34067737 260 16389 VWA2 0 . GRCh38 10 114289538 114289538 + Nonsense_Mutation SNP C C A rs141684486 C3N-00556_T C3N-00556_N C C c.1259C>A p.Ser420Ter p.S420* ENST00000603594 11/11 83 76 7 107 107 0 strelka-varscan-mutect VWA2,stop_gained,p.Ser420Ter,ENST00000603594,;VWA2,intron_variant,,ENST00000392982,NM_001272046.1;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,; A ENST00000603594 Transcript stop_gained 2265/2600 1259/1266 420/421 S/* tCa/tAa rs141684486,COSM5036868 1 1 VWA2 HGNC HGNC:24709 protein_coding ENSP00000473752 Q5GFL6 UPI0000EA39F8 11/11 0,1 HIGH SNV 1 0,1 1 PASS rs141684486 . 0 207 0 0 0 0 0 2 -4.543474 0 0 1 0 0 A 4 1 54 114289538 114289538 C A 1 0 0 0 0 0 1 0 0 17793 838 29 2 2 VWA2 10 114289538 Nonsense_Mutation SNP C C3N-00556_T 14559853 114289538 19507884 261 16390 FRG2B 0 . GRCh38 10 133626682 133626682 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.61C>A p.Gln21Lys p.Q21K ENST00000425520 1/4 250 216 34 289 289 0 varscan-mutect FRG2B,missense_variant,p.Gln21Lys,ENST00000443774,;FRG2B,missense_variant,p.Gln21Lys,ENST00000425520,NM_001080998.1; T ENST00000425520 Transcript missense_variant 114/890 61/837 21/278 Q/K Cag/Aag 1 -1 FRG2B HGNC HGNC:33518 protein_coding YES CCDS44502.1 ENSP00000401310 Q96QU4 UPI00000727C6 NM_001080998.1 tolerated(0.12) 1/4 hmmpanther:PTHR31883,hmmpanther:PTHR31883:SF3,Prints_domain:PR02074 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 133626682 133626682 G T 1 0 0 0 0 1 0 0 0 5916 1357 47 2 2 FRG2B 10 133626682 Missense_Mutation SNP G C3N-00556_T 19337144 133626682 170740 262 16391 ANO9 0 . GRCh38 11 418570 418570 + Missense_Mutation SNP T T C novel C3N-00556_T C3N-00556_N T T c.2150A>G p.Lys717Arg p.K717R ENST00000332826 23/23 138 124 14 150 150 0 strelka-varscan-mutect ANO9,missense_variant,p.Lys717Arg,ENST00000332826,NM_001012302.2;SIGIRR,upstream_gene_variant,,ENST00000431843,NM_001135054.1;SIGIRR,upstream_gene_variant,,ENST00000332725,NM_021805.2,NM_001135053.1;SIGIRR,upstream_gene_variant,,ENST00000397632,;SIGIRR,upstream_gene_variant,,ENST00000528209,;SIGIRR,upstream_gene_variant,,ENST00000530494,;SIGIRR,upstream_gene_variant,,ENST00000528058,;SIGIRR,upstream_gene_variant,,ENST00000529486,;SIGIRR,upstream_gene_variant,,ENST00000534217,;SIGIRR,upstream_gene_variant,,ENST00000528116,;SIGIRR,upstream_gene_variant,,ENST00000525299,;SIGIRR,upstream_gene_variant,,ENST00000526788,;SIGIRR,upstream_gene_variant,,ENST00000527136,;ANO9,non_coding_transcript_exon_variant,,ENST00000532094,;ANO9,non_coding_transcript_exon_variant,,ENST00000526142,;ANO9,non_coding_transcript_exon_variant,,ENST00000528927,;ANO9,non_coding_transcript_exon_variant,,ENST00000534161,;ANO9,non_coding_transcript_exon_variant,,ENST00000524802,;SIGIRR,upstream_gene_variant,,ENST00000527295,;SIGIRR,upstream_gene_variant,,ENST00000525070,;ANO9,downstream_gene_variant,,ENST00000525804,; C ENST00000332826 Transcript missense_variant 2235/2542 2150/2349 717/782 K/R aAg/aGg 1 -1 ANO9 HGNC HGNC:20679 protein_coding YES CCDS31326.1 ENSP00000332788 A1A5B4 UPI0001505B10 NM_001012302.2 deleterious(0.03) 23/23 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF37,Pfam_domain:PF04547 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 418570 418570 T C 1 0 0 0 0 1 0 0 0 811 1609 56 5 5 ANO9 11 418570 Missense_Mutation SNP T C3N-00556_T 418570 134668052 263 16392 RASSF7 0 . GRCh38 11 562453 562453 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.499G>A p.Glu167Lys p.E167K ENST00000397583 3/6 297 272 25 320 320 0 strelka-varscan-mutect RASSF7,missense_variant,p.Glu167Lys,ENST00000397583,NM_003475.3;RASSF7,missense_variant,p.Glu167Lys,ENST00000431809,;RASSF7,missense_variant,p.Glu167Lys,ENST00000397582,NM_001143993.1;RASSF7,missense_variant,p.Glu167Lys,ENST00000454668,NM_001143994.1;LMNTD2,upstream_gene_variant,,ENST00000329451,NM_173573.2;LMNTD2,upstream_gene_variant,,ENST00000441853,;LMNTD2,upstream_gene_variant,,ENST00000486629,;RASSF7,downstream_gene_variant,,ENST00000528736,;MIR210HG,downstream_gene_variant,,ENST00000500447,;MIR210HG,downstream_gene_variant,,ENST00000533920,;MIR210HG,downstream_gene_variant,,ENST00000528245,;RP11-496I9.1,downstream_gene_variant,,ENST00000527620,;RP11-496I9.1,downstream_gene_variant,,ENST00000533844,;RP11-496I9.1,downstream_gene_variant,,ENST00000527113,;RASSF7,non_coding_transcript_exon_variant,,ENST00000524468,;RASSF7,missense_variant,p.Glu24Lys,ENST00000531112,;RASSF7,3_prime_UTR_variant,,ENST00000414138,;LMNTD2,upstream_gene_variant,,ENST00000492515,; A ENST00000397583 Transcript missense_variant 932/1928 499/1122 167/373 E/K Gag/Aag 1 1 RASSF7 HGNC HGNC:1166 protein_coding YES CCDS7702.1 ENSP00000380713 Q02833 A0A024RCE4 UPI0000127A61 NM_003475.3 tolerated(0.52) 3/6 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 562453 562453 G A 1 0 0 0 0 1 0 0 0 13252 1291 45 3 3 RASSF7 11 562453 Missense_Mutation SNP G C3N-00556_T 143883 562453 134524169 264 16393 MUC5AC 0 . GRCh38 11 1191095 1191095 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.12950C>A p.Pro4317His p.P4317H ENST00000621226 31/49 419 392 27 506 506 0 varscan-mutect MUC5AC,missense_variant,p.Pro4317His,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 12997/17448 12950/16965 4317/5654 P/H cCt/cAt 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0.02) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 1191095 1191095 C A 1 0 0 0 0 1 0 0 0 9978 681 24 2 2 MUC5AC 11 1191095 Missense_Mutation SNP C C3N-00556_T 628642 1191095 133895527 265 16394 UBQLN3 0 . GRCh38 11 5507598 5507598 + Missense_Mutation SNP T T A novel C3N-00556_T C3N-00556_N T T c.1961A>T p.Gln654Leu p.Q654L ENST00000311659 2/2 39 35 4 79 79 0 strelka-varscan-mutect UBQLN3,missense_variant,p.Gln654Leu,ENST00000311659,NM_017481.2;HBG2,intron_variant,,ENST00000380259,;HBE1,upstream_gene_variant,,ENST00000380237,;UBQLN3,downstream_gene_variant,,ENST00000445998,;HBG2,upstream_gene_variant,,ENST00000380252,;HBE1,upstream_gene_variant,,ENST00000396895,;AC104389.28,upstream_gene_variant,,ENST00000415970,;AC104389.28,upstream_gene_variant,,ENST00000418729,;AC104389.28,upstream_gene_variant,,ENST00000420465,;AC104389.28,upstream_gene_variant,,ENST00000420726,; A ENST00000311659 Transcript missense_variant 2109/2407 1961/1968 654/655 Q/L cAg/cTg 1 -1 UBQLN3 HGNC HGNC:12510 protein_coding YES CCDS7758.1 ENSP00000347997 Q9H347 A0A140VJZ3 UPI000006E3A0 NM_017481.2 deleterious(0) 2/2 PROSITE_profiles:PS50030,hmmpanther:PTHR10677:SF4,hmmpanther:PTHR10677,SMART_domains:SM00165,Superfamily_domains:SSF46934 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.81769 1 1 1 1 0 A 3 1 54 5507598 5507598 T A 1 0 0 0 0 1 0 0 0 17422 1580 55 4 4 UBQLN3 11 5507598 Missense_Mutation SNP T C3N-00556_T 4316503 5507598 129579024 266 16395 CSNK2A3 0 . GRCh38 11 11352703 11352703 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.417G>C p.Glu139Asp p.E139D ENST00000528848 1/1 407 375 32 534 534 0 strelka-varscan-mutect CSNK2A3,missense_variant,p.Glu139Asp,ENST00000528848,NM_001256686.1;GALNT18,intron_variant,,ENST00000227756,NM_198516.2;RP11-567I13.1,non_coding_transcript_exon_variant,,ENST00000526867,; G ENST00000528848 Transcript missense_variant 655/1416 417/1176 139/391 E/D gaG/gaC 1 -1 CSNK2A3 HGNC HGNC:2458 protein_coding YES CCDS59224.1 ENSP00000473553 Q8NEV1 UPI00001F9D63 NM_001256686.1 deleterious(0.03) 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR24054:SF16,hmmpanther:PTHR24054,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 11352703 11352703 C G 1 0 0 0 0 1 0 0 0 3759 912 32 4 4 CSNK2A3 11 11352703 Missense_Mutation SNP C C3N-00556_T 5845105 11352703 123733919 267 16396 SPON1 0 . GRCh38 11 14041530 14041530 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.355G>A p.Glu119Lys p.E119K ENST00000576479 3/16 87 82 5 115 115 0 varscan-mutect SPON1,missense_variant,p.Glu119Lys,ENST00000576479,NM_006108.3; A ENST00000576479 Transcript missense_variant 571/4837 355/2424 119/807 E/K Gaa/Aaa COSM5689055 1 1 SPON1 HGNC HGNC:11252 protein_coding YES CCDS73262.1 ENSP00000460236 Q9HCB6 UPI000044404A NM_006108.3 tolerated(0.26) 3/16 PROSITE_profiles:PS51019,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF18,Pfam_domain:PF02014 1 MODERATE 1 SNV 1 1 1 PASS rs1287325735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 14041530 14041530 G A 1 0 0 0 0 1 0 0 0 15435 1059 37 1 1 SPON1 11 14041530 Missense_Mutation SNP G C3N-00556_T 2688827 14041530 121045092 268 16397 SPON1 0 . GRCh38 11 14262782 14262782 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.2067G>A p.= p.V689V ENST00000576479 15/16 259 238 21 340 340 0 strelka-varscan-mutect SPON1,synonymous_variant,p.=,ENST00000576479,NM_006108.3;RP11-21L19.1,downstream_gene_variant,,ENST00000534587,;SPON1,non_coding_transcript_exon_variant,,ENST00000591785,; A ENST00000576479 Transcript synonymous_variant 2283/4837 2067/2424 689/807 V gtG/gtA 1 1 SPON1 HGNC HGNC:11252 protein_coding YES CCDS73262.1 ENSP00000460236 Q9HCB6 UPI000044404A NM_006108.3 15/16 PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF18,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 14262782 14262782 G A 1 0 0 0 0 0 0 0 1 15435 1277 45 3 3 SPON1 11 14262782 Silent SNP G C3N-00556_T 221252 14262782 120823840 269 16398 TCP11L1 0 . GRCh38 11 33057966 33057966 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.465G>C p.Gln155His p.Q155H ENST00000334274 5/10 212 199 13 228 228 0 strelka-varscan-mutect TCP11L1,missense_variant,p.Gln155His,ENST00000334274,NM_018393.3;TCP11L1,missense_variant,p.Gln155His,ENST00000432887,NM_001145541.1;TCP11L1,missense_variant,p.Gln155His,ENST00000531632,;TCP11L1,downstream_gene_variant,,ENST00000530419,;TCP11L1,downstream_gene_variant,,ENST00000602733,;TCP11L1,non_coding_transcript_exon_variant,,ENST00000530171,;TCP11L1,missense_variant,p.Gln155His,ENST00000527661,;TCP11L1,3_prime_UTR_variant,,ENST00000528107,; C ENST00000334274 Transcript missense_variant 865/2817 465/1530 155/509 Q/H caG/caC 1 1 TCP11L1 HGNC HGNC:25655 protein_coding YES CCDS7882.1 ENSP00000335595 Q9NUJ3 UPI0000071A1F NM_018393.3 deleterious(0.02) 5/10 Pfam_domain:PF05794,hmmpanther:PTHR12832,hmmpanther:PTHR12832:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 33057966 33057966 G C 1 0 0 0 0 1 0 0 0 16121 933 33 4 4 TCP11L1 11 33057966 Missense_Mutation SNP G C3N-00556_T 18795184 33057966 102028656 270 16399 CKAP5 0 . GRCh38 11 46770063 46770063 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.3222G>A p.= p.E1074E ENST00000529230 26/44 272 258 14 313 313 0 strelka-varscan-mutect CKAP5,synonymous_variant,p.=,ENST00000529230,NM_001008938.3;CKAP5,synonymous_variant,p.=,ENST00000312055,NM_014756.3;CKAP5,synonymous_variant,p.=,ENST00000354558,;CKAP5,non_coding_transcript_exon_variant,,ENST00000533413,;CKAP5,non_coding_transcript_exon_variant,,ENST00000526943,; T ENST00000529230 Transcript synonymous_variant 3269/7121 3222/6099 1074/2032 E gaG/gaA 1 -1 CKAP5 HGNC HGNC:28959 protein_coding YES CCDS31477.1 ENSP00000432768 Q14008 UPI000013F21E NM_001008938.3 26/44 hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609,SMART_domains:SM01349 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 46770063 46770063 C T 1 0 0 0 0 0 0 0 1 3208 912 32 3 3 CKAP5 11 46770063 Silent SNP C C3N-00556_T 13712097 46770063 88316559 271 16400 OR5D18 0 . GRCh38 11 55820565 55820565 + Silent SNP T T G novel C3N-00556_T C3N-00556_N T T c.936T>G p.= p.S312S ENST00000333976 1/1 56 45 11 102 102 0 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; G ENST00000333976 Transcript synonymous_variant 936/942 936/942 312/313 S tcT/tcG 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 55820565 55820565 T G 1 0 0 0 0 0 0 0 1 11227 1596 56 5 5 OR5D18 11 55820565 Silent SNP T C3N-00556_T 9050502 55820565 79266057 272 16401 MS4A2 0 . GRCh38 11 60093972 60093972 + Silent SNP A A T novel C3N-00556_T C3N-00556_N A A c.546A>T p.= p.V182V ENST00000278888 6/7 309 272 37 381 381 0 strelka-mutect MS4A2,synonymous_variant,p.=,ENST00000617306,NM_001256916.1;MS4A2,synonymous_variant,p.=,ENST00000278888,NM_000139.4;MS4A2,downstream_gene_variant,,ENST00000524868,;MS4A2,non_coding_transcript_exon_variant,,ENST00000440896,; T ENST00000278888 Transcript synonymous_variant 648/1152 546/735 182/244 V gtA/gtT 1 1 MS4A2 HGNC HGNC:7316 protein_coding YES CCDS7980.1 ENSP00000278888 Q01362 UPI0000038E6F NM_000139.4 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF66,hmmpanther:PTHR23320,Pfam_domain:PF04103 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 60093972 60093972 A T 1 0 0 0 0 0 0 0 1 9838 407 15 4 4 MS4A2 11 60093972 Silent SNP A C3N-00556_T 4273407 60093972 74992650 273 16402 CD6 0 . GRCh38 11 60971896 60971896 + Silent SNP C C T C3N-00556_T C3N-00556_N C C c.31C>T p.= p.L11L ENST00000313421 1/13 233 203 30 272 272 0 strelka-varscan-mutect CD6,synonymous_variant,p.=,ENST00000313421,NM_006725.4;CD6,synonymous_variant,p.=,ENST00000352009,NM_001254750.1;CD6,synonymous_variant,p.=,ENST00000452451,NM_001254751.1;CD6,synonymous_variant,p.=,ENST00000433107,;CD6,synonymous_variant,p.=,ENST00000542157,;CD6,non_coding_transcript_exon_variant,,ENST00000545105,;CD6,non_coding_transcript_exon_variant,,ENST00000545320,;CD6,synonymous_variant,p.=,ENST00000344931,;CD6,synonymous_variant,p.=,ENST00000542254,; T ENST00000313421 Transcript synonymous_variant 217/3252 31/2007 11/668 L Ctg/Ttg COSM4487538,COSM4487539 1 1 CD6 HGNC HGNC:1691 protein_coding YES CCDS7999.1 ENSP00000323280 P30203 UPI000013F532 NM_006725.4 1/13 Cleavage_site_(Signalp):SignalP-noTM 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 60971896 60971896 C T 1 0 0 0 0 0 0 0 1 2732 796 28 3 3 CD6 11 60971896 Silent SNP C C3N-00556_T 877924 60971896 74114726 274 16403 DAGLA 0 . GRCh38 11 61736296 61736296 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1317C>T p.= p.I439I ENST00000257215 13/20 209 192 17 195 194 1 strelka-varscan-mutect DAGLA,synonymous_variant,p.=,ENST00000257215,NM_006133.2;DAGLA,3_prime_UTR_variant,,ENST00000540717,; T ENST00000257215 Transcript synonymous_variant 1433/5757 1317/3129 439/1042 I atC/atT 1 1 DAGLA HGNC HGNC:1165 protein_coding YES CCDS31578.1 ENSP00000257215 Q9Y4D2 A0A024R517 UPI00001678B3 NM_006133.2 13/20 Gene3D:3.40.50.1820,Pfam_domain:PF01764,hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF102,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 61736296 61736296 C T 1 0 0 0 0 0 0 0 1 4028 816 29 3 3 DAGLA 11 61736296 Silent SNP C C3N-00556_T 764400 61736296 73350326 275 16404 AHNAK 0 . GRCh38 11 62518630 62518630 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.15787G>C p.Glu5263Gln p.E5263Q ENST00000378024 5/5 226 207 19 272 272 0 strelka-varscan-mutect AHNAK,missense_variant,p.Glu5263Gln,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; G ENST00000378024 Transcript missense_variant 16062/18787 15787/17673 5263/5890 E/Q Gaa/Caa 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0.01) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 62518630 62518630 C G 1 0 0 0 0 1 0 0 0 491 835 29 4 4 AHNAK 11 62518630 Missense_Mutation SNP C C3N-00556_T 782334 62518630 72567992 276 16405 SLC22A12 0 . GRCh38 11 64591937 64591937 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.381C>A p.Phe127Leu p.F127L ENST00000377574 1/10 199 162 37 185 185 0 strelka-varscan-mutect SLC22A12,missense_variant,p.Phe127Leu,ENST00000377574,NM_144585.3;SLC22A12,missense_variant,p.Phe127Leu,ENST00000377572,NM_001276327.1;SLC22A12,missense_variant,p.Phe127Leu,ENST00000377567,;SLC22A12,missense_variant,p.Phe127Leu,ENST00000336464,NM_001276326.1;SLC22A12,5_prime_UTR_variant,,ENST00000473690,NM_153378.2; A ENST00000377574 Transcript missense_variant 1128/3206 381/1662 127/553 F/L ttC/ttA 1 1 SLC22A12 HGNC HGNC:17989 protein_coding YES CCDS8075.1 ENSP00000366797 Q96S37 UPI0000040C17 NM_144585.3 deleterious(0.01) 1/10 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF205,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 64591937 64591937 C A 1 0 0 0 0 1 0 0 0 14709 825 29 2 2 SLC22A12 11 64591937 Missense_Mutation SNP C C3N-00556_T 2073307 64591937 70494685 277 16406 PYGM 0 . GRCh38 11 64750423 64750423 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.2130C>T p.= p.F710F ENST00000164139 17/20 383 337 46 365 365 0 strelka-varscan-mutect PYGM,synonymous_variant,p.=,ENST00000164139,NM_005609.2;PYGM,synonymous_variant,p.=,ENST00000377432,NM_001164716.1;RASGRP2,upstream_gene_variant,,ENST00000354024,NM_153819.1;PYGM,downstream_gene_variant,,ENST00000462303,;PYGM,downstream_gene_variant,,ENST00000460413,;PYGM,upstream_gene_variant,,ENST00000483742,; A ENST00000164139 Transcript synonymous_variant 2529/3198 2130/2529 710/842 F ttC/ttT CD941765 1 -1 PYGM HGNC HGNC:9726 protein_coding YES CCDS8079.1 ENSP00000164139 P11217 UPI000013C5AC NM_005609.2 17/20 Gene3D:3.40.50.2000,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF13,Superfamily_domains:SSF53756,TIGRFAM_domain:TIGR02093 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 64750423 64750423 G A 1 0 0 0 0 0 0 0 1 13016 1281 45 3 3 PYGM 11 64750423 Silent SNP G C3N-00556_T 158486 64750423 70336199 278 16407 ZFPL1 0 . GRCh38 11 65084749 65084749 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.51C>G p.Phe17Leu p.F17L ENST00000294258 2/8 240 226 14 254 254 0 strelka-varscan-mutect ZFPL1,missense_variant,p.Phe17Leu,ENST00000294258,NM_006782.3;ZFPL1,missense_variant,p.Phe17Leu,ENST00000532200,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000526334,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000526945,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000525509,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000526791,;CDCA5,upstream_gene_variant,,ENST00000275517,NM_080668.3;CDCA5,upstream_gene_variant,,ENST00000404147,;VPS51,upstream_gene_variant,,ENST00000528588,;TMEM262,downstream_gene_variant,,ENST00000530719,NM_001282448.1;TMEM262,downstream_gene_variant,,ENST00000524603,;TMEM262,downstream_gene_variant,,ENST00000524632,NM_001242631.2;ZFPL1,upstream_gene_variant,,ENST00000530488,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000453524,;ZFPL1,missense_variant,p.Phe17Leu,ENST00000531761,;ZFPL1,non_coding_transcript_exon_variant,,ENST00000533216,;ZFPL1,non_coding_transcript_exon_variant,,ENST00000526289,;ZFPL1,non_coding_transcript_exon_variant,,ENST00000526440,;TMEM262,downstream_gene_variant,,ENST00000528029,;CDCA5,upstream_gene_variant,,ENST00000479032,;CDCA5,upstream_gene_variant,,ENST00000531401,;CDCA5,upstream_gene_variant,,ENST00000524733,;CDCA5,upstream_gene_variant,,ENST00000527430,;TMEM262,downstream_gene_variant,,ENST00000334821,;ZFPL1,upstream_gene_variant,,ENST00000528123,;CDCA5,upstream_gene_variant,,ENST00000462902,;CDCA5,upstream_gene_variant,,ENST00000533015,;ZFPL1,upstream_gene_variant,,ENST00000530744,;TMEM262,downstream_gene_variant,,ENST00000525544,; G ENST00000294258 Transcript missense_variant 203/1371 51/933 17/310 F/L ttC/ttG 1 1 ZFPL1 HGNC HGNC:12868 protein_coding YES CCDS8092.1 ENSP00000294258 O95159 A0A024R576 UPI000007347E NM_006782.3 deleterious(0) 2/8 hmmpanther:PTHR12981,hmmpanther:PTHR12981:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 65084749 65084749 C G 1 0 0 0 0 1 0 0 0 18234 883 31 4 4 ZFPL1 11 65084749 Missense_Mutation SNP C C3N-00556_T 334326 65084749 70001873 279 16408 LTBP3 0 . GRCh38 11 65547775 65547775 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1893C>G p.Ile631Met p.I631M ENST00000301873 13/28 475 447 28 429 428 1 strelka-varscan-mutect LTBP3,missense_variant,p.Ile631Met,ENST00000301873,NM_001130144.2;LTBP3,missense_variant,p.Ile631Met,ENST00000322147,NM_001164266.1,NM_021070.4;LTBP3,missense_variant,p.Ile542Met,ENST00000530866,;LTBP3,missense_variant,p.Ile61Met,ENST00000532932,;LTBP3,missense_variant,p.Ile282Met,ENST00000526927,;LTBP3,upstream_gene_variant,,ENST00000530785,;LTBP3,upstream_gene_variant,,ENST00000529189,;LTBP3,upstream_gene_variant,,ENST00000527339,;LTBP3,downstream_gene_variant,,ENST00000530426,;LTBP3,3_prime_UTR_variant,,ENST00000528516,;LTBP3,upstream_gene_variant,,ENST00000525443,;LTBP3,downstream_gene_variant,,ENST00000526825,;LTBP3,downstream_gene_variant,,ENST00000527792,;LTBP3,downstream_gene_variant,,ENST00000524798,;LTBP3,downstream_gene_variant,,ENST00000528966,;LTBP3,downstream_gene_variant,,ENST00000529764,; C ENST00000301873 Transcript missense_variant 2162/4443 1893/3912 631/1303 I/M atC/atG 1 -1 LTBP3 HGNC HGNC:6716 protein_coding YES CCDS44647.1 ENSP00000301873 Q9NS15 UPI00003667EB NM_001130144.2 tolerated(0.22) 13/28 PROSITE_profiles:PS50026,hmmpanther:PTHR24034:SF46,hmmpanther:PTHR24034,PROSITE_patterns:PS01187,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 65547775 65547775 G C 1 0 0 0 0 1 0 0 0 8981 932 33 4 4 LTBP3 11 65547775 Missense_Mutation SNP G C3N-00556_T 463026 65547775 69538847 280 16409 TSGA10IP 0 . GRCh38 11 65948023 65948023 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1026G>C p.Lys342Asn p.K342N ENST00000532620 4/8 134 125 9 120 120 0 strelka-varscan-mutect TSGA10IP,missense_variant,p.Lys342Asn,ENST00000532620,NM_152762.2;TSGA10IP,intron_variant,,ENST00000608857,;TSGA10IP,intron_variant,,ENST00000534740,;TSGA10IP,downstream_gene_variant,,ENST00000531518,;TSGA10IP,downstream_gene_variant,,ENST00000528291,; C ENST00000532620 Transcript missense_variant 1257/1925 1026/1671 342/556 K/N aaG/aaC 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 tolerated(0.06) 4/8 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 65948023 65948023 G C 1 0 0 0 0 1 0 0 0 17124 933 33 4 4 TSGA10IP 11 65948023 Missense_Mutation SNP G C3N-00556_T 400248 65948023 69138599 281 16410 TSGA10IP 0 . GRCh38 11 65948095 65948095 + Silent SNP C C T rs769002141 C3N-00556_T C3N-00556_N C C c.1098C>T p.= p.F366F ENST00000532620 4/8 210 195 15 182 182 0 strelka-varscan-mutect TSGA10IP,synonymous_variant,p.=,ENST00000532620,NM_152762.2;TSGA10IP,intron_variant,,ENST00000608857,;TSGA10IP,intron_variant,,ENST00000534740,;TSGA10IP,downstream_gene_variant,,ENST00000531518,;TSGA10IP,downstream_gene_variant,,ENST00000528291,; T ENST00000532620 Transcript synonymous_variant 1329/1925 1098/1671 366/556 F ttC/ttT rs769002141,COSM1317276 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 4/8 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5 0,1 LOW 1 SNV 1 0,1 1 PASS rs769002141 . 0 208 0 2 0 0 0 0 -18.96936 0.9999997 1 1 1 0 T 2 4 54 65948095 65948095 C T 1 0 0 0 0 0 0 0 1 17124 883 31 1 1 TSGA10IP 11 65948095 Silent SNP C C3N-00556_T 72 65948095 69138527 282 16411 PPFIA1 0 . GRCh38 11 70339292 70339292 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.1693G>A p.Asp565Asn p.D565N ENST00000253925 14/28 98 91 7 112 112 0 strelka-varscan-mutect PPFIA1,missense_variant,p.Asp565Asn,ENST00000253925,NM_003626.3;PPFIA1,missense_variant,p.Asp565Asn,ENST00000389547,NM_177423.2;PPFIA1,missense_variant,p.Asp117Asn,ENST00000530798,;PPFIA1,upstream_gene_variant,,ENST00000528750,;AP000487.6,intron_variant,,ENST00000528607,;PPFIA1,upstream_gene_variant,,ENST00000530294,;PPFIA1,upstream_gene_variant,,ENST00000526347,;PPFIA1,downstream_gene_variant,,ENST00000532443,;PPFIA1,upstream_gene_variant,,ENST00000526074,;PPFIA1,upstream_gene_variant,,ENST00000528284,;PPFIA1,downstream_gene_variant,,ENST00000530932,;PPFIA1,missense_variant,p.Asp361Asn,ENST00000526262,;PPFIA1,synonymous_variant,p.=,ENST00000532504,;PPFIA1,synonymous_variant,p.=,ENST00000526369,; A ENST00000253925 Transcript missense_variant 1908/5234 1693/3609 565/1202 D/N Gat/Aat COSM1188338 1 1 PPFIA1 HGNC HGNC:9245 protein_coding YES CCDS31627.1 ENSP00000253925 Q13136 UPI0000072426 NM_003626.3 deleterious(0.04) 14/28 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF15 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 70339292 70339292 G A 1 0 0 0 0 1 0 0 0 12418 942 33 3 3 PPFIA1 11 70339292 Missense_Mutation SNP G C3N-00556_T 4391197 70339292 64747330 283 16412 B3GNT6 0 . GRCh38 11 77039938 77039938 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.387C>T p.= p.H129H ENST00000622824 2/2 236 205 31 242 242 0 strelka-varscan-mutect B3GNT6,synonymous_variant,p.=,ENST00000622824,NM_138706.4;B3GNT6,downstream_gene_variant,,ENST00000528622,; T ENST00000622824 Transcript synonymous_variant 468/2503 387/1155 129/384 H caC/caT 1 1 B3GNT6 HGNC HGNC:24141 protein_coding YES CCDS53681.1 ENSP00000484640 Q6ZMB0 A8K9Q8 UPI000006D55A NM_138706.4 2/2 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 77039938 77039938 C T 1 0 0 0 0 0 0 0 1 1417 564 20 3 3 B3GNT6 11 77039938 Silent SNP C C3N-00556_T 6700646 77039938 58046684 284 16413 GRM5 0 . GRCh38 11 88567153 88567153 + Missense_Mutation SNP G G A rs752621407 C3N-00556_T C3N-00556_N G G c.2530C>T p.Arg844Cys p.R844C ENST00000305447 7/9 150 127 23 168 168 0 strelka-varscan-mutect GRM5,missense_variant,p.Arg844Cys,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Arg844Cys,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Arg844Cys,ENST00000305432,; A ENST00000305447 Transcript missense_variant 2680/4571 2530/3639 844/1212 R/C Cgc/Tgc rs752621407,COSM2222117,COSM2222118,COSM311660,COSM311661 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 7/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs752621407 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 54 88567153 88567153 G A 1 0 0 0 0 1 0 0 0 6682 1087 38 1 1 GRM5 11 88567153 Missense_Mutation SNP G C3N-00556_T 11527215 88567153 46519469 285 16414 FAT3 0 . GRCh38 11 92354553 92354553 + Nonsense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1991G>A p.Trp664Ter p.W664* ENST00000525166 1/27 248 227 21 292 292 0 strelka-varscan-mutect FAT3,stop_gained,p.Trp814Ter,ENST00000409404,NM_001008781.2;FAT3,stop_gained,p.Trp664Ter,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; A ENST00000525166 Transcript stop_gained 2013/18699 1991/13320 664/4439 W/* tGg/tAg 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 92354553 92354553 G A 1 0 0 0 0 0 1 0 0 5551 1357 47 3 3 FAT3 11 92354553 Nonsense_Mutation SNP G C3N-00556_T 3787400 92354553 42732069 286 16415 FUT4 0 . GRCh38 11 94544737 94544737 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.604G>A p.Asp202Asn p.D202N ENST00000358752 1/1 143 134 9 148 148 0 strelka-varscan-mutect FUT4,missense_variant,p.Asp202Asn,ENST00000358752,NM_002033.3;RP11-867G2.8,downstream_gene_variant,,ENST00000536540,;RP11-867G2.8,downstream_gene_variant,,ENST00000537874,;PIWIL4,intron_variant,,ENST00000543336,;PIWIL4,upstream_gene_variant,,ENST00000446230,; A ENST00000358752 Transcript missense_variant 898/6059 604/1593 202/530 D/N Gat/Aat COSM5433002 1 1 FUT4 HGNC HGNC:4015 protein_coding YES CCDS8301.1 ENSP00000351602 P22083 UPI000002CC7E NM_002033.3 tolerated(0.31) 1/1 Pfam_domain:PF17039,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF132,Superfamily_domains:SSF53756 1 MODERATE SNV 1 1 PASS rs984644159 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 94544737 94544737 G A 1 0 0 0 0 1 0 0 0 5978 1058 37 1 1 FUT4 11 94544737 Missense_Mutation SNP G C3N-00556_T 2190184 94544737 40541885 287 16416 DYNC2H1 0 . GRCh38 11 103200132 103200132 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.8175G>C p.Met2725Ile p.M2725I ENST00000398093 50/90 217 193 24 274 274 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Met2725Ile,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Met2725Ile,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,;DYNC2H1,upstream_gene_variant,,ENST00000533027,; C ENST00000398093 Transcript missense_variant 8175/12945 8175/12945 2725/4314 M/I atG/atC 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 tolerated(0.36) 50/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Gene3D:3.40.50.300,Pfam_domain:PF12780,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 103200132 103200132 G C 1 0 0 0 0 1 0 0 0 4670 1290 45 4 4 DYNC2H1 11 103200132 Missense_Mutation SNP G C3N-00556_T 8655395 103200132 31886490 288 16417 KMT2A 0 . GRCh38 11 118503798 118503798 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.7906C>T p.Pro2636Ser p.P2636S ENST00000534358 27/36 235 199 36 297 296 1 strelka-varscan-mutect KMT2A,missense_variant,p.Pro2636Ser,ENST00000534358,NM_001197104.1;KMT2A,missense_variant,p.Pro2633Ser,ENST00000389506,NM_005933.3;KMT2A,downstream_gene_variant,,ENST00000528278,;KMT2A,upstream_gene_variant,,ENST00000534085,; T ENST00000534358 Transcript missense_variant 7929/16602 7906/11919 2636/3972 P/S Cca/Tca 1 1 KMT2A HGNC HGNC:7132 protein_coding YES CCDS55791.1 ENSP00000436786 Q03164 UPI0001E5E732 NM_001197104.1 deleterious_low_confidence(0) 27/36 PIRSF_domain:PIRSF010354 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 118503798 118503798 C T 1 0 0 0 0 1 0 0 0 8295 623 22 3 3 KMT2A 11 118503798 Missense_Mutation SNP C C3N-00556_T 15303666 118503798 16582824 289 16418 GRAMD1B 0 . GRCh38 11 123606620 123606620 + Silent SNP G G A rs770078855 C3N-00556_T C3N-00556_N G G c.927G>A p.= p.L309L ENST00000456860 11/21 83 74 9 107 107 0 strelka-varscan-mutect GRAMD1B,synonymous_variant,p.=,ENST00000529750,NM_020716.2;GRAMD1B,synonymous_variant,p.=,ENST00000529432,NM_001286564.1;GRAMD1B,synonymous_variant,p.=,ENST00000638157,;GRAMD1B,synonymous_variant,p.=,ENST00000635736,;GRAMD1B,synonymous_variant,p.=,ENST00000456860,NM_001286563.1;GRAMD1B,synonymous_variant,p.=,ENST00000638086,;GRAMD1B,synonymous_variant,p.=,ENST00000322282,;GRAMD1B,synonymous_variant,p.=,ENST00000534764,;GRAMD1B,upstream_gene_variant,,ENST00000450171,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,; A ENST00000456860 Transcript synonymous_variant 1440/2805 927/2238 309/745 L ctG/ctA rs770078855,COSM1660096,COSM1660097 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 11/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs770078855 . 0 205 4 0 0 0 0 0 -19.22791 1 1 1 1 0 A 2 1 54 123606620 123606620 G A 1 0 0 0 0 0 0 0 1 6627 1306 46 3 3 GRAMD1B 11 123606620 Silent SNP G C3N-00556_T 5102822 123606620 11480002 290 16419 ROBO4 0 . GRCh38 11 124894308 124894308 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1211C>G p.Thr404Ser p.T404S ENST00000306534 8/18 136 128 8 116 116 0 strelka-varscan-mutect ROBO4,missense_variant,p.Thr404Ser,ENST00000306534,NM_019055.5;ROBO4,missense_variant,p.Thr259Ser,ENST00000533054,NM_001301088.1;RP11-664I21.6,downstream_gene_variant,,ENST00000524433,;ROBO4,downstream_gene_variant,,ENST00000526899,;ROBO4,downstream_gene_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000529941,;ROBO4,non_coding_transcript_exon_variant,,ENST00000525182,;ROBO4,upstream_gene_variant,,ENST00000534407,;ROBO4,upstream_gene_variant,,ENST00000532216,;ROBO4,downstream_gene_variant,,ENST00000533337,;ROBO4,downstream_gene_variant,,ENST00000532300,; C ENST00000306534 Transcript missense_variant 1697/4710 1211/3024 404/1007 T/S aCc/aGc 1 -1 ROBO4 HGNC HGNC:17985 protein_coding YES CCDS8455.1 ENSP00000304945 Q8WZ75 UPI000004A023 NM_019055.5 tolerated(0.65) 8/18 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 124894308 124894308 G C 1 0 0 0 0 1 0 0 0 13694 1261 44 4 4 ROBO4 11 124894308 Missense_Mutation SNP G C3N-00556_T 1287688 124894308 10192314 291 16420 WNK1 0 . GRCh38 12 897528 897528 + Nonsense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.7051G>T p.Glu2351Ter p.E2351* ENST00000340908 25/28 434 403 31 485 485 0 strelka-varscan-mutect WNK1,stop_gained,p.Glu2512Ter,ENST00000530271,;WNK1,stop_gained,p.Glu2359Ter,ENST00000537687,NM_001184985.1;WNK1,stop_gained,p.Glu2351Ter,ENST00000340908,NM_213655.4;WNK1,stop_gained,p.Glu2099Ter,ENST00000315939,NM_018979.3;WNK1,stop_gained,p.Glu1851Ter,ENST00000535572,NM_014823.2;WNK1,upstream_gene_variant,,ENST00000544559,;WNK1,upstream_gene_variant,,ENST00000543065,;WNK1,non_coding_transcript_exon_variant,,ENST00000542424,;WNK1,upstream_gene_variant,,ENST00000537603,; T ENST00000340908 Transcript stop_gained 7694/11208 7051/7905 2351/2634 E/* Gaa/Taa 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 25/28 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 897528 897528 G T 1 0 0 0 0 0 1 0 0 17933 1291 45 2 2 WNK1 12 897528 Nonsense_Mutation SNP G C3N-00556_T 897528 132377781 292 16421 CACNA2D4 0 . GRCh38 12 1885014 1885014 + Silent SNP C C G novel C3N-00556_T C3N-00556_N C C c.1131G>C p.= p.L377L ENST00000382722 10/38 230 217 13 256 256 0 strelka-varscan-mutect CACNA2D4,synonymous_variant,p.=,ENST00000382722,NM_172364.4;CACNA2D4,synonymous_variant,p.=,ENST00000587995,;CACNA2D4,synonymous_variant,p.=,ENST00000586184,;CACNA2D4,synonymous_variant,p.=,ENST00000588077,;CACNA2D4,synonymous_variant,p.=,ENST00000585708,;CACNA2D4,synonymous_variant,p.=,ENST00000585732,;CACNA2D4,synonymous_variant,p.=,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,;CACNA2D4,upstream_gene_variant,,ENST00000590880,; G ENST00000382722 Transcript synonymous_variant 1494/5475 1131/3414 377/1137 L ctG/ctC 1 -1 CACNA2D4 HGNC HGNC:20202 protein_coding YES CCDS44785.1 ENSP00000372169 Q7Z3S7 UPI0000E593D9 NM_172364.4 10/38 PROSITE_profiles:PS50234,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF26,Pfam_domain:PF13768,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 1885014 1885014 C G 1 0 0 0 0 0 0 0 1 2239 813 29 4 4 CACNA2D4 12 1885014 Silent SNP C C3N-00556_T 987486 1885014 131390295 293 16422 CACNA1C 0 . GRCh38 12 2688585 2688585 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.6067G>C p.Glu2023Gln p.E2023Q ENST00000347598 48/49 215 199 16 170 170 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Glu2046Gln,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Glu2046Gln,ENST00000406454,;CACNA1C,missense_variant,p.Glu2010Gln,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Glu2000Gln,ENST00000335762,;CACNA1C,missense_variant,p.Glu2023Gln,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Glu2016Gln,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Glu2010Gln,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Glu2003Gln,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Glu1995Gln,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Glu1994Gln,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Glu1994Gln,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Glu1994Gln,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Glu1992Gln,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Glu1983Gln,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Glu1983Gln,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Glu1981Gln,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Glu1975Gln,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Glu666Gln,ENST00000616390,;CACNA1C-AS1,intron_variant,,ENST00000501371,;CACNA1C-AS1,downstream_gene_variant,,ENST00000544517,;CACNA1C-AS1,downstream_gene_variant,,ENST00000541673,; C ENST00000347598 Transcript missense_variant 6067/6655 6067/6561 2023/2186 E/Q Gag/Cag 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 tolerated_low_confidence(0.13) 48/49 MODERATE 1 SNV 1 1 PASS rs910120198 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 2688585 2688585 G C 1 0 0 0 0 1 0 0 0 2228 1291 45 4 4 CACNA1C 12 2688585 Missense_Mutation SNP G C3N-00556_T 803571 2688585 130586724 294 16423 DYRK4 0 . GRCh38 12 4591261 4591261 + Missense_Mutation SNP G G T rs754725794 C3N-00556_T C3N-00556_N G G c.81G>T p.Lys27Asn p.K27N ENST00000540757 3/13 109 98 11 154 153 1 strelka-varscan-mutect DYRK4,missense_variant,p.Lys27Asn,ENST00000540757,NM_003845.2;DYRK4,missense_variant,p.Lys142Asn,ENST00000543431,;DYRK4,missense_variant,p.Lys27Asn,ENST00000010132,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536645,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536157,;DYRK4,non_coding_transcript_exon_variant,,ENST00000542905,;DYRK4,downstream_gene_variant,,ENST00000539309,;DYRK4,downstream_gene_variant,,ENST00000539701,;DYRK4,downstream_gene_variant,,ENST00000537719,;DYRK4,downstream_gene_variant,,ENST00000538520,; T ENST00000540757 Transcript missense_variant 241/3272 81/1563 27/520 K/N aaG/aaT rs754725794 1 1 DYRK4 HGNC HGNC:3095 protein_coding YES CCDS8530.1 ENSP00000441755 Q9NR20 UPI000006E05C NM_003845.2 tolerated(0.13) 3/13 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF22 MODERATE 1 SNV 1 1 PASS rs754725794 . 0 196 9 4 0 0 0 0 -16.56626 0.990976 1 1 1 0 T 3 4 54 4591261 4591261 G T 1 0 0 0 0 1 0 0 0 4682 1020 36 2 2 DYRK4 12 4591261 Missense_Mutation SNP G C3N-00556_T 1902676 4591261 128684048 295 16424 TAPBPL 0 . GRCh38 12 6462063 6462063 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1321G>A p.Glu441Lys p.E441K ENST00000266556 7/7 76 65 11 76 76 0 strelka-varscan-mutect TAPBPL,missense_variant,p.Glu441Lys,ENST00000266556,NM_018009.4;VAMP1,downstream_gene_variant,,ENST00000361716,NM_199245.2;VAMP1,downstream_gene_variant,,ENST00000396308,NM_014231.4;VAMP1,downstream_gene_variant,,ENST00000400911,NM_016830.3;TAPBPL,downstream_gene_variant,,ENST00000544021,;VAMP1,downstream_gene_variant,,ENST00000535180,NM_001297438.1;RP1-102E24.10,upstream_gene_variant,,ENST00000619166,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000545700,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000539384,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000543567,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000544289,;TAPBPL,non_coding_transcript_exon_variant,,ENST00000542160,;VAMP1,downstream_gene_variant,,ENST00000544432,;VAMP1,downstream_gene_variant,,ENST00000539047,;VAMP1,downstream_gene_variant,,ENST00000535927,;VAMP1,downstream_gene_variant,,ENST00000538970,; A ENST00000266556 Transcript missense_variant 1486/1741 1321/1407 441/468 E/K Gaa/Aaa 1 1 TAPBPL HGNC HGNC:30683 protein_coding YES CCDS8546.1 ENSP00000266556 Q9BX59 UPI000013D6F6 NM_018009.4 tolerated_low_confidence(0.08) 7/7 hmmpanther:PTHR23411,hmmpanther:PTHR23411:SF3 MODERATE 1 SNV 1 1 PASS . . 0 202 6 2 0 0 0 0 -18.78163 0.9999124 1 1 1 0 A 3 1 54 6462063 6462063 G A 1 0 0 0 0 1 0 0 0 15952 1291 45 3 3 TAPBPL 12 6462063 Missense_Mutation SNP G C3N-00556_T 1870802 6462063 126813246 296 16425 COPS7A 0 . GRCh38 12 6730680 6730681 + Frame_Shift_Ins INS - - A novel C3N-00556_T C3N-00556_N - - c.655dupA p.Thr219AsnfsTer3 p.T219Nfs*3 ENST00000543155 7/8 102 65 37 145 143 2 sindel-varindel COPS7A,frameshift_variant,p.Thr219AsnfsTer3,ENST00000543155,NM_001164094.1;COPS7A,frameshift_variant,p.Thr219AsnfsTer3,ENST00000534947,NM_001164093.1;COPS7A,frameshift_variant,p.Thr219AsnfsTer3,ENST00000539735,NM_001164095.2;COPS7A,frameshift_variant,p.Thr219AsnfsTer3,ENST00000229251,NM_016319.3;COPS7A,frameshift_variant,p.Thr219AsnfsTer3,ENST00000534877,;COPS7A,3_prime_UTR_variant,,ENST00000626119,;COPS7A,intron_variant,,ENST00000538410,;COPS7A,downstream_gene_variant,,ENST00000541866,;COPS7A,downstream_gene_variant,,ENST00000538753,;COPS7A,downstream_gene_variant,,ENST00000544725,;COPS7A,non_coding_transcript_exon_variant,,ENST00000542150,;COPS7A,3_prime_UTR_variant,,ENST00000543939,;COPS7A,3_prime_UTR_variant,,ENST00000455113,;COPS7A,3_prime_UTR_variant,,ENST00000538375,;COPS7A,3_prime_UTR_variant,,ENST00000543537,;COPS7A,non_coding_transcript_exon_variant,,ENST00000542630,;COPS7A,downstream_gene_variant,,ENST00000536872,;COPS7A,downstream_gene_variant,,ENST00000546229,;COPS7A,downstream_gene_variant,,ENST00000540408,;COPS7A,downstream_gene_variant,,ENST00000543170,;COPS7A,downstream_gene_variant,,ENST00000544316,;COPS7A,downstream_gene_variant,,ENST00000537022,; A ENST00000543155 Transcript frameshift_variant 1130-1131/2127 648-649/828 216-217/275 -/X -/A 1 1 COPS7A HGNC HGNC:16758 protein_coding YES CCDS8558.1 ENSP00000438115 Q9UBW8 UPI0000035DA4 NM_001164094.1 7/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15350:SF7,hmmpanther:PTHR15350 HIGH 1 insertion 1 7 1 PASS . . 0 198 6 6 0 0 0 0 -20 0.9980494 1 1 1 0 A 7 5 54 6730680 6730680 - A 1 0 1 1 0 0 0 0 0 3531 1741 61 0 0 COPS7A 12 6730680 Frame_Shift_Ins INS - C3N-00556_T 268617 6730680 126544629 297 16426 ACSM4 0 . GRCh38 12 7324584 7324584 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1522C>G p.Gln508Glu p.Q508E ENST00000399422 11/13 225 203 22 290 290 0 strelka-varscan-mutect ACSM4,missense_variant,p.Gln508Glu,ENST00000399422,NM_001080454.1; G ENST00000399422 Transcript missense_variant 1570/2142 1522/1743 508/580 Q/E Caa/Gaa 1 1 ACSM4 HGNC HGNC:32016 protein_coding YES CCDS44825.1 ENSP00000382349 P0C7M7 UPI0000DD812A NM_001080454.1 tolerated(0.11) 11/13 hmmpanther:PTHR24095:SF127,hmmpanther:PTHR24095,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 7324584 7324584 C G 1 0 0 0 0 1 0 0 0 228 827 29 4 4 ACSM4 12 7324584 Missense_Mutation SNP C C3N-00556_T 593904 7324584 125950725 298 16427 CLEC4D 0 . GRCh38 12 8515253 8515253 + Missense_Mutation SNP C C A rs766350813 C3N-00556_T C3N-00556_N C C c.46C>A p.Pro16Thr p.P16T ENST00000299665 2/6 150 117 33 204 204 0 strelka-varscan-mutect CLEC4D,missense_variant,p.Pro16Thr,ENST00000299665,NM_080387.4;CLEC4D,missense_variant,p.Pro16Thr,ENST00000382064,;SUPT4H1P2,upstream_gene_variant,,ENST00000501248,; A ENST00000299665 Transcript missense_variant 239/1936 46/648 16/215 P/T Ccc/Acc rs766350813 1 1 CLEC4D HGNC HGNC:14554 protein_coding YES CCDS8593.1 ENSP00000299665 Q8WXI8 UPI0000072EBB NM_080387.4 tolerated(0.38) 2/6 hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF11 MODERATE 1 SNV 1 1 PASS rs766350813 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 8515253 8515253 C A 1 0 0 0 0 1 0 0 0 3282 855 30 2 2 CLEC4D 12 8515253 Missense_Mutation SNP C C3N-00556_T 1190669 8515253 124760056 299 16428 PRB2 0 . GRCh38 12 11393388 11393388 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.690C>A p.Asn230Lys p.N230K ENST00000389362 3/4 186 150 36 281 281 0 strelka-varscan-mutect PRB2,missense_variant,p.Asn230Lys,ENST00000389362,NM_006248.3;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,; T ENST00000389362 Transcript missense_variant 726/1429 690/1251 230/416 N/K aaC/aaA 1 -1 PRB2 HGNC HGNC:9338 protein_coding YES CCDS41757.2 ENSP00000374013 P02812 UPI0000EE5993 NM_006248.3 tolerated(0.95) 3/4 hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF2,SMART_domains:SM01412 MODERATE 1 SNV 5 1 PASS rs1380663850 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 11393388 11393388 G T 1 0 0 0 0 1 0 0 0 12574 1368 48 2 2 PRB2 12 11393388 Missense_Mutation SNP G C3N-00556_T 2878135 11393388 121881921 300 16429 PYROXD1 0 . GRCh38 12 21462800 21462800 + Missense_Mutation SNP G G C rs765266761 C3N-00556_T C3N-00556_N G G c.1054G>C p.Asp352His p.D352H ENST00000240651 10/12 205 182 23 258 258 0 varscan-mutect PYROXD1,missense_variant,p.Asp352His,ENST00000240651,NM_024854.3;PYROXD1,missense_variant,p.Asp281His,ENST00000538582,;PYROXD1,3_prime_UTR_variant,,ENST00000375266,;PYROXD1,3_prime_UTR_variant,,ENST00000544970,;PYROXD1,non_coding_transcript_exon_variant,,ENST00000536851,;PYROXD1,downstream_gene_variant,,ENST00000543476,;PYROXD1,upstream_gene_variant,,ENST00000538615,;PYROXD1,downstream_gene_variant,,ENST00000544187,; C ENST00000240651 Transcript missense_variant 1108/4055 1054/1503 352/500 D/H Gat/Cat rs765266761 1 1 PYROXD1 HGNC HGNC:26162 protein_coding YES CCDS31755.1 ENSP00000240651 Q8WU10 UPI000006CE59 NM_024854.3 deleterious(0.04) 10/12 Gene3D:3.50.50.60,Pfam_domain:PF07992,Prints_domain:PR00368,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF98,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS rs765266761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 21462800 21462800 G C 1 0 0 0 0 1 0 0 0 13021 1290 45 4 4 PYROXD1 12 21462800 Missense_Mutation SNP G C3N-00556_T 10069412 21462800 111812509 301 16430 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-00556_T C3N-00556_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 357 242 115 335 334 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-00556_T 3782551 25245351 108029958 302 16431 ANO6 0 . GRCh38 12 45429296 45429296 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.2781G>T p.= p.R927R ENST00000423947 21/21 340 282 58 366 366 0 strelka-varscan-mutect ANO6,synonymous_variant,p.=,ENST00000320560,NM_001025356.2;ANO6,synonymous_variant,p.=,ENST00000441606,NM_001142678.1;ANO6,synonymous_variant,p.=,ENST00000423947,NM_001204803.1;ANO6,intron_variant,,ENST00000425752,NM_001142679.1; T ENST00000423947 Transcript synonymous_variant 3018/5504 2781/2796 927/931 R cgG/cgT 1 1 ANO6 HGNC HGNC:25240 protein_coding YES CCDS55819.1 ENSP00000409126 Q4KMQ2 UPI000022935A NM_001204803.1 21/21 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 45429296 45429296 G T 1 0 0 0 0 0 0 0 1 808 1190 42 2 2 ANO6 12 45429296 Silent SNP G C3N-00556_T 20183945 45429296 87846013 303 16432 ADCY6 0 . GRCh38 12 48773618 48773618 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.2472C>T p.= p.L824L ENST00000307885 15/21 442 415 27 351 350 1 strelka-varscan-mutect ADCY6,synonymous_variant,p.=,ENST00000307885,NM_015270.3;ADCY6,synonymous_variant,p.=,ENST00000550422,NM_020983.2;ADCY6,synonymous_variant,p.=,ENST00000357869,;ADCY6,downstream_gene_variant,,ENST00000548820,;MIR4701,upstream_gene_variant,,ENST00000583094,;ADCY6,non_coding_transcript_exon_variant,,ENST00000548351,;ADCY6,downstream_gene_variant,,ENST00000552090,;ADCY6,non_coding_transcript_exon_variant,,ENST00000547260,;ADCY6,non_coding_transcript_exon_variant,,ENST00000552099,;ADCY6,downstream_gene_variant,,ENST00000551435,; A ENST00000307885 Transcript synonymous_variant 3167/6464 2472/3507 824/1168 L ctC/ctT 1 -1 ADCY6 HGNC HGNC:237 protein_coding YES CCDS8767.1 ENSP00000311405 O43306 UPI000003EC29 NM_015270.3 15/21 hmmpanther:PTHR11920:SF343,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 48773618 48773618 G A 1 0 0 0 0 0 0 0 1 342 929 33 3 3 ADCY6 12 48773618 Silent SNP G C3N-00556_T 3344322 48773618 84501691 304 16433 KCNH3 0 . GRCh38 12 49555843 49555843 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2360G>A p.Arg787Lys p.R787K ENST00000257981 12/15 106 99 7 90 90 0 strelka-varscan-mutect KCNH3,missense_variant,p.Arg787Lys,ENST00000257981,NM_001314030.1,NM_012284.1;MCRS1,downstream_gene_variant,,ENST00000550165,;MCRS1,downstream_gene_variant,,ENST00000343810,NM_006337.4;MCRS1,downstream_gene_variant,,ENST00000546244,NM_001278341.1;MCRS1,downstream_gene_variant,,ENST00000357123,NM_001012300.1;MCRS1,downstream_gene_variant,,ENST00000553173,;MCRS1,downstream_gene_variant,,ENST00000551598,;MCRS1,downstream_gene_variant,,ENST00000547182,;MCRS1,downstream_gene_variant,,ENST00000551625,;MCRS1,downstream_gene_variant,,ENST00000548602,;MCRS1,downstream_gene_variant,,ENST00000549000,;MCRS1,downstream_gene_variant,,ENST00000552596,;KCNH3,upstream_gene_variant,,ENST00000548675,;MCRS1,downstream_gene_variant,,ENST00000548646,; A ENST00000257981 Transcript missense_variant 2620/3867 2360/3252 787/1083 R/K aGg/aAg 1 1 KCNH3 HGNC HGNC:6252 protein_coding YES CCDS8786.1 ENSP00000257981 Q9ULD8 UPI000012DCA6 NM_001314030.1,NM_012284.1 tolerated(0.81) 12/15 Low_complexity_(Seg):seg,hmmpanther:PTHR10217:SF481,hmmpanther:PTHR10217 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -10.80565 0.999965 1 1 1 0 A 3 1 54 49555843 49555843 G A 1 0 0 0 0 1 0 0 0 7949 1000 35 3 3 KCNH3 12 49555843 Missense_Mutation SNP G C3N-00556_T 782225 49555843 83719466 305 16434 FAM186A 0 . GRCh38 12 50354786 50354786 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2046G>C p.Gln682His p.Q682H ENST00000327337 4/8 124 116 8 149 149 0 strelka-varscan-mutect FAM186A,missense_variant,p.Gln682His,ENST00000543111,;FAM186A,missense_variant,p.Gln682His,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; G ENST00000327337 Transcript missense_variant 2046/7127 2046/7056 682/2351 Q/H caG/caC 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 deleterious(0.02) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS rs1474247998 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 50354786 50354786 C G 1 0 0 0 0 1 0 0 0 5361 912 32 4 4 FAM186A 12 50354786 Missense_Mutation SNP C C3N-00556_T 798943 50354786 82920523 306 16435 KRT6B 0 . GRCh38 12 52449633 52449633 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.913G>C p.Glu305Gln p.E305Q ENST00000252252 5/9 535 506 29 503 502 1 varscan-mutect KRT6B,missense_variant,p.Glu305Gln,ENST00000252252,NM_005555.3; G ENST00000252252 Transcript missense_variant,splice_region_variant 961/2282 913/1695 305/564 E/Q Gag/Cag 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 deleterious(0) 5/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs1187052028 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 52449633 52449633 C G 1 0 0 0 0 1 0 0 0 8363 869 30 4 4 KRT6B 12 52449633 Missense_Mutation SNP C C3N-00556_T 2094847 52449633 80825676 307 16436 PDE1B 0 . GRCh38 12 54569600 54569600 + Silent SNP C C G rs769568392 C3N-00556_T C3N-00556_N C C c.465C>G p.= p.L155L ENST00000243052 5/16 248 221 27 200 200 0 strelka-varscan-mutect PDE1B,synonymous_variant,p.=,ENST00000243052,NM_000924.3;PDE1B,synonymous_variant,p.=,ENST00000550620,NM_001165975.2;PDE1B,synonymous_variant,p.=,ENST00000538346,NM_001288768.1,NM_001288769.1;PDE1B,non_coding_transcript_exon_variant,,ENST00000394277,;PDE1B,intron_variant,,ENST00000542335,;PDE1B,stop_gained,p.Ser176Ter,ENST00000550285,;PDE1B,non_coding_transcript_exon_variant,,ENST00000548855,;PDE1B,downstream_gene_variant,,ENST00000611899,; G ENST00000243052 Transcript synonymous_variant 901/3444 465/1611 155/536 L ctC/ctG rs769568392 1 1 PDE1B HGNC HGNC:8775 protein_coding YES CCDS8882.1 ENSP00000243052 Q01064 A0A024RB59 UPI0000001607 NM_000924.3 5/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF128,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 LOW 1 SNV 1 1 PASS rs769568392 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 54569600 54569600 C G 1 0 0 0 0 0 0 0 1 11722 813 29 4 4 PDE1B 12 54569600 Silent SNP C C3N-00556_T 2119967 54569600 78705709 308 16437 ESYT1 0 . GRCh38 12 56128679 56128679 + Silent SNP C C G novel C3N-00556_T C3N-00556_N C C c.360C>G p.= p.L120L ENST00000267113 1/31 350 300 50 315 315 0 strelka-varscan-mutect ESYT1,synonymous_variant,p.=,ENST00000394048,NM_015292.2;ESYT1,synonymous_variant,p.=,ENST00000267113,NM_001184796.1;ESYT1,5_prime_UTR_variant,,ENST00000551790,;ZC3H10,downstream_gene_variant,,ENST00000257940,NM_032786.2,NM_001303124.1,NM_001303125.1;RP11-603J24.5,non_coding_transcript_exon_variant,,ENST00000549438,;RP11-603J24.5,intron_variant,,ENST00000550947,;ESYT1,upstream_gene_variant,,ENST00000550986,;ESYT1,upstream_gene_variant,,ENST00000550179,; G ENST00000267113 Transcript synonymous_variant 413/3577 360/3345 120/1114 L ctC/ctG 1 1 ESYT1 HGNC HGNC:29534 protein_coding YES CCDS53801.1 ENSP00000267113 Q9BSJ8 A0A024RB16 UPI0000D720B2 NM_001184796.1 1/31 hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 56128679 56128679 C G 1 0 0 0 0 0 0 0 1 5126 900 32 4 4 ESYT1 12 56128679 Silent SNP C C3N-00556_T 1559079 56128679 77146630 309 16438 DPY19L2 0 . GRCh38 12 63644415 63644415 + Frame_Shift_Del DEL C C - novel C3N-00556_T C3N-00556_N C C c.791delG p.Gly264GlufsTer4 p.G264Efs*4 ENST00000324472 6/22 112 101 11 123 123 0 sindel-varindel-pindel DPY19L2,frameshift_variant,p.Gly264GlufsTer4,ENST00000324472,NM_173812.4;RP11-415I12.3,intron_variant,,ENST00000509615,;DPY19L2,3_prime_UTR_variant,,ENST00000306389,; - ENST00000324472 Transcript frameshift_variant 975/4060 791/2277 264/758 G/X gGa/ga 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 6/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99722 1 1 1 1 0 - 7 5 54 63644415 63644415 C - 1 0 1 0 1 0 0 0 0 4556 855 30 0 0 DPY19L2 12 63644415 Frame_Shift_Del DEL C C3N-00556_T 7515736 63644415 69630894 310 16439 ZFC3H1 0 . GRCh38 12 71629001 71629001 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.3863G>T p.Trp1288Leu p.W1288L ENST00000378743 20/35 93 75 18 113 113 0 strelka-varscan-mutect ZFC3H1,missense_variant,p.Trp1288Leu,ENST00000378743,NM_144982.4;ZFC3H1,missense_variant,p.Trp1288Leu,ENST00000552994,;ZFC3H1,downstream_gene_variant,,ENST00000546606,; A ENST00000378743 Transcript missense_variant 4222/7285 3863/5970 1288/1989 W/L tGg/tTg 1 -1 ZFC3H1 HGNC HGNC:28328 protein_coding YES CCDS41813.1 ENSP00000368017 O60293 UPI00003668E9 NM_144982.4 deleterious(0) 20/35 hmmpanther:PTHR21563,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 54 71629001 71629001 C A 1 0 0 0 0 1 0 0 0 18210 595 21 2 2 ZFC3H1 12 71629001 Missense_Mutation SNP C C3N-00556_T 7984586 71629001 61646308 311 16440 TRHDE 0 . GRCh38 12 72652346 72652346 + Silent SNP C C T C3N-00556_T C3N-00556_N C C c.2565C>T p.= p.I855I ENST00000261180 16/19 99 93 6 126 125 1 strelka-varscan-mutect TRHDE,synonymous_variant,p.=,ENST00000261180,NM_013381.2; T ENST00000261180 Transcript synonymous_variant 2661/10733 2565/3075 855/1024 I atC/atT COSM3465131 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 16/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -12.67611 1 1 1 1 0 T 2 4 54 72652346 72652346 C T 1 0 0 0 0 0 0 0 1 16968 874 31 1 1 TRHDE 12 72652346 Silent SNP C C3N-00556_T 1023345 72652346 60622963 312 16441 LRRIQ1 0 . GRCh38 12 85040499 85040499 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.142G>A p.Glu48Lys p.E48K ENST00000393217 3/27 47 43 4 75 75 0 strelka-varscan-mutect LRRIQ1,missense_variant,p.Glu48Lys,ENST00000393217,NM_001079910.1;LRRIQ1,missense_variant,p.Glu48Lys,ENST00000393212,;TSPAN19,upstream_gene_variant,,ENST00000532498,NM_001100917.1;TSPAN19,upstream_gene_variant,,ENST00000547836,;LRRIQ1,upstream_gene_variant,,ENST00000533414,;TSPAN19,upstream_gene_variant,,ENST00000547403,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000529408,;TSPAN19,upstream_gene_variant,,ENST00000532628,;TSPAN19,upstream_gene_variant,,ENST00000552392,;TSPAN19,upstream_gene_variant,,ENST00000433494,; A ENST00000393217 Transcript missense_variant 203/5394 142/5169 48/1722 E/K Gaa/Aaa 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 tolerated(0.09) 3/27 MODERATE 1 SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -10.62708 1 1 1 1 0 A 3 1 54 85040499 85040499 G A 1 0 0 0 0 1 0 0 0 8935 1291 45 3 3 LRRIQ1 12 85040499 Missense_Mutation SNP G C3N-00556_T 12388153 85040499 48234810 313 16442 RASSF9 0 . GRCh38 12 85805939 85805939 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.71C>T p.Ser24Leu p.S24L ENST00000361228 2/2 55 48 7 80 80 0 strelka-varscan-mutect RASSF9,missense_variant,p.Ser24Leu,ENST00000361228,NM_005447.3; A ENST00000361228 Transcript missense_variant 440/5682 71/1308 24/435 S/L tCa/tTa 1 -1 RASSF9 HGNC HGNC:15739 protein_coding YES CCDS44950.1 ENSP00000354884 O75901 UPI000003E7E4 NM_005447.3 tolerated(0.09) 2/2 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF10,SMART_domains:SM00314 MODERATE 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -16.07432 0.9997874 1 1 1 0 A 3 1 54 85805939 85805939 G A 1 0 0 0 0 1 0 0 0 13254 1294 45 3 3 RASSF9 12 85805939 Missense_Mutation SNP G C3N-00556_T 765440 85805939 47469370 314 16443 CFAP54 0 . GRCh38 12 96743540 96743540 + Missense_Mutation SNP A A T novel C3N-00556_T C3N-00556_N A A c.7358A>T p.Asp2453Val p.D2453V ENST00000524981 53/68 178 138 40 187 186 1 strelka-varscan-mutect CFAP54,missense_variant,p.Asp2453Val,ENST00000524981,NM_001306084.1;CFAP54,missense_variant,p.Asp1424Val,ENST00000637336,;CFAP54,non_coding_transcript_exon_variant,,ENST00000342887,; T ENST00000524981 Transcript missense_variant 7381/9766 7358/9291 2453/3096 D/V gAc/gTc 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 deleterious(0) 53/68 hmmpanther:PTHR33487,hmmpanther:PTHR33487:SF2 MODERATE 1 SNV 5 1 PASS rs1489574967 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 96743540 96743540 A T 1 0 0 0 0 1 0 0 0 3025 275 10 4 4 CFAP54 12 96743540 Missense_Mutation SNP A C3N-00556_T 10937601 96743540 36531769 315 16444 STAB2 0 . GRCh38 12 103753317 103753317 + Silent SNP C C A rs200959680 C3N-00556_T C3N-00556_N C C c.6678C>A p.= p.T2226T ENST00000388887 61/69 209 166 43 212 212 0 strelka-varscan-mutect STAB2,synonymous_variant,p.=,ENST00000388887,NM_017564.9;RP11-341G23.4,intron_variant,,ENST00000551299,;STAB2,upstream_gene_variant,,ENST00000548073,;STAB2,upstream_gene_variant,,ENST00000548579,; A ENST00000388887 Transcript synonymous_variant 6882/8251 6678/7656 2226/2551 T acC/acA rs200959680 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 61/69 PROSITE_profiles:PS50963,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,PROSITE_patterns:PS01241,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs200959680 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 103753317 103753317 C A 1 0 0 0 0 0 0 0 1 15616 581 21 2 2 STAB2 12 103753317 Silent SNP C C3N-00556_T 7009777 103753317 29521992 316 16445 DAO 0 . GRCh38 12 108889493 108889493 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.334C>A p.Leu112Met p.L112M ENST00000228476 4/11 328 221 107 294 294 0 strelka-varscan-mutect DAO,missense_variant,p.Leu112Met,ENST00000228476,NM_001917.4;DAO,missense_variant,p.Leu112Met,ENST00000547166,;DAO,5_prime_UTR_variant,,ENST00000547768,;DAO,intron_variant,,ENST00000551281,;DAO,missense_variant,p.Phe73Leu,ENST00000547122,;DAO,intron_variant,,ENST00000549215,; A ENST00000228476 Transcript missense_variant 538/1756 334/1044 112/347 L/M Ctg/Atg 1 1 DAO HGNC HGNC:2671 protein_coding YES CCDS9122.1 ENSP00000228476 P14920 A0A024RBI1 UPI0000130F5F NM_001917.4 deleterious(0) 4/11 Gene3D:3.30.9.10,Pfam_domain:PF01266,PIRSF_domain:PIRSF000189,hmmpanther:PTHR11530,hmmpanther:PTHR11530:SF11,Superfamily_domains:SSF51971 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 108889493 108889493 C A 1 0 0 0 0 1 0 0 0 4032 912 32 2 2 DAO 12 108889493 Missense_Mutation SNP C C3N-00556_T 5136176 108889493 24385816 317 16446 GIT2 0 . GRCh38 12 109959864 109959864 + Missense_Mutation SNP G G C C3N-00556_T C3N-00556_N G G c.1082C>G p.Ser361Cys p.S361C ENST00000355312 12/20 172 161 11 191 191 0 strelka-varscan-mutect GIT2,missense_variant,p.Ser361Cys,ENST00000355312,NM_057169.3;GIT2,missense_variant,p.Ser361Cys,ENST00000361006,NM_001135214.1;GIT2,missense_variant,p.Ser363Cys,ENST00000354574,NM_014776.3;GIT2,missense_variant,p.Ser363Cys,ENST00000457474,NM_001135213.1;GIT2,missense_variant,p.Ser361Cys,ENST00000547815,NM_139201.2;GIT2,missense_variant,p.Ser361Cys,ENST00000553118,NM_057170.3;GIT2,missense_variant,p.Ser360Cys,ENST00000551209,;GIT2,missense_variant,p.Ser361Cys,ENST00000320063,;GIT2,missense_variant,p.Ser299Cys,ENST00000550186,;TCHP,intron_variant,,ENST00000550780,;GIT2,non_coding_transcript_exon_variant,,ENST00000551455,;GIT2,non_coding_transcript_exon_variant,,ENST00000547694,;GIT2,downstream_gene_variant,,ENST00000551721,; C ENST00000355312 Transcript missense_variant 1082/5466 1082/2280 361/759 S/C tCt/tGt COSM1706261,COSM1706262 1 -1 GIT2 HGNC HGNC:4273 protein_coding YES CCDS9138.1 ENSP00000347464 Q14161 UPI000012B4C5 NM_057169.3 deleterious(0.03) 12/20 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF248 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 109959864 109959864 G C 1 0 0 0 0 1 0 0 0 6279 942 33 4 4 GIT2 12 109959864 Missense_Mutation SNP G C3N-00556_T 1070371 109959864 23315445 318 16447 NOS1 0 . GRCh38 12 117234608 117234608 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.3294G>C p.Gln1098His p.Q1098H ENST00000618760 22/30 121 106 15 87 87 0 strelka-varscan-mutect NOS1,missense_variant,p.Gln1098His,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Gln1064His,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Gln1098His,ENST00000338101,;NOS1,missense_variant,p.Gln1063His,ENST00000344089,; G ENST00000618760 Transcript missense_variant 4005/12283 3294/4407 1098/1468 Q/H caG/caC 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 tolerated(0.05) 22/30 PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Gene3D:1.20.990.10,Pfam_domain:PF00667,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380 MODERATE 1 SNV 5 1 PASS . . 0 204 4 2 0 0 0 0 -19.99946 0.9999749 1 1 1 0 G 3 3 54 117234608 117234608 C G 1 0 0 0 0 1 0 0 0 10586 912 32 4 4 NOS1 12 117234608 Missense_Mutation SNP C C3N-00556_T 7274744 117234608 16040701 319 16448 GCN1 0 . GRCh38 12 120190337 120190337 + Missense_Mutation SNP C C G C3N-00556_T C3N-00556_N C C c.82G>C p.Glu28Gln p.E28Q ENST00000300648 2/58 192 182 10 214 214 0 strelka-varscan-mutect GCN1,missense_variant,p.Glu28Gln,ENST00000300648,NM_006836.1; G ENST00000300648 Transcript missense_variant 95/8675 82/8016 28/2671 E/Q Gaa/Caa COSM5478017 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 tolerated(0.42) 2/58 hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7 1 MODERATE 1 SNV 1 1 1 PASS rs1171494851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 120190337 120190337 C G 1 0 0 0 0 1 0 0 0 6169 922 32 4 4 GCN1 12 120190337 Missense_Mutation SNP C C3N-00556_T 2955729 120190337 13084972 320 16449 HNF1A 0 . GRCh38 12 120994336 120994336 + Nonsense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.886G>T p.Gly296Ter p.G296* ENST00000544413 4/10 220 169 51 242 242 0 strelka-varscan-mutect HNF1A,stop_gained,p.Gly296Ter,ENST00000257555,NM_000545.5;HNF1A,stop_gained,p.Gly296Ter,ENST00000541395,;HNF1A,stop_gained,p.Gly296Ter,ENST00000400024,;HNF1A,stop_gained,p.Gly296Ter,ENST00000544413,NM_001306179.1;HNF1A,intron_variant,,ENST00000543427,;HNF1A,intron_variant,,ENST00000617366,;HNF1A,intron_variant,,ENST00000615446,;HNF1A,intron_variant,,ENST00000538626,;HNF1A,intron_variant,,ENST00000535955,;HNF1A,synonymous_variant,p.=,ENST00000538646,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,non_coding_transcript_exon_variant,,ENST00000402929,;HNF1A,intron_variant,,ENST00000560968,;HNF1A,intron_variant,,ENST00000541924,;HNF1A,intron_variant,,ENST00000544574,;HNF1A,upstream_gene_variant,,ENST00000543255,; T ENST00000544413 Transcript stop_gained 906/2014 886/1917 296/638 G/* Gga/Tga 1 1 HNF1A HGNC HGNC:11621 protein_coding YES CCDS76611.1 ENSP00000438804 F5H0K0 UPI000204ABCC NM_001306179.1 4/10 Pfam_domain:PF04812,hmmpanther:PTHR11568,hmmpanther:PTHR11568:SF4,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 120994336 120994336 G T 1 0 0 0 0 0 1 0 0 7142 1233 43 2 2 HNF1A 12 120994336 Nonsense_Mutation SNP G C3N-00556_T 803999 120994336 12280973 321 16450 RNF34 0 . GRCh38 12 121430141 121430141 + Missense_Mutation SNP G G A rs782116976 C3N-00556_T C3N-00556_N G G c.3773C>T p.Ser1258Leu p.S1258L ENST00000377069 23/23 327 305 22 340 340 0 strelka-varscan-mutect KDM2B,missense_variant,p.Ser1258Leu,ENST00000377069,NM_001005366.1;RNF34,missense_variant,p.Glu391Lys,ENST00000392464,;KDM2B,3_prime_UTR_variant,,ENST00000377071,NM_032590.4;KDM2B,3_prime_UTR_variant,,ENST00000611216,;KDM2B,3_prime_UTR_variant,,ENST00000542973,;KDM2B,3_prime_UTR_variant,,ENST00000536437,;KDM2B,3_prime_UTR_variant,,ENST00000543025,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538503,; A ENST00000377069 Transcript missense_variant 4180/5224 3773/3798 1258/1265 S/L tCa/tTa rs782116976 1 -1 KDM2B HGNC HGNC:13610 protein_coding CCDS41849.1 ENSP00000366269 Q8NHM5 UPI000044FEA8 NM_001005366.1 deleterious_low_confidence(0) 23/23 Gene3D:3.80.10.10 MODERATE SNV 2 1 PASS rs782116976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 121430141 121430141 G A 1 0 0 0 0 1 0 0 0 13669 1291 45 3 3 RNF34 12 121430141 Missense_Mutation SNP G C3N-00556_T 435805 121430141 11845168 322 16451 SETD1B 0 . GRCh38 12 121819593 121819593 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3479C>T p.Ser1160Phe p.S1160F ENST00000542440 12/18 396 360 36 360 359 1 strelka-varscan-mutect SETD1B,missense_variant,p.Ser1160Phe,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Ser1203Phe,ENST00000604567,;SETD1B,missense_variant,p.Ser1203Phe,ENST00000619791,;SETD1B,missense_variant,p.Ser1160Phe,ENST00000267197,; T ENST00000542440 Transcript missense_variant 3547/8185 3479/5772 1160/1923 S/F tCt/tTt 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 deleterious_low_confidence(0) 12/18 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 121819593 121819593 C T 1 0 0 0 0 1 0 0 0 14408 913 32 3 3 SETD1B 12 121819593 Missense_Mutation SNP C C3N-00556_T 389452 121819593 11455716 323 16452 KNTC1 0 . GRCh38 12 122586708 122586708 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.3681G>C p.Lys1227Asn p.K1227N ENST00000333479 38/64 111 96 15 91 91 0 strelka-varscan-mutect KNTC1,missense_variant,p.Lys1227Asn,ENST00000333479,NM_014708.4;KNTC1,intron_variant,,ENST00000450485,; C ENST00000333479 Transcript missense_variant 3858/6975 3681/6630 1227/2209 K/N aaG/aaC 1 1 KNTC1 HGNC HGNC:17255 protein_coding YES CCDS45002.1 ENSP00000328236 P50748 UPI0000047FD6 NM_014708.4 deleterious(0.03) 38/64 hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 122586708 122586708 G C 1 0 0 0 0 1 0 0 0 8308 933 33 4 4 KNTC1 12 122586708 Missense_Mutation SNP G C3N-00556_T 767115 122586708 10688601 324 16453 POLE 0 . GRCh38 12 132661613 132661613 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.2778G>A p.= p.E926E ENST00000320574 24/49 228 205 23 193 193 0 strelka-varscan-mutect POLE,synonymous_variant,p.=,ENST00000320574,NM_006231.3;POLE,synonymous_variant,p.=,ENST00000535270,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,upstream_gene_variant,,ENST00000536445,; T ENST00000320574 Transcript synonymous_variant 2822/7840 2778/6861 926/2286 E gaG/gaA 1 -1 POLE HGNC HGNC:9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 UPI00001FBF97 NM_006231.3 24/49 Pfam_domain:PF00136,hmmpanther:PTHR10670,Superfamily_domains:SSF56672 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 132661613 132661613 C T 1 0 0 0 0 0 0 0 1 12306 912 32 3 3 POLE 12 132661613 Silent SNP C C3N-00556_T 10074905 132661613 613696 325 16454 SACS 0 . GRCh38 13 23332113 23332113 + Missense_Mutation SNP G G C rs749093421 C3N-00556_T C3N-00556_N G G c.11763C>G p.Ile3921Met p.I3921M ENST00000382292 9/9 348 327 21 488 488 0 strelka-varscan-mutect SACS,missense_variant,p.Ile3921Met,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Ile3171Met,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; C ENST00000382292 Transcript missense_variant 12037/15324 11763/13740 3921/4579 I/M atC/atG rs749093421 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 tolerated(0.09) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 MODERATE 1 SNV 5 1 PASS rs749093421 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 23332113 23332113 G C 1 0 0 0 0 1 0 0 0 14063 932 33 4 4 SACS 13 23332113 Missense_Mutation SNP G C3N-00556_T 23332113 91032215 326 16455 AMER2 0 . GRCh38 13 25170034 25170034 + Missense_Mutation SNP G G C rs771130477 C3N-00556_T C3N-00556_N G G c.1586C>G p.Thr529Arg p.T529R ENST00000515384 1/1 84 79 5 134 134 0 strelka-varscan-mutect AMER2,missense_variant,p.Thr410Arg,ENST00000357816,NM_199138.2;AMER2,missense_variant,p.Thr529Arg,ENST00000515384,NM_152704.3;LINC00463,downstream_gene_variant,,ENST00000413501,; C ENST00000515384 Transcript missense_variant 2254/3197 1586/2016 529/671 T/R aCg/aGg rs771130477 1 -1 AMER2 HGNC HGNC:26360 protein_coding YES CCDS53859.1 ENSP00000426528 Q8N7J2 UPI0000231C76 NM_152704.3 deleterious(0) 1/1 hmmpanther:PTHR22237:SF1,hmmpanther:PTHR22237,Pfam_domain:PF09422 MODERATE SNV 1 PASS rs771130477 . 0 207 2 0 0 0 0 0 -11.40976 1 1 1 1 0 C 3 2 54 25170034 25170034 G C 1 0 0 0 0 1 0 0 0 668 1145 40 4 4 AMER2 13 25170034 Missense_Mutation SNP G C3N-00556_T 1837921 25170034 89194294 327 16456 TEX26 0 . GRCh38 13 30952720 30952720 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.207G>T p.Gln69His p.Q69H ENST00000380473 3/7 148 122 26 210 210 0 strelka-varscan-mutect TEX26,missense_variant,p.Gln69His,ENST00000380473,NM_152325.1;TEX26,upstream_gene_variant,,ENST00000530916,;TEX26,intron_variant,,ENST00000531960,; T ENST00000380473 Transcript missense_variant 220/1478 207/870 69/289 Q/H caG/caT 1 1 TEX26 HGNC HGNC:28622 protein_coding YES CCDS9339.1 ENSP00000369840 Q8N6G2 UPI0000070D41 NM_152325.1 deleterious(0.01) 3/7 hmmpanther:PTHR33769:SF1,hmmpanther:PTHR33769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 30952720 30952720 G T 1 0 0 0 0 1 0 0 0 16205 933 33 2 2 TEX26 13 30952720 Missense_Mutation SNP G C3N-00556_T 5782686 30952720 83411608 328 16457 B3GLCT 0 . GRCh38 13 31260945 31260945 + Splice_Site SNP G G T novel C3N-00556_T C3N-00556_N G G c.460-1G>T p.X154_splice ENST00000343307 153 129 24 214 214 0 strelka-varscan-mutect B3GLCT,splice_acceptor_variant,,ENST00000343307,NM_194318.3;B3GLCT,splice_acceptor_variant,,ENST00000461652,; T ENST00000343307 Transcript splice_acceptor_variant -/4254 460/1497 154/498 1 1 B3GLCT HGNC HGNC:20207 protein_coding YES CCDS9341.1 ENSP00000343002 Q6Y288 UPI000036695C NM_194318.3 6/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 54 31260945 31260945 G T 1 0 0 0 0 0 0 1 0 1412 1014 35 2 2 B3GLCT 13 31260945 Splice_Site SNP G C3N-00556_T 308225 31260945 83103383 329 16458 FRY 0 . GRCh38 13 32171022 32171022 + Missense_Mutation SNP C C T rs777478179 C3N-00556_T C3N-00556_N C C c.1903C>T p.His635Tyr p.H635Y ENST00000542859 18/61 176 161 15 224 224 0 strelka-varscan-mutect FRY,missense_variant,p.His635Tyr,ENST00000542859,NM_023037.2;FRY,missense_variant,p.His635Tyr,ENST00000380250,; T ENST00000542859 Transcript missense_variant 2399/13200 1903/9042 635/3013 H/Y Cat/Tat rs777478179 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0) 18/61 Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS rs777478179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 32171022 32171022 C T 1 0 0 0 0 1 0 0 0 5935 826 29 3 3 FRY 13 32171022 Missense_Mutation SNP C C3N-00556_T 910077 32171022 82193306 330 16459 FRY 0 . GRCh38 13 32237826 32237826 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.6258G>A p.= p.E2086E ENST00000542859 44/61 194 182 12 231 230 1 strelka-varscan-mutect FRY,synonymous_variant,p.=,ENST00000542859,NM_023037.2;FRY,synonymous_variant,p.=,ENST00000380250,; A ENST00000542859 Transcript synonymous_variant 6754/13200 6258/9042 2086/3013 E gaG/gaA 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 44/61 Pfam_domain:PF14225,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 LOW 1 SNV 5 1 PASS rs762897259 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 32237826 32237826 G A 1 0 0 0 0 0 0 0 1 5935 933 33 3 3 FRY 13 32237826 Silent SNP G C3N-00556_T 66804 32237826 82126502 331 16460 TRPC4 0 . GRCh38 13 37674336 37674336 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1266G>C p.Trp422Cys p.W422C ENST00000625583 4/10 202 176 26 254 254 0 strelka-varscan-mutect TRPC4,missense_variant,p.Trp422Cys,ENST00000379705,NM_016179.2;TRPC4,missense_variant,p.Trp422Cys,ENST00000625583,NM_003306.1;TRPC4,missense_variant,p.Trp422Cys,ENST00000358477,NM_001135955.1;TRPC4,missense_variant,p.Trp249Cys,ENST00000338947,NM_001135958.1;TRPC4,missense_variant,p.Trp422Cys,ENST00000355779,NM_001135957.1;TRPC4,missense_variant,p.Trp422Cys,ENST00000379673,NM_001135956.1;TRPC4,missense_variant,p.Trp422Cys,ENST00000426868,;TRPC4,missense_variant,p.Trp249Cys,ENST00000379679,;TRPC4,non_coding_transcript_exon_variant,,ENST00000494529,;TRPC4,missense_variant,p.Gly310Ala,ENST00000488717,; G ENST00000625583 Transcript missense_variant 1266/3009 1266/2949 422/982 W/C tgG/tgC 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 deleterious(0) 4/10 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,Pfam_domain:PF00520,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 37674336 37674336 C G 1 0 0 0 0 1 0 0 0 17085 624 22 4 4 TRPC4 13 37674336 Missense_Mutation SNP C C3N-00556_T 5436510 37674336 76689992 332 16461 NUFIP1 0 . GRCh38 13 44959408 44959408 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.994C>T p.Leu332Phe p.L332F ENST00000379161 7/10 240 223 17 295 293 2 strelka-varscan-mutect NUFIP1,missense_variant,p.Leu332Phe,ENST00000379161,NM_012345.2; A ENST00000379161 Transcript missense_variant 1041/3492 994/1488 332/495 L/F Ctt/Ttt 1 -1 NUFIP1 HGNC HGNC:8057 protein_coding YES CCDS9393.1 ENSP00000368459 Q9UHK0 UPI000013C768 NM_012345.2 deleterious(0) 7/10 hmmpanther:PTHR13309 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 44959408 44959408 G A 1 0 0 0 0 1 0 0 0 10812 942 33 3 3 NUFIP1 13 44959408 Missense_Mutation SNP G C3N-00556_T 7285072 44959408 69404920 333 16462 ZC3H13 0 . GRCh38 13 45975472 45975472 + Missense_Mutation SNP C C G rs868471939 C3N-00556_T C3N-00556_N C C c.2279G>C p.Arg760Thr p.R760T ENST00000282007 12/17 194 173 21 252 252 0 strelka-varscan-mutect ZC3H13,missense_variant,p.Arg760Thr,ENST00000242848,;ZC3H13,missense_variant,p.Arg760Thr,ENST00000282007,NM_015070.4; G ENST00000282007 Transcript missense_variant 2350/6412 2279/4695 760/1564 R/T aGa/aCa rs868471939 1 -1 ZC3H13 HGNC HGNC:20368 protein_coding YES CCDS9400.1 ENSP00000282007 Q5T200 UPI0000366969 NM_015070.4 deleterious_low_confidence(0.03) 12/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13585,hmmpanther:PTHR13585:SF5 MODERATE 1 SNV 1 1 PASS rs868471939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 45975472 45975472 C G 1 0 0 0 0 1 0 0 0 18140 913 32 4 4 ZC3H13 13 45975472 Missense_Mutation SNP C C3N-00556_T 1016064 45975472 68388856 334 16463 ZC3H13 0 . GRCh38 13 45975533 45975533 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2218G>C p.Glu740Gln p.E740Q ENST00000282007 12/17 173 155 18 285 285 0 strelka-varscan-mutect ZC3H13,missense_variant,p.Glu740Gln,ENST00000242848,;ZC3H13,missense_variant,p.Glu740Gln,ENST00000282007,NM_015070.4; G ENST00000282007 Transcript missense_variant 2289/6412 2218/4695 740/1564 E/Q Gag/Cag 1 -1 ZC3H13 HGNC HGNC:20368 protein_coding YES CCDS9400.1 ENSP00000282007 Q5T200 UPI0000366969 NM_015070.4 tolerated_low_confidence(0.14) 12/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13585,hmmpanther:PTHR13585:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 45975533 45975533 C G 1 0 0 0 0 1 0 0 0 18140 922 32 4 4 ZC3H13 13 45975533 Missense_Mutation SNP C C3N-00556_T 61 45975533 68388795 335 16464 MYCBP2 0 . GRCh38 13 77097809 77097809 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.9231C>G p.Ile3077Met p.I3077M ENST00000544440 56/83 148 132 16 253 253 0 strelka-varscan-mutect MYCBP2,missense_variant,p.Ile3077Met,ENST00000357337,NM_015057.4;MYCBP2,missense_variant,p.Ile3077Met,ENST00000544440,;RP11-226E21.4,intron_variant,,ENST00000638101,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2-AS1,intron_variant,,ENST00000629771,;MYCBP2-AS1,intron_variant,,ENST00000627409,;MYCBP2,downstream_gene_variant,,ENST00000482517,;MYCBP2,downstream_gene_variant,,ENST00000498073,;MYCBP2,upstream_gene_variant,,ENST00000485061,;MYCBP2,downstream_gene_variant,,ENST00000462987,;RP11-226E21.4,intron_variant,,ENST00000637192,; C ENST00000544440 Transcript missense_variant 9249/14664 9231/13923 3077/4640 I/M atC/atG 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 deleterious(0.05) 56/83 MODERATE 1 SNV 1 1 PASS . . 0 203 0 3 4 0 0 0 -7.264409 0.6129769 1 1 1 0 C 3 2 54 77097809 77097809 G C 1 0 0 0 0 1 0 0 0 10018 1280 45 4 4 MYCBP2 13 77097809 Missense_Mutation SNP G C3N-00556_T 31122276 77097809 37266519 336 16465 OR4K14 0 . GRCh38 14 20014668 20014668 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.526G>A p.Asp176Asn p.D176N ENST00000305045 1/1 199 159 40 269 269 0 strelka-varscan-mutect OR4K14,missense_variant,p.Asp176Asn,ENST00000305045,NM_001004712.1; T ENST00000305045 Transcript missense_variant 526/934 526/933 176/310 D/N Gac/Aac 1 -1 OR4K14 HGNC HGNC:15352 protein_coding YES CCDS32027.1 ENSP00000305011 Q8NGD5 A0A126GVP2 UPI0000041CED NM_001004712.1 deleterious(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF31,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 20014668 20014668 C T 1 0 0 0 0 1 0 0 0 11146 913 32 3 3 OR4K14 14 20014668 Missense_Mutation SNP C C3N-00556_T 20014668 87029050 337 16466 PNP 0 . GRCh38 14 20475173 20475173 + Silent SNP C C G novel C3N-00556_T C3N-00556_N C C c.573C>G p.= p.T191T ENST00000361505 5/6 158 133 25 206 206 0 strelka-varscan-mutect PNP,synonymous_variant,p.=,ENST00000361505,NM_000270.3;PNP,downstream_gene_variant,,ENST00000553591,;PNP,downstream_gene_variant,,ENST00000553418,;PNP,downstream_gene_variant,,ENST00000554065,;RP11-203M5.8,intron_variant,,ENST00000554678,;PNP,non_coding_transcript_exon_variant,,ENST00000556754,;PNP,non_coding_transcript_exon_variant,,ENST00000554056,;PNP,downstream_gene_variant,,ENST00000556293,;PNP,downstream_gene_variant,,ENST00000557229,; G ENST00000361505 Transcript synonymous_variant 719/1509 573/870 191/289 T acC/acG 1 1 PNP HGNC HGNC:7892 protein_coding YES CCDS9552.1 ENSP00000354532 P00491 V9HWH6 UPI00001FCF7D NM_000270.3 5/6 hmmpanther:PTHR11904,hmmpanther:PTHR11904:SF12,TIGRFAM_domain:TIGR01700,PIRSF_domain:PIRSF000477,Pfam_domain:PF01048,TIGRFAM_domain:TIGR01697,Gene3D:3.40.50.1580,Superfamily_domains:SSF53167 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 20475173 20475173 C G 1 0 0 0 0 0 0 0 1 12271 668 24 4 4 PNP 14 20475173 Silent SNP C C3N-00556_T 460505 20475173 86568545 338 16467 OR5AU1 0 . GRCh38 14 21155233 21155233 + Missense_Mutation SNP T T A rs763489918 C3N-00556_T C3N-00556_N T T c.793A>T p.Ile265Phe p.I265F ENST00000304418 1/1 238 206 32 336 334 2 strelka-varscan-mutect OR5AU1,missense_variant,p.Ile265Phe,ENST00000304418,NM_001004731.1; A ENST00000304418 Transcript missense_variant 831/1199 793/1089 265/362 I/F Atc/Ttc rs763489918 1 -1 OR5AU1 HGNC HGNC:15362 protein_coding YES CCDS32042.1 ENSP00000302057 Q8NGC0 A0A126GVW7 UPI000015F240 NM_001004731.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF186,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs763489918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 21155233 21155233 T A 1 0 0 0 0 1 0 0 0 11218 1464 51 4 4 OR5AU1 14 21155233 Missense_Mutation SNP T C3N-00556_T 680060 21155233 85888485 339 16468 PRMT5 0 . GRCh38 14 22920923 22920923 + Nonsense_Mutation SNP G G C C3N-00556_T C3N-00556_N G G c.1895C>G p.Ser632Ter p.S632* ENST00000324366 17/17 167 146 21 160 160 0 strelka-varscan-mutect PRMT5,stop_gained,p.Ser632Ter,ENST00000324366,NM_006109.4;PRMT5,stop_gained,p.Ser615Ter,ENST00000397441,NM_001039619.2;PRMT5,stop_gained,p.Ser571Ter,ENST00000216350,NM_001282954.1,NM_001282953.1;PRMT5,stop_gained,p.Ser461Ter,ENST00000397440,NM_001282956.1;PRMT5,stop_gained,p.Ser588Ter,ENST00000553897,NM_001282955.1;PRMT5,stop_gained,p.Ser174Ter,ENST00000454731,;PRMT5,3_prime_UTR_variant,,ENST00000555454,;PRMT5,intron_variant,,ENST00000557443,;RBM23,upstream_gene_variant,,ENST00000359890,NM_001077351.1;RBM23,upstream_gene_variant,,ENST00000399922,NM_018107.4;RBM23,upstream_gene_variant,,ENST00000346528,NM_001077352.1;RBM23,upstream_gene_variant,,ENST00000555209,;RBM23,upstream_gene_variant,,ENST00000542016,NM_001308044.1;PRMT5,downstream_gene_variant,,ENST00000555530,;RBM23,upstream_gene_variant,,ENST00000557403,;PRMT5,downstream_gene_variant,,ENST00000556043,;RBM23,upstream_gene_variant,,ENST00000555722,;RBM23,upstream_gene_variant,,ENST00000554618,;RBM23,upstream_gene_variant,,ENST00000555676,;RBM23,upstream_gene_variant,,ENST00000557549,;RBM23,upstream_gene_variant,,ENST00000554256,;PRMT5,downstream_gene_variant,,ENST00000553550,;RBM23,upstream_gene_variant,,ENST00000557571,;RBM23,upstream_gene_variant,,ENST00000556862,;RBM23,upstream_gene_variant,,ENST00000557227,;RBM23,upstream_gene_variant,,ENST00000557464,;PRMT5,downstream_gene_variant,,ENST00000553502,;RBM23,upstream_gene_variant,,ENST00000553876,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000424245,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000599580,;PRMT5-AS1,non_coding_transcript_exon_variant,,ENST00000457443,;PRMT5-AS1,intron_variant,,ENST00000609885,;PRMT5-AS1,upstream_gene_variant,,ENST00000587245,;PRMT5-AS1,upstream_gene_variant,,ENST00000590290,;PRMT5-AS1,upstream_gene_variant,,ENST00000595662,;PRMT5,non_coding_transcript_exon_variant,,ENST00000476175,;RBM23,upstream_gene_variant,,ENST00000556984,;PRMT5,downstream_gene_variant,,ENST00000554716,;RBM23,upstream_gene_variant,,ENST00000555714,;RBM23,upstream_gene_variant,,ENST00000553920,;RBM23,upstream_gene_variant,,ENST00000556365,;RBM23,upstream_gene_variant,,ENST00000553777,;PRMT5,3_prime_UTR_variant,,ENST00000553915,;RBM23,upstream_gene_variant,,ENST00000557667,;RBM23,upstream_gene_variant,,ENST00000307814,;RBM23,upstream_gene_variant,,ENST00000556687,;RBM23,upstream_gene_variant,,ENST00000554955,;PRMT5,downstream_gene_variant,,ENST00000557758,;RBM23,upstream_gene_variant,,ENST00000553902,;PRMT5,downstream_gene_variant,,ENST00000553787,; C ENST00000324366 Transcript stop_gained 2119/2531 1895/1914 632/637 S/* tCa/tGa COSM1195458,COSM1195459 1 -1 PRMT5 HGNC HGNC:10894 protein_coding YES CCDS9579.1 ENSP00000319169 O14744 UPI000006F09F NM_006109.4 17/17 hmmpanther:PTHR10738,PIRSF_domain:PIRSF015894,Superfamily_domains:SSF53335 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 54 22920923 22920923 G C 1 0 0 0 0 0 1 0 0 12670 1294 45 4 4 PRMT5 14 22920923 Nonsense_Mutation SNP G C3N-00556_T 1765690 22920923 84122795 340 16469 ZFHX2 0 . GRCh38 14 23522708 23522708 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.6973G>T p.Asp2325Tyr p.D2325Y ENST00000419474 10/10 206 189 17 170 170 0 strelka-varscan-mutect ZFHX2,missense_variant,p.Asp2325Tyr,ENST00000419474,NM_033400.2;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;ZFHX2,upstream_gene_variant,,ENST00000606808,;RP11-66N24.4,intron_variant,,ENST00000554403,; A ENST00000419474 Transcript missense_variant 7329/9182 6973/7719 2325/2572 D/Y Gat/Tat 1 -1 ZFHX2 HGNC HGNC:20152 protein_coding YES CCDS55907.1 ENSP00000413418 Q9C0A1 UPI000198D01B NM_033400.2 tolerated(0.09) 10/10 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF119 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 23522708 23522708 C A 1 0 0 0 0 1 0 0 0 18211 826 29 2 2 ZFHX2 14 23522708 Missense_Mutation SNP C C3N-00556_T 601785 23522708 83521010 341 16470 ZFHX2 0 . GRCh38 14 23527621 23527621 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3118G>A p.Glu1040Lys p.E1040K ENST00000419474 7/10 220 195 25 199 199 0 strelka-varscan-mutect ZFHX2,missense_variant,p.Glu1040Lys,ENST00000419474,NM_033400.2;ZFHX2,downstream_gene_variant,,ENST00000615307,;RP11-66N24.4,intron_variant,,ENST00000553985,;RP11-66N24.4,intron_variant,,ENST00000556354,;RP11-66N24.7,upstream_gene_variant,,ENST00000622438,;RP11-66N24.4,intron_variant,,ENST00000554403,; T ENST00000419474 Transcript missense_variant 3474/9182 3118/7719 1040/2572 E/K Gag/Aag 1 -1 ZFHX2 HGNC HGNC:20152 protein_coding YES CCDS55907.1 ENSP00000413418 Q9C0A1 UPI000198D01B NM_033400.2 deleterious(0.03) 7/10 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF119 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 23527621 23527621 C T 1 0 0 0 0 1 0 0 0 18211 835 29 3 3 ZFHX2 14 23527621 Missense_Mutation SNP C C3N-00556_T 4913 23527621 83516097 342 16471 IPO4 0 . GRCh38 14 24181818 24181818 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.2833C>G p.Leu945Val p.L945V ENST00000354464 27/30 50 46 4 78 78 0 varscan-mutect IPO4,missense_variant,p.Leu945Val,ENST00000354464,NM_024658.3;IPO4,missense_variant,p.Leu409Val,ENST00000561462,;IPO4,missense_variant,p.Leu211Val,ENST00000558233,;REC8,downstream_gene_variant,,ENST00000620473,;REC8,downstream_gene_variant,,ENST00000611366,NM_005132.2,NM_001048205.1;REC8,downstream_gene_variant,,ENST00000560501,;REC8,downstream_gene_variant,,ENST00000559939,;RP11-468E2.2,3_prime_UTR_variant,,ENST00000561419,;IPO4,3_prime_UTR_variant,,ENST00000558780,;IPO4,3_prime_UTR_variant,,ENST00000560155,;IPO4,3_prime_UTR_variant,,ENST00000558046,;IPO4,non_coding_transcript_exon_variant,,ENST00000561090,;IPO4,non_coding_transcript_exon_variant,,ENST00000560798,;IPO4,non_coding_transcript_exon_variant,,ENST00000559588,;IPO4,non_coding_transcript_exon_variant,,ENST00000561199,;REC8,downstream_gene_variant,,ENST00000619469,;REC8,downstream_gene_variant,,ENST00000619284,;REC8,downstream_gene_variant,,ENST00000619111,;REC8,downstream_gene_variant,,ENST00000559797,;IPO4,downstream_gene_variant,,ENST00000560935,;IPO4,downstream_gene_variant,,ENST00000561379,;REC8,downstream_gene_variant,,ENST00000558191,;REC8,downstream_gene_variant,,ENST00000560823,;REC8,downstream_gene_variant,,ENST00000558381,; C ENST00000354464 Transcript missense_variant 3010/3646 2833/3246 945/1081 L/V Ctt/Gtt 1 -1 IPO4 HGNC HGNC:19426 protein_coding YES CCDS9616.1 ENSP00000346453 Q8TEX9 UPI000013CCB3 NM_024658.3 deleterious(0.01) 27/30 Gene3D:1.25.10.10,hmmpanther:PTHR10527,hmmpanther:PTHR10527:SF6,Low_complexity_(Seg):seg,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -10.12287 0.9999983 1 1 1 0 C 3 2 54 24181818 24181818 G C 1 0 0 0 0 1 0 0 0 7698 1000 35 4 4 IPO4 14 24181818 Missense_Mutation SNP G C3N-00556_T 654197 24181818 82861900 343 16472 FRMD6 0 . GRCh38 14 51720059 51720059 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.1029G>A p.= p.K343K ENST00000344768 11/14 73 68 5 78 78 0 strelka-varscan-mutect FRMD6,synonymous_variant,p.=,ENST00000395718,NM_152330.3;FRMD6,synonymous_variant,p.=,ENST00000356218,NM_001042481.2;FRMD6,synonymous_variant,p.=,ENST00000554167,;FRMD6,synonymous_variant,p.=,ENST00000344768,NM_001267046.1;FRMD6,synonymous_variant,p.=,ENST00000555197,;FRMD6,5_prime_UTR_variant,,ENST00000553556,NM_001267047.1;FRMD6,5_prime_UTR_variant,,ENST00000555703,;RNU6-301P,upstream_gene_variant,,ENST00000384277,;FRMD6,downstream_gene_variant,,ENST00000557183,;FRMD6,non_coding_transcript_exon_variant,,ENST00000557522,; A ENST00000344768 Transcript synonymous_variant 1225/2972 1029/1869 343/622 K aaG/aaA 1 1 FRMD6 HGNC HGNC:19839 protein_coding YES CCDS58318.1 ENSP00000343899 Q96NE9 UPI00000473F6 NM_001267046.1 11/14 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF9,Superfamily_domains:SSF50729 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 51720059 51720059 G A 1 0 0 0 0 0 0 0 1 5924 956 33 3 3 FRMD6 14 51720059 Silent SNP G C3N-00556_T 27538241 51720059 55323659 344 16473 PPP1R36 0 . GRCh38 14 64589151 64589151 + Splice_Site SNP G G C rs759921647 C3N-00556_T C3N-00556_N G G c.1083-1G>C p.X361_splice ENST00000298705 75 67 8 127 127 0 strelka-varscan-mutect PPP1R36,splice_acceptor_variant,,ENST00000298705,NM_172365.2;RP11-973N13.3,intron_variant,,ENST00000556634,;RP11-973N13.3,intron_variant,,ENST00000554454,;PPP1R36,splice_acceptor_variant,,ENST00000554400,;PPP1R36,splice_acceptor_variant,,ENST00000467261,;PPP1R36,downstream_gene_variant,,ENST00000556023,; C ENST00000298705 Transcript splice_acceptor_variant -/1405 1083/1269 361/422 rs759921647 1 1 PPP1R36 HGNC HGNC:20097 protein_coding YES CCDS9767.1 ENSP00000298705 Q96LQ0 UPI0000070446 NM_172365.2 11/11 HIGH 1 SNV 1 1 PASS rs759921647 . 0 207 3 0 0 0 0 0 -17.71532 1 1 1 1 0 C 5 2 54 64589151 64589151 G C 1 0 0 0 0 0 0 1 0 12490 956 33 4 4 PPP1R36 14 64589151 Splice_Site SNP G C3N-00556_T 12869092 64589151 42454567 345 16474 GALNT16 0 . GRCh38 14 69348015 69348015 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1552G>A p.Ala518Thr p.A518T ENST00000553669 14/14 190 163 27 168 168 0 strelka-varscan-mutect GALNT16,missense_variant,p.Ala518Thr,ENST00000553669,;GALNT16,intron_variant,,ENST00000337827,NM_001168368.1,NM_020692.2;GALNT16,intron_variant,,ENST00000448469,;GALNT16,upstream_gene_variant,,ENST00000556829,;GALNT16,missense_variant,p.Ala518Thr,ENST00000553471,; A ENST00000553669 Transcript missense_variant 1552/1629 1552/1629 518/542 A/T Gcc/Acc 1 1 GALNT16 HGNC HGNC:23233 protein_coding ENSP00000451200 Q8N428 UPI00001FD777 tolerated(0.57) 14/14 Pfam_domain:PF00652 MODERATE SNV 1 1 PASS rs1192532792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 69348015 69348015 G A 1 0 0 0 0 1 0 0 0 6082 1319 46 3 3 GALNT16 14 69348015 Missense_Mutation SNP G C3N-00556_T 4758864 69348015 37695703 346 16475 C14orf1 0 . GRCh38 14 75651877 75651877 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.237C>A p.= p.I79I ENST00000256319 4/5 134 120 14 175 173 2 strelka-varscan-mutect C14orf1,synonymous_variant,p.=,ENST00000256319,NM_007176.3;FLVCR2,intron_variant,,ENST00000553587,;FLVCR2,downstream_gene_variant,,ENST00000238667,NM_017791.2;FLVCR2,downstream_gene_variant,,ENST00000556856,;FLVCR2,intron_variant,,ENST00000556241,;TTLL5,intron_variant,,ENST00000556265,;FLVCR2,intron_variant,,ENST00000555385,;TTLL5,intron_variant,,ENST00000554132,; T ENST00000256319 Transcript synonymous_variant 683/2633 237/423 79/140 I atC/atA 1 -1 C14orf1 HGNC HGNC:1187 protein_coding YES CCDS9845.1 ENSP00000256319 Q9UKR5 Q6FII3 UPI0000127BDF NM_007176.3 4/5 Pfam_domain:PF03694,hmmpanther:PTHR15451,hmmpanther:PTHR15451:SF19,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1438669946 . 0 207 0 0 2 0 0 0 -6.851653 0.9937169 1 1 1 0 T 2 4 54 75651877 75651877 G T 1 0 0 0 0 0 0 0 1 1826 1280 45 2 2 C14orf1 14 75651877 Silent SNP G C3N-00556_T 6303862 75651877 31391841 347 16476 TTLL5 0 . GRCh38 14 75776761 75776761 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.2298G>T p.Met766Ile p.M766I ENST00000298832 23/32 150 135 15 158 158 0 strelka-mutect TTLL5,missense_variant,p.Met766Ile,ENST00000298832,NM_015072.4;TTLL5,missense_variant,p.Met780Ile,ENST00000557636,;TTLL5,missense_variant,p.Met317Ile,ENST00000556893,;TTLL5,missense_variant,p.Met275Ile,ENST00000554510,;TTLL5,non_coding_transcript_exon_variant,,ENST00000555422,; T ENST00000298832 Transcript missense_variant 2503/4683 2298/3846 766/1281 M/I atG/atT 1 1 TTLL5 HGNC HGNC:19963 protein_coding YES CCDS32124.1 ENSP00000298832 Q6EMB2 UPI00003FF22B NM_015072.4 deleterious(0.01) 23/32 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 75776761 75776761 G T 1 0 0 0 0 1 0 0 0 17241 1348 47 2 2 TTLL5 14 75776761 Missense_Mutation SNP G C3N-00556_T 124884 75776761 31266957 348 16477 NOXRED1 0 . GRCh38 14 77407514 77407514 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.481G>C p.Glu161Gln p.E161Q ENST00000380835 3/6 164 148 16 152 152 0 strelka-mutect NOXRED1,missense_variant,p.Glu161Gln,ENST00000380835,NM_001113475.2;NOXRED1,missense_variant,p.Glu161Gln,ENST00000555603,;NOXRED1,non_coding_transcript_exon_variant,,ENST00000555901,; G ENST00000380835 Transcript missense_variant 648/1857 481/1080 161/359 E/Q Gag/Cag 1 -1 NOXRED1 HGNC HGNC:20487 protein_coding YES CCDS45142.1 ENSP00000370215 Q6NXP6 UPI0000407F20 NM_001113475.2 tolerated(0.73) 3/6 Gene3D:3.40.50.720,Pfam_domain:PF03807,hmmpanther:PTHR11645,hmmpanther:PTHR11645:SF7,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99791 0.9999998 1 1 1 0 G 3 3 54 77407514 77407514 C G 1 0 0 0 0 1 0 0 0 10608 835 29 4 4 NOXRED1 14 77407514 Missense_Mutation SNP C C3N-00556_T 1630753 77407514 29636204 349 16478 DIO2 0 . GRCh38 14 80203056 80203056 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.563C>T p.Ser188Leu p.S188L ENST00000555750 3/3 110 97 13 176 175 1 strelka-varscan-mutect DIO2,stop_gained,p.Gln27Ter,ENST00000557125,;DIO2,missense_variant,p.Ser152Leu,ENST00000557010,NM_001324462.1,NM_000793.5;DIO2,missense_variant,p.Ser152Leu,ENST00000438257,NM_013989.4;DIO2,missense_variant,p.Ser188Leu,ENST00000555750,NM_001007023.3;DIO2,3_prime_UTR_variant,,ENST00000422005,NM_001242503.2,NM_001242502.1;DIO2,3_prime_UTR_variant,,ENST00000556811,;DIO2,3_prime_UTR_variant,,ENST00000555844,; A ENST00000555750 Transcript missense_variant 591/1049 563/930 188/309 S/L tCa/tTa 1 -1 DIO2 HGNC HGNC:2884 protein_coding YES CCDS55934.1 ENSP00000450980 A0A0A0MTQ2 UPI000046D384 NM_001007023.3 deleterious(0.04) 3/3 Gene3D:3.40.30.10,Pfam_domain:PF00837,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF3,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 80203056 80203056 G A 1 0 0 0 0 1 0 0 0 4330 1303 45 3 3 DIO2 14 80203056 Missense_Mutation SNP G C3N-00556_T 2795542 80203056 26840662 350 16479 CEP128 0 . GRCh38 14 80831214 80831214 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1138G>T p.Glu380Ter p.E380* ENST00000555265 13/25 252 214 38 281 280 1 strelka-varscan-mutect CEP128,stop_gained,p.Glu380Ter,ENST00000555265,;CEP128,stop_gained,p.Glu380Ter,ENST00000281129,NM_152446.3;CEP128,stop_gained,p.Glu259Ter,ENST00000554827,;CEP128,stop_gained,p.Glu380Ter,ENST00000216517,;CEP128,stop_gained,p.Glu72Ter,ENST00000554502,; A ENST00000555265 Transcript stop_gained 1514/4662 1138/3285 380/1094 E/* Gag/Tag 1 -1 CEP128 HGNC HGNC:20359 protein_coding YES CCDS32130.1 ENSP00000451162 Q6ZU80 UPI000022982E 13/25 hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF205 HIGH 1 SNV 5 1 PASS rs762635519 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 80831214 80831214 C A 1 0 0 0 0 0 1 0 0 2958 835 29 2 2 CEP128 14 80831214 Nonsense_Mutation SNP C C3N-00556_T 628158 80831214 26212504 351 16480 NRDE2 0 . GRCh38 14 90290433 90290433 + Missense_Mutation SNP C C T rs773313077 C3N-00556_T C3N-00556_N C C c.2017G>A p.Asp673Asn p.D673N ENST00000354366 10/14 196 180 16 217 217 0 strelka-varscan-mutect NRDE2,missense_variant,p.Asp673Asn,ENST00000354366,NM_017970.3;NRDE2,downstream_gene_variant,,ENST00000554464,;NRDE2,3_prime_UTR_variant,,ENST00000553409,;NRDE2,3_prime_UTR_variant,,ENST00000556189,;NRDE2,upstream_gene_variant,,ENST00000555903,; T ENST00000354366 Transcript missense_variant 2250/14208 2017/3495 673/1164 D/N Gat/Aat rs773313077 1 -1 NRDE2 HGNC HGNC:20186 protein_coding YES CCDS9890.1 ENSP00000346335 Q9H7Z3 UPI00001FD9DB NM_017970.3 tolerated(0.28) 10/14 hmmpanther:PTHR13471,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs773313077 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 90290433 90290433 C T 1 0 0 0 0 1 0 0 0 10702 826 29 3 3 NRDE2 14 90290433 Missense_Mutation SNP C C3N-00556_T 9459219 90290433 16753285 352 16481 RPS6KA5 0 . GRCh38 14 90978451 90978451 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.249G>C p.Leu83Phe p.L83F ENST00000614987 3/17 108 101 7 163 163 0 strelka-varscan-mutect RPS6KA5,missense_variant,p.Leu83Phe,ENST00000614987,NM_004755.2;RPS6KA5,missense_variant,p.Leu4Phe,ENST00000536315,;RPS6KA5,missense_variant,p.Leu83Phe,ENST00000418736,NM_182398.1;RPS6KA5,missense_variant,p.Leu25Phe,ENST00000556178,;RPS6KA5,missense_variant,p.Leu83Phe,ENST00000554206,;RPS6KA5,3_prime_UTR_variant,,ENST00000556594,; G ENST00000614987 Transcript missense_variant 423/26795 249/2409 83/802 L/F ttG/ttC 1 -1 RPS6KA5 HGNC HGNC:10434 protein_coding YES CCDS9893.1 ENSP00000479667 O75582 UPI0000031C30 NM_004755.2 deleterious(0) 3/17 Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF000606,PROSITE_profiles:PS50011,hmmpanther:PTHR24351,hmmpanther:PTHR24351:SF48,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 90978451 90978451 C G 1 0 0 0 0 1 0 0 0 13909 825 29 4 4 RPS6KA5 14 90978451 Missense_Mutation SNP C C3N-00556_T 688018 90978451 16065267 353 16482 UNC79 0 . GRCh38 14 93538184 93538184 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.787G>A p.Glu263Lys p.E263K ENST00000256339 12/50 58 53 5 80 80 0 strelka-varscan-mutect UNC79,missense_variant,p.Glu440Lys,ENST00000553484,;UNC79,missense_variant,p.Glu440Lys,ENST00000555664,;UNC79,missense_variant,p.Glu263Lys,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Glu440Lys,ENST00000393151,;UNC79,missense_variant,p.Glu263Lys,ENST00000621021,; A ENST00000256339 Transcript missense_variant 1442/8400 787/7377 263/2458 E/K Gag/Aag COSM3956303,COSM3956304,COSM4623047,COSM4623048 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated(0.09) 12/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696,Pfam_domain:PF14776 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 204 6 0 0 0 0 0 -11.91003 0.9999998 1 1 1 0 A 3 1 54 93538184 93538184 G A 1 0 0 0 0 1 0 0 0 17520 1291 45 3 3 UNC79 14 93538184 Missense_Mutation SNP G C3N-00556_T 2559733 93538184 13505534 354 16483 BCL11B 0 . GRCh38 14 99175485 99175485 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.1351G>T p.Gly451Cys p.G451C ENST00000357195 4/4 202 186 16 216 216 0 strelka-mutect BCL11B,missense_variant,p.Gly380Cys,ENST00000345514,NM_001282238.1,NM_022898.2;BCL11B,missense_variant,p.Gly451Cys,ENST00000357195,NM_001282237.1,NM_138576.3;BCL11B,missense_variant,p.Gly257Cys,ENST00000443726,; A ENST00000357195 Transcript missense_variant 1361/7559 1351/2685 451/894 G/C Ggc/Tgc 1 -1 BCL11B HGNC HGNC:13222 protein_coding YES CCDS9950.1 ENSP00000349723 Q9C0K0 L8B7P7 UPI000006E083 NM_001282237.1,NM_138576.3 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF45,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 99175485 99175485 C A 1 0 0 0 0 1 0 0 0 1511 623 22 2 2 BCL11B 14 99175485 Missense_Mutation SNP C C3N-00556_T 5637301 99175485 7868233 355 16484 BEGAIN 0 . GRCh38 14 100543936 100543936 + Silent SNP C C T rs747563702 C3N-00556_T C3N-00556_N C C c.273G>A p.= p.A91A ENST00000443071 4/6 180 160 20 160 160 0 strelka-varscan-mutect BEGAIN,synonymous_variant,p.=,ENST00000637716,;BEGAIN,synonymous_variant,p.=,ENST00000637646,;BEGAIN,synonymous_variant,p.=,ENST00000443071,NM_001159531.1;BEGAIN,synonymous_variant,p.=,ENST00000355173,NM_020836.3;BEGAIN,synonymous_variant,p.=,ENST00000556188,;BEGAIN,synonymous_variant,p.=,ENST00000553553,;BEGAIN,synonymous_variant,p.=,ENST00000554356,;BEGAIN,synonymous_variant,p.=,ENST00000557378,;BEGAIN,synonymous_variant,p.=,ENST00000554140,;CTD-2062F14.3,downstream_gene_variant,,ENST00000553301,;BEGAIN,downstream_gene_variant,,ENST00000554747,;BEGAIN,non_coding_transcript_exon_variant,,ENST00000556751,;BEGAIN,downstream_gene_variant,,ENST00000554274,; T ENST00000443071 Transcript synonymous_variant 419/2744 273/1782 91/593 A gcG/gcA rs747563702 1 -1 BEGAIN HGNC HGNC:24163 protein_coding YES CCDS9962.1 ENSP00000411124 Q9BUH8 UPI00000710B1 NM_001159531.1 4/6 hmmpanther:PTHR28664,hmmpanther:PTHR28664:SF2 LOW 1 SNV 1 1 PASS rs747563702 . 0 207 0 3 0 0 0 0 -20 0.9999883 1 1 1 0 T 2 4 54 100543936 100543936 C T 1 0 0 0 0 0 0 0 1 1545 755 27 1 1 BEGAIN 14 100543936 Silent SNP C C3N-00556_T 1368451 100543936 6499782 356 16485 DYNC1H1 0 . GRCh38 14 102036541 102036541 + Nonsense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.10807G>T p.Glu3603Ter p.E3603* ENST00000360184 57/78 291 274 17 331 331 0 strelka-varscan-mutect DYNC1H1,stop_gained,p.Glu3603Ter,ENST00000360184,NM_001376.4;DYNC1H1,stop_gained,p.Glu79Ter,ENST00000553423,;RP11-1017G21.4,non_coding_transcript_exon_variant,,ENST00000557551,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557242,;RP11-1017G21.4,downstream_gene_variant,,ENST00000553701,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000556791,;DYNC1H1,upstream_gene_variant,,ENST00000556139,;DYNC1H1,upstream_gene_variant,,ENST00000556499,;DYNC1H1,upstream_gene_variant,,ENST00000555800,; T ENST00000360184 Transcript stop_gained 10971/14333 10807/13941 3603/4646 E/* Gaa/Taa 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 57/78 Pfam_domain:PF12781,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 102036541 102036541 G T 1 0 0 0 0 0 1 0 0 4665 1291 45 2 2 DYNC1H1 14 102036541 Nonsense_Mutation SNP G C3N-00556_T 1492605 102036541 5007177 357 16486 CRIP2 0 . GRCh38 14 105479217 105479217 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.721G>A p.Glu241Lys p.E241K ENST00000483017 6/8 115 101 14 141 141 0 strelka-varscan-mutect CRIP2,missense_variant,p.Glu167Lys,ENST00000329146,NM_001312.3;CRIP2,missense_variant,p.Glu241Lys,ENST00000483017,NM_001270837.1;CRIP2,missense_variant,p.Glu151Lys,ENST00000538259,;CRIP2,missense_variant,p.Glu63Lys,ENST00000550577,NM_001270841.1;CRIP2,splice_region_variant,,ENST00000548989,;CRIP2,splice_region_variant,,ENST00000548309,;CRIP2,downstream_gene_variant,,ENST00000548923,;CRIP2,splice_region_variant,,ENST00000552643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000547643,;CRIP2,non_coding_transcript_exon_variant,,ENST00000551738,;CRIP2,downstream_gene_variant,,ENST00000551836,; A ENST00000483017 Transcript missense_variant,splice_region_variant 1007/1176 721/849 241/282 E/K Gag/Aag 1 1 CRIP2 HGNC HGNC:2361 protein_coding YES CCDS59246.1 ENSP00000426119 P52943 UPI0001914E41 NM_001270837.1 deleterious(0) 6/8 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 105479217 105479217 G A 1 0 0 0 0 1 0 0 0 3676 1188 41 3 3 CRIP2 14 105479217 Missense_Mutation SNP G C3N-00556_T 3442676 105479217 1564501 358 16487 MAGEL2 0 . GRCh38 15 23645929 23645929 + Missense_Mutation SNP T T A novel C3N-00556_T C3N-00556_N T T c.1814A>T p.Glu605Val p.E605V ENST00000532292 1/1 230 205 25 248 248 0 strelka-varscan-mutect MAGEL2,missense_variant,p.Glu605Val,ENST00000532292,NM_019066.4; A ENST00000532292 Transcript missense_variant 1913/4298 1814/3750 605/1249 E/V gAa/gTa 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS rs925734791 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 23645929 23645929 T A 1 0 0 0 0 1 0 0 0 9107 1783 62 4 4 MAGEL2 15 23645929 Missense_Mutation SNP T C3N-00556_T 23645929 78345260 359 16488 GOLGA8M 0 . GRCh38 15 28710523 28710523 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.132G>A p.= p.Q44Q ENST00000563027 2/19 79 74 5 119 118 1 varscan-mutect GOLGA8M,synonymous_variant,p.=,ENST00000563027,NM_001282468.1;GOLGA8M,non_coding_transcript_exon_variant,,ENST00000563213,; T ENST00000563027 Transcript synonymous_variant 132/1899 132/1899 44/632 Q caG/caA 1 -1 GOLGA8M HGNC HGNC:44404 protein_coding YES CCDS61572.1 ENSP00000456927 H3BSY2 UPI0001A5E7A0 NM_001282468.1 2/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 28710523 28710523 C T 1 0 0 0 0 0 0 0 1 6454 912 32 3 3 GOLGA8M 15 28710523 Silent SNP C C3N-00556_T 5064594 28710523 73280666 360 16489 STARD9 0 . GRCh38 15 42688335 42688335 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.6757C>T p.Gln2253Ter p.Q2253* ENST00000290607 23/33 180 164 16 236 236 0 strelka-varscan-mutect STARD9,stop_gained,p.Gln2253Ter,ENST00000290607,NM_020759.2;STARD9,upstream_gene_variant,,ENST00000562619,; T ENST00000290607 Transcript stop_gained 6814/15567 6757/14103 2253/4700 Q/* Cag/Tag 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 23/33 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 42688335 42688335 C T 1 0 0 0 0 0 1 0 0 15639 827 29 3 3 STARD9 15 42688335 Nonsense_Mutation SNP C C3N-00556_T 13977812 42688335 59302854 361 16490 PDIA3 0 . GRCh38 15 43746651 43746651 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.112C>T p.Arg38Cys p.R38C ENST00000300289 1/13 226 207 19 249 249 0 strelka-varscan-mutect PDIA3,missense_variant,p.Arg38Cys,ENST00000300289,NM_005313.4;CATSPER2P1,non_coding_transcript_exon_variant,,ENST00000429276,;PDIA3,non_coding_transcript_exon_variant,,ENST00000469684,;CATSPER2P1,upstream_gene_variant,,ENST00000381680,;CATSPER2P1,upstream_gene_variant,,ENST00000416302,;PDIA3,missense_variant,p.Arg38Cys,ENST00000434494,;PDIA3,missense_variant,p.Arg14Cys,ENST00000455250,;PDIA3,missense_variant,p.Arg38Cys,ENST00000446523,;CATSPER2P1,upstream_gene_variant,,ENST00000439564,; T ENST00000300289 Transcript missense_variant 260/3727 112/1518 38/505 R/C Cgc/Tgc COSM5626662 1 1 PDIA3 HGNC HGNC:4606 protein_coding YES CCDS10101.1 ENSP00000300289 P30101 V9HVY3 UPI0000052A4F NM_005313.4 deleterious(0.05) 1/13 PROSITE_profiles:PS51352,hmmpanther:PTHR18929:SF60,hmmpanther:PTHR18929,TIGRFAM_domain:TIGR01130,TIGRFAM_domain:TIGR01126,Pfam_domain:PF00085,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 43746651 43746651 C T 1 0 0 0 0 1 0 0 0 11757 884 31 1 1 PDIA3 15 43746651 Missense_Mutation SNP C C3N-00556_T 1058316 43746651 58244538 362 16491 CCPG1 0 . GRCh38 15 55359751 55359751 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.2022G>A p.Trp674Ter p.W674* ENST00000442196 8/9 135 113 22 189 189 0 strelka-varscan-mutect CCPG1,stop_gained,p.Trp674Ter,ENST00000310958,NM_004748.4,NM_020739.3;CCPG1,stop_gained,p.Trp674Ter,ENST00000442196,NM_001204450.1;CCPG1,stop_gained,p.Trp674Ter,ENST00000569205,;CCPG1,intron_variant,,ENST00000425574,NM_001204451.1;CCPG1,intron_variant,,ENST00000568543,;CCPG1,intron_variant,,ENST00000568592,;PIGB,downstream_gene_variant,,ENST00000164305,NM_004855.4;PIGB,downstream_gene_variant,,ENST00000539642,;CCPG1,upstream_gene_variant,,ENST00000564663,;DYX1C1-CCPG1,non_coding_transcript_exon_variant,,ENST00000565113,;CCPG1,3_prime_UTR_variant,,ENST00000568808,;CCPG1,non_coding_transcript_exon_variant,,ENST00000568372,;PIGB,downstream_gene_variant,,ENST00000563742,;PIGB,downstream_gene_variant,,ENST00000565367,;PIGB,downstream_gene_variant,,ENST00000565502,;PIGB,downstream_gene_variant,,ENST00000562751,; T ENST00000442196 Transcript stop_gained 2070/3453 2022/2424 674/807 W/* tgG/tgA 1 -1 CCPG1 HGNC HGNC:24227 protein_coding YES CCDS55966.1 ENSP00000403400 Q9ULG6 UPI0000D61347 NM_001204450.1 8/9 hmmpanther:PTHR28638,hmmpanther:PTHR28638:SF2 HIGH SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 55359751 55359751 C T 1 0 0 0 0 0 1 0 0 2638 856 30 3 3 CCPG1 15 55359751 Nonsense_Mutation SNP C C3N-00556_T 11613100 55359751 46631438 363 16492 DENND4A 0 . GRCh38 15 65701170 65701170 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2582C>T p.Pro861Leu p.P861L ENST00000443035 19/33 110 93 17 169 169 0 strelka-mutect DENND4A,missense_variant,p.Pro861Leu,ENST00000443035,NM_001320835.1,NM_001144823.1;DENND4A,missense_variant,p.Pro861Leu,ENST00000635620,;DENND4A,missense_variant,p.Pro861Leu,ENST00000431932,NM_005848.3;DENND4A,missense_variant,p.Pro861Leu,ENST00000564674,;snoU13,upstream_gene_variant,,ENST00000459325,;DENND4A,non_coding_transcript_exon_variant,,ENST00000562028,; A ENST00000443035 Transcript missense_variant 2798/8665 2582/5721 861/1906 P/L cCt/cTt 1 -1 DENND4A HGNC HGNC:24321 protein_coding YES CCDS53949.1 ENSP00000391167 Q7Z401 UPI000013EDF7 NM_001320835.1,NM_001144823.1 deleterious(0) 19/33 hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 65701170 65701170 G A 1 0 0 0 0 1 0 0 0 4237 1000 35 3 3 DENND4A 15 65701170 Missense_Mutation SNP G C3N-00556_T 10341419 65701170 36290019 364 16493 SNAPC5 0 . GRCh38 15 66497678 66497678 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.54G>T p.Leu18Phe p.L18F ENST00000316634 1/3 137 128 9 138 138 0 strelka-varscan-mutect SNAPC5,missense_variant,p.Leu18Phe,ENST00000316634,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000563480,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000307979,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000395589,NM_006049.2;SNAPC5,missense_variant,p.Leu18Phe,ENST00000566658,;RPL4,downstream_gene_variant,,ENST00000307961,NM_000968.3;RPL4,downstream_gene_variant,,ENST00000568588,;RPL4,downstream_gene_variant,,ENST00000569696,;RPL4,downstream_gene_variant,,ENST00000569438,;MIR4512,upstream_gene_variant,,ENST00000583257,;SNORD18B,downstream_gene_variant,,ENST00000365659,;snoU18,downstream_gene_variant,,ENST00000629629,;SNORD18C,downstream_gene_variant,,ENST00000362704,;RPL4,downstream_gene_variant,,ENST00000563473,;RPL4,downstream_gene_variant,,ENST00000565723,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000568875,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000565465,;SNAPC5,missense_variant,p.Leu18Phe,ENST00000562411,;RPL4,downstream_gene_variant,,ENST00000567229,;RPL4,downstream_gene_variant,,ENST00000561775,;RPL4,downstream_gene_variant,,ENST00000564647,;RPL4,downstream_gene_variant,,ENST00000566039,;RPL4,downstream_gene_variant,,ENST00000566624,;RPL4,downstream_gene_variant,,ENST00000566622,;RPL4,downstream_gene_variant,,ENST00000564744,;RPL4,downstream_gene_variant,,ENST00000564439,; A ENST00000316634 Transcript missense_variant 136/1002 54/297 18/98 L/F ttG/ttT 1 -1 SNAPC5 HGNC HGNC:15484 protein_coding YES CCDS10217.1 ENSP00000319597 O75971 A0A024R5X1 UPI0000135B25 deleterious_low_confidence(0.01) 1/3 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15333,hmmpanther:PTHR15333:SF2,Pfam_domain:PF15497 MODERATE 1 SNV 1 1 PASS rs1172928359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 66497678 66497678 C A 1 0 0 0 0 1 0 0 0 15159 825 29 2 2 SNAPC5 15 66497678 Missense_Mutation SNP C C3N-00556_T 796508 66497678 35493511 365 16494 TMEM202 0 . GRCh38 15 72398334 72398334 + Missense_Mutation SNP G G A rs148351239 C3N-00556_T C3N-00556_N G G c.8G>A p.Arg3Gln p.R3Q ENST00000341689 1/5 106 98 8 114 114 0 strelka-varscan-mutect TMEM202,missense_variant,p.Arg3Gln,ENST00000341689,NM_001080462.1;TMEM202,missense_variant,p.Arg3Gln,ENST00000567679,;TMEM202,missense_variant,p.Arg3Gln,ENST00000568167,; A ENST00000341689 Transcript missense_variant 62/1012 8/822 3/273 R/Q cGa/cAa rs148351239 1 1 TMEM202 HGNC HGNC:33733 protein_coding YES CCDS32287.1 ENSP00000340212 A6NGA9 UPI000049DDE8 NM_001080462.1 tolerated(0.08) 1/5 MODERATE 1 SNV 5 1 PASS rs148351239 . 0 207 2 0 0 0 0 0 -16.50481 1 1 1 1 0 A 3 1 54 72398334 72398334 G A 1 0 0 0 0 1 0 0 0 16566 1058 37 1 1 TMEM202 15 72398334 Missense_Mutation SNP G C3N-00556_T 5900656 72398334 29592855 366 16495 SH3GL3 0 . GRCh38 15 83618231 83618231 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1012G>A p.Glu338Lys p.E338K ENST00000324537 12/12 177 161 16 241 241 0 strelka-varscan-mutect SH3GL3,missense_variant,p.Glu338Lys,ENST00000324537,NM_001301109.1;SH3GL3,missense_variant,p.Glu330Lys,ENST00000427482,NM_001301108.1,NM_003027.4;SH3GL3,non_coding_transcript_exon_variant,,ENST00000564054,;SH3GL3,non_coding_transcript_exon_variant,,ENST00000467735,;SH3GL3,3_prime_UTR_variant,,ENST00000563901,; A ENST00000324537 Transcript missense_variant 1504/2012 1012/1068 338/355 E/K Gaa/Aaa 1 1 SH3GL3 HGNC HGNC:10832 protein_coding YES CCDS73772.1 ENSP00000320092 Q99963 UPI000002B391 NM_001301109.1 tolerated(0.5) 12/12 PROSITE_profiles:PS50002,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF158,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00452 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 83618231 83618231 G A 1 0 0 0 0 1 0 0 0 14511 943 33 3 3 SH3GL3 15 83618231 Missense_Mutation SNP G C3N-00556_T 11219897 83618231 18372958 367 16496 AGBL1 0 . GRCh38 15 86279703 86279703 + Missense_Mutation SNP A A T C3N-00556_T C3N-00556_N A A c.2140A>T p.Thr714Ser p.T714S ENST00000441037 16/25 205 192 13 184 184 0 strelka-varscan-mutect AGBL1,missense_variant,p.Thr714Ser,ENST00000441037,;AGBL1,missense_variant,p.Thr668Ser,ENST00000635782,NM_152336.2;AGBL1,missense_variant,p.Thr668Ser,ENST00000421325,;AGBL1,non_coding_transcript_exon_variant,,ENST00000567715,;AGBL1,non_coding_transcript_exon_variant,,ENST00000568785,; T ENST00000441037 Transcript missense_variant 2140/3551 2140/3339 714/1112 T/S Acc/Tcc COSM3504946,COSM3504947,COSM4660311,COSM4660312,COSM4660313 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 tolerated(0.1) 16/25 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 86279703 86279703 A T 1 0 0 0 0 1 0 0 0 451 159 6 4 4 AGBL1 15 86279703 Missense_Mutation SNP A C3N-00556_T 2661472 86279703 15711486 368 16497 SV2B 0 . GRCh38 15 91267584 91267584 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1149G>T p.Met383Ile p.M383I ENST00000394232 8/13 192 176 16 231 230 1 strelka-varscan-mutect SV2B,missense_variant,p.Met383Ile,ENST00000394232,NM_001323038.1,NM_001323031.1,NM_001323040.1,NM_001323039.1,NM_001323032.1,NM_001323036.1,NM_001323037.1,NM_014848.4;SV2B,missense_variant,p.Met383Ile,ENST00000330276,;SV2B,missense_variant,p.Met232Ile,ENST00000545111,NM_001167580.1;SV2B,missense_variant,p.Met383Ile,ENST00000557410,;SV2B,downstream_gene_variant,,ENST00000553727,; T ENST00000394232 Transcript missense_variant 1619/11279 1149/2052 383/683 M/I atG/atT 1 1 SV2B HGNC HGNC:16874 protein_coding YES CCDS10370.1 ENSP00000377779 Q7L1I2 UPI000006FCF1 NM_001323038.1,NM_001323031.1,NM_001323040.1,NM_001323039.1,NM_001323032.1,NM_001323036.1,NM_001323037.1,NM_014848.4 tolerated(0.19) 8/13 PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF2,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 91267584 91267584 G T 1 0 0 0 0 1 0 0 0 15802 1348 47 2 2 SV2B 15 91267584 Missense_Mutation SNP G C3N-00556_T 4987881 91267584 10723605 369 16498 RGMA 0 . GRCh38 15 93052113 93052113 + Silent SNP G G A rs375645172 C3N-00556_T C3N-00556_N G G c.549C>T p.= p.T183T ENST00000557301 3/4 188 177 11 188 188 0 strelka-varscan-mutect RGMA,synonymous_variant,p.=,ENST00000329082,NM_020211.2;RGMA,synonymous_variant,p.=,ENST00000543599,NM_001166287.1;RGMA,synonymous_variant,p.=,ENST00000425933,NM_001166288.1,NM_001166289.1;RGMA,synonymous_variant,p.=,ENST00000542321,NM_001166286.1;RGMA,synonymous_variant,p.=,ENST00000557301,NM_001166283.1;RGMA,synonymous_variant,p.=,ENST00000556658,;RGMA,intron_variant,,ENST00000557420,;RGMA,downstream_gene_variant,,ENST00000555598,;RGMA,downstream_gene_variant,,ENST00000555584,;RGMA,3_prime_UTR_variant,,ENST00000554387,; A ENST00000557301 Transcript synonymous_variant 921/1929 549/1377 183/458 T acC/acT rs375645172 1 -1 RGMA HGNC HGNC:30308 protein_coding YES CCDS53974.1 ENSP00000452126 A0A0A0MTQ4 UPI0001BAC468 NM_001166283.1 3/4 Pfam_domain:PF06535,hmmpanther:PTHR31428,hmmpanther:PTHR31428:SF4 LOW 1 SNV 2 1 PASS rs375645172 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 93052113 93052113 G A 1 0 0 0 0 0 0 0 1 13453 1103 39 1 1 RGMA 15 93052113 Silent SNP G C3N-00556_T 1784529 93052113 8939076 370 16499 RAB26 0 . GRCh38 16 2151897 2151897 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.457G>A p.Asp153Asn p.D153N ENST00000210187 5/9 312 293 19 254 254 0 strelka-varscan-mutect RAB26,missense_variant,p.Asp153Asn,ENST00000210187,NM_014353.4;RAB26,missense_variant,p.Asp87Asn,ENST00000541451,NM_001308053.1;TRAF7,upstream_gene_variant,,ENST00000326181,NM_032271.2;TRAF7,upstream_gene_variant,,ENST00000565383,;TRAF7,upstream_gene_variant,,ENST00000567653,;RAB26,upstream_gene_variant,,ENST00000566724,;SNHG19,downstream_gene_variant,,ENST00000563192,;SNORD60,downstream_gene_variant,,ENST00000383903,;snoR1,downstream_gene_variant,,ENST00000628177,;RAB26,3_prime_UTR_variant,,ENST00000565592,;RAB26,non_coding_transcript_exon_variant,,ENST00000564426,;RAB26,non_coding_transcript_exon_variant,,ENST00000562735,;RAB26,non_coding_transcript_exon_variant,,ENST00000561600,;RAB26,non_coding_transcript_exon_variant,,ENST00000567145,;TRAF7,upstream_gene_variant,,ENST00000564067,;TRAF7,upstream_gene_variant,,ENST00000569686,; A ENST00000210187 Transcript missense_variant 617/1675 457/771 153/256 D/N Gac/Aac 1 1 RAB26 HGNC HGNC:14259 protein_coding YES CCDS10460.1 ENSP00000210187 Q9ULW5 UPI00003584E3 NM_014353.4 tolerated(0.06) 5/9 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF531,hmmpanther:PTHR24073,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00176,SMART_domains:SM00177,SMART_domains:SM00173,SMART_domains:SM00174,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 2151897 2151897 G A 1 0 0 0 0 1 0 0 0 13071 1290 45 3 3 RAB26 16 2151897 Missense_Mutation SNP G C3N-00556_T 2151897 88186448 371 16500 GRIN2A 0 . GRCh38 16 9938541 9938541 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.425C>T p.Ser142Phe p.S142F ENST00000396573 4/14 275 254 21 281 281 0 strelka-varscan-mutect GRIN2A,missense_variant,p.Ser142Phe,ENST00000396573,NM_000833.4;GRIN2A,missense_variant,p.Ser5Phe,ENST00000396575,;GRIN2A,missense_variant,p.Ser142Phe,ENST00000330684,NM_001134407.2;GRIN2A,missense_variant,p.Ser142Phe,ENST00000562109,NM_001134408.2;GRIN2A,missense_variant,p.Ser5Phe,ENST00000535259,;GRIN2A,missense_variant,p.Ser6Phe,ENST00000637393,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000568247,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566670,;GRIN2A,intron_variant,,ENST00000566683,; A ENST00000396573 Transcript missense_variant 735/14450 425/4395 142/1464 S/F tCt/tTt 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 deleterious(0.02) 4/14 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF16,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 9938541 9938541 G A 1 0 0 0 0 1 0 0 0 6661 942 33 3 3 GRIN2A 16 9938541 Missense_Mutation SNP G C3N-00556_T 7786644 9938541 80399804 372 16501 UMOD 0 . GRCh38 16 20348658 20348658 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.742G>A p.Glu248Lys p.E248K ENST00000396134 4/12 102 89 13 130 130 0 strelka-mutect UMOD,missense_variant,p.Glu215Lys,ENST00000302509,NM_001008389.2,NM_003361.3;UMOD,missense_variant,p.Glu248Lys,ENST00000396134,NM_001278614.1;UMOD,missense_variant,p.Glu264Lys,ENST00000396138,;UMOD,missense_variant,p.Glu215Lys,ENST00000570689,;UMOD,downstream_gene_variant,,ENST00000574195,;UMOD,downstream_gene_variant,,ENST00000571174,;UMOD,downstream_gene_variant,,ENST00000577168,;UMOD,downstream_gene_variant,,ENST00000570972,;UMOD,downstream_gene_variant,,ENST00000573567,;UMOD,downstream_gene_variant,,ENST00000576546,;UMOD,downstream_gene_variant,,ENST00000570757,;UMOD,downstream_gene_variant,,ENST00000576688,; T ENST00000396134 Transcript missense_variant 866/2408 742/2022 248/673 E/K Gag/Aag 1 -1 UMOD HGNC HGNC:12559 protein_coding YES CCDS61876.1 ENSP00000379438 P07911 UPI000059D336 NM_001278614.1 deleterious(0) 4/12 hmmpanther:PTHR24044:SF263,hmmpanther:PTHR24044 MODERATE 1 SNV 2 1 PASS rs1490168938 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 20348658 20348658 C T 1 0 0 0 0 1 0 0 0 17503 893 31 1 1 UMOD 16 20348658 Missense_Mutation SNP C C3N-00556_T 10410117 20348658 69989687 373 16502 RBBP6 0 . GRCh38 16 24570460 24570460 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.3770G>A p.Gly1257Glu p.G1257E ENST00000319715 17/18 104 86 18 112 112 0 strelka-varscan-mutect RBBP6,missense_variant,p.Gly1257Glu,ENST00000319715,NM_006910.4;RBBP6,missense_variant,p.Gly1223Glu,ENST00000348022,NM_018703.3;RBBP6,intron_variant,,ENST00000381039,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,; A ENST00000319715 Transcript missense_variant 4202/6229 3770/5379 1257/1792 G/E gGa/gAa COSM4059488 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 deleterious_low_confidence(0) 17/18 hmmpanther:PTHR15439:SF3,hmmpanther:PTHR15439 1 MODERATE 1 SNV 1 1 1 PASS rs1450712090 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 24570460 24570460 G A 1 0 0 0 0 1 0 0 0 13264 1174 41 3 3 RBBP6 16 24570460 Missense_Mutation SNP G C3N-00556_T 4221802 24570460 65767885 374 16503 RBBP6 0 . GRCh38 16 24571426 24571426 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.4360G>A p.Asp1454Asn p.D1454N ENST00000319715 18/18 160 139 21 203 203 0 strelka-varscan-mutect RBBP6,missense_variant,p.Asp1454Asn,ENST00000319715,NM_006910.4;RBBP6,missense_variant,p.Asp1420Asn,ENST00000348022,NM_018703.3;RBBP6,missense_variant,p.Asp614Asn,ENST00000381039,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,; A ENST00000319715 Transcript missense_variant 4792/6229 4360/5379 1454/1792 D/N Gat/Aat 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 deleterious_low_confidence(0) 18/18 hmmpanther:PTHR15439:SF3,hmmpanther:PTHR15439 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 24571426 24571426 G A 1 0 0 0 0 1 0 0 0 13264 942 33 3 3 RBBP6 16 24571426 Missense_Mutation SNP G C3N-00556_T 966 24571426 65766919 375 16504 ZKSCAN2 0 . GRCh38 16 25243932 25243932 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.1834G>A p.Glu612Lys p.E612K ENST00000328086 6/7 277 253 24 249 249 0 strelka-varscan-mutect ZKSCAN2,missense_variant,p.Glu612Lys,ENST00000328086,NM_001012981.4;CTD-2547G23.2,downstream_gene_variant,,ENST00000569456,;ZKSCAN2,3_prime_UTR_variant,,ENST00000569150,;ZKSCAN2,downstream_gene_variant,,ENST00000565590,; T ENST00000328086 Transcript missense_variant 2638/7523 1834/2904 612/967 E/K Gaa/Aaa COSM324423 1 -1 ZKSCAN2 HGNC HGNC:25677 protein_coding YES CCDS32410.1 ENSP00000331626 Q63HK3 UPI0000229E7F NM_001012981.4 tolerated(0.08) 6/7 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 25243932 25243932 C T 1 0 0 0 0 1 0 0 0 18265 835 29 3 3 ZKSCAN2 16 25243932 Missense_Mutation SNP C C3N-00556_T 672506 25243932 65094413 376 16505 ZNF764 0 . GRCh38 16 30557842 30557842 + Silent SNP G G A rs770932668 C3N-00556_T C3N-00556_N G G c.201C>T p.= p.I67I ENST00000252797 2/3 135 126 9 148 148 0 strelka-varscan-mutect ZNF764,synonymous_variant,p.=,ENST00000395091,NM_001172679.1;ZNF764,synonymous_variant,p.=,ENST00000252797,NM_033410.3;AC002310.13,intron_variant,,ENST00000568114,;ZNF764,non_coding_transcript_exon_variant,,ENST00000568333,; A ENST00000252797 Transcript synonymous_variant 282/2738 201/1227 67/408 I atC/atT rs770932668,COSM265142 1 -1 ZNF764 HGNC HGNC:28200 protein_coding YES CCDS10683.1 ENSP00000252797 Q96H86 A0A024QZB2 UPI000013CD86 NM_033410.3 2/3 Superfamily_domains:0044637,PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF131,SMART_domains:SM00349 0,1 LOW 1 SNV 1 0,1 1 PASS rs770932668 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 30557842 30557842 G A 1 0 0 0 0 0 0 0 1 18721 1072 37 1 1 ZNF764 16 30557842 Silent SNP G C3N-00556_T 5313910 30557842 59780503 377 16506 SALL1 0 . GRCh38 16 51137222 51137222 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.3865G>C p.Glu1289Gln p.E1289Q ENST00000251020 3/3 139 128 11 207 207 0 strelka-varscan-mutect SALL1,missense_variant,p.Glu1192Gln,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Glu1289Gln,ENST00000251020,NM_002968.2;SALL1,3_prime_UTR_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000570206,; G ENST00000251020 Transcript missense_variant 3899/5146 3865/3975 1289/1324 E/Q Gag/Cag 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.11) 3/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 51137222 51137222 C G 1 0 0 0 0 1 0 0 0 14069 922 32 4 4 SALL1 16 51137222 Missense_Mutation SNP C C3N-00556_T 20579380 51137222 39201123 378 16507 IRX5 0 . GRCh38 16 54933355 54933355 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.934G>T p.Gly312Cys p.G312C ENST00000394636 3/3 121 93 28 121 121 0 strelka-varscan-mutect IRX5,missense_variant,p.Gly312Cys,ENST00000394636,NM_005853.5;IRX5,missense_variant,p.Gly311Cys,ENST00000320990,NM_001252197.1;IRX5,intron_variant,,ENST00000620085,;IRX5,intron_variant,,ENST00000560154,;CRNDE,upstream_gene_variant,,ENST00000560208,;CRNDE,upstream_gene_variant,,ENST00000559598,;CRNDE,upstream_gene_variant,,ENST00000502066,;CRNDE,upstream_gene_variant,,ENST00000501177,;CRNDE,upstream_gene_variant,,ENST00000558952,;CRNDE,upstream_gene_variant,,ENST00000559432,;CTD-3032H12.1,downstream_gene_variant,,ENST00000559802,;CTD-3032H12.1,downstream_gene_variant,,ENST00000558156,;CRNDE,upstream_gene_variant,,ENST00000557792,;CRNDE,upstream_gene_variant,,ENST00000560912,;CTD-3032H12.2,upstream_gene_variant,,ENST00000560487,;IRX5,non_coding_transcript_exon_variant,,ENST00000558597,; T ENST00000394636 Transcript missense_variant 1271/2401 934/1452 312/483 G/C Ggc/Tgc 1 1 IRX5 HGNC HGNC:14361 protein_coding YES CCDS10751.1 ENSP00000378132 P78411 UPI00001FF1CD NM_005853.5 deleterious(0.03) 3/3 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF17,Low_complexity_(Seg):seg MODERATE 1 SNV 3 1 PASS rs1242231944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 54933355 54933355 G T 1 0 0 0 0 1 0 0 0 7755 1116 39 1 1 IRX5 16 54933355 Missense_Mutation SNP G C3N-00556_T 3796133 54933355 35404990 379 16508 CMTR2 0 . GRCh38 16 71283992 71283992 + Frame_Shift_Del DEL C C - novel C3N-00556_T C3N-00556_N C C c.1929delG p.Met643IlefsTer16 p.M643Ifs*16 ENST00000338099 3/3 81 58 23 135 134 1 sindel-varindel CMTR2,frameshift_variant,p.Met643IlefsTer16,ENST00000338099,;CMTR2,frameshift_variant,p.Met643IlefsTer16,ENST00000434935,NM_001324377.1,NM_018348.5,NM_001099642.1;CMTR2,downstream_gene_variant,,ENST00000565850,;CMTR2,downstream_gene_variant,,ENST00000568910,;CMTR2,downstream_gene_variant,,ENST00000563876,;CMTR2,downstream_gene_variant,,ENST00000564183,;CMTR2,downstream_gene_variant,,ENST00000567610,;CMTR2,downstream_gene_variant,,ENST00000564690,; - ENST00000338099 Transcript frameshift_variant 2266/4869 1929/2313 643/770 M/X atG/at 1 -1 CMTR2 HGNC HGNC:25635 protein_coding YES CCDS10898.1 ENSP00000337512 Q8IYT2 UPI000006EA8B 3/3 hmmpanther:PTHR16121,hmmpanther:PTHR16121:SF2 HIGH 1 deletion 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 54 71283992 71283992 C - 1 0 1 0 1 0 0 0 0 3367 826 29 0 0 CMTR2 16 71283992 Frame_Shift_Del DEL C C3N-00556_T 16350637 71283992 19054353 380 16509 PMFBP1 0 . GRCh38 16 72164912 72164912 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.17G>T p.Gly6Val p.G6V ENST00000237353 3/21 32 22 10 45 45 0 strelka-varscan-mutect PMFBP1,missense_variant,p.Gly6Val,ENST00000537465,;PMFBP1,missense_variant,p.Gly6Val,ENST00000237353,NM_031293.2;PMFBP1,missense_variant,p.Gly6Val,ENST00000535461,;PMFBP1,missense_variant,p.Gly6Val,ENST00000539172,;PMFBP1,missense_variant,p.Gly6Val,ENST00000536211,;PMFBP1,missense_variant,p.Gly6Val,ENST00000540440,;PMFBP1,5_prime_UTR_variant,,ENST00000355636,NM_001160213.1;PMFBP1,non_coding_transcript_exon_variant,,ENST00000543746,;PMFBP1,missense_variant,p.Gly6Val,ENST00000379073,; A ENST00000237353 Transcript missense_variant 279/3527 17/3024 6/1007 G/V gGg/gTg 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 deleterious_low_confidence(0.05) 3/21 hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 54 72164912 72164912 C A 1 0 0 0 0 1 0 0 0 12241 637 22 2 2 PMFBP1 16 72164912 Missense_Mutation SNP C C3N-00556_T 880920 72164912 18173433 381 16510 ZFHX3 0 . GRCh38 16 72787673 72787673 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.10603G>A p.Glu3535Lys p.E3535K ENST00000268489 10/10 301 276 25 250 249 1 strelka-varscan-mutect ZFHX3,missense_variant,p.Glu3535Lys,ENST00000268489,NM_006885.3;ZFHX3,missense_variant,p.Glu2621Lys,ENST00000397992,NM_001164766.1;RP5-991G20.1,non_coding_transcript_exon_variant,,ENST00000563328,; T ENST00000268489 Transcript missense_variant 11276/16064 10603/11112 3535/3703 E/K Gag/Aag COSM3672321 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 deleterious_low_confidence(0.01) 10/10 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF84,PROSITE_patterns:PS00028,SMART_domains:SM00451,SMART_domains:SM00355 1 MODERATE 1 SNV 1 1 1 PASS rs1457944892 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 72787673 72787673 C T 1 0 0 0 0 1 0 0 0 18212 893 31 1 1 ZFHX3 16 72787673 Missense_Mutation SNP C C3N-00556_T 622761 72787673 17550672 382 16511 ZNF469 0 . GRCh38 16 88433317 88433317 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.5763G>T p.Lys1921Asn p.K1921N ENST00000437464 2/2 195 139 56 229 229 0 strelka-varscan-mutect ZNF469,missense_variant,p.Lys1949Asn,ENST00000565624,;ZNF469,missense_variant,p.Lys1921Asn,ENST00000437464,NM_001127464.2; T ENST00000437464 Transcript missense_variant 5763/13203 5763/11778 1921/3925 K/N aaG/aaT 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.81) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 88433317 88433317 G T 1 0 0 0 0 1 0 0 0 18500 991 35 2 2 ZNF469 16 88433317 Missense_Mutation SNP G C3N-00556_T 15645644 88433317 1905028 383 16512 WDR81 0 . GRCh38 17 1726555 1726555 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.1596G>T p.= p.L532L ENST00000409644 1/10 139 122 17 152 152 0 strelka-varscan-mutect WDR81,synonymous_variant,p.=,ENST00000409644,NM_001163809.1;WDR81,intron_variant,,ENST00000309182,NM_152348.3;WDR81,intron_variant,,ENST00000419248,NM_001163811.1;WDR81,intron_variant,,ENST00000437219,NM_001163673.1;WDR81,intron_variant,,ENST00000446363,;WDR81,intron_variant,,ENST00000418841,;WDR81,intron_variant,,ENST00000455636,;WDR81,intron_variant,,ENST00000468539,;WDR81,upstream_gene_variant,,ENST00000575206,;RP11-961A15.1,intron_variant,,ENST00000576540,;WDR81,intron_variant,,ENST00000492901,;WDR81,upstream_gene_variant,,ENST00000464528,;WDR81,upstream_gene_variant,,ENST00000479966,;WDR81,upstream_gene_variant,,ENST00000474958,;WDR81,upstream_gene_variant,,ENST00000495411,; T ENST00000409644 Transcript synonymous_variant 1596/6733 1596/5826 532/1941 L ctG/ctT 1 1 WDR81 HGNC HGNC:26600 protein_coding YES CCDS54062.1 ENSP00000386609 Q562E7 UPI0001881A85 NM_001163809.1 1/10 PROSITE_profiles:PS50197,Pfam_domain:PF02138,Gene3D:1t77A02,SMART_domains:SM01026,Superfamily_domains:SSF81837 LOW 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9998731 1 1 1 0 T 2 4 54 1726555 1726555 G T 1 0 0 0 0 0 0 0 1 17885 1335 47 2 2 WDR81 17 1726555 Silent SNP G C3N-00556_T 1726555 81530886 384 16513 CYB5D2 0 . GRCh38 17 4149982 4149982 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.342G>A p.= p.L114L ENST00000301391 2/4 206 186 20 232 231 1 strelka-varscan-mutect CYB5D2,synonymous_variant,p.=,ENST00000301391,NM_144611.3;CYB5D2,synonymous_variant,p.=,ENST00000575251,NM_001254755.1;CYB5D2,synonymous_variant,p.=,ENST00000577075,NM_001254756.1;CYB5D2,synonymous_variant,p.=,ENST00000573984,;CYB5D2,non_coding_transcript_exon_variant,,ENST00000575411,; A ENST00000301391 Transcript synonymous_variant 842/1910 342/795 114/264 L ctG/ctA 1 1 CYB5D2 HGNC HGNC:28471 protein_coding YES CCDS11044.1 ENSP00000301391 Q8WUJ1 UPI000006E3B0 NM_144611.3 2/4 Gene3D:3.10.120.10,Pfam_domain:PF00173,hmmpanther:PTHR10281,hmmpanther:PTHR10281:SF4,SMART_domains:SM01117,Superfamily_domains:SSF55856 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 4149982 4149982 G A 1 0 0 0 0 0 0 0 1 3929 1277 45 3 3 CYB5D2 17 4149982 Silent SNP G C3N-00556_T 2423427 4149982 79107459 385 16514 DHX33 0 . GRCh38 17 5444364 5444364 + Silent SNP C C A rs775681379 C3N-00556_T C3N-00556_N C C c.1965G>T p.= p.S655S ENST00000225296 12/12 354 296 58 352 352 0 strelka-varscan-mutect DHX33,synonymous_variant,p.=,ENST00000225296,NM_020162.3;DHX33,synonymous_variant,p.=,ENST00000572490,NM_001199699.1;DHX33,synonymous_variant,p.=,ENST00000433302,;C1QBP,intron_variant,,ENST00000570805,;DHX33,3_prime_UTR_variant,,ENST00000574023,;DHX33,non_coding_transcript_exon_variant,,ENST00000575153,; A ENST00000225296 Transcript synonymous_variant 2166/5618 1965/2124 655/707 S tcG/tcT rs775681379 1 -1 DHX33 HGNC HGNC:16718 protein_coding YES CCDS11072.1 ENSP00000225296 Q9H6R0 UPI000013C861 NM_020162.3 12/12 hmmpanther:PTHR18934,Pfam_domain:PF07717 LOW 1 SNV 1 1 PASS rs775681379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 5444364 5444364 C A 1 0 0 0 0 0 0 0 1 4310 523 19 1 1 DHX33 17 5444364 Silent SNP C C3N-00556_T 1294382 5444364 77813077 386 16515 NLRP1 0 . GRCh38 17 5558643 5558643 + Missense_Mutation SNP C C G rs200362116 C3N-00556_T C3N-00556_N C C c.2053G>C p.Glu685Gln p.E685Q ENST00000617618 5/18 275 226 49 325 325 0 strelka-varscan-mutect NLRP1,missense_variant,p.Glu685Gln,ENST00000262467,NM_001033053.2;NLRP1,missense_variant,p.Glu685Gln,ENST00000269280,NM_014922.4;NLRP1,missense_variant,p.Glu685Gln,ENST00000617618,NM_033004.3;NLRP1,missense_variant,p.Glu685Gln,ENST00000619223,NM_033006.3;NLRP1,missense_variant,p.Glu685Gln,ENST00000345221,;NLRP1,missense_variant,p.Glu685Gln,ENST00000613500,;NLRP1,missense_variant,p.Glu685Gln,ENST00000572272,;NLRP1,missense_variant,p.Glu685Gln,ENST00000354411,;NLRP1,missense_variant,p.Glu685Gln,ENST00000577119,NM_033007.3;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,missense_variant,p.Glu685Gln,ENST00000571451,;NLRP1,missense_variant,p.Glu685Gln,ENST00000544378,; G ENST00000617618 Transcript missense_variant 2419/4788 2053/4422 685/1473 E/Q Gag/Cag rs200362116 1 -1 NLRP1 HGNC HGNC:14374 protein_coding YES CCDS42246.1 ENSP00000478516 Q9C000 UPI0000038309 NM_033004.3 tolerated(0.09) 5/18 hmmpanther:PTHR24106:SF13,hmmpanther:PTHR24106 MODERATE 1 SNV 5 1 PASS rs200362116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 5558643 5558643 C G 1 0 0 0 0 1 0 0 0 10508 922 32 4 4 NLRP1 17 5558643 Missense_Mutation SNP C C3N-00556_T 114279 5558643 77698798 387 16516 CHD3 0 . GRCh38 17 7894534 7894534 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.1372C>T p.Arg458Cys p.R458C ENST00000380358 8/40 118 106 12 109 109 0 strelka-varscan-mutect CHD3,missense_variant,p.Arg458Cys,ENST00000380358,NM_001005271.2;CHD3,missense_variant,p.Arg399Cys,ENST00000330494,NM_001005273.2;CHD3,missense_variant,p.Arg399Cys,ENST00000358181,NM_005852.3;CHD3,missense_variant,p.Arg270Cys,ENST00000452447,;CHD3,downstream_gene_variant,,ENST00000571249,;CHD3,downstream_gene_variant,,ENST00000570758,;CHD3,downstream_gene_variant,,ENST00000574022,;CHD3,non_coding_transcript_exon_variant,,ENST00000572579,;CHD3,upstream_gene_variant,,ENST00000479080,; T ENST00000380358 Transcript missense_variant 1373/7356 1372/6180 458/2059 R/C Cgt/Tgt COSM3523247 1 1 CHD3 HGNC HGNC:1918 protein_coding YES CCDS32553.2 ENSP00000369716 Q12873 UPI00004DDA7C NM_001005271.2 deleterious(0.01) 8/40 Gene3D:3.30.40.10,Pfam_domain:PF00628,PROSITE_patterns:PS01359,PROSITE_profiles:PS50016,SMART_domains:SM00249,Superfamily_domains:SSF57903 1 MODERATE 1 SNV 2 1 1 PASS rs1178138055 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 7894534 7894534 C T 1 0 0 0 0 1 0 0 0 3085 884 31 1 1 CHD3 17 7894534 Missense_Mutation SNP C C3N-00556_T 2335891 7894534 75362907 388 16517 PFAS 0 . GRCh38 17 8257869 8257869 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1138G>A p.Glu380Lys p.E380K ENST00000314666 10/28 277 263 14 289 289 0 strelka-varscan-mutect PFAS,missense_variant,p.Glu380Lys,ENST00000314666,NM_012393.2;PFAS,downstream_gene_variant,,ENST00000585183,;PFAS,downstream_gene_variant,,ENST00000584044,;PFAS,downstream_gene_variant,,ENST00000581242,;PFAS,downstream_gene_variant,,ENST00000625942,;PFAS,upstream_gene_variant,,ENST00000585319,;PFAS,3_prime_UTR_variant,,ENST00000580356,; A ENST00000314666 Transcript missense_variant 1271/5371 1138/4017 380/1338 E/K Gag/Aag 1 1 PFAS HGNC HGNC:8863 protein_coding YES CCDS11136.1 ENSP00000313490 O15067 UPI00001A95E5 NM_012393.2 tolerated(0.39) 10/28 HAMAP:MF_00419,hmmpanther:PTHR10099,hmmpanther:PTHR10099:SF1,Gene3D:3.30.1330.10,TIGRFAM_domain:TIGR01735,Superfamily_domains:SSF55326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 8257869 8257869 G A 1 0 0 0 0 1 0 0 0 11844 1175 41 3 3 PFAS 17 8257869 Missense_Mutation SNP G C3N-00556_T 363335 8257869 74999572 389 16518 MYH8 0 . GRCh38 17 10400479 10400479 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.3646G>T p.Val1216Phe p.V1216F ENST00000403437 27/40 306 240 66 399 398 1 strelka-varscan-mutect MYH8,missense_variant,p.Val1216Phe,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript missense_variant 3741/6041 3646/5814 1216/1937 V/F Gtc/Ttc 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0) 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 10400479 10400479 C A 1 0 0 0 0 1 0 0 0 10041 507 18 2 2 MYH8 17 10400479 Missense_Mutation SNP C C3N-00556_T 2142610 10400479 72856962 390 16519 SLC5A10 0 . GRCh38 17 19020158 19020158 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1678G>A p.Glu560Lys p.E560K ENST00000395647 14/15 166 152 14 191 191 0 strelka-varscan-mutect SLC5A10,missense_variant,p.Glu514Lys,ENST00000317977,NM_001282417.1;SLC5A10,missense_variant,p.Glu560Lys,ENST00000395647,NM_152351.4;SLC5A10,missense_variant,p.Glu544Lys,ENST00000395645,NM_001042450.2;SLC5A10,missense_variant,p.Glu508Lys,ENST00000417251,NM_001270649.1;SLC5A10,missense_variant,p.Glu517Lys,ENST00000395643,NM_001270648.1;GRAP,downstream_gene_variant,,ENST00000284154,NM_006613.3;GRAP,downstream_gene_variant,,ENST00000573099,;GRAP,downstream_gene_variant,,ENST00000395635,;SLC5A10,downstream_gene_variant,,ENST00000584658,;GRAP,downstream_gene_variant,,ENST00000583020,; A ENST00000395647 Transcript missense_variant 1719/2140 1678/1839 560/612 E/K Gag/Aag 1 1 SLC5A10 HGNC HGNC:23155 protein_coding YES CCDS11201.2 ENSP00000379008 A0PJK1 UPI00001401D2 NM_152351.4 tolerated(0.93) 14/15 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF128 MODERATE SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 19020158 19020158 G A 1 0 0 0 0 1 0 0 0 14945 1304 45 3 3 SLC5A10 17 19020158 Missense_Mutation SNP G C3N-00556_T 8619679 19020158 64237283 391 16520 KCNJ18 0 . GRCh38 17 21703980 21703980 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.1194C>A p.= p.G398G ENST00000567955 3/3 80 61 19 112 112 0 varscan-mutect KCNJ18,synonymous_variant,p.=,ENST00000567955,NM_001194958.2; A ENST00000567955 Transcript synonymous_variant 1564/2196 1194/1302 398/433 G ggC/ggA 1 1 KCNJ18 HGNC HGNC:39080 protein_coding YES CCDS74015.1 ENSP00000457807 B7U540 UPI0002064ECF NM_001194958.2 3/3 Prints_domain:PR01325,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 2 1 54 21703980 21703980 C A 1 0 0 0 0 0 0 0 1 7967 726 26 2 2 KCNJ18 17 21703980 Silent SNP C C3N-00556_T 2683822 21703980 61553461 392 16521 NEK8 0 . GRCh38 17 28737381 28737381 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.694C>T p.Arg232Cys p.R232C ENST00000268766 5/15 510 465 45 417 416 1 strelka-varscan-mutect NEK8,missense_variant,p.Arg232Cys,ENST00000268766,NM_178170.2;NEK8,missense_variant,p.Arg58Cys,ENST00000592510,;NEK8,downstream_gene_variant,,ENST00000579060,;NEK8,downstream_gene_variant,,ENST00000579671,;AC010761.6,intron_variant,,ENST00000584779,;AC010761.6,downstream_gene_variant,,ENST00000582536,;NEK8,downstream_gene_variant,,ENST00000593261,;NEK8,missense_variant,p.Arg232Cys,ENST00000543014,;NEK8,downstream_gene_variant,,ENST00000584342,;NEK8,downstream_gene_variant,,ENST00000581000,; T ENST00000268766 Transcript missense_variant 728/3581 694/2079 232/692 R/C Cgc/Tgc COSM229300 1 1 NEK8 HGNC HGNC:13387 protein_coding YES CCDS32597.1 ENSP00000268766 Q86SG6 UPI000004B820 NM_178170.2 tolerated(0.07) 5/15 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24362,hmmpanther:PTHR24362:SF0,Low_complexity_(Seg):seg,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS rs1199087140 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 28737381 28737381 C T 1 0 0 0 0 1 0 0 0 10358 884 31 1 1 NEK8 17 28737381 Missense_Mutation SNP C C3N-00556_T 7033401 28737381 54520060 393 16522 SLC6A4 0 . GRCh38 17 30211395 30211395 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1234G>C p.Glu412Gln p.E412Q ENST00000261707 10/15 201 181 20 229 229 0 strelka-varscan-mutect SLC6A4,missense_variant,p.Glu412Gln,ENST00000261707,NM_001045.5;SLC6A4,missense_variant,p.Glu412Gln,ENST00000401766,;SLC6A4,missense_variant,p.Glu412Gln,ENST00000394821,;RP11-354P11.4,downstream_gene_variant,,ENST00000581633,;SLC6A4,upstream_gene_variant,,ENST00000579221,; G ENST00000261707 Transcript missense_variant 1810/6604 1234/1893 412/630 E/Q Gaa/Caa 1 -1 SLC6A4 HGNC HGNC:11050 protein_coding YES CCDS11256.1 ENSP00000261707 P31645 UPI0000135493 NM_001045.5 deleterious(0.03) 10/15 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF105,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 30211395 30211395 C G 1 0 0 0 0 1 0 0 0 14969 922 32 4 4 SLC6A4 17 30211395 Missense_Mutation SNP C C3N-00556_T 1474014 30211395 53046046 394 16523 NF1 0 . GRCh38 17 31327795 31327795 + Silent SNP C C G novel C3N-00556_T C3N-00556_N C C c.5565C>G p.= p.L1855L ENST00000358273 38/58 132 122 10 192 192 0 strelka-varscan-mutect NF1,synonymous_variant,p.=,ENST00000358273,NM_001042492.2;NF1,synonymous_variant,p.=,ENST00000356175,NM_000267.3;NF1,synonymous_variant,p.=,ENST00000456735,;NF1,non_coding_transcript_exon_variant,,ENST00000581113,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000479536,; G ENST00000358273 Transcript synonymous_variant 5948/12425 5565/8520 1855/2839 L ctC/ctG 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 38/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 54 31327795 31327795 C G 1 0 0 0 0 0 0 0 1 10393 813 29 4 4 NF1 17 31327795 Silent SNP C C3N-00556_T 1116400 31327795 51929646 395 16524 AP2B1 0 . GRCh38 17 35624440 35624440 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.569C>G p.Ser190Cys p.S190C ENST00000618940 6/22 287 266 21 283 283 0 strelka-varscan-mutect AP2B1,missense_variant,p.Ser190Cys,ENST00000621914,NM_001282.2;AP2B1,missense_variant,p.Ser190Cys,ENST00000618940,;AP2B1,missense_variant,p.Ser152Cys,ENST00000616681,;AP2B1,missense_variant,p.Ser190Cys,ENST00000610402,NM_001030006.1;AP2B1,missense_variant,p.Ser190Cys,ENST00000616784,;AP2B1,missense_variant,p.Ser190Cys,ENST00000614600,;AP2B1,missense_variant,p.Ser190Cys,ENST00000612116,;AP2B1,missense_variant,p.Ser190Cys,ENST00000612035,;AP2B1,missense_variant,p.Ser152Cys,ENST00000621668,;AP2B1,non_coding_transcript_exon_variant,,ENST00000619183,;AP2B1,non_coding_transcript_exon_variant,,ENST00000591561,;AP2B1,3_prime_UTR_variant,,ENST00000620039,;AP2B1,upstream_gene_variant,,ENST00000588116,; G ENST00000618940 Transcript missense_variant 741/3415 569/2856 190/951 S/C tCt/tGt 1 1 AP2B1 HGNC HGNC:563 protein_coding YES CCDS32621.1 ENSP00000482835 P63010 A0A140VJE8 UPI000006DD97 deleterious(0) 6/22 hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF9,Gene3D:1.25.10.10,PIRSF_domain:PIRSF002291,Pfam_domain:PF01602,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 35624440 35624440 C G 1 0 0 0 0 1 0 0 0 857 913 32 4 4 AP2B1 17 35624440 Missense_Mutation SNP C C3N-00556_T 4296645 35624440 47633001 396 16525 TAF15 0 . GRCh38 17 35824094 35824094 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.501G>A p.= p.V167V ENST00000605844 7/16 266 244 22 290 290 0 strelka-varscan-mutect TAF15,synonymous_variant,p.=,ENST00000605844,NM_139215.2;TAF15,synonymous_variant,p.=,ENST00000604841,NM_003487.3;TAF15,synonymous_variant,p.=,ENST00000603777,;TAF15,synonymous_variant,p.=,ENST00000604879,;TAF15,downstream_gene_variant,,ENST00000603427,;AC015849.19,intron_variant,,ENST00000603981,;AC015849.13,downstream_gene_variant,,ENST00000603678,;TAF15,downstream_gene_variant,,ENST00000604360,;TAF15,synonymous_variant,p.=,ENST00000603393,;TAF15,non_coding_transcript_exon_variant,,ENST00000605649,;TAF15,non_coding_transcript_exon_variant,,ENST00000605197,;TAF15,intron_variant,,ENST00000603067,; A ENST00000605844 Transcript synonymous_variant 616/2191 501/1779 167/592 V gtG/gtA 1 1 TAF15 HGNC HGNC:11547 protein_coding YES CCDS32623.1 ENSP00000474096 Q92804 UPI000013317D NM_139215.2 7/16 hmmpanther:PTHR23238,hmmpanther:PTHR23238:SF25 LOW 1 SNV 1 1 PASS rs945006859 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 35824094 35824094 G A 1 0 0 0 0 0 0 0 1 15914 1277 45 3 3 TAF15 17 35824094 Silent SNP G C3N-00556_T 199654 35824094 47433347 397 16526 STARD3 0 . GRCh38 17 39653568 39653568 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.37G>C p.Glu13Gln p.E13Q ENST00000336308 2/15 237 219 18 188 188 0 strelka-varscan-mutect STARD3,missense_variant,p.Glu13Gln,ENST00000336308,NM_006804.3;STARD3,missense_variant,p.Glu13Gln,ENST00000580611,;STARD3,missense_variant,p.Glu13Gln,ENST00000394250,NM_001165938.1;STARD3,missense_variant,p.Glu13Gln,ENST00000544210,NM_001165937.1;STARD3,missense_variant,p.Glu13Gln,ENST00000443521,;STARD3,missense_variant,p.Glu13Gln,ENST00000581894,;STARD3,missense_variant,p.Glu13Gln,ENST00000583419,;STARD3,missense_variant,p.Glu13Gln,ENST00000577248,;STARD3,missense_variant,p.Glu13Gln,ENST00000579479,;STARD3,missense_variant,p.Glu13Gln,ENST00000580331,;STARD3,missense_variant,p.Glu13Gln,ENST00000583718,;STARD3,non_coding_transcript_exon_variant,,ENST00000582874,;STARD3,non_coding_transcript_exon_variant,,ENST00000460894,;STARD3,non_coding_transcript_exon_variant,,ENST00000585214,;STARD3,non_coding_transcript_exon_variant,,ENST00000578254,;STARD3,intron_variant,,ENST00000578232,;STARD3,missense_variant,p.Glu13Gln,ENST00000578577,;STARD3,non_coding_transcript_exon_variant,,ENST00000488876,;STARD3,non_coding_transcript_exon_variant,,ENST00000583582,;STARD3,non_coding_transcript_exon_variant,,ENST00000484773,;STARD3,non_coding_transcript_exon_variant,,ENST00000580551,;STARD3,upstream_gene_variant,,ENST00000481171,;STARD3,upstream_gene_variant,,ENST00000584850,;STARD3,upstream_gene_variant,,ENST00000585269,; C ENST00000336308 Transcript missense_variant 255/2132 37/1338 13/445 E/Q Gag/Cag 1 1 STARD3 HGNC HGNC:17579 protein_coding YES CCDS11341.1 ENSP00000337446 Q14849 UPI000013CE10 NM_006804.3 tolerated_low_confidence(0.13) 2/15 hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF51 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 39653568 39653568 G C 1 0 0 0 0 1 0 0 0 15632 1175 41 4 4 STARD3 17 39653568 Missense_Mutation SNP G C3N-00556_T 3829474 39653568 43603873 398 16527 GSDMA 0 . GRCh38 17 39965807 39965807 + Silent SNP G G C novel C3N-00556_T C3N-00556_N G G c.120G>C p.= p.L40L ENST00000301659 2/12 365 345 20 335 335 0 strelka-varscan GSDMA,synonymous_variant,p.=,ENST00000301659,NM_178171.4;GSDMA,synonymous_variant,p.=,ENST00000635792,;GSDMA,synonymous_variant,p.=,ENST00000577447,; C ENST00000301659 Transcript synonymous_variant 238/2164 120/1338 40/445 L ctG/ctC 1 1 GSDMA HGNC HGNC:13311 protein_coding YES CCDS45669.1 ENSP00000301659 Q96QA5 UPI0000140D2A NM_178171.4 2/12 hmmpanther:PTHR16399:SF18,hmmpanther:PTHR16399,Pfam_domain:PF04598 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 39965807 39965807 G C 1 0 0 0 0 0 0 0 1 6698 1277 45 4 4 GSDMA 17 39965807 Silent SNP G C3N-00556_T 312239 39965807 43291634 399 16528 CASC3 0 . GRCh38 17 40163977 40163977 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1282C>T p.Pro428Ser p.P428S ENST00000264645 7/14 271 255 16 301 301 0 strelka-varscan-mutect CASC3,missense_variant,p.Pro428Ser,ENST00000264645,NM_007359.4;CASC3,downstream_gene_variant,,ENST00000584997,;CASC3,downstream_gene_variant,,ENST00000638146,;CASC3,missense_variant,p.Pro23Ser,ENST00000577605,;CASC3,synonymous_variant,p.=,ENST00000474190,;CASC3,non_coding_transcript_exon_variant,,ENST00000418132,;CASC3,upstream_gene_variant,,ENST00000394114,;CASC3,downstream_gene_variant,,ENST00000581849,;CASC3,upstream_gene_variant,,ENST00000583902,;CASC3,upstream_gene_variant,,ENST00000579238,; T ENST00000264645 Transcript missense_variant 1508/4116 1282/2112 428/703 P/S Cct/Tct 1 1 CASC3 HGNC HGNC:17040 protein_coding YES CCDS11362.1 ENSP00000264645 O15234 UPI000000DAAA NM_007359.4 tolerated_low_confidence(0.31) 7/14 Low_complexity_(Seg):seg,hmmpanther:PTHR13434 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 40163977 40163977 C T 1 0 0 0 0 1 0 0 0 2361 855 30 3 3 CASC3 17 40163977 Missense_Mutation SNP C C3N-00556_T 198170 40163977 43093464 400 16529 KRT27 0 . GRCh38 17 40779620 40779620 + Missense_Mutation SNP G G A rs754672693 C3N-00556_T C3N-00556_N G G c.854C>T p.Ser285Leu p.S285L ENST00000301656 5/8 109 103 6 115 115 0 strelka-varscan KRT27,missense_variant,p.Ser285Leu,ENST00000301656,NM_181537.3;KRT27,upstream_gene_variant,,ENST00000540723,; A ENST00000301656 Transcript missense_variant 895/1612 854/1380 285/459 S/L tCg/tTg rs754672693 1 -1 KRT27 HGNC HGNC:30841 protein_coding YES CCDS11375.1 ENSP00000301656 Q7Z3Y8 UPI0000200C91 NM_181537.3 tolerated(0.15) 5/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF120,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 40779620 40779620 G A 1 0 0 0 0 1 0 0 0 8346 1059 37 1 1 KRT27 17 40779620 Missense_Mutation SNP G C3N-00556_T 615643 40779620 42477821 401 16530 TMEM99 0 . GRCh38 17 40834723 40834723 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.207C>T p.= p.L69L ENST00000622451 3/3 105 98 7 171 171 0 strelka-varscan-mutect TMEM99,synonymous_variant,p.=,ENST00000622451,NM_001195386.1;TMEM99,synonymous_variant,p.=,ENST00000301665,NM_001195387.1,NM_145274.3;TMEM99,synonymous_variant,p.=,ENST00000436612,; T ENST00000622451 Transcript synonymous_variant 522/2073 207/777 69/258 L ctC/ctT 1 1 TMEM99 HGNC HGNC:28305 protein_coding YES CCDS42319.1 ENSP00000482364 Q8N816 A0A024R1X7 UPI0000E5924C NM_001195386.1 3/3 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs1237518912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 40834723 40834723 C T 1 0 0 0 0 0 0 0 1 16701 900 32 3 3 TMEM99 17 40834723 Silent SNP C C3N-00556_T 55103 40834723 42422718 402 16531 FKBP10 0 . GRCh38 17 41813169 41813169 + Silent SNP C C T rs782808931 C3N-00556_T C3N-00556_N C C c.135C>T p.= p.V45V ENST00000321562 1/10 112 90 22 102 102 0 strelka-varscan-mutect FKBP10,synonymous_variant,p.=,ENST00000321562,NM_021939.3;FKBP10,synonymous_variant,p.=,ENST00000585922,;FKBP10,intron_variant,,ENST00000585664,;FKBP10,intron_variant,,ENST00000429461,;P3H4,upstream_gene_variant,,ENST00000355468,;P3H4,upstream_gene_variant,,ENST00000393928,NM_006455.2;P3H4,upstream_gene_variant,,ENST00000592026,;P3H4,upstream_gene_variant,,ENST00000590496,;FKBP10,synonymous_variant,p.=,ENST00000489591,;P3H4,upstream_gene_variant,,ENST00000467164,;P3H4,upstream_gene_variant,,ENST00000587455,; T ENST00000321562 Transcript synonymous_variant 239/2662 135/1749 45/582 V gtC/gtT rs782808931 1 1 FKBP10 HGNC HGNC:18169 protein_coding YES CCDS11409.1 ENSP00000317232 Q96AY3 A0A024R1W3 UPI000012A80A NM_021939.3 1/10 hmmpanther:PTHR10516,hmmpanther:PTHR10516:SF247,Superfamily_domains:SSF54534 LOW 1 SNV 1 1 PASS rs782808931 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 41813169 41813169 C T 1 0 0 0 0 0 0 0 1 5765 813 29 3 3 FKBP10 17 41813169 Silent SNP C C3N-00556_T 978446 41813169 41444272 403 16532 NMT1 0 . GRCh38 17 45061435 45061435 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.106G>A p.Glu36Lys p.E36K ENST00000592782 2/13 172 161 11 147 147 0 strelka-varscan NMT1,missense_variant,p.Glu36Lys,ENST00000592782,;NMT1,missense_variant,p.Glu36Lys,ENST00000258960,NM_021079.4;DCAKD,upstream_gene_variant,,ENST00000310604,NM_024819.5,NM_001288654.1;DCAKD,upstream_gene_variant,,ENST00000342350,;NMT1,upstream_gene_variant,,ENST00000592654,;NMT1,non_coding_transcript_exon_variant,,ENST00000590114,;NMT1,non_coding_transcript_exon_variant,,ENST00000588975,;NMT1,missense_variant,p.Glu36Lys,ENST00000543908,;NMT1,missense_variant,p.Glu35Lys,ENST00000585561,; A ENST00000592782 Transcript missense_variant 237/4999 106/1491 36/496 E/K Gag/Aag 1 1 NMT1 HGNC HGNC:7857 protein_coding YES CCDS11494.1 ENSP00000468424 P30419 UPI0000130275 tolerated_low_confidence(0.07) 2/13 hmmpanther:PTHR11377,hmmpanther:PTHR11377:SF7 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -14.48264 0.9999996 1 1 1 0 A 3 1 54 45061435 45061435 G A 1 0 0 0 0 1 0 0 0 10544 1291 45 3 3 NMT1 17 45061435 Missense_Mutation SNP G C3N-00556_T 3248266 45061435 38196006 404 16533 WNT9B 0 . GRCh38 17 46875141 46875141 + Silent SNP C C T rs368158766 C3N-00556_T C3N-00556_N C C c.375C>T p.= p.A125A ENST00000290015 3/4 210 196 14 180 180 0 strelka-varscan-mutect WNT9B,synonymous_variant,p.=,ENST00000393461,NM_001320458.1;WNT9B,synonymous_variant,p.=,ENST00000290015,NM_003396.1;WNT9B,synonymous_variant,p.=,ENST00000575372,; T ENST00000290015 Transcript synonymous_variant 428/1376 375/1074 125/357 A gcC/gcT rs368158766,COSM3755605,COSM3755606 1 1 WNT9B HGNC HGNC:12779 protein_coding YES CCDS11506.1 ENSP00000290015 O14905 UPI000013DFB5 NM_003396.1 3/4 Pfam_domain:PF00110,Prints_domain:PR01349,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF84,SMART_domains:SM00097 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs368158766 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 46875141 46875141 C T 1 0 0 0 0 0 0 0 1 17955 639 23 1 1 WNT9B 17 46875141 Silent SNP C C3N-00556_T 1813706 46875141 36382300 405 16534 VEZF1 0 . GRCh38 17 57979179 57979179 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1111G>A p.Glu371Lys p.E371K ENST00000581208 5/6 150 140 10 148 148 0 varscan-mutect VEZF1,missense_variant,p.Glu190Lys,ENST00000258963,;VEZF1,missense_variant,p.Glu362Lys,ENST00000584396,;VEZF1,missense_variant,p.Glu371Lys,ENST00000581208,NM_007146.2;VEZF1,downstream_gene_variant,,ENST00000583932,; T ENST00000581208 Transcript missense_variant 1152/2321 1111/1566 371/521 E/K Gaa/Aaa 1 -1 VEZF1 HGNC HGNC:12949 protein_coding YES CCDS32687.1 ENSP00000462337 Q14119 UPI000013D01B NM_007146.2 tolerated_low_confidence(0.46) 5/6 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 57979179 57979179 C T 1 0 0 0 0 1 0 0 0 17701 864 30 3 3 VEZF1 17 57979179 Missense_Mutation SNP C C3N-00556_T 11104038 57979179 25278262 406 16535 VEZF1 0 . GRCh38 17 57979197 57979197 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1093G>C p.Glu365Gln p.E365Q ENST00000581208 5/6 201 188 13 179 179 0 strelka-varscan-mutect VEZF1,missense_variant,p.Glu184Gln,ENST00000258963,;VEZF1,missense_variant,p.Glu356Gln,ENST00000584396,;VEZF1,missense_variant,p.Glu365Gln,ENST00000581208,NM_007146.2;VEZF1,downstream_gene_variant,,ENST00000583932,; G ENST00000581208 Transcript missense_variant 1134/2321 1093/1566 365/521 E/Q Gaa/Caa 1 -1 VEZF1 HGNC HGNC:12949 protein_coding YES CCDS32687.1 ENSP00000462337 Q14119 UPI000013D01B NM_007146.2 tolerated_low_confidence(0.48) 5/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 57979197 57979197 C G 1 0 0 0 0 1 0 0 0 17701 922 32 4 4 VEZF1 17 57979197 Missense_Mutation SNP C C3N-00556_T 18 57979197 25278244 407 16536 TEX14 0 . GRCh38 17 58602532 58602532 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1413G>A p.= p.G471G ENST00000240361 12/33 135 125 10 165 165 0 strelka-varscan-mutect TEX14,synonymous_variant,p.=,ENST00000389934,NM_198393.3;TEX14,synonymous_variant,p.=,ENST00000240361,NM_001201457.1;TEX14,synonymous_variant,p.=,ENST00000349033,NM_031272.4;TEX14,3_prime_UTR_variant,,ENST00000582740,; T ENST00000240361 Transcript synonymous_variant 1499/4911 1413/4494 471/1497 G ggG/ggA 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 12/33 PROSITE_profiles:PS50011,hmmpanther:PTHR23060,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 58602532 58602532 C T 1 0 0 0 0 0 0 0 1 16200 842 30 3 3 TEX14 17 58602532 Silent SNP C C3N-00556_T 623335 58602532 24654909 408 16537 TEX14 0 . GRCh38 17 58605111 58605111 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1221G>C p.Gln407His p.Q407H ENST00000240361 11/33 163 126 37 172 172 0 strelka-varscan-mutect TEX14,missense_variant,p.Gln401His,ENST00000389934,NM_198393.3;TEX14,missense_variant,p.Gln407His,ENST00000240361,NM_001201457.1;TEX14,missense_variant,p.Gln401His,ENST00000349033,NM_031272.4;TEX14,3_prime_UTR_variant,,ENST00000582740,; G ENST00000240361 Transcript missense_variant 1307/4911 1221/4494 407/1497 Q/H caG/caC 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 tolerated(1) 11/33 PROSITE_profiles:PS50011,hmmpanther:PTHR23060,Gene3D:1.10.510.10,Pfam_domain:PF07714,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 58605111 58605111 C G 1 0 0 0 0 1 0 0 0 16200 912 32 4 4 TEX14 17 58605111 Missense_Mutation SNP C C3N-00556_T 2579 58605111 24652330 409 16538 RPS6KB1 0 . GRCh38 17 59934177 59934177 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.696G>A p.= p.V232V ENST00000225577 8/15 113 94 19 151 151 0 strelka-varscan-mutect RPS6KB1,synonymous_variant,p.=,ENST00000393021,NM_001272044.1;RPS6KB1,synonymous_variant,p.=,ENST00000225577,NM_001272060.1,NM_003161.3;RPS6KB1,synonymous_variant,p.=,ENST00000406116,NM_001272043.1;RPS6KB1,synonymous_variant,p.=,ENST00000443572,NM_001272042.1;RPS6KB1,3_prime_UTR_variant,,ENST00000472940,;RPS6KB1,non_coding_transcript_exon_variant,,ENST00000590928,;RPS6KB1,non_coding_transcript_exon_variant,,ENST00000587622,;RPS6KB1,downstream_gene_variant,,ENST00000489824,; A ENST00000225577 Transcript synonymous_variant 717/5375 696/1578 232/525 V gtG/gtA 1 1 RPS6KB1 HGNC HGNC:10436 protein_coding YES CCDS11621.1 ENSP00000225577 P23443 UPI000013C873 NM_001272060.1,NM_003161.3 8/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24351:SF85,hmmpanther:PTHR24351,PIRSF_domain:PIRSF000605,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 59934177 59934177 G A 1 0 0 0 0 0 0 0 1 13911 1277 45 3 3 RPS6KB1 17 59934177 Silent SNP G C3N-00556_T 1329066 59934177 23323264 410 16539 TLK2 0 . GRCh38 17 62600696 62600696 + Missense_Mutation SNP C C G C3N-00556_T C3N-00556_N C C c.1662C>G p.Phe554Leu p.F554L ENST00000326270 19/23 127 117 10 138 138 0 varscan-mutect TLK2,missense_variant,p.Phe383Leu,ENST00000582809,;TLK2,missense_variant,p.Phe554Leu,ENST00000326270,NM_001284333.1;TLK2,missense_variant,p.Phe532Leu,ENST00000346027,NM_006852.3;TLK2,missense_variant,p.Phe500Leu,ENST00000343388,NM_001284363.1;TLK2,missense_variant,p.Phe468Leu,ENST00000581041,;TLK2,intron_variant,,ENST00000578931,;TLK2,non_coding_transcript_exon_variant,,ENST00000582660,; G ENST00000326270 Transcript missense_variant 1930/3512 1662/2319 554/772 F/L ttC/ttG COSM3520530,COSM3520531,COSM3520532 1 1 TLK2 HGNC HGNC:11842 protein_coding YES CCDS62283.1 ENSP00000316512 Q86UE8 UPI00001B6B0E NM_001284333.1 deleterious(0.01) 19/23 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF20,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 62600696 62600696 C G 1 0 0 0 0 1 0 0 0 16390 912 32 4 4 TLK2 17 62600696 Missense_Mutation SNP C C3N-00556_T 2666519 62600696 20656745 411 16540 DDX42 0 . GRCh38 17 63813334 63813334 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1782G>C p.Glu594Asp p.E594D ENST00000578681 16/19 148 135 13 140 140 0 strelka-varscan-mutect DDX42,missense_variant,p.Glu594Asp,ENST00000578681,NM_007372.3;DDX42,missense_variant,p.Glu594Asp,ENST00000583590,;DDX42,missense_variant,p.Glu594Asp,ENST00000389924,NM_203499.2;DDX42,missense_variant,p.Glu475Asp,ENST00000457800,;DDX42,missense_variant,p.Glu475Asp,ENST00000359353,;DDX42,upstream_gene_variant,,ENST00000582985,;DDX42,non_coding_transcript_exon_variant,,ENST00000584010,;DDX42,non_coding_transcript_exon_variant,,ENST00000578593,;DDX42,non_coding_transcript_exon_variant,,ENST00000584951,;DDX42,upstream_gene_variant,,ENST00000581767,;DDX42,downstream_gene_variant,,ENST00000577940,;DDX42,upstream_gene_variant,,ENST00000579539,;DDX42,downstream_gene_variant,,ENST00000581477,; C ENST00000578681 Transcript missense_variant 2383/4337 1782/2817 594/938 E/D gaG/gaC 1 1 DDX42 HGNC HGNC:18676 protein_coding YES CCDS32704.1 ENSP00000464050 Q86XP3 UPI000017DA3D NM_007372.3 tolerated(0.34) 16/19 PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF125,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 63813334 63813334 G C 1 0 0 0 0 1 0 0 0 4165 933 33 4 4 DDX42 17 63813334 Missense_Mutation SNP G C3N-00556_T 1212638 63813334 19444107 412 16541 USP36 0 . GRCh38 17 78814529 78814529 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.1047C>T p.= p.L349L ENST00000542802 11/21 121 110 11 147 147 0 strelka-varscan-mutect USP36,synonymous_variant,p.=,ENST00000542802,NM_001321291.1;USP36,synonymous_variant,p.=,ENST00000312010,NM_025090.3;USP36,synonymous_variant,p.=,ENST00000449938,;USP36,synonymous_variant,p.=,ENST00000586066,;USP36,non_coding_transcript_exon_variant,,ENST00000588467,;USP36,synonymous_variant,p.=,ENST00000589225,;USP36,synonymous_variant,p.=,ENST00000588086,;USP36,non_coding_transcript_exon_variant,,ENST00000590312,;USP36,downstream_gene_variant,,ENST00000589254,; A ENST00000542802 Transcript synonymous_variant 1491/6063 1047/3372 349/1123 L ctC/ctT 1 -1 USP36 HGNC HGNC:20062 protein_coding YES CCDS32755.1 ENSP00000441214 Q9P275 A0A024R8V6 UPI00000398BB NM_001321291.1 11/21 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF409,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 78814529 78814529 G A 1 0 0 0 0 0 0 0 1 17609 1277 45 3 3 USP36 17 78814529 Silent SNP G C3N-00556_T 15001195 78814529 4442912 413 16542 CANT1 0 . GRCh38 17 78993714 78993715 + Frame_Shift_Ins INS - - G novel C3N-00556_T C3N-00556_N - - c.1041dupC p.Lys348GlnfsTer103 p.K348Qfs*103 ENST00000302345 4/4 229 183 46 264 264 0 sindel-varindel-pindel CANT1,frameshift_variant,p.Lys348GlnfsTer103,ENST00000302345,NM_138793.3,NM_001159773.1;CANT1,frameshift_variant,p.Lys348GlnfsTer103,ENST00000620915,;CANT1,frameshift_variant,p.Lys348GlnfsTer103,ENST00000392446,;CANT1,frameshift_variant,p.Lys348GlnfsTer?,ENST00000591773,NM_001159772.1;CANT1,downstream_gene_variant,,ENST00000588611,;CANT1,downstream_gene_variant,,ENST00000588075,;CANT1,downstream_gene_variant,,ENST00000586916,;CANT1,downstream_gene_variant,,ENST00000590370,;CANT1,downstream_gene_variant,,ENST00000591625,;CANT1,downstream_gene_variant,,ENST00000592033,;CANT1,downstream_gene_variant,,ENST00000591811,;CANT1,downstream_gene_variant,,ENST00000591732,;CANT1,downstream_gene_variant,,ENST00000592887,;CANT1,downstream_gene_variant,,ENST00000587242,;CANT1,intron_variant,,ENST00000592228,;CANT1,downstream_gene_variant,,ENST00000588096,; G ENST00000302345 Transcript frameshift_variant 1536-1537/3534 1041-1042/1206 347-348/401 -/X -/C 1 -1 CANT1 HGNC HGNC:19721 protein_coding YES CCDS11760.1 ENSP00000307674 Q8WVQ1 A0A024R8U8 UPI00000734F8 NM_138793.3,NM_001159773.1 4/4 Superfamily_domains:0049295,Pfam_domain:PF06079,hmmpanther:PTHR13023 HIGH 1 insertion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 54 78993714 78993714 - G 1 0 1 1 0 0 0 0 0 2310 1821 63 0 0 CANT1 17 78993714 Frame_Shift_Ins INS - C3N-00556_T 179185 78993714 4263727 414 16543 RAC3 0 . GRCh38 17 82033474 82033474 + Missense_Mutation SNP C C A rs765128571 C3N-00556_T C3N-00556_N C C c.323C>A p.Thr108Lys p.T108K ENST00000306897 5/6 76 61 15 74 73 1 strelka-varscan-mutect RAC3,missense_variant,p.Thr108Lys,ENST00000306897,NM_001316307.1,NM_005052.2;RAC3,missense_variant,p.Thr64Lys,ENST00000580965,;RAC3,missense_variant,p.Thr64Lys,ENST00000584341,;LRRC45,downstream_gene_variant,,ENST00000306688,NM_144999.3;DCXR,downstream_gene_variant,,ENST00000306869,NM_001195218.1,NM_016286.3;DCXR,downstream_gene_variant,,ENST00000581584,;DCXR,downstream_gene_variant,,ENST00000582900,;DCXR,downstream_gene_variant,,ENST00000577532,;DCXR,downstream_gene_variant,,ENST00000579155,;DCXR,downstream_gene_variant,,ENST00000577712,;DCXR,downstream_gene_variant,,ENST00000579004,;RP13-650J16.1,upstream_gene_variant,,ENST00000584705,;RP13-650J16.1,upstream_gene_variant,,ENST00000582558,;RP11-1182P23.5,downstream_gene_variant,,ENST00000623540,;DCXR,downstream_gene_variant,,ENST00000584318,;DCXR,downstream_gene_variant,,ENST00000577996,;RAC3,non_coding_transcript_exon_variant,,ENST00000585014,;LRRC45,downstream_gene_variant,,ENST00000583302,;DCXR,downstream_gene_variant,,ENST00000579334,;LRRC45,downstream_gene_variant,,ENST00000581227,;DCXR,downstream_gene_variant,,ENST00000580750,;DCXR,downstream_gene_variant,,ENST00000578885,;DCXR,downstream_gene_variant,,ENST00000585085,;DCXR,downstream_gene_variant,,ENST00000580320,;DCXR,downstream_gene_variant,,ENST00000578273,;DCXR,downstream_gene_variant,,ENST00000579842,;DCXR,downstream_gene_variant,,ENST00000582074,;DCXR,downstream_gene_variant,,ENST00000582613,;DCXR,downstream_gene_variant,,ENST00000577286,;LRRC45,downstream_gene_variant,,ENST00000582083,;DCXR,downstream_gene_variant,,ENST00000585164,;DCXR,downstream_gene_variant,,ENST00000579821,; A ENST00000306897 Transcript missense_variant 461/1090 323/579 108/192 T/K aCg/aAg rs765128571 1 1 RAC3 HGNC HGNC:9803 protein_coding YES CCDS11798.1 ENSP00000304283 P60763 UPI00000041DA NM_001316307.1,NM_005052.2 deleterious_low_confidence(0.01) 5/6 PROSITE_profiles:PS51420,hmmpanther:PTHR24072,hmmpanther:PTHR24072:SF169,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS rs765128571 . 0 201 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 54 82033474 82033474 C A 1 0 0 0 0 1 0 0 0 13135 536 19 1 1 RAC3 17 82033474 Missense_Mutation SNP C C3N-00556_T 3039760 82033474 1223967 415 16544 SMCHD1 0 . GRCh38 18 2740732 2740732 + Nonsense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3544C>T p.Gln1182Ter p.Q1182* ENST00000320876 28/48 156 126 30 161 161 0 strelka-varscan-mutect SMCHD1,stop_gained,p.Gln1182Ter,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,stop_gained,p.Gln653Ter,ENST00000577880,;SMCHD1,3_prime_UTR_variant,,ENST00000584897,;SMCHD1,downstream_gene_variant,,ENST00000581631,; T ENST00000320876 Transcript stop_gained 3882/8821 3544/6018 1182/2005 Q/* Cag/Tag 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 28/48 hmmpanther:PTHR22640,hmmpanther:PTHR22640:SF2 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 54 2740732 2740732 C T 1 0 0 0 0 0 1 0 0 15081 827 29 3 3 SMCHD1 18 2740732 Nonsense_Mutation SNP C C3N-00556_T 2740732 77632553 416 16545 MYL12B 0 . GRCh38 18 3272995 3272995 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.97G>C p.Glu33Gln p.E33Q ENST00000581193 2/4 147 137 10 157 157 0 varscan-mutect MYL12B,missense_variant,p.Glu33Gln,ENST00000581193,NM_001144945.1;MYL12B,missense_variant,p.Glu33Gln,ENST00000237500,NM_033546.3;MYL12B,missense_variant,p.Glu33Gln,ENST00000584539,;MYL12B,missense_variant,p.Glu33Gln,ENST00000400175,NM_001144944.1; C ENST00000581193 Transcript missense_variant 480/1249 97/519 33/172 E/Q Gag/Cag 1 1 MYL12B HGNC HGNC:29827 protein_coding YES CCDS11831.1 ENSP00000463559 O14950 UPI0000024704 NM_001144945.1 deleterious(0) 2/4 Gene3D:1.10.238.10,Pfam_domain:PF13405,PROSITE_profiles:PS50222,hmmpanther:PTHR23049,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 3272995 3272995 G C 1 0 0 0 0 1 0 0 0 10046 1175 41 4 4 MYL12B 18 3272995 Missense_Mutation SNP G C3N-00556_T 532263 3272995 77100290 417 16546 PPP4R1 0 . GRCh38 18 9553419 9553419 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.2194C>G p.Leu732Val p.L732V ENST00000400556 16/20 169 149 20 193 193 0 strelka-varscan-mutect PPP4R1,missense_variant,p.Leu732Val,ENST00000400556,NM_001042388.2;PPP4R1,missense_variant,p.Leu715Val,ENST00000400555,NM_005134.3;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579609,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000584754,;PPP4R1,3_prime_UTR_variant,,ENST00000285124,;PPP4R1,upstream_gene_variant,,ENST00000582594,;PPP4R1,downstream_gene_variant,,ENST00000583438,;PPP4R1,downstream_gene_variant,,ENST00000577667,;PPP4R1,upstream_gene_variant,,ENST00000578010,;PPP4R1,upstream_gene_variant,,ENST00000578329,; C ENST00000400556 Transcript missense_variant 2268/3925 2194/2853 732/950 L/V Ctt/Gtt 1 -1 PPP4R1 HGNC HGNC:9320 protein_coding YES CCDS42412.1 ENSP00000383402 Q8TF05 UPI000006D6DE NM_001042388.2 deleterious(0) 16/20 Low_complexity_(Seg):seg,hmmpanther:PTHR10648:SF8,hmmpanther:PTHR10648,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 9553419 9553419 G C 1 0 0 0 0 1 0 0 0 12525 956 33 4 4 PPP4R1 18 9553419 Missense_Mutation SNP G C3N-00556_T 6280424 9553419 70819866 418 16547 NOL4 0 . GRCh38 18 33883311 33883311 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.1656C>A p.= p.T552T ENST00000261592 10/11 136 102 34 133 133 0 strelka-varscan-mutect NOL4,synonymous_variant,p.=,ENST00000261592,NM_003787.4;NOL4,synonymous_variant,p.=,ENST00000589544,NM_001198548.1;NOL4,synonymous_variant,p.=,ENST00000538587,NM_001198547.1;NOL4,synonymous_variant,p.=,ENST00000590712,NM_001198546.1;NOL4,synonymous_variant,p.=,ENST00000535384,NM_001198549.1;NOL4,downstream_gene_variant,,ENST00000586553,;NOL4,3_prime_UTR_variant,,ENST00000586314,; T ENST00000261592 Transcript synonymous_variant 1954/3957 1656/1917 552/638 T acC/acA 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 10/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 33883311 33883311 G T 1 0 0 0 0 0 0 0 1 10567 987 35 2 2 NOL4 18 33883311 Silent SNP G C3N-00556_T 24329892 33883311 46489974 419 16548 ALPK2 0 . GRCh38 18 58536763 58536763 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.3424C>A p.Leu1142Met p.L1142M ENST00000361673 5/13 159 118 41 238 237 1 strelka-varscan-mutect ALPK2,missense_variant,p.Leu1142Met,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; T ENST00000361673 Transcript missense_variant 3638/7303 3424/6513 1142/2170 L/M Ctg/Atg 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(0.17) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 58536763 58536763 G T 1 0 0 0 0 1 0 0 0 645 991 35 2 2 ALPK2 18 58536763 Missense_Mutation SNP G C3N-00556_T 24653452 58536763 21836522 420 16549 KIAA1468 0 . GRCh38 18 62287419 62287419 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.3322G>C p.Asp1108His p.D1108H ENST00000398130 26/29 206 169 37 244 244 0 strelka-varscan-mutect KIAA1468,missense_variant,p.Asp1108His,ENST00000398130,NM_020854.3;KIAA1468,missense_variant,p.Asp1142His,ENST00000256858,;KIAA1468,non_coding_transcript_exon_variant,,ENST00000587764,;KIAA1468,downstream_gene_variant,,ENST00000593217,;KIAA1468,downstream_gene_variant,,ENST00000587714,;KIAA1468,non_coding_transcript_exon_variant,,ENST00000587198,; C ENST00000398130 Transcript missense_variant 3554/6178 3322/3651 1108/1216 D/H Gac/Cac 1 1 KIAA1468 HGNC HGNC:29289 protein_coding YES CCDS11979.2 ENSP00000381198 Q9P260 UPI0000DA5AF7 NM_020854.3 deleterious(0) 26/29 hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1275546413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 62287419 62287419 G C 1 0 0 0 0 1 0 0 0 8117 1174 41 4 4 KIAA1468 18 62287419 Missense_Mutation SNP G C3N-00556_T 3750656 62287419 18085866 421 16550 SERPINB3 0 . GRCh38 18 63655828 63655828 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1002G>A p.= p.V334V ENST00000283752 8/8 171 158 13 249 249 0 strelka-varscan-mutect SERPINB3,synonymous_variant,p.=,ENST00000283752,NM_006919.2;SERPINB3,synonymous_variant,p.=,ENST00000332821,;SERPINB11,5_prime_UTR_variant,,ENST00000489748,; T ENST00000283752 Transcript synonymous_variant 1146/1777 1002/1173 334/390 V gtG/gtA 1 -1 SERPINB3 HGNC HGNC:10569 protein_coding YES CCDS11987.1 ENSP00000283752 P29508 UPI0000038A19 NM_006919.2 8/8 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF186,Low_complexity_(Seg):seg,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS rs749066127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 63655828 63655828 C T 1 0 0 0 0 0 0 0 1 14378 581 21 3 3 SERPINB3 18 63655828 Silent SNP C C3N-00556_T 1368409 63655828 16717457 422 16551 SERPINB11 0 . GRCh38 18 63723183 63723183 + Silent SNP A A T novel C3N-00556_T C3N-00556_N A A c.702A>T p.= p.S234S ENST00000623262 5/5 98 72 26 162 162 0 strelka-varscan-mutect SERPINB11,synonymous_variant,p.=,ENST00000382749,NM_080475.3;SERPINB11,synonymous_variant,p.=,ENST00000544088,;SERPINB11,synonymous_variant,p.=,ENST00000623262,NM_001291278.1;SERPINB11,synonymous_variant,p.=,ENST00000624518,;SERPINB11,downstream_gene_variant,,ENST00000489748,;SERPINB11,intron_variant,,ENST00000467649,;SERPINB11,3_prime_UTR_variant,,ENST00000536691,;SERPINB11,downstream_gene_variant,,ENST00000610304,; T ENST00000623262 Transcript synonymous_variant 702/918 702/918 234/305 S tcA/tcT 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 5/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 63723183 63723183 A T 1 0 0 0 0 0 0 0 1 14374 146 6 4 4 SERPINB11 18 63723183 Silent SNP A C3N-00556_T 67355 63723183 16650102 423 16552 ZNF236 0 . GRCh38 18 76925497 76925497 + Missense_Mutation SNP C C G C3N-00556_T C3N-00556_N C C c.3970C>G p.Gln1324Glu p.Q1324E ENST00000320610 22/31 143 134 9 216 216 0 strelka-varscan-mutect ZNF236,missense_variant,p.Gln1322Glu,ENST00000253159,NM_007345.3;ZNF236,missense_variant,p.Gln1324Glu,ENST00000320610,NM_001306089.1;ZNF236,missense_variant,p.Gln1322Glu,ENST00000543926,; G ENST00000320610 Transcript missense_variant 3971/7124 3970/5544 1324/1847 Q/E Cag/Gag COSM4975634,COSM4975635 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 deleterious(0.01) 22/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 76925497 76925497 C G 1 0 0 0 0 1 0 0 0 18366 827 29 4 4 ZNF236 18 76925497 Missense_Mutation SNP C C3N-00556_T 13202314 76925497 3447788 424 16553 PIP5K1C 0 . GRCh38 19 3646020 3646020 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1299G>A p.= p.E433E ENST00000589578 11/17 292 235 57 301 301 0 strelka-varscan-mutect PIP5K1C,synonymous_variant,p.=,ENST00000335312,NM_012398.2;PIP5K1C,synonymous_variant,p.=,ENST00000537021,;PIP5K1C,synonymous_variant,p.=,ENST00000589578,NM_001300849.1;PIP5K1C,synonymous_variant,p.=,ENST00000539785,NM_001195733.1;PIP5K1C,non_coding_transcript_exon_variant,,ENST00000592530,;PIP5K1C,downstream_gene_variant,,ENST00000587482,; T ENST00000589578 Transcript synonymous_variant 1299/2933 1299/2124 433/707 E gaG/gaA 1 -1 PIP5K1C HGNC HGNC:8996 protein_coding YES CCDS74257.1 ENSP00000466363 O60331 UPI0001AAAED7 NM_001300849.1 11/17 Gene3D:1bo1A02,Pfam_domain:PF01504,PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF26,SMART_domains:SM00330,Superfamily_domains:SSF56104 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 3646020 3646020 C T 1 0 0 0 0 0 0 0 1 12036 796 28 3 3 PIP5K1C 19 3646020 Silent SNP C C3N-00556_T 3646020 54971596 425 16554 SEMA6B 0 . GRCh38 19 4550908 4550908 + Missense_Mutation SNP C C A rs769580864 C3N-00556_T C3N-00556_N C C c.1012G>T p.Ala338Ser p.A338S ENST00000586582 11/17 164 120 44 143 141 2 strelka-varscan-mutect SEMA6B,missense_variant,p.Ala338Ser,ENST00000586582,NM_032108.3;SEMA6B,missense_variant,p.Ala338Ser,ENST00000586965,;SEMA6B,upstream_gene_variant,,ENST00000589889,; A ENST00000586582 Transcript missense_variant 1323/3986 1012/2667 338/888 A/S Gcc/Tcc rs769580864 1 -1 SEMA6B HGNC HGNC:10739 protein_coding YES CCDS12131.1 ENSP00000467290 Q9H3T3 UPI000004BA6B NM_032108.3 deleterious(0.02) 11/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS rs769580864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 4550908 4550908 C A 1 0 0 0 0 1 0 0 0 14316 768 27 1 1 SEMA6B 19 4550908 Missense_Mutation SNP C C3N-00556_T 904888 4550908 54066708 426 16555 DPP9 0 . GRCh38 19 4694737 4694737 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.1440C>T p.= p.F480F ENST00000262960 13/22 280 262 18 253 253 0 strelka-varscan-mutect DPP9,synonymous_variant,p.=,ENST00000262960,NM_139159.4;DPP9,synonymous_variant,p.=,ENST00000594671,;DPP9,synonymous_variant,p.=,ENST00000598800,;DPP9,synonymous_variant,p.=,ENST00000597849,;DPP9,upstream_gene_variant,,ENST00000595327,;DPP9,3_prime_UTR_variant,,ENST00000599163,;DPP9,non_coding_transcript_exon_variant,,ENST00000597145,;DPP9,non_coding_transcript_exon_variant,,ENST00000601764,;DPP9,non_coding_transcript_exon_variant,,ENST00000599998,;DPP9,upstream_gene_variant,,ENST00000597253,; A ENST00000262960 Transcript synonymous_variant 1718/4295 1440/2679 480/892 F ttC/ttT 1 -1 DPP9 HGNC HGNC:18648 protein_coding YES CCDS45928.1 ENSP00000262960 Q86TI2 UPI000004DB00 NM_139159.4 13/22 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF109,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 4694737 4694737 G A 1 0 0 0 0 0 0 0 1 4548 933 33 3 3 DPP9 19 4694737 Silent SNP G C3N-00556_T 143829 4694737 53922879 427 16556 C19orf45 0 . GRCh38 19 7501290 7501290 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.468C>A p.= p.S156S ENST00000361664 2/9 193 140 53 140 140 0 strelka-varscan-mutect C19orf45,synonymous_variant,p.=,ENST00000361664,NM_198534.2;C19orf45,synonymous_variant,p.=,ENST00000601176,;C19orf45,synonymous_variant,p.=,ENST00000596132,;C19orf45,synonymous_variant,p.=,ENST00000597207,;PEX11G,upstream_gene_variant,,ENST00000593942,NM_001300881.1;C19orf45,synonymous_variant,p.=,ENST00000596524,;C19orf45,upstream_gene_variant,,ENST00000600112,; A ENST00000361664 Transcript synonymous_variant 609/1679 468/1518 156/505 S tcC/tcA 1 1 C19orf45 HGNC HGNC:24745 protein_coding YES CCDS12179.2 ENSP00000355241 Q8NA69 UPI00001D83AB NM_198534.2 2/9 Pfam_domain:PF15373,hmmpanther:PTHR34828 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 7501290 7501290 C A 1 0 0 0 0 0 0 0 1 1912 610 22 2 2 C19orf45 19 7501290 Silent SNP C C3N-00556_T 2806553 7501290 51116326 428 16557 CAMSAP3 0 . GRCh38 19 7613131 7613131 + Nonsense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.2719G>T p.Glu907Ter p.E907* ENST00000446248 13/19 82 76 6 60 60 0 strelka-varscan-mutect CAMSAP3,stop_gained,p.Glu907Ter,ENST00000446248,NM_001080429.2;CAMSAP3,stop_gained,p.Glu880Ter,ENST00000160298,NM_020902.1;MIR6792,upstream_gene_variant,,ENST00000614460,;CAMSAP3,upstream_gene_variant,,ENST00000595692,;CAMSAP3,upstream_gene_variant,,ENST00000593434,; T ENST00000446248 Transcript stop_gained 2820/4179 2719/3831 907/1276 E/* Gag/Tag 1 1 CAMSAP3 HGNC HGNC:29307 protein_coding YES CCDS45947.1 ENSP00000416797 Q9P1Y5 UPI0000161861 NM_001080429.2 13/19 Low_complexity_(Seg):seg,hmmpanther:PTHR21595:SF2,hmmpanther:PTHR21595 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.13079 1 1 1 1 0 T 4 4 54 7613131 7613131 G T 1 0 0 0 0 0 1 0 0 2305 1175 41 2 2 CAMSAP3 19 7613131 Nonsense_Mutation SNP G C3N-00556_T 111841 7613131 51004485 429 16558 EIF3G 0 . GRCh38 19 10115969 10115969 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.701G>C p.Arg234Thr p.R234T ENST00000253108 8/11 134 125 9 124 124 0 strelka-varscan-mutect EIF3G,missense_variant,p.Arg234Thr,ENST00000253108,NM_003755.3;EIF3G,missense_variant,p.Arg226Thr,ENST00000589454,;EIF3G,missense_variant,p.Arg236Thr,ENST00000588709,;EIF3G,missense_variant,p.Arg199Thr,ENST00000587146,;EIF3G,missense_variant,p.Arg45Thr,ENST00000593054,;PPAN-P2RY11,downstream_gene_variant,,ENST00000428358,NM_001198690.1;PPAN-P2RY11,downstream_gene_variant,,ENST00000393796,NM_001040664.2;P2RY11,downstream_gene_variant,,ENST00000321826,NM_002566.4;PPAN,downstream_gene_variant,,ENST00000253107,NM_020230.5;PPAN,downstream_gene_variant,,ENST00000393793,;PPAN,downstream_gene_variant,,ENST00000444703,;P2RY11,downstream_gene_variant,,ENST00000471843,;EIF3G,downstream_gene_variant,,ENST00000587168,;EIF3G,splice_region_variant,,ENST00000590158,;EIF3G,downstream_gene_variant,,ENST00000589009,;PPAN,downstream_gene_variant,,ENST00000486482,;EIF3G,downstream_gene_variant,,ENST00000592485,;EIF3G,downstream_gene_variant,,ENST00000590940,;EIF3G,downstream_gene_variant,,ENST00000593095,;EIF3G,downstream_gene_variant,,ENST00000589674,;EIF3G,downstream_gene_variant,,ENST00000593066,;EIF3G,downstream_gene_variant,,ENST00000587993,;EIF3G,downstream_gene_variant,,ENST00000587681,; G ENST00000253108 Transcript missense_variant,splice_region_variant 744/1103 701/963 234/320 R/T aGa/aCa 1 -1 EIF3G HGNC HGNC:3274 protein_coding YES CCDS12227.1 ENSP00000253108 O75821 UPI000012D2FE NM_003755.3 tolerated(0.11) 8/11 Gene3D:3.30.70.330,HAMAP:MF_03006,PIRSF_domain:PIRSF037949,hmmpanther:PTHR10352,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs1423685248 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 10115969 10115969 C G 1 0 0 0 0 1 0 0 0 4851 927 32 4 4 EIF3G 19 10115969 Missense_Mutation SNP C C3N-00556_T 2502838 10115969 48501647 430 16559 TYK2 0 . GRCh38 19 10358069 10358069 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.2245G>A p.Glu749Lys p.E749K ENST00000525621 16/25 319 296 23 261 260 1 strelka-varscan-mutect TYK2,missense_variant,p.Glu749Lys,ENST00000525621,NM_003331.4;TYK2,missense_variant,p.Glu749Lys,ENST00000264818,;TYK2,missense_variant,p.Glu564Lys,ENST00000524462,;TYK2,missense_variant,p.Glu749Lys,ENST00000529370,;TYK2,downstream_gene_variant,,ENST00000525220,;TYK2,upstream_gene_variant,,ENST00000530560,;TYK2,upstream_gene_variant,,ENST00000529422,;TYK2,upstream_gene_variant,,ENST00000592137,;TYK2,3_prime_UTR_variant,,ENST00000533334,;TYK2,upstream_gene_variant,,ENST00000529739,;TYK2,upstream_gene_variant,,ENST00000530220,;TYK2,upstream_gene_variant,,ENST00000529412,;TYK2,upstream_gene_variant,,ENST00000527481,;TYK2,upstream_gene_variant,,ENST00000534228,;TYK2,downstream_gene_variant,,ENST00000531620,; T ENST00000525621 Transcript missense_variant 2727/4347 2245/3564 749/1187 E/K Gag/Aag COSM380936 1 -1 TYK2 HGNC HGNC:12440 protein_coding YES CCDS12236.1 ENSP00000431885 P29597 A0A024R7E4 UPI000013D573 NM_003331.4 tolerated(0.21) 16/25 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000636,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF244,SMART_domains:SM00219,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 10358069 10358069 C T 1 0 0 0 0 1 0 0 0 17325 922 32 3 3 TYK2 19 10358069 Missense_Mutation SNP C C3N-00556_T 242100 10358069 48259547 431 16560 CCDC151 0 . GRCh38 19 11424020 11424020 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.973G>T p.Glu325Ter p.E325* ENST00000356392 8/13 84 56 28 94 94 0 strelka-varscan-mutect CCDC151,stop_gained,p.Glu325Ter,ENST00000356392,NM_145045.4,NM_001302453.1;CCDC151,stop_gained,p.Glu265Ter,ENST00000591179,NM_001302454.1;CCDC151,stop_gained,p.Glu134Ter,ENST00000586836,;RGL3,upstream_gene_variant,,ENST00000380456,NM_001035223.3;RGL3,upstream_gene_variant,,ENST00000393423,NM_001161616.2;RGL3,upstream_gene_variant,,ENST00000567080,;RGL3,upstream_gene_variant,,ENST00000561570,;CCDC151,3_prime_UTR_variant,,ENST00000591345,;RGL3,upstream_gene_variant,,ENST00000563726,;RGL3,upstream_gene_variant,,ENST00000562663,;RGL3,upstream_gene_variant,,ENST00000453604,;RGL3,upstream_gene_variant,,ENST00000569439,;RGL3,upstream_gene_variant,,ENST00000568420,; A ENST00000356392 Transcript stop_gained 1061/2107 973/1788 325/595 E/* Gag/Tag 1 -1 CCDC151 HGNC HGNC:28303 protein_coding YES CCDS42501.1 ENSP00000348757 A5D8V7 UPI000040CC83 NM_145045.4,NM_001302453.1 8/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21694,hmmpanther:PTHR21694:SF24 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 11424020 11424020 C A 1 0 0 0 0 0 1 0 0 2472 893 31 1 1 CCDC151 19 11424020 Nonsense_Mutation SNP C C3N-00556_T 1065951 11424020 47193596 432 16561 ZNF563 0 . GRCh38 19 12319657 12319657 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.368G>C p.Arg123Thr p.R123T ENST00000293725 4/4 183 172 11 228 228 0 strelka-varscan-mutect ZNF563,missense_variant,p.Arg123Thr,ENST00000293725,NM_145276.2;ZNF563,missense_variant,p.Arg123Thr,ENST00000595977,;ZNF563,missense_variant,p.Arg35Thr,ENST00000594577,;ZNF563,missense_variant,p.Arg91Thr,ENST00000601858,; G ENST00000293725 Transcript missense_variant 574/2754 368/1431 123/476 R/T aGa/aCa 1 -1 ZNF563 HGNC HGNC:30498 protein_coding YES CCDS12270.1 ENSP00000293725 Q8TA94 UPI0000072E62 NM_145276.2 tolerated(0.1) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF14,hmmpanther:PTHR24379 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 12319657 12319657 C G 1 0 0 0 0 1 0 0 0 18568 913 32 4 4 ZNF563 19 12319657 Missense_Mutation SNP C C3N-00556_T 895637 12319657 46297959 433 16562 ILVBL 0 . GRCh38 19 15117975 15117975 + Silent SNP G G T novel C3N-00556_T C3N-00556_N G G c.1092C>A p.= p.L364L ENST00000263383 10/16 248 210 38 201 200 1 strelka-varscan-mutect ILVBL,synonymous_variant,p.=,ENST00000263383,NM_006844.4;ILVBL,synonymous_variant,p.=,ENST00000534378,;ILVBL,synonymous_variant,p.=,ENST00000598709,;SYDE1,downstream_gene_variant,,ENST00000600252,;SYDE1,downstream_gene_variant,,ENST00000342784,NM_033025.5;SYDE1,downstream_gene_variant,,ENST00000600440,NM_001300910.1;ILVBL,downstream_gene_variant,,ENST00000527093,;ILVBL,downstream_gene_variant,,ENST00000600984,;SYDE1,downstream_gene_variant,,ENST00000602203,;ILVBL,downstream_gene_variant,,ENST00000531635,;ILVBL,3_prime_UTR_variant,,ENST00000533148,;ILVBL,non_coding_transcript_exon_variant,,ENST00000533086,;ILVBL,non_coding_transcript_exon_variant,,ENST00000525880,;ILVBL,upstream_gene_variant,,ENST00000534806,;ILVBL,upstream_gene_variant,,ENST00000524779,;ILVBL,upstream_gene_variant,,ENST00000596093,; T ENST00000263383 Transcript synonymous_variant 1232/2304 1092/1899 364/632 L ctC/ctA 1 -1 ILVBL HGNC HGNC:6041 protein_coding YES CCDS12325.1 ENSP00000263383 A1L0T0 UPI000007055E NM_006844.4 10/16 hmmpanther:PTHR18968,hmmpanther:PTHR18968:SF127,Gene3D:3.40.50.1220,Pfam_domain:PF00205,Superfamily_domains:SSF52467 LOW 1 SNV 1 1 PASS rs1158275083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 15117975 15117975 G T 1 0 0 0 0 0 0 0 1 7618 1277 45 2 2 ILVBL 19 15117975 Silent SNP G C3N-00556_T 2798318 15117975 43499641 434 16563 MYO9B 0 . GRCh38 19 17180957 17180957 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2250C>G p.Ile750Met p.I750M ENST00000595618 15/40 121 105 16 115 115 0 strelka-varscan-mutect MYO9B,missense_variant,p.Ile750Met,ENST00000595618,NM_001130065.1;MYO9B,missense_variant,p.Ile750Met,ENST00000594824,NM_004145.3;MYO9B,missense_variant,p.Ile750Met,ENST00000397274,;MYO9B,missense_variant,p.Ile750Met,ENST00000595641,;MYO9B,intron_variant,,ENST00000602177,;MYO9B,intron_variant,,ENST00000594971,;CTD-3032J10.4,upstream_gene_variant,,ENST00000594678,;MYO9B,non_coding_transcript_exon_variant,,ENST00000601749,;MYO9B,non_coding_transcript_exon_variant,,ENST00000598101,;MYO9B,upstream_gene_variant,,ENST00000601490,;MYO9B,upstream_gene_variant,,ENST00000598464,; G ENST00000595618 Transcript missense_variant 2402/7623 2250/6069 750/2022 I/M atC/atG 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 deleterious(0.05) 15/40 PROSITE_profiles:PS51456,SMART_domains:SM00242 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 17180957 17180957 C G 1 0 0 0 0 1 0 0 0 10086 816 29 4 4 MYO9B 19 17180957 Missense_Mutation SNP C C3N-00556_T 2062982 17180957 41436659 435 16564 MYO9B 0 . GRCh38 19 17192826 17192826 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.2892G>A p.= p.Q964Q ENST00000595618 21/40 148 139 9 105 105 0 strelka-varscan-mutect MYO9B,synonymous_variant,p.=,ENST00000595618,NM_001130065.1;MYO9B,synonymous_variant,p.=,ENST00000594824,NM_004145.3;MYO9B,synonymous_variant,p.=,ENST00000397274,;MYO9B,synonymous_variant,p.=,ENST00000595641,;MYO9B,downstream_gene_variant,,ENST00000602177,;MYO9B,downstream_gene_variant,,ENST00000601749,; A ENST00000595618 Transcript synonymous_variant 3044/7623 2892/6069 964/2022 Q caG/caA 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 21/40 Pfam_domain:PF00612,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,SMART_domains:SM00015,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 17192826 17192826 G A 1 0 0 0 0 0 0 0 1 10086 933 33 3 3 MYO9B 19 17192826 Silent SNP G C3N-00556_T 11869 17192826 41424790 436 16565 KLHL26 0 . GRCh38 19 18668407 18668407 + Missense_Mutation SNP G G T rs772002583 C3N-00556_T C3N-00556_N G G c.1010G>T p.Gly337Val p.G337V ENST00000300976 3/3 188 167 21 214 214 0 strelka-varscan-mutect KLHL26,missense_variant,p.Gly337Val,ENST00000300976,NM_018316.1;KLHL26,intron_variant,,ENST00000599006,;KLHL26,downstream_gene_variant,,ENST00000595423,;KLHL26,downstream_gene_variant,,ENST00000595182,;KLHL26,downstream_gene_variant,,ENST00000596843,;KLHL26,downstream_gene_variant,,ENST00000600657,; T ENST00000300976 Transcript missense_variant 1100/4407 1010/1848 337/615 G/V gGa/gTa rs772002583 1 1 KLHL26 HGNC HGNC:25623 protein_coding YES CCDS12384.1 ENSP00000300976 Q53HC5 A0A024R7N5 UPI0000071AC2 NM_018316.1 tolerated(0.09) 3/3 hmmpanther:PTHR24412:SF56,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS rs772002583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 18668407 18668407 G T 1 0 0 0 0 1 0 0 0 8245 1174 41 2 2 KLHL26 19 18668407 Missense_Mutation SNP G C3N-00556_T 1475581 18668407 39949209 437 16566 ZNF93 0 . GRCh38 19 19933249 19933249 + Silent SNP G G C novel C3N-00556_T C3N-00556_N G G c.294G>C p.= p.V98V ENST00000343769 4/4 48 34 14 80 80 0 strelka-varscan-mutect ZNF93,synonymous_variant,p.=,ENST00000343769,NM_031218.3;ZNF93,synonymous_variant,p.=,ENST00000588146,;ZNF93,downstream_gene_variant,,ENST00000592160,;AC007204.2,intron_variant,,ENST00000592245,;ZNF93,3_prime_UTR_variant,,ENST00000586021,; C ENST00000343769 Transcript synonymous_variant 322/2648 294/1863 98/620 V gtG/gtC 1 1 ZNF93 HGNC HGNC:13169 protein_coding YES CCDS32973.1 ENSP00000342002 P35789 UPI00002263B9 NM_031218.3 4/4 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF374 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 54 19933249 19933249 G C 1 0 0 0 0 0 0 0 1 18795 1277 45 4 4 ZNF93 19 19933249 Silent SNP G C3N-00556_T 1264842 19933249 38684367 438 16567 GPI 0 . GRCh38 19 34396601 34396601 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.1246G>A p.Asp416Asn p.D416N ENST00000415930 14/18 310 290 20 347 347 0 strelka-varscan-mutect GPI,missense_variant,p.Asp416Asn,ENST00000415930,NM_001184722.1;GPI,missense_variant,p.Asp405Asn,ENST00000356487,NM_000175.3,NM_001289790.1;GPI,missense_variant,p.Asp420Asn,ENST00000588991,NM_001289789.1;GPI,missense_variant,p.Asp405Asn,ENST00000586425,;RP11-618P17.4,missense_variant,p.Asp47Asn,ENST00000592740,;RP11-618P17.4,upstream_gene_variant,,ENST00000606020,;GPI,non_coding_transcript_exon_variant,,ENST00000586392,;GPI,non_coding_transcript_exon_variant,,ENST00000589985,;GPI,upstream_gene_variant,,ENST00000586077,; A ENST00000415930 Transcript missense_variant 1416/4000 1246/1710 416/569 D/N Gac/Aac COSM4616511 1 1 GPI HGNC HGNC:4458 protein_coding YES CCDS54246.1 ENSP00000405573 P06744 UPI00017A6DE4 NM_001184722.1 deleterious_low_confidence(0.01) 14/18 Gene3D:3.40.50.10490,HAMAP:MF_00473,Pfam_domain:PF00342,PROSITE_profiles:PS51463,hmmpanther:PTHR11469,hmmpanther:PTHR11469:SF4,Superfamily_domains:SSF53697 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 34396601 34396601 G A 1 0 0 0 0 1 0 0 0 6513 1290 45 3 3 GPI 19 34396601 Missense_Mutation SNP G C3N-00556_T 14463352 34396601 24221015 439 16568 LSR 0 . GRCh38 19 35258944 35258944 + Splice_Site SNP G G T novel C3N-00556_T C3N-00556_N G G c.599-1G>T p.X200_splice ENST00000621372 446 416 30 424 424 0 strelka-varscan-mutect LSR,splice_acceptor_variant,,ENST00000602122,NM_001260489.1;LSR,splice_acceptor_variant,,ENST00000621372,NM_205834.3;LSR,splice_acceptor_variant,,ENST00000361790,;LSR,splice_acceptor_variant,,ENST00000354900,NM_015925.6;LSR,splice_acceptor_variant,,ENST00000360798,NM_205835.3;LSR,splice_acceptor_variant,,ENST00000605618,;LSR,splice_acceptor_variant,,ENST00000347609,;LSR,splice_acceptor_variant,,ENST00000601623,;LSR,splice_acceptor_variant,,ENST00000599658,;LSR,intron_variant,,ENST00000427250,NM_001260490.1;AD000684.2,upstream_gene_variant,,ENST00000602262,;LSR,splice_acceptor_variant,,ENST00000597933,;LSR,splice_acceptor_variant,,ENST00000602044,; T ENST00000621372 Transcript splice_acceptor_variant -/2274 599/1950 200/649 1 1 LSR HGNC HGNC:29572 protein_coding YES CCDS12450.1 ENSP00000480821 Q86X29 UPI000003117A NM_205834.3 2/9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 54 35258944 35258944 G T 1 0 0 0 0 0 0 1 0 8971 956 33 2 2 LSR 19 35258944 Splice_Site SNP G C3N-00556_T 862343 35258944 23358672 440 16569 KMT2B 0 . GRCh38 19 35721298 35721298 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1951C>G p.Gln651Glu p.Q651E ENST00000420124 3/37 202 190 12 222 222 0 strelka-varscan-mutect KMT2B,missense_variant,p.Gln651Glu,ENST00000420124,NM_014727.2;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,NM_014383.1;ZBTB32,downstream_gene_variant,,ENST00000426659,;KMT2B,intron_variant,,ENST00000606995,;ZBTB32,downstream_gene_variant,,ENST00000481182,; G ENST00000420124 Transcript missense_variant 1951/8469 1951/8148 651/2715 Q/E Cag/Gag 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 deleterious_low_confidence(0.01) 3/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 35721298 35721298 C G 1 0 0 0 0 1 0 0 0 8296 827 29 4 4 KMT2B 19 35721298 Missense_Mutation SNP C C3N-00556_T 462354 35721298 22896318 441 16570 C19orf33 0 . GRCh38 19 38304443 38304443 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.294C>T p.His99Tyr p.H99Y ENST00000591889 4/6 101 89 12 168 168 0 strelka-varscan-mutect CTB-102L5.4,missense_variant,p.His99Tyr,ENST00000591889,;C19orf33,missense_variant,p.His31Tyr,ENST00000588605,NM_001317801.1;C19orf33,missense_variant,p.His31Tyr,ENST00000301246,NM_033520.1;CTB-102L5.4,synonymous_variant,p.=,ENST00000587519,;YIF1B,downstream_gene_variant,,ENST00000392124,;YIF1B,downstream_gene_variant,,ENST00000337679,NM_001145463.1;YIF1B,downstream_gene_variant,,ENST00000339413,NM_001039672.2,NM_001039673.2;YIF1B,downstream_gene_variant,,ENST00000592694,;YIF1B,downstream_gene_variant,,ENST00000591755,;YIF1B,downstream_gene_variant,,ENST00000329420,NM_001039671.2,NM_001145461.1;YIF1B,downstream_gene_variant,,ENST00000591784,NM_001145462.1;YIF1B,downstream_gene_variant,,ENST00000592246,;YIF1B,downstream_gene_variant,,ENST00000589247,;YIF1B,downstream_gene_variant,,ENST00000588002,;YIF1B,downstream_gene_variant,,ENST00000587039,;YIF1B,downstream_gene_variant,,ENST00000587361,;C19orf33,non_coding_transcript_exon_variant,,ENST00000591852,;C19orf33,non_coding_transcript_exon_variant,,ENST00000589986,;YIF1B,downstream_gene_variant,,ENST00000589644,;YIF1B,downstream_gene_variant,,ENST00000585563,;YIF1B,downstream_gene_variant,,ENST00000586319,;YIF1B,downstream_gene_variant,,ENST00000589151,; T ENST00000591889 Transcript missense_variant 294/528 295/462 99/153 H/Y Cac/Tac 1 1 CTB-102L5.4 Clone_based_vega_gene protein_coding YES ENSP00000468040 K7EQZ3 UPI0002840CB6 deleterious_low_confidence(0.02) 4/6 hmmpanther:PTHR21830:SF0,hmmpanther:PTHR21830,Pfam_domain:PF15761 MODERATE SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 38304443 38304443 C T 1 0 0 0 0 1 0 0 0 1907 594 21 3 3 C19orf33 19 38304443 Missense_Mutation SNP C C3N-00556_T 2583145 38304443 20313173 442 16571 LTBP4 0 . GRCh38 19 40614003 40614003 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.2846G>T p.Gly949Val p.G949V ENST00000308370 21/33 235 176 59 211 211 0 strelka-varscan-mutect LTBP4,missense_variant,p.Gly912Val,ENST00000204005,NM_003573.2;LTBP4,missense_variant,p.Gly949Val,ENST00000308370,NM_001042544.1;LTBP4,missense_variant,p.Gly882Val,ENST00000396819,NM_001042545.1;LTBP4,missense_variant,p.Gly282Val,ENST00000243562,;LTBP4,missense_variant,p.Gly181Val,ENST00000601032,;LTBP4,missense_variant,p.Gly57Val,ENST00000599724,;LTBP4,missense_variant,p.Gly93Val,ENST00000612121,;LTBP4,missense_variant,p.Gly55Val,ENST00000597071,;LTBP4,missense_variant,p.Gly30Val,ENST00000593463,;LTBP4,missense_variant,p.Gly30Val,ENST00000618486,;LTBP4,upstream_gene_variant,,ENST00000622457,;LTBP4,downstream_gene_variant,,ENST00000598055,;LTBP4,non_coding_transcript_exon_variant,,ENST00000595118,;LTBP4,non_coding_transcript_exon_variant,,ENST00000622565,;LTBP4,non_coding_transcript_exon_variant,,ENST00000602251,;LTBP4,non_coding_transcript_exon_variant,,ENST00000600499,;LTBP4,non_coding_transcript_exon_variant,,ENST00000610893,;LTBP4,non_coding_transcript_exon_variant,,ENST00000612845,;LTBP4,upstream_gene_variant,,ENST00000318809,;LTBP4,downstream_gene_variant,,ENST00000546155,;LTBP4,downstream_gene_variant,,ENST00000598717,;LTBP4,downstream_gene_variant,,ENST00000598256,;LTBP4,upstream_gene_variant,,ENST00000597816,;LTBP4,upstream_gene_variant,,ENST00000622107,;LTBP4,upstream_gene_variant,,ENST00000617753,;LTBP4,upstream_gene_variant,,ENST00000595665,;LTBP4,upstream_gene_variant,,ENST00000594448,;LTBP4,upstream_gene_variant,,ENST00000596351,;LTBP4,upstream_gene_variant,,ENST00000601464,; T ENST00000308370 Transcript missense_variant 2846/4948 2846/4875 949/1624 G/V gGa/gTa 1 1 LTBP4 HGNC HGNC:6717 protein_coding YES CCDS74369.1 ENSP00000311905 Q8N2S1 UPI0000DACAC4 NM_001042544.1 deleterious(0) 21/33 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF43,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 40614003 40614003 G T 1 0 0 0 0 1 0 0 0 8982 1174 41 2 2 LTBP4 19 40614003 Missense_Mutation SNP G C3N-00556_T 2309560 40614003 18003613 443 16572 PSG1 0 . GRCh38 19 42877986 42877986 + Silent SNP G G T rs765139938 C3N-00556_T C3N-00556_N G G c.357C>A p.= p.S119S ENST00000312439 2/6 179 163 16 233 233 0 varscan-mutect PSG1,synonymous_variant,p.=,ENST00000244296,NM_006905.2;PSG1,synonymous_variant,p.=,ENST00000436291,NM_001184825.1;PSG1,synonymous_variant,p.=,ENST00000595356,NM_001184826.1;PSG1,synonymous_variant,p.=,ENST00000312439,NM_001297773.1;PSG1,synonymous_variant,p.=,ENST00000403380,;PSG1,synonymous_variant,p.=,ENST00000595124,;PSG1,synonymous_variant,p.=,ENST00000595930,;PSG1,synonymous_variant,p.=,ENST00000597058,;PSG1,non_coding_transcript_exon_variant,,ENST00000601073,;PSG1,non_coding_transcript_exon_variant,,ENST00000601456,; T ENST00000312439 Transcript synonymous_variant 443/1882 357/1287 119/428 S tcC/tcA rs765139938 1 -1 PSG1 HGNC HGNC:9514 protein_coding YES CCDS74380.1 ENSP00000308970 P11464 UPI000006DB43 NM_001297773.1 2/6 hmmpanther:PTHR10489,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs765139938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 42877986 42877986 G T 1 0 0 0 0 0 0 0 1 12804 987 35 2 2 PSG1 19 42877986 Silent SNP G C3N-00556_T 2263983 42877986 15739630 444 16573 XRCC1 0 . GRCh38 19 43543416 43543416 + Silent SNP G G C novel C3N-00556_T C3N-00556_N G G c.1878C>G p.= p.L626L ENST00000262887 17/17 117 109 8 157 157 0 strelka-varscan-mutect XRCC1,synonymous_variant,p.=,ENST00000262887,NM_006297.2;XRCC1,synonymous_variant,p.=,ENST00000543982,; C ENST00000262887 Transcript synonymous_variant 2426/2802 1878/1902 626/633 L ctC/ctG 1 -1 XRCC1 HGNC HGNC:12828 protein_coding YES CCDS12624.1 ENSP00000262887 P18887 UPI0000231BEC NM_006297.2 17/17 Gene3D:3.40.50.10190,Pfam_domain:PF16589,PROSITE_profiles:PS50172,hmmpanther:PTHR11370,hmmpanther:PTHR11370:SF3,Superfamily_domains:SSF52113 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 43543416 43543416 G C 1 0 0 0 0 0 0 0 1 18011 929 33 4 4 XRCC1 19 43543416 Silent SNP G C3N-00556_T 665430 43543416 15074200 445 16574 SRRM5 0 . GRCh38 19 43612811 43612811 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.690G>C p.Lys230Asn p.K230N ENST00000607544 3/3 255 233 22 296 296 0 strelka-varscan-mutect SRRM5,missense_variant,p.Lys230Asn,ENST00000607544,;SRRM5,missense_variant,p.Lys230Asn,ENST00000417606,NM_001145641.1;ZNF428,intron_variant,,ENST00000300811,NM_182498.3;ZNF428,intron_variant,,ENST00000598676,;ZNF428,downstream_gene_variant,,ENST00000595304,; C ENST00000607544 Transcript missense_variant 1012/2698 690/2148 230/715 K/N aaG/aaC 1 1 SRRM5 HGNC HGNC:37248 protein_coding YES CCDS46095.1 ENSP00000476253 B3KS81 UPI000059D73E tolerated(0.07) 3/3 hmmpanther:PTHR39414,hmmpanther:PTHR39414:SF1 MODERATE SNV 2 1 PASS rs1397238413 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 43612811 43612811 G C 1 0 0 0 0 1 0 0 0 15533 933 33 4 4 SRRM5 19 43612811 Missense_Mutation SNP G C3N-00556_T 69395 43612811 15004805 446 16575 ZNF225 0 . GRCh38 19 44131017 44131017 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.403G>T p.Asp135Tyr p.D135Y ENST00000262894 5/5 152 119 33 230 230 0 strelka-varscan-mutect ZNF225,missense_variant,p.Asp135Tyr,ENST00000262894,NM_001321685.1,NM_013362.2;ZNF225,missense_variant,p.Asp135Tyr,ENST00000590612,;ZNF225,3_prime_UTR_variant,,ENST00000592780,;ZNF225,downstream_gene_variant,,ENST00000589155,;ZNF225,downstream_gene_variant,,ENST00000592360,; T ENST00000262894 Transcript missense_variant 683/4482 403/2121 135/706 D/Y Gat/Tat 1 1 ZNF225 HGNC HGNC:13018 protein_coding YES CCDS46100.1 ENSP00000262894 Q9UK10 UPI000016960F NM_001321685.1,NM_013362.2 deleterious(0.05) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 44131017 44131017 G T 1 0 0 0 0 1 0 0 0 18356 1290 45 2 2 ZNF225 19 44131017 Missense_Mutation SNP G C3N-00556_T 518206 44131017 14486599 447 16576 APOC1 0 . GRCh38 19 44919229 44919229 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.251G>A p.= p.*84* ENST00000588750 5/5 141 117 24 155 155 0 strelka-varscan-mutect APOC1,stop_retained_variant,p.=,ENST00000588750,NM_001321066.1,NM_001645.3;APOC1,stop_retained_variant,p.=,ENST00000588802,;APOC1,3_prime_UTR_variant,,ENST00000592885,;APOC1,3_prime_UTR_variant,,ENST00000586638,;APOC1,3_prime_UTR_variant,,ENST00000589781,;APOC1,downstream_gene_variant,,ENST00000592535,;APOC1,downstream_gene_variant,,ENST00000589078,;CTB-129P6.7,downstream_gene_variant,,ENST00000623895,;APOC1,3_prime_UTR_variant,,ENST00000592176,;APOC1,3_prime_UTR_variant,,ENST00000590334,; A ENST00000588750 Transcript stop_retained_variant 576/689 251/252 84/83 * tGa/tAa COSM459941 1 1 APOC1 HGNC HGNC:607 protein_coding YES CCDS12648.1 ENSP00000465356 P02654 A0A024R0T8 UPI0000125C19 NM_001321066.1,NM_001645.3 5/5 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 44919229 44919229 G A 1 0 0 0 0 0 0 0 1 919 1285 45 3 3 APOC1 19 44919229 Silent SNP G C3N-00556_T 788212 44919229 13698387 448 16577 SYMPK 0 . GRCh38 19 45818105 45818105 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.2935G>C p.Glu979Gln p.E979Q ENST00000245934 23/27 100 94 6 139 139 0 strelka-mutect SYMPK,missense_variant,p.Glu979Gln,ENST00000245934,NM_004819.2;SYMPK,downstream_gene_variant,,ENST00000599814,;SYMPK,downstream_gene_variant,,ENST00000599460,;RSPH6A,upstream_gene_variant,,ENST00000221538,NM_030785.3;RSPH6A,upstream_gene_variant,,ENST00000597055,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598155,;SYMPK,3_prime_UTR_variant,,ENST00000600237,;SYMPK,non_coding_transcript_exon_variant,,ENST00000593504,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598329,;SYMPK,upstream_gene_variant,,ENST00000598364,;SYMPK,upstream_gene_variant,,ENST00000596824,; G ENST00000245934 Transcript missense_variant 3180/4195 2935/3825 979/1274 E/Q Gag/Cag 1 -1 SYMPK HGNC HGNC:22935 protein_coding YES CCDS12676.2 ENSP00000245934 Q92797 A0A024R0R6 UPI00002026C0 NM_004819.2 deleterious(0.01) 23/27 hmmpanther:PTHR15245:SF20,hmmpanther:PTHR15245,Pfam_domain:PF12295 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 45818105 45818105 C G 1 0 0 0 0 1 0 0 0 15829 922 32 4 4 SYMPK 19 45818105 Missense_Mutation SNP C C3N-00556_T 898876 45818105 12799511 449 16578 GLTSCR1 0 . GRCh38 19 47701427 47701427 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.3695C>T p.Pro1232Leu p.P1232L ENST00000396720 15/15 369 345 24 335 335 0 strelka-varscan-mutect GLTSCR1,missense_variant,p.Pro1232Leu,ENST00000396720,NM_015711.3;GLTSCR1,missense_variant,p.Pro1180Leu,ENST00000614245,;CTD-2571L23.8,intron_variant,,ENST00000599924,;GLTSCR1,non_coding_transcript_exon_variant,,ENST00000602258,; T ENST00000396720 Transcript missense_variant 3889/5739 3695/4683 1232/1560 P/L cCc/cTc 1 1 GLTSCR1 HGNC HGNC:4332 protein_coding YES CCDS46134.1 ENSP00000379946 Q9NZM4 UPI00016278EE NM_015711.3 tolerated(0.22) 15/15 hmmpanther:PTHR15572:SF1,hmmpanther:PTHR15572 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 47701427 47701427 C T 1 0 0 0 0 1 0 0 0 6350 623 22 3 3 GLTSCR1 19 47701427 Missense_Mutation SNP C C3N-00556_T 1883322 47701427 10916189 450 16579 CRX 0 . GRCh38 19 47839789 47839789 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.722C>T p.Ser241Phe p.S241F ENST00000221996 4/4 194 171 23 223 223 0 strelka-varscan-mutect CRX,missense_variant,p.Ser241Phe,ENST00000221996,NM_000554.4;CRX,missense_variant,p.Ser241Phe,ENST00000539067,;CRX,3_prime_UTR_variant,,ENST00000613299,;CRX,downstream_gene_variant,,ENST00000566686,;CRX,upstream_gene_variant,,ENST00000602001,;CRX,downstream_gene_variant,,ENST00000556527,; T ENST00000221996 Transcript missense_variant 929/4470 722/900 241/299 S/F tCc/tTc 1 1 CRX HGNC HGNC:2383 protein_coding YES CCDS12706.1 ENSP00000221996 O43186 UPI00001284E0 NM_000554.4 tolerated(0.07) 4/4 Pfam_domain:PF03529,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 47839789 47839789 C T 1 0 0 0 0 1 0 0 0 3704 855 30 3 3 CRX 19 47839789 Missense_Mutation SNP C C3N-00556_T 138362 47839789 10777827 451 16580 POLD1 0 . GRCh38 19 50403137 50403137 + Missense_Mutation SNP G G T rs556862476 C3N-00556_T C3N-00556_N G G c.1055G>T p.Arg352Leu p.R352L ENST00000440232 9/27 144 110 34 131 130 1 strelka-varscan-mutect POLD1,missense_variant,p.Arg352Leu,ENST00000613923,NM_001308632.1;POLD1,missense_variant,p.Arg352Leu,ENST00000440232,NM_002691.3,NM_001256849.1;POLD1,missense_variant,p.Arg352Leu,ENST00000599857,;POLD1,missense_variant,p.Arg352Leu,ENST00000595904,;POLD1,downstream_gene_variant,,ENST00000601098,;POLD1,downstream_gene_variant,,ENST00000593887,;POLD1,upstream_gene_variant,,ENST00000596425,;POLD1,missense_variant,p.Arg352Leu,ENST00000600859,;POLD1,downstream_gene_variant,,ENST00000600746,; T ENST00000440232 Transcript missense_variant 1108/3444 1055/3324 352/1107 R/L cGc/cTc rs556862476 1 1 POLD1 HGNC HGNC:9175 protein_coding YES CCDS12795.1 ENSP00000406046 P28340 A0A024R4F4 UPI000007288E NM_002691.3,NM_001256849.1 deleterious(0) 9/27 hmmpanther:PTHR10322,hmmpanther:PTHR10322:SF23,Pfam_domain:PF03104,Gene3D:3.30.420.10,SMART_domains:SM00486,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS rs556862476 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 50403137 50403137 G T 1 0 0 0 0 1 0 0 0 12300 1087 38 1 1 POLD1 19 50403137 Missense_Mutation SNP G C3N-00556_T 2563348 50403137 8214479 452 16581 RPS9 0 . GRCh38 19 54201540 54201540 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.151G>A p.Ala51Thr p.A51T ENST00000302907 3/5 174 161 13 176 176 0 varscan-mutect RPS9,missense_variant,p.Ala51Thr,ENST00000402367,;RPS9,missense_variant,p.Ala51Thr,ENST00000441429,;RPS9,missense_variant,p.Ala51Thr,ENST00000302907,NM_001013.3;RPS9,missense_variant,p.Ala51Thr,ENST00000391752,NM_001321702.1;RPS9,missense_variant,p.Ala51Thr,ENST00000391753,;RPS9,missense_variant,p.Ala51Thr,ENST00000391751,NM_001321706.1;RPS9,missense_variant,p.Ala51Thr,ENST00000626547,;AC012314.20,upstream_gene_variant,,ENST00000426213,;RPS9,missense_variant,p.Ala51Thr,ENST00000448962,;RPS9,missense_variant,p.Ala51Thr,ENST00000445961,;RPS9,missense_variant,p.Ala51Thr,ENST00000436445,;RPS9,non_coding_transcript_exon_variant,,ENST00000495002,;RPS9,non_coding_transcript_exon_variant,,ENST00000484121,;RPS9,non_coding_transcript_exon_variant,,ENST00000460761,; A ENST00000302907 Transcript missense_variant 323/829 151/585 51/194 A/T Gcc/Acc 1 1 RPS9 HGNC HGNC:10442 protein_coding YES CCDS12884.1 ENSP00000302896 P46781 UPI00000040B2 NM_001013.3 tolerated(0.17) 3/5 hmmpanther:PTHR11831,hmmpanther:PTHR11831:SF10,Pfam_domain:PF00163,TIGRFAM_domain:TIGR01018,SMART_domains:SM01390,Superfamily_domains:SSF55174 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 54201540 54201540 G A 1 0 0 0 0 1 0 0 0 13917 1203 42 3 3 RPS9 19 54201540 Missense_Mutation SNP G C3N-00556_T 3798403 54201540 4416076 453 16582 GP6 0 . GRCh38 19 55014298 55014298 + Silent SNP G G C rs754162124 C3N-00556_T C3N-00556_N G G c.1647C>G p.= p.L549L ENST00000310373 8/8 411 387 24 513 513 0 strelka-varscan-mutect GP6,synonymous_variant,p.=,ENST00000310373,NM_001083899.2;GP6,3_prime_UTR_variant,,ENST00000417454,NM_016363.5;GP6,3_prime_UTR_variant,,ENST00000333884,NM_001256017.2;CTC-550B14.7,intron_variant,,ENST00000593060,;CTC-550B14.7,intron_variant,,ENST00000586845,;GP6,downstream_gene_variant,,ENST00000465648,; C ENST00000310373 Transcript synonymous_variant 1675/2268 1647/1863 549/620 L ctC/ctG rs754162124 1 -1 GP6 HGNC HGNC:14388 protein_coding YES CCDS42626.1 ENSP00000308782 Q9HCN6 UPI000013C631 NM_001083899.2 8/8 LOW 1 SNV 1 1 PASS rs754162124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 54 55014298 55014298 G C 1 0 0 0 0 0 0 0 1 6479 929 33 4 4 GP6 19 55014298 Silent SNP G C3N-00556_T 812758 55014298 3603318 454 16583 DNAAF3 0 . GRCh38 19 55165900 55165900 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.390G>T p.= p.R130R ENST00000527223 3/12 318 226 92 347 347 0 strelka-varscan-mutect DNAAF3,synonymous_variant,p.=,ENST00000527223,NM_001256714.1;DNAAF3,synonymous_variant,p.=,ENST00000391720,NM_178837.4;DNAAF3,synonymous_variant,p.=,ENST00000524407,NM_001256715.1;DNAAF3,synonymous_variant,p.=,ENST00000532817,;DNAAF3,synonymous_variant,p.=,ENST00000526003,;DNAAF3,synonymous_variant,p.=,ENST00000534170,;DNAAF3,5_prime_UTR_variant,,ENST00000455045,NM_001256716.1;snoU13,upstream_gene_variant,,ENST00000459370,;CTD-2587H24.5,intron_variant,,ENST00000591665,;DNAAF3,non_coding_transcript_exon_variant,,ENST00000528476,;DNAAF3,upstream_gene_variant,,ENST00000527166,;DNAAF3,upstream_gene_variant,,ENST00000527292,;DNAAF3,synonymous_variant,p.=,ENST00000528412,;DNAAF3,synonymous_variant,p.=,ENST00000534214,;DNAAF3,upstream_gene_variant,,ENST00000533527,;DNAAF3,upstream_gene_variant,,ENST00000526959,;DNAAF3,downstream_gene_variant,,ENST00000586877,; A ENST00000527223 Transcript synonymous_variant 392/2228 390/1827 130/608 R cgG/cgT 1 -1 DNAAF3 HGNC HGNC:30492 protein_coding YES CCDS58680.1 ENSP00000436975 A0A0C4DH81 UPI00000722C7 NM_001256714.1 3/12 hmmpanther:PTHR22118:SF14,hmmpanther:PTHR22118,Pfam_domain:PF14737 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 55165900 55165900 C A 1 0 0 0 0 0 0 0 1 4408 842 30 2 2 DNAAF3 19 55165900 Silent SNP C C3N-00556_T 151602 55165900 3451716 455 16584 UBE2S 0 . GRCh38 19 55404317 55404317 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.313G>A p.Ala105Thr p.A105T ENST00000264552 3/4 295 251 44 293 293 0 strelka-varscan-mutect UBE2S,missense_variant,p.Ala105Thr,ENST00000264552,NM_014501.2;UBE2S,missense_variant,p.Ala105Thr,ENST00000587845,;UBE2S,missense_variant,p.Gly79Asp,ENST00000589978,;RPL28,downstream_gene_variant,,ENST00000560055,;UBE2S,upstream_gene_variant,,ENST00000592570,; T ENST00000264552 Transcript missense_variant 501/2548 313/669 105/222 A/T Gct/Act 1 -1 UBE2S HGNC HGNC:17895 protein_coding YES CCDS33114.1 ENSP00000264552 Q16763 UPI000000122B NM_014501.2 deleterious(0) 3/4 Gene3D:3.10.110.10,Pfam_domain:PF00179,PROSITE_profiles:PS50127,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF57,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 55404317 55404317 C T 1 0 0 0 0 1 0 0 0 17395 739 26 3 3 UBE2S 19 55404317 Missense_Mutation SNP C C3N-00556_T 238417 55404317 3213299 456 16585 SSC5D 0 . GRCh38 19 55489961 55489961 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.441G>A p.= p.L147L ENST00000389623 4/14 153 143 10 151 151 0 strelka-varscan-mutect SSC5D,synonymous_variant,p.=,ENST00000389623,NM_001144950.1;SSC5D,synonymous_variant,p.=,ENST00000587166,NM_001195267.1;NAT14,downstream_gene_variant,,ENST00000205194,NM_020378.3;NAT14,downstream_gene_variant,,ENST00000591590,;NAT14,downstream_gene_variant,,ENST00000588985,;SSC5D,downstream_gene_variant,,ENST00000594321,;NAT14,downstream_gene_variant,,ENST00000587400,;SSC5D,upstream_gene_variant,,ENST00000589020,;NAT14,downstream_gene_variant,,ENST00000592719,;SSC5D,non_coding_transcript_exon_variant,,ENST00000588254,; A ENST00000389623 Transcript synonymous_variant 464/4845 441/4722 147/1573 L ctG/ctA 1 1 SSC5D HGNC HGNC:26641 protein_coding YES CCDS46196.1 ENSP00000374274 A1L4H1 UPI000192952A NM_001144950.1 4/14 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 55489961 55489961 G A 1 0 0 0 0 0 0 0 1 15558 1277 45 3 3 SSC5D 19 55489961 Silent SNP G C3N-00556_T 85644 55489961 3127655 457 16586 ZNF524 0 . GRCh38 19 55602711 55602711 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.599G>A p.Cys200Tyr p.C200Y ENST00000591046 1/1 288 210 78 210 209 1 strelka-varscan-mutect ZNF524,missense_variant,p.Cys200Tyr,ENST00000591046,;ZNF524,missense_variant,p.Cys200Tyr,ENST00000301073,NM_153219.3;FIZ1,upstream_gene_variant,,ENST00000590714,;ZNF865,upstream_gene_variant,,ENST00000568956,NM_001195605.1;FIZ1,upstream_gene_variant,,ENST00000221665,NM_032836.2;FIZ1,upstream_gene_variant,,ENST00000587678,;ZNF524,downstream_gene_variant,,ENST00000589521,;FIZ1,upstream_gene_variant,,ENST00000592585,;FIZ1,upstream_gene_variant,,ENST00000587414,; A ENST00000591046 Transcript missense_variant 833/1260 599/795 200/264 C/Y tGc/tAc COSM4081625 1 1 ZNF524 HGNC HGNC:28322 protein_coding YES CCDS12929.1 ENSP00000466907 Q96C55 UPI00000735DD deleterious(0) 1/1 Gene3D:3.30.160.60,Pfam_domain:PF13894,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 55602711 55602711 G A 1 0 0 0 0 1 0 0 0 18538 1319 46 3 3 ZNF524 19 55602711 Missense_Mutation SNP G C3N-00556_T 112750 55602711 3014905 458 16587 ZNF787 0 . GRCh38 19 56088727 56088727 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.445C>T p.Pro149Ser p.P149S ENST00000610935 3/3 103 84 19 135 135 0 strelka-varscan-mutect ZNF787,missense_variant,p.Pro149Ser,ENST00000610935,NM_001002836.3;ZNF787,downstream_gene_variant,,ENST00000586787,; A ENST00000610935 Transcript missense_variant 564/1925 445/1149 149/382 P/S Ccc/Tcc 1 -1 ZNF787 HGNC HGNC:26998 protein_coding YES CCDS42634.1 ENSP00000478557 A0A087WUD1 UPI0001596896 NM_001002836.3 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24408:SF1,hmmpanther:PTHR24408,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 56088727 56088727 G A 1 0 0 0 0 1 0 0 0 18743 1203 42 3 3 ZNF787 19 56088727 Missense_Mutation SNP G C3N-00556_T 486016 56088727 2528889 459 16588 ZSCAN5B 0 . GRCh38 19 56192947 56192947 + Missense_Mutation SNP G G A rs374507565 C3N-00556_T C3N-00556_N G G c.106C>T p.His36Tyr p.H36Y ENST00000586855 2/5 148 140 8 166 166 0 varscan-mutect ZSCAN5B,missense_variant,p.His36Tyr,ENST00000586855,;ZSCAN5B,missense_variant,p.His36Tyr,ENST00000358992,NM_001080456.2;ZSCAN5B,missense_variant,p.His36Tyr,ENST00000589938,;ZSCAN5B,missense_variant,p.His36Tyr,ENST00000587032,; A ENST00000586855 Transcript missense_variant 420/2059 106/1488 36/495 H/Y Cac/Tac rs374507565 1 -1 ZSCAN5B HGNC HGNC:34246 protein_coding YES CCDS46203.1 ENSP00000466072 A6NJL1 UPI000059D7BA tolerated(0.06) 2/5 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF164,Superfamily_domains:SSF47353 MODERATE 1 SNV 5 1 PASS rs374507565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 56192947 56192947 G A 1 0 0 0 0 1 0 0 0 18838 1290 45 3 3 ZSCAN5B 19 56192947 Missense_Mutation SNP G C3N-00556_T 104220 56192947 2424669 460 16589 ZNF471 0 . GRCh38 19 56525267 56525267 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1200G>C p.Glu400Asp p.E400D ENST00000308031 5/5 198 187 11 287 287 0 strelka-varscan-mutect ZNF471,missense_variant,p.Glu400Asp,ENST00000308031,NM_001321768.1,NM_020813.2;ZNF471,3_prime_UTR_variant,,ENST00000591537,;ZNF471,intron_variant,,ENST00000593197,; C ENST00000308031 Transcript missense_variant 1333/6287 1200/1881 400/626 E/D gaG/gaC 1 1 ZNF471 HGNC HGNC:23226 protein_coding YES CCDS12945.1 ENSP00000309161 Q9BX82 A0A024R4Q9 UPI0000073465 NM_001321768.1,NM_020813.2 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF309,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 56525267 56525267 G C 1 0 0 0 0 1 0 0 0 18502 933 33 4 4 ZNF471 19 56525267 Missense_Mutation SNP G C3N-00556_T 332320 56525267 2092349 461 16590 ZFP28 0 . GRCh38 19 56554193 56554193 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1408C>T p.His470Tyr p.H470Y ENST00000301318 8/8 172 158 14 230 230 0 strelka-varscan-mutect ZFP28,missense_variant,p.His470Tyr,ENST00000301318,NM_020828.1;ZFP28,downstream_gene_variant,,ENST00000591844,NM_001308440.1;AC007228.11,intron_variant,,ENST00000596587,;ZFP28,downstream_gene_variant,,ENST00000588163,; T ENST00000301318 Transcript missense_variant 1479/4096 1408/2607 470/868 H/Y Cac/Tac 1 1 ZFP28 HGNC HGNC:17801 protein_coding YES CCDS12946.1 ENSP00000301318 Q8NHY6 UPI000006D90E NM_020828.1 deleterious(0.02) 8/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF212,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 56554193 56554193 C T 1 0 0 0 0 1 0 0 0 18217 826 29 3 3 ZFP28 19 56554193 Missense_Mutation SNP C C3N-00556_T 28926 56554193 2063423 462 16591 MGME1 0 . GRCh38 20 17975876 17975876 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.704G>A p.Gly235Asp p.G235D ENST00000377710 3/5 225 211 14 237 237 0 strelka-mutect MGME1,missense_variant,p.Gly235Asp,ENST00000377710,NM_052865.2;MGME1,missense_variant,p.Gly155Asp,ENST00000377709,;MGME1,intron_variant,,ENST00000377704,;MGME1,intron_variant,,ENST00000467391,;MGME1,intron_variant,,ENST00000463219,;OVOL2,intron_variant,,ENST00000486776,; A ENST00000377710 Transcript missense_variant 992/2336 704/1035 235/344 G/D gGt/gAt 1 1 MGME1 HGNC HGNC:16205 protein_coding YES CCDS13131.1 ENSP00000366939 Q9BQP7 UPI00001285E8 NM_052865.2 deleterious(0) 3/5 HAMAP:MF_03030,hmmpanther:PTHR31340,Pfam_domain:PF12705,Superfamily_domains:SSF52980 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 17975876 17975876 G A 1 0 0 0 0 1 0 0 0 9513 1261 44 3 3 MGME1 20 17975876 Missense_Mutation SNP G C3N-00556_T 17975876 46468291 463 16592 NDRG3 0 . GRCh38 20 36707008 36707008 + Splice_Site SNP C C G novel C3N-00556_T C3N-00556_N C C c.58-1G>C p.X20_splice ENST00000349004 115 105 10 100 100 0 strelka-varscan-mutect NDRG3,splice_acceptor_variant,,ENST00000373803,;NDRG3,splice_acceptor_variant,,ENST00000349004,NM_032013.3;NDRG3,splice_acceptor_variant,,ENST00000373773,;NDRG3,intron_variant,,ENST00000359675,NM_022477.3; G ENST00000349004 Transcript splice_acceptor_variant -/2964 58/1128 20/375 1 -1 NDRG3 HGNC HGNC:14462 protein_coding YES CCDS13285.1 ENSP00000345292 Q9UGV2 UPI000012FEDF NM_032013.3 2/15 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 54 36707008 36707008 C G 1 0 0 0 0 0 0 1 0 10274 927 32 4 4 NDRG3 20 36707008 Splice_Site SNP C C3N-00556_T 18731132 36707008 27737159 464 16593 KIAA1755 0 . GRCh38 20 38219710 38219710 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.2476C>A p.Leu826Met p.L826M ENST00000279024 11/14 282 251 31 211 211 0 strelka-varscan-mutect KIAA1755,missense_variant,p.Leu826Met,ENST00000279024,NM_001029864.1;KIAA1755,missense_variant,p.Leu125Met,ENST00000435901,;KIAA1755,non_coding_transcript_exon_variant,,ENST00000484362,;KIAA1755,upstream_gene_variant,,ENST00000460881,;KIAA1755,upstream_gene_variant,,ENST00000487506,; T ENST00000279024 Transcript missense_variant 2748/6429 2476/3603 826/1200 L/M Ctg/Atg 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 deleterious(0) 11/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF125 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 38219710 38219710 G T 1 0 0 0 0 1 0 0 0 8128 933 33 2 2 KIAA1755 20 38219710 Missense_Mutation SNP G C3N-00556_T 1512702 38219710 26224457 465 16594 SLC12A5 0 . GRCh38 20 46043255 46043255 + Missense_Mutation SNP C C A C3N-00556_T C3N-00556_N C C c.1238C>A p.Pro413His p.P413H ENST00000454036 9/26 234 152 82 197 195 2 strelka-varscan-mutect SLC12A5,missense_variant,p.Pro390His,ENST00000243964,NM_020708.4;SLC12A5,missense_variant,p.Pro413His,ENST00000454036,NM_001134771.1;SLC12A5,missense_variant,p.Pro390His,ENST00000616201,;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,non_coding_transcript_exon_variant,,ENST00000608594,;SLC12A5,intron_variant,,ENST00000539566,;SLC12A5,downstream_gene_variant,,ENST00000629054,;SLC12A5,downstream_gene_variant,,ENST00000625683,;SLC12A5,downstream_gene_variant,,ENST00000372315,;SLC12A5,downstream_gene_variant,,ENST00000622711,;SLC12A5,upstream_gene_variant,,ENST00000626144,; A ENST00000454036 Transcript missense_variant 1314/3593 1238/3420 413/1139 P/H cCt/cAt COSM3547175,COSM4958780 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 deleterious(0.01) 9/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,TIGRFAM_domain:TIGR00930 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 46043255 46043255 C A 1 0 0 0 0 1 0 0 0 14651 681 24 2 2 SLC12A5 20 46043255 Missense_Mutation SNP C C3N-00556_T 7823545 46043255 18400912 466 16595 DDX27 0 . GRCh38 20 49219378 49219378 + Missense_Mutation SNP G G T rs745864215 C3N-00556_T C3N-00556_N G G c.23G>T p.Arg8Leu p.R8L ENST00000622530 1/21 95 88 7 83 83 0 strelka-varscan-mutect DDX27,missense_variant,p.Arg8Leu,ENST00000622530,NM_017895.7;DDX27,missense_variant,p.Arg8Leu,ENST00000371764,;DDX27,upstream_gene_variant,,ENST00000618172,;DDX27,non_coding_transcript_exon_variant,,ENST00000484427,;DDX27,upstream_gene_variant,,ENST00000462328,; T ENST00000622530 Transcript missense_variant 84/2693 23/2391 8/796 R/L cGa/cTa rs745864215 1 1 DDX27 HGNC HGNC:15837 protein_coding YES CCDS13416.1 ENSP00000483495 Q96GQ7 UPI0000140DCA NM_017895.7 deleterious_low_confidence(0.03) 1/21 MODERATE 1 SNV 1 1 PASS rs745864215 . 0 206 4 0 0 0 0 0 -14.63158 1 1 1 1 0 T 3 4 54 49219378 49219378 G T 1 0 0 0 0 1 0 0 0 4156 1058 37 1 1 DDX27 20 49219378 Missense_Mutation SNP G C3N-00556_T 3176123 49219378 15224789 467 16596 ZNFX1 0 . GRCh38 20 49270638 49270638 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.1174C>T p.Leu392Phe p.L392F ENST00000396105 3/14 137 128 9 188 188 0 strelka-varscan-mutect ZNFX1,missense_variant,p.Leu392Phe,ENST00000396105,NM_021035.2;ZNFX1,missense_variant,p.Leu392Phe,ENST00000371752,;ZNFX1,missense_variant,p.Leu392Phe,ENST00000371754,;ZNFX1,missense_variant,p.Leu392Phe,ENST00000371744,;ZNFX1,missense_variant,p.Leu196Phe,ENST00000455070,; A ENST00000396105 Transcript missense_variant 1421/7371 1174/5757 392/1918 L/F Ctc/Ttc 1 -1 ZNFX1 HGNC HGNC:29271 protein_coding YES CCDS13417.1 ENSP00000379412 Q9P2E3 UPI000012DD83 NM_021035.2 deleterious(0.02) 3/14 hmmpanther:PTHR10887:SF379,hmmpanther:PTHR10887 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 49270638 49270638 G A 1 0 0 0 0 1 0 0 0 18798 942 33 3 3 ZNFX1 20 49270638 Missense_Mutation SNP G C3N-00556_T 51260 49270638 15173529 468 16597 FAM210B 0 . GRCh38 20 56366098 56366098 + Silent SNP G G A C3N-00556_T C3N-00556_N G G c.390G>A p.= p.L130L ENST00000371384 3/3 219 205 14 219 219 0 varscan-mutect FAM210B,synonymous_variant,p.=,ENST00000371384,NM_080821.2;AURKA,downstream_gene_variant,,ENST00000347343,NM_003600.2;AURKA,downstream_gene_variant,,ENST00000395914,NM_198434.1,NM_198433.1;AURKA,downstream_gene_variant,,ENST00000312783,NM_198436.1;AURKA,downstream_gene_variant,,ENST00000395913,;AURKA,downstream_gene_variant,,ENST00000395911,NM_001323304.1;AURKA,downstream_gene_variant,,ENST00000395915,NM_198435.1,NM_198437.1;AURKA,downstream_gene_variant,,ENST00000371356,;AURKA,downstream_gene_variant,,ENST00000395907,; A ENST00000371384 Transcript synonymous_variant 481/3046 390/579 130/192 L ctG/ctA COSM4842285 1 1 FAM210B HGNC HGNC:16102 protein_coding YES CCDS13450.1 ENSP00000360437 Q96KR6 UPI000003B117 NM_080821.2 3/3 Pfam_domain:PF06916,hmmpanther:PTHR21377,hmmpanther:PTHR21377:SF0 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 56366098 56366098 G A 1 0 0 0 0 0 0 0 1 5397 1277 45 3 3 FAM210B 20 56366098 Silent SNP G C3N-00556_T 7095460 56366098 8078069 469 16598 TFAP2C 0 . GRCh38 20 56631562 56631562 + Missense_Mutation SNP G G A rs771721373 C3N-00556_T C3N-00556_N G G c.406G>A p.Val136Met p.V136M ENST00000201031 2/7 133 118 15 134 134 0 strelka-varscan-mutect TFAP2C,missense_variant,p.Val136Met,ENST00000201031,NM_003222.3;TFAP2C,downstream_gene_variant,,ENST00000416606,; A ENST00000201031 Transcript missense_variant 649/2866 406/1353 136/450 V/M Gtg/Atg rs771721373 1 1 TFAP2C HGNC HGNC:11744 protein_coding YES CCDS13454.1 ENSP00000201031 Q92754 UPI0000125BC8 NM_003222.3 tolerated(0.36) 2/7 hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF9 MODERATE 1 SNV 1 1 PASS rs771721373 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 56631562 56631562 G A 1 0 0 0 0 1 0 0 0 16222 1261 44 3 3 TFAP2C 20 56631562 Missense_Mutation SNP G C3N-00556_T 265464 56631562 7812605 470 16599 FAM217B 0 . GRCh38 20 59944035 59944035 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.92C>T p.Ser31Phe p.S31F ENST00000358293 5/5 231 218 13 222 222 0 strelka-varscan-mutect FAM217B,missense_variant,p.Ser31Phe,ENST00000358293,NM_001190826.1;FAM217B,missense_variant,p.Ser31Phe,ENST00000360816,NM_001190827.1,NM_022106.2;FAM217B,missense_variant,p.Ser31Phe,ENST00000421092,;PPP1R3D,upstream_gene_variant,,ENST00000370996,NM_006242.3;FAM217B,intron_variant,,ENST00000469084,; T ENST00000358293 Transcript missense_variant 507/5152 92/1152 31/383 S/F tCc/tTc 1 1 FAM217B HGNC HGNC:16170 protein_coding YES CCDS13484.1 ENSP00000351040 Q9NTX9 UPI0000128624 NM_001190826.1 deleterious(0.04) 5/5 hmmpanther:PTHR22145,hmmpanther:PTHR22145:SF3 MODERATE 1 SNV 2 1 PASS rs1204849635 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 59944035 59944035 C T 1 0 0 0 0 1 0 0 0 5407 855 30 3 3 FAM217B 20 59944035 Missense_Mutation SNP C C3N-00556_T 3312473 59944035 4500132 471 16600 PSMA7 0 . GRCh38 20 62136892 62136892 + Missense_Mutation SNP C C G rs769374594 C3N-00556_T C3N-00556_N C C c.712G>C p.Glu238Gln p.E238Q ENST00000370873 7/7 249 224 25 196 196 0 strelka-varscan-mutect PSMA7,missense_variant,p.Glu238Gln,ENST00000370873,NM_002792.3;PSMA7,missense_variant,p.Glu168Gln,ENST00000370861,;PSMA7,missense_variant,p.Glu177Gln,ENST00000442551,;LSM14B,downstream_gene_variant,,ENST00000279068,NM_144703.2;PSMA7,downstream_gene_variant,,ENST00000370858,;PSMA7,non_coding_transcript_exon_variant,,ENST00000484488,;PSMA7,downstream_gene_variant,,ENST00000486193,; G ENST00000370873 Transcript missense_variant 839/996 712/747 238/248 E/Q Gaa/Caa rs769374594 1 -1 PSMA7 HGNC HGNC:9536 protein_coding YES CCDS13489.1 ENSP00000359910 O14818 A0A0K0K1K4 UPI00000354E4 NM_002792.3 tolerated(0.39) 7/7 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11599:SF40,hmmpanther:PTHR11599,Gene3D:3.60.20.10 MODERATE 1 SNV 1 1 PASS rs769374594 . 0 207 0 0 0 0 0 2 -6.838335 0 0 1 0 0 G 3 3 54 62136892 62136892 C G 1 0 0 0 0 1 0 0 0 12823 922 32 4 4 PSMA7 20 62136892 Missense_Mutation SNP C C3N-00556_T 2192857 62136892 2307275 472 16601 KRTAP19-5 0 . GRCh38 21 30502026 30502026 + Frame_Shift_Del DEL C C - rs150866063 C3N-00556_T C3N-00556_N C C c.65delG p.Gly22AlafsTer56 p.G22Afs*56 ENST00000334151 1/1 329 294 35 368 368 0 sindel-varindel-pindel KRTAP19-5,frameshift_variant,p.Gly22AlafsTer56,ENST00000334151,NM_181611.1;KRTAP19-4,upstream_gene_variant,,ENST00000334058,NM_181610.1; - ENST00000334151 Transcript frameshift_variant 92/461 65/219 22/72 G/X gGc/gc rs150866063,COSM3963902,COSM4101122 1 -1 KRTAP19-5 HGNC HGNC:18940 protein_coding YES CCDS13597.1 ENSP00000334985 Q3LI72 UPI00001A9E50 NM_181611.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR38140:SF4,hmmpanther:PTHR38140,Pfam_domain:PF11759 0,1,1 HIGH 1 deletion 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 54 30502026 30502026 C - 1 0 1 0 1 0 0 0 0 8416 739 26 0 0 KRTAP19-5 21 30502026 Frame_Shift_Del DEL C C3N-00556_T 30502026 16207957 473 16602 SCAF4 0 . GRCh38 21 31671461 31671461 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.3382G>A p.Glu1128Lys p.E1128K ENST00000286835 20/20 158 146 12 205 205 0 strelka-varscan-mutect SCAF4,missense_variant,p.Glu1128Lys,ENST00000286835,NM_020706.2;SCAF4,missense_variant,p.Glu1106Lys,ENST00000399804,NM_001145445.1;SCAF4,missense_variant,p.Glu1113Lys,ENST00000434667,NM_001145444.1;SOD1,downstream_gene_variant,,ENST00000270142,NM_000454.4;SOD1,downstream_gene_variant,,ENST00000389995,;AP000254.8,upstream_gene_variant,,ENST00000609934,;SOD1,downstream_gene_variant,,ENST00000470944,;SOD1,downstream_gene_variant,,ENST00000476106,; T ENST00000286835 Transcript missense_variant 3765/4193 3382/3444 1128/1147 E/K Gag/Aag COSM1307729 1 -1 SCAF4 HGNC HGNC:19304 protein_coding YES CCDS33537.1 ENSP00000286835 O95104 UPI0000206D66 NM_020706.2 deleterious_low_confidence(0) 20/20 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 31671461 31671461 C T 1 0 0 0 0 1 0 0 0 14134 835 29 3 3 SCAF4 21 31671461 Missense_Mutation SNP C C3N-00556_T 1169435 31671461 15038522 474 16603 URB1 0 . GRCh38 21 32316814 32316814 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.6286G>T p.Ala2096Ser p.A2096S ENST00000382751 38/39 46 37 9 83 83 0 strelka-varscan-mutect URB1,missense_variant,p.Ala2096Ser,ENST00000382751,NM_014825.2;MRAP,downstream_gene_variant,,ENST00000399784,NM_178817.3;MRAP,downstream_gene_variant,,ENST00000303645,;MRAP,downstream_gene_variant,,ENST00000339944,NM_206898.1;MRAP,downstream_gene_variant,,ENST00000497833,; A ENST00000382751 Transcript missense_variant 6402/10832 6286/6816 2096/2271 A/S Gcc/Tcc 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 tolerated(0.32) 38/39 hmmpanther:PTHR13500 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.99179 0.9999989 1 1 1 0 A 3 1 54 32316814 32316814 C A 1 0 0 0 0 1 0 0 0 17554 710 25 2 2 URB1 21 32316814 Missense_Mutation SNP C C3N-00556_T 645353 32316814 14393169 475 16604 RUNX1 0 . GRCh38 21 35048874 35048874 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.26C>T p.Ser9Leu p.S9L ENST00000300305 1/8 398 367 31 419 419 0 strelka-varscan-mutect RUNX1,missense_variant,p.Ser9Leu,ENST00000300305,;RUNX1,missense_variant,p.Ser9Leu,ENST00000437180,NM_001754.4;RUNX1,missense_variant,p.Ser9Leu,ENST00000475045,;RUNX1,missense_variant,p.Ser9Leu,ENST00000455571,;RUNX1,missense_variant,p.Ser9Leu,ENST00000416754,;RUNX1,missense_variant,p.Ser9Leu,ENST00000482318,; A ENST00000300305 Transcript missense_variant 471/6222 26/1443 9/480 S/L tCa/tTa COSM1030466 1 -1 RUNX1 HGNC HGNC:10471 protein_coding YES CCDS13639.1 ENSP00000300305 Q01196 UPI000015FE6A deleterious_low_confidence(0) 1/8 PIRSF_domain:PIRSF009374,hmmpanther:PTHR11950 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 35048874 35048874 G A 1 0 0 0 0 1 0 0 0 14007 1294 45 3 3 RUNX1 21 35048874 Missense_Mutation SNP G C3N-00556_T 2732060 35048874 11661109 476 16605 DIP2A 0 . GRCh38 21 46545257 46545257 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.2297C>T p.Thr766Met p.T766M ENST00000417564 19/38 38 33 5 59 59 0 strelka-varscan-mutect DIP2A,missense_variant,p.Thr762Met,ENST00000400274,NM_001146116.1;DIP2A,missense_variant,p.Thr766Met,ENST00000417564,NM_015151.3;DIP2A,missense_variant,p.Thr766Met,ENST00000457905,NM_206889.2;DIP2A,missense_variant,p.Thr766Met,ENST00000435722,NM_206891.2,NM_206890.2;DIP2A,missense_variant,p.Thr723Met,ENST00000466639,NM_001146115.1;DIP2A,downstream_gene_variant,,ENST00000473752,;DIP2A,non_coding_transcript_exon_variant,,ENST00000494435,;DIP2A,non_coding_transcript_exon_variant,,ENST00000480553,; T ENST00000417564 Transcript missense_variant 2318/6967 2297/4716 766/1571 T/M aCg/aTg 1 1 DIP2A HGNC HGNC:17217 protein_coding YES CCDS46655.1 ENSP00000392066 Q14689 UPI00001B2E47 NM_015151.3 deleterious(0) 19/38 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF24,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -12.97584 0.9999994 1 1 1 0 T 3 4 54 46545257 46545257 C T 1 0 0 0 0 1 0 0 0 4332 536 19 1 1 DIP2A 21 46545257 Missense_Mutation SNP C C3N-00556_T 11496383 46545257 164726 477 16606 RIMBP3 0 . GRCh38 22 18607092 18607092 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.4343C>A p.Thr1448Lys p.T1448K ENST00000619918 1/1 82 70 12 108 108 0 varscan-mutect RIMBP3,missense_variant,p.Thr1448Lys,ENST00000619918,NM_015672.1;SCARNA17,downstream_gene_variant,,ENST00000614296,;RN7SKP131,upstream_gene_variant,,ENST00000410698,; T ENST00000619918 Transcript missense_variant 4828/6105 4343/4920 1448/1639 T/K aCg/aAg 1 -1 RIMBP3 HGNC HGNC:29344 protein_coding YES CCDS46665.1 ENSP00000483386 Q9UFD9 UPI0000237729 NM_015672.1 tolerated(0.28) 1/1 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF21,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 18607092 18607092 G T 1 0 0 0 0 1 0 0 0 13539 1145 40 1 1 RIMBP3 22 18607092 Missense_Mutation SNP G C3N-00556_T 18607092 32211376 478 16607 GAS2L1 0 . GRCh38 22 29308147 29308147 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.42G>C p.Lys14Asn p.K14N ENST00000618518 1/5 46 42 4 42 42 0 strelka-mutect GAS2L1,missense_variant,p.Lys14Asn,ENST00000618518,;GAS2L1,missense_variant,p.Lys14Asn,ENST00000616432,;GAS2L1,missense_variant,p.Lys14Asn,ENST00000621062,NM_006478.4;GAS2L1,missense_variant,p.Lys14Asn,ENST00000611648,NM_152236.2;GAS2L1,missense_variant,p.Lys14Asn,ENST00000610653,;GAS2L1,missense_variant,p.Lys14Asn,ENST00000406549,NM_001278730.1;GAS2L1,missense_variant,p.Lys14Asn,ENST00000416823,;GAS2L1,missense_variant,p.Lys14Asn,ENST00000428622,;RASL10A,downstream_gene_variant,,ENST00000401450,;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.4;GAS2L1,upstream_gene_variant,,ENST00000491016,;GAS2L1,downstream_gene_variant,,ENST00000487341,; C ENST00000618518 Transcript missense_variant 1090/3382 42/2046 14/681 K/N aaG/aaC 1 1 GAS2L1 HGNC HGNC:16955 protein_coding YES CCDS74840.1 ENSP00000481012 A0A5E8 UPI0000073BD7 deleterious(0) 1/5 MODERATE SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -10.67449 1 1 1 1 0 C 3 2 54 29308147 29308147 G C 1 0 0 0 0 1 0 0 0 6116 933 33 4 4 GAS2L1 22 29308147 Missense_Mutation SNP G C3N-00556_T 10701055 29308147 21510321 479 16608 PRR14L 0 . GRCh38 22 31715264 31715264 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.2575G>T p.Asp859Tyr p.D859Y ENST00000327423 4/9 204 179 25 268 268 0 strelka-varscan-mutect PRR14L,missense_variant,p.Asp859Tyr,ENST00000327423,NM_173566.2;PRR14L,upstream_gene_variant,,ENST00000330495,;PRR14L,downstream_gene_variant,,ENST00000461722,;PRR14L,upstream_gene_variant,,ENST00000492705,;PRR14L,upstream_gene_variant,,ENST00000431684,; A ENST00000327423 Transcript missense_variant 2765/10826 2575/6456 859/2151 D/Y Gat/Tat 1 -1 PRR14L HGNC HGNC:28738 protein_coding YES CCDS13900.2 ENSP00000331845 Q5THK1 UPI0000207582 NM_173566.2 deleterious(0.04) 4/9 hmmpanther:PTHR14522,hmmpanther:PTHR14522:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 31715264 31715264 C A 1 0 0 0 0 1 0 0 0 12722 826 29 2 2 PRR14L 22 31715264 Missense_Mutation SNP C C3N-00556_T 2407117 31715264 19103204 480 16609 ISX 0 . GRCh38 22 35067275 35067275 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.188C>T p.Ser63Leu p.S63L ENST00000308700 1/4 238 210 28 286 286 0 strelka-varscan-mutect ISX,missense_variant,p.Ser63Leu,ENST00000308700,;ISX,missense_variant,p.Ser63Leu,ENST00000404699,NM_001303508.1; T ENST00000308700 Transcript missense_variant 1140/3384 188/738 63/245 S/L tCa/tTa 1 1 ISX HGNC HGNC:28084 protein_coding YES CCDS33640.1 ENSP00000311492 Q2M1V0 UPI00001BE8E5 tolerated(0.31) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24329:SF362,hmmpanther:PTHR24329,Gene3D:1.10.10.60 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 35067275 35067275 C T 1 0 0 0 0 1 0 0 0 7773 838 29 3 3 ISX 22 35067275 Missense_Mutation SNP C C3N-00556_T 3352011 35067275 15751193 481 16610 MYH9 0 . GRCh38 22 36320805 36320806 + Frame_Shift_Del DEL GT GT - novel C3N-00556_T C3N-00556_N GT GT c.860_861delAC p.His287ProfsTer74 p.H287Pfs*74 ENST00000216181 8/41 259 212 47 327 327 0 sindel-varindel-pindel MYH9,frameshift_variant,p.His287ProfsTer74,ENST00000216181,NM_002473.5;MYH9,downstream_gene_variant,,ENST00000401701,;MYH9,non_coding_transcript_exon_variant,,ENST00000463027,;MYH9,non_coding_transcript_exon_variant,,ENST00000472210,;MYH9,upstream_gene_variant,,ENST00000477189,; - ENST00000216181 Transcript frameshift_variant 1091-1092/7501 860-861/5883 287/1960 H/X cAC/c 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 8/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF317,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 54 36320805 36320805 GT - 1 0 1 0 1 0 0 0 0 10042 1252 44 0 0 MYH9 22 36320805 Frame_Shift_Del DEL GT C3N-00556_T 1253530 36320805 14497663 482 16611 BAIAP2L2 0 . GRCh38 22 38088794 38088794 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1072G>C p.Glu358Gln p.E358Q ENST00000381669 10/14 176 164 12 141 141 0 strelka-mutect BAIAP2L2,missense_variant,p.Glu358Gln,ENST00000381669,NM_025045.5;BAIAP2L2,missense_variant,p.Glu358Gln,ENST00000332536,;BAIAP2L2,missense_variant,p.Glu49Gln,ENST00000428572,;SLC16A8,upstream_gene_variant,,ENST00000427592,;CTA-228A9.3,upstream_gene_variant,,ENST00000609162,;SLC16A8,upstream_gene_variant,,ENST00000469516,; G ENST00000381669 Transcript missense_variant 1217/2146 1072/1590 358/529 E/Q Gag/Cag 1 -1 BAIAP2L2 HGNC HGNC:26203 protein_coding YES CCDS43018.1 ENSP00000371085 Q6UXY1 UPI00001AECDC NM_025045.5 tolerated(0.06) 10/14 Gene3D:2.30.30.40,Pfam_domain:PF14604,PROSITE_profiles:PS50002,hmmpanther:PTHR14206,hmmpanther:PTHR14206:SF5,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -15.78372 0.9999996 1 1 1 0 G 3 3 54 38088794 38088794 C G 1 0 0 0 0 1 0 0 0 1455 893 31 4 4 BAIAP2L2 22 38088794 Missense_Mutation SNP C C3N-00556_T 1767989 38088794 12729674 483 16612 CCDC134 0 . GRCh38 22 41813315 41813315 + Missense_Mutation SNP G G T rs753415480 C3N-00556_T C3N-00556_N G G c.362G>T p.Arg121Leu p.R121L ENST00000255784 5/7 206 192 14 217 217 0 strelka-varscan-mutect CCDC134,missense_variant,p.Arg121Leu,ENST00000255784,NM_024821.3;CCDC134,intron_variant,,ENST00000402061,NM_001304797.1; T ENST00000255784 Transcript missense_variant 466/1270 362/690 121/229 R/L cGc/cTc rs753415480 1 1 CCDC134 HGNC HGNC:26185 protein_coding YES CCDS33654.1 ENSP00000255784 Q9H6E4 UPI000007311E NM_024821.3 deleterious(0) 5/7 hmmpanther:PTHR14735,Pfam_domain:PF15002 MODERATE 1 SNV 1 1 PASS rs753415480 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 41813315 41813315 G T 1 0 0 0 0 1 0 0 0 2458 1087 38 1 1 CCDC134 22 41813315 Missense_Mutation SNP G C3N-00556_T 3724521 41813315 9005153 484 16613 PHF21B 0 . GRCh38 22 44893482 44893482 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.935C>G p.Ala312Gly p.A312G ENST00000313237 7/13 183 173 10 179 179 0 strelka-mutect PHF21B,missense_variant,p.Ala312Gly,ENST00000313237,NM_138415.4;PHF21B,missense_variant,p.Ala108Gly,ENST00000403565,NM_001284296.1;PHF21B,missense_variant,p.Ala258Gly,ENST00000396103,NM_001242450.1;PHF21B,missense_variant,p.Ala270Gly,ENST00000629843,NM_001135862.2;PHF21B,missense_variant,p.Ala108Gly,ENST00000414269,; C ENST00000313237 Transcript missense_variant 1086/3671 935/1596 312/531 A/G gCc/gGc 1 -1 PHF21B HGNC HGNC:25161 protein_coding YES CCDS14061.1 ENSP00000324403 Q96EK2 A0A0S2Z6R3 UPI0000072111 NM_138415.4 deleterious(0.01) 7/13 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 44893482 44893482 G C 1 0 0 0 0 1 0 0 0 11920 1203 42 4 4 PHF21B 22 44893482 Missense_Mutation SNP G C3N-00556_T 3080167 44893482 5924986 485 16614 GTSE1 0 . GRCh38 22 46329479 46329479 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.2048G>A p.Gly683Glu p.G683E ENST00000454366 11/12 457 432 25 512 512 0 strelka-varscan-mutect GTSE1,missense_variant,p.Gly683Glu,ENST00000454366,NM_016426.6;TRMU,upstream_gene_variant,,ENST00000476901,;TRMU,upstream_gene_variant,,ENST00000486620,;GTSE1,non_coding_transcript_exon_variant,,ENST00000491863,;GTSE1,downstream_gene_variant,,ENST00000466510,;GTSE1,downstream_gene_variant,,ENST00000479645,; A ENST00000454366 Transcript missense_variant 2260/3112 2048/2220 683/739 G/E gGa/gAa 1 1 GTSE1 HGNC HGNC:13698 protein_coding YES CCDS14074.2 ENSP00000415430 Q9NYZ3 UPI000021D19B NM_016426.6 tolerated(0.54) 11/12 hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 46329479 46329479 G A 1 0 0 0 0 1 0 0 0 6766 1174 41 3 3 GTSE1 22 46329479 Missense_Mutation SNP G C3N-00556_T 1435997 46329479 4488989 486 16615 PANX2 0 . GRCh38 22 50177220 50177220 + Missense_Mutation SNP G G A C3N-00556_T C3N-00556_N G G c.508G>A p.Glu170Lys p.E170K ENST00000395842 2/3 151 142 9 170 170 0 strelka-varscan-mutect PANX2,missense_variant,p.Glu170Lys,ENST00000395842,NM_052839.3;PANX2,missense_variant,p.Glu170Lys,ENST00000159647,NM_001160300.1;PANX2,3_prime_UTR_variant,,ENST00000402472,; A ENST00000395842 Transcript missense_variant 508/3051 508/2034 170/677 E/K Gag/Aag COSM4653536,COSM4653537,COSM4833950,COSM4833951 1 1 PANX2 HGNC HGNC:8600 protein_coding YES CCDS14085.2 ENSP00000379183 Q96RD6 UPI0000E070D3 NM_052839.3 tolerated(0.17) 2/3 PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF7,Pfam_domain:PF00876 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS rs1485043074 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 50177220 50177220 G A 1 0 0 0 0 1 0 0 0 11502 1059 37 1 1 PANX2 22 50177220 Missense_Mutation SNP G C3N-00556_T 3847741 50177220 641248 487 16616 SHANK3 0 . GRCh38 22 50720464 50720464 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.2628C>T p.= p.L876L ENST00000262795 24/25 56 49 7 21 21 0 strelka-mutect SHANK3,synonymous_variant,p.=,ENST00000262795,;SHANK3,synonymous_variant,p.=,ENST00000445220,NM_033517.1;SHANK3,non_coding_transcript_exon_variant,,ENST00000414786,; T ENST00000262795 Transcript synonymous_variant 2628/7091 2628/5193 876/1730 L ctC/ctT 1 1 SHANK3 HGNC HGNC:14294 protein_coding YES ENSP00000489147 A0A0U1RQS4 UPI00071AFB18 24/25 hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135 LOW 1 SNV 5 1 PASS rs1158278512 . 0 205 5 0 0 0 0 0 -16.42394 1 1 1 1 0 T 2 4 54 50720464 50720464 C T 1 0 0 0 0 0 0 0 1 14525 871 31 1 1 SHANK3 22 50720464 Silent SNP C C3N-00556_T 543244 50720464 98004 488 16617 SLC25A6 0 . GRCh38 X 1386725 1386725 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.774G>T p.Trp258Cys p.W258C ENST00000381401 4/4 104 98 6 113 113 0 strelka-varscan-mutect SLC25A6,missense_variant,p.Trp258Cys,ENST00000381401,NM_001636.3;IL3RA,downstream_gene_variant,,ENST00000331035,NM_002183.3;IL3RA,downstream_gene_variant,,ENST00000381469,NM_001267713.1;SLC25A6,downstream_gene_variant,,ENST00000475167,;SLC25A6,downstream_gene_variant,,ENST00000484026,; A ENST00000381401 Transcript missense_variant 1489/2062 774/897 258/298 W/C tgG/tgT 1 -1 SLC25A6 HGNC HGNC:10992 protein_coding YES CCDS14114.1 ENSP00000370808 P12236 Q6I9V5 UPI00000015FE NM_001636.3 deleterious(0.04) 4/4 PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF217,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 1386725 1386725 C A 1 0 0 0 0 1 0 0 0 14783 856 30 2 2 SLC25A6 23 1386725 Missense_Mutation SNP C C3N-00556_T 1386725 154654170 489 16618 ARSF 0 . GRCh38 X 3110134 3110134 + Missense_Mutation SNP T T G novel C3N-00556_T C3N-00556_N T T c.1272T>G p.Ile424Met p.I424M ENST00000381127 10/11 18 12 6 15 15 0 strelka-varscan-mutect ARSF,missense_variant,p.Ile424Met,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,missense_variant,p.Ile424Met,ENST00000359361,NM_004042.4;RP13-824C8.2,downstream_gene_variant,,ENST00000443851,; G ENST00000381127 Transcript missense_variant 1493/2164 1272/1773 424/590 I/M atT/atG 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 deleterious(0.04) 10/11 hmmpanther:PTHR10342:SF220,hmmpanther:PTHR10342,Gene3D:3.40.720.10,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 3110134 3110134 T G 1 0 0 0 0 1 0 0 0 1134 1800 63 5 5 ARSF 23 3110134 Missense_Mutation SNP T C3N-00556_T 1723409 3110134 152930761 490 16619 TLR7 0 . GRCh38 X 12886927 12886927 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1419G>C p.Arg473Ser p.R473S ENST00000380659 3/3 44 31 13 82 82 0 strelka-mutect TLR7,missense_variant,p.Arg473Ser,ENST00000380659,NM_016562.3; C ENST00000380659 Transcript missense_variant 1558/5011 1419/3150 473/1049 R/S agG/agC 1 1 TLR7 HGNC HGNC:15631 protein_coding YES CCDS14151.1 ENSP00000370034 Q9NYK1 B2R9N9 UPI000004BAF6 NM_016562.3 tolerated(0.07) 3/3 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF222 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 12886927 12886927 G C 1 0 0 0 0 1 0 0 0 16402 1165 41 4 4 TLR7 23 12886927 Missense_Mutation SNP G C3N-00556_T 9776793 12886927 143153968 491 16620 FANCB 0 . GRCh38 X 14864767 14864767 + Missense_Mutation SNP G G C rs199762452 C3N-00556_T C3N-00556_N G G c.744C>G p.Ile248Met p.I248M ENST00000398334 3/10 133 114 19 210 210 0 strelka-varscan-mutect FANCB,missense_variant,p.Ile248Met,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Ile248Met,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Ile248Met,ENST00000452869,;FANCB,downstream_gene_variant,,ENST00000489126,; C ENST00000398334 Transcript missense_variant 1012/3008 744/2580 248/859 I/M atC/atG rs199762452 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 deleterious(0.01) 3/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS rs199762452 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 14864767 14864767 G C 1 0 0 0 0 1 0 0 0 5522 1280 45 4 4 FANCB 23 14864767 Missense_Mutation SNP G C3N-00556_T 1977840 14864767 141176128 492 16621 DMD 0 . GRCh38 X 32438376 32438376 + Silent SNP C C T rs377156960 C3N-00556_T C3N-00556_N C C c.3936G>A p.= p.L1312L ENST00000357033 29/79 139 129 10 239 239 0 strelka-varscan-mutect DMD,synonymous_variant,p.=,ENST00000357033,NM_000109.3,NM_004006.2;DMD,synonymous_variant,p.=,ENST00000378677,NM_004010.3,NM_004009.3;DMD,synonymous_variant,p.=,ENST00000620040,;DMD,synonymous_variant,p.=,ENST00000619831,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000488902,; T ENST00000357033 Transcript synonymous_variant 4143/13956 3936/11058 1312/3685 L ttG/ttA rs377156960 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 29/79 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS rs377156960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 32438376 32438376 C T 1 0 0 0 0 0 0 0 1 4387 825 29 3 3 DMD 23 32438376 Silent SNP C C3N-00556_T 17573609 32438376 123602519 493 16622 TBC1D25 0 . GRCh38 X 48559663 48559663 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.755G>A p.Arg252Gln p.R252Q ENST00000376771 6/6 67 54 13 77 77 0 strelka-varscan-mutect TBC1D25,missense_variant,p.Arg252Gln,ENST00000376771,NM_002536.2;TBC1D25,downstream_gene_variant,,ENST00000418627,;TBC1D25,non_coding_transcript_exon_variant,,ENST00000476141,;TBC1D25,non_coding_transcript_exon_variant,,ENST00000494495,;TBC1D25,3_prime_UTR_variant,,ENST00000481090,; A ENST00000376771 Transcript missense_variant 1096/4042 755/2067 252/688 R/Q cGa/cAa 1 1 TBC1D25 HGNC HGNC:8092 protein_coding YES CCDS35242.1 ENSP00000365962 Q3MII6 UPI0000160685 NM_002536.2 tolerated(0.98) 6/6 PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF34,hmmpanther:PTHR22957,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 48559663 48559663 G A 1 0 0 0 0 1 0 0 0 16015 1058 37 1 1 TBC1D25 23 48559663 Missense_Mutation SNP G C3N-00556_T 16121287 48559663 107481232 494 16623 GNL3L 0 . GRCh38 X 54558570 54558570 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.1581G>C p.Gln527His p.Q527H ENST00000336470 15/16 219 196 23 190 190 0 strelka-varscan-mutect GNL3L,missense_variant,p.Gln527His,ENST00000336470,NM_019067.5;GNL3L,missense_variant,p.Gln527His,ENST00000360845,NM_001184819.1; C ENST00000336470 Transcript missense_variant 1720/2357 1581/1749 527/582 Q/H caG/caC 1 1 GNL3L HGNC HGNC:25553 protein_coding YES CCDS14360.1 ENSP00000338573 Q9NVN8 A0A024R9Y6 UPI000006CF81 NM_019067.5 deleterious(0) 15/16 hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF27 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 54558570 54558570 G C 1 0 0 0 0 1 0 0 0 6417 933 33 4 4 GNL3L 23 54558570 Missense_Mutation SNP G C3N-00556_T 5998907 54558570 101482325 495 16624 ITIH6 0 . GRCh38 X 54788510 54788510 + Silent SNP C C A novel C3N-00556_T C3N-00556_N C C c.756G>T p.= p.V252V ENST00000218436 5/13 50 33 17 57 57 0 strelka-varscan-mutect ITIH6,synonymous_variant,p.=,ENST00000218436,NM_198510.2;ITIH6,non_coding_transcript_exon_variant,,ENST00000498398,; A ENST00000218436 Transcript synonymous_variant 786/4968 756/3942 252/1313 V gtG/gtT 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 5/13 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 54788510 54788510 C A 1 0 0 0 0 0 0 0 1 7814 581 21 2 2 ITIH6 23 54788510 Silent SNP C C3N-00556_T 229940 54788510 101252385 496 16625 PAGE2 0 . GRCh38 X 55090579 55090579 + Missense_Mutation SNP G G T C3N-00556_T C3N-00556_N G G c.162G>T p.Glu54Asp p.E54D ENST00000374968 3/5 89 75 14 143 143 0 strelka-varscan-mutect PAGE2,missense_variant,p.Glu54Asp,ENST00000374968,NM_207339.3;PAGE2,missense_variant,p.Glu54Asp,ENST00000449097,;PAGE2,intron_variant,,ENST00000374965,; T ENST00000374968 Transcript missense_variant 266/551 162/336 54/111 E/D gaG/gaT COSM1123624 1 1 PAGE2 HGNC HGNC:31804 protein_coding YES CCDS14367.1 ENSP00000364107 Q7Z2X7 UPI0000160CEC NM_207339.3 tolerated(0.18) 3/5 hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF14,Pfam_domain:PF05831,SMART_domains:SM01379 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 55090579 55090579 G T 1 0 0 0 0 1 0 0 0 11468 933 33 2 2 PAGE2 23 55090579 Missense_Mutation SNP G C3N-00556_T 302069 55090579 100950316 497 16626 OGT 0 . GRCh38 X 71573719 71573719 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.3066G>C p.Gln1022His p.Q1022H ENST00000373719 22/22 93 79 14 115 115 0 strelka-varscan-mutect OGT,missense_variant,p.Gln1022His,ENST00000373719,NM_181672.2;OGT,missense_variant,p.Gln1012His,ENST00000373701,NM_181673.2;ACRC,upstream_gene_variant,,ENST00000373696,NM_052957.4;OGT,non_coding_transcript_exon_variant,,ENST00000488174,; C ENST00000373719 Transcript missense_variant 3283/5461 3066/3141 1022/1046 Q/H caG/caC 1 1 OGT HGNC HGNC:8127 protein_coding YES CCDS14414.1 ENSP00000362824 O15294 UPI0000073C9F NM_181672.2 tolerated(0.07) 22/22 Pfam_domain:PF13844 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 71573719 71573719 G C 1 0 0 0 0 1 0 0 0 10922 933 33 4 4 OGT 23 71573719 Missense_Mutation SNP G C3N-00556_T 16483140 71573719 84467176 498 16627 MAGEE2 0 . GRCh38 X 75784620 75784620 + Silent SNP C C T rs369383225 C3N-00556_T C3N-00556_N C C c.432G>A p.= p.L144L ENST00000373359 1/1 94 80 14 116 116 0 strelka-varscan-mutect MAGEE2,synonymous_variant,p.=,ENST00000373359,NM_138703.4; T ENST00000373359 Transcript synonymous_variant 617/2249 432/1572 144/523 L ctG/ctA rs369383225 1 -1 MAGEE2 HGNC HGNC:24935 protein_coding YES CCDS14431.1 ENSP00000362457 Q8TD90 UPI0000071D2B NM_138703.4 1/1 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF7,SMART_domains:SM01373 LOW 1 SNV 1 PASS rs369383225 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 75784620 75784620 C T 1 0 0 0 0 0 0 0 1 9104 813 29 3 3 MAGEE2 23 75784620 Silent SNP C C3N-00556_T 4210901 75784620 80256275 499 16628 ARMCX4 0 . GRCh38 X 101489814 101489814 + Missense_Mutation SNP C C T novel C3N-00556_T C3N-00556_N C C c.1225C>T p.His409Tyr p.H409Y ENST00000423738 2/2 148 134 14 137 137 0 strelka-varscan-mutect ARMCX4,missense_variant,p.His409Tyr,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; T ENST00000423738 Transcript missense_variant 1427/7424 1225/6873 409/2290 H/Y Cac/Tac 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 deleterious(0.01) 2/2 hmmpanther:PTHR15712,hmmpanther:PTHR15712:SF21 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 101489814 101489814 C T 1 0 0 0 0 1 0 0 0 1102 826 29 3 3 ARMCX4 23 101489814 Missense_Mutation SNP C C3N-00556_T 25705194 101489814 54551081 500 16629 TCP11X2 0 . GRCh38 X 102463196 102463196 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.574C>T p.Pro192Ser p.P192S ENST00000453326 7/10 612 530 82 654 654 0 strelka-varscan-mutect TCP11X2,missense_variant,p.Pro192Ser,ENST00000453326,NM_001277423.1;NXF2B,intron_variant,,ENST00000618881,;NXF2B,upstream_gene_variant,,ENST00000618302,;TCP11X2,non_coding_transcript_exon_variant,,ENST00000462555,;TCP11X2,intron_variant,,ENST00000429905,; A ENST00000453326 Transcript missense_variant 903/1747 574/1224 192/407 P/S Cca/Tca 1 -1 TCP11X2 HGNC HGNC:48335 protein_coding YES CCDS59530.1 ENSP00000392879 Q5H9J9 UPI00004A2DFE NM_001277423.1 tolerated(0.1) 7/10 hmmpanther:PTHR12832:SF21,hmmpanther:PTHR12832,Pfam_domain:PF05794 MODERATE 1 SNV 2 1 PASS . . 6 204 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 102463196 102463196 G A 1 0 0 0 0 1 0 0 0 16123 1174 41 3 3 TCP11X2 23 102463196 Missense_Mutation SNP G C3N-00556_T 973382 102463196 53577699 501 16630 TBC1D8B 0 . GRCh38 X 106827358 106827358 + Silent SNP C C T novel C3N-00556_T C3N-00556_N C C c.1224C>T p.= p.I408I ENST00000481617 7/7 84 70 14 103 103 0 strelka-varscan-mutect TBC1D8B,synonymous_variant,p.=,ENST00000481617,;TBC1D8B,intron_variant,,ENST00000357242,NM_017752.2;TBC1D8B,intron_variant,,ENST00000276175,;TBC1D8B,intron_variant,,ENST00000310452,NM_198881.1;MORC4,intron_variant,,ENST00000604604,; T ENST00000481617 Transcript synonymous_variant 1373/4098 1224/1260 408/419 I atC/atT 1 1 TBC1D8B HGNC HGNC:24715 protein_coding ENSP00000421375 D6RFZ2 UPI00005A931C 7/7 LOW SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 106827358 106827358 C T 1 0 0 0 0 0 0 0 1 16031 816 29 3 3 TBC1D8B 23 106827358 Silent SNP C C3N-00556_T 4364162 106827358 49213537 502 16631 MID2 0 . GRCh38 X 107924489 107924489 + Nonsense_Mutation SNP C C T rs777521293 C3N-00556_T C3N-00556_N C C c.1582C>T p.Arg528Ter p.R528* ENST00000262843 8/10 48 36 12 70 70 0 strelka-mutect MID2,stop_gained,p.Arg528Ter,ENST00000262843,NM_012216.3;MID2,stop_gained,p.Arg498Ter,ENST00000443968,NM_052817.2;RP6-191P20.4,intron_variant,,ENST00000430140,;MID2,non_coding_transcript_exon_variant,,ENST00000474517,; T ENST00000262843 Transcript stop_gained 2130/2876 1582/2208 528/735 R/* Cga/Tga rs777521293 1 1 MID2 HGNC HGNC:7096 protein_coding YES CCDS14532.2 ENSP00000262843 Q9UJV3 UPI0000D4F411 NM_012216.3 8/10 Gene3D:2.60.40.10,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF283,Superfamily_domains:SSF49265,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS rs777521293 . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 T 4 4 54 107924489 107924489 C T 1 0 0 0 0 0 1 0 0 9538 644 23 1 1 MID2 23 107924489 Nonsense_Mutation SNP C C3N-00556_T 1097131 107924489 48116406 503 16632 CXorf56 0 . GRCh38 X 119560290 119560290 + Nonsense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.220G>T p.Glu74Ter p.E74* ENST00000536133 2/6 106 67 39 132 132 0 strelka-varscan-mutect CXorf56,stop_gained,p.Glu25Ter,ENST00000320339,NM_001170569.1;CXorf56,stop_gained,p.Glu74Ter,ENST00000536133,NM_022101.3,NM_001170570.1; A ENST00000536133 Transcript stop_gained 273/1089 220/627 74/208 E/* Gag/Tag 1 -1 CXorf56 HGNC HGNC:26239 protein_coding YES CCDS55485.1 ENSP00000441786 Q9H5V9 UPI0001C0B3BE NM_022101.3,NM_001170570.1 2/6 hmmpanther:PTHR13420,hmmpanther:PTHR13420:SF4 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 54 119560290 119560290 C A 1 0 0 0 0 0 1 0 0 3916 835 29 2 2 CXorf56 23 119560290 Nonsense_Mutation SNP C C3N-00556_T 11635801 119560290 36480605 504 16633 THOC2 0 . GRCh38 X 123619408 123619408 + Missense_Mutation SNP G G A novel C3N-00556_T C3N-00556_N G G c.4304C>T p.Ser1435Leu p.S1435L ENST00000245838 33/39 73 42 31 55 55 0 strelka-varscan-mutect THOC2,missense_variant,p.Ser1435Leu,ENST00000245838,NM_001081550.1;THOC2,missense_variant,p.Ser1435Leu,ENST00000355725,;THOC2,missense_variant,p.Ser1320Leu,ENST00000491737,;THOC2,missense_variant,p.Ser230Leu,ENST00000441692,;THOC2,missense_variant,p.Ser256Leu,ENST00000618150,;THOC2,missense_variant,p.Ser31Leu,ENST00000448128,;THOC2,missense_variant,p.Ser24Leu,ENST00000416618,;THOC2,downstream_gene_variant,,ENST00000438358,;THOC2,non_coding_transcript_exon_variant,,ENST00000497887,;THOC2,3_prime_UTR_variant,,ENST00000432353,;THOC2,non_coding_transcript_exon_variant,,ENST00000496830,;THOC2,non_coding_transcript_exon_variant,,ENST00000464992,;THOC2,downstream_gene_variant,,ENST00000459945,;THOC2,downstream_gene_variant,,ENST00000464604,;THOC2,downstream_gene_variant,,ENST00000464161,;THOC2,downstream_gene_variant,,ENST00000464982,; A ENST00000245838 Transcript missense_variant 4336/5609 4304/4782 1435/1593 S/L tCa/tTa 1 -1 THOC2 HGNC HGNC:19073 protein_coding YES CCDS43988.1 ENSP00000245838 Q8NI27 UPI00001D7C42 NM_001081550.1 tolerated(0.05) 33/39 hmmpanther:PTHR21597,hmmpanther:PTHR21597:SF1 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 54 123619408 123619408 G A 1 0 0 0 0 1 0 0 0 16300 1294 45 3 3 THOC2 23 123619408 Missense_Mutation SNP G C3N-00556_T 4059118 123619408 32421487 505 16634 ELF4 0 . GRCh38 X 130069376 130069376 + Missense_Mutation SNP C C G novel C3N-00556_T C3N-00556_N C C c.1111G>C p.Asp371His p.D371H ENST00000308167 8/9 205 185 20 176 176 0 strelka-varscan-mutect ELF4,missense_variant,p.Asp371His,ENST00000308167,NM_001421.3;ELF4,missense_variant,p.Asp371His,ENST00000335997,NM_001127197.1;ELF4,missense_variant,p.Arg370Thr,ENST00000615377,;ELF4,downstream_gene_variant,,ENST00000434609,; G ENST00000308167 Transcript missense_variant 1491/4165 1111/1992 371/663 D/H Gac/Cac 1 -1 ELF4 HGNC HGNC:3319 protein_coding YES CCDS14617.1 ENSP00000311280 Q99607 UPI0000072B32 NM_001421.3 tolerated(0.55) 8/9 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF170 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 54 130069376 130069376 C G 1 0 0 0 0 1 0 0 0 4889 913 32 4 4 ELF4 23 130069376 Missense_Mutation SNP C C3N-00556_T 6449968 130069376 25971519 506 16635 GPR50 0 . GRCh38 X 151180631 151180631 + Missense_Mutation SNP G G T novel C3N-00556_T C3N-00556_N G G c.1048G>T p.Asp350Tyr p.D350Y ENST00000218316 2/2 160 80 80 139 139 0 strelka-varscan-mutect GPR50,missense_variant,p.Asp350Tyr,ENST00000218316,NM_004224.3;AF003625.3,upstream_gene_variant,,ENST00000602313,;GPR50-AS1,upstream_gene_variant,,ENST00000454196,; T ENST00000218316 Transcript missense_variant 1117/1951 1048/1854 350/617 D/Y Gac/Tac 1 1 GPR50 HGNC HGNC:4506 protein_coding YES CCDS44012.1 ENSP00000218316 Q13585 UPI000013C755 NM_004224.3 deleterious(0) 2/2 Low_complexity_(Seg):seg,Prints_domain:PR01151 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 54 151180631 151180631 G T 1 0 0 0 0 1 0 0 0 6582 942 33 2 2 GPR50 23 151180631 Missense_Mutation SNP G C3N-00556_T 21111255 151180631 4860264 507 16636 GABRA3 0 . GRCh38 X 152168293 152168293 + Silent SNP G G A novel C3N-00556_T C3N-00556_N G G c.1414C>T p.= p.L472L ENST00000370314 10/10 141 99 42 117 117 0 strelka-varscan-mutect GABRA3,synonymous_variant,p.=,ENST00000370314,NM_000808.3;GABRA3,synonymous_variant,p.=,ENST00000535043,;RP11-329E24.6,intron_variant,,ENST00000453915,; A ENST00000370314 Transcript synonymous_variant 1653/3712 1414/1479 472/492 L Ctg/Ttg 1 -1 GABRA3 HGNC HGNC:4077 protein_coding YES CCDS14706.1 ENSP00000359337 P34903 UPI000002D730 NM_000808.3 10/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF216,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:1.20.58.390,Superfamily_domains:SSF90112,Prints_domain:PR00253 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 54 152168293 152168293 G A 1 0 0 0 0 0 0 0 1 6033 933 33 3 3 GABRA3 23 152168293 Silent SNP G C3N-00556_T 987662 152168293 3872602 508 16637 BGN 0 . GRCh38 X 153505258 153505258 + Missense_Mutation SNP G G C novel C3N-00556_T C3N-00556_N G G c.259G>C p.Glu87Gln p.E87Q ENST00000331595 3/8 52 40 12 29 29 0 strelka-varscan-mutect BGN,missense_variant,p.Glu87Gln,ENST00000331595,NM_001711.4;BGN,missense_variant,p.Glu87Gln,ENST00000431891,;BGN,splice_acceptor_variant,,ENST00000480756,;BGN,non_coding_transcript_exon_variant,,ENST00000472615,;BGN,upstream_gene_variant,,ENST00000492658,; C ENST00000331595 Transcript missense_variant 445/2402 259/1107 87/368 E/Q Gag/Cag 1 1 BGN HGNC HGNC:1044 protein_coding YES CCDS14721.1 ENSP00000327336 P21810 UPI000003BDBA NM_001711.4 tolerated(0.29) 3/8 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF6,Gene3D:3.80.10.10,PIRSF_domain:PIRSF002490,Pfam_domain:PF01462,SMART_domains:SM00013,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 54 153505258 153505258 G C 1 0 0 0 0 1 0 0 0 1566 943 33 4 4 BGN 23 153505258 Missense_Mutation SNP G C3N-00556_T 1336965 153505258 2535637 509 16638 PDZD4 0 . GRCh38 X 153804198 153804198 + Missense_Mutation SNP C C T C3N-00556_T C3N-00556_N C C c.1483G>A p.Glu495Lys p.E495K ENST00000393758 8/8 58 53 5 59 59 0 strelka-mutect PDZD4,missense_variant,p.Glu495Lys,ENST00000393758,NM_001303515.1,NM_001303513.1,NM_001303512.1;PDZD4,missense_variant,p.Glu489Lys,ENST00000164640,NM_001303516.1,NM_032512.3;PDZD4,missense_variant,p.Glu380Lys,ENST00000544474,NM_001303514.1;PDZD4,downstream_gene_variant,,ENST00000475140,;PDZD4,downstream_gene_variant,,ENST00000483693,;PDZD4,downstream_gene_variant,,ENST00000484792,;PDZD4,downstream_gene_variant,,ENST00000468491,;PDZD4,downstream_gene_variant,,ENST00000480418,;PDZD4,downstream_gene_variant,,ENST00000480650,; T ENST00000393758 Transcript missense_variant 1733/3763 1483/2328 495/775 E/K Gag/Aag COSM3913631 1 -1 PDZD4 HGNC HGNC:21167 protein_coding YES CCDS78518.1 ENSP00000377355 Q17RL8 UPI0000211CB2 NM_001303515.1,NM_001303513.1,NM_001303512.1 deleterious(0.01) 8/8 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF4,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.08612 1 1 1 1 0 T 3 4 54 153804198 153804198 C T 1 0 0 0 0 1 0 0 0 11791 893 31 1 1 PDZD4 23 153804198 Missense_Mutation SNP C C3N-00556_T 298940 153804198 2236697 510 16639 CTAG2 0 . GRCh38 X 154652541 154652541 + Silent SNP C C T C3N-00556_T C3N-00556_N C C c.360G>A p.= p.G120G ENST00000247306 2/2 101 76 25 71 71 0 strelka-varscan-mutect CTAG2,synonymous_variant,p.=,ENST00000247306,NM_020994.4;CTAG2,synonymous_variant,p.=,ENST00000369585,NM_172377.4;IKBKGP1,upstream_gene_variant,,ENST00000612193,;AF277315.13,upstream_gene_variant,,ENST00000442033,; T ENST00000247306 Transcript synonymous_variant 424/993 360/633 120/210 G ggG/ggA COSM5153717,COSM5153718,COSM5153719 1 -1 CTAG2 HGNC HGNC:2492 protein_coding YES CCDS14759.1 ENSP00000247306 O75638 UPI000006D049 NM_020994.4 2/2 Pfam_domain:PF09341,hmmpanther:PTHR31283,hmmpanther:PTHR31283:SF4 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 54 154652541 154652541 C T 1 0 0 0 0 0 0 0 1 3795 610 22 3 3 CTAG2 23 154652541 Silent SNP C C3N-00556_T 848343 154652541 1388354 511 16640 RAB39B 0 . GRCh38 X 155261055 155261055 + Missense_Mutation SNP C C A novel C3N-00556_T C3N-00556_N C C c.390G>T p.Gln130His p.Q130H ENST00000369454 2/2 78 73 5 87 87 0 strelka-varscan-mutect RAB39B,missense_variant,p.Gln130His,ENST00000369454,NM_171998.3; A ENST00000369454 Transcript missense_variant 691/3505 390/642 130/213 Q/H caG/caT 1 -1 RAB39B HGNC HGNC:16499 protein_coding YES CCDS14766.1 ENSP00000358466 Q96DA2 UPI00000412A6 NM_171998.3 tolerated(0.14) 2/2 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF395,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -11.30334 1 1 1 1 0 A 3 1 54 155261055 155261055 C A 1 0 0 0 0 1 0 0 0 13089 912 32 2 2 RAB39B 23 155261055 Missense_Mutation SNP C C3N-00556_T 608514 155261055 779840 512 16641 WDR78 0 . GRCh38 1 66862146 66862146 + Splice_Site SNP C C G novel C3N-00559_T C3N-00559_N C C c.1096+1G>C p.X366_splice ENST00000371026 18 14 4 76 76 0 varscan-mutect WDR78,splice_donor_variant,,ENST00000371026,NM_024763.4;WDR78,splice_donor_variant,,ENST00000464352,;WDR78,splice_donor_variant,,ENST00000371023,NM_207014.2;WDR78,splice_donor_variant,,ENST00000469450,;WDR78,splice_donor_variant,,ENST00000531552,;WDR78,splice_donor_variant,,ENST00000493572,;WDR78,splice_donor_variant,,ENST00000491297,;WDR78,downstream_gene_variant,,ENST00000531980,; G ENST00000371026 Transcript splice_donor_variant -/3848 1096/2547 366/848 1 -1 WDR78 HGNC HGNC:26252 protein_coding YES CCDS635.1 ENSP00000360065 Q5VTH9 UPI00004561EF NM_024763.4 7/16 HIGH 1 SNV 1 1 PASS rs1207293612 . 0 199 6 5 0 0 0 0 -10.18698 0.9979394 1 1 1 0 G 5 3 55 66862146 66862146 C G 1 0 0 0 0 0 0 1 0 17884 579 20 4 4 WDR78 1 66862146 Splice_Site SNP C C3N-00559_T 66862146 182094276 1 16642 62 2 WDR78 0 . GRCh38 1 66862147 66862147 + Missense_Mutation SNP T T C novel C3N-00559_T C3N-00559_N T T c.1096A>G p.Asn366Asp p.N366D ENST00000371026 7/17 19 15 4 76 76 0 varscan-mutect WDR78,missense_variant,p.Asn366Asp,ENST00000371026,NM_024763.4;WDR78,missense_variant,p.Asn132Asp,ENST00000464352,;WDR78,missense_variant,p.Asn366Asp,ENST00000371023,NM_207014.2;WDR78,missense_variant,p.Thr100Ala,ENST00000469450,;WDR78,missense_variant,p.Lys53Glu,ENST00000531552,;WDR78,splice_region_variant,,ENST00000493572,;WDR78,splice_region_variant,,ENST00000491297,;WDR78,downstream_gene_variant,,ENST00000531980,; C ENST00000371026 Transcript missense_variant,splice_region_variant 1152/3848 1096/2547 366/848 N/D Aat/Gat 1 -1 WDR78 HGNC HGNC:26252 protein_coding YES CCDS635.1 ENSP00000360065 Q5VTH9 UPI00004561EF NM_024763.4 tolerated(0.79) 7/17 MODERATE 1 SNV 1 1 PASS . . 0 201 5 3 0 0 0 0 -10.28413 0.9998528 1 1 1 0 C 3 2 55 66862147 66862147 T C 1 0 0 0 0 1 0 0 0 17884 1623 56 5 5 WDR78 1 66862147 Missense_Mutation SNP T C3N-00559_T 1 66862147 182094275 2 16643 62 2 ZC3H6 0 . GRCh38 2 112309957 112309957 + Missense_Mutation SNP T T A novel C3N-00559_T C3N-00559_N T T c.409T>A p.Tyr137Asn p.Y137N ENST00000409871 4/12 56 52 4 311 311 0 varscan-mutect ZC3H6,missense_variant,p.Tyr137Asn,ENST00000409871,NM_198581.2;ZC3H6,missense_variant,p.Tyr137Asn,ENST00000343936,;ZC3H6,non_coding_transcript_exon_variant,,ENST00000476511,; A ENST00000409871 Transcript missense_variant 810/11542 409/3570 137/1189 Y/N Tat/Aat 1 1 ZC3H6 HGNC HGNC:24762 protein_coding YES CCDS46393.1 ENSP00000386764 P61129 UPI00004215E8 NM_198581.2 deleterious(0.01) 4/12 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF22 MODERATE 1 SNV 2 1 PASS rs1280185213 . 0 195 0 0 14 0 0 0 -2.728568 0.01377469 1 1 0 0 A 3 1 55 112309957 112309957 T A 1 0 0 0 0 1 0 0 0 18146 1406 49 4 4 ZC3H6 2 112309957 Missense_Mutation SNP T C3N-00559_T 112309957 129883572 3 16644 HECW2 0 . GRCh38 2 196325112 196325112 + Silent SNP G G A novel C3N-00559_T C3N-00559_N G G c.609C>T p.= p.F203F ENST00000260983 6/29 46 38 8 83 83 0 strelka-mutect HECW2,synonymous_variant,p.=,ENST00000260983,NM_020760.2;HECW2,intron_variant,,ENST00000409111,NM_001304840.1; A ENST00000260983 Transcript synonymous_variant 792/11809 609/4719 203/1572 F ttC/ttT 1 -1 HECW2 HGNC HGNC:29853 protein_coding YES CCDS33354.1 ENSP00000260983 Q9P2P5 UPI00001A75E8 NM_020760.2 6/29 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF127,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.45491 1 1 1 1 0 A 2 1 55 196325112 196325112 G A 1 0 0 0 0 0 0 0 1 6925 1281 45 3 3 HECW2 2 196325112 Silent SNP G C3N-00559_T 84015155 196325112 45868417 4 16645 COL4A3 0 . GRCh38 2 227309241 227309241 + Missense_Mutation SNP G G A rs574102153 C3N-00559_T C3N-00559_N G G c.4678G>A p.Val1560Ile p.V1560I ENST00000396578 50/52 322 292 30 462 462 0 strelka-varscan-mutect COL4A3,missense_variant,p.Val1560Ile,ENST00000396578,NM_000091.4;AC097662.2,intron_variant,,ENST00000439598,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000433324,;COL4A3,non_coding_transcript_exon_variant,,ENST00000469504,;COL4A3,downstream_gene_variant,,ENST00000471862,; A ENST00000396578 Transcript missense_variant 4840/8097 4678/5013 1560/1670 V/I Gtt/Att rs574102153,COSM4092100,COSM4092101 1 1 COL4A3 HGNC HGNC:2204 protein_coding YES CCDS42829.1 ENSP00000379823 Q01955 UPI000013E9F3 NM_000091.4 tolerated(0.25) 50/52 PROSITE_profiles:PS51403,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF598,Pfam_domain:PF01413,Gene3D:1t60D00,SMART_domains:SM00111,Superfamily_domains:SSF56436 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs574102153 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 55 227309241 227309241 G A 1 0 0 0 0 1 0 0 0 3480 1145 40 1 1 COL4A3 2 227309241 Missense_Mutation SNP G C3N-00559_T 30984129 227309241 14884288 5 16646 ALPI 0 . GRCh38 2 232458888 232458888 + Silent SNP G G A C3N-00559_T C3N-00559_N G G c.1329G>A p.= p.A443A ENST00000295463 11/11 297 219 78 133 133 0 strelka-varscan-mutect ALPI,synonymous_variant,p.=,ENST00000295463,NM_001631.4;ALPI,3_prime_UTR_variant,,ENST00000457560,; A ENST00000295463 Transcript synonymous_variant 1406/2550 1329/1587 443/528 A gcG/gcA COSM1406220 1 1 ALPI HGNC HGNC:437 protein_coding YES CCDS2492.1 ENSP00000295463 P09923 A0A024R4A2 UPI0000131FFE NM_001631.4 11/11 hmmpanther:PTHR11596:SF31,hmmpanther:PTHR11596,Pfam_domain:PF00245,Gene3D:3.40.720.10,SMART_domains:SM00098,Superfamily_domains:SSF53649 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 55 232458888 232458888 G A 1 0 0 0 0 0 0 0 1 643 1103 39 1 1 ALPI 2 232458888 Silent SNP G C3N-00559_T 5149647 232458888 9734641 6 16647 WNT7A 0 . GRCh38 3 13818970 13818970 + Missense_Mutation SNP G G A C3N-00559_T C3N-00559_N G G c.1024C>T p.Arg342Cys p.R342C ENST00000285018 4/4 91 81 10 39 39 0 strelka-varscan-mutect WNT7A,missense_variant,p.Arg342Cys,ENST00000285018,NM_004625.3; A ENST00000285018 Transcript missense_variant 1329/4041 1024/1050 342/349 R/C Cgc/Tgc COSM3124098 1 -1 WNT7A HGNC HGNC:12786 protein_coding YES CCDS2616.1 ENSP00000285018 O00755 UPI0000033777 NM_004625.3 deleterious(0) 4/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF78,SMART_domains:SM00097 1 MODERATE 1 SNV 1 1 1 PASS rs1426757027 . 0 200 10 0 0 0 0 0 -19.9074 0.999968 1 1 1 0 A 3 1 55 13818970 13818970 G A 1 0 0 0 0 1 0 0 0 17950 1087 38 1 1 WNT7A 3 13818970 Missense_Mutation SNP G C3N-00559_T 13818970 184476589 7 16648 SCN5A 0 . GRCh38 3 38560229 38560229 + Missense_Mutation SNP T T C novel C3N-00559_T C3N-00559_N T T c.4163A>G p.Asn1388Ser p.N1388S ENST00000413689 23/28 249 157 92 326 326 0 strelka-varscan SCN5A,missense_variant,p.Asn1388Ser,ENST00000413689,NM_001099404.1;SCN5A,missense_variant,p.Asn1388Ser,ENST00000333535,NM_198056.2;SCN5A,missense_variant,p.Asn1388Ser,ENST00000425664,NM_001099405.1;SCN5A,missense_variant,p.Asn1387Ser,ENST00000423572,NM_000335.4;SCN5A,missense_variant,p.Asn1334Ser,ENST00000451551,NM_001160161.1;SCN5A,missense_variant,p.Asn1388Ser,ENST00000414099,;SCN5A,missense_variant,p.Asn1387Ser,ENST00000455624,NM_001160160.1;SCN5A,missense_variant,p.Asn1334Ser,ENST00000450102,;SCN5A,missense_variant,p.Asn1334Ser,ENST00000449557,; C ENST00000413689 Transcript missense_variant 4357/8504 4163/6051 1388/2016 N/S aAc/aGc 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 tolerated(0.09) 23/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 38560229 38560229 T C 1 0 0 0 0 1 0 0 0 14191 1725 60 5 5 SCN5A 3 38560229 Missense_Mutation SNP T C3N-00559_T 24741259 38560229 159735330 8 16649 NR3C2 0 . GRCh38 4 148435572 148435572 + Missense_Mutation SNP T T A novel C3N-00559_T C3N-00559_N T T c.1289A>T p.Glu430Val p.E430V ENST00000358102 2/9 93 81 12 312 312 0 strelka-varscan-mutect NR3C2,missense_variant,p.Glu430Val,ENST00000625323,;NR3C2,missense_variant,p.Glu430Val,ENST00000358102,NM_000901.4;NR3C2,missense_variant,p.Glu430Val,ENST00000344721,;NR3C2,missense_variant,p.Glu430Val,ENST00000512865,NM_001166104.1;NR3C2,missense_variant,p.Glu430Val,ENST00000511528,;NR3C2,missense_variant,p.Glu430Val,ENST00000342437,; A ENST00000358102 Transcript missense_variant 1652/5893 1289/2955 430/984 E/V gAa/gTa 1 -1 NR3C2 HGNC HGNC:7979 protein_coding YES CCDS3772.1 ENSP00000350815 B0ZBF6 UPI000013DC6D NM_000901.4 deleterious_low_confidence(0) 2/9 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF22 MODERATE 1 SNV 1 1 PASS rs971716617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 55 148435572 148435572 T A 1 0 0 0 0 1 0 0 0 10687 1783 62 4 4 NR3C2 4 148435572 Missense_Mutation SNP T C3N-00559_T 148435572 41778983 9 16650 PPARGC1B 0 . GRCh38 5 149833376 149833376 + Nonsense_Mutation SNP G G T novel C3N-00559_T C3N-00559_N G G c.1303G>T p.Glu435Ter p.E435* ENST00000309241 5/12 577 544 33 196 196 0 strelka-varscan-mutect PPARGC1B,stop_gained,p.Glu435Ter,ENST00000309241,NM_133263.3;PPARGC1B,stop_gained,p.Glu435Ter,ENST00000394320,;PPARGC1B,stop_gained,p.Glu371Ter,ENST00000403750,NM_001172699.1;PPARGC1B,stop_gained,p.Glu396Ter,ENST00000360453,NM_001172698.1;PPARGC1B,stop_gained,p.Glu122Ter,ENST00000434684,; T ENST00000309241 Transcript stop_gained 1335/10568 1303/3072 435/1023 E/* Gaa/Taa 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 5/12 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 55 149833376 149833376 G T 1 0 0 0 0 0 1 0 0 12410 1175 41 2 2 PPARGC1B 5 149833376 Nonsense_Mutation SNP G C3N-00559_T 149833376 31704883 10 16651 PDGFRB 0 . GRCh38 5 150121899 150121899 + Silent SNP G G A C3N-00559_T C3N-00559_N G G c.2325C>T p.= p.Y775Y ENST00000261799 16/23 221 201 20 160 160 0 strelka-varscan-mutect PDGFRB,synonymous_variant,p.=,ENST00000261799,NM_002609.3;PDGFRB,non_coding_transcript_exon_variant,,ENST00000519575,;PDGFRB,non_coding_transcript_exon_variant,,ENST00000521723,;PDGFRB,3_prime_UTR_variant,,ENST00000520579,;PDGFRB,downstream_gene_variant,,ENST00000520229,; A ENST00000261799 Transcript synonymous_variant 2795/5717 2325/3321 775/1106 Y taC/taT COSM1064296 1 -1 PDGFRB HGNC HGNC:8804 protein_coding YES CCDS4303.1 ENSP00000261799 P09619 UPI0000131791 NM_002609.3 16/23 Pfam_domain:PF07714,PIRSF_domain:PIRSF000615,PIRSF_domain:PIRSF500948,PROSITE_profiles:PS50011,SMART_domains:SM00219 1 LOW 1 SNV 1 1 1 PASS rs1472203888 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 55 150121899 150121899 G A 1 0 0 0 0 0 0 0 1 11750 1140 40 1 1 PDGFRB 5 150121899 Silent SNP G C3N-00559_T 288523 150121899 31416360 11 16652 SOX30 0 . GRCh38 5 157648807 157648807 + Missense_Mutation SNP G G T novel C3N-00559_T C3N-00559_N G G c.1057C>A p.Pro353Thr p.P353T ENST00000265007 2/5 212 199 13 336 336 0 strelka-varscan-mutect SOX30,missense_variant,p.Pro353Thr,ENST00000265007,NM_178424.1;SOX30,missense_variant,p.Pro353Thr,ENST00000311371,NM_007017.2;SOX30,missense_variant,p.Pro48Thr,ENST00000519442,NM_001308165.1; T ENST00000265007 Transcript missense_variant 1399/3265 1057/2262 353/753 P/T Cca/Aca 1 -1 SOX30 HGNC HGNC:30635 protein_coding YES CCDS4339.1 ENSP00000265007 O94993 UPI00001362BA NM_178424.1 deleterious(0.01) 2/5 Gene3D:1.10.30.10,Pfam_domain:PF00505,PROSITE_profiles:PS50118,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF10,Low_complexity_(Seg):seg,SMART_domains:SM00398,Superfamily_domains:SSF47095 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 157648807 157648807 G T 1 0 0 0 0 1 0 0 0 15278 1261 44 2 2 SOX30 5 157648807 Missense_Mutation SNP G C3N-00559_T 7526908 157648807 23889452 12 16653 FAF2 0 . GRCh38 5 176494057 176494057 + Missense_Mutation SNP A A G novel C3N-00559_T C3N-00559_N A A c.542A>G p.Asp181Gly p.D181G ENST00000261942 6/11 43 38 5 188 188 0 strelka-mutect FAF2,missense_variant,p.Asp181Gly,ENST00000261942,NM_014613.2;FAF2,non_coding_transcript_exon_variant,,ENST00000513627,;FAF2,non_coding_transcript_exon_variant,,ENST00000504983,; G ENST00000261942 Transcript missense_variant 595/4515 542/1338 181/445 D/G gAt/gGt 1 1 FAF2 HGNC HGNC:24666 protein_coding YES CCDS34296.1 ENSP00000261942 Q96CS3 UPI000007478A NM_014613.2 deleterious(0.03) 6/11 hmmpanther:PTHR23322,hmmpanther:PTHR23322:SF1,SMART_domains:SM00594,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 55 176494057 176494057 A G 1 0 0 0 0 1 0 0 0 5242 333 12 5 5 FAF2 5 176494057 Missense_Mutation SNP A C3N-00559_T 18845250 176494057 5044202 13 16654 MCUR1 0 . GRCh38 6 13814303 13814303 + Missense_Mutation SNP A A T novel C3N-00559_T C3N-00559_N A A c.127T>A p.Ser43Thr p.S43T ENST00000379170 1/9 1249 725 524 203 203 0 strelka-varscan-mutect MCUR1,missense_variant,p.Ser43Thr,ENST00000379170,NM_001031713.3;MCUR1,missense_variant,p.Ser43Thr,ENST00000488770,; T ENST00000379170 Transcript missense_variant 266/5471 127/1080 43/359 S/T Tct/Act 1 -1 MCUR1 HGNC HGNC:21097 protein_coding YES CCDS35495.1 ENSP00000368468 Q96AQ8 UPI0000072AC6 NM_001031713.3 tolerated_low_confidence(0.53) 1/9 MODERATE 1 SNV 1 1 PASS rs1434303141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 13814303 13814303 A T 1 0 0 0 0 1 0 0 0 9340 304 11 4 4 MCUR1 6 13814303 Missense_Mutation SNP A C3N-00559_T 13814303 156991676 14 16655 DGKB 0 . GRCh38 7 14574333 14574333 + Missense_Mutation SNP A A T novel C3N-00559_T C3N-00559_N A A c.1652T>A p.Ile551Asn p.I551N ENST00000403951 20/26 28 24 4 151 151 0 strelka-mutect DGKB,missense_variant,p.Ile551Asn,ENST00000403951,;DGKB,missense_variant,p.Ile551Asn,ENST00000399322,NM_004080.2;DGKB,missense_variant,p.Ile550Asn,ENST00000402815,;DGKB,missense_variant,p.Ile543Asn,ENST00000407950,;DGKB,missense_variant,p.Ile551Asn,ENST00000406247,NM_145695.2;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,; T ENST00000403951 Transcript missense_variant 2072/6917 1652/2415 551/804 I/N aTt/aAt 1 -1 DGKB HGNC HGNC:2850 protein_coding YES CCDS47547.1 ENSP00000385780 Q9Y6T7 UPI0000033B9B deleterious(0) 20/26 PROSITE_profiles:PS50146,hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255,Pfam_domain:PF00781,SMART_domains:SM00046,Superfamily_domains:SSF111331 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 14574333 14574333 A T 1 0 0 0 0 1 0 0 0 4272 101 4 4 4 DGKB 7 14574333 Missense_Mutation SNP A C3N-00559_T 14574333 144771640 15 16656 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-00559_T C3N-00559_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 1372 776 596 652 652 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 55 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-00559_T 40600439 55174772 104171201 16 16657 WBSCR17 0 . GRCh38 7 71665437 71665437 + Missense_Mutation SNP G G T novel C3N-00559_T C3N-00559_N G G c.1107G>T p.Glu369Asp p.E369D ENST00000333538 7/11 211 197 14 147 146 1 strelka-varscan-mutect WBSCR17,missense_variant,p.Glu369Asp,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Glu290Asp,ENST00000618959,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; T ENST00000333538 Transcript missense_variant 1741/3884 1107/1797 369/598 E/D gaG/gaT 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 deleterious(0) 7/11 Gene3D:3.90.550.10,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 71665437 71665437 G T 1 0 0 0 0 1 0 0 0 17823 991 35 2 2 WBSCR17 7 71665437 Missense_Mutation SNP G C3N-00559_T 16490665 71665437 87680536 17 16658 ZNF804B 0 . GRCh38 7 89335337 89335337 + Silent SNP C C T novel C3N-00559_T C3N-00559_N C C c.2355C>T p.= p.C785C ENST00000333190 4/4 46 33 13 245 245 0 strelka-varscan-mutect ZNF804B,synonymous_variant,p.=,ENST00000333190,NM_181646.3;ZNF804B,synonymous_variant,p.=,ENST00000611114,; T ENST00000333190 Transcript synonymous_variant 2964/4659 2355/4050 785/1349 C tgC/tgT 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 55 89335337 89335337 C T 1 0 0 0 0 0 0 0 1 18756 718 25 3 3 ZNF804B 7 89335337 Silent SNP C C3N-00559_T 17669900 89335337 70010636 18 16659 UBN2 0 . GRCh38 7 139269525 139269525 + Splice_Site DEL T T - novel C3N-00559_T C3N-00559_N T T c.1596+2delT p.X532_splice ENST00000473989 39 36 3 133 133 0 varindel-pindel UBN2,splice_donor_variant,,ENST00000473989,NM_173569.3;UBN2,splice_donor_variant,,ENST00000483726,; - ENST00000473989 Transcript splice_donor_variant -/14444 1596/4044 532/1347 1 1 UBN2 HGNC HGNC:21931 protein_coding YES CCDS43655.2 ENSP00000418648 Q6ZU65 UPI00001D74DF NM_173569.3 8/17 HIGH 1 deletion 2 1 PASS . . 0 205 4 0 0 0 0 0 -8.771766 1 1 1 1 0 - 8 5 55 139269525 139269525 T - 1 0 1 0 1 0 0 1 0 17417 1652 57 0 0 UBN2 7 139269525 Splice_Site DEL T C3N-00559_T 49934188 139269525 20076448 19 16660 ZNF282 0 . GRCh38 7 149224224 149224224 + Missense_Mutation SNP G G C rs762099755 C3N-00559_T C3N-00559_N G G c.1593G>C p.Lys531Asn p.K531N ENST00000610704 8/8 417 377 40 143 143 0 strelka-varscan-mutect ZNF282,missense_variant,p.Lys531Asn,ENST00000610704,NM_003575.3;ZNF282,intron_variant,,ENST00000479907,NM_001303481.1;ZNF282,non_coding_transcript_exon_variant,,ENST00000470381,; C ENST00000610704 Transcript missense_variant 1698/3722 1593/2016 531/671 K/N aaG/aaC rs762099755 1 1 ZNF282 HGNC HGNC:13076 protein_coding YES CCDS5895.1 ENSP00000477841 Q9UDV7 A0A090N8Y3 UPI000013D255 NM_003575.3 tolerated(0.38) 8/8 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF21,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs762099755 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 149224224 149224224 G C 1 0 0 0 0 1 0 0 0 18395 933 33 4 4 ZNF282 7 149224224 Missense_Mutation SNP G C3N-00559_T 9954699 149224224 10121749 20 16661 KAT6A 0 . GRCh38 8 41933027 41933027 + Missense_Mutation SNP G G C novel C3N-00559_T C3N-00559_N G G c.5193C>G p.Ile1731Met p.I1731M ENST00000396930 18/18 356 313 43 184 184 0 strelka-varscan-mutect KAT6A,missense_variant,p.Ile1731Met,ENST00000396930,NM_001099412.1;KAT6A,missense_variant,p.Ile1731Met,ENST00000406337,NM_001099413.1;KAT6A,missense_variant,p.Ile1731Met,ENST00000265713,NM_006766.3;KAT6A,downstream_gene_variant,,ENST00000418721,; C ENST00000396930 Transcript missense_variant 5737/9285 5193/6015 1731/2004 I/M atC/atG 1 -1 KAT6A HGNC HGNC:13013 protein_coding YES CCDS6124.1 ENSP00000380136 Q92794 UPI000013D666 NM_001099412.1 deleterious(0.01) 18/18 hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 41933027 41933027 G C 1 0 0 0 0 1 0 0 0 7898 932 33 4 4 KAT6A 8 41933027 Missense_Mutation SNP G C3N-00559_T 41933027 103205609 21 16662 KAT6A 0 . GRCh38 8 41933439 41933439 + Missense_Mutation SNP G G A novel C3N-00559_T C3N-00559_N G G c.4781C>T p.Ser1594Phe p.S1594F ENST00000396930 18/18 257 239 18 65 65 0 strelka-varscan-mutect KAT6A,missense_variant,p.Ser1594Phe,ENST00000396930,NM_001099412.1;KAT6A,missense_variant,p.Ser1594Phe,ENST00000406337,NM_001099413.1;KAT6A,missense_variant,p.Ser1594Phe,ENST00000265713,NM_006766.3;KAT6A,downstream_gene_variant,,ENST00000418721,; A ENST00000396930 Transcript missense_variant 5325/9285 4781/6015 1594/2004 S/F tCc/tTc 1 -1 KAT6A HGNC HGNC:13013 protein_coding YES CCDS6124.1 ENSP00000380136 Q92794 UPI000013D666 NM_001099412.1 deleterious(0) 18/18 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -19.99334 0.9999904 1 1 1 0 A 3 1 55 41933439 41933439 G A 1 0 0 0 0 1 0 0 0 7898 1174 41 3 3 KAT6A 8 41933439 Missense_Mutation SNP G C3N-00559_T 412 41933439 103205197 22 16663 ZNF189 0 . GRCh38 9 101409144 101409144 + Missense_Mutation SNP A A T novel C3N-00559_T C3N-00559_N A A c.1376A>T p.Asp459Val p.D459V ENST00000339664 3/3 19 12 7 139 139 0 strelka-varscan-mutect ZNF189,missense_variant,p.Asp445Val,ENST00000374861,NM_001278231.1,NM_001278232.1;ZNF189,missense_variant,p.Asp417Val,ENST00000259395,NM_197977.2;ZNF189,missense_variant,p.Asp459Val,ENST00000339664,NM_003452.3;ZNF189,3_prime_UTR_variant,,ENST00000615466,NM_001278240.1; T ENST00000339664 Transcript missense_variant 1505/3021 1376/1881 459/626 D/V gAt/gTt 1 1 ZNF189 HGNC HGNC:12980 protein_coding YES CCDS6754.1 ENSP00000342019 O75820 UPI000013FAD5 NM_003452.3 deleterious(0.01) 3/3 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF316,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.11736 1 1 1 1 0 T 3 4 55 101409144 101409144 A T 1 0 0 0 0 1 0 0 0 18333 333 12 4 4 ZNF189 9 101409144 Missense_Mutation SNP A C3N-00559_T 101409144 36985573 23 16664 GRIN3A 0 . GRCh38 9 101670210 101670210 + Missense_Mutation SNP G G C rs754316395 C3N-00559_T C3N-00559_N G G c.2202C>G p.Ile734Met p.I734M ENST00000361820 3/9 78 73 5 205 205 0 strelka-varscan GRIN3A,missense_variant,p.Ile734Met,ENST00000361820,NM_133445.2; C ENST00000361820 Transcript missense_variant 2803/7770 2202/3348 734/1115 I/M atC/atG rs754316395 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 tolerated(0.06) 3/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Pfam_domain:PF00060,Gene3D:1.10.287.70,SMART_domains:SM00079 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 101670210 101670210 G C 1 0 0 0 0 1 0 0 0 6665 1280 45 4 4 GRIN3A 9 101670210 Missense_Mutation SNP G C3N-00559_T 261066 101670210 36724507 24 16665 FNBP1 0 . GRCh38 9 129927336 129927336 + Silent SNP T T G rs139863276 C3N-00559_T C3N-00559_N T T c.648A>C p.= p.I216I ENST00000446176 8/17 37 33 4 116 116 0 varscan-mutect FNBP1,synonymous_variant,p.=,ENST00000420781,;FNBP1,synonymous_variant,p.=,ENST00000446176,NM_015033.2;FNBP1,synonymous_variant,p.=,ENST00000443566,;FNBP1,synonymous_variant,p.=,ENST00000449089,;FNBP1,synonymous_variant,p.=,ENST00000355681,;FNBP1,upstream_gene_variant,,ENST00000478129,;FNBP1,upstream_gene_variant,,ENST00000482107,; G ENST00000446176 Transcript synonymous_variant 835/5393 648/1854 216/617 I atA/atC rs139863276 1 -1 FNBP1 HGNC HGNC:17069 protein_coding YES CCDS48040.1 ENSP00000413625 Q96RU3 UPI000022408C NM_015033.2 8/17 PROSITE_profiles:PS51741,hmmpanther:PTHR10663:SF157,hmmpanther:PTHR10663,Gene3D:3.40.50.620,Superfamily_domains:SSF103657 LOW 1 SNV 1 1 PASS rs139863276 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 55 129927336 129927336 T G 1 0 0 0 0 0 0 0 1 5821 1652 57 5 5 FNBP1 9 129927336 Silent SNP T C3N-00559_T 28257126 129927336 8467381 25 16666 MARCH8 0 . GRCh38 10 45458508 45458508 + Missense_Mutation SNP C C T rs756396964 C3N-00559_T C3N-00559_N C C c.1453G>A p.Val485Ile p.V485I ENST00000453424 8/8 34 28 6 87 87 0 varscan-mutect MARCH8,missense_variant,p.Val485Ile,ENST00000453424,NM_001282866.1;MARCH8,missense_variant,p.Val203Ile,ENST00000319836,NM_145021.5;MARCH8,missense_variant,p.Val203Ile,ENST00000395769,NM_001002266.2;MARCH8,downstream_gene_variant,,ENST00000453980,;MARCH8,non_coding_transcript_exon_variant,,ENST00000476962,;MARCH8,downstream_gene_variant,,ENST00000602712,; T ENST00000453424 Transcript missense_variant 1715/5638 1453/1722 485/573 V/I Gtt/Att rs756396964 1 -1 MARCH8 HGNC HGNC:23356 protein_coding YES CCDS60519.1 ENSP00000411848 Q5T0T0 UPI0000EE77CA NM_001282866.1 deleterious(0.05) 8/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR23012:SF71,hmmpanther:PTHR23012 MODERATE 1 SNV 1 1 PASS rs756396964 . 0 208 2 0 0 0 0 0 -16.2041 1 1 1 1 0 T 3 4 55 45458508 45458508 C T 1 0 0 0 0 1 0 0 0 9232 507 18 3 3 MARCH8 10 45458508 Missense_Mutation SNP C C3N-00559_T 45458508 88338914 26 16667 USH1C 0 . GRCh38 11 17509737 17509737 + Silent SNP G G A rs142545736 C3N-00559_T C3N-00559_N G G c.1632C>T p.= p.D544D ENST00000005226 18/27 409 332 77 237 237 0 strelka-varscan-mutect USH1C,synonymous_variant,p.=,ENST00000005226,NM_153676.3;USH1C,intron_variant,,ENST00000527720,;USH1C,intron_variant,,ENST00000318024,NM_005709.3;USH1C,intron_variant,,ENST00000527020,NM_001297764.1;USH1C,intron_variant,,ENST00000529563,;USH1C,downstream_gene_variant,,ENST00000530700,;USH1C,intron_variant,,ENST00000526313,; A ENST00000005226 Transcript synonymous_variant 1632/2700 1632/2700 544/899 D gaC/gaT rs142545736 1 -1 USH1C HGNC HGNC:12597 protein_coding YES CCDS7825.1 ENSP00000005226 Q9Y6N9 UPI00001D965A NM_153676.3 18/27 hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF36 benign LOW 1 SNV 5 1 1 PASS rs142545736 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 55 17509737 17509737 G A 1 0 0 0 0 0 0 0 1 17568 1136 40 1 1 USH1C 11 17509737 Silent SNP G C3N-00559_T 17509737 117576885 27 16668 RCN1 0 . GRCh38 11 32091206 32091225 + Frame_Shift_Del DEL GGTGGCCGCGGCCGCCGCCT GGTGGCCGCGGCCGCCGCCT - novel C3N-00559_T C3N-00559_N GGTGGCCGCGGCCGCCGCCT GGTGGCCGCGGCCGCCGCCT c.12_31delTGGCCGCGGCCGCCGCCTGG p.Gly5ValfsTer40 p.G5Vfs*40 ENST00000054950 1/6 149 136 13 74 74 0 sindel-varindel-pindel RCN1,frameshift_variant,p.Gly5ValfsTer40,ENST00000054950,NM_002901.2;RCN1,intron_variant,,ENST00000532942,;RCN1,intron_variant,,ENST00000530348,;RCN1,upstream_gene_variant,,ENST00000532721,; - ENST00000054950 Transcript frameshift_variant 303-322/2572 10-29/996 4-10/331 GGRGRRL/X GGTGGCCGCGGCCGCCGCCTg/g 1 1 RCN1 HGNC HGNC:9934 protein_coding YES CCDS7876.1 ENSP00000054950 Q15293 V9HW95 UPI0000000CA7 NM_002901.2 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10827,hmmpanther:PTHR10827:SF17,Cleavage_site_(Signalp):SignalP-noTM HIGH 1 deletion 1 2 1 PASS . . 0 204 6 0 0 0 0 0 -19.99998 0.9999998 1 1 1 0 - 7 5 55 32091206 32091206 GGTGGCCGCGGCCGCCGCCT - 1 0 1 0 1 0 0 0 0 13349 1116 39 0 0 RCN1 11 32091206 Frame_Shift_Del DEL GGTGGCCGCGGCCGCCGCCT C3N-00559_T 14581469 32091206 102995416 28 16669 OR4C3 0 . GRCh38 11 48325170 48325170 + Missense_Mutation SNP G G T novel C3N-00559_T C3N-00559_N G G c.230G>T p.Ser77Ile p.S77I ENST00000319856 1/1 107 97 10 195 195 0 strelka-varscan-mutect OR4C3,missense_variant,p.Ser77Ile,ENST00000319856,NM_001004702.1;OR4C3,upstream_gene_variant,,ENST00000611380,; T ENST00000319856 Transcript missense_variant 251/1036 230/990 77/329 S/I aGc/aTc 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 48325170 48325170 G T 1 0 0 0 0 1 0 0 0 11126 971 34 2 2 OR4C3 11 48325170 Missense_Mutation SNP G C3N-00559_T 16233964 48325170 86761452 29 16670 DDB1 0 . GRCh38 11 61332955 61332956 + Frame_Shift_Ins INS - - A novel C3N-00559_T C3N-00559_N - - c.13dupT p.Tyr5LeufsTer88 p.Y5Lfs*88 ENST00000301764 1/27 271 254 17 140 140 0 sindel-varindel-pindel DDB1,frameshift_variant,p.Tyr5LeufsTer88,ENST00000301764,NM_001923.4;DDB1,frameshift_variant,p.Tyr5LeufsTer86,ENST00000543658,;DDB1,frameshift_variant,p.Tyr5LeufsTer88,ENST00000542337,;DDB1,frameshift_variant,p.Tyr5LeufsTer88,ENST00000543627,;TKFC,upstream_gene_variant,,ENST00000394900,NM_015533.3;TKFC,upstream_gene_variant,,ENST00000529479,;DDB1,upstream_gene_variant,,ENST00000535283,;TKFC,upstream_gene_variant,,ENST00000532173,;DDB1,upstream_gene_variant,,ENST00000539426,;TKFC,upstream_gene_variant,,ENST00000524968,;DDB1,non_coding_transcript_exon_variant,,ENST00000543162,;TKFC,upstream_gene_variant,,ENST00000530057,;TKFC,upstream_gene_variant,,ENST00000533393,;TKFC,upstream_gene_variant,,ENST00000530456,;TKFC,upstream_gene_variant,,ENST00000525170,;TKFC,upstream_gene_variant,,ENST00000529620,;DDB1,frameshift_variant,p.Tyr5LeufsTer88,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000537120,;TKFC,upstream_gene_variant,,ENST00000529121,;TKFC,upstream_gene_variant,,ENST00000531820,;DDB1,upstream_gene_variant,,ENST00000538129,; A ENST00000301764 Transcript frameshift_variant 411-412/4506 13-14/3423 5/1140 Y/LX tac/tTac 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 1/27 hmmpanther:PTHR10644 HIGH 1 insertion 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 7 5 55 61332955 61332955 - A 1 0 1 1 0 0 0 0 0 4126 1638 57 0 0 DDB1 11 61332955 Frame_Shift_Ins INS - C3N-00559_T 13007785 61332955 73753667 30 16671 SLCO2B1 0 . GRCh38 11 75193430 75193430 + Missense_Mutation SNP G G A rs374986387 C3N-00559_T C3N-00559_N G G c.1288G>A p.Val430Ile p.V430I ENST00000289575 9/14 173 156 17 82 82 0 strelka-mutect SLCO2B1,missense_variant,p.Val430Ile,ENST00000289575,NM_007256.4;SLCO2B1,missense_variant,p.Val203Ile,ENST00000454962,;SLCO2B1,missense_variant,p.Val314Ile,ENST00000532236,;SLCO2B1,missense_variant,p.Val408Ile,ENST00000428359,NM_001145211.2;SLCO2B1,missense_variant,p.Val286Ile,ENST00000525650,NM_001145212.2;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000531756,;SLCO2B1,upstream_gene_variant,,ENST00000530012,;SLCO2B1,upstream_gene_variant,,ENST00000528108,; A ENST00000289575 Transcript missense_variant 1683/4494 1288/2130 430/709 V/I Gtc/Atc rs374986387 1 1 SLCO2B1 HGNC HGNC:10962 protein_coding YES CCDS8235.1 ENSP00000289575 A0A024R5I4 UPI000000D99A NM_007256.4 tolerated(0.96) 9/14 Gene3D:1.20.1250.20,Pfam_domain:PF03137,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF87,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs374986387 . 0 199 10 0 0 0 0 0 -20 0.999958 1 1 1 0 A 3 1 55 75193430 75193430 G A 1 0 0 0 0 1 0 0 0 15014 1145 40 1 1 SLCO2B1 11 75193430 Missense_Mutation SNP G C3N-00559_T 13860475 75193430 59893192 31 16672 KCNA1 0 . GRCh38 12 4911874 4911874 + Missense_Mutation SNP G G A novel C3N-00559_T C3N-00559_N G G c.496G>A p.Ala166Thr p.A166T ENST00000382545 2/2 336 318 18 119 119 0 strelka-varscan-mutect KCNA1,missense_variant,p.Ala166Thr,ENST00000382545,NM_000217.2;KCNA1,intron_variant,,ENST00000543874,;KCNA1,intron_variant,,ENST00000541095,; A ENST00000382545 Transcript missense_variant 1603/7976 496/1488 166/495 A/T Gcc/Acc 1 1 KCNA1 HGNC HGNC:6218 protein_coding YES CCDS8535.1 ENSP00000371985 Q09470 UPI000013C8E0 NM_000217.2 deleterious(0) 2/2 Gene3D:1.20.120.350,Prints_domain:PR00169,Prints_domain:PR01496,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF24,Superfamily_domains:SSF81324 MODERATE 1 SNV 4 1 PASS rs1179635654 . 0 205 0 3 2 0 0 0 -4.169592 0.8470527 1 1 1 0 A 3 1 55 4911874 4911874 G A 1 0 0 0 0 1 0 0 0 7917 1087 38 1 1 KCNA1 12 4911874 Missense_Mutation SNP G C3N-00559_T 4911874 128363435 32 16673 C2CD5 0 . GRCh38 12 22506710 22506710 + Splice_Site SNP C C A novel C3N-00559_T C3N-00559_N C C c.1120+1G>T p.X374_splice ENST00000545552 59 55 4 167 167 0 varscan-mutect C2CD5,splice_donor_variant,,ENST00000333957,NM_014802.2;C2CD5,splice_donor_variant,,ENST00000536386,NM_001286173.1;C2CD5,splice_donor_variant,,ENST00000446597,NM_001286176.1,NM_001286174.1;C2CD5,splice_donor_variant,,ENST00000545552,NM_001286175.1;C2CD5,splice_donor_variant,,ENST00000396028,NM_001286177.1;C2CD5,splice_donor_variant,,ENST00000542676,;C2CD5,splice_donor_variant,,ENST00000535555,;C2CD5,splice_donor_variant,,ENST00000543855,;C2CD5,splice_donor_variant,,ENST00000541310,;C2CD5,splice_donor_variant,,ENST00000543797,;C2CD5,intron_variant,,ENST00000542683,; A ENST00000545552 Transcript splice_donor_variant -/3471 1120/3165 374/1054 1 -1 C2CD5 HGNC HGNC:29062 protein_coding YES CCDS66339.1 ENSP00000443204 Q86YS7 UPI000204AC3E NM_001286175.1 10/27 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 55 22506710 22506710 C A 1 0 0 0 0 0 0 1 0 2030 521 18 2 2 C2CD5 12 22506710 Splice_Site SNP C C3N-00559_T 17594836 22506710 110768599 33 16674 VEZT 0 . GRCh38 12 95300579 95300579 + Missense_Mutation SNP C C T rs777106680 C3N-00559_T C3N-00559_N C C c.2246C>T p.Ser749Phe p.S749F ENST00000436874 12/12 199 158 41 255 255 0 strelka-varscan-mutect VEZT,missense_variant,p.Ser749Phe,ENST00000436874,NM_017599.3;VEZT,missense_variant,p.Ser705Phe,ENST00000397792,;VEZT,3_prime_UTR_variant,,ENST00000261219,;VEZT,non_coding_transcript_exon_variant,,ENST00000356859,;VEZT,non_coding_transcript_exon_variant,,ENST00000550106,;VEZT,downstream_gene_variant,,ENST00000552306,;VEZT,downstream_gene_variant,,ENST00000551695,;VEZT,downstream_gene_variant,,ENST00000546951,;VEZT,3_prime_UTR_variant,,ENST00000547997,;VEZT,3_prime_UTR_variant,,ENST00000552660,;VEZT,3_prime_UTR_variant,,ENST00000551994,;VEZT,3_prime_UTR_variant,,ENST00000548838,;VEZT,downstream_gene_variant,,ENST00000549192,; T ENST00000436874 Transcript missense_variant 2351/4562 2246/2340 749/779 S/F tCt/tTt rs777106680 1 1 VEZT HGNC HGNC:18258 protein_coding YES CCDS44954.1 ENSP00000410083 Q9HBM0 UPI00001FB2EC NM_017599.3 deleterious(0) 12/12 hmmpanther:PTHR15989:SF5,hmmpanther:PTHR15989 MODERATE 1 SNV 1 1 PASS rs777106680 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 95300579 95300579 C T 1 0 0 0 0 1 0 0 0 17702 913 32 3 3 VEZT 12 95300579 Missense_Mutation SNP C C3N-00559_T 72793869 95300579 37974730 34 16675 MYH7 0 . GRCh38 14 23431603 23431603 + Silent SNP G G A rs202141819 C3N-00559_T C3N-00559_N G G c.714C>T p.= p.N238N ENST00000355349 8/40 1489 1414 75 619 619 0 strelka-varscan MYH7,synonymous_variant,p.=,ENST00000355349,NM_000257.3; A ENST00000355349 Transcript synonymous_variant 877/6087 714/5808 238/1935 N aaC/aaT rs202141819,COSM3983194,COSM698143 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 8/40 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 benign 0,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 55 23431603 23431603 G A 1 0 0 0 0 0 0 0 1 10039 1136 40 1 1 MYH7 14 23431603 Silent SNP G C3N-00559_T 23431603 83612115 35 16676 GPR135 0 . GRCh38 14 59464968 59464968 + Missense_Mutation SNP G G C novel C3N-00559_T C3N-00559_N G G c.259C>G p.Arg87Gly p.R87G ENST00000395116 1/1 396 309 87 137 137 0 strelka-varscan-mutect GPR135,missense_variant,p.Arg87Gly,ENST00000395116,NM_022571.5;L3HYPDH,intron_variant,,ENST00000466522,;GPR135,missense_variant,p.Arg87Gly,ENST00000481661,; C ENST00000395116 Transcript missense_variant 375/4578 259/1485 87/494 R/G Cgg/Ggg 1 -1 GPR135 HGNC HGNC:19991 protein_coding YES CCDS9738.1 ENSP00000378548 Q8IZ08 UPI0000046D5B NM_022571.5 tolerated_low_confidence(0.49) 1/1 hmmpanther:PTHR22752,hmmpanther:PTHR22752:SF3 MODERATE 1 SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 59464968 59464968 G C 1 0 0 0 0 1 0 0 0 6530 1086 38 4 4 GPR135 14 59464968 Missense_Mutation SNP G C3N-00559_T 36033365 59464968 47578750 36 16677 DYNC1H1 0 . GRCh38 14 102039103 102039103 + Missense_Mutation SNP T T C novel C3N-00559_T C3N-00559_N T T c.11309T>C p.Leu3770Pro p.L3770P ENST00000360184 60/78 713 503 210 571 571 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Leu3770Pro,ENST00000360184,NM_001376.4;DYNC1H1,downstream_gene_variant,,ENST00000553423,;RP11-1017G21.4,intron_variant,,ENST00000557551,;RP11-1017G21.4,intron_variant,,ENST00000557242,;RP11-1017G21.4,intron_variant,,ENST00000553701,;DYNC1H1,downstream_gene_variant,,ENST00000556791,;DYNC1H1,upstream_gene_variant,,ENST00000555102,;DYNC1H1,upstream_gene_variant,,ENST00000556139,;DYNC1H1,upstream_gene_variant,,ENST00000556499,;DYNC1H1,downstream_gene_variant,,ENST00000555800,; C ENST00000360184 Transcript missense_variant 11473/14333 11309/13941 3770/4646 L/P cTg/cCg 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0) 60/78 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF12781,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 102039103 102039103 T C 1 0 0 0 0 1 0 0 0 4665 1580 55 5 5 DYNC1H1 14 102039103 Missense_Mutation SNP T C3N-00559_T 42574135 102039103 5004615 37 16678 ZFYVE21 0 . GRCh38 14 103729090 103729090 + Splice_Site SNP G G C novel C3N-00559_T C3N-00559_N G G c.435-1G>C p.X145_splice ENST00000216602 281 211 70 174 174 0 strelka-varscan-mutect ZFYVE21,splice_acceptor_variant,,ENST00000216602,NM_001198953.1;ZFYVE21,splice_acceptor_variant,,ENST00000311141,NM_024071.3;ZFYVE21,splice_acceptor_variant,,ENST00000555163,;PPP1R13B,downstream_gene_variant,,ENST00000202556,NM_015316.2;Y_RNA,upstream_gene_variant,,ENST00000517287,;ZFYVE21,splice_acceptor_variant,,ENST00000555501,;ZFYVE21,splice_acceptor_variant,,ENST00000553724,;ZFYVE21,splice_acceptor_variant,,ENST00000554630,;ZFYVE21,splice_acceptor_variant,,ENST00000556795,;ZFYVE21,splice_acceptor_variant,,ENST00000556610,;PPP1R13B,downstream_gene_variant,,ENST00000556597,;PPP1R13B,downstream_gene_variant,,ENST00000555825,;ZFYVE21,upstream_gene_variant,,ENST00000554757,;PPP1R13B,downstream_gene_variant,,ENST00000557587,;ZFYVE21,downstream_gene_variant,,ENST00000553512,;ZFYVE21,downstream_gene_variant,,ENST00000554255,;ZFYVE21,upstream_gene_variant,,ENST00000602552,; C ENST00000216602 Transcript splice_acceptor_variant -/1521 435/759 145/252 1 1 ZFYVE21 HGNC HGNC:20760 protein_coding YES CCDS55948.1 ENSP00000216602 Q9BQ24 UPI000006E373 NM_001198953.1 4/7 HIGH SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 55 103729090 103729090 G C 1 0 0 0 0 0 0 1 0 18244 956 33 4 4 ZFYVE21 14 103729090 Splice_Site SNP G C3N-00559_T 1689987 103729090 3314628 38 16679 GTF3C1 0 . GRCh38 16 27461442 27461442 + Missense_Mutation SNP T T C novel C3N-00559_T C3N-00559_N T T c.6238A>G p.Met2080Val p.M2080V ENST00000356183 37/37 693 576 117 224 223 1 strelka-varscan-mutect GTF3C1,missense_variant,p.Met2080Val,ENST00000356183,NM_001520.3;GTF3C1,missense_variant,p.Met2055Val,ENST00000561623,NM_001286242.1;GTF3C1,missense_variant,p.Met185Val,ENST00000569653,;GTF3C1,upstream_gene_variant,,ENST00000567806,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000562609,;GTF3C1,non_coding_transcript_exon_variant,,ENST00000564747,; C ENST00000356183 Transcript missense_variant 6254/7018 6238/6330 2080/2109 M/V Atg/Gtg 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 tolerated(0.56) 37/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 55 27461442 27461442 T C 1 0 0 0 0 1 0 0 0 6753 1464 51 5 5 GTF3C1 16 27461442 Missense_Mutation SNP T C3N-00559_T 27461442 62876903 39 16680 APOBR 0 . GRCh38 16 28497625 28497625 + Missense_Mutation SNP A A G novel C3N-00559_T C3N-00559_N A A c.2584A>G p.Thr862Ala p.T862A ENST00000564831 2/4 231 191 40 50 50 0 strelka-varscan-mutect APOBR,missense_variant,p.Thr862Ala,ENST00000564831,NM_018690.3;APOBR,missense_variant,p.Thr853Ala,ENST00000431282,;CLN3,upstream_gene_variant,,ENST00000569430,;IL27,downstream_gene_variant,,ENST00000356897,NM_145659.3;IL27,downstream_gene_variant,,ENST00000568075,;CLN3,upstream_gene_variant,,ENST00000567804,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566472,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,;CLN3,upstream_gene_variant,,ENST00000563874,; G ENST00000564831 Transcript missense_variant 2617/3792 2584/3294 862/1097 T/A Aca/Gca 1 1 APOBR HGNC HGNC:24087 protein_coding YES CCDS58442.1 ENSP00000457539 Q0VD83 UPI000013EFFC NM_018690.3 tolerated(1) 2/4 hmmpanther:PTHR15964:SF0,hmmpanther:PTHR15964 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 55 28497625 28497625 A G 1 0 0 0 0 1 0 0 0 918 275 10 5 5 APOBR 16 28497625 Missense_Mutation SNP A C3N-00559_T 1036183 28497625 61840720 40 16681 ZZEF1 0 . GRCh38 17 4090832 4090832 + Splice_Site SNP T T C novel C3N-00559_T C3N-00559_N T T c.1914-2A>G p.X638_splice ENST00000381638 39 34 5 160 159 1 varscan-mutect ZZEF1,splice_acceptor_variant,,ENST00000381638,NM_015113.3;ZZEF1,splice_acceptor_variant,,ENST00000574474,; C ENST00000381638 Transcript splice_acceptor_variant -/11456 1914/8886 638/2961 1 -1 ZZEF1 HGNC HGNC:29027 protein_coding YES CCDS11043.1 ENSP00000371051 O43149 UPI00004569F7 NM_015113.3 11/54 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 55 4090832 4090832 T C 1 0 0 0 0 0 0 1 0 18859 1594 55 5 5 ZZEF1 17 4090832 Splice_Site SNP T C3N-00559_T 4090832 79166609 41 16682 SPNS2 0 . GRCh38 17 4533806 4533806 + Missense_Mutation SNP G G A novel C3N-00559_T C3N-00559_N G G c.1297G>A p.Glu433Lys p.E433K ENST00000329078 9/13 551 517 34 269 269 0 strelka-varscan-mutect SPNS2,missense_variant,p.Glu433Lys,ENST00000329078,NM_001124758.1;SPNS2,missense_variant,p.Glu103Lys,ENST00000571386,;SPNS2,non_coding_transcript_exon_variant,,ENST00000576635,;SPNS2,non_coding_transcript_exon_variant,,ENST00000573106,;SPNS2,non_coding_transcript_exon_variant,,ENST00000573990,;SPNS2,non_coding_transcript_exon_variant,,ENST00000571668,;SPNS2,upstream_gene_variant,,ENST00000570979,;SPNS2,upstream_gene_variant,,ENST00000570641,; A ENST00000329078 Transcript missense_variant 1507/3447 1297/1650 433/549 E/K Gag/Aag 1 1 SPNS2 HGNC HGNC:26992 protein_coding YES CCDS42237.1 ENSP00000333292 Q8IVW8 UPI00001C1FCB NM_001124758.1 deleterious(0.01) 9/13 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23505:SF4,hmmpanther:PTHR23505,Gene3D:1.20.1250.20,Pfam_domain:PF07690,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 55 4533806 4533806 G A 1 0 0 0 0 1 0 0 0 15428 1175 41 3 3 SPNS2 17 4533806 Missense_Mutation SNP G C3N-00559_T 442974 4533806 78723635 42 16683 TP53 0 . GRCh38 17 7673802 7673802 + Missense_Mutation SNP C C T rs28934576 C3N-00559_T C3N-00559_N C C c.818G>A p.Arg273His p.R273H ENST00000269305 8/11 879 516 363 759 759 0 strelka-varscan-mutect TP53,missense_variant,p.Arg273His,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg273His,ENST00000420246,;TP53,missense_variant,p.Arg234His,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg234His,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg273His,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg234His,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg273His,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg234His,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg273His,ENST00000445888,;TP53,missense_variant,p.Arg234His,ENST00000619485,;TP53,missense_variant,p.Arg141His,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg114His,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg141His,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg114His,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg141His,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg114His,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg273His,ENST00000359597,;TP53,missense_variant,p.Arg262His,ENST00000615910,;TP53,missense_variant,p.Arg141His,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg234His,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 1008/2579 818/1182 273/393 R/H cGt/cAt rs28934576,CM004342,CM010472,CM920677,TP53_g.13798G>C,TP53_g.13798del,TP53_g.13798G>A,TP53_g.13798G>T,COSM10660,COSM10779,COSM1640828,COSM1645335,COSM1646808,COSM165077,COSM318169,COSM3356963,COSM3675521,COSM3726798,COSM43896,COSM44440,COSM99729 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 tolerated(0.13) 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 25105660 MODERATE 1 SNV 1 1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs28934576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 7673802 7673802 C T 1 0 0 0 0 1 0 0 0 16859 536 19 1 1 TP53 17 7673802 Missense_Mutation SNP C C3N-00559_T 3139996 7673802 75583639 43 16684 CDH2 0 . GRCh38 18 28176992 28176992 + Missense_Mutation SNP G G C novel C3N-00559_T C3N-00559_N G G c.31C>G p.Leu11Val p.L11V ENST00000269141 1/16 292 236 56 106 106 0 strelka-varscan-mutect CDH2,missense_variant,p.Leu11Val,ENST00000269141,NM_001792.3; C ENST00000269141 Transcript missense_variant 455/4332 31/2721 11/906 L/V Ctg/Gtg 1 -1 CDH2 HGNC HGNC:1759 protein_coding YES CCDS11891.1 ENSP00000269141 P19022 A0A024RC42 UPI000013D7FD NM_001792.3 tolerated(0.54) 1/16 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1351191506 . 0 206 2 2 0 0 0 0 -20 0.9999988 1 1 1 0 C 3 2 55 28176992 28176992 G C 1 0 0 0 0 1 0 0 0 2808 991 35 4 4 CDH2 18 28176992 Missense_Mutation SNP G C3N-00559_T 28176992 52196293 44 16685 ZNF135 0 . GRCh38 19 58067119 58067119 + Missense_Mutation SNP A A T novel C3N-00559_T C3N-00559_N A A c.707A>T p.Lys236Ile p.K236I ENST00000401053 4/4 217 154 63 339 339 0 strelka-varscan-mutect ZNF135,missense_variant,p.Lys170Ile,ENST00000506786,NM_001289402.1;ZNF135,missense_variant,p.Lys236Ile,ENST00000401053,NM_001164529.1,NM_007134.1;ZNF135,missense_variant,p.Lys212Ile,ENST00000313434,NM_001289401.1;ZNF135,missense_variant,p.Lys224Ile,ENST00000511556,NM_003436.3;ZNF135,missense_variant,p.Lys224Ile,ENST00000359978,NM_001164530.1;RN7SL526P,upstream_gene_variant,,ENST00000469492,;ZNF135,intron_variant,,ENST00000515535,; T ENST00000401053 Transcript missense_variant 710/3346 707/2049 236/682 K/I aAa/aTa 1 1 ZNF135 HGNC HGNC:12919 protein_coding YES CCDS54329.1 ENSP00000441410 P52742 UPI0001B3CB2A NM_001164529.1,NM_007134.1 deleterious(0) 4/4 Gene3D:3.30.160.60,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF250,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 55 58067119 58067119 A T 1 0 0 0 0 1 0 0 0 18306 14 1 4 4 ZNF135 19 58067119 Missense_Mutation SNP A C3N-00559_T 58067119 550497 45 16686 SLC12A5 0 . GRCh38 20 46051831 46051831 + Missense_Mutation SNP C C T rs757395459 C3N-00559_T C3N-00559_N C C c.2407C>T p.Arg803Cys p.R803C ENST00000454036 18/26 355 305 50 127 127 0 strelka-varscan-mutect SLC12A5,missense_variant,p.Arg780Cys,ENST00000243964,NM_020708.4;SLC12A5,missense_variant,p.Arg803Cys,ENST00000454036,NM_001134771.1;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616201,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,downstream_gene_variant,,ENST00000539566,;SLC12A5,upstream_gene_variant,,ENST00000628413,; T ENST00000454036 Transcript missense_variant 2483/3593 2407/3420 803/1139 R/C Cgc/Tgc rs757395459,COSM188914 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 deleterious(0.02) 18/26 hmmpanther:PTHR11827:SF54,hmmpanther:PTHR11827,Pfam_domain:PF03522,TIGRFAM_domain:TIGR00930 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs757395459 . 0 202 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 55 46051831 46051831 C T 1 0 0 0 0 1 0 0 0 14651 768 27 1 1 SLC12A5 20 46051831 Missense_Mutation SNP C C3N-00559_T 46051831 18392336 46 16687 FMR1NB 0 . GRCh38 X 148003231 148003231 + Missense_Mutation SNP A A T rs782753814 C3N-00559_T C3N-00559_N A A c.308A>T p.His103Leu p.H103L ENST00000370467 2/6 50 43 7 176 176 0 strelka-mutect FMR1NB,missense_variant,p.His103Leu,ENST00000370467,NM_152578.2;5S_rRNA,downstream_gene_variant,,ENST00000364415,;FMR1NB,upstream_gene_variant,,ENST00000489034,; T ENST00000370467 Transcript missense_variant 382/1021 308/768 103/255 H/L cAt/cTt rs782753814 1 1 FMR1NB HGNC HGNC:26372 protein_coding YES CCDS14683.1 ENSP00000359498 Q8N0W7 UPI0000062299 NM_152578.2 tolerated(0.61) 2/6 hmmpanther:PTHR37360:SF1,hmmpanther:PTHR37360 MODERATE 1 SNV 1 1 PASS rs782753814 . 0 207 3 0 0 0 0 0 -17.05723 1 1 1 1 0 T 3 4 55 148003231 148003231 A T 1 0 0 0 0 1 0 0 0 5817 217 8 4 4 FMR1NB 23 148003231 Missense_Mutation SNP A C3N-00559_T 148003231 8037664 47 16688 L1CAM 0 . GRCh38 X 153868609 153868609 + Missense_Mutation SNP C C A novel C3N-00559_T C3N-00559_N C C c.1498G>T p.Ala500Ser p.A500S ENST00000370060 13/29 1227 1156 71 545 545 0 strelka-varscan-mutect L1CAM,missense_variant,p.Ala500Ser,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,missense_variant,p.Ala495Ser,ENST00000361981,NM_001143963.2;L1CAM,missense_variant,p.Ala495Ser,ENST00000370055,;L1CAM,missense_variant,p.Ala500Ser,ENST00000361699,NM_024003.3;L1CAM,upstream_gene_variant,,ENST00000370058,;L1CAM,downstream_gene_variant,,ENST00000439496,;L1CAM,downstream_gene_variant,,ENST00000458029,;L1CAM,downstream_gene_variant,,ENST00000407935,;L1CAM,upstream_gene_variant,,ENST00000455590,;L1CAM,downstream_gene_variant,,ENST00000420165,;L1CAM,non_coding_transcript_exon_variant,,ENST00000496122,;L1CAM,non_coding_transcript_exon_variant,,ENST00000484652,;L1CAM,upstream_gene_variant,,ENST00000491983,;L1CAM,downstream_gene_variant,,ENST00000464967,;L1CAM,upstream_gene_variant,,ENST00000474853,;L1CAM,downstream_gene_variant,,ENST00000460553,; A ENST00000370060 Transcript missense_variant 1688/5113 1498/3774 500/1257 A/S Gcc/Tcc 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 tolerated(0.76) 13/29 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 55 153868609 153868609 C A 1 0 0 0 0 1 0 0 0 8489 710 25 2 2 L1CAM 23 153868609 Missense_Mutation SNP C C3N-00559_T 5865378 153868609 2172286 48 16689 PERM1 0 . GRCh38 1 979410 979410 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1620C>A p.= p.A540A ENST00000433179 1/3 56 32 24 54 54 0 strelka-mutect PERM1,synonymous_variant,p.=,ENST00000433179,NM_001291366.1;PERM1,synonymous_variant,p.=,ENST00000341290,NM_001291367.1;PLEKHN1,downstream_gene_variant,,ENST00000379409,;PLEKHN1,downstream_gene_variant,,ENST00000379410,NM_032129.2;PLEKHN1,downstream_gene_variant,,ENST00000379407,NM_001160184.1;PLEKHN1,downstream_gene_variant,,ENST00000491024,;PERM1,upstream_gene_variant,,ENST00000479361,; T ENST00000433179 Transcript synonymous_variant 1620/3340 1620/2373 540/790 A gcC/gcA 1 -1 PERM1 HGNC HGNC:28208 protein_coding YES CCDS76083.1 ENSP00000414022 Q5SV97 UPI0003E30FA7 NM_001291366.1 1/3 hmmpanther:PTHR21712,hmmpanther:PTHR21712:SF34 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 979410 979410 G T 1 0 0 0 0 0 0 0 1 11820 987 35 2 2 PERM1 1 979410 Silent SNP G C3N-00560_T 979410 247977012 1 16690 MIB2 0 . GRCh38 1 1627701 1627701 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.1897C>T p.= p.L633L ENST00000505820 13/20 227 186 41 180 180 0 strelka-mutect MIB2,synonymous_variant,p.=,ENST00000520777,NM_001170686.1;MIB2,synonymous_variant,p.=,ENST00000504599,;MIB2,synonymous_variant,p.=,ENST00000505820,NM_080875.2;MIB2,synonymous_variant,p.=,ENST00000355826,NM_001170687.1;MIB2,synonymous_variant,p.=,ENST00000518681,NM_001170688.1;MIB2,synonymous_variant,p.=,ENST00000378708,;MIB2,synonymous_variant,p.=,ENST00000378712,NM_001170689.1;MIB2,synonymous_variant,p.=,ENST00000514234,;MMP23B,upstream_gene_variant,,ENST00000356026,NM_006983.1;MMP23B,upstream_gene_variant,,ENST00000378675,;MIB2,upstream_gene_variant,,ENST00000483015,;MIB2,downstream_gene_variant,,ENST00000510793,;MIB2,downstream_gene_variant,,ENST00000503789,;MMP23B,upstream_gene_variant,,ENST00000472264,;MIB2,downstream_gene_variant,,ENST00000512004,;MIB2,synonymous_variant,p.=,ENST00000487053,;MIB2,3_prime_UTR_variant,,ENST00000489635,;MIB2,3_prime_UTR_variant,,ENST00000506488,;MIB2,non_coding_transcript_exon_variant,,ENST00000479659,;MIB2,non_coding_transcript_exon_variant,,ENST00000511502,;MIB2,non_coding_transcript_exon_variant,,ENST00000507229,;MIB2,non_coding_transcript_exon_variant,,ENST00000473511,;MIB2,non_coding_transcript_exon_variant,,ENST00000464570,;MIB2,non_coding_transcript_exon_variant,,ENST00000505370,;MMP23B,upstream_gene_variant,,ENST00000512731,;MIB2,downstream_gene_variant,,ENST00000502470,;MIB2,downstream_gene_variant,,ENST00000467597,;MIB2,downstream_gene_variant,,ENST00000514363,;MIB2,upstream_gene_variant,,ENST00000511910,;MIB2,downstream_gene_variant,,ENST00000508148,;MIB2,downstream_gene_variant,,ENST00000486072,;MIB2,downstream_gene_variant,,ENST00000508455,;MIB2,upstream_gene_variant,,ENST00000470373,; T ENST00000505820 Transcript synonymous_variant 1914/3305 1897/3213 633/1070 L Ctg/Ttg 1 1 MIB2 HGNC HGNC:30577 protein_coding YES CCDS41224.2 ENSP00000426103 Q96AX9 UPI0001C0B37A NM_080875.2 13/20 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24202:SF4,hmmpanther:PTHR24202,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 1627701 1627701 C T 1 0 0 0 0 0 0 0 1 9524 680 24 3 3 MIB2 1 1627701 Silent SNP C C3N-00560_T 648291 1627701 247328721 2 16691 CCDC27 0 . GRCh38 1 3752722 3752722 + Missense_Mutation SNP C C T rs760567788 C3N-00560_T C3N-00560_N C C c.241C>T p.Pro81Ser p.P81S ENST00000294600 1/12 287 186 101 257 257 0 strelka-varscan-mutect CCDC27,missense_variant,p.Pro81Ser,ENST00000294600,NM_152492.2;CCDC27,missense_variant,p.Pro81Ser,ENST00000462521,;CCDC27,non_coding_transcript_exon_variant,,ENST00000636250,; T ENST00000294600 Transcript missense_variant 325/2176 241/1971 81/656 P/S Cca/Tca rs760567788 1 1 CCDC27 HGNC HGNC:26546 protein_coding YES CCDS50.1 ENSP00000294600 Q2M243 UPI000013E186 NM_152492.2 tolerated(0.31) 1/12 hmmpanther:PTHR18853:SF8,hmmpanther:PTHR18853 MODERATE 1 SNV 1 1 PASS rs760567788 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 3752722 3752722 C T 1 0 0 0 0 1 0 0 0 2511 623 22 3 3 CCDC27 1 3752722 Missense_Mutation SNP C C3N-00560_T 2125021 3752722 245203700 3 16692 LRRC47 0 . GRCh38 1 3796110 3796110 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.367G>T p.Ala123Ser p.A123S ENST00000378251 1/7 143 113 30 65 65 0 strelka-varscan-mutect LRRC47,missense_variant,p.Ala123Ser,ENST00000378251,NM_020710.2; A ENST00000378251 Transcript missense_variant 395/4310 367/1752 123/583 A/S Gcc/Tcc 1 -1 LRRC47 HGNC HGNC:29207 protein_coding YES CCDS51.1 ENSP00000367498 Q8N1G4 A0A024R4G1 UPI000006DEDC NM_020710.2 tolerated(0.25) 1/7 Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR10947,hmmpanther:PTHR10947:SF3,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 3796110 3796110 C A 1 0 0 0 0 1 0 0 0 8900 768 27 1 1 LRRC47 1 3796110 Missense_Mutation SNP C C3N-00560_T 43388 3796110 245160312 4 16693 NPHP4 0 . GRCh38 1 5879628 5879628 + Missense_Mutation SNP C C A rs774055525 C3N-00560_T C3N-00560_N C C c.2613G>T p.Trp871Cys p.W871C ENST00000622020 20/20 98 41 57 89 89 0 strelka-varscan-mutect NPHP4,missense_variant,p.Trp871Cys,ENST00000622020,;NPHP4,intron_variant,,ENST00000378156,NM_001291594.1,NM_001291593.1,NM_015102.4;NPHP4,intron_variant,,ENST00000478423,;NPHP4,missense_variant,p.Trp871Cys,ENST00000489180,;NPHP4,intron_variant,,ENST00000378169,;NPHP4,intron_variant,,ENST00000470763,;NPHP4,upstream_gene_variant,,ENST00000506941,; A ENST00000622020 Transcript missense_variant 2881/3004 2613/2736 871/911 W/C tgG/tgT rs774055525 1 -1 NPHP4 HGNC HGNC:19104 protein_coding ENSP00000481831 O75161 UPI0000074519 tolerated(0.18) 20/20 MODERATE SNV 5 1 PASS rs774055525 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 5879628 5879628 C A 1 0 0 0 0 1 0 0 0 10629 637 22 2 2 NPHP4 1 5879628 Missense_Mutation SNP C C3N-00560_T 2083518 5879628 243076794 5 16694 NPPB 0 . GRCh38 1 11858269 11858269 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.333C>T p.= p.G111G ENST00000376468 2/3 82 45 37 107 107 0 strelka-varscan-mutect NPPB,synonymous_variant,p.=,ENST00000376468,NM_002521.2; A ENST00000376468 Transcript synonymous_variant 431/694 333/405 111/134 G ggC/ggT 1 -1 NPPB HGNC HGNC:7940 protein_coding YES CCDS140.1 ENSP00000365651 P16860 UPI00000350A5 NM_002521.2 2/3 hmmpanther:PTHR14066,Pfam_domain:PF00212,SMART_domains:SM00183,Prints_domain:PR00712 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 11858269 11858269 G A 1 0 0 0 0 0 0 0 1 10648 958 34 3 3 NPPB 1 11858269 Silent SNP G C3N-00560_T 5978641 11858269 237098153 6 16695 TNFRSF8 0 . GRCh38 1 12142409 12142409 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1666C>A p.His556Asn p.H556N ENST00000263932 15/15 199 189 10 237 237 0 strelka-varscan TNFRSF8,missense_variant,p.His556Asn,ENST00000263932,NM_001243.4;TNFRSF8,missense_variant,p.His444Asn,ENST00000417814,NM_001281430.2;TNFRSF8,missense_variant,p.His93Asn,ENST00000413146,;TNFRSF8,non_coding_transcript_exon_variant,,ENST00000479933,;TNFRSF8,3_prime_UTR_variant,,ENST00000514649,; A ENST00000263932 Transcript missense_variant 1888/3686 1666/1788 556/595 H/N Cat/Aat 1 1 TNFRSF8 HGNC HGNC:11923 protein_coding YES CCDS144.1 ENSP00000263932 P28908 UPI0000000971 NM_001243.4 deleterious(0.04) 15/15 Prints_domain:PR01923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 12142409 12142409 C A 1 0 0 0 0 1 0 0 0 16773 594 21 2 2 TNFRSF8 1 12142409 Missense_Mutation SNP C C3N-00560_T 284140 12142409 236814013 7 16696 VPS13D 0 . GRCh38 1 12261036 12261036 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1301A>T p.Gln434Leu p.Q434L ENST00000620676 12/70 371 204 167 480 480 0 strelka-varscan-mutect VPS13D,missense_variant,p.Gln434Leu,ENST00000620676,NM_015378.3;VPS13D,missense_variant,p.Gln434Leu,ENST00000613099,NM_018156.3;VPS13D,downstream_gene_variant,,ENST00000489961,; T ENST00000620676 Transcript missense_variant 1431/16320 1301/13167 434/4388 Q/L cAg/cTg 1 1 VPS13D HGNC HGNC:23595 protein_coding YES CCDS30588.1 ENSP00000478104 Q5THJ4 UPI0000451CA9 NM_015378.3 deleterious(0.03) 12/70 hmmpanther:PTHR16166:SF104,hmmpanther:PTHR16166 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 12261036 12261036 A T 1 0 0 0 0 1 0 0 0 17739 188 7 4 4 VPS13D 1 12261036 Missense_Mutation SNP A C3N-00560_T 118627 12261036 236695386 8 16697 UBXN10 0 . GRCh38 1 20191183 20191183 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.622G>T p.Gly208Cys p.G208C ENST00000375099 2/2 256 150 106 356 356 0 strelka-varscan-mutect UBXN10,missense_variant,p.Gly208Cys,ENST00000375099,NM_152376.4;UBXN10-AS1,upstream_gene_variant,,ENST00000442226,; T ENST00000375099 Transcript missense_variant 706/5571 622/843 208/280 G/C Ggc/Tgc 1 1 UBXN10 HGNC HGNC:26354 protein_coding YES CCDS205.1 ENSP00000364240 Q96LJ8 UPI000000DBEB NM_152376.4 deleterious(0) 2/2 PROSITE_profiles:PS50033,hmmpanther:PTHR23322:SF28,hmmpanther:PTHR23322,Pfam_domain:PF00789,Gene3D:3.10.20.90,SMART_domains:SM00166,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 20191183 20191183 G T 1 0 0 0 0 1 0 0 0 17436 1000 35 2 2 UBXN10 1 20191183 Missense_Mutation SNP G C3N-00560_T 7930147 20191183 228765239 9 16698 HSPG2 0 . GRCh38 1 21828849 21828849 + Missense_Mutation SNP C C A rs557821484 C3N-00560_T C3N-00560_N C C c.12223G>T p.Gly4075Cys p.G4075C ENST00000374695 88/97 261 146 115 313 312 1 strelka-varscan-mutect HSPG2,missense_variant,p.Gly4075Cys,ENST00000374695,NM_005529.6,NM_001291860.1;LDLRAD2,downstream_gene_variant,,ENST00000344642,NM_001013693.2;LDLRAD2,downstream_gene_variant,,ENST00000543870,;HSPG2,downstream_gene_variant,,ENST00000635682,;HSPG2,non_coding_transcript_exon_variant,,ENST00000486901,;HSPG2,downstream_gene_variant,,ENST00000471322,;HSPG2,upstream_gene_variant,,ENST00000481644,; A ENST00000374695 Transcript missense_variant 12303/14327 12223/13176 4075/4391 G/C Ggc/Tgc rs557821484 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 deleterious(0) 88/97 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF273,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs557821484 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 21828849 21828849 C A 1 0 0 0 0 1 0 0 0 7326 652 23 1 1 HSPG2 1 21828849 Missense_Mutation SNP C C3N-00560_T 1637666 21828849 227127573 10 16699 ARID1A 0 . GRCh38 1 26771246 26771246 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3326G>T p.Arg1109Leu p.R1109L ENST00000324856 12/20 371 298 73 337 337 0 strelka-varscan-mutect ARID1A,missense_variant,p.Arg1109Leu,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Arg728Leu,ENST00000636219,;ARID1A,missense_variant,p.Arg726Leu,ENST00000430799,;ARID1A,missense_variant,p.Arg726Leu,ENST00000374152,;ARID1A,missense_variant,p.Arg1109Leu,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Arg725Leu,ENST00000615191,;ARID1A,upstream_gene_variant,,ENST00000636794,;ARID1A,non_coding_transcript_exon_variant,,ENST00000636110,;ARID1A,upstream_gene_variant,,ENST00000466382,;ARID1A,upstream_gene_variant,,ENST00000532781,;ARID1A,upstream_gene_variant,,ENST00000636072,;ARID1A,downstream_gene_variant,,ENST00000430291,; T ENST00000324856 Transcript missense_variant 3697/8577 3326/6858 1109/2285 R/L cGg/cTg 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 deleterious(0.01) 12/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12,Gene3D:1.10.150.60,SMART_domains:SM00501,Superfamily_domains:SSF46774 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 26771246 26771246 G T 1 0 0 0 0 1 0 0 0 1049 1116 39 1 1 ARID1A 1 26771246 Missense_Mutation SNP G C3N-00560_T 4942397 26771246 222185176 11 16700 PUM1 0 . GRCh38 1 30945399 30945399 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.2941G>A p.Glu981Lys p.E981K ENST00000426105 18/22 262 175 87 252 252 0 strelka-varscan-mutect PUM1,missense_variant,p.Glu982Lys,ENST00000373747,;PUM1,missense_variant,p.Glu979Lys,ENST00000257075,NM_014676.2;PUM1,missense_variant,p.Glu737Lys,ENST00000424085,;PUM1,missense_variant,p.Glu918Lys,ENST00000525843,;PUM1,missense_variant,p.Glu1017Lys,ENST00000373741,;PUM1,missense_variant,p.Glu981Lys,ENST00000426105,NM_001020658.1;PUM1,missense_variant,p.Glu955Lys,ENST00000440538,;PUM1,missense_variant,p.Glu920Lys,ENST00000373742,;PUM1,missense_variant,p.Glu693Lys,ENST00000498419,;PUM1,missense_variant,p.Glu132Lys,ENST00000529846,;PUM1,intron_variant,,ENST00000525997,;PUM1,downstream_gene_variant,,ENST00000527498,;PUM1,upstream_gene_variant,,ENST00000530669,; T ENST00000426105 Transcript missense_variant 3032/4043 2941/3567 981/1188 E/K Gaa/Aaa 1 -1 PUM1 HGNC HGNC:14957 protein_coding YES CCDS44099.1 ENSP00000391723 Q14671 UPI0000203D8E NM_001020658.1 deleterious(0) 18/22 Gene3D:1.25.10.10,Pfam_domain:PF00806,PROSITE_profiles:PS50302,PROSITE_profiles:PS50303,hmmpanther:PTHR12537,hmmpanther:PTHR12537:SF1,SMART_domains:SM00025,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 30945399 30945399 C T 1 0 0 0 0 1 0 0 0 12982 835 29 3 3 PUM1 1 30945399 Missense_Mutation SNP C C3N-00560_T 4174153 30945399 218011023 12 16701 TXLNA 0 . GRCh38 1 32181487 32181487 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.415G>T p.Asp139Tyr p.D139Y ENST00000373609 2/10 179 147 32 180 179 1 strelka-varscan-mutect TXLNA,missense_variant,p.Asp139Tyr,ENST00000373609,;TXLNA,missense_variant,p.Asp139Tyr,ENST00000373610,NM_175852.3;KPNA6,downstream_gene_variant,,ENST00000373625,NM_012316.4;RP4-622L5.2,downstream_gene_variant,,ENST00000515055,; T ENST00000373609 Transcript missense_variant 696/5012 415/1641 139/546 D/Y Gat/Tat 1 1 TXLNA HGNC HGNC:30685 protein_coding YES CCDS353.1 ENSP00000362711 P40222 UPI000000D7D9 deleterious(0.01) 2/10 hmmpanther:PTHR16127,hmmpanther:PTHR16127:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 32181487 32181487 G T 1 0 0 0 0 1 0 0 0 17303 1174 41 2 2 TXLNA 1 32181487 Missense_Mutation SNP G C3N-00560_T 1236088 32181487 216774935 13 16702 ZSCAN20 0 . GRCh38 1 33493287 33493287 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1545G>T p.Gln515His p.Q515H ENST00000361328 7/8 368 232 136 342 342 0 strelka-varscan-mutect ZSCAN20,missense_variant,p.Gln515His,ENST00000361328,NM_145238.3;ZSCAN20,downstream_gene_variant,,ENST00000373413,;ZSCAN20,downstream_gene_variant,,ENST00000480917,; T ENST00000361328 Transcript missense_variant 1698/4316 1545/3132 515/1043 Q/H caG/caT 1 1 ZSCAN20 HGNC HGNC:13093 protein_coding YES CCDS41300.1 ENSP00000355053 P17040 UPI0000D61EC5 NM_145238.3 deleterious(0.02) 7/8 Pfam_domain:PF13837,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF198,SMART_domains:SM00717 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 33493287 33493287 G T 1 0 0 0 0 1 0 0 0 18826 991 35 2 2 ZSCAN20 1 33493287 Missense_Mutation SNP G C3N-00560_T 1311800 33493287 215463135 14 16703 CSMD2 0 . GRCh38 1 33533795 33533795 + Splice_Site SNP C C A C3N-00560_T C3N-00560_N C C c.9991+1G>T p.X3331_splice ENST00000373381 139 94 45 126 126 0 strelka-varscan-mutect CSMD2,splice_donor_variant,,ENST00000373381,NM_001281956.1;CSMD2,splice_donor_variant,,ENST00000619121,;CSMD2,splice_donor_variant,,ENST00000373388,NM_052896.4;CSMD2,splice_donor_variant,,ENST00000241312,; A ENST00000373381 Transcript splice_donor_variant -/13698 9991/10896 3331/3631 COSM1732300,COSM1732301 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 63/70 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 33533795 33533795 C A 1 0 0 0 0 0 0 1 0 3746 550 19 1 1 CSMD2 1 33533795 Splice_Site SNP C C3N-00560_T 40508 33533795 215422627 15 16704 CSMD2 0 . GRCh38 1 33658103 33658103 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.4290C>A p.= p.I1430I ENST00000373381 27/71 90 71 19 74 74 0 strelka-varscan-mutect CSMD2,synonymous_variant,p.=,ENST00000373381,NM_001281956.1;CSMD2,synonymous_variant,p.=,ENST00000619121,;CSMD2,synonymous_variant,p.=,ENST00000373388,NM_052896.4;CSMD2,synonymous_variant,p.=,ENST00000373380,;CSMD2,synonymous_variant,p.=,ENST00000241312,; T ENST00000373381 Transcript synonymous_variant 4467/13698 4290/10896 1430/3631 I atC/atA COSM4994032,COSM4994033 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 27/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 33658103 33658103 G T 1 0 0 0 0 0 0 0 1 3746 1164 41 2 2 CSMD2 1 33658103 Silent SNP G C3N-00560_T 124308 33658103 215298319 16 16705 HIVEP3 0 . GRCh38 1 41512902 41512902 + Missense_Mutation SNP C C A rs141540001 C3N-00560_T C3N-00560_N C C c.6319G>T p.Gly2107Trp p.G2107W ENST00000372583 8/9 114 92 22 114 114 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Gly2107Trp,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Gly2107Trp,ENST00000372583,NM_024503.4;HIVEP3,non_coding_transcript_exon_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 7205/12193 6319/7221 2107/2406 G/W Ggg/Tgg rs141540001 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious(0.04) 8/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS rs141540001 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 41512902 41512902 C A 1 0 0 0 0 1 0 0 0 7077 623 22 2 2 HIVEP3 1 41512902 Missense_Mutation SNP C C3N-00560_T 7854799 41512902 207443520 17 16706 HIVEP3 0 . GRCh38 1 41583590 41583590 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1208A>T p.Gln403Leu p.Q403L ENST00000372583 4/9 247 213 34 257 257 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Gln403Leu,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Gln403Leu,ENST00000372583,NM_024503.4;HIVEP3,upstream_gene_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 2094/12193 1208/7221 403/2406 Q/L cAg/cTg 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious(0) 4/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 41583590 41583590 T A 1 0 0 0 0 1 0 0 0 7077 1580 55 4 4 HIVEP3 1 41583590 Missense_Mutation SNP T C3N-00560_T 70688 41583590 207372832 18 16707 MAST2 0 . GRCh38 1 46025675 46025675 + Splice_Site SNP A A T novel C3N-00560_T C3N-00560_N A A c.1781-2A>T p.X594_splice ENST00000361297 134 87 47 137 136 1 strelka-varscan-mutect MAST2,splice_acceptor_variant,,ENST00000361297,NM_001324320.1,NM_001319245.1,NM_015112.2;MAST2,splice_acceptor_variant,,ENST00000372009,;MAST2,splice_acceptor_variant,,ENST00000372008,;MAST2,upstream_gene_variant,,ENST00000477968,;MAST2,downstream_gene_variant,,ENST00000467367,;MAST2,downstream_gene_variant,,ENST00000498668,; T ENST00000361297 Transcript splice_acceptor_variant -/5738 1781/5397 594/1798 1 1 MAST2 HGNC HGNC:19035 protein_coding YES CCDS41326.1 ENSP00000354671 Q6P0Q8 UPI0000458AEB NM_001324320.1,NM_001319245.1,NM_015112.2 15/28 HIGH 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999924 1 1 1 0 T 5 4 56 46025675 46025675 A T 1 0 0 0 0 0 0 1 0 9251 202 7 4 4 MAST2 1 46025675 Splice_Site SNP A C3N-00560_T 4442085 46025675 202930747 19 16708 AGBL4 0 . GRCh38 1 49697437 49697437 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.158G>T p.Gly53Val p.G53V ENST00000371839 3/14 80 65 15 90 90 0 strelka-varscan-mutect AGBL4,missense_variant,p.Gly53Val,ENST00000371839,NM_032785.3;AGBL4,missense_variant,p.Gly53Val,ENST00000371836,;AGBL4,missense_variant,p.Gly53Val,ENST00000371838,;AGBL4,splice_region_variant,,ENST00000497451,; A ENST00000371839 Transcript missense_variant,splice_region_variant 275/2947 158/1512 53/503 G/V gGt/gTt 1 -1 AGBL4 HGNC HGNC:25892 protein_coding YES CCDS44137.1 ENSP00000360905 Q5VU57 UPI00002042F9 NM_032785.3 deleterious(0) 3/14 hmmpanther:PTHR12756 MODERATE 1 SNV 2 1 PASS rs965723811 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49697437 49697437 C A 1 0 0 0 0 1 0 0 0 454 521 18 2 2 AGBL4 1 49697437 Missense_Mutation SNP C C3N-00560_T 3671762 49697437 199258985 20 16709 GLIS1 0 . GRCh38 1 53594827 53594827 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.76C>G p.Leu26Val p.L26V ENST00000312233 3/10 83 68 15 96 96 0 strelka-varscan-mutect GLIS1,missense_variant,p.Leu26Val,ENST00000312233,NM_147193.2;GLIS1,missense_variant,p.Leu201Val,ENST00000628545,; C ENST00000312233 Transcript missense_variant 643/2812 76/1863 26/620 L/V Ctc/Gtc 1 -1 GLIS1 HGNC HGNC:29525 protein_coding YES CCDS582.1 ENSP00000309653 Q8NBF1 UPI000013F293 NM_147193.2 deleterious_low_confidence(0.02) 3/10 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF93 MODERATE 1 SNV 2 1 PASS . . 0 200 8 2 0 0 0 0 -20 0.9998101 1 1 1 0 C 3 2 56 53594827 53594827 G C 1 0 0 0 0 1 0 0 0 6323 1000 35 4 4 GLIS1 1 53594827 Missense_Mutation SNP G C3N-00560_T 3897390 53594827 195361595 21 16710 PCSK9 0 . GRCh38 1 55061464 55061464 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1771C>A p.His591Asn p.H591N ENST00000302118 11/12 288 176 112 277 277 0 strelka-varscan-mutect PCSK9,missense_variant,p.His591Asn,ENST00000302118,NM_174936.3;USP24,downstream_gene_variant,,ENST00000294383,NM_015306.2;PCSK9,non_coding_transcript_exon_variant,,ENST00000490692,; A ENST00000302118 Transcript missense_variant 2061/3637 1771/2079 591/692 H/N Cac/Aac 1 1 PCSK9 HGNC HGNC:20001 protein_coding YES CCDS603.1 ENSP00000303208 Q8NBP7 UPI00001615E1 NM_174936.3 tolerated(0.08) 11/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 55061464 55061464 C A 1 0 0 0 0 1 0 0 0 11694 594 21 2 2 PCSK9 1 55061464 Missense_Mutation SNP C C3N-00560_T 1466637 55061464 193894958 22 16711 KANK4 0 . GRCh38 1 62273269 62273269 + Nonsense_Mutation SNP G G T rs200228736 C3N-00560_T C3N-00560_N G G c.1835C>A p.Ser612Ter p.S612* ENST00000371153 3/10 30 13 17 12 12 0 strelka-varscan-mutect KANK4,stop_gained,p.Ser612Ter,ENST00000371153,NM_181712.4;KANK4,intron_variant,,ENST00000354381,;KANK4,upstream_gene_variant,,ENST00000371150,; T ENST00000371153 Transcript stop_gained 2214/4665 1835/2988 612/995 S/* tCg/tAg rs200228736 1 -1 KANK4 HGNC HGNC:27263 protein_coding YES CCDS620.1 ENSP00000360195 Q5T7N3 UPI000022AE73 NM_181712.4 3/10 hmmpanther:PTHR24168,hmmpanther:PTHR24168:SF24,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs200228736 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 62273269 62273269 G T 1 0 0 0 0 0 1 0 0 7888 1059 37 1 1 KANK4 1 62273269 Nonsense_Mutation SNP G C3N-00560_T 7211805 62273269 186683153 23 16712 DOCK7 0 . GRCh38 1 62504698 62504698 + Missense_Mutation SNP C C A rs147103646 C3N-00560_T C3N-00560_N C C c.4669G>T p.Gly1557Cys p.G1557C ENST00000454575 37/49 318 285 33 241 241 0 strelka-varscan-mutect DOCK7,missense_variant,p.Gly1557Cys,ENST00000251157,;DOCK7,missense_variant,p.Gly1557Cys,ENST00000454575,NM_001271999.1;DOCK7,missense_variant,p.Gly1535Cys,ENST00000340370,NM_033407.3;DOCK7,missense_variant,p.Gly1566Cys,ENST00000635253,;DOCK7,missense_variant,p.Gly1526Cys,ENST00000634264,NM_001272000.1;DOCK7,missense_variant,p.Gly1526Cys,ENST00000635123,NM_001272001.1;DOCK7,missense_variant,p.Gly657Cys,ENST00000637255,;DOCK7,downstream_gene_variant,,ENST00000635286,;DOCK7,3_prime_UTR_variant,,ENST00000637208,;DOCK7,non_coding_transcript_exon_variant,,ENST00000635983,; A ENST00000454575 Transcript missense_variant 4680/6985 4669/6390 1557/2129 G/C Ggt/Tgt rs147103646 1 -1 DOCK7 HGNC HGNC:19190 protein_coding YES CCDS60156.1 ENSP00000413583 Q96N67 H0Y7L2 UPI0000E45660 NM_001271999.1 deleterious(0.01) 37/49 hmmpanther:PTHR23317:SF78,hmmpanther:PTHR23317 MODERATE 1 SNV 1 1 PASS rs147103646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 62504698 62504698 C A 1 0 0 0 0 1 0 0 0 4507 652 23 1 1 DOCK7 1 62504698 Missense_Mutation SNP C C3N-00560_T 231429 62504698 186451724 24 16713 MIER1 0 . GRCh38 1 66958098 66958098 + Missense_Mutation SNP G G T rs866229137 C3N-00560_T C3N-00560_N G G c.379G>T p.Gly127Cys p.G127C ENST00000401041 5/14 186 161 25 134 134 0 strelka-mutect MIER1,missense_variant,p.Gly91Cys,ENST00000357692,NM_001146112.1,NM_020948.3,NM_001146110.1;MIER1,missense_variant,p.Gly74Cys,ENST00000355356,NM_001077701.2;MIER1,missense_variant,p.Gly91Cys,ENST00000371018,NM_001146111.1;MIER1,missense_variant,p.Gly11Cys,ENST00000355977,NM_001146113.1;MIER1,missense_variant,p.Gly127Cys,ENST00000401041,NM_001077700.2;MIER1,missense_variant,p.Gly91Cys,ENST00000371016,NM_001077702.2;MIER1,missense_variant,p.Gly127Cys,ENST00000371014,NM_001077703.2;MIER1,missense_variant,p.Gly74Cys,ENST00000401042,NM_001077704.2;MIER1,non_coding_transcript_exon_variant,,ENST00000479067,;MIER1,upstream_gene_variant,,ENST00000493357,; T ENST00000401041 Transcript missense_variant 449/2552 379/1698 127/565 G/C Ggt/Tgt rs866229137 1 1 MIER1 HGNC HGNC:29657 protein_coding YES CCDS53326.1 ENSP00000383820 Q8N108 UPI0000204526 NM_001077700.2 deleterious(0.02) 5/14 hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF24 MODERATE 1 SNV 2 1 PASS rs866229137 . 0 207 0 3 0 0 0 0 -20 0.9999921 1 1 1 0 T 3 4 56 66958098 66958098 G T 1 0 0 0 0 1 0 0 0 9543 1348 47 2 2 MIER1 1 66958098 Missense_Mutation SNP G C3N-00560_T 4453400 66958098 181998324 25 16714 RPE65 0 . GRCh38 1 68440953 68440953 + Silent SNP G G T rs746156974 C3N-00560_T C3N-00560_N G G c.543C>A p.= p.P181P ENST00000262340 6/14 372 311 61 261 261 0 strelka-varscan-mutect RPE65,synonymous_variant,p.=,ENST00000262340,NM_000329.2; T ENST00000262340 Transcript synonymous_variant 597/2610 543/1602 181/533 P ccC/ccA rs746156974 1 -1 RPE65 HGNC HGNC:10294 protein_coding YES CCDS643.1 ENSP00000262340 Q16518 UPI000004346C NM_000329.2 6/14 Pfam_domain:PF03055,hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF43 LOW 1 SNV 1 1 PASS rs746156974 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 68440953 68440953 G T 1 0 0 0 0 0 0 0 1 13796 1219 43 2 2 RPE65 1 68440953 Silent SNP G C3N-00560_T 1482855 68440953 180515469 26 16715 CTH 0 . GRCh38 1 70435178 70435178 + Splice_Site SNP G G T rs570239863 C3N-00560_T C3N-00560_N G G c.1052+1G>T p.X351_splice ENST00000370938 422 377 45 365 365 0 strelka-varscan-mutect CTH,splice_donor_variant,,ENST00000411986,NM_001190463.1;CTH,splice_donor_variant,,ENST00000370938,NM_001902.5;CTH,splice_donor_variant,,ENST00000346806,NM_153742.4;Metazoa_SRP,downstream_gene_variant,,ENST00000612213,;CTH,splice_donor_variant,,ENST00000482383,;CTH,downstream_gene_variant,,ENST00000464926,; T ENST00000370938 Transcript splice_donor_variant -/1805 1052/1218 351/405 rs570239863 1 1 CTH HGNC HGNC:2501 protein_coding YES CCDS650.1 ENSP00000359976 P32929 UPI00001275DE NM_001902.5 10/11 HIGH 1 SNV 1 1 PASS rs763437497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 70435178 70435178 G T 1 0 0 0 0 0 0 1 0 3817 1159 40 1 1 CTH 1 70435178 Splice_Site SNP G C3N-00560_T 1994225 70435178 178521244 27 16716 NEGR1 0 . GRCh38 1 71592965 71592965 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.792C>T p.= p.L264L ENST00000357731 6/7 78 61 17 84 84 0 strelka-varscan-mutect NEGR1,synonymous_variant,p.=,ENST00000357731,NM_173808.2;NEGR1,synonymous_variant,p.=,ENST00000306821,; A ENST00000357731 Transcript synonymous_variant 1032/12811 792/1065 264/354 L ctC/ctT 1 -1 NEGR1 HGNC HGNC:17302 protein_coding YES CCDS661.1 ENSP00000350364 Q7Z3B1 UPI00000477EE NM_173808.2 6/7 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF132,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1290717485 . 0 196 14 0 0 0 0 0 -20 0.999867 1 1 1 0 A 2 1 56 71592965 71592965 G A 1 0 0 0 0 0 0 0 1 10345 956 33 3 3 NEGR1 1 71592965 Silent SNP G C3N-00560_T 1157787 71592965 177363457 28 16717 ERICH3 0 . GRCh38 1 74620885 74620885 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.849A>G p.= p.L283L ENST00000326665 8/15 78 56 22 98 98 0 strelka-varscan-mutect ERICH3,synonymous_variant,p.=,ENST00000326665,NM_001002912.4;ERICH3,synonymous_variant,p.=,ENST00000420661,;ERICH3-AS1,intron_variant,,ENST00000612390,;ERICH3-AS1,intron_variant,,ENST00000416017,;ERICH3,3_prime_UTR_variant,,ENST00000479666,; C ENST00000326665 Transcript synonymous_variant 1068/7159 849/4593 283/1530 L ttA/ttG 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 8/15 hmmpanther:PTHR23034 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 74620885 74620885 T C 1 0 0 0 0 0 0 0 1 5083 1635 57 5 5 ERICH3 1 74620885 Silent SNP T C3N-00560_T 3027920 74620885 174335537 29 16718 PIGK 0 . GRCh38 1 77219325 77219325 + Silent SNP G G A rs536087505 C3N-00560_T C3N-00560_N G G c.78C>T p.= p.A26A ENST00000370812 1/11 224 189 35 262 260 2 strelka-varscan-mutect PIGK,synonymous_variant,p.=,ENST00000370812,NM_005482.2;PIGK,synonymous_variant,p.=,ENST00000445065,;PIGK,synonymous_variant,p.=,ENST00000359130,;PIGK,non_coding_transcript_exon_variant,,ENST00000478391,; A ENST00000370812 Transcript synonymous_variant 102/4596 78/1188 26/395 A gcC/gcT rs536087505,COSM5137466 1 -1 PIGK HGNC HGNC:8965 protein_coding YES CCDS674.1 ENSP00000359848 Q92643 UPI000012B9D1 NM_005482.2 1/11 PIRSF_domain:PIRSF019663,PIRSF_domain:PIRSF500138,hmmpanther:PTHR12000,hmmpanther:PTHR12000:SF1,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs536087505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 77219325 77219325 G A 1 0 0 0 0 0 0 0 1 11984 1103 39 1 1 PIGK 1 77219325 Silent SNP G C3N-00560_T 2598440 77219325 171737097 30 16719 AK5 0 . GRCh38 1 77297914 77297914 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.666A>T p.Arg222Ser p.R222S ENST00000354567 5/14 91 76 15 122 122 0 strelka-varscan-mutect AK5,missense_variant,p.Arg196Ser,ENST00000344720,NM_012093.3;AK5,missense_variant,p.Arg222Ser,ENST00000354567,NM_174858.2;AK5,downstream_gene_variant,,ENST00000478407,;AK5,non_coding_transcript_exon_variant,,ENST00000317704,;AK5,non_coding_transcript_exon_variant,,ENST00000524494,;AK5,non_coding_transcript_exon_variant,,ENST00000466114,;AK5,downstream_gene_variant,,ENST00000469394,; T ENST00000354567 Transcript missense_variant 929/3251 666/1689 222/562 R/S agA/agT 1 1 AK5 HGNC HGNC:365 protein_coding YES CCDS675.1 ENSP00000346577 Q9Y6K8 UPI0000167E20 NM_174858.2 deleterious(0) 5/14 HAMAP:MF_00235,hmmpanther:PTHR23359:SF79,hmmpanther:PTHR23359,PROSITE_patterns:PS00113,Pfam_domain:PF00406,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1383094445 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 77297914 77297914 A T 1 0 0 0 0 1 0 0 0 522 301 11 4 4 AK5 1 77297914 Missense_Mutation SNP A C3N-00560_T 78589 77297914 171658508 31 16720 ADGRL4 0 . GRCh38 1 78946294 78946294 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.305A>T p.Asn102Ile p.N102I ENST00000370742 3/15 105 87 18 115 115 0 strelka-varscan-mutect ADGRL4,missense_variant,p.Asn102Ile,ENST00000370742,NM_022159.3; A ENST00000370742 Transcript missense_variant 369/3527 305/2073 102/690 N/I aAt/aTt 1 -1 ADGRL4 HGNC HGNC:20822 protein_coding YES CCDS41352.1 ENSP00000359778 Q9HBW9 UPI00004561FF NM_022159.3 deleterious_low_confidence(0) 3/15 hmmpanther:PTHR12011:SF59,hmmpanther:PTHR12011,Gene3D:2.40.155.10,SMART_domains:SM00181,SMART_domains:SM00179 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 78946294 78946294 T A 1 0 0 0 0 1 0 0 0 378 1493 52 4 4 ADGRL4 1 78946294 Missense_Mutation SNP T C3N-00560_T 1648380 78946294 170010128 32 16721 WDR63 0 . GRCh38 1 85084594 85084594 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.439G>T p.Glu147Ter p.E147* ENST00000294664 6/23 83 50 33 92 92 0 strelka-varscan-mutect WDR63,stop_gained,p.Glu147Ter,ENST00000294664,NM_145172.4;WDR63,stop_gained,p.Glu147Ter,ENST00000370596,;WDR63,stop_gained,p.Glu147Ter,ENST00000326813,NM_001288563.1;WDR63,downstream_gene_variant,,ENST00000528899,;WDR63,stop_gained,p.Glu147Ter,ENST00000464801,; T ENST00000294664 Transcript stop_gained 619/2995 439/2676 147/891 E/* Gaa/Taa 1 1 WDR63 HGNC HGNC:30711 protein_coding YES CCDS702.1 ENSP00000294664 Q8IWG1 A0A140VJZ8 UPI00000744F1 NM_145172.4 6/23 hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF5 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 85084594 85084594 G T 1 0 0 0 0 0 1 0 0 17873 1291 45 2 2 WDR63 1 85084594 Nonsense_Mutation SNP G C3N-00560_T 6138300 85084594 163871828 33 16722 CLCA1 0 . GRCh38 1 86499762 86499762 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2462C>A p.Ser821Tyr p.S821Y ENST00000234701 15/15 173 129 44 199 199 0 strelka-mutect CLCA1,missense_variant,p.Ser821Tyr,ENST00000234701,;CLCA1,missense_variant,p.Ser821Tyr,ENST00000394711,NM_001285.3; A ENST00000234701 Transcript missense_variant 2813/3310 2462/2745 821/914 S/Y tCt/tAt 1 1 CLCA1 HGNC HGNC:2015 protein_coding YES CCDS709.1 ENSP00000234701 A8K7I4 UPI00001AE689 deleterious(0.04) 15/15 hmmpanther:PTHR10579:SF52,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 86499762 86499762 C A 1 0 0 0 0 1 0 0 0 3221 913 32 2 2 CLCA1 1 86499762 Missense_Mutation SNP C C3N-00560_T 1415168 86499762 162456660 34 16723 BARHL2 0 . GRCh38 1 90716901 90716901 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.295G>C p.Ala99Pro p.A99P ENST00000370445 1/3 246 154 92 221 221 0 strelka-varscan-mutect BARHL2,missense_variant,p.Ala99Pro,ENST00000370445,NM_020063.1; G ENST00000370445 Transcript missense_variant 337/1979 295/1164 99/387 A/P Gcg/Ccg 1 -1 BARHL2 HGNC HGNC:954 protein_coding YES CCDS730.1 ENSP00000359474 Q9NY43 UPI00001B50ED NM_020063.1 tolerated_low_confidence(0.34) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24330:SF4,hmmpanther:PTHR24330 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 90716901 90716901 C G 1 0 0 0 0 1 0 0 0 1466 768 27 4 4 BARHL2 1 90716901 Missense_Mutation SNP C C3N-00560_T 4217139 90716901 158239521 35 16724 HFM1 0 . GRCh38 1 91352605 91352605 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.1878A>G p.= p.L626L ENST00000370425 16/39 89 74 15 132 132 0 strelka-varscan-mutect HFM1,synonymous_variant,p.=,ENST00000370425,NM_001017975.4;HFM1,non_coding_transcript_exon_variant,,ENST00000462405,; C ENST00000370425 Transcript synonymous_variant 1977/4931 1878/4308 626/1435 L ctA/ctG 1 -1 HFM1 HGNC HGNC:20193 protein_coding YES CCDS30769.2 ENSP00000359454 A2PYH4 UPI0000F51F79 NM_001017975.4 16/39 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,SMART_domains:SM00490,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 91352605 91352605 T C 1 0 0 0 0 0 0 0 1 6967 1509 53 5 5 HFM1 1 91352605 Silent SNP T C3N-00560_T 635704 91352605 157603817 36 16725 ABCA4 0 . GRCh38 1 94031939 94031939 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.3967G>C p.Gly1323Arg p.G1323R ENST00000370225 27/50 394 323 71 410 409 1 strelka-varscan-mutect ABCA4,missense_variant,p.Gly1323Arg,ENST00000370225,NM_000350.2;ABCA4,missense_variant,p.Gly115Arg,ENST00000536513,; G ENST00000370225 Transcript missense_variant 4054/7309 3967/6822 1323/2273 G/R Ggg/Cgg COSM5447327 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 tolerated(0.13) 27/50 Low_complexity_(Seg):seg,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF97,TIGRFAM_domain:TIGR01257 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 94031939 94031939 C G 1 0 0 0 0 1 0 0 0 38 681 24 4 4 ABCA4 1 94031939 Missense_Mutation SNP C C3N-00560_T 2679334 94031939 154924483 37 16726 PLPPR4 0 . GRCh38 1 99301821 99301821 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.890G>T p.Arg297Leu p.R297L ENST00000370185 6/7 132 96 36 138 138 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Arg297Leu,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Arg139Leu,ENST00000370184,;PLPPR4,intron_variant,,ENST00000457765,NM_001166252.1; T ENST00000370185 Transcript missense_variant 1387/5369 890/2292 297/763 R/L cGg/cTg 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0) 6/7 hmmpanther:PTHR10165:SF13,hmmpanther:PTHR10165,Pfam_domain:PF01569,Gene3D:1.20.144.10,SMART_domains:SM00014,Superfamily_domains:SSF48317 MODERATE 1 SNV 1 1 PASS rs1256827767 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 99301821 99301821 G T 1 0 0 0 0 1 0 0 0 12212 1116 39 1 1 PLPPR4 1 99301821 Missense_Mutation SNP G C3N-00560_T 5269882 99301821 149654601 38 16727 PALMD 0 . GRCh38 1 99689805 99689805 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1545C>A p.Ser515Arg p.S515R ENST00000263174 7/8 131 74 57 106 106 0 strelka-varscan-mutect PALMD,missense_variant,p.Ser515Arg,ENST00000263174,NM_017734.4;PALMD,missense_variant,p.Ser515Arg,ENST00000605497,;PALMD,missense_variant,p.Ser435Arg,ENST00000615664,;PALMD,non_coding_transcript_exon_variant,,ENST00000496843,; A ENST00000263174 Transcript missense_variant 1920/2510 1545/1656 515/551 S/R agC/agA 1 1 PALMD HGNC HGNC:15846 protein_coding YES CCDS758.1 ENSP00000263174 Q9NP74 A0A0S2Z5E7 UPI000006DDD8 NM_017734.4 tolerated(0.36) 7/8 hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF5 MODERATE 1 SNV 1 1 PASS rs924841206 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 99689805 99689805 C A 1 0 0 0 0 1 0 0 0 11491 738 26 2 2 PALMD 1 99689805 Missense_Mutation SNP C C3N-00560_T 387984 99689805 149266617 39 16728 OLFM3 0 . GRCh38 1 101996748 101996749 + Frame_Shift_Ins INS - - T novel C3N-00560_T C3N-00560_N - - c.68dupA p.Thr24AspfsTer4 p.T24Dfs*4 ENST00000370103 1/6 128 77 51 184 184 0 sindel-varindel-pindel OLFM3,frameshift_variant,p.Thr24AspfsTer4,ENST00000370103,NM_058170.3;OLFM3,splice_region_variant,,ENST00000462354,; T ENST00000370103 Transcript frameshift_variant,splice_region_variant 282-283/3255 68-69/1377 23/458 K/KX aag/aaAg 1 -1 OLFM3 HGNC HGNC:17990 protein_coding CCDS30781.1 ENSP00000359121 Q96PB7 UPI000002AF6A NM_058170.3 1/6 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF36 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 7 5 56 101996748 101996748 - T 1 0 1 1 0 0 0 0 0 10929 695 24 0 0 OLFM3 1 101996748 Frame_Shift_Ins INS - C3N-00560_T 2306943 101996748 146959674 40 16729 COL11A1 0 . GRCh38 1 103003226 103003226 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1987C>A p.Pro663Thr p.P663T ENST00000370096 21/67 341 290 51 442 442 0 strelka-varscan-mutect COL11A1,missense_variant,p.Pro675Thr,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro663Thr,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro624Thr,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro547Thr,ENST00000512756,NM_080630.3;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,intron_variant,,ENST00000475980,;COL11A1,missense_variant,p.Pro436Thr,ENST00000635193,; T ENST00000370096 Transcript missense_variant 2300/7286 1987/5421 663/1806 P/T Cca/Aca 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.05) 21/67 Pfam_domain:PF01391,Pfam_domain:PF01391,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 103003226 103003226 G T 1 0 0 0 0 1 0 0 0 3455 1174 41 2 2 COL11A1 1 103003226 Missense_Mutation SNP G C3N-00560_T 1006478 103003226 145953196 41 16730 COL11A1 0 . GRCh38 1 103005858 103005858 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.1825C>A p.Pro609Thr p.P609T ENST00000370096 18/67 237 141 96 233 233 0 strelka-varscan-mutect COL11A1,missense_variant,p.Pro621Thr,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro609Thr,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro570Thr,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro493Thr,ENST00000512756,NM_080630.3;COL11A1,downstream_gene_variant,,ENST00000427239,;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,upstream_gene_variant,,ENST00000475980,;COL11A1,missense_variant,p.Pro382Thr,ENST00000635193,; T ENST00000370096 Transcript missense_variant 2138/7286 1825/5421 609/1806 P/T Cca/Aca COSM5443465,COSM5443466 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 18/67 Pfam_domain:PF01391 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 103005858 103005858 G T 1 0 0 0 0 1 0 0 0 3455 1203 42 2 2 COL11A1 1 103005858 Missense_Mutation SNP G C3N-00560_T 2632 103005858 145950564 42 16731 AMY2A 0 . GRCh38 1 103617449 103617449 + Missense_Mutation SNP C C G rs372297866 C3N-00560_T C3N-00560_N C C c.9C>G p.Phe3Leu p.F3L ENST00000622339 2/11 175 145 30 189 188 1 strelka-varscan-mutect AMY2A,missense_variant,p.Phe3Leu,ENST00000622339,;AMY2A,missense_variant,p.Phe3Leu,ENST00000414303,NM_000699.3;AMY2A,missense_variant,p.Phe2Leu,ENST00000423678,;AMY2A,upstream_gene_variant,,ENST00000497748,; G ENST00000622339 Transcript missense_variant 304/1862 9/1536 3/511 F/L ttC/ttG rs372297866 1 1 AMY2A HGNC HGNC:477 protein_coding YES CCDS783.1 ENSP00000481450 P04746 UPI0000000C80 tolerated(0.87) 2/11 hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF161,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS rs372297866 . 2 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 56 103617449 103617449 C G 1 0 0 0 0 1 0 0 0 691 912 32 4 4 AMY2A 1 103617449 Missense_Mutation SNP C C3N-00560_T 611591 103617449 145338973 43 16732 NTNG1 0 . GRCh38 1 107148717 107148717 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.124G>T p.Gly42Trp p.G42W ENST00000370068 2/8 354 301 53 376 376 0 strelka-varscan-mutect NTNG1,missense_variant,p.Gly42Trp,ENST00000370067,;NTNG1,missense_variant,p.Gly42Trp,ENST00000370068,;NTNG1,missense_variant,p.Gly42Trp,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Gly42Trp,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Gly42Trp,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Gly42Trp,ENST00000370065,;NTNG1,missense_variant,p.Gly42Trp,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000462149,;NTNG1,downstream_gene_variant,,ENST00000370076,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; T ENST00000370068 Transcript missense_variant 970/4034 124/1620 42/539 G/W Ggg/Tgg 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 2/8 hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 107148717 107148717 G T 1 0 0 0 0 1 0 0 0 10769 1000 35 2 2 NTNG1 1 107148717 Missense_Mutation SNP G C3N-00560_T 3531268 107148717 141807705 44 16733 WDR47 0 . GRCh38 1 108983370 108983370 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2031G>C p.Trp677Cys p.W677C ENST00000400794 11/15 155 126 29 130 130 0 strelka-varscan-mutect WDR47,missense_variant,p.Trp670Cys,ENST00000369965,NM_014969.5;WDR47,missense_variant,p.Trp669Cys,ENST00000369962,NM_001142551.1;WDR47,missense_variant,p.Trp641Cys,ENST00000357672,;WDR47,missense_variant,p.Trp677Cys,ENST00000400794,NM_001142550.1;WDR47,missense_variant,p.Trp641Cys,ENST00000361054,;RP5-1065J22.2,downstream_gene_variant,,ENST00000439282,; G ENST00000400794 Transcript missense_variant 2165/4134 2031/2784 677/927 W/C tgG/tgC 1 -1 WDR47 HGNC HGNC:29141 protein_coding YES CCDS44186.1 ENSP00000383599 O94967 UPI0001639B05 NM_001142550.1 deleterious(0) 11/15 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19863,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 108983370 108983370 C G 1 0 0 0 0 1 0 0 0 17860 856 30 4 4 WDR47 1 108983370 Missense_Mutation SNP C C3N-00560_T 1834653 108983370 139973052 45 16734 UBL4B 0 . GRCh38 1 110112754 110112754 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.220T>A p.Leu74Met p.L74M ENST00000334179 1/1 327 215 112 334 334 0 strelka-varscan-mutect UBL4B,missense_variant,p.Leu74Met,ENST00000334179,NM_203412.1;LINC01397,downstream_gene_variant,,ENST00000554808,; A ENST00000334179 Transcript missense_variant 287/1478 220/525 74/174 L/M Ttg/Atg 1 1 UBL4B HGNC HGNC:32309 protein_coding YES CCDS820.1 ENSP00000334044 Q8N7F7 UPI0000072926 NM_203412.1 tolerated(0.05) 1/1 hmmpanther:PTHR10666,hmmpanther:PTHR10666:SF108,Superfamily_domains:SSF54236 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 110112754 110112754 T A 1 0 0 0 0 1 0 0 0 17412 1606 56 4 4 UBL4B 1 110112754 Missense_Mutation SNP T C3N-00560_T 1129384 110112754 138843668 46 16735 MAGI3 0 . GRCh38 1 113585416 113585416 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.583G>T p.Ala195Ser p.A195S ENST00000307546 4/21 281 237 44 243 243 0 strelka-varscan-mutect MAGI3,missense_variant,p.Ala195Ser,ENST00000369615,NM_152900.2;MAGI3,missense_variant,p.Ala195Ser,ENST00000307546,NM_001142782.1;MAGI3,missense_variant,p.Ala195Ser,ENST00000369617,;MAGI3,missense_variant,p.Ala195Ser,ENST00000369611,;MAGI3,downstream_gene_variant,,ENST00000486456,; T ENST00000307546 Transcript missense_variant 658/6430 583/4446 195/1481 A/S Gca/Tca 1 1 MAGI3 HGNC HGNC:29647 protein_coding YES CCDS44196.1 ENSP00000304604 Q5TCQ9 UPI00004589AE NM_001142782.1 tolerated(0.19) 4/21 hmmpanther:PTHR10316:SF10,hmmpanther:PTHR10316,Gene3D:3.30.63.10,SMART_domains:SM00072 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 113585416 113585416 G T 1 0 0 0 0 1 0 0 0 9110 971 34 2 2 MAGI3 1 113585416 Missense_Mutation SNP G C3N-00560_T 3472662 113585416 135371006 47 16736 HSD3B2 0 . GRCh38 1 119422314 119422314 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.813G>T p.= p.L271L ENST00000543831 4/4 420 276 144 339 338 1 strelka-varscan-mutect HSD3B2,synonymous_variant,p.=,ENST00000543831,NM_001166120.1;HSD3B2,synonymous_variant,p.=,ENST00000369416,NM_000198.3;HSD3B2,downstream_gene_variant,,ENST00000433745,;HSD3B2,downstream_gene_variant,,ENST00000471656,;HSD3B2,downstream_gene_variant,,ENST00000443865,;HSD3B2,downstream_gene_variant,,ENST00000448448,; T ENST00000543831 Transcript synonymous_variant 1062/1783 813/1119 271/372 L ctG/ctT 1 1 HSD3B2 HGNC HGNC:5218 protein_coding YES CCDS902.1 ENSP00000445122 P26439 A0A024R0F9 UPI0000001C6C NM_001166120.1 4/4 Gene3D:3.40.50.720,Pfam_domain:PF01073,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF444,Superfamily_domains:SSF51735 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 119422314 119422314 G T 1 0 0 0 0 0 0 0 1 7285 1277 45 2 2 HSD3B2 1 119422314 Silent SNP G C3N-00560_T 5836898 119422314 129534108 48 16737 HSD3B1 0 . GRCh38 1 119513891 119513891 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.368C>G p.Thr123Ser p.T123S ENST00000369413 4/4 141 97 44 123 123 0 strelka-mutect HSD3B1,missense_variant,p.Thr123Ser,ENST00000369413,NM_000862.2;HSD3B1,missense_variant,p.Thr123Ser,ENST00000528909,;HSD3B1,downstream_gene_variant,,ENST00000531340,;HSD3B1,downstream_gene_variant,,ENST00000492140,; G ENST00000369413 Transcript missense_variant 513/1676 368/1122 123/373 T/S aCc/aGc 1 1 HSD3B1 HGNC HGNC:5217 protein_coding YES CCDS903.1 ENSP00000358421 P14060 UPI0000036BD2 NM_000862.2 tolerated(0.07) 4/4 Gene3D:3.40.50.720,Pfam_domain:PF01073,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF378,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 119513891 119513891 C G 1 0 0 0 0 1 0 0 0 7284 507 18 4 4 HSD3B1 1 119513891 Missense_Mutation SNP C C3N-00560_T 91577 119513891 129442531 49 16738 SV2A 0 . GRCh38 1 149906834 149906834 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.1701G>T p.= p.V567V ENST00000369146 11/13 352 247 105 334 333 1 strelka-varscan-mutect SV2A,synonymous_variant,p.=,ENST00000369146,NM_014849.4;SV2A,synonymous_variant,p.=,ENST00000369145,; A ENST00000369146 Transcript synonymous_variant 2192/4416 1701/2229 567/742 V gtG/gtT 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 11/13 Pfam_domain:PF13599,PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF11,Superfamily_domains:SSF141571,TIGRFAM_domain:TIGR01299 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 149906834 149906834 C A 1 0 0 0 0 0 0 0 1 15801 813 29 2 2 SV2A 1 149906834 Silent SNP C C3N-00560_T 30392943 149906834 99049588 50 16739 OTUD7B 0 . GRCh38 1 149967443 149967443 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.353G>A p.Gly118Asp p.G118D ENST00000581312 4/12 172 127 45 133 133 0 strelka-varscan-mutect OTUD7B,missense_variant,p.Gly118Asp,ENST00000581312,NM_020205.3;OTUD7B,missense_variant,p.Gly118Asp,ENST00000417191,;OTUD7B,intron_variant,,ENST00000619871,; T ENST00000581312 Transcript missense_variant 648/8872 353/2532 118/843 G/D gGt/gAt 1 -1 OTUD7B HGNC HGNC:16683 protein_coding YES CCDS72903.1 ENSP00000462729 Q6GQQ9 UPI000020415D NM_020205.3 tolerated(0.41) 4/12 hmmpanther:PTHR13367,hmmpanther:PTHR13367:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 149967443 149967443 C T 1 0 0 0 0 1 0 0 0 11388 507 18 3 3 OTUD7B 1 149967443 Missense_Mutation SNP C C3N-00560_T 60609 149967443 98988979 51 16740 TARS2 0 . GRCh38 1 150506957 150506957 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.2050C>T p.Arg684Trp p.R684W ENST00000369064 18/18 225 146 79 160 160 0 strelka-varscan-mutect TARS2,missense_variant,p.Arg684Trp,ENST00000369064,NM_025150.4;TARS2,missense_variant,p.Arg409Trp,ENST00000438568,;TARS2,missense_variant,p.Arg602Trp,ENST00000606933,NM_001271895.1;TARS2,missense_variant,p.Arg554Trp,ENST00000369054,NM_001271896.1;ECM1,upstream_gene_variant,,ENST00000369047,NM_004425.3;ECM1,upstream_gene_variant,,ENST00000369049,NM_001202858.1;ECM1,upstream_gene_variant,,ENST00000346569,NM_022664.2;ECM1,upstream_gene_variant,,ENST00000470432,;ECM1,upstream_gene_variant,,ENST00000496744,;ECM1,upstream_gene_variant,,ENST00000498579,;TARS2,downstream_gene_variant,,ENST00000463555,;TARS2,downstream_gene_variant,,ENST00000480070,;ECM1,upstream_gene_variant,,ENST00000490346,;TARS2,downstream_gene_variant,,ENST00000483046,;TARS2,3_prime_UTR_variant,,ENST00000369051,;TARS2,3_prime_UTR_variant,,ENST00000467982,; T ENST00000369064 Transcript missense_variant 2084/2729 2050/2157 684/718 R/W Cgg/Tgg 1 1 TARS2 HGNC HGNC:30740 protein_coding YES CCDS952.1 ENSP00000358060 Q9BW92 UPI00000492D1 NM_025150.4 deleterious(0) 18/18 HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF27,TIGRFAM_domain:TIGR00418,Gene3D:3.40.50.800,Pfam_domain:PF03129,Superfamily_domains:SSF52954 MODERATE 1 SNV 1 1 PASS rs1294564776 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 150506957 150506957 C T 1 0 0 0 0 1 0 0 0 15959 875 31 1 1 TARS2 1 150506957 Missense_Mutation SNP C C3N-00560_T 539514 150506957 98449465 52 16741 SEMA6C 0 . GRCh38 1 151136529 151136529 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1025G>T p.Gly342Val p.G342V ENST00000368913 12/20 237 185 52 197 197 0 strelka-varscan-mutect SEMA6C,missense_variant,p.Gly342Val,ENST00000341697,;SEMA6C,missense_variant,p.Gly342Val,ENST00000368914,NM_030913.4;SEMA6C,missense_variant,p.Gly342Val,ENST00000368913,NM_001178061.1;SEMA6C,missense_variant,p.Gly302Val,ENST00000368912,NM_001178062.1;SEMA6C,missense_variant,p.Gly342Val,ENST00000613223,;SEMA6C,missense_variant,p.Gly342Val,ENST00000621728,;RP11-68I18.10,upstream_gene_variant,,ENST00000563624,;SEMA6C,upstream_gene_variant,,ENST00000479820,;SEMA6C,upstream_gene_variant,,ENST00000464018,;SEMA6C,upstream_gene_variant,,ENST00000489944,;SEMA6C,downstream_gene_variant,,ENST00000485745,; A ENST00000368913 Transcript missense_variant 1154/3817 1025/2889 342/962 G/V gGg/gTg 1 -1 SEMA6C HGNC HGNC:10740 protein_coding YES CCDS53364.1 ENSP00000357909 Q9H3T2 UPI00001414D0 NM_001178061.1 tolerated(0.39) 12/20 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF11,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 151136529 151136529 C A 1 0 0 0 0 1 0 0 0 14317 623 22 2 2 SEMA6C 1 151136529 Missense_Mutation SNP C C3N-00560_T 629572 151136529 97819893 53 16742 PSMD4 0 . GRCh38 1 151264891 151264891 + Frame_Shift_Del DEL A A - rs779184227 C3N-00560_T C3N-00560_N A A c.343delA p.Ser115AlafsTer11 p.S115Afs*11 ENST00000368884 4/10 234 165 69 225 225 0 sindel-varindel PSMD4,frameshift_variant,p.Ser115AlafsTer11,ENST00000368884,NM_002810.2;PSMD4,frameshift_variant,p.Ser115AlafsTer11,ENST00000368881,;PSMD4,frameshift_variant,p.Ser100AlafsTer11,ENST00000437736,;PSMD4,frameshift_variant,p.Ser3AlafsTer11,ENST00000445776,;PSMD4,upstream_gene_variant,,ENST00000453615,;PSMD4,non_coding_transcript_exon_variant,,ENST00000469786,;PSMD4,non_coding_transcript_exon_variant,,ENST00000476855,;PSMD4,non_coding_transcript_exon_variant,,ENST00000462970,;PSMD4,downstream_gene_variant,,ENST00000461434,;PSMD4,upstream_gene_variant,,ENST00000427779,;PSMD4,upstream_gene_variant,,ENST00000491857,;PSMD4,upstream_gene_variant,,ENST00000470396,; - ENST00000368884 Transcript frameshift_variant 422/1350 342/1134 114/377 G/X ggA/gg rs779184227 1 1 PSMD4 HGNC HGNC:9561 protein_coding YES CCDS991.1 ENSP00000357879 P55036 UPI0000038DA5 NM_002810.2 4/10 PROSITE_profiles:PS50234,hmmpanther:PTHR10223,Pfam_domain:PF13519,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 151264891 151264891 A - 1 0 1 0 1 0 0 0 0 12851 233 9 0 0 PSMD4 1 151264891 Frame_Shift_Del DEL A C3N-00560_T 128362 151264891 97691531 54 16743 TDRKH 0 . GRCh38 1 151775129 151775129 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1472A>T p.Tyr491Phe p.Y491F ENST00000368822 11/14 215 152 63 186 186 0 strelka-varscan-mutect TDRKH,missense_variant,p.Tyr491Phe,ENST00000368822,;TDRKH,missense_variant,p.Tyr491Phe,ENST00000368824,NM_001083965.1;TDRKH,missense_variant,p.Tyr491Phe,ENST00000458431,NM_001083963.1;TDRKH,missense_variant,p.Tyr487Phe,ENST00000368823,;TDRKH,missense_variant,p.Tyr446Phe,ENST00000368825,NM_001083964.1;TDRKH,missense_variant,p.Tyr491Phe,ENST00000368827,NM_006862.3;TDRKH,missense_variant,p.Tyr491Phe,ENST00000440583,;OAZ3,downstream_gene_variant,,ENST00000479764,;OAZ3,downstream_gene_variant,,ENST00000400999,NM_016178.2;OAZ3,downstream_gene_variant,,ENST00000321531,NM_001134939.1;OAZ3,downstream_gene_variant,,ENST00000627780,;OAZ3,downstream_gene_variant,,ENST00000635322,;OAZ3,downstream_gene_variant,,ENST00000453029,NM_001301371.1;TDRKH,downstream_gene_variant,,ENST00000526378,;OAZ3,downstream_gene_variant,,ENST00000635374,;OAZ3,downstream_gene_variant,,ENST00000582415,;TDRKH,downstream_gene_variant,,ENST00000484421,;TDRKH,3_prime_UTR_variant,,ENST00000525790,;TDRKH,3_prime_UTR_variant,,ENST00000526413,;TDRKH,downstream_gene_variant,,ENST00000486986,;TDRKH,downstream_gene_variant,,ENST00000494725,;TDRKH,downstream_gene_variant,,ENST00000530202,; A ENST00000368822 Transcript missense_variant 2106/3093 1472/1686 491/561 Y/F tAc/tTc 1 -1 TDRKH HGNC HGNC:11713 protein_coding YES CCDS41394.1 ENSP00000357812 Q9Y2W6 UPI0000204267 deleterious(0.03) 11/14 hmmpanther:PTHR22948 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 151775129 151775129 T A 1 0 0 0 0 1 0 0 0 16147 1638 57 4 4 TDRKH 1 151775129 Missense_Mutation SNP T C3N-00560_T 510238 151775129 97181293 55 16744 LCE5A 0 . GRCh38 1 152511732 152511732 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.198C>A p.= p.G66G ENST00000334269 2/2 428 313 115 385 385 0 strelka-varscan-mutect LCE5A,synonymous_variant,p.=,ENST00000334269,NM_178438.4;CRCT1,upstream_gene_variant,,ENST00000368790,NM_019060.2;AL135842.1,downstream_gene_variant,,ENST00000624892,; A ENST00000334269 Transcript synonymous_variant 374/819 198/357 66/118 G ggC/ggA 1 1 LCE5A HGNC HGNC:16614 protein_coding YES CCDS1011.1 ENSP00000333952 Q5TCM9 UPI00001615D7 NM_178438.4 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,Low_complexity_(Seg):seg LOW SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 152511732 152511732 C A 1 0 0 0 0 0 0 0 1 8580 784 28 2 2 LCE5A 1 152511732 Silent SNP C C3N-00560_T 736603 152511732 96444690 56 16745 KPRP 0 . GRCh38 1 152759617 152759617 + Missense_Mutation SNP G G T rs77368440 C3N-00560_T C3N-00560_N G G c.29G>T p.Arg10Leu p.R10L ENST00000606109 1/1 137 87 50 118 118 0 strelka-varscan-mutect KPRP,missense_variant,p.Arg10Leu,ENST00000606109,NM_001025231.1; T ENST00000606109 Transcript missense_variant 57/2492 29/1740 10/579 R/L cGc/cTc rs77368440,COSM2156689 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 tolerated(0.12) 1/1 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 PASS rs77368440 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 152759617 152759617 G T 1 0 0 0 0 1 0 0 0 8316 1087 38 1 1 KPRP 1 152759617 Missense_Mutation SNP G C3N-00560_T 247885 152759617 96196805 57 16746 IVL 0 . GRCh38 1 152911254 152911254 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1457A>T p.Gln486Leu p.Q486L ENST00000368764 2/2 355 260 95 305 305 0 strelka-varscan-mutect IVL,missense_variant,p.Gln486Leu,ENST00000368764,NM_005547.2; T ENST00000368764 Transcript missense_variant 1521/2153 1457/1758 486/585 Q/L cAg/cTg 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 deleterious_low_confidence(0.01) 2/2 Pfam_domain:PF00904 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 152911254 152911254 A T 1 0 0 0 0 1 0 0 0 7835 188 7 4 4 IVL 1 152911254 Missense_Mutation SNP A C3N-00560_T 151637 152911254 96045168 58 16747 LOR 0 . GRCh38 1 153261039 153261039 + Silent SNP C C A rs747858365 C3N-00560_T C3N-00560_N C C c.90C>A p.= p.G30G ENST00000368742 2/2 276 184 92 277 277 0 strelka-varscan-mutect LOR,synonymous_variant,p.=,ENST00000368742,NM_000427.2; A ENST00000368742 Transcript synonymous_variant 147/1230 90/939 30/312 G ggC/ggA rs747858365 1 1 LOR HGNC HGNC:6663 protein_coding YES CCDS30870.1 ENSP00000357731 P23490 UPI0000470BBD NM_000427.2 2/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS51257,hmmpanther:PTHR39228,Pfam_domain:PF15847 LOW 1 SNV 1 1 PASS rs747858365 . 0 181 11 9 6 3 0 0 -8.918183 0.0570761 0 1 0 0 A 2 1 56 153261039 153261039 C A 1 0 0 0 0 0 0 0 1 8799 755 27 1 1 LOR 1 153261039 Silent SNP C C3N-00560_T 349785 153261039 95695383 59 16748 S100A5 0 . GRCh38 1 153540113 153540113 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.79C>G p.Leu27Val p.L27V ENST00000368718 3/4 244 173 71 227 227 0 strelka-varscan-mutect S100A5,missense_variant,p.Leu27Val,ENST00000368718,NM_002962.1;S100A5,missense_variant,p.Leu27Val,ENST00000368717,;S100A6,upstream_gene_variant,,ENST00000368720,;S100A6,upstream_gene_variant,,ENST00000496817,;S100A6,upstream_gene_variant,,ENST00000368719,NM_014624.3;S100A4,downstream_gene_variant,,ENST00000368716,NM_002961.2;S100A4,downstream_gene_variant,,ENST00000368715,;S100A4,downstream_gene_variant,,ENST00000354332,NM_019554.2;S100A4,downstream_gene_variant,,ENST00000368714,;S100A6,upstream_gene_variant,,ENST00000462776,;BX470102.3,downstream_gene_variant,,ENST00000420695,;S100A4,downstream_gene_variant,,ENST00000481009,;S100A4,downstream_gene_variant,,ENST00000468373,;S100A6,upstream_gene_variant,,ENST00000462951,; C ENST00000368718 Transcript missense_variant 361/710 79/279 27/92 L/V Ctg/Gtg 1 -1 S100A5 HGNC HGNC:10495 protein_coding YES CCDS1041.2 ENSP00000357707 P33763 UPI00001353F4 NM_002962.1 tolerated(0.13) 3/4 Gene3D:1.10.238.10,Pfam_domain:PF01023,hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF65,SMART_domains:SM01394,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 153540113 153540113 G C 1 0 0 0 0 1 0 0 0 14040 1020 36 4 4 S100A5 1 153540113 Missense_Mutation SNP G C3N-00560_T 279074 153540113 95416309 60 16749 AQP10 0 . GRCh38 1 154323004 154323004 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.255C>A p.Phe85Leu p.F85L ENST00000324978 3/6 294 190 104 226 226 0 strelka-varscan-mutect AQP10,missense_variant,p.Phe85Leu,ENST00000484864,;AQP10,missense_variant,p.Phe85Leu,ENST00000324978,NM_080429.2;ATP8B2,upstream_gene_variant,,ENST00000368489,NM_020452.3;ATP8B2,upstream_gene_variant,,ENST00000368487,NM_001005855.1;AQP10,non_coding_transcript_exon_variant,,ENST00000355197,;ATP8B2,upstream_gene_variant,,ENST00000368490,; A ENST00000324978 Transcript missense_variant 295/1791 255/906 85/301 F/L ttC/ttA 1 1 AQP10 HGNC HGNC:16029 protein_coding YES CCDS1065.1 ENSP00000318355 Q96PS8 UPI000007028A NM_080429.2 deleterious(0.05) 3/6 hmmpanther:PTHR19139:SF138,hmmpanther:PTHR19139,PROSITE_patterns:PS00221,TIGRFAM_domain:TIGR00861,Pfam_domain:PF00230,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338,Prints_domain:PR00783 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 154323004 154323004 C A 1 0 0 0 0 1 0 0 0 945 912 32 2 2 AQP10 1 154323004 Missense_Mutation SNP C C3N-00560_T 782891 154323004 94633418 61 16750 ATP8B2 0 . GRCh38 1 154330426 154330426 + Missense_Mutation SNP G G T rs149978531 C3N-00560_T C3N-00560_N G G c.161G>T p.Arg54Leu p.R54L ENST00000368489 3/28 178 129 49 114 114 0 strelka-varscan-mutect ATP8B2,missense_variant,p.Arg54Leu,ENST00000368489,NM_020452.3;ATP8B2,missense_variant,p.Arg21Leu,ENST00000368487,NM_001005855.1;ATP8B2,non_coding_transcript_exon_variant,,ENST00000426445,;ATP8B2,non_coding_transcript_exon_variant,,ENST00000368490,;ATP8B2,upstream_gene_variant,,ENST00000514107,; T ENST00000368489 Transcript missense_variant 161/5861 161/3672 54/1223 R/L cGa/cTa rs149978531 1 1 ATP8B2 HGNC HGNC:13534 protein_coding YES CCDS1066.1 ENSP00000357475 P98198 UPI00001B92AB NM_020452.3 deleterious(0) 3/28 Pfam_domain:PF16209,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF46,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs149978531 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 154330426 154330426 G T 1 0 0 0 0 1 0 0 0 1348 1058 37 1 1 ATP8B2 1 154330426 Missense_Mutation SNP G C3N-00560_T 7422 154330426 94625996 62 16751 PKLR 0 . GRCh38 1 155294279 155294279 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1072G>T p.Gly358Trp p.G358W ENST00000342741 7/11 706 483 223 620 619 1 strelka-varscan-mutect PKLR,missense_variant,p.Gly327Trp,ENST00000392414,NM_181871.3;PKLR,missense_variant,p.Gly358Trp,ENST00000342741,NM_000298.5;HCN3,downstream_gene_variant,,ENST00000368358,NM_020897.2;HCN3,downstream_gene_variant,,ENST00000496230,;HCN3,downstream_gene_variant,,ENST00000492035,;PKLR,downstream_gene_variant,,ENST00000434082,; A ENST00000342741 Transcript missense_variant 1111/2083 1072/1725 358/574 G/W Ggg/Tgg CM090466 1 -1 PKLR HGNC HGNC:9020 protein_coding YES CCDS1109.1 ENSP00000339933 P30613 UPI0000001292 NM_000298.5 deleterious(0) 7/11 hmmpanther:PTHR11817,hmmpanther:PTHR11817:SF31,TIGRFAM_domain:TIGR01064,Pfam_domain:PF00224,Gene3D:3.20.20.60,Superfamily_domains:SSF51621,Prints_domain:PR01050 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 155294279 155294279 C A 1 0 0 0 0 1 0 0 0 12072 594 21 2 2 PKLR 1 155294279 Missense_Mutation SNP C C3N-00560_T 963853 155294279 93662143 63 16752 INSRR 0 . GRCh38 1 156841045 156841045 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.3722A>G p.His1241Arg p.H1241R ENST00000368195 22/22 461 316 145 429 429 0 strelka-varscan-mutect INSRR,missense_variant,p.His1241Arg,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; C ENST00000368195 Transcript missense_variant 4119/5101 3722/3894 1241/1297 H/R cAc/cGc 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 deleterious(0.01) 22/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF338,PIRSF_domain:PIRSF000620,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 156841045 156841045 T C 1 0 0 0 0 1 0 0 0 7676 1696 59 5 5 INSRR 1 156841045 Missense_Mutation SNP T C3N-00560_T 1546766 156841045 92115377 64 16753 ETV3L 0 . GRCh38 1 157098754 157098754 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.438C>T p.= p.A146A ENST00000454449 3/5 86 75 11 73 73 0 strelka-varscan-mutect ETV3L,synonymous_variant,p.=,ENST00000454449,NM_001004341.2; A ENST00000454449 Transcript synonymous_variant 723/1976 438/1086 146/361 A gcC/gcT 1 -1 ETV3L HGNC HGNC:33834 protein_coding YES CCDS30893.1 ENSP00000430271 Q6ZN32 UPI000035E7AE NM_001004341.2 3/5 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF30 LOW 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -19.99976 0.9999994 1 1 1 0 A 2 1 56 157098754 157098754 G A 1 0 0 0 0 0 0 0 1 5144 1219 43 3 3 ETV3L 1 157098754 Silent SNP G C3N-00560_T 257709 157098754 91857668 65 16754 FCRL4 0 . GRCh38 1 157587353 157587353 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.770G>T p.Gly257Val p.G257V ENST00000271532 5/12 352 232 120 311 311 0 strelka-varscan-mutect FCRL4,missense_variant,p.Gly257Val,ENST00000271532,NM_031282.2;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,; A ENST00000271532 Transcript missense_variant 906/3459 770/1548 257/515 G/V gGa/gTa COSM3475750 1 -1 FCRL4 HGNC HGNC:18507 protein_coding YES CCDS1166.1 ENSP00000271532 Q96PJ5 UPI000006E26B NM_031282.2 deleterious(0) 5/12 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF59,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 157587353 157587353 C A 1 0 0 0 0 1 0 0 0 5659 855 30 2 2 FCRL4 1 157587353 Missense_Mutation SNP C C3N-00560_T 488599 157587353 91369069 66 16755 KIRREL 0 . GRCh38 1 158089529 158089529 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1072C>A p.Leu358Met p.L358M ENST00000359209 9/15 203 136 67 184 184 0 strelka-varscan-mutect KIRREL,missense_variant,p.Leu258Met,ENST00000368173,NM_001286349.1;KIRREL,missense_variant,p.Leu172Met,ENST00000368172,;KIRREL,missense_variant,p.Leu194Met,ENST00000360089,;KIRREL,missense_variant,p.Leu358Met,ENST00000359209,NM_018240.6; A ENST00000359209 Transcript missense_variant 1139/2874 1072/2274 358/757 L/M Ctg/Atg 1 1 KIRREL HGNC HGNC:15734 protein_coding YES CCDS1172.2 ENSP00000352138 Q96J84 UPI0000443FBD NM_018240.6 deleterious(0) 9/15 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF14,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 158089529 158089529 C A 1 0 0 0 0 1 0 0 0 8188 796 28 2 2 KIRREL 1 158089529 Missense_Mutation SNP C C3N-00560_T 502176 158089529 90866893 67 16756 OR10Z1 0 . GRCh38 1 158606942 158606942 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.504C>A p.Phe168Leu p.F168L ENST00000361284 1/1 407 300 107 372 372 0 strelka-varscan-mutect OR10Z1,missense_variant,p.Phe168Leu,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000485680,; A ENST00000361284 Transcript missense_variant 504/942 504/942 168/313 F/L ttC/ttA 1 1 OR10Z1 HGNC HGNC:14996 protein_coding YES CCDS30901.1 ENSP00000354707 Q8NGY1 A0A126GV63 UPI000004CA23 NM_001004478.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs901144945 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 158606942 158606942 C A 1 0 0 0 0 1 0 0 0 10999 912 32 2 2 OR10Z1 1 158606942 Missense_Mutation SNP C C3N-00560_T 517413 158606942 90349480 68 16757 SPTA1 0 . GRCh38 1 158613855 158613855 + Missense_Mutation SNP C C G rs371341474 C3N-00560_T C3N-00560_N C C c.6855G>C p.Glu2285Asp p.E2285D ENST00000368147 50/52 370 262 108 339 339 0 strelka-varscan-mutect SPTA1,missense_variant,p.Glu2285Asp,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000485680,;SPTA1,non_coding_transcript_exon_variant,,ENST00000481212,;SPTA1,non_coding_transcript_exon_variant,,ENST00000498708,;SPTA1,downstream_gene_variant,,ENST00000492934,; G ENST00000368147 Transcript missense_variant 7036/7999 6855/7260 2285/2419 E/D gaG/gaC rs371341474 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.03) 50/52 PROSITE_profiles:PS50222,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs371341474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 158613855 158613855 C G 1 0 0 0 0 1 0 0 0 15472 912 32 4 4 SPTA1 1 158613855 Missense_Mutation SNP C C3N-00560_T 6913 158613855 90342567 69 16758 SPTA1 0 . GRCh38 1 158620334 158620334 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.6253C>T p.His2085Tyr p.H2085Y ENST00000368147 44/52 410 297 113 369 369 0 strelka-varscan-mutect SPTA1,missense_variant,p.His2085Tyr,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript missense_variant 6434/7999 6253/7260 2085/2419 H/Y Cat/Tat 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 44/52 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 158620334 158620334 G A 1 0 0 0 0 1 0 0 0 15472 1348 47 3 3 SPTA1 1 158620334 Missense_Mutation SNP G C3N-00560_T 6479 158620334 90336088 70 16759 SPTA1 0 . GRCh38 1 158620428 158620428 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.6159A>T p.= p.S2053S ENST00000368147 44/52 214 145 69 183 183 0 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript synonymous_variant 6340/7999 6159/7260 2053/2419 S tcA/tcT 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 44/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 158620428 158620428 T A 1 0 0 0 0 0 0 0 1 15472 1567 55 4 4 SPTA1 1 158620428 Silent SNP T C3N-00560_T 94 158620428 90335994 71 16760 SPTA1 0 . GRCh38 1 158634653 158634653 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.5455C>A p.Leu1819Ile p.L1819I ENST00000368147 39/52 501 355 146 388 388 0 strelka-varscan-mutect SPTA1,missense_variant,p.Leu1819Ile,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,;SPTA1,downstream_gene_variant,,ENST00000465741,; T ENST00000368147 Transcript missense_variant 5636/7999 5455/7260 1819/2419 L/I Cta/Ata 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.01) 39/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Gene3D:1.20.58.60,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs960614315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 158634653 158634653 G T 1 0 0 0 0 1 0 0 0 15472 991 35 2 2 SPTA1 1 158634653 Missense_Mutation SNP G C3N-00560_T 14225 158634653 90321769 72 16761 SPTA1 0 . GRCh38 1 158648520 158648520 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.3703C>G p.Leu1235Val p.L1235V ENST00000368147 26/52 408 283 125 421 421 0 strelka-varscan-mutect SPTA1,missense_variant,p.Leu1235Val,ENST00000368147,NM_003126.2; C ENST00000368147 Transcript missense_variant 3884/7999 3703/7260 1235/2419 L/V Ctg/Gtg 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.02) 26/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS rs1345925946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 158648520 158648520 G C 1 0 0 0 0 1 0 0 0 15472 991 35 4 4 SPTA1 1 158648520 Missense_Mutation SNP G C3N-00560_T 13867 158648520 90307902 73 16762 SPTA1 0 . GRCh38 1 158674639 158674639 + Silent SNP T T A C3N-00560_T C3N-00560_N T T c.1149A>T p.= p.S383S ENST00000368147 9/52 696 497 199 610 610 0 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000467387,; A ENST00000368147 Transcript synonymous_variant 1330/7999 1149/7260 383/2419 S tcA/tcT COSM1986711 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 9/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 158674639 158674639 T A 1 0 0 0 0 0 0 0 1 15472 1567 55 4 4 SPTA1 1 158674639 Silent SNP T C3N-00560_T 26119 158674639 90281783 74 16763 PYHIN1 0 . GRCh38 1 158936948 158936948 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.38G>T p.Gly13Val p.G13V ENST00000368140 2/9 52 38 14 51 51 0 strelka-varscan-mutect PYHIN1,missense_variant,p.Gly13Val,ENST00000368140,NM_152501.4;PYHIN1,missense_variant,p.Gly13Val,ENST00000368138,NM_198928.4;PYHIN1,missense_variant,p.Gly13Val,ENST00000368135,;PYHIN1,missense_variant,p.Gly13Val,ENST00000392254,NM_198929.4;PYHIN1,missense_variant,p.Gly13Val,ENST00000392252,NM_198930.3;PYHIN1,missense_variant,p.Gly13Val,ENST00000458222,; T ENST00000368140 Transcript missense_variant 283/2083 38/1479 13/492 G/V gGa/gTa 1 1 PYHIN1 HGNC HGNC:28894 protein_coding YES CCDS1178.1 ENSP00000357122 Q6K0P9 UPI0000225618 NM_152501.4 deleterious(0) 2/9 Pfam_domain:PF02758,PROSITE_profiles:PS50824,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF14,SMART_domains:SM01289 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 158936948 158936948 G T 1 0 0 0 0 1 0 0 0 13019 1174 41 2 2 PYHIN1 1 158936948 Missense_Mutation SNP G C3N-00560_T 262309 158936948 90019474 75 16764 FCRL6 0 . GRCh38 1 159809463 159809463 + Missense_Mutation SNP C C A rs557324156 C3N-00560_T C3N-00560_N C C c.666C>A p.Asp222Glu p.D222E ENST00000368106 5/10 155 96 59 118 118 0 strelka-varscan-mutect FCRL6,missense_variant,p.Asp229Glu,ENST00000321935,NM_001284217.1;FCRL6,missense_variant,p.Asp222Glu,ENST00000339348,;FCRL6,missense_variant,p.Asp222Glu,ENST00000368106,NM_001004310.2;FCRL6,missense_variant,p.Asp127Glu,ENST00000392235,;FCRL6,downstream_gene_variant,,ENST00000536257,;FCRL6,downstream_gene_variant,,ENST00000540741,;FCRL6,downstream_gene_variant,,ENST00000541729,; A ENST00000368106 Transcript missense_variant 667/1306 666/1305 222/434 D/E gaC/gaA rs557324156 1 1 FCRL6 HGNC HGNC:31910 protein_coding YES CCDS30912.1 ENSP00000357086 Q6DN72 UPI0000D62020 NM_001004310.2 tolerated(0.14) 5/10 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF62,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs557324156 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 159809463 159809463 C A 1 0 0 0 0 1 0 0 0 5661 477 17 2 2 FCRL6 1 159809463 Missense_Mutation SNP C C3N-00560_T 872515 159809463 89146959 76 16765 ATP1A4 0 . GRCh38 1 160177585 160177585 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2657C>A p.Pro886His p.P886H ENST00000368081 18/22 164 128 36 153 152 1 strelka-varscan-mutect ATP1A4,missense_variant,p.Pro886His,ENST00000368081,NM_144699.3;ATP1A4,missense_variant,p.Pro22His,ENST00000470705,NM_001001734.1;ATP1A4,non_coding_transcript_exon_variant,,ENST00000418334,;ATP1A4,non_coding_transcript_exon_variant,,ENST00000466526,;ATP1A4,3_prime_UTR_variant,,ENST00000477338,;ATP1A4,non_coding_transcript_exon_variant,,ENST00000469023,; A ENST00000368081 Transcript missense_variant 3128/3839 2657/3090 886/1029 P/H cCt/cAt 1 1 ATP1A4 HGNC HGNC:14073 protein_coding YES CCDS1197.1 ENSP00000357060 Q13733 UPI0000124FC5 NM_144699.3 deleterious(0) 18/22 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF309,TIGRFAM_domain:TIGR01106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 160177585 160177585 C A 1 0 0 0 0 1 0 0 0 1283 681 24 2 2 ATP1A4 1 160177585 Missense_Mutation SNP C C3N-00560_T 368122 160177585 88778837 77 16766 VANGL2 0 . GRCh38 1 160420540 160420540 + Silent SNP C C A rs781182828 C3N-00560_T C3N-00560_N C C c.930C>A p.= p.L310L ENST00000368061 5/8 365 243 122 301 300 1 strelka-varscan-mutect VANGL2,synonymous_variant,p.=,ENST00000368061,NM_020335.2;VANGL2,intron_variant,,ENST00000483408,; A ENST00000368061 Transcript synonymous_variant 1404/5340 930/1566 310/521 L ctC/ctA rs781182828 1 1 VANGL2 HGNC HGNC:15511 protein_coding YES CCDS30915.1 ENSP00000357040 Q9ULK5 UPI00001C1D79 NM_020335.2 5/8 hmmpanther:PTHR20886,PIRSF_domain:PIRSF007991,Pfam_domain:PF06638 LOW 1 SNV 2 1 PASS rs781182828 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 160420540 160420540 C A 1 0 0 0 0 0 0 0 1 17665 871 31 1 1 VANGL2 1 160420540 Silent SNP C C3N-00560_T 242955 160420540 88535882 78 16767 NECTIN4 0 . GRCh38 1 161077539 161077539 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.644G>T p.Ser215Ile p.S215I ENST00000368012 3/9 482 320 162 368 368 0 strelka-varscan-mutect NECTIN4,missense_variant,p.Ser215Ile,ENST00000368012,NM_030916.2;NECTIN4,upstream_gene_variant,,ENST00000486694,; A ENST00000368012 Transcript missense_variant 947/3502 644/1533 215/510 S/I aGc/aTc 1 -1 NECTIN4 HGNC HGNC:19688 protein_coding YES CCDS1216.1 ENSP00000356991 Q96NY8 K4PZ75 UPI000006F072 NM_030916.2 deleterious(0.01) 3/9 PROSITE_profiles:PS50835,hmmpanther:PTHR23277:SF11,hmmpanther:PTHR23277,Gene3D:2.60.40.10,Pfam_domain:PF08205,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1266573212 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 161077539 161077539 C A 1 0 0 0 0 1 0 0 0 10336 797 28 2 2 NECTIN4 1 161077539 Missense_Mutation SNP C C3N-00560_T 656999 161077539 87878883 79 16768 OLFML2B 0 . GRCh38 1 162000147 162000147 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.918G>T p.Lys306Asn p.K306N ENST00000367940 5/8 74 56 18 78 78 0 strelka-varscan-mutect OLFML2B,missense_variant,p.Lys305Asn,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Lys306Asn,ENST00000367940,NM_001297713.1; A ENST00000367940 Transcript missense_variant 1128/2685 918/2256 306/751 K/N aaG/aaT COSM283483 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 tolerated(0.22) 5/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37,Coiled-coils_(Ncoils):Coil 1 MODERATE 1 SNV 2 1 1 PASS rs1452651565 . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 56 162000147 162000147 C A 1 0 0 0 0 1 0 0 0 10933 680 24 2 2 OLFML2B 1 162000147 Missense_Mutation SNP C C3N-00560_T 922608 162000147 86956275 80 16769 LMX1A 0 . GRCh38 1 165249599 165249599 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.305C>T p.Ala102Val p.A102V ENST00000342310 4/9 327 238 89 257 257 0 strelka-varscan-mutect LMX1A,missense_variant,p.Ala102Val,ENST00000342310,NM_177398.3;LMX1A,missense_variant,p.Ala102Val,ENST00000294816,NM_001174069.1;LMX1A,missense_variant,p.Ala102Val,ENST00000367893,; A ENST00000342310 Transcript missense_variant 688/3545 305/1149 102/382 A/V gCt/gTt 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 deleterious(0.02) 4/9 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88,PROSITE_patterns:PS00478,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 165249599 165249599 G A 1 0 0 0 0 1 0 0 0 8788 971 34 3 3 LMX1A 1 165249599 Missense_Mutation SNP G C3N-00560_T 3249452 165249599 83706823 81 16770 POGK 0 . GRCh38 1 166846708 166846708 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.229A>G p.Arg77Gly p.R77G ENST00000367875 3/5 239 180 59 194 194 0 strelka-varscan-mutect POGK,missense_variant,p.Arg77Gly,ENST00000367875,;POGK,missense_variant,p.Arg77Gly,ENST00000367876,NM_001314014.1,NM_017542.3;POGK,missense_variant,p.Arg77Gly,ENST00000449930,; G ENST00000367875 Transcript missense_variant 589/6254 229/1830 77/609 R/G Agg/Ggg 1 1 POGK HGNC HGNC:18800 protein_coding YES CCDS1254.1 ENSP00000356849 Q9P215 A0A024R8Y1 UPI0000167816 deleterious_low_confidence(0) 3/5 PROSITE_profiles:PS50805,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 166846708 166846708 A G 1 0 0 0 0 1 0 0 0 12294 295 11 5 5 POGK 1 166846708 Missense_Mutation SNP A C3N-00560_T 1597109 166846708 82109714 82 16771 ILDR2 0 . GRCh38 1 166920912 166920912 + Missense_Mutation SNP G G T rs369124503 C3N-00560_T C3N-00560_N G G c.1679C>A p.Pro560Gln p.P560Q ENST00000271417 9/10 140 91 49 76 76 0 strelka-varscan-mutect ILDR2,missense_variant,p.Pro560Gln,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Pro541Gln,ENST00000529071,;ILDR2,missense_variant,p.Pro501Gln,ENST00000528703,;ILDR2,missense_variant,p.Pro452Gln,ENST00000526687,;ILDR2,missense_variant,p.Pro433Gln,ENST00000525740,;ILDR2,intron_variant,,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; T ENST00000271417 Transcript missense_variant 1735/13140 1679/1920 560/639 P/Q cCg/cAg rs369124503 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 tolerated(0.61) 9/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0 MODERATE 1 SNV 1 1 PASS rs369124503 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 166920912 166920912 G T 1 0 0 0 0 1 0 0 0 7613 1116 39 1 1 ILDR2 1 166920912 Missense_Mutation SNP G C3N-00560_T 74204 166920912 82035510 83 16772 ILDR2 0 . GRCh38 1 166921138 166921138 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1453C>A p.Arg485Ser p.R485S ENST00000271417 9/10 159 113 46 115 115 0 strelka-varscan-mutect ILDR2,missense_variant,p.Arg485Ser,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Arg466Ser,ENST00000529071,;ILDR2,missense_variant,p.Arg426Ser,ENST00000528703,;ILDR2,missense_variant,p.Arg377Ser,ENST00000526687,;ILDR2,missense_variant,p.Arg358Ser,ENST00000525740,;ILDR2,intron_variant,,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; T ENST00000271417 Transcript missense_variant 1509/13140 1453/1920 485/639 R/S Cgc/Agc 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 deleterious(0.02) 9/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0 MODERATE 1 SNV 1 1 PASS rs931752264 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 166921138 166921138 G T 1 0 0 0 0 1 0 0 0 7613 1116 39 1 1 ILDR2 1 166921138 Missense_Mutation SNP G C3N-00560_T 226 166921138 82035284 84 16773 F5 0 . GRCh38 1 169560704 169560704 + Silent SNP G G T rs767477438 C3N-00560_T C3N-00560_N G G c.436C>A p.= p.R146R ENST00000367797 4/25 456 340 116 362 361 1 strelka-varscan-mutect F5,synonymous_variant,p.=,ENST00000367796,;F5,synonymous_variant,p.=,ENST00000367797,NM_000130.4; T ENST00000367797 Transcript synonymous_variant 638/7024 436/6675 146/2224 R Cga/Aga rs767477438,COSM2073645 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 4/25 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,PIRSF_domain:PIRSF000354,Gene3D:2.60.40.420,Pfam_domain:PF07732,Superfamily_domains:SSF49503 0,1 LOW 1 SNV 1 0,1 1 PASS rs767477438 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 169560704 169560704 G T 1 0 0 0 0 0 0 0 1 5216 1124 39 1 1 F5 1 169560704 Silent SNP G C3N-00560_T 2639566 169560704 79395718 85 16774 C1orf105 0 . GRCh38 1 172456414 172456414 + Splice_Site SNP G G C C3N-00560_T C3N-00560_N G G c.199-1G>C p.X67_splice ENST00000367727 112 79 33 92 92 0 strelka-varscan-mutect C1orf105,splice_acceptor_variant,,ENST00000367727,NM_139240.3;C1orf105,splice_acceptor_variant,,ENST00000367725,NM_001300760.1;C1orf105,splice_acceptor_variant,,ENST00000488100,;C1orf105,intron_variant,,ENST00000367726,; C ENST00000367727 Transcript splice_acceptor_variant -/985 199/552 67/183 COSM530513 1 1 C1orf105 HGNC HGNC:29591 protein_coding YES CCDS1301.1 ENSP00000356700 O95561 UPI000006D456 NM_139240.3 3/6 1 HIGH 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 56 172456414 172456414 G C 1 0 0 0 0 0 0 1 0 1955 1014 35 4 4 C1orf105 1 172456414 Splice_Site SNP G C3N-00560_T 2895710 172456414 76500008 86 16775 SUCO 0 . GRCh38 1 172589444 172589444 + Silent SNP T T G rs774045411 C3N-00560_T C3N-00560_N T T c.2796T>G p.= p.S932S ENST00000367723 17/23 69 64 5 84 84 0 varscan-mutect SUCO,synonymous_variant,p.=,ENST00000367723,NM_016227.3;SUCO,synonymous_variant,p.=,ENST00000608151,;SUCO,synonymous_variant,p.=,ENST00000263688,NM_014283.4;SUCO,synonymous_variant,p.=,ENST00000616058,NM_001282751.1;SUCO,intron_variant,,ENST00000610051,NM_001282750.1; G ENST00000367723 Transcript synonymous_variant 2920/5916 2796/4218 932/1405 S tcT/tcG rs774045411 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 17/23 hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 LOW 1 SNV 1 1 PASS rs774045411 . 0 206 4 0 0 0 0 0 -11.62632 1 1 1 1 0 G 2 3 56 172589444 172589444 T G 1 0 0 0 0 0 0 0 1 15751 1567 55 5 5 SUCO 1 172589444 Silent SNP T C3N-00560_T 133030 172589444 76366978 87 16776 FASLG 0 . GRCh38 1 172659373 172659373 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.172C>A p.Pro58Thr p.P58T ENST00000367721 1/4 439 303 136 410 410 0 strelka-varscan-mutect FASLG,missense_variant,p.Pro58Thr,ENST00000367721,NM_000639.2;FASLG,missense_variant,p.Pro58Thr,ENST00000340030,NM_001302746.1; A ENST00000367721 Transcript missense_variant 356/1888 172/846 58/281 P/T Ccg/Acg 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 tolerated(0.09) 1/4 hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF33,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 172659373 172659373 C A 1 0 0 0 0 1 0 0 0 5542 739 26 2 2 FASLG 1 172659373 Missense_Mutation SNP C C3N-00560_T 69929 172659373 76297049 88 16777 RFWD2 0 . GRCh38 1 176027613 176027613 + Frame_Shift_Del DEL A A - novel C3N-00560_T C3N-00560_N A A c.1688delT p.Phe563SerfsTer46 p.F563Sfs*46 ENST00000367669 15/20 250 176 74 228 228 0 sindel-varindel-pindel RFWD2,frameshift_variant,p.Phe563SerfsTer46,ENST00000367669,NM_022457.6,NM_001286644.1;RFWD2,frameshift_variant,p.Phe539SerfsTer46,ENST00000308769,NM_001001740.3;RFWD2,frameshift_variant,p.Phe398SerfsTer46,ENST00000367666,;RFWD2,3_prime_UTR_variant,,ENST00000367667,;RFWD2,non_coding_transcript_exon_variant,,ENST00000461830,; - ENST00000367669 Transcript frameshift_variant 2203/3033 1688/2196 563/731 F/X tTc/tc 1 -1 RFWD2 HGNC HGNC:17440 protein_coding YES CCDS30944.1 ENSP00000356641 Q8NHY2 UPI0000061E51 NM_022457.6,NM_001286644.1 15/20 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF451,hmmpanther:PTHR22847,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 176027613 176027613 A - 1 0 1 0 1 0 0 0 0 13434 246 9 0 0 RFWD2 1 176027613 Frame_Shift_Del DEL A C3N-00560_T 3368240 176027613 72928809 89 16778 TDRD5 0 . GRCh38 1 179639916 179639916 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1598G>T p.Cys533Phe p.C533F ENST00000444136 10/18 415 291 124 353 353 0 strelka-varscan-mutect TDRD5,missense_variant,p.Cys533Phe,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,missense_variant,p.Cys533Phe,ENST00000367614,NM_001199091.1;TDRD5,missense_variant,p.Cys533Phe,ENST00000294848,NM_173533.3;TDRD5,upstream_gene_variant,,ENST00000417329,; T ENST00000444136 Transcript missense_variant 2116/3946 1598/3108 533/1035 C/F tGt/tTt 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 deleterious(0) 10/18 Gene3D:2.30.30.140,Pfam_domain:PF00567,PROSITE_profiles:PS50304,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF19,SMART_domains:SM00333,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS rs1273506634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 179639916 179639916 G T 1 0 0 0 0 1 0 0 0 16143 1377 48 2 2 TDRD5 1 179639916 Missense_Mutation SNP G C3N-00560_T 3612303 179639916 69316506 90 16779 SHCBP1L 0 . GRCh38 1 182952949 182952949 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.185delG p.Gly62AlafsTer53 p.G62Afs*53 ENST00000367547 1/10 229 168 61 185 185 0 sindel-varindel-pindel SHCBP1L,frameshift_variant,p.Gly62AlafsTer53,ENST00000367547,NM_030933.2;SHCBP1L,non_coding_transcript_exon_variant,,ENST00000488956,;SHCBP1L,non_coding_transcript_exon_variant,,ENST00000483655,;SHCBP1L,non_coding_transcript_exon_variant,,ENST00000497549,;SHCBP1L,upstream_gene_variant,,ENST00000467208,;RP11-505O17.1,downstream_gene_variant,,ENST00000418657,; - ENST00000367547 Transcript frameshift_variant 422/2317 185/1962 62/653 G/X gGc/gc 1 -1 SHCBP1L HGNC HGNC:16788 protein_coding YES CCDS30955.1 ENSP00000356518 Q9BZQ2 UPI000006F7B9 NM_030933.2 1/10 hmmpanther:PTHR14695,hmmpanther:PTHR14695:SF7 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 182952949 182952949 C - 1 0 1 0 1 0 0 0 0 14534 739 26 0 0 SHCBP1L 1 182952949 Frame_Shift_Del DEL C C3N-00560_T 3313033 182952949 66003473 91 16780 NMNAT2 0 . GRCh38 1 183290199 183290199 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.250C>G p.Pro84Ala p.P84A ENST00000287713 4/11 185 138 47 153 153 0 strelka-varscan-mutect NMNAT2,missense_variant,p.Pro84Ala,ENST00000287713,NM_015039.3;NMNAT2,missense_variant,p.Pro79Ala,ENST00000294868,NM_170706.3;NMNAT2,non_coding_transcript_exon_variant,,ENST00000473046,; C ENST00000287713 Transcript missense_variant 585/5663 250/924 84/307 P/A Cct/Gct 1 -1 NMNAT2 HGNC HGNC:16789 protein_coding YES CCDS1353.1 ENSP00000287713 Q9BZQ4 UPI00000706AB NM_015039.3 deleterious(0.03) 4/11 Gene3D:3.40.50.620,Pfam_domain:PF01467,hmmpanther:PTHR12039,hmmpanther:PTHR12039:SF2,Superfamily_domains:SSF52374 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 183290199 183290199 G C 1 0 0 0 0 1 0 0 0 10538 1232 43 4 4 NMNAT2 1 183290199 Missense_Mutation SNP G C3N-00560_T 337250 183290199 65666223 92 16781 SWT1 0 . GRCh38 1 185204730 185204730 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.1700A>G p.Glu567Gly p.E567G ENST00000367500 12/19 115 88 27 169 168 1 strelka-varscan-mutect SWT1,missense_variant,p.Glu567Gly,ENST00000367500,NM_017673.6;SWT1,missense_variant,p.Glu567Gly,ENST00000367501,NM_001105518.1; G ENST00000367500 Transcript missense_variant 1865/3830 1700/2703 567/900 E/G gAg/gGg 1 1 SWT1 HGNC HGNC:16785 protein_coding YES CCDS1367.1 ENSP00000356470 Q5T5J6 UPI000013D4C5 NM_017673.6 tolerated(0.14) 12/19 hmmpanther:PTHR16161,hmmpanther:PTHR16161:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 185204730 185204730 A G 1 0 0 0 0 1 0 0 0 15813 304 11 5 5 SWT1 1 185204730 Missense_Mutation SNP A C3N-00560_T 1914531 185204730 63751692 93 16782 HMCN1 0 . GRCh38 1 186018182 186018182 + Splice_Site SNP G G T rs762850788 C3N-00560_T C3N-00560_N G G c.5301-1G>T p.X1767_splice ENST00000271588 343 262 81 330 330 0 strelka-varscan-mutect HMCN1,splice_acceptor_variant,,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript splice_acceptor_variant -/18208 5301/16908 1767/5635 rs762850788 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 33/106 HIGH 1 SNV 1 1 PASS rs762850788 . 0 204 0 0 6 0 0 0 -20 0.709545 1 1 1 0 T 5 4 56 186018182 186018182 G T 1 0 0 0 0 0 0 1 0 7111 1014 35 2 2 HMCN1 1 186018182 Splice_Site SNP G C3N-00560_T 813452 186018182 62938240 94 16783 HMCN1 0 . GRCh38 1 186055540 186055540 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.7010A>C p.Lys2337Thr p.K2337T ENST00000271588 45/107 530 457 73 446 446 0 strelka-varscan-mutect HMCN1,missense_variant,p.Lys2337Thr,ENST00000271588,NM_031935.2; C ENST00000271588 Transcript missense_variant 7239/18208 7010/16908 2337/5635 K/T aAg/aCg 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.5) 45/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1461444446 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 186055540 186055540 A C 1 0 0 0 0 1 0 0 0 7111 72 3 5 5 HMCN1 1 186055540 Missense_Mutation SNP A C3N-00560_T 37358 186055540 62900882 95 16784 HMCN1 0 . GRCh38 1 186125675 186125675 + Missense_Mutation SNP G G T rs141096306 C3N-00560_T C3N-00560_N G G c.12571G>T p.Val4191Leu p.V4191L ENST00000271588 82/107 210 145 65 188 188 0 strelka-varscan-mutect HMCN1,missense_variant,p.Val4191Leu,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript missense_variant 12800/18208 12571/16908 4191/5635 V/L Gta/Tta rs141096306 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.12) 82/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs141096306 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 186125675 186125675 G T 1 0 0 0 0 1 0 0 0 7111 1145 40 1 1 HMCN1 1 186125675 Missense_Mutation SNP G C3N-00560_T 70135 186125675 62830747 96 16785 B3GALT2 0 . GRCh38 1 193180715 193180715 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.848T>A p.Met283Lys p.M283K ENST00000367434 2/2 201 131 70 161 161 0 strelka-varscan-mutect B3GALT2,missense_variant,p.Met283Lys,ENST00000367434,NM_003783.3;CDC73,intron_variant,,ENST00000367435,NM_024529.4;CDC73,intron_variant,,ENST00000635846,; T ENST00000367434 Transcript missense_variant 1604/3274 848/1269 283/422 M/K aTg/aAg 1 -1 B3GALT2 HGNC HGNC:917 protein_coding YES CCDS1383.1 ENSP00000356404 O43825 UPI0000073BFF NM_003783.3 deleterious(0) 2/2 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF19,Pfam_domain:PF01762 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 193180715 193180715 A T 1 0 0 0 0 1 0 0 0 1405 217 8 4 4 B3GALT2 1 193180715 Missense_Mutation SNP A C3N-00560_T 7055040 193180715 55775707 97 16786 CFHR2 0 . GRCh38 1 196957958 196957958 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.498A>T p.= p.S166S ENST00000367415 4/5 224 160 64 199 199 0 strelka-varscan-mutect CFHR2,synonymous_variant,p.=,ENST00000367415,NM_005666.2;RP4-608O15.3,synonymous_variant,p.=,ENST00000367421,;CFHR2,synonymous_variant,p.=,ENST00000476712,;CFHR2,non_coding_transcript_exon_variant,,ENST00000496448,;CFHR2,non_coding_transcript_exon_variant,,ENST00000473386,; T ENST00000367415 Transcript synonymous_variant 598/1059 498/813 166/270 S tcA/tcT 1 1 CFHR2 HGNC HGNC:4890 protein_coding YES CCDS30959.1 ENSP00000356385 P36980 UPI000012A73B NM_005666.2 4/5 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 196957958 196957958 A T 1 0 0 0 0 0 0 0 1 3043 175 7 4 4 CFHR2 1 196957958 Silent SNP A C3N-00560_T 3777243 196957958 51998464 98 16787 ASPM 0 . GRCh38 1 197143072 197143072 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1180A>T p.Asn394Tyr p.N394Y ENST00000367409 3/28 158 111 47 190 190 0 strelka-varscan-mutect ASPM,missense_variant,p.Asn394Tyr,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Asn394Tyr,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000612785,;SEPT14P12,upstream_gene_variant,,ENST00000442280,; A ENST00000367409 Transcript missense_variant 1437/10887 1180/10434 394/3477 N/Y Aat/Tat 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 deleterious(0.01) 3/28 MODERATE 1 SNV 1 1 PASS rs199422138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 197143072 197143072 T A 1 0 0 0 0 1 0 0 0 1203 1754 61 4 4 ASPM 1 197143072 Missense_Mutation SNP T C3N-00560_T 185114 197143072 51813350 99 16788 GPR25 0 . GRCh38 1 200873560 200873560 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.523C>A p.Leu175Met p.L175M ENST00000304244 1/1 153 102 51 94 94 0 strelka-varscan-mutect GPR25,missense_variant,p.Leu175Met,ENST00000304244,NM_005298.3; A ENST00000304244 Transcript missense_variant 606/1224 523/1086 175/361 L/M Ctg/Atg 1 1 GPR25 HGNC HGNC:4480 protein_coding YES CCDS1405.1 ENSP00000301917 O00155 UPI000013E957 NM_005298.3 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF9,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 200873560 200873560 C A 1 0 0 0 0 1 0 0 0 6567 680 24 2 2 GPR25 1 200873560 Missense_Mutation SNP C C3N-00560_T 3730488 200873560 48082862 100 16789 C1orf106 0 . GRCh38 1 200907840 200907840 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.527G>T p.Ser176Ile p.S176I ENST00000413687 6/10 191 148 43 161 161 0 strelka-varscan-mutect C1orf106,missense_variant,p.Ser261Ile,ENST00000367342,NM_018265.3;C1orf106,missense_variant,p.Ser176Ile,ENST00000413687,NM_001142569.2;C1orf106,non_coding_transcript_exon_variant,,ENST00000531649,;C1orf106,upstream_gene_variant,,ENST00000465162,;C1orf106,upstream_gene_variant,,ENST00000526172,; T ENST00000413687 Transcript missense_variant 888/2197 527/1737 176/578 S/I aGt/aTt 1 1 C1orf106 HGNC HGNC:25599 protein_coding YES CCDS44292.1 ENSP00000392105 Q3KP66 UPI0000204714 NM_001142569.2 deleterious(0) 6/10 hmmpanther:PTHR16093,hmmpanther:PTHR16093:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 200907840 200907840 G T 1 0 0 0 0 1 0 0 0 1956 1029 36 2 2 C1orf106 1 200907840 Missense_Mutation SNP G C3N-00560_T 34280 200907840 48048582 101 16790 63 2 C1orf106 0 . GRCh38 1 200907842 200907842 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.529G>A p.Ala177Thr p.A177T ENST00000413687 6/10 189 147 42 158 158 0 strelka-varscan-mutect C1orf106,missense_variant,p.Ala262Thr,ENST00000367342,NM_018265.3;C1orf106,missense_variant,p.Ala177Thr,ENST00000413687,NM_001142569.2;C1orf106,non_coding_transcript_exon_variant,,ENST00000531649,;C1orf106,upstream_gene_variant,,ENST00000465162,;C1orf106,upstream_gene_variant,,ENST00000526172,; A ENST00000413687 Transcript missense_variant 890/2197 529/1737 177/578 A/T Gcc/Acc 1 1 C1orf106 HGNC HGNC:25599 protein_coding YES CCDS44292.1 ENSP00000392105 Q3KP66 UPI0000204714 NM_001142569.2 tolerated(0.05) 6/10 hmmpanther:PTHR16093,hmmpanther:PTHR16093:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 200907842 200907842 G A 1 0 0 0 0 1 0 0 0 1956 1319 46 3 3 C1orf106 1 200907842 Missense_Mutation SNP G C3N-00560_T 2 200907842 48048580 102 16791 63 2 KIF21B 0 . GRCh38 1 200988902 200988902 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3162G>T p.Gln1054His p.Q1054H ENST00000422435 22/35 106 80 26 97 97 0 strelka-varscan-mutect KIF21B,missense_variant,p.Gln1054His,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Gln1054His,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Gln1054His,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Gln1054His,ENST00000360529,NM_001252103.1; A ENST00000422435 Transcript missense_variant 3479/5519 3162/4914 1054/1637 Q/H caG/caT 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0) 22/35 hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115,Superfamily_domains:SSF46579 MODERATE 1 SNV 1 1 PASS rs1452561321 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 200988902 200988902 C A 1 0 0 0 0 1 0 0 0 8154 912 32 2 2 KIF21B 1 200988902 Missense_Mutation SNP C C3N-00560_T 81060 200988902 47967520 103 16792 KIF21B 0 . GRCh38 1 201004447 201004447 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.909G>T p.Leu303Phe p.L303F ENST00000422435 7/35 206 127 79 213 211 2 strelka-varscan-mutect KIF21B,missense_variant,p.Leu303Phe,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Leu303Phe,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Leu303Phe,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Leu303Phe,ENST00000360529,NM_001252103.1;KIF21B,non_coding_transcript_exon_variant,,ENST00000534043,; A ENST00000422435 Transcript missense_variant 1226/5519 909/4914 303/1637 L/F ttG/ttT COSM4937018,COSM4937019 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0) 7/35 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 201004447 201004447 C A 1 0 0 0 0 1 0 0 0 8154 593 21 2 2 KIF21B 1 201004447 Missense_Mutation SNP C C3N-00560_T 15545 201004447 47951975 104 16793 CACNA1S 0 . GRCh38 1 201074514 201074514 + Silent SNP C C T rs200844059 C3N-00560_T C3N-00560_N C C c.2055G>A p.= p.K685K ENST00000362061 14/44 597 440 157 454 454 0 strelka-varscan-mutect CACNA1S,synonymous_variant,p.=,ENST00000362061,NM_000069.2;CACNA1S,synonymous_variant,p.=,ENST00000367338,; T ENST00000362061 Transcript synonymous_variant 2282/6166 2055/5622 685/1873 K aaG/aaA rs200844059 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 14/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs200844059 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 201074514 201074514 C T 1 0 0 0 0 0 0 0 1 2235 912 32 3 3 CACNA1S 1 201074514 Silent SNP C C3N-00560_T 70067 201074514 47881908 105 16794 IGFN1 0 . GRCh38 1 201207988 201207988 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3095G>T p.Gly1032Val p.G1032V ENST00000335211 12/24 313 245 68 241 241 0 strelka-varscan-mutect IGFN1,missense_variant,p.Gly1032Val,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,downstream_gene_variant,,ENST00000444705,; T ENST00000335211 Transcript missense_variant 3225/11810 3095/11127 1032/3708 G/V gGg/gTg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 tolerated(0.22) 12/24 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF630 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 201207988 201207988 G T 1 0 0 0 0 1 0 0 0 7497 1232 43 2 2 IGFN1 1 201207988 Missense_Mutation SNP G C3N-00560_T 133474 201207988 47748434 106 16795 IGFN1 0 . GRCh38 1 201215018 201215018 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.8859C>A p.= p.T2953T ENST00000335211 14/24 150 102 48 104 104 0 strelka-varscan-mutect IGFN1,synonymous_variant,p.=,ENST00000335211,NM_001164586.1;IGFN1,synonymous_variant,p.=,ENST00000295591,;IGFN1,synonymous_variant,p.=,ENST00000412892,;IGFN1,synonymous_variant,p.=,ENST00000437879,;IGFN1,non_coding_transcript_exon_variant,,ENST00000473483,; A ENST00000335211 Transcript synonymous_variant 8989/11810 8859/11127 2953/3708 T acC/acA 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 14/24 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF630,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 201215018 201215018 C A 1 0 0 0 0 0 0 0 1 7497 608 21 2 2 IGFN1 1 201215018 Silent SNP C C3N-00560_T 7030 201215018 47741404 107 16796 PKP1 0 . GRCh38 1 201283861 201283861 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.159G>T p.Lys53Asn p.K53N ENST00000263946 1/15 809 569 240 641 641 0 strelka-varscan-mutect PKP1,missense_variant,p.Lys53Asn,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Lys53Asn,ENST00000367324,NM_001005337.2;PKP1,missense_variant,p.Lys53Asn,ENST00000352845,; T ENST00000263946 Transcript missense_variant 410/5447 159/2244 53/747 K/N aaG/aaT 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 deleterious(0.01) 1/15 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 201283861 201283861 G T 1 0 0 0 0 1 0 0 0 12080 1020 36 2 2 PKP1 1 201283861 Missense_Mutation SNP G C3N-00560_T 68843 201283861 47672561 108 16797 TNNT2 0 . GRCh38 1 201361283 201361283 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.806A>T p.Tyr269Phe p.Y269F ENST00000236918 14/16 514 335 179 397 397 0 strelka-varscan-mutect TNNT2,missense_variant,p.Tyr259Phe,ENST00000509001,NM_001276347.1;TNNT2,missense_variant,p.Tyr197Phe,ENST00000458432,;TNNT2,missense_variant,p.Tyr256Phe,ENST00000367322,NM_001001431.2;TNNT2,missense_variant,p.Tyr259Phe,ENST00000367318,NM_001001430.2;TNNT2,missense_variant,p.Tyr269Phe,ENST00000236918,NM_001276345.1,NM_000364.3;TNNT2,missense_variant,p.Tyr197Phe,ENST00000421663,;TNNT2,missense_variant,p.Tyr262Phe,ENST00000367315,;TNNT2,missense_variant,p.Tyr253Phe,ENST00000367317,NM_001001432.2;TNNT2,missense_variant,p.Tyr226Phe,ENST00000367320,NM_001276346.1;TNNT2,missense_variant,p.Tyr226Phe,ENST00000360372,;TNNT2,missense_variant,p.Tyr253Phe,ENST00000438742,;TNNT2,downstream_gene_variant,,ENST00000455702,;TNNT2,downstream_gene_variant,,ENST00000422165,;TNNT2,downstream_gene_variant,,ENST00000412633,;TNNT2,non_coding_transcript_exon_variant,,ENST00000460780,;TNNT2,non_coding_transcript_exon_variant,,ENST00000476888,;TNNT2,non_coding_transcript_exon_variant,,ENST00000477035,;TNNT2,downstream_gene_variant,,ENST00000466570,;TNNT2,non_coding_transcript_exon_variant,,ENST00000491504,;TNNT2,non_coding_transcript_exon_variant,,ENST00000515042,;TNNT2,downstream_gene_variant,,ENST00000503459,; A ENST00000236918 Transcript missense_variant 806/1098 806/897 269/298 Y/F tAt/tTt 1 -1 TNNT2 HGNC HGNC:11949 protein_coding YES CCDS73003.1 ENSP00000236918 P45379 UPI0000186843 NM_001276345.1,NM_000364.3 deleterious(0.01) 14/16 Gene3D:1.20.5.350,Pfam_domain:PF00992,hmmpanther:PTHR11521,hmmpanther:PTHR11521:SF5,Superfamily_domains:SSF90250 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 201361283 201361283 T A 1 0 0 0 0 1 0 0 0 16804 1420 49 4 4 TNNT2 1 201361283 Missense_Mutation SNP T C3N-00560_T 77422 201361283 47595139 109 16798 PPP1R12B 0 . GRCh38 1 202425598 202425598 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.574G>T p.Glu192Ter p.E192* ENST00000608999 4/24 193 133 60 171 171 0 strelka-varscan-mutect PPP1R12B,stop_gained,p.Glu192Ter,ENST00000391959,;PPP1R12B,stop_gained,p.Glu192Ter,ENST00000608999,NM_002481.3;PPP1R12B,stop_gained,p.Glu192Ter,ENST00000480184,NM_001167857.1;PPP1R12B,stop_gained,p.Glu192Ter,ENST00000356764,NM_001167858.1;PPP1R12B,intron_variant,,ENST00000466968,;PPP1R12B,3_prime_UTR_variant,,ENST00000476364,;PPP1R12B,upstream_gene_variant,,ENST00000488330,; T ENST00000608999 Transcript stop_gained 727/15248 574/2949 192/982 E/* Gag/Tag 1 1 PPP1R12B HGNC HGNC:7619 protein_coding YES CCDS1426.1 ENSP00000476755 O60237 UPI0000458A57 NM_002481.3 4/24 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50297,hmmpanther:PTHR24179:SF18,hmmpanther:PTHR24179,Gene3D:1.25.40.20,PIRSF_domain:PIRSF038141,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 202425598 202425598 G T 1 0 0 0 0 0 1 0 0 12465 943 33 2 2 PPP1R12B 1 202425598 Nonsense_Mutation SNP G C3N-00560_T 1064315 202425598 46530824 110 16799 PPFIA4 0 . GRCh38 1 203060250 203060250 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.2551G>A p.Ala851Thr p.A851T ENST00000447715 27/35 261 190 71 233 233 0 strelka-varscan-mutect PPFIA4,missense_variant,p.Ala852Thr,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,missense_variant,p.Ala367Thr,ENST00000295706,;PPFIA4,missense_variant,p.Ala851Thr,ENST00000447715,;PPFIA4,missense_variant,p.Ala367Thr,ENST00000272198,;PPFIA4,missense_variant,p.Ala367Thr,ENST00000599966,;PPFIA4,missense_variant,p.Ala619Thr,ENST00000600426,;PPFIA4,downstream_gene_variant,,ENST00000599514,;PPFIA4,upstream_gene_variant,,ENST00000486360,;PPFIA4,upstream_gene_variant,,ENST00000594656,;PPFIA4,downstream_gene_variant,,ENST00000600447,; A ENST00000447715 Transcript missense_variant 2992/6349 2551/3558 851/1185 A/T Gcc/Acc 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 deleterious(0) 27/35 Gene3D:1.10.150.50,Pfam_domain:PF00536,PROSITE_profiles:PS50105,hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 203060250 203060250 G A 1 0 0 0 0 1 0 0 0 12421 971 34 3 3 PPFIA4 1 203060250 Missense_Mutation SNP G C3N-00560_T 634652 203060250 45896172 111 16800 PRELP 0 . GRCh38 1 203483937 203483937 + Missense_Mutation SNP T T A rs376825552 C3N-00560_T C3N-00560_N T T c.753T>A p.Ser251Arg p.S251R ENST00000343110 2/3 343 251 92 266 265 1 strelka-varscan-mutect PRELP,missense_variant,p.Ser251Arg,ENST00000343110,NM_002725.3,NM_201348.1; A ENST00000343110 Transcript missense_variant 880/5747 753/1149 251/382 S/R agT/agA rs376825552 1 1 PRELP HGNC HGNC:9357 protein_coding YES CCDS1438.1 ENSP00000343924 P51888 UPI000013222E NM_002725.3,NM_201348.1 tolerated(0.71) 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF152,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs376825552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 203483937 203483937 T A 1 0 0 0 0 1 0 0 0 12607 1635 57 4 4 PRELP 1 203483937 Missense_Mutation SNP T C3N-00560_T 423687 203483937 45472485 112 16801 RAB29 0 . GRCh38 1 205770794 205770794 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.439G>A p.Gly147Ser p.G147S ENST00000367139 5/6 432 317 115 331 331 0 strelka-varscan-mutect RAB29,missense_variant,p.Gly147Ser,ENST00000367139,NM_003929.2;RAB29,missense_variant,p.Gly147Ser,ENST00000235932,NM_001135662.1;RAB29,missense_variant,p.Gly123Ser,ENST00000446390,NM_001135663.1;RAB29,missense_variant,p.Gly75Ser,ENST00000437324,NM_001135664.1;RAB29,missense_variant,p.Gly147Ser,ENST00000414729,;RAB29,non_coding_transcript_exon_variant,,ENST00000468887,;RAB29,downstream_gene_variant,,ENST00000533111,;RAB29,3_prime_UTR_variant,,ENST00000528078,;RAB29,downstream_gene_variant,,ENST00000492534,; T ENST00000367139 Transcript missense_variant 743/3272 439/612 147/203 G/S Ggt/Agt COSM1560314 1 -1 RAB29 HGNC HGNC:9789 protein_coding YES CCDS1459.1 ENSP00000356107 O14966 Q6FGU7 UPI0000133181 NM_003929.2 deleterious(0.01) 5/6 PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF315,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00176,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs1372871032 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 205770794 205770794 C T 1 0 0 0 0 1 0 0 0 13075 652 23 1 1 RAB29 1 205770794 Missense_Mutation SNP C C3N-00560_T 2286857 205770794 43185628 113 16802 SLC26A9 0 . GRCh38 1 205931983 205931983 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.429C>A p.= p.A143A ENST00000367134 5/22 236 164 72 203 203 0 strelka-varscan-mutect SLC26A9,synonymous_variant,p.=,ENST00000367135,NM_052934.3;SLC26A9,synonymous_variant,p.=,ENST00000367134,NM_134325.2;SLC26A9,synonymous_variant,p.=,ENST00000340781,;RP4-681L3.2,upstream_gene_variant,,ENST00000421166,;SLC26A9,upstream_gene_variant,,ENST00000491127,;SLC26A9,upstream_gene_variant,,ENST00000469392,; T ENST00000367134 Transcript synonymous_variant 543/4616 429/2664 143/887 A gcC/gcA 1 -1 SLC26A9 HGNC HGNC:14469 protein_coding YES CCDS30989.1 ENSP00000356102 Q7LBE3 UPI000013DF98 NM_134325.2 5/22 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF17,TIGRFAM_domain:TIGR00815 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 205931983 205931983 G T 1 0 0 0 0 0 0 0 1 14794 1219 43 2 2 SLC26A9 1 205931983 Silent SNP G C3N-00560_T 161189 205931983 43024439 114 16803 CR1 0 . GRCh38 1 207496350 207496350 + Missense_Mutation SNP T T A rs752683886 C3N-00560_T C3N-00560_N T T c.83T>A p.Leu28Gln p.L28Q ENST00000367049 1/47 332 247 85 288 288 0 strelka-varscan-mutect CR1,missense_variant,p.Leu28Gln,ENST00000367049,NM_000651.4;CR1,missense_variant,p.Leu28Gln,ENST00000367051,;CR1,missense_variant,p.Leu28Gln,ENST00000367052,;CR1,missense_variant,p.Leu28Gln,ENST00000367053,;CR1,missense_variant,p.Leu28Gln,ENST00000400960,NM_000573.3;CR1,missense_variant,p.Leu4Gln,ENST00000529814,;CR1,non_coding_transcript_exon_variant,,ENST00000367050,;CR1,missense_variant,p.Leu28Gln,ENST00000534202,;CR1,non_coding_transcript_exon_variant,,ENST00000434033,;CR1,non_coding_transcript_exon_variant,,ENST00000436595,;CR1,non_coding_transcript_exon_variant,,ENST00000450439,;CR1,non_coding_transcript_exon_variant,,ENST00000530487,; A ENST00000367049 Transcript missense_variant 83/7470 83/7470 28/2489 L/Q cTg/cAg rs752683886 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 deleterious_low_confidence(0) 1/47 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 5 1 PASS rs752683886 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 207496350 207496350 T A 1 0 0 0 0 1 0 0 0 3638 1580 55 4 4 CR1 1 207496350 Missense_Mutation SNP T C3N-00560_T 1564367 207496350 41460072 115 16804 RPS6KC1 0 . GRCh38 1 213241654 213241654 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2178G>T p.Leu726Phe p.L726F ENST00000366960 11/15 209 149 60 203 203 0 strelka-varscan-mutect RPS6KC1,missense_variant,p.Leu726Phe,ENST00000366960,NM_012424.4;RPS6KC1,missense_variant,p.Leu714Phe,ENST00000366959,NM_001136138.2;RPS6KC1,missense_variant,p.Leu514Phe,ENST00000543470,NM_001287219.1;RPS6KC1,missense_variant,p.Leu514Phe,ENST00000614059,NM_001287218.1;RPS6KC1,missense_variant,p.Leu545Phe,ENST00000543354,NM_001287221.1;RPS6KC1,missense_variant,p.Leu261Phe,ENST00000615329,NM_001287220.1;RPS6KC1,non_coding_transcript_exon_variant,,ENST00000490299,;RPS6KC1,upstream_gene_variant,,ENST00000491616,; T ENST00000366960 Transcript missense_variant 2328/5490 2178/3201 726/1066 L/F ttG/ttT 1 1 RPS6KC1 HGNC HGNC:10439 protein_coding YES CCDS1513.1 ENSP00000355927 Q96S38 UPI0000071B8C NM_012424.4 tolerated_low_confidence(0.15) 11/15 hmmpanther:PTHR15508,hmmpanther:PTHR15508:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 213241654 213241654 G T 1 0 0 0 0 1 0 0 0 13913 1339 47 2 2 RPS6KC1 1 213241654 Missense_Mutation SNP G C3N-00560_T 5745304 213241654 35714768 116 16805 CENPF 0 . GRCh38 1 214618694 214618694 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.481G>T p.Gly161Cys p.G161C ENST00000366955 4/20 122 84 38 115 115 0 strelka-varscan-mutect CENPF,missense_variant,p.Gly161Cys,ENST00000366955,NM_016343.3;CENPF,downstream_gene_variant,,ENST00000464322,;CENPF,downstream_gene_variant,,ENST00000495259,; T ENST00000366955 Transcript missense_variant,splice_region_variant 649/10307 481/9345 161/3114 G/C Ggt/Tgt 1 1 CENPF HGNC HGNC:1857 protein_coding YES CCDS31023.1 ENSP00000355922 P49454 UPI00001AE985 NM_016343.3 deleterious(0.03) 4/20 Pfam_domain:PF10481,hmmpanther:PTHR18874 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 214618694 214618694 G T 1 0 0 0 0 1 0 0 0 2939 1362 47 2 2 CENPF 1 214618694 Missense_Mutation SNP G C3N-00560_T 1377040 214618694 34337728 117 16806 USH2A 0 . GRCh38 1 216207409 216207409 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.3180delC p.Arg1061GlufsTer51 p.R1061Efs*51 ENST00000307340 16/72 255 195 60 289 287 2 sindel-varindel-pindel USH2A,frameshift_variant,p.Arg1061GlufsTer51,ENST00000307340,NM_206933.2;USH2A,frameshift_variant,p.Arg1061GlufsTer51,ENST00000366942,NM_007123.5;RP5-1099E6.3,downstream_gene_variant,,ENST00000420867,; - ENST00000307340 Transcript frameshift_variant 3567/18883 3180/15609 1060/5202 P/X ccC/cc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 16/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 216207409 216207409 G - 1 0 1 0 1 0 0 0 0 17570 1335 47 0 0 USH2A 1 216207409 Frame_Shift_Del DEL G C3N-00560_T 1588715 216207409 32749013 118 16807 USH2A 0 . GRCh38 1 216250927 216250927 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.2143T>G p.Cys715Gly p.C715G ENST00000307340 12/72 368 266 102 389 389 0 strelka-varscan-mutect USH2A,missense_variant,p.Cys715Gly,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Cys715Gly,ENST00000366942,NM_007123.5; C ENST00000307340 Transcript missense_variant 2530/18883 2143/15609 715/5202 C/G Tgc/Ggc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.01) 12/72 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 216250927 216250927 A C 1 0 0 0 0 1 0 0 0 17570 159 6 5 5 USH2A 1 216250927 Missense_Mutation SNP A C3N-00560_T 43518 216250927 32705495 119 16808 USH2A 0 . GRCh38 1 216324195 216324195 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1301A>T p.Asp434Val p.D434V ENST00000307340 7/72 135 95 40 171 170 1 strelka-varscan-mutect USH2A,missense_variant,p.Asp434Val,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Asp434Val,ENST00000366942,NM_007123.5; A ENST00000307340 Transcript missense_variant 1688/18883 1301/15609 434/5202 D/V gAt/gTt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 7/72 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 216324195 216324195 T A 1 0 0 0 0 1 0 0 0 17570 1435 50 4 4 USH2A 1 216324195 Missense_Mutation SNP T C3N-00560_T 73268 216324195 32632227 120 16809 ESRRG 0 . GRCh38 1 216564267 216564267 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.850G>A p.Ala284Thr p.A284T ENST00000366937 6/8 142 127 15 125 125 0 strelka-varscan-mutect ESRRG,missense_variant,p.Ala249Thr,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000360012,NM_001243514.1;ESRRG,missense_variant,p.Ala284Thr,ENST00000366937,NM_001243518.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000361525,NM_206594.2;ESRRG,missense_variant,p.Ala249Thr,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,missense_variant,p.Ala249Thr,ENST00000493603,NM_001243510.2;ESRRG,missense_variant,p.Ala249Thr,ENST00000366938,NM_001243513.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000361395,;ESRRG,missense_variant,p.Ala272Thr,ENST00000408911,NM_001438.3;ESRRG,missense_variant,p.Ala249Thr,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000616180,;ESRRG,missense_variant,p.Ala210Thr,ENST00000463665,NM_001243507.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000487276,NM_001243512.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000493748,NM_001243509.1;ESRRG,missense_variant,p.Ala249Thr,ENST00000475275,;ESRRG,downstream_gene_variant,,ENST00000586199,; T ENST00000366937 Transcript missense_variant 1117/5365 850/1413 284/470 A/T Gcc/Acc 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 tolerated(0.22) 6/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PIRSF_domain:PIRSF500939,Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398 MODERATE 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 216564267 216564267 C T 1 0 0 0 0 1 0 0 0 5124 739 26 3 3 ESRRG 1 216564267 Missense_Mutation SNP C C3N-00560_T 240072 216564267 32392155 121 16810 SPATA17 0 . GRCh38 1 217801741 217801741 + Missense_Mutation SNP A A T rs549452959 C3N-00560_T C3N-00560_N A A c.896A>T p.His299Leu p.H299L ENST00000366933 9/11 55 41 14 108 108 0 strelka-varscan-mutect SPATA17,missense_variant,p.His299Leu,ENST00000366933,NM_138796.3;SPATA17,non_coding_transcript_exon_variant,,ENST00000471021,;SPATA17,non_coding_transcript_exon_variant,,ENST00000492747,; T ENST00000366933 Transcript missense_variant 951/5818 896/1086 299/361 H/L cAt/cTt rs549452959 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 deleterious(0) 9/11 hmmpanther:PTHR22706 MODERATE 1 SNV 1 1 PASS rs549452959 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 217801741 217801741 A T 1 0 0 0 0 1 0 0 0 15332 217 8 4 4 SPATA17 1 217801741 Missense_Mutation SNP A C3N-00560_T 1237474 217801741 31154681 122 16811 ZC3H11B 0 . GRCh38 1 219610431 219610431 + Silent SNP A A T rs534921022 C3N-00560_T C3N-00560_N A A c.1632T>A p.= p.V544V ENST00000636126 2/2 82 56 26 68 68 0 strelka-varscan-mutect ZC3H11B,synonymous_variant,p.=,ENST00000636126,;ZC3H11B,synonymous_variant,p.=,ENST00000367211,; T ENST00000636126 Transcript synonymous_variant 2348/4432 1632/2418 544/805 V gtT/gtA rs534921022 1 -1 ZC3H11B HGNC HGNC:25659 protein_coding YES ENSP00000489836 UPI000013E86C 2/2 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 LOW 1 SNV 1 PASS rs534921022 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 219610431 219610431 A T 1 0 0 0 0 0 0 0 1 18135 117 5 4 4 ZC3H11B 1 219610431 Silent SNP A C3N-00560_T 1808690 219610431 29345991 123 16812 EPRS 0 . GRCh38 1 219983188 219983188 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.3300+1G>T p.X1100_splice ENST00000366923 180 123 57 169 168 1 strelka-varscan-mutect EPRS,splice_donor_variant,,ENST00000366923,NM_004446.2;EPRS,downstream_gene_variant,,ENST00000609181,;EPRS,splice_donor_variant,,ENST00000485821,; A ENST00000366923 Transcript splice_donor_variant -/5014 3300/4539 1100/1512 1 -1 EPRS HGNC HGNC:3418 protein_coding YES CCDS31027.1 ENSP00000355890 P07814 UPI0000205E8C NM_004446.2 22/31 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 219983188 219983188 C A 1 0 0 0 0 0 0 1 0 5039 521 18 2 2 EPRS 1 219983188 Splice_Site SNP C C3N-00560_T 372757 219983188 28973234 124 16813 DUSP10 0 . GRCh38 1 221739736 221739736 + Silent SNP C C A rs776606563 C3N-00560_T C3N-00560_N C C c.9G>T p.= p.P3P ENST00000366899 2/4 39 27 12 44 44 0 strelka-varscan-mutect DUSP10,synonymous_variant,p.=,ENST00000366899,NM_007207.5;DUSP10,intron_variant,,ENST00000477026,;DUSP10,upstream_gene_variant,,ENST00000468085,; A ENST00000366899 Transcript synonymous_variant 248/2676 9/1449 3/482 P ccG/ccT rs776606563,COSM679488 1 -1 DUSP10 HGNC HGNC:3065 protein_coding YES CCDS1528.1 ENSP00000355866 Q9Y6W6 UPI000003473B NM_007207.5 2/4 0,1 LOW 1 SNV 1 0,1 1 PASS rs776606563 . 0 200 9 0 0 0 0 0 -20 0.9999984 1 1 1 0 A 2 1 56 221739736 221739736 C A 1 0 0 0 0 0 0 0 1 4632 523 19 1 1 DUSP10 1 221739736 Silent SNP C C3N-00560_T 1756548 221739736 27216686 125 16814 FAM177B 0 . GRCh38 1 222746692 222746692 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.147G>A p.= p.E49E ENST00000445590 1/4 108 79 29 111 111 0 strelka-varscan-mutect FAM177B,synonymous_variant,p.=,ENST00000445590,;FAM177B,synonymous_variant,p.=,ENST00000360827,NM_207468.2;FAM177B,synonymous_variant,p.=,ENST00000456298,;FAM177B,synonymous_variant,p.=,ENST00000434700,;FAM177B,synonymous_variant,p.=,ENST00000391880,;FAM177B,intron_variant,,ENST00000460763,; A ENST00000445590 Transcript synonymous_variant 164/1096 147/477 49/158 E gaG/gaA 1 1 FAM177B HGNC HGNC:34395 protein_coding YES CCDS1535.2 ENSP00000414451 A6PVY3 UPI00001D75B4 1/4 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14774,hmmpanther:PTHR31206,hmmpanther:PTHR31206:SF9,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 222746692 222746692 G A 1 0 0 0 0 0 0 0 1 5348 962 34 3 3 FAM177B 1 222746692 Silent SNP G C3N-00560_T 1006956 222746692 26209730 126 16815 EPHX1 0 . GRCh38 1 225828762 225828762 + Silent SNP G G C novel C3N-00560_T C3N-00560_N G G c.33G>C p.= p.L11L ENST00000614058 2/9 330 247 83 267 267 0 strelka-varscan-mutect EPHX1,synonymous_variant,p.=,ENST00000614058,NM_001291163.1;EPHX1,synonymous_variant,p.=,ENST00000366837,NM_000120.3;EPHX1,synonymous_variant,p.=,ENST00000272167,NM_001136018.3;EPHX1,synonymous_variant,p.=,ENST00000448202,;EPHX1,synonymous_variant,p.=,ENST00000445856,;EPHX1,upstream_gene_variant,,ENST00000467015,; C ENST00000614058 Transcript synonymous_variant 242/1789 33/1368 11/455 L ctG/ctC 1 1 EPHX1 HGNC HGNC:3401 protein_coding YES CCDS1547.1 ENSP00000480004 P07099 R4SBI6 UPI000012CFF2 NM_001291163.1 2/9 PIRSF_domain:PIRSF001112,hmmpanther:PTHR21661,hmmpanther:PTHR21661:SF34,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 225828762 225828762 G C 1 0 0 0 0 0 0 0 1 5026 1335 47 4 4 EPHX1 1 225828762 Silent SNP G C3N-00560_T 3082070 225828762 23127660 127 16816 PARP1 0 . GRCh38 1 226386347 226386347 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.813A>G p.= p.Q271Q ENST00000366794 6/23 605 434 171 494 494 0 strelka-varscan-mutect PARP1,synonymous_variant,p.=,ENST00000366794,NM_001618.3;PARP1,downstream_gene_variant,,ENST00000469663,; C ENST00000366794 Transcript synonymous_variant 957/3958 813/3045 271/1014 Q caA/caG 1 -1 PARP1 HGNC HGNC:270 protein_coding YES CCDS1554.1 ENSP00000355759 P09874 A0A024R3T8 UPI000013D92D NM_001618.3 6/23 hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF62,PIRSF_domain:PIRSF000489 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 226386347 226386347 T C 1 0 0 0 0 0 0 0 1 11534 1606 56 5 5 PARP1 1 226386347 Silent SNP T C3N-00560_T 557585 226386347 22570075 128 16817 ITPKB 0 . GRCh38 1 226648724 226648724 + Missense_Mutation SNP G G T rs769795552 C3N-00560_T C3N-00560_N G G c.1980C>A p.Phe660Leu p.F660L ENST00000429204 3/8 218 162 56 186 186 0 strelka-varscan-mutect ITPKB,missense_variant,p.Phe660Leu,ENST00000429204,NM_002221.3;ITPKB,missense_variant,p.Phe660Leu,ENST00000272117,; T ENST00000429204 Transcript missense_variant 2320/6162 1980/2841 660/946 F/L ttC/ttA rs769795552 1 -1 ITPKB HGNC HGNC:6179 protein_coding YES CCDS1555.1 ENSP00000411152 P27987 UPI000013D92B NM_002221.3 deleterious(0.05) 3/8 hmmpanther:PTHR12400,hmmpanther:PTHR12400:SF4 MODERATE 1 SNV 5 1 PASS rs769795552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 226648724 226648724 G T 1 0 0 0 0 1 0 0 0 7824 1049 37 1 1 ITPKB 1 226648724 Missense_Mutation SNP G C3N-00560_T 262377 226648724 22307698 129 16818 OBSCN 0 . GRCh38 1 228216431 228216431 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.2106G>T p.= p.G702G ENST00000570156 7/116 94 72 22 82 82 0 strelka-varscan-mutect OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000284548,NM_052843.3;C1orf145,upstream_gene_variant,,ENST00000295012,;OBSCN,non_coding_transcript_exon_variant,,ENST00000493977,;C1orf145,upstream_gene_variant,,ENST00000337335,;C1orf145,upstream_gene_variant,,ENST00000472613,; T ENST00000570156 Transcript synonymous_variant 2180/26925 2106/26772 702/8923 G ggG/ggT 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 7/116 PROSITE_profiles:PS50835,Gene3D:2.60.40.10 LOW SNV 5 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999656 1 1 1 0 T 2 4 56 228216431 228216431 G T 1 0 0 0 0 0 0 0 1 10889 1190 42 2 2 OBSCN 1 228216431 Silent SNP G C3N-00560_T 1567707 228216431 20739991 130 16819 OBSCN 0 . GRCh38 1 228319222 228319222 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.17341G>T p.Gly5781Trp p.G5781W ENST00000570156 65/116 133 98 35 104 104 0 strelka-varscan-mutect OBSCN,missense_variant,p.Gly5781Trp,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Gly5781Trp,ENST00000366707,;OBSCN,missense_variant,p.Gly4824Trp,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Gly4824Trp,ENST00000636875,;OBSCN,missense_variant,p.Gly4824Trp,ENST00000284548,NM_052843.3;OBSCN,intron_variant,,ENST00000483539,; T ENST00000570156 Transcript missense_variant 17415/26925 17341/26772 5781/8923 G/W Ggg/Tgg 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 65/116 hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 228319222 228319222 G T 1 0 0 0 0 1 0 0 0 10889 1348 47 2 2 OBSCN 1 228319222 Missense_Mutation SNP G C3N-00560_T 102791 228319222 20637200 131 16820 CCSAP 0 . GRCh38 1 229342233 229342233 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.233delC p.Pro78ArgfsTer8 p.P78Rfs*8 ENST00000284617 2/4 43 31 12 16 16 0 sindel-varindel-pindel CCSAP,frameshift_variant,p.Pro78ArgfsTer8,ENST00000284617,NM_145257.4;CCSAP,frameshift_variant,p.Pro78ArgfsTer8,ENST00000366687,;CCSAP,upstream_gene_variant,,ENST00000366686,;CCSAP,non_coding_transcript_exon_variant,,ENST00000483092,; - ENST00000284617 Transcript frameshift_variant 311/5121 233/813 78/270 P/X cCg/cg 1 -1 CCSAP HGNC HGNC:29578 protein_coding YES CCDS1577.1 ENSP00000284617 Q6IQ19 UPI0000071365 NM_145257.4 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR31022:SF4,hmmpanther:PTHR31022,Pfam_domain:PF15748 HIGH 1 deletion 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 229342233 229342233 G - 1 0 1 0 1 0 0 0 0 2651 1116 39 0 0 CCSAP 1 229342233 Frame_Shift_Del DEL G C3N-00560_T 1023011 229342233 19614189 132 16821 URB2 0 . GRCh38 1 229647554 229647554 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.3951A>T p.= p.T1317T ENST00000258243 7/10 295 190 105 208 208 0 strelka-varscan-mutect URB2,synonymous_variant,p.=,ENST00000258243,NM_001314021.1,NM_014777.2;URB2,upstream_gene_variant,,ENST00000434387,; T ENST00000258243 Transcript synonymous_variant 4087/5613 3951/4575 1317/1524 T acA/acT 1 1 URB2 HGNC HGNC:28967 protein_coding YES CCDS31052.1 ENSP00000258243 Q14146 UPI000013CFBD NM_001314021.1,NM_014777.2 7/10 hmmpanther:PTHR15682 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 229647554 229647554 A T 1 0 0 0 0 0 0 0 1 17555 175 7 4 4 URB2 1 229647554 Silent SNP A C3N-00560_T 305321 229647554 19308868 133 16822 EGLN1 0 . GRCh38 1 231421618 231421618 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.271C>A p.= p.R91R ENST00000366641 1/5 123 86 37 78 78 0 strelka-varscan-mutect EGLN1,synonymous_variant,p.=,ENST00000366641,NM_022051.2;EGLN1,upstream_gene_variant,,ENST00000476717,; T ENST00000366641 Transcript synonymous_variant 3427/7097 271/1281 91/426 R Cgg/Agg 1 -1 EGLN1 HGNC HGNC:1232 protein_coding YES CCDS1595.1 ENSP00000355601 Q9GZT9 R4SCQ0 UPI0000050C90 NM_022051.2 1/5 hmmpanther:PTHR12907,hmmpanther:PTHR12907:SF4,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 231421618 231421618 G T 1 0 0 0 0 0 0 0 1 4804 1115 39 1 1 EGLN1 1 231421618 Silent SNP G C3N-00560_T 1774064 231421618 17534804 134 16823 DISC1 0 . GRCh38 1 231694115 231694115 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.357G>T p.= p.G119G ENST00000366633 2/10 657 436 221 563 563 0 strelka-varscan-mutect DISC1,synonymous_variant,p.=,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,synonymous_variant,p.=,ENST00000622252,;DISC1,synonymous_variant,p.=,ENST00000366637,NM_001012957.1;DISC1,synonymous_variant,p.=,ENST00000620189,NM_001164540.1;DISC1,synonymous_variant,p.=,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,synonymous_variant,p.=,ENST00000366633,NM_001164539.1;DISC1,synonymous_variant,p.=,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,synonymous_variant,p.=,ENST00000317586,NM_001012958.1;DISC1,synonymous_variant,p.=,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,synonymous_variant,p.=,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,synonymous_variant,p.=,ENST00000537876,;DISC1,synonymous_variant,p.=,ENST00000366636,NM_001012959.1;DISC1,intron_variant,,ENST00000602873,NM_001164556.1;DISC1,downstream_gene_variant,,ENST00000602600,;DISC1,synonymous_variant,p.=,ENST00000535944,;DISC1,synonymous_variant,p.=,ENST00000295051,;DISC1,synonymous_variant,p.=,ENST00000602822,;DISC1,synonymous_variant,p.=,ENST00000602713,;DISC1,synonymous_variant,p.=,ENST00000602700,;DISC1,synonymous_variant,p.=,ENST00000366632,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,non_coding_transcript_exon_variant,,ENST00000468399,; T ENST00000366633 Transcript synonymous_variant 410/2676 357/2268 119/755 G ggG/ggT 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 2/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 231694115 231694115 G T 1 0 0 0 0 0 0 0 1 4344 1161 41 2 2 DISC1 1 231694115 Silent SNP G C3N-00560_T 272497 231694115 17262307 135 16824 DISC1 0 . GRCh38 1 231767210 231767210 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1339A>T p.Ser447Cys p.S447C ENST00000366633 5/10 368 262 106 319 319 0 strelka-varscan-mutect DISC1,missense_variant,p.Ser447Cys,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,missense_variant,p.Ser447Cys,ENST00000366637,NM_001012957.1;DISC1,missense_variant,p.Ser447Cys,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,missense_variant,p.Ser447Cys,ENST00000366633,NM_001164539.1;DISC1,missense_variant,p.Ser447Cys,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,missense_variant,p.Ser447Cys,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,missense_variant,p.Ser447Cys,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,missense_variant,p.Ser447Cys,ENST00000537876,;DISC1,missense_variant,p.Ser447Cys,ENST00000366636,NM_001012959.1;DISC1,missense_variant,p.Ser97Cys,ENST00000602873,NM_001164556.1;DISC1,intron_variant,,ENST00000622252,;DISC1,intron_variant,,ENST00000620189,NM_001164540.1;DISC1,missense_variant,p.Ser447Cys,ENST00000535944,;DISC1,missense_variant,p.Ser447Cys,ENST00000295051,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,3_prime_UTR_variant,,ENST00000602822,;DISC1,3_prime_UTR_variant,,ENST00000602713,;DISC1,3_prime_UTR_variant,,ENST00000602700,;DISC1,3_prime_UTR_variant,,ENST00000366632,; T ENST00000366633 Transcript missense_variant 1392/2676 1339/2268 447/755 S/C Agc/Tgc 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 deleterious(0.03) 5/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 231767210 231767210 A T 1 0 0 0 0 1 0 0 0 4344 188 7 4 4 DISC1 1 231767210 Missense_Mutation SNP A C3N-00560_T 73095 231767210 17189212 136 16825 ARID4B 0 . GRCh38 1 235220360 235220360 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1349G>T p.Arg450Ile p.R450I ENST00000264183 15/24 98 34 64 141 141 0 strelka-varscan-mutect ARID4B,missense_variant,p.Arg450Ile,ENST00000264183,NM_016374.5;ARID4B,missense_variant,p.Arg450Ile,ENST00000366603,NM_001206794.1;ARID4B,missense_variant,p.Arg450Ile,ENST00000349213,NM_031371.3;ARID4B,missense_variant,p.Arg450Ile,ENST00000418304,;ARID4B,missense_variant,p.Arg450Ile,ENST00000421364,;ARID4B,non_coding_transcript_exon_variant,,ENST00000471257,;ARID4B,non_coding_transcript_exon_variant,,ENST00000491632,; A ENST00000264183 Transcript missense_variant 1847/6067 1349/3939 450/1312 R/I aGa/aTa 1 -1 ARID4B HGNC HGNC:15550 protein_coding YES CCDS31061.1 ENSP00000264183 Q4LE39 A0A024R3R1 UPI00000437FE NM_016374.5 deleterious(0.02) 15/24 hmmpanther:PTHR13964:SF24,hmmpanther:PTHR13964 MODERATE 1 SNV 1 1 PASS rs1238160583 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 235220360 235220360 C A 1 0 0 0 0 1 0 0 0 1056 913 32 2 2 ARID4B 1 235220360 Missense_Mutation SNP C C3N-00560_T 3453150 235220360 13736062 137 16826 LYST 0 . GRCh38 1 235808598 235808598 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2220A>T p.Gln740His p.Q740H ENST00000389793 5/53 224 90 134 205 205 0 strelka-varscan-mutect LYST,missense_variant,p.Gln740His,ENST00000389793,NM_000081.3,NM_001301365.1;LYST,missense_variant,p.Gln740His,ENST00000389794,;LYST,non_coding_transcript_exon_variant,,ENST00000489585,;LYST,non_coding_transcript_exon_variant,,ENST00000465349,; A ENST00000389793 Transcript missense_variant 2395/13480 2220/11406 740/3801 Q/H caA/caT 1 -1 LYST HGNC HGNC:1968 protein_coding YES CCDS31062.1 ENSP00000374443 Q99698 UPI000020509E NM_000081.3,NM_001301365.1 tolerated(0.14) 5/53 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF86,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 235808598 235808598 T A 1 0 0 0 0 1 0 0 0 9041 1838 64 4 4 LYST 1 235808598 Missense_Mutation SNP T C3N-00560_T 588238 235808598 13147824 138 16827 NID1 0 . GRCh38 1 236048715 236048715 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.500G>T p.Ser167Ile p.S167I ENST00000264187 2/20 216 79 137 209 209 0 strelka-varscan-mutect NID1,missense_variant,p.Ser167Ile,ENST00000264187,NM_002508.2;NID1,missense_variant,p.Ser167Ile,ENST00000366595,; A ENST00000264187 Transcript missense_variant 583/5864 500/3744 167/1247 S/I aGc/aTc 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 tolerated(0.07) 2/20 PROSITE_profiles:PS51220,SMART_domains:SM00539 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 236048715 236048715 C A 1 0 0 0 0 1 0 0 0 10447 797 28 2 2 NID1 1 236048715 Missense_Mutation SNP C C3N-00560_T 240117 236048715 12907707 139 16828 ACTN2 0 . GRCh38 1 236757588 236757588 + Nonsense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.2257G>T p.Glu753Ter p.E753* ENST00000542672 18/21 477 183 294 441 441 0 strelka-varscan-mutect ACTN2,stop_gained,p.Glu545Ter,ENST00000546208,NM_001278344.1;ACTN2,stop_gained,p.Glu753Ter,ENST00000542672,NM_001278343.1;ACTN2,stop_gained,p.Glu753Ter,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; T ENST00000542672 Transcript stop_gained 2477/4906 2257/2685 753/894 E/* Gag/Tag COSM137805 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 18/21 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,Superfamily_domains:SSF47473 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 236757588 236757588 G T 1 0 0 0 0 0 1 0 0 249 1175 41 2 2 ACTN2 1 236757588 Nonsense_Mutation SNP G C3N-00560_T 708873 236757588 12198834 140 16829 RYR2 0 . GRCh38 1 237610823 237610824 + Frame_Shift_Ins INS - - CC rs766543639 C3N-00560_T C3N-00560_N - - c.4750_4751dupCC p.Leu1586AlafsTer20 p.L1586Afs*20 ENST00000366574 36/105 204 73 131 172 169 3 sindel-varindel-pindel RYR2,frameshift_variant,p.Leu1586AlafsTer20,ENST00000366574,NM_001035.2;RYR2,frameshift_variant,p.Leu1570AlafsTer20,ENST00000360064,; CC ENST00000366574 Transcript frameshift_variant 5062-5063/16562 4745-4746/14904 1582/4967 C/CX tgc/tgCCc rs766543639 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 36/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 HIGH 1 insertion 1 6 1 PASS . . 0 204 0 5 0 0 0 0 -20 0.9999683 1 1 1 0 CC 7 5 56 237610823 237610823 - CC 1 0 1 1 0 0 0 0 0 14029 1319 46 0 0 RYR2 1 237610823 Frame_Shift_Ins INS - C3N-00560_T 853235 237610823 11345599 141 16830 RYR2 0 . GRCh38 1 237784311 237784311 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.12599T>A p.Met4200Lys p.M4200K ENST00000366574 90/105 293 116 177 269 269 0 strelka-varscan-mutect RYR2,missense_variant,p.Met4200Lys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Met4184Lys,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript missense_variant 12916/16562 12599/14904 4200/4967 M/K aTg/aAg 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 90/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 237784311 237784311 T A 1 0 0 0 0 1 0 0 0 14029 1464 51 4 4 RYR2 1 237784311 Missense_Mutation SNP T C3N-00560_T 173488 237784311 11172111 142 16831 CHRM3 0 . GRCh38 1 239907736 239907736 + Silent SNP C C G rs781176638 C3N-00560_T C3N-00560_N C C c.285C>G p.= p.V95V ENST00000255380 5/5 241 145 96 352 352 0 strelka-varscan-mutect CHRM3,synonymous_variant,p.=,ENST00000255380,NM_000740.2;CHRM3,synonymous_variant,p.=,ENST00000615928,;CHRM3,synonymous_variant,p.=,ENST00000448020,; G ENST00000255380 Transcript synonymous_variant 1064/8780 285/1773 95/590 V gtC/gtG rs781176638 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 5/5 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00243,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF61,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs781176638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 239907736 239907736 C G 1 0 0 0 0 0 0 0 1 3138 813 29 4 4 CHRM3 1 239907736 Silent SNP C C3N-00560_T 2123425 239907736 9048686 143 16832 CHRM3 0 . GRCh38 1 239907837 239907837 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.386T>C p.Ile129Thr p.I129T ENST00000255380 5/5 165 127 38 206 206 0 strelka-varscan-mutect CHRM3,missense_variant,p.Ile129Thr,ENST00000255380,NM_000740.2;CHRM3,missense_variant,p.Ile129Thr,ENST00000615928,;CHRM3,downstream_gene_variant,,ENST00000448020,; C ENST00000255380 Transcript missense_variant 1165/8780 386/1773 129/590 I/T aTc/aCc 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 deleterious(0) 5/5 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF61,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 239907837 239907837 T C 1 0 0 0 0 1 0 0 0 3138 1435 50 5 5 CHRM3 1 239907837 Missense_Mutation SNP T C3N-00560_T 101 239907837 9048585 144 16833 FMN2 0 . GRCh38 1 240206907 240206908 + Frame_Shift_Ins INS - - C novel C3N-00560_T C3N-00560_N - - c.2098dupC p.Leu700ProfsTer13 p.L700Pfs*13 ENST00000319653 5/18 177 101 76 260 260 0 sindel-varindel-pindel FMN2,frameshift_variant,p.Leu700ProfsTer13,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,frameshift_variant,p.Leu137ProfsTer13,ENST00000447095,; C ENST00000319653 Transcript frameshift_variant 2325-2326/6434 2095-2096/5169 699/1722 A/AX gcc/gCcc 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 5/18 Coiled-coils_(Ncoils):Coil HIGH 1 insertion 5 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 56 240206907 240206907 - C 1 0 1 1 0 0 0 0 0 5806 1319 46 0 0 FMN2 1 240206907 Frame_Shift_Ins INS - C3N-00560_T 299070 240206907 8749515 145 16834 FMN2 0 . GRCh38 1 240207892 240207892 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.3080G>C p.Gly1027Ala p.G1027A ENST00000319653 5/18 61 49 12 91 91 0 varscan-mutect FMN2,missense_variant,p.Gly1027Ala,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; C ENST00000319653 Transcript missense_variant 3310/6434 3080/5169 1027/1722 G/A gGa/gCa 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 tolerated_low_confidence(0.4) 5/18 Pfam_domain:PF06346,Prints_domain:PR01217,Low_complexity_(Seg):seg,SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 240207892 240207892 G C 1 0 0 0 0 1 0 0 0 5806 1174 41 4 4 FMN2 1 240207892 Missense_Mutation SNP G C3N-00560_T 985 240207892 8748530 146 16835 PLD5 0 . GRCh38 1 242220070 242220070 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.653G>T p.Arg218Leu p.R218L ENST00000536534 5/10 184 113 71 243 243 0 strelka-varscan-mutect PLD5,missense_variant,p.Arg218Leu,ENST00000536534,;PLD5,missense_variant,p.Arg218Leu,ENST00000442594,NM_001320272.1,NM_152666.2;PLD5,missense_variant,p.Arg156Leu,ENST00000427495,NM_001195812.1,NM_001195811.1;PLD5,3_prime_UTR_variant,,ENST00000314833,;PLD5,3_prime_UTR_variant,,ENST00000366545,;PLD5,3_prime_UTR_variant,,ENST00000467561,; A ENST00000536534 Transcript missense_variant 895/8721 653/1611 218/536 R/L cGg/cTg 1 -1 PLD5 HGNC HGNC:26879 protein_coding YES CCDS1621.2 ENSP00000440896 Q8N7P1 UPI000040E1A4 tolerated(0.72) 5/10 hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Gene3D:3.30.870.10,SMART_domains:SM00155,Superfamily_domains:SSF56024 MODERATE 1 SNV 1 1 PASS rs1161348547 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 242220070 242220070 C A 1 0 0 0 0 1 0 0 0 12143 652 23 1 1 PLD5 1 242220070 Missense_Mutation SNP C C3N-00560_T 2012178 242220070 6736352 147 16836 PLD5 0 . GRCh38 1 242288428 242288428 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.429delC p.Lys145SerfsTer5 p.K145Sfs*5 ENST00000536534 3/10 121 74 47 152 152 0 sindel-varindel-pindel PLD5,frameshift_variant,p.Lys145SerfsTer5,ENST00000536534,;PLD5,frameshift_variant,p.Lys145SerfsTer5,ENST00000442594,NM_001320272.1,NM_152666.2;PLD5,frameshift_variant,p.Lys83SerfsTer5,ENST00000427495,NM_001195812.1,NM_001195811.1;PLD5,frameshift_variant,p.Lys83SerfsTer5,ENST00000459864,;PLD5,frameshift_variant,p.Lys145SerfsTer5,ENST00000467561,;PLD5,3_prime_UTR_variant,,ENST00000366545,;PLD5,intron_variant,,ENST00000314833,; - ENST00000536534 Transcript frameshift_variant 671/8721 429/1611 143/536 A/X gcC/gc 1 -1 PLD5 HGNC HGNC:26879 protein_coding YES CCDS1621.2 ENSP00000440896 Q8N7P1 UPI000040E1A4 3/10 hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 242288428 242288428 G - 1 0 1 0 1 0 0 0 0 12143 1335 47 0 0 PLD5 1 242288428 Frame_Shift_Del DEL G C3N-00560_T 68358 242288428 6667994 148 16837 ADSS 0 . GRCh38 1 244417726 244417726 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.972G>T p.Arg324Ser p.R324S ENST00000366535 10/13 91 46 45 142 142 0 strelka-varscan-mutect ADSS,missense_variant,p.Arg324Ser,ENST00000366535,NM_001126.3;ADSS,non_coding_transcript_exon_variant,,ENST00000468215,;ADSS,downstream_gene_variant,,ENST00000462358,; A ENST00000366535 Transcript missense_variant 1289/2780 972/1371 324/456 R/S agG/agT 1 -1 ADSS HGNC HGNC:292 protein_coding YES CCDS1624.1 ENSP00000355493 P30520 A0A024R5Q7 UPI0000132AF5 NM_001126.3 tolerated(0.6) 10/13 HAMAP:MF_00011,HAMAP:MF_03127,hmmpanther:PTHR11846:SF1,hmmpanther:PTHR11846,Pfam_domain:PF00709,TIGRFAM_domain:TIGR00184,Gene3D:2v40A03,SMART_domains:SM00788,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 244417726 244417726 C A 1 0 0 0 0 1 0 0 0 421 622 22 2 2 ADSS 1 244417726 Missense_Mutation SNP C C3N-00560_T 2129298 244417726 4538696 149 16838 OR2G3 0 . GRCh38 1 247605739 247605739 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.154G>C p.Asp52His p.D52H ENST00000320002 1/1 151 97 54 217 217 0 strelka-varscan-mutect OR2G3,missense_variant,p.Asp52His,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; C ENST00000320002 Transcript missense_variant 154/930 154/930 52/309 D/H Gat/Cat COSM262578 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 247605739 247605739 G C 1 0 0 0 0 1 0 0 0 11077 1174 41 4 4 OR2G3 1 247605739 Missense_Mutation SNP G C3N-00560_T 3188013 247605739 1350683 150 16839 OR2M2 0 . GRCh38 1 248180658 248180658 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.673G>T p.Val225Phe p.V225F ENST00000359682 1/1 352 199 153 512 511 1 strelka-varscan-mutect OR2M2,missense_variant,p.Val225Phe,ENST00000359682,NM_001004688.1; T ENST00000359682 Transcript missense_variant 673/1044 673/1044 225/347 V/F Gtc/Ttc 1 1 OR2M2 HGNC HGNC:8268 protein_coding YES CCDS31106.1 ENSP00000352710 Q96R28 A0A126GWI7 UPI00001612E4 NM_001004688.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 248180658 248180658 G T 1 0 0 0 0 1 0 0 0 11088 1377 48 2 2 OR2M2 1 248180658 Missense_Mutation SNP G C3N-00560_T 574919 248180658 775764 151 16840 OR2T3 0 . GRCh38 1 248473806 248473806 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.456C>A p.= p.A152A ENST00000359594 1/1 44 40 4 88 88 0 varscan-mutect OR2T3,synonymous_variant,p.=,ENST00000359594,NM_001005495.1; A ENST00000359594 Transcript synonymous_variant 456/957 456/957 152/318 A gcC/gcA 1 1 OR2T3 HGNC HGNC:14727 protein_coding YES CCDS31117.1 ENSP00000352604 Q8NH03 A0A126GVW5 UPI00001D7CA5 NM_001005495.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF4,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -10.55074 1 1 1 1 0 A 2 1 56 248473806 248473806 C A 1 0 0 0 0 0 0 0 1 11100 668 24 2 2 OR2T3 1 248473806 Silent SNP C C3N-00560_T 293148 248473806 482616 152 16841 OR2T34 0 . GRCh38 1 248574302 248574302 + Silent SNP G G T rs763747813 C3N-00560_T C3N-00560_N G G c.456C>A p.= p.A152A ENST00000328782 1/1 95 55 40 146 146 0 strelka-varscan-mutect OR2T34,synonymous_variant,p.=,ENST00000328782,NM_001001821.1; T ENST00000328782 Transcript synonymous_variant 456/957 456/957 152/318 A gcC/gcA rs763747813 1 -1 OR2T34 HGNC HGNC:31256 protein_coding YES CCDS31120.1 ENSP00000330904 Q8NGX1 UPI0000061ED4 NM_001001821.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF4,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs763747813 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 248574302 248574302 G T 1 0 0 0 0 0 0 0 1 11102 987 35 2 2 OR2T34 1 248574302 Silent SNP G C3N-00560_T 100496 248574302 382120 153 16842 FAM110C 0 . GRCh38 2 46189 46189 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.197G>T p.Gly66Val p.G66V ENST00000327669 1/2 52 33 19 28 28 0 strelka-varscan-mutect FAM110C,missense_variant,p.Gly66Val,ENST00000327669,NM_001077710.2;FAM110C,intron_variant,,ENST00000461026,;FAM110C,upstream_gene_variant,,ENST00000460464,; A ENST00000327669 Transcript missense_variant 197/3760 197/966 66/321 G/V gGg/gTg 1 -1 FAM110C HGNC HGNC:33340 protein_coding YES CCDS42645.1 ENSP00000328347 Q1W6H9 UPI0000579458 NM_001077710.2 tolerated(0.33) 1/2 hmmpanther:PTHR14758:SF5,hmmpanther:PTHR14758 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 46189 46189 C A 1 0 0 0 0 1 0 0 0 5262 623 22 2 2 FAM110C 2 46189 Missense_Mutation SNP C C3N-00560_T 46189 242147340 154 16843 MYT1L 0 . GRCh38 2 1922533 1922533 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.1236C>T p.= p.T412T ENST00000399161 10/25 356 286 70 366 366 0 strelka-varscan-mutect MYT1L,synonymous_variant,p.=,ENST00000399161,NM_001303052.1;MYT1L,synonymous_variant,p.=,ENST00000428368,NM_015025.3;MYT1L,synonymous_variant,p.=,ENST00000602387,; A ENST00000399161 Transcript synonymous_variant 1984/7063 1236/3561 412/1186 T acC/acT 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 10/25 hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 1922533 1922533 G A 1 0 0 0 0 0 0 0 1 10106 1335 47 3 3 MYT1L 2 1922533 Silent SNP G C3N-00560_T 1876344 1922533 240270996 155 16844 TSSC1 0 . GRCh38 2 3192437 3192437 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.966G>T p.Gln322His p.Q322H ENST00000382125 8/9 86 68 18 79 79 0 strelka-varscan-mutect TSSC1,missense_variant,p.Gln349His,ENST00000398659,;TSSC1,missense_variant,p.Gln322His,ENST00000382125,NM_003310.2;TSSC1,missense_variant,p.Gln171His,ENST00000441271,;TSSC1,non_coding_transcript_exon_variant,,ENST00000478754,;TSSC1,downstream_gene_variant,,ENST00000463662,;TSSC1,3_prime_UTR_variant,,ENST00000455162,;TSSC1,non_coding_transcript_exon_variant,,ENST00000496433,;TSSC1,downstream_gene_variant,,ENST00000435721,;TSSC1,downstream_gene_variant,,ENST00000482570,;TSSC1,downstream_gene_variant,,ENST00000470625,; A ENST00000382125 Transcript missense_variant 1159/1766 966/1164 322/387 Q/H caG/caT 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 tolerated(0.11) 8/9 hmmpanther:PTHR14205:SF15,hmmpanther:PTHR14205,Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999795 1 1 1 0 A 3 1 56 3192437 3192437 C A 1 0 0 0 0 1 0 0 0 17174 680 24 2 2 TSSC1 2 3192437 Missense_Mutation SNP C C3N-00560_T 1269904 3192437 239001092 156 16845 ADAM17 0 . GRCh38 2 9509983 9509983 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.1340A>G p.Asn447Ser p.N447S ENST00000310823 11/19 128 76 52 96 96 0 strelka-varscan-mutect ADAM17,missense_variant,p.Asn447Ser,ENST00000310823,NM_003183.4;RP11-400L8.2,intron_variant,,ENST00000480764,;RP11-400L8.2,intron_variant,,ENST00000472619,; C ENST00000310823 Transcript missense_variant 1523/4349 1340/2475 447/824 N/S aAt/aGt 1 -1 ADAM17 HGNC HGNC:195 protein_coding YES CCDS1665.1 ENSP00000309968 P78536 B2RNB2 UPI00001254D4 NM_003183.4 deleterious(0.05) 11/19 PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF152,Pfam_domain:PF13688,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 9509983 9509983 T C 1 0 0 0 0 1 0 0 0 282 1507 52 5 5 ADAM17 2 9509983 Missense_Mutation SNP T C3N-00560_T 6317546 9509983 232683546 157 16846 APOB 0 . GRCh38 2 21005162 21005162 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.11706G>T p.Leu3902Phe p.L3902F ENST00000233242 26/29 270 160 110 281 281 0 strelka-varscan-mutect APOB,missense_variant,p.Leu3902Phe,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; A ENST00000233242 Transcript missense_variant 11834/14121 11706/13692 3902/4563 L/F ttG/ttT 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0.03) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 21005162 21005162 C A 1 0 0 0 0 1 0 0 0 907 825 29 2 2 APOB 2 21005162 Missense_Mutation SNP C C3N-00560_T 11495179 21005162 221188367 158 16847 APOB 0 . GRCh38 2 21005786 21005786 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.11082C>A p.= p.T3694T ENST00000233242 26/29 162 131 31 148 148 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; T ENST00000233242 Transcript synonymous_variant 11210/14121 11082/13692 3694/4563 T acC/acA COSM3962322 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 1 LOW 1 SNV 1 1 1 PASS rs1311037335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 21005786 21005786 G T 1 0 0 0 0 0 0 0 1 907 1335 47 2 2 APOB 2 21005786 Silent SNP G C3N-00560_T 624 21005786 221187743 159 16848 APOB 0 . GRCh38 2 21008338 21008338 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.8530C>A p.Leu2844Met p.L2844M ENST00000233242 26/29 120 78 42 129 129 0 strelka-varscan-mutect APOB,missense_variant,p.Leu2844Met,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 8658/14121 8530/13692 2844/4563 L/M Ctg/Atg COSM1015923 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0.05) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 21008338 21008338 G T 1 0 0 0 0 1 0 0 0 907 962 34 2 2 APOB 2 21008338 Missense_Mutation SNP G C3N-00560_T 2552 21008338 221185191 160 16849 APOB 0 . GRCh38 2 21011394 21011394 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.5474G>T p.Gly1825Val p.G1825V ENST00000233242 26/29 226 141 85 212 212 0 strelka-varscan-mutect APOB,missense_variant,p.Gly1825Val,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript missense_variant 5602/14121 5474/13692 1825/4563 G/V gGt/gTt 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 21011394 21011394 C A 1 0 0 0 0 1 0 0 0 907 507 18 2 2 APOB 2 21011394 Missense_Mutation SNP C C3N-00560_T 3056 21011394 221182135 161 16850 EFR3B 0 . GRCh38 2 25103658 25103658 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.234G>A p.= p.E78E ENST00000403714 4/23 130 112 18 97 97 0 strelka-varscan-mutect EFR3B,synonymous_variant,p.=,ENST00000403714,NM_001319099.1,NM_014971.1;EFR3B,synonymous_variant,p.=,ENST00000401432,;EFR3B,synonymous_variant,p.=,ENST00000402191,; A ENST00000403714 Transcript synonymous_variant 417/7434 234/2454 78/817 E gaG/gaA 1 1 EFR3B HGNC HGNC:29155 protein_coding YES CCDS46231.1 ENSP00000384081 Q9Y2G0 UPI0000208069 NM_001319099.1,NM_014971.1 4/23 Gene3D:1.25.10.10,hmmpanther:PTHR12444,hmmpanther:PTHR12444:SF4,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 25103658 25103658 G A 1 0 0 0 0 0 0 0 1 4795 991 35 3 3 EFR3B 2 25103658 Silent SNP G C3N-00560_T 4092264 25103658 217089871 162 16851 OTOF 0 . GRCh38 2 26465989 26465989 + Nonsense_Mutation SNP C C A rs769672854 C3N-00560_T C3N-00560_N C C c.4588G>T p.Glu1530Ter p.E1530* ENST00000272371 37/47 788 474 314 718 718 0 strelka-varscan-mutect OTOF,stop_gained,p.Glu1530Ter,ENST00000272371,NM_194248.2;OTOF,stop_gained,p.Glu1530Ter,ENST00000403946,NM_001287489.1;OTOF,stop_gained,p.Glu840Ter,ENST00000402415,NM_194322.2;OTOF,stop_gained,p.Glu763Ter,ENST00000338581,NM_004802.3;OTOF,stop_gained,p.Glu763Ter,ENST00000339598,NM_194323.2;OTOF,non_coding_transcript_exon_variant,,ENST00000464574,; A ENST00000272371 Transcript stop_gained 4715/7156 4588/5994 1530/1997 E/* Gag/Tag rs769672854 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 37/47 PROSITE_profiles:PS50004,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 HIGH 1 SNV 1 1 PASS rs769672854 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 26465989 26465989 C A 1 0 0 0 0 0 1 0 0 11369 864 30 2 2 OTOF 2 26465989 Nonsense_Mutation SNP C C3N-00560_T 1362331 26465989 215727540 163 16852 SLC35F6 0 . GRCh38 2 26778073 26778073 + Silent SNP G G C novel C3N-00560_T C3N-00560_N G G c.678G>C p.= p.L226L ENST00000344420 6/6 92 81 11 86 86 0 strelka-varscan-mutect SLC35F6,synonymous_variant,p.=,ENST00000344420,NM_017877.3;SLC35F6,non_coding_transcript_exon_variant,,ENST00000482746,;CENPA,intron_variant,,ENST00000475662,;SLC35F6,3_prime_UTR_variant,,ENST00000429494,;SLC35F6,3_prime_UTR_variant,,ENST00000414029,; C ENST00000344420 Transcript synonymous_variant 740/3898 678/1116 226/371 L ctG/ctC 1 1 SLC35F6 HGNC HGNC:26055 protein_coding YES CCDS1728.1 ENSP00000345528 Q8N357 UPI0000071B52 NM_017877.3 6/6 PIRSF_domain:PIRSF036436,hmmpanther:PTHR13146,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.99944 0.9999993 1 1 1 0 C 2 2 56 26778073 26778073 G C 1 0 0 0 0 0 0 0 1 14864 1306 46 4 4 SLC35F6 2 26778073 Silent SNP G C3N-00560_T 312084 26778073 215415456 164 16853 GTF3C2 0 . GRCh38 2 27333757 27333757 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1630G>C p.Gly544Arg p.G544R ENST00000359541 12/19 90 76 14 82 82 0 strelka-varscan-mutect GTF3C2,missense_variant,p.Gly544Arg,ENST00000359541,NM_001318909.1;GTF3C2,missense_variant,p.Gly544Arg,ENST00000264720,NM_001521.3,NM_001035521.2;GTF3C2,missense_variant,p.Gly544Arg,ENST00000622534,;GTF3C2,missense_variant,p.Gly53Arg,ENST00000454704,;GTF3C2,upstream_gene_variant,,ENST00000457098,;GTF3C2-AS1,upstream_gene_variant,,ENST00000416453,;GTF3C2-AS1,upstream_gene_variant,,ENST00000625728,;GTF3C2-AS1,upstream_gene_variant,,ENST00000626256,;GTF3C2-AS1,upstream_gene_variant,,ENST00000585326,;GTF3C2-AS1,upstream_gene_variant,,ENST00000590383,;GTF3C2-AS1,upstream_gene_variant,,ENST00000592265,;GTF3C2-AS1,upstream_gene_variant,,ENST00000588707,;GTF3C2-AS1,upstream_gene_variant,,ENST00000608473,;GTF3C2-AS1,upstream_gene_variant,,ENST00000589853,;GTF3C2-AS1,upstream_gene_variant,,ENST00000587586,;GTF3C2-AS1,upstream_gene_variant,,ENST00000590754,;GTF3C2-AS1,upstream_gene_variant,,ENST00000585645,;GTF3C2-AS1,upstream_gene_variant,,ENST00000589232,;GTF3C2,upstream_gene_variant,,ENST00000415683,;GTF3C2,downstream_gene_variant,,ENST00000493511,;GTF3C2,downstream_gene_variant,,ENST00000470115,;GTF3C2,downstream_gene_variant,,ENST00000480989,;GTF3C2,upstream_gene_variant,,ENST00000484680,; G ENST00000359541 Transcript missense_variant 2060/3992 1630/2736 544/911 G/R Ggg/Cgg 1 -1 GTF3C2 HGNC HGNC:4665 protein_coding YES CCDS1749.1 ENSP00000352536 Q8WUA4 UPI0000074025 NM_001318909.1 deleterious(0.02) 12/19 Gene3D:2.130.10.10,hmmpanther:PTHR15052,hmmpanther:PTHR15052:SF2,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 27333757 27333757 C G 1 0 0 0 0 1 0 0 0 6754 623 22 4 4 GTF3C2 2 27333757 Missense_Mutation SNP C C3N-00560_T 555684 27333757 214859772 165 16854 GCKR 0 . GRCh38 2 27497385 27497385 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.202C>A p.Leu68Met p.L68M ENST00000264717 2/19 455 272 183 385 384 1 strelka-varscan-mutect GCKR,missense_variant,p.Leu68Met,ENST00000264717,NM_001486.3;GCKR,missense_variant,p.Leu40Met,ENST00000453813,;FNDC4,upstream_gene_variant,,ENST00000264703,NM_022823.2;GCKR,missense_variant,p.Leu68Met,ENST00000417872,;GCKR,non_coding_transcript_exon_variant,,ENST00000472290,;FNDC4,upstream_gene_variant,,ENST00000491414,;FNDC4,upstream_gene_variant,,ENST00000476197,; A ENST00000264717 Transcript missense_variant 265/2186 202/1878 68/625 L/M Ctg/Atg 1 1 GCKR HGNC HGNC:4196 protein_coding YES CCDS1757.1 ENSP00000264717 A0A0C4DFN2 UPI000013D55B NM_001486.3 tolerated(0.92) 2/19 hmmpanther:PTHR10088,hmmpanther:PTHR10088:SF4,Gene3D:3.40.50.10490,Superfamily_domains:SSF53697 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 27497385 27497385 C A 1 0 0 0 0 1 0 0 0 6164 680 24 2 2 GCKR 2 27497385 Missense_Mutation SNP C C3N-00560_T 163628 27497385 214696144 166 16855 CAPN14 0 . GRCh38 2 31200500 31200500 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.677T>A p.Ile226Asn p.I226N ENST00000403897 6/22 137 103 34 121 121 0 strelka-varscan-mutect CAPN14,missense_variant,p.Ile226Asn,ENST00000403897,NM_001145122.1;CAPN14,3_prime_UTR_variant,,ENST00000398824,NM_001321270.1; T ENST00000403897 Transcript missense_variant 819/2197 677/2055 226/684 I/N aTc/aAc 1 -1 CAPN14 HGNC HGNC:16664 protein_coding YES CCDS46254.1 ENSP00000385247 A8MX76 UPI000173A463 NM_001145122.1 tolerated(0.12) 6/22 PROSITE_profiles:PS50203,hmmpanther:PTHR10183:SF302,hmmpanther:PTHR10183,Pfam_domain:PF00648,Gene3D:3.90.70.10,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 31200500 31200500 A T 1 0 0 0 0 1 0 0 0 2319 333 12 4 4 CAPN14 2 31200500 Missense_Mutation SNP A C3N-00560_T 3703115 31200500 210993029 167 16856 SLC8A1 0 . GRCh38 2 40139444 40139444 + Silent SNP A A T rs112067970 C3N-00560_T C3N-00560_N A A c.2502T>A p.= p.S834S ENST00000403092 10/11 269 225 44 234 234 0 strelka-varscan-mutect SLC8A1,synonymous_variant,p.=,ENST00000406785,;SLC8A1,synonymous_variant,p.=,ENST00000403092,;SLC8A1,synonymous_variant,p.=,ENST00000405901,NM_001112800.1;SLC8A1,synonymous_variant,p.=,ENST00000402441,NM_001112802.1;SLC8A1,synonymous_variant,p.=,ENST00000405269,;SLC8A1,synonymous_variant,p.=,ENST00000332839,NM_021097.2;SLC8A1,synonymous_variant,p.=,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,synonymous_variant,p.=,ENST00000406391,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000625324,;SLC8A1-AS1,intron_variant,,ENST00000593848,;SLC8A1-AS1,intron_variant,,ENST00000625780,;SLC8A1-AS1,intron_variant,,ENST00000598247,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000625234,;SLC8A1-AS1,intron_variant,,ENST00000631022,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000631142,;SLC8A1-AS1,intron_variant,,ENST00000628471,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000435515,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000627219,;SLC8A1-AS1,intron_variant,,ENST00000629329,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000629180,;SLC8A1-AS1,intron_variant,,ENST00000629157,;SLC8A1-AS1,intron_variant,,ENST00000631204,;SLC8A1-AS1,intron_variant,,ENST00000630783,;SLC8A1-AS1,intron_variant,,ENST00000625381,;SLC8A1-AS1,intron_variant,,ENST00000631137,;SLC8A1-AS1,intron_variant,,ENST00000627108,;SLC8A1-AS1,intron_variant,,ENST00000626098,;SLC8A1-AS1,intron_variant,,ENST00000631330,;SLC8A1-AS1,intron_variant,,ENST00000630006,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1,3_prime_UTR_variant,,ENST00000407929,; T ENST00000403092 Transcript synonymous_variant 2536/3178 2502/2922 834/973 S tcT/tcA rs112067970 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 10/11 Pfam_domain:PF01699,Prints_domain:PR01259,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs112067970 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 40139444 40139444 A T 1 0 0 0 0 0 0 0 1 14989 175 7 4 4 SLC8A1 2 40139444 Silent SNP A C3N-00560_T 8938944 40139444 202054085 168 16857 SLC8A1 0 . GRCh38 2 40139676 40139676 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.2270G>A p.Gly757Glu p.G757E ENST00000403092 10/11 84 68 16 84 84 0 strelka-varscan-mutect SLC8A1,missense_variant,p.Gly721Glu,ENST00000406785,;SLC8A1,missense_variant,p.Gly757Glu,ENST00000403092,;SLC8A1,missense_variant,p.Gly752Glu,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Gly721Glu,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Gly721Glu,ENST00000405269,;SLC8A1,missense_variant,p.Gly757Glu,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Gly749Glu,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Gly721Glu,ENST00000406391,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000625324,;SLC8A1-AS1,intron_variant,,ENST00000593848,;SLC8A1-AS1,intron_variant,,ENST00000625780,;SLC8A1-AS1,intron_variant,,ENST00000598247,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000625234,;SLC8A1-AS1,intron_variant,,ENST00000631022,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000631142,;SLC8A1-AS1,intron_variant,,ENST00000628471,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000435515,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000627219,;SLC8A1-AS1,intron_variant,,ENST00000629329,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000629180,;SLC8A1-AS1,intron_variant,,ENST00000629157,;SLC8A1-AS1,intron_variant,,ENST00000631204,;SLC8A1-AS1,intron_variant,,ENST00000630783,;SLC8A1-AS1,intron_variant,,ENST00000625381,;SLC8A1-AS1,intron_variant,,ENST00000631137,;SLC8A1-AS1,intron_variant,,ENST00000627108,;SLC8A1-AS1,intron_variant,,ENST00000626098,;SLC8A1-AS1,intron_variant,,ENST00000631330,;SLC8A1-AS1,intron_variant,,ENST00000630006,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1,splice_region_variant,,ENST00000407929,; T ENST00000403092 Transcript missense_variant,splice_region_variant 2304/3178 2270/2922 757/973 G/E gGg/gAg 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 tolerated(0.07) 10/11 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40139676 40139676 C T 1 0 0 0 0 1 0 0 0 14989 637 22 3 3 SLC8A1 2 40139676 Missense_Mutation SNP C C3N-00560_T 232 40139676 202053853 169 16858 SLC8A1 0 . GRCh38 2 40164974 40164974 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2049T>A p.Asp683Glu p.D683E ENST00000403092 8/11 148 120 28 129 128 1 strelka-varscan-mutect SLC8A1,missense_variant,p.Asp647Glu,ENST00000406785,;SLC8A1,missense_variant,p.Asp683Glu,ENST00000403092,;SLC8A1,missense_variant,p.Asp678Glu,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Asp647Glu,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Asp647Glu,ENST00000405269,;SLC8A1,missense_variant,p.Asp683Glu,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Asp675Glu,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Asp647Glu,ENST00000406391,;SLC8A1-AS1,intron_variant,,ENST00000444629,;SLC8A1-AS1,intron_variant,,ENST00000625324,;SLC8A1-AS1,intron_variant,,ENST00000593848,;SLC8A1-AS1,intron_variant,,ENST00000625780,;SLC8A1-AS1,intron_variant,,ENST00000598247,;SLC8A1-AS1,intron_variant,,ENST00000593878,;SLC8A1-AS1,intron_variant,,ENST00000596532,;SLC8A1-AS1,intron_variant,,ENST00000625234,;SLC8A1-AS1,intron_variant,,ENST00000631022,;SLC8A1-AS1,intron_variant,,ENST00000599268,;SLC8A1-AS1,intron_variant,,ENST00000631142,;SLC8A1-AS1,intron_variant,,ENST00000628471,;SLC8A1-AS1,intron_variant,,ENST00000601679,;SLC8A1-AS1,intron_variant,,ENST00000435515,;SLC8A1-AS1,intron_variant,,ENST00000597385,;SLC8A1-AS1,intron_variant,,ENST00000627219,;SLC8A1-AS1,intron_variant,,ENST00000629329,;SLC8A1-AS1,intron_variant,,ENST00000599956,;SLC8A1-AS1,intron_variant,,ENST00000597170,;SLC8A1-AS1,intron_variant,,ENST00000629180,;SLC8A1-AS1,intron_variant,,ENST00000629157,;SLC8A1-AS1,intron_variant,,ENST00000631204,;SLC8A1-AS1,intron_variant,,ENST00000630783,;SLC8A1-AS1,intron_variant,,ENST00000625381,;SLC8A1-AS1,intron_variant,,ENST00000631137,;SLC8A1-AS1,intron_variant,,ENST00000627108,;SLC8A1-AS1,intron_variant,,ENST00000626098,;SLC8A1-AS1,intron_variant,,ENST00000631330,;SLC8A1-AS1,intron_variant,,ENST00000630006,;SLC8A1-AS1,intron_variant,,ENST00000599740,;SLC8A1,3_prime_UTR_variant,,ENST00000407929,; T ENST00000403092 Transcript missense_variant 2083/3178 2049/2922 683/973 D/E gaT/gaA 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 tolerated(0.85) 8/11 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,Superfamily_domains:SSF141072,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS rs879239752 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40164974 40164974 A T 1 0 0 0 0 1 0 0 0 14989 214 8 4 4 SLC8A1 2 40164974 Missense_Mutation SNP A C3N-00560_T 25298 40164974 202028555 170 16859 SLC8A1 0 . GRCh38 2 40429114 40429114 + Missense_Mutation SNP C C A rs763837333 C3N-00560_T C3N-00560_N C C c.1167G>T p.Lys389Asn p.K389N ENST00000403092 2/11 197 169 28 216 216 0 strelka-varscan-mutect SLC8A1,missense_variant,p.Lys389Asn,ENST00000406785,;SLC8A1,missense_variant,p.Lys389Asn,ENST00000403092,;SLC8A1,missense_variant,p.Lys389Asn,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Lys389Asn,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Lys389Asn,ENST00000405269,;SLC8A1,missense_variant,p.Lys389Asn,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Lys389Asn,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Lys389Asn,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,missense_variant,p.Lys386Asn,ENST00000407929,; A ENST00000403092 Transcript missense_variant 1201/3178 1167/2922 389/973 K/N aaG/aaT rs763837333 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 deleterious(0.03) 2/11 Pfam_domain:PF16494,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS rs763837333 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 40429114 40429114 C A 1 0 0 0 0 1 0 0 0 14989 680 24 2 2 SLC8A1 2 40429114 Missense_Mutation SNP C C3N-00560_T 264140 40429114 201764415 171 16860 EML4 0 . GRCh38 2 42256587 42256587 + Missense_Mutation SNP G G C rs773766836 C3N-00560_T C3N-00560_N G G c.295G>C p.Val99Leu p.V99L ENST00000318522 3/23 139 120 19 127 127 0 strelka-varscan-mutect EML4,missense_variant,p.Val99Leu,ENST00000318522,NM_019063.4;EML4,missense_variant,p.Val99Leu,ENST00000401738,;EML4,missense_variant,p.Val99Leu,ENST00000402711,NM_001145076.2;EML4,non_coding_transcript_exon_variant,,ENST00000409040,; C ENST00000318522 Transcript missense_variant 557/5549 295/2946 99/981 V/L Gtc/Ctc rs773766836 1 1 EML4 HGNC HGNC:1316 protein_coding YES CCDS1807.1 ENSP00000320663 Q9HC35 UPI0000140350 NM_019063.4 tolerated(0.45) 3/23 hmmpanther:PTHR13720:SF11,hmmpanther:PTHR13720 MODERATE 1 SNV 1 1 PASS rs773766836 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 42256587 42256587 G C 1 0 0 0 0 1 0 0 0 4942 1377 48 4 4 EML4 2 42256587 Missense_Mutation SNP G C3N-00560_T 1827473 42256587 199936942 172 16861 DYNC2LI1 0 . GRCh38 2 43776855 43776855 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.82G>T p.Glu28Ter p.E28* ENST00000605786 2/13 94 71 23 137 137 0 strelka-varscan-mutect DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000398823,;DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000260605,NM_016008.3;DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000605786,NM_001193464.1;DYNC2LI1,stop_gained,p.Glu12Ter,ENST00000378587,;DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000406852,NM_015522.3;RN7SKP66,upstream_gene_variant,,ENST00000516681,;DYNC2LI1,intron_variant,,ENST00000489222,;DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000479242,;DYNC2LI1,stop_gained,p.Glu28Ter,ENST00000496980,;DYNC2LI1,synonymous_variant,p.=,ENST00000462426,; T ENST00000605786 Transcript stop_gained 139/1346 82/1059 28/352 E/* Gaa/Taa 1 1 DYNC2LI1 HGNC HGNC:24595 protein_coding YES CCDS62903.1 ENSP00000474032 Q8TCX1 UPI00000704B1 NM_001193464.1 2/13 hmmpanther:PTHR13236 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 43776855 43776855 G T 1 0 0 0 0 0 1 0 0 4671 1291 45 2 2 DYNC2LI1 2 43776855 Nonsense_Mutation SNP G C3N-00560_T 1520268 43776855 198416674 173 16862 KCNK12 0 . GRCh38 2 47521335 47521335 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.865T>A p.Cys289Ser p.C289S ENST00000327876 2/2 214 173 41 189 189 0 strelka-varscan-mutect KCNK12,missense_variant,p.Cys289Ser,ENST00000327876,NM_022055.1;MSH2,intron_variant,,ENST00000461394,; T ENST00000327876 Transcript missense_variant 1473/6227 865/1293 289/430 C/S Tgc/Agc 1 -1 KCNK12 HGNC HGNC:6274 protein_coding YES CCDS1835.1 ENSP00000327611 Q9HB15 UPI000000DC4C NM_022055.1 tolerated(0.06) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF11,Pfam_domain:PF07885,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR01588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 47521335 47521335 A T 1 0 0 0 0 1 0 0 0 7977 159 6 4 4 KCNK12 2 47521335 Missense_Mutation SNP A C3N-00560_T 3744480 47521335 194672194 174 16863 PPP1R21 0 . GRCh38 2 48511340 48511340 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2185G>T p.Asp729Tyr p.D729Y ENST00000294952 21/22 102 72 30 97 97 0 strelka-varscan-mutect PPP1R21,missense_variant,p.Asp729Tyr,ENST00000294952,NM_001135629.2;PPP1R21,missense_variant,p.Asp718Tyr,ENST00000281394,NM_152994.4;PPP1R21,missense_variant,p.Asp687Tyr,ENST00000449090,NM_001193475.1;PPP1R21,splice_region_variant,,ENST00000476199,;PPP1R21,splice_region_variant,,ENST00000416913,;PPP1R21,splice_region_variant,,ENST00000431614,; T ENST00000294952 Transcript missense_variant,splice_region_variant 2342/3142 2185/2343 729/780 D/Y Gat/Tat 1 1 PPP1R21 HGNC HGNC:30595 protein_coding YES CCDS46278.1 ENSP00000294952 Q6ZMI0 UPI000015C523 NM_001135629.2 deleterious(0) 21/22 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10212,hmmpanther:PTHR21448 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 48511340 48511340 G T 1 0 0 0 0 1 0 0 0 12483 1188 41 2 2 PPP1R21 2 48511340 Missense_Mutation SNP G C3N-00560_T 990005 48511340 193682189 175 16864 NRXN1 0 . GRCh38 2 50621226 50621226 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1257G>T p.Met419Ile p.M419I ENST00000404971 8/24 113 94 19 119 119 0 strelka-varscan-mutect NRXN1,missense_variant,p.Met386Ile,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Met419Ile,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Met386Ile,ENST00000401669,;NRXN1,missense_variant,p.Met109Ile,ENST00000406859,;NRXN1,intron_variant,,ENST00000625672,;NRXN1,intron_variant,,ENST00000405472,;NRXN1,intron_variant,,ENST00000630543,;NRXN1,intron_variant,,ENST00000628515,;NRXN1,intron_variant,,ENST00000402717,;NRXN1,intron_variant,,ENST00000625891,;NRXN1,upstream_gene_variant,,ENST00000495871,;RP11-358H12.1,intron_variant,,ENST00000634985,;NRXN1,intron_variant,,ENST00000636298,;NRXN1,intron_variant,,ENST00000628761,;NRXN1,downstream_gene_variant,,ENST00000630431,;NRXN1,upstream_gene_variant,,ENST00000637605,;NRXN1,intron_variant,,ENST00000331040,;NRXN1,intron_variant,,ENST00000626249,; A ENST00000404971 Transcript missense_variant 2597/7578 1257/4644 419/1547 M/I atG/atT COSM5287221,COSM5287222,COSM5287223 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.04) 8/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 50621226 50621226 C A 1 0 0 0 0 1 0 0 0 10724 594 21 2 2 NRXN1 2 50621226 Missense_Mutation SNP C C3N-00560_T 2109886 50621226 191572303 176 16865 RTN4 0 . GRCh38 2 55050274 55050274 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.27G>T p.= p.L9L ENST00000337526 1/9 37 24 13 32 32 0 strelka-mutect RTN4,synonymous_variant,p.=,ENST00000337526,NM_020532.4;RTN4,synonymous_variant,p.=,ENST00000357732,NM_207520.1;RTN4,synonymous_variant,p.=,ENST00000317610,NM_153828.2;RTN4,intron_variant,,ENST00000394611,NM_001321860.1;RTN4,intron_variant,,ENST00000404909,NM_001321859.1;RTN4,intron_variant,,ENST00000402434,;RTN4,intron_variant,,ENST00000427710,;RTN4,upstream_gene_variant,,ENST00000357376,NM_001321861.1,NM_207521.1;RTN4,upstream_gene_variant,,ENST00000405240,NM_001321863.1;RTN4,upstream_gene_variant,,ENST00000438462,; A ENST00000337526 Transcript synonymous_variant 271/4790 27/3579 9/1192 L ctG/ctT 1 -1 RTN4 HGNC HGNC:14085 protein_coding YES CCDS42684.1 ENSP00000337838 Q9NQC3 UPI000000D81D NM_020532.4 1/9 hmmpanther:PTHR10994,hmmpanther:PTHR10994:SF25 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 55050274 55050274 C A 1 0 0 0 0 0 0 0 1 13988 581 21 2 2 RTN4 2 55050274 Silent SNP C C3N-00560_T 4429048 55050274 187143255 177 16866 CCDC85A 0 . GRCh38 2 56184656 56184656 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.32C>T p.Ala11Val p.A11V ENST00000407595 1/6 112 82 30 109 109 0 strelka-varscan-mutect CCDC85A,missense_variant,p.Ala11Val,ENST00000407595,NM_001080433.1;RP11-481J13.1,downstream_gene_variant,,ENST00000606639,;AC007743.1,non_coding_transcript_exon_variant,,ENST00000596663,;AC007743.1,non_coding_transcript_exon_variant,,ENST00000447423,;AC007743.1,intron_variant,,ENST00000432793,;RP11-482H16.1,intron_variant,,ENST00000607540,; T ENST00000407595 Transcript missense_variant 534/3982 32/1662 11/553 A/V gCt/gTt 1 1 CCDC85A HGNC HGNC:29400 protein_coding YES CCDS46290.1 ENSP00000384040 Q96PX6 UPI00001C1DC1 NM_001080433.1 tolerated_low_confidence(0.12) 1/6 hmmpanther:PTHR13546,hmmpanther:PTHR13546:SF16,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 56184656 56184656 C T 1 0 0 0 0 1 0 0 0 2557 797 28 3 3 CCDC85A 2 56184656 Missense_Mutation SNP C C3N-00560_T 1134382 56184656 186008873 178 16867 CLEC4F 0 . GRCh38 2 70819828 70819828 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.125C>A p.Pro42Gln p.P42Q ENST00000272367 2/7 45 35 10 41 41 0 strelka-varscan-mutect CLEC4F,missense_variant,p.Pro42Gln,ENST00000272367,NM_001258027.1,NM_173535.2;CLEC4F,missense_variant,p.Pro42Gln,ENST00000426626,; T ENST00000272367 Transcript missense_variant 202/2475 125/1770 42/589 P/Q cCg/cAg COSM2997082 1 -1 CLEC4F HGNC HGNC:25357 protein_coding YES CCDS1910.1 ENSP00000272367 Q8N1N0 UPI0000376BCC NM_001258027.1,NM_173535.2 deleterious(0.01) 2/7 Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 2 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 56 70819828 70819828 G T 1 0 0 0 0 1 0 0 0 3284 1116 39 1 1 CLEC4F 2 70819828 Missense_Mutation SNP G C3N-00560_T 14635172 70819828 171373701 179 16868 TET3 0 . GRCh38 2 74092929 74092929 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.3067G>C p.Asp1023His p.D1023H ENST00000409262 8/11 189 157 32 222 222 0 strelka-varscan-mutect TET3,missense_variant,p.Asp1023His,ENST00000409262,NM_001287491.1;TET3,missense_variant,p.Asp930His,ENST00000305799,; C ENST00000409262 Transcript missense_variant 3067/11388 3067/5388 1023/1795 D/H Gac/Cac 1 1 TET3 HGNC HGNC:28313 protein_coding YES CCDS46339.2 ENSP00000386869 O43151 K9JJH7 UPI0002A87FCB NM_001287491.1 tolerated(0.12) 8/11 hmmpanther:PTHR23358:SF4,hmmpanther:PTHR23358,Pfam_domain:PF12851,SMART_domains:SM01333 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 74092929 74092929 G C 1 0 0 0 0 1 0 0 0 16192 1174 41 4 4 TET3 2 74092929 Missense_Mutation SNP G C3N-00560_T 3273101 74092929 168100600 180 16869 LOXL3 0 . GRCh38 2 74536461 74536461 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.923G>T p.Arg308Leu p.R308L ENST00000264094 6/14 107 68 39 110 110 0 strelka-varscan-mutect LOXL3,missense_variant,p.Arg308Leu,ENST00000264094,NM_032603.3;LOXL3,missense_variant,p.Arg308Leu,ENST00000409549,;LOXL3,missense_variant,p.Arg308Leu,ENST00000409249,;LOXL3,missense_variant,p.Arg163Leu,ENST00000393937,NM_001289164.1;LOXL3,missense_variant,p.Arg163Leu,ENST00000409986,;LOXL3,missense_variant,p.Arg35Leu,ENST00000420535,;HTRA2,downstream_gene_variant,,ENST00000258080,NM_013247.4;HTRA2,downstream_gene_variant,,ENST00000437202,;HTRA2,downstream_gene_variant,,ENST00000352222,NM_145074.2;LOXL3,downstream_gene_variant,,ENST00000413469,;LOXL3,non_coding_transcript_exon_variant,,ENST00000481835,;HTRA2,downstream_gene_variant,,ENST00000467961,;HTRA2,downstream_gene_variant,,ENST00000462909,;LOXL3,downstream_gene_variant,,ENST00000484369,;HTRA2,downstream_gene_variant,,ENST00000484881,;LOXL3,non_coding_transcript_exon_variant,,ENST00000470907,;HTRA2,downstream_gene_variant,,ENST00000484352,;HTRA2,downstream_gene_variant,,ENST00000482331,; A ENST00000264094 Transcript missense_variant 995/3502 923/2262 308/753 R/L cGt/cTt 1 -1 LOXL3 HGNC HGNC:13869 protein_coding YES CCDS1953.1 ENSP00000264094 P58215 UPI0000044959 NM_032603.3 deleterious(0) 6/14 Gene3D:3.10.250.10,Prints_domain:PR00258,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF305,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS rs1315777875 . 0 201 9 0 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 56 74536461 74536461 C A 1 0 0 0 0 1 0 0 0 8804 536 19 1 1 LOXL3 2 74536461 Missense_Mutation SNP C C3N-00560_T 443532 74536461 167657068 181 16870 REG3G 0 . GRCh38 2 79027055 79027055 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.217T>A p.Ser73Thr p.S73T ENST00000272324 4/6 168 142 26 164 163 1 strelka-varscan-mutect REG3G,missense_variant,p.Ser73Thr,ENST00000272324,NM_001008387.2;REG3G,missense_variant,p.Ser73Thr,ENST00000393897,NM_198448.3;REG3G,intron_variant,,ENST00000409471,NM_001270040.1;REG3G,non_coding_transcript_exon_variant,,ENST00000490944,;REG3G,downstream_gene_variant,,ENST00000498312,; A ENST00000272324 Transcript missense_variant 401/938 217/528 73/175 S/T Tct/Act 1 1 REG3G HGNC HGNC:29595 protein_coding YES CCDS1962.1 ENSP00000272324 Q6UW15 UPI0000048F1E NM_001008387.2 deleterious(0) 4/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF60,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 79027055 79027055 T A 1 0 0 0 0 1 0 0 0 13383 1551 54 4 4 REG3G 2 79027055 Missense_Mutation SNP T C3N-00560_T 4490594 79027055 163166474 182 16871 REG3A 0 . GRCh38 2 79158362 79158362 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.297C>A p.Tyr99Ter p.Y99* ENST00000393878 3/5 142 84 58 133 133 0 strelka-varscan-mutect REG3A,stop_gained,p.Tyr99Ter,ENST00000393878,NM_138938.2;REG3A,stop_gained,p.Tyr99Ter,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,stop_gained,p.Tyr99Ter,ENST00000305165,;AC011754.1,upstream_gene_variant,,ENST00000415201,;REG3A,downstream_gene_variant,,ENST00000464746,;REG3A,downstream_gene_variant,,ENST00000490901,; T ENST00000393878 Transcript stop_gained 645/1095 297/528 99/175 Y/* taC/taA 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 3/5 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 HIGH 1 SNV 1 1 PASS rs1383969235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 79158362 79158362 G T 1 0 0 0 0 0 1 0 0 13382 1024 36 2 2 REG3A 2 79158362 Nonsense_Mutation SNP G C3N-00560_T 131307 79158362 163035167 183 16872 CTNNA2 0 . GRCh38 2 79744573 79744573 + Missense_Mutation SNP C C G rs373818447 C3N-00560_T C3N-00560_N C C c.289C>G p.Arg97Gly p.R97G ENST00000402739 2/18 91 75 16 99 99 0 strelka-varscan-mutect CTNNA2,missense_variant,p.Arg97Gly,ENST00000466387,;CTNNA2,missense_variant,p.Arg97Gly,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Arg97Gly,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Arg97Gly,ENST00000629316,NM_001164883.1;CTNNA2,missense_variant,p.Arg97Gly,ENST00000409971,;CTNNA2,downstream_gene_variant,,ENST00000451966,;CTNNA2,non_coding_transcript_exon_variant,,ENST00000508970,; G ENST00000402739 Transcript missense_variant 294/3684 289/2862 97/953 R/G Cgc/Ggc rs373818447,COSM3000679,COSM4315409 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0.02) 2/18 Gene3D:1.20.120.230,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23,Superfamily_domains:SSF47220 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs373818447 . 0 199 10 0 0 0 0 0 -20 0.999987 1 1 1 0 G 3 3 56 79744573 79744573 C G 1 0 0 0 0 1 0 0 0 3822 768 27 4 4 CTNNA2 2 79744573 Missense_Mutation SNP C C3N-00560_T 586211 79744573 162448956 184 16873 CTNNA2 0 . GRCh38 2 79909607 79909607 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.866T>A p.Leu289Gln p.L289Q ENST00000402739 6/18 146 114 32 142 142 0 strelka-varscan-mutect CTNNA2,missense_variant,p.Leu289Gln,ENST00000466387,;CTNNA2,missense_variant,p.Leu289Gln,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Leu289Gln,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Leu289Gln,ENST00000629316,NM_001164883.1; A ENST00000402739 Transcript missense_variant 871/3684 866/2862 289/953 L/Q cTg/cAg 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0.04) 6/18 Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 79909607 79909607 T A 1 0 0 0 0 1 0 0 0 3822 1580 55 4 4 CTNNA2 2 79909607 Missense_Mutation SNP T C3N-00560_T 165034 79909607 162283922 185 16874 LRRTM1 0 . GRCh38 2 80303560 80303560 + Missense_Mutation SNP C C G rs759656049 C3N-00560_T C3N-00560_N C C c.260G>C p.Gly87Ala p.G87A ENST00000295057 2/2 237 208 29 276 276 0 strelka-varscan-mutect LRRTM1,missense_variant,p.Gly87Ala,ENST00000295057,;LRRTM1,missense_variant,p.Gly87Ala,ENST00000409148,NM_178839.4;LRRTM1,missense_variant,p.Gly87Ala,ENST00000416268,;LRRTM1,missense_variant,p.Gly87Ala,ENST00000452811,;LRRTM1,missense_variant,p.Gly87Ala,ENST00000415098,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Gly87Ala,ENST00000433224,;LRRTM1,missense_variant,p.Gly87Ala,ENST00000417012,; G ENST00000295057 Transcript missense_variant 917/2599 260/1569 87/522 G/A gGg/gCg rs759656049 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE tolerated(0.05) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs759656049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 80303560 80303560 C G 1 0 0 0 0 1 0 0 0 8945 623 22 4 4 LRRTM1 2 80303560 Missense_Mutation SNP C C3N-00560_T 393953 80303560 161889969 186 16875 THNSL2 0 . GRCh38 2 88173228 88173228 + Frame_Shift_Del DEL C C - rs114858196 C3N-00560_T C3N-00560_N C C c.78delC p.Asp26GlufsTer30 p.D26Efs*30 ENST00000324166 1/8 93 57 36 103 103 0 sindel-varindel THNSL2,frameshift_variant,p.Asp26GlufsTer30,ENST00000324166,NM_018271.4;THNSL2,frameshift_variant,p.Asp26GlufsTer30,ENST00000343544,NM_001244676.1;THNSL2,frameshift_variant,p.Asp26GlufsTer30,ENST00000419759,;THNSL2,intron_variant,,ENST00000449349,;THNSL2,intron_variant,,ENST00000377254,NM_001244678.1;THNSL2,upstream_gene_variant,,ENST00000496844,;THNSL2,upstream_gene_variant,,ENST00000475910,; - ENST00000324166 Transcript frameshift_variant 1769/3649 78/1455 26/484 D/X gaC/ga rs114858196 1 1 THNSL2 HGNC HGNC:25602 protein_coding YES CCDS2002.2 ENSP00000327323 Q86YJ6 UPI00002088D9 NM_018271.4 1/8 Gene3D:1kl7A01,Pfam_domain:PF14821,hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF1,Superfamily_domains:SSF53686 HIGH 1 deletion 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 - 7 5 56 88173228 88173228 C - 1 0 1 0 1 0 0 0 0 16298 535 19 0 0 THNSL2 2 88173228 Frame_Shift_Del DEL C C3N-00560_T 7869668 88173228 154020301 187 16876 THNSL2 0 . GRCh38 2 88183073 88183073 + Missense_Mutation SNP G G T rs569834072 C3N-00560_T C3N-00560_N G G c.1077G>T p.Lys359Asn p.K359N ENST00000324166 6/8 75 69 6 77 77 0 strelka-varscan-mutect THNSL2,missense_variant,p.Lys359Asn,ENST00000324166,NM_018271.4;THNSL2,missense_variant,p.Lys359Asn,ENST00000343544,NM_001244676.1;THNSL2,missense_variant,p.Lys201Asn,ENST00000377254,NM_001244678.1;THNSL2,intron_variant,,ENST00000449349,;THNSL2,splice_region_variant,,ENST00000496844,;THNSL2,splice_region_variant,,ENST00000496165,;THNSL2,non_coding_transcript_exon_variant,,ENST00000476349,;THNSL2,non_coding_transcript_exon_variant,,ENST00000464022,; T ENST00000324166 Transcript missense_variant,splice_region_variant 2768/3649 1077/1455 359/484 K/N aaG/aaT rs569834072 1 1 THNSL2 HGNC HGNC:25602 protein_coding YES CCDS2002.2 ENSP00000327323 Q86YJ6 UPI00002088D9 NM_018271.4 deleterious(0.03) 6/8 Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686,TIGRFAM_domain:TIGR00260 MODERATE 1 SNV 1 1 PASS rs569834072 . 0 204 6 0 0 0 0 0 -13.2306 0.9999998 1 1 1 0 T 3 4 56 88183073 88183073 G T 1 0 0 0 0 1 0 0 0 16298 1014 35 2 2 THNSL2 2 88183073 Missense_Mutation SNP G C3N-00560_T 9845 88183073 154010456 188 16877 THNSL2 0 . GRCh38 2 88185906 88185906 + Missense_Mutation SNP G G T rs533962054 C3N-00560_T C3N-00560_N G G c.1238G>T p.Arg413Leu p.R413L ENST00000324166 8/8 189 124 65 192 192 0 strelka-varscan-mutect THNSL2,missense_variant,p.Arg413Leu,ENST00000324166,NM_018271.4;THNSL2,missense_variant,p.Gly239Cys,ENST00000449349,;THNSL2,synonymous_variant,p.=,ENST00000377254,NM_001244678.1;THNSL2,3_prime_UTR_variant,,ENST00000343544,NM_001244676.1;THNSL2,non_coding_transcript_exon_variant,,ENST00000496844,;THNSL2,downstream_gene_variant,,ENST00000496165,;THNSL2,downstream_gene_variant,,ENST00000476349,;THNSL2,downstream_gene_variant,,ENST00000464022,; T ENST00000324166 Transcript missense_variant 2929/3649 1238/1455 413/484 R/L cGg/cTg rs533962054 1 1 THNSL2 HGNC HGNC:25602 protein_coding YES CCDS2002.2 ENSP00000327323 Q86YJ6 UPI00002088D9 NM_018271.4 deleterious(0.04) 8/8 Gene3D:3.40.50.1100,hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF1,Superfamily_domains:SSF53686,TIGRFAM_domain:TIGR00260 MODERATE 1 SNV 1 1 PASS rs533962054 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 88185906 88185906 G T 1 0 0 0 0 1 0 0 0 16298 1116 39 1 1 THNSL2 2 88185906 Missense_Mutation SNP G C3N-00560_T 2833 88185906 154007623 189 16878 MAL 0 . GRCh38 2 95049704 95049704 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.385G>T p.Val129Leu p.V129L ENST00000309988 3/4 151 108 43 140 140 0 strelka-varscan-mutect MAL,missense_variant,p.Val129Leu,ENST00000309988,NM_002371.3;MAL,missense_variant,p.Val73Leu,ENST00000354078,NM_022439.2;MAL,intron_variant,,ENST00000353004,NM_022438.2;MAL,intron_variant,,ENST00000349807,NM_022440.2;AC103563.9,downstream_gene_variant,,ENST00000442200,; T ENST00000309988 Transcript missense_variant,splice_region_variant 494/1112 385/462 129/153 V/L Gtg/Ttg 1 1 MAL HGNC HGNC:6817 protein_coding YES CCDS2006.1 ENSP00000310880 P21145 A0A024RE19 UPI000004494A NM_002371.3 deleterious(0.01) 3/4 Pfam_domain:PF01284,Prints_domain:PR01884,PROSITE_profiles:PS51225,hmmpanther:PTHR22776,hmmpanther:PTHR22776:SF12,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1256810902 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 95049704 95049704 G T 1 0 0 0 0 1 0 0 0 9118 1159 40 1 1 MAL 2 95049704 Missense_Mutation SNP G C3N-00560_T 6863798 95049704 147143825 190 16879 NCAPH 0 . GRCh38 2 96343210 96343211 + Frame_Shift_Del DEL GC GC - novel C3N-00560_T C3N-00560_N GC GC c.504_505delCG p.Val169GlyfsTer30 p.V169Gfs*30 ENST00000240423 5/18 129 96 33 181 181 0 sindel-varindel-pindel NCAPH,frameshift_variant,p.Val158GlyfsTer30,ENST00000455200,;NCAPH,frameshift_variant,p.Val169GlyfsTer30,ENST00000240423,NM_015341.4,NM_001281710.1,NM_001281711.1;NCAPH,frameshift_variant,p.Val33GlyfsTer30,ENST00000427946,NM_001281712.1;NCAPH,frameshift_variant,p.Val158GlyfsTer30,ENST00000435975,;NCAPH,intron_variant,,ENST00000456906,;NCAPH,non_coding_transcript_exon_variant,,ENST00000477409,; - ENST00000240423 Transcript frameshift_variant 544-545/2763 501-502/2226 167-168/741 VR/VX gtGCgc/gtgc 1 1 NCAPH HGNC HGNC:1112 protein_coding YES CCDS2021.1 ENSP00000240423 Q15003 UPI0000163F72 NM_015341.4,NM_001281710.1,NM_001281711.1 5/18 hmmpanther:PTHR13108,Pfam_domain:PF05786,PIRSF_domain:PIRSF017126 HIGH 1 deletion 1 3 1 PASS . . 0 205 0 5 0 0 0 0 -20 0.9998355 1 1 1 0 - 7 5 56 96343210 96343210 GC - 1 0 1 0 1 0 0 0 0 10225 1306 46 0 0 NCAPH 2 96343210 Frame_Shift_Del DEL GC C3N-00560_T 1293506 96343210 145850319 191 16880 ANKRD39 0 . GRCh38 2 96857970 96857970 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.18C>T p.= p.P6P ENST00000393537 1/4 218 145 73 153 153 0 strelka-varscan-mutect ANKRD39,synonymous_variant,p.=,ENST00000393537,NM_016466.5;SEMA4C,downstream_gene_variant,,ENST00000305476,NM_017789.4;ANKRD23,upstream_gene_variant,,ENST00000462692,;ANKRD39,synonymous_variant,p.=,ENST00000443120,;SEMA4C,downstream_gene_variant,,ENST00000482925,;SEMA4C,downstream_gene_variant,,ENST00000467747,;SEMA4C,downstream_gene_variant,,ENST00000474420,; A ENST00000393537 Transcript synonymous_variant 126/976 18/552 6/183 P ccC/ccT 1 -1 ANKRD39 HGNC HGNC:28640 protein_coding YES CCDS2028.1 ENSP00000377170 Q53RE8 UPI0000207C9D NM_016466.5 1/4 hmmpanther:PTHR24148,hmmpanther:PTHR24148:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 96857970 96857970 G A 1 0 0 0 0 0 0 0 1 774 987 35 3 3 ANKRD39 2 96857970 Silent SNP G C3N-00560_T 514760 96857970 145335559 192 16881 INPP4A 0 . GRCh38 2 98539534 98539534 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.677G>T p.Gly226Val p.G226V ENST00000074304 10/26 95 57 38 70 70 0 strelka-varscan-mutect INPP4A,missense_variant,p.Gly226Val,ENST00000409016,NM_004027.2;INPP4A,missense_variant,p.Gly226Val,ENST00000074304,NM_001134224.1;INPP4A,missense_variant,p.Gly226Val,ENST00000409851,NM_001134225.1;INPP4A,missense_variant,p.Gly226Val,ENST00000409540,NM_001566.2;INPP4A,missense_variant,p.Gly226Val,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,; T ENST00000074304 Transcript missense_variant 1070/6752 677/2934 226/977 G/V gGt/gTt COSM2914124,COSM2914125,COSM2914126,COSM4317084 1 1 INPP4A HGNC HGNC:6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1 tolerated(0.05) 10/26 hmmpanther:PTHR12187,hmmpanther:PTHR12187:SF4 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs1379669602 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 98539534 98539534 G T 1 0 0 0 0 1 0 0 0 7655 1261 44 2 2 INPP4A 2 98539534 Missense_Mutation SNP G C3N-00560_T 1681564 98539534 143653995 193 16882 TBC1D8 0 . GRCh38 2 101029540 101029540 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2128G>C p.Asp710His p.D710H ENST00000376840 12/20 189 140 49 107 107 0 varscan-mutect TBC1D8,missense_variant,p.Asp725His,ENST00000409318,;TBC1D8,missense_variant,p.Asp710His,ENST00000376840,NM_001102426.1;TBC1D8,non_coding_transcript_exon_variant,,ENST00000481317,;TBC1D8,non_coding_transcript_exon_variant,,ENST00000473937,;TBC1D8,non_coding_transcript_exon_variant,,ENST00000485875,; G ENST00000376840 Transcript missense_variant 2128/3627 2128/3423 710/1140 D/H Gac/Cac 1 -1 TBC1D8 HGNC HGNC:17791 protein_coding YES CCDS46375.1 ENSP00000366036 O95759 UPI00015ADD19 NM_001102426.1 deleterious(0.03) 12/20 Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF260,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 101029540 101029540 C G 1 0 0 0 0 1 0 0 0 16030 855 30 4 4 TBC1D8 2 101029540 Missense_Mutation SNP C C3N-00560_T 2490006 101029540 141163989 194 16883 RFX8 0 . GRCh38 2 101406008 101406008 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.863T>A p.Leu288Gln p.L288Q ENST00000428343 10/12 170 129 41 141 141 0 strelka-varscan-mutect RFX8,missense_variant,p.Leu288Gln,ENST00000428343,NM_001145664.1;RFX8,3_prime_UTR_variant,,ENST00000481179,; T ENST00000428343 Transcript missense_variant 983/1686 863/1422 288/473 L/Q cTg/cAg 1 -1 RFX8 HGNC HGNC:37253 protein_coding YES CCDS46376.1 ENSP00000401536 Q6ZV50 UPI0001AE76D5 NM_001145664.1 deleterious(0) 10/12 hmmpanther:PTHR12619:SF24,hmmpanther:PTHR12619 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 101406008 101406008 A T 1 0 0 0 0 1 0 0 0 13443 188 7 4 4 RFX8 2 101406008 Missense_Mutation SNP A C3N-00560_T 376468 101406008 140787521 195 16884 IL1RL1 0 . GRCh38 2 102340758 102340758 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.540C>A p.= p.T180T ENST00000233954 5/11 135 87 48 146 146 0 strelka-mutect IL1RL1,synonymous_variant,p.=,ENST00000311734,NM_003856.3;IL1RL1,synonymous_variant,p.=,ENST00000404917,NM_001282408.1;IL1RL1,synonymous_variant,p.=,ENST00000409584,;IL1RL1,synonymous_variant,p.=,ENST00000233954,NM_016232.4;IL18R1,intron_variant,,ENST00000410040,;IL1RL1,downstream_gene_variant,,ENST00000447231,;IL1RL1,intron_variant,,ENST00000482701,;IL1RL1,downstream_gene_variant,,ENST00000473175,;IL1RL1,synonymous_variant,p.=,ENST00000427077,;IL1RL1,downstream_gene_variant,,ENST00000463990,; A ENST00000233954 Transcript synonymous_variant 811/2058 540/1671 180/556 T acC/acA 1 1 IL1RL1 HGNC HGNC:5998 protein_coding YES CCDS2057.1 ENSP00000233954 Q01638 UPI000013C992 NM_016232.4 5/11 Gene3D:2.60.40.10,Prints_domain:PR01536,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF7,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1251146420 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 102340758 102340758 C A 1 0 0 0 0 0 0 0 1 7566 668 24 2 2 IL1RL1 2 102340758 Silent SNP C C3N-00560_T 934750 102340758 139852771 196 16885 RGPD4 0 . GRCh38 2 107890720 107890720 + Splice_Site SNP G G T rs778358827 C3N-00560_T C3N-00560_N G G c.5267-1G>T p.X1756_splice ENST00000408999 88 50 38 117 117 0 strelka-varscan-mutect RGPD4,splice_acceptor_variant,,ENST00000408999,NM_182588.2; T ENST00000408999 Transcript splice_acceptor_variant -/5464 5267/5277 1756/1758 rs778358827 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 22/22 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 107890720 107890720 G T 1 0 0 0 0 0 0 1 0 13460 1014 35 2 2 RGPD4 2 107890720 Splice_Site SNP G C3N-00560_T 5549962 107890720 134302809 197 16886 RANBP2 0 . GRCh38 2 108765429 108765429 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.4890G>C p.Gln1630His p.Q1630H ENST00000283195 20/29 117 58 59 127 127 0 strelka-varscan-mutect RANBP2,missense_variant,p.Gln1630His,ENST00000283195,NM_006267.4; C ENST00000283195 Transcript missense_variant 5016/11711 4890/9675 1630/3224 Q/H caG/caC 1 1 RANBP2 HGNC HGNC:9848 protein_coding YES CCDS2079.1 ENSP00000283195 P49792 UPI0000207FB9 NM_006267.4 deleterious(0.03) 20/29 PROSITE_profiles:PS50199,Pfam_domain:PF00641,SMART_domains:SM00547,Superfamily_domains:SSF90209 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 108765429 108765429 G C 1 0 0 0 0 1 0 0 0 13187 933 33 4 4 RANBP2 2 108765429 Missense_Mutation SNP G C3N-00560_T 874709 108765429 133428100 198 16887 SLC35F5 0 . GRCh38 2 113731587 113731587 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.982G>C p.Val328Leu p.V328L ENST00000245680 10/16 113 61 52 132 132 0 strelka-varscan-mutect SLC35F5,missense_variant,p.Val328Leu,ENST00000245680,NM_025181.3;SLC35F5,missense_variant,p.Val91Leu,ENST00000447673,;SLC35F5,upstream_gene_variant,,ENST00000470204,;SLC35F5,missense_variant,p.Val322Leu,ENST00000409106,; G ENST00000245680 Transcript missense_variant 1396/4412 982/1572 328/523 V/L Gta/Cta 1 -1 SLC35F5 HGNC HGNC:23617 protein_coding YES CCDS2119.1 ENSP00000245680 Q8WV83 A0A024RAD4 UPI000004C648 NM_025181.3 tolerated(0.84) 10/16 hmmpanther:PTHR23051,hmmpanther:PTHR23051:SF0,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1359735479 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 113731587 113731587 C G 1 0 0 0 0 1 0 0 0 14863 579 20 4 4 SLC35F5 2 113731587 Missense_Mutation SNP C C3N-00560_T 4966158 113731587 128461942 199 16888 DDX18 0 . GRCh38 2 117828967 117828967 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1654G>C p.Asp552His p.D552H ENST00000263239 12/14 42 24 18 93 93 0 strelka-varscan-mutect DDX18,missense_variant,p.Asp552His,ENST00000263239,NM_006773.3;DDX18,downstream_gene_variant,,ENST00000415038,;AC009404.2,upstream_gene_variant,,ENST00000420330,;DDX18,downstream_gene_variant,,ENST00000474694,;DDX18,non_coding_transcript_exon_variant,,ENST00000476149,;DDX18,downstream_gene_variant,,ENST00000461443,; C ENST00000263239 Transcript missense_variant 1782/3796 1654/2013 552/670 D/H Gac/Cac 1 1 DDX18 HGNC HGNC:2741 protein_coding YES CCDS2120.1 ENSP00000263239 Q9NVP1 A0A024RAH8 UPI000012907E NM_006773.3 deleterious(0) 12/14 PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF301 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 117828967 117828967 G C 1 0 0 0 0 1 0 0 0 4148 1290 45 4 4 DDX18 2 117828967 Missense_Mutation SNP G C3N-00560_T 4097380 117828967 124364562 200 16889 MYO7B 0 . GRCh38 2 127632347 127632347 + Missense_Mutation SNP G G T rs532416210 C3N-00560_T C3N-00560_N G G c.5273G>T p.Arg1758Leu p.R1758L ENST00000428314 38/47 79 41 38 78 78 0 strelka-varscan-mutect MYO7B,missense_variant,p.Arg1758Leu,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.Arg1758Leu,ENST00000409816,;MYO7B,missense_variant,p.Arg611Leu,ENST00000409090,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,;MYO7B,upstream_gene_variant,,ENST00000494959,; T ENST00000428314 Transcript missense_variant 5326/6715 5273/6351 1758/2116 R/L cGg/cTg rs532416210,COSM4084712,COSM4084713 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 deleterious(0.01) 38/47 Pfam_domain:PF00784,PROSITE_profiles:PS51016,SMART_domains:SM00139 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs532416210 . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 56 127632347 127632347 G T 1 0 0 0 0 1 0 0 0 10084 1116 39 1 1 MYO7B 2 127632347 Missense_Mutation SNP G C3N-00560_T 9803380 127632347 114561182 201 16890 MYO7B 0 . GRCh38 2 127636581 127636581 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.6082A>T p.Ile2028Phe p.I2028F ENST00000428314 45/47 229 122 107 223 223 0 strelka-varscan-mutect MYO7B,missense_variant,p.Ile2028Phe,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.Ile2028Phe,ENST00000409816,;MYO7B,missense_variant,p.Ile881Phe,ENST00000409090,;LIMS2,downstream_gene_variant,,ENST00000409455,;LIMS2,downstream_gene_variant,,ENST00000410011,NM_001161404.1;LIMS2,downstream_gene_variant,,ENST00000409808,;LIMS2,downstream_gene_variant,,ENST00000324938,NM_017980.4;LIMS2,downstream_gene_variant,,ENST00000355119,NM_001161403.1;LIMS2,downstream_gene_variant,,ENST00000545738,NM_001136037.2;LIMS2,downstream_gene_variant,,ENST00000410038,NM_001256542.1;LIMS2,downstream_gene_variant,,ENST00000409286,;LIMS2,downstream_gene_variant,,ENST00000409754,;LIMS2,downstream_gene_variant,,ENST00000426981,;LIMS2,downstream_gene_variant,,ENST00000409254,;LIMS2,downstream_gene_variant,,ENST00000494613,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,;MYO7B,non_coding_transcript_exon_variant,,ENST00000494959,;LIMS2,downstream_gene_variant,,ENST00000469300,;LIMS2,downstream_gene_variant,,ENST00000466410,;LIMS2,downstream_gene_variant,,ENST00000476932,;LIMS2,downstream_gene_variant,,ENST00000484252,;LIMS2,downstream_gene_variant,,ENST00000413578,; T ENST00000428314 Transcript missense_variant 6135/6715 6082/6351 2028/2116 I/F Atc/Ttc 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 deleterious(0) 45/47 Gene3D:2.30.29.30,PROSITE_profiles:PS50057,Superfamily_domains:SSF50729 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 127636581 127636581 A T 1 0 0 0 0 1 0 0 0 10084 217 8 4 4 MYO7B 2 127636581 Missense_Mutation SNP A C3N-00560_T 4234 127636581 114556948 202 16891 POTEE 0 . GRCh38 2 131218897 131218897 + Missense_Mutation SNP C C A rs779199454 C3N-00560_T C3N-00560_N C C c.495C>A p.Asp165Glu p.D165E ENST00000356920 1/15 432 333 99 478 478 0 strelka-varscan-mutect POTEE,missense_variant,p.Asp165Glu,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.Asp165Glu,ENST00000626191,;POTEE,missense_variant,p.Asp165Glu,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,missense_variant,p.Asp165Glu,ENST00000358087,;POTEE,missense_variant,p.Asp165Glu,ENST00000514256,; A ENST00000356920 Transcript missense_variant 831/4159 495/3228 165/1075 D/E gaC/gaA rs779199454,COSM4392134,COSM4392135 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 deleterious_low_confidence(0) 1/15 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs779199454 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 131218897 131218897 C A 1 0 0 0 0 1 0 0 0 12378 535 19 1 1 POTEE 2 131218897 Missense_Mutation SNP C C3N-00560_T 3582316 131218897 110974632 203 16892 NCKAP5 0 . GRCh38 2 132784551 132784551 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2260G>T p.Val754Leu p.V754L ENST00000409261 14/20 18 10 8 42 42 0 strelka-varscan-mutect NCKAP5,missense_variant,p.Val754Leu,ENST00000409261,NM_207363.2;NCKAP5,missense_variant,p.Val754Leu,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; A ENST00000409261 Transcript missense_variant 2634/7594 2260/5730 754/1909 V/L Gtg/Ttg 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 tolerated(0.05) 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 A 3 1 56 132784551 132784551 C A 1 0 0 0 0 1 0 0 0 10241 507 18 2 2 NCKAP5 2 132784551 Missense_Mutation SNP C C3N-00560_T 1565654 132784551 109408978 204 16893 LCT 0 . GRCh38 2 135817887 135817887 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1161C>A p.= p.L387L ENST00000264162 6/17 327 173 154 400 400 0 strelka-varscan-mutect LCT,synonymous_variant,p.=,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; T ENST00000264162 Transcript synonymous_variant 1172/6279 1161/5784 387/1927 L ctC/ctA 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 6/17 PROSITE_patterns:PS00653,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 135817887 135817887 G T 1 0 0 0 0 0 0 0 1 8599 929 33 2 2 LCT 2 135817887 Silent SNP G C3N-00560_T 3033336 135817887 106375642 205 16894 EPC2 0 . GRCh38 2 148762679 148762679 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.827delG p.Gly276GlufsTer11 p.G276Efs*11 ENST00000258484 6/14 27 20 7 93 93 0 sindel-varindel-pindel EPC2,frameshift_variant,p.Gly276GlufsTer11,ENST00000258484,NM_015630.3;EPC2,downstream_gene_variant,,ENST00000397424,;EPC2,downstream_gene_variant,,ENST00000491099,; - ENST00000258484 Transcript frameshift_variant 859/3649 825/2424 275/807 L/X ttG/tt 1 1 EPC2 HGNC HGNC:24543 protein_coding YES CCDS46422.1 ENSP00000258484 Q52LR7 UPI00005A7FE2 NM_015630.3 6/14 hmmpanther:PTHR14898,hmmpanther:PTHR14898:SF4 HIGH 1 deletion 1 2 1 PASS . . 0 207 2 0 0 0 0 0 -19.40805 1 1 1 1 0 - 7 5 56 148762679 148762679 G - 1 0 1 0 1 0 0 0 0 5007 1339 47 0 0 EPC2 2 148762679 Frame_Shift_Del DEL G C3N-00560_T 12944792 148762679 93430850 206 16895 BAZ2B 0 . GRCh38 2 159478599 159478599 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.121C>T p.Leu41Phe p.L41F ENST00000392783 3/37 107 52 55 112 112 0 strelka-varscan-mutect BAZ2B,missense_variant,p.Leu41Phe,ENST00000392783,NM_013450.3;BAZ2B,missense_variant,p.Leu41Phe,ENST00000392782,NM_001289975.1;BAZ2B,missense_variant,p.Leu41Phe,ENST00000437839,;BAZ2B,missense_variant,p.Leu41Phe,ENST00000541068,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000483316,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000482503,;BAZ2B,non_coding_transcript_exon_variant,,ENST00000467184,; A ENST00000392783 Transcript missense_variant 617/8289 121/6507 41/2168 L/F Ctt/Ttt 1 -1 BAZ2B HGNC HGNC:963 protein_coding YES CCDS2209.2 ENSP00000376534 Q9UIF8 UPI0000D74C4A NM_013450.3 deleterious_low_confidence(0.02) 3/37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 159478599 159478599 G A 1 0 0 0 0 1 0 0 0 1477 1029 36 3 3 BAZ2B 2 159478599 Missense_Mutation SNP G C3N-00560_T 10715920 159478599 82714930 207 16896 GCG 0 . GRCh38 2 162149133 162149133 + Missense_Mutation SNP G G T rs767533221 C3N-00560_T C3N-00560_N G G c.46C>A p.Gln16Lys p.Q16K ENST00000418842 2/6 106 68 38 160 160 0 strelka-varscan-mutect GCG,missense_variant,p.Gln16Lys,ENST00000418842,NM_002054.4;GCG,missense_variant,p.Gln16Lys,ENST00000375497,;GCG,non_coding_transcript_exon_variant,,ENST00000492913,;GCG,upstream_gene_variant,,ENST00000497568,;GCG,upstream_gene_variant,,ENST00000483769,; T ENST00000418842 Transcript missense_variant 301/1289 46/543 16/180 Q/K Caa/Aaa rs767533221 1 -1 GCG HGNC HGNC:4191 protein_coding YES CCDS46439.1 ENSP00000387662 P01275 UPI000012B832 NM_002054.4 deleterious(0.03) 2/6 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11418:SF0,hmmpanther:PTHR11418 MODERATE 1 SNV 1 1 PASS rs767533221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 162149133 162149133 G T 1 0 0 0 0 1 0 0 0 6159 1386 48 2 2 GCG 2 162149133 Missense_Mutation SNP G C3N-00560_T 2670534 162149133 80044396 208 16897 KCNH7 0 . GRCh38 2 162446394 162446394 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1178C>A p.Pro393Gln p.P393Q ENST00000332142 7/16 90 53 37 132 131 1 strelka-varscan-mutect KCNH7,missense_variant,p.Pro393Gln,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Pro293Gln,ENST00000618399,;KCNH7,missense_variant,p.Pro386Gln,ENST00000328032,NM_173162.2;KCNH7,missense_variant,p.Pro284Gln,ENST00000621889,; T ENST00000332142 Transcript missense_variant 1278/4113 1178/3591 393/1196 P/Q cCa/cAa 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 deleterious(0.02) 7/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 162446394 162446394 G T 1 0 0 0 0 1 0 0 0 7953 1348 47 2 2 KCNH7 2 162446394 Missense_Mutation SNP G C3N-00560_T 297261 162446394 79747135 209 16898 XIRP2 0 . GRCh38 2 167239879 167239879 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.883G>A p.Gly295Ser p.G295S ENST00000409195 6/11 250 111 139 198 198 0 strelka-varscan-mutect XIRP2,missense_variant,p.Gly295Ser,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Gly73Ser,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Gly120Ser,ENST00000628543,;XIRP2,missense_variant,p.Gly328Ser,ENST00000409728,NM_001199143.1;XIRP2,missense_variant,p.Gly295Ser,ENST00000409043,NM_001079810.3;XIRP2,missense_variant,p.Gly73Ser,ENST00000409605,NM_001199145.1; A ENST00000409195 Transcript missense_variant 972/12675 883/10650 295/3549 G/S Ggc/Agc 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.55) 6/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 167239879 167239879 G A 1 0 0 0 0 1 0 0 0 17989 1348 47 3 3 XIRP2 2 167239879 Missense_Mutation SNP G C3N-00560_T 4793485 167239879 74953650 210 16899 XIRP2 0 . GRCh38 2 167247084 167247084 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.5692G>T p.Ala1898Ser p.A1898S ENST00000409195 9/11 184 158 26 162 162 0 strelka-varscan-mutect XIRP2,missense_variant,p.Ala1898Ser,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ala1676Ser,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ala1723Ser,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; T ENST00000409195 Transcript missense_variant 5781/12675 5692/10650 1898/3549 A/S Gct/Tct 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.02) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 167247084 167247084 G T 1 0 0 0 0 1 0 0 0 17989 971 34 2 2 XIRP2 2 167247084 Missense_Mutation SNP G C3N-00560_T 7205 167247084 74946445 211 16900 B3GALT1 0 . GRCh38 2 167869681 167869681 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.642G>T p.= p.R214R ENST00000392690 1/1 107 95 12 96 96 0 strelka-varscan-mutect B3GALT1,synonymous_variant,p.=,ENST00000392690,NM_020981.3;AC016723.4,intron_variant,,ENST00000436982,;AC016723.4,intron_variant,,ENST00000430546,; T ENST00000392690 Transcript synonymous_variant 734/5094 642/981 214/326 R cgG/cgT 1 1 B3GALT1 HGNC HGNC:916 protein_coding YES CCDS2227.1 ENSP00000376456 Q9Y5Z6 UPI00000255A2 NM_020981.3 1/1 hmmpanther:PTHR11214:SF20,hmmpanther:PTHR11214,Pfam_domain:PF01762,Superfamily_domains:SSF53448 LOW SNV 1 PASS . . 0 206 2 2 0 0 0 0 -18.60218 0.9999965 1 1 1 0 T 2 4 56 167869681 167869681 G T 1 0 0 0 0 0 0 0 1 1404 1219 43 2 2 B3GALT1 2 167869681 Silent SNP G C3N-00560_T 622597 167869681 74323848 212 16901 OSBPL6 0 . GRCh38 2 178361758 178361758 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.1305G>A p.= p.Q435Q ENST00000392505 14/26 226 95 131 281 281 0 strelka-varscan-mutect OSBPL6,synonymous_variant,p.=,ENST00000190611,NM_032523.3;OSBPL6,synonymous_variant,p.=,ENST00000359685,NM_001201482.1;OSBPL6,synonymous_variant,p.=,ENST00000392505,NM_001201480.1;OSBPL6,synonymous_variant,p.=,ENST00000409045,NM_001201481.1;OSBPL6,synonymous_variant,p.=,ENST00000409631,;OSBPL6,synonymous_variant,p.=,ENST00000315022,NM_145739.2;OSBPL6,synonymous_variant,p.=,ENST00000357080,; A ENST00000392505 Transcript synonymous_variant 1849/3637 1305/2880 435/959 Q caG/caA 1 1 OSBPL6 HGNC HGNC:16388 protein_coding YES CCDS56150.1 ENSP00000376293 Q9BZF3 UPI0000E5A29F NM_001201480.1 14/26 hmmpanther:PTHR10972:SF76,hmmpanther:PTHR10972 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 178361758 178361758 G A 1 0 0 0 0 0 0 0 1 11347 991 35 3 3 OSBPL6 2 178361758 Silent SNP G C3N-00560_T 10492077 178361758 63831771 213 16902 TTN 0 . GRCh38 2 178632544 178632544 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.43462G>T p.Gly14488Cys p.G14488C ENST00000589042 235/363 187 94 93 319 319 0 strelka-varscan-mutect TTN,missense_variant,p.Gly14488Cys,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gly12847Cys,ENST00000591111,;TTN,missense_variant,p.Gly12847Cys,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gly11920Cys,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Gly5423Cys,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Gly5615Cys,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Gly5548Cys,ENST00000359218,NM_133432.3;TTN,downstream_gene_variant,,ENST00000414766,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000630096,;TTN-AS1,upstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000418062,;TTN-AS1,downstream_gene_variant,,ENST00000628296,; A ENST00000589042 Transcript missense_variant 43687/109224 43462/107976 14488/35991 G/C Ggc/Tgc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 235/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 178632544 178632544 C A 1 0 0 0 0 1 0 0 0 17245 594 21 2 2 TTN 2 178632544 Missense_Mutation SNP C C3N-00560_T 270786 178632544 63560985 214 16903 TTN 0 . GRCh38 2 178702498 178702498 + Missense_Mutation SNP C C A rs373355159 C3N-00560_T C3N-00560_N C C c.30389G>T p.Arg10130Leu p.R10130L ENST00000589042 107/363 106 62 44 129 129 0 strelka-varscan-mutect TTN,missense_variant,p.Arg10130Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Arg9813Leu,ENST00000591111,;TTN,missense_variant,p.Arg9813Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Arg8886Leu,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Arg8Leu,ENST00000414766,;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; A ENST00000589042 Transcript missense_variant 30614/109224 30389/107976 10130/35991 R/L cGc/cTc rs373355159 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 107/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 not_provided MODERATE 1 SNV 5 1 1 PASS rs373355159 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 178702498 178702498 C A 1 0 0 0 0 1 0 0 0 17245 768 27 1 1 TTN 2 178702498 Missense_Mutation SNP C C3N-00560_T 69954 178702498 63491031 215 16904 TTN 0 . GRCh38 2 178728531 178728531 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.19395C>A p.Ser6465Arg p.S6465R ENST00000589042 66/363 69 45 24 77 77 0 strelka-varscan-mutect TTN,missense_variant,p.Ser6465Arg,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser6148Arg,ENST00000591111,;TTN,missense_variant,p.Ser6148Arg,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser5221Arg,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;TTN-AS1,upstream_gene_variant,,ENST00000582847,; T ENST00000589042 Transcript missense_variant 19620/109224 19395/107976 6465/35991 S/R agC/agA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 66/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 178728531 178728531 G T 1 0 0 0 0 1 0 0 0 17245 1310 46 2 2 TTN 2 178728531 Missense_Mutation SNP G C3N-00560_T 26033 178728531 63464998 216 16905 TTN 0 . GRCh38 2 178728743 178728743 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.19183G>C p.Asp6395His p.D6395H ENST00000589042 66/363 61 49 12 84 84 0 strelka-varscan-mutect TTN,missense_variant,p.Asp6395His,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Asp6078His,ENST00000591111,;TTN,missense_variant,p.Asp6078His,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Asp5151His,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;TTN-AS1,upstream_gene_variant,,ENST00000582847,; G ENST00000589042 Transcript missense_variant 19408/109224 19183/107976 6395/35991 D/H Gat/Cat 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 66/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 178728743 178728743 C G 1 0 0 0 0 1 0 0 0 17245 826 29 4 4 TTN 2 178728743 Missense_Mutation SNP C C3N-00560_T 212 178728743 63464786 217 16906 ZNF804A 0 . GRCh38 2 184937069 184937070 + Frame_Shift_Ins INS - - A novel C3N-00560_T C3N-00560_N - - c.1674dupA p.Glu559ArgfsTer4 p.E559Rfs*4 ENST00000302277 4/4 37 23 14 76 76 0 sindel-varindel-pindel ZNF804A,frameshift_variant,p.Glu559ArgfsTer4,ENST00000302277,NM_194250.1;ZNF804A,frameshift_variant,p.Glu474ArgfsTer4,ENST00000613975,; A ENST00000302277 Transcript frameshift_variant 2267-2268/4690 1673-1674/3630 558/1209 T/TX aca/acAa 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 HIGH 1 insertion 1 1 1 PASS . . 1 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 56 184937069 184937069 - A 1 0 1 1 0 0 0 0 0 18755 478 17 0 0 ZNF804A 2 184937069 Frame_Shift_Ins INS - C3N-00560_T 6208326 184937069 57256460 218 16907 FSIP2 0 . GRCh38 2 185801001 185801001 + Nonsense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.11962A>T p.Lys3988Ter p.K3988* ENST00000343098 17/23 67 40 27 120 120 0 strelka-varscan-mutect FSIP2,stop_gained,p.Lys3988Ter,ENST00000343098,NM_173651.2;FSIP2,stop_gained,p.Lys3899Ter,ENST00000424728,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; T ENST00000343098 Transcript stop_gained 11962/21054 11962/20991 3988/6996 K/* Aaa/Taa 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 17/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 HIGH SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 185801001 185801001 A T 1 0 0 0 0 0 1 0 0 5949 363 13 4 4 FSIP2 2 185801001 Nonsense_Mutation SNP A C3N-00560_T 863932 185801001 56392528 219 16908 COL5A2 0 . GRCh38 2 189179570 189179570 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.35T>A p.Leu12His p.L12H ENST00000374866 1/54 250 137 113 381 380 1 strelka-varscan-mutect COL5A2,missense_variant,p.Leu12His,ENST00000374866,NM_000393.3;COL5A2,5_prime_UTR_variant,,ENST00000618828,; T ENST00000374866 Transcript missense_variant 310/6949 35/4500 12/1499 L/H cTc/cAc 1 -1 COL5A2 HGNC HGNC:2210 protein_coding YES CCDS33350.1 ENSP00000364000 P05997 UPI00006C511C NM_000393.3 deleterious(0) 1/54 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 189179570 189179570 A T 1 0 0 0 0 1 0 0 0 3486 304 11 4 4 COL5A2 2 189179570 Missense_Mutation SNP A C3N-00560_T 3378569 189179570 53013959 220 16909 MARS2 0 . GRCh38 2 197706887 197706887 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1482G>T p.Lys494Asn p.K494N ENST00000282276 1/1 207 108 99 281 280 1 strelka-varscan-mutect MARS2,missense_variant,p.Lys494Asn,ENST00000282276,NM_138395.3;AC011997.1,intron_variant,,ENST00000409845,; T ENST00000282276 Transcript missense_variant 1519/3019 1482/1782 494/593 K/N aaG/aaT 1 1 MARS2 HGNC HGNC:25133 protein_coding YES CCDS33358.1 ENSP00000282276 Q96GW9 UPI00000492CE NM_138395.3 deleterious(0) 1/1 Gene3D:1.10.730.10,hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF88,Superfamily_domains:SSF47323,TIGRFAM_domain:TIGR00398 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 197706887 197706887 G T 1 0 0 0 0 1 0 0 0 9242 962 34 2 2 MARS2 2 197706887 Missense_Mutation SNP G C3N-00560_T 8527317 197706887 44486642 221 16910 NBEAL1 0 . GRCh38 2 203138278 203138278 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.4595C>T p.Ser1532Leu p.S1532L ENST00000449802 29/55 175 156 19 198 198 0 strelka-varscan-mutect NBEAL1,missense_variant,p.Ser1532Leu,ENST00000449802,NM_001114132.1; T ENST00000449802 Transcript missense_variant 4928/10938 4595/8085 1532/2694 S/L tCa/tTa 1 1 NBEAL1 HGNC HGNC:20681 protein_coding YES CCDS46495.1 ENSP00000399903 Q6ZS30 UPI000194EC27 NM_001114132.1 deleterious(0.01) 29/55 hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 56 203138278 203138278 C T 1 0 0 0 0 1 0 0 0 10199 838 29 3 3 NBEAL1 2 203138278 Missense_Mutation SNP C C3N-00560_T 5431391 203138278 39055251 222 16911 PARD3B 0 . GRCh38 2 205615466 205615466 + Missense_Mutation SNP G G T rs370015965 C3N-00560_T C3N-00560_N G G c.3271G>T p.Ala1091Ser p.A1091S ENST00000406610 23/23 43 21 22 73 73 0 strelka-varscan-mutect PARD3B,missense_variant,p.Ala1091Ser,ENST00000406610,NM_001302769.1;PARD3B,missense_variant,p.Ala955Ser,ENST00000613457,;PARD3B,missense_variant,p.Ala948Ser,ENST00000614500,;PARD3B,missense_variant,p.Ala916Ser,ENST00000622699,;PARD3B,missense_variant,p.Ala1029Ser,ENST00000358768,NM_152526.5;PARD3B,missense_variant,p.Ala1022Ser,ENST00000351153,NM_057177.6;PARD3B,missense_variant,p.Ala990Ser,ENST00000349953,NM_205863.3;PARD3B,non_coding_transcript_exon_variant,,ENST00000488622,; T ENST00000406610 Transcript missense_variant 3478/8174 3271/3618 1091/1205 A/S Gca/Tca rs370015965 1 1 PARD3B HGNC HGNC:14446 protein_coding YES CCDS77511.1 ENSP00000385848 Q8TEW8 UPI0000070178 NM_001302769.1 tolerated(0.48) 23/23 hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF4 MODERATE 1 SNV 1 1 PASS rs370015965 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 205615466 205615466 G T 1 0 0 0 0 1 0 0 0 11524 1087 38 1 1 PARD3B 2 205615466 Missense_Mutation SNP G C3N-00560_T 2477188 205615466 36578063 223 16912 ZDBF2 0 . GRCh38 2 206307792 206307792 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3264G>T p.Gln1088His p.Q1088H ENST00000374423 5/5 70 35 35 121 121 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Gln1088His,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Gln1086His,ENST00000611847,NM_001285549.1; T ENST00000374423 Transcript missense_variant 3650/10286 3264/7065 1088/2354 Q/H caG/caT 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.39) 5/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 206307792 206307792 G T 1 0 0 0 0 1 0 0 0 18174 991 35 2 2 ZDBF2 2 206307792 Missense_Mutation SNP G C3N-00560_T 692326 206307792 35885737 224 16913 CRYGD 0 . GRCh38 2 208121869 208121869 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.329C>A p.Ser110Tyr p.S110Y ENST00000264376 3/3 286 155 131 318 317 1 strelka-varscan-mutect CRYGD,missense_variant,p.Ser110Tyr,ENST00000264376,NM_006891.3; T ENST00000264376 Transcript missense_variant 357/619 329/525 110/174 S/Y tCc/tAc 1 -1 CRYGD HGNC HGNC:2411 protein_coding YES CCDS2378.1 ENSP00000264376 P07320 A0A140CTX7 UPI0000161BE3 NM_006891.3 deleterious(0) 3/3 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF63,Pfam_domain:PF00030,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 208121869 208121869 G T 1 0 0 0 0 1 0 0 0 3719 1174 41 2 2 CRYGD 2 208121869 Missense_Mutation SNP G C3N-00560_T 1814077 208121869 34071660 225 16914 MAP2 0 . GRCh38 2 209729849 209729849 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.5156-1G>T p.X1719_splice ENST00000360351 69 33 36 90 90 0 strelka-varscan-mutect MAP2,splice_acceptor_variant,,ENST00000360351,NM_002374.3;MAP2,splice_acceptor_variant,,ENST00000447185,;MAP2,splice_acceptor_variant,,ENST00000392194,NM_031845.2;MAP2,splice_acceptor_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,splice_acceptor_variant,,ENST00000361559,;MAP2,splice_acceptor_variant,,ENST00000475600,; T ENST00000360351 Transcript splice_acceptor_variant -/9711 5156/5484 1719/1827 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 13/14 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 209729849 209729849 G T 1 0 0 0 0 0 0 1 0 9157 1014 35 2 2 MAP2 2 209729849 Splice_Site SNP G C3N-00560_T 1607980 209729849 32463680 226 16915 SPAG16 0 . GRCh38 2 214410153 214410153 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.1734T>A p.= p.A578A ENST00000331683 16/16 182 105 77 262 262 0 strelka-varscan-mutect SPAG16,synonymous_variant,p.=,ENST00000331683,NM_024532.4;SPAG16,synonymous_variant,p.=,ENST00000451561,;VWC2L,upstream_gene_variant,,ENST00000312504,NM_001080500.2;VWC2L,upstream_gene_variant,,ENST00000427124,;AC107218.3,intron_variant,,ENST00000437883,;AC107218.3,intron_variant,,ENST00000412896,;SPAG16,non_coding_transcript_exon_variant,,ENST00000480494,;SPAG16,3_prime_UTR_variant,,ENST00000406979,;VWC2L,upstream_gene_variant,,ENST00000477752,; A ENST00000331683 Transcript synonymous_variant 1829/2177 1734/1896 578/631 A gcT/gcA 1 1 SPAG16 HGNC HGNC:23225 protein_coding YES CCDS2396.1 ENSP00000332592 Q8N0X2 UPI00001AFF12 NM_024532.4 16/16 PROSITE_profiles:PS50294,hmmpanther:PTHR14604:SF3,hmmpanther:PTHR14604,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 214410153 214410153 T A 1 0 0 0 0 0 0 0 1 15309 1538 54 4 4 SPAG16 2 214410153 Silent SNP T C3N-00560_T 4680304 214410153 27783376 227 16916 WNT10A 0 . GRCh38 2 218890176 218890176 + Missense_Mutation SNP A A T rs766421951 C3N-00560_T C3N-00560_N A A c.569A>T p.His190Leu p.H190L ENST00000258411 3/4 193 107 86 258 258 0 strelka-varscan-mutect WNT10A,missense_variant,p.His190Leu,ENST00000258411,NM_025216.2;WNT10A,intron_variant,,ENST00000458582,;WNT10A,downstream_gene_variant,,ENST00000483911,;WNT10A,upstream_gene_variant,,ENST00000489887,; T ENST00000258411 Transcript missense_variant 1202/2547 569/1254 190/417 H/L cAt/cTt rs766421951 1 1 WNT10A HGNC HGNC:13829 protein_coding YES CCDS2426.1 ENSP00000258411 Q9GZT5 UPI0000032F2A NM_025216.2 tolerated(0.11) 3/4 Pfam_domain:PF00110,Prints_domain:PR01893,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS rs766421951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 218890176 218890176 A T 1 0 0 0 0 1 0 0 0 17938 217 8 4 4 WNT10A 2 218890176 Missense_Mutation SNP A C3N-00560_T 4480023 218890176 23303353 228 16917 SPEG 0 . GRCh38 2 219477729 219477729 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4770G>T p.Glu1590Asp p.E1590D ENST00000312358 21/41 38 23 15 51 51 0 strelka-mutect SPEG,missense_variant,p.Glu1590Asp,ENST00000312358,NM_005876.4;AC053503.11,downstream_gene_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,downstream_gene_variant,,ENST00000485069,; T ENST00000312358 Transcript missense_variant 4902/10782 4770/9804 1590/3267 E/D gaG/gaT 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.12) 21/41 MODERATE SNV 5 1 PASS rs1459937250 . 0 200 9 0 0 0 0 0 -20 0.999999 1 1 1 0 T 3 4 56 219477729 219477729 G T 1 0 0 0 0 1 0 0 0 15387 991 35 2 2 SPEG 2 219477729 Missense_Mutation SNP G C3N-00560_T 587553 219477729 22715800 229 16918 ASB18 0 . GRCh38 2 236214416 236214416 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.1047G>T p.= p.V349V ENST00000409749 4/6 276 159 117 307 307 0 strelka-varscan-mutect ASB18,synonymous_variant,p.=,ENST00000409749,NM_212556.2;ASB18,synonymous_variant,p.=,ENST00000447030,;ASB18,downstream_gene_variant,,ENST00000430053,;RNU1-31P,upstream_gene_variant,,ENST00000363875,;AC079135.1,intron_variant,,ENST00000415226,;AC079135.1,downstream_gene_variant,,ENST00000483218,; A ENST00000409749 Transcript synonymous_variant 1047/1401 1047/1401 349/466 V gtG/gtT 1 -1 ASB18 HGNC HGNC:19770 protein_coding YES CCDS46548.1 ENSP00000386532 Q6ZVZ8 UPI00015D60A6 NM_212556.2 4/6 Gene3D:1.25.40.20,hmmpanther:PTHR24188,hmmpanther:PTHR24188:SF7 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 236214416 236214416 C A 1 0 0 0 0 0 0 0 1 1164 697 25 2 2 ASB18 2 236214416 Silent SNP C C3N-00560_T 16736687 236214416 5979113 230 16919 KIF1A 0 . GRCh38 2 240740322 240740322 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.3792C>T p.= p.C1264C ENST00000498729 36/49 89 42 47 91 91 0 strelka-varscan-mutect KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,synonymous_variant,p.=,ENST00000404283,;KIF1A,synonymous_variant,p.=,ENST00000431776,;KIF1A,downstream_gene_variant,,ENST00000415042,;KIF1A,upstream_gene_variant,,ENST00000494452,; A ENST00000498729 Transcript synonymous_variant 4039/9223 3792/5376 1264/1791 C tgC/tgT 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 36/49 Pfam_domain:PF12473,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 240740322 240740322 G A 1 0 0 0 0 0 0 0 1 8147 1311 46 3 3 KIF1A 2 240740322 Silent SNP G C3N-00560_T 4525906 240740322 1453207 231 16920 C2orf54 0 . GRCh38 2 240888383 240888383 + Missense_Mutation SNP C C A rs372313713 C3N-00560_T C3N-00560_N C C c.1160G>T p.Arg387Leu p.R387L ENST00000388934 4/5 77 46 31 108 108 0 strelka-varscan-mutect C2orf54,missense_variant,p.Arg238Leu,ENST00000307486,NM_001282921.1;C2orf54,missense_variant,p.Arg219Leu,ENST00000402775,NM_024861.3;C2orf54,missense_variant,p.Arg387Leu,ENST00000388934,NM_001085437.2; A ENST00000388934 Transcript missense_variant 1319/1911 1160/1344 387/447 R/L cGc/cTc rs372313713 1 -1 C2orf54 HGNC HGNC:26216 protein_coding YES CCDS42839.1 ENSP00000373586 Q08AI8 UPI000049DF42 NM_001085437.2 deleterious(0.01) 4/5 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF7 MODERATE 1 SNV 2 1 PASS rs372313713 . 0 203 3 4 0 0 0 0 -20 0.9999288 1 1 1 0 A 3 1 56 240888383 240888383 C A 1 0 0 0 0 1 0 0 0 2038 768 27 1 1 C2orf54 2 240888383 Missense_Mutation SNP C C3N-00560_T 148061 240888383 1305146 232 16921 NEU4 0 . GRCh38 2 241814924 241814924 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.273C>A p.= p.A91A ENST00000325935 3/4 106 45 61 143 143 0 strelka-varscan-mutect NEU4,synonymous_variant,p.=,ENST00000391969,NM_001167602.2;NEU4,synonymous_variant,p.=,ENST00000404257,NM_080741.3;NEU4,synonymous_variant,p.=,ENST00000325935,NM_001167599.2;NEU4,synonymous_variant,p.=,ENST00000407683,NM_001167601.2,NM_001167600.2;NEU4,synonymous_variant,p.=,ENST00000405370,;NEU4,synonymous_variant,p.=,ENST00000420288,;NEU4,synonymous_variant,p.=,ENST00000423583,;NEU4,synonymous_variant,p.=,ENST00000428592,;NEU4,intron_variant,,ENST00000415936,;NEU4,intron_variant,,ENST00000426032,;NEU4,downstream_gene_variant,,ENST00000435894,;NEU4,downstream_gene_variant,,ENST00000435934,;AC114730.3,upstream_gene_variant,,ENST00000413820,;AC114730.3,upstream_gene_variant,,ENST00000420272,;AC114730.3,upstream_gene_variant,,ENST00000439270,;NEU4,synonymous_variant,p.=,ENST00000435855,;NEU4,non_coding_transcript_exon_variant,,ENST00000618597,;NEU4,non_coding_transcript_exon_variant,,ENST00000488997,;NEU4,non_coding_transcript_exon_variant,,ENST00000476542,;NEU4,downstream_gene_variant,,ENST00000494678,; A ENST00000325935 Transcript synonymous_variant 702/2288 273/1494 91/497 A gcC/gcA 1 1 NEU4 HGNC HGNC:21328 protein_coding YES CCDS54441.1 ENSP00000320318 Q8WWR8 UPI0000EE378E NM_001167599.2 3/4 Gene3D:2.120.10.10,Pfam_domain:PF13088,hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF22,Superfamily_domains:SSF50939 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 241814924 241814924 C A 1 0 0 0 0 0 0 0 1 10379 610 22 2 2 NEU4 2 241814924 Silent SNP C C3N-00560_T 926541 241814924 378605 233 16922 ITPR1 0 . GRCh38 3 4670917 4670917 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.2150G>T p.Ser717Ile p.S717I ENST00000302640 19/61 31 17 14 31 31 0 strelka-varscan-mutect ITPR1,missense_variant,p.Ser732Ile,ENST00000354582,;ITPR1,missense_variant,p.Ser717Ile,ENST00000302640,NM_001168272.1;ITPR1,missense_variant,p.Ser732Ile,ENST00000357086,NM_001099952.2;ITPR1,missense_variant,p.Ser717Ile,ENST00000456211,NM_002222.5;ITPR1,missense_variant,p.Ser717Ile,ENST00000443694,;ITPR1,intron_variant,,ENST00000544951,;ITPR1,non_coding_transcript_exon_variant,,ENST00000477577,; T ENST00000302640 Transcript missense_variant 2500/10197 2150/8232 717/2743 S/I aGc/aTc COSM4823456,COSM4823457,COSM4823458 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 deleterious(0.04) 19/61 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs1464623729 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 4670917 4670917 G T 1 0 0 0 0 1 0 0 0 7826 971 34 2 2 ITPR1 3 4670917 Missense_Mutation SNP G C3N-00560_T 4670917 193624642 234 16923 GRM7 0 . GRCh38 3 7578809 7578809 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1903G>T p.Gly635Cys p.G635C ENST00000357716 8/10 117 57 60 148 147 1 strelka-varscan-mutect GRM7,missense_variant,p.Gly635Cys,ENST00000486284,NM_181874.2;GRM7,missense_variant,p.Gly635Cys,ENST00000357716,NM_000844.3;GRM7,missense_variant,p.Gly635Cys,ENST00000389336,;GRM7,missense_variant,p.Gly390Cys,ENST00000402647,;GRM7,downstream_gene_variant,,ENST00000445087,;GRM7,non_coding_transcript_exon_variant,,ENST00000458641,;GRM7,missense_variant,p.Gly635Cys,ENST00000467425,;GRM7,missense_variant,p.Gly635Cys,ENST00000440923,;GRM7,missense_variant,p.Gly635Cys,ENST00000389335,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,; T ENST00000357716 Transcript missense_variant 2177/4127 1903/2748 635/915 G/C Ggc/Tgc 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 deleterious(0) 8/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Pfam_domain:PF00003,Prints_domain:PR00248 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 7578809 7578809 G T 1 0 0 0 0 1 0 0 0 6684 1232 43 2 2 GRM7 3 7578809 Missense_Mutation SNP G C3N-00560_T 2907892 7578809 190716750 235 16924 GRM7 0 . GRCh38 3 7578976 7578976 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.2070A>T p.= p.S690S ENST00000357716 8/10 206 107 99 240 240 0 strelka-varscan-mutect GRM7,synonymous_variant,p.=,ENST00000486284,NM_181874.2;GRM7,synonymous_variant,p.=,ENST00000357716,NM_000844.3;GRM7,synonymous_variant,p.=,ENST00000389336,;GRM7,synonymous_variant,p.=,ENST00000402647,;GRM7,downstream_gene_variant,,ENST00000445087,;GRM7,non_coding_transcript_exon_variant,,ENST00000458641,;GRM7,synonymous_variant,p.=,ENST00000467425,;GRM7,synonymous_variant,p.=,ENST00000440923,;GRM7,synonymous_variant,p.=,ENST00000389335,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,; T ENST00000357716 Transcript synonymous_variant 2344/4127 2070/2748 690/915 S tcA/tcT 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 8/10 PROSITE_profiles:PS50259,hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Pfam_domain:PF00003 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 7578976 7578976 A T 1 0 0 0 0 0 0 0 1 6684 175 7 4 4 GRM7 3 7578976 Silent SNP A C3N-00560_T 167 7578976 190716583 236 16925 SCN10A 0 . GRCh38 3 38760729 38760729 + Missense_Mutation SNP T T A rs370912250 C3N-00560_T C3N-00560_N T T c.902A>T p.Lys301Met p.K301M ENST00000449082 7/27 194 118 76 251 251 0 strelka-varscan-mutect SCN10A,missense_variant,p.Lys301Met,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; A ENST00000449082 Transcript missense_variant 902/6418 902/5871 301/1956 K/M aAg/aTg rs370912250,COSM3392389 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 tolerated(0.08) 7/27 hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037,Pfam_domain:PF00520 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs370912250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 38760729 38760729 T A 1 0 0 0 0 1 0 0 0 14181 1609 56 4 4 SCN10A 3 38760729 Missense_Mutation SNP T C3N-00560_T 31181753 38760729 159534830 237 16926 SCN11A 0 . GRCh38 3 38921226 38921226 + Missense_Mutation SNP G G A rs764550088 C3N-00560_T C3N-00560_N G G c.742C>T p.Arg248Cys p.R248C ENST00000302328 6/26 116 65 51 112 112 0 strelka-varscan-mutect SCN11A,missense_variant,p.Arg248Cys,ENST00000302328,NM_014139.2,NM_001287223.1;SCN11A,missense_variant,p.Arg248Cys,ENST00000444237,;SCN11A,missense_variant,p.Arg248Cys,ENST00000456224,; A ENST00000302328 Transcript missense_variant 941/6500 742/5376 248/1791 R/C Cgc/Tgc rs764550088,COSM446467 1 -1 SCN11A HGNC HGNC:10583 protein_coding YES CCDS33737.1 ENSP00000307599 Q9UI33 UPI000006CCD7 NM_014139.2,NM_001287223.1 deleterious(0) 6/26 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF210,Superfamily_domains:SSF81324 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs764550088 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 38921226 38921226 G A 1 0 0 0 0 1 0 0 0 14182 1145 40 1 1 SCN11A 3 38921226 Missense_Mutation SNP G C3N-00560_T 160497 38921226 159374333 238 16927 KLHL40 0 . GRCh38 3 42686741 42686741 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1123G>T p.Glu375Ter p.E375* ENST00000287777 1/6 83 47 36 102 102 0 strelka-varscan-mutect KLHL40,stop_gained,p.Glu375Ter,ENST00000287777,NM_152393.3; T ENST00000287777 Transcript stop_gained 1223/2517 1123/1866 375/621 E/* Gag/Tag 1 1 KLHL40 HGNC HGNC:30372 protein_coding YES CCDS2703.1 ENSP00000287777 Q2TBA0 UPI000000D866 NM_152393.3 1/6 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF22,SMART_domains:SM00612 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 42686741 42686741 G T 1 0 0 0 0 0 1 0 0 8258 943 33 2 2 KLHL40 3 42686741 Nonsense_Mutation SNP G C3N-00560_T 3765515 42686741 155608818 239 16928 PTH1R 0 . GRCh38 3 46893970 46893970 + Missense_Mutation SNP C C A rs138009937 C3N-00560_T C3N-00560_N C C c.139C>A p.Gln47Lys p.Q47K ENST00000313049 2/14 200 103 97 220 220 0 strelka-varscan-mutect PTH1R,missense_variant,p.Gln47Lys,ENST00000313049,;PTH1R,missense_variant,p.Gln47Lys,ENST00000449590,NM_000316.2;PTH1R,missense_variant,p.Gln47Lys,ENST00000418619,;PTH1R,missense_variant,p.Gln47Lys,ENST00000430002,NM_001184744.1;PTH1R,missense_variant,p.Gln47Lys,ENST00000427125,;PTH1R,non_coding_transcript_exon_variant,,ENST00000490109,;PTH1R,missense_variant,p.Gln47Lys,ENST00000428220,; A ENST00000313049 Transcript missense_variant 342/2123 139/1782 47/593 Q/K Cag/Aag rs138009937 1 1 PTH1R HGNC HGNC:9608 protein_coding YES CCDS2747.1 ENSP00000321999 Q03431 A0A024R2Z8 UPI000005041F tolerated(0.57) 2/14 PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF24 MODERATE 1 SNV 1 1 PASS rs138009937 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 46893970 46893970 C A 1 0 0 0 0 1 0 0 0 12914 595 21 2 2 PTH1R 3 46893970 Missense_Mutation SNP C C3N-00560_T 4207229 46893970 151401589 240 16929 CDHR4 0 . GRCh38 3 49793803 49793803 + Missense_Mutation SNP C C A rs144675334 C3N-00560_T C3N-00560_N C C c.1483G>T p.Gly495Trp p.G495W ENST00000412678 11/19 131 74 57 146 146 0 strelka-varscan-mutect CDHR4,missense_variant,p.Gly495Trp,ENST00000412678,NM_001007540.3;CDHR4,downstream_gene_variant,,ENST00000343366,;CDHR4,downstream_gene_variant,,ENST00000487256,;CDHR4,upstream_gene_variant,,ENST00000487666,;CDHR4,upstream_gene_variant,,ENST00000462108,;CDHR4,upstream_gene_variant,,ENST00000460430,; A ENST00000412678 Transcript missense_variant,splice_region_variant 1492/2476 1483/2367 495/788 G/W Ggg/Tgg rs144675334 1 -1 CDHR4 HGNC HGNC:34527 protein_coding YES CCDS46829.1 ENSP00000391409 A6H8M9 UPI0001574E5E NM_001007540.3 deleterious(0) 11/19 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF123,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS rs144675334 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49793803 49793803 C A 1 0 0 0 0 1 0 0 0 2824 666 23 1 1 CDHR4 3 49793803 Missense_Mutation SNP C C3N-00560_T 2899833 49793803 148501756 241 16930 DOCK3 0 . GRCh38 3 51270978 51270978 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2519C>G p.Thr840Arg p.T840R ENST00000266037 24/53 91 42 49 112 112 0 strelka-varscan-mutect DOCK3,missense_variant,p.Thr840Arg,ENST00000266037,NM_004947.4; G ENST00000266037 Transcript missense_variant 2542/8755 2519/6093 840/2030 T/R aCa/aGa 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 deleterious(0) 24/53 hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 51270978 51270978 C G 1 0 0 0 0 1 0 0 0 4503 478 17 4 4 DOCK3 3 51270978 Missense_Mutation SNP C C3N-00560_T 1477175 51270978 147024581 242 16931 ITIH4 0 . GRCh38 3 52823709 52823709 + Silent SNP C C A rs368475731 C3N-00560_T C3N-00560_N C C c.1386G>T p.= p.L462L ENST00000266041 11/24 160 88 72 146 145 1 strelka-varscan-mutect ITIH4,synonymous_variant,p.=,ENST00000266041,NM_002218.4;ITIH4,synonymous_variant,p.=,ENST00000485816,;ITIH4,synonymous_variant,p.=,ENST00000406595,NM_001166449.1;ITIH4,synonymous_variant,p.=,ENST00000441637,;ITIH4-AS1,upstream_gene_variant,,ENST00000478366,;ITIH4,upstream_gene_variant,,ENST00000467462,;ITIH4,upstream_gene_variant,,ENST00000471505,;ITIH4,upstream_gene_variant,,ENST00000484632,;RP5-966M1.6,3_prime_UTR_variant,,ENST00000468472,;ITIH4,non_coding_transcript_exon_variant,,ENST00000491663,;ITIH4,non_coding_transcript_exon_variant,,ENST00000537897,;ITIH4,non_coding_transcript_exon_variant,,ENST00000485894,;ITIH4,upstream_gene_variant,,ENST00000461966,;ITIH4,upstream_gene_variant,,ENST00000481977,;ITIH4,downstream_gene_variant,,ENST00000483372,; A ENST00000266041 Transcript synonymous_variant 1483/3336 1386/2793 462/930 L ctG/ctT rs368475731 1 -1 ITIH4 HGNC HGNC:6169 protein_coding YES CCDS2865.1 ENSP00000266041 Q14624 UPI000013D6C3 NM_002218.4 11/24 hmmpanther:PTHR10338:SF119,hmmpanther:PTHR10338 LOW 1 SNV 1 1 PASS rs368475731 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 52823709 52823709 C A 1 0 0 0 0 0 0 0 1 7812 813 29 2 2 ITIH4 3 52823709 Silent SNP C C3N-00560_T 1552731 52823709 145471850 243 16932 DNAH12 0 . GRCh38 3 57323539 57323539 + Missense_Mutation SNP C C A rs751401968 C3N-00560_T C3N-00560_N C C c.10059G>T p.Lys3353Asn p.K3353N ENST00000495027 63/74 50 31 19 105 105 0 strelka-varscan-mutect DNAH12,missense_variant,p.Lys3353Asn,ENST00000495027,NM_001291661.1;DNAH12,missense_variant,p.Lys2485Asn,ENST00000351747,;DNAH12,missense_variant,p.Lys179Asn,ENST00000466540,; A ENST00000495027 Transcript missense_variant 10240/12146 10059/11883 3353/3960 K/N aaG/aaT rs751401968 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 tolerated(0.19) 63/74 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255 MODERATE 1 SNV 5 1 PASS rs751401968 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 57323539 57323539 C A 1 0 0 0 0 1 0 0 0 4414 912 32 2 2 DNAH12 3 57323539 Missense_Mutation SNP C C3N-00560_T 4499830 57323539 140972020 244 16933 FOXP1 0 . GRCh38 3 71047084 71047084 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.522G>T p.= p.V174V ENST00000615603 10/21 301 178 123 438 438 0 strelka-varscan-mutect FOXP1,synonymous_variant,p.=,ENST00000615603,NM_001244810.1;FOXP1,synonymous_variant,p.=,ENST00000318789,NM_032682.5;FOXP1,synonymous_variant,p.=,ENST00000614176,NM_001244813.1;FOXP1,synonymous_variant,p.=,ENST00000475937,NM_001244816.1;FOXP1,synonymous_variant,p.=,ENST00000493089,NM_001244808.1;FOXP1,synonymous_variant,p.=,ENST00000498215,NM_001244814.1;FOXP1,synonymous_variant,p.=,ENST00000491238,NM_001244815.1;FOXP1,synonymous_variant,p.=,ENST00000484350,NM_001244812.1;FOXP1,synonymous_variant,p.=,ENST00000468577,;FOXP1,synonymous_variant,p.=,ENST00000497355,;FOXP1,synonymous_variant,p.=,ENST00000485326,;FOXP1,synonymous_variant,p.=,ENST00000472382,;FOXP1,synonymous_variant,p.=,ENST00000497553,;FOXP1,synonymous_variant,p.=,ENST00000327590,; A ENST00000615603 Transcript synonymous_variant 1048/7140 522/2082 174/693 V gtG/gtT 1 -1 FOXP1 HGNC HGNC:3823 protein_coding YES CCDS74964.1 ENSP00000484803 A0A087X299 UPI00022AEF64 NM_001244810.1 10/21 Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF176,hmmpanther:PTHR11829 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 71047084 71047084 C A 1 0 0 0 0 0 0 0 1 5891 581 21 2 2 FOXP1 3 71047084 Silent SNP C C3N-00560_T 13723545 71047084 127248475 245 16934 EPHA3 0 . GRCh38 3 89210280 89210280 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.574T>A p.Leu192Met p.L192M ENST00000336596 3/17 107 61 46 154 154 0 strelka-varscan-mutect EPHA3,missense_variant,p.Leu192Met,ENST00000336596,NM_005233.5;EPHA3,missense_variant,p.Leu192Met,ENST00000494014,;EPHA3,missense_variant,p.Leu192Met,ENST00000452448,NM_182644.2; A ENST00000336596 Transcript missense_variant 799/5809 574/2952 192/983 L/M Ttg/Atg 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 deleterious(0) 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PROSITE_patterns:PS00790,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 89210280 89210280 T A 1 0 0 0 0 1 0 0 0 5015 1606 56 4 4 EPHA3 3 89210280 Missense_Mutation SNP T C3N-00560_T 18163196 89210280 109085279 246 16935 EPHA6 0 . GRCh38 3 96866841 96866841 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.402A>T p.= p.T134T ENST00000389672 2/18 75 60 15 144 144 0 strelka-varscan-mutect EPHA6,synonymous_variant,p.=,ENST00000389672,NM_001080448.2;EPHA6,synonymous_variant,p.=,ENST00000470610,;EPHA6,synonymous_variant,p.=,ENST00000506569,NM_001278301.1; T ENST00000389672 Transcript synonymous_variant 440/3971 402/3393 134/1130 T acA/acT 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 2/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 2 1 PASS rs917664284 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 96866841 96866841 A T 1 0 0 0 0 0 0 0 1 5018 117 5 4 4 EPHA6 3 96866841 Silent SNP A C3N-00560_T 7656561 96866841 101428718 247 16936 MYH15 0 . GRCh38 3 108399099 108399099 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.4965G>T p.= p.L1655L ENST00000273353 35/42 74 49 25 72 72 0 varscan-mutect MYH15,synonymous_variant,p.=,ENST00000273353,NM_014981.1; A ENST00000273353 Transcript synonymous_variant 5022/7074 4965/5841 1655/1946 L ctG/ctT 1 -1 MYH15 HGNC HGNC:31073 protein_coding YES CCDS43127.1 ENSP00000273353 Q9Y2K3 UPI0000253B6F NM_014981.1 35/42 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF475,Pfam_domain:PF01576 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 2 1 56 108399099 108399099 C A 1 0 0 0 0 0 0 0 1 10034 581 21 2 2 MYH15 3 108399099 Silent SNP C C3N-00560_T 11532258 108399099 89896460 248 16937 DPPA2 0 . GRCh38 3 109309196 109309196 + Missense_Mutation SNP G G T rs747560868 C3N-00560_T C3N-00560_N G G c.316C>A p.Gln106Lys p.Q106K ENST00000478945 4/9 257 179 78 221 221 0 strelka-varscan-mutect DPPA2,missense_variant,p.Gln106Lys,ENST00000478945,NM_138815.3; T ENST00000478945 Transcript missense_variant 563/1383 316/897 106/298 Q/K Caa/Aaa rs747560868 1 -1 DPPA2 HGNC HGNC:19197 protein_coding YES CCDS2956.1 ENSP00000417710 Q7Z7J5 UPI000007143F NM_138815.3 deleterious(0.02) 4/9 Gene3D:1.10.720.30,PROSITE_profiles:PS50800,hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF10 MODERATE 1 SNV 1 1 PASS rs747560868 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 109309196 109309196 G T 1 0 0 0 0 1 0 0 0 4549 1386 48 2 2 DPPA2 3 109309196 Missense_Mutation SNP G C3N-00560_T 910097 109309196 88986363 249 16938 CASR 0 . GRCh38 3 122275915 122275915 + Nonsense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1481G>A p.Trp494Ter p.W494* ENST00000498619 5/7 419 273 146 382 381 1 strelka-varscan-mutect CASR,stop_gained,p.Trp494Ter,ENST00000498619,NM_001178065.1;CASR,stop_gained,p.Trp494Ter,ENST00000490131,NM_000388.3; A ENST00000498619 Transcript stop_gained 1919/5011 1481/3267 494/1088 W/* tGg/tAg 1 1 CASR HGNC HGNC:1514 protein_coding YES CCDS54632.1 ENSP00000420194 E7ENE0 UPI000020A065 NM_001178065.1 5/7 Pfam_domain:PF01094,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF358,Superfamily_domains:SSF53822 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 122275915 122275915 G A 1 0 0 0 0 0 1 0 0 2381 1357 47 3 3 CASR 3 122275915 Nonsense_Mutation SNP G C3N-00560_T 12966719 122275915 76019644 250 16939 MYLK 0 . GRCh38 3 123647414 123647414 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4429C>A p.Gln1477Lys p.Q1477K ENST00000360304 26/33 372 309 63 408 407 1 strelka-varscan-mutect MYLK,missense_variant,p.Gln1477Lys,ENST00000360772,;MYLK,missense_variant,p.Gln1477Lys,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,missense_variant,p.Gln1477Lys,ENST00000359169,NM_053027.3;MYLK,missense_variant,p.Gln1408Lys,ENST00000354792,;MYLK,missense_variant,p.Gln1408Lys,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,missense_variant,p.Gln1477Lys,ENST00000475616,;MYLK-AS1,downstream_gene_variant,,ENST00000485162,;MYLK,intron_variant,,ENST00000514895,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,non_coding_transcript_exon_variant,,ENST00000513111,; T ENST00000360304 Transcript missense_variant 4615/7738 4429/5745 1477/1914 Q/K Cag/Aag 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 tolerated(0.11) 26/33 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 123647414 123647414 G T 1 0 0 0 0 1 0 0 0 10056 1386 48 2 2 MYLK 3 123647414 Missense_Mutation SNP G C3N-00560_T 1371499 123647414 74648145 251 16940 SNX4 0 . GRCh38 3 125489442 125489442 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.619C>T p.Leu207Phe p.L207F ENST00000251775 6/14 176 151 25 271 270 1 strelka-varscan-mutect SNX4,missense_variant,p.Leu207Phe,ENST00000251775,NM_003794.3;SNX4,intron_variant,,ENST00000473417,;SNX4,3_prime_UTR_variant,,ENST00000471751,;SNX4,intron_variant,,ENST00000465505,; A ENST00000251775 Transcript missense_variant 644/2513 619/1353 207/450 L/F Ctt/Ttt 1 -1 SNX4 HGNC HGNC:11175 protein_coding YES CCDS3032.1 ENSP00000251775 O95219 UPI000003586D NM_003794.3 tolerated(0.06) 6/14 hmmpanther:PTHR10555:SF139,hmmpanther:PTHR10555 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 125489442 125489442 G A 1 0 0 0 0 1 0 0 0 15225 971 34 3 3 SNX4 3 125489442 Missense_Mutation SNP G C3N-00560_T 1842028 125489442 72806117 252 16941 PLXNA1 0 . GRCh38 3 127027947 127027947 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.4370C>T p.Ala1457Val p.A1457V ENST00000393409 23/31 455 291 164 464 464 0 strelka-varscan-mutect PLXNA1,missense_variant,p.Ala1457Val,ENST00000393409,NM_032242.3;PLXNA1,upstream_gene_variant,,ENST00000505278,;PLXNA1,non_coding_transcript_exon_variant,,ENST00000503234,;PLXNA1,upstream_gene_variant,,ENST00000503363,; T ENST00000393409 Transcript missense_variant 4370/9066 4370/5691 1457/1896 A/V gCt/gTt 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 deleterious(0) 23/31 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 127027947 127027947 C T 1 0 0 0 0 1 0 0 0 12225 797 28 3 3 PLXNA1 3 127027947 Missense_Mutation SNP C C3N-00560_T 1538505 127027947 71267612 253 16942 RPN1 0 . GRCh38 3 128650677 128650677 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.124C>G p.Leu42Val p.L42V ENST00000296255 1/10 223 155 68 213 213 0 strelka-varscan-mutect RPN1,missense_variant,p.Leu42Val,ENST00000296255,NM_002950.3;RPN1,intron_variant,,ENST00000497289,;RPN1,non_coding_transcript_exon_variant,,ENST00000497415,;RPN1,intron_variant,,ENST00000495462,;RPN1,missense_variant,p.Leu42Val,ENST00000476931,;RPN1,non_coding_transcript_exon_variant,,ENST00000481168,; C ENST00000296255 Transcript missense_variant 173/2314 124/1824 42/607 L/V Cta/Gta 1 -1 RPN1 HGNC HGNC:10381 protein_coding YES CCDS3051.1 ENSP00000296255 P04843 UPI00001338BA NM_002950.3 tolerated(0.2) 1/10 hmmpanther:PTHR21049,hmmpanther:PTHR21049:SF0,Pfam_domain:PF04597 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 128650677 128650677 G C 1 0 0 0 0 1 0 0 0 13860 991 35 4 4 RPN1 3 128650677 Missense_Mutation SNP G C3N-00560_T 1622730 128650677 69644882 254 16943 COL6A5 0 . GRCh38 3 130379984 130379984 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.1234A>G p.Lys412Glu p.K412E ENST00000265379 4/43 151 117 34 144 144 0 strelka-varscan-mutect COL6A5,missense_variant,p.Lys412Glu,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Lys412Glu,ENST00000312481,; G ENST00000265379 Transcript missense_variant 1728/9214 1234/7836 412/2611 K/E Aag/Gag 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0.02) 4/43 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 130379984 130379984 A G 1 0 0 0 0 1 0 0 0 3491 15 1 5 5 COL6A5 3 130379984 Missense_Mutation SNP A C3N-00560_T 1729307 130379984 67915575 255 16944 PIK3R4 0 . GRCh38 3 130679321 130679321 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.4071G>C p.Trp1357Cys p.W1357C ENST00000356763 20/20 91 72 19 102 101 1 strelka-varscan-mutect PIK3R4,missense_variant,p.Trp1357Cys,ENST00000356763,NM_014602.2;COL6A6,downstream_gene_variant,,ENST00000358511,NM_001102608.1;PIK3R4,downstream_gene_variant,,ENST00000512677,;PIK3R4,non_coding_transcript_exon_variant,,ENST00000511760,;COL6A6,downstream_gene_variant,,ENST00000506143,;PIK3R4,downstream_gene_variant,,ENST00000512362,; G ENST00000356763 Transcript missense_variant 4629/5015 4071/4077 1357/1358 W/C tgG/tgC 1 -1 PIK3R4 HGNC HGNC:8982 protein_coding YES CCDS3067.1 ENSP00000349205 Q99570 UPI0000071EF3 NM_014602.2 deleterious(0) 20/20 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR17583,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999912 1 1 1 0 G 3 3 56 130679321 130679321 C G 1 0 0 0 0 1 0 0 0 12016 856 30 4 4 PIK3R4 3 130679321 Missense_Mutation SNP C C3N-00560_T 299337 130679321 67616238 256 16945 SLCO2A1 0 . GRCh38 3 133973804 133973804 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.256A>G p.Ile86Val p.I86V ENST00000310926 3/14 168 133 35 145 145 0 strelka-mutect SLCO2A1,missense_variant,p.Ile86Val,ENST00000310926,NM_005630.2;SLCO2A1,missense_variant,p.Ile86Val,ENST00000493729,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000478651,;SLCO2A1,missense_variant,p.Ile86Val,ENST00000481359,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000462770,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000464676,; C ENST00000310926 Transcript missense_variant 530/4223 256/1932 86/643 I/V Atc/Gtc 1 -1 SLCO2A1 HGNC HGNC:10955 protein_coding YES CCDS3084.1 ENSP00000311291 Q92959 UPI000013F0AD NM_005630.2 tolerated(1) 3/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF14,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 133973804 133973804 T C 1 0 0 0 0 1 0 0 0 15013 1464 51 5 5 SLCO2A1 3 133973804 Missense_Mutation SNP T C3N-00560_T 3294483 133973804 64321755 257 16946 PRR23B 0 . GRCh38 3 139020589 139020589 + Missense_Mutation SNP G G T rs748085369 C3N-00560_T C3N-00560_N G G c.73C>A p.Pro25Thr p.P25T ENST00000329447 1/1 144 121 23 135 133 2 strelka-varscan-mutect PRR23B,missense_variant,p.Pro25Thr,ENST00000329447,NM_001013650.2;MRPS22,intron_variant,,ENST00000495075,; T ENST00000329447 Transcript missense_variant 338/1896 73/798 25/265 P/T Cct/Act rs748085369 1 -1 PRR23B HGNC HGNC:33764 protein_coding YES CCDS33868.1 ENSP00000328768 Q6ZRT6 UPI00001C0F1A NM_001013650.2 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF7,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE SNV 1 PASS rs748085369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 139020589 139020589 G T 1 0 0 0 0 1 0 0 0 12730 1232 43 2 2 PRR23B 3 139020589 Missense_Mutation SNP G C3N-00560_T 5046785 139020589 59274970 258 16947 TRIM42 0 . GRCh38 3 140687965 140687965 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1283C>G p.Ala428Gly p.A428G ENST00000286349 3/5 267 218 49 268 268 0 strelka-varscan-mutect TRIM42,missense_variant,p.Ala428Gly,ENST00000286349,NM_152616.4; G ENST00000286349 Transcript missense_variant 1474/2539 1283/2172 428/723 A/G gCc/gGc 1 1 TRIM42 HGNC HGNC:19014 protein_coding YES CCDS3113.1 ENSP00000286349 Q8IWZ5 UPI00001AEAE0 NM_152616.4 tolerated(0.1) 3/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF269 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 140687965 140687965 C G 1 0 0 0 0 1 0 0 0 17007 739 26 4 4 TRIM42 3 140687965 Missense_Mutation SNP C C3N-00560_T 1667376 140687965 57607594 259 16948 GK5 0 . GRCh38 3 142185965 142185965 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.780A>T p.Glu260Asp p.E260D ENST00000392993 9/16 110 59 51 145 145 0 strelka-varscan-mutect GK5,missense_variant,p.Glu260Asp,ENST00000392993,NM_001039547.2;GK5,upstream_gene_variant,,ENST00000486459,;GK5,missense_variant,p.Glu260Asp,ENST00000480757,;GK5,missense_variant,p.Glu260Asp,ENST00000492097,;GK5,upstream_gene_variant,,ENST00000460515,;GK5,downstream_gene_variant,,ENST00000460544,;GK5,upstream_gene_variant,,ENST00000460630,; A ENST00000392993 Transcript missense_variant 932/9837 780/1590 260/529 E/D gaA/gaT 1 -1 GK5 HGNC HGNC:28635 protein_coding YES CCDS33871.1 ENSP00000418001 Q6ZS86 UPI000069B0CB NM_001039547.2 tolerated(0.23) 9/16 Gene3D:3.30.420.40,Pfam_domain:PF00370,PIRSF_domain:PIRSF000538,hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF68,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 142185965 142185965 T A 1 0 0 0 0 1 0 0 0 6300 1606 56 4 4 GK5 3 142185965 Missense_Mutation SNP T C3N-00560_T 1498000 142185965 56109594 260 16949 CPB1 0 . GRCh38 3 148834612 148834612 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.262C>T p.= p.L88L ENST00000491148 4/12 142 109 33 150 150 0 strelka-varscan-mutect CPB1,synonymous_variant,p.=,ENST00000491148,;CPB1,synonymous_variant,p.=,ENST00000282957,NM_001871.2;CPB1,synonymous_variant,p.=,ENST00000468341,;CPB1,synonymous_variant,p.=,ENST00000462345,;CPB1,downstream_gene_variant,,ENST00000494888,;CPB1,upstream_gene_variant,,ENST00000484877,;CPB1,non_coding_transcript_exon_variant,,ENST00000465718,; T ENST00000491148 Transcript synonymous_variant 596/1773 262/1254 88/417 L Cta/Tta 1 1 CPB1 HGNC HGNC:2299 protein_coding YES CCDS33874.1 ENSP00000417222 P15086 UPI00001271CD 4/12 hmmpanther:PTHR11705:SF20,hmmpanther:PTHR11705,Gene3D:3.30.70.340,Pfam_domain:PF02244,Superfamily_domains:SSF54897 LOW 1 SNV 5 1 PASS rs1355424538 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 56 148834612 148834612 C T 1 0 0 0 0 0 0 0 1 3590 564 20 3 3 CPB1 3 148834612 Silent SNP C C3N-00560_T 6648647 148834612 49460947 261 16950 CP 0 . GRCh38 3 149199739 149199739 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1474T>A p.Ser492Thr p.S492T ENST00000264613 8/19 431 356 75 369 369 0 strelka-varscan-mutect CP,missense_variant,p.Ser492Thr,ENST00000264613,NM_000096.3;CP,missense_variant,p.Ser275Thr,ENST00000494544,;CP,upstream_gene_variant,,ENST00000462336,;CP,missense_variant,p.Ser492Thr,ENST00000481169,;CP,non_coding_transcript_exon_variant,,ENST00000490639,;CP,non_coding_transcript_exon_variant,,ENST00000489736,;CP,non_coding_transcript_exon_variant,,ENST00000471356,;CP,non_coding_transcript_exon_variant,,ENST00000497797,; T ENST00000264613 Transcript missense_variant 1737/4676 1474/3198 492/1065 S/T Tcc/Acc 1 -1 CP HGNC HGNC:2295 protein_coding YES CCDS3141.1 ENSP00000264613 P00450 UPI000045718B NM_000096.3 tolerated(0.56) 8/19 hmmpanther:PTHR10127:SF664,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 149199739 149199739 A T 1 0 0 0 0 1 0 0 0 3582 246 9 4 4 CP 3 149199739 Missense_Mutation SNP A C3N-00560_T 365127 149199739 49095820 262 16951 CP 0 . GRCh38 3 149207530 149207530 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.869A>T p.Asn290Ile p.N290I ENST00000264613 5/19 386 266 120 281 281 0 strelka-varscan-mutect CP,missense_variant,p.Asn290Ile,ENST00000264613,NM_000096.3;CP,missense_variant,p.Asn73Ile,ENST00000494544,;CP,downstream_gene_variant,,ENST00000455472,;CP,missense_variant,p.Asn290Ile,ENST00000481169,;CP,non_coding_transcript_exon_variant,,ENST00000490639,;CP,non_coding_transcript_exon_variant,,ENST00000489736,; A ENST00000264613 Transcript missense_variant 1132/4676 869/3198 290/1065 N/I aAt/aTt 1 -1 CP HGNC HGNC:2295 protein_coding YES CCDS3141.1 ENSP00000264613 P00450 UPI000045718B NM_000096.3 deleterious(0) 5/19 hmmpanther:PTHR10127:SF664,hmmpanther:PTHR10127,Gene3D:2.60.40.420,Pfam_domain:PF00394,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 149207530 149207530 T A 1 0 0 0 0 1 0 0 0 3582 1493 52 4 4 CP 3 149207530 Missense_Mutation SNP T C3N-00560_T 7791 149207530 49088029 263 16952 P2RY1 0 . GRCh38 3 152836565 152836565 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.783G>T p.= p.L261L ENST00000305097 1/1 229 157 72 245 245 0 strelka-varscan-mutect P2RY1,synonymous_variant,p.=,ENST00000305097,NM_002563.3; T ENST00000305097 Transcript synonymous_variant 1873/6747 783/1122 261/373 L ctG/ctT 1 1 P2RY1 HGNC HGNC:8539 protein_coding YES CCDS3169.1 ENSP00000304767 P47900 UPI0000001C06 NM_002563.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF2,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 152836565 152836565 G T 1 0 0 0 0 0 0 0 1 11419 1335 47 2 2 P2RY1 3 152836565 Silent SNP G C3N-00560_T 3629035 152836565 45458994 264 16953 SHOX2 0 . GRCh38 3 158098044 158098044 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1051G>C p.Ala351Pro p.A351P ENST00000389589 6/6 65 39 26 66 66 0 strelka-varscan-mutect SHOX2,missense_variant,p.Ala327Pro,ENST00000441443,NM_006884.3;SHOX2,missense_variant,p.Ala351Pro,ENST00000389589,NM_003030.4;SHOX2,missense_variant,p.Ala315Pro,ENST00000483851,NM_001163678.1;SHOX2,missense_variant,p.Ala186Pro,ENST00000425436,;SHOX2,downstream_gene_variant,,ENST00000554685,;SHOX2,non_coding_transcript_exon_variant,,ENST00000490689,; G ENST00000389589 Transcript missense_variant 1187/2072 1051/1068 351/355 A/P Gca/Cca 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 tolerated(0.08) 6/6 Pfam_domain:PF03826,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -20 0.9999761 1 1 1 0 G 3 3 56 158098044 158098044 C G 1 0 0 0 0 1 0 0 0 14552 768 27 4 4 SHOX2 3 158098044 Missense_Mutation SNP C C3N-00560_T 5261479 158098044 40197515 265 16954 SHOX2 0 . GRCh38 3 158098193 158098193 + Frame_Shift_Del DEL A A - novel C3N-00560_T C3N-00560_N A A c.902delT p.Phe301SerfsTer23 p.F301Sfs*23 ENST00000389589 6/6 276 243 33 276 276 0 sindel-varindel SHOX2,frameshift_variant,p.Phe277SerfsTer23,ENST00000441443,NM_006884.3;SHOX2,frameshift_variant,p.Phe301SerfsTer23,ENST00000389589,NM_003030.4;SHOX2,frameshift_variant,p.Phe265SerfsTer23,ENST00000483851,NM_001163678.1;SHOX2,frameshift_variant,p.Phe136SerfsTer23,ENST00000425436,;SHOX2,downstream_gene_variant,,ENST00000554685,;SHOX2,non_coding_transcript_exon_variant,,ENST00000490689,; - ENST00000389589 Transcript frameshift_variant 1038/2072 902/1068 301/355 F/X tTc/tc 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 6/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 158098193 158098193 A - 1 0 1 0 1 0 0 0 0 14552 246 9 0 0 SHOX2 3 158098193 Frame_Shift_Del DEL A C3N-00560_T 149 158098193 40197366 266 16955 SHOX2 0 . GRCh38 3 158105867 158105867 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.158G>T p.Ser53Ile p.S53I ENST00000389589 1/6 172 141 31 134 134 0 strelka-varscan-mutect SHOX2,missense_variant,p.Ser53Ile,ENST00000441443,NM_006884.3;SHOX2,missense_variant,p.Ser53Ile,ENST00000389589,NM_003030.4;SHOX2,missense_variant,p.Ser53Ile,ENST00000483851,NM_001163678.1;RSRC1,5_prime_UTR_variant,,ENST00000480820,;RSRC1,upstream_gene_variant,,ENST00000464171,;RSRC1,upstream_gene_variant,,ENST00000611884,NM_001271838.1;RSRC1,upstream_gene_variant,,ENST00000295930,NM_016625.3;SHOX2,upstream_gene_variant,,ENST00000425436,;RSRC1,upstream_gene_variant,,ENST00000312179,NM_001271834.1;RSRC1,upstream_gene_variant,,ENST00000475278,;RSRC1,upstream_gene_variant,,ENST00000476899,;RSRC1,upstream_gene_variant,,ENST00000471994,;RSRC1,upstream_gene_variant,,ENST00000494002,;SHOX2,upstream_gene_variant,,ENST00000554685,;RSRC1,upstream_gene_variant,,ENST00000471911,;RSRC1,upstream_gene_variant,,ENST00000468344,;SHOX2,upstream_gene_variant,,ENST00000490689,;RSRC1,upstream_gene_variant,,ENST00000480119,; A ENST00000389589 Transcript missense_variant 294/2072 158/1068 53/355 S/I aGc/aTc 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 tolerated_low_confidence(0.16) 1/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 158105867 158105867 C A 1 0 0 0 0 1 0 0 0 14552 797 28 2 2 SHOX2 3 158105867 Missense_Mutation SNP C C3N-00560_T 7674 158105867 40189692 267 16956 BCHE 0 . GRCh38 3 165830037 165830037 + Missense_Mutation SNP T T C rs765307050 C3N-00560_T C3N-00560_N T T c.997A>G p.Ile333Val p.I333V ENST00000264381 2/4 87 58 29 101 101 0 strelka-varscan-mutect BCHE,missense_variant,p.Ile333Val,ENST00000264381,NM_000055.2;BCHE,intron_variant,,ENST00000488954,;BCHE,intron_variant,,ENST00000479451,;BCHE,missense_variant,p.Ile333Val,ENST00000482958,;BCHE,missense_variant,p.Ile333Val,ENST00000497011,; C ENST00000264381 Transcript missense_variant 1164/2454 997/1809 333/602 I/V Ata/Gta rs765307050,COSM1040854 1 -1 BCHE HGNC HGNC:983 protein_coding YES CCDS3198.1 ENSP00000264381 P06276 UPI0000127866 NM_000055.2 tolerated(0.35) 2/4 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF215,Superfamily_domains:SSF53474 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765307050 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 165830037 165830037 T C 1 0 0 0 0 1 0 0 0 1505 1464 51 5 5 BCHE 3 165830037 Missense_Mutation SNP T C3N-00560_T 7724170 165830037 32465522 268 16957 WDR49 0 . GRCh38 3 167620582 167620582 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.805G>C p.Ala269Pro p.A269P ENST00000479765 5/10 130 74 56 117 117 0 strelka-varscan-mutect WDR49,missense_variant,p.Ala269Pro,ENST00000479765,;WDR49,intron_variant,,ENST00000308378,NM_178824.3;WDR49,intron_variant,,ENST00000466760,;WDR49,upstream_gene_variant,,ENST00000472600,;WDR49,downstream_gene_variant,,ENST00000488012,;WDR49,intron_variant,,ENST00000460448,; G ENST00000479765 Transcript missense_variant 1029/2108 805/1557 269/518 A/P Gca/Cca 1 -1 WDR49 HGNC HGNC:26587 protein_coding ENSP00000419749 E9PDB0 UPI000013ED1E deleterious(0.05) 5/10 Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE SNV 2 1 PASS rs907179390 . 0 196 13 0 0 0 0 0 -20 0.9999784 1 1 1 0 G 3 3 56 167620582 167620582 C G 1 0 0 0 0 1 0 0 0 17862 768 27 4 4 WDR49 3 167620582 Missense_Mutation SNP C C3N-00560_T 1790545 167620582 30674977 269 16958 PLD1 0 . GRCh38 3 171687510 171687510 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1614G>T p.Gln538His p.Q538H ENST00000351298 15/27 231 148 83 228 228 0 strelka-varscan-mutect PLD1,missense_variant,p.Gln538His,ENST00000356327,NM_001130081.2;PLD1,missense_variant,p.Gln538His,ENST00000351298,NM_002662.4;PLD1,downstream_gene_variant,,ENST00000481505,; A ENST00000351298 Transcript missense_variant 1741/5604 1614/3225 538/1074 Q/H caG/caT 1 -1 PLD1 HGNC HGNC:9067 protein_coding YES CCDS3216.1 ENSP00000342793 Q13393 UPI0000131BDC NM_002662.4 tolerated(0.15) 15/27 PIRSF_domain:PIRSF009376 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 171687510 171687510 C A 1 0 0 0 0 1 0 0 0 12139 912 32 2 2 PLD1 3 171687510 Missense_Mutation SNP C C3N-00560_T 4066928 171687510 26608049 270 16959 SPATA16 0 . GRCh38 3 172956802 172956802 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.956C>A p.Thr319Asn p.T319N ENST00000351008 6/11 330 279 51 318 318 0 strelka-varscan-mutect SPATA16,missense_variant,p.Thr319Asn,ENST00000351008,NM_031955.5; T ENST00000351008 Transcript missense_variant 1140/2106 956/1710 319/569 T/N aCc/aAc 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 deleterious(0) 6/11 Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 172956802 172956802 G T 1 0 0 0 0 1 0 0 0 15331 1261 44 2 2 SPATA16 3 172956802 Missense_Mutation SNP G C3N-00560_T 1269292 172956802 25338757 271 16960 NLGN1 0 . GRCh38 3 174281013 174281013 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2182G>T p.Glu728Ter p.E728* ENST00000457714 7/7 192 137 55 240 239 1 strelka-varscan-mutect NLGN1,stop_gained,p.Glu728Ter,ENST00000457714,NM_014932.3;NLGN1,stop_gained,p.Glu728Ter,ENST00000361589,;NLGN1,stop_gained,p.Glu513Ter,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,; T ENST00000457714 Transcript stop_gained 2611/8242 2182/2472 728/823 E/* Gag/Tag 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 7/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 174281013 174281013 G T 1 0 0 0 0 0 1 0 0 10498 943 33 2 2 NLGN1 3 174281013 Nonsense_Mutation SNP G C3N-00560_T 1324211 174281013 24014546 272 16961 MCCC1 0 . GRCh38 3 183039079 183039079 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1324G>T p.Ala442Ser p.A442S ENST00000265594 12/19 408 260 148 425 425 0 strelka-varscan-mutect MCCC1,missense_variant,p.Ala333Ser,ENST00000492597,;MCCC1,missense_variant,p.Ala442Ser,ENST00000265594,NM_020166.4;MCCC1,missense_variant,p.Ala292Ser,ENST00000610757,NM_001293273.1;MCCC1,missense_variant,p.Ala404Ser,ENST00000629669,;MCCC1,missense_variant,p.Ala395Ser,ENST00000476176,;MCCC1,upstream_gene_variant,,ENST00000489909,;MCCC1,missense_variant,p.Ala404Ser,ENST00000497959,;MCCC1,3_prime_UTR_variant,,ENST00000497830,;MCCC1,3_prime_UTR_variant,,ENST00000495767,; A ENST00000265594 Transcript missense_variant 1471/2545 1324/2178 442/725 A/S Gca/Tca 1 -1 MCCC1 HGNC HGNC:6936 protein_coding YES CCDS3241.1 ENSP00000265594 Q96RQ3 A0A0S2Z693 UPI000013D646 NM_020166.4 tolerated(0.31) 12/19 PROSITE_profiles:PS50979,hmmpanther:PTHR18866,Pfam_domain:PF02785,Gene3D:3.30.470.20,SMART_domains:SM00878,Superfamily_domains:SSF51246 MODERATE 1 SNV 1 1 PASS rs1386085483 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 183039079 183039079 C A 1 0 0 0 0 1 0 0 0 9304 797 28 2 2 MCCC1 3 183039079 Missense_Mutation SNP C C3N-00560_T 8758066 183039079 15256480 273 16962 ABCC5 0 . GRCh38 3 183950109 183950109 + Silent SNP C C G rs201096049 C3N-00560_T C3N-00560_N C C c.2961G>C p.= p.P987P ENST00000334444 21/30 146 119 27 140 140 0 strelka-varscan-mutect ABCC5,synonymous_variant,p.=,ENST00000334444,NM_005688.2;ABCC5,synonymous_variant,p.=,ENST00000265586,;ABCC5,3_prime_UTR_variant,,ENST00000437205,NM_001320032.1; G ENST00000334444 Transcript synonymous_variant 3202/5921 2961/4314 987/1437 P ccG/ccC rs201096049 1 -1 ABCC5 HGNC HGNC:56 protein_coding YES CCDS43176.1 ENSP00000333926 O15440 UPI000004A33C NM_005688.2 21/30 PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF196,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS rs201096049 . 0 207 0 3 0 0 0 0 -20 0.9999959 1 1 1 0 G 2 3 56 183950109 183950109 C G 1 0 0 0 0 0 0 0 1 60 523 19 4 4 ABCC5 3 183950109 Silent SNP C C3N-00560_T 911030 183950109 14345450 274 16963 HTR3E 0 . GRCh38 3 184104222 184104222 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.320G>T p.Cys107Phe p.C107F ENST00000440596 2/7 154 131 23 116 116 0 strelka-varscan-mutect HTR3E,missense_variant,p.Cys107Phe,ENST00000415389,NM_001256613.1;HTR3E,missense_variant,p.Cys122Phe,ENST00000335304,NM_182589.2;HTR3E,missense_variant,p.Cys107Phe,ENST00000440596,NM_001256614.1;HTR3E,missense_variant,p.Cys107Phe,ENST00000436361,NM_198314.2;HTR3E,missense_variant,p.Cys92Phe,ENST00000425359,NM_198313.2;HTR3E,missense_variant,p.Cys36Phe,ENST00000431041,;HTR3E-AS1,non_coding_transcript_exon_variant,,ENST00000431427,; T ENST00000440596 Transcript missense_variant 320/1449 320/1449 107/482 C/F tGt/tTt 1 1 HTR3E HGNC HGNC:24005 protein_coding YES CCDS58871.1 ENSP00000406050 A5X5Y0 UPI000198CB5D NM_001256614.1 deleterious(0) 2/7 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF378,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 184104222 184104222 G T 1 0 0 0 0 1 0 0 0 7344 1377 48 2 2 HTR3E 3 184104222 Missense_Mutation SNP G C3N-00560_T 154113 184104222 14191337 275 16964 DGKG 0 . GRCh38 3 186275595 186275595 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.862T>A p.Cys288Ser p.C288S ENST00000265022 10/25 219 180 39 219 219 0 strelka-varscan-mutect DGKG,missense_variant,p.Cys288Ser,ENST00000265022,NM_001346.2;DGKG,missense_variant,p.Cys288Ser,ENST00000344484,NM_001080744.1;DGKG,missense_variant,p.Cys288Ser,ENST00000382164,NM_001080745.1;DGKG,missense_variant,p.Cys39Ser,ENST00000437018,;DGKG,non_coding_transcript_exon_variant,,ENST00000480809,;DGKG,non_coding_transcript_exon_variant,,ENST00000472506,;DGKG,downstream_gene_variant,,ENST00000482566,; T ENST00000265022 Transcript missense_variant 1402/5805 862/2376 288/791 C/S Tgc/Agc 1 -1 DGKG HGNC HGNC:2853 protein_coding YES CCDS3274.1 ENSP00000265022 P49619 UPI000013D5AB NM_001346.2 deleterious(0) 10/25 PROSITE_profiles:PS50081,hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF36,PROSITE_patterns:PS00479,Pfam_domain:PF00130,Gene3D:3.30.60.20,SMART_domains:SM00109,Superfamily_domains:SSF57889 MODERATE 1 SNV 1 1 PASS rs1222063890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 186275595 186275595 A T 1 0 0 0 0 1 0 0 0 4275 188 7 4 4 DGKG 3 186275595 Missense_Mutation SNP A C3N-00560_T 2171373 186275595 12019964 276 16965 RFC4 0 . GRCh38 3 186804670 186804670 + Missense_Mutation SNP G G A rs146612878 C3N-00560_T C3N-00560_N G G c.44C>T p.Pro15Leu p.P15L ENST00000392481 2/11 181 151 30 206 206 0 strelka-varscan-mutect RFC4,missense_variant,p.Pro15Leu,ENST00000392481,NM_181573.2;RFC4,missense_variant,p.Pro15Leu,ENST00000296273,NM_002916.3;RFC4,missense_variant,p.Pro15Leu,ENST00000433496,;RFC4,missense_variant,p.Pro15Leu,ENST00000447345,;RFC4,missense_variant,p.Pro15Leu,ENST00000418288,;RFC4,missense_variant,p.Pro15Leu,ENST00000411792,;RFC4,missense_variant,p.Pro15Leu,ENST00000427785,;RFC4,missense_variant,p.Pro15Leu,ENST00000448497,;RP11-573D15.3,upstream_gene_variant,,ENST00000434957,;RFC4,missense_variant,p.Pro15Leu,ENST00000449502,;RFC4,non_coding_transcript_exon_variant,,ENST00000494047,;RFC4,upstream_gene_variant,,ENST00000489028,; A ENST00000392481 Transcript missense_variant 326/1448 44/1092 15/363 P/L cCg/cTg rs146612878,COSM78411 1 -1 RFC4 HGNC HGNC:9972 protein_coding YES CCDS3283.1 ENSP00000376272 P35249 UPI0000125167 NM_181573.2 tolerated(0.33) 2/11 0,1 MODERATE SNV 5 0,1 1 PASS rs146612878 . 0 207 0 3 0 0 0 0 -20 0.9999948 1 1 1 0 A 3 1 56 186804670 186804670 G A 1 0 0 0 0 1 0 0 0 13418 1116 39 1 1 RFC4 3 186804670 Missense_Mutation SNP G C3N-00560_T 529075 186804670 11490889 277 16966 RPL39L 0 . GRCh38 3 187121271 187121271 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.30G>T p.Lys10Asn p.K10N ENST00000296277 3/3 124 111 13 102 102 0 strelka-varscan-mutect RPL39L,missense_variant,p.Lys10Asn,ENST00000296277,NM_052969.1;RPL39L,missense_variant,p.Lys10Asn,ENST00000433055,;RPL39L,missense_variant,p.Lys10Asn,ENST00000455270,; A ENST00000296277 Transcript missense_variant 433/756 30/156 10/51 K/N aaG/aaT 1 -1 RPL39L HGNC HGNC:17094 protein_coding YES CCDS3286.1 ENSP00000296277 Q96EH5 UPI0000001BE0 NM_052969.1 deleterious(0.01) 3/3 HAMAP:MF_00629,hmmpanther:PTHR19970,hmmpanther:PTHR19970:SF1,Pfam_domain:PF00832,Gene3D:1vq8200,Superfamily_domains:0037553,PD007914 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 187121271 187121271 C A 1 0 0 0 0 1 0 0 0 13846 796 28 2 2 RPL39L 3 187121271 Missense_Mutation SNP C C3N-00560_T 316601 187121271 11174288 278 16967 CPN2 0 . GRCh38 3 194341973 194341973 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.730G>T p.Glu244Ter p.E244* ENST00000323830 2/2 234 183 51 213 213 0 strelka-varscan-mutect CPN2,stop_gained,p.Glu244Ter,ENST00000323830,NM_001291988.1,NM_001080513.3;CPN2,stop_gained,p.Glu244Ter,ENST00000429275,; A ENST00000323830 Transcript stop_gained 820/3028 730/1638 244/545 E/* Gag/Tag 1 -1 CPN2 HGNC HGNC:2313 protein_coding YES CCDS33920.1 ENSP00000319464 P22792 UPI0001AE76B7 NM_001291988.1,NM_001080513.3 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF278,SMART_domains:SM00369,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 194341973 194341973 C A 1 0 0 0 0 0 1 0 0 3605 922 32 2 2 CPN2 3 194341973 Nonsense_Mutation SNP C C3N-00560_T 7220702 194341973 3953586 279 16968 TM4SF19 0 . GRCh38 3 196324365 196324365 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.355C>A p.Leu119Met p.L119M ENST00000273695 4/5 219 179 40 209 209 0 strelka-varscan-mutect TM4SF19,missense_variant,p.Leu119Met,ENST00000446879,;TM4SF19,missense_variant,p.Leu93Met,ENST00000454715,NM_001204898.1;TM4SF19,missense_variant,p.Leu119Met,ENST00000273695,NM_138461.3,NM_001204897.1;TM4SF19,upstream_gene_variant,,ENST00000440822,;TM4SF19-AS1,non_coding_transcript_exon_variant,,ENST00000452051,;TM4SF19-AS1,downstream_gene_variant,,ENST00000444939,;TM4SF19-AS1,downstream_gene_variant,,ENST00000420226,;TM4SF19-TCTEX1D2,missense_variant,p.Leu119Met,ENST00000442633,; T ENST00000273695 Transcript missense_variant 481/1022 355/630 119/209 L/M Ctg/Atg 1 -1 TM4SF19 HGNC HGNC:25167 protein_coding YES CCDS3316.1 ENSP00000273695 Q96DZ7 UPI000013D9CC NM_138461.3,NM_001204897.1 deleterious(0) 4/5 Pfam_domain:PF05805,hmmpanther:PTHR14198,hmmpanther:PTHR14198:SF22,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 196324365 196324365 G T 1 0 0 0 0 1 0 0 0 16413 933 33 2 2 TM4SF19 3 196324365 Missense_Mutation SNP G C3N-00560_T 1982392 196324365 1971194 280 16969 NAT8L 0 . GRCh38 4 2059788 2059788 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.277C>A p.Arg93Ser p.R93S ENST00000423729 1/3 189 107 82 175 175 0 strelka-varscan-mutect NAT8L,missense_variant,p.Arg93Ser,ENST00000423729,NM_178557.3;NAT8L,upstream_gene_variant,,ENST00000331662,; A ENST00000423729 Transcript missense_variant 277/5870 277/909 93/302 R/S Cgc/Agc 1 1 NAT8L HGNC HGNC:26742 protein_coding YES CCDS3359.2 ENSP00000413064 Q8N9F0 UPI0000EE6EE5 NM_178557.3 deleterious(0.05) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR13947,hmmpanther:PTHR13947:SF11,Gene3D:3.40.630.30 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 2059788 2059788 C A 1 0 0 0 0 1 0 0 0 10189 652 23 1 1 NAT8L 4 2059788 Missense_Mutation SNP C C3N-00560_T 2059788 188154767 281 16970 HTT 0 . GRCh38 4 3212589 3212589 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.6654G>T p.= p.L2218L ENST00000355072 49/67 92 50 42 116 116 0 strelka-varscan-mutect HTT,synonymous_variant,p.=,ENST00000355072,NM_002111.7;HTT,non_coding_transcript_exon_variant,,ENST00000510626,;HTT,non_coding_transcript_exon_variant,,ENST00000509751,; T ENST00000355072 Transcript synonymous_variant 6799/13474 6654/9429 2218/3142 L ctG/ctT 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 49/67 hmmpanther:PTHR10170,hmmpanther:PTHR10170:SF10 LOW 1 SNV 1 1 PASS rs898508972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 3212589 3212589 G T 1 0 0 0 0 0 0 0 1 7353 1306 46 2 2 HTT 4 3212589 Silent SNP G C3N-00560_T 1152801 3212589 187001966 282 16971 HTT 0 . GRCh38 4 3228614 3228614 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.7849-1G>T p.X2617_splice ENST00000355072 21 12 9 35 35 0 strelka-varscan-mutect HTT,splice_acceptor_variant,,ENST00000355072,NM_002111.7;HTT,upstream_gene_variant,,ENST00000513806,;HTT,splice_acceptor_variant,,ENST00000510626,;HTT,upstream_gene_variant,,ENST00000512068,; T ENST00000355072 Transcript splice_acceptor_variant -/13474 7849/9429 2617/3142 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 57/66 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 3228614 3228614 G T 1 0 0 0 0 0 0 1 0 7353 1014 35 2 2 HTT 4 3228614 Splice_Site SNP G C3N-00560_T 16025 3228614 186985941 283 16972 DOK7 0 . GRCh38 4 3473440 3473440 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.135G>T p.= p.S45S ENST00000340083 3/7 184 105 79 193 193 0 strelka-varscan-mutect DOK7,synonymous_variant,p.=,ENST00000340083,NM_173660.4;DOK7,synonymous_variant,p.=,ENST00000507039,NM_001164673.1;DOK7,intron_variant,,ENST00000503688,;DOK7,non_coding_transcript_exon_variant,,ENST00000511267,; T ENST00000340083 Transcript synonymous_variant 200/2562 135/1515 45/504 S tcG/tcT COSM1054932,COSM1594534 1 1 DOK7 HGNC HGNC:26594 protein_coding YES CCDS3370.2 ENSP00000344432 Q18PE1 UPI0000DA4A17 NM_173660.4 3/7 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR21636,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1 LOW 1 SNV 1 1,1 1 PASS rs1336271146 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 3473440 3473440 G T 1 0 0 0 0 0 0 0 1 4517 1103 39 1 1 DOK7 4 3473440 Silent SNP G C3N-00560_T 244826 3473440 186741115 284 16973 DOK7 0 . GRCh38 4 3485623 3485623 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.617C>T p.Thr206Ile p.T206I ENST00000340083 5/7 48 31 17 72 72 0 strelka-varscan-mutect DOK7,missense_variant,p.Thr206Ile,ENST00000340083,NM_173660.4;DOK7,synonymous_variant,p.=,ENST00000507039,NM_001164673.1;DOK7,non_coding_transcript_exon_variant,,ENST00000503688,;DOK7,non_coding_transcript_exon_variant,,ENST00000515886,;DOK7,non_coding_transcript_exon_variant,,ENST00000513995,; T ENST00000340083 Transcript missense_variant 682/2562 617/1515 206/504 T/I aCc/aTc COSM5264754,COSM5264755 1 1 DOK7 HGNC HGNC:26594 protein_coding YES CCDS3370.2 ENSP00000344432 Q18PE1 UPI0000DA4A17 NM_173660.4 deleterious(0) 5/7 PROSITE_profiles:PS51064,hmmpanther:PTHR21636,Superfamily_domains:SSF50729 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1338126929 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 3485623 3485623 C T 1 0 0 0 0 1 0 0 0 4517 507 18 3 3 DOK7 4 3485623 Missense_Mutation SNP C C3N-00560_T 12183 3485623 186728932 285 16974 OTOP1 0 . GRCh38 4 4226587 4226587 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.278T>A p.Leu93Gln p.L93Q ENST00000296358 1/6 172 125 47 187 187 0 strelka-varscan-mutect OTOP1,missense_variant,p.Leu93Gln,ENST00000296358,NM_177998.1; T ENST00000296358 Transcript missense_variant 303/1864 278/1839 93/612 L/Q cTg/cAg 1 -1 OTOP1 HGNC HGNC:19656 protein_coding YES CCDS3372.1 ENSP00000296358 Q7RTM1 UPI0000186945 NM_177998.1 tolerated(0.06) 1/6 hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF19,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 4226587 4226587 A T 1 0 0 0 0 1 0 0 0 11373 188 7 4 4 OTOP1 4 4226587 Missense_Mutation SNP A C3N-00560_T 740964 4226587 185987968 286 16975 C4orf50 0 . GRCh38 4 5988671 5988671 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.3375C>T p.= p.A1125A ENST00000531445 6/12 157 90 67 220 220 0 strelka-varscan-mutect C4orf50,synonymous_variant,p.=,ENST00000531445,;C4orf50,5_prime_UTR_variant,,ENST00000324058,; A ENST00000531445 Transcript synonymous_variant 3451/6860 3375/4527 1125/1508 A gcC/gcT 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 6/12 hmmpanther:PTHR36866 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 5988671 5988671 G A 1 0 0 0 0 0 0 0 1 2089 1335 47 3 3 C4orf50 4 5988671 Silent SNP G C3N-00560_T 1762084 5988671 184225884 287 16976 JAKMIP1 0 . GRCh38 4 6105953 6105953 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.144C>A p.= p.R48R ENST00000409021 3/21 48 20 28 57 57 0 strelka-varscan-mutect JAKMIP1,synonymous_variant,p.=,ENST00000409021,NM_001099433.1;JAKMIP1,synonymous_variant,p.=,ENST00000282924,NM_144720.3;JAKMIP1,synonymous_variant,p.=,ENST00000409831,NM_001306133.1;JAKMIP1,intron_variant,,ENST00000409371,;JAKMIP1,intron_variant,,ENST00000410077,NM_001306134.1;JAKMIP1,intron_variant,,ENST00000457227,;JAKMIP1,synonymous_variant,p.=,ENST00000473053,; T ENST00000409021 Transcript synonymous_variant 594/2975 144/2496 48/831 R cgC/cgA 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 3/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 2 4 56 6105953 6105953 G T 1 0 0 0 0 0 0 0 1 7853 1074 38 1 1 JAKMIP1 4 6105953 Silent SNP G C3N-00560_T 117282 6105953 184108602 288 16977 SH3TC1 0 . GRCh38 4 8214487 8214487 + Silent SNP A A C novel C3N-00560_T C3N-00560_N A A c.388A>C p.= p.R130R ENST00000245105 5/18 169 93 76 197 197 0 strelka-varscan-mutect SH3TC1,synonymous_variant,p.=,ENST00000245105,NM_018986.3;SH3TC1,synonymous_variant,p.=,ENST00000509119,;SH3TC1,downstream_gene_variant,,ENST00000457650,;SH3TC1,upstream_gene_variant,,ENST00000508641,;AC104650.1,downstream_gene_variant,,ENST00000625822,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000503284,;SH3TC1,downstream_gene_variant,,ENST00000510763,;SH3TC1,synonymous_variant,p.=,ENST00000502669,;SH3TC1,3_prime_UTR_variant,,ENST00000515682,NM_001318480.1;SH3TC1,non_coding_transcript_exon_variant,,ENST00000506360,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000512100,;SH3TC1,downstream_gene_variant,,ENST00000504223,;SH3TC1,upstream_gene_variant,,ENST00000507891,; C ENST00000245105 Transcript synonymous_variant 455/4226 388/4011 130/1336 R Agg/Cgg 1 1 SH3TC1 HGNC HGNC:26009 protein_coding YES CCDS3399.1 ENSP00000245105 Q8TE82 UPI000013CB93 NM_018986.3 5/18 hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 8214487 8214487 A C 1 0 0 0 0 0 0 0 1 14520 179 7 5 5 SH3TC1 4 8214487 Silent SNP A C3N-00560_T 2108534 8214487 182000068 289 16978 ZNF518B 0 . GRCh38 4 10444864 10444864 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1465G>T p.Val489Leu p.V489L ENST00000326756 3/3 81 47 34 101 101 0 strelka-varscan-mutect ZNF518B,missense_variant,p.Val489Leu,ENST00000326756,NM_053042.2;ZNF518B,downstream_gene_variant,,ENST00000507515,; A ENST00000326756 Transcript missense_variant 1904/6894 1465/3225 489/1074 V/L Gta/Tta 1 -1 ZNF518B HGNC HGNC:29365 protein_coding YES CCDS33960.1 ENSP00000317614 Q9C0D4 UPI0000160B97 NM_053042.2 tolerated(0.62) 3/3 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF188 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 10444864 10444864 C A 1 0 0 0 0 1 0 0 0 18535 478 17 2 2 ZNF518B 4 10444864 Missense_Mutation SNP C C3N-00560_T 2230377 10444864 179769691 290 16979 KLB 0 . GRCh38 4 39407677 39407677 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.728A>T p.Tyr243Phe p.Y243F ENST00000257408 1/5 128 51 77 118 118 0 strelka-varscan-mutect KLB,missense_variant,p.Tyr243Phe,ENST00000257408,NM_175737.3;MIR5591,upstream_gene_variant,,ENST00000578248,; T ENST00000257408 Transcript missense_variant 825/6082 728/3135 243/1044 Y/F tAt/tTt 1 1 KLB HGNC HGNC:15527 protein_coding YES CCDS3451.1 ENSP00000257408 Q86Z14 UPI000000D726 NM_175737.3 tolerated(0.2) 1/5 Gene3D:3.20.20.80,Pfam_domain:PF00232,hmmpanther:PTHR10353,hmmpanther:PTHR10353:SF68,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 39407677 39407677 A T 1 0 0 0 0 1 0 0 0 8197 449 16 4 4 KLB 4 39407677 Missense_Mutation SNP A C3N-00560_T 28962813 39407677 150806878 291 16980 N4BP2 0 . GRCh38 4 40103075 40103076 + Frame_Shift_Ins INS - - T novel C3N-00560_T C3N-00560_N - - c.1231dupT p.Trp411LeufsTer4 p.W411Lfs*4 ENST00000261435 4/18 245 102 143 228 228 0 sindel-varindel-pindel N4BP2,frameshift_variant,p.Trp411LeufsTer4,ENST00000261435,NM_018177.4;N4BP2,frameshift_variant,p.Trp58LeufsTer4,ENST00000513269,;N4BP2,downstream_gene_variant,,ENST00000515550,;N4BP2,3_prime_UTR_variant,,ENST00000511480,NM_001318359.1; T ENST00000261435 Transcript frameshift_variant 1646-1647/9744 1230-1231/5313 410-411/1770 -/X -/T 1 1 N4BP2 HGNC HGNC:29851 protein_coding YES CCDS3457.1 ENSP00000261435 Q86UW6 UPI00001A962C NM_018177.4 4/18 hmmpanther:PTHR13308,hmmpanther:PTHR13308:SF21 HIGH 1 insertion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 56 40103075 40103075 - T 1 0 1 1 0 0 0 0 0 10114 436 16 0 0 N4BP2 4 40103075 Frame_Shift_Ins INS - C3N-00560_T 695398 40103075 150111480 292 16981 ATP10D 0 . GRCh38 4 47546686 47546686 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1459A>T p.Ser487Cys p.S487C ENST00000273859 10/23 415 213 202 301 300 1 strelka-varscan-mutect ATP10D,missense_variant,p.Ser487Cys,ENST00000273859,NM_020453.3;ATP10D,missense_variant,p.Ser472Cys,ENST00000504445,;ATP10D,missense_variant,p.Ser135Cys,ENST00000503288,; T ENST00000273859 Transcript missense_variant 1728/6655 1459/4281 487/1426 S/C Agt/Tgt 1 1 ATP10D HGNC HGNC:13549 protein_coding YES CCDS3476.1 ENSP00000273859 Q9P241 UPI00001AE9B7 NM_020453.3 tolerated(0.27) 10/23 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF84,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 47546686 47546686 A T 1 0 0 0 0 1 0 0 0 1270 188 7 4 4 ATP10D 4 47546686 Missense_Mutation SNP A C3N-00560_T 7443611 47546686 142667869 293 16982 KIAA1211 0 . GRCh38 4 56316556 56316556 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.3054C>A p.= p.P1018P ENST00000504228 6/9 166 116 50 272 270 2 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,;MRPL22P1,downstream_gene_variant,,ENST00000505398,; A ENST00000504228 Transcript synonymous_variant 3159/4628 3054/3702 1018/1233 P ccC/ccA 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1324528359 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 56316556 56316556 C A 1 0 0 0 0 0 0 0 1 8107 610 22 2 2 KIAA1211 4 56316556 Silent SNP C C3N-00560_T 8769870 56316556 133897999 294 16983 UGT2B4 0 . GRCh38 4 69486667 69486667 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.1032A>T p.= p.P344P ENST00000305107 4/6 62 49 13 128 128 0 strelka-varscan-mutect UGT2B4,synonymous_variant,p.=,ENST00000305107,NM_021139.2;UGT2B4,synonymous_variant,p.=,ENST00000512583,NM_001297615.1;UGT2B4,non_coding_transcript_exon_variant,,ENST00000506580,;UGT2B4,non_coding_transcript_exon_variant,,ENST00000502655,;UGT2B4,downstream_gene_variant,,ENST00000503836,; A ENST00000305107 Transcript synonymous_variant 1079/2103 1032/1587 344/528 P ccA/ccT 1 -1 UGT2B4 HGNC HGNC:12553 protein_coding YES CCDS43234.1 ENSP00000305221 P06133 UPI000000087F NM_021139.2 4/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF198,Pfam_domain:PF00201,Gene3D:3.40.50.2000,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 69486667 69486667 T A 1 0 0 0 0 0 0 0 1 17485 1567 55 4 4 UGT2B4 4 69486667 Silent SNP T C3N-00560_T 13170111 69486667 120727888 295 16984 PRR27 0 . GRCh38 4 70158795 70158795 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.543G>T p.Glu181Asp p.E181D ENST00000344526 3/5 167 132 35 274 273 1 strelka-varscan-mutect PRR27,missense_variant,p.Glu181Asp,ENST00000344526,NM_214711.3;PRR27,missense_variant,p.Glu181Asp,ENST00000502294,;PRR27,downstream_gene_variant,,ENST00000502441,;PRR27,missense_variant,p.Glu23Asp,ENST00000512173,;PRR27,3_prime_UTR_variant,,ENST00000509633,; T ENST00000344526 Transcript missense_variant 732/3127 543/660 181/219 E/D gaG/gaT COSM296350 1 1 PRR27 HGNC HGNC:33193 protein_coding YES CCDS3535.1 ENSP00000343172 Q6MZM9 UPI0000036170 NM_214711.3 tolerated(0.37) 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR39415,hmmpanther:PTHR39415:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 70158795 70158795 G T 1 0 0 0 0 1 0 0 0 12734 991 35 2 2 PRR27 4 70158795 Missense_Mutation SNP G C3N-00560_T 672128 70158795 120055760 296 16985 SMR3A 0 . GRCh38 4 70362139 70362139 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.24G>T p.Leu8Phe p.L8F ENST00000226460 2/3 115 90 25 235 234 1 strelka-varscan-mutect SMR3A,missense_variant,p.Leu8Phe,ENST00000226460,NM_012390.3; T ENST00000226460 Transcript missense_variant 120/665 24/405 8/134 L/F ttG/ttT 1 1 SMR3A HGNC HGNC:19216 protein_coding YES CCDS34000.1 ENSP00000226460 Q99954 UPI000013C8A0 NM_012390.3 deleterious_low_confidence(0) 2/3 Pfam_domain:PF15621,PROSITE_profiles:PS51257,hmmpanther:PTHR14179,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 70362139 70362139 G T 1 0 0 0 0 1 0 0 0 15132 1339 47 2 2 SMR3A 4 70362139 Missense_Mutation SNP G C3N-00560_T 203344 70362139 119852416 297 16986 ENAM 0 . GRCh38 4 70644784 70644784 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.3359delC p.Pro1120HisfsTer38 p.P1120Hfs*38 ENST00000396073 9/9 70 54 16 107 107 0 sindel-varindel-pindel ENAM,frameshift_variant,p.Pro1120HisfsTer38,ENST00000396073,NM_031889.2;ENAM,intron_variant,,ENST00000472903,;ENAM,downstream_gene_variant,,ENST00000472597,; - ENST00000396073 Transcript frameshift_variant 3639/5679 3358/3429 1120/1142 P/X Cca/ca 1 1 ENAM HGNC HGNC:3344 protein_coding YES CCDS3544.2 ENSP00000379383 Q9NRM1 UPI000013CE60 NM_031889.2 9/9 hmmpanther:PTHR16784:SF2,hmmpanther:PTHR16784 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 70644784 70644784 C - 1 0 1 0 1 0 0 0 0 4954 855 30 0 0 ENAM 4 70644784 Frame_Shift_Del DEL C C3N-00560_T 282645 70644784 119569771 298 16987 GC 0 . GRCh38 4 71756876 71756876 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.927C>A p.= p.S309S ENST00000504199 9/14 177 125 52 275 273 2 strelka-varscan-mutect GC,synonymous_variant,p.=,ENST00000273951,NM_000583.3,NM_001204306.1;GC,synonymous_variant,p.=,ENST00000504199,NM_001204307.1;GC,synonymous_variant,p.=,ENST00000513476,;RNA5SP163,downstream_gene_variant,,ENST00000410304,;GC,non_coding_transcript_exon_variant,,ENST00000503472,;GC,upstream_gene_variant,,ENST00000503364,;GC,synonymous_variant,p.=,ENST00000509740,; T ENST00000504199 Transcript synonymous_variant 1022/1777 927/1482 309/493 S tcC/tcA COSM5603640,COSM5603641 1 -1 GC HGNC HGNC:4187 protein_coding YES CCDS56332.1 ENSP00000421725 P02774 UPI0001D3B4EE NM_001204307.1 9/14 Gene3D:1.10.246.10,Pfam_domain:PF00273,PROSITE_profiles:PS51438,hmmpanther:PTHR11385,hmmpanther:PTHR11385:SF11,SMART_domains:SM00103,Superfamily_domains:SSF48552 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 71756876 71756876 G T 1 0 0 0 0 0 0 0 1 6152 1335 47 2 2 GC 4 71756876 Silent SNP G C3N-00560_T 1112092 71756876 118457679 299 16988 SHROOM3 0 . GRCh38 4 76741346 76741346 + Missense_Mutation SNP G G T rs374140337 C3N-00560_T C3N-00560_N G G c.3173G>T p.Arg1058Leu p.R1058L ENST00000296043 5/11 343 252 91 522 522 0 strelka-varscan-mutect SHROOM3,missense_variant,p.Arg1058Leu,ENST00000296043,NM_020859.3;SHROOM3,intron_variant,,ENST00000469923,;SHROOM3,downstream_gene_variant,,ENST00000473602,;SHROOM3,downstream_gene_variant,,ENST00000481002,;SHROOM3,non_coding_transcript_exon_variant,,ENST00000486758,; T ENST00000296043 Transcript missense_variant 4126/11020 3173/5991 1058/1996 R/L cGc/cTc rs374140337 1 1 SHROOM3 HGNC HGNC:30422 protein_coding YES CCDS3579.2 ENSP00000296043 Q8TF72 UPI0000E5AC1C NM_020859.3 deleterious(0) 5/11 hmmpanther:PTHR15012:SF33,hmmpanther:PTHR15012,Pfam_domain:PF08688 MODERATE 1 SNV 1 1 PASS rs374140337 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 76741346 76741346 G T 1 0 0 0 0 1 0 0 0 14558 1087 38 1 1 SHROOM3 4 76741346 Missense_Mutation SNP G C3N-00560_T 4984470 76741346 113473209 300 16989 FRAS1 0 . GRCh38 4 78237615 78237615 + Nonsense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.214A>T p.Lys72Ter p.K72* ENST00000512123 3/74 21 16 5 51 51 0 strelka-varscan-mutect FRAS1,stop_gained,p.Lys72Ter,ENST00000512123,NM_025074.6;FRAS1,stop_gained,p.Lys72Ter,ENST00000325942,NM_001166133.1;FRAS1,stop_gained,p.Lys72Ter,ENST00000264899,; T ENST00000512123 Transcript stop_gained,splice_region_variant 654/15624 214/12039 72/4012 K/* Aag/Tag 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 3/74 PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 HIGH 1 SNV 5 1 PASS rs1417951751 . 0 208 2 0 0 0 0 0 -15.15433 1 1 1 1 0 T 4 4 56 78237615 78237615 A T 1 0 0 0 0 0 1 0 0 5908 260 9 4 4 FRAS1 4 78237615 Nonsense_Mutation SNP A C3N-00560_T 1496269 78237615 111976940 301 16990 FRAS1 0 . GRCh38 4 78450161 78450161 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.6285A>G p.= p.A2095A ENST00000512123 45/74 61 41 20 94 94 0 strelka-varscan-mutect FRAS1,synonymous_variant,p.=,ENST00000512123,NM_025074.6;FRAS1,downstream_gene_variant,,ENST00000325942,NM_001166133.1;FRAS1,downstream_gene_variant,,ENST00000264899,;FRAS1,downstream_gene_variant,,ENST00000510944,;FRAS1,non_coding_transcript_exon_variant,,ENST00000509802,; G ENST00000512123 Transcript synonymous_variant 6725/15624 6285/12039 2095/4012 A gcA/gcG 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 45/74 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29 LOW 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 78450161 78450161 A G 1 0 0 0 0 0 0 0 1 5908 146 6 5 5 FRAS1 4 78450161 Silent SNP A C3N-00560_T 212546 78450161 111764394 302 16991 PRDM8 0 . GRCh38 4 80202340 80202340 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.878G>T p.Gly293Val p.G293V ENST00000339711 10/10 158 109 49 207 207 0 strelka-varscan-mutect PRDM8,missense_variant,p.Gly293Val,ENST00000339711,NM_020226.3;PRDM8,missense_variant,p.Gly293Val,ENST00000504452,;PRDM8,missense_variant,p.Gly293Val,ENST00000415738,NM_001099403.1;PRDM8,missense_variant,p.Gly293Val,ENST00000515013,; T ENST00000339711 Transcript missense_variant 2109/4095 878/2070 293/689 G/V gGc/gTc 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 tolerated_low_confidence(0.34) 10/10 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80202340 80202340 G T 1 0 0 0 0 1 0 0 0 12594 1203 42 2 2 PRDM8 4 80202340 Missense_Mutation SNP G C3N-00560_T 1752179 80202340 110012215 303 16992 PRDM8 0 . GRCh38 4 80202396 80202396 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.934G>T p.Gly312Ter p.G312* ENST00000339711 10/10 127 83 44 199 199 0 strelka-varscan-mutect PRDM8,stop_gained,p.Gly312Ter,ENST00000339711,NM_020226.3;PRDM8,stop_gained,p.Gly312Ter,ENST00000504452,;PRDM8,stop_gained,p.Gly312Ter,ENST00000415738,NM_001099403.1;PRDM8,stop_gained,p.Gly312Ter,ENST00000515013,; T ENST00000339711 Transcript stop_gained 2165/4095 934/2070 312/689 G/* Gga/Tga 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 10/10 hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 80202396 80202396 G T 1 0 0 0 0 0 1 0 0 12594 1001 35 2 2 PRDM8 4 80202396 Nonsense_Mutation SNP G C3N-00560_T 56 80202396 110012159 304 16993 C4orf22 0 . GRCh38 4 80870028 80870028 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.420G>T p.= p.G140G ENST00000508675 5/7 92 70 22 166 166 0 strelka-mutect C4orf22,synonymous_variant,p.=,ENST00000358105,NM_152770.2;C4orf22,synonymous_variant,p.=,ENST00000508675,NM_001206997.1;C4orf22,upstream_gene_variant,,ENST00000508314,;C4orf22,3_prime_UTR_variant,,ENST00000513920,; T ENST00000508675 Transcript synonymous_variant 420/753 420/753 140/250 G ggG/ggT 1 1 C4orf22 HGNC HGNC:28554 protein_coding YES CCDS56336.1 ENSP00000425786 Q6V702 UPI0000D61589 NM_001206997.1 5/7 Pfam_domain:PF14713,hmmpanther:PTHR33588,hmmpanther:PTHR33588:SF1 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 80870028 80870028 G T 1 0 0 0 0 0 0 0 1 2080 1190 42 2 2 C4orf22 4 80870028 Silent SNP G C3N-00560_T 667632 80870028 109344527 305 16994 SPARCL1 0 . GRCh38 4 87479452 87479452 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1944C>A p.= p.G648G ENST00000418378 11/12 83 52 31 116 116 0 strelka-varscan-mutect SPARCL1,synonymous_variant,p.=,ENST00000418378,NM_001128310.2;SPARCL1,synonymous_variant,p.=,ENST00000282470,NM_004684.5;SPARCL1,synonymous_variant,p.=,ENST00000503414,NM_001291977.1,NM_001291976.1; T ENST00000418378 Transcript synonymous_variant 2516/2994 1944/1995 648/664 G ggC/ggA 1 -1 SPARCL1 HGNC HGNC:11220 protein_coding YES CCDS3622.1 ENSP00000414856 Q14515 A0A024RDE1 UPI000013DCE3 NM_001128310.2 11/12 PROSITE_profiles:PS50222,hmmpanther:PTHR13866:SF16,hmmpanther:PTHR13866,PIRSF_domain:PIRSF002574,Gene3D:1.10.238.10,Pfam_domain:PF10591,Superfamily_domains:SSF47473 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 87479452 87479452 G T 1 0 0 0 0 0 0 0 1 15327 1190 42 2 2 SPARCL1 4 87479452 Silent SNP G C3N-00560_T 6609424 87479452 102735103 306 16995 CCDC109B 0 . GRCh38 4 109660230 109660230 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.211G>T p.Val71Leu p.V71L ENST00000394650 3/8 124 58 66 82 82 0 strelka-varscan-mutect CCDC109B,missense_variant,p.Val71Leu,ENST00000394650,NM_017918.4;CCDC109B,non_coding_transcript_exon_variant,,ENST00000452915,;CCDC109B,non_coding_transcript_exon_variant,,ENST00000515114,;CCDC109B,non_coding_transcript_exon_variant,,ENST00000472310,; T ENST00000394650 Transcript missense_variant 344/2278 211/1011 71/336 V/L Gta/Tta 1 1 CCDC109B HGNC HGNC:26076 protein_coding YES CCDS3683.2 ENSP00000378145 Q9NWR8 UPI000037446B NM_017918.4 tolerated(0.17) 3/8 hmmpanther:PTHR13462,hmmpanther:PTHR13462:SF6 MODERATE 1 SNV 1 1 PASS rs1229246607 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 109660230 109660230 G T 1 0 0 0 0 1 0 0 0 2440 1261 44 2 2 CCDC109B 4 109660230 Missense_Mutation SNP G C3N-00560_T 22180778 109660230 80554325 307 16996 ZGRF1 0 . GRCh38 4 112547383 112547383 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.5500G>A p.Val1834Ile p.V1834I ENST00000505019 24/28 184 90 94 144 144 0 strelka-varscan-mutect ZGRF1,missense_variant,p.Val1834Ile,ENST00000505019,NM_018392.4;ZGRF1,missense_variant,p.Val1834Ile,ENST00000445203,;ZGRF1,5_prime_UTR_variant,,ENST00000612287,;RP11-402J6.1,downstream_gene_variant,,ENST00000504009,;ZGRF1,3_prime_UTR_variant,,ENST00000445413,;ZGRF1,non_coding_transcript_exon_variant,,ENST00000506675,; T ENST00000505019 Transcript missense_variant 5626/6652 5500/6315 1834/2104 V/I Gtt/Att 1 -1 ZGRF1 HGNC HGNC:25654 protein_coding YES CCDS3700.2 ENSP00000424737 Q86YA3 UPI0000EE2F8F NM_018392.4 deleterious(0) 24/28 Gene3D:3.40.50.300,Pfam_domain:PF13086,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs1476930091 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 112547383 112547383 C T 1 0 0 0 0 1 0 0 0 18253 478 17 3 3 ZGRF1 4 112547383 Missense_Mutation SNP C C3N-00560_T 2887153 112547383 77667172 308 16997 ANK2 0 . GRCh38 4 113348306 113348306 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4402G>T p.Glu1468Ter p.E1468* ENST00000357077 36/46 378 212 166 298 298 0 strelka-varscan-mutect ANK2,stop_gained,p.Glu1468Ter,ENST00000357077,NM_001148.4;ANK2,stop_gained,p.Glu1435Ter,ENST00000264366,;ANK2,stop_gained,p.Glu1459Ter,ENST00000506722,NM_001127493.1;ANK2,stop_gained,p.Glu1468Ter,ENST00000394537,NM_020977.3;ANK2,stop_gained,p.Glu1483Ter,ENST00000504454,;ANK2,stop_gained,p.Glu1381Ter,ENST00000503423,;ANK2,stop_gained,p.Glu644Ter,ENST00000509550,;ANK2,stop_gained,p.Glu120Ter,ENST00000510275,;ANK2,stop_gained,p.Glu121Ter,ENST00000504415,;ANK2,intron_variant,,ENST00000514960,;ANK2,splice_region_variant,,ENST00000508007,;ANK2,splice_region_variant,,ENST00000512298,; T ENST00000357077 Transcript stop_gained,splice_region_variant 4455/14196 4402/11874 1468/3957 E/* Gag/Tag 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 36/46 Low_complexity_(Seg):seg,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 113348306 113348306 G T 1 0 0 0 0 0 1 0 0 721 956 33 2 2 ANK2 4 113348306 Nonsense_Mutation SNP G C3N-00560_T 800923 113348306 76866249 309 16998 ANK2 0 . GRCh38 4 113354446 113354446 + Missense_Mutation SNP G G T rs764180060 C3N-00560_T C3N-00560_N G G c.5828G>T p.Gly1943Val p.G1943V ENST00000357077 38/46 257 131 126 197 197 0 strelka-varscan-mutect ANK2,missense_variant,p.Gly1943Val,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Gly1910Val,ENST00000264366,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000612754,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,;ANK2,downstream_gene_variant,,ENST00000512298,; T ENST00000357077 Transcript missense_variant 5881/14196 5828/11874 1943/3957 G/V gGa/gTa rs764180060 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0.01) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS rs764180060 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 113354446 113354446 G T 1 0 0 0 0 1 0 0 0 721 1174 41 2 2 ANK2 4 113354446 Missense_Mutation SNP G C3N-00560_T 6140 113354446 76860109 310 16999 CAMK2D 0 . GRCh38 4 113455822 113455822 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.1434-1G>T p.X478_splice ENST00000342666 128 68 60 96 96 0 strelka-varscan-mutect CAMK2D,splice_acceptor_variant,,ENST00000511664,;CAMK2D,splice_acceptor_variant,,ENST00000342666,NM_001221.3;CAMK2D,splice_acceptor_variant,,ENST00000515496,;CAMK2D,splice_acceptor_variant,,ENST00000514328,;CAMK2D,intron_variant,,ENST00000296402,NM_172127.2;CAMK2D,intron_variant,,ENST00000394524,NM_001321576.1,NM_172128.2;CAMK2D,intron_variant,,ENST00000513132,;CAMK2D,downstream_gene_variant,,ENST00000394522,NM_172114.1;CAMK2D,downstream_gene_variant,,ENST00000505990,;CAMK2D,downstream_gene_variant,,ENST00000379773,NM_172115.2;CAMK2D,downstream_gene_variant,,ENST00000508738,NM_172129.1;CAMK2D,downstream_gene_variant,,ENST00000509594,; A ENST00000342666 Transcript splice_acceptor_variant -/1940 1434/1500 478/499 1 -1 CAMK2D HGNC HGNC:1462 protein_coding YES CCDS3703.1 ENSP00000339740 Q13557 A0A024RDK3 UPI000013FFDA NM_001221.3 17/18 HIGH 1 SNV 5 1 PASS rs1248293531 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 113455822 113455822 C A 1 0 0 0 0 0 0 1 0 2292 695 24 2 2 CAMK2D 4 113455822 Splice_Site SNP C C3N-00560_T 101376 113455822 76758733 311 17000 ARSJ 0 . GRCh38 4 113903501 113903501 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.573A>G p.= p.R191R ENST00000315366 2/2 375 188 187 302 302 0 strelka-varscan-mutect ARSJ,synonymous_variant,p.=,ENST00000315366,NM_024590.3;ARSJ,downstream_gene_variant,,ENST00000636527,;ARSJ,3_prime_UTR_variant,,ENST00000509829,; C ENST00000315366 Transcript synonymous_variant 1440/4657 573/1800 191/599 R agA/agG 1 -1 ARSJ HGNC HGNC:26286 protein_coding YES CCDS43264.1 ENSP00000320219 Q5FYB0 UPI000003FD84 NM_024590.3 2/2 hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF69,Pfam_domain:PF00884,Gene3D:3.40.720.10,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS rs1354445732 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 113903501 113903501 T C 1 0 0 0 0 0 0 0 1 1138 1548 54 5 5 ARSJ 4 113903501 Silent SNP T C3N-00560_T 447679 113903501 76311054 312 17001 TRPC3 0 . GRCh38 4 121907485 121907485 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.1875G>T p.= p.R625R ENST00000379645 7/12 270 246 24 210 210 0 strelka-varscan-mutect TRPC3,synonymous_variant,p.=,ENST00000264811,NM_003305.2;TRPC3,synonymous_variant,p.=,ENST00000379645,NM_001130698.1;TRPC3,synonymous_variant,p.=,ENST00000513531,;TRPC3,3_prime_UTR_variant,,ENST00000506449,; A ENST00000379645 Transcript synonymous_variant 1949/3548 1875/2766 625/921 R cgG/cgT 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 7/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 121907485 121907485 C A 1 0 0 0 0 0 0 0 1 17084 842 30 2 2 TRPC3 4 121907485 Silent SNP C C3N-00560_T 8003984 121907485 68307070 313 17002 KIAA1109 0 . GRCh38 4 122308063 122308063 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.9956G>T p.Gly3319Val p.G3319V ENST00000264501 58/86 509 285 224 424 423 1 strelka-varscan-mutect KIAA1109,missense_variant,p.Gly3319Val,ENST00000264501,;KIAA1109,missense_variant,p.Gly3319Val,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Gly1277Val,ENST00000419325,;KIAA1109,upstream_gene_variant,,ENST00000438707,;KIAA1109,upstream_gene_variant,,ENST00000421930,; T ENST00000264501 Transcript missense_variant 10329/15896 9956/15018 3319/5005 G/V gGt/gTt 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 tolerated(0.5) 58/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 122308063 122308063 G T 1 0 0 0 0 1 0 0 0 8101 1261 44 2 2 KIAA1109 4 122308063 Missense_Mutation SNP G C3N-00560_T 400578 122308063 67906492 314 17003 KIAA1109 0 . GRCh38 4 122343536 122343536 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.12479A>G p.Tyr4160Cys p.Y4160C ENST00000264501 73/86 314 268 46 205 205 0 strelka-varscan-mutect KIAA1109,missense_variant,p.Tyr4160Cys,ENST00000264501,;KIAA1109,missense_variant,p.Tyr4160Cys,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Tyr829Cys,ENST00000438707,;KIAA1109,missense_variant,p.Tyr536Cys,ENST00000306802,;KIAA1109,missense_variant,p.Tyr106Cys,ENST00000442707,; G ENST00000264501 Transcript missense_variant 12852/15896 12479/15018 4160/5005 Y/C tAt/tGt 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 deleterious(0) 73/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 122343536 122343536 A G 1 0 0 0 0 1 0 0 0 8101 449 16 5 5 KIAA1109 4 122343536 Missense_Mutation SNP A C3N-00560_T 35473 122343536 67871019 315 17004 BBS12 0 . GRCh38 4 122742507 122742507 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.615G>T p.Lys205Asn p.K205N ENST00000542236 3/3 175 85 90 108 108 0 strelka-varscan-mutect BBS12,missense_variant,p.Lys205Asn,ENST00000542236,NM_001178007.1;BBS12,missense_variant,p.Lys205Asn,ENST00000314218,NM_152618.2;BBS12,downstream_gene_variant,,ENST00000433287,; T ENST00000542236 Transcript missense_variant 996/3431 615/2133 205/710 K/N aaG/aaT 1 1 BBS12 HGNC HGNC:26648 protein_coding YES CCDS3728.1 ENSP00000438273 Q6ZW61 UPI0000231CAC NM_001178007.1 tolerated(0.16) 3/3 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 122742507 122742507 G T 1 0 0 0 0 1 0 0 0 1484 991 35 2 2 BBS12 4 122742507 Missense_Mutation SNP G C3N-00560_T 398971 122742507 67472048 316 17005 FAT4 0 . GRCh38 4 125408521 125408521 + Missense_Mutation SNP G G T rs778560998 C3N-00560_T C3N-00560_N G G c.5647G>T p.Asp1883Tyr p.D1883Y ENST00000394329 4/17 116 100 16 112 112 0 strelka-varscan-mutect FAT4,missense_variant,p.Asp1883Tyr,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Asp181Tyr,ENST00000335110,; T ENST00000394329 Transcript missense_variant 5660/16123 5647/14946 1883/4981 D/Y Gat/Tat rs778560998,COSM1206634,COSM1206635 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0) 4/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs778560998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 125408521 125408521 G T 1 0 0 0 0 1 0 0 0 5552 942 33 2 2 FAT4 4 125408521 Missense_Mutation SNP G C3N-00560_T 2666014 125408521 64806034 317 17006 FAT4 0 . GRCh38 4 125452713 125452713 + Silent SNP A A G C3N-00560_T C3N-00560_N A A c.11697A>G p.= p.R3899R ENST00000394329 9/17 201 107 94 162 162 0 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,synonymous_variant,p.=,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; G ENST00000394329 Transcript synonymous_variant 11710/16123 11697/14946 3899/4981 R agA/agG COSM1736676,COSM1736677 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 9/17 Gene3D:2gy5A03,Superfamily_domains:SSF57184 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 125452713 125452713 A G 1 0 0 0 0 0 0 0 1 5552 301 11 5 5 FAT4 4 125452713 Silent SNP A C3N-00560_T 44192 125452713 64761842 318 17007 PLK4 0 . GRCh38 4 127891578 127891578 + Splice_Site SNP G G C novel C3N-00560_T C3N-00560_N G G c.1936-1G>C p.X646_splice ENST00000270861 83 64 19 83 83 0 strelka-varscan-mutect PLK4,splice_acceptor_variant,,ENST00000270861,NM_014264.4;PLK4,splice_acceptor_variant,,ENST00000515069,;PLK4,splice_acceptor_variant,,ENST00000507249,;PLK4,splice_acceptor_variant,,ENST00000513090,NM_001190799.1;PLK4,splice_acceptor_variant,,ENST00000514379,NM_001190801.1;PLK4,intron_variant,,ENST00000508113,;RNU6-583P,upstream_gene_variant,,ENST00000516012,;PLK4,splice_acceptor_variant,,ENST00000507454,;PLK4,upstream_gene_variant,,ENST00000510192,;PLK4,downstream_gene_variant,,ENST00000510605,; C ENST00000270861 Transcript splice_acceptor_variant -/3841 1936/2913 646/970 1 1 PLK4 HGNC HGNC:11397 protein_coding YES CCDS3735.1 ENSP00000270861 O00444 UPI000007426E NM_014264.4 8/15 HIGH 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 5 2 56 127891578 127891578 G C 1 0 0 0 0 0 0 1 0 12193 956 33 4 4 PLK4 4 127891578 Splice_Site SNP G C3N-00560_T 2438865 127891578 62322977 319 17008 PCDH10 0 . GRCh38 4 133151535 133151535 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1395G>C p.Gln465His p.Q465H ENST00000264360 1/5 323 175 148 330 330 0 strelka-varscan-mutect PCDH10,missense_variant,p.Gln465His,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Gln465His,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; C ENST00000264360 Transcript missense_variant 2221/8489 1395/3123 465/1040 Q/H caG/caC 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 deleterious(0.02) 1/5 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1157153017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 133151535 133151535 G C 1 0 0 0 0 1 0 0 0 11594 962 34 4 4 PCDH10 4 133151535 Missense_Mutation SNP G C3N-00560_T 5259957 133151535 57063020 320 17009 INPP4B 0 . GRCh38 4 142122148 142122148 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2115G>C p.Leu705Phe p.L705F ENST00000513000 22/27 210 83 127 148 148 0 strelka-varscan-mutect INPP4B,missense_variant,p.Leu705Phe,ENST00000513000,NM_003866.2;INPP4B,missense_variant,p.Leu705Phe,ENST00000509777,;INPP4B,missense_variant,p.Leu705Phe,ENST00000262992,NM_001101669.1;INPP4B,missense_variant,p.Leu705Phe,ENST00000508116,;INPP4B,missense_variant,p.Leu705Phe,ENST00000510812,;INPP4B,missense_variant,p.Leu520Phe,ENST00000511838,;INPP4B,missense_variant,p.Leu576Phe,ENST00000514525,;INPP4B,3_prime_UTR_variant,,ENST00000512630,; G ENST00000513000 Transcript missense_variant 2549/8831 2115/2775 705/924 L/F ttG/ttC 1 -1 INPP4B HGNC HGNC:6075 protein_coding YES CCDS3757.1 ENSP00000425487 O15327 UPI000013D37A NM_003866.2 deleterious(0.04) 22/27 hmmpanther:PTHR12187,hmmpanther:PTHR12187:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 142122148 142122148 C G 1 0 0 0 0 1 0 0 0 7656 709 25 4 4 INPP4B 4 142122148 Missense_Mutation SNP C C3N-00560_T 8970613 142122148 48092407 321 17010 ARHGAP10 0 . GRCh38 4 147909741 147909741 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.1126A>G p.Ser376Gly p.S376G ENST00000336498 12/23 155 77 78 170 170 0 strelka-varscan-mutect ARHGAP10,missense_variant,p.Ser376Gly,ENST00000336498,NM_024605.3;ARHGAP10,missense_variant,p.Ser54Gly,ENST00000507661,;ARHGAP10,non_coding_transcript_exon_variant,,ENST00000506054,; G ENST00000336498 Transcript missense_variant 1365/3299 1126/2361 376/786 S/G Agt/Ggt 1 1 ARHGAP10 HGNC HGNC:26099 protein_coding YES CCDS34075.1 ENSP00000336923 A1A4S6 UPI000013EA63 NM_024605.3 tolerated(0.28) 12/23 hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 147909741 147909741 A G 1 0 0 0 0 1 0 0 0 986 420 15 5 5 ARHGAP10 4 147909741 Missense_Mutation SNP A C3N-00560_T 5787593 147909741 42304814 322 17011 RPS3A 0 . GRCh38 4 151102886 151102886 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.370C>G p.His124Asp p.H124D ENST00000274065 4/6 165 156 9 201 201 0 varscan-mutect RPS3A,missense_variant,p.His87Asp,ENST00000514682,;RPS3A,missense_variant,p.His124Asp,ENST00000274065,NM_001006.4;RPS3A,missense_variant,p.His87Asp,ENST00000506126,;RPS3A,missense_variant,p.His124Asp,ENST00000512690,;RPS3A,missense_variant,p.His104Asp,ENST00000510993,;RPS3A,missense_variant,p.His119Asp,ENST00000512797,;RPS3A,missense_variant,p.His87Asp,ENST00000507327,;RPS3A,missense_variant,p.His68Asp,ENST00000515792,;RPS3A,missense_variant,p.His87Asp,ENST00000505243,;RPS3A,missense_variant,p.His87Asp,ENST00000508783,;RPS3A,missense_variant,p.His5Asp,ENST00000509736,;RPS3A,downstream_gene_variant,,ENST00000503002,;SNORD73B,downstream_gene_variant,,ENST00000364394,;SNORD73A,upstream_gene_variant,,ENST00000386062,;SH3D19,non_coding_transcript_exon_variant,,ENST00000604922,;RPS3A,3_prime_UTR_variant,,ENST00000515818,;RPS3A,non_coding_transcript_exon_variant,,ENST00000507485,; G ENST00000274065 Transcript missense_variant 450/934 370/795 124/264 H/D Cac/Gac COSM1319371 1 1 RPS3A HGNC HGNC:10421 protein_coding YES CCDS3775.1 ENSP00000346050 P61247 UPI000013D9EC NM_001006.4 deleterious(0.01) 4/6 HAMAP:MF_03122,Pfam_domain:PF01015,hmmpanther:PTHR11830,SMART_domains:SM01397 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 151102886 151102886 C G 1 0 0 0 0 1 0 0 0 13899 826 29 4 4 RPS3A 4 151102886 Missense_Mutation SNP C C3N-00560_T 3193145 151102886 39111669 323 17012 ARFIP1 0 . GRCh38 4 152870752 152870752 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.203-1G>T p.X68_splice ENST00000451320 104 83 21 106 106 0 strelka-varscan-mutect ARFIP1,splice_acceptor_variant,,ENST00000451320,NM_001287431.1;ARFIP1,splice_acceptor_variant,,ENST00000353617,NM_001287432.1,NM_001025595.2;ARFIP1,intron_variant,,ENST00000405727,NM_014447.3,NM_001287433.1;ARFIP1,intron_variant,,ENST00000429148,;ARFIP1,intron_variant,,ENST00000356064,NM_001025593.2;ARFIP1,splice_acceptor_variant,,ENST00000511289,;ARFIP1,splice_acceptor_variant,,ENST00000513361,; T ENST00000451320 Transcript splice_acceptor_variant -/3424 203/1122 68/373 1 1 ARFIP1 HGNC HGNC:21496 protein_coding YES CCDS34080.1 ENSP00000395083 P53367 B4E273 UPI0000125668 NM_001287431.1 3/8 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 152870752 152870752 G T 1 0 0 0 0 0 0 1 0 978 1014 35 2 2 ARFIP1 4 152870752 Splice_Site SNP G C3N-00560_T 1767866 152870752 37343803 324 17013 NPY2R 0 . GRCh38 4 155214911 155214911 + Silent SNP C C A C3N-00560_T C3N-00560_N C C c.972C>A p.= p.L324L ENST00000329476 2/2 104 73 31 127 127 0 strelka-varscan-mutect NPY2R,synonymous_variant,p.=,ENST00000329476,NM_000910.3;NPY2R,synonymous_variant,p.=,ENST00000506608,;AC097467.2,intron_variant,,ENST00000630664,; A ENST00000329476 Transcript synonymous_variant 1461/3626 972/1146 324/381 L ctC/ctA COSM1539615 1 1 NPY2R HGNC HGNC:7957 protein_coding YES CCDS3791.1 ENSP00000332591 P49146 UPI000003B342 NM_000910.3 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF42,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR01012 1 LOW 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 155214911 155214911 C A 1 0 0 0 0 0 0 0 1 10664 900 32 2 2 NPY2R 4 155214911 Silent SNP C C3N-00560_T 2344159 155214911 34999644 325 17014 GUCY1B3 0 . GRCh38 4 155759802 155759802 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.19C>T p.His7Tyr p.H7Y ENST00000502959 2/15 81 75 6 121 121 0 strelka-varscan-mutect GUCY1B3,missense_variant,p.His7Tyr,ENST00000264424,NM_000857.3;GUCY1B3,missense_variant,p.His7Tyr,ENST00000502959,NM_001291951.1;GUCY1B3,missense_variant,p.His7Tyr,ENST00000503520,NM_001291954.1;GUCY1B3,5_prime_UTR_variant,,ENST00000507146,NM_001291953.1;GUCY1B3,5_prime_UTR_variant,,ENST00000505764,NM_001291952.1;GUCY1B3,5_prime_UTR_variant,,ENST00000513437,;GUCY1B3,intron_variant,,ENST00000505154,NM_001291955.1; T ENST00000502959 Transcript missense_variant 139/2255 19/1926 7/641 H/Y Cac/Tac 1 1 GUCY1B3 HGNC HGNC:4687 protein_coding YES CCDS77975.1 ENSP00000426786 E9PCN2 UPI0001D3B9A4 NM_001291951.1 tolerated(1) 2/15 hmmpanther:PTHR11920:SF318,hmmpanther:PTHR11920,Pfam_domain:PF07700,Gene3D:3sj5A00,Superfamily_domains:SSF111126 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 155759802 155759802 C T 1 0 0 0 0 1 0 0 0 6777 826 29 3 3 GUCY1B3 4 155759802 Missense_Mutation SNP C C3N-00560_T 544891 155759802 34454753 326 17015 FAM218A 0 . GRCh38 4 164957043 164957043 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.21G>T p.= p.R7R ENST00000513876 1/1 33 24 9 31 31 0 strelka-varscan-mutect FAM218A,synonymous_variant,p.=,ENST00000513876,NM_153027.1;TRIM61,intron_variant,,ENST00000329314,NM_001012414.2; T ENST00000513876 Transcript synonymous_variant 96/2175 21/474 7/157 R cgG/cgT 1 1 FAM218A HGNC HGNC:26466 protein_coding YES CCDS3807.1 ENSP00000427428 Q96MZ4 UPI000006D0F5 NM_153027.1 1/1 LOW SNV 1 PASS . . 0 202 8 0 0 0 0 0 -19.99979 0.9999994 1 1 1 0 T 2 4 56 164957043 164957043 G T 1 0 0 0 0 0 0 0 1 5408 1190 42 2 2 FAM218A 4 164957043 Silent SNP G C3N-00560_T 9197241 164957043 25257512 327 17016 DDX60L 0 . GRCh38 4 168391576 168391576 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.3879A>G p.= p.Q1293Q ENST00000260184 29/38 149 121 28 172 172 0 strelka-varscan-mutect DDX60L,synonymous_variant,p.=,ENST00000511577,;DDX60L,synonymous_variant,p.=,ENST00000260184,NM_001012967.2;DDX60L,synonymous_variant,p.=,ENST00000505890,NM_001291510.1;DDX60L,synonymous_variant,p.=,ENST00000514580,;DDX60L,downstream_gene_variant,,ENST00000505863,;DDX60L,downstream_gene_variant,,ENST00000503190,; C ENST00000260184 Transcript synonymous_variant 4100/6754 3879/5121 1293/1706 Q caA/caG 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 29/38 PROSITE_profiles:PS51194,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 168391576 168391576 T C 1 0 0 0 0 0 0 0 1 4182 1606 56 5 5 DDX60L 4 168391576 Silent SNP T C3N-00560_T 3434533 168391576 21822979 328 17017 DDX60L 0 . GRCh38 4 168394543 168394543 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.3732delG p.Ile1245LeufsTer21 p.I1245Lfs*21 ENST00000260184 28/38 105 85 20 182 182 0 sindel-varindel-pindel DDX60L,frameshift_variant,p.Ile1245LeufsTer21,ENST00000511577,;DDX60L,frameshift_variant,p.Ile1245LeufsTer21,ENST00000260184,NM_001012967.2;DDX60L,frameshift_variant,p.Ile1246LeufsTer21,ENST00000505890,NM_001291510.1;DDX60L,frameshift_variant,p.Ile133LeufsTer21,ENST00000514580,;DDX60L,downstream_gene_variant,,ENST00000505863,;DDX60L,downstream_gene_variant,,ENST00000503190,; - ENST00000260184 Transcript frameshift_variant 3953/6754 3732/5121 1244/1706 G/X ggG/gg 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 28/38 PROSITE_profiles:PS51194,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 HIGH 1 deletion 5 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999961 1 1 1 0 - 7 5 56 168394543 168394543 C - 1 0 1 0 1 0 0 0 0 4182 842 30 0 0 DDX60L 4 168394543 Frame_Shift_Del DEL C C3N-00560_T 2967 168394543 21820012 329 17018 GALNT7 0 . GRCh38 4 173298216 173298216 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1067G>T p.Trp356Leu p.W356L ENST00000265000 6/12 97 69 28 113 112 1 strelka-varscan-mutect GALNT7,missense_variant,p.Trp356Leu,ENST00000265000,NM_017423.2;GALNT7,3_prime_UTR_variant,,ENST00000512285,;GALNT7,intron_variant,,ENST00000505308,;GALNT7,downstream_gene_variant,,ENST00000502407,;GALNT7,non_coding_transcript_exon_variant,,ENST00000506317,; T ENST00000265000 Transcript missense_variant 1150/4307 1067/1974 356/657 W/L tGg/tTg 1 1 GALNT7 HGNC HGNC:4129 protein_coding YES CCDS3815.1 ENSP00000265000 Q86SF2 UPI000000DB3C NM_017423.2 deleterious(0.01) 6/12 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF60,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 173298216 173298216 G T 1 0 0 0 0 1 0 0 0 6089 1357 47 2 2 GALNT7 4 173298216 Missense_Mutation SNP G C3N-00560_T 4903673 173298216 16916339 330 17019 TENM3 0 . GRCh38 4 182736857 182736857 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.3017A>T p.Tyr1006Phe p.Y1006F ENST00000511685 17/28 189 155 34 236 236 0 strelka-varscan-mutect TENM3,missense_variant,p.Tyr1006Phe,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,; T ENST00000511685 Transcript missense_variant 3140/10896 3017/8100 1006/2699 Y/F tAc/tTc 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 deleterious(0.02) 17/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 182736857 182736857 A T 1 0 0 0 0 1 0 0 0 16173 391 14 4 4 TENM3 4 182736857 Missense_Mutation SNP A C3N-00560_T 9438641 182736857 7477698 331 17020 CENPU 0 . GRCh38 4 184728971 184728971 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.161G>T p.Ser54Ile p.S54I ENST00000281453 3/13 120 99 21 150 150 0 strelka-varscan-mutect CENPU,missense_variant,p.Ser54Ile,ENST00000281453,NM_024629.3;CENPU,missense_variant,p.Ser25Ile,ENST00000514781,;CENPU,missense_variant,p.Ser54Ile,ENST00000510146,; A ENST00000281453 Transcript missense_variant 232/1998 161/1257 54/418 S/I aGc/aTc 1 -1 CENPU HGNC HGNC:21348 protein_coding YES CCDS3838.1 ENSP00000281453 Q71F23 UPI00001BFAF6 NM_024629.3 deleterious(0.04) 3/13 hmmpanther:PTHR32222:SF1,hmmpanther:PTHR32222 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 184728971 184728971 C A 1 0 0 0 0 1 0 0 0 2951 797 28 2 2 CENPU 4 184728971 Missense_Mutation SNP C C3N-00560_T 1992114 184728971 5485584 332 17021 TRIML2 0 . GRCh38 4 188099082 188099082 + Missense_Mutation SNP C C A rs141642320 C3N-00560_T C3N-00560_N C C c.574G>T p.Val192Leu p.V192L ENST00000512729 4/7 175 140 35 207 207 0 strelka-varscan-mutect TRIML2,missense_variant,p.Val192Leu,ENST00000512729,NM_173553.2;TRIML2,missense_variant,p.Val152Leu,ENST00000326754,NM_001303419.1;TRIML2,missense_variant,p.Val97Leu,ENST00000503141,;TRIML2,missense_variant,p.Val97Leu,ENST00000503475,;TRIML2,non_coding_transcript_exon_variant,,ENST00000511771,; A ENST00000512729 Transcript missense_variant 799/1639 574/1314 192/437 V/L Gtg/Ttg rs141642320 1 -1 TRIML2 HGNC HGNC:26378 protein_coding YES ENSP00000422581 Q8N7C3 UPI000020B818 NM_173553.2 tolerated(0.33) 4/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103:SF347,hmmpanther:PTHR24103 MODERATE 1 SNV 1 1 PASS rs141642320 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 188099082 188099082 C A 1 0 0 0 0 1 0 0 0 17048 536 19 1 1 TRIML2 4 188099082 Missense_Mutation SNP C C3N-00560_T 3370111 188099082 2115473 333 17022 AHRR 0 . GRCh38 5 434302 434302 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1628A>T p.Asp543Val p.D543V ENST00000316418 12/12 160 134 26 81 81 0 strelka-varscan-mutect AHRR,missense_variant,p.Asp543Val,ENST00000316418,NM_020731.4;AHRR,missense_variant,p.Asp381Val,ENST00000506456,;AHRR,missense_variant,p.Asp525Val,ENST00000505113,NM_001242412.1;AHRR,missense_variant,p.Asp371Val,ENST00000512529,;AHRR,missense_variant,p.Asp180Val,ENST00000511487,;AHRR,non_coding_transcript_exon_variant,,ENST00000507048,; T ENST00000316418 Transcript missense_variant 1672/5661 1628/2160 543/719 D/V gAc/gTc 1 1 AHRR HGNC HGNC:346 protein_coding YES CCDS43297.1 ENSP00000323816 A9YTQ3 UPI00004572BE NM_020731.4 tolerated(0.15) 12/12 hmmpanther:PTHR10649:SF3,hmmpanther:PTHR10649 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 434302 434302 A T 1 0 0 0 0 1 0 0 0 494 275 10 4 4 AHRR 5 434302 Missense_Mutation SNP A C3N-00560_T 434302 181103957 334 17023 SLC9A3 0 . GRCh38 5 482105 482105 + Missense_Mutation SNP T T G novel C3N-00560_T C3N-00560_N T T c.1409A>C p.His470Pro p.H470P ENST00000264938 8/17 710 505 205 318 318 0 strelka-varscan-mutect SLC9A3,missense_variant,p.His470Pro,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.His461Pro,ENST00000514375,NM_001284351.1;CTD-2228K2.7,downstream_gene_variant,,ENST00000607286,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606288,;CTD-2228K2.7,downstream_gene_variant,,ENST00000607005,;SLC9A3,non_coding_transcript_exon_variant,,ENST00000507407,;CTD-2228K2.7,downstream_gene_variant,,ENST00000534918,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606074,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606107,; G ENST00000264938 Transcript missense_variant 1419/2584 1409/2505 470/834 H/P cAc/cCc 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 tolerated(0.28) 8/17 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840,Prints_domain:PR01087 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 482105 482105 T G 1 0 0 0 0 1 0 0 0 14995 1696 59 5 5 SLC9A3 5 482105 Missense_Mutation SNP T C3N-00560_T 47803 482105 181056154 335 17024 NKD2 0 . GRCh38 5 1038090 1038090 + Missense_Mutation SNP C C A rs182715653 C3N-00560_T C3N-00560_N C C c.1073C>A p.Pro358Gln p.P358Q ENST00000296849 10/10 315 259 56 110 110 0 strelka-varscan-mutect NKD2,missense_variant,p.Pro358Gln,ENST00000296849,NM_033120.3;NKD2,3_prime_UTR_variant,,ENST00000274150,NM_001271082.1;NKD2,non_coding_transcript_exon_variant,,ENST00000513296,;NKD2,non_coding_transcript_exon_variant,,ENST00000523688,;NKD2,downstream_gene_variant,,ENST00000519933,; A ENST00000296849 Transcript missense_variant 1302/2155 1073/1356 358/451 P/Q cCg/cAg rs182715653 1 1 NKD2 HGNC HGNC:17046 protein_coding YES CCDS3859.1 ENSP00000296849 Q969F2 UPI0000073E19 NM_033120.3 tolerated(0.1) 10/10 hmmpanther:PTHR22611:SF1,hmmpanther:PTHR22611 MODERATE 1 SNV 1 1 PASS rs182715653 . 0 206 0 2 0 0 0 2 -2.782174 0 0 1 0 0 A 3 1 56 1038090 1038090 C A 1 0 0 0 0 1 0 0 0 10477 652 23 1 1 NKD2 5 1038090 Missense_Mutation SNP C C3N-00560_T 555985 1038090 180500169 336 17025 ADAMTS16 0 . GRCh38 5 5146279 5146279 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.325C>A p.His109Asn p.H109N ENST00000274181 3/23 681 546 135 415 415 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.His109Asn,ENST00000274181,NM_139056.2;ADAMTS16,missense_variant,p.His109Asn,ENST00000511368,;CTD-2297D10.1,intron_variant,,ENST00000514848,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript missense_variant 463/4979 325/3675 109/1224 H/N Cac/Aac 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 3/23 Pfam_domain:PF01562 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 5146279 5146279 C A 1 0 0 0 0 1 0 0 0 305 594 21 2 2 ADAMTS16 5 5146279 Missense_Mutation SNP C C3N-00560_T 4108189 5146279 176391980 337 17026 ADAMTS16 0 . GRCh38 5 5146380 5146380 + Silent SNP G G A rs753444967 C3N-00560_T C3N-00560_N G G c.426G>A p.= p.E142E ENST00000274181 3/23 355 283 72 228 228 0 strelka-varscan-mutect ADAMTS16,synonymous_variant,p.=,ENST00000274181,NM_139056.2;ADAMTS16,synonymous_variant,p.=,ENST00000511368,;CTD-2297D10.1,intron_variant,,ENST00000514848,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript synonymous_variant 564/4979 426/3675 142/1224 E gaG/gaA rs753444967 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 3/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF01562 LOW 1 SNV 2 1 PASS rs753444967 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 5146380 5146380 G A 1 0 0 0 0 0 0 0 1 305 991 35 3 3 ADAMTS16 5 5146380 Silent SNP G C3N-00560_T 101 5146380 176391879 338 17027 ADAMTS16 0 . GRCh38 5 5182144 5182144 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.602C>T p.Ser201Phe p.S201F ENST00000274181 4/23 350 284 66 227 227 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.Ser201Phe,ENST00000274181,NM_139056.2;ADAMTS16,missense_variant,p.Ser201Phe,ENST00000511368,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 740/4979 602/3675 201/1224 S/F tCc/tTc COSM2151002,COSM2151003,COSM333009,COSM333010 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 4/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF01562 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 5182144 5182144 C T 1 0 0 0 0 1 0 0 0 305 855 30 3 3 ADAMTS16 5 5182144 Missense_Mutation SNP C C3N-00560_T 35764 5182144 176356115 339 17028 ADAMTS16 0 . GRCh38 5 5200244 5200244 + Missense_Mutation SNP C C A rs755888082 C3N-00560_T C3N-00560_N C C c.1426C>A p.Arg476Ser p.R476S ENST00000274181 9/23 307 244 63 176 176 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.Arg476Ser,ENST00000274181,NM_139056.2;ADAMTS16,missense_variant,p.Arg476Ser,ENST00000511368,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript missense_variant 1564/4979 1426/3675 476/1224 R/S Cgc/Agc rs755888082 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 9/23 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 2 1 PASS rs755888082 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 5200244 5200244 C A 1 0 0 0 0 1 0 0 0 305 652 23 1 1 ADAMTS16 5 5200244 Missense_Mutation SNP C C3N-00560_T 18100 5200244 176338015 340 17029 ICE1 0 . GRCh38 5 5441191 5441192 + Frame_Shift_Ins INS - - T novel C3N-00560_T C3N-00560_N - - c.277_278insT p.Gly93ValfsTer35 p.G93Vfs*35 ENST00000296564 5/19 98 80 18 132 132 0 sindel-varindel ICE1,frameshift_variant,p.Gly93ValfsTer35,ENST00000296564,NM_015325.2;ICE1,frameshift_variant,p.Gly16ValfsTer35,ENST00000512608,;ICE1,downstream_gene_variant,,ENST00000505464,; T ENST00000296564 Transcript frameshift_variant 499-500/7927 277-278/6801 93/2266 G/VX gga/gTga 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 5/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 56 5441191 5441191 - T 1 0 1 1 0 0 0 0 0 7384 1233 43 0 0 ICE1 5 5441191 Frame_Shift_Ins INS - C3N-00560_T 240947 5441191 176097068 341 17030 ADCY2 0 . GRCh38 5 7414698 7414698 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.336G>T p.= p.V112V ENST00000338316 2/25 277 219 58 208 208 0 strelka-varscan-mutect ADCY2,synonymous_variant,p.=,ENST00000338316,NM_020546.2;ADCY2,non_coding_transcript_exon_variant,,ENST00000498598,;ADCY2,non_coding_transcript_exon_variant,,ENST00000484965,; T ENST00000338316 Transcript synonymous_variant 425/6575 336/3276 112/1091 V gtG/gtT 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 2/25 Pfam_domain:PF16214,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1160232625 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 7414698 7414698 G T 1 0 0 0 0 0 0 0 1 338 1277 45 2 2 ADCY2 5 7414698 Silent SNP G C3N-00560_T 1973507 7414698 174123561 342 17031 ADCY2 0 . GRCh38 5 7707748 7707748 + Silent SNP C C A rs112493968 C3N-00560_T C3N-00560_N C C c.1311C>A p.= p.G437G ENST00000338316 9/25 246 230 16 189 189 0 strelka-varscan-mutect ADCY2,synonymous_variant,p.=,ENST00000338316,NM_020546.2;RP11-711G10.1,downstream_gene_variant,,ENST00000514105,; A ENST00000338316 Transcript synonymous_variant 1400/6575 1311/3276 437/1091 G ggC/ggA rs112493968,COSM3373954,COSM3373955 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 9/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs112493968 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 7707748 7707748 C A 1 0 0 0 0 0 0 0 1 338 755 27 1 1 ADCY2 5 7707748 Silent SNP C C3N-00560_T 293050 7707748 173830511 343 17032 SEMA5A 0 . GRCh38 5 9108179 9108179 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.2034G>C p.Arg678Ser p.R678S ENST00000382496 16/23 145 105 40 125 125 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Arg678Ser,ENST00000382496,NM_003966.2; G ENST00000382496 Transcript missense_variant 2700/11762 2034/3225 678/1074 R/S agG/agC COSM5430432 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0) 16/23 PROSITE_profiles:PS50092,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 9108179 9108179 C G 1 0 0 0 0 1 0 0 0 14313 854 30 4 4 SEMA5A 5 9108179 Missense_Mutation SNP C C3N-00560_T 1400431 9108179 172430080 344 17033 CTNND2 0 . GRCh38 5 11022810 11022810 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.2958C>T p.= p.G986G ENST00000304623 17/22 488 323 165 299 298 1 strelka-varscan-mutect CTNND2,synonymous_variant,p.=,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,synonymous_variant,p.=,ENST00000511377,NM_001288715.1;CTNND2,synonymous_variant,p.=,ENST00000503622,NM_001288716.1;CTNND2,synonymous_variant,p.=,ENST00000458100,;RNU6-429P,upstream_gene_variant,,ENST00000384582,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,upstream_gene_variant,,ENST00000506324,;CTNND2,synonymous_variant,p.=,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; A ENST00000304623 Transcript synonymous_variant 3148/5481 2958/3678 986/1225 G ggC/ggT 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 17/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 11022810 11022810 G A 1 0 0 0 0 0 0 0 1 3829 1306 46 3 3 CTNND2 5 11022810 Silent SNP G C3N-00560_T 1914631 11022810 170515449 345 17034 CTNND2 0 . GRCh38 5 11384761 11384761 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1081C>A p.Pro361Thr p.P361T ENST00000304623 7/22 455 348 107 268 267 1 strelka-varscan-mutect CTNND2,missense_variant,p.Pro361Thr,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Pro270Thr,ENST00000511377,NM_001288715.1;CTNND2,intron_variant,,ENST00000503622,NM_001288716.1;CTNND2,intron_variant,,ENST00000502551,;CTNND2,downstream_gene_variant,,ENST00000513598,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506735,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,intron_variant,,ENST00000511278,;CTNND2,downstream_gene_variant,,ENST00000514132,;CTNND2,non_coding_transcript_exon_variant,,ENST00000507430,;CTNND2,intron_variant,,ENST00000513588,;CTNND2,intron_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 1271/5481 1081/3678 361/1225 P/T Ccc/Acc 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.13) 7/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 11384761 11384761 G T 1 0 0 0 0 1 0 0 0 3829 1203 42 2 2 CTNND2 5 11384761 Missense_Mutation SNP G C3N-00560_T 361951 11384761 170153498 346 17035 DNAH5 0 . GRCh38 5 13839530 13839530 + Splice_Site SNP T T A rs548521732 C3N-00560_T C3N-00560_N T T c.5710-2A>T p.X1904_splice ENST00000265104 302 233 69 207 207 0 strelka-varscan-mutect DNAH5,splice_acceptor_variant,,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript splice_acceptor_variant -/15633 5710/13875 1904/4624 rs548521732,CS091944 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 34/78 HIGH 1 SNV 1 0,1 1 PASS rs548521732 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 13839530 13839530 T A 1 0 0 0 0 0 0 1 0 4419 1594 55 4 4 DNAH5 5 13839530 Splice_Site SNP T C3N-00560_T 2454769 13839530 167698729 347 17036 FBXL7 0 . GRCh38 5 15928097 15928097 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.335C>A p.Ala112Asp p.A112D ENST00000504595 3/4 228 192 36 189 189 0 strelka-varscan-mutect FBXL7,missense_variant,p.Ala112Asp,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Ala70Asp,ENST00000329673,;FBXL7,missense_variant,p.Ala65Asp,ENST00000510662,NM_001278317.1; A ENST00000504595 Transcript missense_variant 816/4562 335/1476 112/491 A/D gCc/gAc 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.19) 3/4 Gene3D:3.80.10.10,PROSITE_profiles:PS50181,hmmpanther:PTHR24006,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 15928097 15928097 C A 1 0 0 0 0 1 0 0 0 5587 739 26 2 2 FBXL7 5 15928097 Missense_Mutation SNP C C3N-00560_T 2088567 15928097 165610162 348 17037 CDH18 0 . GRCh38 5 19473604 19473604 + Missense_Mutation SNP C C A rs764127448 C3N-00560_T C3N-00560_N C C c.1995G>T p.Glu665Asp p.E665D ENST00000507958 15/15 282 214 68 220 220 0 strelka-varscan-mutect CDH18,missense_variant,p.Glu665Asp,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Glu665Asp,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Glu665Asp,ENST00000274170,;CDH18,3_prime_UTR_variant,,ENST00000506372,NM_001291957.1;CDH18,3_prime_UTR_variant,,ENST00000502796,NM_001167667.1;CDH18,downstream_gene_variant,,ENST00000515257,;CDH18,non_coding_transcript_exon_variant,,ENST00000510297,; A ENST00000507958 Transcript missense_variant 2986/3542 1995/2373 665/790 E/D gaG/gaT rs764127448,COSM3947361,COSM3947362 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 15/15 Low_complexity_(Seg):seg,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Pfam_domain:PF01049 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs764127448 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 19473604 19473604 C A 1 0 0 0 0 1 0 0 0 2806 680 24 2 2 CDH18 5 19473604 Missense_Mutation SNP C C3N-00560_T 3545507 19473604 162064655 349 17038 CDH18 0 . GRCh38 5 19838891 19838891 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.96G>T p.Lys32Asn p.K32N ENST00000507958 5/15 617 492 125 455 455 0 strelka-varscan-mutect CDH18,missense_variant,p.Lys32Asn,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Lys32Asn,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Lys32Asn,ENST00000274170,;CDH18,missense_variant,p.Lys32Asn,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Lys32Asn,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Lys32Asn,ENST00000511273,;CDH18,upstream_gene_variant,,ENST00000515257,;CDH18,downstream_gene_variant,,ENST00000507632,;CDH18,downstream_gene_variant,,ENST00000511423,;CDH18,downstream_gene_variant,,ENST00000503132,; A ENST00000507958 Transcript missense_variant 1087/3542 96/2373 32/790 K/N aaG/aaT 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 tolerated(0.3) 5/15 hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 19838891 19838891 C A 1 0 0 0 0 1 0 0 0 2806 680 24 2 2 CDH18 5 19838891 Missense_Mutation SNP C C3N-00560_T 365287 19838891 161699368 350 17039 CDH12 0 . GRCh38 5 22078450 22078450 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.227delG p.Gly76GlufsTer7 p.G76Efs*7 ENST00000382254 5/15 238 178 60 164 164 0 sindel-varindel-pindel CDH12,frameshift_variant,p.Gly76GlufsTer7,ENST00000382254,NM_004061.3;CDH12,frameshift_variant,p.Gly76GlufsTer7,ENST00000504376,;CDH12,frameshift_variant,p.Gly76GlufsTer7,ENST00000522262,;CDH12,downstream_gene_variant,,ENST00000518209,;CDH12,downstream_gene_variant,,ENST00000521745,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; - ENST00000382254 Transcript frameshift_variant 1314/4164 227/2385 76/794 G/X gGa/ga 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 5/15 Pfam_domain:PF00028,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,Superfamily_domains:SSF49313 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 22078450 22078450 C - 1 0 1 0 1 0 0 0 0 2801 869 30 0 0 CDH12 5 22078450 Frame_Shift_Del DEL C C3N-00560_T 2239559 22078450 159459809 351 17040 PRDM9 0 . GRCh38 5 23527144 23527144 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2056C>A p.His686Asn p.H686N ENST00000296682 11/11 210 195 15 150 150 0 varscan-mutect PRDM9,missense_variant,p.His686Asn,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; A ENST00000296682 Transcript missense_variant 2238/3691 2056/2685 686/894 H/N Cac/Aac 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR16515:SF10,hmmpanther:PTHR16515,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 23527144 23527144 C A 1 0 0 0 0 1 0 0 0 12595 478 17 2 2 PRDM9 5 23527144 Missense_Mutation SNP C C3N-00560_T 1448694 23527144 158011115 352 17041 CDH9 0 . GRCh38 5 26906734 26906734 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.628G>A p.Val210Met p.V210M ENST00000231021 4/12 379 266 113 254 254 0 strelka-varscan-mutect CDH9,missense_variant,p.Val210Met,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505045,; T ENST00000231021 Transcript missense_variant 801/3079 628/2370 210/789 V/M Gtg/Atg 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0) 4/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 26906734 26906734 C T 1 0 0 0 0 1 0 0 0 2820 565 20 3 3 CDH9 5 26906734 Missense_Mutation SNP C C3N-00560_T 3379590 26906734 154631525 353 17042 TARS 0 . GRCh38 5 33448682 33448682 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.280G>C p.Asp94His p.D94H ENST00000455217 3/20 195 146 49 118 118 0 strelka-varscan-mutect TARS,missense_variant,p.Asp94His,ENST00000265112,NM_152295.4;TARS,missense_variant,p.Asp94His,ENST00000502553,NM_001258437.1;TARS,missense_variant,p.Asp94His,ENST00000455217,NM_001258438.1;TARS,missense_variant,p.Asp35His,ENST00000506040,;TARS,missense_variant,p.Asp94His,ENST00000514259,;TARS,intron_variant,,ENST00000627006,;TARS,downstream_gene_variant,,ENST00000626210,;TARS,downstream_gene_variant,,ENST00000502508,;TARS,missense_variant,p.Asp94His,ENST00000507716,;TARS,missense_variant,p.Asp94His,ENST00000505012,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,3_prime_UTR_variant,,ENST00000513066,;TARS,intron_variant,,ENST00000508361,; C ENST00000455217 Transcript missense_variant 402/2523 280/2271 94/756 D/H Gat/Cat COSM4792231 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 deleterious(0.03) 3/20 hmmpanther:PTHR11451:SF36,hmmpanther:PTHR11451,Gene3D:3.10.20.30 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 33448682 33448682 G C 1 0 0 0 0 1 0 0 0 15958 1290 45 4 4 TARS 5 33448682 Missense_Mutation SNP G C3N-00560_T 6541948 33448682 148089577 354 17043 UGT3A2 0 . GRCh38 5 36049038 36049038 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.694G>T p.Gly232Cys p.G232C ENST00000282507 4/7 546 454 92 260 260 0 strelka-varscan-mutect UGT3A2,missense_variant,p.Gly232Cys,ENST00000282507,NM_174914.3;UGT3A2,missense_variant,p.Gly198Cys,ENST00000513300,NM_001168316.1;UGT3A2,downstream_gene_variant,,ENST00000515131,;UGT3A2,intron_variant,,ENST00000504954,;UGT3A2,intron_variant,,ENST00000504685,; A ENST00000282507 Transcript missense_variant 796/2355 694/1572 232/523 G/C Ggc/Tgc 1 -1 UGT3A2 HGNC HGNC:27266 protein_coding YES CCDS3914.1 ENSP00000282507 Q3SY77 UPI000013DCE8 NM_174914.3 deleterious(0.02) 4/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF320,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 36049038 36049038 C A 1 0 0 0 0 1 0 0 0 17488 681 24 2 2 UGT3A2 5 36049038 Missense_Mutation SNP C C3N-00560_T 2600356 36049038 145489221 355 17044 C5orf42 0 . GRCh38 5 37205367 37205367 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.3237A>T p.= p.P1079P ENST00000425232 18/52 249 208 41 142 142 0 strelka-varscan-mutect C5orf42,synonymous_variant,p.=,ENST00000425232,NM_023073.3;C5orf42,synonymous_variant,p.=,ENST00000508244,;C5orf42,synonymous_variant,p.=,ENST00000514429,;C5orf42,synonymous_variant,p.=,ENST00000509849,;C5orf42,non_coding_transcript_exon_variant,,ENST00000505431,;OFD1P17,upstream_gene_variant,,ENST00000437639,; A ENST00000425232 Transcript synonymous_variant 3468/11199 3237/9594 1079/3197 P ccA/ccT 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 18/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 37205367 37205367 T A 1 0 0 0 0 0 0 0 1 2100 1567 55 4 4 C5orf42 5 37205367 Silent SNP T C3N-00560_T 1156329 37205367 144332892 356 17045 C9 0 . GRCh38 5 39308344 39308344 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1126G>T p.Asp376Tyr p.D376Y ENST00000263408 8/11 370 300 70 260 260 0 strelka-varscan-mutect C9,missense_variant,p.Asp376Tyr,ENST00000263408,NM_001737.3; A ENST00000263408 Transcript missense_variant 1222/2713 1126/1680 376/559 D/Y Gac/Tac 1 -1 C9 HGNC HGNC:1358 protein_coding YES CCDS3929.1 ENSP00000263408 P02748 UPI0000001065 NM_001737.3 deleterious(0) 8/11 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF362,hmmpanther:PTHR19325,Pfam_domain:PF01823,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS rs1195276908 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 39308344 39308344 C A 1 0 0 0 0 1 0 0 0 2169 913 32 2 2 C9 5 39308344 Missense_Mutation SNP C C3N-00560_T 2102977 39308344 142229915 357 17046 C7 0 . GRCh38 5 40934417 40934417 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.231A>T p.Arg77Ser p.R77S ENST00000313164 4/18 350 279 71 209 209 0 strelka-varscan-mutect C7,missense_variant,p.Arg77Ser,ENST00000313164,NM_000587.2;C7,upstream_gene_variant,,ENST00000489457,;C7,non_coding_transcript_exon_variant,,ENST00000508185,; T ENST00000313164 Transcript missense_variant 590/4257 231/2532 77/843 R/S agA/agT 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 4/18 Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00209 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40934417 40934417 A T 1 0 0 0 0 1 0 0 0 2134 301 11 4 4 C7 5 40934417 Missense_Mutation SNP A C3N-00560_T 1626073 40934417 140603842 358 17047 C7 0 . GRCh38 5 40937597 40937597 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.474C>A p.= p.T158T ENST00000313164 6/18 163 114 49 90 90 0 strelka-varscan-mutect C7,synonymous_variant,p.=,ENST00000313164,NM_000587.2;C7,downstream_gene_variant,,ENST00000489457,;C7,non_coding_transcript_exon_variant,,ENST00000508185,; A ENST00000313164 Transcript synonymous_variant 833/4257 474/2532 158/843 T acC/acA 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 6/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389 LOW 1 SNV 1 1 PASS rs1204257939 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 40937597 40937597 C A 1 0 0 0 0 0 0 0 1 2134 581 21 2 2 C7 5 40937597 Silent SNP C C3N-00560_T 3180 40937597 140600662 359 17048 C7 0 . GRCh38 5 40958159 40958159 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1387G>T p.Gly463Cys p.G463C ENST00000313164 11/18 217 171 46 113 112 1 strelka-varscan-mutect C7,missense_variant,p.Gly463Cys,ENST00000313164,NM_000587.2; T ENST00000313164 Transcript missense_variant 1746/4257 1387/2532 463/843 G/C Ggt/Tgt 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 11/18 Gene3D:2.10.25.10,Prints_domain:PR00764,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40958159 40958159 G T 1 0 0 0 0 1 0 0 0 2134 1348 47 2 2 C7 5 40958159 Missense_Mutation SNP G C3N-00560_T 20562 40958159 140580100 360 17049 C7 0 . GRCh38 5 40959502 40959502 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.1543G>T p.Gly515Trp p.G515W ENST00000313164 12/18 260 211 49 141 141 0 strelka-varscan-mutect C7,missense_variant,p.Gly515Trp,ENST00000313164,NM_000587.2;C7,upstream_gene_variant,,ENST00000486779,; T ENST00000313164 Transcript missense_variant 1902/4257 1543/2532 515/843 G/W Ggg/Tgg COSM3616461 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 12/18 Gene3D:2.20.100.10,Pfam_domain:PF00090,Prints_domain:PR01705,PROSITE_profiles:PS50092,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40959502 40959502 G T 1 0 0 0 0 1 0 0 0 2134 1000 35 2 2 C7 5 40959502 Missense_Mutation SNP G C3N-00560_T 1343 40959502 140578757 361 17050 C7 0 . GRCh38 5 40981442 40981442 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2401G>T p.Gly801Trp p.G801W ENST00000313164 18/18 426 351 75 267 265 2 strelka-varscan-mutect C7,missense_variant,p.Gly801Trp,ENST00000313164,NM_000587.2;C7,downstream_gene_variant,,ENST00000494960,;C7,non_coding_transcript_exon_variant,,ENST00000464864,;C7,downstream_gene_variant,,ENST00000513922,; T ENST00000313164 Transcript missense_variant 2760/4257 2401/2532 801/843 G/W Ggg/Tgg 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 18/18 SMART_domains:SM00057 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40981442 40981442 G T 1 0 0 0 0 1 0 0 0 2134 1000 35 2 2 C7 5 40981442 Missense_Mutation SNP G C3N-00560_T 21940 40981442 140556817 362 17051 MROH2B 0 . GRCh38 5 41009990 41009990 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.3225C>A p.= p.S1075S ENST00000399564 31/42 222 180 42 118 118 0 strelka-varscan-mutect MROH2B,synonymous_variant,p.=,ENST00000399564,NM_173489.4;MROH2B,synonymous_variant,p.=,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,; T ENST00000399564 Transcript synonymous_variant 3676/5239 3225/4758 1075/1585 S tcC/tcA 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 31/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 41009990 41009990 G T 1 0 0 0 0 0 0 0 1 9745 1219 43 2 2 MROH2B 5 41009990 Silent SNP G C3N-00560_T 28548 41009990 140528269 363 17052 C6 0 . GRCh38 5 41149347 41149347 + Missense_Mutation SNP G G T rs567176554 C3N-00560_T C3N-00560_N G G c.2517C>A p.Asp839Glu p.D839E ENST00000263413 17/18 722 618 104 418 418 0 strelka-varscan-mutect C6,missense_variant,p.Asp839Glu,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Asp839Glu,ENST00000337836,NM_000065.3;C6,downstream_gene_variant,,ENST00000461473,; T ENST00000263413 Transcript missense_variant 2782/3661 2517/2805 839/934 D/E gaC/gaA rs567176554,COSM1166373 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 tolerated(0.41) 17/18 PROSITE_profiles:PS51465,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,SMART_domains:SM00057 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs567176554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 41149347 41149347 G T 1 0 0 0 0 1 0 0 0 2111 1136 40 1 1 C6 5 41149347 Missense_Mutation SNP G C3N-00560_T 139357 41149347 140388912 364 17053 C6 0 . GRCh38 5 41159116 41159116 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1822G>T p.Glu608Ter p.E608* ENST00000263413 12/18 452 361 91 264 263 1 strelka-varscan-mutect C6,stop_gained,p.Glu608Ter,ENST00000263413,NM_001115131.2;C6,stop_gained,p.Glu608Ter,ENST00000337836,NM_000065.3;C6,downstream_gene_variant,,ENST00000475349,;C6,upstream_gene_variant,,ENST00000461473,;C6,downstream_gene_variant,,ENST00000473450,;C6,non_coding_transcript_exon_variant,,ENST00000511470,; A ENST00000263413 Transcript stop_gained 2087/3661 1822/2805 608/934 E/* Gag/Tag 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 12/18 PROSITE_profiles:PS50092,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 41159116 41159116 C A 1 0 0 0 0 0 1 0 0 2111 922 32 2 2 C6 5 41159116 Nonsense_Mutation SNP C C3N-00560_T 9769 41159116 140379143 365 17054 HCN1 0 . GRCh38 5 45695776 45695776 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.318C>A p.= p.V106V ENST00000303230 1/8 1063 532 531 603 603 0 strelka-varscan-mutect HCN1,synonymous_variant,p.=,ENST00000303230,NM_021072.3;HCN1,synonymous_variant,p.=,ENST00000634658,;HCN1,upstream_gene_variant,,ENST00000638054,; T ENST00000303230 Transcript synonymous_variant 559/9885 318/2673 106/890 V gtC/gtA 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 1/8 Pfam_domain:PF08412,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 45695776 45695776 G T 1 0 0 0 0 0 0 0 1 6883 1277 45 2 2 HCN1 5 45695776 Silent SNP G C3N-00560_T 4536660 45695776 135842483 366 17055 MAP1B 0 . GRCh38 5 72199573 72199573 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.6218C>A p.Pro2073His p.P2073H ENST00000296755 5/7 248 157 91 307 307 0 strelka-varscan-mutect MAP1B,missense_variant,p.Pro2073His,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; A ENST00000296755 Transcript missense_variant 6516/12036 6218/7407 2073/2468 P/H cCc/cAc 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 tolerated(0.55) 5/7 hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 72199573 72199573 C A 1 0 0 0 0 1 0 0 0 9151 623 22 2 2 MAP1B 5 72199573 Missense_Mutation SNP C C3N-00560_T 26503797 72199573 109338686 367 17056 ARHGEF28 0 . GRCh38 5 73909583 73909583 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.4333C>T p.His1445Tyr p.H1445Y ENST00000545377 34/37 188 108 80 216 216 0 strelka-varscan-mutect ARHGEF28,missense_variant,p.His1445Tyr,ENST00000545377,NM_001080479.2;ARHGEF28,missense_variant,p.His1445Tyr,ENST00000513042,NM_001177693.1;ARHGEF28,missense_variant,p.His1445Tyr,ENST00000426542,;ARHGEF28,missense_variant,p.His1445Tyr,ENST00000437974,;ARHGEF28,missense_variant,p.His1445Tyr,ENST00000296794,;ARHGEF28,missense_variant,p.His1132Tyr,ENST00000296799,NM_001244364.1;ARHGEF28,missense_variant,p.His365Tyr,ENST00000512883,;ARHGEF28,non_coding_transcript_exon_variant,,ENST00000503341,;ARHGEF28,downstream_gene_variant,,ENST00000510312,; T ENST00000545377 Transcript missense_variant 4509/6351 4333/5196 1445/1731 H/Y Cac/Tac 1 1 ARHGEF28 HGNC HGNC:30322 protein_coding YES CCDS47231.2 ENSP00000441913 Q8N1W1 UPI00004DF58E NM_001080479.2 tolerated(1) 34/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF133,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 73909583 73909583 C T 1 0 0 0 0 1 0 0 0 1036 710 25 3 3 ARHGEF28 5 73909583 Missense_Mutation SNP C C3N-00560_T 1710010 73909583 107628676 368 17057 IQGAP2 0 . GRCh38 5 76683114 76683114 + Splice_Site SNP G G T rs113692837 C3N-00560_T C3N-00560_N G G c.3661-1G>T p.X1221_splice ENST00000274364 76 40 36 103 103 0 strelka-varscan-mutect IQGAP2,splice_acceptor_variant,,ENST00000274364,NM_006633.3;IQGAP2,splice_acceptor_variant,,ENST00000379730,NM_001285460.1;IQGAP2,splice_acceptor_variant,,ENST00000505766,;IQGAP2,splice_acceptor_variant,,ENST00000502745,NM_001285462.1;IQGAP2,splice_acceptor_variant,,ENST00000396234,NM_001285461.1;IQGAP2,splice_acceptor_variant,,ENST00000504477,;IQGAP2,splice_acceptor_variant,,ENST00000512256,; T ENST00000274364 Transcript splice_acceptor_variant -/5844 3661/4728 1221/1575 rs113692837 1 1 IQGAP2 HGNC HGNC:6111 protein_coding YES CCDS34188.1 ENSP00000274364 Q13576 UPI000020CB2C NM_006633.3 28/35 HIGH 1 SNV 1 1 PASS rs113692837 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 76683114 76683114 G T 1 0 0 0 0 0 0 1 0 7721 985 34 2 2 IQGAP2 5 76683114 Splice_Site SNP G C3N-00560_T 2773531 76683114 104855145 369 17058 BHMT 0 . GRCh38 5 79130969 79130969 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.1074C>T p.= p.A358A ENST00000274353 8/8 99 52 47 123 123 0 strelka-varscan-mutect BHMT,synonymous_variant,p.=,ENST00000274353,NM_001713.2;BHMT,synonymous_variant,p.=,ENST00000524080,;DMGDH,intron_variant,,ENST00000520388,;DMGDH,intron_variant,,ENST00000518707,;BHMT,downstream_gene_variant,,ENST00000521279,;BHMT,downstream_gene_variant,,ENST00000523508,; T ENST00000274353 Transcript synonymous_variant 1181/2502 1074/1221 358/406 A gcC/gcT 1 1 BHMT HGNC HGNC:1047 protein_coding YES CCDS4046.1 ENSP00000274353 Q93088 V9HWA4 UPI000006D864 NM_001713.2 8/8 hmmpanther:PTHR21091:SF116,hmmpanther:PTHR21091,Gene3D:3.20.20.330,PIRSF_domain:PIRSF037505,Superfamily_domains:SSF82282 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 79130969 79130969 C T 1 0 0 0 0 0 0 0 1 1574 668 24 3 3 BHMT 5 79130969 Silent SNP C C3N-00560_T 2447855 79130969 102407290 370 17059 RASGRF2 0 . GRCh38 5 81070519 81070519 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.571C>A p.= p.R191R ENST00000265080 4/27 91 56 35 148 148 0 strelka-varscan-mutect RASGRF2,synonymous_variant,p.=,ENST00000265080,NM_006909.2;RASGRF2,non_coding_transcript_exon_variant,,ENST00000502677,;RASGRF2,non_coding_transcript_exon_variant,,ENST00000514946,;RASGRF2,synonymous_variant,p.=,ENST00000503795,; A ENST00000265080 Transcript synonymous_variant 638/8167 571/3714 191/1237 R Cga/Aga 1 1 RASGRF2 HGNC HGNC:9876 protein_coding YES CCDS4052.1 ENSP00000265080 O14827 UPI0000047ABF NM_006909.2 4/27 hmmpanther:PTHR23113:SF187,hmmpanther:PTHR23113 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 81070519 81070519 C A 1 0 0 0 0 0 0 0 1 13234 528 19 1 1 RASGRF2 5 81070519 Silent SNP C C3N-00560_T 1939550 81070519 100467740 371 17060 HAPLN1 0 . GRCh38 5 83641691 83641691 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.870C>A p.= p.G290G ENST00000274341 5/5 252 163 89 312 312 0 strelka-varscan-mutect HAPLN1,synonymous_variant,p.=,ENST00000274341,NM_001884.3;HAPLN1,downstream_gene_variant,,ENST00000510978,;HAPLN1,downstream_gene_variant,,ENST00000504713,;HAPLN1,downstream_gene_variant,,ENST00000508307,;HAPLN1,downstream_gene_variant,,ENST00000503117,; T ENST00000274341 Transcript synonymous_variant 1721/5607 870/1065 290/354 G ggC/ggA 1 -1 HAPLN1 HGNC HGNC:2380 protein_coding YES CCDS4061.1 ENSP00000274341 P10915 A0A024RAK9 UPI0000131BFF NM_001884.3 5/5 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF10,hmmpanther:PTHR22804,PROSITE_patterns:PS01241,Gene3D:3.10.100.10,Pfam_domain:PF00193,SMART_domains:SM00445,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 83641691 83641691 G T 1 0 0 0 0 0 0 0 1 6840 1190 42 2 2 HAPLN1 5 83641691 Silent SNP G C3N-00560_T 2571172 83641691 97896568 372 17061 TTC37 0 . GRCh38 5 95528119 95528119 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1028G>A p.Gly343Asp p.G343D ENST00000358746 13/43 180 108 72 258 258 0 strelka-varscan-mutect TTC37,missense_variant,p.Gly343Asp,ENST00000358746,NM_014639.3;TTC37,missense_variant,p.Gly295Asp,ENST00000514952,;TTC37,non_coding_transcript_exon_variant,,ENST00000504421,;TTC37,intron_variant,,ENST00000505578,;TTC37,upstream_gene_variant,,ENST00000513232,;TTC37,downstream_gene_variant,,ENST00000503279,; T ENST00000358746 Transcript missense_variant 1327/5706 1028/4695 343/1564 G/D gGt/gAt 1 -1 TTC37 HGNC HGNC:23639 protein_coding YES CCDS4072.1 ENSP00000351596 Q6PGP7 UPI00000709BD NM_014639.3 tolerated(0.12) 13/43 PROSITE_profiles:PS50293,hmmpanther:PTHR15704,hmmpanther:PTHR15704:SF7,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs1290716289 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 95528119 95528119 C T 1 0 0 0 0 1 0 0 0 17214 507 18 3 3 TTC37 5 95528119 Missense_Mutation SNP C C3N-00560_T 11886428 95528119 86010140 373 17062 MAN2A1 0 . GRCh38 5 109865060 109865060 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3196G>T p.Ala1066Ser p.A1066S ENST00000261483 21/22 148 79 69 203 203 0 strelka-varscan-mutect MAN2A1,missense_variant,p.Ala1066Ser,ENST00000261483,NM_002372.3;MAN2A1,non_coding_transcript_exon_variant,,ENST00000505313,;MAN2A1,non_coding_transcript_exon_variant,,ENST00000503970,;MAN2A1,non_coding_transcript_exon_variant,,ENST00000513921,; T ENST00000261483 Transcript missense_variant 4248/4667 3196/3435 1066/1144 A/S Gca/Tca 1 1 MAN2A1 HGNC HGNC:6824 protein_coding YES CCDS34209.1 ENSP00000261483 Q16706 UPI000013D193 NM_002372.3 tolerated(0.1) 21/22 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF4,Pfam_domain:PF07748,Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 109865060 109865060 G T 1 0 0 0 0 1 0 0 0 9135 1203 42 2 2 MAN2A1 5 109865060 Missense_Mutation SNP G C3N-00560_T 14336941 109865060 71673199 374 17063 TRIM36 0 . GRCh38 5 115163571 115163571 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.245G>T p.Arg82Leu p.R82L ENST00000282369 2/10 253 132 121 283 283 0 strelka-varscan-mutect TRIM36,missense_variant,p.Arg70Leu,ENST00000513154,NM_001300759.1;TRIM36,missense_variant,p.Arg82Leu,ENST00000282369,NM_018700.3;TRIM36,missense_variant,p.Arg70Leu,ENST00000508894,;TRIM36,intron_variant,,ENST00000514154,NM_001300752.1;TRIM36,non_coding_transcript_exon_variant,,ENST00000515104,;TRIM36,intron_variant,,ENST00000510222,; A ENST00000282369 Transcript missense_variant 367/4050 245/2187 82/728 R/L cGa/cTa COSM420445,COSM4812093 1 -1 TRIM36 HGNC HGNC:16280 protein_coding YES CCDS4115.1 ENSP00000282369 Q9NQ86 UPI000013DCD9 NM_018700.3 deleterious(0.01) 2/10 PROSITE_profiles:PS50089,Low_complexity_(Seg):seg,SMART_domains:SM00184 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs957625882 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 115163571 115163571 C A 1 0 0 0 0 1 0 0 0 16999 884 31 1 1 TRIM36 5 115163571 Missense_Mutation SNP C C3N-00560_T 5298511 115163571 66374688 375 17064 SLC12A2 0 . GRCh38 5 128135709 128135709 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1309G>T p.Val437Phe p.V437F ENST00000262461 7/27 134 83 51 192 192 0 strelka-varscan-mutect SLC12A2,missense_variant,p.Val437Phe,ENST00000262461,NM_001046.2;SLC12A2,missense_variant,p.Val437Phe,ENST00000343225,NM_001256461.1;SLC12A2,missense_variant,p.Val437Phe,ENST00000628403,;SLC12A2,missense_variant,p.Val437Phe,ENST00000509205,; T ENST00000262461 Transcript missense_variant 1498/6885 1309/3639 437/1212 V/F Gtt/Ttt 1 1 SLC12A2 HGNC HGNC:10911 protein_coding YES CCDS4144.1 ENSP00000262461 P55011 Q53ZR1 UPI000013541A NM_001046.2 tolerated(0.24) 7/27 Pfam_domain:PF00324,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF58,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00930,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 128135709 128135709 G T 1 0 0 0 0 1 0 0 0 14648 1377 48 2 2 SLC12A2 5 128135709 Missense_Mutation SNP G C3N-00560_T 12972138 128135709 53402550 376 17065 ANKHD1 0 . GRCh38 5 140449282 140449282 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.1219A>C p.Thr407Pro p.T407P ENST00000532219 7/36 117 74 43 159 159 0 strelka-varscan-mutect ANKHD1-EIF4EBP3,missense_variant,p.Thr407Pro,ENST00000532219,NM_020690.5;ANKHD1,missense_variant,p.Thr407Pro,ENST00000360839,NM_017747.2;ANKHD1,missense_variant,p.Thr407Pro,ENST00000421134,;ANKHD1,missense_variant,p.Thr407Pro,ENST00000394723,NM_024668.3;ANKHD1,missense_variant,p.Thr407Pro,ENST00000616482,NM_001197030.1;ANKHD1,missense_variant,p.Thr396Pro,ENST00000394722,NM_017978.2;ANKHD1,5_prime_UTR_variant,,ENST00000297183,;ANKHD1,downstream_gene_variant,,ENST00000511151,; C ENST00000532219 Transcript missense_variant 1279/8246 1219/7854 407/2617 T/P Act/Cct 1 1 ANKHD1-EIF4EBP3 HGNC HGNC:33530 protein_coding YES CCDS4224.1 ENSP00000432016 UPI0000074448 NM_020690.5 deleterious(0) 7/36 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR23206:SF5,hmmpanther:PTHR23206,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403,Superfamily_domains:SSF48403 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 140449282 140449282 A C 1 0 0 0 0 1 0 0 0 730 159 6 5 5 ANKHD1 5 140449282 Missense_Mutation SNP A C3N-00560_T 12313573 140449282 41088977 377 17066 PCDHA4 0 . GRCh38 5 140808069 140808069 + Missense_Mutation SNP C C A rs781875261 C3N-00560_T C3N-00560_N C C c.882C>A p.His294Gln p.H294Q ENST00000530339 1/4 77 41 36 154 154 0 strelka-varscan-mutect PCDHA4,missense_variant,p.His294Gln,ENST00000618834,NM_031500.2;PCDHA4,missense_variant,p.His294Gln,ENST00000530339,NM_018907.3;PCDHA4,missense_variant,p.His294Gln,ENST00000512229,;PCDHA4,missense_variant,p.His293Gln,ENST00000378125,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,downstream_gene_variant,,ENST00000532566,NM_031497.1;PCDHA2,downstream_gene_variant,,ENST00000520672,NM_031496.1;AC005609.16,intron_variant,,ENST00000624712,; A ENST00000530339 Transcript missense_variant 882/5251 882/2844 294/947 H/Q caC/caA rs781875261 1 1 PCDHA4 HGNC HGNC:8670 protein_coding YES CCDS54916.1 ENSP00000435300 Q9UN74 UPI00001273CC NM_018907.3 tolerated_low_confidence(0.31) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs781875261 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 140808069 140808069 C A 1 0 0 0 0 1 0 0 0 11613 477 17 2 2 PCDHA4 5 140808069 Missense_Mutation SNP C C3N-00560_T 358787 140808069 40730190 378 17067 PCDHA4 0 . GRCh38 5 140808691 140808691 + Missense_Mutation SNP C C A rs140993559 C3N-00560_T C3N-00560_N C C c.1504C>A p.Arg502Ser p.R502S ENST00000530339 1/4 621 317 304 781 780 1 strelka-varscan-mutect PCDHA4,missense_variant,p.Arg502Ser,ENST00000618834,NM_031500.2;PCDHA4,missense_variant,p.Arg502Ser,ENST00000530339,NM_018907.3;PCDHA4,missense_variant,p.Arg502Ser,ENST00000512229,;PCDHA4,missense_variant,p.Arg501Ser,ENST00000378125,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,downstream_gene_variant,,ENST00000532566,NM_031497.1;PCDHA2,downstream_gene_variant,,ENST00000520672,NM_031496.1;AC005609.16,intron_variant,,ENST00000624712,; A ENST00000530339 Transcript missense_variant 1504/5251 1504/2844 502/947 R/S Cgc/Agc rs140993559 1 1 PCDHA4 HGNC HGNC:8670 protein_coding YES CCDS54916.1 ENSP00000435300 Q9UN74 UPI00001273CC NM_018907.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs140993559 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 140808691 140808691 C A 1 0 0 0 0 1 0 0 0 11613 768 27 1 1 PCDHA4 5 140808691 Missense_Mutation SNP C C3N-00560_T 622 140808691 40729568 379 17068 PCDHA9 0 . GRCh38 5 140849778 140849778 + Missense_Mutation SNP G G A rs781905467 C3N-00560_T C3N-00560_N G G c.1283G>A p.Arg428Gln p.R428Q ENST00000532602 1/4 348 187 161 435 435 0 strelka-varscan-mutect PCDHA9,missense_variant,p.Arg428Gln,ENST00000378122,NM_014005.4;PCDHA9,missense_variant,p.Arg428Gln,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; A ENST00000532602 Transcript missense_variant 2316/6293 1283/2853 428/950 R/Q cGg/cAg rs781905467,COSM4524630,COSM4524631 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 tolerated_low_confidence(0.14) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs781905467 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 140849778 140849778 G A 1 0 0 0 0 1 0 0 0 11618 1116 39 1 1 PCDHA9 5 140849778 Missense_Mutation SNP G C3N-00560_T 41087 140849778 40688481 380 17069 PCDHA10 0 . GRCh38 5 140857428 140857428 + Silent SNP G G T rs782142394 C3N-00560_T C3N-00560_N G G c.1380G>T p.= p.T460T ENST00000307360 1/4 649 361 288 774 773 1 strelka-varscan-mutect PCDHA10,synonymous_variant,p.=,ENST00000562220,NM_031859.2;PCDHA10,synonymous_variant,p.=,ENST00000307360,NM_018901.3;PCDHA10,synonymous_variant,p.=,ENST00000506939,NM_031860.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; T ENST00000307360 Transcript synonymous_variant 1380/5254 1380/2847 460/948 T acG/acT rs782142394,COSM1633993,COSM1633994,COSM1633995 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,Superfamily_domains:SSF49313 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs782142394 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 140857428 140857428 G T 1 0 0 0 0 0 0 0 1 11607 1103 39 1 1 PCDHA10 5 140857428 Silent SNP G C3N-00560_T 7650 140857428 40680831 381 17070 PCDHGA9 0 . GRCh38 5 141404226 141404226 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1274C>T p.Thr425Ile p.T425I ENST00000573521 1/4 148 91 57 202 202 0 strelka-varscan-mutect PCDHGA9,missense_variant,p.Thr425Ile,ENST00000573521,NM_018921.2;PCDHGA9,missense_variant,p.Thr425Ile,ENST00000616887,NM_032089.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGB6,upstream_gene_variant,,ENST00000616430,NM_032100.1;PCDHGB6,upstream_gene_variant,,ENST00000520790,NM_018926.2;PCDHGB5,downstream_gene_variant,,ENST00000621169,NM_032099.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000573521 Transcript missense_variant 1274/4605 1274/2799 425/932 T/I aCa/aTa 1 1 PCDHGA9 HGNC HGNC:8707 protein_coding YES CCDS58981.1 ENSP00000460274 Q9Y5G4 UPI00000721C3 NM_018921.2 tolerated_low_confidence(0.08) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF86,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 141404226 141404226 C T 1 0 0 0 0 1 0 0 0 11648 478 17 3 3 PCDHGA9 5 141404226 Missense_Mutation SNP C C3N-00560_T 546798 141404226 40134033 382 17071 AFAP1L1 0 . GRCh38 5 149310112 149310112 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.904G>A p.Glu302Lys p.E302K ENST00000296721 8/19 78 43 35 88 88 0 strelka-varscan-mutect AFAP1L1,missense_variant,p.Glu302Lys,ENST00000296721,NM_152406.2;AFAP1L1,missense_variant,p.Glu302Lys,ENST00000515000,NM_001146337.1;AFAP1L1,downstream_gene_variant,,ENST00000522492,;AFAP1L1,non_coding_transcript_exon_variant,,ENST00000455574,; A ENST00000296721 Transcript missense_variant 1002/4177 904/2307 302/768 E/K Gag/Aag 1 1 AFAP1L1 HGNC HGNC:26714 protein_coding YES CCDS34274.1 ENSP00000296721 Q8TED9 UPI00001C1E2F NM_152406.2 deleterious(0) 8/19 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF1,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 149310112 149310112 G A 1 0 0 0 0 1 0 0 0 431 943 33 3 3 AFAP1L1 5 149310112 Missense_Mutation SNP G C3N-00560_T 7905886 149310112 32228147 383 17072 GRPEL2 0 . GRCh38 5 149349652 149349652 + Splice_Site SNP A A T novel C3N-00560_T C3N-00560_N A A c.232-2A>T p.X78_splice ENST00000329271 77 34 43 91 91 0 strelka-varscan-mutect GRPEL2,splice_acceptor_variant,,ENST00000329271,NM_152407.3;GRPEL2,splice_acceptor_variant,,ENST00000513661,;GRPEL2,intron_variant,,ENST00000416916,;GRPEL2-AS1,intron_variant,,ENST00000521295,;GRPEL2,splice_acceptor_variant,,ENST00000507562,; T ENST00000329271 Transcript splice_acceptor_variant -/4089 232/678 78/225 1 1 GRPEL2 HGNC HGNC:21060 protein_coding YES CCDS4295.1 ENSP00000329558 Q8TAA5 UPI000004A0F1 NM_152407.3 2/3 HIGH 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 149349652 149349652 A T 1 0 0 0 0 0 0 1 0 6689 202 7 4 4 GRPEL2 5 149349652 Splice_Site SNP A C3N-00560_T 39540 149349652 32188607 384 17073 ZNF300 0 . GRCh38 5 150895855 150895855 + Nonsense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1432G>T p.Glu478Ter p.E478* ENST00000446148 7/7 137 78 59 166 166 0 strelka-varscan-mutect ZNF300,stop_gained,p.Glu478Ter,ENST00000446148,NM_001172831.1;ZNF300,stop_gained,p.Glu462Ter,ENST00000274599,NM_052860.2;ZNF300,stop_gained,p.Glu462Ter,ENST00000394226,;ZNF300,stop_gained,p.Glu426Ter,ENST00000418587,NM_001172832.1;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,; A ENST00000446148 Transcript stop_gained 1860/3323 1432/1863 478/620 E/* Gaa/Taa COSM5413859,COSM5413860 1 -1 ZNF300 HGNC HGNC:13091 protein_coding YES CCDS54940.1 ENSP00000397178 Q96RE9 UPI0001AE74AD NM_001172831.1 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF320,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 150895855 150895855 C A 1 0 0 0 0 0 1 0 0 18406 864 30 2 2 ZNF300 5 150895855 Nonsense_Mutation SNP C C3N-00560_T 1546203 150895855 30642404 385 17074 ZNF300 0 . GRCh38 5 150896741 150896741 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.546A>G p.= p.P182P ENST00000446148 7/7 200 116 84 290 289 1 strelka-varscan-mutect ZNF300,synonymous_variant,p.=,ENST00000446148,NM_001172831.1;ZNF300,synonymous_variant,p.=,ENST00000274599,NM_052860.2;ZNF300,synonymous_variant,p.=,ENST00000394226,;ZNF300,synonymous_variant,p.=,ENST00000418587,NM_001172832.1;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,; C ENST00000446148 Transcript synonymous_variant 974/3323 546/1863 182/620 P ccA/ccG 1 -1 ZNF300 HGNC HGNC:13091 protein_coding YES CCDS54940.1 ENSP00000397178 Q96RE9 UPI0001AE74AD NM_001172831.1 7/7 hmmpanther:PTHR24377:SF320,hmmpanther:PTHR24377 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 150896741 150896741 T C 1 0 0 0 0 0 0 0 1 18406 1683 59 5 5 ZNF300 5 150896741 Silent SNP T C3N-00560_T 886 150896741 30641518 386 17075 FAT2 0 . GRCh38 5 151565686 151565686 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.3246C>T p.= p.I1082I ENST00000261800 1/23 38 20 18 35 35 0 strelka-varscan-mutect FAT2,synonymous_variant,p.=,ENST00000261800,NM_001447.2; A ENST00000261800 Transcript synonymous_variant 3259/14534 3246/13050 1082/4349 I atC/atT 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 1/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 56 151565686 151565686 G A 1 0 0 0 0 0 0 0 1 5550 1280 45 3 3 FAT2 5 151565686 Silent SNP G C3N-00560_T 668945 151565686 29972573 387 17076 FAM71B 0 . GRCh38 5 157162899 157162899 + Nonsense_Mutation SNP T T A rs746344491 C3N-00560_T C3N-00560_N T T c.1366A>T p.Arg456Ter p.R456* ENST00000302938 2/2 212 103 109 284 284 0 strelka-varscan-mutect FAM71B,stop_gained,p.Arg456Ter,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; A ENST00000302938 Transcript stop_gained 1462/2515 1366/1818 456/605 R/* Aga/Tga rs746344491 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 HIGH 1 SNV 1 1 PASS rs746344491 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 157162899 157162899 T A 1 0 0 0 0 0 1 0 0 5472 1559 54 4 4 FAM71B 5 157162899 Nonsense_Mutation SNP T C3N-00560_T 5597213 157162899 24375360 388 17077 UBLCP1 0 . GRCh38 5 159269009 159269022 + Frame_Shift_Del DEL CTCAAGACCCTTAC CTCAAGACCCTTAC - novel C3N-00560_T C3N-00560_N CTCAAGACCCTTAC CTCAAGACCCTTAC c.94_107delCTCAAGACCCTTAC p.Leu32ArgfsTer15 p.L32Rfs*15 ENST00000296786 2/11 174 118 56 239 239 0 sindel-varindel-pindel UBLCP1,frameshift_variant,p.Leu32ArgfsTer15,ENST00000296786,NM_145049.3; - ENST00000296786 Transcript frameshift_variant 420-433/2392 94-107/957 32-36/318 LKTLT/X CTCAAGACCCTTACa/a 1 1 UBLCP1 HGNC HGNC:28110 protein_coding YES CCDS4345.1 ENSP00000296786 Q8WVY7 UPI0000071EAA NM_145049.3 2/11 PROSITE_profiles:PS50053,hmmpanther:PTHR32054,Pfam_domain:PF00240,Gene3D:3.10.20.90,SMART_domains:SM00213,Superfamily_domains:SSF54236 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 159269009 159269009 CTCAAGACCCTTAC - 1 0 1 0 1 0 0 0 0 17415 913 32 0 0 UBLCP1 5 159269009 Frame_Shift_Del DEL CTCAAGACCCTTAC C3N-00560_T 2106110 159269009 22269250 389 17078 IL12B 0 . GRCh38 5 159323053 159323053 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.364+1G>T p.X122_splice ENST00000231228 149 88 61 244 243 1 strelka-varscan-mutect IL12B,splice_donor_variant,,ENST00000231228,NM_002187.2;RNU4ATAC2P,downstream_gene_variant,,ENST00000408674,;AC008697.1,intron_variant,,ENST00000521472,; A ENST00000231228 Transcript splice_donor_variant -/2761 364/987 122/328 1 -1 IL12B HGNC HGNC:5970 protein_coding YES CCDS4346.1 ENSP00000231228 P29460 UPI00000358B7 NM_002187.2 3/7 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 159323053 159323053 C A 1 0 0 0 0 0 0 1 0 7533 521 18 2 2 IL12B 5 159323053 Splice_Site SNP C C3N-00560_T 54044 159323053 22215206 390 17079 GABRB2 0 . GRCh38 5 161294408 161294408 + Missense_Mutation SNP G G C rs770274870 C3N-00560_T C3N-00560_N G G c.1212C>G p.Ile404Met p.I404M ENST00000274547 11/11 76 45 31 114 114 0 strelka-varscan-mutect GABRB2,missense_variant,p.Ile404Met,ENST00000274547,NM_021911.2;GABRB2,missense_variant,p.Ile404Met,ENST00000393959,;GABRB2,missense_variant,p.Ile366Met,ENST00000520240,;GABRB2,missense_variant,p.Ile366Met,ENST00000353437,NM_000813.2;GABRB2,missense_variant,p.Ile303Met,ENST00000517901,;GABRB2,missense_variant,p.Ile206Met,ENST00000517547,; C ENST00000274547 Transcript missense_variant 1430/7409 1212/1539 404/512 I/M atC/atG rs770274870 1 -1 GABRB2 HGNC HGNC:4082 protein_coding YES CCDS4355.1 ENSP00000274547 P47870 UPI000002AA29 NM_021911.2 tolerated(0.09) 11/11 TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112 MODERATE 1 SNV 5 1 PASS rs770274870 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 161294408 161294408 G C 1 0 0 0 0 1 0 0 0 6038 932 33 4 4 GABRB2 5 161294408 Missense_Mutation SNP G C3N-00560_T 1971355 161294408 20243851 391 17080 STC2 0 . GRCh38 5 173317910 173317910 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.846G>A p.= p.Q282Q ENST00000265087 4/4 63 34 29 51 51 0 strelka-varscan-mutect STC2,synonymous_variant,p.=,ENST00000265087,NM_003714.2;STC2,downstream_gene_variant,,ENST00000520593,; T ENST00000265087 Transcript synonymous_variant 2156/5353 846/909 282/302 Q caG/caA 1 -1 STC2 HGNC HGNC:11374 protein_coding YES CCDS4388.1 ENSP00000265087 O76061 Q6FHC9 UPI00001360B8 NM_003714.2 4/4 hmmpanther:PTHR11245:SF2,hmmpanther:PTHR11245 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 173317910 173317910 C T 1 0 0 0 0 0 0 0 1 15652 680 24 3 3 STC2 5 173317910 Silent SNP C C3N-00560_T 12023502 173317910 8220349 392 17081 DDX41 0 . GRCh38 5 177514948 177514948 + Missense_Mutation SNP C C G rs746011550 C3N-00560_T C3N-00560_N C C c.766G>C p.Glu256Gln p.E256Q ENST00000507955 8/17 143 106 37 179 179 0 strelka-varscan-mutect DDX41,missense_variant,p.Glu256Gln,ENST00000507955,NM_016222.2;DDX41,missense_variant,p.Glu274Gln,ENST00000330503,;FAM193B,downstream_gene_variant,,ENST00000514747,NM_001190946.1;DOK3,upstream_gene_variant,,ENST00000312943,NM_001144875.1;FAM193B,downstream_gene_variant,,ENST00000524677,;DOK3,upstream_gene_variant,,ENST00000377112,NM_001144876.1;DOK3,upstream_gene_variant,,ENST00000501403,NM_001308236.1,NM_001308235.1;DDX41,downstream_gene_variant,,ENST00000629036,;DOK3,upstream_gene_variant,,ENST00000509310,;DOK3,upstream_gene_variant,,ENST00000510389,;DDX41,downstream_gene_variant,,ENST00000625286,;DDX41,downstream_gene_variant,,ENST00000506965,;FAM193B,downstream_gene_variant,,ENST00000504130,;DDX41,missense_variant,p.Glu82Gln,ENST00000508279,;DDX41,3_prime_UTR_variant,,ENST00000504781,;DDX41,non_coding_transcript_exon_variant,,ENST00000505081,;DDX41,non_coding_transcript_exon_variant,,ENST00000503078,;DDX41,non_coding_transcript_exon_variant,,ENST00000507900,;DDX41,non_coding_transcript_exon_variant,,ENST00000512431,;DDX41,non_coding_transcript_exon_variant,,ENST00000511040,;DDX41,non_coding_transcript_exon_variant,,ENST00000513562,;FAM193B,downstream_gene_variant,,ENST00000506955,;FAM193B,downstream_gene_variant,,ENST00000510479,;FAM193B,downstream_gene_variant,,ENST00000510163,;FAM193B,downstream_gene_variant,,ENST00000505569,;DDX41,downstream_gene_variant,,ENST00000515562,;DOK3,upstream_gene_variant,,ENST00000502380,;DDX41,downstream_gene_variant,,ENST00000509576,;DDX41,upstream_gene_variant,,ENST00000504807,;DDX41,upstream_gene_variant,,ENST00000512334,;FAM193B,downstream_gene_variant,,ENST00000513282,;DDX41,upstream_gene_variant,,ENST00000512027,;FAM193B,downstream_gene_variant,,ENST00000506879,;DDX41,downstream_gene_variant,,ENST00000510171,; G ENST00000507955 Transcript missense_variant 1290/2607 766/1869 256/622 E/Q Gag/Cag rs746011550,COSM4558399 1 -1 DDX41 HGNC HGNC:18674 protein_coding YES CCDS4427.1 ENSP00000422753 Q9UJV9 UPI0000125164 NM_016222.2 deleterious(0.01) 8/17 PROSITE_profiles:PS51192,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF20,Gene3D:3.40.50.300,Pfam_domain:PF00270,SMART_domains:SM00487,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746011550 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 177514948 177514948 C G 1 0 0 0 0 1 0 0 0 4164 893 31 4 4 DDX41 5 177514948 Missense_Mutation SNP C C3N-00560_T 4197038 177514948 4023311 393 17082 ZNF354A 0 . GRCh38 5 178712949 178712949 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.929G>T p.Arg310Met p.R310M ENST00000335815 5/5 169 96 73 263 263 0 strelka-varscan-mutect ZNF354A,missense_variant,p.Arg310Met,ENST00000335815,NM_001324339.1,NM_005649.2;ZNF354A,downstream_gene_variant,,ENST00000520331,; A ENST00000335815 Transcript missense_variant 1127/2484 929/1818 310/605 R/M aGg/aTg 1 -1 ZNF354A HGNC HGNC:11628 protein_coding YES CCDS4438.1 ENSP00000337122 O60765 V9HWI2 UPI000013EB5E NM_001324339.1,NM_005649.2 tolerated(0.17) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF146,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 178712949 178712949 C A 1 0 0 0 0 1 0 0 0 18436 681 24 2 2 ZNF354A 5 178712949 Missense_Mutation SNP C C3N-00560_T 1198001 178712949 2825310 394 17083 RUFY1 0 . GRCh38 5 179591649 179591649 + Missense_Mutation SNP G G C rs762453287 C3N-00560_T C3N-00560_N G G c.1153G>C p.Glu385Gln p.E385Q ENST00000319449 10/18 152 114 38 174 174 0 strelka-varscan-mutect RUFY1,missense_variant,p.Glu385Gln,ENST00000319449,NM_025158.4;RUFY1,missense_variant,p.Glu277Gln,ENST00000437570,NM_001040451.2;RUFY1,missense_variant,p.Glu277Gln,ENST00000393438,NM_001040452.2;RUFY1,missense_variant,p.Glu63Gln,ENST00000502434,;RUFY1,missense_variant,p.Glu174Gln,ENST00000508609,;RP11-1379J22.2,downstream_gene_variant,,ENST00000500262,;RUFY1,downstream_gene_variant,,ENST00000514238,;RUFY1,3_prime_UTR_variant,,ENST00000393448,;RUFY1,non_coding_transcript_exon_variant,,ENST00000509797,;RUFY1,upstream_gene_variant,,ENST00000502531,; C ENST00000319449 Transcript missense_variant 1165/2646 1153/2127 385/708 E/Q Gag/Cag rs762453287 1 1 RUFY1 HGNC HGNC:19760 protein_coding YES CCDS4445.2 ENSP00000325594 Q96T51 UPI0000D74C3F NM_025158.4 deleterious(0.01) 10/18 hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF84 MODERATE 1 SNV 1 1 PASS rs762453287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 179591649 179591649 G C 1 0 0 0 0 1 0 0 0 14000 1291 45 4 4 RUFY1 5 179591649 Missense_Mutation SNP G C3N-00560_T 878700 179591649 1946610 395 17084 FOXF2 0 . GRCh38 6 1390539 1390539 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.592C>T p.Arg198Trp p.R198W ENST00000259806 1/2 318 114 204 223 223 0 strelka-varscan-mutect FOXF2,missense_variant,p.Arg198Trp,ENST00000259806,NM_001452.1;MIR6720,upstream_gene_variant,,ENST00000611664,; T ENST00000259806 Transcript missense_variant 706/2187 592/1335 198/444 R/W Cgg/Tgg COSM4685354 1 1 FOXF2 HGNC HGNC:3810 protein_coding YES CCDS4472.1 ENSP00000259806 Q12947 UPI000012ADD6 NM_001452.1 deleterious(0) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF224 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 56 1390539 1390539 C T 1 0 0 0 0 1 0 0 0 5868 759 27 1 1 FOXF2 6 1390539 Missense_Mutation SNP C C3N-00560_T 1390539 169415440 396 17085 SERPINB9 0 . GRCh38 6 2896135 2896135 + Missense_Mutation SNP G G T rs769613099 C3N-00560_T C3N-00560_N G G c.224C>A p.Thr75Asn p.T75N ENST00000380698 3/7 268 105 163 205 205 0 strelka-varscan-mutect SERPINB9,missense_variant,p.Thr75Asn,ENST00000380698,NM_004155.5; T ENST00000380698 Transcript missense_variant 314/4118 224/1131 75/376 T/N aCt/aAt rs769613099 1 -1 SERPINB9 HGNC HGNC:8955 protein_coding YES CCDS4478.1 ENSP00000370074 P50453 A0A024QZT4 UPI000000121F NM_004155.5 tolerated(0.16) 3/7 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF67,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs769613099 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 2896135 2896135 G T 1 0 0 0 0 1 0 0 0 14384 1029 36 2 2 SERPINB9 6 2896135 Missense_Mutation SNP G C3N-00560_T 1505596 2896135 167909844 397 17086 F13A1 0 . GRCh38 6 6174637 6174637 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1690G>T p.Val564Phe p.V564F ENST00000264870 12/15 442 153 289 360 360 0 strelka-varscan-mutect F13A1,missense_variant,p.Val564Phe,ENST00000264870,NM_000129.3; A ENST00000264870 Transcript missense_variant 1956/3999 1690/2199 564/732 V/F Gtc/Ttc COSM5171604 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 deleterious(0) 12/15 Gene3D:2.60.40.10,Pfam_domain:PF00927,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF42,Superfamily_domains:SSF49309 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 6174637 6174637 C A 1 0 0 0 0 1 0 0 0 5208 507 18 2 2 F13A1 6 6174637 Missense_Mutation SNP C C3N-00560_T 3278502 6174637 164631342 398 17087 CAGE1 0 . GRCh38 6 7374077 7374077 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.742G>T p.Val248Phe p.V248F ENST00000502583 5/14 166 42 124 125 125 0 strelka-varscan-mutect CAGE1,missense_variant,p.Val248Phe,ENST00000502583,NM_001170692.1;CAGE1,missense_variant,p.Val248Phe,ENST00000379918,;CAGE1,missense_variant,p.Val112Phe,ENST00000296742,NM_205864.2;CAGE1,missense_variant,p.Val248Phe,ENST00000338150,NM_001170693.1;CAGE1,missense_variant,p.Val248Phe,ENST00000512086,;CAGE1,missense_variant,p.Val260Phe,ENST00000512691,;CAGE1,non_coding_transcript_exon_variant,,ENST00000509324,;CAGE1,missense_variant,p.Val248Phe,ENST00000458291,;CAGE1,3_prime_UTR_variant,,ENST00000442019,; A ENST00000502583 Transcript missense_variant 1307/3284 742/2520 248/839 V/F Gtc/Ttc COSM319207,COSM319208 1 -1 CAGE1 HGNC HGNC:21622 protein_coding YES CCDS54965.1 ENSP00000425493 Q8TC20 UPI0001C0B380 NM_001170692.1 tolerated(0.05) 5/14 hmmpanther:PTHR36864,Pfam_domain:PF15066 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 7374077 7374077 C A 1 0 0 0 0 1 0 0 0 2262 565 20 2 2 CAGE1 6 7374077 Missense_Mutation SNP C C3N-00560_T 1199440 7374077 163431902 399 17088 SYCP2L 0 . GRCh38 6 10893875 10893875 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.87A>G p.= p.S29S ENST00000283141 3/30 161 119 42 194 194 0 strelka-varscan-mutect SYCP2L,synonymous_variant,p.=,ENST00000283141,NM_001040274.2;SYCP2L,synonymous_variant,p.=,ENST00000543878,;SYCP2L,synonymous_variant,p.=,ENST00000341041,;RP11-637O19.3,3_prime_UTR_variant,,ENST00000480294,;SYCP2L,upstream_gene_variant,,ENST00000487561,; G ENST00000283141 Transcript synonymous_variant 383/3130 87/2439 29/812 S tcA/tcG 1 1 SYCP2L HGNC HGNC:21537 protein_coding YES CCDS43423.1 ENSP00000283141 Q5T4T6 UPI000022CA18 NM_001040274.2 3/30 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF14 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 10893875 10893875 A G 1 0 0 0 0 0 0 0 1 15823 146 6 5 5 SYCP2L 6 10893875 Silent SNP A C3N-00560_T 3519798 10893875 159912104 400 17089 DEK 0 . GRCh38 6 18257981 18257981 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.329A>T p.His110Leu p.H110L ENST00000397239 4/11 51 31 20 78 78 0 strelka-varscan-mutect DEK,missense_variant,p.His110Leu,ENST00000397239,NM_003472.3;DEK,missense_variant,p.His76Leu,ENST00000244776,NM_001134709.1;DEK,missense_variant,p.His115Leu,ENST00000515742,;DEK,missense_variant,p.His43Leu,ENST00000503715,;DEK,missense_variant,p.His82Leu,ENST00000505224,;DEK,upstream_gene_variant,,ENST00000512145,;DEK,upstream_gene_variant,,ENST00000515770,; A ENST00000397239 Transcript missense_variant 777/3427 329/1128 110/375 H/L cAc/cTc 1 -1 DEK HGNC HGNC:2768 protein_coding YES CCDS34344.1 ENSP00000380414 P35659 UPI0000001C2C NM_003472.3 deleterious(0) 4/11 hmmpanther:PTHR13468 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 18257981 18257981 T A 1 0 0 0 0 1 0 0 0 4229 1696 59 4 4 DEK 6 18257981 Missense_Mutation SNP T C3N-00560_T 7364106 18257981 152547998 401 17090 HIST1H4E 0 . GRCh38 6 26204927 26204927 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.283G>C p.Gly95Arg p.G95R ENST00000615164 1/1 98 41 57 99 99 0 strelka-varscan-mutect HIST1H4E,missense_variant,p.Gly95Arg,ENST00000615164,NM_003545.3;HIST1H2BF,downstream_gene_variant,,ENST00000356530,NM_003522.3;RP1-34B20.4,downstream_gene_variant,,ENST00000405418,; C ENST00000615164 Transcript missense_variant 376/1487 283/312 95/103 G/R Gga/Cga 1 1 HIST1H4E HGNC HGNC:4790 protein_coding YES CCDS4593.1 ENSP00000484789 P62805 B2R4R0 UPI000000003C NM_003545.3 deleterious(0.02) 1/1 hmmpanther:PTHR10484,Gene3D:1.10.20.10,Pfam_domain:PF15511,Superfamily_domains:SSF47113,Prints_domain:PR00623 MODERATE 1 SNV 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 C 3 2 56 26204927 26204927 G C 1 0 0 0 0 1 0 0 0 7057 1233 43 4 4 HIST1H4E 6 26204927 Missense_Mutation SNP G C3N-00560_T 7946946 26204927 144601052 402 17091 ZSCAN23 0 . GRCh38 6 28434607 28434607 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1028G>A p.Ser343Asn p.S343N ENST00000289788 4/4 161 123 38 160 160 0 strelka-varscan-mutect ZSCAN23,missense_variant,p.Ser343Asn,ENST00000289788,NM_001012455.1;ZSCAN23,downstream_gene_variant,,ENST00000486481,;ZSCAN23,3_prime_UTR_variant,,ENST00000481983,; T ENST00000289788 Transcript missense_variant 1174/3126 1028/1170 343/389 S/N aGt/aAt 1 -1 ZSCAN23 HGNC HGNC:21193 protein_coding YES CCDS47393.1 ENSP00000289788 Q3MJ62 UPI000019874A NM_001012455.1 tolerated(0.11) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF76,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 28434607 28434607 C T 1 0 0 0 0 1 0 0 0 18829 565 20 3 3 ZSCAN23 6 28434607 Missense_Mutation SNP C C3N-00560_T 2229680 28434607 142371372 403 17092 OR2B3 0 . GRCh38 6 29087024 29087024 + Silent SNP T T G novel C3N-00560_T C3N-00560_N T T c.225A>C p.= p.T75T ENST00000377173 1/1 271 145 126 292 292 0 strelka-varscan-mutect OR2B3,synonymous_variant,p.=,ENST00000377173,NM_001005226.2; G ENST00000377173 Transcript synonymous_variant 290/1007 225/942 75/313 T acA/acC 1 -1 OR2B3 HGNC HGNC:8238 protein_coding YES CCDS34358.1 ENSP00000366378 O76000 A0A126GV76 UPI0000041DB9 NM_001005226.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF103,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 29087024 29087024 T G 1 0 0 0 0 0 0 0 1 11069 1799 63 5 5 OR2B3 6 29087024 Silent SNP T C3N-00560_T 652417 29087024 141718955 404 17093 OR2J3 0 . GRCh38 6 29111981 29111981 + Missense_Mutation SNP T T G novel C3N-00560_T C3N-00560_N T T c.91T>G p.Phe31Val p.F31V ENST00000377169 1/1 163 145 18 210 210 0 strelka-varscan-mutect OR2J3,missense_variant,p.Phe31Val,ENST00000377169,NM_001005216.3; G ENST00000377169 Transcript missense_variant 91/936 91/936 31/311 F/V Ttt/Gtt 1 1 OR2J3 HGNC HGNC:8261 protein_coding YES CCDS43433.1 ENSP00000366374 O76001 A0A126GWT2 UPI000014073A NM_001005216.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF209,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 29111981 29111981 T G 1 0 0 0 0 1 0 0 0 11082 1609 56 5 5 OR2J3 6 29111981 Missense_Mutation SNP T C3N-00560_T 24957 29111981 141693998 405 17094 OR14J1 0 . GRCh38 6 29307037 29307037 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.348G>T p.Met116Ile p.M116I ENST00000377160 1/1 428 197 231 417 416 1 strelka-varscan-mutect OR14J1,missense_variant,p.Met116Ile,ENST00000377160,NM_030946.1; T ENST00000377160 Transcript missense_variant 348/966 348/966 116/321 M/I atG/atT 1 1 OR14J1 HGNC HGNC:13971 protein_coding YES CCDS34362.1 ENSP00000366365 Q9UGF5 A0A126GW10 UPI0000041CEC NM_030946.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF42,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 29307037 29307037 G T 1 0 0 0 0 1 0 0 0 11025 1377 48 2 2 OR14J1 6 29307037 Missense_Mutation SNP G C3N-00560_T 195056 29307037 141498942 406 17095 OR11A1 0 . GRCh38 6 29427156 29427156 + Silent SNP G G T rs112976090 C3N-00560_T C3N-00560_N G G c.486C>A p.= p.A162A ENST00000377149 5/5 136 58 78 133 133 0 strelka-varscan-mutect OR11A1,synonymous_variant,p.=,ENST00000377149,;OR11A1,synonymous_variant,p.=,ENST00000377148,;OR11A1,synonymous_variant,p.=,ENST00000377147,NM_013937.3;OR5V1,intron_variant,,ENST00000377154,; T ENST00000377149 Transcript synonymous_variant 959/2611 486/948 162/315 A gcC/gcA rs112976090 1 -1 OR11A1 HGNC HGNC:8176 protein_coding YES CCDS34363.1 ENSP00000366354 Q9GZK7 A0A024RCH9 UPI000000DCA8 5/5 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF178,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs112976090 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 29427156 29427156 G T 1 0 0 0 0 0 0 0 1 11000 1219 43 2 2 OR11A1 6 29427156 Silent SNP G C3N-00560_T 120119 29427156 141378823 407 17096 OR2H2 0 . GRCh38 6 29588751 29588751 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.807C>A p.= p.G269G ENST00000383640 1/1 225 114 111 245 245 0 strelka-varscan-mutect OR2H2,synonymous_variant,p.=,ENST00000383640,NM_007160.3;GABBR1,intron_variant,,ENST00000355973,; A ENST00000383640 Transcript synonymous_variant 1297/1584 807/939 269/312 G ggC/ggA 1 1 OR2H2 HGNC HGNC:8253 protein_coding YES CCDS34365.1 ENSP00000373136 O95918 UPI00001404DC NM_007160.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF199,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 29588751 29588751 C A 1 0 0 0 0 0 0 0 1 11080 697 25 2 2 OR2H2 6 29588751 Silent SNP C C3N-00560_T 161595 29588751 141217228 408 17097 GABBR1 0 . GRCh38 6 29604861 29604861 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.2567A>G p.Lys856Arg p.K856R ENST00000377034 21/23 68 26 42 70 70 0 strelka-varscan-mutect GABBR1,missense_variant,p.Lys856Arg,ENST00000377034,NM_001470.2;GABBR1,missense_variant,p.Lys794Arg,ENST00000377016,NM_021904.2;GABBR1,missense_variant,p.Lys739Arg,ENST00000377012,NM_021903.2;GABBR1,missense_variant,p.Lys739Arg,ENST00000355973,;GABBR1,downstream_gene_variant,,ENST00000376977,;GABBR1,splice_region_variant,,ENST00000472823,;GABBR1,splice_region_variant,,ENST00000491829,;GABBR1,splice_region_variant,,ENST00000478931,;GABBR1,downstream_gene_variant,,ENST00000494877,;GABBR1,downstream_gene_variant,,ENST00000473774,;GABBR1,downstream_gene_variant,,ENST00000488334,;GABBR1,downstream_gene_variant,,ENST00000486434,;GABBR1,downstream_gene_variant,,ENST00000489839,; C ENST00000377034 Transcript missense_variant,splice_region_variant 2903/4527 2567/2886 856/961 K/R aAg/aGg 1 -1 GABBR1 HGNC HGNC:4070 protein_coding YES CCDS4663.1 ENSP00000366233 Q9UBS5 UPI000004618A NM_001470.2 deleterious(0) 21/23 PROSITE_profiles:PS50259,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF42,Pfam_domain:PF00003,Prints_domain:PR01176 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 29604861 29604861 T C 1 0 0 0 0 1 0 0 0 6026 1623 56 5 5 GABBR1 6 29604861 Missense_Mutation SNP T C3N-00560_T 16110 29604861 141201118 409 17098 GNL1 0 . GRCh38 6 30552587 30552587 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.979G>T p.Glu327Ter p.E327* ENST00000376621 8/12 103 40 63 127 127 0 strelka-varscan-mutect GNL1,stop_gained,p.Glu327Ter,ENST00000376621,NM_005275.3;PRR3,upstream_gene_variant,,ENST00000376560,NM_025263.3;PRR3,upstream_gene_variant,,ENST00000376557,NM_001077497.2;GNL1,downstream_gene_variant,,ENST00000433809,;PRR3,upstream_gene_variant,,ENST00000498336,;PRR3,upstream_gene_variant,,ENST00000481741,;GNL1,non_coding_transcript_exon_variant,,ENST00000487166,;GNL1,upstream_gene_variant,,ENST00000462708,;GNL1,upstream_gene_variant,,ENST00000464231,;PRR3,upstream_gene_variant,,ENST00000491173,; A ENST00000376621 Transcript stop_gained 1950/7490 979/1824 327/607 E/* Gag/Tag 1 -1 GNL1 HGNC HGNC:4413 protein_coding YES CCDS4680.1 ENSP00000365806 P36915 A0A024RCR2 UPI0000073F2B NM_005275.3 8/12 PROSITE_profiles:PS51721,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 30552587 30552587 C A 1 0 0 0 0 0 1 0 0 6414 864 30 2 2 GNL1 6 30552587 Nonsense_Mutation SNP C C3N-00560_T 947726 30552587 140253392 410 17099 GTF2H4 0 . GRCh38 6 30909057 30909057 + Missense_Mutation SNP G G C rs373085246 C3N-00560_T C3N-00560_N G G c.21G>C p.Arg7Ser p.R7S ENST00000259895 2/14 368 178 190 394 393 1 strelka-varscan-mutect GTF2H4,missense_variant,p.Arg7Ser,ENST00000259895,NM_001517.4;GTF2H4,missense_variant,p.Arg7Ser,ENST00000376316,;GTF2H4,non_coding_transcript_exon_variant,,ENST00000453897,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;GTF2H4,upstream_gene_variant,,ENST00000487746,;GTF2H4,upstream_gene_variant,,ENST00000483318,;GTF2H4,upstream_gene_variant,,ENST00000475845,; C ENST00000259895 Transcript missense_variant 244/1735 21/1389 7/462 R/S agG/agC rs373085246 1 1 GTF2H4 HGNC HGNC:4658 protein_coding YES CCDS34386.1 ENSP00000259895 Q92759 UPI000000D741 NM_001517.4 tolerated_low_confidence(0.46) 2/14 MODERATE 1 SNV 1 1 PASS rs373085246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 30909057 30909057 G C 1 0 0 0 0 1 0 0 0 6746 1223 43 4 4 GTF2H4 6 30909057 Missense_Mutation SNP G C3N-00560_T 356470 30909057 139896922 411 17100 NEU1 0 . GRCh38 6 31860463 31860463 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.774T>A p.Asn258Lys p.N258K ENST00000375631 4/6 490 225 265 457 457 0 strelka-varscan-mutect NEU1,missense_variant,p.Asn258Lys,ENST00000375631,NM_000434.3;SLC44A4,downstream_gene_variant,,ENST00000544672,NM_001178045.1;SLC44A4,downstream_gene_variant,,ENST00000229729,NM_025257.2;SLC44A4,downstream_gene_variant,,ENST00000375562,NM_001178044.1;SLC44A4,downstream_gene_variant,,ENST00000487680,;NEU1,missense_variant,p.Asn258Lys,ENST00000491768,;NEU1,non_coding_transcript_exon_variant,,ENST00000495807,;NEU1,non_coding_transcript_exon_variant,,ENST00000480384,; T ENST00000375631 Transcript missense_variant 904/2045 774/1248 258/415 N/K aaT/aaA 1 -1 NEU1 HGNC HGNC:7758 protein_coding YES CCDS4723.1 ENSP00000364782 Q99519 Q5JQI0 UPI000012FF46 NM_000434.3 tolerated(0.33) 4/6 Gene3D:2.120.10.10,Pfam_domain:PF13088,hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF21,Superfamily_domains:SSF50939 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 31860463 31860463 A T 1 0 0 0 0 1 0 0 0 10376 214 8 4 4 NEU1 6 31860463 Missense_Mutation SNP A C3N-00560_T 951406 31860463 138945516 412 17101 KIF6 0 . GRCh38 6 39586318 39586318 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.933A>T p.= p.G311G ENST00000287152 8/23 190 90 100 175 175 0 strelka-varscan-mutect KIF6,synonymous_variant,p.=,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,synonymous_variant,p.=,ENST00000458470,;KIF6,synonymous_variant,p.=,ENST00000441975,;KIF6,5_prime_UTR_variant,,ENST00000538893,; A ENST00000287152 Transcript synonymous_variant 1028/9082 933/2445 311/814 G ggA/ggT 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 8/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 39586318 39586318 T A 1 0 0 0 0 0 0 0 1 8173 1538 54 4 4 KIF6 6 39586318 Silent SNP T C3N-00560_T 7725855 39586318 131219661 413 17102 UNC5CL 0 . GRCh38 6 41033931 41033931 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.636G>T p.= p.P212P ENST00000244565 3/9 204 73 131 152 152 0 strelka-varscan-mutect UNC5CL,synonymous_variant,p.=,ENST00000244565,NM_173561.2;UNC5CL,synonymous_variant,p.=,ENST00000373164,;UNC5CL,upstream_gene_variant,,ENST00000470102,;OARD1,3_prime_UTR_variant,,ENST00000482853,; A ENST00000244565 Transcript synonymous_variant 753/3136 636/1557 212/518 P ccG/ccT 1 -1 UNC5CL HGNC HGNC:21203 protein_coding YES CCDS4847.1 ENSP00000244565 Q8IV45 H8YHX0 UPI00001609DB NM_173561.2 3/9 hmmpanther:PTHR12582 LOW 1 SNV 1 1 PASS rs939516044 . 0 207 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 A 2 1 56 41033931 41033931 C A 1 0 0 0 0 0 0 0 1 17518 639 23 1 1 UNC5CL 6 41033931 Silent SNP C C3N-00560_T 1447613 41033931 129772048 414 17103 GUCA1A 0 . GRCh38 6 42173707 42173707 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.94G>T p.Gly32Cys p.G32C ENST00000394237 3/6 633 282 351 585 585 0 strelka-varscan-mutect GUCA1A,missense_variant,p.Gly32Cys,ENST00000394237,NM_001319061.1;GUCA1A,missense_variant,p.Gly28Cys,ENST00000541991,;GUCA1A,missense_variant,p.Gly32Cys,ENST00000053469,NM_000409.3;GUCA1A,missense_variant,p.Gly32Cys,ENST00000372958,;GUCA1A,missense_variant,p.Gly32Cys,ENST00000418175,; T ENST00000394237 Transcript missense_variant 1070/2233 94/606 32/201 G/C Ggc/Tgc 1 1 GUCA1A HGNC HGNC:4678 protein_coding YES CCDS4864.1 ENSP00000377784 P43080 UPI0000001C22 NM_001319061.1 deleterious(0.02) 3/6 PROSITE_profiles:PS50222,hmmpanther:PTHR23055:SF13,hmmpanther:PTHR23055,Gene3D:1.10.238.10,Superfamily_domains:SSF47473,Prints_domain:PR00450 MODERATE 1 SNV 2 1 PASS rs1045675208 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 42173707 42173707 G T 1 0 0 0 0 1 0 0 0 6769 1348 47 2 2 GUCA1A 6 42173707 Missense_Mutation SNP G C3N-00560_T 1139776 42173707 128632272 415 17104 TTBK1 0 . GRCh38 6 43283980 43283980 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.3240C>G p.Ser1080Arg p.S1080R ENST00000259750 14/15 139 61 78 126 126 0 strelka-varscan-mutect TTBK1,missense_variant,p.Ser1080Arg,ENST00000259750,NM_032538.1; G ENST00000259750 Transcript missense_variant 3323/6932 3240/3966 1080/1321 S/R agC/agG 1 1 TTBK1 HGNC HGNC:19140 protein_coding YES CCDS34455.1 ENSP00000259750 Q5TCY1 UPI000041512B NM_032538.1 tolerated_low_confidence(0.35) 14/15 MODERATE 1 SNV 1 1 PASS rs1033890642 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 43283980 43283980 C G 1 0 0 0 0 1 0 0 0 17186 709 25 4 4 TTBK1 6 43283980 Missense_Mutation SNP C C3N-00560_T 1110273 43283980 127521999 416 17105 HSP90AB1 0 . GRCh38 6 44253372 44253372 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2059G>T p.Gly687Cys p.G687C ENST00000371554 11/12 132 64 68 132 132 0 strelka-varscan-mutect HSP90AB1,missense_variant,p.Gly687Cys,ENST00000371554,;HSP90AB1,missense_variant,p.Gly687Cys,ENST00000620073,NM_001271970.1;HSP90AB1,missense_variant,p.Gly687Cys,ENST00000353801,NM_001271969.1;HSP90AB1,missense_variant,p.Gly687Cys,ENST00000371646,NM_001271971.1,NM_007355.3,NM_001271972.1;NFKBIE,downstream_gene_variant,,ENST00000275015,NM_004556.2;NFKBIE,downstream_gene_variant,,ENST00000619360,;SLC35B2,downstream_gene_variant,,ENST00000619636,NM_001286510.1,NM_001286512.1;SLC35B2,downstream_gene_variant,,ENST00000393812,NM_178148.3,NM_001286509.1;SLC35B2,downstream_gene_variant,,ENST00000615337,NM_001286511.1;SLC35B2,downstream_gene_variant,,ENST00000538577,NM_001286513.1;SLC35B2,downstream_gene_variant,,ENST00000393810,;SLC35B2,downstream_gene_variant,,ENST00000537814,NM_001286519.1,NM_001286520.1;SLC35B2,downstream_gene_variant,,ENST00000583964,;SLC35B2,downstream_gene_variant,,ENST00000495706,; T ENST00000371554 Transcript missense_variant 2273/2674 2059/2175 687/724 G/C Ggt/Tgt 1 1 HSP90AB1 HGNC HGNC:5258 protein_coding YES CCDS4909.1 ENSP00000360609 P08238 A0A024RD80 UPI00001411EF deleterious(0.02) 11/12 Pfam_domain:PF00183,PIRSF_domain:PIRSF002583,hmmpanther:PTHR11528 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 44253372 44253372 G T 1 0 0 0 0 1 0 0 0 7298 1000 35 2 2 HSP90AB1 6 44253372 Missense_Mutation SNP G C3N-00560_T 969392 44253372 126552607 417 17106 CDC5L 0 . GRCh38 6 44403972 44403972 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.703C>G p.Leu235Val p.L235V ENST00000371477 6/16 219 100 119 256 256 0 strelka-varscan-mutect CDC5L,missense_variant,p.Leu235Val,ENST00000371477,NM_001253.3; G ENST00000371477 Transcript missense_variant 1002/6423 703/2409 235/802 L/V Ctt/Gtt COSM3830651 1 1 CDC5L HGNC HGNC:1743 protein_coding YES CCDS4912.1 ENSP00000360532 Q99459 UPI000006EE42 NM_001253.3 tolerated(0.55) 6/16 Coiled-coils_(Ncoils):Coil 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 44403972 44403972 C G 1 0 0 0 0 1 0 0 0 2785 913 32 4 4 CDC5L 6 44403972 Missense_Mutation SNP C C3N-00560_T 150600 44403972 126402007 418 17107 TFAP2B 0 . GRCh38 6 50823466 50823466 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.141C>A p.= p.S47S ENST00000393655 2/7 222 101 121 231 231 0 strelka-varscan-mutect TFAP2B,synonymous_variant,p.=,ENST00000393655,NM_003221.3;TFAP2B,synonymous_variant,p.=,ENST00000344788,;TFAP2B,non_coding_transcript_exon_variant,,ENST00000489228,; A ENST00000393655 Transcript synonymous_variant 310/5773 141/1383 47/460 S tcC/tcA 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 2/7 Prints_domain:PR01750,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 50823466 50823466 C A 1 0 0 0 0 0 0 0 1 16221 610 22 2 2 TFAP2B 6 50823466 Silent SNP C C3N-00560_T 6419494 50823466 119982513 419 17108 GSTA5 0 . GRCh38 6 52834160 52834160 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.395A>T p.Tyr132Phe p.Y132F ENST00000370989 4/6 237 122 115 224 224 0 strelka-varscan-mutect GSTA5,missense_variant,p.Tyr132Phe,ENST00000370989,;GSTA5,missense_variant,p.Tyr132Phe,ENST00000284562,NM_153699.1;GSTA5,non_coding_transcript_exon_variant,,ENST00000475052,; A ENST00000370989 Transcript missense_variant 425/892 395/669 132/222 Y/F tAc/tTc 1 -1 GSTA5 HGNC HGNC:19662 protein_coding YES CCDS4946.1 ENSP00000360028 Q7RTV2 UPI0000049038 tolerated(0.12) 4/6 Gene3D:1.20.1050.10,Pfam_domain:PF14497,PROSITE_profiles:PS50405,hmmpanther:PTHR11571,hmmpanther:PTHR11571:SF131,Superfamily_domains:SSF47616 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 52834160 52834160 T A 1 0 0 0 0 1 0 0 0 6718 1638 57 4 4 GSTA5 6 52834160 Missense_Mutation SNP T C3N-00560_T 2010694 52834160 117971819 420 17109 GSTA5 0 . GRCh38 6 52836323 52836323 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.185G>T p.Gly62Val p.G62V ENST00000370989 3/6 216 127 89 237 237 0 strelka-varscan-mutect GSTA5,missense_variant,p.Gly62Val,ENST00000370989,;GSTA5,missense_variant,p.Gly62Val,ENST00000284562,NM_153699.1;GSTA5,intron_variant,,ENST00000475052,; A ENST00000370989 Transcript missense_variant 215/892 185/669 62/222 G/V gGg/gTg 1 -1 GSTA5 HGNC HGNC:19662 protein_coding YES CCDS4946.1 ENSP00000360028 Q7RTV2 UPI0000049038 deleterious(0) 3/6 Gene3D:3.40.30.10,Pfam_domain:PF02798,PROSITE_profiles:PS50404,hmmpanther:PTHR11571,hmmpanther:PTHR11571:SF131,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 52836323 52836323 C A 1 0 0 0 0 1 0 0 0 6718 623 22 2 2 GSTA5 6 52836323 Missense_Mutation SNP C C3N-00560_T 2163 52836323 117969656 421 17110 TINAG 0 . GRCh38 6 54326889 54326889 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.597C>A p.= p.P199P ENST00000259782 4/11 141 57 84 159 159 0 strelka-varscan-mutect TINAG,synonymous_variant,p.=,ENST00000259782,NM_014464.3;TINAG,synonymous_variant,p.=,ENST00000370869,;TINAG,synonymous_variant,p.=,ENST00000370864,;TINAG,downstream_gene_variant,,ENST00000486436,; A ENST00000259782 Transcript synonymous_variant 693/1754 597/1431 199/476 P ccC/ccA 1 1 TINAG HGNC HGNC:14599 protein_coding YES CCDS4955.1 ENSP00000259782 Q9UJW2 UPI000013D078 NM_014464.3 4/11 hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF274,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS rs1184886174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 54326889 54326889 C A 1 0 0 0 0 0 0 0 1 16362 581 21 2 2 TINAG 6 54326889 Silent SNP C C3N-00560_T 1490566 54326889 116479090 422 17111 EYS 0 . GRCh38 6 64388800 64388801 + Frame_Shift_Ins INS - - T novel C3N-00560_T C3N-00560_N - - c.5967dupA p.Gly1990ArgfsTer56 p.G1990Rfs*56 ENST00000370621 29/44 148 69 79 172 172 0 sindel-varindel-pindel EYS,frameshift_variant,p.Gly1990ArgfsTer56,ENST00000503581,NM_001142800.1;EYS,frameshift_variant,p.Gly1990ArgfsTer56,ENST00000370621,NM_001292009.1;RP11-349P19.1,intron_variant,,ENST00000424274,; T ENST00000370621 Transcript frameshift_variant 6494-6495/10485 5967-5968/9498 1989-1990/3165 -/X -/A 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 29/44 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 56 64388800 64388800 - T 1 0 1 1 0 0 0 0 0 5200 681 24 0 0 EYS 6 64388800 Frame_Shift_Ins INS - C3N-00560_T 10061911 64388800 106417179 423 17112 EYS 0 . GRCh38 6 64591415 64591415 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4452G>T p.Trp1484Cys p.W1484C ENST00000370621 26/44 353 170 183 364 364 0 strelka-varscan-mutect EYS,missense_variant,p.Trp1484Cys,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Trp1484Cys,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; A ENST00000370621 Transcript missense_variant 4979/10485 4452/9498 1484/3165 W/C tgG/tgT 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0.05) 26/44 MODERATE 1 SNV 1 1 PASS rs1428994453 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 64591415 64591415 C A 1 0 0 0 0 1 0 0 0 5200 856 30 2 2 EYS 6 64591415 Missense_Mutation SNP C C3N-00560_T 202615 64591415 106214564 424 17113 ADGRB3 0 . GRCh38 6 69327826 69327826 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2972C>A p.Pro991Gln p.P991Q ENST00000370598 22/32 134 61 73 150 149 1 strelka-varscan-mutect ADGRB3,missense_variant,p.Pro991Gln,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Pro991Gln,ENST00000546190,;ADGRB3,missense_variant,p.Pro197Gln,ENST00000238918,;ADGRB3,downstream_gene_variant,,ENST00000603207,; A ENST00000370598 Transcript missense_variant 3793/6010 2972/4569 991/1522 P/Q cCa/cAa 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 deleterious(0.02) 22/32 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF00002,Prints_domain:PR00249 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 69327826 69327826 C A 1 0 0 0 0 1 0 0 0 357 594 21 2 2 ADGRB3 6 69327826 Missense_Mutation SNP C C3N-00560_T 4736411 69327826 101478153 425 17114 RIMS1 0 . GRCh38 6 72258229 72258229 + Missense_Mutation SNP G G T rs763404266 C3N-00560_T C3N-00560_N G G c.2875G>T p.Gly959Cys p.G959C ENST00000521978 17/34 154 68 86 162 162 0 strelka-varscan-mutect RIMS1,missense_variant,p.Gly959Cys,ENST00000264839,;RIMS1,missense_variant,p.Gly959Cys,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Gly959Cys,ENST00000491071,;RIMS1,missense_variant,p.Gly958Cys,ENST00000520567,;RIMS1,missense_variant,p.Gly958Cys,ENST00000517960,;RIMS1,missense_variant,p.Gly959Cys,ENST00000518273,;RIMS1,missense_variant,p.Gly958Cys,ENST00000522291,;RIMS1,missense_variant,p.Gly432Cys,ENST00000401910,NM_001168407.1;RIMS1,missense_variant,p.Gly533Cys,ENST00000517433,;RIMS1,missense_variant,p.Gly433Cys,ENST00000523963,NM_001168408.1;RIMS1,missense_variant,p.Gly418Cys,ENST00000517827,NM_001168410.1;RIMS1,missense_variant,p.Gly352Cys,ENST00000425662,NM_001168409.1;RIMS1,missense_variant,p.Gly352Cys,ENST00000453976,;RIMS1,missense_variant,p.Gly50Cys,ENST00000522211,;RIMS1,missense_variant,p.Gly184Cys,ENST00000370420,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,;RIMS1,non_coding_transcript_exon_variant,,ENST00000524197,;RIMS1,upstream_gene_variant,,ENST00000463023,; T ENST00000521978 Transcript missense_variant 2875/5079 2875/5079 959/1692 G/C Ggc/Tgc rs763404266 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 deleterious_low_confidence(0.03) 17/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS rs763404266 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 72258229 72258229 G T 1 0 0 0 0 1 0 0 0 13542 1116 39 1 1 RIMS1 6 72258229 Missense_Mutation SNP G C3N-00560_T 2930403 72258229 98547750 426 17115 CD109 0 . GRCh38 6 73809991 73809991 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3363G>T p.Met1121Ile p.M1121I ENST00000287097 27/33 250 116 134 254 254 0 strelka-varscan-mutect CD109,missense_variant,p.Met1121Ile,ENST00000437994,NM_001159587.2;CD109,missense_variant,p.Met1044Ile,ENST00000422508,NM_001159588.2;CD109,missense_variant,p.Met1121Ile,ENST00000287097,NM_133493.4; T ENST00000287097 Transcript missense_variant 3475/9130 3363/4338 1121/1445 M/I atG/atT 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 tolerated(0.32) 27/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80,Gene3D:1.50.10.20,Pfam_domain:PF07678,Superfamily_domains:SSF48239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 73809991 73809991 G T 1 0 0 0 0 1 0 0 0 2666 1319 46 2 2 CD109 6 73809991 Missense_Mutation SNP G C3N-00560_T 1551762 73809991 96995988 427 17116 CD109 0 . GRCh38 6 73823486 73823486 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.4191T>C p.= p.S1397S ENST00000287097 33/33 98 44 54 98 98 0 strelka-varscan-mutect CD109,synonymous_variant,p.=,ENST00000437994,NM_001159587.2;CD109,synonymous_variant,p.=,ENST00000422508,NM_001159588.2;CD109,synonymous_variant,p.=,ENST00000287097,NM_133493.4; C ENST00000287097 Transcript synonymous_variant 4303/9130 4191/4338 1397/1445 S tcT/tcC 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 33/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80,Gene3D:1ayoA00,Superfamily_domains:SSF49410 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 73823486 73823486 T C 1 0 0 0 0 0 0 0 1 2666 1567 55 5 5 CD109 6 73823486 Silent SNP T C3N-00560_T 13495 73823486 96982493 428 17117 COL12A1 0 . GRCh38 6 75130851 75130851 + Splice_Site SNP C C A C3N-00560_T C3N-00560_N C C c.6067+1G>T p.X2023_splice ENST00000322507 135 51 84 118 117 1 strelka-varscan-mutect COL12A1,splice_donor_variant,,ENST00000322507,NM_004370.5;COL12A1,splice_donor_variant,,ENST00000615798,;COL12A1,splice_donor_variant,,ENST00000483888,;COL12A1,splice_donor_variant,,ENST00000416123,;COL12A1,splice_donor_variant,,ENST00000345356,NM_080645.2;COL12A1,downstream_gene_variant,,ENST00000419671,; A ENST00000322507 Transcript splice_donor_variant -/11723 6067/9192 2023/3063 COSM3411283 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 36/65 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 75130851 75130851 C A 1 0 0 0 0 0 0 1 0 3457 550 19 1 1 COL12A1 6 75130851 Splice_Site SNP C C3N-00560_T 1307365 75130851 95675128 429 17118 TBX18 0 . GRCh38 6 84737368 84737368 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1141G>C p.Gly381Arg p.G381R ENST00000369663 8/8 21 8 13 36 36 0 strelka-mutect TBX18,missense_variant,p.Gly381Arg,ENST00000369663,NM_001080508.2;TBX18,intron_variant,,ENST00000606784,;TBX18,downstream_gene_variant,,ENST00000606521,;TBX18,downstream_gene_variant,,ENST00000607343,; G ENST00000369663 Transcript missense_variant 1479/6245 1141/1824 381/607 G/R Ggc/Cgc 1 -1 TBX18 HGNC HGNC:11595 protein_coding YES CCDS34495.1 ENSP00000358677 O95935 UPI00001A3A8A NM_001080508.2 deleterious(0.01) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF20 MODERATE 1 SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 84737368 84737368 C G 1 0 0 0 0 1 0 0 0 16058 594 21 4 4 TBX18 6 84737368 Missense_Mutation SNP C C3N-00560_T 9606517 84737368 86068611 430 17119 ZNF292 0 . GRCh38 6 87260956 87260956 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.7327G>T p.Gly2443Cys p.G2443C ENST00000369577 8/8 138 73 65 207 206 1 strelka-varscan-mutect ZNF292,missense_variant,p.Gly2443Cys,ENST00000369577,NM_015021.1;ZNF292,missense_variant,p.Gly2438Cys,ENST00000339907,;ZNF292,downstream_gene_variant,,ENST00000496806,; T ENST00000369577 Transcript missense_variant 7370/10610 7327/8172 2443/2723 G/C Ggt/Tgt 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 deleterious(0.05) 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 87260956 87260956 G T 1 0 0 0 0 1 0 0 0 18402 1000 35 2 2 ZNF292 6 87260956 Missense_Mutation SNP G C3N-00560_T 2523588 87260956 83545023 431 17120 CNR1 0 . GRCh38 6 88144114 88144114 + Silent SNP C C A C3N-00560_T C3N-00560_N C C c.1161G>T p.= p.L387L ENST00000369501 2/2 246 110 136 253 253 0 strelka-varscan-mutect CNR1,synonymous_variant,p.=,ENST00000369501,NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1;CNR1,synonymous_variant,p.=,ENST00000369499,;CNR1,synonymous_variant,p.=,ENST00000549890,;CNR1,synonymous_variant,p.=,ENST00000428600,;CNR1,synonymous_variant,p.=,ENST00000468898,NM_033181.3;CNR1,3_prime_UTR_variant,,ENST00000362094,;CNR1,downstream_gene_variant,,ENST00000551417,; A ENST00000369501 Transcript synonymous_variant 1781/6031 1161/1419 387/472 L ctG/ctT COSM743917 1 -1 CNR1 HGNC HGNC:2159 protein_coding YES CCDS5015.1 ENSP00000358513 P21554 S5TLS4 UPI00000008AA NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF47,hmmpanther:PTHR22750,Pfam_domain:PF00001,Gene3D:1.20.1070.10,PIRSF_domain:PIRSF037995,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 88144114 88144114 C A 1 0 0 0 0 0 0 0 1 3413 697 25 2 2 CNR1 6 88144114 Silent SNP C C3N-00560_T 883158 88144114 82661865 432 17121 BEND3 0 . GRCh38 6 107069868 107069868 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1323G>C p.Gln441His p.Q441H ENST00000429433 5/5 183 130 53 198 198 0 strelka-varscan-mutect BEND3,missense_variant,p.Gln441His,ENST00000429433,NM_001080450.2;BEND3,missense_variant,p.Gln441His,ENST00000369042,; G ENST00000429433 Transcript missense_variant 1973/6654 1323/2487 441/828 Q/H caG/caC 1 -1 BEND3 HGNC HGNC:23040 protein_coding YES CCDS34507.1 ENSP00000411268 Q5T5X7 UPI00001D80D7 NM_001080450.2 tolerated(0.66) 5/5 Pfam_domain:PF10523,PROSITE_profiles:PS51457,hmmpanther:PTHR28665,SMART_domains:SM01025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 107069868 107069868 C G 1 0 0 0 0 1 0 0 0 1547 680 24 4 4 BEND3 6 107069868 Missense_Mutation SNP C C3N-00560_T 18925754 107069868 63736111 433 17122 SOBP 0 . GRCh38 6 107634057 107634057 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1213C>A p.Gln405Lys p.Q405K ENST00000317357 6/7 80 41 39 97 97 0 strelka-varscan-mutect SOBP,missense_variant,p.Gln405Lys,ENST00000317357,NM_018013.3;SOBP,upstream_gene_variant,,ENST00000494935,; A ENST00000317357 Transcript missense_variant 1872/5245 1213/2622 405/873 Q/K Cag/Aag 1 1 SOBP HGNC HGNC:29256 protein_coding YES CCDS43488.1 ENSP00000318900 A7XYQ1 UPI0000E6A8ED NM_018013.3 deleterious(0.02) 6/7 hmmpanther:PTHR23186:SF2,hmmpanther:PTHR23186,Pfam_domain:PF15279 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 107634057 107634057 C A 1 0 0 0 0 1 0 0 0 15233 711 25 2 2 SOBP 6 107634057 Missense_Mutation SNP C C3N-00560_T 564189 107634057 63171922 434 17123 LAMA4 0 . GRCh38 6 112120439 112120439 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.4509C>A p.= p.S1503S ENST00000230538 33/39 182 90 92 238 238 0 strelka-varscan-mutect LAMA4,synonymous_variant,p.=,ENST00000230538,NM_001105206.2;LAMA4,synonymous_variant,p.=,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,synonymous_variant,p.=,ENST00000389463,;LAMA4,synonymous_variant,p.=,ENST00000424408,;LAMA4,downstream_gene_variant,,ENST00000604740,;LAMA4,downstream_gene_variant,,ENST00000521693,; T ENST00000230538 Transcript synonymous_variant 4907/6547 4509/5472 1503/1823 S tcC/tcA 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 33/39 PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 112120439 112120439 G T 1 0 0 0 0 0 0 0 1 8512 987 35 2 2 LAMA4 6 112120439 Silent SNP G C3N-00560_T 4486382 112120439 58685540 435 17124 RFPL4B 0 . GRCh38 6 112350476 112350476 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.768C>A p.= p.G256G ENST00000441065 3/3 54 28 26 59 59 0 strelka-varscan-mutect RFPL4B,synonymous_variant,p.=,ENST00000441065,NM_001013734.2;RP11-506B6.7,downstream_gene_variant,,ENST00000585611,;RP11-506B6.7,downstream_gene_variant,,ENST00000587816,;RP11-506B6.7,downstream_gene_variant,,ENST00000590673,; A ENST00000441065 Transcript synonymous_variant 1080/1900 768/792 256/263 G ggC/ggA 1 1 RFPL4B HGNC HGNC:33264 protein_coding YES CCDS34515.1 ENSP00000423391 Q6ZWI9 UPI00001972F0 NM_001013734.2 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF223,Superfamily_domains:SSF49899 LOW 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 112350476 112350476 C A 1 0 0 0 0 0 0 0 1 13430 697 25 2 2 RFPL4B 6 112350476 Silent SNP C C3N-00560_T 230037 112350476 58455503 436 17125 GPRC6A 0 . GRCh38 6 116792487 116792487 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.2436T>A p.= p.A812A ENST00000310357 6/6 108 48 60 164 164 0 strelka-varscan-mutect GPRC6A,synonymous_variant,p.=,ENST00000310357,NM_148963.3;GPRC6A,synonymous_variant,p.=,ENST00000368549,NM_001286355.1;GPRC6A,synonymous_variant,p.=,ENST00000530250,NM_001286354.1; T ENST00000310357 Transcript synonymous_variant 2458/2860 2436/2781 812/926 A gcT/gcA 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 6/6 PROSITE_profiles:PS50259,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF00003 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 116792487 116792487 A T 1 0 0 0 0 0 0 0 1 6607 175 7 4 4 GPRC6A 6 116792487 Silent SNP A C3N-00560_T 4442011 116792487 54013492 437 17126 GPRC6A 0 . GRCh38 6 116806879 116806879 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.826G>T p.Val276Leu p.V276L ENST00000310357 3/6 150 73 77 184 184 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Val276Leu,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Val276Leu,ENST00000368549,NM_001286355.1;GPRC6A,intron_variant,,ENST00000530250,NM_001286354.1; A ENST00000310357 Transcript missense_variant 848/2860 826/2781 276/926 V/L Gta/Tta 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated(0.18) 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 116806879 116806879 C A 1 0 0 0 0 1 0 0 0 6607 507 18 2 2 GPRC6A 6 116806879 Missense_Mutation SNP C C3N-00560_T 14392 116806879 53999100 438 17127 LAMA2 0 . GRCh38 6 129291634 129291634 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2770G>T p.Gly924Cys p.G924C ENST00000421865 20/65 414 200 214 451 451 0 strelka-varscan-mutect LAMA2,missense_variant,p.Gly924Cys,ENST00000618192,;LAMA2,missense_variant,p.Gly924Cys,ENST00000617695,;LAMA2,missense_variant,p.Gly924Cys,ENST00000421865,NM_001079823.1,NM_000426.3; T ENST00000421865 Transcript missense_variant 2819/9640 2770/9369 924/3122 G/C Ggc/Tgc 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 deleterious(0) 20/65 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 129291634 129291634 G T 1 0 0 0 0 1 0 0 0 8510 1348 47 2 2 LAMA2 6 129291634 Missense_Mutation SNP G C3N-00560_T 12484755 129291634 41514345 439 17128 ENPP1 0 . GRCh38 6 131879935 131879935 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2001G>T p.Lys667Asn p.K667N ENST00000360971 20/25 217 108 109 274 273 1 strelka-varscan-mutect ENPP1,missense_variant,p.Lys667Asn,ENST00000360971,NM_006208.2;ENPP1,3_prime_UTR_variant,,ENST00000513998,;ENPP1,downstream_gene_variant,,ENST00000459624,; T ENST00000360971 Transcript missense_variant 2021/7442 2001/2778 667/925 K/N aaG/aaT 1 1 ENPP1 HGNC HGNC:3356 protein_coding YES CCDS5150.2 ENSP00000354238 P22413 UPI00001303F0 NM_006208.2 tolerated(0.2) 20/25 Gene3D:1g8tA00,hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF77 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 131879935 131879935 G T 1 0 0 0 0 1 0 0 0 4974 991 35 2 2 ENPP1 6 131879935 Missense_Mutation SNP G C3N-00560_T 2588301 131879935 38926044 440 17129 MOXD1 0 . GRCh38 6 132374755 132374755 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.287G>T p.Arg96Ile p.R96I ENST00000367963 2/12 131 64 67 278 277 1 strelka-varscan-mutect MOXD1,missense_variant,p.Arg96Ile,ENST00000367963,NM_015529.3;MOXD1,missense_variant,p.Arg28Ile,ENST00000336749,; A ENST00000367963 Transcript missense_variant 406/3059 287/1842 96/613 R/I aGa/aTa 1 -1 MOXD1 HGNC HGNC:21063 protein_coding YES CCDS5152.2 ENSP00000356940 Q6UVY6 UPI000003F04F NM_015529.3 tolerated(0.11) 2/12 PROSITE_profiles:PS50836,hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF28,Pfam_domain:PF03351,SMART_domains:SM00664 MODERATE 1 SNV 1 1 PASS rs1275504589 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 132374755 132374755 C A 1 0 0 0 0 1 0 0 0 9682 913 32 2 2 MOXD1 6 132374755 Missense_Mutation SNP C C3N-00560_T 494820 132374755 38431224 441 17130 TXLNB 0 . GRCh38 6 139288648 139288648 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.252G>T p.Arg84Ser p.R84S ENST00000358430 2/10 332 136 196 355 355 0 strelka-varscan-mutect TXLNB,missense_variant,p.Arg84Ser,ENST00000358430,NM_153235.3;RP11-445F6.2,downstream_gene_variant,,ENST00000441249,;RP11-445F6.2,downstream_gene_variant,,ENST00000440518,; A ENST00000358430 Transcript missense_variant 485/4753 252/2055 84/684 R/S agG/agT 1 -1 TXLNB HGNC HGNC:21617 protein_coding YES CCDS34545.1 ENSP00000351206 Q8N3L3 UPI0000072983 NM_153235.3 tolerated(0.33) 2/10 hmmpanther:PTHR16127,hmmpanther:PTHR16127:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 139288648 139288648 C A 1 0 0 0 0 1 0 0 0 17304 622 22 2 2 TXLNB 6 139288648 Missense_Mutation SNP C C3N-00560_T 6913893 139288648 31517331 442 17131 GRM1 0 . GRCh38 6 146029790 146029790 + Silent SNP G G T rs771323107 C3N-00560_T C3N-00560_N G G c.273G>T p.= p.A91A ENST00000361719 2/9 354 164 190 417 417 0 strelka-varscan-mutect GRM1,synonymous_variant,p.=,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,synonymous_variant,p.=,ENST00000361719,;GRM1,synonymous_variant,p.=,ENST00000282753,NM_001278064.1;GRM1,synonymous_variant,p.=,ENST00000355289,NM_001278067.1;GRM1,synonymous_variant,p.=,ENST00000507907,;GRM1,non_coding_transcript_exon_variant,,ENST00000502405,;GRM1,non_coding_transcript_exon_variant,,ENST00000507005,; T ENST00000361719 Transcript synonymous_variant 640/6754 273/3585 91/1194 A gcG/gcT rs771323107 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD 2/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00248 LOW 1 SNV 5 1 PASS rs771323107 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 146029790 146029790 G T 1 0 0 0 0 0 0 0 1 6678 1103 39 1 1 GRM1 6 146029790 Silent SNP G C3N-00560_T 6741142 146029790 24776189 443 17132 ADGB 0 . GRCh38 6 146784677 146784677 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.4095G>C p.Leu1365Phe p.L1365F ENST00000397944 31/36 99 53 46 120 120 0 strelka-varscan-mutect ADGB,missense_variant,p.Leu1365Phe,ENST00000397944,NM_024694.3;ADGB,missense_variant,p.Leu323Phe,ENST00000367490,;ADGB,missense_variant,p.Leu88Phe,ENST00000326916,;ADGB,intron_variant,,ENST00000470716,;ADGB,splice_region_variant,,ENST00000523560,;ADGB,splice_region_variant,,ENST00000480328,;ADGB,3_prime_UTR_variant,,ENST00000493950,; C ENST00000397944 Transcript missense_variant 4171/5325 4095/5004 1365/1667 L/F ttG/ttC 1 1 ADGB HGNC HGNC:21212 protein_coding YES ENSP00000381036 Q8N7X0 UPI000020E382 NM_024694.3 deleterious(0.02) 31/36 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 146784677 146784677 G C 1 0 0 0 0 1 0 0 0 351 1339 47 4 4 ADGB 6 146784677 Missense_Mutation SNP G C3N-00560_T 754887 146784677 24021302 444 17133 AKAP12 0 . GRCh38 6 151350265 151350265 + Missense_Mutation SNP G G C rs774124521 C3N-00560_T C3N-00560_N G G c.1874G>C p.Arg625Pro p.R625P ENST00000402676 4/5 222 113 109 238 238 0 strelka-varscan-mutect AKAP12,missense_variant,p.Arg625Pro,ENST00000402676,NM_005100.3;AKAP12,missense_variant,p.Arg625Pro,ENST00000253332,;AKAP12,missense_variant,p.Arg527Pro,ENST00000354675,NM_144497.2;AKAP12,missense_variant,p.Arg520Pro,ENST00000359755,;AKAP12,downstream_gene_variant,,ENST00000490177,; C ENST00000402676 Transcript missense_variant 2114/8432 1874/5349 625/1782 R/P cGg/cCg rs774124521,COSM1074563 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 deleterious(0) 4/5 hmmpanther:PTHR23209,Pfam_domain:PF03832 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs774124521 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 151350265 151350265 G C 1 0 0 0 0 1 0 0 0 531 1116 39 4 4 AKAP12 6 151350265 Missense_Mutation SNP G C3N-00560_T 4565588 151350265 19455714 445 17134 CCDC170 0 . GRCh38 6 151596403 151596403 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.1536C>A p.= p.A512A ENST00000239374 9/11 278 114 164 304 302 2 strelka-varscan-mutect CCDC170,synonymous_variant,p.=,ENST00000239374,NM_025059.3;CCDC170,non_coding_transcript_exon_variant,,ENST00000537358,; A ENST00000239374 Transcript synonymous_variant 1635/5293 1536/2148 512/715 A gcC/gcA 1 1 CCDC170 HGNC HGNC:21177 protein_coding YES CCDS43515.1 ENSP00000239374 Q8IYT3 UPI000020D0BA NM_025059.3 9/11 hmmpanther:PTHR18863:SF4,hmmpanther:PTHR18863,Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 151596403 151596403 C A 1 0 0 0 0 0 0 0 1 2487 610 22 2 2 CCDC170 6 151596403 Silent SNP C C3N-00560_T 246138 151596403 19209576 446 17135 SYNE1 0 . GRCh38 6 152149595 152149595 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.24524A>T p.Glu8175Val p.E8175V ENST00000367255 136/146 266 131 135 286 286 0 strelka-varscan-mutect SYNE1,missense_variant,p.Glu8175Val,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Glu8104Val,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Glu7770Val,ENST00000341594,;SYNE1,missense_variant,p.Glu1097Val,ENST00000367251,;SYNE1,missense_variant,p.Glu821Val,ENST00000367257,;SYNE1,missense_variant,p.Glu330Val,ENST00000539504,;SYNE1,missense_variant,p.Glu330Val,ENST00000354674,;SYNE1,non_coding_transcript_exon_variant,,ENST00000347037,;SYNE1,non_coding_transcript_exon_variant,,ENST00000460912,;SYNE1,non_coding_transcript_exon_variant,,ENST00000536990,;SYNE1,downstream_gene_variant,,ENST00000476519,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;SYNE1,upstream_gene_variant,,ENST00000478916,;SYNE1,downstream_gene_variant,,ENST00000490866,;SYNE1,upstream_gene_variant,,ENST00000472563,; A ENST00000367255 Transcript missense_variant 25126/27748 24524/26394 8175/8797 E/V gAa/gTa 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 136/146 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 152149595 152149595 T A 1 0 0 0 0 1 0 0 0 15837 1783 62 4 4 SYNE1 6 152149595 Missense_Mutation SNP T C3N-00560_T 553192 152149595 18656384 447 17136 PLG 0 . GRCh38 6 160731806 160731806 + Silent SNP G G A rs775623839 C3N-00560_T C3N-00560_N G G c.1500G>A p.= p.T500T ENST00000308192 12/19 423 198 225 395 394 1 strelka-varscan-mutect PLG,synonymous_variant,p.=,ENST00000308192,NM_000301.3;PLG,downstream_gene_variant,,ENST00000297289,;PLG,non_coding_transcript_exon_variant,,ENST00000493435,; A ENST00000308192 Transcript synonymous_variant 1563/2741 1500/2433 500/810 T acG/acA rs775623839,COSM4978081 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 12/19 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001150,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 0,1 LOW 1 SNV 1 0,1 1 PASS rs775623839 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 160731806 160731806 G A 1 0 0 0 0 0 0 0 1 12181 1074 38 1 1 PLG 6 160731806 Silent SNP G C3N-00560_T 8582211 160731806 10074173 448 17137 DACT2 0 . GRCh38 6 168319589 168319589 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.45C>A p.= p.R15R ENST00000366795 1/4 45 17 28 33 33 0 strelka-varscan-mutect DACT2,synonymous_variant,p.=,ENST00000366795,NM_214462.4;DACT2,synonymous_variant,p.=,ENST00000366796,NM_001286351.1;DACT2,5_prime_UTR_variant,,ENST00000607983,;DACT2,intron_variant,,ENST00000610183,NM_001286350.1; T ENST00000366795 Transcript synonymous_variant 134/2942 45/2325 15/774 R cgC/cgA 1 -1 DACT2 HGNC HGNC:21231 protein_coding YES CCDS47519.1 ENSP00000355760 Q5SW24 UPI00001D8145 NM_214462.4 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15919:SF13,hmmpanther:PTHR15919 LOW 1 SNV 2 1 PASS rs1254053062 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 168319589 168319589 G T 1 0 0 0 0 0 0 0 1 4024 1190 42 2 2 DACT2 6 168319589 Silent SNP G C3N-00560_T 7587783 168319589 2486390 449 17138 THBS2 0 . GRCh38 6 169223333 169223333 + Silent SNP G G C novel C3N-00560_T C3N-00560_N G G c.2916C>G p.= p.T972T ENST00000366787 19/23 233 108 125 256 256 0 strelka-varscan-mutect THBS2,synonymous_variant,p.=,ENST00000366787,NM_003247.3;THBS2,synonymous_variant,p.=,ENST00000617924,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,non_coding_transcript_exon_variant,,ENST00000488355,; C ENST00000366787 Transcript synonymous_variant 3166/5811 2916/3519 972/1172 T acC/acG 1 -1 THBS2 HGNC HGNC:11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 UPI0000231C7F NM_003247.3 19/23 PROSITE_profiles:PS51236,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF10,Gene3D:2.60.120.200,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 169223333 169223333 G C 1 0 0 0 0 0 0 0 1 16287 1335 47 4 4 THBS2 6 169223333 Silent SNP G C3N-00560_T 903744 169223333 1582646 450 17139 FAM120B 0 . GRCh38 6 170318927 170318927 + Missense_Mutation SNP G G T rs766907261 C3N-00560_T C3N-00560_N G G c.1606G>T p.Asp536Tyr p.D536Y ENST00000537664 2/11 179 76 103 190 190 0 strelka-varscan-mutect FAM120B,missense_variant,p.Asp513Tyr,ENST00000476287,NM_032448.2;FAM120B,missense_variant,p.Asp525Tyr,ENST00000630384,NM_001286379.1;FAM120B,missense_variant,p.Asp536Tyr,ENST00000537664,NM_001286380.1;FAM120B,intron_variant,,ENST00000625626,NM_001286381.1; T ENST00000537664 Transcript missense_variant 1691/3212 1606/2802 536/933 D/Y Gat/Tat rs766907261 1 1 FAM120B HGNC HGNC:21109 protein_coding YES CCDS75555.1 ENSP00000440125 F5GY05 UPI00020654A4 NM_001286380.1 tolerated_low_confidence(0.17) 2/11 hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF17 MODERATE 1 SNV 2 1 PASS rs766907261 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 170318927 170318927 G T 1 0 0 0 0 1 0 0 0 5274 942 33 2 2 FAM120B 6 170318927 Missense_Mutation SNP G C3N-00560_T 1095594 170318927 487052 451 17140 PRKAR1B 0 . GRCh38 7 680685 680685 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.219A>G p.= p.S73S ENST00000406797 3/11 271 183 88 213 213 0 strelka-varscan-mutect PRKAR1B,synonymous_variant,p.=,ENST00000406797,NM_001164761.1;PRKAR1B,synonymous_variant,p.=,ENST00000537384,NM_001164760.1;PRKAR1B,synonymous_variant,p.=,ENST00000544935,NM_001164759.1,NM_001164762.1;PRKAR1B,synonymous_variant,p.=,ENST00000360274,NM_002735.2;PRKAR1B,synonymous_variant,p.=,ENST00000403562,NM_001164758.1;PRKAR1B,synonymous_variant,p.=,ENST00000430040,;PRKAR1B,synonymous_variant,p.=,ENST00000414568,;PRKAR1B,synonymous_variant,p.=,ENST00000417852,;PRKAR1B,synonymous_variant,p.=,ENST00000456696,; C ENST00000406797 Transcript synonymous_variant 394/2553 219/1146 73/381 S tcA/tcG 1 -1 PRKAR1B HGNC HGNC:9390 protein_coding YES CCDS34579.1 ENSP00000385749 P31321 UPI000021C478 NM_001164761.1 3/11 PIRSF_domain:PIRSF000548,hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF126 LOW 1 SNV 1 1 PASS rs1214785921 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 680685 680685 T C 1 0 0 0 0 0 0 0 1 12637 1683 59 5 5 PRKAR1B 7 680685 Silent SNP T C3N-00560_T 680685 158665288 452 17141 CYP2W1 0 . GRCh38 7 984442 984442 + Missense_Mutation SNP G G T rs535558848 C3N-00560_T C3N-00560_N G G c.205G>T p.Val69Leu p.V69L ENST00000308919 2/9 267 184 83 256 256 0 strelka-varscan-mutect CYP2W1,missense_variant,p.Val13Leu,ENST00000340150,;CYP2W1,missense_variant,p.Val69Leu,ENST00000308919,NM_017781.2;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000462453,;CYP2W1,upstream_gene_variant,,ENST00000468456,; T ENST00000308919 Transcript missense_variant 218/2304 205/1473 69/490 V/L Gtg/Ttg rs535558848 1 1 CYP2W1 HGNC HGNC:20243 protein_coding YES CCDS5319.2 ENSP00000310149 Q8TAV3 UPI000013C59A NM_017781.2 tolerated(0.2) 2/9 hmmpanther:PTHR24300:SF183,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS rs535558848 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 984442 984442 G T 1 0 0 0 0 1 0 0 0 3979 1145 40 1 1 CYP2W1 7 984442 Missense_Mutation SNP G C3N-00560_T 303757 984442 158361531 453 17142 ELFN1 0 . GRCh38 7 1744695 1744695 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.99G>T p.Glu33Asp p.E33D ENST00000424383 3/3 360 265 95 242 242 0 strelka-varscan-mutect ELFN1,missense_variant,p.Glu33Asp,ENST00000424383,;ELFN1,missense_variant,p.Glu33Asp,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; T ENST00000424383 Transcript missense_variant 586/3845 99/2487 33/828 E/D gaG/gaT 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 deleterious(0.01) 3/3 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF34 MODERATE SNV 5 1 PASS rs1285420106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 1744695 1744695 G T 1 0 0 0 0 1 0 0 0 4891 991 35 2 2 ELFN1 7 1744695 Missense_Mutation SNP G C3N-00560_T 760253 1744695 157601278 454 17143 NUDT1 0 . GRCh38 7 2249978 2249978 + Nonsense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.343C>T p.Gln115Ter p.Q115* ENST00000397048 4/5 382 257 125 288 288 0 strelka-varscan-mutect NUDT1,stop_gained,p.Gln115Ter,ENST00000397048,NM_198952.1;NUDT1,stop_gained,p.Gln115Ter,ENST00000343985,NM_198949.1,NM_198954.1;NUDT1,stop_gained,p.Gln92Ter,ENST00000397049,;NUDT1,stop_gained,p.Gln92Ter,ENST00000397046,NM_198950.1;NUDT1,stop_gained,p.Gln92Ter,ENST00000339737,NM_198953.1;NUDT1,stop_gained,p.Gln92Ter,ENST00000356714,NM_002452.3,NM_198948.1;SNX8,downstream_gene_variant,,ENST00000222990,NM_013321.3;NUDT1,non_coding_transcript_exon_variant,,ENST00000487426,;NUDT1,downstream_gene_variant,,ENST00000471348,; T ENST00000397048 Transcript stop_gained 442/783 343/540 115/179 Q/* Cag/Tag 1 1 NUDT1 HGNC HGNC:8048 protein_coding YES CCDS5329.1 ENSP00000380241 P36639 A0A024R858 UPI000013C81F NM_198952.1 4/5 Gene3D:3.90.79.10,Pfam_domain:PF00293,Prints_domain:PR01403,PROSITE_profiles:PS51462,hmmpanther:PTHR22769,hmmpanther:PTHR22769:SF20,Superfamily_domains:SSF55811 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 2249978 2249978 C T 1 0 0 0 0 0 1 0 0 10791 595 21 3 3 NUDT1 7 2249978 Nonsense_Mutation SNP C C3N-00560_T 505283 2249978 157095995 455 17144 EIF3B 0 . GRCh38 7 2369530 2369530 + Missense_Mutation SNP G G A C3N-00560_T C3N-00560_N G G c.1462G>A p.Asp488Asn p.D488N ENST00000360876 10/19 608 429 179 478 477 1 strelka-varscan-mutect EIF3B,missense_variant,p.Asp488Asn,ENST00000360876,NM_001037283.1;EIF3B,missense_variant,p.Asp488Asn,ENST00000397011,NM_003751.3;EIF3B,downstream_gene_variant,,ENST00000431643,;EIF3B,non_coding_transcript_exon_variant,,ENST00000466199,;EIF3B,upstream_gene_variant,,ENST00000475415,;EIF3B,downstream_gene_variant,,ENST00000463026,;EIF3B,downstream_gene_variant,,ENST00000468250,;EIF3B,downstream_gene_variant,,ENST00000463229,; A ENST00000360876 Transcript missense_variant 1518/3055 1462/2445 488/814 D/N Gat/Aat COSM600543 1 1 EIF3B HGNC HGNC:3280 protein_coding YES CCDS5332.1 ENSP00000354125 P55884 A0A024R821 UPI000013F934 NM_001037283.1 tolerated(0.61) 10/19 HAMAP:MF_03001,hmmpanther:PTHR14068:SF0,hmmpanther:PTHR14068,Gene3D:2.130.10.10,PIRSF_domain:PIRSF036424,Superfamily_domains:0047732 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 2369530 2369530 G A 1 0 0 0 0 1 0 0 0 4847 942 33 3 3 EIF3B 7 2369530 Missense_Mutation SNP G C3N-00560_T 119552 2369530 156976443 456 17145 TNRC18 0 . GRCh38 7 5388429 5388429 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.1395G>T p.= p.L465L ENST00000430969 5/30 213 153 60 120 120 0 strelka-varscan-mutect TNRC18,synonymous_variant,p.=,ENST00000399537,;TNRC18,synonymous_variant,p.=,ENST00000430969,NM_001080495.2;TNRC18,downstream_gene_variant,,ENST00000399434,;TNRC18,upstream_gene_variant,,ENST00000413081,;TNRC18,downstream_gene_variant,,ENST00000434361,; A ENST00000430969 Transcript synonymous_variant 1744/10562 1395/8907 465/2968 L ctG/ctT 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 5/30 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF21 LOW 1 SNV 5 1 PASS rs1378760359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 5388429 5388429 C A 1 0 0 0 0 0 0 0 1 16812 697 25 2 2 TNRC18 7 5388429 Silent SNP C C3N-00560_T 3018899 5388429 153957544 457 17146 TNRC18 0 . GRCh38 7 5421124 5421124 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.123G>T p.= p.S41S ENST00000430969 2/30 25 19 6 16 16 0 strelka-mutect TNRC18,synonymous_variant,p.=,ENST00000399537,;TNRC18,synonymous_variant,p.=,ENST00000430969,NM_001080495.2;TNRC18,intron_variant,,ENST00000399434,;RP11-1275H24.2,upstream_gene_variant,,ENST00000609130,;AC092171.2,intron_variant,,ENST00000455866,;AC093620.5,downstream_gene_variant,,ENST00000342963,; A ENST00000430969 Transcript synonymous_variant 472/10562 123/8907 41/2968 S tcG/tcT 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 2/30 Low_complexity_(Seg):seg LOW SNV 5 1 PASS rs1221886256 . 3 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 5421124 5421124 C A 1 0 0 0 0 0 0 0 1 16812 639 23 1 1 TNRC18 7 5421124 Silent SNP C C3N-00560_T 32695 5421124 153924849 458 17147 USP42 0 . GRCh38 7 6139101 6139101 + Missense_Mutation SNP G G T rs752099114 C3N-00560_T C3N-00560_N G G c.563G>T p.Arg188Met p.R188M ENST00000306177 5/18 149 106 43 101 101 0 strelka-varscan-mutect USP42,missense_variant,p.Arg188Met,ENST00000306177,NM_032172.2;USP42,missense_variant,p.Arg34Met,ENST00000426246,;USP42,missense_variant,p.Arg121Met,ENST00000465073,;USP42,missense_variant,p.Arg188Met,ENST00000521713,;USP42,3_prime_UTR_variant,,ENST00000404008,;USP42,non_coding_transcript_exon_variant,,ENST00000479544,; T ENST00000306177 Transcript missense_variant 721/5155 563/3951 188/1316 R/M aGg/aTg rs752099114 1 1 USP42 HGNC HGNC:20068 protein_coding YES CCDS47535.1 ENSP00000301962 Q9H9J4 UPI0000416754 NM_032172.2 deleterious(0) 5/18 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF409,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS rs752099114 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 6139101 6139101 G T 1 0 0 0 0 1 0 0 0 17616 1000 35 2 2 USP42 7 6139101 Missense_Mutation SNP G C3N-00560_T 717977 6139101 153206872 459 17148 ZNF853 0 . GRCh38 7 6622589 6622589 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.1598G>C p.Arg533Pro p.R533P ENST00000457543 3/3 288 208 80 184 184 0 strelka-varscan-mutect ZNF853,missense_variant,p.Arg533Pro,ENST00000457543,NM_017560.1; C ENST00000457543 Transcript missense_variant 2156/3857 1598/1980 533/659 R/P cGc/cCc COSM5472430,COSM5472431 1 1 ZNF853 HGNC HGNC:21767 protein_coding YES CCDS59048.1 ENSP00000455585 P0CG23 UPI00018E24EF NM_017560.1 deleterious_low_confidence(0) 3/3 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 3 1,1 1 PASS rs1457638924 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 6622589 6622589 G C 1 0 0 0 0 1 0 0 0 18784 1087 38 4 4 ZNF853 7 6622589 Missense_Mutation SNP G C3N-00560_T 483488 6622589 152723384 460 17149 ZNF12 0 . GRCh38 7 6691430 6691430 + Missense_Mutation SNP C C A rs746237527 C3N-00560_T C3N-00560_N C C c.1512G>T p.Gln504His p.Q504H ENST00000405858 5/5 238 164 74 165 165 0 strelka-varscan-mutect ZNF12,missense_variant,p.Gln504His,ENST00000405858,NM_016265.3;ZNF12,missense_variant,p.Gln430His,ENST00000404360,;ZNF12,missense_variant,p.Gln466His,ENST00000342651,NM_006956.2;AC073343.13,intron_variant,,ENST00000366167,; A ENST00000405858 Transcript missense_variant 2054/5051 1512/2094 504/697 Q/H caG/caT rs746237527 1 -1 ZNF12 HGNC HGNC:12902 protein_coding YES CCDS47538.1 ENSP00000385939 P17014 UPI000020EAF7 NM_016265.3 tolerated(0.28) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF85,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs746237527 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 6691430 6691430 C A 1 0 0 0 0 1 0 0 0 18299 564 20 2 2 ZNF12 7 6691430 Missense_Mutation SNP C C3N-00560_T 68841 6691430 152654543 461 17150 COL28A1 0 . GRCh38 7 7443654 7443654 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.1582-1G>T p.X528_splice ENST00000399429 151 99 52 152 152 0 strelka-varscan-mutect COL28A1,splice_acceptor_variant,,ENST00000399429,NM_001037763.2;COL28A1,splice_acceptor_variant,,ENST00000444268,; A ENST00000399429 Transcript splice_acceptor_variant -/4277 1582/3378 528/1125 1 -1 COL28A1 HGNC HGNC:22442 protein_coding YES CCDS43553.1 ENSP00000382356 Q2UY09 UPI000155D64E NM_001037763.2 19/34 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 7443654 7443654 C A 1 0 0 0 0 0 0 1 0 3475 695 24 2 2 COL28A1 7 7443654 Splice_Site SNP C C3N-00560_T 752224 7443654 151902319 462 17151 TSPAN13 0 . GRCh38 7 16753981 16753981 + Missense_Mutation SNP G G A rs200364974 C3N-00560_T C3N-00560_N G G c.14G>A p.Gly5Asp p.G5D ENST00000262067 1/6 563 390 173 372 372 0 strelka-varscan-mutect TSPAN13,missense_variant,p.Gly5Asp,ENST00000262067,NM_014399.3; A ENST00000262067 Transcript missense_variant 447/2093 14/615 5/204 G/D gGc/gAc rs200364974 1 1 TSPAN13 HGNC HGNC:21643 protein_coding YES CCDS5363.1 ENSP00000262067 O95857 Q6FGK0 UPI0000048EB9 NM_014399.3 deleterious(0) 1/6 hmmpanther:PTHR19282:SF203,hmmpanther:PTHR19282,PIRSF_domain:PIRSF002419 MODERATE 1 SNV 1 1 PASS rs200364974 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 16753981 16753981 G A 1 0 0 0 0 1 0 0 0 17142 1203 42 3 3 TSPAN13 7 16753981 Missense_Mutation SNP G C3N-00560_T 9310327 16753981 142591992 463 17152 TMEM196 0 . GRCh38 7 19724313 19724313 + Missense_Mutation SNP G G T rs748067485 C3N-00560_T C3N-00560_N G G c.500C>A p.Pro167Gln p.P167Q ENST00000405844 4/5 241 175 66 231 231 0 strelka-varscan-mutect TMEM196,missense_variant,p.Pro167Gln,ENST00000405844,;TMEM196,missense_variant,p.Pro99Gln,ENST00000422233,;TMEM196,3_prime_UTR_variant,,ENST00000433641,;TMEM196,intron_variant,,ENST00000405764,NM_152774.3;TMEM196,intron_variant,,ENST00000493519,; T ENST00000405844 Transcript missense_variant 1196/4054 500/540 167/179 P/Q cCg/cAg rs748067485 1 -1 TMEM196 HGNC HGNC:22431 protein_coding ENSP00000385087 B7WNR7 UPI0000469AC8 deleterious_low_confidence(0.01) 4/5 hmmpanther:PTHR28681 MODERATE SNV 5 1 PASS rs748067485 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 19724313 19724313 G T 1 0 0 0 0 1 0 0 0 16558 1116 39 1 1 TMEM196 7 19724313 Missense_Mutation SNP G C3N-00560_T 2970332 19724313 139621660 464 17153 TMEM196 0 . GRCh38 7 19725626 19725626 + Missense_Mutation SNP C C A rs780657033 C3N-00560_T C3N-00560_N C C c.347G>T p.Gly116Val p.G116V ENST00000405764 3/4 309 228 81 277 277 0 strelka-varscan-mutect TMEM196,missense_variant,p.Gly116Val,ENST00000405844,;TMEM196,missense_variant,p.Gly116Val,ENST00000405764,NM_152774.3;TMEM196,missense_variant,p.Gly48Val,ENST00000422233,;TMEM196,missense_variant,p.Gly48Val,ENST00000433641,;TMEM196,missense_variant,p.Gly48Val,ENST00000493519,; A ENST00000405764 Transcript missense_variant 1044/3975 347/519 116/172 G/V gGg/gTg rs780657033 1 -1 TMEM196 HGNC HGNC:22431 protein_coding YES CCDS34607.2 ENSP00000384234 Q5HYL7 UPI00005A9078 NM_152774.3 tolerated_low_confidence(0.16) 3/4 hmmpanther:PTHR28681,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs780657033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 19725626 19725626 C A 1 0 0 0 0 1 0 0 0 16558 623 22 2 2 TMEM196 7 19725626 Missense_Mutation SNP C C3N-00560_T 1313 19725626 139620347 465 17154 NPVF 0 . GRCh38 7 25226848 25226853 + In_Frame_Del DEL GCTGTT GCTGTT - novel C3N-00560_T C3N-00560_N GCTGTT GCTGTT c.312_317delAACAGC p.Thr105_Ala106del p.T105_A106del ENST00000222674 2/3 215 134 81 209 209 0 sindel-varindel-pindel NPVF,inframe_deletion,p.Thr105_Ala106del,ENST00000222674,NM_022150.3; - ENST00000222674 Transcript inframe_deletion 359-364/1190 312-317/591 104-106/196 ATA/A gcAACAGCc/gcc 1 -1 NPVF HGNC HGNC:13782 protein_coding YES CCDS5395.1 ENSP00000222674 Q9HCQ7 UPI000013380C NM_022150.3 2/3 hmmpanther:PTHR14403 MODERATE 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 25226848 25226848 GCTGTT - 1 0 1 0 1 0 0 0 0 10661 1203 42 0 0 NPVF 7 25226848 In_Frame_Del DEL GCTGTT C3N-00560_T 5501222 25226848 134119125 466 17155 SKAP2 0 . GRCh38 7 26726903 26726903 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.573T>A p.= p.A191A ENST00000345317 7/13 56 38 18 112 112 0 strelka-varscan-mutect SKAP2,synonymous_variant,p.=,ENST00000345317,NM_003930.4,NM_001303468.1;SKAP2,non_coding_transcript_exon_variant,,ENST00000489977,;SKAP2,non_coding_transcript_exon_variant,,ENST00000495802,;SKAP2,non_coding_transcript_exon_variant,,ENST00000468712,; T ENST00000345317 Transcript synonymous_variant 887/3998 573/1080 191/359 A gcT/gcA 1 -1 SKAP2 HGNC HGNC:15687 protein_coding YES CCDS5400.1 ENSP00000005587 O75563 UPI0000073C8C NM_003930.4,NM_001303468.1 7/13 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR15129,hmmpanther:PTHR15129:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 26726903 26726903 A T 1 0 0 0 0 0 0 0 1 14618 291 11 4 4 SKAP2 7 26726903 Silent SNP A C3N-00560_T 1500055 26726903 132619070 467 17156 HOXA2 0 . GRCh38 7 27102261 27102261 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.240C>A p.Ser80Arg p.S80R ENST00000222718 1/2 267 167 100 130 130 0 strelka-varscan-mutect HOXA2,missense_variant,p.Ser80Arg,ENST00000222718,NM_006735.3;HOXA3,downstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA3,downstream_gene_variant,,ENST00000396352,NM_030661.4;HOXA3,downstream_gene_variant,,ENST00000317201,;HOTAIRM1,downstream_gene_variant,,ENST00000428939,;HOTAIRM1,downstream_gene_variant,,ENST00000429611,;HOTAIRM1,downstream_gene_variant,,ENST00000434063,;HOTAIRM1,downstream_gene_variant,,ENST00000593300,;HOTAIRM1,downstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,downstream_gene_variant,,ENST00000616712,;HOTAIRM1_5,downstream_gene_variant,,ENST00000619311,;HOTAIRM1_4,downstream_gene_variant,,ENST00000617934,;HOTAIRM1_3,downstream_gene_variant,,ENST00000619974,;HOXA2,non_coding_transcript_exon_variant,,ENST00000612779,; T ENST00000222718 Transcript missense_variant 551/1814 240/1131 80/376 S/R agC/agA 1 -1 HOXA2 HGNC HGNC:5103 protein_coding YES CCDS5403.1 ENSP00000222718 O43364 UPI0000049C49 NM_006735.3 tolerated(0.53) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF179 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 27102261 27102261 G T 1 0 0 0 0 1 0 0 0 7186 1194 42 2 2 HOXA2 7 27102261 Missense_Mutation SNP G C3N-00560_T 375358 27102261 132243712 468 17157 CREB5 0 . GRCh38 7 28804334 28804334 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.838C>A p.Gln280Lys p.Q280K ENST00000357727 8/11 588 408 180 510 510 0 strelka-varscan-mutect CREB5,missense_variant,p.Gln280Lys,ENST00000357727,NM_182898.3;CREB5,missense_variant,p.Gln273Lys,ENST00000396300,NM_004904.3;CREB5,missense_variant,p.Gln247Lys,ENST00000396299,NM_182899.4;CREB5,missense_variant,p.Gln141Lys,ENST00000396298,NM_001011666.2;CREB5,missense_variant,p.Gln247Lys,ENST00000409603,;CREB5,missense_variant,p.Gln106Lys,ENST00000426500,; A ENST00000357727 Transcript missense_variant 1228/8532 838/1527 280/508 Q/K Cag/Aag 1 1 CREB5 HGNC HGNC:16844 protein_coding YES CCDS5417.1 ENSP00000350359 Q02930 UPI0000457534 NM_182898.3 deleterious(0.05) 8/11 PIRSF_domain:PIRSF003153,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 28804334 28804334 C A 1 0 0 0 0 1 0 0 0 3660 827 29 2 2 CREB5 7 28804334 Missense_Mutation SNP C C3N-00560_T 1702073 28804334 130541639 469 17158 AQP1 0 . GRCh38 7 30921836 30921836 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.133C>G p.Gln45Glu p.Q45E ENST00000441328 2/5 138 97 41 93 93 0 strelka-varscan-mutect AQP1,missense_variant,p.Gln45Glu,ENST00000441328,NM_001185060.1;AQP1,missense_variant,p.Gln77Glu,ENST00000409611,NM_001185061.1;AQP1,intron_variant,,ENST00000311813,NM_198098.2;RP5-877J2.1,intron_variant,,ENST00000509504,;AQP1,intron_variant,,ENST00000409899,NM_001185062.1;AQP1,intron_variant,,ENST00000482461,; G ENST00000441328 Transcript missense_variant,splice_region_variant 172/2487 133/561 45/186 Q/E Cag/Gag 1 1 AQP1 HGNC HGNC:633 protein_coding CCDS55098.1 ENSP00000405698 P29972 UPI000189292C NM_001185060.1 tolerated(0.72) 2/5 hmmpanther:PTHR19139,hmmpanther:PTHR19139:SF161,Gene3D:1.20.1080.10,Pfam_domain:PF00230 MODERATE SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 30921836 30921836 C G 1 0 0 0 0 1 0 0 0 944 724 25 4 4 AQP1 7 30921836 Missense_Mutation SNP C C3N-00560_T 2117502 30921836 128424137 470 17159 PDE1C 0 . GRCh38 7 31828315 31828315 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1442C>T p.Thr481Ile p.T481I ENST00000396193 13/19 222 173 49 168 168 0 strelka-varscan-mutect PDE1C,missense_variant,p.Thr421Ile,ENST00000396184,NM_001322057.1,NM_001322056.1,NM_001322059.1,NM_005020.3;PDE1C,missense_variant,p.Thr481Ile,ENST00000396193,NM_001191058.2;PDE1C,missense_variant,p.Thr421Ile,ENST00000396191,NM_001191057.2;PDE1C,missense_variant,p.Thr421Ile,ENST00000321453,NM_001191059.2;PDE1C,missense_variant,p.Thr421Ile,ENST00000396182,NM_001191056.2; A ENST00000396193 Transcript missense_variant 2036/5109 1442/2310 481/769 T/I aCt/aTt 1 -1 PDE1C HGNC HGNC:8776 protein_coding YES CCDS55100.1 ENSP00000379496 A0A0A0MS69 UPI00043788D1 NM_001191058.2 tolerated(0.05) 13/19 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Superfamily_domains:SSF109604 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 31828315 31828315 G A 1 0 0 0 0 1 0 0 0 11723 1029 36 3 3 PDE1C 7 31828315 Missense_Mutation SNP G C3N-00560_T 906479 31828315 127517658 471 17160 FKBP9 0 . GRCh38 7 32974756 32974756 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.520G>T p.Gly174Ter p.G174* ENST00000538336 3/11 132 124 8 110 110 0 varscan-mutect FKBP9,stop_gained,p.Gly174Ter,ENST00000538336,NM_001284341.1;FKBP9,stop_gained,p.Gly121Ter,ENST00000242209,NM_007270.4;FKBP9,upstream_gene_variant,,ENST00000490776,NM_001284343.1;FKBP9,upstream_gene_variant,,ENST00000418354,;FKBP9,intron_variant,,ENST00000469202,;FKBP9,upstream_gene_variant,,ENST00000489038,;FKBP9,upstream_gene_variant,,ENST00000472007,;FKBP9,downstream_gene_variant,,ENST00000464334,;FKBP9,non_coding_transcript_exon_variant,,ENST00000494374,;FKBP9,non_coding_transcript_exon_variant,,ENST00000485309,; T ENST00000538336 Transcript stop_gained 690/3621 520/1872 174/623 G/* Gga/Tga 1 1 FKBP9 HGNC HGNC:3725 protein_coding YES CCDS64622.1 ENSP00000439250 O95302 UPI0001914EC6 NM_001284341.1 3/11 PROSITE_profiles:PS50059,hmmpanther:PTHR10516:SF111,hmmpanther:PTHR10516,Pfam_domain:PF00254,Gene3D:3.10.50.40,Superfamily_domains:SSF54534 HIGH 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -11.43771 0.9999995 1 1 1 0 T 4 4 56 32974756 32974756 G T 1 0 0 0 0 0 1 0 0 5778 1001 35 2 2 FKBP9 7 32974756 Nonsense_Mutation SNP G C3N-00560_T 1146441 32974756 126371217 472 17161 BMPER 0 . GRCh38 7 33970411 33970411 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.485C>T p.Thr162Ile p.T162I ENST00000297161 6/16 417 295 122 374 374 0 strelka-varscan-mutect BMPER,missense_variant,p.Thr162Ile,ENST00000297161,NM_133468.4;BMPER,missense_variant,p.His129Tyr,ENST00000436222,;BMPER,downstream_gene_variant,,ENST00000444773,; T ENST00000297161 Transcript missense_variant 859/5031 485/2058 162/685 T/I aCa/aTa 1 1 BMPER HGNC HGNC:24154 protein_coding YES CCDS5442.1 ENSP00000297161 Q8N8U9 A0A090N7U6 UPI000006D462 NM_133468.4 deleterious(0.01) 6/16 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF272,SMART_domains:SM00214,Superfamily_domains:SSF57603,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS rs1245250061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 33970411 33970411 C T 1 0 0 0 0 1 0 0 0 1623 478 17 3 3 BMPER 7 33970411 Missense_Mutation SNP C C3N-00560_T 995655 33970411 125375562 473 17162 NPSR1 0 . GRCh38 7 34684684 34684684 + Missense_Mutation SNP G G T rs761286205 C3N-00560_T C3N-00560_N G G c.280G>T p.Asp94Tyr p.D94Y ENST00000381539 2/10 100 73 27 91 91 0 varscan-mutect NPSR1,stop_gained,p.Glu94Ter,ENST00000381542,NM_001300934.1;NPSR1,missense_variant,p.Asp94Tyr,ENST00000360581,NM_207172.1;NPSR1,missense_variant,p.Asp94Tyr,ENST00000359791,NM_207173.1;NPSR1,missense_variant,p.Asp94Tyr,ENST00000531252,NM_001300933.1;NPSR1,missense_variant,p.Asp94Tyr,ENST00000381539,NM_001300935.1;NPSR1,missense_variant,p.Asp94Tyr,ENST00000381553,;NPSR1,missense_variant,p.Val94Leu,ENST00000465305,;NPSR1-AS1,intron_variant,,ENST00000419766,;NPSR1-AS1,intron_variant,,ENST00000539747,;NPSR1-AS1,intron_variant,,ENST00000439852,;NPSR1-AS1,intron_variant,,ENST00000358772,;NPSR1-AS1,intron_variant,,ENST00000431669,;NPSR1,missense_variant,p.Asp94Tyr,ENST00000396095,;NPSR1,missense_variant,p.Gly94Cys,ENST00000381544,; T ENST00000381539 Transcript missense_variant,splice_region_variant 284/1233 280/1173 94/390 D/Y Gat/Tat rs761286205,COSM5326320,COSM5326321,COSM5326322,COSM5326323 1 1 NPSR1 HGNC HGNC:23631 protein_coding YES CCDS75579.1 ENSP00000370950 Q6W5P4 UPI00004F9C01 NM_001300935.1 deleterious(0) 2/10 PROSITE_profiles:PS50262,hmmpanther:PTHR24244,hmmpanther:PTHR24244:SF2,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs761286205 . 0 201 9 0 0 0 0 0 -20 0.9999981 1 1 1 0 T 3 4 56 34684684 34684684 G T 1 0 0 0 0 1 0 0 0 10656 1014 35 2 2 NPSR1 7 34684684 Missense_Mutation SNP G C3N-00560_T 714273 34684684 124661289 474 17163 HECW1 0 . GRCh38 7 43554619 43554619 + Missense_Mutation SNP G G T rs139970379 C3N-00560_T C3N-00560_N G G c.4538G>T p.Arg1513Leu p.R1513L ENST00000395891 29/30 309 225 84 277 277 0 strelka-varscan-mutect HECW1,missense_variant,p.Arg1513Leu,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Arg1479Leu,ENST00000453890,NM_001287059.1; T ENST00000395891 Transcript missense_variant 5143/9501 4538/4821 1513/1606 R/L cGc/cTc rs139970379 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious(0.04) 29/30 PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS rs139970379 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 43554619 43554619 G T 1 0 0 0 0 1 0 0 0 6924 1087 38 1 1 HECW1 7 43554619 Missense_Mutation SNP G C3N-00560_T 8869935 43554619 115791354 475 17164 AEBP1 0 . GRCh38 7 44108922 44108922 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.964C>A p.Pro322Thr p.P322T ENST00000223357 7/21 261 181 80 191 189 2 strelka-varscan-mutect AEBP1,missense_variant,p.Pro322Thr,ENST00000223357,NM_001129.4;AEBP1,missense_variant,p.Pro215Thr,ENST00000455443,;AEBP1,upstream_gene_variant,,ENST00000450684,;AEBP1,downstream_gene_variant,,ENST00000449162,;AEBP1,upstream_gene_variant,,ENST00000582839,;AEBP1,upstream_gene_variant,,ENST00000454218,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,upstream_gene_variant,,ENST00000453052,;AEBP1,upstream_gene_variant,,ENST00000434445,; A ENST00000223357 Transcript missense_variant 1269/4081 964/3477 322/1158 P/T Ccg/Acg COSM1698613 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 tolerated_low_confidence(0.08) 7/21 hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF48 1 MODERATE 1 SNV 1 1 1 PASS rs1187616022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44108922 44108922 C A 1 0 0 0 0 1 0 0 0 424 855 30 2 2 AEBP1 7 44108922 Missense_Mutation SNP C C3N-00560_T 554303 44108922 115237051 476 17165 AEBP1 0 . GRCh38 7 44111914 44111914 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1901T>A p.Leu634Gln p.L634Q ENST00000223357 16/21 299 212 87 250 250 0 strelka-varscan-mutect AEBP1,missense_variant,p.Leu634Gln,ENST00000223357,NM_001129.4;AEBP1,missense_variant,p.Leu209Gln,ENST00000450684,;POLD2,downstream_gene_variant,,ENST00000406581,NM_001256879.1;POLD2,downstream_gene_variant,,ENST00000452185,NM_001127218.2;POLD2,downstream_gene_variant,,ENST00000610533,NM_006230.3;POLD2,downstream_gene_variant,,ENST00000223361,;POLD2,downstream_gene_variant,,ENST00000436844,;AEBP1,downstream_gene_variant,,ENST00000455443,;AEBP1,downstream_gene_variant,,ENST00000449162,;POLD2,downstream_gene_variant,,ENST00000436400,;AEBP1,downstream_gene_variant,,ENST00000582839,;AEBP1,downstream_gene_variant,,ENST00000454218,;AEBP1,3_prime_UTR_variant,,ENST00000413907,;AEBP1,3_prime_UTR_variant,,ENST00000431035,;AEBP1,downstream_gene_variant,,ENST00000453052,;AEBP1,downstream_gene_variant,,ENST00000434445,;POLD2,downstream_gene_variant,,ENST00000481104,;POLD2,downstream_gene_variant,,ENST00000489883,; A ENST00000223357 Transcript missense_variant 2206/4081 1901/3477 634/1158 L/Q cTg/cAg 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 deleterious(0) 16/21 Gene3D:3.40.630.10,Pfam_domain:PF00246,PROSITE_patterns:PS00132,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF48,Low_complexity_(Seg):seg,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44111914 44111914 T A 1 0 0 0 0 1 0 0 0 424 1580 55 4 4 AEBP1 7 44111914 Missense_Mutation SNP T C3N-00560_T 2992 44111914 115234059 477 17166 CCM2 0 . GRCh38 7 45074371 45074371 + Silent SNP G G T rs771358794 C3N-00560_T C3N-00560_N G G c.1080G>T p.= p.R360R ENST00000381112 9/10 435 292 143 330 330 0 strelka-varscan-mutect CCM2,synonymous_variant,p.=,ENST00000475551,;CCM2,synonymous_variant,p.=,ENST00000258781,NM_031443.3;CCM2,synonymous_variant,p.=,ENST00000381112,NM_001029835.2;CCM2,synonymous_variant,p.=,ENST00000541586,NM_001167934.1;CCM2,synonymous_variant,p.=,ENST00000544363,NM_001167935.1;CCM2,synonymous_variant,p.=,ENST00000474617,;CCM2,downstream_gene_variant,,ENST00000480382,;CCM2,non_coding_transcript_exon_variant,,ENST00000461377,;CCM2,downstream_gene_variant,,ENST00000482714,;CCM2,downstream_gene_variant,,ENST00000472223,;CCM2,downstream_gene_variant,,ENST00000478582,;CCM2,3_prime_UTR_variant,,ENST00000488727,;CCM2,non_coding_transcript_exon_variant,,ENST00000481194,;CCM2,non_coding_transcript_exon_variant,,ENST00000477605,;CCM2,downstream_gene_variant,,ENST00000480658,;CCM2,downstream_gene_variant,,ENST00000492883,;CCM2,downstream_gene_variant,,ENST00000470837,; T ENST00000381112 Transcript synonymous_variant 1151/1881 1080/1398 360/465 R cgG/cgT rs771358794,COSM5482124 1 1 CCM2 HGNC HGNC:21708 protein_coding YES CCDS34630.1 ENSP00000370503 Q9BSQ5 UPI0000563237 NM_001029835.2 9/10 hmmpanther:PTHR21642,hmmpanther:PTHR21642:SF4,Pfam_domain:PF16545 0,1 LOW 1 SNV 2 0,1 1 PASS rs771358794 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 45074371 45074371 G T 1 0 0 0 0 0 0 0 1 2606 1190 42 2 2 CCM2 7 45074371 Silent SNP G C3N-00560_T 962457 45074371 114271602 478 17167 UPP1 0 . GRCh38 7 48107492 48107492 + Missense_Mutation SNP G G T rs753891294 C3N-00560_T C3N-00560_N G G c.778G>T p.Ala260Ser p.A260S ENST00000331803 9/10 91 68 23 58 57 1 strelka-varscan-mutect UPP1,missense_variant,p.Ala260Ser,ENST00000331803,NM_001287426.1;UPP1,missense_variant,p.Ala260Ser,ENST00000395564,NM_003364.3;UPP1,downstream_gene_variant,,ENST00000436673,;UPP1,downstream_gene_variant,,ENST00000416681,;UPP1,non_coding_transcript_exon_variant,,ENST00000482015,;UPP1,3_prime_UTR_variant,,ENST00000457596,;UPP1,3_prime_UTR_variant,,ENST00000395560,;UPP1,3_prime_UTR_variant,,ENST00000417464,;UPP1,non_coding_transcript_exon_variant,,ENST00000495446,;UPP1,downstream_gene_variant,,ENST00000421046,;UPP1,downstream_gene_variant,,ENST00000444999,; T ENST00000331803 Transcript missense_variant 1401/1932 778/933 260/310 A/S Gcc/Tcc rs753891294 1 1 UPP1 HGNC HGNC:12576 protein_coding YES CCDS5507.1 ENSP00000330032 Q16831 UPI0000137AC5 NM_001287426.1 tolerated(0.41) 9/10 Gene3D:3.40.50.1580,Pfam_domain:PF01048,hmmpanther:PTHR21234,hmmpanther:PTHR21234:SF15,Superfamily_domains:SSF53167,TIGRFAM_domain:TIGR01719 MODERATE 1 SNV 1 1 PASS rs753891294 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 48107492 48107492 G T 1 0 0 0 0 1 0 0 0 17538 1087 38 1 1 UPP1 7 48107492 Missense_Mutation SNP G C3N-00560_T 3033121 48107492 111238481 479 17168 FIGNL1 0 . GRCh38 7 50445451 50445451 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.1837A>G p.Arg613Gly p.R613G ENST00000419119 2/2 115 73 42 93 93 0 strelka-varscan-mutect FIGNL1,missense_variant,p.Arg613Gly,ENST00000419119,;FIGNL1,missense_variant,p.Arg613Gly,ENST00000433017,NM_001287492.1;FIGNL1,missense_variant,p.Arg613Gly,ENST00000611938,;FIGNL1,missense_variant,p.Arg613Gly,ENST00000395556,NM_001042762.2,NM_022116.4;FIGNL1,missense_variant,p.Arg613Gly,ENST00000356889,;FIGNL1,missense_variant,p.Arg613Gly,ENST00000615084,NM_001287496.1,NM_001287494.1,NM_001287493.1;FIGNL1,missense_variant,p.Arg613Gly,ENST00000617389,NM_001287495.1;FIGNL1,missense_variant,p.Arg613Gly,ENST00000613602,;FIGNL1,downstream_gene_variant,,ENST00000440350,;FIGNL1,downstream_gene_variant,,ENST00000435566,;FIGNL1,downstream_gene_variant,,ENST00000420829,;FIGNL1,downstream_gene_variant,,ENST00000422854,;FIGNL1,downstream_gene_variant,,ENST00000448788,;FIGNL1,downstream_gene_variant,,ENST00000436590,; C ENST00000419119 Transcript missense_variant 3391/3700 1837/2025 613/674 R/G Agg/Ggg 1 -1 FIGNL1 HGNC HGNC:13286 protein_coding YES CCDS5510.1 ENSP00000410811 Q6PIW4 UPI000013CE5D deleterious(0) 2/2 hmmpanther:PTHR23074:SF75,hmmpanther:PTHR23074,Gene3D:1.10.8.60,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 50445451 50445451 T C 1 0 0 0 0 1 0 0 0 5756 1579 55 5 5 FIGNL1 7 50445451 Missense_Mutation SNP T C3N-00560_T 2337959 50445451 108900522 480 17169 VSTM2A 0 . GRCh38 7 54549951 54549951 + Missense_Mutation SNP G G A rs761935287 C3N-00560_T C3N-00560_N G G c.415G>A p.Glu139Lys p.E139K ENST00000402613 4/5 328 242 86 307 306 1 strelka-varscan-mutect VSTM2A,missense_variant,p.Glu139Lys,ENST00000302287,NM_001317843.1;VSTM2A,missense_variant,p.Glu139Lys,ENST00000407838,NM_182546.3;VSTM2A,missense_variant,p.Glu139Lys,ENST00000404951,;VSTM2A,missense_variant,p.Glu139Lys,ENST00000402613,NM_001301009.1;VSTM2A,non_coding_transcript_exon_variant,,ENST00000498834,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000466888,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000469952,;VSTM2A,downstream_gene_variant,,ENST00000495904,; A ENST00000402613 Transcript missense_variant 541/1076 415/723 139/240 E/K Gaa/Aaa rs761935287 1 1 VSTM2A HGNC HGNC:28499 protein_coding YES CCDS75604.1 ENSP00000384103 F8W8J5 UPI00003E58E7 NM_001301009.1 deleterious(0) 4/5 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF23,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS rs761935287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 54549951 54549951 G A 1 0 0 0 0 1 0 0 0 17780 1175 41 3 3 VSTM2A 7 54549951 Missense_Mutation SNP G C3N-00560_T 4104500 54549951 104796022 481 17170 ZNF716 0 . GRCh38 7 57469690 57469690 + Missense_Mutation SNP G G T rs782774321 C3N-00560_T C3N-00560_N G G c.1229G>T p.Cys410Phe p.C410F ENST00000420713 4/4 265 200 65 278 278 0 strelka-varscan-mutect ZNF716,missense_variant,p.Cys410Phe,ENST00000420713,NM_001159279.1; T ENST00000420713 Transcript missense_variant 1341/5197 1229/1488 410/495 C/F tGt/tTt rs782774321 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS rs782774321 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57469690 57469690 G T 1 0 0 0 0 1 0 0 0 18694 1377 48 2 2 ZNF716 7 57469690 Missense_Mutation SNP G C3N-00560_T 2919739 57469690 101876283 482 17171 VKORC1L1 0 . GRCh38 7 65873528 65873528 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.157G>A p.Gly53Arg p.G53R ENST00000434382 1/2 313 252 61 179 179 0 strelka-varscan-mutect VKORC1L1,missense_variant,p.Gly53Arg,ENST00000360768,NM_173517.4;VKORC1L1,missense_variant,p.Gly53Arg,ENST00000434382,NM_001284342.1; A ENST00000434382 Transcript missense_variant 160/1541 157/534 53/177 G/R Ggg/Agg 1 1 VKORC1L1 HGNC HGNC:21492 protein_coding YES CCDS64663.1 ENSP00000403077 Q8N0U8 UPI0000423DF4 NM_001284342.1 deleterious(0) 1/2 hmmpanther:PTHR14519,hmmpanther:PTHR14519:SF4,Pfam_domain:PF07884 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 65873528 65873528 G A 1 0 0 0 0 1 0 0 0 17720 1232 43 3 3 VKORC1L1 7 65873528 Missense_Mutation SNP G C3N-00560_T 8403838 65873528 93472445 483 17172 WBSCR27 0 . GRCh38 7 73840431 73840431 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.371C>T p.Pro124Leu p.P124L ENST00000297873 4/6 210 154 56 194 194 0 strelka-varscan-mutect WBSCR27,missense_variant,p.Pro124Leu,ENST00000297873,NM_152559.2;WBSCR27,intron_variant,,ENST00000493174,;WBSCR27,intron_variant,,ENST00000458679,; A ENST00000297873 Transcript missense_variant 421/941 371/738 124/245 P/L cCt/cTt 1 -1 WBSCR27 HGNC HGNC:19068 protein_coding YES CCDS5561.1 ENSP00000297873 Q8N6F8 UPI000013E466 NM_152559.2 tolerated(0.06) 4/6 hmmpanther:PTHR10108,hmmpanther:PTHR10108:SF888,Pfam_domain:PF13649,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 73840431 73840431 G A 1 0 0 0 0 1 0 0 0 17825 1000 35 3 3 WBSCR27 7 73840431 Missense_Mutation SNP G C3N-00560_T 7966903 73840431 85505542 484 17173 SPDYE5 0 . GRCh38 7 75494143 75494143 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.96C>A p.= p.P32P ENST00000625065 1/8 423 285 138 329 328 1 strelka-varscan-mutect SPDYE5,synonymous_variant,p.=,ENST00000625065,;SPDYE5,synonymous_variant,p.=,ENST00000455862,;SPDYE5,upstream_gene_variant,,ENST00000624640,NM_001099435.2; A ENST00000625065 Transcript synonymous_variant 519/1700 96/1209 32/402 P ccC/ccA 1 1 SPDYE5 HGNC HGNC:35464 protein_coding YES CCDS78241.1 ENSP00000485398 A0A096LPK5 UPI000387D8EA 1/8 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF15 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 75494143 75494143 C A 1 0 0 0 0 0 0 0 1 15381 610 22 2 2 SPDYE5 7 75494143 Silent SNP C C3N-00560_T 1653712 75494143 83851830 485 17174 HGF 0 . GRCh38 7 81743425 81743425 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.793G>C p.Gly265Arg p.G265R ENST00000222390 7/18 458 338 120 347 347 0 strelka-varscan-mutect HGF,missense_variant,p.Gly265Arg,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Gly260Arg,ENST00000457544,NM_001010932.1;HGF,missense_variant,p.Gly265Arg,ENST00000444829,NM_001010931.1;HGF,missense_variant,p.Gly260Arg,ENST00000453411,NM_001010933.1; G ENST00000222390 Transcript missense_variant 1020/5989 793/2187 265/728 G/R Ggc/Cgc 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 deleterious(0.01) 7/18 PROSITE_profiles:PS50070,hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PROSITE_patterns:PS00021,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440,Prints_domain:PR00018 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 81743425 81743425 C G 1 0 0 0 0 1 0 0 0 6969 594 21 4 4 HGF 7 81743425 Missense_Mutation SNP C C3N-00560_T 6249282 81743425 77602548 486 17175 CACNA2D1 0 . GRCh38 7 82014452 82014452 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1171C>A p.Gln391Lys p.Q391K ENST00000356860 13/39 223 170 53 273 272 1 strelka-varscan-mutect CACNA2D1,missense_variant,p.Gln391Lys,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Gln391Lys,ENST00000356253,;AC006145.4,intron_variant,,ENST00000439234,;AC006145.4,intron_variant,,ENST00000454066,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000464354,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000492734,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000475237,;CACNA2D1,upstream_gene_variant,,ENST00000466806,; T ENST00000356860 Transcript missense_variant 1510/7563 1171/3276 391/1091 Q/K Caa/Aaa 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 tolerated(0.06) 13/39 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 82014452 82014452 G T 1 0 0 0 0 1 0 0 0 2236 1299 45 2 2 CACNA2D1 7 82014452 Missense_Mutation SNP G C3N-00560_T 271027 82014452 77331521 487 17176 CACNA2D1 0 . GRCh38 7 82014476 82014476 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1147C>A p.Arg383Ser p.R383S ENST00000356860 13/39 205 150 55 246 246 0 strelka-varscan-mutect CACNA2D1,missense_variant,p.Arg383Ser,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Arg383Ser,ENST00000356253,;AC006145.4,intron_variant,,ENST00000439234,;AC006145.4,intron_variant,,ENST00000454066,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000464354,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000492734,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000475237,;CACNA2D1,upstream_gene_variant,,ENST00000466806,; T ENST00000356860 Transcript missense_variant 1486/7563 1147/3276 383/1091 R/S Cgt/Agt 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 deleterious(0.01) 13/39 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 82014476 82014476 G T 1 0 0 0 0 1 0 0 0 2236 1159 40 1 1 CACNA2D1 7 82014476 Missense_Mutation SNP G C3N-00560_T 24 82014476 77331497 488 17177 KIAA1324L 0 . GRCh38 7 86912076 86912076 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2165A>T p.His722Leu p.H722L ENST00000450689 15/22 84 62 22 90 90 0 strelka-varscan-mutect KIAA1324L,missense_variant,p.His722Leu,ENST00000450689,NM_001142749.2;KIAA1324L,missense_variant,p.His651Leu,ENST00000444627,;KIAA1324L,missense_variant,p.His555Leu,ENST00000416314,NM_152748.3,NM_001291990.1;KIAA1324L,missense_variant,p.His683Leu,ENST00000423294,;KIAA1324L,downstream_gene_variant,,ENST00000490995,;KIAA1324L,downstream_gene_variant,,ENST00000474609,;KIAA1324L,missense_variant,p.His43Leu,ENST00000427812,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,;KIAA1324L,non_coding_transcript_exon_variant,,ENST00000470853,; A ENST00000450689 Transcript missense_variant 2351/6841 2165/3090 722/1029 H/L cAt/cTt 1 -1 KIAA1324L HGNC HGNC:21945 protein_coding YES CCDS47632.1 ENSP00000413445 A8MWY0 UPI000173AA00 NM_001142749.2 tolerated(0.09) 15/22 hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Superfamily_domains:SSF50911 MODERATE 1 SNV 5 1 PASS rs1283059824 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 86912076 86912076 T A 1 0 0 0 0 1 0 0 0 8112 1478 51 4 4 KIAA1324L 7 86912076 Missense_Mutation SNP T C3N-00560_T 4897600 86912076 72433897 489 17178 DBF4 0 . GRCh38 7 87907836 87907836 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.1699delG p.Asp567IlefsTer12 p.D567Ifs*12 ENST00000265728 12/12 127 96 31 148 148 0 sindel-varindel DBF4,frameshift_variant,p.Asp567IlefsTer12,ENST00000265728,NM_006716.3;DBF4,3_prime_UTR_variant,,ENST00000413643,;DBF4,3_prime_UTR_variant,,ENST00000431138,;DBF4,downstream_gene_variant,,ENST00000430279,;DBF4,downstream_gene_variant,,ENST00000498144,; - ENST00000265728 Transcript frameshift_variant 2202/3907 1698/2025 566/674 M/X atG/at 1 1 DBF4 HGNC HGNC:17364 protein_coding YES CCDS5611.1 ENSP00000265728 Q9UBU7 UPI000000DC33 NM_006716.3 12/12 hmmpanther:PTHR15375 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 87907836 87907836 G - 1 0 1 0 1 0 0 0 0 4048 1348 47 0 0 DBF4 7 87907836 Frame_Shift_Del DEL G C3N-00560_T 995760 87907836 71438137 490 17179 CFAP69 0 . GRCh38 7 90271594 90271594 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.601G>T p.Val201Phe p.V201F ENST00000389297 7/23 194 143 51 187 187 0 strelka-varscan-mutect CFAP69,missense_variant,p.Val201Phe,ENST00000389297,NM_001039706.2;CFAP69,missense_variant,p.Val183Phe,ENST00000497910,NM_001160138.1;CFAP69,missense_variant,p.Val141Phe,ENST00000457170,;CFAP69,missense_variant,p.Val3Phe,ENST00000418199,;AC002064.4,upstream_gene_variant,,ENST00000420245,;CFAP69,non_coding_transcript_exon_variant,,ENST00000463311,;CFAP69,missense_variant,p.Val201Phe,ENST00000451029,;CFAP69,3_prime_UTR_variant,,ENST00000427396,;CFAP69,upstream_gene_variant,,ENST00000475031,; T ENST00000389297 Transcript missense_variant 852/3902 601/2826 201/941 V/F Gtc/Ttc 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 deleterious(0) 7/23 hmmpanther:PTHR14716:SF0,hmmpanther:PTHR14716,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 90271594 90271594 G T 1 0 0 0 0 1 0 0 0 3030 1261 44 2 2 CFAP69 7 90271594 Missense_Mutation SNP G C3N-00560_T 2363758 90271594 69074379 491 17180 CFAP69 0 . GRCh38 7 90310067 90310067 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.2656-1G>T p.X886_splice ENST00000389297 127 76 51 108 108 0 strelka-varscan-mutect CFAP69,splice_acceptor_variant,,ENST00000389297,NM_001039706.2;CFAP69,splice_acceptor_variant,,ENST00000497910,NM_001160138.1;CFAP69,splice_acceptor_variant,,ENST00000449577,;CFAP69,splice_acceptor_variant,,ENST00000445156,;CFAP69,splice_acceptor_variant,,ENST00000412839,;AC002064.5,upstream_gene_variant,,ENST00000445784,;CFAP69,splice_acceptor_variant,,ENST00000475031,;CFAP69,downstream_gene_variant,,ENST00000427396,; T ENST00000389297 Transcript splice_acceptor_variant -/3902 2656/2826 886/941 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 22/22 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 90310067 90310067 G T 1 0 0 0 0 0 0 1 0 3030 1014 35 2 2 CFAP69 7 90310067 Splice_Site SNP G C3N-00560_T 38473 90310067 69035906 492 17181 AKAP9 0 . GRCh38 7 92002054 92002054 + Nonsense_Mutation SNP A A T C3N-00560_T C3N-00560_N A A c.2137A>T p.Lys713Ter p.K713* ENST00000356239 8/50 46 32 14 103 103 0 strelka-varscan-mutect AKAP9,stop_gained,p.Lys713Ter,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,stop_gained,p.Lys724Ter,ENST00000359028,;AKAP9,stop_gained,p.Lys713Ter,ENST00000358100,;AKAP9,stop_gained,p.Lys721Ter,ENST00000619023,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; T ENST00000356239 Transcript stop_gained 2370/12471 2137/11724 713/3907 K/* Aag/Tag COSM338037,COSM338038 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 8/50 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 92002054 92002054 A T 1 0 0 0 0 0 1 0 0 543 15 1 4 4 AKAP9 7 92002054 Nonsense_Mutation SNP A C3N-00560_T 1691987 92002054 67343919 493 17182 CYP51A1 0 . GRCh38 7 92131800 92131800 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.265G>A p.Glu89Lys p.E89K ENST00000003100 2/10 105 71 34 129 128 1 strelka-varscan-mutect CYP51A1,missense_variant,p.Glu89Lys,ENST00000003100,NM_000786.3;CYP51A1,5_prime_UTR_variant,,ENST00000450723,NM_001146152.1;CYP51A1,downstream_gene_variant,,ENST00000435873,;CYP51A1-AS1,upstream_gene_variant,,ENST00000453068,;LRRD1,non_coding_transcript_exon_variant,,ENST00000422722,; T ENST00000003100 Transcript missense_variant 431/3210 265/1530 89/509 E/K Gaa/Aaa COSM1092997 1 -1 CYP51A1 HGNC HGNC:2649 protein_coding YES CCDS5623.1 ENSP00000003100 A0A0C4DFL7 UPI000013C4D5 NM_000786.3 tolerated(0.4) 2/10 hmmpanther:PTHR24286:SF24,hmmpanther:PTHR24286,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00465 1 MODERATE 1 SNV 1 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 56 92131800 92131800 C T 1 0 0 0 0 1 0 0 0 3998 835 29 3 3 CYP51A1 7 92131800 Missense_Mutation SNP C C3N-00560_T 129746 92131800 67214173 494 17183 PEX1 0 . GRCh38 7 92517352 92517352 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1163G>T p.Trp388Leu p.W388L ENST00000248633 5/24 210 164 46 226 225 1 strelka-varscan-mutect PEX1,missense_variant,p.Trp388Leu,ENST00000248633,NM_000466.2;PEX1,missense_variant,p.Trp388Leu,ENST00000428214,NM_001282677.1;PEX1,intron_variant,,ENST00000438045,NM_001282678.1;PEX1,missense_variant,p.Trp22Leu,ENST00000422866,;PEX1,non_coding_transcript_exon_variant,,ENST00000484913,;PEX1,upstream_gene_variant,,ENST00000476923,; A ENST00000248633 Transcript missense_variant 1259/4385 1163/3852 388/1283 W/L tGg/tTg 1 -1 PEX1 HGNC HGNC:8850 protein_coding YES CCDS5627.1 ENSP00000248633 O43933 UPI0000001C39 NM_000466.2 tolerated(0.11) 5/24 hmmpanther:PTHR23077,hmmpanther:PTHR23077:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 92517352 92517352 C A 1 0 0 0 0 1 0 0 0 11825 595 21 2 2 PEX1 7 92517352 Missense_Mutation SNP C C3N-00560_T 385552 92517352 66828621 495 17184 COL1A2 0 . GRCh38 7 94430312 94430312 + Silent SNP C C T rs138451009 C3N-00560_T C3N-00560_N C C c.4020C>T p.= p.P1340P ENST00000297268 52/52 357 273 84 306 306 0 strelka-varscan-mutect COL1A2,synonymous_variant,p.=,ENST00000297268,NM_000089.3;COL1A2,synonymous_variant,p.=,ENST00000620463,;COL1A2,non_coding_transcript_exon_variant,,ENST00000481570,;COL1A2,non_coding_transcript_exon_variant,,ENST00000464916,;COL1A2,downstream_gene_variant,,ENST00000478215,;COL1A2,downstream_gene_variant,,ENST00000469732,;COL1A2,downstream_gene_variant,,ENST00000492110,;COL1A2,downstream_gene_variant,,ENST00000488121,; T ENST00000297268 Transcript synonymous_variant 4491/5411 4020/4101 1340/1366 P ccC/ccT rs138451009 1 1 COL1A2 HGNC HGNC:2198 protein_coding YES CCDS34682.1 ENSP00000297268 P08123 A0A0S2Z3H5 UPI00003B0CFC NM_000089.3 52/52 PD002078,Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF568,SMART_domains:SM00038 LOW 1 SNV 1 1 PASS rs138451009 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 94430312 94430312 C T 1 0 0 0 0 0 0 0 1 3466 668 24 3 3 COL1A2 7 94430312 Silent SNP C C3N-00560_T 1912960 94430312 64915661 496 17185 LMTK2 0 . GRCh38 7 98191927 98191927 + Nonsense_Mutation SNP G G T rs756530538 C3N-00560_T C3N-00560_N G G c.1462G>T p.Glu488Ter p.E488* ENST00000297293 11/14 292 227 65 274 274 0 strelka-varscan-mutect LMTK2,stop_gained,p.Glu488Ter,ENST00000297293,NM_014916.3; T ENST00000297293 Transcript stop_gained 1755/8946 1462/4512 488/1503 E/* Gag/Tag rs756530538 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 11/14 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF357 HIGH 1 SNV 1 1 PASS rs756530538 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 98191927 98191927 G T 1 0 0 0 0 0 1 0 0 8786 1059 37 1 1 LMTK2 7 98191927 Nonsense_Mutation SNP G C3N-00560_T 3761615 98191927 61154046 497 17186 OR2AE1 0 . GRCh38 7 99876800 99876800 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.234C>A p.= p.I78I ENST00000316368 1/1 253 175 78 213 213 0 strelka-varscan-mutect OR2AE1,synonymous_variant,p.=,ENST00000316368,NM_001005276.1;TRIM4,downstream_gene_variant,,ENST00000447480,;CYP3A52P,downstream_gene_variant,,ENST00000563326,; T ENST00000316368 Transcript synonymous_variant 258/1071 234/972 78/323 I atC/atA COSM377294 1 -1 OR2AE1 HGNC HGNC:15087 protein_coding YES CCDS34696.1 ENSP00000313936 Q8NHA4 UPI000004B1E7 NM_001005276.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF196,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 99876800 99876800 G T 1 0 0 0 0 0 0 0 1 11060 1164 41 2 2 OR2AE1 7 99876800 Silent SNP G C3N-00560_T 1684873 99876800 59469173 498 17187 NYAP1 0 . GRCh38 7 100491059 100491059 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.2232C>T p.= p.P744P ENST00000300179 6/7 192 127 65 144 144 0 strelka-varscan-mutect NYAP1,synonymous_variant,p.=,ENST00000300179,NM_173564.3;NYAP1,synonymous_variant,p.=,ENST00000454988,;NYAP1,non_coding_transcript_exon_variant,,ENST00000496985,;NYAP1,non_coding_transcript_exon_variant,,ENST00000489641,; T ENST00000300179 Transcript synonymous_variant 2391/3581 2232/2526 744/841 P ccC/ccT 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 6/7 Pfam_domain:PF15452,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 LOW 1 SNV 2 1 PASS rs1383745759 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 100491059 100491059 C T 1 0 0 0 0 0 0 0 1 10872 610 22 3 3 NYAP1 7 100491059 Silent SNP C C3N-00560_T 614259 100491059 58854914 499 17188 EPHB4 0 . GRCh38 7 100818556 100818556 + Silent SNP C C A rs776463916 C3N-00560_T C3N-00560_N C C c.1386G>T p.= p.G462G ENST00000358173 7/17 300 215 85 215 215 0 strelka-varscan-mutect EPHB4,synonymous_variant,p.=,ENST00000358173,NM_004444.4;EPHB4,synonymous_variant,p.=,ENST00000360620,;EPHB4,intron_variant,,ENST00000616502,;RN7SL750P,downstream_gene_variant,,ENST00000582814,;EPHB4,non_coding_transcript_exon_variant,,ENST00000477446,;EPHB4,intron_variant,,ENST00000489808,;EPHB4,non_coding_transcript_exon_variant,,ENST00000487222,;EPHB4,non_coding_transcript_exon_variant,,ENST00000492878,;EPHB4,upstream_gene_variant,,ENST00000478459,; A ENST00000358173 Transcript synonymous_variant 1855/4329 1386/2964 462/987 G ggG/ggT rs776463916 1 -1 EPHB4 HGNC HGNC:3395 protein_coding YES CCDS5706.1 ENSP00000350896 P54760 Q541P7 UPI0000000DBB NM_004444.4 7/17 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF296,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs776463916 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 100818556 100818556 C A 1 0 0 0 0 0 0 0 1 5024 610 22 2 2 EPHB4 7 100818556 Silent SNP C C3N-00560_T 327497 100818556 58527417 500 17189 ACHE 0 . GRCh38 7 100892524 100892524 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1363C>A p.= p.R455R ENST00000302913 3/5 79 56 23 52 52 0 strelka-varscan-mutect ACHE,synonymous_variant,p.=,ENST00000302913,NM_015831.2;ACHE,synonymous_variant,p.=,ENST00000412389,;ACHE,synonymous_variant,p.=,ENST00000411582,NM_001302621.1;ACHE,synonymous_variant,p.=,ENST00000241069,NM_000665.4;ACHE,synonymous_variant,p.=,ENST00000428317,NM_001302622.1;ACHE,synonymous_variant,p.=,ENST00000419336,NM_001282449.1;ACHE,intron_variant,,ENST00000430554,;ACHE,intron_variant,,ENST00000426415,;SRRT,downstream_gene_variant,,ENST00000614484,NM_001128852.1;SRRT,downstream_gene_variant,,ENST00000618262,NM_001128853.1;SRRT,downstream_gene_variant,,ENST00000611405,NM_015908.5;SRRT,downstream_gene_variant,,ENST00000618411,NM_001128854.1;SRRT,downstream_gene_variant,,ENST00000448764,;UFSP1,upstream_gene_variant,,ENST00000388761,NM_001015072.3;ACHE,downstream_gene_variant,,ENST00000441605,;ACHE,downstream_gene_variant,,ENST00000445236,;ACHE,downstream_gene_variant,,ENST00000619863,;ACHE,3_prime_UTR_variant,,ENST00000442452,;ACHE,intron_variant,,ENST00000454485,;ACHE,intron_variant,,ENST00000440755,;SRRT,downstream_gene_variant,,ENST00000478693,;SRRT,downstream_gene_variant,,ENST00000477529,;SRRT,downstream_gene_variant,,ENST00000445337,; T ENST00000302913 Transcript synonymous_variant 1502/2956 1363/1854 455/617 R Cgg/Agg 1 -1 ACHE HGNC HGNC:108 protein_coding YES CCDS5710.1 ENSP00000303211 P22303 UPI0000140DF0 NM_015831.2 3/5 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF154,Low_complexity_(Seg):seg,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS rs1296445238 . 0 200 9 0 0 0 0 0 -20 0.9999983 1 1 1 0 T 2 4 56 100892524 100892524 G T 1 0 0 0 0 0 0 0 1 179 1115 39 1 1 ACHE 7 100892524 Silent SNP G C3N-00560_T 73968 100892524 58453449 501 17190 ACHE 0 . GRCh38 7 100894075 100894075 + Missense_Mutation SNP A A T rs747647567 C3N-00560_T C3N-00560_N A A c.158T>A p.Leu53Gln p.L53Q ENST00000302913 2/5 44 32 12 57 56 1 strelka-varscan-mutect ACHE,missense_variant,p.Leu53Gln,ENST00000302913,NM_015831.2;ACHE,missense_variant,p.Leu53Gln,ENST00000412389,;ACHE,missense_variant,p.Leu53Gln,ENST00000411582,NM_001302621.1;ACHE,missense_variant,p.Leu53Gln,ENST00000241069,NM_000665.4;ACHE,missense_variant,p.Leu53Gln,ENST00000428317,NM_001302622.1;ACHE,missense_variant,p.Leu53Gln,ENST00000419336,NM_001282449.1;ACHE,missense_variant,p.Leu53Gln,ENST00000430554,;ACHE,missense_variant,p.Leu53Gln,ENST00000426415,;ACHE,missense_variant,p.Leu53Gln,ENST00000441605,;UFSP1,upstream_gene_variant,,ENST00000388761,NM_001015072.3;ACHE,downstream_gene_variant,,ENST00000445236,;ACHE,downstream_gene_variant,,ENST00000619863,;ACHE,missense_variant,p.Leu53Gln,ENST00000454485,;ACHE,missense_variant,p.Leu53Gln,ENST00000440755,;ACHE,intron_variant,,ENST00000442452,; T ENST00000302913 Transcript missense_variant 297/2956 158/1854 53/617 L/Q cTg/cAg rs747647567 1 -1 ACHE HGNC HGNC:108 protein_coding YES CCDS5710.1 ENSP00000303211 P22303 UPI0000140DF0 NM_015831.2 deleterious(0.03) 2/5 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF154,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs747647567 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 100894075 100894075 A T 1 0 0 0 0 1 0 0 0 179 188 7 4 4 ACHE 7 100894075 Missense_Mutation SNP A C3N-00560_T 1551 100894075 58451898 502 17191 MUC12 0 . GRCh38 7 100999151 100999151 + Nonsense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.8588C>G p.Ser2863Ter p.S2863* ENST00000536621 2/12 1510 1400 110 1333 1333 0 varscan-mutect MUC12,stop_gained,p.Ser3006Ter,ENST00000379442,;MUC12,stop_gained,p.Ser2863Ter,ENST00000536621,NM_001164462.1; G ENST00000536621 Transcript stop_gained 8588/16321 8588/16008 2863/5335 S/* tCa/tGa 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 2/12 HIGH 1 SNV 5 1 PASS . . 3 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 56 100999151 100999151 C G 1 0 0 0 0 0 1 0 0 9969 838 29 4 4 MUC12 7 100999151 Nonsense_Mutation SNP C C3N-00560_T 105076 100999151 58346822 503 17192 MUC17 0 . GRCh38 7 101038010 101038010 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.6594C>A p.= p.A2198A ENST00000306151 3/13 149 107 42 100 100 0 strelka-varscan-mutect MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; A ENST00000306151 Transcript synonymous_variant 6658/14247 6594/13482 2198/4493 A gcC/gcA 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 101038010 101038010 C A 1 0 0 0 0 0 0 0 1 9973 610 22 2 2 MUC17 7 101038010 Silent SNP C C3N-00560_T 38859 101038010 58307963 504 17193 MUC17 0 . GRCh38 7 101043604 101043604 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.12188C>A p.Pro4063Gln p.P4063Q ENST00000306151 3/13 189 128 61 151 151 0 strelka-varscan-mutect MUC17,missense_variant,p.Pro4063Gln,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Pro4063Gln,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; A ENST00000306151 Transcript missense_variant 12252/14247 12188/13482 4063/4493 P/Q cCa/cAa 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0.01) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999:SF1,hmmpanther:PTHR37999 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 101043604 101043604 C A 1 0 0 0 0 1 0 0 0 9973 594 21 2 2 MUC17 7 101043604 Missense_Mutation SNP C C3N-00560_T 5594 101043604 58302369 505 17194 CUX1 0 . GRCh38 7 102248567 102248567 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4076G>T p.Gly1359Val p.G1359V ENST00000360264 24/24 245 176 69 147 147 0 strelka-varscan-mutect CUX1,missense_variant,p.Gly1359Val,ENST00000360264,NM_001202543.1;CUX1,missense_variant,p.Gly1348Val,ENST00000292535,NM_181552.3;CUX1,missense_variant,p.Gly1326Val,ENST00000549414,;CUX1,missense_variant,p.Gly1292Val,ENST00000550008,;CUX1,missense_variant,p.Gly1246Val,ENST00000546411,;CUX1,missense_variant,p.Gly1190Val,ENST00000556210,;CUX1,intron_variant,,ENST00000437600,NM_001913.4;CUX1,intron_variant,,ENST00000622516,NM_181500.3;CUX1,intron_variant,,ENST00000292538,;CUX1,intron_variant,,ENST00000547394,NM_001202544.2;CUX1,intron_variant,,ENST00000425244,NM_001202545.2;CUX1,intron_variant,,ENST00000393824,NM_001202546.2;CUX1,intron_variant,,ENST00000560541,;CUX1,intron_variant,,ENST00000558836,; T ENST00000360264 Transcript missense_variant 4096/13762 4076/4551 1359/1516 G/V gGc/gTc 1 1 CUX1 HGNC HGNC:2557 protein_coding YES CCDS56498.1 ENSP00000353401 P39880 UPI00001AEB98 NM_001202543.1 tolerated(0.2) 24/24 hmmpanther:PTHR14043:SF4,hmmpanther:PTHR14043 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 102248567 102248567 G T 1 0 0 0 0 1 0 0 0 3874 1203 42 2 2 CUX1 7 102248567 Missense_Mutation SNP G C3N-00560_T 1204963 102248567 57097406 506 17195 PSMC2 0 . GRCh38 7 103366117 103366117 + Silent SNP A A T C3N-00560_T C3N-00560_N A A c.798A>T p.= p.T266T ENST00000435765 10/13 152 109 43 167 167 0 strelka-varscan-mutect PSMC2,synonymous_variant,p.=,ENST00000435765,;PSMC2,synonymous_variant,p.=,ENST00000292644,NM_002803.3;SLC26A5,intron_variant,,ENST00000339444,NM_206883.2;SLC26A5,intron_variant,,ENST00000393735,NM_206884.2;SLC26A5,intron_variant,,ENST00000356767,NM_206885.2;PSMC2,downstream_gene_variant,,ENST00000457587,;PSMC2,downstream_gene_variant,,ENST00000425206,NM_001204453.1;PSMC2,downstream_gene_variant,,ENST00000460021,; T ENST00000435765 Transcript synonymous_variant 1209/3054 798/1302 266/433 T acA/acT COSM3083863 1 1 PSMC2 HGNC HGNC:9548 protein_coding YES CCDS5731.1 ENSP00000391211 P35998 A0A140VK70 UPI000013237A 10/13 hmmpanther:PTHR23073,TIGRFAM_domain:TIGR01242,Pfam_domain:PF00004,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1 LOW 1 SNV 5 1 1 PASS rs1429473692 . 0 203 0 0 5 0 0 0 -20 0.8757031 1 1 1 0 T 2 4 56 103366117 103366117 A T 1 0 0 0 0 0 0 0 1 12837 117 5 4 4 PSMC2 7 103366117 Silent SNP A C3N-00560_T 1117550 103366117 55979856 507 17196 SLC26A5 0 . GRCh38 7 103413066 103413066 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.339G>T p.= p.L113L ENST00000306312 5/20 388 269 119 337 337 0 strelka-varscan-mutect SLC26A5,synonymous_variant,p.=,ENST00000306312,NM_198999.2;SLC26A5,synonymous_variant,p.=,ENST00000354356,;SLC26A5,synonymous_variant,p.=,ENST00000432958,NM_001167962.1;SLC26A5,synonymous_variant,p.=,ENST00000393730,;SLC26A5,synonymous_variant,p.=,ENST00000339444,NM_206883.2;SLC26A5,synonymous_variant,p.=,ENST00000393727,;SLC26A5,synonymous_variant,p.=,ENST00000393723,;SLC26A5,synonymous_variant,p.=,ENST00000393735,NM_206884.2;SLC26A5,synonymous_variant,p.=,ENST00000356767,NM_206885.2;SLC26A5,intron_variant,,ENST00000393729,;SLC26A5,synonymous_variant,p.=,ENST00000423416,;SLC26A5,synonymous_variant,p.=,ENST00000445809,;SLC26A5,synonymous_variant,p.=,ENST00000454864,;SLC26A5,intron_variant,,ENST00000456463,;SLC26A5,intron_variant,,ENST00000487407,; A ENST00000306312 Transcript synonymous_variant 601/2689 339/2235 113/744 L ctG/ctT 1 -1 SLC26A5 HGNC HGNC:9359 protein_coding YES CCDS5733.1 ENSP00000304783 P58743 UPI0000132195 NM_198999.2 5/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR11814:SF32,hmmpanther:PTHR11814,PROSITE_patterns:PS01130,TIGRFAM_domain:TIGR00815,Pfam_domain:PF00916 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 103413066 103413066 C A 1 0 0 0 0 0 0 0 1 14790 465 17 2 2 SLC26A5 7 103413066 Silent SNP C C3N-00560_T 46949 103413066 55932907 508 17197 SLC26A3 0 . GRCh38 7 107783353 107783353 + Splice_Site SNP C C T novel C3N-00560_T C3N-00560_N C C c.972-1G>A p.X324_splice ENST00000340010 274 182 92 262 262 0 strelka-varscan-mutect SLC26A3,splice_acceptor_variant,,ENST00000340010,NM_000111.2;SLC26A3,splice_acceptor_variant,,ENST00000379083,;SLC26A3,splice_acceptor_variant,,ENST00000468551,; T ENST00000340010 Transcript splice_acceptor_variant -/2863 972/2295 324/764 1 -1 SLC26A3 HGNC HGNC:3018 protein_coding YES CCDS5748.1 ENSP00000345873 P40879 UPI000000128C NM_000111.2 8/20 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 107783353 107783353 C T 1 0 0 0 0 0 0 1 0 14788 927 32 3 3 SLC26A3 7 107783353 Splice_Site SNP C C3N-00560_T 4370287 107783353 51562620 509 17198 LAMB4 0 . GRCh38 7 108057843 108057843 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3368G>T p.Gly1123Val p.G1123V ENST00000388781 24/34 220 144 76 181 181 0 strelka-varscan-mutect LAMB4,missense_variant,p.Gly1123Val,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Gly1123Val,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Gly149Val,ENST00000422975,;LAMB4,downstream_gene_variant,,ENST00000475469,;LAMB4,downstream_gene_variant,,ENST00000471677,; A ENST00000388781 Transcript missense_variant 3452/5858 3368/5286 1123/1761 G/V gGg/gTg 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 tolerated(0.51) 24/34 Gene3D:2.10.25.10,Prints_domain:PR00011,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00180 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 108057843 108057843 C A 1 0 0 0 0 1 0 0 0 8517 623 22 2 2 LAMB4 7 108057843 Missense_Mutation SNP C C3N-00560_T 274490 108057843 51288130 510 17199 GPR85 0 . GRCh38 7 113083824 113083824 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.898C>A p.Pro300Thr p.P300T ENST00000297146 3/3 204 135 69 175 175 0 strelka-varscan-mutect GPR85,missense_variant,p.Pro300Thr,ENST00000297146,NM_001146265.1,NM_018970.6;GPR85,missense_variant,p.Pro300Thr,ENST00000424100,NM_001146267.1;GPR85,missense_variant,p.Pro300Thr,ENST00000449591,NM_001146266.1;GPR85,downstream_gene_variant,,ENST00000438062,;GPR85,downstream_gene_variant,,ENST00000449735,;GPR85,downstream_gene_variant,,ENST00000487573,;GPR85,missense_variant,p.Pro300Thr,ENST00000610164,; T ENST00000297146 Transcript missense_variant 1502/5079 898/1113 300/370 P/T Ccc/Acc COSM3928758,COSM598655 1 -1 GPR85 HGNC HGNC:4536 protein_coding YES CCDS5758.1 ENSP00000297146 P60893 A4D0T8 UPI0000004048 NM_001146265.1,NM_018970.6 deleterious(0) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 113083824 113083824 G T 1 0 0 0 0 1 0 0 0 6596 1232 43 2 2 GPR85 7 113083824 Missense_Mutation SNP G C3N-00560_T 5025981 113083824 46262149 511 17200 ST7 0 . GRCh38 7 117129830 117129830 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.432G>C p.Arg144Ser p.R144S ENST00000265437 4/16 302 246 56 215 214 1 strelka-varscan-mutect ST7,missense_variant,p.Arg144Ser,ENST00000265437,NM_021908.2;ST7,missense_variant,p.Arg94Ser,ENST00000393443,;ST7,missense_variant,p.Arg101Ser,ENST00000393447,;ST7,missense_variant,p.Arg101Ser,ENST00000465133,;ST7,missense_variant,p.Arg144Ser,ENST00000323984,;ST7,missense_variant,p.Arg144Ser,ENST00000393449,;ST7,missense_variant,p.Arg144Ser,ENST00000393446,;ST7,missense_variant,p.Arg101Ser,ENST00000393444,;ST7,missense_variant,p.Arg144Ser,ENST00000393451,NM_018412.3;ST7,missense_variant,p.Arg98Ser,ENST00000432298,;ST7,missense_variant,p.Arg98Ser,ENST00000422922,;ST7,missense_variant,p.Arg144Ser,ENST00000446490,;ST7,missense_variant,p.Arg92Ser,ENST00000490039,;ST7,missense_variant,p.Arg92Ser,ENST00000477742,;ST7,missense_variant,p.Arg92Ser,ENST00000420755,;ST7,downstream_gene_variant,,ENST00000449366,;ST7-AS2,intron_variant,,ENST00000432541,;ST7-AS2,intron_variant,,ENST00000434993,;ST7-AS2,intron_variant,,ENST00000442719,;ST7,non_coding_transcript_exon_variant,,ENST00000487459,;ST7,non_coding_transcript_exon_variant,,ENST00000489293,;ST7,non_coding_transcript_exon_variant,,ENST00000467538,;ST7,3_prime_UTR_variant,,ENST00000438863,;ST7,intron_variant,,ENST00000443979,; C ENST00000265437 Transcript missense_variant 646/2899 432/1758 144/585 R/S agG/agC 1 1 ST7 HGNC HGNC:11351 protein_coding YES CCDS5770.1 ENSP00000265437 Q9NRC1 X5DRA0 UPI00000702A3 NM_021908.2 deleterious(0) 4/16 hmmpanther:PTHR12745,Pfam_domain:PF04184 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 117129830 117129830 G C 1 0 0 0 0 1 0 0 0 15607 1223 43 4 4 ST7 7 117129830 Missense_Mutation SNP G C3N-00560_T 4046006 117129830 42216143 512 17201 PTPRZ1 0 . GRCh38 7 122012031 122012031 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2985A>T p.Glu995Asp p.E995D ENST00000393386 12/30 304 215 89 252 252 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.Glu995Asp,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; T ENST00000393386 Transcript missense_variant 3396/8175 2985/6948 995/2315 E/D gaA/gaT 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 tolerated_low_confidence(0.76) 12/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 122012031 122012031 A T 1 0 0 0 0 1 0 0 0 12969 98 4 4 4 PTPRZ1 7 122012031 Missense_Mutation SNP A C3N-00560_T 4882201 122012031 37333942 513 17202 RNF148 0 . GRCh38 7 122702562 122702562 + Frame_Shift_Del DEL C C - rs751949808 C3N-00560_T C3N-00560_N C C c.189delG p.Asn64IlefsTer26 p.N64Ifs*26 ENST00000434824 1/1 155 105 50 156 156 0 sindel-varindel-pindel RNF148,frameshift_variant,p.Asn64IlefsTer26,ENST00000434824,NM_198085.1;CADPS2,intron_variant,,ENST00000615869,;CADPS2,intron_variant,,ENST00000313070,NM_001167940.1;CADPS2,intron_variant,,ENST00000334010,;CADPS2,intron_variant,,ENST00000412584,NM_001009571.3;CADPS2,intron_variant,,ENST00000449022,NM_017954.10;RNF148,intron_variant,,ENST00000447240,;RNF133,upstream_gene_variant,,ENST00000340112,NM_139175.1; - ENST00000434824 Transcript frameshift_variant 406/1304 189/918 63/305 G/X ggG/gg rs751949808 1 -1 RNF148 HGNC HGNC:22411 protein_coding YES CCDS47692.1 ENSP00000388207 Q8N7C7 UPI000006FF1E NM_198085.1 1/1 hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF53 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 122702562 122702562 C - 1 0 1 0 1 0 0 0 0 13627 842 30 0 0 RNF148 7 122702562 Frame_Shift_Del DEL C C3N-00560_T 690531 122702562 36643411 514 17203 LMOD2 0 . GRCh38 7 123663135 123663135 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1549C>A p.Pro517Thr p.P517T ENST00000458573 2/3 293 224 69 260 260 0 strelka-varscan-mutect LMOD2,missense_variant,p.Pro517Thr,ENST00000458573,NM_207163.1;LMOD2,missense_variant,p.Pro124Thr,ENST00000456238,; A ENST00000458573 Transcript missense_variant 1706/2346 1549/1644 517/547 P/T Cca/Aca 1 1 LMOD2 HGNC HGNC:6648 protein_coding YES CCDS47693.1 ENSP00000411932 Q6P5Q4 UPI0001572CCA NM_207163.1 deleterious(0.01) 2/3 hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF12 MODERATE 1 SNV 2 1 PASS rs1256156410 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 123663135 123663135 C A 1 0 0 0 0 1 0 0 0 8784 623 22 2 2 LMOD2 7 123663135 Missense_Mutation SNP C C3N-00560_T 960573 123663135 35682838 515 17204 GRM8 0 . GRCh38 7 127106676 127106676 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.547C>A p.Leu183Ile p.L183I ENST00000339582 3/11 388 276 112 314 313 1 strelka-varscan-mutect GRM8,missense_variant,p.Leu183Ile,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Leu183Ile,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Leu183Ile,ENST00000457830,;GRM8,upstream_gene_variant,,ENST00000465844,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,non_coding_transcript_exon_variant,,ENST00000448250,;GRM8,non_coding_transcript_exon_variant,,ENST00000473254,;GRM8,missense_variant,p.Leu183Ile,ENST00000472701,;GRM8,missense_variant,p.Leu183Ile,ENST00000341617,; T ENST00000339582 Transcript missense_variant 1356/4057 547/2727 183/908 L/I Cta/Ata 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious(0) 3/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 127106676 127106676 G T 1 0 0 0 0 1 0 0 0 6685 962 34 2 2 GRM8 7 127106676 Missense_Mutation SNP G C3N-00560_T 3443541 127106676 32239297 516 17205 FAM71F1 0 . GRCh38 7 128718890 128718890 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.494A>T p.Gln165Leu p.Q165L ENST00000315184 3/7 260 184 76 195 195 0 strelka-varscan-mutect FAM71F1,splice_acceptor_variant,,ENST00000621392,;FAM71F1,splice_acceptor_variant,,ENST00000485070,NM_001282789.1;FAM71F1,missense_variant,p.Gln165Leu,ENST00000315184,NM_001282788.1,NM_032599.3;FAM71F1,missense_variant,p.Gln21Leu,ENST00000466842,;FAM71F1,splice_acceptor_variant,,ENST00000483459,;FAM71F1,intron_variant,,ENST00000469348,;FAM71F1,splice_acceptor_variant,,ENST00000484425,;FAM71F1,missense_variant,p.Gln165Leu,ENST00000471558,;FAM71F1,non_coding_transcript_exon_variant,,ENST00000493738,; T ENST00000315184 Transcript missense_variant 547/1718 494/1035 165/344 Q/L cAg/cTg 1 1 FAM71F1 HGNC HGNC:30704 protein_coding YES CCDS5804.1 ENSP00000326652 Q96KD3 A0A140VJJ3 UPI000006D961 NM_001282788.1,NM_032599.3 deleterious(0) 3/7 Pfam_domain:PF12480,hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF13 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999983 1 1 1 0 T 3 4 56 128718890 128718890 A T 1 0 0 0 0 1 0 0 0 5477 202 7 4 4 FAM71F1 7 128718890 Missense_Mutation SNP A C3N-00560_T 1612214 128718890 30627083 517 17206 FLNC 0 . GRCh38 7 128843466 128843466 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.2700C>A p.= p.A900A ENST00000325888 18/48 482 319 163 385 385 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;FLNC,downstream_gene_variant,,ENST00000388853,; A ENST00000325888 Transcript synonymous_variant 2961/9188 2700/8178 900/2725 A gcC/gcA 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 18/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 128843466 128843466 C A 1 0 0 0 0 0 0 0 1 5791 581 21 2 2 FLNC 7 128843466 Silent SNP C C3N-00560_T 124576 128843466 30502507 518 17207 FLNC 0 . GRCh38 7 128848708 128848708 + Silent SNP C C A C3N-00560_T C3N-00560_N C C c.4728C>A p.= p.V1576V ENST00000325888 27/48 665 483 182 486 486 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,; A ENST00000325888 Transcript synonymous_variant 4989/9188 4728/8178 1576/2725 V gtC/gtA COSM390309 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 27/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 1 LOW 1 SNV 1 1 1 PASS rs1222823077 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 128848708 128848708 C A 1 0 0 0 0 0 0 0 1 5791 842 30 2 2 FLNC 7 128848708 Silent SNP C C3N-00560_T 5242 128848708 30497265 519 17208 SMO 0 . GRCh38 7 129208814 129208814 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1320G>T p.Lys440Asn p.K440N ENST00000249373 7/12 261 184 77 197 197 0 strelka-varscan-mutect SMO,missense_variant,p.Lys440Asn,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,missense_variant,p.Lys134Asn,ENST00000462420,;SMO,non_coding_transcript_exon_variant,,ENST00000495998,;SMO,upstream_gene_variant,,ENST00000475779,; T ENST00000249373 Transcript missense_variant 1600/3738 1320/2364 440/787 K/N aaG/aaT 1 1 SMO HGNC HGNC:11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 UPI0000050447 NM_005631.4 deleterious(0.01) 7/12 PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF35,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE 1 SNV 1 1 PASS rs1374043825 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 129208814 129208814 G T 1 0 0 0 0 1 0 0 0 15121 991 35 2 2 SMO 7 129208814 Missense_Mutation SNP G C3N-00560_T 360106 129208814 30137159 520 17209 AHCYL2 0 . GRCh38 7 129425097 129425097 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1664A>T p.Glu555Val p.E555V ENST00000325006 15/17 360 251 109 278 278 0 strelka-varscan-mutect AHCYL2,missense_variant,p.Glu555Val,ENST00000325006,NM_015328.3;AHCYL2,missense_variant,p.Glu554Val,ENST00000446544,NM_001130720.2;AHCYL2,missense_variant,p.Glu452Val,ENST00000474594,NM_001130723.2;AHCYL2,missense_variant,p.Glu452Val,ENST00000490911,NM_001130722.2;AHCYL2,missense_variant,p.Glu462Val,ENST00000466924,;AHCYL2,non_coding_transcript_exon_variant,,ENST00000477028,; T ENST00000325006 Transcript missense_variant 1718/5056 1664/1836 555/611 E/V gAg/gTg 1 1 AHCYL2 HGNC HGNC:22204 protein_coding YES CCDS5812.1 ENSP00000315931 Q96HN2 UPI00001354E4 NM_015328.3 deleterious(0.03) 15/17 hmmpanther:PTHR23420:SF2,hmmpanther:PTHR23420,TIGRFAM_domain:TIGR00936,Gene3D:3.40.50.1480,SMART_domains:SM00996,Superfamily_domains:SSF52283 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 129425097 129425097 A T 1 0 0 0 0 1 0 0 0 488 304 11 4 4 AHCYL2 7 129425097 Missense_Mutation SNP A C3N-00560_T 216283 129425097 29920876 521 17210 SLC35B4 0 . GRCh38 7 134296467 134296467 + Splice_Site SNP C C T novel C3N-00560_T C3N-00560_N C C c.674-1G>A p.X225_splice ENST00000378509 242 192 50 157 157 0 strelka-varscan-mutect SLC35B4,splice_acceptor_variant,,ENST00000378509,NM_032826.4;SLC35B4,downstream_gene_variant,,ENST00000470969,;SLC35B4,upstream_gene_variant,,ENST00000466599,;SLC35B4,splice_acceptor_variant,,ENST00000416907,; T ENST00000378509 Transcript splice_acceptor_variant -/6797 674/996 225/331 1 -1 SLC35B4 HGNC HGNC:20584 protein_coding YES CCDS34756.1 ENSP00000367770 Q969S0 UPI00000377B5 NM_032826.4 8/9 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 134296467 134296467 C T 1 0 0 0 0 0 0 1 0 14848 927 32 3 3 SLC35B4 7 134296467 Splice_Site SNP C C3N-00560_T 4871370 134296467 25049506 522 17211 AKR1B10 0 . GRCh38 7 134538257 134538257 + Missense_Mutation SNP C C A rs142388608 C3N-00560_T C3N-00560_N C C c.805C>A p.Arg269Ser p.R269S ENST00000359579 8/10 320 187 133 220 220 0 strelka-varscan-mutect AKR1B10,missense_variant,p.Arg269Ser,ENST00000359579,NM_020299.4;AKR1B10,non_coding_transcript_exon_variant,,ENST00000498818,;AKR1B10,non_coding_transcript_exon_variant,,ENST00000496435,;AKR1B10,downstream_gene_variant,,ENST00000475559,; A ENST00000359579 Transcript missense_variant 1125/1590 805/951 269/316 R/S Cgc/Agc rs142388608,COSM5241234 1 1 AKR1B10 HGNC HGNC:382 protein_coding YES CCDS5832.1 ENSP00000352584 O60218 UPI00000362E9 NM_020299.4 deleterious(0) 8/10 Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,PROSITE_patterns:PS00063,hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF238,Superfamily_domains:SSF51430 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs142388608 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 134538257 134538257 C A 1 0 0 0 0 1 0 0 0 551 536 19 1 1 AKR1B10 7 134538257 Missense_Mutation SNP C C3N-00560_T 241790 134538257 24807716 523 17212 AKR1B15 0 . GRCh38 7 134575833 134575833 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.649C>A p.Pro217Thr p.P217T ENST00000457545 8/12 489 428 61 308 308 0 varscan-mutect AKR1B15,missense_variant,p.Pro217Thr,ENST00000457545,NM_001080538.2;AKR1B15,missense_variant,p.Pro217Thr,ENST00000423958,; A ENST00000457545 Transcript missense_variant 909/1621 649/1035 217/344 P/T Cca/Aca 1 1 AKR1B15 HGNC HGNC:37281 protein_coding YES CCDS47715.2 ENSP00000389289 C9JRZ8 UPI00004193E1 NM_001080538.2 deleterious(0) 8/12 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF197,Pfam_domain:PF00248,Gene3D:3.20.20.100,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430,Prints_domain:PR00069 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 134575833 134575833 C A 1 0 0 0 0 1 0 0 0 552 623 22 2 2 AKR1B15 7 134575833 Missense_Mutation SNP C C3N-00560_T 37576 134575833 24770140 524 17213 STRA8 0 . GRCh38 7 135258428 135258428 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.929T>A p.Phe310Tyr p.F310Y ENST00000275764 9/9 174 95 79 88 87 1 strelka-varscan-mutect STRA8,missense_variant,p.Phe310Tyr,ENST00000275764,NM_182489.1;RP11-260N14.1,intron_variant,,ENST00000637483,; A ENST00000275764 Transcript missense_variant 929/993 929/993 310/330 F/Y tTt/tAt 1 1 STRA8 HGNC HGNC:30653 protein_coding YES CCDS5839.1 ENSP00000275764 Q7Z7C7 UPI00001A36D9 NM_182489.1 tolerated(0.28) 9/9 hmmpanther:PTHR35254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 135258428 135258428 T A 1 0 0 0 0 1 0 0 0 15704 1841 64 4 4 STRA8 7 135258428 Missense_Mutation SNP T C3N-00560_T 682595 135258428 24087545 525 17214 CHRM2 0 . GRCh38 7 137015554 137015554 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.689C>T p.Pro230Leu p.P230L ENST00000445907 3/3 509 384 125 427 427 0 strelka-varscan-mutect CHRM2,missense_variant,p.Pro230Leu,ENST00000445907,NM_001006630.1,NM_001006627.1;CHRM2,missense_variant,p.Pro230Leu,ENST00000401861,NM_000739.2,NM_001006626.1,NM_001006628.1;CHRM2,missense_variant,p.Pro230Leu,ENST00000453373,NM_001006631.1,NM_001006629.1;CHRM2,missense_variant,p.Pro230Leu,ENST00000320658,NM_001006632.1;AC009264.1,intron_variant,,ENST00000439694,;AC009264.1,intron_variant,,ENST00000425981,;AC009264.1,intron_variant,,ENST00000586239,;AC009264.1,intron_variant,,ENST00000597642,;AC009264.1,intron_variant,,ENST00000598184,;AC009264.1,intron_variant,,ENST00000593789,;AC009264.1,intron_variant,,ENST00000592183,; T ENST00000445907 Transcript missense_variant 1217/5918 689/1401 230/466 P/L cCc/cTc COSM3633697 1 1 CHRM2 HGNC HGNC:1951 protein_coding YES CCDS5843.1 ENSP00000399745 P08172 A4D1Q0 UPI0000050410 NM_001006630.1,NM_001006627.1 tolerated(0.19) 3/3 Pfam_domain:PF00001,Prints_domain:PR00539,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF57,SMART_domains:SM01381 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 137015554 137015554 C T 1 0 0 0 0 1 0 0 0 3137 623 22 3 3 CHRM2 7 137015554 Missense_Mutation SNP C C3N-00560_T 1757126 137015554 22330419 526 17215 SVOPL 0 . GRCh38 7 138644722 138644722 + Missense_Mutation SNP C C A rs143599875 C3N-00560_T C3N-00560_N C C c.784G>T p.Val262Phe p.V262F ENST00000419765 8/15 144 70 74 91 91 0 strelka-varscan-mutect SVOPL,missense_variant,p.Val142Phe,ENST00000421622,;SVOPL,missense_variant,p.Val262Phe,ENST00000419765,NM_001139456.1;SVOPL,missense_variant,p.Val110Phe,ENST00000436657,NM_174959.3;SVOPL,missense_variant,p.Val110Phe,ENST00000288513,;SVOPL,missense_variant,p.Val15Phe,ENST00000441685,;AC013429.4,downstream_gene_variant,,ENST00000456604,; A ENST00000419765 Transcript missense_variant 818/1523 784/1479 262/492 V/F Gtc/Ttc rs143599875 1 -1 SVOPL HGNC HGNC:27034 protein_coding YES CCDS47721.1 ENSP00000405482 Q8N434 UPI0001565476 NM_001139456.1 tolerated(0.36) 8/15 Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF168,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS rs143599875 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 138644722 138644722 C A 1 0 0 0 0 1 0 0 0 15809 550 19 1 1 SVOPL 7 138644722 Missense_Mutation SNP C C3N-00560_T 1629168 138644722 20701251 527 17216 BRAF 0 . GRCh38 7 140924700 140924700 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4G>T p.Ala2Ser p.A2S ENST00000288602 1/18 248 184 64 164 164 0 strelka-varscan-mutect BRAF,missense_variant,p.Ala2Ser,ENST00000288602,NM_004333.4;BRAF,non_coding_transcript_exon_variant,,ENST00000469930,;BRAF,upstream_gene_variant,,ENST00000497784,; A ENST00000288602 Transcript missense_variant 65/2480 4/2301 2/766 A/S Gcg/Tcg 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious_low_confidence(0) 1/18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 140924700 140924700 C A 1 0 0 0 0 1 0 0 0 1665 739 26 2 2 BRAF 7 140924700 Missense_Mutation SNP C C3N-00560_T 2279978 140924700 18421273 528 17217 WEE2 0 . GRCh38 7 141714292 141714292 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.426C>A p.= p.P142P ENST00000397541 2/12 207 146 61 199 199 0 strelka-varscan-mutect WEE2,synonymous_variant,p.=,ENST00000397541,NM_001105558.1;WEE2,upstream_gene_variant,,ENST00000493845,;WEE2-AS1,non_coding_transcript_exon_variant,,ENST00000488785,;WEE2-AS1,non_coding_transcript_exon_variant,,ENST00000478332,;WEE2-AS1,non_coding_transcript_exon_variant,,ENST00000462383,;WEE2-AS1,non_coding_transcript_exon_variant,,ENST00000471512,;WEE2-AS1,intron_variant,,ENST00000495800,;WEE2-AS1,intron_variant,,ENST00000465110,;WEE2-AS1,intron_variant,,ENST00000459753,; A ENST00000397541 Transcript synonymous_variant 832/3061 426/1704 142/567 P ccC/ccA 1 1 WEE2 HGNC HGNC:19684 protein_coding YES CCDS43660.1 ENSP00000380675 P0C1S8 UPI000004E9D3 NM_001105558.1 2/12 hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF75,PIRSF_domain:PIRSF037281 LOW 1 SNV 2 1 PASS rs1404838196 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 141714292 141714292 C A 1 0 0 0 0 0 0 0 1 17902 610 22 2 2 WEE2 7 141714292 Silent SNP C C3N-00560_T 789592 141714292 17631681 529 17218 OR9A4 0 . GRCh38 7 141919348 141919348 + Missense_Mutation SNP G G T rs781997058 C3N-00560_T C3N-00560_N G G c.473G>T p.Trp158Leu p.W158L ENST00000548136 1/1 280 196 84 215 215 0 strelka-varscan-mutect OR9A4,missense_variant,p.Trp158Leu,ENST00000548136,NM_001001656.1;MGAM,intron_variant,,ENST00000465654,;MGAM,intron_variant,,ENST00000497554,; T ENST00000548136 Transcript missense_variant 532/1093 473/945 158/314 W/L tGg/tTg rs781997058 1 1 OR9A4 HGNC HGNC:15095 protein_coding YES CCDS43661.1 ENSP00000448789 Q8NGU2 A0A126GVB1 UPI0000041D24 NM_001001656.1 tolerated(0.67) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF216,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs781997058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 141919348 141919348 G T 1 0 0 0 0 1 0 0 0 11316 1357 47 2 2 OR9A4 7 141919348 Missense_Mutation SNP G C3N-00560_T 205056 141919348 17426625 530 17219 MGAM 0 . GRCh38 7 142036215 142036215 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2006T>A p.Leu669His p.L669H ENST00000549489 17/48 289 212 77 277 277 0 strelka-varscan-mutect MGAM,missense_variant,p.Leu669His,ENST00000475668,;MGAM,missense_variant,p.Leu669His,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Leu669His,ENST00000620571,;MGAM,downstream_gene_variant,,ENST00000495045,;MGAM,upstream_gene_variant,,ENST00000490593,; A ENST00000549489 Transcript missense_variant 2101/6525 2006/5574 669/1857 L/H cTc/cAc 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 17/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,PROSITE_patterns:PS00707,Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 142036215 142036215 T A 1 0 0 0 0 1 0 0 0 9499 1551 54 4 4 MGAM 7 142036215 Missense_Mutation SNP T C3N-00560_T 116867 142036215 17309758 531 17220 TRPV6 0 . GRCh38 7 142873588 142873588 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1768G>T p.Asp590Tyr p.D590Y ENST00000359396 13/15 461 346 115 404 404 0 strelka-varscan-mutect TRPV6,missense_variant,p.Asp590Tyr,ENST00000359396,NM_018646.5;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;TRPV6,downstream_gene_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000619250,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; A ENST00000359396 Transcript missense_variant 1894/2928 1768/2298 590/765 D/Y Gac/Tac 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 tolerated(0.29) 13/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS rs1158903250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 142873588 142873588 C A 1 0 0 0 0 1 0 0 0 17106 855 30 2 2 TRPV6 7 142873588 Missense_Mutation SNP C C3N-00560_T 837373 142873588 16472385 532 17221 TRPV5 0 . GRCh38 7 142915355 142915355 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1238C>A p.Ser413Tyr p.S413Y ENST00000265310 10/15 136 102 34 123 123 0 strelka-varscan-mutect TRPV5,missense_variant,p.Ser413Tyr,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Ser358Tyr,ENST00000439304,; T ENST00000265310 Transcript missense_variant 1587/2952 1238/2190 413/729 S/Y tCt/tAt 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 deleterious(0.03) 10/15 Pfam_domain:PF00520,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 142915355 142915355 G T 1 0 0 0 0 1 0 0 0 17105 942 33 2 2 TRPV5 7 142915355 Missense_Mutation SNP G C3N-00560_T 41767 142915355 16430618 533 17222 TRPV5 0 . GRCh38 7 142925635 142925635 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1016A>T p.Tyr339Phe p.Y339F ENST00000265310 8/15 477 328 149 403 403 0 strelka-varscan-mutect TRPV5,missense_variant,p.Tyr339Phe,ENST00000265310,NM_019841.6;TRPV5,missense_variant,p.Tyr339Phe,ENST00000442623,;TRPV5,missense_variant,p.Tyr284Phe,ENST00000439304,; A ENST00000265310 Transcript missense_variant 1365/2952 1016/2190 339/729 Y/F tAc/tTc 1 -1 TRPV5 HGNC HGNC:3145 protein_coding YES CCDS5875.1 ENSP00000265310 A0A0A6YY98 UPI0004620D64 NM_019841.6 deleterious(0.01) 8/15 Pfam_domain:PF00520,hmmpanther:PTHR10582,hmmpanther:PTHR10582:SF11,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 142925635 142925635 T A 1 0 0 0 0 1 0 0 0 17105 1638 57 4 4 TRPV5 7 142925635 Missense_Mutation SNP T C3N-00560_T 10280 142925635 16420338 534 17223 C7orf34 0 . GRCh38 7 142940545 142940545 + Silent SNP G G A rs550423222 C3N-00560_T C3N-00560_N G G c.402G>A p.= p.R134R ENST00000409607 2/2 305 197 108 277 277 0 strelka-varscan-mutect C7orf34,synonymous_variant,p.=,ENST00000409607,NM_178829.4;C7orf34,synonymous_variant,p.=,ENST00000458732,;KEL,downstream_gene_variant,,ENST00000355265,NM_000420.2;KEL,downstream_gene_variant,,ENST00000470850,;KEL,downstream_gene_variant,,ENST00000465697,;KEL,downstream_gene_variant,,ENST00000478969,; A ENST00000409607 Transcript synonymous_variant 443/766 402/444 134/147 R cgG/cgA rs550423222 1 1 C7orf34 HGNC HGNC:21750 protein_coding YES CCDS5876.2 ENSP00000386450 Q96L11 UPI00005A76EA NM_178829.4 2/2 LOW 1 SNV 1 1 PASS rs550423222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 142940545 142940545 G A 1 0 0 0 0 0 0 0 1 2139 1161 41 3 3 C7orf34 7 142940545 Silent SNP G C3N-00560_T 14910 142940545 16405428 535 17224 OR9A2 0 . GRCh38 7 143027120 143027120 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.13C>A p.His5Asn p.H5N ENST00000350513 1/1 35 20 15 22 22 0 strelka-varscan-mutect OR9A2,missense_variant,p.His5Asn,ENST00000350513,NM_001001658.1; T ENST00000350513 Transcript missense_variant 76/1038 13/933 5/310 H/N Cac/Aac 1 -1 OR9A2 HGNC HGNC:15093 protein_coding YES CCDS34767.1 ENSP00000316518 Q8NGT5 UPI0000041C18 NM_001001658.1 tolerated(0.28) 1/1 hmmpanther:PTHR24242:SF216,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 143027120 143027120 G T 1 0 0 0 0 1 0 0 0 11315 1348 47 2 2 OR9A2 7 143027120 Missense_Mutation SNP G C3N-00560_T 86575 143027120 16318853 536 17225 TCAF2 0 . GRCh38 7 143720468 143720468 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1409G>T p.Arg470Leu p.R470L ENST00000444908 3/7 40 27 13 50 50 0 strelka-varscan-mutect TCAF2,missense_variant,p.Arg470Leu,ENST00000441159,;TCAF2,missense_variant,p.Arg470Leu,ENST00000444908,NM_001130025.1;TCAF2,missense_variant,p.Arg470Leu,ENST00000357344,NM_173678.2;TCAF2,missense_variant,p.Arg306Leu,ENST00000411935,;TCAF2,missense_variant,p.Arg306Leu,ENST00000425618,NM_001130026.2;TCAF2,missense_variant,p.Arg285Leu,ENST00000518791,;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,; T ENST00000444908 Transcript missense_variant 1494/2976 1409/2538 470/845 R/L cGa/cTa 1 1 TCAF2 HGNC HGNC:26878 protein_coding YES CCDS34769.1 ENSP00000412724 A6NFQ2 UPI00001AF3A8 NM_001130025.1 tolerated(0.12) 3/7 hmmpanther:PTHR15730,hmmpanther:PTHR15730:SF4 MODERATE 1 SNV 1 1 PASS rs1435713501 . 27 179 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 143720468 143720468 G T 1 0 0 0 0 1 0 0 0 16071 1058 37 1 1 TCAF2 7 143720468 Missense_Mutation SNP G C3N-00560_T 693348 143720468 15625505 537 17226 OR2A14 0 . GRCh38 7 144130010 144130010 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.898C>G p.Leu300Val p.L300V ENST00000408899 1/1 101 75 26 95 95 0 strelka-varscan-mutect OR2A14,missense_variant,p.Leu300Val,ENST00000408899,NM_001001659.1;OR2A14,missense_variant,p.Leu300Val,ENST00000627593,; G ENST00000408899 Transcript missense_variant 953/1012 898/933 300/310 L/V Ctg/Gtg 1 1 OR2A14 HGNC HGNC:15084 protein_coding YES CCDS43672.1 ENSP00000386137 Q96R47 A0A126GVB0 UPI0000061E6E NM_001001659.1 deleterious(0.03) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF27,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs953814616 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 144130010 144130010 C G 1 0 0 0 0 1 0 0 0 11053 680 24 4 4 OR2A14 7 144130010 Missense_Mutation SNP C C3N-00560_T 409542 144130010 15215963 538 17227 NOBOX 0 . GRCh38 7 144398467 144398467 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1589C>T p.Ser530Phe p.S530F ENST00000467773 9/10 222 153 69 186 186 0 strelka-varscan-mutect NOBOX,missense_variant,p.Ser530Phe,ENST00000467773,NM_001080413.3;NOBOX,missense_variant,p.Ser498Phe,ENST00000483238,; A ENST00000467773 Transcript missense_variant 1589/2076 1589/2076 530/691 S/F tCc/tTc 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 tolerated(0.45) 9/10 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF282 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 144398467 144398467 G A 1 0 0 0 0 1 0 0 0 10554 1174 41 3 3 NOBOX 7 144398467 Missense_Mutation SNP G C3N-00560_T 268457 144398467 14947506 539 17228 CNTNAP2 0 . GRCh38 7 146839856 146839856 + Missense_Mutation SNP C C A rs141831869 C3N-00560_T C3N-00560_N C C c.354C>A p.Ser118Arg p.S118R ENST00000361727 3/24 310 200 110 286 286 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Ser118Arg,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Ser118Arg,ENST00000625365,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; A ENST00000361727 Transcript missense_variant 872/9896 354/3996 118/1331 S/R agC/agA rs141831869 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 3/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,SMART_domains:SM00231,Superfamily_domains:SSF49785 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs141831869 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 146839856 146839856 C A 1 0 0 0 0 1 0 0 0 3428 767 27 1 1 CNTNAP2 7 146839856 Missense_Mutation SNP C C3N-00560_T 2441389 146839856 12506117 540 17229 ZNF746 0 . GRCh38 7 149474823 149474823 + Missense_Mutation SNP C C G rs553710582 C3N-00560_T C3N-00560_N C C c.1499G>C p.Ser500Thr p.S500T ENST00000458143 7/7 122 87 35 49 49 0 strelka-varscan-mutect ZNF746,missense_variant,p.Ser499Thr,ENST00000340622,NM_152557.4;ZNF746,missense_variant,p.Ser500Thr,ENST00000458143,NM_001163474.1;ZNF746,downstream_gene_variant,,ENST00000471735,; G ENST00000458143 Transcript missense_variant 1770/3797 1499/1938 500/645 S/T aGc/aCc rs553710582 1 -1 ZNF746 HGNC HGNC:21948 protein_coding YES CCDS55180.1 ENSP00000395007 Q6NUN9 UPI00015DA840 NM_001163474.1 tolerated_low_confidence(0.49) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs553710582 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 149474823 149474823 C G 1 0 0 0 0 1 0 0 0 18712 797 28 4 4 ZNF746 7 149474823 Missense_Mutation SNP C C3N-00560_T 2634967 149474823 9871150 541 17230 ZNF746 0 . GRCh38 7 149494208 149494208 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.320C>G p.Pro107Arg p.P107R ENST00000458143 2/7 220 154 66 188 188 0 strelka-varscan-mutect ZNF746,missense_variant,p.Pro107Arg,ENST00000461958,;ZNF746,missense_variant,p.Pro107Arg,ENST00000340622,NM_152557.4;ZNF746,missense_variant,p.Pro107Arg,ENST00000458143,NM_001163474.1; C ENST00000458143 Transcript missense_variant 591/3797 320/1938 107/645 P/R cCt/cGt 1 -1 ZNF746 HGNC HGNC:21948 protein_coding YES CCDS55180.1 ENSP00000395007 Q6NUN9 UPI00015DA840 NM_001163474.1 deleterious(0) 2/7 PROSITE_profiles:PS50805,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF13,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 149494208 149494208 G C 1 0 0 0 0 1 0 0 0 18712 1014 35 4 4 ZNF746 7 149494208 Missense_Mutation SNP G C3N-00560_T 19385 149494208 9851765 542 17231 ZNF467 0 . GRCh38 7 149765002 149765002 + Silent SNP C C A rs546115312 C3N-00560_T C3N-00560_N C C c.1500G>T p.= p.S500S ENST00000302017 5/5 136 102 34 84 84 0 strelka-varscan-mutect ZNF467,synonymous_variant,p.=,ENST00000302017,NM_207336.1;ZNF467,intron_variant,,ENST00000484747,; A ENST00000302017 Transcript synonymous_variant 1914/2553 1500/1788 500/595 S tcG/tcT rs546115312 1 -1 ZNF467 HGNC HGNC:23154 protein_coding YES CCDS5899.1 ENSP00000304769 Q7Z7K2 UPI0000160B41 NM_207336.1 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF227,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs546115312 . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 56 149765002 149765002 C A 1 0 0 0 0 0 0 0 1 18498 755 27 1 1 ZNF467 7 149765002 Silent SNP C C3N-00560_T 270794 149765002 9580971 543 17232 SSPO 0 . GRCh38 7 149789289 149789289 + Silent SNP G G C rs115279959 C3N-00560_T C3N-00560_N G G c.4356G>C p.= p.P1452P ENST00000378016 29/107 431 292 139 322 322 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,;SSPO,downstream_gene_variant,,ENST00000493502,; C ENST00000378016 Transcript synonymous_variant 4356/15589 4356/15453 1452/5150 P ccG/ccC rs115279959 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 29/107 Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424,Superfamily_domains:SSF57424,PROSITE_profiles:PS50068,PROSITE_profiles:PS50068,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294,PROSITE_patterns:PS01209 LOW 1 SNV 5 1 PASS rs115279959 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 149789289 149789289 G C 1 0 0 0 0 0 0 0 1 15566 1132 40 4 4 SSPO 7 149789289 Silent SNP G C3N-00560_T 24287 149789289 9556684 544 17233 SSPO 0 . GRCh38 7 149809109 149809109 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.9192C>A p.= p.R3064R ENST00000378016 62/107 284 190 94 277 277 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,upstream_gene_variant,,ENST00000481772,; A ENST00000378016 Transcript synonymous_variant 9192/15589 9192/15453 3064/5150 R cgC/cgA 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 62/107 Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895,PROSITE_profiles:PS50092 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 149809109 149809109 C A 1 0 0 0 0 0 0 0 1 15566 697 25 2 2 SSPO 7 149809109 Silent SNP C C3N-00560_T 19820 149809109 9536864 545 17234 SSPO 0 . GRCh38 7 149827817 149827817 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.14823G>T p.= p.G4941G ENST00000378016 102/107 72 46 26 52 52 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000492965,;SSPO,non_coding_transcript_exon_variant,,ENST00000488835,;SSPO,non_coding_transcript_exon_variant,,ENST00000461331,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,; T ENST00000378016 Transcript synonymous_variant 14823/15589 14823/15453 4941/5150 G ggG/ggT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 102/107 Gene3D:2.10.25.10,Superfamily_domains:SSF57567 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 149827817 149827817 G T 1 0 0 0 0 0 0 0 1 15566 1190 42 2 2 SSPO 7 149827817 Silent SNP G C3N-00560_T 18708 149827817 9518156 546 17235 ZNF775 0 . GRCh38 7 150397237 150397237 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.756G>T p.Trp252Cys p.W252C ENST00000329630 3/3 38 22 16 19 19 0 strelka-varscan-mutect ZNF775,missense_variant,p.Trp252Cys,ENST00000329630,NM_173680.3;ZNF775,downstream_gene_variant,,ENST00000490973,;ZNF775,downstream_gene_variant,,ENST00000478789,;ZNF775,intron_variant,,ENST00000486297,;ZNF775,intron_variant,,ENST00000483664,; T ENST00000329630 Transcript missense_variant 863/2257 756/1614 252/537 W/C tgG/tgT 1 1 ZNF775 HGNC HGNC:28501 protein_coding YES CCDS43678.1 ENSP00000330838 Q96BV0 UPI00001BDA25 NM_173680.3 tolerated(0.29) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 150397237 150397237 G T 1 0 0 0 0 1 0 0 0 18731 1212 42 2 2 ZNF775 7 150397237 Missense_Mutation SNP G C3N-00560_T 569420 150397237 8948736 547 17236 GIMAP6 0 . GRCh38 7 150627867 150627867 + Missense_Mutation SNP C C A rs774492534 C3N-00560_T C3N-00560_N C C c.941G>T p.Arg314Leu p.R314L ENST00000618759 3/3 489 350 139 411 411 0 strelka-varscan-mutect GIMAP6,missense_variant,p.Arg314Leu,ENST00000618759,NM_001244072.1;GIMAP6,missense_variant,p.Arg244Leu,ENST00000328902,NM_024711.5;GIMAP6,3_prime_UTR_variant,,ENST00000493969,NM_001244071.1; A ENST00000618759 Transcript missense_variant 1421/3910 941/1089 314/362 R/L cGg/cTg rs774492534 1 -1 GIMAP6 HGNC HGNC:21918 protein_coding YES CCDS75676.1 ENSP00000479580 B4DH95 UPI00017A6DF2 NM_001244072.1 tolerated(0.71) 3/3 hmmpanther:PTHR10903:SF51,hmmpanther:PTHR10903,Pfam_domain:PF04548 MODERATE 1 SNV 2 1 PASS rs774492534 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 150627867 150627867 C A 1 0 0 0 0 1 0 0 0 6263 652 23 1 1 GIMAP6 7 150627867 Missense_Mutation SNP C C3N-00560_T 230630 150627867 8718106 548 17237 GIMAP6 0 . GRCh38 7 150628097 150628097 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.711C>T p.= p.D237D ENST00000618759 3/3 474 348 126 428 428 0 strelka-varscan-mutect GIMAP6,synonymous_variant,p.=,ENST00000618759,NM_001244072.1;GIMAP6,synonymous_variant,p.=,ENST00000328902,NM_024711.5;GIMAP6,3_prime_UTR_variant,,ENST00000493969,NM_001244071.1; A ENST00000618759 Transcript synonymous_variant 1191/3910 711/1089 237/362 D gaC/gaT 1 -1 GIMAP6 HGNC HGNC:21918 protein_coding YES CCDS75676.1 ENSP00000479580 B4DH95 UPI00017A6DF2 NM_001244072.1 3/3 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF51,hmmpanther:PTHR10903,Pfam_domain:PF04548,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS rs1408493110 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 150628097 150628097 G A 1 0 0 0 0 0 0 0 1 6263 1252 44 3 3 GIMAP6 7 150628097 Silent SNP G C3N-00560_T 230 150628097 8717876 549 17238 GIMAP1 0 . GRCh38 7 150720333 150720333 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.329C>A p.Pro110His p.P110H ENST00000307194 3/3 130 89 41 96 96 0 strelka-varscan-mutect GIMAP1,missense_variant,p.Pro110His,ENST00000307194,NM_130759.3;GIMAP1-GIMAP5,missense_variant,p.Pro110His,ENST00000611999,NM_001199577.1;GIMAP5,upstream_gene_variant,,ENST00000498181,;GIMAP1,downstream_gene_variant,,ENST00000464461,; A ENST00000307194 Transcript missense_variant 469/4420 329/921 110/306 P/H cCc/cAc 1 1 GIMAP1 HGNC HGNC:23237 protein_coding YES CCDS5906.1 ENSP00000302833 Q8WWP7 A0A090N8Z4 UPI0000073C9B NM_130759.3 deleterious(0) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF04548,PROSITE_profiles:PS51720,hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF74,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 56 150720333 150720333 C A 1 0 0 0 0 1 0 0 0 6259 623 22 2 2 GIMAP1 7 150720333 Missense_Mutation SNP C C3N-00560_T 92236 150720333 8625640 550 17239 ATG9B 0 . GRCh38 7 151018836 151018836 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1502C>A p.Ala501Glu p.A501E ENST00000605952 6/17 44 22 22 11 11 0 strelka-varscan-mutect ATG9B,missense_variant,p.Ala501Glu,ENST00000469530,NM_173681.5;NOS3,downstream_gene_variant,,ENST00000297494,NM_000603.4;NOS3,downstream_gene_variant,,ENST00000461406,;ATG9B,intron_variant,,ENST00000617967,;ATG9B,upstream_gene_variant,,ENST00000611177,;ATG9B,downstream_gene_variant,,ENST00000473409,;NOS3,downstream_gene_variant,,ENST00000477227,;ATG9B,upstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000466157,;ATG9B,missense_variant,p.Ala501Glu,ENST00000605952,;ATG9B,upstream_gene_variant,,ENST00000404733,;ATG9B,downstream_gene_variant,,ENST00000473134,;ATG9B,upstream_gene_variant,,ENST00000471797,; T ENST00000605952 Transcript missense_variant,NMD_transcript_variant 1578/4572 1502/2775 501/924 A/E gCg/gAg 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 deleterious(0.03) 6/17 Low_complexity_(Seg):seg,hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038,Pfam_domain:PF04109 MODERATE SNV 1 1 PASS . . 5 202 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 151018836 151018836 G T 1 0 0 0 0 1 0 0 0 1255 1087 38 1 1 ATG9B 7 151018836 Missense_Mutation SNP G C3N-00560_T 298503 151018836 8327137 551 17240 ATG9B 0 . GRCh38 7 151019333 151019333 + Silent SNP G G T rs763437227 C3N-00560_T C3N-00560_N G G c.1005C>A p.= p.R335R ENST00000605952 6/17 62 46 16 43 43 0 strelka-varscan-mutect ATG9B,synonymous_variant,p.=,ENST00000469530,NM_173681.5;NOS3,downstream_gene_variant,,ENST00000297494,NM_000603.4;NOS3,downstream_gene_variant,,ENST00000461406,;ATG9B,intron_variant,,ENST00000617967,;ATG9B,upstream_gene_variant,,ENST00000611177,;ATG9B,downstream_gene_variant,,ENST00000473409,;ATG9B,upstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000466157,;ATG9B,synonymous_variant,p.=,ENST00000605952,;ATG9B,downstream_gene_variant,,ENST00000473134,;ATG9B,upstream_gene_variant,,ENST00000471797,; T ENST00000605952 Transcript synonymous_variant,NMD_transcript_variant 1081/4572 1005/2775 335/924 R cgC/cgA rs763437227 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 6/17 hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038,Pfam_domain:PF04109 LOW SNV 1 1 PASS rs763437227 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 151019333 151019333 G T 1 0 0 0 0 0 0 0 1 1255 1190 42 2 2 ATG9B 7 151019333 Silent SNP G C3N-00560_T 497 151019333 8326640 552 17241 KMT2C 0 . GRCh38 7 152229993 152229993 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2906G>T p.Gly969Val p.G969V ENST00000262189 18/59 191 180 11 262 262 0 varscan-mutect KMT2C,missense_variant,p.Gly969Val,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Gly969Val,ENST00000355193,;KMT2C,missense_variant,p.Gly125Val,ENST00000418673,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; A ENST00000262189 Transcript missense_variant 3125/16862 2906/14736 969/4911 G/V gGa/gTa 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 deleterious(0.02) 18/59 PROSITE_profiles:PS50016,hmmpanther:PTHR22884:SF373,hmmpanther:PTHR22884,Gene3D:3.30.40.10,SMART_domains:SM00184,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 152229993 152229993 C A 1 0 0 0 0 1 0 0 0 8297 855 30 2 2 KMT2C 7 152229993 Missense_Mutation SNP C C3N-00560_T 1210660 152229993 7115980 553 17242 ACTR3B 0 . GRCh38 7 152854507 152854507 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1211G>T p.Gly404Val p.G404V ENST00000256001 12/12 308 219 89 232 232 0 strelka-varscan-mutect ACTR3B,missense_variant,p.Gly404Val,ENST00000256001,NM_020445.5;ACTR3B,missense_variant,p.Gly316Val,ENST00000397282,;ACTR3B,missense_variant,p.Gly334Val,ENST00000377776,NM_001040135.2;ACTR3B,non_coding_transcript_exon_variant,,ENST00000479402,; T ENST00000256001 Transcript missense_variant 1345/2216 1211/1257 404/418 G/V gGg/gTg 1 1 ACTR3B HGNC HGNC:17256 protein_coding YES CCDS5934.1 ENSP00000256001 Q9P1U1 UPI0000073AC7 NM_020445.5 deleterious(0) 12/12 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF170,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 152854507 152854507 G T 1 0 0 0 0 1 0 0 0 256 1232 43 2 2 ACTR3B 7 152854507 Missense_Mutation SNP G C3N-00560_T 624514 152854507 6491466 554 17243 DPP6 0 . GRCh38 7 154807092 154807092 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1646T>A p.Phe549Tyr p.F549Y ENST00000377770 16/26 113 85 28 103 103 0 strelka-varscan-mutect DPP6,missense_variant,p.Phe485Tyr,ENST00000404039,NM_001039350.2;DPP6,missense_variant,p.Phe487Tyr,ENST00000332007,NM_001936.4;DPP6,missense_variant,p.Phe549Tyr,ENST00000377770,NM_130797.3;DPP6,missense_variant,p.Phe442Tyr,ENST00000427557,NM_001290252.1;DPP6,non_coding_transcript_exon_variant,,ENST00000493268,; A ENST00000377770 Transcript missense_variant 1787/3710 1646/2598 549/865 F/Y tTc/tAc 1 1 DPP6 HGNC HGNC:3010 protein_coding YES CCDS75683.1 ENSP00000367001 P42658 UPI00001AE746 NM_130797.3 tolerated(1) 16/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 154807092 154807092 T A 1 0 0 0 0 1 0 0 0 4545 1783 62 4 4 DPP6 7 154807092 Missense_Mutation SNP T C3N-00560_T 1952585 154807092 4538881 555 17244 CSMD1 0 . GRCh38 8 2942483 2942483 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.10527C>A p.= p.L3509L ENST00000520002 70/71 58 29 29 76 76 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,; T ENST00000520002 Transcript synonymous_variant 11083/11740 10527/10698 3509/3565 L ctC/ctA 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 70/71 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 2942483 2942483 G T 1 0 0 0 0 0 0 0 1 3745 929 33 2 2 CSMD1 8 2942483 Silent SNP G C3N-00560_T 2942483 142196153 556 17245 CSMD1 0 . GRCh38 8 3188962 3188962 + Silent SNP G G T rs200934039 C3N-00560_T C3N-00560_N G G c.5451C>A p.= p.P1817P ENST00000520002 36/71 88 49 39 126 126 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; T ENST00000520002 Transcript synonymous_variant 6007/11740 5451/10698 1817/3565 P ccC/ccA rs200934039 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 36/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 5 1 PASS rs200934039 . 0 203 0 5 0 0 0 0 -20 0.9999358 1 1 1 0 T 2 4 56 3188962 3188962 G T 1 0 0 0 0 0 0 0 1 3745 1103 39 1 1 CSMD1 8 3188962 Silent SNP G C3N-00560_T 246479 3188962 141949674 557 17246 CSMD1 0 . GRCh38 8 3396308 3396308 + Nonsense_Mutation SNP C C A rs775334589 C3N-00560_T C3N-00560_N C C c.2482G>T p.Glu828Ter p.E828* ENST00000520002 18/71 127 81 46 182 182 0 strelka-varscan-mutect CSMD1,stop_gained,p.Glu689Ter,ENST00000537824,;CSMD1,stop_gained,p.Glu308Ter,ENST00000335551,;CSMD1,stop_gained,p.Glu828Ter,ENST00000520002,;CSMD1,stop_gained,p.Glu828Ter,ENST00000602557,;CSMD1,stop_gained,p.Glu827Ter,ENST00000635120,NM_033225.5;CSMD1,stop_gained,p.Glu828Ter,ENST00000400186,;CSMD1,stop_gained,p.Glu828Ter,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; A ENST00000520002 Transcript stop_gained 3038/11740 2482/10698 828/3565 E/* Gag/Tag rs775334589,COSM3648490,COSM3648491,COSM3648492 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 18/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1,1 HIGH 1 SNV 5 0,1,1,1 1 PASS rs775334589 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 3396308 3396308 C A 1 0 0 0 0 0 1 0 0 3745 893 31 1 1 CSMD1 8 3396308 Nonsense_Mutation SNP C C3N-00560_T 207346 3396308 141742328 558 17247 XKR5 0 . GRCh38 8 6811213 6811213 + Silent SNP C C A rs368947710 C3N-00560_T C3N-00560_N C C c.2046G>T p.= p.P682P ENST00000618742 7/7 71 36 35 101 101 0 strelka-varscan-mutect XKR5,synonymous_variant,p.=,ENST00000618742,NM_207411.4,NM_001289973.1;XKR5,3_prime_UTR_variant,,ENST00000618990,; A ENST00000618742 Transcript synonymous_variant 2197/4893 2046/2061 682/686 P ccG/ccT rs368947710 1 -1 XKR5 HGNC HGNC:20782 protein_coding YES ENSP00000483879 A0A087X143 UPI0000EE786F NM_207411.4,NM_001289973.1 7/7 LOW 1 SNV 1 1 PASS rs368947710 . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 56 6811213 6811213 C A 1 0 0 0 0 0 0 0 1 17993 871 31 1 1 XKR5 8 6811213 Silent SNP C C3N-00560_T 3414905 6811213 138327423 559 17248 FAM160B2 0 . GRCh38 8 22100915 22100915 + Missense_Mutation SNP G G T rs547583857 C3N-00560_T C3N-00560_N G G c.1559G>T p.Arg520Leu p.R520L ENST00000289921 12/17 197 126 71 289 289 0 strelka-varscan-mutect FAM160B2,missense_variant,p.Arg520Leu,ENST00000289921,NM_022749.5;FAM160B2,missense_variant,p.Arg520Leu,ENST00000450006,;FAM160B2,non_coding_transcript_exon_variant,,ENST00000491733,;FAM160B2,non_coding_transcript_exon_variant,,ENST00000462914,;FAM160B2,downstream_gene_variant,,ENST00000488968,;FAM160B2,upstream_gene_variant,,ENST00000496599,;FAM160B2,downstream_gene_variant,,ENST00000427751,;FAM160B2,downstream_gene_variant,,ENST00000498344,;FAM160B2,downstream_gene_variant,,ENST00000464226,;FAM160B2,upstream_gene_variant,,ENST00000523633,;FAM160B2,upstream_gene_variant,,ENST00000477614,;FAM160B2,downstream_gene_variant,,ENST00000474579,; T ENST00000289921 Transcript missense_variant 1605/4245 1559/2232 520/743 R/L cGc/cTc rs547583857 1 1 FAM160B2 HGNC HGNC:16492 protein_coding YES CCDS6021.2 ENSP00000289921 Q86V87 UPI00006C5119 NM_022749.5 tolerated(0.34) 12/17 hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF9 MODERATE 1 SNV 5 1 PASS rs547583857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 22100915 22100915 G T 1 0 0 0 0 1 0 0 0 5320 1087 38 1 1 FAM160B2 8 22100915 Missense_Mutation SNP G C3N-00560_T 15289702 22100915 123037721 560 17249 ESCO2 0 . GRCh38 8 27803362 27803362 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1730C>T p.Pro577Leu p.P577L ENST00000305188 11/11 226 109 117 264 264 0 strelka-varscan-mutect ESCO2,missense_variant,p.Pro577Leu,ENST00000305188,NM_001017420.2;ESCO2,missense_variant,p.Pro225Leu,ENST00000397418,;ESCO2,downstream_gene_variant,,ENST00000518262,;ESCO2,3_prime_UTR_variant,,ENST00000522378,; T ENST00000305188 Transcript missense_variant 1968/3922 1730/1806 577/601 P/L cCa/cTa 1 1 ESCO2 HGNC HGNC:27230 protein_coding YES CCDS34872.1 ENSP00000306999 Q56NI9 UPI0000160D17 NM_001017420.2 deleterious(0) 11/11 Pfam_domain:PF13880,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 27803362 27803362 C T 1 0 0 0 0 1 0 0 0 5111 594 21 3 3 ESCO2 8 27803362 Missense_Mutation SNP C C3N-00560_T 5702447 27803362 117335274 561 17250 RAB11FIP1 0 . GRCh38 8 37873030 37873030 + Missense_Mutation SNP C C A rs769998709 C3N-00560_T C3N-00560_N C C c.1772G>T p.Ser591Ile p.S591I ENST00000330843 4/6 218 90 128 202 202 0 strelka-varscan-mutect RAB11FIP1,missense_variant,p.Ser591Ile,ENST00000330843,NM_001002814.2;RAB11FIP1,intron_variant,,ENST00000287263,NM_025151.4;RAB11FIP1,intron_variant,,ENST00000524118,;RAB11FIP1,intron_variant,,ENST00000522727,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000523182,;RAB11FIP1,non_coding_transcript_exon_variant,,ENST00000522774,; A ENST00000330843 Transcript missense_variant 1785/7811 1772/3852 591/1283 S/I aGt/aTt rs769998709 1 -1 RAB11FIP1 HGNC HGNC:30265 protein_coding YES CCDS34882.1 ENSP00000331342 Q6WKZ4 UPI0000D624B1 NM_001002814.2 deleterious(0) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR15746,hmmpanther:PTHR15746:SF22 MODERATE 1 SNV 1 1 PASS rs769998709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 37873030 37873030 C A 1 0 0 0 0 1 0 0 0 13051 565 20 2 2 RAB11FIP1 8 37873030 Missense_Mutation SNP C C3N-00560_T 10069668 37873030 107265606 562 17251 PCMTD1 0 . GRCh38 8 51861062 51861062 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.90G>T p.Glu30Asp p.E30D ENST00000360540 3/7 373 279 94 223 223 0 strelka-varscan-mutect PCMTD1,missense_variant,p.Glu30Asp,ENST00000360540,NM_052937.3;PCMTD1,missense_variant,p.Glu30Asp,ENST00000521344,;PCMTD1,missense_variant,p.Glu30Asp,ENST00000522514,;PCMTD1,intron_variant,,ENST00000544451,NM_001286782.1;PCMTD1,intron_variant,,ENST00000519559,;PCMTD1,non_coding_transcript_exon_variant,,ENST00000521046,;PCMTD1,upstream_gene_variant,,ENST00000519975,; A ENST00000360540 Transcript missense_variant 497/4252 90/1074 30/357 E/D gaG/gaT 1 -1 PCMTD1 HGNC HGNC:30483 protein_coding YES CCDS6148.1 ENSP00000353739 Q96MG8 UPI0000047CC0 NM_052937.3 deleterious(0.01) 3/7 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF4 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 51861062 51861062 C A 1 0 0 0 0 1 0 0 0 11674 796 28 2 2 PCMTD1 8 51861062 Missense_Mutation SNP C C3N-00560_T 13988032 51861062 93277574 563 17252 PENK 0 . GRCh38 8 56445681 56445681 + Silent SNP C C G novel C3N-00560_T C3N-00560_N C C c.273G>C p.= p.P91P ENST00000518770 3/3 88 40 48 44 44 0 strelka-varscan-mutect PENK,synonymous_variant,p.=,ENST00000518770,;PENK,intron_variant,,ENST00000314922,NM_006211.3;PENK,intron_variant,,ENST00000451791,NM_001135690.1;PENK,intron_variant,,ENST00000523051,;PENK,intron_variant,,ENST00000517415,;PENK,intron_variant,,ENST00000518974,;RP11-17A4.2,upstream_gene_variant,,ENST00000518662,;PENK,upstream_gene_variant,,ENST00000523274,;PENK,downstream_gene_variant,,ENST00000521153,; G ENST00000518770 Transcript synonymous_variant 427/863 273/279 91/92 P ccG/ccC 1 -1 PENK HGNC HGNC:8831 protein_coding ENSP00000430592 E5RJ72 UPI000189235A 3/3 LOW SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 2 3 56 56445681 56445681 C G 1 0 0 0 0 0 0 0 1 11815 523 19 4 4 PENK 8 56445681 Silent SNP C C3N-00560_T 4584619 56445681 88692955 564 17253 FAM110B 0 . GRCh38 8 58147039 58147039 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.809T>A p.Val270Glu p.V270E ENST00000361488 5/5 440 323 117 231 230 1 strelka-varscan-mutect FAM110B,missense_variant,p.Val270Glu,ENST00000361488,NM_147189.2;FAM110B,intron_variant,,ENST00000520369,;FAM110B,intron_variant,,ENST00000523486,;FAM110B,downstream_gene_variant,,ENST00000519262,;FAM110B,downstream_gene_variant,,ENST00000522059,;FAM110B,downstream_gene_variant,,ENST00000521413,; A ENST00000361488 Transcript missense_variant 1689/3438 809/1113 270/370 V/E gTg/gAg 1 1 FAM110B HGNC HGNC:28587 protein_coding YES CCDS6170.1 ENSP00000355204 Q8TC76 A0A024R7V5 UPI000006E853 NM_147189.2 deleterious(0) 5/5 Pfam_domain:PF14160,hmmpanther:PTHR14758,hmmpanther:PTHR14758:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 58147039 58147039 T A 1 0 0 0 0 1 0 0 0 5261 1696 59 4 4 FAM110B 8 58147039 Missense_Mutation SNP T C3N-00560_T 1701358 58147039 86991597 565 17254 UBXN2B 0 . GRCh38 8 58446059 58446059 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.824G>C p.Ser275Thr p.S275T ENST00000399598 7/8 60 30 30 69 69 0 strelka-varscan-mutect UBXN2B,missense_variant,p.Ser275Thr,ENST00000399598,NM_001077619.1;UBXN2B,3_prime_UTR_variant,,ENST00000523409,;UBXN2B,3_prime_UTR_variant,,ENST00000520732,; C ENST00000399598 Transcript missense_variant 946/5068 824/996 275/331 S/T aGt/aCt 1 1 UBXN2B HGNC HGNC:27035 protein_coding YES CCDS43741.1 ENSP00000382507 Q14CS0 UPI000013F1FC NM_001077619.1 tolerated(0.13) 7/8 Gene3D:3.10.20.90,Pfam_domain:PF00789,PROSITE_profiles:PS50033,hmmpanther:PTHR23333,hmmpanther:PTHR23333:SF14,SMART_domains:SM00166,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS rs1410479667 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 58446059 58446059 G C 1 0 0 0 0 1 0 0 0 17439 1029 36 4 4 UBXN2B 8 58446059 Missense_Mutation SNP G C3N-00560_T 299020 58446059 86692577 566 17255 TOX 0 . GRCh38 8 58815508 58815508 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1222G>T p.Val408Phe p.V408F ENST00000361421 7/9 150 79 71 132 132 0 strelka-varscan-mutect TOX,missense_variant,p.Val408Phe,ENST00000361421,NM_014729.2;RNU4-50P,upstream_gene_variant,,ENST00000364361,; A ENST00000361421 Transcript missense_variant 1443/4131 1222/1581 408/526 V/F Gtc/Ttc 1 -1 TOX HGNC HGNC:18988 protein_coding YES CCDS34897.1 ENSP00000354842 O94900 UPI0000070A73 NM_014729.2 tolerated(0.06) 7/9 hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF155 MODERATE 1 SNV 1 1 PASS rs1247571532 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 58815508 58815508 C A 1 0 0 0 0 1 0 0 0 16855 478 17 2 2 TOX 8 58815508 Missense_Mutation SNP C C3N-00560_T 369449 58815508 86323128 567 17256 BHLHE22 0 . GRCh38 8 64581222 64581222 + Silent SNP C C A rs780153535 C3N-00560_T C3N-00560_N C C c.432C>A p.= p.G144G ENST00000321870 1/1 128 109 19 44 44 0 strelka-varscan-mutect BHLHE22,synonymous_variant,p.=,ENST00000321870,NM_152414.4;RP11-21C4.1,intron_variant,,ENST00000517909,;RP11-21C4.1,upstream_gene_variant,,ENST00000520834,; A ENST00000321870 Transcript synonymous_variant 856/3262 432/1146 144/381 G ggC/ggA rs780153535 1 1 BHLHE22 HGNC HGNC:11963 protein_coding YES CCDS6179.1 ENSP00000318799 Q8NFJ8 UPI0000070A3C NM_152414.4 1/1 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF52 LOW SNV 1 PASS rs780153535 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 64581222 64581222 C A 1 0 0 0 0 0 0 0 1 1569 755 27 1 1 BHLHE22 8 64581222 Silent SNP C C3N-00560_T 5765714 64581222 80557414 568 17257 VCPIP1 0 . GRCh38 8 66665161 66665161 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1798G>T p.Gly600Ter p.G600* ENST00000310421 1/3 94 61 33 52 52 0 strelka-varscan-mutect VCPIP1,stop_gained,p.Gly600Ter,ENST00000310421,NM_025054.4;C8orf44-SGK3,upstream_gene_variant,,ENST00000519289,NM_001204173.1;C8orf44,upstream_gene_variant,,ENST00000519561,NM_019607.2;C8orf44,upstream_gene_variant,,ENST00000521889,;C8orf44-SGK3,upstream_gene_variant,,ENST00000520044,;C8orf44,upstream_gene_variant,,ENST00000521113,; A ENST00000310421 Transcript stop_gained 2057/9942 1798/3669 600/1222 G/* Gga/Tga 1 -1 VCPIP1 HGNC HGNC:30897 protein_coding YES CCDS6192.1 ENSP00000309031 Q96JH7 UPI00001D3EF3 NM_025054.4 1/3 hmmpanther:PTHR14843,hmmpanther:PTHR14843:SF2 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 66665161 66665161 C A 1 0 0 0 0 0 1 0 0 17686 603 21 2 2 VCPIP1 8 66665161 Nonsense_Mutation SNP C C3N-00560_T 2083939 66665161 78473475 569 17258 VCPIP1 0 . GRCh38 8 66666462 66666462 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.497G>T p.Arg166Leu p.R166L ENST00000310421 1/3 319 229 90 200 200 0 strelka-varscan-mutect VCPIP1,missense_variant,p.Arg166Leu,ENST00000310421,NM_025054.4;C8orf44-SGK3,upstream_gene_variant,,ENST00000519289,NM_001204173.1;C8orf44,upstream_gene_variant,,ENST00000519561,NM_019607.2;C8orf44,upstream_gene_variant,,ENST00000521889,;C8orf44-SGK3,upstream_gene_variant,,ENST00000520044,;C8orf44,upstream_gene_variant,,ENST00000521113,; A ENST00000310421 Transcript missense_variant 756/9942 497/3669 166/1222 R/L cGc/cTc 1 -1 VCPIP1 HGNC HGNC:30897 protein_coding YES CCDS6192.1 ENSP00000309031 Q96JH7 UPI00001D3EF3 NM_025054.4 deleterious(0) 1/3 hmmpanther:PTHR14843,hmmpanther:PTHR14843:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 66666462 66666462 C A 1 0 0 0 0 1 0 0 0 17686 768 27 1 1 VCPIP1 8 66666462 Missense_Mutation SNP C C3N-00560_T 1301 66666462 78472174 570 17259 NCOA2 0 . GRCh38 8 70157050 70157050 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1315G>T p.Gly439Cys p.G439C ENST00000452400 11/23 354 309 45 249 249 0 strelka-varscan-mutect NCOA2,missense_variant,p.Gly439Cys,ENST00000452400,NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2;NCOA2,intron_variant,,ENST00000524223,;NCOA2,missense_variant,p.Gly439Cys,ENST00000518287,; A ENST00000452400 Transcript missense_variant 1497/8447 1315/4395 439/1464 G/C Ggc/Tgc 1 -1 NCOA2 HGNC HGNC:7669 protein_coding YES CCDS47872.1 ENSP00000399968 Q15596 UPI000012FE42 NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2 tolerated(0.12) 11/23 Low_complexity_(Seg):seg,hmmpanther:PTHR10684,hmmpanther:PTHR10684:SF2,PIRSF_domain:PIRSF038181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 70157050 70157050 C A 1 0 0 0 0 1 0 0 0 10248 623 22 2 2 NCOA2 8 70157050 Missense_Mutation SNP C C3N-00560_T 3490588 70157050 74981586 571 17260 TRPA1 0 . GRCh38 8 72033649 72033649 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2863T>A p.Leu955Ile p.L955I ENST00000262209 23/27 280 258 22 210 210 0 strelka-varscan-mutect TRPA1,missense_variant,p.Leu955Ile,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Leu807Ile,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000512290,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;TRPA1,downstream_gene_variant,,ENST00000519720,; T ENST00000262209 Transcript missense_variant 3071/5223 2863/3360 955/1119 L/I Tta/Ata 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 23/27 Pfam_domain:PF00520,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 72033649 72033649 A T 1 0 0 0 0 1 0 0 0 17082 28 1 4 4 TRPA1 8 72033649 Missense_Mutation SNP A C3N-00560_T 1876599 72033649 73104987 572 17261 KCNB2 0 . GRCh38 8 72936439 72936439 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1084G>A p.Ala362Thr p.A362T ENST00000523207 3/3 219 152 67 146 146 0 strelka-varscan-mutect KCNB2,missense_variant,p.Ala362Thr,ENST00000523207,NM_004770.2; A ENST00000523207 Transcript missense_variant 1672/3582 1084/2736 362/911 A/T Gct/Act 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 tolerated(0.58) 3/3 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF134,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 72936439 72936439 G A 1 0 0 0 0 1 0 0 0 7929 1319 46 3 3 KCNB2 8 72936439 Missense_Mutation SNP G C3N-00560_T 902790 72936439 72202197 573 17262 KCNB2 0 . GRCh38 8 72937269 72937269 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.1914A>T p.= p.P638P ENST00000523207 3/3 572 513 59 303 302 1 strelka-varscan-mutect KCNB2,synonymous_variant,p.=,ENST00000523207,NM_004770.2; T ENST00000523207 Transcript synonymous_variant 2502/3582 1914/2736 638/911 P ccA/ccT 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 3/3 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF134,Pfam_domain:PF03521 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 72937269 72937269 A T 1 0 0 0 0 0 0 0 1 7929 175 7 4 4 KCNB2 8 72937269 Silent SNP A C3N-00560_T 830 72937269 72201367 574 17263 CRISPLD1 0 . GRCh38 8 75032218 75032218 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.1479A>G p.= p.A493A ENST00000262207 15/15 108 101 7 117 117 0 varscan-mutect CRISPLD1,synonymous_variant,p.=,ENST00000262207,NM_031461.5;CRISPLD1,synonymous_variant,p.=,ENST00000523524,NM_001286778.1;CRISPLD1,synonymous_variant,p.=,ENST00000517786,NM_001286777.1;RP11-300E4.2,upstream_gene_variant,,ENST00000520778,; G ENST00000262207 Transcript synonymous_variant 1947/4287 1479/1503 493/500 A gcA/gcG 1 1 CRISPLD1 HGNC HGNC:18206 protein_coding YES CCDS6219.1 ENSP00000262207 Q9H336 UPI00000422F5 NM_031461.5 15/15 Gene3D:1jbiA00,Superfamily_domains:0039469 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -14.3044 1 1 1 1 0 G 2 3 56 75032218 75032218 A G 1 0 0 0 0 0 0 0 1 3683 204 8 5 5 CRISPLD1 8 75032218 Silent SNP A C3N-00560_T 2094949 75032218 70106418 575 17264 HNF4G 0 . GRCh38 8 75559038 75559038 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.1093+1G>T p.X365_splice ENST00000396423 238 93 145 151 151 0 strelka-varscan-mutect HNF4G,splice_donor_variant,,ENST00000396423,NM_004133.4;HNF4G,splice_donor_variant,,ENST00000354370,; T ENST00000396423 Transcript splice_donor_variant -/4209 1093/1338 365/445 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 8/9 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 75559038 75559038 G T 1 0 0 0 0 0 0 1 0 7145 1275 44 2 2 HNF4G 8 75559038 Splice_Site SNP G C3N-00560_T 526820 75559038 69579598 576 17265 ZFHX4 0 . GRCh38 8 76705024 76705024 + Silent SNP C C A rs759670574 C3N-00560_T C3N-00560_N C C c.936C>A p.= p.L312L ENST00000521891 2/11 289 195 94 192 192 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript synonymous_variant 1384/14019 936/10851 312/3616 L ctC/ctA rs759670574 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 LOW 1 SNV 5 1 PASS rs759670574 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 76705024 76705024 C A 1 0 0 0 0 0 0 0 1 18213 842 30 2 2 ZFHX4 8 76705024 Silent SNP C C3N-00560_T 1145986 76705024 68433612 577 17266 ZFHX4 0 . GRCh38 8 76852550 76852550 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.5629G>T p.Glu1877Ter p.E1877* ENST00000521891 10/11 237 212 25 175 175 0 strelka-varscan-mutect ZFHX4,stop_gained,p.Glu1877Ter,ENST00000521891,NM_024721.4;ZFHX4,stop_gained,p.Glu1851Ter,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; T ENST00000521891 Transcript stop_gained 6077/14019 5629/10851 1877/3616 E/* Gaa/Taa 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 76852550 76852550 G T 1 0 0 0 0 0 1 0 0 18213 1291 45 2 2 ZFHX4 8 76852550 Nonsense_Mutation SNP G C3N-00560_T 147526 76852550 68286086 578 17267 ZFHX4 0 . GRCh38 8 76855952 76855952 + Missense_Mutation SNP C C A rs762923975 C3N-00560_T C3N-00560_N C C c.9031C>A p.Leu3011Ile p.L3011I ENST00000521891 10/11 339 305 34 205 204 1 strelka-varscan-mutect ZFHX4,missense_variant,p.Leu3011Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Leu2985Ile,ENST00000518282,; A ENST00000521891 Transcript missense_variant 9479/14019 9031/10851 3011/3616 L/I Ctc/Atc rs762923975 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(0.07) 10/11 PROSITE_patterns:PS00028,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,SMART_domains:SM00451,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs762923975 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 76855952 76855952 C A 1 0 0 0 0 1 0 0 0 18213 681 24 2 2 ZFHX4 8 76855952 Missense_Mutation SNP C C3N-00560_T 3402 76855952 68282684 579 17268 ZBTB10 0 . GRCh38 8 80487522 80487522 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.712C>T p.Arg238Trp p.R238W ENST00000430430 2/7 409 162 247 214 213 1 strelka-varscan-mutect ZBTB10,missense_variant,p.Arg238Trp,ENST00000430430,;ZBTB10,missense_variant,p.Arg238Trp,ENST00000426744,NM_023929.4;ZBTB10,missense_variant,p.Arg238Trp,ENST00000455036,NM_001105539.2;ZBTB10,missense_variant,p.Arg65Trp,ENST00000610895,;ZBTB10,intron_variant,,ENST00000379091,NM_001277145.1;RP11-48B3.5,upstream_gene_variant,,ENST00000605948,;Y_RNA,upstream_gene_variant,,ENST00000516058,; T ENST00000430430 Transcript missense_variant 1491/10132 712/2616 238/871 R/W Cgg/Tgg 1 1 ZBTB10 HGNC HGNC:30953 protein_coding YES CCDS47880.1 ENSP00000387462 Q96DT7 UPI0000E5AEF3 deleterious_low_confidence(0) 2/7 hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80487522 80487522 C T 1 0 0 0 0 1 0 0 0 18089 759 27 1 1 ZBTB10 8 80487522 Missense_Mutation SNP C C3N-00560_T 3631570 80487522 64651114 580 17269 ZBTB10 0 . GRCh38 8 80499883 80499883 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.1362T>C p.= p.T454T ENST00000430430 3/7 275 256 19 172 172 0 strelka-varscan-mutect ZBTB10,synonymous_variant,p.=,ENST00000430430,;ZBTB10,synonymous_variant,p.=,ENST00000426744,NM_023929.4;ZBTB10,synonymous_variant,p.=,ENST00000455036,NM_001105539.2;ZBTB10,synonymous_variant,p.=,ENST00000610895,;ZBTB10,synonymous_variant,p.=,ENST00000379091,NM_001277145.1; C ENST00000430430 Transcript synonymous_variant 2141/10132 1362/2616 454/871 T acT/acC 1 1 ZBTB10 HGNC HGNC:30953 protein_coding YES CCDS47880.1 ENSP00000387462 Q96DT7 UPI0000E5AEF3 3/7 Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF27,SMART_domains:SM00225,Superfamily_domains:SSF54695 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 80499883 80499883 T C 1 0 0 0 0 0 0 0 1 18089 1596 56 5 5 ZBTB10 8 80499883 Silent SNP T C3N-00560_T 12361 80499883 64638753 581 17270 PMP2 0 . GRCh38 8 81444856 81444856 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.207G>T p.Gln69His p.Q69H ENST00000256103 2/4 242 220 22 175 175 0 strelka-varscan-mutect PMP2,missense_variant,p.Gln69His,ENST00000256103,NM_002677.3;PMP2,intron_variant,,ENST00000519260,;RP11-157I4.4,intron_variant,,ENST00000524085,; A ENST00000256103 Transcript missense_variant 344/3608 207/399 69/132 Q/H caG/caT 1 -1 PMP2 HGNC HGNC:9117 protein_coding YES CCDS6229.1 ENSP00000256103 P02689 UPI000013CEEB NM_002677.3 deleterious(0.01) 2/4 hmmpanther:PTHR11955:SF64,hmmpanther:PTHR11955,Gene3D:2.40.128.20,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR00178 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 81444856 81444856 C A 1 0 0 0 0 1 0 0 0 12245 680 24 2 2 PMP2 8 81444856 Missense_Mutation SNP C C3N-00560_T 944973 81444856 63693780 582 17271 CNGB3 0 . GRCh38 8 86604200 86604200 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.1674C>T p.= p.G558G ENST00000320005 15/18 326 281 45 263 263 0 strelka-varscan-mutect CNGB3,synonymous_variant,p.=,ENST00000320005,NM_019098.4; A ENST00000320005 Transcript synonymous_variant 1722/4347 1674/2430 558/809 G ggC/ggT 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 15/18 PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385,PROSITE_patterns:PS00888,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 86604200 86604200 G A 1 0 0 0 0 0 0 0 1 3381 1306 46 3 3 CNGB3 8 86604200 Silent SNP G C3N-00560_T 5159344 86604200 58534436 583 17272 DCAF4L2 0 . GRCh38 8 87873898 87873898 + Missense_Mutation SNP G G T rs185686116 C3N-00560_T C3N-00560_N G G c.74C>A p.Ala25Glu p.A25E ENST00000319675 1/1 391 184 207 301 301 0 strelka-varscan-mutect DCAF4L2,missense_variant,p.Ala25Glu,ENST00000319675,NM_152418.3; T ENST00000319675 Transcript missense_variant 171/3326 74/1188 25/395 A/E gCa/gAa rs185686116 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 deleterious(0.03) 1/1 hmmpanther:PTHR22847:SF457,hmmpanther:PTHR22847 MODERATE 1 SNV 1 PASS rs185686116 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 87873898 87873898 G T 1 0 0 0 0 1 0 0 0 4073 1319 46 2 2 DCAF4L2 8 87873898 Missense_Mutation SNP G C3N-00560_T 1269698 87873898 57264738 584 17273 NECAB1 0 . GRCh38 8 90824774 90824774 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.182G>A p.Ser61Asn p.S61N ENST00000417640 3/13 129 108 21 127 127 0 strelka-varscan-mutect NECAB1,missense_variant,p.Ser61Asn,ENST00000417640,NM_022351.4;RP11-662G23.1,intron_variant,,ENST00000517884,;NECAB1,non_coding_transcript_exon_variant,,ENST00000521954,;NECAB1,non_coding_transcript_exon_variant,,ENST00000523962,;NECAB1,non_coding_transcript_exon_variant,,ENST00000522729,; A ENST00000417640 Transcript missense_variant 519/5289 182/1056 61/351 S/N aGt/aAt 1 1 NECAB1 HGNC HGNC:20983 protein_coding YES CCDS47889.1 ENSP00000387380 Q8N987 UPI0000070EEA NM_022351.4 tolerated(0.14) 3/13 PROSITE_profiles:PS50222,hmmpanther:PTHR12178,hmmpanther:PTHR12178:SF11,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 90824774 90824774 G A 1 0 0 0 0 1 0 0 0 10328 1029 36 3 3 NECAB1 8 90824774 Missense_Mutation SNP G C3N-00560_T 2950876 90824774 54313862 585 17274 DPY19L4 0 . GRCh38 8 94765753 94765753 + Missense_Mutation SNP G G T rs770626744 C3N-00560_T C3N-00560_N G G c.1045G>T p.Val349Leu p.V349L ENST00000414645 10/19 113 101 12 112 112 0 strelka-varscan-mutect DPY19L4,missense_variant,p.Val349Leu,ENST00000414645,NM_181787.2;DPY19L4,missense_variant,p.Val149Leu,ENST00000523020,; T ENST00000414645 Transcript missense_variant 1144/6197 1045/2172 349/723 V/L Gtg/Ttg rs770626744 1 1 DPY19L4 HGNC HGNC:27829 protein_coding YES CCDS34924.1 ENSP00000389630 Q7Z388 A0A024R9F2 UPI00001A9D7A NM_181787.2 tolerated(1) 10/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 1 1 PASS rs780973978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 94765753 94765753 G T 1 0 0 0 0 1 0 0 0 4558 1029 36 2 2 DPY19L4 8 94765753 Missense_Mutation SNP G C3N-00560_T 3940979 94765753 50372883 586 17275 MATN2 0 . GRCh38 8 97961424 97961424 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.852C>A p.= p.A284A ENST00000254898 5/19 160 82 78 106 106 0 strelka-varscan-mutect MATN2,synonymous_variant,p.=,ENST00000254898,NM_002380.3;MATN2,synonymous_variant,p.=,ENST00000521689,NM_030583.2;MATN2,synonymous_variant,p.=,ENST00000520016,;MATN2,synonymous_variant,p.=,ENST00000524308,;MATN2,synonymous_variant,p.=,ENST00000521041,;MATN2,5_prime_UTR_variant,,ENST00000522025,;MATN2,5_prime_UTR_variant,,ENST00000519585,;MATN2,intron_variant,,ENST00000518154,;MATN2,upstream_gene_variant,,ENST00000522270,;MATN2,non_coding_transcript_exon_variant,,ENST00000523490,; A ENST00000254898 Transcript synonymous_variant 1083/4106 852/2871 284/956 A gcC/gcA 1 1 MATN2 HGNC HGNC:6908 protein_coding YES CCDS55264.1 ENSP00000254898 O00339 A0A140VKH7 UPI000021037B NM_002380.3 5/19 Gene3D:2.10.25.10,Pfam_domain:PF07645,hmmpanther:PTHR11132,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 97961424 97961424 C A 1 0 0 0 0 0 0 0 1 9260 581 21 2 2 MATN2 8 97961424 Silent SNP C C3N-00560_T 3195671 97961424 47177212 587 17276 DPYS 0 . GRCh38 8 104381264 104381264 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.1494C>T p.= p.A498A ENST00000351513 9/10 492 400 92 402 402 0 strelka-varscan-mutect DPYS,synonymous_variant,p.=,ENST00000351513,NM_001385.2;DPYS,intron_variant,,ENST00000533874,;DPYS,non_coding_transcript_exon_variant,,ENST00000521601,;DPYS,non_coding_transcript_exon_variant,,ENST00000521372,;DPYS,non_coding_transcript_exon_variant,,ENST00000520483,;DPYS,non_coding_transcript_exon_variant,,ENST00000520806,; A ENST00000351513 Transcript synonymous_variant 1627/2127 1494/1560 498/519 A gcC/gcT 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 9/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 104381264 104381264 G A 1 0 0 0 0 0 0 0 1 4561 1335 47 3 3 DPYS 8 104381264 Silent SNP G C3N-00560_T 6419840 104381264 40757372 588 17277 LRP12 0 . GRCh38 8 104491071 104491071 + Missense_Mutation SNP T T C C3N-00560_T C3N-00560_N T T c.2182A>G p.Ser728Gly p.S728G ENST00000276654 7/7 240 124 116 208 208 0 strelka-varscan-mutect LRP12,missense_variant,p.Ser728Gly,ENST00000276654,NM_013437.4;LRP12,missense_variant,p.Ser709Gly,ENST00000424843,NM_001135703.2;LRP12,downstream_gene_variant,,ENST00000523007,;LRP12,non_coding_transcript_exon_variant,,ENST00000518375,;LRP12,downstream_gene_variant,,ENST00000522046,; C ENST00000276654 Transcript missense_variant 2291/4112 2182/2580 728/859 S/G Agt/Ggt COSM603651 1 -1 LRP12 HGNC HGNC:31708 protein_coding YES CCDS6303.1 ENSP00000276654 Q9Y561 UPI0000047A9F NM_013437.4 deleterious(0.04) 7/7 hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF216 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 104491071 104491071 T C 1 0 0 0 0 1 0 0 0 8849 1609 56 5 5 LRP12 8 104491071 Missense_Mutation SNP T C3N-00560_T 109807 104491071 40647565 589 17278 64 2 LRP12 0 . GRCh38 8 104491073 104491073 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2180C>A p.Thr727Lys p.T727K ENST00000276654 7/7 236 120 116 210 210 0 strelka-varscan-mutect LRP12,missense_variant,p.Thr727Lys,ENST00000276654,NM_013437.4;LRP12,missense_variant,p.Thr708Lys,ENST00000424843,NM_001135703.2;LRP12,downstream_gene_variant,,ENST00000523007,;LRP12,non_coding_transcript_exon_variant,,ENST00000518375,;LRP12,downstream_gene_variant,,ENST00000522046,; T ENST00000276654 Transcript missense_variant 2289/4112 2180/2580 727/859 T/K aCa/aAa 1 -1 LRP12 HGNC HGNC:31708 protein_coding YES CCDS6303.1 ENSP00000276654 Q9Y561 UPI0000047A9F NM_013437.4 deleterious(0.02) 7/7 hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF216 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 104491073 104491073 G T 1 0 0 0 0 1 0 0 0 8849 1377 48 2 2 LRP12 8 104491073 Missense_Mutation SNP G C3N-00560_T 2 104491073 40647563 590 17279 64 2 ZFPM2 0 . GRCh38 8 105802563 105802563 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.2481C>A p.Asp827Glu p.D827E ENST00000407775 8/8 535 407 128 376 376 0 strelka-varscan-mutect ZFPM2,missense_variant,p.Asp827Glu,ENST00000407775,NM_012082.3;ZFPM2,missense_variant,p.Asp695Glu,ENST00000520492,;ZFPM2,missense_variant,p.Asp695Glu,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; A ENST00000407775 Transcript missense_variant 2731/4700 2481/3456 827/1151 D/E gaC/gaA COSM5065737 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 tolerated(0.09) 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 1 MODERATE 1 SNV 1 1 1 PASS rs1286201473 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 105802563 105802563 C A 1 0 0 0 0 1 0 0 0 18236 535 19 1 1 ZFPM2 8 105802563 Missense_Mutation SNP C C3N-00560_T 1311490 105802563 39336073 591 17280 ABRA 0 . GRCh38 8 106761050 106761050 + Missense_Mutation SNP G G A rs200631708 C3N-00560_T C3N-00560_N G G c.1133C>T p.Thr378Met p.T378M ENST00000311955 2/2 142 109 33 94 94 0 strelka-varscan-mutect ABRA,missense_variant,p.Thr378Met,ENST00000311955,NM_139166.4; A ENST00000311955 Transcript missense_variant 1188/2755 1133/1146 378/381 T/M aCg/aTg rs200631708,COSM3271409 1 -1 ABRA HGNC HGNC:30655 protein_coding YES CCDS6305.1 ENSP00000311436 Q8N0Z2 UPI000006F0DE NM_139166.4 deleterious(0) 2/2 hmmpanther:PTHR22739,hmmpanther:PTHR22739:SF7,Pfam_domain:PF14705,SMART_domains:SM01283 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200631708 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 106761050 106761050 G A 1 0 0 0 0 1 0 0 0 109 1145 40 1 1 ABRA 8 106761050 Missense_Mutation SNP G C3N-00560_T 958487 106761050 38377586 592 17281 TRHR 0 . GRCh38 8 109087744 109087744 + Missense_Mutation SNP G G T rs754288192 C3N-00560_T C3N-00560_N G G c.232G>T p.Ala78Ser p.A78S ENST00000518632 2/3 359 309 50 265 264 1 strelka-varscan-mutect TRHR,missense_variant,p.Ala78Ser,ENST00000518632,;TRHR,missense_variant,p.Ala78Ser,ENST00000311762,NM_003301.5; T ENST00000518632 Transcript missense_variant 583/1660 232/1197 78/398 A/S Gca/Tca rs754288192,COSM3271597 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 tolerated(0.05) 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115,Low_complexity_(Seg):seg,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs754288192 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 109087744 109087744 G T 1 0 0 0 0 1 0 0 0 16969 1087 38 1 1 TRHR 8 109087744 Missense_Mutation SNP G C3N-00560_T 2326694 109087744 36050892 593 17282 PKHD1L1 0 . GRCh38 8 109445284 109445284 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.5415C>A p.= p.L1805L ENST00000378402 38/78 360 326 34 299 299 0 strelka-varscan-mutect PKHD1L1,synonymous_variant,p.=,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript synonymous_variant 5519/13076 5415/12732 1805/4243 L ctC/ctA 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 38/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS rs1301194481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 109445284 109445284 C A 1 0 0 0 0 0 0 0 1 12068 842 30 2 2 PKHD1L1 8 109445284 Silent SNP C C3N-00560_T 357540 109445284 35693352 594 17283 KCNV1 0 . GRCh38 8 109974030 109974030 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.359G>T p.Gly120Val p.G120V ENST00000524391 2/4 414 359 55 326 326 0 strelka-varscan-mutect KCNV1,missense_variant,p.Gly120Val,ENST00000524391,;KCNV1,missense_variant,p.Gly120Val,ENST00000297404,NM_014379.2;RP11-696P8.2,splice_region_variant,,ENST00000530667,; A ENST00000524391 Transcript missense_variant 1392/6979 359/1503 120/500 G/V gGc/gTc 1 -1 KCNV1 HGNC HGNC:18861 protein_coding YES CCDS6314.1 ENSP00000435954 Q6PIU1 UPI0000073DA5 deleterious(0) 2/4 Gene3D:3.30.710.10,Pfam_domain:PF02214,Prints_domain:PR01493,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF38,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 109974030 109974030 C A 1 0 0 0 0 1 0 0 0 8010 739 26 2 2 KCNV1 8 109974030 Missense_Mutation SNP C C3N-00560_T 528746 109974030 35164606 595 17284 CSMD3 0 . GRCh38 8 112682541 112682541 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2578T>A p.Cys860Ser p.C860S ENST00000297405 16/71 166 102 64 157 157 0 strelka-varscan-mutect CSMD3,missense_variant,p.Cys860Ser,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Cys820Ser,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Cys756Ser,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Cys200Ser,ENST00000339701,; T ENST00000297405 Transcript missense_variant 2823/13212 2578/11124 860/3707 C/S Tgt/Agt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.02) 16/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 112682541 112682541 A T 1 0 0 0 0 1 0 0 0 3747 130 5 4 4 CSMD3 8 112682541 Missense_Mutation SNP A C3N-00560_T 2708511 112682541 32456095 596 17285 CSMD3 0 . GRCh38 8 113314727 113314727 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.245C>A p.Pro82Gln p.P82Q ENST00000297405 2/71 217 191 26 277 276 1 strelka-varscan-mutect CSMD3,missense_variant,p.Pro82Gln,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro42Gln,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro82Gln,ENST00000455883,NM_052900.2;CSMD3,non_coding_transcript_exon_variant,,ENST00000493303,;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,; T ENST00000297405 Transcript missense_variant 490/13212 245/11124 82/3707 P/Q cCa/cAa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 2/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 113314727 113314727 G T 1 0 0 0 0 1 0 0 0 3747 1348 47 2 2 CSMD3 8 113314727 Missense_Mutation SNP G C3N-00560_T 632186 113314727 31823909 597 17286 EXT1 0 . GRCh38 8 117807332 117807332 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1768G>T p.Val590Leu p.V590L ENST00000378204 9/11 501 235 266 398 397 1 strelka-varscan-mutect EXT1,missense_variant,p.Val590Leu,ENST00000378204,NM_000127.2;EXT1,3_prime_UTR_variant,,ENST00000437196,; A ENST00000378204 Transcript missense_variant 2575/8270 1768/2241 590/746 V/L Gtg/Ttg 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 deleterious(0) 9/11 Gene3D:3.90.550.10,Pfam_domain:PF09258,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 117807332 117807332 C A 1 0 0 0 0 1 0 0 0 5191 478 17 2 2 EXT1 8 117807332 Missense_Mutation SNP C C3N-00560_T 4492605 117807332 27331304 598 17287 EXT1 0 . GRCh38 8 117807355 117807355 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1745G>T p.Trp582Leu p.W582L ENST00000378204 9/11 518 447 71 416 416 0 strelka-varscan-mutect EXT1,missense_variant,p.Trp582Leu,ENST00000378204,NM_000127.2;EXT1,3_prime_UTR_variant,,ENST00000437196,; A ENST00000378204 Transcript missense_variant 2552/8270 1745/2241 582/746 W/L tGg/tTg CM012094 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 deleterious(0) 9/11 Gene3D:3.90.550.10,Pfam_domain:PF09258,hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF97,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 117807355 117807355 C A 1 0 0 0 0 1 0 0 0 5191 595 21 2 2 EXT1 8 117807355 Missense_Mutation SNP C C3N-00560_T 23 117807355 27331281 599 17288 FER1L6 0 . GRCh38 8 123970098 123970098 + Splice_Site SNP G G A rs755495488 C3N-00560_T C3N-00560_N G G c.447+1G>A p.X149_splice ENST00000522917 211 148 63 215 215 0 strelka-varscan-mutect FER1L6,splice_donor_variant,,ENST00000522917,NM_001039112.2; A ENST00000522917 Transcript splice_donor_variant -/6051 447/5574 149/1857 rs755495488,COSM4168173 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 6/40 0,1 HIGH 1 SNV 1 0,1 1 PASS rs1254088849 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 123970098 123970098 G A 1 0 0 0 0 0 0 1 0 5678 1159 40 1 1 FER1L6 8 123970098 Splice_Site SNP G C3N-00560_T 6162743 123970098 21168538 600 17289 FER1L6 0 . GRCh38 8 124094961 124094961 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4618G>T p.Glu1540Ter p.E1540* ENST00000522917 35/41 498 441 57 387 386 1 strelka-varscan-mutect FER1L6,stop_gained,p.Glu1540Ter,ENST00000522917,NM_001039112.2;FER1L6-AS2,intron_variant,,ENST00000520031,; T ENST00000522917 Transcript stop_gained 4824/6051 4618/5574 1540/1857 E/* Gaa/Taa 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 35/41 hmmpanther:PTHR12546:SF37,hmmpanther:PTHR12546 HIGH 1 SNV 1 1 PASS rs1402824205 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 124094961 124094961 G T 1 0 0 0 0 0 1 0 0 5678 1175 41 2 2 FER1L6 8 124094961 Nonsense_Mutation SNP G C3N-00560_T 124863 124094961 21043675 601 17290 FAM49B 0 . GRCh38 8 129849242 129849242 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.840+1G>T p.X280_splice ENST00000519824 109 82 27 82 82 0 strelka-varscan-mutect FAM49B,splice_donor_variant,,ENST00000519824,NM_016623.4;FAM49B,splice_donor_variant,,ENST00000522746,;FAM49B,splice_donor_variant,,ENST00000401979,;FAM49B,splice_donor_variant,,ENST00000519540,NM_001256763.1;FAM49B,splice_donor_variant,,ENST00000523509,;FAM49B,splice_donor_variant,,ENST00000519110,;FAM49B,splice_donor_variant,,ENST00000517654,;FAM49B,splice_donor_variant,,ENST00000522941,;FAM49B,splice_donor_variant,,ENST00000522250,;FAM49B,splice_donor_variant,,ENST00000615041,;RP11-473O4.5,downstream_gene_variant,,ENST00000524100,;FAM49B,splice_donor_variant,,ENST00000523288,;FAM49B,downstream_gene_variant,,ENST00000517801,;FAM49B,upstream_gene_variant,,ENST00000520887,; A ENST00000519824 Transcript splice_donor_variant -/3798 840/975 280/324 1 -1 FAM49B HGNC HGNC:25216 protein_coding YES CCDS6361.1 ENSP00000429150 Q9NUQ9 A0A024R9G4 UPI0000073D89 NM_016623.4 10/11 HIGH 1 SNV 2 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999937 1 1 1 0 A 5 1 56 129849242 129849242 C A 1 0 0 0 0 0 0 1 0 5452 492 17 2 2 FAM49B 8 129849242 Splice_Site SNP C C3N-00560_T 5754281 129849242 15289394 602 17291 ASAP1 0 . GRCh38 8 130054793 130054793 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3328G>T p.Glu1110Ter p.E1110* ENST00000518721 30/30 279 222 57 194 194 0 strelka-varscan-mutect ASAP1,stop_gained,p.Glu1103Ter,ENST00000357668,NM_001247996.1;ASAP1,stop_gained,p.Glu1110Ter,ENST00000518721,NM_018482.3;ASAP1,stop_gained,p.Glu931Ter,ENST00000524124,;ASAP1,stop_gained,p.Glu467Ter,ENST00000519483,;ASAP1,3_prime_UTR_variant,,ENST00000521075,; A ENST00000518721 Transcript stop_gained 3556/5507 3328/3390 1110/1129 E/* Gaa/Taa 1 -1 ASAP1 HGNC HGNC:2720 protein_coding YES CCDS6362.1 ENSP00000429900 Q9ULH1 UPI0000351D6E NM_018482.3 30/30 PROSITE_profiles:PS50002,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF192,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 130054793 130054793 C A 1 0 0 0 0 0 1 0 0 1152 893 31 1 1 ASAP1 8 130054793 Nonsense_Mutation SNP C C3N-00560_T 205551 130054793 15083843 603 17292 LRRC6 0 . GRCh38 8 132611293 132611293 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.1044+1G>T p.X348_splice ENST00000620350 144 74 70 109 109 0 strelka-varscan-mutect LRRC6,splice_donor_variant,,ENST00000620350,NM_012472.4;LRRC6,splice_donor_variant,,ENST00000618342,;LRRC6,splice_donor_variant,,ENST00000519595,;LRRC6,splice_donor_variant,,ENST00000518642,;LRRC6,splice_donor_variant,,ENST00000250173,;LRRC6,splice_donor_variant,,ENST00000522789,;LRRC6,splice_donor_variant,,ENST00000519085,;LRRC6,splice_donor_variant,,ENST00000522597,; A ENST00000620350 Transcript splice_donor_variant -/1878 1044/1401 348/466 1 -1 LRRC6 HGNC HGNC:16725 protein_coding YES CCDS6365.1 ENSP00000484634 Q86X45 UPI000000DBC5 NM_012472.4 9/11 HIGH 1 SNV 1 1 PASS rs1234742897 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 132611293 132611293 C A 1 0 0 0 0 0 0 1 0 8911 521 18 2 2 LRRC6 8 132611293 Splice_Site SNP C C3N-00560_T 2556500 132611293 12527343 604 17293 FAM135B 0 . GRCh38 8 138139064 138139064 + Missense_Mutation SNP C C A rs374711628 C3N-00560_T C3N-00560_N C C c.3823G>T p.Gly1275Trp p.G1275W ENST00000395297 18/20 151 89 62 147 147 0 strelka-varscan-mutect FAM135B,missense_variant,p.Gly1275Trp,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,;FAM135B,downstream_gene_variant,,ENST00000467365,;FAM135B,downstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 3994/6962 3823/4221 1275/1406 G/W Ggg/Tgg rs374711628 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 18/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482,Gene3D:3.40.50.1820,Pfam_domain:PF05057,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS rs374711628 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 138139064 138139064 C A 1 0 0 0 0 1 0 0 0 5299 652 23 1 1 FAM135B 8 138139064 Missense_Mutation SNP C C3N-00560_T 5527771 138139064 6999572 605 17294 FAM135B 0 . GRCh38 8 138153119 138153119 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.1356C>A p.Ser452Arg p.S452R ENST00000395297 13/20 151 129 22 122 122 0 strelka-varscan-mutect FAM135B,missense_variant,p.Ser452Arg,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Ser452Arg,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; T ENST00000395297 Transcript missense_variant 1527/6962 1356/4221 452/1406 S/R agC/agA COSM5358753,COSM5358754 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.88) 13/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 138153119 138153119 G T 1 0 0 0 0 1 0 0 0 5299 1310 46 2 2 FAM135B 8 138153119 Missense_Mutation SNP G C3N-00560_T 14055 138153119 6985517 606 17295 COL22A1 0 . GRCh38 8 138594126 138594126 + Silent SNP T T G novel C3N-00560_T C3N-00560_N T T c.4506A>C p.= p.P1502P ENST00000303045 63/65 147 127 20 140 140 0 strelka-varscan-mutect COL22A1,synonymous_variant,p.=,ENST00000303045,NM_152888.2;COL22A1,synonymous_variant,p.=,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; G ENST00000303045 Transcript synonymous_variant 4953/6346 4506/4881 1502/1626 P ccA/ccC 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 63/65 Low_complexity_(Seg):seg,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS rs1374502999 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 2 3 56 138594126 138594126 T G 1 0 0 0 0 0 0 0 1 3469 1567 55 5 5 COL22A1 8 138594126 Silent SNP T C3N-00560_T 441007 138594126 6544510 607 17296 COL22A1 0 . GRCh38 8 138594199 138594199 + Missense_Mutation SNP G G T rs759271482 C3N-00560_T C3N-00560_N G G c.4433C>A p.Thr1478Asn p.T1478N ENST00000303045 63/65 171 150 21 167 167 0 strelka-varscan-mutect COL22A1,missense_variant,p.Thr1478Asn,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Thr1171Asn,ENST00000435777,;COL22A1,splice_region_variant,,ENST00000341807,; T ENST00000303045 Transcript missense_variant,splice_region_variant 4880/6346 4433/4881 1478/1626 T/N aCc/aAc rs759271482 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.45) 63/65 MODERATE 1 SNV 1 1 PASS rs759271482 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 56 138594199 138594199 G T 1 0 0 0 0 1 0 0 0 3469 1217 42 2 2 COL22A1 8 138594199 Missense_Mutation SNP G C3N-00560_T 73 138594199 6544437 608 17297 JRK 0 . GRCh38 8 142664484 142664484 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1575G>T p.Gln525His p.Q525H ENST00000612905 2/2 214 101 113 163 162 1 strelka-varscan-mutect JRK,missense_variant,p.Gln525His,ENST00000612905,NM_003724.3;JRK,missense_variant,p.Gln525His,ENST00000614134,;JRK,missense_variant,p.Gln525His,ENST00000615982,NM_001279352.1;JRK,missense_variant,p.Gln525His,ENST00000571961,NM_001077527.2;JRK,downstream_gene_variant,,ENST00000503272,;JRK,downstream_gene_variant,,ENST00000591357,;JRK,upstream_gene_variant,,ENST00000506774,; A ENST00000612905 Transcript missense_variant 2100/9124 1575/1707 525/568 Q/H caG/caT 1 -1 JRK HGNC HGNC:6199 protein_coding YES CCDS75796.1 ENSP00000482410 Q86XJ5 UPI000000DA37 NM_003724.3 tolerated(0.05) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 142664484 142664484 C A 1 0 0 0 0 1 0 0 0 7876 796 28 2 2 JRK 8 142664484 Missense_Mutation SNP C C3N-00560_T 4070285 142664484 2474152 609 17298 CYP11B2 0 . GRCh38 8 142917740 142917740 + Missense_Mutation SNP G G T rs753988592 C3N-00560_T C3N-00560_N G G c.101C>A p.Thr34Lys p.T34K ENST00000323110 1/9 616 425 191 426 425 1 strelka-varscan-mutect CYP11B2,missense_variant,p.Thr34Lys,ENST00000323110,NM_000498.3;GML,downstream_gene_variant,,ENST00000522728,; T ENST00000323110 Transcript missense_variant 104/2936 101/1512 34/503 T/K aCg/aAg rs753988592,COSM4762248 1 -1 CYP11B2 HGNC HGNC:2592 protein_coding YES CCDS6393.1 ENSP00000325822 P19099 UPI00001282CF NM_000498.3 tolerated(0.34) 1/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753988592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 142917740 142917740 G T 1 0 0 0 0 1 0 0 0 3949 1145 40 1 1 CYP11B2 8 142917740 Missense_Mutation SNP G C3N-00560_T 253256 142917740 2220896 610 17299 LY6E 0 . GRCh38 8 143021771 143021771 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.378G>T p.= p.L126L ENST00000520466 5/5 154 123 31 81 81 0 strelka-varscan-mutect LY6E,synonymous_variant,p.=,ENST00000520466,;LY6E,synonymous_variant,p.=,ENST00000521699,;LY6E,synonymous_variant,p.=,ENST00000292494,NM_002346.2;LY6E,synonymous_variant,p.=,ENST00000429120,NM_001127213.1;LY6E,synonymous_variant,p.=,ENST00000522024,;LY6E,synonymous_variant,p.=,ENST00000522971,;LY6E,synonymous_variant,p.=,ENST00000521003,;LY6E,3_prime_UTR_variant,,ENST00000517503,;LY6E,3_prime_UTR_variant,,ENST00000521182,;LY6E,3_prime_UTR_variant,,ENST00000519546,;LY6E,3_prime_UTR_variant,,ENST00000519611,;LY6E,3_prime_UTR_variant,,ENST00000522528,;LY6E,intron_variant,,ENST00000523847,;LY6E,downstream_gene_variant,,ENST00000520531,;RP11-273G15.2,upstream_gene_variant,,ENST00000502167,;RP11-273G15.2,upstream_gene_variant,,ENST00000517833,;RP11-273G15.2,upstream_gene_variant,,ENST00000522060,;RP11-273G15.2,upstream_gene_variant,,ENST00000518831,;LY6E,upstream_gene_variant,,ENST00000519615,; T ENST00000520466 Transcript synonymous_variant 781/1419 378/396 126/131 L ctG/ctT 1 1 LY6E HGNC HGNC:6727 protein_coding YES CCDS6394.1 ENSP00000428572 Q16553 UPI00000374A7 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16983:SF13,hmmpanther:PTHR16983 LOW SNV 2 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 2 4 56 143021771 143021771 G T 1 0 0 0 0 0 0 0 1 9001 1306 46 2 2 LY6E 8 143021771 Silent SNP G C3N-00560_T 104031 143021771 2116865 611 17300 WDR97 0 . GRCh38 8 144109522 144109522 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1188G>T p.Trp396Cys p.W396C ENST00000323662 5/24 322 224 98 186 186 0 strelka-varscan-mutect WDR97,missense_variant,p.Trp396Cys,ENST00000323662,;MAF1,downstream_gene_variant,,ENST00000534585,;MAF1,downstream_gene_variant,,ENST00000322428,NM_032272.4;MAF1,downstream_gene_variant,,ENST00000532522,;MAF1,downstream_gene_variant,,ENST00000527058,;MAF1,downstream_gene_variant,,ENST00000527572,;MAF1,downstream_gene_variant,,ENST00000534811,;WDR97,upstream_gene_variant,,ENST00000533108,;SHARPIN,upstream_gene_variant,,ENST00000533184,;WDR97,missense_variant,p.Trp396Cys,ENST00000534167,;WDR97,upstream_gene_variant,,ENST00000528691,;WDR97,upstream_gene_variant,,ENST00000525150,;WDR97,upstream_gene_variant,,ENST00000529209,; T ENST00000323662 Transcript missense_variant 1213/6916 1188/4869 396/1622 W/C tgG/tgT 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 deleterious(0.04) 5/24 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF497,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS rs897281478 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 144109522 144109522 G T 1 0 0 0 0 1 0 0 0 17897 1212 42 2 2 WDR97 8 144109522 Missense_Mutation SNP G C3N-00560_T 1087751 144109522 1029114 612 17301 LRRC24 0 . GRCh38 8 144523123 144523123 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.894G>C p.Gln298His p.Q298H ENST00000529415 5/5 453 416 37 331 331 0 strelka-varscan-mutect LRRC24,missense_variant,p.Gln298His,ENST00000529415,NM_001024678.3;LRRC24,missense_variant,p.Gln295His,ENST00000533758,;LRRC14,3_prime_UTR_variant,,ENST00000292524,NM_014665.3;C8orf82,downstream_gene_variant,,ENST00000524821,NM_001001795.1;LRRC14,downstream_gene_variant,,ENST00000529022,NM_001272036.1;C8orf82,downstream_gene_variant,,ENST00000313465,;LRRC14,downstream_gene_variant,,ENST00000527730,;C8orf82,downstream_gene_variant,,ENST00000532827,;LRRC14,downstream_gene_variant,,ENST00000530854,;LRRC14,downstream_gene_variant,,ENST00000525766,;LRRC14,non_coding_transcript_exon_variant,,ENST00000528528,;LRRC14,upstream_gene_variant,,ENST00000529995,;LRRC14,upstream_gene_variant,,ENST00000530242,;C8orf82,downstream_gene_variant,,ENST00000534680,;LRRC14,downstream_gene_variant,,ENST00000531310,; G ENST00000529415 Transcript missense_variant 1012/1758 894/1542 298/513 Q/H caG/caC 1 -1 LRRC24 HGNC HGNC:28947 protein_coding YES CCDS34969.1 ENSP00000434849 Q50LG9 UPI0000419443 NM_001024678.3 tolerated(0.49) 5/5 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF255,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 144523123 144523123 C G 1 0 0 0 0 1 0 0 0 8874 796 28 4 4 LRRC24 8 144523123 Missense_Mutation SNP C C3N-00560_T 413601 144523123 615513 613 17302 INSL4 0 . GRCh38 9 5233726 5233726 + Nonsense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.269C>A p.Ser90Ter p.S90* ENST00000239316 2/2 240 149 91 307 305 2 strelka-varscan-mutect INSL4,stop_gained,p.Ser90Ter,ENST00000239316,NM_002195.1; A ENST00000239316 Transcript stop_gained 374/1952 269/420 90/139 S/* tCa/tAa COSM1725209 1 1 INSL4 HGNC HGNC:6087 protein_coding YES CCDS6459.1 ENSP00000239316 Q14641 UPI0000032F5A NM_002195.1 2/2 Prints_domain:PR02004,hmmpanther:PTHR12004,hmmpanther:PTHR12004:SF3 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 5233726 5233726 C A 1 0 0 0 0 0 1 0 0 7670 838 29 2 2 INSL4 9 5233726 Nonsense_Mutation SNP C C3N-00560_T 5233726 133160991 614 17303 KIAA2026 0 . GRCh38 9 5929139 5929139 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2403G>C p.Arg801Ser p.R801S ENST00000399933 6/8 72 45 27 148 148 0 strelka-varscan-mutect KIAA2026,missense_variant,p.Arg801Ser,ENST00000399933,NM_001017969.2;KIAA2026,missense_variant,p.Arg771Ser,ENST00000381461,;KIAA2026,missense_variant,p.Gly129Ala,ENST00000540714,; G ENST00000399933 Transcript missense_variant 2403/6988 2403/6312 801/2103 R/S agG/agC 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 deleterious(0) 6/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 5929139 5929139 C G 1 0 0 0 0 1 0 0 0 8134 738 26 4 4 KIAA2026 9 5929139 Missense_Mutation SNP C C3N-00560_T 695413 5929139 132465578 615 17304 UHRF2 0 . GRCh38 9 6433995 6433995 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.466G>A p.Asp156Asn p.D156N ENST00000276893 3/16 160 79 81 187 187 0 strelka-varscan-mutect UHRF2,missense_variant,p.Asp156Asn,ENST00000276893,NM_152896.2;UHRF2,intron_variant,,ENST00000450508,;RP11-307L3.4,intron_variant,,ENST00000411561,;UHRF2,non_coding_transcript_exon_variant,,ENST00000469298,;UHRF2,non_coding_transcript_exon_variant,,ENST00000481049,;UHRF2,non_coding_transcript_exon_variant,,ENST00000461236,;UHRF2,missense_variant,p.Asp156Asn,ENST00000468435,;UHRF2,upstream_gene_variant,,ENST00000484159,; A ENST00000276893 Transcript missense_variant 634/3452 466/2409 156/802 D/N Gat/Aat 1 1 UHRF2 HGNC HGNC:12557 protein_coding YES CCDS6469.1 ENSP00000276893 Q96PU4 UPI000006E524 NM_152896.2 tolerated(0.34) 3/16 hmmpanther:PTHR14140:SF3,hmmpanther:PTHR14140,Pfam_domain:PF12148 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 6433995 6433995 G A 1 0 0 0 0 1 0 0 0 17494 1290 45 3 3 UHRF2 9 6433995 Missense_Mutation SNP G C3N-00560_T 504856 6433995 131960722 616 17305 GLDC 0 . GRCh38 9 6610261 6610261 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.566T>G p.Leu189Arg p.L189R ENST00000321612 4/25 256 159 97 282 282 0 strelka-varscan-mutect GLDC,missense_variant,p.Leu189Arg,ENST00000321612,NM_000170.2;GLDC,upstream_gene_variant,,ENST00000463305,; C ENST00000321612 Transcript missense_variant 717/3767 566/3063 189/1020 L/R cTg/cGg 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0) 4/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Gene3D:3.40.640.10,Pfam_domain:PF02347,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 6610261 6610261 A C 1 0 0 0 0 1 0 0 0 6311 188 7 5 5 GLDC 9 6610261 Missense_Mutation SNP A C3N-00560_T 176266 6610261 131784456 617 17306 BNC2 0 . GRCh38 9 16727843 16727843 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.284C>A p.Thr95Lys p.T95K ENST00000380672 3/7 256 142 114 326 326 0 strelka-varscan-mutect BNC2,missense_variant,p.Thr95Lys,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Thr52Lys,ENST00000418777,;BNC2,missense_variant,p.Thr17Lys,ENST00000380666,;BNC2,missense_variant,p.Thr17Lys,ENST00000603713,;BNC2,missense_variant,p.Thr53Lys,ENST00000486514,;BNC2,missense_variant,p.Thr17Lys,ENST00000617779,;BNC2,missense_variant,p.Thr52Lys,ENST00000468187,;BNC2,missense_variant,p.Thr17Lys,ENST00000613349,;BNC2,missense_variant,p.Thr17Lys,ENST00000603313,;BNC2,5_prime_UTR_variant,,ENST00000545497,;BNC2,intron_variant,,ENST00000380667,;RP11-62F24.2,downstream_gene_variant,,ENST00000450445,;BNC2,missense_variant,p.Thr95Lys,ENST00000484726,; T ENST00000380672 Transcript missense_variant 342/12844 284/3300 95/1099 T/K aCa/aAa 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 deleterious_low_confidence(0) 3/7 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 16727843 16727843 G T 1 0 0 0 0 1 0 0 0 1631 1377 48 2 2 BNC2 9 16727843 Missense_Mutation SNP G C3N-00560_T 10117582 16727843 121666874 618 17307 FOCAD 0 . GRCh38 9 20770216 20770216 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.884A>T p.His295Leu p.H295L ENST00000380249 10/46 176 100 76 258 258 0 strelka-varscan-mutect FOCAD,missense_variant,p.His295Leu,ENST00000380249,NM_017794.4;FOCAD,missense_variant,p.His295Leu,ENST00000338382,;FOCAD,downstream_gene_variant,,ENST00000604103,;FOCAD,downstream_gene_variant,,ENST00000605031,; T ENST00000380249 Transcript missense_variant 1248/6096 884/5406 295/1801 H/L cAc/cTc 1 1 FOCAD HGNC HGNC:23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 UPI0000EE4244 NM_017794.4 tolerated(0.13) 10/46 hmmpanther:PTHR16212,hmmpanther:PTHR16212:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 20770216 20770216 A T 1 0 0 0 0 1 0 0 0 5839 159 6 4 4 FOCAD 9 20770216 Missense_Mutation SNP A C3N-00560_T 4042373 20770216 117624501 619 17308 IFNA13 0 . GRCh38 9 21367978 21367978 + Silent SNP G G C C3N-00560_T C3N-00560_N G G c.33C>G p.= p.A11A ENST00000610660 1/1 211 116 95 272 272 0 strelka-varscan-mutect IFNA13,synonymous_variant,p.=,ENST00000610660,NM_006900.3;IFNA13,synonymous_variant,p.=,ENST00000449498,; C ENST00000610660 Transcript synonymous_variant 985/1539 33/573 11/190 A gcC/gcG COSM753762 1 -1 IFNA13 HGNC HGNC:5419 protein_coding YES CCDS6505.2 ENSP00000480467 A0A087WWS6 UPI0000D4C125 NM_006900.3 1/1 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF30 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 21367978 21367978 G C 1 0 0 0 0 0 0 0 1 7433 1219 43 4 4 IFNA13 9 21367978 Silent SNP G C3N-00560_T 597762 21367978 117026739 620 17309 TEK 0 . GRCh38 9 27212781 27212781 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2761G>T p.Glu921Ter p.E921* ENST00000380036 17/23 748 547 201 627 626 1 strelka-varscan-mutect TEK,stop_gained,p.Glu921Ter,ENST00000380036,NM_000459.4;TEK,stop_gained,p.Glu878Ter,ENST00000406359,NM_001290077.1;TEK,stop_gained,p.Glu773Ter,ENST00000519097,NM_001290078.1;TEK,3_prime_UTR_variant,,ENST00000615002,;RP11-179D22.1,downstream_gene_variant,,ENST00000422804,; T ENST00000380036 Transcript stop_gained 3203/4760 2761/3375 921/1124 E/* Gag/Tag 1 1 TEK HGNC HGNC:11724 protein_coding YES CCDS6519.1 ENSP00000369375 Q02763 UPI000021121E NM_000459.4 17/23 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF125,SMART_domains:SM00219,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 27212781 27212781 G T 1 0 0 0 0 0 1 0 0 16163 1175 41 2 2 TEK 9 27212781 Nonsense_Mutation SNP G C3N-00560_T 5844803 27212781 111181936 621 17310 TOPORS 0 . GRCh38 9 32542667 32542667 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1858G>T p.Gly620Trp p.G620W ENST00000360538 3/3 701 481 220 622 619 3 strelka-varscan-mutect TOPORS,missense_variant,p.Gly620Trp,ENST00000360538,NM_005802.4;TOPORS,missense_variant,p.Gly555Trp,ENST00000379858,NM_001195622.1; A ENST00000360538 Transcript missense_variant 1975/4098 1858/3138 620/1045 G/W Ggg/Tgg 1 -1 TOPORS HGNC HGNC:21653 protein_coding YES CCDS6527.1 ENSP00000353735 Q9NS56 UPI000006F223 NM_005802.4 deleterious_low_confidence(0.01) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22937:SF61,hmmpanther:PTHR22937 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 32542667 32542667 C A 1 0 0 0 0 1 0 0 0 16847 594 21 2 2 TOPORS 9 32542667 Missense_Mutation SNP C C3N-00560_T 5329886 32542667 105852050 622 17311 TAF1L 0 . GRCh38 9 32633026 32633026 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2554G>C p.Ala852Pro p.A852P ENST00000242310 1/1 599 435 164 543 543 0 strelka-varscan-mutect TAF1L,missense_variant,p.Ala852Pro,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; G ENST00000242310 Transcript missense_variant 2644/6216 2554/5481 852/1826 A/P Gcc/Ccc 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0) 1/1 Pfam_domain:PF12157,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 32633026 32633026 C G 1 0 0 0 0 1 0 0 0 15919 797 28 4 4 TAF1L 9 32633026 Missense_Mutation SNP C C3N-00560_T 90359 32633026 105761691 623 17312 TAF1L 0 . GRCh38 9 32633579 32633579 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.2001G>C p.Lys667Asn p.K667N ENST00000242310 1/1 322 223 99 269 269 0 strelka-varscan-mutect TAF1L,missense_variant,p.Lys667Asn,ENST00000242310,NM_153809.2;RP11-555J4.4,non_coding_transcript_exon_variant,,ENST00000430787,; G ENST00000242310 Transcript missense_variant 2091/6216 2001/5481 667/1826 K/N aaG/aaC COSM3952656 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0) 1/1 Pfam_domain:PF12157,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 32633579 32633579 C G 1 0 0 0 0 1 0 0 0 15919 912 32 4 4 TAF1L 9 32633579 Missense_Mutation SNP C C3N-00560_T 553 32633579 105761138 624 17313 UNC13B 0 . GRCh38 9 35403544 35403544 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.4435A>T p.Thr1479Ser p.T1479S ENST00000378495 38/39 172 108 64 124 124 0 strelka-varscan-mutect UNC13B,missense_variant,p.Thr4228Ser,ENST00000635942,;UNC13B,missense_variant,p.Thr1878Ser,ENST00000636694,;UNC13B,missense_variant,p.Thr1085Ser,ENST00000617908,;UNC13B,missense_variant,p.Thr1498Ser,ENST00000619578,;UNC13B,missense_variant,p.Thr1479Ser,ENST00000378495,NM_006377.3;UNC13B,missense_variant,p.Thr1510Ser,ENST00000396787,;UNC13B,missense_variant,p.Thr1085Ser,ENST00000378496,;UNC13B,downstream_gene_variant,,ENST00000481299,;UNC13B,non_coding_transcript_exon_variant,,ENST00000637271,;ATP8B5P,upstream_gene_variant,,ENST00000430846,;ATP8B5P,upstream_gene_variant,,ENST00000329395,;ATP8B5P,upstream_gene_variant,,ENST00000439972,;UNC13B,3_prime_UTR_variant,,ENST00000634487,; T ENST00000378495 Transcript missense_variant 4657/6303 4435/4776 1479/1591 T/S Aca/Tca 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 tolerated(0.35) 38/39 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10480,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 35403544 35403544 A T 1 0 0 0 0 1 0 0 0 17509 159 6 4 4 UNC13B 9 35403544 Missense_Mutation SNP A C3N-00560_T 2769965 35403544 102991173 625 17314 ALDH1B1 0 . GRCh38 9 38395771 38395771 + Missense_Mutation SNP G G T rs61757680 C3N-00560_T C3N-00560_N G G c.23G>T p.Arg8Leu p.R8L ENST00000377698 2/2 60 42 18 44 44 0 strelka-varscan-mutect ALDH1B1,missense_variant,p.Arg8Leu,ENST00000377698,NM_000692.4;ALDH1B1,missense_variant,p.Arg8Leu,ENST00000635162,; T ENST00000377698 Transcript missense_variant 176/3066 23/1554 8/517 R/L cGg/cTg rs61757680,COSM3907431 1 1 ALDH1B1 HGNC HGNC:407 protein_coding YES CCDS6615.1 ENSP00000366927 P30837 UPI0000073000 NM_000692.4 tolerated(0.18) 2/2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs61757680 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 56 38395771 38395771 G T 1 0 0 0 0 1 0 0 0 593 1116 39 1 1 ALDH1B1 9 38395771 Missense_Mutation SNP G C3N-00560_T 2992227 38395771 99998946 626 17315 CNTNAP3 0 . GRCh38 9 39086808 39086808 + Missense_Mutation SNP G G T rs267602246 C3N-00560_T C3N-00560_N G G c.3262C>A p.Pro1088Thr p.P1088T ENST00000297668 20/24 250 184 66 297 297 0 strelka-varscan-mutect CNTNAP3,missense_variant,p.Pro1088Thr,ENST00000297668,NM_033655.3;CNTNAP3,missense_variant,p.Pro1007Thr,ENST00000377656,;CNTNAP3,missense_variant,p.Pro1000Thr,ENST00000358144,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000493965,;CNTNAP3,upstream_gene_variant,,ENST00000477002,; T ENST00000297668 Transcript missense_variant 3336/5064 3262/3867 1088/1288 P/T Cct/Act rs267602246 1 -1 CNTNAP3 HGNC HGNC:13834 protein_coding YES CCDS6616.1 ENSP00000297668 Q9BZ76 UPI000013E43B NM_033655.3 tolerated(0.09) 20/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs267602246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 39086808 39086808 G T 1 0 0 0 0 1 0 0 0 3429 1174 41 2 2 CNTNAP3 9 39086808 Missense_Mutation SNP G C3N-00560_T 691037 39086808 99307909 627 17316 SPATA31A1 0 . GRCh38 9 39355836 39355836 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.148C>A p.Leu50Met p.L50M ENST00000377647 1/4 15 8 7 21 21 0 strelka-varscan-mutect SPATA31A1,missense_variant,p.Leu50Met,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,upstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 168/4256 148/4086 50/1361 L/M Ctg/Atg 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 deleterious(0.03) 1/4 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 39355836 39355836 C A 1 0 0 0 0 1 0 0 0 15343 680 24 2 2 SPATA31A1 9 39355836 Missense_Mutation SNP C C3N-00560_T 269028 39355836 99038881 628 17317 SPATA31A1 0 . GRCh38 9 39359401 39359401 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.1679delC p.Pro560LeufsTer3 p.P560Lfs*3 ENST00000377647 4/4 281 237 44 230 230 0 sindel-varindel-pindel SPATA31A1,frameshift_variant,p.Pro560LeufsTer3,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; - ENST00000377647 Transcript frameshift_variant 1698/4256 1678/4086 560/1361 P/X Cct/ct 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF14650 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 2 -3.473107 0 0 1 0 0 - 7 5 56 39359401 39359401 C - 1 0 1 0 1 0 0 0 0 15343 739 26 0 0 SPATA31A1 9 39359401 Frame_Shift_Del DEL C C3N-00560_T 3565 39359401 99035316 629 17318 SPATA31A3 0 . GRCh38 9 66990127 66990127 + Missense_Mutation SNP C C A rs199602513 C3N-00560_T C3N-00560_N C C c.371G>T p.Gly124Val p.G124V ENST00000428649 4/4 225 161 64 213 213 0 strelka-varscan-mutect SPATA31A3,missense_variant,p.Gly124Val,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; A ENST00000428649 Transcript missense_variant 433/4256 371/4044 124/1347 G/V gGt/gTt rs199602513 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 deleterious(0) 4/4 Pfam_domain:PF15371,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS rs199602513 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 66990127 66990127 C A 1 0 0 0 0 1 0 0 0 15344 507 18 2 2 SPATA31A3 9 66990127 Missense_Mutation SNP C C3N-00560_T 27630726 66990127 71404590 630 17319 TRPM3 0 . GRCh38 9 70537080 70537080 + Missense_Mutation SNP G G C rs149067881 C3N-00560_T C3N-00560_N G G c.3997C>G p.Arg1333Gly p.R1333G ENST00000377110 25/25 102 71 31 141 141 0 strelka-varscan-mutect TRPM3,missense_variant,p.Arg1333Gly,ENST00000377110,NM_001007471.2;TRPM3,missense_variant,p.Arg1195Gly,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,missense_variant,p.Arg1192Gly,ENST00000377105,NM_024971.5;TRPM3,missense_variant,p.Arg1337Gly,ENST00000357533,;TRPM3,missense_variant,p.Arg1205Gly,ENST00000396292,NM_206946.3;TRPM3,missense_variant,p.Arg1195Gly,ENST00000358082,;TRPM3,missense_variant,p.Arg1192Gly,ENST00000396285,NM_020952.4;TRPM3,missense_variant,p.Arg1192Gly,ENST00000408909,;TRPM3,missense_variant,p.Arg1182Gly,ENST00000396280,NM_206945.3;TRPM3,intron_variant,,ENST00000377111,; C ENST00000377110 Transcript missense_variant 4241/12258 3997/5124 1333/1707 R/G Cgt/Ggt rs149067881 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 deleterious_low_confidence(0.04) 25/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 MODERATE 1 SNV 1 1 PASS rs149067881 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 70537080 70537080 G C 1 0 0 0 0 1 0 0 0 17093 1116 39 4 4 TRPM3 9 70537080 Missense_Mutation SNP G C3N-00560_T 3546953 70537080 67857637 631 17320 TRPM3 0 . GRCh38 9 70625326 70625326 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1638C>A p.Asn546Lys p.N546K ENST00000377110 13/25 121 66 55 146 146 0 strelka-varscan-mutect TRPM3,missense_variant,p.Asn546Lys,ENST00000377110,NM_001007471.2;TRPM3,missense_variant,p.Asn418Lys,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,missense_variant,p.Asn405Lys,ENST00000377105,NM_024971.5;TRPM3,missense_variant,p.Asn560Lys,ENST00000357533,;TRPM3,missense_variant,p.Asn418Lys,ENST00000396292,NM_206946.3;TRPM3,missense_variant,p.Asn418Lys,ENST00000358082,;TRPM3,missense_variant,p.Asn393Lys,ENST00000396285,NM_020952.4;TRPM3,missense_variant,p.Asn405Lys,ENST00000408909,;TRPM3,missense_variant,p.Asn405Lys,ENST00000396280,NM_206945.3;TRPM3,missense_variant,p.Asn546Lys,ENST00000377111,; T ENST00000377110 Transcript missense_variant 1882/12258 1638/5124 546/1707 N/K aaC/aaA 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 deleterious(0.01) 13/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 70625326 70625326 G T 1 0 0 0 0 1 0 0 0 17093 1275 44 2 2 TRPM3 9 70625326 Missense_Mutation SNP G C3N-00560_T 88246 70625326 67769391 632 17321 PRUNE2 0 . GRCh38 9 76705800 76705800 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.6474A>T p.= p.A2158A ENST00000376718 8/19 175 92 83 178 178 0 strelka-varscan-mutect PRUNE2,synonymous_variant,p.=,ENST00000376718,NM_015225.2;PRUNE2,synonymous_variant,p.=,ENST00000428286,;PRUNE2,synonymous_variant,p.=,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,synonymous_variant,p.=,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; A ENST00000376718 Transcript synonymous_variant 6598/12584 6474/9267 2158/3088 A gcA/gcT 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 8/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 76705800 76705800 T A 1 0 0 0 0 0 0 0 1 12791 1567 55 4 4 PRUNE2 9 76705800 Silent SNP T C3N-00560_T 6080474 76705800 61688917 633 17322 SPATA31D1 0 . GRCh38 9 81992889 81992889 + Missense_Mutation SNP A A G C3N-00560_T C3N-00560_N A A c.2419A>G p.Thr807Ala p.T807A ENST00000344803 4/4 343 205 138 405 403 2 strelka-varscan-mutect SPATA31D1,missense_variant,p.Thr807Ala,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; G ENST00000344803 Transcript missense_variant 2466/4833 2419/4731 807/1576 T/A Act/Gct COSM487593,COSM487594 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated(0.17) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12,Pfam_domain:PF14650 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 81992889 81992889 A G 1 0 0 0 0 1 0 0 0 15347 43 2 5 5 SPATA31D1 9 81992889 Missense_Mutation SNP A C3N-00560_T 5287089 81992889 56401828 634 17323 GAS1 0 . GRCh38 9 86946528 86946528 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.252G>T p.= p.A84A ENST00000298743 1/1 216 111 105 154 154 0 strelka-varscan-mutect GAS1,synonymous_variant,p.=,ENST00000298743,NM_002048.2;GAS1RR,upstream_gene_variant,,ENST00000415801,; A ENST00000298743 Transcript synonymous_variant 662/2827 252/1038 84/345 A gcG/gcT 1 -1 GAS1 HGNC HGNC:4165 protein_coding YES CCDS6674.1 ENSP00000298743 P54826 UPI0000140B67 NM_002048.2 1/1 hmmpanther:PTHR16840,hmmpanther:PTHR16840:SF3,Low_complexity_(Seg):seg,SMART_domains:SM00907 LOW SNV 1 PASS . . 0 203 4 3 0 0 0 0 -20 0.9999833 1 1 1 0 A 2 1 56 86946528 86946528 C A 1 0 0 0 0 0 0 0 1 6114 755 27 1 1 GAS1 9 86946528 Silent SNP C C3N-00560_T 4953639 86946528 51448189 635 17324 S1PR3 0 . GRCh38 9 89001499 89001499 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.299G>T p.Gly100Val p.G100V ENST00000375846 1/1 154 124 30 197 197 0 strelka-varscan-mutect S1PR3,missense_variant,p.Gly100Val,ENST00000375846,;S1PR3,missense_variant,p.Gly100Val,ENST00000358157,NM_005226.3;SHC3,downstream_gene_variant,,ENST00000375835,NM_016848.5; T ENST00000375846 Transcript missense_variant 4994/8505 299/1137 100/378 G/V gGc/gTc 1 1 S1PR3 HGNC HGNC:3167 protein_coding YES CCDS6680.1 ENSP00000365006 Q99500 UPI0000140B93 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF24,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01523 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 89001499 89001499 G T 1 0 0 0 0 1 0 0 0 14054 1203 42 2 2 S1PR3 9 89001499 Missense_Mutation SNP G C3N-00560_T 2054971 89001499 49393218 636 17325 PTCH1 0 . GRCh38 9 95476794 95476794 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1567A>T p.Ser523Cys p.S523C ENST00000331920 11/24 355 214 141 390 390 0 strelka-varscan-mutect PTCH1,missense_variant,p.Ser457Cys,ENST00000430669,;PTCH1,missense_variant,p.Ser523Cys,ENST00000331920,NM_000264.3;PTCH1,missense_variant,p.Ser457Cys,ENST00000437951,NM_001083602.1;PTCH1,missense_variant,p.Ser372Cys,ENST00000418258,NM_001083607.1;PTCH1,missense_variant,p.Ser372Cys,ENST00000421141,NM_001083604.1,NM_001083605.1;PTCH1,missense_variant,p.Ser372Cys,ENST00000429896,NM_001083606.1;PTCH1,missense_variant,p.Ser522Cys,ENST00000375274,NM_001083603.1;PTCH1,missense_variant,p.Ser188Cys,ENST00000375271,;PTCH1,downstream_gene_variant,,ENST00000553011,;PTCH1,downstream_gene_variant,,ENST00000547672,;PTCH1,downstream_gene_variant,,ENST00000546820,;PTCH1,downstream_gene_variant,,ENST00000551845,;PTCH1,downstream_gene_variant,,ENST00000548420,;PTCH1,downstream_gene_variant,,ENST00000548379,;PTCH1,downstream_gene_variant,,ENST00000553256,;PTCH1,downstream_gene_variant,,ENST00000548945,;PTCH1,missense_variant,p.Ser402Cys,ENST00000375290,;PTCH1,downstream_gene_variant,,ENST00000550914,;PTCH1,downstream_gene_variant,,ENST00000488809,; A ENST00000331920 Transcript missense_variant 1867/8057 1567/4344 523/1447 S/C Agt/Tgt 1 -1 PTCH1 HGNC HGNC:9585 protein_coding YES CCDS6714.1 ENSP00000332353 Q13635 UPI00001AFF9C NM_000264.3 deleterious(0.01) 11/24 Gene3D:2j8sB01,Pfam_domain:PF02460,PROSITE_profiles:PS50156,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF61,Superfamily_domains:SSF82866,TIGRFAM_domain:TIGR00918 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 95476794 95476794 T A 1 0 0 0 0 1 0 0 0 12883 1580 55 4 4 PTCH1 9 95476794 Missense_Mutation SNP T C3N-00560_T 6475295 95476794 42917923 637 17326 ZNF367 0 . GRCh38 9 96388453 96388454 + Frame_Shift_Ins INS - - A novel C3N-00560_T C3N-00560_N - - c.836_837insT p.Trp279CysfsTer20 p.W279Cfs*20 ENST00000375256 5/5 102 50 52 128 128 0 sindel-varindel-pindel ZNF367,frameshift_variant,p.Trp279CysfsTer20,ENST00000375256,NM_153695.3;SLC35D2,upstream_gene_variant,,ENST00000253270,NM_007001.2;SLC35D2,upstream_gene_variant,,ENST00000375259,NM_001286990.1;SLC35D2,upstream_gene_variant,,ENST00000375257,;SLC35D2,upstream_gene_variant,,ENST00000482643,; A ENST00000375256 Transcript frameshift_variant 1133-1134/3646 836-837/1053 279/350 W/CX tgg/tgTg 1 -1 ZNF367 HGNC HGNC:18320 protein_coding YES CCDS6718.1 ENSP00000364405 Q7RTV3 UPI000013E47A NM_153695.3 5/5 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 56 96388453 96388453 - A 1 0 1 1 0 0 0 0 0 18443 624 22 0 0 ZNF367 9 96388453 Frame_Shift_Ins INS - C3N-00560_T 911659 96388453 42006264 638 17327 HEMGN 0 . GRCh38 9 97931099 97931099 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.296A>T p.Lys99Ile p.K99I ENST00000616898 3/4 230 136 94 262 262 0 strelka-varscan-mutect HEMGN,missense_variant,p.Lys99Ile,ENST00000616898,NM_197978.2;HEMGN,missense_variant,p.Lys99Ile,ENST00000259456,NM_018437.4; A ENST00000616898 Transcript missense_variant 553/2305 296/1455 99/484 K/I aAa/aTa 1 -1 HEMGN HGNC HGNC:17509 protein_coding YES CCDS6731.1 ENSP00000480020 Q9BXL5 A0A024R162 UPI000004D311 NM_197978.2 deleterious(0.03) 3/4 hmmpanther:PTHR15993,hmmpanther:PTHR15993:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 97931099 97931099 T A 1 0 0 0 0 1 0 0 0 6933 1841 64 4 4 HEMGN 9 97931099 Missense_Mutation SNP T C3N-00560_T 1542646 97931099 40463618 639 17328 ERP44 0 . GRCh38 9 100006564 100006564 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.958G>T p.Val320Leu p.V320L ENST00000262455 10/12 129 88 41 194 194 0 strelka-varscan-mutect ERP44,missense_variant,p.Val320Leu,ENST00000262455,NM_015051.2; A ENST00000262455 Transcript missense_variant 1158/4854 958/1221 320/406 V/L Gta/Tta 1 -1 ERP44 HGNC HGNC:18311 protein_coding YES CCDS35082.1 ENSP00000262455 Q9BS26 UPI0000072130 NM_015051.2 tolerated(0.94) 10/12 Pfam_domain:PF13848,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF107,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 100006564 100006564 C A 1 0 0 0 0 1 0 0 0 5101 478 17 2 2 ERP44 9 100006564 Missense_Mutation SNP C C3N-00560_T 2075465 100006564 38388153 640 17329 TXN 0 . GRCh38 9 110244203 110244203 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.272G>T p.Gly91Val p.G91V ENST00000374517 5/5 72 50 22 135 134 1 strelka-varscan-mutect TXN,missense_variant,p.Gly91Val,ENST00000374517,NM_003329.3;TXN,missense_variant,p.Gly71Val,ENST00000374515,NM_001244938.1;TXN,non_coding_transcript_exon_variant,,ENST00000487892,; A ENST00000374517 Transcript missense_variant 477/869 272/318 91/105 G/V gGa/gTa 1 -1 TXN HGNC HGNC:12435 protein_coding YES CCDS35103.1 ENSP00000363641 P10599 H9ZYJ2 UPI000011065C NM_003329.3 deleterious(0) 5/5 Gene3D:3.40.30.10,Pfam_domain:PF00085,PIRSF_domain:PIRSF000077,PROSITE_profiles:PS51352,hmmpanther:PTHR10438,hmmpanther:PTHR10438:SF18,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 110244203 110244203 C A 1 0 0 0 0 1 0 0 0 17306 855 30 2 2 TXN 9 110244203 Missense_Mutation SNP C C3N-00560_T 10237639 110244203 28150514 641 17330 ZFP37 0 . GRCh38 9 113043387 113043387 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1276G>T p.Gly426Trp p.G426W ENST00000553380 4/4 144 90 54 230 230 0 strelka-varscan-mutect ZFP37,missense_variant,p.Gly411Trp,ENST00000374227,NM_003408.2;ZFP37,missense_variant,p.Gly412Trp,ENST00000555206,NM_001282518.1;ZFP37,missense_variant,p.Gly426Trp,ENST00000553380,NM_001282515.1;ZNF883,intron_variant,,ENST00000619044,NM_001101338.1; A ENST00000553380 Transcript missense_variant 1276/1969 1276/1938 426/645 G/W Ggg/Tgg 1 -1 ZFP37 HGNC HGNC:12863 protein_coding YES CCDS65110.1 ENSP00000452552 Q9Y6Q3 UPI0001B04BC3 NM_001282515.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF147,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 113043387 113043387 C A 1 0 0 0 0 1 0 0 0 18223 594 21 2 2 ZFP37 9 113043387 Missense_Mutation SNP C C3N-00560_T 2799184 113043387 25351330 642 17331 ASTN2 0 . GRCh38 9 116440695 116440695 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3543G>T p.Met1181Ile p.M1181I ENST00000361209 21/22 149 86 63 185 185 0 strelka-varscan-mutect ASTN2,missense_variant,p.Met1232Ile,ENST00000313400,;ASTN2,missense_variant,p.Met1181Ile,ENST00000361209,NM_014010.4;ASTN2,missense_variant,p.Met284Ile,ENST00000361477,NM_198187.3;ASTN2,missense_variant,p.Met955Ile,ENST00000373986,;ASTN2,missense_variant,p.Met333Ile,ENST00000288520,NM_198186.3;ASTN2,missense_variant,p.Met284Ile,ENST00000341734,NM_001184734.1,NM_198188.2;ASTN2,missense_variant,p.Met14Ile,ENST00000417725,; A ENST00000361209 Transcript missense_variant 3675/4622 3543/3867 1181/1288 M/I atG/atT 1 -1 ASTN2 HGNC HGNC:17021 protein_coding YES CCDS6815.1 ENSP00000354504 O75129 UPI00002116D7 NM_014010.4 tolerated(0.09) 21/22 hmmpanther:PTHR16592,hmmpanther:PTHR16592:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 116440695 116440695 C A 1 0 0 0 0 1 0 0 0 1212 710 25 2 2 ASTN2 9 116440695 Missense_Mutation SNP C C3N-00560_T 3397308 116440695 21954022 643 17332 RBM18 0 . GRCh38 9 122241994 122241994 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.463G>T p.Glu155Ter p.E155* ENST00000417201 6/6 163 93 70 184 184 0 strelka-varscan-mutect RBM18,stop_gained,p.Glu155Ter,ENST00000417201,NM_033117.3;RBM18,non_coding_transcript_exon_variant,,ENST00000483428,;RBM18,non_coding_transcript_exon_variant,,ENST00000491850,; A ENST00000417201 Transcript stop_gained 604/4974 463/573 155/190 E/* Gaa/Taa 1 -1 RBM18 HGNC HGNC:28413 protein_coding YES CCDS6839.1 ENSP00000409315 Q96H35 UPI0000046802 NM_033117.3 6/6 hmmpanther:PTHR21245:SF2,hmmpanther:PTHR21245 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 122241994 122241994 C A 1 0 0 0 0 0 1 0 0 13285 864 30 2 2 RBM18 9 122241994 Nonsense_Mutation SNP C C3N-00560_T 5801299 122241994 16152723 644 17333 OR1L1 0 . GRCh38 9 122661813 122661813 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.98C>T p.Pro33Leu p.P33L ENST00000309623 1/1 132 75 57 160 160 0 strelka-varscan-mutect OR1L1,missense_variant,p.Pro83Leu,ENST00000373686,;OR1L1,missense_variant,p.Pro33Leu,ENST00000309623,NM_001005236.3; T ENST00000309623 Transcript missense_variant 98/933 98/933 33/310 P/L cCc/cTc 1 1 OR1L1 HGNC HGNC:8213 protein_coding YES CCDS35127.2 ENSP00000310773 A0A0B4J1S0 UPI0000041E03 NM_001005236.3 tolerated(0.66) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF39,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 122661813 122661813 C T 1 0 0 0 0 1 0 0 0 11041 623 22 3 3 OR1L1 9 122661813 Missense_Mutation SNP C C3N-00560_T 419819 122661813 15732904 645 17334 SH3GLB2 0 . GRCh38 9 129014489 129014489 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.483C>T p.= p.L161L ENST00000372554 5/13 227 171 56 186 185 1 strelka-varscan-mutect SH3GLB2,synonymous_variant,p.=,ENST00000372564,NM_001287046.1,NM_020145.3;SH3GLB2,synonymous_variant,p.=,ENST00000372554,NM_001287045.1;SH3GLB2,synonymous_variant,p.=,ENST00000417224,;SH3GLB2,synonymous_variant,p.=,ENST00000416629,;SH3GLB2,synonymous_variant,p.=,ENST00000372559,;SH3GLB2,3_prime_UTR_variant,,ENST00000455407,;SH3GLB2,3_prime_UTR_variant,,ENST00000416230,;SH3GLB2,3_prime_UTR_variant,,ENST00000425236,;SH3GLB2,non_coding_transcript_exon_variant,,ENST00000483980,;SH3GLB2,upstream_gene_variant,,ENST00000461811,;SH3GLB2,upstream_gene_variant,,ENST00000479237,;SH3GLB2,upstream_gene_variant,,ENST00000477165,; A ENST00000372554 Transcript synonymous_variant 608/1985 483/1215 161/404 L ctC/ctT 1 -1 SH3GLB2 HGNC HGNC:10834 protein_coding YES CCDS69680.1 ENSP00000361634 Q9NR46 UPI000004A0D5 NM_001287045.1 5/13 Gene3D:1.20.1270.60,Pfam_domain:PF03114,PROSITE_profiles:PS51021,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF161,Low_complexity_(Seg):seg,SMART_domains:SM00721,Superfamily_domains:SSF103657 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 129014489 129014489 G A 1 0 0 0 0 0 0 0 1 14513 1161 41 3 3 SH3GLB2 9 129014489 Silent SNP G C3N-00560_T 6352676 129014489 9380228 646 17335 FAM73B 0 . GRCh38 9 129049390 129049390 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.430G>T p.Val144Leu p.V144L ENST00000358369 5/16 249 162 87 175 175 0 strelka-varscan-mutect FAM73B,missense_variant,p.Val144Leu,ENST00000358369,NM_032809.2;FAM73B,downstream_gene_variant,,ENST00000474534,;FAM73B,missense_variant,p.Val144Leu,ENST00000439290,;FAM73B,missense_variant,p.Val144Leu,ENST00000445183,; T ENST00000358369 Transcript missense_variant 656/3637 430/1782 144/593 V/L Gtg/Ttg 1 1 FAM73B HGNC HGNC:23621 protein_coding YES CCDS6917.1 ENSP00000351138 Q7L4E1 UPI00001B4EFD NM_032809.2 tolerated(0.16) 5/16 Low_complexity_(Seg):seg,hmmpanther:PTHR21508,hmmpanther:PTHR21508:SF2,Pfam_domain:PF10265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 129049390 129049390 G T 1 0 0 0 0 1 0 0 0 5484 1029 36 2 2 FAM73B 9 129049390 Missense_Mutation SNP G C3N-00560_T 34901 129049390 9345327 647 17336 PTPA 0 . GRCh38 9 129120521 129120521 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.40G>A p.Glu14Lys p.E14K ENST00000393370 2/10 228 201 27 131 131 0 strelka-varscan-mutect PTPA,missense_variant,p.Glu14Lys,ENST00000337738,NM_178001.2;PTPA,missense_variant,p.Glu14Lys,ENST00000348141,;PTPA,missense_variant,p.Glu14Lys,ENST00000393370,NM_178000.2;PTPA,missense_variant,p.Glu14Lys,ENST00000358994,NM_021131.4;PTPA,missense_variant,p.Glu14Lys,ENST00000357197,NM_001271832.1;PTPA,missense_variant,p.Glu14Lys,ENST00000355007,NM_178003.2;PTPA,missense_variant,p.Glu14Lys,ENST00000347048,;PTPA,missense_variant,p.Glu14Lys,ENST00000445241,;PTPA,missense_variant,p.Glu14Lys,ENST00000455292,;PTPA,missense_variant,p.Glu31Lys,ENST00000417504,;PTPA,5_prime_UTR_variant,,ENST00000452489,NM_001193397.1;PTPA,5_prime_UTR_variant,,ENST00000417728,;PTPA,5_prime_UTR_variant,,ENST00000453358,;PTPA,5_prime_UTR_variant,,ENST00000440346,;PTPA,intron_variant,,ENST00000414331,; A ENST00000393370 Transcript missense_variant 323/2737 40/972 14/323 E/K Gag/Aag 1 1 PTPA HGNC HGNC:9308 protein_coding YES CCDS6920.1 ENSP00000377036 Q15257 UPI000013D6D6 NM_178000.2 tolerated(0.17) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR10012,PIRSF_domain:PIRSF016325,Superfamily_domains:SSF140984 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 129120521 129120521 G A 1 0 0 0 0 1 0 0 0 12929 943 33 3 3 PTPA 9 129120521 Missense_Mutation SNP G C3N-00560_T 71131 129120521 9274196 648 17337 HMCN2 0 . GRCh38 9 130360436 130360436 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.5779T>A p.Trp1927Arg p.W1927R ENST00000624552 38/98 145 106 39 97 97 0 varscan-mutect HMCN2,missense_variant,p.Trp1927Arg,ENST00000624552,NM_001291815.1; A ENST00000624552 Transcript missense_variant 5779/15610 5779/15180 1927/5059 W/R Tgg/Agg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0) 38/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 130360436 130360436 T A 1 0 0 0 0 1 0 0 0 7112 1580 55 4 4 HMCN2 9 130360436 Missense_Mutation SNP T C3N-00560_T 1239915 130360436 8034281 649 17338 HMCN2 0 . GRCh38 9 130393907 130393907 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.10397T>A p.Leu3466Gln p.L3466Q ENST00000624552 68/98 230 152 78 204 204 0 strelka-varscan-mutect HMCN2,missense_variant,p.Leu3466Gln,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,; A ENST00000624552 Transcript missense_variant 10397/15610 10397/15180 3466/5059 L/Q cTg/cAg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0) 68/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 130393907 130393907 T A 1 0 0 0 0 1 0 0 0 7112 1580 55 4 4 HMCN2 9 130393907 Missense_Mutation SNP T C3N-00560_T 33471 130393907 8000810 650 17339 HMCN2 0 . GRCh38 9 130406009 130406009 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.12334C>G p.Arg4112Gly p.R4112G ENST00000624552 82/98 221 136 85 161 161 0 strelka-varscan-mutect HMCN2,missense_variant,p.Arg4112Gly,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,non_coding_transcript_exon_variant,,ENST00000480829,; G ENST00000624552 Transcript missense_variant 12334/15610 12334/15180 4112/5059 R/G Cgc/Ggc 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 tolerated(0.14) 82/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs986624800 . 0 207 0 3 0 0 0 0 -20 0.999999 1 1 1 0 G 3 3 56 130406009 130406009 C G 1 0 0 0 0 1 0 0 0 7112 652 23 4 4 HMCN2 9 130406009 Missense_Mutation SNP C C3N-00560_T 12102 130406009 7988708 651 17340 HMCN2 0 . GRCh38 9 130407612 130407612 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.12535G>A p.Ala4179Thr p.A4179T ENST00000624552 83/98 226 166 60 159 159 0 strelka-varscan-mutect HMCN2,missense_variant,p.Ala4179Thr,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,downstream_gene_variant,,ENST00000480829,; A ENST00000624552 Transcript missense_variant 12535/15610 12535/15180 4179/5059 A/T Gcc/Acc 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 tolerated(0.53) 83/98 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 130407612 130407612 G A 1 0 0 0 0 1 0 0 0 7112 1203 42 3 3 HMCN2 9 130407612 Missense_Mutation SNP G C3N-00560_T 1603 130407612 7987105 652 17341 ASS1 0 . GRCh38 9 130480400 130480400 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.789G>T p.= p.V263V ENST00000372394 12/16 707 523 184 539 538 1 strelka-varscan-mutect ASS1,synonymous_variant,p.=,ENST00000372394,;ASS1,synonymous_variant,p.=,ENST00000352480,NM_054012.3;ASS1,synonymous_variant,p.=,ENST00000372393,NM_000050.4;ASS1,non_coding_transcript_exon_variant,,ENST00000372386,;ASS1,non_coding_transcript_exon_variant,,ENST00000492400,;ASS1,non_coding_transcript_exon_variant,,ENST00000493984,;ASS1,non_coding_transcript_exon_variant,,ENST00000470849,;ASS1,downstream_gene_variant,,ENST00000467695,; T ENST00000372394 Transcript synonymous_variant 1270/1973 789/1239 263/412 V gtG/gtT 1 1 ASS1 HGNC HGNC:758 protein_coding YES CCDS6933.1 ENSP00000361471 P00966 Q5T6L4 UPI00000015D6 12/16 Gene3D:3.90.1260.10,HAMAP:MF_00005,Pfam_domain:PF00764,hmmpanther:PTHR11587,Superfamily_domains:SSF69864,TIGRFAM_domain:TIGR00032 LOW 1 SNV 2 1 PASS rs1419381608 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 130480400 130480400 G T 1 0 0 0 0 0 0 0 1 1208 1335 47 2 2 ASS1 9 130480400 Silent SNP G C3N-00560_T 72788 130480400 7914317 653 17342 GFI1B 0 . GRCh38 9 132988417 132988417 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.459C>A p.Ser153Arg p.S153R ENST00000339463 8/11 215 157 58 166 166 0 strelka-varscan-mutect GFI1B,missense_variant,p.Ser153Arg,ENST00000339463,NM_004188.5;GFI1B,missense_variant,p.Ser153Arg,ENST00000636137,;GFI1B,missense_variant,p.Ser153Arg,ENST00000372122,;GFI1B,missense_variant,p.Ser153Arg,ENST00000636263,;GFI1B,missense_variant,p.Ser153Arg,ENST00000372123,NM_001135031.1; A ENST00000339463 Transcript missense_variant 1278/2449 459/993 153/330 S/R agC/agA 1 1 GFI1B HGNC HGNC:4238 protein_coding YES CCDS6957.1 ENSP00000344782 Q5VTD9 UPI000013E4EE NM_004188.5 tolerated(0.07) 8/11 Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 132988417 132988417 C A 1 0 0 0 0 1 0 0 0 6214 738 26 2 2 GFI1B 9 132988417 Missense_Mutation SNP C C3N-00560_T 2508017 132988417 5406300 654 17343 CEL 0 . GRCh38 9 133064429 133064429 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.101G>T p.Gly34Val p.G34V ENST00000372080 2/11 615 496 119 493 492 1 strelka-varscan-mutect CEL,missense_variant,p.Gly34Val,ENST00000372080,NM_001807.4;CEL,intron_variant,,ENST00000621209,; T ENST00000372080 Transcript missense_variant 117/2384 101/2271 34/756 G/V gGg/gTg 1 1 CEL HGNC HGNC:1848 protein_coding YES CCDS43896.1 ENSP00000361151 X6R868 UPI000013E8C6 NM_001807.4 deleterious(0) 2/11 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 133064429 133064429 G T 1 0 0 0 0 1 0 0 0 2916 1232 43 2 2 CEL 9 133064429 Missense_Mutation SNP G C3N-00560_T 76012 133064429 5330288 655 17344 ADAMTSL2 0 . GRCh38 9 133544486 133544486 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.699C>A p.= p.T233T ENST00000354484 8/19 633 452 181 569 568 1 strelka-varscan-mutect ADAMTSL2,synonymous_variant,p.=,ENST00000393061,;ADAMTSL2,synonymous_variant,p.=,ENST00000354484,NM_001145320.1;ADAMTSL2,synonymous_variant,p.=,ENST00000393060,NM_014694.3; A ENST00000354484 Transcript synonymous_variant 1256/4068 699/2856 233/951 T acC/acA 1 1 ADAMTSL2 HGNC HGNC:14631 protein_coding YES CCDS6976.1 ENSP00000346478 Q86TH1 UPI000018CEA2 NM_001145320.1 8/19 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF147,Pfam_domain:PF05986 LOW 1 SNV 1 1 PASS rs1374421192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 133544486 133544486 C A 1 0 0 0 0 0 0 0 1 319 610 22 2 2 ADAMTSL2 9 133544486 Silent SNP C C3N-00560_T 480057 133544486 4850231 656 17345 RXRA 0 . GRCh38 9 134401791 134401791 + Missense_Mutation SNP C C T rs531899705 C3N-00560_T C3N-00560_N C C c.188C>T p.Pro63Leu p.P63L ENST00000481739 2/10 260 246 14 222 222 0 strelka-varscan-mutect RXRA,missense_variant,p.Pro63Leu,ENST00000481739,NM_002957.5,NM_001291920.1;RXRA,non_coding_transcript_exon_variant,,ENST00000356384,;RXRA,non_coding_transcript_exon_variant,,ENST00000484822,; T ENST00000481739 Transcript missense_variant 240/1846 188/1389 63/462 P/L cCg/cTg rs531899705 1 1 RXRA HGNC HGNC:10477 protein_coding YES CCDS35172.1 ENSP00000419692 P19793 F1D8Q5 UPI0000042A9A NM_002957.5,NM_001291920.1 tolerated(0.18) 2/10 Pfam_domain:PF11825,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF39 MODERATE 1 SNV 1 1 PASS rs531899705 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 134401791 134401791 C T 1 0 0 0 0 1 0 0 0 14024 652 23 1 1 RXRA 9 134401791 Missense_Mutation SNP C C3N-00560_T 857305 134401791 3992926 657 17346 COL5A1 0 . GRCh38 9 134753850 134753850 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1720G>T p.Gly574Cys p.G574C ENST00000371817 15/66 262 181 81 264 264 0 strelka-varscan-mutect COL5A1,missense_variant,p.Gly574Cys,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly574Cys,ENST00000618395,NM_001278074.1; T ENST00000371817 Transcript missense_variant,splice_region_variant 2134/8471 1720/5517 574/1838 G/C Ggt/Tgt 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0) 15/66 Pfam_domain:PF01391,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 134753850 134753850 G T 1 0 0 0 0 1 0 0 0 3485 1246 43 2 2 COL5A1 9 134753850 Missense_Mutation SNP G C3N-00560_T 352059 134753850 3640867 658 17347 COL5A1 0 . GRCh38 9 134825794 134825794 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4957G>T p.Glu1653Ter p.E1653* ENST00000371817 63/66 482 341 141 381 378 3 strelka-varscan-mutect COL5A1,stop_gained,p.Glu1653Ter,ENST00000371817,NM_000093.4;COL5A1,stop_gained,p.Glu1653Ter,ENST00000618395,NM_001278074.1;COL5A1,stop_gained,p.Glu73Ter,ENST00000371820,;COL5A1,splice_region_variant,,ENST00000460264,;COL5A1,splice_region_variant,,ENST00000465877,; T ENST00000371817 Transcript stop_gained,splice_region_variant 5371/8471 4957/5517 1653/1838 E/* Gaa/Taa 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 63/66 Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF387,SMART_domains:SM00038 HIGH 1 SNV 1 1 PASS rs1286248077 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 134825794 134825794 G T 1 0 0 0 0 0 1 0 0 3485 1304 45 2 2 COL5A1 9 134825794 Nonsense_Mutation SNP G C3N-00560_T 71944 134825794 3568923 659 17348 NOTCH1 0 . GRCh38 9 136509827 136509827 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2875A>T p.Asn959Tyr p.N959Y ENST00000277541 18/34 701 488 213 548 547 1 strelka-varscan-mutect NOTCH1,missense_variant,p.Asn959Tyr,ENST00000277541,NM_017617.3;NOTCH1,upstream_gene_variant,,ENST00000494783,; A ENST00000277541 Transcript missense_variant 2951/9371 2875/7668 959/2555 N/Y Aac/Tac 1 -1 NOTCH1 HGNC HGNC:7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 UPI0000210F68 NM_017617.3 deleterious(0) 18/34 Gene3D:2.10.25.10,PIRSF_domain:PIRSF002279,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF69,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 136509827 136509827 T A 1 0 0 0 0 1 0 0 0 10592 1812 63 4 4 NOTCH1 9 136509827 Missense_Mutation SNP T C3N-00560_T 1684033 136509827 1884890 660 17349 SAPCD2 0 . GRCh38 9 137065656 137065656 + Nonsense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.697A>T p.Lys233Ter p.K233* ENST00000409687 3/6 123 90 33 67 67 0 strelka-varscan-mutect SAPCD2,stop_gained,p.Lys233Ter,ENST00000409687,NM_178448.3;RP11-229P13.23,downstream_gene_variant,,ENST00000456356,;RP11-229P13.22,downstream_gene_variant,,ENST00000435463,; A ENST00000409687 Transcript stop_gained 825/3848 697/1185 233/394 K/* Aag/Tag 1 -1 SAPCD2 HGNC HGNC:28055 protein_coding YES CCDS7027.2 ENSP00000386348 Q86UD0 UPI00005A8C06 NM_178448.3 3/6 Low_complexity_(Seg):seg,hmmpanther:PTHR14907,hmmpanther:PTHR14907:SF3,Pfam_domain:PF11414 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 137065656 137065656 T A 1 0 0 0 0 0 1 0 0 14098 1792 62 4 4 SAPCD2 9 137065656 Nonsense_Mutation SNP T C3N-00560_T 555829 137065656 1329061 661 17350 NSMF 0 . GRCh38 9 137452369 137452369 + Missense_Mutation SNP C C A rs761488406 C3N-00560_T C3N-00560_N C C c.1232G>T p.Cys411Phe p.C411F ENST00000371475 12/16 450 320 130 303 303 0 strelka-varscan-mutect NSMF,missense_variant,p.Cys411Phe,ENST00000371475,NM_001130969.1;NSMF,missense_variant,p.Cys409Phe,ENST00000265663,NM_015537.4;NSMF,missense_variant,p.Cys388Phe,ENST00000437259,NM_001130970.1;NSMF,missense_variant,p.Cys386Phe,ENST00000371474,NM_001130971.1;NSMF,missense_variant,p.Cys381Phe,ENST00000371473,NM_001178064.1;NSMF,missense_variant,p.Cys244Phe,ENST00000339554,;NSMF,missense_variant,p.Cys409Phe,ENST00000371472,;NSMF,missense_variant,p.Cys101Phe,ENST00000482448,;NSMF,upstream_gene_variant,,ENST00000611474,;NSMF,non_coding_transcript_exon_variant,,ENST00000371482,;NSMF,non_coding_transcript_exon_variant,,ENST00000484316,;NSMF,downstream_gene_variant,,ENST00000371468,; A ENST00000371475 Transcript missense_variant 1464/3646 1232/1593 411/530 C/F tGc/tTc rs761488406 1 -1 NSMF HGNC HGNC:29843 protein_coding YES CCDS48069.1 ENSP00000360530 Q6X4W1 UPI000035198D NM_001130969.1 deleterious(0) 12/16 hmmpanther:PTHR32061 MODERATE 1 SNV 1 1 PASS rs761488406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 137452369 137452369 C A 1 0 0 0 0 1 0 0 0 10739 724 25 2 2 NSMF 9 137452369 Missense_Mutation SNP C C3N-00560_T 386713 137452369 942348 662 17351 CACNA1B 0 . GRCh38 9 137986844 137986844 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1964C>A p.Thr655Asn p.T655N ENST00000371372 15/47 328 232 96 270 270 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Thr655Asn,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Thr655Asn,ENST00000371363,;CACNA1B,missense_variant,p.Thr656Asn,ENST00000371355,;CACNA1B,missense_variant,p.Thr656Asn,ENST00000371357,;CACNA1B,missense_variant,p.Thr655Asn,ENST00000277549,;CACNA1B,missense_variant,p.Thr655Asn,ENST00000277551,NM_001243812.1; A ENST00000371372 Transcript missense_variant 2109/9790 1964/7020 655/2339 T/N aCt/aAt 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 deleterious(0) 15/47 Pfam_domain:PF00520,Prints_domain:PR00167,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 137986844 137986844 C A 1 0 0 0 0 1 0 0 0 2227 565 20 2 2 CACNA1B 9 137986844 Missense_Mutation SNP C C3N-00560_T 534475 137986844 407873 663 17352 CACNA1B 0 . GRCh38 9 138052123 138052123 + Frame_Shift_Del DEL A A - novel C3N-00560_T C3N-00560_N A A c.3743delA p.Lys1248SerfsTer3 p.K1248Sfs*3 ENST00000371372 25/47 207 154 53 154 154 0 sindel-varindel CACNA1B,frameshift_variant,p.Lys1248SerfsTer3,ENST00000371372,NM_000718.3;CACNA1B,frameshift_variant,p.Lys1248SerfsTer3,ENST00000371363,;CACNA1B,frameshift_variant,p.Lys1249SerfsTer3,ENST00000371355,;CACNA1B,frameshift_variant,p.Lys1249SerfsTer3,ENST00000371357,;CACNA1B,frameshift_variant,p.Lys1248SerfsTer3,ENST00000277549,;CACNA1B,frameshift_variant,p.Lys1248SerfsTer3,ENST00000277551,NM_001243812.1; - ENST00000371372 Transcript frameshift_variant 3887/9790 3742/7020 1248/2339 K/X Aag/ag 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 25/47 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324 HIGH 1 deletion 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 138052123 138052123 A - 1 0 1 0 1 0 0 0 0 2227 131 5 0 0 CACNA1B 9 138052123 Frame_Shift_Del DEL A C3N-00560_T 65279 138052123 342594 664 17353 CACNA1B 0 . GRCh38 9 138120671 138120671 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.6279G>A p.= p.E2093E ENST00000371372 46/47 71 51 20 69 69 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; A ENST00000371372 Transcript synonymous_variant 6424/9790 6279/7020 2093/2339 E gaG/gaA 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 46/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 138120671 138120671 G A 1 0 0 0 0 0 0 0 1 2227 991 35 3 3 CACNA1B 9 138120671 Silent SNP G C3N-00560_T 68548 138120671 274046 665 17354 AKR1C3 0 . GRCh38 10 5098859 5098859 + Missense_Mutation SNP G G T rs782456698 C3N-00560_T C3N-00560_N G G c.427G>T p.Asp143Tyr p.D143Y ENST00000380554 4/9 109 76 33 132 132 0 strelka-varscan-mutect AKR1C3,missense_variant,p.Asp143Tyr,ENST00000380554,NM_003739.5;AKR1C3,missense_variant,p.Asp120Tyr,ENST00000605149,;AKR1C3,missense_variant,p.Asp143Tyr,ENST00000439082,NM_001253908.1;AKR1C3,missense_variant,p.Asp120Tyr,ENST00000602997,;AKR1C3,non_coding_transcript_exon_variant,,ENST00000605781,;AKR1C3,downstream_gene_variant,,ENST00000470862,;AKR1C3,downstream_gene_variant,,ENST00000480822,;AKR1C3,intron_variant,,ENST00000605322,;AKR1C3,downstream_gene_variant,,ENST00000480697,;AKR1C3,downstream_gene_variant,,ENST00000603312,; T ENST00000380554 Transcript missense_variant 1079/1807 427/972 143/323 D/Y Gat/Tat rs782456698 1 1 AKR1C3 HGNC HGNC:386 protein_coding YES CCDS7063.1 ENSP00000369927 P42330 UPI0000140951 NM_003739.5 deleterious(0.01) 4/9 Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF201,Superfamily_domains:SSF51430 MODERATE 1 SNV 1 1 PASS rs782456698 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 5098859 5098859 G T 1 0 0 0 0 1 0 0 0 555 1174 41 2 2 AKR1C3 10 5098859 Missense_Mutation SNP G C3N-00560_T 5098859 128698563 666 17355 ITIH5 0 . GRCh38 10 7566316 7566316 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.2241C>A p.= p.L747L ENST00000397146 13/14 156 108 48 140 140 0 strelka-varscan-mutect ITIH5,synonymous_variant,p.=,ENST00000397146,NM_030569.6;ITIH5,synonymous_variant,p.=,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000473591,;ITIH5,downstream_gene_variant,,ENST00000492668,; T ENST00000397146 Transcript synonymous_variant 2320/6721 2241/2829 747/942 L ctC/ctA 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 13/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,Pfam_domain:PF06668 LOW 1 SNV 1 1 PASS rs1183933551 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 7566316 7566316 G T 1 0 0 0 0 0 0 0 1 7813 1277 45 2 2 ITIH5 10 7566316 Silent SNP G C3N-00560_T 2467457 7566316 126231106 667 17356 ITIH5 0 . GRCh38 10 7576708 7576708 + Missense_Mutation SNP G G C rs377411908 C3N-00560_T C3N-00560_N G G c.1723C>G p.Arg575Gly p.R575G ENST00000397146 10/14 253 190 63 250 250 0 strelka-varscan-mutect ITIH5,missense_variant,p.Arg575Gly,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Arg575Gly,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Arg361Gly,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,;ITIH5,non_coding_transcript_exon_variant,,ENST00000468389,;ITIH5,downstream_gene_variant,,ENST00000461751,;ITIH5,upstream_gene_variant,,ENST00000492668,; C ENST00000397146 Transcript missense_variant 1802/6721 1723/2829 575/942 R/G Cgt/Ggt rs377411908 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 deleterious(0) 10/14 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62 MODERATE 1 SNV 1 1 PASS rs377411908 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 7576708 7576708 G C 1 0 0 0 0 1 0 0 0 7813 1087 38 4 4 ITIH5 10 7576708 Missense_Mutation SNP G C3N-00560_T 10392 7576708 126220714 668 17357 CAMK1D 0 . GRCh38 10 12825691 12825691 + Splice_Site SNP G G C novel C3N-00560_T C3N-00560_N G G c.1039+1G>C p.X347_splice ENST00000619168 187 147 40 170 170 0 strelka-varscan-mutect CAMK1D,splice_donor_variant,,ENST00000619168,NM_153498.3;CAMK1D,splice_donor_variant,,ENST00000615792,;CAMK1D,missense_variant,p.Cys347Ser,ENST00000378845,NM_020397.3; C ENST00000619168 Transcript splice_donor_variant -/8153 1039/1158 347/385 1 1 CAMK1D HGNC HGNC:19341 protein_coding YES CCDS7091.1 ENSP00000478874 Q8IU85 UPI000003CA33 NM_153498.3 10/10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 56 12825691 12825691 G C 1 0 0 0 0 0 0 1 0 2288 1391 48 4 4 CAMK1D 10 12825691 Splice_Site SNP G C3N-00560_T 5248983 12825691 120971731 669 17358 PHYH 0 . GRCh38 10 13283782 13283782 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.736G>T p.Val246Leu p.V246L ENST00000263038 7/9 575 476 99 538 538 0 strelka-varscan-mutect PHYH,missense_variant,p.Val229Leu,ENST00000396920,;PHYH,missense_variant,p.Val146Leu,ENST00000396913,NM_001323084.1,NM_001037537.1;PHYH,missense_variant,p.Val246Leu,ENST00000263038,NM_001323082.1,NM_006214.3;PHYH,missense_variant,p.Val146Leu,ENST00000453759,;PHYH,downstream_gene_variant,,ENST00000479604,; A ENST00000263038 Transcript missense_variant 795/1577 736/1017 246/338 V/L Gtg/Ttg 1 -1 PHYH HGNC HGNC:8940 protein_coding YES CCDS7097.1 ENSP00000263038 O14832 UPI0000131215 NM_001323082.1,NM_006214.3 deleterious(0.03) 7/9 hmmpanther:PTHR21308:SF1,hmmpanther:PTHR21308,Gene3D:2.60.120.620,Pfam_domain:PF05721,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 13283782 13283782 C A 1 0 0 0 0 1 0 0 0 11952 507 18 2 2 PHYH 10 13283782 Missense_Mutation SNP C C3N-00560_T 458091 13283782 120513640 670 17359 C1QL3 0 . GRCh38 10 16520860 16520860 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.206C>A p.Pro69His p.P69H ENST00000298943 1/2 78 50 28 80 80 0 strelka-varscan-mutect C1QL3,missense_variant,p.Pro69His,ENST00000298943,NM_001010908.1;C1QL3,intron_variant,,ENST00000619991,; T ENST00000298943 Transcript missense_variant 1146/2493 206/768 69/255 P/H cCc/cAc 1 -1 C1QL3 HGNC HGNC:19359 protein_coding YES CCDS31156.1 ENSP00000298943 Q5VWW1 UPI000013E53F NM_001010908.1 tolerated(0.07) 1/2 Low_complexity_(Seg):seg,Pfam_domain:PF01391 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 16520860 16520860 G T 1 0 0 0 0 1 0 0 0 1938 1232 43 2 2 C1QL3 10 16520860 Missense_Mutation SNP G C3N-00560_T 3237078 16520860 117276562 671 17360 CUBN 0 . GRCh38 10 16903984 16903984 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.8044G>C p.Ala2682Pro p.A2682P ENST00000377833 51/67 226 143 83 264 264 0 strelka-varscan-mutect CUBN,missense_variant,p.Ala2682Pro,ENST00000377833,NM_001081.3; G ENST00000377833 Transcript missense_variant 8110/11949 8044/10872 2682/3623 A/P Gca/Cca 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 deleterious(0.01) 51/67 PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 16903984 16903984 C G 1 0 0 0 0 1 0 0 0 3861 710 25 4 4 CUBN 10 16903984 Missense_Mutation SNP C C3N-00560_T 383124 16903984 116893438 672 17361 CUBN 0 . GRCh38 10 16940184 16940184 + Missense_Mutation SNP C C A rs758077332 C3N-00560_T C3N-00560_N C C c.5396G>T p.Arg1799Leu p.R1799L ENST00000377833 37/67 296 199 97 293 293 0 strelka-varscan-mutect CUBN,missense_variant,p.Arg1799Leu,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript missense_variant 5462/11949 5396/10872 1799/3623 R/L cGt/cTt rs758077332 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 deleterious(0.02) 37/67 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF645,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs758077332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 16940184 16940184 C A 1 0 0 0 0 1 0 0 0 3861 536 19 1 1 CUBN 10 16940184 Missense_Mutation SNP C C3N-00560_T 36200 16940184 116857238 673 17362 SLC39A12 0 . GRCh38 10 17977915 17977915 + Silent SNP C C A rs543733651 C3N-00560_T C3N-00560_N C C c.765C>A p.= p.L255L ENST00000377369 5/13 34 24 10 31 31 0 strelka-varscan-mutect SLC39A12,synonymous_variant,p.=,ENST00000377369,NM_001145195.1;SLC39A12,synonymous_variant,p.=,ENST00000377371,NM_001282733.1;SLC39A12,synonymous_variant,p.=,ENST00000377374,NM_152725.3;SLC39A12,synonymous_variant,p.=,ENST00000539911,NM_001282734.1; A ENST00000377369 Transcript synonymous_variant 1038/2808 765/2076 255/691 L ctC/ctA rs543733651 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 5/13 hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191 LOW 1 SNV 1 1 PASS rs543733651 . 1 201 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 56 17977915 17977915 C A 1 0 0 0 0 0 0 0 1 14893 842 30 2 2 SLC39A12 10 17977915 Silent SNP C C3N-00560_T 1037731 17977915 115819507 674 17363 PLXDC2 0 . GRCh38 10 20001842 20001842 + Silent SNP G G T rs149037714 C3N-00560_T C3N-00560_N G G c.180G>T p.= p.A60A ENST00000377252 2/14 356 238 118 420 419 1 strelka-varscan-mutect PLXDC2,synonymous_variant,p.=,ENST00000377252,NM_032812.8;PLXDC2,synonymous_variant,p.=,ENST00000377242,NM_001282736.1; T ENST00000377252 Transcript synonymous_variant 1021/12468 180/1590 60/529 A gcG/gcT rs149037714,COSM4013250 1 1 PLXDC2 HGNC HGNC:21013 protein_coding YES CCDS7132.1 ENSP00000366460 Q6UX71 UPI0000048F2C NM_032812.8 2/14 hmmpanther:PTHR13055:SF11,hmmpanther:PTHR13055 0,1 LOW 1 SNV 1 0,1 1 PASS rs149037714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 20001842 20001842 G T 1 0 0 0 0 0 0 0 1 12224 1132 40 1 1 PLXDC2 10 20001842 Silent SNP G C3N-00560_T 2023927 20001842 113795580 675 17364 SKIDA1 0 . GRCh38 10 21517271 21517271 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.552C>G p.Ile184Met p.I184M ENST00000449193 4/4 125 76 49 130 130 0 strelka-varscan-mutect SKIDA1,missense_variant,p.Ile184Met,ENST00000449193,NM_207371.3;SKIDA1,missense_variant,p.Ile184Met,ENST00000444772,;SKIDA1,downstream_gene_variant,,ENST00000633225,;SKIDA1,downstream_gene_variant,,ENST00000487107,; C ENST00000449193 Transcript missense_variant 2805/6598 552/2727 184/908 I/M atC/atG 1 -1 SKIDA1 HGNC HGNC:32697 protein_coding YES CCDS44363.1 ENSP00000410041 E9PAX1 UPI00015386B3 NM_207371.3 tolerated(0.12) 4/4 hmmpanther:PTHR23187:SF2,hmmpanther:PTHR23187 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 21517271 21517271 G C 1 0 0 0 0 1 0 0 0 14620 1048 37 4 4 SKIDA1 10 21517271 Missense_Mutation SNP G C3N-00560_T 1515429 21517271 112280151 676 17365 PTF1A 0 . GRCh38 10 23192722 23192722 + Missense_Mutation SNP C C A rs749956400 C3N-00560_T C3N-00560_N C C c.192C>A p.Asp64Glu p.D64E ENST00000376504 1/2 121 99 22 104 104 0 strelka-varscan-mutect PTF1A,missense_variant,p.Asp64Glu,ENST00000376504,NM_178161.2; A ENST00000376504 Transcript missense_variant 396/1537 192/987 64/328 D/E gaC/gaA rs749956400 1 1 PTF1A HGNC HGNC:23734 protein_coding YES CCDS7143.1 ENSP00000365687 Q7RTS3 UPI000018F612 NM_178161.2 tolerated_low_confidence(0.18) 1/2 hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF59 MODERATE 1 SNV 2 1 PASS rs749956400 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 56 23192722 23192722 C A 1 0 0 0 0 1 0 0 0 12893 535 19 1 1 PTF1A 10 23192722 Missense_Mutation SNP C C3N-00560_T 1675451 23192722 110604700 677 17366 KIAA1217 0 . GRCh38 10 24474002 24474002 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1621A>T p.Met541Leu p.M541L ENST00000376454 6/21 133 81 52 112 112 0 strelka-varscan-mutect KIAA1217,missense_variant,p.Met259Leu,ENST00000376451,;KIAA1217,missense_variant,p.Met541Leu,ENST00000376454,NM_019590.4;KIAA1217,missense_variant,p.Met461Leu,ENST00000376462,NM_001098500.2;KIAA1217,missense_variant,p.Met541Leu,ENST00000376452,NM_001282767.1;KIAA1217,missense_variant,p.Met541Leu,ENST00000458595,NM_001282768.1;KIAA1217,missense_variant,p.Met461Leu,ENST00000430453,;KIAA1217,missense_variant,p.Met259Leu,ENST00000396445,;KIAA1217,missense_variant,p.Met259Leu,ENST00000307544,NM_001282769.1;KIAA1217,missense_variant,p.Met541Leu,ENST00000376456,;KIAA1217,missense_variant,p.Met259Leu,ENST00000396446,NM_001282770.1;KIAA1217,missense_variant,p.Met391Leu,ENST00000438429,; T ENST00000376454 Transcript missense_variant 1651/7381 1621/5832 541/1943 M/L Atg/Ttg 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 tolerated(0.82) 6/21 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 24474002 24474002 A T 1 0 0 0 0 1 0 0 0 8109 101 4 4 4 KIAA1217 10 24474002 Missense_Mutation SNP A C3N-00560_T 1281280 24474002 109323420 678 17367 GPR158 0 . GRCh38 10 25596775 25596775 + Missense_Mutation SNP C C G C3N-00560_T C3N-00560_N C C c.2131C>G p.Pro711Ala p.P711A ENST00000376351 10/11 139 108 31 102 102 0 strelka-varscan-mutect GPR158,missense_variant,p.Pro711Ala,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; G ENST00000376351 Transcript missense_variant 2490/6959 2131/3648 711/1215 P/A Cca/Gca COSM230654 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0) 10/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 25596775 25596775 C G 1 0 0 0 0 1 0 0 0 6549 855 30 4 4 GPR158 10 25596775 Missense_Mutation SNP C C3N-00560_T 1122773 25596775 108200647 679 17368 LYZL2 0 . GRCh38 10 30612821 30612821 + Splice_Site SNP C C T rs753953857 C3N-00560_T C3N-00560_N C C c.515+1G>A p.X172_splice ENST00000375318 117 94 23 98 98 0 strelka-varscan-mutect LYZL2,splice_donor_variant,,ENST00000375318,NM_183058.2; T ENST00000375318 Transcript splice_donor_variant -/818 515/585 172/194 rs753953857 1 -1 LYZL2 HGNC HGNC:29613 protein_coding YES CCDS7167.2 ENSP00000364467 Q7Z4W2 A0A080YUZ9 UPI0000160E06 NM_183058.2 4/4 HIGH 1 SNV 1 1 PASS rs753953857 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 30612821 30612821 C T 1 0 0 0 0 0 0 1 0 9045 521 18 3 3 LYZL2 10 30612821 Splice_Site SNP C C3N-00560_T 5016046 30612821 103184601 680 17369 PARD3 0 . GRCh38 10 34377988 34377988 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1518G>C p.Lys506Asn p.K506N ENST00000374789 10/25 116 78 38 89 89 0 strelka-varscan-mutect PARD3,missense_variant,p.Lys506Asn,ENST00000374789,NM_019619.3;PARD3,missense_variant,p.Lys506Asn,ENST00000374788,NM_001184785.1;PARD3,missense_variant,p.Lys506Asn,ENST00000545693,NM_001184786.1;PARD3,missense_variant,p.Lys506Asn,ENST00000346874,NM_001184787.1;PARD3,missense_variant,p.Lys506Asn,ENST00000350537,NM_001184789.1,NM_001184788.1;PARD3,missense_variant,p.Lys462Asn,ENST00000374790,;PARD3,missense_variant,p.Lys462Asn,ENST00000545260,NM_001184790.1;PARD3,missense_variant,p.Lys462Asn,ENST00000374794,NM_001184791.1;PARD3,missense_variant,p.Lys506Asn,ENST00000340077,NM_001184792.1;PARD3,missense_variant,p.Lys506Asn,ENST00000374773,NM_001184793.1;PARD3,missense_variant,p.Lys506Asn,ENST00000374776,NM_001184794.1;PARD3,missense_variant,p.Lys236Asn,ENST00000544292,; G ENST00000374789 Transcript missense_variant 1844/6005 1518/4071 506/1356 K/N aaG/aaC 1 -1 PARD3 HGNC HGNC:16051 protein_coding YES CCDS7178.1 ENSP00000363921 Q8TEW0 UPI0000073A9F NM_019619.3 deleterious(0) 10/25 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 34377988 34377988 C G 1 0 0 0 0 1 0 0 0 11523 680 24 4 4 PARD3 10 34377988 Missense_Mutation SNP C C3N-00560_T 3765167 34377988 99419434 681 17370 AGAP14P 0 . GRCh38 10 46358456 46358456 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1800G>C p.Gln600His p.Q600H ENST00000624701 9/9 485 391 94 453 453 0 strelka-varscan-mutect AGAP14P,missense_variant,p.Gln600His,ENST00000624701,; C ENST00000624701 Transcript missense_variant 1800/2058 1800/2058 600/685 Q/H caG/caC 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF tolerated(0.05) 9/9 PROSITE_profiles:PS50297,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,Pfam_domain:PF12796,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 46358456 46358456 G C 1 0 0 0 0 1 0 0 0 444 933 33 4 4 AGAP14P 10 46358456 Missense_Mutation SNP G C3N-00560_T 11980468 46358456 87438966 682 17371 GDF2 0 . GRCh38 10 47325415 47325415 + Missense_Mutation SNP C C G rs368331513 C3N-00560_T C3N-00560_N C C c.921C>G p.His307Gln p.H307Q ENST00000581492 2/2 200 127 73 195 195 0 strelka-varscan-mutect GDF2,missense_variant,p.His307Gln,ENST00000581492,NM_016204.2; G ENST00000581492 Transcript missense_variant 1100/1955 921/1290 307/429 H/Q caC/caG rs368331513 1 1 GDF2 HGNC HGNC:4217 protein_coding YES CCDS73118.1 ENSP00000463051 Q9UK05 UPI000012B394 NM_016204.2 tolerated(0.3) 2/2 MODERATE 1 SNV 1 1 PASS rs368331513 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 47325415 47325415 C G 1 0 0 0 0 1 0 0 0 6186 535 19 4 4 GDF2 10 47325415 Missense_Mutation SNP C C3N-00560_T 966959 47325415 86472007 683 17372 ZNF488 0 . GRCh38 10 47367920 47367920 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.910G>T p.Gly304Trp p.G304W ENST00000585316 2/2 275 225 50 305 305 0 strelka-varscan-mutect ZNF488,missense_variant,p.Gly304Trp,ENST00000585316,NM_153034.2;ZNF488,missense_variant,p.Gly197Trp,ENST00000591025,; A ENST00000585316 Transcript missense_variant 1072/3496 910/1023 304/340 G/W Ggg/Tgg 1 -1 ZNF488 HGNC HGNC:23535 protein_coding YES CCDS73120.1 ENSP00000462269 Q96MN9 UPI00000736CF NM_153034.2 deleterious(0) 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR16516:SF5,hmmpanther:PTHR16516,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 47367920 47367920 C A 1 0 0 0 0 1 0 0 0 18513 623 22 2 2 ZNF488 10 47367920 Missense_Mutation SNP C C3N-00560_T 42505 47367920 86429502 684 17373 AGAP9 0 . GRCh38 10 47503072 47503072 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1057G>A p.Ala353Thr p.A353T ENST00000452145 8/8 1242 1146 96 1246 1246 0 varscan-mutect AGAP9,missense_variant,p.Ala353Thr,ENST00000452145,NM_001190810.1;RP11-144G6.4,downstream_gene_variant,,ENST00000434533,; T ENST00000452145 Transcript missense_variant 1169/2387 1057/1977 353/658 A/T Gca/Aca 1 -1 AGAP9 HGNC HGNC:23463 protein_coding YES CCDS73125.1 ENSP00000392206 Q5VTM2 UPI000019733B NM_001190810.1 tolerated(0.14) 8/8 PROSITE_profiles:PS50003,SMART_domains:SM00233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 47503072 47503072 C T 1 0 0 0 0 1 0 0 0 450 710 25 3 3 AGAP9 10 47503072 Missense_Mutation SNP C C3N-00560_T 135152 47503072 86294350 685 17374 FRMPD2 0 . GRCh38 10 48251609 48251609 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.108C>A p.= p.L36L ENST00000374201 2/29 200 159 41 167 167 0 strelka-varscan-mutect FRMPD2,synonymous_variant,p.=,ENST00000374201,NM_001018071.3;FRMPD2,synonymous_variant,p.=,ENST00000305531,NM_001318191.1;FRMPD2,synonymous_variant,p.=,ENST00000636244,;FRMPD2,synonymous_variant,p.=,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000492045,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000468556,; T ENST00000374201 Transcript synonymous_variant 411/4997 108/3930 36/1309 L ctC/ctA 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 2/29 PROSITE_profiles:PS51377,hmmpanther:PTHR19964:SF42,hmmpanther:PTHR19964,SMART_domains:SM00750 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 48251609 48251609 G T 1 0 0 0 0 0 0 0 1 5928 1161 41 2 2 FRMPD2 10 48251609 Silent SNP G C3N-00560_T 748537 48251609 85545813 686 17375 WDFY4 0 . GRCh38 10 48974987 48974987 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.9054C>A p.= p.T3018T ENST00000325239 57/61 317 217 100 289 289 0 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1;WDFY4,synonymous_variant,p.=,ENST00000265453,;RP11-523O18.5,downstream_gene_variant,,ENST00000428825,;WDFY4,non_coding_transcript_exon_variant,,ENST00000465910,;WDFY4,non_coding_transcript_exon_variant,,ENST00000497480,;WDFY4,upstream_gene_variant,,ENST00000490507,;RP11-523O18.5,downstream_gene_variant,,ENST00000610464,; A ENST00000325239 Transcript synonymous_variant 9054/9555 9054/9555 3018/3184 T acC/acA 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 57/61 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS rs1393133594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 48974987 48974987 C A 1 0 0 0 0 0 0 0 1 17831 610 22 2 2 WDFY4 10 48974987 Silent SNP C C3N-00560_T 723378 48974987 84822435 687 17376 C10orf71 0 . GRCh38 10 49323392 49323392 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.847C>A p.His283Asn p.H283N ENST00000374144 3/3 256 173 83 288 288 0 strelka-varscan-mutect C10orf71,missense_variant,p.His283Asn,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript missense_variant 1135/5230 847/4308 283/1435 H/N Cac/Aac 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0.01) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49323392 49323392 C A 1 0 0 0 0 1 0 0 0 1769 594 21 2 2 C10orf71 10 49323392 Missense_Mutation SNP C C3N-00560_T 348405 49323392 84474030 688 17377 CHAT 0 . GRCh38 10 49616549 49616549 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.334C>T p.= p.L112L ENST00000337653 2/15 543 434 109 530 530 0 strelka-varscan-mutect CHAT,synonymous_variant,p.=,ENST00000395562,NM_001142933.1;CHAT,synonymous_variant,p.=,ENST00000337653,NM_020549.4;CHAT,5_prime_UTR_variant,,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,5_prime_UTR_variant,,ENST00000339797,NM_020984.3;CHAT,5_prime_UTR_variant,,ENST00000395559,NM_020986.3;SLC18A3,downstream_gene_variant,,ENST00000374115,NM_003055.2;CHAT,non_coding_transcript_exon_variant,,ENST00000460699,;CHAT,non_coding_transcript_exon_variant,,ENST00000490270,;CHAT,non_coding_transcript_exon_variant,,ENST00000481336,;CHAT,3_prime_UTR_variant,,ENST00000466590,; T ENST00000337653 Transcript synonymous_variant 487/2458 334/2247 112/748 L Ctg/Ttg 1 1 CHAT HGNC HGNC:1912 protein_coding YES CCDS7232.1 ENSP00000337103 P28329 UPI000013F1B9 NM_020549.4 2/15 hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 49616549 49616549 C T 1 0 0 0 0 0 0 0 1 3073 680 24 3 3 CHAT 10 49616549 Silent SNP C C3N-00560_T 293157 49616549 84180873 689 17378 CHAT 0 . GRCh38 10 49646597 49646597 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1204C>A p.His402Asn p.H402N ENST00000337653 8/15 227 193 34 231 231 0 strelka-varscan-mutect CHAT,missense_variant,p.His320Asn,ENST00000395562,NM_001142933.1;CHAT,missense_variant,p.His402Asn,ENST00000337653,NM_020549.4;CHAT,missense_variant,p.His284Asn,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,missense_variant,p.His284Asn,ENST00000339797,NM_020984.3;CHAT,missense_variant,p.His284Asn,ENST00000395559,NM_020986.3;CHAT,3_prime_UTR_variant,,ENST00000466590,; A ENST00000337653 Transcript missense_variant 1357/2458 1204/2247 402/748 H/N Cac/Aac 1 1 CHAT HGNC HGNC:1912 protein_coding YES CCDS7232.1 ENSP00000337103 P28329 UPI000013F1B9 NM_020549.4 tolerated(1) 8/15 Pfam_domain:PF00755,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF14,Superfamily_domains:SSF52777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49646597 49646597 C A 1 0 0 0 0 1 0 0 0 3073 594 21 2 2 CHAT 10 49646597 Missense_Mutation SNP C C3N-00560_T 30048 49646597 84150825 690 17379 CHAT 0 . GRCh38 10 49655128 49655128 + Missense_Mutation SNP C C A rs55702495 C3N-00560_T C3N-00560_N C C c.1668C>A p.Ser556Arg p.S556R ENST00000337653 12/15 468 378 90 425 424 1 strelka-varscan-mutect CHAT,missense_variant,p.Ser474Arg,ENST00000395562,NM_001142933.1;CHAT,missense_variant,p.Ser556Arg,ENST00000337653,NM_020549.4;CHAT,missense_variant,p.Ser438Arg,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,missense_variant,p.Ser438Arg,ENST00000339797,NM_020984.3;CHAT,missense_variant,p.Ser438Arg,ENST00000395559,NM_020986.3;CHAT,3_prime_UTR_variant,,ENST00000466590,; A ENST00000337653 Transcript missense_variant 1821/2458 1668/2247 556/748 S/R agC/agA rs55702495,COSM1348109,COSM5161564,COSM5292476,COSM5292477 1 1 CHAT HGNC HGNC:1912 protein_coding YES CCDS7232.1 ENSP00000337103 P28329 UPI000013F1B9 NM_020549.4 deleterious(0.01) 12/15 Pfam_domain:PF00755,hmmpanther:PTHR22589,hmmpanther:PTHR22589:SF14,Superfamily_domains:SSF52777 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs55702495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49655128 49655128 C A 1 0 0 0 0 1 0 0 0 3073 767 27 1 1 CHAT 10 49655128 Missense_Mutation SNP C C3N-00560_T 8531 49655128 84142294 691 17380 FAM21A 0 . GRCh38 10 50119737 50119737 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2446A>T p.Ile816Phe p.I816F ENST00000282633 23/31 146 122 24 197 197 0 strelka-varscan-mutect FAM21A,missense_variant,p.Ile816Phe,ENST00000351071,NM_001291398.1;FAM21A,missense_variant,p.Ile816Phe,ENST00000314664,;FAM21A,missense_variant,p.Ile741Phe,ENST00000611324,;FAM21A,missense_variant,p.Ile728Phe,ENST00000399339,;FAM21A,missense_variant,p.Ile816Phe,ENST00000282633,NM_001005751.2;FAM21A,missense_variant,p.Ile30Phe,ENST00000454806,;FAM21A,3_prime_UTR_variant,,ENST00000434114,; T ENST00000282633 Transcript missense_variant 2491/4272 2446/4026 816/1341 I/F Att/Ttt 1 1 FAM21A HGNC HGNC:23416 protein_coding YES CCDS41527.1 ENSP00000282633 Q641Q2 UPI000044FEAB NM_001005751.2 deleterious(0.04) 23/31 hmmpanther:PTHR21669,hmmpanther:PTHR21669:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 50119737 50119737 A T 1 0 0 0 0 1 0 0 0 5411 217 8 4 4 FAM21A 10 50119737 Missense_Mutation SNP A C3N-00560_T 464609 50119737 83677685 692 17381 ASAH2 0 . GRCh38 10 50245252 50245252 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.330C>A p.Asp110Glu p.D110E ENST00000395526 2/20 280 219 61 297 297 0 strelka-varscan-mutect ASAH2,missense_variant,p.Asp110Glu,ENST00000395526,NM_019893.2;ASAH2,missense_variant,p.Asp110Glu,ENST00000447815,NM_001143974.1;ASAH2,missense_variant,p.Asp91Glu,ENST00000329428,;ASAH2,upstream_gene_variant,,ENST00000443575,; T ENST00000395526 Transcript missense_variant 330/6880 330/2343 110/780 D/E gaC/gaA 1 -1 ASAH2 HGNC HGNC:18860 protein_coding YES CCDS7239.2 ENSP00000378897 Q9NR71 UPI00004042A7 NM_019893.2 deleterious(0) 2/20 hmmpanther:PTHR12670,Pfam_domain:PF04734 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 50245252 50245252 G T 1 0 0 0 0 1 0 0 0 1150 1020 36 2 2 ASAH2 10 50245252 Missense_Mutation SNP G C3N-00560_T 125515 50245252 83552170 693 17382 PCDH15 0 . GRCh38 10 53866788 53866788 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3586G>T p.Gly1196Ter p.G1196* ENST00000373957 28/35 279 195 84 387 387 0 strelka-varscan-mutect PCDH15,stop_gained,p.Gly1196Ter,ENST00000614895,;PCDH15,stop_gained,p.Gly1191Ter,ENST00000373965,NM_001142772.1;PCDH15,stop_gained,p.Gly1191Ter,ENST00000414778,;PCDH15,stop_gained,p.Gly1196Ter,ENST00000617051,;PCDH15,stop_gained,p.Gly1196Ter,ENST00000373957,NM_001142763.1;PCDH15,stop_gained,p.Gly1191Ter,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,stop_gained,p.Gly1191Ter,ENST00000395430,NM_001142766.1;PCDH15,stop_gained,p.Gly1169Ter,ENST00000395433,NM_001142773.1;PCDH15,stop_gained,p.Gly1154Ter,ENST00000395432,NM_001142767.1;PCDH15,stop_gained,p.Gly1191Ter,ENST00000320301,NM_033056.3;PCDH15,stop_gained,p.Gly1120Ter,ENST00000622048,;PCDH15,stop_gained,p.Gly1120Ter,ENST00000437009,NM_001142765.1;PCDH15,stop_gained,p.Gly1191Ter,ENST00000617271,NM_001142770.1;PCDH15,stop_gained,p.Gly1203Ter,ENST00000613657,NM_001142769.1;PCDH15,stop_gained,p.Gly1198Ter,ENST00000395445,;PCDH15,stop_gained,p.Gly1191Ter,ENST00000616114,;PCDH15,stop_gained,p.Gly1191Ter,ENST00000395438,;PCDH15,stop_gained,p.Gly1203Ter,ENST00000612394,;PCDH15,stop_gained,p.Gly1196Ter,ENST00000621708,NM_001142771.1;PCDH15,stop_gained,p.Gly802Ter,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,non_coding_transcript_exon_variant,,ENST00000463095,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript stop_gained 3981/7032 3586/5889 1196/1962 G/* Gga/Tga 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 28/35 PROSITE_profiles:PS50268,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 SNV 5 1 PASS rs1288942478 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 53866788 53866788 C A 1 0 0 0 0 0 1 0 0 11598 632 22 2 2 PCDH15 10 53866788 Nonsense_Mutation SNP C C3N-00560_T 3621536 53866788 79930634 694 17383 PCDH15 0 . GRCh38 10 53959753 53959753 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.3116G>T p.Arg1039Leu p.R1039L ENST00000373957 24/35 293 242 51 343 343 0 strelka-varscan-mutect PCDH15,missense_variant,p.Arg1039Leu,ENST00000614895,;PCDH15,missense_variant,p.Arg1034Leu,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Arg1034Leu,ENST00000414778,;PCDH15,missense_variant,p.Arg1039Leu,ENST00000617051,;PCDH15,missense_variant,p.Arg1039Leu,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Arg1034Leu,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Arg1034Leu,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Arg1012Leu,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Arg997Leu,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Arg1034Leu,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Arg963Leu,ENST00000622048,;PCDH15,missense_variant,p.Arg963Leu,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Arg1034Leu,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Arg1046Leu,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Arg1041Leu,ENST00000395445,;PCDH15,missense_variant,p.Arg1034Leu,ENST00000616114,;PCDH15,missense_variant,p.Arg1034Leu,ENST00000395438,;PCDH15,missense_variant,p.Arg1046Leu,ENST00000612394,;PCDH15,missense_variant,p.Arg1039Leu,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Arg645Leu,ENST00000409834,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript missense_variant 3511/7032 3116/5889 1039/1962 R/L cGc/cTc COSM125167,COSM125168,COSM125169,COSM5009170 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.34) 24/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs907693214 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 53959753 53959753 C A 1 0 0 0 0 1 0 0 0 11598 768 27 1 1 PCDH15 10 53959753 Missense_Mutation SNP C C3N-00560_T 92965 53959753 79837669 695 17384 PCDH15 0 . GRCh38 10 54664188 54664188 + Missense_Mutation SNP C C A rs772829621 C3N-00560_T C3N-00560_N C C c.75G>T p.Leu25Phe p.L25F ENST00000373957 2/35 360 307 53 390 388 2 strelka-varscan-mutect PCDH15,missense_variant,p.Leu25Phe,ENST00000614895,;PCDH15,missense_variant,p.Leu25Phe,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000414778,;PCDH15,missense_variant,p.Leu25Phe,ENST00000617051,;PCDH15,missense_variant,p.Leu25Phe,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Leu25Phe,ENST00000622048,;PCDH15,missense_variant,p.Leu25Phe,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000395445,;PCDH15,missense_variant,p.Leu25Phe,ENST00000616114,;PCDH15,missense_variant,p.Leu25Phe,ENST00000395438,;PCDH15,missense_variant,p.Leu25Phe,ENST00000612394,;PCDH15,missense_variant,p.Leu25Phe,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Leu25Phe,ENST00000373955,;PCDH15,missense_variant,p.Leu25Phe,ENST00000395446,;PCDH15,missense_variant,p.Leu25Phe,ENST00000395440,;PCDH15,missense_variant,p.Leu25Phe,ENST00000395442,;PCDH15,missense_variant,p.Leu25Phe,ENST00000613346,;PCDH15,missense_variant,p.Leu25Phe,ENST00000458638,;PCDH15,5_prime_UTR_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Leu25Phe,ENST00000448885,;PCDH15,missense_variant,p.Leu25Phe,ENST00000373956,;PCDH15,missense_variant,p.Leu25Phe,ENST00000414367,; A ENST00000373957 Transcript missense_variant 470/7032 75/5889 25/1962 L/F ttG/ttT rs772829621 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated_low_confidence(0.23) 2/35 Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 5 1 PASS rs772829621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 54664188 54664188 C A 1 0 0 0 0 1 0 0 0 11598 593 21 2 2 PCDH15 10 54664188 Missense_Mutation SNP C C3N-00560_T 704435 54664188 79133234 696 17385 JMJD1C 0 . GRCh38 10 63189180 63189180 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.6558delG p.Trp2186Ter p.W2186* ENST00000399262 18/26 30 25 5 48 48 0 sindel-varindel-pindel JMJD1C,frameshift_variant,p.Trp2186Ter,ENST00000399262,NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2;JMJD1C,frameshift_variant,p.Trp2004Ter,ENST00000542921,NM_001318153.1,NM_001282948.1;JMJD1C,frameshift_variant,p.Trp733Ter,ENST00000327520,;JMJD1C,non_coding_transcript_exon_variant,,ENST00000402544,;JMJD1C,downstream_gene_variant,,ENST00000497922,;JMJD1C,downstream_gene_variant,,ENST00000483298,;JMJD1C,downstream_gene_variant,,ENST00000490669,; - ENST00000399262 Transcript frameshift_variant 6777/8666 6558/7623 2186/2540 W/X tgG/tg 1 -1 JMJD1C HGNC HGNC:12313 protein_coding YES CCDS41532.1 ENSP00000382204 Q15652 UPI0000198BEF NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2 18/26 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF6,Superfamily_domains:SSF51197 HIGH 1 deletion 5 1 PASS . . 1 194 13 2 0 0 0 0 -11.31595 0.9980934 1 1 1 0 - 7 5 56 63189180 63189180 C - 1 0 1 0 1 0 0 0 0 7864 856 30 0 0 JMJD1C 10 63189180 Frame_Shift_Del DEL C C3N-00560_T 8524992 63189180 70608242 697 17386 LRRTM3 0 . GRCh38 10 66927491 66927491 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.575G>T p.Arg192Leu p.R192L ENST00000361320 2/3 221 175 46 242 242 0 strelka-varscan-mutect LRRTM3,missense_variant,p.Arg192Leu,ENST00000361320,NM_178011.4;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2,NM_013266.3;CTNNA3,intron_variant,,ENST00000494580,; T ENST00000361320 Transcript missense_variant 1153/4358 575/1746 192/581 R/L cGg/cTg 1 1 LRRTM3 HGNC HGNC:19410 protein_coding YES CCDS7270.1 ENSP00000355187 Q86VH5 UPI0000088C0F NM_178011.4 deleterious(0) 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 66927491 66927491 G T 1 0 0 0 0 1 0 0 0 8947 1116 39 1 1 LRRTM3 10 66927491 Missense_Mutation SNP G C3N-00560_T 3738311 66927491 66869931 698 17387 DNAJC12 0 . GRCh38 10 67811542 67811542 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.279G>T p.Leu93Phe p.L93F ENST00000225171 3/5 209 181 28 224 224 0 strelka-varscan-mutect DNAJC12,missense_variant,p.Leu93Phe,ENST00000225171,NM_021800.2;DNAJC12,missense_variant,p.Leu93Phe,ENST00000339758,NM_201262.1;DNAJC12,missense_variant,p.Leu123Phe,ENST00000483798,;RNU6-1250P,downstream_gene_variant,,ENST00000391218,;DNAJC12,3_prime_UTR_variant,,ENST00000480963,;DNAJC12,3_prime_UTR_variant,,ENST00000480180,; A ENST00000225171 Transcript missense_variant 432/1201 279/597 93/198 L/F ttG/ttT 1 -1 DNAJC12 HGNC HGNC:28908 protein_coding YES CCDS7271.1 ENSP00000225171 Q9UKB3 Q6IAH1 UPI000012DAAA NM_021800.2 deleterious(0) 3/5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 67811542 67811542 C A 1 0 0 0 0 1 0 0 0 4445 825 29 2 2 DNAJC12 10 67811542 Missense_Mutation SNP C C3N-00560_T 884051 67811542 65985880 699 17388 DNA2 0 . GRCh38 10 68470144 68470144 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.94G>T p.Ala32Ser p.A32S ENST00000358410 2/21 126 103 23 117 117 0 strelka-varscan-mutect DNA2,missense_variant,p.Ala32Ser,ENST00000358410,NM_001080449.2;DNA2,missense_variant,p.Ala32Ser,ENST00000551118,;DNA2,missense_variant,p.Ala32Ser,ENST00000399180,;DNA2,missense_variant,p.Ala32Ser,ENST00000399179,;DNA2,3_prime_UTR_variant,,ENST00000550357,; A ENST00000358410 Transcript missense_variant 145/4208 94/3183 32/1060 A/S Gct/Tct 1 -1 DNA2 HGNC HGNC:2939 protein_coding YES CCDS44415.2 ENSP00000351185 P51530 UPI00001C1EDB NM_001080449.2 tolerated_low_confidence(0.2) 2/21 hmmpanther:PTHR10887:SF14,hmmpanther:PTHR10887 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 68470144 68470144 C A 1 0 0 0 0 1 0 0 0 4405 797 28 2 2 DNA2 10 68470144 Missense_Mutation SNP C C3N-00560_T 658602 68470144 65327278 700 17389 TET1 0 . GRCh38 10 68574235 68574235 + Missense_Mutation SNP G G C rs546506706 C3N-00560_T C3N-00560_N G G c.1897G>C p.Val633Leu p.V633L ENST00000373644 2/12 89 77 12 89 88 1 strelka-varscan-mutect TET1,missense_variant,p.Val633Leu,ENST00000373644,NM_030625.2; C ENST00000373644 Transcript missense_variant 2106/9288 1897/6411 633/2136 V/L Gtt/Ctt rs546506706 1 1 TET1 HGNC HGNC:29484 protein_coding YES CCDS7281.1 ENSP00000362748 Q8NFU7 UPI000013D114 NM_030625.2 tolerated(0.23) 2/12 hmmpanther:PTHR23358,hmmpanther:PTHR23358:SF2 MODERATE 1 SNV 1 1 PASS rs546506706 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 68574235 68574235 G C 1 0 0 0 0 1 0 0 0 16190 1377 48 4 4 TET1 10 68574235 Missense_Mutation SNP G C3N-00560_T 104091 68574235 65223187 701 17390 COL13A1 0 . GRCh38 10 69875155 69875155 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.427G>A p.Gly143Arg p.G143R ENST00000398978 5/40 243 209 34 265 265 0 strelka-varscan-mutect COL13A1,missense_variant,p.Gly143Arg,ENST00000398978,NM_001130103.1;COL13A1,missense_variant,p.Gly143Arg,ENST00000354547,NM_080801.3;COL13A1,missense_variant,p.Gly143Arg,ENST00000357811,;COL13A1,missense_variant,p.Gly143Arg,ENST00000522165,NM_080800.3;COL13A1,missense_variant,p.Gly143Arg,ENST00000517713,NM_080802.3;COL13A1,intron_variant,,ENST00000520267,NM_080798.3;COL13A1,intron_variant,,ENST00000398969,;COL13A1,intron_variant,,ENST00000520133,NM_080805.3;COL13A1,upstream_gene_variant,,ENST00000484990,;COL13A1,missense_variant,p.Gly143Arg,ENST00000479733,; A ENST00000398978 Transcript missense_variant 919/3093 427/2154 143/717 G/R Gga/Aga 1 1 COL13A1 HGNC HGNC:2190 protein_coding YES CCDS44419.1 ENSP00000381949 Q5TAT6 UPI000046FD72 NM_001130103.1 deleterious(0) 5/40 hmmpanther:PTHR24023:SF537,hmmpanther:PTHR24023 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 69875155 69875155 G A 1 0 0 0 0 1 0 0 0 3458 1349 47 3 3 COL13A1 10 69875155 Missense_Mutation SNP G C3N-00560_T 1300920 69875155 63922267 702 17391 ADAMTS14 0 . GRCh38 10 70702447 70702447 + Missense_Mutation SNP G G T rs764128541 C3N-00560_T C3N-00560_N G G c.658G>T p.Asp220Tyr p.D220Y ENST00000373208 3/22 97 65 32 77 77 0 strelka-varscan-mutect ADAMTS14,missense_variant,p.Asp220Tyr,ENST00000373208,NM_139155.2;ADAMTS14,missense_variant,p.Asp220Tyr,ENST00000373207,NM_080722.3; T ENST00000373208 Transcript missense_variant 658/5269 658/3681 220/1226 D/Y Gac/Tac rs764128541 1 1 ADAMTS14 HGNC HGNC:14899 protein_coding YES CCDS7307.1 ENSP00000362304 Q8WXS8 UPI000013E57B NM_139155.2 deleterious(0.04) 3/22 hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723 MODERATE 1 SNV 2 1 PASS rs764128541 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 70702447 70702447 G T 1 0 0 0 0 1 0 0 0 303 1290 45 2 2 ADAMTS14 10 70702447 Missense_Mutation SNP G C3N-00560_T 827292 70702447 63094975 703 17392 ADAMTS14 0 . GRCh38 10 70738950 70738950 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1717G>C p.Gly573Arg p.G573R ENST00000373208 11/22 182 144 38 146 146 0 strelka-varscan-mutect ADAMTS14,missense_variant,p.Gly573Arg,ENST00000373208,NM_139155.2;ADAMTS14,missense_variant,p.Gly570Arg,ENST00000373207,NM_080722.3; C ENST00000373208 Transcript missense_variant 1717/5269 1717/3681 573/1226 G/R Ggc/Cgc 1 1 ADAMTS14 HGNC HGNC:14899 protein_coding YES CCDS7307.1 ENSP00000362304 Q8WXS8 UPI000013E57B NM_139155.2 deleterious(0.03) 11/22 Low_complexity_(Seg):seg,PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,Prints_domain:PR01857 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 70738950 70738950 G C 1 0 0 0 0 1 0 0 0 303 1232 43 4 4 ADAMTS14 10 70738950 Missense_Mutation SNP G C3N-00560_T 36503 70738950 63058472 704 17393 CHST3 0 . GRCh38 10 72005934 72005934 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.92T>A p.Val31Glu p.V31E ENST00000373115 2/3 512 332 180 479 479 0 strelka-varscan-mutect CHST3,missense_variant,p.Val31Glu,ENST00000373115,NM_004273.4; A ENST00000373115 Transcript missense_variant 529/6970 92/1440 31/479 V/E gTg/gAg 1 1 CHST3 HGNC HGNC:1971 protein_coding YES CCDS7312.1 ENSP00000362207 Q7LGC8 UPI000013CB04 NM_004273.4 deleterious_low_confidence(0) 2/3 PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF38,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 72005934 72005934 T A 1 0 0 0 0 1 0 0 0 3165 1696 59 4 4 CHST3 10 72005934 Missense_Mutation SNP T C3N-00560_T 1266984 72005934 61791488 705 17394 SPOCK2 0 . GRCh38 10 72072237 72072237 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.266C>A p.Pro89His p.P89H ENST00000373109 4/11 56 40 16 57 57 0 strelka-varscan-mutect SPOCK2,missense_variant,p.Pro89His,ENST00000373109,NM_001244950.1;SPOCK2,missense_variant,p.Pro89His,ENST00000317376,NM_014767.2;SPOCK2,missense_variant,p.Pro88His,ENST00000536168,;SPOCK2,upstream_gene_variant,,ENST00000460053,;SPOCK2,upstream_gene_variant,,ENST00000469121,;SPOCK2,upstream_gene_variant,,ENST00000463279,; T ENST00000373109 Transcript missense_variant 711/5445 266/1275 89/424 P/H cCc/cAc 1 -1 SPOCK2 HGNC HGNC:13564 protein_coding YES CCDS7313.1 ENSP00000362201 Q92563 UPI0000136F51 NM_001244950.1 deleterious(0) 4/11 Gene3D:3.40.50.1820,hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF13 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 72072237 72072237 G T 1 0 0 0 0 1 0 0 0 15433 1232 43 2 2 SPOCK2 10 72072237 Missense_Mutation SNP G C3N-00560_T 66303 72072237 61725185 706 17395 KCNMA1 0 . GRCh38 10 76944820 76944820 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.2855C>T p.Ser952Phe p.S952F ENST00000286628 23/28 461 297 164 501 501 0 strelka-varscan-mutect KCNMA1,missense_variant,p.Ser759Phe,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,missense_variant,p.Ser894Phe,ENST00000286627,NM_002247.3;KCNMA1,missense_variant,p.Ser952Phe,ENST00000286628,NM_001161352.1;KCNMA1,missense_variant,p.Ser787Phe,ENST00000354353,;KCNMA1,missense_variant,p.Ser729Phe,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,missense_variant,p.Ser894Phe,ENST00000372443,;KCNMA1,missense_variant,p.Ser894Phe,ENST00000372440,NM_001014797.2;KCNMA1,missense_variant,p.Ser952Phe,ENST00000404771,;KCNMA1,missense_variant,p.Ser926Phe,ENST00000457953,;KCNMA1,missense_variant,p.Ser935Phe,ENST00000626620,NM_001161353.1;KCNMA1,missense_variant,p.Ser887Phe,ENST00000372437,;KCNMA1,missense_variant,p.Ser868Phe,ENST00000372421,;KCNMA1,missense_variant,p.Ser831Phe,ENST00000372408,;KCNMA1,missense_variant,p.Ser845Phe,ENST00000372403,;KCNMA1,missense_variant,p.Ser730Phe,ENST00000404857,NM_001271518.1;KCNMA1,missense_variant,p.Ser602Phe,ENST00000434208,;KCNMA1-AS1,intron_variant,,ENST00000600782,;KCNMA1-AS1,intron_variant,,ENST00000598613,;KCNMA1-AS1,intron_variant,,ENST00000617241,;KCNMA1-AS1,intron_variant,,ENST00000426234,;KCNMA1-AS1,intron_variant,,ENST00000458661,;KCNMA1-AS1,intron_variant,,ENST00000608791,;KCNMA1-AS1,intron_variant,,ENST00000611475,; A ENST00000286628 Transcript missense_variant 2855/6100 2855/3711 952/1236 S/F tCt/tTt 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 deleterious(0) 23/28 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 76944820 76944820 G A 1 0 0 0 0 1 0 0 0 7990 942 33 3 3 KCNMA1 10 76944820 Missense_Mutation SNP G C3N-00560_T 4872583 76944820 56852602 707 17396 SFTPA1 0 . GRCh38 10 79614016 79614016 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.695delC p.Ala232GlufsTer27 p.A232Efs*27 ENST00000419470 6/6 322 282 40 390 390 0 sindel-varindel SFTPA1,frameshift_variant,p.Ala217GlufsTer27,ENST00000398636,NM_001164646.1,NM_005411.4,NM_001164644.1;SFTPA1,frameshift_variant,p.Ala232GlufsTer27,ENST00000419470,NM_001093770.2,NM_001164645.1;SFTPA1,frameshift_variant,p.Ala217GlufsTer27,ENST00000428376,NM_001164647.1;SFTPA1,downstream_gene_variant,,ENST00000439264,;SFTPA1,downstream_gene_variant,,ENST00000429958,;SFTPA1,downstream_gene_variant,,ENST00000486922,; - ENST00000419470 Transcript frameshift_variant 771/2210 695/792 232/263 A/X gCa/ga 1 1 SFTPA1 HGNC HGNC:10798 protein_coding YES CCDS44444.2 ENSP00000397082 Q8IWL2 UPI00006C104C NM_001093770.2,NM_001164645.1 6/6 PROSITE_profiles:PS50041,hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF21,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 79614016 79614016 C - 1 0 1 0 1 0 0 0 0 14449 710 25 0 0 SFTPA1 10 79614016 Frame_Shift_Del DEL C C3N-00560_T 2669196 79614016 54183406 708 17397 SH2D4B 0 . GRCh38 10 80644014 80644014 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1007G>C p.Arg336Thr p.R336T ENST00000339284 7/7 187 124 63 207 207 0 strelka-varscan-mutect SH2D4B,missense_variant,p.Arg336Thr,ENST00000339284,NM_207372.2;SH2D4B,missense_variant,p.Arg288Thr,ENST00000313455,NM_001145719.1;SH2D4B,non_coding_transcript_exon_variant,,ENST00000372150,;SH2D4B,non_coding_transcript_exon_variant,,ENST00000481537,; C ENST00000339284 Transcript missense_variant 1437/3983 1007/1074 336/357 R/T aGg/aCg 1 1 SH2D4B HGNC HGNC:31440 protein_coding YES CCDS7370.1 ENSP00000345295 Q5SQS7 UPI00002289C3 NM_207372.2 tolerated_low_confidence(0.39) 7/7 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 80644014 80644014 G C 1 0 0 0 0 1 0 0 0 14494 1000 35 4 4 SH2D4B 10 80644014 Missense_Mutation SNP G C3N-00560_T 1029998 80644014 53153408 709 17398 CDHR1 0 . GRCh38 10 84214464 84214464 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.2423A>C p.Gln808Pro p.Q808P ENST00000623527 17/17 238 174 64 195 194 1 strelka-varscan-mutect CDHR1,missense_variant,p.Gln808Pro,ENST00000623527,NM_033100.3;CDHR1,missense_variant,p.Gln547Pro,ENST00000372117,;CDHR1,intron_variant,,ENST00000332904,NM_001171971.2;CDHR1,intron_variant,,ENST00000623399,;CDHR1,non_coding_transcript_exon_variant,,ENST00000459673,;CDHR1,downstream_gene_variant,,ENST00000622973,; C ENST00000623527 Transcript missense_variant 2549/6781 2423/2580 808/859 Q/P cAg/cCg 1 1 CDHR1 HGNC HGNC:14550 protein_coding YES CCDS7372.1 ENSP00000485478 Q96JP9 F1T0L2 UPI0000161C2F NM_033100.3 tolerated_low_confidence(0.3) 17/17 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF340 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 84214464 84214464 A C 1 0 0 0 0 1 0 0 0 2821 188 7 5 5 CDHR1 10 84214464 Missense_Mutation SNP A C3N-00560_T 3570450 84214464 49582958 710 17399 LIPK 0 . GRCh38 10 88737663 88737663 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.698C>A p.Pro233His p.P233H ENST00000404190 6/9 162 115 47 145 145 0 strelka-varscan-mutect LIPK,missense_variant,p.Pro233His,ENST00000404190,NM_001080518.1; A ENST00000404190 Transcript missense_variant 698/1230 698/1200 233/399 P/H cCt/cAt 1 1 LIPK HGNC HGNC:23444 protein_coding YES CCDS44455.1 ENSP00000383900 Q5VXJ0 UPI00000497BC NM_001080518.1 tolerated(0.1) 6/9 hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF45,PIRSF_domain:PIRSF000862,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 88737663 88737663 C A 1 0 0 0 0 1 0 0 0 8748 681 24 2 2 LIPK 10 88737663 Missense_Mutation SNP C C3N-00560_T 4523199 88737663 45059759 711 17400 HTR7 0 . GRCh38 10 90749338 90749338 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.796G>T p.Ala266Ser p.A266S ENST00000336152 2/4 253 181 72 217 217 0 strelka-varscan-mutect HTR7,missense_variant,p.Ala266Ser,ENST00000336152,NM_019859.3;HTR7,missense_variant,p.Ala266Ser,ENST00000371719,NM_019860.3;HTR7,missense_variant,p.Ala266Ser,ENST00000277874,NM_000872.4; A ENST00000336152 Transcript missense_variant 823/3126 796/1440 266/479 A/S Gcc/Tcc 1 -1 HTR7 HGNC HGNC:5302 protein_coding YES CCDS7408.1 ENSP00000337949 P34969 UPI0000049B68 NM_019859.3 tolerated(0.14) 2/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF116,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00652 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 90749338 90749338 C A 1 0 0 0 0 1 0 0 0 7348 710 25 2 2 HTR7 10 90749338 Missense_Mutation SNP C C3N-00560_T 2011675 90749338 43048084 712 17401 RRP12 0 . GRCh38 10 97370233 97370233 + Missense_Mutation SNP C C A rs750295475 C3N-00560_T C3N-00560_N C C c.2731G>T p.Val911Leu p.V911L ENST00000536831 25/35 154 103 51 140 140 0 strelka-varscan-mutect RRP12,missense_variant,p.Val911Leu,ENST00000536831,;RRP12,missense_variant,p.Val911Leu,ENST00000370992,NM_015179.3;RRP12,missense_variant,p.Val850Leu,ENST00000414986,NM_001145114.1;RRP12,missense_variant,p.Val811Leu,ENST00000315563,NM_001284337.1;RRP12,upstream_gene_variant,,ENST00000487612,;RRP12,non_coding_transcript_exon_variant,,ENST00000479481,;RRP12,downstream_gene_variant,,ENST00000490815,;RRP12,upstream_gene_variant,,ENST00000491313,; A ENST00000536831 Transcript missense_variant 2920/4476 2731/3894 911/1297 V/L Gtg/Ttg rs750295475 1 -1 RRP12 HGNC HGNC:29100 protein_coding YES CCDS7457.1 ENSP00000446184 Q5JTH9 UPI000013E51C tolerated(0.25) 25/35 hmmpanther:PTHR21576,hmmpanther:PTHR21576:SF2,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs750295475 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 97370233 97370233 C A 1 0 0 0 0 1 0 0 0 13941 507 18 2 2 RRP12 10 97370233 Missense_Mutation SNP C C3N-00560_T 6620895 97370233 36427189 713 17402 ZFYVE27 0 . GRCh38 10 97757713 97757713 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.1176G>T p.Met392Ile p.M392I ENST00000423811 12/13 235 155 80 174 174 0 strelka-varscan-mutect ZFYVE27,missense_variant,p.Met387Ile,ENST00000393677,NM_144588.6;ZFYVE27,missense_variant,p.Met392Ile,ENST00000423811,NM_001002261.3;ZFYVE27,missense_variant,p.Met380Ile,ENST00000359980,NM_001002262.3;ZFYVE27,missense_variant,p.Met348Ile,ENST00000337540,NM_001174119.1;ZFYVE27,missense_variant,p.Met287Ile,ENST00000370610,NM_001174121.1;ZFYVE27,missense_variant,p.Met294Ile,ENST00000357540,NM_001174120.1;ZFYVE27,missense_variant,p.Met262Ile,ENST00000370613,NM_001174122.1;ZFYVE27,non_coding_transcript_exon_variant,,ENST00000477521,;ZFYVE27,non_coding_transcript_exon_variant,,ENST00000473237,; T ENST00000423811 Transcript missense_variant 1375/3045 1176/1251 392/416 M/I atG/atT COSM4742751 1 1 ZFYVE27 HGNC HGNC:26559 protein_coding YES CCDS31262.1 ENSP00000409594 Q5T4F4 UPI00003FE526 NM_001002261.3 deleterious(0.01) 12/13 PROSITE_profiles:PS50178,hmmpanther:PTHR14543,Gene3D:3.30.40.10,Pfam_domain:PF01363,SMART_domains:SM00064,Superfamily_domains:SSF57903 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 97757713 97757713 G T 1 0 0 0 0 1 0 0 0 18246 1348 47 2 2 ZFYVE27 10 97757713 Missense_Mutation SNP G C3N-00560_T 387480 97757713 36039709 714 17403 DNMBP 0 . GRCh38 10 99898213 99898213 + Silent SNP C C A rs866818939 C3N-00560_T C3N-00560_N C C c.2793G>T p.= p.L931L ENST00000324109 9/17 392 287 105 342 342 0 strelka-varscan-mutect DNMBP,synonymous_variant,p.=,ENST00000324109,NM_015221.2;DNMBP,synonymous_variant,p.=,ENST00000636706,NM_001318326.1;DNMBP,synonymous_variant,p.=,ENST00000543621,NM_001318327.1; A ENST00000324109 Transcript synonymous_variant 2885/6400 2793/4734 931/1577 L ctG/ctT rs866818939 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 9/17 PROSITE_profiles:PS50010,hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834,PROSITE_patterns:PS00741,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 1 1 PASS rs866818939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 99898213 99898213 C A 1 0 0 0 0 0 0 0 1 4487 465 17 2 2 DNMBP 10 99898213 Silent SNP C C3N-00560_T 2140500 99898213 33899209 715 17404 CPN1 0 . GRCh38 10 100065212 100065212 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.735G>T p.= p.T245T ENST00000370418 4/9 104 75 29 98 98 0 strelka-varscan-mutect CPN1,synonymous_variant,p.=,ENST00000370418,NM_001308.2;CPN1,synonymous_variant,p.=,ENST00000441382,; A ENST00000370418 Transcript synonymous_variant 987/1863 735/1377 245/458 T acG/acT 1 -1 CPN1 HGNC HGNC:2312 protein_coding YES CCDS7486.1 ENSP00000359446 P15169 UPI00000012AC NM_001308.2 4/9 hmmpanther:PTHR11532:SF7,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS rs986069911 . 0 200 10 0 0 0 0 0 -20 0.999995 1 1 1 0 A 2 1 56 100065212 100065212 C A 1 0 0 0 0 0 0 0 1 3604 755 27 1 1 CPN1 10 100065212 Silent SNP C C3N-00560_T 166999 100065212 33732210 716 17405 PAX2 0 . GRCh38 10 100749851 100749851 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.149G>T p.Arg50Leu p.R50L ENST00000370296 2/11 117 85 32 121 121 0 strelka-varscan-mutect PAX2,missense_variant,p.Arg50Leu,ENST00000370296,NM_003988.3;PAX2,missense_variant,p.Arg50Leu,ENST00000428433,NM_003987.3,NM_003990.3;PAX2,missense_variant,p.Arg50Leu,ENST00000355243,NM_001304569.1,NM_000278.3,NM_003989.3;PAX2,missense_variant,p.Arg49Leu,ENST00000361791,;PAX2,missense_variant,p.Arg54Leu,ENST00000554172,;PAX2,missense_variant,p.Arg50Leu,ENST00000427256,;PAX2,intron_variant,,ENST00000554363,;PAX2,intron_variant,,ENST00000553492,;PAX2,non_coding_transcript_exon_variant,,ENST00000483202,; T ENST00000370296 Transcript missense_variant 699/4140 149/1191 50/396 R/L cGg/cTg 1 1 PAX2 HGNC HGNC:8616 protein_coding YES CCDS7499.1 ENSP00000359319 Q02962 UPI000016AE71 NM_003988.3 deleterious(0) 2/11 PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF172,PROSITE_patterns:PS00034,Gene3D:1.10.10.10,Pfam_domain:PF00292,SMART_domains:SM00351,Superfamily_domains:SSF46689,Prints_domain:PR00027 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 100749851 100749851 G T 1 0 0 0 0 1 0 0 0 11564 1116 39 1 1 PAX2 10 100749851 Missense_Mutation SNP G C3N-00560_T 684639 100749851 33047571 717 17406 C10orf76 0 . GRCh38 10 101939903 101939903 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.1741delG p.Glu581LysfsTer6 p.E581Kfs*6 ENST00000370033 23/26 218 164 54 204 204 0 sindel-varindel-pindel C10orf76,frameshift_variant,p.Glu581LysfsTer6,ENST00000370033,NM_024541.2; - ENST00000370033 Transcript frameshift_variant 1861/4119 1741/2070 581/689 E/X Gaa/aa 1 -1 C10orf76 HGNC HGNC:25788 protein_coding YES CCDS41563.1 ENSP00000359050 Q5T2E6 UPI000047005B NM_024541.2 23/26 hmmpanther:PTHR13608,hmmpanther:PTHR13608:SF3,Pfam_domain:PF08427,SMART_domains:SM01158,Superfamily_domains:SSF48371 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 101939903 101939903 C - 1 0 1 0 1 0 0 0 0 1770 864 30 0 0 C10orf76 10 101939903 Frame_Shift_Del DEL C C3N-00560_T 1190052 101939903 31857519 718 17407 PSD 0 . GRCh38 10 102416664 102416664 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.375G>T p.= p.R125R ENST00000020673 2/17 126 83 43 99 99 0 strelka-varscan-mutect PSD,synonymous_variant,p.=,ENST00000020673,NM_002779.4;PSD,synonymous_variant,p.=,ENST00000406432,NM_001270965.1;PSD,intron_variant,,ENST00000611678,NM_001270966.1;FBXL15,upstream_gene_variant,,ENST00000224862,NM_024326.3;FBXL15,upstream_gene_variant,,ENST00000369956,;FBXL15,upstream_gene_variant,,ENST00000432590,;FBXL15,upstream_gene_variant,,ENST00000440407,;FBXL15,upstream_gene_variant,,ENST00000425536,;FBXL15,upstream_gene_variant,,ENST00000457067,;PSD,non_coding_transcript_exon_variant,,ENST00000472685,;PSD,downstream_gene_variant,,ENST00000492902,;FBXL15,upstream_gene_variant,,ENST00000481808,;PSD,upstream_gene_variant,,ENST00000488194,; A ENST00000020673 Transcript synonymous_variant 902/4183 375/3075 125/1024 R cgG/cgT 1 -1 PSD HGNC HGNC:9507 protein_coding YES CCDS31272.1 ENSP00000020673 A5PKW4 UPI0000404928 NM_002779.4 2/17 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 102416664 102416664 C A 1 0 0 0 0 0 0 0 1 12797 842 30 2 2 PSD 10 102416664 Silent SNP C C3N-00560_T 476761 102416664 31380758 719 17408 CFAP43 0 . GRCh38 10 104207746 104207746 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.814G>T p.Glu272Ter p.E272* ENST00000357060 6/38 173 129 44 153 153 0 strelka-varscan-mutect CFAP43,stop_gained,p.Glu272Ter,ENST00000357060,NM_025145.5;CFAP43,stop_gained,p.Glu202Ter,ENST00000278064,;CFAP43,stop_gained,p.Glu202Ter,ENST00000369720,;CFAP43,stop_gained,p.Glu202Ter,ENST00000369719,; A ENST00000357060 Transcript stop_gained 930/5365 814/4998 272/1665 E/* Gaa/Taa 1 -1 CFAP43 HGNC HGNC:26684 protein_coding YES CCDS31281.1 ENSP00000349568 Q8NDM7 UPI0000D60FC7 NM_025145.5 6/38 hmmpanther:PTHR14885,hmmpanther:PTHR14885:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 104207746 104207746 C A 1 0 0 0 0 0 1 0 0 3018 835 29 2 2 CFAP43 10 104207746 Nonsense_Mutation SNP C C3N-00560_T 1791082 104207746 29589676 720 17409 CFAP58 0 . GRCh38 10 104400815 104400815 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1951G>C p.Asp651His p.D651H ENST00000369704 13/18 273 190 83 228 228 0 strelka-varscan-mutect CFAP58,missense_variant,p.Asp651His,ENST00000369704,NM_001008723.1; C ENST00000369704 Transcript missense_variant 2085/3313 1951/2619 651/872 D/H Gac/Cac 1 1 CFAP58 HGNC HGNC:26676 protein_coding YES CCDS31282.1 ENSP00000358718 Q5T655 UPI0000160405 NM_001008723.1 deleterious(0) 13/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 104400815 104400815 G C 1 0 0 0 0 1 0 0 0 3027 1174 41 4 4 CFAP58 10 104400815 Missense_Mutation SNP G C3N-00560_T 193069 104400815 29396607 721 17410 SORCS3 0 . GRCh38 10 105262417 105262417 + Missense_Mutation SNP C C G rs759046110 C3N-00560_T C3N-00560_N C C c.3530C>G p.Ala1177Gly p.A1177G ENST00000369701 26/27 223 173 50 224 224 0 strelka-varscan-mutect SORCS3,missense_variant,p.Ala1177Gly,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Ala1177Gly,ENST00000369699,; G ENST00000369701 Transcript missense_variant 3757/5757 3530/3669 1177/1222 A/G gCc/gGc rs759046110,COSM3952795 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 tolerated(0.15) 26/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759046110 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 105262417 105262417 C G 1 0 0 0 0 1 0 0 0 15254 739 26 4 4 SORCS3 10 105262417 Missense_Mutation SNP C C3N-00560_T 861602 105262417 28535005 722 17411 GPAM 0 . GRCh38 10 112160750 112160750 + Missense_Mutation SNP T T A rs750371327 C3N-00560_T C3N-00560_N T T c.1613A>T p.Gln538Leu p.Q538L ENST00000348367 16/22 512 376 136 481 481 0 strelka-varscan-mutect GPAM,missense_variant,p.Gln538Leu,ENST00000348367,NM_001244949.1,NM_020918.5;GPAM,missense_variant,p.Gln538Leu,ENST00000369425,; A ENST00000348367 Transcript missense_variant 1811/6371 1613/2487 538/828 Q/L cAg/cTg rs750371327 1 -1 GPAM HGNC HGNC:24865 protein_coding YES CCDS7570.1 ENSP00000265276 Q9HCL2 UPI000004AC02 NM_001244949.1,NM_020918.5 tolerated(0.22) 16/22 hmmpanther:PTHR12563,hmmpanther:PTHR12563:SF16,PIRSF_domain:PIRSF500064,PIRSF_domain:PIRSF000437 MODERATE 1 SNV 1 1 PASS rs750371327 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 112160750 112160750 T A 1 0 0 0 0 1 0 0 0 6484 1580 55 4 4 GPAM 10 112160750 Missense_Mutation SNP T C3N-00560_T 6898333 112160750 21636672 723 17412 HABP2 0 . GRCh38 10 113575974 113575974 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.301G>T p.Ala101Ser p.A101S ENST00000351270 4/13 172 125 47 151 151 0 strelka-varscan-mutect HABP2,missense_variant,p.Ala101Ser,ENST00000351270,NM_004132.3;HABP2,missense_variant,p.Ala75Ser,ENST00000542051,NM_001177660.1; T ENST00000351270 Transcript missense_variant 397/3009 301/1683 101/560 A/S Gct/Tct COSM1739635 1 1 HABP2 HGNC HGNC:4798 protein_coding YES CCDS7577.1 ENSP00000277903 Q14520 UPI0000049411 NM_004132.3 tolerated(0.61) 4/13 PROSITE_profiles:PS50026,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Pfam_domain:PF00008,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999744 1 1 1 0 T 3 4 56 113575974 113575974 G T 1 0 0 0 0 1 0 0 0 6820 1203 42 2 2 HABP2 10 113575974 Missense_Mutation SNP G C3N-00560_T 1415224 113575974 20221448 724 17413 PNLIP 0 . GRCh38 10 116548391 116548391 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.233G>T p.Gly78Val p.G78V ENST00000369221 4/13 100 66 34 100 100 0 strelka-varscan-mutect PNLIP,missense_variant,p.Gly78Val,ENST00000369221,NM_000936.2;PNLIP,non_coding_transcript_exon_variant,,ENST00000470562,; T ENST00000369221 Transcript missense_variant 261/1483 233/1398 78/465 G/V gGc/gTc 1 1 PNLIP HGNC HGNC:9155 protein_coding YES CCDS7594.1 ENSP00000358223 P16233 UPI000004F1A0 NM_000936.2 tolerated(0.06) 4/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Prints_domain:PR00821,Prints_domain:PR00823,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF85,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs1274565673 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 116548391 116548391 G T 1 0 0 0 0 1 0 0 0 12257 1203 42 2 2 PNLIP 10 116548391 Missense_Mutation SNP G C3N-00560_T 2972417 116548391 17249031 725 17414 HSPA12A 0 . GRCh38 10 116698641 116698641 + Silent SNP C C A rs545779576 C3N-00560_T C3N-00560_N C C c.540G>T p.= p.A180A ENST00000369209 5/12 130 82 48 67 67 0 strelka-varscan-mutect HSPA12A,synonymous_variant,p.=,ENST00000635765,;HSPA12A,synonymous_variant,p.=,ENST00000369209,NM_025015.2;HSPA12A,downstream_gene_variant,,ENST00000468935,;HSPA12A,non_coding_transcript_exon_variant,,ENST00000481291,; A ENST00000369209 Transcript synonymous_variant 645/5722 540/2028 180/675 A gcG/gcT rs545779576,COSM1474392 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 5/12 Gene3D:3.30.420.40,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46,Superfamily_domains:SSF53067 0,1 LOW 1 SNV 1 0,1 1 PASS rs545779576 . 0 200 9 0 0 0 0 0 -20 0.9999989 1 1 1 0 A 2 1 56 116698641 116698641 C A 1 0 0 0 0 0 0 0 1 7300 755 27 1 1 HSPA12A 10 116698641 Silent SNP C C3N-00560_T 150250 116698641 17098781 726 17415 EIF3A 0 . GRCh38 10 119036057 119036057 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4131G>T p.Trp1377Cys p.W1377C ENST00000369144 22/22 249 177 72 171 171 0 varscan-mutect EIF3A,missense_variant,p.Trp1377Cys,ENST00000369144,NM_003750.2;EIF3A,missense_variant,p.Trp1377Cys,ENST00000541549,;NANOS1,downstream_gene_variant,,ENST00000425699,NM_199461.2;NANOS1,downstream_gene_variant,,ENST00000340087,; A ENST00000369144 Transcript missense_variant 4259/6646 4131/4149 1377/1382 W/C tgG/tgT 1 -1 EIF3A HGNC HGNC:3271 protein_coding YES CCDS7608.1 ENSP00000358140 Q14152 UPI000012D311 NM_003750.2 deleterious_low_confidence(0) 22/22 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 119036057 119036057 C A 1 0 0 0 0 1 0 0 0 4846 856 30 2 2 EIF3A 10 119036057 Missense_Mutation SNP C C3N-00560_T 2337416 119036057 14761365 727 17416 FGFR2 0 . GRCh38 10 121551370 121551370 + Missense_Mutation SNP C C A rs200766273 C3N-00560_T C3N-00560_N C C c.544G>T p.Gly182Trp p.G182W ENST00000457416 5/18 413 296 117 304 303 1 strelka-varscan-mutect FGFR2,missense_variant,p.Gly93Trp,ENST00000613048,NM_023029.2;FGFR2,missense_variant,p.Gly182Trp,ENST00000358487,NM_001320658.1,NM_000141.4;FGFR2,missense_variant,p.Gly182Trp,ENST00000369061,NM_001144914.1;FGFR2,missense_variant,p.Gly93Trp,ENST00000357555,NM_001144915.1;FGFR2,missense_variant,p.Gly67Trp,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,missense_variant,p.Gly182Trp,ENST00000369060,NM_001144917.1;FGFR2,missense_variant,p.Gly182Trp,ENST00000457416,NM_022970.3;FGFR2,missense_variant,p.Gly67Trp,ENST00000369059,;FGFR2,missense_variant,p.Gly93Trp,ENST00000360144,NM_001144919.1;FGFR2,missense_variant,p.Gly182Trp,ENST00000369058,;FGFR2,missense_variant,p.Gly182Trp,ENST00000369056,NM_001144913.1;FGFR2,missense_variant,p.Gly93Trp,ENST00000336553,;FGFR2,missense_variant,p.Gly182Trp,ENST00000351936,;FGFR2,missense_variant,p.Gly182Trp,ENST00000346997,;FGFR2,missense_variant,p.Gly182Trp,ENST00000359354,;FGFR2,non_coding_transcript_exon_variant,,ENST00000490349,;FGFR2,missense_variant,p.Gly67Trp,ENST00000604236,; A ENST00000457416 Transcript missense_variant 1136/3061 544/2469 182/822 G/W Ggg/Tgg rs200766273 1 -1 FGFR2 HGNC HGNC:3689 protein_coding YES CCDS7620.2 ENSP00000410294 P21802 UPI000002A99A NM_022970.3 deleterious(0.02) 5/18 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF130,Gene3D:2.60.40.10,Pfam_domain:PF07679,PIRSF_domain:PIRSF000628,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs200766273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 121551370 121551370 C A 1 0 0 0 0 1 0 0 0 5730 652 23 1 1 FGFR2 10 121551370 Missense_Mutation SNP C C3N-00560_T 2515313 121551370 12246052 728 17417 TACC2 0 . GRCh38 10 122085809 122085809 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3309G>T p.Trp1103Cys p.W1103C ENST00000369005 4/23 121 80 41 128 128 0 strelka-varscan-mutect TACC2,missense_variant,p.Trp1103Cys,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Trp1103Cys,ENST00000334433,;TACC2,missense_variant,p.Trp1103Cys,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Trp1103Cys,ENST00000453444,;TACC2,missense_variant,p.Trp1103Cys,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; T ENST00000369005 Transcript missense_variant 3649/9673 3309/8847 1103/2948 W/C tgG/tgT 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious(0) 4/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 122085809 122085809 G T 1 0 0 0 0 1 0 0 0 15898 1241 43 2 2 TACC2 10 122085809 Missense_Mutation SNP G C3N-00560_T 534439 122085809 11711613 729 17418 DMBT1 0 . GRCh38 10 122598954 122598955 + Frame_Shift_Ins INS - - T novel C3N-00560_T C3N-00560_N - - c.3137_3138insT p.Arg1047ProfsTer13 p.R1047Pfs*13 ENST00000368909 26/53 621 444 177 565 565 0 sindel-varindel DMBT1,frameshift_variant,p.Arg1047ProfsTer13,ENST00000338354,NM_001320644.1;DMBT1,frameshift_variant,p.Arg1047ProfsTer13,ENST00000368909,NM_001320644.1,NM_007329.2;DMBT1,frameshift_variant,p.Arg1047ProfsTer13,ENST00000619379,NM_001320644.1;DMBT1,frameshift_variant,p.Arg1037ProfsTer13,ENST00000344338,;DMBT1,frameshift_variant,p.Arg1037ProfsTer13,ENST00000368955,NM_017579.2;DMBT1,frameshift_variant,p.Arg548ProfsTer13,ENST00000330163,;DMBT1,frameshift_variant,p.Arg548ProfsTer13,ENST00000368956,NM_004406.2;DMBT1,intron_variant,,ENST00000359586,; T ENST00000368909 Transcript frameshift_variant 3243-3244/7686 3137-3138/7242 1046/2413 A/AX gcc/gcTc 1 1 DMBT1 HGNC HGNC:2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 UPI000047021C NM_001320644.1,NM_007329.2 26/53 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF22,SMART_domains:SM00202,Superfamily_domains:SSF56487 HIGH 1 insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 56 122598954 122598954 - T 1 0 1 1 0 0 0 0 0 4384 739 26 0 0 DMBT1 10 122598954 Frame_Shift_Ins INS - C3N-00560_T 513145 122598954 11198468 730 17419 CTBP2 0 . GRCh38 10 125026447 125026447 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1313G>C p.Gly438Ala p.G438A ENST00000309035 1/9 67 51 16 59 59 0 strelka-varscan-mutect CTBP2,missense_variant,p.Gly438Ala,ENST00000309035,NM_022802.2;CTBP2,intron_variant,,ENST00000337195,NM_001329.2;CTBP2,intron_variant,,ENST00000411419,NM_001083914.1;CTBP2,intron_variant,,ENST00000494626,NM_001290214.1;CTBP2,intron_variant,,ENST00000531469,NM_001290215.1;CTBP2,intron_variant,,ENST00000460976,;CTBP2,intron_variant,,ENST00000493552,; G ENST00000309035 Transcript missense_variant 1444/3669 1313/2958 438/985 G/A gGg/gCg 1 -1 CTBP2 HGNC HGNC:2495 protein_coding YES CCDS7644.1 ENSP00000311825 P56545 UPI000013EE11 NM_022802.2 tolerated_low_confidence(0.11) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 125026447 125026447 C G 1 0 0 0 0 1 0 0 0 3804 623 22 4 4 CTBP2 10 125026447 Missense_Mutation SNP C C3N-00560_T 2427493 125026447 8770975 731 17420 DPYSL4 0 . GRCh38 10 132192712 132192712 + Missense_Mutation SNP C C G rs749104221 C3N-00560_T C3N-00560_N C C c.183C>G p.His61Gln p.H61Q ENST00000338492 3/14 166 118 48 112 112 0 strelka-varscan-mutect DPYSL4,missense_variant,p.His61Gln,ENST00000338492,NM_006426.2;DPYSL4,upstream_gene_variant,,ENST00000368627,;DPYSL4,non_coding_transcript_exon_variant,,ENST00000493882,;DPYSL4,non_coding_transcript_exon_variant,,ENST00000493927,; G ENST00000338492 Transcript missense_variant 347/2729 183/1719 61/572 H/Q caC/caG rs749104221 1 1 DPYSL4 HGNC HGNC:3016 protein_coding YES CCDS7665.1 ENSP00000339850 O14531 UPI000013DC70 NM_006426.2 tolerated(0.6) 3/14 Gene3D:2.30.40.10,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF55,Superfamily_domains:SSF51338,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS rs749104221 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 132192712 132192712 C G 1 0 0 0 0 1 0 0 0 4564 535 19 4 4 DPYSL4 10 132192712 Missense_Mutation SNP C C3N-00560_T 7166265 132192712 1604710 732 17421 INPP5A 0 . GRCh38 10 132780889 132780889 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1130G>C p.Gly377Ala p.G377A ENST00000368594 14/16 276 210 66 240 239 1 strelka-varscan-mutect INPP5A,missense_variant,p.Gly377Ala,ENST00000368594,NM_005539.3;INPP5A,missense_variant,p.Gly59Ala,ENST00000445580,;NKX6-2,downstream_gene_variant,,ENST00000368592,NM_177400.2;INPP5A,downstream_gene_variant,,ENST00000368593,;INPP5A,downstream_gene_variant,,ENST00000342652,;NKX6-2,downstream_gene_variant,,ENST00000441365,; C ENST00000368594 Transcript missense_variant 1407/2967 1130/1239 377/412 G/A gGg/gCg 1 1 INPP5A HGNC HGNC:6076 protein_coding YES CCDS7669.2 ENSP00000357583 Q14642 UPI000012D085 NM_005539.3 deleterious(0) 14/16 hmmpanther:PTHR12997,hmmpanther:PTHR12997:SF9,Gene3D:3.60.10.10,Pfam_domain:PF03372,SMART_domains:SM00128,Superfamily_domains:SSF56219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 132780889 132780889 G C 1 0 0 0 0 1 0 0 0 7657 1232 43 4 4 INPP5A 10 132780889 Missense_Mutation SNP G C3N-00560_T 588177 132780889 1016533 733 17422 MUC6 0 . GRCh38 11 1018566 1018566 + Missense_Mutation SNP G G T rs771673875 C3N-00560_T C3N-00560_N G G c.4235C>A p.Ala1412Glu p.A1412E ENST00000421673 31/33 148 80 68 178 178 0 strelka-varscan-mutect MUC6,missense_variant,p.Ala1412Glu,ENST00000421673,NM_005961.2;MUC6,upstream_gene_variant,,ENST00000532016,;MUC6,downstream_gene_variant,,ENST00000527242,; T ENST00000421673 Transcript missense_variant 4286/8006 4235/7320 1412/2439 A/E gCg/gAg rs771673875 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 tolerated_low_confidence(0.6) 31/33 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs771673875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 1018566 1018566 G T 1 0 0 0 0 1 0 0 0 9980 1087 38 1 1 MUC6 11 1018566 Missense_Mutation SNP G C3N-00560_T 1018566 134068056 734 17423 MUC5AC 0 . GRCh38 11 1188846 1188846 + Silent SNP C C G novel C3N-00560_T C3N-00560_N C C c.10701C>G p.= p.L3567L ENST00000621226 31/49 72 38 34 58 58 0 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; G ENST00000621226 Transcript synonymous_variant 10748/17448 10701/16965 3567/5654 L ctC/ctG 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 31/49 Pfam_domain:PF13330 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 1188846 1188846 C G 1 0 0 0 0 0 0 0 1 9978 842 30 4 4 MUC5AC 11 1188846 Silent SNP C C3N-00560_T 170280 1188846 133897776 735 17424 IGF2 0 . GRCh38 11 2133586 2133586 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.405C>A p.= p.L135L ENST00000434045 4/5 158 82 76 204 204 0 strelka-varscan-mutect IGF2,synonymous_variant,p.=,ENST00000416167,NM_000612.5;IGF2,synonymous_variant,p.=,ENST00000381406,;IGF2,synonymous_variant,p.=,ENST00000381395,NM_001007139.5,NM_001291861.2;IGF2,synonymous_variant,p.=,ENST00000434045,NM_001127598.2;IGF2,synonymous_variant,p.=,ENST00000381389,NM_001291862.2;IGF2,synonymous_variant,p.=,ENST00000381392,;IGF2,synonymous_variant,p.=,ENST00000418738,;MIR483,downstream_gene_variant,,ENST00000385070,;AC132217.4,upstream_gene_variant,,ENST00000430034,;INS-IGF2,3_prime_UTR_variant,,ENST00000356578,; T ENST00000434045 Transcript synonymous_variant 790/1583 405/711 135/236 L ctC/ctA 1 -1 IGF2 HGNC HGNC:5466 protein_coding YES CCDS44517.1 ENSP00000391826 P01344 UPI0001751501 NM_001127598.2 4/5 Gene3D:1.10.100.10,Pfam_domain:PF00049,Prints_domain:PR00276,Prints_domain:PR02002,Prints_domain:PR02006,PROSITE_patterns:PS00262,hmmpanther:PTHR11454,hmmpanther:PTHR11454:SF10,SMART_domains:SM00078,Superfamily_domains:SSF56994 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 2133586 2133586 G T 1 0 0 0 0 0 0 0 1 7478 1161 41 2 2 IGF2 11 2133586 Silent SNP G C3N-00560_T 944740 2133586 132953036 736 17425 OR51T1 0 . GRCh38 11 4882592 4882593 + Frame_Shift_Del DEL GG GG - novel C3N-00560_T C3N-00560_N GG GG c.774_775delGG p.Ala259ProfsTer44 p.A259Pfs*44 ENST00000380378 1/1 138 101 37 215 215 0 sindel-varindel-pindel OR51T1,frameshift_variant,p.Ala259ProfsTer44,ENST00000380378,NM_001004759.1;OR51T1,frameshift_variant,p.Ala232ProfsTer44,ENST00000322049,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; - ENST00000380378 Transcript frameshift_variant 774-775/1065 774-775/1065 258-259/354 VA/VX gtGGcc/gtcc 1 1 OR51T1 HGNC HGNC:15205 protein_coding YES CCDS31363.1 ENSP00000369738 A0A0C4DFX5 UPI000015F1FF NM_001004759.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF6,Superfamily_domains:SSF81321 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 4882592 4882592 GG - 1 0 1 0 1 0 0 0 0 11180 1335 47 0 0 OR51T1 11 4882592 Frame_Shift_Del DEL GG C3N-00560_T 2749006 4882592 130204030 737 17426 OR51A4 0 . GRCh38 11 4946993 4946993 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.108G>A p.Met36Ile p.M36I ENST00000380373 1/1 206 166 40 246 246 0 strelka-varscan-mutect OR51A4,missense_variant,p.Met36Ile,ENST00000380373,NM_001005329.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000380373 Transcript missense_variant 108/942 108/942 36/313 M/I atG/atA 1 -1 OR51A4 HGNC HGNC:14795 protein_coding YES CCDS31367.1 ENSP00000369731 Q8NGJ6 UPI0000047195 NM_001005329.1 tolerated(0.24) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF168,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 4946993 4946993 C T 1 0 0 0 0 1 0 0 0 11162 478 17 3 3 OR51A4 11 4946993 Missense_Mutation SNP C C3N-00560_T 64401 4946993 130139629 738 17427 OR51A2 0 . GRCh38 11 4955606 4955606 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.108G>A p.Met36Ile p.M36I ENST00000380371 1/1 16 11 5 20 20 0 strelka-varscan-mutect OR51A2,missense_variant,p.Met36Ile,ENST00000380371,NM_001004748.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000380371 Transcript missense_variant 108/942 108/942 36/313 M/I atG/atA 1 -1 OR51A2 HGNC HGNC:14764 protein_coding YES CCDS31368.1 ENSP00000369729 Q8NGJ7 A0A126GWD5 UPI0000041B7B NM_001004748.1 tolerated(0.26) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF168,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 1 206 3 0 0 0 0 0 -15.75659 1 1 1 1 0 T 3 4 56 4955606 4955606 C T 1 0 0 0 0 1 0 0 0 11161 478 17 3 3 OR51A2 11 4955606 Missense_Mutation SNP C C3N-00560_T 8613 4955606 130131016 739 17428 OR51B5 0 . GRCh38 11 5342936 5342936 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.589C>G p.Pro197Ala p.P197A ENST00000300773 1/1 125 80 45 154 154 0 strelka-varscan-mutect OR51B5,missense_variant,p.Pro197Ala,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,;AC104389.28,downstream_gene_variant,,ENST00000418729,; C ENST00000300773 Transcript missense_variant 589/939 589/939 197/312 P/A Cca/Gca 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 tolerated(0.36) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 5342936 5342936 G C 1 0 0 0 0 1 0 0 0 11165 1232 43 4 4 OR51B5 11 5342936 Missense_Mutation SNP G C3N-00560_T 387330 5342936 129743686 740 17429 OR52N2 0 . GRCh38 11 5820497 5820497 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.162G>C p.Glu54Asp p.E54D ENST00000317037 1/1 98 47 51 96 96 0 strelka-varscan-mutect OR52N2,missense_variant,p.Glu54Asp,ENST00000317037,NM_001005174.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; C ENST00000317037 Transcript missense_variant 184/1035 162/966 54/321 E/D gaG/gaC 1 1 OR52N2 HGNC HGNC:15228 protein_coding YES CCDS31399.1 ENSP00000322801 Q8NGI0 UPI0000041BEB NM_001005174.1 tolerated(0.1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF185,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs895070476 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 5820497 5820497 G C 1 0 0 0 0 1 0 0 0 11201 991 35 4 4 OR52N2 11 5820497 Missense_Mutation SNP G C3N-00560_T 477561 5820497 129266125 741 17430 OR6A2 0 . GRCh38 11 6795192 6795192 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.517T>A p.Tyr173Asn p.Y173N ENST00000332601 1/1 364 259 105 267 267 0 strelka-varscan-mutect OR6A2,missense_variant,p.Tyr173Asn,ENST00000332601,NM_003696.2; T ENST00000332601 Transcript missense_variant 592/1157 517/984 173/327 Y/N Tac/Aac 1 -1 OR6A2 HGNC HGNC:15301 protein_coding YES CCDS7772.1 ENSP00000330384 O95222 A0A126GW91 UPI0000061E92 NM_003696.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF234,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs768106044 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 6795192 6795192 A T 1 0 0 0 0 1 0 0 0 11254 362 13 4 4 OR6A2 11 6795192 Missense_Mutation SNP A C3N-00560_T 974695 6795192 128291430 742 17431 DKK3 0 . GRCh38 11 11998719 11998719 + Missense_Mutation SNP C C A rs765767133 C3N-00560_T C3N-00560_N C C c.412G>T p.Asp138Tyr p.D138Y ENST00000396505 4/8 417 286 131 277 277 0 strelka-varscan-mutect DKK3,missense_variant,p.Asp138Tyr,ENST00000396505,NM_015881.5;DKK3,missense_variant,p.Asp138Tyr,ENST00000326932,NM_001018057.1,NM_013253.4;DKK3,missense_variant,p.Asp138Tyr,ENST00000525493,;DKK3,missense_variant,p.Asp138Tyr,ENST00000533813,;DKK3,intron_variant,,ENST00000534511,;DKK3,intron_variant,,ENST00000529338,;DKK3,non_coding_transcript_exon_variant,,ENST00000526218,;DKK3,non_coding_transcript_exon_variant,,ENST00000532873,;DKK3,intron_variant,,ENST00000527132,;DKK3,downstream_gene_variant,,ENST00000533900,;DKK3,downstream_gene_variant,,ENST00000530694,;DKK3,upstream_gene_variant,,ENST00000528188,;DKK3,non_coding_transcript_exon_variant,,ENST00000531309,;DKK3,downstream_gene_variant,,ENST00000534479,; A ENST00000396505 Transcript missense_variant 651/2650 412/1053 138/350 D/Y Gac/Tac rs765767133 1 -1 DKK3 HGNC HGNC:2893 protein_coding YES CCDS7808.1 ENSP00000379762 Q9UBP4 UPI00001694CA NM_015881.5 deleterious(0.01) 4/8 hmmpanther:PTHR12113:SF8,hmmpanther:PTHR12113 MODERATE 1 SNV 1 1 PASS rs765767133 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 11998719 11998719 C A 1 0 0 0 0 1 0 0 0 4352 913 32 2 2 DKK3 11 11998719 Missense_Mutation SNP C C3N-00560_T 5203527 11998719 123087903 743 17432 RASSF10 0 . GRCh38 11 13010784 13010784 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1208G>T p.Arg403Leu p.R403L ENST00000529419 1/1 248 161 87 191 190 1 strelka-varscan-mutect RASSF10,missense_variant,p.Arg403Leu,ENST00000529419,NM_001080521.2;CTC-497E21.3,upstream_gene_variant,,ENST00000533002,; T ENST00000529419 Transcript missense_variant 1208/2530 1208/1524 403/507 R/L cGg/cTg 1 1 RASSF10 HGNC HGNC:33984 protein_coding YES ENSP00000485526 A6NK89 UPI0001722D5E NM_001080521.2 deleterious(0) 1/1 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF13 MODERATE SNV 1 PASS rs1384812045 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 13010784 13010784 G T 1 0 0 0 0 1 0 0 0 13246 1116 39 1 1 RASSF10 11 13010784 Missense_Mutation SNP G C3N-00560_T 1012065 13010784 122075838 744 17433 PLEKHA7 0 . GRCh38 11 16817018 16817018 + Missense_Mutation SNP C C A rs775610890 C3N-00560_T C3N-00560_N C C c.1648G>T p.Asp550Tyr p.D550Y ENST00000355661 11/23 72 44 28 61 61 0 strelka-varscan-mutect PLEKHA7,missense_variant,p.Asp550Tyr,ENST00000355661,NM_175058.4;PLEKHA7,missense_variant,p.Asp550Tyr,ENST00000531066,;PLEKHA7,missense_variant,p.Asp181Tyr,ENST00000530489,;PLEKHA7,missense_variant,p.Asp449Tyr,ENST00000637162,;PLEKHA7,intron_variant,,ENST00000532079,;PLEKHA7,upstream_gene_variant,,ENST00000636113,;PLEKHA7,upstream_gene_variant,,ENST00000525581,;PLEKHA7,non_coding_transcript_exon_variant,,ENST00000525781,;PLEKHA7,upstream_gene_variant,,ENST00000525049,; A ENST00000355661 Transcript missense_variant 1659/4980 1648/3366 550/1121 D/Y Gac/Tac rs775610890,COSM5248496 1 -1 PLEKHA7 HGNC HGNC:27049 protein_coding YES CCDS31434.1 ENSP00000347883 Q6IQ23 UPI0000456498 NM_175058.4 tolerated(0.13) 11/23 hmmpanther:PTHR12752:SF4,hmmpanther:PTHR12752 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775610890 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 16817018 16817018 C A 1 0 0 0 0 1 0 0 0 12154 884 31 1 1 PLEKHA7 11 16817018 Missense_Mutation SNP C C3N-00560_T 3806234 16817018 118269604 745 17434 SPTY2D1 0 . GRCh38 11 18614719 18614719 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1555G>T p.Gly519Ter p.G519* ENST00000336349 3/6 142 92 50 104 104 0 strelka-varscan-mutect SPTY2D1,stop_gained,p.Gly519Ter,ENST00000336349,NM_194285.2;SPTY2D1-AS1,downstream_gene_variant,,ENST00000636011,;SPTY2D1,downstream_gene_variant,,ENST00000543776,;SPTY2D1,non_coding_transcript_exon_variant,,ENST00000536336,;SPTY2D1-AS1,downstream_gene_variant,,ENST00000501599,; A ENST00000336349 Transcript stop_gained 1791/5754 1555/2058 519/685 G/* Gga/Tga 1 -1 SPTY2D1 HGNC HGNC:26818 protein_coding YES CCDS31441.1 ENSP00000337991 Q68D10 UPI00001607F0 NM_194285.2 3/6 hmmpanther:PTHR22691,hmmpanther:PTHR22691:SF8 HIGH 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 4 1 56 18614719 18614719 C A 1 0 0 0 0 0 1 0 0 15484 632 22 2 2 SPTY2D1 11 18614719 Nonsense_Mutation SNP C C3N-00560_T 1797701 18614719 116471903 746 17435 SLC17A6 0 . GRCh38 11 22370147 22370147 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1000C>A p.Pro334Thr p.P334T ENST00000263160 8/12 137 102 35 213 213 0 strelka-varscan-mutect SLC17A6,missense_variant,p.Pro334Thr,ENST00000263160,NM_020346.2; A ENST00000263160 Transcript missense_variant 1437/3949 1000/1749 334/582 P/T Cca/Aca 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 deleterious(0.01) 8/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 22370147 22370147 C A 1 0 0 0 0 1 0 0 0 14686 739 26 2 2 SLC17A6 11 22370147 Missense_Mutation SNP C C3N-00560_T 3755428 22370147 112716475 747 17436 KCNA4 0 . GRCh38 11 30012504 30012504 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.175G>T p.Gly59Trp p.G59W ENST00000328224 2/2 164 125 39 176 176 0 strelka-varscan-mutect KCNA4,missense_variant,p.Gly59Trp,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript missense_variant 1409/4172 175/1962 59/653 G/W Ggg/Tgg COSM3670751 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 deleterious_low_confidence(0) 2/2 Gene3D:1kn7A00,Pfam_domain:PF07941,Prints_domain:PR01511,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 30012504 30012504 C A 1 0 0 0 0 1 0 0 0 7921 594 21 2 2 KCNA4 11 30012504 Missense_Mutation SNP C C3N-00560_T 7642357 30012504 105074118 748 17437 KIAA1549L 0 . GRCh38 11 33542675 33542675 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.221G>C p.Ser74Thr p.S74T ENST00000321505 1/20 129 87 42 106 106 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Ser74Thr,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Ser74Thr,ENST00000265654,;KIAA1549L,intron_variant,,ENST00000526400,; C ENST00000321505 Transcript missense_variant 401/11678 221/5550 74/1849 S/T aGc/aCc 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 tolerated_low_confidence(1) 1/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 MODERATE 1 SNV 1 1 PASS rs1340350622 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 33542675 33542675 G C 1 0 0 0 0 1 0 0 0 8121 971 34 4 4 KIAA1549L 11 33542675 Missense_Mutation SNP G C3N-00560_T 3530171 33542675 101543947 749 17438 LRRC4C 0 . GRCh38 11 40115230 40115230 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1063G>T p.Val355Leu p.V355L ENST00000278198 2/2 152 74 78 212 211 1 strelka-varscan-mutect LRRC4C,missense_variant,p.Val355Leu,ENST00000278198,;LRRC4C,missense_variant,p.Val355Leu,ENST00000527150,;LRRC4C,missense_variant,p.Val355Leu,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Val355Leu,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Val355Leu,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; A ENST00000278198 Transcript missense_variant 3027/4054 1063/1923 355/640 V/L Gtg/Ttg 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 tolerated(0.3) 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Pfam_domain:PF07679,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 40115230 40115230 C A 1 0 0 0 0 1 0 0 0 8903 507 18 2 2 LRRC4C 11 40115230 Missense_Mutation SNP C C3N-00560_T 6572555 40115230 94971392 750 17439 TTC17 0 . GRCh38 11 43391481 43391481 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.436G>A p.Asp146Asn p.D146N ENST00000039989 4/24 84 54 30 128 128 0 strelka-varscan-mutect TTC17,missense_variant,p.Asp146Asn,ENST00000039989,NM_018259.5;TTC17,missense_variant,p.Asp146Asn,ENST00000299240,NM_001307943.1;RP11-484D2.4,intron_variant,,ENST00000394183,;TTC17,upstream_gene_variant,,ENST00000526774,;TTC17,3_prime_UTR_variant,,ENST00000534347,;TTC17,non_coding_transcript_exon_variant,,ENST00000530469,; A ENST00000039989 Transcript missense_variant 450/4469 436/3426 146/1141 D/N Gac/Aac 1 1 TTC17 HGNC HGNC:25596 protein_coding YES CCDS31466.1 ENSP00000039989 Q96AE7 UPI000006E6C7 NM_018259.5 tolerated(0.09) 4/24 hmmpanther:PTHR16091 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 43391481 43391481 G A 1 0 0 0 0 1 0 0 0 17193 942 33 3 3 TTC17 11 43391481 Missense_Mutation SNP G C3N-00560_T 3276251 43391481 91695141 751 17440 ACCS 0 . GRCh38 11 44083295 44083295 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1238G>T p.Trp413Leu p.W413L ENST00000263776 13/15 123 74 49 136 136 0 strelka-varscan-mutect ACCS,missense_variant,p.Trp413Leu,ENST00000263776,NM_001127219.1,NM_032592.3;ACCS,non_coding_transcript_exon_variant,,ENST00000527346,;ACCS,non_coding_transcript_exon_variant,,ENST00000534035,;ACCS,downstream_gene_variant,,ENST00000531940,;ACCS,downstream_gene_variant,,ENST00000531505,;ACCS,downstream_gene_variant,,ENST00000531190,;ACCS,downstream_gene_variant,,ENST00000532122,;ACCS,downstream_gene_variant,,ENST00000527557,; T ENST00000263776 Transcript missense_variant 1672/2362 1238/1506 413/501 W/L tGg/tTg 1 1 ACCS HGNC HGNC:23989 protein_coding YES CCDS7907.1 ENSP00000263776 Q96QU6 A0A0S2Z622 UPI000006D45A NM_001127219.1,NM_032592.3 deleterious(0) 13/15 hmmpanther:PTHR11751,hmmpanther:PTHR11751:SF375,Gene3D:3.90.1150.10,Pfam_domain:PF00155,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs1417232724 . 0 206 0 4 0 0 0 0 -20 0.9999875 1 1 1 0 T 3 4 56 44083295 44083295 G T 1 0 0 0 0 1 0 0 0 171 1357 47 2 2 ACCS 11 44083295 Missense_Mutation SNP G C3N-00560_T 691814 44083295 91003327 752 17441 LRP4 0 . GRCh38 11 46869022 46869022 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4803G>T p.Met1601Ile p.M1601I ENST00000378623 32/38 479 255 224 574 574 0 strelka-varscan-mutect LRP4,missense_variant,p.Met1601Ile,ENST00000378623,NM_002334.3;LRP4-AS1,intron_variant,,ENST00000502049,;LRP4-AS1,intron_variant,,ENST00000531719,;LRP4,downstream_gene_variant,,ENST00000527656,; A ENST00000378623 Transcript missense_variant 5046/8076 4803/5718 1601/1905 M/I atG/atT 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 deleterious(0.03) 32/38 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 46869022 46869022 C A 1 0 0 0 0 1 0 0 0 8854 594 21 2 2 LRP4 11 46869022 Missense_Mutation SNP C C3N-00560_T 2785727 46869022 88217600 753 17442 TRIM49B 0 . GRCh38 11 49034177 49034177 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.539G>T p.Arg180Ile p.R180I ENST00000622138 5/8 247 156 91 409 409 0 strelka-varscan-mutect TRIM49B,missense_variant,p.Arg180Ile,ENST00000622138,;TRIM49B,missense_variant,p.Arg180Ile,ENST00000332682,NM_001206626.1; T ENST00000622138 Transcript missense_variant 868/2162 539/1359 180/452 R/I aGa/aTa 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 deleterious(0) 5/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310 MODERATE 1 SNV 5 1 PASS rs1319639592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 49034177 49034177 G T 1 0 0 0 0 1 0 0 0 17015 942 33 2 2 TRIM49B 11 49034177 Missense_Mutation SNP G C3N-00560_T 2165155 49034177 86052445 754 17443 OR8H2 0 . GRCh38 11 56105179 56105179 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.137T>C p.Met46Thr p.M46T ENST00000313503 1/1 195 131 64 262 261 1 strelka-varscan-mutect OR8H2,missense_variant,p.Met45Thr,ENST00000618136,;OR8H2,missense_variant,p.Met46Thr,ENST00000313503,NM_001005200.1; C ENST00000313503 Transcript missense_variant 137/939 137/939 46/312 M/T aTg/aCg 1 1 OR8H2 HGNC HGNC:15308 protein_coding YES CCDS31518.1 ENSP00000323982 Q8N162 UPI0000041D0C NM_001005200.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 56105179 56105179 T C 1 0 0 0 0 1 0 0 0 11306 1464 51 5 5 OR8H2 11 56105179 Missense_Mutation SNP T C3N-00560_T 7071002 56105179 78981443 755 17444 OR5T2 0 . GRCh38 11 56232322 56232322 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.864A>G p.= p.S288S ENST00000313264 1/1 61 31 30 48 48 0 strelka-varscan-mutect OR5T2,synonymous_variant,p.=,ENST00000313264,NM_001004746.1; C ENST00000313264 Transcript synonymous_variant 864/1080 864/1080 288/359 S tcA/tcG 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 56232322 56232322 T C 1 0 0 0 0 0 0 0 1 11250 1799 63 5 5 OR5T2 11 56232322 Silent SNP T C3N-00560_T 127143 56232322 78854300 756 17445 OR5T3 0 . GRCh38 11 56252813 56252813 + Missense_Mutation SNP G G T rs867632332 C3N-00560_T C3N-00560_N G G c.614G>T p.Arg205Met p.R205M ENST00000303059 1/1 226 146 80 295 295 0 strelka-varscan-mutect OR5T3,missense_variant,p.Arg205Met,ENST00000303059,NM_001004747.1; T ENST00000303059 Transcript missense_variant 614/1023 614/1023 205/340 R/M aGg/aTg rs867632332 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs867632332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 56252813 56252813 G T 1 0 0 0 0 1 0 0 0 11251 1000 35 2 2 OR5T3 11 56252813 Missense_Mutation SNP G C3N-00560_T 20491 56252813 78833809 757 17446 OR8J1 0 . GRCh38 11 56360397 56360397 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.151G>A p.Val51Ile p.V51I ENST00000303039 1/1 145 83 62 203 203 0 strelka-varscan-mutect OR8J1,missense_variant,p.Val51Ile,ENST00000303039,NM_001005205.2;RPL5P29,downstream_gene_variant,,ENST00000482972,; A ENST00000303039 Transcript missense_variant 183/1074 151/951 51/316 V/I Gtt/Att 1 1 OR8J1 HGNC HGNC:14855 protein_coding YES CCDS31529.1 ENSP00000304060 Q8NGP2 UPI000004BE58 NM_001005205.2 tolerated(0.37) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF317,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 56360397 56360397 G A 1 0 0 0 0 1 0 0 0 11309 1377 48 3 3 OR8J1 11 56360397 Missense_Mutation SNP G C3N-00560_T 107584 56360397 78726225 758 17447 OR9G1 0 . GRCh38 11 56701036 56701036 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.649T>A p.Tyr217Asn p.Y217N ENST00000312153 1/1 355 262 93 452 452 0 strelka-varscan-mutect OR9G1,missense_variant,p.Tyr217Asn,ENST00000312153,NM_001005213.1; A ENST00000312153 Transcript missense_variant 649/918 649/918 217/305 Y/N Tac/Aac 1 1 OR9G1 HGNC HGNC:15319 protein_coding YES CCDS31536.1 ENSP00000309012 Q8NH87 UPI0000061E7E NM_001005213.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF158,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 56701036 56701036 T A 1 0 0 0 0 1 0 0 0 11317 1522 53 4 4 OR9G1 11 56701036 Missense_Mutation SNP T C3N-00560_T 340639 56701036 78385586 759 17448 CLP1 0 . GRCh38 11 57660940 57660940 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.782G>T p.Arg261Leu p.R261L ENST00000533682 3/3 203 130 73 237 237 0 strelka-varscan-mutect CLP1,missense_variant,p.Arg261Leu,ENST00000533682,;CLP1,missense_variant,p.Arg272Leu,ENST00000529430,;CLP1,missense_variant,p.Arg197Leu,ENST00000302731,NM_001142597.1;CLP1,missense_variant,p.Arg261Leu,ENST00000525602,NM_006831.2;CLP1,downstream_gene_variant,,ENST00000529773,;CLP1,downstream_gene_variant,,ENST00000533905,; T ENST00000533682 Transcript missense_variant 1507/2435 782/1278 261/425 R/L cGa/cTa 1 1 CLP1 HGNC HGNC:16999 protein_coding YES CCDS7964.1 ENSP00000434995 Q92989 UPI000012754A tolerated(0.06) 3/3 HAMAP:MF_03035,hmmpanther:PTHR12755,Pfam_domain:PF16575,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57660940 57660940 G T 1 0 0 0 0 1 0 0 0 3320 1058 37 1 1 CLP1 11 57660940 Missense_Mutation SNP G C3N-00560_T 959904 57660940 77425682 760 17449 DTX4 0 . GRCh38 11 59204786 59204786 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1737G>T p.Lys579Asn p.K579N ENST00000227451 9/9 313 170 143 398 398 0 strelka-varscan-mutect DTX4,missense_variant,p.Lys579Asn,ENST00000227451,NM_015177.1;DTX4,missense_variant,p.Lys473Asn,ENST00000532982,NM_001300727.1;MPEG1,downstream_gene_variant,,ENST00000361050,NM_001039396.1;DTX4,downstream_gene_variant,,ENST00000527475,; T ENST00000227451 Transcript missense_variant 1841/5642 1737/1860 579/619 K/N aaG/aaT 1 1 DTX4 HGNC HGNC:29151 protein_coding YES CCDS44612.1 ENSP00000227451 Q9Y2E6 UPI00001C1F00 NM_015177.1 deleterious(0) 9/9 hmmpanther:PTHR12622:SF5,hmmpanther:PTHR12622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 59204786 59204786 G T 1 0 0 0 0 1 0 0 0 4620 933 33 2 2 DTX4 11 59204786 Missense_Mutation SNP G C3N-00560_T 1543846 59204786 75881836 761 17450 ZP1 0 . GRCh38 11 60867578 60867578 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.17C>G p.Ala6Gly p.A6G ENST00000278853 1/12 90 56 34 120 120 0 strelka-varscan-mutect ZP1,missense_variant,p.Ala6Gly,ENST00000278853,NM_207341.3;ZP1,upstream_gene_variant,,ENST00000537203,;ZP1,upstream_gene_variant,,ENST00000542971,;ZP1,upstream_gene_variant,,ENST00000540908,; G ENST00000278853 Transcript missense_variant 17/1954 17/1917 6/638 A/G gCc/gGc 1 1 ZP1 HGNC HGNC:13187 protein_coding YES CCDS31572.1 ENSP00000278853 P60852 V9HWI9 UPI0000351AA0 NM_207341.3 deleterious_low_confidence(0.05) 1/12 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999934 1 1 1 0 G 3 3 56 60867578 60867578 C G 1 0 0 0 0 1 0 0 0 18807 739 26 4 4 ZP1 11 60867578 Missense_Mutation SNP C C3N-00560_T 1662792 60867578 74219044 762 17451 PGA5 0 . GRCh38 11 61248350 61248350 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.126G>T p.Glu42Asp p.E42D ENST00000451616 1/4 519 289 230 567 567 0 strelka-varscan-mutect PGA5,missense_variant,p.Glu42Asp,ENST00000451616,;PGA5,intron_variant,,ENST00000312403,NM_014224.3;PGA5,upstream_gene_variant,,ENST00000541528,;CTD-2331C18.5,intron_variant,,ENST00000537594,;PGA5,downstream_gene_variant,,ENST00000536269,;PGA5,downstream_gene_variant,,ENST00000535568,; T ENST00000451616 Transcript missense_variant 229/971 126/705 42/234 E/D gaG/gaT 1 1 PGA5 HGNC HGNC:8887 protein_coding ENSP00000408739 C9JM59 UPI000204AD8D tolerated_low_confidence(0.21) 1/4 PROSITE_profiles:PS51767 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 61248350 61248350 G T 1 0 0 0 0 1 0 0 0 11862 991 35 2 2 PGA5 11 61248350 Missense_Mutation SNP G C3N-00560_T 380772 61248350 73838272 763 17452 DDB1 0 . GRCh38 11 61311820 61311820 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.2241G>T p.= p.G747G ENST00000301764 18/27 111 68 43 125 123 2 strelka-varscan-mutect DDB1,synonymous_variant,p.=,ENST00000301764,NM_001923.4;DDB1,intron_variant,,ENST00000543658,;DDB1,downstream_gene_variant,,ENST00000545930,;DDB1,downstream_gene_variant,,ENST00000538280,;DDB1,synonymous_variant,p.=,ENST00000540166,;DDB1,non_coding_transcript_exon_variant,,ENST00000535147,;DDB1,downstream_gene_variant,,ENST00000414411,;DDB1,upstream_gene_variant,,ENST00000539332,;DDB1,downstream_gene_variant,,ENST00000539739,;DDB1,downstream_gene_variant,,ENST00000535967,;DDB1,downstream_gene_variant,,ENST00000537877,;DDB1,downstream_gene_variant,,ENST00000540784,;DDB1,downstream_gene_variant,,ENST00000535174,; A ENST00000301764 Transcript synonymous_variant 2639/4506 2241/3423 747/1140 G ggG/ggT 1 -1 DDB1 HGNC HGNC:2717 protein_coding YES CCDS31576.1 ENSP00000301764 Q16531 UPI0000000CB7 NM_001923.4 18/27 hmmpanther:PTHR10644 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 61311820 61311820 C A 1 0 0 0 0 0 0 0 1 4126 610 22 2 2 DDB1 11 61311820 Silent SNP C C3N-00560_T 63470 61311820 73774802 764 17453 PPP1R32 0 . GRCh38 11 61482427 61482427 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.226G>T p.Gly76Trp p.G76W ENST00000338608 3/14 95 47 48 136 136 0 strelka-mutect PPP1R32,missense_variant,p.Gly76Trp,ENST00000338608,NM_145017.2;PPP1R32,missense_variant,p.Gly76Trp,ENST00000432063,NM_001170753.1;PPP1R32,upstream_gene_variant,,ENST00000542951,;RP11-286N22.8,downstream_gene_variant,,ENST00000541135,;PPP1R32,upstream_gene_variant,,ENST00000535545,;RP11-286N22.8,intron_variant,,ENST00000544880,;RP11-286N22.8,downstream_gene_variant,,ENST00000544025,;RP11-286N22.8,splice_region_variant,,ENST00000544801,;RP11-286N22.8,intron_variant,,ENST00000538594,;RP11-286N22.8,downstream_gene_variant,,ENST00000543044,; T ENST00000338608 Transcript missense_variant,splice_region_variant 351/1535 226/1278 76/425 G/W Ggg/Tgg 1 1 PPP1R32 HGNC HGNC:28869 protein_coding YES CCDS8008.1 ENSP00000344140 Q7Z5V6 G3F4G3 UPI000013E13F NM_145017.2 deleterious(0) 3/14 Pfam_domain:PF15691,hmmpanther:PTHR34349 MODERATE 1 SNV 1 1 PASS rs902541948 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 61482427 61482427 G T 1 0 0 0 0 1 0 0 0 12488 1246 43 2 2 PPP1R32 11 61482427 Missense_Mutation SNP G C3N-00560_T 170607 61482427 73604195 765 17454 MTA2 0 . GRCh38 11 62594040 62594040 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1842G>T p.Arg614Ser p.R614S ENST00000278823 18/18 67 36 31 65 65 0 strelka-varscan-mutect MTA2,missense_variant,p.Arg614Ser,ENST00000278823,NM_004739.3;MTA2,missense_variant,p.Arg441Ser,ENST00000524902,;MTA2,missense_variant,p.Arg441Ser,ENST00000527204,;TUT1,upstream_gene_variant,,ENST00000476907,;TUT1,upstream_gene_variant,,ENST00000308436,NM_022830.2;TUT1,upstream_gene_variant,,ENST00000494385,;TUT1,upstream_gene_variant,,ENST00000278279,;RP11-864I4.1,upstream_gene_variant,,ENST00000496634,;TUT1,upstream_gene_variant,,ENST00000478537,;MTA2,downstream_gene_variant,,ENST00000526844,;MTA2,downstream_gene_variant,,ENST00000531179,;MTA2,downstream_gene_variant,,ENST00000531261,;MTA2,downstream_gene_variant,,ENST00000532239,; A ENST00000278823 Transcript missense_variant,splice_region_variant 2232/3058 1842/2007 614/668 R/S agG/agT 1 -1 MTA2 HGNC HGNC:7411 protein_coding YES CCDS8022.1 ENSP00000278823 O94776 A0A024R534 UPI000012F743 NM_004739.3 deleterious_low_confidence(0.03) 18/18 hmmpanther:PTHR10865:SF4,hmmpanther:PTHR10865 MODERATE 1 SNV 1 1 PASS rs1460436914 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 62594040 62594040 C A 1 0 0 0 0 1 0 0 0 9894 637 22 2 2 MTA2 11 62594040 Missense_Mutation SNP C C3N-00560_T 1111613 62594040 72492582 766 17455 LRRN4CL 0 . GRCh38 11 62688295 62688295 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.214C>T p.= p.L72L ENST00000317449 2/2 151 72 79 177 177 0 strelka-varscan-mutect LRRN4CL,synonymous_variant,p.=,ENST00000317449,NM_203422.3;BSCL2,downstream_gene_variant,,ENST00000405837,;BSCL2,downstream_gene_variant,,ENST00000403550,;BSCL2,downstream_gene_variant,,ENST00000360796,NM_001122955.3;BSCL2,downstream_gene_variant,,ENST00000407022,NM_032667.6;BSCL2,downstream_gene_variant,,ENST00000421906,;BSCL2,downstream_gene_variant,,ENST00000278893,NM_001130702.2;BSCL2,downstream_gene_variant,,ENST00000448568,;BSCL2,downstream_gene_variant,,ENST00000524862,;BSCL2,downstream_gene_variant,,ENST00000531524,;BSCL2,downstream_gene_variant,,ENST00000449636,;BSCL2,downstream_gene_variant,,ENST00000403098,;BSCL2,downstream_gene_variant,,ENST00000412351,;BSCL2,downstream_gene_variant,,ENST00000526426,;BSCL2,downstream_gene_variant,,ENST00000532115,;HNRNPUL2-BSCL2,downstream_gene_variant,,ENST00000403734,;BSCL2,downstream_gene_variant,,ENST00000301781,;BSCL2,downstream_gene_variant,,ENST00000463679,;BSCL2,downstream_gene_variant,,ENST00000468505,;BSCL2,downstream_gene_variant,,ENST00000470529,; A ENST00000317449 Transcript synonymous_variant 692/2585 214/717 72/238 L Ctg/Ttg 1 -1 LRRN4CL HGNC HGNC:33724 protein_coding YES CCDS8030.1 ENSP00000325808 Q8ND94 UPI00000359F7 NM_203422.3 2/2 hmmpanther:PTHR24366 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 62688295 62688295 G A 1 0 0 0 0 0 0 0 1 8944 991 35 3 3 LRRN4CL 11 62688295 Silent SNP G C3N-00560_T 94255 62688295 72398327 767 17456 RTN3 0 . GRCh38 11 63704907 63704907 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.199G>T p.Glu67Ter p.E67* ENST00000377819 2/9 128 74 54 176 176 0 strelka-varscan-mutect RTN3,stop_gained,p.Glu67Ter,ENST00000377819,NM_001265589.1;RTN3,missense_variant,p.Val67Leu,ENST00000356000,NM_201429.2;RTN3,missense_variant,p.Ala67Ser,ENST00000545432,;RTN3,intron_variant,,ENST00000339997,NM_201428.2;RTN3,intron_variant,,ENST00000540798,NM_001265590.1;RTN3,intron_variant,,ENST00000537981,NM_006054.3;RTN3,intron_variant,,ENST00000341307,NM_201430.2;RTN3,intron_variant,,ENST00000354497,NM_001265591.1;RTN3,intron_variant,,ENST00000542238,;RTN3,intron_variant,,ENST00000543552,;RTN3,splice_region_variant,,ENST00000338850,;RTN3,intron_variant,,ENST00000538995,;RTN3,intron_variant,,ENST00000536011,;RTN3,intron_variant,,ENST00000543123,; T ENST00000377819 Transcript stop_gained,splice_region_variant 353/4937 199/3099 67/1032 E/* Gag/Tag 1 1 RTN3 HGNC HGNC:10469 protein_coding YES CCDS58141.1 ENSP00000367050 O95197 UPI00004546A2 NM_001265589.1 2/9 hmmpanther:PTHR10994,hmmpanther:PTHR10994:SF1 HIGH 1 SNV 1 1 PASS rs1274064715 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 63704907 63704907 G T 1 0 0 0 0 0 1 0 0 13987 1014 35 2 2 RTN3 11 63704907 Nonsense_Mutation SNP G C3N-00560_T 1016612 63704907 71381715 768 17457 SLC22A12 0 . GRCh38 11 64593655 64593655 + Silent SNP C C A rs748654094 C3N-00560_T C3N-00560_N C C c.682C>A p.= p.R228R ENST00000377574 4/10 257 152 105 302 302 0 strelka-varscan-mutect SLC22A12,synonymous_variant,p.=,ENST00000377574,NM_144585.3;SLC22A12,synonymous_variant,p.=,ENST00000473690,NM_153378.2;SLC22A12,synonymous_variant,p.=,ENST00000336464,NM_001276326.1;SLC22A12,intron_variant,,ENST00000377572,NM_001276327.1;SLC22A12,intron_variant,,ENST00000377567,; A ENST00000377574 Transcript synonymous_variant 1429/3206 682/1662 228/553 R Cgg/Agg rs748654094,COSM5213971 1 1 SLC22A12 HGNC HGNC:17989 protein_coding YES CCDS8075.1 ENSP00000366797 Q96S37 UPI0000040C17 NM_144585.3 4/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF205,Superfamily_domains:SSF103473 0,1 LOW 1 SNV 1 0,1 1 PASS rs748654094 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 64593655 64593655 C A 1 0 0 0 0 0 0 0 1 14709 527 19 1 1 SLC22A12 11 64593655 Silent SNP C C3N-00560_T 888748 64593655 70492967 769 17458 NRXN2 0 . GRCh38 11 64685670 64685670 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1128C>A p.= p.V376V ENST00000265459 6/23 406 222 184 511 511 0 strelka-varscan-mutect NRXN2,synonymous_variant,p.=,ENST00000265459,NM_015080.3;NRXN2,synonymous_variant,p.=,ENST00000377559,NM_138732.2;NRXN2,synonymous_variant,p.=,ENST00000409571,;NRXN2,synonymous_variant,p.=,ENST00000377551,;NRXN2,synonymous_variant,p.=,ENST00000442300,;NRXN2,synonymous_variant,p.=,ENST00000437746,;NRXN2,synonymous_variant,p.=,ENST00000417749,;NRXN2,non_coding_transcript_exon_variant,,ENST00000466324,; T ENST00000265459 Transcript synonymous_variant 1590/6621 1128/5139 376/1712 V gtC/gtA 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 6/23 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF593,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 64685670 64685670 G T 1 0 0 0 0 0 0 0 1 10725 1161 41 2 2 NRXN2 11 64685670 Silent SNP G C3N-00560_T 92015 64685670 70400952 770 17459 ZFPL1 0 . GRCh38 11 65086586 65086586 + Missense_Mutation SNP G G T rs747733761 C3N-00560_T C3N-00560_N G G c.386G>T p.Arg129Leu p.R129L ENST00000294258 4/8 124 66 58 163 163 0 strelka-varscan-mutect ZFPL1,missense_variant,p.Arg129Leu,ENST00000294258,NM_006782.3;ZFPL1,missense_variant,p.Arg129Leu,ENST00000532200,;ZFPL1,missense_variant,p.Arg129Leu,ENST00000526334,;ZFPL1,missense_variant,p.Arg123Leu,ENST00000526945,;ZFPL1,intron_variant,,ENST00000530488,;CDCA5,upstream_gene_variant,,ENST00000275517,NM_080668.3;CDCA5,upstream_gene_variant,,ENST00000404147,;VPS51,upstream_gene_variant,,ENST00000528588,;TMEM262,downstream_gene_variant,,ENST00000530719,NM_001282448.1;ZFPL1,downstream_gene_variant,,ENST00000525509,;TMEM262,downstream_gene_variant,,ENST00000524603,;TMEM262,downstream_gene_variant,,ENST00000524632,NM_001242631.2;ZFPL1,downstream_gene_variant,,ENST00000526791,;ZFPL1,3_prime_UTR_variant,,ENST00000453524,;ZFPL1,3_prime_UTR_variant,,ENST00000531761,;TMEM262,non_coding_transcript_exon_variant,,ENST00000528029,;ZFPL1,non_coding_transcript_exon_variant,,ENST00000528123,;ZFPL1,intron_variant,,ENST00000530744,;ZFPL1,downstream_gene_variant,,ENST00000533216,;CDCA5,upstream_gene_variant,,ENST00000479032,;ZFPL1,downstream_gene_variant,,ENST00000526289,;CDCA5,upstream_gene_variant,,ENST00000531401,;CDCA5,upstream_gene_variant,,ENST00000524733,;ZFPL1,downstream_gene_variant,,ENST00000526440,;CDCA5,upstream_gene_variant,,ENST00000527430,;TMEM262,downstream_gene_variant,,ENST00000334821,;CDCA5,upstream_gene_variant,,ENST00000462902,;CDCA5,upstream_gene_variant,,ENST00000533015,;TMEM262,downstream_gene_variant,,ENST00000525544,; T ENST00000294258 Transcript missense_variant 538/1371 386/933 129/310 R/L cGg/cTg rs747733761,COSM1676170,COSM2165020 1 1 ZFPL1 HGNC HGNC:12868 protein_coding YES CCDS8092.1 ENSP00000294258 O95159 A0A024R576 UPI000007347E NM_006782.3 deleterious(0) 4/8 hmmpanther:PTHR12981,hmmpanther:PTHR12981:SF0 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747733761 . 0 205 0 5 0 0 0 0 -20 0.9999458 1 1 1 0 T 3 4 56 65086586 65086586 G T 1 0 0 0 0 1 0 0 0 18234 1116 39 1 1 ZFPL1 11 65086586 Missense_Mutation SNP G C3N-00560_T 400916 65086586 70000036 771 17460 NPAS4 0 . GRCh38 11 66422842 66422842 + Missense_Mutation SNP G G T rs777027579 C3N-00560_T C3N-00560_N G G c.599G>T p.Arg200Leu p.R200L ENST00000311034 4/8 296 153 143 323 322 1 strelka-varscan-mutect NPAS4,missense_variant,p.Arg200Leu,ENST00000311034,NM_178864.3;NPAS4,missense_variant,p.Arg200Leu,ENST00000525148,;NPAS4,upstream_gene_variant,,ENST00000524617,; T ENST00000311034 Transcript missense_variant 775/3303 599/2409 200/802 R/L cGc/cTc rs777027579,COSM194386 1 1 NPAS4 HGNC HGNC:18983 protein_coding YES CCDS8138.1 ENSP00000311196 Q8IUM7 UPI0000074744 NM_178864.3 deleterious(0.01) 4/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF24,hmmpanther:PTHR23043 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777027579 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 66422842 66422842 G T 1 0 0 0 0 1 0 0 0 10613 1087 38 1 1 NPAS4 11 66422842 Missense_Mutation SNP G C3N-00560_T 1336256 66422842 68663780 772 17461 LRFN4 0 . GRCh38 11 66858561 66858561 + Missense_Mutation SNP G G A C3N-00560_T C3N-00560_N G G c.817G>A p.Glu273Lys p.E273K ENST00000309602 1/2 53 26 27 68 68 0 strelka-varscan-mutect LRFN4,missense_variant,p.Glu273Lys,ENST00000309602,NM_024036.4;LRFN4,missense_variant,p.Glu273Lys,ENST00000393952,;PC,intron_variant,,ENST00000393960,NM_001040716.1;PC,intron_variant,,ENST00000393958,NM_000920.3;PC,intron_variant,,ENST00000393955,NM_022172.2;PC,downstream_gene_variant,,ENST00000524491,;PC,downstream_gene_variant,,ENST00000628663,;PC,intron_variant,,ENST00000530187,;LRFN4,downstream_gene_variant,,ENST00000531590,; A ENST00000309602 Transcript missense_variant 1060/2431 817/1908 273/635 E/K Gag/Aag COSM4559746 1 1 LRFN4 HGNC HGNC:28456 protein_coding YES CCDS8153.1 ENSP00000312535 Q6PJG9 A0A024R5I6 UPI0000001C10 NM_024036.4 deleterious(0) 1/2 hmmpanther:PTHR24373:SF151,hmmpanther:PTHR24373,Gene3D:3.80.10.10,SMART_domains:SM00082,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS rs1162648844 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 66858561 66858561 G A 1 0 0 0 0 1 0 0 0 8834 1059 37 1 1 LRFN4 11 66858561 Missense_Mutation SNP G C3N-00560_T 435719 66858561 68228061 773 17462 TESMIN 0 . GRCh38 11 68713403 68713403 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1025G>A p.Cys342Tyr p.C342Y ENST00000255087 8/10 151 84 67 159 159 0 strelka-varscan-mutect TESMIN,missense_variant,p.Cys342Tyr,ENST00000255087,NM_004923.3;TESMIN,missense_variant,p.Cys35Tyr,ENST00000543240,;TESMIN,upstream_gene_variant,,ENST00000544398,; T ENST00000255087 Transcript missense_variant 1209/2579 1025/1527 342/508 C/Y tGt/tAt 1 -1 TESMIN HGNC HGNC:7446 protein_coding YES CCDS8184.1 ENSP00000255087 Q9Y4I5 UPI00001FAE07 NM_004923.3 deleterious(0.02) 8/10 PROSITE_profiles:PS51634,hmmpanther:PTHR12446:SF22,hmmpanther:PTHR12446 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 68713403 68713403 C T 1 0 0 0 0 1 0 0 0 16188 492 17 3 3 TESMIN 11 68713403 Missense_Mutation SNP C C3N-00560_T 1854842 68713403 66373219 774 17463 MRGPRF 0 . GRCh38 11 69005427 69005427 + Missense_Mutation SNP C C G rs758658446 C3N-00560_T C3N-00560_N C C c.883G>C p.Gly295Arg p.G295R ENST00000309099 3/3 188 127 61 231 231 0 strelka-varscan-mutect MRGPRF,missense_variant,p.Gly295Arg,ENST00000309099,NM_145015.4;MRGPRF,missense_variant,p.Gly295Arg,ENST00000441623,NM_001098515.1;MRGPRF,downstream_gene_variant,,ENST00000320913,;RP11-554A11.4,upstream_gene_variant,,ENST00000562276,;RP11-554A11.5,downstream_gene_variant,,ENST00000562506,; G ENST00000309099 Transcript missense_variant 1266/2295 883/1032 295/343 G/R Ggg/Cgg rs758658446 1 -1 MRGPRF HGNC HGNC:24828 protein_coding YES CCDS8188.1 ENSP00000309782 Q96AM1 A0A024R5F0 UPI000012F566 NM_145015.4 deleterious(0) 3/3 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF3,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs758658446 . 0 208 0 0 2 0 0 0 -20 0.9992325 1 1 1 0 G 3 3 56 69005427 69005427 C G 1 0 0 0 0 1 0 0 0 9731 652 23 4 4 MRGPRF 11 69005427 Missense_Mutation SNP C C3N-00560_T 292024 69005427 66081195 775 17464 ANO1 0 . GRCh38 11 70170974 70170974 + Missense_Mutation SNP G G T rs770919354 C3N-00560_T C3N-00560_N G G c.2285G>T p.Arg762Leu p.R762L ENST00000355303 22/26 154 94 60 200 200 0 strelka-varscan-mutect ANO1,missense_variant,p.Arg762Leu,ENST00000355303,NM_018043.5;ANO1,missense_variant,p.Arg471Leu,ENST00000531349,;ANO1,missense_variant,p.Arg616Leu,ENST00000530676,;ANO1,non_coding_transcript_exon_variant,,ENST00000525494,;ANO1,non_coding_transcript_exon_variant,,ENST00000529636,; T ENST00000355303 Transcript missense_variant 2590/4790 2285/2961 762/986 R/L cGc/cTc rs770919354 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 deleterious(0) 22/26 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 MODERATE 1 SNV 1 1 PASS rs770919354 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 70170974 70170974 G T 1 0 0 0 0 1 0 0 0 802 1087 38 1 1 ANO1 11 70170974 Missense_Mutation SNP G C3N-00560_T 1165547 70170974 64915648 776 17465 PCF11 0 . GRCh38 11 83184772 83184772 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4546G>T p.Glu1516Ter p.E1516* ENST00000298281 16/16 105 58 47 151 151 0 strelka-varscan-mutect PCF11,stop_gained,p.Glu1516Ter,ENST00000298281,NM_015885.3;PCF11,downstream_gene_variant,,ENST00000530906,;RP11-727A23.5,non_coding_transcript_exon_variant,,ENST00000602381,;PCF11-AS1,downstream_gene_variant,,ENST00000602322,;RP11-727A23.4,downstream_gene_variant,,ENST00000528133,;PCF11,downstream_gene_variant,,ENST00000528336,; T ENST00000298281 Transcript stop_gained 4998/7677 4546/4668 1516/1555 E/* Gaa/Taa 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 16/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 83184772 83184772 G T 1 0 0 0 0 0 1 0 0 11661 1175 41 2 2 PCF11 11 83184772 Nonsense_Mutation SNP G C3N-00560_T 13013798 83184772 51901850 777 17466 DLG2 0 . GRCh38 11 83786732 83786732 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.1783delG p.Ala595LeufsTer5 p.A595Lfs*5 ENST00000376104 18/28 177 107 70 230 230 0 sindel-varindel-pindel DLG2,frameshift_variant,p.Ala490LeufsTer5,ENST00000398309,NM_001364.3;DLG2,frameshift_variant,p.Ala529LeufsTer5,ENST00000280241,NM_001206769.1;DLG2,frameshift_variant,p.Ala595LeufsTer5,ENST00000376104,NM_001142699.1;DLG2,frameshift_variant,p.Ala387LeufsTer5,ENST00000418306,NM_001142700.1;DLG2,frameshift_variant,p.Ala457LeufsTer5,ENST00000531015,;DLG2,frameshift_variant,p.Ala490LeufsTer5,ENST00000532653,NM_001300983.1;DLG2,frameshift_variant,p.Ala490LeufsTer5,ENST00000524982,;DLG2,frameshift_variant,p.Ala429LeufsTer5,ENST00000330014,;DLG2,frameshift_variant,p.Ala529LeufsTer5,ENST00000398301,;DLG2,non_coding_transcript_exon_variant,,ENST00000529111,;RP11-160H12.3,downstream_gene_variant,,ENST00000528055,; - ENST00000376104 Transcript frameshift_variant 2095/5139 1783/2928 595/975 A/X Gct/ct 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 18/28 PROSITE_profiles:PS50106,hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119,PIRSF_domain:PIRSF001741,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 83786732 83786732 C - 1 0 1 0 1 0 0 0 0 4362 739 26 0 0 DLG2 11 83786732 Frame_Shift_Del DEL C C3N-00560_T 601960 83786732 51299890 778 17467 GRM5 0 . GRCh38 11 88567938 88567938 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1745C>A p.Ala582Glu p.A582E ENST00000305447 7/9 82 50 32 107 107 0 strelka-varscan-mutect GRM5,missense_variant,p.Ala582Glu,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Ala582Glu,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Ala582Glu,ENST00000305432,; T ENST00000305447 Transcript missense_variant 1895/4571 1745/3639 582/1212 A/E gCa/gAa 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0.02) 7/9 Prints_domain:PR01055,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs998009435 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 88567938 88567938 G T 1 0 0 0 0 1 0 0 0 6682 1319 46 2 2 GRM5 11 88567938 Missense_Mutation SNP G C3N-00560_T 4781206 88567938 46518684 779 17468 GRM5 0 . GRCh38 11 89047619 89047619 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.254T>C p.Leu85Pro p.L85P ENST00000305447 1/9 251 148 103 341 341 0 strelka-varscan-mutect GRM5,missense_variant,p.Leu85Pro,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Leu85Pro,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Leu85Pro,ENST00000305432,;GRM5,missense_variant,p.Leu85Pro,ENST00000393294,;GRM5,upstream_gene_variant,,ENST00000449371,; G ENST00000305447 Transcript missense_variant 404/4571 254/3639 85/1212 L/P cTc/cCc 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 1/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,Prints_domain:PR00248,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 89047619 89047619 A G 1 0 0 0 0 1 0 0 0 6682 304 11 5 5 GRM5 11 89047619 Missense_Mutation SNP A C3N-00560_T 479681 89047619 46039003 780 17469 FAT3 0 . GRCh38 11 92800517 92800517 + Missense_Mutation SNP G G T rs757504785 C3N-00560_T C3N-00560_N G G c.7054G>T p.Val2352Leu p.V2352L ENST00000525166 9/27 188 102 86 200 200 0 strelka-varscan-mutect FAT3,missense_variant,p.Val2502Leu,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Val2352Leu,ENST00000525166,; T ENST00000525166 Transcript missense_variant 7076/18699 7054/13320 2352/4439 V/L Gta/Tta rs757504785,COSM258557,COSM258558,COSM5691171,COSM5691172 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.85) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs757504785 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 92800517 92800517 G T 1 0 0 0 0 1 0 0 0 5551 1145 40 1 1 FAT3 11 92800517 Missense_Mutation SNP G C3N-00560_T 3752898 92800517 42286105 781 17470 FAT3 0 . GRCh38 11 92883236 92883236 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.12330C>A p.His4110Gln p.H4110Q ENST00000525166 23/27 223 126 97 300 300 0 strelka-varscan-mutect FAT3,missense_variant,p.His4260Gln,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.His4110Gln,ENST00000525166,;FAT3,missense_variant,p.His595Gln,ENST00000533797,;FAT3,upstream_gene_variant,,ENST00000489716,;FAT3,upstream_gene_variant,,ENST00000469900,; A ENST00000525166 Transcript missense_variant 12352/18699 12330/13320 4110/4439 H/Q caC/caA 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.16) 23/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 92883236 92883236 C A 1 0 0 0 0 1 0 0 0 5551 506 18 2 2 FAT3 11 92883236 Missense_Mutation SNP C C3N-00560_T 82719 92883236 42203386 782 17471 CNTN5 0 . GRCh38 11 100193546 100193546 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.1767T>A p.= p.I589I ENST00000524871 15/25 185 107 78 194 194 0 strelka-varscan-mutect CNTN5,synonymous_variant,p.=,ENST00000524871,NM_014361.3;CNTN5,synonymous_variant,p.=,ENST00000279463,;CNTN5,synonymous_variant,p.=,ENST00000619298,;CNTN5,synonymous_variant,p.=,ENST00000527185,NM_001243271.1;CNTN5,synonymous_variant,p.=,ENST00000528682,NM_001243270.1;CNTN5,synonymous_variant,p.=,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; A ENST00000524871 Transcript synonymous_variant 2057/6258 1767/3303 589/1100 I atT/atA 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 15/25 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 100193546 100193546 T A 1 0 0 0 0 0 0 0 1 3425 1800 63 4 4 CNTN5 11 100193546 Silent SNP T C3N-00560_T 7310310 100193546 34893076 783 17472 CNTN5 0 . GRCh38 11 100340467 100340467 + Missense_Mutation SNP G G T rs201931804 C3N-00560_T C3N-00560_N G G c.2735G>T p.Gly912Val p.G912V ENST00000524871 22/25 39 22 17 49 49 0 strelka-varscan-mutect CNTN5,missense_variant,p.Gly912Val,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Gly896Val,ENST00000279463,;CNTN5,missense_variant,p.Gly834Val,ENST00000619298,;CNTN5,missense_variant,p.Gly912Val,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Gly838Val,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,;RPA2P3,downstream_gene_variant,,ENST00000533268,; T ENST00000524871 Transcript missense_variant 3025/6258 2735/3303 912/1100 G/V gGt/gTt rs201931804 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 tolerated(0.55) 22/25 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs201931804 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 100340467 100340467 G T 1 0 0 0 0 1 0 0 0 3425 1275 44 2 2 CNTN5 11 100340467 Missense_Mutation SNP G C3N-00560_T 146921 100340467 34746155 784 17473 MMP10 0 . GRCh38 11 102779688 102779688 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.163G>T p.Asp55Tyr p.D55Y ENST00000279441 2/10 165 98 67 255 255 0 strelka-varscan-mutect MMP10,missense_variant,p.Asp55Tyr,ENST00000279441,NM_002425.2;MMP10,missense_variant,p.Asp55Tyr,ENST00000539681,;WTAPP1,intron_variant,,ENST00000371455,;WTAPP1,upstream_gene_variant,,ENST00000525739,;WTAPP1,upstream_gene_variant,,ENST00000544704,; A ENST00000279441 Transcript missense_variant 200/1758 163/1431 55/476 D/Y Gac/Tac 1 -1 MMP10 HGNC HGNC:7156 protein_coding YES CCDS8321.1 ENSP00000279441 P09238 UPI00000422C0 NM_002425.2 deleterious(0) 2/10 Gene3D:3.40.390.10,Pfam_domain:PF01471,PIRSF_domain:PIRSF001191,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF153,Superfamily_domains:SSF47090 MODERATE 1 SNV 1 1 PASS rs964227800 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 102779688 102779688 C A 1 0 0 0 0 1 0 0 0 9612 855 30 2 2 MMP10 11 102779688 Missense_Mutation SNP C C3N-00560_T 2439221 102779688 32306934 785 17474 MMP12 0 . GRCh38 11 102871673 102871673 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.546C>A p.= p.A182A ENST00000571244 4/10 250 167 83 303 301 2 strelka-varscan-mutect MMP12,synonymous_variant,p.=,ENST00000571244,NM_002426.4; T ENST00000571244 Transcript synonymous_variant 643/1874 546/1413 182/470 A gcC/gcA 1 -1 MMP12 HGNC HGNC:7158 protein_coding YES CCDS73375.1 ENSP00000458585 P39900 UPI00000422BE NM_002426.4 4/10 Gene3D:3.40.390.10,Pfam_domain:PF00413,PIRSF_domain:PIRSF001191,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF32,SMART_domains:SM00235,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 102871673 102871673 G T 1 0 0 0 0 0 0 0 1 9614 1219 43 2 2 MMP12 11 102871673 Silent SNP G C3N-00560_T 91985 102871673 32214949 786 17475 DYNC2H1 0 . GRCh38 11 103259945 103259945 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.10684G>A p.Val3562Ile p.V3562I ENST00000398093 71/90 30 15 15 107 107 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Val3555Ile,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Val3562Ile,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,; A ENST00000398093 Transcript missense_variant 10684/12945 10684/12945 3562/4314 V/I Gta/Ata 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 tolerated(0.12) 71/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282 MODERATE 1 SNV 5 1 PASS rs1238053472 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 103259945 103259945 G A 1 0 0 0 0 1 0 0 0 4670 1261 44 3 3 DYNC2H1 11 103259945 Missense_Mutation SNP G C3N-00560_T 388272 103259945 31826677 787 17476 KBTBD3 0 . GRCh38 11 106053603 106053603 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.1086T>A p.= p.I362I ENST00000526793 3/3 153 76 77 201 201 0 strelka-varscan-mutect KBTBD3,synonymous_variant,p.=,ENST00000526793,NM_152433.3;KBTBD3,synonymous_variant,p.=,ENST00000534815,;KBTBD3,synonymous_variant,p.=,ENST00000531837,NM_198439.2;KBTBD3,downstream_gene_variant,,ENST00000531482,;KBTBD3,downstream_gene_variant,,ENST00000532662,; T ENST00000526793 Transcript synonymous_variant 1246/3751 1086/1839 362/612 I atT/atA 1 -1 KBTBD3 HGNC HGNC:22934 protein_coding YES CCDS8334.1 ENSP00000436262 Q8NAB2 A0A024R3B5 UPI00001BDB79 NM_152433.3 3/3 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF5,SMART_domains:SM00612 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 106053603 106053603 A T 1 0 0 0 0 0 0 0 1 7911 126 5 4 4 KBTBD3 11 106053603 Silent SNP A C3N-00560_T 2793658 106053603 29033019 788 17477 NCAM1 0 . GRCh38 11 113235105 113235105 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1844T>A p.Leu615His p.L615H ENST00000619839 15/21 155 94 61 184 184 0 strelka-varscan-mutect NCAM1,missense_variant,p.Leu615His,ENST00000615285,;NCAM1,missense_variant,p.Leu589His,ENST00000615112,;NCAM1,missense_variant,p.Leu579His,ENST00000618266,;NCAM1,missense_variant,p.Leu589His,ENST00000316851,NM_181351.4;NCAM1,missense_variant,p.Leu579His,ENST00000621518,;NCAM1,missense_variant,p.Leu579His,ENST00000621128,NM_001242608.1;NCAM1,missense_variant,p.Leu615His,ENST00000619839,NM_001242607.1;NCAM1,missense_variant,p.Leu579His,ENST00000531044,NM_000615.6;NCAM1,missense_variant,p.Leu579His,ENST00000621850,NM_001076682.3;NCAM1,missense_variant,p.Leu579His,ENST00000401611,;NCAM1,missense_variant,p.Leu89His,ENST00000533073,;NCAM1,missense_variant,p.Leu124His,ENST00000526322,;NCAM1,missense_variant,p.Leu82His,ENST00000528590,;NCAM1,missense_variant,p.Leu145His,ENST00000530543,;NCAM1,intron_variant,,ENST00000620046,;NCAM1,downstream_gene_variant,,ENST00000613217,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,missense_variant,p.Leu89His,ENST00000531817,;NCAM1,non_coding_transcript_exon_variant,,ENST00000525355,;NCAM1,downstream_gene_variant,,ENST00000534046,; A ENST00000619839 Transcript missense_variant 2182/2993 1844/2655 615/884 L/H cTc/cAc 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 deleterious(0) 15/21 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 113235105 113235105 T A 1 0 0 0 0 1 0 0 0 10218 1551 54 4 4 NCAM1 11 113235105 Missense_Mutation SNP T C3N-00560_T 7181502 113235105 21851517 789 17478 NXPE4 0 . GRCh38 11 114580184 114580184 + Missense_Mutation SNP C C A rs542613181 C3N-00560_T C3N-00560_N C C c.1047G>T p.Met349Ile p.M349I ENST00000375478 5/6 292 178 114 340 340 0 strelka-varscan-mutect NXPE4,missense_variant,p.Met349Ile,ENST00000375478,NM_001077639.1;NXPE4,missense_variant,p.Met65Ile,ENST00000424261,NM_017678.2;RP11-172C16.4,upstream_gene_variant,,ENST00000536916,; A ENST00000375478 Transcript missense_variant 1228/1822 1047/1635 349/544 M/I atG/atT rs542613181,COSM3443665 1 -1 NXPE4 HGNC HGNC:23117 protein_coding YES CCDS41718.1 ENSP00000364627 Q6UWF7 UPI00000477F3 NM_001077639.1 tolerated(0.2) 5/6 hmmpanther:PTHR16165,hmmpanther:PTHR16165:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs542613181 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 114580184 114580184 C A 1 0 0 0 0 1 0 0 0 10865 594 21 2 2 NXPE4 11 114580184 Missense_Mutation SNP C C3N-00560_T 1345079 114580184 20506438 790 17479 SIK3 0 . GRCh38 11 116858245 116858245 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3076G>T p.Asp1026Tyr p.D1026Y ENST00000375300 20/24 75 41 34 85 85 0 strelka-varscan-mutect SIK3,missense_variant,p.Asp1068Tyr,ENST00000445177,;SIK3,missense_variant,p.Asp1026Tyr,ENST00000375300,NM_025164.4,NM_001281748.1;SIK3,missense_variant,p.Asp966Tyr,ENST00000446921,NM_001281749.1;APOA1-AS,downstream_gene_variant,,ENST00000444200,;SIK3,non_coding_transcript_exon_variant,,ENST00000488337,;SIK3,3_prime_UTR_variant,,ENST00000415541,;SIK3,non_coding_transcript_exon_variant,,ENST00000465421,;SIK3,non_coding_transcript_exon_variant,,ENST00000480468,; A ENST00000375300 Transcript missense_variant 3082/6213 3076/3966 1026/1321 D/Y Gat/Tat 1 -1 SIK3 HGNC HGNC:29165 protein_coding YES CCDS8379.2 ENSP00000364449 J3KPC8 UPI000066D90F NM_025164.4,NM_001281748.1 deleterious_low_confidence(0) 20/24 hmmpanther:PTHR22971,hmmpanther:PTHR22971:SF3 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 116858245 116858245 C A 1 0 0 0 0 1 0 0 0 14583 855 30 2 2 SIK3 11 116858245 Missense_Mutation SNP C C3N-00560_T 2278061 116858245 18228377 791 17480 FXYD6 0 . GRCh38 11 117840348 117840348 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.230C>T p.Ala77Val p.A77V ENST00000526014 6/8 149 97 52 170 169 1 strelka-varscan-mutect FXYD6,missense_variant,p.Ala77Val,ENST00000526014,NM_001164832.2,NM_022003.3;FXYD6,missense_variant,p.Ala77Val,ENST00000539526,NM_001164837.2;FXYD6,missense_variant,p.Ala77Val,ENST00000260282,NM_001164836.2;FXYD6,missense_variant,p.Ala77Val,ENST00000527717,NM_001164831.2;FXYD6,missense_variant,p.Ala77Val,ENST00000524656,;FXYD6,missense_variant,p.Ala76Val,ENST00000529335,;FXYD6-FXYD2,missense_variant,p.Pro65Ser,ENST00000532984,NM_001243598.2;FXYD6,missense_variant,p.Ala77Val,ENST00000530956,;FXYD6,missense_variant,p.Ala77Val,ENST00000584230,;FXYD6,intron_variant,,ENST00000584394,;FXYD6-FXYD2,intron_variant,,ENST00000614497,NM_001204268.1;RP11-728F11.4,downstream_gene_variant,,ENST00000534150,;RP11-728F11.4,downstream_gene_variant,,ENST00000525260,;RP11-728F11.4,downstream_gene_variant,,ENST00000581173,;FXYD6,non_coding_transcript_exon_variant,,ENST00000583233,;FXYD6,non_coding_transcript_exon_variant,,ENST00000579486,;FXYD6,missense_variant,p.Ala77Val,ENST00000524841,;FXYD6,non_coding_transcript_exon_variant,,ENST00000527429,;FXYD6,non_coding_transcript_exon_variant,,ENST00000540359,;FXYD6,non_coding_transcript_exon_variant,,ENST00000583660,;FXYD6,downstream_gene_variant,,ENST00000527053,;FXYD6,downstream_gene_variant,,ENST00000534125,; A ENST00000526014 Transcript missense_variant 826/2171 230/288 77/95 A/V gCc/gTc 1 -1 FXYD6 HGNC HGNC:4030 protein_coding YES CCDS8387.1 ENSP00000433312 Q9H0Q3 A0A024R3J8 UPI0000037BAF NM_001164832.2,NM_022003.3 deleterious(0.03) 6/8 Gene3D:1.20.5.780,hmmpanther:PTHR14132,hmmpanther:PTHR14132:SF15 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 56 117840348 117840348 G A 1 0 0 0 0 1 0 0 0 5993 1217 42 3 3 FXYD6 11 117840348 Missense_Mutation SNP G C3N-00560_T 982103 117840348 17246274 792 17481 TRIM29 0 . GRCh38 11 120137318 120137318 + Silent SNP G G C C3N-00560_T C3N-00560_N G G c.714C>G p.= p.T238T ENST00000341846 1/9 301 181 120 376 376 0 strelka-varscan-mutect TRIM29,synonymous_variant,p.=,ENST00000341846,NM_012101.3;TRIM29,downstream_gene_variant,,ENST00000532833,;TRIM29,downstream_gene_variant,,ENST00000529495,;TRIM29,downstream_gene_variant,,ENST00000529040,;TRIM29,downstream_gene_variant,,ENST00000529011,;TRIM29,downstream_gene_variant,,ENST00000627238,;TRIM29,3_prime_UTR_variant,,ENST00000475051,; C ENST00000341846 Transcript synonymous_variant 1136/3328 714/1767 238/588 T acC/acG COSM338427 1 -1 TRIM29 HGNC HGNC:17274 protein_coding YES CCDS8428.1 ENSP00000343129 Q14134 A0A024R3J1 UPI0000073FDE NM_012101.3 1/9 Gene3D:1freA00,Pfam_domain:PF00643,PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF412,SMART_domains:SM00336,Superfamily_domains:SSF57845 1 LOW 1 SNV 1 1 1 PASS rs1185002346 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 120137318 120137318 G C 1 0 0 0 0 0 0 0 1 16992 1103 39 4 4 TRIM29 11 120137318 Silent SNP G C3N-00560_T 2296970 120137318 14949304 793 17482 OR8B4 0 . GRCh38 11 124424145 124424145 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.727C>A p.His243Asn p.H243N ENST00000356130 1/1 112 70 42 136 136 0 strelka-varscan-mutect OR8B4,missense_variant,p.His243Asn,ENST00000356130,NM_001005196.1; T ENST00000356130 Transcript missense_variant 749/990 727/930 243/309 H/N Cac/Aac COSM348376 1 -1 OR8B4 HGNC HGNC:8473 protein_coding YES CCDS31710.1 ENSP00000348449 Q96RC9 UPI00000015B0 NM_001005196.1 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF208,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 124424145 124424145 G T 1 0 0 0 0 1 0 0 0 11299 1348 47 2 2 OR8B4 11 124424145 Missense_Mutation SNP G C3N-00560_T 4286827 124424145 10662477 794 17483 PKNOX2 0 . GRCh38 11 125429976 125429976 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1027C>G p.Arg343Gly p.R343G ENST00000298282 12/13 86 46 40 89 89 0 strelka-varscan-mutect PKNOX2,missense_variant,p.Arg343Gly,ENST00000298282,NM_022062.2;PKNOX2,non_coding_transcript_exon_variant,,ENST00000530517,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000531116,;PKNOX2,3_prime_UTR_variant,,ENST00000532623,;PKNOX2,non_coding_transcript_exon_variant,,ENST00000526955,; G ENST00000298282 Transcript missense_variant 1298/3687 1027/1419 343/472 R/G Cgg/Ggg 1 1 PKNOX2 HGNC HGNC:16714 protein_coding YES CCDS41730.1 ENSP00000298282 Q96KN3 UPI000023271E NM_022062.2 deleterious(0) 12/13 PROSITE_profiles:PS50071,hmmpanther:PTHR11850:SF53,hmmpanther:PTHR11850,Gene3D:1.10.10.60,Pfam_domain:PF05920,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 125429976 125429976 C G 1 0 0 0 0 1 0 0 0 12079 643 23 4 4 PKNOX2 11 125429976 Missense_Mutation SNP C C3N-00560_T 1005831 125429976 9656646 795 17484 KCNJ5 0 . GRCh38 11 128911852 128911852 + Silent SNP C C G novel C3N-00560_T C3N-00560_N C C c.579C>G p.= p.P193P ENST00000529694 2/3 138 72 66 186 186 0 strelka-varscan-mutect KCNJ5,synonymous_variant,p.=,ENST00000529694,NM_000890.3;KCNJ5,synonymous_variant,p.=,ENST00000338350,;KCNJ5,synonymous_variant,p.=,ENST00000533599,; G ENST00000529694 Transcript synonymous_variant 955/5940 579/1260 193/419 P ccC/ccG 1 1 KCNJ5 HGNC HGNC:6266 protein_coding YES CCDS8479.1 ENSP00000433295 P48544 UPI000013D428 NM_000890.3 2/3 hmmpanther:PTHR11767:SF52,hmmpanther:PTHR11767,Pfam_domain:PF01007,Gene3D:2.60.40.1400,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 128911852 128911852 C G 1 0 0 0 0 0 0 0 1 7971 581 21 4 4 KCNJ5 11 128911852 Silent SNP C C3N-00560_T 3481876 128911852 6174770 796 17485 ST14 0 . GRCh38 11 130197871 130197871 + Missense_Mutation SNP G G T rs753425257 C3N-00560_T C3N-00560_N G G c.1385G>T p.Gly462Val p.G462V ENST00000278742 12/19 126 65 61 130 130 0 strelka-varscan-mutect ST14,missense_variant,p.Gly462Val,ENST00000278742,NM_021978.3;ST14,downstream_gene_variant,,ENST00000530532,;ST14,downstream_gene_variant,,ENST00000524718,;ST14,downstream_gene_variant,,ENST00000530376,; T ENST00000278742 Transcript missense_variant 1803/3539 1385/2568 462/855 G/V gGg/gTg rs753425257 1 1 ST14 HGNC HGNC:11344 protein_coding YES CCDS8487.1 ENSP00000278742 Q9Y5Y6 UPI00000012E9 NM_021978.3 deleterious(0) 12/19 Gene3D:4.10.400.10,Pfam_domain:PF00057,PIRSF_domain:PIRSF036370,Prints_domain:PR00261,PROSITE_profiles:PS50068,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF226,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS rs753425257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 130197871 130197871 G T 1 0 0 0 0 1 0 0 0 15589 1232 43 2 2 ST14 11 130197871 Missense_Mutation SNP G C3N-00560_T 1286019 130197871 4888751 797 17486 ADAMTS8 0 . GRCh38 11 130405986 130405986 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.2242C>G p.Leu748Val p.L748V ENST00000257359 9/9 164 96 68 248 248 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Leu748Val,ENST00000257359,NM_007037.4;RP11-121M22.1,downstream_gene_variant,,ENST00000602376,;RP11-121M22.1,downstream_gene_variant,,ENST00000616197,;ADAMTS8,non_coding_transcript_exon_variant,,ENST00000531752,; C ENST00000257359 Transcript missense_variant 2949/4010 2242/2670 748/889 L/V Ctg/Gtg 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 deleterious(0) 9/9 hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 130405986 130405986 G C 1 0 0 0 0 1 0 0 0 316 991 35 4 4 ADAMTS8 11 130405986 Missense_Mutation SNP G C3N-00560_T 208115 130405986 4680636 798 17487 ADAMTS8 0 . GRCh38 11 130414806 130414806 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1291G>A p.Ala431Thr p.A431T ENST00000257359 5/9 84 64 20 124 123 1 strelka-varscan-mutect ADAMTS8,missense_variant,p.Ala431Thr,ENST00000257359,NM_007037.4;ADAMTS8,upstream_gene_variant,,ENST00000531752,; T ENST00000257359 Transcript missense_variant 1998/4010 1291/2670 431/889 A/T Gcg/Acg 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 tolerated(0.11) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,Gene3D:3.40.390.10 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 130414806 130414806 C T 1 0 0 0 0 1 0 0 0 316 710 25 3 3 ADAMTS8 11 130414806 Missense_Mutation SNP C C3N-00560_T 8820 130414806 4671816 799 17488 WNK1 0 . GRCh38 12 868005 868005 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.2534G>T p.Arg845Leu p.R845L ENST00000340908 10/28 375 314 61 398 398 0 strelka-varscan-mutect WNK1,missense_variant,p.Arg760Leu,ENST00000530271,;WNK1,missense_variant,p.Arg760Leu,ENST00000537687,NM_001184985.1;WNK1,missense_variant,p.Arg845Leu,ENST00000340908,NM_213655.4;WNK1,missense_variant,p.Arg59Leu,ENST00000574564,;WNK1,intron_variant,,ENST00000315939,NM_018979.3;WNK1,intron_variant,,ENST00000535572,NM_014823.2;WNK1,intron_variant,,ENST00000535698,;WNK1,intron_variant,,ENST00000544965,;WNK1,intron_variant,,ENST00000545285,;WNK1,upstream_gene_variant,,ENST00000574679,; T ENST00000340908 Transcript missense_variant 3177/11208 2534/7905 845/2634 R/L cGt/cTt COSM1513743,COSM3813266,COSM5202542,COSM5324297 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 deleterious_low_confidence(0) 10/28 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs1427290653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 868005 868005 G T 1 0 0 0 0 1 0 0 0 17933 1145 40 1 1 WNK1 12 868005 Missense_Mutation SNP G C3N-00560_T 868005 132407304 800 17489 FOXM1 0 . GRCh38 12 2864704 2864704 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1069A>T p.Thr357Ser p.T357S ENST00000342628 7/10 244 205 39 222 221 1 strelka-varscan-mutect FOXM1,missense_variant,p.Thr342Ser,ENST00000627656,NM_001243088.1;FOXM1,missense_variant,p.Thr357Ser,ENST00000342628,NM_202002.2;FOXM1,missense_variant,p.Thr342Ser,ENST00000361953,NM_202003.2,NM_001243089.1;FOXM1,missense_variant,p.Thr357Ser,ENST00000359843,NM_021953.3;FOXM1,missense_variant,p.Thr83Ser,ENST00000535350,;ITFG2,downstream_gene_variant,,ENST00000545509,;ITFG2,downstream_gene_variant,,ENST00000537710,;FOXM1,downstream_gene_variant,,ENST00000537018,;FOXM1,3_prime_UTR_variant,,ENST00000538564,;FOXM1,non_coding_transcript_exon_variant,,ENST00000536066,;FOXM1,non_coding_transcript_exon_variant,,ENST00000366362,;FOXM1,downstream_gene_variant,,ENST00000545049,; A ENST00000342628 Transcript missense_variant 1183/3475 1069/2406 357/801 T/S Acc/Tcc 1 -1 FOXM1 HGNC HGNC:3818 protein_coding YES CCDS8516.1 ENSP00000342307 Q08050 UPI000016B22B NM_202002.2 tolerated(0.18) 7/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 2864704 2864704 T A 1 0 0 0 0 1 0 0 0 5882 1725 60 4 4 FOXM1 12 2864704 Missense_Mutation SNP T C3N-00560_T 1996699 2864704 130410605 801 17490 DYRK4 0 . GRCh38 12 4607371 4607371 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.999G>T p.Arg333Ser p.R333S ENST00000540757 10/13 206 171 35 198 197 1 strelka-varscan-mutect DYRK4,missense_variant,p.Arg333Ser,ENST00000540757,NM_003845.2;DYRK4,missense_variant,p.Arg448Ser,ENST00000543431,;DYRK4,missense_variant,p.Arg333Ser,ENST00000010132,;DYRK4,upstream_gene_variant,,ENST00000544671,;DYRK4,non_coding_transcript_exon_variant,,ENST00000536137,;DYRK4,non_coding_transcript_exon_variant,,ENST00000540644,;DYRK4,intron_variant,,ENST00000545571,;RP11-500M8.7,intron_variant,,ENST00000536588,;DYRK4,upstream_gene_variant,,ENST00000541024,;RP11-234B24.5,upstream_gene_variant,,ENST00000538921,; T ENST00000540757 Transcript missense_variant 1159/3272 999/1563 333/520 R/S agG/agT 1 1 DYRK4 HGNC HGNC:3095 protein_coding YES CCDS8530.1 ENSP00000441755 Q9NR20 UPI000006E05C NM_003845.2 deleterious(0) 10/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF22,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 4607371 4607371 G T 1 0 0 0 0 1 0 0 0 4682 1165 41 2 2 DYRK4 12 4607371 Missense_Mutation SNP G C3N-00560_T 1742667 4607371 128667938 802 17491 GALNT8 0 . GRCh38 12 4810134 4810134 + Silent SNP C C A C3N-00560_T C3N-00560_N C C c.93C>A p.= p.A31A ENST00000280684 1/1 62 40 22 59 59 0 strelka-varscan-mutect GALNT8,synonymous_variant,p.=,ENST00000433855,NM_002235.3;KCNA6,synonymous_variant,p.=,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; A ENST00000280684 Transcript synonymous_variant 959/4237 93/1590 31/529 A gcC/gcA COSM4513473 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD 1/1 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104 1 LOW SNV 1 1 PASS . . 0 197 11 2 0 0 0 0 -20 0.9997796 1 1 1 0 A 2 1 56 4810134 4810134 C A 1 0 0 0 0 0 0 0 1 6090 639 23 1 1 GALNT8 12 4810134 Silent SNP C C3N-00560_T 202763 4810134 128465175 803 17492 GALNT8 0 . GRCh38 12 4810917 4810917 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.876C>A p.Phe292Leu p.F292L ENST00000280684 1/1 150 125 25 146 146 0 strelka-varscan-mutect GALNT8,missense_variant,p.Phe292Leu,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Phe292Leu,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; A ENST00000280684 Transcript missense_variant 1742/4237 876/1590 292/529 F/L ttC/ttA 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD deleterious(0.03) 1/1 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104,Superfamily_domains:SSF81324 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 4810917 4810917 C A 1 0 0 0 0 1 0 0 0 6090 854 30 2 2 GALNT8 12 4810917 Missense_Mutation SNP C C3N-00560_T 783 4810917 128464392 804 17493 LPAR5 0 . GRCh38 12 6621096 6621096 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.153G>T p.= p.L51L ENST00000329858 2/2 57 36 21 47 47 0 strelka-varscan-mutect LPAR5,synonymous_variant,p.=,ENST00000329858,NM_020400.5;LPAR5,synonymous_variant,p.=,ENST00000431922,NM_001142961.1;LPAR5,non_coding_transcript_exon_variant,,ENST00000540335,; A ENST00000329858 Transcript synonymous_variant 910/3171 153/1119 51/372 L ctG/ctT 1 -1 LPAR5 HGNC HGNC:13307 protein_coding YES CCDS8553.1 ENSP00000327875 Q9H1C0 Q5KU18 UPI0000036A45 NM_020400.5 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24234,hmmpanther:PTHR24234:SF6,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 6621096 6621096 C A 1 0 0 0 0 0 0 0 1 8811 697 25 2 2 LPAR5 12 6621096 Silent SNP C C3N-00560_T 1810179 6621096 126654213 805 17494 ZNF384 0 . GRCh38 12 6678140 6678140 + Missense_Mutation SNP C C A rs551677880 C3N-00560_T C3N-00560_N C C c.673G>T p.Gly225Cys p.G225C ENST00000396801 6/11 81 48 33 103 103 0 strelka-varscan-mutect ZNF384,missense_variant,p.Gly225Cys,ENST00000319770,NM_133476.4;ZNF384,missense_variant,p.Gly225Cys,ENST00000396801,NM_001135734.2;ZNF384,missense_variant,p.Gly225Cys,ENST00000361959,;ZNF384,missense_variant,p.Gly170Cys,ENST00000355772,NM_001039920.2;ZNF384,missense_variant,p.Gly225Cys,ENST00000417772,;ZNF384,missense_variant,p.Gly209Cys,ENST00000436774,;ZNF384,downstream_gene_variant,,ENST00000540915,;ZNF384,downstream_gene_variant,,ENST00000535485,;ZNF384,downstream_gene_variant,,ENST00000542351,;ZNF384,downstream_gene_variant,,ENST00000544482,;ZNF384,downstream_gene_variant,,ENST00000538829,;ZNF384,non_coding_transcript_exon_variant,,ENST00000542519,;ZNF384,upstream_gene_variant,,ENST00000537383,;ZNF384,downstream_gene_variant,,ENST00000537248,;ZNF384,downstream_gene_variant,,ENST00000542605,; A ENST00000396801 Transcript missense_variant 881/3008 673/1734 225/577 G/C Ggc/Tgc rs551677880 1 -1 ZNF384 HGNC HGNC:11955 protein_coding YES CCDS44817.1 ENSP00000380019 Q8TF68 UPI00001AE6F8 NM_001135734.2 deleterious(0) 6/11 hmmpanther:PTHR24409,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs551677880 . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 56 6678140 6678140 C A 1 0 0 0 0 1 0 0 0 18447 652 23 1 1 ZNF384 12 6678140 Missense_Mutation SNP C C3N-00560_T 57044 6678140 126597169 806 17495 CD163 0 . GRCh38 12 7487944 7487944 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1564G>T p.Gly522Cys p.G522C ENST00000359156 7/17 248 159 89 268 268 0 strelka-varscan-mutect CD163,missense_variant,p.Gly522Cys,ENST00000359156,NM_004244.5;CD163,missense_variant,p.Gly522Cys,ENST00000396620,;CD163,missense_variant,p.Gly522Cys,ENST00000432237,NM_203416.3;CD163,missense_variant,p.Gly510Cys,ENST00000541972,;CD163,upstream_gene_variant,,ENST00000537626,;CD163,upstream_gene_variant,,ENST00000542280,;CD163,upstream_gene_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;CD163,upstream_gene_variant,,ENST00000538840,; A ENST00000359156 Transcript missense_variant 1767/4268 1564/3471 522/1156 G/C Ggc/Tgc 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 deleterious(0) 7/17 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF324,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 7487944 7487944 C A 1 0 0 0 0 1 0 0 0 2670 594 21 2 2 CD163 12 7487944 Missense_Mutation SNP C C3N-00560_T 809804 7487944 125787365 807 17496 APOBEC1 0 . GRCh38 12 7649611 7649611 + Missense_Mutation SNP T T A rs774597050 C3N-00560_T C3N-00560_N T T c.647A>T p.Gln216Leu p.Q216L ENST00000229304 5/5 186 164 22 184 184 0 strelka-varscan-mutect APOBEC1,missense_variant,p.Gln216Leu,ENST00000229304,NM_001304566.1,NM_001644.4;APOBEC1,3_prime_UTR_variant,,ENST00000467171,NM_005889.3; A ENST00000229304 Transcript missense_variant 668/879 647/711 216/236 Q/L cAa/cTa rs774597050 1 -1 APOBEC1 HGNC HGNC:604 protein_coding YES CCDS8579.1 ENSP00000229304 P41238 UPI000013C8F4 NM_001304566.1,NM_001644.4 deleterious(0.01) 5/5 hmmpanther:PTHR13857:SF26,hmmpanther:PTHR13857 MODERATE 1 SNV 1 1 PASS rs774597050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 7649611 7649611 T A 1 0 0 0 0 1 0 0 0 908 1812 63 4 4 APOBEC1 12 7649611 Missense_Mutation SNP T C3N-00560_T 161667 7649611 125625698 808 17497 CLEC12B 0 . GRCh38 12 10018432 10018432 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.782G>T p.Trp261Leu p.W261L ENST00000338896 6/6 212 186 26 263 263 0 strelka-varscan-mutect CLEC12B,missense_variant,p.Trp261Leu,ENST00000338896,NM_001129998.1;CLEC12B,downstream_gene_variant,,ENST00000396502,NM_001319242.1,NM_205852.2;RP11-133L14.5,intron_variant,,ENST00000544225,;CLEC12B,3_prime_UTR_variant,,ENST00000544853,;CLEC12B,downstream_gene_variant,,ENST00000539155,; T ENST00000338896 Transcript missense_variant 910/1097 782/831 261/276 W/L tGg/tTg 1 1 CLEC12B HGNC HGNC:31966 protein_coding YES CCDS44830.1 ENSP00000344563 Q2HXU8 A0A140VK10 UPI000036687A NM_001129998.1 tolerated(0.75) 6/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22800:SF8,hmmpanther:PTHR22800,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 187 0 0 23 0 0 0 -10.35798 0 0 1 0 0 T 3 4 56 10018432 10018432 G T 1 0 0 0 0 1 0 0 0 3264 1357 47 2 2 CLEC12B 12 10018432 Missense_Mutation SNP G C3N-00560_T 2368821 10018432 123256877 809 17498 GRIN2B 0 . GRCh38 12 13567263 13567263 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.2360G>A p.Gly787Glu p.G787E ENST00000609686 12/13 273 237 36 260 260 0 strelka-varscan-mutect GRIN2B,missense_variant,p.Gly787Glu,ENST00000609686,NM_000834.3;GRIN2B,intron_variant,,ENST00000637214,;GRIN2B,splice_region_variant,,ENST00000628166,;GRIN2B,upstream_gene_variant,,ENST00000636207,; T ENST00000609686 Transcript missense_variant,splice_region_variant 2814/30355 2360/4455 787/1484 G/E gGg/gAg COSM1511571 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 deleterious(0) 12/13 Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF192,SMART_domains:SM00079,Superfamily_domains:SSF53850 1 MODERATE 1 SNV 1 1 1 PASS rs898581464 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 13567263 13567263 C T 1 0 0 0 0 1 0 0 0 6662 637 22 3 3 GRIN2B 12 13567263 Missense_Mutation SNP C C3N-00560_T 3548831 13567263 119708046 810 17499 GRIN2B 0 . GRCh38 12 13753881 13753881 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.446C>A p.Ser149Ter p.S149* ENST00000609686 3/13 133 87 46 151 150 1 strelka-varscan-mutect GRIN2B,stop_gained,p.Ser149Ter,ENST00000609686,NM_000834.3; T ENST00000609686 Transcript stop_gained 900/30355 446/4455 149/1484 S/* tCa/tAa 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 3/13 Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF192,Superfamily_domains:SSF53822 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 13753881 13753881 G T 1 0 0 0 0 0 1 0 0 6662 1294 45 2 2 GRIN2B 12 13753881 Nonsense_Mutation SNP G C3N-00560_T 186618 13753881 119521428 811 17500 PIK3C2G 0 . GRCh38 12 18538283 18538283 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.3451A>T p.Ser1151Cys p.S1151C ENST00000538779 25/33 121 77 44 147 147 0 varscan-mutect PIK3C2G,missense_variant,p.Ser1151Cys,ENST00000538779,NM_001288772.1,NM_001288774.1;PIK3C2G,missense_variant,p.Ser1110Cys,ENST00000433979,NM_004570.5;PIK3C2G,missense_variant,p.Ser1110Cys,ENST00000266497,;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,; T ENST00000538779 Transcript missense_variant 3567/4963 3451/4461 1151/1486 S/C Agc/Tgc 1 1 PIK3C2G HGNC HGNC:8973 protein_coding YES CCDS73452.1 ENSP00000445381 F5H369 UPI00020655D2 NM_001288772.1,NM_001288774.1 deleterious(0) 25/33 PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF29,hmmpanther:PTHR10048,Pfam_domain:PF00454,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 18538283 18538283 A T 1 0 0 0 0 1 0 0 0 12006 188 7 4 4 PIK3C2G 12 18538283 Missense_Mutation SNP A C3N-00560_T 4784402 18538283 114737026 812 17501 PLEKHA5 0 . GRCh38 12 19255166 19255166 + Splice_Site SNP G G A C3N-00560_T C3N-00560_N G G c.432+1G>A p.X144_splice ENST00000429027 40 26 14 47 47 0 strelka-varscan-mutect PLEKHA5,splice_donor_variant,,ENST00000538714,NM_001143821.2;PLEKHA5,splice_donor_variant,,ENST00000429027,NM_001256470.1;PLEKHA5,splice_donor_variant,,ENST00000424268,NM_001256787.1;PLEKHA5,splice_donor_variant,,ENST00000299275,NM_019012.5;PLEKHA5,splice_donor_variant,,ENST00000539256,;PLEKHA5,splice_donor_variant,,ENST00000536974,;PLEKHA5,splice_donor_variant,,ENST00000538305,;PLEKHA5,splice_donor_variant,,ENST00000538034,;PLEKHA5,upstream_gene_variant,,ENST00000510738,;PLEKHA5,downstream_gene_variant,,ENST00000534979,; A ENST00000429027 Transcript splice_donor_variant -/4762 432/3849 144/1282 COSM3935860,COSM3935861,COSM3935862 1 1 PLEKHA5 HGNC HGNC:30036 protein_coding YES CCDS58213.1 ENSP00000404296 Q9HAU0 UPI000204ABA8 NM_001256470.1 5/31 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999924 1 1 1 0 A 5 1 56 19255166 19255166 G A 1 0 0 0 0 0 0 1 0 12152 1043 36 3 3 PLEKHA5 12 19255166 Splice_Site SNP G C3N-00560_T 716883 19255166 114020143 813 17502 SLCO1B3 0 . GRCh38 12 20916028 20916028 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.1890A>G p.Ile630Met p.I630M ENST00000261196 14/14 66 57 9 105 105 0 strelka-varscan-mutect SLCO1B3,missense_variant,p.Ile630Met,ENST00000261196,;SLCO1B3,missense_variant,p.Ile630Met,ENST00000381545,NM_019844.3;RP11-545J16.1,intron_variant,,ENST00000540229,;RP11-545J16.1,intron_variant,,ENST00000381541,; G ENST00000261196 Transcript missense_variant 1957/2840 1890/2109 630/702 I/M atA/atG 1 1 SLCO1B3 HGNC HGNC:10961 protein_coding YES CCDS8684.1 ENSP00000261196 Q9NPD5 UPI000013544A tolerated(0.44) 14/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388:SF89,hmmpanther:PTHR11388,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.83908 1 1 1 1 0 G 3 3 56 20916028 20916028 A G 1 0 0 0 0 1 0 0 0 15010 410 15 5 5 SLCO1B3 12 20916028 Missense_Mutation SNP A C3N-00560_T 1660862 20916028 112359281 814 17503 SLCO1B1 0 . GRCh38 12 21172734 21172734 + Silent SNP C C A rs139257324 C3N-00560_T C3N-00560_N C C c.169C>A p.= p.R57R ENST00000256958 3/15 197 131 66 288 288 0 strelka-varscan-mutect SLCO1B1,synonymous_variant,p.=,ENST00000256958,NM_006446.4;RP11-125O5.2,intron_variant,,ENST00000543498,; A ENST00000256958 Transcript synonymous_variant 265/2229 169/2076 57/691 R Cgg/Agg rs139257324,CM120188,COSM182981 1 1 SLCO1B1 HGNC HGNC:10959 protein_coding YES CCDS8685.1 ENSP00000256958 Q9Y6L6 A0A024RAU7 UPI0000043BED NM_006446.4 3/15 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805 0,0,1 LOW 1 SNV 1 0,1,1 1 PASS rs139257324 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 21172734 21172734 C A 1 0 0 0 0 0 0 0 1 15009 527 19 1 1 SLCO1B1 12 21172734 Silent SNP C C3N-00560_T 256706 21172734 112102575 815 17504 SLCO1B1 0 . GRCh38 12 21178644 21178644 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.553delG p.Glu185ArgfsTer4 p.E185Rfs*4 ENST00000256958 6/15 130 91 39 186 186 0 sindel-varindel-pindel SLCO1B1,frameshift_variant,p.Glu185ArgfsTer4,ENST00000256958,NM_006446.4;RP11-125O5.2,downstream_gene_variant,,ENST00000543498,; - ENST00000256958 Transcript frameshift_variant 646/2229 550/2076 184/691 G/X Ggg/gg 1 1 SLCO1B1 HGNC HGNC:10959 protein_coding YES CCDS8685.1 ENSP00000256958 Q9Y6L6 A0A024RAU7 UPI0000043BED NM_006446.4 6/15 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805 HIGH 1 deletion 1 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 21178644 21178644 G - 1 0 1 0 1 0 0 0 0 15009 1000 35 0 0 SLCO1B1 12 21178644 Frame_Shift_Del DEL G C3N-00560_T 5910 21178644 112096665 816 17505 RECQL 0 . GRCh38 12 21491658 21491658 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.75T>G p.Ile25Met p.I25M ENST00000444129 3/15 210 176 34 208 208 0 strelka-varscan-mutect RECQL,missense_variant,p.Ile25Met,ENST00000444129,NM_032941.2,NM_002907.3;RECQL,missense_variant,p.Ile25Met,ENST00000421138,;RECQL,missense_variant,p.Ile25Met,ENST00000314748,;RECQL,missense_variant,p.Ile25Met,ENST00000396093,;RECQL,missense_variant,p.Ile25Met,ENST00000542432,;RECQL,missense_variant,p.Ile25Met,ENST00000539672,;RECQL,missense_variant,p.Ile25Met,ENST00000536964,;RECQL,missense_variant,p.Ile25Met,ENST00000536240,; C ENST00000444129 Transcript missense_variant 544/3702 75/1950 25/649 I/M atT/atG 1 -1 RECQL HGNC HGNC:9948 protein_coding YES CCDS31756.1 ENSP00000416739 P46063 A0A024RAV2 UPI0000167E2F NM_032941.2,NM_002907.3 tolerated(0.06) 3/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF72 MODERATE 1 SNV 2 1 PASS rs1327715764 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 21491658 21491658 A C 1 0 0 0 0 1 0 0 0 13371 242 9 5 5 RECQL 12 21491658 Missense_Mutation SNP A C3N-00560_T 313014 21491658 111783651 817 17506 ETNK1 0 . GRCh38 12 22625250 22625250 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.87C>T p.= p.T29T ENST00000266517 1/8 196 124 72 157 157 0 strelka-varscan-mutect ETNK1,synonymous_variant,p.=,ENST00000266517,NM_018638.4;ETNK1,synonymous_variant,p.=,ENST00000538218,;ETNK1,synonymous_variant,p.=,ENST00000335148,NM_001039481.1;ETNK1,upstream_gene_variant,,ENST00000545979,;RP11-268P4.4,upstream_gene_variant,,ENST00000542076,; T ENST00000266517 Transcript synonymous_variant 176/7159 87/1359 29/452 T acC/acT 1 1 ETNK1 HGNC HGNC:24649 protein_coding YES CCDS8698.1 ENSP00000266517 Q9HBU6 UPI0000129E2F NM_018638.4 1/8 hmmpanther:PTHR22603,hmmpanther:PTHR22603:SF22 LOW 1 SNV 1 1 PASS rs1434311430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 22625250 22625250 C T 1 0 0 0 0 0 0 0 1 5136 610 22 3 3 ETNK1 12 22625250 Silent SNP C C3N-00560_T 1133592 22625250 110650059 818 17507 ASUN 0 . GRCh38 12 26917715 26917715 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.908G>C p.Gly303Ala p.G303A ENST00000261191 9/17 128 107 21 167 167 0 strelka-varscan-mutect ASUN,missense_variant,p.Gly303Ala,ENST00000261191,NM_018164.2;ASUN,missense_variant,p.Gly7Ala,ENST00000538155,;ASUN,intron_variant,,ENST00000536232,;ASUN,non_coding_transcript_exon_variant,,ENST00000542392,; G ENST00000261191 Transcript missense_variant 1445/2974 908/2121 303/706 G/A gGc/gCc 1 -1 ASUN HGNC HGNC:20174 protein_coding YES CCDS8708.1 ENSP00000261191 Q9NVM9 UPI0000044950 NM_018164.2 tolerated(0.77) 9/17 hmmpanther:PTHR12955,hmmpanther:PTHR12955:SF1,Pfam_domain:PF10221 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 26917715 26917715 C G 1 0 0 0 0 1 0 0 0 1213 739 26 4 4 ASUN 12 26917715 Missense_Mutation SNP C C3N-00560_T 4292465 26917715 106357594 819 17508 OVCH1 0 . GRCh38 12 29471891 29471891 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.1767G>A p.= p.Q589Q ENST00000318184 16/28 220 179 41 231 231 0 strelka-varscan-mutect OVCH1,synonymous_variant,p.=,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; T ENST00000318184 Transcript synonymous_variant 1767/3405 1767/3405 589/1134 Q caG/caA 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 16/28 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 29471891 29471891 C T 1 0 0 0 0 0 0 0 1 11393 680 24 3 3 OVCH1 12 29471891 Silent SNP C C3N-00560_T 2554176 29471891 103803418 820 17509 TSPAN11 0 . GRCh38 12 30979625 30979625 + Silent SNP C C A C3N-00560_T C3N-00560_N C C c.411C>A p.= p.P137P ENST00000261177 5/8 271 203 68 208 208 0 strelka-varscan-mutect TSPAN11,synonymous_variant,p.=,ENST00000261177,NM_001080509.2;TSPAN11,synonymous_variant,p.=,ENST00000546076,;TSPAN11,synonymous_variant,p.=,ENST00000535215,;RP11-551L14.4,intron_variant,,ENST00000613860,;RP11-551L14.4,upstream_gene_variant,,ENST00000612219,; A ENST00000261177 Transcript synonymous_variant 470/5505 411/762 137/253 P ccC/ccA COSM938678 1 1 TSPAN11 HGNC HGNC:30795 protein_coding YES CCDS31765.1 ENSP00000261177 A1L157 UPI00001AE7E4 NM_001080509.2 5/8 hmmpanther:PTHR19282:SF198,hmmpanther:PTHR19282,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Superfamily_domains:0037997 1 LOW 1 SNV 1 1 1 PASS rs1450737382 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 30979625 30979625 C A 1 0 0 0 0 0 0 0 1 17140 639 23 1 1 TSPAN11 12 30979625 Silent SNP C C3N-00560_T 1507734 30979625 102295684 821 17510 BICD1 0 . GRCh38 12 32328418 32328418 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1963G>T p.Ala655Ser p.A655S ENST00000281474 5/10 243 160 83 269 269 0 strelka-varscan-mutect BICD1,missense_variant,p.Ala655Ser,ENST00000548411,NM_001003398.1;BICD1,missense_variant,p.Ala655Ser,ENST00000281474,NM_001714.2;BICD1,missense_variant,p.Ala7Ser,ENST00000547680,;BICD1,missense_variant,p.Ala655Ser,ENST00000395758,; T ENST00000281474 Transcript missense_variant 2066/3281 1963/2928 655/975 A/S Gcg/Tcg 1 1 BICD1 HGNC HGNC:1049 protein_coding YES CCDS8726.1 ENSP00000281474 Q96G01 UPI00001AEA67 NM_001714.2 tolerated(0.07) 5/10 hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF3,Pfam_domain:PF09730 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 32328418 32328418 G T 1 0 0 0 0 1 0 0 0 1577 971 34 2 2 BICD1 12 32328418 Missense_Mutation SNP G C3N-00560_T 1348793 32328418 100946891 822 17511 PKP2 0 . GRCh38 12 32869023 32869023 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1074T>A p.Ser358Arg p.S358R ENST00000070846 4/14 355 296 59 337 337 0 strelka-varscan-mutect PKP2,missense_variant,p.Ser358Arg,ENST00000340811,NM_001005242.2;PKP2,missense_variant,p.Ser358Arg,ENST00000070846,NM_004572.3; T ENST00000070846 Transcript missense_variant 1099/4241 1074/2646 358/881 S/R agT/agA 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 deleterious(0.03) 4/14 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 32869023 32869023 A T 1 0 0 0 0 1 0 0 0 12081 388 14 4 4 PKP2 12 32869023 Missense_Mutation SNP A C3N-00560_T 540605 32869023 100406286 823 17512 CPNE8 0 . GRCh38 12 38829404 38829404 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.382G>T p.Gly128Ter p.G128* ENST00000331366 6/20 140 99 41 166 166 0 strelka-varscan-mutect CPNE8,stop_gained,p.Gly128Ter,ENST00000331366,NM_153634.2;CPNE8,stop_gained,p.Gly116Ter,ENST00000360449,;CPNE8,5_prime_UTR_variant,,ENST00000550863,; A ENST00000331366 Transcript stop_gained 479/3489 382/1695 128/564 G/* Gga/Tga 1 -1 CPNE8 HGNC HGNC:23498 protein_coding YES CCDS8733.1 ENSP00000329748 Q86YQ8 UPI000015FF59 NM_153634.2 6/20 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF9,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 HIGH 1 SNV 1 1 PASS rs1415696432 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 38829404 38829404 C A 1 0 0 0 0 0 1 0 0 3613 632 22 2 2 CPNE8 12 38829404 Nonsense_Mutation SNP C C3N-00560_T 5960381 38829404 94445905 824 17513 SLC2A13 0 . GRCh38 12 40028487 40028487 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.739G>C p.Val247Leu p.V247L ENST00000280871 3/10 191 160 31 198 197 1 varscan-mutect SLC2A13,missense_variant,p.Val247Leu,ENST00000280871,NM_052885.3;SLC2A13,missense_variant,p.Val247Leu,ENST00000380858,; G ENST00000280871 Transcript missense_variant 790/7003 739/1947 247/648 V/L Gtt/Ctt 1 -1 SLC2A13 HGNC HGNC:15956 protein_coding YES CCDS8736.2 ENSP00000280871 Q96QE2 UPI000066D913 NM_052885.3 tolerated(0.32) 3/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23500,hmmpanther:PTHR23500:SF89,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 40028487 40028487 C G 1 0 0 0 0 1 0 0 0 14812 565 20 4 4 SLC2A13 12 40028487 Missense_Mutation SNP C C3N-00560_T 1199083 40028487 93246822 825 17514 CNTN1 0 . GRCh38 12 40929860 40929860 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.561A>T p.= p.R187R ENST00000551295 7/24 350 294 56 418 418 0 strelka-varscan-mutect CNTN1,synonymous_variant,p.=,ENST00000551295,NM_001843.3;CNTN1,synonymous_variant,p.=,ENST00000347616,;CNTN1,synonymous_variant,p.=,ENST00000348761,NM_175038.2;CNTN1,synonymous_variant,p.=,ENST00000547849,NM_001256064.1;CNTN1,synonymous_variant,p.=,ENST00000547702,NM_001256063.1; T ENST00000551295 Transcript synonymous_variant 678/5557 561/3057 187/1018 R cgA/cgT 1 1 CNTN1 HGNC HGNC:2171 protein_coding YES CCDS8737.1 ENSP00000447006 Q12860 A0A024R104 UPI0000127EBA NM_001843.3 7/24 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 40929860 40929860 A T 1 0 0 0 0 0 0 0 1 3421 320 12 4 4 CNTN1 12 40929860 Silent SNP A C3N-00560_T 901373 40929860 92345449 826 17515 PDZRN4 0 . GRCh38 12 41188674 41188674 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.219C>A p.= p.L73L ENST00000402685 1/10 235 195 40 227 227 0 strelka-varscan-mutect PDZRN4,synonymous_variant,p.=,ENST00000402685,NM_001164595.1; A ENST00000402685 Transcript synonymous_variant 227/3347 219/3111 73/1036 L ctC/ctA 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 1/10 Gene3D:3.30.40.10,Superfamily_domains:SSF57850 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 41188674 41188674 C A 1 0 0 0 0 0 0 0 1 11798 813 29 2 2 PDZRN4 12 41188674 Silent SNP C C3N-00560_T 258814 41188674 92086635 827 17516 ADAMTS20 0 . GRCh38 12 43375493 43375493 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.5332T>C p.Cys1778Arg p.C1778R ENST00000389420 36/39 120 94 26 180 180 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Cys1778Arg,ENST00000389420,NM_025003.3; G ENST00000389420 Transcript missense_variant 5332/6076 5332/5733 1778/1910 C/R Tgt/Cgt 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0) 36/39 PROSITE_profiles:PS51046,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF08685 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 43375493 43375493 A G 1 0 0 0 0 1 0 0 0 310 217 8 5 5 ADAMTS20 12 43375493 Missense_Mutation SNP A C3N-00560_T 2186819 43375493 89899816 828 17517 ADAMTS20 0 . GRCh38 12 43383599 43383599 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.4756C>G p.Pro1586Ala p.P1586A ENST00000389420 31/39 66 44 22 88 88 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Pro1586Ala,ENST00000389420,NM_025003.3; C ENST00000389420 Transcript missense_variant 4756/6076 4756/5733 1586/1910 P/A Cct/Gct 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(0.77) 31/39 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 43383599 43383599 G C 1 0 0 0 0 1 0 0 0 310 1232 43 4 4 ADAMTS20 12 43383599 Missense_Mutation SNP G C3N-00560_T 8106 43383599 89891710 829 17518 ARID2 0 . GRCh38 12 45839443 45839443 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1445G>T p.Arg482Met p.R482M ENST00000334344 11/21 148 109 39 132 132 0 strelka-varscan-mutect ARID2,missense_variant,p.Arg482Met,ENST00000334344,NM_152641.2;ARID2,missense_variant,p.Arg92Met,ENST00000444670,;ARID2,missense_variant,p.Arg333Met,ENST00000422737,;ARID2,non_coding_transcript_exon_variant,,ENST00000479608,;ARID2,non_coding_transcript_exon_variant,,ENST00000480128,; T ENST00000334344 Transcript missense_variant 1617/8642 1445/5508 482/1835 R/M aGg/aTg 1 1 ARID2 HGNC HGNC:18037 protein_coding YES CCDS31783.1 ENSP00000335044 Q68CP9 UPI00001D7973 NM_152641.2 deleterious(0) 11/21 hmmpanther:PTHR22970,hmmpanther:PTHR22970:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 45839443 45839443 G T 1 0 0 0 0 1 0 0 0 1051 1000 35 2 2 ARID2 12 45839443 Missense_Mutation SNP G C3N-00560_T 2455844 45839443 87435866 830 17519 COL2A1 0 . GRCh38 12 47997683 47997683 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.454G>T p.Asp152Tyr p.D152Y ENST00000380518 7/54 396 318 78 387 387 0 strelka-varscan-mutect COL2A1,missense_variant,p.Asp152Tyr,ENST00000380518,NM_001844.4;COL2A1,missense_variant,p.Asp83Tyr,ENST00000337299,NM_033150.2;COL2A1,non_coding_transcript_exon_variant,,ENST00000474996,;COL2A1,downstream_gene_variant,,ENST00000465743,;COL2A1,downstream_gene_variant,,ENST00000466884,;COL2A1,downstream_gene_variant,,ENST00000490609,; A ENST00000380518 Transcript missense_variant 619/5071 454/4464 152/1487 D/Y Gat/Tat 1 -1 COL2A1 HGNC HGNC:2200 protein_coding YES CCDS41778.1 ENSP00000369889 P02458 UPI0000D79713 NM_001844.4 deleterious(0) 7/54 Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 47997683 47997683 C A 1 0 0 0 0 1 0 0 0 3476 913 32 2 2 COL2A1 12 47997683 Missense_Mutation SNP C C3N-00560_T 2158240 47997683 85277626 831 17520 SPATS2 0 . GRCh38 12 49526169 49526169 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1552G>T p.Glu518Ter p.E518* ENST00000553127 15/15 298 245 53 274 274 0 strelka-varscan-mutect SPATS2,stop_gained,p.Glu518Ter,ENST00000553127,NM_001293285.1;SPATS2,stop_gained,p.Glu518Ter,ENST00000321898,NM_001293286.1;SPATS2,stop_gained,p.Glu518Ter,ENST00000552918,NM_023071.3;SPATS2,non_coding_transcript_exon_variant,,ENST00000547003,;SPATS2,3_prime_UTR_variant,,ENST00000549412,;SPATS2,downstream_gene_variant,,ENST00000548727,; T ENST00000553127 Transcript stop_gained 2065/3320 1552/1638 518/545 E/* Gag/Tag 1 1 SPATS2 HGNC HGNC:18650 protein_coding YES CCDS31794.1 ENSP00000448228 Q86XZ4 A0A024R101 UPI0000171C5F NM_001293285.1 15/15 hmmpanther:PTHR15623,hmmpanther:PTHR15623:SF10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 49526169 49526169 G T 1 0 0 0 0 0 1 0 0 15365 1175 41 2 2 SPATS2 12 49526169 Nonsense_Mutation SNP G C3N-00560_T 1528486 49526169 83749140 832 17521 KCNH3 0 . GRCh38 12 49549139 49549139 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1434G>T p.Glu478Asp p.E478D ENST00000257981 8/15 80 66 14 59 59 0 strelka-varscan-mutect KCNH3,missense_variant,p.Glu478Asp,ENST00000257981,NM_001314030.1,NM_012284.1;KCNH3,downstream_gene_variant,,ENST00000551415,; T ENST00000257981 Transcript missense_variant 1694/3867 1434/3252 478/1083 E/D gaG/gaT 1 1 KCNH3 HGNC HGNC:6252 protein_coding YES CCDS8786.1 ENSP00000257981 Q9ULD8 UPI000012DCA6 NM_001314030.1,NM_012284.1 deleterious(0.01) 8/15 hmmpanther:PTHR10217:SF481,hmmpanther:PTHR10217,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR01463 MODERATE 1 SNV 1 1 PASS rs1211350694 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 49549139 49549139 G T 1 0 0 0 0 1 0 0 0 7949 933 33 2 2 KCNH3 12 49549139 Missense_Mutation SNP G C3N-00560_T 22970 49549139 83726170 833 17522 NCKAP5L 0 . GRCh38 12 49796601 49796601 + Missense_Mutation SNP C C G rs775598664 C3N-00560_T C3N-00560_N C C c.1259G>C p.Arg420Pro p.R420P ENST00000335999 8/13 34 22 12 45 45 0 strelka-varscan-mutect NCKAP5L,missense_variant,p.Arg420Pro,ENST00000335999,NM_001037806.3;NCKAP5L,missense_variant,p.Arg135Pro,ENST00000433948,; G ENST00000335999 Transcript missense_variant 1461/4900 1259/4005 420/1334 R/P cGg/cCg rs775598664 1 -1 NCKAP5L HGNC HGNC:29321 protein_coding YES CCDS41781.2 ENSP00000337998 Q9HCH0 UPI00006C1298 NM_001037806.3 deleterious_low_confidence(0.05) 8/13 hmmpanther:PTHR21740 MODERATE 1 SNV 5 1 PASS rs775598664 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 56 49796601 49796601 C G 1 0 0 0 0 1 0 0 0 10242 652 23 4 4 NCKAP5L 12 49796601 Missense_Mutation SNP C C3N-00560_T 247462 49796601 83478708 834 17523 FAM186A 0 . GRCh38 12 50352439 50352439 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4393C>A p.Gln1465Lys p.Q1465K ENST00000327337 4/8 336 305 31 394 393 1 varscan-mutect FAM186A,missense_variant,p.Gln1465Lys,ENST00000543111,;FAM186A,missense_variant,p.Gln1465Lys,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; T ENST00000327337 Transcript missense_variant 4393/7127 4393/7056 1465/2351 Q/K Cag/Aag 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 tolerated(0.1) 4/8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 50352439 50352439 G T 1 0 0 0 0 1 0 0 0 5361 1299 45 2 2 FAM186A 12 50352439 Missense_Mutation SNP G C3N-00560_T 555838 50352439 82922870 835 17524 FAM186A 0 . GRCh38 12 50352605 50352605 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.4227C>A p.= p.I1409I ENST00000327337 4/8 335 273 62 426 426 0 strelka-varscan-mutect FAM186A,synonymous_variant,p.=,ENST00000543111,;FAM186A,synonymous_variant,p.=,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; T ENST00000327337 Transcript synonymous_variant 4227/7127 4227/7056 1409/2351 I atC/atA 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 50352605 50352605 G T 1 0 0 0 0 0 0 0 1 5361 1164 41 2 2 FAM186A 12 50352605 Silent SNP G C3N-00560_T 166 50352605 82922704 836 17525 FAM186A 0 . GRCh38 12 50352983 50352983 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3849G>T p.Gln1283His p.Q1283H ENST00000327337 4/8 196 159 37 216 216 0 strelka-varscan-mutect FAM186A,missense_variant,p.Gln1283His,ENST00000543111,;FAM186A,missense_variant,p.Gln1283His,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; A ENST00000327337 Transcript missense_variant 3849/7127 3849/7056 1283/2351 Q/H caG/caT 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 deleterious(0.03) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 50352983 50352983 C A 1 0 0 0 0 1 0 0 0 5361 680 24 2 2 FAM186A 12 50352983 Missense_Mutation SNP C C3N-00560_T 378 50352983 82922326 837 17526 NR4A1 0 . GRCh38 12 52054988 52054988 + Silent SNP G G A rs749848012 C3N-00560_T C3N-00560_N G G c.822G>A p.= p.E274E ENST00000545748 3/8 246 156 90 234 234 0 strelka-varscan-mutect NR4A1,synonymous_variant,p.=,ENST00000545748,NM_001202234.1;NR4A1,synonymous_variant,p.=,ENST00000243050,NM_002135.4;NR4A1,synonymous_variant,p.=,ENST00000394824,;NR4A1,synonymous_variant,p.=,ENST00000360284,NM_001202233.1;NR4A1,synonymous_variant,p.=,ENST00000394825,NM_173157.2;NR4A1,synonymous_variant,p.=,ENST00000550082,;NR4A1,synonymous_variant,p.=,ENST00000546842,;NR4A1,synonymous_variant,p.=,ENST00000548232,;NR4A1,intron_variant,,ENST00000550763,;NR4A1,downstream_gene_variant,,ENST00000562373,;NR4A1,upstream_gene_variant,,ENST00000550582,;NR4A1,downstream_gene_variant,,ENST00000548977,;RP11-1100L3.8,downstream_gene_variant,,ENST00000564363,;RP11-1100L3.8,downstream_gene_variant,,ENST00000564531,;NR4A1,intron_variant,,ENST00000548733,;NR4A1,downstream_gene_variant,,ENST00000547206,;NR4A1,non_coding_transcript_exon_variant,,ENST00000550557,;NR4A1,non_coding_transcript_exon_variant,,ENST00000478250,;NR4A1,upstream_gene_variant,,ENST00000564201,;NR4A1,upstream_gene_variant,,ENST00000565848,;NR4A1,upstream_gene_variant,,ENST00000567890,;NR4A1,downstream_gene_variant,,ENST00000549102,;NR4A1,upstream_gene_variant,,ENST00000550339,; A ENST00000545748 Transcript synonymous_variant 1817/3511 822/1959 274/652 E gaG/gaA rs749848012 1 1 NR4A1 HGNC HGNC:7980 protein_coding YES CCDS73471.1 ENSP00000440864 F5GXF0 UPI0000D621F3 NM_001202234.1 3/8 hmmpanther:PTHR24085:SF1,hmmpanther:PTHR24085,Prints_domain:PR01285 LOW 1 SNV 2 1 PASS rs749848012 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 52054988 52054988 G A 1 0 0 0 0 0 0 0 1 10688 991 35 3 3 NR4A1 12 52054988 Silent SNP G C3N-00560_T 1702005 52054988 81220321 838 17527 KRT71 0 . GRCh38 12 52550043 52550043 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.642G>A p.= p.E214E ENST00000267119 2/9 235 191 44 207 207 0 strelka-varscan-mutect KRT71,synonymous_variant,p.=,ENST00000267119,NM_033448.2; T ENST00000267119 Transcript synonymous_variant 712/2265 642/1572 214/523 E gaG/gaA 1 -1 KRT71 HGNC HGNC:28927 protein_coding YES CCDS8831.1 ENSP00000267119 Q3SY84 UPI0000052B57 NM_033448.2 2/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01276,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF116,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999996 1 1 1 0 T 2 4 56 52550043 52550043 C T 1 0 0 0 0 0 0 0 1 8366 680 24 3 3 KRT71 12 52550043 Silent SNP C C3N-00560_T 495055 52550043 80725266 839 17528 PFDN5 0 . GRCh38 12 53295602 53295602 + Missense_Mutation SNP T T A rs199718276 C3N-00560_T C3N-00560_N T T c.35T>A p.Leu12Gln p.L12Q ENST00000551018 1/6 202 130 72 226 225 1 strelka-varscan-mutect PFDN5,missense_variant,p.Leu12Gln,ENST00000551018,NM_002624.3;PFDN5,missense_variant,p.Leu12Gln,ENST00000334478,;PFDN5,missense_variant,p.Leu8Gln,ENST00000549759,;PFDN5,missense_variant,p.Leu12Gln,ENST00000351500,NM_145897.2;PFDN5,missense_variant,p.Leu12Gln,ENST00000550846,;PFDN5,missense_variant,p.Leu12Gln,ENST00000628881,;ESPL1,downstream_gene_variant,,ENST00000257934,NM_012291.4;ESPL1,downstream_gene_variant,,ENST00000552462,;C12orf10,upstream_gene_variant,,ENST00000267103,NM_021640.3;C12orf10,upstream_gene_variant,,ENST00000548632,;C12orf10,upstream_gene_variant,,ENST00000549488,;RP11-680A11.5,downstream_gene_variant,,ENST00000550263,;PFDN5,missense_variant,p.Leu12Gln,ENST00000550880,;PFDN5,missense_variant,p.Leu12Gln,ENST00000552742,;PFDN5,missense_variant,p.Leu12Gln,ENST00000243040,;PFDN5,missense_variant,p.Leu12Gln,ENST00000547130,;PFDN5,non_coding_transcript_exon_variant,,ENST00000552341,;PFDN5,non_coding_transcript_exon_variant,,ENST00000550513,;PFDN5,non_coding_transcript_exon_variant,,ENST00000547228,;PFDN5,non_coding_transcript_exon_variant,,ENST00000550069,;PFDN5,non_coding_transcript_exon_variant,,ENST00000549995,;PFDN5,non_coding_transcript_exon_variant,,ENST00000551223,;ESPL1,downstream_gene_variant,,ENST00000552671,;ESPL1,downstream_gene_variant,,ENST00000549154,;C12orf10,upstream_gene_variant,,ENST00000548845,;C12orf10,upstream_gene_variant,,ENST00000551670,;PFDN5,upstream_gene_variant,,ENST00000550964,;C12orf10,upstream_gene_variant,,ENST00000551131,;PFDN5,upstream_gene_variant,,ENST00000548984,;PFDN5,upstream_gene_variant,,ENST00000552548,;PFDN5,upstream_gene_variant,,ENST00000553171,; A ENST00000551018 Transcript missense_variant 312/847 35/465 12/154 L/Q cTg/cAg rs199718276,COSM1261971 1 1 PFDN5 HGNC HGNC:8869 protein_coding YES CCDS8853.1 ENSP00000447942 Q99471 UPI00000009FD NM_002624.3 deleterious(0) 1/6 HAMAP:MF_00308,hmmpanther:PTHR12674:SF2,hmmpanther:PTHR12674,TIGRFAM_domain:TIGR00293,Gene3D:1.10.287.370,Superfamily_domains:SSF46579 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199718276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 53295602 53295602 T A 1 0 0 0 0 1 0 0 0 11848 1580 55 4 4 PFDN5 12 53295602 Missense_Mutation SNP T C3N-00560_T 745559 53295602 79979707 840 17529 PMEL 0 . GRCh38 12 55961704 55961704 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.105C>T p.= p.V35V ENST00000449260 2/11 185 151 34 185 185 0 strelka-varscan-mutect PMEL,synonymous_variant,p.=,ENST00000548747,;PMEL,synonymous_variant,p.=,ENST00000552882,;PMEL,synonymous_variant,p.=,ENST00000548493,NM_006928.4;PMEL,synonymous_variant,p.=,ENST00000449260,NM_001200054.1;PMEL,synonymous_variant,p.=,ENST00000547137,;PMEL,synonymous_variant,p.=,ENST00000546543,;PMEL,synonymous_variant,p.=,ENST00000548803,;PMEL,synonymous_variant,p.=,ENST00000549233,;PMEL,synonymous_variant,p.=,ENST00000549418,;PMEL,intron_variant,,ENST00000550464,NM_001200053.1;PMEL,intron_variant,,ENST00000550447,;PMEL,upstream_gene_variant,,ENST00000549404,;PMEL,non_coding_transcript_exon_variant,,ENST00000548689,;PMEL,upstream_gene_variant,,ENST00000549564,;PMEL,non_coding_transcript_exon_variant,,ENST00000550590,;PMEL,non_coding_transcript_exon_variant,,ENST00000549430,;PMEL,non_coding_transcript_exon_variant,,ENST00000549413,;PMEL,upstream_gene_variant,,ENST00000556802,; A ENST00000449260 Transcript synonymous_variant 116/2127 105/2007 35/668 V gtC/gtT 1 -1 PMEL HGNC HGNC:10880 protein_coding YES CCDS55834.1 ENSP00000402758 P40967 UPI0000EE2701 NM_001200054.1 2/11 hmmpanther:PTHR11861,hmmpanther:PTHR11861:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 55961704 55961704 G A 1 0 0 0 0 0 0 0 1 12238 929 33 3 3 PMEL 12 55961704 Silent SNP G C3N-00560_T 2666102 55961704 77313605 841 17530 STAT2 0 . GRCh38 12 56349258 56349258 + Missense_Mutation SNP C C G rs766306027 C3N-00560_T C3N-00560_N C C c.1345G>C p.Asp449His p.D449H ENST00000314128 16/24 183 151 32 177 177 0 strelka-varscan-mutect STAT2,missense_variant,p.Asp449His,ENST00000314128,NM_005419.3;STAT2,missense_variant,p.Asp445His,ENST00000557235,NM_198332.1;STAT2,intron_variant,,ENST00000418572,;RNU7-40P,downstream_gene_variant,,ENST00000516397,;STAT2,non_coding_transcript_exon_variant,,ENST00000556539,;STAT2,downstream_gene_variant,,ENST00000557252,;STAT2,downstream_gene_variant,,ENST00000557156,;STAT2,downstream_gene_variant,,ENST00000556140,;STAT2,upstream_gene_variant,,ENST00000557199,;STAT2,downstream_gene_variant,,ENST00000555519,;STAT2,upstream_gene_variant,,ENST00000555488,; G ENST00000314128 Transcript missense_variant 1369/3259 1345/2556 449/851 D/H Gac/Cac rs766306027 1 -1 STAT2 HGNC HGNC:11363 protein_coding YES CCDS8917.1 ENSP00000315768 P52630 R9QE65 UPI00000473FC NM_005419.3 deleterious(0.01) 16/24 Gene3D:2.60.40.630,Pfam_domain:PF02864,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF41,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS rs766306027 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 56349258 56349258 C G 1 0 0 0 0 1 0 0 0 15641 869 30 4 4 STAT2 12 56349258 Missense_Mutation SNP C C3N-00560_T 387554 56349258 76926051 842 17531 ZBTB39 0 . GRCh38 12 57002872 57002872 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.2046G>T p.= p.V682V ENST00000300101 2/2 254 166 88 208 208 0 strelka-varscan-mutect ZBTB39,synonymous_variant,p.=,ENST00000300101,NM_014830.2;GPR182,downstream_gene_variant,,ENST00000300098,NM_007264.3;GPR182,downstream_gene_variant,,ENST00000556850,; A ENST00000300101 Transcript synonymous_variant 2132/6170 2046/2139 682/712 V gtG/gtT 1 -1 ZBTB39 HGNC HGNC:29014 protein_coding YES CCDS31839.1 ENSP00000300101 O15060 UPI0000139682 NM_014830.2 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF218,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 57002872 57002872 C A 1 0 0 0 0 0 0 0 1 18109 697 25 2 2 ZBTB39 12 57002872 Silent SNP C C3N-00560_T 653614 57002872 76272437 843 17532 ARHGAP9 0 . GRCh38 12 57476924 57476924 + Missense_Mutation SNP G G T rs533374298 C3N-00560_T C3N-00560_N G G c.910C>A p.Pro304Thr p.P304T ENST00000393791 6/18 435 368 67 441 441 0 strelka-varscan-mutect ARHGAP9,missense_variant,p.Pro375Thr,ENST00000393797,NM_001319850.1;ARHGAP9,missense_variant,p.Pro383Thr,ENST00000550288,;ARHGAP9,missense_variant,p.Pro304Thr,ENST00000393791,NM_032496.2;ARHGAP9,missense_variant,p.Pro304Thr,ENST00000424809,NM_001080157.1;ARHGAP9,missense_variant,p.Pro120Thr,ENST00000430041,NM_001080156.1;ARHGAP9,missense_variant,p.Pro120Thr,ENST00000548139,;ARHGAP9,missense_variant,p.Pro120Thr,ENST00000552066,;ARHGAP9,missense_variant,p.Pro157Thr,ENST00000551452,;ARHGAP9,intron_variant,,ENST00000552604,;GLI1,downstream_gene_variant,,ENST00000228682,NM_005269.2;GLI1,downstream_gene_variant,,ENST00000546141,NM_001167609.1;GLI1,downstream_gene_variant,,ENST00000543426,NM_001160045.1;GLI1,downstream_gene_variant,,ENST00000528467,;ARHGAP9,upstream_gene_variant,,ENST00000550399,;ARHGAP9,downstream_gene_variant,,ENST00000552249,;ARHGAP9,downstream_gene_variant,,ENST00000549602,;ARHGAP9,upstream_gene_variant,,ENST00000550130,;ARHGAP9,intron_variant,,ENST00000550454,;MARS,intron_variant,,ENST00000549133,;ARHGAP9,upstream_gene_variant,,ENST00000547200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000546200,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000552420,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000548148,;ARHGAP9,non_coding_transcript_exon_variant,,ENST00000551574,;ARHGAP9,upstream_gene_variant,,ENST00000552953,;ARHGAP9,upstream_gene_variant,,ENST00000550440,;ARHGAP9,downstream_gene_variant,,ENST00000547216,;ARHGAP9,upstream_gene_variant,,ENST00000546704,;ARHGAP9,downstream_gene_variant,,ENST00000551000,; T ENST00000393791 Transcript missense_variant 1049/2597 910/2196 304/731 P/T Cct/Act rs533374298 1 -1 ARHGAP9 HGNC HGNC:14130 protein_coding YES CCDS8941.2 ENSP00000377380 Q9BRR9 UPI000007131B NM_032496.2 tolerated(0.19) 6/18 Low_complexity_(Seg):seg,hmmpanther:PTHR23181:SF4,hmmpanther:PTHR23181 MODERATE 1 SNV 1 1 PASS rs533374298 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57476924 57476924 G T 1 0 0 0 0 1 0 0 0 1019 1232 43 2 2 ARHGAP9 12 57476924 Missense_Mutation SNP G C3N-00560_T 474052 57476924 75798385 844 17533 WIF1 0 . GRCh38 12 65062511 65062511 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.796C>A p.Pro266Thr p.P266T ENST00000286574 7/10 143 85 58 173 172 1 strelka-varscan-mutect WIF1,missense_variant,p.Pro266Thr,ENST00000286574,NM_007191.4;WIF1,missense_variant,p.Pro29Thr,ENST00000543094,; T ENST00000286574 Transcript missense_variant 1171/2238 796/1140 266/379 P/T Cca/Aca 1 -1 WIF1 HGNC HGNC:18081 protein_coding YES CCDS8971.1 ENSP00000286574 Q9Y5W5 UPI0000038BEE NM_007191.4 tolerated(0.13) 7/10 Gene3D:2gy5A03,Pfam_domain:PF12661,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs1482903439 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 65062511 65062511 G T 1 0 0 0 0 1 0 0 0 17922 1174 41 2 2 WIF1 12 65062511 Missense_Mutation SNP G C3N-00560_T 7585587 65062511 68212798 845 17534 KCNC2 0 . GRCh38 12 75207454 75207454 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.530G>C p.Gly177Ala p.G177A ENST00000549446 2/5 260 211 49 286 286 0 strelka-varscan-mutect KCNC2,missense_variant,p.Gly177Ala,ENST00000549446,NM_139137.3;KCNC2,missense_variant,p.Gly177Ala,ENST00000298972,NM_139136.3;KCNC2,missense_variant,p.Gly177Ala,ENST00000350228,NM_153748.2;KCNC2,missense_variant,p.Gly177Ala,ENST00000548513,;KCNC2,missense_variant,p.Gly177Ala,ENST00000550433,NM_001260498.1;KCNC2,missense_variant,p.Gly177Ala,ENST00000393288,NM_001260497.1;KCNC2,missense_variant,p.Gly177Ala,ENST00000540018,NM_001260499.1; G ENST00000549446 Transcript missense_variant 1211/5625 530/1917 177/638 G/A gGc/gCc 1 -1 KCNC2 HGNC HGNC:6234 protein_coding YES CCDS9007.1 ENSP00000449253 Q96PR1 A0A024RBA5 UPI000004DB9B NM_139137.3 tolerated(0.37) 2/5 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 75207454 75207454 C G 1 0 0 0 0 1 0 0 0 7931 739 26 4 4 KCNC2 12 75207454 Missense_Mutation SNP C C3N-00560_T 10144943 75207454 58067855 846 17535 GLIPR1L1 0 . GRCh38 12 75366955 75366955 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.101C>A p.Pro34His p.P34H ENST00000548623 1/2 458 366 92 401 400 1 strelka-varscan-mutect GLIPR1L1,missense_variant,p.Pro34His,ENST00000548623,;GLIPR1L1,missense_variant,p.Pro7His,ENST00000547144,;GLIPR1L1,intron_variant,,ENST00000312442,NM_152779.3;GLIPR1L1,intron_variant,,ENST00000378695,NM_001304964.1;CAPS2,intron_variant,,ENST00000436898,;CAPS2,intron_variant,,ENST00000552497,;CAPS2,intron_variant,,ENST00000551829,;CAPS2,intron_variant,,ENST00000548958,;CAPS2,intron_variant,,ENST00000486196,;CAPS2,intron_variant,,ENST00000547320,;CAPS2,intron_variant,,ENST00000328705,;CAPS2,intron_variant,,ENST00000336815,; A ENST00000548623 Transcript missense_variant 123/484 101/174 34/57 P/H cCc/cAc 1 1 GLIPR1L1 HGNC HGNC:28392 protein_coding ENSP00000487263 A0A0D9SG94 UPI0005C122A5 1/2 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 75366955 75366955 C A 1 0 0 0 0 1 0 0 0 6320 623 22 2 2 GLIPR1L1 12 75366955 Missense_Mutation SNP C C3N-00560_T 159501 75366955 57908354 847 17536 OTOGL 0 . GRCh38 12 80305581 80305581 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3192G>T p.Lys1064Asn p.K1064N ENST00000458043 28/58 49 33 16 83 83 0 strelka-varscan-mutect OTOGL,missense_variant,p.Lys1064Asn,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Lys1064Asn,ENST00000547103,; T ENST00000458043 Transcript missense_variant 3198/8083 3192/7035 1064/2344 K/N aaG/aaT 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0.01) 28/58 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Pfam_domain:PF00094,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80305581 80305581 G T 1 0 0 0 0 1 0 0 0 11371 985 34 2 2 OTOGL 12 80305581 Missense_Mutation SNP G C3N-00560_T 4938626 80305581 52969728 848 17537 PTPRQ 0 . GRCh38 12 80635073 80635073 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.5915G>T p.Arg1972Leu p.R1972L ENST00000614701 35/45 165 133 32 205 205 0 strelka-mutect PTPRQ,missense_variant,p.Arg1972Leu,ENST00000614701,NM_001145026.1;PTPRQ,missense_variant,p.Arg2014Leu,ENST00000616559,;PTPRQ,missense_variant,p.Arg67Leu,ENST00000547881,;PTPRQ,splice_region_variant,,ENST00000549355,; T ENST00000614701 Transcript missense_variant,splice_region_variant 6093/8289 5915/6900 1972/2299 R/L cGg/cTg 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 deleterious(0.03) 35/45 MODERATE 1 SNV 5 1 PASS rs1314753637 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80635073 80635073 G T 1 0 0 0 0 1 0 0 0 12964 1130 39 1 1 PTPRQ 12 80635073 Missense_Mutation SNP G C3N-00560_T 329492 80635073 52640236 849 17538 PTPRQ 0 . GRCh38 12 80673220 80673220 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.6654A>G p.= p.Q2218Q ENST00000614701 43/45 173 146 27 217 217 0 strelka-varscan-mutect PTPRQ,synonymous_variant,p.=,ENST00000614701,NM_001145026.1;PTPRQ,synonymous_variant,p.=,ENST00000616559,; G ENST00000614701 Transcript synonymous_variant 6832/8289 6654/6900 2218/2299 Q caA/caG 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 43/45 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 LOW 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -14.26646 0.9971074 1 1 1 0 G 2 3 56 80673220 80673220 A G 1 0 0 0 0 0 0 0 1 12964 40 2 5 5 PTPRQ 12 80673220 Silent SNP A C3N-00560_T 38147 80673220 52602089 850 17539 MYF6 0 . GRCh38 12 80708926 80708926 + Missense_Mutation SNP A A T rs747177260 C3N-00560_T C3N-00560_N A A c.695A>T p.Lys232Ile p.K232I ENST00000228641 3/3 365 260 105 397 397 0 strelka-varscan-mutect MYF6,missense_variant,p.Lys232Ile,ENST00000228641,NM_002469.2; T ENST00000228641 Transcript missense_variant 917/1465 695/729 232/242 K/I aAa/aTa rs747177260 1 1 MYF6 HGNC HGNC:7566 protein_coding YES CCDS9019.1 ENSP00000228641 P23409 UPI0000001050 NM_002469.2 tolerated(0.06) 3/3 hmmpanther:PTHR11534,hmmpanther:PTHR11534:SF4 MODERATE 1 SNV 1 1 PASS rs747177260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80708926 80708926 A T 1 0 0 0 0 1 0 0 0 10028 14 1 4 4 MYF6 12 80708926 Missense_Mutation SNP A C3N-00560_T 35706 80708926 52566383 851 17540 SLC6A15 0 . GRCh38 12 84892069 84892069 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.52G>T p.Glu18Ter p.E18* ENST00000266682 2/12 161 110 51 199 199 0 strelka-varscan-mutect SLC6A15,stop_gained,p.Glu18Ter,ENST00000266682,NM_182767.5;SLC6A15,stop_gained,p.Glu18Ter,ENST00000450363,NM_018057.6;SLC6A15,stop_gained,p.Glu18Ter,ENST00000549540,;SLC6A15,stop_gained,p.Glu18Ter,ENST00000551010,;SLC6A15,intron_variant,,ENST00000552192,NM_001146335.2;SLC6A15,intron_variant,,ENST00000551612,;SLC6A15,intron_variant,,ENST00000551388,;SLC6A15,intron_variant,,ENST00000547240,; A ENST00000266682 Transcript stop_gained 594/4879 52/2193 18/730 E/* Gag/Tag 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 2/12 hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 84892069 84892069 C A 1 0 0 0 0 0 1 0 0 14961 835 29 2 2 SLC6A15 12 84892069 Nonsense_Mutation SNP C C3N-00560_T 4183143 84892069 48383240 852 17541 LRRIQ1 0 . GRCh38 12 85104039 85104039 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3245C>A p.Ser1082Ter p.S1082* ENST00000393217 14/27 51 40 11 144 144 0 strelka-varscan-mutect LRRIQ1,stop_gained,p.Ser1082Ter,ENST00000393217,NM_001079910.1;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,; A ENST00000393217 Transcript stop_gained 3306/5394 3245/5169 1082/1722 S/* tCa/tAa 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 14/27 PROSITE_profiles:PS51450,hmmpanther:PTHR24365:SF66,hmmpanther:PTHR24365,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 85104039 85104039 C A 1 0 0 0 0 0 1 0 0 8935 838 29 2 2 LRRIQ1 12 85104039 Nonsense_Mutation SNP C C3N-00560_T 211970 85104039 48171270 853 17542 POC1B 0 . GRCh38 12 89425344 89425344 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1149G>T p.Lys383Asn p.K383N ENST00000313546 11/12 242 205 37 190 190 0 strelka-varscan-mutect POC1B,missense_variant,p.Lys253Asn,ENST00000393179,;POC1B,missense_variant,p.Lys383Asn,ENST00000313546,NM_172240.2;POC1B,missense_variant,p.Lys341Asn,ENST00000549035,NM_001199777.1;POC1B,3_prime_UTR_variant,,ENST00000549504,;POC1B,non_coding_transcript_exon_variant,,ENST00000546740,;POC1B,3_prime_UTR_variant,,ENST00000547496,;POC1B,3_prime_UTR_variant,,ENST00000548715,;POC1B,non_coding_transcript_exon_variant,,ENST00000549591,; A ENST00000313546 Transcript missense_variant 1278/3001 1149/1437 383/478 K/N aaG/aaT 1 -1 POC1B HGNC HGNC:30836 protein_coding YES CCDS31869.1 ENSP00000323302 Q8TC44 A0MNP0 UPI000006E6B9 NM_172240.2 tolerated(0.43) 11/12 MODERATE 1 SNV 1 1 PASS rs1414322338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 89425344 89425344 C A 1 0 0 0 0 1 0 0 0 12285 680 24 2 2 POC1B 12 89425344 Missense_Mutation SNP C C3N-00560_T 4321305 89425344 43849965 854 17543 CCER1 0 . GRCh38 12 90954025 90954025 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.718A>T p.Ser240Cys p.S240C ENST00000358859 1/1 308 268 40 271 271 0 strelka-varscan-mutect CCER1,missense_variant,p.Ser240Cys,ENST00000358859,NM_152638.3;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,; A ENST00000358859 Transcript missense_variant 1152/2962 718/1221 240/406 S/C Agc/Tgc 1 -1 CCER1 HGNC HGNC:28373 protein_coding YES CCDS9036.1 ENSP00000351727 Q8TC90 UPI000006EE70 NM_152638.3 tolerated(0.23) 1/1 hmmpanther:PTHR37337:SF1,hmmpanther:PTHR37337 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 90954025 90954025 T A 1 0 0 0 0 1 0 0 0 2574 1580 55 4 4 CCER1 12 90954025 Missense_Mutation SNP T C3N-00560_T 1528681 90954025 42321284 855 17544 LUM 0 . GRCh38 12 91108716 91108716 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.264T>C p.= p.N88N ENST00000266718 2/3 310 162 148 259 259 0 strelka-varscan-mutect LUM,synonymous_variant,p.=,ENST00000266718,NM_002345.3;LUM,intron_variant,,ENST00000548071,;LUM,intron_variant,,ENST00000546642,; G ENST00000266718 Transcript synonymous_variant 719/3008 264/1017 88/338 N aaT/aaC 1 -1 LUM HGNC HGNC:6724 protein_coding YES CCDS9038.1 ENSP00000266718 P51884 UPI0000001C4D NM_002345.3 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF119,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 91108716 91108716 A G 1 0 0 0 0 0 0 0 1 8992 214 8 5 5 LUM 12 91108716 Silent SNP A C3N-00560_T 154691 91108716 42166593 856 17545 CLLU1 0 . GRCh38 12 92424792 92424792 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.112C>A p.Leu38Met p.L38M ENST00000378485 1/2 59 50 9 94 94 0 strelka-varscan-mutect CLLU1,missense_variant,p.Leu38Met,ENST00000378485,NM_001025233.1;CLLU1OS,intron_variant,,ENST00000378487,NM_001025232.1;RP11-693J15.4,intron_variant,,ENST00000508671,;CLLU1,intron_variant,,ENST00000472839,;CLLU1,intron_variant,,ENST00000512817,;CLLU1,non_coding_transcript_exon_variant,,ENST00000586526,;CLLU1,downstream_gene_variant,,ENST00000589406,; A ENST00000378485 Transcript missense_variant 834/3897 112/366 38/121 L/M Ctg/Atg 1 1 CLLU1 HGNC HGNC:29841 protein_coding YES ENSP00000367746 Q5K131 UPI00004A1179 NM_001025233.1 1/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 92424792 92424792 C A 1 0 0 0 0 1 0 0 0 3309 912 32 2 2 CLLU1 12 92424792 Missense_Mutation SNP C C3N-00560_T 1316076 92424792 40850517 857 17546 CEP83 0 . GRCh38 12 94412375 94412375 + Missense_Mutation SNP C C A rs149856098 C3N-00560_T C3N-00560_N C C c.116G>T p.Arg39Met p.R39M ENST00000397809 3/17 201 114 87 153 153 0 strelka-varscan-mutect CEP83,missense_variant,p.Arg39Met,ENST00000397809,NM_016122.2;CEP83,missense_variant,p.Arg39Met,ENST00000339839,NM_001042399.1;CEP83,missense_variant,p.Arg39Met,ENST00000547575,;CEP83,5_prime_UTR_variant,,ENST00000397807,;CEP83,downstream_gene_variant,,ENST00000546527,;CEP83,upstream_gene_variant,,ENST00000549352,;CEP83,missense_variant,p.Arg6Met,ENST00000547232,;CEP83,non_coding_transcript_exon_variant,,ENST00000551596,;CEP83,upstream_gene_variant,,ENST00000551078,; A ENST00000397809 Transcript missense_variant 666/3773 116/2106 39/701 R/M aGg/aTg rs149856098 1 -1 CEP83 HGNC HGNC:17966 protein_coding YES CCDS41820.1 ENSP00000380911 J3KNW7 UPI0000D4BD6F NM_016122.2 deleterious(0) 3/17 hmmpanther:PTHR23170,hmmpanther:PTHR23170:SF2 MODERATE 1 SNV 1 1 PASS rs149856098 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 94412375 94412375 C A 1 0 0 0 0 1 0 0 0 2984 681 24 2 2 CEP83 12 94412375 Missense_Mutation SNP C C3N-00560_T 1987583 94412375 38862934 858 17547 FGD6 0 . GRCh38 12 95141413 95141413 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2812G>T p.Glu938Ter p.E938* ENST00000343958 6/21 161 95 66 122 121 1 strelka-varscan-mutect FGD6,stop_gained,p.Glu938Ter,ENST00000343958,NM_018351.3;FGD6,stop_gained,p.Glu938Ter,ENST00000546711,;FGD6,stop_gained,p.Glu938Ter,ENST00000549499,;FGD6,3_prime_UTR_variant,,ENST00000451107,; A ENST00000343958 Transcript stop_gained 3036/9288 2812/4293 938/1430 E/* Gaa/Taa 1 -1 FGD6 HGNC HGNC:21740 protein_coding YES CCDS31878.1 ENSP00000344446 Q6ZV73 UPI00001FB2F4 NM_018351.3 6/21 PROSITE_profiles:PS50010,hmmpanther:PTHR12673:SF12,hmmpanther:PTHR12673,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 95141413 95141413 C A 1 0 0 0 0 0 1 0 0 5701 864 30 2 2 FGD6 12 95141413 Nonsense_Mutation SNP C C3N-00560_T 729038 95141413 38133896 859 17548 UHRF1BP1L 0 . GRCh38 12 100051128 100051128 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.3518A>G p.Asp1173Gly p.D1173G ENST00000279907 16/21 291 147 144 258 258 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Asp1173Gly,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Asp823Gly,ENST00000545232,;UHRF1BP1L,upstream_gene_variant,,ENST00000548712,;UHRF1BP1L,non_coding_transcript_exon_variant,,ENST00000547504,; C ENST00000279907 Transcript missense_variant 3731/5168 3518/4395 1173/1464 D/G gAt/gGt 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 tolerated(0.06) 16/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS rs1266958698 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 100051128 100051128 T C 1 0 0 0 0 1 0 0 0 17493 1435 50 5 5 UHRF1BP1L 12 100051128 Missense_Mutation SNP T C3N-00560_T 4909715 100051128 33224181 860 17549 ANO4 0 . GRCh38 12 101086821 101086821 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.1698T>C p.= p.N566N ENST00000392977 17/28 103 57 46 100 100 0 strelka-varscan-mutect ANO4,synonymous_variant,p.=,ENST00000392979,NM_178826.3;ANO4,synonymous_variant,p.=,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,synonymous_variant,p.=,ENST00000550015,;ANO4,downstream_gene_variant,,ENST00000548940,; C ENST00000392977 Transcript synonymous_variant 1908/3509 1698/2868 566/955 N aaT/aaC 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 17/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 101086821 101086821 T C 1 0 0 0 0 0 0 0 1 806 1478 51 5 5 ANO4 12 101086821 Silent SNP T C3N-00560_T 1035693 101086821 32188488 861 17550 ANO4 0 . GRCh38 12 101096573 101096573 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1776C>A p.Phe592Leu p.F592L ENST00000392977 19/28 196 127 69 183 183 0 strelka-varscan-mutect ANO4,missense_variant,p.Phe557Leu,ENST00000392979,NM_178826.3;ANO4,missense_variant,p.Phe592Leu,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,missense_variant,p.Phe112Leu,ENST00000550015,; A ENST00000392977 Transcript missense_variant 1986/3509 1776/2868 592/955 F/L ttC/ttA 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 tolerated(1) 19/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 101096573 101096573 C A 1 0 0 0 0 1 0 0 0 806 825 29 2 2 ANO4 12 101096573 Missense_Mutation SNP C C3N-00560_T 9752 101096573 32178736 862 17551 SLC5A8 0 . GRCh38 12 101193644 101193644 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.673G>A p.Gly225Arg p.G225R ENST00000536262 5/15 120 67 53 113 113 0 strelka-varscan-mutect SLC5A8,missense_variant,p.Gly225Arg,ENST00000536262,NM_145913.3; T ENST00000536262 Transcript missense_variant 1232/4178 673/1833 225/610 G/R Gga/Aga 1 -1 SLC5A8 HGNC HGNC:19119 protein_coding YES CCDS9080.1 ENSP00000445340 Q8N695 UPI000004DAF6 NM_145913.3 deleterious(0.01) 5/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF121,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 101193644 101193644 C T 1 0 0 0 0 1 0 0 0 14954 603 21 3 3 SLC5A8 12 101193644 Missense_Mutation SNP C C3N-00560_T 97071 101193644 32081665 863 17552 PAH 0 . GRCh38 12 102917098 102917098 + Missense_Mutation SNP C C A rs772557951 C3N-00560_T C3N-00560_N C C c.33G>T p.Leu11Phe p.L11F ENST00000553106 1/13 662 557 105 515 515 0 strelka-varscan-mutect PAH,missense_variant,p.Leu11Phe,ENST00000553106,NM_000277.1;PAH,missense_variant,p.Leu11Phe,ENST00000546844,;PAH,missense_variant,p.Leu11Phe,ENST00000551337,;PAH,missense_variant,p.Leu6Phe,ENST00000550978,;PAH,5_prime_UTR_variant,,ENST00000307000,;PAH,non_coding_transcript_exon_variant,,ENST00000551988,;PAH,non_coding_transcript_exon_variant,,ENST00000547319,;PAH,intron_variant,,ENST00000635500,;PAH,downstream_gene_variant,,ENST00000546708,;PAH,upstream_gene_variant,,ENST00000548928,;PAH,upstream_gene_variant,,ENST00000548677,;PAH,non_coding_transcript_exon_variant,,ENST00000549111,; A ENST00000553106 Transcript missense_variant 506/4122 33/1359 11/452 L/F ttG/ttT rs772557951 1 -1 PAH HGNC HGNC:8582 protein_coding YES CCDS9092.1 ENSP00000448059 P00439 A0A024RBG4 UPI00001318A0 NM_000277.1 tolerated(0.11) 1/13 hmmpanther:PTHR11473,PIRSF_domain:PIRSF000336 MODERATE 1 SNV 1 1 PASS rs772557951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 102917098 102917098 C A 1 0 0 0 0 1 0 0 0 11474 593 21 2 2 PAH 12 102917098 Missense_Mutation SNP C C3N-00560_T 1723454 102917098 30358211 864 17553 STAB2 0 . GRCh38 12 103725015 103725015 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4724C>A p.Thr1575Asn p.T1575N ENST00000388887 45/69 240 152 88 199 199 0 strelka-varscan-mutect STAB2,missense_variant,p.Thr1575Asn,ENST00000388887,NM_017564.9; A ENST00000388887 Transcript missense_variant 4928/8251 4724/7656 1575/2551 T/N aCt/aAt 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 deleterious(0) 45/69 PROSITE_profiles:PS50026,hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2.40.155.10,Pfam_domain:PF12947,SMART_domains:SM00181,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 103725015 103725015 C A 1 0 0 0 0 1 0 0 0 15616 565 20 2 2 STAB2 12 103725015 Missense_Mutation SNP C C3N-00560_T 807917 103725015 29550294 865 17554 ALDH1L2 0 . GRCh38 12 105052150 105052150 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1475C>T p.Ala492Val p.A492V ENST00000258494 12/23 176 105 71 193 193 0 strelka-varscan-mutect ALDH1L2,missense_variant,p.Ala492Val,ENST00000258494,NM_001034173.3;C12orf45,intron_variant,,ENST00000622317,;C12orf45,downstream_gene_variant,,ENST00000637147,;C12orf45,downstream_gene_variant,,ENST00000548583,;ALDH1L2,3_prime_UTR_variant,,ENST00000552270,;ALDH1L2,non_coding_transcript_exon_variant,,ENST00000549335,;C12orf45,intron_variant,,ENST00000547750,; A ENST00000258494 Transcript missense_variant 1616/7547 1475/2772 492/923 A/V gCt/gTt 1 -1 ALDH1L2 HGNC HGNC:26777 protein_coding YES CCDS31891.1 ENSP00000258494 Q3SY69 UPI00000477A9 NM_001034173.3 deleterious(0) 12/23 Gene3D:3.40.605.10,Pfam_domain:PF00171,PIRSF_domain:PIRSF036489,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF131,Low_complexity_(Seg):seg,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS rs1349183264 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 105052150 105052150 G A 1 0 0 0 0 1 0 0 0 595 971 34 3 3 ALDH1L2 12 105052150 Missense_Mutation SNP G C3N-00560_T 1327135 105052150 28223159 866 17555 RFX4 0 . GRCh38 12 106689356 106689356 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.688T>A p.Phe230Ile p.F230I ENST00000357881 7/18 236 155 81 177 177 0 strelka-mutect RFX4,missense_variant,p.Phe221Ile,ENST00000392842,NM_213594.2;RFX4,missense_variant,p.Phe127Ile,ENST00000229387,NM_032491.5;RFX4,missense_variant,p.Phe230Ile,ENST00000357881,NM_001206691.1;RFX4,missense_variant,p.Phe166Ile,ENST00000551640,;RFX4,intron_variant,,ENST00000539967,;RFX4,downstream_gene_variant,,ENST00000549040,;RP11-144F15.1,intron_variant,,ENST00000551505,;RP11-144F15.1,intron_variant,,ENST00000549203,;RP11-482D24.2,upstream_gene_variant,,ENST00000547531,;RFX4,non_coding_transcript_exon_variant,,ENST00000552866,;RFX4,missense_variant,p.Phe230Ile,ENST00000536722,;RFX4,3_prime_UTR_variant,,ENST00000552917,;RFX4,non_coding_transcript_exon_variant,,ENST00000536688,; A ENST00000357881 Transcript missense_variant 828/2565 688/2235 230/744 F/I Ttt/Att 1 1 RFX4 HGNC HGNC:9985 protein_coding YES CCDS55880.1 ENSP00000350552 Q33E94 UPI00001FB460 NM_001206691.1 deleterious(0) 7/18 hmmpanther:PTHR12619:SF25,hmmpanther:PTHR12619 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 106689356 106689356 T A 1 0 0 0 0 1 0 0 0 13439 1609 56 4 4 RFX4 12 106689356 Missense_Mutation SNP T C3N-00560_T 1637206 106689356 26585953 867 17556 CMKLR1 0 . GRCh38 12 108292217 108292217 + Missense_Mutation SNP C C A rs760204829 C3N-00560_T C3N-00560_N C C c.746G>T p.Arg249Leu p.R249L ENST00000312143 3/3 281 144 137 227 226 1 strelka-varscan-mutect CMKLR1,missense_variant,p.Arg249Leu,ENST00000312143,NM_001142344.1;CMKLR1,missense_variant,p.Arg249Leu,ENST00000412676,NM_001142345.1;CMKLR1,missense_variant,p.Arg249Leu,ENST00000550402,NM_001142343.1;CMKLR1,missense_variant,p.Arg247Leu,ENST00000552995,NM_004072.2;CMKLR1,downstream_gene_variant,,ENST00000550573,;CMKLR1,downstream_gene_variant,,ENST00000549466,; A ENST00000312143 Transcript missense_variant 1110/5283 746/1122 249/373 R/L cGc/cTc rs760204829 1 -1 CMKLR1 HGNC HGNC:2121 protein_coding YES CCDS44965.1 ENSP00000311733 Q99788 UPI0000127BD4 NM_001142344.1 deleterious(0) 3/3 PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF696,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01126 MODERATE 1 SNV 2 1 PASS rs760204829 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 108292217 108292217 C A 1 0 0 0 0 1 0 0 0 3354 768 27 1 1 CMKLR1 12 108292217 Missense_Mutation SNP C C3N-00560_T 1602861 108292217 24983092 868 17557 FAM222A 0 . GRCh38 12 109768558 109768558 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.629G>T p.Cys210Phe p.C210F ENST00000538780 3/3 89 73 16 75 75 0 strelka-varscan-mutect FAM222A,missense_variant,p.Cys210Phe,ENST00000538780,NM_032829.2;FAM222A,missense_variant,p.Cys210Phe,ENST00000358906,;FAM222A-AS1,intron_variant,,ENST00000541723,;FAM222A-AS1,intron_variant,,ENST00000541460,; T ENST00000538780 Transcript missense_variant 1345/3294 629/1359 210/452 C/F tGc/tTc 1 1 FAM222A HGNC HGNC:25915 protein_coding YES CCDS9133.1 ENSP00000443292 Q5U5X8 A0A024RBN3 UPI000013D712 NM_032829.2 deleterious(0.01) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR16070 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 109768558 109768558 G T 1 0 0 0 0 1 0 0 0 5416 1319 46 2 2 FAM222A 12 109768558 Missense_Mutation SNP G C3N-00560_T 1476341 109768558 23506751 869 17558 GCN1 0 . GRCh38 12 120164377 120164377 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1807G>T p.Gly603Ter p.G603* ENST00000300648 18/58 179 151 28 158 158 0 strelka-varscan-mutect GCN1,stop_gained,p.Gly603Ter,ENST00000300648,NM_006836.1;GCN1,upstream_gene_variant,,ENST00000550471,;GCN1,upstream_gene_variant,,ENST00000547369,;GCN1,downstream_gene_variant,,ENST00000551549,; A ENST00000300648 Transcript stop_gained 1820/8675 1807/8016 603/2671 G/* Gga/Tga 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 18/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 56 120164377 120164377 C A 1 0 0 0 0 0 1 0 0 6169 661 23 1 1 GCN1 12 120164377 Nonsense_Mutation SNP C C3N-00560_T 10395819 120164377 13110932 870 17559 HNF1A 0 . GRCh38 12 120997591 120997591 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1427T>A p.Leu476His p.L476H ENST00000544413 7/10 319 175 144 299 298 1 strelka-varscan-mutect HNF1A,missense_variant,p.Leu476His,ENST00000257555,NM_000545.5;HNF1A,missense_variant,p.Leu476His,ENST00000541395,;HNF1A,missense_variant,p.Leu297His,ENST00000543427,;HNF1A,missense_variant,p.Leu72His,ENST00000615446,;HNF1A,missense_variant,p.Leu476His,ENST00000400024,;HNF1A,missense_variant,p.Leu476His,ENST00000544413,NM_001306179.1;HNF1A,intron_variant,,ENST00000617366,;C12orf43,downstream_gene_variant,,ENST00000288757,NM_022895.2,NM_001286192.1;C12orf43,downstream_gene_variant,,ENST00000445832,NM_001286198.1;HNF1A,non_coding_transcript_exon_variant,,ENST00000538626,;HNF1A,non_coding_transcript_exon_variant,,ENST00000535955,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,3_prime_UTR_variant,,ENST00000560968,;HNF1A,3_prime_UTR_variant,,ENST00000538646,;HNF1A,3_prime_UTR_variant,,ENST00000541924,;HNF1A,3_prime_UTR_variant,,ENST00000544574,;HNF1A,non_coding_transcript_exon_variant,,ENST00000402929,;HNF1A,non_coding_transcript_exon_variant,,ENST00000543255,; A ENST00000544413 Transcript missense_variant 1447/2014 1427/1917 476/638 L/H cTc/cAc 1 1 HNF1A HGNC HGNC:11621 protein_coding YES CCDS76611.1 ENSP00000438804 F5H0K0 UPI000204ABCC NM_001306179.1 deleterious(0) 7/10 Pfam_domain:PF04812,hmmpanther:PTHR11568,hmmpanther:PTHR11568:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 120997591 120997591 T A 1 0 0 0 0 1 0 0 0 7142 1551 54 4 4 HNF1A 12 120997591 Missense_Mutation SNP T C3N-00560_T 833214 120997591 12277718 871 17560 CAMKK2 0 . GRCh38 12 121260326 121260326 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.789G>T p.= p.L263L ENST00000324774 7/17 281 241 40 221 221 0 strelka-varscan-mutect CAMKK2,synonymous_variant,p.=,ENST00000324774,NM_006549.3;CAMKK2,synonymous_variant,p.=,ENST00000337174,NM_153499.2;CAMKK2,synonymous_variant,p.=,ENST00000347034,NM_172216.1;CAMKK2,synonymous_variant,p.=,ENST00000538733,NM_153500.1;CAMKK2,synonymous_variant,p.=,ENST00000392474,NM_001270486.1;CAMKK2,synonymous_variant,p.=,ENST00000545538,;CAMKK2,synonymous_variant,p.=,ENST00000392473,NM_172214.2;CAMKK2,synonymous_variant,p.=,ENST00000446440,NM_172215.2;CAMKK2,synonymous_variant,p.=,ENST00000404169,NM_001270485.1;CAMKK2,synonymous_variant,p.=,ENST00000402834,;CAMKK2,synonymous_variant,p.=,ENST00000412367,NM_172226.2;CAMKK2,intron_variant,,ENST00000535524,;CAMKK2,downstream_gene_variant,,ENST00000542540,; A ENST00000324774 Transcript synonymous_variant 1618/5598 789/1767 263/588 L ctG/ctT 1 -1 CAMKK2 HGNC HGNC:1470 protein_coding YES CCDS9216.1 ENSP00000312741 Q96RR4 A0A024RBQ0 UPI000013D208 NM_006549.3 7/17 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF204,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 121260326 121260326 C A 1 0 0 0 0 0 0 0 1 2298 465 17 2 2 CAMKK2 12 121260326 Silent SNP C C3N-00560_T 262735 121260326 12014983 872 17561 NCOR2 0 . GRCh38 12 124336973 124336973 + Silent SNP C C T rs781638122 C3N-00560_T C3N-00560_N C C c.5895G>A p.= p.G1965G ENST00000405201 38/47 51 40 11 36 36 0 strelka-varscan-mutect NCOR2,synonymous_variant,p.=,ENST00000405201,NM_006312.5;NCOR2,synonymous_variant,p.=,ENST00000404621,NM_001077261.3;NCOR2,synonymous_variant,p.=,ENST00000429285,NM_001206654.1;NCOR2,synonymous_variant,p.=,ENST00000356219,;NCOR2,synonymous_variant,p.=,ENST00000404121,;NCOR2,upstream_gene_variant,,ENST00000440337,;NCOR2,downstream_gene_variant,,ENST00000453428,;NCOR2,upstream_gene_variant,,ENST00000418829,;NCOR2,downstream_gene_variant,,ENST00000440187,;MIR6880,downstream_gene_variant,,ENST00000622851,;NCOR2,upstream_gene_variant,,ENST00000461081,;NCOR2,upstream_gene_variant,,ENST00000443451,;NCOR2,upstream_gene_variant,,ENST00000474079,; T ENST00000405201 Transcript synonymous_variant 5896/8533 5895/7545 1965/2514 G ggG/ggA rs781638122 1 -1 NCOR2 HGNC HGNC:7673 protein_coding YES CCDS41858.2 ENSP00000384018 C9JFD3 UPI000013D737 NM_006312.5 38/47 hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF21 LOW 1 SNV 1 1 PASS rs781638122 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 124336973 124336973 C T 1 0 0 0 0 0 0 0 1 10255 726 26 3 3 NCOR2 12 124336973 Silent SNP C C3N-00560_T 3076647 124336973 8938336 873 17562 TMEM132B 0 . GRCh38 12 125519439 125519439 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1092G>T p.Arg364Ser p.R364S ENST00000299308 4/9 134 62 72 113 113 0 strelka-varscan-mutect TMEM132B,missense_variant,p.Arg364Ser,ENST00000299308,NM_052907.3;TMEM132B,splice_region_variant,,ENST00000534945,; T ENST00000299308 Transcript missense_variant,splice_region_variant 1100/10906 1092/3237 364/1078 R/S agG/agT 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 tolerated(0.27) 4/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 125519439 125519439 G T 1 0 0 0 0 1 0 0 0 16490 1246 43 2 2 TMEM132B 12 125519439 Missense_Mutation SNP G C3N-00560_T 1182466 125519439 7755870 874 17563 TMEM132B 0 . GRCh38 12 125644197 125644197 + Missense_Mutation SNP C C T C3N-00560_T C3N-00560_N C C c.1544C>T p.Pro515Leu p.P515L ENST00000299308 6/9 395 227 168 370 370 0 strelka-varscan-mutect TMEM132B,missense_variant,p.Pro515Leu,ENST00000299308,NM_052907.3;TMEM132B,missense_variant,p.Pro27Leu,ENST00000613307,NM_001286219.1;TMEM132B,non_coding_transcript_exon_variant,,ENST00000535886,; T ENST00000299308 Transcript missense_variant 1552/10906 1544/3237 515/1078 P/L cCc/cTc COSM2227506 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 deleterious(0) 6/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388,Pfam_domain:PF16070 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 125644197 125644197 C T 1 0 0 0 0 1 0 0 0 16490 623 22 3 3 TMEM132B 12 125644197 Missense_Mutation SNP C C3N-00560_T 124758 125644197 7631112 875 17564 TMEM132C 0 . GRCh38 12 128415565 128415565 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.919G>T p.Val307Phe p.V307F ENST00000435159 2/9 102 55 47 63 63 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Val307Phe,ENST00000435159,NM_001136103.2; T ENST00000435159 Transcript missense_variant 919/4947 919/3327 307/1108 V/F Gtc/Ttc 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0.03) 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 128415565 128415565 G T 1 0 0 0 0 1 0 0 0 16491 1261 44 2 2 TMEM132C 12 128415565 Missense_Mutation SNP G C3N-00560_T 2771368 128415565 4859744 876 17565 FZD10 0 . GRCh38 12 130163902 130163902 + Silent SNP C C A rs747438554 C3N-00560_T C3N-00560_N C C c.960C>A p.= p.G320G ENST00000229030 1/1 340 188 152 323 323 0 strelka-varscan-mutect FZD10,missense_variant,p.His288Asn,ENST00000539839,;FZD10,synonymous_variant,p.=,ENST00000229030,NM_007197.3;FZD10-AS1,upstream_gene_variant,,ENST00000505807,;FZD10-AS1,upstream_gene_variant,,ENST00000509760,;FZD10-AS1,upstream_gene_variant,,ENST00000537095,;FZD10-AS1,upstream_gene_variant,,ENST00000542000,; A ENST00000229030 Transcript synonymous_variant 1444/3281 960/1746 320/581 G ggC/ggA rs747438554 1 1 FZD10 HGNC HGNC:4039 protein_coding YES CCDS9267.1 ENSP00000229030 Q9ULW2 UPI000004EC92 NM_007197.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF86,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330,Prints_domain:PR00489 LOW SNV 1 PASS rs747438554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 130163902 130163902 C A 1 0 0 0 0 0 0 0 1 6000 710 25 2 2 FZD10 12 130163902 Silent SNP C C3N-00560_T 1748337 130163902 3111407 877 17566 PIWIL1 0 . GRCh38 12 130363105 130363105 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.2156A>C p.Gln719Pro p.Q719P ENST00000245255 18/21 263 152 111 205 205 0 strelka-varscan-mutect PIWIL1,missense_variant,p.Gln719Pro,ENST00000245255,NM_004764.4,NM_001190971.1;PIWIL1,upstream_gene_variant,,ENST00000541480,; C ENST00000245255 Transcript missense_variant 2428/3897 2156/2586 719/861 Q/P cAg/cCg 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 deleterious(0) 18/21 Gene3D:3.30.420.10,Pfam_domain:PF02171,PROSITE_profiles:PS50822,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF46,SMART_domains:SM00950,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 130363105 130363105 A C 1 0 0 0 0 1 0 0 0 12053 188 7 5 5 PIWIL1 12 130363105 Missense_Mutation SNP A C3N-00560_T 199203 130363105 2912204 878 17567 SFSWAP 0 . GRCh38 12 131725460 131725460 + Missense_Mutation SNP G G T rs142183661 C3N-00560_T C3N-00560_N G G c.662G>T p.Arg221Met p.R221M ENST00000541286 5/19 526 453 73 404 403 1 strelka-varscan-mutect SFSWAP,missense_variant,p.Arg221Met,ENST00000261674,NM_004592.3;SFSWAP,missense_variant,p.Arg221Met,ENST00000541286,NM_001261411.1;SFSWAP,non_coding_transcript_exon_variant,,ENST00000542813,;SFSWAP,3_prime_UTR_variant,,ENST00000538548,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000535236,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000540469,;SFSWAP,upstream_gene_variant,,ENST00000535202,; T ENST00000541286 Transcript missense_variant 755/3219 662/3012 221/1003 R/M aGg/aTg rs142183661 1 1 SFSWAP HGNC HGNC:10790 protein_coding YES CCDS58290.1 ENSP00000437738 Q12872 UPI000204AB4C NM_001261411.1 deleterious(0) 5/19 Pfam_domain:PF01805,PROSITE_profiles:PS50128,hmmpanther:PTHR13161,hmmpanther:PTHR13161:SF15,SMART_domains:SM00648,Superfamily_domains:SSF109905 MODERATE 1 SNV 1 1 PASS rs142183661 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 131725460 131725460 G T 1 0 0 0 0 1 0 0 0 14444 1000 35 2 2 SFSWAP 12 131725460 Missense_Mutation SNP G C3N-00560_T 1362355 131725460 1549849 879 17568 ZNF268 0 . GRCh38 12 133202520 133202520 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.834C>A p.Cys278Ter p.C278* ENST00000536435 6/6 180 146 34 124 124 0 strelka-varscan-mutect ZNF268,stop_gained,p.Cys278Ter,ENST00000536435,NM_003415.2;ZNF268,stop_gained,p.Cys278Ter,ENST00000228289,NM_001165881.2;ZNF268,3_prime_UTR_variant,,ENST00000541009,NM_152943.2;ZNF268,3_prime_UTR_variant,,ENST00000542986,;ZNF268,3_prime_UTR_variant,,ENST00000536899,NM_001165884.2;ZNF268,3_prime_UTR_variant,,ENST00000542711,NM_001165886.1;CTD-2140B24.4,downstream_gene_variant,,ENST00000540096,;ZNF268,downstream_gene_variant,,ENST00000541211,NM_001165885.1;ZNF268,downstream_gene_variant,,ENST00000539248,NM_001165883.1;ZNF268,downstream_gene_variant,,ENST00000500625,NM_001165882.2;ZNF268,downstream_gene_variant,,ENST00000592241,NM_001165887.1;ZNF268,downstream_gene_variant,,ENST00000591951,;ZNF268,downstream_gene_variant,,ENST00000585488,;ZNF268,downstream_gene_variant,,ENST00000588312,;ZNF268,downstream_gene_variant,,ENST00000534953,; A ENST00000536435 Transcript stop_gained 1164/13475 834/2844 278/947 C/* tgC/tgA 1 1 ZNF268 HGNC HGNC:13061 protein_coding YES CCDS45012.1 ENSP00000444412 Q14587 UPI000013C33E NM_003415.2 6/6 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 133202520 133202520 C A 1 0 0 0 0 0 1 0 0 18383 718 25 2 2 ZNF268 12 133202520 Nonsense_Mutation SNP C C3N-00560_T 1477060 133202520 72789 880 17569 TUBA3C 0 . GRCh38 13 19178276 19178276 + Silent SNP G G T rs552346334 C3N-00560_T C3N-00560_N G G c.345C>A p.= p.V115V ENST00000400113 3/5 105 52 53 130 130 0 strelka-varscan-mutect TUBA3C,synonymous_variant,p.=,ENST00000400113,NM_006001.2;TUBA3C,synonymous_variant,p.=,ENST00000618094,; T ENST00000400113 Transcript synonymous_variant 450/1551 345/1353 115/450 V gtC/gtA rs552346334,COSM5376469 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 3/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.40.50.1440,Pfam_domain:PF00091,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161 0,1 LOW 1 SNV 5 0,1 1 PASS rs552346334 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 19178276 19178276 G T 1 0 0 0 0 0 0 0 1 17256 1045 37 1 1 TUBA3C 13 19178276 Silent SNP G C3N-00560_T 19178276 95186052 881 17570 SACS 0 . GRCh38 13 23333393 23333393 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.10483G>T p.Glu3495Ter p.E3495* ENST00000382292 9/9 32 14 18 74 74 0 strelka-varscan-mutect SACS,stop_gained,p.Glu3495Ter,ENST00000382292,NM_014363.5;SACS,stop_gained,p.Glu2745Ter,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; A ENST00000382292 Transcript stop_gained 10757/15324 10483/13740 3495/4579 E/* Gag/Tag 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 HIGH 1 SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 23333393 23333393 C A 1 0 0 0 0 0 1 0 0 14063 922 32 2 2 SACS 13 23333393 Nonsense_Mutation SNP C C3N-00560_T 4155117 23333393 91030935 882 17571 SACS 0 . GRCh38 13 23333464 23333464 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.10412T>C p.Val3471Ala p.V3471A ENST00000382292 9/9 110 60 50 146 146 0 strelka-varscan-mutect SACS,missense_variant,p.Val3471Ala,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Val2721Ala,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; G ENST00000382292 Transcript missense_variant 10686/15324 10412/13740 3471/4579 V/A gTa/gCa 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 deleterious(0) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 23333464 23333464 A G 1 0 0 0 0 1 0 0 0 14063 391 14 5 5 SACS 13 23333464 Missense_Mutation SNP A C3N-00560_T 71 23333464 91030864 883 17572 C1QTNF9 0 . GRCh38 13 24318872 24318872 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.221G>T p.Gly74Val p.G74V ENST00000382071 3/4 229 194 35 278 278 0 strelka-varscan-mutect C1QTNF9,missense_variant,p.Gly74Val,ENST00000382071,NM_001303138.1;C1QTNF9,missense_variant,p.Gly74Val,ENST00000332018,NM_001303137.1,NM_178540.4;C1QTNF9B-AS1,downstream_gene_variant,,ENST00000626707,;C1QTNF9-AS1,intron_variant,,ENST00000449656,;RP11-307N16.6,3_prime_UTR_variant,,ENST00000382141,;RP11-307N16.7,upstream_gene_variant,,ENST00000621992,; T ENST00000382071 Transcript missense_variant 306/1854 221/1002 74/333 G/V gGa/gTa COSM3467802,COSM469260 1 1 C1QTNF9 HGNC HGNC:28732 protein_coding YES CCDS9306.1 ENSP00000371503 P0C862 UPI000004F06F NM_001303138.1 deleterious(0) 3/4 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF557 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 24318872 24318872 G T 1 0 0 0 0 1 0 0 0 1948 1174 41 2 2 C1QTNF9 13 24318872 Missense_Mutation SNP G C3N-00560_T 985408 24318872 90045456 884 17573 ATP8A2 0 . GRCh38 13 25559746 25559746 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1378C>A p.Pro460Thr p.P460T ENST00000381655 15/37 150 107 43 202 202 0 strelka-varscan-mutect ATP8A2,missense_variant,p.Pro460Thr,ENST00000381655,NM_016529.4;ATP8A2,missense_variant,p.Pro420Thr,ENST00000255283,;ATP8A2,missense_variant,p.Pro300Thr,ENST00000281620,; A ENST00000381655 Transcript missense_variant 1520/9575 1378/3567 460/1188 P/T Ccg/Acg 1 1 ATP8A2 HGNC HGNC:13533 protein_coding YES CCDS41873.1 ENSP00000371070 Q9NTI2 UPI0000229592 NM_016529.4 tolerated(0.95) 15/37 hmmpanther:PTHR24092:SF66,hmmpanther:PTHR24092,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Superfamily_domains:SSF81660 MODERATE 1 SNV 2 1 PASS rs1317025985 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 25559746 25559746 C A 1 0 0 0 0 1 0 0 0 1346 739 26 2 2 ATP8A2 13 25559746 Missense_Mutation SNP C C3N-00560_T 1240874 25559746 88804582 885 17574 ALOX5AP 0 . GRCh38 13 30764082 30764082 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.633C>A p.= p.I211I ENST00000617770 6/6 94 51 43 115 115 0 strelka-varscan-mutect ALOX5AP,synonymous_variant,p.=,ENST00000617770,NM_001204406.1;ALOX5AP,synonymous_variant,p.=,ENST00000380490,NM_001629.3; A ENST00000617770 Transcript synonymous_variant 881/1224 633/657 211/218 I atC/atA 1 1 ALOX5AP HGNC HGNC:436 protein_coding YES CCDS73558.1 ENSP00000479870 A0A087WW23 UPI0000E00F64 NM_001204406.1 6/6 hmmpanther:PTHR10250:SF2,hmmpanther:PTHR10250,Gene3D:1.20.120.550 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 30764082 30764082 C A 1 0 0 0 0 0 0 0 1 641 903 32 2 2 ALOX5AP 13 30764082 Silent SNP C C3N-00560_T 5204336 30764082 83600246 886 17575 FRY 0 . GRCh38 13 32228544 32228544 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.5295G>T p.= p.L1765L ENST00000542859 40/61 278 152 126 308 308 0 strelka-varscan-mutect FRY,synonymous_variant,p.=,ENST00000542859,NM_023037.2;FRY,synonymous_variant,p.=,ENST00000380250,; T ENST00000542859 Transcript synonymous_variant 5791/13200 5295/9042 1765/3013 L ctG/ctT 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 40/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1218590316 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 32228544 32228544 G T 1 0 0 0 0 0 0 0 1 5935 1335 47 2 2 FRY 13 32228544 Silent SNP G C3N-00560_T 1464462 32228544 82135784 887 17576 BRCA2 0 . GRCh38 13 32338302 32338302 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.3947A>T p.Asn1316Ile p.N1316I ENST00000380152 11/27 22 18 4 55 55 0 strelka-varscan-mutect BRCA2,missense_variant,p.Asn1316Ile,ENST00000380152,;BRCA2,missense_variant,p.Asn1316Ile,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,; T ENST00000380152 Transcript missense_variant 4180/11986 3947/10257 1316/3418 N/I aAt/aTt 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC deleterious(0) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 MODERATE 1 SNV 5 1 PASS . . 2 205 3 0 0 0 0 0 -12.32464 1 1 1 1 0 T 3 4 56 32338302 32338302 A T 1 0 0 0 0 1 0 0 0 1669 101 4 4 4 BRCA2 13 32338302 Missense_Mutation SNP A C3N-00560_T 109758 32338302 82026026 888 17577 POSTN 0 . GRCh38 13 37579040 37579040 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1873G>T p.Asp625Tyr p.D625Y ENST00000379747 14/23 56 27 29 158 158 0 strelka-varscan-mutect POSTN,missense_variant,p.Asp625Tyr,ENST00000379747,NM_006475.2;POSTN,missense_variant,p.Asp625Tyr,ENST00000541179,NM_001135936.1,NM_001135935.1;POSTN,missense_variant,p.Asp625Tyr,ENST00000379749,;POSTN,missense_variant,p.Asp625Tyr,ENST00000379743,NM_001286665.1;POSTN,missense_variant,p.Asp625Tyr,ENST00000541481,NM_001286666.1,NM_001286667.1;POSTN,missense_variant,p.Asp625Tyr,ENST00000379742,NM_001135934.1; A ENST00000379747 Transcript missense_variant 1991/3373 1873/2511 625/836 D/Y Gat/Tat 1 -1 POSTN HGNC HGNC:16953 protein_coding YES CCDS9364.1 ENSP00000369071 Q15063 A0A024RDS2 UPI000013CEB8 NM_006475.2 deleterious(0) 14/23 Gene3D:2.30.180.10,Pfam_domain:PF02469,PIRSF_domain:PIRSF016553,PROSITE_profiles:PS50213,hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF12,SMART_domains:SM00554,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 37579040 37579040 C A 1 0 0 0 0 1 0 0 0 12373 913 32 2 2 POSTN 13 37579040 Missense_Mutation SNP C C3N-00560_T 5240738 37579040 76785288 889 17578 MRPS31 0 . GRCh38 13 40749263 40749263 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.833G>T p.Trp278Leu p.W278L ENST00000323563 6/7 83 40 43 108 108 0 strelka-varscan-mutect MRPS31,missense_variant,p.Trp278Leu,ENST00000323563,NM_005830.3;MRPS31,non_coding_transcript_exon_variant,,ENST00000498078,;MRPS31,non_coding_transcript_exon_variant,,ENST00000461675,; A ENST00000323563 Transcript missense_variant 870/1462 833/1188 278/395 W/L tGg/tTg 1 -1 MRPS31 HGNC HGNC:16632 protein_coding YES CCDS9372.1 ENSP00000315397 Q92665 UPI000013D1D3 NM_005830.3 deleterious(0) 6/7 hmmpanther:PTHR13231,Pfam_domain:PF15433 MODERATE 1 SNV 1 1 PASS rs866441224 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 40749263 40749263 C A 1 0 0 0 0 1 0 0 0 9818 595 21 2 2 MRPS31 13 40749263 Missense_Mutation SNP C C3N-00560_T 3170223 40749263 73615065 890 17579 TNFSF11 0 . GRCh38 13 42606841 42606841 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.877G>C p.Val293Leu p.V293L ENST00000398795 5/5 99 60 39 142 142 0 strelka-varscan-mutect TNFSF11,missense_variant,p.Val293Leu,ENST00000398795,NM_003701.3;TNFSF11,missense_variant,p.Val220Leu,ENST00000405262,;TNFSF11,missense_variant,p.Val220Leu,ENST00000358545,NM_033012.3;TNFSF11,missense_variant,p.Val246Leu,ENST00000239849,;TNFSF11,missense_variant,p.Val220Leu,ENST00000544862,; C ENST00000398795 Transcript missense_variant 1028/2199 877/954 293/317 V/L Gtc/Ctc COSM3704639 1 1 TNFSF11 HGNC HGNC:11926 protein_coding YES CCDS9384.1 ENSP00000381775 O14788 Q5T9Y4 UPI000003BC8E NM_003701.3 deleterious(0.01) 5/5 PROSITE_profiles:PS50049,hmmpanther:PTHR11471:SF3,hmmpanther:PTHR11471,Pfam_domain:PF00229,Gene3D:2.60.120.40,PIRSF_domain:PIRSF038013,SMART_domains:SM00207,Superfamily_domains:SSF49842 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 42606841 42606841 G C 1 0 0 0 0 1 0 0 0 16776 1261 44 4 4 TNFSF11 13 42606841 Missense_Mutation SNP G C3N-00560_T 1857578 42606841 71757487 891 17580 FAM216B 0 . GRCh38 13 42788771 42788771 + Missense_Mutation SNP G G A rs749283387 C3N-00560_T C3N-00560_N G G c.401G>A p.Arg134His p.R134H ENST00000537894 4/4 92 53 39 98 98 0 strelka-varscan-mutect FAM216B,missense_variant,p.Arg134His,ENST00000537894,NM_001318932.1,NM_182508.2;FAM216B,missense_variant,p.Arg134His,ENST00000313851,; A ENST00000537894 Transcript missense_variant 524/3300 401/420 134/139 R/H cGc/cAc rs749283387,COSM3955608 1 1 FAM216B HGNC HGNC:26883 protein_coding YES CCDS9386.1 ENSP00000445786 Q8N7L0 UPI0000070E45 NM_001318932.1,NM_182508.2 tolerated_low_confidence(0.22) 4/4 hmmpanther:PTHR16476,hmmpanther:PTHR16476:SF3 0,1 MODERATE 1 SNV 4 0,1 1 PASS rs749283387 . 0 205 2 3 0 0 0 0 -20 0.9999947 1 1 1 0 A 3 1 56 42788771 42788771 G A 1 0 0 0 0 1 0 0 0 5405 1087 38 1 1 FAM216B 13 42788771 Missense_Mutation SNP G C3N-00560_T 181930 42788771 71575557 892 17581 PCDH8 0 . GRCh38 13 52846922 52846922 + Silent SNP C C A rs761213188 C3N-00560_T C3N-00560_N C C c.1515G>T p.= p.S505S ENST00000377942 1/3 155 80 75 162 161 1 strelka-varscan-mutect PCDH8,synonymous_variant,p.=,ENST00000377942,NM_002590.3;PCDH8,synonymous_variant,p.=,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; A ENST00000377942 Transcript synonymous_variant 1719/5088 1515/3213 505/1070 S tcG/tcT rs761213188,COSM4048117 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,Superfamily_domains:SSF49313 0,1 LOW 1 SNV 1 0,1 1 PASS rs761213188 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 52846922 52846922 C A 1 0 0 0 0 0 0 0 1 11604 639 23 1 1 PCDH8 13 52846922 Silent SNP C C3N-00560_T 10058151 52846922 61517406 893 17582 PCDH17 0 . GRCh38 13 57634153 57634153 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1607C>A p.Ala536Asp p.A536D ENST00000377918 1/4 341 187 154 465 464 1 strelka-varscan-mutect PCDH17,missense_variant,p.Ala536Asp,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,upstream_gene_variant,,ENST00000610846,;PCDH17,missense_variant,p.Ala536Asp,ENST00000484979,; A ENST00000377918 Transcript missense_variant 2342/8232 1607/3480 536/1159 A/D gCc/gAc COSM551856 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 deleterious(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 57634153 57634153 C A 1 0 0 0 0 1 0 0 0 11599 739 26 2 2 PCDH17 13 57634153 Missense_Mutation SNP C C3N-00560_T 4787231 57634153 56730175 894 17583 KLHL1 0 . GRCh38 13 69796896 69796896 + Missense_Mutation SNP C C G rs111395379 C3N-00560_T C3N-00560_N C C c.1481G>C p.Gly494Ala p.G494A ENST00000377844 7/11 308 272 36 301 301 0 strelka-varscan-mutect KLHL1,missense_variant,p.Gly494Ala,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Gly433Ala,ENST00000545028,NM_001286725.1; G ENST00000377844 Transcript missense_variant 2241/4115 1481/2247 494/748 G/A gGc/gCc rs111395379 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 tolerated(0.07) 7/11 hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS rs111395379 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 69796896 69796896 C G 1 0 0 0 0 1 0 0 0 8229 739 26 4 4 KLHL1 13 69796896 Missense_Mutation SNP C C3N-00560_T 12162743 69796896 44567432 895 17584 TBC1D4 0 . GRCh38 13 75362184 75362184 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.922G>T p.Glu308Ter p.E308* ENST00000377636 2/21 378 311 67 425 424 1 strelka-varscan-mutect TBC1D4,stop_gained,p.Glu308Ter,ENST00000377636,NM_014832.3;TBC1D4,stop_gained,p.Glu308Ter,ENST00000431480,NM_001286658.1;TBC1D4,stop_gained,p.Glu308Ter,ENST00000377625,NM_001286659.1; A ENST00000377636 Transcript stop_gained 1269/6364 922/3897 308/1298 E/* Gag/Tag 1 -1 TBC1D4 HGNC HGNC:19165 protein_coding YES CCDS41901.1 ENSP00000366863 O60343 UPI00001AE7B3 NM_014832.3 2/21 SMART_domains:SM00462 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 75362184 75362184 C A 1 0 0 0 0 0 1 0 0 16027 835 29 2 2 TBC1D4 13 75362184 Nonsense_Mutation SNP C C3N-00560_T 5565288 75362184 39002144 896 17585 RBM26 0 . GRCh38 13 79366868 79366868 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.900G>T p.Lys300Asn p.K300N ENST00000622611 7/22 62 48 14 67 67 0 strelka-varscan-mutect RBM26,missense_variant,p.Lys300Asn,ENST00000622611,NM_001286631.1;RBM26,missense_variant,p.Lys300Asn,ENST00000438724,NM_001286632.1;RBM26,missense_variant,p.Lys300Asn,ENST00000438737,;RBM26,missense_variant,p.Lys300Asn,ENST00000267229,NM_022118.4;RBM26,upstream_gene_variant,,ENST00000461008,; A ENST00000622611 Transcript missense_variant 1347/5230 900/3030 300/1009 K/N aaG/aaT 1 -1 RBM26 HGNC HGNC:20327 protein_coding YES CCDS73591.1 ENSP00000483408 A0A087X0H9 UPI00016378C8 NM_001286631.1 deleterious(0) 7/22 Gene3D:1m9oA00,PROSITE_profiles:PS50103,hmmpanther:PTHR14398,hmmpanther:PTHR14398:SF2,SMART_domains:SM00356 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 79366868 79366868 C A 1 0 0 0 0 1 0 0 0 13292 695 24 2 2 RBM26 13 79366868 Missense_Mutation SNP C C3N-00560_T 4004684 79366868 34997460 897 17586 SLITRK1 0 . GRCh38 13 83880101 83880101 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1407C>A p.= p.A469A ENST00000377084 1/1 138 82 56 146 146 0 strelka-varscan-mutect SLITRK1,synonymous_variant,p.=,ENST00000377084,NM_052910.2,NM_001281503.1; T ENST00000377084 Transcript synonymous_variant 2293/5189 1407/2091 469/696 A gcC/gcA 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 83880101 83880101 G T 1 0 0 0 0 0 0 0 1 15033 1335 47 2 2 SLITRK1 13 83880101 Silent SNP G C3N-00560_T 4513233 83880101 30484227 898 17587 CCDC168 0 . GRCh38 13 102729931 102729931 + Silent SNP A A G novel C3N-00560_T C3N-00560_N A A c.20766T>C p.= p.N6922N ENST00000322527 4/4 268 121 147 229 229 0 strelka-varscan-mutect CCDC168,synonymous_variant,p.=,ENST00000322527,NM_001146197.1; G ENST00000322527 Transcript synonymous_variant 20904/21466 20766/21246 6922/7081 N aaT/aaC 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 102729931 102729931 A G 1 0 0 0 0 0 0 0 1 2484 446 16 5 5 CCDC168 13 102729931 Silent SNP A C3N-00560_T 18849830 102729931 11634397 899 17588 MYO16 0 . GRCh38 13 108964819 108964819 + Frame_Shift_Del DEL G G - C3N-00560_T C3N-00560_N G G c.2287delG p.Ala763ProfsTer13 p.A763Pfs*13 ENST00000457511 20/35 170 67 103 171 171 0 sindel-varindel-pindel MYO16,frameshift_variant,p.Ala763ProfsTer13,ENST00000457511,NM_001198950.1;MYO16,frameshift_variant,p.Ala741ProfsTer13,ENST00000356711,NM_015011.1;MYO16,frameshift_variant,p.Ala741ProfsTer13,ENST00000357550,;MYO16,frameshift_variant,p.Ala741ProfsTer13,ENST00000251041,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,; - ENST00000457511 Transcript frameshift_variant 2908/7436 2286/5643 762/1880 L/X ttG/tt COSM5034596,COSM5034597,COSM5034598 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 20/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,SMART_domains:SM00242,Superfamily_domains:SSF52540 1,1,1 HIGH 1 deletion 1 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 108964819 108964819 G - 1 0 1 0 1 0 0 0 0 10065 1339 47 0 0 MYO16 13 108964819 Frame_Shift_Del DEL G C3N-00560_T 6234888 108964819 5399509 900 17589 IRS2 0 . GRCh38 13 109785147 109785147 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.907C>T p.Arg303Cys p.R303C ENST00000375856 1/2 444 134 310 269 269 0 strelka-varscan-mutect IRS2,missense_variant,p.Arg303Cys,ENST00000375856,NM_003749.2;RP11-40E6.1,upstream_gene_variant,,ENST00000615635,; A ENST00000375856 Transcript missense_variant 1422/8138 907/4017 303/1338 R/C Cgc/Tgc 1 -1 IRS2 HGNC HGNC:6126 protein_coding YES CCDS9510.1 ENSP00000365016 Q9Y4H2 UPI000006E4A8 NM_003749.2 deleterious(0) 1/2 hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 109785147 109785147 G A 1 0 0 0 0 1 0 0 0 7749 1087 38 1 1 IRS2 13 109785147 Missense_Mutation SNP G C3N-00560_T 820328 109785147 4579181 901 17590 COL4A2 0 . GRCh38 13 110457381 110457381 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1378G>T p.Gly460Cys p.G460C ENST00000360467 21/48 598 205 393 487 487 0 strelka-varscan-mutect COL4A2,missense_variant,p.Gly460Cys,ENST00000360467,NM_001846.2;COL4A2,upstream_gene_variant,,ENST00000617564,;COL4A2-AS2,intron_variant,,ENST00000458403,;COL4A2,upstream_gene_variant,,ENST00000478681,; T ENST00000360467 Transcript missense_variant 1684/6281 1378/5139 460/1712 G/C Ggc/Tgc 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 deleterious(0) 21/48 Pfam_domain:PF01391 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 110457381 110457381 G T 1 0 0 0 0 1 0 0 0 3479 1000 35 2 2 COL4A2 13 110457381 Missense_Mutation SNP G C3N-00560_T 672234 110457381 3906947 902 17591 POTEM 0 . GRCh38 14 18967499 18967499 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.14C>A p.Ala5Asp p.A5D ENST00000547889 1/11 91 78 13 121 121 0 varscan-mutect POTEM,missense_variant,p.Ala5Asp,ENST00000547889,NM_001145442.1;POTEM,missense_variant,p.Ala5Asp,ENST00000552966,;POTEM,missense_variant,p.Ala5Asp,ENST00000616847,; A ENST00000547889 Transcript missense_variant 66/1817 14/1527 5/508 A/D gCt/gAt 1 1 POTEM HGNC HGNC:37096 protein_coding YES CCDS73609.1 ENSP00000448062 A6NI47 UPI00006C1407 NM_001145442.1 deleterious_low_confidence(0) 1/11 MODERATE 1 SNV 1 1 PASS rs1231316269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 18967499 18967499 C A 1 0 0 0 0 1 0 0 0 12384 797 28 2 2 POTEM 14 18967499 Missense_Mutation SNP C C3N-00560_T 18967499 88076219 903 17592 POTEG 0 . GRCh38 14 19433970 19433970 + Missense_Mutation SNP G G T rs768540032 C3N-00560_T C3N-00560_N G G c.320C>A p.Pro107His p.P107H ENST00000547848 1/11 1316 1152 164 1764 1764 0 varscan-mutect POTEG,missense_variant,p.Pro107His,ENST00000547848,NM_001005356.2;POTEG,missense_variant,p.Pro107His,ENST00000547722,;POTEG,missense_variant,p.Pro107His,ENST00000622767,; T ENST00000547848 Transcript missense_variant 372/2204 320/1527 107/508 P/H cCc/cAc rs768540032 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 deleterious_low_confidence(0) 1/11 hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118 MODERATE 1 SNV 1 1 PASS rs768540032 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 19433970 19433970 G T 1 0 0 0 0 1 0 0 0 12380 1232 43 2 2 POTEG 14 19433970 Missense_Mutation SNP G C3N-00560_T 466471 19433970 87609748 904 17593 POTEG 0 . GRCh38 14 19434276 19434276 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.14C>A p.Ala5Asp p.A5D ENST00000547848 1/11 350 313 37 511 511 0 varscan-mutect POTEG,missense_variant,p.Ala5Asp,ENST00000547848,NM_001005356.2;POTEG,missense_variant,p.Ala5Asp,ENST00000547722,;POTEG,missense_variant,p.Ala5Asp,ENST00000622767,; T ENST00000547848 Transcript missense_variant 66/2204 14/1527 5/508 A/D gCt/gAt 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 deleterious_low_confidence(0) 1/11 MODERATE 1 SNV 1 1 PASS rs1380408511 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 19434276 19434276 G T 1 0 0 0 0 1 0 0 0 12380 971 34 2 2 POTEG 14 19434276 Missense_Mutation SNP G C3N-00560_T 306 19434276 87609442 905 17594 KLHL33 0 . GRCh38 14 20430157 20430157 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.519G>T p.= p.R173R ENST00000344581 2/4 266 178 88 220 220 0 strelka-varscan-mutect KLHL33,synonymous_variant,p.=,ENST00000637228,;KLHL33,synonymous_variant,p.=,ENST00000636854,;KLHL33,synonymous_variant,p.=,ENST00000344581,NM_001109997.2; A ENST00000344581 Transcript synonymous_variant 742/1863 519/1602 173/533 R cgG/cgT 1 -1 KLHL33 HGNC HGNC:31952 protein_coding YES CCDS53882.1 ENSP00000341549 A6NCF5 UPI00016630E8 NM_001109997.2 2/4 hmmpanther:PTHR24412:SF195,hmmpanther:PTHR24412,Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,SMART_domains:SM00875 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 20430157 20430157 C A 1 0 0 0 0 0 0 0 1 8252 842 30 2 2 KLHL33 14 20430157 Silent SNP C C3N-00560_T 995881 20430157 86613561 906 17595 OXA1L 0 . GRCh38 14 22771349 22771349 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.1363+1G>T p.X455_splice ENST00000612549 96 57 39 87 87 0 strelka-varscan-mutect OXA1L,splice_donor_variant,,ENST00000612549,;OXA1L,splice_donor_variant,,ENST00000358043,;OXA1L,splice_donor_variant,,ENST00000285848,NM_005015.3;OXA1L,splice_donor_variant,,ENST00000604262,;OXA1L,intron_variant,,ENST00000412791,;SLC7A7,downstream_gene_variant,,ENST00000397532,;SLC7A7,downstream_gene_variant,,ENST00000555702,NM_001126106.2;SLC7A7,downstream_gene_variant,,ENST00000285850,;SLC7A7,downstream_gene_variant,,ENST00000397528,NM_001126105.2;SLC7A7,downstream_gene_variant,,ENST00000397529,;SLC7A7,downstream_gene_variant,,ENST00000554517,;OXA1L,downstream_gene_variant,,ENST00000431881,;SLC7A7,downstream_gene_variant,,ENST00000556350,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554857,;CTD-2555K7.2,upstream_gene_variant,,ENST00000553792,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554730,;SLC7A7,downstream_gene_variant,,ENST00000554061,;OXA1L,splice_donor_variant,,ENST00000495424,;OXA1L,splice_donor_variant,,ENST00000481218,;SLC7A7,downstream_gene_variant,,ENST00000556287,;OXA1L,downstream_gene_variant,,ENST00000483939,;SLC7A7,downstream_gene_variant,,ENST00000555678,;OXA1L,downstream_gene_variant,,ENST00000473744,;OXA1L,downstream_gene_variant,,ENST00000442110,;OXA1L,downstream_gene_variant,,ENST00000556473,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554194,;OXA1L,downstream_gene_variant,,ENST00000557299,; T ENST00000612549 Transcript splice_donor_variant -/2971 1363/1488 455/495 1 1 OXA1L HGNC HGNC:8526 protein_coding YES CCDS9573.1 ENSP00000483491 J3KNA0 UPI000013DE11 9/9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 22771349 22771349 G T 1 0 0 0 0 0 0 1 0 11400 1275 44 2 2 OXA1L 14 22771349 Splice_Site SNP G C3N-00560_T 2341192 22771349 84272369 907 17596 CEBPE 0 . GRCh38 14 23118671 23118671 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.421C>A p.Leu141Met p.L141M ENST00000206513 1/2 154 117 37 130 130 0 strelka-varscan-mutect CEBPE,missense_variant,p.Leu141Met,ENST00000206513,NM_001805.3; T ENST00000206513 Transcript missense_variant 946/1554 421/846 141/281 L/M Ctg/Atg COSM1470674 1 -1 CEBPE HGNC HGNC:1836 protein_coding YES CCDS9589.1 ENSP00000206513 Q15744 UPI000013C660 NM_001805.3 tolerated(0.12) 1/2 PIRSF_domain:PIRSF005879,hmmpanther:PTHR23334,hmmpanther:PTHR23334:SF27 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 23118671 23118671 G T 1 0 0 0 0 1 0 0 0 2908 991 35 2 2 CEBPE 14 23118671 Missense_Mutation SNP G C3N-00560_T 347322 23118671 83925047 908 17597 EMC9 0 . GRCh38 14 24141294 24141294 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.11T>C p.Val4Ala p.V4A ENST00000419198 1/5 282 186 96 231 231 0 strelka-varscan-mutect EMC9,missense_variant,p.Val4Ala,ENST00000419198,;EMC9,missense_variant,p.Val4Ala,ENST00000216799,NM_016049.3;EMC9,intron_variant,,ENST00000560403,;PSME2,downstream_gene_variant,,ENST00000216802,NM_002818.2;PSME1,downstream_gene_variant,,ENST00000382708,NM_176783.2;PSME1,downstream_gene_variant,,ENST00000559123,;PSME1,downstream_gene_variant,,ENST00000206451,NM_001281529.1,NM_006263.3;PSME1,downstream_gene_variant,,ENST00000561435,NM_001281528.1;PSME2,downstream_gene_variant,,ENST00000615264,;PSME2,downstream_gene_variant,,ENST00000560410,;PSME2,downstream_gene_variant,,ENST00000559056,;PSME2,downstream_gene_variant,,ENST00000630027,;RP11-468E2.5,downstream_gene_variant,,ENST00000558478,;PSME2,downstream_gene_variant,,ENST00000620784,;EMC9,non_coding_transcript_exon_variant,,ENST00000558200,;PSME2,downstream_gene_variant,,ENST00000471700,;PSME1,downstream_gene_variant,,ENST00000470718,;PSME2,downstream_gene_variant,,ENST00000559613,;EMC9,missense_variant,p.Val4Ala,ENST00000560600,;PSME2,downstream_gene_variant,,ENST00000558931,;PSME2,downstream_gene_variant,,ENST00000559453,;PSME2,downstream_gene_variant,,ENST00000558273,;PSME1,downstream_gene_variant,,ENST00000561059,;PSME1,downstream_gene_variant,,ENST00000560420,;PSME1,downstream_gene_variant,,ENST00000561142,;PSME2,downstream_gene_variant,,ENST00000560788,;PSME1,downstream_gene_variant,,ENST00000559741,;PSME2,downstream_gene_variant,,ENST00000560592,;PSME2,downstream_gene_variant,,ENST00000559493,;PSME1,downstream_gene_variant,,ENST00000558112,;PSME2,downstream_gene_variant,,ENST00000559042,;PSME2,downstream_gene_variant,,ENST00000560370,;EMC9,upstream_gene_variant,,ENST00000558045,;EMC9,upstream_gene_variant,,ENST00000559101,;PSME2,downstream_gene_variant,,ENST00000559005,;PSME2,downstream_gene_variant,,ENST00000559359,; G ENST00000419198 Transcript missense_variant 292/953 11/627 4/208 V/A gTg/gCg 1 -1 EMC9 HGNC HGNC:20273 protein_coding YES CCDS9613.1 ENSP00000403210 Q9Y3B6 UPI000013C709 deleterious(0) 1/5 Pfam_domain:PF03665,hmmpanther:PTHR12941,hmmpanther:PTHR12941:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 24141294 24141294 A G 1 0 0 0 0 1 0 0 0 4929 159 6 5 5 EMC9 14 24141294 Missense_Mutation SNP A C3N-00560_T 1022623 24141294 82902424 909 17598 NFATC4 0 . GRCh38 14 24373861 24373861 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1915G>T p.Glu639Ter p.E639* ENST00000413692 6/10 497 353 144 434 434 0 strelka-varscan-mutect NFATC4,stop_gained,p.Glu639Ter,ENST00000413692,NM_001136022.2;NFATC4,stop_gained,p.Glu608Ter,ENST00000539237,;NFATC4,stop_gained,p.Glu506Ter,ENST00000557451,;NFATC4,stop_gained,p.Glu564Ter,ENST00000422617,NM_001288802.1;NFATC4,stop_gained,p.Glu589Ter,ENST00000424781,;NFATC4,stop_gained,p.Glu576Ter,ENST00000553708,;NFATC4,stop_gained,p.Glu576Ter,ENST00000250373,NM_001320043.1,NM_004554.4;NFATC4,stop_gained,p.Glu111Ter,ENST00000555167,;NFATC4,stop_gained,p.Glu564Ter,ENST00000555453,;NFATC4,stop_gained,p.Glu576Ter,ENST00000554050,NM_001198965.1;NFATC4,stop_gained,p.Glu506Ter,ENST00000554344,;NFATC4,stop_gained,p.Glu608Ter,ENST00000556279,;NFATC4,stop_gained,p.Glu639Ter,ENST00000554591,NM_001198967.2;NFATC4,stop_gained,p.Glu589Ter,ENST00000555590,;NFATC4,stop_gained,p.Glu506Ter,ENST00000553879,NM_001198966.2;NFATC4,stop_gained,p.Glu506Ter,ENST00000554661,;NFATC4,stop_gained,p.Glu608Ter,ENST00000553469,;NFATC4,stop_gained,p.Glu564Ter,ENST00000556169,;NFATC4,stop_gained,p.Glu589Ter,ENST00000554966,;NFATC4,stop_gained,p.Glu111Ter,ENST00000556759,;NFATC4,stop_gained,p.Glu111Ter,ENST00000554473,;NFATC4,upstream_gene_variant,,ENST00000555393,;NFATC4,upstream_gene_variant,,ENST00000555802,;NFATC4,downstream_gene_variant,,ENST00000557674,;NFATC4,upstream_gene_variant,,ENST00000557767,;NFATC4,downstream_gene_variant,,ENST00000554779,;NFATC4,downstream_gene_variant,,ENST00000554903,;NFATC4,downstream_gene_variant,,ENST00000440487,;NFATC4,upstream_gene_variant,,ENST00000555821,;NFATC4,non_coding_transcript_exon_variant,,ENST00000554655,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556302,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556957,;NFATC4,non_coding_transcript_exon_variant,,ENST00000557028,; T ENST00000413692 Transcript stop_gained 2059/5700 1915/2895 639/964 E/* Gag/Tag 1 1 NFATC4 HGNC HGNC:7778 protein_coding YES CCDS45089.1 ENSP00000388910 Q14934 UPI00017BD050 NM_001136022.2 6/10 PROSITE_profiles:PS50254,hmmpanther:PTHR12533:SF11,hmmpanther:PTHR12533,Pfam_domain:PF00554,Gene3D:2.60.40.340,Superfamily_domains:SSF49417,Prints_domain:PR01789 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 24373861 24373861 G T 1 0 0 0 0 0 1 0 0 10402 1059 37 1 1 NFATC4 14 24373861 Nonsense_Mutation SNP G C3N-00560_T 232567 24373861 82669857 910 17599 CMA1 0 . GRCh38 14 24506038 24506038 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.590C>G p.Ser197Cys p.S197C ENST00000250378 4/5 176 111 65 167 167 0 strelka-varscan-mutect CMA1,missense_variant,p.Ser197Cys,ENST00000250378,NM_001836.3;CMA1,missense_variant,p.Ser86Cys,ENST00000206446,NM_001308083.1;RP11-80A15.1,intron_variant,,ENST00000555109,; C ENST00000250378 Transcript missense_variant 620/937 590/744 197/247 S/C tCt/tGt 1 -1 CMA1 HGNC HGNC:2097 protein_coding YES CCDS9630.1 ENSP00000250378 P23946 UPI000012EDED NM_001836.3 deleterious(0.04) 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF24,PROSITE_patterns:PS00135,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 MODERATE 1 SNV 1 1 PASS rs1462507754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 24506038 24506038 G C 1 0 0 0 0 1 0 0 0 3347 942 33 4 4 CMA1 14 24506038 Missense_Mutation SNP G C3N-00560_T 132177 24506038 82537680 911 17600 NPAS3 0 . GRCh38 14 33793978 33793978 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1235C>A p.Ala412Asp p.A412D ENST00000356141 10/12 183 142 41 199 199 0 strelka-varscan-mutect NPAS3,missense_variant,p.Ala380Asp,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Ala382Asp,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Ala417Asp,ENST00000551492,;NPAS3,missense_variant,p.Ala412Asp,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Ala399Asp,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Ala389Asp,ENST00000551634,; A ENST00000356141 Transcript missense_variant 1235/2802 1235/2802 412/933 A/D gCc/gAc COSM1726657,COSM1726658,COSM1726659 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious(0.01) 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043,Pfam_domain:PF08447,Gene3D:3.30.450.20,Superfamily_domains:SSF55785 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 33793978 33793978 C A 1 0 0 0 0 1 0 0 0 10612 739 26 2 2 NPAS3 14 33793978 Missense_Mutation SNP C C3N-00560_T 9287940 33793978 73249740 912 17601 LRFN5 0 . GRCh38 14 41891362 41891362 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1498A>T p.Thr500Ser p.T500S ENST00000298119 4/6 312 219 93 288 287 1 strelka-varscan-mutect LRFN5,missense_variant,p.Thr500Ser,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; T ENST00000298119 Transcript missense_variant 2687/3723 1498/2160 500/719 T/S Aca/Tca 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0) 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 MODERATE 1 SNV 1 1 PASS rs1161531791 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 41891362 41891362 A T 1 0 0 0 0 1 0 0 0 8835 159 6 4 4 LRFN5 14 41891362 Missense_Mutation SNP A C3N-00560_T 8097384 41891362 65152356 913 17602 MDGA2 0 . GRCh38 14 47061387 47061387 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1180G>C p.Asp394His p.D394H ENST00000399232 7/17 193 127 66 225 225 0 strelka-varscan-mutect MDGA2,missense_variant,p.Asp264His,ENST00000426342,;MDGA2,missense_variant,p.Asp394His,ENST00000399232,NM_001113498.2;MDGA2,missense_variant,p.Asp165His,ENST00000357362,NM_182830.4;MDGA2,missense_variant,p.Asp169His,ENST00000554762,;MDGA2,missense_variant,p.Asp165His,ENST00000557238,;MDGA2,missense_variant,p.Asp165His,ENST00000482848,; G ENST00000399232 Transcript missense_variant 1545/5075 1180/2871 394/956 D/H Gat/Cat 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 deleterious(0) 7/17 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 47061387 47061387 C G 1 0 0 0 0 1 0 0 0 9345 826 29 4 4 MDGA2 14 47061387 Missense_Mutation SNP C C3N-00560_T 5170025 47061387 59982331 914 17603 KTN1 0 . GRCh38 14 55640425 55640425 + Missense_Mutation SNP G G T rs374085889 C3N-00560_T C3N-00560_N G G c.1966G>T p.Ala656Ser p.A656S ENST00000395314 15/44 45 30 15 125 125 0 strelka-varscan-mutect KTN1,missense_variant,p.Ala656Ser,ENST00000395314,NM_001271014.1,NM_001079521.1;KTN1,missense_variant,p.Ala656Ser,ENST00000395311,NM_001079522.1;KTN1,missense_variant,p.Ala656Ser,ENST00000413890,;KTN1,missense_variant,p.Ala656Ser,ENST00000438792,NM_004986.3;KTN1,missense_variant,p.Ala656Ser,ENST00000395308,;KTN1,missense_variant,p.Ala656Ser,ENST00000395309,;KTN1,upstream_gene_variant,,ENST00000554507,;KTN1,downstream_gene_variant,,ENST00000554567,;KTN1,upstream_gene_variant,,ENST00000554890,;KTN1,missense_variant,p.Ala656Ser,ENST00000459737,;KTN1,upstream_gene_variant,,ENST00000553360,; T ENST00000395314 Transcript missense_variant 2034/4618 1966/4074 656/1357 A/S Gcc/Tcc rs374085889 1 1 KTN1 HGNC HGNC:6467 protein_coding YES CCDS41957.1 ENSP00000378725 Q86UP2 A0A024R663 UPI0000190F88 NM_001271014.1,NM_001079521.1 deleterious(0.05) 15/44 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18864 MODERATE 1 SNV 1 1 PASS rs374085889 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 55640425 55640425 G T 1 0 0 0 0 1 0 0 0 8483 1203 42 2 2 KTN1 14 55640425 Missense_Mutation SNP G C3N-00560_T 8579038 55640425 51403293 915 17604 SYNE2 0 . GRCh38 14 64020071 64020071 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.5129G>T p.Ser1710Ile p.S1710I ENST00000358025 35/116 124 81 43 253 253 0 strelka-varscan-mutect SYNE2,missense_variant,p.Ser1710Ile,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Ser1710Ile,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Ser1710Ile,ENST00000357395,;SYNE2,missense_variant,p.Ser1710Ile,ENST00000554584,;SYNE2,non_coding_transcript_exon_variant,,ENST00000557005,; T ENST00000358025 Transcript missense_variant 5341/21842 5129/20724 1710/6907 S/I aGt/aTt 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 deleterious(0.01) 35/116 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 64020071 64020071 G T 1 0 0 0 0 1 0 0 0 15838 1029 36 2 2 SYNE2 14 64020071 Missense_Mutation SNP G C3N-00560_T 8379646 64020071 43023647 916 17605 HSPA2 0 . GRCh38 14 64541386 64541386 + Silent SNP G G A C3N-00560_T C3N-00560_N G G c.537G>A p.= p.A179A ENST00000394709 2/2 325 166 159 359 359 0 strelka-varscan-mutect HSPA2,synonymous_variant,p.=,ENST00000394709,;HSPA2,synonymous_variant,p.=,ENST00000247207,NM_021979.3;RP11-973N13.4,upstream_gene_variant,,ENST00000554918,;HSPA2,non_coding_transcript_exon_variant,,ENST00000554883,; A ENST00000394709 Transcript synonymous_variant 613/5400 537/1920 179/639 A gcG/gcA COSM5509257 1 1 HSPA2 HGNC HGNC:5235 protein_coding YES CCDS9766.1 ENSP00000378199 P54652 A0A024R6B5 UPI000012CC6A 2/2 Gene3D:3.30.420.40,Pfam_domain:PF00012,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF216,Superfamily_domains:SSF53067 1 LOW 1 SNV 1 1 1 PASS rs1158063213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 64541386 64541386 G A 1 0 0 0 0 0 0 0 1 7307 1103 39 1 1 HSPA2 14 64541386 Silent SNP G C3N-00560_T 521315 64541386 42502332 917 17606 MAP3K9 0 . GRCh38 14 70732988 70732988 + Missense_Mutation SNP C C A rs745488869 C3N-00560_T C3N-00560_N C C c.2423G>T p.Arg808Leu p.R808L ENST00000555993 12/13 172 93 79 198 198 0 strelka-varscan-mutect MAP3K9,missense_variant,p.Arg794Leu,ENST00000554752,NM_001284230.1;MAP3K9,missense_variant,p.Arg570Leu,ENST00000611979,NM_001284231.1;MAP3K9,missense_variant,p.Arg808Leu,ENST00000555993,NM_033141.3;MAP3K9,missense_variant,p.Arg771Leu,ENST00000381250,;MAP3K9,missense_variant,p.Arg527Leu,ENST00000553414,NM_001284232.1;MAP3K9,missense_variant,p.Arg522Leu,ENST00000554146,; A ENST00000555993 Transcript missense_variant 2786/4449 2423/3357 808/1118 R/L cGg/cTg rs745488869,COSM195156,COSM5237818 1 -1 MAP3K9 HGNC HGNC:6861 protein_coding YES CCDS32112.1 ENSP00000451263 P80192 UPI00001D7B5C NM_033141.3 tolerated(0.09) 12/13 Low_complexity_(Seg):seg,PIRSF_domain:PIRSF000556 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs745488869 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 70732988 70732988 C A 1 0 0 0 0 1 0 0 0 9181 652 23 1 1 MAP3K9 14 70732988 Missense_Mutation SNP C C3N-00560_T 6191602 70732988 36310730 918 17607 ALDH6A1 0 . GRCh38 14 74067413 74067413 + Missense_Mutation SNP C C A rs778508150 C3N-00560_T C3N-00560_N C C c.1009G>T p.Val337Leu p.V337L ENST00000553458 8/12 279 154 125 389 389 0 strelka-varscan-mutect ALDH6A1,missense_variant,p.Val337Leu,ENST00000553458,NM_001278594.1,NM_005589.3;ALDH6A1,missense_variant,p.Val324Leu,ENST00000350259,NM_001278593.1;ALDH6A1,missense_variant,p.Val54Leu,ENST00000555126,;BBOF1,downstream_gene_variant,,ENST00000394009,NM_025057.2;BBOF1,intron_variant,,ENST00000492026,;ALDH6A1,downstream_gene_variant,,ENST00000556852,;ALDH6A1,downstream_gene_variant,,ENST00000553814,;ALDH6A1,non_coding_transcript_exon_variant,,ENST00000554501,;ALDH6A1,downstream_gene_variant,,ENST00000554231,; A ENST00000553458 Transcript missense_variant 1108/5499 1009/1608 337/535 V/L Gtg/Ttg rs778508150 1 -1 ALDH6A1 HGNC HGNC:7179 protein_coding YES CCDS9826.1 ENSP00000450436 Q02252 A0A024R6G4 UPI0000001610 NM_001278594.1,NM_005589.3 tolerated(0.07) 8/12 hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF183,TIGRFAM_domain:TIGR01722,Pfam_domain:PF00171,Gene3D:3.40.309.10,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS rs778508150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 74067413 74067413 C A 1 0 0 0 0 1 0 0 0 603 507 18 2 2 ALDH6A1 14 74067413 Missense_Mutation SNP C C3N-00560_T 3334425 74067413 32976305 919 17608 LRRC74A 0 . GRCh38 14 76852419 76852419 + Missense_Mutation SNP G G A rs764157721 C3N-00560_T C3N-00560_N G G c.782G>A p.Arg261Lys p.R261K ENST00000393774 8/14 133 68 65 141 141 0 strelka-varscan-mutect LRRC74A,missense_variant,p.Arg261Lys,ENST00000393774,NM_194287.2;LRRC74A,3_prime_UTR_variant,,ENST00000484640,;LRRC74A,3_prime_UTR_variant,,ENST00000216450,; A ENST00000393774 Transcript missense_variant 906/1648 782/1467 261/488 R/K aGg/aAg rs764157721 1 1 LRRC74A HGNC HGNC:23346 protein_coding YES CCDS9853.2 ENSP00000377369 Q0VAA2 UPI000155D520 NM_194287.2 tolerated(1) 8/14 hmmpanther:PTHR24114,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 76852419 76852419 G A 1 0 0 0 0 1 0 0 0 8921 1000 35 3 3 LRRC74A 14 76852419 Missense_Mutation SNP G C3N-00560_T 2785006 76852419 30191299 920 17609 DIO2 0 . GRCh38 14 80203072 80203072 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.547G>A p.Val183Met p.V183M ENST00000555750 3/3 108 60 48 150 150 0 strelka-varscan-mutect DIO2,stop_gained,p.Trp21Ter,ENST00000557125,;DIO2,missense_variant,p.Val147Met,ENST00000557010,NM_001324462.1,NM_000793.5;DIO2,missense_variant,p.Val147Met,ENST00000438257,NM_013989.4;DIO2,missense_variant,p.Val183Met,ENST00000555750,NM_001007023.3;DIO2,3_prime_UTR_variant,,ENST00000422005,NM_001242503.2,NM_001242502.1;DIO2,3_prime_UTR_variant,,ENST00000556811,;DIO2,3_prime_UTR_variant,,ENST00000555844,; T ENST00000555750 Transcript missense_variant 575/1049 547/930 183/309 V/M Gtg/Atg 1 -1 DIO2 HGNC HGNC:2884 protein_coding YES CCDS55934.1 ENSP00000450980 A0A0A0MTQ2 UPI000046D384 NM_001007023.3 deleterious(0.05) 3/3 Gene3D:3.40.30.10,Pfam_domain:PF00837,hmmpanther:PTHR11781,hmmpanther:PTHR11781:SF3,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 80203072 80203072 C T 1 0 0 0 0 1 0 0 0 4330 508 18 3 3 DIO2 14 80203072 Missense_Mutation SNP C C3N-00560_T 3350653 80203072 26840646 921 17610 PPP4R3A 0 . GRCh38 14 91475966 91475966 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1111G>T p.Gly371Cys p.G371C ENST00000554684 7/15 59 35 24 59 59 0 strelka-varscan PPP4R3A,missense_variant,p.Gly371Cys,ENST00000554684,NM_001284280.1;PPP4R3A,missense_variant,p.Gly371Cys,ENST00000554943,;PPP4R3A,missense_variant,p.Gly132Cys,ENST00000555462,NM_001284281.1;PPP4R3A,missense_variant,p.Gly151Cys,ENST00000555470,;PPP4R3A,missense_variant,p.Gly132Cys,ENST00000555029,;PPP4R3A,missense_variant,p.Gly371Cys,ENST00000554390,;PPP4R3A,missense_variant,p.Gly374Cys,ENST00000554308,;PPP4R3A,splice_region_variant,,ENST00000554574,; A ENST00000554684 Transcript missense_variant,splice_region_variant 1608/4108 1111/2463 371/820 G/C Ggc/Tgc 1 -1 PPP4R3A HGNC HGNC:20219 protein_coding YES CCDS9895.1 ENSP00000450864 Q6IN85 A0A024R6M2 UPI00001A95E2 NM_001284280.1 tolerated(0.07) 7/15 hmmpanther:PTHR23318:SF3,hmmpanther:PTHR23318,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 181 26 2 0 0 0 0 -20 0.9916791 0 1 1 0 A 3 1 56 91475966 91475966 C A 1 0 0 0 0 1 0 0 0 12527 637 22 2 2 PPP4R3A 14 91475966 Missense_Mutation SNP C C3N-00560_T 11272894 91475966 15567752 922 17611 UNC79 0 . GRCh38 14 93572034 93572034 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1365C>G p.Ile455Met p.I455M ENST00000256339 15/50 129 70 59 141 141 0 strelka-mutect UNC79,missense_variant,p.Ile632Met,ENST00000553484,;UNC79,missense_variant,p.Ile632Met,ENST00000555664,;UNC79,missense_variant,p.Ile455Met,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Ile632Met,ENST00000393151,;UNC79,missense_variant,p.Ile455Met,ENST00000621021,; G ENST00000256339 Transcript missense_variant 2020/8400 1365/7377 455/2458 I/M atC/atG 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated(0.13) 15/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696,Pfam_domain:PF14776 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 93572034 93572034 C G 1 0 0 0 0 1 0 0 0 17520 816 29 4 4 UNC79 14 93572034 Missense_Mutation SNP C C3N-00560_T 2096068 93572034 13471684 923 17612 CLMN 0 . GRCh38 14 95203302 95203302 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2047G>T p.Gly683Cys p.G683C ENST00000298912 9/13 228 133 95 259 259 0 strelka-varscan-mutect CLMN,missense_variant,p.Gly683Cys,ENST00000298912,NM_024734.3;CLMN,non_coding_transcript_exon_variant,,ENST00000556454,;RP11-725G5.3,downstream_gene_variant,,ENST00000555482,; A ENST00000298912 Transcript missense_variant 2161/12747 2047/3009 683/1002 G/C Ggc/Tgc 1 -1 CLMN HGNC HGNC:19972 protein_coding YES CCDS9933.1 ENSP00000298912 Q96JQ2 UPI000006DB99 NM_024734.3 tolerated(0.07) 9/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 95203302 95203302 C A 1 0 0 0 0 1 0 0 0 3311 623 22 2 2 CLMN 14 95203302 Missense_Mutation SNP C C3N-00560_T 1631268 95203302 11840416 924 17613 WDR20 0 . GRCh38 14 102139981 102139981 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.58C>A p.= p.R20R ENST00000454394 1/4 232 110 122 244 244 0 strelka-varscan-mutect WDR20,synonymous_variant,p.=,ENST00000322340,NM_001242415.1;WDR20,synonymous_variant,p.=,ENST00000424963,;WDR20,synonymous_variant,p.=,ENST00000335263,NM_181291.2;WDR20,synonymous_variant,p.=,ENST00000342702,NM_144574.3,NM_001242418.1;WDR20,synonymous_variant,p.=,ENST00000556807,NM_001242416.1;WDR20,synonymous_variant,p.=,ENST00000299135,NM_001242414.1;WDR20,synonymous_variant,p.=,ENST00000556511,NM_181308.2;WDR20,synonymous_variant,p.=,ENST00000454394,NM_001242417.1;WDR20,synonymous_variant,p.=,ENST00000558567,;HSP90AA1,upstream_gene_variant,,ENST00000334701,NM_001017963.2;HSP90AA1,upstream_gene_variant,,ENST00000558600,;WDR20,non_coding_transcript_exon_variant,,ENST00000557186,;WDR20,non_coding_transcript_exon_variant,,ENST00000561154,;WDR20,intron_variant,,ENST00000557485,;WDR20,synonymous_variant,p.=,ENST00000555879,;WDR20,synonymous_variant,p.=,ENST00000556094,;HSP90AA1,upstream_gene_variant,,ENST00000557234,; A ENST00000454394 Transcript synonymous_variant 68/2067 58/1803 20/600 R Cgg/Agg 1 1 WDR20 HGNC HGNC:19667 protein_coding YES CCDS55943.1 ENSP00000406084 Q8TBZ3 UPI0000E23AC1 NM_001242417.1 1/4 hmmpanther:PTHR14107,hmmpanther:PTHR14107:SF5 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 102139981 102139981 C A 1 0 0 0 0 0 0 0 1 17840 643 23 1 1 WDR20 14 102139981 Silent SNP C C3N-00560_T 6936679 102139981 4903737 925 17614 KIF26A 0 . GRCh38 14 104176422 104176422 + Silent SNP C C A rs200700317 C3N-00560_T C3N-00560_N C C c.3634C>A p.= p.R1212R ENST00000423312 12/15 56 30 26 51 51 0 strelka-varscan-mutect KIF26A,synonymous_variant,p.=,ENST00000315264,;KIF26A,synonymous_variant,p.=,ENST00000423312,NM_015656.1; A ENST00000423312 Transcript synonymous_variant 3634/5649 3634/5649 1212/1882 R Cgg/Agg rs200700317 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 12/15 LOW 1 SNV 5 1 PASS rs200700317 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 104176422 104176422 C A 1 0 0 0 0 0 0 0 1 8159 643 23 1 1 KIF26A 14 104176422 Silent SNP C C3N-00560_T 2036441 104176422 2867296 926 17615 KIF26A 0 . GRCh38 14 104176711 104176711 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3923G>T p.Arg1308Met p.R1308M ENST00000423312 12/15 51 27 24 59 59 0 strelka-varscan-mutect KIF26A,missense_variant,p.Arg1169Met,ENST00000315264,;KIF26A,missense_variant,p.Arg1308Met,ENST00000423312,NM_015656.1; T ENST00000423312 Transcript missense_variant 3923/5649 3923/5649 1308/1882 R/M aGg/aTg 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 deleterious(0) 12/15 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 104176711 104176711 G T 1 0 0 0 0 1 0 0 0 8159 1000 35 2 2 KIF26A 14 104176711 Missense_Mutation SNP G C3N-00560_T 289 104176711 2867007 927 17616 CEP170B 0 . GRCh38 14 104886873 104886873 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.2634A>T p.= p.P878P ENST00000414716 12/19 173 96 77 229 229 0 strelka-varscan-mutect CEP170B,synonymous_variant,p.=,ENST00000453495,;CEP170B,synonymous_variant,p.=,ENST00000414716,NM_001112726.2;CEP170B,synonymous_variant,p.=,ENST00000556508,NM_015005.2; T ENST00000414716 Transcript synonymous_variant 2862/6705 2634/4665 878/1554 P ccA/ccT 1 1 CEP170B HGNC HGNC:20362 protein_coding YES CCDS45175.1 ENSP00000404151 Q9Y4F5 UPI00001FDCF7 NM_001112726.2 12/19 Pfam_domain:PF15308,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 104886873 104886873 A T 1 0 0 0 0 0 0 0 1 2965 175 7 4 4 CEP170B 14 104886873 Silent SNP A C3N-00560_T 710162 104886873 2156845 928 17617 AHNAK2 0 . GRCh38 14 104945179 104945179 + Missense_Mutation SNP C C A rs372010769 C3N-00560_T C3N-00560_N C C c.10272G>T p.Lys3424Asn p.K3424N ENST00000333244 7/7 427 215 212 478 476 2 strelka-varscan-mutect AHNAK2,missense_variant,p.Lys3424Asn,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript missense_variant 10392/18254 10272/17388 3424/5795 K/N aaG/aaT rs372010769 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0.01) 7/7 MODERATE 1 SNV 5 1 PASS rs372010769 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 104945179 104945179 C A 1 0 0 0 0 1 0 0 0 492 680 24 2 2 AHNAK2 14 104945179 Missense_Mutation SNP C C3N-00560_T 58306 104945179 2098539 929 17618 NPAP1 0 . GRCh38 15 24676257 24676257 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.390A>T p.= p.P130P ENST00000329468 1/1 14 7 7 11 11 0 strelka-varscan-mutect NPAP1,synonymous_variant,p.=,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript synonymous_variant 390/7526 390/3471 130/1156 P ccA/ccT 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15 LOW 1 SNV 1 PASS . . 24 184 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 24676257 24676257 A T 1 0 0 0 0 0 0 0 1 10609 146 6 4 4 NPAP1 15 24676257 Silent SNP A C3N-00560_T 24676257 77314932 930 17619 GABRB3 0 . GRCh38 15 26772681 26772681 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.172G>T p.Gly58Cys p.G58C ENST00000311550 2/9 261 141 120 275 275 0 strelka-varscan-mutect GABRB3,missense_variant,p.Gly114Cys,ENST00000541819,;GABRB3,missense_variant,p.Gly58Cys,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Gly58Cys,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Gly25Cys,ENST00000638099,;GABRB3,splice_region_variant,,ENST00000622697,NM_001278631.1;GABRB3,upstream_gene_variant,,ENST00000636466,;GABRB3,splice_region_variant,,ENST00000557641,;GABRB3,splice_region_variant,,ENST00000554722,;GABRB3,missense_variant,p.Gly58Cys,ENST00000555632,;GABRB3,missense_variant,p.Gly58Cys,ENST00000554556,; A ENST00000311550 Transcript missense_variant,splice_region_variant 284/5781 172/1422 58/473 G/C Ggt/Tgt COSM5339144,COSM5339145,COSM5339146 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 deleterious(0) 2/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 26772681 26772681 C A 1 0 0 0 0 1 0 0 0 6039 637 22 2 2 GABRB3 15 26772681 Missense_Mutation SNP C C3N-00560_T 2096424 26772681 75218508 931 17620 OCA2 0 . GRCh38 15 28014815 28014815 + Silent SNP C C A rs763586305 C3N-00560_T C3N-00560_N C C c.1005G>T p.= p.T335T ENST00000354638 9/24 318 171 147 339 339 0 strelka-varscan-mutect OCA2,synonymous_variant,p.=,ENST00000354638,NM_000275.2;OCA2,synonymous_variant,p.=,ENST00000353809,NM_001300984.1;OCA2,downstream_gene_variant,,ENST00000431101,;OCA2,downstream_gene_variant,,ENST00000445578,; A ENST00000354638 Transcript synonymous_variant 1161/3186 1005/2517 335/838 T acG/acT rs763586305,COSM4868598,COSM960084 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 9/24 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs763586305 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 28014815 28014815 C A 1 0 0 0 0 0 0 0 1 10892 639 23 1 1 OCA2 15 28014815 Silent SNP C C3N-00560_T 1242134 28014815 73976374 932 17621 HERC2 0 . GRCh38 15 28263069 28263069 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1971G>T p.Leu657Phe p.L657F ENST00000261609 15/93 343 216 127 440 440 0 strelka-varscan-mutect HERC2,missense_variant,p.Leu657Phe,ENST00000261609,NM_004667.5;HERC2,3_prime_UTR_variant,,ENST00000564734,; A ENST00000261609 Transcript missense_variant 2080/15337 1971/14505 657/4834 L/F ttG/ttT COSM4627306,COSM4627307 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 deleterious(0.04) 15/93 Gene3D:2.130.10.30,Pfam_domain:PF00415,PROSITE_profiles:PS50012,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF325,SMART_domains:SM00706,Superfamily_domains:SSF50985 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 28263069 28263069 C A 1 0 0 0 0 1 0 0 0 6942 593 21 2 2 HERC2 15 28263069 Missense_Mutation SNP C C3N-00560_T 248254 28263069 73728120 933 17622 GOLGA8M 0 . GRCh38 15 28706472 28706472 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.713G>T p.Arg238Ile p.R238I ENST00000563027 10/19 144 135 9 161 161 0 varscan-mutect GOLGA8M,missense_variant,p.Arg238Ile,ENST00000563027,NM_001282468.1;RN7SL719P,upstream_gene_variant,,ENST00000620196,;GOLGA8M,downstream_gene_variant,,ENST00000563213,; A ENST00000563027 Transcript missense_variant 713/1899 713/1899 238/632 R/I aGa/aTa 1 -1 GOLGA8M HGNC HGNC:44404 protein_coding YES CCDS61572.1 ENSP00000456927 H3BSY2 UPI0001A5E7A0 NM_001282468.1 deleterious(0) 10/19 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 28706472 28706472 C A 1 0 0 0 0 1 0 0 0 6454 913 32 2 2 GOLGA8M 15 28706472 Missense_Mutation SNP C C3N-00560_T 443403 28706472 73284717 934 17623 TRPM1 0 . GRCh38 15 31026188 31026188 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.3631G>A p.Asp1211Asn p.D1211N ENST00000542188 26/27 416 219 197 486 486 0 strelka-varscan-mutect TRPM1,missense_variant,p.Asp1211Asn,ENST00000542188,NM_001252020.1;TRPM1,missense_variant,p.Asp1172Asn,ENST00000397795,NM_002420.5;TRPM1,missense_variant,p.Asp1194Asn,ENST00000256552,NM_001252024.1;TRPM1,missense_variant,p.Asp1095Asn,ENST00000558768,;TRPM1,missense_variant,p.Asp1172Asn,ENST00000558445,;TRPM1,missense_variant,p.Asp287Asn,ENST00000559177,;RP11-348B17.1,intron_variant,,ENST00000561299,;RP11-348B17.1,upstream_gene_variant,,ENST00000558755,;TRPM1,3_prime_UTR_variant,,ENST00000560801,;TRPM1,downstream_gene_variant,,ENST00000558212,;TRPM1,downstream_gene_variant,,ENST00000557948,; T ENST00000542188 Transcript missense_variant 3945/6004 3631/4929 1211/1642 D/N Gat/Aat 1 -1 TRPM1 HGNC HGNC:7146 protein_coding YES CCDS58347.1 ENSP00000437849 Q7Z4N2 UPI0001DBB3A9 NM_001252020.1 deleterious(0.02) 26/27 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 31026188 31026188 C T 1 0 0 0 0 1 0 0 0 17091 855 30 3 3 TRPM1 15 31026188 Missense_Mutation SNP C C3N-00560_T 2319716 31026188 70965001 935 17624 RYR3 0 . GRCh38 15 33660269 33660269 + Missense_Mutation SNP C C A rs74005937 C3N-00560_T C3N-00560_N C C c.4468C>A p.Leu1490Met p.L1490M ENST00000634891 34/104 181 105 76 217 217 0 strelka-varscan-mutect RYR3,missense_variant,p.Leu1490Met,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Leu1490Met,ENST00000622037,;RYR3,missense_variant,p.Leu1490Met,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Leu1490Met,ENST00000389232,;RYR3,missense_variant,p.Leu1490Met,ENST00000634418,; A ENST00000634891 Transcript missense_variant 4569/15591 4468/14613 1490/4870 L/M Ctg/Atg rs74005937 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 34/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS rs74005937 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 33660269 33660269 C A 1 0 0 0 0 1 0 0 0 14030 796 28 2 2 RYR3 15 33660269 Missense_Mutation SNP C C3N-00560_T 2634081 33660269 68330920 936 17625 RYR3 0 . GRCh38 15 33819791 33819791 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.10742C>G p.Ser3581Cys p.S3581C ENST00000634891 77/104 139 94 45 187 187 0 strelka-varscan-mutect RYR3,missense_variant,p.Ser3581Cys,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Ser3584Cys,ENST00000622037,;RYR3,missense_variant,p.Ser3576Cys,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Ser3580Cys,ENST00000389232,;RYR3,missense_variant,p.Ser3576Cys,ENST00000634418,;RYR3,downstream_gene_variant,,ENST00000638038,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,upstream_gene_variant,,ENST00000558060,;RYR3,upstream_gene_variant,,ENST00000557931,; G ENST00000634891 Transcript missense_variant 10843/15591 10742/14613 3581/4870 S/C tCc/tGc 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 77/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 33819791 33819791 C G 1 0 0 0 0 1 0 0 0 14030 855 30 4 4 RYR3 15 33819791 Missense_Mutation SNP C C3N-00560_T 159522 33819791 68171398 937 17626 RYR3 0 . GRCh38 15 33838374 33838374 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.12394G>T p.Glu4132Ter p.E4132* ENST00000634891 89/104 293 157 136 355 354 1 strelka-varscan-mutect RYR3,stop_gained,p.Glu4132Ter,ENST00000634891,NM_001036.4;RYR3,stop_gained,p.Glu4135Ter,ENST00000622037,;RYR3,stop_gained,p.Glu4127Ter,ENST00000415757,NM_001243996.2;RYR3,stop_gained,p.Glu4131Ter,ENST00000389232,;RYR3,stop_gained,p.Glu4121Ter,ENST00000634418,;RYR3,upstream_gene_variant,,ENST00000634730,;RYR3,upstream_gene_variant,,ENST00000636568,;RYR3,downstream_gene_variant,,ENST00000635842,;RYR3,downstream_gene_variant,,ENST00000638032,;RYR3,non_coding_transcript_exon_variant,,ENST00000635749,;RYR3,upstream_gene_variant,,ENST00000638052,;RYR3,upstream_gene_variant,,ENST00000636656,;RYR3,upstream_gene_variant,,ENST00000637615,;RYR3,upstream_gene_variant,,ENST00000637984,;RYR3,stop_gained,p.Glu10Ter,ENST00000637948,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,upstream_gene_variant,,ENST00000636845,; T ENST00000634891 Transcript stop_gained 12495/15591 12394/14613 4132/4870 E/* Gaa/Taa 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 89/104 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 33838374 33838374 G T 1 0 0 0 0 0 1 0 0 14030 943 33 2 2 RYR3 15 33838374 Nonsense_Mutation SNP G C3N-00560_T 18583 33838374 68152815 938 17627 DPH6 0 . GRCh38 15 35538330 35538330 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.256A>T p.Thr86Ser p.T86S ENST00000256538 3/9 148 77 71 171 171 0 strelka-varscan-mutect DPH6,missense_variant,p.Thr86Ser,ENST00000440392,NM_001141972.1;DPH6,missense_variant,p.Thr86Ser,ENST00000256538,NM_080650.3;DPH6,missense_variant,p.Thr38Ser,ENST00000561411,;DPH6,non_coding_transcript_exon_variant,,ENST00000559585,;DPH6,non_coding_transcript_exon_variant,,ENST00000559784,;DPH6,non_coding_transcript_exon_variant,,ENST00000560526,; A ENST00000256538 Transcript missense_variant 283/2099 256/804 86/267 T/S Acc/Tcc 1 -1 DPH6 HGNC HGNC:30543 protein_coding YES CCDS10043.1 ENSP00000256538 Q7L8W6 UPI000007296C NM_080650.3 tolerated(0.83) 3/9 Gene3D:3.40.50.620,Pfam_domain:PF01902,PIRSF_domain:PIRSF039123,hmmpanther:PTHR12196,Superfamily_domains:SSF52402,TIGRFAM_domain:TIGR00290 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 35538330 35538330 T A 1 0 0 0 0 1 0 0 0 4537 1696 59 4 4 DPH6 15 35538330 Missense_Mutation SNP T C3N-00560_T 1699956 35538330 66452859 939 17628 GANC 0 . GRCh38 15 42351391 42351391 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.2594G>C p.Gly865Ala p.G865A ENST00000318010 23/24 146 84 62 198 198 0 strelka-varscan-mutect GANC,missense_variant,p.Gly865Ala,ENST00000318010,NM_198141.2;GANC,missense_variant,p.Gly74Ala,ENST00000566690,;GANC,missense_variant,p.Gly74Ala,ENST00000567596,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000495723,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000466369,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000549793,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000483208,; C ENST00000318010 Transcript missense_variant 2834/7781 2594/2745 865/914 G/A gGc/gCc COSM5098369 1 1 GANC HGNC HGNC:4139 protein_coding YES CCDS10084.1 ENSP00000326227 Q8TET4 UPI00001FE303 NM_198141.2 23/24 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF60 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 42351391 42351391 G C 1 0 0 0 0 1 0 0 0 6102 1203 42 4 4 GANC 15 42351391 Missense_Mutation SNP G C3N-00560_T 6813061 42351391 59639798 940 17629 STRC 0 . GRCh38 15 43604766 43604766 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.4011A>T p.= p.T1337T ENST00000450892 20/29 786 523 263 597 596 1 strelka-varscan-mutect STRC,synonymous_variant,p.=,ENST00000450892,NM_153700.2;STRC,synonymous_variant,p.=,ENST00000541030,;RNU6-554P,downstream_gene_variant,,ENST00000410466,;CKMT1B,intron_variant,,ENST00000411560,;STRC,3_prime_UTR_variant,,ENST00000428650,;STRC,3_prime_UTR_variant,,ENST00000440125,;STRC,3_prime_UTR_variant,,ENST00000455136,;STRC,non_coding_transcript_exon_variant,,ENST00000485556,;STRC,non_coding_transcript_exon_variant,,ENST00000471703,;STRC,intron_variant,,ENST00000448437,;STRC,upstream_gene_variant,,ENST00000460952,;STRC,upstream_gene_variant,,ENST00000493750,; A ENST00000450892 Transcript synonymous_variant 4089/5680 4011/5328 1337/1775 T acA/acT 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 20/29 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF14 LOW 1 SNV 5 1 PASS rs1231379897 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 43604766 43604766 T A 1 0 0 0 0 0 0 0 1 15709 1683 59 4 4 STRC 15 43604766 Silent SNP T C3N-00560_T 1253375 43604766 58386423 941 17630 SPG11 0 . GRCh38 15 44659297 44659297 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.449C>T p.Ser150Phe p.S150F ENST00000261866 3/40 181 129 52 147 147 0 strelka-varscan-mutect SPG11,missense_variant,p.Ser150Phe,ENST00000261866,NM_025137.3;SPG11,missense_variant,p.Ser150Phe,ENST00000535302,NM_001160227.1;SPG11,missense_variant,p.Ser150Phe,ENST00000427534,;SPG11,missense_variant,p.Ser150Phe,ENST00000558319,;SPG11,missense_variant,p.Ser150Phe,ENST00000559193,; A ENST00000261866 Transcript missense_variant 466/7774 449/7332 150/2443 S/F tCc/tTc 1 -1 SPG11 HGNC HGNC:11226 protein_coding YES CCDS10112.1 ENSP00000261866 Q96JI7 UPI0000456840 NM_025137.3 deleterious(0) 3/40 Low_complexity_(Seg):seg,hmmpanther:PTHR13650,hmmpanther:PTHR13650:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44659297 44659297 G A 1 0 0 0 0 1 0 0 0 15392 1174 41 3 3 SPG11 15 44659297 Missense_Mutation SNP G C3N-00560_T 1054531 44659297 57331892 942 17631 PATL2 0 . GRCh38 15 44667145 44667145 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1424A>T p.His475Leu p.H475L ENST00000434130 14/16 252 192 60 212 212 0 strelka-varscan-mutect PATL2,missense_variant,p.His475Leu,ENST00000434130,NM_001145112.1;PATL2,missense_variant,p.His475Leu,ENST00000560775,;PATL2,missense_variant,p.His286Leu,ENST00000560780,;PATL2,intron_variant,,ENST00000558809,;SPG11,upstream_gene_variant,,ENST00000261866,NM_025137.3;SPG11,upstream_gene_variant,,ENST00000535302,NM_001160227.1;SPG11,upstream_gene_variant,,ENST00000427534,;SPG11,upstream_gene_variant,,ENST00000558319,;SPG11,upstream_gene_variant,,ENST00000559193,;PATL2,downstream_gene_variant,,ENST00000560110,;PATL2,non_coding_transcript_exon_variant,,ENST00000561082,;PATL2,upstream_gene_variant,,ENST00000558159,;PATL2,downstream_gene_variant,,ENST00000558481,; A ENST00000434130 Transcript missense_variant 1522/1950 1424/1632 475/543 H/L cAt/cTt 1 -1 PATL2 HGNC HGNC:33630 protein_coding YES CCDS45253.1 ENSP00000416673 C9JE40 UPI00006C1508 NM_001145112.1 deleterious(0) 14/16 hmmpanther:PTHR21551,hmmpanther:PTHR21551:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44667145 44667145 T A 1 0 0 0 0 1 0 0 0 11560 1464 51 4 4 PATL2 15 44667145 Missense_Mutation SNP T C3N-00560_T 7848 44667145 57324044 943 17632 PATL2 0 . GRCh38 15 44673322 44673322 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.359C>A p.Ser120Tyr p.S120Y ENST00000434130 5/16 380 261 119 252 252 0 strelka-varscan-mutect PATL2,missense_variant,p.Ser120Tyr,ENST00000434130,NM_001145112.1;PATL2,missense_variant,p.Ser120Tyr,ENST00000560775,;PATL2,missense_variant,p.Ser33Tyr,ENST00000560110,;PATL2,5_prime_UTR_variant,,ENST00000560780,;PATL2,upstream_gene_variant,,ENST00000558809,;PATL2,downstream_gene_variant,,ENST00000558573,;PATL2,missense_variant,p.Ser91Tyr,ENST00000558481,; T ENST00000434130 Transcript missense_variant 457/1950 359/1632 120/543 S/Y tCt/tAt 1 -1 PATL2 HGNC HGNC:33630 protein_coding YES CCDS45253.1 ENSP00000416673 C9JE40 UPI00006C1508 NM_001145112.1 deleterious(0.05) 5/16 Low_complexity_(Seg):seg,hmmpanther:PTHR21551,hmmpanther:PTHR21551:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 44673322 44673322 G T 1 0 0 0 0 1 0 0 0 11560 942 33 2 2 PATL2 15 44673322 Missense_Mutation SNP G C3N-00560_T 6177 44673322 57317867 944 17633 DUOX2 0 . GRCh38 15 45109960 45109960 + Missense_Mutation SNP C C A rs370954970 C3N-00560_T C3N-00560_N C C c.1061G>T p.Arg354Leu p.R354L ENST00000603300 10/34 627 448 179 486 486 0 strelka-varscan-mutect DUOX2,missense_variant,p.Arg354Leu,ENST00000389039,;DUOX2,missense_variant,p.Arg354Leu,ENST00000603300,NM_014080.4;DUOXA2,upstream_gene_variant,,ENST00000323030,NM_207581.3;DUOX2,non_coding_transcript_exon_variant,,ENST00000558383,;DUOXA2,upstream_gene_variant,,ENST00000491993,;DUOXA2,upstream_gene_variant,,ENST00000350243,; A ENST00000603300 Transcript missense_variant 1264/6345 1061/4647 354/1548 R/L cGg/cTg rs370954970 1 -1 DUOX2 HGNC HGNC:13273 protein_coding YES CCDS10117.1 ENSP00000475084 Q9NRD8 UPI000013D775 NM_014080.4 deleterious(0.04) 10/34 Gene3D:1.10.640.10,Pfam_domain:PF03098,PROSITE_profiles:PS50292,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS rs370954970 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45109960 45109960 C A 1 0 0 0 0 1 0 0 0 4623 652 23 1 1 DUOX2 15 45109960 Missense_Mutation SNP C C3N-00560_T 436638 45109960 56881229 945 17634 BCL2L10 0 . GRCh38 15 52109973 52109973 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.560G>C p.Gly187Ala p.G187A ENST00000561198 2/2 94 68 26 73 73 0 strelka-varscan-mutect BCL2L10,missense_variant,p.Asp164His,ENST00000260442,NM_020396.2;BCL2L10,missense_variant,p.Gly187Ala,ENST00000561198,NM_001306168.1; G ENST00000561198 Transcript missense_variant,splice_region_variant 602/825 560/726 187/241 G/A gGa/gCa 1 -1 BCL2L10 HGNC HGNC:993 protein_coding YES CCDS76756.1 ENSP00000453562 H0YMD5 UPI00022F852C NM_001306168.1 2/2 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 52109973 52109973 C G 1 0 0 0 0 1 0 0 0 1515 869 30 4 4 BCL2L10 15 52109973 Missense_Mutation SNP C C3N-00560_T 7000013 52109973 49881216 946 17635 MYO5C 0 . GRCh38 15 52211807 52211807 + Missense_Mutation SNP C C G rs754670620 C3N-00560_T C3N-00560_N C C c.4219G>C p.Ala1407Pro p.A1407P ENST00000261839 35/41 174 122 52 146 146 0 strelka-varscan-mutect MYO5C,missense_variant,p.Ala1407Pro,ENST00000261839,NM_018728.3;MYO5C,3_prime_UTR_variant,,ENST00000560809,;MYO5C,non_coding_transcript_exon_variant,,ENST00000559696,; G ENST00000261839 Transcript missense_variant 4381/6971 4219/5229 1407/1742 A/P Gca/Cca rs754670620 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 deleterious(0) 35/41 hmmpanther:PTHR13140:SF313,hmmpanther:PTHR13140 MODERATE 1 SNV 1 1 PASS rs754670620 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 52211807 52211807 C G 1 0 0 0 0 1 0 0 0 10081 768 27 4 4 MYO5C 15 52211807 Missense_Mutation SNP C C3N-00560_T 101834 52211807 49779382 947 17636 ONECUT1 0 . GRCh38 15 52789189 52789189 + Missense_Mutation SNP C C A rs529209684 C3N-00560_T C3N-00560_N C C c.696G>T p.Gln232His p.Q232H ENST00000305901 1/2 43 30 13 44 44 0 strelka-varscan-mutect ONECUT1,missense_variant,p.Gln232His,ENST00000305901,NM_004498.2;ONECUT1,intron_variant,,ENST00000561401,;ONECUT1,missense_variant,p.Gln70His,ENST00000570208,; A ENST00000305901 Transcript missense_variant 824/2092 696/1398 232/465 Q/H caG/caT rs529209684 1 -1 ONECUT1 HGNC HGNC:8138 protein_coding YES CCDS10150.1 ENSP00000302630 Q9UBC0 UPI000012CA91 NM_004498.2 deleterious(0.04) 1/2 hmmpanther:PTHR14057:SF9,hmmpanther:PTHR14057 MODERATE 1 SNV 1 1 PASS rs529209684 . 0 201 9 0 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 56 52789189 52789189 C A 1 0 0 0 0 1 0 0 0 10943 796 28 2 2 ONECUT1 15 52789189 Missense_Mutation SNP C C3N-00560_T 577382 52789189 49202000 948 17637 VPS13C 0 . GRCh38 15 61856375 61856375 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.10987G>T p.Gly3663Cys p.G3663C ENST00000261517 83/85 218 148 70 258 257 1 strelka-varscan-mutect VPS13C,missense_variant,p.Gly3663Cys,ENST00000261517,NM_020821.2;VPS13C,missense_variant,p.Gly3620Cys,ENST00000249837,NM_017684.4;RP11-16B9.1,downstream_gene_variant,,ENST00000559251,;VPS13C,non_coding_transcript_exon_variant,,ENST00000560637,;VPS13C,non_coding_transcript_exon_variant,,ENST00000559119,; A ENST00000261517 Transcript missense_variant 11061/13400 10987/11262 3663/3753 G/C Ggc/Tgc 1 -1 VPS13C HGNC HGNC:23594 protein_coding YES CCDS32257.1 ENSP00000261517 Q709C8 UPI000023B7D3 NM_020821.2 deleterious(0.01) 83/85 hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF69 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -20 0.9991937 1 1 1 0 A 3 1 56 61856375 61856375 C A 1 0 0 0 0 1 0 0 0 17738 623 22 2 2 VPS13C 15 61856375 Missense_Mutation SNP C C3N-00560_T 9067186 61856375 40134814 949 17638 HERC1 0 . GRCh38 15 63661813 63661813 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.9110G>T p.Gly3037Val p.G3037V ENST00000443617 45/78 300 215 85 253 253 0 strelka-varscan-mutect HERC1,missense_variant,p.Gly3037Val,ENST00000443617,NM_003922.3; A ENST00000443617 Transcript missense_variant 9198/15137 9110/14586 3037/4861 G/V gGc/gTc 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 tolerated(0.43) 45/78 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 63661813 63661813 C A 1 0 0 0 0 1 0 0 0 6941 739 26 2 2 HERC1 15 63661813 Missense_Mutation SNP C C3N-00560_T 1805438 63661813 38329376 950 17639 RASL12 0 . GRCh38 15 65054991 65054991 + Missense_Mutation SNP G G T rs765723325 C3N-00560_T C3N-00560_N G G c.709C>A p.Gln237Lys p.Q237K ENST00000220062 5/5 309 210 99 199 199 0 strelka-varscan-mutect RASL12,missense_variant,p.Gln237Lys,ENST00000220062,NM_016563.2;RASL12,missense_variant,p.Gln218Lys,ENST00000421977,NM_001307930.1;RASL12,missense_variant,p.Gln226Lys,ENST00000434605,;SLC51B,downstream_gene_variant,,ENST00000334287,NM_178859.3; T ENST00000220062 Transcript missense_variant 986/2640 709/801 237/266 Q/K Cag/Aag rs765723325 1 -1 RASL12 HGNC HGNC:30289 protein_coding YES CCDS10200.1 ENSP00000220062 Q9NYN1 A0A024R5Y3 UPI000006F3CC NM_016563.2 deleterious(0.04) 5/5 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF252 MODERATE 1 SNV 1 1 PASS rs765723325 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 65054991 65054991 G T 1 0 0 0 0 1 0 0 0 13244 1357 47 2 2 RASL12 15 65054991 Missense_Mutation SNP G C3N-00560_T 1393178 65054991 36936198 951 17640 IGDCC4 0 . GRCh38 15 65388865 65388865 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2650C>A p.Leu884Met p.L884M ENST00000352385 15/20 282 188 94 226 224 2 strelka-varscan-mutect IGDCC4,missense_variant,p.Leu884Met,ENST00000352385,NM_020962.2;IGDCC4,upstream_gene_variant,,ENST00000558048,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,;IGDCC4,upstream_gene_variant,,ENST00000560319,;IGDCC4,upstream_gene_variant,,ENST00000561309,; T ENST00000352385 Transcript missense_variant 2860/6508 2650/3753 884/1250 L/M Ctg/Atg 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 deleterious(0.03) 15/20 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 65388865 65388865 G T 1 0 0 0 0 1 0 0 0 7475 991 35 2 2 IGDCC4 15 65388865 Missense_Mutation SNP G C3N-00560_T 333874 65388865 36602324 952 17641 DENND4A 0 . GRCh38 15 65741770 65741770 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.576A>G p.= p.V192V ENST00000443035 5/33 182 124 58 190 190 0 strelka-varscan-mutect DENND4A,synonymous_variant,p.=,ENST00000443035,NM_001320835.1,NM_001144823.1;DENND4A,synonymous_variant,p.=,ENST00000635620,;DENND4A,synonymous_variant,p.=,ENST00000431932,NM_005848.3;DENND4A,synonymous_variant,p.=,ENST00000564674,;RAB11A,intron_variant,,ENST00000569304,;DENND4A,non_coding_transcript_exon_variant,,ENST00000568515,; C ENST00000443035 Transcript synonymous_variant 792/8665 576/5721 192/1906 V gtA/gtG 1 -1 DENND4A HGNC HGNC:24321 protein_coding YES CCDS53949.1 ENSP00000391167 Q7Z401 UPI000013EDF7 NM_001320835.1,NM_001144823.1 5/33 PROSITE_profiles:PS51498,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF16,SMART_domains:SM00800 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 65741770 65741770 T C 1 0 0 0 0 0 0 0 1 4237 1393 49 5 5 DENND4A 15 65741770 Silent SNP T C3N-00560_T 352905 65741770 36249419 953 17642 DENND4A 0 . GRCh38 15 65752501 65752501 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.439G>A p.Ala147Thr p.A147T ENST00000443035 4/33 356 268 88 281 281 0 strelka-varscan-mutect DENND4A,missense_variant,p.Ala147Thr,ENST00000443035,NM_001320835.1,NM_001144823.1;DENND4A,missense_variant,p.Ala147Thr,ENST00000635620,;DENND4A,missense_variant,p.Ala147Thr,ENST00000431932,NM_005848.3;DENND4A,missense_variant,p.Ala147Thr,ENST00000564674,;RAB11A,intron_variant,,ENST00000569304,;DENND4A,non_coding_transcript_exon_variant,,ENST00000568515,; T ENST00000443035 Transcript missense_variant 655/8665 439/5721 147/1906 A/T Gcc/Acc 1 -1 DENND4A HGNC HGNC:24321 protein_coding YES CCDS53949.1 ENSP00000391167 Q7Z401 UPI000013EDF7 NM_001320835.1,NM_001144823.1 deleterious(0) 4/33 PROSITE_profiles:PS51498,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 65752501 65752501 C T 1 0 0 0 0 1 0 0 0 4237 797 28 3 3 DENND4A 15 65752501 Missense_Mutation SNP C C3N-00560_T 10731 65752501 36238688 954 17643 TMEM202 0 . GRCh38 15 72406668 72406668 + Nonsense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.404G>A p.Trp135Ter p.W135* ENST00000341689 3/5 266 201 65 201 201 0 strelka-varscan-mutect TMEM202,stop_gained,p.Trp135Ter,ENST00000341689,NM_001080462.1;TMEM202,missense_variant,p.Gly50Ser,ENST00000567679,;RP11-1007O24.3,downstream_gene_variant,,ENST00000562573,;TMEM202,missense_variant,p.Gly50Ser,ENST00000568167,; A ENST00000341689 Transcript stop_gained 458/1012 404/822 135/273 W/* tGg/tAg 1 1 TMEM202 HGNC HGNC:33733 protein_coding YES CCDS32287.1 ENSP00000340212 A6NGA9 UPI000049DDE8 NM_001080462.1 3/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR10671:SF42,hmmpanther:PTHR10671 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 72406668 72406668 G A 1 0 0 0 0 0 1 0 0 16566 1357 47 3 3 TMEM202 15 72406668 Nonsense_Mutation SNP G C3N-00560_T 6654167 72406668 29584521 955 17644 CSK 0 . GRCh38 15 74801057 74801057 + Silent SNP G G C rs753705973 C3N-00560_T C3N-00560_N G G c.768G>C p.= p.V256V ENST00000220003 9/13 499 376 123 297 297 0 strelka-varscan-mutect CSK,synonymous_variant,p.=,ENST00000220003,NM_004383.2;CSK,synonymous_variant,p.=,ENST00000567571,;CSK,synonymous_variant,p.=,ENST00000439220,NM_001127190.1;CSK,downstream_gene_variant,,ENST00000569915,;CSK,downstream_gene_variant,,ENST00000567123,;CSK,downstream_gene_variant,,ENST00000569462,;CSK,non_coding_transcript_exon_variant,,ENST00000568329,;CSK,non_coding_transcript_exon_variant,,ENST00000564216,;CSK,non_coding_transcript_exon_variant,,ENST00000567135,;CSK,non_coding_transcript_exon_variant,,ENST00000569321,;CSK,non_coding_transcript_exon_variant,,ENST00000566464,;CSK,downstream_gene_variant,,ENST00000563894,;CSK,upstream_gene_variant,,ENST00000563010,;CSK,downstream_gene_variant,,ENST00000562066,; C ENST00000220003 Transcript synonymous_variant 1497/2767 768/1353 256/450 V gtG/gtC rs753705973 1 1 CSK HGNC HGNC:2444 protein_coding YES CCDS10269.1 ENSP00000220003 P41240 B2R6Q4 UPI0000128541 NM_004383.2 9/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF52,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs753705973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 74801057 74801057 G C 1 0 0 0 0 0 0 0 1 3744 1335 47 4 4 CSK 15 74801057 Silent SNP G C3N-00560_T 2394389 74801057 27190132 956 17645 SIN3A 0 . GRCh38 15 75380724 75380724 + Splice_Site SNP C C A novel C3N-00560_T C3N-00560_N C C c.3289-1G>T p.X1097_splice ENST00000394947 237 155 82 169 169 0 strelka-varscan-mutect SIN3A,splice_acceptor_variant,,ENST00000394947,NM_001145358.1;SIN3A,splice_acceptor_variant,,ENST00000360439,NM_001145357.1;SIN3A,splice_acceptor_variant,,ENST00000394949,NM_015477.2;SIN3A,non_coding_transcript_exon_variant,,ENST00000570124,;SIN3A,upstream_gene_variant,,ENST00000566640,;SIN3A,downstream_gene_variant,,ENST00000570021,; A ENST00000394947 Transcript splice_acceptor_variant -/6737 3289/3822 1097/1273 1 -1 SIN3A HGNC HGNC:19353 protein_coding YES CCDS10279.1 ENSP00000378402 Q96ST3 UPI000013EAD4 NM_001145358.1 18/20 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 75380724 75380724 C A 1 0 0 0 0 0 0 1 0 14589 811 28 2 2 SIN3A 15 75380724 Splice_Site SNP C C3N-00560_T 579667 75380724 26610465 957 17646 CSPG4 0 . GRCh38 15 75676340 75676340 + Missense_Mutation SNP G G T rs572735955 C3N-00560_T C3N-00560_N G G c.6179C>A p.Thr2060Asn p.T2060N ENST00000308508 10/10 184 110 74 133 133 0 strelka-varscan-mutect CSPG4,missense_variant,p.Thr2060Asn,ENST00000308508,NM_001897.4;CTD-2026K11.1,non_coding_transcript_exon_variant,,ENST00000569467,;CTD-2026K11.6,upstream_gene_variant,,ENST00000435356,; T ENST00000308508 Transcript missense_variant 6272/8290 6179/6969 2060/2322 T/N aCc/aAc rs572735955 1 -1 CSPG4 HGNC HGNC:2466 protein_coding YES CCDS10284.1 ENSP00000312506 Q6UVK1 UPI00001AEEB6 NM_001897.4 deleterious(0) 10/10 hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF16 MODERATE 1 SNV 1 1 PASS rs572735955 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 75676340 75676340 G T 1 0 0 0 0 1 0 0 0 3761 1261 44 2 2 CSPG4 15 75676340 Missense_Mutation SNP G C3N-00560_T 295616 75676340 26314849 958 17647 SCAPER 0 . GRCh38 15 76753835 76753835 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.1839G>A p.= p.V613V ENST00000563290 15/32 112 68 44 106 106 0 strelka-varscan-mutect SCAPER,synonymous_variant,p.=,ENST00000563290,;SCAPER,synonymous_variant,p.=,ENST00000538941,NM_001145923.1;SCAPER,synonymous_variant,p.=,ENST00000324767,NM_020843.2;SCAPER,synonymous_variant,p.=,ENST00000564590,;SCAPER,synonymous_variant,p.=,ENST00000565970,;SCAPER,3_prime_UTR_variant,,ENST00000565507,;SCAPER,non_coding_transcript_exon_variant,,ENST00000303521,; T ENST00000563290 Transcript synonymous_variant 1935/5028 1839/4203 613/1400 V gtG/gtA 1 -1 SCAPER HGNC HGNC:13081 protein_coding YES CCDS53962.1 ENSP00000454973 Q9BY12 UPI0000E59CC3 15/32 hmmpanther:PTHR31434:SF2,hmmpanther:PTHR31434 LOW 1 SNV 5 1 PASS . . 0 189 7 9 5 0 0 0 -20 0.5795814 1 1 1 0 T 2 4 56 76753835 76753835 C T 1 0 0 0 0 0 0 0 1 14144 813 29 3 3 SCAPER 15 76753835 Silent SNP C C3N-00560_T 1077495 76753835 25237354 959 17648 HYKK 0 . GRCh38 15 78513109 78513109 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.21G>T p.Gln7His p.Q7H ENST00000569878 1/4 151 102 49 131 131 0 strelka-varscan-mutect HYKK,missense_variant,p.Gln7His,ENST00000569878,;HYKK,missense_variant,p.Gln7His,ENST00000566332,;HYKK,missense_variant,p.Gln7His,ENST00000388988,NM_001013619.2;HYKK,missense_variant,p.Gln7His,ENST00000408962,NM_001083612.1;HYKK,missense_variant,p.Gln7His,ENST00000563233,;HYKK,missense_variant,p.Gln7His,ENST00000566289,; T ENST00000569878 Transcript missense_variant 21/4097 21/1122 7/373 Q/H caG/caT 1 1 HYKK HGNC HGNC:34403 protein_coding YES CCDS42063.1 ENSP00000455459 A2RU49 UPI0000366A7F tolerated_low_confidence(0.46) 1/4 hmmpanther:PTHR21064,hmmpanther:PTHR21064:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 78513109 78513109 G T 1 0 0 0 0 1 0 0 0 7365 962 34 2 2 HYKK 15 78513109 Missense_Mutation SNP G C3N-00560_T 1759274 78513109 23478080 960 17649 ADAMTS7 0 . GRCh38 15 78774295 78774295 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1882C>G p.Pro628Ala p.P628A ENST00000388820 13/24 147 108 39 100 100 0 strelka-varscan-mutect ADAMTS7,missense_variant,p.Pro628Ala,ENST00000388820,NM_014272.3;ADAMTS7,intron_variant,,ENST00000566303,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000565793,;ADAMTS7,non_coding_transcript_exon_variant,,ENST00000568712,; C ENST00000388820 Transcript missense_variant 2093/5490 1882/5061 628/1686 P/A Ccc/Gcc 1 -1 ADAMTS7 HGNC HGNC:223 protein_coding YES CCDS32303.1 ENSP00000373472 Q9UKP4 UPI00002263B3 NM_014272.3 deleterious(0) 13/24 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF142 MODERATE 1 SNV 1 1 PASS rs1225249427 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 78774295 78774295 G C 1 0 0 0 0 1 0 0 0 315 1246 43 4 4 ADAMTS7 15 78774295 Missense_Mutation SNP G C3N-00560_T 261186 78774295 23216894 961 17650 GOLGA6L10 0 . GRCh38 15 82347513 82347513 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.201G>A p.= p.G67G ENST00000610657 2/9 972 843 129 1051 1051 0 varscan-mutect GOLGA6L10,synonymous_variant,p.=,ENST00000619556,;GOLGA6L10,synonymous_variant,p.=,ENST00000621197,;GOLGA6L10,synonymous_variant,p.=,ENST00000610657,NM_001164465.3;GOLGA6L10,non_coding_transcript_exon_variant,,ENST00000558035,; T ENST00000610657 Transcript synonymous_variant 301/1705 201/1569 67/522 G ggG/ggA 1 -1 GOLGA6L10 HGNC HGNC:37228 protein_coding YES CCDS45325.2 ENSP00000479362 A6NI86 UPI0003EAF95A NM_001164465.3 2/9 hmmpanther:PTHR23143:SF12,hmmpanther:PTHR23143 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 82347513 82347513 C T 1 0 0 0 0 0 0 0 1 6439 637 22 3 3 GOLGA6L10 15 82347513 Silent SNP C C3N-00560_T 3573218 82347513 19643676 962 17651 RPS17 0 . GRCh38 15 82538967 82538967 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.174G>T p.Met58Ile p.M58I ENST00000330244 3/5 432 262 170 503 502 1 strelka-varscan-mutect RPS17,missense_variant,p.Met58Ile,ENST00000561157,;RPS17,missense_variant,p.Met58Ile,ENST00000330244,NM_001021.4;CPEB1,downstream_gene_variant,,ENST00000614918,;CPEB1,downstream_gene_variant,,ENST00000611031,;CPEB1,downstream_gene_variant,,ENST00000617958,;CPEB1,downstream_gene_variant,,ENST00000618449,NM_001079533.1;RP11-152F13.10,downstream_gene_variant,,ENST00000562833,;RP11-379H8.1,upstream_gene_variant,,ENST00000621893,;RPS17,missense_variant,p.Met58Ile,ENST00000558397,;RPS17,3_prime_UTR_variant,,ENST00000561068,;RPS17,non_coding_transcript_exon_variant,,ENST00000561440,;RPS17,non_coding_transcript_exon_variant,,ENST00000560612,;RPS17,non_coding_transcript_exon_variant,,ENST00000560639,;RPS17,non_coding_transcript_exon_variant,,ENST00000560229,;RPS17,non_coding_transcript_exon_variant,,ENST00000559776,;CPEB1,downstream_gene_variant,,ENST00000618698,;RPS17,downstream_gene_variant,,ENST00000559273,;DNM1P38,upstream_gene_variant,,ENST00000560794,; A ENST00000330244 Transcript missense_variant 310/592 174/408 58/135 M/I atG/atT 1 -1 RPS17 HGNC HGNC:10397 protein_coding YES CCDS10320.1 ENSP00000346046 P08708 UPI0000167B0C NM_001021.4 deleterious(0.04) 3/5 HAMAP:MF_00511,hmmpanther:PTHR10732,Gene3D:1rq6A00,Pfam_domain:PF00833,Superfamily_domains:0049231 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 82538967 82538967 C A 1 0 0 0 0 1 0 0 0 13882 826 29 2 2 RPS17 15 82538967 Missense_Mutation SNP C C3N-00560_T 191454 82538967 19452222 963 17652 BNC1 0 . GRCh38 15 83264571 83264571 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.680C>A p.Pro227His p.P227H ENST00000345382 4/5 165 90 75 198 198 0 strelka-varscan-mutect BNC1,missense_variant,p.Pro227His,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Pro220His,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; T ENST00000345382 Transcript missense_variant 766/4610 680/2985 227/994 P/H cCc/cAc COSM5328333 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0) 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 83264571 83264571 G T 1 0 0 0 0 1 0 0 0 1630 1232 43 2 2 BNC1 15 83264571 Missense_Mutation SNP G C3N-00560_T 725604 83264571 18726618 964 17653 ACAN 0 . GRCh38 15 88841860 88841860 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.750G>A p.= p.E250E ENST00000439576 5/18 118 59 59 112 112 0 strelka-varscan-mutect ACAN,synonymous_variant,p.=,ENST00000439576,NM_013227.3;ACAN,synonymous_variant,p.=,ENST00000617301,;ACAN,synonymous_variant,p.=,ENST00000559004,;ACAN,synonymous_variant,p.=,ENST00000561243,;ACAN,synonymous_variant,p.=,ENST00000352105,NM_001135.3;ACAN,synonymous_variant,p.=,ENST00000558207,; A ENST00000439576 Transcript synonymous_variant 1124/8840 750/7593 250/2530 E gaG/gaA 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 5/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Gene3D:3.10.100.10,Superfamily_domains:SSF56436,Prints_domain:PR01265 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 88841860 88841860 G A 1 0 0 0 0 0 0 0 1 160 933 33 3 3 ACAN 15 88841860 Silent SNP G C3N-00560_T 5577289 88841860 13149329 965 17654 MFGE8 0 . GRCh38 15 88901604 88901604 + Missense_Mutation SNP C C A rs141275837 C3N-00560_T C3N-00560_N C C c.817G>T p.Gly273Cys p.G273C ENST00000268150 6/8 235 116 119 222 222 0 strelka-varscan-mutect MFGE8,missense_variant,p.Gly273Cys,ENST00000268150,NM_005928.2;MFGE8,missense_variant,p.Gly273Cys,ENST00000268151,NM_001114614.1;MFGE8,missense_variant,p.Gly273Cys,ENST00000566497,;MFGE8,missense_variant,p.Gly229Cys,ENST00000542878,;MFGE8,missense_variant,p.Arg251Ser,ENST00000558029,;MFGE8,downstream_gene_variant,,ENST00000617199,;MFGE8,downstream_gene_variant,,ENST00000559997,;MFGE8,downstream_gene_variant,,ENST00000560553,;MFGE8,3_prime_UTR_variant,,ENST00000558018,NM_001310320.1;MFGE8,non_coding_transcript_exon_variant,,ENST00000560937,;MFGE8,downstream_gene_variant,,ENST00000558352,;MFGE8,downstream_gene_variant,,ENST00000559259,;MFGE8,downstream_gene_variant,,ENST00000613965,; A ENST00000268150 Transcript missense_variant 909/1937 817/1164 273/387 G/C Ggc/Tgc rs141275837 1 -1 MFGE8 HGNC HGNC:7036 protein_coding YES CCDS10347.1 ENSP00000268150 Q08431 UPI000013D7A3 NM_005928.2 deleterious(0) 6/8 PROSITE_profiles:PS50022,hmmpanther:PTHR10127:SF303,hmmpanther:PTHR10127,Pfam_domain:PF00754,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS rs141275837 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 88901604 88901604 C A 1 0 0 0 0 1 0 0 0 9473 623 22 2 2 MFGE8 15 88901604 Missense_Mutation SNP C C3N-00560_T 59744 88901604 13089585 966 17655 ANPEP 0 . GRCh38 15 89803491 89803491 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1454G>T p.Arg485Met p.R485M ENST00000300060 9/21 143 80 63 134 134 0 strelka-varscan-mutect ANPEP,missense_variant,p.Arg485Met,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,stop_gained,p.Gly93Ter,ENST00000560030,;ANPEP,downstream_gene_variant,,ENST00000560028,;ANPEP,downstream_gene_variant,,ENST00000559887,;ANPEP,upstream_gene_variant,,ENST00000559761,; A ENST00000300060 Transcript missense_variant 1768/3678 1454/2904 485/967 R/M aGg/aTg 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 deleterious(0) 9/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Gene3D:1.10.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 89803491 89803491 C A 1 0 0 0 0 1 0 0 0 817 681 24 2 2 ANPEP 15 89803491 Missense_Mutation SNP C C3N-00560_T 901887 89803491 12187698 967 17656 MCTP2 0 . GRCh38 15 94442922 94442922 + Missense_Mutation SNP A A G novel C3N-00560_T C3N-00560_N A A c.2212A>G p.Ser738Gly p.S738G ENST00000357742 18/22 111 65 46 125 125 0 strelka-varscan-mutect MCTP2,missense_variant,p.Ser738Gly,ENST00000357742,NM_018349.3;MCTP2,intron_variant,,ENST00000451018,NM_001159643.1;MCTP2,3_prime_UTR_variant,,ENST00000456504,; G ENST00000357742 Transcript missense_variant 2212/7555 2212/2637 738/878 S/G Agc/Ggc 1 1 MCTP2 HGNC HGNC:25636 protein_coding YES CCDS32338.1 ENSP00000350377 Q6DN12 UPI0000D613A2 NM_018349.3 tolerated(0.34) 18/22 Pfam_domain:PF08372,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF78,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 94442922 94442922 A G 1 0 0 0 0 1 0 0 0 9337 318 11 5 5 MCTP2 15 94442922 Missense_Mutation SNP A C3N-00560_T 4639431 94442922 7548267 968 17657 LRRC28 0 . GRCh38 15 99363110 99363110 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.876G>T p.Leu292Phe p.L292F ENST00000301981 9/10 173 129 44 140 140 0 strelka-varscan-mutect LRRC28,missense_variant,p.Leu292Phe,ENST00000301981,NM_001321680.1,NM_001321675.1,NM_001321679.1,NM_144598.3;LRRC28,missense_variant,p.Leu247Phe,ENST00000561276,;LRRC28,intron_variant,,ENST00000447360,NM_001284400.1;LRRC28,intron_variant,,ENST00000331450,;LRRC28,intron_variant,,ENST00000558879,;LRRC28,downstream_gene_variant,,ENST00000558172,;LRRC28,3_prime_UTR_variant,,ENST00000559433,;LRRC28,non_coding_transcript_exon_variant,,ENST00000559819,;LRRC28,non_coding_transcript_exon_variant,,ENST00000558890,;LRRC28,non_coding_transcript_exon_variant,,ENST00000560483,;LRRC28,downstream_gene_variant,,ENST00000558471,;LRRC28,upstream_gene_variant,,ENST00000560236,; T ENST00000301981 Transcript missense_variant 1116/5971 876/1104 292/367 L/F ttG/ttT 1 1 LRRC28 HGNC HGNC:28355 protein_coding YES CCDS10380.1 ENSP00000304923 Q86X40 UPI000000DBCB NM_001321680.1,NM_001321675.1,NM_001321679.1,NM_144598.3 tolerated(0.24) 9/10 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 99363110 99363110 G T 1 0 0 0 0 1 0 0 0 8877 1304 45 2 2 LRRC28 15 99363110 Missense_Mutation SNP G C3N-00560_T 4920188 99363110 2628079 969 17658 PRR35 0 . GRCh38 16 563819 563819 + Silent SNP G G T rs535166629 C3N-00560_T C3N-00560_N G G c.525G>T p.= p.A175A ENST00000409413 2/3 24 14 10 33 33 0 strelka-varscan-mutect PRR35,synonymous_variant,p.=,ENST00000409413,NM_145270.2;NHLRC4,upstream_gene_variant,,ENST00000424439,NM_176677.2,NM_001301159.1;NHLRC4,upstream_gene_variant,,ENST00000540585,;PIGQ,upstream_gene_variant,,ENST00000409527,;PIGQ,upstream_gene_variant,,ENST00000293874,; T ENST00000409413 Transcript synonymous_variant 804/2216 525/1716 175/571 A gcG/gcT rs535166629 1 1 PRR35 HGNC HGNC:14139 protein_coding YES CCDS45365.1 ENSP00000386499 P0CG20 UPI000006F4B0 NM_145270.2 2/3 hmmpanther:PTHR14678:SF2,hmmpanther:PTHR14678 LOW 1 SNV 1 1 PASS rs535166629 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 563819 563819 G T 1 0 0 0 0 0 0 0 1 12740 1103 39 1 1 PRR35 16 563819 Silent SNP G C3N-00560_T 563819 89774526 970 17659 CACNA1H 0 . GRCh38 16 1220899 1220899 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.6967G>C p.Gly2323Arg p.G2323R ENST00000348261 35/35 174 91 83 146 146 0 strelka-varscan-mutect CACNA1H,missense_variant,p.Gly2323Arg,ENST00000348261,NM_021098.2;CACNA1H,missense_variant,p.Gly2317Arg,ENST00000358590,NM_001005407.1;CACNA1H,missense_variant,p.Gly2317Arg,ENST00000565831,;CACNA1H,missense_variant,p.Gly1070Arg,ENST00000569107,;CACNA1H,missense_variant,p.Gly1054Arg,ENST00000564231,;CACNA1H,missense_variant,p.Gly1048Arg,ENST00000562079,;TPSG1,downstream_gene_variant,,ENST00000234798,NM_012467.3;RP11-616M22.12,upstream_gene_variant,,ENST00000621827,;TPSG1,downstream_gene_variant,,ENST00000564684,; C ENST00000348261 Transcript missense_variant 7335/8208 6967/7062 2323/2353 G/R Ggg/Cgg 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 deleterious_low_confidence(0.02) 35/35 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 1220899 1220899 G C 1 0 0 0 0 1 0 0 0 2233 1232 43 4 4 CACNA1H 16 1220899 Missense_Mutation SNP G C3N-00560_T 657080 1220899 89117446 971 17660 ABCA3 0 . GRCh38 16 2278354 2278354 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.4652G>T p.Arg1551Leu p.R1551L ENST00000301732 30/33 236 120 116 229 229 0 strelka-varscan-mutect ABCA3,missense_variant,p.Arg1551Leu,ENST00000301732,NM_001089.2;ABCA3,missense_variant,p.Arg1493Leu,ENST00000382381,;MIR940,downstream_gene_variant,,ENST00000563734,;MIR4717,downstream_gene_variant,,ENST00000584656,;ABCA3,non_coding_transcript_exon_variant,,ENST00000566200,;ABCA3,downstream_gene_variant,,ENST00000569062,; A ENST00000301732 Transcript missense_variant 5353/6609 4652/5115 1551/1704 R/L cGc/cTc 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 deleterious(0) 30/33 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1333633950 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 2278354 2278354 C A 1 0 0 0 0 1 0 0 0 37 768 27 1 1 ABCA3 16 2278354 Missense_Mutation SNP C C3N-00560_T 1057455 2278354 88059991 972 17661 CCNF 0 . GRCh38 16 2439826 2439826 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.777G>T p.Gln259His p.Q259H ENST00000397066 8/17 170 106 64 231 230 1 strelka-varscan-mutect CCNF,missense_variant,p.Gln259His,ENST00000397066,NM_001761.2;CCNF,splice_region_variant,,ENST00000293968,NM_001323538.1;CCNF,downstream_gene_variant,,ENST00000564333,;CCNF,downstream_gene_variant,,ENST00000569093,;CCNF,upstream_gene_variant,,ENST00000564236,; T ENST00000397066 Transcript missense_variant,splice_region_variant 865/4283 777/2361 259/786 Q/H caG/caT 1 1 CCNF HGNC HGNC:1591 protein_coding YES CCDS10467.1 ENSP00000380256 P41002 UPI0000127595 NM_001761.2 deleterious(0) 8/17 hmmpanther:PTHR10177:SF252,hmmpanther:PTHR10177,Gene3D:1.25.40.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 2439826 2439826 G T 1 0 0 0 0 1 0 0 0 2621 1014 35 2 2 CCNF 16 2439826 Missense_Mutation SNP G C3N-00560_T 161472 2439826 87898519 973 17662 AMDHD2 0 . GRCh38 16 2527950 2527950 + Missense_Mutation SNP G G T rs563365209 C3N-00560_T C3N-00560_N G G c.593G>T p.Arg198Leu p.R198L ENST00000413459 5/11 174 95 79 177 177 0 strelka-varscan-mutect AMDHD2,missense_variant,p.Arg198Leu,ENST00000302956,NM_015944.3;AMDHD2,missense_variant,p.Arg198Leu,ENST00000413459,NM_001145815.1;AMDHD2,missense_variant,p.Arg198Leu,ENST00000293971,;RP11-20I23.3,missense_variant,p.Arg151Leu,ENST00000569317,;AMDHD2,5_prime_UTR_variant,,ENST00000568263,;AMDHD2,intron_variant,,ENST00000566706,;AMDHD2,intron_variant,,ENST00000569879,;CEMP1,downstream_gene_variant,,ENST00000567119,NM_001048212.3;CEMP1,downstream_gene_variant,,ENST00000565480,;AMDHD2,downstream_gene_variant,,ENST00000563556,;MIR3178,downstream_gene_variant,,ENST00000581887,;AMDHD2,intron_variant,,ENST00000565570,;AMDHD2,3_prime_UTR_variant,,ENST00000563633,;AMDHD2,non_coding_transcript_exon_variant,,ENST00000565963,;AMDHD2,non_coding_transcript_exon_variant,,ENST00000567475,;AMDHD2,non_coding_transcript_exon_variant,,ENST00000561487,;AMDHD2,non_coding_transcript_exon_variant,,ENST00000570028,;AMDHD2,non_coding_transcript_exon_variant,,ENST00000566947,;AMDHD2,upstream_gene_variant,,ENST00000563145,;AMDHD2,downstream_gene_variant,,ENST00000569219,;AMDHD2,upstream_gene_variant,,ENST00000563453,;AMDHD2,upstream_gene_variant,,ENST00000563444,; T ENST00000413459 Transcript missense_variant 662/2049 593/1785 198/594 R/L cGg/cTg rs563365209,COSM5384590,COSM5384591 1 1 AMDHD2 HGNC HGNC:24262 protein_coding YES CCDS53984.1 ENSP00000391596 Q9Y303 UPI00017A73A4 NM_001145815.1 tolerated(0.08) 5/11 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11113,hmmpanther:PTHR11113:SF1,Superfamily_domains:SSF51556 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs563365209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 2527950 2527950 G T 1 0 0 0 0 1 0 0 0 664 1116 39 1 1 AMDHD2 16 2527950 Missense_Mutation SNP G C3N-00560_T 88124 2527950 87810395 974 17663 ZSCAN10 0 . GRCh38 16 3089989 3089989 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1034G>T p.Gly345Val p.G345V ENST00000538082 5/5 273 148 125 227 227 0 strelka-varscan-mutect ZSCAN10,missense_variant,p.Gly482Val,ENST00000576985,NM_032805.2;ZSCAN10,missense_variant,p.Gly427Val,ENST00000252463,;ZSCAN10,missense_variant,p.Gly345Val,ENST00000538082,NM_001282416.1;ZSCAN10,missense_variant,p.Gly88Val,ENST00000575108,NM_001282415.1;ZSCAN10,downstream_gene_variant,,ENST00000576483,;ZSCAN10,downstream_gene_variant,,ENST00000572548,;ZSCAN10,downstream_gene_variant,,ENST00000572431,;RP11-473M20.9,upstream_gene_variant,,ENST00000571404,;RP11-473M20.9,upstream_gene_variant,,ENST00000574387,;RNU1-22P,downstream_gene_variant,,ENST00000363334,;ZSCAN10,downstream_gene_variant,,ENST00000571903,;ZSCAN10,downstream_gene_variant,,ENST00000577059,; A ENST00000538082 Transcript missense_variant 1350/2350 1034/1932 345/643 G/V gGc/gTc 1 -1 ZSCAN10 HGNC HGNC:12997 protein_coding YES CCDS61814.1 ENSP00000440047 Q96SZ4 UPI0001639829 NM_001282416.1 deleterious(0.02) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF13894,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF369,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 3089989 3089989 C A 1 0 0 0 0 1 0 0 0 18821 739 26 2 2 ZSCAN10 16 3089989 Missense_Mutation SNP C C3N-00560_T 562039 3089989 87248356 975 17664 CORO7 0 . GRCh38 16 4365060 4365060 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.841G>T p.Gly281Cys p.G281C ENST00000251166 11/28 141 84 57 186 185 1 strelka-varscan-mutect CORO7,missense_variant,p.Gly281Cys,ENST00000251166,NM_024535.4;CORO7,missense_variant,p.Gly263Cys,ENST00000537233,NM_001201472.1;CORO7-PAM16,missense_variant,p.Gly281Cys,ENST00000572467,NM_001201479.1;CORO7,missense_variant,p.Gly196Cys,ENST00000574025,NM_001201473.1;CORO7,missense_variant,p.Gly126Cys,ENST00000572549,;CORO7,missense_variant,p.Gly113Cys,ENST00000572044,;CORO7-PAM16,missense_variant,p.Gly281Cys,ENST00000575334,;CORO7,missense_variant,p.Gly113Cys,ENST00000574311,;CORO7,splice_region_variant,,ENST00000571227,;CORO7,splice_region_variant,,ENST00000575714,;CORO7,splice_region_variant,,ENST00000571756,;CORO7,intron_variant,,ENST00000576437,;CORO7,upstream_gene_variant,,ENST00000575531,;CORO7,upstream_gene_variant,,ENST00000572666,;CORO7,upstream_gene_variant,,ENST00000573773,; A ENST00000251166 Transcript missense_variant,splice_region_variant 987/3540 841/2778 281/925 G/C Ggc/Tgc 1 -1 CORO7 HGNC HGNC:26161 protein_coding YES CCDS10513.1 ENSP00000251166 P57737 UPI00001FF898 NM_024535.4 deleterious(0) 11/28 hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF20,Gene3D:2.130.10.10,SMART_domains:SM01167,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 4365060 4365060 C A 1 0 0 0 0 1 0 0 0 3553 637 22 2 2 CORO7 16 4365060 Missense_Mutation SNP C C3N-00560_T 1275071 4365060 85973285 976 17665 C16orf71 0 . GRCh38 16 4737875 4737875 + Missense_Mutation SNP C C A rs780545004 C3N-00560_T C3N-00560_N C C c.205C>A p.Leu69Met p.L69M ENST00000299320 3/10 175 112 63 196 196 0 strelka-varscan-mutect C16orf71,missense_variant,p.Leu69Met,ENST00000299320,NM_139170.2;C16orf71,missense_variant,p.Leu69Met,ENST00000590191,;C16orf71,missense_variant,p.Leu69Met,ENST00000586724,;ANKS3,upstream_gene_variant,,ENST00000304283,NM_133450.3;ANKS3,upstream_gene_variant,,ENST00000450067,NM_001242929.1;ANKS3,upstream_gene_variant,,ENST00000585773,;ANKS3,upstream_gene_variant,,ENST00000592421,;ANKS3,upstream_gene_variant,,ENST00000592698,;ANKS3,upstream_gene_variant,,ENST00000586605,;C16orf71,upstream_gene_variant,,ENST00000619274,;ANKS3,upstream_gene_variant,,ENST00000590147,;ANKS3,upstream_gene_variant,,ENST00000586166,;ANKS3,upstream_gene_variant,,ENST00000592711,;ANKS3,upstream_gene_variant,,ENST00000592190,;ANKS3,upstream_gene_variant,,ENST00000589065,;RP11-127I20.7,non_coding_transcript_exon_variant,,ENST00000588099,;C16orf71,non_coding_transcript_exon_variant,,ENST00000586256,;ANKS3,upstream_gene_variant,,ENST00000592077,;ANKS3,upstream_gene_variant,,ENST00000590193,;ANKS3,upstream_gene_variant,,ENST00000590730,;ANKS3,upstream_gene_variant,,ENST00000592068,;ANKS3,upstream_gene_variant,,ENST00000586159,;ANKS3,upstream_gene_variant,,ENST00000590689,;ANKS3,upstream_gene_variant,,ENST00000593120,;ANKS3,upstream_gene_variant,,ENST00000587005,;ANKS3,upstream_gene_variant,,ENST00000591281,; A ENST00000299320 Transcript missense_variant 683/2722 205/1563 69/520 L/M Ctg/Atg rs780545004 1 1 C16orf71 HGNC HGNC:25081 protein_coding YES CCDS10521.1 ENSP00000299320 Q8IYS4 UPI000013E57E NM_139170.2 deleterious(0) 3/10 hmmpanther:PTHR35977,hmmpanther:PTHR35977:SF1,Pfam_domain:PF15773 MODERATE 1 SNV 1 1 PASS rs780545004 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 4737875 4737875 C A 1 0 0 0 0 1 0 0 0 1863 796 28 2 2 C16orf71 16 4737875 Missense_Mutation SNP C C3N-00560_T 372815 4737875 85600470 977 17666 CPPED1 0 . GRCh38 16 12704977 12704977 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.362T>A p.Leu121Gln p.L121Q ENST00000381774 3/4 187 86 101 188 188 0 strelka-varscan-mutect CPPED1,missense_variant,p.Leu121Gln,ENST00000381774,NM_018340.2;CPPED1,intron_variant,,ENST00000433677,NM_001099455.1;CPPED1,intron_variant,,ENST00000261660,; T ENST00000381774 Transcript missense_variant 603/6273 362/945 121/314 L/Q cTg/cAg 1 -1 CPPED1 HGNC HGNC:25632 protein_coding YES CCDS42120.1 ENSP00000371193 Q9BRF8 UPI000013D1D1 NM_018340.2 deleterious(0) 3/4 hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF34,Pfam_domain:PF00149,Gene3D:3.60.21.10,Superfamily_domains:SSF56300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 12704977 12704977 A T 1 0 0 0 0 1 0 0 0 3617 188 7 4 4 CPPED1 16 12704977 Missense_Mutation SNP A C3N-00560_T 7967102 12704977 77633368 978 17667 SHISA9 0 . GRCh38 16 13235381 13235381 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1247C>A p.Thr416Asn p.T416N ENST00000558583 5/5 74 38 36 121 121 0 strelka-varscan-mutect SHISA9,missense_variant,p.Thr416Asn,ENST00000558583,NM_001145204.2;SHISA9,downstream_gene_variant,,ENST00000566106,; A ENST00000558583 Transcript missense_variant 1692/6724 1247/1275 416/424 T/N aCc/aAc 1 1 SHISA9 HGNC HGNC:37231 protein_coding YES CCDS45417.2 ENSP00000454014 B4DS77 UPI0001CE6F1C NM_001145204.2 deleterious(0) 5/5 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 13235381 13235381 C A 1 0 0 0 0 1 0 0 0 14546 507 18 2 2 SHISA9 16 13235381 Missense_Mutation SNP C C3N-00560_T 530404 13235381 77102964 979 17668 POLR3E 0 . GRCh38 16 22315169 22315169 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.603A>T p.= p.A201A ENST00000299853 9/21 143 85 58 146 146 0 strelka-varscan-mutect POLR3E,synonymous_variant,p.=,ENST00000299853,NM_018119.3;POLR3E,synonymous_variant,p.=,ENST00000615879,NM_001258035.1;POLR3E,synonymous_variant,p.=,ENST00000418581,NM_001258034.1;POLR3E,synonymous_variant,p.=,ENST00000359210,NM_001258036.1;POLR3E,synonymous_variant,p.=,ENST00000564209,NM_001258033.1;POLR3E,5_prime_UTR_variant,,ENST00000569757,;POLR3E,downstream_gene_variant,,ENST00000565358,;POLR3E,downstream_gene_variant,,ENST00000563024,;POLR3E,3_prime_UTR_variant,,ENST00000564750,;POLR3E,3_prime_UTR_variant,,ENST00000565551,;POLR3E,non_coding_transcript_exon_variant,,ENST00000564061,;POLR3E,downstream_gene_variant,,ENST00000563766,;POLR3E,upstream_gene_variant,,ENST00000569787,; T ENST00000299853 Transcript synonymous_variant 770/3697 603/2127 201/708 A gcA/gcT 1 1 POLR3E HGNC HGNC:30347 protein_coding YES CCDS10605.1 ENSP00000299853 Q9NVU0 UPI000006D8F8 NM_018119.3 9/21 hmmpanther:PTHR12069,Pfam_domain:PF04801 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 22315169 22315169 A T 1 0 0 0 0 0 0 0 1 12343 175 7 4 4 POLR3E 16 22315169 Silent SNP A C3N-00560_T 9079788 22315169 68023176 980 17669 IL21R 0 . GRCh38 16 27444651 27444651 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.617C>G p.Pro206Arg p.P206R ENST00000337929 6/9 56 37 19 54 54 0 strelka-varscan-mutect IL21R,missense_variant,p.Pro206Arg,ENST00000337929,NM_181078.2;IL21R,missense_variant,p.Pro206Arg,ENST00000564089,NM_181079.4;IL21R,missense_variant,p.Pro206Arg,ENST00000395754,NM_021798.3;IL21R-AS1,downstream_gene_variant,,ENST00000563191,;IL21R,non_coding_transcript_exon_variant,,ENST00000564583,;IL21R,non_coding_transcript_exon_variant,,ENST00000561953,; G ENST00000337929 Transcript missense_variant 1090/4849 617/1617 206/538 P/R cCt/cGt 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 deleterious(0) 6/9 Gene3D:2.60.40.10,PROSITE_patterns:PS01355,PROSITE_profiles:PS50853,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 27444651 27444651 C G 1 0 0 0 0 1 0 0 0 7574 681 24 4 4 IL21R 16 27444651 Missense_Mutation SNP C C3N-00560_T 5129482 27444651 62893694 981 17670 GTF3C1 0 . GRCh38 16 27505925 27505925 + Nonsense_Mutation SNP C C A rs777212155 C3N-00560_T C3N-00560_N C C c.1744G>T p.Glu582Ter p.E582* ENST00000356183 10/37 195 129 66 158 158 0 strelka-varscan-mutect GTF3C1,stop_gained,p.Glu582Ter,ENST00000356183,NM_001520.3;GTF3C1,stop_gained,p.Glu582Ter,ENST00000561623,NM_001286242.1;GTF3C1,upstream_gene_variant,,ENST00000569653,; A ENST00000356183 Transcript stop_gained 1760/7018 1744/6330 582/2109 E/* Gag/Tag rs777212155 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 10/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 HIGH 1 SNV 1 1 PASS rs777212155 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 27505925 27505925 C A 1 0 0 0 0 0 1 0 0 6753 893 31 1 1 GTF3C1 16 27505925 Nonsense_Mutation SNP C C3N-00560_T 61274 27505925 62832420 982 17671 APOBR 0 . GRCh38 16 28496014 28496014 + Missense_Mutation SNP G G T rs199560946 C3N-00560_T C3N-00560_N G G c.973G>T p.Gly325Trp p.G325W ENST00000564831 2/4 69 52 17 54 54 0 strelka-varscan-mutect APOBR,missense_variant,p.Gly325Trp,ENST00000564831,NM_018690.3;APOBR,missense_variant,p.Gly325Trp,ENST00000431282,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000636147,NM_001042432.1;CLN3,upstream_gene_variant,,ENST00000359984,NM_000086.2;CLN3,upstream_gene_variant,,ENST00000360019,NM_001286104.1;CLN3,upstream_gene_variant,,ENST00000357857,NM_001286110.1;CLN3,upstream_gene_variant,,ENST00000333496,;CLN3,upstream_gene_variant,,ENST00000631023,;CLN3,upstream_gene_variant,,ENST00000357806,;CLN3,upstream_gene_variant,,ENST00000567963,NM_001286109.1;CLN3,upstream_gene_variant,,ENST00000395653,;CLN3,upstream_gene_variant,,ENST00000565316,;CLN3,upstream_gene_variant,,ENST00000637100,;CLN3,upstream_gene_variant,,ENST00000636228,;CLN3,upstream_gene_variant,,ENST00000355477,;CLN3,upstream_gene_variant,,ENST00000635973,;IL27,downstream_gene_variant,,ENST00000356897,NM_145659.3;CLN3,upstream_gene_variant,,ENST00000568443,;CLN3,upstream_gene_variant,,ENST00000568497,;CLN3,upstream_gene_variant,,ENST00000565778,;CLN3,upstream_gene_variant,,ENST00000565688,;CLN3,upstream_gene_variant,,ENST00000568558,;CLN3,upstream_gene_variant,,ENST00000567804,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000565236,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566472,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,;CLN3,upstream_gene_variant,,ENST00000565047,;CLN3,upstream_gene_variant,,ENST00000563874,;CLN3,upstream_gene_variant,,ENST00000636977,;RP11-435I10.4,upstream_gene_variant,,ENST00000635887,;RP11-435I10.4,upstream_gene_variant,,ENST00000636503,;RP11-435I10.4,upstream_gene_variant,,ENST00000637376,;RP11-435I10.4,upstream_gene_variant,,ENST00000636866,;RP11-435I10.4,upstream_gene_variant,,ENST00000636078,;CLN3,upstream_gene_variant,,ENST00000636853,;RP11-435I10.4,upstream_gene_variant,,ENST00000636017,;RP11-435I10.4,upstream_gene_variant,,ENST00000636766,;CLN3,upstream_gene_variant,,ENST00000636839,;CLN3,upstream_gene_variant,,ENST00000568076,;CLN3,upstream_gene_variant,,ENST00000561689,;RP11-435I10.4,upstream_gene_variant,,ENST00000637299,;CLN3,upstream_gene_variant,,ENST00000637107,;CLN3,upstream_gene_variant,,ENST00000635958,;CLN3,upstream_gene_variant,,ENST00000637184,;RP11-435I10.4,upstream_gene_variant,,ENST00000568224,;CLN3,upstream_gene_variant,,ENST00000568452,;CLN3,upstream_gene_variant,,ENST00000637871,;CLN3,upstream_gene_variant,,ENST00000637578,;CLN3,upstream_gene_variant,,ENST00000636172,;CLN3,upstream_gene_variant,,ENST00000566083,;CLN3,upstream_gene_variant,,ENST00000635861,;CLN3,upstream_gene_variant,,ENST00000566824,;CLN3,upstream_gene_variant,,ENST00000637699,;CLN3,upstream_gene_variant,,ENST00000565140,;CLN3,upstream_gene_variant,,ENST00000628023,;CLN3,upstream_gene_variant,,ENST00000568422,;CLN3,upstream_gene_variant,,ENST00000564574,;CLN3,upstream_gene_variant,,ENST00000569030,;CLN3,upstream_gene_variant,,ENST00000568472,;CLN3,upstream_gene_variant,,ENST00000566057,;CLN3,upstream_gene_variant,,ENST00000567495,;CLN3,upstream_gene_variant,,ENST00000637985,;CLN3,upstream_gene_variant,,ENST00000561505,; T ENST00000564831 Transcript missense_variant 1006/3792 973/3294 325/1097 G/W Ggg/Tgg rs199560946 1 1 APOBR HGNC HGNC:24087 protein_coding YES CCDS58442.1 ENSP00000457539 Q0VD83 UPI000013EFFC NM_018690.3 deleterious(0.04) 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15964:SF0,hmmpanther:PTHR15964 MODERATE 1 SNV 1 1 PASS rs199560946 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 28496014 28496014 G T 1 0 0 0 0 1 0 0 0 918 1116 39 1 1 APOBR 16 28496014 Missense_Mutation SNP G C3N-00560_T 990089 28496014 61842331 983 17672 ITGAL 0 . GRCh38 16 30517015 30517015 + Missense_Mutation SNP C C A rs771190771 C3N-00560_T C3N-00560_N C C c.2905C>A p.Leu969Met p.L969M ENST00000356798 26/31 230 163 67 161 161 0 strelka-varscan-mutect ITGAL,missense_variant,p.Leu969Met,ENST00000356798,NM_002209.2;ITGAL,missense_variant,p.Leu885Met,ENST00000358164,NM_001114380.1;ITGAL,missense_variant,p.Leu203Met,ENST00000433423,;ITGAL,non_coding_transcript_exon_variant,,ENST00000566267,;ITGAL,upstream_gene_variant,,ENST00000564632,; A ENST00000356798 Transcript missense_variant 3085/5213 2905/3513 969/1170 L/M Ctg/Atg rs771190771,COSM435108 1 1 ITGAL HGNC HGNC:6148 protein_coding YES CCDS32433.1 ENSP00000349252 P20701 UPI000013C4FF NM_002209.2 deleterious(0.04) 26/31 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF84 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771190771 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 30517015 30517015 C A 1 0 0 0 0 1 0 0 0 7793 680 24 2 2 ITGAL 16 30517015 Missense_Mutation SNP C C3N-00560_T 2021001 30517015 59821330 984 17673 SRCAP 0 . GRCh38 16 30720204 30720204 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.2860C>T p.Arg954Cys p.R954C ENST00000262518 19/34 172 146 26 120 120 0 strelka-varscan-mutect SRCAP,missense_variant,p.Arg954Cys,ENST00000262518,NM_006662.2;SRCAP,missense_variant,p.Arg757Cys,ENST00000395059,;SRCAP,missense_variant,p.Arg654Cys,ENST00000483083,;RP11-2C24.9,missense_variant,p.Arg935Cys,ENST00000380361,; T ENST00000262518 Transcript missense_variant 3245/11754 2860/9693 954/3230 R/C Cgt/Tgt 1 1 SRCAP HGNC HGNC:16974 protein_coding YES CCDS10689.2 ENSP00000262518 Q6ZRS2 UPI000059D368 NM_006662.2 deleterious(0.01) 19/34 MODERATE 1 SNV 2 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999832 1 1 1 0 T 3 4 56 30720204 30720204 C T 1 0 0 0 0 1 0 0 0 15493 884 31 1 1 SRCAP 16 30720204 Missense_Mutation SNP C C3N-00560_T 203189 30720204 59618141 985 17674 ITGAD 0 . GRCh38 16 31423398 31423398 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2906G>T p.Trp969Leu p.W969L ENST00000389202 25/30 280 199 81 208 208 0 strelka-varscan-mutect ITGAD,missense_variant,p.Trp969Leu,ENST00000389202,NM_001318185.1,NM_005353.2;COX6A2,downstream_gene_variant,,ENST00000287490,NM_005205.3;RP11-452L6.8,upstream_gene_variant,,ENST00000615068,;ITGAD,upstream_gene_variant,,ENST00000567308,;COX6A2,downstream_gene_variant,,ENST00000565462,; T ENST00000389202 Transcript missense_variant 2955/3912 2906/3486 969/1161 W/L tGg/tTg 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 tolerated(0.15) 25/30 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 31423398 31423398 G T 1 0 0 0 0 1 0 0 0 7791 1357 47 2 2 ITGAD 16 31423398 Missense_Mutation SNP G C3N-00560_T 703194 31423398 58914947 986 17675 ARMC5 0 . GRCh38 16 31459858 31459858 + Missense_Mutation SNP T T A rs777779636 C3N-00560_T C3N-00560_N T T c.619T>A p.Ser207Thr p.S207T ENST00000408912 3/8 476 393 83 287 286 1 strelka-varscan-mutect ARMC5,missense_variant,p.Ser112Thr,ENST00000457010,NM_024742.2;ARMC5,missense_variant,p.Ser207Thr,ENST00000408912,NM_001288767.1;ARMC5,missense_variant,p.Ser112Thr,ENST00000268314,NM_001105247.1;ARMC5,missense_variant,p.Ser112Thr,ENST00000563544,NM_001301820.1;ARMC5,5_prime_UTR_variant,,ENST00000538189,;ARMC5,upstream_gene_variant,,ENST00000564900,;RP11-452L6.5,upstream_gene_variant,,ENST00000564629,;ARMC5,upstream_gene_variant,,ENST00000564514,; A ENST00000408912 Transcript missense_variant 936/3626 619/3093 207/1030 S/T Tcc/Acc rs777779636 1 1 ARMC5 HGNC HGNC:25781 protein_coding YES CCDS73874.1 ENSP00000386125 J3KQ26 UPI0001AE681E NM_001288767.1 tolerated_low_confidence(0.07) 3/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23312 MODERATE 1 SNV 2 1 PASS rs777779636 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 31459858 31459858 T A 1 0 0 0 0 1 0 0 0 1095 1551 54 4 4 ARMC5 16 31459858 Missense_Mutation SNP T C3N-00560_T 36460 31459858 58878487 987 17676 NETO2 0 . GRCh38 16 47083636 47083636 + Missense_Mutation SNP C C G rs572763783 C3N-00560_T C3N-00560_N C C c.1163G>C p.Gly388Ala p.G388A ENST00000562435 9/9 217 128 89 259 259 0 strelka-varscan-mutect NETO2,missense_variant,p.Gly388Ala,ENST00000562435,NM_018092.4;NETO2,missense_variant,p.Gly381Ala,ENST00000303155,NM_001201477.1;NETO2,missense_variant,p.Gly228Ala,ENST00000562559,;NETO2,missense_variant,p.Gly91Ala,ENST00000564667,;NETO2,missense_variant,p.Gly187Ala,ENST00000563078,; G ENST00000562435 Transcript missense_variant 1548/7481 1163/1578 388/525 G/A gGg/gCg rs572763783,COSM1679063 1 -1 NETO2 HGNC HGNC:14644 protein_coding YES CCDS10727.1 ENSP00000455169 Q8NC67 UPI000003C718 NM_018092.4 tolerated(0.84) 9/9 hmmpanther:PTHR10127:SF314,hmmpanther:PTHR10127 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs572763783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 47083636 47083636 C G 1 0 0 0 0 1 0 0 0 10375 623 22 4 4 NETO2 16 47083636 Missense_Mutation SNP C C3N-00560_T 15623778 47083636 43254709 988 17677 ZNF423 0 . GRCh38 16 49636649 49636649 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.2503G>C p.Ala835Pro p.A835P ENST00000561648 5/9 158 84 74 198 197 1 strelka-varscan-mutect ZNF423,missense_variant,p.Ala835Pro,ENST00000561648,;ZNF423,missense_variant,p.Ala775Pro,ENST00000563137,;ZNF423,missense_variant,p.Ala835Pro,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Ala775Pro,ENST00000562871,;ZNF423,missense_variant,p.Ala718Pro,ENST00000535559,;ZNF423,missense_variant,p.Ala775Pro,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Ala718Pro,ENST00000567169,; G ENST00000561648 Transcript missense_variant 2804/7907 2503/3855 835/1284 A/P Gct/Cct 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC tolerated(0.23) 5/9 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 49636649 49636649 C G 1 0 0 0 0 1 0 0 0 18470 710 25 4 4 ZNF423 16 49636649 Missense_Mutation SNP C C3N-00560_T 2553013 49636649 40701696 989 17678 CYLD 0 . GRCh38 16 50792651 50792651 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.2296T>C p.Phe766Leu p.F766L ENST00000427738 15/18 80 39 41 150 150 0 strelka-varscan-mutect CYLD,missense_variant,p.Phe766Leu,ENST00000427738,;CYLD,missense_variant,p.Phe766Leu,ENST00000311559,NM_015247.2;CYLD,missense_variant,p.Phe763Leu,ENST00000398568,NM_001042412.1;CYLD,missense_variant,p.Phe763Leu,ENST00000569418,NM_001042355.1;CYLD,missense_variant,p.Phe581Leu,ENST00000568704,;CYLD,missense_variant,p.Phe763Leu,ENST00000564326,;CYLD,missense_variant,p.Phe763Leu,ENST00000566206,;CYLD,upstream_gene_variant,,ENST00000562884,;CYLD,upstream_gene_variant,,ENST00000566024,;RP11-327F22.4,intron_variant,,ENST00000564510,;RP11-327F22.4,intron_variant,,ENST00000575917,;CYLD,downstream_gene_variant,,ENST00000563629,; C ENST00000427738 Transcript missense_variant 2501/8503 2296/2871 766/956 F/L Ttt/Ctt 1 1 CYLD HGNC HGNC:2584 protein_coding YES CCDS45482.1 ENSP00000392025 Q9NQC7 UPI0000073A15 deleterious(0.04) 15/18 PROSITE_profiles:PS50235,hmmpanther:PTHR11830:SF3,hmmpanther:PTHR11830,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE SNV 5 1 PASS . . 0 202 2 4 2 0 0 0 -20 0.9923869 1 1 1 0 C 3 2 56 50792651 50792651 T C 1 0 0 0 0 1 0 0 0 3946 1493 52 5 5 CYLD 16 50792651 Missense_Mutation SNP T C3N-00560_T 1156002 50792651 39545694 990 17679 SALL1 0 . GRCh38 16 51139506 51139506 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2716G>T p.Gly906Cys p.G906C ENST00000251020 2/3 238 146 92 266 266 0 strelka-varscan-mutect SALL1,missense_variant,p.Gly809Cys,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Gly906Cys,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Gly809Cys,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 2750/5146 2716/3975 906/1324 G/C Ggt/Tgt 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.18) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 51139506 51139506 C A 1 0 0 0 0 1 0 0 0 14069 623 22 2 2 SALL1 16 51139506 Missense_Mutation SNP C C3N-00560_T 346855 51139506 39198839 991 17680 MT1B 0 . GRCh38 16 56653070 56653070 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.189G>T p.Leu63Phe p.L63F ENST00000562399 3/3 164 92 72 217 217 0 strelka-varscan-mutect MT1B,missense_variant,p.Leu63Phe,ENST00000562399,;MT1B,3_prime_UTR_variant,,ENST00000334346,NM_005947.2;MT1F,upstream_gene_variant,,ENST00000334350,NM_005949.3;MT1F,upstream_gene_variant,,ENST00000568475,NM_001301272.1;RP11-249C24.11,downstream_gene_variant,,ENST00000568608,;MT1F,upstream_gene_variant,,ENST00000564295,;MT1CP,downstream_gene_variant,,ENST00000567054,; T ENST00000562399 Transcript missense_variant 217/351 189/213 63/70 L/F ttG/ttT 1 1 MT1B HGNC HGNC:7394 protein_coding ENSP00000456056 H3BR34 UPI0000E02B21 tolerated_low_confidence(0.08) 3/3 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 56653070 56653070 G T 1 0 0 0 0 1 0 0 0 9882 1339 47 2 2 MT1B 16 56653070 Missense_Mutation SNP G C3N-00560_T 5513564 56653070 33685275 992 17681 NLRC5 0 . GRCh38 16 57079572 57079572 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.5264A>T p.Gln1755Leu p.Q1755L ENST00000262510 46/49 204 124 80 268 268 0 strelka-varscan-mutect NLRC5,missense_variant,p.Gln1755Leu,ENST00000262510,;NLRC5,missense_variant,p.Gln1755Leu,ENST00000436936,NM_032206.4;NLRC5,missense_variant,p.Gln1726Leu,ENST00000539144,;NLRC5,3_prime_UTR_variant,,ENST00000545081,;NLRC5,3_prime_UTR_variant,,ENST00000538453,;NLRC5,3_prime_UTR_variant,,ENST00000540182,;NLRC5,3_prime_UTR_variant,,ENST00000537056,;NLRC5,non_coding_transcript_exon_variant,,ENST00000534927,;NLRC5,upstream_gene_variant,,ENST00000543103,;NLRC5,downstream_gene_variant,,ENST00000544189,;NLRC5,downstream_gene_variant,,ENST00000545349,;NLRC5,upstream_gene_variant,,ENST00000543049,; T ENST00000262510 Transcript missense_variant 5489/6822 5264/5601 1755/1866 Q/L cAg/cTg 1 1 NLRC5 HGNC HGNC:29933 protein_coding YES CCDS10773.1 ENSP00000262510 Q86WI3 UPI00001AEE94 tolerated(0.12) 46/49 Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF16,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57079572 57079572 A T 1 0 0 0 0 1 0 0 0 10507 188 7 4 4 NLRC5 16 57079572 Missense_Mutation SNP A C3N-00560_T 426502 57079572 33258773 993 17682 CDH8 0 . GRCh38 16 61825092 61825092 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.755A>T p.His252Leu p.H252L ENST00000577390 5/12 200 110 90 248 248 0 strelka-varscan-mutect CDH8,missense_variant,p.His252Leu,ENST00000577390,NM_001796.4;CDH8,missense_variant,p.His252Leu,ENST00000577730,;CDH8,missense_variant,p.His252Leu,ENST00000584337,;CDH8,missense_variant,p.His252Leu,ENST00000299345,;CDH8,missense_variant,p.His252Leu,ENST00000583382,;CDH8,missense_variant,p.His252Leu,ENST00000585315,; A ENST00000577390 Transcript missense_variant 1710/9721 755/2400 252/799 H/L cAc/cTc 1 -1 CDH8 HGNC HGNC:1767 protein_coding YES CCDS10802.1 ENSP00000462701 P55286 UPI0000126D9F NM_001796.4 deleterious(0.04) 5/12 Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF273,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 61825092 61825092 T A 1 0 0 0 0 1 0 0 0 2819 1696 59 4 4 CDH8 16 61825092 Missense_Mutation SNP T C3N-00560_T 4745520 61825092 28513253 994 17683 C16orf70 0 . GRCh38 16 67144373 67144373 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.959A>T p.Asn320Ile p.N320I ENST00000219139 11/16 106 64 42 138 138 0 strelka-varscan-mutect C16orf70,missense_variant,p.Asn320Ile,ENST00000219139,NM_001320541.1,NM_001320540.1,NM_001320542.1,NM_025187.3;C16orf70,missense_variant,p.Asn320Ile,ENST00000569600,;C16orf70,missense_variant,p.Asn320Ile,ENST00000563853,;B3GNT9,downstream_gene_variant,,ENST00000449549,NM_033309.2;C16orf70,downstream_gene_variant,,ENST00000569914,;C16orf70,upstream_gene_variant,,ENST00000569277,;C16orf70,non_coding_transcript_exon_variant,,ENST00000567162,; T ENST00000219139 Transcript missense_variant 1147/2865 959/1269 320/422 N/I aAc/aTc 1 1 C16orf70 HGNC HGNC:29564 protein_coding YES CCDS10828.1 ENSP00000219139 Q9BSU1 A0A024R6W4 UPI0000137911 NM_001320541.1,NM_001320540.1,NM_001320542.1,NM_025187.3 deleterious(0) 11/16 hmmpanther:PTHR13465,Pfam_domain:PF03676 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 67144373 67144373 A T 1 0 0 0 0 1 0 0 0 1862 57 2 4 4 C16orf70 16 67144373 Missense_Mutation SNP A C3N-00560_T 5319281 67144373 23193972 995 17684 PRMT7 0 . GRCh38 16 68348414 68348414 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1396G>T p.Asp466Tyr p.D466Y ENST00000339507 14/19 83 46 37 111 111 0 strelka-varscan-mutect PRMT7,missense_variant,p.Asp466Tyr,ENST00000339507,NM_001290018.1;PRMT7,missense_variant,p.Asp466Tyr,ENST00000441236,NM_019023.2;PRMT7,missense_variant,p.Asp416Tyr,ENST00000449359,NM_001184824.1;PRMT7,non_coding_transcript_exon_variant,,ENST00000566708,;PRMT7,downstream_gene_variant,,ENST00000564050,;PRMT7,missense_variant,p.Asp466Tyr,ENST00000568975,;PRMT7,non_coding_transcript_exon_variant,,ENST00000566687,;PRMT7,intron_variant,,ENST00000567542,;PRMT7,intron_variant,,ENST00000565356,;PRMT7,upstream_gene_variant,,ENST00000563608,; T ENST00000339507 Transcript missense_variant 2226/4238 1396/2079 466/692 D/Y Gac/Tac 1 1 PRMT7 HGNC HGNC:25557 protein_coding YES CCDS10866.1 ENSP00000343103 Q9NVM4 A0A024R726 UPI0000041857 NM_001290018.1 deleterious(0.04) 14/19 PROSITE_profiles:PS51678,PIRSF_domain:PIRSF036946,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 68348414 68348414 G T 1 0 0 0 0 1 0 0 0 12672 1174 41 2 2 PRMT7 16 68348414 Missense_Mutation SNP G C3N-00560_T 1204041 68348414 21989931 996 17685 COG4 0 . GRCh38 16 70496323 70496323 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1590A>T p.Gln530His p.Q530H ENST00000323786 12/19 430 225 205 519 519 0 strelka-varscan-mutect COG4,missense_variant,p.Gln530His,ENST00000323786,NM_015386.2;COG4,missense_variant,p.Gln530His,ENST00000393612,NM_001195139.1;COG4,3_prime_UTR_variant,,ENST00000564415,;COG4,3_prime_UTR_variant,,ENST00000482252,;COG4,non_coding_transcript_exon_variant,,ENST00000530314,;COG4,non_coding_transcript_exon_variant,,ENST00000526700,;COG4,non_coding_transcript_exon_variant,,ENST00000564315,;COG4,downstream_gene_variant,,ENST00000567244,; A ENST00000323786 Transcript missense_variant 1612/2833 1590/2370 530/789 Q/H caA/caT 1 -1 COG4 HGNC HGNC:18620 protein_coding YES CCDS10892.2 ENSP00000315775 J3KNI1 UPI000059D3B0 NM_015386.2 tolerated(0.13) 12/19 hmmpanther:PTHR24016:SF0,hmmpanther:PTHR24016 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 70496323 70496323 T A 1 0 0 0 0 1 0 0 0 3448 1606 56 4 4 COG4 16 70496323 Missense_Mutation SNP T C3N-00560_T 2147909 70496323 19842022 997 17686 PMFBP1 0 . GRCh38 16 72136579 72136579 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1072C>T p.His358Tyr p.H358Y ENST00000237353 9/21 158 89 69 203 203 0 strelka-varscan-mutect PMFBP1,missense_variant,p.His358Tyr,ENST00000537465,;PMFBP1,missense_variant,p.His358Tyr,ENST00000237353,NM_031293.2;PMFBP1,missense_variant,p.His213Tyr,ENST00000355636,NM_001160213.1;PMFBP1,missense_variant,p.His161Tyr,ENST00000537392,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,; A ENST00000237353 Transcript missense_variant 1334/3527 1072/3024 358/1007 H/Y Cac/Tac 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 deleterious(0) 9/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 72136579 72136579 G A 1 0 0 0 0 1 0 0 0 12241 1319 46 3 3 PMFBP1 16 72136579 Missense_Mutation SNP G C3N-00560_T 1640256 72136579 18201766 998 17687 CMIP 0 . GRCh38 16 81672024 81672024 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.988G>T p.Val330Leu p.V330L ENST00000537098 9/21 89 50 39 133 133 0 strelka-varscan-mutect CMIP,missense_variant,p.Val330Leu,ENST00000537098,NM_198390.2;CMIP,missense_variant,p.Val235Leu,ENST00000621537,;CMIP,missense_variant,p.Val236Leu,ENST00000539778,NM_030629.2;CMIP,missense_variant,p.Val177Leu,ENST00000398040,;CMIP,missense_variant,p.Val143Leu,ENST00000566513,;CMIP,downstream_gene_variant,,ENST00000566462,; T ENST00000537098 Transcript missense_variant 1060/4357 988/2322 330/773 V/L Gtg/Ttg 1 1 CMIP HGNC HGNC:24319 protein_coding YES CCDS54044.1 ENSP00000446100 Q8IY22 UPI00001FFCBD NM_198390.2 tolerated(0.07) 9/21 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999891 1 1 1 0 T 3 4 56 81672024 81672024 G T 1 0 0 0 0 1 0 0 0 3353 1145 40 1 1 CMIP 16 81672024 Missense_Mutation SNP G C3N-00560_T 9535445 81672024 8666321 999 17688 CRISPLD2 0 . GRCh38 16 84873106 84873106 + Missense_Mutation SNP G G T rs138350685 C3N-00560_T C3N-00560_N G G c.1096G>T p.Gly366Cys p.G366C ENST00000262424 10/15 89 43 46 98 98 0 strelka-varscan-mutect CRISPLD2,missense_variant,p.Gly366Cys,ENST00000262424,NM_031476.3;CRISPLD2,missense_variant,p.Gly365Cys,ENST00000567845,;CRISPLD2,missense_variant,p.Gly366Cys,ENST00000564567,;CRISPLD2,missense_variant,p.Gly209Cys,ENST00000563066,;CRISPLD2,non_coding_transcript_exon_variant,,ENST00000569262,; T ENST00000262424 Transcript missense_variant 1320/4586 1096/1494 366/497 G/C Ggc/Tgc rs138350685 1 1 CRISPLD2 HGNC HGNC:25248 protein_coding YES CCDS10949.1 ENSP00000262424 Q9H0B8 A0A140VK80 UPI00000411B0 NM_031476.3 deleterious(0) 10/15 Superfamily_domains:0039469,Gene3D:1jbiA00,Pfam_domain:PF03815,PROSITE_profiles:PS50820,SMART_domains:SM00603 MODERATE 1 SNV 1 1 PASS rs138350685 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 84873106 84873106 G T 1 0 0 0 0 1 0 0 0 3684 1116 39 1 1 CRISPLD2 16 84873106 Missense_Mutation SNP G C3N-00560_T 3201082 84873106 5465239 1000 17689 ANKRD11 0 . GRCh38 16 89279435 89279435 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.7107C>T p.= p.A2369A ENST00000301030 9/13 79 59 20 107 107 0 strelka-varscan-mutect ANKRD11,synonymous_variant,p.=,ENST00000301030,NM_013275.5,NM_001256183.1;ANKRD11,synonymous_variant,p.=,ENST00000378330,NM_001256182.1;ANKRD11,intron_variant,,ENST00000562194,;ANKRD11,non_coding_transcript_exon_variant,,ENST00000623388,;ANKRD11,3_prime_UTR_variant,,ENST00000330736,; A ENST00000301030 Transcript synonymous_variant 7568/9301 7107/7992 2369/2663 A gcC/gcT 1 -1 ANKRD11 HGNC HGNC:21316 protein_coding YES CCDS32513.1 ENSP00000301030 Q6UB99 UPI00004569E1 NM_013275.5,NM_001256183.1 9/13 hmmpanther:PTHR24145:SF3,hmmpanther:PTHR24145 LOW 1 SNV 5 1 PASS rs1430139628 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 89279435 89279435 G A 1 0 0 0 0 0 0 0 1 740 1335 47 3 3 ANKRD11 16 89279435 Silent SNP G C3N-00560_T 4406329 89279435 1058910 1001 17690 NXN 0 . GRCh38 17 819473 819473 + Silent SNP C C G novel C3N-00560_T C3N-00560_N C C c.786G>C p.= p.R262R ENST00000336868 5/8 229 85 144 192 192 0 strelka-varscan-mutect NXN,synonymous_variant,p.=,ENST00000336868,NM_022463.4;NXN,synonymous_variant,p.=,ENST00000575801,NM_001205319.1;NXN,synonymous_variant,p.=,ENST00000537628,;NXN,synonymous_variant,p.=,ENST00000571684,;NXN,downstream_gene_variant,,ENST00000577098,;NXN,downstream_gene_variant,,ENST00000571338,;NXN,non_coding_transcript_exon_variant,,ENST00000575455,; G ENST00000336868 Transcript synonymous_variant 878/3036 786/1308 262/435 R cgG/cgC 1 -1 NXN HGNC HGNC:18008 protein_coding YES CCDS10998.1 ENSP00000337443 Q6DKJ4 UPI00001B31EB NM_022463.4 5/8 PROSITE_profiles:PS51352,hmmpanther:PTHR13871,hmmpanther:PTHR13871:SF52,Gene3D:3.40.30.10,Pfam_domain:PF13905,Superfamily_domains:SSF52833 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 819473 819473 C G 1 0 0 0 0 0 0 0 1 10859 726 26 4 4 NXN 17 819473 Silent SNP C C3N-00560_T 819473 82437968 1002 17691 RTN4RL1 0 . GRCh38 17 1937674 1937674 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.148G>T p.Glu50Ter p.E50* ENST00000331238 2/2 353 132 221 300 300 0 strelka-varscan-mutect RTN4RL1,stop_gained,p.Glu50Ter,ENST00000331238,NM_178568.3; A ENST00000331238 Transcript stop_gained 628/3625 148/1326 50/441 E/* Gag/Tag 1 -1 RTN4RL1 HGNC HGNC:21329 protein_coding YES CCDS45569.1 ENSP00000330631 Q86UN2 UPI000018CD23 NM_178568.3 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF11,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 1937674 1937674 C A 1 0 0 0 0 0 1 0 0 13991 864 30 2 2 RTN4RL1 17 1937674 Nonsense_Mutation SNP C C3N-00560_T 1118201 1937674 81319767 1003 17692 MNT 0 . GRCh38 17 2394937 2394937 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.591G>T p.= p.G197G ENST00000174618 2/6 288 119 169 246 245 1 strelka-varscan-mutect MNT,synonymous_variant,p.=,ENST00000174618,NM_020310.2;MNT,intron_variant,,ENST00000575394,;MNT,upstream_gene_variant,,ENST00000575374,;MNT,downstream_gene_variant,,ENST00000574559,;MNT,upstream_gene_variant,,ENST00000572892,;MNT,downstream_gene_variant,,ENST00000571836,;MNT,upstream_gene_variant,,ENST00000571232,;MNT,upstream_gene_variant,,ENST00000575402,; A ENST00000174618 Transcript synonymous_variant 997/4996 591/1749 197/582 G ggG/ggT 1 -1 MNT HGNC HGNC:7188 protein_coding YES CCDS11018.1 ENSP00000174618 Q99583 UPI000012F2C6 NM_020310.2 2/6 hmmpanther:PTHR11969,hmmpanther:PTHR11969:SF15,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 2394937 2394937 C A 1 0 0 0 0 0 0 0 1 9642 842 30 2 2 MNT 17 2394937 Silent SNP C C3N-00560_T 457263 2394937 80862504 1004 17693 AIPL1 0 . GRCh38 17 6427049 6427049 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.474C>A p.= p.A158A ENST00000381129 4/6 375 140 235 298 297 1 strelka-varscan-mutect AIPL1,synonymous_variant,p.=,ENST00000381129,NM_014336.4;AIPL1,synonymous_variant,p.=,ENST00000250087,NM_001033054.2;AIPL1,synonymous_variant,p.=,ENST00000575265,;AIPL1,synonymous_variant,p.=,ENST00000574506,NM_001285399.2,NM_001285402.1;AIPL1,synonymous_variant,p.=,ENST00000570466,NM_001285400.2;AIPL1,synonymous_variant,p.=,ENST00000576776,NM_001285401.2;AIPL1,synonymous_variant,p.=,ENST00000576307,NM_001033055.2;AIPL1,synonymous_variant,p.=,ENST00000574913,;AIPL1,intron_variant,,ENST00000571740,NM_001285403.2;AIPL1,intron_variant,,ENST00000570584,;AIPL1,3_prime_UTR_variant,,ENST00000381128,; T ENST00000381129 Transcript synonymous_variant 555/2959 474/1155 158/384 A gcC/gcA COSM4397208 1 -1 AIPL1 HGNC HGNC:359 protein_coding YES CCDS11075.1 ENSP00000370521 Q9NZN9 F1T0B6 UPI0000125741 NM_014336.4 4/6 Gene3D:3.10.50.40,hmmpanther:PTHR11242,hmmpanther:PTHR11242:SF2 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 6427049 6427049 G T 1 0 0 0 0 0 0 0 1 513 1219 43 2 2 AIPL1 17 6427049 Silent SNP G C3N-00560_T 4032112 6427049 76830392 1005 17694 DLG4 0 . GRCh38 17 7191949 7191949 + Silent SNP C C A rs754740263 C3N-00560_T C3N-00560_N C C c.2049G>T p.= p.A683A ENST00000399510 20/22 32 14 18 25 25 0 strelka-varscan-mutect DLG4,synonymous_variant,p.=,ENST00000399510,NM_001321074.1,NM_001365.3;DLG4,synonymous_variant,p.=,ENST00000399506,NM_001321076.1,NM_001321075.1;DLG4,synonymous_variant,p.=,ENST00000302955,NM_001321077.1,NM_001128827.1;CTD-2545G14.4,downstream_gene_variant,,ENST00000623840,;DLG4,non_coding_transcript_exon_variant,,ENST00000489885,;DLG4,intron_variant,,ENST00000491753,; A ENST00000399510 Transcript synonymous_variant 2902/3975 2049/2304 683/767 A gcG/gcT rs754740263 1 -1 DLG4 HGNC HGNC:2903 protein_coding YES CCDS45599.1 ENSP00000382428 P78352 UPI0000048D63 NM_001321074.1,NM_001365.3 20/22 Gene3D:3.40.50.300,Pfam_domain:PF00625,PROSITE_profiles:PS50052,hmmpanther:PTHR23119,hmmpanther:PTHR23119:SF33,SMART_domains:SM00072,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs754740263 . 1 206 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 7191949 7191949 C A 1 0 0 0 0 0 0 0 1 4364 639 23 1 1 DLG4 17 7191949 Silent SNP C C3N-00560_T 764900 7191949 76065492 1006 17695 NEURL4 0 . GRCh38 17 7321739 7321739 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2920G>T p.Gly974Trp p.G974W ENST00000399464 18/29 323 123 200 212 212 0 strelka-varscan-mutect NEURL4,missense_variant,p.Gly974Trp,ENST00000399464,NM_032442.2;NEURL4,missense_variant,p.Gly972Trp,ENST00000315614,NM_001005408.1;NEURL4,missense_variant,p.Gly950Trp,ENST00000570460,;NEURL4,missense_variant,p.Gly937Trp,ENST00000571887,;NEURL4,upstream_gene_variant,,ENST00000574120,;NEURL4,missense_variant,p.Gly719Trp,ENST00000573186,;NEURL4,3_prime_UTR_variant,,ENST00000573651,;NEURL4,non_coding_transcript_exon_variant,,ENST00000571508,;RP11-542C16.2,upstream_gene_variant,,ENST00000575474,;RP11-542C16.2,upstream_gene_variant,,ENST00000315601,;NEURL4,upstream_gene_variant,,ENST00000576794,;NEURL4,upstream_gene_variant,,ENST00000572680,;NEURL4,downstream_gene_variant,,ENST00000576966,;NEURL4,downstream_gene_variant,,ENST00000576485,;NEURL4,upstream_gene_variant,,ENST00000572029,;NEURL4,downstream_gene_variant,,ENST00000571243,; A ENST00000399464 Transcript missense_variant 2936/5200 2920/4689 974/1562 G/W Ggg/Tgg 1 -1 NEURL4 HGNC HGNC:34410 protein_coding YES CCDS42251.1 ENSP00000382390 Q96JN8 UPI000020081C NM_032442.2 deleterious(0) 18/29 PROSITE_profiles:PS51065,hmmpanther:PTHR12429:SF14,hmmpanther:PTHR12429,Pfam_domain:PF07177,SMART_domains:SM00588 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 7321739 7321739 C A 1 0 0 0 0 1 0 0 0 10384 623 22 2 2 NEURL4 17 7321739 Missense_Mutation SNP C C3N-00560_T 129790 7321739 75935702 1007 17696 TMEM95 0 . GRCh38 17 7355213 7355213 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.9G>C p.Arg3Ser p.R3S ENST00000330767 1/7 260 181 79 219 219 0 strelka-varscan-mutect TMEM95,missense_variant,p.Arg3Ser,ENST00000389982,NM_001320435.1,NM_001320436.1;TMEM95,missense_variant,p.Arg3Ser,ENST00000330767,NM_198154.1;TMEM95,missense_variant,p.Arg3Ser,ENST00000576060,;KCTD11,downstream_gene_variant,,ENST00000333751,NM_001002914.2;ACAP1,downstream_gene_variant,,ENST00000158762,NM_014716.3;ACAP1,downstream_gene_variant,,ENST00000574499,;ACAP1,downstream_gene_variant,,ENST00000571471,;ACAP1,downstream_gene_variant,,ENST00000575415,;ACAP1,downstream_gene_variant,,ENST00000570504,;RP11-542C16.1,upstream_gene_variant,,ENST00000572417,;KCTD11,downstream_gene_variant,,ENST00000576980,;ACAP1,downstream_gene_variant,,ENST00000570439,; C ENST00000330767 Transcript missense_variant 36/1169 9/555 3/184 R/S agG/agC 1 1 TMEM95 HGNC HGNC:27898 protein_coding YES CCDS32546.1 ENSP00000331466 Q3KNT9 UPI00001D6946 NM_198154.1 tolerated(0.08) 1/7 Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS51257,hmmpanther:PTHR38808,hmmpanther:PTHR38808:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 7355213 7355213 G C 1 0 0 0 0 1 0 0 0 16698 1194 42 4 4 TMEM95 17 7355213 Missense_Mutation SNP G C3N-00560_T 33474 7355213 75902228 1008 17697 TP53 0 . GRCh38 17 7675237 7675237 + Splice_Site SNP C C A rs868137297 C3N-00560_T C3N-00560_N C C c.376-1G>T p.X126_splice ENST00000269305 321 126 195 277 277 0 strelka-varscan-mutect TP53,splice_acceptor_variant,,ENST00000617185,NM_001126114.2;TP53,splice_acceptor_variant,,ENST00000420246,;TP53,splice_acceptor_variant,,ENST00000622645,NM_001276696.1;TP53,splice_acceptor_variant,,ENST00000610292,NM_001126118.1;TP53,splice_acceptor_variant,,ENST00000455263,NM_001126113.2;TP53,splice_acceptor_variant,,ENST00000610538,NM_001276695.1;TP53,splice_acceptor_variant,,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,splice_acceptor_variant,,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,splice_acceptor_variant,,ENST00000445888,;TP53,splice_acceptor_variant,,ENST00000619485,;TP53,splice_acceptor_variant,,ENST00000359597,;TP53,splice_acceptor_variant,,ENST00000413465,;TP53,splice_acceptor_variant,,ENST00000509690,;TP53,splice_acceptor_variant,,ENST00000508793,;TP53,splice_acceptor_variant,,ENST00000503591,;TP53,splice_acceptor_variant,,ENST00000514944,;TP53,missense_variant,p.Lys114Asn,ENST00000615910,;TP53,5_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000504937,NM_001126115.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,splice_acceptor_variant,,ENST00000635293,;TP53,splice_acceptor_variant,,ENST00000505014,; A ENST00000269305 Transcript splice_acceptor_variant -/2579 376/1182 126/393 rs868137297,TP53_g.12363del,TP53_g.12363G>A,TP53_g.12363G>T,TP53_g.12363G>C,COSM1167885,COSM1167886,COSM1167887,COSM2156353,COSM21572,COSM218536,COSM218537,COSM218538,COSM22908,COSM2744965,COSM3378369,COSM3388229,COSM4271994,COSM4271995,COSM4271996,COSM4271997,COSM4271998,COSM45364,COSM45809,COSM6900 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 4/10 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs751253294 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 7675237 7675237 C A 1 0 0 0 0 0 0 1 0 16859 579 20 2 2 TP53 17 7675237 Splice_Site SNP C C3N-00560_T 320024 7675237 75582204 1009 17698 CTC1 0 . GRCh38 17 8232063 8232063 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.2225T>A p.Met742Lys p.M742K ENST00000315684 13/23 48 25 23 40 40 0 strelka-varscan-mutect CTC1,missense_variant,p.Met742Lys,ENST00000315684,NM_025099.5;CTC1,upstream_gene_variant,,ENST00000581729,;CTC1,upstream_gene_variant,,ENST00000580299,;CTC1,downstream_gene_variant,,ENST00000581671,;CTC1,missense_variant,p.Met707Lys,ENST00000449476,;CTC1,missense_variant,p.Met41Lys,ENST00000578537,;CTC1,non_coding_transcript_exon_variant,,ENST00000578240,;CTC1,upstream_gene_variant,,ENST00000578441,;CTC1,upstream_gene_variant,,ENST00000584439,;CTC1,downstream_gene_variant,,ENST00000581967,;CTC1,downstream_gene_variant,,ENST00000579066,;CTC1,downstream_gene_variant,,ENST00000583254,; T ENST00000315684 Transcript missense_variant 2233/7021 2225/3654 742/1217 M/K aTg/aAg 1 -1 CTC1 HGNC HGNC:26169 protein_coding YES CCDS42259.1 ENSP00000313759 Q2NKJ3 UPI000041A9A9 NM_025099.5 deleterious(0) 13/23 Pfam_domain:PF15489,hmmpanther:PTHR14865 MODERATE 1 SNV 1 1 PASS rs1351626756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 8232063 8232063 A T 1 0 0 0 0 1 0 0 0 3806 217 8 4 4 CTC1 17 8232063 Missense_Mutation SNP A C3N-00560_T 556826 8232063 75025378 1010 17699 CCDC42 0 . GRCh38 17 8741577 8741577 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.389A>T p.Gln130Leu p.Q130L ENST00000293845 4/7 485 185 300 429 429 0 strelka-varscan-mutect CCDC42,missense_variant,p.Gln130Leu,ENST00000293845,NM_144681.2;CCDC42,missense_variant,p.Gln130Leu,ENST00000539522,NM_001158261.1;CCDC42,downstream_gene_variant,,ENST00000581598,; A ENST00000293845 Transcript missense_variant 616/1374 389/951 130/316 Q/L cAg/cTg 1 -1 CCDC42 HGNC HGNC:26528 protein_coding YES CCDS11145.1 ENSP00000293845 Q96M95 UPI000013E127 NM_144681.2 tolerated(0.25) 4/7 hmmpanther:PTHR21683:SF8,hmmpanther:PTHR21683,Pfam_domain:PF13863 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 8741577 8741577 T A 1 0 0 0 0 1 0 0 0 2522 1580 55 4 4 CCDC42 17 8741577 Missense_Mutation SNP T C3N-00560_T 509514 8741577 74515864 1011 17700 DHRS7C 0 . GRCh38 17 9779905 9779905 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.401G>T p.Gly134Val p.G134V ENST00000330255 3/6 506 195 311 469 468 1 strelka-varscan-mutect DHRS7C,missense_variant,p.Gly134Val,ENST00000330255,NM_001220493.1;DHRS7C,missense_variant,p.Gly133Val,ENST00000571134,NM_001105571.2;DHRS7C,missense_variant,p.Gly6Val,ENST00000571771,;RP11-477N12.6,intron_variant,,ENST00000634974,; A ENST00000330255 Transcript missense_variant 414/1006 401/939 134/312 G/V gGg/gTg COSM4960797 1 -1 DHRS7C HGNC HGNC:32423 protein_coding YES CCDS56020.1 ENSP00000327975 A6NNS2 UPI000178DECB NM_001220493.1 deleterious(0) 3/6 hmmpanther:PTHR24322:SF254,hmmpanther:PTHR24322,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 1 MODERATE 1 SNV 1 1 1 PASS rs1227994979 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 9779905 9779905 C A 1 0 0 0 0 1 0 0 0 4301 623 22 2 2 DHRS7C 17 9779905 Missense_Mutation SNP C C3N-00560_T 1038328 9779905 73477536 1012 17701 MYH1 0 . GRCh38 17 10501313 10501313 + Missense_Mutation SNP G G T rs755825265 C3N-00560_T C3N-00560_N G G c.3535C>A p.Arg1179Ser p.R1179S ENST00000226207 27/40 568 222 346 545 545 0 strelka-varscan-mutect MYH1,missense_variant,p.Arg1179Ser,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript missense_variant 3630/6024 3535/5820 1179/1939 R/S Cgc/Agc rs755825265 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0.01) 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS rs755825265 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 10501313 10501313 G T 1 0 0 0 0 1 0 0 0 10029 1087 38 1 1 MYH1 17 10501313 Missense_Mutation SNP G C3N-00560_T 721408 10501313 72756128 1013 17702 SHISA6 0 . GRCh38 17 11555746 11555746 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.959C>A p.Pro320Gln p.P320Q ENST00000441885 5/6 67 24 43 55 55 0 strelka-varscan-mutect SHISA6,missense_variant,p.Pro320Gln,ENST00000441885,NM_207386.3;SHISA6,missense_variant,p.Pro301Gln,ENST00000432116,NM_001173462.1;SHISA6,missense_variant,p.Pro269Gln,ENST00000409168,NM_001173461.1; A ENST00000441885 Transcript missense_variant 1119/7575 959/1656 320/551 P/Q cCa/cAa 1 1 SHISA6 HGNC HGNC:34491 protein_coding YES CCDS45615.1 ENSP00000390084 Q6ZSJ9 UPI000183CBD8 NM_207386.3 tolerated(0.1) 5/6 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF0 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 11555746 11555746 C A 1 0 0 0 0 1 0 0 0 14544 594 21 2 2 SHISA6 17 11555746 Missense_Mutation SNP C C3N-00560_T 1054433 11555746 71701695 1014 17703 DNAH9 0 . GRCh38 17 11608301 11608301 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.590T>C p.Phe197Ser p.F197S ENST00000262442 2/69 114 49 65 102 102 0 strelka-varscan-mutect DNAH9,missense_variant,p.Phe197Ser,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Phe197Ser,ENST00000454412,;DNAH9,missense_variant,p.Phe197Ser,ENST00000579828,;DNAH9,upstream_gene_variant,,ENST00000579602,;DNAH9,upstream_gene_variant,,ENST00000579813,;DNAH9,non_coding_transcript_exon_variant,,ENST00000579406,; C ENST00000262442 Transcript missense_variant 658/13750 590/13461 197/4486 F/S tTt/tCt 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 tolerated(0.46) 2/69 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS rs757635352 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 11608301 11608301 T C 1 0 0 0 0 1 0 0 0 4423 1841 64 5 5 DNAH9 17 11608301 Missense_Mutation SNP T C3N-00560_T 52555 11608301 71649140 1015 17704 HS3ST3B1 0 . GRCh38 17 14345391 14345391 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.918G>T p.= p.G306G ENST00000360954 2/2 67 24 43 52 52 0 strelka-varscan-mutect HS3ST3B1,synonymous_variant,p.=,ENST00000360954,NM_006041.2;HS3ST3B1,synonymous_variant,p.=,ENST00000466596,; T ENST00000360954 Transcript synonymous_variant 1354/5367 918/1173 306/390 G ggG/ggT 1 1 HS3ST3B1 HGNC HGNC:5198 protein_coding YES CCDS11167.1 ENSP00000354213 Q9Y662 UPI0000038167 NM_006041.2 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF7,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 14345391 14345391 G T 1 0 0 0 0 0 0 0 1 7260 1219 43 2 2 HS3ST3B1 17 14345391 Silent SNP G C3N-00560_T 2737090 14345391 68912050 1016 17705 ADORA2B 0 . GRCh38 17 15945275 15945275 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.27G>T p.= p.L9L ENST00000304222 1/2 37 15 22 45 45 0 strelka-varscan-mutect ADORA2B,synonymous_variant,p.=,ENST00000304222,NM_000676.2; T ENST00000304222 Transcript synonymous_variant 359/1735 27/999 9/332 L ctG/ctT 1 1 ADORA2B HGNC HGNC:264 protein_coding YES CCDS11173.1 ENSP00000304501 P29275 UPI00000503E3 NM_000676.2 1/2 hmmpanther:PTHR24246,hmmpanther:PTHR24246:SF18,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00424 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 15945275 15945275 G T 1 0 0 0 0 0 0 0 1 403 1364 48 2 2 ADORA2B 17 15945275 Silent SNP G C3N-00560_T 1599884 15945275 67312166 1017 17706 MYO15A 0 . GRCh38 17 18120846 18120846 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.2046G>T p.= p.P682P ENST00000205890 2/66 76 39 37 50 50 0 strelka-varscan-mutect MYO15A,synonymous_variant,p.=,ENST00000205890,NM_016239.3;MYO15A,synonymous_variant,p.=,ENST00000615845,;MYO15A,non_coding_transcript_exon_variant,,ENST00000583079,; T ENST00000205890 Transcript synonymous_variant 2384/11863 2046/10593 682/3530 P ccG/ccT 1 1 MYO15A HGNC HGNC:7594 protein_coding YES CCDS42271.1 ENSP00000205890 Q9UKN7 UPI0000E59E6E NM_016239.3 2/66 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1284228904 . 6 198 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 18120846 18120846 G T 1 0 0 0 0 0 0 0 1 10063 1103 39 1 1 MYO15A 17 18120846 Silent SNP G C3N-00560_T 2175571 18120846 65136595 1018 17707 TOP3A 0 . GRCh38 17 18302394 18302394 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.684G>T p.Arg228Ser p.R228S ENST00000542570 7/19 103 56 47 116 116 0 strelka-varscan-mutect TOP3A,missense_variant,p.Arg228Ser,ENST00000542570,NM_004618.3;TOP3A,missense_variant,p.Arg228Ser,ENST00000321105,;TOP3A,missense_variant,p.Arg203Ser,ENST00000580095,;TOP3A,downstream_gene_variant,,ENST00000584669,;TOP3A,3_prime_UTR_variant,,ENST00000584582,;TOP3A,3_prime_UTR_variant,,ENST00000582981,;TOP3A,non_coding_transcript_exon_variant,,ENST00000469739,;TOP3A,non_coding_transcript_exon_variant,,ENST00000583804,;TOP3A,downstream_gene_variant,,ENST00000472959,;TOP3A,downstream_gene_variant,,ENST00000461127,;TOP3A,upstream_gene_variant,,ENST00000581536,;TOP3A,downstream_gene_variant,,ENST00000583328,;TOP3A,downstream_gene_variant,,ENST00000585031,; A ENST00000542570 Transcript missense_variant 913/4116 684/3006 228/1001 R/S agG/agT 1 -1 TOP3A HGNC HGNC:11992 protein_coding YES CCDS11194.1 ENSP00000442336 Q13472 UPI00001371A0 NM_004618.3 deleterious(0) 7/19 hmmpanther:PTHR11390:SF21,hmmpanther:PTHR11390,Gene3D:1.10.460.10,Pfam_domain:PF01131,SMART_domains:SM00436,Superfamily_domains:SSF56712 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 18302394 18302394 C A 1 0 0 0 0 1 0 0 0 16843 854 30 2 2 TOP3A 17 18302394 Missense_Mutation SNP C C3N-00560_T 181548 18302394 64955047 1019 17708 LGALS9B 0 . GRCh38 17 20460375 20460375 + Silent SNP G G T rs772797556 C3N-00560_T C3N-00560_N G G c.108C>A p.= p.A36A ENST00000324290 2/11 290 162 128 422 421 1 strelka-varscan-mutect LGALS9B,synonymous_variant,p.=,ENST00000423676,;LGALS9B,synonymous_variant,p.=,ENST00000324290,NM_001042685.1;LGALS9B,intron_variant,,ENST00000578481,;LGALS9B,upstream_gene_variant,,ENST00000584703,; T ENST00000324290 Transcript synonymous_variant 173/1243 108/1068 36/355 A gcC/gcA rs772797556 1 -1 LGALS9B HGNC HGNC:24842 protein_coding YES CCDS42283.1 ENSP00000315564 Q3B8N2 UPI00001AF401 NM_001042685.1 2/11 Gene3D:2.60.120.200,Pfam_domain:PF00337,PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF91,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 LOW 1 SNV 5 1 PASS rs772797556 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 20460375 20460375 G T 1 0 0 0 0 0 0 0 1 8658 1103 39 1 1 LGALS9B 17 20460375 Silent SNP G C3N-00560_T 2157981 20460375 62797066 1020 17709 KCNJ12 0 . GRCh38 17 21415660 21415660 + Silent SNP G G T rs149095815 C3N-00560_T C3N-00560_N G G c.318G>T p.= p.A106A ENST00000583088 3/3 423 249 174 481 481 0 strelka-varscan-mutect KCNJ12,synonymous_variant,p.=,ENST00000583088,NM_021012.4;KCNJ12,synonymous_variant,p.=,ENST00000331718,; T ENST00000583088 Transcript synonymous_variant 1213/5425 318/1302 106/433 A gcG/gcT rs149095815 1 1 KCNJ12 HGNC HGNC:6258 protein_coding YES CCDS11219.1 ENSP00000463778 Q14500 UPI00000725C7 NM_021012.4 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14,Pfam_domain:PF01007,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR01320 LOW 1 SNV 1 1 PASS rs149095815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 21415660 21415660 G T 1 0 0 0 0 0 0 0 1 7962 1103 39 1 1 KCNJ12 17 21415660 Silent SNP G C3N-00560_T 955285 21415660 61841781 1021 17710 KCNJ12 0 . GRCh38 17 21416627 21416627 + Silent SNP C C A rs781867776 C3N-00560_T C3N-00560_N C C c.1285C>A p.= p.R429R ENST00000583088 3/3 61 50 11 69 68 1 strelka-varscan-mutect KCNJ12,synonymous_variant,p.=,ENST00000583088,NM_021012.4;KCNJ12,synonymous_variant,p.=,ENST00000331718,; A ENST00000583088 Transcript synonymous_variant 2180/5425 1285/1302 429/433 R Cgg/Agg rs781867776 1 1 KCNJ12 HGNC HGNC:6258 protein_coding YES CCDS11219.1 ENSP00000463778 Q14500 UPI00000725C7 NM_021012.4 3/3 hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14 LOW 1 SNV 1 1 PASS rs781867776 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 21416627 21416627 C A 1 0 0 0 0 0 0 0 1 7962 527 19 1 1 KCNJ12 17 21416627 Silent SNP C C3N-00560_T 967 21416627 61840814 1022 17711 FNDC8 0 . GRCh38 17 35127248 35127248 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.416C>A p.Pro139His p.P139H ENST00000158009 2/4 61 39 22 84 84 0 strelka-varscan-mutect FNDC8,missense_variant,p.Pro139His,ENST00000158009,NM_017559.2;NLE1,downstream_gene_variant,,ENST00000586869,NM_001014445.2;NLE1,downstream_gene_variant,,ENST00000442241,NM_018096.4;NLE1,downstream_gene_variant,,ENST00000360831,;NLE1,downstream_gene_variant,,ENST00000588019,; A ENST00000158009 Transcript missense_variant 531/1388 416/975 139/324 P/H cCc/cAc 1 1 FNDC8 HGNC HGNC:25286 protein_coding YES CCDS11290.1 ENSP00000158009 Q8TC99 UPI000006D671 NM_017559.2 tolerated_low_confidence(0.09) 2/4 hmmpanther:PTHR32430 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 56 35127248 35127248 C A 1 0 0 0 0 1 0 0 0 5831 623 22 2 2 FNDC8 17 35127248 Missense_Mutation SNP C C3N-00560_T 13710621 35127248 48130193 1023 17712 KRT26 0 . GRCh38 17 40769971 40769971 + Missense_Mutation SNP A A C novel C3N-00560_T C3N-00560_N A A c.833T>G p.Phe278Cys p.F278C ENST00000335552 4/8 316 227 89 223 223 0 strelka-varscan-mutect KRT26,missense_variant,p.Phe278Cys,ENST00000335552,NM_181539.4; C ENST00000335552 Transcript missense_variant 882/1733 833/1407 278/468 F/C tTc/tGc 1 -1 KRT26 HGNC HGNC:30840 protein_coding YES CCDS11374.1 ENSP00000334798 Q7Z3Y9 UPI0000200C8F NM_181539.4 deleterious(0) 4/8 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF162,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs1429800484 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 40769971 40769971 A C 1 0 0 0 0 1 0 0 0 8345 246 9 5 5 KRT26 17 40769971 Missense_Mutation SNP A C3N-00560_T 5642723 40769971 42487470 1024 17713 KRT40 0 . GRCh38 17 40982374 40982374 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.620C>A p.Ser207Tyr p.S207Y ENST00000377755 3/7 128 89 39 95 95 0 strelka-varscan-mutect KRT40,missense_variant,p.Ser207Tyr,ENST00000377755,;KRT40,missense_variant,p.Ser207Tyr,ENST00000398486,NM_182497.3;KRT40,missense_variant,p.Ser207Tyr,ENST00000461923,; T ENST00000377755 Transcript missense_variant 655/1812 620/1296 207/431 S/Y tCt/tAt 1 -1 KRT40 HGNC HGNC:26707 protein_coding YES CCDS42320.1 ENSP00000366984 Q6A162 UPI00003B288A deleterious(0) 3/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01248,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF90,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs1165763233 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 40982374 40982374 G T 1 0 0 0 0 1 0 0 0 8360 942 33 2 2 KRT40 17 40982374 Missense_Mutation SNP G C3N-00560_T 212403 40982374 42275067 1025 17714 KRTAP4-16 0 . GRCh38 17 41101976 41101976 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.234C>T p.= p.C78C ENST00000440582 1/1 416 307 109 298 298 0 strelka-varscan-mutect KRTAP4-16,synonymous_variant,p.=,ENST00000440582,;KRTAP4-7,intron_variant,,ENST00000612231,;KRTAP4-8,upstream_gene_variant,,ENST00000333822,NM_031960.2;KRTAP4-9,upstream_gene_variant,,ENST00000391415,NM_001146041.1;KRTAP4-9,upstream_gene_variant,,ENST00000617453,;KRTAP4-8,upstream_gene_variant,,ENST00000318329,; A ENST00000440582 Transcript synonymous_variant 234/708 234/708 78/235 C tgC/tgT 1 -1 KRTAP4-16 HGNC HGNC:18921 protein_coding YES ENSP00000411198 G5E9R7 UPI0000E59F68 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF37,Pfam_domain:PF13885 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 41101976 41101976 G A 1 0 0 0 0 0 0 0 1 8444 963 34 3 3 KRTAP4-16 17 41101976 Silent SNP G C3N-00560_T 119602 41101976 42155465 1026 17715 KRTAP4-4 0 . GRCh38 17 41160264 41160264 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.428C>A p.Thr143Asn p.T143N ENST00000390661 1/1 321 279 42 225 225 0 strelka-mutect KRTAP4-4,missense_variant,p.Thr143Asn,ENST00000390661,NM_032524.1; T ENST00000390661 Transcript missense_variant 468/1081 428/501 143/166 T/N aCc/aAc 1 -1 KRTAP4-4 HGNC HGNC:16928 protein_coding YES CCDS11383.1 ENSP00000375076 Q9BYR3 UPI000006DEC1 NM_032524.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF57 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 41160264 41160264 G T 1 0 0 0 0 1 0 0 0 8447 1261 44 2 2 KRTAP4-4 17 41160264 Missense_Mutation SNP G C3N-00560_T 58288 41160264 42097177 1027 17716 KRT33A 0 . GRCh38 17 41347065 41347065 + Missense_Mutation SNP G G T rs151338884 C3N-00560_T C3N-00560_N G G c.746C>A p.Thr249Lys p.T249K ENST00000007735 4/7 108 72 36 91 91 0 strelka-varscan-mutect KRT33A,missense_variant,p.Thr249Lys,ENST00000007735,NM_004138.3; T ENST00000007735 Transcript missense_variant 791/1287 746/1215 249/404 T/K aCg/aAg rs151338884 1 -1 KRT33A HGNC HGNC:6450 protein_coding YES CCDS11388.1 ENSP00000007735 O76009 UPI000013C503 NM_004138.3 tolerated(0.11) 4/7 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF98,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs151338884 . 0 201 9 0 0 0 0 0 -20 0.9999987 1 1 1 0 T 3 4 56 41347065 41347065 G T 1 0 0 0 0 1 0 0 0 8351 1159 40 1 1 KRT33A 17 41347065 Missense_Mutation SNP G C3N-00560_T 186801 41347065 41910376 1028 17717 KRT31 0 . GRCh38 17 41394934 41394934 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.1011G>A p.= p.Q337Q ENST00000251645 6/7 502 388 114 403 403 0 strelka-varscan-mutect KRT31,synonymous_variant,p.=,ENST00000251645,NM_002277.2; T ENST00000251645 Transcript synonymous_variant 1064/1596 1011/1251 337/416 Q caG/caA 1 -1 KRT31 HGNC HGNC:6448 protein_coding YES CCDS11391.1 ENSP00000251645 Q15323 UPI000006F564 NM_002277.2 6/7 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF99,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 41394934 41394934 C T 1 0 0 0 0 0 0 0 1 8349 680 24 3 3 KRT31 17 41394934 Silent SNP C C3N-00560_T 47869 41394934 41862507 1029 17718 KRT31 0 . GRCh38 17 41395299 41395299 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.822G>T p.Glu274Asp p.E274D ENST00000251645 5/7 354 272 82 314 314 0 strelka-varscan-mutect KRT31,missense_variant,p.Glu274Asp,ENST00000251645,NM_002277.2; A ENST00000251645 Transcript missense_variant 875/1596 822/1251 274/416 E/D gaG/gaT 1 -1 KRT31 HGNC HGNC:6448 protein_coding YES CCDS11391.1 ENSP00000251645 Q15323 UPI000006F564 NM_002277.2 tolerated(0.17) 5/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF99,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 41395299 41395299 C A 1 0 0 0 0 1 0 0 0 8349 796 28 2 2 KRT31 17 41395299 Missense_Mutation SNP C C3N-00560_T 365 41395299 41862142 1030 17719 KRT37 0 . GRCh38 17 41424238 41424238 + Missense_Mutation SNP C C G rs759503740 C3N-00560_T C3N-00560_N C C c.286G>C p.Gly96Arg p.G96R ENST00000225550 1/7 661 481 180 538 538 0 strelka-varscan-mutect KRT37,missense_variant,p.Gly96Arg,ENST00000225550,NM_003770.4;AC003958.2,non_coding_transcript_exon_variant,,ENST00000432258,; G ENST00000225550 Transcript missense_variant 286/1475 286/1350 96/449 G/R Ggc/Cgc rs759503740 1 -1 KRT37 HGNC HGNC:6455 protein_coding YES CCDS32653.1 ENSP00000225550 O76014 UPI000000DC9A NM_003770.4 tolerated(0.36) 1/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF197 MODERATE 1 SNV 1 1 PASS rs759503740 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 41424238 41424238 C G 1 0 0 0 0 1 0 0 0 8356 652 23 4 4 KRT37 17 41424238 Missense_Mutation SNP C C3N-00560_T 28939 41424238 41833203 1031 17720 KRT36 0 . GRCh38 17 41489699 41489699 + Missense_Mutation SNP G G T rs759806098 C3N-00560_T C3N-00560_N G G c.166C>A p.Leu56Ile p.L56I ENST00000328119 1/7 556 393 163 475 475 0 strelka-varscan-mutect KRT36,missense_variant,p.Leu6Ile,ENST00000393986,;KRT36,missense_variant,p.Leu56Ile,ENST00000328119,NM_003771.4; T ENST00000328119 Transcript missense_variant 166/1644 166/1404 56/467 L/I Ctc/Atc rs759806098 1 -1 KRT36 HGNC HGNC:6454 protein_coding YES CCDS11395.1 ENSP00000329165 O76013 UPI000012DAFA NM_003771.4 tolerated(0.42) 1/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF193,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 41489699 41489699 G T 1 0 0 0 0 1 0 0 0 8355 1000 35 2 2 KRT36 17 41489699 Missense_Mutation SNP G C3N-00560_T 65461 41489699 41767742 1032 17721 ATXN7L3 0 . GRCh38 17 44194622 44194622 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.811G>C p.Asp271His p.D271H ENST00000454077 11/12 202 147 55 168 168 0 strelka-varscan-mutect ATXN7L3,missense_variant,p.Asp264His,ENST00000389384,NM_001098833.1;ATXN7L3,missense_variant,p.Asp271His,ENST00000454077,NM_020218.1;ATXN7L3,missense_variant,p.Asp103His,ENST00000591295,;ATXN7L3,missense_variant,p.Asp264His,ENST00000587097,;ATXN7L3,missense_variant,p.Asp46His,ENST00000590537,;TMUB2,downstream_gene_variant,,ENST00000319511,NM_177441.2;TMUB2,downstream_gene_variant,,ENST00000592825,;TMUB2,downstream_gene_variant,,ENST00000587989,;TMUB2,downstream_gene_variant,,ENST00000538716,NM_001076674.1;TMUB2,downstream_gene_variant,,ENST00000357984,NM_024107.2;TMUB2,downstream_gene_variant,,ENST00000589785,;TMUB2,downstream_gene_variant,,ENST00000589184,;TMUB2,downstream_gene_variant,,ENST00000587172,;TMUB2,downstream_gene_variant,,ENST00000446571,;TMUB2,downstream_gene_variant,,ENST00000590235,;TMUB2,downstream_gene_variant,,ENST00000589856,;TMUB2,downstream_gene_variant,,ENST00000587630,;ATXN7L3,downstream_gene_variant,,ENST00000589805,;ATXN7L3,downstream_gene_variant,,ENST00000590169,;CTB-175E5.7,upstream_gene_variant,,ENST00000586560,;ATXN7L3,non_coding_transcript_exon_variant,,ENST00000593073,;ATXN7L3,non_coding_transcript_exon_variant,,ENST00000586688,;TMUB2,downstream_gene_variant,,ENST00000587326,;TMUB2,downstream_gene_variant,,ENST00000588413,;ATXN7L3,downstream_gene_variant,,ENST00000589607,;TMUB2,downstream_gene_variant,,ENST00000587775,;ATXN7L3,downstream_gene_variant,,ENST00000591807,;ATXN7L3,downstream_gene_variant,,ENST00000587022,; G ENST00000454077 Transcript missense_variant 811/3523 811/1065 271/354 D/H Gac/Cac 1 -1 ATXN7L3 HGNC HGNC:25416 protein_coding YES CCDS45697.1 ENSP00000397259 Q14CW9 UPI00001613AC NM_020218.1 deleterious(0) 11/12 hmmpanther:PTHR15117,hmmpanther:PTHR15117:SF10 MODERATE 1 SNV 1 1 PASS rs1308317354 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 44194622 44194622 C G 1 0 0 0 0 1 0 0 0 1372 826 29 4 4 ATXN7L3 17 44194622 Missense_Mutation SNP C C3N-00560_T 2704923 44194622 39062819 1033 17722 ITGA2B 0 . GRCh38 17 44375667 44375667 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2651A>T p.His884Leu p.H884L ENST00000262407 26/30 152 115 37 136 136 0 strelka-varscan-mutect ITGA2B,missense_variant,p.His884Leu,ENST00000262407,NM_000419.3;ITGA2B,intron_variant,,ENST00000587295,;ITGA2B,upstream_gene_variant,,ENST00000588098,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592462,;ITGA2B,downstream_gene_variant,,ENST00000592226,; A ENST00000262407 Transcript missense_variant 2683/3333 2651/3120 884/1039 H/L cAt/cTt 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 tolerated(0.11) 26/30 Low_complexity_(Seg):seg,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Gene3D:1jv2A04,Pfam_domain:PF08441,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44375667 44375667 T A 1 0 0 0 0 1 0 0 0 7783 1464 51 4 4 ITGA2B 17 44375667 Missense_Mutation SNP T C3N-00560_T 181045 44375667 38881774 1034 17723 ADAM11 0 . GRCh38 17 44776796 44776796 + Splice_Site SNP G G T rs780946704 C3N-00560_T C3N-00560_N G G c.1617+1G>T p.X539_splice ENST00000200557 222 158 64 156 156 0 strelka-varscan-mutect ADAM11,splice_donor_variant,,ENST00000200557,NM_001318933.1,NM_002390.4;ADAM11,splice_donor_variant,,ENST00000535346,;ADAM11,splice_donor_variant,,ENST00000355638,;ADAM11,splice_donor_variant,,ENST00000587773,;ADAM11,splice_donor_variant,,ENST00000588363,; T ENST00000200557 Transcript splice_donor_variant -/4571 1617/2310 539/769 rs780946704 1 1 ADAM11 HGNC HGNC:189 protein_coding YES CCDS11486.1 ENSP00000200557 O75078 UPI000013C629 NM_001318933.1,NM_002390.4 19/26 HIGH 1 SNV 1 1 PASS rs780946704 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 44776796 44776796 G T 1 0 0 0 0 0 0 1 0 279 1275 44 2 2 ADAM11 17 44776796 Splice_Site SNP G C3N-00560_T 401129 44776796 38480645 1035 17724 MAPT 0 . GRCh38 17 45996566 45996566 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1729C>A p.Arg577Ser p.R577S ENST00000344290 11/15 518 401 117 458 458 0 strelka-varscan-mutect MAPT,missense_variant,p.Arg577Ser,ENST00000344290,NM_001123066.3;MAPT,missense_variant,p.Arg559Ser,ENST00000262410,NM_016835.4;MAPT,missense_variant,p.Arg242Ser,ENST00000351559,NM_005910.5;MAPT,missense_variant,p.Arg213Ser,ENST00000340799,NM_001123067.3;MAPT,missense_variant,p.Arg242Ser,ENST00000535772,NM_001203251.1,NM_001203252.1;MAPT,missense_variant,p.Arg184Ser,ENST00000446361,NM_016834.4;MAPT,missense_variant,p.Arg577Ser,ENST00000415613,;MAPT,missense_variant,p.Arg559Ser,ENST00000571987,;MAPT,missense_variant,p.Arg242Ser,ENST00000574436,;MAPT,missense_variant,p.Arg213Ser,ENST00000420682,;MAPT,missense_variant,p.Arg242Ser,ENST00000431008,;MAPT,missense_variant,p.Arg184Ser,ENST00000334239,NM_016841.4;STH,upstream_gene_variant,,ENST00000537309,NM_001007532.2;MAPT,non_coding_transcript_exon_variant,,ENST00000570299,;MAPT,non_coding_transcript_exon_variant,,ENST00000576518,; A ENST00000344290 Transcript missense_variant 2051/6816 1729/2331 577/776 R/S Cgc/Agc 1 1 MAPT HGNC HGNC:6893 protein_coding YES CCDS45715.1 ENSP00000340820 P10636 UPI0001AE66E9 NM_001123066.3 deleterious(0) 11/15 hmmpanther:PTHR11501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45996566 45996566 C A 1 0 0 0 0 1 0 0 0 9220 652 23 1 1 MAPT 17 45996566 Missense_Mutation SNP C C3N-00560_T 1219770 45996566 37260875 1036 17725 GNGT2 0 . GRCh38 17 49206768 49206768 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.199C>A p.Leu67Met p.L67M ENST00000511277 4/4 116 73 43 73 73 0 strelka-varscan-mutect GNGT2,missense_variant,p.Leu67Met,ENST00000511277,NM_001198756.1;GNGT2,missense_variant,p.Leu67Met,ENST00000300406,NM_031498.2,NM_001198755.1;GNGT2,missense_variant,p.Leu67Met,ENST00000515635,;GNGT2,missense_variant,p.Leu67Met,ENST00000507680,NM_001198754.1;GNGT2,missense_variant,p.Leu67Met,ENST00000511673,;GNGT2,intron_variant,,ENST00000503070,;ABI3,upstream_gene_variant,,ENST00000225941,NM_016428.2;ABI3,upstream_gene_variant,,ENST00000419580,NM_001135186.1; T ENST00000511277 Transcript missense_variant 379/918 199/210 67/69 L/M Ctg/Atg 1 -1 GNGT2 HGNC HGNC:4412 protein_coding YES CCDS11545.1 ENSP00000426022 O14610 UPI000012B236 NM_001198756.1 tolerated(0.24) 4/4 Gene3D:4.10.260.10,Pfam_domain:PF00631,PROSITE_profiles:PS50058,hmmpanther:PTHR13809,hmmpanther:PTHR13809:SF28,SMART_domains:SM00224,SMART_domains:SM01224 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 49206768 49206768 G T 1 0 0 0 0 1 0 0 0 6413 933 33 2 2 GNGT2 17 49206768 Missense_Mutation SNP G C3N-00560_T 3210202 49206768 34050673 1037 17726 ZNF652 0 . GRCh38 17 49317229 49317229 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.497G>T p.Ser166Ile p.S166I ENST00000362063 2/6 343 255 88 336 335 1 strelka-varscan-mutect ZNF652,missense_variant,p.Ser166Ile,ENST00000362063,NM_014897.2;ZNF652,missense_variant,p.Ser166Ile,ENST00000430262,NM_001145365.1;ZNF652,intron_variant,,ENST00000508237,; A ENST00000362063 Transcript missense_variant 816/5988 497/1821 166/606 S/I aGc/aTc 1 -1 ZNF652 HGNC HGNC:29147 protein_coding YES CCDS32677.1 ENSP00000354686 Q9Y2D9 UPI000006D93D NM_014897.2 tolerated(0.11) 2/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 49317229 49317229 C A 1 0 0 0 0 1 0 0 0 18638 797 28 2 2 ZNF652 17 49317229 Missense_Mutation SNP C C3N-00560_T 110461 49317229 33940212 1038 17727 FAM117A 0 . GRCh38 17 49717696 49717696 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.727G>C p.Gly243Arg p.G243R ENST00000240364 6/8 64 29 35 63 63 0 strelka-varscan-mutect FAM117A,missense_variant,p.Gly243Arg,ENST00000240364,NM_030802.3;FAM117A,missense_variant,p.Gly133Arg,ENST00000511743,;FAM117A,missense_variant,p.Gly211Arg,ENST00000506156,;FAM117A,5_prime_UTR_variant,,ENST00000513602,;RP11-613C6.2,intron_variant,,ENST00000512720,;FAM117A,non_coding_transcript_exon_variant,,ENST00000514018,;FAM117A,non_coding_transcript_exon_variant,,ENST00000505159,;FAM117A,non_coding_transcript_exon_variant,,ENST00000515240,;FAM117A,non_coding_transcript_exon_variant,,ENST00000503855,;FAM117A,downstream_gene_variant,,ENST00000509347,;FAM117A,downstream_gene_variant,,ENST00000503720,;FAM117A,3_prime_UTR_variant,,ENST00000503573,;FAM117A,downstream_gene_variant,,ENST00000514841,; G ENST00000240364 Transcript missense_variant 807/2365 727/1362 243/453 G/R Ggg/Cgg 1 -1 FAM117A HGNC HGNC:24179 protein_coding YES CCDS11553.1 ENSP00000240364 Q9C073 UPI00000503DC NM_030802.3 deleterious(0.01) 6/8 Pfam_domain:PF15388,hmmpanther:PTHR14972,hmmpanther:PTHR14972:SF7 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 49717696 49717696 C G 1 0 0 0 0 1 0 0 0 5268 594 21 4 4 FAM117A 17 49717696 Missense_Mutation SNP C C3N-00560_T 400467 49717696 33539745 1039 17728 ACSF2 0 . GRCh38 17 50461308 50461308 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.466G>C p.Gly156Arg p.G156R ENST00000427954 4/17 332 240 92 344 344 0 strelka-varscan-mutect ACSF2,missense_variant,p.Gly156Arg,ENST00000427954,NM_001288968.1;ACSF2,missense_variant,p.Gly131Arg,ENST00000300441,NM_025149.5;ACSF2,missense_variant,p.Gly131Arg,ENST00000502667,NM_001288969.1;ACSF2,intron_variant,,ENST00000504392,NM_001288972.1,NM_001288970.1,NM_001288971.1;ACSF2,intron_variant,,ENST00000506582,;CHAD,downstream_gene_variant,,ENST00000508540,NM_001267.2;CHAD,downstream_gene_variant,,ENST00000258969,;CHAD,downstream_gene_variant,,ENST00000506187,;ACSF2,upstream_gene_variant,,ENST00000509806,;ACSF2,non_coding_transcript_exon_variant,,ENST00000570356,;ACSF2,intron_variant,,ENST00000510410,;ACSF2,upstream_gene_variant,,ENST00000506052,;ACSF2,upstream_gene_variant,,ENST00000508245,;ACSF2,upstream_gene_variant,,ENST00000507769,;ACSF2,upstream_gene_variant,,ENST00000513101,;ACSF2,downstream_gene_variant,,ENST00000503408,;ACSF2,downstream_gene_variant,,ENST00000504945,;ACSF2,upstream_gene_variant,,ENST00000510262,; C ENST00000427954 Transcript missense_variant 509/2251 466/1923 156/640 G/R Gga/Cga 1 1 ACSF2 HGNC HGNC:26101 protein_coding YES CCDS74103.1 ENSP00000401831 Q96CM8 UPI00017A6F63 NM_001288968.1 deleterious(0.01) 4/17 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,Superfamily_domains:SSF56801 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 50461308 50461308 G C 1 0 0 0 0 1 0 0 0 217 1233 43 4 4 ACSF2 17 50461308 Missense_Mutation SNP G C3N-00560_T 743612 50461308 32796133 1040 17729 CACNA1G 0 . GRCh38 17 50572622 50572622 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.815C>A p.Ser272Tyr p.S272Y ENST00000359106 6/38 95 62 33 86 86 0 strelka-varscan-mutect CACNA1G,missense_variant,p.Ser272Tyr,ENST00000354983,NM_198396.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000352832,NM_198387.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000359106,NM_018896.4;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000360761,NM_198382.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000442258,NM_198388.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000429973,NM_198386.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000507336,NM_198377.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000358244,NM_198376.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000507510,NM_198385.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000515765,NM_198380.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000515411,NM_001256324.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000502264,NM_198383.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000510115,NM_198379.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000514079,NM_001256325.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000513689,NM_001256326.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000515165,NM_198384.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000507609,NM_001256327.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000512389,NM_198378.2;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000514181,NM_001256328.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000510366,NM_001256331.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000514717,NM_001256332.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000505165,NM_001256333.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000507896,NM_001256334.1;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000416767,;CACNA1G,missense_variant,p.Ser154Tyr,ENST00000570567,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000506406,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000504076,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000511765,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000503436,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000511768,;CACNA1G,missense_variant,p.Ser272Tyr,ENST00000503607,; A ENST00000359106 Transcript missense_variant 815/7648 815/7134 272/2377 S/Y tCc/tAc 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 deleterious(0) 6/38 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 50572622 50572622 C A 1 0 0 0 0 1 0 0 0 2232 855 30 2 2 CACNA1G 17 50572622 Missense_Mutation SNP C C3N-00560_T 111314 50572622 32684819 1041 17730 CACNA1G 0 . GRCh38 17 50606974 50606974 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.4497G>T p.= p.V1499V ENST00000359106 24/38 571 387 184 463 463 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CACNA1G,synonymous_variant,p.=,ENST00000506520,;CACNA1G,downstream_gene_variant,,ENST00000416767,;CACNA1G,synonymous_variant,p.=,ENST00000506406,;CACNA1G,synonymous_variant,p.=,ENST00000504076,;CACNA1G,synonymous_variant,p.=,ENST00000511765,;CACNA1G,synonymous_variant,p.=,ENST00000503436,;CACNA1G,synonymous_variant,p.=,ENST00000511768,;CACNA1G,synonymous_variant,p.=,ENST00000503607,; T ENST00000359106 Transcript synonymous_variant 4497/7648 4497/7134 1499/2377 V gtG/gtT 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 24/38 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 50606974 50606974 G T 1 0 0 0 0 0 0 0 1 2232 1335 47 2 2 CACNA1G 17 50606974 Silent SNP G C3N-00560_T 34352 50606974 32650467 1042 17731 MKS1 0 . GRCh38 17 58210726 58210726 + Splice_Site SNP T T A novel C3N-00560_T C3N-00560_N T T c.959-2A>T p.X320_splice ENST00000393119 494 358 136 437 437 0 strelka-varscan-mutect MKS1,splice_acceptor_variant,,ENST00000393119,NM_017777.3;MKS1,splice_acceptor_variant,,ENST00000313863,;MKS1,splice_acceptor_variant,,ENST00000537529,NM_001165927.1;MKS1,splice_acceptor_variant,,ENST00000577824,;MKS1,splice_acceptor_variant,,ENST00000585134,;MKS1,splice_acceptor_variant,,ENST00000577315,;MKS1,splice_acceptor_variant,,ENST00000393120,;MKS1,splice_acceptor_variant,,ENST00000581761,;MKS1,non_coding_transcript_exon_variant,,ENST00000579358,;MKS1,downstream_gene_variant,,ENST00000581180,;MKS1,downstream_gene_variant,,ENST00000580127,;MKS1,upstream_gene_variant,,ENST00000583577,;MKS1,downstream_gene_variant,,ENST00000578789,; A ENST00000393119 Transcript splice_acceptor_variant -/2397 959/1680 320/559 1 -1 MKS1 HGNC HGNC:7121 protein_coding YES CCDS11603.2 ENSP00000376827 Q9NXB0 UPI00002010BB NM_017777.3 10/17 HIGH 1 SNV 1 1 PASS rs1273591389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 58210726 58210726 T A 1 0 0 0 0 0 0 1 0 9577 1536 53 4 4 MKS1 17 58210726 Splice_Site SNP T C3N-00560_T 7603752 58210726 25046715 1043 17732 MPO 0 . GRCh38 17 58273466 58273466 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1569C>A p.= p.P523P ENST00000225275 9/12 473 323 150 348 347 1 strelka-varscan-mutect MPO,synonymous_variant,p.=,ENST00000225275,NM_000250.1;MPO,synonymous_variant,p.=,ENST00000577220,;LPO,downstream_gene_variant,,ENST00000262290,NM_006151.2;LPO,downstream_gene_variant,,ENST00000421678,NM_001160102.1;MPO,downstream_gene_variant,,ENST00000578493,;LPO,downstream_gene_variant,,ENST00000389576,; T ENST00000225275 Transcript synonymous_variant 1746/3215 1569/2238 523/745 P ccC/ccA 1 -1 MPO HGNC HGNC:7218 protein_coding YES CCDS11604.1 ENSP00000225275 P05164 UPI0000131634 NM_000250.1 9/12 PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 LOW 1 SNV 1 1 PASS rs963955387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 58273466 58273466 G T 1 0 0 0 0 0 0 0 1 9698 1219 43 2 2 MPO 17 58273466 Silent SNP G C3N-00560_T 62740 58273466 24983975 1044 17733 TSPOAP1 0 . GRCh38 17 58316079 58316079 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.2042C>T p.Thr681Ile p.T681I ENST00000343736 16/32 340 259 81 299 299 0 strelka-varscan-mutect TSPOAP1,missense_variant,p.Thr621Ile,ENST00000268893,NM_024418.2;TSPOAP1,missense_variant,p.Thr681Ile,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1,upstream_gene_variant,,ENST00000585149,; A ENST00000343736 Transcript missense_variant 2206/5947 2042/5574 681/1857 T/I aCa/aTa 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 deleterious(0.01) 16/32 Gene3D:2.30.30.40,Pfam_domain:PF14604,PROSITE_profiles:PS50002,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 58316079 58316079 G A 1 0 0 0 0 1 0 0 0 17163 1377 48 3 3 TSPOAP1 17 58316079 Missense_Mutation SNP G C3N-00560_T 42613 58316079 24941362 1045 17734 HSF5 0 . GRCh38 17 58488206 58488206 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.69C>A p.Asn23Lys p.N23K ENST00000323777 1/6 58 46 12 33 33 0 strelka-varscan-mutect HSF5,missense_variant,p.Asn23Lys,ENST00000323777,NM_001080439.2;HSF5,missense_variant,p.Asn23Lys,ENST00000617946,;MTMR4,downstream_gene_variant,,ENST00000323456,NM_004687.4;MTMR4,downstream_gene_variant,,ENST00000579925,;MTMR4,downstream_gene_variant,,ENST00000578259,; T ENST00000323777 Transcript missense_variant 179/4094 69/1791 23/596 N/K aaC/aaA 1 -1 HSF5 HGNC HGNC:26862 protein_coding YES CCDS32690.1 ENSP00000313243 Q4G112 UPI000056D414 NM_001080439.2 deleterious(0) 1/6 Gene3D:1.10.10.10,Pfam_domain:PF00447,hmmpanther:PTHR10015,hmmpanther:PTHR10015:SF138,SMART_domains:SM00415,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 58488206 58488206 G T 1 0 0 0 0 1 0 0 0 7293 1368 48 2 2 HSF5 17 58488206 Missense_Mutation SNP G C3N-00560_T 172127 58488206 24769235 1046 17735 RAD51C 0 . GRCh38 17 58709949 58709949 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.796G>T p.Ala266Ser p.A266S ENST00000337432 5/9 413 299 114 308 308 0 strelka-varscan-mutect RAD51C,missense_variant,p.Ala266Ser,ENST00000337432,NM_058216.2;RAD51C,missense_variant,p.Ala266Ser,ENST00000583539,;RAD51C,missense_variant,p.Ala146Ser,ENST00000413590,;RAD51C,missense_variant,p.Ala31Ser,ENST00000584804,;RAD51C,downstream_gene_variant,,ENST00000461271,;RAD51C,downstream_gene_variant,,ENST00000425173,;RAD51C,downstream_gene_variant,,ENST00000487921,;RAD51C,3_prime_UTR_variant,,ENST00000475762,;RAD51C,3_prime_UTR_variant,,ENST00000487525,;RAD51C,3_prime_UTR_variant,,ENST00000482007,;RAD51C,3_prime_UTR_variant,,ENST00000584617,;RAD51C,non_coding_transcript_exon_variant,,ENST00000581221,;RAD51C,non_coding_transcript_exon_variant,,ENST00000578151,; T ENST00000337432 Transcript missense_variant 867/2591 796/1131 266/376 A/S Gcc/Tcc 1 1 RAD51C HGNC HGNC:9820 protein_coding YES CCDS11611.1 ENSP00000336701 O43502 UPI0000133007 NM_058216.2 tolerated(0.17) 5/9 PROSITE_profiles:PS50162,hmmpanther:PTHR22942:SF14,hmmpanther:PTHR22942,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005856,Pfam_domain:PF08423,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 58709949 58709949 G T 1 0 0 0 0 1 0 0 0 13150 971 34 2 2 RAD51C 17 58709949 Missense_Mutation SNP G C3N-00560_T 221743 58709949 24547492 1047 17736 TRIM37 0 . GRCh38 17 59070949 59070949 + Splice_Site SNP T T A novel C3N-00560_T C3N-00560_N T T c.685-2A>T p.X229_splice ENST00000262294 211 155 56 217 217 0 strelka-varscan-mutect TRIM37,splice_acceptor_variant,,ENST00000262294,NM_015294.3;TRIM37,splice_acceptor_variant,,ENST00000393066,NM_001005207.2;TRIM37,splice_acceptor_variant,,ENST00000393065,;TRIM37,splice_acceptor_variant,,ENST00000581468,;TRIM37,splice_acceptor_variant,,ENST00000577554,NM_001320990.1;TRIM37,splice_acceptor_variant,,ENST00000582852,;TRIM37,downstream_gene_variant,,ENST00000580973,; A ENST00000262294 Transcript splice_acceptor_variant -/4330 685/2895 229/964 1 -1 TRIM37 HGNC HGNC:7523 protein_coding YES CCDS32694.1 ENSP00000262294 O94972 UPI0000167B57 NM_015294.3 8/23 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 59070949 59070949 T A 1 0 0 0 0 0 0 1 0 17000 1594 55 4 4 TRIM37 17 59070949 Splice_Site SNP T C3N-00560_T 361000 59070949 24186492 1048 17737 USP32 0 . GRCh38 17 60219751 60219751 + Nonsense_Mutation SNP C C A rs768692573 C3N-00560_T C3N-00560_N C C c.1786G>T p.Glu596Ter p.E596* ENST00000300896 16/34 125 66 59 141 141 0 strelka-varscan-mutect USP32,stop_gained,p.Glu596Ter,ENST00000300896,NM_032582.3;USP32,stop_gained,p.Glu266Ter,ENST00000592339,;USP32,stop_gained,p.Glu593Ter,ENST00000590133,;USP32,stop_gained,p.Glu127Ter,ENST00000591768,;USP32,3_prime_UTR_variant,,ENST00000589552,;USP32,non_coding_transcript_exon_variant,,ENST00000587651,; A ENST00000300896 Transcript stop_gained 1981/5171 1786/4815 596/1604 E/* Gaa/Taa rs768692573 1 -1 USP32 HGNC HGNC:19143 protein_coding YES CCDS32697.1 ENSP00000300896 Q8NFA0 UPI0000047AF8 NM_032582.3 16/34 Gene3D:3jyuB01 HIGH 1 SNV 1 1 PASS rs768692573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 60219751 60219751 C A 1 0 0 0 0 0 1 0 0 17605 864 30 2 2 USP32 17 60219751 Nonsense_Mutation SNP C C3N-00560_T 1148802 60219751 23037690 1049 17738 RGS9 0 . GRCh38 17 65225120 65225120 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1526C>T p.Ser509Leu p.S509L ENST00000262406 18/19 152 76 76 206 206 0 strelka-varscan-mutect RGS9,missense_variant,p.Ser506Leu,ENST00000449996,NM_001081955.2;RGS9,missense_variant,p.Ser509Leu,ENST00000262406,NM_003835.3;RGS9,missense_variant,p.Ser509Leu,ENST00000635833,;RGS9,missense_variant,p.Ser506Leu,ENST00000443584,NM_001165933.1;RGS9,3_prime_UTR_variant,,ENST00000584234,;RGS9,non_coding_transcript_exon_variant,,ENST00000577595,; T ENST00000262406 Transcript missense_variant 1593/2375 1526/2025 509/674 S/L tCa/tTa 1 1 RGS9 HGNC HGNC:10004 protein_coding YES CCDS42373.1 ENSP00000262406 O75916 UPI000013382A NM_003835.3 tolerated_low_confidence(0.11) 18/19 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF170 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 65225120 65225120 C T 1 0 0 0 0 1 0 0 0 13484 838 29 3 3 RGS9 17 65225120 Missense_Mutation SNP C C3N-00560_T 5005369 65225120 18032321 1050 17739 SDK2 0 . GRCh38 17 73394245 73394245 + Silent SNP G G C rs371857762 C3N-00560_T C3N-00560_N G G c.3672C>G p.= p.P1224P ENST00000392650 26/45 34 17 17 52 52 0 strelka-varscan-mutect SDK2,synonymous_variant,p.=,ENST00000392650,NM_001144952.1;SDK2,synonymous_variant,p.=,ENST00000424778,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; C ENST00000392650 Transcript synonymous_variant 3673/10723 3672/6519 1224/2172 P ccC/ccG rs371857762 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 26/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs371857762 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 73394245 73394245 G C 1 0 0 0 0 0 0 0 1 14244 1103 39 4 4 SDK2 17 73394245 Silent SNP G C3N-00560_T 8169125 73394245 9863196 1051 17740 KIF19 0 . GRCh38 17 74353506 74353506 + Missense_Mutation SNP G G T rs753223269 C3N-00560_T C3N-00560_N G G c.2233G>T p.Asp745Tyr p.D745Y ENST00000389916 17/20 258 148 110 308 308 0 strelka-varscan-mutect KIF19,missense_variant,p.Asp745Tyr,ENST00000389916,NM_153209.3;KIF19,downstream_gene_variant,,ENST00000551294,;BTBD17,downstream_gene_variant,,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000547389,;KIF19,downstream_gene_variant,,ENST00000359939,;KIF19,downstream_gene_variant,,ENST00000549637,; T ENST00000389916 Transcript missense_variant 2371/3643 2233/2997 745/998 D/Y Gac/Tac rs753223269 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 tolerated(0.08) 17/20 MODERATE SNV 5 1 PASS rs753223269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 74353506 74353506 G T 1 0 0 0 0 1 0 0 0 8146 1174 41 2 2 KIF19 17 74353506 Missense_Mutation SNP G C3N-00560_T 959261 74353506 8903935 1052 17741 TSEN54 0 . GRCh38 17 75521906 75521906 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.825G>T p.= p.V275V ENST00000333213 8/11 257 133 124 275 275 0 strelka-varscan-mutect TSEN54,synonymous_variant,p.=,ENST00000333213,NM_207346.2;LLGL2,upstream_gene_variant,,ENST00000392550,NM_001031803.1;LLGL2,upstream_gene_variant,,ENST00000167462,NM_004524.2;LLGL2,upstream_gene_variant,,ENST00000578363,;LLGL2,upstream_gene_variant,,ENST00000375227,NM_001015002.1;TSEN54,upstream_gene_variant,,ENST00000545228,;TSEN54,downstream_gene_variant,,ENST00000434205,;LLGL2,upstream_gene_variant,,ENST00000580578,;LLGL2,upstream_gene_variant,,ENST00000579392,;TSEN54,downstream_gene_variant,,ENST00000580013,;TSEN54,3_prime_UTR_variant,,ENST00000578415,;TSEN54,intron_variant,,ENST00000583173,;TSEN54,upstream_gene_variant,,ENST00000579449,;TSEN54,downstream_gene_variant,,ENST00000583818,;TSEN54,downstream_gene_variant,,ENST00000583454,;TSEN54,upstream_gene_variant,,ENST00000577197,;TSEN54,downstream_gene_variant,,ENST00000583634,; T ENST00000333213 Transcript synonymous_variant 861/1944 825/1581 275/526 V gtG/gtT 1 1 TSEN54 HGNC HGNC:27561 protein_coding YES CCDS11724.1 ENSP00000327487 Q7Z6J9 UPI00001C1FD2 NM_207346.2 8/11 hmmpanther:PTHR21027 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 75521906 75521906 G T 1 0 0 0 0 0 0 0 1 17120 1335 47 2 2 TSEN54 17 75521906 Silent SNP G C3N-00560_T 1168400 75521906 7735535 1053 17742 MRPL38 0 . GRCh38 17 75902025 75902025 + Missense_Mutation SNP C C A rs200385750 C3N-00560_T C3N-00560_N C C c.377G>T p.Arg126Leu p.R126L ENST00000309352 3/9 105 59 46 113 113 0 strelka-varscan-mutect MRPL38,missense_variant,p.Arg126Leu,ENST00000309352,NM_032478.3;RP11-552F3.10,downstream_gene_variant,,ENST00000587267,;MRPL38,non_coding_transcript_exon_variant,,ENST00000585475,;MRPL38,downstream_gene_variant,,ENST00000410030,;MRPL38,upstream_gene_variant,,ENST00000480203,;MRPL38,upstream_gene_variant,,ENST00000588620,;MRPL38,upstream_gene_variant,,ENST00000477023,;RP11-552F3.12,3_prime_UTR_variant,,ENST00000590947,;RP11-552F3.12,non_coding_transcript_exon_variant,,ENST00000593156,;MRPL38,non_coding_transcript_exon_variant,,ENST00000493104,;MRPL38,non_coding_transcript_exon_variant,,ENST00000461602,;MRPL38,non_coding_transcript_exon_variant,,ENST00000494179,;MRPL38,non_coding_transcript_exon_variant,,ENST00000477736,;MRPL38,non_coding_transcript_exon_variant,,ENST00000464758,;MRPL38,non_coding_transcript_exon_variant,,ENST00000493383,;MRPL38,non_coding_transcript_exon_variant,,ENST00000474548,;MRPL38,upstream_gene_variant,,ENST00000486101,;MRPL38,upstream_gene_variant,,ENST00000477371,;MRPL38,upstream_gene_variant,,ENST00000471434,;RP11-552F3.12,downstream_gene_variant,,ENST00000587556,;MRPL38,upstream_gene_variant,,ENST00000483393,; A ENST00000309352 Transcript missense_variant 915/1888 377/1143 126/380 R/L cGc/cTc rs200385750,COSM5513362 1 -1 MRPL38 HGNC HGNC:14033 protein_coding YES CCDS11733.2 ENSP00000308275 Q96DV4 UPI0000038D66 NM_032478.3 tolerated(0.1) 3/9 hmmpanther:PTHR11362,hmmpanther:PTHR11362:SF6 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200385750 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 75902025 75902025 C A 1 0 0 0 0 1 0 0 0 9776 782 27 1 1 MRPL38 17 75902025 Missense_Mutation SNP C C3N-00560_T 380119 75902025 7355416 1054 17743 RPTOR 0 . GRCh38 17 80923558 80923558 + Missense_Mutation SNP G G T rs780000343 C3N-00560_T C3N-00560_N G G c.2693G>T p.Ser898Ile p.S898I ENST00000306801 23/34 287 153 134 329 329 0 strelka-varscan-mutect RPTOR,missense_variant,p.Ser898Ile,ENST00000306801,NM_020761.2;RPTOR,missense_variant,p.Ser740Ile,ENST00000544334,NM_001163034.1;RPTOR,missense_variant,p.Ser58Ile,ENST00000576366,;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,; T ENST00000306801 Transcript missense_variant 3055/6408 2693/4008 898/1335 S/I aGc/aTc rs780000343 1 1 RPTOR HGNC HGNC:30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 UPI000007000F NM_020761.2 deleterious(0.02) 23/34 hmmpanther:PTHR12848 MODERATE 1 SNV 1 1 PASS rs780000343 . 0 208 0 0 2 0 0 0 -20 0.9995972 1 1 1 0 T 3 4 56 80923558 80923558 G T 1 0 0 0 0 1 0 0 0 13920 971 34 2 2 RPTOR 17 80923558 Missense_Mutation SNP G C3N-00560_T 5021533 80923558 2333883 1055 17744 BAHCC1 0 . GRCh38 17 81447569 81447569 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.3790G>C p.Gly1264Arg p.G1264R ENST00000584436 12/29 272 138 134 281 281 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Gly1264Arg,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Gly1233Arg,ENST00000307745,;MIR3186,downstream_gene_variant,,ENST00000577404,;BAHCC1,downstream_gene_variant,,ENST00000585224,; C ENST00000584436 Transcript missense_variant 4157/10801 3790/7920 1264/2639 G/R Ggg/Cgg 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 tolerated(0.45) 12/29 Low_complexity_(Seg):seg,hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 81447569 81447569 G C 1 0 0 0 0 1 0 0 0 1451 1232 43 4 4 BAHCC1 17 81447569 Missense_Mutation SNP G C3N-00560_T 524011 81447569 1809872 1056 17745 ADCYAP1 0 . GRCh38 18 907764 907764 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.216C>A p.= p.A72A ENST00000579794 2/4 193 140 53 104 104 0 strelka-varscan-mutect ADCYAP1,synonymous_variant,p.=,ENST00000579794,NM_001117.4;ADCYAP1,synonymous_variant,p.=,ENST00000450565,NM_001099733.1;RP11-672L10.2,upstream_gene_variant,,ENST00000582921,;RP11-672L10.2,upstream_gene_variant,,ENST00000581719,;RP11-672L10.2,upstream_gene_variant,,ENST00000577358,;RP11-672L10.2,upstream_gene_variant,,ENST00000580612,;RP11-672L10.3,upstream_gene_variant,,ENST00000582554,;ADCYAP1,non_coding_transcript_exon_variant,,ENST00000269200,;ADCYAP1,upstream_gene_variant,,ENST00000581602,; A ENST00000579794 Transcript synonymous_variant 494/3346 216/531 72/176 A gcC/gcA 1 1 ADCYAP1 HGNC HGNC:241 protein_coding YES CCDS11825.1 ENSP00000462647 P18509 UPI000013D805 NM_001117.4 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11213:SF1,hmmpanther:PTHR11213 LOW 1 SNV 1 1 PASS rs1298234471 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 907764 907764 C A 1 0 0 0 0 0 0 0 1 346 639 23 1 1 ADCYAP1 18 907764 Silent SNP C C3N-00560_T 907764 79465521 1057 17746 LPIN2 0 . GRCh38 18 2960689 2960689 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.152G>T p.Arg51Leu p.R51L ENST00000261596 2/20 526 451 75 379 378 1 strelka-varscan-mutect LPIN2,missense_variant,p.Arg51Leu,ENST00000261596,NM_014646.2;LPIN2,missense_variant,p.Arg51Leu,ENST00000584294,;LPIN2,missense_variant,p.Arg88Leu,ENST00000584915,;RP11-737O24.2,non_coding_transcript_exon_variant,,ENST00000584431,; A ENST00000261596 Transcript missense_variant 391/6229 152/2691 51/896 R/L cGg/cTg 1 -1 LPIN2 HGNC HGNC:14450 protein_coding YES CCDS11829.1 ENSP00000261596 Q92539 UPI000012E865 NM_014646.2 deleterious(0) 2/20 hmmpanther:PTHR12181,hmmpanther:PTHR12181:SF11,Pfam_domain:PF04571 MODERATE 1 SNV 1 1 PASS rs1264741042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 2960689 2960689 C A 1 0 0 0 0 1 0 0 0 8819 652 23 1 1 LPIN2 18 2960689 Missense_Mutation SNP C C3N-00560_T 2052925 2960689 77412596 1058 17747 LAMA1 0 . GRCh38 18 7049158 7049158 + Missense_Mutation SNP G G T rs200844421 C3N-00560_T C3N-00560_N G G c.688C>A p.Arg230Ser p.R230S ENST00000389658 5/63 279 170 109 404 404 0 strelka-varscan-mutect LAMA1,missense_variant,p.Arg230Ser,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; T ENST00000389658 Transcript missense_variant 782/9657 688/9228 230/3075 R/S Cgc/Agc rs200844421,COSM287127 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 5/63 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00136 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs200844421 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 7049158 7049158 G T 1 0 0 0 0 1 0 0 0 8509 1145 40 1 1 LAMA1 18 7049158 Missense_Mutation SNP G C3N-00560_T 4088469 7049158 73324127 1059 17748 PTPRM 0 . GRCh38 18 7888212 7888212 + Nonsense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.303T>A p.Tyr101Ter p.Y101* ENST00000580170 3/33 359 297 62 272 272 0 strelka-varscan-mutect PTPRM,stop_gained,p.Tyr101Ter,ENST00000332175,NM_002845.3;PTPRM,stop_gained,p.Tyr101Ter,ENST00000580170,NM_001105244.1;PTPRM,stop_gained,p.Tyr39Ter,ENST00000400053,;PTPRM,5_prime_UTR_variant,,ENST00000400060,; A ENST00000580170 Transcript stop_gained 1340/5941 303/4398 101/1465 Y/* taT/taA 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 3/33 Pfam_domain:PF00629,Prints_domain:PR00020,PROSITE_patterns:PS00740,PROSITE_profiles:PS50060,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206,SMART_domains:SM00137,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 7888212 7888212 T A 1 0 0 0 0 0 1 0 0 12960 1500 52 4 4 PTPRM 18 7888212 Nonsense_Mutation SNP T C3N-00560_T 839054 7888212 72485073 1060 17749 CEP192 0 . GRCh38 18 13049436 13049436 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2645G>T p.Cys882Phe p.C882F ENST00000506447 16/45 163 122 41 189 189 0 strelka-varscan-mutect CEP192,missense_variant,p.Cys882Phe,ENST00000506447,NM_032142.3;CEP192,missense_variant,p.Cys407Phe,ENST00000325971,;CEP192,missense_variant,p.Cys421Phe,ENST00000511820,;CEP192,missense_variant,p.Cys623Phe,ENST00000589596,;CEP192,missense_variant,p.Cys482Phe,ENST00000510237,;CEP192,3_prime_UTR_variant,,ENST00000513432,; T ENST00000506447 Transcript missense_variant 2725/7960 2645/7614 882/2537 C/F tGt/tTt 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 tolerated(0.69) 16/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 13049436 13049436 G T 1 0 0 0 0 1 0 0 0 2967 1377 48 2 2 CEP192 18 13049436 Missense_Mutation SNP G C3N-00560_T 5161224 13049436 67323849 1061 17750 FAM210A 0 . GRCh38 18 13681799 13681799 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.279G>T p.Arg93Ser p.R93S ENST00000322247 3/5 460 335 125 467 467 0 strelka-varscan-mutect FAM210A,missense_variant,p.Arg93Ser,ENST00000322247,;FAM210A,missense_variant,p.Arg93Ser,ENST00000402563,NM_001098801.1,NM_152352.3;FAM210A,missense_variant,p.Arg93Ser,ENST00000592976,;FAM210A,missense_variant,p.Arg93Ser,ENST00000591269,;FAM210A,non_coding_transcript_exon_variant,,ENST00000588475,;FAM210A,intron_variant,,ENST00000585785,; A ENST00000322247 Transcript missense_variant 667/4340 279/819 93/272 R/S agG/agT 1 -1 FAM210A HGNC HGNC:28346 protein_coding YES CCDS11866.1 ENSP00000323635 Q96ND0 UPI000006D5B2 tolerated(0.13) 3/5 hmmpanther:PTHR21377,hmmpanther:PTHR21377:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 13681799 13681799 C A 1 0 0 0 0 1 0 0 0 5396 854 30 2 2 FAM210A 18 13681799 Missense_Mutation SNP C C3N-00560_T 632363 13681799 66691486 1062 17751 POTEC 0 . GRCh38 18 14522254 14522254 + Missense_Mutation SNP C C A rs556974559 C3N-00560_T C3N-00560_N C C c.1409G>T p.Ser470Ile p.S470I ENST00000358970 9/11 47 33 14 62 62 0 strelka-varscan-mutect POTEC,missense_variant,p.Ser470Ile,ENST00000358970,NM_001137671.1;POTEC,splice_region_variant,,ENST00000511306,; A ENST00000358970 Transcript missense_variant,splice_region_variant 1409/1629 1409/1629 470/542 S/I aGt/aTt rs556974559 1 -1 POTEC HGNC HGNC:33894 protein_coding YES CCDS45835.1 ENSP00000351856 B2RU33 UPI0000197B83 NM_001137671.1 deleterious(0.02) 9/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38 MODERATE 1 SNV 1 1 PASS rs556974559 . 1 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 56 14522254 14522254 C A 1 0 0 0 0 1 0 0 0 12376 695 24 2 2 POTEC 18 14522254 Missense_Mutation SNP C C3N-00560_T 840455 14522254 65851031 1063 17752 LAMA3 0 . GRCh38 18 23928232 23928232 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.8287G>A p.Asp2763Asn p.D2763N ENST00000313654 63/75 518 358 160 391 391 0 strelka-varscan-mutect LAMA3,missense_variant,p.Asp2763Asn,ENST00000313654,NM_198129.2;LAMA3,missense_variant,p.Asp2707Asn,ENST00000399516,NM_001127717.2;LAMA3,missense_variant,p.Asp1154Asn,ENST00000269217,NM_000227.4;LAMA3,missense_variant,p.Asp1098Asn,ENST00000587184,NM_001127718.2;LAMA3,missense_variant,p.Asp1023Asn,ENST00000586751,;LAMA3,upstream_gene_variant,,ENST00000588164,;LAMA3,non_coding_transcript_exon_variant,,ENST00000588770,;LAMA3,upstream_gene_variant,,ENST00000592442,; A ENST00000313654 Transcript missense_variant 8528/10661 8287/10002 2763/3333 D/N Gac/Aac 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 deleterious(0.02) 63/75 Gene3D:2.60.120.200,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 23928232 23928232 G A 1 0 0 0 0 1 0 0 0 8511 942 33 3 3 LAMA3 18 23928232 Missense_Mutation SNP G C3N-00560_T 9405978 23928232 56445053 1064 17753 KCTD1 0 . GRCh38 18 26501128 26501128 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.108G>T p.= p.V36V ENST00000408011 2/5 130 84 46 114 114 0 strelka-varscan-mutect KCTD1,synonymous_variant,p.=,ENST00000408011,NM_001136205.2;KCTD1,synonymous_variant,p.=,ENST00000579973,NM_198991.3;KCTD1,synonymous_variant,p.=,ENST00000317932,;KCTD1,synonymous_variant,p.=,ENST00000417602,NM_001258221.1;KCTD1,synonymous_variant,p.=,ENST00000580059,;KCTD1,synonymous_variant,p.=,ENST00000580191,NM_001258222.1;KCTD1,synonymous_variant,p.=,ENST00000580638,;KCTD1,synonymous_variant,p.=,ENST00000578973,; A ENST00000408011 Transcript synonymous_variant 668/2103 108/774 36/257 V gtG/gtT 1 -1 KCTD1 HGNC HGNC:18249 protein_coding YES CCDS11888.1 ENSP00000384367 Q719H9 A0A024RC45 UPI00001CDFF1 NM_001136205.2 2/5 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF65,SMART_domains:SM00225,Superfamily_domains:SSF54695 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 26501128 26501128 C A 1 0 0 0 0 0 0 0 1 8013 581 21 2 2 KCTD1 18 26501128 Silent SNP C C3N-00560_T 2572896 26501128 53872157 1065 17754 CCDC178 0 . GRCh38 18 33346327 33346327 + Missense_Mutation SNP C C T rs779422806 C3N-00560_T C3N-00560_N C C c.542G>A p.Arg181Gln p.R181Q ENST00000583930 8/23 241 182 59 252 252 0 strelka-varscan-mutect CCDC178,missense_variant,p.Arg181Gln,ENST00000383096,;CCDC178,missense_variant,p.Arg181Gln,ENST00000403303,NM_001105528.1;CCDC178,missense_variant,p.Arg181Gln,ENST00000583930,;CCDC178,missense_variant,p.Arg181Gln,ENST00000300227,NM_198995.2;CCDC178,missense_variant,p.Arg181Gln,ENST00000406524,;CCDC178,missense_variant,p.Arg181Gln,ENST00000579947,;CCDC178,intron_variant,,ENST00000579916,;CCDC178,missense_variant,p.Arg181Gln,ENST00000399177,;CCDC178,upstream_gene_variant,,ENST00000577268,; T ENST00000583930 Transcript missense_variant 621/3094 542/2676 181/891 R/Q cGg/cAg rs779422806,COSM1640956,COSM1640957 1 -1 CCDC178 HGNC HGNC:29588 protein_coding YES CCDS77174.1 ENSP00000463254 F8W7A7 UPI00020655A5 deleterious(0) 8/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR35088:SF1,hmmpanther:PTHR35088 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs779422806 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 33346327 33346327 C T 1 0 0 0 0 1 0 0 0 2493 652 23 1 1 CCDC178 18 33346327 Missense_Mutation SNP C C3N-00560_T 6845199 33346327 47026958 1066 17755 NOL4 0 . GRCh38 18 34019326 34019326 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1048G>T p.Gly350Ter p.G350* ENST00000261592 6/11 100 79 21 113 113 0 strelka-varscan-mutect NOL4,stop_gained,p.Gly350Ter,ENST00000261592,NM_003787.4;NOL4,stop_gained,p.Gly350Ter,ENST00000589544,NM_001198548.1;NOL4,stop_gained,p.Gly276Ter,ENST00000538587,NM_001198547.1;NOL4,stop_gained,p.Gly334Ter,ENST00000590712,NM_001198546.1;NOL4,stop_gained,p.Gly65Ter,ENST00000535384,NM_001198549.1;NOL4,stop_gained,p.Gly99Ter,ENST00000586553,;NOL4,3_prime_UTR_variant,,ENST00000586314,; A ENST00000261592 Transcript stop_gained 1346/3957 1048/1917 350/638 G/* Gga/Tga 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 6/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 HIGH 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999913 1 1 1 0 A 4 1 56 34019326 34019326 C A 1 0 0 0 0 0 1 0 0 10567 603 21 2 2 NOL4 18 34019326 Nonsense_Mutation SNP C C3N-00560_T 672999 34019326 46353959 1067 17756 DTNA 0 . GRCh38 18 34766018 34766018 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.125G>A p.Arg42Lys p.R42K ENST00000598334 4/20 418 314 104 393 393 0 strelka-varscan-mutect DTNA,missense_variant,p.Arg42Lys,ENST00000283365,NM_032975.3;DTNA,missense_variant,p.Arg42Lys,ENST00000399121,NM_001198939.1;DTNA,missense_variant,p.Arg42Lys,ENST00000444659,NM_001390.4;DTNA,missense_variant,p.Arg42Lys,ENST00000595022,NM_001198940.1;DTNA,missense_variant,p.Arg42Lys,ENST00000348997,NM_032978.6,NM_001391.5;DTNA,missense_variant,p.Arg42Lys,ENST00000598334,NM_001198938.1;DTNA,missense_variant,p.Arg42Lys,ENST00000598142,;DTNA,missense_variant,p.Arg42Lys,ENST00000598774,NM_032979.4;DTNA,missense_variant,p.Arg42Lys,ENST00000399113,;DTNA,missense_variant,p.Arg42Lys,ENST00000597599,NM_001198941.1;DTNA,missense_variant,p.Arg42Lys,ENST00000315456,NM_001392.4;DTNA,missense_variant,p.Arg42Lys,ENST00000554864,NM_001128175.1;DTNA,missense_variant,p.Arg42Lys,ENST00000596745,NM_001198945.1;DTNA,missense_variant,p.Arg42Lys,ENST00000590598,;DTNA,missense_variant,p.Arg42Lys,ENST00000590412,;DTNA,missense_variant,p.Arg42Lys,ENST00000588125,;DTNA,missense_variant,p.Arg44Lys,ENST00000588949,;DTNA,missense_variant,p.Arg31Lys,ENST00000591816,;RP11-138H11.1,intron_variant,,ENST00000596954,;DTNA,intron_variant,,ENST00000585446,; A ENST00000598334 Transcript missense_variant 451/3201 125/2175 42/724 R/K aGg/aAg 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 deleterious(0.01) 4/20 hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204,Pfam_domain:PF09068,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 34766018 34766018 G A 1 0 0 0 0 1 0 0 0 4611 1000 35 3 3 DTNA 18 34766018 Missense_Mutation SNP G C3N-00560_T 746692 34766018 45607267 1068 17757 DTNA 0 . GRCh38 18 34812033 34812033 + Frame_Shift_Del DEL C C - novel C3N-00560_T C3N-00560_N C C c.523delC p.Leu175SerfsTer32 p.L175Sfs*32 ENST00000598334 7/20 283 203 80 307 307 0 sindel-varindel-pindel DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000283365,NM_032975.3;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000399121,NM_001198939.1;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000444659,NM_001390.4;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000595022,NM_001198940.1;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000348997,NM_032978.6,NM_001391.5;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000598334,NM_001198938.1;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000598142,;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000598774,NM_032979.4;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000399113,;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000597599,NM_001198941.1;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000315456,NM_001392.4;DTNA,frameshift_variant,p.Leu175SerfsTer32,ENST00000554864,NM_001128175.1;DTNA,frameshift_variant,p.Leu175SerfsTer51,ENST00000596745,NM_001198945.1;DTNA,non_coding_transcript_exon_variant,,ENST00000585446,;DTNA,upstream_gene_variant,,ENST00000592114,; - ENST00000598334 Transcript frameshift_variant 849/3201 523/2175 175/724 L/X Ctc/tc 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 7/20 hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,Gene3D:1.10.238.10,Pfam_domain:PF09069,PIRSF_domain:PIRSF038204,Superfamily_domains:SSF47473 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 34812033 34812033 C - 1 0 1 0 1 0 0 0 0 4611 913 32 0 0 DTNA 18 34812033 Frame_Shift_Del DEL C C3N-00560_T 46015 34812033 45561252 1069 17758 SLC14A2 0 . GRCh38 18 45673746 45673746 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2441T>A p.Leu814His p.L814H ENST00000255226 18/20 261 184 77 228 228 0 strelka-varscan-mutect SLC14A2,missense_variant,p.Leu814His,ENST00000255226,NM_007163.3;SLC14A2,missense_variant,p.Leu814His,ENST00000586448,NM_001242692.1;RP11-116O18.3,intron_variant,,ENST00000589510,; A ENST00000255226 Transcript missense_variant 3257/4746 2441/2763 814/920 L/H cTc/cAc 1 1 SLC14A2 HGNC HGNC:10919 protein_coding YES CCDS11924.1 ENSP00000255226 Q15849 UPI000013CE99 NM_007163.3 deleterious(0) 18/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR10464:SF6,hmmpanther:PTHR10464,Pfam_domain:PF03253,Gene3D:1.10.3430.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45673746 45673746 T A 1 0 0 0 0 1 0 0 0 14662 1551 54 4 4 SLC14A2 18 45673746 Missense_Mutation SNP T C3N-00560_T 10861713 45673746 34699539 1070 17759 EPG5 0 . GRCh38 18 45943232 45943232 + Silent SNP C C A rs777606681 C3N-00560_T C3N-00560_N C C c.1872G>T p.= p.L624L ENST00000282041 9/44 249 195 54 259 258 1 strelka-varscan-mutect EPG5,synonymous_variant,p.=,ENST00000282041,NM_020964.2;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,; A ENST00000282041 Transcript synonymous_variant 1907/12633 1872/7740 624/2579 L ctG/ctT rs777606681 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 9/44 hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 LOW 1 SNV 2 1 PASS rs777606681 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 45943232 45943232 C A 1 0 0 0 0 0 0 0 1 5010 581 21 2 2 EPG5 18 45943232 Silent SNP C C3N-00560_T 269486 45943232 34430053 1071 17760 LOXHD1 0 . GRCh38 18 46533324 46533324 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.880G>C p.Gly294Arg p.G294R ENST00000300591 10/24 157 98 59 104 104 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Gly1405Arg,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Gly1199Arg,ENST00000441551,;LOXHD1,missense_variant,p.Gly294Arg,ENST00000300591,NM_001145472.2;LOXHD1,missense_variant,p.Gly294Arg,ENST00000582408,;LOXHD1,missense_variant,p.Gly198Arg,ENST00000579038,NM_001308013.1;LOXHD1,splice_region_variant,,ENST00000335730,;LOXHD1,splice_region_variant,,ENST00000536111,; G ENST00000300591 Transcript missense_variant,splice_region_variant 1294/3970 880/3345 294/1114 G/R Ggt/Cgt 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 deleterious(0) 10/24 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137,Superfamily_domains:SSF49723 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 46533324 46533324 C G 1 0 0 0 0 1 0 0 0 8801 637 22 4 4 LOXHD1 18 46533324 Missense_Mutation SNP C C3N-00560_T 590092 46533324 33839961 1072 17761 LOXHD1 0 . GRCh38 18 46610852 46610852 + Missense_Mutation SNP G G T rs372408513 C3N-00560_T C3N-00560_N G G c.683C>A p.Pro228Gln p.P228Q ENST00000536736 6/40 169 113 56 147 147 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Pro228Gln,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Pro228Gln,ENST00000441551,; T ENST00000536736 Transcript missense_variant 683/6848 683/6636 228/2211 P/Q cCg/cAg rs372408513 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 deleterious(0.04) 6/40 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE 1 SNV 5 1 PASS rs372408513 . 0 206 0 0 3 0 0 0 -20 0.9916815 1 1 1 0 T 3 4 56 46610852 46610852 G T 1 0 0 0 0 1 0 0 0 8801 1116 39 1 1 LOXHD1 18 46610852 Missense_Mutation SNP G C3N-00560_T 77528 46610852 33762433 1073 17762 DCC 0 . GRCh38 18 52340859 52340859 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.72C>G p.Ser24Arg p.S24R ENST00000442544 1/29 614 458 156 541 541 0 strelka-varscan-mutect DCC,missense_variant,p.Ser24Arg,ENST00000442544,NM_005215.3;RP11-25O3.1,upstream_gene_variant,,ENST00000582700,; G ENST00000442544 Transcript missense_variant 688/10206 72/4344 24/1447 S/R agC/agG 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 tolerated(0.36) 1/29 PROSITE_profiles:PS50835,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 52340859 52340859 C G 1 0 0 0 0 1 0 0 0 4084 767 27 4 4 DCC 18 52340859 Missense_Mutation SNP C C3N-00560_T 5730007 52340859 28032426 1074 17763 DCC 0 . GRCh38 18 52752137 52752137 + Missense_Mutation SNP C C T rs762319358 C3N-00560_T C3N-00560_N C C c.175C>T p.Leu59Phe p.L59F ENST00000442544 2/29 213 156 57 228 228 0 strelka-varscan-mutect DCC,missense_variant,p.Leu59Phe,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Leu36Phe,ENST00000412726,;DCC,missense_variant,p.Leu27Phe,ENST00000578080,;DCC,upstream_gene_variant,,ENST00000582875,;DCC,upstream_gene_variant,,ENST00000580024,;DCC,upstream_gene_variant,,ENST00000579666,;DCC,upstream_gene_variant,,ENST00000582595,;DCC,upstream_gene_variant,,ENST00000304775,;DCC,upstream_gene_variant,,ENST00000579349,;DCC,upstream_gene_variant,,ENST00000581559,; T ENST00000442544 Transcript missense_variant 791/10206 175/4344 59/1447 L/F Ctc/Ttc rs762319358,COSM5608240 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 deleterious(0) 2/29 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762319358 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 52752137 52752137 C T 1 0 0 0 0 1 0 0 0 4084 681 24 3 3 DCC 18 52752137 Missense_Mutation SNP C C3N-00560_T 411278 52752137 27621148 1075 17764 DCC 0 . GRCh38 18 53450621 53450621 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.3351G>T p.= p.V1117V ENST00000442544 23/29 586 418 168 560 557 3 strelka-varscan-mutect DCC,synonymous_variant,p.=,ENST00000442544,NM_005215.3;DCC,synonymous_variant,p.=,ENST00000412726,;DCC,synonymous_variant,p.=,ENST00000581580,; T ENST00000442544 Transcript synonymous_variant 3967/10206 3351/4344 1117/1447 V gtG/gtT 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 23/29 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs967763926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 53450621 53450621 G T 1 0 0 0 0 0 0 0 1 4084 1335 47 2 2 DCC 18 53450621 Silent SNP G C3N-00560_T 698484 53450621 26922664 1076 17765 ONECUT2 0 . GRCh38 18 57476678 57476678 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1470C>A p.Ser490Arg p.S490R ENST00000491143 2/2 279 194 85 241 241 0 strelka-varscan-mutect ONECUT2,missense_variant,p.Ser490Arg,ENST00000491143,NM_004852.2;ONECUT2,non_coding_transcript_exon_variant,,ENST00000481727,; A ENST00000491143 Transcript missense_variant 1502/16121 1470/1515 490/504 S/R agC/agA 1 1 ONECUT2 HGNC HGNC:8139 protein_coding YES CCDS42440.1 ENSP00000419185 O95948 UPI0000201DC1 NM_004852.2 tolerated_low_confidence(0.16) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR14057,hmmpanther:PTHR14057:SF10,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 57476678 57476678 C A 1 0 0 0 0 1 0 0 0 10944 709 25 2 2 ONECUT2 18 57476678 Missense_Mutation SNP C C3N-00560_T 4026057 57476678 22896607 1077 17766 NEDD4L 0 . GRCh38 18 58396243 58396243 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.2902G>C p.Ala968Pro p.A968P ENST00000400345 31/31 222 156 66 186 186 0 strelka-varscan-mutect NEDD4L,missense_variant,p.Ala847Pro,ENST00000456986,NM_001144964.1,NM_001144965.1;NEDD4L,missense_variant,p.Ala948Pro,ENST00000382850,NM_015277.5;NEDD4L,missense_variant,p.Ala827Pro,ENST00000456173,NM_001144970.2;NEDD4L,missense_variant,p.Ala1247Pro,ENST00000635997,;NEDD4L,missense_variant,p.Ala968Pro,ENST00000400345,NM_001144967.2;NEDD4L,missense_variant,p.Ala960Pro,ENST00000357895,NM_001144968.1;NEDD4L,missense_variant,p.Ala827Pro,ENST00000435432,NM_001144971.1;NEDD4L,missense_variant,p.Ala940Pro,ENST00000586263,NM_001144969.1;NEDD4L,missense_variant,p.Ala847Pro,ENST00000431212,NM_001144966.2;NEDD4L,missense_variant,p.Ala904Pro,ENST00000356462,NM_001243960.1;NEDD4L,missense_variant,p.Ala864Pro,ENST00000256830,;NEDD4L,missense_variant,p.Ala632Pro,ENST00000587881,;NEDD4L,missense_variant,p.Ala99Pro,ENST00000589054,;RP11-845C23.3,downstream_gene_variant,,ENST00000590318,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000590506,;NEDD4L,non_coding_transcript_exon_variant,,ENST00000588712,;NEDD4L,downstream_gene_variant,,ENST00000592097,; C ENST00000400345 Transcript missense_variant 3185/3647 2902/2928 968/975 A/P Gct/Cct 1 1 NEDD4L HGNC HGNC:7728 protein_coding YES CCDS45872.1 ENSP00000383199 Q96PU5 UPI000058E3AE NM_001144967.2 deleterious(0.01) 31/31 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF310,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 58396243 58396243 G C 1 0 0 0 0 1 0 0 0 10339 1319 46 4 4 NEDD4L 18 58396243 Missense_Mutation SNP G C3N-00560_T 919565 58396243 21977042 1078 17767 ALPK2 0 . GRCh38 18 58536339 58536339 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3848C>A p.Ala1283Asp p.A1283D ENST00000361673 5/13 262 195 67 236 236 0 strelka-varscan-mutect ALPK2,missense_variant,p.Ala1283Asp,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; T ENST00000361673 Transcript missense_variant 4062/7303 3848/6513 1283/2170 A/D gCt/gAt 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0.04) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 58536339 58536339 G T 1 0 0 0 0 1 0 0 0 645 971 34 2 2 ALPK2 18 58536339 Missense_Mutation SNP G C3N-00560_T 140096 58536339 21836946 1079 17768 KIAA1468 0 . GRCh38 18 62187887 62187887 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.382C>T p.Arg128Cys p.R128C ENST00000398130 1/29 158 128 30 128 128 0 strelka-varscan-mutect KIAA1468,missense_variant,p.Arg128Cys,ENST00000398130,NM_020854.3;KIAA1468,missense_variant,p.Arg128Cys,ENST00000256858,;PIGN,upstream_gene_variant,,ENST00000357637,NM_176787.4;PIGN,upstream_gene_variant,,ENST00000400334,NM_012327.5;PIGN,upstream_gene_variant,,ENST00000589720,;PIGN,upstream_gene_variant,,ENST00000587134,;PIGN,upstream_gene_variant,,ENST00000585923,;PIGN,upstream_gene_variant,,ENST00000585344,;PIGN,upstream_gene_variant,,ENST00000588571,;PIGN,upstream_gene_variant,,ENST00000589339,;PIGN,upstream_gene_variant,,ENST00000590765,;PIGN,upstream_gene_variant,,ENST00000585926,;PIGN,upstream_gene_variant,,ENST00000585458,;PIGN,upstream_gene_variant,,ENST00000593225,;KIAA1468,missense_variant,p.Arg128Cys,ENST00000587725,; T ENST00000398130 Transcript missense_variant 614/6178 382/3651 128/1216 R/C Cgc/Tgc 1 1 KIAA1468 HGNC HGNC:29289 protein_coding YES CCDS11979.2 ENSP00000381198 Q9P260 UPI0000DA5AF7 NM_020854.3 deleterious(0) 1/29 hmmpanther:PTHR32059:SF0,hmmpanther:PTHR32059 MODERATE 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999752 1 1 1 0 T 3 4 56 62187887 62187887 C T 1 0 0 0 0 1 0 0 0 8117 768 27 1 1 KIAA1468 18 62187887 Missense_Mutation SNP C C3N-00560_T 3651548 62187887 18185398 1080 17769 KIAA1468 0 . GRCh38 18 62305441 62305441 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.3558G>A p.= p.V1186V ENST00000398130 29/29 172 118 54 155 155 0 strelka-varscan-mutect KIAA1468,synonymous_variant,p.=,ENST00000398130,NM_020854.3;KIAA1468,synonymous_variant,p.=,ENST00000256858,;RP11-173A16.1,upstream_gene_variant,,ENST00000591014,; A ENST00000398130 Transcript synonymous_variant 3790/6178 3558/3651 1186/1216 V gtG/gtA 1 1 KIAA1468 HGNC HGNC:29289 protein_coding YES CCDS11979.2 ENSP00000381198 Q9P260 UPI0000DA5AF7 NM_020854.3 29/29 hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 62305441 62305441 G A 1 0 0 0 0 0 0 0 1 8117 1277 45 3 3 KIAA1468 18 62305441 Silent SNP G C3N-00560_T 117554 62305441 18067844 1081 17770 KDSR 0 . GRCh38 18 63331854 63331854 + Silent SNP T T A rs751892868 C3N-00560_T C3N-00560_N T T c.927A>T p.= p.G309G ENST00000406396 10/10 186 146 40 159 159 0 strelka-varscan-mutect KDSR,synonymous_variant,p.=,ENST00000406396,NM_002035.2;KDSR,synonymous_variant,p.=,ENST00000326575,;KDSR,synonymous_variant,p.=,ENST00000591902,;KDSR,non_coding_transcript_exon_variant,,ENST00000589592,;KDSR,non_coding_transcript_exon_variant,,ENST00000586791,;KDSR,non_coding_transcript_exon_variant,,ENST00000588089,; A ENST00000406396 Transcript synonymous_variant 1319/5447 927/999 309/332 G ggA/ggT rs751892868 1 -1 KDSR HGNC HGNC:4021 protein_coding YES CCDS11982.1 ENSP00000385083 Q06136 A0A024R292 UPI000004C798 NM_002035.2 10/10 LOW 1 SNV 1 1 PASS rs751892868 . 0 207 0 3 0 0 0 0 -20 0.9999969 1 1 1 0 A 2 1 56 63331854 63331854 T A 1 0 0 0 0 0 0 0 1 8060 1770 62 4 4 KDSR 18 63331854 Silent SNP T C3N-00560_T 1026413 63331854 17041431 1082 17771 SERPINB12 0 . GRCh38 18 63566695 63566695 + Frame_Shift_Del DEL G G - rs755221725 C3N-00560_T C3N-00560_N G G c.963delG p.Phe322SerfsTer? p.F322Sfs*? ENST00000382768 7/7 182 134 48 205 205 0 sindel-varindel-pindel SERPINB12,frameshift_variant,p.Phe322SerfsTer?,ENST00000382768,NM_001307928.1;SERPINB12,frameshift_variant,p.Phe302SerfsTer?,ENST00000269491,NM_080474.1; - ENST00000382768 Transcript frameshift_variant 962/1278 962/1278 321/425 R/X cGg/cg rs755221725 1 1 SERPINB12 HGNC HGNC:14220 protein_coding YES CCDS77194.1 ENSP00000372218 Q96P63 UPI00003DA003 NM_001307928.1 7/7 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF125,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999998 1 1 1 0 - 7 5 56 63566695 63566695 G - 1 0 1 0 1 0 0 0 0 14375 1116 39 0 0 SERPINB12 18 63566695 Frame_Shift_Del DEL G C3N-00560_T 234841 63566695 16806590 1083 17772 SERPINB4 0 . GRCh38 18 63643181 63643181 + Frame_Shift_Del DEL C C - C3N-00560_T C3N-00560_N C C c.202delG p.Glu68LysfsTer22 p.E68Kfs*22 ENST00000341074 3/8 237 194 43 269 269 0 sindel-varindel-pindel SERPINB4,frameshift_variant,p.Glu68LysfsTer22,ENST00000341074,NM_002974.3;SERPINB4,frameshift_variant,p.Glu70LysfsTer22,ENST00000413673,NM_175041.1;SERPINB4,frameshift_variant,p.Glu68LysfsTer10,ENST00000436264,;SERPINB11,upstream_gene_variant,,ENST00000489748,;SERPINB4,non_coding_transcript_exon_variant,,ENST00000498496,; - ENST00000341074 Transcript frameshift_variant 318/1749 202/1173 68/390 E/X Gaa/aa COSM5588911 1 -1 SERPINB4 HGNC HGNC:10570 protein_coding YES CCDS11986.1 ENSP00000343445 P48594 UPI0000038A1A NM_002974.3 3/8 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF186,SMART_domains:SM00093,Superfamily_domains:SSF56574 1 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 2 -2.612657 0 0 1 0 0 - 7 5 56 63643181 63643181 C - 1 0 1 0 1 0 0 0 0 14379 922 32 0 0 SERPINB4 18 63643181 Frame_Shift_Del DEL C C3N-00560_T 76486 63643181 16730104 1084 17773 SERPINB11 0 . GRCh38 18 63712622 63712622 + Nonsense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.286C>T p.Gln96Ter p.Q96* ENST00000623262 3/5 152 117 35 158 158 0 strelka-varscan-mutect SERPINB11,stop_gained,p.Gln96Ter,ENST00000382749,NM_080475.3;SERPINB11,stop_gained,p.Gln96Ter,ENST00000544088,;SERPINB11,stop_gained,p.Gln96Ter,ENST00000489748,;SERPINB11,stop_gained,p.Gln96Ter,ENST00000623262,NM_001291278.1;SERPINB11,intron_variant,,ENST00000624518,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000467649,;SERPINB11,stop_gained,p.Gln96Ter,ENST00000536691,;SERPINB11,non_coding_transcript_exon_variant,,ENST00000610304,; T ENST00000623262 Transcript stop_gained 286/918 286/918 96/305 Q/* Cag/Tag 1 1 SERPINB11 HGNC HGNC:14221 protein_coding YES CCDS77196.1 ENSP00000485532 A0A096LPD5 UPI0003EAEE70 NM_001291278.1 3/5 hmmpanther:PTHR11461:SF199,hmmpanther:PTHR11461,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 63712622 63712622 C T 1 0 0 0 0 0 1 0 0 14374 595 21 3 3 SERPINB11 18 63712622 Nonsense_Mutation SNP C C3N-00560_T 69441 63712622 16660663 1085 17774 CDH7 0 . GRCh38 18 65880583 65880583 + Silent SNP C C A rs779582603 C3N-00560_T C3N-00560_N C C c.2047C>A p.= p.R683R ENST00000397968 12/12 133 93 40 103 103 0 strelka-varscan-mutect CDH7,synonymous_variant,p.=,ENST00000397968,NM_004361.2;CDH7,synonymous_variant,p.=,ENST00000323011,NM_033646.1; A ENST00000397968 Transcript synonymous_variant 2473/12231 2047/2358 683/785 R Cgg/Agg rs779582603 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 12/12 Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91 LOW 1 SNV 1 1 PASS rs779582603 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 65880583 65880583 C A 1 0 0 0 0 0 0 0 1 2818 643 23 1 1 CDH7 18 65880583 Silent SNP C C3N-00560_T 2167961 65880583 14492702 1086 17775 DSEL 0 . GRCh38 18 67511282 67511282 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.3357A>T p.= p.A1119A ENST00000310045 2/2 258 188 70 246 245 1 strelka-varscan-mutect DSEL,synonymous_variant,p.=,ENST00000310045,NM_032160.2;CTD-2541J13.2,non_coding_transcript_exon_variant,,ENST00000583493,;CTD-2541J13.2,non_coding_transcript_exon_variant,,ENST00000581951,; A ENST00000310045 Transcript synonymous_variant 4831/9531 3357/3669 1119/1222 A gcA/gcT 1 -1 DSEL HGNC HGNC:18144 protein_coding YES CCDS11995.1 ENSP00000310565 Q8IZU8 UPI00000740A1 NM_032160.2 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF2,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 67511282 67511282 T A 1 0 0 0 0 0 0 0 1 4596 1567 55 4 4 DSEL 18 67511282 Silent SNP T C3N-00560_T 1630699 67511282 12862003 1087 17776 CD226 0 . GRCh38 18 69864333 69864333 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.992G>T p.Arg331Ile p.R331I ENST00000280200 7/7 134 93 41 121 121 0 strelka-varscan-mutect CD226,missense_variant,p.Arg331Ile,ENST00000280200,NM_006566.3;CD226,missense_variant,p.Arg176Ile,ENST00000581982,NM_001303619.1;CD226,missense_variant,p.Arg331Ile,ENST00000582621,NM_001303618.1;CD226,missense_variant,p.Arg176Ile,ENST00000577287,;CD226,intron_variant,,ENST00000578928,; A ENST00000280200 Transcript missense_variant 1261/12319 992/1011 331/336 R/I aGa/aTa 1 -1 CD226 HGNC HGNC:16961 protein_coding YES CCDS11997.1 ENSP00000280200 Q15762 UPI000013DC05 NM_006566.3 deleterious(0) 7/7 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF58 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 56 69864333 69864333 C A 1 0 0 0 0 1 0 0 0 2689 913 32 2 2 CD226 18 69864333 Missense_Mutation SNP C C3N-00560_T 2353051 69864333 10508952 1088 17777 NETO1 0 . GRCh38 18 72783748 72783748 + Silent SNP C C T C3N-00560_T C3N-00560_N C C c.798G>A p.= p.V266V ENST00000327305 7/11 389 311 78 393 393 0 strelka-varscan-mutect NETO1,synonymous_variant,p.=,ENST00000327305,NM_138966.3;NETO1,synonymous_variant,p.=,ENST00000583169,NM_001201465.1;NETO1,downstream_gene_variant,,ENST00000579730,; T ENST00000327305 Transcript synonymous_variant 1456/3058 798/1602 266/533 V gtG/gtA COSM3527476 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 7/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,SMART_domains:SM00042,Superfamily_domains:SSF49854 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 72783748 72783748 C T 1 0 0 0 0 0 0 0 1 10374 813 29 3 3 NETO1 18 72783748 Silent SNP C C3N-00560_T 2919415 72783748 7589537 1089 17778 C18orf63 0 . GRCh38 18 74322754 74322754 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.270G>T p.Lys90Asn p.K90N ENST00000579455 4/14 42 33 9 57 56 1 strelka-varscan-mutect C18orf63,missense_variant,p.Lys90Asn,ENST00000579455,NM_001174123.1; T ENST00000579455 Transcript missense_variant,splice_region_variant 599/5127 270/2058 90/685 K/N aaG/aaT 1 1 C18orf63 HGNC HGNC:40037 protein_coding YES CCDS54189.1 ENSP00000464330 Q68DL7 UPI00006C192C NM_001174123.1 deleterious(0.03) 4/14 Pfam_domain:PF15813,hmmpanther:PTHR28495,hmmpanther:PTHR28495:SF1 MODERATE 1 SNV 1 1 PASS rs1175876880 . 0 206 4 0 0 0 0 0 -19.99846 1 1 1 1 0 T 3 4 56 74322754 74322754 G T 1 0 0 0 0 1 0 0 0 1901 1014 35 2 2 C18orf63 18 74322754 Missense_Mutation SNP G C3N-00560_T 1539006 74322754 6050531 1090 17779 CNDP1 0 . GRCh38 18 74580251 74580252 + Frame_Shift_Ins INS - - AA novel C3N-00560_T C3N-00560_N - - c.1293_1294dupAA p.Arg432LysfsTer14 p.R432Kfs*14 ENST00000358821 10/12 121 82 39 96 96 0 sindel-pindel CNDP1,frameshift_variant,p.Arg389LysfsTer14,ENST00000582365,;CNDP1,frameshift_variant,p.Arg432LysfsTer14,ENST00000358821,NM_032649.5;CNDP1,downstream_gene_variant,,ENST00000578498,;CNDP1,non_coding_transcript_exon_variant,,ENST00000582461,;CNDP1,non_coding_transcript_exon_variant,,ENST00000584004,;CNDP1,downstream_gene_variant,,ENST00000584316,; AA ENST00000358821 Transcript frameshift_variant 1517-1518/2215 1289-1290/1524 430/507 A/AX gca/gcAAa 1 1 CNDP1 HGNC HGNC:20675 protein_coding YES CCDS12007.1 ENSP00000351682 Q96KN2 UPI00000463FC NM_032649.5 10/12 Gene3D:3.40.630.10,Pfam_domain:PF01546,PIRSF_domain:PIRSF037242,hmmpanther:PTHR11014,hmmpanther:PTHR11014:SF58,Superfamily_domains:SSF53187 HIGH 1 insertion 1 5 1 PASS . . 0 196 3 10 0 0 0 0 -20 0.9855644 1 1 1 0 AA 7 5 56 74580251 74580251 - AA 1 0 1 1 0 0 0 0 0 3372 710 25 0 0 CNDP1 18 74580251 Frame_Shift_Ins INS - C3N-00560_T 257497 74580251 5793034 1091 17780 ZNF516 0 . GRCh38 18 76441263 76441263 + Missense_Mutation SNP C C A rs758621513 C3N-00560_T C3N-00560_N C C c.1792G>T p.Ala598Ser p.A598S ENST00000443185 3/7 226 156 70 184 184 0 strelka-mutect ZNF516,missense_variant,p.Ala598Ser,ENST00000443185,NM_014643.3;ZNF516,downstream_gene_variant,,ENST00000532857,; A ENST00000443185 Transcript missense_variant 2110/8118 1792/3492 598/1163 A/S Gcc/Tcc rs758621513,COSM1234181 1 -1 ZNF516 HGNC HGNC:28990 protein_coding YES CCDS74234.1 ENSP00000394757 Q92618 UPI00001394A1 NM_014643.3 tolerated(0.4) 3/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs758621513 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 76441263 76441263 C A 1 0 0 0 0 1 0 0 0 18532 768 27 1 1 ZNF516 18 76441263 Missense_Mutation SNP C C3N-00560_T 1861012 76441263 3932022 1092 17781 SALL3 0 . GRCh38 18 78992756 78992756 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.765C>A p.= p.P255P ENST00000537592 2/3 61 40 21 33 33 0 strelka-varscan-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000536229,;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,intron_variant,,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; A ENST00000537592 Transcript synonymous_variant 765/6555 765/3903 255/1300 P ccC/ccA 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 LOW 1 SNV 5 1 PASS rs1183300472 . 2 204 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 78992756 78992756 C A 1 0 0 0 0 0 0 0 1 14071 581 21 2 2 SALL3 18 78992756 Silent SNP C C3N-00560_T 2551493 78992756 1380529 1093 17782 ADNP2 0 . GRCh38 18 80137260 80137260 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1847C>A p.Thr616Lys p.T616K ENST00000262198 4/4 344 271 73 297 297 0 strelka-varscan-mutect ADNP2,missense_variant,p.Thr616Lys,ENST00000262198,NM_014913.3;ADNP2,intron_variant,,ENST00000561195,;ADNP2,downstream_gene_variant,,ENST00000560752,;ADNP2,downstream_gene_variant,,ENST00000559951,;ADNP2,downstream_gene_variant,,ENST00000560561,; A ENST00000262198 Transcript missense_variant 2302/5393 1847/3396 616/1131 T/K aCg/aAg 1 1 ADNP2 HGNC HGNC:23803 protein_coding YES CCDS32853.1 ENSP00000262198 Q6IQ32 A0A024R377 UPI0000071DEA NM_014913.3 deleterious(0) 4/4 hmmpanther:PTHR15740 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 80137260 80137260 C A 1 0 0 0 0 1 0 0 0 399 536 19 1 1 ADNP2 18 80137260 Missense_Mutation SNP C C3N-00560_T 1144504 80137260 236025 1094 17783 RNF126 0 . GRCh38 19 651759 651759 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.295G>C p.Gly99Arg p.G99R ENST00000292363 4/9 143 78 65 158 158 0 strelka-varscan-mutect RNF126,missense_variant,p.Gly99Arg,ENST00000292363,NM_194460.2;RNF126,missense_variant,p.Gly99Arg,ENST00000589762,;RNF126,non_coding_transcript_exon_variant,,ENST00000590885,;RNF126,3_prime_UTR_variant,,ENST00000605891,;RNF126,non_coding_transcript_exon_variant,,ENST00000591394,;RNF126,upstream_gene_variant,,ENST00000586749,;RNF126,downstream_gene_variant,,ENST00000592626,; G ENST00000292363 Transcript missense_variant 451/1694 295/936 99/311 G/R Ggg/Cgg 1 -1 RNF126 HGNC HGNC:21151 protein_coding YES CCDS12039.1 ENSP00000292363 Q9BV68 A0A024R206 UPI000006F904 NM_194460.2 tolerated(0.13) 4/9 hmmpanther:PTHR22763:SF81,hmmpanther:PTHR22763 MODERATE 1 SNV 1 1 PASS rs1170960424 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 651759 651759 C G 1 0 0 0 0 1 0 0 0 13613 594 21 4 4 RNF126 19 651759 Missense_Mutation SNP C C3N-00560_T 651759 57965857 1095 17784 R3HDM4 0 . GRCh38 19 901488 901488 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.285G>A p.= p.G95G ENST00000361574 3/8 203 82 121 192 192 0 strelka-varscan-mutect R3HDM4,synonymous_variant,p.=,ENST00000361574,NM_138774.3;R3HDM4,synonymous_variant,p.=,ENST00000587975,;R3HDM4,downstream_gene_variant,,ENST00000626716,;R3HDM4,non_coding_transcript_exon_variant,,ENST00000591829,;R3HDM4,3_prime_UTR_variant,,ENST00000590454,;R3HDM4,intron_variant,,ENST00000589428,;R3HDM4,downstream_gene_variant,,ENST00000589445,;R3HDM4,upstream_gene_variant,,ENST00000586080,; T ENST00000361574 Transcript synonymous_variant 359/1815 285/807 95/268 G ggG/ggA 1 -1 R3HDM4 HGNC HGNC:28270 protein_coding YES CCDS12048.1 ENSP00000355385 Q96D70 UPI00001B50F1 NM_138774.3 3/8 Pfam_domain:PF13902,hmmpanther:PTHR32019,hmmpanther:PTHR32019:SF2,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 901488 901488 C T 1 0 0 0 0 0 0 0 1 13046 610 22 3 3 R3HDM4 19 901488 Silent SNP C C3N-00560_T 249729 901488 57716128 1096 17785 SBNO2 0 . GRCh38 19 1110829 1110829 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2944G>T p.Ala982Ser p.A982S ENST00000361757 26/32 195 100 95 199 199 0 strelka-varscan-mutect SBNO2,missense_variant,p.Ala982Ser,ENST00000361757,NM_014963.2;SBNO2,missense_variant,p.Ala972Ser,ENST00000587024,;SBNO2,missense_variant,p.Ala925Ser,ENST00000438103,NM_001100122.1;GPX4,downstream_gene_variant,,ENST00000622390,NM_001039848.2;GPX4,downstream_gene_variant,,ENST00000616066,NM_001039847.2;GPX4,downstream_gene_variant,,ENST00000354171,NM_002085.4;GPX4,downstream_gene_variant,,ENST00000589115,;GPX4,downstream_gene_variant,,ENST00000588919,;GPX4,downstream_gene_variant,,ENST00000611653,;GPX4,downstream_gene_variant,,ENST00000593032,;GPX4,downstream_gene_variant,,ENST00000587648,;SBNO2,non_coding_transcript_exon_variant,,ENST00000587673,;SBNO2,non_coding_transcript_exon_variant,,ENST00000586109,;SBNO2,downstream_gene_variant,,ENST00000592222,;GPX4,downstream_gene_variant,,ENST00000592940,;GPX4,downstream_gene_variant,,ENST00000585480,; A ENST00000361757 Transcript missense_variant 3182/4923 2944/4101 982/1366 A/S Gcc/Tcc 1 -1 SBNO2 HGNC HGNC:29158 protein_coding YES CCDS45894.1 ENSP00000354733 Q9Y2G9 UPI0000140680 NM_014963.2 tolerated(0.37) 26/32 Pfam_domain:PF13871,hmmpanther:PTHR12706,hmmpanther:PTHR12706:SF5 MODERATE 1 SNV 1 1 PASS rs1276168951 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 1110829 1110829 C A 1 0 0 0 0 1 0 0 0 14128 768 27 1 1 SBNO2 19 1110829 Missense_Mutation SNP C C3N-00560_T 209341 1110829 57506787 1097 17786 DAZAP1 0 . GRCh38 19 1428869 1428869 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.574G>T p.Asp192Tyr p.D192Y ENST00000233078 8/12 202 97 105 170 170 0 strelka-varscan-mutect DAZAP1,missense_variant,p.Asp192Tyr,ENST00000336761,NM_170711.2;DAZAP1,missense_variant,p.Asp192Tyr,ENST00000233078,NM_018959.3;DAZAP1,missense_variant,p.Asp192Tyr,ENST00000592522,;DAZAP1,missense_variant,p.Asp191Tyr,ENST00000587079,;DAZAP1,missense_variant,p.Asp170Tyr,ENST00000592453,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000586579,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000585485,;DAZAP1,non_coding_transcript_exon_variant,,ENST00000589484,;DAZAP1,upstream_gene_variant,,ENST00000589874,; T ENST00000233078 Transcript missense_variant 735/2160 574/1224 192/407 D/Y Gac/Tac 1 1 DAZAP1 HGNC HGNC:2683 protein_coding YES CCDS12065.1 ENSP00000233078 Q96EP5 A0A0S2Z569 UPI00000728D6 NM_018959.3 deleterious(0) 8/12 hmmpanther:PTHR24012:SF489,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 1428869 1428869 G T 1 0 0 0 0 1 0 0 0 4045 1174 41 2 2 DAZAP1 19 1428869 Missense_Mutation SNP G C3N-00560_T 318040 1428869 57188747 1098 17787 MATK 0 . GRCh38 19 3783920 3783920 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.479G>T p.Cys160Phe p.C160F ENST00000395045 6/14 222 94 128 265 265 0 strelka-varscan-mutect MATK,missense_variant,p.Cys159Phe,ENST00000310132,NM_139355.2;MATK,missense_variant,p.Cys160Phe,ENST00000395045,NM_002378.3;MATK,missense_variant,p.Cys159Phe,ENST00000585778,;MATK,missense_variant,p.Cys118Phe,ENST00000395040,NM_139354.2;MATK,missense_variant,p.Cys160Phe,ENST00000619596,;MATK,missense_variant,p.Cys48Phe,ENST00000590493,;MATK,missense_variant,p.Cys40Phe,ENST00000587180,;MATK,missense_variant,p.Cys159Phe,ENST00000590028,;MATK,upstream_gene_variant,,ENST00000588983,;MATK,downstream_gene_variant,,ENST00000591059,;MATK,downstream_gene_variant,,ENST00000590849,;MATK,downstream_gene_variant,,ENST00000590980,;MATK,downstream_gene_variant,,ENST00000590821,; A ENST00000395045 Transcript missense_variant 817/2073 479/1527 160/508 C/F tGc/tTc 1 -1 MATK HGNC HGNC:6906 protein_coding YES CCDS12113.1 ENSP00000378485 P42679 UPI000013FB32 NM_002378.3 deleterious(0) 6/14 PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF268,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401 MODERATE 1 SNV 2 1 PASS rs1330705409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 3783920 3783920 C A 1 0 0 0 0 1 0 0 0 9258 710 25 2 2 MATK 19 3783920 Missense_Mutation SNP C C3N-00560_T 2355051 3783920 54833696 1099 17788 ZFR2 0 . GRCh38 19 3827556 3827556 + Missense_Mutation SNP G G T rs564576533 C3N-00560_T C3N-00560_N G G c.950C>A p.Ala317Glu p.A317E ENST00000262961 6/19 207 86 121 233 233 0 strelka-varscan-mutect ZFR2,missense_variant,p.Ala317Glu,ENST00000262961,NM_015174.1;ZFR2,downstream_gene_variant,,ENST00000591965,;ZFR2,missense_variant,p.Ala317Glu,ENST00000438164,; T ENST00000262961 Transcript missense_variant 961/4756 950/2820 317/939 A/E gCg/gAg rs564576533 1 -1 ZFR2 HGNC HGNC:29189 protein_coding YES CCDS45921.1 ENSP00000262961 Q9UPR6 UPI0000DD84BE NM_015174.1 tolerated(0.1) 6/19 hmmpanther:PTHR10910:SF85,hmmpanther:PTHR10910,SMART_domains:SM00451,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs564576533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 3827556 3827556 G T 1 0 0 0 0 1 0 0 0 18238 1087 38 1 1 ZFR2 19 3827556 Missense_Mutation SNP G C3N-00560_T 43636 3827556 54790060 1100 17789 MAP2K2 0 . GRCh38 19 4101032 4101032 + Missense_Mutation SNP C C A rs730880511 C3N-00560_T C3N-00560_N C C c.692G>T p.Arg231Leu p.R231L ENST00000262948 6/11 170 90 80 190 190 0 strelka-varscan-mutect MAP2K2,missense_variant,p.Arg231Leu,ENST00000262948,NM_030662.3;MAP2K2,missense_variant,p.Arg134Leu,ENST00000394867,;MAP2K2,synonymous_variant,p.=,ENST00000599021,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000593364,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000597263,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000602167,;MAP2K2,downstream_gene_variant,,ENST00000599345,;MAP2K2,upstream_gene_variant,,ENST00000595715,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000601786,;MAP2K2,non_coding_transcript_exon_variant,,ENST00000597008,;MAP2K2,upstream_gene_variant,,ENST00000600584,; A ENST00000262948 Transcript missense_variant 946/1734 692/1203 231/400 R/L cGc/cTc rs730880511 1 -1 MAP2K2 HGNC HGNC:6842 protein_coding YES CCDS12120.1 ENSP00000262948 P36507 UPI000012F489 NM_030662.3 deleterious(0) 6/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF314,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 likely_pathogenic MODERATE 1 SNV 1 1 1 PASS rs730880511 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 4101032 4101032 C A 1 0 0 0 0 1 0 0 0 9159 768 27 1 1 MAP2K2 19 4101032 Missense_Mutation SNP C C3N-00560_T 273476 4101032 54516584 1101 17790 ADGRE1 0 . GRCh38 19 6897253 6897253 + Frame_Shift_Del DEL C C - rs755844453 C3N-00560_T C3N-00560_N C C c.345delC p.Thr116LeufsTer95 p.T116Lfs*95 ENST00000312053 4/21 170 80 90 152 152 0 sindel-varindel-pindel ADGRE1,frameshift_variant,p.Thr116LeufsTer95,ENST00000312053,NM_001974.4;ADGRE1,frameshift_variant,p.Thr116LeufsTer95,ENST00000250572,NM_001256253.1;ADGRE1,frameshift_variant,p.Thr116LeufsTer34,ENST00000450315,NM_001256255.1;ADGRE1,frameshift_variant,p.Thr82LeufsTer95,ENST00000595026,;ADGRE1,intron_variant,,ENST00000381404,NM_001256252.1;ADGRE1,intron_variant,,ENST00000381407,NM_001256254.1;ADGRE1,non_coding_transcript_exon_variant,,ENST00000601198,;CTC-312O10.3,upstream_gene_variant,,ENST00000624996,;ADGRE1,non_coding_transcript_exon_variant,,ENST00000596944,;CTC-312O10.2,upstream_gene_variant,,ENST00000595362,; - ENST00000312053 Transcript frameshift_variant 380/3128 343/2661 115/886 P/X Ccc/cc rs755844453,COSM3541120 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 4/21 PROSITE_profiles:PS50026,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181 0,1 HIGH 1 deletion 1 2 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 6897253 6897253 C - 1 0 1 0 1 0 0 0 0 359 855 30 0 0 ADGRE1 19 6897253 Frame_Shift_Del DEL C C3N-00560_T 2796221 6897253 51720363 1102 17791 INSR 0 . GRCh38 19 7132257 7132257 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.2743G>T p.Gly915Trp p.G915W ENST00000302850 14/22 390 167 223 360 359 1 strelka-varscan-mutect INSR,missense_variant,p.Gly903Trp,ENST00000341500,NM_001079817.1;INSR,missense_variant,p.Gly915Trp,ENST00000302850,NM_000208.2; A ENST00000302850 Transcript missense_variant 2886/4721 2743/4149 915/1382 G/W Ggg/Tgg COSM4648348,COSM4648349 1 -1 INSR HGNC HGNC:6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 UPI000020324D NM_000208.2 deleterious(0.02) 14/22 Gene3D:2.60.40.10,PIRSF_domain:PIRSF000620,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF325,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 7132257 7132257 C A 1 0 0 0 0 1 0 0 0 7675 594 21 2 2 INSR 19 7132257 Missense_Mutation SNP C C3N-00560_T 235004 7132257 51485359 1103 17792 ZNF358 0 . GRCh38 19 7519896 7519896 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.654G>T p.Trp218Cys p.W218C ENST00000597229 2/2 138 62 76 109 109 0 strelka-varscan-mutect ZNF358,missense_variant,p.Trp218Cys,ENST00000597229,NM_018083.4;MCOLN1,upstream_gene_variant,,ENST00000264079,NM_020533.2;MCOLN1,upstream_gene_variant,,ENST00000601003,;ZNF358,downstream_gene_variant,,ENST00000596712,;CTD-2207O23.12,downstream_gene_variant,,ENST00000599312,;CTD-2207O23.11,downstream_gene_variant,,ENST00000602083,;MCOLN1,upstream_gene_variant,,ENST00000394321,;MCOLN1,upstream_gene_variant,,ENST00000596390,;CTD-2207O23.12,downstream_gene_variant,,ENST00000597384,; T ENST00000597229 Transcript missense_variant 824/1954 654/1707 218/568 W/C tgG/tgT 1 1 ZNF358 HGNC HGNC:16838 protein_coding YES CCDS32890.2 ENSP00000472305 Q9NW07 UPI0000201F0C NM_018083.4 tolerated(0.18) 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 7519896 7519896 G T 1 0 0 0 0 1 0 0 0 18439 1212 42 2 2 ZNF358 19 7519896 Missense_Mutation SNP G C3N-00560_T 387639 7519896 51097720 1104 17793 FCER2 0 . GRCh38 19 7697011 7697011 + Splice_Site SNP A A T novel C3N-00560_T C3N-00560_N A A c.379+2T>A p.X127_splice ENST00000346664 180 85 95 174 173 1 strelka-varscan-mutect FCER2,splice_donor_variant,,ENST00000346664,NM_002002.4,NM_001220500.1;FCER2,splice_donor_variant,,ENST00000597921,;FCER2,splice_donor_variant,,ENST00000360067,NM_001207019.2;FCER2,intron_variant,,ENST00000593418,;FCER2,splice_donor_variant,,ENST00000597312,;FCER2,splice_donor_variant,,ENST00000598803,;FCER2,splice_donor_variant,,ENST00000597934,; T ENST00000346664 Transcript splice_donor_variant -/1596 379/966 127/321 1 -1 FCER2 HGNC HGNC:3612 protein_coding YES CCDS12184.1 ENSP00000264072 P06734 UPI000002BEF3 NM_002002.4,NM_001220500.1 7/10 HIGH 1 SNV 1 1 PASS . . 0 202 0 7 0 0 0 0 -20 0.999541 1 1 1 0 T 5 4 56 7697011 7697011 A T 1 0 0 0 0 0 0 1 0 5639 173 6 4 4 FCER2 19 7697011 Splice_Site SNP A C3N-00560_T 177115 7697011 50920605 1105 17794 MUC16 0 . GRCh38 19 8958917 8958917 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.17853C>A p.= p.P5951P ENST00000397910 3/84 248 122 126 207 206 1 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 18057/43816 17853/43524 5951/14507 P ccC/ccA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 8958917 8958917 G T 1 0 0 0 0 0 0 0 1 9972 1335 47 2 2 MUC16 19 8958917 Silent SNP G C3N-00560_T 1261906 8958917 49658699 1106 17795 MUC16 0 . GRCh38 19 8976386 8976386 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.4753delC p.His1585IlefsTer63 p.H1585Ifs*63 ENST00000397910 1/84 163 65 98 191 191 0 sindel-varindel-pindel MUC16,frameshift_variant,p.His1585IlefsTer63,ENST00000397910,NM_024690.2; - ENST00000397910 Transcript frameshift_variant 4957/43816 4753/43524 1585/14507 H/X Cat/at 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 56 8976386 8976386 G - 1 0 1 0 1 0 0 0 0 9972 1348 47 0 0 MUC16 19 8976386 Frame_Shift_Del DEL G C3N-00560_T 17469 8976386 49641230 1107 17796 MUC16 0 . GRCh38 19 8978816 8978816 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.2323C>G p.Leu775Val p.L775V ENST00000397910 1/84 167 141 26 181 181 0 strelka-mutect MUC16,missense_variant,p.Leu775Val,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 2527/43816 2323/43524 775/14507 L/V Cta/Gta 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 8978816 8978816 G C 1 0 0 0 0 1 0 0 0 9972 991 35 4 4 MUC16 19 8978816 Missense_Mutation SNP G C3N-00560_T 2430 8978816 49638800 1108 17797 ICAM5 0 . GRCh38 19 10292815 10292815 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1165G>T p.Val389Leu p.V389L ENST00000221980 5/11 208 96 112 218 218 0 strelka-varscan-mutect ICAM5,missense_variant,p.Val389Leu,ENST00000221980,NM_003259.3;ICAM4,downstream_gene_variant,,ENST00000393717,NM_022377.3;ICAM4,downstream_gene_variant,,ENST00000380770,NM_001544.4;ICAM4,downstream_gene_variant,,ENST00000340992,NM_001039132.2;ICAM5,downstream_gene_variant,,ENST00000587398,;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,downstream_gene_variant,,ENST00000586004,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,; T ENST00000221980 Transcript missense_variant 1228/3000 1165/2775 389/924 V/L Gtg/Ttg 1 1 ICAM5 HGNC HGNC:5348 protein_coding YES CCDS12233.1 ENSP00000221980 Q9UMF0 UPI000013C7E4 NM_003259.3 tolerated(0.1) 5/11 Gene3D:2.60.40.10,hmmpanther:PTHR13771,hmmpanther:PTHR13771:SF9,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 10292815 10292815 G T 1 0 0 0 0 1 0 0 0 7383 1377 48 2 2 ICAM5 19 10292815 Missense_Mutation SNP G C3N-00560_T 1313999 10292815 48324801 1109 17798 SMARCA4 0 . GRCh38 19 11025482 11025482 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.3142C>T p.His1048Tyr p.H1048Y ENST00000429416 23/36 503 252 251 453 453 0 strelka-varscan-mutect SMARCA4,missense_variant,p.His1048Tyr,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.His1112Tyr,ENST00000413806,;SMARCA4,missense_variant,p.His1048Tyr,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.His1048Tyr,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.His1048Tyr,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.His1048Tyr,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.His1048Tyr,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.His1048Tyr,ENST00000444061,NM_001128848.1;SMARCA4,downstream_gene_variant,,ENST00000586122,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,downstream_gene_variant,,ENST00000587988,; T ENST00000429416 Transcript missense_variant 3423/5691 3142/4944 1048/1647 H/Y Cac/Tac 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 deleterious(0) 23/36 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Pfam_domain:PF00176,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 11025482 11025482 C T 1 0 0 0 0 1 0 0 0 15063 594 21 3 3 SMARCA4 19 11025482 Missense_Mutation SNP C C3N-00560_T 732667 11025482 47592134 1110 17799 ZNF700 0 . GRCh38 19 11947196 11947196 + Nonsense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.88G>T p.Glu30Ter p.E30* ENST00000622593 2/4 140 77 63 138 138 0 strelka-varscan-mutect ZNF700,stop_gained,p.Glu9Ter,ENST00000482090,;ZNF700,stop_gained,p.Glu30Ter,ENST00000622593,NM_001271848.1;ZNF700,stop_gained,p.Glu27Ter,ENST00000254321,NM_144566.2;CTD-2006C1.13,intron_variant,,ENST00000590798,;CTD-2006C1.13,intron_variant,,ENST00000591944,;CTD-2006C1.12,intron_variant,,ENST00000586394,;CTD-2006C1.13,intron_variant,,ENST00000591441,;CTD-2006C1.13,upstream_gene_variant,,ENST00000586354,; T ENST00000622593 Transcript stop_gained 231/2901 88/2238 30/745 E/* Gag/Tag COSM3959539 1 1 ZNF700 HGNC HGNC:25292 protein_coding YES CCDS74289.1 ENSP00000479449 A0A087WVH9 UPI0002A097BD NM_001271848.1 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24379,hmmpanther:PTHR24379:SF24,SMART_domains:SM00349 1 HIGH SNV 4 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 11947196 11947196 G T 1 0 0 0 0 0 1 0 0 18677 1291 45 2 2 ZNF700 19 11947196 Nonsense_Mutation SNP G C3N-00560_T 921714 11947196 46670420 1111 17800 CACNA1A 0 . GRCh38 19 13455145 13455145 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.361C>A p.Leu121Met p.L121M ENST00000360228 2/47 111 47 64 102 102 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Leu121Met,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Leu121Met,ENST00000635895,;CACNA1A,missense_variant,p.Leu121Met,ENST00000637769,;CACNA1A,missense_variant,p.Leu121Met,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Leu121Met,ENST00000614285,;CACNA1A,missense_variant,p.Leu121Met,ENST00000636389,;CACNA1A,missense_variant,p.Leu121Met,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Leu121Met,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Leu121Met,ENST00000573710,;CACNA1A,missense_variant,p.Leu121Met,ENST00000635727,;CACNA1A,missense_variant,p.Leu121Met,ENST00000636012,;CACNA1A,missense_variant,p.Leu121Met,ENST00000637276,;CACNA1A,missense_variant,p.Leu121Met,ENST00000637927,;CACNA1A,missense_variant,p.Leu121Met,ENST00000636549,NM_001174080.1;CACNA1A,missense_variant,p.Leu38Met,ENST00000574974,;CACNA1A,intron_variant,,ENST00000637736,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637966,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636966,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637616,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000593160,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637981,; T ENST00000360228 Transcript missense_variant 596/8627 361/7521 121/2506 L/M Ctg/Atg 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0) 2/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 13455145 13455145 G T 1 0 0 0 0 1 0 0 0 2226 933 33 2 2 CACNA1A 19 13455145 Missense_Mutation SNP G C3N-00560_T 1507949 13455145 45162471 1112 17801 ADGRE2 0 . GRCh38 19 14743663 14743663 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2305C>A p.Leu769Met p.L769M ENST00000315576 19/21 191 89 102 159 159 0 strelka-varscan-mutect ADGRE2,missense_variant,p.Leu769Met,ENST00000315576,NM_013447.3;ADGRE2,missense_variant,p.Leu758Met,ENST00000601345,;ADGRE2,missense_variant,p.Leu758Met,ENST00000596991,;ADGRE2,missense_variant,p.Leu711Met,ENST00000392965,NM_001271052.1;ADGRE2,missense_variant,p.Leu720Met,ENST00000594294,;ADGRE2,missense_variant,p.Leu676Met,ENST00000594076,;ADGRE2,missense_variant,p.Leu627Met,ENST00000595839,;ADGRE2,non_coding_transcript_exon_variant,,ENST00000360222,;ADGRE2,downstream_gene_variant,,ENST00000595208,; T ENST00000315576 Transcript missense_variant 2757/6767 2305/2472 769/823 L/M Ctg/Atg 1 -1 ADGRE2 HGNC HGNC:3337 protein_coding YES CCDS32935.1 ENSP00000319883 Q9UHX3 UPI000016393A NM_013447.3 deleterious(0) 19/21 Pfam_domain:PF00002,Prints_domain:PR00249,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF286,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 14743663 14743663 G T 1 0 0 0 0 1 0 0 0 360 991 35 2 2 ADGRE2 19 14743663 Missense_Mutation SNP G C3N-00560_T 1288518 14743663 43873953 1113 17802 ADGRE2 0 . GRCh38 19 14765774 14765774 + Missense_Mutation SNP T T A rs762072283 C3N-00560_T C3N-00560_N T T c.665A>T p.Gln222Leu p.Q222L ENST00000315576 8/21 204 141 63 190 190 0 strelka-varscan-mutect ADGRE2,missense_variant,p.Gln222Leu,ENST00000315576,NM_013447.3;ADGRE2,missense_variant,p.Gln222Leu,ENST00000601345,;ADGRE2,missense_variant,p.Gln222Leu,ENST00000596991,;ADGRE2,missense_variant,p.Gln222Leu,ENST00000392965,NM_001271052.1;ADGRE2,missense_variant,p.Gln173Leu,ENST00000594294,;ADGRE2,missense_variant,p.Gln129Leu,ENST00000594076,;ADGRE2,intron_variant,,ENST00000595839,;ADGRE2,downstream_gene_variant,,ENST00000599423,;ADGRE2,downstream_gene_variant,,ENST00000601619,;ADGRE2,missense_variant,p.Gln66Leu,ENST00000595208,;ADGRE2,missense_variant,p.Gln173Leu,ENST00000392962,;ADGRE2,non_coding_transcript_exon_variant,,ENST00000360222,; A ENST00000315576 Transcript missense_variant 1117/6767 665/2472 222/823 Q/L cAg/cTg rs762072283 1 -1 ADGRE2 HGNC HGNC:3337 protein_coding YES CCDS32935.1 ENSP00000319883 Q9UHX3 UPI000016393A NM_013447.3 tolerated(0.08) 8/21 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF286,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs762072283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 14765774 14765774 T A 1 0 0 0 0 1 0 0 0 360 1580 55 4 4 ADGRE2 19 14765774 Missense_Mutation SNP T C3N-00560_T 22111 14765774 43851842 1114 17803 KCNN1 0 . GRCh38 19 17974050 17974050 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.162C>A p.= p.P54P ENST00000222249 3/11 197 79 118 167 167 0 strelka-varscan-mutect KCNN1,synonymous_variant,p.=,ENST00000222249,NM_002248.4;KCNN1,synonymous_variant,p.=,ENST00000615435,;KCNN1,synonymous_variant,p.=,ENST00000609922,;RNA5SP468,downstream_gene_variant,,ENST00000516782,; A ENST00000222249 Transcript synonymous_variant 481/3625 162/1632 54/543 P ccC/ccA 1 1 KCNN1 HGNC HGNC:6290 protein_coding YES CCDS67611.1 ENSP00000476519 Q92952 UPI00001649F9 NM_002248.4 3/11 Low_complexity_(Seg):seg,hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF38 LOW 1 SNV 1 1 PASS rs1299315675 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 17974050 17974050 C A 1 0 0 0 0 0 0 0 1 7994 668 24 2 2 KCNN1 19 17974050 Silent SNP C C3N-00560_T 3208276 17974050 40643566 1115 17804 SLC25A42 0 . GRCh38 19 19110667 19110667 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.748G>T p.Val250Leu p.V250L ENST00000318596 8/8 174 76 98 169 169 0 strelka-varscan-mutect SLC25A42,missense_variant,p.Val250Leu,ENST00000318596,NM_001321544.1,NM_178526.4;SLC25A42,downstream_gene_variant,,ENST00000600275,;SLC25A42,downstream_gene_variant,,ENST00000594070,;SLC25A42,downstream_gene_variant,,ENST00000596819,;SLC25A42,downstream_gene_variant,,ENST00000597661,; T ENST00000318596 Transcript missense_variant 899/3120 748/957 250/318 V/L Gtg/Ttg COSM4632203 1 1 SLC25A42 HGNC HGNC:28380 protein_coding YES CCDS32966.1 ENSP00000326693 Q86VD7 A0A024R7K2 UPI0000198748 NM_001321544.1,NM_178526.4 deleterious(0.01) 8/8 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF242,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588,Prints_domain:PR00926 1 MODERATE 1 SNV 1 1 1 PASS rs1375781278 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 19110667 19110667 G T 1 0 0 0 0 1 0 0 0 14772 1261 44 2 2 SLC25A42 19 19110667 Missense_Mutation SNP G C3N-00560_T 1136617 19110667 39506949 1116 17805 NCAN 0 . GRCh38 19 19249820 19249820 + Missense_Mutation SNP A A T rs775943135 C3N-00560_T C3N-00560_N A A c.3875A>T p.Gln1292Leu p.Q1292L ENST00000252575 15/15 109 49 60 101 101 0 strelka-varscan-mutect NCAN,missense_variant,p.Gln1292Leu,ENST00000252575,NM_004386.2;NCAN,missense_variant,p.Gln146Leu,ENST00000588231,;AC138430.4,downstream_gene_variant,,ENST00000586064,;NCAN,downstream_gene_variant,,ENST00000585410,; T ENST00000252575 Transcript missense_variant 3974/6387 3875/3966 1292/1321 Q/L cAg/cTg rs775943135,COSM4075902,COSM4075903 1 1 NCAN HGNC HGNC:2465 protein_coding YES CCDS12397.1 ENSP00000252575 O14594 A0A024R7M3 UPI000013CD70 NM_004386.2 tolerated(0.06) 15/15 Low_complexity_(Seg):seg,hmmpanther:PTHR22804:SF24,hmmpanther:PTHR22804 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs775943135 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 19249820 19249820 A T 1 0 0 0 0 1 0 0 0 10220 188 7 4 4 NCAN 19 19249820 Missense_Mutation SNP A C3N-00560_T 139153 19249820 39367796 1117 17806 CILP2 0 . GRCh38 19 19544453 19544453 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.1908A>T p.= p.P636P ENST00000291495 8/8 184 87 97 174 174 0 strelka-varscan-mutect CILP2,synonymous_variant,p.=,ENST00000586018,;CILP2,synonymous_variant,p.=,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; T ENST00000291495 Transcript synonymous_variant 1993/4199 1908/3471 636/1156 P ccA/ccT 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 LOW 1 SNV 1 1 PASS rs1182711800 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 19544453 19544453 A T 1 0 0 0 0 0 0 0 1 3192 146 6 4 4 CILP2 19 19544453 Silent SNP A C3N-00560_T 294633 19544453 39073163 1118 17807 ZNF91 0 . GRCh38 19 23373777 23373777 + Missense_Mutation SNP T T C rs757869359 C3N-00560_T C3N-00560_N T T c.218A>G p.Asn73Ser p.N73S ENST00000300619 3/4 103 67 36 136 136 0 strelka-varscan-mutect ZNF91,missense_variant,p.Asn73Ser,ENST00000300619,NM_003430.3;ZNF91,missense_variant,p.Asn73Ser,ENST00000599743,;ZNF91,intron_variant,,ENST00000397082,NM_001300951.1;ZNF91,intron_variant,,ENST00000595533,;ZNF91,non_coding_transcript_exon_variant,,ENST00000596989,; C ENST00000300619 Transcript missense_variant 424/5489 218/3576 73/1191 N/S aAt/aGt rs757869359 1 -1 ZNF91 HGNC HGNC:13166 protein_coding YES CCDS42541.1 ENSP00000300619 Q05481 UPI00002038F9 NM_003430.3 tolerated(0.73) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF195,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS rs757869359 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 23373777 23373777 T C 1 0 0 0 0 1 0 0 0 18793 1493 52 5 5 ZNF91 19 23373777 Missense_Mutation SNP T C3N-00560_T 3829324 23373777 35243839 1119 17808 ZNF536 0 . GRCh38 19 30444779 30444779 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1217C>G p.Pro406Arg p.P406R ENST00000355537 2/5 448 354 94 283 283 0 strelka-varscan-mutect ZNF536,missense_variant,p.Pro406Arg,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Pro406Arg,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; G ENST00000355537 Transcript missense_variant 1364/4945 1217/3903 406/1300 P/R cCc/cGc 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated(0.14) 2/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 30444779 30444779 C G 1 0 0 0 0 1 0 0 0 18547 623 22 4 4 ZNF536 19 30444779 Missense_Mutation SNP C C3N-00560_T 7071002 30444779 28172837 1120 17809 ZNF536 0 . GRCh38 19 30445194 30445194 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1632G>T p.= p.L544L ENST00000355537 2/5 320 245 75 208 208 0 strelka-varscan-mutect ZNF536,synonymous_variant,p.=,ENST00000355537,NM_014717.1;ZNF536,synonymous_variant,p.=,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript synonymous_variant 1779/4945 1632/3903 544/1300 L ctG/ctT 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 2/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 LOW 1 SNV 1 1 PASS rs1286116407 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 30445194 30445194 G T 1 0 0 0 0 0 0 0 1 18547 1306 46 2 2 ZNF536 19 30445194 Silent SNP G C3N-00560_T 415 30445194 28172422 1121 17810 TSHZ3 0 . GRCh38 19 31277127 31277127 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.2666A>G p.Gln889Arg p.Q889R ENST00000240587 2/2 37 23 14 41 41 0 strelka-varscan-mutect TSHZ3,missense_variant,p.Gln889Arg,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; C ENST00000240587 Transcript missense_variant 2994/5176 2666/3246 889/1081 Q/R cAg/cGg 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0.01) 2/2 Gene3D:1.10.10.60,PROSITE_profiles:PS50071,hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 MODERATE 1 SNV 1 1 PASS rs1245684737 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 31277127 31277127 T C 1 0 0 0 0 1 0 0 0 17130 1580 55 5 5 TSHZ3 19 31277127 Missense_Mutation SNP T C3N-00560_T 831933 31277127 27340489 1122 17811 TSHZ3 0 . GRCh38 19 31279504 31279504 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.289G>T p.Glu97Ter p.E97* ENST00000240587 2/2 63 38 25 68 68 0 strelka-mutect TSHZ3,stop_gained,p.Glu97Ter,ENST00000240587,NM_020856.2;TSHZ3,non_coding_transcript_exon_variant,,ENST00000560707,; A ENST00000240587 Transcript stop_gained 617/5176 289/3246 97/1081 E/* Gag/Tag 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 31279504 31279504 C A 1 0 0 0 0 0 1 0 0 17130 922 32 2 2 TSHZ3 19 31279504 Nonsense_Mutation SNP C C3N-00560_T 2377 31279504 27338112 1123 17812 PEPD 0 . GRCh38 19 33401846 33401846 + Missense_Mutation SNP T T A rs766027294 C3N-00560_T C3N-00560_N T T c.842A>T p.Tyr281Phe p.Y281F ENST00000244137 12/15 1185 793 392 524 523 1 strelka-varscan-mutect PEPD,missense_variant,p.Tyr281Phe,ENST00000244137,NM_000285.3;PEPD,missense_variant,p.Tyr240Phe,ENST00000397032,NM_001166056.1;PEPD,missense_variant,p.Tyr217Phe,ENST00000436370,NM_001166057.1;PEPD,missense_variant,p.Tyr112Phe,ENST00000588328,;PEPD,missense_variant,p.Tyr92Phe,ENST00000609145,;PEPD,non_coding_transcript_exon_variant,,ENST00000590731,;PEPD,non_coding_transcript_exon_variant,,ENST00000588719,;PEPD,non_coding_transcript_exon_variant,,ENST00000593163,; A ENST00000244137 Transcript missense_variant 876/1910 842/1482 281/493 Y/F tAt/tTt rs766027294 1 -1 PEPD HGNC HGNC:8840 protein_coding YES CCDS42544.1 ENSP00000244137 P12955 A0A140VJR2 UPI000006F8BF NM_000285.3 deleterious(0.02) 12/15 hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF100,Pfam_domain:PF00557,Gene3D:3.90.230.10,Superfamily_domains:SSF55920 MODERATE 1 SNV 1 1 PASS rs766027294 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 33401846 33401846 T A 1 0 0 0 0 1 0 0 0 11816 1406 49 4 4 PEPD 19 33401846 Missense_Mutation SNP T C3N-00560_T 2122342 33401846 25215770 1124 17813 PROSER3 0 . GRCh38 19 35759788 35759788 + Splice_Site SNP G G A novel C3N-00560_T C3N-00560_N G G c.109-1G>A p.X37_splice ENST00000396908 215 156 59 147 147 0 strelka-varscan-mutect PROSER3,splice_acceptor_variant,,ENST00000396908,NM_001039887.2;PROSER3,splice_acceptor_variant,,ENST00000536950,;PROSER3,splice_acceptor_variant,,ENST00000301165,;PROSER3,splice_acceptor_variant,,ENST00000537459,;PROSER3,splice_acceptor_variant,,ENST00000545674,;PROSER3,splice_acceptor_variant,,ENST00000444637,;PROSER3,intron_variant,,ENST00000421853,;HSPB6,upstream_gene_variant,,ENST00000592984,;HSPB6,upstream_gene_variant,,ENST00000004982,NM_144617.2;HSPB6,upstream_gene_variant,,ENST00000587965,;PROSER3,upstream_gene_variant,,ENST00000542134,;AC002398.12,downstream_gene_variant,,ENST00000587767,;PROSER3,intron_variant,,ENST00000544876,;PROSER3,splice_acceptor_variant,,ENST00000620918,;PROSER3,splice_acceptor_variant,,ENST00000601095,;PROSER3,non_coding_transcript_exon_variant,,ENST00000600988,;PROSER3,intron_variant,,ENST00000539771,; A ENST00000396908 Transcript splice_acceptor_variant -/2149 109/1443 37/480 1 1 PROSER3 HGNC HGNC:25204 protein_coding YES ENSP00000380116 Q2NL68 UPI000067CA4C NM_001039887.2 2/10 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 56 35759788 35759788 G A 1 0 0 0 0 0 0 1 0 12695 956 33 3 3 PROSER3 19 35759788 Splice_Site SNP G C3N-00560_T 2357942 35759788 22857828 1125 17814 PROSER3 0 . GRCh38 19 35766922 35766922 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.924G>T p.Trp308Cys p.W308C ENST00000396908 8/11 136 89 47 93 93 0 strelka-varscan-mutect PROSER3,missense_variant,p.Trp308Cys,ENST00000396908,NM_001039887.2;PROSER3,downstream_gene_variant,,ENST00000536950,;PROSER3,downstream_gene_variant,,ENST00000301165,;PROSER3,downstream_gene_variant,,ENST00000537459,;PROSER3,downstream_gene_variant,,ENST00000421853,;PROSER3,downstream_gene_variant,,ENST00000545674,;PROSER3,downstream_gene_variant,,ENST00000444637,;PROSER3,downstream_gene_variant,,ENST00000542134,;AC002398.13,downstream_gene_variant,,ENST00000589397,;PROSER3,non_coding_transcript_exon_variant,,ENST00000542591,;PROSER3,intron_variant,,ENST00000544876,;PROSER3,upstream_gene_variant,,ENST00000536037,;PROSER3,missense_variant,p.Trp296Cys,ENST00000620918,;PROSER3,downstream_gene_variant,,ENST00000600988,;PROSER3,upstream_gene_variant,,ENST00000544158,;PROSER3,downstream_gene_variant,,ENST00000601095,;PROSER3,downstream_gene_variant,,ENST00000539771,; T ENST00000396908 Transcript missense_variant 987/2149 924/1443 308/480 W/C tgG/tgT COSM239034 1 1 PROSER3 HGNC HGNC:25204 protein_coding YES ENSP00000380116 Q2NL68 UPI000067CA4C NM_001039887.2 deleterious(0.02) 8/11 hmmpanther:PTHR22045,hmmpanther:PTHR22045:SF6 1 MODERATE 1 SNV 1 1 1 PASS rs907280072 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 35766922 35766922 G T 1 0 0 0 0 1 0 0 0 12695 1241 43 2 2 PROSER3 19 35766922 Missense_Mutation SNP G C3N-00560_T 7134 35766922 22850694 1126 17815 ZNF793 0 . GRCh38 19 37537512 37537512 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.854G>T p.Cys285Phe p.C285F ENST00000445217 4/4 218 188 30 159 158 1 strelka-varscan-mutect ZNF793,missense_variant,p.Cys285Phe,ENST00000445217,NM_001013659.2;ZNF793,missense_variant,p.Cys191Phe,ENST00000542455,;ZNF793,missense_variant,p.Cys285Phe,ENST00000627814,;ZNF793,missense_variant,p.Cys285Phe,ENST00000587143,;ZNF793,3_prime_UTR_variant,,ENST00000588578,;ZNF793,intron_variant,,ENST00000589319,;ZNF793,downstream_gene_variant,,ENST00000587986,;ZNF793,downstream_gene_variant,,ENST00000586138,;ZNF793,downstream_gene_variant,,ENST00000587490,;ZNF793,intron_variant,,ENST00000586187,; T ENST00000445217 Transcript missense_variant 889/6712 854/1221 285/406 C/F tGt/tTt 1 1 ZNF793 HGNC HGNC:33115 protein_coding YES CCDS46062.1 ENSP00000396402 Q6ZN11 UPI0001536771 NM_001013659.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF42,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs766943226 . 0 138 0 25 47 0 0 0 -12.58937 0 0 1 0 0 T 3 4 56 37537512 37537512 G T 1 0 0 0 0 1 0 0 0 18750 1391 48 2 2 ZNF793 19 37537512 Missense_Mutation SNP G C3N-00560_T 1770590 37537512 21080104 1127 17816 WDR87 0 . GRCh38 19 37887669 37887669 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.6002C>T p.Ala2001Val p.A2001V ENST00000447313 6/6 209 72 137 152 151 1 strelka-varscan-mutect WDR87,missense_variant,p.Ala2001Val,ENST00000447313,NM_001291088.1;WDR87,missense_variant,p.Ala1962Val,ENST00000303868,NM_031951.4; A ENST00000447313 Transcript missense_variant 6163/9009 6002/8739 2001/2912 A/V gCa/gTa 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 deleterious(0.01) 6/6 PD936484 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 37887669 37887669 G A 1 0 0 0 0 1 0 0 0 17890 1319 46 3 3 WDR87 19 37887669 Missense_Mutation SNP G C3N-00560_T 350157 37887669 20729947 1128 17817 WDR87 0 . GRCh38 19 37893693 37893693 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2010C>A p.Tyr670Ter p.Y670* ENST00000447313 4/6 254 71 183 162 162 0 strelka-varscan-mutect WDR87,stop_gained,p.Tyr670Ter,ENST00000447313,NM_001291088.1;WDR87,stop_gained,p.Tyr631Ter,ENST00000303868,NM_031951.4;WDR87,downstream_gene_variant,,ENST00000473328,; T ENST00000447313 Transcript stop_gained 2171/9009 2010/8739 670/2912 Y/* taC/taA 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 4/6 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF465 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 37893693 37893693 G T 1 0 0 0 0 0 1 0 0 17890 1256 44 2 2 WDR87 19 37893693 Nonsense_Mutation SNP G C3N-00560_T 6024 37893693 20723923 1129 17818 SIPA1L3 0 . GRCh38 19 38082627 38082627 + Missense_Mutation SNP G G T rs146812141 C3N-00560_T C3N-00560_N G G c.1062G>T p.Glu354Asp p.E354D ENST00000222345 3/22 301 95 206 223 223 0 strelka-varscan-mutect SIPA1L3,missense_variant,p.Glu354Asp,ENST00000222345,NM_015073.2;SIPA1L3,downstream_gene_variant,,ENST00000476317,; T ENST00000222345 Transcript missense_variant 1571/7987 1062/5346 354/1781 E/D gaG/gaT rs146812141 1 1 SIPA1L3 HGNC HGNC:23801 protein_coding YES CCDS33007.1 ENSP00000222345 O60292 UPI00001D8160 NM_015073.2 deleterious(0.03) 3/22 hmmpanther:PTHR15711:SF15,hmmpanther:PTHR15711 MODERATE 1 SNV 1 1 PASS rs146812141 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 38082627 38082627 G T 1 0 0 0 0 1 0 0 0 14594 991 35 2 2 SIPA1L3 19 38082627 Missense_Mutation SNP G C3N-00560_T 188934 38082627 20534989 1130 17819 RYR1 0 . GRCh38 19 38469118 38469118 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3534C>A p.Phe1178Leu p.F1178L ENST00000359596 26/106 718 230 488 476 476 0 strelka-varscan-mutect RYR1,missense_variant,p.Phe1178Leu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Phe1178Leu,ENST00000359596,NM_000540.2;RYR1,downstream_gene_variant,,ENST00000594111,; A ENST00000359596 Transcript missense_variant 3534/15117 3534/15117 1178/5038 F/L ttC/ttA 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.01) 26/106 PROSITE_profiles:PS50188,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 38469118 38469118 C A 1 0 0 0 0 1 0 0 0 14028 854 30 2 2 RYR1 19 38469118 Missense_Mutation SNP C C3N-00560_T 386491 38469118 20148498 1131 17820 ACP7 0 . GRCh38 19 39085324 39085324 + Missense_Mutation SNP T T A rs780329718 C3N-00560_T C3N-00560_N T T c.55T>A p.Leu19Met p.L19M ENST00000331256 2/13 129 52 77 111 111 0 strelka-varscan-mutect ACP7,missense_variant,p.Leu19Met,ENST00000331256,NM_001004318.2;ACP7,missense_variant,p.Leu19Met,ENST00000594229,;ACP7,missense_variant,p.Leu19Met,ENST00000601575,; A ENST00000331256 Transcript missense_variant 329/2966 55/1317 19/438 L/M Ttg/Atg rs780329718 1 1 ACP7 HGNC HGNC:33781 protein_coding YES CCDS33018.1 ENSP00000327557 Q6ZNF0 UPI000041AA68 NM_001004318.2 deleterious(0.03) 2/13 hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF9,Cleavage_site_(Signalp):SignalP-noTM,Superfamily_domains:SSF49363 MODERATE 1 SNV 2 1 PASS rs780329718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 39085324 39085324 T A 1 0 0 0 0 1 0 0 0 208 1606 56 4 4 ACP7 19 39085324 Missense_Mutation SNP T C3N-00560_T 616206 39085324 19532292 1132 17821 AXL 0 . GRCh38 19 41220803 41220803 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.253C>A p.Gln85Lys p.Q85K ENST00000301178 2/20 350 257 93 329 329 0 strelka-varscan-mutect AXL,missense_variant,p.Gln85Lys,ENST00000301178,NM_021913.4;AXL,missense_variant,p.Gln85Lys,ENST00000359092,NM_001699.5;CTD-2195B23.3,downstream_gene_variant,,ENST00000598541,;AXL,non_coding_transcript_exon_variant,,ENST00000594880,;AXL,non_coding_transcript_exon_variant,,ENST00000599659,; A ENST00000301178 Transcript missense_variant 443/4737 253/2685 85/894 Q/K Cag/Aag 1 1 AXL HGNC HGNC:905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 UPI000014319B NM_021913.4 deleterious(0.02) 2/20 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF323,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 41220803 41220803 C A 1 0 0 0 0 1 0 0 0 1395 595 21 2 2 AXL 19 41220803 Missense_Mutation SNP C C3N-00560_T 2135479 41220803 17396813 1133 17822 HNRNPUL1 0 . GRCh38 19 41279094 41279094 + Silent SNP C C T rs758565657 C3N-00560_T C3N-00560_N C C c.804C>T p.= p.S268S ENST00000392006 6/15 225 82 143 184 184 0 strelka-varscan-mutect HNRNPUL1,synonymous_variant,p.=,ENST00000392006,NM_007040.4;HNRNPUL1,synonymous_variant,p.=,ENST00000352456,;HNRNPUL1,synonymous_variant,p.=,ENST00000263367,;HNRNPUL1,synonymous_variant,p.=,ENST00000602130,;HNRNPUL1,synonymous_variant,p.=,ENST00000595018,NM_144732.3;HNRNPUL1,synonymous_variant,p.=,ENST00000593587,;HNRNPUL1,synonymous_variant,p.=,ENST00000599614,;HNRNPUL1,synonymous_variant,p.=,ENST00000599719,;HNRNPUL1,synonymous_variant,p.=,ENST00000597725,;HNRNPUL1,intron_variant,,ENST00000378215,;HNRNPUL1,intron_variant,,ENST00000617305,;HNRNPUL1,intron_variant,,ENST00000617774,;HNRNPUL1,downstream_gene_variant,,ENST00000601336,;HNRNPUL1,downstream_gene_variant,,ENST00000601309,;HNRNPUL1,non_coding_transcript_exon_variant,,ENST00000594207,;HNRNPUL1,synonymous_variant,p.=,ENST00000600596,;HNRNPUL1,3_prime_UTR_variant,,ENST00000595196,;HNRNPUL1,downstream_gene_variant,,ENST00000600332,; T ENST00000392006 Transcript synonymous_variant 977/3555 804/2571 268/856 S tcC/tcT rs758565657 1 1 HNRNPUL1 HGNC HGNC:17011 protein_coding YES CCDS12576.1 ENSP00000375863 Q9BUJ2 UPI000013D3F4 NM_007040.4 6/15 PROSITE_profiles:PS50188,hmmpanther:PTHR12381,hmmpanther:PTHR12381:SF41,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs758565657 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 41279094 41279094 C T 1 0 0 0 0 0 0 0 1 7169 639 23 1 1 HNRNPUL1 19 41279094 Silent SNP C C3N-00560_T 58291 41279094 17338522 1134 17823 GRIK5 0 . GRCh38 19 42006661 42006661 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2021C>A p.Thr674Asn p.T674N ENST00000301218 15/19 224 78 146 189 189 0 strelka-varscan-mutect GRIK5,missense_variant,p.Thr674Asn,ENST00000262895,NM_002088.4;GRIK5,missense_variant,p.Thr674Asn,ENST00000301218,NM_001301030.1;GRIK5,missense_variant,p.Thr674Asn,ENST00000593562,;GRIK5,non_coding_transcript_exon_variant,,ENST00000454993,;GRIK5,upstream_gene_variant,,ENST00000602210,; T ENST00000301218 Transcript missense_variant 2056/3310 2021/2946 674/981 T/N aCc/aAc 1 -1 GRIK5 HGNC HGNC:4583 protein_coding YES CCDS77305.1 ENSP00000301218 Q16478 UPI000006E81F NM_001301030.1 deleterious(0) 15/19 Gene3D:1.10.287.70,Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF34,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 42006661 42006661 G T 1 0 0 0 0 1 0 0 0 6659 1261 44 2 2 GRIK5 19 42006661 Missense_Mutation SNP G C3N-00560_T 727567 42006661 16610955 1135 17824 PSG9 0 . GRCh38 19 43258873 43258873 + Silent SNP G G T rs745937029 C3N-00560_T C3N-00560_N G G c.972C>A p.= p.V324V ENST00000270077 4/6 292 215 77 136 136 0 varscan-mutect PSG9,synonymous_variant,p.=,ENST00000621109,;PSG9,synonymous_variant,p.=,ENST00000418820,;PSG9,synonymous_variant,p.=,ENST00000270077,NM_002784.4;PSG9,synonymous_variant,p.=,ENST00000443718,NM_001301707.1;PSG9,intron_variant,,ENST00000244293,;PSG9,intron_variant,,ENST00000596730,;PSG9,intron_variant,,ENST00000593948,NM_001301708.1;PSG9,intron_variant,,ENST00000291752,NM_001301709.1;PSG9,non_coding_transcript_exon_variant,,ENST00000595404,; T ENST00000270077 Transcript synonymous_variant 1069/1705 972/1281 324/426 V gtC/gtA rs745937029 1 -1 PSG9 HGNC HGNC:9526 protein_coding YES CCDS12618.1 ENSP00000270077 Q00887 UPI00001327A5 NM_002784.4 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs745937029 . 14 193 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 43258873 43258873 G T 1 0 0 0 0 0 0 0 1 12813 1277 45 2 2 PSG9 19 43258873 Silent SNP G C3N-00560_T 1252212 43258873 15358743 1136 17825 ZNF221 0 . GRCh38 19 43967082 43967082 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1580G>T p.Cys527Phe p.C527F ENST00000251269 6/6 307 193 114 246 246 0 strelka-varscan-mutect ZNF221,missense_variant,p.Cys527Phe,ENST00000251269,NM_013359.2;ZNF221,missense_variant,p.Cys527Phe,ENST00000592350,;ZNF221,missense_variant,p.Cys527Phe,ENST00000622072,;ZNF221,missense_variant,p.Cys527Phe,ENST00000587682,NM_001297589.1,NM_001297588.1;ZNF221,downstream_gene_variant,,ENST00000591168,;ZNF155,upstream_gene_variant,,ENST00000590411,; T ENST00000251269 Transcript missense_variant 1908/2535 1580/1854 527/617 C/F tGc/tTc 1 1 ZNF221 HGNC HGNC:13014 protein_coding YES CCDS12633.1 ENSP00000251269 A0A087WT08 UPI00015CFC02 NM_013359.2 deleterious(0) 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24388,hmmpanther:PTHR24388:SF3,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 43967082 43967082 G T 1 0 0 0 0 1 0 0 0 18352 1319 46 2 2 ZNF221 19 43967082 Missense_Mutation SNP G C3N-00560_T 708209 43967082 14650534 1137 17826 ZNF230 0 . GRCh38 19 44011204 44011204 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1165G>T p.Glu389Ter p.E389* ENST00000429154 5/5 486 366 120 312 311 1 strelka-varscan-mutect ZNF230,stop_gained,p.Glu389Ter,ENST00000429154,NM_006300.3;ZNF230,downstream_gene_variant,,ENST00000585491,;ZNF230,downstream_gene_variant,,ENST00000585632,;ZNF230,3_prime_UTR_variant,,ENST00000585568,; T ENST00000429154 Transcript stop_gained 1393/4115 1165/1425 389/474 E/* Gag/Tag 1 1 ZNF230 HGNC HGNC:13024 protein_coding YES CCDS33044.1 ENSP00000409318 Q9UIE0 UPI000016960C NM_006300.3 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF176,hmmpanther:PTHR24402,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 44011204 44011204 G T 1 0 0 0 0 0 1 0 0 18361 943 33 2 2 ZNF230 19 44011204 Nonsense_Mutation SNP G C3N-00560_T 44122 44011204 14606412 1138 17827 ZNF233 0 . GRCh38 19 44274277 44274277 + Missense_Mutation SNP G G C rs752266706 C3N-00560_T C3N-00560_N G G c.1617G>C p.Glu539Asp p.E539D ENST00000391958 5/5 303 232 71 172 172 0 strelka-varscan-mutect ZNF233,missense_variant,p.Glu539Asp,ENST00000391958,NM_001207005.1,NM_181756.2;ZNF233,3_prime_UTR_variant,,ENST00000592581,;ZNF235,intron_variant,,ENST00000589799,;ZNF233,downstream_gene_variant,,ENST00000590668,;ZNF235,downstream_gene_variant,,ENST00000589248,;ZNF235,intron_variant,,ENST00000592844,; C ENST00000391958 Transcript missense_variant 1744/2784 1617/2013 539/670 E/D gaG/gaC rs752266706 1 1 ZNF233 HGNC HGNC:30946 protein_coding YES CCDS33047.1 ENSP00000375820 A6NK53 UPI000049DEBE NM_001207005.1,NM_181756.2 tolerated(0.32) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs752266706 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 44274277 44274277 G C 1 0 0 0 0 1 0 0 0 18363 933 33 4 4 ZNF233 19 44274277 Missense_Mutation SNP G C3N-00560_T 263073 44274277 14343339 1139 17828 ZNF229 0 . GRCh38 19 44428544 44428544 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.2237G>T p.Gly746Val p.G746V ENST00000614049 6/6 389 305 84 200 200 0 strelka-varscan-mutect ZNF229,missense_variant,p.Gly740Val,ENST00000613197,NM_001278510.2;ZNF229,missense_variant,p.Gly746Val,ENST00000614049,NM_014518.3;ZNF229,downstream_gene_variant,,ENST00000592308,;CTC-512J12.4,intron_variant,,ENST00000588655,;ZNF229,intron_variant,,ENST00000591289,;ZNF229,3_prime_UTR_variant,,ENST00000620012,; A ENST00000614049 Transcript missense_variant 2671/4507 2237/2478 746/825 G/V gGg/gTg 1 -1 ZNF229 HGNC HGNC:13022 protein_coding YES CCDS42574.1 ENSP00000479884 Q9UJW7 UPI0001747B51 NM_014518.3 deleterious(0) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF348,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 44428544 44428544 C A 1 0 0 0 0 1 0 0 0 18359 623 22 2 2 ZNF229 19 44428544 Missense_Mutation SNP C C3N-00560_T 154267 44428544 14189072 1140 17829 APOC4 0 . GRCh38 19 44945299 44945299 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.378G>A p.= p.Q126Q ENST00000592954 3/3 142 38 104 80 80 0 strelka-varscan-mutect APOC4,synonymous_variant,p.=,ENST00000592954,NM_001646.2;APOC4-APOC2,intron_variant,,ENST00000589057,;APOC2,upstream_gene_variant,,ENST00000585786,;APOC2,upstream_gene_variant,,ENST00000590360,;APOC4-APOC2,upstream_gene_variant,,ENST00000252490,NM_000483.4;APOC2,upstream_gene_variant,,ENST00000591597,;APOC2,upstream_gene_variant,,ENST00000592257,;APOC4,downstream_gene_variant,,ENST00000591600,;CTB-129P6.11,downstream_gene_variant,,ENST00000591646,;APOC4-APOC2,synonymous_variant,p.=,ENST00000585685,; A ENST00000592954 Transcript synonymous_variant 418/615 378/384 126/127 Q caG/caA 1 1 APOC4 HGNC HGNC:611 protein_coding YES CCDS12649.1 ENSP00000468236 P55056 UPI0000125C2A NM_001646.2 3/3 PD020932,hmmpanther:PTHR32288 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 44945299 44945299 G A 1 0 0 0 0 0 0 0 1 922 991 35 3 3 APOC4 19 44945299 Silent SNP G C3N-00560_T 516755 44945299 13672317 1141 17830 CLPTM1 0 . GRCh38 19 44990477 44990477 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1215G>T p.= p.V405V ENST00000337392 10/14 238 84 154 185 184 1 strelka-varscan-mutect CLPTM1,synonymous_variant,p.=,ENST00000541297,NM_001282175.1;CLPTM1,synonymous_variant,p.=,ENST00000337392,NM_001294.3;CLPTM1,synonymous_variant,p.=,ENST00000546079,NM_001282176.1;CLPTM1,upstream_gene_variant,,ENST00000586915,;CLPTM1,downstream_gene_variant,,ENST00000589158,;CLPTM1,synonymous_variant,p.=,ENST00000589347,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000588274,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000586975,;CLPTM1,downstream_gene_variant,,ENST00000588855,;CLPTM1,downstream_gene_variant,,ENST00000587537,; T ENST00000337392 Transcript synonymous_variant 1365/2604 1215/2010 405/669 V gtG/gtT 1 1 CLPTM1 HGNC HGNC:2087 protein_coding YES CCDS12651.1 ENSP00000336994 O96005 A0A0S2Z3H2 UPI0000072CBA NM_001294.3 10/14 Pfam_domain:PF05602,hmmpanther:PTHR21347,hmmpanther:PTHR21347:SF0,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 44990477 44990477 G T 1 0 0 0 0 0 0 0 1 3326 1335 47 2 2 CLPTM1 19 44990477 Silent SNP G C3N-00560_T 45178 44990477 13627139 1142 17831 PPP1R13L 0 . GRCh38 19 45396220 45396220 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.851A>T p.Gln284Leu p.Q284L ENST00000418234 6/13 169 109 60 265 265 0 strelka-varscan-mutect PPP1R13L,missense_variant,p.Gln284Leu,ENST00000418234,NM_001142502.1;PPP1R13L,missense_variant,p.Gln284Leu,ENST00000360957,NM_006663.3;PPP1R13L,downstream_gene_variant,,ENST00000593226,;PPP1R13L,downstream_gene_variant,,ENST00000592134,;PPP1R13L,non_coding_transcript_exon_variant,,ENST00000585905,;PPP1R13L,upstream_gene_variant,,ENST00000587270,; A ENST00000418234 Transcript missense_variant 930/3118 851/2487 284/828 Q/L cAg/cTg 1 -1 PPP1R13L HGNC HGNC:18838 protein_coding YES CCDS33050.1 ENSP00000403902 Q8WUF5 A0A024R0Q5 UPI00001400F1 NM_001142502.1 tolerated(0.1) 6/13 hmmpanther:PTHR24164,hmmpanther:PTHR24164:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45396220 45396220 T A 1 0 0 0 0 1 0 0 0 12468 1580 55 4 4 PPP1R13L 19 45396220 Missense_Mutation SNP T C3N-00560_T 405743 45396220 13221396 1143 17832 BHMG1 0 . GRCh38 19 45754629 45754629 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.707C>A p.Pro236His p.P236H ENST00000457052 7/15 276 176 100 314 314 0 strelka-varscan-mutect BHMG1,missense_variant,p.Pro236His,ENST00000457052,NM_001310124.1; A ENST00000457052 Transcript missense_variant 1123/2749 707/1917 236/638 P/H cCt/cAt 1 1 BHMG1 HGNC HGNC:44318 protein_coding YES ENSP00000402674 C9JSJ3 UPI0002840CC6 NM_001310124.1 deleterious_low_confidence(0.01) 7/15 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45754629 45754629 C A 1 0 0 0 0 1 0 0 0 1573 681 24 2 2 BHMG1 19 45754629 Missense_Mutation SNP C C3N-00560_T 358409 45754629 12862987 1144 17833 CCDC9 0 . GRCh38 19 47260742 47260742 + Missense_Mutation SNP G G C C3N-00560_T C3N-00560_N G G c.365G>C p.Gly122Ala p.G122A ENST00000221922 5/12 69 30 39 91 91 0 strelka-varscan-mutect CCDC9,missense_variant,p.Gly122Ala,ENST00000221922,NM_015603.2;CCDC9,missense_variant,p.Gly122Ala,ENST00000599398,;CCDC9,downstream_gene_variant,,ENST00000596938,;CCDC9,downstream_gene_variant,,ENST00000595659,;CCDC9,downstream_gene_variant,,ENST00000601154,; C ENST00000221922 Transcript missense_variant 587/2093 365/1596 122/531 G/A gGa/gCa COSM4544876 1 1 CCDC9 HGNC HGNC:24560 protein_coding YES CCDS12698.1 ENSP00000221922 Q9Y3X0 UPI0000073E41 NM_015603.2 tolerated(0.26) 5/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15635,hmmpanther:PTHR15635:SF11 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 47260742 47260742 G C 1 0 0 0 0 1 0 0 0 2566 1174 41 4 4 CCDC9 19 47260742 Missense_Mutation SNP G C3N-00560_T 1506113 47260742 11356874 1145 17834 KPTN 0 . GRCh38 19 47484035 47484035 + Silent SNP C C A rs760344382 C3N-00560_T C3N-00560_N C C c.126G>T p.= p.L42L ENST00000338134 1/12 210 121 89 286 285 1 strelka-varscan-mutect KPTN,synonymous_variant,p.=,ENST00000338134,NM_007059.3,NM_001291296.1;KPTN,synonymous_variant,p.=,ENST00000595554,;KPTN,intron_variant,,ENST00000600271,;NAPA,downstream_gene_variant,,ENST00000263354,NM_003827.3;NAPA,downstream_gene_variant,,ENST00000595227,;NAPA-AS1,upstream_gene_variant,,ENST00000593284,;NAPA-AS1,upstream_gene_variant,,ENST00000594367,;KPTN,non_coding_transcript_exon_variant,,ENST00000595484,;KPTN,non_coding_transcript_exon_variant,,ENST00000602193,;RP11-43N16.4,downstream_gene_variant,,ENST00000624088,;KPTN,upstream_gene_variant,,ENST00000598699,;KPTN,synonymous_variant,p.=,ENST00000594208,;NAPA,downstream_gene_variant,,ENST00000597778,;NAPA,downstream_gene_variant,,ENST00000597271,;NAPA,downstream_gene_variant,,ENST00000594001,;KPTN,upstream_gene_variant,,ENST00000594139,;NAPA,downstream_gene_variant,,ENST00000594217,; A ENST00000338134 Transcript synonymous_variant 234/1691 126/1311 42/436 L ctG/ctT rs760344382 1 -1 KPTN HGNC HGNC:6404 protein_coding YES CCDS42583.1 ENSP00000337850 Q9Y664 UPI000007002E NM_007059.3,NM_001291296.1 1/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15435,hmmpanther:PTHR15435:SF2 LOW 1 SNV 1 1 PASS rs760344382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 47484035 47484035 C A 1 0 0 0 0 0 0 0 1 8317 581 21 2 2 KPTN 19 47484035 Silent SNP C C3N-00560_T 223293 47484035 11133581 1146 17835 KLK7 0 . GRCh38 19 50977620 50977620 + Missense_Mutation SNP G G C rs17855561 C3N-00560_T C3N-00560_N G G c.678C>G p.Cys226Trp p.C226W ENST00000391807 6/6 140 83 57 193 193 0 strelka-varscan-mutect KLK7,missense_variant,p.Cys226Trp,ENST00000391807,NM_139277.2;KLK7,missense_variant,p.Cys226Trp,ENST00000595820,NM_005046.3;KLK7,missense_variant,p.Cys154Trp,ENST00000597707,NM_001207053.1;KLK7,downstream_gene_variant,,ENST00000593904,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK7,downstream_gene_variant,,ENST00000595638,;KLK7,3_prime_UTR_variant,,ENST00000304045,NM_001243126.1; C ENST00000391807 Transcript missense_variant 780/1912 678/762 226/253 C/W tgC/tgG rs17855561,COSM713227 1 -1 KLK7 HGNC HGNC:6368 protein_coding YES CCDS12812.1 ENSP00000375683 P49862 A0A024R4H6 UPI0000001BC4 NM_139277.2 deleterious(0) 6/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF231,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE SNV 5 0,1 1 PASS rs17855561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 50977620 50977620 G C 1 0 0 0 0 1 0 0 0 8278 1079 38 4 4 KLK7 19 50977620 Missense_Mutation SNP G C3N-00560_T 3493585 50977620 7639996 1147 17836 SIGLEC8 0 . GRCh38 19 51452537 51452537 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.1342G>A p.Ala448Thr p.A448T ENST00000321424 7/7 108 48 60 100 100 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Ala448Thr,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Ala339Thr,ENST00000430817,;SIGLEC8,missense_variant,p.Ala355Thr,ENST00000340550,;SIGLEC8,downstream_gene_variant,,ENST00000597352,; T ENST00000321424 Transcript missense_variant 1409/2949 1342/1500 448/499 A/T Gca/Aca 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 deleterious(0.04) 7/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 51452537 51452537 C T 1 0 0 0 0 1 0 0 0 14578 710 25 3 3 SIGLEC8 19 51452537 Missense_Mutation SNP C C3N-00560_T 474917 51452537 7165079 1148 17837 SIGLEC8 0 . GRCh38 19 51457545 51457545 + Missense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.649G>A p.Asp217Asn p.D217N ENST00000321424 2/7 201 94 107 203 203 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Asp217Asn,ENST00000321424,NM_014442.2;SIGLEC8,intron_variant,,ENST00000430817,;SIGLEC8,intron_variant,,ENST00000340550,;SIGLEC8,non_coding_transcript_exon_variant,,ENST00000597352,; T ENST00000321424 Transcript missense_variant 716/2949 649/1500 217/499 D/N Gac/Aac 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 deleterious(0) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 51457545 51457545 C T 1 0 0 0 0 1 0 0 0 14578 855 30 3 3 SIGLEC8 19 51457545 Missense_Mutation SNP C C3N-00560_T 5008 51457545 7160071 1149 17838 HAS1 0 . GRCh38 19 51719535 51719535 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.373C>A p.Arg125Ser p.R125S ENST00000222115 2/5 198 96 102 209 209 0 strelka-varscan-mutect HAS1,missense_variant,p.Arg124Ser,ENST00000540069,NM_001297436.1;HAS1,missense_variant,p.Arg125Ser,ENST00000222115,NM_001523.3;HAS1,missense_variant,p.Arg132Ser,ENST00000601714,;HAS1,upstream_gene_variant,,ENST00000594621,;HAS1,upstream_gene_variant,,ENST00000601667,; T ENST00000222115 Transcript missense_variant 408/2087 373/1737 125/578 R/S Cgc/Agc 1 -1 HAS1 HGNC HGNC:4818 protein_coding YES CCDS12838.1 ENSP00000222115 Q92839 UPI000006D531 NM_001523.3 tolerated(0.74) 2/5 Low_complexity_(Seg):seg,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF4,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs1167931448 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 51719535 51719535 G T 1 0 0 0 0 1 0 0 0 6847 1087 38 1 1 HAS1 19 51719535 Missense_Mutation SNP G C3N-00560_T 261990 51719535 6898081 1150 17839 FPR1 0 . GRCh38 19 51746146 51746146 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.849G>T p.= p.V283V ENST00000595042 3/3 382 200 182 399 399 0 strelka-varscan-mutect FPR1,synonymous_variant,p.=,ENST00000595042,NM_001193306.1;FPR1,synonymous_variant,p.=,ENST00000304748,NM_002029.3;FPR1,downstream_gene_variant,,ENST00000600815,;FPR1,downstream_gene_variant,,ENST00000594900,; A ENST00000595042 Transcript synonymous_variant 991/1965 849/1053 283/350 V gtG/gtT 1 -1 FPR1 HGNC HGNC:3826 protein_coding YES CCDS12839.1 ENSP00000471493 P21462 UPI0000050484 NM_001193306.1 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF15,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 51746146 51746146 C A 1 0 0 0 0 0 0 0 1 5904 581 21 2 2 FPR1 19 51746146 Silent SNP C C3N-00560_T 26611 51746146 6871470 1151 17840 FPR3 0 . GRCh38 19 51824324 51824324 + Missense_Mutation SNP C C A rs147264707 C3N-00560_T C3N-00560_N C C c.576C>A p.Asn192Lys p.N192K ENST00000339223 2/2 150 71 79 147 147 0 strelka-varscan-mutect FPR3,missense_variant,p.Asn192Lys,ENST00000339223,NM_002030.3;FPR3,missense_variant,p.Asn192Lys,ENST00000595991,; A ENST00000339223 Transcript missense_variant 755/2620 576/1062 192/353 N/K aaC/aaA rs147264707,COSM4080717 1 1 FPR3 HGNC HGNC:3828 protein_coding YES CCDS12841.1 ENSP00000341821 P25089 Q6L5J4 UPI000011DFC1 NM_002030.3 tolerated(1) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF16,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs147264707 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 51824324 51824324 C A 1 0 0 0 0 1 0 0 0 5906 535 19 1 1 FPR3 19 51824324 Missense_Mutation SNP C C3N-00560_T 78178 51824324 6793292 1152 17841 65 2 FPR3 0 . GRCh38 19 51824326 51824326 + Missense_Mutation SNP T T G rs866353243 C3N-00560_T C3N-00560_N T T c.578T>G p.Val193Gly p.V193G ENST00000339223 2/2 150 71 79 144 143 1 strelka-varscan-mutect FPR3,missense_variant,p.Val193Gly,ENST00000339223,NM_002030.3;FPR3,missense_variant,p.Val193Gly,ENST00000595991,; G ENST00000339223 Transcript missense_variant 757/2620 578/1062 193/353 V/G gTg/gGg rs866353243 1 1 FPR3 HGNC HGNC:3828 protein_coding YES CCDS12841.1 ENSP00000341821 P25089 Q6L5J4 UPI000011DFC1 NM_002030.3 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF16,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs866353243 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 51824326 51824326 T G 1 0 0 0 0 1 0 0 0 5906 1696 59 5 5 FPR3 19 51824326 Missense_Mutation SNP T C3N-00560_T 2 51824326 6793290 1153 17842 65 2 VN1R2 0 . GRCh38 19 53258639 53258639 + Silent SNP G G T rs781134003 C3N-00560_T C3N-00560_N G G c.264G>T p.= p.V88V ENST00000341702 1/1 156 69 87 138 138 0 strelka-varscan-mutect VN1R2,synonymous_variant,p.=,ENST00000341702,NM_173856.2;ZNF677,upstream_gene_variant,,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,upstream_gene_variant,,ENST00000594681,;ZNF677,upstream_gene_variant,,ENST00000599012,;ZNF677,upstream_gene_variant,,ENST00000601828,;ZNF677,upstream_gene_variant,,ENST00000601413,;ZNF677,upstream_gene_variant,,ENST00000598806,;ZNF677,upstream_gene_variant,,ENST00000594517,;ZNF677,upstream_gene_variant,,ENST00000595293,;VN1R2,upstream_gene_variant,,ENST00000598458,; T ENST00000341702 Transcript synonymous_variant 348/1311 264/1188 88/395 V gtG/gtT rs781134003 1 1 VN1R2 HGNC HGNC:19872 protein_coding YES CCDS12862.1 ENSP00000351244 Q8NFZ6 UPI0000062046 NM_173856.2 1/1 LOW SNV 1 PASS rs781134003 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 53258639 53258639 G T 1 0 0 0 0 0 0 0 1 17727 1335 47 2 2 VN1R2 19 53258639 Silent SNP G C3N-00560_T 1434313 53258639 5358977 1154 17843 LILRA4 0 . GRCh38 19 54338118 54338118 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.473G>T p.Gly158Val p.G158V ENST00000291759 4/8 291 133 158 269 269 0 strelka-varscan-mutect LILRA4,missense_variant,p.Gly158Val,ENST00000291759,NM_012276.4;AC008984.2,upstream_gene_variant,,ENST00000616950,;LILRA4,downstream_gene_variant,,ENST00000421056,;LILRA4,upstream_gene_variant,,ENST00000595581,; A ENST00000291759 Transcript missense_variant 530/1944 473/1500 158/499 G/V gGa/gTa 1 -1 LILRA4 HGNC HGNC:15503 protein_coding YES CCDS12890.1 ENSP00000291759 P59901 UPI00034F238A NM_012276.4 deleterious(0.02) 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF98,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF00047,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 54338118 54338118 C A 1 0 0 0 0 1 0 0 0 8695 855 30 2 2 LILRA4 19 54338118 Missense_Mutation SNP C C3N-00560_T 1079479 54338118 4279498 1155 17844 LILRA1 0 . GRCh38 19 54600709 54600709 + Silent SNP C C A rs540116375 C3N-00560_T C3N-00560_N C C c.1362C>A p.= p.P454P ENST00000251372 10/10 221 93 128 187 187 0 strelka-varscan-mutect LILRA1,synonymous_variant,p.=,ENST00000453777,NM_001278318.1;LILRA1,synonymous_variant,p.=,ENST00000251372,NM_006863.3;LILRA1,downstream_gene_variant,,ENST00000618665,;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,downstream_gene_variant,,ENST00000495417,;LILRA1,downstream_gene_variant,,ENST00000477255,; A ENST00000251372 Transcript synonymous_variant 1544/1910 1362/1470 454/489 P ccC/ccA rs540116375 1 1 LILRA1 HGNC HGNC:6602 protein_coding YES CCDS12901.1 ENSP00000251372 O75019 UPI0000034C00 NM_006863.3 10/10 PIRSF_domain:PIRSF001979 LOW 1 SNV 1 1 PASS rs540116375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 54600709 54600709 C A 1 0 0 0 0 0 0 0 1 8693 610 22 2 2 LILRA1 19 54600709 Silent SNP C C3N-00560_T 262591 54600709 4016907 1156 17845 LILRB4 0 . GRCh38 19 54664253 54664253 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.423C>A p.= p.T141T ENST00000391736 6/14 201 87 114 166 166 0 strelka-varscan-mutect LILRB4,synonymous_variant,p.=,ENST00000391736,NM_001278426.3;LILRB4,synonymous_variant,p.=,ENST00000430952,NM_001278427.3;LILRB4,synonymous_variant,p.=,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,synonymous_variant,p.=,ENST00000391734,;LILRB4,synonymous_variant,p.=,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000470943,; A ENST00000391736 Transcript synonymous_variant 738/4002 423/1347 141/448 T acC/acA 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 6/14 PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Pfam_domain:PF00047,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 54664253 54664253 C A 1 0 0 0 0 0 0 0 1 8701 610 22 2 2 LILRB4 19 54664253 Silent SNP C C3N-00560_T 63544 54664253 3953363 1157 17846 NLRP7 0 . GRCh38 19 54941682 54941682 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.30G>T p.= p.L10L ENST00000588756 4/13 119 57 62 107 107 0 strelka-varscan-mutect NLRP7,synonymous_variant,p.=,ENST00000588756,;NLRP7,synonymous_variant,p.=,ENST00000328092,NM_139176.3;NLRP7,synonymous_variant,p.=,ENST00000592784,NM_001127255.1;NLRP7,synonymous_variant,p.=,ENST00000340844,NM_206828.3;NLRP7,synonymous_variant,p.=,ENST00000590030,;NLRP7,synonymous_variant,p.=,ENST00000590659,;NLRP7,synonymous_variant,p.=,ENST00000587103,;NLRP7,synonymous_variant,p.=,ENST00000587844,;NLRP7,synonymous_variant,p.=,ENST00000586379,; A ENST00000588756 Transcript synonymous_variant 517/3826 30/3114 10/1037 L ctG/ctT 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 4/13 Low_complexity_(Seg):seg,PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF14,hmmpanther:PTHR24106,Pfam_domain:PF02758,Gene3D:1.10.533.10,SMART_domains:SM01289,Superfamily_domains:SSF47986 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 54941682 54941682 C A 1 0 0 0 0 0 0 0 1 10520 697 25 2 2 NLRP7 19 54941682 Silent SNP C C3N-00560_T 277429 54941682 3675934 1158 17847 SHISA7 0 . GRCh38 19 55442380 55442380 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.484G>C p.Ala162Pro p.A162P ENST00000376325 1/4 121 58 63 40 40 0 strelka-varscan-mutect SHISA7,missense_variant,p.Ala162Pro,ENST00000376325,NM_001145176.1;SHISA7,upstream_gene_variant,,ENST00000416792,; G ENST00000376325 Transcript missense_variant 484/6033 484/1617 162/538 A/P Gcc/Ccc 1 -1 SHISA7 HGNC HGNC:35409 protein_coding YES CCDS46193.1 ENSP00000365503 A6NL88 UPI000193055E NM_001145176.1 tolerated(0.27) 1/4 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1280741709 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 55442380 55442380 C G 1 0 0 0 0 1 0 0 0 14545 739 26 4 4 SHISA7 19 55442380 Missense_Mutation SNP C C3N-00560_T 500698 55442380 3175236 1159 17848 EPN1 0 . GRCh38 19 55691879 55691879 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1146G>T p.Trp382Cys p.W382C ENST00000411543 7/11 79 38 41 88 88 0 strelka-varscan-mutect EPN1,missense_variant,p.Trp296Cys,ENST00000270460,NM_001130072.1;EPN1,missense_variant,p.Trp382Cys,ENST00000411543,NM_001130071.1;EPN1,missense_variant,p.Trp271Cys,ENST00000085079,NM_013333.3;EPN1,upstream_gene_variant,,ENST00000589704,;AC010525.4,downstream_gene_variant,,ENST00000585559,;EPN1,downstream_gene_variant,,ENST00000591743,;EPN1,upstream_gene_variant,,ENST00000587937,;EPN1,upstream_gene_variant,,ENST00000586194,; T ENST00000411543 Transcript missense_variant 1693/2621 1146/1989 382/662 W/C tgG/tgT 1 1 EPN1 HGNC HGNC:21604 protein_coding YES CCDS46198.1 ENSP00000406209 Q9Y6I3 UPI000059D7B7 NM_001130071.1 deleterious(0) 7/11 hmmpanther:PTHR12276,hmmpanther:PTHR12276:SF48,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 55691879 55691879 G T 1 0 0 0 0 1 0 0 0 5032 1241 43 2 2 EPN1 19 55691879 Missense_Mutation SNP G C3N-00560_T 249499 55691879 2925737 1160 17849 NLRP13 0 . GRCh38 19 55896012 55896012 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3065C>A p.Thr1022Asn p.T1022N ENST00000342929 11/11 133 56 77 134 134 0 strelka-varscan-mutect NLRP13,missense_variant,p.Thr1022Asn,ENST00000588751,NM_001321057.1;NLRP13,missense_variant,p.Thr1022Asn,ENST00000342929,NM_176810.2; T ENST00000342929 Transcript missense_variant 3065/3132 3065/3132 1022/1043 T/N aCt/aAt 1 -1 NLRP13 HGNC HGNC:22937 protein_coding YES CCDS33119.1 ENSP00000343891 Q86W25 UPI00001AEEC8 NM_176810.2 tolerated(0.31) 11/11 Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 55896012 55896012 G T 1 0 0 0 0 1 0 0 0 10512 1029 36 2 2 NLRP13 19 55896012 Missense_Mutation SNP G C3N-00560_T 204133 55896012 2721604 1161 17850 ZNF543 0 . GRCh38 19 57329185 57329185 + Missense_Mutation SNP G G T rs561081582 C3N-00560_T C3N-00560_N G G c.1723G>T p.Ala575Ser p.A575S ENST00000321545 4/4 139 70 69 164 163 1 strelka-varscan-mutect ZNF543,missense_variant,p.Ala575Ser,ENST00000321545,NM_213598.3; T ENST00000321545 Transcript missense_variant 2068/3659 1723/1803 575/600 A/S Gca/Tca rs561081582 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 tolerated(0.98) 4/4 MODERATE 1 SNV 1 1 PASS rs561081582 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57329185 57329185 G T 1 0 0 0 0 1 0 0 0 18550 1319 46 2 2 ZNF543 19 57329185 Missense_Mutation SNP G C3N-00560_T 1433173 57329185 1288431 1162 17851 ZNF417 0 . GRCh38 19 57910088 57910088 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.190G>T p.Glu64Ter p.E64* ENST00000312026 3/3 52 46 6 63 63 0 varscan-mutect ZNF417,stop_gained,p.Glu64Ter,ENST00000312026,NM_152475.2;ZNF417,stop_gained,p.Glu63Ter,ENST00000595559,NM_001297734.1;ZNF417,stop_gained,p.Glu21Ter,ENST00000598526,;ZNF417,stop_gained,p.Glu21Ter,ENST00000597515,;ZNF417,stop_gained,p.Glu21Ter,ENST00000598629,;ZNF417,intron_variant,,ENST00000594396,;ZNF417,downstream_gene_variant,,ENST00000599251,;CTD-2583A14.9,intron_variant,,ENST00000602124,; A ENST00000312026 Transcript stop_gained 355/3597 190/1728 64/575 E/* Gag/Tag 1 -1 ZNF417 HGNC HGNC:20646 protein_coding YES CCDS12965.1 ENSP00000311319 Q8TAU3 UPI000013F249 NM_152475.2 3/3 Superfamily_domains:0044637,PROSITE_profiles:PS50805,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF22,SMART_domains:SM00349 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.67465 1 1 1 1 0 A 4 1 56 57910088 57910088 C A 1 0 0 0 0 0 1 0 0 18466 864 30 2 2 ZNF417 19 57910088 Nonsense_Mutation SNP C C3N-00560_T 580903 57910088 707528 1163 17852 ZNF324B 0 . GRCh38 19 58455543 58455543 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.599A>T p.Gln200Leu p.Q200L ENST00000336614 4/4 256 130 126 286 286 0 strelka-varscan-mutect ZNF324B,missense_variant,p.Gln200Leu,ENST00000336614,NM_207395.2;ZNF324B,missense_variant,p.Gln200Leu,ENST00000545523,;ZNF324B,downstream_gene_variant,,ENST00000598244,;ZNF324B,downstream_gene_variant,,ENST00000599193,;ZNF324B,downstream_gene_variant,,ENST00000594214,;ZNF324B,downstream_gene_variant,,ENST00000599194,; T ENST00000336614 Transcript missense_variant 706/2996 599/1635 200/544 Q/L cAg/cTg 1 1 ZNF324B HGNC HGNC:33107 protein_coding YES CCDS33138.1 ENSP00000337473 Q6AW86 UPI000022AA2D NM_207395.2 tolerated(0.16) 4/4 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF159 MODERATE 1 SNV 1 1 PASS rs1159685356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 58455543 58455543 A T 1 0 0 0 0 1 0 0 0 18417 188 7 4 4 ZNF324B 19 58455543 Missense_Mutation SNP A C3N-00560_T 545455 58455543 162073 1164 17853 TGM3 0 . GRCh38 20 2332085 2332085 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1417G>T p.Gly473Cys p.G473C ENST00000381458 10/13 225 163 62 166 166 0 strelka-varscan-mutect TGM3,missense_variant,p.Gly473Cys,ENST00000381458,NM_003245.3; T ENST00000381458 Transcript missense_variant 1480/2642 1417/2082 473/693 G/C Ggt/Tgt 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 deleterious(0.02) 10/13 PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 2332085 2332085 G T 1 0 0 0 0 1 0 0 0 16264 1232 43 2 2 TGM3 20 2332085 Missense_Mutation SNP G C3N-00560_T 2332085 62112082 1165 17854 TMC2 0 . GRCh38 20 2594823 2594823 + Splice_Site SNP A A C novel C3N-00560_T C3N-00560_N A A c.934-2A>C p.X312_splice ENST00000358864 116 79 37 87 86 1 strelka-varscan-mutect TMC2,splice_acceptor_variant,,ENST00000358864,NM_080751.2; C ENST00000358864 Transcript splice_acceptor_variant -/3169 934/2721 312/906 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 8/19 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 56 2594823 2594823 A C 1 0 0 0 0 0 0 1 0 16431 202 7 5 5 TMC2 20 2594823 Splice_Site SNP A C3N-00560_T 262738 2594823 61849344 1166 17855 TMC2 0 . GRCh38 20 2597280 2597280 + Silent SNP C C G novel C3N-00560_T C3N-00560_N C C c.1206C>G p.= p.S402S ENST00000358864 10/20 155 111 44 79 79 0 strelka-varscan-mutect TMC2,synonymous_variant,p.=,ENST00000358864,NM_080751.2;TMC2,upstream_gene_variant,,ENST00000496948,; G ENST00000358864 Transcript synonymous_variant 1221/3169 1206/2721 402/906 S tcC/tcG 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 10/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 2597280 2597280 C G 1 0 0 0 0 0 0 0 1 16431 581 21 4 4 TMC2 20 2597280 Silent SNP C C3N-00560_T 2457 2597280 61846887 1167 17856 ITPA 0 . GRCh38 20 3213384 3213384 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.189+1G>T p.X63_splice ENST00000380113 568 322 246 454 454 0 strelka-varscan-mutect ITPA,splice_donor_variant,,ENST00000380113,NM_033453.3;ITPA,splice_donor_variant,,ENST00000455664,NM_181493.2;ITPA,intron_variant,,ENST00000399838,NM_001267623.1;ITPA,splice_donor_variant,,ENST00000490838,;ITPA,non_coding_transcript_exon_variant,,ENST00000460676,;ITPA,intron_variant,,ENST00000483354,;ITPA,intron_variant,,ENST00000460550,;ITPA,upstream_gene_variant,,ENST00000461029,;ITPA,splice_donor_variant,,ENST00000609835,; T ENST00000380113 Transcript splice_donor_variant -/1185 189/585 63/194 1 1 ITPA HGNC HGNC:6176 protein_coding YES CCDS13051.1 ENSP00000369456 Q9BY32 A0A0S2Z3W7 UPI0000072BC2 NM_033453.3 3/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 3213384 3213384 G T 1 0 0 0 0 0 0 1 0 7821 1275 44 2 2 ITPA 20 3213384 Splice_Site SNP G C3N-00560_T 616104 3213384 61230783 1168 17857 C20orf194 0 . GRCh38 20 3381382 3381382 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.280G>T p.Asp94Tyr p.D94Y ENST00000252032 3/37 102 71 31 88 88 0 strelka-varscan-mutect C20orf194,missense_variant,p.Asp94Tyr,ENST00000252032,NM_001009984.2;U3,upstream_gene_variant,,ENST00000364476,; A ENST00000252032 Transcript missense_variant 348/6869 280/3534 94/1177 D/Y Gat/Tat 1 -1 C20orf194 HGNC HGNC:17721 protein_coding YES CCDS42851.1 ENSP00000252032 Q5TEA3 UPI0000470A8D NM_001009984.2 deleterious(0) 3/37 hmmpanther:PTHR33664,hmmpanther:PTHR33664:SF1 MODERATE 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 56 3381382 3381382 C A 1 0 0 0 0 1 0 0 0 2005 927 32 2 2 C20orf194 20 3381382 Missense_Mutation SNP C C3N-00560_T 167998 3381382 61062785 1169 17858 SIGLEC1 0 . GRCh38 20 3692563 3692563 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.3988C>A p.Gln1330Lys p.Q1330K ENST00000344754 15/21 286 196 90 170 170 0 strelka-varscan-mutect SIGLEC1,missense_variant,p.Gln1330Lys,ENST00000344754,NM_023068.3;SIGLEC1,missense_variant,p.Gln144Lys,ENST00000419548,; T ENST00000344754 Transcript missense_variant 3988/6720 3988/5130 1330/1709 Q/K Cag/Aag 1 -1 SIGLEC1 HGNC HGNC:11127 protein_coding YES CCDS13060.1 ENSP00000341141 Q9BZZ2 UPI0000049BA6 NM_023068.3 tolerated(0.15) 15/21 Gene3D:2.60.40.10,Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF70,SMART_domains:SM00408,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 3692563 3692563 G T 1 0 0 0 0 1 0 0 0 14569 1357 47 2 2 SIGLEC1 20 3692563 Missense_Mutation SNP G C3N-00560_T 311181 3692563 60751604 1170 17859 HSPA12B 0 . GRCh38 20 3745543 3745543 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.504C>A p.= p.P168P ENST00000254963 6/13 342 251 91 275 275 0 strelka-varscan-mutect HSPA12B,synonymous_variant,p.=,ENST00000254963,NM_052970.4,NM_001197327.1;HSPA12B,synonymous_variant,p.=,ENST00000399701,NM_001318322.1; A ENST00000254963 Transcript synonymous_variant 649/3151 504/2061 168/686 P ccC/ccA 1 1 HSPA12B HGNC HGNC:16193 protein_coding YES CCDS13061.1 ENSP00000254963 Q96MM6 UPI00001285E5 NM_052970.4,NM_001197327.1 6/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF39,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS rs1229963734 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 3745543 3745543 C A 1 0 0 0 0 0 0 0 1 7301 639 23 1 1 HSPA12B 20 3745543 Silent SNP C C3N-00560_T 52980 3745543 60698624 1171 17860 PROKR2 0 . GRCh38 20 5302464 5302464 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.731C>A p.Ala244Asp p.A244D ENST00000217270 2/2 599 385 214 490 489 1 strelka-varscan-mutect PROKR2,missense_variant,p.Ala244Asp,ENST00000217270,NM_144773.2; T ENST00000217270 Transcript missense_variant 731/1155 731/1155 244/384 A/D gCc/gAc 1 -1 PROKR2 HGNC HGNC:15836 protein_coding YES CCDS13089.1 ENSP00000217270 Q8NFJ6 UPI000003BCC6 NM_144773.2 deleterious(0.02) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF234,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 5302464 5302464 G T 1 0 0 0 0 1 0 0 0 12686 1203 42 2 2 PROKR2 20 5302464 Missense_Mutation SNP G C3N-00560_T 1556921 5302464 59141703 1172 17861 C20orf196 0 . GRCh38 20 5772872 5772872 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.7G>T p.Ala3Ser p.A3S ENST00000303142 2/3 94 60 34 78 78 0 strelka-varscan-mutect C20orf196,missense_variant,p.Ala3Ser,ENST00000303142,NM_001303477.1,NM_152504.3;C20orf196,missense_variant,p.Ala50Ser,ENST00000442185,;C20orf196,missense_variant,p.Ala3Ser,ENST00000378979,NM_001303479.1;C20orf196,missense_variant,p.Ala3Ser,ENST00000445603,; T ENST00000303142 Transcript missense_variant 94/1154 7/618 3/205 A/S Gcc/Tcc 1 1 C20orf196 HGNC HGNC:26318 protein_coding YES CCDS13091.1 ENSP00000305875 Q8IYI0 UPI0000074251 NM_001303477.1,NM_152504.3 tolerated(0.36) 2/3 Pfam_domain:PF15021,hmmpanther:PTHR36863,hmmpanther:PTHR36863:SF1 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 56 5772872 5772872 G T 1 0 0 0 0 1 0 0 0 2006 971 34 2 2 C20orf196 20 5772872 Missense_Mutation SNP G C3N-00560_T 470408 5772872 58671295 1173 17862 PAX1 0 . GRCh38 20 21705811 21705811 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.99C>A p.= p.L33L ENST00000398485 1/5 78 62 16 11 11 0 strelka-mutect PAX1,synonymous_variant,p.=,ENST00000613128,NM_001257096.1;PAX1,synonymous_variant,p.=,ENST00000398485,NM_006192.4;PAX1,upstream_gene_variant,,ENST00000444366,;RP5-1065O2.4,upstream_gene_variant,,ENST00000624692,;PAX1,intron_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,; A ENST00000398485 Transcript synonymous_variant 153/2838 99/1605 33/534 L ctC/ctA 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 1/5 LOW SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 21705811 21705811 C A 1 0 0 0 0 0 0 0 1 11563 842 30 2 2 PAX1 20 21705811 Silent SNP C C3N-00560_T 15932939 21705811 42738356 1174 17863 SSTR4 0 . GRCh38 20 23036168 23036168 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.685C>A p.Leu229Met p.L229M ENST00000255008 1/1 148 98 50 108 108 0 strelka-varscan-mutect SSTR4,missense_variant,p.Leu229Met,ENST00000255008,NM_001052.2;RP4-753D10.3,intron_variant,,ENST00000440921,;RP4-753D10.3,upstream_gene_variant,,ENST00000419734,; A ENST00000255008 Transcript missense_variant 783/1427 685/1167 229/388 L/M Ctg/Atg COSM5559010 1 1 SSTR4 HGNC HGNC:11333 protein_coding YES CCDS42856.1 ENSP00000255008 P31391 UPI000013CE7A NM_001052.2 tolerated(0.07) 1/1 Transmembrane_helices:TMhelix,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF0,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS rs1047538726 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 23036168 23036168 C A 1 0 0 0 0 1 0 0 0 15577 680 24 2 2 SSTR4 20 23036168 Missense_Mutation SNP C C3N-00560_T 1330357 23036168 41407999 1175 17864 CST4 0 . GRCh38 20 23688873 23688873 + Missense_Mutation SNP C C A rs761780683 C3N-00560_T C3N-00560_N C C c.97G>T p.Gly33Cys p.G33C ENST00000217423 1/3 490 385 105 320 320 0 strelka-varscan-mutect CST4,missense_variant,p.Gly33Cys,ENST00000217423,NM_001899.2; A ENST00000217423 Transcript missense_variant 168/751 97/426 33/141 G/C Ggc/Tgc rs761780683 1 -1 CST4 HGNC HGNC:2476 protein_coding YES CCDS13159.1 ENSP00000217423 P01036 UPI0000049812 NM_001899.2 tolerated(0.07) 1/3 Gene3D:3.10.450.10,Pfam_domain:PF00031,hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF54,SMART_domains:SM00043,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS rs761780683 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 23688873 23688873 C A 1 0 0 0 0 1 0 0 0 3774 594 21 2 2 CST4 20 23688873 Missense_Mutation SNP C C3N-00560_T 652705 23688873 40755294 1176 17865 CST2 0 . GRCh38 20 23825239 23825239 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.313G>C p.Ala105Pro p.A105P ENST00000304725 2/3 395 252 143 224 224 0 strelka-varscan-mutect CST2,missense_variant,p.Ala105Pro,ENST00000304725,NM_001322.2; G ENST00000304725 Transcript missense_variant 384/748 313/426 105/141 A/P Gcc/Ccc 1 -1 CST2 HGNC HGNC:2474 protein_coding YES CCDS13161.1 ENSP00000307540 P09228 UPI0000128D74 NM_001322.2 tolerated(1) 2/3 hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF48,Pfam_domain:PF00031,Gene3D:3.10.450.10,SMART_domains:SM00043,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 23825239 23825239 C G 1 0 0 0 0 1 0 0 0 3772 710 25 4 4 CST2 20 23825239 Missense_Mutation SNP C C3N-00560_T 136366 23825239 40618928 1177 17866 ACSS1 0 . GRCh38 20 25013968 25013968 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1445A>T p.Asp482Val p.D482V ENST00000323482 9/14 124 58 66 122 122 0 strelka-varscan-mutect ACSS1,missense_variant,p.Asp482Val,ENST00000323482,NM_032501.3,NM_001252675.1;ACSS1,missense_variant,p.Asp361Val,ENST00000537502,NM_001252676.1;ACSS1,missense_variant,p.Asp482Val,ENST00000432802,NM_001252677.1;ACSS1,upstream_gene_variant,,ENST00000484396,; A ENST00000323482 Transcript missense_variant 1525/3680 1445/2070 482/689 D/V gAt/gTt 1 -1 ACSS1 HGNC HGNC:16091 protein_coding YES CCDS13167.1 ENSP00000316924 Q9NUB1 UPI00001615FE NM_032501.3,NM_001252675.1 deleterious(0) 9/14 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF110,Superfamily_domains:SSF56801,TIGRFAM_domain:TIGR02188 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 25013968 25013968 T A 1 0 0 0 0 1 0 0 0 231 1435 50 4 4 ACSS1 20 25013968 Missense_Mutation SNP T C3N-00560_T 1188729 25013968 39430199 1178 17867 DNMT3B 0 . GRCh38 20 32795527 32795527 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1245G>T p.Gln415His p.Q415H ENST00000328111 11/23 297 157 140 393 392 1 strelka-varscan-mutect DNMT3B,missense_variant,p.Gln415His,ENST00000328111,NM_006892.3;DNMT3B,missense_variant,p.Gln407His,ENST00000201963,NM_175850.2;DNMT3B,missense_variant,p.Gln395His,ENST00000353855,NM_175848.1;DNMT3B,missense_variant,p.Gln395His,ENST00000348286,NM_175849.1;DNMT3B,missense_variant,p.Gln353His,ENST00000443239,NM_001207055.1;DNMT3B,missense_variant,p.Gln319His,ENST00000456297,NM_001207056.1; T ENST00000328111 Transcript missense_variant 1566/4336 1245/2562 415/853 Q/H caG/caT 1 1 DNMT3B HGNC HGNC:2979 protein_coding YES CCDS13205.1 ENSP00000328547 Q9UBC3 UPI0000001046 NM_006892.3 deleterious(0.03) 11/23 hmmpanther:PTHR23068:SF9,hmmpanther:PTHR23068 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 32795527 32795527 G T 1 0 0 0 0 1 0 0 0 4490 933 33 2 2 DNMT3B 20 32795527 Missense_Mutation SNP G C3N-00560_T 7781559 32795527 31648640 1179 17868 SOGA1 0 . GRCh38 20 36815358 36815358 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.2084A>T p.His695Leu p.H695L ENST00000237536 5/15 179 101 78 192 192 0 strelka-varscan-mutect SOGA1,missense_variant,p.His695Leu,ENST00000237536,NM_080627.2;SOGA1,missense_variant,p.His457Leu,ENST00000279034,NM_199181.2;SOGA1,missense_variant,p.His309Leu,ENST00000465671,; A ENST00000237536 Transcript missense_variant 2426/14371 2084/4986 695/1661 H/L cAt/cTt 1 -1 SOGA1 HGNC HGNC:16111 protein_coding YES CCDS54459.1 ENSP00000237536 O94964 UPI0000E5A319 NM_080627.2 tolerated(0.39) 5/15 hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 36815358 36815358 T A 1 0 0 0 0 1 0 0 0 15244 1464 51 4 4 SOGA1 20 36815358 Missense_Mutation SNP T C3N-00560_T 4019831 36815358 27628809 1180 17869 KIAA1755 0 . GRCh38 20 38241669 38241669 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.462C>T p.= p.N154N ENST00000279024 3/14 334 176 158 386 386 0 strelka-varscan-mutect KIAA1755,synonymous_variant,p.=,ENST00000279024,NM_001029864.1;KIAA1755,synonymous_variant,p.=,ENST00000496900,;KIAA1755,upstream_gene_variant,,ENST00000611812,; A ENST00000279024 Transcript synonymous_variant 734/6429 462/3603 154/1200 N aaC/aaT 1 -1 KIAA1755 HGNC HGNC:29372 protein_coding YES CCDS33467.1 ENSP00000279024 Q5JYT7 UPI000041AADF NM_001029864.1 3/14 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF125 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 38241669 38241669 G A 1 0 0 0 0 0 0 0 1 8128 1368 48 3 3 KIAA1755 20 38241669 Silent SNP G C3N-00560_T 1426311 38241669 26202498 1181 17870 PPP1R16B 0 . GRCh38 20 38836124 38836124 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.199G>T p.Glu67Ter p.E67* ENST00000299824 2/11 141 67 74 163 163 0 strelka-varscan-mutect PPP1R16B,stop_gained,p.Glu67Ter,ENST00000299824,NM_015568.2;PPP1R16B,stop_gained,p.Glu67Ter,ENST00000373331,NM_001172735.1;PPP1R16B,non_coding_transcript_exon_variant,,ENST00000468265,;PPP1R16B,upstream_gene_variant,,ENST00000463749,; T ENST00000299824 Transcript stop_gained 388/6251 199/1704 67/567 E/* Gag/Tag 1 1 PPP1R16B HGNC HGNC:15850 protein_coding YES CCDS13309.1 ENSP00000299824 Q96T49 UPI0000132059 NM_015568.2 2/11 PROSITE_profiles:PS50297,hmmpanther:PTHR24186,hmmpanther:PTHR24186:SF6,PIRSF_domain:PIRSF038159,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS rs1251633174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 38836124 38836124 G T 1 0 0 0 0 0 1 0 0 12476 1059 37 1 1 PPP1R16B 20 38836124 Nonsense_Mutation SNP G C3N-00560_T 594455 38836124 25608043 1182 17871 L3MBTL1 0 . GRCh38 20 43534845 43534845 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1662G>T p.Trp554Cys p.W554C ENST00000418998 16/22 158 75 83 159 159 0 strelka-varscan-mutect L3MBTL1,missense_variant,p.Trp272Cys,ENST00000422861,;L3MBTL1,missense_variant,p.Trp554Cys,ENST00000418998,NM_032107.4;L3MBTL1,missense_variant,p.Trp486Cys,ENST00000373135,NM_015478.6;L3MBTL1,missense_variant,p.Trp554Cys,ENST00000427442,;L3MBTL1,missense_variant,p.Trp486Cys,ENST00000373134,;L3MBTL1,3_prime_UTR_variant,,ENST00000445228,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000373133,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000497347,;L3MBTL1,non_coding_transcript_exon_variant,,ENST00000483547,;L3MBTL1,upstream_gene_variant,,ENST00000494117,;L3MBTL1,downstream_gene_variant,,ENST00000485334,; T ENST00000418998 Transcript missense_variant 1738/3365 1662/2523 554/840 W/C tgG/tgT 1 1 L3MBTL1 HGNC HGNC:15905 protein_coding YES CCDS46602.2 ENSP00000398516 Q9Y468 UPI0001E18E26 NM_032107.4 deleterious(0) 16/22 PROSITE_profiles:PS51079,hmmpanther:PTHR12247:SF69,hmmpanther:PTHR12247,Pfam_domain:PF02820,Gene3D:2.30.30.160,SMART_domains:SM00561,Superfamily_domains:SSF63748 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 43534845 43534845 G T 1 0 0 0 0 1 0 0 0 8493 1183 41 2 2 L3MBTL1 20 43534845 Missense_Mutation SNP G C3N-00560_T 4698721 43534845 20909322 1183 17872 DBNDD2 0 . GRCh38 20 45406498 45406498 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.47C>A p.Ala16Glu p.A16E ENST00000372720 1/4 120 67 53 119 119 0 strelka-varscan-mutect DBNDD2,missense_variant,p.Ala16Glu,ENST00000372720,NM_018478.3;DBNDD2,intron_variant,,ENST00000372722,NM_001048222.2;DBNDD2,intron_variant,,ENST00000372723,NM_001048221.2;DBNDD2,intron_variant,,ENST00000357275,NM_001197140.1;DBNDD2,upstream_gene_variant,,ENST00000372712,;DBNDD2,upstream_gene_variant,,ENST00000372710,NM_001048225.2;DBNDD2,upstream_gene_variant,,ENST00000443296,NM_001048226.2;DBNDD2,upstream_gene_variant,,ENST00000372717,NM_001048224.2;DBNDD2,upstream_gene_variant,,ENST00000360981,NM_001197139.1,NM_001048223.2;TP53TG5,intron_variant,,ENST00000494455,;SYS1-DBNDD2,intron_variant,,ENST00000475242,;TP53TG5,intron_variant,,ENST00000468375,;TP53TG5,upstream_gene_variant,,ENST00000488588,;SYS1-DBNDD2,intron_variant,,ENST00000419593,;SYS1-DBNDD2,intron_variant,,ENST00000452133,;SYS1-DBNDD2,intron_variant,,ENST00000458187,; A ENST00000372720 Transcript missense_variant 278/1481 47/780 16/259 A/E gCg/gAg 1 1 DBNDD2 HGNC HGNC:15881 protein_coding CCDS56193.1 ENSP00000361805 Q9BQY9 UPI0000071AED NM_018478.3 deleterious_low_confidence(0) 1/4 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS rs1394579358 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 45406498 45406498 C A 1 0 0 0 0 1 0 0 0 4054 768 27 1 1 DBNDD2 20 45406498 Missense_Mutation SNP C C3N-00560_T 1871653 45406498 19037669 1184 17873 DNTTIP1 0 . GRCh38 20 45811187 45811187 + Nonsense_Mutation SNP C C T novel C3N-00560_T C3N-00560_N C C c.982C>T p.Gln328Ter p.Q328* ENST00000372622 13/13 50 23 27 45 45 0 strelka-varscan-mutect DNTTIP1,stop_gained,p.Gln328Ter,ENST00000372622,NM_052951.2;DNTTIP1,stop_gained,p.Gln279Ter,ENST00000456939,;DNTTIP1,stop_gained,p.Gln231Ter,ENST00000435014,;UBE2C,upstream_gene_variant,,ENST00000372568,NM_181801.3;UBE2C,upstream_gene_variant,,ENST00000356455,NM_007019.3;UBE2C,upstream_gene_variant,,ENST00000335046,NM_181799.2;UBE2C,upstream_gene_variant,,ENST00000617055,NM_001281741.1;UBE2C,upstream_gene_variant,,ENST00000352551,NM_181800.2;UBE2C,upstream_gene_variant,,ENST00000405520,NM_001281742.1;UBE2C,upstream_gene_variant,,ENST00000243893,;UBE2C,upstream_gene_variant,,ENST00000496085,; T ENST00000372622 Transcript stop_gained 1050/1290 982/990 328/329 Q/* Cag/Tag 1 1 DNTTIP1 HGNC HGNC:16160 protein_coding YES CCDS13369.1 ENSP00000361705 Q9H147 UPI0000136B4E NM_052951.2 13/13 hmmpanther:PTHR23399 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 45811187 45811187 C T 1 0 0 0 0 0 1 0 0 4495 479 17 3 3 DNTTIP1 20 45811187 Nonsense_Mutation SNP C C3N-00560_T 404689 45811187 18632980 1185 17874 MOCS3 0 . GRCh38 20 50960105 50960105 + Silent SNP C C T rs766995677 C3N-00560_T C3N-00560_N C C c.1263C>T p.= p.A421A ENST00000244051 1/1 573 483 90 237 237 0 strelka-varscan-mutect MOCS3,synonymous_variant,p.=,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; T ENST00000244051 Transcript synonymous_variant 1280/5106 1263/1383 421/460 A gcC/gcT rs766995677 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 1/1 Gene3D:3.40.250.10,HAMAP:MF_03049,Pfam_domain:PF00581,PROSITE_profiles:PS50206,hmmpanther:PTHR10953,SMART_domains:SM00450,Superfamily_domains:SSF69572 LOW SNV 1 PASS rs766995677 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 50960105 50960105 C T 1 0 0 0 0 0 0 0 1 9655 639 23 1 1 MOCS3 20 50960105 Silent SNP C C3N-00560_T 5148918 50960105 13484062 1186 17875 MOCS3 0 . GRCh38 20 50960216 50960216 + Silent SNP A A T novel C3N-00560_T C3N-00560_N A A c.1374A>T p.= p.P458P ENST00000244051 1/1 155 52 103 43 43 0 strelka-varscan-mutect MOCS3,synonymous_variant,p.=,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; T ENST00000244051 Transcript synonymous_variant 1391/5106 1374/1383 458/460 P ccA/ccT 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 1/1 HAMAP:MF_03049,PROSITE_profiles:PS50206,hmmpanther:PTHR10953 LOW SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 50960216 50960216 A T 1 0 0 0 0 0 0 0 1 9655 146 6 4 4 MOCS3 20 50960216 Silent SNP A C3N-00560_T 111 50960216 13483951 1187 17876 ZFP64 0 . GRCh38 20 52084685 52084685 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1810G>T p.Asp604Tyr p.D604Y ENST00000361387 9/9 242 143 99 345 345 0 strelka-varscan-mutect ZFP64,missense_variant,p.Asp604Tyr,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.Asp385Tyr,ENST00000371523,NM_001319146.1;ZFP64,intron_variant,,ENST00000371518,;ZFP64,downstream_gene_variant,,ENST00000395989,;ZFP64,downstream_gene_variant,,ENST00000456175,;ZFP64,downstream_gene_variant,,ENST00000477786,;ZFP64,downstream_gene_variant,,ENST00000467811,; A ENST00000361387 Transcript missense_variant 1871/2545 1810/1938 604/645 D/Y Gat/Tat 1 -1 ZFP64 HGNC HGNC:15940 protein_coding CCDS13439.1 ENSP00000355179 Q9NTW7 UPI000013C56C NM_199427.2 deleterious(0.03) 9/9 PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF34,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1404427482 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 52084685 52084685 C A 1 0 0 0 0 1 0 0 0 18228 826 29 2 2 ZFP64 20 52084685 Missense_Mutation SNP C C3N-00560_T 1124469 52084685 12359482 1188 17877 ZFP64 0 . GRCh38 20 52088456 52088456 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.1164C>G p.Cys388Trp p.C388W ENST00000361387 8/9 377 200 177 502 502 0 strelka-varscan-mutect ZFP64,missense_variant,p.Cys388Trp,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.Cys169Trp,ENST00000371523,NM_001319146.1;ZFP64,missense_variant,p.Cys388Trp,ENST00000371518,;ZFP64,missense_variant,p.Cys191Trp,ENST00000395989,;ZFP64,missense_variant,p.Cys94Trp,ENST00000456175,;ZFP64,non_coding_transcript_exon_variant,,ENST00000467811,;ZFP64,downstream_gene_variant,,ENST00000477786,; C ENST00000361387 Transcript missense_variant 1225/2545 1164/1938 388/645 C/W tgC/tgG 1 -1 ZFP64 HGNC HGNC:15940 protein_coding CCDS13439.1 ENSP00000355179 Q9NTW7 UPI000013C56C NM_199427.2 deleterious(0) 8/9 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 52088456 52088456 G C 1 0 0 0 0 1 0 0 0 18228 1195 42 4 4 ZFP64 20 52088456 Missense_Mutation SNP G C3N-00560_T 3771 52088456 12355711 1189 17878 CYP24A1 0 . GRCh38 20 54158158 54158158 + Silent SNP C C G rs373504037 C3N-00560_T C3N-00560_N C C c.1164G>C p.= p.T388T ENST00000216862 9/12 288 182 106 351 351 0 strelka-varscan-mutect CYP24A1,synonymous_variant,p.=,ENST00000216862,NM_000782.4;CYP24A1,synonymous_variant,p.=,ENST00000395955,NM_001128915.1;CYP24A1,synonymous_variant,p.=,ENST00000395954,;CYP24A1,upstream_gene_variant,,ENST00000460643,;CYP24A1,downstream_gene_variant,,ENST00000487593,; G ENST00000216862 Transcript synonymous_variant 1558/3262 1164/1545 388/514 T acG/acC rs373504037 1 -1 CYP24A1 HGNC HGNC:2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 9/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF5,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264,Prints_domain:PR00385,Prints_domain:PR00463 LOW 1 SNV 1 1 PASS rs373504037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 56 54158158 54158158 C G 1 0 0 0 0 0 0 0 1 3957 755 27 4 4 CYP24A1 20 54158158 Silent SNP C C3N-00560_T 2069702 54158158 10286009 1190 17879 CASS4 0 . GRCh38 20 56437314 56437314 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.187G>T p.Ala63Ser p.A63S ENST00000360314 3/7 154 112 42 130 130 0 strelka-varscan-mutect CASS4,missense_variant,p.Ala63Ser,ENST00000434344,NM_001164115.1;CASS4,missense_variant,p.Ala63Ser,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; T ENST00000360314 Transcript missense_variant 412/2619 187/2361 63/786 A/S Gcc/Tcc 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0) 3/7 PROSITE_profiles:PS50002,hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 56437314 56437314 G T 1 0 0 0 0 1 0 0 0 2382 1203 42 2 2 CASS4 20 56437314 Missense_Mutation SNP G C3N-00560_T 2279156 56437314 8006853 1191 17880 FAM209B 0 . GRCh38 20 56533420 56533420 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.79C>A p.Gln27Lys p.Q27K ENST00000371325 1/2 504 352 152 456 456 0 strelka-varscan-mutect FAM209B,missense_variant,p.Gln27Lys,ENST00000371325,NM_001013646.3; A ENST00000371325 Transcript missense_variant 175/694 79/516 27/171 Q/K Cag/Aag 1 1 FAM209B HGNC HGNC:16101 protein_coding YES CCDS33494.1 ENSP00000360376 Q5JX69 UPI00001D82E0 NM_001013646.3 tolerated(0.05) 1/2 hmmpanther:PTHR35157:SF2,hmmpanther:PTHR35157,Pfam_domain:PF15206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 56533420 56533420 C A 1 0 0 0 0 1 0 0 0 5392 479 17 2 2 FAM209B 20 56533420 Missense_Mutation SNP C C3N-00560_T 96106 56533420 7910747 1192 17881 ZBP1 0 . GRCh38 20 57610302 57610302 + Missense_Mutation SNP G G T rs778416170 C3N-00560_T C3N-00560_N G G c.940C>A p.Pro314Thr p.P314T ENST00000371173 7/8 514 347 167 353 352 1 strelka-varscan-mutect ZBP1,missense_variant,p.Pro314Thr,ENST00000371173,NM_001160417.1,NM_030776.2;ZBP1,missense_variant,p.Pro239Thr,ENST00000395822,NM_001160418.1;ZBP1,downstream_gene_variant,,ENST00000541799,NM_001160419.2;ZBP1,upstream_gene_variant,,ENST00000453793,;ZBP1,downstream_gene_variant,,ENST00000538947,;ZBP1,downstream_gene_variant,,ENST00000432548,;ZBP1,downstream_gene_variant,,ENST00000546110,;ZBP1,non_coding_transcript_exon_variant,,ENST00000461547,;ZBP1,downstream_gene_variant,,ENST00000480037,; T ENST00000371173 Transcript missense_variant 1118/2195 940/1290 314/429 P/T Cct/Act rs778416170 1 -1 ZBP1 HGNC HGNC:16176 protein_coding YES CCDS13461.1 ENSP00000360215 Q9H171 UPI000013CB5B NM_001160417.1,NM_030776.2 tolerated(0.1) 7/8 hmmpanther:PTHR14966 MODERATE 1 SNV 1 1 PASS rs778416170 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 57610302 57610302 G T 1 0 0 0 0 1 0 0 0 18087 1232 43 2 2 ZBP1 20 57610302 Missense_Mutation SNP G C3N-00560_T 1076882 57610302 6833865 1193 17882 RAB22A 0 . GRCh38 20 58353480 58353480 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.319G>T p.Gly107Cys p.G107C ENST00000244040 5/7 285 255 30 298 298 0 strelka-varscan-mutect RAB22A,missense_variant,p.Gly107Cys,ENST00000244040,NM_020673.2; T ENST00000244040 Transcript missense_variant 600/8670 319/585 107/194 G/C Ggc/Tgc 1 1 RAB22A HGNC HGNC:9764 protein_coding YES CCDS33497.1 ENSP00000244040 Q9UL26 UPI0000132F68 NM_020673.2 deleterious(0.01) 5/7 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF401,hmmpanther:PTHR24073,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,Pfam_domain:PF00071,SMART_domains:SM00176,SMART_domains:SM00174,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 58353480 58353480 G T 1 0 0 0 0 1 0 0 0 13067 1348 47 2 2 RAB22A 20 58353480 Missense_Mutation SNP G C3N-00560_T 743178 58353480 6090687 1194 17883 APCDD1L 0 . GRCh38 20 58461327 58461327 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.969C>A p.Cys323Ter p.C323* ENST00000371149 4/4 58 42 16 59 59 0 strelka-varscan-mutect APCDD1L,stop_gained,p.Cys323Ter,ENST00000371149,NM_153360.2;APCDD1L,non_coding_transcript_exon_variant,,ENST00000491015,; T ENST00000371149 Transcript stop_gained 1200/3426 969/1506 323/501 C/* tgC/tgA 1 -1 APCDD1L HGNC HGNC:26892 protein_coding YES CCDS13467.1 ENSP00000360191 Q8NCL9 UPI000006F69F NM_153360.2 4/4 Pfam_domain:PF14921,hmmpanther:PTHR31021,hmmpanther:PTHR31021:SF3,SMART_domains:SM01352 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 58461327 58461327 G T 1 0 0 0 0 0 1 0 0 886 1195 42 2 2 APCDD1L 20 58461327 Nonsense_Mutation SNP G C3N-00560_T 107847 58461327 5982840 1195 17884 GNAS 0 . GRCh38 20 58853776 58853776 + Missense_Mutation SNP C C A rs747313993 C3N-00560_T C3N-00560_N C C c.511C>A p.Gln171Lys p.Q171K ENST00000371100 1/13 855 605 250 743 743 0 strelka-varscan-mutect GNAS,missense_variant,p.Gln171Lys,ENST00000371100,NM_080425.2;GNAS,missense_variant,p.Gln171Lys,ENST00000371099,;GNAS,missense_variant,p.Gln171Lys,ENST00000371102,;GNAS,synonymous_variant,p.=,ENST00000306120,NM_001077490.1;GNAS,intron_variant,,ENST00000313949,;GNAS,intron_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000371098,;GNAS,intron_variant,,ENST00000419558,;GNAS,intron_variant,,ENST00000453292,;GNAS,upstream_gene_variant,,ENST00000423897,;GNAS,upstream_gene_variant,,ENST00000450130,;GNAS,upstream_gene_variant,,ENST00000349036,;GNAS-AS1,upstream_gene_variant,,ENST00000424094,;GNAS-AS1,upstream_gene_variant,,ENST00000598163,;GNAS-AS1_5,downstream_gene_variant,,ENST00000614281,;GNAS-AS1_4,downstream_gene_variant,,ENST00000616546,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,intron_variant,,ENST00000491348,;GNAS,intron_variant,,ENST00000472183,;GNAS,intron_variant,,ENST00000493744,;GNAS,intron_variant,,ENST00000482112,;GNAS,intron_variant,,ENST00000490374,;GNAS,intron_variant,,ENST00000467227,;GNAS,intron_variant,,ENST00000462499,;GNAS,upstream_gene_variant,,ENST00000481768,; A ENST00000371100 Transcript missense_variant 1063/4029 511/3114 171/1037 Q/K Cag/Aag rs747313993 1 1 GNAS HGNC HGNC:4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 UPI0000E444AE NM_080425.2 deleterious_low_confidence(0.03) 1/13 MODERATE 1 SNV 5 1 PASS rs747313993 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 58853776 58853776 C A 1 0 0 0 0 1 0 0 0 6390 595 21 2 2 GNAS 20 58853776 Missense_Mutation SNP C C3N-00560_T 392449 58853776 5590391 1196 17885 CDH4 0 . GRCh38 20 61743570 61743570 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.177C>A p.Phe59Leu p.F59L ENST00000614565 3/16 209 143 66 162 162 0 strelka-varscan-mutect CDH4,missense_variant,p.Phe59Leu,ENST00000614565,NM_001794.4;CDH4,missense_variant,p.Phe19Leu,ENST00000611855,;CDH4,5_prime_UTR_variant,,ENST00000543233,NM_001252338.2,NM_001252339.2;RP11-429E11.2,intron_variant,,ENST00000447909,;RP11-429E11.2,intron_variant,,ENST00000442888,; A ENST00000614565 Transcript missense_variant 265/6513 177/2751 59/916 F/L ttC/ttA 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 deleterious(0.03) 3/16 hmmpanther:PTHR24027:SF81,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF08758,SMART_domains:SM01055,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 61743570 61743570 C A 1 0 0 0 0 1 0 0 0 2815 825 29 2 2 CDH4 20 61743570 Missense_Mutation SNP C C3N-00560_T 2889794 61743570 2700597 1197 17886 PRPF6 0 . GRCh38 20 64027659 64027659 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.2262G>T p.Glu754Asp p.E754D ENST00000266079 17/21 935 736 199 545 545 0 strelka-varscan-mutect PRPF6,missense_variant,p.Glu754Asp,ENST00000266079,NM_012469.3; T ENST00000266079 Transcript missense_variant 2373/3044 2262/2826 754/941 E/D gaG/gaT COSM1177800 1 1 PRPF6 HGNC HGNC:15860 protein_coding YES CCDS13550.1 ENSP00000266079 O94906 UPI0000132356 NM_012469.3 deleterious(0.02) 17/21 Gene3D:1.25.40.10,Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50293,hmmpanther:PTHR11246,SMART_domains:SM00028,SMART_domains:SM00386,Superfamily_domains:SSF48452 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 64027659 64027659 G T 1 0 0 0 0 1 0 0 0 12710 933 33 2 2 PRPF6 20 64027659 Missense_Mutation SNP G C3N-00560_T 2284089 64027659 416508 1198 17887 ADAMTS5 0 . GRCh38 21 26934552 26934552 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1603C>A p.Pro535Thr p.P535T ENST00000284987 4/8 418 346 72 482 482 0 strelka-varscan-mutect ADAMTS5,missense_variant,p.Pro535Thr,ENST00000284987,NM_007038.3;AP001601.2,intron_variant,,ENST00000426771,; T ENST00000284987 Transcript missense_variant 1725/9056 1603/2793 535/930 P/T Cct/Act 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 deleterious(0.01) 4/8 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 26934552 26934552 G T 1 0 0 0 0 1 0 0 0 313 1203 42 2 2 ADAMTS5 21 26934552 Missense_Mutation SNP G C3N-00560_T 26934552 19775431 1199 17888 ADAMTS5 0 . GRCh38 21 26966323 26966323 + Frame_Shift_Del DEL G G - novel C3N-00560_T C3N-00560_N G G c.69delC p.Ala24ArgfsTer142 p.A24Rfs*142 ENST00000284987 1/8 51 38 13 69 69 0 sindel-varindel-pindel ADAMTS5,frameshift_variant,p.Ala24ArgfsTer142,ENST00000284987,NM_007038.3; - ENST00000284987 Transcript frameshift_variant 191/9056 69/2793 23/930 A/X gcC/gc 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 1/8 Prints_domain:PR01860 HIGH 1 deletion 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 56 26966323 26966323 G - 1 0 1 0 1 0 0 0 0 313 1103 39 0 0 ADAMTS5 21 26966323 Frame_Shift_Del DEL G C3N-00560_T 31771 26966323 19743660 1200 17889 CLDN17 0 . GRCh38 21 30166236 30166236 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.382C>A p.Leu128Met p.L128M ENST00000286808 1/1 216 163 53 265 265 0 strelka-varscan-mutect CLDN17,missense_variant,p.Leu128Met,ENST00000286808,NM_012131.2; T ENST00000286808 Transcript missense_variant 521/1193 382/675 128/224 L/M Ctg/Atg 1 -1 CLDN17 HGNC HGNC:2038 protein_coding YES CCDS13586.1 ENSP00000286808 P56750 UPI000004E655 NM_012131.2 tolerated(0.18) 1/1 Pfam_domain:PF00822,Prints_domain:PR01077,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF75,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 30166236 30166236 G T 1 0 0 0 0 1 0 0 0 3242 991 35 2 2 CLDN17 21 30166236 Missense_Mutation SNP G C3N-00560_T 3199913 30166236 16543747 1201 17890 TIAM1 0 . GRCh38 21 31146938 31146938 + Silent SNP G G T rs759007864 C3N-00560_T C3N-00560_N G G c.3432C>A p.= p.A1144A ENST00000286827 21/29 281 231 50 330 330 0 strelka-varscan-mutect TIAM1,synonymous_variant,p.=,ENST00000286827,NM_003253.2;TIAM1,synonymous_variant,p.=,ENST00000541036,;TIAM1,synonymous_variant,p.=,ENST00000636887,; T ENST00000286827 Transcript synonymous_variant 3904/7200 3432/4776 1144/1591 A gcC/gcA rs759007864 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 21/29 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 1 1 PASS rs759007864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 31146938 31146938 G T 1 0 0 0 0 0 0 0 1 16324 987 35 2 2 TIAM1 21 31146938 Silent SNP G C3N-00560_T 980702 31146938 15563045 1202 17891 SOD1 0 . GRCh38 21 31659801 31659801 + Missense_Mutation SNP G G A C3N-00560_T C3N-00560_N G G c.32G>A p.Gly11Asp p.G11D ENST00000270142 1/5 281 221 60 299 299 0 strelka-varscan-mutect SOD1,missense_variant,p.Gly11Asp,ENST00000270142,NM_000454.4;SOD1,intron_variant,,ENST00000389995,;AP000253.1,upstream_gene_variant,,ENST00000449339,;SNORA81,upstream_gene_variant,,ENST00000458922,;SOD1,non_coding_transcript_exon_variant,,ENST00000470944,;SOD1,non_coding_transcript_exon_variant,,ENST00000476106,; A ENST00000270142 Transcript missense_variant 180/966 32/465 11/154 G/D gGc/gAc CP035469 1 1 SOD1 HGNC HGNC:11179 protein_coding YES CCDS33536.1 ENSP00000270142 P00441 V9HWC9 UPI0000000C20 NM_000454.4 deleterious(0) 1/5 hmmpanther:PTHR10003,Gene3D:2.60.40.200,Superfamily_domains:SSF49329 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 31659801 31659801 G A 1 0 0 0 0 1 0 0 0 15241 1203 42 3 3 SOD1 21 31659801 Missense_Mutation SNP G C3N-00560_T 512863 31659801 15050182 1203 17892 TRPM2 0 . GRCh38 21 44369265 44369265 + Silent SNP C C T novel C3N-00560_T C3N-00560_N C C c.693C>T p.= p.Y231Y ENST00000397928 5/32 93 75 18 102 102 0 strelka-varscan-mutect TRPM2,synonymous_variant,p.=,ENST00000397928,NM_003307.3;TRPM2,synonymous_variant,p.=,ENST00000300482,;TRPM2,synonymous_variant,p.=,ENST00000300481,;TRPM2,synonymous_variant,p.=,ENST00000397932,;TRPM2,downstream_gene_variant,,ENST00000431901,;TRPM2,non_coding_transcript_exon_variant,,ENST00000498430,; T ENST00000397928 Transcript synonymous_variant 1138/6221 693/4512 231/1503 Y taC/taT 1 1 TRPM2 HGNC HGNC:12339 protein_coding YES CCDS13710.1 ENSP00000381023 O94759 UPI0000169D60 NM_003307.3 5/32 hmmpanther:PTHR13800:SF2,hmmpanther:PTHR13800,Gene3D:3.40.50.450 LOW 1 SNV 1 1 PASS rs1183340309 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 44369265 44369265 C T 1 0 0 0 0 0 0 0 1 17092 489 17 3 3 TRPM2 21 44369265 Silent SNP C C3N-00560_T 12709464 44369265 2340718 1204 17893 KRTAP10-8 0 . GRCh38 21 44612771 44612771 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.671C>G p.Pro224Arg p.P224R ENST00000334662 1/1 419 329 90 488 488 0 strelka-varscan-mutect KRTAP10-8,missense_variant,p.Pro224Arg,ENST00000334662,NM_198695.2;KRTAP10-7,missense_variant,p.Pro210Arg,ENST00000616689,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; G ENST00000334662 Transcript missense_variant 693/876 671/780 224/259 P/R cCt/cGt 1 1 KRTAP10-8 HGNC HGNC:20525 protein_coding YES CCDS13713.1 ENSP00000335565 P60410 UPI000036709C NM_198695.2 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262:SF74,hmmpanther:PTHR23262 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 44612771 44612771 C G 1 0 0 0 0 1 0 0 0 8398 681 24 4 4 KRTAP10-8 21 44612771 Missense_Mutation SNP C C3N-00560_T 243506 44612771 2097212 1205 17894 COL18A1 0 . GRCh38 21 45475532 45475532 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2040G>T p.Glu680Asp p.E680D ENST00000359759 4/41 141 111 30 178 178 0 strelka-varscan-mutect COL18A1,missense_variant,p.Glu680Asp,ENST00000359759,NM_130444.2;COL18A1,missense_variant,p.Glu445Asp,ENST00000355480,NM_030582.3;COL18A1,missense_variant,p.Glu265Asp,ENST00000400337,NM_130445.3;MIR6815,upstream_gene_variant,,ENST00000611994,; T ENST00000359759 Transcript missense_variant 2040/6586 2040/5265 680/1754 E/D gaG/gaT 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 tolerated(0.51) 4/41 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 45475532 45475532 G T 1 0 0 0 0 1 0 0 0 3463 956 33 2 2 COL18A1 21 45475532 Missense_Mutation SNP G C3N-00560_T 862761 45475532 1234451 1206 17895 AIFM3 0 . GRCh38 22 20973428 20973428 + Silent SNP G G T rs748543747 C3N-00560_T C3N-00560_N G G c.153G>T p.= p.T51T ENST00000399167 3/21 380 258 122 319 319 0 strelka-varscan-mutect AIFM3,synonymous_variant,p.=,ENST00000399167,NM_144704.2;AIFM3,synonymous_variant,p.=,ENST00000440238,;AIFM3,synonymous_variant,p.=,ENST00000405089,NM_001146288.1;AIFM3,synonymous_variant,p.=,ENST00000399163,NM_001018060.2;AIFM3,synonymous_variant,p.=,ENST00000434714,;AIFM3,synonymous_variant,p.=,ENST00000441376,;AIFM3,non_coding_transcript_exon_variant,,ENST00000468124,;AIFM3,non_coding_transcript_exon_variant,,ENST00000496097,;AIFM3,upstream_gene_variant,,ENST00000465606,;AIFM3,upstream_gene_variant,,ENST00000483107,;AIFM3,missense_variant,p.Arg30Leu,ENST00000426113,;AIFM3,synonymous_variant,p.=,ENST00000417515,;AIFM3,non_coding_transcript_exon_variant,,ENST00000484206,;AIFM3,non_coding_transcript_exon_variant,,ENST00000472575,;AIFM3,non_coding_transcript_exon_variant,,ENST00000467926,;AIFM3,upstream_gene_variant,,ENST00000486003,; T ENST00000399167 Transcript synonymous_variant 393/2387 153/1818 51/605 T acG/acT rs748543747 1 1 AIFM3 HGNC HGNC:26398 protein_coding YES CCDS13786.1 ENSP00000382120 Q96NN9 UPI0000071A61 NM_144704.2 3/21 LOW 1 SNV 2 1 PASS rs748543747 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 20973428 20973428 G T 1 0 0 0 0 0 0 0 1 505 1103 39 1 1 AIFM3 22 20973428 Silent SNP G C3N-00560_T 20973428 29845040 1207 17896 PRAME 0 . GRCh38 22 22548116 22548116 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1481C>A p.Thr494Asn p.T494N ENST00000543184 5/5 154 106 48 186 186 0 strelka-varscan-mutect PRAME,missense_variant,p.Thr494Asn,ENST00000543184,NM_206953.2;PRAME,missense_variant,p.Thr494Asn,ENST00000398741,NM_206955.2;PRAME,missense_variant,p.Thr494Asn,ENST00000398743,NM_206954.2,NM_001291715.1,NM_006115.4;PRAME,missense_variant,p.Thr494Asn,ENST00000405655,NM_206956.2,NM_001291716.1;PRAME,missense_variant,p.Thr494Asn,ENST00000402697,;PRAME,downstream_gene_variant,,ENST00000439106,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000420709,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,downstream_gene_variant,,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000485532,;PRAME,downstream_gene_variant,,ENST00000476336,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,; T ENST00000543184 Transcript missense_variant 2344/2758 1481/1530 494/509 T/N aCc/aAc 1 -1 PRAME HGNC HGNC:9336 protein_coding YES CCDS13801.1 ENSP00000445675 P78395 A0A024R1E6 UPI0000000DDA NM_206953.2 tolerated(0.07) 5/5 hmmpanther:PTHR14224:SF4,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 22548116 22548116 G T 1 0 0 0 0 1 0 0 0 12553 1261 44 2 2 PRAME 22 22548116 Missense_Mutation SNP G C3N-00560_T 1574688 22548116 28270352 1208 17897 PRAME 0 . GRCh38 22 22549823 22549823 + Missense_Mutation SNP C C G rs752912693 C3N-00560_T C3N-00560_N C C c.856G>C p.Ala286Pro p.A286P ENST00000543184 4/5 232 159 73 232 232 0 strelka-varscan-mutect PRAME,missense_variant,p.Ala286Pro,ENST00000543184,NM_206953.2;PRAME,missense_variant,p.Ala286Pro,ENST00000398741,NM_206955.2;PRAME,missense_variant,p.Ala286Pro,ENST00000398743,NM_206954.2,NM_001291715.1,NM_006115.4;PRAME,missense_variant,p.Ala286Pro,ENST00000405655,NM_206956.2,NM_001291716.1;PRAME,missense_variant,p.Ala286Pro,ENST00000402697,;PRAME,downstream_gene_variant,,ENST00000439106,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000420709,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,downstream_gene_variant,,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000485532,;PRAME,downstream_gene_variant,,ENST00000476336,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,; G ENST00000543184 Transcript missense_variant 1719/2758 856/1530 286/509 A/P Gcc/Ccc rs752912693,COSM3424061,COSM5679056 1 -1 PRAME HGNC HGNC:9336 protein_coding YES CCDS13801.1 ENSP00000445675 P78395 A0A024R1E6 UPI0000000DDA NM_206953.2 tolerated(0.21) 4/5 hmmpanther:PTHR14224:SF4,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs752912693 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 22549823 22549823 C G 1 0 0 0 0 1 0 0 0 12553 768 27 4 4 PRAME 22 22549823 Missense_Mutation SNP C C3N-00560_T 1707 22549823 28268645 1209 17898 SGSM1 0 . GRCh38 22 24874432 24874432 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.1309G>A p.Gly437Ser p.G437S ENST00000400359 13/26 122 77 45 99 99 0 strelka-varscan-mutect SGSM1,missense_variant,p.Gly437Ser,ENST00000610372,NM_133454.3,NM_001098498.2;SGSM1,missense_variant,p.Gly437Ser,ENST00000400359,NM_001039948.3;SGSM1,intron_variant,,ENST00000400358,NM_001098497.2;SGSM1,intron_variant,,ENST00000473458,;SGSM1,intron_variant,,ENST00000480523,; A ENST00000400359 Transcript missense_variant 1316/4317 1309/3447 437/1148 G/S Ggc/Agc 1 1 SGSM1 HGNC HGNC:29410 protein_coding YES CCDS46674.1 ENSP00000383212 Q2NKQ1 UPI00006EB130 NM_001039948.3 tolerated(0.72) 13/26 hmmpanther:PTHR22957:SF187,hmmpanther:PTHR22957 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 24874432 24874432 G A 1 0 0 0 0 1 0 0 0 14480 1232 43 3 3 SGSM1 22 24874432 Missense_Mutation SNP G C3N-00560_T 2324609 24874432 25944036 1210 17899 MYO18B 0 . GRCh38 22 25908353 25908353 + Missense_Mutation SNP G G T rs201899118 C3N-00560_T C3N-00560_N G G c.5180G>T p.Arg1727Leu p.R1727L ENST00000335473 32/44 277 221 56 156 156 0 strelka-varscan-mutect MYO18B,missense_variant,p.Arg1727Leu,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Arg1728Leu,ENST00000407587,;MYO18B,missense_variant,p.Arg1727Leu,ENST00000536101,;MYO18B,downstream_gene_variant,,ENST00000536204,;MYO18B,downstream_gene_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript missense_variant 5430/8565 5180/7704 1727/2567 R/L cGg/cTg rs201899118,COSM2935266 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0) 32/44 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201899118 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 25908353 25908353 G T 1 0 0 0 0 1 0 0 0 10067 1116 39 1 1 MYO18B 22 25908353 Missense_Mutation SNP G C3N-00560_T 1033921 25908353 24910115 1211 17900 GAS2L1 0 . GRCh38 22 29311937 29311937 + Missense_Mutation SNP G G T rs747846620 C3N-00560_T C3N-00560_N G G c.1486G>T p.Gly496Cys p.G496C ENST00000618518 5/5 438 289 149 323 322 1 strelka-varscan-mutect GAS2L1,missense_variant,p.Gly496Cys,ENST00000618518,;GAS2L1,missense_variant,p.Gly496Cys,ENST00000616432,;GAS2L1,missense_variant,p.Gly496Cys,ENST00000621062,NM_006478.4;GAS2L1,missense_variant,p.Gly496Cys,ENST00000611648,NM_152236.2;GAS2L1,3_prime_UTR_variant,,ENST00000610653,;GAS2L1,intron_variant,,ENST00000406549,NM_001278730.1;RASL10A,downstream_gene_variant,,ENST00000401450,;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.4;GAS2L1,downstream_gene_variant,,ENST00000416823,;GAS2L1,downstream_gene_variant,,ENST00000428622,;AC002059.10,downstream_gene_variant,,ENST00000608014,;RASL10A,downstream_gene_variant,,ENST00000608559,;RASL10A,downstream_gene_variant,,ENST00000474590,;GAS2L1,downstream_gene_variant,,ENST00000491016,;GAS2L1,downstream_gene_variant,,ENST00000487341,; T ENST00000618518 Transcript missense_variant 2534/3382 1486/2046 496/681 G/C Ggc/Tgc rs747846620 1 1 GAS2L1 HGNC HGNC:16955 protein_coding YES CCDS74840.1 ENSP00000481012 A0A5E8 UPI0000073BD7 deleterious(0.01) 5/5 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF296 MODERATE SNV 2 1 PASS rs747846620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 29311937 29311937 G T 1 0 0 0 0 1 0 0 0 6116 1232 43 2 2 GAS2L1 22 29311937 Missense_Mutation SNP G C3N-00560_T 3403584 29311937 21506531 1212 17901 SEC14L3 0 . GRCh38 22 30461347 30461347 + Silent SNP G G T rs369303021 C3N-00560_T C3N-00560_N G G c.1044C>A p.= p.P348P ENST00000215812 11/12 79 65 14 62 62 0 strelka-varscan-mutect SEC14L3,synonymous_variant,p.=,ENST00000403066,;SEC14L3,synonymous_variant,p.=,ENST00000540910,;SEC14L3,synonymous_variant,p.=,ENST00000215812,NM_174975.4;SEC14L3,synonymous_variant,p.=,ENST00000402286,NM_001257378.1;SEC14L3,synonymous_variant,p.=,ENST00000401751,NM_001257379.1,NM_001257382.1;SEC14L3,downstream_gene_variant,,ENST00000435069,;SEC14L3,3_prime_UTR_variant,,ENST00000434642,; T ENST00000215812 Transcript synonymous_variant 1135/2086 1044/1203 348/400 P ccC/ccA rs369303021 1 -1 SEC14L3 HGNC HGNC:18655 protein_coding YES CCDS13877.1 ENSP00000215812 Q9UDX4 UPI000000D83C NM_174975.4 11/12 PROSITE_profiles:PS50866,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF62,Superfamily_domains:0041713 LOW 1 SNV 1 1 PASS rs369303021 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 30461347 30461347 G T 1 0 0 0 0 0 0 0 1 14259 1103 39 1 1 SEC14L3 22 30461347 Silent SNP G C3N-00560_T 1149410 30461347 20357121 1213 17902 GAL3ST1 0 . GRCh38 22 30556039 30556039 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.186G>T p.= p.V62V ENST00000402321 3/3 159 113 46 128 128 0 strelka-varscan-mutect GAL3ST1,synonymous_variant,p.=,ENST00000402321,;GAL3ST1,synonymous_variant,p.=,ENST00000406361,NM_001318104.1,NM_001318113.1;GAL3ST1,synonymous_variant,p.=,ENST00000401975,NM_001318110.1,NM_001318115.1,NM_004861.1;GAL3ST1,synonymous_variant,p.=,ENST00000338911,;GAL3ST1,synonymous_variant,p.=,ENST00000402369,NM_001318103.1,NM_001318109.1;GAL3ST1,synonymous_variant,p.=,ENST00000406955,NM_001318112.1,NM_001318114.1;GAL3ST1,synonymous_variant,p.=,ENST00000441967,;GAL3ST1,synonymous_variant,p.=,ENST00000452827,;GAL3ST1,synonymous_variant,p.=,ENST00000431313,;GAL3ST1,synonymous_variant,p.=,ENST00000437282,;GAL3ST1,synonymous_variant,p.=,ENST00000423299,;GAL3ST1,synonymous_variant,p.=,ENST00000423371,;GAL3ST1,synonymous_variant,p.=,ENST00000453479,;GAL3ST1,synonymous_variant,p.=,ENST00000443136,;GAL3ST1,synonymous_variant,p.=,ENST00000416358,;GAL3ST1,synonymous_variant,p.=,ENST00000448604,;GAL3ST1,synonymous_variant,p.=,ENST00000411821,;GAL3ST1,synonymous_variant,p.=,ENST00000445645,;GAL3ST1,synonymous_variant,p.=,ENST00000447224,;GAL3ST1,synonymous_variant,p.=,ENST00000426220,;GAL3ST1,synonymous_variant,p.=,ENST00000428682,;GAL3ST1,synonymous_variant,p.=,ENST00000427899,; A ENST00000402321 Transcript synonymous_variant 504/1908 186/1272 62/423 V gtG/gtT 1 -1 GAL3ST1 HGNC HGNC:24240 protein_coding YES CCDS13879.1 ENSP00000385735 Q99999 A0A024R1D7 UPI00001285C2 3/3 Pfam_domain:PF06990,hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF56 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 30556039 30556039 C A 1 0 0 0 0 0 0 0 1 6065 813 29 2 2 GAL3ST1 22 30556039 Silent SNP C C3N-00560_T 94692 30556039 20262429 1214 17903 SFI1 0 . GRCh38 22 31606415 31606415 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.2142G>T p.Arg714Ser p.R714S ENST00000400288 21/33 169 125 44 124 124 0 strelka-varscan-mutect SFI1,missense_variant,p.Arg659Ser,ENST00000540643,NM_001258325.1;SFI1,missense_variant,p.Arg683Ser,ENST00000432498,NM_014775.3;SFI1,missense_variant,p.Arg714Ser,ENST00000400288,NM_001007467.2;SFI1,missense_variant,p.Arg632Ser,ENST00000400289,NM_001258326.1,NM_001258327.1;SFI1,missense_variant,p.Arg561Ser,ENST00000443011,;SFI1,missense_variant,p.Arg297Ser,ENST00000417682,;SFI1,non_coding_transcript_exon_variant,,ENST00000466991,;SFI1,3_prime_UTR_variant,,ENST00000524296,;SFI1,non_coding_transcript_exon_variant,,ENST00000382162,;SFI1,non_coding_transcript_exon_variant,,ENST00000488883,;SFI1,intron_variant,,ENST00000452250,;SFI1,upstream_gene_variant,,ENST00000491973,; T ENST00000400288 Transcript missense_variant 2247/4002 2142/3729 714/1242 R/S agG/agT 1 1 SFI1 HGNC HGNC:29064 protein_coding YES CCDS43004.1 ENSP00000383145 A8K8P3 UPI00004703B1 NM_001007467.2 deleterious(0) 21/33 hmmpanther:PTHR22028,hmmpanther:PTHR22028:SF4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 31606415 31606415 G T 1 0 0 0 0 1 0 0 0 14434 1165 41 2 2 SFI1 22 31606415 Missense_Mutation SNP G C3N-00560_T 1050376 31606415 19212053 1215 17904 RFPL2 0 . GRCh38 22 32191176 32191176 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.733G>T p.Val245Leu p.V245L ENST00000400237 5/5 278 135 143 323 323 0 strelka-varscan-mutect RFPL2,missense_variant,p.Val245Leu,ENST00000400237,NM_001098527.2;RFPL2,missense_variant,p.Val184Leu,ENST00000248980,NM_001159545.1,NM_006605.3,NM_001159546.1;RFPL2,missense_variant,p.Val245Leu,ENST00000248983,;AL008723.1,missense_variant,p.His25Gln,ENST00000623133,;RFPL3-AS1_1,upstream_gene_variant,,ENST00000618747,;RFPL2,non_coding_transcript_exon_variant,,ENST00000489846,;RFPL2,3_prime_UTR_variant,,ENST00000626996,;RFPL2,3_prime_UTR_variant,,ENST00000628378,; A ENST00000400237 Transcript missense_variant 1669/2407 733/1137 245/378 V/L Gtg/Ttg 1 -1 RFPL2 HGNC HGNC:9979 protein_coding YES CCDS43009.2 ENSP00000383096 O75678 UPI000013CC66 NM_001098527.2 deleterious(0.02) 5/5 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF225,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9996602 1 1 1 0 A 3 1 56 32191176 32191176 C A 1 0 0 0 0 1 0 0 0 13425 507 18 2 2 RFPL2 22 32191176 Missense_Mutation SNP C C3N-00560_T 584761 32191176 18627292 1216 17905 APOL6 0 . GRCh38 22 35659369 35659369 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.805G>T p.Glu269Ter p.E269* ENST00000409652 3/3 201 118 83 272 272 0 strelka-varscan-mutect APOL6,stop_gained,p.Glu269Ter,ENST00000409652,NM_030641.3; T ENST00000409652 Transcript stop_gained 1081/10121 805/1032 269/343 E/* Gaa/Taa 1 1 APOL6 HGNC HGNC:14870 protein_coding YES CCDS13919.1 ENSP00000386280 Q9BWW8 B3KTP4 UPI000000DC62 NM_030641.3 3/3 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05461,hmmpanther:PTHR14096,hmmpanther:PTHR14096:SF7,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 35659369 35659369 G T 1 0 0 0 0 0 1 0 0 932 1175 41 2 2 APOL6 22 35659369 Nonsense_Mutation SNP G C3N-00560_T 3468193 35659369 15159099 1217 17906 CACNG2 0 . GRCh38 22 36702561 36702561 + Silent SNP G G T C3N-00560_T C3N-00560_N G G c.16C>A p.= p.R6R ENST00000300105 1/4 246 151 95 315 314 1 strelka-varscan-mutect CACNG2,synonymous_variant,p.=,ENST00000300105,NM_006078.3;RP1-293L6.1,upstream_gene_variant,,ENST00000430281,; T ENST00000300105 Transcript synonymous_variant 998/2384 16/972 6/323 R Cga/Aga COSM259914 1 -1 CACNG2 HGNC HGNC:1406 protein_coding YES CCDS13931.1 ENSP00000300105 Q9Y698 UPI00001272AC NM_006078.3 1/4 hmmpanther:PTHR12107,hmmpanther:PTHR12107:SF1 1 LOW 1 SNV 1 1 1 PASS rs1327899143 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 36702561 36702561 G T 1 0 0 0 0 0 0 0 1 2245 1066 37 1 1 CACNG2 22 36702561 Silent SNP G C3N-00560_T 1043192 36702561 14115907 1218 17907 NCF4 0 . GRCh38 22 36870438 36870438 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.366G>T p.Trp122Cys p.W122C ENST00000397147 5/9 442 267 175 551 551 0 strelka-varscan-mutect NCF4,missense_variant,p.Trp122Cys,ENST00000397147,NM_013416.3;NCF4,missense_variant,p.Trp122Cys,ENST00000248899,NM_000631.4;NCF4,missense_variant,p.Trp19Cys,ENST00000447071,;CTA-833B7.2,non_coding_transcript_exon_variant,,ENST00000619915,;CTA-833B7.2,upstream_gene_variant,,ENST00000431290,;NCF4,upstream_gene_variant,,ENST00000415063,; T ENST00000397147 Transcript missense_variant 550/1641 366/1047 122/348 W/C tgG/tgT 1 1 NCF4 HGNC HGNC:7662 protein_coding YES CCDS13935.1 ENSP00000380334 Q15080 UPI000013CC59 NM_013416.3 tolerated(0.09) 5/9 PROSITE_profiles:PS50195,hmmpanther:PTHR10663:SF209,hmmpanther:PTHR10663,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS rs1219261355 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 36870438 36870438 G T 1 0 0 0 0 1 0 0 0 10236 1241 43 2 2 NCF4 22 36870438 Missense_Mutation SNP G C3N-00560_T 167877 36870438 13948030 1219 17908 SSTR3 0 . GRCh38 22 37207021 37207021 + Silent SNP G G T rs144127697 C3N-00560_T C3N-00560_N G G c.783C>A p.= p.A261A ENST00000610913 2/2 260 126 134 303 303 0 strelka-varscan-mutect SSTR3,synonymous_variant,p.=,ENST00000610913,NM_001051.4;SSTR3,synonymous_variant,p.=,ENST00000617123,NM_001278687.2; T ENST00000610913 Transcript synonymous_variant 1317/4100 783/1257 261/418 A gcC/gcA rs144127697 1 -1 SSTR3 HGNC HGNC:11332 protein_coding YES CCDS13944.1 ENSP00000480971 P32745 UPI0000050435 NM_001051.4 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF42,Low_complexity_(Seg):seg,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs144127697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 37207021 37207021 G T 1 0 0 0 0 0 0 0 1 15576 1103 39 1 1 SSTR3 22 37207021 Silent SNP G C3N-00560_T 336583 37207021 13611447 1220 17909 TNRC6B 0 . GRCh38 22 40280071 40280071 + Silent SNP G G A C3N-00560_T C3N-00560_N G G c.3339G>A p.= p.K1113K ENST00000454349 10/23 119 73 46 160 160 0 strelka-varscan-mutect TNRC6B,synonymous_variant,p.=,ENST00000454349,NM_001162501.1;TNRC6B,synonymous_variant,p.=,ENST00000335727,NM_015088.2;TNRC6B,synonymous_variant,p.=,ENST00000301923,NM_001024843.1;TNRC6B,synonymous_variant,p.=,ENST00000446273,;TNRC6B,synonymous_variant,p.=,ENST00000402203,;TNRC6B,non_coding_transcript_exon_variant,,ENST00000497559,; A ENST00000454349 Transcript synonymous_variant 3550/18279 3339/5502 1113/1833 K aaG/aaA COSM1159108,COSM1159109 1 1 TNRC6B HGNC HGNC:29190 protein_coding YES CCDS54533.1 ENSP00000401946 Q9UPQ9 UPI00017A6F19 NM_001162501.1 10/23 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF32 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 40280071 40280071 G A 1 0 0 0 0 0 0 0 1 16814 991 35 3 3 TNRC6B 22 40280071 Silent SNP G C3N-00560_T 3073050 40280071 10538397 1221 17910 PNPLA3 0 . GRCh38 22 43937236 43937236 + Missense_Mutation SNP A A G C3N-00560_T C3N-00560_N A A c.943A>G p.Ser315Gly p.S315G ENST00000216180 6/9 245 126 119 305 305 0 strelka-varscan-mutect PNPLA3,missense_variant,p.Ser315Gly,ENST00000216180,NM_025225.2;PNPLA3,missense_variant,p.Ser311Gly,ENST00000423180,;PNPLA3,non_coding_transcript_exon_variant,,ENST00000497129,;PNPLA3,downstream_gene_variant,,ENST00000478713,;PNPLA3,3_prime_UTR_variant,,ENST00000406117,; G ENST00000216180 Transcript missense_variant 1116/2805 943/1446 315/481 S/G Agc/Ggc COSM273130 1 1 PNPLA3 HGNC HGNC:18590 protein_coding YES CCDS14054.1 ENSP00000216180 Q9NST1 UPI000006CED5 NM_025225.2 tolerated(0.21) 6/9 hmmpanther:PTHR12406:SF22,hmmpanther:PTHR12406 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 43937236 43937236 A G 1 0 0 0 0 1 0 0 0 12274 304 11 5 5 PNPLA3 22 43937236 Missense_Mutation SNP A C3N-00560_T 3657165 43937236 6881232 1222 17911 PKDREJ 0 . GRCh38 22 46262811 46262811 + Missense_Mutation SNP G G T rs776386876 C3N-00560_T C3N-00560_N G G c.512C>A p.Pro171Gln p.P171Q ENST00000253255 1/1 21 10 11 20 20 0 strelka-varscan-mutect PKDREJ,missense_variant,p.Pro171Gln,ENST00000253255,NM_006071.1; T ENST00000253255 Transcript missense_variant 545/7693 512/6762 171/2253 P/Q cCg/cAg rs776386876,COSM4939771 1 -1 PKDREJ HGNC HGNC:9015 protein_coding YES CCDS14073.1 ENSP00000253255 Q9NTG1 UPI0000031D01 NM_006071.1 deleterious(0.02) 1/1 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 PASS rs776386876 . 2 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 46262811 46262811 G T 1 0 0 0 0 1 0 0 0 12066 1116 39 1 1 PKDREJ 22 46262811 Missense_Mutation SNP G C3N-00560_T 2325575 46262811 4555657 1223 17912 CSF2RA 0 . GRCh38 X 1300570 1300570 + Missense_Mutation SNP G G T C3N-00560_T C3N-00560_N G G c.890G>T p.Arg297Ile p.R297I ENST00000417535 10/14 927 809 118 480 478 2 strelka-varscan-mutect CSF2RA,missense_variant,p.Arg297Ile,ENST00000381524,;CSF2RA,missense_variant,p.Arg297Ile,ENST00000417535,NM_001161530.1;CSF2RA,missense_variant,p.Arg297Ile,ENST00000432318,NM_001161529.1;CSF2RA,missense_variant,p.Arg297Ile,ENST00000381529,NM_006140.4,NM_172245.2;CSF2RA,missense_variant,p.Arg297Ile,ENST00000355432,NM_172246.2;CSF2RA,missense_variant,p.Arg164Ile,ENST00000501036,NM_001161532.1;CSF2RA,missense_variant,p.Arg297Ile,ENST00000381509,NM_001161531.1;CSF2RA,missense_variant,p.Arg297Ile,ENST00000381500,NM_172247.2;CSF2RA,intron_variant,,ENST00000355805,NM_172249.2;CSF2RA,intron_variant,,ENST00000494969,;RNA5SP498,upstream_gene_variant,,ENST00000411342,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000498153,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000475259,;CSF2RA,downstream_gene_variant,,ENST00000493312,;CSF2RA,downstream_gene_variant,,ENST00000491683,;CSF2RA,intron_variant,,ENST00000486791,; T ENST00000417535 Transcript missense_variant 1084/1955 890/1305 297/434 R/I aGa/aTa COSM4770857,COSM4770858,COSM4770859 1 1 CSF2RA HGNC HGNC:2435 protein_coding YES CCDS55359.1 ENSP00000394227 P15509 UPI000159C3E4 NM_001161530.1 deleterious(0) 10/14 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF94,hmmpanther:PTHR23036,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 1300570 1300570 G T 1 0 0 0 0 1 0 0 0 3735 942 33 2 2 CSF2RA 23 1300570 Missense_Mutation SNP G C3N-00560_T 1300570 154740325 1224 17913 IL3RA 0 . GRCh38 X 1341815 1341815 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.50T>A p.Leu17Gln p.L17Q ENST00000331035 2/12 296 224 72 346 346 0 strelka-varscan-mutect IL3RA,missense_variant,p.Leu17Gln,ENST00000331035,NM_002183.3;IL3RA,missense_variant,p.Leu17Gln,ENST00000381469,NM_001267713.1;IL3RA,missense_variant,p.Leu17Gln,ENST00000432757,; A ENST00000331035 Transcript missense_variant 399/1706 50/1137 17/378 L/Q cTg/cAg 1 1 IL3RA HGNC HGNC:6012 protein_coding YES CCDS14113.1 ENSP00000327890 P26951 UPI0000001C31 NM_002183.3 tolerated(0.08) 2/12 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF94 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 1341815 1341815 T A 1 0 0 0 0 1 0 0 0 7599 1580 55 4 4 IL3RA 23 1341815 Missense_Mutation SNP T C3N-00560_T 41245 1341815 154699080 1225 17914 ASMT 0 . GRCh38 X 1624306 1624306 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.282G>T p.= p.L94L ENST00000381241 3/9 713 303 410 368 368 0 strelka-varscan-mutect ASMT,synonymous_variant,p.=,ENST00000381241,NM_004043.2,NM_001171038.1;ASMT,synonymous_variant,p.=,ENST00000381229,;ASMT,synonymous_variant,p.=,ENST00000381233,NM_001171039.1;ASMT,upstream_gene_variant,,ENST00000509780,; T ENST00000381241 Transcript synonymous_variant 481/1388 282/1122 94/373 L ctG/ctT 1 1 ASMT HGNC HGNC:750 protein_coding YES CCDS14117.1 ENSP00000370639 P46597 A0A024RBT9 UPI00001AEDD0 NM_004043.2,NM_001171038.1 3/9 PROSITE_profiles:PS51683,hmmpanther:PTHR11746:SF71,hmmpanther:PTHR11746,Pfam_domain:PF16864 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 1624306 1624306 G T 1 0 0 0 0 0 0 0 1 1192 1277 45 2 2 ASMT 23 1624306 Silent SNP G C3N-00560_T 282491 1624306 154416589 1226 17915 ASMT 0 . GRCh38 X 1642933 1642933 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1041G>T p.Met347Ile p.M347I ENST00000381241 9/9 1199 550 649 651 651 0 strelka-varscan-mutect ASMT,missense_variant,p.Met347Ile,ENST00000381241,NM_004043.2,NM_001171038.1;ASMT,missense_variant,p.Met319Ile,ENST00000381229,;ASMT,missense_variant,p.Met272Ile,ENST00000381233,NM_001171039.1;ASMT,missense_variant,p.Met98Ile,ENST00000432523,; T ENST00000381241 Transcript missense_variant 1240/1388 1041/1122 347/373 M/I atG/atT 1 1 ASMT HGNC HGNC:750 protein_coding YES CCDS14117.1 ENSP00000370639 P46597 A0A024RBT9 UPI00001AEDD0 NM_004043.2,NM_001171038.1 tolerated(0.13) 9/9 PROSITE_profiles:PS51683,hmmpanther:PTHR11746:SF71,hmmpanther:PTHR11746,Pfam_domain:PF00891,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 1642933 1642933 G T 1 0 0 0 0 1 0 0 0 1192 1319 46 2 2 ASMT 23 1642933 Missense_Mutation SNP G C3N-00560_T 18627 1642933 154397962 1227 17916 MXRA5 0 . GRCh38 X 3317430 3317430 + Missense_Mutation SNP C C A rs188082959 C3N-00560_T C3N-00560_N C C c.6251G>T p.Gly2084Val p.G2084V ENST00000217939 6/7 98 33 65 97 97 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gly2084Val,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 6406/9793 6251/8487 2084/2828 G/V gGg/gTg rs188082959 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.5) 6/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs188082959 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 3317430 3317430 C A 1 0 0 0 0 1 0 0 0 10002 623 22 2 2 MXRA5 23 3317430 Missense_Mutation SNP C C3N-00560_T 1674497 3317430 152723465 1228 17917 NLGN4X 0 . GRCh38 X 6151459 6151459 + Missense_Mutation SNP C C A rs139587269 C3N-00560_T C3N-00560_N C C c.8G>T p.Arg3Leu p.R3L ENST00000381095 2/6 172 69 103 143 143 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Arg3Leu,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Arg3Leu,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Arg3Leu,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Arg3Leu,ENST00000381092,;NLGN4X,upstream_gene_variant,,ENST00000538097,;NLGN4X,non_coding_transcript_exon_variant,,ENST00000469740,;NLGN4X,non_coding_transcript_exon_variant,,ENST00000483337,; A ENST00000381095 Transcript missense_variant 636/5870 8/2451 3/816 R/L cGg/cTg rs139587269 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 tolerated_low_confidence(0.08) 2/6 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260 MODERATE 1 SNV 1 1 PASS rs139587269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 6151459 6151459 C A 1 0 0 0 0 1 0 0 0 10501 652 23 1 1 NLGN4X 23 6151459 Missense_Mutation SNP C C3N-00560_T 2834029 6151459 149889436 1229 17918 SHROOM2 0 . GRCh38 X 9895385 9895385 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1477G>T p.Gly493Ter p.G493* ENST00000380913 4/10 48 14 34 39 39 0 strelka-varscan-mutect SHROOM2,stop_gained,p.Gly493Ter,ENST00000380913,NM_001649.2;SHROOM2,upstream_gene_variant,,ENST00000493668,; T ENST00000380913 Transcript stop_gained 1567/7447 1477/4851 493/1616 G/* Gga/Tga 1 1 SHROOM2 HGNC HGNC:630 protein_coding YES CCDS14135.1 ENSP00000370299 Q13796 UPI0000125D05 NM_001649.2 4/10 hmmpanther:PTHR15012:SF8,hmmpanther:PTHR15012 HIGH 1 SNV 1 1 PASS rs935978898 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 9895385 9895385 G T 1 0 0 0 0 0 1 0 0 14557 1233 43 2 2 SHROOM2 23 9895385 Nonsense_Mutation SNP G C3N-00560_T 3743926 9895385 146145510 1230 17919 FRMPD4 0 . GRCh38 X 12609882 12609882 + Splice_Site SNP G G T novel C3N-00560_T C3N-00560_N G G c.319+1G>T p.X107_splice ENST00000380682 63 27 36 45 45 0 strelka-varscan-mutect FRMPD4,splice_donor_variant,,ENST00000380682,NM_014728.3;FRMPD4,splice_donor_variant,,ENST00000616992,;RN7SKP290,downstream_gene_variant,,ENST00000606842,; T ENST00000380682 Transcript splice_donor_variant -/8465 319/3969 107/1322 1 1 FRMPD4 HGNC HGNC:29007 protein_coding YES CCDS35201.1 ENSP00000370057 Q14CM0 UPI00001C2066 NM_014728.3 3/16 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 56 12609882 12609882 G T 1 0 0 0 0 0 0 1 0 5930 1275 44 2 2 FRMPD4 23 12609882 Splice_Site SNP G C3N-00560_T 2714497 12609882 143431013 1231 17920 ZNF645 0 . GRCh38 X 22273628 22273628 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.637C>A p.Pro213Thr p.P213T ENST00000323684 1/1 85 33 52 95 95 0 strelka-varscan-mutect ZNF645,missense_variant,p.Pro213Thr,ENST00000323684,NM_152577.3;PTCHD1-AS,intron_variant,,ENST00000608254,; A ENST00000323684 Transcript missense_variant 686/1519 637/1278 213/425 P/T Cca/Aca 1 1 ZNF645 HGNC HGNC:26371 protein_coding YES CCDS14205.1 ENSP00000323348 Q8N7E2 UPI0000073BD5 NM_152577.3 tolerated(0.75) 1/1 hmmpanther:PTHR13480,hmmpanther:PTHR13480:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs1239511357 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 22273628 22273628 C A 1 0 0 0 0 1 0 0 0 18634 623 22 2 2 ZNF645 23 22273628 Missense_Mutation SNP C C3N-00560_T 9663746 22273628 133767267 1232 17921 IL1RAPL1 0 . GRCh38 X 29955460 29955460 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1731G>T p.Glu577Asp p.E577D ENST00000378993 11/11 198 77 121 141 141 0 strelka-varscan-mutect IL1RAPL1,missense_variant,p.Glu577Asp,ENST00000378993,NM_014271.3;IL1RAPL1,missense_variant,p.Glu318Asp,ENST00000302196,; T ENST00000378993 Transcript missense_variant 2404/3667 1731/2091 577/696 E/D gaG/gaT 1 1 IL1RAPL1 HGNC HGNC:5996 protein_coding YES CCDS14218.1 ENSP00000368278 Q9NZN1 X5DNQ7 UPI000006D1BF NM_014271.3 deleterious(0.01) 11/11 hmmpanther:PTHR11890:SF22,hmmpanther:PTHR11890 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 29955460 29955460 G T 1 0 0 0 0 1 0 0 0 7564 962 34 2 2 IL1RAPL1 23 29955460 Missense_Mutation SNP G C3N-00560_T 7681832 29955460 126085435 1233 17922 DMD 0 . GRCh38 X 31146365 31146365 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.10847C>T p.Thr3616Ile p.T3616I ENST00000357033 76/79 317 295 22 256 256 0 strelka-varscan-mutect DMD,missense_variant,p.Thr3616Ile,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Thr3612Ile,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Thr3615Ile,ENST00000620040,;DMD,missense_variant,p.Thr3611Ile,ENST00000619831,;DMD,missense_variant,p.Thr1156Ile,ENST00000378707,NM_004013.2;DMD,missense_variant,p.Thr1143Ile,ENST00000359836,NM_004022.2;DMD,missense_variant,p.Thr1046Ile,ENST00000541735,NM_004020.3,NM_004023.2;DMD,missense_variant,p.Thr1299Ile,ENST00000358062,;DMD,missense_variant,p.Thr887Ile,ENST00000343523,NM_004014.2;DMD,missense_variant,p.Thr1156Ile,ENST00000474231,NM_004021.2;DMD,missense_variant,p.Thr548Ile,ENST00000378723,NM_004016.2;DMD,missense_variant,p.Thr548Ile,ENST00000378702,NM_004015.2,NM_004017.2;DMD,missense_variant,p.Thr535Ile,ENST00000361471,NM_004018.2;DMD,missense_variant,p.Thr438Ile,ENST00000378680,;DMD,intron_variant,,ENST00000481143,; A ENST00000357033 Transcript missense_variant 11054/13956 10847/11058 3616/3685 T/I aCc/aTc 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0.01) 76/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 31146365 31146365 G A 1 0 0 0 0 1 0 0 0 4387 1261 44 3 3 DMD 23 31146365 Missense_Mutation SNP G C3N-00560_T 1190905 31146365 124894530 1234 17923 DMD 0 . GRCh38 X 32844826 32844826 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.221T>A p.Leu74Gln p.L74Q ENST00000357033 4/79 298 133 165 234 234 0 strelka-varscan-mutect DMD,missense_variant,p.Leu74Gln,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Leu70Gln,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Leu74Gln,ENST00000620040,;DMD,missense_variant,p.Leu70Gln,ENST00000619831,;DMD,missense_variant,p.Leu66Gln,ENST00000288447,;DMD,missense_variant,p.Leu37Gln,ENST00000447523,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000488902,;DMD,downstream_gene_variant,,ENST00000472681,; T ENST00000357033 Transcript missense_variant 428/13956 221/11058 74/3685 L/Q cTg/cAg 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0) 4/79 PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,Gene3D:1.10.418.10,Pfam_domain:PF00307,PIRSF_domain:PIRSF002341,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs398123880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 32844826 32844826 A T 1 0 0 0 0 1 0 0 0 4387 188 7 4 4 DMD 23 32844826 Missense_Mutation SNP A C3N-00560_T 1698461 32844826 123196069 1235 17924 FAM47A 0 . GRCh38 X 34130609 34130609 + Missense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.1670A>T p.His557Leu p.H557L ENST00000346193 1/1 101 39 62 91 91 0 strelka-varscan-mutect FAM47A,missense_variant,p.His557Leu,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.His544Leu,ENST00000613251,; A ENST00000346193 Transcript missense_variant 1703/2556 1670/2376 557/791 H/L cAc/cTc 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 tolerated(0.64) 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200 MODERATE 1 SNV 1 PASS . . 0 201 4 3 2 0 0 0 -20 0.9951716 1 1 1 0 A 3 1 56 34130609 34130609 T A 1 0 0 0 0 1 0 0 0 5447 1696 59 4 4 FAM47A 23 34130609 Missense_Mutation SNP T C3N-00560_T 1285783 34130609 121910286 1236 17925 FAM47C 0 . GRCh38 X 37009553 37009553 + Missense_Mutation SNP A A C rs782492678 C3N-00560_T C3N-00560_N A A c.1143A>C p.Glu381Asp p.E381D ENST00000358047 1/1 156 109 47 140 140 0 strelka-varscan-mutect FAM47C,missense_variant,p.Glu381Asp,ENST00000358047,NM_001013736.2; C ENST00000358047 Transcript missense_variant 1157/3270 1143/3108 381/1035 E/D gaA/gaC rs782492678 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0.01) 1/1 Pfam_domain:PF14642,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS rs782492678 . 0 168 0 17 24 0 0 0 -20 0.0132273 0 1 0 0 C 3 2 56 37009553 37009553 A C 1 0 0 0 0 1 0 0 0 5449 40 2 5 5 FAM47C 23 37009553 Missense_Mutation SNP A C3N-00560_T 2878944 37009553 119031342 1237 17926 1 11 3 3 218 N G_C_A 3.940048e-05 FAM47C 0 . GRCh38 X 37009587 37009587 + Nonsense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1177G>T p.Glu393Ter p.E393* ENST00000358047 1/1 158 75 83 158 158 0 strelka-varscan-mutect FAM47C,stop_gained,p.Glu393Ter,ENST00000358047,NM_001013736.2; T ENST00000358047 Transcript stop_gained 1191/3270 1177/3108 393/1035 E/* Gag/Tag 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 1/1 Pfam_domain:PF14642 HIGH 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 56 37009587 37009587 G T 1 0 0 0 0 0 1 0 0 5449 943 33 2 2 FAM47C 23 37009587 Nonsense_Mutation SNP G C3N-00560_T 34 37009587 119031308 1238 17927 1 11 3 3 218 N G_C_A 3.940048e-05 FAM47C 0 . GRCh38 X 37009770 37009770 + Missense_Mutation SNP C C A rs782169623 C3N-00560_T C3N-00560_N C C c.1360C>A p.Pro454Thr p.P454T ENST00000358047 1/1 196 101 95 240 239 1 strelka-varscan-mutect FAM47C,missense_variant,p.Pro454Thr,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript missense_variant 1374/3270 1360/3108 454/1035 P/T Cct/Act rs782169623 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0.02) 1/1 Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS rs782169623 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 37009770 37009770 C A 1 0 0 0 0 1 0 0 0 5449 739 26 2 2 FAM47C 23 37009770 Missense_Mutation SNP C C3N-00560_T 183 37009770 119031125 1239 17928 1 11 3 3 218 N G_C_A 3.940048e-05 SYTL5 0 . GRCh38 X 38073632 38073632 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.488C>A p.Ala163Glu p.A163E ENST00000456733 4/17 78 29 49 55 55 0 strelka-varscan-mutect SYTL5,missense_variant,p.Ala163Glu,ENST00000297875,NM_138780.2,NM_001163335.1;SYTL5,missense_variant,p.Ala163Glu,ENST00000456733,NM_001163334.1;RP5-972B16.2,intron_variant,,ENST00000465127,; A ENST00000456733 Transcript missense_variant 844/4704 488/2259 163/752 A/E gCa/gAa 1 1 SYTL5 HGNC HGNC:15589 protein_coding YES CCDS55399.1 ENSP00000395220 Q8TDW5 UPI0000F0599F NM_001163334.1 tolerated(0.3) 4/17 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF13 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 38073632 38073632 C A 1 0 0 0 0 1 0 0 0 15880 710 25 2 2 SYTL5 23 38073632 Missense_Mutation SNP C C3N-00560_T 1063862 38073632 117967263 1240 17929 NYX 0 . GRCh38 X 41473859 41473859 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.406C>A p.Arg136Ser p.R136S ENST00000342595 2/2 63 24 39 41 41 0 strelka-varscan-mutect NYX,missense_variant,p.Arg136Ser,ENST00000342595,NM_022567.2;NYX,missense_variant,p.Arg136Ser,ENST00000378220,;NYX,downstream_gene_variant,,ENST00000486842,;RP1-169I5.4,upstream_gene_variant,,ENST00000451718,; A ENST00000342595 Transcript missense_variant 862/2713 406/1446 136/481 R/S Cgc/Agc 1 1 NYX HGNC HGNC:8082 protein_coding YES CCDS14256.1 ENSP00000340328 Q9GZU5 UPI0000130B37 NM_022567.2 tolerated(0.18) 2/2 Gene3D:3.80.10.10,Low_complexity_(Seg):seg,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 41473859 41473859 C A 1 0 0 0 0 1 0 0 0 10875 652 23 1 1 NYX 23 41473859 Missense_Mutation SNP C C3N-00560_T 3400227 41473859 114567036 1241 17930 ZNF630 0 . GRCh38 X 48059703 48059703 + Nonsense_Mutation SNP T T A novel C3N-00560_T C3N-00560_N T T c.739A>T p.Lys247Ter p.K247* ENST00000442455 5/5 71 26 45 81 81 0 strelka-varscan-mutect ZNF630,stop_gained,p.Lys247Ter,ENST00000442455,NM_001190255.2,NM_001282201.1;ZNF630,stop_gained,p.Lys123Ter,ENST00000276054,NM_001282202.1;ZNF630,stop_gained,p.Lys247Ter,ENST00000409324,NM_001037735.3;ZNF630,stop_gained,p.Lys233Ter,ENST00000616492,;ZNF630,downstream_gene_variant,,ENST00000428686,;ZNF630,downstream_gene_variant,,ENST00000627643,;ZNF630,downstream_gene_variant,,ENST00000421903,;ZNF630-AS1,intron_variant,,ENST00000614448,;ZNF630,intron_variant,,ENST00000428463,; A ENST00000442455 Transcript stop_gained 1306/2829 739/1974 247/657 K/* Aag/Tag 1 -1 ZNF630 HGNC HGNC:28855 protein_coding YES CCDS35237.2 ENSP00000393163 Q2M218 UPI0000160BE4 NM_001190255.2,NM_001282201.1 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF216,Superfamily_domains:SSF57667 HIGH SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 48059703 48059703 T A 1 0 0 0 0 0 1 0 0 18629 1763 61 4 4 ZNF630 23 48059703 Nonsense_Mutation SNP T C3N-00560_T 6585844 48059703 107981192 1242 17931 CCNB3 0 . GRCh38 X 50308652 50308652 + Silent SNP G G A C3N-00560_T C3N-00560_N G G c.483G>A p.= p.K161K ENST00000376042 6/13 126 66 60 106 106 0 strelka-varscan-mutect CCNB3,synonymous_variant,p.=,ENST00000376042,;CCNB3,synonymous_variant,p.=,ENST00000276014,NM_033031.2;CCNB3,intron_variant,,ENST00000348603,NM_033670.2;CCNB3,intron_variant,,ENST00000376038,;CCNB3,intron_variant,,ENST00000476167,; A ENST00000376042 Transcript synonymous_variant 781/4693 483/4188 161/1395 K aaG/aaA COSM3562140 1 1 CCNB3 HGNC HGNC:18709 protein_coding YES CCDS14331.1 ENSP00000365210 Q8WWL7 UPI000022DC76 6/13 1 LOW 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 50308652 50308652 G A 1 0 0 0 0 0 0 0 1 2613 991 35 3 3 CCNB3 23 50308652 Silent SNP G C3N-00560_T 2248949 50308652 105732243 1243 17932 DGKK 0 . GRCh38 X 50378157 50378157 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.3052A>G p.Arg1018Gly p.R1018G ENST00000611977 22/28 138 54 84 111 111 0 strelka-varscan-mutect DGKK,missense_variant,p.Arg1018Gly,ENST00000611977,NM_001013742.3; C ENST00000611977 Transcript missense_variant 3112/7407 3052/3816 1018/1271 R/G Aga/Gga 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 deleterious(0.02) 22/28 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF33,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 50378157 50378157 T C 1 0 0 0 0 1 0 0 0 4278 1559 54 5 5 DGKK 23 50378157 Missense_Mutation SNP T C3N-00560_T 69505 50378157 105662738 1244 17933 MAGED2 0 . GRCh38 X 54810849 54810849 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.566G>C p.Gly189Ala p.G189A ENST00000375068 4/13 40 12 28 42 42 0 strelka-varscan-mutect MAGED2,missense_variant,p.Gly189Ala,ENST00000375068,NM_177433.2;MAGED2,missense_variant,p.Gly171Ala,ENST00000347546,;MAGED2,missense_variant,p.Gly189Ala,ENST00000375053,;MAGED2,missense_variant,p.Gly189Ala,ENST00000375058,NM_014599.5;MAGED2,missense_variant,p.Gly189Ala,ENST00000396224,NM_201222.2;MAGED2,missense_variant,p.Gly189Ala,ENST00000218439,;MAGED2,missense_variant,p.Gly151Ala,ENST00000627068,;MAGED2,missense_variant,p.Gly151Ala,ENST00000375060,;SNORA11,upstream_gene_variant,,ENST00000408789,;MAGED2,non_coding_transcript_exon_variant,,ENST00000497484,;MAGED2,non_coding_transcript_exon_variant,,ENST00000463787,;MAGED2,downstream_gene_variant,,ENST00000485483,;MAGED2,upstream_gene_variant,,ENST00000487463,;MAGED2,upstream_gene_variant,,ENST00000487482,; C ENST00000375068 Transcript missense_variant 799/2189 566/1821 189/606 G/A gGc/gCc 1 1 MAGED2 HGNC HGNC:16353 protein_coding YES CCDS14362.1 ENSP00000364209 Q9UNF1 A0A024R9Y7 UPI000000123B NM_177433.2 tolerated(0.08) 4/13 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 54810849 54810849 G C 1 0 0 0 0 1 0 0 0 9102 1203 42 4 4 MAGED2 23 54810849 Missense_Mutation SNP G C3N-00560_T 4432692 54810849 101230046 1245 17934 ZC4H2 0 . GRCh38 X 64921832 64921832 + Missense_Mutation SNP G G T rs376951408 C3N-00560_T C3N-00560_N G G c.210C>A p.His70Gln p.H70Q ENST00000374839 2/5 81 27 54 70 70 0 strelka-varscan-mutect ZC4H2,missense_variant,p.His70Gln,ENST00000447788,NM_001178033.2;ZC4H2,missense_variant,p.His47Gln,ENST00000337990,NM_001178032.2,NM_001243804.1;ZC4H2,missense_variant,p.His70Gln,ENST00000374839,NM_018684.3;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488608,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000476032,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000492653,;ZC4H2,non_coding_transcript_exon_variant,,ENST00000488831,;ZC4H2,upstream_gene_variant,,ENST00000488406,; T ENST00000374839 Transcript missense_variant 317/2184 210/675 70/224 H/Q caC/caA rs376951408,COSM5505496,COSM5505497 1 -1 ZC4H2 HGNC HGNC:24931 protein_coding YES CCDS14380.1 ENSP00000363972 Q9NQZ6 UPI0000025CAA NM_018684.3 deleterious(0) 2/5 Pfam_domain:PF10146,hmmpanther:PTHR31058 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs376951408 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 64921832 64921832 G T 1 0 0 0 0 1 0 0 0 18153 1136 40 1 1 ZC4H2 23 64921832 Missense_Mutation SNP G C3N-00560_T 10110983 64921832 91119063 1246 17935 FAM155B 0 . GRCh38 X 69505896 69505896 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.614G>T p.Trp205Leu p.W205L ENST00000252338 1/3 253 99 154 253 253 0 strelka-varscan-mutect FAM155B,missense_variant,p.Trp205Leu,ENST00000252338,NM_015686.2; T ENST00000252338 Transcript missense_variant 656/4013 614/1419 205/472 W/L tGg/tTg 1 1 FAM155B HGNC HGNC:30701 protein_coding YES CCDS35317.1 ENSP00000252338 O75949 UPI0000070EAA NM_015686.2 tolerated(0.73) 1/3 hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 69505896 69505896 G T 1 0 0 0 0 1 0 0 0 5314 1357 47 2 2 FAM155B 23 69505896 Missense_Mutation SNP G C3N-00560_T 4584064 69505896 86534999 1247 17936 TEX11 0 . GRCh38 X 70651468 70651468 + Missense_Mutation SNP C C G novel C3N-00560_T C3N-00560_N C C c.1510G>C p.Glu504Gln p.E504Q ENST00000395889 18/31 60 22 38 58 58 0 strelka-varscan-mutect TEX11,missense_variant,p.Glu504Gln,ENST00000395889,NM_001003811.1;TEX11,missense_variant,p.Glu489Gln,ENST00000374333,NM_031276.2;TEX11,missense_variant,p.Glu504Gln,ENST00000344304,;TEX11,missense_variant,p.Glu179Gln,ENST00000374320,; G ENST00000395889 Transcript missense_variant 1666/3133 1510/2823 504/940 E/Q Gag/Cag 1 -1 TEX11 HGNC HGNC:11733 protein_coding YES CCDS35323.1 ENSP00000379226 Q8IYF3 UPI000013CA89 NM_001003811.1 tolerated(0.14) 18/31 Gene3D:1.25.40.10,Superfamily_domains:SSF48452 MODERATE 1 SNV 2 1 PASS rs1483378881 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 56 70651468 70651468 C G 1 0 0 0 0 1 0 0 0 16195 922 32 4 4 TEX11 23 70651468 Missense_Mutation SNP C C3N-00560_T 1145572 70651468 85389427 1248 17937 ZDHHC15 0 . GRCh38 X 75505831 75505831 + Silent SNP T T A novel C3N-00560_T C3N-00560_N T T c.153A>T p.= p.P51P ENST00000373367 2/12 76 31 45 71 71 0 strelka-varscan-mutect ZDHHC15,synonymous_variant,p.=,ENST00000373367,NM_144969.2;ZDHHC15,intron_variant,,ENST00000541184,NM_001146256.1;ZDHHC15,intron_variant,,ENST00000482827,; A ENST00000373367 Transcript synonymous_variant 384/5796 153/1014 51/337 P ccA/ccT 1 -1 ZDHHC15 HGNC HGNC:20342 protein_coding YES CCDS14430.1 ENSP00000362465 Q96MV8 UPI000006DB5A NM_144969.2 2/12 hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF68 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 75505831 75505831 T A 1 0 0 0 0 0 0 0 1 18181 1567 55 4 4 ZDHHC15 23 75505831 Silent SNP T C3N-00560_T 4854363 75505831 80535064 1249 17938 FAM46D 0 . GRCh38 X 80442999 80442999 + Missense_Mutation SNP G G A novel C3N-00560_T C3N-00560_N G G c.460G>A p.Gly154Arg p.G154R ENST00000538312 5/5 121 56 65 117 117 0 strelka-varscan-mutect FAM46D,missense_variant,p.Gly154Arg,ENST00000538312,NM_001170574.1;FAM46D,missense_variant,p.Gly154Arg,ENST00000308293,NM_152630.4; A ENST00000538312 Transcript missense_variant 794/3106 460/1170 154/389 G/R Ggg/Agg 1 1 FAM46D HGNC HGNC:28399 protein_coding YES CCDS14446.1 ENSP00000443410 Q8NEK8 UPI0000073CF3 NM_001170574.1 deleterious(0.01) 5/5 hmmpanther:PTHR12974:SF30,hmmpanther:PTHR12974,Pfam_domain:PF07984,SMART_domains:SM01153 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 80442999 80442999 G A 1 0 0 0 0 1 0 0 0 5446 1348 47 3 3 FAM46D 23 80442999 Missense_Mutation SNP G C3N-00560_T 4937168 80442999 75597896 1250 17939 SATL1 0 . GRCh38 X 85107587 85107587 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1382C>A p.Thr461Asn p.T461N ENST00000509231 1/5 168 61 107 153 153 0 strelka-varscan-mutect SATL1,missense_variant,p.Thr461Asn,ENST00000509231,NM_001012980.2;SATL1,missense_variant,p.Thr274Asn,ENST00000395409,; T ENST00000509231 Transcript missense_variant 1462/2224 1382/1899 461/632 T/N aCt/aAt 1 -1 SATL1 HGNC HGNC:27992 protein_coding YES CCDS35343.2 ENSP00000425421 Q86VE3 UPI000041ABBC NM_001012980.2 tolerated(0.33) 1/5 hmmpanther:PTHR10545,hmmpanther:PTHR10545:SF28 MODERATE 1 SNV 1 1 PASS rs1185598409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 85107587 85107587 G T 1 0 0 0 0 1 0 0 0 14116 1029 36 2 2 SATL1 23 85107587 Missense_Mutation SNP G C3N-00560_T 4664588 85107587 70933308 1251 17940 PCDH11X 0 . GRCh38 X 91835911 91835911 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.407C>A p.Ala136Glu p.A136E ENST00000373094 1/7 155 70 85 152 151 1 strelka-varscan-mutect PCDH11X,missense_variant,p.Ala136Glu,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Ala136Glu,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Ala136Glu,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Ala136Glu,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Ala136Glu,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Ala136Glu,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Ala136Glu,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; A ENST00000373094 Transcript missense_variant 1252/9179 407/4044 136/1347 A/E gCa/gAa 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0) 1/7 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 91835911 91835911 C A 1 0 0 0 0 1 0 0 0 11595 710 25 2 2 PCDH11X 23 91835911 Missense_Mutation SNP C C3N-00560_T 6728324 91835911 64204984 1252 17941 PCDH11X 0 . GRCh38 X 91876961 91876961 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.721G>T p.Asp241Tyr p.D241Y ENST00000373094 2/7 266 109 157 295 294 1 strelka-varscan-mutect PCDH11X,missense_variant,p.Asp241Tyr,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Asp241Tyr,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 1566/9179 721/4044 241/1347 D/Y Gat/Tat 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0) 2/7 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 91876961 91876961 G T 1 0 0 0 0 1 0 0 0 11595 1290 45 2 2 PCDH11X 23 91876961 Missense_Mutation SNP G C3N-00560_T 41050 91876961 64163934 1253 17942 PCDH11X 0 . GRCh38 X 92618544 92618544 + Silent SNP G G A novel C3N-00560_T C3N-00560_N G G c.3648G>A p.= p.V1216V ENST00000373094 7/7 528 218 310 510 510 0 strelka-varscan-mutect PCDH11X,synonymous_variant,p.=,ENST00000373094,NM_032968.4;PCDH11X,synonymous_variant,p.=,ENST00000373097,NM_032969.4;PCDH11X,synonymous_variant,p.=,ENST00000406881,NM_001168360.1;PCDH11X,synonymous_variant,p.=,ENST00000361655,NM_001168363.1;PCDH11X,synonymous_variant,p.=,ENST00000373088,NM_001168362.1;PCDH11X,3_prime_UTR_variant,,ENST00000504220,NM_001168361.1; A ENST00000373094 Transcript synonymous_variant 4493/9179 3648/4044 1216/1347 V gtG/gtA 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 7/7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 92618544 92618544 G A 1 0 0 0 0 0 0 0 1 11595 1364 48 3 3 PCDH11X 23 92618544 Silent SNP G C3N-00560_T 741583 92618544 63422351 1254 17943 PCDH19 0 . GRCh38 X 100406777 100406777 + Missense_Mutation SNP C C A C3N-00560_T C3N-00560_N C C c.1821G>T p.Met607Ile p.M607I ENST00000373034 1/6 400 151 249 332 331 1 strelka-varscan-mutect PCDH19,missense_variant,p.Met607Ile,ENST00000373034,NM_001184880.1;PCDH19,missense_variant,p.Met607Ile,ENST00000255531,NM_001105243.1;PCDH19,missense_variant,p.Met607Ile,ENST00000420881,NM_020766.2;PCDH19,upstream_gene_variant,,ENST00000636150,; A ENST00000373034 Transcript missense_variant 3497/9756 1821/3447 607/1148 M/I atG/atT COSM3564173,COSM3564174 1 -1 PCDH19 HGNC HGNC:14270 protein_coding YES CCDS55462.1 ENSP00000362125 Q8TAB3 UPI00001D7BCD NM_001184880.1 tolerated(1) 1/6 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF40,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 100406777 100406777 C A 1 0 0 0 0 1 0 0 0 11601 826 29 2 2 PCDH19 23 100406777 Missense_Mutation SNP C C3N-00560_T 7788233 100406777 55634118 1255 17944 SYTL4 0 . GRCh38 X 100690130 100690130 + Silent SNP C C A novel C3N-00560_T C3N-00560_N C C c.753G>T p.= p.V251V ENST00000372989 10/19 82 33 49 88 88 0 strelka-varscan-mutect SYTL4,synonymous_variant,p.=,ENST00000372981,;SYTL4,synonymous_variant,p.=,ENST00000372989,NM_080737.2;SYTL4,synonymous_variant,p.=,ENST00000276141,NM_001174068.1;SYTL4,synonymous_variant,p.=,ENST00000263033,NM_001129896.2; A ENST00000372989 Transcript synonymous_variant 1085/3885 753/2016 251/671 V gtG/gtT 1 -1 SYTL4 HGNC HGNC:15588 protein_coding YES CCDS14472.1 ENSP00000362080 Q96C24 A0A024RCF8 UPI00001AE9F2 NM_080737.2 10/19 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF9 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 56 100690130 100690130 C A 1 0 0 0 0 0 0 0 1 15879 581 21 2 2 SYTL4 23 100690130 Silent SNP C C3N-00560_T 283353 100690130 55350765 1256 17945 ARMCX4 0 . GRCh38 X 101493326 101493326 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.4737G>T p.Gln1579His p.Q1579H ENST00000423738 2/2 92 28 64 81 81 0 strelka-varscan-mutect ARMCX4,missense_variant,p.Gln1579His,ENST00000423738,NM_001256155.2;ARMCX4,intron_variant,,ENST00000433011,;ARMCX4,intron_variant,,ENST00000452188,;ARMCX4,intron_variant,,ENST00000354842,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,;ARMCX4,intron_variant,,ENST00000455331,; T ENST00000423738 Transcript missense_variant 4939/7424 4737/6873 1579/2290 Q/H caG/caT 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 deleterious(0) 2/2 MODERATE 1 SNV 5 1 PASS rs1041030727 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 101493326 101493326 G T 1 0 0 0 0 1 0 0 0 1102 991 35 2 2 ARMCX4 23 101493326 Missense_Mutation SNP G C3N-00560_T 803196 101493326 54547569 1257 17946 H2BFM 0 . GRCh38 X 104040843 104040843 + Silent SNP G G T rs782543925 C3N-00560_T C3N-00560_N G G c.444G>T p.= p.A148A ENST00000355016 2/3 97 41 56 93 92 1 strelka-varscan-mutect H2BFM,synonymous_variant,p.=,ENST00000355016,NM_001164416.1;H2BFM,synonymous_variant,p.=,ENST00000417637,;H2BFM,synonymous_variant,p.=,ENST00000598335,; T ENST00000355016 Transcript synonymous_variant 472/1882 444/465 148/154 A gcG/gcT rs782543925,COSM1112347,COSM1598637 1 1 H2BFM HGNC HGNC:27867 protein_coding YES CCDS55468.1 ENSP00000347119 P0C1H6 W0TYI6 UPI0000161AB5 NM_001164416.1 2/3 hmmpanther:PTHR23428,hmmpanther:PTHR23428:SF34 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs782543925 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 104040843 104040843 G T 1 0 0 0 0 0 0 0 1 6813 1045 37 1 1 H2BFM 23 104040843 Silent SNP G C3N-00560_T 2547517 104040843 52000052 1258 17947 NRK 0 . GRCh38 X 105909266 105909266 + Missense_Mutation SNP A A T novel C3N-00560_T C3N-00560_N A A c.1625A>T p.His542Leu p.H542L ENST00000243300 13/29 113 44 69 130 130 0 strelka-varscan-mutect NRK,missense_variant,p.His542Leu,ENST00000243300,NM_198465.3;NRK,3_prime_UTR_variant,,ENST00000428173,; T ENST00000243300 Transcript missense_variant 1928/8062 1625/4749 542/1582 H/L cAc/cTc 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0.02) 13/29 hmmpanther:PTHR24361:SF417,hmmpanther:PTHR24361,Gene3D:1.10.510.10 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 105909266 105909266 A T 1 0 0 0 0 1 0 0 0 10713 159 6 4 4 NRK 23 105909266 Missense_Mutation SNP A C3N-00560_T 1868423 105909266 50131629 1259 17948 NRK 0 . GRCh38 X 105909542 105909542 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1901G>T p.Gly634Val p.G634V ENST00000243300 13/29 115 43 72 105 105 0 strelka-varscan-mutect NRK,missense_variant,p.Gly634Val,ENST00000243300,NM_198465.3;NRK,3_prime_UTR_variant,,ENST00000428173,; T ENST00000243300 Transcript missense_variant 2204/8062 1901/4749 634/1582 G/V gGc/gTc 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0) 13/29 hmmpanther:PTHR24361:SF417,hmmpanther:PTHR24361 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.999999 1 1 1 0 T 3 4 56 105909542 105909542 G T 1 0 0 0 0 1 0 0 0 10713 1203 42 2 2 NRK 23 105909542 Missense_Mutation SNP G C3N-00560_T 276 105909542 50131353 1260 17949 ZCCHC16 0 . GRCh38 X 112455565 112455565 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.837G>T p.Leu279Phe p.L279F ENST00000340433 1/1 118 60 58 109 109 0 strelka-varscan-mutect ZCCHC16,missense_variant,p.Leu279Phe,ENST00000340433,NM_001004308.2; T ENST00000340433 Transcript missense_variant 1066/2613 837/933 279/310 L/F ttG/ttT 1 1 ZCCHC16 HGNC HGNC:25214 protein_coding YES CCDS35369.1 ENSP00000340590 Q6ZR62 UPI00001975B5 NM_001004308.2 deleterious(0.03) 1/1 hmmpanther:PTHR15503:SF8,hmmpanther:PTHR15503,Gene3D:4.10.60.10,Superfamily_domains:SSF57756 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 112455565 112455565 G T 1 0 0 0 0 1 0 0 0 18159 1368 48 2 2 ZCCHC16 23 112455565 Missense_Mutation SNP G C3N-00560_T 6546023 112455565 43585330 1261 17950 KIAA1210 0 . GRCh38 X 119087444 119087444 + Silent SNP T T C novel C3N-00560_T C3N-00560_N T T c.3786A>G p.= p.L1262L ENST00000402510 11/14 80 20 60 86 86 0 strelka-varscan-mutect KIAA1210,synonymous_variant,p.=,ENST00000402510,NM_020721.1; C ENST00000402510 Transcript synonymous_variant 3786/7824 3786/5130 1262/1709 L ttA/ttG 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 11/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 56 119087444 119087444 T C 1 0 0 0 0 0 0 0 1 8106 1635 57 5 5 KIAA1210 23 119087444 Silent SNP T C3N-00560_T 6631879 119087444 36953451 1262 17951 KIAA1210 0 . GRCh38 X 119088091 119088091 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.3139G>T p.Glu1047Ter p.E1047* ENST00000402510 11/14 161 72 89 122 122 0 strelka-varscan-mutect KIAA1210,stop_gained,p.Glu1047Ter,ENST00000402510,NM_020721.1; A ENST00000402510 Transcript stop_gained 3139/7824 3139/5130 1047/1709 E/* Gaa/Taa 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 11/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 119088091 119088091 C A 1 0 0 0 0 0 1 0 0 8106 864 30 2 2 KIAA1210 23 119088091 Nonsense_Mutation SNP C C3N-00560_T 647 119088091 36952804 1263 17952 TMEM255A 0 . GRCh38 X 120268308 120268308 + Missense_Mutation SNP G G C novel C3N-00560_T C3N-00560_N G G c.827C>G p.Ala276Gly p.A276G ENST00000309720 9/10 83 37 46 83 83 0 strelka-varscan-mutect TMEM255A,missense_variant,p.Ala252Gly,ENST00000371369,NM_001104544.1;TMEM255A,missense_variant,p.Ala276Gly,ENST00000309720,NM_017938.3;TMEM255A,missense_variant,p.Ala168Gly,ENST00000440464,NM_001104545.1;TMEM255A,missense_variant,p.Ala112Gly,ENST00000371352,;TMEM255A,downstream_gene_variant,,ENST00000519908,;RP11-45J1.1,upstream_gene_variant,,ENST00000439244,; C ENST00000309720 Transcript missense_variant 951/3394 827/1050 276/349 A/G gCa/gGa 1 -1 TMEM255A HGNC HGNC:26086 protein_coding YES CCDS14597.1 ENSP00000310110 Q5JRV8 UPI0000246DA1 NM_017938.3 deleterious(0.02) 9/10 Pfam_domain:PF14967,hmmpanther:PTHR33721,hmmpanther:PTHR33721:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 120268308 120268308 G C 1 0 0 0 0 1 0 0 0 16614 1319 46 4 4 TMEM255A 23 120268308 Missense_Mutation SNP G C3N-00560_T 1180217 120268308 35772587 1264 17953 TEX13C 0 . GRCh38 X 125321611 125321611 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1492G>T p.Gly498Trp p.G498W ENST00000632600 1/1 281 126 155 229 229 0 strelka-varscan-mutect TEX13C,missense_variant,p.Gly498Trp,ENST00000632600,NM_001195272.1; T ENST00000632600 Transcript missense_variant 1492/5095 1492/2982 498/993 G/W Ggg/Tgg 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 tolerated(0.05) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 125321611 125321611 G T 1 0 0 0 0 1 0 0 0 16199 1232 43 2 2 TEX13C 23 125321611 Missense_Mutation SNP G C3N-00560_T 5053303 125321611 30719284 1265 17954 PRR32 0 . GRCh38 X 126821118 126821118 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.480G>T p.Leu160Phe p.L160F ENST00000371125 2/2 90 41 49 105 105 0 strelka-varscan-mutect PRR32,missense_variant,p.Leu160Phe,ENST00000371125,NM_001122716.1; T ENST00000371125 Transcript missense_variant 560/1228 480/897 160/298 L/F ttG/ttT 1 1 PRR32 HGNC HGNC:34498 protein_coding YES CCDS48163.1 ENSP00000360166 B1ATL7 UPI00004A3B00 NM_001122716.1 tolerated(0.28) 2/2 Pfam_domain:PF15488,hmmpanther:PTHR37343,hmmpanther:PTHR37343:SF1 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 126821118 126821118 G T 1 0 0 0 0 1 0 0 0 12738 1310 46 2 2 PRR32 23 126821118 Missense_Mutation SNP G C3N-00560_T 1499507 126821118 29219777 1266 17955 IGSF1 0 . GRCh38 X 131283213 131283213 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.719C>A p.Pro240His p.P240H ENST00000370903 6/20 119 39 80 73 73 0 strelka-varscan-mutect IGSF1,missense_variant,p.Pro231His,ENST00000370904,;IGSF1,missense_variant,p.Pro240His,ENST00000370903,NM_001170961.1;IGSF1,missense_variant,p.Pro231His,ENST00000370910,NM_001170962.1;IGSF1,missense_variant,p.Pro240His,ENST00000361420,NM_001555.4;IGSF1,downstream_gene_variant,,ENST00000370901,NM_205833.3;IGSF1,downstream_gene_variant,,ENST00000370900,NM_001170963.1;IGSF1,upstream_gene_variant,,ENST00000469836,; T ENST00000370903 Transcript missense_variant 1002/4594 719/4026 240/1341 P/H cCt/cAt 1 -1 IGSF1 HGNC HGNC:5948 protein_coding YES CCDS55491.1 ENSP00000359940 Q8N6C5 UPI0000E0C769 NM_001170961.1 deleterious(0) 6/20 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 56 131283213 131283213 G T 1 0 0 0 0 1 0 0 0 7503 1000 35 2 2 IGSF1 23 131283213 Missense_Mutation SNP G C3N-00560_T 4462095 131283213 24757682 1267 17956 USP26 0 . GRCh38 X 133026900 133026900 + Nonsense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.1321G>T p.Glu441Ter p.E441* ENST00000511190 6/6 285 106 179 281 280 1 strelka-varscan-mutect USP26,stop_gained,p.Glu441Ter,ENST00000511190,;USP26,stop_gained,p.Glu441Ter,ENST00000370832,NM_031907.1; A ENST00000511190 Transcript stop_gained 1791/3665 1321/2742 441/913 E/* Gag/Tag 1 -1 USP26 HGNC HGNC:13485 protein_coding YES CCDS14635.1 ENSP00000423390 Q9BXU7 UPI00000421FD 6/6 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF390,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 56 133026900 133026900 C A 1 0 0 0 0 0 1 0 0 17598 922 32 2 2 USP26 23 133026900 Nonsense_Mutation SNP C C3N-00560_T 1743687 133026900 23013995 1268 17957 HTATSF1 0 . GRCh38 X 136509099 136509099 + Silent SNP G G T rs752281014 C3N-00560_T C3N-00560_N G G c.843G>T p.= p.P281P ENST00000535601 8/10 95 38 57 67 67 0 strelka-varscan-mutect HTATSF1,synonymous_variant,p.=,ENST00000535601,NM_001163280.1;HTATSF1,synonymous_variant,p.=,ENST00000218364,NM_014500.4; T ENST00000535601 Transcript synonymous_variant 1265/3019 843/2268 281/755 P ccG/ccT rs752281014 1 1 HTATSF1 HGNC HGNC:5276 protein_coding YES CCDS14657.1 ENSP00000442699 O43719 UPI000006D876 NM_001163280.1 8/10 Gene3D:3.30.70.330,PROSITE_profiles:PS50102,hmmpanther:PTHR15608,SMART_domains:SM00360 LOW 1 SNV 1 1 PASS rs752281014 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 136509099 136509099 G T 1 0 0 0 0 0 0 0 1 7329 1132 40 1 1 HTATSF1 23 136509099 Silent SNP G C3N-00560_T 3482199 136509099 19531796 1269 17958 MAGEC1 0 . GRCh38 X 141908061 141908061 + Missense_Mutation SNP T T C novel C3N-00560_T C3N-00560_N T T c.2657T>C p.Leu886Pro p.L886P ENST00000285879 4/4 86 26 60 66 66 0 strelka-varscan-mutect MAGEC1,missense_variant,p.Leu886Pro,ENST00000285879,NM_005462.4;MAGEC1,intron_variant,,ENST00000406005,; C ENST00000285879 Transcript missense_variant 2943/4270 2657/3429 886/1142 L/P cTa/cCa 1 1 MAGEC1 HGNC HGNC:6812 protein_coding YES CCDS35417.1 ENSP00000285879 O60732 UPI000006F2FD NM_005462.4 deleterious_low_confidence(0) 4/4 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 56 141908061 141908061 T C 1 0 0 0 0 1 0 0 0 9098 1522 53 5 5 MAGEC1 23 141908061 Missense_Mutation SNP T C3N-00560_T 5398962 141908061 14132834 1270 17959 SPANXN2 0 . GRCh38 X 143712271 143712271 + Missense_Mutation SNP C C A novel C3N-00560_T C3N-00560_N C C c.307G>T p.Asp103Tyr p.D103Y ENST00000598475 2/2 277 107 170 296 295 1 strelka-varscan-mutect SPANXN2,missense_variant,p.Asp103Tyr,ENST00000598475,NM_001009615.2; A ENST00000598475 Transcript missense_variant 1062/1378 307/543 103/180 D/Y Gac/Tac 1 -1 SPANXN2 HGNC HGNC:33175 protein_coding YES CCDS35419.1 ENSP00000470584 Q5MJ10 UPI000049D98C NM_001009615.2 tolerated(0.07) 2/2 hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 56 143712271 143712271 C A 1 0 0 0 0 1 0 0 0 15322 855 30 2 2 SPANXN2 23 143712271 Missense_Mutation SNP C C3N-00560_T 1804210 143712271 12328624 1271 17960 PNMA3 0 . GRCh38 X 153058296 153058296 + Missense_Mutation SNP G G T novel C3N-00560_T C3N-00560_N G G c.1241G>T p.Cys414Phe p.C414F ENST00000593810 1/1 170 47 123 159 159 0 strelka-varscan-mutect PNMA3,missense_variant,p.Cys414Phe,ENST00000619635,NM_001282535.1;PNMA3,missense_variant,p.Cys414Phe,ENST00000593810,NM_013364.5;PNMA3,missense_variant,p.Cys414Phe,ENST00000424805,; T ENST00000593810 Transcript missense_variant 1261/1432 1241/1392 414/463 C/F tGc/tTc 1 1 PNMA3 HGNC HGNC:18742 protein_coding YES CCDS35435.2 ENSP00000469445 Q9UL41 UPI0000070F18 NM_013364.5 tolerated(0.27) 1/1 PROSITE_profiles:PS50158,hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF22,Superfamily_domains:SSF57756 MODERATE 1 SNV 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 56 153058296 153058296 G T 1 0 0 0 0 1 0 0 0 12262 1319 46 2 2 PNMA3 23 153058296 Missense_Mutation SNP G C3N-00560_T 9346025 153058296 2982599 1272 17961 TMLHE 0 . GRCh38 X 155491631 155491631 + Silent SNP G G T novel C3N-00560_T C3N-00560_N G G c.1170C>A p.= p.G390G ENST00000334398 8/8 43 27 16 26 26 0 varscan-mutect TMLHE,synonymous_variant,p.=,ENST00000334398,NM_018196.3;TMLHE,downstream_gene_variant,,ENST00000369439,NM_001184797.1;TMLHE-AS1,intron_variant,,ENST00000433624,;TMLHE-AS1,intron_variant,,ENST00000452506,;RP11-218L14.4,downstream_gene_variant,,ENST00000447347,;TMLHE,non_coding_transcript_exon_variant,,ENST00000449645,; T ENST00000334398 Transcript synonymous_variant 1316/2832 1170/1266 390/421 G ggC/ggA 1 -1 TMLHE HGNC HGNC:18308 protein_coding YES CCDS14768.1 ENSP00000335261 Q9NVH6 UPI000013707B NM_018196.3 8/8 hmmpanther:PTHR10696:SF3,hmmpanther:PTHR10696,Gene3D:3.60.130.10,Pfam_domain:PF02668,TIGRFAM_domain:TIGR02410,Superfamily_domains:SSF51197 LOW 1 SNV 1 1 PASS rs1236434929 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 56 155491631 155491631 G T 1 0 0 0 0 0 0 0 1 16708 1306 46 2 2 TMLHE 23 155491631 Silent SNP G C3N-00560_T 2433335 155491631 549264 1273 17962 TBCE 0 . GRCh38 1 235414585 235414585 + Missense_Mutation SNP C C G rs766820945 C3N-00572_T C3N-00572_N C C c.338C>G p.Thr113Ser p.T113S ENST00000543662 4/18 354 299 55 417 417 0 strelka-varscan-mutect TBCE,missense_variant,p.Thr113Ser,ENST00000543662,NM_001287801.1;TBCE,missense_variant,p.Thr113Ser,ENST00000406207,NM_001079515.2;TBCE,missense_variant,p.Thr113Ser,ENST00000366601,NM_001287802.1,NM_003193.4;TBCE,non_coding_transcript_exon_variant,,ENST00000472011,;TBCE,non_coding_transcript_exon_variant,,ENST00000482230,;TBCE,upstream_gene_variant,,ENST00000461651,; G ENST00000543662 Transcript missense_variant 514/2117 338/1737 113/578 T/S aCt/aGt rs766820945 1 1 TBCE HGNC HGNC:11582 protein_coding YES CCDS73052.1 ENSP00000439170 Q15813 UPI0001914D1A NM_001287801.1 tolerated(0.4) 4/18 hmmpanther:PTHR15140:SF13,hmmpanther:PTHR15140,Superfamily_domains:SSF52047,Superfamily_domains:SSF74924 MODERATE 1 SNV 2 1 PASS rs766820945 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 57 235414585 235414585 C G 1 0 0 0 0 1 0 0 0 16039 565 20 4 4 TBCE 1 235414585 Missense_Mutation SNP C C3N-00572_T 235414585 13541837 1 17963 HEATR1 0 . GRCh38 1 236554609 236554609 + Silent SNP G G A rs749182893 C3N-00572_T C3N-00572_N G G c.6067C>T p.= p.L2023L ENST00000366582 42/45 250 220 30 354 354 0 strelka-varscan-mutect HEATR1,synonymous_variant,p.=,ENST00000366582,NM_018072.5;HEATR1,synonymous_variant,p.=,ENST00000366581,;LGALS8,downstream_gene_variant,,ENST00000526589,;LGALS8,downstream_gene_variant,,ENST00000450372,NM_006499.4;LGALS8,downstream_gene_variant,,ENST00000416919,;LGALS8,downstream_gene_variant,,ENST00000366584,NM_201544.2;RP11-385F5.4,upstream_gene_variant,,ENST00000433131,; A ENST00000366582 Transcript synonymous_variant 6182/8447 6067/6435 2023/2144 L Ctg/Ttg rs749182893 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 42/45 hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371 LOW SNV 5 1 PASS rs749182893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 57 236554609 236554609 G A 1 0 0 0 0 0 0 0 1 6910 933 33 3 3 HEATR1 1 236554609 Silent SNP G C3N-00572_T 1140024 236554609 12401813 2 17964 ASAP2 0 . GRCh38 2 9374879 9374879 + Nonsense_Mutation SNP G G T novel C3N-00572_T C3N-00572_N G G c.1681G>T p.Gly561Ter p.G561* ENST00000281419 17/28 186 174 12 250 250 0 strelka-varscan-mutect ASAP2,stop_gained,p.Gly561Ter,ENST00000281419,NM_003887.2;ASAP2,stop_gained,p.Gly561Ter,ENST00000315273,NM_001135191.1; T ENST00000281419 Transcript stop_gained 2021/5712 1681/3021 561/1006 G/* Gga/Tga 1 1 ASAP2 HGNC HGNC:2721 protein_coding YES CCDS1661.1 ENSP00000281419 O43150 UPI0000073459 NM_003887.2 17/28 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF238,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS rs1334115239 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 57 9374879 9374879 G T 1 0 0 0 0 0 1 0 0 1153 1349 47 2 2 ASAP2 2 9374879 Nonsense_Mutation SNP G C3N-00572_T 9374879 232818650 3 17965 TFRC 0 . GRCh38 3 196055120 196055120 + Missense_Mutation SNP G G A novel C3N-00572_T C3N-00572_N G G c.1859C>T p.Ser620Leu p.S620L ENST00000360110 17/19 438 359 79 465 465 0 strelka-varscan-mutect TFRC,missense_variant,p.Ser620Leu,ENST00000360110,NM_001128148.1;TFRC,missense_variant,p.Ser620Leu,ENST00000392396,NM_003234.2;TFRC,missense_variant,p.Ser539Leu,ENST00000420415,NM_001313966.1,NM_001313965.1;TFRC,missense_variant,p.Ser32Leu,ENST00000426789,;TFRC,downstream_gene_variant,,ENST00000465288,;TFRC,downstream_gene_variant,,ENST00000463356,;TFRC,non_coding_transcript_exon_variant,,ENST00000475593,;TFRC,non_coding_transcript_exon_variant,,ENST00000483983,;TFRC,non_coding_transcript_exon_variant,,ENST00000463047,;TFRC,downstream_gene_variant,,ENST00000477148,;TFRC,downstream_gene_variant,,ENST00000482479,; A ENST00000360110 Transcript missense_variant 2029/5111 1859/2283 620/760 S/L tCa/tTa 1 -1 TFRC HGNC HGNC:11763 protein_coding YES CCDS3312.1 ENSP00000353224 P02786 UPI0000049ADE NM_001128148.1 tolerated(0.11) 17/19 hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF26,Gene3D:3kasA03,Superfamily_domains:SSF47672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 57 196055120 196055120 G A 1 0 0 0 0 1 0 0 0 16245 1294 45 3 3 TFRC 3 196055120 Missense_Mutation SNP G C3N-00572_T 196055120 2240439 4 17966 SENP5 0 . GRCh38 3 196899748 196899748 + Silent SNP C C T C3N-00572_T C3N-00572_N C C c.1596C>T p.= p.V532V ENST00000323460 3/10 110 89 21 200 200 0 strelka-varscan-mutect SENP5,synonymous_variant,p.=,ENST00000323460,NM_152699.4;SENP5,synonymous_variant,p.=,ENST00000445299,NM_001308045.1;SENP5,synonymous_variant,p.=,ENST00000419026,;SENP5,upstream_gene_variant,,ENST00000489744,; T ENST00000323460 Transcript synonymous_variant 1845/6308 1596/2268 532/755 V gtC/gtT COSM263573 1 1 SENP5 HGNC HGNC:28407 protein_coding YES CCDS3322.1 ENSP00000327197 Q96HI0 UPI00001AF3BE NM_152699.4 3/10 hmmpanther:PTHR12606:SF10,hmmpanther:PTHR12606 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 57 196899748 196899748 C T 1 0 0 0 0 0 0 0 1 14325 900 32 3 3 SENP5 3 196899748 Silent SNP C C3N-00572_T 844628 196899748 1395811 5 17967 MAN2A1 0 . GRCh38 5 109855189 109855191 + In_Frame_Del DEL CTT CTT - rs750925456 C3N-00572_T C3N-00572_N CTT CTT c.3031_3033delTCT p.Ser1011del p.S1011del ENST00000261483 20/22 62 57 5 90 90 0 sindel-varindel-pindel MAN2A1,inframe_deletion,p.Ser1011del,ENST00000261483,NM_002372.3;MAN2A1,non_coding_transcript_exon_variant,,ENST00000505313,;MAN2A1,non_coding_transcript_exon_variant,,ENST00000513921,; - ENST00000261483 Transcript inframe_deletion 4078-4080/4667 3026-3028/3435 1009-1010/1144 TS/T aCTTct/act rs750925456,COSM1257205 1 1 MAN2A1 HGNC HGNC:6824 protein_coding YES CCDS34209.1 ENSP00000261483 Q16706 UPI000013D193 NM_002372.3 20/22 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF4,Pfam_domain:PF07748,Superfamily_domains:SSF74650 0,1 MODERATE 1 deletion 1 5 0,1 1 PASS . . 0 205 4 0 0 0 0 0 -11.90922 1 1 1 1 0 - 7 5 57 109855189 109855189 CTT - 1 0 1 0 1 0 0 0 0 9135 565 20 0 0 MAN2A1 5 109855189 In_Frame_Del DEL CTT C3N-00572_T 109855189 71683070 6 17968 DPP6 0 . GRCh38 7 154889324 154889324 + Missense_Mutation SNP T T A novel C3N-00572_T C3N-00572_N T T c.2357T>A p.Ile786Asn p.I786N ENST00000377770 24/26 173 141 32 226 226 0 strelka-varscan-mutect DPP6,missense_variant,p.Ile722Asn,ENST00000404039,NM_001039350.2;DPP6,missense_variant,p.Ile724Asn,ENST00000332007,NM_001936.4;DPP6,missense_variant,p.Ile786Asn,ENST00000377770,NM_130797.3;DPP6,missense_variant,p.Ile679Asn,ENST00000427557,NM_001290252.1;DPP6,non_coding_transcript_exon_variant,,ENST00000480367,; A ENST00000377770 Transcript missense_variant 2498/3710 2357/2598 786/865 I/N aTc/aAc 1 1 DPP6 HGNC HGNC:3010 protein_coding YES CCDS75683.1 ENSP00000367001 P42658 UPI00001AE746 NM_130797.3 deleterious(0) 24/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20,Gene3D:3.40.50.1820,Pfam_domain:PF00326,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 57 154889324 154889324 T A 1 0 0 0 0 1 0 0 0 4545 1435 50 4 4 DPP6 7 154889324 Missense_Mutation SNP T C3N-00572_T 154889324 4456649 7 17969 ACVR1B 0 . GRCh38 12 51991982 51991982 + Nonsense_Mutation SNP C C T C3N-00572_T C3N-00572_N C C c.1504C>T p.Gln502Ter p.Q502* ENST00000541224 9/10 252 214 38 413 413 0 strelka-varscan-mutect ACVR1B,stop_gained,p.Gln461Ter,ENST00000257963,NM_004302.4;ACVR1B,stop_gained,p.Gln409Ter,ENST00000542485,NM_020327.3;ACVR1B,stop_gained,p.Gln502Ter,ENST00000541224,NM_020328.3;ACVR1B,stop_gained,p.Gln461Ter,ENST00000426655,;ACVR1B,downstream_gene_variant,,ENST00000415850,;RNU6-574P,downstream_gene_variant,,ENST00000384265,;ACVR1B,non_coding_transcript_exon_variant,,ENST00000563121,; T ENST00000541224 Transcript stop_gained 1547/1791 1504/1641 502/546 Q/* Cag/Tag COSM1362434 1 1 ACVR1B HGNC HGNC:172 protein_coding YES CCDS44894.2 ENSP00000442656 P36896 UPI0001915052 NM_020328.3 9/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF22,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 HIGH 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 57 51991982 51991982 C T 1 0 0 0 0 0 1 0 0 265 711 25 3 3 ACVR1B 12 51991982 Nonsense_Mutation SNP C C3N-00572_T 51991982 81283327 8 17970 ZNF768 0 . GRCh38 16 30524745 30524745 + Silent SNP G G C novel C3N-00572_T C3N-00572_N G G c.1395C>G p.= p.T465T ENST00000380412 2/2 215 177 38 270 270 0 strelka-varscan-mutect ZNF768,synonymous_variant,p.=,ENST00000380412,NM_024671.3;ZNF768,synonymous_variant,p.=,ENST00000562803,;ITGAL,downstream_gene_variant,,ENST00000356798,NM_002209.2;ITGAL,downstream_gene_variant,,ENST00000358164,NM_001114380.1;ITGAL,downstream_gene_variant,,ENST00000433423,;AC002310.14,upstream_gene_variant,,ENST00000624451,;AC002310.11,downstream_gene_variant,,ENST00000569360,;ITGAL,downstream_gene_variant,,ENST00000564632,; C ENST00000380412 Transcript synonymous_variant 1571/2315 1395/1623 465/540 T acC/acG 1 -1 ZNF768 HGNC HGNC:26273 protein_coding YES CCDS10681.2 ENSP00000369777 Q9H5H4 A0A024QZC8 UPI00001FFEED NM_024671.3 2/2 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF208,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs1343537361 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 57 30524745 30524745 G C 1 0 0 0 0 0 0 0 1 18724 987 35 4 4 ZNF768 16 30524745 Silent SNP G C3N-00572_T 30524745 59813600 9 17971 TP53 0 . GRCh38 17 7670687 7670687 + Missense_Mutation SNP A A T C3N-00572_T C3N-00572_N A A c.1022T>A p.Phe341Tyr p.F341Y ENST00000269305 10/11 282 236 46 416 416 0 strelka-varscan-mutect TP53,missense_variant,p.Phe302Tyr,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Phe341Tyr,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Phe302Tyr,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Phe341Tyr,ENST00000445888,;TP53,missense_variant,p.Phe302Tyr,ENST00000619485,;TP53,missense_variant,p.Phe209Tyr,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Phe182Tyr,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Phe330Tyr,ENST00000615910,;TP53,3_prime_UTR_variant,,ENST00000617185,NM_001126114.2;TP53,3_prime_UTR_variant,,ENST00000420246,;TP53,3_prime_UTR_variant,,ENST00000622645,NM_001276696.1;TP53,3_prime_UTR_variant,,ENST00000455263,NM_001126113.2;TP53,3_prime_UTR_variant,,ENST00000610538,NM_001276695.1;TP53,3_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,3_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,3_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,3_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,intron_variant,,ENST00000359597,;TP53,intron_variant,,ENST00000413465,;TP53,intron_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Phe302Tyr,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 1212/2579 1022/1182 341/393 F/Y tTc/tAc TP53_g.16913del,TP53_g.16913T>G,COSM45744,COSM46016 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.01) 10/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:1olgA00,Pfam_domain:PF07710,Superfamily_domains:SSF47719,Prints_domain:PR00386 0,0,1,1 MODERATE 1 SNV 1 0,0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 57 7670687 7670687 A T 1 0 0 0 0 1 0 0 0 16859 246 9 4 4 TP53 17 7670687 Missense_Mutation SNP A C3N-00572_T 7670687 75586754 10 17972 TMEM132E 0 . GRCh38 17 34637708 34637708 + Missense_Mutation SNP G G A novel C3N-00572_T C3N-00572_N G G c.2431G>A p.Ala811Thr p.A811T ENST00000321639 10/10 227 191 36 291 291 0 strelka-varscan-mutect TMEM132E,missense_variant,p.Ala901Thr,ENST00000631683,NM_001304438.1;TMEM132E,missense_variant,p.Ala811Thr,ENST00000321639,;TMEM132E,downstream_gene_variant,,ENST00000577271,; A ENST00000321639 Transcript missense_variant 2759/4369 2431/2955 811/984 A/T Gcc/Acc 1 1 TMEM132E HGNC HGNC:26991 protein_coding YES ENSP00000316532 Q6IEE7 UPI000035960F deleterious(0) 10/10 Pfam_domain:PF15706,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF7,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 204 0 4 0 0 0 0 -20 0.9999209 1 1 1 0 A 3 1 57 34637708 34637708 G A 1 0 0 0 0 1 0 0 0 16493 1087 38 1 1 TMEM132E 17 34637708 Missense_Mutation SNP G C3N-00572_T 26967021 34637708 48619733 11 17973 HID1 0 . GRCh38 17 74959020 74959020 + Missense_Mutation SNP C C A rs750214001 C3N-00572_T C3N-00572_N C C c.1040G>T p.Arg347Leu p.R347L ENST00000425042 9/19 43 33 10 58 58 0 strelka-varscan-mutect HID1,missense_variant,p.Arg347Leu,ENST00000425042,NM_030630.2;HID1,missense_variant,p.Arg239Leu,ENST00000530857,;HID1,missense_variant,p.Arg54Leu,ENST00000318565,;HID1,downstream_gene_variant,,ENST00000581676,;HID1,downstream_gene_variant,,ENST00000532900,;HID1,downstream_gene_variant,,ENST00000579818,;HID1,downstream_gene_variant,,ENST00000530904,;HID1,upstream_gene_variant,,ENST00000578002,;HID1,3_prime_UTR_variant,,ENST00000534480,;HID1,non_coding_transcript_exon_variant,,ENST00000532894,;HID1,downstream_gene_variant,,ENST00000528902,;HID1,upstream_gene_variant,,ENST00000532395,;HID1,downstream_gene_variant,,ENST00000525128,;HID1,upstream_gene_variant,,ENST00000583244,; A ENST00000425042 Transcript missense_variant 1118/3271 1040/2367 347/788 R/L cGg/cTg rs750214001 1 -1 HID1 HGNC HGNC:15736 protein_coding YES CCDS32726.1 ENSP00000413520 Q8IV36 UPI00000746AC NM_030630.2 deleterious(0.01) 9/19 Pfam_domain:PF12722,hmmpanther:PTHR21575,hmmpanther:PTHR21575:SF12 MODERATE 1 SNV 1 1 PASS rs750214001 . 0 204 6 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 57 74959020 74959020 C A 1 0 0 0 0 1 0 0 0 6987 652 23 1 1 HID1 17 74959020 Missense_Mutation SNP C C3N-00572_T 40321312 74959020 8298421 12 17974 ZNF773 0 . GRCh38 19 57506379 57506379 + Missense_Mutation SNP C C T novel C3N-00572_T C3N-00572_N C C c.284C>T p.Ala95Val p.A95V ENST00000282292 4/4 100 91 9 134 134 0 strelka-varscan-mutect ZNF773,missense_variant,p.Ala95Val,ENST00000282292,NM_198542.2;ZNF773,missense_variant,p.Ala94Val,ENST00000598770,NM_001304336.1,NM_001304334.1;ZNF773,intron_variant,,ENST00000599847,NM_001304335.1;ZNF773,intron_variant,,ENST00000593916,NM_001304337.1;ZNF773,non_coding_transcript_exon_variant,,ENST00000601958,;ZNF773,intron_variant,,ENST00000597061,;AC003005.4,downstream_gene_variant,,ENST00000601674,;AC003005.4,downstream_gene_variant,,ENST00000599674,; T ENST00000282292 Transcript missense_variant 424/2206 284/1329 95/442 A/V gCt/gTt 1 1 ZNF773 HGNC HGNC:30487 protein_coding YES CCDS33134.1 ENSP00000282292 Q6PK81 UPI00001BD93D NM_198542.2 tolerated(0.54) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF40 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.74849 1 1 1 1 0 T 3 4 57 57506379 57506379 C T 1 0 0 0 0 1 0 0 0 18729 797 28 3 3 ZNF773 19 57506379 Missense_Mutation SNP C C3N-00572_T 57506379 1111237 13 17975 LAMP5 0 . GRCh38 20 9518038 9518038 + Splice_Site SNP A A G novel C3N-00572_T C3N-00572_N A A c.476-2A>G p.X159_splice ENST00000246070 94 82 12 105 105 0 strelka-varscan-mutect LAMP5,splice_acceptor_variant,,ENST00000246070,NM_012261.3;LAMP5,splice_acceptor_variant,,ENST00000427562,NM_001199897.1;LAMP5-AS1,upstream_gene_variant,,ENST00000443469,; G ENST00000246070 Transcript splice_acceptor_variant -/2039 476/843 159/280 1 1 LAMP5 HGNC HGNC:16097 protein_coding YES CCDS13106.1 ENSP00000246070 Q9UJQ1 UPI0000128675 NM_012261.3 4/5 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999994 1 1 1 0 G 5 3 57 9518038 9518038 A G 1 0 0 0 0 0 0 1 0 8524 434 15 5 5 LAMP5 20 9518038 Splice_Site SNP A C3N-00572_T 9518038 54926129 14 17976 1 12 2 2 131 A 8.839513e-05 LAMP5 0 . GRCh38 20 9518168 9518168 + Missense_Mutation SNP A A C novel C3N-00572_T C3N-00572_N A A c.604A>C p.Ile202Leu p.I202L ENST00000246070 5/6 221 191 30 240 240 0 strelka-varscan-mutect LAMP5,missense_variant,p.Ile202Leu,ENST00000246070,NM_012261.3;LAMP5,missense_variant,p.Ile158Leu,ENST00000427562,NM_001199897.1;LAMP5-AS1,upstream_gene_variant,,ENST00000443469,; C ENST00000246070 Transcript missense_variant 1096/2039 604/843 202/280 I/L Atc/Ctc 1 1 LAMP5 HGNC HGNC:16097 protein_coding YES CCDS13106.1 ENSP00000246070 Q9UJQ1 UPI0000128675 NM_012261.3 tolerated(1) 5/6 hmmpanther:PTHR11506,Pfam_domain:PF01299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 57 9518168 9518168 A C 1 0 0 0 0 1 0 0 0 8524 333 12 5 5 LAMP5 20 9518168 Missense_Mutation SNP A C3N-00572_T 130 9518168 54925999 15 17977 1 12 2 2 131 A 8.839513e-05 JAG1 0 . GRCh38 20 10641646 10641646 + Silent SNP C C T novel C3N-00572_T C3N-00572_N C C c.2730G>A p.= p.E910E ENST00000254958 23/26 444 368 76 607 607 0 strelka-varscan-mutect JAG1,synonymous_variant,p.=,ENST00000254958,NM_000214.2;JAG1,downstream_gene_variant,,ENST00000613518,;JAG1,non_coding_transcript_exon_variant,,ENST00000423891,;JAG1,downstream_gene_variant,,ENST00000488480,;SLX4IP,downstream_gene_variant,,ENST00000488816,;JAG1,downstream_gene_variant,,ENST00000612857,;JAG1,upstream_gene_variant,,ENST00000617357,; T ENST00000254958 Transcript synonymous_variant 3307/6048 2730/3657 910/1218 E gaG/gaA 1 -1 JAG1 HGNC HGNC:6188 protein_coding YES CCDS13112.1 ENSP00000254958 P78504 UPI00000498B5 NM_000214.2 23/26 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF269,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 57 10641646 10641646 C T 1 0 0 0 0 0 0 0 1 7847 564 20 3 3 JAG1 20 10641646 Silent SNP C C3N-00572_T 1123478 10641646 53802521 16 17978 ZNF512B 0 . GRCh38 20 63961944 63961944 + Nonsense_Mutation SNP T T A novel C3N-00572_T C3N-00572_N T T c.2326A>T p.Lys776Ter p.K776* ENST00000369888 15/17 213 191 22 199 199 0 strelka-varscan-mutect ZNF512B,stop_gained,p.Lys776Ter,ENST00000369888,NM_020713.2;UCKL1-AS1,downstream_gene_variant,,ENST00000623569,; A ENST00000369888 Transcript stop_gained,splice_region_variant 2380/5919 2326/2679 776/892 K/* Aag/Tag 1 -1 ZNF512B HGNC HGNC:29212 protein_coding YES CCDS13548.1 ENSP00000358904 Q96KM6 UPI000013A290 NM_020713.2 15/17 hmmpanther:PTHR22979,hmmpanther:PTHR22979:SF3,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 57 63961944 63961944 T A 1 0 0 0 0 0 1 0 0 18529 1768 61 4 4 ZNF512B 20 63961944 Nonsense_Mutation SNP T C3N-00572_T 53320298 63961944 482223 17 17979 MGAT3 0 . GRCh38 22 39487677 39487677 + Silent SNP C C A novel C3N-00572_T C3N-00572_N C C c.330C>A p.= p.R110R ENST00000341184 2/2 83 68 15 145 145 0 strelka-varscan-mutect MGAT3,synonymous_variant,p.=,ENST00000341184,NM_002409.4,NM_001098270.1;MGAT3,synonymous_variant,p.=,ENST00000429402,;MGAT3,downstream_gene_variant,,ENST00000418314,; A ENST00000341184 Transcript synonymous_variant 545/5062 330/1602 110/533 R cgC/cgA 1 1 MGAT3 HGNC HGNC:7046 protein_coding YES CCDS13994.2 ENSP00000345270 Q09327 UPI00003765B6 NM_002409.4,NM_001098270.1 2/2 hmmpanther:PTHR12224:SF0,hmmpanther:PTHR12224 LOW 1 SNV 1 1 PASS rs1205519736 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 57 39487677 39487677 C A 1 0 0 0 0 0 0 0 1 9504 697 25 2 2 MGAT3 22 39487677 Silent SNP C C3N-00572_T 39487677 11330791 18 17980 MAP7D2 0 . GRCh38 X 20025035 20025035 + Missense_Mutation SNP T T C novel C3N-00572_T C3N-00572_N T T c.1328A>G p.Lys443Arg p.K443R ENST00000379643 10/17 221 181 40 255 255 0 strelka-varscan-mutect MAP7D2,missense_variant,p.Lys402Arg,ENST00000379651,NM_152780.3;MAP7D2,missense_variant,p.Lys443Arg,ENST00000379643,NM_001168465.1;MAP7D2,missense_variant,p.Lys357Arg,ENST00000443379,NM_001168466.1;MAP7D2,missense_variant,p.Lys350Arg,ENST00000452324,NM_001168467.1;MAP7D2,non_coding_transcript_exon_variant,,ENST00000466145,; C ENST00000379643 Transcript missense_variant 1366/3918 1328/2322 443/773 K/R aAg/aGg 1 -1 MAP7D2 HGNC HGNC:25899 protein_coding YES CCDS55386.1 ENSP00000368964 Q96T17 UPI00015E039B NM_001168465.1 tolerated(0.24) 10/17 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05672,hmmpanther:PTHR15073,hmmpanther:PTHR15073:SF3 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 57 20025035 20025035 T C 1 0 0 0 0 1 0 0 0 9192 1609 56 5 5 MAP7D2 23 20025035 Missense_Mutation SNP T C3N-00572_T 20025035 136015860 19 17981 TAB3 0 . GRCh38 X 30859511 30859511 + Silent SNP G G A rs763138676 C3N-00572_T C3N-00572_N G G c.78C>T p.= p.G26G ENST00000378933 6/12 279 238 41 311 311 0 strelka-varscan-mutect TAB3,synonymous_variant,p.=,ENST00000378933,NM_152787.4;TAB3,synonymous_variant,p.=,ENST00000378930,;TAB3,synonymous_variant,p.=,ENST00000378932,;TAB3,synonymous_variant,p.=,ENST00000288422,;TAB3-AS2,downstream_gene_variant,,ENST00000445240,;TAB3,synonymous_variant,p.=,ENST00000467136,; A ENST00000378933 Transcript synonymous_variant 625/6671 78/2139 26/712 G ggC/ggT rs763138676,COSM185140 1 -1 TAB3 HGNC HGNC:30681 protein_coding YES CCDS14226.1 ENSP00000368215 Q8N5C8 UPI0000071648 NM_152787.4 6/12 PROSITE_profiles:PS51140,hmmpanther:PTHR10351:SF45,hmmpanther:PTHR10351,Pfam_domain:PF02845,SMART_domains:SM00546 0,1 LOW 1 SNV 1 0,1 1 PASS rs763138676 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 57 30859511 30859511 G A 1 0 0 0 0 0 0 0 1 15893 1074 38 1 1 TAB3 23 30859511 Silent SNP G C3N-00572_T 10834476 30859511 125181384 20 17982 ARHGAP36 0 . GRCh38 X 131081750 131081751 + Frame_Shift_Ins INS - - T novel C3N-00572_T C3N-00572_N - - c.92dupT p.Leu31PhefsTer27 p.L31Ffs*27 ENST00000276211 2/12 306 259 47 430 429 1 sindel-varindel ARHGAP36,frameshift_variant,p.Leu31PhefsTer27,ENST00000276211,NM_144967.3;ARHGAP36,intron_variant,,ENST00000370922,NM_001282607.1;ARHGAP36,intron_variant,,ENST00000412432,;ARHGAP36,intron_variant,,ENST00000423277,;ARHGAP36,upstream_gene_variant,,ENST00000370921,; T ENST00000276211 Transcript frameshift_variant 430-431/3083 85-86/1644 29/547 I/IX att/aTtt 1 1 ARHGAP36 HGNC HGNC:26388 protein_coding YES CCDS14628.1 ENSP00000276211 Q6ZRI8 UPI0000041347 NM_144967.3 2/12 hmmpanther:PTHR12635,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix HIGH 1 insertion 2 7 1 PASS . . 0 200 0 4 6 0 0 0 -19.98256 0.3610029 1 1 0 0 T 7 5 57 131081750 131081750 - T 1 0 1 1 0 0 0 0 0 1009 217 8 0 0 ARHGAP36 23 131081750 Frame_Shift_Ins INS - C3N-00572_T 100222239 131081750 24959145 21 17983 CSMD2 0 . GRCh38 1 33605986 33605986 + Missense_Mutation SNP A A T novel C3N-00574_T C3N-00574_N A A c.6226T>A p.Leu2076Met p.L2076M ENST00000373388 42/70 161 149 12 120 120 0 strelka-varscan-mutect CSMD2,missense_variant,p.Leu2076Met,ENST00000373388,NM_052896.4;CSMD2,intron_variant,,ENST00000373381,NM_001281956.1;CSMD2,intron_variant,,ENST00000619121,;CSMD2,intron_variant,,ENST00000373380,;CSMD2,intron_variant,,ENST00000373377,;CSMD2,upstream_gene_variant,,ENST00000489419,;CSMD2,missense_variant,p.Leu2076Met,ENST00000241312,; T ENST00000373388 Transcript missense_variant,splice_region_variant 6255/13118 6226/10464 2076/3487 L/M Ttg/Atg 1 -1 CSMD2 HGNC HGNC:19290 protein_coding CCDS380.1 ENSP00000362486 Q7Z408 UPI00004561AB NM_052896.4 tolerated_low_confidence(0.11) 42/70 PROSITE_profiles:PS01180,SMART_domains:SM00042 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 33605986 33605986 A T 1 0 0 0 0 1 0 0 0 3746 28 1 4 4 CSMD2 1 33605986 Missense_Mutation SNP A C3N-00574_T 33605986 215350436 1 17984 MACF1 0 . GRCh38 1 39353086 39353086 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.5093C>T p.Ser1698Phe p.S1698F ENST00000361689 38/93 184 174 10 153 153 0 strelka-varscan-mutect MACF1,missense_variant,p.Ser3760Phe,ENST00000564288,;MACF1,missense_variant,p.Ser3797Phe,ENST00000567887,;MACF1,missense_variant,p.Ser3765Phe,ENST00000372915,;MACF1,missense_variant,p.Ser2200Phe,ENST00000289893,;MACF1,missense_variant,p.Ser1698Phe,ENST00000361689,NM_012090.5;MACF1,missense_variant,p.Ser832Phe,ENST00000372925,;MACF1,missense_variant,p.Ser1847Phe,ENST00000530262,;MACF1,non_coding_transcript_exon_variant,,ENST00000476350,; T ENST00000361689 Transcript missense_variant 5145/17538 5093/16293 1698/5430 S/F tCt/tTt 1 1 MACF1 HGNC HGNC:13664 protein_coding YES CCDS435.1 ENSP00000354573 Q9UPN3 UPI00001B3DC6 NM_012090.5 deleterious(0.02) 38/93 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 39353086 39353086 C T 1 0 0 0 0 1 0 0 0 9060 913 32 3 3 MACF1 1 39353086 Missense_Mutation SNP C C3N-00574_T 5747100 39353086 209603336 2 17985 PATJ 0 . GRCh38 1 61901430 61901430 + Missense_Mutation SNP G G A rs545651035 C3N-00574_T C3N-00574_N G G c.3352G>A p.Ala1118Thr p.A1118T ENST00000371158 24/43 203 187 16 244 243 1 strelka-varscan-mutect PATJ,missense_variant,p.Ala1118Thr,ENST00000371158,NM_176877.2;PATJ,missense_variant,p.Ala1118Thr,ENST00000613764,;PATJ,missense_variant,p.Ala1118Thr,ENST00000316485,;PATJ,missense_variant,p.Ala577Thr,ENST00000484937,;PATJ,3_prime_UTR_variant,,ENST00000635023,;PATJ,non_coding_transcript_exon_variant,,ENST00000484562,;PATJ,non_coding_transcript_exon_variant,,ENST00000459752,;PATJ,non_coding_transcript_exon_variant,,ENST00000635214,; A ENST00000371158 Transcript missense_variant 3466/8505 3352/5406 1118/1801 A/T Gca/Aca rs545651035,COSM911279 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 tolerated(0.17) 24/43 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF11,SMART_domains:SM00228,Superfamily_domains:SSF50156 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs545651035 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 58 61901430 61901430 G A 1 0 0 0 0 1 0 0 0 11558 1087 38 1 1 PATJ 1 61901430 Missense_Mutation SNP G C3N-00574_T 22548344 61901430 187054992 3 17986 FLG 0 . GRCh38 1 152311573 152311573 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.3313G>A p.Asp1105Asn p.D1105N ENST00000368799 3/3 565 508 57 442 441 1 strelka-varscan-mutect FLG,missense_variant,p.Asp1105Asn,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 3349/12747 3313/12186 1105/4061 D/N Gac/Aac 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.21) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 152311573 152311573 C T 1 0 0 0 0 1 0 0 0 5784 826 29 3 3 FLG 1 152311573 Missense_Mutation SNP C C3N-00574_T 90410143 152311573 96644849 4 17987 SRGAP2 0 . GRCh38 1 206446269 206446269 + Missense_Mutation SNP A A G novel C3N-00574_T C3N-00574_N A A c.2069A>G p.Tyr690Cys p.Y690C ENST00000573034 17/22 308 290 18 204 204 0 strelka-varscan SRGAP2,missense_variant,p.Tyr690Cys,ENST00000573034,NM_015326.4;SRGAP2,missense_variant,p.Tyr689Cys,ENST00000624873,NM_001170637.3;SRGAP2,missense_variant,p.Tyr689Cys,ENST00000605610,NM_001300952.1;SRGAP2,missense_variant,p.Tyr304Cys,ENST00000605476,;SRGAP2,missense_variant,p.Tyr73Cys,ENST00000604925,;SRGAP2,downstream_gene_variant,,ENST00000604419,; G ENST00000573034 Transcript missense_variant 2131/6301 2069/3216 690/1071 Y/C tAc/tGc 1 1 SRGAP2 HGNC HGNC:19751 protein_coding YES CCDS73017.1 ENSP00000459615 A2RUF3 UPI0000DC3AA7 NM_015326.4 deleterious(0) 17/22 hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 58 206446269 206446269 A G 1 0 0 0 0 1 0 0 0 15505 391 14 5 5 SRGAP2 1 206446269 Missense_Mutation SNP A C3N-00574_T 54134696 206446269 42510153 5 17988 RYR2 0 . GRCh38 1 237711775 237711775 + Missense_Mutation SNP G G T novel C3N-00574_T C3N-00574_N G G c.10261G>T p.Val3421Leu p.V3421L ENST00000366574 71/105 161 123 38 235 235 0 strelka-varscan RYR2,missense_variant,p.Val3421Leu,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Val3405Leu,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript missense_variant 10578/16562 10261/14904 3421/4967 V/L Gta/Tta 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.01) 71/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 237711775 237711775 G T 1 0 0 0 0 1 0 0 0 14029 1377 48 2 2 RYR2 1 237711775 Missense_Mutation SNP G C3N-00574_T 31265506 237711775 11244647 6 17989 OR2M2 0 . GRCh38 1 248180434 248180434 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.449T>C p.Ile150Thr p.I150T ENST00000359682 1/1 386 342 44 357 357 0 strelka-varscan OR2M2,missense_variant,p.Ile150Thr,ENST00000359682,NM_001004688.1; C ENST00000359682 Transcript missense_variant 449/1044 449/1044 150/347 I/T aTc/aCc 1 1 OR2M2 HGNC HGNC:8268 protein_coding YES CCDS31106.1 ENSP00000352710 Q96R28 A0A126GWI7 UPI00001612E4 NM_001004688.1 tolerated(0.06) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 248180434 248180434 T C 1 0 0 0 0 1 0 0 0 11088 1435 50 5 5 OR2M2 1 248180434 Missense_Mutation SNP T C3N-00574_T 10468659 248180434 775988 7 17990 OR2T4 0 . GRCh38 1 248361854 248361854 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.274T>C p.Tyr92His p.Y92H ENST00000366475 1/1 420 366 54 355 355 0 strelka-varscan OR2T4,missense_variant,p.Tyr92His,ENST00000366475,NM_001004696.1; C ENST00000366475 Transcript missense_variant 274/1047 274/1047 92/348 Y/H Tac/Cac 1 1 OR2T4 HGNC HGNC:15016 protein_coding YES CCDS31113.1 ENSP00000355431 Q8NH00 UPI000004B9CC NM_001004696.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF241,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 248361854 248361854 T C 1 0 0 0 0 1 0 0 0 11104 1638 57 5 5 OR2T4 1 248361854 Missense_Mutation SNP T C3N-00574_T 181420 248361854 594568 8 17991 SLC5A6 0 . GRCh38 2 27203804 27203804 + Missense_Mutation SNP C C A novel C3N-00574_T C3N-00574_N C C c.1069G>T p.Ala357Ser p.A357S ENST00000310574 10/17 330 219 111 221 221 0 strelka-varscan SLC5A6,missense_variant,p.Ala357Ser,ENST00000310574,NM_021095.2;SLC5A6,missense_variant,p.Ala357Ser,ENST00000408041,;SLC5A6,downstream_gene_variant,,ENST00000412471,;SLC5A6,downstream_gene_variant,,ENST00000414408,;SLC5A6,downstream_gene_variant,,ENST00000401463,;SLC5A6,downstream_gene_variant,,ENST00000432106,;SLC5A6,downstream_gene_variant,,ENST00000426119,;SLC5A6,downstream_gene_variant,,ENST00000430186,;SLC5A6,downstream_gene_variant,,ENST00000428518,;SLC5A6,downstream_gene_variant,,ENST00000442731,;SLC5A6,upstream_gene_variant,,ENST00000461319,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000488743,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000476319,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000492069,;SLC5A6,upstream_gene_variant,,ENST00000461757,;SLC5A6,downstream_gene_variant,,ENST00000445802,;SLC5A6,downstream_gene_variant,,ENST00000464538,;SLC5A6,upstream_gene_variant,,ENST00000481751,; A ENST00000310574 Transcript missense_variant 1543/3231 1069/1908 357/635 A/S Gcc/Tcc 1 -1 SLC5A6 HGNC HGNC:11041 protein_coding YES CCDS1740.1 ENSP00000310208 Q9Y289 UPI000006DE33 NM_021095.2 tolerated(0.09) 10/17 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF140,TIGRFAM_domain:TIGR00813,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 58 27203804 27203804 C A 1 0 0 0 0 1 0 0 0 14952 710 25 2 2 SLC5A6 2 27203804 Missense_Mutation SNP C C3N-00574_T 27203804 214989725 9 17992 PELI1 0 . GRCh38 2 64096535 64096535 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.379A>G p.Thr127Ala p.T127A ENST00000358912 5/7 171 132 39 138 138 0 strelka-varscan PELI1,missense_variant,p.Thr127Ala,ENST00000358912,NM_020651.3;PELI1,downstream_gene_variant,,ENST00000466177,; C ENST00000358912 Transcript missense_variant 822/3750 379/1257 127/418 T/A Aca/Gca 1 -1 PELI1 HGNC HGNC:8827 protein_coding YES CCDS1876.1 ENSP00000351789 Q96FA3 Q53T26 UPI00000443B7 NM_020651.3 tolerated(1) 5/7 hmmpanther:PTHR12098:SF4,hmmpanther:PTHR12098,PIRSF_domain:PIRSF038886,Pfam_domain:PF04710 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 64096535 64096535 T C 1 0 0 0 0 1 0 0 0 11809 1638 57 5 5 PELI1 2 64096535 Missense_Mutation SNP T C3N-00574_T 36892731 64096535 178096994 10 17993 ERMN 0 . GRCh38 2 157321638 157321638 + Missense_Mutation SNP C C T rs554539666 C3N-00574_T C3N-00574_N C C c.527G>A p.Arg176Gln p.R176Q ENST00000397283 4/4 313 295 18 248 248 0 strelka-varscan ERMN,missense_variant,p.Arg163Gln,ENST00000410096,NM_001304344.1,NM_001304345.1,NM_020711.2;ERMN,missense_variant,p.Arg176Gln,ENST00000397283,NM_001009959.2;ERMN,missense_variant,p.Arg143Gln,ENST00000420719,NM_001304346.1;ERMN,downstream_gene_variant,,ENST00000409216,;ERMN,downstream_gene_variant,,ENST00000419116,;ERMN,downstream_gene_variant,,ENST00000411762,;ERMN,downstream_gene_variant,,ENST00000409925,;ERMN,downstream_gene_variant,,ENST00000420317,;ERMN,3_prime_UTR_variant,,ENST00000409395,; T ENST00000397283 Transcript missense_variant 761/3760 527/894 176/297 R/Q cGa/cAa rs554539666 1 -1 ERMN HGNC HGNC:29208 protein_coding YES CCDS42764.1 ENSP00000380453 Q8TAM6 UPI0000208F55 NM_001009959.2 tolerated(1) 4/4 hmmpanther:PTHR23281,hmmpanther:PTHR23281:SF22 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 157321638 157321638 C T 1 0 0 0 0 1 0 0 0 5093 884 31 1 1 ERMN 2 157321638 Missense_Mutation SNP C C3N-00574_T 93225103 157321638 84871891 11 17994 CSRNP3 0 . GRCh38 2 165679416 165679416 + Missense_Mutation SNP C C T rs766623860 C3N-00574_T C3N-00574_N C C c.1421C>T p.Pro474Leu p.P474L ENST00000314499 7/7 271 240 31 266 265 1 strelka-varscan CSRNP3,missense_variant,p.Pro474Leu,ENST00000314499,NM_001172173.1;CSRNP3,missense_variant,p.Pro474Leu,ENST00000342316,NM_024969.3;CSRNP3,missense_variant,p.Pro506Leu,ENST00000409420,;CSRNP3,downstream_gene_variant,,ENST00000421875,;CSRNP3,downstream_gene_variant,,ENST00000409664,; T ENST00000314499 Transcript missense_variant 1797/11788 1421/1758 474/585 P/L cCg/cTg rs766623860,COSM32890 1 1 CSRNP3 HGNC HGNC:30729 protein_coding YES CCDS2225.1 ENSP00000318258 Q8WYN3 UPI0000136882 NM_001172173.1 deleterious_low_confidence(0.03) 7/7 hmmpanther:PTHR13580,hmmpanther:PTHR13580:SF13 0,1 MODERATE 1 SNV 5 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 165679416 165679416 C T 1 0 0 0 0 1 0 0 0 3766 652 23 1 1 CSRNP3 2 165679416 Missense_Mutation SNP C C3N-00574_T 8357778 165679416 76514113 12 17995 CALCRL 0 . GRCh38 2 187346314 187346314 + Missense_Mutation SNP G G A rs761424831 C3N-00574_T C3N-00574_N G G c.1256C>T p.Ala419Val p.A419V ENST00000409998 16/16 254 227 27 233 233 0 strelka-varscan-mutect CALCRL,missense_variant,p.Ala419Val,ENST00000409998,;CALCRL,missense_variant,p.Ala419Val,ENST00000392370,NM_005795.5;CALCRL,missense_variant,p.Ala419Val,ENST00000410068,NM_001271751.1;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; A ENST00000409998 Transcript missense_variant 2038/5223 1256/1386 419/461 A/V gCg/gTg rs761424831 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF tolerated(0.08) 16/16 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF67,Prints_domain:PR01351 MODERATE 1 SNV 5 1 PASS rs761424831 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 58 187346314 187346314 G A 1 0 0 0 0 1 0 0 0 2270 1087 38 1 1 CALCRL 2 187346314 Missense_Mutation SNP G C3N-00574_T 21666898 187346314 54847215 13 17996 BAP1 0 . GRCh38 3 52406261 52406261 + Silent SNP G G A novel C3N-00574_T C3N-00574_N G G c.775C>T p.= p.L259L ENST00000460680 9/17 392 270 122 274 274 0 strelka-varscan-mutect BAP1,synonymous_variant,p.=,ENST00000460680,NM_004656.3;BAP1,synonymous_variant,p.=,ENST00000296288,;PHF7,upstream_gene_variant,,ENST00000327906,NM_016483.5;BAP1,upstream_gene_variant,,ENST00000469613,;PHF7,upstream_gene_variant,,ENST00000347025,;BAP1,upstream_gene_variant,,ENST00000478368,;BAP1,downstream_gene_variant,,ENST00000470173,;BAP1,upstream_gene_variant,,ENST00000615113,;PHF7,upstream_gene_variant,,ENST00000482327,;BAP1,non_coding_transcript_exon_variant,,ENST00000471532,;BAP1,upstream_gene_variant,,ENST00000466093,;PHF7,upstream_gene_variant,,ENST00000473145,;BAP1,upstream_gene_variant,,ENST00000490804,;BAP1,downstream_gene_variant,,ENST00000483984,;BAP1,downstream_gene_variant,,ENST00000490917,; A ENST00000460680 Transcript synonymous_variant 1247/3937 775/2190 259/729 L Ctg/Ttg 1 -1 BAP1 HGNC HGNC:950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 A0A024R305 UPI0000071B3D NM_004656.3 9/17 hmmpanther:PTHR10589:SF28,hmmpanther:PTHR10589 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 58 52406261 52406261 G A 1 0 0 0 0 0 0 0 1 1463 933 33 3 3 BAP1 3 52406261 Silent SNP G C3N-00574_T 52406261 145889298 14 17997 PLXNA1 0 . GRCh38 3 127030019 127030019 + Silent SNP C C T novel C3N-00574_T C3N-00574_N C C c.5016C>T p.= p.S1672S ENST00000393409 27/31 125 96 29 83 83 0 strelka-varscan-mutect PLXNA1,synonymous_variant,p.=,ENST00000393409,NM_032242.3;PLXNA1,upstream_gene_variant,,ENST00000505278,;PLXNA1,non_coding_transcript_exon_variant,,ENST00000503234,;PLXNA1,downstream_gene_variant,,ENST00000503363,; T ENST00000393409 Transcript synonymous_variant 5016/9066 5016/5691 1672/1896 S agC/agT 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 27/31 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 58 127030019 127030019 C T 1 0 0 0 0 0 0 0 1 12225 709 25 3 3 PLXNA1 3 127030019 Silent SNP C C3N-00574_T 74623758 127030019 71265540 15 17998 NAALADL2 0 . GRCh38 3 175097045 175097045 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.299T>C p.Leu100Pro p.L100P ENST00000454872 2/14 315 282 33 268 268 0 strelka-varscan-mutect NAALADL2,missense_variant,p.Leu100Pro,ENST00000454872,NM_207015.2;NAALADL2,missense_variant,p.Leu83Pro,ENST00000434257,;NAALADL2-AS3,intron_variant,,ENST00000453180,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000485853,;NAALADL2-AS3,intron_variant,,ENST00000436929,; C ENST00000454872 Transcript missense_variant 427/9865 299/2388 100/795 L/P cTt/cCt 1 1 NAALADL2 HGNC HGNC:23219 protein_coding YES CCDS46960.1 ENSP00000404705 Q58DX5 UPI0000161608 NM_207015.2 deleterious(0) 2/14 hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 175097045 175097045 T C 1 0 0 0 0 1 0 0 0 10134 1609 56 5 5 NAALADL2 3 175097045 Missense_Mutation SNP T C3N-00574_T 48067026 175097045 23198514 16 17999 FAM184B 0 . GRCh38 4 17709131 17709131 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.655G>A p.Glu219Lys p.E219K ENST00000265018 2/18 216 190 26 181 181 0 strelka-varscan-mutect FAM184B,missense_variant,p.Glu219Lys,ENST00000265018,NM_015688.1; T ENST00000265018 Transcript missense_variant 868/6622 655/3183 219/1060 E/K Gag/Aag 1 -1 FAM184B HGNC HGNC:29235 protein_coding YES CCDS47033.1 ENSP00000265018 Q9ULE4 UPI000020BD7C NM_015688.1 tolerated(0.22) 2/18 hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870,Pfam_domain:PF15665,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS rs899848754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 17709131 17709131 C T 1 0 0 0 0 1 0 0 0 5359 893 31 1 1 FAM184B 4 17709131 Missense_Mutation SNP C C3N-00574_T 17709131 172505424 17 18000 ADGRL3 0 . GRCh38 4 62070683 62070683 + Silent SNP C C G novel C3N-00574_T C3N-00574_N C C c.4185C>G p.= p.T1395T ENST00000514591 25/25 212 187 25 171 171 0 strelka-varscan-mutect ADGRL3,synonymous_variant,p.=,ENST00000514591,NM_015236.4;ADGRL3,synonymous_variant,p.=,ENST00000506720,;ADGRL3,synonymous_variant,p.=,ENST00000506746,;ADGRL3,synonymous_variant,p.=,ENST00000507625,;ADGRL3,synonymous_variant,p.=,ENST00000508946,;ADGRL3,synonymous_variant,p.=,ENST00000514996,;ADGRL3,synonymous_variant,p.=,ENST00000502815,;ADGRL3,3_prime_UTR_variant,,ENST00000512091,NM_001322246.1;ADGRL3,3_prime_UTR_variant,,ENST00000509896,;ADGRL3,3_prime_UTR_variant,,ENST00000511324,;ADGRL3,3_prime_UTR_variant,,ENST00000508693,;ADGRL3,3_prime_UTR_variant,,ENST00000507164,;ADGRL3,3_prime_UTR_variant,,ENST00000506700,;ADGRL3,3_prime_UTR_variant,,ENST00000504896,;ADGRL3,3_prime_UTR_variant,,ENST00000514157,;ADGRL3-AS1,downstream_gene_variant,,ENST00000506704,;ADGRL3-AS1,downstream_gene_variant,,ENST00000504135,;ADGRL3-AS1,downstream_gene_variant,,ENST00000509461,; G ENST00000514591 Transcript synonymous_variant 4514/6297 4185/4410 1395/1469 T acC/acG 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 25/25 Pfam_domain:PF02354 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 58 62070683 62070683 C G 1 0 0 0 0 0 0 0 1 377 581 21 4 4 ADGRL3 4 62070683 Silent SNP C C3N-00574_T 44361552 62070683 128143872 18 18001 FAM218A 0 . GRCh38 4 164957285 164957286 + Frame_Shift_Del DEL CT CT - novel C3N-00574_T C3N-00574_N CT CT c.263_264delCT p.Pro88ArgfsTer12 p.P88Rfs*12 ENST00000513876 1/1 392 357 35 289 289 0 sindel-varindel-pindel FAM218A,frameshift_variant,p.Pro88ArgfsTer12,ENST00000513876,NM_153027.1;TRIM61,intron_variant,,ENST00000329314,NM_001012414.2; - ENST00000513876 Transcript frameshift_variant 338-339/2175 263-264/474 88/157 P/X cCT/c 1 1 FAM218A HGNC HGNC:26466 protein_coding YES CCDS3807.1 ENSP00000427428 Q96MZ4 UPI000006D0F5 NM_153027.1 1/1 HIGH deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 58 164957285 164957285 CT - 1 0 1 0 1 0 0 0 0 5408 681 24 0 0 FAM218A 4 164957285 Frame_Shift_Del DEL CT C3N-00574_T 102886602 164957285 25257270 19 18002 RASGRF2 0 . GRCh38 5 81180265 81180265 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.2777T>C p.Val926Ala p.V926A ENST00000265080 18/27 136 118 18 115 115 0 strelka-varscan-mutect RASGRF2,missense_variant,p.Val926Ala,ENST00000265080,NM_006909.2;RASGRF2,missense_variant,p.Val926Ala,ENST00000503795,; C ENST00000265080 Transcript missense_variant 2844/8167 2777/3714 926/1237 V/A gTc/gCc 1 1 RASGRF2 HGNC HGNC:9876 protein_coding YES CCDS4052.1 ENSP00000265080 O14827 UPI0000047ABF NM_006909.2 deleterious(0.03) 18/27 hmmpanther:PTHR23113:SF187,hmmpanther:PTHR23113,Gene3D:2ii0A01,SMART_domains:SM00229,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 81180265 81180265 T C 1 0 0 0 0 1 0 0 0 13234 1667 58 5 5 RASGRF2 5 81180265 Missense_Mutation SNP T C3N-00574_T 81180265 100357994 20 18003 UBTD2 0 . GRCh38 5 172234181 172234181 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.248G>A p.Ser83Asn p.S83N ENST00000393792 2/3 384 356 28 294 294 0 strelka-mutect UBTD2,missense_variant,p.Ser83Asn,ENST00000393792,NM_152277.2; T ENST00000393792 Transcript missense_variant 654/3301 248/705 83/234 S/N aGc/aAc 1 -1 UBTD2 HGNC HGNC:24463 protein_coding YES CCDS4379.2 ENSP00000377381 Q8WUN7 UPI000020C12C NM_152277.2 tolerated(0.19) 2/3 Pfam_domain:PF16455,hmmpanther:PTHR13609,hmmpanther:PTHR13609:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 172234181 172234181 C T 1 0 0 0 0 1 0 0 0 17432 797 28 3 3 UBTD2 5 172234181 Missense_Mutation SNP C C3N-00574_T 91053916 172234181 9304078 21 18004 KCNK17 0 . GRCh38 6 39304116 39304116 + Missense_Mutation SNP G G C rs566450809 C3N-00574_T C3N-00574_N G G c.529C>G p.Arg177Gly p.R177G ENST00000373231 4/5 183 159 24 94 94 0 strelka-varscan-mutect KCNK17,missense_variant,p.Arg177Gly,ENST00000453413,NM_001135111.1;KCNK17,missense_variant,p.Arg177Gly,ENST00000373231,NM_031460.3;KCNK17,non_coding_transcript_exon_variant,,ENST00000503878,; C ENST00000373231 Transcript missense_variant 762/1658 529/999 177/332 R/G Cgg/Ggg rs566450809 1 -1 KCNK17 HGNC HGNC:14465 protein_coding YES CCDS4842.1 ENSP00000362328 Q96T54 UPI0000127A59 NM_031460.3 deleterious(0.03) 4/5 hmmpanther:PTHR11003:SF24,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs566450809 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 58 39304116 39304116 G C 1 0 0 0 0 1 0 0 0 7981 1086 38 4 4 KCNK17 6 39304116 Missense_Mutation SNP G C3N-00574_T 39304116 131501863 22 18005 POU6F2 0 . GRCh38 7 39433236 39433236 + Missense_Mutation SNP A A G novel C3N-00574_T C3N-00574_N A A c.1186A>G p.Ile396Val p.I396V ENST00000403058 8/11 218 186 32 163 163 0 strelka-varscan-mutect POU6F2,missense_variant,p.Ile396Val,ENST00000518318,NM_001166018.1;POU6F2,missense_variant,p.Ile341Val,ENST00000559001,;POU6F2,missense_variant,p.Ile396Val,ENST00000403058,NM_007252.3;POU6F2,missense_variant,p.Ile341Val,ENST00000524147,;POU6F2,missense_variant,p.Ile388Val,ENST00000520104,;POU6F2,missense_variant,p.Ile95Val,ENST00000416452,; G ENST00000403058 Transcript missense_variant 1340/2335 1186/2076 396/691 I/V Atc/Gtc 1 1 POU6F2 HGNC HGNC:21694 protein_coding YES CCDS34620.2 ENSP00000384004 P78424 UPI0000480E81 NM_007252.3 tolerated(0.24) 8/11 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF68 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 58 39433236 39433236 A G 1 0 0 0 0 1 0 0 0 12401 333 12 5 5 POU6F2 7 39433236 Missense_Mutation SNP A C3N-00574_T 39433236 119912737 23 18006 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-00574_T C3N-00574_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 3484 212 3272 432 432 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 58 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-00574_T 15741536 55174772 104171201 24 18007 FLNC 0 . GRCh38 7 128837209 128837209 + Silent SNP C C T rs370425863 C3N-00574_T C3N-00574_N C C c.651C>T p.= p.N217N ENST00000325888 3/48 222 200 22 134 134 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;FLNC,upstream_gene_variant,,ENST00000388853,; T ENST00000325888 Transcript synonymous_variant 912/9188 651/8178 217/2725 N aaC/aaT rs370425863 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 3/48 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS rs370425863 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 58 128837209 128837209 C T 1 0 0 0 0 0 0 0 1 5791 535 19 1 1 FLNC 7 128837209 Silent SNP C C3N-00574_T 73662437 128837209 30508764 25 18008 PRSS1 0 . GRCh38 7 142750650 142750650 + Missense_Mutation SNP C C A novel C3N-00574_T C3N-00574_N C C c.136C>A p.His46Asn p.H46N ENST00000311737 2/5 379 348 31 335 335 0 varscan-mutect PRSS1,missense_variant,p.His46Asn,ENST00000486171,;PRSS1,missense_variant,p.His46Asn,ENST00000612126,;PRSS1,missense_variant,p.His46Asn,ENST00000311737,NM_002769.4;PRSS1,missense_variant,p.His46Asn,ENST00000619214,;TRBC2,intron_variant,,ENST00000637077,;TRBC2,intron_variant,,ENST00000610416,;TRBC2,intron_variant,,ENST00000636844,;PRSS1,upstream_gene_variant,,ENST00000492062,;PRSS1,non_coding_transcript_exon_variant,,ENST00000485223,;PRSS1,non_coding_transcript_exon_variant,,ENST00000497041,;PRSS1,upstream_gene_variant,,ENST00000463701,; A ENST00000311737 Transcript missense_variant 142/800 136/744 46/247 H/N Cac/Aac 1 1 PRSS1 HGNC HGNC:9475 protein_coding YES CCDS5872.1 ENSP00000308720 P07477 UPI0000001309 NM_002769.4 tolerated(0.08) 2/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24264:SF12,hmmpanther:PTHR24264,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 58 142750650 142750650 C A 1 0 0 0 0 1 0 0 0 12761 594 21 2 2 PRSS1 7 142750650 Missense_Mutation SNP C C3N-00574_T 13913441 142750650 16595323 26 18009 PIP4K2A 0 . GRCh38 10 22573424 22573424 + Missense_Mutation SNP G G A novel C3N-00574_T C3N-00574_N G G c.526C>T p.Pro176Ser p.P176S ENST00000376573 5/10 198 182 16 175 175 0 strelka-varscan-mutect PIP4K2A,missense_variant,p.Pro176Ser,ENST00000376573,NM_005028.4;PIP4K2A,missense_variant,p.Pro117Ser,ENST00000545335,;PIP4K2A,missense_variant,p.Pro22Ser,ENST00000323883,;PIP4K2A,missense_variant,p.Pro22Ser,ENST00000604912,;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000422321,; A ENST00000376573 Transcript missense_variant 755/3802 526/1221 176/406 P/S Ccc/Tcc 1 -1 PIP4K2A HGNC HGNC:8997 protein_coding YES CCDS7141.1 ENSP00000365757 P48426 UPI0000001052 NM_005028.4 deleterious(0) 5/10 Gene3D:2gk9B01,Pfam_domain:PF01504,PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF21,SMART_domains:SM00330,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 58 22573424 22573424 G A 1 0 0 0 0 1 0 0 0 12031 1174 41 3 3 PIP4K2A 10 22573424 Missense_Mutation SNP G C3N-00574_T 22573424 111223998 27 18010 MUC5B 0 . GRCh38 11 1251315 1251315 + Missense_Mutation SNP C C G rs751375768 C3N-00574_T C3N-00574_N C C c.14435C>G p.Thr4812Ser p.T4812S ENST00000529681 31/49 482 385 97 268 268 0 strelka-varscan-mutect MUC5B,missense_variant,p.Thr4812Ser,ENST00000529681,NM_002458.2;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,; G ENST00000529681 Transcript missense_variant 14493/17911 14435/17289 4812/5762 T/S aCt/aGt rs751375768 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.39) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs751375768 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 58 1251315 1251315 C G 1 0 0 0 0 1 0 0 0 9979 565 20 4 4 MUC5B 11 1251315 Missense_Mutation SNP C C3N-00574_T 1251315 133835307 28 18011 APOA4 0 . GRCh38 11 116821446 116821446 + Silent SNP G G A rs201385362 C3N-00574_T C3N-00574_N G G c.612C>T p.= p.Y204Y ENST00000357780 3/3 545 490 55 421 421 0 strelka-varscan-mutect APOA4,synonymous_variant,p.=,ENST00000357780,NM_000482.3; A ENST00000357780 Transcript synonymous_variant 727/1473 612/1191 204/396 Y taC/taT rs201385362 1 -1 APOA4 HGNC HGNC:602 protein_coding YES CCDS31681.1 ENSP00000350425 P06727 UPI00001AE660 NM_000482.3 3/3 hmmpanther:PTHR18976:SF1,hmmpanther:PTHR18976,Gene3D:1.20.120.20,Pfam_domain:PF01442,Pfam_domain:PF01442,Superfamily_domains:0053393 LOW 1 SNV 1 1 PASS rs201385362 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 58 116821446 116821446 G A 1 0 0 0 0 0 0 0 1 905 1140 40 1 1 APOA4 11 116821446 Silent SNP G C3N-00574_T 115570131 116821446 18265176 29 18012 SIAE 0 . GRCh38 11 124669489 124669489 + Missense_Mutation SNP T T C novel C3N-00574_T C3N-00574_N T T c.100A>G p.Asn34Asp p.N34D ENST00000263593 2/10 501 365 136 447 447 0 strelka-varscan-mutect SIAE,missense_variant,p.Asn34Asp,ENST00000263593,NM_170601.4;SIAE,5_prime_UTR_variant,,ENST00000545756,;SIAE,5_prime_UTR_variant,,ENST00000618733,NM_001199922.1;SPA17,upstream_gene_variant,,ENST00000532692,;SPA17,upstream_gene_variant,,ENST00000227135,NM_017425.3;SIAE,non_coding_transcript_exon_variant,,ENST00000525730,;SPA17,upstream_gene_variant,,ENST00000529498,;SIAE,non_coding_transcript_exon_variant,,ENST00000436137,;SIAE,non_coding_transcript_exon_variant,,ENST00000533613,; C ENST00000263593 Transcript missense_variant 273/5583 100/1572 34/523 N/D Aat/Gat 1 -1 SIAE HGNC HGNC:18187 protein_coding YES CCDS8449.1 ENSP00000263593 Q9HAT2 UPI0000073B2D NM_170601.4 tolerated(1) 2/10 hmmpanther:PTHR22901,hmmpanther:PTHR22901:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 124669489 124669489 T C 1 0 0 0 0 1 0 0 0 14562 1754 61 5 5 SIAE 11 124669489 Missense_Mutation SNP T C3N-00574_T 7848043 124669489 10417133 30 18013 SLC6A12 0 . GRCh38 12 197399 197399 + Silent SNP G G T rs753915121 C3N-00574_T C3N-00574_N G G c.1053C>A p.= p.P351P ENST00000424061 11/17 159 143 16 102 102 0 strelka-varscan-mutect SLC6A12,synonymous_variant,p.=,ENST00000424061,NM_003044.4;SLC6A12,synonymous_variant,p.=,ENST00000397296,;SLC6A12,synonymous_variant,p.=,ENST00000359674,NM_001122847.2,NM_001122848.2;SLC6A12,synonymous_variant,p.=,ENST00000536824,NM_001206931.1;RP11-283I3.1,downstream_gene_variant,,ENST00000544067,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000535498,;SLC6A12,downstream_gene_variant,,ENST00000538272,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000545058,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000542825,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000544782,;SLC6A12,downstream_gene_variant,,ENST00000538580,;SLC6A12,downstream_gene_variant,,ENST00000540094,; T ENST00000424061 Transcript synonymous_variant 1608/3332 1053/1845 351/614 P ccC/ccA rs753915121 1 -1 SLC6A12 HGNC HGNC:11045 protein_coding YES CCDS8501.1 ENSP00000399136 P48065 UPI000013C8DB NM_003044.4 11/17 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF118 LOW 1 SNV 1 1 PASS rs753915121 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 58 197399 197399 G T 1 0 0 0 0 0 0 0 1 14958 1335 47 2 2 SLC6A12 12 197399 Silent SNP G C3N-00574_T 197399 133077910 31 18014 H1FNT 0 . GRCh38 12 48329588 48329588 + Silent SNP G G T C3N-00574_T C3N-00574_N G G c.297G>T p.= p.A99A ENST00000335017 1/1 350 306 44 245 244 1 strelka-varscan-mutect H1FNT,synonymous_variant,p.=,ENST00000335017,NM_181788.1;RP11-370I10.10,upstream_gene_variant,,ENST00000612739,;RP11-370I10.4,downstream_gene_variant,,ENST00000549699,; T ENST00000335017 Transcript synonymous_variant 609/1300 297/768 99/255 A gcG/gcT COSM3792621 1 1 H1FNT HGNC HGNC:24893 protein_coding YES CCDS8762.1 ENSP00000334805 Q75WM6 A0A140VK96 UPI00001AA15C NM_181788.1 1/1 hmmpanther:PTHR11467,hmmpanther:PTHR11467:SF14 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 58 48329588 48329588 G T 1 0 0 0 0 0 0 0 1 6803 1074 38 1 1 H1FNT 12 48329588 Silent SNP G C3N-00574_T 48132189 48329588 84945721 32 18015 KRT2 0 . GRCh38 12 52649923 52649923 + Silent SNP C C G rs780098277 C3N-00574_T C3N-00574_N C C c.852G>C p.= p.T284T ENST00000309680 3/9 428 276 152 339 339 0 strelka-varscan-mutect KRT2,synonymous_variant,p.=,ENST00000309680,NM_000423.2;KRT2,non_coding_transcript_exon_variant,,ENST00000547106,; G ENST00000309680 Transcript synonymous_variant 874/2403 852/1920 284/639 T acG/acC rs780098277,COSM401351,COSM940803 1 -1 KRT2 HGNC HGNC:6439 protein_coding YES CCDS8835.1 ENSP00000310861 P35908 UPI0000367804 NM_000423.2 3/9 hmmpanther:PTHR23239:SF134,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593,Prints_domain:PR01276 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs780098277 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 58 52649923 52649923 C G 1 0 0 0 0 0 0 0 1 8339 755 27 4 4 KRT2 12 52649923 Silent SNP C C3N-00574_T 4320335 52649923 80625386 33 18016 LRIG3 0 . GRCh38 12 58877752 58877752 + Silent SNP C C T novel C3N-00574_T C3N-00574_N C C c.2184G>A p.= p.L728L ENST00000320743 15/19 2372 1306 1066 314 314 0 strelka-varscan-mutect LRIG3,synonymous_variant,p.=,ENST00000320743,NM_153377.4;LRIG3,synonymous_variant,p.=,ENST00000379141,NM_001136051.2;LRIG3,upstream_gene_variant,,ENST00000550825,;LRIG3,3_prime_UTR_variant,,ENST00000433272,;LRIG3,upstream_gene_variant,,ENST00000552646,;LRIG3,downstream_gene_variant,,ENST00000547329,; T ENST00000320743 Transcript synonymous_variant 2471/4070 2184/3360 728/1119 L ctG/ctA 1 -1 LRIG3 HGNC HGNC:30991 protein_coding YES CCDS8960.1 ENSP00000326759 Q6UXM1 UPI0000035BB5 NM_153377.4 15/19 PROSITE_profiles:PS50835,hmmpanther:PTHR24367:SF242,hmmpanther:PTHR24367,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 58 58877752 58877752 C T 1 0 0 0 0 0 0 0 1 8841 813 29 3 3 LRIG3 12 58877752 Silent SNP C C3N-00574_T 6227829 58877752 74397557 34 18017 MED4 0 . GRCh38 13 48077176 48077176 + Nonsense_Mutation SNP G G C novel C3N-00574_T C3N-00574_N G G c.776C>G p.Ser259Ter p.S259* ENST00000258648 7/7 110 73 37 163 163 0 strelka-varscan-mutect MED4,stop_gained,p.Ser259Ter,ENST00000258648,NM_014166.3;MED4,stop_gained,p.Ser213Ter,ENST00000378586,NM_001270629.1;MED4,stop_gained,p.Ser237Ter,ENST00000417167,;MED4-AS1,non_coding_transcript_exon_variant,,ENST00000422483,;MED4,stop_gained,p.Ser90Ter,ENST00000495013,; C ENST00000258648 Transcript stop_gained 802/2022 776/813 259/270 S/* tCa/tGa 1 -1 MED4 HGNC HGNC:17903 protein_coding YES CCDS9408.1 ENSP00000258648 Q9NPJ6 A0A024RDY7 UPI0000129871 NM_014166.3 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR13208,hmmpanther:PTHR13208:SF2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 58 48077176 48077176 G C 1 0 0 0 0 0 1 0 0 9389 1294 45 4 4 MED4 13 48077176 Nonsense_Mutation SNP G C3N-00574_T 48077176 66287152 35 18018 PCDH8 0 . GRCh38 13 52848309 52848309 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.128G>A p.Gly43Asp p.G43D ENST00000377942 1/3 188 161 27 168 168 0 strelka-varscan-mutect PCDH8,missense_variant,p.Gly43Asp,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Gly43Asp,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; T ENST00000377942 Transcript missense_variant 332/5088 128/3213 43/1070 G/D gGc/gAc 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 deleterious(0.02) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 52848309 52848309 C T 1 0 0 0 0 1 0 0 0 11604 739 26 3 3 PCDH8 13 52848309 Missense_Mutation SNP C C3N-00574_T 4771133 52848309 61516019 36 18019 SPRY2 0 . GRCh38 13 80337233 80337235 + In_Frame_Del DEL AGC AGC - novel C3N-00574_T C3N-00574_N AGC AGC c.471_473delGCT p.Glu157_Leu158delinsAsp p.E157_L158delinsD ENST00000377102 2/2 76 70 6 75 75 0 sindel-varindel-pindel SPRY2,inframe_deletion,p.Glu157_Leu158delinsAsp,ENST00000377102,NM_001318537.1;SPRY2,inframe_deletion,p.Glu157_Leu158delinsAsp,ENST00000377104,NM_005842.2; - ENST00000377102 Transcript inframe_deletion 1449-1451/2708 471-473/948 157-158/315 EL/D gaGCTc/gac 1 -1 SPRY2 HGNC HGNC:11270 protein_coding YES CCDS9463.1 ENSP00000366306 O43597 UPI0000001301 NM_001318537.1 2/2 hmmpanther:PTHR12365,hmmpanther:PTHR12365:SF8 MODERATE 1 deletion 1 1 PASS . . 0 200 10 0 0 0 0 0 -12.96774 0.9999367 1 1 1 0 - 7 5 58 80337233 80337233 AGC - 1 0 1 0 1 0 0 0 0 15462 304 11 0 0 SPRY2 13 80337233 In_Frame_Del DEL AGC C3N-00574_T 27488924 80337233 34027095 37 18020 CHD2 0 . GRCh38 15 92953430 92953430 + Missense_Mutation SNP C C G novel C3N-00574_T C3N-00574_N C C c.1576C>G p.Leu526Val p.L526V ENST00000394196 14/39 418 339 79 379 379 0 strelka-mutect CHD2,missense_variant,p.Leu526Val,ENST00000394196,NM_001271.3;CHD2,missense_variant,p.Leu526Val,ENST00000626874,;CHD2,downstream_gene_variant,,ENST00000420239,NM_001042572.2;CHD2,downstream_gene_variant,,ENST00000626782,;CHD2,downstream_gene_variant,,ENST00000637613,;CHD2,non_coding_transcript_exon_variant,,ENST00000635856,;CHD2,non_coding_transcript_exon_variant,,ENST00000628181,;CHD2,upstream_gene_variant,,ENST00000627200,;CHD2,missense_variant,p.Leu317Val,ENST00000636881,;CHD2,non_coding_transcript_exon_variant,,ENST00000637572,;RP11-437B10.1,downstream_gene_variant,,ENST00000630790,;CHD2,downstream_gene_variant,,ENST00000630016,; G ENST00000394196 Transcript missense_variant 2152/9363 1576/5487 526/1828 L/V Ctg/Gtg 1 1 CHD2 HGNC HGNC:1917 protein_coding YES CCDS10374.2 ENSP00000377747 O14647 UPI0000E8A85C NM_001271.3 deleterious(0) 14/39 PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF538,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 58 92953430 92953430 C G 1 0 0 0 0 1 0 0 0 3084 680 24 4 4 CHD2 15 92953430 Missense_Mutation SNP C C3N-00574_T 92953430 9037759 38 18021 TP53 0 . GRCh38 17 7674250 7674254 + Frame_Shift_Del DEL CACAT CACAT - C3N-00574_T C3N-00574_N CACAT CACAT c.709_713delATGTG p.Met237Ter p.M237* ENST00000269305 7/11 366 195 171 303 303 0 sindel-varindel-pindel TP53,frameshift_variant,p.Met237Ter,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.Met237Ter,ENST00000420246,;TP53,frameshift_variant,p.Met198Ter,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.Met198Ter,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.Met237Ter,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.Met198Ter,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.Met237Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.Met198Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.Met237Ter,ENST00000445888,;TP53,frameshift_variant,p.Met198Ter,ENST00000619485,;TP53,frameshift_variant,p.Met105Ter,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.Met78Ter,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.Met105Ter,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.Met78Ter,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.Met105Ter,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.Met78Ter,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.Met237Ter,ENST00000359597,;TP53,frameshift_variant,p.Met226Ter,ENST00000615910,;TP53,frameshift_variant,p.Met237Ter,ENST00000413465,;TP53,frameshift_variant,p.Met105Ter,ENST00000509690,;TP53,frameshift_variant,p.Met144Ter,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,frameshift_variant,p.Met198Ter,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; - ENST00000269305 Transcript frameshift_variant 899-903/2579 709-713/1182 237-238/393 MC/X ATGTGt/t TP53_g.13346_13350del,COSM4437812,COSM4437813,COSM4437814,COSM4437815,COSM4437816,COSM45503 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,1,1,1,1,1,1 HIGH 1 deletion 1 0,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 58 7674250 7674250 CACAT - 1 0 1 0 1 0 0 0 0 16859 478 17 0 0 TP53 17 7674250 Frame_Shift_Del DEL CACAT C3N-00574_T 7674250 75583191 39 18022 MYH1 0 . GRCh38 17 10514014 10514015 + Frame_Shift_Ins INS - - T novel C3N-00574_T C3N-00574_N - - c.643dupA p.Met215AsnfsTer28 p.M215Nfs*28 ENST00000226207 7/40 333 307 26 278 278 0 sindel-varindel MYH1,frameshift_variant,p.Met215AsnfsTer28,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript frameshift_variant 738-739/6024 643-644/5820 215/1939 M/NX atg/aAtg 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 7/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 58 10514014 10514014 - T 1 0 1 1 0 0 0 0 0 10029 231 8 0 0 MYH1 17 10514014 Frame_Shift_Ins INS - C3N-00574_T 2839764 10514014 72743427 40 18023 FMNL1 0 . GRCh38 17 45246229 45246229 + Missense_Mutation SNP G G A rs780634604 C3N-00574_T C3N-00574_N G G c.3110G>A p.Arg1037Gln p.R1037Q ENST00000331495 25/27 103 91 12 63 63 0 strelka-varscan-mutect FMNL1,missense_variant,p.Arg1037Gln,ENST00000331495,NM_005892.3;FMNL1,missense_variant,p.Arg615Gln,ENST00000587489,;FMNL1,missense_variant,p.Arg367Gln,ENST00000586643,;FMNL1,missense_variant,p.Arg70Gln,ENST00000586092,;FMNL1,3_prime_UTR_variant,,ENST00000328118,;FMNL1,3_prime_UTR_variant,,ENST00000589911,;CTD-2020K17.4,intron_variant,,ENST00000420431,;CTD-2020K17.3,upstream_gene_variant,,ENST00000587534,;MAP3K14-AS1,upstream_gene_variant,,ENST00000590100,;MAP3K14-AS1,upstream_gene_variant,,ENST00000592422,;CTD-2020K17.4,downstream_gene_variant,,ENST00000591361,;MAP3K14-AS1,upstream_gene_variant,,ENST00000588504,;MAP3K14-AS1,upstream_gene_variant,,ENST00000585346,;MAP3K14-AS1,upstream_gene_variant,,ENST00000588698,;MAP3K14-AS1,upstream_gene_variant,,ENST00000591263,;CTD-2020K17.4,downstream_gene_variant,,ENST00000589518,;FMNL1,non_coding_transcript_exon_variant,,ENST00000587856,; A ENST00000331495 Transcript missense_variant 3446/4101 3110/3303 1037/1100 R/Q cGg/cAg rs780634604 1 1 FMNL1 HGNC HGNC:1212 protein_coding YES CCDS11497.1 ENSP00000329219 O95466 UPI0000246EE9 NM_005892.3 tolerated(0.22) 25/27 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF188,Low_complexity_(Seg):seg,SMART_domains:SM00498 MODERATE 1 SNV 1 1 PASS rs780634604 . 0 204 6 0 0 0 0 0 -19.99999 0.9999999 1 1 1 0 A 3 1 58 45246229 45246229 G A 1 0 0 0 0 1 0 0 0 5807 1116 39 1 1 FMNL1 17 45246229 Missense_Mutation SNP G C3N-00574_T 34732215 45246229 38011212 41 18024 BRD4 0 . GRCh38 19 15257159 15257159 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.1356G>A p.Met452Ile p.M452I ENST00000263377 8/20 78 66 12 72 72 0 strelka-varscan-mutect BRD4,missense_variant,p.Met452Ile,ENST00000263377,NM_058243.2;BRD4,missense_variant,p.Met452Ile,ENST00000371835,NM_014299.2;BRD4,missense_variant,p.Met452Ile,ENST00000360016,;BRD4,missense_variant,p.Met452Ile,ENST00000594841,;BRD4,non_coding_transcript_exon_variant,,ENST00000602230,;BRD4,non_coding_transcript_exon_variant,,ENST00000594842,;BRD4,upstream_gene_variant,,ENST00000595926,; T ENST00000263377 Transcript missense_variant 1578/7169 1356/4089 452/1362 M/I atG/atA 1 -1 BRD4 HGNC HGNC:13575 protein_coding YES CCDS12328.1 ENSP00000263377 O60885 UPI0000126ACE NM_058243.2 deleterious(0.02) 8/20 Gene3D:1.20.920.10,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF143,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 15257159 15257159 C T 1 0 0 0 0 1 0 0 0 1674 710 25 3 3 BRD4 19 15257159 Missense_Mutation SNP C C3N-00574_T 15257159 43360457 42 18025 ZNF181 0 . GRCh38 19 34741436 34741436 + Missense_Mutation SNP G G A rs748135943 C3N-00574_T C3N-00574_N G G c.1055G>A p.Arg352His p.R352H ENST00000492450 4/4 108 101 7 121 121 0 varscan-mutect ZNF181,missense_variant,p.Arg352His,ENST00000492450,NM_001029997.3;ZNF181,missense_variant,p.Arg396His,ENST00000392232,;ZNF181,missense_variant,p.Arg351His,ENST00000459757,NM_001145665.1;ZNF181,downstream_gene_variant,,ENST00000595708,;ZNF181,downstream_gene_variant,,ENST00000599244,;ZNF181,downstream_gene_variant,,ENST00000593781,;ZNF181,non_coding_transcript_exon_variant,,ENST00000448715,; A ENST00000492450 Transcript missense_variant 1144/5086 1055/1716 352/571 R/H cGt/cAt rs748135943,COSM3404098,COSM3404099,COSM3404100 1 1 ZNF181 HGNC HGNC:12971 protein_coding YES CCDS32990.2 ENSP00000420727 Q2M3W8 UPI000020207A NM_001029997.3 tolerated(0.14) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs748135943 . 0 206 4 0 0 0 0 0 -14.17946 1 1 1 1 0 A 3 1 58 34741436 34741436 G A 1 0 0 0 0 1 0 0 0 18329 1145 40 1 1 ZNF181 19 34741436 Missense_Mutation SNP G C3N-00574_T 19484277 34741436 23876180 43 18026 CPT1C 0 . GRCh38 19 49700724 49700724 + Missense_Mutation SNP G G A C3N-00574_T C3N-00574_N G G c.322G>A p.Ala108Thr p.A108T ENST00000392518 5/20 237 223 14 151 150 1 strelka-varscan-mutect CPT1C,missense_variant,p.Ala108Thr,ENST00000392518,NM_001199752.2;CPT1C,missense_variant,p.Ala108Thr,ENST00000405931,NM_001136052.2;CPT1C,missense_variant,p.Ala108Thr,ENST00000323446,NM_152359.2;CPT1C,missense_variant,p.Ala108Thr,ENST00000598293,NM_001199753.1;CPT1C,missense_variant,p.Ala108Thr,ENST00000598396,;CPT1C,missense_variant,p.Ala108Thr,ENST00000594587,;CPT1C,intron_variant,,ENST00000595969,;CPT1C,downstream_gene_variant,,ENST00000602019,;CPT1C,downstream_gene_variant,,ENST00000598714,;CPT1C,3_prime_UTR_variant,,ENST00000598259,;CPT1C,non_coding_transcript_exon_variant,,ENST00000599023,;CPT1C,intron_variant,,ENST00000295404,;CPT1C,intron_variant,,ENST00000595568,;CPT1C,upstream_gene_variant,,ENST00000596701,;CPT1C,downstream_gene_variant,,ENST00000600944,;CPT1C,downstream_gene_variant,,ENST00000596922,;CPT1C,upstream_gene_variant,,ENST00000594431,;CPT1C,downstream_gene_variant,,ENST00000594038,; A ENST00000392518 Transcript missense_variant 694/2910 322/2412 108/803 A/T Gcg/Acg COSM3389220 1 1 CPT1C HGNC HGNC:18540 protein_coding YES CCDS12779.1 ENSP00000376303 Q8TCG5 A0A024QZE3 UPI0000071C78 NM_001199752.2 tolerated(0.36) 5/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR22589:SF55,hmmpanther:PTHR22589 1 MODERATE 1 SNV 2 1 1 PASS rs1243005888 . 0 208 0 2 0 0 0 0 -16.79998 0.9999995 1 1 1 0 A 3 1 58 49700724 49700724 G A 1 0 0 0 0 1 0 0 0 3630 1087 38 1 1 CPT1C 19 49700724 Missense_Mutation SNP G C3N-00574_T 14959288 49700724 8916892 44 18027 ACPT 0 . GRCh38 19 50791769 50791769 + Silent SNP C C T novel C3N-00574_T C3N-00574_N C C c.417C>T p.= p.I139I ENST00000270593 4/11 136 126 10 71 71 0 strelka-varscan-mutect ACPT,synonymous_variant,p.=,ENST00000270593,NM_033068.2;CTD-2568A17.1,intron_variant,,ENST00000636757,;CTD-2568A17.8,downstream_gene_variant,,ENST00000594114,; T ENST00000270593 Transcript synonymous_variant 417/1347 417/1281 139/426 I atC/atT 1 1 ACPT HGNC HGNC:14376 protein_coding YES CCDS12802.1 ENSP00000270593 Q9BZG2 UPI0000048D54 NM_033068.2 4/11 hmmpanther:PTHR11567,hmmpanther:PTHR11567:SF110,Gene3D:3.40.50.1240,Pfam_domain:PF00328,Superfamily_domains:SSF53254 LOW 1 SNV 2 1 PASS rs1449685112 . 0 206 2 2 0 0 0 0 -14.19957 0.9999914 1 1 1 0 T 2 4 58 50791769 50791769 C T 1 0 0 0 0 0 0 0 1 210 845 30 3 3 ACPT 19 50791769 Silent SNP C C3N-00574_T 1091045 50791769 7825847 45 18028 KIR2DL3 0 . GRCh38 19 54741992 54741992 + Missense_Mutation SNP A A C novel C3N-00574_T C3N-00574_N A A c.83A>C p.Lys28Thr p.K28T ENST00000342376 3/8 260 237 23 155 154 1 varscan-mutect KIR2DL3,missense_variant,p.Lys28Thr,ENST00000342376,NM_015868.2;CTB-61M7.1,intron_variant,,ENST00000400864,; C ENST00000342376 Transcript missense_variant 114/1590 83/1026 28/341 K/T aAa/aCa 1 1 KIR2DL3 HGNC HGNC:6331 protein_coding YES CCDS33107.1 ENSP00000342215 P43628 E3NZD8 UPI000012DB1C NM_015868.2 deleterious(0) 3/8 hmmpanther:PTHR11738:SF119,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 58 54741992 54741992 A C 1 0 0 0 0 1 0 0 0 8182 14 1 5 5 KIR2DL3 19 54741992 Missense_Mutation SNP A C3N-00574_T 3950223 54741992 3875624 46 18029 NLRP9 0 . GRCh38 19 55733246 55733246 + Missense_Mutation SNP C C G novel C3N-00574_T C3N-00574_N C C c.585G>C p.Glu195Asp p.E195D ENST00000332836 2/9 288 263 25 165 165 0 strelka-varscan-mutect NLRP9,missense_variant,p.Glu195Asp,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Glu195Asp,ENST00000590200,;RN7SKP109,upstream_gene_variant,,ENST00000410592,; G ENST00000332836 Transcript missense_variant 613/3484 585/2976 195/991 E/D gaG/gaC 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 deleterious(0.05) 2/9 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 G 3 3 58 55733246 55733246 C G 1 0 0 0 0 1 0 0 0 10522 912 32 4 4 NLRP9 19 55733246 Missense_Mutation SNP C C3N-00574_T 991254 55733246 2884370 47 18030 SNTA1 0 . GRCh38 20 33438977 33438977 + Silent SNP T T A novel C3N-00574_T C3N-00574_N T T c.360A>T p.= p.G120G ENST00000217381 2/8 910 812 98 431 430 1 strelka-varscan-mutect SNTA1,synonymous_variant,p.=,ENST00000217381,NM_003098.2; A ENST00000217381 Transcript synonymous_variant 632/2342 360/1518 120/505 G ggA/ggT 1 -1 SNTA1 HGNC HGNC:11167 protein_coding YES CCDS13220.1 ENSP00000217381 Q13424 UPI0000135B08 NM_003098.2 2/8 PROSITE_profiles:PS50106,PROSITE_profiles:PS50003,hmmpanther:PTHR10554:SF6,hmmpanther:PTHR10554,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,SMART_domains:SM00233,Superfamily_domains:SSF50156 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 58 33438977 33438977 T A 1 0 0 0 0 0 0 0 1 15191 1422 50 4 4 SNTA1 20 33438977 Silent SNP T C3N-00574_T 33438977 31005190 48 18031 PLCG1 0 . GRCh38 20 41163396 41163396 + Missense_Mutation SNP C C T C3N-00574_T C3N-00574_N C C c.808C>T p.Arg270Cys p.R270C ENST00000244007 10/33 296 184 112 180 178 2 strelka-varscan-mutect PLCG1,missense_variant,p.Arg270Cys,ENST00000373271,NM_182811.1;PLCG1,missense_variant,p.Arg270Cys,ENST00000244007,NM_002660.2;PLCG1,downstream_gene_variant,,ENST00000483646,;PLCG1,upstream_gene_variant,,ENST00000617873,;PLCG1,non_coding_transcript_exon_variant,,ENST00000492148,;PLCG1,non_coding_transcript_exon_variant,,ENST00000470528,;PLCG1,upstream_gene_variant,,ENST00000483175,;PLCG1,upstream_gene_variant,,ENST00000477870,;PLCG1,upstream_gene_variant,,ENST00000465571,;PLCG1,downstream_gene_variant,,ENST00000490253,;PLCG1,upstream_gene_variant,,ENST00000473632,; T ENST00000244007 Transcript missense_variant 1005/5285 808/3876 270/1291 R/C Cgc/Tgc COSM3911298 1 1 PLCG1 HGNC HGNC:9065 protein_coding YES CCDS13313.1 ENSP00000244007 P19174 UPI00001B94DD NM_002660.2 deleterious(0.05) 10/33 hmmpanther:PTHR10336:SF52,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000952,Superfamily_domains:SSF47473 1 MODERATE 1 SNV 5 1 1 PASS rs1422530185 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 58 41163396 41163396 C T 1 0 0 0 0 1 0 0 0 12129 884 31 1 1 PLCG1 20 41163396 Missense_Mutation SNP C C3N-00574_T 7724419 41163396 23280771 49 18032 HUWE1 0 . GRCh38 X 53575698 53575698 + Missense_Mutation SNP C C T rs199846544 C3N-00574_T C3N-00574_N C C c.5975G>A p.Arg1992Gln p.R1992Q ENST00000342160 44/83 141 110 31 96 95 1 strelka-varscan-mutect HUWE1,missense_variant,p.Arg1992Gln,ENST00000342160,;HUWE1,missense_variant,p.Arg1992Gln,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Arg1983Gln,ENST00000612484,; T ENST00000342160 Transcript missense_variant 6433/14796 5975/13125 1992/4374 R/Q cGg/cAg rs199846544,COSM2968491,COSM2968492 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC deleterious_low_confidence(0.01) 44/83 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs199846544 . 0 205 3 2 0 0 0 0 -20 0.9999971 1 1 1 0 T 3 4 58 53575698 53575698 C T 1 0 0 0 0 1 0 0 0 7357 652 23 1 1 HUWE1 23 53575698 Missense_Mutation SNP C C3N-00574_T 53575698 102465197 50 18033 RRAGB 0 . GRCh38 X 55722265 55722265 + Missense_Mutation SNP C C T novel C3N-00574_T C3N-00574_N C C c.206C>T p.Thr69Ile p.T69I ENST00000262850 3/11 49 43 6 37 37 0 strelka-mutect RRAGB,missense_variant,p.Thr69Ile,ENST00000374941,NM_006064.4;RRAGB,missense_variant,p.Thr69Ile,ENST00000262850,NM_016656.3;RRAGB,missense_variant,p.Thr31Ile,ENST00000414239,;RRAGB,non_coding_transcript_exon_variant,,ENST00000498762,; T ENST00000262850 Transcript missense_variant 649/1573 206/1125 69/374 T/I aCa/aTa 1 1 RRAGB HGNC HGNC:19901 protein_coding YES CCDS14372.1 ENSP00000262850 Q5VZM2 UPI00001AE856 NM_016656.3 deleterious(0) 3/11 Gene3D:3.40.50.300,Pfam_domain:PF04670,hmmpanther:PTHR11259,hmmpanther:PTHR11259:SF4,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -14.737 1 1 1 1 0 T 3 4 58 55722265 55722265 C T 1 0 0 0 0 1 0 0 0 13927 478 17 3 3 RRAGB 23 55722265 Missense_Mutation SNP C C3N-00574_T 2146567 55722265 100318630 51 18034 EDA2R 0 . GRCh38 X 66604490 66604490 + Missense_Mutation SNP G G A rs755280381 C3N-00574_T C3N-00574_N G G c.283C>T p.Arg95Cys p.R95C ENST00000396050 3/7 62 52 10 32 32 0 strelka-varscan-mutect EDA2R,missense_variant,p.Arg95Cys,ENST00000451436,NM_001199687.2;EDA2R,missense_variant,p.Arg95Cys,ENST00000396050,NM_001242310.1;EDA2R,missense_variant,p.Arg95Cys,ENST00000374719,NM_001324206.1,NM_021783.3;EDA2R,missense_variant,p.Arg95Cys,ENST00000253392,; A ENST00000396050 Transcript missense_variant 293/3429 283/957 95/318 R/C Cgc/Tgc rs755280381 1 -1 EDA2R HGNC HGNC:17756 protein_coding YES CCDS56603.1 ENSP00000379365 Q9HAV5 UPI00001B037F NM_001242310.1 tolerated(0.1) 3/7 hmmpanther:PTHR12120:SF8,hmmpanther:PTHR12120 MODERATE 1 SNV 5 1 PASS rs755280381 . 0 202 8 0 0 0 0 0 -19.99903 0.9999984 1 1 1 0 A 3 1 58 66604490 66604490 G A 1 0 0 0 0 1 0 0 0 4732 1145 40 1 1 EDA2R 23 66604490 Missense_Mutation SNP G C3N-00574_T 10882225 66604490 89436405 52 18035 TGIF2LX 0 . GRCh38 X 89922685 89922685 + Silent SNP G G A novel C3N-00574_T C3N-00574_N G G c.600G>A p.= p.P200P ENST00000561129 1/1 258 242 16 213 213 0 varscan-mutect TGIF2LX,synonymous_variant,p.=,ENST00000561129,;TGIF2LX,synonymous_variant,p.=,ENST00000283891,NM_138960.3; A ENST00000561129 Transcript synonymous_variant 730/928 600/726 200/241 P ccG/ccA 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11850:SF16,hmmpanther:PTHR11850 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -18.92762 0.9999996 1 1 1 0 A 2 1 58 89922685 89922685 G A 1 0 0 0 0 0 0 0 1 16260 1132 40 1 1 TGIF2LX 23 89922685 Silent SNP G C3N-00574_T 23318195 89922685 66118210 53 18036 CAPN6 0 . GRCh38 X 111251648 111251648 + Missense_Mutation SNP C C G novel C3N-00574_T C3N-00574_N C C c.794G>C p.Gly265Ala p.G265A ENST00000324068 6/13 124 111 13 88 88 0 strelka-varscan-mutect CAPN6,missense_variant,p.Gly265Ala,ENST00000324068,NM_014289.3; G ENST00000324068 Transcript missense_variant 962/3568 794/1926 265/641 G/A gGa/gCa 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 deleterious(0.03) 6/13 PROSITE_profiles:PS50203,hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183,Pfam_domain:PF00648,Gene3D:3.90.70.10,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 58 111251648 111251648 C G 1 0 0 0 0 1 0 0 0 2324 855 30 4 4 CAPN6 23 111251648 Missense_Mutation SNP C C3N-00574_T 21328963 111251648 44789247 54 18037 MAGEA12 0 . GRCh38 X 152736947 152736947 + Silent SNP C C T rs782159959 C3N-00574_T C3N-00574_N C C c.786C>T p.= p.P262P ENST00000393900 3/3 363 304 59 209 209 0 strelka-varscan-mutect MAGEA12,synonymous_variant,p.=,ENST00000393900,NM_001166386.3;MAGEA12,synonymous_variant,p.=,ENST00000393869,NM_001166387.3;MAGEA12,synonymous_variant,p.=,ENST00000357916,NM_005367.6;CSAG1,upstream_gene_variant,,ENST00000370291,;CSAG1,upstream_gene_variant,,ENST00000370287,NM_153478.2;CSAG1,upstream_gene_variant,,ENST00000452779,NM_001102576.2;CSAG4,intron_variant,,ENST00000361201,;CSAG1,upstream_gene_variant,,ENST00000361211,;CSAG4,upstream_gene_variant,,ENST00000583763,; T ENST00000393900 Transcript synonymous_variant 1140/1853 786/945 262/314 P ccC/ccT rs782159959,COSM175949 1 1 MAGEA12 HGNC HGNC:6799 protein_coding YES CCDS76048.1 ENSP00000377478 P43365 Q6FHH8 UPI0000000C51 NM_001166386.3 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF74,Pfam_domain:PF01454,SMART_domains:SM01373 0,1 LOW 1 SNV 1 0,1 1 PASS rs782159959 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 58 152736947 152736947 C T 1 0 0 0 0 0 0 0 1 9082 639 23 1 1 MAGEA12 23 152736947 Silent SNP C C3N-00574_T 41485299 152736947 3303948 55 18038 SGIP1 0 . GRCh38 1 66635959 66635959 + Missense_Mutation SNP G G A rs372902905 C3N-00578_T C3N-00578_N G G c.115G>A p.Glu39Lys p.E39K ENST00000371037 4/25 318 216 102 276 276 0 strelka-varscan-mutect SGIP1,missense_variant,p.Glu39Lys,ENST00000371037,NM_032291.2;SGIP1,missense_variant,p.Glu39Lys,ENST00000424320,;SGIP1,intron_variant,,ENST00000371039,NM_001308203.1;SGIP1,intron_variant,,ENST00000237247,;SGIP1,non_coding_transcript_exon_variant,,ENST00000483060,;SGIP1,intron_variant,,ENST00000468286,; A ENST00000371037 Transcript missense_variant 192/7768 115/2487 39/828 E/K Gaa/Aaa rs372902905,COSM911719 1 1 SGIP1 HGNC HGNC:25412 protein_coding YES CCDS30744.1 ENSP00000360076 Q9BQI5 UPI000045891B NM_032291.2 tolerated_low_confidence(0.38) 4/25 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372902905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 59 66635959 66635959 G A 1 0 0 0 0 1 0 0 0 14466 1059 37 1 1 SGIP1 1 66635959 Missense_Mutation SNP G C3N-00578_T 66635959 182320463 1 18039 TDRKH 0 . GRCh38 1 151776575 151776575 + Missense_Mutation SNP T T A novel C3N-00578_T C3N-00578_N T T c.908A>T p.His303Leu p.H303L ENST00000368822 7/14 144 100 44 85 85 0 strelka-varscan-mutect TDRKH,missense_variant,p.His303Leu,ENST00000368822,;TDRKH,missense_variant,p.His303Leu,ENST00000368824,NM_001083965.1;TDRKH,missense_variant,p.His303Leu,ENST00000458431,NM_001083963.1;TDRKH,missense_variant,p.His299Leu,ENST00000368823,;TDRKH,missense_variant,p.His258Leu,ENST00000368825,NM_001083964.1;TDRKH,missense_variant,p.His303Leu,ENST00000368827,NM_006862.3;TDRKH,missense_variant,p.His303Leu,ENST00000440583,;TDRKH,downstream_gene_variant,,ENST00000526378,;TDRKH,downstream_gene_variant,,ENST00000484421,;TDRKH,3_prime_UTR_variant,,ENST00000525790,;TDRKH,3_prime_UTR_variant,,ENST00000526413,;TDRKH,downstream_gene_variant,,ENST00000486986,;TDRKH,downstream_gene_variant,,ENST00000494725,;TDRKH,downstream_gene_variant,,ENST00000530202,; A ENST00000368822 Transcript missense_variant 1542/3093 908/1686 303/561 H/L cAt/cTt 1 -1 TDRKH HGNC HGNC:11713 protein_coding YES CCDS41394.1 ENSP00000357812 Q9Y2W6 UPI0000204267 tolerated(0.09) 7/14 hmmpanther:PTHR22948 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 59 151776575 151776575 T A 1 0 0 0 0 1 0 0 0 16147 1464 51 4 4 TDRKH 1 151776575 Missense_Mutation SNP T C3N-00578_T 85140616 151776575 97179847 2 18040 SPEG 0 . GRCh38 2 219448060 219448060 + Missense_Mutation SNP C C T novel C3N-00578_T C3N-00578_N C C c.902C>T p.Pro301Leu p.P301L ENST00000312358 4/41 273 219 54 277 277 0 strelka-varscan-mutect SPEG,missense_variant,p.Pro301Leu,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Pro197Leu,ENST00000396698,;SPEG,missense_variant,p.Pro148Leu,ENST00000431523,;SPEG,missense_variant,p.Pro151Leu,ENST00000435853,;SPEG,missense_variant,p.Pro152Leu,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,non_coding_transcript_exon_variant,,ENST00000491248,;SPEG,non_coding_transcript_exon_variant,,ENST00000497065,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,3_prime_UTR_variant,,ENST00000452101,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; T ENST00000312358 Transcript missense_variant 1034/10782 902/9804 301/3267 P/L cCg/cTg 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.51) 4/41 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1156992455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 219448060 219448060 C T 1 0 0 0 0 1 0 0 0 15387 652 23 1 1 SPEG 2 219448060 Missense_Mutation SNP C C3N-00578_T 219448060 22745469 3 18041 DHX30 0 . GRCh38 3 47827407 47827407 + Missense_Mutation SNP G G A novel C3N-00578_T C3N-00578_N G G c.185G>A p.Gly62Glu p.G62E ENST00000445061 5/22 251 208 43 176 176 0 strelka-varscan-mutect DHX30,missense_variant,p.Gly62Glu,ENST00000445061,NM_138615.2;DHX30,missense_variant,p.Gly34Glu,ENST00000348968,;DHX30,missense_variant,p.Gly90Glu,ENST00000457607,;DHX30,missense_variant,p.Gly62Glu,ENST00000446256,;DHX30,missense_variant,p.Gly23Glu,ENST00000619982,NM_014966.3;DHX30,non_coding_transcript_exon_variant,,ENST00000470959,;DHX30,non_coding_transcript_exon_variant,,ENST00000471082,;DHX30,downstream_gene_variant,,ENST00000492893,;DHX30,3_prime_UTR_variant,,ENST00000395745,;DHX30,3_prime_UTR_variant,,ENST00000441384,;DHX30,downstream_gene_variant,,ENST00000415400,; A ENST00000445061 Transcript missense_variant 592/4065 185/3585 62/1194 G/E gGa/gAa 1 1 DHX30 HGNC HGNC:16716 protein_coding YES CCDS2759.1 ENSP00000405620 Q7L2E3 A0A024R2T6 UPI000007112B NM_138615.2 tolerated(0.99) 5/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 59 47827407 47827407 G A 1 0 0 0 0 1 0 0 0 4308 1174 41 3 3 DHX30 3 47827407 Missense_Mutation SNP G C3N-00578_T 47827407 150468152 4 18042 CELSR3 0 . GRCh38 3 48656263 48656263 + Missense_Mutation SNP T T C novel C3N-00578_T C3N-00578_N T T c.4502A>G p.Gln1501Arg p.Q1501R ENST00000164024 3/35 327 257 70 297 297 0 strelka-varscan-mutect CELSR3,missense_variant,p.Gln1501Arg,ENST00000164024,NM_001407.2; C ENST00000164024 Transcript missense_variant 4783/11956 4502/9939 1501/3312 Q/R cAg/cGg 1 -1 CELSR3 HGNC HGNC:3230 protein_coding YES CCDS2775.1 ENSP00000164024 Q9NYQ7 UPI00001AE5A6 NM_001407.2 tolerated(0.21) 3/35 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF38,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 59 48656263 48656263 T C 1 0 0 0 0 1 0 0 0 2930 1580 55 5 5 CELSR3 3 48656263 Missense_Mutation SNP T C3N-00578_T 828856 48656263 149639296 5 18043 USP4 0 . GRCh38 3 49325830 49325830 + Missense_Mutation SNP G G C C3N-00578_T C3N-00578_N G G c.376C>G p.Leu126Val p.L126V ENST00000265560 4/22 206 155 51 128 128 0 strelka-varscan-mutect USP4,missense_variant,p.Leu126Val,ENST00000351842,NM_199443.2;USP4,missense_variant,p.Leu126Val,ENST00000265560,NM_003363.3;USP4,missense_variant,p.Leu126Val,ENST00000416417,NM_001251877.1;USP4,missense_variant,p.Leu126Val,ENST00000415188,;USP4,non_coding_transcript_exon_variant,,ENST00000491791,;USP4,non_coding_transcript_exon_variant,,ENST00000464168,;USP4,intron_variant,,ENST00000486549,; C ENST00000265560 Transcript missense_variant 423/3126 376/2892 126/963 L/V Ctg/Gtg COSM1309262 1 -1 USP4 HGNC HGNC:12627 protein_coding YES CCDS2793.1 ENSP00000265560 Q13107 A0A024R2T0 UPI000013D63C NM_003363.3 tolerated(0.08) 4/22 Gene3D:3jyuB01 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 59 49325830 49325830 G C 1 0 0 0 0 1 0 0 0 17613 991 35 4 4 USP4 3 49325830 Missense_Mutation SNP G C3N-00578_T 669567 49325830 148969729 6 18044 ECT2 0 . GRCh38 3 172762720 172762720 + Missense_Mutation SNP A A G novel C3N-00578_T C3N-00578_N A A c.919A>G p.Arg307Gly p.R307G ENST00000392692 10/25 147 109 38 93 93 0 strelka-mutect ECT2,missense_variant,p.Arg276Gly,ENST00000540509,NM_001258316.1;ECT2,missense_variant,p.Arg275Gly,ENST00000417960,;ECT2,missense_variant,p.Arg307Gly,ENST00000392692,NM_001258315.1;ECT2,missense_variant,p.Arg276Gly,ENST00000232458,NM_018098.5;ECT2,missense_variant,p.Arg276Gly,ENST00000441497,;ECT2,downstream_gene_variant,,ENST00000428567,;ECT2,downstream_gene_variant,,ENST00000415665,;ECT2,upstream_gene_variant,,ENST00000444250,; G ENST00000392692 Transcript missense_variant 1095/4158 919/2745 307/914 R/G Aga/Gga 1 1 ECT2 HGNC HGNC:3155 protein_coding YES CCDS58860.1 ENSP00000376457 Q9H8V3 UPI00003DFD0A NM_001258315.1 tolerated(0.13) 10/25 Gene3D:3.40.50.10190,Pfam_domain:PF00533,PROSITE_profiles:PS50172,hmmpanther:PTHR16777,hmmpanther:PTHR16777:SF2,SMART_domains:SM00292,Superfamily_domains:SSF52113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 59 172762720 172762720 A G 1 0 0 0 0 1 0 0 0 4729 64 3 5 5 ECT2 3 172762720 Missense_Mutation SNP A C3N-00578_T 123436890 172762720 25532839 7 18045 PCDHA8 0 . GRCh38 5 140843570 140843570 + Missense_Mutation SNP A A G novel C3N-00578_T C3N-00578_N A A c.2249A>G p.Tyr750Cys p.Y750C ENST00000531613 1/4 306 275 31 251 251 0 strelka-varscan-mutect PCDHA8,missense_variant,p.Tyr750Cys,ENST00000531613,NM_018911.2;PCDHA8,missense_variant,p.Tyr750Cys,ENST00000378123,NM_031856.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,upstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA9,upstream_gene_variant,,ENST00000532602,NM_031857.1; G ENST00000531613 Transcript missense_variant 2249/5260 2249/2853 750/950 Y/C tAc/tGc 1 1 PCDHA8 HGNC HGNC:8674 protein_coding YES CCDS54919.1 ENSP00000434655 Q9Y5H6 UPI00001273D0 NM_018911.2 tolerated_low_confidence(0.07) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF125 MODERATE 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 59 140843570 140843570 A G 1 0 0 0 0 1 0 0 0 11617 391 14 5 5 PCDHA8 5 140843570 Missense_Mutation SNP A C3N-00578_T 140843570 40694689 8 18046 PCDHGA2 0 . GRCh38 5 141340738 141340738 + Silent SNP C C A rs777268988 C3N-00578_T C3N-00578_N C C c.1767C>A p.= p.T589T ENST00000394576 1/4 488 407 81 430 429 1 strelka-varscan-mutect PCDHGA2,synonymous_variant,p.=,ENST00000394576,NM_018915.3;PCDHGA2,synonymous_variant,p.=,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; A ENST00000394576 Transcript synonymous_variant 1767/4605 1767/2799 589/932 T acC/acA rs777268988 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs777268988 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 59 141340738 141340738 C A 1 0 0 0 0 0 0 0 1 11641 581 21 2 2 PCDHGA2 5 141340738 Silent SNP C C3N-00578_T 497168 141340738 40197521 9 18047 SLC17A4 0 . GRCh38 6 25779088 25779088 + Missense_Mutation SNP T T C novel C3N-00578_T C3N-00578_N T T c.1394T>C p.Leu465Pro p.L465P ENST00000377905 12/12 210 171 39 207 207 0 strelka-mutect SLC17A4,missense_variant,p.Leu411Pro,ENST00000439485,NM_001286121.1;SLC17A4,missense_variant,p.Leu465Pro,ENST00000377905,NM_005495.2;SLC17A4,3_prime_UTR_variant,,ENST00000397076,;SLC17A1,downstream_gene_variant,,ENST00000244527,NM_005074.3;SLC17A1,downstream_gene_variant,,ENST00000377886,; C ENST00000377905 Transcript missense_variant 1513/3616 1394/1494 465/497 L/P cTt/cCt 1 1 SLC17A4 HGNC HGNC:10932 protein_coding YES CCDS4564.1 ENSP00000367137 Q9Y2C5 A0A024R013 UPI0000073585 NM_005495.2 deleterious(0) 12/12 Gene3D:1.20.1250.20,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF284,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 59 25779088 25779088 T C 1 0 0 0 0 1 0 0 0 14684 1609 56 5 5 SLC17A4 6 25779088 Missense_Mutation SNP T C3N-00578_T 25779088 145026891 10 18048 TRIB1 0 . GRCh38 8 125436165 125436165 + Silent SNP G G A novel C3N-00578_T C3N-00578_N G G c.813G>A p.= p.G271G ENST00000311922 3/3 485 359 126 379 378 1 strelka-varscan-mutect TRIB1,synonymous_variant,p.=,ENST00000311922,NM_025195.3;TRIB1,synonymous_variant,p.=,ENST00000519576,;TRIB1,synonymous_variant,p.=,ENST00000520847,NM_001282985.1;TRIB1,downstream_gene_variant,,ENST00000521778,; A ENST00000311922 Transcript synonymous_variant 1395/3635 813/1119 271/372 G ggG/ggA 1 1 TRIB1 HGNC HGNC:16891 protein_coding YES CCDS6357.1 ENSP00000312150 Q96RU8 UPI00000717B2 NM_025195.3 3/3 PROSITE_profiles:PS50011,hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF17,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 59 125436165 125436165 G A 1 0 0 0 0 0 0 0 1 16971 1219 43 3 3 TRIB1 8 125436165 Silent SNP G C3N-00578_T 125436165 19702471 11 18049 OTUD1 0 . GRCh38 10 23439627 23439627 + Missense_Mutation SNP C C A novel C3N-00578_T C3N-00578_N C C c.170C>A p.Ala57Glu p.A57E ENST00000376495 1/1 75 69 6 72 72 0 strelka-mutect OTUD1,missense_variant,p.Ala57Glu,ENST00000376495,NM_001145373.2; A ENST00000376495 Transcript missense_variant 170/2933 170/1446 57/481 A/E gCg/gAg 1 1 OTUD1 HGNC HGNC:27346 protein_coding YES CCDS44366.1 ENSP00000365678 Q5VV17 UPI0000458A32 NM_001145373.2 tolerated(0.3) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR12419:SF15,hmmpanther:PTHR12419 MODERATE 1 SNV 1 PASS . . 0 205 2 3 0 0 0 0 -10.24429 0.9998596 1 1 1 0 A 3 1 59 23439627 23439627 C A 1 0 0 0 0 1 0 0 0 11381 768 27 1 1 OTUD1 10 23439627 Missense_Mutation SNP C C3N-00578_T 23439627 110357795 12 18050 OR5M3 0 . GRCh38 11 56470040 56470040 + Missense_Mutation SNP G G A C3N-00578_T C3N-00578_N G G c.458C>T p.Thr153Met p.T153M ENST00000312240 1/1 294 265 29 205 205 0 strelka-varscan-mutect OR5M3,missense_variant,p.Thr153Met,ENST00000312240,NM_001004742.2; A ENST00000312240 Transcript missense_variant 458/924 458/924 153/307 T/M aCg/aTg COSM2149020 1 -1 OR5M3 HGNC HGNC:14806 protein_coding YES CCDS31532.1 ENSP00000312208 Q8NGP4 UPI0000041BAA NM_001004742.2 tolerated(0.25) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF17,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS rs1406730292 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 59 56470040 56470040 G A 1 0 0 0 0 1 0 0 0 11244 1145 40 1 1 OR5M3 11 56470040 Missense_Mutation SNP G C3N-00578_T 56470040 78616582 13 18051 FEN1 0 . GRCh38 11 61796266 61796266 + Missense_Mutation SNP A A G novel C3N-00578_T C3N-00578_N A A c.905A>G p.Asn302Ser p.N302S ENST00000305885 2/2 724 578 146 522 522 0 strelka-varscan-mutect FEN1,missense_variant,p.Asn302Ser,ENST00000305885,NM_004111.5;FEN1,missense_variant,p.Asn110Ser,ENST00000535307,;FADS2,intron_variant,,ENST00000574708,;FADS1,downstream_gene_variant,,ENST00000350997,NM_013402.4;TMEM258,upstream_gene_variant,,ENST00000543510,;FEN1,downstream_gene_variant,,ENST00000535723,;TMEM258,upstream_gene_variant,,ENST00000537328,NM_014206.3;TMEM258,upstream_gene_variant,,ENST00000384869,;TMEM258,upstream_gene_variant,,ENST00000545210,;TMEM258,upstream_gene_variant,,ENST00000540434,;TMEM258,upstream_gene_variant,,ENST00000541893,;TMEM258,upstream_gene_variant,,ENST00000257262,;TMEM258,upstream_gene_variant,,ENST00000535297,; G ENST00000305885 Transcript missense_variant 1318/2296 905/1143 302/380 N/S aAt/aGt 1 1 FEN1 HGNC HGNC:3650 protein_coding YES CCDS8010.1 ENSP00000305480 P39748 Q6FHX6 UPI0000050E0F NM_004111.5 deleterious(0.01) 2/2 HAMAP:MF_00614,hmmpanther:PTHR11081,hmmpanther:PTHR11081:SF31,Superfamily_domains:SSF47807 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 59 61796266 61796266 A G 1 0 0 0 0 1 0 0 0 5675 101 4 5 5 FEN1 11 61796266 Missense_Mutation SNP A C3N-00578_T 5326226 61796266 73290356 14 18052 LRFN4 0 . GRCh38 11 66857807 66857807 + Nonsense_Mutation SNP C C A novel C3N-00578_T C3N-00578_N C C c.63C>A p.Cys21Ter p.C21* ENST00000309602 1/2 330 248 82 158 158 0 strelka-varscan-mutect LRFN4,stop_gained,p.Cys21Ter,ENST00000309602,NM_024036.4;LRFN4,stop_gained,p.Cys21Ter,ENST00000393952,;PC,intron_variant,,ENST00000393960,NM_001040716.1;PC,intron_variant,,ENST00000393958,NM_000920.3;PC,intron_variant,,ENST00000393955,NM_022172.2;PC,downstream_gene_variant,,ENST00000524491,;PC,downstream_gene_variant,,ENST00000628663,;PC,upstream_gene_variant,,ENST00000530259,;PC,downstream_gene_variant,,ENST00000530187,;LRFN4,downstream_gene_variant,,ENST00000531590,; A ENST00000309602 Transcript stop_gained 306/2431 63/1908 21/635 C/* tgC/tgA 1 1 LRFN4 HGNC HGNC:28456 protein_coding YES CCDS8153.1 ENSP00000312535 Q6PJG9 A0A024R5I6 UPI0000001C10 NM_024036.4 1/2 hmmpanther:PTHR24373:SF151,hmmpanther:PTHR24373,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS rs1028163083 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 59 66857807 66857807 C A 1 0 0 0 0 0 1 0 0 8834 776 27 1 1 LRFN4 11 66857807 Nonsense_Mutation SNP C C3N-00578_T 5061541 66857807 68228815 15 18053 KMT2D 0 . GRCh38 12 49052935 49052935 + Silent SNP C C T novel C3N-00578_T C3N-00578_N C C c.1092G>A p.= p.Q364Q ENST00000301067 8/54 204 181 23 149 149 0 strelka-varscan-mutect KMT2D,synonymous_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000547610,; T ENST00000301067 Transcript synonymous_variant 1092/19419 1092/16614 364/5537 Q caG/caA 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 8/54 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 59 49052935 49052935 C T 1 0 0 0 0 0 0 0 1 8298 796 28 3 3 KMT2D 12 49052935 Silent SNP C C3N-00578_T 49052935 84222374 16 18054 EML5 0 . GRCh38 14 88696922 88696922 + Missense_Mutation SNP C C T novel C3N-00578_T C3N-00578_N C C c.2269G>A p.Asp757Asn p.D757N ENST00000554922 15/44 188 173 15 91 91 0 strelka-varscan-mutect EML5,missense_variant,p.Asp757Asn,ENST00000554922,NM_183387.2;EML5,missense_variant,p.Asp757Asn,ENST00000380664,;EML5,3_prime_UTR_variant,,ENST00000553281,; T ENST00000554922 Transcript missense_variant 2518/9570 2269/5934 757/1977 D/N Gat/Aat 1 -1 EML5 HGNC HGNC:18197 protein_coding YES CCDS45148.1 ENSP00000451998 Q05BV3 UPI00001C0438 NM_183387.2 tolerated(0.07) 15/44 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF16,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 88696922 88696922 C T 1 0 0 0 0 1 0 0 0 4943 855 30 3 3 EML5 14 88696922 Missense_Mutation SNP C C3N-00578_T 88696922 18346796 17 18055 TRPM1 0 . GRCh38 15 31068053 31068053 + Missense_Mutation SNP G G A rs779477918 C3N-00578_T C3N-00578_N G G c.370C>T p.Leu124Phe p.L124F ENST00000542188 4/27 435 386 49 453 453 0 strelka-varscan-mutect TRPM1,missense_variant,p.Leu124Phe,ENST00000542188,NM_001252020.1;TRPM1,missense_variant,p.Leu85Phe,ENST00000397795,NM_002420.5;TRPM1,missense_variant,p.Leu107Phe,ENST00000256552,NM_001252024.1;TRPM1,missense_variant,p.Leu14Phe,ENST00000558768,;TRPM1,missense_variant,p.Leu85Phe,ENST00000558445,;TRPM1,missense_variant,p.Leu85Phe,ENST00000559177,;TRPM1,downstream_gene_variant,,ENST00000559179,NM_001252030.1;MIR211,upstream_gene_variant,,ENST00000384969,;TRPM1,missense_variant,p.Leu14Phe,ENST00000560801,;TRPM1,missense_variant,p.Leu85Phe,ENST00000560658,; A ENST00000542188 Transcript missense_variant 684/6004 370/4929 124/1642 L/F Ctc/Ttc rs779477918 1 -1 TRPM1 HGNC HGNC:7146 protein_coding YES CCDS58347.1 ENSP00000437849 Q7Z4N2 UPI0001DBB3A9 NM_001252020.1 deleterious(0.01) 4/27 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF13 MODERATE 1 SNV 1 1 PASS rs779477918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 59 31068053 31068053 G A 1 0 0 0 0 1 0 0 0 17091 971 34 3 3 TRPM1 15 31068053 Missense_Mutation SNP G C3N-00578_T 31068053 70923136 18 18056 SLC12A6 0 . GRCh38 15 34254383 34254383 + Silent SNP T T A rs754403127 C3N-00578_T C3N-00578_N T T c.1083A>T p.= p.G361G ENST00000354181 9/26 441 317 124 442 442 0 strelka-varscan-mutect SLC12A6,synonymous_variant,p.=,ENST00000290209,NM_005135.2;SLC12A6,synonymous_variant,p.=,ENST00000354181,;SLC12A6,synonymous_variant,p.=,ENST00000458406,NM_001042494.1;SLC12A6,synonymous_variant,p.=,ENST00000560611,NM_133647.1;SLC12A6,synonymous_variant,p.=,ENST00000397707,NM_001042497.1;SLC12A6,synonymous_variant,p.=,ENST00000397702,NM_001042495.1;SLC12A6,synonymous_variant,p.=,ENST00000558589,NM_001042496.1;SLC12A6,synonymous_variant,p.=,ENST00000560164,;SLC12A6,synonymous_variant,p.=,ENST00000558667,;SLC12A6,downstream_gene_variant,,ENST00000561120,;SLC12A6,downstream_gene_variant,,ENST00000560332,;RP11-1084A12.2,upstream_gene_variant,,ENST00000559867,;SLC12A6,synonymous_variant,p.=,ENST00000561080,;SLC12A6,synonymous_variant,p.=,ENST00000559664,;SLC12A6,synonymous_variant,p.=,ENST00000559523,; A ENST00000354181 Transcript synonymous_variant 1576/4568 1083/3453 361/1150 G ggA/ggT rs754403127 1 -1 SLC12A6 HGNC HGNC:10914 protein_coding YES CCDS58352.1 ENSP00000346112 Q9UHW9 A0A024R9I5 UPI0000135427 9/26 Pfam_domain:PF00324,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF66,TIGRFAM_domain:TIGR00930,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs754403127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 59 34254383 34254383 T A 1 0 0 0 0 0 0 0 1 14652 1538 54 4 4 SLC12A6 15 34254383 Silent SNP T C3N-00578_T 3186330 34254383 67736806 19 18057 POU2F2 0 . GRCh38 19 42099612 42099612 + Missense_Mutation SNP A A C novel C3N-00578_T C3N-00578_N A A c.416T>G p.Leu139Arg p.L139R ENST00000526816 7/14 299 263 36 268 268 0 strelka-varscan-mutect POU2F2,missense_variant,p.Leu139Arg,ENST00000389341,NM_002698.4;POU2F2,missense_variant,p.Leu139Arg,ENST00000342301,;POU2F2,missense_variant,p.Leu100Arg,ENST00000560558,;POU2F2,missense_variant,p.Leu139Arg,ENST00000526816,NM_001207025.2;POU2F2,missense_variant,p.Leu139Arg,ENST00000529067,NM_001247994.1;POU2F2,missense_variant,p.Leu157Arg,ENST00000560804,;POU2F2,missense_variant,p.Leu161Arg,ENST00000560398,;POU2F2,missense_variant,p.Leu139Arg,ENST00000529952,NM_001207026.1;POU2F2,missense_variant,p.Leu198Arg,ENST00000526831,;POU2F2,missense_variant,p.Leu133Arg,ENST00000528894,;POU2F2,upstream_gene_variant,,ENST00000533548,;POU2F2,upstream_gene_variant,,ENST00000598842,;POU2F2,downstream_gene_variant,,ENST00000531773,;POU2F2,3_prime_UTR_variant,,ENST00000534559,;POU2F2,non_coding_transcript_exon_variant,,ENST00000530982,; C ENST00000526816 Transcript missense_variant 432/3218 416/1440 139/479 L/R cTa/cGa 1 -1 POU2F2 HGNC HGNC:9213 protein_coding YES CCDS56095.1 ENSP00000431603 P09086 UPI0000186851 NM_001207025.2 deleterious(0) 7/14 Prints_domain:PR00029,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF46 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 59 42099612 42099612 A C 1 0 0 0 0 1 0 0 0 12388 420 15 5 5 POU2F2 19 42099612 Missense_Mutation SNP A C3N-00578_T 42099612 16518004 20 18058 GIPR 0 . GRCh38 19 45669574 45669574 + Silent SNP G G A novel C3N-00578_T C3N-00578_N G G c.54G>A p.= p.L18L ENST00000590918 2/14 310 259 51 205 205 0 strelka-varscan-mutect GIPR,synonymous_variant,p.=,ENST00000590918,NM_000164.2;GIPR,synonymous_variant,p.=,ENST00000263281,;GIPR,synonymous_variant,p.=,ENST00000304207,;GIPR,upstream_gene_variant,,ENST00000591322,;GIPR,synonymous_variant,p.=,ENST00000585889,;GIPR,upstream_gene_variant,,ENST00000588816,; A ENST00000590918 Transcript synonymous_variant 153/3289 54/1401 18/466 L ctG/ctA 1 1 GIPR HGNC HGNC:4271 protein_coding YES CCDS12671.1 ENSP00000467494 P48546 UPI00000503FD NM_000164.2 2/14 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF315,Prints_domain:PR01129 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 59 45669574 45669574 G A 1 0 0 0 0 0 0 0 1 6277 1306 46 3 3 GIPR 19 45669574 Silent SNP G C3N-00578_T 3569962 45669574 12948042 21 18059 PTPN1 0 . GRCh38 20 50579907 50579907 + Missense_Mutation SNP G G T rs781220884 C3N-00578_T C3N-00578_N G G c.1069G>T p.Ala357Ser p.A357S ENST00000371621 8/10 287 237 50 195 195 0 strelka-varscan-mutect PTPN1,missense_variant,p.Ala357Ser,ENST00000371621,NM_002827.3;PTPN1,missense_variant,p.Ala284Ser,ENST00000541713,NM_001278618.1;RP4-530I15.9,upstream_gene_variant,,ENST00000431019,; T ENST00000371621 Transcript missense_variant 1243/4008 1069/1308 357/435 A/S Gca/Tca rs781220884 1 1 PTPN1 HGNC HGNC:9642 protein_coding YES CCDS13430.1 ENSP00000360683 P18031 A8K3M3 UPI000011DD79 NM_002827.3 tolerated(0.87) 8/10 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF239,PIRSF_domain:PIRSF000926 MODERATE 1 SNV 1 1 PASS rs781220884 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 50579907 50579907 G T 1 0 0 0 0 1 0 0 0 12932 1087 38 1 1 PTPN1 20 50579907 Missense_Mutation SNP G C3N-00578_T 50579907 13864260 22 18060 KCNQ2 0 . GRCh38 20 63414950 63414950 + Missense_Mutation SNP C C T rs774040213 C3N-00578_T C3N-00578_N C C c.1478G>A p.Arg493His p.R493H ENST00000359125 13/17 402 378 24 238 237 1 strelka-varscan-mutect KCNQ2,missense_variant,p.Arg475His,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Arg493His,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Arg465His,ENST00000370224,;KCNQ2,missense_variant,p.Arg292His,ENST00000637193,;KCNQ2,missense_variant,p.Arg453His,ENST00000625514,;KCNQ2,missense_variant,p.Arg465His,ENST00000629241,;KCNQ2,missense_variant,p.Arg465His,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Arg463His,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Arg349His,ENST00000357249,;KCNQ2,missense_variant,p.Arg465His,ENST00000629676,;KCNQ2,missense_variant,p.Arg180His,ENST00000627221,;KCNQ2,missense_variant,p.Arg29His,ENST00000629318,;KCNQ2,upstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000635867,;KCNQ2,upstream_gene_variant,,ENST00000636499,;KCNQ2,downstream_gene_variant,,ENST00000637584,; T ENST00000359125 Transcript missense_variant 1605/3253 1478/2619 493/872 R/H cGc/cAc rs774040213 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious(0.02) 13/17 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF6,Pfam_domain:PF03520 MODERATE 1 SNV 1 1 PASS rs774040213 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 63414950 63414950 C T 1 0 0 0 0 1 0 0 0 7999 768 27 1 1 KCNQ2 20 63414950 Missense_Mutation SNP C C3N-00578_T 12835043 63414950 1029217 23 18061 ZBED1 0 . GRCh38 X 2489457 2489457 + Missense_Mutation SNP C C T novel C3N-00578_T C3N-00578_N C C c.1263G>A p.Met421Ile p.M421I ENST00000381223 2/2 543 434 109 429 428 1 strelka-varscan-mutect ZBED1,missense_variant,p.Met421Ile,ENST00000381223,NM_001171136.1,NM_004729.3;ZBED1,missense_variant,p.Met421Ile,ENST00000381222,;ZBED1,missense_variant,p.Met421Ile,ENST00000381218,NM_001171135.1;DHRSX,intron_variant,,ENST00000334651,NM_145177.2;DHRSX,intron_variant,,ENST00000444280,;DHRSX,intron_variant,,ENST00000412516,;ZBED1,downstream_gene_variant,,ENST00000461691,;DHRSX,intron_variant,,ENST00000430536,;ZBED1,upstream_gene_variant,,ENST00000515319,;DHRSX,intron_variant,,ENST00000478825,;DHRSX,intron_variant,,ENST00000441131,; T ENST00000381223 Transcript missense_variant 1467/4510 1263/2085 421/694 M/I atG/atA 1 -1 ZBED1 HGNC HGNC:447 protein_coding YES CCDS14118.1 ENSP00000370621 O96006 A0A024RBU4 UPI0000073DE9 NM_001171136.1,NM_004729.3 tolerated(0.13) 2/2 hmmpanther:PTHR23272,hmmpanther:PTHR23272:SF35,Superfamily_domains:SSF53098 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 2489457 2489457 C T 1 0 0 0 0 1 0 0 0 18079 594 21 3 3 ZBED1 23 2489457 Missense_Mutation SNP C C3N-00578_T 2489457 153551438 24 18062 NLGN4X 0 . GRCh38 X 5903472 5903472 + Missense_Mutation SNP G G T rs771730382 C3N-00578_T C3N-00578_N G G c.1206C>A p.Phe402Leu p.F402L ENST00000381095 5/6 192 101 91 143 143 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Phe402Leu,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Phe402Leu,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Phe402Leu,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Phe402Leu,ENST00000381092,;NLGN4X,missense_variant,p.Phe403Leu,ENST00000538097,;NLGN4X,upstream_gene_variant,,ENST00000477079,; T ENST00000381095 Transcript missense_variant 1834/5870 1206/2451 402/816 F/L ttC/ttA rs771730382 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0) 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs771730382 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 59 5903472 5903472 G T 1 0 0 0 0 1 0 0 0 10501 1049 37 1 1 NLGN4X 23 5903472 Missense_Mutation SNP G C3N-00578_T 3414015 5903472 150137423 25 18063 TAF1 0 . GRCh38 X 71382632 71382632 + Missense_Mutation SNP A A G novel C3N-00578_T C3N-00578_N A A c.1694A>G p.Lys565Arg p.K565R ENST00000423759 10/39 92 52 40 103 103 0 strelka-varscan-mutect TAF1,missense_variant,p.Lys565Arg,ENST00000423759,NM_001286074.1;TAF1,missense_variant,p.Lys544Arg,ENST00000373790,NM_138923.3;TAF1,missense_variant,p.Lys565Arg,ENST00000276072,NM_004606.4;TAF1,upstream_gene_variant,,ENST00000478305,;TAF1,downstream_gene_variant,,ENST00000483365,;TAF1,upstream_gene_variant,,ENST00000472567,; G ENST00000423759 Transcript missense_variant 1770/7722 1694/5688 565/1895 K/R aAa/aGa 1 1 TAF1 HGNC HGNC:11535 protein_coding YES CCDS69783.1 ENSP00000406549 P21675 UPI000171708A NM_001286074.1 tolerated(0.07) 10/39 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 59 71382632 71382632 A G 1 0 0 0 0 1 0 0 0 15909 14 1 5 5 TAF1 23 71382632 Missense_Mutation SNP A C3N-00578_T 65479160 71382632 84658263 26 18064 ZC3H11A 0 . GRCh38 1 203838052 203838052 + Missense_Mutation SNP A A G novel C3N-00579_T C3N-00579_N A A c.961A>G p.Thr321Ala p.T321A ENST00000545588 10/17 213 153 60 119 119 0 strelka-varscan-mutect ZC3H11A,missense_variant,p.Thr321Ala,ENST00000545588,;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000332127,NM_001319239.1;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000367210,;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000367214,;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000367212,NM_014827.4;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000453771,;ZC3H11A,missense_variant,p.Thr321Ala,ENST00000495527,;RP11-397P13.7,upstream_gene_variant,,ENST00000427282,; G ENST00000545588 Transcript missense_variant 4788/7979 961/2433 321/810 T/A Aca/Gca 1 1 ZC3H11A HGNC HGNC:29093 protein_coding YES CCDS30978.1 ENSP00000438527 O75152 UPI000006F3FD tolerated(1) 10/17 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 60 203838052 203838052 A G 1 0 0 0 0 1 0 0 0 18134 43 2 5 5 ZC3H11A 1 203838052 Missense_Mutation SNP A C3N-00579_T 203838052 45118370 1 18065 OBSCN 0 . GRCh38 1 228372312 228372312 + Silent SNP C C T novel C3N-00579_T C3N-00579_N C C c.24405C>T p.= p.S8135S ENST00000570156 105/116 379 337 42 173 173 0 strelka-varscan-mutect OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000636476,; T ENST00000570156 Transcript synonymous_variant 24479/26925 24405/26772 8135/8923 S tcC/tcT 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 105/116 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 60 228372312 228372312 C T 1 0 0 0 0 0 0 0 1 10889 610 22 3 3 OBSCN 1 228372312 Silent SNP C C3N-00579_T 24534260 228372312 20584110 2 18066 SOX11 0 . GRCh38 2 5694041 5694042 + Frame_Shift_Ins INS - - T novel C3N-00579_T C3N-00579_N - - c.1321dupT p.Tyr441LeufsTer61 p.Y441Lfs*61 ENST00000322002 1/1 83 74 9 60 60 0 sindel-varindel-pindel SOX11,frameshift_variant,p.Tyr441LeufsTer61,ENST00000322002,NM_003108.3;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC010729.1,upstream_gene_variant,,ENST00000455579,;LINC01248,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,; T ENST00000322002 Transcript frameshift_variant 1375-1376/8719 1320-1321/1326 440-441/441 -/X -/T 1 1 SOX11 HGNC HGNC:11191 protein_coding YES CCDS1654.1 ENSP00000322568 P35716 UPI00001362AD NM_003108.3 1/1 PIRSF_domain:PIRSF038098,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF113 HIGH insertion 1 1 PASS . . 0 194 16 0 0 0 0 0 -18.68471 0.9986771 1 1 1 0 T 7 5 60 5694041 5694041 - T 1 0 1 1 0 0 0 0 0 15268 204 8 0 0 SOX11 2 5694041 Frame_Shift_Ins INS - C3N-00579_T 5694041 236499488 3 18067 APOB 0 . GRCh38 2 21013479 21013479 + Silent SNP A A C novel C3N-00579_T C3N-00579_N A A c.3897T>G p.= p.P1299P ENST00000233242 25/29 239 196 43 131 131 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2; C ENST00000233242 Transcript synonymous_variant 4025/14121 3897/13692 1299/4563 P ccT/ccG 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 25/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 60 21013479 21013479 A C 1 0 0 0 0 0 0 0 1 907 59 3 5 5 APOB 2 21013479 Silent SNP A C3N-00579_T 15319438 21013479 221180050 4 18068 SCN2A 0 . GRCh38 2 165388719 165388738 + Frame_Shift_Del DEL GTCTGATCAAAGGAGCAAAG GTCTGATCAAAGGAGCAAAG - novel C3N-00579_T C3N-00579_N GTCTGATCAAAGGAGCAAAG GTCTGATCAAAGGAGCAAAG c.4914_4933delTCTGATCAAAGGAGCAAAGG p.Leu1639AspfsTer17 p.L1639Dfs*17 ENST00000636071 28/28 471 423 48 553 553 0 sindel-varindel-pindel SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000636071,;SCN2A,frameshift_variant,p.Leu1507AspfsTer17,ENST00000636985,;SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000637266,;SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000375437,NM_001040142.1;SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000283256,NM_021007.2;SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000375427,NM_001040143.1;SCN2A,frameshift_variant,p.Leu1639AspfsTer17,ENST00000631182,;SCN2A,3_prime_UTR_variant,,ENST00000636662,;SCN2A,3_prime_UTR_variant,,ENST00000636384,;SCN2A,3_prime_UTR_variant,,ENST00000636769,;SCN2A,3_prime_UTR_variant,,ENST00000636135,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,; - ENST00000636071 Transcript frameshift_variant 5290-5309/9303 4913-4932/6018 1638-1644/2005 RLIKGAK/X cGTCTGATCAAAGGAGCAAAG/c 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 28/28 Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 HIGH 1 deletion 1 1 PASS . . 0 125 2 0 0 0 0 82 -8.613378 0 0 1 0 0 - 7 5 60 165388719 165388719 GTCTGATCAAAGGAGCAAAG - 1 0 1 0 1 0 0 0 0 14185 1145 40 0 0 SCN2A 2 165388719 Frame_Shift_Del DEL GTCTGATCAAAGGAGCAAAG C3N-00579_T 144375240 165388719 76804810 5 18069 LRP2 0 . GRCh38 2 169241098 169241098 + Missense_Mutation SNP C C T novel C3N-00579_T C3N-00579_N C C c.3935G>A p.Cys1312Tyr p.C1312Y ENST00000263816 25/79 110 90 20 80 80 0 strelka-varscan-mutect LRP2,missense_variant,p.Cys1312Tyr,ENST00000263816,NM_004525.2;LRP2,missense_variant,p.Cys1175Tyr,ENST00000443831,; T ENST00000263816 Transcript missense_variant 4221/15808 3935/13968 1312/4655 C/Y tGt/tAt 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 deleterious(0) 25/79 Gene3D:4.10.400.10,PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF232,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 169241098 169241098 C T 1 0 0 0 0 1 0 0 0 8851 478 17 3 3 LRP2 2 169241098 Missense_Mutation SNP C C3N-00579_T 3852379 169241098 72952431 6 18070 TTN 0 . GRCh38 2 178601081 178601081 + Missense_Mutation SNP C C G novel C3N-00579_T C3N-00579_N C C c.55823G>C p.Gly18608Ala p.G18608A ENST00000589042 288/363 79 68 11 42 42 0 strelka-varscan-mutect TTN,missense_variant,p.Gly18608Ala,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Gly16967Ala,ENST00000591111,;TTN,missense_variant,p.Gly16967Ala,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Gly16040Ala,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Gly9543Ala,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Gly9735Ala,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Gly9668Ala,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000592689,;TTN-AS1,downstream_gene_variant,,ENST00000629117,;TTN-AS1,downstream_gene_variant,,ENST00000590932,;TTN-AS1,downstream_gene_variant,,ENST00000591332,;TTN-AS1,downstream_gene_variant,,ENST00000626517,; G ENST00000589042 Transcript missense_variant 56048/109224 55823/107976 18608/35991 G/A gGc/gCc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 288/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -19.99989 0.9999926 1 1 1 0 G 3 3 60 178601081 178601081 C G 1 0 0 0 0 1 0 0 0 17245 739 26 4 4 TTN 2 178601081 Missense_Mutation SNP C C3N-00579_T 9359983 178601081 63592448 7 18071 KAT2B 0 . GRCh38 3 20101391 20101391 + Missense_Mutation SNP G G T novel C3N-00579_T C3N-00579_N G G c.774G>T p.Trp258Cys p.W258C ENST00000263754 5/18 345 274 71 184 183 1 strelka-varscan-mutect KAT2B,missense_variant,p.Trp258Cys,ENST00000263754,NM_003884.4;KAT2B,downstream_gene_variant,,ENST00000426228,; T ENST00000263754 Transcript missense_variant 1229/4833 774/2499 258/832 W/C tgG/tgT 1 1 KAT2B HGNC HGNC:8638 protein_coding YES CCDS2634.1 ENSP00000263754 Q92831 UPI00002132DE NM_003884.4 deleterious(0) 5/18 Pfam_domain:PF06466,PIRSF_domain:PIRSF003048,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF116 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 20101391 20101391 G T 1 0 0 0 0 1 0 0 0 7896 1212 42 2 2 KAT2B 3 20101391 Missense_Mutation SNP G C3N-00579_T 20101391 178194168 8 18072 DCP1A 0 . GRCh38 3 53347392 53347392 + Silent SNP G G A novel C3N-00579_T C3N-00579_N G G c.126C>T p.= p.A42A ENST00000294241 1/9 88 67 21 61 61 0 strelka-varscan-mutect DCP1A,synonymous_variant,p.=,ENST00000610213,NM_018403.6,NM_001290206.1,NM_001290205.1;DCP1A,synonymous_variant,p.=,ENST00000294241,NM_001290204.1;DCP1A,synonymous_variant,p.=,ENST00000559748,;CACNA1D,intron_variant,,ENST00000637424,;DCP1A,intron_variant,,ENST00000560624,;DCP1A,synonymous_variant,p.=,ENST00000560076,; A ENST00000294241 Transcript synonymous_variant 134/1853 126/1635 42/544 A gcC/gcT 1 -1 DCP1A HGNC HGNC:18714 protein_coding YES CCDS74946.1 ENSP00000476046 Q9NPI6 UPI00017A7307 NM_001290204.1 1/9 Gene3D:2.30.29.30,Pfam_domain:PF06058,hmmpanther:PTHR16290,hmmpanther:PTHR16290:SF4,Superfamily_domains:SSF50729 LOW 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 60 53347392 53347392 G A 1 0 0 0 0 0 0 0 1 4100 1335 47 3 3 DCP1A 3 53347392 Silent SNP G C3N-00579_T 33246001 53347392 144948167 9 18073 CACNA2D3 0 . GRCh38 3 54899788 54899788 + Missense_Mutation SNP G G T novel C3N-00579_T C3N-00579_N G G c.2369G>T p.Gly790Val p.G790V ENST00000474759 27/38 247 207 40 163 163 0 strelka-varscan-mutect CACNA2D3,missense_variant,p.Gly790Val,ENST00000474759,NM_018398.2;CACNA2D3,missense_variant,p.Gly790Val,ENST00000288197,;CACNA2D3,missense_variant,p.Gly790Val,ENST00000415676,;CACNA2D3,missense_variant,p.Gly696Val,ENST00000490478,;CACNA2D3,splice_region_variant,,ENST00000620722,;CACNA2D3-AS1,intron_variant,,ENST00000471265,;CACNA2D3,splice_region_variant,,ENST00000471363,; T ENST00000474759 Transcript missense_variant,splice_region_variant 2417/3675 2369/3276 790/1091 G/V gGa/gTa 1 1 CACNA2D3 HGNC HGNC:15460 protein_coding YES CCDS54598.1 ENSP00000419101 Q8IZS8 UPI000004A7BF NM_018398.2 tolerated(0.07) 27/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF25,Pfam_domain:PF08473 MODERATE 1 SNV 1 1 PASS rs1189495439 . 0 207 0 0 2 0 0 0 -19.69855 0.9972153 1 1 1 0 T 3 4 60 54899788 54899788 G T 1 0 0 0 0 1 0 0 0 2238 1188 41 2 2 CACNA2D3 3 54899788 Missense_Mutation SNP G C3N-00579_T 1552396 54899788 143395771 10 18074 DNAH12 0 . GRCh38 3 57453376 57453376 + Nonsense_Mutation SNP G G A novel C3N-00579_T C3N-00579_N G G c.3484C>T p.Gln1162Ter p.Q1162* ENST00000495027 24/74 137 121 16 117 116 1 strelka-varscan-mutect DNAH12,stop_gained,p.Gln1162Ter,ENST00000495027,NM_001291661.1;DNAH12,stop_gained,p.Gln1139Ter,ENST00000351747,; A ENST00000495027 Transcript stop_gained 3665/12146 3484/11883 1162/3960 Q/* Cag/Tag 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 24/74 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 60 57453376 57453376 G A 1 0 0 0 0 0 1 0 0 4414 1299 45 3 3 DNAH12 3 57453376 Nonsense_Mutation SNP G C3N-00579_T 2553588 57453376 140842183 11 18075 DPPA4 0 . GRCh38 3 109330758 109330759 + Frame_Shift_Ins INS - - T rs765696593 C3N-00579_T C3N-00579_N - - c.444dupA p.Leu149IlefsTer14 p.L149Ifs*14 ENST00000335658 5/7 191 141 50 125 124 1 sindel-varindel DPPA4,frameshift_variant,p.Leu149IlefsTer14,ENST00000335658,NM_018189.3;DPPA4,downstream_gene_variant,,ENST00000477303,;DPPA4,non_coding_transcript_exon_variant,,ENST00000478791,;DPPA4,intron_variant,,ENST00000463966,;DPPA4,3_prime_UTR_variant,,ENST00000495679,;DPPA4,non_coding_transcript_exon_variant,,ENST00000475135,;DPPA4,non_coding_transcript_exon_variant,,ENST00000487299,;DPPA4,downstream_gene_variant,,ENST00000489281,; T ENST00000335658 Transcript frameshift_variant 499-500/2817 444-445/915 148-149/304 -/X -/A rs765696593 1 -1 DPPA4 HGNC HGNC:19200 protein_coding YES CCDS33814.1 ENSP00000335306 Q7L190 UPI000022C153 NM_018189.3 5/7 hmmpanther:PTHR16073,hmmpanther:PTHR16073:SF8,Pfam_domain:PF14049 HIGH 1 insertion 1 1 PASS . . 0 159 0 29 20 0 0 0 -20 0.01109156 0 1 0 0 T 7 5 60 109330758 109330758 - T 1 0 1 1 0 0 0 0 0 4551 98 4 0 0 DPPA4 3 109330758 Frame_Shift_Ins INS - C3N-00579_T 51877382 109330758 88964801 12 18076 SH3TC1 0 . GRCh38 4 8233395 8233395 + Missense_Mutation SNP G G A C3N-00579_T C3N-00579_N G G c.3164G>A p.Arg1055Gln p.R1055Q ENST00000245105 14/18 103 88 15 95 95 0 strelka-varscan-mutect SH3TC1,missense_variant,p.Arg1055Gln,ENST00000245105,NM_018986.3;SH3TC1,downstream_gene_variant,,ENST00000507801,;SH3TC1,3_prime_UTR_variant,,ENST00000515682,NM_001318480.1;SH3TC1,3_prime_UTR_variant,,ENST00000502669,;SH3TC1,3_prime_UTR_variant,,ENST00000511002,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000506360,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000502559,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000502350,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000508183,;SH3TC1,non_coding_transcript_exon_variant,,ENST00000513495,; A ENST00000245105 Transcript missense_variant 3231/4226 3164/4011 1055/1336 R/Q cGa/cAa COSM1694137 1 1 SH3TC1 HGNC HGNC:26009 protein_coding YES CCDS3399.1 ENSP00000245105 Q8TE82 UPI000013CB93 NM_018986.3 tolerated(0.09) 14/18 Gene3D:1.25.40.10,hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF3,Superfamily_domains:SSF48452 1 MODERATE 1 SNV 2 1 1 PASS rs1309187912 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 8233395 8233395 G A 1 0 0 0 0 1 0 0 0 14520 1058 37 1 1 SH3TC1 4 8233395 Missense_Mutation SNP G C3N-00579_T 8233395 181981160 13 18077 FRAS1 0 . GRCh38 4 78445575 78445575 + Nonsense_Mutation SNP C C T C3N-00579_T C3N-00579_N C C c.5719C>T p.Gln1907Ter p.Q1907* ENST00000512123 42/74 77 68 9 67 67 0 strelka-varscan-mutect FRAS1,stop_gained,p.Gln1907Ter,ENST00000512123,NM_025074.6;FRAS1,stop_gained,p.Gln1907Ter,ENST00000325942,NM_001166133.1;FRAS1,stop_gained,p.Gln357Ter,ENST00000510944,;FRAS1,3_prime_UTR_variant,,ENST00000264899,;FRAS1,upstream_gene_variant,,ENST00000509802,; T ENST00000512123 Transcript stop_gained 6159/15624 5719/12039 1907/4012 Q/* Caa/Taa COSM3826279,COSM3826280,COSM3826281 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 42/74 Pfam_domain:PF16184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29 1,1,1 HIGH 1 SNV 5 1,1,1 1 PASS . . 0 207 3 0 0 0 0 0 -19.57028 1 1 1 1 0 T 4 4 60 78445575 78445575 C T 1 0 0 0 0 0 1 0 0 5908 827 29 3 3 FRAS1 4 78445575 Nonsense_Mutation SNP C C3N-00579_T 70212180 78445575 111768980 14 18078 ANK2 0 . GRCh38 4 113292492 113292492 + Missense_Mutation SNP C C A novel C3N-00579_T C3N-00579_N C C c.2354C>A p.Ala785Asp p.A785D ENST00000357077 21/46 725 607 118 568 568 0 strelka-varscan-mutect ANK2,missense_variant,p.Ala785Asp,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala785Asp,ENST00000264366,;ANK2,missense_variant,p.Ala764Asp,ENST00000506722,NM_001127493.1;ANK2,missense_variant,p.Ala785Asp,ENST00000394537,NM_020977.3;ANK2,missense_variant,p.Ala800Asp,ENST00000504454,;ANK2,missense_variant,p.Ala731Asp,ENST00000503423,;ANK2,missense_variant,p.Ala757Asp,ENST00000634436,;ANK2,missense_variant,p.Ala764Asp,ENST00000503271,;ANK2,upstream_gene_variant,,ENST00000509550,;ANK2,upstream_gene_variant,,ENST00000502701,; A ENST00000357077 Transcript missense_variant 2407/14196 2354/11874 785/3957 A/D gCc/gAc 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious(0.02) 21/46 Low_complexity_(Seg):seg,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Pfam_domain:PF13857,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 113292492 113292492 C A 1 0 0 0 0 1 0 0 0 721 739 26 2 2 ANK2 4 113292492 Missense_Mutation SNP C C3N-00579_T 34846917 113292492 76922063 15 18079 DNAH5 0 . GRCh38 5 13770861 13770861 + Nonsense_Mutation SNP G G A C3N-00579_T C3N-00579_N G G c.9493C>T p.Gln3165Ter p.Q3165* ENST00000265104 56/79 693 622 71 377 377 0 strelka-varscan-mutect DNAH5,stop_gained,p.Gln3165Ter,ENST00000265104,NM_001369.2;DNAH5,non_coding_transcript_exon_variant,,ENST00000504001,; A ENST00000265104 Transcript stop_gained 9598/15633 9493/13875 3165/4624 Q/* Cag/Tag COSM5529978 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 56/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF12780,Superfamily_domains:SSF52540 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 60 13770861 13770861 G A 1 0 0 0 0 0 1 0 0 4419 1299 45 3 3 DNAH5 5 13770861 Nonsense_Mutation SNP G C3N-00579_T 13770861 167767398 16 18080 OXCT1 0 . GRCh38 5 41870302 41870302 + Silent SNP T T G novel C3N-00579_T C3N-00579_N T T c.57A>C p.= p.G19G ENST00000196371 1/17 708 644 64 407 407 0 strelka-varscan-mutect OXCT1,synonymous_variant,p.=,ENST00000196371,NM_000436.3;OXCT1-AS1,non_coding_transcript_exon_variant,,ENST00000508458,;OXCT1-AS1,non_coding_transcript_exon_variant,,ENST00000510509,; G ENST00000196371 Transcript synonymous_variant 218/3388 57/1563 19/520 G ggA/ggC 1 -1 OXCT1 HGNC HGNC:8527 protein_coding YES CCDS3937.1 ENSP00000196371 P55809 A0A024R040 UPI0000000C9A NM_000436.3 1/17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 60 41870302 41870302 T G 1 0 0 0 0 0 0 0 1 11401 1422 50 5 5 OXCT1 5 41870302 Silent SNP T C3N-00579_T 28099441 41870302 139667957 17 18081 GABBR1 0 . GRCh38 6 29606958 29606958 + Missense_Mutation SNP C C A novel C3N-00579_T C3N-00579_N C C c.2156G>T p.Gly719Val p.G719V ENST00000377034 18/23 352 263 89 269 269 0 strelka-varscan-mutect GABBR1,missense_variant,p.Gly719Val,ENST00000377034,NM_001470.2;GABBR1,missense_variant,p.Gly657Val,ENST00000377016,NM_021904.2;GABBR1,missense_variant,p.Gly602Val,ENST00000377012,NM_021903.2;GABBR1,missense_variant,p.Gly602Val,ENST00000355973,;GABBR1,downstream_gene_variant,,ENST00000376977,;GABBR1,3_prime_UTR_variant,,ENST00000472823,;GABBR1,3_prime_UTR_variant,,ENST00000491829,;GABBR1,3_prime_UTR_variant,,ENST00000494877,;GABBR1,upstream_gene_variant,,ENST00000478931,;GABBR1,downstream_gene_variant,,ENST00000473774,;GABBR1,upstream_gene_variant,,ENST00000488334,;GABBR1,upstream_gene_variant,,ENST00000486434,;GABBR1,downstream_gene_variant,,ENST00000489839,; A ENST00000377034 Transcript missense_variant 2492/4527 2156/2886 719/961 G/V gGc/gTc 1 -1 GABBR1 HGNC HGNC:4070 protein_coding YES CCDS4663.1 ENSP00000366233 Q9UBS5 UPI000004618A NM_001470.2 tolerated(0.57) 18/23 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF42,Pfam_domain:PF00003,Prints_domain:PR01176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 29606958 29606958 C A 1 0 0 0 0 1 0 0 0 6026 739 26 2 2 GABBR1 6 29606958 Missense_Mutation SNP C C3N-00579_T 29606958 141199021 18 18082 TAP1 0 . GRCh38 6 32848792 32848792 + Missense_Mutation SNP C C G novel C3N-00579_T C3N-00579_N C C c.1606G>C p.Glu536Gln p.E536Q ENST00000354258 7/11 488 348 140 335 335 0 strelka-varscan-mutect TAP1,missense_variant,p.Glu536Gln,ENST00000354258,NM_000593.5,NM_001292022.1;PSMB9,intron_variant,,ENST00000395330,;PSMB9,intron_variant,,ENST00000414474,;PSMB8,upstream_gene_variant,,ENST00000374881,NM_004159.4;PSMB8,upstream_gene_variant,,ENST00000374882,NM_148919.3;PSMB8,upstream_gene_variant,,ENST00000395339,;PSMB8-AS1,downstream_gene_variant,,ENST00000453426,;PSMB8-AS1,downstream_gene_variant,,ENST00000412095,;PSMB8-AS1,downstream_gene_variant,,ENST00000429600,;PSMB8-AS1,downstream_gene_variant,,ENST00000458296,;PSMB8-AS1,downstream_gene_variant,,ENST00000413039,;PSMB8-AS1,downstream_gene_variant,,ENST00000415067,;TAP1,non_coding_transcript_exon_variant,,ENST00000486332,;PSMB8,upstream_gene_variant,,ENST00000484003,;TAP1,upstream_gene_variant,,ENST00000487296,; G ENST00000354258 Transcript missense_variant 1768/2959 1606/2427 536/808 E/Q Gag/Cag 1 -1 TAP1 HGNC HGNC:43 protein_coding YES CCDS4758.1 ENSP00000346206 Q03518 A0A0S2Z5A6 UPI000002D4E6 NM_000593.5,NM_001292022.1 deleterious(0.01) 7/11 hmmpanther:PTHR24221:SF249,hmmpanther:PTHR24221,TIGRFAM_domain:TIGR00958,PIRSF_domain:PIRSF002773,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 60 32848792 32848792 C G 1 0 0 0 0 1 0 0 0 15949 922 32 4 4 TAP1 6 32848792 Missense_Mutation SNP C C3N-00579_T 3241834 32848792 137957187 19 18083 PACSIN1 0 . GRCh38 6 34530271 34530271 + Missense_Mutation SNP C C A novel C3N-00579_T C3N-00579_N C C c.817C>A p.Gln273Lys p.Q273K ENST00000620693 7/10 164 125 39 82 82 0 strelka-varscan-mutect PACSIN1,missense_variant,p.Gln273Lys,ENST00000620693,NM_020804.4;PACSIN1,missense_variant,p.Gln273Lys,ENST00000538621,NM_001199583.2;PACSIN1,missense_variant,p.Gln273Lys,ENST00000244458,;PACSIN1,missense_variant,p.Gln231Lys,ENST00000374043,;PACSIN1,downstream_gene_variant,,ENST00000486120,;PACSIN1,downstream_gene_variant,,ENST00000487760,;PACSIN1,downstream_gene_variant,,ENST00000493633,; A ENST00000620693 Transcript missense_variant 1090/4299 817/1335 273/444 Q/K Cag/Aag 1 1 PACSIN1 HGNC HGNC:8570 protein_coding YES CCDS4793.1 ENSP00000484060 Q9BY11 Q5TZC3 UPI000000D983 NM_020804.4 deleterious(0.03) 7/10 PROSITE_profiles:PS51741,hmmpanther:PTHR23065:SF16,hmmpanther:PTHR23065,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS rs1452745537 . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 60 34530271 34530271 C A 1 0 0 0 0 1 0 0 0 11452 711 25 2 2 PACSIN1 6 34530271 Missense_Mutation SNP C C3N-00579_T 1681479 34530271 136275708 20 18084 ABCC10 0 . GRCh38 6 43445842 43445842 + Silent SNP C C T novel C3N-00579_T C3N-00579_N C C c.3274C>T p.= p.L1092L ENST00000372530 15/22 417 324 93 245 245 0 strelka-varscan-mutect ABCC10,synonymous_variant,p.=,ENST00000244533,NM_033450.2;ABCC10,synonymous_variant,p.=,ENST00000372530,NM_001198934.1;DLK2,downstream_gene_variant,,ENST00000357338,NM_206539.2;DLK2,downstream_gene_variant,,ENST00000372488,NM_023932.3;DLK2,downstream_gene_variant,,ENST00000372485,NM_001286656.1,NM_001286655.1;DLK2,downstream_gene_variant,,ENST00000430324,;ABCC10,downstream_gene_variant,,ENST00000372515,;ABCC10,upstream_gene_variant,,ENST00000505344,;ABCC10,non_coding_transcript_exon_variant,,ENST00000463024,;ABCC10,intron_variant,,ENST00000372512,;ABCC10,upstream_gene_variant,,ENST00000437104,;ABCC10,downstream_gene_variant,,ENST00000469856,; T ENST00000372530 Transcript synonymous_variant 3489/5033 3274/4479 1092/1492 L Ctg/Ttg 1 1 ABCC10 HGNC HGNC:52 protein_coding YES CCDS56430.1 ENSP00000361608 Q5T3U5 A0A024RD21 UPI000004A062 NM_001198934.1 15/22 PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF235,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 60 43445842 43445842 C T 1 0 0 0 0 0 0 0 1 54 796 28 3 3 ABCC10 6 43445842 Silent SNP C C3N-00579_T 8915571 43445842 127360137 21 18085 HECW1 0 . GRCh38 7 43444316 43444316 + Missense_Mutation SNP T T A novel C3N-00579_T C3N-00579_N T T c.1144T>A p.Ser382Thr p.S382T ENST00000395891 11/30 274 241 33 150 150 0 strelka-mutect HECW1,missense_variant,p.Ser382Thr,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Ser382Thr,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript missense_variant 1749/9501 1144/4821 382/1606 S/T Tct/Act 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated_low_confidence(0.67) 11/30 Low_complexity_(Seg):seg,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 43444316 43444316 T A 1 0 0 0 0 1 0 0 0 6924 1667 58 4 4 HECW1 7 43444316 Missense_Mutation SNP T C3N-00579_T 43444316 115901657 22 18086 1 13 2 2 17 N T_C 3.678372e-05 HECW1 0 . GRCh38 7 43444332 43444332 + Missense_Mutation SNP C C A C3N-00579_T C3N-00579_N C C c.1160C>A p.Ser387Tyr p.S387Y ENST00000395891 11/30 301 262 39 157 156 1 strelka-mutect HECW1,missense_variant,p.Ser387Tyr,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Ser387Tyr,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript missense_variant 1765/9501 1160/4821 387/1606 S/Y tCc/tAc COSM390862 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated_low_confidence(0.66) 11/30 Low_complexity_(Seg):seg,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 43444332 43444332 C A 1 0 0 0 0 1 0 0 0 6924 855 30 2 2 HECW1 7 43444332 Missense_Mutation SNP C C3N-00579_T 16 43444332 115901641 23 18087 1 13 2 2 17 N T_C 3.678372e-05 ABCA13 0 . GRCh38 7 48275377 48275377 + Missense_Mutation SNP C C T novel C3N-00579_T C3N-00579_N C C c.5711C>T p.Ser1904Phe p.S1904F ENST00000435803 17/62 657 552 105 374 374 0 strelka-varscan-mutect ABCA13,missense_variant,p.Ser1904Phe,ENST00000435803,NM_152701.4;ABCA13,upstream_gene_variant,,ENST00000544596,;ABCA13,upstream_gene_variant,,ENST00000611776,;ABCA13,downstream_gene_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant 5735/17184 5711/15177 1904/5058 S/F tCt/tTt 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.09) 17/62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 48275377 48275377 C T 1 0 0 0 0 1 0 0 0 35 913 32 3 3 ABCA13 7 48275377 Missense_Mutation SNP C C3N-00579_T 4831045 48275377 111070596 24 18088 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-00579_T C3N-00579_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 786 592 194 452 451 1 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 60 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-00579_T 6916445 55191822 104154151 25 18089 LHFPL3 0 . GRCh38 7 104329208 104329208 + Missense_Mutation SNP G G C novel C3N-00579_T C3N-00579_N G G c.387G>C p.Trp129Cys p.W129C ENST00000424859 1/3 106 98 8 47 47 0 strelka-varscan-mutect LHFPL3,missense_variant,p.Trp129Cys,ENST00000424859,NM_199000.2;LHFPL3,missense_variant,p.Trp129Cys,ENST00000401970,; C ENST00000424859 Transcript missense_variant 553/1852 387/669 129/222 W/C tgG/tgC 1 1 LHFPL3 HGNC HGNC:6589 protein_coding YES ENSP00000393128 Q86UP9 UPI000020F876 NM_199000.2 deleterious(0) 1/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR12489,hmmpanther:PTHR12489:SF13,Pfam_domain:PF10242 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.20385 1 1 1 1 0 C 3 2 60 104329208 104329208 G C 1 0 0 0 0 1 0 0 0 8675 1183 41 4 4 LHFPL3 7 104329208 Missense_Mutation SNP G C3N-00579_T 49137386 104329208 55016765 26 18090 GRM8 0 . GRCh38 7 126609456 126609456 + Missense_Mutation SNP G G A novel C3N-00579_T C3N-00579_N G G c.1400C>T p.Ala467Val p.A467V ENST00000339582 8/11 268 234 34 163 163 0 strelka-varscan-mutect GRM8,missense_variant,p.Ala467Val,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Ala467Val,ENST00000358373,NM_001127323.1;GRM8,intron_variant,,ENST00000480995,;GRM8,missense_variant,p.Ala467Val,ENST00000472701,;GRM8,missense_variant,p.Leu491Phe,ENST00000341617,; A ENST00000339582 Transcript missense_variant 2209/4057 1400/2727 467/908 A/V gCt/gTt 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious(0.01) 8/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS rs1469354095 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 126609456 126609456 G A 1 0 0 0 0 1 0 0 0 6685 971 34 3 3 GRM8 7 126609456 Missense_Mutation SNP G C3N-00579_T 22280248 126609456 32736517 27 18091 PDIA4 0 . GRCh38 7 149011972 149011972 + Missense_Mutation SNP G G T novel C3N-00579_T C3N-00579_N G G c.853C>A p.Pro285Thr p.P285T ENST00000286091 6/10 47 42 5 35 35 0 strelka-mutect PDIA4,missense_variant,p.Pro285Thr,ENST00000286091,NM_004911.4; T ENST00000286091 Transcript missense_variant 1086/2903 853/1938 285/645 P/T Cct/Act 1 -1 PDIA4 HGNC HGNC:30167 protein_coding YES CCDS5893.1 ENSP00000286091 P13667 A0A090N8Y2 UPI000004062C NM_004911.4 deleterious(0) 6/10 PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF110,TIGRFAM_domain:TIGR01130,PIRSF_domain:PIRSF036862,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -12.6469 1 1 1 1 0 T 3 4 60 149011972 149011972 G T 1 0 0 0 0 1 0 0 0 11758 1203 42 2 2 PDIA4 7 149011972 Missense_Mutation SNP G C3N-00579_T 22402516 149011972 10334001 28 18092 ZCCHC7 0 . GRCh38 9 37349409 37349409 + Nonsense_Mutation SNP T T A novel C3N-00579_T C3N-00579_N T T c.1040T>A p.Leu347Ter p.L347* ENST00000534928 7/9 329 282 47 141 141 0 strelka-varscan-mutect ZCCHC7,stop_gained,p.Leu347Ter,ENST00000534928,NM_001289121.1,NM_001289120.1;ZCCHC7,stop_gained,p.Leu347Ter,ENST00000336755,NM_032226.2,NM_001289119.1;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000461038,;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000481507,;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000488607,;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000463625,;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000496099,;ZCCHC7,non_coding_transcript_exon_variant,,ENST00000497924,; A ENST00000534928 Transcript stop_gained 1358/2828 1040/1632 347/543 L/* tTa/tAa 1 1 ZCCHC7 HGNC HGNC:26209 protein_coding YES CCDS6608.2 ENSP00000443113 Q8N3Z6 UPI0000036027 NM_001289121.1,NM_001289120.1 7/9 hmmpanther:PTHR23002:SF11,hmmpanther:PTHR23002,Gene3D:4.10.60.10 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 60 37349409 37349409 T A 1 0 0 0 0 0 1 0 0 18168 1764 61 4 4 ZCCHC7 9 37349409 Nonsense_Mutation SNP T C3N-00579_T 37349409 101045308 29 18093 TRPM6 0 . GRCh38 9 74742612 74742612 + Missense_Mutation SNP T T C novel C3N-00579_T C3N-00579_N T T c.5149A>G p.Asn1717Asp p.N1717D ENST00000360774 33/39 474 419 55 305 305 0 strelka-varscan-mutect TRPM6,missense_variant,p.Asn1717Asp,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Asn1712Asp,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Asn1712Asp,ENST00000449912,NM_001177310.1; C ENST00000360774 Transcript missense_variant 5387/8425 5149/6069 1717/2022 N/D Aat/Gat 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 deleterious(0.01) 33/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 74742612 74742612 T C 1 0 0 0 0 1 0 0 0 17096 1754 61 5 5 TRPM6 9 74742612 Missense_Mutation SNP T C3N-00579_T 37393203 74742612 63652105 30 18094 SPTAN1 0 . GRCh38 9 128582734 128582734 + Missense_Mutation SNP G G A rs201168391 C3N-00579_T C3N-00579_N G G c.1691G>A p.Arg564His p.R564H ENST00000372739 14/57 473 379 94 335 335 0 strelka-varscan-mutect SPTAN1,missense_variant,p.Arg564His,ENST00000372731,NM_003127.3;SPTAN1,missense_variant,p.Arg564His,ENST00000372739,NM_001130438.2;SPTAN1,missense_variant,p.Arg564His,ENST00000630804,;SPTAN1,missense_variant,p.Arg564His,ENST00000358161,NM_001195532.1;SPTAN1,missense_variant,p.Arg564His,ENST00000630866,;SPTAN1,non_coding_transcript_exon_variant,,ENST00000635853,;SPTAN1,non_coding_transcript_exon_variant,,ENST00000625282,;SPTAN1,downstream_gene_variant,,ENST00000472211,; A ENST00000372739 Transcript missense_variant 1801/7868 1691/7434 564/2477 R/H cGt/cAt rs201168391 1 1 SPTAN1 HGNC HGNC:11273 protein_coding YES CCDS48036.1 ENSP00000361824 Q13813 UPI000045894C NM_001130438.2 tolerated(0.3) 14/57 hmmpanther:PTHR11915:SF283,hmmpanther:PTHR11915,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs201168391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 128582734 128582734 G A 1 0 0 0 0 1 0 0 0 15473 1145 40 1 1 SPTAN1 9 128582734 Missense_Mutation SNP G C3N-00579_T 53840122 128582734 9811983 31 18095 GTF3C5 0 . GRCh38 9 133042151 133042151 + Missense_Mutation SNP C C T novel C3N-00579_T C3N-00579_N C C c.218C>T p.Pro73Leu p.P73L ENST00000372108 2/12 376 316 60 352 352 0 strelka-varscan-mutect GTF3C5,missense_variant,p.Pro73Leu,ENST00000372097,NM_012087.3;GTF3C5,missense_variant,p.Pro73Leu,ENST00000372108,NM_001122823.1;GTF3C5,missense_variant,p.Pro73Leu,ENST00000342018,;GTF3C5,missense_variant,p.Pro26Leu,ENST00000440319,;GTF3C5,intron_variant,,ENST00000372099,NM_001286709.1;GTF3C5,intron_variant,,ENST00000439697,;GTF3C5,intron_variant,,ENST00000485692,; T ENST00000372108 Transcript missense_variant 226/2110 218/1581 73/526 P/L cCa/cTa 1 1 GTF3C5 HGNC HGNC:4668 protein_coding YES CCDS48050.1 ENSP00000361180 Q9Y5Q8 UPI000046FE5A NM_001122823.1 deleterious(0) 2/12 Pfam_domain:PF09734,hmmpanther:PTHR13230 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 133042151 133042151 C T 1 0 0 0 0 1 0 0 0 6757 594 21 3 3 GTF3C5 9 133042151 Missense_Mutation SNP C C3N-00579_T 4459417 133042151 5352566 32 18096 WAC 0 . GRCh38 10 28608213 28608213 + Nonsense_Mutation SNP C C G C3N-00579_T C3N-00579_N C C c.947C>G p.Ser316Ter p.S316* ENST00000354911 8/14 325 297 28 266 266 0 strelka-varscan-mutect WAC,stop_gained,p.Ser271Ter,ENST00000375664,NM_100264.2;WAC,stop_gained,p.Ser316Ter,ENST00000354911,NM_016628.4;WAC,stop_gained,p.Ser213Ter,ENST00000347934,NM_100486.3;WAC,stop_gained,p.Ser168Ter,ENST00000375646,;WAC,3_prime_UTR_variant,,ENST00000628285,;WAC,3_prime_UTR_variant,,ENST00000428935,;WAC,stop_gained,p.Ser271Ter,ENST00000439676,;WAC,3_prime_UTR_variant,,ENST00000424454,;WAC,non_coding_transcript_exon_variant,,ENST00000345541,;WAC,non_coding_transcript_exon_variant,,ENST00000476046,;WAC,upstream_gene_variant,,ENST00000495268,; G ENST00000354911 Transcript stop_gained 1108/3042 947/1944 316/647 S/* tCa/tGa COSM1297202 1 1 WAC HGNC HGNC:17327 protein_coding YES CCDS7159.1 ENSP00000346986 Q9BTA9 UPI000013D398 NM_016628.4 8/14 hmmpanther:PTHR15911,hmmpanther:PTHR15911:SF6 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 60 28608213 28608213 C G 1 0 0 0 0 0 1 0 0 17807 838 29 4 4 WAC 10 28608213 Nonsense_Mutation SNP C C3N-00579_T 28608213 105189209 33 18097 F2 0 . GRCh38 11 46719826 46719826 + Missense_Mutation SNP G G C novel C3N-00579_T C3N-00579_N G G c.204G>C p.Glu68Asp p.E68D ENST00000311907 2/14 392 338 54 323 323 0 strelka-varscan-mutect F2,missense_variant,p.Glu68Asp,ENST00000311907,NM_001311257.1,NM_000506.3;F2,missense_variant,p.Glu68Asp,ENST00000530231,;F2,missense_variant,p.Glu58Asp,ENST00000442468,;F2,non_coding_transcript_exon_variant,,ENST00000469189,;F2,upstream_gene_variant,,ENST00000490274,; C ENST00000311907 Transcript missense_variant 260/2023 204/1869 68/622 E/D gaG/gaC 1 1 F2 HGNC HGNC:3535 protein_coding YES CCDS31476.1 ENSP00000308541 P00734 UPI0000136ECD NM_001311257.1,NM_000506.3 deleterious(0) 2/14 Gene3D:4.10.740.10,Pfam_domain:PF00594,PIRSF_domain:PIRSF001149,Prints_domain:PR00001,PROSITE_patterns:PS00011,PROSITE_profiles:PS50998,hmmpanther:PTHR24254,hmmpanther:PTHR24254:SF10,SMART_domains:SM00069,Superfamily_domains:SSF57630 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 46719826 46719826 G C 1 0 0 0 0 1 0 0 0 5210 991 35 4 4 F2 11 46719826 Missense_Mutation SNP G C3N-00579_T 46719826 88366796 34 18098 OR5M8 0 . GRCh38 11 56490769 56490769 + Missense_Mutation SNP A A T novel C3N-00579_T C3N-00579_N A A c.602T>A p.Val201Glu p.V201E ENST00000327216 1/1 250 225 25 224 224 0 strelka-varscan-mutect OR5M8,missense_variant,p.Val201Glu,ENST00000327216,NM_001005282.1;CTD-3051L14.13,upstream_gene_variant,,ENST00000525853,; T ENST00000327216 Transcript missense_variant 602/936 602/936 201/311 V/E gTg/gAg 1 -1 OR5M8 HGNC HGNC:14846 protein_coding YES CCDS31533.1 ENSP00000323354 Q8NGP6 A0A126GWD6 UPI00000405CC NM_001005282.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF146,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 56490769 56490769 A T 1 0 0 0 0 1 0 0 0 11245 159 6 4 4 OR5M8 11 56490769 Missense_Mutation SNP A C3N-00579_T 9770943 56490769 78595853 35 18099 RBM14 0 . GRCh38 11 66625460 66625469 + Frame_Shift_Del DEL TGCTGCCCAG TGCTGCCCAG - novel C3N-00579_T C3N-00579_N TGCTGCCCAG TGCTGCCCAG c.1584_1593delTGCTGCCCAG p.Ala529SerfsTer77 p.A529Sfs*77 ENST00000310137 2/3 150 126 24 120 120 0 sindel-varindel-pindel RBM14,frameshift_variant,p.Ala529SerfsTer77,ENST00000310137,NM_006328.3;RBM14-RBM4,intron_variant,,ENST00000412278,NM_001198845.1;RBM14,intron_variant,,ENST00000393979,NM_001198836.1;RBM14-RBM4,intron_variant,,ENST00000500635,NM_001198846.1;RBM14,intron_variant,,ENST00000409738,NM_001198837.1;RBM14,downstream_gene_variant,,ENST00000409372,;RBM14,downstream_gene_variant,,ENST00000443702,;RBM14-RBM4,intron_variant,,ENST00000511114,;RBM14,downstream_gene_variant,,ENST00000461478,;RBM14,downstream_gene_variant,,ENST00000496694,;RBM14-RBM4,intron_variant,,ENST00000421355,; - ENST00000310137 Transcript frameshift_variant 1723-1732/2828 1584-1593/2010 528-531/669 YAAQ/X taTGCTGCCCAG/ta 1 1 RBM14 HGNC HGNC:14219 protein_coding YES CCDS8147.1 ENSP00000311747 Q96PK6 A0A0S2Z4Z0 UPI0000073D46 NM_006328.3 2/3 Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 60 66625460 66625460 TGCTGCCCAG - 1 0 1 0 1 0 0 0 0 13281 1471 51 0 0 RBM14 11 66625460 Frame_Shift_Del DEL TGCTGCCCAG C3N-00579_T 10134691 66625460 68461162 36 18100 KDM2A 0 . GRCh38 11 67231877 67231877 + Missense_Mutation SNP G G A C3N-00579_T C3N-00579_N G G c.1396G>A p.Asp466Asn p.D466N ENST00000529006 12/21 263 248 15 199 199 0 strelka-varscan-mutect KDM2A,missense_variant,p.Asp466Asn,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Asp466Asn,ENST00000398645,;KDM2A,missense_variant,p.Asp449Asn,ENST00000308783,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000525041,; A ENST00000529006 Transcript missense_variant 1842/6967 1396/3489 466/1162 D/N Gat/Aat COSM3953703 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 tolerated(0.18) 12/21 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 67231877 67231877 G A 1 0 0 0 0 1 0 0 0 8042 942 33 3 3 KDM2A 11 67231877 Missense_Mutation SNP G C3N-00579_T 606417 67231877 67854745 37 18101 SSH3 0 . GRCh38 11 67311799 67311799 + Missense_Mutation SNP G G C novel C3N-00579_T C3N-00579_N G G c.1892G>C p.Gly631Ala p.G631A ENST00000308127 14/14 228 194 34 308 308 0 strelka-varscan-mutect SSH3,missense_variant,p.Gly485Ala,ENST00000376757,;SSH3,missense_variant,p.Gly631Ala,ENST00000308127,NM_017857.3;SSH3,missense_variant,p.Gly366Ala,ENST00000308298,;SSH3,downstream_gene_variant,,ENST00000532181,;SSH3,downstream_gene_variant,,ENST00000527821,;SSH3,intron_variant,,ENST00000525913,;SSH3,downstream_gene_variant,,ENST00000529224,;SSH3,downstream_gene_variant,,ENST00000531495,;SSH3,3_prime_UTR_variant,,ENST00000532881,;SSH3,downstream_gene_variant,,ENST00000532600,; C ENST00000308127 Transcript missense_variant 2070/2871 1892/1980 631/659 G/A gGa/gCa 1 1 SSH3 HGNC HGNC:30581 protein_coding YES CCDS8157.1 ENSP00000312081 Q8TE77 A0A024R5J4 UPI0000038D01 NM_017857.3 tolerated_low_confidence(0.22) 14/14 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 67311799 67311799 G C 1 0 0 0 0 1 0 0 0 15562 1174 41 4 4 SSH3 11 67311799 Missense_Mutation SNP G C3N-00579_T 79922 67311799 67774823 38 18102 GPR152 0 . GRCh38 11 67451924 67451924 + Silent SNP G G C novel C3N-00579_T C3N-00579_N G G c.801C>G p.= p.V267V ENST00000312457 1/1 340 315 25 259 259 0 strelka-varscan-mutect GPR152,synonymous_variant,p.=,ENST00000312457,NM_206997.1;CABP4,upstream_gene_variant,,ENST00000325656,NM_145200.3;CABP4,upstream_gene_variant,,ENST00000438189,NM_001300896.1,NM_001300895.1;CABP4,upstream_gene_variant,,ENST00000542025,;CABP4,upstream_gene_variant,,ENST00000538060,;CABP4,upstream_gene_variant,,ENST00000542233,;CABP4,upstream_gene_variant,,ENST00000545040,;CABP4,upstream_gene_variant,,ENST00000545777,; C ENST00000312457 Transcript synonymous_variant 806/1429 801/1413 267/470 V gtC/gtG 1 -1 GPR152 HGNC HGNC:23622 protein_coding YES CCDS8165.1 ENSP00000310255 Q8TDT2 A0A0I9RJ67 UPI000003B364 NM_206997.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF1,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW SNV 1 PASS rs1018548389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 60 67451924 67451924 G C 1 0 0 0 0 0 0 0 1 6544 929 33 4 4 GPR152 11 67451924 Silent SNP G C3N-00579_T 140125 67451924 67634698 39 18103 EMSY 0 . GRCh38 11 76544696 76544696 + Silent SNP G G C novel C3N-00579_T C3N-00579_N G G c.3192G>C p.= p.V1064V ENST00000524767 19/21 442 388 54 330 330 0 strelka-varscan-mutect EMSY,synonymous_variant,p.=,ENST00000529032,;EMSY,synonymous_variant,p.=,ENST00000334736,NM_020193.4;EMSY,synonymous_variant,p.=,ENST00000525038,NM_001300944.1;EMSY,synonymous_variant,p.=,ENST00000524767,NM_001300942.1;EMSY,synonymous_variant,p.=,ENST00000525919,NM_001300943.1;EMSY,synonymous_variant,p.=,ENST00000524490,;EMSY,synonymous_variant,p.=,ENST00000533248,;EMSY,synonymous_variant,p.=,ENST00000532719,;EMSY,downstream_gene_variant,,ENST00000524451,;EMSY,upstream_gene_variant,,ENST00000531793,;EMSY,non_coding_transcript_exon_variant,,ENST00000531641,;EMSY,downstream_gene_variant,,ENST00000534573,; C ENST00000524767 Transcript synonymous_variant 3231/4116 3192/4014 1064/1337 V gtG/gtC 1 1 EMSY HGNC HGNC:18071 protein_coding YES CCDS73349.1 ENSP00000433205 Q7Z589 UPI000191704B NM_001300942.1 19/21 hmmpanther:PTHR16500,hmmpanther:PTHR16500:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 60 76544696 76544696 G C 1 0 0 0 0 0 0 0 1 4948 1277 45 4 4 EMSY 11 76544696 Silent SNP G C3N-00579_T 9092772 76544696 58541926 40 18104 C11orf88 0 . GRCh38 11 111533781 111533781 + Frame_Shift_Del DEL A A - novel C3N-00579_T C3N-00579_N A A c.459delA p.Lys153AsnfsTer11 p.K153Nfs*11 ENST00000332814 5/7 58 53 5 76 76 0 sindel-varindel-pindel C11orf88,frameshift_variant,p.Lys153AsnfsTer11,ENST00000529167,;C11orf88,frameshift_variant,p.Lys153AsnfsTer11,ENST00000332814,NM_207430.2;C11orf88,frameshift_variant,p.Lys126AsnfsTer11,ENST00000375618,NM_001100388.1;C11orf88,3_prime_UTR_variant,,ENST00000529661,; - ENST00000332814 Transcript frameshift_variant 456/795 456/591 152/196 R/X agA/ag 1 1 C11orf88 HGNC HGNC:25061 protein_coding YES CCDS41712.1 ENSP00000333845 Q6PI97 UPI00001D7746 NM_207430.2 5/7 hmmpanther:PTHR16213,hmmpanther:PTHR16213:SF61 HIGH 1 deletion 5 3 1 PASS . . 0 207 3 0 0 0 0 0 -12.21106 1 1 1 1 0 - 7 5 60 111533781 111533781 A - 1 0 1 0 1 0 0 0 0 1800 243 9 0 0 C11orf88 11 111533781 Frame_Shift_Del DEL A C3N-00579_T 34989085 111533781 23552841 41 18105 OR10G7 0 . GRCh38 11 124038263 124038263 + Missense_Mutation SNP C C T novel C3N-00579_T C3N-00579_N C C c.739G>A p.Val247Ile p.V247I ENST00000330487 1/1 176 151 25 120 120 0 strelka-varscan-mutect OR10G7,missense_variant,p.Val247Ile,ENST00000330487,NM_001004463.1; T ENST00000330487 Transcript missense_variant 748/945 739/936 247/311 V/I Gtc/Atc 1 -1 OR10G7 HGNC HGNC:14842 protein_coding YES CCDS31705.1 ENSP00000329689 Q8NGN6 A0A126GWF3 UPI0000040A84 NM_001004463.1 tolerated(0.43) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 124038263 124038263 C T 1 0 0 0 0 1 0 0 0 10979 507 18 3 3 OR10G7 11 124038263 Missense_Mutation SNP C C3N-00579_T 12504482 124038263 11048359 42 18106 GALNT8 0 . GRCh38 12 4720692 4720692 + Silent SNP G G A novel C3N-00579_T C3N-00579_N G G c.15G>A p.= p.R5R ENST00000252318 1/11 327 302 25 183 182 1 strelka-varscan-mutect GALNT8,synonymous_variant,p.=,ENST00000252318,NM_017417.1;RP11-234B24.2,upstream_gene_variant,,ENST00000527518,;RP11-234B24.6,intron_variant,,ENST00000543979,;RP11-234B24.6,intron_variant,,ENST00000544741,; A ENST00000252318 Transcript synonymous_variant 352/2380 15/1914 5/637 R agG/agA 1 1 GALNT8 HGNC HGNC:4130 protein_coding YES CCDS8533.1 ENSP00000252318 Q9NY28 UPI0000070DEC NM_017417.1 1/11 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF50 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 60 4720692 4720692 G A 1 0 0 0 0 0 0 0 1 6090 1165 41 3 3 GALNT8 12 4720692 Silent SNP G C3N-00579_T 4720692 128554617 43 18107 SLCO1C1 0 . GRCh38 12 20717183 20717183 + Missense_Mutation SNP G G A novel C3N-00579_T C3N-00579_N G G c.728G>A p.Gly243Asp p.G243D ENST00000545604 8/16 208 184 24 216 216 0 strelka-varscan-mutect SLCO1C1,missense_variant,p.Gly243Asp,ENST00000266509,NM_017435.4;SLCO1C1,missense_variant,p.Gly125Asp,ENST00000545102,NM_001145944.1;SLCO1C1,missense_variant,p.Gly243Asp,ENST00000545604,NM_001145946.1;SLCO1C1,missense_variant,p.Gly194Asp,ENST00000540354,NM_001145945.1;SLCO1C1,3_prime_UTR_variant,,ENST00000539415,; A ENST00000545604 Transcript missense_variant 958/2557 728/2193 243/730 G/D gGc/gAc 1 1 SLCO1C1 HGNC HGNC:13819 protein_coding YES CCDS53757.1 ENSP00000444149 Q9NYB5 UPI00004C3E1B NM_001145946.1 deleterious(0) 8/16 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF99,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs1418759177 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 20717183 20717183 G A 1 0 0 0 0 1 0 0 0 15012 1203 42 3 3 SLCO1C1 12 20717183 Missense_Mutation SNP G C3N-00579_T 15996491 20717183 112558126 44 18108 ELK3 0 . GRCh38 12 96247240 96247240 + Frame_Shift_Del DEL C C - novel C3N-00579_T C3N-00579_N C C c.510delC p.Glu171LysfsTer12 p.E171Kfs*12 ENST00000228741 3/5 544 434 110 531 531 0 sindel-varindel-pindel ELK3,frameshift_variant,p.Glu171LysfsTer12,ENST00000228741,NM_005230.3;ELK3,intron_variant,,ENST00000552142,;ELK3,downstream_gene_variant,,ENST00000547860,;ELK3,frameshift_variant,p.Glu39LysfsTer12,ENST00000549985,; - ENST00000228741 Transcript frameshift_variant 834/4205 508/1224 170/407 P/X Ccc/cc 1 1 ELK3 HGNC HGNC:3325 protein_coding YES CCDS9060.1 ENSP00000228741 P41970 A0A024RBE2 UPI0000000E09 NM_005230.3 3/5 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF172,Low_complexity_(Seg):seg HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 60 96247240 96247240 C - 1 0 1 0 1 0 0 0 0 4894 739 26 0 0 ELK3 12 96247240 Frame_Shift_Del DEL C C3N-00579_T 75530057 96247240 37028069 45 18109 RB1 0 . GRCh38 13 48465249 48465249 + Nonsense_Mutation SNP C C G rs794727372 C3N-00579_T C3N-00579_N C C c.2370C>G p.Tyr790Ter p.Y790* ENST00000267163 23/27 308 235 73 224 224 0 strelka-varscan-mutect RB1,stop_gained,p.Tyr790Ter,ENST00000267163,NM_000321.2; G ENST00000267163 Transcript stop_gained 2508/4840 2370/2787 790/928 Y/* taC/taG rs794727372,CM011479,CM034906,COSM3733248,COSM3733249 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 23/27 Pfam_domain:PF08934,hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21,SMART_domains:SM01369 pathogenic 0,0,0,1,1 HIGH 1 SNV 1 1,1,1,1,1 1 PASS rs794727372 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 60 48465249 48465249 C G 1 0 0 0 0 0 1 0 0 13259 489 17 4 4 RB1 13 48465249 Nonsense_Mutation SNP C C3N-00579_T 48465249 65899079 46 18110 MDGA2 0 . GRCh38 14 47144234 47144234 + Silent SNP A A G novel C3N-00579_T C3N-00579_N A A c.429T>C p.= p.G143G ENST00000399232 4/17 154 108 46 115 115 0 strelka-varscan-mutect MDGA2,synonymous_variant,p.=,ENST00000426342,;MDGA2,synonymous_variant,p.=,ENST00000399232,NM_001113498.2;MDGA2,5_prime_UTR_variant,,ENST00000357362,NM_182830.4;MDGA2,5_prime_UTR_variant,,ENST00000557238,;MDGA2,5_prime_UTR_variant,,ENST00000482848,; G ENST00000399232 Transcript synonymous_variant 794/5075 429/2871 143/956 G ggT/ggC 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 4/17 PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 60 47144234 47144234 A G 1 0 0 0 0 0 0 0 1 9345 146 6 5 5 MDGA2 14 47144234 Silent SNP A C3N-00579_T 47144234 59899484 47 18111 NUMB 0 . GRCh38 14 73284173 73284173 + Missense_Mutation SNP T T C novel C3N-00579_T C3N-00579_N T T c.857A>G p.Lys286Arg p.K286R ENST00000555238 10/13 596 445 151 442 442 0 strelka-varscan-mutect NUMB,missense_variant,p.Lys142Arg,ENST00000556772,;NUMB,missense_variant,p.Lys275Arg,ENST00000554546,NM_001005745.1;NUMB,missense_variant,p.Lys286Arg,ENST00000555238,NM_001005743.1;NUMB,missense_variant,p.Lys275Arg,ENST00000557597,NM_003744.5;NUMB,missense_variant,p.Lys286Arg,ENST00000356296,NM_001320114.1;NUMB,missense_variant,p.Lys286Arg,ENST00000355058,;NUMB,missense_variant,p.Lys275Arg,ENST00000359560,;NUMB,missense_variant,p.Lys286Arg,ENST00000535282,;NUMB,missense_variant,p.Lys286Arg,ENST00000555394,NM_001005744.1;NUMB,intron_variant,,ENST00000544991,;NUMB,intron_variant,,ENST00000560335,;NUMB,intron_variant,,ENST00000555738,;NUMB,intron_variant,,ENST00000559312,;NUMB,intron_variant,,ENST00000554521,;NUMB,downstream_gene_variant,,ENST00000555307,;NUMB,downstream_gene_variant,,ENST00000554394,;NUMB,downstream_gene_variant,,ENST00000555859,;NUMB,non_coding_transcript_exon_variant,,ENST00000553997,;NUMB,non_coding_transcript_exon_variant,,ENST00000554014,;NUMB,non_coding_transcript_exon_variant,,ENST00000557486,;NUMB,downstream_gene_variant,,ENST00000556989,;NUMB,downstream_gene_variant,,ENST00000554315,; C ENST00000555238 Transcript missense_variant 1127/3588 857/1956 286/651 K/R aAg/aGg 1 -1 NUMB HGNC HGNC:8060 protein_coding YES CCDS32116.1 ENSP00000451300 P49757 A0A024R6F4 UPI00001309BF NM_001005743.1 tolerated(0.06) 10/13 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF33,Pfam_domain:PF06311,PIRSF_domain:PIRSF017607 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 73284173 73284173 T C 1 0 0 0 0 1 0 0 0 10816 1609 56 5 5 NUMB 14 73284173 Missense_Mutation SNP T C3N-00579_T 26139939 73284173 33759545 48 18112 TECPR2 0 . GRCh38 14 102438126 102438126 + Missense_Mutation SNP C C G rs539429220 C3N-00579_T C3N-00579_N C C c.2499C>G p.Phe833Leu p.F833L ENST00000359520 10/20 294 268 26 280 280 0 strelka-varscan-mutect TECPR2,missense_variant,p.Phe833Leu,ENST00000359520,NM_014844.3;TECPR2,missense_variant,p.Phe833Leu,ENST00000558678,NM_001172631.1;TECPR2,non_coding_transcript_exon_variant,,ENST00000560060,;TECPR2,upstream_gene_variant,,ENST00000557786,; G ENST00000359520 Transcript missense_variant 2725/8686 2499/4236 833/1411 F/L ttC/ttG rs539429220 1 1 TECPR2 HGNC HGNC:19957 protein_coding YES CCDS32162.1 ENSP00000352510 O15040 UPI00001FDC38 NM_014844.3 deleterious(0.01) 10/20 hmmpanther:PTHR23287,hmmpanther:PTHR23287:SF16 MODERATE 1 SNV 1 1 PASS rs539429220 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 60 102438126 102438126 C G 1 0 0 0 0 1 0 0 0 16155 912 32 4 4 TECPR2 14 102438126 Missense_Mutation SNP C C3N-00579_T 29153953 102438126 4605592 49 18113 OTUD7A 0 . GRCh38 15 31483412 31483412 + Missense_Mutation SNP C C T novel C3N-00579_T C3N-00579_N C C c.2663G>A p.Arg888Gln p.R888Q ENST00000307050 11/11 63 54 9 46 46 0 strelka-varscan-mutect OTUD7A,missense_variant,p.Arg888Gln,ENST00000307050,NM_130901.1; T ENST00000307050 Transcript missense_variant 2756/10770 2663/2781 888/926 R/Q cGg/cAg 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 tolerated_low_confidence(0.28) 11/11 PROSITE_profiles:PS51036,hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367,SMART_domains:SM00259 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.91864 1 1 1 1 0 T 3 4 60 31483412 31483412 C T 1 0 0 0 0 1 0 0 0 11387 652 23 1 1 OTUD7A 15 31483412 Missense_Mutation SNP C C3N-00579_T 31483412 70507777 50 18114 ANPEP 0 . GRCh38 15 89790464 89790464 + Missense_Mutation SNP T T G novel C3N-00579_T C3N-00579_N T T c.2747A>C p.Gln916Pro p.Q916P ENST00000300060 20/21 212 137 75 215 215 0 strelka-varscan-mutect ANPEP,missense_variant,p.Gln916Pro,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000558740,; G ENST00000300060 Transcript missense_variant 3061/3678 2747/2904 916/967 Q/P cAg/cCg 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 deleterious(0) 20/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Pfam_domain:PF11838 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 60 89790464 89790464 T G 1 0 0 0 0 1 0 0 0 817 1594 55 5 5 ANPEP 15 89790464 Missense_Mutation SNP T C3N-00579_T 58307052 89790464 12200725 51 18115 ABCA3 0 . GRCh38 16 2286968 2286968 + Splice_Site SNP C C T C3N-00579_T C3N-00579_N C C c.3005-1G>A p.X1002_splice ENST00000301732 307 250 57 208 208 0 strelka-varscan-mutect ABCA3,splice_acceptor_variant,,ENST00000301732,NM_001089.2;ABCA3,splice_acceptor_variant,,ENST00000382381,;ABCA3,downstream_gene_variant,,ENST00000563623,;ABCA3,upstream_gene_variant,,ENST00000566200,;ABCA3,upstream_gene_variant,,ENST00000569062,; T ENST00000301732 Transcript splice_acceptor_variant -/6609 3005/5115 1002/1704 CS066265 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 21/32 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 60 2286968 2286968 C T 1 0 0 0 0 0 0 1 0 37 695 24 3 3 ABCA3 16 2286968 Splice_Site SNP C C3N-00579_T 2286968 88051377 52 18116 GRIN2A 0 . GRCh38 16 9763752 9763752 + Silent SNP C C T novel C3N-00579_T C3N-00579_N C C c.3792G>A p.= p.E1264E ENST00000396573 14/14 949 830 119 564 564 0 strelka-varscan-mutect GRIN2A,synonymous_variant,p.=,ENST00000396573,NM_000833.4;GRIN2A,synonymous_variant,p.=,ENST00000396575,;GRIN2A,synonymous_variant,p.=,ENST00000330684,NM_001134407.2;GRIN2A,intron_variant,,ENST00000562109,NM_001134408.2;GRIN2A,intron_variant,,ENST00000535259,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,intron_variant,,ENST00000461292,;GRIN2A,downstream_gene_variant,,ENST00000463531,; T ENST00000396573 Transcript synonymous_variant 4102/14450 3792/4395 1264/1464 E gaG/gaA 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 14/14 Pfam_domain:PF10565 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 60 9763752 9763752 C T 1 0 0 0 0 0 0 0 1 6661 796 28 3 3 GRIN2A 16 9763752 Silent SNP C C3N-00579_T 7476784 9763752 80574593 53 18117 NFATC2IP 0 . GRCh38 16 28959090 28959090 + Missense_Mutation SNP C C T C3N-00579_T C3N-00579_N C C c.1091C>T p.Ser364Leu p.S364L ENST00000320805 7/8 173 160 13 107 107 0 strelka-varscan-mutect NFATC2IP,missense_variant,p.Ser364Leu,ENST00000320805,NM_032815.3;NFATC2IP,missense_variant,p.Ser85Leu,ENST00000564978,;NFATC2IP,missense_variant,p.Ser72Leu,ENST00000568148,;NFATC2IP,downstream_gene_variant,,ENST00000578855,;RP11-264B17.2,intron_variant,,ENST00000569974,;RP11-264B17.2,upstream_gene_variant,,ENST00000568057,;NFATC2IP,downstream_gene_variant,,ENST00000562977,;NFATC2IP,downstream_gene_variant,,ENST00000568998,; T ENST00000320805 Transcript missense_variant 1166/4569 1091/1260 364/419 S/L tCa/tTa COSM3724803 1 1 NFATC2IP HGNC HGNC:25906 protein_coding YES CCDS10645.1 ENSP00000324792 Q8NCF5 UPI00000316E2 NM_032815.3 tolerated(0.05) 7/8 Gene3D:3.10.20.90,Pfam_domain:PF11976,PROSITE_profiles:PS50053,hmmpanther:PTHR10562,hmmpanther:PTHR10562:SF28,SMART_domains:SM00213,Superfamily_domains:SSF54236 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 28959090 28959090 C T 1 0 0 0 0 1 0 0 0 10400 838 29 3 3 NFATC2IP 16 28959090 Missense_Mutation SNP C C3N-00579_T 19195338 28959090 61379255 54 18118 TP53 0 . GRCh38 17 7674230 7674230 + Missense_Mutation SNP C C T rs28934575 C3N-00579_T C3N-00579_N C C c.733G>A p.Gly245Ser p.G245S ENST00000269305 7/11 285 213 72 300 299 1 strelka-varscan-mutect TP53,missense_variant,p.Gly245Ser,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly245Ser,ENST00000420246,;TP53,missense_variant,p.Gly206Ser,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly206Ser,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly245Ser,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly206Ser,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly245Ser,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly206Ser,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly245Ser,ENST00000445888,;TP53,missense_variant,p.Gly206Ser,ENST00000619485,;TP53,missense_variant,p.Gly113Ser,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly86Ser,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly113Ser,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly86Ser,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly113Ser,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly86Ser,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly245Ser,ENST00000359597,;TP53,missense_variant,p.Gly234Ser,ENST00000615910,;TP53,missense_variant,p.Gly245Ser,ENST00000413465,;TP53,missense_variant,p.Gly113Ser,ENST00000509690,;TP53,missense_variant,p.Gly152Ser,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly206Ser,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 923/2579 733/1182 245/393 G/S Ggc/Agc rs28934575,CM010463,CM900210,CM920674,TP53_g.13370G>T,TP53_g.13370G>C,TP53_g.13370del,TP53_g.13370G>A,COSM10957,COSM11081,COSM121035,COSM121036,COSM121037,COSM1610835,COSM1610836,COSM1610837,COSM1640833,COSM1646855,COSM3356965,COSM3388190,COSM3717639,COSM3717640,COSM3726870,COSM3726871,COSM3726872,COSM3726873,COSM3726874,COSM44642,COSM562651,COSM562652,COSM562653,COSM6932 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic,pathogenic 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 2.50327002510566e+23 MODERATE 1 SNV 1 1,1,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs28934575 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 60 7674230 7674230 C T 1 0 0 0 0 1 0 0 0 16859 652 23 1 1 TP53 17 7674230 Missense_Mutation SNP C C3N-00579_T 7674230 75583211 55 18119 USP43 0 . GRCh38 17 9709960 9709960 + Nonsense_Mutation SNP C C A novel C3N-00579_T C3N-00579_N C C c.2016C>A p.Tyr672Ter p.Y672* ENST00000285199 13/15 39 35 4 25 25 0 strelka-mutect USP43,stop_gained,p.Tyr672Ter,ENST00000285199,NM_153210.4;USP43,stop_gained,p.Tyr667Ter,ENST00000570475,NM_001267576.1;USP43,stop_gained,p.Tyr459Ter,ENST00000574408,;USP43,stop_gained,p.Tyr197Ter,ENST00000573955,;USP43,non_coding_transcript_exon_variant,,ENST00000570827,; A ENST00000285199 Transcript stop_gained 2112/4169 2016/3372 672/1123 Y/* taC/taA 1 1 USP43 HGNC HGNC:20072 protein_coding YES CCDS45610.1 ENSP00000285199 Q70EL4 UPI0000047AFB NM_153210.4 13/15 PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF462,Pfam_domain:PF00443,Superfamily_domains:SSF54001 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -10.7385 0.9999999 1 1 1 0 A 4 1 60 9709960 9709960 C A 1 0 0 0 0 0 1 0 0 17617 579 20 2 2 USP43 17 9709960 Nonsense_Mutation SNP C C3N-00579_T 2035730 9709960 73547481 56 18120 FAM171A2 0 . GRCh38 17 44355132 44355132 + Missense_Mutation SNP T T C novel C3N-00579_T C3N-00579_N T T c.1082A>G p.Asp361Gly p.D361G ENST00000293443 8/8 250 214 36 250 250 0 strelka-varscan-mutect FAM171A2,missense_variant,p.Asp361Gly,ENST00000293443,NM_198475.2;GRN,downstream_gene_variant,,ENST00000053867,NM_002087.3;GRN,downstream_gene_variant,,ENST00000589265,;GRN,downstream_gene_variant,,ENST00000586443,;GRN,downstream_gene_variant,,ENST00000593167,;GRN,downstream_gene_variant,,ENST00000586242,;GRN,downstream_gene_variant,,ENST00000587387,;GRN,downstream_gene_variant,,ENST00000591740,;GRN,downstream_gene_variant,,ENST00000588237,;GRN,downstream_gene_variant,,ENST00000588143,;GRN,downstream_gene_variant,,ENST00000592783,;GRN,downstream_gene_variant,,ENST00000587518,;GRN,downstream_gene_variant,,ENST00000589923,;FAM171A2,downstream_gene_variant,,ENST00000589407,;FAM171A2,downstream_gene_variant,,ENST00000588067,;GRN,downstream_gene_variant,,ENST00000586782,;FAM171A2,downstream_gene_variant,,ENST00000592560,;GRN,downstream_gene_variant,,ENST00000585348,;GRN,downstream_gene_variant,,ENST00000590984,; C ENST00000293443 Transcript missense_variant 1243/3160 1082/2481 361/826 D/G gAc/gGc 1 -1 FAM171A2 HGNC HGNC:30480 protein_coding YES CCDS45701.1 ENSP00000293443 A8MVW0 UPI0000E59FC0 NM_198475.2 deleterious(0.02) 8/8 Pfam_domain:PF10577,hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 44355132 44355132 T C 1 0 0 0 0 1 0 0 0 5338 1667 58 5 5 FAM171A2 17 44355132 Missense_Mutation SNP T C3N-00579_T 34645172 44355132 38902309 57 18121 TMEM94 0 . GRCh38 17 75485978 75485978 + Nonsense_Mutation SNP C C A rs543706878 C3N-00579_T C3N-00579_N C C c.252C>A p.Cys84Ter p.C84* ENST00000314256 4/32 80 63 17 66 66 0 strelka-varscan-mutect TMEM94,stop_gained,p.Cys84Ter,ENST00000314256,NM_001321149.1,NM_014738.4;TMEM94,stop_gained,p.Cys94Ter,ENST00000375248,;TMEM94,stop_gained,p.Cys12Ter,ENST00000582186,;TMEM94,stop_gained,p.Cys84Ter,ENST00000577380,;TMEM94,stop_gained,p.Cys84Ter,ENST00000581519,;TMEM94,intron_variant,,ENST00000579208,;TMEM94,intron_variant,,ENST00000581252,;TMEM94,downstream_gene_variant,,ENST00000582455,;TMEM94,intron_variant,,ENST00000580416,;TMEM94,upstream_gene_variant,,ENST00000583795,;TMEM94,stop_gained,p.Cys94Ter,ENST00000579707,;TMEM94,non_coding_transcript_exon_variant,,ENST00000585105,;TMEM94,non_coding_transcript_exon_variant,,ENST00000581085,;TMEM94,non_coding_transcript_exon_variant,,ENST00000584383,;TMEM94,upstream_gene_variant,,ENST00000579241,;TMEM94,downstream_gene_variant,,ENST00000585277,;TMEM94,upstream_gene_variant,,ENST00000580441,;TMEM94,upstream_gene_variant,,ENST00000580849,; A ENST00000314256 Transcript stop_gained 646/5213 252/4071 84/1356 C/* tgC/tgA rs543706878 1 1 TMEM94 HGNC HGNC:28983 protein_coding YES CCDS32732.1 ENSP00000313885 Q12767 A0A024R8S6 UPI0000139439 NM_001321149.1,NM_014738.4 4/32 Transmembrane_helices:TMhelix,hmmpanther:PTHR13219,hmmpanther:PTHR13219:SF6,Superfamily_domains:0049473 HIGH 1 SNV 1 1 PASS rs543706878 . 0 201 6 3 0 0 0 0 -20 0.9997672 1 1 1 0 A 4 1 60 75485978 75485978 C A 1 0 0 0 0 0 1 0 0 16697 776 27 1 1 TMEM94 17 75485978 Nonsense_Mutation SNP C C3N-00579_T 31130846 75485978 7771463 58 18122 TMC6 0 . GRCh38 17 78120679 78120679 + Silent SNP G G A novel C3N-00579_T C3N-00579_N G G c.1689C>T p.= p.D563D ENST00000590602 13/20 614 512 102 485 485 0 strelka-varscan-mutect TMC6,synonymous_variant,p.=,ENST00000590602,NM_001127198.1;TMC6,synonymous_variant,p.=,ENST00000392467,;TMC6,synonymous_variant,p.=,ENST00000322914,NM_007267.6;TMC6,3_prime_UTR_variant,,ENST00000589553,;TMC6,intron_variant,,ENST00000306591,;TMC6,intron_variant,,ENST00000591436,;TMC6,downstream_gene_variant,,ENST00000589271,;TMC6,downstream_gene_variant,,ENST00000592063,;TMC6,non_coding_transcript_exon_variant,,ENST00000590934,;TMC6,intron_variant,,ENST00000592076,;TMC6,non_coding_transcript_exon_variant,,ENST00000593044,;TMC6,non_coding_transcript_exon_variant,,ENST00000588087,;TMC6,non_coding_transcript_exon_variant,,ENST00000591756,;TMC6,downstream_gene_variant,,ENST00000586271,;TMC6,downstream_gene_variant,,ENST00000591594,;TMC6,upstream_gene_variant,,ENST00000589933,;TMC6,downstream_gene_variant,,ENST00000585849,; A ENST00000590602 Transcript synonymous_variant 1849/5268 1689/2418 563/805 D gaC/gaT 1 -1 TMC6 HGNC HGNC:18021 protein_coding YES CCDS32748.1 ENSP00000465261 Q7Z403 A0A024R8V2 UPI000013D819 NM_001127198.1 13/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR23302:SF4,hmmpanther:PTHR23302,Pfam_domain:PF07810 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 60 78120679 78120679 G A 1 0 0 0 0 0 0 0 1 16435 1368 48 3 3 TMC6 17 78120679 Silent SNP G C3N-00579_T 2634701 78120679 5136762 59 18123 MUC16 0 . GRCh38 19 8947108 8947108 + Missense_Mutation SNP T T C novel C3N-00579_T C3N-00579_N T T c.29662A>G p.Thr9888Ala p.T9888A ENST00000397910 3/84 175 148 27 101 101 0 strelka-varscan-mutect MUC16,missense_variant,p.Thr9888Ala,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 29866/43816 29662/43524 9888/14507 T/A Acc/Gcc 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 60 8947108 8947108 T C 1 0 0 0 0 1 0 0 0 9972 1667 58 5 5 MUC16 19 8947108 Missense_Mutation SNP T C3N-00579_T 8947108 49670508 60 18124 NR2C2AP 0 . GRCh38 19 19201475 19201475 + Nonstop_Mutation SNP T T A rs187406875 C3N-00579_T C3N-00579_N T T c.503A>T p.Ter168LeuextTer8 p.*168Lext*8 ENST00000420605 6/6 369 295 74 313 313 0 strelka-varscan-mutect NR2C2AP,stop_lost,p.Ter168LeuextTer8,ENST00000420605,NM_001300945.1;NR2C2AP,3_prime_UTR_variant,,ENST00000331552,NM_176880.5;RFXANK,intron_variant,,ENST00000303088,NM_003721.3;RFXANK,intron_variant,,ENST00000456252,NM_001278727.1;RFXANK,intron_variant,,ENST00000407360,;RFXANK,intron_variant,,ENST00000392324,NM_134440.2,NM_001278728.1;RFXANK,intron_variant,,ENST00000536253,;RFXANK,intron_variant,,ENST00000544923,;NR2C2AP,downstream_gene_variant,,ENST00000544883,;NR2C2AP,downstream_gene_variant,,ENST00000538165,;RFXANK,downstream_gene_variant,,ENST00000593273,;RFXANK,downstream_gene_variant,,ENST00000421262,;RFXANK,downstream_gene_variant,,ENST00000540981,;RFXANK,downstream_gene_variant,,ENST00000535017,;NR2C2AP,downstream_gene_variant,,ENST00000539678,;NR2C2AP,non_coding_transcript_exon_variant,,ENST00000537399,;RFXANK,intron_variant,,ENST00000540977,;RFXANK,downstream_gene_variant,,ENST00000541873,;NR2C2AP,downstream_gene_variant,,ENST00000539693,;RFXANK,downstream_gene_variant,,ENST00000543157,;RFXANK,downstream_gene_variant,,ENST00000545522,;RFXANK,downstream_gene_variant,,ENST00000543118,; A ENST00000420605 Transcript stop_lost 800/859 503/504 168/167 */L tAa/tTa rs187406875 1 -1 NR2C2AP HGNC HGNC:30763 protein_coding YES CCDS74316.1 ENSP00000402756 Q86WQ0 UPI0000203824 NM_001300945.1 6/6 HIGH SNV 2 1 PASS rs187406875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 60 19201475 19201475 T A 1 0 0 0 0 0 0 0 0 10680 1761 61 4 4 NR2C2AP 19 19201475 Nonstop_Mutation SNP T C3N-00579_T 10254367 19201475 39416141 61 18125 CEACAM20 0 . GRCh38 19 44511133 44511133 + Missense_Mutation SNP C C T rs372851437 C3N-00579_T C3N-00579_N C C c.1634G>A p.Arg545His p.R545H ENST00000614924 11/12 159 122 37 117 117 0 strelka-varscan-mutect CEACAM20,missense_variant,p.Arg545His,ENST00000621342,;CEACAM20,missense_variant,p.Arg545His,ENST00000617951,;CEACAM20,missense_variant,p.Arg545His,ENST00000614924,NM_001102597.2;CEACAM20,missense_variant,p.Arg533His,ENST00000611497,NM_001102600.2;CEACAM20,missense_variant,p.Arg452His,ENST00000614577,NM_001102599.2;CEACAM20,missense_variant,p.Arg440His,ENST00000620096,NM_001102598.2; T ENST00000614924 Transcript missense_variant 1650/1809 1634/1791 545/596 R/H cGt/cAt rs372851437,COSM50870 1 -1 CEACAM20 HGNC HGNC:24879 protein_coding YES CCDS74393.1 ENSP00000481937 A0A087WYM6 UPI0003EC04B5 NM_001102597.2 tolerated(0.29) 11/12 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372851437 . 0 207 0 3 0 0 0 0 -20 0.9999974 1 1 1 0 T 3 4 60 44511133 44511133 C T 1 0 0 0 0 1 0 0 0 2897 536 19 1 1 CEACAM20 19 44511133 Missense_Mutation SNP C C3N-00579_T 25309658 44511133 14106483 62 18126 IGLON5 0 . GRCh38 19 51327102 51327102 + Silent SNP G G A novel C3N-00579_T C3N-00579_N G G c.669G>A p.= p.V223V ENST00000270642 6/8 111 85 26 88 87 1 strelka-varscan-mutect IGLON5,synonymous_variant,p.=,ENST00000270642,NM_001101372.1;VSIG10L,downstream_gene_variant,,ENST00000335624,NM_001163922.1;VSIG10L,downstream_gene_variant,,ENST00000600663,; A ENST00000270642 Transcript synonymous_variant 669/2606 669/1011 223/336 V gtG/gtA 1 1 IGLON5 HGNC HGNC:34550 protein_coding YES CCDS46158.1 ENSP00000270642 A6NGN9 UPI000058F1A8 NM_001101372.1 6/8 Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF148,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 60 51327102 51327102 G A 1 0 0 0 0 0 0 0 1 7502 1277 45 3 3 IGLON5 19 51327102 Silent SNP G C3N-00579_T 6815969 51327102 7290514 63 18127 SLC13A3 0 . GRCh38 20 46566298 46566298 + Silent SNP G G A rs147641404 C3N-00579_T C3N-00579_N G G c.1425C>T p.= p.I475I ENST00000279027 11/13 221 179 42 195 194 1 strelka-varscan-mutect SLC13A3,synonymous_variant,p.=,ENST00000279027,NM_022829.5;SLC13A3,synonymous_variant,p.=,ENST00000290317,NM_001193342.1,NM_001011554.2;SLC13A3,synonymous_variant,p.=,ENST00000472148,NM_001193340.1;SLC13A3,synonymous_variant,p.=,ENST00000413164,NM_001193339.1;SLC13A3,synonymous_variant,p.=,ENST00000495082,;SLC13A3,downstream_gene_variant,,ENST00000468915,; A ENST00000279027 Transcript synonymous_variant 1444/4017 1425/1809 475/602 I atC/atT rs147641404,COSM1412200 1 -1 SLC13A3 HGNC HGNC:14430 protein_coding YES CCDS13400.1 ENSP00000279027 Q8WWT9 UPI000013542F NM_022829.5 11/13 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF62,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 1 0,1 1 PASS rs147641404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 60 46566298 46566298 G A 1 0 0 0 0 0 0 0 1 14658 1048 37 1 1 SLC13A3 20 46566298 Silent SNP G C3N-00579_T 46566298 17877869 64 18128 CDH26 0 . GRCh38 20 59989041 59989041 + Silent SNP G G C novel C3N-00579_T C3N-00579_N G G c.1161G>C p.= p.V387V ENST00000348616 9/18 1132 980 152 497 497 0 strelka-varscan-mutect CDH26,synonymous_variant,p.=,ENST00000348616,NM_177980.2;CDH26,upstream_gene_variant,,ENST00000370991,;CDH26,non_coding_transcript_exon_variant,,ENST00000477058,; C ENST00000348616 Transcript synonymous_variant 1461/3182 1161/2499 387/832 V gtG/gtC 1 1 CDH26 HGNC HGNC:15902 protein_coding YES CCDS13485.1 ENSP00000339390 Q8IXH8 UPI000013CB55 NM_177980.2 9/18 Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF78,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 60 59989041 59989041 G C 1 0 0 0 0 0 0 0 1 2813 1277 45 4 4 CDH26 20 59989041 Silent SNP G C3N-00579_T 13422743 59989041 4455126 65 18129 MICAL3 0 . GRCh38 22 17896762 17896762 + Nonsense_Mutation SNP G G A novel C3N-00579_T C3N-00579_N G G c.1168C>T p.Gln390Ter p.Q390* ENST00000441493 8/32 203 188 15 154 154 0 strelka-varscan-mutect MICAL3,stop_gained,p.Gln390Ter,ENST00000441493,NM_015241.2;MICAL3,stop_gained,p.Gln390Ter,ENST00000414725,;MICAL3,stop_gained,p.Gln390Ter,ENST00000585038,NM_001136004.3;MICAL3,stop_gained,p.Gln390Ter,ENST00000400561,NM_001122731.2;MICAL3,stop_gained,p.Gln390Ter,ENST00000383094,;MICAL3,upstream_gene_variant,,ENST00000461307,;MICAL3,3_prime_UTR_variant,,ENST00000495076,; A ENST00000441493 Transcript stop_gained 1521/9445 1168/6009 390/2002 Q/* Cag/Tag 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 8/32 Superfamily_domains:SSF51905,Superfamily_domains:SSF47576 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 60 17896762 17896762 G A 1 0 0 0 0 0 1 0 0 9528 1357 47 3 3 MICAL3 22 17896762 Nonsense_Mutation SNP G C3N-00579_T 17896762 32921706 66 18130 PPARA 0 . GRCh38 22 46215334 46215334 + Splice_Site SNP G G A novel C3N-00579_T C3N-00579_N G G c.369+1G>A p.X123_splice ENST00000407236 495 385 110 451 451 0 strelka-varscan-mutect PPARA,splice_donor_variant,,ENST00000407236,;PPARA,splice_donor_variant,,ENST00000262735,NM_005036.4,NM_001001928.2;PPARA,splice_donor_variant,,ENST00000402126,;PPARA,missense_variant,p.Val124Ile,ENST00000420804,;PPARA,splice_donor_variant,,ENST00000493286,; A ENST00000407236 Transcript splice_donor_variant -/9995 369/1407 123/468 1 1 PPARA HGNC HGNC:9232 protein_coding YES CCDS33669.1 ENSP00000385523 Q07869 F1D8S4 UPI000000D8E0 4/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 60 46215334 46215334 G A 1 0 0 0 0 0 0 1 0 12406 1275 44 3 3 PPARA 22 46215334 Splice_Site SNP G C3N-00579_T 28318572 46215334 4603134 67 18131 HCCS 0 . GRCh38 X 11114923 11114923 + Silent SNP C C T rs138058070 C3N-00579_T C3N-00579_N C C c.189C>T p.= p.Y63Y ENST00000321143 3/7 383 311 72 166 166 0 strelka-varscan-mutect HCCS,synonymous_variant,p.=,ENST00000321143,NM_005333.4,NM_001122608.2,NM_001171991.2;HCCS,synonymous_variant,p.=,ENST00000380762,;HCCS,synonymous_variant,p.=,ENST00000380763,;RP11-120D5.1,upstream_gene_variant,,ENST00000608176,;RP11-120D5.1,upstream_gene_variant,,ENST00000608576,;RP11-120D5.1,upstream_gene_variant,,ENST00000433747,;RP11-120D5.1,upstream_gene_variant,,ENST00000608916,;Y_RNA,downstream_gene_variant,,ENST00000384422,; T ENST00000321143 Transcript synonymous_variant 391/2277 189/807 63/268 Y taC/taT rs138058070,COSM3939745 1 1 HCCS HGNC HGNC:4837 protein_coding YES CCDS14139.1 ENSP00000326579 P53701 A0A024RBY9 UPI00001272B7 NM_005333.4,NM_001122608.2,NM_001171991.2 3/7 Pfam_domain:PF01265,hmmpanther:PTHR12743,hmmpanther:PTHR12743:SF0 0,1 LOW 1 SNV 2 0,1 1 PASS rs138058070 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 60 11114923 11114923 C T 1 0 0 0 0 0 0 0 1 6878 547 19 1 1 HCCS 23 11114923 Silent SNP C C3N-00579_T 11114923 144925972 68 18132 CYLC1 0 . GRCh38 X 83873127 83873127 + Frame_Shift_Del DEL C C - novel C3N-00579_T C3N-00579_N C C c.419delC p.Thr140LysfsTer8 p.T140Kfs*8 ENST00000329312 4/5 48 39 9 41 41 0 sindel-varindel-pindel CYLC1,frameshift_variant,p.Thr140LysfsTer8,ENST00000329312,NM_021118.2;CYLC1,intron_variant,,ENST00000621735,NM_001271680.1; - ENST00000329312 Transcript frameshift_variant 456/2106 419/1956 140/651 T/X aCa/aa 1 1 CYLC1 HGNC HGNC:2582 protein_coding YES CCDS35341.1 ENSP00000331556 P35663 UPI0000251E1D NM_021118.2 4/5 hmmpanther:PTHR16742,hmmpanther:PTHR16742:SF1 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99349 1 1 1 1 0 - 7 5 60 83873127 83873127 C - 1 0 1 0 1 0 0 0 0 3944 478 17 0 0 CYLC1 23 83873127 Frame_Shift_Del DEL C C3N-00579_T 72758204 83873127 72167768 69 18133 PRPS1 0 . GRCh38 X 107647631 107647631 + Missense_Mutation SNP G G A novel C3N-00579_T C3N-00579_N G G c.730G>A p.Val244Ile p.V244I ENST00000372435 6/7 315 263 52 134 134 0 strelka-varscan-mutect PRPS1,missense_variant,p.Val244Ile,ENST00000372435,NM_002764.3;PRPS1,missense_variant,p.Val40Ile,ENST00000372428,NM_001204402.1;PRPS1,missense_variant,p.Val144Ile,ENST00000372418,; A ENST00000372435 Transcript missense_variant 852/2073 730/957 244/318 V/I Gtt/Att 1 1 PRPS1 HGNC HGNC:9462 protein_coding YES CCDS14529.1 ENSP00000361512 P60891 UPI00000000A5 NM_002764.3 tolerated(0.13) 6/7 Gene3D:3.40.50.2020,HAMAP:MF_00583_B,Pfam_domain:PF14572,hmmpanther:PTHR10210,hmmpanther:PTHR10210:SF60,Superfamily_domains:SSF53271,TIGRFAM_domain:TIGR01251 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 60 107647631 107647631 G A 1 0 0 0 0 1 0 0 0 12714 1029 36 3 3 PRPS1 23 107647631 Missense_Mutation SNP G C3N-00579_T 23774504 107647631 48393264 70 18134 ADGRG4 0 . GRCh38 X 136349082 136349082 + Silent SNP T T A novel C3N-00579_T C3N-00579_N T T c.5376T>A p.= p.S1792S ENST00000394143 6/26 70 64 6 48 48 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; A ENST00000394143 Transcript synonymous_variant 5667/9931 5376/9243 1792/3080 S tcT/tcA 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -10.63015 0.9998781 1 1 1 0 A 2 1 60 136349082 136349082 T A 1 0 0 0 0 0 0 0 1 371 1596 56 4 4 ADGRG4 23 136349082 Silent SNP T C3N-00579_T 28701451 136349082 19691813 71 18135 CFAP74 0 . GRCh38 1 1923446 1923446 + Missense_Mutation SNP G G T rs768973631 C3N-00580_T C3N-00580_N G G c.4443C>A p.Phe1481Leu p.F1481L ENST00000493964 36/38 203 184 19 229 228 1 strelka-varscan-mutect CFAP74,missense_variant,p.Phe1481Leu,ENST00000493964,NM_001304360.1;TMEM52,upstream_gene_variant,,ENST00000378602,;TMEM52,upstream_gene_variant,,ENST00000310991,NM_178545.3;TMEM52,upstream_gene_variant,,ENST00000378598,;TMEM52,upstream_gene_variant,,ENST00000416272,;CFAP74,non_coding_transcript_exon_variant,,ENST00000464311,;CFAP74,non_coding_transcript_exon_variant,,ENST00000412120,;TMEM52,upstream_gene_variant,,ENST00000602604,;TMEM52,upstream_gene_variant,,ENST00000470931,; T ENST00000493964 Transcript missense_variant 4599/5247 4443/4755 1481/1584 F/L ttC/ttA rs768973631 1 -1 CFAP74 HGNC HGNC:29368 protein_coding YES ENSP00000417061 Q9C0B2 UPI0004620AE2 NM_001304360.1 deleterious(0.01) 36/38 hmmpanther:PTHR22538 MODERATE SNV 5 1 PASS rs768973631 . 0 205 0 4 0 0 0 0 -20 0.9997835 1 1 1 0 T 3 4 61 1923446 1923446 G T 1 0 0 0 0 1 0 0 0 3033 1049 37 1 1 CFAP74 1 1923446 Missense_Mutation SNP G C3N-00580_T 1923446 247032976 1 18136 CHD5 0 . GRCh38 1 6106687 6106687 + Silent SNP G G T rs371741094 C3N-00580_T C3N-00580_N G G c.5671C>A p.= p.R1891R ENST00000262450 39/42 150 130 20 122 122 0 strelka-varscan-mutect CHD5,synonymous_variant,p.=,ENST00000262450,NM_015557.2;CHD5,synonymous_variant,p.=,ENST00000475121,;CHD5,3_prime_UTR_variant,,ENST00000496404,;CHD5,3_prime_UTR_variant,,ENST00000462991,;CHD5,3_prime_UTR_variant,,ENST00000377999,; T ENST00000262450 Transcript synonymous_variant 5771/9646 5671/5865 1891/1954 R Cgg/Agg rs371741094 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 39/42 Pfam_domain:PF08074 LOW 1 SNV 1 1 PASS rs371741094 . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 61 6106687 6106687 G T 1 0 0 0 0 0 0 0 1 3087 1115 39 1 1 CHD5 1 6106687 Silent SNP G C3N-00580_T 4183241 6106687 242849735 2 18137 TAS1R1 0 . GRCh38 1 6574643 6574643 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.511G>T p.Ala171Ser p.A171S ENST00000333172 3/6 85 77 8 85 85 0 strelka-varscan-mutect TAS1R1,missense_variant,p.Ala171Ser,ENST00000333172,NM_138697.3;TAS1R1,missense_variant,p.Ala97Ser,ENST00000411823,;TAS1R1,intron_variant,,ENST00000351136,NM_177540.2;TAS1R1,intron_variant,,ENST00000415267,; T ENST00000333172 Transcript missense_variant 704/2892 511/2526 171/841 A/S Gcc/Tcc 1 1 TAS1R1 HGNC HGNC:14448 protein_coding YES CCDS81.1 ENSP00000331867 Q7RTX1 UPI000004737B NM_138697.3 deleterious(0.03) 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF3,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS rs1470993468 . 0 200 10 0 0 0 0 0 -16.68948 0.999956 1 1 1 0 T 3 4 61 6574643 6574643 G T 1 0 0 0 0 1 0 0 0 15961 1203 42 2 2 TAS1R1 1 6574643 Missense_Mutation SNP G C3N-00580_T 467956 6574643 242381779 3 18138 CAMTA1 0 . GRCh38 1 7664269 7664269 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1722C>A p.= p.G574G ENST00000303635 9/23 291 143 148 183 183 0 strelka-varscan-mutect CAMTA1,synonymous_variant,p.=,ENST00000303635,NM_015215.3; A ENST00000303635 Transcript synonymous_variant 1929/8444 1722/5022 574/1673 G ggC/ggA 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 9/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 7664269 7664269 C A 1 0 0 0 0 0 0 0 1 2306 726 26 2 2 CAMTA1 1 7664269 Silent SNP C C3N-00580_T 1089626 7664269 241292153 4 18139 MTOR 0 . GRCh38 1 11241664 11241664 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1430A>T p.Gln477Leu p.Q477L ENST00000361445 10/58 195 116 79 155 155 0 strelka-varscan-mutect MTOR,missense_variant,p.Gln477Leu,ENST00000361445,NM_004958.3; A ENST00000361445 Transcript missense_variant 1507/8677 1430/7650 477/2549 Q/L cAg/cTg 1 -1 MTOR HGNC HGNC:3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 UPI000012ABD3 NM_004958.3 tolerated(0.46) 10/58 hmmpanther:PTHR11139:SF9,hmmpanther:PTHR11139,Gene3D:1.25.10.10,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 196 10 4 0 0 0 0 -20 0.9990529 1 1 1 0 A 3 1 61 11241664 11241664 T A 1 0 0 0 0 1 0 0 0 9941 1580 55 4 4 MTOR 1 11241664 Missense_Mutation SNP T C3N-00580_T 3577395 11241664 237714758 5 18140 PRAMEF15 0 . GRCh38 1 13321860 13321860 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.1033A>C p.Ile345Leu p.I345L ENST00000376152 4/4 948 885 63 832 832 0 varscan-mutect PRAMEF15,missense_variant,p.Ile345Leu,ENST00000376152,NM_001098376.2;PRAMEF15,missense_variant,p.Ile343Leu,ENST00000613530,;RP11-219C24.10,upstream_gene_variant,,ENST00000432559,; C ENST00000376152 Transcript missense_variant 1127/1865 1033/1437 345/478 I/L Att/Ctt 1 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES CCDS44059.1 ENSP00000365322 Q5VWM5 UPI0000199BA7 NM_001098376.2 tolerated(0.09) 4/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 13321860 13321860 A C 1 0 0 0 0 1 0 0 0 12559 101 4 5 5 PRAMEF15 1 13321860 Missense_Mutation SNP A C3N-00580_T 2080196 13321860 235634562 6 18141 PLEKHM2 0 . GRCh38 1 15728352 15728352 + Missense_Mutation SNP G G T rs368652190 C3N-00580_T C3N-00580_N G G c.1916G>T p.Arg639Leu p.R639L ENST00000375799 11/20 151 56 95 172 172 0 strelka-varscan-mutect PLEKHM2,missense_variant,p.Arg639Leu,ENST00000375799,NM_015164.2;PLEKHM2,missense_variant,p.Arg619Leu,ENST00000375793,;RP11-288I21.1,intron_variant,,ENST00000615472,;RP11-288I21.1,intron_variant,,ENST00000623689,;RP11-288I21.1,intron_variant,,ENST00000453804,;PLEKHM2,upstream_gene_variant,,ENST00000477849,; T ENST00000375799 Transcript missense_variant 2143/4122 1916/3060 639/1019 R/L cGg/cTg rs368652190,COSM4715724,COSM4715725 1 1 PLEKHM2 HGNC HGNC:29131 protein_coding YES CCDS44063.1 ENSP00000364956 Q8IWE5 UPI00001C1D9C NM_015164.2 deleterious(0) 11/20 hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF155 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs368652190 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 15728352 15728352 G T 1 0 0 0 0 1 0 0 0 12174 1130 39 1 1 PLEKHM2 1 15728352 Missense_Mutation SNP G C3N-00580_T 2406492 15728352 233228070 7 18142 PLEKHM2 0 . GRCh38 1 15732375 15732375 + Missense_Mutation SNP G G T rs768068764 C3N-00580_T C3N-00580_N G G c.2651G>T p.Ser884Ile p.S884I ENST00000375799 18/20 157 64 93 143 143 0 strelka-varscan-mutect PLEKHM2,missense_variant,p.Ser884Ile,ENST00000375799,NM_015164.2;PLEKHM2,missense_variant,p.Ser864Ile,ENST00000375793,;SLC25A34,upstream_gene_variant,,ENST00000294454,NM_207348.2;RP11-288I21.1,intron_variant,,ENST00000615472,;RP11-288I21.1,intron_variant,,ENST00000623689,;RP11-288I21.1,intron_variant,,ENST00000453804,;PLEKHM2,non_coding_transcript_exon_variant,,ENST00000477849,; T ENST00000375799 Transcript missense_variant 2878/4122 2651/3060 884/1019 S/I aGc/aTc rs768068764 1 1 PLEKHM2 HGNC HGNC:29131 protein_coding YES CCDS44063.1 ENSP00000364956 Q8IWE5 UPI00001C1D9C NM_015164.2 deleterious(0.03) 18/20 MODERATE 1 SNV 1 1 PASS rs768068764 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 15732375 15732375 G T 1 0 0 0 0 1 0 0 0 12174 971 34 2 2 PLEKHM2 1 15732375 Missense_Mutation SNP G C3N-00580_T 4023 15732375 233224047 8 18143 PLEKHM2 0 . GRCh38 1 15732612 15732612 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.2806G>A p.Glu936Lys p.E936K ENST00000375799 19/20 125 73 52 136 135 1 strelka-varscan-mutect PLEKHM2,missense_variant,p.Glu936Lys,ENST00000375799,NM_015164.2;PLEKHM2,missense_variant,p.Glu916Lys,ENST00000375793,;SLC25A34,upstream_gene_variant,,ENST00000294454,NM_207348.2;RP11-288I21.1,intron_variant,,ENST00000453804,;RP11-288I21.1,upstream_gene_variant,,ENST00000615472,;RP11-288I21.1,upstream_gene_variant,,ENST00000623689,;PLEKHM2,splice_region_variant,,ENST00000477849,; A ENST00000375799 Transcript missense_variant,splice_region_variant 3033/4122 2806/3060 936/1019 E/K Gag/Aag 1 1 PLEKHM2 HGNC HGNC:29131 protein_coding YES CCDS44063.1 ENSP00000364956 Q8IWE5 UPI00001C1D9C NM_015164.2 deleterious(0.01) 19/20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 15732612 15732612 G A 1 0 0 0 0 1 0 0 0 12174 1188 41 3 3 PLEKHM2 1 15732612 Missense_Mutation SNP G C3N-00580_T 237 15732612 233223810 9 18144 CROCC 0 . GRCh38 1 16924441 16924441 + Missense_Mutation SNP G G A rs201480427 C3N-00580_T C3N-00580_N G G c.313G>A p.Asp105Asn p.D105N ENST00000375541 3/37 438 347 91 342 342 0 strelka-varscan-mutect CROCC,missense_variant,p.Asp105Asn,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Asp55Asn,ENST00000445545,;CROCC,intron_variant,,ENST00000467938,;CROCC,intron_variant,,ENST00000466256,; A ENST00000375541 Transcript missense_variant 382/6656 313/6054 105/2017 D/N Gat/Aat rs201480427,COSM3966035 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 deleterious(0) 3/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs201480427 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 16924441 16924441 G A 1 0 0 0 0 1 0 0 0 3694 1058 37 1 1 CROCC 1 16924441 Missense_Mutation SNP G C3N-00580_T 1191829 16924441 232031981 10 18145 CROCC 0 . GRCh38 1 16966561 16966561 + Missense_Mutation SNP G G T rs566509715 C3N-00580_T C3N-00580_N G G c.4850G>T p.Arg1617Leu p.R1617L ENST00000375541 30/37 64 60 4 65 65 0 strelka-mutect CROCC,missense_variant,p.Arg1617Leu,ENST00000375541,NM_014675.4;CROCC,non_coding_transcript_exon_variant,,ENST00000465021,;CROCC,upstream_gene_variant,,ENST00000465291,; T ENST00000375541 Transcript missense_variant 4919/6656 4850/6054 1617/2017 R/L cGg/cTg rs566509715 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 deleterious(0) 30/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17,Superfamily_domains:SSF57997 MODERATE 1 SNV 5 1 PASS rs566509715 . 0 205 5 0 0 0 0 0 -9.727984 1 1 1 1 0 T 3 4 61 16966561 16966561 G T 1 0 0 0 0 1 0 0 0 3694 1116 39 1 1 CROCC 1 16966561 Missense_Mutation SNP G C3N-00580_T 42120 16966561 231989861 11 18146 PADI2 0 . GRCh38 1 17095909 17095909 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.411G>T p.Lys137Asn p.K137N ENST00000375486 4/16 107 96 11 107 106 1 strelka-mutect PADI2,missense_variant,p.Lys137Asn,ENST00000375486,NM_007365.2;PADI2,missense_variant,p.Lys137Asn,ENST00000375481,; A ENST00000375486 Transcript missense_variant,splice_region_variant 475/4345 411/1998 137/665 K/N aaG/aaT 1 -1 PADI2 HGNC HGNC:18341 protein_coding YES CCDS177.1 ENSP00000364635 Q9Y2J8 A0A024RA98 UPI00001314AF NM_007365.2 deleterious(0) 4/16 Superfamily_domains:0044952,PD936484,Pfam_domain:PF08527,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF12 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -19.99371 0.9998274 1 1 1 0 A 3 1 61 17095909 17095909 C A 1 0 0 0 0 1 0 0 0 11456 695 24 2 2 PADI2 1 17095909 Missense_Mutation SNP C C3N-00580_T 129348 17095909 231860513 12 18147 PADI6 0 . GRCh38 1 17398730 17398730 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1734C>A p.= p.G578G ENST00000619609 15/16 246 223 23 186 186 0 strelka-varscan-mutect PADI6,synonymous_variant,p.=,ENST00000619609,NM_207421.4; A ENST00000619609 Transcript synonymous_variant 1784/2396 1734/2085 578/694 G ggC/ggA 1 1 PADI6 HGNC HGNC:20449 protein_coding YES CCDS72715.1 ENSP00000483125 Q6TGC4 UPI0000253BE7 NM_207421.4 15/16 hmmpanther:PTHR10837:SF4,hmmpanther:PTHR10837,PIRSF_domain:PIRSF001247,Pfam_domain:PF03068,Superfamily_domains:SSF55909 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 17398730 17398730 C A 1 0 0 0 0 0 0 0 1 11459 726 26 2 2 PADI6 1 17398730 Silent SNP C C3N-00580_T 302821 17398730 231557692 13 18148 IGSF21 0 . GRCh38 1 18365513 18365513 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.831G>T p.Trp277Cys p.W277C ENST00000251296 6/10 557 500 57 599 599 0 strelka-varscan-mutect IGSF21,missense_variant,p.Trp277Cys,ENST00000251296,NM_032880.4;IGSF21,non_coding_transcript_exon_variant,,ENST00000412684,;IGSF21,non_coding_transcript_exon_variant,,ENST00000497331,; T ENST00000251296 Transcript missense_variant 1214/1943 831/1404 277/467 W/C tgG/tgT 1 1 IGSF21 HGNC HGNC:28246 protein_coding YES CCDS184.1 ENSP00000251296 Q96ID5 UPI000006FCF2 NM_032880.4 deleterious(0) 6/10 hmmpanther:PTHR10489:SF442,hmmpanther:PTHR10489 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 18365513 18365513 G T 1 0 0 0 0 1 0 0 0 7506 1241 43 2 2 IGSF21 1 18365513 Missense_Mutation SNP G C3N-00580_T 966783 18365513 230590909 14 18149 UBR4 0 . GRCh38 1 19184025 19184025 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2089G>T p.Gly697Ter p.G697* ENST00000375254 16/106 174 151 23 134 134 0 strelka-varscan-mutect UBR4,stop_gained,p.Gly697Ter,ENST00000375254,NM_020765.2; A ENST00000375254 Transcript stop_gained 2117/15906 2089/15552 697/5183 G/* Gga/Tga 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 16/106 hmmpanther:PTHR21725 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 19184025 19184025 C A 1 0 0 0 0 0 1 0 0 17428 603 21 2 2 UBR4 1 19184025 Nonsense_Mutation SNP C C3N-00580_T 818512 19184025 229772397 15 18150 VWA5B1 0 . GRCh38 1 20354005 20354005 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.3405G>T p.Arg1135Ser p.R1135S ENST00000375079 22/22 409 355 54 430 430 0 strelka-varscan-mutect VWA5B1,missense_variant,p.Arg1130Ser,ENST00000289815,NM_001039500.2;VWA5B1,missense_variant,p.Arg1135Ser,ENST00000375079,;VWA5B1,non_coding_transcript_exon_variant,,ENST00000525343,;VWA5B1,3_prime_UTR_variant,,ENST00000485375,;VWA5B1,3_prime_UTR_variant,,ENST00000467486,; T ENST00000375079 Transcript missense_variant 3601/3859 3405/3663 1135/1220 R/S agG/agT 1 1 VWA5B1 HGNC HGNC:26538 protein_coding YES ENSP00000364220 Q5TIE3 UPI000066D8B8 tolerated(0.76) 22/22 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF109 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20354005 20354005 G T 1 0 0 0 0 1 0 0 0 17797 1223 43 2 2 VWA5B1 1 20354005 Missense_Mutation SNP G C3N-00580_T 1169980 20354005 228602417 16 18151 EIF4G3 0 . GRCh38 1 20904923 20904923 + Missense_Mutation SNP C C A rs772664825 C3N-00580_T C3N-00580_N C C c.1541G>T p.Arg514Leu p.R514L ENST00000400422 12/35 184 157 27 194 194 0 strelka-varscan-mutect EIF4G3,missense_variant,p.Arg521Leu,ENST00000602326,NM_001198802.1;EIF4G3,missense_variant,p.Arg515Leu,ENST00000264211,NM_003760.4;EIF4G3,missense_variant,p.Arg514Leu,ENST00000400422,NM_001198801.1;EIF4G3,missense_variant,p.Arg235Leu,ENST00000374935,;EIF4G3,missense_variant,p.Arg704Leu,ENST00000634879,;EIF4G3,non_coding_transcript_exon_variant,,ENST00000374933,; A ENST00000400422 Transcript missense_variant 2122/5762 1541/4866 514/1621 R/L cGg/cTg rs772664825,COSM1238771,COSM1238772 1 -1 EIF4G3 HGNC HGNC:3298 protein_coding YES CCDS72723.1 ENSP00000383274 A0A0A0MSA7 UPI0000D4C1EC NM_001198801.1 tolerated_low_confidence(0.3) 12/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF23 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs772664825 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 61 20904923 20904923 C A 1 0 0 0 0 1 0 0 0 4871 652 23 1 1 EIF4G3 1 20904923 Missense_Mutation SNP C C3N-00580_T 550918 20904923 228051499 17 18152 HSPG2 0 . GRCh38 1 21890664 21890664 + Missense_Mutation SNP C C T rs554613529 C3N-00580_T C3N-00580_N C C c.275G>A p.Arg92His p.R92H ENST00000374695 4/97 622 356 266 766 765 1 strelka-varscan-mutect HSPG2,missense_variant,p.Arg92His,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,intron_variant,,ENST00000412328,;HSPG2,upstream_gene_variant,,ENST00000374673,;HSPG2,non_coding_transcript_exon_variant,,ENST00000439717,; T ENST00000374695 Transcript missense_variant 355/14327 275/13176 92/4391 R/H cGc/cAc rs554613529 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 tolerated(0.59) 4/97 PROSITE_profiles:PS50024,SMART_domains:SM00200 MODERATE 1 SNV 1 1 PASS rs554613529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 21890664 21890664 C T 1 0 0 0 0 1 0 0 0 7326 768 27 1 1 HSPG2 1 21890664 Missense_Mutation SNP C C3N-00580_T 985741 21890664 227065758 18 18153 C1QC 0 . GRCh38 1 22647279 22647279 + Silent SNP C C A rs112294511 C3N-00580_T C3N-00580_N C C c.234C>A p.= p.P78P ENST00000374639 3/3 226 188 38 215 215 0 strelka-varscan-mutect C1QC,synonymous_variant,p.=,ENST00000374639,NM_001114101.1;C1QC,synonymous_variant,p.=,ENST00000374640,NM_172369.3;C1QC,synonymous_variant,p.=,ENST00000374637,; A ENST00000374639 Transcript synonymous_variant 352/1183 234/738 78/245 P ccC/ccA rs112294511 1 1 C1QC HGNC HGNC:1245 protein_coding YES CCDS227.1 ENSP00000363770 P02747 A0A024RAA7 UPI0000126BF3 NM_001114101.1 3/3 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF558 LOW 1 SNV 2 1 PASS rs112294511 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 22647279 22647279 C A 1 0 0 0 0 0 0 0 1 1935 639 23 1 1 C1QC 1 22647279 Silent SNP C C3N-00580_T 756615 22647279 226309143 19 18154 MYOM3 0 . GRCh38 1 24107099 24107099 + Silent SNP G G T rs761928788 C3N-00580_T C3N-00580_N G G c.376C>A p.= p.R126R ENST00000374434 4/37 126 114 12 168 168 0 strelka-varscan-mutect MYOM3,synonymous_variant,p.=,ENST00000374434,NM_152372.3;MYOM3,non_coding_transcript_exon_variant,,ENST00000475306,; T ENST00000374434 Transcript synonymous_variant 539/5804 376/4314 126/1437 R Cgg/Agg rs761928788 1 -1 MYOM3 HGNC HGNC:26679 protein_coding YES CCDS41281.1 ENSP00000363557 Q5VTT5 UPI0000203A5D NM_152372.3 4/37 Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs761928788 . 0 206 2 2 0 0 0 0 -17.67532 0.999995 1 1 1 0 T 2 4 61 24107099 24107099 G T 1 0 0 0 0 0 0 0 1 10094 1086 38 1 1 MYOM3 1 24107099 Silent SNP G C3N-00580_T 1459820 24107099 224849323 20 18155 IL22RA1 0 . GRCh38 1 24138596 24138596 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.162C>T p.= p.S54S ENST00000270800 2/7 215 179 36 188 188 0 strelka-varscan-mutect IL22RA1,synonymous_variant,p.=,ENST00000270800,NM_021258.3; A ENST00000270800 Transcript synonymous_variant 201/2798 162/1725 54/574 S agC/agT 1 -1 IL22RA1 HGNC HGNC:13700 protein_coding YES CCDS247.1 ENSP00000270800 Q8N6P7 UPI0000071143 NM_021258.3 2/7 Gene3D:2.60.40.10,Pfam_domain:PF01108,PROSITE_profiles:PS50853,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF20,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 24138596 24138596 G A 1 0 0 0 0 0 0 0 1 7576 1310 46 3 3 IL22RA1 1 24138596 Silent SNP G C3N-00580_T 31497 24138596 224817826 21 18156 SLC30A2 0 . GRCh38 1 26039843 26039843 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.907C>T p.= p.L303L ENST00000374276 7/8 351 295 56 369 369 0 strelka-varscan-mutect SLC30A2,synonymous_variant,p.=,ENST00000374278,NM_032513.4;SLC30A2,synonymous_variant,p.=,ENST00000374276,NM_001004434.2;EXTL1,downstream_gene_variant,,ENST00000374280,NM_004455.2;SLC30A2,downstream_gene_variant,,ENST00000498060,;EXTL1,downstream_gene_variant,,ENST00000470037,; A ENST00000374276 Transcript synonymous_variant 1144/2494 907/1119 303/372 L Ctg/Ttg 1 -1 SLC30A2 HGNC HGNC:11013 protein_coding YES CCDS30644.1 ENSP00000363394 Q9BRI3 UPI0000049F98 NM_001004434.2 7/8 hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF51,TIGRFAM_domain:TIGR01297,Superfamily_domains:SSF160240 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 26039843 26039843 G A 1 0 0 0 0 0 0 0 1 14825 991 35 3 3 SLC30A2 1 26039843 Silent SNP G C3N-00580_T 1901247 26039843 222916579 22 18157 AIM1L 0 . GRCh38 1 26336691 26336691 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.3953A>G p.Tyr1318Cys p.Y1318C ENST00000308182 12/20 267 240 27 585 585 0 strelka-varscan-mutect AIM1L,missense_variant,p.Tyr1318Cys,ENST00000308182,NM_001039775.3;AIM1L,missense_variant,p.Tyr444Cys,ENST00000527815,;AIM1L,missense_variant,p.Tyr211Cys,ENST00000429942,;AIM1L,non_coding_transcript_exon_variant,,ENST00000522993,;AIM1L,non_coding_transcript_exon_variant,,ENST00000522923,;AIM1L,upstream_gene_variant,,ENST00000520372,; C ENST00000308182 Transcript missense_variant 4103/5245 3953/4986 1318/1661 Y/C tAc/tGc 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 deleterious(0.01) 12/20 Gene3D:2.60.20.10,Pfam_domain:PF00030,PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF50,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 26336691 26336691 T C 1 0 0 0 0 1 0 0 0 508 1638 57 5 5 AIM1L 1 26336691 Missense_Mutation SNP T C3N-00580_T 296848 26336691 222619731 23 18158 PUM1 0 . GRCh38 1 30964686 30964717 + Frame_Shift_Del DEL TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA - novel C3N-00580_T C3N-00580_N TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA c.2280_2311delTCCTTCCCTCTCTTCACATGGATCCTCTTCAA p.Pro761LeufsTer21 p.P761Lfs*21 ENST00000426105 14/22 321 280 41 385 384 1 sindel-pindel PUM1,frameshift_variant,p.Pro762LeufsTer21,ENST00000373747,;PUM1,frameshift_variant,p.Pro761LeufsTer21,ENST00000257075,NM_014676.2;PUM1,frameshift_variant,p.Pro519LeufsTer21,ENST00000424085,;PUM1,frameshift_variant,p.Pro797LeufsTer21,ENST00000373741,;PUM1,frameshift_variant,p.Pro761LeufsTer21,ENST00000426105,NM_001020658.1;PUM1,frameshift_variant,p.Pro735LeufsTer21,ENST00000440538,;PUM1,frameshift_variant,p.Pro702LeufsTer21,ENST00000373742,;PUM1,frameshift_variant,p.Pro473LeufsTer21,ENST00000498419,;PUM1,intron_variant,,ENST00000525843,;PUM1,downstream_gene_variant,,ENST00000532678,;PUM1,downstream_gene_variant,,ENST00000490546,;PUM1,frameshift_variant,p.Pro53LeufsTer?,ENST00000527498,;PUM1,downstream_gene_variant,,ENST00000471894,;PUM1,downstream_gene_variant,,ENST00000498627,; - ENST00000426105 Transcript frameshift_variant 2371-2402/4043 2280-2311/3567 760-771/1188 PPSLSSHGSSSS/PX ccTCCTTCCCTCTCTTCACATGGATCCTCTTCAAgc/ccgc 1 -1 PUM1 HGNC HGNC:14957 protein_coding YES CCDS44099.1 ENSP00000391723 Q14671 UPI0000203D8E NM_001020658.1 14/22 hmmpanther:PTHR12537,hmmpanther:PTHR12537:SF1,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 30964686 30964686 TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA - 1 0 1 0 1 0 0 0 0 12982 1609 56 0 0 PUM1 1 30964686 Frame_Shift_Del DEL TTGAAGAGGATCCATGTGAAGAGAGGGAAGGA C3N-00580_T 4627995 30964686 217991736 24 18159 C1orf94 0 . GRCh38 1 34200964 34200964 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1202C>A p.Ala401Asp p.A401D ENST00000488417 3/7 454 339 115 472 472 0 strelka-varscan-mutect C1orf94,missense_variant,p.Ala401Asp,ENST00000488417,NM_001134734.1;C1orf94,missense_variant,p.Ala211Asp,ENST00000373374,NM_032884.4; A ENST00000488417 Transcript missense_variant 1322/2287 1202/1797 401/598 A/D gCc/gAc 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 deleterious_low_confidence(0.05) 3/7 hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1,Pfam_domain:PF15752 MODERATE 1 SNV 1 1 PASS rs1412312966 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 34200964 34200964 C A 1 0 0 0 0 1 0 0 0 2000 739 26 2 2 C1orf94 1 34200964 Missense_Mutation SNP C C3N-00580_T 3236278 34200964 214755458 25 18160 HIVEP3 0 . GRCh38 1 41584182 41584182 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.616G>T p.Val206Leu p.V206L ENST00000372583 4/9 210 101 109 198 198 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Val206Leu,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Val206Leu,ENST00000372583,NM_024503.4;HIVEP3,upstream_gene_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 1502/12193 616/7221 206/2406 V/L Gtg/Ttg 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious(0.01) 4/9 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 41584182 41584182 C A 1 0 0 0 0 1 0 0 0 7077 536 19 1 1 HIVEP3 1 41584182 Missense_Mutation SNP C C3N-00580_T 7383218 41584182 207372240 26 18161 YBX1 0 . GRCh38 1 42696672 42696672 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.385G>T p.Gly129Cys p.G129C ENST00000321358 5/8 36 19 17 29 29 0 strelka-varscan-mutect YBX1,missense_variant,p.Gly179Cys,ENST00000436427,;YBX1,missense_variant,p.Gly129Cys,ENST00000321358,NM_004559.3;YBX1,missense_variant,p.Gly99Cys,ENST00000332220,;YBX1,non_coding_transcript_exon_variant,,ENST00000467957,; T ENST00000321358 Transcript missense_variant 524/1514 385/975 129/324 G/C Ggt/Tgt 1 1 YBX1 HGNC HGNC:8014 protein_coding YES CCDS470.1 ENSP00000361626 P67809 UPI0000001C6B NM_004559.3 deleterious(0.02) 5/8 hmmpanther:PTHR11544 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 42696672 42696672 G T 1 0 0 0 0 1 0 0 0 18030 1348 47 2 2 YBX1 1 42696672 Missense_Mutation SNP G C3N-00580_T 1112490 42696672 206259750 27 18162 MAST2 0 . GRCh38 1 45824557 45824557 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.302G>C p.Gly101Ala p.G101A ENST00000361297 2/29 123 85 38 135 135 0 strelka-varscan-mutect MAST2,missense_variant,p.Gly101Ala,ENST00000361297,NM_001324320.1,NM_001319245.1,NM_015112.2;MAST2,non_coding_transcript_exon_variant,,ENST00000470809,; C ENST00000361297 Transcript missense_variant 585/5738 302/5397 101/1798 G/A gGa/gCa 1 1 MAST2 HGNC HGNC:19035 protein_coding YES CCDS41326.1 ENSP00000354671 Q6P0Q8 UPI0000458AEB NM_001324320.1,NM_001319245.1,NM_015112.2 deleterious_low_confidence(0.01) 2/29 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 45824557 45824557 G C 1 0 0 0 0 1 0 0 0 9251 1174 41 4 4 MAST2 1 45824557 Missense_Mutation SNP G C3N-00580_T 3127885 45824557 203131865 28 18163 CYP4X1 0 . GRCh38 1 47046498 47046498 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1105A>T p.Met369Leu p.M369L ENST00000371901 9/12 244 122 122 199 199 0 strelka-varscan-mutect CYP4X1,missense_variant,p.Met369Leu,ENST00000371901,NM_178033.1; T ENST00000371901 Transcript missense_variant 1355/2357 1105/1530 369/509 M/L Atg/Ttg 1 1 CYP4X1 HGNC HGNC:20244 protein_coding YES CCDS544.1 ENSP00000360968 Q8N118 UPI000003F043 NM_178033.1 tolerated(0.06) 9/12 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00385,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF55,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs916282190 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 47046498 47046498 A T 1 0 0 0 0 1 0 0 0 3996 101 4 4 4 CYP4X1 1 47046498 Missense_Mutation SNP A C3N-00580_T 1221941 47046498 201909924 29 18164 TTC39A 0 . GRCh38 1 51302517 51302517 + Silent SNP G G T rs367944910 C3N-00580_T C3N-00580_N G G c.928C>A p.= p.R310R ENST00000447632 10/18 337 195 142 397 397 0 strelka-varscan-mutect TTC39A,synonymous_variant,p.=,ENST00000262676,;TTC39A,synonymous_variant,p.=,ENST00000447632,NM_001297665.1;TTC39A,synonymous_variant,p.=,ENST00000413473,NM_001144832.2;TTC39A,synonymous_variant,p.=,ENST00000262675,NM_001297664.1,NM_001297663.1;TTC39A,synonymous_variant,p.=,ENST00000371750,NM_001080494.3;TTC39A,synonymous_variant,p.=,ENST00000371747,NM_001297662.1;TTC39A,synonymous_variant,p.=,ENST00000439482,;TTC39A,synonymous_variant,p.=,ENST00000411642,;TTC39A,upstream_gene_variant,,ENST00000530004,NM_001297667.1,NM_001297666.1;TTC39A,downstream_gene_variant,,ENST00000422925,;TTC39A,downstream_gene_variant,,ENST00000380849,;TTC39A,non_coding_transcript_exon_variant,,ENST00000431927,;TTC39A,non_coding_transcript_exon_variant,,ENST00000524442,;TTC39A,upstream_gene_variant,,ENST00000534098,; T ENST00000447632 Transcript synonymous_variant 977/2790 928/1842 310/613 R Cgg/Agg rs367944910 1 -1 TTC39A HGNC HGNC:18657 protein_coding YES CCDS72790.1 ENSP00000393952 Q5SRH9 UPI000046FE6B NM_001297665.1 10/18 Gene3D:1.25.40.10,Pfam_domain:PF10300,hmmpanther:PTHR31859,hmmpanther:PTHR31859:SF3,Superfamily_domains:SSF81901 LOW 1 SNV 1 1 PASS rs367944910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 51302517 51302517 G T 1 0 0 0 0 0 0 0 1 17216 1115 39 1 1 TTC39A 1 51302517 Silent SNP G C3N-00580_T 4256019 51302517 197653905 30 18165 NRDC 0 . GRCh38 1 51834102 51834102 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.985G>T p.Gly329Cys p.G329C ENST00000354831 6/33 211 151 60 241 241 0 strelka-varscan-mutect NRDC,missense_variant,p.Gly329Cys,ENST00000354831,NM_002525.2;NRDC,missense_variant,p.Gly261Cys,ENST00000544028,;NRDC,missense_variant,p.Gly261Cys,ENST00000352171,NM_001101662.1;NRDC,missense_variant,p.Gly197Cys,ENST00000539524,NM_001242361.1;NRDC,downstream_gene_variant,,ENST00000390787,;NRDC,non_coding_transcript_exon_variant,,ENST00000485608,;NRDC,non_coding_transcript_exon_variant,,ENST00000475715,;NRDC,upstream_gene_variant,,ENST00000473805,; A ENST00000354831 Transcript missense_variant 1175/3895 985/3660 329/1219 G/C Ggt/Tgt 1 -1 NRDC HGNC HGNC:7995 protein_coding YES CCDS559.1 ENSP00000346890 B1AKJ5 UPI0000458A53 NM_002525.2 deleterious(0) 6/33 hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF123,Gene3D:3.30.830.10,Pfam_domain:PF00675,Superfamily_domains:SSF63411 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 51834102 51834102 C A 1 0 0 0 0 1 0 0 0 10701 623 22 2 2 NRDC 1 51834102 Missense_Mutation SNP C C3N-00580_T 531585 51834102 197122320 31 18166 TTC4 0 . GRCh38 1 54731622 54731622 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.818G>T p.Arg273Met p.R273M ENST00000371281 7/10 367 209 158 443 443 0 strelka-varscan-mutect TTC4,missense_variant,p.Arg273Met,ENST00000371281,NM_004623.4;TTC4,non_coding_transcript_exon_variant,,ENST00000371284,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000414150,;MROH7-TTC4,non_coding_transcript_exon_variant,,ENST00000460155,;MROH7-TTC4,intron_variant,,ENST00000606515,; T ENST00000371281 Transcript missense_variant 905/2395 818/1164 273/387 R/M aGg/aTg COSM910943 1 1 TTC4 HGNC HGNC:12394 protein_coding YES CCDS596.1 ENSP00000360329 O95801 UPI000013E156 NM_004623.4 tolerated(0.19) 7/10 hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF365 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 54731622 54731622 G T 1 0 0 0 0 1 0 0 0 17219 1000 35 2 2 TTC4 1 54731622 Missense_Mutation SNP G C3N-00580_T 2897520 54731622 194224800 32 18167 L1TD1 0 . GRCh38 1 62210040 62210040 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.1266A>T p.= p.S422S ENST00000498273 4/4 240 132 108 245 244 1 strelka-varscan-mutect L1TD1,synonymous_variant,p.=,ENST00000498273,NM_001164835.1,NM_019079.4;Y_RNA,upstream_gene_variant,,ENST00000363304,;RP5-1155K23.4,upstream_gene_variant,,ENST00000450606,; T ENST00000498273 Transcript synonymous_variant 1561/3849 1266/2598 422/865 S tcA/tcT 1 1 L1TD1 HGNC HGNC:25595 protein_coding YES CCDS619.1 ENSP00000419901 Q5T7N2 UPI000013E18E NM_001164835.1,NM_019079.4 4/4 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 62210040 62210040 A T 1 0 0 0 0 0 0 0 1 8490 175 7 4 4 L1TD1 1 62210040 Silent SNP A C3N-00580_T 7478418 62210040 186746382 33 18168 DOCK7 0 . GRCh38 1 62494354 62494354 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.5111A>T p.His1704Leu p.H1704L ENST00000454575 40/49 244 202 42 285 284 1 strelka-varscan-mutect DOCK7,missense_variant,p.His1704Leu,ENST00000251157,;DOCK7,missense_variant,p.His1704Leu,ENST00000454575,NM_001271999.1;DOCK7,missense_variant,p.His1682Leu,ENST00000340370,NM_033407.3;DOCK7,missense_variant,p.His1713Leu,ENST00000635253,;DOCK7,missense_variant,p.His1673Leu,ENST00000634264,NM_001272000.1;DOCK7,missense_variant,p.His1673Leu,ENST00000635123,NM_001272001.1;DOCK7,missense_variant,p.His804Leu,ENST00000637255,;DOCK7,downstream_gene_variant,,ENST00000637144,;DOCK7,3_prime_UTR_variant,,ENST00000637208,;DOCK7,non_coding_transcript_exon_variant,,ENST00000635983,;DOCK7,non_coding_transcript_exon_variant,,ENST00000479983,;DOCK7,upstream_gene_variant,,ENST00000635088,; A ENST00000454575 Transcript missense_variant 5122/6985 5111/6390 1704/2129 H/L cAc/cTc 1 -1 DOCK7 HGNC HGNC:19190 protein_coding YES CCDS60156.1 ENSP00000413583 Q96N67 H0Y7L2 UPI0000E45660 NM_001271999.1 deleterious(0) 40/49 PROSITE_profiles:PS51651,hmmpanther:PTHR23317:SF78,hmmpanther:PTHR23317,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 62494354 62494354 T A 1 0 0 0 0 1 0 0 0 4507 1696 59 4 4 DOCK7 1 62494354 Missense_Mutation SNP T C3N-00580_T 284314 62494354 186462068 34 18169 ROR1 0 . GRCh38 1 64177527 64177527 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1486G>T p.Gly496Cys p.G496C ENST00000371079 9/9 334 207 127 356 356 0 strelka-varscan-mutect ROR1,missense_variant,p.Gly496Cys,ENST00000371079,NM_005012.3;ROR1,missense_variant,p.Gly441Cys,ENST00000545203,; T ENST00000371079 Transcript missense_variant 1861/5832 1486/2814 496/937 G/C Ggc/Tgc 1 1 ROR1 HGNC HGNC:10256 protein_coding YES CCDS626.1 ENSP00000360120 Q01973 UPI00001AF82C NM_005012.3 deleterious(0) 9/9 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF134,Pfam_domain:PF07714,PIRSF_domain:PIRSF000624,Gene3D:3.30.200.20,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 64177527 64177527 G T 1 0 0 0 0 1 0 0 0 13703 1000 35 2 2 ROR1 1 64177527 Missense_Mutation SNP G C3N-00580_T 1683173 64177527 184778895 35 18170 SSX2IP 0 . GRCh38 1 84658441 84658441 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.955G>T p.Gly319Trp p.G319W ENST00000342203 9/14 168 149 19 176 176 0 strelka-varscan-mutect SSX2IP,missense_variant,p.Gly292Trp,ENST00000437941,NM_001166294.1,NM_001166295.1;SSX2IP,missense_variant,p.Gly319Trp,ENST00000342203,NM_014021.3,NM_001166293.1,NM_001166417.1;SSX2IP,missense_variant,p.Gly292Trp,ENST00000605755,;SSX2IP,intron_variant,,ENST00000603677,;SSX2IP,missense_variant,p.Gly319Trp,ENST00000481102,;SSX2IP,missense_variant,p.Gly315Trp,ENST00000476905,;SSX2IP,non_coding_transcript_exon_variant,,ENST00000460500,;SSX2IP,upstream_gene_variant,,ENST00000459708,; A ENST00000342203 Transcript missense_variant 1219/5835 955/1845 319/614 G/W Ggg/Tgg COSM4144203,COSM4144204 1 -1 SSX2IP HGNC HGNC:16509 protein_coding YES CCDS699.1 ENSP00000340279 Q9Y2D8 UPI00000728CA NM_014021.3,NM_001166293.1,NM_001166417.1 tolerated(0.05) 9/14 hmmpanther:PTHR21736,hmmpanther:PTHR21736:SF21 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1171194235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 84658441 84658441 C A 1 0 0 0 0 1 0 0 0 15583 652 23 1 1 SSX2IP 1 84658441 Missense_Mutation SNP C C3N-00580_T 20480914 84658441 164297981 36 18171 GBP3 0 . GRCh38 1 89013183 89013183 + Splice_Site SNP A A G novel C3N-00580_T C3N-00580_N A A c.868+2T>C p.X290_splice ENST00000370481 152 137 15 118 118 0 strelka-varscan-mutect GBP3,splice_donor_variant,,ENST00000370481,NM_018284.2;GBP3,intron_variant,,ENST00000445969,;GBP3,upstream_gene_variant,,ENST00000461384,;GBP3,downstream_gene_variant,,ENST00000564665,;GBP3,downstream_gene_variant,,ENST00000475853,;GBP3,splice_donor_variant,,ENST00000370482,;GBP3,splice_donor_variant,,ENST00000493594,;GBP3,splice_donor_variant,,ENST00000489444,;GBP3,splice_donor_variant,,ENST00000235878,;GBP3,downstream_gene_variant,,ENST00000568006,; G ENST00000370481 Transcript splice_donor_variant -/3067 868/1788 290/595 1 -1 GBP3 HGNC HGNC:4184 protein_coding YES CCDS717.2 ENSP00000359512 Q9H0R5 UPI0000204D81 NM_018284.2 6/10 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 61 89013183 89013183 A G 1 0 0 0 0 0 0 1 0 6145 405 14 5 5 GBP3 1 89013183 Splice_Site SNP A C3N-00580_T 4354742 89013183 159943239 37 18172 LRRC8C 0 . GRCh38 1 89713811 89713811 + Missense_Mutation SNP T T G novel C3N-00580_T C3N-00580_N T T c.1241T>G p.Leu414Arg p.L414R ENST00000370454 3/3 229 206 23 170 170 0 strelka-varscan-mutect LRRC8C,missense_variant,p.Leu414Arg,ENST00000370454,NM_032270.4;LRRC8C,intron_variant,,ENST00000479252,;RP11-302M6.4,intron_variant,,ENST00000370453,; G ENST00000370454 Transcript missense_variant 1496/7218 1241/2412 414/803 L/R cTg/cGg 1 1 LRRC8C HGNC HGNC:25075 protein_coding YES CCDS725.1 ENSP00000359483 Q8TDW0 UPI000013E814 NM_032270.4 deleterious(0) 3/3 hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF250 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 89713811 89713811 T G 1 0 0 0 0 1 0 0 0 8927 1580 55 5 5 LRRC8C 1 89713811 Missense_Mutation SNP T C3N-00580_T 700628 89713811 159242611 38 18173 DPYD 0 . GRCh38 1 97234995 97234995 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.2300-1G>T p.X767_splice ENST00000370192 410 228 182 460 460 0 strelka-varscan-mutect DPYD,splice_acceptor_variant,,ENST00000370192,NM_000110.3;DPYD-AS1,intron_variant,,ENST00000422980,; A ENST00000370192 Transcript splice_acceptor_variant -/4412 2300/3078 767/1025 1 -1 DPYD HGNC HGNC:3012 protein_coding YES CCDS30777.1 ENSP00000359211 Q12882 UPI00000727C7 NM_000110.3 18/22 HIGH 1 SNV 1 1 PASS rs984858263 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 97234995 97234995 C A 1 0 0 0 0 0 0 1 0 4560 695 24 2 2 DPYD 1 97234995 Splice_Site SNP C C3N-00580_T 7521184 97234995 151721427 39 18174 GPR88 0 . GRCh38 1 100539852 100539852 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.886G>T p.Ala296Ser p.A296S ENST00000315033 2/2 173 94 79 192 192 0 strelka-varscan-mutect GPR88,missense_variant,p.Ala296Ser,ENST00000315033,NM_022049.2; T ENST00000315033 Transcript missense_variant 1325/3491 886/1155 296/384 A/S Gcc/Tcc 1 1 GPR88 HGNC HGNC:4539 protein_coding YES CCDS772.1 ENSP00000314223 Q9GZN0 UPI00001403B3 NM_022049.2 tolerated(0.93) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF233,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 100539852 100539852 G T 1 0 0 0 0 1 0 0 0 6598 1203 42 2 2 GPR88 1 100539852 Missense_Mutation SNP G C3N-00580_T 3304857 100539852 148416570 40 18175 VCAM1 0 . GRCh38 1 100720575 100720575 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.164C>A p.Pro55Gln p.P55Q ENST00000294728 2/9 298 191 107 289 289 0 strelka-varscan-mutect VCAM1,missense_variant,p.Pro55Gln,ENST00000294728,NM_001078.3;VCAM1,missense_variant,p.Pro55Gln,ENST00000347652,NM_080682.2;VCAM1,missense_variant,p.Pro55Gln,ENST00000370115,;VCAM1,intron_variant,,ENST00000370119,NM_001199834.1; A ENST00000294728 Transcript missense_variant 265/3083 164/2220 55/739 P/Q cCa/cAa COSM3470315 1 1 VCAM1 HGNC HGNC:12663 protein_coding YES CCDS773.1 ENSP00000294728 P19320 UPI0000000E06 NM_001078.3 deleterious(0) 2/9 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF729,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 100720575 100720575 C A 1 0 0 0 0 1 0 0 0 17682 594 21 2 2 VCAM1 1 100720575 Missense_Mutation SNP C C3N-00580_T 180723 100720575 148235847 41 18176 S1PR1 0 . GRCh38 1 101239283 101239283 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.299C>A p.Ala100Asp p.A100D ENST00000305352 2/2 183 96 87 164 163 1 strelka-varscan-mutect S1PR1,missense_variant,p.Ala100Asp,ENST00000305352,NM_001320730.1,NM_001400.4;RP4-575N6.5,upstream_gene_variant,,ENST00000561748,;RP4-575N6.4,upstream_gene_variant,,ENST00000432195,;S1PR1,non_coding_transcript_exon_variant,,ENST00000475821,;S1PR1,downstream_gene_variant,,ENST00000475289,; A ENST00000305352 Transcript missense_variant 674/2909 299/1149 100/382 A/D gCt/gAt 1 1 S1PR1 HGNC HGNC:3165 protein_coding YES CCDS777.1 ENSP00000305416 P21453 UPI0000050421 NM_001320730.1,NM_001400.4 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR01523,PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF16,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 101239283 101239283 C A 1 0 0 0 0 1 0 0 0 14052 797 28 2 2 S1PR1 1 101239283 Missense_Mutation SNP C C3N-00580_T 518708 101239283 147717139 42 18177 COL11A1 0 . GRCh38 1 102978906 102978906 + Missense_Mutation SNP C C A rs779814887 C3N-00580_T C3N-00580_N C C c.2663G>T p.Arg888Leu p.R888L ENST00000370096 34/67 579 352 227 538 537 1 strelka-varscan-mutect COL11A1,missense_variant,p.Arg900Leu,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Arg888Leu,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Arg849Leu,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Arg772Leu,ENST00000512756,NM_080630.3;COL11A1,synonymous_variant,p.=,ENST00000635193,; A ENST00000370096 Transcript missense_variant 2976/7286 2663/5421 888/1806 R/L cGa/cTa rs779814887,COSM4759632,COSM4759633 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.01) 34/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs779814887 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 102978906 102978906 C A 1 0 0 0 0 1 0 0 0 3455 884 31 1 1 COL11A1 1 102978906 Missense_Mutation SNP C C3N-00580_T 1739623 102978906 145977516 43 18178 COL11A1 0 . GRCh38 1 103017883 103017883 + Splice_Site SNP C C T novel C3N-00580_T C3N-00580_N C C c.1351-1G>A p.X451_splice ENST00000370096 283 230 53 276 276 0 strelka-varscan-mutect COL11A1,splice_acceptor_variant,,ENST00000358392,NM_080629.2;COL11A1,splice_acceptor_variant,,ENST00000370096,NM_001854.3;COL11A1,splice_acceptor_variant,,ENST00000353414,NM_001190709.1;COL11A1,splice_acceptor_variant,,ENST00000512756,NM_080630.3;COL11A1,splice_acceptor_variant,,ENST00000427239,;COL11A1,splice_acceptor_variant,,ENST00000635193,; T ENST00000370096 Transcript splice_acceptor_variant -/7286 1351/5421 451/1806 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 10/66 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 103017883 103017883 C T 1 0 0 0 0 0 0 1 0 3455 695 24 3 3 COL11A1 1 103017883 Splice_Site SNP C C3N-00580_T 38977 103017883 145938539 44 18179 WDR47 0 . GRCh38 1 109002323 109002323 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1358A>T p.Gln453Leu p.Q453L ENST00000400794 7/15 220 199 21 215 215 0 strelka-varscan-mutect WDR47,missense_variant,p.Gln446Leu,ENST00000369965,NM_014969.5;WDR47,missense_variant,p.Gln445Leu,ENST00000369962,NM_001142551.1;WDR47,missense_variant,p.Gln417Leu,ENST00000357672,;WDR47,missense_variant,p.Gln453Leu,ENST00000400794,NM_001142550.1;WDR47,missense_variant,p.Gln417Leu,ENST00000361054,; A ENST00000400794 Transcript missense_variant 1492/4134 1358/2784 453/927 Q/L cAa/cTa 1 -1 WDR47 HGNC HGNC:29141 protein_coding YES CCDS44186.1 ENSP00000383599 O94967 UPI0001639B05 NM_001142550.1 deleterious(0.01) 7/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19863,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 109002323 109002323 T A 1 0 0 0 0 1 0 0 0 17860 1812 63 4 4 WDR47 1 109002323 Missense_Mutation SNP T C3N-00580_T 5984440 109002323 139954099 45 18180 CASQ2 0 . GRCh38 1 115768489 115768489 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.53G>A p.Arg18Lys p.R18K ENST00000261448 1/11 415 246 169 316 315 1 strelka-varscan-mutect CASQ2,missense_variant,p.Arg18Lys,ENST00000261448,NM_001232.3; T ENST00000261448 Transcript missense_variant 293/2674 53/1200 18/399 R/K aGg/aAg COSM3471840 1 -1 CASQ2 HGNC HGNC:1513 protein_coding YES CCDS884.1 ENSP00000261448 O14958 UPI0000126F16 NM_001232.3 tolerated(0.31) 1/11 Pfam_domain:PF01216,hmmpanther:PTHR10033,hmmpanther:PTHR10033:SF15,Cleavage_site_(Signalp):SignalP-noTM 1 MODERATE 1 SNV 1 1 1 PASS rs1324526301 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 115768489 115768489 C T 1 0 0 0 0 1 0 0 0 2380 681 24 3 3 CASQ2 1 115768489 Missense_Mutation SNP C C3N-00580_T 6766166 115768489 133187933 46 18181 IGSF3 0 . GRCh38 1 116616458 116616458 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.44-1G>T p.X15_splice ENST00000369483 70 46 24 54 54 0 strelka-varscan-mutect IGSF3,splice_acceptor_variant,,ENST00000369483,NM_001542.3;IGSF3,splice_acceptor_variant,,ENST00000369486,NM_001007237.2;IGSF3,splice_acceptor_variant,,ENST00000318837,;IGSF3,splice_acceptor_variant,,ENST00000481589,; A ENST00000369483 Transcript splice_acceptor_variant -/7326 44/3645 15/1214 1 -1 IGSF3 HGNC HGNC:5950 protein_coding YES CCDS30814.1 ENSP00000358495 O75054 UPI0000140437 NM_001542.3 2/11 HIGH 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 5 1 61 116616458 116616458 C A 1 0 0 0 0 0 0 1 0 7509 695 24 2 2 IGSF3 1 116616458 Splice_Site SNP C C3N-00580_T 847969 116616458 132339964 47 18182 TTF2 0 . GRCh38 1 117098838 117098838 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3275C>A p.Pro1092Gln p.P1092Q ENST00000369466 22/23 194 152 42 193 193 0 strelka-varscan-mutect TTF2,missense_variant,p.Pro1092Gln,ENST00000369466,NM_003594.3;TTF2,missense_variant,p.Pro73Gln,ENST00000427271,;MIR942,downstream_gene_variant,,ENST00000401111,;TTF2,non_coding_transcript_exon_variant,,ENST00000480701,;TTF2,non_coding_transcript_exon_variant,,ENST00000492682,;TTF2,non_coding_transcript_exon_variant,,ENST00000463696,; A ENST00000369466 Transcript missense_variant 3319/9462 3275/3489 1092/1162 P/Q cCa/cAa 1 1 TTF2 HGNC HGNC:12398 protein_coding YES CCDS892.1 ENSP00000358478 Q9UNY4 A0A024R0F1 UPI000013CCE7 NM_003594.3 deleterious(0) 22/23 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF573,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 117098838 117098838 C A 1 0 0 0 0 1 0 0 0 17229 608 21 2 2 TTF2 1 117098838 Missense_Mutation SNP C C3N-00580_T 482380 117098838 131857584 48 18183 HSD3B1 0 . GRCh38 1 119514471 119514471 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.948C>A p.Asn316Lys p.N316K ENST00000369413 4/4 283 251 32 202 202 0 strelka-varscan-mutect HSD3B1,missense_variant,p.Asn316Lys,ENST00000369413,NM_000862.2;HSD3B1,missense_variant,p.Asn316Lys,ENST00000528909,;HSD3B1,downstream_gene_variant,,ENST00000531340,;HSD3B1,downstream_gene_variant,,ENST00000492140,; A ENST00000369413 Transcript missense_variant 1093/1676 948/1122 316/373 N/K aaC/aaA 1 1 HSD3B1 HGNC HGNC:5217 protein_coding YES CCDS903.1 ENSP00000358421 P14060 UPI0000036BD2 NM_000862.2 deleterious(0) 4/4 hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF378,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 119514471 119514471 C A 1 0 0 0 0 1 0 0 0 7284 506 18 2 2 HSD3B1 1 119514471 Missense_Mutation SNP C C3N-00580_T 2415633 119514471 129441951 49 18184 PDE4DIP 0 . GRCh38 1 149004979 149004979 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.3957G>T p.= p.R1319R ENST00000369356 27/44 231 211 20 136 136 0 varscan-mutect PDE4DIP,synonymous_variant,p.=,ENST00000585156,;PDE4DIP,synonymous_variant,p.=,ENST00000369356,NM_001198834.3;PDE4DIP,synonymous_variant,p.=,ENST00000524974,;PDE4DIP,synonymous_variant,p.=,ENST00000369354,NM_014644.5;PDE4DIP,synonymous_variant,p.=,ENST00000618462,NM_001198832.2;RP4-791M13.5,downstream_gene_variant,,ENST00000531288,;PDE4DIP,intron_variant,,ENST00000530062,;PDE4DIP,upstream_gene_variant,,ENST00000479369,; T ENST00000369356 Transcript synonymous_variant 4248/8307 3957/7089 1319/2362 R cgG/cgT 1 1 PDE4DIP HGNC HGNC:15580 protein_coding YES CCDS72892.1 ENSP00000358363 A0A0A0MRM1 UPI000292EFC6 NM_001198834.3 27/44 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 149004979 149004979 G T 1 0 0 0 0 0 0 0 1 11731 1219 43 2 2 PDE4DIP 1 149004979 Silent SNP G C3N-00580_T 29490508 149004979 99951443 50 18185 NBPF9 0 . GRCh38 1 149079198 149079198 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.302C>T p.Ser101Phe p.S101F ENST00000615421 8/29 168 148 20 96 96 0 varscan-mutect NBPF9,missense_variant,p.Ser101Phe,ENST00000615421,;NBPF9,missense_variant,p.Ser101Phe,ENST00000621645,;NBPF9,missense_variant,p.Ser101Phe,ENST00000584027,NM_001277444.1;NBPF9,missense_variant,p.Ser101Phe,ENST00000613969,NM_001037501.2;NBPF9,missense_variant,p.Ser101Phe,ENST00000613595,NM_001037675.3;NBPF9,missense_variant,p.Ser101Phe,ENST00000621074,;NBPF9,missense_variant,p.Ser101Phe,ENST00000610300,;NBPF9,upstream_gene_variant,,ENST00000483630,; A ENST00000615421 Transcript missense_variant 1172/5835 302/3336 101/1111 S/F tCt/tTt 1 -1 NBPF9 HGNC HGNC:31991 protein_coding YES CCDS72896.1 ENSP00000477979 A0A075B761 UPI000292EE30 deleterious(0) 8/29 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 149079198 149079198 G A 1 0 0 0 0 1 0 0 0 10215 942 33 3 3 NBPF9 1 149079198 Missense_Mutation SNP G C3N-00580_T 74219 149079198 99877224 51 18186 CIART 0 . GRCh38 1 150284502 150284502 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.519G>T p.Met173Ile p.M173I ENST00000290363 3/5 353 205 148 295 295 0 strelka-varscan-mutect CIART,missense_variant,p.Met173Ile,ENST00000290363,NM_144697.3;CIART,missense_variant,p.Met173Ile,ENST00000369095,NM_001300838.1;CIART,missense_variant,p.Met85Ile,ENST00000369094,NM_001300840.1,NM_001300839.1,NM_001300841.1;CIART,missense_variant,p.Met85Ile,ENST00000417398,;CIART,missense_variant,p.Met85Ile,ENST00000447007,;C1orf54,downstream_gene_variant,,ENST00000369102,NM_001301040.1,NM_001301039.1;C1orf54,downstream_gene_variant,,ENST00000369099,NM_024579.3;C1orf54,downstream_gene_variant,,ENST00000369098,NM_001301042.1;CIART,splice_region_variant,,ENST00000497211,;CIART,splice_region_variant,,ENST00000469255,; T ENST00000290363 Transcript missense_variant,splice_region_variant 968/1746 519/1158 173/385 M/I atG/atT 1 1 CIART HGNC HGNC:25200 protein_coding YES CCDS949.1 ENSP00000290363 Q8N365 UPI000000DBBF NM_144697.3 deleterious(0.03) 3/5 Pfam_domain:PF15673,hmmpanther:PTHR35441 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 150284502 150284502 G T 1 0 0 0 0 1 0 0 0 3181 1362 47 2 2 CIART 1 150284502 Missense_Mutation SNP G C3N-00580_T 1205304 150284502 98671920 52 18187 KPRP 0 . GRCh38 1 152759617 152759617 + Missense_Mutation SNP G G T rs77368440 C3N-00580_T C3N-00580_N G G c.29G>T p.Arg10Leu p.R10L ENST00000606109 1/1 210 133 77 131 131 0 strelka-varscan-mutect KPRP,missense_variant,p.Arg10Leu,ENST00000606109,NM_001025231.1; T ENST00000606109 Transcript missense_variant 57/2492 29/1740 10/579 R/L cGc/cTc rs77368440,COSM2156689 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 tolerated(0.12) 1/1 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 0,1 1 PASS rs77368440 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 152759617 152759617 G T 1 0 0 0 0 1 0 0 0 8316 1087 38 1 1 KPRP 1 152759617 Missense_Mutation SNP G C3N-00580_T 2475115 152759617 96196805 53 18188 KPRP 0 . GRCh38 1 152760725 152760725 + Silent SNP C C A C3N-00580_T C3N-00580_N C C c.1137C>A p.= p.L379L ENST00000606109 1/1 434 276 158 411 411 0 strelka-varscan-mutect KPRP,synonymous_variant,p.=,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript synonymous_variant 1165/2492 1137/1740 379/579 L ctC/ctA COSM2207304,COSM5242816 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 1/1 1,1 LOW 1 SNV 1,1 1 PASS rs1191021657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 152760725 152760725 C A 1 0 0 0 0 0 0 0 1 8316 842 30 2 2 KPRP 1 152760725 Silent SNP C C3N-00580_T 1108 152760725 96195697 54 18189 S100A7 0 . GRCh38 1 153457819 153457819 + Missense_Mutation SNP C C T rs138333032 C3N-00580_T C3N-00580_N C C c.293G>A p.Gly98Glu p.G98E ENST00000368723 3/3 238 129 109 141 141 0 strelka-varscan-mutect S100A7,missense_variant,p.Gly98Glu,ENST00000368723,NM_002963.3;S100A7,missense_variant,p.Gly98Glu,ENST00000368722,; T ENST00000368723 Transcript missense_variant 404/479 293/306 98/101 G/E gGg/gAg rs138333032,COSM106364 1 -1 S100A7 HGNC HGNC:10497 protein_coding YES CCDS1039.1 ENSP00000357712 P31151 UPI000013D90F NM_002963.3 tolerated(0.24) 3/3 hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF64,Gene3D:1.10.238.10 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs138333032 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 153457819 153457819 C T 1 0 0 0 0 1 0 0 0 14042 623 22 3 3 S100A7 1 153457819 Missense_Mutation SNP C C3N-00580_T 697094 153457819 95498603 55 18190 NUP210L 0 . GRCh38 1 154060562 154060562 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.2828T>A p.Met943Lys p.M943K ENST00000368559 20/40 228 159 69 185 185 0 strelka-varscan-mutect NUP210L,missense_variant,p.Met943Lys,ENST00000368559,NM_207308.2;NUP210L,missense_variant,p.Met943Lys,ENST00000271854,NM_001159484.1;NUP210L,upstream_gene_variant,,ENST00000368553,; T ENST00000368559 Transcript missense_variant 2900/5889 2828/5667 943/1888 M/K aTg/aAg 1 -1 NUP210L HGNC HGNC:29915 protein_coding YES CCDS41399.1 ENSP00000357547 Q5VU65 UPI000023724F NM_207308.2 tolerated(0.58) 20/40 hmmpanther:PTHR23019,hmmpanther:PTHR23019:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 154060562 154060562 A T 1 0 0 0 0 1 0 0 0 10826 217 8 4 4 NUP210L 1 154060562 Missense_Mutation SNP A C3N-00580_T 602743 154060562 94895860 56 18191 FAM189B 0 . GRCh38 1 155248132 155248132 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1751G>T p.Gly584Val p.G584V ENST00000361361 11/12 353 281 72 220 219 1 strelka-varscan-mutect FAM189B,missense_variant,p.Gly584Val,ENST00000361361,NM_006589.2;FAM189B,missense_variant,p.Gly566Val,ENST00000368368,NM_001267608.1;FAM189B,missense_variant,p.Gly488Val,ENST00000350210,NM_198264.1;FAM189B,missense_variant,p.Gly306Val,ENST00000491082,;FAM189B,intron_variant,,ENST00000621094,;GBA,upstream_gene_variant,,ENST00000327247,NM_001005741.2,NM_001005742.2;GBA,upstream_gene_variant,,ENST00000428024,NM_001171811.1;GBA,upstream_gene_variant,,ENST00000493842,;FAM189B,downstream_gene_variant,,ENST00000472550,;GBA,upstream_gene_variant,,ENST00000473570,;GBA,upstream_gene_variant,,ENST00000467918,;FAM189B,3_prime_UTR_variant,,ENST00000487649,;FAM189B,non_coding_transcript_exon_variant,,ENST00000368366,;FAM189B,downstream_gene_variant,,ENST00000481822,;FAM189B,downstream_gene_variant,,ENST00000497941,; A ENST00000361361 Transcript missense_variant 2261/3082 1751/2007 584/668 G/V gGt/gTt 1 -1 FAM189B HGNC HGNC:1233 protein_coding YES CCDS1103.1 ENSP00000354958 P81408 UPI00000710DE NM_006589.2 tolerated(0.21) 11/12 hmmpanther:PTHR17615,hmmpanther:PTHR17615:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 155248132 155248132 C A 1 0 0 0 0 1 0 0 0 5369 507 18 2 2 FAM189B 1 155248132 Missense_Mutation SNP C C3N-00580_T 1187570 155248132 93708290 57 18192 LMNA 0 . GRCh38 1 156137714 156137714 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1669G>T p.Asp557Tyr p.D557Y ENST00000368300 10/12 884 638 246 584 584 0 strelka-varscan-mutect LMNA,missense_variant,p.Asp557Tyr,ENST00000368300,NM_170707.3;LMNA,missense_variant,p.Asp557Tyr,ENST00000368301,NM_001282625.1,NM_005572.3;LMNA,missense_variant,p.Asp557Tyr,ENST00000368299,NM_001282626.1;LMNA,missense_variant,p.Asp458Tyr,ENST00000473598,;LMNA,missense_variant,p.Asp445Tyr,ENST00000448611,NM_001257374.2;LMNA,missense_variant,p.Asp472Tyr,ENST00000361308,;LMNA,missense_variant,p.Asp476Tyr,ENST00000368297,NM_001282624.1;LMNA,intron_variant,,ENST00000347559,NM_170708.3;LMNA,intron_variant,,ENST00000508500,;LMNA,downstream_gene_variant,,ENST00000504687,;LMNA,non_coding_transcript_exon_variant,,ENST00000496738,;LMNA,downstream_gene_variant,,ENST00000459904,;LMNA,downstream_gene_variant,,ENST00000469565,;LMNA,downstream_gene_variant,,ENST00000502751,;LMNA,downstream_gene_variant,,ENST00000470199,;LMNA,downstream_gene_variant,,ENST00000502357,;LMNA,non_coding_transcript_exon_variant,,ENST00000498722,;LMNA,non_coding_transcript_exon_variant,,ENST00000506981,;LMNA,downstream_gene_variant,,ENST00000368298,;LMNA,downstream_gene_variant,,ENST00000515459,;LMNA,downstream_gene_variant,,ENST00000515824,; T ENST00000368300 Transcript missense_variant 1881/3190 1669/1995 557/664 D/Y Gat/Tat 1 1 LMNA HGNC HGNC:6636 protein_coding YES CCDS1129.1 ENSP00000357283 P02545 UPI000012E20D NM_170707.3 deleterious(0.01) 10/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 156137714 156137714 G T 1 0 0 0 0 1 0 0 0 8772 1174 41 2 2 LMNA 1 156137714 Missense_Mutation SNP G C3N-00580_T 889582 156137714 92818708 58 18193 RHBG 0 . GRCh38 1 156382804 156382804 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1169C>G p.Ala390Gly p.A390G ENST00000537040 8/10 494 463 31 372 372 0 strelka-varscan-mutect RHBG,missense_variant,p.Ala390Gly,ENST00000537040,NM_001256395.1,NM_020407.4,NM_001256396.1;RHBG,non_coding_transcript_exon_variant,,ENST00000494874,;RHBG,3_prime_UTR_variant,,ENST00000620376,;RHBG,3_prime_UTR_variant,,ENST00000451864,;RHBG,3_prime_UTR_variant,,ENST00000613460,;RHBG,3_prime_UTR_variant,,ENST00000612897,;RHBG,non_coding_transcript_exon_variant,,ENST00000618120,;RHBG,non_coding_transcript_exon_variant,,ENST00000622297,; G ENST00000537040 Transcript missense_variant 1207/1789 1169/1377 390/458 A/G gCc/gGc 1 1 RHBG HGNC HGNC:14572 protein_coding YES ENSP00000441197 Q9H310 UPI000004F267 NM_001256395.1,NM_020407.4,NM_001256396.1 tolerated(1) 8/10 Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 156382804 156382804 C G 1 0 0 0 0 1 0 0 0 13496 739 26 4 4 RHBG 1 156382804 Missense_Mutation SNP C C3N-00580_T 245090 156382804 92573618 59 18194 NTRK1 0 . GRCh38 1 156861011 156861011 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.77T>C p.Leu26Pro p.L26P ENST00000524377 1/17 442 310 132 333 333 0 strelka-varscan-mutect NTRK1,missense_variant,p.Leu26Pro,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Leu26Pro,ENST00000358660,;NTRK1,missense_variant,p.Leu26Pro,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;INSRR,upstream_gene_variant,,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000489021,;NTRK1,non_coding_transcript_exon_variant,,ENST00000533630,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; C ENST00000524377 Transcript missense_variant 118/2432 77/2391 26/796 L/P cTg/cCg 1 1 NTRK1 HGNC HGNC:8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 deleterious(0.04) 1/17 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF370 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 156861011 156861011 T C 1 0 0 0 0 1 0 0 0 10772 1580 55 5 5 NTRK1 1 156861011 Missense_Mutation SNP T C3N-00580_T 478207 156861011 92095411 60 18195 CD1E 0 . GRCh38 1 158356081 158356081 + Missense_Mutation SNP G G T rs772268165 C3N-00580_T C3N-00580_N G G c.880G>T p.Gly294Cys p.G294C ENST00000368167 4/6 152 92 60 93 93 0 strelka-varscan-mutect CD1E,missense_variant,p.Gly195Cys,ENST00000444681,NM_001185114.1;CD1E,missense_variant,p.Gly294Cys,ENST00000368160,NM_001042583.2;CD1E,missense_variant,p.Gly294Cys,ENST00000368167,NM_030893.3;CD1E,missense_variant,p.Gly105Cys,ENST00000368166,NM_001042586.2;CD1E,missense_variant,p.Gly204Cys,ENST00000368165,NM_001185107.1;CD1E,missense_variant,p.Gly204Cys,ENST00000368156,NM_001185115.1;CD1E,missense_variant,p.Gly105Cys,ENST00000452291,NM_001185112.1;CD1E,intron_variant,,ENST00000368161,NM_001042584.2;CD1E,intron_variant,,ENST00000368163,NM_001042585.2;CD1E,intron_variant,,ENST00000368162,;CD1E,intron_variant,,ENST00000368164,NM_001042587.2;CD1E,intron_variant,,ENST00000368155,NM_001185108.1;CD1E,intron_variant,,ENST00000368154,NM_001185113.1;CD1E,intron_variant,,ENST00000368157,NM_001185110.1;CD1E,downstream_gene_variant,,ENST00000464822,; T ENST00000368167 Transcript missense_variant 1119/1458 880/1167 294/388 G/C Ggc/Tgc rs772268165 1 1 CD1E HGNC HGNC:1638 protein_coding YES CCDS41417.1 ENSP00000357149 P15812 UPI000046F8C2 NM_030893.3 deleterious(0) 4/6 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF146,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs772268165 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 158356081 158356081 G T 1 0 0 0 0 1 0 0 0 2681 1232 43 2 2 CD1E 1 158356081 Missense_Mutation SNP G C3N-00580_T 1495070 158356081 90600341 61 18196 SPTA1 0 . GRCh38 1 158647594 158647594 + Missense_Mutation SNP G G T rs199685020 C3N-00580_T C3N-00580_N G G c.3841C>A p.Arg1281Ser p.R1281S ENST00000368147 27/52 693 444 249 457 456 1 strelka-varscan-mutect SPTA1,missense_variant,p.Arg1281Ser,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 4022/7999 3841/7260 1281/2419 R/S Cgt/Agt rs199685020,COSM229892 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 27/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199685020 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 158647594 158647594 G T 1 0 0 0 0 1 0 0 0 15472 1058 37 1 1 SPTA1 1 158647594 Missense_Mutation SNP G C3N-00580_T 291513 158647594 90308828 62 18197 AIM2 0 . GRCh38 1 159066183 159066183 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.543G>A p.= p.V181V ENST00000368130 4/6 523 382 141 286 286 0 strelka-varscan-mutect AIM2,synonymous_variant,p.=,ENST00000368130,NM_004833.1;AIM2,synonymous_variant,p.=,ENST00000368129,;AIM2,intron_variant,,ENST00000481829,;AIM2,downstream_gene_variant,,ENST00000411768,; T ENST00000368130 Transcript synonymous_variant 832/1529 543/1032 181/343 V gtG/gtA 1 -1 AIM2 HGNC HGNC:357 protein_coding YES CCDS1181.1 ENSP00000357112 O14862 UPI000012573B NM_004833.1 4/6 PROSITE_profiles:PS50834,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF17,Pfam_domain:PF02760,Gene3D:2.40.50.140,Superfamily_domains:SSF159141 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 159066183 159066183 C T 1 0 0 0 0 0 0 0 1 509 581 21 3 3 AIM2 1 159066183 Silent SNP C C3N-00580_T 418589 159066183 89890239 63 18198 ACKR1 0 . GRCh38 1 159205851 159205851 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.418G>T p.Gly140Cys p.G140C ENST00000368121 1/1 231 140 91 115 115 0 strelka-varscan-mutect ACKR1,missense_variant,p.Gly138Cys,ENST00000537147,;ACKR1,missense_variant,p.Gly138Cys,ENST00000368122,NM_002036.3;ACKR1,missense_variant,p.Gly140Cys,ENST00000368121,NM_001122951.2;ACKR1,missense_variant,p.Gly140Cys,ENST00000435307,;CADM3,downstream_gene_variant,,ENST00000368125,NM_001127173.1;CADM3,downstream_gene_variant,,ENST00000368124,NM_021189.3;CADM3-AS1,intron_variant,,ENST00000609696,;CADM3-AS1,upstream_gene_variant,,ENST00000415675,; T ENST00000368121 Transcript missense_variant 593/1240 418/1017 140/338 G/C Ggc/Tgc 1 1 ACKR1 HGNC HGNC:4035 protein_coding YES CCDS44252.1 ENSP00000357103 Q16570 Q5Y7A1 UPI000013E1B0 NM_001122951.2 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR14181,Prints_domain:PR01559 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 159205851 159205851 G T 1 0 0 0 0 1 0 0 0 181 1348 47 2 2 ACKR1 1 159205851 Missense_Mutation SNP G C3N-00580_T 139668 159205851 89750571 64 18199 ITLN1 0 . GRCh38 1 160879414 160879414 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.686G>T p.Arg229Leu p.R229L ENST00000326245 7/8 235 163 72 145 145 0 strelka-varscan-mutect ITLN1,missense_variant,p.Arg229Leu,ENST00000326245,NM_017625.2;ITLN1,splice_region_variant,,ENST00000487531,;ITLN1,downstream_gene_variant,,ENST00000464077,; A ENST00000326245 Transcript missense_variant,splice_region_variant 802/1183 686/942 229/313 R/L cGg/cTg 1 -1 ITLN1 HGNC HGNC:18259 protein_coding YES CCDS1211.1 ENSP00000323587 Q8WWA0 UPI0000032AA3 NM_017625.2 tolerated(0.3) 7/8 hmmpanther:PTHR16146,hmmpanther:PTHR16146:SF38,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS rs878960498 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 160879414 160879414 C A 1 0 0 0 0 1 0 0 0 7816 637 22 2 2 ITLN1 1 160879414 Missense_Mutation SNP C C3N-00580_T 1673563 160879414 88077008 65 18200 66 2 ITLN1 0 . GRCh38 1 160879416 160879416 + Splice_Site SNP T T A novel C3N-00580_T C3N-00580_N T T c.686-2A>T p.X229_splice ENST00000326245 235 164 71 146 146 0 strelka-varscan-mutect ITLN1,splice_acceptor_variant,,ENST00000326245,NM_017625.2;ITLN1,splice_acceptor_variant,,ENST00000487531,;ITLN1,downstream_gene_variant,,ENST00000464077,; A ENST00000326245 Transcript splice_acceptor_variant -/1183 686/942 229/313 1 -1 ITLN1 HGNC HGNC:18259 protein_coding YES CCDS1211.1 ENSP00000323587 Q8WWA0 UPI0000032AA3 NM_017625.2 6/7 HIGH 1 SNV 1 1 PASS rs1221467356 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 160879416 160879416 T A 1 0 0 0 0 0 0 1 0 7816 1594 55 4 4 ITLN1 1 160879416 Splice_Site SNP T C3N-00580_T 2 160879416 88077006 66 18201 66 2 FCGR3A 0 . GRCh38 1 161544911 161544911 + Missense_Mutation SNP G G T rs765857580 C3N-00580_T C3N-00580_N G G c.475C>A p.Pro159Thr p.P159T ENST00000367969 4/5 661 461 200 422 422 0 strelka-varscan-mutect FCGR3A,missense_variant,p.Pro159Thr,ENST00000367969,NM_001127592.1,NM_000569.6;FCGR3A,missense_variant,p.Pro123Thr,ENST00000443193,;FCGR3A,missense_variant,p.Pro123Thr,ENST00000436743,NM_001127595.1,NM_001127596.1,NM_001127593.1;FCGR3A,missense_variant,p.Pro123Thr,ENST00000367967,;FCGR3A,missense_variant,p.Pro140Thr,ENST00000426740,;FCGR3A,downstream_gene_variant,,ENST00000442336,;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR3A,downstream_gene_variant,,ENST00000476031,; T ENST00000367969 Transcript missense_variant 659/2310 475/873 159/290 P/T Cct/Act rs765857580 1 -1 FCGR3A HGNC HGNC:3619 protein_coding YES CCDS1232.1 ENSP00000356946 M9MML0 UPI000013E1BC NM_001127592.1,NM_000569.6 tolerated(0.54) 4/5 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF14,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs765857580 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 161544911 161544911 G T 1 0 0 0 0 1 0 0 0 5646 1232 43 2 2 FCGR3A 1 161544911 Missense_Mutation SNP G C3N-00580_T 665495 161544911 87411511 67 18202 OLFML2B 0 . GRCh38 1 161983798 161983799 + Frame_Shift_Del DEL GG GG - novel C3N-00580_T C3N-00580_N GG GG c.2132_2133delCC p.Pro711GlnfsTer7 p.P711Qfs*7 ENST00000367940 8/8 625 591 34 383 382 1 varindel-pindel OLFML2B,frameshift_variant,p.Pro710GlnfsTer7,ENST00000294794,NM_015441.2;OLFML2B,frameshift_variant,p.Pro711GlnfsTer7,ENST00000367940,NM_001297713.1;OLFML2B,frameshift_variant,p.Pro193GlnfsTer7,ENST00000367938,;OLFML2B,frameshift_variant,p.Pro48GlnfsTer7,ENST00000525589,;OLFML2B,frameshift_variant,p.Pro50GlnfsTer7,ENST00000533556,; - ENST00000367940 Transcript frameshift_variant 2342-2343/2685 2132-2133/2256 711/751 P/X cCC/c 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 8/8 PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF37,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 161983798 161983798 GG - 1 0 1 0 1 0 0 0 0 10933 1335 47 0 0 OLFML2B 1 161983798 Frame_Shift_Del DEL GG C3N-00580_T 438887 161983798 86972624 68 18203 OLFML2B 0 . GRCh38 1 162020180 162020180 + Missense_Mutation SNP C C A rs765388090 C3N-00580_T C3N-00580_N C C c.177G>T p.Leu59Phe p.L59F ENST00000367940 2/8 262 152 110 216 216 0 strelka-varscan-mutect OLFML2B,missense_variant,p.Leu59Phe,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Leu59Phe,ENST00000367940,NM_001297713.1; A ENST00000367940 Transcript missense_variant,splice_region_variant 387/2685 177/2256 59/751 L/F ttG/ttT rs765388090 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 deleterious(0.01) 2/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37 MODERATE 1 SNV 2 1 PASS rs765388090 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 162020180 162020180 C A 1 0 0 0 0 1 0 0 0 10933 724 25 2 2 OLFML2B 1 162020180 Missense_Mutation SNP C C3N-00580_T 36382 162020180 86936242 69 18204 DUSP27 0 . GRCh38 1 167127806 167127806 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.2675C>A p.Ala892Asp p.A892D ENST00000361200 6/6 427 340 87 257 257 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ala892Asp,ENST00000361200,;DUSP27,missense_variant,p.Ala892Asp,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ala892Asp,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; A ENST00000361200 Transcript missense_variant 2841/4164 2675/3477 892/1158 A/D gCc/gAc COSM677337 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0.01) 6/6 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 167127806 167127806 C A 1 0 0 0 0 1 0 0 0 4646 739 26 2 2 DUSP27 1 167127806 Missense_Mutation SNP C C3N-00580_T 5107626 167127806 81828616 70 18205 CD247 0 . GRCh38 1 167518441 167518441 + Missense_Mutation SNP C C A rs750366836 C3N-00580_T C3N-00580_N C C c.25G>T p.Ala9Ser p.A9S ENST00000362089 1/8 758 441 317 543 543 0 strelka-varscan-mutect CD247,missense_variant,p.Ala9Ser,ENST00000392122,NM_000734.3;CD247,missense_variant,p.Ala9Ser,ENST00000362089,NM_198053.2;CD247,non_coding_transcript_exon_variant,,ENST00000483825,;CD247,non_coding_transcript_exon_variant,,ENST00000479979,;AKR1D1P1,upstream_gene_variant,,ENST00000457236,; A ENST00000362089 Transcript missense_variant 98/1609 25/495 9/164 A/S Gcg/Tcg rs750366836 1 -1 CD247 HGNC HGNC:1677 protein_coding YES CCDS1261.1 ENSP00000354782 P20963 UPI0000127362 NM_198053.2 tolerated(0.49) 1/8 Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR10035 MODERATE 1 SNV 1 1 PASS rs750366836 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 167518441 167518441 C A 1 0 0 0 0 1 0 0 0 2692 768 27 1 1 CD247 1 167518441 Missense_Mutation SNP C C3N-00580_T 390635 167518441 81437981 71 18206 MROH9 0 . GRCh38 1 170986657 170986657 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.826G>A p.Ala276Thr p.A276T ENST00000367759 10/22 265 170 95 182 182 0 strelka-varscan-mutect MROH9,missense_variant,p.Ala276Thr,ENST00000367759,NM_001163629.1;MROH9,missense_variant,p.Ala276Thr,ENST00000367758,NM_025063.2; A ENST00000367759 Transcript missense_variant 980/3165 826/2586 276/861 A/T Gca/Aca 1 1 MROH9 HGNC HGNC:26287 protein_coding YES CCDS53429.1 ENSP00000356733 Q5TGP6 UPI0001B09232 NM_001163629.1 deleterious(0) 10/22 Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF5 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 170986657 170986657 G A 1 0 0 0 0 1 0 0 0 9748 1319 46 3 3 MROH9 1 170986657 Missense_Mutation SNP G C3N-00580_T 3468216 170986657 77969765 72 18207 SUCO 0 . GRCh38 1 172557745 172557745 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1157G>T p.Gly386Val p.G386V ENST00000367723 6/23 163 147 16 148 148 0 strelka-varscan-mutect SUCO,missense_variant,p.Gly386Val,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Gly386Val,ENST00000608151,;SUCO,missense_variant,p.Gly228Val,ENST00000263688,NM_014283.4;SUCO,missense_variant,p.Gly191Val,ENST00000610051,NM_001282750.1;SUCO,5_prime_UTR_variant,,ENST00000616058,NM_001282751.1;SUCO,non_coding_transcript_exon_variant,,ENST00000608804,; T ENST00000367723 Transcript missense_variant 1281/5916 1157/4218 386/1405 G/V gGt/gTt 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 deleterious_low_confidence(0.02) 6/23 hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 172557745 172557745 G T 1 0 0 0 0 1 0 0 0 15751 1261 44 2 2 SUCO 1 172557745 Missense_Mutation SNP G C3N-00580_T 1571088 172557745 76398677 73 18208 SUCO 0 . GRCh38 1 172585926 172585926 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2089T>A p.Ser697Thr p.S697T ENST00000367723 16/23 226 210 16 131 131 0 strelka-varscan-mutect SUCO,missense_variant,p.Ser697Thr,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Ser697Thr,ENST00000608151,;SUCO,missense_variant,p.Ser546Thr,ENST00000263688,NM_014283.4;SUCO,missense_variant,p.Ser509Thr,ENST00000610051,NM_001282750.1;SUCO,intron_variant,,ENST00000616058,NM_001282751.1; A ENST00000367723 Transcript missense_variant 2213/5916 2089/4218 697/1405 S/T Tca/Aca 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 deleterious(0.04) 16/23 Low_complexity_(Seg):seg,hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.66473 0.9999997 1 1 1 0 A 3 1 61 172585926 172585926 T A 1 0 0 0 0 1 0 0 0 15751 1783 62 4 4 SUCO 1 172585926 Missense_Mutation SNP T C3N-00580_T 28181 172585926 76370496 74 18209 SUCO 0 . GRCh38 1 172589604 172589604 + Missense_Mutation SNP G G T rs547712281 C3N-00580_T C3N-00580_N G G c.2956G>T p.Asp986Tyr p.D986Y ENST00000367723 17/23 347 189 158 168 167 1 strelka-varscan-mutect SUCO,missense_variant,p.Asp986Tyr,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Asp986Tyr,ENST00000608151,;SUCO,missense_variant,p.Asp835Tyr,ENST00000263688,NM_014283.4;SUCO,missense_variant,p.Asp272Tyr,ENST00000616058,NM_001282751.1;SUCO,intron_variant,,ENST00000610051,NM_001282750.1; T ENST00000367723 Transcript missense_variant 3080/5916 2956/4218 986/1405 D/Y Gac/Tac rs547712281,COSM1198487,COSM1198488 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 deleterious(0) 17/23 hmmpanther:PTHR12953:SF0,hmmpanther:PTHR12953 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs547712281 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 172589604 172589604 G T 1 0 0 0 0 1 0 0 0 15751 1058 37 1 1 SUCO 1 172589604 Missense_Mutation SNP G C3N-00580_T 3678 172589604 76366818 75 18210 TNR 0 . GRCh38 1 175403305 175403313 + In_Frame_Del DEL AACAGTCCC AACAGTCCC - novel C3N-00580_T C3N-00580_N AACAGTCCC AACAGTCCC c.803_811delGGGACTGTT p.Gly268_Ser271delinsAla p.G268_S271delinsA ENST00000367674 4/23 567 355 212 448 448 0 sindel-varindel-pindel TNR,inframe_deletion,p.Gly268_Ser271delinsAla,ENST00000367674,;TNR,inframe_deletion,p.Gly268_Ser271delinsAla,ENST00000263525,NM_003285.2;TNR,intron_variant,,ENST00000422274,; - ENST00000367674 Transcript inframe_deletion 1512-1520/12949 803-811/4077 268-271/1358 GDCS/A gGGGACTGTTcg/gcg 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 4/23 Gene3D:2.10.25.10,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00181 MODERATE 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 175403305 175403305 AACAGTCCC - 1 0 1 0 1 0 0 0 0 16811 246 9 0 0 TNR 1 175403305 In_Frame_Del DEL AACAGTCCC C3N-00580_T 2813701 175403305 73553117 76 18211 SEC16B 0 . GRCh38 1 177937330 177937330 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2387G>T p.Arg796Met p.R796M ENST00000308284 19/26 447 340 107 371 370 1 strelka-varscan-mutect SEC16B,missense_variant,p.Arg796Met,ENST00000308284,NM_033127.2;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000354921,;SEC16B,non_coding_transcript_exon_variant,,ENST00000327037,;SEC16B,upstream_gene_variant,,ENST00000495165,;SEC16B,3_prime_UTR_variant,,ENST00000528461,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000466953,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,; A ENST00000308284 Transcript missense_variant 2477/3985 2387/3183 796/1060 R/M aGg/aTg 1 -1 SEC16B HGNC HGNC:30301 protein_coding YES CCDS44281.1 ENSP00000308339 Q96JE7 UPI0000203C4D NM_033127.2 tolerated(0.12) 19/26 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 177937330 177937330 C A 1 0 0 0 0 1 0 0 0 14264 681 24 2 2 SEC16B 1 177937330 Missense_Mutation SNP C C3N-00580_T 2534025 177937330 71019092 77 18212 CACNA1E 0 . GRCh38 1 181771292 181771292 + Splice_Site SNP G G T C3N-00580_T C3N-00580_N G G c.4882-1G>T p.X1628_splice ENST00000367573 161 91 70 59 59 0 strelka-varscan-mutect CACNA1E,splice_acceptor_variant,,ENST00000621791,NM_001205294.1;CACNA1E,splice_acceptor_variant,,ENST00000621551,;CACNA1E,splice_acceptor_variant,,ENST00000367567,;CACNA1E,splice_acceptor_variant,,ENST00000358338,;CACNA1E,splice_acceptor_variant,,ENST00000367570,NM_000721.3;CACNA1E,splice_acceptor_variant,,ENST00000367573,NM_001205293.1;CACNA1E,splice_acceptor_variant,,ENST00000357570,;CACNA1E,splice_acceptor_variant,,ENST00000360108,;RNA5SP70,upstream_gene_variant,,ENST00000517168,; T ENST00000367573 Transcript splice_acceptor_variant -/7067 4882/6942 1628/2313 COSM4450200,COSM4450201,COSM4450202,COSM4450203,COSM5527993 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 35/47 1,1,1,1,1 HIGH 1 SNV 1 1,1,1,1,1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 5 4 61 181771292 181771292 G T 1 0 0 0 0 0 0 1 0 2230 1014 35 2 2 CACNA1E 1 181771292 Splice_Site SNP G C3N-00580_T 3833962 181771292 67185130 78 18213 CDC73 0 . GRCh38 1 193125179 193125179 + Missense_Mutation SNP G G T rs748952219 C3N-00580_T C3N-00580_N G G c.199G>T p.Val67Leu p.V67L ENST00000367435 2/17 583 450 133 332 331 1 strelka-varscan-mutect CDC73,missense_variant,p.Val67Leu,ENST00000367435,NM_024529.4;CDC73,missense_variant,p.Val67Leu,ENST00000635846,;CDC73,non_coding_transcript_exon_variant,,ENST00000482484,; T ENST00000367435 Transcript missense_variant 383/4969 199/1596 67/531 V/L Gtg/Ttg rs748952219,COSM3689228 1 1 CDC73 HGNC HGNC:16783 protein_coding YES CCDS1382.1 ENSP00000356405 Q6P1J9 UPI0000021592 NM_024529.4 tolerated(0.07) 2/17 Pfam_domain:PF16050,hmmpanther:PTHR12466,hmmpanther:PTHR12466:SF8 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748952219 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 193125179 193125179 G T 1 0 0 0 0 1 0 0 0 2788 1145 40 1 1 CDC73 1 193125179 Missense_Mutation SNP G C3N-00580_T 11353887 193125179 55831243 79 18214 KCNT2 0 . GRCh38 1 196228228 196228228 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.3404T>G p.Leu1135Arg p.L1135R ENST00000294725 28/28 246 229 17 192 192 0 strelka-varscan-mutect KCNT2,missense_variant,p.Leu1111Arg,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Leu1135Arg,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Leu1068Arg,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,; C ENST00000294725 Transcript missense_variant 4320/4409 3404/3408 1135/1135 L/R cTt/cGt 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 deleterious_low_confidence(0) 28/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 196228228 196228228 A C 1 0 0 0 0 1 0 0 0 8008 72 3 5 5 KCNT2 1 196228228 Missense_Mutation SNP A C3N-00580_T 3103049 196228228 52728194 80 18215 KCNT2 0 . GRCh38 1 196258329 196258329 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.3076C>A p.Pro1026Thr p.P1026T ENST00000294725 26/28 414 293 121 223 222 1 strelka-varscan-mutect KCNT2,missense_variant,p.Pro1002Thr,ENST00000367433,NM_001287819.1;KCNT2,missense_variant,p.Pro1026Thr,ENST00000294725,NM_198503.3;KCNT2,missense_variant,p.Pro959Thr,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; T ENST00000294725 Transcript missense_variant 3992/4409 3076/3408 1026/1135 P/T Cca/Aca COSM5585554,COSM5585555 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 tolerated(0.25) 26/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 196258329 196258329 G T 1 0 0 0 0 1 0 0 0 8008 1232 43 2 2 KCNT2 1 196258329 Missense_Mutation SNP G C3N-00580_T 30101 196258329 52698093 81 18216 CFHR1 0 . GRCh38 1 196831895 196831895 + Nonsense_Mutation SNP G G T rs201995028 C3N-00580_T C3N-00580_N G G c.889G>T p.Glu297Ter p.E297* ENST00000320493 6/6 1038 809 229 680 680 0 strelka-varscan-mutect CFHR1,stop_gained,p.Glu297Ter,ENST00000320493,NM_002113.2;CFHR1,stop_gained,p.Glu238Ter,ENST00000367424,;RP4-608O15.3,intron_variant,,ENST00000367421,;CFHR1,downstream_gene_variant,,ENST00000480960,; T ENST00000320493 Transcript stop_gained 977/1271 889/993 297/330 E/* Gaa/Taa rs201995028,COSM3480853 1 1 CFHR1 HGNC HGNC:4888 protein_coding YES CCDS1386.1 ENSP00000314299 Q03591 UPI000013CCFE NM_002113.2 6/6 PROSITE_profiles:PS50923,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1 HIGH 1 SNV 1 0,1 1 PASS rs201995028 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 196831895 196831895 G T 1 0 0 0 0 0 1 0 0 3042 1291 45 2 2 CFHR1 1 196831895 Nonsense_Mutation SNP G C3N-00580_T 573566 196831895 52124527 82 18217 CFHR5 0 . GRCh38 1 196994233 196994233 + Nonsense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.584C>G p.Ser195Ter p.S195* ENST00000256785 4/10 353 282 71 249 249 0 strelka-varscan-mutect CFHR5,stop_gained,p.Ser195Ter,ENST00000256785,NM_030787.3; G ENST00000256785 Transcript stop_gained 693/2810 584/1710 195/569 S/* tCa/tGa 1 1 CFHR5 HGNC HGNC:24668 protein_coding YES CCDS1387.1 ENSP00000256785 Q9BXR6 UPI0000043814 NM_030787.3 4/10 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF381,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 SNV 1 1 PASS rs765183774 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 61 196994233 196994233 C G 1 0 0 0 0 0 1 0 0 3046 838 29 4 4 CFHR5 1 196994233 Nonsense_Mutation SNP C C3N-00580_T 162338 196994233 51962189 83 18218 ASPM 0 . GRCh38 1 197101587 197101587 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.7664A>G p.Lys2555Arg p.K2555R ENST00000367409 18/28 419 321 98 317 317 0 strelka-varscan-mutect ASPM,missense_variant,p.Lys2555Arg,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Lys541Arg,ENST00000612785,;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000367408,; C ENST00000367409 Transcript missense_variant 7921/10887 7664/10434 2555/3477 K/R aAa/aGa 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.73) 18/28 PROSITE_profiles:PS50096,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 197101587 197101587 T C 1 0 0 0 0 1 0 0 0 1203 1841 64 5 5 ASPM 1 197101587 Missense_Mutation SNP T C3N-00580_T 107354 197101587 51854835 84 18219 CACNA1S 0 . GRCh38 1 201085546 201085546 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1040G>T p.Arg347Met p.R347M ENST00000362061 8/44 393 294 99 260 260 0 strelka-varscan-mutect CACNA1S,missense_variant,p.Arg347Met,ENST00000362061,NM_000069.2;CACNA1S,missense_variant,p.Arg347Met,ENST00000367338,; A ENST00000362061 Transcript missense_variant 1267/6166 1040/5622 347/1873 R/M aGg/aTg 1 -1 CACNA1S HGNC HGNC:1397 protein_coding YES CCDS1407.1 ENSP00000355192 Q13698 UPI000020471D NM_000069.2 deleterious(0) 8/44 Prints_domain:PR00167,Prints_domain:PR01630,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF190 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 201085546 201085546 C A 1 0 0 0 0 1 0 0 0 2235 681 24 2 2 CACNA1S 1 201085546 Missense_Mutation SNP C C3N-00580_T 3983959 201085546 47870876 85 18220 LMOD1 0 . GRCh38 1 201900389 201900389 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.624A>G p.= p.R208R ENST00000367288 2/3 473 261 212 270 270 0 strelka-varscan-mutect LMOD1,synonymous_variant,p.=,ENST00000367288,NM_012134.2;LMOD1,synonymous_variant,p.=,ENST00000616739,;RP11-307B6.3,downstream_gene_variant,,ENST00000458139,;RP11-307B6.3,downstream_gene_variant,,ENST00000414927,; C ENST00000367288 Transcript synonymous_variant 871/3970 624/1803 208/600 R agA/agG 1 -1 LMOD1 HGNC HGNC:6647 protein_coding YES CCDS53457.1 ENSP00000356257 P29536 UPI00003665F4 NM_012134.2 2/3 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 201900389 201900389 T C 1 0 0 0 0 0 0 0 1 8783 1548 54 5 5 LMOD1 1 201900389 Silent SNP T C3N-00580_T 814843 201900389 47056033 86 18221 PPFIA4 0 . GRCh38 1 203049739 203049739 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1495G>T p.Gly499Trp p.G499W ENST00000447715 17/35 105 73 32 80 80 0 strelka-varscan-mutect PPFIA4,missense_variant,p.Gly474Trp,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,missense_variant,p.Gly499Trp,ENST00000447715,;PPFIA4,missense_variant,p.Gly241Trp,ENST00000600426,;PPFIA4,5_prime_UTR_variant,,ENST00000295706,;PPFIA4,upstream_gene_variant,,ENST00000272198,;PPFIA4,upstream_gene_variant,,ENST00000599966,;PPFIA4,upstream_gene_variant,,ENST00000599514,;PPFIA4,downstream_gene_variant,,ENST00000601609,;PPFIA4,upstream_gene_variant,,ENST00000600447,; T ENST00000447715 Transcript missense_variant 1936/6349 1495/3558 499/1185 G/W Ggg/Tgg 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 deleterious(0.01) 17/35 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 203049739 203049739 G T 1 0 0 0 0 1 0 0 0 12421 1232 43 2 2 PPFIA4 1 203049739 Missense_Mutation SNP G C3N-00580_T 1149350 203049739 45906683 87 18222 CHIT1 0 . GRCh38 1 203219682 203219682 + Silent SNP C C A rs202073190 C3N-00580_T C3N-00580_N C C c.897G>T p.= p.G299G ENST00000367229 8/11 666 541 125 420 420 0 strelka-varscan-mutect CHIT1,synonymous_variant,p.=,ENST00000367229,NM_001270509.1,NM_003465.2;CHIT1,synonymous_variant,p.=,ENST00000255427,NM_001256125.1;CHIT1,non_coding_transcript_exon_variant,,ENST00000484834,;CHIT1,non_coding_transcript_exon_variant,,ENST00000506427,;CHIT1,downstream_gene_variant,,ENST00000513472,;CHIT1,upstream_gene_variant,,ENST00000479483,;CHIT1,synonymous_variant,p.=,ENST00000491855,;CHIT1,synonymous_variant,p.=,ENST00000503786,; A ENST00000367229 Transcript synonymous_variant 932/2246 897/1401 299/466 G ggG/ggT rs202073190,COSM4561739 1 -1 CHIT1 HGNC HGNC:1936 protein_coding YES CCDS1436.1 ENSP00000356198 Q13231 UPI00000399C1 NM_001270509.1,NM_003465.2 8/11 hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF211,Gene3D:3.10.50.10,Pfam_domain:PF00704,SMART_domains:SM00636,Superfamily_domains:SSF54556 0,1 LOW 1 SNV 1 0,1 1 PASS rs202073190 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 203219682 203219682 C A 1 0 0 0 0 0 0 0 1 3105 842 30 2 2 CHIT1 1 203219682 Silent SNP C C3N-00580_T 169943 203219682 45736740 88 18223 PPP1R15B 0 . GRCh38 1 204411275 204411275 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.137G>T p.Gly46Val p.G46V ENST00000367188 1/2 627 383 244 533 533 0 strelka-varscan-mutect PPP1R15B,missense_variant,p.Gly46Val,ENST00000367188,NM_032833.4;RP11-739N20.2,intron_variant,,ENST00000443515,; A ENST00000367188 Transcript missense_variant 517/5227 137/2142 46/713 G/V gGg/gTg 1 -1 PPP1R15B HGNC HGNC:14951 protein_coding YES CCDS1445.1 ENSP00000356156 Q5SWA1 UPI0000EE3EB3 NM_032833.4 deleterious_low_confidence(0) 1/2 Pfam_domain:PF10472 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 204411275 204411275 C A 1 0 0 0 0 1 0 0 0 12474 623 22 2 2 PPP1R15B 1 204411275 Missense_Mutation SNP C C3N-00580_T 1191593 204411275 44545147 89 18224 FAM72A 0 . GRCh38 1 206202017 206202017 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.9C>A p.= p.T3T ENST00000367128 1/4 49 39 10 45 45 0 strelka-varscan-mutect FAM72A,synonymous_variant,p.=,ENST00000367128,NM_001123168.1;FAM72A,synonymous_variant,p.=,ENST00000341209,;FAM72A,synonymous_variant,p.=,ENST00000607379,;FAM72A,intron_variant,,ENST00000431655,;FAM72A,intron_variant,,ENST00000367129,;SRGAP2,upstream_gene_variant,,ENST00000573034,NM_015326.4;SRGAP2,upstream_gene_variant,,ENST00000624873,NM_001170637.3;SRGAP2,upstream_gene_variant,,ENST00000605610,NM_001300952.1;SRGAP2,upstream_gene_variant,,ENST00000419187,;SRGAP2,upstream_gene_variant,,ENST00000579225,;FAM72A,downstream_gene_variant,,ENST00000468509,;FAM72A,intron_variant,,ENST00000470041,;FAM72A,intron_variant,,ENST00000481737,;SRGAP2,upstream_gene_variant,,ENST00000624686,;SRGAP2,upstream_gene_variant,,ENST00000603708,;SRGAP2,upstream_gene_variant,,ENST00000603575,; T ENST00000367128 Transcript synonymous_variant 857/2398 9/450 3/149 T acC/acA 1 -1 FAM72A HGNC HGNC:24044 protein_coding YES CCDS73016.1 ENSP00000356096 Q5TYM5 UPI0000046C34 NM_001123168.1 1/4 hmmpanther:PTHR31841 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99997 1 1 1 1 0 T 2 4 61 206202017 206202017 G T 1 0 0 0 0 0 0 0 1 5479 1335 47 2 2 FAM72A 1 206202017 Silent SNP G C3N-00580_T 1790742 206202017 42754405 90 18225 SRGAP2 0 . GRCh38 1 206446296 206446296 + Missense_Mutation SNP A A T rs782181909 C3N-00580_T C3N-00580_N A A c.2096A>T p.Tyr699Phe p.Y699F ENST00000573034 17/22 368 346 22 225 225 0 strelka-varscan-mutect SRGAP2,missense_variant,p.Tyr699Phe,ENST00000573034,NM_015326.4;SRGAP2,missense_variant,p.Tyr698Phe,ENST00000624873,NM_001170637.3;SRGAP2,missense_variant,p.Tyr698Phe,ENST00000605610,NM_001300952.1;SRGAP2,missense_variant,p.Tyr313Phe,ENST00000605476,;SRGAP2,missense_variant,p.Tyr82Phe,ENST00000604925,;SRGAP2,downstream_gene_variant,,ENST00000604419,; T ENST00000573034 Transcript missense_variant 2158/6301 2096/3216 699/1071 Y/F tAc/tTc rs782181909 1 1 SRGAP2 HGNC HGNC:19751 protein_coding YES CCDS73017.1 ENSP00000459615 A2RUF3 UPI0000DC3AA7 NM_015326.4 tolerated(0.16) 17/22 hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF6 MODERATE 1 SNV 1 1 PASS rs782181909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 206446296 206446296 A T 1 0 0 0 0 1 0 0 0 15505 405 14 4 4 SRGAP2 1 206446296 Missense_Mutation SNP A C3N-00580_T 244279 206446296 42510126 91 18226 CR1 0 . GRCh38 1 207575609 207575609 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.4466G>C p.Gly1489Ala p.G1489A ENST00000367049 28/47 629 542 87 406 406 0 strelka-varscan-mutect CR1,missense_variant,p.Gly1489Ala,ENST00000367049,NM_000651.4;CR1,missense_variant,p.Gly1039Ala,ENST00000367051,;CR1,missense_variant,p.Gly1039Ala,ENST00000367052,;CR1,missense_variant,p.Gly1039Ala,ENST00000367053,;CR1,missense_variant,p.Gly1039Ala,ENST00000400960,NM_000573.3;CR1,intron_variant,,ENST00000529814,;RP11-78B10.2,intron_variant,,ENST00000623503,;RP11-78B10.2,intron_variant,,ENST00000597497,;RP11-78B10.2,intron_variant,,ENST00000596003,;CR1,3_prime_UTR_variant,,ENST00000534202,;CR1,downstream_gene_variant,,ENST00000436595,;CR1,downstream_gene_variant,,ENST00000450439,; C ENST00000367049 Transcript missense_variant 4466/7470 4466/7470 1489/2489 G/A gGt/gCt 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 deleterious(0.02) 28/47 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF354,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 207575609 207575609 G C 1 0 0 0 0 1 0 0 0 3638 1261 44 4 4 CR1 1 207575609 Missense_Mutation SNP G C3N-00580_T 1129313 207575609 41380813 92 18227 TRAF3IP3 0 . GRCh38 1 209760078 209760078 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.39C>A p.= p.A13A ENST00000367024 3/17 244 140 104 155 154 1 strelka-varscan-mutect TRAF3IP3,synonymous_variant,p.=,ENST00000367024,NM_001320143.1;TRAF3IP3,synonymous_variant,p.=,ENST00000367025,NM_025228.3;TRAF3IP3,synonymous_variant,p.=,ENST00000367026,NM_001320144.1;TRAF3IP3,synonymous_variant,p.=,ENST00000400959,;TRAF3IP3,synonymous_variant,p.=,ENST00000479796,;TRAF3IP3,intron_variant,,ENST00000468672,;TRAF3IP3,synonymous_variant,p.=,ENST00000478359,; A ENST00000367024 Transcript synonymous_variant 555/2331 39/1656 13/551 A gcC/gcA 1 1 TRAF3IP3 HGNC HGNC:30766 protein_coding YES CCDS1490.2 ENSP00000355991 Q9Y228 UPI00005190E1 NM_001320143.1 3/17 hmmpanther:PTHR15715:SF21,hmmpanther:PTHR15715 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 209760078 209760078 C A 1 0 0 0 0 0 0 0 1 16925 610 22 2 2 TRAF3IP3 1 209760078 Silent SNP C C3N-00580_T 2184469 209760078 39196344 93 18228 PTPN14 0 . GRCh38 1 214384002 214384002 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1853A>T p.His618Leu p.H618L ENST00000366956 13/19 173 100 73 107 107 0 strelka-varscan PTPN14,missense_variant,p.His618Leu,ENST00000366956,NM_005401.4;PTPN14,3_prime_UTR_variant,,ENST00000543945,; A ENST00000366956 Transcript missense_variant 2048/12985 1853/3564 618/1187 H/L cAt/cTt 1 -1 PTPN14 HGNC HGNC:9647 protein_coding YES CCDS1514.1 ENSP00000355923 Q15678 UPI000013DCA6 NM_005401.4 deleterious(0) 13/19 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF77,PIRSF_domain:PIRSF000934 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 214384002 214384002 T A 1 0 0 0 0 1 0 0 0 12936 1464 51 4 4 PTPN14 1 214384002 Missense_Mutation SNP T C3N-00580_T 4623924 214384002 34572420 94 18229 CENPF 0 . GRCh38 1 214644631 214644631 + Missense_Mutation SNP G G T rs763114507 C3N-00580_T C3N-00580_N G G c.5061G>T p.Lys1687Asn p.K1687N ENST00000366955 13/20 154 122 32 104 104 0 strelka-varscan CENPF,missense_variant,p.Lys1687Asn,ENST00000366955,NM_016343.3;CENPF,upstream_gene_variant,,ENST00000614578,;CENPF,upstream_gene_variant,,ENST00000467765,; T ENST00000366955 Transcript missense_variant 5229/10307 5061/9345 1687/3114 K/N aaG/aaT rs763114507 1 1 CENPF HGNC HGNC:1857 protein_coding YES CCDS31023.1 ENSP00000355922 P49454 UPI00001AE985 NM_016343.3 tolerated(0.13) 13/20 hmmpanther:PTHR18874 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 214644631 214644631 G T 1 0 0 0 0 1 0 0 0 2939 962 34 2 2 CENPF 1 214644631 Missense_Mutation SNP G C3N-00580_T 260629 214644631 34311791 95 18230 USH2A 0 . GRCh38 1 215634602 215634602 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.15154T>C p.= p.L5052L ENST00000307340 70/72 649 601 48 322 322 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;SNORD116,upstream_gene_variant,,ENST00000365628,; G ENST00000307340 Transcript synonymous_variant 15541/18883 15154/15609 5052/5202 L Ttg/Ctg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 70/72 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 215634602 215634602 A G 1 0 0 0 0 0 0 0 1 17570 69 3 5 5 USH2A 1 215634602 Silent SNP A C3N-00580_T 989971 215634602 33321820 96 18231 USH2A 0 . GRCh38 1 215674387 215674387 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.13524A>T p.= p.T4508T ENST00000307340 63/72 274 158 116 167 167 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript synonymous_variant 13911/18883 13524/15609 4508/5202 T acA/acT 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 63/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 215674387 215674387 T A 1 0 0 0 0 0 0 0 1 17570 1567 55 4 4 USH2A 1 215674387 Silent SNP T C3N-00580_T 39785 215674387 33282035 97 18232 USH2A 0 . GRCh38 1 216246885 216246885 + Silent SNP G G T rs142655448 C3N-00580_T C3N-00580_N G G c.2509C>A p.= p.R837R ENST00000307340 13/72 486 420 66 268 268 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;USH2A,synonymous_variant,p.=,ENST00000366942,NM_007123.5; T ENST00000307340 Transcript synonymous_variant 2896/18883 2509/15609 837/5202 R Cgg/Agg rs142655448,COSM252908 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 13/72 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00180,Superfamily_domains:SSF57196 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 216246885 216246885 G T 1 0 0 0 0 0 0 0 1 17570 1144 40 1 1 USH2A 1 216246885 Silent SNP G C3N-00580_T 572498 216246885 32709537 98 18233 EPRS 0 . GRCh38 1 219997128 219997128 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.2396A>G p.Tyr799Cys p.Y799C ENST00000366923 18/32 385 347 38 277 277 0 strelka-varscan EPRS,missense_variant,p.Tyr799Cys,ENST00000366923,NM_004446.2;EPRS,missense_variant,p.Tyr806Cys,ENST00000609181,;EPRS,downstream_gene_variant,,ENST00000477030,;EPRS,downstream_gene_variant,,ENST00000464052,; C ENST00000366923 Transcript missense_variant 2666/5014 2396/4539 799/1512 Y/C tAt/tGt 1 -1 EPRS HGNC HGNC:3418 protein_coding YES CCDS31027.1 ENSP00000355890 P07814 UPI0000205E8C NM_004446.2 deleterious(0) 18/32 Gene3D:1.10.287.10,Pfam_domain:PF00458,PROSITE_profiles:PS51185,SMART_domains:SM00991,Superfamily_domains:SSF47060 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 219997128 219997128 T C 1 0 0 0 0 1 0 0 0 5039 1406 49 5 5 EPRS 1 219997128 Missense_Mutation SNP T C3N-00580_T 3750243 219997128 28959294 99 18234 DNAH14 0 . GRCh38 1 225333370 225333370 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.9665G>T p.Cys3222Phe p.C3222F ENST00000430092 64/84 439 384 55 316 316 0 strelka-varscan DNAH14,missense_variant,p.Cys3222Phe,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Cys3222Phe,ENST00000439375,;DNAH14,intron_variant,,ENST00000445597,;DNAH14,intron_variant,,ENST00000327794,; T ENST00000430092 Transcript missense_variant 9880/13763 9665/13548 3222/4515 C/F tGc/tTc 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 tolerated(0.2) 64/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676,Pfam_domain:PF12777 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 225333370 225333370 G T 1 0 0 0 0 1 0 0 0 4415 1319 46 2 2 DNAH14 1 225333370 Missense_Mutation SNP G C3N-00580_T 5336242 225333370 23623052 100 18235 PRSS38 0 . GRCh38 1 227816157 227816157 + Silent SNP G G T rs759710941 C3N-00580_T C3N-00580_N G G c.216G>T p.= p.P72P ENST00000366757 2/5 282 221 61 182 182 0 strelka-varscan PRSS38,synonymous_variant,p.=,ENST00000366757,NM_183062.2; T ENST00000366757 Transcript synonymous_variant 240/1267 216/981 72/326 P ccG/ccT rs759710941,COSM1962633 1 1 PRSS38 HGNC HGNC:29625 protein_coding YES CCDS1563.1 ENSP00000355719 A1L453 UPI00001BBB34 NM_183062.2 2/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24250,hmmpanther:PTHR24250:SF30,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 227816157 227816157 G T 1 0 0 0 0 0 0 0 1 12774 1132 40 1 1 PRSS38 1 227816157 Silent SNP G C3N-00580_T 2482787 227816157 21140265 101 18236 OBSCN 0 . GRCh38 1 228335205 228335205 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.19183G>T p.Asp6395Tyr p.D6395Y ENST00000570156 73/116 618 458 160 461 461 0 strelka-varscan OBSCN,missense_variant,p.Asp6395Tyr,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Asp6395Tyr,ENST00000366707,;OBSCN,missense_variant,p.Asp5438Tyr,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Asp5438Tyr,ENST00000636875,;OBSCN,missense_variant,p.Asp5438Tyr,ENST00000284548,NM_052843.3;OBSCN,missense_variant,p.Asp54Tyr,ENST00000636476,;OBSCN,intron_variant,,ENST00000483539,; T ENST00000570156 Transcript missense_variant 19257/26925 19183/26772 6395/8923 D/Y Gac/Tac 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 73/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 228335205 228335205 G T 1 0 0 0 0 1 0 0 0 10889 1174 41 2 2 OBSCN 1 228335205 Missense_Mutation SNP G C3N-00580_T 519048 228335205 20621217 102 18237 HIST3H3 0 . GRCh38 1 228425255 228425255 + Missense_Mutation SNP T T G novel C3N-00580_T C3N-00580_N T T c.71A>C p.Lys24Thr p.K24T ENST00000366696 1/1 344 310 34 245 245 0 strelka-varscan HIST3H3,missense_variant,p.Lys24Thr,ENST00000366696,NM_003493.2; G ENST00000366696 Transcript missense_variant 71/481 71/411 24/136 K/T aAg/aCg 1 -1 HIST3H3 HGNC HGNC:4778 protein_coding YES CCDS1572.1 ENSP00000355657 Q16695 UPI000000D7E2 NM_003493.2 deleterious_low_confidence(0) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 228425255 228425255 T G 1 0 0 0 0 1 0 0 0 7073 1609 56 5 5 HIST3H3 1 228425255 Missense_Mutation SNP T C3N-00580_T 90050 228425255 20531167 103 18238 URB2 0 . GRCh38 1 229659191 229659191 + Frame_Shift_Del DEL G G - rs138399002 C3N-00580_T C3N-00580_N G G c.4471delG p.Ala1491ProfsTer7 p.A1491Pfs*7 ENST00000258243 10/10 355 202 153 220 220 0 sindel-varindel-pindel URB2,frameshift_variant,p.Ala1491ProfsTer7,ENST00000258243,NM_001314021.1,NM_014777.2;URB2,downstream_gene_variant,,ENST00000434387,; - ENST00000258243 Transcript frameshift_variant 4605/5613 4469/4575 1490/1524 R/X cGg/cg rs138399002,COSM533273 1 1 URB2 HGNC HGNC:28967 protein_coding YES CCDS31052.1 ENSP00000258243 Q14146 UPI000013CFBD NM_001314021.1,NM_014777.2 10/10 Pfam_domain:PF10441,hmmpanther:PTHR15682 0,1 HIGH 1 deletion 1 2 0,1 1 PASS . . 0 204 0 5 0 0 0 0 -20 0.9999348 1 1 1 0 - 7 5 61 229659191 229659191 G - 1 0 1 0 1 0 0 0 0 17555 1116 39 0 0 URB2 1 229659191 Frame_Shift_Del DEL G C3N-00580_T 1233936 229659191 19297231 104 18239 RYR2 0 . GRCh38 1 237454473 237454473 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1375C>T p.Leu459Phe p.L459F ENST00000366574 15/105 372 331 41 206 206 0 strelka-varscan RYR2,missense_variant,p.Leu459Phe,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu443Phe,ENST00000360064,; T ENST00000366574 Transcript missense_variant 1692/16562 1375/14904 459/4967 L/F Ctc/Ttc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 15/105 Superfamily_domains:0048280,Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237454473 237454473 C T 1 0 0 0 0 1 0 0 0 14029 913 32 3 3 RYR2 1 237454473 Missense_Mutation SNP C C3N-00580_T 7795282 237454473 11501949 105 18240 67 2 RYR2 0 . GRCh38 1 237454476 237454476 + Missense_Mutation SNP A A T C3N-00580_T C3N-00580_N A A c.1378A>T p.Ile460Phe p.I460F ENST00000366574 15/105 386 348 38 218 218 0 strelka-varscan RYR2,missense_variant,p.Ile460Phe,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ile444Phe,ENST00000360064,; T ENST00000366574 Transcript missense_variant 1695/16562 1378/14904 460/4967 I/F Att/Ttt COSM1340412,COSM5157820 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 15/105 Superfamily_domains:0048280,Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237454476 237454476 A T 1 0 0 0 0 1 0 0 0 14029 217 8 4 4 RYR2 1 237454476 Missense_Mutation SNP A C3N-00580_T 3 237454476 11501946 106 18241 67 2 RYR2 0 . GRCh38 1 237496753 237496753 + Splice_Site SNP G G T novel C3N-00580_T C3N-00580_N G G c.2203+1G>T p.X735_splice ENST00000366574 139 108 31 71 71 0 strelka-varscan RYR2,splice_donor_variant,,ENST00000366574,NM_001035.2;RYR2,splice_donor_variant,,ENST00000360064,; T ENST00000366574 Transcript splice_donor_variant -/16562 2203/14904 735/4967 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 20/104 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 237496753 237496753 G T 1 0 0 0 0 0 0 1 0 14029 1275 44 2 2 RYR2 1 237496753 Splice_Site SNP G C3N-00580_T 42277 237496753 11459669 107 18242 RYR2 0 . GRCh38 1 237614532 237614532 + Missense_Mutation SNP G G T rs773181830 C3N-00580_T C3N-00580_N G G c.5404G>T p.Gly1802Cys p.G1802C ENST00000366574 37/105 666 485 181 379 378 1 strelka-varscan RYR2,missense_variant,p.Gly1802Cys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gly1786Cys,ENST00000360064,; T ENST00000366574 Transcript missense_variant 5721/16562 5404/14904 1802/4967 G/C Ggc/Tgc rs773181830 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.1) 37/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237614532 237614532 G T 1 0 0 0 0 1 0 0 0 14029 1232 43 2 2 RYR2 1 237614532 Missense_Mutation SNP G C3N-00580_T 117779 237614532 11341890 108 18243 RYR2 0 . GRCh38 1 237623828 237623828 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5980G>T p.Asp1994Tyr p.D1994Y ENST00000366574 39/105 195 122 73 210 209 1 strelka-varscan RYR2,missense_variant,p.Asp1994Tyr,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp1978Tyr,ENST00000360064,; T ENST00000366574 Transcript missense_variant 6297/16562 5980/14904 1994/4967 D/Y Gac/Tac 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.01) 39/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237623828 237623828 G T 1 0 0 0 0 1 0 0 0 14029 1290 45 2 2 RYR2 1 237623828 Missense_Mutation SNP G C3N-00580_T 9296 237623828 11332594 109 18244 RYR2 0 . GRCh38 1 237786025 237786025 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.13317T>A p.= p.P4439P ENST00000366574 91/105 164 111 53 108 108 0 strelka-varscan RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,intron_variant,,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript synonymous_variant 13634/16562 13317/14904 4439/4967 P ccT/ccA 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 91/105 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 237786025 237786025 T A 1 0 0 0 0 0 0 0 1 14029 1567 55 4 4 RYR2 1 237786025 Silent SNP T C3N-00580_T 162197 237786025 11170397 110 18245 ZP4 0 . GRCh38 1 237887377 237887377 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.738A>G p.= p.R246R ENST00000611898 5/13 143 129 14 133 133 0 strelka-varscan ZP4,synonymous_variant,p.=,ENST00000611898,NM_021186.3;ZP4,synonymous_variant,p.=,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; C ENST00000611898 Transcript synonymous_variant 1025/2474 738/1623 246/540 R agA/agG 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 5/13 Pfam_domain:PF00100,Prints_domain:PR00023,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 LOW SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 237887377 237887377 T C 1 0 0 0 0 0 0 0 1 18810 1681 58 5 5 ZP4 1 237887377 Silent SNP T C3N-00580_T 101352 237887377 11069045 111 18246 ZNF695 0 . GRCh38 1 246987640 246987640 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.875G>T p.Gly292Val p.G292V ENST00000339986 4/4 70 56 14 73 73 0 strelka-varscan ZNF695,missense_variant,p.Gly292Val,ENST00000339986,NM_020394.4;ZNF695,intron_variant,,ENST00000487338,NM_001204221.1;ZNF695,intron_variant,,ENST00000498046,;ZNF670-ZNF695,intron_variant,,ENST00000474541,;ZNF670-ZNF695,intron_variant,,ENST00000465049,;ZNF695,intron_variant,,ENST00000479214,;ZNF695,intron_variant,,ENST00000366504,;ZNF695,intron_variant,,ENST00000491337,; A ENST00000339986 Transcript missense_variant 1023/3340 875/1548 292/515 G/V gGa/gTa 1 -1 ZNF695 HGNC HGNC:30954 protein_coding YES CCDS44344.1 ENSP00000341236 Q8IW36 UPI0000F734A8 NM_020394.4 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF119,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 246987640 246987640 C A 1 0 0 0 0 1 0 0 0 18671 855 30 2 2 ZNF695 1 246987640 Missense_Mutation SNP C C3N-00580_T 9100263 246987640 1968782 112 18247 OR2G3 0 . GRCh38 1 247605639 247605639 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.54A>G p.= p.S18S ENST00000320002 1/1 142 128 14 90 90 0 strelka-varscan OR2G3,synonymous_variant,p.=,ENST00000320002,NM_001001914.1;U6,downstream_gene_variant,,ENST00000637707,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; G ENST00000320002 Transcript synonymous_variant 54/930 54/930 18/309 S tcA/tcG 1 1 OR2G3 HGNC HGNC:15008 protein_coding YES CCDS31093.1 ENSP00000326301 Q8NGZ4 A0A126GVX0 UPI0000041CD9 NM_001001914.1 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF300,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 247605639 247605639 A G 1 0 0 0 0 0 0 0 1 11077 175 7 5 5 OR2G3 1 247605639 Silent SNP A C3N-00580_T 617999 247605639 1350783 113 18248 OR2M4 0 . GRCh38 1 248239612 248239612 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.684G>T p.Met228Ile p.M228I ENST00000306687 1/1 296 215 81 214 214 0 strelka-varscan OR2M4,missense_variant,p.Met228Ile,ENST00000306687,NM_017504.1; T ENST00000306687 Transcript missense_variant 684/936 684/936 228/311 M/I atG/atT 1 1 OR2M4 HGNC HGNC:8270 protein_coding YES CCDS31108.1 ENSP00000306688 Q96R27 A0A126GV73 UPI000004B233 NM_017504.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF91,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 248239612 248239612 G T 1 0 0 0 0 1 0 0 0 11090 1348 47 2 2 OR2M4 1 248239612 Missense_Mutation SNP G C3N-00580_T 633973 248239612 716810 114 18249 OR2T33 0 . GRCh38 1 248272985 248272985 + Missense_Mutation SNP G G T rs113045980 C3N-00580_T C3N-00580_N G G c.830C>A p.Thr277Asn p.T277N ENST00000318021 1/1 473 381 92 351 351 0 strelka-varscan OR2T33,missense_variant,p.Thr277Asn,ENST00000318021,NM_001004695.1; T ENST00000318021 Transcript missense_variant 830/963 830/963 277/320 T/N aCt/aAt rs113045980 1 -1 OR2T33 HGNC HGNC:31255 protein_coding YES CCDS31109.1 ENSP00000324687 Q8NG76 UPI000004B237 NM_001004695.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 248272985 248272985 G T 1 0 0 0 0 1 0 0 0 11101 1029 36 2 2 OR2T33 1 248272985 Missense_Mutation SNP G C3N-00580_T 33373 248272985 683437 115 18250 OR14C36 0 . GRCh38 1 248349004 248349004 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.230C>G p.Pro77Arg p.P77R ENST00000317861 1/1 245 138 107 137 137 0 strelka-varscan OR14C36,missense_variant,p.Pro77Arg,ENST00000317861,NM_001001918.1; G ENST00000317861 Transcript missense_variant 230/939 230/939 77/312 P/R cCt/cGt 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 248349004 248349004 C G 1 0 0 0 0 1 0 0 0 11023 681 24 4 4 OR14C36 1 248349004 Missense_Mutation SNP C C3N-00580_T 76019 248349004 607418 116 18251 OR2T6 0 . GRCh38 1 248387948 248387948 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.340C>A p.Leu114Met p.L114M ENST00000355728 1/1 75 47 28 43 43 0 strelka-varscan OR2T6,missense_variant,p.Leu114Met,ENST00000355728,NM_001005471.1; A ENST00000355728 Transcript missense_variant 340/927 340/927 114/308 L/M Ctg/Atg 1 1 OR2T6 HGNC HGNC:15018 protein_coding YES CCDS31114.1 ENSP00000347965 Q8NHC8 UPI0000199147 NM_001005471.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF57,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 248387948 248387948 C A 1 0 0 0 0 1 0 0 0 11106 680 24 2 2 OR2T6 1 248387948 Missense_Mutation SNP C C3N-00580_T 38944 248387948 568474 117 18252 OR2T1 0 . GRCh38 1 248406714 248406714 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.720A>T p.= p.A240A ENST00000366474 1/1 201 174 27 170 170 0 strelka-varscan OR2T1,synonymous_variant,p.=,ENST00000366474,NM_030904.1; T ENST00000366474 Transcript synonymous_variant 720/1110 720/1110 240/369 A gcA/gcT 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 61 248406714 248406714 A T 1 0 0 0 0 0 0 0 1 11094 175 7 4 4 OR2T1 1 248406714 Silent SNP A C3N-00580_T 18766 248406714 549708 118 18253 OR2T3 0 . GRCh38 1 248474225 248474225 + Missense_Mutation SNP C C G C3N-00580_T C3N-00580_N C C c.875C>G p.Pro292Arg p.P292R ENST00000359594 1/1 592 449 143 391 391 0 strelka-varscan OR2T3,missense_variant,p.Pro292Arg,ENST00000359594,NM_001005495.1; G ENST00000359594 Transcript missense_variant 875/957 875/957 292/318 P/R cCc/cGc COSM3487220 1 1 OR2T3 HGNC HGNC:14727 protein_coding YES CCDS31117.1 ENSP00000352604 Q8NH03 A0A126GVW5 UPI00001D7CA5 NM_001005495.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF4,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 248474225 248474225 C G 1 0 0 0 0 1 0 0 0 11100 623 22 4 4 OR2T3 1 248474225 Missense_Mutation SNP C C3N-00580_T 67511 248474225 482197 119 18254 TPO 0 . GRCh38 2 1477517 1477517 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1251G>T p.= p.L417L ENST00000345913 8/17 267 165 102 525 524 1 strelka-varscan-mutect TPO,synonymous_variant,p.=,ENST00000422464,;TPO,synonymous_variant,p.=,ENST00000345913,NM_000547.5;TPO,synonymous_variant,p.=,ENST00000329066,NM_001206744.1;TPO,synonymous_variant,p.=,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,synonymous_variant,p.=,ENST00000346956,NM_175721.3;TPO,intron_variant,,ENST00000382198,NM_175722.3;TPO,intron_variant,,ENST00000497517,; T ENST00000345913 Transcript synonymous_variant 1342/3145 1251/2802 417/933 L ctG/ctT 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 8/17 Low_complexity_(Seg):seg,PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 1477517 1477517 G T 1 0 0 0 0 0 0 0 1 16891 1335 47 2 2 TPO 2 1477517 Silent SNP G C3N-00580_T 1477517 240716012 120 18255 PXDN 0 . GRCh38 2 1676978 1676978 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.797C>T p.Thr266Ile p.T266I ENST00000252804 8/23 180 94 86 184 184 0 strelka-varscan-mutect PXDN,missense_variant,p.Thr266Ile,ENST00000252804,NM_012293.2;PXDN,missense_variant,p.Thr262Ile,ENST00000433670,;PXDN,missense_variant,p.Thr190Ile,ENST00000447941,;PXDN,downstream_gene_variant,,ENST00000425171,;PXDN,upstream_gene_variant,,ENST00000483018,;PXDN,upstream_gene_variant,,ENST00000467191,;PXDN,upstream_gene_variant,,ENST00000477810,;PXDN,downstream_gene_variant,,ENST00000485177,;PXDN,upstream_gene_variant,,ENST00000478155,; A ENST00000252804 Transcript missense_variant 848/6808 797/4440 266/1479 T/I aCc/aTc 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 deleterious(0.03) 8/23 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1676978 1676978 G A 1 0 0 0 0 1 0 0 0 13001 1261 44 3 3 PXDN 2 1676978 Missense_Mutation SNP G C3N-00580_T 199461 1676978 240516551 121 18256 OSR1 0 . GRCh38 2 19353722 19353722 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.84C>A p.Asn28Lys p.N28K ENST00000272223 2/3 260 230 30 219 219 0 strelka-varscan-mutect OSR1,missense_variant,p.Asn28Lys,ENST00000272223,NM_145260.2;OSR1,downstream_gene_variant,,ENST00000498844,;OSR1,non_coding_transcript_exon_variant,,ENST00000487581,; T ENST00000272223 Transcript missense_variant 429/1936 84/801 28/266 N/K aaC/aaA COSM3743494 1 -1 OSR1 HGNC HGNC:8111 protein_coding YES CCDS1694.1 ENSP00000272223 Q8TAX0 UPI000006EA6A NM_145260.2 deleterious_low_confidence(0.01) 2/3 hmmpanther:PTHR14196,hmmpanther:PTHR14196:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9998629 1 1 1 0 T 3 4 61 19353722 19353722 G T 1 0 0 0 0 1 0 0 0 11360 1136 40 1 1 OSR1 2 19353722 Missense_Mutation SNP G C3N-00580_T 17676744 19353722 222839807 122 18257 APOB 0 . GRCh38 2 21033504 21033504 + Missense_Mutation SNP C C A rs770369582 C3N-00580_T C3N-00580_N C C c.919G>T p.Gly307Cys p.G307C ENST00000233242 9/29 415 240 175 365 365 0 strelka-varscan-mutect APOB,missense_variant,p.Gly307Cys,ENST00000233242,NM_000384.2;APOB,missense_variant,p.Gly307Cys,ENST00000399256,; A ENST00000233242 Transcript missense_variant 1047/14121 919/13692 307/4563 G/C Ggc/Tgc rs770369582,COSM1136594 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 9/29 PROSITE_profiles:PS51211,hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF01347,SMART_domains:SM00638,Superfamily_domains:SSF56968 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs770369582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 21033504 21033504 C A 1 0 0 0 0 1 0 0 0 907 623 22 2 2 APOB 2 21033504 Missense_Mutation SNP C C3N-00580_T 1679782 21033504 221160025 123 18258 C2orf71 0 . GRCh38 2 29074082 29074082 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.180G>C p.Glu60Asp p.E60D ENST00000331664 1/2 546 289 257 372 372 0 strelka-varscan C2orf71,missense_variant,p.Glu60Asp,ENST00000331664,NM_001029883.2; G ENST00000331664 Transcript missense_variant 180/7044 180/3867 60/1288 E/D gaG/gaC 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.11) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 29074082 29074082 C G 1 0 0 0 0 1 0 0 0 2045 796 28 4 4 C2orf71 2 29074082 Missense_Mutation SNP C C3N-00580_T 8040578 29074082 213119447 124 18259 C2orf71 0 . GRCh38 2 29074093 29074093 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.169C>A p.Leu57Met p.L57M ENST00000331664 1/2 473 260 213 337 337 0 strelka-varscan C2orf71,missense_variant,p.Leu57Met,ENST00000331664,NM_001029883.2; T ENST00000331664 Transcript missense_variant 169/7044 169/3867 57/1288 L/M Ctg/Atg 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.08) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 29074093 29074093 G T 1 0 0 0 0 1 0 0 0 2045 991 35 2 2 C2orf71 2 29074093 Missense_Mutation SNP G C3N-00580_T 11 29074093 213119436 125 18260 ALK 0 . GRCh38 2 29296960 29296960 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1745G>T p.Trp582Leu p.W582L ENST00000389048 9/29 429 280 149 380 380 0 strelka-varscan ALK,missense_variant,p.Trp582Leu,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Trp205Leu,ENST00000618119,;ALK,non_coding_transcript_exon_variant,,ENST00000498037,; A ENST00000389048 Transcript missense_variant 2652/6220 1745/4863 582/1620 W/L tGg/tTg 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 deleterious(0) 9/29 PROSITE_profiles:PS50060,Pfam_domain:PF00629,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 29296960 29296960 C A 1 0 0 0 0 1 0 0 0 625 595 21 2 2 ALK 2 29296960 Missense_Mutation SNP C C3N-00580_T 222867 29296960 212896569 126 18261 EHD3 0 . GRCh38 2 31266288 31266288 + Missense_Mutation SNP C C T rs144717418 C3N-00580_T C3N-00580_N C C c.1192C>T p.Arg398Cys p.R398C ENST00000322054 6/6 355 266 89 225 225 0 strelka-varscan EHD3,missense_variant,p.Arg398Cys,ENST00000322054,NM_014600.2; T ENST00000322054 Transcript missense_variant 1477/4636 1192/1608 398/535 R/C Cgc/Tgc rs144717418 1 1 EHD3 HGNC HGNC:3244 protein_coding YES CCDS1774.1 ENSP00000327116 Q9NZN3 UPI0000140D07 NM_014600.2 deleterious(0.01) 6/6 hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF67 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 31266288 31266288 C T 1 0 0 0 0 1 0 0 0 4815 768 27 1 1 EHD3 2 31266288 Missense_Mutation SNP C C3N-00580_T 1969328 31266288 210927241 127 18262 SRD5A2 0 . GRCh38 2 31580885 31580885 + Missense_Mutation SNP G G C rs9332960 C3N-00580_T C3N-00580_N G G c.16C>G p.Gln6Glu p.Q6E ENST00000622030 1/5 183 137 46 127 127 0 strelka-varscan SRD5A2,missense_variant,p.Gln6Glu,ENST00000622030,NM_000348.3; C ENST00000622030 Transcript missense_variant 183/4648 16/765 6/254 Q/E Cag/Gag rs9332960 1 -1 SRD5A2 HGNC HGNC:11285 protein_coding YES CCDS74503.1 ENSP00000477587 P31213 UPI000017954A NM_000348.3 tolerated(0.17) 1/5 PIRSF_domain:PIRSF015596 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 31580885 31580885 G C 1 0 0 0 0 1 0 0 0 15496 1357 47 4 4 SRD5A2 2 31580885 Missense_Mutation SNP G C3N-00580_T 314597 31580885 210612644 128 18263 LTBP1 0 . GRCh38 2 33134958 33134958 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1199T>A p.Val400Glu p.V400E ENST00000404816 5/34 103 75 28 91 91 0 strelka-varscan LTBP1,missense_variant,p.Val400Glu,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Val74Glu,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Val74Glu,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Val74Glu,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Val74Glu,ENST00000402934,;LTBP1,splice_region_variant,,ENST00000432635,; A ENST00000404816 Transcript missense_variant,splice_region_variant 1552/6333 1199/5166 400/1721 V/E gTg/gAg 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0) 5/34 PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 33134958 33134958 T A 1 0 0 0 0 1 0 0 0 8979 1710 59 4 4 LTBP1 2 33134958 Missense_Mutation SNP T C3N-00580_T 1554073 33134958 209058571 129 18264 LTBP1 0 . GRCh38 2 33257329 33257329 + Missense_Mutation SNP C C A rs765745245 C3N-00580_T C3N-00580_N C C c.2213C>A p.Ser738Tyr p.S738Y ENST00000404816 12/34 404 315 89 260 260 0 strelka-varscan LTBP1,missense_variant,p.Ser738Tyr,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Ser412Tyr,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Ser412Tyr,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Ser55Tyr,ENST00000468091,;LTBP1,intron_variant,,ENST00000404525,NM_001166265.1;LTBP1,intron_variant,,ENST00000402934,;LTBP1,intron_variant,,ENST00000413303,; A ENST00000404816 Transcript missense_variant 2566/6333 2213/5166 738/1721 S/Y tCt/tAt rs765745245 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0) 12/34 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 33257329 33257329 C A 1 0 0 0 0 1 0 0 0 8979 913 32 2 2 LTBP1 2 33257329 Missense_Mutation SNP C C3N-00580_T 122371 33257329 208936200 130 18265 SLC3A1 0 . GRCh38 2 44320400 44320400 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1819C>G p.Leu607Val p.L607V ENST00000260649 10/10 618 452 166 413 413 0 strelka-varscan SLC3A1,missense_variant,p.Leu607Val,ENST00000260649,NM_000341.3;SLC3A1,missense_variant,p.Leu329Val,ENST00000409380,;SLC3A1,missense_variant,p.Leu238Val,ENST00000409740,;PREPL,3_prime_UTR_variant,,ENST00000541738,NM_001171617.1;PREPL,3_prime_UTR_variant,,ENST00000409936,NM_001171606.1;PREPL,3_prime_UTR_variant,,ENST00000409411,NM_001171613.1;PREPL,3_prime_UTR_variant,,ENST00000409957,;PREPL,3_prime_UTR_variant,,ENST00000444696,;PREPL,downstream_gene_variant,,ENST00000260648,NM_006036.4;PREPL,downstream_gene_variant,,ENST00000410081,;PREPL,downstream_gene_variant,,ENST00000409272,NM_001171603.1;SLC3A1,downstream_gene_variant,,ENST00000409387,;PREPL,downstream_gene_variant,,ENST00000378511,NM_001042385.2;PREPL,downstream_gene_variant,,ENST00000378520,NM_001042386.2;SLC3A1,downstream_gene_variant,,ENST00000611973,;PREPL,downstream_gene_variant,,ENST00000420756,;PREPL,3_prime_UTR_variant,,ENST00000426481,;PREPL,3_prime_UTR_variant,,ENST00000425263,; G ENST00000260649 Transcript missense_variant 1895/2989 1819/2058 607/685 L/V Cta/Gta 1 1 SLC3A1 HGNC HGNC:11025 protein_coding YES CCDS1819.1 ENSP00000260649 Q07837 A0A0S2Z4E1 UPI000013D0F2 NM_000341.3 deleterious(0.03) 10/10 hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 44320400 44320400 C G 1 0 0 0 0 1 0 0 0 14904 912 32 4 4 SLC3A1 2 44320400 Missense_Mutation SNP C C3N-00580_T 11063071 44320400 197873129 131 18266 CAMKMT 0 . GRCh38 2 44706310 44706310 + Missense_Mutation SNP G G T rs533364037 C3N-00580_T C3N-00580_N G G c.461G>T p.Gly154Val p.G154V ENST00000378494 5/11 380 254 126 248 248 0 strelka-varscan CAMKMT,missense_variant,p.Gly154Val,ENST00000378494,NM_024766.4;CAMKMT,missense_variant,p.Gly28Val,ENST00000613618,;CAMKMT,non_coding_transcript_exon_variant,,ENST00000477830,; T ENST00000378494 Transcript missense_variant 505/1495 461/972 154/323 G/V gGg/gTg rs533364037 1 1 CAMKMT HGNC HGNC:26276 protein_coding YES CCDS1820.1 ENSP00000367755 Q7Z624 UPI0000070B33 NM_024766.4 deleterious(0) 5/11 Gene3D:3.40.50.150,Pfam_domain:PF10294,PROSITE_profiles:PS51610,hmmpanther:PTHR13539,hmmpanther:PTHR13539:SF5,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 44706310 44706310 G T 1 0 0 0 0 1 0 0 0 2299 1232 43 2 2 CAMKMT 2 44706310 Missense_Mutation SNP G C3N-00580_T 385910 44706310 197487219 132 18267 NRXN1 0 . GRCh38 2 50236900 50236900 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.3555C>A p.= p.P1185P ENST00000404971 19/24 308 273 35 299 299 0 strelka-varscan NRXN1,synonymous_variant,p.=,ENST00000406316,NM_004801.4;NRXN1,synonymous_variant,p.=,ENST00000625672,;NRXN1,synonymous_variant,p.=,ENST00000404971,NM_001135659.1;NRXN1,synonymous_variant,p.=,ENST00000401669,;NRXN1,synonymous_variant,p.=,ENST00000405472,;NRXN1,synonymous_variant,p.=,ENST00000630543,;NRXN1,synonymous_variant,p.=,ENST00000342183,NM_138735.2;NRXN1,synonymous_variant,p.=,ENST00000401710,;NRXN1,synonymous_variant,p.=,ENST00000628364,;NRXN1,synonymous_variant,p.=,ENST00000625320,;NRXN1,5_prime_UTR_variant,,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,upstream_gene_variant,,ENST00000636736,;NRXN1,downstream_gene_variant,,ENST00000636818,;NRXN1,synonymous_variant,p.=,ENST00000331040,;NRXN1,synonymous_variant,p.=,ENST00000637906,; T ENST00000404971 Transcript synonymous_variant 4895/7578 3555/4644 1185/1547 P ccC/ccA COSM3962890,COSM3962891,COSM3962892,COSM3962893,COSM3962894 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 19/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,Superfamily_domains:SSF49899 1,1,1,1,1 LOW 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 50236900 50236900 G T 1 0 0 0 0 0 0 0 1 10724 1335 47 2 2 NRXN1 2 50236900 Silent SNP G C3N-00580_T 5530590 50236900 191956629 133 18268 PLEK 0 . GRCh38 2 68393213 68393213 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.814C>A p.Pro272Thr p.P272T ENST00000234313 7/9 355 284 71 262 262 0 strelka-varscan PLEK,missense_variant,p.Pro272Thr,ENST00000234313,NM_002664.2;PLEK,non_coding_transcript_exon_variant,,ENST00000474788,; A ENST00000234313 Transcript missense_variant 993/2869 814/1053 272/350 P/T Cct/Act 1 1 PLEK HGNC HGNC:9070 protein_coding YES CCDS1887.1 ENSP00000234313 P08567 UPI00002085C1 NM_002664.2 deleterious(0) 7/9 PROSITE_profiles:PS50003,hmmpanther:PTHR12092,hmmpanther:PTHR12092:SF1,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 68393213 68393213 C A 1 0 0 0 0 1 0 0 0 12146 623 22 2 2 PLEK 2 68393213 Missense_Mutation SNP C C3N-00580_T 18156313 68393213 173800316 134 18269 ADD2 0 . GRCh38 2 70674777 70674777 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1642G>T p.Asp548Tyr p.D548Y ENST00000264436 14/16 214 152 62 222 222 0 strelka-varscan ADD2,missense_variant,p.Asp548Tyr,ENST00000264436,NM_001617.3;ADD2,missense_variant,p.Asp548Tyr,ENST00000407644,NM_001185054.1;ADD2,missense_variant,p.Asp548Tyr,ENST00000355733,NM_017488.3;ADD2,missense_variant,p.Asp300Tyr,ENST00000456320,;ADD2,missense_variant,p.Asp242Tyr,ENST00000522886,;ADD2,downstream_gene_variant,,ENST00000413157,NM_017482.3;ADD2,downstream_gene_variant,,ENST00000430656,NM_001185055.1;ADD2,missense_variant,p.Asp548Tyr,ENST00000403045,;ADD2,upstream_gene_variant,,ENST00000481675,; A ENST00000264436 Transcript missense_variant 2087/9267 1642/2181 548/726 D/Y Gat/Tat COSM3582805,COSM3582806 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 deleterious(0.05) 14/16 hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 70674777 70674777 C A 1 0 0 0 0 1 0 0 0 349 884 31 1 1 ADD2 2 70674777 Missense_Mutation SNP C C3N-00580_T 2281564 70674777 171518752 135 18270 MPHOSPH10 0 . GRCh38 2 71133018 71133018 + Frame_Shift_Del DEL T T - novel C3N-00580_T C3N-00580_N T T c.213delT p.Phe71LeufsTer52 p.F71Lfs*52 ENST00000244230 2/11 333 268 65 252 252 0 sindel-varindel-pindel MPHOSPH10,frameshift_variant,p.Phe71LeufsTer52,ENST00000244230,NM_005791.2;MPHOSPH10,frameshift_variant,p.Phe71LeufsTer52,ENST00000498451,;MCEE,upstream_gene_variant,,ENST00000494660,;MCEE,upstream_gene_variant,,ENST00000244217,NM_032601.3;MCEE,upstream_gene_variant,,ENST00000486135,;MPHOSPH10,non_coding_transcript_exon_variant,,ENST00000468427,; - ENST00000244230 Transcript frameshift_variant 562/2484 210/2046 70/681 N/X aaT/aa 1 1 MPHOSPH10 HGNC HGNC:7213 protein_coding YES CCDS1916.1 ENSP00000244230 O00566 UPI000012F41D NM_005791.2 2/11 hmmpanther:PTHR17039,hmmpanther:PTHR17039:SF1,Pfam_domain:PF04006,PIRSF_domain:PIRSF017300 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 71133018 71133018 T - 1 0 1 0 1 0 0 0 0 9690 1490 52 0 0 MPHOSPH10 2 71133018 Frame_Shift_Del DEL T C3N-00580_T 458241 71133018 171060511 136 18271 ALMS1 0 . GRCh38 2 73450586 73450586 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.4059A>T p.= p.P1353P ENST00000613296 8/23 428 289 139 267 266 1 strelka-varscan ALMS1,synonymous_variant,p.=,ENST00000613296,NM_015120.4;ALMS1,synonymous_variant,p.=,ENST00000484298,;ALMS1,synonymous_variant,p.=,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; T ENST00000613296 Transcript synonymous_variant 4170/12925 4059/12507 1353/4168 P ccA/ccT 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 8/23 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 73450586 73450586 A T 1 0 0 0 0 0 0 0 1 635 117 5 4 4 ALMS1 2 73450586 Silent SNP A C3N-00580_T 2317568 73450586 168742943 137 18272 CCDC142 0 . GRCh38 2 74475394 74475394 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.1606A>G p.Ser536Gly p.S536G ENST00000290418 7/9 76 46 30 64 64 0 strelka-varscan CCDC142,missense_variant,p.Ser543Gly,ENST00000393965,;CCDC142,missense_variant,p.Ser536Gly,ENST00000290418,NM_032779.3;MRPL53,upstream_gene_variant,,ENST00000258105,NM_053050.4;MRPL53,upstream_gene_variant,,ENST00000409710,;CCDC142,missense_variant,p.Ser445Gly,ENST00000454193,;CCDC142,non_coding_transcript_exon_variant,,ENST00000473278,;CCDC142,non_coding_transcript_exon_variant,,ENST00000497232,;CCDC142,non_coding_transcript_exon_variant,,ENST00000486335,;MRPL53,upstream_gene_variant,,ENST00000468875,;MRPL53,upstream_gene_variant,,ENST00000467349,; C ENST00000290418 Transcript missense_variant 1765/2835 1606/2232 536/743 S/G Agt/Ggt 1 -1 CCDC142 HGNC HGNC:25889 protein_coding YES CCDS1945.1 ENSP00000290418 Q17RM4 UPI000013CFB5 NM_032779.3 deleterious(0.05) 7/9 Pfam_domain:PF14923,hmmpanther:PTHR21436 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 74475394 74475394 T C 1 0 0 0 0 1 0 0 0 2464 1580 55 5 5 CCDC142 2 74475394 Missense_Mutation SNP T C3N-00580_T 1024808 74475394 167718135 138 18273 DQX1 0 . GRCh38 2 74523349 74523349 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.1005C>T p.= p.S335S ENST00000404568 5/12 637 369 268 506 506 0 strelka-varscan DQX1,synonymous_variant,p.=,ENST00000404568,NM_133637.2;DQX1,synonymous_variant,p.=,ENST00000393951,;AUP1,downstream_gene_variant,,ENST00000377526,NM_181575.4;DQX1,downstream_gene_variant,,ENST00000451518,;DQX1,non_coding_transcript_exon_variant,,ENST00000495597,;DQX1,downstream_gene_variant,,ENST00000498552,;DQX1,synonymous_variant,p.=,ENST00000418139,;DQX1,non_coding_transcript_exon_variant,,ENST00000473508,;AUP1,downstream_gene_variant,,ENST00000466894,;AUP1,downstream_gene_variant,,ENST00000463900,;AUP1,downstream_gene_variant,,ENST00000425118,;AUP1,downstream_gene_variant,,ENST00000486234,;AUP1,downstream_gene_variant,,ENST00000464887,;DQX1,upstream_gene_variant,,ENST00000483555,;AUP1,downstream_gene_variant,,ENST00000462297,; A ENST00000404568 Transcript synonymous_variant 1225/2689 1005/2154 335/717 S tcC/tcT 1 -1 DQX1 HGNC HGNC:20410 protein_coding YES CCDS1949.2 ENSP00000384621 Q8TE96 UPI0000208758 NM_133637.2 5/12 PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF108,Superfamily_domains:SSF52540 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 74523349 74523349 G A 1 0 0 0 0 0 0 0 1 4566 1335 47 3 3 DQX1 2 74523349 Silent SNP G C3N-00580_T 47955 74523349 167670180 139 18274 M1AP 0 . GRCh38 2 74560208 74560208 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1365C>A p.= p.I455I ENST00000290536 9/11 162 106 56 179 179 0 strelka-varscan M1AP,synonymous_variant,p.=,ENST00000290536,NM_138804.4;M1AP,synonymous_variant,p.=,ENST00000536235,NM_001321739.1,NM_001281296.1;M1AP,synonymous_variant,p.=,ENST00000409585,;DOK1,downstream_gene_variant,,ENST00000233668,NM_001318866.1,NM_001381.3;DOK1,downstream_gene_variant,,ENST00000409429,NM_001197260.1;DOK1,downstream_gene_variant,,ENST00000340004,;LOXL3,upstream_gene_variant,,ENST00000413469,;M1AP,non_coding_transcript_exon_variant,,ENST00000464686,;M1AP,intron_variant,,ENST00000485997,;DOK1,downstream_gene_variant,,ENST00000480318,;DOK1,downstream_gene_variant,,ENST00000489958,;DOK1,downstream_gene_variant,,ENST00000496966,;DOK1,downstream_gene_variant,,ENST00000485132,;DOK1,downstream_gene_variant,,ENST00000488613,;DOK1,downstream_gene_variant,,ENST00000464613,;DOK1,downstream_gene_variant,,ENST00000429631,;DOK1,downstream_gene_variant,,ENST00000482206,;DOK1,downstream_gene_variant,,ENST00000474924,;DOK1,downstream_gene_variant,,ENST00000475191,; T ENST00000290536 Transcript synonymous_variant 1482/2543 1365/1593 455/530 I atC/atA 1 -1 M1AP HGNC HGNC:25183 protein_coding YES CCDS33229.1 ENSP00000290536 Q8TC57 UPI0000072570 NM_138804.4 9/11 hmmpanther:PTHR28642,hmmpanther:PTHR28642:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 74560208 74560208 G T 1 0 0 0 0 0 0 0 1 9053 932 33 2 2 M1AP 2 74560208 Silent SNP G C3N-00580_T 36859 74560208 167633321 140 18275 CTNNA2 0 . GRCh38 2 79651634 79651634 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.78G>T p.Arg26Ser p.R26S ENST00000402739 1/18 367 313 54 217 217 0 strelka-varscan CTNNA2,missense_variant,p.Arg26Ser,ENST00000466387,;CTNNA2,missense_variant,p.Arg26Ser,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Arg26Ser,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Arg26Ser,ENST00000629316,NM_001164883.1;CTNNA2,missense_variant,p.Arg26Ser,ENST00000409971,;CTNNA2,missense_variant,p.Arg26Ser,ENST00000451966,;CTNNA2,missense_variant,p.Arg26Ser,ENST00000409266,;MIR4264,upstream_gene_variant,,ENST00000583520,; T ENST00000402739 Transcript missense_variant 83/3684 78/2862 26/953 R/S agG/agT 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0.02) 1/18 Pfam_domain:PF01044,Prints_domain:PR00805,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 79651634 79651634 G T 1 0 0 0 0 1 0 0 0 3822 1194 42 2 2 CTNNA2 2 79651634 Missense_Mutation SNP G C3N-00580_T 5091426 79651634 162541895 141 18276 ZNF2 0 . GRCh38 2 95181290 95181290 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.501A>T p.Lys167Asn p.K167N ENST00000611147 5/5 225 126 99 187 187 0 strelka-varscan ZNF2,missense_variant,p.Lys112Asn,ENST00000617923,NM_001017396.2;ZNF2,missense_variant,p.Lys74Asn,ENST00000611463,NM_001291604.1;ZNF2,missense_variant,p.Lys154Asn,ENST00000614034,NM_021088.3;ZNF2,missense_variant,p.Lys116Asn,ENST00000622059,NM_001282398.1;ZNF2,missense_variant,p.Lys167Asn,ENST00000611147,NM_001291605.1; T ENST00000611147 Transcript missense_variant 584/1465 501/1317 167/438 K/N aaA/aaT 1 1 ZNF2 HGNC HGNC:12991 protein_coding YES CCDS77434.1 ENSP00000482030 A0A087WYR5 UPI0004438063 NM_001291605.1 tolerated(0.1) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF364 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 95181290 95181290 A T 1 0 0 0 0 1 0 0 0 18337 69 3 4 4 ZNF2 2 95181290 Missense_Mutation SNP A C3N-00580_T 15529656 95181290 147012239 142 18277 STARD7 0 . GRCh38 2 96193304 96193304 + Nonsense_Mutation SNP C C A rs372858958 C3N-00580_T C3N-00580_N C C c.598G>T p.Glu200Ter p.E200* ENST00000337288 4/8 465 338 127 476 476 0 strelka-varscan STARD7,stop_gained,p.Glu200Ter,ENST00000337288,NM_020151.3;STARD7,stop_gained,p.Glu99Ter,ENST00000443962,;STARD7,splice_region_variant,,ENST00000462501,;STARD7,non_coding_transcript_exon_variant,,ENST00000495687,;STARD7,downstream_gene_variant,,ENST00000488084,; A ENST00000337288 Transcript stop_gained 982/3368 598/1113 200/370 E/* Gag/Tag rs372858958 1 -1 STARD7 HGNC HGNC:18063 protein_coding YES CCDS2017.2 ENSP00000338030 Q9NQZ5 UPI0000001C0C NM_020151.3 4/8 PROSITE_profiles:PS50848,hmmpanther:PTHR19308,Gene3D:3.30.530.20,Pfam_domain:PF01852,SMART_domains:SM00234,Superfamily_domains:SSF55961 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 96193304 96193304 C A 1 0 0 0 0 0 1 0 0 15637 864 30 2 2 STARD7 2 96193304 Nonsense_Mutation SNP C C3N-00580_T 1012014 96193304 146000225 143 18278 SNRNP200 0 . GRCh38 2 96284459 96284459 + Nonsense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.4291A>T p.Lys1431Ter p.K1431* ENST00000323853 31/45 747 511 236 601 600 1 strelka-varscan SNRNP200,stop_gained,p.Lys1431Ter,ENST00000323853,NM_014014.4;SNRNP200,5_prime_UTR_variant,,ENST00000429650,;SNRNP200,non_coding_transcript_exon_variant,,ENST00000480242,;SNRNP200,non_coding_transcript_exon_variant,,ENST00000497539,;SNRNP200,downstream_gene_variant,,ENST00000480615,;SNRNP200,upstream_gene_variant,,ENST00000493271,;SNRNP200,upstream_gene_variant,,ENST00000484372,; A ENST00000323853 Transcript stop_gained 4369/7165 4291/6411 1431/2136 K/* Aag/Tag 1 -1 SNRNP200 HGNC HGNC:30859 protein_coding YES CCDS2020.1 ENSP00000317123 O75643 UPI0000207C53 NM_014014.4 31/45 PROSITE_profiles:PS51192,PIRSF_domain:PIRSF039073,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 96284459 96284459 T A 1 0 0 0 0 0 1 0 0 15172 1792 62 4 4 SNRNP200 2 96284459 Nonsense_Mutation SNP T C3N-00580_T 91155 96284459 145909070 144 18279 ANKRD36B 0 . GRCh38 2 97558995 97558995 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.866-1G>T p.X289_splice ENST00000258459 87 63 24 114 114 0 strelka-varscan ANKRD36B,splice_acceptor_variant,,ENST00000438709,;ANKRD36B,splice_acceptor_variant,,ENST00000258459,NM_025190.3;ANKRD36B,splice_acceptor_variant,,ENST00000359901,;ANKRD36B,splice_acceptor_variant,,ENST00000443455,;ANKRD36B,splice_acceptor_variant,,ENST00000419390,; A ENST00000258459 Transcript splice_acceptor_variant -/5986 866/4062 289/1353 1 -1 ANKRD36B HGNC HGNC:29333 protein_coding YES CCDS74543.1 ENSP00000481149 Q8N2N9 UPI000155D57B NM_025190.3 8/43 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 97558995 97558995 C A 1 0 0 0 0 0 0 1 0 772 579 20 2 2 ANKRD36B 2 97558995 Splice_Site SNP C C3N-00580_T 1274536 97558995 144634534 145 18280 VWA3B 0 . GRCh38 2 98236670 98236670 + Silent SNP G G T rs377277436 C3N-00580_T C3N-00580_N G G c.2613G>T p.= p.P871P ENST00000477737 19/28 235 174 61 250 250 0 strelka-varscan VWA3B,synonymous_variant,p.=,ENST00000477737,NM_144992.4;VWA3B,synonymous_variant,p.=,ENST00000473149,;VWA3B,synonymous_variant,p.=,ENST00000465555,;VWA3B,non_coding_transcript_exon_variant,,ENST00000485216,;VWA3B,3_prime_UTR_variant,,ENST00000432242,;VWA3B,3_prime_UTR_variant,,ENST00000416277,;VWA3B,3_prime_UTR_variant,,ENST00000495571,;VWA3B,3_prime_UTR_variant,,ENST00000489630,;VWA3B,3_prime_UTR_variant,,ENST00000448638,;VWA3B,non_coding_transcript_exon_variant,,ENST00000409460,; T ENST00000477737 Transcript synonymous_variant 2817/4454 2613/3885 871/1294 P ccG/ccT rs377277436 1 1 VWA3B HGNC HGNC:28385 protein_coding YES CCDS42718.1 ENSP00000417955 Q502W6 UPI0000E9B173 NM_144992.4 19/28 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 98236670 98236670 G T 1 0 0 0 0 0 0 0 1 17795 1074 38 1 1 VWA3B 2 98236670 Silent SNP G C3N-00580_T 677675 98236670 143956859 146 18281 LONRF2 0 . GRCh38 2 100294322 100294322 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1664A>T p.His555Leu p.H555L ENST00000393437 9/12 72 56 16 105 105 0 strelka-varscan LONRF2,missense_variant,p.His555Leu,ENST00000393437,NM_198461.3;LONRF2,missense_variant,p.His312Leu,ENST00000409647,; A ENST00000393437 Transcript missense_variant 2304/13912 1664/2265 555/754 H/L cAc/cTc 1 -1 LONRF2 HGNC HGNC:24788 protein_coding YES CCDS2046.2 ENSP00000377086 Q1L5Z9 UPI000152B4EF NM_198461.3 deleterious(0) 9/12 hmmpanther:PTHR23327:SF5,hmmpanther:PTHR23327,Pfam_domain:PF02190,SMART_domains:SM00464,Superfamily_domains:SSF88697 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 100294322 100294322 T A 1 0 0 0 0 1 0 0 0 8797 1696 59 4 4 LONRF2 2 100294322 Missense_Mutation SNP T C3N-00580_T 2057652 100294322 141899207 147 18282 RPL31 0 . GRCh38 2 101019005 101019005 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.354G>A p.= p.V118V ENST00000409028 5/5 283 240 43 252 252 0 strelka-varscan RPL31,synonymous_variant,p.=,ENST00000409028,NM_001098577.2;TBC1D8,intron_variant,,ENST00000409318,;TBC1D8,intron_variant,,ENST00000376840,NM_001102426.1;RPL31,intron_variant,,ENST00000441435,;RPL31,downstream_gene_variant,,ENST00000409038,;RPL31,downstream_gene_variant,,ENST00000409650,;TBC1D8,intron_variant,,ENST00000494011,; A ENST00000409028 Transcript synonymous_variant 387/1110 354/387 118/128 V gtG/gtA 1 1 RPL31 HGNC HGNC:10334 protein_coding YES CCDS46373.1 ENSP00000386717 P62899 UPI0000EE6D67 NM_001098577.2 5/5 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 101019005 101019005 G A 1 0 0 0 0 0 0 0 1 13833 1306 46 3 3 RPL31 2 101019005 Silent SNP G C3N-00580_T 724683 101019005 141174524 148 18283 IL18RAP 0 . GRCh38 2 102445224 102445224 + Missense_Mutation SNP G G T rs768468042 C3N-00580_T C3N-00580_N G G c.956G>T p.Arg319Leu p.R319L ENST00000264260 9/12 260 179 81 156 156 0 strelka-varscan IL18RAP,missense_variant,p.Arg319Leu,ENST00000264260,NM_003853.3;IL18RAP,missense_variant,p.Arg177Leu,ENST00000409369,;AC007278.3,downstream_gene_variant,,ENST00000450893,; T ENST00000264260 Transcript missense_variant 1545/2773 956/1800 319/599 R/L cGt/cTt rs768468042,COSM1613241 1 1 IL18RAP HGNC HGNC:5989 protein_coding YES CCDS2061.1 ENSP00000264260 O95256 UPI0000071CAF NM_003853.3 tolerated(0.62) 9/12 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF23,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 102445224 102445224 G T 1 0 0 0 0 1 0 0 0 7556 1145 40 1 1 IL18RAP 2 102445224 Missense_Mutation SNP G C3N-00580_T 1426219 102445224 139748305 149 18284 NCK2 0 . GRCh38 2 105881932 105881932 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.831C>A p.Ser277Arg p.S277R ENST00000233154 4/5 38 25 13 35 35 0 strelka-varscan NCK2,missense_variant,p.Ser277Arg,ENST00000233154,NM_003581.4;NCK2,missense_variant,p.Ser277Arg,ENST00000393349,NM_001004720.2;NCK2,intron_variant,,ENST00000451463,NM_001004722.3;NCK2,intron_variant,,ENST00000522586,;NCK2,downstream_gene_variant,,ENST00000393348,;NCK2,downstream_gene_variant,,ENST00000425756,; A ENST00000233154 Transcript missense_variant 1273/2683 831/1143 277/380 S/R agC/agA 1 1 NCK2 HGNC HGNC:7665 protein_coding YES CCDS33266.1 ENSP00000233154 O43639 A0A0S2Z4M6 UPI000012FE3F NM_003581.4 tolerated(0.54) 4/5 PIRSF_domain:PIRSF037874,Superfamily_domains:SSF50044,Superfamily_domains:SSF55550 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 105881932 105881932 C A 1 0 0 0 0 1 0 0 0 10238 767 27 1 1 NCK2 2 105881932 Missense_Mutation SNP C C3N-00580_T 3436708 105881932 136311597 150 18285 CCDC93 0 . GRCh38 2 117920370 117920370 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1869G>T p.= p.L623L ENST00000376300 24/24 107 73 34 119 119 0 strelka-varscan CCDC93,synonymous_variant,p.=,ENST00000376300,NM_019044.4;CCDC93,synonymous_variant,p.=,ENST00000319432,;HTR5BP,intron_variant,,ENST00000434708,;CCDC93,3_prime_UTR_variant,,ENST00000437999,; A ENST00000376300 Transcript synonymous_variant 2007/6899 1869/1896 623/631 L ctG/ctT 1 -1 CCDC93 HGNC HGNC:25611 protein_coding YES CCDS2121.2 ENSP00000365477 Q567U6 UPI0000207DEC NM_019044.4 24/24 hmmpanther:PTHR16441 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 117920370 117920370 C A 1 0 0 0 0 0 0 0 1 2570 465 17 2 2 CCDC93 2 117920370 Silent SNP C C3N-00580_T 12038438 117920370 124273159 151 18286 TSN 0 . GRCh38 2 121765238 121765238 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.558G>A p.= p.L186L ENST00000389682 6/6 522 335 187 524 524 0 strelka-varscan TSN,synonymous_variant,p.=,ENST00000389682,NM_004622.2;TSN,synonymous_variant,p.=,ENST00000409193,;TSN,3_prime_UTR_variant,,ENST00000536142,NM_001261401.1;TSN,downstream_gene_variant,,ENST00000455432,;TSN,non_coding_transcript_exon_variant,,ENST00000498545,;TSN,non_coding_transcript_exon_variant,,ENST00000495112,;TSN,3_prime_UTR_variant,,ENST00000467324,;TSN,3_prime_UTR_variant,,ENST00000490104,;TSN,downstream_gene_variant,,ENST00000478165,;TSN,downstream_gene_variant,,ENST00000490717,; A ENST00000389682 Transcript synonymous_variant 805/3420 558/687 186/228 L ctG/ctA 1 1 TSN HGNC HGNC:12379 protein_coding YES CCDS33284.1 ENSP00000374332 Q15631 UPI0000000C3D NM_004622.2 6/6 hmmpanther:PTHR10741,hmmpanther:PTHR10741:SF2,Gene3D:1j1jA02,Pfam_domain:PF01997,Superfamily_domains:0047790 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 121765238 121765238 G A 1 0 0 0 0 0 0 0 1 17134 1277 45 3 3 TSN 2 121765238 Silent SNP G C3N-00580_T 3844868 121765238 120428291 152 18287 MYO7B 0 . GRCh38 2 127559737 127559737 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.15G>T p.Arg5Ser p.R5S ENST00000428314 2/47 284 216 68 256 255 1 strelka-varscan MYO7B,missense_variant,p.Arg5Ser,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.Arg5Ser,ENST00000409816,; T ENST00000428314 Transcript missense_variant 68/6715 15/6351 5/2116 R/S agG/agT 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 tolerated(0.15) 2/47 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 127559737 127559737 G T 1 0 0 0 0 1 0 0 0 10084 1217 42 2 2 MYO7B 2 127559737 Missense_Mutation SNP G C3N-00580_T 5794499 127559737 114633792 153 18288 MYO7B 0 . GRCh38 2 127581935 127581935 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1125C>A p.= p.I375I ENST00000428314 11/47 371 238 133 344 344 0 strelka-varscan MYO7B,synonymous_variant,p.=,ENST00000428314,NM_001080527.1;MYO7B,synonymous_variant,p.=,ENST00000409816,; A ENST00000428314 Transcript synonymous_variant 1178/6715 1125/6351 375/2116 I atC/atA 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 11/47 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF505,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 127581935 127581935 C A 1 0 0 0 0 0 0 0 1 10084 845 30 2 2 MYO7B 2 127581935 Silent SNP C C3N-00580_T 22198 127581935 114611594 154 18289 POTEF 0 . GRCh38 2 130102156 130102156 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1151A>T p.Glu384Val p.E384V ENST00000409914 9/17 217 157 60 191 191 0 strelka-varscan POTEF,missense_variant,p.Glu384Val,ENST00000409914,NM_001099771.2;POTEF,downstream_gene_variant,,ENST00000361163,; A ENST00000409914 Transcript missense_variant 1551/3842 1151/3228 384/1075 E/V gAg/gTg 1 -1 POTEF HGNC HGNC:33905 protein_coding YES CCDS46409.1 ENSP00000386786 A5A3E0 UPI0000418FEA NM_001099771.2 deleterious_low_confidence(0) 9/17 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 130102156 130102156 T A 1 0 0 0 0 1 0 0 0 12379 1551 54 4 4 POTEF 2 130102156 Missense_Mutation SNP T C3N-00580_T 2520221 130102156 112091373 155 18290 TISP43 0 . GRCh38 2 130576763 130576763 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.290C>A p.Pro97His p.P97H ENST00000409982 3/3 56 44 12 59 59 0 strelka-varscan-mutect TISP43,missense_variant,p.Pro97His,ENST00000623376,;TISP43,missense_variant,p.Pro97His,ENST00000409982,;TISP43,missense_variant,p.Pro97His,ENST00000440359,;TISP43,intron_variant,,ENST00000409793,;TISP43,non_coding_transcript_exon_variant,,ENST00000419965,;TISP43,intron_variant,,ENST00000414595,; A ENST00000409982 Transcript missense_variant 461/1039 290/483 97/160 P/H cCc/cAc 1 1 TISP43 EntrezGene protein_coding YES ENSP00000387081 B9A030 UPI000188179A tolerated(0.07) 3/3 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF221,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999592 1 1 1 0 A 3 1 61 130576763 130576763 C A 1 0 0 0 0 1 0 0 0 16369 623 22 2 2 TISP43 2 130576763 Missense_Mutation SNP C C3N-00580_T 474607 130576763 111616766 156 18291 TISP43 0 . GRCh38 2 130580613 130580613 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.434C>A p.Pro145His p.P145H ENST00000623376 5/5 150 124 26 148 148 0 strelka-varscan-mutect TISP43,missense_variant,p.Pro145His,ENST00000623376,;TISP43,intron_variant,,ENST00000440359,;TISP43,intron_variant,,ENST00000409793,;TISP43,downstream_gene_variant,,ENST00000409982,;AC140481.4,downstream_gene_variant,,ENST00000457169,;TISP43,intron_variant,,ENST00000419965,;TISP43,intron_variant,,ENST00000414595,; A ENST00000623376 Transcript missense_variant 630/1653 434/450 145/149 P/H cCc/cAc 1 1 TISP43 EntrezGene protein_coding ENSP00000485065 A0A096LNJ3 UPI00006C04F9 5/5 PROSITE_profiles:PS50240,SMART_domains:SM00020 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 130580613 130580613 C A 1 0 0 0 0 1 0 0 0 16369 623 22 2 2 TISP43 2 130580613 Missense_Mutation SNP C C3N-00580_T 3850 130580613 111612916 157 18292 POTEJ 0 . GRCh38 2 130657221 130657221 + Missense_Mutation SNP G G T rs771270515 C3N-00580_T C3N-00580_N G G c.2461G>T p.Gly821Trp p.G821W ENST00000409602 15/15 160 109 51 146 146 0 strelka-varscan-mutect POTEJ,missense_variant,p.Gly821Trp,ENST00000409602,NM_001277083.1; T ENST00000409602 Transcript missense_variant 2513/3383 2461/3117 821/1038 G/W Ggg/Tgg rs771270515 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0) 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 5 1 PASS rs771270515 . 5 202 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 130657221 130657221 G T 1 0 0 0 0 1 0 0 0 12383 1116 39 1 1 POTEJ 2 130657221 Missense_Mutation SNP G C3N-00580_T 76608 130657221 111536308 158 18293 ARHGEF4 0 . GRCh38 2 131041836 131041836 + Silent SNP C C A rs774222755 C3N-00580_T C3N-00580_N C C c.1359C>A p.= p.A453A ENST00000326016 10/14 221 149 72 182 182 0 strelka-varscan-mutect ARHGEF4,synonymous_variant,p.=,ENST00000409359,;ARHGEF4,synonymous_variant,p.=,ENST00000525839,NM_032995.2;ARHGEF4,synonymous_variant,p.=,ENST00000392953,;ARHGEF4,synonymous_variant,p.=,ENST00000326016,NM_015320.3;ARHGEF4,synonymous_variant,p.=,ENST00000611048,;ARHGEF4,synonymous_variant,p.=,ENST00000409303,;ARHGEF4,synonymous_variant,p.=,ENST00000355771,;ARHGEF4,synonymous_variant,p.=,ENST00000532720,;ARHGEF4,intron_variant,,ENST00000428230,;ARHGEF4,intron_variant,,ENST00000438985,;ARHGEF4,downstream_gene_variant,,ENST00000439368,;ARHGEF4,downstream_gene_variant,,ENST00000496764,;ARHGEF4,downstream_gene_variant,,ENST00000528247,;ARHGEF4,3_prime_UTR_variant,,ENST00000636987,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000490728,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000525092,;ARHGEF4,non_coding_transcript_exon_variant,,ENST00000527365,; A ENST00000326016 Transcript synonymous_variant 1878/3666 1359/2073 453/690 A gcC/gcA rs774222755 1 1 ARHGEF4 HGNC HGNC:684 protein_coding YES CCDS2165.1 ENSP00000316845 Q9NR80 UPI00001417F6 NM_015320.3 10/14 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF103,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 2 1 PASS rs774222755 . 0 207 0 3 0 0 0 0 -20 0.9999987 1 1 1 0 A 2 1 61 131041836 131041836 C A 1 0 0 0 0 0 0 0 1 1043 639 23 1 1 ARHGEF4 2 131041836 Silent SNP C C3N-00580_T 384615 131041836 111151693 159 18294 POTEE 0 . GRCh38 2 131218895 131218895 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.493G>T p.Asp165Tyr p.D165Y ENST00000356920 1/15 394 281 113 393 393 0 strelka-varscan-mutect POTEE,missense_variant,p.Asp165Tyr,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.Asp165Tyr,ENST00000626191,;POTEE,missense_variant,p.Asp165Tyr,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,missense_variant,p.Asp165Tyr,ENST00000358087,;POTEE,missense_variant,p.Asp165Tyr,ENST00000514256,; T ENST00000356920 Transcript missense_variant 829/4159 493/3228 165/1075 D/Y Gac/Tac 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 deleterious_low_confidence(0) 1/15 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 131218895 131218895 G T 1 0 0 0 0 1 0 0 0 12378 1290 45 2 2 POTEE 2 131218895 Missense_Mutation SNP G C3N-00580_T 177059 131218895 110974634 160 18295 POTEE 0 . GRCh38 2 131228279 131228279 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.953C>A p.Ala318Glu p.A318E ENST00000356920 5/15 414 315 99 402 401 1 strelka-varscan-mutect POTEE,missense_variant,p.Ala318Glu,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.Ala318Glu,ENST00000626191,;POTEE,missense_variant,p.Ala318Glu,ENST00000613282,;PLEKHB2,intron_variant,,ENST00000404460,;RNU6-127P,upstream_gene_variant,,ENST00000390897,;POTEE,missense_variant,p.Ala328Glu,ENST00000358087,;POTEE,missense_variant,p.Ala318Glu,ENST00000514256,; A ENST00000356920 Transcript missense_variant 1289/4159 953/3228 318/1075 A/E gCa/gAa 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 tolerated_low_confidence(0.06) 5/15 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 131228279 131228279 C A 1 0 0 0 0 1 0 0 0 12378 710 25 2 2 POTEE 2 131228279 Missense_Mutation SNP C C3N-00580_T 9384 131228279 110965250 161 18296 DARS 0 . GRCh38 2 135920489 135920489 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.923A>T p.Asp308Val p.D308V ENST00000264161 10/16 180 133 47 164 164 0 strelka-mutect DARS,missense_variant,p.Asp308Val,ENST00000264161,NM_001293312.1,NM_001349.3;DARS,missense_variant,p.Asp22Val,ENST00000422708,;DARS,downstream_gene_variant,,ENST00000456565,;DARS,downstream_gene_variant,,ENST00000441323,; A ENST00000264161 Transcript missense_variant 1139/2361 923/1506 308/501 D/V gAc/gTc 1 -1 DARS HGNC HGNC:2678 protein_coding YES CCDS2180.1 ENSP00000264161 P14868 A0A140VJW5 UPI000013639B NM_001293312.1,NM_001349.3 deleterious(0.04) 10/16 Gene3D:3.30.930.10,Pfam_domain:PF00152,PROSITE_profiles:PS50862,hmmpanther:PTHR22594,hmmpanther:PTHR22594:SF33,Superfamily_domains:SSF55681,TIGRFAM_domain:TIGR00458 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 135920489 135920489 T A 1 0 0 0 0 1 0 0 0 4041 1667 58 4 4 DARS 2 135920489 Missense_Mutation SNP T C3N-00580_T 4692210 135920489 106273040 162 18297 THSD7B 0 . GRCh38 2 137667810 137667810 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4694G>T p.Gly1565Val p.G1565V ENST00000272643 26/27 238 154 84 258 257 1 strelka-varscan-mutect THSD7B,missense_variant,p.Gly1563Val,ENST00000409968,NM_001316349.1;THSD7B,missense_variant,p.Gly1565Val,ENST00000272643,;THSD7B,missense_variant,p.Gly1534Val,ENST00000413152,NM_001080427.1; T ENST00000272643 Transcript missense_variant 4694/5939 4694/4827 1565/1608 G/V gGt/gTt 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A deleterious(0.04) 26/27 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs1171966414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 137667810 137667810 G T 1 0 0 0 0 1 0 0 0 16314 1261 44 2 2 THSD7B 2 137667810 Missense_Mutation SNP G C3N-00580_T 1747321 137667810 104525719 163 18298 LRP1B 0 . GRCh38 2 140487639 140487639 + Missense_Mutation SNP C C T rs778965587 C3N-00580_T C3N-00580_N C C c.9221G>A p.Cys3074Tyr p.C3074Y ENST00000389484 58/91 123 88 35 143 143 0 strelka-varscan-mutect LRP1B,missense_variant,p.Cys3074Tyr,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript missense_variant 10193/16535 9221/13800 3074/4599 C/Y tGt/tAt rs778965587 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(1) 58/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Pfam_domain:PF16472,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS rs778965587 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 140487639 140487639 C T 1 0 0 0 0 1 0 0 0 8850 478 17 3 3 LRP1B 2 140487639 Missense_Mutation SNP C C3N-00580_T 2819829 140487639 101705890 164 18299 TNFAIP6 0 . GRCh38 2 151370074 151370074 + Missense_Mutation SNP G G T rs140516340 C3N-00580_T C3N-00580_N G G c.449G>T p.Gly150Val p.G150V ENST00000243347 4/6 354 257 97 205 205 0 strelka-varscan-mutect TNFAIP6,missense_variant,p.Gly150Val,ENST00000243347,NM_007115.3;MIR4773-1,downstream_gene_variant,,ENST00000585225,;hsa-mir-4773-1,upstream_gene_variant,,ENST00000637203,;RN7SL124P,upstream_gene_variant,,ENST00000498656,;TNFAIP6,non_coding_transcript_exon_variant,,ENST00000460812,; T ENST00000243347 Transcript missense_variant 524/1424 449/834 150/277 G/V gGc/gTc rs140516340 1 1 TNFAIP6 HGNC HGNC:11898 protein_coding YES CCDS2193.1 ENSP00000243347 P98066 UPI0000071080 NM_007115.3 deleterious(0) 4/6 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR24038,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs140516340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 151370074 151370074 G T 1 0 0 0 0 1 0 0 0 16749 1203 42 2 2 TNFAIP6 2 151370074 Missense_Mutation SNP G C3N-00580_T 10882435 151370074 90823455 165 18300 NEB 0 . GRCh38 2 151619679 151619679 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.10644G>T p.Trp3548Cys p.W3548C ENST00000618972 73/183 315 233 82 191 191 0 strelka-varscan-mutect NEB,missense_variant,p.Trp3548Cys,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Trp3548Cys,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Trp3548Cys,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Trp3548Cys,ENST00000603639,;NEB,missense_variant,p.Trp3548Cys,ENST00000604864,;NEB,missense_variant,p.Trp3305Cys,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Trp3305Cys,ENST00000172853,;NEB,upstream_gene_variant,,ENST00000486320,; A ENST00000618972 Transcript missense_variant 10847/26307 10644/25683 3548/8560 W/C tgG/tgT 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 deleterious(0.01) 73/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,Pfam_domain:PF00880,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 151619679 151619679 C A 1 0 0 0 0 1 0 0 0 10326 508 18 2 2 NEB 2 151619679 Missense_Mutation SNP C C3N-00580_T 249605 151619679 90573850 166 18301 GALNT5 0 . GRCh38 2 157259164 157259164 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1082G>T p.Arg361Met p.R361M ENST00000259056 1/10 25 17 8 17 17 0 strelka-varscan-mutect GALNT5,missense_variant,p.Arg361Met,ENST00000259056,NM_014568.1; T ENST00000259056 Transcript missense_variant 1567/6171 1082/2823 361/940 R/M aGg/aTg 1 1 GALNT5 HGNC HGNC:4127 protein_coding YES CCDS2203.1 ENSP00000259056 Q7Z7M9 UPI000019AD19 NM_014568.1 deleterious(0.03) 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR11675:SF16,hmmpanther:PTHR11675 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 157259164 157259164 G T 1 0 0 0 0 1 0 0 0 6087 1000 35 2 2 GALNT5 2 157259164 Missense_Mutation SNP G C3N-00580_T 5639485 157259164 84934365 167 18302 KCNH7 0 . GRCh38 2 162536932 162536932 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.456T>A p.= p.T152T ENST00000332142 3/16 164 132 32 87 87 0 strelka-varscan-mutect KCNH7,synonymous_variant,p.=,ENST00000332142,NM_033272.3;KCNH7,synonymous_variant,p.=,ENST00000618399,;KCNH7,synonymous_variant,p.=,ENST00000328032,NM_173162.2;KCNH7,synonymous_variant,p.=,ENST00000621889,; T ENST00000332142 Transcript synonymous_variant 556/4113 456/3591 152/1196 T acT/acA 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 3/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 162536932 162536932 A T 1 0 0 0 0 0 0 0 1 7953 175 7 4 4 KCNH7 2 162536932 Silent SNP A C3N-00580_T 5277768 162536932 79656597 168 18303 SCN7A 0 . GRCh38 2 166472392 166472392 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.497G>A p.Arg166Lys p.R166K ENST00000409855 5/25 203 136 67 191 191 0 strelka-varscan-mutect SCN7A,missense_variant,p.Arg166Lys,ENST00000619410,;SCN7A,missense_variant,p.Arg166Lys,ENST00000621965,;SCN7A,missense_variant,p.Arg166Lys,ENST00000409855,NM_002976.3;SCN7A,missense_variant,p.Arg166Lys,ENST00000419992,;SCN7A,missense_variant,p.Arg166Lys,ENST00000441411,;SCN7A,missense_variant,p.Arg166Lys,ENST00000424326,; T ENST00000409855 Transcript missense_variant 624/7183 497/5049 166/1682 R/K aGa/aAa 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0.03) 5/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 166472392 166472392 C T 1 0 0 0 0 1 0 0 0 14192 913 32 3 3 SCN7A 2 166472392 Missense_Mutation SNP C C3N-00580_T 3935460 166472392 75721137 169 18304 XIRP2 0 . GRCh38 2 167246841 167246841 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5449G>T p.Val1817Phe p.V1817F ENST00000409195 9/11 268 246 22 226 226 0 strelka-varscan-mutect XIRP2,missense_variant,p.Val1817Phe,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Val1595Phe,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Val1642Phe,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; T ENST00000409195 Transcript missense_variant 5538/12675 5449/10650 1817/3549 V/F Gtt/Ttt 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 167246841 167246841 G T 1 0 0 0 0 1 0 0 0 17989 1029 36 2 2 XIRP2 2 167246841 Missense_Mutation SNP G C3N-00580_T 774449 167246841 74946688 170 18305 XIRP2 0 . GRCh38 2 167247543 167247543 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.6151C>A p.His2051Asn p.H2051N ENST00000409195 9/11 222 153 69 191 191 0 strelka-varscan-mutect XIRP2,missense_variant,p.His2051Asn,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.His1829Asn,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.His1876Asn,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 6240/12675 6151/10650 2051/3549 H/N Cat/Aat COSM242277 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious_low_confidence(0.04) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 167247543 167247543 C A 1 0 0 0 0 1 0 0 0 17989 594 21 2 2 XIRP2 2 167247543 Missense_Mutation SNP C C3N-00580_T 702 167247543 74945986 171 18306 NOSTRIN 0 . GRCh38 2 168834310 168834310 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.489G>C p.Glu163Asp p.E163D ENST00000444448 9/19 195 180 15 140 140 0 strelka-varscan-mutect NOSTRIN,missense_variant,p.Glu163Asp,ENST00000444448,;NOSTRIN,missense_variant,p.Glu163Asp,ENST00000458381,NM_001171631.1;NOSTRIN,missense_variant,p.Glu163Asp,ENST00000317647,NM_001039724.3;NOSTRIN,missense_variant,p.Glu85Asp,ENST00000445023,NM_052946.3;NOSTRIN,missense_variant,p.Glu85Asp,ENST00000397206,;NOSTRIN,missense_variant,p.Glu135Asp,ENST00000397209,NM_001171632.1;NOSTRIN,missense_variant,p.Glu85Asp,ENST00000447264,;SPC25,intron_variant,,ENST00000479309,;NOSTRIN,downstream_gene_variant,,ENST00000439509,; C ENST00000444448 Transcript missense_variant 965/2537 489/1692 163/563 E/D gaG/gaC 1 1 NOSTRIN HGNC HGNC:20203 protein_coding YES CCDS54415.1 ENSP00000394051 Q8IVI9 UPI00001400FD tolerated(0.18) 9/19 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51741,hmmpanther:PTHR14167,Superfamily_domains:SSF103657 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 168834310 168834310 G C 1 0 0 0 0 1 0 0 0 10591 933 33 4 4 NOSTRIN 2 168834310 Missense_Mutation SNP G C3N-00580_T 1586767 168834310 73359219 172 18307 LRP2 0 . GRCh38 2 169140491 169140491 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.13163A>T p.Asn4388Ile p.N4388I ENST00000263816 72/79 436 387 49 348 348 0 strelka-varscan-mutect LRP2,missense_variant,p.Asn4388Ile,ENST00000263816,NM_004525.2;LRP2,upstream_gene_variant,,ENST00000491228,; A ENST00000263816 Transcript missense_variant 13449/15808 13163/13968 4388/4655 N/I aAt/aTt 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 tolerated(0.31) 72/79 Gene3D:2gy5A03,PROSITE_profiles:PS50026,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 169140491 169140491 T A 1 0 0 0 0 1 0 0 0 8851 1493 52 4 4 LRP2 2 169140491 Missense_Mutation SNP T C3N-00580_T 306181 169140491 73053038 173 18308 LRP2 0 . GRCh38 2 169320839 169320839 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.125C>T p.Pro42Leu p.P42L ENST00000263816 2/79 893 572 321 683 682 1 strelka-varscan-mutect LRP2,missense_variant,p.Pro42Leu,ENST00000263816,NM_004525.2;LRP2,missense_variant,p.Pro42Leu,ENST00000443831,; A ENST00000263816 Transcript missense_variant 411/15808 125/13968 42/4655 P/L cCt/cTt COSM3315154 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 tolerated(0.1) 2/79 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,SMART_domains:SM00192,Superfamily_domains:SSF57424 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 169320839 169320839 G A 1 0 0 0 0 1 0 0 0 8851 1000 35 3 3 LRP2 2 169320839 Missense_Mutation SNP G C3N-00580_T 180348 169320839 72872690 174 18309 DLX2 0 . GRCh38 2 172102466 172102466 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.73C>A p.Gln25Lys p.Q25K ENST00000234198 1/3 156 105 51 214 214 0 strelka-varscan-mutect DLX2,missense_variant,p.Gln25Lys,ENST00000234198,NM_004405.3;DLX2,missense_variant,p.Gln25Lys,ENST00000466293,;DLX2-AS1,upstream_gene_variant,,ENST00000448117,; T ENST00000234198 Transcript missense_variant 435/2453 73/987 25/328 Q/K Cag/Aag 1 -1 DLX2 HGNC HGNC:2915 protein_coding YES CCDS2248.1 ENSP00000234198 Q07687 Q53QU7,X5D7D8 UPI00001294AC NM_004405.3 deleterious_low_confidence(0.01) 1/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 172102466 172102466 G T 1 0 0 0 0 1 0 0 0 4378 1357 47 2 2 DLX2 2 172102466 Missense_Mutation SNP G C3N-00580_T 2781627 172102466 70091063 175 18310 AC013461.1 0 . GRCh38 2 173191115 173191115 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.520G>A p.Ala174Thr p.A174T ENST00000375213 7/20 316 237 79 257 256 1 strelka-varscan-mutect AC013461.1,missense_variant,p.Ala174Thr,ENST00000338983,NM_133646.2;AC013461.1,missense_variant,p.Ala174Thr,ENST00000375213,NM_016653.2;AC013461.1,missense_variant,p.Ala174Thr,ENST00000409176,;AC013461.1,missense_variant,p.Ala174Thr,ENST00000539448,;AC013461.1,downstream_gene_variant,,ENST00000422149,;MLK7-AS1,intron_variant,,ENST00000419609,;MLK7-AS1,intron_variant,,ENST00000422703,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000480606,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000468408,;AC013461.1,non_coding_transcript_exon_variant,,ENST00000476618,; A ENST00000375213 Transcript missense_variant 598/3741 520/2403 174/800 A/T Gct/Act 1 1 AC013461.1 Clone_based_vega_gene protein_coding YES CCDS42777.1 ENSP00000364361 Q9NYL2 UPI0000073F69 NM_016653.2 deleterious(0) 7/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF424,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 173191115 173191115 G A 1 0 0 0 0 1 0 0 0 124 1203 42 3 3 AC013461.1 2 173191115 Missense_Mutation SNP G C3N-00580_T 1088649 173191115 69002414 176 18311 ATP5G3 0 . GRCh38 2 175180107 175180107 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.111G>A p.= p.R37R ENST00000284727 3/5 177 157 20 301 301 0 strelka-varscan-mutect ATP5G3,synonymous_variant,p.=,ENST00000284727,NM_001689.4;ATP5G3,synonymous_variant,p.=,ENST00000392541,NM_001002258.4;ATP5G3,synonymous_variant,p.=,ENST00000409194,;Y_RNA,upstream_gene_variant,,ENST00000363251,;ATP5G3,non_coding_transcript_exon_variant,,ENST00000497075,;ATP5G3,non_coding_transcript_exon_variant,,ENST00000472782,;AC096649.1,upstream_gene_variant,,ENST00000416186,; T ENST00000284727 Transcript synonymous_variant 3136/5484 111/429 37/142 R agG/agA 1 -1 ATP5G3 HGNC HGNC:843 protein_coding YES CCDS2263.1 ENSP00000284727 P48201 UPI0000000B4F NM_001689.4 3/5 hmmpanther:PTHR10031,hmmpanther:PTHR10031:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 175180107 175180107 C T 1 0 0 0 0 0 0 0 1 1308 854 30 3 3 ATP5G3 2 175180107 Silent SNP C C3N-00580_T 1988992 175180107 67013422 177 18312 HOXD9 0 . GRCh38 2 176124003 176124003 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.887A>T p.Gln296Leu p.Q296L ENST00000249499 2/2 309 225 84 336 336 0 strelka-varscan-mutect HOXD9,missense_variant,p.Gln296Leu,ENST00000249499,NM_014213.3;HOXD10,downstream_gene_variant,,ENST00000249501,NM_002148.3;HOXD-AS2,intron_variant,,ENST00000440016,;HOXD10,downstream_gene_variant,,ENST00000490088,;HOXD10,downstream_gene_variant,,ENST00000549469,; T ENST00000249499 Transcript missense_variant 936/1870 887/1059 296/352 Q/L cAg/cTg 1 1 HOXD9 HGNC HGNC:5140 protein_coding YES CCDS2267.2 ENSP00000249499 P28356 UPI000004A10E NM_014213.3 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF113,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 176124003 176124003 A T 1 0 0 0 0 1 0 0 0 7220 188 7 4 4 HOXD9 2 176124003 Missense_Mutation SNP A C3N-00580_T 943896 176124003 66069526 178 18313 TTN 0 . GRCh38 2 178552711 178552711 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.90189A>G p.= p.T30063T ENST00000589042 335/363 426 395 31 281 281 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; C ENST00000589042 Transcript synonymous_variant 90414/109224 90189/107976 30063/35991 T acA/acG 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 335/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW SNV 5 1 PASS rs758914867 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 178552711 178552711 T C 1 0 0 0 0 0 0 0 1 17245 1567 55 5 5 TTN 2 178552711 Silent SNP T C3N-00580_T 2428708 178552711 63640818 179 18314 TTN 0 . GRCh38 2 178688202 178688202 + Missense_Mutation SNP A A C C3N-00580_T C3N-00580_N A A c.32220T>G p.Ser10740Arg p.S10740R ENST00000589042 127/363 246 231 15 214 214 0 strelka-varscan-mutect TTN,missense_variant,p.Ser10740Arg,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser10423Arg,ENST00000591111,;TTN,missense_variant,p.Ser10423Arg,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser9496Arg,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; C ENST00000589042 Transcript missense_variant 32445/109224 32220/107976 10740/35991 S/R agT/agG COSM1269377 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 127/363 Low_complexity_(Seg):seg,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 178688202 178688202 A C 1 0 0 0 0 1 0 0 0 17245 40 2 5 5 TTN 2 178688202 Missense_Mutation SNP A C3N-00580_T 135491 178688202 63505327 180 18315 TTN 0 . GRCh38 2 178735764 178735764 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.14682A>G p.= p.L4894L ENST00000589042 50/363 365 255 110 251 249 2 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000582847,;TTN-AS1,non_coding_transcript_exon_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,upstream_gene_variant,,ENST00000627661,;TTN-AS1,upstream_gene_variant,,ENST00000590773,;TTN-AS1,upstream_gene_variant,,ENST00000631319,; C ENST00000589042 Transcript synonymous_variant 14907/109224 14682/107976 4894/35991 L ttA/ttG 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 50/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 178735764 178735764 T C 1 0 0 0 0 0 0 0 1 17245 1519 53 5 5 TTN 2 178735764 Silent SNP T C3N-00580_T 47562 178735764 63457765 181 18316 ZNF804A 0 . GRCh38 2 184938039 184938039 + Frame_Shift_Del DEL C C - novel C3N-00580_T C3N-00580_N C C c.2644delC p.His882ThrfsTer17 p.H882Tfs*17 ENST00000302277 4/4 379 341 38 299 299 0 sindel-varindel-pindel ZNF804A,frameshift_variant,p.His882ThrfsTer17,ENST00000302277,NM_194250.1;ZNF804A,frameshift_variant,p.His797ThrfsTer17,ENST00000613975,; - ENST00000302277 Transcript frameshift_variant 3237/4690 2643/3630 881/1209 F/X ttC/tt 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 184938039 184938039 C - 1 0 1 0 1 0 0 0 0 18755 854 30 0 0 ZNF804A 2 184938039 Frame_Shift_Del DEL C C3N-00580_T 6202275 184938039 57255490 182 18317 COL3A1 0 . GRCh38 2 188985707 188985707 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.376C>A p.Pro126Thr p.P126T ENST00000304636 4/51 314 216 98 226 226 0 strelka-varscan-mutect COL3A1,missense_variant,p.Pro126Thr,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Pro126Thr,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000470167,; A ENST00000304636 Transcript missense_variant 546/5543 376/4401 126/1466 P/T Cca/Aca 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 tolerated(0.12) 4/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 188985707 188985707 C A 1 0 0 0 0 1 0 0 0 3477 855 30 2 2 COL3A1 2 188985707 Missense_Mutation SNP C C3N-00580_T 4047668 188985707 53207822 183 18318 WDR75 0 . GRCh38 2 189459366 189459366 + Silent SNP G G T rs115249680 C3N-00580_T C3N-00580_N G G c.720G>T p.= p.T240T ENST00000314761 8/21 148 104 44 279 279 0 strelka-varscan-mutect WDR75,synonymous_variant,p.=,ENST00000314761,NM_032168.2,NM_001303096.1;WDR75,3_prime_UTR_variant,,ENST00000427960,;WDR75,3_prime_UTR_variant,,ENST00000436347,;WDR75,downstream_gene_variant,,ENST00000472286,;WDR75,upstream_gene_variant,,ENST00000498365,; T ENST00000314761 Transcript synonymous_variant 780/2701 720/2493 240/830 T acG/acT rs115249680 1 1 WDR75 HGNC HGNC:25725 protein_coding YES CCDS2298.1 ENSP00000314193 Q8IWA0 UPI000007452C NM_032168.2,NM_001303096.1 8/21 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF359,SMART_domains:SM00320,Superfamily_domains:SSF50998 LOW 1 SNV 1 1 PASS rs115249680 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 189459366 189459366 G T 1 0 0 0 0 0 0 0 1 17881 1132 40 1 1 WDR75 2 189459366 Silent SNP G C3N-00580_T 473659 189459366 52734163 184 18319 PLCL1 0 . GRCh38 2 198083820 198083820 + Silent SNP G G C rs757356633 C3N-00580_T C3N-00580_N G G c.303G>C p.= p.S101S ENST00000428675 2/6 119 56 63 93 93 0 strelka-varscan-mutect PLCL1,synonymous_variant,p.=,ENST00000437704,;PLCL1,synonymous_variant,p.=,ENST00000428675,NM_006226.3;PLCL1,synonymous_variant,p.=,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; C ENST00000428675 Transcript synonymous_variant 701/5125 303/3288 101/1095 S tcG/tcC rs757356633 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 2/6 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102 LOW 1 SNV 1 1 PASS rs757356633 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 198083820 198083820 G C 1 0 0 0 0 0 0 0 1 12133 1103 39 4 4 PLCL1 2 198083820 Silent SNP G C3N-00580_T 8624454 198083820 44109709 185 18320 AOX1 0 . GRCh38 2 200609087 200609087 + Silent SNP C C A C3N-00580_T C3N-00580_N C C c.1011C>A p.= p.L337L ENST00000374700 11/35 229 189 40 225 224 1 strelka-varscan-mutect AOX1,synonymous_variant,p.=,ENST00000374700,NM_001159.3;AOX1,upstream_gene_variant,,ENST00000485106,;AOX1,upstream_gene_variant,,ENST00000465297,;AOX1,upstream_gene_variant,,ENST00000485965,; A ENST00000374700 Transcript synonymous_variant 1252/5074 1011/4017 337/1338 L ctC/ctA COSM2906491 1 1 AOX1 HGNC HGNC:553 protein_coding YES CCDS33360.1 ENSP00000363832 Q06278 UPI0000071863 NM_001159.3 11/35 PROSITE_profiles:PS51387,hmmpanther:PTHR11908:SF86,hmmpanther:PTHR11908,Pfam_domain:PF00941,Gene3D:3.30.465.10,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02969,Superfamily_domains:SSF56176 1 LOW 1 SNV 1 1 1 PASS rs1355744253 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 200609087 200609087 C A 1 0 0 0 0 0 0 0 1 839 842 30 2 2 AOX1 2 200609087 Silent SNP C C3N-00580_T 2525267 200609087 41584442 186 18321 CFLAR 0 . GRCh38 2 201163857 201163857 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1327C>A p.His443Asn p.H443N ENST00000309955 10/10 146 85 61 113 113 0 strelka-varscan-mutect CFLAR,missense_variant,p.His443Asn,ENST00000309955,NM_003879.5;CFLAR,missense_variant,p.His443Asn,ENST00000423241,NM_001127183.2;CFLAR,missense_variant,p.His408Asn,ENST00000341582,NM_001202516.1;CFLAR,missense_variant,p.His347Asn,ENST00000443227,NM_001202517.1;CFLAR,downstream_gene_variant,,ENST00000457277,NM_001308042.1;CFLAR,downstream_gene_variant,,ENST00000479953,NM_001202519.1,NM_001202518.1;CFLAR,downstream_gene_variant,,ENST00000340870,;AC007283.5,upstream_gene_variant,,ENST00000434645,;CFLAR,non_coding_transcript_exon_variant,,ENST00000474842,;CFLAR,downstream_gene_variant,,ENST00000439154,;AC007283.4,upstream_gene_variant,,ENST00000424739,; A ENST00000309955 Transcript missense_variant 1842/14672 1327/1443 443/480 H/N Cac/Aac 1 1 CFLAR HGNC HGNC:1876 protein_coding YES CCDS2337.1 ENSP00000312455 O15519 A0A024R3Z7 UPI0000030475 NM_003879.5 deleterious(0) 10/10 Gene3D:3.40.50.1460,Pfam_domain:PF00656,hmmpanther:PTHR10454,hmmpanther:PTHR10454:SF8,SMART_domains:SM00115,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999992 1 1 1 0 A 3 1 61 201163857 201163857 C A 1 0 0 0 0 1 0 0 0 3050 826 29 2 2 CFLAR 2 201163857 Missense_Mutation SNP C C3N-00580_T 554770 201163857 41029672 187 18322 CDK15 0 . GRCh38 2 201835749 201835749 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.837T>A p.= p.S279S ENST00000450471 8/14 163 108 55 151 151 0 strelka-varscan-mutect CDK15,synonymous_variant,p.=,ENST00000450471,NM_001261435.1;CDK15,synonymous_variant,p.=,ENST00000434439,NM_001261436.1;CDK15,synonymous_variant,p.=,ENST00000410091,;CDK15,synonymous_variant,p.=,ENST00000260967,NM_139158.2;CDK15,non_coding_transcript_exon_variant,,ENST00000488419,;CDK15,3_prime_UTR_variant,,ENST00000451080,; A ENST00000450471 Transcript synonymous_variant 923/3659 837/1290 279/429 S tcT/tcA 1 1 CDK15 HGNC HGNC:14434 protein_coding YES CCDS58747.1 ENSP00000406472 Q96Q40 UPI0001D3BDAF NM_001261435.1 8/14 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 201835749 201835749 T A 1 0 0 0 0 0 0 0 1 2835 1567 55 4 4 CDK15 2 201835749 Silent SNP T C3N-00580_T 671892 201835749 40357780 188 18323 ZDBF2 0 . GRCh38 2 206308396 206308396 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3868C>A p.His1290Asn p.H1290N ENST00000374423 5/5 128 102 26 165 165 0 strelka-varscan-mutect ZDBF2,missense_variant,p.His1290Asn,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.His1288Asn,ENST00000611847,NM_001285549.1; A ENST00000374423 Transcript missense_variant 4254/10286 3868/7065 1290/2354 H/N Cat/Aat 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.77) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 206308396 206308396 C A 1 0 0 0 0 1 0 0 0 18174 826 29 2 2 ZDBF2 2 206308396 Missense_Mutation SNP C C3N-00580_T 4472647 206308396 35885133 189 18324 ZDBF2 0 . GRCh38 2 206308929 206308929 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.4401C>A p.Asp1467Glu p.D1467E ENST00000374423 5/5 138 124 14 148 148 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Asp1467Glu,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Asp1465Glu,ENST00000611847,NM_001285549.1; A ENST00000374423 Transcript missense_variant 4787/10286 4401/7065 1467/2354 D/E gaC/gaA 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.05) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.76804 0.9999858 1 1 1 0 A 3 1 61 206308929 206308929 C A 1 0 0 0 0 1 0 0 0 18174 506 18 2 2 ZDBF2 2 206308929 Missense_Mutation SNP C C3N-00580_T 533 206308929 35884600 190 18325 ADAM23 0 . GRCh38 2 206594822 206594822 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.2164G>C p.Asp722His p.D722H ENST00000264377 23/26 315 262 53 287 287 0 strelka-varscan-mutect ADAM23,missense_variant,p.Asp722His,ENST00000264377,NM_003812.3;ADAM23,missense_variant,p.Asp722His,ENST00000374415,;ADAM23,upstream_gene_variant,,ENST00000444281,; C ENST00000264377 Transcript missense_variant 2492/6330 2164/2499 722/832 D/H Gat/Cat 1 1 ADAM23 HGNC HGNC:202 protein_coding YES CCDS2369.1 ENSP00000264377 O75077 A0A024R3W8 UPI0000044543 NM_003812.3 deleterious(0) 23/26 hmmpanther:PTHR11905:SF13,hmmpanther:PTHR11905,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 206594822 206594822 G C 1 0 0 0 0 1 0 0 0 289 942 33 4 4 ADAM23 2 206594822 Missense_Mutation SNP G C3N-00580_T 285893 206594822 35598707 191 18326 DYTN 0 . GRCh38 2 206707365 206707365 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.233C>A p.Pro78Gln p.P78Q ENST00000452335 3/12 445 247 198 452 452 0 strelka-varscan-mutect DYTN,missense_variant,p.Pro78Gln,ENST00000452335,NM_001093730.1;DYTN,upstream_gene_variant,,ENST00000477734,; T ENST00000452335 Transcript missense_variant 350/2051 233/1737 78/578 P/Q cCa/cAa 1 -1 DYTN HGNC HGNC:23279 protein_coding YES CCDS46502.1 ENSP00000396593 A2CJ06 UPI0000EE0AB9 NM_001093730.1 deleterious(0) 3/12 hmmpanther:PTHR11915:SF282,hmmpanther:PTHR11915,Pfam_domain:PF09068,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 206707365 206707365 G T 1 0 0 0 0 1 0 0 0 4684 1348 47 2 2 DYTN 2 206707365 Missense_Mutation SNP G C3N-00580_T 112543 206707365 35486164 192 18327 PIKFYVE 0 . GRCh38 2 208340097 208340098 + Frame_Shift_Ins INS - - CA novel C3N-00580_T C3N-00580_N - - c.4898_4899dupCA p.Gly1634GlnfsTer19 p.G1634Qfs*19 ENST00000264380 31/42 386 361 25 335 335 0 varindel-pindel PIKFYVE,frameshift_variant,p.Gly1634GlnfsTer19,ENST00000264380,NM_015040.3;PIKFYVE,downstream_gene_variant,,ENST00000452564,;PIKFYVE,downstream_gene_variant,,ENST00000474721,; CA ENST00000264380 Transcript frameshift_variant 5055-5056/9901 4897-4898/6297 1633/2098 P/PX cca/cCAca 1 1 PIKFYVE HGNC HGNC:23785 protein_coding YES CCDS2382.1 ENSP00000264380 Q9Y2I7 UPI0000366FD6 NM_015040.3 31/42 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF57 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 CA 7 5 61 208340097 208340097 - CA 1 0 1 1 0 0 0 0 0 12019 855 30 0 0 PIKFYVE 2 208340097 Frame_Shift_Ins INS - C3N-00580_T 1632732 208340097 33853432 193 18328 MAP2 0 . GRCh38 2 209694634 209694634 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.2464G>C p.Val822Leu p.V822L ENST00000360351 7/15 194 158 36 186 186 0 strelka-varscan-mutect MAP2,missense_variant,p.Val822Leu,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Val818Leu,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; C ENST00000360351 Transcript missense_variant 2970/9711 2464/5484 822/1827 V/L Gtg/Ctg 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious(0.01) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 209694634 209694634 G C 1 0 0 0 0 1 0 0 0 9157 1377 48 4 4 MAP2 2 209694634 Missense_Mutation SNP G C3N-00580_T 1354537 209694634 32498895 194 18329 CPS1 0 . GRCh38 2 210590189 210590189 + Silent SNP G G A C3N-00580_T C3N-00580_N G G c.813G>A p.= p.P271P ENST00000430249 9/39 338 294 44 286 286 0 strelka-varscan-mutect CPS1,synonymous_variant,p.=,ENST00000233072,NM_001875.4;CPS1,synonymous_variant,p.=,ENST00000430249,NM_001122633.2;CPS1,synonymous_variant,p.=,ENST00000619804,;CPS1,upstream_gene_variant,,ENST00000451903,NM_001122634.3; A ENST00000430249 Transcript synonymous_variant 868/5698 813/4521 271/1506 P ccG/ccA COSM5632378,COSM5632379 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 9/39 HAMAP:MF_01209,PROSITE_profiles:PS51273,hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,Pfam_domain:PF00117,Gene3D:3.40.50.880,TIGRFAM_domain:TIGR01368,Superfamily_domains:SSF52317,Prints_domain:PR00099 1,1 LOW 1 SNV 1 1,1 1 PASS rs1174421173 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 210590189 210590189 G A 1 0 0 0 0 0 0 0 1 3619 1103 39 1 1 CPS1 2 210590189 Silent SNP G C3N-00580_T 895555 210590189 31603340 195 18330 CPS1 0 . GRCh38 2 210654058 210654058 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.3532G>T p.Gly1178Trp p.G1178W ENST00000430249 30/39 555 313 242 571 571 0 strelka-varscan-mutect CPS1,missense_variant,p.Gly1172Trp,ENST00000233072,NM_001875.4;CPS1,missense_variant,p.Gly1178Trp,ENST00000430249,NM_001122633.2;CPS1,missense_variant,p.Gly721Trp,ENST00000451903,NM_001122634.3;CPS1,upstream_gene_variant,,ENST00000470791,; T ENST00000430249 Transcript missense_variant 3587/5698 3532/4521 1178/1506 G/W Ggg/Tgg 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 deleterious(0) 30/39 PROSITE_profiles:PS50975,hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,TIGRFAM_domain:TIGR01369,Pfam_domain:PF02786,Gene3D:3.30.470.20,Superfamily_domains:SSF56059 MODERATE 1 SNV 1 1 PASS rs1489457084 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 210654058 210654058 G T 1 0 0 0 0 1 0 0 0 3619 1000 35 2 2 CPS1 2 210654058 Missense_Mutation SNP G C3N-00580_T 63869 210654058 31539471 196 18331 ATIC 0 . GRCh38 2 215349106 215349106 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.1516A>G p.Ile506Val p.I506V ENST00000236959 15/16 231 142 89 225 225 0 strelka-varscan-mutect ATIC,missense_variant,p.Ile505Val,ENST00000435675,;ATIC,missense_variant,p.Ile506Val,ENST00000236959,NM_004044.6;ATIC,missense_variant,p.Ile175Val,ENST00000426233,;ATIC,non_coding_transcript_exon_variant,,ENST00000442048,;ATIC,downstream_gene_variant,,ENST00000446622,;ATIC,3_prime_UTR_variant,,ENST00000443953,;ATIC,non_coding_transcript_exon_variant,,ENST00000479093,;ATIC,non_coding_transcript_exon_variant,,ENST00000478734,;ATIC,downstream_gene_variant,,ENST00000459796,;ATIC,downstream_gene_variant,,ENST00000467388,; G ENST00000236959 Transcript missense_variant 1842/2213 1516/1779 506/592 I/V Ata/Gta 1 1 ATIC HGNC HGNC:794 protein_coding YES CCDS2398.1 ENSP00000236959 P31939 V9HWH7 UPI000000122D NM_004044.6 tolerated(0.46) 15/16 HAMAP:MF_00139,hmmpanther:PTHR11692:SF0,hmmpanther:PTHR11692,Gene3D:1g8mA01,PIRSF_domain:PIRSF000414,TIGRFAM_domain:TIGR00355,Superfamily_domains:SSF53927 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 215349106 215349106 A G 1 0 0 0 0 1 0 0 0 1257 333 12 5 5 ATIC 2 215349106 Missense_Mutation SNP A C3N-00580_T 4695048 215349106 26844423 197 18332 PTPRN 0 . GRCh38 2 219300238 219300238 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1183G>T p.Gly395Cys p.G395C ENST00000295718 9/23 53 34 19 56 56 0 strelka-varscan-mutect PTPRN,missense_variant,p.Gly395Cys,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Gly395Cys,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Gly305Cys,ENST00000423636,NM_001199764.1;PTPRN,upstream_gene_variant,,ENST00000443981,;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,upstream_gene_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,; A ENST00000295718 Transcript missense_variant 1424/3784 1183/2940 395/979 G/C Ggc/Tgc 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 tolerated(0.09) 9/23 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 219300238 219300238 C A 1 0 0 0 0 1 0 0 0 12961 623 22 2 2 PTPRN 2 219300238 Missense_Mutation SNP C C3N-00580_T 3951132 219300238 22893291 198 18333 SPEG 0 . GRCh38 2 219449172 219449172 + Nonsense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.2014A>T p.Arg672Ter p.R672* ENST00000312358 4/41 32 23 9 40 40 0 strelka-varscan-mutect SPEG,stop_gained,p.Arg672Ter,ENST00000312358,NM_005876.4;SPEG,stop_gained,p.Arg568Ter,ENST00000396698,;SPEG,downstream_gene_variant,,ENST00000431523,;SPEG,downstream_gene_variant,,ENST00000435853,;SPEG,downstream_gene_variant,,ENST00000451076,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,upstream_gene_variant,,ENST00000462545,;SPEG,downstream_gene_variant,,ENST00000491248,;SPEG,upstream_gene_variant,,ENST00000463218,;SPEG,downstream_gene_variant,,ENST00000497065,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,intron_variant,,ENST00000409595,;SPEG,downstream_gene_variant,,ENST00000452101,;SPEG,downstream_gene_variant,,ENST00000420132,;SPEG,downstream_gene_variant,,ENST00000403148,; T ENST00000312358 Transcript stop_gained 2146/10782 2014/9804 672/3267 R/* Aga/Tga 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 4/41 HIGH 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 4 4 61 219449172 219449172 A T 1 0 0 0 0 0 1 0 0 15387 180 7 4 4 SPEG 2 219449172 Nonsense_Mutation SNP A C3N-00580_T 148934 219449172 22744357 199 18334 DNER 0 . GRCh38 2 229388389 229388389 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1731G>T p.Glu577Asp p.E577D ENST00000341772 11/13 103 62 41 142 142 0 strelka-varscan-mutect DNER,missense_variant,p.Glu577Asp,ENST00000341772,NM_139072.3; A ENST00000341772 Transcript missense_variant 1866/3260 1731/2214 577/737 E/D gaG/gaT 1 -1 DNER HGNC HGNC:24456 protein_coding YES CCDS33390.1 ENSP00000345229 Q8NFT8 UPI0000048EB8 NM_139072.3 tolerated(0.29) 11/13 PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF275,hmmpanther:PTHR24044,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 229388389 229388389 C A 1 0 0 0 0 1 0 0 0 4480 564 20 2 2 DNER 2 229388389 Missense_Mutation SNP C C3N-00580_T 9939217 229388389 12805140 200 18335 GPR55 0 . GRCh38 2 230910485 230910485 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.478C>A p.His160Asn p.H160N ENST00000392040 2/2 317 268 49 275 275 0 strelka-varscan-mutect GPR55,missense_variant,p.His160Asn,ENST00000392040,NM_005683.3;GPR55,missense_variant,p.His160Asn,ENST00000622008,;GPR55,missense_variant,p.His160Asn,ENST00000392039,;GPR55,missense_variant,p.His160Asn,ENST00000438398,;AC012507.4,downstream_gene_variant,,ENST00000454890,;GPR55,missense_variant,p.His160Asn,ENST00000444078,; T ENST00000392040 Transcript missense_variant 671/3828 478/960 160/319 H/N Cat/Aat 1 -1 GPR55 HGNC HGNC:4511 protein_coding YES CCDS2480.1 ENSP00000375894 Q9Y2T6 A8K858 UPI000006D64F NM_005683.3 deleterious(0.01) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF56,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 230910485 230910485 G T 1 0 0 0 0 1 0 0 0 6584 1348 47 2 2 GPR55 2 230910485 Missense_Mutation SNP G C3N-00580_T 1522096 230910485 11283044 201 18336 USP40 0 . GRCh38 2 233529513 233529513 + Splice_Site SNP C C T novel C3N-00580_T C3N-00580_N C C c.1505-1G>A p.X502_splice ENST00000450966 132 68 64 161 161 0 strelka-varscan-mutect USP40,splice_acceptor_variant,,ENST00000251722,;USP40,splice_acceptor_variant,,ENST00000450966,NM_018218.2;USP40,splice_acceptor_variant,,ENST00000427112,;USP40,splice_acceptor_variant,,ENST00000485943,; T ENST00000450966 Transcript splice_acceptor_variant -/5616 1505/3744 502/1247 1 -1 USP40 HGNC HGNC:20069 protein_coding YES CCDS46547.1 ENSP00000415434 Q9NVE5 UPI0000232F06 NM_018218.2 10/30 HIGH 1 SNV 1 1 PASS . . 0 204 2 4 0 0 0 0 -20 0.99997 1 1 1 0 T 5 4 61 233529513 233529513 C T 1 0 0 0 0 0 0 1 0 17614 811 28 3 3 USP40 2 233529513 Splice_Site SNP C C3N-00580_T 2619028 233529513 8664016 202 18337 UGT1A9 0 . GRCh38 2 233672639 233672639 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.705C>A p.= p.L235L ENST00000354728 1/5 461 380 81 354 353 1 strelka-varscan-mutect UGT1A9,synonymous_variant,p.=,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A10,intron_variant,,ENST00000373445,; A ENST00000354728 Transcript synonymous_variant 787/2416 705/1593 235/530 L ctC/ctA 1 1 UGT1A9 HGNC HGNC:12541 protein_coding YES CCDS2505.1 ENSP00000346768 O60656 Q5DSZ5 UPI0000044213 NM_021027.2 1/5 hmmpanther:PTHR11926:SF173,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 233672639 233672639 C A 1 0 0 0 0 0 0 0 1 17477 842 30 2 2 UGT1A9 2 233672639 Silent SNP C C3N-00580_T 143126 233672639 8520890 203 18338 COL6A3 0 . GRCh38 2 237372317 237372317 + Missense_Mutation SNP C C T rs747082651 C3N-00580_T C3N-00580_N C C c.3700G>A p.Val1234Met p.V1234M ENST00000295550 9/44 468 398 70 457 457 0 strelka-varscan-mutect COL6A3,missense_variant,p.Val1234Met,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Val1028Met,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Val1028Met,ENST00000409809,;COL6A3,missense_variant,p.Val627Met,ENST00000472056,NM_057166.4;COL6A3,missense_variant,p.Val627Met,ENST00000347401,;COL6A3,missense_variant,p.Val1028Met,ENST00000392004,NM_057165.4;COL6A3,missense_variant,p.Val827Met,ENST00000392003,NM_057164.4;COL6A3,downstream_gene_variant,,ENST00000433762,; T ENST00000295550 Transcript missense_variant 4153/10749 3700/9534 1234/3177 V/M Gtg/Atg rs747082651,COSM5461615,COSM5461616 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 deleterious(0) 9/44 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747082651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237372317 237372317 C T 1 0 0 0 0 1 0 0 0 3490 536 19 1 1 COL6A3 2 237372317 Missense_Mutation SNP C C3N-00580_T 3699678 237372317 4821212 204 18339 COL6A3 0 . GRCh38 2 237387642 237387642 + Missense_Mutation SNP A A T C3N-00580_T C3N-00580_N A A c.1252T>A p.Tyr418Asn p.Y418N ENST00000295550 4/44 471 266 205 424 424 0 strelka-varscan-mutect COL6A3,missense_variant,p.Tyr418Asn,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Tyr212Asn,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Tyr212Asn,ENST00000409809,;COL6A3,missense_variant,p.Tyr212Asn,ENST00000392004,NM_057165.4;COL6A3,missense_variant,p.Tyr418Asn,ENST00000433762,;COL6A3,missense_variant,p.Tyr146Asn,ENST00000491233,;COL6A3,intron_variant,,ENST00000472056,NM_057166.4;COL6A3,intron_variant,,ENST00000347401,;COL6A3,intron_variant,,ENST00000392003,NM_057164.4; T ENST00000295550 Transcript missense_variant 1705/10749 1252/9534 418/3177 Y/N Tac/Aac COSM4648549,COSM4648550 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 tolerated(0.31) 4/44 PROSITE_profiles:PS50234,Superfamily_domains:SSF53300 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1321462371 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 237387642 237387642 A T 1 0 0 0 0 1 0 0 0 3490 391 14 4 4 COL6A3 2 237387642 Missense_Mutation SNP A C3N-00580_T 15325 237387642 4805887 205 18340 ANKMY1 0 . GRCh38 2 240523973 240523973 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.1744C>T p.His582Tyr p.H582Y ENST00000401804 8/18 414 240 174 466 465 1 strelka-varscan-mutect ANKMY1,missense_variant,p.His263Tyr,ENST00000405002,;ANKMY1,missense_variant,p.His582Tyr,ENST00000401804,NM_001282771.1;ANKMY1,missense_variant,p.His493Tyr,ENST00000272972,NM_016552.3;ANKMY1,missense_variant,p.His431Tyr,ENST00000403283,NM_001308375.1;ANKMY1,missense_variant,p.His352Tyr,ENST00000361678,NM_017844.3;ANKMY1,missense_variant,p.His352Tyr,ENST00000373318,NM_001282780.1;ANKMY1,missense_variant,p.His254Tyr,ENST00000406958,NM_001282781.1;ANKMY1,missense_variant,p.His352Tyr,ENST00000405523,;ANKMY1,3_prime_UTR_variant,,ENST00000391987,;ANKMY1,upstream_gene_variant,,ENST00000391988,;ANKMY1,downstream_gene_variant,,ENST00000443318,;ANKMY1,downstream_gene_variant,,ENST00000441168,;ANKMY1,downstream_gene_variant,,ENST00000462004,;ANKMY1,non_coding_transcript_exon_variant,,ENST00000480230,;ANKMY1,non_coding_transcript_exon_variant,,ENST00000459901,;ANKMY1,non_coding_transcript_exon_variant,,ENST00000484526,;ANKMY1,non_coding_transcript_exon_variant,,ENST00000496300,; A ENST00000401804 Transcript missense_variant 1883/3232 1744/3093 582/1030 H/Y Cac/Tac 1 -1 ANKMY1 HGNC HGNC:20987 protein_coding YES CCDS63185.1 ENSP00000385887 J3KQ21 UPI0000209839 NM_001282771.1 tolerated(0.75) 8/18 hmmpanther:PTHR15897 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 240523973 240523973 G A 1 0 0 0 0 1 0 0 0 735 1348 47 3 3 ANKMY1 2 240523973 Missense_Mutation SNP G C3N-00580_T 3136331 240523973 1669556 206 18341 KIF1A 0 . GRCh38 2 240758373 240758373 + Missense_Mutation SNP G G A rs372544960 C3N-00580_T C3N-00580_N G G c.2569C>T p.Arg857Trp p.R857W ENST00000498729 26/49 69 62 7 97 97 0 strelka-mutect KIF1A,missense_variant,p.Arg857Trp,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Arg848Trp,ENST00000320389,NM_004321.6;KIF1A,missense_variant,p.Arg857Trp,ENST00000404283,; A ENST00000498729 Transcript missense_variant 2816/9223 2569/5376 857/1791 R/W Cgg/Tgg rs372544960,COSM2909861,COSM4311613 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 deleterious(0) 26/49 Pfam_domain:PF12423,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs372544960 . 0 203 6 0 0 0 0 0 -15.593 0.9999998 1 1 1 0 A 3 1 61 240758373 240758373 G A 1 0 0 0 0 1 0 0 0 8147 1115 39 1 1 KIF1A 2 240758373 Missense_Mutation SNP G C3N-00580_T 234400 240758373 1435156 207 18342 ATG4B 0 . GRCh38 2 241653521 241653521 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.194G>T p.Gly65Val p.G65V ENST00000404914 4/13 175 145 30 257 257 0 strelka-varscan-mutect ATG4B,missense_variant,p.Gly65Val,ENST00000405546,NM_178326.2;ATG4B,missense_variant,p.Gly65Val,ENST00000404914,NM_013325.4;ATG4B,missense_variant,p.Gly65Val,ENST00000425239,;ATG4B,missense_variant,p.Gly65Val,ENST00000400771,;ATG4B,5_prime_UTR_variant,,ENST00000402096,;ATG4B,5_prime_UTR_variant,,ENST00000430617,;ATG4B,5_prime_UTR_variant,,ENST00000419606,;ATG4B,5_prime_UTR_variant,,ENST00000429899,;ATG4B,downstream_gene_variant,,ENST00000625810,;ATG4B,downstream_gene_variant,,ENST00000491867,;ATG4B,3_prime_UTR_variant,,ENST00000344376,;ATG4B,3_prime_UTR_variant,,ENST00000400772,;ATG4B,3_prime_UTR_variant,,ENST00000415107,;ATG4B,non_coding_transcript_exon_variant,,ENST00000482507,;ATG4B,non_coding_transcript_exon_variant,,ENST00000494465,;ATG4B,non_coding_transcript_exon_variant,,ENST00000483778,;ATG4B,non_coding_transcript_exon_variant,,ENST00000493618,;ATG4B,non_coding_transcript_exon_variant,,ENST00000475195,;ATG4B,non_coding_transcript_exon_variant,,ENST00000468018,;ATG4B,non_coding_transcript_exon_variant,,ENST00000465399,;ATG4B,non_coding_transcript_exon_variant,,ENST00000479554,; T ENST00000404914 Transcript missense_variant 297/2878 194/1182 65/393 G/V gGc/gTc 1 1 ATG4B HGNC HGNC:20790 protein_coding YES CCDS46564.1 ENSP00000384259 Q9Y4P1 UPI00001AF16F NM_013325.4 deleterious(0) 4/13 Pfam_domain:PF03416,hmmpanther:PTHR22624,hmmpanther:PTHR22624:SF39,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 241653521 241653521 G T 1 0 0 0 0 1 0 0 0 1249 1203 42 2 2 ATG4B 2 241653521 Missense_Mutation SNP G C3N-00580_T 895148 241653521 540008 208 18343 RTP5 0 . GRCh38 2 241871981 241871981 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.426C>A p.= p.G142G ENST00000343216 2/2 97 57 40 144 144 0 strelka-varscan-mutect RTP5,synonymous_variant,p.=,ENST00000343216,NM_173821.2;RTP5,3_prime_UTR_variant,,ENST00000419912,; A ENST00000343216 Transcript synonymous_variant 454/2296 426/1719 142/572 G ggC/ggA 1 1 RTP5 HGNC HGNC:26585 protein_coding YES CCDS42843.1 ENSP00000345374 Q14D33 UPI000014050F NM_173821.2 2/2 Pfam_domain:PF13695,hmmpanther:PTHR14402,hmmpanther:PTHR14402:SF2,SMART_domains:SM01328 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 241871981 241871981 C A 1 0 0 0 0 0 0 0 1 13997 784 28 2 2 RTP5 2 241871981 Silent SNP C C3N-00580_T 218460 241871981 321548 209 18344 CPNE9 0 . GRCh38 3 9705475 9705475 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.272A>C p.Asp91Ala p.D91A ENST00000383832 5/21 103 56 47 137 137 0 strelka-varscan-mutect CPNE9,missense_variant,p.Asp91Ala,ENST00000383832,NM_153635.2;CPNE9,missense_variant,p.Asp91Ala,ENST00000383831,NM_001308388.1;CPNE9,missense_variant,p.Asp91Ala,ENST00000613455,;MTMR14,downstream_gene_variant,,ENST00000296003,NM_001077525.2;MTMR14,downstream_gene_variant,,ENST00000353332,NM_001077526.2;MTMR14,downstream_gene_variant,,ENST00000351233,NM_022485.4;MTMR14,downstream_gene_variant,,ENST00000420925,;MTMR14,downstream_gene_variant,,ENST00000606184,;MTMR14,downstream_gene_variant,,ENST00000414996,;MTMR14,downstream_gene_variant,,ENST00000447144,;CPNE9,downstream_gene_variant,,ENST00000491802,; C ENST00000383832 Transcript missense_variant 462/2068 272/1662 91/553 D/A gAc/gCc 1 1 CPNE9 HGNC HGNC:24336 protein_coding YES CCDS2574.2 ENSP00000373343 Q8IYJ1 UPI0000412048 NM_153635.2 deleterious(0) 5/21 PROSITE_profiles:PS50004,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF10,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 9705475 9705475 A C 1 0 0 0 0 1 0 0 0 3614 275 10 5 5 CPNE9 3 9705475 Missense_Mutation SNP A C3N-00580_T 9705475 188590084 210 18345 TIMP4 0 . GRCh38 3 12158821 12158821 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.20C>A p.Pro7His p.P7H ENST00000287814 1/5 76 49 27 109 109 0 strelka-varscan-mutect TIMP4,missense_variant,p.Pro7His,ENST00000287814,NM_003256.3;SYN2,intron_variant,,ENST00000620175,NM_003178.5;SYN2,intron_variant,,ENST00000621198,NM_133625.4;SYN2,non_coding_transcript_exon_variant,,ENST00000447752,;SYN2,intron_variant,,ENST00000439861,;SYN2,upstream_gene_variant,,ENST00000425297,; T ENST00000287814 Transcript missense_variant 531/1650 20/675 7/224 P/H cCc/cAc 1 -1 TIMP4 HGNC HGNC:11823 protein_coding YES CCDS2608.1 ENSP00000287814 Q99727 UPI0000136FA3 NM_003256.3 deleterious(0.04) 1/5 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11844 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 3 4 61 12158821 12158821 G T 1 0 0 0 0 1 0 0 0 16361 1232 43 2 2 TIMP4 3 12158821 Missense_Mutation SNP G C3N-00580_T 2453346 12158821 186136738 211 18346 PPARG 0 . GRCh38 3 12392744 12392744 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.611C>A p.Ser204Tyr p.S204Y ENST00000287820 4/7 386 348 38 377 377 0 strelka-varscan-mutect PPARG,missense_variant,p.Ser182Tyr,ENST00000397026,;PPARG,missense_variant,p.Ser176Tyr,ENST00000397010,;PPARG,missense_variant,p.Ser176Tyr,ENST00000397012,NM_138711.3;PPARG,missense_variant,p.Ser176Tyr,ENST00000309576,NM_138712.3;PPARG,missense_variant,p.Ser204Tyr,ENST00000287820,NM_015869.4;PPARG,missense_variant,p.Ser176Tyr,ENST00000397015,NM_005037.5;PPARG,missense_variant,p.Ser176Tyr,ENST00000397000,;PPARG,missense_variant,p.Ser176Tyr,ENST00000396999,;PPARG,3_prime_UTR_variant,,ENST00000397023,;PPARG,non_coding_transcript_exon_variant,,ENST00000477039,;PPARG,non_coding_transcript_exon_variant,,ENST00000497594,; A ENST00000287820 Transcript missense_variant 732/1850 611/1518 204/505 S/Y tCt/tAt 1 1 PPARG HGNC HGNC:9236 protein_coding YES CCDS2609.1 ENSP00000287820 P37231 UPI0000055911 NM_015869.4 deleterious(0) 4/7 PROSITE_profiles:PS51030,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF14,Pfam_domain:PF00105,Gene3D:1.10.565.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00398 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 12392744 12392744 C A 1 0 0 0 0 1 0 0 0 12408 913 32 2 2 PPARG 3 12392744 Missense_Mutation SNP C C3N-00580_T 233923 12392744 185902815 212 18347 RBMS3 0 . GRCh38 3 29762910 29762910 + Missense_Mutation SNP A A T rs779082369 C3N-00580_T C3N-00580_N A A c.558A>T p.Arg186Ser p.R186S ENST00000383767 6/15 106 91 15 208 207 1 strelka-varscan-mutect RBMS3,missense_variant,p.Arg185Ser,ENST00000434693,;RBMS3,missense_variant,p.Arg185Ser,ENST00000383766,NM_001003792.2;RBMS3,missense_variant,p.Arg186Ser,ENST00000383767,NM_001003793.2;RBMS3,missense_variant,p.Arg252Ser,ENST00000636680,;RBMS3,missense_variant,p.Arg186Ser,ENST00000273139,NM_014483.3;RBMS3,missense_variant,p.Arg186Ser,ENST00000452462,NM_001177711.1;RBMS3,missense_variant,p.Arg186Ser,ENST00000456853,NM_001177712.1;RBMS3,missense_variant,p.Arg186Ser,ENST00000445033,;RBMS3,upstream_gene_variant,,ENST00000497319,;RP11-9J18.1,splice_region_variant,,ENST00000635992,;RBMS3,splice_region_variant,,ENST00000637842,; T ENST00000383767 Transcript missense_variant,splice_region_variant 894/1864 558/1314 186/437 R/S agA/agT rs779082369 1 1 RBMS3 HGNC HGNC:13427 protein_coding YES CCDS33724.1 ENSP00000373277 Q6XE24 UPI000023FE75 NM_001003793.2 deleterious(0.03) 6/15 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF473,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs779082369 . 0 194 0 10 5 0 0 0 -8.478474 0.2421289 1 1 0 0 T 3 4 61 29762910 29762910 A T 1 0 0 0 0 1 0 0 0 13316 260 9 4 4 RBMS3 3 29762910 Missense_Mutation SNP A C3N-00580_T 17370166 29762910 168532649 213 18348 STT3B 0 . GRCh38 3 31576463 31576463 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.382G>T p.Glu128Ter p.E128* ENST00000295770 2/16 42 34 8 92 92 0 strelka-varscan-mutect STT3B,stop_gained,p.Glu128Ter,ENST00000295770,NM_178862.2;STT3B,non_coding_transcript_exon_variant,,ENST00000453168,;STT3B,non_coding_transcript_exon_variant,,ENST00000423527,;STT3B,non_coding_transcript_exon_variant,,ENST00000462235,; T ENST00000295770 Transcript stop_gained 591/4248 382/2481 128/826 E/* Gaa/Taa 1 1 STT3B HGNC HGNC:30611 protein_coding YES CCDS2650.1 ENSP00000295770 Q8TCJ2 UPI000006D7FB NM_178862.2 2/16 hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF25,Pfam_domain:PF02516 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.74926 1 1 1 1 0 T 4 4 61 31576463 31576463 G T 1 0 0 0 0 0 1 0 0 15717 1291 45 2 2 STT3B 3 31576463 Nonsense_Mutation SNP G C3N-00580_T 1813553 31576463 166719096 214 18349 SCN5A 0 . GRCh38 3 38585765 38585765 + Frame_Shift_Del DEL C C - C3N-00580_T C3N-00580_N C C c.2713delG p.Asp905ThrfsTer27 p.D905Tfs*27 ENST00000413689 16/28 205 168 37 174 174 0 sindel-varindel-pindel SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000413689,NM_001099404.1;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000333535,NM_198056.2;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000425664,NM_001099405.1;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000423572,NM_000335.4;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000451551,NM_001160161.1;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000414099,;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000455624,NM_001160160.1;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000450102,;SCN5A,frameshift_variant,p.Asp905ThrfsTer27,ENST00000449557,; - ENST00000413689 Transcript frameshift_variant 2907/8504 2713/6051 905/2016 D/X Gac/ac COSM126042 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 16/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206,Superfamily_domains:SSF81324 1 HIGH 1 deletion 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 38585765 38585765 C - 1 0 1 0 1 0 0 0 0 14191 855 30 0 0 SCN5A 3 38585765 Frame_Shift_Del DEL C C3N-00580_T 7009302 38585765 159709794 215 18350 CSRNP1 0 . GRCh38 3 39146675 39146675 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.8G>T p.Gly3Val p.G3V ENST00000273153 2/5 157 100 57 247 247 0 strelka-varscan-mutect CSRNP1,missense_variant,p.Gly3Val,ENST00000273153,NM_001320560.1,NM_001320559.1,NM_033027.3;CSRNP1,missense_variant,p.Gly3Val,ENST00000514182,; A ENST00000273153 Transcript missense_variant 186/3148 8/1770 3/589 G/V gGg/gTg 1 -1 CSRNP1 HGNC HGNC:14300 protein_coding YES CCDS2682.1 ENSP00000273153 Q96S65 A0A024R2N7 UPI0000044242 NM_001320560.1,NM_001320559.1,NM_033027.3 deleterious(0.02) 2/5 PROSITE_profiles:PS51257,hmmpanther:PTHR13580,hmmpanther:PTHR13580:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39146675 39146675 C A 1 0 0 0 0 1 0 0 0 3764 623 22 2 2 CSRNP1 3 39146675 Missense_Mutation SNP C C3N-00580_T 560910 39146675 159148884 216 18351 XIRP1 0 . GRCh38 3 39185170 39185170 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4276C>A p.Pro1426Thr p.P1426T ENST00000340369 2/2 69 56 13 88 88 0 strelka-varscan-mutect XIRP1,missense_variant,p.Pro1426Thr,ENST00000340369,NM_194293.2;XIRP1,missense_variant,p.Pro109Thr,ENST00000421646,;XIRP1,3_prime_UTR_variant,,ENST00000396251,NM_001198621.2; T ENST00000340369 Transcript missense_variant 4505/6460 4276/5532 1426/1843 P/T Ccc/Acc 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 tolerated_low_confidence(0.5) 2/2 hmmpanther:PTHR22591 MODERATE 1 SNV 1 1 PASS rs1421701853 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 39185170 39185170 G T 1 0 0 0 0 1 0 0 0 17988 1232 43 2 2 XIRP1 3 39185170 Missense_Mutation SNP G C3N-00580_T 38495 39185170 159110389 217 18352 FAM198A 0 . GRCh38 3 43032507 43032507 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.244G>C p.Ala82Pro p.A82P ENST00000430121 2/5 176 150 26 177 177 0 strelka-varscan-mutect FAM198A,missense_variant,p.Ala82Pro,ENST00000430121,NM_001129908.2;FAM198A,intron_variant,,ENST00000488863,;RP11-136C24.3,downstream_gene_variant,,ENST00000446977,;RP11-136C24.3,non_coding_transcript_exon_variant,,ENST00000418093,;RP11-136C24.3,downstream_gene_variant,,ENST00000451200,;FAM198A,missense_variant,p.Ala82Pro,ENST00000273146,;FAM198A,non_coding_transcript_exon_variant,,ENST00000434206,;FAM198A,intron_variant,,ENST00000492161,;RP11-136C24.3,intron_variant,,ENST00000443313,;RP11-136C24.1,upstream_gene_variant,,ENST00000417304,; C ENST00000430121 Transcript missense_variant 339/3121 244/1728 82/575 A/P Gct/Cct 1 1 FAM198A HGNC HGNC:24485 protein_coding YES CCDS46808.1 ENSP00000407301 Q9UFP1 UPI000016146E NM_001129908.2 deleterious_low_confidence(0.04) 2/5 hmmpanther:PTHR15905,hmmpanther:PTHR15905:SF5 MODERATE SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 43032507 43032507 G C 1 0 0 0 0 1 0 0 0 5375 1319 46 4 4 FAM198A 3 43032507 Missense_Mutation SNP G C3N-00580_T 3847337 43032507 155263052 218 18353 FYCO1 0 . GRCh38 3 45958561 45958561 + Missense_Mutation SNP C C A rs780377697 C3N-00580_T C3N-00580_N C C c.3646G>T p.Gly1216Cys p.G1216C ENST00000296137 13/18 635 386 249 665 664 1 strelka-varscan-mutect FYCO1,missense_variant,p.Gly1216Cys,ENST00000535325,;FYCO1,missense_variant,p.Gly1216Cys,ENST00000296137,NM_024513.3;FYCO1,missense_variant,p.Gly5Cys,ENST00000433878,;FYCO1,5_prime_UTR_variant,,ENST00000438446,; A ENST00000296137 Transcript missense_variant 3852/8504 3646/4437 1216/1478 G/C Ggt/Tgt rs780377697 1 -1 FYCO1 HGNC HGNC:14673 protein_coding YES CCDS2734.1 ENSP00000296137 Q9BQS8 UPI000013E307 NM_024513.3 deleterious(0.02) 13/18 Gene3D:3.30.40.10,Pfam_domain:PF01363,PROSITE_profiles:PS50178,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF57,SMART_domains:SM00064,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS rs780377697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 45958561 45958561 C A 1 0 0 0 0 1 0 0 0 5996 652 23 1 1 FYCO1 3 45958561 Missense_Mutation SNP C C3N-00580_T 2926054 45958561 152336998 219 18354 TMEM110 0 . GRCh38 3 52855402 52855402 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.203G>T p.Arg68Met p.R68M ENST00000355083 2/8 232 211 21 239 238 1 strelka-varscan-mutect TMEM110,missense_variant,p.Arg68Met,ENST00000355083,NM_198563.2;TMEM110-MUSTN1,missense_variant,p.Arg68Met,ENST00000504329,NM_001198974.2;TMEM110,upstream_gene_variant,,ENST00000485356,;TMEM110,3_prime_UTR_variant,,ENST00000467979,; A ENST00000355083 Transcript missense_variant 349/4769 203/885 68/294 R/M aGg/aTg 1 -1 TMEM110 HGNC HGNC:30526 protein_coding YES CCDS2866.1 ENSP00000347195 Q86TL2 UPI000000DB9A NM_198563.2 tolerated(0.06) 2/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR31735,hmmpanther:PTHR31735:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 61 52855402 52855402 C A 1 0 0 0 0 1 0 0 0 16471 681 24 2 2 TMEM110 3 52855402 Missense_Mutation SNP C C3N-00580_T 6896841 52855402 145440157 220 18355 CACNA1D 0 . GRCh38 3 53723556 53723556 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1849G>T p.Gly617Cys p.G617C ENST00000288139 14/49 584 229 355 440 439 1 strelka-varscan-mutect CACNA1D,missense_variant,p.Gly617Cys,ENST00000288139,NM_000720.3;CACNA1D,missense_variant,p.Gly597Cys,ENST00000350061,NM_001128840.2;CACNA1D,missense_variant,p.Gly597Cys,ENST00000636938,;CACNA1D,missense_variant,p.Gly621Cys,ENST00000637424,;CACNA1D,missense_variant,p.Gly597Cys,ENST00000636570,;CACNA1D,missense_variant,p.Gly597Cys,ENST00000422281,NM_001128839.2;CACNA1D,missense_variant,p.Gly290Cys,ENST00000481478,;CACNA1D,missense_variant,p.Gly364Cys,ENST00000636627,;CACNA1D,downstream_gene_variant,,ENST00000481085,;CACNA1D,downstream_gene_variant,,ENST00000637301,; T ENST00000288139 Transcript missense_variant 2317/9341 1849/6546 617/2181 G/C Ggt/Tgt 1 1 CACNA1D HGNC HGNC:1391 protein_coding YES CCDS2872.1 ENSP00000288139 Q01668 UPI000005031A NM_000720.3 deleterious(0.05) 14/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR01630,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF139,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 53723556 53723556 G T 1 0 0 0 0 1 0 0 0 2229 1348 47 2 2 CACNA1D 3 53723556 Missense_Mutation SNP G C3N-00580_T 868154 53723556 144572003 221 18356 CACNA1D 0 . GRCh38 3 53803449 53803449 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.5522C>A p.Pro1841Gln p.P1841Q ENST00000288139 45/49 699 640 59 613 613 0 strelka-varscan-mutect CACNA1D,missense_variant,p.Pro1841Gln,ENST00000288139,NM_000720.3;CACNA1D,missense_variant,p.Pro1821Gln,ENST00000350061,NM_001128840.2;CACNA1D,missense_variant,p.Pro1830Gln,ENST00000637424,;CACNA1D,missense_variant,p.Pro1806Gln,ENST00000636570,;CACNA1D,missense_variant,p.Pro1797Gln,ENST00000422281,NM_001128839.2;CACNA1D,missense_variant,p.Pro1514Gln,ENST00000481478,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636629,;CACNA1D,3_prime_UTR_variant,,ENST00000636448,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636633,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636999,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000637844,;CACNA1D,upstream_gene_variant,,ENST00000636581,;CACNA1D,downstream_gene_variant,,ENST00000637589,; A ENST00000288139 Transcript missense_variant 5990/9341 5522/6546 1841/2181 P/Q cCa/cAa 1 1 CACNA1D HGNC HGNC:1391 protein_coding YES CCDS2872.1 ENSP00000288139 Q01668 UPI000005031A NM_000720.3 deleterious_low_confidence(0.02) 45/49 Pfam_domain:PF16885,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF139 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 53803449 53803449 C A 1 0 0 0 0 1 0 0 0 2229 594 21 2 2 CACNA1D 3 53803449 Missense_Mutation SNP C C3N-00580_T 79893 53803449 144492110 222 18357 CADPS 0 . GRCh38 3 62650846 62650846 + Splice_Site SNP C C T novel C3N-00580_T C3N-00580_N C C c.1203+1G>A p.X401_splice ENST00000383710 194 83 111 137 137 0 strelka-varscan-mutect CADPS,splice_donor_variant,,ENST00000383710,NM_003716.3;CADPS,splice_donor_variant,,ENST00000612439,;CADPS,splice_donor_variant,,ENST00000357948,NM_183393.2;CADPS,splice_donor_variant,,ENST00000283269,NM_183394.2;CADPS,splice_donor_variant,,ENST00000490353,; T ENST00000383710 Transcript splice_donor_variant -/5471 1203/4062 401/1353 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 5/29 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 62650846 62650846 C T 1 0 0 0 0 0 0 1 0 2260 521 18 3 3 CADPS 3 62650846 Splice_Site SNP C C3N-00580_T 8847397 62650846 135644713 223 18358 ADAMTS9 0 . GRCh38 3 64681254 64681254 + Missense_Mutation SNP C C G rs146464879 C3N-00580_T C3N-00580_N C C c.626G>C p.Arg209Pro p.R209P ENST00000498707 3/40 247 215 32 188 188 0 strelka-varscan-mutect ADAMTS9,missense_variant,p.Arg209Pro,ENST00000498707,NM_182920.1;ADAMTS9,missense_variant,p.Arg209Pro,ENST00000295903,NM_001318781.1;ADAMTS9,missense_variant,p.Arg209Pro,ENST00000459780,;ADAMTS9-AS2,upstream_gene_variant,,ENST00000460833,;ADAMTS9-AS2,upstream_gene_variant,,ENST00000474768,;ADAMTS9-AS2,upstream_gene_variant,,ENST00000481312,;ADAMTS9-AS2,upstream_gene_variant,,ENST00000485174,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000482490,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000475557,; G ENST00000498707 Transcript missense_variant 969/7624 626/5808 209/1935 R/P cGc/cCc rs146464879,COSM1048065 1 -1 ADAMTS9 HGNC HGNC:13202 protein_coding YES CCDS2903.1 ENSP00000418735 Q9P2N4 UPI00000463F0 NM_182920.1 deleterious(0.02) 3/40 hmmpanther:PTHR13723:SF33,hmmpanther:PTHR13723 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs146464879 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 61 64681254 64681254 C G 1 0 0 0 0 1 0 0 0 317 768 27 4 4 ADAMTS9 3 64681254 Missense_Mutation SNP C C3N-00580_T 2030408 64681254 133614305 224 18359 EIF4E3 0 . GRCh38 3 71696488 71696488 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.377G>T p.Trp126Leu p.W126L ENST00000425534 4/7 245 226 19 200 200 0 strelka-varscan-mutect EIF4E3,missense_variant,p.Trp126Leu,ENST00000425534,NM_001134651.1;EIF4E3,missense_variant,p.Trp20Leu,ENST00000448225,NM_001134649.2;EIF4E3,missense_variant,p.Trp20Leu,ENST00000389826,NM_001134650.1;EIF4E3,missense_variant,p.Trp20Leu,ENST00000295612,NM_001282886.1;EIF4E3,missense_variant,p.Trp20Leu,ENST00000421769,NM_173359.4;EIF4E3,missense_variant,p.Trp20Leu,ENST00000497838,;EIF4E3,missense_variant,p.Trp20Leu,ENST00000496214,;EIF4E3,missense_variant,p.Trp20Leu,ENST00000469524,;EIF4E3,intron_variant,,ENST00000468147,;EIF4E3,intron_variant,,ENST00000481525,; A ENST00000425534 Transcript missense_variant 385/9949 377/675 126/224 W/L tGg/tTg 1 -1 EIF4E3 HGNC HGNC:31837 protein_coding YES CCDS46867.1 ENSP00000393324 Q8N5X7 UPI00015887BF NM_001134651.1 deleterious(0) 4/7 Gene3D:3.30.760.10,Pfam_domain:PF01652,hmmpanther:PTHR11960,hmmpanther:PTHR11960:SF6,Superfamily_domains:SSF55418 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71696488 71696488 C A 1 0 0 0 0 1 0 0 0 4865 595 21 2 2 EIF4E3 3 71696488 Missense_Mutation SNP C C3N-00580_T 7015234 71696488 126599071 225 18360 SHQ1 0 . GRCh38 3 72848239 72848239 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.102G>T p.Glu34Asp p.E34D ENST00000325599 1/11 351 324 27 340 340 0 strelka-varscan-mutect SHQ1,missense_variant,p.Glu34Asp,ENST00000325599,NM_018130.2;SHQ1,intron_variant,,ENST00000482785,;SHQ1,upstream_gene_variant,,ENST00000463369,;SHQ1,missense_variant,p.Glu34Asp,ENST00000444040,;SHQ1,missense_variant,p.Glu34Asp,ENST00000471526,; A ENST00000325599 Transcript missense_variant 242/2879 102/1734 34/577 E/D gaG/gaT 1 -1 SHQ1 HGNC HGNC:25543 protein_coding YES CCDS33788.1 ENSP00000315182 Q6PI26 UPI00001416C5 NM_018130.2 tolerated(0.5) 1/11 PROSITE_profiles:PS51203,hmmpanther:PTHR12967,hmmpanther:PTHR12967:SF0,Superfamily_domains:SSF49764 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 72848239 72848239 C A 1 0 0 0 0 1 0 0 0 14555 680 24 2 2 SHQ1 3 72848239 Missense_Mutation SNP C C3N-00580_T 1151751 72848239 125447320 226 18361 ZNF717 0 . GRCh38 3 75739135 75739135 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.338A>T p.Gln113Leu p.Q113L ENST00000478296 4/4 83 39 44 82 82 0 strelka-varscan-mutect ZNF717,missense_variant,p.Gln113Leu,ENST00000478296,NM_001290209.1;ZNF717,intron_variant,,ENST00000477374,NM_001290210.1;ZNF717,downstream_gene_variant,,ENST00000468296,;ZNF717,downstream_gene_variant,,ENST00000471541,;MIR4273,downstream_gene_variant,,ENST00000582824,;ZNF717,intron_variant,,ENST00000491507,; A ENST00000478296 Transcript missense_variant 615/3875 338/2595 113/864 Q/L cAg/cTg 1 -1 ZNF717 HGNC HGNC:29448 protein_coding YES CCDS77773.1 ENSP00000419377 C9JVC3 UPI0001B794C0 NM_001290209.1 tolerated(0.22) 4/4 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 75739135 75739135 T A 1 0 0 0 0 1 0 0 0 18695 1580 55 4 4 ZNF717 3 75739135 Missense_Mutation SNP T C3N-00580_T 2890896 75739135 122556424 227 18362 ABI3BP 0 . GRCh38 3 100750591 100750591 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.3132C>A p.= p.R1044R ENST00000284322 35/35 201 177 24 180 180 0 strelka-varscan-mutect ABI3BP,synonymous_variant,p.=,ENST00000471714,;ABI3BP,synonymous_variant,p.=,ENST00000284322,NM_015429.3;ABI3BP,synonymous_variant,p.=,ENST00000495591,;TFG,downstream_gene_variant,,ENST00000240851,NM_006070.5,NM_001195478.1;TFG,downstream_gene_variant,,ENST00000476228,NM_001195479.1;TFG,downstream_gene_variant,,ENST00000418917,;TFG,downstream_gene_variant,,ENST00000490574,NM_001007565.2;TFG,downstream_gene_variant,,ENST00000620299,;TFG,downstream_gene_variant,,ENST00000615993,;TFG,downstream_gene_variant,,ENST00000481203,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000470336,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,;ABI3BP,downstream_gene_variant,,ENST00000497021,; T ENST00000284322 Transcript synonymous_variant 3242/4498 3132/3228 1044/1075 R cgC/cgA 1 -1 ABI3BP HGNC HGNC:17265 protein_coding YES CCDS46880.1 ENSP00000284322 Q7Z7G0 UPI000011C136 NM_015429.3 35/35 hmmpanther:PTHR23197:SF10,hmmpanther:PTHR23197 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 100750591 100750591 G T 1 0 0 0 0 0 0 0 1 101 1190 42 2 2 ABI3BP 3 100750591 Silent SNP G C3N-00580_T 25011456 100750591 97544968 228 18363 ABI3BP 0 . GRCh38 3 100834750 100834750 + Nonsense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2236A>T p.Arg746Ter p.R746* ENST00000471714 29/67 267 239 28 209 209 0 strelka-varscan-mutect ABI3BP,stop_gained,p.Arg746Ter,ENST00000471714,;ABI3BP,stop_gained,p.Arg746Ter,ENST00000495063,;ABI3BP,stop_gained,p.Arg153Ter,ENST00000495591,;ABI3BP,stop_gained,p.Arg112Ter,ENST00000533795,;ABI3BP,stop_gained,p.Arg78Ter,ENST00000528490,;ABI3BP,stop_gained,p.Arg29Ter,ENST00000466947,;ABI3BP,stop_gained,p.Arg89Ter,ENST00000534413,;ABI3BP,intron_variant,,ENST00000284322,NM_015429.3;ABI3BP,intron_variant,,ENST00000528305,;ABI3BP,upstream_gene_variant,,ENST00000471901,;ABI3BP,downstream_gene_variant,,ENST00000533855,;ABI3BP,upstream_gene_variant,,ENST00000478235,;ABI3BP,downstream_gene_variant,,ENST00000534256,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487249,;ABI3BP,intron_variant,,ENST00000470336,; A ENST00000471714 Transcript stop_gained 2346/6783 2236/5334 746/1777 R/* Aga/Tga 1 -1 ABI3BP HGNC HGNC:17265 protein_coding ENSP00000420524 D3YTG3 UPI00004225FE 29/67 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF10,Low_complexity_(Seg):seg HIGH SNV 5 1 PASS rs1268838091 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 100834750 100834750 T A 1 0 0 0 0 0 1 0 0 101 1617 56 4 4 ABI3BP 3 100834750 Nonsense_Mutation SNP T C3N-00580_T 84159 100834750 97460809 229 18364 DZIP3 0 . GRCh38 3 108625883 108625883 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.495G>A p.= p.K165K ENST00000361582 7/33 109 50 59 114 114 0 strelka-mutect DZIP3,synonymous_variant,p.=,ENST00000361582,NM_014648.3;DZIP3,synonymous_variant,p.=,ENST00000463306,;DZIP3,synonymous_variant,p.=,ENST00000479138,;DZIP3,synonymous_variant,p.=,ENST00000486815,;DZIP3,synonymous_variant,p.=,ENST00000495008,; A ENST00000361582 Transcript synonymous_variant 725/5350 495/3627 165/1208 K aaG/aaA 1 1 DZIP3 HGNC HGNC:30938 protein_coding YES CCDS2952.1 ENSP00000355028 Q86Y13 UPI000006E7D4 NM_014648.3 7/33 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 108625883 108625883 G A 1 0 0 0 0 0 0 0 1 4689 933 33 3 3 DZIP3 3 108625883 Silent SNP G C3N-00580_T 7791133 108625883 89669676 230 18365 AC026348.1 0 . GRCh38 3 113305037 113305037 + Missense_Mutation SNP T T A rs748163260 C3N-00580_T C3N-00580_N T T c.4874A>T p.Gln1625Leu p.Q1625L ENST00000393845 30/34 173 95 78 186 186 0 strelka-varscan-mutect AC026348.1,missense_variant,p.Gln1625Leu,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Gln762Leu,ENST00000465636,;CFAP44,missense_variant,p.Gln246Leu,ENST00000461734,;CFAP44,upstream_gene_variant,,ENST00000489244,;CFAP44,upstream_gene_variant,,ENST00000465510,; A ENST00000393845 Transcript missense_variant,splice_region_variant 4874/5565 4874/5565 1625/1854 Q/L cAg/cTg rs748163260 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 deleterious(0) 30/34 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18 MODERATE 1 SNV 5 1 PASS rs748163260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 113305037 113305037 T A 1 0 0 0 0 1 0 0 0 128 1594 55 4 4 AC026348.1 3 113305037 Missense_Mutation SNP T C3N-00580_T 4679154 113305037 84990522 231 18366 DRD3 0 . GRCh38 3 114171906 114171906 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.87T>A p.His29Gln p.H29Q ENST00000383673 2/7 124 107 17 120 120 0 strelka-varscan-mutect DRD3,missense_variant,p.His29Gln,ENST00000383673,NM_000796.5;DRD3,missense_variant,p.His29Gln,ENST00000460779,NM_001282563.2;DRD3,missense_variant,p.His29Gln,ENST00000467632,NM_001290809.1;DRD3,missense_variant,p.His29Gln,ENST00000295881,NM_033663.5; T ENST00000383673 Transcript missense_variant 518/1640 87/1203 29/400 H/Q caT/caA 1 -1 DRD3 HGNC HGNC:3024 protein_coding YES CCDS2978.1 ENSP00000373169 P35462 X5D2G4 UPI000013E2C2 NM_000796.5 deleterious(0.03) 2/7 hmmpanther:PTHR24249:SF38,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00568 MODERATE 1 SNV 1 1 PASS rs1158923776 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 114171906 114171906 A T 1 0 0 0 0 1 0 0 0 4577 214 8 4 4 DRD3 3 114171906 Missense_Mutation SNP A C3N-00580_T 866869 114171906 84123653 232 18367 GAP43 0 . GRCh38 3 115676392 115676392 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.518C>A p.Ser173Ter p.S173* ENST00000393780 3/4 160 116 44 143 142 1 strelka-varscan-mutect GAP43,stop_gained,p.Ser173Ter,ENST00000393780,NM_001130064.1;GAP43,stop_gained,p.Ser137Ter,ENST00000305124,NM_002045.3; A ENST00000393780 Transcript stop_gained 986/1901 518/825 173/274 S/* tCa/tAa 1 1 GAP43 HGNC HGNC:4140 protein_coding YES CCDS46890.1 ENSP00000377372 P17677 UPI0000209FC5 NM_001130064.1 3/4 hmmpanther:PTHR10699:SF15,hmmpanther:PTHR10699,Pfam_domain:PF06614 HIGH 1 SNV 1 1 PASS rs1185272164 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 115676392 115676392 C A 1 0 0 0 0 0 1 0 0 6103 838 29 2 2 GAP43 3 115676392 Nonsense_Mutation SNP C C3N-00580_T 1504486 115676392 82619167 233 18368 LSAMP 0 . GRCh38 3 116086527 116086528 + Frame_Shift_Ins INS - - G novel C3N-00580_T C3N-00580_N - - c.184_185insC p.Val62AlafsTer15 p.V62Afs*15 ENST00000490035 2/7 305 153 152 255 255 0 sindel-varindel LSAMP,frameshift_variant,p.Val62AlafsTer15,ENST00000490035,NM_002338.3;LSAMP,frameshift_variant,p.Val12AlafsTer15,ENST00000539563,;LSAMP,frameshift_variant,p.Val46AlafsTer15,ENST00000333617,;LSAMP,frameshift_variant,p.Val96AlafsTer15,ENST00000474851,; G ENST00000490035 Transcript frameshift_variant 684-685/9446 184-185/1017 62/338 V/AX gtg/gCtg 1 -1 LSAMP HGNC HGNC:6705 protein_coding YES CCDS2982.1 ENSP00000419000 Q13449 UPI00000746A0 NM_002338.3 2/7 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF118,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 61 116086527 116086527 - G 1 0 1 1 0 0 0 0 0 8954 159 6 0 0 LSAMP 3 116086527 Frame_Shift_Ins INS - C3N-00580_T 410135 116086527 82209032 234 18369 STXBP5L 0 . GRCh38 3 121378853 121378853 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2386T>A p.Cys796Ser p.C796S ENST00000273666 22/28 173 147 26 131 131 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Cys796Ser,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Cys772Ser,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Cys796Ser,ENST00000492541,;STXBP5L,missense_variant,p.Cys772Ser,ENST00000472879,;STXBP5L,intron_variant,,ENST00000471262,;STXBP5L,intron_variant,,ENST00000497029,; A ENST00000273666 Transcript missense_variant 2657/9496 2386/3561 796/1186 C/S Tgc/Agc 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 tolerated(0.28) 22/28 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 121378853 121378853 T A 1 0 0 0 0 1 0 0 0 15741 1580 55 4 4 STXBP5L 3 121378853 Missense_Mutation SNP T C3N-00580_T 5292326 121378853 76916706 235 18370 STXBP5L 0 . GRCh38 3 121407600 121407600 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.3017T>A p.Met1006Lys p.M1006K ENST00000273666 24/28 249 206 43 229 229 0 strelka-varscan-mutect STXBP5L,missense_variant,p.Met1006Lys,ENST00000273666,NM_014980.2;STXBP5L,missense_variant,p.Met982Lys,ENST00000471454,NM_001308330.1;STXBP5L,missense_variant,p.Met949Lys,ENST00000471262,;STXBP5L,missense_variant,p.Met1006Lys,ENST00000492541,;STXBP5L,missense_variant,p.Met982Lys,ENST00000472879,;STXBP5L,missense_variant,p.Met980Lys,ENST00000497029,; A ENST00000273666 Transcript missense_variant 3288/9496 3017/3561 1006/1186 M/K aTg/aAg 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 deleterious(0.01) 24/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF19,Pfam_domain:PF08596,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1247746178 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 121407600 121407600 T A 1 0 0 0 0 1 0 0 0 15741 1478 51 4 4 STXBP5L 3 121407600 Missense_Mutation SNP T C3N-00580_T 28747 121407600 76887959 236 18371 POLQ 0 . GRCh38 3 121487737 121487737 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.5194A>T p.Asn1732Tyr p.N1732Y ENST00000264233 16/30 207 175 32 193 193 0 strelka-varscan-mutect POLQ,missense_variant,p.Asn1867Tyr,ENST00000621776,;POLQ,missense_variant,p.Asn1732Tyr,ENST00000264233,NM_199420.3; A ENST00000264233 Transcript missense_variant 5323/8775 5194/7773 1732/2590 N/Y Aat/Tat 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious(0) 16/30 MODERATE 1 SNV 1 1 PASS rs1264076375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 121487737 121487737 T A 1 0 0 0 0 1 0 0 0 12318 1754 61 4 4 POLQ 3 121487737 Missense_Mutation SNP T C3N-00580_T 80137 121487737 76807822 237 18372 SEMA5B 0 . GRCh38 3 122948647 122948647 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.349G>T p.Gly117Cys p.G117C ENST00000451055 3/23 177 146 31 156 156 0 strelka-varscan-mutect SEMA5B,missense_variant,p.Gly63Cys,ENST00000616742,NM_001256346.1;SEMA5B,missense_variant,p.Gly63Cys,ENST00000357599,NM_001031702.3;SEMA5B,missense_variant,p.Gly117Cys,ENST00000451055,NM_001256347.1;SEMA5B,missense_variant,p.Gly5Cys,ENST00000195173,NM_001256348.1;SEMA5B,missense_variant,p.Gly63Cys,ENST00000393583,;SEMA5B,missense_variant,p.Gly63Cys,ENST00000421053,;SEMA5B,missense_variant,p.Gly63Cys,ENST00000449546,;SEMA5B,non_coding_transcript_exon_variant,,ENST00000465147,;SEMA5B,non_coding_transcript_exon_variant,,ENST00000477001,;SEMA5B,missense_variant,p.Gly63Cys,ENST00000475244,; A ENST00000451055 Transcript missense_variant 360/4579 349/3618 117/1205 G/C Ggc/Tgc 1 -1 SEMA5B HGNC HGNC:10737 protein_coding YES CCDS58848.1 ENSP00000389588 Q9P283 UPI0002065011 NM_001256347.1 deleterious_low_confidence(0.02) 3/23 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 122948647 122948647 C A 1 0 0 0 0 1 0 0 0 14314 681 24 2 2 SEMA5B 3 122948647 Missense_Mutation SNP C C3N-00580_T 1460910 122948647 75346912 238 18373 SLC41A3 0 . GRCh38 3 126015539 126015539 + Nonsense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.925A>T p.Lys309Ter p.K309* ENST00000315891 8/12 238 207 31 237 237 0 strelka-varscan-mutect SLC41A3,stop_gained,p.Lys283Ter,ENST00000383598,NM_001008487.1;SLC41A3,stop_gained,p.Lys309Ter,ENST00000360370,NM_017836.3;SLC41A3,stop_gained,p.Lys309Ter,ENST00000315891,NM_001008485.1;SLC41A3,stop_gained,p.Lys273Ter,ENST00000346785,NM_001008486.1;SLC41A3,stop_gained,p.Lys192Ter,ENST00000508835,NM_001164475.1;SLC41A3,downstream_gene_variant,,ENST00000514677,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000512557,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000506102,;SLC41A3,downstream_gene_variant,,ENST00000507008,; A ENST00000315891 Transcript stop_gained 1164/1797 925/1524 309/507 K/* Aaa/Taa 1 -1 SLC41A3 HGNC HGNC:31046 protein_coding YES CCDS33843.1 ENSP00000326070 Q96GZ6 UPI000013D523 NM_001008485.1 8/12 hmmpanther:PTHR16228:SF22,hmmpanther:PTHR16228,Gene3D:2zy9B03,Superfamily_domains:0054748 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 126015539 126015539 T A 1 0 0 0 0 0 1 0 0 14909 1763 61 4 4 SLC41A3 3 126015539 Nonsense_Mutation SNP T C3N-00580_T 3066892 126015539 72280020 239 18374 PLXND1 0 . GRCh38 3 129605966 129605967 + Frame_Shift_Ins INS - - G novel C3N-00580_T C3N-00580_N - - c.673dupC p.Arg225ProfsTer207 p.R225Pfs*207 ENST00000324093 1/36 319 278 41 397 397 0 sindel-varindel-pindel PLXND1,frameshift_variant,p.Arg225ProfsTer207,ENST00000324093,NM_015103.2; G ENST00000324093 Transcript frameshift_variant 852-853/7094 673-674/5778 225/1925 R/PX cgc/cCgc 1 -1 PLXND1 HGNC HGNC:9107 protein_coding YES CCDS33854.1 ENSP00000317128 Q9Y4D7 UPI00003671AD NM_015103.2 1/36 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF7,SMART_domains:SM00630,Superfamily_domains:SSF101912 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 61 129605966 129605966 - G 1 0 1 1 0 0 0 0 0 12233 768 27 0 0 PLXND1 3 129605966 Frame_Shift_Ins INS - C3N-00580_T 3590427 129605966 68689593 240 18375 EPHB1 0 . GRCh38 3 135166076 135166076 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1694G>C p.Arg565Thr p.R565T ENST00000398015 8/16 180 146 34 142 142 0 strelka-varscan-mutect EPHB1,missense_variant,p.Arg565Thr,ENST00000398015,NM_004441.4;EPHB1,missense_variant,p.Arg126Thr,ENST00000493838,; C ENST00000398015 Transcript missense_variant,splice_region_variant 2064/4672 1694/2955 565/984 R/T aGg/aCg 1 1 EPHB1 HGNC HGNC:3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 UPI000012A07E NM_004441.4 deleterious(0.01) 8/16 Pfam_domain:PF14575,PIRSF_domain:PIRSF000666,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999988 1 1 1 0 C 3 2 61 135166076 135166076 G C 1 0 0 0 0 1 0 0 0 5021 1014 35 4 4 EPHB1 3 135166076 Missense_Mutation SNP G C3N-00580_T 5560110 135166076 63129483 241 18376 PRR23C 0 . GRCh38 3 139044593 139044593 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.28G>A p.Ala10Thr p.A10T ENST00000413199 1/1 137 115 22 160 160 0 strelka-varscan-mutect PRR23C,missense_variant,p.Ala10Thr,ENST00000413199,NM_001134657.1;MRPS22,intron_variant,,ENST00000495075,; T ENST00000413199 Transcript missense_variant 300/2791 28/789 10/262 A/T Gcc/Acc 1 -1 PRR23C HGNC HGNC:37173 protein_coding YES CCDS46924.1 ENSP00000396648 Q6ZRP0 UPI00001C0F48 NM_001134657.1 deleterious(0.02) 1/1 hmmpanther:PTHR31813:SF6,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 139044593 139044593 C T 1 0 0 0 0 1 0 0 0 12731 768 27 1 1 PRR23C 3 139044593 Missense_Mutation SNP C C3N-00580_T 3878517 139044593 59250966 242 18377 XRN1 0 . GRCh38 3 142375852 142375852 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2924G>T p.Ser975Ile p.S975I ENST00000264951 25/42 182 163 19 184 184 0 strelka-varscan-mutect XRN1,missense_variant,p.Ser975Ile,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Ser441Ile,ENST00000498077,;XRN1,missense_variant,p.Ser975Ile,ENST00000392981,NM_001282857.1;XRN1,non_coding_transcript_exon_variant,,ENST00000472625,;XRN1,downstream_gene_variant,,ENST00000472697,; A ENST00000264951 Transcript missense_variant 3042/10143 2924/5121 975/1706 S/I aGt/aTt 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 tolerated(0.06) 25/42 hmmpanther:PTHR12341:SF7,hmmpanther:PTHR12341 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 142375852 142375852 C A 1 0 0 0 0 1 0 0 0 18017 565 20 2 2 XRN1 3 142375852 Missense_Mutation SNP C C3N-00580_T 3331259 142375852 55919707 243 18378 ATR 0 . GRCh38 3 142562712 142562712 + Frame_Shift_Del DEL C C - novel C3N-00580_T C3N-00580_N C C c.690delG p.Trp230CysfsTer3 p.W230Cfs*3 ENST00000350721 4/47 164 81 83 181 181 0 sindel-varindel-pindel ATR,frameshift_variant,p.Trp230CysfsTer3,ENST00000350721,NM_001184.3;ATR,upstream_gene_variant,,ENST00000515149,;ATR,intron_variant,,ENST00000507148,;ATR,upstream_gene_variant,,ENST00000515863,; - ENST00000350721 Transcript frameshift_variant 812/8249 690/7935 230/2644 W/X tgG/tg 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 4/47 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 142562712 142562712 C - 1 0 1 0 1 0 0 0 0 1356 740 26 0 0 ATR 3 142562712 Frame_Shift_Del DEL C C3N-00580_T 186860 142562712 55732847 244 18379 CHST2 0 . GRCh38 3 143121971 143121971 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1155C>T p.= p.G385G ENST00000309575 2/2 75 67 8 86 86 0 strelka-varscan-mutect CHST2,synonymous_variant,p.=,ENST00000309575,NM_004267.4;RP11-80H8.4,upstream_gene_variant,,ENST00000483262,; T ENST00000309575 Transcript synonymous_variant 2539/4582 1155/1593 385/530 G ggC/ggT 1 1 CHST2 HGNC HGNC:1970 protein_coding YES CCDS3129.1 ENSP00000307911 Q9Y4C5 V9HVX9 UPI0000073CBC NM_004267.4 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF3,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -17.08023 0.999699 1 1 1 0 T 2 4 61 143121971 143121971 C T 1 0 0 0 0 0 0 0 1 3164 726 26 3 3 CHST2 3 143121971 Silent SNP C C3N-00580_T 559259 143121971 55173588 245 18380 AGTR1 0 . GRCh38 3 148742079 148742079 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1044C>A p.= p.S348S ENST00000497524 2/2 370 189 181 364 364 0 strelka-varscan-mutect AGTR1,synonymous_variant,p.=,ENST00000497524,NM_009585.3;AGTR1,synonymous_variant,p.=,ENST00000349243,NM_000685.4;AGTR1,synonymous_variant,p.=,ENST00000404754,;AGTR1,synonymous_variant,p.=,ENST00000402260,NM_032049.3;AGTR1,synonymous_variant,p.=,ENST00000418473,NM_004835.4,NM_031850.3;AGTR1,synonymous_variant,p.=,ENST00000474935,;AGTR1,synonymous_variant,p.=,ENST00000475347,;AGTR1,synonymous_variant,p.=,ENST00000461609,; A ENST00000497524 Transcript synonymous_variant 1435/2359 1044/1080 348/359 S tcC/tcA 1 1 AGTR1 HGNC HGNC:336 protein_coding YES CCDS3137.1 ENSP00000419422 P30556 Q53YY0 UPI0000039D66 NM_009585.3 2/2 hmmpanther:PTHR24228:SF30,hmmpanther:PTHR24228,Prints_domain:PR00635 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 148742079 148742079 C A 1 0 0 0 0 0 0 0 1 480 581 21 2 2 AGTR1 3 148742079 Silent SNP C C3N-00580_T 5620108 148742079 49553480 246 18381 LEKR1 0 . GRCh38 3 157011446 157011446 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.231C>A p.= p.I77I ENST00000470811 11/14 249 224 25 255 255 0 strelka-varscan-mutect LEKR1,synonymous_variant,p.=,ENST00000470811,;LEKR1,synonymous_variant,p.=,ENST00000356539,NM_001004316.2; A ENST00000470811 Transcript synonymous_variant 1566/2881 231/1167 77/388 I atC/atA 1 1 LEKR1 HGNC HGNC:33765 protein_coding ENSP00000418214 Q6ZMV7 UPI0000425F3D 11/14 hmmpanther:PTHR34251 LOW 1 SNV 2 1 PASS rs949576025 . 0 207 0 3 0 0 0 0 -20 0.9999855 1 1 1 0 A 2 1 61 157011446 157011446 C A 1 0 0 0 0 0 0 0 1 8625 874 31 1 1 LEKR1 3 157011446 Silent SNP C C3N-00580_T 8269367 157011446 41284113 247 18382 NMD3 0 . GRCh38 3 161222017 161222017 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4G>T p.Glu2Ter p.E2* ENST00000460469 1/15 208 172 36 217 217 0 strelka-varscan-mutect NMD3,stop_gained,p.Glu2Ter,ENST00000460469,;NMD3,stop_gained,p.Glu2Ter,ENST00000351193,NM_015938.3;NMD3,stop_gained,p.Glu2Ter,ENST00000472947,NM_001320227.1;NMD3,stop_gained,p.Glu2Ter,ENST00000463518,;NMD3,stop_gained,p.Glu2Ter,ENST00000493066,;NMD3,stop_gained,p.Glu2Ter,ENST00000476237,;NMD3,stop_gained,p.Glu2Ter,ENST00000468606,;NMD3,stop_gained,p.Glu2Ter,ENST00000460503,;NMD3,upstream_gene_variant,,ENST00000478160,;NMD3,non_coding_transcript_exon_variant,,ENST00000473909,;RP11-479I16.2,downstream_gene_variant,,ENST00000603703,; T ENST00000460469 Transcript stop_gained 459/3061 4/1512 2/503 E/* Gag/Tag 1 1 NMD3 HGNC HGNC:24250 protein_coding YES CCDS3194.1 ENSP00000419004 Q96D46 UPI0000035FBE 1/15 hmmpanther:PTHR12746 HIGH 1 SNV 1 1 PASS rs1451861872 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 161222017 161222017 G T 1 0 0 0 0 0 1 0 0 10526 1175 41 2 2 NMD3 3 161222017 Nonsense_Mutation SNP G C3N-00580_T 4210571 161222017 37073542 248 18383 SI 0 . GRCh38 3 165063512 165063512 + Silent SNP T T A rs571049231 C3N-00580_T C3N-00580_N T T c.837A>T p.= p.T279T ENST00000264382 8/48 103 85 18 80 80 0 strelka-varscan-mutect SI,synonymous_variant,p.=,ENST00000264382,NM_001041.3; A ENST00000264382 Transcript synonymous_variant 900/6011 837/5484 279/1827 T acA/acT rs571049231 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 8/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Superfamily_domains:SSF74650 LOW 1 SNV 1 1 PASS rs571049231 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 165063512 165063512 T A 1 0 0 0 0 0 0 0 1 14561 1451 51 4 4 SI 3 165063512 Silent SNP T C3N-00580_T 3841495 165063512 33232047 249 18384 SLITRK3 0 . GRCh38 3 165188121 165188121 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.2710T>C p.Tyr904His p.Y904H ENST00000475390 2/2 94 43 51 102 102 0 strelka-varscan-mutect SLITRK3,missense_variant,p.Tyr904His,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Tyr904His,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; G ENST00000475390 Transcript missense_variant 3154/4555 2710/2934 904/977 Y/H Tat/Cat 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 deleterious(0) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 165188121 165188121 A G 1 0 0 0 0 1 0 0 0 15035 420 15 5 5 SLITRK3 3 165188121 Missense_Mutation SNP A C3N-00580_T 124609 165188121 33107438 250 18385 BCHE 0 . GRCh38 3 165773470 165773470 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1721G>T p.Gly574Val p.G574V ENST00000264381 4/4 344 302 42 323 322 1 strelka-varscan-mutect BCHE,missense_variant,p.Gly574Val,ENST00000264381,NM_000055.2;BCHE,missense_variant,p.Gly104Val,ENST00000479451,;BCHE,downstream_gene_variant,,ENST00000488954,;BCHE,3_prime_UTR_variant,,ENST00000482958,;BCHE,3_prime_UTR_variant,,ENST00000497011,; A ENST00000264381 Transcript missense_variant 1888/2454 1721/1809 574/602 G/V gGa/gTa 1 -1 BCHE HGNC HGNC:983 protein_coding YES CCDS3198.1 ENSP00000264381 P06276 UPI0000127866 NM_000055.2 tolerated(0.05) 4/4 PD415333,Pfam_domain:PF08674,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF215 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 165773470 165773470 C A 1 0 0 0 0 1 0 0 0 1505 855 30 2 2 BCHE 3 165773470 Missense_Mutation SNP C C3N-00580_T 585349 165773470 32522089 251 18386 PRKCI 0 . GRCh38 3 170259993 170259993 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.248A>T p.Gln83Leu p.Q83L ENST00000295797 3/18 124 61 63 166 166 0 strelka-varscan-mutect PRKCI,missense_variant,p.Gln83Leu,ENST00000295797,NM_002740.5; T ENST00000295797 Transcript missense_variant 553/4950 248/1791 83/596 Q/L cAg/cTg 1 1 PRKCI HGNC HGNC:9404 protein_coding YES CCDS3212.2 ENSP00000295797 P41743 UPI000020A798 NM_002740.5 tolerated(0.06) 3/18 Gene3D:3.10.20.240,Pfam_domain:PF00564,PIRSF_domain:PIRSF000554,PROSITE_profiles:PS51745,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF214,SMART_domains:SM00666,Superfamily_domains:SSF54277 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 170259993 170259993 A T 1 0 0 0 0 1 0 0 0 12647 188 7 4 4 PRKCI 3 170259993 Missense_Mutation SNP A C3N-00580_T 4486523 170259993 28035566 252 18387 NAALADL2 0 . GRCh38 3 175096976 175096976 + Missense_Mutation SNP C C T rs758174571 C3N-00580_T C3N-00580_N C C c.230C>T p.Ser77Leu p.S77L ENST00000454872 2/14 242 168 74 189 189 0 strelka-varscan-mutect NAALADL2,missense_variant,p.Ser77Leu,ENST00000454872,NM_207015.2;NAALADL2,missense_variant,p.Ser60Leu,ENST00000434257,;NAALADL2-AS3,intron_variant,,ENST00000453180,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000485853,;NAALADL2-AS3,intron_variant,,ENST00000436929,; T ENST00000454872 Transcript missense_variant 358/9865 230/2388 77/795 S/L tCa/tTa rs758174571 1 1 NAALADL2 HGNC HGNC:23219 protein_coding YES CCDS46960.1 ENSP00000404705 Q58DX5 UPI0000161608 NM_207015.2 deleterious(0.01) 2/14 hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404 MODERATE 1 SNV 1 1 PASS rs758174571 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 175096976 175096976 C T 1 0 0 0 0 1 0 0 0 10134 838 29 3 3 NAALADL2 3 175096976 Missense_Mutation SNP C C3N-00580_T 4836983 175096976 23198583 253 18388 FXR1 0 . GRCh38 3 180968231 180968231 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1379G>T p.Gly460Val p.G460V ENST00000357559 14/17 306 245 61 229 229 0 strelka-varscan-mutect FXR1,missense_variant,p.Gly460Val,ENST00000357559,NM_005087.3;FXR1,missense_variant,p.Gly375Val,ENST00000305586,NM_001013439.2;FXR1,missense_variant,p.Gly460Val,ENST00000445140,NM_001013438.2;FXR1,missense_variant,p.Gly447Val,ENST00000480918,;FXR1,missense_variant,p.Gly375Val,ENST00000468861,;FXR1,missense_variant,p.Gly411Val,ENST00000491062,;FXR1,missense_variant,p.Gly61Val,ENST00000482125,;FXR1,non_coding_transcript_exon_variant,,ENST00000475315,;FXR1,non_coding_transcript_exon_variant,,ENST00000472339,;FXR1,non_coding_transcript_exon_variant,,ENST00000476672,;FXR1,non_coding_transcript_exon_variant,,ENST00000498658,;FXR1,upstream_gene_variant,,ENST00000481383,; T ENST00000357559 Transcript missense_variant 1763/8711 1379/1866 460/621 G/V gGt/gTt 1 1 FXR1 HGNC HGNC:4023 protein_coding YES CCDS3238.1 ENSP00000350170 P51114 UPI000013EA6E NM_005087.3 deleterious_low_confidence(0.03) 14/17 Low_complexity_(Seg):seg,hmmpanther:PTHR10603:SF6,hmmpanther:PTHR10603,Pfam_domain:PF16096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 180968231 180968231 G T 1 0 0 0 0 1 0 0 0 5986 1261 44 2 2 FXR1 3 180968231 Missense_Mutation SNP G C3N-00580_T 5871255 180968231 17327328 254 18389 SOX2 0 . GRCh38 3 181713008 181713008 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.648C>A p.Tyr216Ter p.Y216* ENST00000325404 1/1 689 606 83 869 867 2 strelka-varscan-mutect SOX2,stop_gained,p.Tyr216Ter,ENST00000325404,NM_003106.3;SOX2-OT,intron_variant,,ENST00000498731,;SOX2-OT,intron_variant,,ENST00000492337,;SOX2-OT,intron_variant,,ENST00000493521,;SOX2-OT,intron_variant,,ENST00000466034,;SOX2-OT,intron_variant,,ENST00000630553,;SOX2-OT,intron_variant,,ENST00000477928,;SOX2-OT,intron_variant,,ENST00000491282,;SOX2-OT,intron_variant,,ENST00000627530,;SOX2-OT,intron_variant,,ENST00000597828,;SOX2-OT,intron_variant,,ENST00000595084,;SOX2-OT,intron_variant,,ENST00000599082,;SOX2-OT,intron_variant,,ENST00000628496,;SOX2-OT,intron_variant,,ENST00000600386,;SOX2-OT,intron_variant,,ENST00000627501,;SOX2-OT,intron_variant,,ENST00000600778,;SOX2-OT,intron_variant,,ENST00000629112,;SOX2-OT,intron_variant,,ENST00000593549,;SOX2-OT,intron_variant,,ENST00000630887,;SOX2-OT,intron_variant,,ENST00000628343,;SOX2-OT,intron_variant,,ENST00000629781,;SOX2-OT,intron_variant,,ENST00000627738,;SOX2-OT,intron_variant,,ENST00000629830,;SOX2-OT,intron_variant,,ENST00000600801,;SOX2-OT,intron_variant,,ENST00000626619,;SOX2-OT,intron_variant,,ENST00000597651,;SOX2-OT,intron_variant,,ENST00000626299,;SOX2-OT,intron_variant,,ENST00000628810,;SOX2-OT,intron_variant,,ENST00000596250,;SOX2-OT,intron_variant,,ENST00000476964,;SOX2-OT,intron_variant,,ENST00000595287,;SOX2-OT,intron_variant,,ENST00000629552,;SOX2-OT,intron_variant,,ENST00000469278,;SOX2-OT,intron_variant,,ENST00000498226,;SOX2-OT,intron_variant,,ENST00000598474,;SOX2-OT,intron_variant,,ENST00000593330,;SOX2-OT,downstream_gene_variant,,ENST00000476125,;SOX2-OT,downstream_gene_variant,,ENST00000631025,;SOX2-OT,downstream_gene_variant,,ENST00000600962,;SOX2OT_exon4,upstream_gene_variant,,ENST00000610449,; A ENST00000325404 Transcript stop_gained 1085/2513 648/954 216/317 Y/* taC/taA 1 1 SOX2 HGNC HGNC:11195 protein_coding YES CCDS3239.1 ENSP00000323588 P48431 A0A0U3FYV6 UPI000003F545 NM_003106.3 1/1 hmmpanther:PTHR10270:SF231,hmmpanther:PTHR10270 HIGH SNV 1 PASS rs1020803542 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 181713008 181713008 C A 1 0 0 0 0 0 1 0 0 15275 489 17 2 2 SOX2 3 181713008 Nonsense_Mutation SNP C C3N-00580_T 744777 181713008 16582551 255 18390 ATP11B 0 . GRCh38 3 182872456 182872456 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1967A>T p.Gln656Leu p.Q656L ENST00000323116 18/30 222 200 22 126 126 0 strelka-varscan-mutect ATP11B,missense_variant,p.Gln656Leu,ENST00000323116,NM_014616.2;ATP11B,missense_variant,p.Gln457Leu,ENST00000498086,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,;ATP11B,upstream_gene_variant,,ENST00000466758,; T ENST00000323116 Transcript missense_variant 2227/7325 1967/3534 656/1177 Q/L cAg/cTg 1 1 ATP11B HGNC HGNC:13553 protein_coding YES CCDS33896.1 ENSP00000321195 Q9Y2G3 UPI000004124E NM_014616.2 deleterious(0.01) 18/30 Gene3D:3.40.1110.10,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 182872456 182872456 A T 1 0 0 0 0 1 0 0 0 1272 188 7 4 4 ATP11B 3 182872456 Missense_Mutation SNP A C3N-00580_T 1159448 182872456 15423103 256 18391 KLHL24 0 . GRCh38 3 183651231 183651231 + Missense_Mutation SNP A A G C3N-00580_T C3N-00580_N A A c.875A>G p.His292Arg p.H292R ENST00000454652 4/9 178 158 20 110 110 0 strelka-varscan-mutect KLHL24,missense_variant,p.His292Arg,ENST00000454652,NM_017644.3;KLHL24,missense_variant,p.His292Arg,ENST00000242810,;KLHL24,missense_variant,p.His292Arg,ENST00000476808,;KLHL24,downstream_gene_variant,,ENST00000493074,;KLHL24,downstream_gene_variant,,ENST00000468001,;KLHL24,downstream_gene_variant,,ENST00000454495,;KLHL24,downstream_gene_variant,,ENST00000482138,;KLHL24,downstream_gene_variant,,ENST00000468101,;KLHL24,downstream_gene_variant,,ENST00000437402,;KLHL24,downstream_gene_variant,,ENST00000427201,;KLHL24,downstream_gene_variant,,ENST00000473045,;KLHL24,intron_variant,,ENST00000475827,; G ENST00000454652 Transcript missense_variant 1261/7380 875/1803 292/600 H/R cAc/cGc COSM402400 1 1 KLHL24 HGNC HGNC:25947 protein_coding YES CCDS3246.1 ENSP00000395012 Q6TFL4 UPI000020A86F NM_017644.3 deleterious(0.02) 4/9 Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF257 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 183651231 183651231 A G 1 0 0 0 0 1 0 0 0 8243 159 6 5 5 KLHL24 3 183651231 Missense_Mutation SNP A C3N-00580_T 778775 183651231 14644328 257 18392 AHSG 0 . GRCh38 3 186620628 186620628 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.802G>T p.Val268Phe p.V268F ENST00000411641 7/7 129 69 60 95 95 0 strelka-varscan-mutect AHSG,missense_variant,p.Val268Phe,ENST00000411641,NM_001622.2;AHSG,missense_variant,p.Val269Phe,ENST00000273784,;RP11-573D15.8,intron_variant,,ENST00000630178,;RP11-573D15.8,intron_variant,,ENST00000628505,;RP11-573D15.8,intron_variant,,ENST00000625386,;AHSG,downstream_gene_variant,,ENST00000478441,; T ENST00000411641 Transcript missense_variant 1021/1711 802/1104 268/367 V/F Gtc/Ttc 1 1 AHSG HGNC HGNC:349 protein_coding YES CCDS3278.1 ENSP00000393887 P02765 UPI000013D9D0 NM_001622.2 tolerated(0.06) 7/7 hmmpanther:PTHR13814,hmmpanther:PTHR13814:SF6,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1199583206 . 0 201 9 0 0 0 0 0 -20 0.9999993 1 1 1 0 T 3 4 61 186620628 186620628 G T 1 0 0 0 0 1 0 0 0 497 1029 36 2 2 AHSG 3 186620628 Missense_Mutation SNP G C3N-00580_T 2969397 186620628 11674931 258 18393 IL1RAP 0 . GRCh38 3 190645731 190645731 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.1234G>A p.Ala412Thr p.A412T ENST00000317757 11/12 148 128 20 143 143 0 strelka-varscan-mutect IL1RAP,missense_variant,p.Ala412Thr,ENST00000317757,NM_001167931.1;IL1RAP,missense_variant,p.Ala412Thr,ENST00000412504,;IL1RAP,missense_variant,p.Ala412Thr,ENST00000447382,NM_002182.3;IL1RAP,missense_variant,p.Ala412Thr,ENST00000072516,NM_001167929.1;IL1RAP,missense_variant,p.Ala412Thr,ENST00000443369,;IL1RAP,missense_variant,p.Ala412Thr,ENST00000439062,NM_001167928.1;RN7SKP296,downstream_gene_variant,,ENST00000411185,;IL1RAP,3_prime_UTR_variant,,ENST00000413869,;IL1RAP,3_prime_UTR_variant,,ENST00000342550,; A ENST00000317757 Transcript missense_variant 1440/5413 1234/2064 412/687 A/T Gca/Aca 1 1 IL1RAP HGNC HGNC:5995 protein_coding YES CCDS54696.1 ENSP00000314807 Q9NPH3 UPI000020A9C1 NM_001167931.1 deleterious(0) 11/12 PROSITE_profiles:PS50104,hmmpanther:PTHR11890:SF20,hmmpanther:PTHR11890,Pfam_domain:PF01582,Gene3D:3.40.50.10140,SMART_domains:SM00255,Superfamily_domains:SSF52200,Prints_domain:PR01537 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 190645731 190645731 G A 1 0 0 0 0 1 0 0 0 7563 1319 46 3 3 IL1RAP 3 190645731 Missense_Mutation SNP G C3N-00580_T 4025103 190645731 7649828 259 18394 SMCO1 0 . GRCh38 3 196509662 196509662 + Missense_Mutation SNP G G C rs9869292 C3N-00580_T C3N-00580_N G G c.58C>G p.His20Asp p.H20D ENST00000397537 2/3 119 103 16 95 95 0 strelka-varscan SMCO1,missense_variant,p.His20Asp,ENST00000397537,NM_001077657.1;SMCO1,3_prime_UTR_variant,,ENST00000452776,NM_001320473.1; C ENST00000397537 Transcript missense_variant 215/1812 58/645 20/214 H/D Cac/Gac rs9869292 1 -1 SMCO1 HGNC HGNC:27407 protein_coding YES CCDS43192.1 ENSP00000380671 Q147U7 UPI000020AF14 NM_001077657.1 tolerated(0.22) 2/3 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15080,hmmpanther:PTHR35979 MODERATE 1 SNV 1 1 PASS . . 0 202 6 0 0 0 0 2 -3.432753 0 0 1 0 0 C 3 2 61 196509662 196509662 G C 1 0 0 0 0 1 0 0 0 15082 1348 47 4 4 SMCO1 3 196509662 Missense_Mutation SNP G C3N-00580_T 5863931 196509662 1785897 260 18395 FGFR3 0 . GRCh38 4 1804449 1804449 + Missense_Mutation SNP C C T rs370064407 C3N-00580_T C3N-00580_N C C c.1201C>T p.Arg401Cys p.R401C ENST00000340107 9/18 71 64 7 116 116 0 strelka-varscan-mutect FGFR3,missense_variant,p.Arg401Cys,ENST00000340107,NM_001163213.1;FGFR3,missense_variant,p.Arg399Cys,ENST00000440486,NM_000142.4;FGFR3,missense_variant,p.Arg399Cys,ENST00000481110,;FGFR3,missense_variant,p.Arg399Cys,ENST00000260795,;FGFR3,3_prime_UTR_variant,,ENST00000613647,;FGFR3,intron_variant,,ENST00000412135,NM_022965.3;FGFR3,intron_variant,,ENST00000352904,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,upstream_gene_variant,,ENST00000469068,; T ENST00000340107 Transcript missense_variant 1457/4293 1201/2427 401/808 R/C Cgc/Tgc rs370064407,COSM296687 1 1 FGFR3 HGNC HGNC:3690 protein_coding YES CCDS54706.1 ENSP00000339824 P22607 UPI000002A9AC NM_001163213.1 tolerated(0.07) 9/18 Gene3D:3.30.200.20,PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF353 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs370064407 . 0 201 7 2 0 0 0 0 -12.20012 0.9996482 1 1 1 0 T 3 4 61 1804449 1804449 C T 1 0 0 0 0 1 0 0 0 5731 768 27 1 1 FGFR3 4 1804449 Missense_Mutation SNP C C3N-00580_T 1804449 188410106 261 18396 CFAP99 0 . GRCh38 4 2449735 2449735 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.708C>A p.Asn236Lys p.N236K ENST00000616117 6/15 231 170 61 246 246 0 strelka-varscan-mutect CFAP99,missense_variant,p.Asn236Lys,ENST00000635017,;CFAP99,missense_variant,p.Asn236Lys,ENST00000616117,NM_001193282.2;CFAP99,upstream_gene_variant,,ENST00000506607,;CFAP99,non_coding_transcript_exon_variant,,ENST00000511731,;CFAP99,non_coding_transcript_exon_variant,,ENST00000514556,;CFAP99,non_coding_transcript_exon_variant,,ENST00000515732,; A ENST00000616117 Transcript missense_variant 708/1941 708/1941 236/646 N/K aaC/aaA 1 1 CFAP99 HGNC HGNC:51180 protein_coding YES CCDS75092.1 ENSP00000480601 A0A087WWY8 UPI00043788D2 NM_001193282.2 deleterious(0) 6/15 hmmpanther:PTHR34649,hmmpanther:PTHR34649:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 2449735 2449735 C A 1 0 0 0 0 1 0 0 0 3036 506 18 2 2 CFAP99 4 2449735 Missense_Mutation SNP C C3N-00580_T 645286 2449735 187764820 262 18397 STX18 0 . GRCh38 4 4423554 4423554 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.795A>T p.Arg265Ser p.R265S ENST00000306200 9/11 205 165 40 351 351 0 strelka-varscan-mutect STX18,missense_variant,p.Arg265Ser,ENST00000306200,NM_016930.2;STX18,missense_variant,p.Arg265Ser,ENST00000505286,;NSG1,downstream_gene_variant,,ENST00000421177,;NSG1,downstream_gene_variant,,ENST00000513555,;NSG1,downstream_gene_variant,,ENST00000397958,NM_001287763.1;NSG1,downstream_gene_variant,,ENST00000433139,NM_001287764.1,NM_001040101.1;NSG1,downstream_gene_variant,,ENST00000621129,NM_014392.4;STX18,downstream_gene_variant,,ENST00000507908,;STX18,non_coding_transcript_exon_variant,,ENST00000503861,;STX18,downstream_gene_variant,,ENST00000512195,;STX18,non_coding_transcript_exon_variant,,ENST00000503692,;STX18,non_coding_transcript_exon_variant,,ENST00000515687,;STX18,non_coding_transcript_exon_variant,,ENST00000510296,;STX18,non_coding_transcript_exon_variant,,ENST00000502267,;NSG1,downstream_gene_variant,,ENST00000513829,; A ENST00000306200 Transcript missense_variant 859/2138 795/1008 265/335 R/S agA/agT 1 -1 STX18 HGNC HGNC:15942 protein_coding YES CCDS3377.1 ENSP00000305810 Q9P2W9 UPI0000049FDD NM_016930.2 deleterious(0.01) 9/11 Gene3D:1.20.5.110,PROSITE_patterns:PS00914,hmmpanther:PTHR15959,hmmpanther:PTHR15959:SF0,Superfamily_domains:SSF58038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 4423554 4423554 T A 1 0 0 0 0 1 0 0 0 15725 1664 58 4 4 STX18 4 4423554 Missense_Mutation SNP T C3N-00580_T 1973819 4423554 185791001 263 18398 EVC2 0 . GRCh38 4 5689156 5689156 + Splice_Site SNP C C G novel C3N-00580_T C3N-00580_N C C c.706+1G>C p.X236_splice ENST00000344408 364 265 99 359 359 0 strelka-mutect EVC2,splice_donor_variant,,ENST00000310917,NM_001166136.1;EVC2,splice_donor_variant,,ENST00000344408,NM_147127.4;EVC2,splice_donor_variant,,ENST00000475313,;EVC2,splice_donor_variant,,ENST00000509670,; G ENST00000344408 Transcript splice_donor_variant -/4390 706/3927 236/1308 1 -1 EVC2 HGNC HGNC:19747 protein_coding YES CCDS3382.2 ENSP00000342144 Q86UK5 UPI00001910B5 NM_147127.4 5/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 61 5689156 5689156 C G 1 0 0 0 0 0 0 1 0 5153 521 18 4 4 EVC2 4 5689156 Splice_Site SNP C C3N-00580_T 1265602 5689156 184525399 264 18399 CPZ 0 . GRCh38 4 8619302 8619302 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1644C>A p.= p.I548I ENST00000360986 11/11 229 188 41 393 393 0 strelka-varscan-mutect CPZ,synonymous_variant,p.=,ENST00000382480,NM_001014448.2;CPZ,synonymous_variant,p.=,ENST00000360986,NM_001014447.2;CPZ,synonymous_variant,p.=,ENST00000315782,NM_003652.3;GPR78,3_prime_UTR_variant,,ENST00000514302,;CPZ,3_prime_UTR_variant,,ENST00000515606,;GPR78,non_coding_transcript_exon_variant,,ENST00000513120,;CPZ,non_coding_transcript_exon_variant,,ENST00000513486,; A ENST00000360986 Transcript synonymous_variant 1818/2267 1644/1959 548/652 I atC/atA 1 1 CPZ HGNC HGNC:2333 protein_coding YES CCDS33953.1 ENSP00000354255 Q66K79 UPI000020BCC5 NM_001014447.2 11/11 Gene3D:2.60.40.1120,Pfam_domain:PF13620,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF55,SMART_domains:SM00631,Superfamily_domains:SSF49464 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 8619302 8619302 C A 1 0 0 0 0 0 0 0 1 3637 845 30 2 2 CPZ 4 8619302 Silent SNP C C3N-00580_T 2930146 8619302 181595253 265 18400 WDR1 0 . GRCh38 4 10088367 10088367 + Missense_Mutation SNP T T C rs367695543 C3N-00580_T C3N-00580_N T T c.643A>G p.Ile215Val p.I215V ENST00000499869 7/15 507 409 98 560 560 0 strelka-varscan-mutect WDR1,missense_variant,p.Ile215Val,ENST00000382452,;WDR1,missense_variant,p.Ile215Val,ENST00000499869,NM_017491.3;WDR1,missense_variant,p.Ile75Val,ENST00000382451,;WDR1,missense_variant,p.Ile75Val,ENST00000502702,NM_005112.4;WDR1,missense_variant,p.Ile219Val,ENST00000508079,;WDR1,non_coding_transcript_exon_variant,,ENST00000515743,;WDR1,non_coding_transcript_exon_variant,,ENST00000502962,;WDR1,non_coding_transcript_exon_variant,,ENST00000505543,;WDR1,non_coding_transcript_exon_variant,,ENST00000506246,;WDR1,non_coding_transcript_exon_variant,,ENST00000504739,;WDR1,non_coding_transcript_exon_variant,,ENST00000510848,;WDR1,non_coding_transcript_exon_variant,,ENST00000508949,;WDR1,non_coding_transcript_exon_variant,,ENST00000509695,; C ENST00000499869 Transcript missense_variant 837/3054 643/1821 215/606 I/V Atc/Gtc rs367695543 1 -1 WDR1 HGNC HGNC:12754 protein_coding YES CCDS54740.1 ENSP00000427687 O75083 V9HWG7 UPI0000138EDA NM_017491.3 tolerated(0.45) 7/15 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19856,SMART_domains:SM00320,Superfamily_domains:SSF50974 MODERATE 1 SNV 5 1 PASS rs367695543 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 10088367 10088367 T C 1 0 0 0 0 1 0 0 0 17834 1464 51 5 5 WDR1 4 10088367 Missense_Mutation SNP T C3N-00580_T 1469065 10088367 180126188 266 18401 NKX3-2 0 . GRCh38 4 13542289 13542289 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.706C>G p.Arg236Gly p.R236G ENST00000382438 2/2 195 121 74 169 169 0 strelka-varscan-mutect NKX3-2,missense_variant,p.Arg236Gly,ENST00000382438,NM_001189.3;LINC01096,downstream_gene_variant,,ENST00000501050,;LINC01096,downstream_gene_variant,,ENST00000503938,; C ENST00000382438 Transcript missense_variant 1342/2801 706/1002 236/333 R/G Cgc/Ggc 1 -1 NKX3-2 HGNC HGNC:951 protein_coding YES CCDS3410.1 ENSP00000371875 P78367 UPI00001301F5 NM_001189.3 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24340:SF34,hmmpanther:PTHR24340,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 13542289 13542289 G C 1 0 0 0 0 1 0 0 0 10493 1087 38 4 4 NKX3-2 4 13542289 Missense_Mutation SNP G C3N-00580_T 3453922 13542289 176672266 267 18402 BOD1L1 0 . GRCh38 4 13602633 13602633 + Nonsense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.4267A>T p.Lys1423Ter p.K1423* ENST00000040738 10/26 331 215 116 290 290 0 strelka-varscan-mutect BOD1L1,stop_gained,p.Lys1423Ter,ENST00000040738,NM_148894.2; A ENST00000040738 Transcript stop_gained 4403/10565 4267/9156 1423/3051 K/* Aag/Tag 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 10/26 hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 13602633 13602633 T A 1 0 0 0 0 0 1 0 0 1639 1850 64 4 4 BOD1L1 4 13602633 Nonsense_Mutation SNP T C3N-00580_T 60344 13602633 176611922 268 18403 PROM1 0 . GRCh38 4 15985821 15985821 + Missense_Mutation SNP T T A rs113820099 C3N-00580_T C3N-00580_N T T c.2219A>T p.Lys740Met p.K740M ENST00000510224 22/28 103 77 26 169 169 0 strelka-varscan-mutect PROM1,missense_variant,p.Lys731Met,ENST00000505450,NM_001145848.1;PROM1,missense_variant,p.Lys731Met,ENST00000508167,NM_001145847.1;PROM1,missense_variant,p.Lys740Met,ENST00000510224,;PROM1,missense_variant,p.Lys740Met,ENST00000447510,NM_006017.2;PROM1,missense_variant,p.Lys740Met,ENST00000540805,NM_001145849.1,NM_001145851.1;PROM1,missense_variant,p.Lys740Met,ENST00000539194,NM_001145850.1,NM_001145852.1;PROM1,upstream_gene_variant,,ENST00000513946,;PROM1,non_coding_transcript_exon_variant,,ENST00000511270,;PROM1,upstream_gene_variant,,ENST00000503884,; A ENST00000510224 Transcript missense_variant 2468/4006 2219/2598 740/865 K/M aAg/aTg rs113820099 1 -1 PROM1 HGNC HGNC:9454 protein_coding YES CCDS47029.1 ENSP00000426809 O43490 UPI000004ECD6 deleterious(0.04) 22/28 hmmpanther:PTHR22730,hmmpanther:PTHR22730:SF3,Pfam_domain:PF05478 MODERATE 1 SNV 5 1 PASS rs113820099 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 15985821 15985821 T A 1 0 0 0 0 1 0 0 0 12687 1609 56 4 4 PROM1 4 15985821 Missense_Mutation SNP T C3N-00580_T 2383188 15985821 174228734 269 18404 SLC34A2 0 . GRCh38 4 25662611 25662614 + Splice_Site DEL AAGT AAGT - novel C3N-00580_T C3N-00580_N AAGT AAGT c.112+3_112+6delAAGT p.X38_splice ENST00000382051 2/13 744 680 64 728 728 0 sindel-varindel-pindel SLC34A2,splice_donor_variant,,ENST00000382051,NM_006424.2;SLC34A2,splice_donor_variant,,ENST00000503434,NM_001177999.1;SLC34A2,splice_donor_variant,,ENST00000504570,NM_001177998.1;SLC34A2,splice_donor_variant,,ENST00000507530,;SLC34A2,splice_donor_variant,,ENST00000513204,;SLC34A2,upstream_gene_variant,,ENST00000510033,; - ENST00000382051 Transcript splice_donor_variant,coding_sequence_variant 161-?/4122 111-?/2073 37-?/690 1 1 SLC34A2 HGNC HGNC:11020 protein_coding YES CCDS3435.1 ENSP00000371483 O95436 UPI000013DF24 NM_006424.2 2/13 2/12 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 61 25662611 25662611 AAGT - 1 0 1 0 1 0 0 1 0 14838 28 1 0 0 SLC34A2 4 25662611 Splice_Site DEL AAGT C3N-00580_T 9676790 25662611 164551944 270 18405 PCDH7 0 . GRCh38 4 30722436 30722436 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1014G>T p.= p.G338G ENST00000543491 1/1 177 96 81 172 172 0 strelka-varscan-mutect PCDH7,synonymous_variant,p.=,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,synonymous_variant,p.=,ENST00000361762,NM_002589.2;PCDH7,synonymous_variant,p.=,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; T ENST00000543491 Transcript synonymous_variant 1584/4457 1014/3219 338/1072 G ggG/ggT 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF321,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 30722436 30722436 G T 1 0 0 0 0 0 0 0 1 11603 1219 43 2 2 PCDH7 4 30722436 Silent SNP G C3N-00580_T 5059825 30722436 159492119 271 18406 C4orf19 0 . GRCh38 4 37590980 37590980 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.925G>T p.Asp309Tyr p.D309Y ENST00000284437 3/3 66 56 10 72 71 1 strelka-varscan-mutect C4orf19,missense_variant,p.Asp309Tyr,ENST00000284437,NM_018302.2;C4orf19,missense_variant,p.Asp309Tyr,ENST00000381980,NM_001104629.1;RELL1,3_prime_UTR_variant,,ENST00000314117,NM_001085399.1;C4orf19,intron_variant,,ENST00000508175,;RP11-36B15.1,upstream_gene_variant,,ENST00000503034,; T ENST00000284437 Transcript missense_variant 1103/1949 925/945 309/314 D/Y Gat/Tat COSM5487186 1 1 C4orf19 HGNC HGNC:25618 protein_coding YES CCDS3442.1 ENSP00000284437 Q8IY42 A0A024R9R1 UPI00000742D7 NM_018302.2 deleterious(0) 3/3 Pfam_domain:PF15770,hmmpanther:PTHR16106,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99849 0.9999999 1 1 1 0 T 3 4 61 37590980 37590980 G T 1 0 0 0 0 1 0 0 0 2079 942 33 2 2 C4orf19 4 37590980 Missense_Mutation SNP G C3N-00580_T 6868544 37590980 152623575 272 18407 PDS5A 0 . GRCh38 4 39879798 39879798 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1922G>T p.Gly641Val p.G641V ENST00000303538 18/33 305 206 99 261 261 0 strelka-varscan-mutect PDS5A,missense_variant,p.Gly641Val,ENST00000303538,NM_001100399.1; A ENST00000303538 Transcript missense_variant 2462/7176 1922/4014 641/1337 G/V gGg/gTg 1 -1 PDS5A HGNC HGNC:29088 protein_coding YES CCDS47045.1 ENSP00000303427 Q29RF7 G1UI16 UPI00006C6A7E NM_001100399.1 deleterious(0) 18/33 hmmpanther:PTHR12663:SF2,hmmpanther:PTHR12663 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39879798 39879798 C A 1 0 0 0 0 1 0 0 0 11779 623 22 2 2 PDS5A 4 39879798 Missense_Mutation SNP C C3N-00580_T 2288818 39879798 150334757 273 18408 SCFD2 0 . GRCh38 4 53145336 53145336 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1558A>T p.Thr520Ser p.T520S ENST00000401642 5/9 200 167 33 103 103 0 strelka-varscan-mutect SCFD2,missense_variant,p.Thr520Ser,ENST00000401642,NM_152540.3;SCFD2,missense_variant,p.Thr520Ser,ENST00000388940,; A ENST00000401642 Transcript missense_variant 1692/3176 1558/2055 520/684 T/S Acg/Tcg 1 -1 SCFD2 HGNC HGNC:30676 protein_coding YES CCDS33984.1 ENSP00000384182 Q8WU76 UPI000006FB05 NM_152540.3 tolerated(0.18) 5/9 Pfam_domain:PF00995,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF29,Superfamily_domains:SSF56815 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 53145336 53145336 T A 1 0 0 0 0 1 0 0 0 14156 1652 57 4 4 SCFD2 4 53145336 Missense_Mutation SNP T C3N-00580_T 13265538 53145336 137069219 274 18409 KIT 0 . GRCh38 4 54731936 54731936 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.2299G>C p.Glu767Gln p.E767Q ENST00000288135 16/21 709 516 193 405 405 0 strelka-varscan-mutect KIT,missense_variant,p.Glu767Gln,ENST00000288135,NM_000222.2;KIT,missense_variant,p.Glu763Gln,ENST00000412167,NM_001093772.1;KIT,non_coding_transcript_exon_variant,,ENST00000512959,; C ENST00000288135 Transcript missense_variant 2396/5186 2299/2931 767/976 E/Q Gaa/Caa 1 1 KIT HGNC HGNC:6342 protein_coding YES CCDS3496.1 ENSP00000288135 P10721 A0A024RDA0 UPI000003F17D NM_000222.2 deleterious(0.04) 16/21 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000615,PIRSF_domain:PIRSF500951,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF46,Low_complexity_(Seg):seg,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 54731936 54731936 G C 1 0 0 0 0 1 0 0 0 8193 943 33 4 4 KIT 4 54731936 Missense_Mutation SNP G C3N-00580_T 1586600 54731936 135482619 275 18410 SRD5A3 0 . GRCh38 4 55364073 55364073 + Splice_Site SNP G G A novel C3N-00580_T C3N-00580_N G G c.365-1G>A p.X122_splice ENST00000264228 533 317 216 276 276 0 strelka-varscan-mutect SRD5A3,splice_acceptor_variant,,ENST00000264228,NM_024592.4;SRD5A3,intron_variant,,ENST00000505210,;SRD5A3-AS1,non_coding_transcript_exon_variant,,ENST00000433175,;SRD5A3-AS1,downstream_gene_variant,,ENST00000510637,;SRD5A3-AS1,downstream_gene_variant,,ENST00000595734,;SRD5A3-AS1,downstream_gene_variant,,ENST00000596289,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609573,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609051,;SRD5A3-AS1,downstream_gene_variant,,ENST00000596312,;SRD5A3-AS1,downstream_gene_variant,,ENST00000598906,;SRD5A3-AS1,downstream_gene_variant,,ENST00000608086,;SRD5A3-AS1,downstream_gene_variant,,ENST00000608265,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609580,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609487,;SRD5A3-AS1,downstream_gene_variant,,ENST00000608558,;SRD5A3-AS1,downstream_gene_variant,,ENST00000595103,;SRD5A3-AS1,downstream_gene_variant,,ENST00000619912,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609700,;SRD5A3-AS1,downstream_gene_variant,,ENST00000609500,;SRD5A3-AS1,downstream_gene_variant,,ENST00000613794,;SRD5A3,splice_acceptor_variant,,ENST00000514398,;SRD5A3-AS1,downstream_gene_variant,,ENST00000610396,;SRD5A3-AS1,downstream_gene_variant,,ENST00000619685,; A ENST00000264228 Transcript splice_acceptor_variant -/4190 365/957 122/318 1 1 SRD5A3 HGNC HGNC:25812 protein_coding YES CCDS3498.1 ENSP00000264228 Q9H8P0 UPI0000043F70 NM_024592.4 2/4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 55364073 55364073 G A 1 0 0 0 0 0 0 1 0 15497 1014 35 3 3 SRD5A3 4 55364073 Splice_Site SNP G C3N-00580_T 632137 55364073 134850482 276 18411 ADGRL3 0 . GRCh38 4 61732816 61732816 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.457C>A p.His153Asn p.H153N ENST00000514591 7/25 270 151 119 124 124 0 strelka-varscan-mutect ADGRL3,missense_variant,p.His153Asn,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.His153Asn,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.His221Asn,ENST00000509896,;ADGRL3,missense_variant,p.His221Asn,ENST00000511324,;ADGRL3,missense_variant,p.His221Asn,ENST00000508693,;ADGRL3,missense_variant,p.His221Asn,ENST00000507164,;ADGRL3,missense_variant,p.His221Asn,ENST00000506720,;ADGRL3,missense_variant,p.His221Asn,ENST00000506746,;ADGRL3,missense_variant,p.His221Asn,ENST00000507625,;ADGRL3,missense_variant,p.His153Asn,ENST00000506700,;ADGRL3,missense_variant,p.His153Asn,ENST00000504896,;ADGRL3,missense_variant,p.His153Asn,ENST00000514157,;ADGRL3,missense_variant,p.His153Asn,ENST00000508946,;ADGRL3,missense_variant,p.His153Asn,ENST00000514996,; A ENST00000514591 Transcript missense_variant 786/6297 457/4410 153/1469 H/N Cac/Aac 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0.02) 7/25 PROSITE_profiles:PS51132,hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF02191,SMART_domains:SM00284 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 61732816 61732816 C A 1 0 0 0 0 1 0 0 0 377 594 21 2 2 ADGRL3 4 61732816 Missense_Mutation SNP C C3N-00580_T 6368743 61732816 128481739 277 18412 ADGRL3 0 . GRCh38 4 62037776 62037776 + Frame_Shift_Del DEL G G - novel C3N-00580_T C3N-00580_N G G c.3434delG p.Gly1145AlafsTer51 p.G1145Afs*51 ENST00000514591 23/25 431 268 163 293 293 0 sindel-varindel-pindel ADGRL3,frameshift_variant,p.Gly1145AlafsTer51,ENST00000512091,NM_001322246.1;ADGRL3,frameshift_variant,p.Gly1145AlafsTer51,ENST00000514591,NM_015236.4;ADGRL3,frameshift_variant,p.Gly1213AlafsTer51,ENST00000509896,;ADGRL3,frameshift_variant,p.Gly1204AlafsTer51,ENST00000511324,;ADGRL3,frameshift_variant,p.Gly1213AlafsTer51,ENST00000508693,;ADGRL3,frameshift_variant,p.Gly1204AlafsTer51,ENST00000507164,;ADGRL3,frameshift_variant,p.Gly1213AlafsTer51,ENST00000506720,;ADGRL3,frameshift_variant,p.Gly1204AlafsTer51,ENST00000506746,;ADGRL3,frameshift_variant,p.Gly1204AlafsTer51,ENST00000507625,;ADGRL3,frameshift_variant,p.Gly1136AlafsTer51,ENST00000506700,;ADGRL3,frameshift_variant,p.Gly1145AlafsTer51,ENST00000504896,;ADGRL3,frameshift_variant,p.Gly1136AlafsTer51,ENST00000514157,;ADGRL3,frameshift_variant,p.Gly1145AlafsTer51,ENST00000508946,;ADGRL3,frameshift_variant,p.Gly1136AlafsTer51,ENST00000514996,;ADGRL3,frameshift_variant,p.Gly594AlafsTer51,ENST00000502815,; - ENST00000514591 Transcript frameshift_variant 3762/6297 3433/4410 1145/1469 G/X Ggc/gc 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 23/25 hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF02354,Superfamily_domains:SSF81321 HIGH 1 deletion 5 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 62037776 62037776 G - 1 0 1 0 1 0 0 0 0 377 1348 47 0 0 ADGRL3 4 62037776 Frame_Shift_Del DEL G C3N-00580_T 304960 62037776 128176779 278 18413 EPHA5 0 . GRCh38 4 65643384 65643384 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.225G>T p.Trp75Cys p.W75C ENST00000622150 2/18 440 291 149 301 299 2 strelka-varscan-mutect EPHA5,missense_variant,p.Trp75Cys,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Trp75Cys,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Trp75Cys,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Trp75Cys,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Trp75Cys,ENST00000432638,;EPHA5,missense_variant,p.Trp75Cys,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 978/8421 225/3117 75/1038 W/C tgG/tgT 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 2/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 65643384 65643384 C A 1 0 0 0 0 1 0 0 0 5017 856 30 2 2 EPHA5 4 65643384 Missense_Mutation SNP C C3N-00580_T 3605608 65643384 124571171 279 18414 TMPRSS11E 0 . GRCh38 4 68461862 68461862 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.53C>A p.Pro18His p.P18H ENST00000305363 2/10 202 103 99 222 221 1 strelka-varscan-mutect TMPRSS11E,missense_variant,p.Pro18His,ENST00000305363,NM_014058.3;TMPRSS11E,missense_variant,p.Pro15His,ENST00000510647,; A ENST00000305363 Transcript missense_variant 117/2136 53/1272 18/423 P/H cCc/cAc 1 1 TMPRSS11E HGNC HGNC:24465 protein_coding YES CCDS33993.1 ENSP00000307519 Q9UL52 UPI00000389F7 NM_014058.3 deleterious(0) 2/10 hmmpanther:PTHR24256:SF101,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037941 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 68461862 68461862 C A 1 0 0 0 0 1 0 0 0 16718 623 22 2 2 TMPRSS11E 4 68461862 Missense_Mutation SNP C C3N-00580_T 2818478 68461862 121752693 280 18415 NPFFR2 0 . GRCh38 4 72128862 72128862 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.577G>A p.Asp193Asn p.D193N ENST00000308744 2/4 156 67 89 145 145 0 strelka-varscan-mutect NPFFR2,missense_variant,p.Asp193Asn,ENST00000308744,NM_004885.2;NPFFR2,missense_variant,p.Asp94Asn,ENST00000395999,NM_001144756.1;NPFFR2,missense_variant,p.Asp91Asn,ENST00000358749,NM_053036.2;NPFFR2,intron_variant,,ENST00000344413,; A ENST00000308744 Transcript missense_variant 675/1922 577/1569 193/522 D/N Gat/Aat 1 1 NPFFR2 HGNC HGNC:4525 protein_coding YES CCDS3551.1 ENSP00000307822 Q9Y5X5 UPI000012FFBD NM_004885.2 deleterious(0) 2/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF3,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 72128862 72128862 G A 1 0 0 0 0 1 0 0 0 10626 1290 45 3 3 NPFFR2 4 72128862 Missense_Mutation SNP G C3N-00580_T 3667000 72128862 118085693 281 18416 MMRN1 0 . GRCh38 4 89936467 89936467 + Silent SNP A A T rs773351612 C3N-00580_T C3N-00580_N A A c.2787A>T p.= p.T929T ENST00000394980 7/9 147 113 34 178 178 0 strelka-varscan-mutect MMRN1,synonymous_variant,p.=,ENST00000394980,;MMRN1,synonymous_variant,p.=,ENST00000264790,NM_007351.2;MMRN1,synonymous_variant,p.=,ENST00000508372,; T ENST00000394980 Transcript synonymous_variant 3106/5217 2787/3687 929/1228 T acA/acT rs773351612,COSM588910 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 7/9 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 0,1 LOW 1 SNV 5 0,1 1 PASS rs773351612 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 89936467 89936467 A T 1 0 0 0 0 0 0 0 1 9633 117 5 4 4 MMRN1 4 89936467 Silent SNP A C3N-00580_T 17807605 89936467 100278088 282 18417 C4orf17 0 . GRCh38 4 99529947 99529947 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.535C>A p.Gln179Lys p.Q179K ENST00000326581 5/9 90 66 24 83 83 0 strelka-varscan-mutect C4orf17,missense_variant,p.Gln179Lys,ENST00000514652,;C4orf17,missense_variant,p.Gln179Lys,ENST00000326581,NM_032149.2;C4orf17,non_coding_transcript_exon_variant,,ENST00000503257,;C4orf17,missense_variant,p.Gln179Lys,ENST00000477187,; A ENST00000326581 Transcript missense_variant 897/1636 535/1080 179/359 Q/K Cag/Aag 1 1 C4orf17 HGNC HGNC:25274 protein_coding YES CCDS3649.1 ENSP00000322582 Q53FE4 UPI0000141987 NM_032149.2 deleterious(0.01) 5/9 Pfam_domain:PF15256,hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF2 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 61 99529947 99529947 C A 1 0 0 0 0 1 0 0 0 2078 827 29 2 2 C4orf17 4 99529947 Missense_Mutation SNP C C3N-00580_T 9593480 99529947 90684608 283 18418 MANBA 0 . GRCh38 4 102690626 102690626 + Frame_Shift_Del DEL C C - novel C3N-00580_T C3N-00580_N C C c.819delG p.Ile274LeufsTer6 p.I274Lfs*6 ENST00000226578 6/17 317 300 17 355 354 1 varindel-pindel MANBA,frameshift_variant,p.Ile274LeufsTer6,ENST00000226578,NM_005908.3;MANBA,frameshift_variant,p.Ile217LeufsTer6,ENST00000505239,;MANBA,non_coding_transcript_exon_variant,,ENST00000514430,; - ENST00000226578 Transcript frameshift_variant 919/2904 819/2640 273/879 R/X agG/ag 1 -1 MANBA HGNC HGNC:6831 protein_coding YES CCDS3658.1 ENSP00000226578 O00462 UPI000013C8A2 NM_005908.3 6/17 Gene3D:2.60.40.320,hmmpanther:PTHR10066,hmmpanther:PTHR10066:SF65,Superfamily_domains:SSF49303 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 102690626 102690626 C - 1 0 1 0 1 0 0 0 0 9140 854 30 0 0 MANBA 4 102690626 Frame_Shift_Del DEL C C3N-00580_T 3160679 102690626 87523929 284 18419 ETNPPL 0 . GRCh38 4 108746517 108746517 + Frame_Shift_Del DEL T T - novel C3N-00580_T C3N-00580_N T T c.1185delA p.Lys395AsnfsTer17 p.K395Nfs*17 ENST00000296486 11/13 68 56 12 78 78 0 sindel-varindel-pindel ETNPPL,frameshift_variant,p.Lys395AsnfsTer17,ENST00000296486,NM_031279.3;ETNPPL,frameshift_variant,p.Lys389AsnfsTer17,ENST00000411864,NM_001146590.1;ETNPPL,frameshift_variant,p.Lys355AsnfsTer17,ENST00000510706,;ETNPPL,frameshift_variant,p.Lys337AsnfsTer17,ENST00000512646,NM_001146627.1;ETNPPL,downstream_gene_variant,,ENST00000505233,;ETNPPL,downstream_gene_variant,,ENST00000503912,; - ENST00000296486 Transcript frameshift_variant 1340/2099 1185/1500 395/499 K/X aaA/aa 1 -1 ETNPPL HGNC HGNC:14404 protein_coding YES CCDS3682.1 ENSP00000296486 Q8TBG4 UPI000004B638 NM_031279.3 11/13 hmmpanther:PTHR11986:SF63,hmmpanther:PTHR11986,Gene3D:3.90.1150.10,Pfam_domain:PF00202,Superfamily_domains:SSF53383 HIGH 1 deletion 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 108746517 108746517 T - 1 0 1 0 1 0 0 0 0 5138 1722 60 0 0 ETNPPL 4 108746517 Frame_Shift_Del DEL T C3N-00580_T 6055891 108746517 81468038 285 18420 ANK2 0 . GRCh38 4 113357127 113357127 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.8509G>T p.Ala2837Ser p.A2837S ENST00000357077 38/46 480 319 161 463 463 0 strelka-varscan-mutect ANK2,missense_variant,p.Ala2837Ser,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala2804Ser,ENST00000264366,;ANK2,missense_variant,p.Ala139Ser,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; T ENST00000357077 Transcript missense_variant 8562/14196 8509/11874 2837/3957 A/S Gca/Tca 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(0.08) 38/46 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 113357127 113357127 G T 1 0 0 0 0 1 0 0 0 721 971 34 2 2 ANK2 4 113357127 Missense_Mutation SNP G C3N-00580_T 4610610 113357127 76857428 286 18421 TRPC3 0 . GRCh38 4 121932292 121932292 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.966C>A p.= p.A322A ENST00000379645 2/12 128 97 31 104 104 0 strelka-varscan-mutect TRPC3,synonymous_variant,p.=,ENST00000264811,NM_003305.2;TRPC3,synonymous_variant,p.=,ENST00000379645,NM_001130698.1;TRPC3,synonymous_variant,p.=,ENST00000513531,;TRPC3,downstream_gene_variant,,ENST00000502968,;TRPC3,synonymous_variant,p.=,ENST00000506449,; T ENST00000379645 Transcript synonymous_variant 1040/3548 966/2766 322/921 A gcC/gcA 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 2/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Pfam_domain:PF08344 LOW 1 SNV 1 1 PASS rs1485877040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 121932292 121932292 G T 1 0 0 0 0 0 0 0 1 17084 1335 47 2 2 TRPC3 4 121932292 Silent SNP G C3N-00580_T 8575165 121932292 68282263 287 18422 IL2 0 . GRCh38 4 122453719 122453719 + Silent SNP C C G rs753489414 C3N-00580_T C3N-00580_N C C c.342G>C p.= p.L114L ENST00000226730 3/4 87 66 21 126 126 0 strelka-varscan-mutect IL2,synonymous_variant,p.=,ENST00000226730,NM_000586.3;IL2,non_coding_transcript_exon_variant,,ENST00000477645,; G ENST00000226730 Transcript synonymous_variant 627/1029 342/462 114/153 L ctG/ctC rs753489414 1 -1 IL2 HGNC HGNC:6001 protein_coding YES CCDS3726.1 ENSP00000226730 P60568 Q0GK43 UPI000002BE7B NM_000586.3 3/4 Gene3D:1.20.1250.10,PD003649,Pfam_domain:PF00715,Prints_domain:PR00265,hmmpanther:PTHR11443,SMART_domains:SM00189,Superfamily_domains:SSF47266 LOW 1 SNV 1 1 PASS rs753489414 . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 G 2 3 61 122453719 122453719 C G 1 0 0 0 0 0 0 0 1 7569 581 21 4 4 IL2 4 122453719 Silent SNP C C3N-00580_T 521427 122453719 67760836 288 18423 DCHS2 0 . GRCh38 4 154489955 154489955 + Silent SNP G G T rs769774270 C3N-00580_T C3N-00580_N G G c.1401C>A p.= p.I467I ENST00000339452 1/8 54 25 29 61 60 1 strelka-varscan-mutect DCHS2,synonymous_variant,p.=,ENST00000339452,NM_001142552.1;DCHS2,non_coding_transcript_exon_variant,,ENST00000456341,; T ENST00000339452 Transcript synonymous_variant 1762/5064 1401/4110 467/1369 I atC/atA rs769774270 1 -1 DCHS2 HGNC HGNC:23111 protein_coding CCDS47150.1 ENSP00000345062 A0A0A0MRC0 UPI00002372F1 NM_001142552.1 1/8 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,Low_complexity_(Seg):seg,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs769774270 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 154489955 154489955 G T 1 0 0 0 0 0 0 0 1 4091 932 33 2 2 DCHS2 4 154489955 Silent SNP G C3N-00580_T 32036236 154489955 35724600 289 18424 RBM46 0 . GRCh38 4 154798013 154798013 + Silent SNP C C T rs750760222 C3N-00580_T C3N-00580_N C C c.354C>T p.= p.I118I ENST00000281722 3/5 95 43 52 111 111 0 strelka-varscan-mutect RBM46,synonymous_variant,p.=,ENST00000510397,NM_001277173.1;RBM46,synonymous_variant,p.=,ENST00000281722,NM_144979.4;RBM46,synonymous_variant,p.=,ENST00000514866,NM_001277171.1;RBM46,synonymous_variant,p.=,ENST00000512640,; T ENST00000281722 Transcript synonymous_variant 589/2583 354/1602 118/533 I atC/atT rs750760222,COSM5278244 1 1 RBM46 HGNC HGNC:28401 protein_coding YES CCDS3790.1 ENSP00000281722 Q8TBY0 UPI000007173F NM_144979.4 3/5 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF272,hmmpanther:PTHR24012,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01648,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 0,1 LOW 1 SNV 1 0,1 1 PASS rs750760222 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 154798013 154798013 C T 1 0 0 0 0 0 0 0 1 13306 816 29 3 3 RBM46 4 154798013 Silent SNP C C3N-00580_T 308058 154798013 35416542 290 18425 TMEM144 0 . GRCh38 4 158217368 158217368 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.280G>T p.Gly94Ter p.G94* ENST00000296529 5/13 136 94 42 131 131 0 strelka-varscan-mutect TMEM144,stop_gained,p.Gly94Ter,ENST00000514558,;TMEM144,stop_gained,p.Gly94Ter,ENST00000296529,NM_018342.4;TMEM144,stop_gained,p.Gly94Ter,ENST00000508243,;TMEM144,stop_gained,p.Gly94Ter,ENST00000504569,;TMEM144,stop_gained,p.Gly94Ter,ENST00000503200,;TMEM144,downstream_gene_variant,,ENST00000509278,;TMEM144,downstream_gene_variant,,ENST00000505189,;TMEM144,downstream_gene_variant,,ENST00000512481,;TMEM144,downstream_gene_variant,,ENST00000502698,;TMEM144,downstream_gene_variant,,ENST00000505049,;TMEM144,downstream_gene_variant,,ENST00000511038,;TMEM144,downstream_gene_variant,,ENST00000514971,;TMEM144,stop_gained,p.Gly94Ter,ENST00000511532,; T ENST00000296529 Transcript stop_gained 800/3442 280/1038 94/345 G/* Gga/Tga 1 1 TMEM144 HGNC HGNC:25633 protein_coding YES CCDS3799.1 ENSP00000296529 Q7Z5S9 UPI0000140BEC NM_018342.4 5/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR16119:SF17,hmmpanther:PTHR16119,Pfam_domain:PF07857 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 158217368 158217368 G T 1 0 0 0 0 0 1 0 0 16503 1349 47 2 2 TMEM144 4 158217368 Nonsense_Mutation SNP G C3N-00580_T 3419355 158217368 31997187 291 18426 SH3RF1 0 . GRCh38 4 169136489 169136489 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.897C>T p.= p.T299T ENST00000284637 5/12 116 90 26 166 166 0 strelka-varscan-mutect SH3RF1,synonymous_variant,p.=,ENST00000284637,NM_020870.3;SH3RF1,non_coding_transcript_exon_variant,,ENST00000508685,;SH3RF1,synonymous_variant,p.=,ENST00000511421,; A ENST00000284637 Transcript synonymous_variant 1239/5272 897/2667 299/888 T acC/acT 1 -1 SH3RF1 HGNC HGNC:17650 protein_coding YES CCDS34099.1 ENSP00000284637 Q7Z6J0 UPI0000160033 NM_020870.3 5/12 LOW 1 SNV 1 1 PASS . . 0 177 0 22 11 0 0 0 -17.15337 0.03963595 0 1 0 0 A 2 1 61 169136489 169136489 G A 1 0 0 0 0 0 0 0 1 14517 1335 47 3 3 SH3RF1 4 169136489 Silent SNP G C3N-00580_T 10919121 169136489 21078066 292 18427 GALNTL6 0 . GRCh38 4 171814610 171814610 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.30G>A p.= p.Q10Q ENST00000506823 2/13 214 100 114 347 347 0 strelka-varscan-mutect GALNTL6,synonymous_variant,p.=,ENST00000506823,NM_001034845.2;GALNTL6,synonymous_variant,p.=,ENST00000511251,;GALNTL6,non_coding_transcript_exon_variant,,ENST00000513061,;GALNTL6,non_coding_transcript_exon_variant,,ENST00000504379,; A ENST00000506823 Transcript synonymous_variant 687/3922 30/1806 10/601 Q caG/caA 1 1 GALNTL6 HGNC HGNC:33844 protein_coding YES CCDS34104.1 ENSP00000423313 Q49A17 E5D8G0 UPI000058EB5C NM_001034845.2 2/13 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF40 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 171814610 171814610 G A 1 0 0 0 0 0 0 0 1 6093 933 33 3 3 GALNTL6 4 171814610 Silent SNP G C3N-00580_T 2678121 171814610 18399945 293 18428 GALNTL6 0 . GRCh38 4 172311749 172311749 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.383C>G p.Ala128Gly p.A128G ENST00000506823 4/13 69 29 40 68 68 0 strelka-varscan-mutect GALNTL6,missense_variant,p.Ala128Gly,ENST00000506823,NM_001034845.2;GALNTL6,missense_variant,p.Ala111Gly,ENST00000508122,;GALNTL6,non_coding_transcript_exon_variant,,ENST00000457021,; G ENST00000506823 Transcript missense_variant 1040/3922 383/1806 128/601 A/G gCt/gGt 1 1 GALNTL6 HGNC HGNC:33844 protein_coding YES CCDS34104.1 ENSP00000423313 Q49A17 E5D8G0 UPI000058EB5C NM_001034845.2 deleterious(0.03) 4/13 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF40,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 172311749 172311749 C G 1 0 0 0 0 1 0 0 0 6093 811 28 4 4 GALNTL6 4 172311749 Missense_Mutation SNP C C3N-00580_T 497139 172311749 17902806 294 18429 FBXO8 0 . GRCh38 4 174262968 174262968 + Missense_Mutation SNP T T C C3N-00580_T C3N-00580_N T T c.125A>G p.Asn42Ser p.N42S ENST00000393674 2/6 437 195 242 416 416 0 strelka-varscan-mutect FBXO8,missense_variant,p.Asn42Ser,ENST00000393674,NM_012180.2;FBXO8,missense_variant,p.Asn42Ser,ENST00000615392,;FBXO8,missense_variant,p.Asn42Ser,ENST00000503293,;FBXO8,missense_variant,p.Asn42Ser,ENST00000513696,;FBXO8,missense_variant,p.Asn42Ser,ENST00000515664,; C ENST00000393674 Transcript missense_variant 988/2577 125/960 42/319 N/S aAt/aGt COSM1618601 1 -1 FBXO8 HGNC HGNC:13587 protein_coding YES CCDS3820.1 ENSP00000377280 Q9NRD0 A0A0S2Z5D1 UPI000012A588 NM_012180.2 tolerated_low_confidence(0.5) 2/6 1 MODERATE 1 SNV 1 1 1 PASS rs1365701819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 174262968 174262968 T C 1 0 0 0 0 1 0 0 0 5624 1493 52 5 5 FBXO8 4 174262968 Missense_Mutation SNP T C3N-00580_T 1951219 174262968 15951587 295 18430 ADAM29 0 . GRCh38 4 174976394 174976394 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.869C>A p.Thr290Lys p.T290K ENST00000615367 6/6 45 20 25 57 57 0 strelka-varscan-mutect ADAM29,missense_variant,p.Thr290Lys,ENST00000615367,NM_001278125.1;ADAM29,missense_variant,p.Thr290Lys,ENST00000359240,NM_014269.4,NM_001278126.1;ADAM29,missense_variant,p.Thr290Lys,ENST00000445694,NM_001130703.1;ADAM29,missense_variant,p.Thr290Lys,ENST00000404450,NM_001130704.1;ADAM29,missense_variant,p.Thr290Lys,ENST00000514159,NM_001130705.1;ADAM29,missense_variant,p.Thr290Lys,ENST00000618444,NM_001278127.1;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000505141,;ADAM29,downstream_gene_variant,,ENST00000502940,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,; A ENST00000615367 Transcript missense_variant 1600/3386 869/2463 290/820 T/K aCa/aAa 1 1 ADAM29 HGNC HGNC:207 protein_coding YES CCDS3823.1 ENSP00000484862 Q9UKF5 A0A140VJD8 UPI000013E9DE NM_001278125.1 deleterious(0) 6/6 PROSITE_profiles:PS50215,hmmpanther:PTHR11905:SF34,hmmpanther:PTHR11905,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 174976394 174976394 C A 1 0 0 0 0 1 0 0 0 291 478 17 2 2 ADAM29 4 174976394 Missense_Mutation SNP C C3N-00580_T 713426 174976394 15238161 296 18431 CENPU 0 . GRCh38 4 184716456 184716456 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.559G>T p.Gly187Ter p.G187* ENST00000281453 6/13 288 130 158 421 421 0 strelka-varscan-mutect CENPU,stop_gained,p.Gly187Ter,ENST00000281453,NM_024629.3;CENPU,stop_gained,p.Gly158Ter,ENST00000514781,;CENPU,upstream_gene_variant,,ENST00000506535,;CENPU,stop_gained,p.Gly187Ter,ENST00000510146,; A ENST00000281453 Transcript stop_gained 630/1998 559/1257 187/418 G/* Gga/Tga 1 -1 CENPU HGNC HGNC:21348 protein_coding YES CCDS3838.1 ENSP00000281453 Q71F23 UPI00001BFAF6 NM_024629.3 6/13 hmmpanther:PTHR32222:SF1,hmmpanther:PTHR32222,Pfam_domain:PF13097 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 184716456 184716456 C A 1 0 0 0 0 0 1 0 0 2951 690 24 2 2 CENPU 4 184716456 Nonsense_Mutation SNP C C3N-00580_T 9740062 184716456 5498099 297 18432 SORBS2 0 . GRCh38 4 185623977 185623977 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1740C>A p.Tyr580Ter p.Y580* ENST00000355634 16/24 340 137 203 307 307 0 strelka-varscan-mutect SORBS2,stop_gained,p.Tyr480Ter,ENST00000284776,NM_021069.4;SORBS2,stop_gained,p.Tyr384Ter,ENST00000418609,NM_001145675.1,NM_001145674.1;SORBS2,stop_gained,p.Tyr580Ter,ENST00000355634,NM_001270771.1;SORBS2,intron_variant,,ENST00000448662,NM_001145672.1;SORBS2,intron_variant,,ENST00000437304,NM_001145673.1;SORBS2,intron_variant,,ENST00000449407,NM_001145670.1;SORBS2,intron_variant,,ENST00000393528,NM_003603.6;SORBS2,intron_variant,,ENST00000319471,NM_001145671.2;SORBS2,intron_variant,,ENST00000319454,;SORBS2,intron_variant,,ENST00000451974,;SORBS2,intron_variant,,ENST00000438278,;SORBS2,downstream_gene_variant,,ENST00000445625,;SORBS2,intron_variant,,ENST00000498125,;SORBS2,downstream_gene_variant,,ENST00000487836,;SORBS2,downstream_gene_variant,,ENST00000495932,;SORBS2,downstream_gene_variant,,ENST00000487184,; T ENST00000355634 Transcript stop_gained 2454/4622 1740/3603 580/1200 Y/* taC/taA 1 -1 SORBS2 HGNC HGNC:24098 protein_coding YES CCDS59482.1 ENSP00000347852 O94875 UPI000198C7F0 NM_001270771.1 16/24 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 185623977 185623977 G T 1 0 0 0 0 0 1 0 0 15250 1140 40 1 1 SORBS2 4 185623977 Nonsense_Mutation SNP G C3N-00580_T 907521 185623977 4590578 298 18433 F11 0 . GRCh38 4 186271664 186271664 + Silent SNP G G C rs762996950 C3N-00580_T C3N-00580_N G G c.111G>C p.= p.T37T ENST00000403665 3/15 559 483 76 574 574 0 strelka-varscan-mutect F11,synonymous_variant,p.=,ENST00000403665,NM_000128.3;F11,synonymous_variant,p.=,ENST00000264692,;F11,synonymous_variant,p.=,ENST00000492972,;F11,upstream_gene_variant,,ENST00000452239,;F11,upstream_gene_variant,,ENST00000514715,; C ENST00000403665 Transcript synonymous_variant 463/2396 111/1878 37/625 T acG/acC rs762996950 1 1 F11 HGNC HGNC:3529 protein_coding YES CCDS3847.1 ENSP00000384957 P03951 UPI000000D8B7 NM_000128.3 3/15 PROSITE_profiles:PS50948,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF258,PROSITE_patterns:PS00495,Gene3D:3.50.4.10,Pfam_domain:PF00024,SMART_domains:SM00223 LOW 1 SNV 1 1 PASS rs762996950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 186271664 186271664 G C 1 0 0 0 0 0 0 0 1 5205 1103 39 4 4 F11 4 186271664 Silent SNP G C3N-00580_T 647687 186271664 3942891 299 18434 FAT1 0 . GRCh38 4 186708803 186708803 + Missense_Mutation SNP C C T rs377127443 C3N-00580_T C3N-00580_N C C c.1025G>A p.Gly342Glu p.G342E ENST00000441802 2/27 269 204 65 216 216 0 strelka-varscan-mutect FAT1,missense_variant,p.Gly342Glu,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Gly342Glu,ENST00000614102,;FAT1,missense_variant,p.Gly342Glu,ENST00000509647,; T ENST00000441802 Transcript missense_variant 1235/14786 1025/13767 342/4588 G/E gGa/gAa rs377127443 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0.02) 2/27 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112 MODERATE 1 SNV 5 1 PASS rs377127443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 186708803 186708803 C T 1 0 0 0 0 1 0 0 0 5549 855 30 3 3 FAT1 4 186708803 Missense_Mutation SNP C C3N-00580_T 437139 186708803 3505752 300 18435 SDHA 0 . GRCh38 5 225506 225506 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.400G>T p.Gly134Trp p.G134W ENST00000264932 4/15 651 542 109 563 563 0 strelka-varscan-mutect SDHA,missense_variant,p.Gly134Trp,ENST00000264932,NM_004168.3;SDHA,missense_variant,p.Gly134Trp,ENST00000504309,;SDHA,intron_variant,,ENST00000510361,NM_001294332.1;SDHA,intron_variant,,ENST00000617470,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,3_prime_UTR_variant,,ENST00000509632,;SDHA,non_coding_transcript_exon_variant,,ENST00000505555,;SDHA,non_coding_transcript_exon_variant,,ENST00000504824,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,upstream_gene_variant,,ENST00000509420,; T ENST00000264932 Transcript missense_variant 515/2390 400/1995 134/664 G/W Ggg/Tgg 1 1 SDHA HGNC HGNC:10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 A0A024QZ30 UPI0000000C2C NM_004168.3 deleterious_low_confidence(0) 4/15 Gene3D:3.50.50.60,Pfam_domain:PF00890,PIRSF_domain:PIRSF000171,hmmpanther:PTHR11632,hmmpanther:PTHR11632:SF51,Superfamily_domains:SSF51905,TIGRFAM_domain:TIGR01812,TIGRFAM_domain:TIGR01816 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 225506 225506 G T 1 0 0 0 0 1 0 0 0 14235 1232 43 2 2 SDHA 5 225506 Missense_Mutation SNP G C3N-00580_T 225506 181312753 301 18436 SLC9A3 0 . GRCh38 5 488454 488454 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.537G>T p.= p.L179L ENST00000264938 3/17 119 100 19 95 95 0 strelka-varscan-mutect SLC9A3,synonymous_variant,p.=,ENST00000264938,NM_004174.2;SLC9A3,synonymous_variant,p.=,ENST00000514375,NM_001284351.1; A ENST00000264938 Transcript synonymous_variant 547/2584 537/2505 179/834 L ctG/ctT 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 3/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 488454 488454 C A 1 0 0 0 0 0 0 0 1 14995 581 21 2 2 SLC9A3 5 488454 Silent SNP C C3N-00580_T 262948 488454 181049805 302 18437 ADCY2 0 . GRCh38 5 7804584 7804584 + Splice_Site SNP G G T C3N-00580_T C3N-00580_N G G c.2776-1G>T p.X926_splice ENST00000338316 600 534 66 435 435 0 strelka-varscan-mutect ADCY2,splice_acceptor_variant,,ENST00000338316,NM_020546.2;ADCY2,splice_acceptor_variant,,ENST00000382531,;ADCY2,splice_acceptor_variant,,ENST00000489501,;ADCY2,splice_acceptor_variant,,ENST00000493243,; T ENST00000338316 Transcript splice_acceptor_variant -/6575 2776/3276 926/1091 COSM1070365 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 21/24 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 7804584 7804584 G T 1 0 0 0 0 0 0 1 0 338 985 34 2 2 ADCY2 5 7804584 Splice_Site SNP G C3N-00580_T 7316130 7804584 173733675 303 18438 C5orf49 0 . GRCh38 5 7835407 7835407 + Missense_Mutation SNP C C A rs369384970 C3N-00580_T C3N-00580_N C C c.239G>T p.Ser80Ile p.S80I ENST00000399810 2/3 270 248 22 165 165 0 strelka-varscan-mutect C5orf49,missense_variant,p.Ser80Ile,ENST00000399810,NM_001089584.2;C5orf49,missense_variant,p.Ser80Ile,ENST00000509627,; A ENST00000399810 Transcript missense_variant 708/2385 239/444 80/147 S/I aGc/aTc rs369384970 1 -1 C5orf49 HGNC HGNC:27028 protein_coding YES CCDS43300.1 ENSP00000382708 A4QMS7 UPI0000160436 NM_001089584.2 deleterious(0.01) 2/3 hmmpanther:PTHR34444,Pfam_domain:PF15074 MODERATE 1 SNV 1 1 PASS rs369384970 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 7835407 7835407 C A 1 0 0 0 0 1 0 0 0 2104 797 28 2 2 C5orf49 5 7835407 Missense_Mutation SNP C C3N-00580_T 30823 7835407 173702852 304 18439 BASP1 0 . GRCh38 5 17275221 17275221 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5G>T p.Gly2Val p.G2V ENST00000322611 2/2 267 136 131 221 221 0 strelka-varscan-mutect BASP1,missense_variant,p.Gly2Val,ENST00000322611,NM_006317.4;BASP1,missense_variant,p.Gly2Val,ENST00000616743,NM_001271606.1;BASP1,missense_variant,p.Gly2Val,ENST00000606445,; T ENST00000322611 Transcript missense_variant 265/1878 5/684 2/227 G/V gGa/gTa 1 1 BASP1 HGNC HGNC:957 protein_coding YES CCDS3888.1 ENSP00000319281 P80723 UPI0000140E98 NM_006317.4 deleterious_low_confidence(0) 2/2 hmmpanther:PTHR23212,hmmpanther:PTHR23212:SF0,Pfam_domain:PF05466 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 17275221 17275221 G T 1 0 0 0 0 1 0 0 0 1469 1174 41 2 2 BASP1 5 17275221 Missense_Mutation SNP G C3N-00580_T 9439814 17275221 164263038 305 18440 CDH6 0 . GRCh38 5 31305403 31305403 + Missense_Mutation SNP C C A rs200424636 C3N-00580_T C3N-00580_N C C c.1229C>A p.Pro410Gln p.P410Q ENST00000265071 7/12 230 194 36 144 144 0 strelka-varscan-mutect CDH6,missense_variant,p.Pro410Gln,ENST00000265071,NM_004932.3;CDH6,missense_variant,p.Pro355Gln,ENST00000514738,;CDH6,downstream_gene_variant,,ENST00000508132,; A ENST00000265071 Transcript missense_variant 1494/8476 1229/2373 410/790 P/Q cCa/cAa rs200424636 1 1 CDH6 HGNC HGNC:1765 protein_coding YES CCDS3894.1 ENSP00000265071 P55285 UPI0000126D9B NM_004932.3 deleterious(0.01) 7/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF322,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS rs200424636 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 31305403 31305403 C A 1 0 0 0 0 1 0 0 0 2817 594 21 2 2 CDH6 5 31305403 Missense_Mutation SNP C C3N-00580_T 14030182 31305403 150232856 306 18441 ADAMTS12 0 . GRCh38 5 33576931 33576931 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.3095T>A p.Leu1032Gln p.L1032Q ENST00000504830 19/24 393 163 230 301 301 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Leu1032Gln,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Leu947Gln,ENST00000352040,;ADAMTS12,downstream_gene_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 3431/8774 3095/4785 1032/1594 L/Q cTg/cAg 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.38) 19/24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 33576931 33576931 A T 1 0 0 0 0 1 0 0 0 301 188 7 4 4 ADAMTS12 5 33576931 Missense_Mutation SNP A C3N-00580_T 2271528 33576931 147961328 307 18442 ADAMTS12 0 . GRCh38 5 33630899 33630899 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1903C>A p.Leu635Ile p.L635I ENST00000504830 13/24 355 163 192 214 214 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Leu635Ile,ENST00000504830,NM_030955.2;ADAMTS12,intron_variant,,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant 2239/8774 1903/4785 635/1594 L/I Ctc/Atc 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 13/24 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 MODERATE 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 33630899 33630899 G T 1 0 0 0 0 1 0 0 0 301 971 34 2 2 ADAMTS12 5 33630899 Missense_Mutation SNP G C3N-00580_T 53968 33630899 147907360 308 18443 SPEF2 0 . GRCh38 5 35691092 35691092 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1580C>T p.Ser527Phe p.S527F ENST00000356031 11/37 453 194 259 277 277 0 strelka-varscan-mutect SPEF2,missense_variant,p.Ser527Phe,ENST00000637569,;SPEF2,missense_variant,p.Ser527Phe,ENST00000440995,;SPEF2,missense_variant,p.Ser527Phe,ENST00000356031,NM_024867.3;SPEF2,missense_variant,p.Ser527Phe,ENST00000509059,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,non_coding_transcript_exon_variant,,ENST00000504054,;SPEF2,non_coding_transcript_exon_variant,,ENST00000503074,; T ENST00000356031 Transcript missense_variant 1734/5681 1580/5469 527/1822 S/F tCc/tTc 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 tolerated(0.1) 11/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 35691092 35691092 C T 1 0 0 0 0 1 0 0 0 15386 855 30 3 3 SPEF2 5 35691092 Missense_Mutation SNP C C3N-00580_T 2060193 35691092 145847167 309 18444 FYB 0 . GRCh38 5 39134927 39134927 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1633G>T p.Glu545Ter p.E545* ENST00000512982 8/19 411 371 40 218 218 0 strelka-varscan-mutect FYB,stop_gained,p.Glu535Ter,ENST00000351578,NM_199335.3;FYB,stop_gained,p.Glu535Ter,ENST00000505428,NM_001465.4;FYB,stop_gained,p.Glu545Ter,ENST00000512982,NM_001243093.1;FYB,stop_gained,p.Glu535Ter,ENST00000515010,; A ENST00000512982 Transcript stop_gained 1719/2747 1633/2520 545/839 E/* Gag/Tag 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 8/19 Gene3D:2.30.30.40,Pfam_domain:PF07653,hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF13,SMART_domains:SM00326,Superfamily_domains:SSF50044 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 39134927 39134927 C A 1 0 0 0 0 0 1 0 0 5995 922 32 2 2 FYB 5 39134927 Nonsense_Mutation SNP C C3N-00580_T 3443835 39134927 142403332 310 18445 PLCXD3 0 . GRCh38 5 41382438 41382438 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.200C>A p.Thr67Asn p.T67N ENST00000377801 2/3 366 313 53 259 259 0 strelka-varscan-mutect PLCXD3,missense_variant,p.Thr67Asn,ENST00000377801,;PLCXD3,missense_variant,p.Thr67Asn,ENST00000328457,NM_001005473.2; T ENST00000377801 Transcript missense_variant 275/7704 200/966 67/321 T/N aCt/aAt 1 -1 PLCXD3 HGNC HGNC:31822 protein_coding YES CCDS34150.1 ENSP00000367032 Q63HM9 UPI0000049DBB tolerated(0.27) 2/3 Gene3D:3.20.20.190,PROSITE_profiles:PS50007,hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF33,SMART_domains:SM00148,Superfamily_domains:SSF51695 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 61 41382438 41382438 G T 1 0 0 0 0 1 0 0 0 12137 1029 36 2 2 PLCXD3 5 41382438 Missense_Mutation SNP G C3N-00580_T 2247511 41382438 140155821 311 18446 HCN1 0 . GRCh38 5 45645409 45645409 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.625G>A p.Asp209Asn p.D209N ENST00000303230 2/8 283 261 22 158 158 0 strelka-varscan-mutect HCN1,missense_variant,p.Asp209Asn,ENST00000303230,NM_021072.3;HCN1,missense_variant,p.Asp209Asn,ENST00000634658,;HCN1,upstream_gene_variant,,ENST00000637256,; T ENST00000303230 Transcript missense_variant 866/9885 625/2673 209/890 D/N Gac/Aac COSM5271836,COSM5403583 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated(0.06) 2/8 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,Superfamily_domains:SSF81324 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 45645409 45645409 C T 1 0 0 0 0 1 0 0 0 6883 855 30 3 3 HCN1 5 45645409 Missense_Mutation SNP C C3N-00580_T 4262971 45645409 135892850 312 18447 ESM1 0 . GRCh38 5 54985475 54985475 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.43C>A p.His15Asn p.H15N ENST00000381405 1/3 94 64 30 132 131 1 strelka-varscan-mutect ESM1,missense_variant,p.His15Asn,ENST00000381405,NM_007036.4;ESM1,missense_variant,p.His15Asn,ENST00000381403,NM_001135604.1;ESM1,missense_variant,p.His15Asn,ENST00000601836,;ESM1,intron_variant,,ENST00000598310,; T ENST00000381405 Transcript missense_variant 189/2169 43/555 15/184 H/N Cac/Aac 1 -1 ESM1 HGNC HGNC:3466 protein_coding YES CCDS3963.1 ENSP00000370812 Q9NQ30 UPI000012A1BA NM_007036.4 tolerated(0.15) 1/3 hmmpanther:PTHR15428,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 54985475 54985475 G T 1 0 0 0 0 1 0 0 0 5114 1377 48 2 2 ESM1 5 54985475 Missense_Mutation SNP G C3N-00580_T 9340066 54985475 126552784 313 18448 RNF180 0 . GRCh38 5 64214179 64214179 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.853A>C p.Ser285Arg p.S285R ENST00000389100 4/8 202 165 37 201 201 0 strelka-varscan-mutect RNF180,missense_variant,p.Ser285Arg,ENST00000389100,NM_001113561.1;RNF180,missense_variant,p.Ser285Arg,ENST00000296615,NM_178532.3;RNF180,downstream_gene_variant,,ENST00000504296,; C ENST00000389100 Transcript missense_variant 925/4906 853/1779 285/592 S/R Agt/Cgt 1 1 RNF180 HGNC HGNC:27752 protein_coding YES CCDS47219.1 ENSP00000373752 Q86T96 UPI0000141201 NM_001113561.1 tolerated(0.07) 4/8 hmmpanther:PTHR23327,hmmpanther:PTHR23327:SF18 MODERATE 1 SNV 1 1 PASS rs1271978809 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 64214179 64214179 A C 1 0 0 0 0 1 0 0 0 13641 188 7 5 5 RNF180 5 64214179 Missense_Mutation SNP A C3N-00580_T 9228704 64214179 117324080 314 18449 NAIP 0 . GRCh38 5 71012703 71012703 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.213G>A p.= p.E71E ENST00000517649 4/17 147 95 52 165 165 0 strelka-varscan-mutect NAIP,synonymous_variant,p.=,ENST00000517649,NM_004536.2;NAIP,synonymous_variant,p.=,ENST00000194097,;NAIP,synonymous_variant,p.=,ENST00000508426,;NAIP,intron_variant,,ENST00000503719,;NAIP,intron_variant,,ENST00000523981,NM_022892.1;NAIP,synonymous_variant,p.=,ENST00000519014,;NAIP,intron_variant,,ENST00000508794,;NAIP,upstream_gene_variant,,ENST00000447012,; T ENST00000517649 Transcript synonymous_variant 504/6124 213/4212 71/1403 E gaG/gaA 1 -1 NAIP HGNC HGNC:7634 protein_coding YES CCDS4009.1 ENSP00000428657 Q13075 UPI000013C609 NM_004536.2 4/17 PROSITE_profiles:PS50143,hmmpanther:PTHR10044,PROSITE_patterns:PS01282,Gene3D:1.10.1170.10,Pfam_domain:PF00653,SMART_domains:SM00238,Superfamily_domains:SSF57924 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 71012703 71012703 C T 1 0 0 0 0 0 0 0 1 10154 796 28 3 3 NAIP 5 71012703 Silent SNP C C3N-00580_T 6798524 71012703 110525556 315 18450 ANKDD1B 0 . GRCh38 5 75620324 75620324 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.307A>G p.Thr103Ala p.T103A ENST00000601380 3/14 132 84 48 121 121 0 strelka-varscan-mutect ANKDD1B,missense_variant,p.Thr103Ala,ENST00000601380,NM_001276713.1;ANKDD1B,intron_variant,,ENST00000506596,; G ENST00000601380 Transcript missense_variant 483/2569 307/1587 103/528 T/A Aca/Gca 1 1 ANKDD1B HGNC HGNC:32525 protein_coding YES CCDS64180.1 ENSP00000471417 A6NHY2 UPI0002A4709F NM_001276713.1 deleterious(0.01) 3/14 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24125,hmmpanther:PTHR24125:SF1,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 75620324 75620324 A G 1 0 0 0 0 1 0 0 0 725 159 6 5 5 ANKDD1B 5 75620324 Missense_Mutation SNP A C3N-00580_T 4607621 75620324 105917935 316 18451 PDE8B 0 . GRCh38 5 77331426 77331426 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.675A>T p.= p.S225S ENST00000264917 5/22 535 465 70 595 595 0 strelka-varscan-mutect PDE8B,synonymous_variant,p.=,ENST00000264917,NM_003719.3;PDE8B,synonymous_variant,p.=,ENST00000340978,NM_001029854.2;PDE8B,synonymous_variant,p.=,ENST00000346042,NM_001029851.2;PDE8B,synonymous_variant,p.=,ENST00000342343,NM_001029853.2;PDE8B,synonymous_variant,p.=,ENST00000333194,NM_001029852.2;PDE8B,synonymous_variant,p.=,ENST00000505926,;PDE8B,synonymous_variant,p.=,ENST00000502945,;PDE8B,5_prime_UTR_variant,,ENST00000503963,; T ENST00000264917 Transcript synonymous_variant 720/5956 675/2658 225/885 S tcA/tcT 1 1 PDE8B HGNC HGNC:8794 protein_coding YES CCDS4037.1 ENSP00000264917 O95263 UPI0000001BBE NM_003719.3 5/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF98 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 77331426 77331426 A T 1 0 0 0 0 0 0 0 1 11742 175 7 4 4 PDE8B 5 77331426 Silent SNP A C3N-00580_T 1711102 77331426 104206833 317 18452 OTP 0 . GRCh38 5 77630484 77630484 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.758C>A p.Ser253Tyr p.S253Y ENST00000306422 3/3 236 177 59 466 466 0 strelka-varscan-mutect OTP,missense_variant,p.Ser253Tyr,ENST00000306422,NM_032109.2; T ENST00000306422 Transcript missense_variant 1897/3669 758/978 253/325 S/Y tCc/tAc 1 -1 OTP HGNC HGNC:8518 protein_coding YES CCDS4039.1 ENSP00000302814 Q5XKR4 UPI0000021CAA NM_032109.2 deleterious(0.04) 3/3 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF316 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 77630484 77630484 G T 1 0 0 0 0 1 0 0 0 11378 1174 41 2 2 OTP 5 77630484 Missense_Mutation SNP G C3N-00580_T 299058 77630484 103907775 318 18453 CMYA5 0 . GRCh38 5 79738725 79738725 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.9960G>T p.Gln3320His p.Q3320H ENST00000446378 2/13 247 178 69 351 351 0 strelka-varscan-mutect CMYA5,missense_variant,p.Gln3320His,ENST00000446378,NM_153610.4;CMYA5,non_coding_transcript_exon_variant,,ENST00000506603,; T ENST00000446378 Transcript missense_variant 9991/12847 9960/12210 3320/4069 Q/H caG/caT 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 deleterious(0.02) 2/13 hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7 MODERATE 1 SNV 5 1 PASS rs1447821740 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 79738725 79738725 G T 1 0 0 0 0 1 0 0 0 3368 933 33 2 2 CMYA5 5 79738725 Missense_Mutation SNP G C3N-00580_T 2108241 79738725 101799534 319 18454 ACOT12 0 . GRCh38 5 81359968 81359968 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.431G>T p.Arg144Met p.R144M ENST00000307624 5/15 97 90 7 251 251 0 strelka-varscan-mutect ACOT12,missense_variant,p.Arg144Met,ENST00000307624,NM_130767.2;ACOT12,missense_variant,p.Arg144Met,ENST00000513751,; A ENST00000307624 Transcript missense_variant 460/2086 431/1668 144/555 R/M aGg/aTg 1 -1 ACOT12 HGNC HGNC:24436 protein_coding YES CCDS4055.1 ENSP00000303246 Q8WYK0 UPI0000126D7B NM_130767.2 deleterious(0) 5/15 Gene3D:3.10.129.10,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF3,Superfamily_domains:SSF54637 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 81359968 81359968 C A 1 0 0 0 0 1 0 0 0 192 681 24 2 2 ACOT12 5 81359968 Missense_Mutation SNP C C3N-00580_T 1621243 81359968 100178291 320 18455 HAPLN1 0 . GRCh38 5 83644558 83644558 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.580C>A p.Leu194Met p.L194M ENST00000274341 4/5 80 66 14 125 125 0 strelka-varscan-mutect HAPLN1,missense_variant,p.Leu194Met,ENST00000274341,NM_001884.3;HAPLN1,missense_variant,p.Leu194Met,ENST00000510978,;HAPLN1,missense_variant,p.Leu194Met,ENST00000508307,;HAPLN1,downstream_gene_variant,,ENST00000504713,;HAPLN1,downstream_gene_variant,,ENST00000503117,; T ENST00000274341 Transcript missense_variant 1431/5607 580/1065 194/354 L/M Ctg/Atg COSM4440967 1 -1 HAPLN1 HGNC HGNC:2380 protein_coding YES CCDS4061.1 ENSP00000274341 P10915 A0A024RAK9 UPI0000131BFF NM_001884.3 deleterious(0) 4/5 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF10,hmmpanther:PTHR22804,PROSITE_patterns:PS01241,Gene3D:3.10.100.10,Pfam_domain:PF00193,SMART_domains:SM00445,Superfamily_domains:SSF56436 1 MODERATE 1 SNV 1 1 1 PASS rs1228942084 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 83644558 83644558 G T 1 0 0 0 0 1 0 0 0 6840 962 34 2 2 HAPLN1 5 83644558 Missense_Mutation SNP G C3N-00580_T 2284590 83644558 97893701 321 18456 EDIL3 0 . GRCh38 5 84060341 84060341 + Missense_Mutation SNP C C A rs368032066 C3N-00580_T C3N-00580_N C C c.1096G>T p.Ala366Ser p.A366S ENST00000296591 9/11 185 139 46 242 242 0 strelka-varscan-mutect EDIL3,missense_variant,p.Ala366Ser,ENST00000296591,NM_005711.4;EDIL3,missense_variant,p.Ala356Ser,ENST00000380138,NM_001278642.1;EDIL3,non_coding_transcript_exon_variant,,ENST00000510271,; A ENST00000296591 Transcript missense_variant 1515/4727 1096/1443 366/480 A/S Gcc/Tcc rs368032066 1 -1 EDIL3 HGNC HGNC:3173 protein_coding YES CCDS4062.1 ENSP00000296591 O43854 UPI000004D126 NM_005711.4 deleterious(0) 9/11 PROSITE_profiles:PS50022,hmmpanther:PTHR10127:SF29,hmmpanther:PTHR10127,PROSITE_patterns:PS01285,Gene3D:2.60.120.260,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS rs368032066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 84060341 84060341 C A 1 0 0 0 0 1 0 0 0 4743 710 25 2 2 EDIL3 5 84060341 Missense_Mutation SNP C C3N-00580_T 415783 84060341 97477918 322 18457 NUDT12 0 . GRCh38 5 103560044 103560044 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.205G>T p.Gly69Trp p.G69W ENST00000230792 2/7 158 127 31 133 133 0 strelka-varscan-mutect NUDT12,missense_variant,p.Gly69Trp,ENST00000230792,NM_031438.3;NUDT12,intron_variant,,ENST00000507423,NM_001300741.1;NUDT12,upstream_gene_variant,,ENST00000515407,;NUDT12,non_coding_transcript_exon_variant,,ENST00000508889,; A ENST00000230792 Transcript missense_variant,splice_region_variant 302/3492 205/1389 69/462 G/W Ggg/Tgg 1 -1 NUDT12 HGNC HGNC:18826 protein_coding YES CCDS4096.1 ENSP00000230792 Q9BQG2 UPI0000073C53 NM_031438.3 deleterious(0.02) 2/7 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 103560044 103560044 C A 1 0 0 0 0 1 0 0 0 10792 695 24 2 2 NUDT12 5 103560044 Missense_Mutation SNP C C3N-00580_T 19499703 103560044 77978215 323 18458 TSSK1B 0 . GRCh38 5 113434511 113434511 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.329A>T p.Glu110Val p.E110V ENST00000390666 1/1 105 72 33 113 113 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Glu110Val,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; A ENST00000390666 Transcript missense_variant 521/2478 329/1104 110/367 E/V gAg/gTg 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 deleterious(0) 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 113434511 113434511 T A 1 0 0 0 0 1 0 0 0 17176 1551 54 4 4 TSSK1B 5 113434511 Missense_Mutation SNP T C3N-00580_T 9874467 113434511 68103748 324 18459 KCNN2 0 . GRCh38 5 114493422 114493422 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1402G>T p.Glu468Ter p.E468* ENST00000512097 8/9 172 113 59 198 198 0 strelka-varscan-mutect KCNN2,stop_gained,p.Glu468Ter,ENST00000512097,;KCNN2,stop_gained,p.Glu468Ter,ENST00000264773,NM_021614.3;KCNN2,stop_gained,p.Glu471Ter,ENST00000631899,;KCNN2,stop_gained,p.Glu120Ter,ENST00000610748,NM_001278204.1;KCNN2,stop_gained,p.Glu120Ter,ENST00000503706,NM_170775.2;RP11-492A10.1,intron_variant,,ENST00000514115,;KCNN2,non_coding_transcript_exon_variant,,ENST00000507750,;KCNN2,3_prime_UTR_variant,,ENST00000505491,;KCNN2,non_coding_transcript_exon_variant,,ENST00000506812,;KCNN2,non_coding_transcript_exon_variant,,ENST00000632892,; T ENST00000512097 Transcript stop_gained 2420/3076 1402/1740 468/579 E/* Gag/Tag 1 1 KCNN2 HGNC HGNC:6291 protein_coding YES CCDS4114.1 ENSP00000427120 Q9H2S1 UPI000013D56A 8/9 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF43,Pfam_domain:PF02888,Gene3D:1.10.287.70,SMART_domains:SM01053,Superfamily_domains:SSF81327 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 114493422 114493422 G T 1 0 0 0 0 0 1 0 0 7995 1175 41 2 2 KCNN2 5 114493422 Nonsense_Mutation SNP G C3N-00580_T 1058911 114493422 67044837 325 18460 AP3S1 0 . GRCh38 5 115913429 115913429 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.521C>A p.Pro174Gln p.P174Q ENST00000316788 6/6 196 178 18 143 143 0 varscan-mutect AP3S1,missense_variant,p.Pro174Gln,ENST00000316788,NM_001284.2;AP3S1,non_coding_transcript_exon_variant,,ENST00000505423,;AP3S1,3_prime_UTR_variant,,ENST00000506430,;AP3S1,non_coding_transcript_exon_variant,,ENST00000395548,; A ENST00000316788 Transcript missense_variant 1078/1730 521/582 174/193 P/Q cCa/cAa 1 1 AP3S1 HGNC HGNC:2013 protein_coding YES CCDS4123.1 ENSP00000325369 Q92572 UPI000002236E NM_001284.2 tolerated_low_confidence(0.19) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 115913429 115913429 C A 1 0 0 0 0 1 0 0 0 865 594 21 2 2 AP3S1 5 115913429 Missense_Mutation SNP C C3N-00580_T 1420007 115913429 65624830 326 18461 FBN2 0 . GRCh38 5 128395221 128395221 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1132G>A p.Glu378Lys p.E378K ENST00000508053 15/71 464 413 51 502 501 1 strelka-varscan-mutect FBN2,missense_variant,p.Glu378Lys,ENST00000508053,;FBN2,missense_variant,p.Glu378Lys,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Glu377Lys,ENST00000619499,;FBN2,missense_variant,p.Glu345Lys,ENST00000508989,; T ENST00000508053 Transcript missense_variant 2107/11132 1132/8739 378/2912 E/K Gag/Aag 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.16) 15/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 128395221 128395221 C T 1 0 0 0 0 1 0 0 0 5566 922 32 3 3 FBN2 5 128395221 Missense_Mutation SNP C C3N-00580_T 12481792 128395221 53143038 327 18462 TRPC7 0 . GRCh38 5 136357323 136357323 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.65G>T p.Arg22Leu p.R22L ENST00000513104 2/12 122 87 35 131 131 0 strelka-varscan-mutect TRPC7,missense_variant,p.Arg22Leu,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Arg22Leu,ENST00000502753,;TRPC7,missense_variant,p.Arg22Leu,ENST00000378459,NM_001167577.1;TRPC7,missense_variant,p.Arg22Leu,ENST00000352189,NM_001167576.1;TRPC7,missense_variant,p.Arg22Leu,ENST00000503275,;TRPC7,missense_variant,p.Arg22Leu,ENST00000514963,; A ENST00000513104 Transcript missense_variant 348/2987 65/2589 22/862 R/L cGt/cTt 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 deleterious(0) 2/12 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9 MODERATE 1 SNV 5 1 PASS rs955730809 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 136357323 136357323 C A 1 0 0 0 0 1 0 0 0 17090 536 19 1 1 TRPC7 5 136357323 Missense_Mutation SNP C C3N-00580_T 7962102 136357323 45180936 328 18463 SIL1 0 . GRCh38 5 138947188 138947188 + Missense_Mutation SNP C C A rs772617071 C3N-00580_T C3N-00580_N C C c.1315G>T p.Asp439Tyr p.D439Y ENST00000394817 10/10 201 152 49 225 225 0 strelka-varscan-mutect SIL1,missense_variant,p.Asp439Tyr,ENST00000394817,NM_022464.4;SIL1,missense_variant,p.Asp439Tyr,ENST00000265195,NM_001037633.1;SIL1,missense_variant,p.Asp446Tyr,ENST00000509534,;SIL1,downstream_gene_variant,,ENST00000505945,;SIL1,non_coding_transcript_exon_variant,,ENST00000515008,;SIL1,downstream_gene_variant,,ENST00000503732,; A ENST00000394817 Transcript missense_variant 1455/1923 1315/1386 439/461 D/Y Gat/Tat rs772617071 1 -1 SIL1 HGNC HGNC:24624 protein_coding YES CCDS4209.1 ENSP00000378294 Q9H173 A0A0S2Z6B4 UPI000003ED21 NM_022464.4 deleterious(0.04) 10/10 hmmpanther:PTHR19316:SF6,hmmpanther:PTHR19316 MODERATE 1 SNV 1 1 PASS rs772617071 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 138947188 138947188 C A 1 0 0 0 0 1 0 0 0 14585 855 30 2 2 SIL1 5 138947188 Missense_Mutation SNP C C3N-00580_T 2589865 138947188 42591071 329 18464 MATR3 0 . GRCh38 5 139308124 139308124 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.709G>T p.Gly237Cys p.G237C ENST00000618441 2/15 265 191 74 322 318 4 strelka-varscan-mutect MATR3,missense_variant,p.Gly237Cys,ENST00000394800,;MATR3,missense_variant,p.Gly237Cys,ENST00000618441,NM_001194955.1;MATR3,missense_variant,p.Gly237Cys,ENST00000394805,NM_018834.5;MATR3,missense_variant,p.Gly237Cys,ENST00000502929,;MATR3,missense_variant,p.Gly237Cys,ENST00000361059,NM_199189.2;MATR3,missense_variant,p.Gly237Cys,ENST00000509990,NM_001194954.1;MATR3,missense_variant,p.Gly237Cys,ENST00000510056,;MATR3,missense_variant,p.Gly237Cys,ENST00000504045,;MATR3,missense_variant,p.Gly11Cys,ENST00000515833,;MATR3,intron_variant,,ENST00000620916,;MATR3,intron_variant,,ENST00000502499,;MATR3,intron_variant,,ENST00000503811,NM_001194956.1;MATR3,intron_variant,,ENST00000504203,NM_001282278.1;MATR3,intron_variant,,ENST00000509644,;MATR3,intron_variant,,ENST00000506147,;MATR3,intron_variant,,ENST00000512107,;MATR3,intron_variant,,ENST00000512876,;MATR3,intron_variant,,ENST00000514528,;MATR3,intron_variant,,ENST00000511249,;MATR3,intron_variant,,ENST00000513678,;MATR3,intron_variant,,ENST00000504311,;MATR3,downstream_gene_variant,,ENST00000504023,;MATR3,downstream_gene_variant,,ENST00000503340,;MATR3,downstream_gene_variant,,ENST00000505016,;MATR3,downstream_gene_variant,,ENST00000514694,;MATR3,downstream_gene_variant,,ENST00000514488,;MATR3,downstream_gene_variant,,ENST00000508689,;MATR3,downstream_gene_variant,,ENST00000511378,;MATR3,intron_variant,,ENST00000511978,;MATR3,intron_variant,,ENST00000509918,;MATR3,intron_variant,,ENST00000504643,;MATR3,intron_variant,,ENST00000513121,;MATR3,intron_variant,,ENST00000507860,;MATR3,upstream_gene_variant,,ENST00000505625,;MATR3,downstream_gene_variant,,ENST00000502394,;MATR3,upstream_gene_variant,,ENST00000514402,; T ENST00000618441 Transcript missense_variant 1165/5282 709/2544 237/847 G/C Ggt/Tgt 1 1 MATR3 EntrezGene HGNC:6912 protein_coding YES CCDS4210.1 ENSP00000482895 UPI0000000DEE NM_001194955.1 tolerated(0.12) 2/15 hmmpanther:PTHR15592 MODERATE SNV 1 1 PASS . . 0 162 0 0 48 0 0 0 -20 0 0 1 0 0 T 3 4 61 139308124 139308124 G T 1 0 0 0 0 1 0 0 0 9263 1348 47 2 2 MATR3 5 139308124 Missense_Mutation SNP G C3N-00580_T 360936 139308124 42230135 330 18465 PCDHA8 0 . GRCh38 5 140841595 140841595 + Missense_Mutation SNP C C A rs566154248 C3N-00580_T C3N-00580_N C C c.274C>A p.Arg92Ser p.R92S ENST00000531613 1/4 685 488 197 907 907 0 strelka-varscan-mutect PCDHA8,missense_variant,p.Arg92Ser,ENST00000531613,NM_018911.2;PCDHA8,missense_variant,p.Arg92Ser,ENST00000378123,NM_031856.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA7,downstream_gene_variant,,ENST00000356878,NM_031852.1; A ENST00000531613 Transcript missense_variant 274/5260 274/2853 92/950 R/S Cgc/Agc rs566154248 1 1 PCDHA8 HGNC HGNC:8674 protein_coding YES CCDS54919.1 ENSP00000434655 Q9Y5H6 UPI00001273D0 NM_018911.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF125,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs566154248 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 140841595 140841595 C A 1 0 0 0 0 1 0 0 0 11617 652 23 1 1 PCDHA8 5 140841595 Missense_Mutation SNP C C3N-00580_T 1533471 140841595 40696664 331 18466 PCDHA10 0 . GRCh38 5 140856516 140856516 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.468A>G p.= p.A156A ENST00000307360 1/4 329 253 76 391 391 0 strelka-varscan-mutect PCDHA10,synonymous_variant,p.=,ENST00000562220,NM_031859.2;PCDHA10,synonymous_variant,p.=,ENST00000307360,NM_018901.3;PCDHA10,synonymous_variant,p.=,ENST00000506939,NM_031860.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,downstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA14,upstream_gene_variant,,ENST00000506751,; G ENST00000307360 Transcript synonymous_variant 468/5254 468/2847 156/948 A gcA/gcG 1 1 PCDHA10 HGNC HGNC:8664 protein_coding YES CCDS54921.1 ENSP00000304234 Q9Y5I2 UPI00001273D3 NM_018901.3 1/4 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF124,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 140856516 140856516 A G 1 0 0 0 0 0 0 0 1 11607 204 8 5 5 PCDHA10 5 140856516 Silent SNP A C3N-00580_T 14921 140856516 40681743 332 18467 PCDHB2 0 . GRCh38 5 141096532 141096532 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1742C>A p.Ala581Glu p.A581E ENST00000194155 1/1 317 218 99 367 367 0 strelka-varscan-mutect PCDHB2,missense_variant,p.Ala581Glu,ENST00000194155,NM_018936.3;PCDHB2,3_prime_UTR_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000624874,;PCDHB2,downstream_gene_variant,,ENST00000625033,;PCDHB2,upstream_gene_variant,,ENST00000624994,;AC005754.7,downstream_gene_variant,,ENST00000607216,;CTC-270D5.1,upstream_gene_variant,,ENST00000623615,;AC005754.7,downstream_gene_variant,,ENST00000625128,;CTC-270D5.1,upstream_gene_variant,,ENST00000623741,;AC005754.7,downstream_gene_variant,,ENST00000625066,;AC005754.7,downstream_gene_variant,,ENST00000624802,; A ENST00000194155 Transcript missense_variant 1955/4126 1742/2397 581/798 A/E gCg/gAg 1 1 PCDHB2 HGNC HGNC:8687 protein_coding YES CCDS4244.1 ENSP00000194155 Q9Y5E7 UPI00001273DC NM_018936.3 deleterious_low_confidence(0.01) 1/1 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 141096532 141096532 C A 1 0 0 0 0 1 0 0 0 11629 768 27 1 1 PCDHB2 5 141096532 Missense_Mutation SNP C C3N-00580_T 240016 141096532 40441727 333 18468 PCDHB4 0 . GRCh38 5 141123993 141123993 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1995C>T p.= p.F665F ENST00000194152 1/1 458 337 121 602 602 0 strelka-varscan-mutect PCDHB4,synonymous_variant,p.=,ENST00000194152,NM_018938.3;AC005754.8,downstream_gene_variant,,ENST00000606030,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB4,non_coding_transcript_exon_variant,,ENST00000623478,; T ENST00000194152 Transcript synonymous_variant 2195/3825 1995/2388 665/795 F ttC/ttT 1 1 PCDHB4 HGNC HGNC:8689 protein_coding YES CCDS4246.1 ENSP00000194152 Q9Y5E5 UPI00001273DF NM_018938.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF55,SMART_domains:SM00112 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 141123993 141123993 C T 1 0 0 0 0 0 0 0 1 11631 912 32 3 3 PCDHB4 5 141123993 Silent SNP C C3N-00580_T 27461 141123993 40414266 334 18469 PCDHB5 0 . GRCh38 5 141137595 141137595 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2161G>T p.Val721Phe p.V721F ENST00000231134 1/1 288 217 71 335 335 0 strelka-varscan-mutect PCDHB5,missense_variant,p.Val721Phe,ENST00000231134,NM_015669.4;PCDHB5,downstream_gene_variant,,ENST00000623915,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; T ENST00000231134 Transcript missense_variant 2378/3408 2161/2388 721/795 V/F Gtc/Ttc 1 1 PCDHB5 HGNC HGNC:8690 protein_coding YES CCDS4247.1 ENSP00000231134 Q9Y5E4 UPI0000169DEA NM_015669.4 tolerated_low_confidence(0.19) 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 141137595 141137595 G T 1 0 0 0 0 1 0 0 0 11632 1261 44 2 2 PCDHB5 5 141137595 Missense_Mutation SNP G C3N-00580_T 13602 141137595 40400664 335 18470 PCDHB7 0 . GRCh38 5 141174380 141174380 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1545C>A p.= p.A515A ENST00000231137 1/1 855 680 175 1031 1031 0 strelka-varscan-mutect PCDHB7,synonymous_variant,p.=,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;AC005754.7,non_coding_transcript_exon_variant,,ENST00000624802,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; A ENST00000231137 Transcript synonymous_variant 1762/3765 1545/2382 515/793 A gcC/gcA 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW SNV 1 PASS rs1301232056 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 141174380 141174380 C A 1 0 0 0 0 0 0 0 1 11634 610 22 2 2 PCDHB7 5 141174380 Silent SNP C C3N-00580_T 36785 141174380 40363879 336 18471 PCDHB8 0 . GRCh38 5 141178047 141178047 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.13G>A p.Gly5Arg p.G5R ENST00000239444 1/1 387 327 60 493 493 0 strelka-varscan-mutect PCDHB8,missense_variant,p.Gly5Arg,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,non_coding_transcript_exon_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; A ENST00000239444 Transcript missense_variant 258/2740 13/2406 5/801 G/R Ggg/Agg 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 tolerated_low_confidence(0.54) 1/1 hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 141178047 141178047 G A 1 0 0 0 0 1 0 0 0 11635 1116 39 1 1 PCDHB8 5 141178047 Missense_Mutation SNP G C3N-00580_T 3667 141178047 40360212 337 18472 PCDHB10 0 . GRCh38 5 141194217 141194217 + Missense_Mutation SNP C C A rs549814048 C3N-00580_T C3N-00580_N C C c.1665C>A p.Asn555Lys p.N555K ENST00000239446 1/1 396 306 90 437 436 1 strelka-varscan-mutect PCDHB10,missense_variant,p.Asn555Lys,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,upstream_gene_variant,,ENST00000625144,; A ENST00000239446 Transcript missense_variant 1865/3290 1665/2403 555/800 N/K aaC/aaA rs549814048 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 deleterious_low_confidence(0.01) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE SNV 1 PASS rs549814048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 141194217 141194217 C A 1 0 0 0 0 1 0 0 0 11622 535 19 1 1 PCDHB10 5 141194217 Missense_Mutation SNP C C3N-00580_T 16170 141194217 40344042 338 18473 PCDHGA2 0 . GRCh38 5 141340497 141340497 + Missense_Mutation SNP C C A rs758184570 C3N-00580_T C3N-00580_N C C c.1526C>A p.Ser509Tyr p.S509Y ENST00000394576 1/4 158 112 46 235 235 0 strelka-varscan-mutect PCDHGA2,missense_variant,p.Ser509Tyr,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Ser509Tyr,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; A ENST00000394576 Transcript missense_variant 1526/4605 1526/2799 509/932 S/Y tCc/tAc rs758184570 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs758184570 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 141340497 141340497 C A 1 0 0 0 0 1 0 0 0 11641 855 30 2 2 PCDHGA2 5 141340497 Missense_Mutation SNP C C3N-00580_T 146280 141340497 40197762 339 18474 PCDHGB2 0 . GRCh38 5 141360907 141360907 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.772G>T p.Gly258Cys p.G258C ENST00000522605 1/4 175 139 36 236 236 0 strelka-varscan-mutect PCDHGB2,missense_variant,p.Gly258Cys,ENST00000522605,NM_018923.2;PCDHGB2,missense_variant,p.Gly258Cys,ENST00000622527,NM_032096.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA5,upstream_gene_variant,,ENST00000518069,NM_018918.2;PCDHGA5,upstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA4,downstream_gene_variant,,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000522605 Transcript missense_variant 772/4602 772/2796 258/931 G/C Ggc/Tgc 1 1 PCDHGB2 HGNC HGNC:8709 protein_coding YES CCDS54924.1 ENSP00000429018 Q9Y5G2 UPI000006EE67 NM_018923.2 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF73,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 141360907 141360907 G T 1 0 0 0 0 1 0 0 0 11650 1232 43 2 2 PCDHGB2 5 141360907 Missense_Mutation SNP G C3N-00580_T 20410 141360907 40177352 340 18475 PCDHGB3 0 . GRCh38 5 141372729 141372729 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2335G>T p.Asp779Tyr p.D779Y ENST00000576222 1/4 189 154 35 263 263 0 strelka-varscan-mutect PCDHGB3,missense_variant,p.Asp779Tyr,ENST00000576222,NM_018924.4;PCDHGB3,missense_variant,p.Asp779Tyr,ENST00000618934,NM_032097.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,upstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGA6,upstream_gene_variant,,ENST00000517434,NM_018919.2;PCDHGA5,downstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000576222 Transcript missense_variant 2466/4727 2335/2790 779/929 D/Y Gat/Tat 1 1 PCDHGB3 HGNC HGNC:8710 protein_coding YES CCDS58980.1 ENSP00000461862 Q9Y5G1 UPI0000EE35B5 NM_018924.4 deleterious(0) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 141372729 141372729 G T 1 0 0 0 0 1 0 0 0 11651 942 33 2 2 PCDHGB3 5 141372729 Missense_Mutation SNP G C3N-00580_T 11822 141372729 40165530 341 18476 PCDH1 0 . GRCh38 5 141864128 141864128 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2203A>T p.Thr735Ser p.T735S ENST00000287008 3/5 105 56 49 60 60 0 strelka-varscan-mutect PCDH1,missense_variant,p.Thr735Ser,ENST00000287008,NM_032420.3;PCDH1,missense_variant,p.Thr735Ser,ENST00000394536,NM_001278613.1,NM_002587.4;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,downstream_gene_variant,,ENST00000514773,;PCDH1,non_coding_transcript_exon_variant,,ENST00000357517,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,downstream_gene_variant,,ENST00000505937,; A ENST00000287008 Transcript missense_variant 2351/4793 2203/3714 735/1237 T/S Acg/Tcg 1 -1 PCDH1 HGNC HGNC:8655 protein_coding YES CCDS4267.1 ENSP00000287008 Q08174 UPI000016158F NM_032420.3 deleterious(0.04) 3/5 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF326,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999954 1 1 1 0 A 3 1 61 141864128 141864128 T A 1 0 0 0 0 1 0 0 0 11593 1667 58 4 4 PCDH1 5 141864128 Missense_Mutation SNP T C3N-00580_T 491399 141864128 39674131 342 18477 PPARGC1B 0 . GRCh38 5 149833319 149833319 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1246G>C p.Val416Leu p.V416L ENST00000309241 5/12 306 169 137 238 238 0 strelka-varscan-mutect PPARGC1B,missense_variant,p.Val416Leu,ENST00000309241,NM_133263.3;PPARGC1B,missense_variant,p.Val416Leu,ENST00000394320,;PPARGC1B,missense_variant,p.Val352Leu,ENST00000403750,NM_001172699.1;PPARGC1B,missense_variant,p.Val377Leu,ENST00000360453,NM_001172698.1;PPARGC1B,missense_variant,p.Val103Leu,ENST00000434684,; C ENST00000309241 Transcript missense_variant 1278/10568 1246/3072 416/1023 V/L Gtg/Ctg 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 tolerated(0.18) 5/12 hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 MODERATE 1 SNV 1 1 PASS rs1202471627 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 149833319 149833319 G C 1 0 0 0 0 1 0 0 0 12410 1261 44 4 4 PPARGC1B 5 149833319 Missense_Mutation SNP G C3N-00580_T 7969191 149833319 31704940 343 18478 NDST1 0 . GRCh38 5 150521507 150521507 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.253G>T p.Val85Leu p.V85L ENST00000261797 2/15 890 696 194 731 731 0 strelka-varscan-mutect NDST1,missense_variant,p.Val85Leu,ENST00000261797,NM_001543.4;NDST1,missense_variant,p.Val85Leu,ENST00000523767,NM_001301063.1;NDST1,missense_variant,p.Val85Leu,ENST00000519157,;NDST1,downstream_gene_variant,,ENST00000522491,;NDST1,downstream_gene_variant,,ENST00000518299,;NDST1,downstream_gene_variant,,ENST00000518346,;NDST1,downstream_gene_variant,,ENST00000524161,; T ENST00000261797 Transcript missense_variant 755/8030 253/2649 85/882 V/L Gtg/Ttg 1 1 NDST1 HGNC HGNC:7680 protein_coding YES CCDS34277.1 ENSP00000261797 P52848 UPI000012CDA5 NM_001543.4 deleterious(0.02) 2/15 Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF30 MODERATE 1 SNV 1 1 PASS rs1045644220 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 150521507 150521507 G T 1 0 0 0 0 1 0 0 0 10276 1261 44 2 2 NDST1 5 150521507 Missense_Mutation SNP G C3N-00580_T 688188 150521507 31016752 344 18479 FAT2 0 . GRCh38 5 151566371 151566371 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2561G>T p.Arg854Met p.R854M ENST00000261800 1/23 163 131 32 185 185 0 strelka-varscan-mutect FAT2,missense_variant,p.Arg854Met,ENST00000261800,NM_001447.2; A ENST00000261800 Transcript missense_variant 2574/14534 2561/13050 854/4349 R/M aGg/aTg 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 tolerated(0.06) 1/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 151566371 151566371 C A 1 0 0 0 0 1 0 0 0 5550 681 24 2 2 FAT2 5 151566371 Missense_Mutation SNP C C3N-00580_T 1044864 151566371 29971888 345 18480 FAT2 0 . GRCh38 5 151566530 151566530 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.2402C>T p.Ser801Phe p.S801F ENST00000261800 1/23 162 122 40 171 171 0 strelka-varscan-mutect FAT2,missense_variant,p.Ser801Phe,ENST00000261800,NM_001447.2; A ENST00000261800 Transcript missense_variant 2415/14534 2402/13050 801/4349 S/F tCc/tTc 1 -1 FAT2 HGNC HGNC:3596 protein_coding YES CCDS4317.1 ENSP00000261800 Q9NYQ8 UPI0000055B22 NM_001447.2 deleterious(0) 1/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF37,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 151566530 151566530 G A 1 0 0 0 0 1 0 0 0 5550 1174 41 3 3 FAT2 5 151566530 Missense_Mutation SNP G C3N-00580_T 159 151566530 29971729 346 18481 GLRA1 0 . GRCh38 5 151855170 151855170 + Nonsense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.567T>A p.Tyr189Ter p.Y189* ENST00000455880 6/9 364 286 78 334 334 0 strelka-varscan-mutect GLRA1,stop_gained,p.Tyr189Ter,ENST00000274576,NM_000171.3,NM_001292000.1;GLRA1,stop_gained,p.Tyr189Ter,ENST00000455880,NM_001146040.1;GLRA1,non_coding_transcript_exon_variant,,ENST00000471351,;GLRA1,3_prime_UTR_variant,,ENST00000462581,;RP11-54C4.2,downstream_gene_variant,,ENST00000603996,; T ENST00000455880 Transcript stop_gained 854/1707 567/1374 189/457 Y/* taT/taA 1 -1 GLRA1 HGNC HGNC:4326 protein_coding YES CCDS54942.1 ENSP00000411593 P23415 UPI0000DA6BF2 NM_001146040.1 6/9 hmmpanther:PTHR18945:SF213,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 151855170 151855170 A T 1 0 0 0 0 0 1 0 0 6333 456 16 4 4 GLRA1 5 151855170 Nonsense_Mutation SNP A C3N-00580_T 288640 151855170 29683089 347 18482 GRIA1 0 . GRCh38 5 153811225 153811225 + Nonstop_Mutation SNP A A C C3N-00580_T C3N-00580_N A A c.2751A>C p.Ter917TyrextTer52 p.*917Yext*52 ENST00000518783 16/16 270 240 30 211 211 0 strelka-varscan-mutect GRIA1,stop_lost,p.Ter907TyrextTer52,ENST00000285900,NM_000827.3;GRIA1,stop_lost,p.Ter917TyrextTer52,ENST00000518783,NM_001258021.1;GRIA1,stop_lost,p.Ter907TyrextTer52,ENST00000340592,NM_001114183.1,NM_001258020.1;GRIA1,stop_lost,p.Ter838TyrextTer52,ENST00000521843,NM_001258023.1;GRIA1,stop_lost,p.Ter917TyrextTer?,ENST00000448073,NM_001258022.1;GRIA1,stop_lost,p.Ter827TyrextTer?,ENST00000518142,NM_001258019.1; C ENST00000518783 Transcript stop_lost 2778/5233 2751/2751 917/916 */Y taA/taC COSM1208882,COSM1208883 1 1 GRIA1 HGNC HGNC:4571 protein_coding YES CCDS58987.1 ENSP00000428994 P42261 UPI0001E8F433 NM_001258021.1 16/16 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 61 153811225 153811225 A C 1 0 0 0 0 0 0 0 0 6647 50 2 5 5 GRIA1 5 153811225 Nonstop_Mutation SNP A C3N-00580_T 1956055 153811225 27727034 348 18483 HAVCR2 0 . GRCh38 5 157104678 157104678 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.466G>T p.Gly156Ter p.G156* ENST00000307851 3/7 183 149 34 122 122 0 strelka-varscan-mutect HAVCR2,stop_gained,p.Gly156Ter,ENST00000307851,NM_032782.4;HAVCR2,stop_gained,p.Gly39Ter,ENST00000524219,;HAVCR2,intron_variant,,ENST00000522593,;CTB-120L21.1,upstream_gene_variant,,ENST00000517708,;HAVCR2,downstream_gene_variant,,ENST00000517358,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000521665,;HAVCR2,downstream_gene_variant,,ENST00000522902,; A ENST00000307851 Transcript stop_gained 1197/2907 466/906 156/301 G/* Gga/Tga 1 -1 HAVCR2 HGNC HGNC:18437 protein_coding YES CCDS4333.1 ENSP00000312002 Q8TDQ0 UPI000011AAFA NM_032782.4 3/7 hmmpanther:PTHR15498:SF45,hmmpanther:PTHR15498 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 157104678 157104678 C A 1 0 0 0 0 0 1 0 0 6860 632 22 2 2 HAVCR2 5 157104678 Nonsense_Mutation SNP C C3N-00580_T 3293453 157104678 24433581 349 18484 HAVCR2 0 . GRCh38 5 157104735 157104735 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.409G>T p.Ala137Ser p.A137S ENST00000307851 3/7 198 125 73 113 113 0 strelka-varscan-mutect HAVCR2,missense_variant,p.Ala137Ser,ENST00000307851,NM_032782.4;HAVCR2,missense_variant,p.Ala20Ser,ENST00000524219,;HAVCR2,intron_variant,,ENST00000522593,;CTB-120L21.1,upstream_gene_variant,,ENST00000517708,;HAVCR2,downstream_gene_variant,,ENST00000517358,;HAVCR2,non_coding_transcript_exon_variant,,ENST00000521665,;HAVCR2,downstream_gene_variant,,ENST00000522902,; A ENST00000307851 Transcript missense_variant 1140/2907 409/906 137/301 A/S Gca/Tca 1 -1 HAVCR2 HGNC HGNC:18437 protein_coding YES CCDS4333.1 ENSP00000312002 Q8TDQ0 UPI000011AAFA NM_032782.4 deleterious(0.03) 3/7 hmmpanther:PTHR15498:SF45,hmmpanther:PTHR15498 MODERATE 1 SNV 1 1 PASS rs1241964348 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 157104735 157104735 C A 1 0 0 0 0 1 0 0 0 6860 710 25 2 2 HAVCR2 5 157104735 Missense_Mutation SNP C C3N-00580_T 57 157104735 24433524 350 18485 FAM71B 0 . GRCh38 5 157165583 157165583 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.586G>A p.Glu196Lys p.E196K ENST00000302938 1/2 67 54 13 42 42 0 strelka-varscan-mutect FAM71B,missense_variant,p.Glu196Lys,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,; T ENST00000302938 Transcript missense_variant 682/2515 586/1818 196/605 E/K Gaa/Aaa COSM1064909 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 deleterious(0.03) 1/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999506 1 1 1 0 T 3 4 61 157165583 157165583 C T 1 0 0 0 0 1 0 0 0 5472 893 31 1 1 FAM71B 5 157165583 Missense_Mutation SNP C C3N-00580_T 60848 157165583 24372676 351 18486 CYFIP2 0 . GRCh38 5 157339168 157339168 + Missense_Mutation SNP G G T rs377031549 C3N-00580_T C3N-00580_N G G c.2572G>T p.Ala858Ser p.A858S ENST00000616178 23/32 318 216 102 299 299 0 strelka-varscan-mutect CYFIP2,missense_variant,p.Ala807Ser,ENST00000521420,NM_001291721.1;CYFIP2,missense_variant,p.Ala833Ser,ENST00000618329,NM_014376.3;CYFIP2,missense_variant,p.Ala858Ser,ENST00000616178,NM_001291722.1;CYFIP2,missense_variant,p.Ala833Ser,ENST00000620254,NM_001037333.2;CYFIP2,missense_variant,p.Ala697Ser,ENST00000435847,;CYFIP2,missense_variant,p.Ala637Ser,ENST00000522463,;FNDC9,downstream_gene_variant,,ENST00000312349,NM_001001343.3;FNDC9,downstream_gene_variant,,ENST00000520782,;CYFIP2,non_coding_transcript_exon_variant,,ENST00000520424,; T ENST00000616178 Transcript missense_variant 2712/4210 2572/3837 858/1278 A/S Gcc/Tcc rs377031549 1 1 CYFIP2 HGNC HGNC:13760 protein_coding YES CCDS78077.1 ENSP00000479719 Q96F07 UPI0000DC89D8 NM_001291722.1 tolerated(0.52) 23/32 Pfam_domain:PF05994,hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF1 MODERATE 1 SNV 1 1 PASS rs377031549 . 0 205 0 0 5 0 0 0 -20 0.9004577 1 1 1 0 T 3 4 61 157339168 157339168 G T 1 0 0 0 0 1 0 0 0 3941 1087 38 1 1 CYFIP2 5 157339168 Missense_Mutation SNP G C3N-00580_T 173585 157339168 24199091 352 18487 WWC1 0 . GRCh38 5 168385383 168385383 + Silent SNP C C G novel C3N-00580_T C3N-00580_N C C c.402C>G p.= p.V134V ENST00000521089 3/23 293 238 55 258 258 0 strelka-varscan-mutect WWC1,synonymous_variant,p.=,ENST00000265293,NM_015238.2;WWC1,synonymous_variant,p.=,ENST00000393895,;WWC1,synonymous_variant,p.=,ENST00000521089,NM_001161662.1,NM_001161661.1;WWC1,non_coding_transcript_exon_variant,,ENST00000523043,;WWC1,non_coding_transcript_exon_variant,,ENST00000519859,; G ENST00000521089 Transcript synonymous_variant 405/3562 402/3360 134/1119 V gtC/gtG 1 1 WWC1 HGNC HGNC:29435 protein_coding YES CCDS54945.1 ENSP00000427772 Q8IX03 UPI00017A7149 NM_001161662.1,NM_001161661.1 3/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14791,hmmpanther:PTHR14791:SF22 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 168385383 168385383 C G 1 0 0 0 0 0 0 0 1 17969 900 32 4 4 WWC1 5 168385383 Silent SNP C C3N-00580_T 11046215 168385383 13152876 353 18488 SNCB 0 . GRCh38 5 176626407 176626407 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.273T>A p.= p.T91T ENST00000310112 5/7 670 594 76 630 630 0 strelka-varscan-mutect SNCB,synonymous_variant,p.=,ENST00000614675,NM_001318034.1;SNCB,synonymous_variant,p.=,ENST00000310112,NM_001001502.1;SNCB,synonymous_variant,p.=,ENST00000393693,NM_003085.3;SNCB,synonymous_variant,p.=,ENST00000510387,;SNCB,synonymous_variant,p.=,ENST00000506696,;EIF4E1B,upstream_gene_variant,,ENST00000318682,NM_001099408.1;EIF4E1B,upstream_gene_variant,,ENST00000510660,;MIR4281,downstream_gene_variant,,ENST00000580852,;EIF4E1B,upstream_gene_variant,,ENST00000510473,;SNCB,non_coding_transcript_exon_variant,,ENST00000508006,;EIF4E1B,upstream_gene_variant,,ENST00000515458,; T ENST00000310112 Transcript synonymous_variant 524/1383 273/405 91/134 T acT/acA 1 -1 SNCB HGNC HGNC:11140 protein_coding YES CCDS4406.1 ENSP00000308057 Q16143 UPI000003173C NM_001001502.1 5/7 hmmpanther:PTHR13820,hmmpanther:PTHR13820:SF4,Pfam_domain:PF01387,Gene3D:1xq8A00,Superfamily_domains:0053543,Prints_domain:PR01213 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 176626407 176626407 A T 1 0 0 0 0 0 0 0 1 15163 175 7 4 4 SNCB 5 176626407 Silent SNP A C3N-00580_T 8241024 176626407 4911852 354 18489 MAML1 0 . GRCh38 5 179765828 179765828 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.818A>G p.Glu273Gly p.E273G ENST00000292599 2/5 214 144 70 211 211 0 strelka-varscan-mutect MAML1,missense_variant,p.Glu273Gly,ENST00000292599,NM_014757.4;MAML1,non_coding_transcript_exon_variant,,ENST00000503050,;MAML1,upstream_gene_variant,,ENST00000507385,; G ENST00000292599 Transcript missense_variant 1081/5723 818/3051 273/1016 E/G gAg/gGg 1 1 MAML1 HGNC HGNC:13632 protein_coding YES CCDS34315.1 ENSP00000292599 Q92585 UPI0000071286 NM_014757.4 deleterious(0) 2/5 hmmpanther:PTHR15692:SF19,hmmpanther:PTHR15692 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 179765828 179765828 A G 1 0 0 0 0 1 0 0 0 9126 304 11 5 5 MAML1 5 179765828 Missense_Mutation SNP A C3N-00580_T 3139421 179765828 1772431 355 18490 RASGEF1C 0 . GRCh38 5 180138016 180138016 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.37C>G p.Pro13Ala p.P13A ENST00000393371 1/13 69 43 26 87 87 0 strelka-varscan-mutect RASGEF1C,missense_variant,p.Pro13Ala,ENST00000393371,;RASGEF1C,missense_variant,p.Pro13Ala,ENST00000361132,NM_175062.3;RASGEF1C,5_prime_UTR_variant,,ENST00000615330,;RASGEF1C,upstream_gene_variant,,ENST00000522500,;RASGEF1C,upstream_gene_variant,,ENST00000519883,;RASGEF1C,upstream_gene_variant,,ENST00000520209,; C ENST00000393371 Transcript missense_variant 334/2395 37/1401 13/466 P/A Cca/Gca 1 -1 RASGEF1C HGNC HGNC:27400 protein_coding YES CCDS4452.1 ENSP00000377037 Q8N431 UPI0000037308 deleterious(0.02) 1/13 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF186 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 61 180138016 180138016 G C 1 0 0 0 0 1 0 0 0 13232 1232 43 4 4 RASGEF1C 5 180138016 Missense_Mutation SNP G C3N-00580_T 372188 180138016 1400243 356 18491 GFPT2 0 . GRCh38 5 180316796 180316796 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1120G>T p.Gly374Cys p.G374C ENST00000253778 12/19 199 145 54 241 241 0 strelka-varscan-mutect GFPT2,missense_variant,p.Gly374Cys,ENST00000253778,NM_005110.2;GFPT2,downstream_gene_variant,,ENST00000518906,;GFPT2,non_coding_transcript_exon_variant,,ENST00000520165,;GFPT2,downstream_gene_variant,,ENST00000518185,;GFPT2,downstream_gene_variant,,ENST00000510122,; A ENST00000253778 Transcript missense_variant 1290/3093 1120/2049 374/682 G/C Ggc/Tgc 1 -1 GFPT2 HGNC HGNC:4242 protein_coding YES CCDS43411.1 ENSP00000253778 O94808 A0A0S2Z4X9 UPI000014F5AC NM_005110.2 deleterious(0) 12/19 Gene3D:3.40.50.10490,Pfam_domain:PF01380,PROSITE_profiles:PS51464,hmmpanther:PTHR10937,hmmpanther:PTHR10937:SF10,Superfamily_domains:SSF53697,TIGRFAM_domain:TIGR01135 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 180316796 180316796 C A 1 0 0 0 0 1 0 0 0 6220 594 21 2 2 GFPT2 5 180316796 Missense_Mutation SNP C C3N-00580_T 178780 180316796 1221463 357 18492 FLT4 0 . GRCh38 5 180616906 180616906 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.3090C>G p.= p.S1030S ENST00000261937 22/30 599 437 162 688 688 0 strelka-varscan-mutect FLT4,synonymous_variant,p.=,ENST00000261937,NM_182925.4;FLT4,synonymous_variant,p.=,ENST00000393347,NM_002020.4;FLT4,synonymous_variant,p.=,ENST00000502649,;FLT4,synonymous_variant,p.=,ENST00000512795,;FLT4,3_prime_UTR_variant,,ENST00000619105,;FLT4,downstream_gene_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,non_coding_transcript_exon_variant,,ENST00000514810,;FLT4,upstream_gene_variant,,ENST00000510000,; C ENST00000261937 Transcript synonymous_variant 3169/5857 3090/4092 1030/1363 S tcC/tcG 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 22/30 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF49,hmmpanther:PTHR24416,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 180616906 180616906 G C 1 0 0 0 0 0 0 0 1 5800 1219 43 4 4 FLT4 5 180616906 Silent SNP G C3N-00580_T 300110 180616906 921353 358 18493 FOXC1 0 . GRCh38 6 1611266 1611266 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.821C>T p.Pro274Leu p.P274L ENST00000380874 1/1 130 117 13 259 259 0 strelka-varscan-mutect FOXC1,missense_variant,p.Pro274Leu,ENST00000380874,NM_001453.2; T ENST00000380874 Transcript missense_variant 1295/3926 821/1662 274/553 P/L cCg/cTg CD121393 1 1 FOXC1 HGNC HGNC:3800 protein_coding YES CCDS4473.1 ENSP00000370256 Q12948 W6CJ52 UPI000012ADC5 NM_001453.2 tolerated(0.07) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11829:SF166,hmmpanther:PTHR11829 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.04414 0.9999998 1 1 1 0 T 3 4 61 1611266 1611266 C T 1 0 0 0 0 1 0 0 0 5854 652 23 1 1 FOXC1 6 1611266 Missense_Mutation SNP C C3N-00580_T 1611266 169194713 359 18494 GMDS 0 . GRCh38 6 1960834 1960834 + Missense_Mutation SNP C C A rs199870515 C3N-00580_T C3N-00580_N C C c.478G>T p.Gly160Trp p.G160W ENST00000380815 5/11 142 99 43 114 114 0 strelka-mutect GMDS,missense_variant,p.Gly160Trp,ENST00000380815,NM_001500.3;GMDS,missense_variant,p.Gly130Trp,ENST00000530927,NM_001253846.1;GMDS,non_coding_transcript_exon_variant,,ENST00000530459,;GMDS,upstream_gene_variant,,ENST00000531690,;GMDS,non_coding_transcript_exon_variant,,ENST00000530075,; A ENST00000380815 Transcript missense_variant 748/1752 478/1119 160/372 G/W Ggg/Tgg rs199870515 1 -1 GMDS HGNC HGNC:4369 protein_coding YES CCDS4474.1 ENSP00000370194 O60547 UPI000012B8AA NM_001500.3 deleterious_low_confidence(0) 5/11 HAMAP:MF_00955,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF429,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR01472,Pfam_domain:PF16363,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs199870515 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1960834 1960834 C A 1 0 0 0 0 1 0 0 0 6365 594 21 2 2 GMDS 6 1960834 Missense_Mutation SNP C C3N-00580_T 349568 1960834 168845145 360 18495 CAGE1 0 . GRCh38 6 7373278 7373278 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1541C>A p.Thr514Asn p.T514N ENST00000502583 5/14 176 89 87 118 118 0 strelka-varscan-mutect CAGE1,missense_variant,p.Thr514Asn,ENST00000502583,NM_001170692.1;CAGE1,missense_variant,p.Thr514Asn,ENST00000379918,;CAGE1,missense_variant,p.Thr378Asn,ENST00000296742,NM_205864.2;CAGE1,missense_variant,p.Thr514Asn,ENST00000338150,NM_001170693.1;CAGE1,missense_variant,p.Thr514Asn,ENST00000512086,;CAGE1,missense_variant,p.Thr526Asn,ENST00000512691,;CAGE1,downstream_gene_variant,,ENST00000509324,;CAGE1,missense_variant,p.Thr514Asn,ENST00000458291,;CAGE1,3_prime_UTR_variant,,ENST00000442019,; T ENST00000502583 Transcript missense_variant 2106/3284 1541/2520 514/839 T/N aCt/aAt 1 -1 CAGE1 HGNC HGNC:21622 protein_coding YES CCDS54965.1 ENSP00000425493 Q8TC20 UPI0001C0B380 NM_001170692.1 deleterious(0.01) 5/14 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR36864,Pfam_domain:PF15066 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 7373278 7373278 G T 1 0 0 0 0 1 0 0 0 2262 1029 36 2 2 CAGE1 6 7373278 Missense_Mutation SNP G C3N-00580_T 5412444 7373278 163432701 361 18496 RIOK1 0 . GRCh38 6 7417394 7417394 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1660G>T p.Val554Leu p.V554L ENST00000379834 17/17 146 118 28 108 108 0 strelka-varscan-mutect RIOK1,missense_variant,p.Val554Leu,ENST00000379834,NM_031480.2;RIOK1,non_coding_transcript_exon_variant,,ENST00000264874,; T ENST00000379834 Transcript missense_variant 2167/2810 1660/1707 554/568 V/L Gtg/Ttg 1 1 RIOK1 HGNC HGNC:18656 protein_coding YES CCDS4500.1 ENSP00000369162 Q9BRS2 UPI000003FDCE NM_031480.2 deleterious(0.03) 17/17 PIRSF_domain:PIRSF038147,hmmpanther:PTHR10593,hmmpanther:PTHR10593:SF23,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 3 3 0 0 0 0 -20 0.9999474 1 1 1 0 T 3 4 61 7417394 7417394 G T 1 0 0 0 0 1 0 0 0 13551 1377 48 2 2 RIOK1 6 7417394 Missense_Mutation SNP G C3N-00580_T 44116 7417394 163388585 362 18497 CD83 0 . GRCh38 6 14131642 14131642 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.276G>C p.= p.L92L ENST00000379153 3/5 610 527 83 569 569 0 strelka-varscan-mutect CD83,synonymous_variant,p.=,ENST00000379153,NM_004233.3,NM_001040280.1;CD83,synonymous_variant,p.=,ENST00000612003,NM_001251901.1; C ENST00000379153 Transcript synonymous_variant 447/2471 276/618 92/205 L ctG/ctC 1 1 CD83 HGNC HGNC:1703 protein_coding YES CCDS4532.1 ENSP00000368450 Q01151 UPI000004C561 NM_004233.3,NM_001040280.1 3/5 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR15193,hmmpanther:PTHR15193:SF1,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 14131642 14131642 G C 1 0 0 0 0 0 0 0 1 2745 1277 45 4 4 CD83 6 14131642 Silent SNP G C3N-00580_T 6714248 14131642 156674337 363 18498 E2F3 0 . GRCh38 6 20479916 20479916 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.464G>T p.Gly155Val p.G155V ENST00000346618 2/7 378 322 56 289 289 0 strelka-varscan-mutect E2F3,missense_variant,p.Gly155Val,ENST00000346618,NM_001949.4;E2F3,missense_variant,p.Gly30Val,ENST00000535432,NM_001243076.2;E2F3,missense_variant,p.Gly40Val,ENST00000613242,; T ENST00000346618 Transcript missense_variant 530/4749 464/1398 155/465 G/V gGc/gTc 1 1 E2F3 HGNC HGNC:3115 protein_coding YES CCDS4545.1 ENSP00000262904 O00716 UPI0000129AC2 NM_001949.4 deleterious(0) 2/7 hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF44 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20479916 20479916 G T 1 0 0 0 0 1 0 0 0 4692 1203 42 2 2 E2F3 6 20479916 Missense_Mutation SNP G C3N-00580_T 6348274 20479916 150326063 364 18499 ZNF311 0 . GRCh38 6 28996426 28996426 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.576G>C p.Glu192Asp p.E192D ENST00000377179 7/7 271 214 57 206 206 0 strelka-varscan ZNF311,missense_variant,p.Glu192Asp,ENST00000377179,NM_001010877.2;ZNF311,non_coding_transcript_exon_variant,,ENST00000483450,; G ENST00000377179 Transcript missense_variant 1089/2730 576/2001 192/666 E/D gaG/gaC 1 -1 ZNF311 HGNC HGNC:13847 protein_coding YES CCDS34357.1 ENSP00000366384 Q5JNZ3 UPI000020D71E NM_001010877.2 tolerated(0.19) 7/7 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF273 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 28996426 28996426 C G 1 0 0 0 0 1 0 0 0 18409 912 32 4 4 ZNF311 6 28996426 Missense_Mutation SNP C C3N-00580_T 8516510 28996426 141809553 365 18500 GABBR1 0 . GRCh38 6 29627604 29627604 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.539G>T p.Gly180Val p.G180V ENST00000377034 6/23 330 286 44 488 488 0 strelka-varscan GABBR1,missense_variant,p.Gly180Val,ENST00000377034,NM_001470.2;GABBR1,missense_variant,p.Gly118Val,ENST00000377016,NM_021904.2;GABBR1,missense_variant,p.Gly63Val,ENST00000377012,NM_021903.2;GABBR1,missense_variant,p.Gly63Val,ENST00000355973,;GABBR1,missense_variant,p.Gly180Val,ENST00000376977,;GABBR1,downstream_gene_variant,,ENST00000462632,;GABBR1,downstream_gene_variant,,ENST00000476670,;GABBR1,missense_variant,p.Gly180Val,ENST00000494877,;GABBR1,3_prime_UTR_variant,,ENST00000472823,;GABBR1,3_prime_UTR_variant,,ENST00000491829,;GABBR1,3_prime_UTR_variant,,ENST00000489385,;GABBR1,intron_variant,,ENST00000485508,;GABBR1,downstream_gene_variant,,ENST00000467259,;GABBR1,upstream_gene_variant,,ENST00000477029,; A ENST00000377034 Transcript missense_variant 875/4527 539/2886 180/961 G/V gGg/gTg 1 -1 GABBR1 HGNC HGNC:4070 protein_coding YES CCDS4663.1 ENSP00000366233 Q9UBS5 UPI000004618A NM_001470.2 deleterious(0) 6/23 hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF42,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822,Prints_domain:PR01177 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 29627604 29627604 C A 1 0 0 0 0 1 0 0 0 6026 623 22 2 2 GABBR1 6 29627604 Missense_Mutation SNP C C3N-00580_T 631178 29627604 141178375 366 18501 PPP1R18 0 . GRCh38 6 30684617 30684617 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1402A>T p.Ser468Cys p.S468C ENST00000274853 1/3 54 29 25 64 64 0 strelka-varscan PPP1R18,missense_variant,p.Ser468Cys,ENST00000274853,NM_133471.3;PPP1R18,missense_variant,p.Ser468Cys,ENST00000615527,;PPP1R18,missense_variant,p.Ser468Cys,ENST00000399199,NM_001134870.1;PPP1R18,missense_variant,p.Ser20Cys,ENST00000615892,;NRM,downstream_gene_variant,,ENST00000259953,NM_007243.2;NRM,downstream_gene_variant,,ENST00000376421,NM_001270707.1;NRM,downstream_gene_variant,,ENST00000444096,;NRM,downstream_gene_variant,,ENST00000376420,NM_001270709.1;PPP1R18,intron_variant,,ENST00000488324,;PPP1R18,intron_variant,,ENST00000467662,;NRM,downstream_gene_variant,,ENST00000470733,;NRM,downstream_gene_variant,,ENST00000462857,;NRM,downstream_gene_variant,,ENST00000495946,;NRM,downstream_gene_variant,,ENST00000482141,;NRM,downstream_gene_variant,,ENST00000474864,; A ENST00000274853 Transcript missense_variant 3279/4599 1402/1842 468/613 S/C Agt/Tgt 1 -1 PPP1R18 HGNC HGNC:29413 protein_coding YES CCDS43444.1 ENSP00000274853 Q6NYC8 A0A024RCJ8 UPI00001C1E5E NM_133471.3 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR21685:SF0,hmmpanther:PTHR21685,Pfam_domain:PF13914 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 30684617 30684617 T A 1 0 0 0 0 1 0 0 0 12478 1580 55 4 4 PPP1R18 6 30684617 Missense_Mutation SNP T C3N-00580_T 1057013 30684617 140121362 367 18502 MDC1 0 . GRCh38 6 30700584 30700584 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.6151A>G p.Ile2051Val p.I2051V ENST00000376406 15/15 322 237 85 205 205 0 strelka-varscan MDC1,missense_variant,p.Ile2051Val,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,upstream_gene_variant,,ENST00000442150,;MDC1,non_coding_transcript_exon_variant,,ENST00000489540,;MDC1,downstream_gene_variant,,ENST00000492462,;RPL7P4,upstream_gene_variant,,ENST00000430239,; C ENST00000376406 Transcript missense_variant 6799/7576 6151/6270 2051/2089 I/V Att/Gtt 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 tolerated(0.65) 15/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 30700584 30700584 T C 1 0 0 0 0 1 0 0 0 9341 1464 51 5 5 MDC1 6 30700584 Missense_Mutation SNP T C3N-00580_T 15967 30700584 140105395 368 18503 LY6G5B 0 . GRCh38 6 31672171 31672171 + Silent SNP C C G novel C3N-00580_T C3N-00580_N C C c.495C>G p.= p.S165S ENST00000375864 3/3 581 454 127 515 515 0 strelka-varscan LY6G5B,synonymous_variant,p.=,ENST00000375864,NM_021221.2;XXbac-BPG32J3.22,synonymous_variant,p.=,ENST00000409691,;LY6G5B,synonymous_variant,p.=,ENST00000409525,;XXbac-BPG32J3.22,synonymous_variant,p.=,ENST00000617558,;XXbac-BPG32J3.22,3_prime_UTR_variant,,ENST00000375880,;CSNK2B,downstream_gene_variant,,ENST00000375885,;LY6G5C,downstream_gene_variant,,ENST00000375863,;CSNK2B,downstream_gene_variant,,ENST00000375882,NM_001320.6,NM_001282385.1;CSNK2B,downstream_gene_variant,,ENST00000375866,;CSNK2B,downstream_gene_variant,,ENST00000375865,;LY6G5C,downstream_gene_variant,,ENST00000383237,NM_025262.3;LY6G5C,downstream_gene_variant,,ENST00000474395,;LY6G5B,upstream_gene_variant,,ENST00000471088,;LY6G5C,downstream_gene_variant,,ENST00000467098,;CSNK2B,downstream_gene_variant,,ENST00000468255,;LY6G5C,downstream_gene_variant,,ENST00000460141,;CSNK2B,downstream_gene_variant,,ENST00000481269,;CSNK2B,downstream_gene_variant,,ENST00000475875,;CSNK2B,downstream_gene_variant,,ENST00000465481,;LY6G5C,downstream_gene_variant,,ENST00000474678,; G ENST00000375864 Transcript synonymous_variant 1279/2654 495/606 165/201 S tcC/tcG 1 1 LY6G5B HGNC HGNC:13931 protein_coding YES CCDS34400.1 ENSP00000365024 Q8NDX9 N0E641 UPI0000071C7A NM_021221.2 3/3 hmmpanther:PTHR14313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 31672171 31672171 C G 1 0 0 0 0 0 0 0 1 9002 610 22 4 4 LY6G5B 6 31672171 Silent SNP C C3N-00580_T 971587 31672171 139133808 369 18504 TNXB 0 . GRCh38 6 32046289 32046289 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.10492G>C p.Asp3498His p.D3498H ENST00000375244 31/44 517 412 105 789 789 0 strelka-varscan TNXB,missense_variant,p.Asp3498His,ENST00000375244,NM_019105.6;TNXB,missense_variant,p.Asp1216His,ENST00000611016,;TNXB,upstream_gene_variant,,ENST00000451343,NM_032470.3;CYP21A2,downstream_gene_variant,,ENST00000418967,NM_000500.7;CYP21A2,downstream_gene_variant,,ENST00000435122,NM_001128590.3;TNXB,non_coding_transcript_exon_variant,,ENST00000490077,;CYP21A2,downstream_gene_variant,,ENST00000479074,;CYP21A2,downstream_gene_variant,,ENST00000479730,;CYP21A2,downstream_gene_variant,,ENST00000486063,;TNXB,upstream_gene_variant,,ENST00000498094,; G ENST00000375244 Transcript missense_variant 10694/13132 10492/12735 3498/4244 D/H Gac/Cac 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 tolerated(0.08) 31/44 PROSITE_profiles:PS50853,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 7 203 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 32046289 32046289 C G 1 0 0 0 0 1 0 0 0 16820 913 32 4 4 TNXB 6 32046289 Missense_Mutation SNP C C3N-00580_T 374118 32046289 138759690 370 18505 TNXB 0 . GRCh38 6 32070324 32070324 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.5081G>T p.Trp1694Leu p.W1694L ENST00000375244 14/44 347 305 42 332 332 0 strelka-varscan TNXB,missense_variant,p.Trp1694Leu,ENST00000375244,NM_019105.6;TNXB,3_prime_UTR_variant,,ENST00000613214,; A ENST00000375244 Transcript missense_variant 5283/13132 5081/12735 1694/4244 W/L tGg/tTg 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 deleterious(0.02) 14/44 PROSITE_profiles:PS50853,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 32070324 32070324 C A 1 0 0 0 0 1 0 0 0 16820 595 21 2 2 TNXB 6 32070324 Missense_Mutation SNP C C3N-00580_T 24035 32070324 138735655 371 18506 COL11A2 0 . GRCh38 6 33177020 33177020 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1784C>A p.Pro595His p.P595H ENST00000374708 23/64 450 403 47 659 658 1 strelka-varscan-mutect COL11A2,missense_variant,p.Pro681His,ENST00000341947,NM_080680.2;COL11A2,missense_variant,p.Pro595His,ENST00000374708,NM_080681.2;COL11A2,missense_variant,p.Pro574His,ENST00000361917,NM_080679.2;COL11A2,downstream_gene_variant,,ENST00000457788,;COL11A2,non_coding_transcript_exon_variant,,ENST00000477772,; T ENST00000374708 Transcript missense_variant 2043/6209 1784/4953 595/1650 P/H cCc/cAc 1 -1 COL11A2 HGNC HGNC:2187 protein_coding YES CCDS43452.1 ENSP00000363840 Q4VXY6 UPI000013E9A5 NM_080681.2 deleterious(0.03) 23/64 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF509 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 33177020 33177020 G T 1 0 0 0 0 1 0 0 0 3456 1232 43 2 2 COL11A2 6 33177020 Missense_Mutation SNP G C3N-00580_T 1106696 33177020 137628959 372 18507 PI16 0 . GRCh38 6 36954839 36954839 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.79G>T p.Ala27Ser p.A27S ENST00000373674 1/7 379 330 49 306 306 0 strelka-varscan-mutect PI16,missense_variant,p.Ala27Ser,ENST00000373674,NM_153370.2;PI16,missense_variant,p.Ala27Ser,ENST00000611814,NM_001199159.1; T ENST00000373674 Transcript missense_variant 407/2190 79/1392 27/463 A/S Gcc/Tcc 1 1 PI16 HGNC HGNC:21245 protein_coding YES CCDS34440.1 ENSP00000362778 Q6UXB8 UPI000004C657 NM_153370.2 tolerated(0.33) 1/7 Gene3D:3.40.33.10,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF197,Cleavage_site_(Signalp):SignalP-noTM,Superfamily_domains:SSF55797,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 36954839 36954839 G T 1 0 0 0 0 1 0 0 0 11958 971 34 2 2 PI16 6 36954839 Missense_Mutation SNP G C3N-00580_T 3777819 36954839 133851140 373 18508 MDGA1 0 . GRCh38 6 37658317 37658317 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.310G>T p.Gly104Cys p.G104C ENST00000434837 3/17 228 182 46 219 219 0 strelka-varscan-mutect MDGA1,missense_variant,p.Gly104Cys,ENST00000434837,NM_153487.3;MDGA1,missense_variant,p.Gly104Cys,ENST00000505425,;MDGA1,missense_variant,p.Gly48Cys,ENST00000515437,;MDGA1,missense_variant,p.Gly48Cys,ENST00000508399,;MDGA1,non_coding_transcript_exon_variant,,ENST00000478143,; A ENST00000434837 Transcript missense_variant 1489/10736 310/2868 104/955 G/C Ggc/Tgc COSM1444173,COSM5160270 1 -1 MDGA1 HGNC HGNC:19267 protein_coding YES CCDS47417.1 ENSP00000402584 Q8NFP4 UPI0000071D28 NM_153487.3 tolerated(0.17) 3/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF66,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 37658317 37658317 C A 1 0 0 0 0 1 0 0 0 9344 652 23 1 1 MDGA1 6 37658317 Missense_Mutation SNP C C3N-00580_T 703478 37658317 133147662 374 18509 GLP1R 0 . GRCh38 6 39085933 39085933 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.1252G>A p.Glu418Lys p.E418K ENST00000373256 13/13 232 176 56 215 215 0 strelka-varscan-mutect GLP1R,missense_variant,p.Glu418Lys,ENST00000373256,NM_002062.3; A ENST00000373256 Transcript missense_variant 1295/3105 1252/1392 418/463 E/K Gag/Aag 1 1 GLP1R HGNC HGNC:4324 protein_coding YES CCDS4839.1 ENSP00000362353 P43220 UPI0000061F20 NM_002062.3 tolerated(0.78) 13/13 hmmpanther:PTHR12011:SF245,hmmpanther:PTHR12011,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39085933 39085933 G A 1 0 0 0 0 1 0 0 0 6331 1175 41 3 3 GLP1R 6 39085933 Missense_Mutation SNP G C3N-00580_T 1427616 39085933 131720046 375 18510 LRFN2 0 . GRCh38 6 40432457 40432457 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.657C>T p.= p.A219A ENST00000338305 2/3 470 256 214 272 272 0 strelka-varscan-mutect LRFN2,synonymous_variant,p.=,ENST00000338305,NM_020737.2; A ENST00000338305 Transcript synonymous_variant 1200/3270 657/2370 219/789 A gcC/gcT 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 40432457 40432457 G A 1 0 0 0 0 0 0 0 1 8832 1219 43 3 3 LRFN2 6 40432457 Silent SNP G C3N-00580_T 1346524 40432457 130373522 376 18511 LRFN2 0 . GRCh38 6 40432667 40432667 + Silent SNP C C A rs762137082 C3N-00580_T C3N-00580_N C C c.447G>T p.= p.L149L ENST00000338305 2/3 625 472 153 499 499 0 strelka-varscan-mutect LRFN2,synonymous_variant,p.=,ENST00000338305,NM_020737.2; A ENST00000338305 Transcript synonymous_variant 990/3270 447/2370 149/789 L ctG/ctT rs762137082 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs762137082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 40432667 40432667 C A 1 0 0 0 0 0 0 0 1 8832 813 29 2 2 LRFN2 6 40432667 Silent SNP C C3N-00580_T 210 40432667 130373312 377 18512 CUL9 0 . GRCh38 6 43203960 43203960 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.4132C>G p.Pro1378Ala p.P1378A ENST00000252050 20/41 157 136 21 114 114 0 strelka-varscan-mutect CUL9,missense_variant,p.Pro1378Ala,ENST00000252050,NM_015089.3;CUL9,missense_variant,p.Pro1378Ala,ENST00000372647,;CUL9,upstream_gene_variant,,ENST00000502937,;CUL9,non_coding_transcript_exon_variant,,ENST00000515773,;CUL9,non_coding_transcript_exon_variant,,ENST00000515344,;CUL9,upstream_gene_variant,,ENST00000502719,;CUL9,upstream_gene_variant,,ENST00000512408,;CUL9,upstream_gene_variant,,ENST00000504485,;CUL9,upstream_gene_variant,,ENST00000505172,; G ENST00000252050 Transcript missense_variant 4216/7780 4132/7554 1378/2517 P/A Ccc/Gcc 1 1 CUL9 HGNC HGNC:15982 protein_coding YES CCDS4890.1 ENSP00000252050 Q8IWT3 UPI000006F22F NM_015089.3 deleterious(0) 20/41 hmmpanther:PTHR22771:SF2,hmmpanther:PTHR22771,Pfam_domain:PF00888,Gene3D:1.25.10.10 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 43203960 43203960 C G 1 0 0 0 0 1 0 0 0 3871 623 22 4 4 CUL9 6 43203960 Missense_Mutation SNP C C3N-00580_T 2771293 43203960 127602019 378 18513 SLC22A7 0 . GRCh38 6 43301199 43301199 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.892T>A p.Leu298Met p.L298M ENST00000372585 6/11 501 378 123 486 486 0 strelka-varscan-mutect SLC22A7,missense_variant,p.Leu298Met,ENST00000372585,NM_153320.2;SLC22A7,missense_variant,p.Leu296Met,ENST00000372589,NM_006672.3;SLC22A7,missense_variant,p.Leu296Met,ENST00000372574,;CRIP3,intron_variant,,ENST00000416431,;CRIP3,downstream_gene_variant,,ENST00000372569,NM_206922.2;SLC22A7,downstream_gene_variant,,ENST00000449231,;SLC22A7,downstream_gene_variant,,ENST00000451757,;CRIP3,downstream_gene_variant,,ENST00000274990,;SLC22A7,upstream_gene_variant,,ENST00000436107,;CRIP3,downstream_gene_variant,,ENST00000451294,;SLC22A7,non_coding_transcript_exon_variant,,ENST00000487175,;SLC22A7,downstream_gene_variant,,ENST00000480882,;SLC22A7,downstream_gene_variant,,ENST00000498232,;CRIP3,downstream_gene_variant,,ENST00000477866,; A ENST00000372585 Transcript missense_variant 987/2555 892/1647 298/548 L/M Ttg/Atg 1 1 SLC22A7 HGNC HGNC:10971 protein_coding YES CCDS4893.2 ENSP00000361666 Q9Y694 UPI000006F307 NM_153320.2 deleterious(0) 6/11 Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF33,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00898 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 43301199 43301199 T A 1 0 0 0 0 1 0 0 0 14725 1606 56 4 4 SLC22A7 6 43301199 Missense_Mutation SNP T C3N-00580_T 97239 43301199 127504780 379 18514 POLH 0 . GRCh38 6 43597799 43597799 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.594G>T p.Glu198Asp p.E198D ENST00000372236 5/11 562 294 268 348 348 0 strelka-varscan-mutect POLH,missense_variant,p.Glu198Asp,ENST00000372236,NM_006502.2;POLH,missense_variant,p.Glu198Asp,ENST00000372226,NM_001291970.1; T ENST00000372236 Transcript missense_variant 889/3540 594/2142 198/713 E/D gaG/gaT 1 1 POLH HGNC HGNC:9181 protein_coding YES CCDS4902.1 ENSP00000361310 Q9Y253 A0A024RD62 UPI000006F8FD NM_006502.2 deleterious(0) 5/11 PROSITE_profiles:PS50173,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF11,PIRSF_domain:PIRSF036603,Gene3D:3.30.70.270,Pfam_domain:PF00817,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 43597799 43597799 G T 1 0 0 0 0 1 0 0 0 12312 991 35 2 2 POLH 6 43597799 Missense_Mutation SNP G C3N-00580_T 296600 43597799 127208180 380 18515 TMEM151B 0 . GRCh38 6 44275556 44275556 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.730G>A p.Glu244Lys p.E244K ENST00000451188 3/3 365 230 135 286 286 0 strelka-varscan-mutect TMEM151B,missense_variant,p.Glu244Lys,ENST00000451188,NM_001137560.1;TMEM151B,intron_variant,,ENST00000438774,;TCTE1,downstream_gene_variant,,ENST00000371505,NM_182539.3;TCTE1,downstream_gene_variant,,ENST00000371504,;RP11-444E17.6,intron_variant,,ENST00000505802,; A ENST00000451188 Transcript missense_variant 1007/4895 730/1701 244/566 E/K Gag/Aag 1 1 TMEM151B HGNC HGNC:21315 protein_coding YES CCDS47437.1 ENSP00000393161 Q8IW70 UPI00006C0A4E NM_001137560.1 tolerated(0.06) 3/3 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF4 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 44275556 44275556 G A 1 0 0 0 0 1 0 0 0 16513 1175 41 3 3 TMEM151B 6 44275556 Missense_Mutation SNP G C3N-00580_T 677757 44275556 126530423 381 18516 PLA2G7 0 . GRCh38 6 46709363 46709363 + Missense_Mutation SNP G G A rs147252565 C3N-00580_T C3N-00580_N G G c.833C>T p.Thr278Met p.T278M ENST00000274793 9/12 305 284 21 329 329 0 strelka-varscan-mutect PLA2G7,missense_variant,p.Thr278Met,ENST00000274793,NM_005084.3;PLA2G7,missense_variant,p.Thr278Met,ENST00000537365,NM_001168357.1; A ENST00000274793 Transcript missense_variant 1030/1882 833/1326 278/441 T/M aCg/aTg rs147252565 1 -1 PLA2G7 HGNC HGNC:9040 protein_coding YES CCDS4917.1 ENSP00000274793 Q13093 UPI000002FED1 NM_005084.3 deleterious(0) 9/12 Gene3D:3.40.50.1820,Pfam_domain:PF03403,PIRSF_domain:PIRSF018169,hmmpanther:PTHR10272,hmmpanther:PTHR10272:SF12,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs147252565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 46709363 46709363 G A 1 0 0 0 0 1 0 0 0 12105 1145 40 1 1 PLA2G7 6 46709363 Missense_Mutation SNP G C3N-00580_T 2433807 46709363 124096616 382 18517 PKHD1 0 . GRCh38 6 52050295 52050295 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.2141T>G p.Val714Gly p.V714G ENST00000371117 22/67 783 738 45 560 560 0 strelka-varscan-mutect PKHD1,missense_variant,p.Val714Gly,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Val714Gly,ENST00000340994,NM_170724.2; C ENST00000371117 Transcript missense_variant,splice_region_variant 2417/16282 2141/12225 714/4074 V/G gTt/gGt 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0) 22/67 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 52050295 52050295 A C 1 0 0 0 0 1 0 0 0 12067 57 2 5 5 PKHD1 6 52050295 Missense_Mutation SNP A C3N-00580_T 5340932 52050295 118755684 383 18518 FAM83B 0 . GRCh38 6 54940713 54940713 + Missense_Mutation SNP C C A rs201414733 C3N-00580_T C3N-00580_N C C c.1742C>A p.Pro581Gln p.P581Q ENST00000306858 5/5 288 203 85 210 210 0 strelka-varscan-mutect FAM83B,missense_variant,p.Pro581Gln,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; A ENST00000306858 Transcript missense_variant 1858/3167 1742/3036 581/1011 P/Q cCa/cAa rs201414733 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 tolerated(0.1) 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 MODERATE 1 SNV 1 1 PASS rs201414733 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 54940713 54940713 C A 1 0 0 0 0 1 0 0 0 5492 594 21 2 2 FAM83B 6 54940713 Missense_Mutation SNP C C3N-00580_T 2890418 54940713 115865266 384 18519 ZNF451 0 . GRCh38 6 57148424 57148424 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2339G>T p.Ser780Ile p.S780I ENST00000370706 10/15 419 246 173 239 238 1 strelka-varscan ZNF451,missense_variant,p.Ser780Ile,ENST00000370706,NM_001031623.2;ZNF451,missense_variant,p.Ser780Ile,ENST00000357489,NM_015555.2;ZNF451,missense_variant,p.Ser780Ile,ENST00000491832,;RP11-203B9.4,intron_variant,,ENST00000416069,;RP11-203B9.4,intron_variant,,ENST00000586432,;RP11-203B9.4,intron_variant,,ENST00000592038,;RP11-203B9.4,intron_variant,,ENST00000588811,;RP11-203B9.4,intron_variant,,ENST00000589549,;RP11-203B9.4,intron_variant,,ENST00000586053,;RP11-203B9.4,intron_variant,,ENST00000586668,;RP11-203B9.4,intron_variant,,ENST00000591553,;RP11-203B9.4,intron_variant,,ENST00000587815,;RP11-203B9.4,intron_variant,,ENST00000585792,;RP11-203B9.4,intron_variant,,ENST00000592500,;RP11-203B9.4,downstream_gene_variant,,ENST00000589263,;RP11-203B9.4,downstream_gene_variant,,ENST00000586466,;ZNF451,non_coding_transcript_exon_variant,,ENST00000444273,;ZNF451,intron_variant,,ENST00000504603,;ZNF451,upstream_gene_variant,,ENST00000508548,; T ENST00000370706 Transcript missense_variant 2583/5268 2339/3186 780/1061 S/I aGt/aTt 1 1 ZNF451 HGNC HGNC:21091 protein_coding YES CCDS43477.1 ENSP00000359740 Q9Y4E5 UPI000004A571 NM_001031623.2 tolerated(0.21) 10/15 hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 57148424 57148424 G T 1 0 0 0 0 1 0 0 0 18493 1029 36 2 2 ZNF451 6 57148424 Missense_Mutation SNP G C3N-00580_T 2207711 57148424 113657555 385 18520 EYS 0 . GRCh38 6 63789115 63789115 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.7521G>T p.= p.L2507L ENST00000370621 38/44 301 195 106 193 193 0 strelka-varscan EYS,synonymous_variant,p.=,ENST00000503581,NM_001142800.1;EYS,synonymous_variant,p.=,ENST00000370621,NM_001292009.1;EYS,synonymous_variant,p.=,ENST00000398580,;EYS,non_coding_transcript_exon_variant,,ENST00000486069,; A ENST00000370621 Transcript synonymous_variant 8048/10485 7521/9498 2507/3165 L ctG/ctT 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 38/44 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 63789115 63789115 C A 1 0 0 0 0 0 0 0 1 5200 813 29 2 2 EYS 6 63789115 Silent SNP C C3N-00580_T 6640691 63789115 107016864 386 18521 EYS 0 . GRCh38 6 63864282 63864282 + Missense_Mutation SNP T T G novel C3N-00580_T C3N-00580_N T T c.7132A>C p.Asn2378His p.N2378H ENST00000370621 36/44 194 134 60 138 138 0 strelka-varscan EYS,missense_variant,p.Asn2378His,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Asn2378His,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Asn150His,ENST00000398580,; G ENST00000370621 Transcript missense_variant 7659/10485 7132/9498 2378/3165 N/H Aac/Cac 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0.01) 36/44 PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 63864282 63864282 T G 1 0 0 0 0 1 0 0 0 5200 1812 63 5 5 EYS 6 63864282 Missense_Mutation SNP T C3N-00580_T 75167 63864282 106941697 387 18522 COL12A1 0 . GRCh38 6 75124053 75124053 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.6766A>T p.Ser2256Cys p.S2256C ENST00000322507 42/66 174 109 65 118 118 0 strelka-varscan-mutect COL12A1,missense_variant,p.Ser2256Cys,ENST00000322507,NM_004370.5;COL12A1,missense_variant,p.Ser1067Cys,ENST00000615798,;COL12A1,missense_variant,p.Ser2256Cys,ENST00000483888,;COL12A1,missense_variant,p.Ser2256Cys,ENST00000416123,;COL12A1,missense_variant,p.Ser1092Cys,ENST00000345356,NM_080645.2;COL12A1,upstream_gene_variant,,ENST00000425443,;COL12A1,upstream_gene_variant,,ENST00000493109,; A ENST00000322507 Transcript missense_variant 7076/11723 6766/9192 2256/3063 S/C Agt/Tgt 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 deleterious(0) 42/66 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 75124053 75124053 T A 1 0 0 0 0 1 0 0 0 3457 1580 55 4 4 COL12A1 6 75124053 Missense_Mutation SNP T C3N-00580_T 11259771 75124053 95681926 388 18523 PHIP 0 . GRCh38 6 78963134 78963134 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.3498A>T p.Glu1166Asp p.E1166D ENST00000275034 30/40 87 73 14 107 107 0 varscan-mutect PHIP,missense_variant,p.Glu1166Asp,ENST00000275034,NM_017934.5;PHIP,non_coding_transcript_exon_variant,,ENST00000479165,; A ENST00000275034 Transcript missense_variant 3666/10460 3498/5466 1166/1821 E/D gaA/gaT 1 -1 PHIP HGNC HGNC:15673 protein_coding YES CCDS4987.1 ENSP00000275034 Q8WWQ0 UPI000013DA40 NM_017934.5 tolerated(0.2) 30/40 Gene3D:1.20.920.10,Pfam_domain:PF00439,hmmpanther:PTHR16266,hmmpanther:PTHR16266:SF4,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 78963134 78963134 T A 1 0 0 0 0 1 0 0 0 11930 1838 64 4 4 PHIP 6 78963134 Missense_Mutation SNP T C3N-00580_T 3839081 78963134 91842845 389 18524 RRAGD 0 . GRCh38 6 89387592 89387592 + Splice_Site SNP T T A novel C3N-00580_T C3N-00580_N T T c.149-2A>T p.X50_splice ENST00000369415 73 57 16 69 69 0 strelka-varscan-mutect RRAGD,splice_acceptor_variant,,ENST00000369415,NM_021244.4;RRAGD,intron_variant,,ENST00000359203,;RRAGD,splice_acceptor_variant,,ENST00000492783,; A ENST00000369415 Transcript splice_acceptor_variant -/4900 149/1203 50/400 1 -1 RRAGD HGNC HGNC:19903 protein_coding YES CCDS5022.1 ENSP00000358423 Q9NQL2 UPI000006E549 NM_021244.4 1/6 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 89387592 89387592 T A 1 0 0 0 0 0 0 1 0 13929 1594 55 4 4 RRAGD 6 89387592 Splice_Site SNP T C3N-00580_T 10424458 89387592 81418387 390 18525 MDN1 0 . GRCh38 6 89719144 89719144 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.6049G>T p.Asp2017Tyr p.D2017Y ENST00000369393 41/102 181 80 101 215 215 0 strelka-varscan-mutect MDN1,missense_variant,p.Asp2017Tyr,ENST00000369393,NM_014611.2;MDN1,missense_variant,p.Asp2017Tyr,ENST00000629399,; A ENST00000369393 Transcript missense_variant 6165/18413 6049/16791 2017/5596 D/Y Gat/Tat 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 deleterious(0.04) 41/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 89719144 89719144 C A 1 0 0 0 0 1 0 0 0 9353 826 29 2 2 MDN1 6 89719144 Missense_Mutation SNP C C3N-00580_T 331552 89719144 81086835 391 18526 EPHA7 0 . GRCh38 6 93410800 93410800 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.533C>A p.Ser178Tyr p.S178Y ENST00000369303 3/17 117 65 52 123 122 1 strelka-varscan-mutect EPHA7,missense_variant,p.Ser178Tyr,ENST00000369303,NM_001288629.1,NM_004440.3;EPHA7,missense_variant,p.Ser178Tyr,ENST00000369297,NM_001288630.1; T ENST00000369303 Transcript missense_variant 718/6588 533/2997 178/998 S/Y tCc/tAc COSM5405977,COSM5405978 1 -1 EPHA7 HGNC HGNC:3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_001288629.1,NM_004440.3 deleterious(0.01) 3/17 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF377,SMART_domains:SM00615,Superfamily_domains:SSF49785 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 194 8 7 0 0 0 0 -20 0.9957976 1 1 1 0 T 3 4 61 93410800 93410800 G T 1 0 0 0 0 1 0 0 0 5019 1174 41 2 2 EPHA7 6 93410800 Missense_Mutation SNP G C3N-00580_T 3691656 93410800 77395179 392 18527 FHL5 0 . GRCh38 6 96610682 96610682 + Missense_Mutation SNP C C A rs61732222 C3N-00580_T C3N-00580_N C C c.615C>A p.Asp205Glu p.D205E ENST00000326771 6/7 164 137 27 209 209 0 strelka-varscan-mutect FHL5,missense_variant,p.Asp205Glu,ENST00000326771,NM_020482.4;FHL5,missense_variant,p.Asp205Glu,ENST00000541107,NM_001170807.1;FHL5,missense_variant,p.Asp205Glu,ENST00000450218,; A ENST00000326771 Transcript missense_variant 995/2031 615/855 205/284 D/E gaC/gaA rs61732222 1 1 FHL5 HGNC HGNC:17371 protein_coding YES CCDS5035.1 ENSP00000326022 Q5TD97 UPI000006F158 NM_020482.4 tolerated(0.35) 6/7 PROSITE_profiles:PS50023,hmmpanther:PTHR24205:SF7,hmmpanther:PTHR24205,Gene3D:2.10.110.10,Pfam_domain:PF00412,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS rs61732222 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 96610682 96610682 C A 1 0 0 0 0 1 0 0 0 5746 535 19 1 1 FHL5 6 96610682 Missense_Mutation SNP C C3N-00580_T 3199882 96610682 74195297 393 18528 ASCC3 0 . GRCh38 6 100650703 100650703 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3087G>T p.Glu1029Asp p.E1029D ENST00000369162 20/42 114 65 49 197 197 0 strelka-varscan-mutect ASCC3,missense_variant,p.Glu1029Asp,ENST00000369162,NM_006828.3;ASCC3,3_prime_UTR_variant,,ENST00000324696,; A ENST00000369162 Transcript missense_variant 3432/8146 3087/6609 1029/2202 E/D gaG/gaT 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 tolerated(0.95) 20/42 Gene3D:2q0zX01,Pfam_domain:PF02889,PIRSF_domain:PIRSF039073,SMART_domains:SM00973,Superfamily_domains:SSF158702 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 100650703 100650703 C A 1 0 0 0 0 1 0 0 0 1175 680 24 2 2 ASCC3 6 100650703 Missense_Mutation SNP C C3N-00580_T 4040021 100650703 70155276 394 18529 ASCC3 0 . GRCh38 6 100800299 100800299 + Splice_Site SNP C C G novel C3N-00580_T C3N-00580_N C C c.1127+1G>C p.X376_splice ENST00000369162 241 183 58 326 326 0 strelka-varscan-mutect ASCC3,splice_donor_variant,,ENST00000369162,NM_006828.3;ASCC3,splice_donor_variant,,ENST00000522650,NM_001284271.1;ASCC3,splice_donor_variant,,ENST00000324696,; G ENST00000369162 Transcript splice_donor_variant -/8146 1127/6609 376/2202 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 6/41 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 61 100800299 100800299 C G 1 0 0 0 0 0 0 1 0 1175 521 18 4 4 ASCC3 6 100800299 Splice_Site SNP C C3N-00580_T 149596 100800299 70005680 395 18530 DSE 0 . GRCh38 6 116436926 116436926 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2458G>T p.Asp820Tyr p.D820Y ENST00000452085 6/6 185 98 87 246 244 2 strelka-varscan-mutect DSE,missense_variant,p.Asp820Tyr,ENST00000452085,NM_001080976.1;DSE,missense_variant,p.Asp820Tyr,ENST00000331677,;DSE,missense_variant,p.Asp820Tyr,ENST00000359564,NM_013352.2;DSE,non_coding_transcript_exon_variant,,ENST00000606712,; T ENST00000452085 Transcript missense_variant 2652/10586 2458/2877 820/958 D/Y Gat/Tat 1 1 DSE HGNC HGNC:21144 protein_coding YES CCDS5107.1 ENSP00000404049 Q9UL01 UPI0000073CB8 NM_001080976.1 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR15532,hmmpanther:PTHR15532:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 116436926 116436926 G T 1 0 0 0 0 1 0 0 0 4595 1174 41 2 2 DSE 6 116436926 Missense_Mutation SNP G C3N-00580_T 15636627 116436926 54369053 396 18531 ROS1 0 . GRCh38 6 117344107 117344107 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.4477G>T p.Glu1493Ter p.E1493* ENST00000368508 27/43 242 133 109 252 252 0 strelka-varscan-mutect ROS1,stop_gained,p.Glu1493Ter,ENST00000368508,NM_002944.2;ROS1,stop_gained,p.Glu1487Ter,ENST00000368507,;RP1-179P9.3,intron_variant,,ENST00000467125,; A ENST00000368508 Transcript stop_gained 4676/7435 4477/7044 1493/2347 E/* Gaa/Taa 1 -1 ROS1 HGNC HGNC:10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 27/43 PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 117344107 117344107 C A 1 0 0 0 0 0 1 0 0 13708 922 32 2 2 ROS1 6 117344107 Nonsense_Mutation SNP C C3N-00580_T 907181 117344107 53461872 397 18532 HSF2 0 . GRCh38 6 122423675 122423675 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1165C>A p.Leu389Ile p.L389I ENST00000368455 10/13 75 60 15 96 96 0 strelka-varscan HSF2,missense_variant,p.Leu389Ile,ENST00000452194,NM_001135564.1;HSF2,missense_variant,p.Leu389Ile,ENST00000368455,NM_004506.3;HSF2,missense_variant,p.Leu160Ile,ENST00000465214,; A ENST00000368455 Transcript missense_variant 1357/2549 1165/1611 389/536 L/I Ctc/Atc 1 1 HSF2 HGNC HGNC:5225 protein_coding YES CCDS5124.1 ENSP00000357440 Q03933 UPI000012CCE8 NM_004506.3 tolerated(0.57) 10/13 hmmpanther:PTHR10015:SF185,hmmpanther:PTHR10015,Pfam_domain:PF06546 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 122423675 122423675 C A 1 0 0 0 0 1 0 0 0 7290 913 32 2 2 HSF2 6 122423675 Missense_Mutation SNP C C3N-00580_T 5079568 122423675 48382304 398 18533 LAMA2 0 . GRCh38 6 128883343 128883343 + Missense_Mutation SNP C C A rs750280423 C3N-00580_T C3N-00580_N C C c.98C>A p.Ala33Glu p.A33E ENST00000421865 1/65 334 193 141 438 438 0 strelka-varscan LAMA2,missense_variant,p.Ala33Glu,ENST00000618192,;LAMA2,missense_variant,p.Ala33Glu,ENST00000617695,;LAMA2,missense_variant,p.Ala33Glu,ENST00000421865,NM_001079823.1,NM_000426.3;LAMA2,non_coding_transcript_exon_variant,,ENST00000466230,; A ENST00000421865 Transcript missense_variant 147/9640 98/9369 33/3122 A/E gCa/gAa rs750280423,COSM1634478 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.28) 1/65 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,Low_complexity_(Seg):seg,SMART_domains:SM00136 0,1 MODERATE 1 SNV 5 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 128883343 128883343 C A 1 0 0 0 0 1 0 0 0 8510 710 25 2 2 LAMA2 6 128883343 Missense_Mutation SNP C C3N-00580_T 6459668 128883343 41922636 399 18534 LAMA2 0 . GRCh38 6 129192833 129192833 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.1762G>T p.Ala588Ser p.A588S ENST00000421865 12/65 307 208 99 302 301 1 strelka-varscan LAMA2,missense_variant,p.Ala588Ser,ENST00000618192,;LAMA2,missense_variant,p.Ala588Ser,ENST00000617695,;LAMA2,missense_variant,p.Ala588Ser,ENST00000421865,NM_001079823.1,NM_000426.3; T ENST00000421865 Transcript missense_variant 1811/9640 1762/9369 588/3122 A/S Gct/Tct LAMA2:c.1762delG 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.6) 12/65 Pfam_domain:PF00052,PROSITE_profiles:PS51115,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,SMART_domains:SM00281 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 129192833 129192833 G T 1 0 0 0 0 1 0 0 0 8510 1203 42 2 2 LAMA2 6 129192833 Missense_Mutation SNP G C3N-00580_T 309490 129192833 41613146 400 18535 TCF21 0 . GRCh38 6 133891783 133891783 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.521G>A p.Cys174Tyr p.C174Y ENST00000367882 2/2 265 189 76 270 270 0 strelka-varscan TCF21,missense_variant,p.Cys174Tyr,ENST00000367882,NM_003206.3;TCF21,missense_variant,p.Cys174Tyr,ENST00000237316,NM_198392.2;TARID,non_coding_transcript_exon_variant,,ENST00000630728,;TARID,non_coding_transcript_exon_variant,,ENST00000607641,;TARID,non_coding_transcript_exon_variant,,ENST00000630119,;TARID,non_coding_transcript_exon_variant,,ENST00000626104,;TARID,non_coding_transcript_exon_variant,,ENST00000631362,;TARID,non_coding_transcript_exon_variant,,ENST00000607573,;TARID,upstream_gene_variant,,ENST00000607033,;TARID,upstream_gene_variant,,ENST00000606544,; A ENST00000367882 Transcript missense_variant 781/4551 521/540 174/179 C/Y tGt/tAt 1 1 TCF21 HGNC HGNC:11632 protein_coding YES CCDS5167.1 ENSP00000356857 O43680 UPI0000001290 NM_003206.3 deleterious_low_confidence(0) 2/2 hmmpanther:PTHR23349:SF67,hmmpanther:PTHR23349 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999982 1 1 1 0 A 3 1 61 133891783 133891783 G A 1 0 0 0 0 1 0 0 0 16098 1377 48 3 3 TCF21 6 133891783 Missense_Mutation SNP G C3N-00580_T 4698950 133891783 36914196 401 18536 AHI1 0 . GRCh38 6 135457550 135457550 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1095G>T p.Met365Ile p.M365I ENST00000367800 7/27 231 125 106 232 232 0 strelka-varscan AHI1,missense_variant,p.Met365Ile,ENST00000367800,NM_001134830.1;AHI1,missense_variant,p.Met365Ile,ENST00000457866,NM_017651.4;AHI1,missense_variant,p.Met365Ile,ENST00000265602,NM_001134831.1;AHI1,missense_variant,p.Met365Ile,ENST00000327035,NM_001134832.1;AHI1,missense_variant,p.Met365Ile,ENST00000531788,; A ENST00000367800 Transcript missense_variant 1312/5921 1095/3591 365/1196 M/I atG/atT 1 -1 AHI1 HGNC HGNC:21575 protein_coding YES CCDS47483.1 ENSP00000356774 Q8N157 UPI00000701FB NM_001134830.1 tolerated(0.06) 7/27 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF361 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 135457550 135457550 C A 1 0 0 0 0 1 0 0 0 490 594 21 2 2 AHI1 6 135457550 Missense_Mutation SNP C C3N-00580_T 1565767 135457550 35348429 402 18537 BCLAF1 0 . GRCh38 6 136278322 136278322 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.559C>A p.Pro187Thr p.P187T ENST00000531224 4/13 126 101 25 116 116 0 strelka-varscan BCLAF1,missense_variant,p.Pro187Thr,ENST00000531224,NM_014739.2;BCLAF1,missense_variant,p.Pro185Thr,ENST00000353331,NM_001077440.1;BCLAF1,missense_variant,p.Pro187Thr,ENST00000527536,;BCLAF1,missense_variant,p.Pro185Thr,ENST00000527759,NM_001301038.1;BCLAF1,missense_variant,p.Pro187Thr,ENST00000530767,NM_001077441.1;BCLAF1,missense_variant,p.Pro185Thr,ENST00000392348,;BCLAF1,missense_variant,p.Pro187Thr,ENST00000628517,;BCLAF1,missense_variant,p.Pro187Thr,ENST00000529826,;BCLAF1,missense_variant,p.Pro187Thr,ENST00000527613,;BCLAF1,missense_variant,p.Pro185Thr,ENST00000534269,;BCLAF1,missense_variant,p.Pro187Thr,ENST00000532384,;BCLAF1,missense_variant,p.Pro185Thr,ENST00000530429,;BCLAF1,upstream_gene_variant,,ENST00000476194,;BCLAF1,upstream_gene_variant,,ENST00000533621,;BCLAF1,downstream_gene_variant,,ENST00000528229,; T ENST00000531224 Transcript missense_variant 812/7263 559/2763 187/920 P/T Ccg/Acg 1 -1 BCLAF1 HGNC HGNC:16863 protein_coding YES CCDS5177.1 ENSP00000435210 Q9NYF8 UPI000006FCE7 NM_014739.2 tolerated_low_confidence(0.1) 4/13 Pfam_domain:PF15440,hmmpanther:PTHR15268,hmmpanther:PTHR15268:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 136278322 136278322 G T 1 0 0 0 0 1 0 0 0 1530 1261 44 2 2 BCLAF1 6 136278322 Missense_Mutation SNP G C3N-00580_T 820772 136278322 34527657 403 18538 GRM1 0 . GRCh38 6 146029764 146029764 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.247T>A p.Phe83Ile p.F83I ENST00000361719 2/9 425 206 219 481 481 0 strelka-varscan GRM1,missense_variant,p.Phe83Ile,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,missense_variant,p.Phe83Ile,ENST00000361719,;GRM1,missense_variant,p.Phe83Ile,ENST00000282753,NM_001278064.1;GRM1,missense_variant,p.Phe83Ile,ENST00000355289,NM_001278067.1;GRM1,missense_variant,p.Phe83Ile,ENST00000507907,;GRM1,non_coding_transcript_exon_variant,,ENST00000502405,;GRM1,non_coding_transcript_exon_variant,,ENST00000507005,; A ENST00000361719 Transcript missense_variant 614/6754 247/3585 83/1194 F/I Ttc/Atc 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD deleterious(0.02) 2/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR00248 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 146029764 146029764 T A 1 0 0 0 0 1 0 0 0 6678 1725 60 4 4 GRM1 6 146029764 Missense_Mutation SNP T C3N-00580_T 9751442 146029764 24776215 404 18539 GRM1 0 . GRCh38 6 146304619 146304619 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.959G>T p.Trp320Leu p.W320L ENST00000361719 4/9 384 312 72 498 498 0 strelka-varscan GRM1,missense_variant,p.Trp320Leu,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,missense_variant,p.Trp320Leu,ENST00000361719,;GRM1,missense_variant,p.Trp320Leu,ENST00000282753,NM_001278064.1;GRM1,missense_variant,p.Trp320Leu,ENST00000355289,NM_001278067.1;GRM1,missense_variant,p.Trp320Leu,ENST00000507907,; T ENST00000361719 Transcript missense_variant 1326/6754 959/3585 320/1194 W/L tGg/tTg 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD deleterious(0) 4/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 146304619 146304619 G T 1 0 0 0 0 1 0 0 0 6678 1357 47 2 2 GRM1 6 146304619 Missense_Mutation SNP G C3N-00580_T 274855 146304619 24501360 405 18540 SYNE1 0 . GRCh38 6 152220886 152220886 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.21817G>A p.Asp7273Asn p.D7273N ENST00000367255 119/146 476 262 214 517 517 0 strelka-varscan SYNE1,missense_variant,p.Asp7273Asn,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Asp7202Asn,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Asp6868Asn,ENST00000341594,;SYNE1,missense_variant,p.Asp195Asn,ENST00000367251,;SYNE1,upstream_gene_variant,,ENST00000367257,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,; T ENST00000367255 Transcript missense_variant 22419/27748 21817/26394 7273/8797 D/N Gac/Aac 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 119/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 152220886 152220886 C T 1 0 0 0 0 1 0 0 0 15837 855 30 3 3 SYNE1 6 152220886 Missense_Mutation SNP C C3N-00580_T 5916267 152220886 18585093 406 18541 TAGAP 0 . GRCh38 6 159039310 159039310 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.588-1G>T p.X196_splice ENST00000367066 195 150 45 222 222 0 strelka-varscan-mutect TAGAP,splice_acceptor_variant,,ENST00000367066,NM_054114.4;TAGAP,splice_acceptor_variant,,ENST00000326965,NM_152133.2;TAGAP,splice_acceptor_variant,,ENST00000338313,NM_138810.3;RP1-111C20.4,intron_variant,,ENST00000607391,;RP1-111C20.4,intron_variant,,ENST00000606466,;RP1-111C20.4,intron_variant,,ENST00000607796,;RP1-111C20.4,intron_variant,,ENST00000606470,; A ENST00000367066 Transcript splice_acceptor_variant -/3887 588/2196 196/731 1 -1 TAGAP HGNC HGNC:15669 protein_coding YES CCDS5261.1 ENSP00000356033 Q8N103 UPI0000071CD5 NM_054114.4 7/9 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 159039310 159039310 C A 1 0 0 0 0 0 0 1 0 15933 695 24 2 2 TAGAP 6 159039310 Splice_Site SNP C C3N-00580_T 6818424 159039310 11766669 407 18542 LPA 0 . GRCh38 6 160650438 160650438 + Missense_Mutation SNP G G C rs121912503 C3N-00580_T C3N-00580_N G G c.109C>G p.Arg37Gly p.R37G ENST00000316300 2/39 394 232 162 446 446 0 strelka-varscan-mutect LPA,missense_variant,p.Arg37Gly,ENST00000316300,NM_005577.2; C ENST00000316300 Transcript missense_variant 154/6414 109/6123 37/2040 R/G Cga/Gga rs121912503,COSM3622586 1 -1 LPA HGNC HGNC:6667 protein_coding YES CCDS43523.1 ENSP00000321334 P08519 UPI0000458AC9 NM_005577.2 deleterious(0.01) 2/39 Gene3D:2.40.20.10,Pfam_domain:PF00051,PROSITE_profiles:PS50070,SMART_domains:SM00130,Superfamily_domains:SSF57440 pathogenic 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs121912503 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 160650438 160650438 G C 1 0 0 0 0 1 0 0 0 8806 1066 37 4 4 LPA 6 160650438 Missense_Mutation SNP G C3N-00580_T 1611128 160650438 10155541 408 18543 MAP3K4 0 . GRCh38 6 161092108 161092108 + Silent SNP G G T rs780920080 C3N-00580_T C3N-00580_N G G c.3234G>T p.= p.L1078L ENST00000392142 13/27 114 95 19 183 183 0 strelka-varscan-mutect MAP3K4,synonymous_variant,p.=,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,synonymous_variant,p.=,ENST00000366920,NM_001301072.1;MAP3K4,synonymous_variant,p.=,ENST00000366919,NM_006724.3;MAP3K4,synonymous_variant,p.=,ENST00000348824,;MAP3K4,synonymous_variant,p.=,ENST00000544041,;MAP3K4,3_prime_UTR_variant,,ENST00000490904,;MAP3K4,upstream_gene_variant,,ENST00000543421,; T ENST00000392142 Transcript synonymous_variant 3382/5490 3234/4827 1078/1608 L ctG/ctT rs780920080,COSM3622637,COSM3622638 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 13/27 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs780920080 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 161092108 161092108 G T 1 0 0 0 0 0 0 0 1 9175 1277 45 2 2 MAP3K4 6 161092108 Silent SNP G C3N-00580_T 441670 161092108 9713871 409 18544 SDK1 0 . GRCh38 7 4017326 4017326 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2576C>A p.Ala859Glu p.A859E ENST00000404826 17/45 139 128 11 126 126 0 strelka-varscan-mutect SDK1,missense_variant,p.Ala859Glu,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Ala859Glu,ENST00000615806,;SDK1,missense_variant,p.Ala859Glu,ENST00000389531,; A ENST00000404826 Transcript missense_variant 2715/10397 2576/6642 859/2213 A/E gCa/gAa 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 tolerated(0.89) 17/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 4017326 4017326 C A 1 0 0 0 0 1 0 0 0 14243 710 25 2 2 SDK1 7 4017326 Missense_Mutation SNP C C3N-00580_T 4017326 155328647 410 18545 RADIL 0 . GRCh38 7 4817327 4817327 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1640G>T p.Cys547Phe p.C547F ENST00000399583 7/15 190 150 40 197 197 0 strelka-varscan-mutect RADIL,missense_variant,p.Cys547Phe,ENST00000399583,NM_018059.4;RADIL,3_prime_UTR_variant,,ENST00000445392,;RADIL,non_coding_transcript_exon_variant,,ENST00000473130,;RADIL,non_coding_transcript_exon_variant,,ENST00000484211,;RADIL,upstream_gene_variant,,ENST00000469399,; A ENST00000399583 Transcript missense_variant 1828/3689 1640/3228 547/1075 C/F tGc/tTc 1 -1 RADIL HGNC HGNC:22226 protein_coding YES CCDS43544.1 ENSP00000382492 Q96JH8 UPI0000E0A787 NM_018059.4 deleterious(0.02) 7/15 PROSITE_profiles:PS51126,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF3 MODERATE 1 SNV 5 1 PASS rs749888829 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 4817327 4817327 C A 1 0 0 0 0 1 0 0 0 13158 710 25 2 2 RADIL 7 4817327 Missense_Mutation SNP C C3N-00580_T 800001 4817327 154528646 411 18546 OCM 0 . GRCh38 7 5880906 5880906 + Missense_Mutation SNP T T A rs755888287 C3N-00580_T C3N-00580_N T T c.17T>A p.Val6Glu p.V6E ENST00000242104 1/4 259 180 79 197 197 0 strelka-varscan-mutect OCM,missense_variant,p.Val6Glu,ENST00000242104,NM_001097622.1;OCM,missense_variant,p.Val6Glu,ENST00000416608,; A ENST00000242104 Transcript missense_variant 109/695 17/330 6/109 V/E gTg/gAg rs755888287 1 1 OCM HGNC HGNC:8105 protein_coding YES CCDS43548.1 ENSP00000242104 P0CE72 UPI00001D7522 NM_001097622.1 deleterious(0) 1/4 hmmpanther:PTHR11653,hmmpanther:PTHR11653:SF8 MODERATE 1 SNV 1 1 PASS rs755888287 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 5880906 5880906 T A 1 0 0 0 0 1 0 0 0 10898 1696 59 4 4 OCM 7 5880906 Missense_Mutation SNP T C3N-00580_T 1063579 5880906 153465067 412 18547 GRID2IP 0 . GRCh38 7 6511033 6511033 + Missense_Mutation SNP G G T rs747318372 C3N-00580_T C3N-00580_N G G c.1430C>A p.Pro477Gln p.P477Q ENST00000457091 9/22 142 119 23 144 143 1 strelka-varscan-mutect GRID2IP,missense_variant,p.Pro477Gln,ENST00000457091,NM_001145118.1;GRID2IP,missense_variant,p.Pro286Gln,ENST00000452113,;GRID2IP,missense_variant,p.Pro293Gln,ENST00000435185,; T ENST00000457091 Transcript missense_variant 1430/3636 1430/3636 477/1211 P/Q cCg/cAg rs747318372 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 tolerated(0.05) 9/22 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs747318372 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 6511033 6511033 G T 1 0 0 0 0 1 0 0 0 6653 1130 39 1 1 GRID2IP 7 6511033 Missense_Mutation SNP G C3N-00580_T 630127 6511033 152834940 413 18548 TMEM106B 0 . GRCh38 7 12231972 12231972 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.822G>C p.Gln274His p.Q274H ENST00000396667 9/9 121 80 41 75 75 0 strelka-varscan-mutect TMEM106B,missense_variant,p.Gln274His,ENST00000396667,NM_018374.3;TMEM106B,missense_variant,p.Gln274His,ENST00000396668,NM_001134232.1;TMEM106B,non_coding_transcript_exon_variant,,ENST00000462754,;TMEM106B,downstream_gene_variant,,ENST00000420833,;TMEM106B,downstream_gene_variant,,ENST00000492762,; C ENST00000396667 Transcript missense_variant 1144/12539 822/825 274/274 Q/H caG/caC 1 1 TMEM106B HGNC HGNC:22407 protein_coding YES CCDS5358.1 ENSP00000379901 Q9NUM4 A0A024R9Z1 UPI000003ED3C NM_018374.3 deleterious_low_confidence(0) 9/9 hmmpanther:PTHR28556,hmmpanther:PTHR28556:SF1 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999919 1 1 1 0 C 3 2 61 12231972 12231972 G C 1 0 0 0 0 1 0 0 0 16465 1020 36 4 4 TMEM106B 7 12231972 Missense_Mutation SNP G C3N-00580_T 5720939 12231972 147114001 414 18549 MEOX2 0 . GRCh38 7 15612611 15612611 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.691G>T p.Val231Leu p.V231L ENST00000262041 3/3 294 172 122 208 208 0 strelka-varscan-mutect MEOX2,missense_variant,p.Val231Leu,ENST00000262041,NM_005924.4; A ENST00000262041 Transcript missense_variant,splice_region_variant 1101/2500 691/915 231/304 V/L Gtg/Ttg 1 -1 MEOX2 HGNC HGNC:7014 protein_coding YES CCDS34605.1 ENSP00000262041 P50222 UPI000013D247 NM_005924.4 deleterious(0.01) 3/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24328,hmmpanther:PTHR24328:SF1,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 15612611 15612611 C A 1 0 0 0 0 1 0 0 0 9419 521 18 2 2 MEOX2 7 15612611 Missense_Mutation SNP C C3N-00580_T 3380639 15612611 143733362 415 18550 SOSTDC1 0 . GRCh38 7 16462850 16462850 + Missense_Mutation SNP G G C rs780662318 C3N-00580_T C3N-00580_N G G c.319C>G p.Leu107Val p.L107V ENST00000307068 2/2 194 143 51 135 135 0 strelka-varscan-mutect SOSTDC1,missense_variant,p.Leu131Val,ENST00000396652,;SOSTDC1,missense_variant,p.Leu107Val,ENST00000307068,NM_015464.2; C ENST00000307068 Transcript missense_variant 500/1869 319/621 107/206 L/V Ctg/Gtg rs780662318 1 -1 SOSTDC1 HGNC HGNC:21748 protein_coding YES CCDS5360.1 ENSP00000304930 Q6X4U4 A4D125 UPI000004BA5E NM_015464.2 tolerated(0.13) 2/2 PROSITE_profiles:PS01225,hmmpanther:PTHR14903,hmmpanther:PTHR14903:SF5,Pfam_domain:PF05463 MODERATE 1 SNV 1 1 PASS rs780662318 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 16462850 16462850 G C 1 0 0 0 0 1 0 0 0 15261 991 35 4 4 SOSTDC1 7 16462850 Missense_Mutation SNP G C3N-00580_T 850239 16462850 142883123 416 18551 SP8 0 . GRCh38 7 20785160 20785160 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.657G>T p.Glu219Asp p.E219D ENST00000418710 2/2 219 172 47 224 224 0 strelka-varscan SP8,missense_variant,p.Glu177Asp,ENST00000617581,;SP8,missense_variant,p.Glu201Asp,ENST00000361443,NM_198956.3;SP8,missense_variant,p.Glu219Asp,ENST00000418710,NM_182700.5; A ENST00000418710 Transcript missense_variant 745/1618 657/1527 219/508 E/D gaG/gaT 1 -1 SP8 HGNC HGNC:19196 protein_coding YES CCDS43555.1 ENSP00000408792 Q8IXZ3 UPI00001AADF2 NM_182700.5 tolerated(0.71) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 20785160 20785160 C A 1 0 0 0 0 1 0 0 0 15296 680 24 2 2 SP8 7 20785160 Missense_Mutation SNP C C3N-00580_T 4322310 20785160 138560813 417 18552 IL6 0 . GRCh38 7 22727610 22727610 + Missense_Mutation SNP C C A rs764720869 C3N-00580_T C3N-00580_N C C c.186C>A p.Asp62Glu p.D62E ENST00000404625 3/6 58 44 14 32 32 0 strelka-varscan IL6,missense_variant,p.Asp62Glu,ENST00000404625,;IL6,missense_variant,p.Asp62Glu,ENST00000258743,NM_000600.3;IL6,missense_variant,p.Asp39Glu,ENST00000401630,;IL6,missense_variant,p.Asp62Glu,ENST00000406575,;IL6,missense_variant,p.Asp62Glu,ENST00000426291,;IL6,intron_variant,,ENST00000407492,NM_001318095.1;IL6,intron_variant,,ENST00000401651,;AC073072.5,non_coding_transcript_exon_variant,,ENST00000325042,;IL6,non_coding_transcript_exon_variant,,ENST00000485300,;IL6,upstream_gene_variant,,ENST00000464710,; A ENST00000404625 Transcript missense_variant 645/1527 186/639 62/212 D/E gaC/gaA rs764720869 1 1 IL6 HGNC HGNC:6018 protein_coding YES CCDS5375.1 ENSP00000385675 P05231 Q75MH2 UPI000002C4A6 tolerated(1) 3/6 hmmpanther:PTHR11457:SF0,hmmpanther:PTHR11457,PIRSF_domain:PIRSF001935,Pfam_domain:PF00489,Gene3D:1.20.1250.10,SMART_domains:SM00126,Superfamily_domains:SSF47266,Prints_domain:PR00433,Prints_domain:PR00434 MODERATE SNV 5 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 61 22727610 22727610 C A 1 0 0 0 0 1 0 0 0 7605 535 19 1 1 IL6 7 22727610 Missense_Mutation SNP C C3N-00580_T 1942450 22727610 136618363 418 18553 IL6 0 . GRCh38 7 22728796 22728796 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.314G>T p.Gly105Val p.G105V ENST00000404625 4/6 247 222 25 169 169 0 strelka-varscan IL6,missense_variant,p.Gly105Val,ENST00000404625,;IL6,missense_variant,p.Gly105Val,ENST00000258743,NM_000600.3;IL6,missense_variant,p.Gly29Val,ENST00000407492,NM_001318095.1;IL6,missense_variant,p.Gly82Val,ENST00000401630,;IL6,missense_variant,p.Gly105Val,ENST00000406575,;IL6,missense_variant,p.Gly105Val,ENST00000426291,;IL6,missense_variant,p.Gly29Val,ENST00000401651,;AC073072.5,upstream_gene_variant,,ENST00000325042,;IL6,non_coding_transcript_exon_variant,,ENST00000485300,;IL6,non_coding_transcript_exon_variant,,ENST00000464710,; T ENST00000404625 Transcript missense_variant 773/1527 314/639 105/212 G/V gGa/gTa COSM4542244,COSM4542245 1 1 IL6 HGNC HGNC:6018 protein_coding YES CCDS5375.1 ENSP00000385675 P05231 Q75MH2 UPI000002C4A6 deleterious(0.01) 4/6 hmmpanther:PTHR11457:SF0,hmmpanther:PTHR11457,PROSITE_patterns:PS00254,PIRSF_domain:PIRSF001935,Pfam_domain:PF00489,Gene3D:1.20.1250.10,SMART_domains:SM00126,Superfamily_domains:SSF47266,Prints_domain:PR00433,Prints_domain:PR00434 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 22728796 22728796 G T 1 0 0 0 0 1 0 0 0 7605 1174 41 2 2 IL6 7 22728796 Missense_Mutation SNP G C3N-00580_T 1186 22728796 136617177 419 18554 HOXA2 0 . GRCh38 7 27101200 27101200 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.657C>G p.Asp219Glu p.D219E ENST00000222718 2/2 522 377 145 506 505 1 strelka-varscan HOXA2,missense_variant,p.Asp219Glu,ENST00000222718,NM_006735.3;HOXA3,downstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA3,downstream_gene_variant,,ENST00000396352,NM_030661.4;HOTAIRM1,downstream_gene_variant,,ENST00000428939,;HOTAIRM1,downstream_gene_variant,,ENST00000429611,;HOTAIRM1,downstream_gene_variant,,ENST00000434063,;HOTAIRM1,downstream_gene_variant,,ENST00000593300,;HOTAIRM1,downstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,downstream_gene_variant,,ENST00000616712,;HOTAIRM1,downstream_gene_variant,,ENST00000495032,;HOTAIRM1_5,downstream_gene_variant,,ENST00000619311,;HOTAIRM1_1,downstream_gene_variant,,ENST00000622675,;HOTAIRM1_4,downstream_gene_variant,,ENST00000617934,;HOTAIRM1_3,downstream_gene_variant,,ENST00000619974,;HOXA2,non_coding_transcript_exon_variant,,ENST00000612779,; C ENST00000222718 Transcript missense_variant 968/1814 657/1131 219/376 D/E gaC/gaG 1 -1 HOXA2 HGNC HGNC:5103 protein_coding YES CCDS5403.1 ENSP00000222718 O43364 UPI0000049C49 NM_006735.3 tolerated(0.2) 2/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF179,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 27101200 27101200 G C 1 0 0 0 0 1 0 0 0 7186 1020 36 4 4 HOXA2 7 27101200 Missense_Mutation SNP G C3N-00580_T 4372404 27101200 132244773 420 18555 TRIL 0 . GRCh38 7 28957472 28957472 + Missense_Mutation SNP C C A rs751295953 C3N-00580_T C3N-00580_N C C c.575G>T p.Arg192Leu p.R192L ENST00000539664 1/1 355 248 107 314 314 0 strelka-varscan TRIL,missense_variant,p.Arg192Leu,ENST00000539664,NM_014817.3;AC005013.5,upstream_gene_variant,,ENST00000436594,; A ENST00000539664 Transcript missense_variant 821/4935 575/2436 192/811 R/L cGc/cTc rs751295953 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 deleterious(0.04) 1/1 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 28957472 28957472 C A 1 0 0 0 0 1 0 0 0 16974 768 27 1 1 TRIL 7 28957472 Missense_Mutation SNP C C3N-00580_T 1856272 28957472 130388501 421 18556 FAM188B 0 . GRCh38 7 30875607 30875607 + Missense_Mutation SNP G G T rs201694248 C3N-00580_T C3N-00580_N G G c.1922G>T p.Arg641Leu p.R641L ENST00000265299 15/18 181 169 12 191 191 0 strelka-varscan FAM188B,missense_variant,p.Arg641Leu,ENST00000265299,NM_032222.2;RP5-877J2.1,missense_variant,p.Arg107Leu,ENST00000509504,;INMT-FAM188B,3_prime_UTR_variant,,ENST00000458257,;FAM188B,non_coding_transcript_exon_variant,,ENST00000409881,; T ENST00000265299 Transcript missense_variant 1999/2733 1922/2274 641/757 R/L cGc/cTc rs201694248 1 1 FAM188B HGNC HGNC:21916 protein_coding YES CCDS43565.1 ENSP00000265299 Q4G0A6 UPI0000D60E7B NM_032222.2 deleterious(0) 15/18 Pfam_domain:PF13898,hmmpanther:PTHR12473,hmmpanther:PTHR12473:SF4,SMART_domains:SM01174 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 30875607 30875607 G T 1 0 0 0 0 1 0 0 0 5366 1087 38 1 1 FAM188B 7 30875607 Missense_Mutation SNP G C3N-00580_T 1918135 30875607 128470366 422 18557 AOAH 0 . GRCh38 7 36673975 36673975 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.258C>A p.= p.V86V ENST00000617267 3/22 157 128 29 148 148 0 strelka-varscan AOAH,synonymous_variant,p.=,ENST00000617267,NM_001177506.1;AOAH,synonymous_variant,p.=,ENST00000617537,NM_001637.3;AOAH,synonymous_variant,p.=,ENST00000612871,NM_001177507.1;AOAH,synonymous_variant,p.=,ENST00000435386,; T ENST00000617267 Transcript synonymous_variant 559/2398 258/2067 86/688 V gtC/gtA COSM387748 1 -1 AOAH HGNC HGNC:548 protein_coding YES CCDS75584.1 ENSP00000479664 A0A087WVT3 UPI0001D043BB NM_001177506.1 3/22 Gene3D:1.10.225.10,Pfam_domain:PF03489,PROSITE_profiles:PS50015,hmmpanther:PTHR15010,SMART_domains:SM00741,Superfamily_domains:SSF47862 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 36673975 36673975 G T 1 0 0 0 0 0 0 0 1 835 1277 45 2 2 AOAH 7 36673975 Silent SNP G C3N-00580_T 5798368 36673975 122671998 423 18558 HECW1 0 . GRCh38 7 43311909 43311909 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.174C>A p.His58Gln p.H58Q ENST00000395891 4/30 599 447 152 413 413 0 strelka-varscan HECW1,missense_variant,p.His58Gln,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.His58Gln,ENST00000453890,NM_001287059.1;HECW1,non_coding_transcript_exon_variant,,ENST00000492310,;HECW1,non_coding_transcript_exon_variant,,ENST00000464944,;HECW1,non_coding_transcript_exon_variant,,ENST00000490954,; A ENST00000395891 Transcript missense_variant 779/9501 174/4821 58/1606 H/Q caC/caA COSM3412052,COSM3412053 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated_low_confidence(0.39) 4/30 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 43311909 43311909 C A 1 0 0 0 0 1 0 0 0 6924 535 19 1 1 HECW1 7 43311909 Missense_Mutation SNP C C3N-00580_T 6637934 43311909 116034064 424 18559 NACAD 0 . GRCh38 7 45084835 45084835 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1345C>A p.Pro449Thr p.P449T ENST00000490531 2/8 191 115 76 165 165 0 strelka-varscan NACAD,missense_variant,p.Pro449Thr,ENST00000490531,NM_001146334.1;NACAD,upstream_gene_variant,,ENST00000460409,; T ENST00000490531 Transcript missense_variant 1365/4780 1345/4689 449/1562 P/T Cct/Act 1 -1 NACAD HGNC HGNC:22196 protein_coding YES CCDS47582.1 ENSP00000420477 O15069 UPI00001D747D NM_001146334.1 tolerated(0.1) 2/8 hmmpanther:PTHR21713:SF1,hmmpanther:PTHR21713 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 45084835 45084835 G T 1 0 0 0 0 1 0 0 0 10141 1174 41 2 2 NACAD 7 45084835 Missense_Mutation SNP G C3N-00580_T 1772926 45084835 114261138 425 18560 PKD1L1 0 . GRCh38 7 47840551 47840551 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.5462G>T p.Cys1821Phe p.C1821F ENST00000289672 35/57 237 189 48 209 208 1 strelka-varscan PKD1L1,missense_variant,p.Cys1821Phe,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; A ENST00000289672 Transcript missense_variant 5513/9092 5462/8550 1821/2849 C/F tGt/tTt 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.51) 35/57 PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF145,Gene3D:2.60.60.20,Pfam_domain:PF01477,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 47840551 47840551 C A 1 0 0 0 0 1 0 0 0 12060 478 17 2 2 PKD1L1 7 47840551 Missense_Mutation SNP C C3N-00580_T 2755716 47840551 111505422 426 18561 ZNF679 0 . GRCh38 7 64266453 64266453 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.820G>T p.Gly274Cys p.G274C ENST00000421025 5/5 178 124 54 104 104 0 strelka-varscan ZNF679,missense_variant,p.Gly274Cys,ENST00000421025,NM_153363.2;ZNF679,missense_variant,p.Gly274Cys,ENST00000255746,; T ENST00000421025 Transcript missense_variant 1089/1567 820/1236 274/411 G/C Ggc/Tgc COSM5237478 1 1 ZNF679 HGNC HGNC:28650 protein_coding YES CCDS47592.1 ENSP00000416809 Q8IYX0 UPI000045756A NM_153363.2 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF91,hmmpanther:PTHR24384,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 64266453 64266453 G T 1 0 0 0 0 1 0 0 0 18659 1348 47 2 2 ZNF679 7 64266453 Missense_Mutation SNP G C3N-00580_T 16425902 64266453 95079520 427 18562 WBSCR17 0 . GRCh38 7 71421000 71421000 + Missense_Mutation SNP A A G rs772568078 C3N-00580_T C3N-00580_N A A c.857A>G p.Gln286Arg p.Q286R ENST00000333538 5/11 680 611 69 501 501 0 strelka-varscan-mutect WBSCR17,missense_variant,p.Gln286Arg,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Gln207Arg,ENST00000618959,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; G ENST00000333538 Transcript missense_variant 1491/3884 857/1797 286/598 Q/R cAg/cGg rs772568078,COSM1270351 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 tolerated(0.14) 5/11 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772568078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 71421000 71421000 A G 1 0 0 0 0 1 0 0 0 17823 188 7 5 5 WBSCR17 7 71421000 Missense_Mutation SNP A C3N-00580_T 7154547 71421000 87924973 428 18563 CLIP2 0 . GRCh38 7 74357468 74357468 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1206G>T p.Gln402His p.Q402H ENST00000223398 6/17 260 144 116 243 242 1 strelka-varscan-mutect CLIP2,missense_variant,p.Gln402His,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Gln402His,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Gln402His,ENST00000395060,; T ENST00000223398 Transcript missense_variant 1533/5563 1206/3141 402/1046 Q/H caG/caT 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 deleterious(0.03) 6/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 74357468 74357468 G T 1 0 0 0 0 1 0 0 0 3302 962 34 2 2 CLIP2 7 74357468 Missense_Mutation SNP G C3N-00580_T 2936468 74357468 84988505 429 18564 RSBN1L 0 . GRCh38 7 77749618 77749618 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.898A>G p.Ile300Val p.I300V ENST00000334955 3/8 223 201 22 190 190 0 strelka-varscan-mutect RSBN1L,missense_variant,p.Ile300Val,ENST00000334955,NM_198467.2;RSBN1L,missense_variant,p.Ile30Val,ENST00000445288,; G ENST00000334955 Transcript missense_variant 925/6422 898/2541 300/846 I/V Ata/Gta 1 1 RSBN1L HGNC HGNC:24765 protein_coding YES CCDS43607.1 ENSP00000334040 Q6PCB5 UPI000020F469 NM_198467.2 tolerated(0.36) 3/8 hmmpanther:PTHR13354:SF9,hmmpanther:PTHR13354 MODERATE 1 SNV 1 1 PASS rs1404707318 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 77749618 77749618 A G 1 0 0 0 0 1 0 0 0 13953 217 8 5 5 RSBN1L 7 77749618 Missense_Mutation SNP A C3N-00580_T 3392150 77749618 81596355 430 18565 GNAI1 0 . GRCh38 7 80189208 80189208 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.280G>T p.Asp94Tyr p.D94Y ENST00000351004 3/8 91 85 6 206 206 0 strelka-mutect GNAI1,missense_variant,p.Asp94Tyr,ENST00000351004,NM_002069.5;GNAI1,missense_variant,p.Asp42Tyr,ENST00000457358,NM_001256414.1;GNAI1,missense_variant,p.Asp42Tyr,ENST00000418742,;GNAI1,incomplete_terminal_codon_variant,p.=,ENST00000447650,;GNAI1,non_coding_transcript_exon_variant,,ENST00000490206,; T ENST00000351004 Transcript missense_variant 653/3347 280/1065 94/354 D/Y Gac/Tac 1 1 GNAI1 HGNC HGNC:4384 protein_coding YES CCDS5595.1 ENSP00000343027 P63096 UPI000000124A NM_002069.5 deleterious(0) 3/8 Gene3D:1.10.400.10,Pfam_domain:PF00503,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF227,SMART_domains:SM00275,Superfamily_domains:SSF47895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 80189208 80189208 G T 1 0 0 0 0 1 0 0 0 6384 942 33 2 2 GNAI1 7 80189208 Missense_Mutation SNP G C3N-00580_T 2439590 80189208 79156765 431 18566 GRM3 0 . GRCh38 7 86839252 86839252 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1738C>A p.Pro580Thr p.P580T ENST00000361669 4/6 284 168 116 212 212 0 strelka-varscan-mutect GRM3,missense_variant,p.Pro580Thr,ENST00000361669,NM_000840.2;GRM3,intron_variant,,ENST00000439827,; A ENST00000361669 Transcript missense_variant 2837/4268 1738/2640 580/879 P/T Cca/Aca 1 1 GRM3 HGNC HGNC:4595 protein_coding YES CCDS5600.1 ENSP00000355316 Q14832 A4D1D0 UPI0000153EFC NM_000840.2 deleterious(0.02) 4/6 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF107 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 86839252 86839252 C A 1 0 0 0 0 1 0 0 0 6680 623 22 2 2 GRM3 7 86839252 Missense_Mutation SNP C C3N-00580_T 6650044 86839252 72506721 432 18567 ABCB1 0 . GRCh38 7 87505954 87505954 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3579G>T p.Gln1193His p.Q1193H ENST00000622132 27/28 541 413 128 391 390 1 strelka-varscan-mutect ABCB1,missense_variant,p.Gln1193His,ENST00000622132,;ABCB1,missense_variant,p.Gln1193His,ENST00000265724,NM_000927.4;ABCB1,missense_variant,p.Gln1129His,ENST00000543898,;ABCB1,non_coding_transcript_exon_variant,,ENST00000488737,;ABCB1,non_coding_transcript_exon_variant,,ENST00000475929,;ABCB1,non_coding_transcript_exon_variant,,ENST00000491360,; A ENST00000622132 Transcript missense_variant 3904/4778 3579/3843 1193/1280 Q/H caG/caT 1 -1 ABCB1 HGNC HGNC:40 protein_coding YES CCDS5608.1 ENSP00000478255 P08183 A4D1D2 UPI000013D66C tolerated(0.09) 27/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 87505954 87505954 C A 1 0 0 0 0 1 0 0 0 44 796 28 2 2 ABCB1 7 87505954 Missense_Mutation SNP C C3N-00580_T 666702 87505954 71840019 433 18568 C7orf62 0 . GRCh38 7 88794866 88794866 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.77C>A p.Pro26Gln p.P26Q ENST00000297203 2/2 143 83 60 122 122 0 strelka-varscan-mutect C7orf62,missense_variant,p.Pro26Gln,ENST00000297203,NM_152706.3;ZNF804B,intron_variant,,ENST00000333190,NM_181646.3; T ENST00000297203 Transcript missense_variant 263/1023 77/762 26/253 P/Q cCa/cAa 1 -1 C7orf62 HGNC HGNC:22402 protein_coding YES CCDS34678.1 ENSP00000297203 Q8TBZ9 UPI000005034C NM_152706.3 deleterious_low_confidence(0.01) 2/2 hmmpanther:PTHR34035,hmmpanther:PTHR34035:SF1 MODERATE 1 SNV 1 1 PASS rs1226326431 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 88794866 88794866 G T 1 0 0 0 0 1 0 0 0 2146 1348 47 2 2 C7orf62 7 88794866 Missense_Mutation SNP G C3N-00580_T 1288912 88794866 70551107 434 18569 AKAP9 0 . GRCh38 7 92076935 92076935 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.6693G>A p.Met2231Ile p.M2231I ENST00000356239 29/50 80 66 14 49 49 0 strelka-varscan-mutect AKAP9,missense_variant,p.Met2231Ile,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,missense_variant,p.Met2242Ile,ENST00000359028,;AKAP9,missense_variant,p.Met2184Ile,ENST00000358100,;AKAP9,missense_variant,p.Met77Ile,ENST00000394534,; A ENST00000356239 Transcript missense_variant 6926/12471 6693/11724 2231/3907 M/I atG/atA 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 deleterious(0) 29/50 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF252 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 92076935 92076935 G A 1 0 0 0 0 1 0 0 0 543 1319 46 3 3 AKAP9 7 92076935 Missense_Mutation SNP G C3N-00580_T 3282069 92076935 67269038 435 18570 KRIT1 0 . GRCh38 7 92237681 92237681 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.341C>T p.Pro114Leu p.P114L ENST00000394507 7/20 168 127 41 225 225 0 strelka-varscan-mutect KRIT1,missense_variant,p.Pro114Leu,ENST00000394507,NM_194456.1;KRIT1,missense_variant,p.Pro114Leu,ENST00000340022,NM_194455.1,NM_004912.3;KRIT1,missense_variant,p.Pro114Leu,ENST00000412043,;KRIT1,missense_variant,p.Pro114Leu,ENST00000394505,NM_194454.1;KRIT1,missense_variant,p.Pro114Leu,ENST00000394503,NM_001013406.1;KRIT1,missense_variant,p.Pro114Leu,ENST00000458177,;KRIT1,missense_variant,p.Pro114Leu,ENST00000454017,;KRIT1,missense_variant,p.Pro114Leu,ENST00000433016,;KRIT1,downstream_gene_variant,,ENST00000444960,;KRIT1,downstream_gene_variant,,ENST00000430102,;KRIT1,downstream_gene_variant,,ENST00000452773,;KRIT1,downstream_gene_variant,,ENST00000425919,;KRIT1,upstream_gene_variant,,ENST00000445516,;KRIT1,downstream_gene_variant,,ENST00000440209,;KRIT1,downstream_gene_variant,,ENST00000413688,;KRIT1,downstream_gene_variant,,ENST00000425073,;KRIT1,downstream_gene_variant,,ENST00000458493,;KRIT1,downstream_gene_variant,,ENST00000422347,;KRIT1,non_coding_transcript_exon_variant,,ENST00000486261,;KRIT1,upstream_gene_variant,,ENST00000475770,;KRIT1,downstream_gene_variant,,ENST00000470309,; A ENST00000394507 Transcript missense_variant 1125/4762 341/2211 114/736 P/L cCa/cTa 1 -1 KRIT1 HGNC HGNC:1573 protein_coding YES CCDS5624.1 ENSP00000378015 O00522 A4D1F7 UPI000006F5AA NM_194456.1 deleterious(0) 7/20 hmmpanther:PTHR13283,Pfam_domain:PF16705 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 92237681 92237681 G A 1 0 0 0 0 1 0 0 0 8327 1348 47 3 3 KRIT1 7 92237681 Missense_Mutation SNP G C3N-00580_T 160746 92237681 67108292 436 18571 CDK6 0 . GRCh38 7 92833095 92833095 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.229G>C p.Val77Leu p.V77L ENST00000265734 2/8 202 158 44 137 137 0 strelka-varscan-mutect CDK6,missense_variant,p.Val77Leu,ENST00000265734,NM_001259.6;CDK6,missense_variant,p.Val77Leu,ENST00000424848,NM_001145306.1;AC002454.1,upstream_gene_variant,,ENST00000435695,;AC002454.1,upstream_gene_variant,,ENST00000452050,;CDK6,downstream_gene_variant,,ENST00000491250,; G ENST00000265734 Transcript missense_variant 641/11612 229/981 77/326 V/L Gtc/Ctc 1 -1 CDK6 HGNC HGNC:1777 protein_coding YES CCDS5628.1 ENSP00000265734 Q00534 UPI00001108FA NM_001259.6 deleterious(0.01) 2/8 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF130,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 92833095 92833095 C G 1 0 0 0 0 1 0 0 0 2852 521 18 4 4 CDK6 7 92833095 Missense_Mutation SNP C C3N-00580_T 595414 92833095 66512878 437 18572 DLX6 0 . GRCh38 7 97009952 97009952 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.787G>T p.Gly263Cys p.G263C ENST00000518156 3/3 621 520 101 508 508 0 strelka-varscan-mutect DLX6,missense_variant,p.Gly263Cys,ENST00000518156,NM_005222.3;DLX6,missense_variant,p.Gly135Cys,ENST00000555308,;DLX6-AS1,intron_variant,,ENST00000430027,;DLX6-AS1,intron_variant,,ENST00000605417,;DLX6-AS1,intron_variant,,ENST00000437331,;DLX6-AS1,intron_variant,,ENST00000452769,;DLX6-AS1,intron_variant,,ENST00000458352,;DLX6-AS1,intron_variant,,ENST00000430404,;DLX6-AS1,intron_variant,,ENST00000437541,;Evf-2_5p,downstream_gene_variant,,ENST00000614213,;DLX6,non_coding_transcript_exon_variant,,ENST00000493273,; T ENST00000518156 Transcript missense_variant 1217/2304 787/882 263/293 G/C Ggt/Tgt 1 1 DLX6 HGNC HGNC:2919 protein_coding YES CCDS47647.2 ENSP00000428480 P56179 UPI0000EE57E0 NM_005222.3 deleterious(0) 3/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF26 MODERATE 1 SNV 1 1 PASS rs1160525363 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 97009952 97009952 G T 1 0 0 0 0 1 0 0 0 4382 1232 43 2 2 DLX6 7 97009952 Missense_Mutation SNP G C3N-00580_T 4176857 97009952 62336021 438 18573 TMEM130 0 . GRCh38 7 98848594 98848594 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1108G>T p.Asp370Tyr p.D370Y ENST00000416379 7/8 293 187 106 212 212 0 strelka-varscan-mutect TMEM130,missense_variant,p.Asp286Tyr,ENST00000450876,;TMEM130,missense_variant,p.Asp370Tyr,ENST00000339375,NM_152913.2;TMEM130,missense_variant,p.Asp370Tyr,ENST00000416379,NM_001134450.1;TMEM130,missense_variant,p.Asp268Tyr,ENST00000345589,NM_001134451.1;TMEM130,upstream_gene_variant,,ENST00000474857,;TMEM130,downstream_gene_variant,,ENST00000461092,; A ENST00000416379 Transcript missense_variant 1113/2881 1108/1308 370/435 D/Y Gac/Tac 1 -1 TMEM130 HGNC HGNC:25429 protein_coding YES CCDS47650.1 ENSP00000413163 Q8N3G9 UPI000006EF2E NM_001134450.1 deleterious(0) 7/8 hmmpanther:PTHR11861:SF10,hmmpanther:PTHR11861 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 98848594 98848594 C A 1 0 0 0 0 1 0 0 0 16487 855 30 2 2 TMEM130 7 98848594 Missense_Mutation SNP C C3N-00580_T 1838642 98848594 60497379 439 18574 68 2 TMEM130 0 . GRCh38 7 98848599 98848599 + Missense_Mutation SNP T T G novel C3N-00580_T C3N-00580_N T T c.1103A>C p.Gln368Pro p.Q368P ENST00000416379 7/8 321 207 114 230 229 1 strelka-varscan-mutect TMEM130,missense_variant,p.Gln284Pro,ENST00000450876,;TMEM130,missense_variant,p.Gln368Pro,ENST00000339375,NM_152913.2;TMEM130,missense_variant,p.Gln368Pro,ENST00000416379,NM_001134450.1;TMEM130,missense_variant,p.Gln266Pro,ENST00000345589,NM_001134451.1;TMEM130,upstream_gene_variant,,ENST00000474857,;TMEM130,downstream_gene_variant,,ENST00000461092,; G ENST00000416379 Transcript missense_variant 1108/2881 1103/1308 368/435 Q/P cAa/cCa 1 -1 TMEM130 HGNC HGNC:25429 protein_coding YES CCDS47650.1 ENSP00000413163 Q8N3G9 UPI000006EF2E NM_001134450.1 tolerated(0.11) 7/8 hmmpanther:PTHR11861:SF10,hmmpanther:PTHR11861 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 98848599 98848599 T G 1 0 0 0 0 1 0 0 0 16487 1812 63 5 5 TMEM130 7 98848599 Missense_Mutation SNP T C3N-00580_T 5 98848599 60497374 440 18575 68 2 STAG3 0 . GRCh38 7 100202502 100202502 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.2612G>A p.Arg871His p.R871H ENST00000615138 25/34 194 142 52 163 163 0 strelka-varscan-mutect STAG3,missense_variant,p.Arg871His,ENST00000426455,NM_001282716.1;STAG3,missense_variant,p.Arg871His,ENST00000615138,NM_001282717.1;STAG3,missense_variant,p.Arg813His,ENST00000620100,;STAG3,missense_variant,p.Arg871His,ENST00000317296,NM_012447.3;STAG3,missense_variant,p.Arg813His,ENST00000394018,NM_001282718.1;GATS,3_prime_UTR_variant,,ENST00000436886,NM_178831.6;GATS,3_prime_UTR_variant,,ENST00000454084,;STAG3,upstream_gene_variant,,ENST00000412190,;STAG3,non_coding_transcript_exon_variant,,ENST00000440830,;STAG3,non_coding_transcript_exon_variant,,ENST00000491498,;GATS,non_coding_transcript_exon_variant,,ENST00000440058,;GATS,non_coding_transcript_exon_variant,,ENST00000414997,;GATS,non_coding_transcript_exon_variant,,ENST00000437485,;GATS,3_prime_UTR_variant,,ENST00000328453,;GATS,3_prime_UTR_variant,,ENST00000543273,;STAG3,intron_variant,,ENST00000496157,;STAG3,upstream_gene_variant,,ENST00000451963,;STAG3,downstream_gene_variant,,ENST00000479359,;STAG3,downstream_gene_variant,,ENST00000477469,;STAG3,downstream_gene_variant,,ENST00000476057,; A ENST00000615138 Transcript missense_variant 2939/4380 2612/3681 871/1226 R/H cGc/cAc 1 1 STAG3 HGNC HGNC:11356 protein_coding YES CCDS75642.1 ENSP00000477973 D6W5U7 UPI000048108A NM_001282717.1 deleterious(0) 25/34 hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF9 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 100202502 100202502 G A 1 0 0 0 0 1 0 0 0 15622 1087 38 1 1 STAG3 7 100202502 Missense_Mutation SNP G C3N-00580_T 1353903 100202502 59143471 441 18576 ZCWPW1 0 . GRCh38 7 100401076 100401076 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1885G>T p.Gly629Trp p.G629W ENST00000398027 18/18 193 174 19 209 209 0 strelka-varscan-mutect ZCWPW1,missense_variant,p.Gly629Trp,ENST00000398027,NM_017984.4;ZCWPW1,missense_variant,p.Gly458Trp,ENST00000490721,;ZCWPW1,3_prime_UTR_variant,,ENST00000360951,NM_001258008.1;PILRA,downstream_gene_variant,,ENST00000198536,NM_013439.2;PILRA,downstream_gene_variant,,ENST00000453419,;PILRA,downstream_gene_variant,,ENST00000350573,NM_178272.1;PILRA,downstream_gene_variant,,ENST00000394000,NM_178273.1;ZCWPW1,downstream_gene_variant,,ENST00000471336,;PILRA,downstream_gene_variant,,ENST00000432297,;ZCWPW1,non_coding_transcript_exon_variant,,ENST00000490089,;ZCWPW1,non_coding_transcript_exon_variant,,ENST00000479315,; A ENST00000398027 Transcript missense_variant 2133/2356 1885/1947 629/648 G/W Ggg/Tgg COSM3412592 1 -1 ZCWPW1 HGNC HGNC:23486 protein_coding YES CCDS43623.1 ENSP00000381109 Q9H0M4 UPI000014146E NM_017984.4 deleterious_low_confidence(0.03) 18/18 hmmpanther:PTHR15999,hmmpanther:PTHR15999:SF4 1 MODERATE 1 SNV 1 1 1 PASS rs1368756919 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 61 100401076 100401076 C A 1 0 0 0 0 1 0 0 0 18172 652 23 1 1 ZCWPW1 7 100401076 Missense_Mutation SNP C C3N-00580_T 198574 100401076 58944897 442 18577 POP7 0 . GRCh38 7 100707047 100707047 + Missense_Mutation SNP G G T rs758799064 C3N-00580_T C3N-00580_N G G c.217G>T p.Gly73Cys p.G73C ENST00000303151 2/2 791 648 143 519 518 1 strelka-varscan-mutect POP7,missense_variant,p.Gly73Cys,ENST00000303151,NM_005837.2;POP7,missense_variant,p.Gly73Cys,ENST00000457480,; T ENST00000303151 Transcript missense_variant 479/927 217/423 73/140 G/C Ggc/Tgc rs758799064 1 1 POP7 HGNC HGNC:19949 protein_coding YES CCDS5704.1 ENSP00000304353 O75817 UPI000006E530 NM_005837.2 deleterious(0) 2/2 hmmpanther:PTHR15314,PIRSF_domain:PIRSF036572,Gene3D:3.30.110.20,Pfam_domain:PF12328,Superfamily_domains:SSF82704 MODERATE 1 SNV 1 1 PASS rs758799064 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 100707047 100707047 G T 1 0 0 0 0 1 0 0 0 12368 1116 39 1 1 POP7 7 100707047 Missense_Mutation SNP G C3N-00580_T 305971 100707047 58638926 443 18578 MUC12 0 . GRCh38 7 101003862 101003862 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.13299T>A p.= p.R4433R ENST00000536621 2/12 3027 2829 198 2911 2910 1 varscan-mutect MUC12,synonymous_variant,p.=,ENST00000379442,;MUC12,synonymous_variant,p.=,ENST00000536621,NM_001164462.1; A ENST00000536621 Transcript synonymous_variant 13299/16321 13299/16008 4433/5335 R cgT/cgA 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 2/12 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs1360826339 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 101003862 101003862 T A 1 0 0 0 0 0 0 0 1 9969 1683 59 4 4 MUC12 7 101003862 Silent SNP T C3N-00580_T 296815 101003862 58342111 444 18579 MUC17 0 . GRCh38 7 101033278 101033278 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1862C>T p.Thr621Ile p.T621I ENST00000306151 3/13 284 181 103 223 223 0 strelka-varscan-mutect MUC17,missense_variant,p.Thr621Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Thr621Ile,ENST00000379439,; T ENST00000306151 Transcript missense_variant 1926/14247 1862/13482 621/4493 T/I aCc/aTc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.23) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS rs1339341695 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 101033278 101033278 C T 1 0 0 0 0 1 0 0 0 9973 507 18 3 3 MUC17 7 101033278 Missense_Mutation SNP C C3N-00580_T 29416 101033278 58312695 445 18580 MUC17 0 . GRCh38 7 101035516 101035516 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.4100C>G p.Pro1367Arg p.P1367R ENST00000306151 3/13 105 74 31 91 91 0 strelka-varscan-mutect MUC17,missense_variant,p.Pro1367Arg,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Pro1367Arg,ENST00000379439,; G ENST00000306151 Transcript missense_variant 4164/14247 4100/13482 1367/4493 P/R cCt/cGt 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0.01) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 101035516 101035516 C G 1 0 0 0 0 1 0 0 0 9973 681 24 4 4 MUC17 7 101035516 Missense_Mutation SNP C C3N-00580_T 2238 101035516 58310457 446 18581 MUC17 0 . GRCh38 7 101036459 101036459 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.5043A>T p.= p.P1681P ENST00000306151 3/13 175 133 42 133 133 0 strelka-varscan-mutect MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; T ENST00000306151 Transcript synonymous_variant 5107/14247 5043/13482 1681/4493 P ccA/ccT 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 101036459 101036459 A T 1 0 0 0 0 0 0 0 1 9973 117 5 4 4 MUC17 7 101036459 Silent SNP A C3N-00580_T 943 101036459 58309514 447 18582 CUX1 0 . GRCh38 7 102273416 102273416 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1306A>T p.Thr436Ser p.T436S ENST00000437600 15/23 288 205 83 312 312 0 strelka-varscan-mutect CUX1,missense_variant,p.Thr436Ser,ENST00000437600,NM_001913.4;CUX1,missense_variant,p.Thr434Ser,ENST00000622516,NM_181500.3;CUX1,missense_variant,p.Thr436Ser,ENST00000292538,;CUX1,missense_variant,p.Thr420Ser,ENST00000547394,NM_001202544.2;CUX1,missense_variant,p.Thr390Ser,ENST00000425244,NM_001202545.2;CUX1,missense_variant,p.Thr397Ser,ENST00000393824,NM_001202546.2;CUX1,non_coding_transcript_exon_variant,,ENST00000560541,;CUX1,non_coding_transcript_exon_variant,,ENST00000558836,;CUX1,upstream_gene_variant,,ENST00000487284,; T ENST00000437600 Transcript missense_variant 1433/3031 1306/2037 436/678 T/S Act/Tct 1 1 CUX1 HGNC HGNC:2557 protein_coding CCDS5720.1 ENSP00000414091 Q13948 UPI00001A95D5 NM_001913.4 tolerated(1) 15/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14043:SF15,hmmpanther:PTHR14043,Pfam_domain:PF08172 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 102273416 102273416 A T 1 0 0 0 0 1 0 0 0 3874 159 6 4 4 CUX1 7 102273416 Missense_Mutation SNP A C3N-00580_T 1236957 102273416 57072557 448 18583 ARMC10 0 . GRCh38 7 103086703 103086703 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.467A>G p.Glu156Gly p.E156G ENST00000323716 4/7 105 89 16 136 136 0 strelka-varscan-mutect ARMC10,missense_variant,p.Glu156Gly,ENST00000323716,NM_031905.4;ARMC10,missense_variant,p.Glu121Gly,ENST00000441711,NM_001161009.2;ARMC10,missense_variant,p.Glu156Gly,ENST00000428183,NM_001161010.2;ARMC10,missense_variant,p.Glu121Gly,ENST00000425331,NM_001161011.2;ARMC10,missense_variant,p.Glu121Gly,ENST00000454559,NM_001161012.2;ARMC10,missense_variant,p.Glu121Gly,ENST00000541300,NM_001161013.2;ARMC10,missense_variant,p.Glu167Gly,ENST00000434153,;ARMC10,missense_variant,p.Glu22Gly,ENST00000431642,;ARMC10,missense_variant,p.Glu156Gly,ENST00000323735,;ARMC10,3_prime_UTR_variant,,ENST00000306450,;CRYZP1,downstream_gene_variant,,ENST00000428923,; G ENST00000323716 Transcript missense_variant 859/2635 467/1032 156/343 E/G gAg/gGg 1 1 ARMC10 HGNC HGNC:21706 protein_coding YES CCDS5728.1 ENSP00000319412 Q8N2F6 UPI0000039E55 NM_031905.4 deleterious(0) 4/7 Gene3D:1.25.10.10,Pfam_domain:PF04826,hmmpanther:PTHR15712,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 103086703 103086703 A G 1 0 0 0 0 1 0 0 0 1090 304 11 5 5 ARMC10 7 103086703 Missense_Mutation SNP A C3N-00580_T 813287 103086703 56259270 449 18584 RELN 0 . GRCh38 7 103700965 103700965 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.847A>T p.Ile283Phe p.I283F ENST00000428762 9/65 580 389 191 462 462 0 strelka-varscan-mutect RELN,missense_variant,p.Ile283Phe,ENST00000424685,;RELN,missense_variant,p.Ile283Phe,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Ile283Phe,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 1007/11571 847/10383 283/3460 I/F Atc/Ttc 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.06) 9/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 103700965 103700965 T A 1 0 0 0 0 1 0 0 0 13390 1464 51 4 4 RELN 7 103700965 Missense_Mutation SNP T C3N-00580_T 614262 103700965 55645008 450 18585 IFRD1 0 . GRCh38 7 112456032 112456032 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.230A>T p.Gln77Leu p.Q77L ENST00000403825 3/12 555 415 140 416 416 0 strelka-varscan-mutect IFRD1,missense_variant,p.Gln27Leu,ENST00000535603,NM_001197079.1;IFRD1,missense_variant,p.Gln27Leu,ENST00000621379,NM_001197080.1;IFRD1,missense_variant,p.Gln77Leu,ENST00000403825,NM_001550.3;IFRD1,missense_variant,p.Gln77Leu,ENST00000429071,;IFRD1,missense_variant,p.Gln77Leu,ENST00000005558,NM_001007245.2;IFRD1,missense_variant,p.Gln27Leu,ENST00000440625,;IFRD1,missense_variant,p.Gln27Leu,ENST00000476927,;IFRD1,missense_variant,p.Gln27Leu,ENST00000443101,;IFRD1,downstream_gene_variant,,ENST00000445335,;IFRD1,upstream_gene_variant,,ENST00000486688,;IFRD1,upstream_gene_variant,,ENST00000466459,; T ENST00000403825 Transcript missense_variant 491/2290 230/1356 77/451 Q/L cAa/cTa 1 1 IFRD1 HGNC HGNC:5456 protein_coding YES CCDS34736.1 ENSP00000384477 O00458 A4D0U1 UPI00000304DC NM_001550.3 deleterious(0.01) 3/12 hmmpanther:PTHR12354:SF6,hmmpanther:PTHR12354,Pfam_domain:PF05004 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 112456032 112456032 A T 1 0 0 0 0 1 0 0 0 7457 130 5 4 4 IFRD1 7 112456032 Missense_Mutation SNP A C3N-00580_T 8755067 112456032 46889941 451 18586 PTPRZ1 0 . GRCh38 7 122012665 122012665 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.3619A>T p.Ile1207Leu p.I1207L ENST00000393386 12/30 265 191 74 215 215 0 strelka-varscan-mutect PTPRZ1,missense_variant,p.Ile1207Leu,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; T ENST00000393386 Transcript missense_variant 4030/8175 3619/6948 1207/2315 I/L Ata/Tta 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 tolerated_low_confidence(0.15) 12/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 122012665 122012665 A T 1 0 0 0 0 1 0 0 0 12969 101 4 4 4 PTPRZ1 7 122012665 Missense_Mutation SNP A C3N-00580_T 9556633 122012665 37333308 452 18587 PTPRZ1 0 . GRCh38 7 122051441 122051441 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.6098C>A p.Ser2033Ter p.S2033* ENST00000393386 24/30 194 154 40 163 163 0 strelka-varscan-mutect PTPRZ1,stop_gained,p.Ser2033Ter,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,stop_gained,p.Ser1166Ter,ENST00000449182,NM_001206839.1; A ENST00000393386 Transcript stop_gained 6509/8175 6098/6948 2033/2315 S/* tCa/tAa 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 24/30 PROSITE_profiles:PS50055,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.999999 1 1 1 0 A 4 1 61 122051441 122051441 C A 1 0 0 0 0 0 1 0 0 12969 838 29 2 2 PTPRZ1 7 122051441 Nonsense_Mutation SNP C C3N-00580_T 38776 122051441 37294532 453 18588 FEZF1 0 . GRCh38 7 122302138 122302138 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1287G>T p.= p.L429L ENST00000442488 4/4 444 324 120 454 454 0 strelka-varscan-mutect FEZF1,synonymous_variant,p.=,ENST00000442488,NM_001024613.3;FEZF1,synonymous_variant,p.=,ENST00000427185,NM_001160264.2;FEZF1,downstream_gene_variant,,ENST00000418046,;FEZF1-AS1,upstream_gene_variant,,ENST00000428449,;FEZF1-AS1,upstream_gene_variant,,ENST00000437317,;FEZF1-AS1,upstream_gene_variant,,ENST00000424404,; A ENST00000442488 Transcript synonymous_variant 1355/2099 1287/1428 429/475 L ctG/ctT 1 -1 FEZF1 HGNC HGNC:22788 protein_coding YES CCDS34741.2 ENSP00000411145 A0PJY2 UPI00004193D6 NM_001024613.3 4/4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 122302138 122302138 C A 1 0 0 0 0 0 0 0 1 5688 581 21 2 2 FEZF1 7 122302138 Silent SNP C C3N-00580_T 250697 122302138 37043835 454 18589 LMOD2 0 . GRCh38 7 123662237 123662237 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.651T>A p.Asn217Lys p.N217K ENST00000458573 2/3 325 246 79 297 297 0 strelka-varscan-mutect LMOD2,missense_variant,p.Asn217Lys,ENST00000458573,NM_207163.1;LMOD2,intron_variant,,ENST00000456238,; A ENST00000458573 Transcript missense_variant 808/2346 651/1644 217/547 N/K aaT/aaA 1 1 LMOD2 HGNC HGNC:6648 protein_coding YES CCDS47693.1 ENSP00000411932 Q6P5Q4 UPI0001572CCA NM_207163.1 deleterious(0) 2/3 Gene3D:3.80.10.10,hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF12,Superfamily_domains:SSF52047 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 123662237 123662237 T A 1 0 0 0 0 1 0 0 0 8784 1490 52 4 4 LMOD2 7 123662237 Missense_Mutation SNP T C3N-00580_T 1360099 123662237 35683736 455 18590 TMEM229A 0 . GRCh38 7 124031967 124031967 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.1037T>C p.Met346Thr p.M346T ENST00000455783 1/1 374 328 46 275 275 0 strelka-varscan-mutect TMEM229A,missense_variant,p.Met346Thr,ENST00000455783,NM_001136002.1;RP5-921G16.1,upstream_gene_variant,,ENST00000484322,;RP4-630C24.3,downstream_gene_variant,,ENST00000472838,; G ENST00000455783 Transcript missense_variant 1057/2108 1037/1143 346/380 M/T aTg/aCg 1 -1 TMEM229A HGNC HGNC:37279 protein_coding YES CCDS47694.1 ENSP00000395244 B2RXF0 UPI0001823FDC NM_001136002.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR31746,hmmpanther:PTHR31746:SF2 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 124031967 124031967 A G 1 0 0 0 0 1 0 0 0 16589 217 8 5 5 TMEM229A 7 124031967 Missense_Mutation SNP A C3N-00580_T 369730 124031967 35314006 456 18591 LEP 0 . GRCh38 7 128252138 128252138 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.120C>A p.= p.T40T ENST00000308868 2/3 761 632 129 493 493 0 strelka-varscan-mutect LEP,synonymous_variant,p.=,ENST00000308868,NM_000230.2; A ENST00000308868 Transcript synonymous_variant 171/3420 120/504 40/167 T acC/acA 1 1 LEP HGNC HGNC:6553 protein_coding YES CCDS5800.1 ENSP00000312652 P41159 A4D0Y8 UPI00000308D4 NM_000230.2 2/3 hmmpanther:PTHR11724:SF1,hmmpanther:PTHR11724,Gene3D:1.20.1250.10,PIRSF_domain:PIRSF001837,Pfam_domain:PF02024,Superfamily_domains:SSF47266,Prints_domain:PR00495,PD005698 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 128252138 128252138 C A 1 0 0 0 0 0 0 0 1 8635 581 21 2 2 LEP 7 128252138 Silent SNP C C3N-00580_T 4220171 128252138 31093835 457 18592 FAM71F1 0 . GRCh38 7 128716893 128716893 + Silent SNP C C T rs115473588 C3N-00580_T C3N-00580_N C C c.330C>T p.= p.C110C ENST00000315184 2/7 256 193 63 216 216 0 strelka-varscan-mutect FAM71F1,missense_variant,p.Pro32Ser,ENST00000621392,;FAM71F1,missense_variant,p.Pro32Ser,ENST00000485070,NM_001282789.1;FAM71F1,synonymous_variant,p.=,ENST00000315184,NM_001282788.1,NM_032599.3;FAM71F1,upstream_gene_variant,,ENST00000466842,;FAM71F1,non_coding_transcript_exon_variant,,ENST00000469348,;FAM71F1,non_coding_transcript_exon_variant,,ENST00000483459,;FAM71F1,synonymous_variant,p.=,ENST00000471558,;FAM71F1,5_prime_UTR_variant,,ENST00000484425,;FAM71F1,non_coding_transcript_exon_variant,,ENST00000493738,; T ENST00000315184 Transcript synonymous_variant 383/1718 330/1035 110/344 C tgC/tgT rs115473588 1 1 FAM71F1 HGNC HGNC:30704 protein_coding YES CCDS5804.1 ENSP00000326652 Q96KD3 A0A140VJJ3 UPI000006D961 NM_001282788.1,NM_032599.3 2/7 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF13 LOW 1 SNV 1 1 PASS rs115473588 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 128716893 128716893 C T 1 0 0 0 0 0 0 0 1 5477 748 26 3 3 FAM71F1 7 128716893 Silent SNP C C3N-00580_T 464755 128716893 30629080 458 18593 FLNC 0 . GRCh38 7 128852743 128852743 + Silent SNP C C A rs746182820 C3N-00580_T C3N-00580_N C C c.5995C>A p.= p.R1999R ENST00000325888 36/48 323 197 126 238 238 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; A ENST00000325888 Transcript synonymous_variant 6256/9188 5995/8178 1999/2725 R Cgg/Agg rs746182820,COSM260963 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 36/48 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 0,1 LOW 1 SNV 1 0,1 1 PASS rs746182820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 128852743 128852743 C A 1 0 0 0 0 0 0 0 1 5791 643 23 1 1 FLNC 7 128852743 Silent SNP C C3N-00580_T 135850 128852743 30493230 459 18594 FLNC 0 . GRCh38 7 128854612 128854612 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.6927G>T p.= p.L2309L ENST00000325888 41/48 449 327 122 348 348 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; T ENST00000325888 Transcript synonymous_variant 7188/9188 6927/8178 2309/2725 L ctG/ctT 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 41/48 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 128854612 128854612 G T 1 0 0 0 0 0 0 0 1 5791 1335 47 2 2 FLNC 7 128854612 Silent SNP G C3N-00580_T 1869 128854612 30491361 460 18595 FLNC 0 . GRCh38 7 128857310 128857310 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.7754G>C p.Gly2585Ala p.G2585A ENST00000325888 46/48 341 238 103 289 289 0 strelka-mutect FLNC,missense_variant,p.Gly2585Ala,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Gly2552Ala,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; C ENST00000325888 Transcript missense_variant 8015/9188 7754/8178 2585/2725 G/A gGc/gCc 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 deleterious(0) 46/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs1261253482 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 128857310 128857310 G C 1 0 0 0 0 1 0 0 0 5791 1203 42 4 4 FLNC 7 128857310 Missense_Mutation SNP G C3N-00580_T 2698 128857310 30488663 461 18596 FLNC 0 . GRCh38 7 128858449 128858449 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.8104G>T p.Gly2702Trp p.G2702W ENST00000325888 48/48 452 322 130 364 364 0 strelka-varscan-mutect FLNC,missense_variant,p.Gly2702Trp,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Gly2669Trp,ENST00000346177,NM_001127487.1;ATP6V1F,upstream_gene_variant,,ENST00000492758,NM_001198909.1;ATP6V1F,upstream_gene_variant,,ENST00000249289,NM_004231.3;RP11-309L24.2,intron_variant,,ENST00000469965,;KCP,downstream_gene_variant,,ENST00000492679,; T ENST00000325888 Transcript missense_variant 8365/9188 8104/8178 2702/2725 G/W Ggg/Tgg 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 deleterious(0) 48/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs1274809025 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 128858449 128858449 G T 1 0 0 0 0 1 0 0 0 5791 1000 35 2 2 FLNC 7 128858449 Missense_Mutation SNP G C3N-00580_T 1139 128858449 30487524 462 18597 IRF5 0 . GRCh38 7 128947921 128947921 + Missense_Mutation SNP G G A rs368255860 C3N-00580_T C3N-00580_N G G c.980G>A p.Arg327His p.R327H ENST00000357234 7/9 358 325 33 273 273 0 strelka-varscan-mutect IRF5,missense_variant,p.Arg311His,ENST00000402030,NM_001098630.2;IRF5,missense_variant,p.Arg311His,ENST00000249375,NM_032643.4;IRF5,missense_variant,p.Arg311His,ENST00000473745,NM_001098627.3;IRF5,missense_variant,p.Arg327His,ENST00000357234,NM_001098629.2;IRF5,missense_variant,p.Arg225His,ENST00000477535,NM_001242452.2;IRF5,3_prime_UTR_variant,,ENST00000619830,;IRF5,downstream_gene_variant,,ENST00000489702,;IRF5,downstream_gene_variant,,ENST00000479582,;IRF5,downstream_gene_variant,,ENST00000613821,;IRF5,downstream_gene_variant,,ENST00000464557,;RP11-309L24.10,downstream_gene_variant,,ENST00000613068,;IRF5,3_prime_UTR_variant,,ENST00000465603,;IRF5,downstream_gene_variant,,ENST00000461416,;IRF5,downstream_gene_variant,,ENST00000488569,;IRF5,downstream_gene_variant,,ENST00000473787,; A ENST00000357234 Transcript missense_variant 1101/1680 980/1545 327/514 R/H cGc/cAc rs368255860 1 1 IRF5 HGNC HGNC:6120 protein_coding YES CCDS43645.1 ENSP00000349770 Q13568 A0A024R763 UPI000013CC7D NM_001098629.2 deleterious(0) 7/9 Gene3D:2.60.200.10,Pfam_domain:PF10401,hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF10,SMART_domains:SM01243,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS rs368255860 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 128947921 128947921 G A 1 0 0 0 0 1 0 0 0 7740 1087 38 1 1 IRF5 7 128947921 Missense_Mutation SNP G C3N-00580_T 89472 128947921 30398052 463 18598 CPA5 0 . GRCh38 7 130363450 130363450 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.779G>C p.Arg260Thr p.R260T ENST00000485477 9/12 260 177 83 244 244 0 strelka-varscan-mutect CPA5,missense_variant,p.Arg260Thr,ENST00000485477,;CPA5,missense_variant,p.Arg260Thr,ENST00000466363,;CPA5,missense_variant,p.Arg260Thr,ENST00000474905,NM_080385.4,NM_001127441.1;CPA5,missense_variant,p.Arg260Thr,ENST00000431780,NM_001127442.1;CPA5,missense_variant,p.Arg260Thr,ENST00000461828,NM_001318223.1;CPA5,missense_variant,p.Arg260Thr,ENST00000393213,;CPA5,missense_variant,p.Arg4Thr,ENST00000479492,;CPA5,downstream_gene_variant,,ENST00000463587,;CPA5,non_coding_transcript_exon_variant,,ENST00000495736,; C ENST00000485477 Transcript missense_variant 1908/2573 779/1311 260/436 R/T aGa/aCa 1 1 CPA5 HGNC HGNC:15722 protein_coding YES CCDS5819.1 ENSP00000420237 Q8WXQ8 A4D1M2 UPI000000D837 tolerated(0.25) 9/12 hmmpanther:PTHR11705:SF16,hmmpanther:PTHR11705,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 130363450 130363450 G C 1 0 0 0 0 1 0 0 0 3587 942 33 4 4 CPA5 7 130363450 Missense_Mutation SNP G C3N-00580_T 1415529 130363450 28982523 464 18599 PLXNA4 0 . GRCh38 7 132228433 132228433 + Missense_Mutation SNP C C A rs762976412 C3N-00580_T C3N-00580_N C C c.1641G>T p.Glu547Asp p.E547D ENST00000359827 6/32 290 188 102 265 264 1 strelka-varscan-mutect PLXNA4,missense_variant,p.Glu547Asp,ENST00000359827,;PLXNA4,missense_variant,p.Glu547Asp,ENST00000321063,NM_020911.1; A ENST00000359827 Transcript missense_variant 2604/13786 1641/5685 547/1894 E/D gaG/gaT rs762976412 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B tolerated(0.48) 6/32 Gene3D:3.30.1680.10,Pfam_domain:PF01437,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,SMART_domains:SM00423,Superfamily_domains:SSF103575 MODERATE 1 SNV 5 1 PASS rs762976412 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 132228433 132228433 C A 1 0 0 0 0 1 0 0 0 12228 796 28 2 2 PLXNA4 7 132228433 Missense_Mutation SNP C C3N-00580_T 1864983 132228433 27117540 465 18600 KIAA1549 0 . GRCh38 7 138838094 138838094 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.5665A>T p.Arg1889Trp p.R1889W ENST00000422774 20/20 119 72 47 112 112 0 strelka-varscan-mutect KIAA1549,missense_variant,p.Arg1873Trp,ENST00000440172,NM_020910.2;KIAA1549,missense_variant,p.Arg1889Trp,ENST00000422774,NM_001164665.1;TMEM213,3_prime_UTR_variant,,ENST00000413208,; A ENST00000422774 Transcript missense_variant 5714/6283 5665/5853 1889/1950 R/W Agg/Tgg 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 deleterious(0) 20/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590 MODERATE 1 SNV 1 1 PASS rs1340191687 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 138838094 138838094 T A 1 0 0 0 0 1 0 0 0 8120 1579 55 4 4 KIAA1549 7 138838094 Missense_Mutation SNP T C3N-00580_T 6609661 138838094 20507879 466 18601 OR9A4 0 . GRCh38 7 141919585 141919585 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.710C>T p.Ser237Phe p.S237F ENST00000548136 1/1 199 163 36 147 147 0 strelka-varscan-mutect OR9A4,missense_variant,p.Ser237Phe,ENST00000548136,NM_001001656.1;MGAM,intron_variant,,ENST00000465654,;MGAM,intron_variant,,ENST00000497554,; T ENST00000548136 Transcript missense_variant 769/1093 710/945 237/314 S/F tCc/tTc 1 1 OR9A4 HGNC HGNC:15095 protein_coding YES CCDS43661.1 ENSP00000448789 Q8NGU2 A0A126GVB1 UPI0000041D24 NM_001001656.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF216,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1476621765 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 141919585 141919585 C T 1 0 0 0 0 1 0 0 0 11316 855 30 3 3 OR9A4 7 141919585 Missense_Mutation SNP C C3N-00580_T 3081491 141919585 17426388 467 18602 MGAM 0 . GRCh38 7 142030663 142030663 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1376C>A p.Ser459Tyr p.S459Y ENST00000549489 12/48 211 128 83 185 185 0 strelka-varscan-mutect MGAM,missense_variant,p.Ser459Tyr,ENST00000475668,;MGAM,missense_variant,p.Ser459Tyr,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Ser459Tyr,ENST00000620571,;MGAM,non_coding_transcript_exon_variant,,ENST00000495045,; A ENST00000549489 Transcript missense_variant 1471/6525 1376/5574 459/1857 S/Y tCt/tAt COSM5248080,COSM5248081,COSM5248082 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0.02) 12/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055,Superfamily_domains:SSF51445 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 142030663 142030663 C A 1 0 0 0 0 1 0 0 0 9499 913 32 2 2 MGAM 7 142030663 Missense_Mutation SNP C C3N-00580_T 111078 142030663 17315310 468 18603 MGAM2 0 . GRCh38 7 142141098 142141098 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1296C>A p.Ser432Arg p.S432R ENST00000477922 12/48 228 178 50 165 165 0 strelka-varscan-mutect MGAM2,missense_variant,p.Ser432Arg,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Ser432Arg,ENST00000550469,; A ENST00000477922 Transcript missense_variant 1350/7867 1296/7548 432/2515 S/R agC/agA 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.01) 12/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51445 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 142141098 142141098 C A 1 0 0 0 0 1 0 0 0 9500 709 25 2 2 MGAM2 7 142141098 Missense_Mutation SNP C C3N-00580_T 110435 142141098 17204875 469 18604 OR9A2 0 . GRCh38 7 143026301 143026301 + Frame_Shift_Del DEL T T - novel C3N-00580_T C3N-00580_N T T c.832delA p.Thr278ProfsTer4 p.T278Pfs*4 ENST00000350513 1/1 149 137 12 116 116 0 sindel-varindel-pindel OR9A2,frameshift_variant,p.Thr278ProfsTer4,ENST00000350513,NM_001001658.1; - ENST00000350513 Transcript frameshift_variant 895/1038 832/933 278/310 T/X Acc/cc 1 -1 OR9A2 HGNC HGNC:15093 protein_coding YES CCDS34767.1 ENSP00000316518 Q8NGT5 UPI0000041C18 NM_001001658.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF216,hmmpanther:PTHR24242,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH 1 deletion 1 PASS . . 0 208 0 2 0 0 0 0 -16.72167 0.9999998 1 1 1 0 - 7 5 61 143026301 143026301 T - 1 0 1 0 1 0 0 0 0 11315 1725 60 0 0 OR9A2 7 143026301 Frame_Shift_Del DEL T C3N-00580_T 885203 143026301 16319672 470 18605 OR6B1 0 . GRCh38 7 144004157 144004157 + Missense_Mutation SNP C C T rs756975238 C3N-00580_T C3N-00580_N C C c.161C>T p.Pro54Leu p.P54L ENST00000408922 1/1 251 143 108 222 222 0 strelka-varscan-mutect OR6B1,missense_variant,p.Pro54Leu,ENST00000408922,NM_001005281.1; T ENST00000408922 Transcript missense_variant 229/1055 161/936 54/311 P/L cCa/cTa rs756975238 1 1 OR6B1 HGNC HGNC:8354 protein_coding YES CCDS43667.1 ENSP00000386151 O95007 UPI0000041B18 NM_001005281.1 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF284,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs756975238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 144004157 144004157 C T 1 0 0 0 0 1 0 0 0 11255 594 21 3 3 OR6B1 7 144004157 Missense_Mutation SNP C C3N-00580_T 977856 144004157 15341816 471 18606 OR2A12 0 . GRCh38 7 144095450 144095450 + Missense_Mutation SNP G G T rs755561676 C3N-00580_T C3N-00580_N G G c.343G>T p.Val115Leu p.V115L ENST00000408949 1/1 242 171 71 164 164 0 strelka-varscan-mutect OR2A12,missense_variant,p.Val115Leu,ENST00000408949,NM_001004135.1; T ENST00000408949 Transcript missense_variant 403/1046 343/933 115/310 V/L Gtg/Ttg rs755561676 1 1 OR2A12 HGNC HGNC:15082 protein_coding YES CCDS43670.1 ENSP00000386174 Q8NGT7 A4D2G4 UPI0000061E6F NM_001004135.1 tolerated(0.08) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF50,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs755561676 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 144095450 144095450 G T 1 0 0 0 0 1 0 0 0 11052 1261 44 2 2 OR2A12 7 144095450 Missense_Mutation SNP G C3N-00580_T 91293 144095450 15250523 472 18607 SSPO 0 . GRCh38 7 149825937 149825937 + Missense_Mutation SNP T T A rs764697985 C3N-00580_T C3N-00580_N T T c.14254T>A p.Cys4752Ser p.C4752S ENST00000378016 97/107 153 82 71 148 148 0 strelka-varscan-mutect SSPO,missense_variant,p.Cys4752Ser,ENST00000378016,NM_198455.2;SSPO,splice_region_variant,,ENST00000623373,;SSPO,splice_region_variant,,ENST00000492965,;SSPO,intron_variant,,ENST00000488835,;SSPO,intron_variant,,ENST00000461331,;SSPO,splice_region_variant,,ENST00000465639,;SSPO,splice_region_variant,,ENST00000472850,; A ENST00000378016 Transcript missense_variant,splice_region_variant 14254/15589 14254/15453 4752/5150 C/S Tgc/Agc rs764697985 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 97/107 hmmpanther:PTHR11339:SF294,hmmpanther:PTHR11339 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 149825937 149825937 T A 1 0 0 0 0 1 0 0 0 15566 1594 55 4 4 SSPO 7 149825937 Missense_Mutation SNP T C3N-00580_T 5730487 149825937 9520036 473 18608 GIMAP4 0 . GRCh38 7 150572707 150572707 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.637G>T p.Val213Leu p.V213L ENST00000255945 3/3 317 191 126 209 209 0 strelka-varscan-mutect GIMAP4,missense_variant,p.Val213Leu,ENST00000255945,NM_018326.2;GIMAP4,missense_variant,p.Val227Leu,ENST00000461940,;GIMAP4,downstream_gene_variant,,ENST00000479232,;GIMAP4,non_coding_transcript_exon_variant,,ENST00000494750,;GIMAP4,downstream_gene_variant,,ENST00000478135,; T ENST00000255945 Transcript missense_variant 812/2060 637/990 213/329 V/L Gtg/Ttg 1 1 GIMAP4 HGNC HGNC:21872 protein_coding YES CCDS5904.1 ENSP00000255945 Q9NUV9 A0A090N7X0 UPI0000073CB0 NM_018326.2 deleterious(0.04) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF04548,PROSITE_profiles:PS51720,hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF57,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1291974882 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 150572707 150572707 G T 1 0 0 0 0 1 0 0 0 6261 1261 44 2 2 GIMAP4 7 150572707 Missense_Mutation SNP G C3N-00580_T 746770 150572707 8773266 474 18609 GIMAP2 0 . GRCh38 7 150692776 150692776 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.490G>T p.Asp164Tyr p.D164Y ENST00000223293 3/3 338 280 58 252 251 1 strelka-varscan-mutect GIMAP2,missense_variant,p.Asp164Tyr,ENST00000223293,NM_015660.2;GIMAP2,downstream_gene_variant,,ENST00000474605,; T ENST00000223293 Transcript missense_variant 584/1449 490/1014 164/337 D/Y Gat/Tat 1 1 GIMAP2 HGNC HGNC:21789 protein_coding YES CCDS5905.1 ENSP00000223293 Q9UG22 A0A090N8H4 UPI000006D114 NM_015660.2 deleterious(0) 3/3 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF7,hmmpanther:PTHR10903,Pfam_domain:PF04548,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 150692776 150692776 G T 1 0 0 0 0 1 0 0 0 6260 942 33 2 2 GIMAP2 7 150692776 Missense_Mutation SNP G C3N-00580_T 120069 150692776 8653197 475 18610 KCNH2 0 . GRCh38 7 150951769 150951769 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1624T>A p.Tyr542Asn p.Y542N ENST00000262186 7/15 150 110 40 96 96 0 strelka-varscan-mutect KCNH2,missense_variant,p.Tyr542Asn,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Tyr202Asn,ENST00000330883,NM_172057.2;KCNH2,missense_variant,p.Tyr426Asn,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; T ENST00000262186 Transcript missense_variant 2026/4286 1624/3480 542/1159 Y/N Tac/Aac 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0) 7/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 150951769 150951769 A T 1 0 0 0 0 1 0 0 0 7948 420 15 4 4 KCNH2 7 150951769 Missense_Mutation SNP A C3N-00580_T 258993 150951769 8394204 476 18611 GBX1 0 . GRCh38 7 151167334 151167334 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.215C>A p.Pro72His p.P72H ENST00000297537 1/2 141 85 56 161 161 0 strelka-varscan-mutect GBX1,missense_variant,p.Pro72His,ENST00000297537,NM_001098834.2;GBX1,intron_variant,,ENST00000475831,; T ENST00000297537 Transcript missense_variant 215/1092 215/1092 72/363 P/H cCc/cAc 1 -1 GBX1 HGNC HGNC:4185 protein_coding YES CCDS43682.1 ENSP00000297537 Q14549 UPI0000E2658B NM_001098834.2 deleterious(0) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24334,hmmpanther:PTHR24334:SF2 MODERATE 1 SNV 2 1 PASS rs1214690453 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 151167334 151167334 G T 1 0 0 0 0 1 0 0 0 6150 1232 43 2 2 GBX1 7 151167334 Missense_Mutation SNP G C3N-00580_T 215565 151167334 8178639 477 18612 KMT2C 0 . GRCh38 7 152265039 152265039 + Nonsense_Mutation SNP T T A C3N-00580_T C3N-00580_N T T c.1183A>T p.Lys395Ter p.K395* ENST00000262189 8/59 298 280 18 288 288 0 varscan-mutect KMT2C,stop_gained,p.Lys395Ter,ENST00000262189,NM_170606.2;KMT2C,stop_gained,p.Lys395Ter,ENST00000355193,;KMT2C,stop_gained,p.Lys395Ter,ENST00000558084,; A ENST00000262189 Transcript stop_gained,splice_region_variant 1402/16862 1183/14736 395/4911 K/* Aaa/Taa COSM3411840,COSM3411841 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 8/59 PROSITE_profiles:PS50016,Gene3D:3.30.40.10,Pfam_domain:PF00628,SMART_domains:SM00184,SMART_domains:SM00249,Superfamily_domains:SSF57903 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 152265039 152265039 T A 1 0 0 0 0 0 1 0 0 8297 1826 63 4 4 KMT2C 7 152265039 Nonsense_Mutation SNP T C3N-00580_T 1097705 152265039 7080934 478 18613 KMT2C 0 . GRCh38 7 152310076 152310076 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.740-1G>T p.X247_splice ENST00000262189 232 137 95 214 214 0 strelka-varscan-mutect KMT2C,splice_acceptor_variant,,ENST00000262189,NM_170606.2;KMT2C,splice_acceptor_variant,,ENST00000355193,;KMT2C,splice_acceptor_variant,,ENST00000558084,;KMT2C,splice_acceptor_variant,,ENST00000490130,; A ENST00000262189 Transcript splice_acceptor_variant -/16862 740/14736 247/4911 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 5/58 HIGH 1 SNV 1 1 PASS . . 0 203 0 5 2 0 0 0 -20 0.9871867 1 1 1 0 A 5 1 61 152310076 152310076 C A 1 0 0 0 0 0 0 1 0 8297 695 24 2 2 KMT2C 7 152310076 Splice_Site SNP C C3N-00580_T 45037 152310076 7035897 479 18614 SHH 0 . GRCh38 7 155811822 155811822 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.300+1G>T p.X100_splice ENST00000297261 604 476 128 483 483 0 strelka-varscan-mutect SHH,splice_donor_variant,,ENST00000297261,NM_000193.2;SHH,upstream_gene_variant,,ENST00000430104,NM_001310462.1;SHH,upstream_gene_variant,,ENST00000472308,;SHH,upstream_gene_variant,,ENST00000441114,;SHH,upstream_gene_variant,,ENST00000435425,; A ENST00000297261 Transcript splice_donor_variant -/4454 300/1389 100/462 1 -1 SHH HGNC HGNC:10848 protein_coding YES CCDS5942.1 ENSP00000297261 Q15465 UPI0000135942 NM_000193.2 1/2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 155811822 155811822 C A 1 0 0 0 0 0 0 1 0 14539 521 18 2 2 SHH 7 155811822 Splice_Site SNP C C3N-00580_T 3501746 155811822 3534151 480 18615 MYOM2 0 . GRCh38 8 2129216 2129216 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.3784G>C p.Val1262Leu p.V1262L ENST00000262113 32/37 129 72 57 180 180 0 strelka-varscan-mutect MYOM2,missense_variant,p.Val1262Leu,ENST00000262113,NM_003970.3;MYOM2,missense_variant,p.Val687Leu,ENST00000523438,;MYOM2,non_coding_transcript_exon_variant,,ENST00000520072,;MYOM2,non_coding_transcript_exon_variant,,ENST00000612167,;MYOM2,non_coding_transcript_exon_variant,,ENST00000519631,;MYOM2,non_coding_transcript_exon_variant,,ENST00000621894,;MYOM2,downstream_gene_variant,,ENST00000523443,; C ENST00000262113 Transcript missense_variant 3925/5014 3784/4398 1262/1465 V/L Gtg/Ctg 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 deleterious(0.04) 32/37 Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1233888967 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 2129216 2129216 G C 1 0 0 0 0 1 0 0 0 10093 1029 36 4 4 MYOM2 8 2129216 Missense_Mutation SNP G C3N-00580_T 2129216 143009420 481 18616 MYOM2 0 . GRCh38 8 2144856 2144856 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4273G>T p.Gly1425Cys p.G1425C ENST00000262113 37/37 137 88 49 366 366 0 strelka-varscan-mutect MYOM2,missense_variant,p.Gly1425Cys,ENST00000262113,NM_003970.3;MYOM2,missense_variant,p.Gly850Cys,ENST00000523438,;MYOM2,non_coding_transcript_exon_variant,,ENST00000520298,;MYOM2,non_coding_transcript_exon_variant,,ENST00000612167,;MYOM2,intron_variant,,ENST00000520779,;MYOM2,downstream_gene_variant,,ENST00000520072,;MYOM2,downstream_gene_variant,,ENST00000519631,;MYOM2,downstream_gene_variant,,ENST00000621894,;MYOM2,downstream_gene_variant,,ENST00000518513,; T ENST00000262113 Transcript missense_variant 4414/5014 4273/4398 1425/1465 G/C Ggc/Tgc 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 deleterious(0) 37/37 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 2144856 2144856 G T 1 0 0 0 0 1 0 0 0 10093 1348 47 2 2 MYOM2 8 2144856 Missense_Mutation SNP G C3N-00580_T 15640 2144856 142993780 482 18617 CSMD1 0 . GRCh38 8 3096973 3096973 + Silent SNP C C T C3N-00580_T C3N-00580_N C C c.7017G>A p.= p.P2339P ENST00000520002 48/71 80 53 27 136 136 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,intron_variant,,ENST00000335551,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523062,; T ENST00000520002 Transcript synonymous_variant 7573/11740 7017/10698 2339/3565 P ccG/ccA COSM5469249,COSM5469250 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 48/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1 LOW 1 SNV 5 1,1 1 PASS rs1397116647 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 3096973 3096973 C T 1 0 0 0 0 0 0 0 1 3745 639 23 1 1 CSMD1 8 3096973 Silent SNP C C3N-00580_T 952117 3096973 142041663 483 18618 XKR5 0 . GRCh38 8 6811600 6811600 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1659C>A p.= p.S553S ENST00000618742 7/7 111 69 42 188 188 0 strelka-varscan-mutect XKR5,synonymous_variant,p.=,ENST00000618742,NM_207411.4,NM_001289973.1;XKR5,3_prime_UTR_variant,,ENST00000618990,; T ENST00000618742 Transcript synonymous_variant 1810/4893 1659/2061 553/686 S tcC/tcA 1 -1 XKR5 HGNC HGNC:20782 protein_coding YES ENSP00000483879 A0A087X143 UPI0000EE786F NM_207411.4,NM_001289973.1 7/7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 6811600 6811600 G T 1 0 0 0 0 0 0 0 1 17993 987 35 2 2 XKR5 8 6811600 Silent SNP G C3N-00580_T 3714627 6811600 138327036 484 18619 DEFA6 0 . GRCh38 8 6925873 6925873 + Missense_Mutation SNP C C T rs778595451 C3N-00580_T C3N-00580_N C C c.163G>A p.Glu55Lys p.E55K ENST00000297436 1/2 63 39 24 129 129 0 strelka-varscan-mutect DEFA6,missense_variant,p.Glu55Lys,ENST00000297436,NM_001926.3;GS1-24F4.3,upstream_gene_variant,,ENST00000526235,; T ENST00000297436 Transcript missense_variant 204/469 163/303 55/100 E/K Gag/Aag rs778595451,COSM5409778 1 -1 DEFA6 HGNC HGNC:2765 protein_coding YES CCDS5960.1 ENSP00000297436 Q01524 UPI0000129125 NM_001926.3 tolerated(1) 1/2 Pfam_domain:PF00879,PIRSF_domain:PIRSF001875,hmmpanther:PTHR11876,hmmpanther:PTHR11876:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778595451 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 6925873 6925873 C T 1 0 0 0 0 1 0 0 0 4194 922 32 3 3 DEFA6 8 6925873 Missense_Mutation SNP C C3N-00580_T 114273 6925873 138212763 485 18620 USP17L1 0 . GRCh38 8 7333213 7333213 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.827T>A p.Leu276His p.L276H ENST00000529559 1/1 88 53 35 144 144 0 varscan-mutect USP17L1,missense_variant,p.Leu276His,ENST00000529559,NM_001256873.1;USP17L4,upstream_gene_variant,,ENST00000526929,NM_001256874.1;FAM66B,intron_variant,,ENST00000606573,;FAM66B,intron_variant,,ENST00000529456,; A ENST00000529559 Transcript missense_variant 827/1593 827/1593 276/530 L/H cTc/cAc 1 1 USP17L1 HGNC HGNC:37182 protein_coding YES CCDS78298.1 ENSP00000485364 Q7RTZ2 UPI00001D9634 NM_001256873.1 deleterious(0) 1/1 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 MODERATE SNV 1 PASS . . 6 201 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 7333213 7333213 T A 1 0 0 0 0 1 0 0 0 17582 1551 54 4 4 USP17L1 8 7333213 Missense_Mutation SNP T C3N-00580_T 407340 7333213 137805423 486 18621 MTMR9 0 . GRCh38 8 11309676 11309676 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.959A>T p.Gln320Leu p.Q320L ENST00000221086 6/10 90 44 46 112 112 0 varscan-mutect MTMR9,missense_variant,p.Gln320Leu,ENST00000221086,NM_015458.3;MTMR9,missense_variant,p.Gln235Leu,ENST00000526292,;MTMR9,3_prime_UTR_variant,,ENST00000530200,; T ENST00000221086 Transcript missense_variant 1432/7481 959/1650 320/549 Q/L cAg/cTg 1 1 MTMR9 HGNC HGNC:14596 protein_coding YES CCDS5979.1 ENSP00000221086 Q96QG7 UPI0000073CA7 NM_015458.3 deleterious(0) 6/10 PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF56,Pfam_domain:PF06602,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 11309676 11309676 A T 1 0 0 0 0 1 0 0 0 9937 188 7 4 4 MTMR9 8 11309676 Missense_Mutation SNP A C3N-00580_T 3976463 11309676 133828960 487 18622 ERLIN2 0 . GRCh38 8 37749582 37749582 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.448C>T p.= p.L150L ENST00000276461 7/12 1062 1000 62 591 590 1 strelka-varscan-mutect ERLIN2,synonymous_variant,p.=,ENST00000276461,NM_007175.6;ERLIN2,synonymous_variant,p.=,ENST00000519638,;ERLIN2,synonymous_variant,p.=,ENST00000521644,;ERLIN2,synonymous_variant,p.=,ENST00000518526,;ERLIN2,downstream_gene_variant,,ENST00000518586,;ERLIN2,downstream_gene_variant,,ENST00000523887,;ERLIN2,downstream_gene_variant,,ENST00000335171,NM_001003790.3;ERLIN2,downstream_gene_variant,,ENST00000397228,NM_001003791.2;ERLIN2,downstream_gene_variant,,ENST00000523107,;ERLIN2,non_coding_transcript_exon_variant,,ENST00000521993,;RP11-863K10.4,upstream_gene_variant,,ENST00000521192,; T ENST00000276461 Transcript synonymous_variant 515/6073 448/1020 150/339 L Ctg/Ttg 1 1 ERLIN2 HGNC HGNC:1356 protein_coding YES CCDS6095.1 ENSP00000276461 O94905 UPI0000073DE1 NM_007175.6 7/12 Pfam_domain:PF01145,hmmpanther:PTHR15351,hmmpanther:PTHR15351:SF4,SMART_domains:SM00244 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 37749582 37749582 C T 1 0 0 0 0 0 0 0 1 5090 564 20 3 3 ERLIN2 8 37749582 Silent SNP C C3N-00580_T 26439906 37749582 107389054 488 18623 VDAC3 0 . GRCh38 8 42402001 42402001 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.540G>T p.Gln180His p.Q180H ENST00000521158 8/11 367 296 71 265 265 0 strelka-varscan-mutect VDAC3,missense_variant,p.Gln179His,ENST00000022615,NM_005662.6;VDAC3,missense_variant,p.Gln180His,ENST00000521158,NM_001135694.2;VDAC3,intron_variant,,ENST00000522572,;VDAC3,downstream_gene_variant,,ENST00000518563,;VDAC3,downstream_gene_variant,,ENST00000522069,;VDAC3,downstream_gene_variant,,ENST00000520115,;VDAC3,3_prime_UTR_variant,,ENST00000522010,;VDAC3,non_coding_transcript_exon_variant,,ENST00000521348,;VDAC3,downstream_gene_variant,,ENST00000519072,;VDAC3,upstream_gene_variant,,ENST00000524291,;VDAC3,downstream_gene_variant,,ENST00000518495,;VDAC3,downstream_gene_variant,,ENST00000522178,; T ENST00000521158 Transcript missense_variant 608/949 540/855 180/284 Q/H caG/caT 1 1 VDAC3 HGNC HGNC:12674 protein_coding YES CCDS47850.1 ENSP00000428845 Q9Y277 UPI000002B16C NM_001135694.2 tolerated(0.16) 8/11 hmmpanther:PTHR11743,hmmpanther:PTHR11743:SF28,Pfam_domain:PF01459,Gene3D:2.40.160.10 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 42402001 42402001 G T 1 0 0 0 0 1 0 0 0 17693 962 34 2 2 VDAC3 8 42402001 Missense_Mutation SNP G C3N-00580_T 4652419 42402001 102736635 489 18624 SLC20A2 0 . GRCh38 8 42459906 42459906 + Silent SNP T T A rs375338138 C3N-00580_T C3N-00580_N T T c.603A>T p.= p.T201T ENST00000342228 5/11 199 90 109 141 141 0 strelka-varscan-mutect SLC20A2,synonymous_variant,p.=,ENST00000342228,NM_006749.4;SLC20A2,synonymous_variant,p.=,ENST00000520262,NM_001257180.1;SLC20A2,synonymous_variant,p.=,ENST00000520179,NM_001257181.1;SLC20A2,non_coding_transcript_exon_variant,,ENST00000518660,;SLC20A2,non_coding_transcript_exon_variant,,ENST00000522401,;SLC20A2,downstream_gene_variant,,ENST00000524211,; A ENST00000342228 Transcript synonymous_variant 973/3657 603/1959 201/652 T acA/acT rs375338138 1 -1 SLC20A2 HGNC HGNC:10947 protein_coding YES CCDS6132.1 ENSP00000340465 Q08357 UPI000006DC58 NM_006749.4 5/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR11101,hmmpanther:PTHR11101:SF15,Pfam_domain:PF01384 LOW 1 SNV 1 1 PASS rs375338138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 42459906 42459906 T A 1 0 0 0 0 0 0 0 1 14705 1567 55 4 4 SLC20A2 8 42459906 Silent SNP T C3N-00580_T 57905 42459906 102678730 490 18625 PXDNL 0 . GRCh38 8 51409023 51409023 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.2601C>A p.= p.P867P ENST00000356297 17/23 273 143 130 201 201 0 strelka-varscan-mutect PXDNL,synonymous_variant,p.=,ENST00000356297,NM_144651.4;PXDNL,upstream_gene_variant,,ENST00000522933,;PXDNL,synonymous_variant,p.=,ENST00000522628,; T ENST00000356297 Transcript synonymous_variant 2702/4805 2601/4392 867/1463 P ccC/ccA COSM4482403,COSM4482404,COSM4879067,COSM4879068 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Pfam_domain:PF03098,Superfamily_domains:SSF48113 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 51409023 51409023 G T 1 0 0 0 0 0 0 0 1 13002 1103 39 1 1 PXDNL 8 51409023 Silent SNP G C3N-00580_T 8949117 51409023 93729613 491 18626 PXDNL 0 . GRCh38 8 51449012 51449012 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1356G>C p.Trp452Cys p.W452C ENST00000356297 11/23 414 339 75 334 334 0 strelka-varscan-mutect PXDNL,missense_variant,p.Trp452Cys,ENST00000356297,NM_144651.4; G ENST00000356297 Transcript missense_variant 1457/4805 1356/4392 452/1463 W/C tgG/tgC 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 11/23 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1375885496 . 0 204 0 0 6 0 0 0 -20 0.6120115 1 1 1 0 G 3 3 61 51449012 51449012 C G 1 0 0 0 0 1 0 0 0 13002 856 30 4 4 PXDNL 8 51449012 Missense_Mutation SNP C C3N-00580_T 39989 51449012 93689624 492 18627 XKR4 0 . GRCh38 8 55523536 55523536 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1262C>A p.Thr421Lys p.T421K ENST00000327381 3/3 328 159 169 234 234 0 strelka-varscan-mutect XKR4,missense_variant,p.Thr421Lys,ENST00000327381,NM_052898.1;XKR4,missense_variant,p.Thr421Lys,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; A ENST00000327381 Transcript missense_variant 1362/19880 1262/1953 421/650 T/K aCa/aAa COSM3951732 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 deleterious(0) 3/3 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14,Pfam_domain:PF09815 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 55523536 55523536 C A 1 0 0 0 0 1 0 0 0 17992 478 17 2 2 XKR4 8 55523536 Missense_Mutation SNP C C3N-00580_T 4074524 55523536 89615100 493 18628 NKAIN3 0 . GRCh38 8 62589731 62589731 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.210C>A p.= p.A70A ENST00000523211 3/7 202 181 21 140 140 0 strelka-varscan-mutect NKAIN3,synonymous_variant,p.=,ENST00000523211,;NKAIN3,intron_variant,,ENST00000524201,;NKAIN3,non_coding_transcript_exon_variant,,ENST00000519049,;NKAIN3,non_coding_transcript_exon_variant,,ENST00000523367,; A ENST00000523211 Transcript synonymous_variant 342/1988 210/594 70/197 A gcC/gcA 1 1 NKAIN3 HGNC HGNC:26829 protein_coding YES ENSP00000429073 Q8N8D7 UPI000006F596 3/7 hmmpanther:PTHR13084:SF2,hmmpanther:PTHR13084,Pfam_domain:PF05640,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 62589731 62589731 C A 1 0 0 0 0 0 0 0 1 10472 610 22 2 2 NKAIN3 8 62589731 Silent SNP C C3N-00580_T 7066195 62589731 82548905 494 18629 DNAJC5B 0 . GRCh38 8 66080521 66080521 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.478G>A p.Glu160Lys p.E160K ENST00000276570 5/6 204 190 14 101 101 0 strelka-varscan-mutect DNAJC5B,missense_variant,p.Glu160Lys,ENST00000276570,NM_033105.4;DNAJC5B,downstream_gene_variant,,ENST00000522619,;DNAJC5B,non_coding_transcript_exon_variant,,ENST00000519330,;DNAJC5B,downstream_gene_variant,,ENST00000524076,; A ENST00000276570 Transcript missense_variant 765/1382 478/600 160/199 E/K Gag/Aag COSM3650212 1 1 DNAJC5B HGNC HGNC:24138 protein_coding YES CCDS6183.1 ENSP00000276570 Q9UF47 A0A024R7Z1 UPI0000050F10 NM_033105.4 tolerated(0.13) 5/6 1 MODERATE 1 SNV 1 1 1 PASS rs1217304685 . 0 207 2 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 61 66080521 66080521 G A 1 0 0 0 0 1 0 0 0 4464 1175 41 3 3 DNAJC5B 8 66080521 Missense_Mutation SNP G C3N-00580_T 3490790 66080521 79058115 495 18630 MYBL1 0 . GRCh38 8 66576280 66576280 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1197G>A p.= p.Q399Q ENST00000522677 10/16 512 199 313 327 327 0 strelka-varscan-mutect MYBL1,synonymous_variant,p.=,ENST00000522677,NM_001080416.3;MYBL1,synonymous_variant,p.=,ENST00000524176,NM_001294282.1,NM_001144755.2;MYBL1,intron_variant,,ENST00000517885,; T ENST00000522677 Transcript synonymous_variant 1608/5192 1197/2259 399/752 Q caG/caA 1 -1 MYBL1 HGNC HGNC:7547 protein_coding YES CCDS47867.1 ENSP00000429633 P10243 UPI000012FADE NM_001080416.3 10/16 hmmpanther:PTHR10641:SF492,hmmpanther:PTHR10641 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 66576280 66576280 C T 1 0 0 0 0 0 0 0 1 10009 796 28 3 3 MYBL1 8 66576280 Silent SNP C C3N-00580_T 495759 66576280 78562356 496 18631 XKR9 0 . GRCh38 8 70681109 70681109 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.51C>A p.= p.I17I ENST00000408926 3/5 255 101 154 145 144 1 strelka-varscan-mutect XKR9,synonymous_variant,p.=,ENST00000408926,NM_001287258.1,NM_001011720.1,NM_001287260.1;XKR9,synonymous_variant,p.=,ENST00000520030,NM_001287259.1;XKR9,synonymous_variant,p.=,ENST00000519350,;XKR9,intron_variant,,ENST00000520273,;XKR9,synonymous_variant,p.=,ENST00000520092,; A ENST00000408926 Transcript synonymous_variant 585/3174 51/1122 17/373 I atC/atA 1 1 XKR9 HGNC HGNC:20937 protein_coding YES CCDS34905.1 ENSP00000386141 Q5GH70 UPI00004C7A9F NM_001287258.1,NM_001011720.1,NM_001287260.1 3/5 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF6,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 70681109 70681109 C A 1 0 0 0 0 0 0 0 1 17997 903 32 2 2 XKR9 8 70681109 Silent SNP C C3N-00580_T 4104829 70681109 74457527 497 18632 HNF4G 0 . GRCh38 8 75556013 75556013 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.647A>T p.His216Leu p.H216L ENST00000396423 6/10 107 58 49 99 99 0 strelka-varscan-mutect HNF4G,missense_variant,p.His216Leu,ENST00000396423,NM_004133.4;HNF4G,missense_variant,p.His179Leu,ENST00000354370,;HNF4G,downstream_gene_variant,,ENST00000396419,; T ENST00000396423 Transcript missense_variant 771/4209 647/1338 216/445 H/L cAc/cTc 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 deleterious(0.01) 6/10 hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Pfam_domain:PF00104,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398 MODERATE 1 SNV 1 1 PASS rs1200797943 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 75556013 75556013 A T 1 0 0 0 0 1 0 0 0 7145 159 6 4 4 HNF4G 8 75556013 Missense_Mutation SNP A C3N-00580_T 4874904 75556013 69582623 498 18633 ZFHX4 0 . GRCh38 8 76778310 76778310 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.3196G>A p.Val1066Ile p.V1066I ENST00000521891 4/11 654 260 394 588 588 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Val1066Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Val1040Ile,ENST00000518282,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000517683,;ZFHX4,missense_variant,p.Val11Ile,ENST00000523625,;ZFHX4,missense_variant,p.Val9Ile,ENST00000519536,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000524290,; A ENST00000521891 Transcript missense_variant 3644/14019 3196/10851 1066/3616 V/I Gtc/Atc 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0.01) 4/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,SMART_domains:SM00451 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 76778310 76778310 G A 1 0 0 0 0 1 0 0 0 18213 1377 48 3 3 ZFHX4 8 76778310 Missense_Mutation SNP G C3N-00580_T 1222297 76778310 68360326 499 18634 ZFHX4 0 . GRCh38 8 76855491 76855491 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.8570C>A p.Thr2857Lys p.T2857K ENST00000521891 10/11 181 64 117 143 143 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Thr2857Lys,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Thr2831Lys,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript missense_variant 9018/14019 8570/10851 2857/3616 T/K aCg/aAg 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0.03) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS rs1230902501 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 76855491 76855491 C A 1 0 0 0 0 1 0 0 0 18213 536 19 1 1 ZFHX4 8 76855491 Missense_Mutation SNP C C3N-00580_T 77181 76855491 68283145 500 18635 CNGB3 0 . GRCh38 8 86739703 86739703 + Missense_Mutation SNP T T G C3N-00580_T C3N-00580_N T T c.163A>C p.Thr55Pro p.T55P ENST00000320005 2/18 666 599 67 394 394 0 strelka-varscan-mutect CNGB3,missense_variant,p.Thr55Pro,ENST00000320005,NM_019098.4;RP11-386D6.1,intron_variant,,ENST00000519041,;CNGB3,non_coding_transcript_exon_variant,,ENST00000519777,; G ENST00000320005 Transcript missense_variant 211/4347 163/2430 55/809 T/P Acc/Ccc COSM751545,COSM85131 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 tolerated(0.16) 2/18 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs778795284 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 86739703 86739703 T G 1 0 0 0 0 1 0 0 0 3381 1725 60 5 5 CNGB3 8 86739703 Missense_Mutation SNP T C3N-00580_T 9884212 86739703 58398933 501 18636 NBN 0 . GRCh38 8 89953351 89953351 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1738G>C p.Val580Leu p.V580L ENST00000265433 11/16 253 232 21 201 201 0 strelka-varscan-mutect NBN,missense_variant,p.Val580Leu,ENST00000265433,NM_002485.4;NBN,missense_variant,p.Val498Leu,ENST00000409330,;NBN,missense_variant,p.Val2Leu,ENST00000613033,;NBN,3_prime_UTR_variant,,ENST00000396252,NM_001024688.2; G ENST00000265433 Transcript missense_variant 1893/4666 1738/2265 580/754 V/L Gtt/Ctt 1 -1 NBN HGNC HGNC:7652 protein_coding YES CCDS6249.1 ENSP00000265433 O60934 UPI0000073BF4 NM_002485.4 tolerated(0.31) 11/16 hmmpanther:PTHR12162,hmmpanther:PTHR12162:SF0,PIRSF_domain:PIRSF011869 MODERATE 1 SNV 1 1 PASS rs878854506 . 0 205 0 4 0 0 0 0 -20 0.9997242 1 1 1 0 G 3 3 61 89953351 89953351 C G 1 0 0 0 0 1 0 0 0 10202 565 20 4 4 NBN 8 89953351 Missense_Mutation SNP C C3N-00580_T 3213648 89953351 55185285 502 18637 POP1 0 . GRCh38 8 98127631 98127631 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.179G>T p.Arg60Ile p.R60I ENST00000401707 3/16 946 745 201 611 611 0 strelka-varscan-mutect POP1,missense_variant,p.Arg60Ile,ENST00000401707,NM_001145860.1,NM_001145861.1;POP1,missense_variant,p.Arg60Ile,ENST00000349693,NM_015029.2;POP1,missense_variant,p.Arg60Ile,ENST00000522319,; T ENST00000401707 Transcript missense_variant 260/4719 179/3075 60/1024 R/I aGa/aTa 1 1 POP1 HGNC HGNC:30129 protein_coding YES CCDS6277.1 ENSP00000385787 Q99575 UPI0000131F33 NM_001145860.1,NM_001145861.1 deleterious(0.01) 3/16 hmmpanther:PTHR22731,hmmpanther:PTHR22731:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 98127631 98127631 G T 1 0 0 0 0 1 0 0 0 12365 942 33 2 2 POP1 8 98127631 Missense_Mutation SNP G C3N-00580_T 8174280 98127631 47011005 503 18638 UBR5 0 . GRCh38 8 102329374 102329374 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1124G>T p.Gly375Val p.G375V ENST00000520539 10/59 253 181 72 198 197 1 strelka-varscan-mutect UBR5,missense_variant,p.Gly375Val,ENST00000520539,NM_015902.5;UBR5,missense_variant,p.Gly375Val,ENST00000220959,NM_001282873.1;UBR5,missense_variant,p.Gly369Val,ENST00000521922,; A ENST00000520539 Transcript missense_variant 1731/10297 1124/8400 375/2799 G/V gGg/gTg 1 -1 UBR5 HGNC HGNC:16806 protein_coding YES CCDS34933.1 ENSP00000429084 O95071 UPI0000129BCB NM_015902.5 tolerated(0.09) 10/59 Gene3D:2.130.10.30,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF337,Superfamily_domains:SSF50985 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 102329374 102329374 C A 1 0 0 0 0 1 0 0 0 17429 623 22 2 2 UBR5 8 102329374 Missense_Mutation SNP C C3N-00580_T 4201743 102329374 42809262 504 18639 RIMS2 0 . GRCh38 8 103885535 103885535 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.936G>T p.Glu312Asp p.E312D ENST00000504942 4/24 297 123 174 193 193 0 strelka-varscan-mutect RIMS2,missense_variant,p.Glu120Asp,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Glu90Asp,ENST00000436393,;RIMS2,missense_variant,p.Glu312Asp,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Glu254Asp,ENST00000626043,;RIMS2,missense_variant,p.Glu120Asp,ENST00000408894,;RIMS2,missense_variant,p.Glu120Asp,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Glu316Asp,ENST00000632716,;RIMS2,missense_variant,p.Glu120Asp,ENST00000515551,; T ENST00000504942 Transcript missense_variant 1075/4228 936/4050 312/1349 E/D gaG/gaT COSM4428876,COSM4428877,COSM4428878,COSM4428879,COSM4428880 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 tolerated_low_confidence(0.13) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 1,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 103885535 103885535 G T 1 0 0 0 0 1 0 0 0 13543 991 35 2 2 RIMS2 8 103885535 Missense_Mutation SNP G C3N-00580_T 1556161 103885535 41253101 505 18640 RIMS2 0 . GRCh38 8 103885777 103885777 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1178G>C p.Arg393Thr p.R393T ENST00000504942 4/24 383 308 75 219 219 0 strelka-varscan-mutect RIMS2,missense_variant,p.Arg201Thr,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Arg171Thr,ENST00000436393,;RIMS2,missense_variant,p.Arg393Thr,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Arg335Thr,ENST00000626043,;RIMS2,missense_variant,p.Arg201Thr,ENST00000408894,;RIMS2,missense_variant,p.Arg201Thr,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Arg397Thr,ENST00000632716,;RIMS2,missense_variant,p.Arg201Thr,ENST00000515551,; C ENST00000504942 Transcript missense_variant 1317/4228 1178/4050 393/1349 R/T aGg/aCg 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0.05) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 103885777 103885777 G C 1 0 0 0 0 1 0 0 0 13543 1000 35 4 4 RIMS2 8 103885777 Missense_Mutation SNP G C3N-00580_T 242 103885777 41252859 506 18641 DPYS 0 . GRCh38 8 104466755 104466755 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.166G>T p.Gly56Cys p.G56C ENST00000351513 1/10 574 473 101 402 402 0 strelka-varscan-mutect DPYS,missense_variant,p.Gly56Cys,ENST00000351513,NM_001385.2;DPYS,missense_variant,p.Gly56Cys,ENST00000521573,; A ENST00000351513 Transcript missense_variant 299/2127 166/1560 56/519 G/C Ggc/Tgc 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 deleterious(0) 1/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,Gene3D:2.30.40.10,TIGRFAM_domain:TIGR02033,Superfamily_domains:SSF51338 MODERATE 1 SNV 1 1 PASS rs1373451792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 104466755 104466755 C A 1 0 0 0 0 1 0 0 0 4561 652 23 1 1 DPYS 8 104466755 Missense_Mutation SNP C C3N-00580_T 580978 104466755 40671881 507 18642 CSMD3 0 . GRCh38 8 112650287 112650287 + Missense_Mutation SNP C C G rs372047417 C3N-00580_T C3N-00580_N C C c.3067G>C p.Gly1023Arg p.G1023R ENST00000297405 19/71 559 248 311 398 398 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gly1023Arg,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly983Arg,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly919Arg,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gly363Arg,ENST00000339701,; G ENST00000297405 Transcript missense_variant 3312/13212 3067/11124 1023/3707 G/R Ggt/Cgt rs372047417,COSM3644340,COSM3644341 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 19/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs372047417 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 112650287 112650287 C G 1 0 0 0 0 1 0 0 0 3747 594 21 4 4 CSMD3 8 112650287 Missense_Mutation SNP C C3N-00580_T 8183532 112650287 32488349 508 18643 CSMD3 0 . GRCh38 8 112947870 112947870 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1428G>C p.Glu476Asp p.E476D ENST00000297405 9/71 355 146 209 281 281 0 strelka-varscan-mutect CSMD3,missense_variant,p.Glu476Asp,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Glu436Asp,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Glu372Asp,ENST00000455883,NM_052900.2; G ENST00000297405 Transcript missense_variant 1673/13212 1428/11124 476/3707 E/D gaG/gaC 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.03) 9/71 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 112947870 112947870 C G 1 0 0 0 0 1 0 0 0 3747 680 24 4 4 CSMD3 8 112947870 Missense_Mutation SNP C C3N-00580_T 297583 112947870 32190766 509 18644 RAD21 0 . GRCh38 8 116854328 116854328 + Missense_Mutation SNP A A C rs565975762 C3N-00580_T C3N-00580_N A A c.1078T>G p.Leu360Val p.L360V ENST00000297338 9/14 486 448 38 363 361 2 strelka-varscan-mutect RAD21,missense_variant,p.Leu360Val,ENST00000297338,NM_006265.2;RAD21,upstream_gene_variant,,ENST00000523986,;RAD21,upstream_gene_variant,,ENST00000517749,;RAD21,upstream_gene_variant,,ENST00000518055,;RAD21,downstream_gene_variant,,ENST00000517485,;RAD21,downstream_gene_variant,,ENST00000520992,;UTP23,downstream_gene_variant,,ENST00000517820,;AC087350.1,downstream_gene_variant,,ENST00000626876,;RAD21,downstream_gene_variant,,ENST00000523547,; C ENST00000297338 Transcript missense_variant 1366/3749 1078/1896 360/631 L/V Ttg/Gtg rs565975762 1 -1 RAD21 HGNC HGNC:9811 protein_coding YES CCDS6321.1 ENSP00000297338 O60216 A0A024R9J0 UPI0000133018 NM_006265.2 deleterious(0) 9/14 hmmpanther:PTHR12585,hmmpanther:PTHR12585:SF20 MODERATE 1 SNV 1 1 PASS rs565975762 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 116854328 116854328 A C 1 0 0 0 0 1 0 0 0 13141 98 4 5 5 RAD21 8 116854328 Missense_Mutation SNP A C3N-00580_T 3906458 116854328 28284308 510 18645 EXT1 0 . GRCh38 8 118110792 118110792 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.255G>C p.Lys85Asn p.K85N ENST00000378204 1/11 249 196 53 153 153 0 strelka-varscan-mutect EXT1,missense_variant,p.Lys85Asn,ENST00000378204,NM_000127.2;EXT1,upstream_gene_variant,,ENST00000436216,;EXT1,intron_variant,,ENST00000437196,; G ENST00000378204 Transcript missense_variant 1062/8270 255/2241 85/746 K/N aaG/aaC 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 tolerated(0.11) 1/11 hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF97 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 118110792 118110792 C G 1 0 0 0 0 1 0 0 0 5191 796 28 4 4 EXT1 8 118110792 Missense_Mutation SNP C C3N-00580_T 1256464 118110792 27027844 511 18646 SAMD12 0 . GRCh38 8 118580867 118580867 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.40G>T p.Gly14Cys p.G14C ENST00000314727 2/4 186 149 37 123 123 0 strelka-varscan-mutect SAMD12,missense_variant,p.Gly14Cys,ENST00000409003,NM_001101676.1;SAMD12,missense_variant,p.Gly14Cys,ENST00000314727,NM_207506.2;SAMD12,missense_variant,p.Gly11Cys,ENST00000453675,;SAMD12,missense_variant,p.Gly6Cys,ENST00000524796,;SAMD12,missense_variant,p.Gly14Cys,ENST00000526328,;SAMD12,missense_variant,p.Gly29Cys,ENST00000526765,;SAMD12,missense_variant,p.Gly14Cys,ENST00000445741,; A ENST00000314727 Transcript missense_variant 177/2172 40/606 14/201 G/C Ggt/Tgt 1 -1 SAMD12 HGNC HGNC:31750 protein_coding YES CCDS6325.1 ENSP00000314173 Q8N8I0 UPI000013F8F1 NM_207506.2 deleterious_low_confidence(0) 2/4 hmmpanther:PTHR20843:SF2,hmmpanther:PTHR20843 MODERATE 1 SNV 1 1 PASS rs1304967359 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 118580867 118580867 C A 1 0 0 0 0 1 0 0 0 14076 623 22 2 2 SAMD12 8 118580867 Missense_Mutation SNP C C3N-00580_T 470075 118580867 26557769 512 18647 TBC1D31 0 . GRCh38 8 123097335 123097335 + Missense_Mutation SNP G G T rs767911030 C3N-00580_T C3N-00580_N G G c.725G>T p.Cys242Phe p.C242F ENST00000287380 6/22 421 345 76 312 312 0 strelka-varscan-mutect TBC1D31,missense_variant,p.Cys242Phe,ENST00000287380,NM_145647.3;TBC1D31,missense_variant,p.Cys137Phe,ENST00000521676,;TBC1D31,missense_variant,p.Cys137Phe,ENST00000522420,;TBC1D31,missense_variant,p.Cys242Phe,ENST00000327098,NM_001145088.1;TBC1D31,missense_variant,p.Cys46Phe,ENST00000521914,;TBC1D31,missense_variant,p.Cys232Phe,ENST00000522276,;TBC1D31,intron_variant,,ENST00000519418,;TBC1D31,upstream_gene_variant,,ENST00000518805,;TBC1D31,downstream_gene_variant,,ENST00000518684,;TBC1D31,3_prime_UTR_variant,,ENST00000524307,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000521980,;TBC1D31,non_coding_transcript_exon_variant,,ENST00000518099,; T ENST00000287380 Transcript missense_variant 815/3502 725/3201 242/1066 C/F tGc/tTc rs767911030 1 1 TBC1D31 HGNC HGNC:30888 protein_coding YES CCDS6338.1 ENSP00000287380 Q96DN5 UPI000013DEAB NM_145647.3 deleterious(0.01) 6/22 PROSITE_profiles:PS50294,hmmpanther:PTHR19853:SF1,hmmpanther:PTHR19853,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs767911030 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 123097335 123097335 G T 1 0 0 0 0 1 0 0 0 16021 1319 46 2 2 TBC1D31 8 123097335 Missense_Mutation SNP G C3N-00580_T 4516468 123097335 22041301 513 18648 WISP1 0 . GRCh38 8 133220707 133220707 + Missense_Mutation SNP G G T rs147638897 C3N-00580_T C3N-00580_N G G c.476G>T p.Arg159Leu p.R159L ENST00000250160 3/5 681 525 156 415 414 1 strelka-varscan-mutect WISP1,missense_variant,p.Arg159Leu,ENST00000250160,NM_003882.3;WISP1,intron_variant,,ENST00000220856,NM_080838.2;WISP1,intron_variant,,ENST00000517423,NM_001204869.1;WISP1,intron_variant,,ENST00000519433,NM_001204870.1;WISP1,intron_variant,,ENST00000377862,; T ENST00000250160 Transcript missense_variant 582/3844 476/1104 159/367 R/L cGa/cTa rs147638897 1 1 WISP1 HGNC HGNC:12769 protein_coding YES CCDS6371.1 ENSP00000250160 O95388 UPI00000359FE NM_003882.3 tolerated(0.26) 3/5 PROSITE_profiles:PS50184,hmmpanther:PTHR11348:SF4,hmmpanther:PTHR11348,PROSITE_patterns:PS01208,PIRSF_domain:PIRSF036495,Pfam_domain:PF00093,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS rs147638897 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 133220707 133220707 G T 1 0 0 0 0 1 0 0 0 17928 1058 37 1 1 WISP1 8 133220707 Missense_Mutation SNP G C3N-00580_T 10123372 133220707 11917929 514 18649 FAM135B 0 . GRCh38 8 138152551 138152551 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1924G>T p.Asp642Tyr p.D642Y ENST00000395297 13/20 263 129 134 185 185 0 strelka-varscan-mutect FAM135B,missense_variant,p.Asp642Tyr,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Asp642Tyr,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 2095/6962 1924/4221 642/1406 D/Y Gat/Tat COSM4532835,COSM4532836 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.09) 13/20 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 138152551 138152551 C A 1 0 0 0 0 1 0 0 0 5299 826 29 2 2 FAM135B 8 138152551 Missense_Mutation SNP C C3N-00580_T 4931844 138152551 6986085 515 18650 KCNK9 0 . GRCh38 8 139618544 139618544 + Missense_Mutation SNP C C A rs750174835 C3N-00580_T C3N-00580_N C C c.839G>T p.Arg280Leu p.R280L ENST00000520439 2/2 378 162 216 225 225 0 strelka-varscan-mutect KCNK9,missense_variant,p.Arg280Leu,ENST00000520439,NM_001282534.1;KCNK9,missense_variant,p.Arg280Leu,ENST00000303015,;KCNK9,upstream_gene_variant,,ENST00000523477,;KCNK9,upstream_gene_variant,,ENST00000519923,;KCNK9,missense_variant,p.Arg280Leu,ENST00000522317,; A ENST00000520439 Transcript missense_variant 903/1441 839/1125 280/374 R/L cGg/cTg rs750174835 1 -1 KCNK9 HGNC HGNC:6283 protein_coding YES CCDS6377.1 ENSP00000430676 Q9NPC2 A0A024R9H3 UPI000000D8AC NM_001282534.1 tolerated(0.53) 2/2 hmmpanther:PTHR11003:SF75,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061 MODERATE 1 SNV 1 1 PASS rs750174835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 139618544 139618544 C A 1 0 0 0 0 1 0 0 0 7989 652 23 1 1 KCNK9 8 139618544 Missense_Mutation SNP C C3N-00580_T 1465993 139618544 5520092 516 18651 TSNARE1 0 . GRCh38 8 142344466 142344466 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.245G>C p.Gly82Ala p.G82A ENST00000524325 4/14 111 44 67 79 79 0 strelka-varscan-mutect TSNARE1,missense_variant,p.Gly82Ala,ENST00000524325,NM_145003.4;TSNARE1,missense_variant,p.Gly82Ala,ENST00000307180,;TSNARE1,missense_variant,p.Gly82Ala,ENST00000520166,;TSNARE1,missense_variant,p.Gly82Ala,ENST00000520462,;TSNARE1,missense_variant,p.Gly98Ala,ENST00000518720,;TSNARE1,intron_variant,,ENST00000519651,NM_001291931.1; G ENST00000524325 Transcript missense_variant 421/1963 245/1542 82/513 G/A gGg/gCg 1 -1 TSNARE1 HGNC HGNC:26437 protein_coding YES CCDS6384.1 ENSP00000428763 Q96NA8 UPI00001AEE5E NM_145003.4 deleterious_low_confidence(0) 4/14 MODERATE 1 SNV 2 1 PASS rs1206522947 . 0 200 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 G 3 3 61 142344466 142344466 C G 1 0 0 0 0 1 0 0 0 17135 623 22 4 4 TSNARE1 8 142344466 Missense_Mutation SNP C C3N-00580_T 2725922 142344466 2794170 517 18652 ARC 0 . GRCh38 8 142613702 142613702 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.570G>T p.Glu190Asp p.E190D ENST00000356613 1/3 84 70 14 65 65 0 strelka-varscan-mutect ARC,missense_variant,p.Glu190Asp,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; A ENST00000356613 Transcript missense_variant 771/2948 570/1191 190/396 E/D gaG/gaT 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 tolerated_low_confidence(0.34) 1/3 hmmpanther:PTHR15962 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 61 142613702 142613702 C A 1 0 0 0 0 1 0 0 0 963 680 24 2 2 ARC 8 142613702 Missense_Mutation SNP C C3N-00580_T 269236 142613702 2524934 518 18653 MAFA 0 . GRCh38 8 143429971 143429971 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.436G>T p.Gly146Cys p.G146C ENST00000333480 1/1 89 75 14 94 94 0 strelka-varscan-mutect MAFA,missense_variant,p.Gly146Cys,ENST00000333480,NM_201589.3;MAFA,upstream_gene_variant,,ENST00000528185,; A ENST00000333480 Transcript missense_variant 436/2347 436/1062 146/353 G/C Ggc/Tgc 1 -1 MAFA HGNC HGNC:23145 protein_coding YES CCDS34955.1 ENSP00000328364 Q8NHW3 UPI00001B0366 NM_201589.3 deleterious(0.01) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR10129:SF30,hmmpanther:PTHR10129 MODERATE 1 SNV 1 PASS rs1344529699 . 0 200 10 0 0 0 0 0 -20 0.9999845 1 1 1 0 A 3 1 61 143429971 143429971 C A 1 0 0 0 0 1 0 0 0 9073 652 23 1 1 MAFA 8 143429971 Missense_Mutation SNP C C3N-00580_T 816269 143429971 1708665 519 18654 MROH1 0 . GRCh38 8 144261239 144261239 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1683C>A p.His561Gln p.H561Q ENST00000544576 25/26 622 499 123 543 541 2 strelka-varscan-mutect MROH1,missense_variant,p.His561Gln,ENST00000544576,;MROH1,intron_variant,,ENST00000528919,NM_032450.2;MROH1,intron_variant,,ENST00000326134,;MROH1,intron_variant,,ENST00000534366,NM_001288814.1;BOP1,downstream_gene_variant,,ENST00000569669,NM_015201.4;BOP1,downstream_gene_variant,,ENST00000569403,;BOP1,downstream_gene_variant,,ENST00000616126,;BOP1,downstream_gene_variant,,ENST00000563210,;BOP1,downstream_gene_variant,,ENST00000568812,;BOP1,downstream_gene_variant,,ENST00000569160,; A ENST00000544576 Transcript missense_variant 3292/3673 1683/1848 561/615 H/Q caC/caA 1 1 MROH1 HGNC HGNC:26958 protein_coding ENSP00000437866 Q8NDA8 UPI0000072B53 deleterious_low_confidence(0.04) 25/26 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 144261239 144261239 C A 1 0 0 0 0 1 0 0 0 9743 506 18 2 2 MROH1 8 144261239 Missense_Mutation SNP C C3N-00580_T 831268 144261239 877397 520 18655 TONSL 0 . GRCh38 8 144442120 144442120 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.782C>T p.Ala261Val p.A261V ENST00000409379 7/26 269 209 60 202 202 0 strelka-varscan-mutect TONSL,missense_variant,p.Ala261Val,ENST00000409379,NM_013432.4;TONSL,synonymous_variant,p.=,ENST00000613741,;TONSL-AS1,downstream_gene_variant,,ENST00000442850,;TONSL,non_coding_transcript_exon_variant,,ENST00000497613,; A ENST00000409379 Transcript missense_variant 812/4502 782/4137 261/1378 A/V gCc/gTc 1 -1 TONSL HGNC HGNC:7801 protein_coding YES CCDS34968.2 ENSP00000386239 Q96HA7 UPI0000424A3B NM_013432.4 deleterious(0) 7/26 Low_complexity_(Seg):seg,PROSITE_profiles:PS50293,hmmpanther:PTHR24139,hmmpanther:PTHR24139:SF31,Gene3D:1.25.40.10,Pfam_domain:PF13181,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 144442120 144442120 G A 1 0 0 0 0 1 0 0 0 16838 1204 42 3 3 TONSL 8 144442120 Missense_Mutation SNP G C3N-00580_T 180881 144442120 696516 521 18656 KIFC2 0 . GRCh38 8 144467614 144467614 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.599A>T p.Gln200Leu p.Q200L ENST00000301332 5/17 76 42 34 50 50 0 strelka-varscan-mutect KIFC2,missense_variant,p.Gln200Leu,ENST00000301332,NM_145754.3;CYHR1,upstream_gene_variant,,ENST00000438911,NM_138496.1;CYHR1,upstream_gene_variant,,ENST00000530374,;CYHR1,upstream_gene_variant,,ENST00000403000,NM_032687.3;CYHR1,upstream_gene_variant,,ENST00000306145,;CYHR1,upstream_gene_variant,,ENST00000424149,NM_001129888.1;CYHR1,upstream_gene_variant,,ENST00000526887,;CYHR1,upstream_gene_variant,,ENST00000533764,;CYHR1,upstream_gene_variant,,ENST00000530637,;CTD-2517M22.16,downstream_gene_variant,,ENST00000525461,;KIFC2,upstream_gene_variant,,ENST00000531423,;KIFC2,non_coding_transcript_exon_variant,,ENST00000533114,;KIFC2,non_coding_transcript_exon_variant,,ENST00000529644,;KIFC2,upstream_gene_variant,,ENST00000531425,;CYHR1,upstream_gene_variant,,ENST00000524623,;KIFC2,upstream_gene_variant,,ENST00000529864,; T ENST00000301332 Transcript missense_variant 976/3646 599/2517 200/838 Q/L cAg/cTg 1 1 KIFC2 HGNC HGNC:29530 protein_coding YES CCDS6427.1 ENSP00000301332 Q96AC6 UPI000006D3B2 NM_145754.3 deleterious(0.03) 5/17 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 144467614 144467614 A T 1 0 0 0 0 1 0 0 0 8178 188 7 4 4 KIFC2 8 144467614 Missense_Mutation SNP A C3N-00580_T 25494 144467614 671022 522 18657 IFNA21 0 . GRCh38 9 21166375 21166375 + Missense_Mutation SNP G G T rs746640260 C3N-00580_T C3N-00580_N G G c.238C>A p.Leu80Ile p.L80I ENST00000380225 1/1 390 299 91 383 383 0 strelka-varscan-mutect IFNA21,missense_variant,p.Leu80Ile,ENST00000380225,NM_002175.2; T ENST00000380225 Transcript missense_variant 286/1024 238/570 80/189 L/I Ctc/Atc rs746640260 1 -1 IFNA21 HGNC HGNC:5424 protein_coding YES CCDS6497.1 ENSP00000369574 P01568 UPI000002C35A NM_002175.2 deleterious(0.03) 1/1 Gene3D:1.20.1250.10,Pfam_domain:PF00143,Prints_domain:PR00266,hmmpanther:PTHR11691,hmmpanther:PTHR11691:SF23,SMART_domains:SM00076,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 PASS rs746640260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 21166375 21166375 G T 1 0 0 0 0 1 0 0 0 7438 1000 35 2 2 IFNA21 9 21166375 Missense_Mutation SNP G C3N-00580_T 21166375 117228342 523 18658 DNAJA1 0 . GRCh38 9 33038896 33038896 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1187C>A p.Thr396Asn p.T396N ENST00000330899 9/9 307 274 33 295 294 1 strelka-varscan-mutect DNAJA1,missense_variant,p.Thr396Asn,ENST00000330899,NM_001539.2;SMU1,downstream_gene_variant,,ENST00000397149,NM_018225.2;DNAJA1,downstream_gene_variant,,ENST00000495015,;DNAJA1,downstream_gene_variant,,ENST00000465677,; A ENST00000330899 Transcript missense_variant 1370/2381 1187/1194 396/397 T/N aCc/aAc 1 1 DNAJA1 HGNC HGNC:5229 protein_coding YES CCDS6533.1 ENSP00000369127 P31689 UPI0000129431 NM_001539.2 deleterious(0.02) 9/9 hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF227 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 33038896 33038896 C A 1 0 0 0 0 1 0 0 0 4426 507 18 2 2 DNAJA1 9 33038896 Missense_Mutation SNP C C3N-00580_T 11872521 33038896 105355821 524 18659 ALDH1B1 0 . GRCh38 9 38396617 38396617 + Missense_Mutation SNP G G C rs758839785 C3N-00580_T C3N-00580_N G G c.869G>C p.Ser290Thr p.S290T ENST00000377698 2/2 265 89 176 241 241 0 strelka-varscan-mutect ALDH1B1,missense_variant,p.Ser290Thr,ENST00000377698,NM_000692.4;ALDH1B1,downstream_gene_variant,,ENST00000635162,; C ENST00000377698 Transcript missense_variant 1022/3066 869/1554 290/517 S/T aGc/aCc rs758839785 1 1 ALDH1B1 HGNC HGNC:407 protein_coding YES CCDS6615.1 ENSP00000366927 P30837 UPI0000073000 NM_000692.4 deleterious(0) 2/2 hmmpanther:PTHR11699:SF211,hmmpanther:PTHR11699,PROSITE_patterns:PS00687,Gene3D:3.40.605.10,Pfam_domain:PF00171,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS rs758839785 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 38396617 38396617 G C 1 0 0 0 0 1 0 0 0 593 971 34 4 4 ALDH1B1 9 38396617 Missense_Mutation SNP G C3N-00580_T 5357721 38396617 99998100 525 18660 SPATA31A1 0 . GRCh38 9 39359005 39359005 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1282C>A p.Gln428Lys p.Q428K ENST00000377647 4/4 283 180 103 274 274 0 strelka-varscan-mutect SPATA31A1,missense_variant,p.Gln428Lys,ENST00000377647,NM_001085452.2;RP11-347J14.4,downstream_gene_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 1302/4256 1282/4086 428/1361 Q/K Cag/Aag 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 deleterious(0) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18,Pfam_domain:PF14650 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39359005 39359005 C A 1 0 0 0 0 1 0 0 0 15343 595 21 2 2 SPATA31A1 9 39359005 Missense_Mutation SNP C C3N-00580_T 962388 39359005 99035712 526 18661 SPATA31A3 0 . GRCh38 9 66987188 66987188 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.3310T>G p.Phe1104Val p.F1104V ENST00000428649 4/4 1155 1056 99 1089 1089 0 varscan-mutect SPATA31A3,missense_variant,p.Phe1104Val,ENST00000428649,NM_001083124.1;RP11-395E19.2,non_coding_transcript_exon_variant,,ENST00000616253,; C ENST00000428649 Transcript missense_variant 3372/4256 3310/4044 1104/1347 F/V Ttt/Gtt 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 tolerated(0.51) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 35 175 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 66987188 66987188 A C 1 0 0 0 0 1 0 0 0 15344 43 2 5 5 SPATA31A3 9 66987188 Missense_Mutation SNP A C3N-00580_T 27628183 66987188 71407529 527 18662 SPATA31A3 0 . GRCh38 9 66988625 66988625 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1873C>A p.Gln625Lys p.Q625K ENST00000428649 4/4 1143 916 227 1033 1031 2 strelka-varscan-mutect SPATA31A3,missense_variant,p.Gln625Lys,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; T ENST00000428649 Transcript missense_variant 1935/4256 1873/4044 625/1347 Q/K Cag/Aag 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 tolerated(0.09) 4/4 Pfam_domain:PF14650,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 32 177 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 66988625 66988625 G T 1 0 0 0 0 1 0 0 0 15344 1328 46 2 2 SPATA31A3 9 66988625 Missense_Mutation SNP G C3N-00580_T 1437 66988625 71406092 528 18663 TRPM3 0 . GRCh38 9 70776472 70776472 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.780C>A p.= p.T260T ENST00000396283 9/9 51 18 33 50 50 0 strelka-varscan-mutect TRPM3,synonymous_variant,p.=,ENST00000396283,NM_001007470.1;TRPM3,intron_variant,,ENST00000377110,NM_001007471.2;TRPM3,intron_variant,,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,intron_variant,,ENST00000377105,NM_024971.5;TRPM3,intron_variant,,ENST00000357533,;TRPM3,intron_variant,,ENST00000396292,NM_206946.3;TRPM3,intron_variant,,ENST00000358082,;TRPM3,intron_variant,,ENST00000396285,NM_020952.4;TRPM3,intron_variant,,ENST00000408909,;TRPM3,intron_variant,,ENST00000396280,NM_206945.3;TRPM3,intron_variant,,ENST00000377111,;TRPM3,intron_variant,,ENST00000377101,; T ENST00000396283 Transcript synonymous_variant 1100/3484 780/828 260/275 T acC/acA 1 -1 TRPM3 HGNC HGNC:17992 protein_coding ENSP00000379579 Q4VXD4 UPI000006DB66 NM_001007470.1 9/9 LOW SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 61 70776472 70776472 G T 1 0 0 0 0 0 0 0 1 17093 1335 47 2 2 TRPM3 9 70776472 Silent SNP G C3N-00580_T 3787847 70776472 67618245 529 18664 ALDH1A1 0 . GRCh38 9 72930896 72930896 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.295G>A p.Asp99Asn p.D99N ENST00000297785 3/13 195 65 130 195 195 0 strelka-varscan-mutect ALDH1A1,missense_variant,p.Asp99Asn,ENST00000297785,NM_000689.4;ALDH1A1,missense_variant,p.Asp99Asn,ENST00000376939,;ALDH1A1,missense_variant,p.Asp99Asn,ENST00000419959,;ALDH1A1,missense_variant,p.Asp99Asn,ENST00000446946,;ALDH1A1,non_coding_transcript_exon_variant,,ENST00000482210,;ALDH1A1,non_coding_transcript_exon_variant,,ENST00000493113,; T ENST00000297785 Transcript missense_variant 350/2107 295/1506 99/501 D/N Gat/Aat 1 -1 ALDH1A1 HGNC HGNC:402 protein_coding YES CCDS6644.1 ENSP00000297785 P00352 V9HW83 UPI0000000DC0 NM_000689.4 tolerated(0.08) 3/13 Gene3D:3.40.605.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF140,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 72930896 72930896 C T 1 0 0 0 0 1 0 0 0 590 913 32 3 3 ALDH1A1 9 72930896 Missense_Mutation SNP C C3N-00580_T 2154424 72930896 65463821 530 18665 PRUNE2 0 . GRCh38 9 76706152 76706152 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.6122G>T p.Ser2041Ile p.S2041I ENST00000376718 8/19 311 143 168 279 279 0 strelka-varscan-mutect PRUNE2,missense_variant,p.Ser2041Ile,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Ser1682Ile,ENST00000428286,;PRUNE2,missense_variant,p.Ser2041Ile,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,missense_variant,p.Ser1363Ile,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; A ENST00000376718 Transcript missense_variant 6246/12584 6122/9267 2041/3088 S/I aGt/aTt 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 deleterious(0.02) 8/19 hmmpanther:PTHR12112:SF11,hmmpanther:PTHR12112 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 76706152 76706152 C A 1 0 0 0 0 1 0 0 0 12791 565 20 2 2 PRUNE2 9 76706152 Missense_Mutation SNP C C3N-00580_T 3775256 76706152 61688565 531 18666 KIF27 0 . GRCh38 9 83903101 83903101 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1417G>A p.Val473Ile p.V473I ENST00000297814 4/18 192 178 14 155 155 0 strelka-varscan-mutect KIF27,missense_variant,p.Val473Ile,ENST00000297814,NM_017576.2;KIF27,missense_variant,p.Val473Ile,ENST00000413982,NM_001271927.1;KIF27,missense_variant,p.Val473Ile,ENST00000334204,NM_001271928.1;KIF27,intron_variant,,ENST00000495062,; T ENST00000297814 Transcript missense_variant 1561/4653 1417/4206 473/1401 V/I Gtt/Att 1 -1 KIF27 HGNC HGNC:18632 protein_coding YES CCDS6665.1 ENSP00000297814 Q86VH2 UPI000018F32F NM_017576.2 tolerated(1) 4/18 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 83903101 83903101 C T 1 0 0 0 0 1 0 0 0 8161 478 17 3 3 KIF27 9 83903101 Missense_Mutation SNP C C3N-00580_T 7196949 83903101 54491616 532 18667 BICD2 0 . GRCh38 9 92720489 92720489 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.873G>T p.Glu291Asp p.E291D ENST00000356884 4/7 519 251 268 397 397 0 strelka-varscan-mutect BICD2,missense_variant,p.Glu291Asp,ENST00000356884,NM_001003800.1;BICD2,missense_variant,p.Glu291Asp,ENST00000375512,NM_015250.3; A ENST00000356884 Transcript missense_variant 941/6427 873/2568 291/855 E/D gaG/gaT 1 -1 BICD2 HGNC HGNC:17208 protein_coding YES CCDS35064.1 ENSP00000349351 Q8TD16 UPI00001BBAF1 NM_001003800.1 tolerated(0.11) 4/7 Pfam_domain:PF09730,hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF7,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1430942149 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 92720489 92720489 C A 1 0 0 0 0 1 0 0 0 1578 796 28 2 2 BICD2 9 92720489 Missense_Mutation SNP C C3N-00580_T 8817388 92720489 45674228 533 18668 COL15A1 0 . GRCh38 9 99055289 99055289 + Frame_Shift_Del DEL G G - novel C3N-00580_T C3N-00580_N G G c.3110delG p.Gly1037ValfsTer116 p.G1037Vfs*116 ENST00000375001 34/42 200 137 63 200 200 0 sindel-varindel-pindel COL15A1,frameshift_variant,p.Gly1037ValfsTer116,ENST00000375001,NM_001855.4;COL15A1,frameshift_variant,p.Gly1023ValfsTer116,ENST00000610452,; - ENST00000375001 Transcript frameshift_variant 3532/5496 3109/4167 1037/1388 G/X Ggt/gt 1 1 COL15A1 HGNC HGNC:2192 protein_coding YES CCDS35081.1 ENSP00000364140 P39059 UPI0000211506 NM_001855.4 34/42 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF559,hmmpanther:PTHR24023 HIGH 1 deletion 1 1 1 PASS . . 0 205 0 2 3 0 0 0 -20 0.9772178 1 1 1 0 - 7 5 61 99055289 99055289 G - 1 0 1 0 1 0 0 0 0 3460 1000 35 0 0 COL15A1 9 99055289 Frame_Shift_Del DEL G C3N-00580_T 6334800 99055289 39339428 534 18669 OR13C2 0 . GRCh38 9 104605350 104605350 + Missense_Mutation SNP G G C C3N-00580_T C3N-00580_N G G c.278C>G p.Ser93Cys p.S93C ENST00000542196 1/1 274 246 28 284 284 0 varscan-mutect OR13C2,missense_variant,p.Ser93Cys,ENST00000542196,NM_001004481.1; C ENST00000542196 Transcript missense_variant 278/957 278/957 93/318 S/C tCc/tGc COSM1314342 1 -1 OR13C2 HGNC HGNC:14701 protein_coding YES CCDS35092.1 ENSP00000438815 Q8NGS9 A0A126GWR7 UPI0000041B29 NM_001004481.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF279,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 104605350 104605350 G C 1 0 0 0 0 1 0 0 0 11010 1174 41 4 4 OR13C2 9 104605350 Missense_Mutation SNP G C3N-00580_T 5550061 104605350 33789367 535 18670 OR13D1 0 . GRCh38 9 104695422 104695439 + In_Frame_Del DEL AGAAAGTCCTGAGCAGAC AGAAAGTCCTGAGCAGAC - novel C3N-00580_T C3N-00580_N AGAAAGTCCTGAGCAGAC AGAAAGTCCTGAGCAGAC c.1002_1019delGAAAGTCCTGAGCAGACA p.Lys334_His340delinsAsn p.K334_H340delinsN ENST00000318763 1/1 47 22 25 47 47 0 sindel-varindel-pindel OR13D1,inframe_deletion,p.Lys334_His340delinsAsn,ENST00000318763,NM_001004484.1; - ENST00000318763 Transcript inframe_deletion 1001-1018/1041 1001-1018/1041 334-340/346 KKVLSRH/N aAGAAAGTCCTGAGCAGACat/aat 1 1 OR13D1 HGNC HGNC:14695 protein_coding YES CCDS35094.1 ENSP00000317357 Q8NGV5 UPI0000061E68 NM_001004484.1 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF268,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 deletion 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 104695422 104695422 AGAAAGTCCTGAGCAGAC - 1 0 1 0 1 0 0 0 0 11016 72 3 0 0 OR13D1 9 104695422 In_Frame_Del DEL AGAAAGTCCTGAGCAGAC C3N-00580_T 90072 104695422 33699295 536 18671 PAPPA 0 . GRCh38 9 116187781 116187781 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.1043G>A p.Arg348His p.R348H ENST00000328252 2/22 497 448 49 435 435 0 strelka-varscan-mutect PAPPA,missense_variant,p.Arg348His,ENST00000328252,NM_002581.3; A ENST00000328252 Transcript missense_variant 1412/10959 1043/4884 348/1627 R/H cGc/cAc COSM202128 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 2/22 Gene3D:3.40.390.10 1 MODERATE 1 SNV 1 1 1 PASS rs1025262255 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 116187781 116187781 G A 1 0 0 0 0 1 0 0 0 11512 1087 38 1 1 PAPPA 9 116187781 Missense_Mutation SNP G C3N-00580_T 11492359 116187781 22206936 537 18672 TLR4 0 . GRCh38 9 117712844 117712844 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.716G>T p.Ser239Ile p.S239I ENST00000355622 3/3 312 145 167 261 261 0 strelka-varscan-mutect TLR4,missense_variant,p.Ser239Ile,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Ser199Ile,ENST00000394487,NM_003266.3;RNU6-1082P,upstream_gene_variant,,ENST00000364574,;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; T ENST00000355622 Transcript missense_variant 817/4844 716/2520 239/839 S/I aGt/aTt 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 deleterious(0) 3/3 hmmpanther:PTHR24365:SF230,hmmpanther:PTHR24365,Gene3D:3.80.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 117712844 117712844 G T 1 0 0 0 0 1 0 0 0 16399 1029 36 2 2 TLR4 9 117712844 Missense_Mutation SNP G C3N-00580_T 1525063 117712844 20681873 538 18673 OR1L3 0 . GRCh38 9 122675637 122675637 + Missense_Mutation SNP A A T C3N-00580_T C3N-00580_N A A c.508A>T p.Thr170Ser p.T170S ENST00000304820 1/1 191 157 34 232 231 1 strelka-varscan-mutect OR1L3,missense_variant,p.Thr170Ser,ENST00000304820,NM_001005234.1; T ENST00000304820 Transcript missense_variant 508/975 508/975 170/324 T/S Aca/Tca COSM3903834 1 1 OR1L3 HGNC HGNC:8215 protein_coding YES CCDS35128.1 ENSP00000302863 Q8NH93 A0A126GVD1 UPI000004618D NM_001005234.1 tolerated(0.31) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF198,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 122675637 122675637 A T 1 0 0 0 0 1 0 0 0 11042 391 14 4 4 OR1L3 9 122675637 Missense_Mutation SNP A C3N-00580_T 4962793 122675637 15719080 539 18674 CRB2 0 . GRCh38 9 123370936 123370936 + Missense_Mutation SNP G G T rs765111298 C3N-00580_T C3N-00580_N G G c.1883G>T p.Arg628Leu p.R628L ENST00000373631 7/13 109 47 62 120 120 0 strelka-varscan-mutect CRB2,missense_variant,p.Arg628Leu,ENST00000373631,NM_173689.6;CRB2,missense_variant,p.Arg628Leu,ENST00000359999,;CRB2,missense_variant,p.Arg296Leu,ENST00000460253,; T ENST00000373631 Transcript missense_variant 1884/5550 1883/3858 628/1285 R/L cGt/cTt rs765111298,COSM3324259,COSM3664073 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 deleterious(0.04) 7/13 Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_patterns:PS00010,PROSITE_profiles:PS50026,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF49899 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs765111298 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 123370936 123370936 G T 1 0 0 0 0 1 0 0 0 3649 1145 40 1 1 CRB2 9 123370936 Missense_Mutation SNP G C3N-00580_T 695299 123370936 15023781 540 18675 HMCN2 0 . GRCh38 9 130302884 130302884 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1301G>T p.Arg434Met p.R434M ENST00000624552 9/98 88 69 19 112 112 0 strelka-varscan-mutect HMCN2,missense_variant,p.Arg434Met,ENST00000624552,NM_001291815.1;HMCN2,upstream_gene_variant,,ENST00000611173,; T ENST00000624552 Transcript missense_variant 1301/15610 1301/15180 434/5059 R/M aGg/aTg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.04) 9/98 SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 61 130302884 130302884 G T 1 0 0 0 0 1 0 0 0 7112 1000 35 2 2 HMCN2 9 130302884 Missense_Mutation SNP G C3N-00580_T 6931948 130302884 8091833 541 18676 TSC1 0 . GRCh38 9 132905874 132905874 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.1704A>T p.= p.G568G ENST00000298552 15/23 110 86 24 117 117 0 strelka-varscan-mutect TSC1,synonymous_variant,p.=,ENST00000298552,NM_000368.4,NM_001162426.1;TSC1,synonymous_variant,p.=,ENST00000440111,;TSC1,synonymous_variant,p.=,ENST00000545250,NM_001162427.1;TSC1,downstream_gene_variant,,ENST00000493467,; A ENST00000298552 Transcript synonymous_variant 1926/8604 1704/3495 568/1164 G ggA/ggT 1 -1 TSC1 HGNC HGNC:12362 protein_coding YES CCDS6956.1 ENSP00000298552 Q92574 X5D9D2 UPI000013773E NM_000368.4,NM_001162426.1 15/23 Pfam_domain:PF04388,hmmpanther:PTHR15154 LOW 1 SNV 1 1 PASS rs1171240569 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 2 1 61 132905874 132905874 T A 1 0 0 0 0 0 0 0 1 17111 1538 54 4 4 TSC1 9 132905874 Silent SNP T C3N-00580_T 2602990 132905874 5488843 542 18677 GFI1B 0 . GRCh38 9 132988345 132988345 + Silent SNP C C A rs146898098 C3N-00580_T C3N-00580_N C C c.387C>A p.= p.A129A ENST00000339463 8/11 445 210 235 522 522 0 strelka-varscan-mutect GFI1B,synonymous_variant,p.=,ENST00000339463,NM_004188.5;GFI1B,synonymous_variant,p.=,ENST00000636137,;GFI1B,synonymous_variant,p.=,ENST00000372122,;GFI1B,synonymous_variant,p.=,ENST00000636263,;GFI1B,synonymous_variant,p.=,ENST00000372123,NM_001135031.1; A ENST00000339463 Transcript synonymous_variant 1206/2449 387/993 129/330 A gcC/gcA rs146898098 1 1 GFI1B HGNC HGNC:4238 protein_coding YES CCDS6957.1 ENSP00000344782 Q5VTD9 UPI000013E4EE NM_004188.5 8/11 LOW 1 SNV 1 1 PASS rs146898098 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 132988345 132988345 C A 1 0 0 0 0 0 0 0 1 6214 668 24 2 2 GFI1B 9 132988345 Silent SNP C C3N-00580_T 82471 132988345 5406372 543 18678 SNAPC4 0 . GRCh38 9 136388473 136388473 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.1094G>A p.Arg365His p.R365H ENST00000298532 10/23 174 146 28 171 171 0 strelka-varscan-mutect SNAPC4,missense_variant,p.Arg365His,ENST00000298532,NM_003086.2;SNAPC4,missense_variant,p.Arg365His,ENST00000637388,; T ENST00000298532 Transcript missense_variant 1463/5010 1094/4410 365/1469 R/H cGc/cAc COSM1461068 1 -1 SNAPC4 HGNC HGNC:11137 protein_coding YES CCDS6998.1 ENSP00000298532 Q5SXM2 A0A024R8F4 UPI000013E4EC NM_003086.2 deleterious(0) 10/23 Gene3D:1.10.10.60,PROSITE_profiles:PS50090,SMART_domains:SM00717,Superfamily_domains:SSF46689 1 MODERATE 1 SNV 1 1 1 PASS rs1221816864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 136388473 136388473 C T 1 0 0 0 0 1 0 0 0 15158 768 27 1 1 SNAPC4 9 136388473 Missense_Mutation SNP C C3N-00580_T 3400128 136388473 2006244 544 18679 SDCCAG3 0 . GRCh38 9 136402791 136402791 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.1305T>C p.= p.S435S ENST00000357365 10/10 166 78 88 178 178 0 strelka-varscan-mutect SDCCAG3,synonymous_variant,p.=,ENST00000298537,NM_006643.3;SDCCAG3,synonymous_variant,p.=,ENST00000357365,NM_001039707.1;SDCCAG3,synonymous_variant,p.=,ENST00000371725,NM_001039708.1;SDCCAG3,synonymous_variant,p.=,ENST00000417512,;SNAPC4,upstream_gene_variant,,ENST00000298532,NM_003086.2;SNAPC4,upstream_gene_variant,,ENST00000637388,;SDCCAG3,downstream_gene_variant,,ENST00000371723,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000461693,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000466579,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000481114,;SDCCAG3,downstream_gene_variant,,ENST00000468963,;SDCCAG3,downstream_gene_variant,,ENST00000486441,; G ENST00000357365 Transcript synonymous_variant 1435/2304 1305/1308 435/435 S tcT/tcC 1 -1 SDCCAG3 HGNC HGNC:10667 protein_coding YES CCDS43904.1 ENSP00000349929 Q96C92 UPI00006C511A NM_001039707.1 10/10 hmmpanther:PTHR31259 LOW SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 136402791 136402791 A G 1 0 0 0 0 0 0 0 1 14229 59 3 5 5 SDCCAG3 9 136402791 Silent SNP A C3N-00580_T 14318 136402791 1991926 545 18680 RABL6 0 . GRCh38 9 136823595 136823595 + Silent SNP G G A rs368002409 C3N-00580_T C3N-00580_N G G c.201G>A p.= p.P67P ENST00000425121 2/15 168 151 17 225 224 1 strelka-varscan-mutect RABL6,synonymous_variant,p.=,ENST00000311502,NM_024718.4;RABL6,synonymous_variant,p.=,ENST00000436380,;RABL6,synonymous_variant,p.=,ENST00000371663,;RABL6,synonymous_variant,p.=,ENST00000425121,NM_001173988.1;RABL6,synonymous_variant,p.=,ENST00000357466,;RABL6,synonymous_variant,p.=,ENST00000371671,NM_001173989.2;RABL6,synonymous_variant,p.=,ENST00000629216,;RABL6,upstream_gene_variant,,ENST00000466096,;RABL6,upstream_gene_variant,,ENST00000461992,;RABL6,synonymous_variant,p.=,ENST00000464941,;RABL6,synonymous_variant,p.=,ENST00000484471,;RP11-216L13.18,non_coding_transcript_exon_variant,,ENST00000471502,; A ENST00000425121 Transcript synonymous_variant 201/2193 201/2193 67/730 P ccG/ccA rs368002409 1 1 RABL6 HGNC HGNC:24703 protein_coding YES CCDS55352.1 ENSP00000395490 H0Y4Z8 UPI0000E0C208 NM_001173988.1 2/15 PROSITE_profiles:PS51419,hmmpanther:PTHR14932,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00175,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW 1 SNV 1 1 PASS rs368002409 . 0 208 0 2 0 0 0 0 -19.99992 0.9999999 1 1 1 0 A 2 1 61 136823595 136823595 G A 1 0 0 0 0 0 0 0 1 13132 1132 40 1 1 RABL6 9 136823595 Silent SNP G C3N-00580_T 420804 136823595 1571122 546 18681 PTGDS 0 . GRCh38 9 136977629 136977629 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.51G>T p.= p.L17L ENST00000371625 1/7 98 44 54 201 201 0 strelka-varscan-mutect PTGDS,synonymous_variant,p.=,ENST00000371625,NM_000954.5;PTGDS,synonymous_variant,p.=,ENST00000457950,;PTGDS,upstream_gene_variant,,ENST00000446677,;PTGDS,upstream_gene_variant,,ENST00000444903,;RP11-229P13.19,downstream_gene_variant,,ENST00000413913,;PTGDS,synonymous_variant,p.=,ENST00000471521,;PTGDS,non_coding_transcript_exon_variant,,ENST00000371623,;LCNL1,upstream_gene_variant,,ENST00000482657,;PTGDS,upstream_gene_variant,,ENST00000492068,;PTGDS,upstream_gene_variant,,ENST00000460340,;PTGDS,upstream_gene_variant,,ENST00000462514,; T ENST00000371625 Transcript synonymous_variant 125/807 51/573 17/190 L ctG/ctT 1 1 PTGDS HGNC HGNC:9592 protein_coding YES CCDS7019.1 ENSP00000360687 P41222 A0A024R8G3 UPI00001317A4 NM_000954.5 1/7 Gene3D:2.40.128.20,hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF86,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 136977629 136977629 G T 1 0 0 0 0 0 0 0 1 12896 1335 47 2 2 PTGDS 9 136977629 Silent SNP G C3N-00580_T 154034 136977629 1417088 547 18682 DIP2C 0 . GRCh38 10 419110 419110 + Frame_Shift_Del DEL T T - rs200266725 C3N-00580_T C3N-00580_N T T c.694delA p.Thr232GlnfsTer19 p.T232Qfs*19 ENST00000280886 6/37 293 202 91 337 337 0 sindel-varindel-pindel DIP2C,frameshift_variant,p.Thr232GlnfsTer19,ENST00000280886,NM_014974.2;DIP2C,frameshift_variant,p.Thr213GlnfsTer19,ENST00000381496,;DIP2C,frameshift_variant,p.Thr288GlnfsTer19,ENST00000634311,; - ENST00000280886 Transcript frameshift_variant 784/7888 694/4671 232/1556 T/X Aca/ca rs200266725 1 -1 DIP2C HGNC HGNC:29150 protein_coding YES CCDS7054.1 ENSP00000280886 Q9Y2E4 UPI00001833B9 NM_014974.2 6/37 hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF25 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 419110 419110 T - 1 0 1 0 1 0 0 0 0 4334 1667 58 0 0 DIP2C 10 419110 Frame_Shift_Del DEL T C3N-00580_T 419110 133378312 548 18683 GTPBP4 0 . GRCh38 10 1012574 1012574 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1454A>T p.Lys485Met p.K485M ENST00000360803 14/17 336 270 66 366 366 0 strelka-varscan-mutect GTPBP4,missense_variant,p.Lys485Met,ENST00000360803,NM_012341.2;GTPBP4,non_coding_transcript_exon_variant,,ENST00000483839,;GTPBP4,downstream_gene_variant,,ENST00000491635,; T ENST00000360803 Transcript missense_variant 1915/5075 1454/1905 485/634 K/M aAg/aTg 1 1 GTPBP4 HGNC HGNC:21535 protein_coding YES CCDS31132.1 ENSP00000354040 Q9BZE4 D2CFK9 UPI000000D960 NM_012341.2 tolerated(0.05) 14/17 Low_complexity_(Seg):seg,hmmpanther:PTHR11702:SF4,hmmpanther:PTHR11702,PIRSF_domain:PIRSF038919 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 1012574 1012574 A T 1 0 0 0 0 1 0 0 0 6763 72 3 4 4 GTPBP4 10 1012574 Missense_Mutation SNP A C3N-00580_T 593464 1012574 132784848 549 18684 ADARB2 0 . GRCh38 10 1233726 1233726 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1481G>T p.Arg494Ile p.R494I ENST00000381312 6/10 167 110 57 199 199 0 strelka-varscan-mutect ADARB2,missense_variant,p.Arg494Ile,ENST00000381312,NM_018702.3;ADARB2,non_coding_transcript_exon_variant,,ENST00000469464,; A ENST00000381312 Transcript missense_variant 1807/8421 1481/2220 494/739 R/I aGa/aTa COSM158919 1 -1 ADARB2 HGNC HGNC:227 protein_coding YES CCDS7058.1 ENSP00000370713 Q9NS39 UPI0000071776 NM_018702.3 deleterious(0) 6/10 PROSITE_profiles:PS50141,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF17,Pfam_domain:PF02137,SMART_domains:SM00552 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1233726 1233726 C A 1 0 0 0 0 1 0 0 0 327 913 32 2 2 ADARB2 10 1233726 Missense_Mutation SNP C C3N-00580_T 221152 1233726 132563696 550 18685 IL2RA 0 . GRCh38 10 6021490 6021490 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.571A>T p.Ser191Cys p.S191C ENST00000379959 4/8 418 331 87 432 432 0 strelka-varscan-mutect IL2RA,missense_variant,p.Ser191Cys,ENST00000379959,NM_000417.2;IL2RA,intron_variant,,ENST00000379954,NM_001308242.1;IL2RA,intron_variant,,ENST00000256876,;IL2RA,intron_variant,,ENST00000447847,;SNORA14,upstream_gene_variant,,ENST00000516113,;RP11-536K7.5,upstream_gene_variant,,ENST00000440436,; A ENST00000379959 Transcript missense_variant 745/3176 571/819 191/272 S/C Agt/Tgt 1 -1 IL2RA HGNC HGNC:6008 protein_coding YES CCDS7076.1 ENSP00000369293 P01589 UPI000012D4A3 NM_000417.2 tolerated(0.05) 4/8 hmmpanther:PTHR10573,hmmpanther:PTHR10573:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 6021490 6021490 T A 1 0 0 0 0 1 0 0 0 7585 1580 55 4 4 IL2RA 10 6021490 Missense_Mutation SNP T C3N-00580_T 4787764 6021490 127775932 551 18686 PRKCQ 0 . GRCh38 10 6483593 6483593 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1026G>T p.Gln342His p.Q342H ENST00000263125 11/18 158 99 59 146 146 0 strelka-varscan-mutect PRKCQ,missense_variant,p.Gln342His,ENST00000263125,NM_001323265.1,NM_006257.4,NM_001282644.1;PRKCQ,missense_variant,p.Gln217His,ENST00000539722,NM_001323266.1,NM_001282645.1;PRKCQ,missense_variant,p.Gln342His,ENST00000397176,NM_001242413.2;PRKCQ,missense_variant,p.Gln306His,ENST00000610727,; A ENST00000263125 Transcript missense_variant 1126/3285 1026/2121 342/706 Q/H caG/caT 1 -1 PRKCQ HGNC HGNC:9410 protein_coding YES CCDS7079.1 ENSP00000263125 Q04759 UPI000012DF74 NM_001323265.1,NM_006257.4,NM_001282644.1 tolerated(0.22) 11/18 PIRSF_domain:PIRSF000551,PIRSF_domain:PIRSF501105 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 6483593 6483593 C A 1 0 0 0 0 1 0 0 0 12648 680 24 2 2 PRKCQ 10 6483593 Missense_Mutation SNP C C3N-00580_T 462103 6483593 127313829 552 18687 ECHDC3 0 . GRCh38 10 11742636 11742636 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.60C>A p.= p.R20R ENST00000379215 1/5 37 32 5 33 33 0 strelka-varscan-mutect ECHDC3,synonymous_variant,p.=,ENST00000379215,NM_024693.4;ECHDC3,synonymous_variant,p.=,ENST00000420401,;ECHDC3,upstream_gene_variant,,ENST00000422887,;ECHDC3,non_coding_transcript_exon_variant,,ENST00000496136,;ECHDC3,upstream_gene_variant,,ENST00000495787,; A ENST00000379215 Transcript synonymous_variant 271/1649 60/912 20/303 R cgC/cgA 1 1 ECHDC3 HGNC HGNC:23489 protein_coding YES CCDS7084.1 ENSP00000368517 Q96DC8 UPI00001F8B44 NM_024693.4 1/5 LOW 1 SNV 1 1 PASS rs1268601230 . 0 208 2 0 0 0 0 0 -13.59209 1 1 1 1 0 A 2 1 61 11742636 11742636 C A 1 0 0 0 0 0 0 0 1 4721 755 27 1 1 ECHDC3 10 11742636 Silent SNP C C3N-00580_T 5259043 11742636 122054786 553 18688 MCM10 0 . GRCh38 10 13195153 13195153 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1861C>T p.Pro621Ser p.P621S ENST00000484800 14/20 483 387 96 427 427 0 strelka-varscan-mutect MCM10,missense_variant,p.Pro620Ser,ENST00000378694,;MCM10,missense_variant,p.Pro620Ser,ENST00000378714,NM_018518.4;MCM10,missense_variant,p.Pro621Ser,ENST00000484800,NM_182751.2;MCM10,non_coding_transcript_exon_variant,,ENST00000481292,;MCM10,non_coding_transcript_exon_variant,,ENST00000459751,;MCM10,upstream_gene_variant,,ENST00000485659,; T ENST00000484800 Transcript missense_variant 1964/3157 1861/2628 621/875 P/S Ccg/Tcg 1 1 MCM10 HGNC HGNC:18043 protein_coding YES CCDS7096.1 ENSP00000418268 Q7L590 UPI000013C5E2 NM_182751.2 tolerated(0.57) 14/20 Pfam_domain:PF09332,hmmpanther:PTHR13454,SMART_domains:SM01280 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 13195153 13195153 C T 1 0 0 0 0 1 0 0 0 9317 623 22 3 3 MCM10 10 13195153 Missense_Mutation SNP C C3N-00580_T 1452517 13195153 120602269 554 18689 MRC1 0 . GRCh38 10 17809479 17809479 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.14T>A p.Leu5Gln p.L5Q ENST00000569591 1/30 852 484 368 809 809 0 strelka-varscan-mutect MRC1,missense_variant,p.Leu5Gln,ENST00000569591,NM_002438.3; A ENST00000569591 Transcript missense_variant 136/5198 14/4371 5/1456 L/Q cTg/cAg 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 tolerated(0.06) 1/30 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 17809479 17809479 T A 1 0 0 0 0 1 0 0 0 9722 1580 55 4 4 MRC1 10 17809479 Missense_Mutation SNP T C3N-00580_T 4614326 17809479 115987943 555 18690 SLC39A12 0 . GRCh38 10 17961835 17961835 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.516G>C p.Arg172Ser p.R172S ENST00000377369 3/13 136 112 24 107 107 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Arg172Ser,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Arg172Ser,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Arg172Ser,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Arg38Ser,ENST00000539911,NM_001282734.1; C ENST00000377369 Transcript missense_variant 789/2808 516/2076 172/691 R/S agG/agC 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 tolerated(0.08) 3/13 hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 C 3 2 61 17961835 17961835 G C 1 0 0 0 0 1 0 0 0 14893 1194 42 4 4 SLC39A12 10 17961835 Missense_Mutation SNP G C3N-00580_T 152356 17961835 115835587 556 18691 PLXDC2 0 . GRCh38 10 20245500 20245500 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1468A>T p.Ile490Phe p.I490F ENST00000377252 13/14 116 72 44 98 98 0 strelka-varscan-mutect PLXDC2,missense_variant,p.Ile490Phe,ENST00000377252,NM_032812.8;PLXDC2,missense_variant,p.Ile441Phe,ENST00000377242,NM_001282736.1;PLXDC2,non_coding_transcript_exon_variant,,ENST00000377238,; T ENST00000377252 Transcript missense_variant 2309/12468 1468/1590 490/529 I/F Att/Ttt 1 1 PLXDC2 HGNC HGNC:21013 protein_coding YES CCDS7132.1 ENSP00000366460 Q6UX71 UPI0000048F2C NM_032812.8 deleterious(0.01) 13/14 hmmpanther:PTHR13055:SF11,hmmpanther:PTHR13055 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20245500 20245500 A T 1 0 0 0 0 1 0 0 0 12224 463 16 4 4 PLXDC2 10 20245500 Missense_Mutation SNP A C3N-00580_T 2283665 20245500 113551922 557 18692 MYO3A 0 . GRCh38 10 25996503 25996503 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.317G>T p.Gly106Val p.G106V ENST00000265944 5/35 447 361 86 444 444 0 strelka-varscan-mutect MYO3A,missense_variant,p.Gly106Val,ENST00000265944,NM_017433.4;MYO3A,missense_variant,p.Gly106Val,ENST00000376302,;MYO3A,missense_variant,p.Gly106Val,ENST00000543632,;MYO3A,missense_variant,p.Gly106Val,ENST00000376301,; T ENST00000265944 Transcript missense_variant 483/5581 317/4851 106/1616 G/V gGa/gTa 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0) 5/35 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1254755444 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 25996503 25996503 G T 1 0 0 0 0 1 0 0 0 10077 1174 41 2 2 MYO3A 10 25996503 Missense_Mutation SNP G C3N-00580_T 5751003 25996503 107800919 558 18693 MYO3A 0 . GRCh38 10 26096386 26096386 + Missense_Mutation SNP A A G rs763004892 C3N-00580_T C3N-00580_N A A c.1568A>G p.Glu523Gly p.E523G ENST00000265944 16/35 262 150 112 212 212 0 strelka-varscan-mutect MYO3A,missense_variant,p.Glu523Gly,ENST00000265944,NM_017433.4;MYO3A,missense_variant,p.Glu523Gly,ENST00000543632,; G ENST00000265944 Transcript missense_variant 1734/5581 1568/4851 523/1616 E/G gAa/gGa rs763004892 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 deleterious(0) 16/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 26096386 26096386 A G 1 0 0 0 0 1 0 0 0 10077 260 9 5 5 MYO3A 10 26096386 Missense_Mutation SNP A C3N-00580_T 99883 26096386 107701036 559 18694 ARHGAP12 0 . GRCh38 10 31808722 31808722 + Missense_Mutation SNP C C A rs34750454 C3N-00580_T C3N-00580_N C C c.2293G>T p.Val765Phe p.V765F ENST00000344936 19/20 227 183 44 253 253 0 strelka-varscan-mutect ARHGAP12,missense_variant,p.Val760Phe,ENST00000396144,NM_001270695.1;ARHGAP12,missense_variant,p.Val718Phe,ENST00000375245,NM_001270697.1;ARHGAP12,missense_variant,p.Val735Phe,ENST00000375250,NM_001270696.1,NM_001270698.1;ARHGAP12,missense_variant,p.Val713Phe,ENST00000311380,NM_001270699.1;ARHGAP12,missense_variant,p.Val765Phe,ENST00000344936,NM_018287.6;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000492028,;ARHGAP12,non_coding_transcript_exon_variant,,ENST00000493008,;ARHGAP12,upstream_gene_variant,,ENST00000497085,;ARHGAP12,downstream_gene_variant,,ENST00000497103,; A ENST00000344936 Transcript missense_variant 2528/4128 2293/2541 765/846 V/F Gtt/Ttt rs34750454 1 -1 ARHGAP12 HGNC HGNC:16348 protein_coding YES CCDS7170.1 ENSP00000345808 Q8IWW6 UPI000007445E NM_018287.6 deleterious(0.03) 19/20 PROSITE_profiles:PS50238,hmmpanther:PTHR23181:SF3,hmmpanther:PTHR23181,Pfam_domain:PF00620,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS rs34750454 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 31808722 31808722 C A 1 0 0 0 0 1 0 0 0 989 478 17 2 2 ARHGAP12 10 31808722 Missense_Mutation SNP C C3N-00580_T 5712336 31808722 101988700 560 18695 ZNF37A 0 . GRCh38 10 38118833 38118833 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1682G>T p.Gly561Val p.G561V ENST00000361085 7/7 33 16 17 26 26 0 strelka-varscan-mutect ZNF37A,missense_variant,p.Gly561Val,ENST00000361085,NM_001178101.1,NM_003421.2;ZNF37A,missense_variant,p.Gly561Val,ENST00000351773,NM_001324248.1,NM_001324246.1,NM_001324249.1,NM_001007094.2;ZNF37A,intron_variant,,ENST00000638053,NM_001324256.1;ZNF37A,downstream_gene_variant,,ENST00000479469,;ZNF37A,downstream_gene_variant,,ENST00000477790,; T ENST00000361085 Transcript missense_variant 2027/8738 1682/1686 561/561 G/V gGg/gTg 1 1 ZNF37A HGNC HGNC:13102 protein_coding YES CCDS31183.1 ENSP00000354377 P17032 UPI000006E045 NM_001178101.1,NM_003421.2 deleterious_low_confidence(0) 7/7 MODERATE 1 SNV 2 1 PASS rs1263606238 . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 38118833 38118833 G T 1 0 0 0 0 1 0 0 0 18444 1232 43 2 2 ZNF37A 10 38118833 Missense_Mutation SNP G C3N-00580_T 6310111 38118833 95678589 561 18696 AGAP14P 0 . GRCh38 10 46358142 46358142 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1486C>A p.Leu496Ile p.L496I ENST00000624701 9/9 1446 1203 243 1390 1390 0 strelka-varscan-mutect AGAP14P,missense_variant,p.Leu496Ile,ENST00000624701,; A ENST00000624701 Transcript missense_variant 1486/2058 1486/2058 496/685 L/I Ctc/Atc 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF deleterious(0.02) 9/9 PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,Pfam_domain:PF01412,SMART_domains:SM00105,Superfamily_domains:SSF57863,Prints_domain:PR00405 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 46358142 46358142 C A 1 0 0 0 0 1 0 0 0 444 681 24 2 2 AGAP14P 10 46358142 Missense_Mutation SNP C C3N-00580_T 8239309 46358142 87439280 562 18697 PTPN20 0 . GRCh38 10 46984540 46984540 + Silent SNP A A C novel C3N-00580_T C3N-00580_N A A c.894A>C p.= p.R298R ENST00000374339 7/10 183 95 88 146 146 0 strelka-varscan-mutect PTPN20,synonymous_variant,p.=,ENST00000374218,NM_001320686.1,NM_001042363.3;PTPN20,synonymous_variant,p.=,ENST00000395721,NM_001320681.1,NM_001320685.1;PTPN20,synonymous_variant,p.=,ENST00000506080,;PTPN20,synonymous_variant,p.=,ENST00000374339,NM_001042357.3;PTPN20,synonymous_variant,p.=,ENST00000511769,NM_001042358.3;PTPN20,synonymous_variant,p.=,ENST00000505814,;PTPN20,synonymous_variant,p.=,ENST00000395727,NM_001042360.2;PTPN20,intron_variant,,ENST00000374346,NM_001320683.1,NM_015605.7;PTPN20,intron_variant,,ENST00000395725,NM_001042364.3;PTPN20,intron_variant,,ENST00000395722,NM_001320682.1,NM_001320690.1;PTPN20,intron_variant,,ENST00000374342,NM_001042365.2;PTPN20,intron_variant,,ENST00000509599,;PTPN20,intron_variant,,ENST00000513156,NM_001042359.2;PTPN20,intron_variant,,ENST00000502705,;PTPN20,intron_variant,,ENST00000513266,;PTPN20,intron_variant,,ENST00000509774,NM_001042361.3;PTPN20,intron_variant,,ENST00000508602,;PTPN20,intron_variant,,ENST00000509900,;PTPN20,intron_variant,,ENST00000513756,;PTPN20,intron_variant,,ENST00000502254,;PTPN20,intron_variant,,ENST00000508715,;PTPN20,intron_variant,,ENST00000417004,;PTPN20,intron_variant,,ENST00000503851,NM_001042362.2;PTPN20,intron_variant,,ENST00000513159,;PTPN20,3_prime_UTR_variant,,ENST00000437863,;PTPN20,3_prime_UTR_variant,,ENST00000510335,;PTPN20,downstream_gene_variant,,ENST00000508357,; C ENST00000374339 Transcript synonymous_variant 971/1388 894/1263 298/420 R cgA/cgC 1 1 PTPN20 HGNC HGNC:23423 protein_coding YES CCDS73110.1 ENSP00000363459 Q4JDL3 UPI00000473F4 NM_001042357.3 7/10 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF271,hmmpanther:PTHR19134,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00194,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 46984540 46984540 A C 1 0 0 0 0 0 0 0 1 12939 233 9 5 5 PTPN20 10 46984540 Silent SNP A C3N-00580_T 626398 46984540 86812882 563 18698 WDFY4 0 . GRCh38 10 48810645 48810645 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.4954G>A p.Ala1652Thr p.A1652T ENST00000325239 28/61 253 208 45 228 227 1 strelka-varscan-mutect WDFY4,missense_variant,p.Ala1652Thr,ENST00000325239,NM_020945.1;WDFY4,missense_variant,p.Ala199Thr,ENST00000374161,; A ENST00000325239 Transcript missense_variant 4954/9555 4954/9555 1652/3184 A/T Gca/Aca 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 tolerated(0.05) 28/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 48810645 48810645 G A 1 0 0 0 0 1 0 0 0 17831 1203 42 3 3 WDFY4 10 48810645 Missense_Mutation SNP G C3N-00580_T 1826105 48810645 84986777 564 18699 WDFY4 0 . GRCh38 10 48820314 48820314 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5586G>T p.Gln1862His p.Q1862H ENST00000325239 32/61 597 355 242 438 438 0 strelka-varscan-mutect WDFY4,missense_variant,p.Gln1862His,ENST00000325239,NM_020945.1;WDFY4,missense_variant,p.Gln409His,ENST00000374161,;WDFY4,upstream_gene_variant,,ENST00000265453,; T ENST00000325239 Transcript missense_variant 5586/9555 5586/9555 1862/3184 Q/H caG/caT 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 deleterious(0.04) 32/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 MODERATE 1 SNV 5 1 PASS rs1402503654 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 48820314 48820314 G T 1 0 0 0 0 1 0 0 0 17831 991 35 2 2 WDFY4 10 48820314 Missense_Mutation SNP G C3N-00580_T 9669 48820314 84977108 565 18700 WDFY4 0 . GRCh38 10 48900220 48900220 + Splice_Site SNP G G A novel C3N-00580_T C3N-00580_N G G c.7438-1G>A p.X2480_splice ENST00000325239 134 107 27 159 159 0 strelka-varscan-mutect WDFY4,splice_acceptor_variant,,ENST00000325239,NM_020945.1;WDFY4,splice_acceptor_variant,,ENST00000265453,;RP11-523O18.7,intron_variant,,ENST00000430438,; A ENST00000325239 Transcript splice_acceptor_variant -/9555 7438/9555 2480/3184 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 44/60 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 48900220 48900220 G A 1 0 0 0 0 0 0 1 0 17831 1014 35 3 3 WDFY4 10 48900220 Splice_Site SNP G C3N-00580_T 79906 48900220 84897202 566 18701 C10orf71 0 . GRCh38 10 49325444 49325444 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2899G>T p.Gly967Trp p.G967W ENST00000374144 3/3 124 70 54 114 114 0 strelka-varscan-mutect C10orf71,missense_variant,p.Gly967Trp,ENST00000374144,NM_001135196.1; T ENST00000374144 Transcript missense_variant 3187/5230 2899/4308 967/1435 G/W Ggg/Tgg 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 49325444 49325444 G T 1 0 0 0 0 1 0 0 0 1769 1232 43 2 2 C10orf71 10 49325444 Missense_Mutation SNP G C3N-00580_T 425224 49325444 84471978 567 18702 PGBD3 0 . GRCh38 10 49515670 49515670 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2849G>T p.Trp950Leu p.W950L ENST00000515869 6/6 214 114 100 179 178 1 strelka-varscan-mutect ERCC6,missense_variant,p.Trp950Leu,ENST00000515869,NM_001277059.1;ERCC6,missense_variant,p.Trp950Leu,ENST00000447839,NM_001277058.1;PGBD3,missense_variant,p.Trp482Leu,ENST00000374127,NM_170753.3;ERCC6,intron_variant,,ENST00000355832,NM_000124.3; A ENST00000515869 Transcript missense_variant 2970/3439 2849/3186 950/1061 W/L tGg/tTg 1 -1 ERCC6 HGNC HGNC:3438 protein_coding CCDS60529.1 ENSP00000423550 E7EV46 UPI00001F98BA NM_001277059.1 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR28576:SF3,hmmpanther:PTHR28576,Pfam_domain:PF13843 MODERATE SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 49515670 49515670 C A 1 0 0 0 0 1 0 0 0 11872 595 21 2 2 PGBD3 10 49515670 Missense_Mutation SNP C C3N-00580_T 190226 49515670 84281752 568 18703 SLC18A3 0 . GRCh38 10 49611296 49611296 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.556G>T p.Gly186Cys p.G186C ENST00000374115 1/1 383 228 155 385 385 0 strelka-varscan-mutect SLC18A3,missense_variant,p.Gly186Cys,ENST00000374115,NM_003055.2;CHAT,intron_variant,,ENST00000339797,NM_020984.3;CHAT,upstream_gene_variant,,ENST00000395562,NM_001142933.1;CHAT,upstream_gene_variant,,ENST00000337653,NM_020549.4;CHAT,upstream_gene_variant,,ENST00000351556,NM_020985.3,NM_001142934.1,NM_001142929.1;CHAT,upstream_gene_variant,,ENST00000395559,NM_020986.3;CHAT,upstream_gene_variant,,ENST00000460699,;CHAT,upstream_gene_variant,,ENST00000490270,;CHAT,upstream_gene_variant,,ENST00000481336,;CHAT,upstream_gene_variant,,ENST00000466590,; T ENST00000374115 Transcript missense_variant 996/2420 556/1599 186/532 G/C Ggc/Tgc 1 1 SLC18A3 HGNC HGNC:10936 protein_coding YES CCDS7231.1 ENSP00000363229 Q16572 UPI00001F98C1 NM_003055.2 deleterious(0) 1/1 PROSITE_profiles:PS50850,hmmpanther:PTHR23506,hmmpanther:PTHR23506:SF13,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 49611296 49611296 G T 1 0 0 0 0 1 0 0 0 14692 1232 43 2 2 SLC18A3 10 49611296 Missense_Mutation SNP G C3N-00580_T 95626 49611296 84186126 569 18704 CTNNA3 0 . GRCh38 10 66280613 66280613 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1741G>C p.Glu581Gln p.E581Q ENST00000433211 13/18 147 130 17 134 134 0 strelka-varscan-mutect CTNNA3,missense_variant,p.Glu581Gln,ENST00000433211,NM_001127384.2,NM_013266.3; G ENST00000433211 Transcript missense_variant 1916/10675 1741/2688 581/895 E/Q Gaa/Caa 1 -1 CTNNA3 HGNC HGNC:2511 protein_coding YES CCDS7269.1 ENSP00000389714 Q9UI47 UPI000004A0E6 NM_001127384.2,NM_013266.3 tolerated(0.66) 13/18 hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF21,Gene3D:1.20.120.230,Pfam_domain:PF01044,Superfamily_domains:SSF47220 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 66280613 66280613 C G 1 0 0 0 0 1 0 0 0 3823 835 29 4 4 CTNNA3 10 66280613 Missense_Mutation SNP C C3N-00580_T 16669317 66280613 67516809 570 18705 LRRTM3 0 . GRCh38 10 66927036 66927036 + Missense_Mutation SNP T T G novel C3N-00580_T C3N-00580_N T T c.120T>G p.Cys40Trp p.C40W ENST00000361320 2/3 212 181 31 210 210 0 strelka-varscan-mutect LRRTM3,missense_variant,p.Cys40Trp,ENST00000361320,NM_178011.4;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2,NM_013266.3;CTNNA3,intron_variant,,ENST00000494580,; G ENST00000361320 Transcript missense_variant 698/4358 120/1746 40/581 C/W tgT/tgG 1 1 LRRTM3 HGNC HGNC:19410 protein_coding YES CCDS7270.1 ENSP00000355187 Q86VH5 UPI0000088C0F NM_178011.4 deleterious(0) 2/3 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54,SMART_domains:SM00013,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 66927036 66927036 T G 1 0 0 0 0 1 0 0 0 8947 1702 59 5 5 LRRTM3 10 66927036 Missense_Mutation SNP T C3N-00580_T 646423 66927036 66870386 571 18706 PALD1 0 . GRCh38 10 70532633 70532633 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.646G>T p.Ala216Ser p.A216S ENST00000263563 6/20 166 86 80 126 126 0 strelka-varscan-mutect PALD1,missense_variant,p.Ala216Ser,ENST00000263563,NM_014431.2; T ENST00000263563 Transcript missense_variant 914/4555 646/2571 216/856 A/S Gcc/Tcc 1 1 PALD1 HGNC HGNC:23530 protein_coding YES CCDS31215.1 ENSP00000263563 Q9ULE6 A0A024QZM5 UPI00001C1EDC NM_014431.2 deleterious(0) 6/20 hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF54,Pfam_domain:PF14566,SMART_domains:SM01301,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 70532633 70532633 G T 1 0 0 0 0 1 0 0 0 11486 1319 46 2 2 PALD1 10 70532633 Missense_Mutation SNP G C3N-00580_T 3605597 70532633 63264789 572 18707 TBATA 0 . GRCh38 10 70777241 70777241 + Missense_Mutation SNP C C A rs761828147 C3N-00580_T C3N-00580_N C C c.602G>T p.Arg201Leu p.R201L ENST00000299290 7/11 233 84 149 323 323 0 strelka-varscan-mutect TBATA,missense_variant,p.Arg202Leu,ENST00000456372,NM_001318241.1;TBATA,missense_variant,p.Arg201Leu,ENST00000299290,NM_001318243.1,NM_152710.2;TBATA,upstream_gene_variant,,ENST00000394982,; A ENST00000299290 Transcript missense_variant 992/1583 602/1056 201/351 R/L cGc/cTc rs761828147 1 -1 TBATA HGNC HGNC:23511 protein_coding YES CCDS7308.1 ENSP00000299290 Q96M53 UPI000013E57C NM_001318243.1,NM_152710.2 deleterious(0.02) 7/11 Low_complexity_(Seg):seg,hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF3,Pfam_domain:PF15256 MODERATE 1 SNV 1 1 PASS rs761828147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 70777241 70777241 C A 1 0 0 0 0 1 0 0 0 15996 768 27 1 1 TBATA 10 70777241 Missense_Mutation SNP C C3N-00580_T 244608 70777241 63020181 573 18708 CDH23 0 . GRCh38 10 71811515 71811515 + Missense_Mutation SNP C C A rs372434845 C3N-00580_T C3N-00580_N C C c.2483C>A p.Ala828Glu p.A828E ENST00000398788 17/23 443 159 284 349 349 0 strelka-varscan-mutect CDH23,missense_variant,p.Ala3073Glu,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Ala3068Glu,ENST00000622827,;CDH23,missense_variant,p.Ala828Glu,ENST00000398788,NM_001171933.1;CDH23,missense_variant,p.Ala828Glu,ENST00000619887,NM_001171934.1;PSAP,downstream_gene_variant,,ENST00000394936,NM_002778.2,NM_001042465.1,NM_001042466.1;PSAP,downstream_gene_variant,,ENST00000394934,;PSAP,downstream_gene_variant,,ENST00000610929,;CDH23,non_coding_transcript_exon_variant,,ENST00000475158,; A ENST00000398788 Transcript missense_variant 2800/4329 2483/3345 828/1114 A/E gCg/gAg rs372434845 1 1 CDH23 HGNC HGNC:13733 protein_coding YES CCDS53540.1 ENSP00000381768 Q9H251 UPI0000496839 NM_001171933.1 deleterious(0.03) 17/23 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs372434845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71811515 71811515 C A 1 0 0 0 0 1 0 0 0 2811 782 27 1 1 CDH23 10 71811515 Missense_Mutation SNP C C3N-00580_T 1034274 71811515 61985907 574 18709 KCNMA1 0 . GRCh38 10 77086498 77086498 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.1430C>T p.Ala477Val p.A477V ENST00000286628 11/28 559 212 347 517 517 0 strelka-varscan-mutect KCNMA1,missense_variant,p.Ala338Val,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,missense_variant,p.Ala477Val,ENST00000286627,NM_002247.3;KCNMA1,missense_variant,p.Ala477Val,ENST00000286628,NM_001161352.1;KCNMA1,missense_variant,p.Ala309Val,ENST00000354353,;KCNMA1,missense_variant,p.Ala309Val,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,missense_variant,p.Ala477Val,ENST00000372443,;KCNMA1,missense_variant,p.Ala477Val,ENST00000372440,NM_001014797.2;KCNMA1,missense_variant,p.Ala477Val,ENST00000404771,;KCNMA1,missense_variant,p.Ala451Val,ENST00000457953,;KCNMA1,missense_variant,p.Ala477Val,ENST00000626620,NM_001161353.1;KCNMA1,missense_variant,p.Ala412Val,ENST00000372437,;KCNMA1,missense_variant,p.Ala451Val,ENST00000372421,;KCNMA1,missense_variant,p.Ala414Val,ENST00000372408,;KCNMA1,missense_variant,p.Ala428Val,ENST00000372403,;KCNMA1,missense_variant,p.Ala309Val,ENST00000404857,NM_001271518.1;KCNMA1,missense_variant,p.Ala156Val,ENST00000434208,;KCNMA1,upstream_gene_variant,,ENST00000484507,; A ENST00000286628 Transcript missense_variant 1430/6100 1430/3711 477/1236 A/V gCa/gTa 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 tolerated(0.07) 11/28 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 77086498 77086498 G A 1 0 0 0 0 1 0 0 0 7990 1319 46 3 3 KCNMA1 10 77086498 Missense_Mutation SNP G C3N-00580_T 5274983 77086498 56710924 575 18710 BMPR1A 0 . GRCh38 10 86921679 86921679 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.1326T>C p.= p.R442R ENST00000372037 11/13 487 448 39 478 478 0 varscan-mutect BMPR1A,synonymous_variant,p.=,ENST00000372037,NM_004329.2;BMPR1A,synonymous_variant,p.=,ENST00000635816,;BMPR1A,synonymous_variant,p.=,ENST00000636056,; C ENST00000372037 Transcript synonymous_variant 1863/11255 1326/1599 442/532 R cgT/cgC 1 1 BMPR1A HGNC HGNC:1076 protein_coding YES CCDS7378.1 ENSP00000361107 P36894 UPI000006EB08 NM_004329.2 11/13 PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF50,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 86921679 86921679 T C 1 0 0 0 0 0 0 0 1 1624 1654 58 5 5 BMPR1A 10 86921679 Silent SNP T C3N-00580_T 9835181 86921679 46875743 576 18711 LCOR 0 . GRCh38 10 96983419 96983419 + Missense_Mutation SNP G G T rs752493286 C3N-00580_T C3N-00580_N G G c.2029G>T p.Val677Leu p.V677L ENST00000286067 1/1 306 115 191 331 331 0 strelka-varscan-mutect LCOR,missense_variant,p.Val959Leu,ENST00000421806,;LCOR,missense_variant,p.Val677Leu,ENST00000286067,NM_015652.2; T ENST00000286067 Transcript missense_variant 2136/4542 2029/3744 677/1247 V/L Gtg/Ttg rs752493286 1 1 LCOR HGNC HGNC:29503 protein_coding YES CCDS7452.1 ENSP00000286067 Q8N655 UPI000006F242 NM_015652.2 tolerated(0.29) 1/1 hmmpanther:PTHR14931,hmmpanther:PTHR14931:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs752493286 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 96983419 96983419 G T 1 0 0 0 0 1 0 0 0 8595 1377 48 2 2 LCOR 10 96983419 Missense_Mutation SNP G C3N-00580_T 10061740 96983419 36814003 577 18712 SORCS1 0 . GRCh38 10 106579223 106579223 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2674C>A p.Gln892Lys p.Q892K ENST00000612154 25/26 210 90 120 280 280 0 strelka-varscan-mutect SORCS1,missense_variant,p.Gln892Lys,ENST00000612154,;SORCS1,missense_variant,p.Gln892Lys,ENST00000344440,;SORCS1,missense_variant,p.Gln669Lys,ENST00000369698,;SORCS1,missense_variant,p.Gln149Lys,ENST00000452214,;SORCS1,intron_variant,,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,intron_variant,,ENST00000622431,;SORCS1,non_coding_transcript_exon_variant,,ENST00000473866,; T ENST00000612154 Transcript missense_variant 2845/6862 2674/2814 892/937 Q/K Cag/Aag 1 -1 SORCS1 HGNC HGNC:16697 protein_coding ENSP00000478065 A0A087WTQ9 UPI0004E4CC23 deleterious(0) 25/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 106579223 106579223 G T 1 0 0 0 0 1 0 0 0 15252 1357 47 2 2 SORCS1 10 106579223 Missense_Mutation SNP G C3N-00580_T 9595804 106579223 27218199 578 18713 ADRA2A 0 . GRCh38 10 111078495 111078495 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.499G>A p.Ala167Thr p.A167T ENST00000280155 1/1 139 64 75 177 177 0 strelka-varscan-mutect ADRA2A,missense_variant,p.Ala167Thr,ENST00000280155,NM_000681.3; A ENST00000280155 Transcript missense_variant 1333/3745 499/1398 167/465 A/T Gcc/Acc 1 1 ADRA2A HGNC HGNC:281 protein_coding YES CCDS7569.2 ENSP00000280155 P08913 UPI000018CE86 NM_000681.3 tolerated(0.07) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF24,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 111078495 111078495 G A 1 0 0 0 0 1 0 0 0 413 1203 42 3 3 ADRA2A 10 111078495 Missense_Mutation SNP G C3N-00580_T 4499272 111078495 22718927 579 18714 NRAP 0 . GRCh38 10 113597118 113597118 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.4399C>A p.His1467Asn p.H1467N ENST00000369358 37/42 203 106 97 261 261 0 strelka-varscan-mutect NRAP,missense_variant,p.His1467Asn,ENST00000359988,NM_198060.3;NRAP,missense_variant,p.His1440Asn,ENST00000369360,;NRAP,missense_variant,p.His1467Asn,ENST00000369358,NM_001261463.1;NRAP,missense_variant,p.His1432Asn,ENST00000360478,NM_006175.4; T ENST00000369358 Transcript missense_variant 4587/5534 4399/5196 1467/1731 H/N Cat/Aat COSM4494748 1 -1 NRAP HGNC HGNC:7988 protein_coding YES CCDS73199.1 ENSP00000358365 A0A0A0MRM2 UPI000264ECBD NM_001261463.1 deleterious(0.03) 37/42 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,SMART_domains:SM00227 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 113597118 113597118 G T 1 0 0 0 0 1 0 0 0 10694 1290 45 2 2 NRAP 10 113597118 Missense_Mutation SNP G C3N-00580_T 2518623 113597118 20200304 580 18715 GFRA1 0 . GRCh38 10 116064406 116064406 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1390A>T p.Thr464Ser p.T464S ENST00000355422 11/11 408 199 209 349 347 2 strelka-varscan-mutect GFRA1,missense_variant,p.Thr459Ser,ENST00000439649,NM_001145453.1;GFRA1,missense_variant,p.Thr459Ser,ENST00000369236,NM_145793.3;GFRA1,missense_variant,p.Thr464Ser,ENST00000355422,NM_005264.4;GFRA1,missense_variant,p.Thr464Ser,ENST00000369234,; A ENST00000355422 Transcript missense_variant 1941/2583 1390/1398 464/465 T/S Aca/Tca 1 -1 GFRA1 HGNC HGNC:4243 protein_coding YES CCDS44481.1 ENSP00000347591 P56159 UPI000012B3A8 NM_005264.4 tolerated_low_confidence(0.45) 11/11 PIRSF_domain:PIRSF038071 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 116064406 116064406 T A 1 0 0 0 0 1 0 0 0 6221 1725 60 4 4 GFRA1 10 116064406 Missense_Mutation SNP T C3N-00580_T 2467288 116064406 17733016 581 18716 FAM24A 0 . GRCh38 10 122911703 122911703 + Silent SNP G G T rs371905795 C3N-00580_T C3N-00580_N G G c.69G>T p.= p.A23A ENST00000368894 2/3 185 86 99 281 281 0 strelka-varscan-mutect FAM24A,synonymous_variant,p.=,ENST00000368894,NM_001029888.1; T ENST00000368894 Transcript synonymous_variant 190/596 69/318 23/105 A gcG/gcT rs371905795,COSM915725 1 1 FAM24A HGNC HGNC:23470 protein_coding YES CCDS31304.1 ENSP00000357889 A6NFZ4 UPI0000160DCE NM_001029888.1 2/3 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR35860,hmmpanther:PTHR35860:SF3 0,1 LOW 1 SNV 3 0,1 1 PASS rs371905795 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 122911703 122911703 G T 1 0 0 0 0 0 0 0 1 5426 1045 37 1 1 FAM24A 10 122911703 Silent SNP G C3N-00580_T 6847297 122911703 10885719 582 18717 LHPP 0 . GRCh38 10 124517272 124517272 + Splice_Site SNP G G T rs745797938 C3N-00580_T C3N-00580_N G G c.716+1G>T p.X239_splice ENST00000368842 69 19 50 97 96 1 strelka-varscan-mutect LHPP,splice_donor_variant,,ENST00000368842,NM_022126.3;LHPP,intron_variant,,ENST00000368839,NM_001167880.1;LHPP,non_coding_transcript_exon_variant,,ENST00000481452,; T ENST00000368842 Transcript splice_donor_variant -/1622 716/813 239/270 rs745797938 1 1 LHPP HGNC HGNC:30042 protein_coding YES CCDS7640.1 ENSP00000357835 Q9H008 UPI00001402EE NM_022126.3 6/6 HIGH 1 SNV 1 1 PASS rs745797938 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 124517272 124517272 G T 1 0 0 0 0 0 0 1 0 8678 1275 44 2 2 LHPP 10 124517272 Splice_Site SNP G C3N-00580_T 1605569 124517272 9280150 583 18718 PTPRE 0 . GRCh38 10 128073466 128073466 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1594G>T p.Glu532Ter p.E532* ENST00000254667 17/21 108 48 60 129 129 0 strelka-mutect PTPRE,stop_gained,p.Glu532Ter,ENST00000254667,NM_001323355.1,NM_001316676.1,NM_001323356.1,NM_006504.4;PTPRE,stop_gained,p.Glu474Ter,ENST00000306042,NM_001323357.1,NM_130435.3;PTPRE,3_prime_UTR_variant,,ENST00000479896,;PTPRE,downstream_gene_variant,,ENST00000463727,;PTPRE,downstream_gene_variant,,ENST00000495530,;PTPRE,downstream_gene_variant,,ENST00000492479,; T ENST00000254667 Transcript stop_gained 1873/5331 1594/2103 532/700 E/* Gag/Tag 1 1 PTPRE HGNC HGNC:9669 protein_coding YES CCDS7657.1 ENSP00000254667 P23469 UPI0000132991 NM_001323355.1,NM_001316676.1,NM_001323356.1,NM_006504.4 17/21 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF002006,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 128073466 128073466 G T 1 0 0 0 0 0 1 0 0 12954 956 33 2 2 PTPRE 10 128073466 Nonsense_Mutation SNP G C3N-00580_T 3556194 128073466 5723956 584 18719 MKI67 0 . GRCh38 10 128106862 128106863 + Frame_Shift_Ins INS - - AGTC novel C3N-00580_T C3N-00580_N - - c.4974_4977dupGACT p.Thr1660AspfsTer13 p.T1660Dfs*13 ENST00000368654 13/15 217 90 127 260 260 0 sindel-varindel-pindel MKI67,frameshift_variant,p.Thr1660AspfsTer13,ENST00000368654,NM_002417.4;MKI67,frameshift_variant,p.Thr1300AspfsTer13,ENST00000368653,NM_001145966.1;MKI67,downstream_gene_variant,,ENST00000484853,;MKI67,upstream_gene_variant,,ENST00000464771,; AGTC ENST00000368654 Transcript frameshift_variant 5353-5354/12678 4977-4978/9771 1659-1660/3256 -/DX -/GACT 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 13/15 Pfam_domain:PF08065,Low_complexity_(Seg):seg,SMART_domains:SM01295 HIGH 1 insertion 2 1 PASS . . 0 207 0 0 2 0 0 0 -20 0.9997202 1 1 1 0 AGTC 7 5 61 128106862 128106862 - AGTC 1 0 1 1 0 0 0 0 0 9566 1638 57 0 0 MKI67 10 128106862 Frame_Shift_Ins INS - C3N-00580_T 33396 128106862 5690560 585 18720 TCERG1L 0 . GRCh38 10 131134402 131134402 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1236A>T p.Gln412His p.Q412H ENST00000368642 8/12 207 109 98 315 315 0 strelka-varscan-mutect TCERG1L,missense_variant,p.Gln412His,ENST00000368642,NM_174937.3;TCERG1L,non_coding_transcript_exon_variant,,ENST00000483040,; A ENST00000368642 Transcript missense_variant 1322/2618 1236/1761 412/586 Q/H caA/caT 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 tolerated(0.26) 8/12 hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 131134402 131134402 T A 1 0 0 0 0 1 0 0 0 16093 1606 56 4 4 TCERG1L 10 131134402 Missense_Mutation SNP T C3N-00580_T 3027540 131134402 2663020 586 18721 TCERG1L 0 . GRCh38 10 131146635 131146635 + Silent SNP G G T rs776171772 C3N-00580_T C3N-00580_N G G c.1060C>A p.= p.R354R ENST00000368642 7/12 137 65 72 112 112 0 strelka-varscan-mutect TCERG1L,synonymous_variant,p.=,ENST00000368642,NM_174937.3;TCERG1L,non_coding_transcript_exon_variant,,ENST00000483040,; T ENST00000368642 Transcript synonymous_variant 1146/2618 1060/1761 354/586 R Cga/Aga rs776171772 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 7/12 Gene3D:2.20.70.10,PROSITE_profiles:PS50020,hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5,SMART_domains:SM00456,Superfamily_domains:SSF51045 LOW 1 SNV 1 1 PASS rs776171772 . 0 204 4 2 0 0 0 0 -20 0.9999985 1 1 1 0 T 2 4 61 131146635 131146635 G T 1 0 0 0 0 0 0 0 1 16093 1124 39 1 1 TCERG1L 10 131146635 Silent SNP G C3N-00580_T 12233 131146635 2650787 587 18722 KNDC1 0 . GRCh38 10 133186317 133186317 + Silent SNP G G A rs754784016 C3N-00580_T C3N-00580_N G G c.969G>A p.= p.P323P ENST00000304613 6/30 193 181 12 244 244 0 strelka-varscan-mutect KNDC1,synonymous_variant,p.=,ENST00000304613,NM_152643.6;KNDC1,synonymous_variant,p.=,ENST00000368571,; A ENST00000304613 Transcript synonymous_variant 990/6793 969/5250 323/1749 P ccG/ccA rs754784016,COSM1560871,COSM4175708 1 1 KNDC1 HGNC HGNC:29374 protein_coding YES CCDS7674.1 ENSP00000304437 Q76NI1 UPI00003529F7 NM_152643.6 6/30 hmmpanther:PTHR21560,hmmpanther:PTHR21560:SF0 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs754784016 . 0 207 0 2 0 0 0 0 -15.26895 0.9999995 1 1 1 0 A 2 1 61 133186317 133186317 G A 1 0 0 0 0 0 0 0 1 8304 1074 38 1 1 KNDC1 10 133186317 Silent SNP G C3N-00580_T 2039682 133186317 611105 588 18723 CALY 0 . GRCh38 10 133328881 133328881 + Nonsense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.109C>T p.Gln37Ter p.Q37* ENST00000252939 2/6 142 119 23 183 183 0 strelka-varscan-mutect CALY,stop_gained,p.Gln37Ter,ENST00000252939,NM_015722.3;CALY,stop_gained,p.Gln37Ter,ENST00000368558,;CALY,stop_gained,p.Gln37Ter,ENST00000368555,;ZNF511-PRAP1,intron_variant,,ENST00000368554,;CALY,upstream_gene_variant,,ENST00000467611,;CALY,upstream_gene_variant,,ENST00000467433,; A ENST00000252939 Transcript stop_gained 203/2271 109/654 37/217 Q/* Cag/Tag 1 -1 CALY HGNC HGNC:17938 protein_coding YES CCDS7678.1 ENSP00000252939 Q9NYX4 UPI0000001C76 NM_015722.3 2/6 Pfam_domain:PF06387,PIRSF_domain:PIRSF002383,hmmpanther:PTHR28546 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 133328881 133328881 G A 1 0 0 0 0 0 1 0 0 2286 1357 47 3 3 CALY 10 133328881 Nonsense_Mutation SNP G C3N-00580_T 142564 133328881 468541 589 18724 SYCE1 0 . GRCh38 10 133555651 133555651 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.776A>T p.Gln259Leu p.Q259L ENST00000343131 11/13 233 115 118 256 256 0 strelka-varscan-mutect SYCE1,missense_variant,p.Gln223Leu,ENST00000368517,NM_130784.2;SYCE1,missense_variant,p.Gln259Leu,ENST00000343131,NM_001143764.1;SYCE1,missense_variant,p.Gln259Leu,ENST00000303903,NM_001143763.1;CYP2E1,non_coding_transcript_exon_variant,,ENST00000368520,;SYCE1,non_coding_transcript_exon_variant,,ENST00000479535,; A ENST00000343131 Transcript missense_variant 881/1309 776/1056 259/351 Q/L cAg/cTg 1 -1 SYCE1 HGNC HGNC:28852 protein_coding YES CCDS44501.1 ENSP00000341282 Q8N0S2 UPI000013F901 NM_001143764.1 tolerated(0.19) 11/13 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21731:SF0,hmmpanther:PTHR21731 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 133555651 133555651 T A 1 0 0 0 0 1 0 0 0 15816 1580 55 4 4 SYCE1 10 133555651 Missense_Mutation SNP T C3N-00580_T 226770 133555651 241771 590 18725 AP2A2 0 . GRCh38 11 1010706 1010706 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.1136G>A p.= p.*379* ENST00000534328 9/9 161 118 43 165 165 0 strelka-varscan-mutect AP2A2,stop_retained_variant,p.=,ENST00000534328,;AP2A2,3_prime_UTR_variant,,ENST00000332231,NM_001242837.1;AP2A2,3_prime_UTR_variant,,ENST00000448903,NM_012305.3;MUC6,downstream_gene_variant,,ENST00000421673,NM_005961.2;MUC6,downstream_gene_variant,,ENST00000532016,;AP2A2,downstream_gene_variant,,ENST00000525891,;AP2A2,downstream_gene_variant,,ENST00000529438,;AP2A2,3_prime_UTR_variant,,ENST00000528815,;AP2A2,non_coding_transcript_exon_variant,,ENST00000531497,;AP2A2,downstream_gene_variant,,ENST00000526401,;AP2A2,downstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526376,;AP2A2,downstream_gene_variant,,ENST00000529427,; A ENST00000534328 Transcript stop_retained_variant 1278/1491 1136/1137 379/378 * tGa/tAa 1 1 AP2A2 HGNC HGNC:562 protein_coding ENSP00000436059 E9PR62 UPI0001F782A3 9/9 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 1010706 1010706 G A 1 0 0 0 0 0 0 0 1 856 1285 45 3 3 AP2A2 11 1010706 Silent SNP G C3N-00580_T 1010706 134075916 591 18726 MUC5AC 0 . GRCh38 11 1163968 1163968 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.766C>A p.Pro256Thr p.P256T ENST00000621226 7/49 311 230 81 418 417 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Pro256Thr,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 813/17448 766/16965 256/5654 P/T Ccg/Acg 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated(0.24) 7/49 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1163968 1163968 C A 1 0 0 0 0 1 0 0 0 9978 623 22 2 2 MUC5AC 11 1163968 Missense_Mutation SNP C C3N-00580_T 153262 1163968 133922654 592 18727 MUC5AC 0 . GRCh38 11 1186825 1186825 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.8680T>A p.Ser2894Thr p.S2894T ENST00000621226 31/49 355 256 99 357 356 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Ser2894Thr,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 8727/17448 8680/16965 2894/5654 S/T Tct/Act 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated_low_confidence(0.34) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1186825 1186825 T A 1 0 0 0 0 1 0 0 0 9978 1551 54 4 4 MUC5AC 11 1186825 Missense_Mutation SNP T C3N-00580_T 22857 1186825 133899797 593 18728 MUC5AC 0 . GRCh38 11 1187520 1187520 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.9375C>A p.Ser3125Arg p.S3125R ENST00000621226 31/49 260 236 24 291 291 0 strelka-varscan-mutect MUC5AC,missense_variant,p.Ser3125Arg,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 9422/17448 9375/16965 3125/5654 S/R agC/agA 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated(0.24) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs748427101 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1187520 1187520 C A 1 0 0 0 0 1 0 0 0 9978 738 26 2 2 MUC5AC 11 1187520 Missense_Mutation SNP C C3N-00580_T 695 1187520 133899102 594 18729 MUC5B 0 . GRCh38 11 1247217 1247217 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.10337C>A p.Pro3446Gln p.P3446Q ENST00000529681 31/49 669 473 196 850 849 1 strelka-varscan-mutect MUC5B,missense_variant,p.Pro3446Gln,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; A ENST00000529681 Transcript missense_variant 10395/17911 10337/17289 3446/5762 P/Q cCa/cAa 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.58) 31/49 MODERATE 1 SNV 5 1 PASS rs1242109246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 1247217 1247217 C A 1 0 0 0 0 1 0 0 0 9979 594 21 2 2 MUC5B 11 1247217 Missense_Mutation SNP C C3N-00580_T 59697 1247217 133839405 595 18730 OR51E2 0 . GRCh38 11 4682504 4682504 + Missense_Mutation SNP G G T rs765350267 C3N-00580_T C3N-00580_N G G c.208C>A p.Leu70Met p.L70M ENST00000396950 2/2 293 183 110 228 228 0 strelka-varscan-mutect OR51E2,missense_variant,p.Leu70Met,ENST00000396950,NM_030774.3;OR51E2,missense_variant,p.Leu70Met,ENST00000532598,; T ENST00000396950 Transcript missense_variant 448/2781 208/963 70/320 L/M Ctg/Atg rs765350267 1 -1 OR51E2 HGNC HGNC:15195 protein_coding YES CCDS7751.1 ENSP00000380153 Q9H255 A0A126GVK0 UPI000003B49B NM_030774.3 deleterious(0.04) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs765350267 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 4682504 4682504 G T 1 0 0 0 0 1 0 0 0 11169 991 35 2 2 OR51E2 11 4682504 Missense_Mutation SNP G C3N-00580_T 3435287 4682504 130404118 596 18731 OR52A5 0 . GRCh38 11 5132445 5132445 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.198C>A p.= p.A66A ENST00000307388 1/1 118 96 22 85 85 0 strelka-varscan-mutect OR52A5,synonymous_variant,p.=,ENST00000307388,NM_001005160.2; T ENST00000307388 Transcript synonymous_variant 198/951 198/951 66/316 A gcC/gcA COSM689110 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 176 15 18 0 0 0 0 -20 0.4753004 0 1 0 0 T 2 4 61 5132445 5132445 G T 1 0 0 0 0 0 0 0 1 11183 1335 47 2 2 OR52A5 11 5132445 Silent SNP G C3N-00580_T 449941 5132445 129954177 597 18732 OR52N4 0 . GRCh38 11 5755447 5755447 + Missense_Mutation SNP G G T rs565267255 C3N-00580_T C3N-00580_N G G c.707G>T p.Arg236Leu p.R236L ENST00000317254 1/1 363 234 129 373 373 0 strelka-varscan-mutect OR52N4,missense_variant,p.Arg236Leu,ENST00000317254,NM_001005175.3;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000317254 Transcript missense_variant 755/1037 707/966 236/321 R/L cGg/cTg rs565267255 1 1 OR52N4 HGNC HGNC:15230 protein_coding YES CCDS44528.1 ENSP00000323224 Q8NGI2 UPI00001AF18B NM_001005175.3 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF74,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs565267255 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 5755447 5755447 G T 1 0 0 0 0 1 0 0 0 11202 1116 39 1 1 OR52N4 11 5755447 Missense_Mutation SNP G C3N-00580_T 623002 5755447 129331175 598 18733 OR52N1 0 . GRCh38 11 5788750 5788750 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.67G>T p.Glu23Ter p.E23* ENST00000317078 1/1 118 80 38 138 138 0 strelka-varscan-mutect OR52N1,stop_gained,p.Glu23Ter,ENST00000317078,NM_001001913.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000317078 Transcript stop_gained 67/963 67/963 23/320 E/* Gaa/Taa 1 -1 OR52N1 HGNC HGNC:14853 protein_coding YES CCDS31398.1 ENSP00000322823 Q8NH53 UPI0000041BDD NM_001001913.1 1/1 hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF145,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 5788750 5788750 C A 1 0 0 0 0 0 1 0 0 11200 864 30 2 2 OR52N1 11 5788750 Nonsense_Mutation SNP C C3N-00580_T 33303 5788750 129297872 599 18734 APBB1 0 . GRCh38 11 6403151 6403151 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1098G>T p.= p.G366G ENST00000609360 6/15 72 54 18 83 82 1 strelka-varscan-mutect APBB1,synonymous_variant,p.=,ENST00000389906,;APBB1,synonymous_variant,p.=,ENST00000609360,NM_001164.4;APBB1,synonymous_variant,p.=,ENST00000299402,;APBB1,synonymous_variant,p.=,ENST00000311051,NM_145689.2;APBB1,synonymous_variant,p.=,ENST00000610474,;APBB1,synonymous_variant,p.=,ENST00000608394,NM_001257321.2;APBB1,synonymous_variant,p.=,ENST00000618005,;APBB1,synonymous_variant,p.=,ENST00000608704,NM_001257320.2;APBB1,synonymous_variant,p.=,ENST00000608645,NM_001257326.2;APBB1,synonymous_variant,p.=,ENST00000608655,NM_001257319.2;APBB1,synonymous_variant,p.=,ENST00000621678,;APBB1,synonymous_variant,p.=,ENST00000530885,NM_001257323.2;APBB1,synonymous_variant,p.=,ENST00000609331,NM_001257325.2;APBB1,synonymous_variant,p.=,ENST00000529890,;APBB1,intron_variant,,ENST00000529519,;APBB1,downstream_gene_variant,,ENST00000532020,;APBB1,synonymous_variant,p.=,ENST00000608435,;APBB1,non_coding_transcript_exon_variant,,ENST00000533407,;APBB1,non_coding_transcript_exon_variant,,ENST00000526925,;APBB1,non_coding_transcript_exon_variant,,ENST00000534188,;APBB1,non_coding_transcript_exon_variant,,ENST00000533139,;APBB1,upstream_gene_variant,,ENST00000524626,;APBB1,upstream_gene_variant,,ENST00000529778,; A ENST00000609360 Transcript synonymous_variant 1198/2642 1098/2133 366/710 G ggG/ggT 1 -1 APBB1 HGNC HGNC:581 protein_coding YES CCDS66018.1 ENSP00000477213 O00213 UPI000012510B NM_001164.4 6/15 Gene3D:2.30.29.30,hmmpanther:PTHR14058,hmmpanther:PTHR14058:SF5,SMART_domains:SM00462,Superfamily_domains:SSF50729 LOW 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 6403151 6403151 C A 1 0 0 0 0 0 0 0 1 879 842 30 2 2 APBB1 11 6403151 Silent SNP C C3N-00580_T 614401 6403151 128683471 600 18735 DCHS1 0 . GRCh38 11 6641145 6641145 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.469G>T p.Ala157Ser p.A157S ENST00000299441 2/21 415 327 88 352 352 0 strelka-varscan-mutect DCHS1,missense_variant,p.Ala157Ser,ENST00000299441,NM_003737.3; A ENST00000299441 Transcript missense_variant 881/10765 469/9897 157/3298 A/S Gct/Tct 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 tolerated(0.22) 2/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 6641145 6641145 C A 1 0 0 0 0 1 0 0 0 4090 797 28 2 2 DCHS1 11 6641145 Missense_Mutation SNP C C3N-00580_T 237994 6641145 128445477 601 18736 OR10A5 0 . GRCh38 11 6845830 6845831 + Frame_Shift_Del DEL AC AC - novel C3N-00580_T C3N-00580_N AC AC c.148_149delAC p.Thr50ProfsTer3 p.T50Pfs*3 ENST00000299454 1/1 497 382 115 631 631 0 sindel-varindel OR10A5,frameshift_variant,p.Thr50ProfsTer3,ENST00000299454,NM_178168.1;RP11-413N10.3,intron_variant,,ENST00000637205,;RP11-560B16.5,upstream_gene_variant,,ENST00000530632,; - ENST00000299454 Transcript frameshift_variant 179-180/1054 148-149/954 50/317 T/X ACc/c 1 1 OR10A5 HGNC HGNC:15131 protein_coding YES CCDS7773.1 ENSP00000299454 Q9H207 A0A126GWR0 UPI000004C155 NM_178168.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 6845830 6845830 AC - 1 0 1 0 1 0 0 0 0 10969 391 14 0 0 OR10A5 11 6845830 Frame_Shift_Del DEL AC C3N-00580_T 204685 6845830 128240792 602 18737 OR10A5 0 . GRCh38 11 6846463 6846463 + Missense_Mutation SNP T T G C3N-00580_T C3N-00580_N T T c.781T>G p.Phe261Val p.F261V ENST00000299454 1/1 182 172 10 196 196 0 strelka-varscan-mutect OR10A5,missense_variant,p.Phe261Val,ENST00000299454,NM_178168.1;RP11-413N10.3,intron_variant,,ENST00000637205,;RP11-560B16.5,upstream_gene_variant,,ENST00000530632,; G ENST00000299454 Transcript missense_variant 812/1054 781/954 261/317 F/V Ttc/Gtc COSM1259969 1 1 OR10A5 HGNC HGNC:15131 protein_coding YES CCDS7773.1 ENSP00000299454 Q9H207 A0A126GWR0 UPI000004C155 NM_178168.1 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 6846463 6846463 T G 1 0 0 0 0 1 0 0 0 10969 1609 56 5 5 OR10A5 11 6846463 Missense_Mutation SNP T C3N-00580_T 633 6846463 128240159 603 18738 OR10A3 0 . GRCh38 11 7938973 7938973 + Missense_Mutation SNP G G T rs200724726 C3N-00580_T C3N-00580_N G G c.548C>A p.Pro183Gln p.P183Q ENST00000360759 1/1 167 150 17 180 180 0 strelka-varscan-mutect OR10A3,missense_variant,p.Pro183Gln,ENST00000360759,NM_001003745.1; T ENST00000360759 Transcript missense_variant 622/1061 548/945 183/314 P/Q cCg/cAg rs200724726 1 -1 OR10A3 HGNC HGNC:8162 protein_coding YES CCDS31421.1 ENSP00000353988 P58181 A0A126GVZ2 UPI00000015AD NM_001003745.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF30,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs200724726 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 7938973 7938973 G T 1 0 0 0 0 1 0 0 0 10967 1116 39 1 1 OR10A3 11 7938973 Missense_Mutation SNP G C3N-00580_T 1092510 7938973 127147649 604 18739 TMEM41B 0 . GRCh38 11 9286514 9286514 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.647A>G p.Asn216Ser p.N216S ENST00000528080 6/7 91 64 27 115 115 0 strelka-varscan-mutect TMEM41B,missense_variant,p.Asn216Ser,ENST00000528080,NM_015012.3;TMEM41B,missense_variant,p.Asn216Ser,ENST00000611268,;TMEM41B,intron_variant,,ENST00000527813,;TMEM41B,missense_variant,p.Asn216Ser,ENST00000299596,;TMEM41B,3_prime_UTR_variant,,ENST00000524543,;TMEM41B,non_coding_transcript_exon_variant,,ENST00000533867,; C ENST00000528080 Transcript missense_variant 986/3968 647/876 216/291 N/S aAt/aGt 1 -1 TMEM41B HGNC HGNC:28948 protein_coding YES CCDS31424.1 ENSP00000433126 Q5BJD5 UPI00001C1EF6 NM_015012.3 deleterious(0) 6/7 Pfam_domain:PF09335,hmmpanther:PTHR12677,hmmpanther:PTHR12677:SF15,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 9286514 9286514 T C 1 0 0 0 0 1 0 0 0 16642 1493 52 5 5 TMEM41B 11 9286514 Missense_Mutation SNP T C3N-00580_T 1347541 9286514 125800108 605 18740 CALCB 0 . GRCh38 11 15075067 15075067 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.93C>A p.= p.A31A ENST00000533448 3/5 252 201 51 275 275 0 strelka-varscan-mutect CALCB,synonymous_variant,p.=,ENST00000523376,;CALCB,synonymous_variant,p.=,ENST00000533448,;CALCB,synonymous_variant,p.=,ENST00000324229,NM_000728.3; A ENST00000533448 Transcript synonymous_variant 204/2097 93/384 31/127 A gcC/gcA 1 1 CALCB HGNC HGNC:1438 protein_coding YES CCDS7820.1 ENSP00000433490 P10092 UPI0000126E36 3/5 Pfam_domain:PF00214,hmmpanther:PTHR10505,hmmpanther:PTHR10505:SF12 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 15075067 15075067 C A 1 0 0 0 0 0 0 0 1 2266 610 22 2 2 CALCB 11 15075067 Silent SNP C C3N-00580_T 5788553 15075067 120011555 606 18741 INSC 0 . GRCh38 11 15221624 15221624 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1108G>T p.Glu370Ter p.E370* ENST00000379554 8/13 133 88 45 142 142 0 strelka-varscan-mutect INSC,stop_gained,p.Glu370Ter,ENST00000379554,NM_001031853.4;INSC,stop_gained,p.Glu357Ter,ENST00000424273,NM_001278314.1;INSC,stop_gained,p.Glu323Ter,ENST00000379556,NM_001042536.2;INSC,stop_gained,p.Glu323Ter,ENST00000528567,NM_001278315.1;INSC,stop_gained,p.Glu323Ter,ENST00000530161,NM_001278313.1;INSC,stop_gained,p.Glu281Ter,ENST00000525218,NM_001278316.1;INSC,non_coding_transcript_exon_variant,,ENST00000447214,; T ENST00000379554 Transcript stop_gained 1154/2954 1108/1740 370/579 E/* Gag/Tag 1 1 INSC HGNC HGNC:33116 protein_coding YES CCDS41621.1 ENSP00000368872 Q1MX18 UPI0000D63F1D NM_001031853.4 8/13 hmmpanther:PTHR21386:SF0,hmmpanther:PTHR21386,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 15221624 15221624 G T 1 0 0 0 0 0 1 0 0 7666 1175 41 2 2 INSC 11 15221624 Nonsense_Mutation SNP G C3N-00580_T 146557 15221624 119864998 607 18742 USH1C 0 . GRCh38 11 17505933 17505933 + Missense_Mutation SNP G G T rs749424126 C3N-00580_T C3N-00580_N G G c.2030C>A p.Pro677Gln p.P677Q ENST00000005226 19/27 490 346 144 560 560 0 strelka-varscan-mutect USH1C,missense_variant,p.Pro677Gln,ENST00000005226,NM_153676.3;USH1C,intron_variant,,ENST00000527720,;USH1C,intron_variant,,ENST00000318024,NM_005709.3;USH1C,intron_variant,,ENST00000527020,NM_001297764.1;USH1C,intron_variant,,ENST00000529563,;USH1C,intron_variant,,ENST00000526313,;USH1C,upstream_gene_variant,,ENST00000534556,; T ENST00000005226 Transcript missense_variant 2030/2700 2030/2700 677/899 P/Q cCa/cAa rs749424126 1 -1 USH1C HGNC HGNC:12597 protein_coding YES CCDS7825.1 ENSP00000005226 Q9Y6N9 UPI00001D965A NM_153676.3 deleterious_low_confidence(0) 19/27 hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF36 MODERATE 1 SNV 5 1 PASS rs749424126 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 17505933 17505933 G T 1 0 0 0 0 1 0 0 0 17568 1348 47 2 2 USH1C 11 17505933 Missense_Mutation SNP G C3N-00580_T 2284309 17505933 117580689 608 18743 OTOG 0 . GRCh38 11 17633769 17633769 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.7198C>G p.Leu2400Val p.L2400V ENST00000399391 42/55 169 120 49 184 184 0 strelka-varscan-mutect OTOG,missense_variant,p.Leu2388Val,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Leu2400Val,ENST00000399391,NM_001277269.1;OTOG,missense_variant,p.Leu1406Val,ENST00000342528,; G ENST00000399391 Transcript missense_variant 7198/8778 7198/8778 2400/2925 L/V Ctg/Gtg 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 tolerated(0.13) 42/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 17633769 17633769 C G 1 0 0 0 0 1 0 0 0 11370 912 32 4 4 OTOG 11 17633769 Missense_Mutation SNP C C3N-00580_T 127836 17633769 117452853 609 18744 HPS5 0 . GRCh38 11 18283795 18283795 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3058G>T p.Gly1020Cys p.G1020C ENST00000349215 21/23 295 215 80 351 351 0 strelka-varscan-mutect HPS5,missense_variant,p.Gly906Cys,ENST00000396253,NM_007216.3;HPS5,missense_variant,p.Gly1020Cys,ENST00000349215,NM_181507.1;HPS5,missense_variant,p.Gly906Cys,ENST00000438420,NM_181508.1;HPS5,missense_variant,p.Gly127Cys,ENST00000537258,;HPS5,downstream_gene_variant,,ENST00000544218,;HPS5,splice_region_variant,,ENST00000352460,;HPS5,downstream_gene_variant,,ENST00000543728,;HPS5,non_coding_transcript_exon_variant,,ENST00000545561,; A ENST00000349215 Transcript missense_variant,splice_region_variant 3336/4491 3058/3390 1020/1129 G/C Ggt/Tgt 1 -1 HPS5 HGNC HGNC:17022 protein_coding YES CCDS7836.1 ENSP00000265967 Q9UPZ3 UPI000000D7E9 NM_181507.1 deleterious(0) 21/23 hmmpanther:PTHR23287 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 18283795 18283795 C A 1 0 0 0 0 1 0 0 0 7237 608 21 2 2 HPS5 11 18283795 Missense_Mutation SNP C C3N-00580_T 650026 18283795 116802827 610 18745 MRGPRX2 0 . GRCh38 11 19055677 19055677 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.726G>T p.Gln242His p.Q242H ENST00000329773 2/2 238 215 23 199 198 1 strelka-varscan-mutect MRGPRX2,missense_variant,p.Gln242His,ENST00000329773,NM_001303615.1,NM_054030.3; A ENST00000329773 Transcript missense_variant 814/2036 726/993 242/330 Q/H caG/caT 1 -1 MRGPRX2 HGNC HGNC:17983 protein_coding YES CCDS7847.1 ENSP00000333800 Q96LB1 UPI0000038C81 NM_001303615.1,NM_054030.3 tolerated(0.61) 2/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF35,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 19055677 19055677 C A 1 0 0 0 0 1 0 0 0 9734 564 20 2 2 MRGPRX2 11 19055677 Missense_Mutation SNP C C3N-00580_T 771882 19055677 116030945 611 18746 DBX1 0 . GRCh38 11 20156484 20156484 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.762C>A p.= p.T254T ENST00000524983 4/4 521 416 105 483 483 0 strelka-varscan-mutect DBX1,synonymous_variant,p.=,ENST00000524983,NM_001029865.2; T ENST00000524983 Transcript synonymous_variant 1051/1380 762/1032 254/343 T acC/acA 1 -1 DBX1 HGNC HGNC:33185 protein_coding YES ENSP00000436881 A6NMT0 UPI000013C8B1 NM_001029865.2 4/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF6 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 20156484 20156484 G T 1 0 0 0 0 0 0 0 1 4059 1219 43 2 2 DBX1 11 20156484 Silent SNP G C3N-00580_T 1100807 20156484 114930138 612 18747 SLC6A5 0 . GRCh38 11 20628074 20628074 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.1490A>C p.Asn497Thr p.N497T ENST00000525748 9/16 546 491 55 542 541 1 strelka-varscan-mutect SLC6A5,missense_variant,p.Asn497Thr,ENST00000525748,NM_004211.3;SLC6A5,upstream_gene_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; C ENST00000525748 Transcript missense_variant 1763/7084 1490/2394 497/797 N/T aAc/aCc 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 deleterious(0) 9/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 20628074 20628074 A C 1 0 0 0 0 1 0 0 0 14970 43 2 5 5 SLC6A5 11 20628074 Missense_Mutation SNP A C3N-00580_T 471590 20628074 114458548 613 18748 NELL1 0 . GRCh38 11 20928455 20928455 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1057G>T p.Gly353Cys p.G353C ENST00000298925 10/21 452 349 103 503 502 1 strelka-varscan-mutect NELL1,missense_variant,p.Gly353Cys,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Gly268Cys,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Gly325Cys,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Gly325Cys,ENST00000532434,NM_201551.2;NELL1,downstream_gene_variant,,ENST00000528495,; T ENST00000298925 Transcript missense_variant 1210/3329 1057/2517 353/838 G/C Ggc/Tgc 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 deleterious(0) 10/21 Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20928455 20928455 G T 1 0 0 0 0 1 0 0 0 10364 1348 47 2 2 NELL1 11 20928455 Missense_Mutation SNP G C3N-00580_T 300381 20928455 114158167 614 18749 NELL1 0 . GRCh38 11 21370894 21370894 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1675G>T p.Ala559Ser p.A559S ENST00000298925 16/21 208 135 73 195 194 1 strelka-varscan-mutect NELL1,missense_variant,p.Ala559Ser,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Ala474Ser,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Ala531Ser,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Ala531Ser,ENST00000532434,NM_201551.2;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,;NELL1,non_coding_transcript_exon_variant,,ENST00000534263,; T ENST00000298925 Transcript missense_variant 1828/3329 1675/2517 559/838 A/S Gct/Tct 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 tolerated(0.45) 16/21 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 2 1 PASS rs986560571 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 21370894 21370894 G T 1 0 0 0 0 1 0 0 0 10364 1203 42 2 2 NELL1 11 21370894 Missense_Mutation SNP G C3N-00580_T 442439 21370894 113715728 615 18750 FANCF 0 . GRCh38 11 22625445 22625445 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.366G>A p.= p.R122R ENST00000327470 1/1 483 326 157 526 526 0 strelka-varscan-mutect FANCF,synonymous_variant,p.=,ENST00000327470,NM_022725.3;GAS2,upstream_gene_variant,,ENST00000528582,; T ENST00000327470 Transcript synonymous_variant 1343/4269 366/1125 122/374 R cgG/cgA 1 -1 FANCF HGNC HGNC:3587 protein_coding YES CCDS7857.1 ENSP00000330875 Q9NPI8 A3KME0 UPI000012A4CA NM_022725.3 1/1 hmmpanther:PTHR14449:SF2,hmmpanther:PTHR14449,Pfam_domain:PF11107,PD321645 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 22625445 22625445 C T 1 0 0 0 0 0 0 0 1 5527 610 22 3 3 FANCF 11 22625445 Silent SNP C C3N-00580_T 1254551 22625445 112461177 616 18751 SLC5A12 0 . GRCh38 11 26678799 26678799 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.1492A>G p.Thr498Ala p.T498A ENST00000396005 13/15 143 129 14 102 102 0 strelka-varscan-mutect SLC5A12,missense_variant,p.Thr498Ala,ENST00000396005,NM_178498.3;SLC5A12,3_prime_UTR_variant,,ENST00000527405,; C ENST00000396005 Transcript missense_variant 1802/6250 1492/1857 498/618 T/A Acc/Gcc 1 -1 SLC5A12 HGNC HGNC:28750 protein_coding YES CCDS7860.2 ENSP00000379326 Q1EHB4 UPI000003ED2C NM_178498.3 tolerated(0.09) 13/15 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF152 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 26678799 26678799 T C 1 0 0 0 0 1 0 0 0 14947 1638 57 5 5 SLC5A12 11 26678799 Missense_Mutation SNP T C3N-00580_T 4053354 26678799 108407823 617 18752 DCDC1 0 . GRCh38 11 30878593 30878593 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.2664C>A p.= p.L888L ENST00000406071 19/20 123 104 19 123 123 0 strelka-varscan-mutect DCDC1,synonymous_variant,p.=,ENST00000597505,;DCDC1,synonymous_variant,p.=,ENST00000406071,NM_020869.3;DCDC1,synonymous_variant,p.=,ENST00000444572,;DCDC1,3_prime_UTR_variant,,ENST00000303697,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,; T ENST00000406071 Transcript synonymous_variant 2980/4758 2664/2673 888/890 L ctC/ctA 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 19/20 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 30878593 30878593 G T 1 0 0 0 0 0 0 0 1 4086 1161 41 2 2 DCDC1 11 30878593 Silent SNP G C3N-00580_T 4199794 30878593 104208029 618 18753 ELP4 0 . GRCh38 11 31520055 31520055 + Splice_Site SNP G G T novel C3N-00580_T C3N-00580_N G G c.224-1G>T p.X75_splice ENST00000395934 123 104 19 158 157 1 strelka-varscan-mutect ELP4,splice_acceptor_variant,,ENST00000395934,NM_001288726.1;ELP4,splice_acceptor_variant,,ENST00000350638,NM_019040.4;ELP4,splice_acceptor_variant,,ENST00000379163,NM_001288725.1;ELP4,splice_acceptor_variant,,ENST00000474374,; T ENST00000395934 Transcript splice_acceptor_variant -/1961 224/1608 75/535 1 1 ELP4 HGNC HGNC:1171 protein_coding YES CCDS73272.1 ENSP00000379267 G5E9D4 UPI000013FA14 NM_001288726.1 1/11 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 31520055 31520055 G T 1 0 0 0 0 0 0 1 0 4916 1014 35 2 2 ELP4 11 31520055 Splice_Site SNP G C3N-00580_T 641462 31520055 103566567 619 18754 PAMR1 0 . GRCh38 11 35435955 35435955 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1332G>A p.= p.R444R ENST00000622144 10/12 421 267 154 238 238 0 strelka-varscan-mutect PAMR1,synonymous_variant,p.=,ENST00000619888,NM_001001991.2;PAMR1,synonymous_variant,p.=,ENST00000621476,NM_001282675.1;PAMR1,synonymous_variant,p.=,ENST00000615849,NM_001282676.1;PAMR1,synonymous_variant,p.=,ENST00000622144,NM_015430.3;PAMR1,synonymous_variant,p.=,ENST00000611014,;PAMR1,synonymous_variant,p.=,ENST00000527605,;PAMR1,non_coding_transcript_exon_variant,,ENST00000531219,; T ENST00000622144 Transcript synonymous_variant 1370/2785 1332/2214 444/737 R agG/agA 1 -1 PAMR1 HGNC HGNC:24554 protein_coding YES CCDS7898.1 ENSP00000482899 Q6UXH9 UPI000013DB70 NM_015430.3 10/12 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR24254,hmmpanther:PTHR24254:SF9,SMART_domains:SM00032,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 35435955 35435955 C T 1 0 0 0 0 0 0 0 1 11494 854 30 3 3 PAMR1 11 35435955 Silent SNP C C3N-00580_T 3915900 35435955 99650667 620 18755 RAG1 0 . GRCh38 11 36573960 36573960 + Missense_Mutation SNP G G T rs764179803 C3N-00580_T C3N-00580_N G G c.656G>T p.Arg219Leu p.R219L ENST00000299440 2/2 461 352 109 262 261 1 strelka-varscan-mutect RAG1,missense_variant,p.Arg219Leu,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Arg219Leu,ENST00000534663,; T ENST00000299440 Transcript missense_variant 768/6564 656/3132 219/1043 R/L cGg/cTg rs764179803 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 tolerated_low_confidence(0.16) 2/2 Pfam_domain:PF12560,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 MODERATE 1 SNV 1 1 PASS rs764179803 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 36573960 36573960 G T 1 0 0 0 0 1 0 0 0 13164 1116 39 1 1 RAG1 11 36573960 Missense_Mutation SNP G C3N-00580_T 1138005 36573960 98512662 621 18756 CREB3L1 0 . GRCh38 11 46320397 46320397 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1392G>T p.= p.R464R ENST00000621158 11/12 455 258 197 372 372 0 strelka-varscan-mutect CREB3L1,synonymous_variant,p.=,ENST00000621158,NM_052854.3;CREB3L1,downstream_gene_variant,,ENST00000534616,;CREB3L1,non_coding_transcript_exon_variant,,ENST00000616094,; T ENST00000621158 Transcript synonymous_variant 1843/2687 1392/1560 464/519 R cgG/cgT 1 1 CREB3L1 HGNC HGNC:18856 protein_coding YES CCDS53620.1 ENSP00000481956 Q96BA8 UPI000004ABFF NM_052854.3 11/12 hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 46320397 46320397 G T 1 0 0 0 0 0 0 0 1 3656 1219 43 2 2 CREB3L1 11 46320397 Silent SNP G C3N-00580_T 9746437 46320397 88766225 622 18757 CKAP5 0 . GRCh38 11 46809489 46809489 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.775G>T p.Gly259Cys p.G259C ENST00000529230 7/44 195 128 67 157 157 0 strelka-varscan-mutect CKAP5,missense_variant,p.Gly259Cys,ENST00000529230,NM_001008938.3;CKAP5,missense_variant,p.Gly259Cys,ENST00000312055,NM_014756.3;CKAP5,missense_variant,p.Gly259Cys,ENST00000354558,; A ENST00000529230 Transcript missense_variant 822/7121 775/6099 259/2032 G/C Ggt/Tgt 1 -1 CKAP5 HGNC HGNC:28959 protein_coding YES CCDS31477.1 ENSP00000432768 Q14008 UPI000013F21E NM_001008938.3 deleterious(0.02) 7/44 Low_complexity_(Seg):seg,hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 46809489 46809489 C A 1 0 0 0 0 1 0 0 0 3208 594 21 2 2 CKAP5 11 46809489 Missense_Mutation SNP C C3N-00580_T 489092 46809489 88277133 623 18758 OR4C3 0 . GRCh38 11 48325776 48325776 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.836G>A p.Cys279Tyr p.C279Y ENST00000319856 1/1 90 65 25 104 103 1 strelka-mutect OR4C3,missense_variant,p.Cys279Tyr,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.Cys142Tyr,ENST00000611380,; A ENST00000319856 Transcript missense_variant 857/1036 836/990 279/329 C/Y tGt/tAt 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1325223004 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 48325776 48325776 G A 1 0 0 0 0 1 0 0 0 11126 1377 48 3 3 OR4C3 11 48325776 Missense_Mutation SNP G C3N-00580_T 1516287 48325776 86760846 624 18759 OR4C3 0 . GRCh38 11 48325847 48325847 + Missense_Mutation SNP C C G rs774687598 C3N-00580_T C3N-00580_N C C c.907C>G p.Leu303Val p.L303V ENST00000319856 1/1 39 27 12 36 36 0 strelka-varscan-mutect OR4C3,missense_variant,p.Leu303Val,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.Leu166Val,ENST00000611380,; G ENST00000319856 Transcript missense_variant 928/1036 907/990 303/329 L/V Ctg/Gtg rs774687598 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 tolerated(0.38) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs774687598 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 48325847 48325847 C G 1 0 0 0 0 1 0 0 0 11126 912 32 4 4 OR4C3 11 48325847 Missense_Mutation SNP C C3N-00580_T 71 48325847 86760775 625 18760 OR4A47 0 . GRCh38 11 48489508 48489508 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.716G>T p.Ser239Ile p.S239I ENST00000446524 1/1 451 310 141 316 316 0 strelka-varscan-mutect OR4A47,missense_variant,p.Ser239Ile,ENST00000446524,NM_001005512.2;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,; T ENST00000446524 Transcript missense_variant 792/1064 716/930 239/309 S/I aGt/aTt COSM1719789 1 1 OR4A47 HGNC HGNC:31266 protein_coding YES CCDS31490.1 ENSP00000412752 Q6IF82 UPI00001971E5 NM_001005512.2 tolerated_low_confidence(0.12) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF87,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 48489508 48489508 G T 1 0 0 0 0 1 0 0 0 11119 1029 36 2 2 OR4A47 11 48489508 Missense_Mutation SNP G C3N-00580_T 163661 48489508 86597114 626 18761 TRIM64C 0 . GRCh38 11 49058167 49058167 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.418C>G p.Leu140Val p.L140V ENST00000617704 2/6 85 63 22 123 123 0 strelka-varscan-mutect TRIM64C,missense_variant,p.Leu140Val,ENST00000617704,NM_001206631.1;TRIM64C,missense_variant,p.Leu140Val,ENST00000530230,; C ENST00000617704 Transcript missense_variant 418/1353 418/1353 140/450 L/V Ctt/Gtt 1 -1 TRIM64C HGNC HGNC:37148 protein_coding YES CCDS73287.1 ENSP00000481815 A0A087WYH8 UPI00006C1130 NM_001206631.1 tolerated(0.05) 2/6 hmmpanther:PTHR24103:SF354,hmmpanther:PTHR24103 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 49058167 49058167 G C 1 0 0 0 0 1 0 0 0 17033 1043 36 4 4 TRIM64C 11 49058167 Missense_Mutation SNP G C3N-00580_T 568659 49058167 86028455 627 18762 OR4C13 0 . GRCh38 11 49953214 49953214 + Silent SNP C C A C3N-00580_T C3N-00580_N C C c.792C>A p.= p.P264P ENST00000555099 1/1 177 106 71 128 128 0 strelka-varscan-mutect OR4C13,synonymous_variant,p.=,ENST00000555099,NM_001001955.2; A ENST00000555099 Transcript synonymous_variant 824/1029 792/930 264/309 P ccC/ccA COSM397419 1 1 OR4C13 HGNC HGNC:15169 protein_coding YES CCDS31495.1 ENSP00000452277 Q8NGP0 UPI000013F7D1 NM_001001955.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF60,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 49953214 49953214 C A 1 0 0 0 0 0 0 0 1 11124 581 21 2 2 OR4C13 11 49953214 Silent SNP C C3N-00580_T 895047 49953214 85133408 628 18763 OR5D16 0 . GRCh38 11 55839209 55839209 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.458G>T p.Trp153Leu p.W153L ENST00000378396 1/1 203 119 84 176 175 1 strelka-varscan-mutect OR5D16,missense_variant,p.Trp153Leu,ENST00000378396,NM_001005496.1; T ENST00000378396 Transcript missense_variant 458/987 458/987 153/328 W/L tGg/tTg 1 1 OR5D16 HGNC HGNC:15283 protein_coding YES CCDS31512.1 ENSP00000367649 Q8NGK9 UPI0000046198 NM_001005496.1 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 55839209 55839209 G T 1 0 0 0 0 1 0 0 0 11226 1357 47 2 2 OR5D16 11 55839209 Missense_Mutation SNP G C3N-00580_T 5885995 55839209 79247413 629 18764 OR5W2 0 . GRCh38 11 55913926 55913926 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.657T>C p.= p.C219C ENST00000344514 1/1 304 198 106 213 213 0 strelka-varscan-mutect OR5W2,synonymous_variant,p.=,ENST00000344514,NM_001001960.1; G ENST00000344514 Transcript synonymous_variant 657/933 657/933 219/310 C tgT/tgC 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 55913926 55913926 A G 1 0 0 0 0 0 0 0 1 11253 41 2 5 5 OR5W2 11 55913926 Silent SNP A C3N-00580_T 74717 55913926 79172696 630 18765 OR5F1 0 . GRCh38 11 55994213 55994213 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.413G>T p.Arg138Met p.R138M ENST00000278409 1/1 198 119 79 200 200 0 strelka-varscan-mutect OR5F1,missense_variant,p.Arg138Met,ENST00000278409,NM_003697.1; A ENST00000278409 Transcript missense_variant 413/945 413/945 138/314 R/M aGg/aTg 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 55994213 55994213 C A 1 0 0 0 0 1 0 0 0 11228 681 24 2 2 OR5F1 11 55994213 Missense_Mutation SNP C C3N-00580_T 80287 55994213 79092409 631 18766 OR5T2 0 . GRCh38 11 56232547 56232547 + Silent SNP A A T C3N-00580_T C3N-00580_N A A c.639T>A p.= p.I213I ENST00000313264 1/1 118 91 27 105 105 0 strelka-varscan-mutect OR5T2,synonymous_variant,p.=,ENST00000313264,NM_001004746.1; T ENST00000313264 Transcript synonymous_variant 639/1080 639/1080 213/359 I atT/atA COSM4168396 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 56232547 56232547 A T 1 0 0 0 0 0 0 0 1 11250 358 13 4 4 OR5T2 11 56232547 Silent SNP A C3N-00580_T 238334 56232547 78854075 632 18767 ZFP91 0 . GRCh38 11 58611713 58611713 + Nonsense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.832A>T p.Arg278Ter p.R278* ENST00000316059 6/11 145 99 46 141 141 0 strelka-varscan-mutect ZFP91,stop_gained,p.Arg278Ter,ENST00000316059,NM_053023.4,NM_001197051.1;CMB9-55A18.1,non_coding_transcript_exon_variant,,ENST00000601906,;ZFP91-CNTF,stop_gained,p.Arg278Ter,ENST00000389919,;ZFP91-CNTF,stop_gained,p.Arg105Ter,ENST00000422974,; T ENST00000316059 Transcript stop_gained 1003/5220 832/1713 278/570 R/* Aga/Tga 1 1 ZFP91 HGNC HGNC:14983 protein_coding YES CCDS31553.1 ENSP00000339030 Q96JP5 A0A024R4Z1 UPI0000070D45 NM_053023.4,NM_001197051.1 6/11 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 58611713 58611713 A T 1 0 0 0 0 0 1 0 0 18232 412 15 4 4 ZFP91 11 58611713 Nonsense_Mutation SNP A C3N-00580_T 2379166 58611713 76474909 633 18768 GLYATL2 0 . GRCh38 11 58838289 58838289 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.158A>G p.Gln53Arg p.Q53R ENST00000287275 3/6 186 170 16 164 164 0 strelka-varscan-mutect GLYATL2,missense_variant,p.Gln53Arg,ENST00000287275,NM_145016.3;GLYATL2,missense_variant,p.Gln53Arg,ENST00000532258,;GLYATL2,non_coding_transcript_exon_variant,,ENST00000533636,; C ENST00000287275 Transcript missense_variant 549/1640 158/885 53/294 Q/R cAg/cGg 1 -1 GLYATL2 HGNC HGNC:24178 protein_coding YES CCDS41649.1 ENSP00000287275 Q8WU03 A0A024R4Z5 UPI000003FFB7 NM_145016.3 tolerated(0.1) 3/6 hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF4,Pfam_domain:PF06021,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 58838289 58838289 T C 1 0 0 0 0 1 0 0 0 6359 1580 55 5 5 GLYATL2 11 58838289 Missense_Mutation SNP T C3N-00580_T 226576 58838289 76248333 634 18769 MPEG1 0 . GRCh38 11 59211048 59211048 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.1818C>G p.= p.A606A ENST00000361050 1/1 311 239 72 261 261 0 strelka-varscan-mutect MPEG1,synonymous_variant,p.=,ENST00000361050,NM_001039396.1;DTX4,downstream_gene_variant,,ENST00000227451,NM_015177.1;RN7SL42P,downstream_gene_variant,,ENST00000579786,; C ENST00000361050 Transcript synonymous_variant 1904/4442 1818/2151 606/716 A gcC/gcG 1 -1 MPEG1 HGNC HGNC:29619 protein_coding YES CCDS41650.1 ENSP00000354335 Q2M385 UPI0000049D9F NM_001039396.1 1/1 hmmpanther:PTHR31463,hmmpanther:PTHR31463:SF4 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 59211048 59211048 G C 1 0 0 0 0 0 0 0 1 9688 1335 47 4 4 MPEG1 11 59211048 Silent SNP G C3N-00580_T 372759 59211048 75875574 635 18770 TMEM132A 0 . GRCh38 11 60930548 60930548 + Missense_Mutation SNP G G T rs538143219 C3N-00580_T C3N-00580_N G G c.905G>T p.Arg302Leu p.R302L ENST00000005286 5/11 137 78 59 151 151 0 strelka-varscan-mutect TMEM132A,missense_variant,p.Arg302Leu,ENST00000005286,NM_017870.3;TMEM132A,missense_variant,p.Arg302Leu,ENST00000453848,NM_178031.2;TMEM132A,missense_variant,p.Arg40Leu,ENST00000544065,;TMEM132A,upstream_gene_variant,,ENST00000540112,;TMEM132A,upstream_gene_variant,,ENST00000535480,;TMEM132A,upstream_gene_variant,,ENST00000536409,;TMEM132A,downstream_gene_variant,,ENST00000543732,;TMEM132A,upstream_gene_variant,,ENST00000536928,;TMEM132A,downstream_gene_variant,,ENST00000540276,;TMEM132A,downstream_gene_variant,,ENST00000537110,;TMEM132A,downstream_gene_variant,,ENST00000537065,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000544098,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000534983,;TMEM132A,upstream_gene_variant,,ENST00000538090,; T ENST00000005286 Transcript missense_variant 1058/3480 905/3075 302/1024 R/L cGc/cTc rs538143219 1 1 TMEM132A HGNC HGNC:31092 protein_coding YES CCDS7997.1 ENSP00000005286 Q24JP5 UPI0000190977 NM_017870.3 deleterious(0) 5/11 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF9 MODERATE 1 SNV 5 1 PASS rs538143219 . 0 199 5 6 0 0 0 0 -20 0.9988805 1 1 1 0 T 3 4 61 60930548 60930548 G T 1 0 0 0 0 1 0 0 0 16489 1087 38 1 1 TMEM132A 11 60930548 Missense_Mutation SNP G C3N-00580_T 1719500 60930548 74156074 636 18771 DAGLA 0 . GRCh38 11 61720695 61720695 + Missense_Mutation SNP G G T rs777615529 C3N-00580_T C3N-00580_N G G c.112G>T p.Val38Leu p.V38L ENST00000257215 3/20 313 236 77 338 338 0 strelka-varscan-mutect DAGLA,missense_variant,p.Val38Leu,ENST00000257215,NM_006133.2;DAGLA,missense_variant,p.Val38Leu,ENST00000540717,; T ENST00000257215 Transcript missense_variant 228/5757 112/3129 38/1042 V/L Gtg/Ttg rs777615529 1 1 DAGLA HGNC HGNC:1165 protein_coding YES CCDS31578.1 ENSP00000257215 Q9Y4D2 A0A024R517 UPI00001678B3 NM_006133.2 tolerated(0.14) 3/20 hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF102,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs777615529 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 61720695 61720695 G T 1 0 0 0 0 1 0 0 0 4028 1145 40 1 1 DAGLA 11 61720695 Missense_Mutation SNP G C3N-00580_T 790147 61720695 73365927 637 18772 DAGLA 0 . GRCh38 11 61737747 61737747 + Silent SNP C C A rs766345907 C3N-00580_T C3N-00580_N C C c.1575C>A p.= p.L525L ENST00000257215 15/20 246 189 57 248 248 0 strelka-varscan-mutect DAGLA,synonymous_variant,p.=,ENST00000257215,NM_006133.2;DAGLA,3_prime_UTR_variant,,ENST00000540717,; A ENST00000257215 Transcript synonymous_variant 1691/5757 1575/3129 525/1042 L ctC/ctA rs766345907,COSM127774 1 1 DAGLA HGNC HGNC:1165 protein_coding YES CCDS31578.1 ENSP00000257215 Q9Y4D2 A0A024R517 UPI00001678B3 NM_006133.2 15/20 Gene3D:3.40.50.1820,Pfam_domain:PF01764,hmmpanther:PTHR21493,hmmpanther:PTHR21493:SF102,Superfamily_domains:SSF53474 0,1 LOW 1 SNV 1 0,1 1 PASS rs766345907 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 61737747 61737747 C A 1 0 0 0 0 0 0 0 1 4028 871 31 1 1 DAGLA 11 61737747 Silent SNP C C3N-00580_T 17052 61737747 73348875 638 18773 SCGB1A1 0 . GRCh38 11 62419122 62419122 + Frame_Shift_Del DEL G G - rs764980269 C3N-00580_T C3N-00580_N G G c.28delG p.Val10SerfsTer46 p.V10Sfs*46 ENST00000278282 1/3 87 74 13 76 76 0 sindel-varindel-pindel SCGB1A1,frameshift_variant,p.Val10SerfsTer46,ENST00000278282,NM_003357.4;SCGB1A1,intron_variant,,ENST00000534397,;CTD-2531D15.4,downstream_gene_variant,,ENST00000528983,; - ENST00000278282 Transcript frameshift_variant 88/441 27/276 9/91 L/X ctG/ct rs764980269 1 1 SCGB1A1 HGNC HGNC:12523 protein_coding YES CCDS8020.1 ENSP00000278282 P11684 A0A0S2Z4R6 UPI00000369D1 NM_003357.4 1/3 Prints_domain:PR00486,hmmpanther:PTHR10136,hmmpanther:PTHR10136:SF6,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM HIGH 1 deletion 1 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 61 62419122 62419122 G - 1 0 1 0 1 0 0 0 0 14160 1335 47 0 0 SCGB1A1 11 62419122 Frame_Shift_Del DEL G C3N-00580_T 681375 62419122 72667500 639 18774 RPS6KA4 0 . GRCh38 11 64368166 64368166 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1106A>T p.Asp369Val p.D369V ENST00000334205 10/17 273 216 57 281 281 0 strelka-mutect RPS6KA4,missense_variant,p.Asp369Val,ENST00000528057,NM_001300802.1,NM_001006944.1;RPS6KA4,missense_variant,p.Asp369Val,ENST00000334205,NM_001318361.1,NM_003942.2;RPS6KA4,missense_variant,p.Asp353Val,ENST00000530504,;MIR1237,upstream_gene_variant,,ENST00000408346,;RPS6KA4,3_prime_UTR_variant,,ENST00000528355,;RPS6KA4,non_coding_transcript_exon_variant,,ENST00000532885,; T ENST00000334205 Transcript missense_variant 1171/3119 1106/2319 369/772 D/V gAc/gTc 1 1 RPS6KA4 HGNC HGNC:10433 protein_coding YES CCDS8073.1 ENSP00000333896 O75676 UPI000006F835 NM_001318361.1,NM_003942.2 tolerated(0.1) 10/17 PIRSF_domain:PIRSF000606,PROSITE_profiles:PS51285,hmmpanther:PTHR24351,hmmpanther:PTHR24351:SF41 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 64368166 64368166 A T 1 0 0 0 0 1 0 0 0 13908 275 10 4 4 RPS6KA4 11 64368166 Missense_Mutation SNP A C3N-00580_T 1949044 64368166 70718456 640 18775 SYVN1 0 . GRCh38 11 65131320 65131320 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.712C>T p.His238Tyr p.H238Y ENST00000377190 8/16 408 249 159 456 456 0 strelka-varscan-mutect SYVN1,missense_variant,p.His238Tyr,ENST00000526060,;SYVN1,missense_variant,p.His238Tyr,ENST00000377190,NM_172230.2;SYVN1,missense_variant,p.His238Tyr,ENST00000294256,NM_032431.2;SYVN1,missense_variant,p.His187Tyr,ENST00000307289,;SYVN1,missense_variant,p.His178Tyr,ENST00000531018,;SYVN1,missense_variant,p.His223Tyr,ENST00000528487,;MRPL49,downstream_gene_variant,,ENST00000279242,NM_004927.3;MRPL49,downstream_gene_variant,,ENST00000531705,;SYVN1,upstream_gene_variant,,ENST00000610479,;SYVN1,non_coding_transcript_exon_variant,,ENST00000526121,;MRPL49,downstream_gene_variant,,ENST00000524482,;SYVN1,upstream_gene_variant,,ENST00000527765,;SYVN1,3_prime_UTR_variant,,ENST00000527142,;SYVN1,3_prime_UTR_variant,,ENST00000532771,;SYVN1,non_coding_transcript_exon_variant,,ENST00000449943,;SYVN1,non_coding_transcript_exon_variant,,ENST00000529207,;MRPL49,downstream_gene_variant,,ENST00000532671,;MRPL49,downstream_gene_variant,,ENST00000526319,;SYVN1,upstream_gene_variant,,ENST00000530451,;SYVN1,downstream_gene_variant,,ENST00000533685,;SYVN1,downstream_gene_variant,,ENST00000525874,; A ENST00000377190 Transcript missense_variant 807/3052 712/1854 238/617 H/Y Cac/Tac 1 -1 SYVN1 HGNC HGNC:20738 protein_coding YES CCDS31605.1 ENSP00000366395 Q86TM6 UPI000004EE90 NM_172230.2 tolerated(0.56) 8/16 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF25 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 65131320 65131320 G A 1 0 0 0 0 1 0 0 0 15881 1319 46 3 3 SYVN1 11 65131320 Missense_Mutation SNP G C3N-00580_T 763154 65131320 69955302 641 18776 PPP6R3 0 . GRCh38 11 68601893 68601893 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.2223A>T p.= p.P741P ENST00000393801 21/25 171 153 18 183 183 0 strelka-varscan-mutect PPP6R3,synonymous_variant,p.=,ENST00000393800,NM_001164161.1;PPP6R3,synonymous_variant,p.=,ENST00000393801,NM_001164160.1;PPP6R3,synonymous_variant,p.=,ENST00000527403,;PPP6R3,synonymous_variant,p.=,ENST00000265636,NM_018312.4;PPP6R3,synonymous_variant,p.=,ENST00000265637,;PPP6R3,synonymous_variant,p.=,ENST00000524904,NM_001164162.1;PPP6R3,synonymous_variant,p.=,ENST00000529710,NM_001164164.1;PPP6R3,synonymous_variant,p.=,ENST00000534534,;PPP6R3,synonymous_variant,p.=,ENST00000524845,NM_001164163.1;PPP6R3,synonymous_variant,p.=,ENST00000534190,;PPP6R3,synonymous_variant,p.=,ENST00000526593,;PPP6R3,non_coding_transcript_exon_variant,,ENST00000526307,; T ENST00000393801 Transcript synonymous_variant 2438/5069 2223/2640 741/879 P ccA/ccT 1 1 PPP6R3 HGNC HGNC:1173 protein_coding YES CCDS53671.1 ENSP00000377390 Q5H9R7 UPI0000688150 NM_001164160.1 21/25 hmmpanther:PTHR12634:SF12,hmmpanther:PTHR12634 LOW 1 SNV 1 1 PASS rs1273793827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 68601893 68601893 A T 1 0 0 0 0 0 0 0 1 12536 175 7 4 4 PPP6R3 11 68601893 Silent SNP A C3N-00580_T 3470573 68601893 66484729 642 18777 MRGPRF 0 . GRCh38 11 69009675 69009675 + Missense_Mutation SNP G G T rs748006591 C3N-00580_T C3N-00580_N G G c.227C>A p.Pro76His p.P76H ENST00000320913 2/2 98 75 23 102 102 0 strelka-varscan-mutect MRGPRF,missense_variant,p.Pro76His,ENST00000320913,;MRGPRF,intron_variant,,ENST00000309099,NM_145015.4;MRGPRF,intron_variant,,ENST00000441623,NM_001098515.1;MRGPRF-AS1,upstream_gene_variant,,ENST00000538407,;MRGPRF-AS1,upstream_gene_variant,,ENST00000569432,;MRGPRF-AS1,upstream_gene_variant,,ENST00000569428,;RP11-554A11.5,downstream_gene_variant,,ENST00000562506,; T ENST00000320913 Transcript missense_variant 447/705 227/315 76/104 P/H cCt/cAt rs748006591 1 -1 MRGPRF HGNC HGNC:24828 protein_coding ENSP00000323414 F5H5R4 UPI0001EE2DBA 2/2 Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS rs748006591 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 69009675 69009675 G T 1 0 0 0 0 1 0 0 0 9731 1000 35 2 2 MRGPRF 11 69009675 Missense_Mutation SNP G C3N-00580_T 407782 69009675 66076947 643 18778 MYO7A 0 . GRCh38 11 77182089 77182089 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3043C>A p.His1015Asn p.H1015N ENST00000409709 24/49 496 324 172 464 464 0 strelka-varscan-mutect MYO7A,missense_variant,p.His1015Asn,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.His1015Asn,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.His1004Asn,ENST00000409619,;MYO7A,missense_variant,p.His196Asn,ENST00000458169,;MYO7A,missense_variant,p.His1015Asn,ENST00000409893,NM_001127179.2;MYO7A,missense_variant,p.His1015Asn,ENST00000620575,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,;MYO7A,upstream_gene_variant,,ENST00000467137,; A ENST00000409709 Transcript missense_variant 3315/7462 3043/6648 1015/2215 H/N Cac/Aac 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.1) 24/49 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 77182089 77182089 C A 1 0 0 0 0 1 0 0 0 10083 710 25 2 2 MYO7A 11 77182089 Missense_Mutation SNP C C3N-00580_T 8172414 77182089 57904533 644 18779 TENM4 0 . GRCh38 11 79064963 79064963 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.268C>A p.Pro90Thr p.P90T ENST00000278550 6/34 37 32 5 43 43 0 strelka-varscan-mutect TENM4,missense_variant,p.Pro90Thr,ENST00000278550,NM_001098816.2;TENM4,downstream_gene_variant,,ENST00000527736,;TENM4,downstream_gene_variant,,ENST00000533038,;TENM4,non_coding_transcript_exon_variant,,ENST00000532654,; T ENST00000278550 Transcript missense_variant 731/14000 268/8310 90/2769 P/T Ccc/Acc 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 tolerated_low_confidence(0.37) 6/34 Pfam_domain:PF06484,PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9 MODERATE 1 SNV 5 1 PASS rs1051681862 . 0 203 7 0 0 0 0 0 -13.04802 0.9999995 1 1 1 0 T 3 4 61 79064963 79064963 G T 1 0 0 0 0 1 0 0 0 16174 1203 42 2 2 TENM4 11 79064963 Missense_Mutation SNP G C3N-00580_T 1882874 79064963 56021659 645 18780 GRM5 0 . GRCh38 11 88984743 88984743 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.857T>A p.Leu286His p.L286H ENST00000393294 4/4 84 54 30 86 86 0 strelka-varscan-mutect GRM5,missense_variant,p.Leu286His,ENST00000393294,;GRM5,intron_variant,,ENST00000455756,NM_000842.4;GRM5,intron_variant,,ENST00000305447,NM_001143831.2;GRM5,intron_variant,,ENST00000305432,;GRM5,intron_variant,,ENST00000449371,; T ENST00000393294 Transcript missense_variant 1227/1268 857/897 286/298 L/H cTt/cAt 1 -1 GRM5 HGNC HGNC:4597 protein_coding ENSP00000376972 A8MT20 UPI0000E593A0 tolerated_low_confidence(0.06) 4/4 MODERATE SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 88984743 88984743 A T 1 0 0 0 0 1 0 0 0 6682 72 3 4 4 GRM5 11 88984743 Missense_Mutation SNP A C3N-00580_T 9919780 88984743 46101879 646 18781 TRIM77 0 . GRCh38 11 89717725 89717725 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1206G>T p.Arg402Ser p.R402S ENST00000398290 6/6 215 160 55 202 202 0 strelka-varscan-mutect TRIM77,missense_variant,p.Arg402Ser,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,missense_variant,p.Arg208Ser,ENST00000534392,; T ENST00000398290 Transcript missense_variant 1206/1353 1206/1353 402/450 R/S agG/agT 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 deleterious(0) 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353,Pfam_domain:PF00622,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 5 1 PASS rs1464892306 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 89717725 89717725 G T 1 0 0 0 0 1 0 0 0 17044 1194 42 2 2 TRIM77 11 89717725 Missense_Mutation SNP G C3N-00580_T 732982 89717725 45368897 647 18782 FAT3 0 . GRCh38 11 92352664 92352664 + Silent SNP C C T rs536537428 C3N-00580_T C3N-00580_N C C c.102C>T p.= p.D34D ENST00000525166 1/27 179 169 10 144 144 0 strelka-varscan-mutect FAT3,synonymous_variant,p.=,ENST00000409404,NM_001008781.2;FAT3,synonymous_variant,p.=,ENST00000525166,;FAT3,upstream_gene_variant,,ENST00000528921,; T ENST00000525166 Transcript synonymous_variant 124/18699 102/13320 34/4439 D gaC/gaT rs536537428,COSM467542,COSM467543 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 1/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs536537428 . 0 205 0 4 0 0 0 0 -12.60213 0.9993798 1 1 1 0 T 2 4 61 92352664 92352664 C T 1 0 0 0 0 0 0 0 1 5551 535 19 1 1 FAT3 11 92352664 Silent SNP C C3N-00580_T 2634939 92352664 42733958 648 18783 KDM4E 0 . GRCh38 11 95026850 95026850 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1293C>A p.= p.S431S ENST00000450979 1/1 444 324 120 356 356 0 strelka-varscan-mutect KDM4E,synonymous_variant,p.=,ENST00000450979,NM_001161630.1;RP11-60C6.8,upstream_gene_variant,,ENST00000616726,; A ENST00000450979 Transcript synonymous_variant 1593/2339 1293/1521 431/506 S tcC/tcA 1 1 KDM4E HGNC HGNC:37098 protein_coding YES CCDS44713.1 ENSP00000397239 B2RXH2 UPI00001607E8 NM_001161630.1 1/1 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 95026850 95026850 C A 1 0 0 0 0 0 0 0 1 8050 581 21 2 2 KDM4E 11 95026850 Silent SNP C C3N-00580_T 2674186 95026850 40059772 649 18784 ARHGAP42 0 . GRCh38 11 100976057 100976057 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1856G>T p.Ser619Ile p.S619I ENST00000298815 20/24 28 16 12 26 26 0 strelka-varscan-mutect ARHGAP42,missense_variant,p.Ser585Ile,ENST00000524892,;ARHGAP42,missense_variant,p.Ser619Ile,ENST00000298815,NM_152432.2;ARHGAP42,missense_variant,p.Ser243Ile,ENST00000529535,; T ENST00000298815 Transcript missense_variant,splice_region_variant 1859/4752 1856/2625 619/874 S/I aGt/aTt 1 1 ARHGAP42 HGNC HGNC:26545 protein_coding YES ENSP00000298815 A6NI28 UPI00005778C9 NM_152432.2 deleterious(0.03) 20/24 Low_complexity_(Seg):seg,hmmpanther:PTHR12552,hmmpanther:PTHR12552:SF3 MODERATE 1 SNV 5 1 PASS rs1225658414 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 100976057 100976057 G T 1 0 0 0 0 1 0 0 0 1013 1275 44 2 2 ARHGAP42 11 100976057 Missense_Mutation SNP G C3N-00580_T 5949207 100976057 34110565 650 18785 DYNC2H1 0 . GRCh38 11 103135568 103135568 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.2279A>T p.Gln760Leu p.Q760L ENST00000398093 16/90 123 94 29 149 149 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Gln760Leu,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Gln760Leu,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,; T ENST00000398093 Transcript missense_variant 2279/12945 2279/12945 760/4314 Q/L cAg/cTg 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0) 16/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 103135568 103135568 A T 1 0 0 0 0 1 0 0 0 4670 188 7 4 4 DYNC2H1 11 103135568 Missense_Mutation SNP A C3N-00580_T 2159511 103135568 31951054 651 18786 DDI1 0 . GRCh38 11 104037511 104037511 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.689C>T p.Ala230Val p.A230V ENST00000302259 1/1 344 241 103 242 241 1 strelka-varscan-mutect DDI1,missense_variant,p.Ala230Val,ENST00000302259,NM_001001711.2;PDGFD,intron_variant,,ENST00000302251,NM_033135.3;PDGFD,intron_variant,,ENST00000393158,NM_025208.4;PDGFD,upstream_gene_variant,,ENST00000529268,; T ENST00000302259 Transcript missense_variant 932/2609 689/1191 230/396 A/V gCg/gTg 1 1 DDI1 HGNC HGNC:18961 protein_coding YES CCDS31660.1 ENSP00000302805 Q8WTU0 UPI0000047AEA NM_001001711.2 deleterious(0) 1/1 Pfam_domain:PF09668,hmmpanther:PTHR12917,hmmpanther:PTHR12917:SF15,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 104037511 104037511 C T 1 0 0 0 0 1 0 0 0 4131 768 27 1 1 DDI1 11 104037511 Missense_Mutation SNP C C3N-00580_T 901943 104037511 31049111 652 18787 C11orf53 0 . GRCh38 11 111284260 111284260 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.192C>A p.= p.P64P ENST00000637637 3/4 457 403 54 434 434 0 strelka-varscan-mutect C11orf53,synonymous_variant,p.=,ENST00000280325,;C11orf53,synonymous_variant,p.=,ENST00000637637,NM_198498.2;C11orf53,missense_variant,p.Pro102His,ENST00000635886,; A ENST00000637637 Transcript synonymous_variant 339/1049 192/711 64/236 P ccC/ccA 1 1 C11orf53 HGNC HGNC:30527 protein_coding YES CCDS31674.1 ENSP00000489630 UPI0000074367 NM_198498.2 3/4 hmmpanther:PTHR28376 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 111284260 111284260 C A 1 0 0 0 0 0 0 0 1 1786 668 24 2 2 C11orf53 11 111284260 Silent SNP C C3N-00580_T 7246749 111284260 23802362 653 18788 HTR3B 0 . GRCh38 11 113946033 113946033 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1222C>A p.Leu408Ile p.L408I ENST00000260191 9/9 491 333 158 458 457 1 strelka-varscan-mutect HTR3B,missense_variant,p.Leu408Ile,ENST00000260191,NM_006028.4;HTR3B,missense_variant,p.Leu397Ile,ENST00000537778,;HTR3B,downstream_gene_variant,,ENST00000543092,; A ENST00000260191 Transcript missense_variant 1479/2011 1222/1326 408/441 L/I Ctc/Atc 1 1 HTR3B HGNC HGNC:5298 protein_coding YES CCDS8364.1 ENSP00000260191 O95264 UPI0000073DA3 NM_006028.4 tolerated(0.14) 9/9 hmmpanther:PTHR18945:SF53,hmmpanther:PTHR18945,Gene3D:1.20.120.370,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS rs1226404585 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 113946033 113946033 C A 1 0 0 0 0 1 0 0 0 7341 681 24 2 2 HTR3B 11 113946033 Missense_Mutation SNP C C3N-00580_T 2661773 113946033 21140589 654 18789 CADM1 0 . GRCh38 11 115504341 115504341 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.54G>T p.= p.A18A ENST00000331581 1/12 354 274 80 386 386 0 strelka-varscan-mutect CADM1,synonymous_variant,p.=,ENST00000452722,NM_014333.3;CADM1,synonymous_variant,p.=,ENST00000542447,NM_001098517.1;CADM1,synonymous_variant,p.=,ENST00000537058,NM_001301044.1;CADM1,synonymous_variant,p.=,ENST00000536727,NM_001301045.1;CADM1,synonymous_variant,p.=,ENST00000545380,;CADM1,synonymous_variant,p.=,ENST00000331581,NM_001301043.1;CADM1,intron_variant,,ENST00000543249,;CADM1,non_coding_transcript_exon_variant,,ENST00000537140,;CADM1,non_coding_transcript_exon_variant,,ENST00000536781,;CADM1,synonymous_variant,p.=,ENST00000540951,;CADM1,non_coding_transcript_exon_variant,,ENST00000541434,; A ENST00000331581 Transcript synonymous_variant 225/1766 54/1416 18/471 A gcG/gcT 1 -1 CADM1 HGNC HGNC:5951 protein_coding YES CCDS73399.1 ENSP00000329797 Q9BY67 X5D7A8 UPI000204AF0D NM_001301043.1 1/12 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF53,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs907370867 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 115504341 115504341 C A 1 0 0 0 0 0 0 0 1 2256 639 23 1 1 CADM1 11 115504341 Silent SNP C C3N-00580_T 1558308 115504341 19582281 655 18790 FXYD2 0 . GRCh38 11 117820879 117820879 + Nonsense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.156T>A p.Cys52Ter p.C52* ENST00000292079 4/6 459 314 145 406 406 0 strelka-varscan-mutect FXYD2,stop_gained,p.Cys50Ter,ENST00000528014,;FXYD6-FXYD2,stop_gained,p.Cys130Ter,ENST00000614497,NM_001204268.1;FXYD2,stop_gained,p.Cys52Ter,ENST00000292079,NM_001680.4;FXYD2,stop_gained,p.Cys50Ter,ENST00000532119,;FXYD2,stop_gained,p.Cys50Ter,ENST00000260287,NM_021603.3;FXYD6-FXYD2,missense_variant,p.Trp110Arg,ENST00000532984,NM_001243598.2;DSCAML1,upstream_gene_variant,,ENST00000525836,;RP11-728F11.3,intron_variant,,ENST00000531850,;FXYD2,upstream_gene_variant,,ENST00000514385,;FXYD2,non_coding_transcript_exon_variant,,ENST00000534383,;FXYD2,non_coding_transcript_exon_variant,,ENST00000533281,;FXYD2,downstream_gene_variant,,ENST00000317594,; T ENST00000292079 Transcript stop_gained 222/571 156/201 52/66 C/* tgT/tgA 1 -1 FXYD2 HGNC HGNC:4026 protein_coding YES CCDS8386.1 ENSP00000292079 P54710 UPI00001262A8 NM_001680.4 4/6 Gene3D:1.20.5.780,PD005989,Pfam_domain:PF02038,hmmpanther:PTHR14132,hmmpanther:PTHR14132:SF3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 117820879 117820879 A T 1 0 0 0 0 0 1 0 0 5989 160 6 4 4 FXYD2 11 117820879 Nonsense_Mutation SNP A C3N-00580_T 2316538 117820879 17265743 656 18791 TMEM136 0 . GRCh38 11 120330226 120330226 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.515G>T p.Gly172Val p.G172V ENST00000314475 3/3 333 228 105 338 338 0 strelka-varscan-mutect TMEM136,missense_variant,p.Gly150Val,ENST00000375095,NM_001198672.1,NM_001198671.1,NM_001198673.1;TMEM136,missense_variant,p.Gly172Val,ENST00000314475,NM_001198670.1;TMEM136,intron_variant,,ENST00000529187,NM_001198674.1,NM_174926.2;TMEM136,non_coding_transcript_exon_variant,,ENST00000531346,;TMEM136,downstream_gene_variant,,ENST00000524680,; T ENST00000314475 Transcript missense_variant 842/1434 515/804 172/267 G/V gGg/gTg 1 1 TMEM136 HGNC HGNC:28280 protein_coding YES CCDS55792.1 ENSP00000312672 Q6ZRR5 UPI0000D4D33E NM_001198670.1 deleterious(0) 3/3 Pfam_domain:PF03798,PROSITE_profiles:PS50922,hmmpanther:PTHR31898,hmmpanther:PTHR31898:SF1,SMART_domains:SM00724 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 120330226 120330226 G T 1 0 0 0 0 1 0 0 0 16497 1232 43 2 2 TMEM136 11 120330226 Missense_Mutation SNP G C3N-00580_T 2509347 120330226 14756396 657 18792 ARHGEF12 0 . GRCh38 11 120451533 120451533 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1865A>T p.Gln622Leu p.Q622L ENST00000397843 22/41 367 273 94 303 303 0 strelka-varscan-mutect ARHGEF12,missense_variant,p.Gln622Leu,ENST00000397843,NM_015313.2;ARHGEF12,missense_variant,p.Gln519Leu,ENST00000532993,NM_001301084.1;ARHGEF12,missense_variant,p.Gln603Leu,ENST00000356641,NM_001198665.1;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000529970,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000525222,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000528225,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000532823,;ARHGEF12,downstream_gene_variant,,ENST00000525960,; T ENST00000397843 Transcript missense_variant 2031/9660 1865/4635 622/1544 Q/L cAg/cTg 1 1 ARHGEF12 HGNC HGNC:14193 protein_coding YES CCDS41727.1 ENSP00000380942 Q9NZN5 UPI00000708ED NM_015313.2 deleterious(0.04) 22/41 hmmpanther:PTHR12673:SF126,hmmpanther:PTHR12673 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 120451533 120451533 A T 1 0 0 0 0 1 0 0 0 1027 188 7 4 4 ARHGEF12 11 120451533 Missense_Mutation SNP A C3N-00580_T 121307 120451533 14635089 658 18793 OR10D3 0 . GRCh38 11 124185758 124185758 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.489C>A p.= p.T163T ENST00000318666 1/1 482 340 142 437 437 0 strelka-varscan-mutect OR10D3,synonymous_variant,p.=,ENST00000318666,; A ENST00000318666 Transcript synonymous_variant 543/1030 489/939 163/312 T acC/acA 1 1 OR10D3 HGNC HGNC:8168 protein_coding YES ENSP00000323895 Q8NH80 UPI000004B22A 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF221,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 124185758 124185758 C A 1 0 0 0 0 0 0 0 1 10974 668 24 2 2 OR10D3 11 124185758 Silent SNP C C3N-00580_T 3734225 124185758 10900864 659 18794 OR8B8 0 . GRCh38 11 124440721 124440721 + Missense_Mutation SNP C C A rs144609364 C3N-00580_T C3N-00580_N C C c.365G>T p.Arg122Leu p.R122L ENST00000328064 1/1 292 205 87 212 212 0 strelka-varscan-mutect OR8B8,missense_variant,p.Arg122Leu,ENST00000328064,NM_012378.1; A ENST00000328064 Transcript missense_variant 438/1033 365/936 122/311 R/L cGc/cTc rs144609364 1 -1 OR8B8 HGNC HGNC:8477 protein_coding YES CCDS8446.1 ENSP00000330280 Q15620 A0A126GW73 UPI00000015B1 NM_012378.1 deleterious_low_confidence(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF214,hmmpanther:PTHR26452,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs144609364 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 124440721 124440721 C A 1 0 0 0 0 1 0 0 0 11300 768 27 1 1 OR8B8 11 124440721 Missense_Mutation SNP C C3N-00580_T 254963 124440721 10645901 660 18795 SLC6A12 0 . GRCh38 12 197491 197491 + Missense_Mutation SNP C C T rs373249721 C3N-00580_T C3N-00580_N C C c.961G>A p.Ala321Thr p.A321T ENST00000424061 11/17 102 90 12 139 139 0 strelka-varscan-mutect SLC6A12,missense_variant,p.Ala321Thr,ENST00000424061,NM_003044.4;SLC6A12,missense_variant,p.Ala321Thr,ENST00000397296,;SLC6A12,missense_variant,p.Ala321Thr,ENST00000359674,NM_001122847.2,NM_001122848.2;SLC6A12,missense_variant,p.Ala321Thr,ENST00000536824,NM_001206931.1;RP11-283I3.1,downstream_gene_variant,,ENST00000544067,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000535498,;SLC6A12,downstream_gene_variant,,ENST00000538272,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000545058,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000542825,;SLC6A12,non_coding_transcript_exon_variant,,ENST00000544782,;SLC6A12,downstream_gene_variant,,ENST00000538580,;SLC6A12,downstream_gene_variant,,ENST00000540094,; T ENST00000424061 Transcript missense_variant 1516/3332 961/1845 321/614 A/T Gcc/Acc rs373249721 1 -1 SLC6A12 HGNC HGNC:11045 protein_coding YES CCDS8501.1 ENSP00000399136 P48065 UPI000013C8DB NM_003044.4 tolerated(0.39) 11/17 Superfamily_domains:0053687,Pfam_domain:PF00209,Prints_domain:PR00176,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF118 MODERATE 1 SNV 1 1 PASS rs373249721 . 0 204 4 2 0 0 0 0 -18.86498 0.9999721 1 1 1 0 T 3 4 61 197491 197491 C T 1 0 0 0 0 1 0 0 0 14958 768 27 1 1 SLC6A12 12 197491 Missense_Mutation SNP C C3N-00580_T 197491 133077818 661 18796 KCNA1 0 . GRCh38 12 4912670 4912670 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1292G>T p.Ser431Ile p.S431I ENST00000382545 2/2 240 86 154 252 252 0 strelka-varscan-mutect KCNA1,missense_variant,p.Ser431Ile,ENST00000382545,NM_000217.2;KCNA1,intron_variant,,ENST00000543874,;KCNA1,intron_variant,,ENST00000541095,; T ENST00000382545 Transcript missense_variant 2399/7976 1292/1488 431/495 S/I aGt/aTt 1 1 KCNA1 HGNC HGNC:6218 protein_coding YES CCDS8535.1 ENSP00000371985 Q09470 UPI000013C8E0 NM_000217.2 tolerated_low_confidence(0.09) 2/2 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF24 MODERATE 1 SNV 4 1 PASS rs1241721668 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 4912670 4912670 G T 1 0 0 0 0 1 0 0 0 7917 1029 36 2 2 KCNA1 12 4912670 Missense_Mutation SNP G C3N-00580_T 4715179 4912670 128362639 662 18797 GPR162 0 . GRCh38 12 6827204 6827204 + Nonstop_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1767A>T p.Ter589CysextTer13 p.*589Cext*13 ENST00000311268 5/5 73 24 49 92 92 0 strelka-varscan-mutect GPR162,stop_lost,p.Ter589CysextTer13,ENST00000311268,NM_019858.1;GPR162,stop_lost,p.Ter305CysextTer13,ENST00000428545,NM_014449.1;GPR162,stop_lost,p.Ter285CysextTer13,ENST00000382315,;GPR162,intron_variant,,ENST00000545321,;P3H3,upstream_gene_variant,,ENST00000290510,NM_014262.4;GPR162,non_coding_transcript_exon_variant,,ENST00000542330,;GPR162,downstream_gene_variant,,ENST00000541431,;P3H3,upstream_gene_variant,,ENST00000538102,;P3H3,upstream_gene_variant,,ENST00000544813,;P3H3,upstream_gene_variant,,ENST00000536140,;P3H3,upstream_gene_variant,,ENST00000612048,;GPR162,downstream_gene_variant,,ENST00000535220,;P3H3,upstream_gene_variant,,ENST00000541956,;P3H3,upstream_gene_variant,,ENST00000544200,;P3H3,upstream_gene_variant,,ENST00000544949,; T ENST00000311268 Transcript stop_lost 2554/2768 1767/1767 589/588 */C tgA/tgT 1 1 GPR162 HGNC HGNC:16693 protein_coding YES CCDS8563.1 ENSP00000311528 Q16538 A0A0I9QPQ8 UPI000005046E NM_019858.1 5/5 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 6827204 6827204 A T 1 0 0 0 0 0 0 0 0 6552 317 11 4 4 GPR162 12 6827204 Nonstop_Mutation SNP A C3N-00580_T 1914534 6827204 126448105 663 18798 A2M 0 . GRCh38 12 9104321 9104321 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.1184C>T p.Ser395Phe p.S395F ENST00000318602 11/36 215 89 126 301 300 1 strelka-varscan-mutect A2M,missense_variant,p.Ser395Phe,ENST00000318602,NM_000014.4;A2M,non_coding_transcript_exon_variant,,ENST00000545828,;A2M,upstream_gene_variant,,ENST00000472360,;A2M,upstream_gene_variant,,ENST00000546069,; A ENST00000318602 Transcript missense_variant 1492/4844 1184/4425 395/1474 S/F tCc/tTc COSM229215 1 -1 A2M HGNC HGNC:7 protein_coding YES CCDS44827.1 ENSP00000323929 P01023 UPI000014038F NM_000014.4 tolerated(0.54) 11/36 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF103 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 9104321 9104321 G A 1 0 0 0 0 1 0 0 0 3 1174 41 3 3 A2M 12 9104321 Missense_Mutation SNP G C3N-00580_T 2277117 9104321 124170988 664 18799 PZP 0 . GRCh38 12 9196668 9196668 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.885C>A p.Cys295Ter p.C295* ENST00000261336 9/36 303 144 159 208 208 0 strelka-varscan-mutect PZP,stop_gained,p.Cys295Ter,ENST00000261336,NM_002864.2;PZP,3_prime_UTR_variant,,ENST00000535230,; T ENST00000261336 Transcript stop_gained 914/4610 885/4449 295/1482 C/* tgC/tgA 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 9/36 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 9196668 9196668 G T 1 0 0 0 0 0 1 0 0 13025 1311 46 2 2 PZP 12 9196668 Nonsense_Mutation SNP G C3N-00580_T 92347 9196668 124078641 665 18800 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C T rs121913530 C3N-00580_T C3N-00580_N C C c.34G>A p.Gly12Ser p.G12S ENST00000256078 2/6 394 139 255 358 357 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Ser,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Ser,ENST00000556131,;KRAS,missense_variant,p.Gly12Ser,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Ser,ENST00000557334,; T ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/S Ggt/Agt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.03) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 25245351 25245351 C T 1 0 0 0 0 1 0 0 0 8318 594 21 3 3 KRAS 12 25245351 Missense_Mutation SNP C C3N-00580_T 16048683 25245351 108029958 666 18801 DDX11 0 . GRCh38 12 31089141 31089141 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.782G>T p.Gly261Val p.G261V ENST00000545668 7/27 396 296 100 457 457 0 strelka-varscan-mutect DDX11,missense_variant,p.Gly261Val,ENST00000545668,NM_152438.1,NM_001257144.1;DDX11,missense_variant,p.Gly261Val,ENST00000350437,NM_004399.2;DDX11,missense_variant,p.Gly235Val,ENST00000228264,NM_001257145.1;DDX11,missense_variant,p.Gly261Val,ENST00000542838,NM_030653.3;DDX11,missense_variant,p.Gly232Val,ENST00000438391,;DDX11,downstream_gene_variant,,ENST00000415475,;DDX11,downstream_gene_variant,,ENST00000535317,;DDX11,downstream_gene_variant,,ENST00000544652,;DDX11,non_coding_transcript_exon_variant,,ENST00000545717,;DDX11,upstream_gene_variant,,ENST00000539673,;DDX11,missense_variant,p.Gly261Val,ENST00000539049,;DDX11,missense_variant,p.Gly261Val,ENST00000542129,;DDX11,missense_variant,p.Gly235Val,ENST00000540935,;DDX11,3_prime_UTR_variant,,ENST00000435753,;DDX11,3_prime_UTR_variant,,ENST00000542244,;DDX11,non_coding_transcript_exon_variant,,ENST00000536265,;DDX11,non_coding_transcript_exon_variant,,ENST00000543026,;DDX11,non_coding_transcript_exon_variant,,ENST00000535158,;DDX11,non_coding_transcript_exon_variant,,ENST00000542242,;DDX11,intron_variant,,ENST00000538345,;DDX11,upstream_gene_variant,,ENST00000536580,;DDX11,downstream_gene_variant,,ENST00000543756,; T ENST00000545668 Transcript missense_variant 862/3751 782/2913 261/970 G/V gGc/gTc 1 1 DDX11 HGNC HGNC:2736 protein_coding YES CCDS44856.1 ENSP00000440402 Q96FC9 UPI000006F88F NM_152438.1,NM_001257144.1 deleterious(0) 7/27 Pfam_domain:PF06733,PROSITE_profiles:PS51193,hmmpanther:PTHR11472,hmmpanther:PTHR11472:SF36,SMART_domains:SM00488,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00604 MODERATE 1 SNV 1 1 PASS rs1169571267 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 31089141 31089141 G T 1 0 0 0 0 1 0 0 0 4147 1203 42 2 2 DDX11 12 31089141 Missense_Mutation SNP G C3N-00580_T 5843790 31089141 102186168 667 18802 OVOS2 0 . GRCh38 12 31136621 31136621 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2204A>T p.Asp735Val p.D735V ENST00000632817 16/34 123 83 40 107 107 0 strelka-varscan-mutect OVOS2,missense_variant,p.Asp735Val,ENST00000398963,;OVOS2,missense_variant,p.Asp735Val,ENST00000632817,; A ENST00000632817 Transcript missense_variant,splice_region_variant 2204/4299 2204/4299 735/1432 D/V gAt/gTt 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 deleterious(0) 16/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412,Pfam_domain:PF00207,SMART_domains:SM01360 MODERATE 1 SNV 5 1 PASS rs1443230410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 31136621 31136621 T A 1 0 0 0 0 1 0 0 0 11399 1565 54 4 4 OVOS2 12 31136621 Missense_Mutation SNP T C3N-00580_T 47480 31136621 102138688 668 18803 ABCD2 0 . GRCh38 12 39619413 39619413 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.203G>A p.Cys68Tyr p.C68Y ENST00000308666 1/10 248 169 79 226 225 1 strelka-varscan-mutect ABCD2,missense_variant,p.Cys68Tyr,ENST00000308666,NM_005164.3; T ENST00000308666 Transcript missense_variant 339/6238 203/2223 68/740 C/Y tGc/tAc 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 deleterious(0.04) 1/10 hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 39619413 39619413 C T 1 0 0 0 0 1 0 0 0 65 710 25 3 3 ABCD2 12 39619413 Missense_Mutation SNP C C3N-00580_T 8482792 39619413 93655896 669 18804 LRRK2 0 . GRCh38 12 40305945 40305945 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.3938G>C p.Cys1313Ser p.C1313S ENST00000298910 28/51 107 72 35 114 114 0 strelka-varscan-mutect LRRK2,missense_variant,p.Cys1313Ser,ENST00000298910,NM_198578.3;LRRK2,downstream_gene_variant,,ENST00000343742,;LRRK2,3_prime_UTR_variant,,ENST00000430804,;LRRK2,non_coding_transcript_exon_variant,,ENST00000479187,; C ENST00000298910 Transcript missense_variant 3996/9158 3938/7584 1313/2527 C/S tGt/tCt 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 tolerated(0.78) 28/51 Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 40305945 40305945 G C 1 0 0 0 0 1 0 0 0 8939 1377 48 4 4 LRRK2 12 40305945 Missense_Mutation SNP G C3N-00580_T 686532 40305945 92969364 670 18805 CNTN1 0 . GRCh38 12 41025162 41025162 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2536G>T p.Ala846Ser p.A846S ENST00000551295 21/24 343 273 70 289 289 0 strelka-varscan-mutect CNTN1,missense_variant,p.Ala846Ser,ENST00000551295,NM_001843.3;CNTN1,missense_variant,p.Ala846Ser,ENST00000347616,;CNTN1,missense_variant,p.Ala835Ser,ENST00000348761,NM_175038.2;CNTN1,non_coding_transcript_exon_variant,,ENST00000550305,;CNTN1,upstream_gene_variant,,ENST00000548481,; T ENST00000551295 Transcript missense_variant 2653/5557 2536/3057 846/1018 A/S Gct/Tct 1 1 CNTN1 HGNC HGNC:2171 protein_coding YES CCDS8737.1 ENSP00000447006 Q12860 A0A024R104 UPI0000127EBA NM_001843.3 tolerated(0.12) 21/24 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 41025162 41025162 G T 1 0 0 0 0 1 0 0 0 3421 1203 42 2 2 CNTN1 12 41025162 Missense_Mutation SNP G C3N-00580_T 719217 41025162 92250147 671 18806 ADCY6 0 . GRCh38 12 48769025 48769025 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3293G>T p.Gly1098Val p.G1098V ENST00000307885 20/21 107 77 30 127 127 0 strelka-varscan-mutect ADCY6,missense_variant,p.Gly1098Val,ENST00000307885,NM_015270.3;ADCY6,missense_variant,p.Gly1045Val,ENST00000550422,NM_020983.2;ADCY6,missense_variant,p.Gly1045Val,ENST00000357869,;LINC00935,downstream_gene_variant,,ENST00000548380,;MIR4701,downstream_gene_variant,,ENST00000583094,;RP11-579D7.2,downstream_gene_variant,,ENST00000548742,;ADCY6,downstream_gene_variant,,ENST00000552090,;ADCY6,downstream_gene_variant,,ENST00000548351,;ADCY6,non_coding_transcript_exon_variant,,ENST00000547260,;ADCY6,downstream_gene_variant,,ENST00000552099,;LINC00935,downstream_gene_variant,,ENST00000548054,; A ENST00000307885 Transcript missense_variant 3988/6464 3293/3507 1098/1168 G/V gGg/gTg 1 -1 ADCY6 HGNC HGNC:237 protein_coding YES CCDS8767.1 ENSP00000311405 O43306 UPI000003EC29 NM_015270.3 deleterious(0) 20/21 PROSITE_profiles:PS50125,hmmpanther:PTHR11920:SF343,hmmpanther:PTHR11920,PROSITE_patterns:PS00452,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 48769025 48769025 C A 1 0 0 0 0 1 0 0 0 342 623 22 2 2 ADCY6 12 48769025 Missense_Mutation SNP C C3N-00580_T 7743863 48769025 84506284 672 18807 ACVRL1 0 . GRCh38 12 51913270 51913270 + Frame_Shift_Del DEL G G - novel C3N-00580_T C3N-00580_N G G c.237delG p.Arg80AlafsTer42 p.R80Afs*42 ENST00000388922 3/10 499 333 166 776 776 0 sindel-varindel-pindel ACVRL1,frameshift_variant,p.Arg94AlafsTer42,ENST00000550683,;ACVRL1,frameshift_variant,p.Arg80AlafsTer42,ENST00000388922,NM_000020.2,NM_001077401.1;ACVRL1,frameshift_variant,p.Arg94AlafsTer?,ENST00000547400,;ACVRL1,frameshift_variant,p.Arg80AlafsTer?,ENST00000551576,;ACVRL1,intron_variant,,ENST00000419526,;ACVRL1,upstream_gene_variant,,ENST00000552678,;ACVRL1,upstream_gene_variant,,ENST00000547632,; - ENST00000388922 Transcript frameshift_variant 516/1971 233/1512 78/503 R/X aGg/ag 1 1 ACVRL1 HGNC HGNC:175 protein_coding YES CCDS31804.1 ENSP00000373574 P37023 A0A0S2Z310 UPI000000D9F4 NM_000020.2,NM_001077401.1 3/10 hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF66,Gene3D:2.10.60.10,Superfamily_domains:SSF57302,Prints_domain:PR00653 HIGH 1 deletion 1 4 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999824 1 1 1 0 - 7 5 61 51913270 51913270 G - 1 0 1 0 1 0 0 0 0 269 1000 35 0 0 ACVRL1 12 51913270 Frame_Shift_Del DEL G C3N-00580_T 3144245 51913270 81362039 673 18808 KRT6B 0 . GRCh38 12 52449767 52449767 + Missense_Mutation SNP C C A rs781409851 C3N-00580_T C3N-00580_N C C c.903G>T p.Leu301Phe p.L301F ENST00000252252 4/9 796 554 242 819 818 1 strelka-varscan-mutect KRT6B,missense_variant,p.Leu301Phe,ENST00000252252,NM_005555.3; A ENST00000252252 Transcript missense_variant 951/2282 903/1695 301/564 L/F ttG/ttT rs781409851 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 tolerated(0.24) 4/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs781409851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 52449767 52449767 C A 1 0 0 0 0 1 0 0 0 8363 477 17 2 2 KRT6B 12 52449767 Missense_Mutation SNP C C3N-00580_T 536497 52449767 80825542 674 18809 KRT72 0 . GRCh38 12 52590937 52590937 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.988G>T p.Gly330Cys p.G330C ENST00000293745 6/9 86 63 23 72 72 0 strelka-varscan-mutect KRT72,missense_variant,p.Gly330Cys,ENST00000293745,NM_080747.2;KRT72,missense_variant,p.Gly330Cys,ENST00000537672,NM_001146225.1;KRT72,intron_variant,,ENST00000354310,NM_001146226.1;KRT72,3_prime_UTR_variant,,ENST00000550829,; A ENST00000293745 Transcript missense_variant 1074/2015 988/1536 330/511 G/C Ggc/Tgc 1 -1 KRT72 HGNC HGNC:28932 protein_coding YES CCDS8833.1 ENSP00000293745 Q14CN4 UPI0000055AC8 NM_080747.2 deleterious(0) 6/9 Pfam_domain:PF00038,Prints_domain:PR01276,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF86,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 52590937 52590937 C A 1 0 0 0 0 1 0 0 0 8367 681 24 2 2 KRT72 12 52590937 Missense_Mutation SNP C C3N-00580_T 141170 52590937 80684372 675 18810 KRT78 0 . GRCh38 12 52839477 52839477 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1279G>T p.Glu427Ter p.E427* ENST00000304620 8/9 79 62 17 80 80 0 strelka-varscan-mutect KRT78,stop_gained,p.Glu317Ter,ENST00000359499,NM_001300814.1;KRT78,stop_gained,p.Glu427Ter,ENST00000304620,NM_173352.3;KRT78,intron_variant,,ENST00000547920,;RP11-153F5.3,downstream_gene_variant,,ENST00000550463,; A ENST00000304620 Transcript stop_gained 1343/1778 1279/1563 427/520 E/* Gag/Tag 1 -1 KRT78 HGNC HGNC:28926 protein_coding YES CCDS8840.1 ENSP00000306261 Q8N1N4 UPI00001AEDBE NM_173352.3 8/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF127 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 52839477 52839477 C A 1 0 0 0 0 0 1 0 0 8373 864 30 2 2 KRT78 12 52839477 Nonsense_Mutation SNP C C3N-00580_T 248540 52839477 80435832 676 18811 PDE1B 0 . GRCh38 12 54573354 54573354 + Splice_Site SNP G G C novel C3N-00580_T C3N-00580_N G G c.837-1G>C p.X279_splice ENST00000243052 236 167 69 248 248 0 strelka-varscan-mutect PDE1B,splice_acceptor_variant,,ENST00000243052,NM_000924.3;PDE1B,splice_acceptor_variant,,ENST00000550620,NM_001165975.2;PDE1B,splice_acceptor_variant,,ENST00000538346,NM_001288768.1,NM_001288769.1;PPP1R1A,downstream_gene_variant,,ENST00000547431,;PDE1B,splice_acceptor_variant,,ENST00000394277,;PDE1B,splice_acceptor_variant,,ENST00000542335,;PDE1B,splice_acceptor_variant,,ENST00000548855,;PDE1B,splice_acceptor_variant,,ENST00000550285,;PDE1B,upstream_gene_variant,,ENST00000552774,;PDE1B,downstream_gene_variant,,ENST00000611899,; C ENST00000243052 Transcript splice_acceptor_variant -/3444 837/1611 279/536 1 1 PDE1B HGNC HGNC:8775 protein_coding YES CCDS8882.1 ENSP00000243052 Q01064 A0A024RB59 UPI0000001607 NM_000924.3 8/15 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 61 54573354 54573354 G C 1 0 0 0 0 0 0 1 0 11722 1014 35 4 4 PDE1B 12 54573354 Splice_Site SNP G C3N-00580_T 1733877 54573354 78701955 677 18812 OR6C74 0 . GRCh38 12 55247601 55247602 + Frame_Shift_Ins INS - - GG novel C3N-00580_T C3N-00580_N - - c.318_319dupGG p.Ala107GlyfsTer29 p.A107Gfs*29 ENST00000343870 1/1 83 64 19 83 83 0 sindel-varindel-pindel OR6C74,frameshift_variant,p.Ala107GlyfsTer29,ENST00000343870,NM_001005490.1; GG ENST00000343870 Transcript frameshift_variant 404-405/1105 314-315/939 105/312 L/LX ttg/ttGGg 1 1 OR6C74 HGNC HGNC:31303 protein_coding YES CCDS31816.1 ENSP00000342836 A6NCV1 A0A126GW13 UPI000016150B NM_001005490.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF72,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH 1 insertion 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 GG 7 5 61 55247601 55247601 - GG 1 0 1 1 0 0 0 0 0 11266 1821 63 0 0 OR6C74 12 55247601 Frame_Shift_Ins INS - C3N-00580_T 674247 55247601 78027708 678 18813 STAT6 0 . GRCh38 12 57096900 57096900 + Silent SNP C C A rs780219389 C3N-00580_T C3N-00580_N C C c.2304G>T p.= p.V768V ENST00000300134 21/22 164 112 52 219 218 1 strelka-varscan-mutect STAT6,synonymous_variant,p.=,ENST00000300134,NM_003153.4,NM_001178078.1;STAT6,synonymous_variant,p.=,ENST00000543873,NM_001178079.1;STAT6,synonymous_variant,p.=,ENST00000454075,;STAT6,synonymous_variant,p.=,ENST00000556155,;STAT6,synonymous_variant,p.=,ENST00000537215,NM_001178080.1;STAT6,synonymous_variant,p.=,ENST00000538913,NM_001178081.1;NAB2,downstream_gene_variant,,ENST00000300131,NM_005967.3;NAB2,downstream_gene_variant,,ENST00000342556,;STAT6,downstream_gene_variant,,ENST00000553533,;STAT6,downstream_gene_variant,,ENST00000555375,;STAT6,downstream_gene_variant,,ENST00000555318,;STAT6,3_prime_UTR_variant,,ENST00000554764,;STAT6,non_coding_transcript_exon_variant,,ENST00000555222,;STAT6,non_coding_transcript_exon_variant,,ENST00000557563,;NAB2,downstream_gene_variant,,ENST00000554839,;STAT6,downstream_gene_variant,,ENST00000554202,; A ENST00000300134 Transcript synonymous_variant 2630/4034 2304/2544 768/847 V gtG/gtT rs780219389 1 -1 STAT6 HGNC HGNC:11368 protein_coding YES CCDS8931.1 ENSP00000300134 P42226 UPI00000473FE NM_003153.4,NM_001178078.1 21/22 Pfam_domain:PF14596 LOW 1 SNV 1 1 PASS rs780219389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 57096900 57096900 C A 1 0 0 0 0 0 0 0 1 15646 581 21 2 2 STAT6 12 57096900 Silent SNP C C3N-00580_T 1849299 57096900 76178409 679 18814 DPY19L2 0 . GRCh38 12 63618203 63618203 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1079T>A p.Val360Asp p.V360D ENST00000324472 10/22 30 21 9 52 52 0 strelka-varscan-mutect DPY19L2,missense_variant,p.Val360Asp,ENST00000324472,NM_173812.4;DPY19L2,missense_variant,p.Val26Asp,ENST00000541083,;DPY19L2,3_prime_UTR_variant,,ENST00000306389,; T ENST00000324472 Transcript missense_variant 1263/4060 1079/2277 360/758 V/D gTt/gAt 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 deleterious(0) 10/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -19.99998 1 1 1 1 0 T 3 4 61 63618203 63618203 A T 1 0 0 0 0 1 0 0 0 4556 43 2 4 4 DPY19L2 12 63618203 Missense_Mutation SNP A C3N-00580_T 6521303 63618203 69657106 680 18815 HELB 0 . GRCh38 12 66309723 66309723 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.795G>T p.Trp265Cys p.W265C ENST00000247815 4/13 67 48 19 51 51 0 strelka-varscan-mutect HELB,missense_variant,p.Trp265Cys,ENST00000247815,NM_033647.3;HELB,missense_variant,p.Trp265Cys,ENST00000545134,;HELB,missense_variant,p.Trp265Cys,ENST00000542394,;HELB,missense_variant,p.Trp265Cys,ENST00000440906,; T ENST00000247815 Transcript missense_variant 854/12866 795/3264 265/1087 W/C tgG/tgT 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 deleterious(0) 4/13 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 66309723 66309723 G T 1 0 0 0 0 1 0 0 0 6927 1183 41 2 2 HELB 12 66309723 Missense_Mutation SNP G C3N-00580_T 2691520 66309723 66965586 681 18816 CPM 0 . GRCh38 12 68885875 68885875 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.175G>T p.Val59Phe p.V59F ENST00000551568 3/9 203 142 61 282 282 0 strelka-varscan-mutect CPM,missense_variant,p.Val59Phe,ENST00000551568,NM_001005502.2,NM_198320.3;CPM,missense_variant,p.Val59Phe,ENST00000338356,;CPM,missense_variant,p.Val59Phe,ENST00000546373,NM_001874.4;CPM,missense_variant,p.Val59Phe,ENST00000548954,;CPM,missense_variant,p.Val59Phe,ENST00000548262,;CPM,synonymous_variant,p.=,ENST00000549781,;CPM,non_coding_transcript_exon_variant,,ENST00000547924,;CPM,intron_variant,,ENST00000551728,;CPM,intron_variant,,ENST00000547134,; A ENST00000551568 Transcript missense_variant 236/6655 175/1332 59/443 V/F Gtt/Ttt 1 -1 CPM HGNC HGNC:2311 protein_coding YES CCDS8987.1 ENSP00000448517 P14384 UPI00001271D4 NM_001005502.2,NM_198320.3 deleterious(0) 3/9 hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF40,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187,Prints_domain:PR00765 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 68885875 68885875 C A 1 0 0 0 0 1 0 0 0 3603 507 18 2 2 CPM 12 68885875 Missense_Mutation SNP C C3N-00580_T 2576152 68885875 64389434 682 18817 PTPRB 0 . GRCh38 12 70559421 70559421 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.4636T>C p.Tyr1546His p.Y1546H ENST00000334414 18/34 618 496 122 457 457 0 strelka-varscan-mutect PTPRB,missense_variant,p.Tyr1546His,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Tyr1458His,ENST00000550358,;PTPRB,missense_variant,p.Tyr1328His,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Tyr1238His,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Tyr1238His,ENST00000550857,NM_001206971.1;PTPRB,missense_variant,p.Tyr1545His,ENST00000551525,;PTPRB,downstream_gene_variant,,ENST00000548122,; G ENST00000334414 Transcript missense_variant 4681/12316 4636/6648 1546/2215 Y/H Tat/Cat 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious(0) 18/34 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 70559421 70559421 A G 1 0 0 0 0 1 0 0 0 12950 420 15 5 5 PTPRB 12 70559421 Missense_Mutation SNP A C3N-00580_T 1673546 70559421 62715888 683 18818 LGR5 0 . GRCh38 12 71580313 71580313 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1442C>A p.Ala481Glu p.A481E ENST00000266674 16/18 109 79 30 137 137 0 strelka-mutect LGR5,missense_variant,p.Ala481Glu,ENST00000266674,NM_003667.3;LGR5,missense_variant,p.Ala457Glu,ENST00000540815,NM_001277226.1;LGR5,missense_variant,p.Ala409Glu,ENST00000536515,NM_001277227.1;RP11-186F10.2,downstream_gene_variant,,ENST00000546601,;LGR5,non_coding_transcript_exon_variant,,ENST00000550851,;LGR5,downstream_gene_variant,,ENST00000547310,; A ENST00000266674 Transcript missense_variant 1753/4611 1442/2724 481/907 A/E gCa/gAa 1 1 LGR5 HGNC HGNC:4504 protein_coding YES CCDS9000.1 ENSP00000266674 O75473 A0A0A8K8C7 UPI000004B65C NM_003667.3 deleterious(0.01) 16/18 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF259 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71580313 71580313 C A 1 0 0 0 0 1 0 0 0 8667 710 25 2 2 LGR5 12 71580313 Missense_Mutation SNP C C3N-00580_T 1020892 71580313 61694996 684 18819 ZFC3H1 0 . GRCh38 12 71614606 71614606 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.5455A>T p.Thr1819Ser p.T1819S ENST00000378743 30/35 148 101 47 158 158 0 strelka-varscan-mutect ZFC3H1,missense_variant,p.Thr1819Ser,ENST00000378743,NM_144982.4;ZFC3H1,missense_variant,p.Thr1819Ser,ENST00000552994,;ZFC3H1,non_coding_transcript_exon_variant,,ENST00000546475,;ZFC3H1,upstream_gene_variant,,ENST00000550963,;ZFC3H1,upstream_gene_variant,,ENST00000551487,;ZFC3H1,upstream_gene_variant,,ENST00000547398,;ZFC3H1,downstream_gene_variant,,ENST00000546771,; A ENST00000378743 Transcript missense_variant 5814/7285 5455/5970 1819/1989 T/S Aca/Tca 1 -1 ZFC3H1 HGNC HGNC:28328 protein_coding YES CCDS41813.1 ENSP00000368017 O60293 UPI00003668E9 NM_144982.4 tolerated(0.19) 30/35 hmmpanther:PTHR21563,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71614606 71614606 T A 1 0 0 0 0 1 0 0 0 18210 1638 57 4 4 ZFC3H1 12 71614606 Missense_Mutation SNP T C3N-00580_T 34293 71614606 61660703 685 18820 NAV3 0 . GRCh38 12 78006672 78006672 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1134C>A p.= p.P378P ENST00000397909 8/40 441 368 73 370 370 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,synonymous_variant,p.=,ENST00000550042,;NAV3,synonymous_variant,p.=,ENST00000550503,;NAV3,downstream_gene_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,; A ENST00000397909 Transcript synonymous_variant 1307/9821 1134/7158 378/2385 P ccC/ccA 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 8/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 78006672 78006672 C A 1 0 0 0 0 0 0 0 1 10194 668 24 2 2 NAV3 12 78006672 Silent SNP C C3N-00580_T 6392066 78006672 55268637 686 18821 OTOGL 0 . GRCh38 12 80339093 80339093 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4852G>T p.Val1618Phe p.V1618F ENST00000458043 42/58 101 63 38 107 107 0 strelka-varscan-mutect OTOGL,missense_variant,p.Val1618Phe,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Val1606Phe,ENST00000547103,;OTOGL,missense_variant,p.Val61Phe,ENST00000298820,;RN7SKP261,downstream_gene_variant,,ENST00000410948,; T ENST00000458043 Transcript missense_variant 4858/8083 4852/7035 1618/2344 V/F Gtt/Ttt 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 tolerated(0.7) 42/58 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Pfam_domain:PF00094,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 80339093 80339093 G T 1 0 0 0 0 1 0 0 0 11371 1377 48 2 2 OTOGL 12 80339093 Missense_Mutation SNP G C3N-00580_T 2332421 80339093 52936216 687 18822 TMTC2 0 . GRCh38 12 82896174 82896174 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1011C>T p.= p.C337C ENST00000321196 3/12 202 136 66 171 171 0 strelka-varscan-mutect TMTC2,synonymous_variant,p.=,ENST00000549919,;TMTC2,synonymous_variant,p.=,ENST00000321196,NM_152588.1;TMTC2,synonymous_variant,p.=,ENST00000548305,NM_001320322.1;TMTC2,3_prime_UTR_variant,,ENST00000546590,NM_001320321.1;TMTC2,non_coding_transcript_exon_variant,,ENST00000551915,; T ENST00000321196 Transcript synonymous_variant 1718/5681 1011/2511 337/836 C tgC/tgT 1 1 TMTC2 HGNC HGNC:25440 protein_coding YES CCDS9025.1 ENSP00000322300 Q8N394 UPI0000073F0F NM_152588.1 3/12 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF390 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 82896174 82896174 C T 1 0 0 0 0 0 0 0 1 16735 718 25 3 3 TMTC2 12 82896174 Silent SNP C C3N-00580_T 2557081 82896174 50379135 688 18823 TSPAN19 0 . GRCh38 12 85029881 85029881 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.66G>T p.Leu22Phe p.L22F ENST00000532498 2/9 59 48 11 48 48 0 strelka-varscan-mutect TSPAN19,missense_variant,p.Leu22Phe,ENST00000532498,NM_001100917.1;TSPAN19,missense_variant,p.Leu22Phe,ENST00000547836,;TSPAN19,intron_variant,,ENST00000547403,;TSPAN19,missense_variant,p.Leu22Phe,ENST00000552392,;TSPAN19,missense_variant,p.Leu22Phe,ENST00000433494,;TSPAN19,splice_region_variant,,ENST00000532628,; A ENST00000532498 Transcript missense_variant,splice_region_variant 147/998 66/747 22/248 L/F ttG/ttT 1 -1 TSPAN19 HGNC HGNC:31886 protein_coding YES CCDS44949.1 ENSP00000433816 P0C672 UPI000003F7BD NM_001100917.1 deleterious(0) 2/9 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR19282:SF211,hmmpanther:PTHR19282,PIRSF_domain:PIRSF002419,Pfam_domain:PF00335,Prints_domain:PR00259 MODERATE 1 SNV 5 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 85029881 85029881 C A 1 0 0 0 0 1 0 0 0 17148 608 21 2 2 TSPAN19 12 85029881 Missense_Mutation SNP C C3N-00580_T 2133707 85029881 48245428 689 18824 C12orf29 0 . GRCh38 12 88046891 88046891 + Missense_Mutation SNP A A G rs750066464 C3N-00580_T C3N-00580_N A A c.704A>G p.Asn235Ser p.N235S ENST00000356891 6/7 102 94 8 146 146 0 strelka-varscan C12orf29,missense_variant,p.Asn235Ser,ENST00000356891,NM_001009894.2;CEP290,downstream_gene_variant,,ENST00000552810,NM_025114.3;CEP290,downstream_gene_variant,,ENST00000309041,;CEP290,downstream_gene_variant,,ENST00000547691,;RNA5SP364,upstream_gene_variant,,ENST00000516938,;C12orf29,non_coding_transcript_exon_variant,,ENST00000548757,;C12orf29,downstream_gene_variant,,ENST00000549345,;C12orf29,3_prime_UTR_variant,,ENST00000550333,;C12orf29,3_prime_UTR_variant,,ENST00000552121,;C12orf29,3_prime_UTR_variant,,ENST00000453037,;C12orf29,non_coding_transcript_exon_variant,,ENST00000548511,;C12orf29,non_coding_transcript_exon_variant,,ENST00000547468,;C12orf29,downstream_gene_variant,,ENST00000552847,;C12orf29,downstream_gene_variant,,ENST00000552803,; G ENST00000356891 Transcript missense_variant 907/2919 704/978 235/325 N/S aAt/aGt rs750066464,COSM1364695 1 1 C12orf29 HGNC HGNC:25322 protein_coding YES CCDS31866.1 ENSP00000349358 Q8N999 UPI000019908D NM_001009894.2 tolerated(0.89) 6/7 hmmpanther:PTHR31219:SF2,hmmpanther:PTHR31219 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 88046891 88046891 A G 1 0 0 0 0 1 0 0 0 1807 101 4 5 5 C12orf29 12 88046891 Missense_Mutation SNP A C3N-00580_T 3017010 88046891 45228418 690 18825 69 2 C12orf29 0 . GRCh38 12 88046901 88046901 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.714G>T p.= p.V238V ENST00000356891 6/7 98 90 8 145 145 0 strelka-varscan C12orf29,synonymous_variant,p.=,ENST00000356891,NM_001009894.2;CEP290,downstream_gene_variant,,ENST00000552810,NM_025114.3;CEP290,downstream_gene_variant,,ENST00000309041,;CEP290,downstream_gene_variant,,ENST00000547691,;RNA5SP364,upstream_gene_variant,,ENST00000516938,;C12orf29,non_coding_transcript_exon_variant,,ENST00000548757,;C12orf29,downstream_gene_variant,,ENST00000549345,;C12orf29,3_prime_UTR_variant,,ENST00000550333,;C12orf29,3_prime_UTR_variant,,ENST00000552121,;C12orf29,3_prime_UTR_variant,,ENST00000453037,;C12orf29,non_coding_transcript_exon_variant,,ENST00000548511,;C12orf29,non_coding_transcript_exon_variant,,ENST00000547468,;C12orf29,downstream_gene_variant,,ENST00000552847,;C12orf29,downstream_gene_variant,,ENST00000552803,; T ENST00000356891 Transcript synonymous_variant 917/2919 714/978 238/325 V gtG/gtT 1 1 C12orf29 HGNC HGNC:25322 protein_coding YES CCDS31866.1 ENSP00000349358 Q8N999 UPI000019908D NM_001009894.2 6/7 hmmpanther:PTHR31219:SF2,hmmpanther:PTHR31219 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 88046901 88046901 G T 1 0 0 0 0 0 0 0 1 1807 1364 48 2 2 C12orf29 12 88046901 Silent SNP G C3N-00580_T 10 88046901 45228408 691 18826 69 2 CCER1 0 . GRCh38 12 90954352 90954352 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.391C>A p.Pro131Thr p.P131T ENST00000358859 1/1 161 95 66 150 150 0 strelka-varscan-mutect CCER1,missense_variant,p.Pro131Thr,ENST00000358859,NM_152638.3;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,; T ENST00000358859 Transcript missense_variant 825/2962 391/1221 131/406 P/T Cct/Act COSM1606744 1 -1 CCER1 HGNC HGNC:28373 protein_coding YES CCDS9036.1 ENSP00000351727 Q8TC90 UPI000006EE70 NM_152638.3 deleterious(0) 1/1 hmmpanther:PTHR37337:SF1,hmmpanther:PTHR37337,Pfam_domain:PF15482 1 MODERATE 1 SNV 1 1 PASS . . 0 205 3 0 2 0 0 0 -20 0.9987803 1 1 1 0 T 3 4 61 90954352 90954352 G T 1 0 0 0 0 1 0 0 0 2574 1232 43 2 2 CCER1 12 90954352 Missense_Mutation SNP G C3N-00580_T 2907451 90954352 42320957 692 18827 TMPO 0 . GRCh38 12 98533699 98533699 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1442A>T p.Gln481Leu p.Q481L ENST00000266732 4/4 679 463 216 645 645 0 strelka-varscan-mutect TMPO,missense_variant,p.Gln481Leu,ENST00000266732,NM_003276.2;TMPO,intron_variant,,ENST00000556029,NM_001032283.2;TMPO,intron_variant,,ENST00000343315,NM_001307975.1;TMPO,intron_variant,,ENST00000393053,NM_001032284.2;TMPO,intron_variant,,ENST00000261210,;TMPO,intron_variant,,ENST00000556678,;TMPO,downstream_gene_variant,,ENST00000547214,;TMPO,downstream_gene_variant,,ENST00000549938,;TMPO,downstream_gene_variant,,ENST00000546828,;TMPO,intron_variant,,ENST00000552831,; T ENST00000266732 Transcript missense_variant 1680/3615 1442/2085 481/694 Q/L cAg/cTg 1 1 TMPO HGNC HGNC:11875 protein_coding YES CCDS9064.1 ENSP00000266732 P42166 UPI000013D709 NM_003276.2 deleterious_low_confidence(0) 4/4 hmmpanther:PTHR12019,hmmpanther:PTHR12019:SF10,Pfam_domain:PF11560 MODERATE 1 SNV 1 1 PASS rs1167615537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 98533699 98533699 A T 1 0 0 0 0 1 0 0 0 16713 188 7 4 4 TMPO 12 98533699 Missense_Mutation SNP A C3N-00580_T 7579347 98533699 34741610 693 18828 ANKS1B 0 . GRCh38 12 99806485 99806485 + Silent SNP C C T rs565638822 C3N-00580_T C3N-00580_N C C c.588G>A p.= p.T196T ENST00000547776 4/26 421 365 56 373 372 1 strelka-varscan-mutect ANKS1B,synonymous_variant,p.=,ENST00000547776,NM_152788.4;ANKS1B,synonymous_variant,p.=,ENST00000549866,;ANKS1B,synonymous_variant,p.=,ENST00000329257,;ANKS1B,intron_variant,,ENST00000547010,; T ENST00000547776 Transcript synonymous_variant 588/3885 588/3747 196/1248 T acG/acA rs565638822,COSM3739361,COSM4661979 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 4/26 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3,SMART_domains:SM00248,Superfamily_domains:SSF48403 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs565638822 . 0 208 0 0 2 0 0 0 -19.99754 0.9961127 1 1 1 0 T 2 4 61 99806485 99806485 C T 1 0 0 0 0 0 0 0 1 795 755 27 1 1 ANKS1B 12 99806485 Silent SNP C C3N-00580_T 1272786 99806485 33468824 694 18829 GNPTAB 0 . GRCh38 12 101764492 101764492 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.2425G>C p.Asp809His p.D809H ENST00000299314 13/21 143 100 43 110 110 0 strelka-varscan-mutect GNPTAB,missense_variant,p.Asp809His,ENST00000299314,NM_024312.4;GNPTAB,downstream_gene_variant,,ENST00000549940,;GNPTAB,upstream_gene_variant,,ENST00000550718,;RNU6-101P,downstream_gene_variant,,ENST00000410323,;GNPTAB,downstream_gene_variant,,ENST00000552009,;GNPTAB,upstream_gene_variant,,ENST00000549194,; G ENST00000299314 Transcript missense_variant 2688/5701 2425/3771 809/1256 D/H Gac/Cac 1 -1 GNPTAB HGNC HGNC:29670 protein_coding YES CCDS9088.1 ENSP00000299314 Q3T906 UPI000004CC0C NM_024312.4 tolerated(0.12) 13/21 Pfam_domain:PF06464,SMART_domains:SM01137 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 101764492 101764492 C G 1 0 0 0 0 1 0 0 0 6424 855 30 4 4 GNPTAB 12 101764492 Missense_Mutation SNP C C3N-00580_T 1958007 101764492 31510817 695 18830 GLT8D2 0 . GRCh38 12 103993392 103993392 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.880G>A p.Gly294Ser p.G294S ENST00000360814 10/11 210 179 31 281 281 0 strelka-varscan-mutect GLT8D2,missense_variant,p.Gly294Ser,ENST00000360814,NM_031302.3;GLT8D2,missense_variant,p.Gly294Ser,ENST00000548660,;GLT8D2,missense_variant,p.Gly294Ser,ENST00000546436,;TDG,downstream_gene_variant,,ENST00000392872,NM_003211.4;GLT8D2,downstream_gene_variant,,ENST00000552572,; T ENST00000360814 Transcript missense_variant,splice_region_variant 1286/1880 880/1050 294/349 G/S Ggc/Agc 1 -1 GLT8D2 HGNC HGNC:24890 protein_coding YES CCDS9096.1 ENSP00000354053 Q9H1C3 UPI000004B633 NM_031302.3 deleterious(0.01) 10/11 Gene3D:3.90.550.10,Pfam_domain:PF01501,hmmpanther:PTHR13778,hmmpanther:PTHR13778:SF2,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 103993392 103993392 C T 1 0 0 0 0 1 0 0 0 6347 637 22 3 3 GLT8D2 12 103993392 Missense_Mutation SNP C C3N-00580_T 2228900 103993392 29281917 696 18831 BTBD11 0 . GRCh38 12 107610322 107610322 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1776G>T p.= p.L592L ENST00000280758 5/17 319 256 63 229 229 0 strelka-varscan-mutect BTBD11,synonymous_variant,p.=,ENST00000280758,NM_001018072.1;BTBD11,synonymous_variant,p.=,ENST00000490090,;BTBD11,synonymous_variant,p.=,ENST00000357167,NM_001017523.1;BTBD11,synonymous_variant,p.=,ENST00000420571,;BTBD11,synonymous_variant,p.=,ENST00000415943,;BTBD11,downstream_gene_variant,,ENST00000550706,;RP11-128P10.1,non_coding_transcript_exon_variant,,ENST00000548473,; T ENST00000280758 Transcript synonymous_variant 2304/5767 1776/3315 592/1104 L ctG/ctT 1 1 BTBD11 HGNC HGNC:23844 protein_coding YES CCDS31893.1 ENSP00000280758 A6QL63 UPI000051901E NM_001018072.1 5/17 Gene3D:1.25.40.20,Superfamily_domains:SSF48403 LOW SNV 5 1 PASS rs1478456203 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 107610322 107610322 G T 1 0 0 0 0 0 0 0 1 1714 1335 47 2 2 BTBD11 12 107610322 Silent SNP G C3N-00580_T 3616930 107610322 25664987 697 18832 SELPLG 0 . GRCh38 12 108623194 108623194 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1162G>T p.Gly388Trp p.G388W ENST00000228463 2/2 113 69 44 102 102 0 strelka-varscan-mutect SELPLG,missense_variant,p.Gly372Trp,ENST00000550948,NM_003006.4;SELPLG,missense_variant,p.Gly388Trp,ENST00000228463,NM_001206609.1;SELPLG,missense_variant,p.Gly362Trp,ENST00000388962,; A ENST00000228463 Transcript missense_variant 1339/1704 1162/1287 388/428 G/W Ggg/Tgg 1 -1 SELPLG HGNC HGNC:10722 protein_coding YES CCDS55881.1 ENSP00000228463 Q14242 UPI0002065776 NM_001206609.1 deleterious(0) 2/2 hmmpanther:PTHR17384,hmmpanther:PTHR17384:SF0 MODERATE 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 108623194 108623194 C A 1 0 0 0 0 1 0 0 0 14297 594 21 2 2 SELPLG 12 108623194 Missense_Mutation SNP C C3N-00580_T 1012872 108623194 24652115 698 18833 IFT81 0 . GRCh38 12 110128048 110128048 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.147A>T p.Gln49His p.Q49H ENST00000242591 3/19 171 141 30 147 147 0 strelka-varscan-mutect IFT81,missense_variant,p.Gln49His,ENST00000242591,NM_014055.3;IFT81,missense_variant,p.Gln49His,ENST00000361948,NM_031473.3;IFT81,missense_variant,p.Gln49His,ENST00000552912,NM_001143779.1;IFT81,missense_variant,p.Gln49His,ENST00000546374,;IFT81,missense_variant,p.Gln19His,ENST00000550156,;IFT81,upstream_gene_variant,,ENST00000551273,; T ENST00000242591 Transcript missense_variant,splice_region_variant 653/3108 147/2031 49/676 Q/H caA/caT 1 1 IFT81 HGNC HGNC:14313 protein_coding YES CCDS41831.1 ENSP00000242591 Q8WYA0 A0A024RBJ1 UPI000000D78F NM_014055.3 tolerated(0.7) 3/19 hmmpanther:PTHR15614,hmmpanther:PTHR15614:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 110128048 110128048 A T 1 0 0 0 0 1 0 0 0 7471 57 2 4 4 IFT81 12 110128048 Missense_Mutation SNP A C3N-00580_T 1504854 110128048 23147261 699 18834 CUX2 0 . GRCh38 12 111310439 111310439 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1657C>A p.Leu553Met p.L553M ENST00000261726 15/22 181 144 37 128 128 0 strelka-varscan-mutect CUX2,missense_variant,p.Leu553Met,ENST00000261726,NM_015267.3; A ENST00000261726 Transcript missense_variant 1811/6844 1657/4461 553/1486 L/M Ctg/Atg 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 tolerated(0.34) 15/22 PROSITE_profiles:PS51042,hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5,Gene3D:1.10.260.40,Pfam_domain:PF02376,SMART_domains:SM01109,Superfamily_domains:SSF47413 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 111310439 111310439 C A 1 0 0 0 0 1 0 0 0 3875 796 28 2 2 CUX2 12 111310439 Missense_Mutation SNP C C3N-00580_T 1182391 111310439 21964870 700 18835 ALDH2 0 . GRCh38 12 111803903 111803903 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1451G>C p.Gly484Ala p.G484A ENST00000261733 12/13 169 136 33 203 203 0 strelka-varscan-mutect ALDH2,missense_variant,p.Gly484Ala,ENST00000261733,NM_000690.3;ALDH2,missense_variant,p.Gly437Ala,ENST00000416293,NM_001204889.1;MIR6761,downstream_gene_variant,,ENST00000617899,;ALDH2,3_prime_UTR_variant,,ENST00000548536,;ALDH2,3_prime_UTR_variant,,ENST00000549106,; C ENST00000261733 Transcript missense_variant 1512/9569 1451/1554 484/517 G/A gGc/gCc 1 1 ALDH2 HGNC HGNC:404 protein_coding YES CCDS9155.1 ENSP00000261733 P05091 UPI0000129293 NM_000690.3 deleterious(0) 12/13 Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF211,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 111803903 111803903 G C 1 0 0 0 0 1 0 0 0 596 1203 42 4 4 ALDH2 12 111803903 Missense_Mutation SNP G C3N-00580_T 493464 111803903 21471406 701 18836 OAS2 0 . GRCh38 12 112987376 112987376 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.516C>A p.= p.L172L ENST00000449768 2/2 65 36 29 45 45 0 strelka-varscan-mutect OAS2,synonymous_variant,p.=,ENST00000449768,NM_001032731.1;OAS2,intron_variant,,ENST00000392583,NM_002535.2;OAS2,intron_variant,,ENST00000342315,NM_016817.2;OAS2,intron_variant,,ENST00000620097,;OAS2,intron_variant,,ENST00000552756,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS2,intron_variant,,ENST00000551603,; A ENST00000449768 Transcript synonymous_variant 643/2072 516/519 172/172 L ctC/ctA 1 1 OAS2 HGNC HGNC:8087 protein_coding CCDS44982.1 ENSP00000411763 P29728 UPI00001BDA97 NM_001032731.1 2/2 LOW SNV 1 1 PASS rs1217498705 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 112987376 112987376 C A 1 0 0 0 0 0 0 0 1 10879 900 32 2 2 OAS2 12 112987376 Silent SNP C C3N-00580_T 1183473 112987376 20287933 702 18837 RASAL1 0 . GRCh38 12 113128180 113128180 + Splice_Site SNP T T A novel C3N-00580_T C3N-00580_N T T c.123-2A>T p.X41_splice ENST00000546530 155 96 59 124 124 0 strelka-varscan-mutect RASAL1,splice_acceptor_variant,,ENST00000546530,NM_001193520.1;RASAL1,splice_acceptor_variant,,ENST00000261729,NM_004658.2;RASAL1,splice_acceptor_variant,,ENST00000446861,NM_001193521.1;RASAL1,splice_acceptor_variant,,ENST00000548055,NM_001301202.1;RASAL1,splice_acceptor_variant,,ENST00000418411,;RASAL1,splice_acceptor_variant,,ENST00000548972,;RASAL1,intron_variant,,ENST00000547810,;RASAL1,splice_acceptor_variant,,ENST00000551051,;RASAL1,splice_acceptor_variant,,ENST00000546727,; A ENST00000546530 Transcript splice_acceptor_variant -/3817 123/2421 41/806 1 -1 RASAL1 HGNC HGNC:9873 protein_coding YES CCDS55889.1 ENSP00000450244 O95294 UPI0001DD37FE NM_001193520.1 3/21 HIGH 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.999999 1 1 1 0 A 5 1 61 113128180 113128180 T A 1 0 0 0 0 0 0 1 0 13224 1594 55 4 4 RASAL1 12 113128180 Splice_Site SNP T C3N-00580_T 140804 113128180 20147129 703 18838 SDS 0 . GRCh38 12 113397287 113397287 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.531C>A p.= p.V177V ENST00000257549 6/8 304 178 126 284 283 1 strelka-varscan-mutect SDS,missense_variant,p.Pro87Thr,ENST00000552280,;SDS,synonymous_variant,p.=,ENST00000257549,NM_006843.2;SDS,downstream_gene_variant,,ENST00000547342,;SDS,non_coding_transcript_exon_variant,,ENST00000553112,;SDS,downstream_gene_variant,,ENST00000546639,;SDS,downstream_gene_variant,,ENST00000546785,; T ENST00000257549 Transcript synonymous_variant 654/1606 531/987 177/328 V gtC/gtA 1 -1 SDS HGNC HGNC:10691 protein_coding YES CCDS9169.1 ENSP00000257549 P20132 UPI000013CF6B NM_006843.2 6/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10314:SF103,hmmpanther:PTHR10314,Pfam_domain:PF00291,Gene3D:3.40.50.1100,Superfamily_domains:SSF53686 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 113397287 113397287 G T 1 0 0 0 0 0 0 0 1 14251 1161 41 2 2 SDS 12 113397287 Silent SNP G C3N-00580_T 269107 113397287 19878022 704 18839 RBM19 0 . GRCh38 12 113957997 113957997 + Missense_Mutation SNP C C A rs757503823 C3N-00580_T C3N-00580_N C C c.625G>T p.Asp209Tyr p.D209Y ENST00000545145 6/25 143 83 60 129 129 0 strelka-varscan-mutect RBM19,missense_variant,p.Asp209Tyr,ENST00000545145,NM_001146699.1;RBM19,missense_variant,p.Asp209Tyr,ENST00000261741,NM_016196.3;RBM19,missense_variant,p.Asp209Tyr,ENST00000392561,NM_001146698.1;RBM19,non_coding_transcript_exon_variant,,ENST00000546876,; A ENST00000545145 Transcript missense_variant 704/4422 625/2883 209/960 D/Y Gat/Tat rs757503823 1 -1 RBM19 HGNC HGNC:29098 protein_coding YES CCDS9172.1 ENSP00000442053 Q9Y4C8 UPI000013D1EC NM_001146699.1 deleterious(0) 6/25 MODERATE 1 SNV 2 1 PASS rs757503823 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 113957997 113957997 C A 1 0 0 0 0 1 0 0 0 13286 855 30 2 2 RBM19 12 113957997 Missense_Mutation SNP C C3N-00580_T 560710 113957997 19317312 705 18840 NOS1 0 . GRCh38 12 117311540 117311540 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.778C>A p.= p.R260R ENST00000618760 3/30 194 108 86 158 158 0 strelka-varscan-mutect NOS1,synonymous_variant,p.=,ENST00000618760,NM_001204218.1;NOS1,synonymous_variant,p.=,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,synonymous_variant,p.=,ENST00000338101,;NOS1,synonymous_variant,p.=,ENST00000344089,; T ENST00000618760 Transcript synonymous_variant 1489/12283 778/4407 260/1468 R Cga/Aga 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 3/30 PIRSF_domain:PIRSF000333 LOW 1 SNV 5 1 PASS rs1245846929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 117311540 117311540 G T 1 0 0 0 0 0 0 0 1 10586 1124 39 1 1 NOS1 12 117311540 Silent SNP G C3N-00580_T 3353543 117311540 15963769 706 18841 SETD1B 0 . GRCh38 12 121827571 121827571 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5261G>T p.Arg1754Leu p.R1754L ENST00000542440 15/18 171 146 25 188 188 0 strelka-varscan-mutect SETD1B,missense_variant,p.Arg1754Leu,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Arg1797Leu,ENST00000604567,;SETD1B,missense_variant,p.Arg1797Leu,ENST00000619791,;SETD1B,missense_variant,p.Arg1754Leu,ENST00000267197,; T ENST00000542440 Transcript missense_variant 5329/8185 5261/5772 1754/1923 R/L cGg/cTg 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 tolerated(0.16) 15/18 Pfam_domain:PF11764,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,Low_complexity_(Seg):seg,SMART_domains:SM01291 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 121827571 121827571 G T 1 0 0 0 0 1 0 0 0 14408 1116 39 1 1 SETD1B 12 121827571 Missense_Mutation SNP G C3N-00580_T 4516031 121827571 11447738 707 18842 VPS33A 0 . GRCh38 12 122232420 122232420 + Silent SNP C C A rs765167095 C3N-00580_T C3N-00580_N C C c.1617G>T p.= p.P539P ENST00000267199 13/13 164 79 85 135 135 0 strelka-varscan-mutect VPS33A,synonymous_variant,p.=,ENST00000267199,NM_022916.4;DIABLO,upstream_gene_variant,,ENST00000443649,NM_019887.5;DIABLO,upstream_gene_variant,,ENST00000485724,;VPS33A,downstream_gene_variant,,ENST00000541169,;DIABLO,upstream_gene_variant,,ENST00000475784,;RP11-512M8.5,synonymous_variant,p.=,ENST00000535844,;VPS33A,3_prime_UTR_variant,,ENST00000543633,; A ENST00000267199 Transcript synonymous_variant 1730/4586 1617/1791 539/596 P ccG/ccT rs765167095 1 -1 VPS33A HGNC HGNC:18179 protein_coding YES CCDS9231.1 ENSP00000267199 Q96AX1 UPI000000D7AA NM_022916.4 13/13 hmmpanther:PTHR11679:SF36,hmmpanther:PTHR11679,Gene3D:3.40.50.1910,Pfam_domain:PF00995,Superfamily_domains:SSF56815 LOW 1 SNV 1 1 PASS rs765167095 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 122232420 122232420 C A 1 0 0 0 0 0 0 0 1 17747 639 23 1 1 VPS33A 12 122232420 Silent SNP C C3N-00580_T 404849 122232420 11042889 708 18843 KMT5A 0 . GRCh38 12 123390732 123390732 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.235C>A p.His79Asn p.H79N ENST00000402868 3/8 397 341 56 450 448 2 strelka-varscan-mutect KMT5A,missense_variant,p.His79Asn,ENST00000402868,NM_020382.3;KMT5A,missense_variant,p.His49Asn,ENST00000330479,;KMT5A,missense_variant,p.His70Asn,ENST00000437502,;KMT5A,non_coding_transcript_exon_variant,,ENST00000478781,;KMT5A,upstream_gene_variant,,ENST00000485469,;KMT5A,downstream_gene_variant,,ENST00000537270,;KMT5A,stop_gained,p.Ser38Ter,ENST00000437519,;KMT5A,non_coding_transcript_exon_variant,,ENST00000461103,;KMT5A,non_coding_transcript_exon_variant,,ENST00000462311,; A ENST00000402868 Transcript missense_variant 661/3140 235/1059 79/352 H/N Cac/Aac 1 1 KMT5A HGNC HGNC:29489 protein_coding YES CCDS9247.1 ENSP00000384629 Q9NQR1 UPI000002B371 NM_020382.3 tolerated(0.06) 3/8 PIRSF_domain:PIRSF027717,PROSITE_profiles:PS51571 MODERATE 1 SNV 1 1 PASS rs1452212440 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 123390732 123390732 C A 1 0 0 0 0 1 0 0 0 8300 826 29 2 2 KMT5A 12 123390732 Missense_Mutation SNP C C3N-00580_T 1158312 123390732 9884577 709 18844 ATP6V0A2 0 . GRCh38 12 123756973 123756973 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.2452A>G p.Ile818Val p.I818V ENST00000330342 19/20 444 407 37 475 475 0 strelka-varscan-mutect ATP6V0A2,missense_variant,p.Ile818Val,ENST00000330342,NM_012463.3;ATP6V0A2,missense_variant,p.Ile98Val,ENST00000534943,;ATP6V0A2,missense_variant,p.Ile100Val,ENST00000544833,;ATP6V0A2,non_coding_transcript_exon_variant,,ENST00000543687,;RP11-338K17.10,upstream_gene_variant,,ENST00000623681,; G ENST00000330342 Transcript missense_variant 2700/6542 2452/2571 818/856 I/V Ata/Gta 1 1 ATP6V0A2 HGNC HGNC:18481 protein_coding YES CCDS9254.1 ENSP00000332247 Q9Y487 UPI00001AFC09 NM_012463.3 deleterious(0.03) 19/20 hmmpanther:PTHR11629:SF22,hmmpanther:PTHR11629,Pfam_domain:PF01496,PIRSF_domain:PIRSF001293 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 123756973 123756973 A G 1 0 0 0 0 1 0 0 0 1322 217 8 5 5 ATP6V0A2 12 123756973 Missense_Mutation SNP A C3N-00580_T 366241 123756973 9518336 710 18845 TMEM132D 0 . GRCh38 12 129700431 129700431 + Missense_Mutation SNP G G T rs777436470 C3N-00580_T C3N-00580_N G G c.347C>A p.Pro116Gln p.P116Q ENST00000422113 2/9 453 362 91 377 377 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Pro116Gln,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; T ENST00000422113 Transcript missense_variant 674/5776 347/3300 116/1099 P/Q cCa/cAa rs777436470 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 tolerated(0.08) 2/9 Pfam_domain:PF15705,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS rs777436470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 129700431 129700431 G T 1 0 0 0 0 1 0 0 0 16492 1348 47 2 2 TMEM132D 12 129700431 Missense_Mutation SNP G C3N-00580_T 5943458 129700431 3574878 711 18846 POLE 0 . GRCh38 12 132672275 132672275 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1734G>T p.Leu578Phe p.L578F ENST00000320574 16/49 322 181 141 372 372 0 strelka-varscan-mutect POLE,missense_variant,p.Leu578Phe,ENST00000320574,NM_006231.3;POLE,missense_variant,p.Leu551Phe,ENST00000535270,;POLE,downstream_gene_variant,,ENST00000539215,;POLE,3_prime_UTR_variant,,ENST00000537064,;POLE,downstream_gene_variant,,ENST00000535934,;POLE,downstream_gene_variant,,ENST00000545015,; A ENST00000320574 Transcript missense_variant 1778/7840 1734/6861 578/2286 L/F ttG/ttT 1 -1 POLE HGNC HGNC:9177 protein_coding YES CCDS9278.1 ENSP00000322570 Q07864 UPI00001FBF97 NM_006231.3 deleterious(0) 16/49 hmmpanther:PTHR10670,SMART_domains:SM00486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 132672275 132672275 C A 1 0 0 0 0 1 0 0 0 12306 709 25 2 2 POLE 12 132672275 Missense_Mutation SNP C C3N-00580_T 2971844 132672275 603034 712 18847 GOLGA3 0 . GRCh38 12 132782323 132782323 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3438G>T p.Glu1146Asp p.E1146D ENST00000204726 17/24 507 305 202 466 464 2 strelka-varscan-mutect GOLGA3,missense_variant,p.Glu1146Asp,ENST00000204726,NM_005895.3;GOLGA3,missense_variant,p.Glu1146Asp,ENST00000450791,;GOLGA3,missense_variant,p.Glu1146Asp,ENST00000456883,;AC127070.1,downstream_gene_variant,,ENST00000545875,NM_001172557.1;GOLGA3,downstream_gene_variant,,ENST00000537452,; A ENST00000204726 Transcript missense_variant 3997/9252 3438/4497 1146/1498 E/D gaG/gaT 1 -1 GOLGA3 HGNC HGNC:4426 protein_coding YES CCDS9281.1 ENSP00000204726 Q08378 UPI0000190979 NM_005895.3 deleterious(0) 17/24 hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF26 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 132782323 132782323 C A 1 0 0 0 0 1 0 0 0 6432 680 24 2 2 GOLGA3 12 132782323 Missense_Mutation SNP C C3N-00580_T 110048 132782323 492986 713 18848 ZNF140 0 . GRCh38 12 133105902 133105902 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.625A>G p.Met209Val p.M209V ENST00000355557 5/5 354 329 25 312 312 0 strelka-varscan-mutect ZNF140,missense_variant,p.Met209Val,ENST00000355557,NM_003440.3;ZNF140,missense_variant,p.Met106Val,ENST00000544426,NM_001300776.1,NM_001300778.1,NM_001300777.1;ZNF140,3_prime_UTR_variant,,ENST00000440550,;ZNF891,downstream_gene_variant,,ENST00000537226,NM_001277291.1;ZNF140,downstream_gene_variant,,ENST00000429434,;ZNF140,downstream_gene_variant,,ENST00000356456,;ZNF140,downstream_gene_variant,,ENST00000319849,;ZNF140,downstream_gene_variant,,ENST00000412146,;ZNF140,3_prime_UTR_variant,,ENST00000536790,;ZNF140,downstream_gene_variant,,ENST00000392041,; G ENST00000355557 Transcript missense_variant 1908/3550 625/1374 209/457 M/V Atg/Gtg 1 1 ZNF140 HGNC HGNC:12925 protein_coding YES CCDS9282.1 ENSP00000347755 P52738 UPI0000074687 NM_003440.3 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF36,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 133105902 133105902 A G 1 0 0 0 0 1 0 0 0 18310 101 4 5 5 ZNF140 12 133105902 Missense_Mutation SNP A C3N-00580_T 323579 133105902 169407 714 18849 KBTBD7 0 . GRCh38 13 41193232 41193232 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.1026C>G p.= p.A342A ENST00000379483 1/1 263 229 34 297 297 0 varscan-mutect KBTBD7,synonymous_variant,p.=,ENST00000379483,NM_032138.4;RP11-74J13.8,intron_variant,,ENST00000619407,;RP11-74J13.8,downstream_gene_variant,,ENST00000615685,; C ENST00000379483 Transcript synonymous_variant 1335/4734 1026/2055 342/684 A gcC/gcG 1 -1 KBTBD7 HGNC HGNC:25266 protein_coding YES CCDS9377.1 ENSP00000368797 Q8WVZ9 UPI0000071F8F NM_032138.4 1/1 hmmpanther:PTHR24412:SF132,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 41193232 41193232 G C 1 0 0 0 0 0 0 0 1 7914 1335 47 4 4 KBTBD7 13 41193232 Silent SNP G C3N-00580_T 41193232 73171096 715 18850 KLHL1 0 . GRCh38 13 69961338 69961338 + Missense_Mutation SNP G G C C3N-00580_T C3N-00580_N G G c.787C>G p.Leu263Val p.L263V ENST00000377844 3/11 182 77 105 187 187 0 strelka-varscan-mutect KLHL1,missense_variant,p.Leu263Val,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Leu202Val,ENST00000545028,NM_001286725.1; C ENST00000377844 Transcript missense_variant 1547/4115 787/2247 263/748 L/V Ctc/Gtc COSM4854261 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 deleterious(0.02) 3/11 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 69961338 69961338 G C 1 0 0 0 0 1 0 0 0 8229 942 33 4 4 KLHL1 13 69961338 Missense_Mutation SNP G C3N-00580_T 28768106 69961338 44402990 716 18851 TGDS 0 . GRCh38 13 94581166 94581166 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.480A>G p.= p.K160K ENST00000261296 6/12 122 48 74 229 229 0 strelka-varscan-mutect TGDS,synonymous_variant,p.=,ENST00000261296,NM_001304430.1,NM_014305.3;TGDS,non_coding_transcript_exon_variant,,ENST00000498294,;TGDS,non_coding_transcript_exon_variant,,ENST00000470480,; C ENST00000261296 Transcript synonymous_variant 601/1905 480/1053 160/350 K aaA/aaG 1 -1 TGDS HGNC HGNC:20324 protein_coding YES CCDS9471.1 ENSP00000261296 O95455 UPI000006E8F4 NM_001304430.1,NM_014305.3 6/12 hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF41,Pfam_domain:PF16363,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 94581166 94581166 T C 1 0 0 0 0 0 0 0 1 16247 1722 60 5 5 TGDS 13 94581166 Silent SNP T C3N-00580_T 24619828 94581166 19783162 717 18852 DZIP1 0 . GRCh38 13 95641672 95641672 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.220G>T p.Ala74Ser p.A74S ENST00000347108 3/21 148 67 81 154 154 0 strelka-varscan-mutect DZIP1,missense_variant,p.Ala74Ser,ENST00000361396,NM_014934.4;DZIP1,missense_variant,p.Ala74Ser,ENST00000347108,;DZIP1,missense_variant,p.Ala74Ser,ENST00000361156,;DZIP1,missense_variant,p.Ala74Ser,ENST00000376829,NM_198968.3;DZIP1,non_coding_transcript_exon_variant,,ENST00000466027,;DZIP1,missense_variant,p.Ala120Ser,ENST00000466569,; A ENST00000347108 Transcript missense_variant 653/7068 220/2604 74/867 A/S Gcc/Tcc 1 -1 DZIP1 HGNC HGNC:20908 protein_coding YES CCDS9478.1 ENSP00000257312 Q86YF9 UPI000000D9B8 deleterious(0.04) 3/21 hmmpanther:PTHR21502,hmmpanther:PTHR21502:SF5,Pfam_domain:PF13815 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 95641672 95641672 C A 1 0 0 0 0 1 0 0 0 4687 768 27 1 1 DZIP1 13 95641672 Missense_Mutation SNP C C3N-00580_T 1060506 95641672 18722656 718 18853 ITGBL1 0 . GRCh38 13 101453937 101453937 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.153C>A p.Cys51Ter p.C51* ENST00000376180 2/11 76 30 46 66 66 0 strelka-varscan-mutect ITGBL1,stop_gained,p.Cys51Ter,ENST00000376180,NM_004791.2;ITGBL1,stop_gained,p.Cys51Ter,ENST00000618057,NM_001271755.1;ITGBL1,intron_variant,,ENST00000545560,NM_001271754.1;ITGBL1,intron_variant,,ENST00000622834,; A ENST00000376180 Transcript stop_gained 372/2494 153/1485 51/494 C/* tgC/tgA 1 1 ITGBL1 HGNC HGNC:6164 protein_coding YES CCDS9499.1 ENSP00000365351 O95965 A0A024RDW7 UPI0000073C95 NM_004791.2 2/11 HIGH 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 4 1 61 101453937 101453937 C A 1 0 0 0 0 0 1 0 0 7808 747 26 2 2 ITGBL1 13 101453937 Nonsense_Mutation SNP C C3N-00580_T 5812265 101453937 12910391 719 18854 OR4K15 0 . GRCh38 14 19976001 19976001 + Missense_Mutation SNP C C A rs373552565 C3N-00580_T C3N-00580_N C C c.483C>A p.Ser161Arg p.S161R ENST00000305051 1/1 352 241 111 334 334 0 strelka-varscan-mutect OR4K15,missense_variant,p.Ser161Arg,ENST00000305051,NM_001005486.1; A ENST00000305051 Transcript missense_variant 558/1216 483/1047 161/348 S/R agC/agA rs373552565 1 1 OR4K15 HGNC HGNC:15353 protein_coding YES CCDS32026.1 ENSP00000304077 Q8NH41 UPI000015F249 NM_001005486.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF287,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs373552565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 19976001 19976001 C A 1 0 0 0 0 1 0 0 0 11147 738 26 2 2 OR4K15 14 19976001 Missense_Mutation SNP C C3N-00580_T 19976001 87067717 720 18855 OR4K17 0 . GRCh38 14 20117837 20117837 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.431T>A p.Val144Glu p.V144E ENST00000315543 1/1 338 214 124 259 259 0 strelka-varscan-mutect OR4K17,missense_variant,p.Val144Glu,ENST00000315543,NM_001004715.1; A ENST00000315543 Transcript missense_variant 431/1032 431/1032 144/343 V/E gTa/gAa 1 1 OR4K17 HGNC HGNC:15355 protein_coding YES CCDS32030.1 ENSP00000319197 Q8NGC6 A0A126GVZ4 UPI000004B1EA NM_001004715.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF322,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1333529363 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 20117837 20117837 T A 1 0 0 0 0 1 0 0 0 11148 1638 57 4 4 OR4K17 14 20117837 Missense_Mutation SNP T C3N-00580_T 141836 20117837 86925881 721 18856 OR4N5 0 . GRCh38 14 20144253 20144253 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.518A>T p.Gln173Leu p.Q173L ENST00000333629 1/1 410 361 49 340 339 1 strelka-varscan-mutect OR4N5,missense_variant,p.Gln173Leu,ENST00000333629,NM_001004724.1;PSMB7P1,upstream_gene_variant,,ENST00000556349,; T ENST00000333629 Transcript missense_variant 518/927 518/927 173/308 Q/L cAg/cTg 1 1 OR4N5 HGNC HGNC:15358 protein_coding YES CCDS32031.1 ENSP00000332110 Q8IXE1 A0A126GVN4 UPI0000041C40 NM_001004724.1 tolerated(0.25) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF40,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1388585514 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20144253 20144253 A T 1 0 0 0 0 1 0 0 0 11155 188 7 4 4 OR4N5 14 20144253 Missense_Mutation SNP A C3N-00580_T 26416 20144253 86899465 722 18857 PARP2 0 . GRCh38 14 20351084 20351084 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.498A>T p.= p.S166S ENST00000250416 6/16 241 183 58 217 217 0 strelka-varscan-mutect PARP2,synonymous_variant,p.=,ENST00000527915,;PARP2,synonymous_variant,p.=,ENST00000250416,NM_005484.3;PARP2,synonymous_variant,p.=,ENST00000429687,NM_001042618.1;PARP2,upstream_gene_variant,,ENST00000539930,;RP11-203M5.2,upstream_gene_variant,,ENST00000528210,;PARP2,upstream_gene_variant,,ENST00000555140,;PARP2,non_coding_transcript_exon_variant,,ENST00000528465,;PARP2,intron_variant,,ENST00000529465,;PARP2,upstream_gene_variant,,ENST00000532299,;PARP2,upstream_gene_variant,,ENST00000530598,;PARP2,upstream_gene_variant,,ENST00000534664,;PARP2,upstream_gene_variant,,ENST00000527384,; T ENST00000250416 Transcript synonymous_variant 525/1886 498/1752 166/583 S tcA/tcT 1 1 PARP2 HGNC HGNC:272 protein_coding YES CCDS41910.1 ENSP00000250416 Q9UGN5 UPI0000035DCA NM_005484.3 6/16 hmmpanther:PTHR10459:SF41,hmmpanther:PTHR10459,Gene3D:2ra8A01,Pfam_domain:PF05406,SMART_domains:SM00773,Superfamily_domains:0052256 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 20351084 20351084 A T 1 0 0 0 0 0 0 0 1 11541 175 7 4 4 PARP2 14 20351084 Silent SNP A C3N-00580_T 206831 20351084 86692634 723 18858 TEP1 0 . GRCh38 14 20408303 20408303 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.137C>G p.Ser46Cys p.S46C ENST00000262715 2/55 451 403 48 418 418 0 strelka-varscan-mutect TEP1,missense_variant,p.Ser46Cys,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Ser46Cys,ENST00000556935,;TEP1,missense_variant,p.Ser46Cys,ENST00000556549,;TEP1,missense_variant,p.Ser46Cys,ENST00000555727,;TEP1,upstream_gene_variant,,ENST00000557627,; C ENST00000262715 Transcript missense_variant 178/10695 137/7884 46/2627 S/C tCc/tGc 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 deleterious_low_confidence(0) 2/55 PROSITE_profiles:PS51226,Pfam_domain:PF05386 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 20408303 20408303 G C 1 0 0 0 0 1 0 0 0 16175 1174 41 4 4 TEP1 14 20408303 Missense_Mutation SNP G C3N-00580_T 57219 20408303 86635415 724 18859 MMP14 0 . GRCh38 14 22844728 22844728 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1249G>T p.Ala417Ser p.A417S ENST00000311852 8/10 362 272 90 347 346 1 strelka-varscan-mutect MMP14,missense_variant,p.Ala417Ser,ENST00000311852,NM_004995.3;MMP14,downstream_gene_variant,,ENST00000548761,;MMP14,non_coding_transcript_exon_variant,,ENST00000548162,;MMP14,downstream_gene_variant,,ENST00000547596,;MMP14,downstream_gene_variant,,ENST00000547074,; T ENST00000311852 Transcript missense_variant 1510/3732 1249/1749 417/582 A/S Gct/Tct 1 1 MMP14 HGNC HGNC:7160 protein_coding YES CCDS9577.1 ENSP00000308208 P50281 UPI0000048136 NM_004995.3 tolerated(0.18) 8/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201:SF24,hmmpanther:PTHR10201,Gene3D:2.110.10.10,Pfam_domain:PF00045,PIRSF_domain:PIRSF001191,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 22844728 22844728 G T 1 0 0 0 0 1 0 0 0 9616 1319 46 2 2 MMP14 14 22844728 Missense_Mutation SNP G C3N-00580_T 2436425 22844728 84198990 725 18860 MYH6 0 . GRCh38 14 23397027 23397027 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2104G>T p.Glu702Ter p.E702* ENST00000405093 18/39 722 480 242 554 552 2 strelka-varscan-mutect MYH6,stop_gained,p.Glu702Ter,ENST00000405093,NM_002471.3;MYH6,stop_gained,p.Glu702Ter,ENST00000356287,;MYH6,downstream_gene_variant,,ENST00000557461,; A ENST00000405093 Transcript stop_gained 2175/5941 2104/5820 702/1939 E/* Gag/Tag 1 -1 MYH6 HGNC HGNC:7576 protein_coding YES CCDS9600.1 ENSP00000386041 P13533 UPI0000160969 NM_002471.3 18/39 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 23397027 23397027 C A 1 0 0 0 0 0 1 0 0 10038 864 30 2 2 MYH6 14 23397027 Nonsense_Mutation SNP C C3N-00580_T 552299 23397027 83646691 726 18861 CARMIL3 0 . GRCh38 14 24060668 24060668 + Missense_Mutation SNP G G T rs774706113 C3N-00580_T C3N-00580_N G G c.2102G>T p.Arg701Leu p.R701L ENST00000342740 25/40 225 176 49 174 174 0 strelka-varscan-mutect CARMIL3,missense_variant,p.Arg701Leu,ENST00000342740,NM_138360.3;CARMIL3,non_coding_transcript_exon_variant,,ENST00000559694,;CARMIL3,upstream_gene_variant,,ENST00000560349,;CARMIL3,upstream_gene_variant,,ENST00000561354,; T ENST00000342740 Transcript missense_variant 2256/4597 2102/4119 701/1372 R/L cGg/cTg rs774706113,COSM5268622 1 1 CARMIL3 HGNC HGNC:20272 protein_coding YES CCDS32054.1 ENSP00000340467 Q8ND23 UPI0000DBEF11 NM_138360.3 tolerated(0.14) 25/40 hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF43 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs774706113 . 0 207 0 3 0 0 0 0 -20 0.999997 1 1 1 0 T 3 4 61 24060668 24060668 G T 1 0 0 0 0 1 0 0 0 2353 1116 39 1 1 CARMIL3 14 24060668 Missense_Mutation SNP G C3N-00580_T 663641 24060668 82983050 727 18862 IRF9 0 . GRCh38 14 24163094 24163094 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.309G>A p.Met103Ile p.M103I ENST00000396864 3/9 265 148 117 299 299 0 strelka-varscan-mutect IRF9,start_lost,p.Met1?,ENST00000557894,;IRF9,missense_variant,p.Met103Ile,ENST00000396864,NM_006084.4;IRF9,missense_variant,p.Met103Ile,ENST00000560275,;IRF9,missense_variant,p.Met33Ile,ENST00000324076,;IRF9,missense_variant,p.Met103Ile,ENST00000559284,;RNF31,downstream_gene_variant,,ENST00000324103,NM_017999.4;RNF31,downstream_gene_variant,,ENST00000559275,NM_001310332.1;RNF31,downstream_gene_variant,,ENST00000560787,;RNF31,downstream_gene_variant,,ENST00000559719,;RNA5SP383,downstream_gene_variant,,ENST00000362934,;RP11-468E2.4,3_prime_UTR_variant,,ENST00000558468,;IRF9,3_prime_UTR_variant,,ENST00000561342,;IRF9,3_prime_UTR_variant,,ENST00000560852,;IRF9,non_coding_transcript_exon_variant,,ENST00000561415,;IRF9,non_coding_transcript_exon_variant,,ENST00000560365,;IRF9,non_coding_transcript_exon_variant,,ENST00000561009,;RNF31,downstream_gene_variant,,ENST00000559071,;RNF31,downstream_gene_variant,,ENST00000491351,;IRF9,upstream_gene_variant,,ENST00000560542,;RNF31,downstream_gene_variant,,ENST00000559449,;RNF31,downstream_gene_variant,,ENST00000483895,;IRF9,upstream_gene_variant,,ENST00000560311,;IRF9,downstream_gene_variant,,ENST00000561412,;IRF9,upstream_gene_variant,,ENST00000559863,;IRF9,upstream_gene_variant,,ENST00000559229,;RNF31,downstream_gene_variant,,ENST00000559491,;RNF31,downstream_gene_variant,,ENST00000560631,; A ENST00000396864 Transcript missense_variant 596/1838 309/1182 103/393 M/I atG/atA 1 1 IRF9 HGNC HGNC:6131 protein_coding YES CCDS9615.1 ENSP00000380073 Q00978 UPI000012D8C2 NM_006084.4 tolerated(0.07) 3/9 Gene3D:1.10.10.10,Pfam_domain:PF00605,PROSITE_profiles:PS51507,hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF26,SMART_domains:SM00348,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 24163094 24163094 G A 1 0 0 0 0 1 0 0 0 7744 1348 47 3 3 IRF9 14 24163094 Missense_Mutation SNP G C3N-00580_T 102426 24163094 82880624 728 18863 SCFD1 0 . GRCh38 14 30628259 30628259 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.112A>T p.Thr38Ser p.T38S ENST00000458591 2/25 129 115 14 154 154 0 strelka-varscan-mutect SCFD1,missense_variant,p.Thr38Ser,ENST00000458591,NM_016106.3;SCFD1,missense_variant,p.Thr13Ser,ENST00000557076,;SCFD1,intron_variant,,ENST00000544052,NM_182835.2;SCFD1,intron_variant,,ENST00000396629,NM_001283032.1,NM_001283033.1,NM_001283031.1,NM_001257376.1;SCFD1,intron_variant,,ENST00000553693,;SCFD1,missense_variant,p.Thr38Ser,ENST00000311943,;SCFD1,missense_variant,p.Thr38Ser,ENST00000463622,;SCFD1,missense_variant,p.Thr38Ser,ENST00000556768,;SCFD1,missense_variant,p.Thr38Ser,ENST00000555259,;SCFD1,missense_variant,p.Thr18Ser,ENST00000554776,;SCFD1,missense_variant,p.Thr13Ser,ENST00000557713,;SCFD1,non_coding_transcript_exon_variant,,ENST00000556413,;SCFD1,intron_variant,,ENST00000484733,; T ENST00000458591 Transcript missense_variant 339/2359 112/1929 38/642 T/S Aca/Tca 1 1 SCFD1 HGNC HGNC:20726 protein_coding YES CCDS9639.1 ENSP00000390783 Q8WVM8 UPI000013C6E3 NM_016106.3 tolerated(0.79) 2/25 Gene3D:3.40.50.2060,PIRSF_domain:PIRSF005715,hmmpanther:PTHR11679,hmmpanther:PTHR11679:SF2,Superfamily_domains:SSF56815 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 30628259 30628259 A T 1 0 0 0 0 1 0 0 0 14155 159 6 4 4 SCFD1 14 30628259 Missense_Mutation SNP A C3N-00580_T 6465165 30628259 76415459 729 18864 SEC23A 0 . GRCh38 14 39091536 39091536 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.544G>T p.Gly182Cys p.G182C ENST00000307712 5/20 582 315 267 384 383 1 strelka-varscan-mutect SEC23A,missense_variant,p.Gly182Cys,ENST00000307712,NM_006364.2;SEC23A,missense_variant,p.Gly153Cys,ENST00000545328,;SEC23A,upstream_gene_variant,,ENST00000537403,;SEC23A,downstream_gene_variant,,ENST00000548032,;SEC23A,downstream_gene_variant,,ENST00000555017,;SEC23A,downstream_gene_variant,,ENST00000557437,;SEC23A,downstream_gene_variant,,ENST00000553970,;SEC23A,downstream_gene_variant,,ENST00000556092,;SEC23A,downstream_gene_variant,,ENST00000557280,;SEC23A,downstream_gene_variant,,ENST00000555425,;SEC23A,downstream_gene_variant,,ENST00000625395,;SEC23A,non_coding_transcript_exon_variant,,ENST00000555682,;RP11-545M17.2,downstream_gene_variant,,ENST00000554037,; A ENST00000307712 Transcript missense_variant 1062/4135 544/2298 182/765 G/C Ggc/Tgc 1 -1 SEC23A HGNC HGNC:10701 protein_coding YES CCDS9668.1 ENSP00000306881 Q15436 UPI000013EC46 NM_006364.2 deleterious(0.03) 5/20 Gene3D:3.40.50.410,Pfam_domain:PF04811,hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF7,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39091536 39091536 C A 1 0 0 0 0 1 0 0 0 14268 681 24 2 2 SEC23A 14 39091536 Missense_Mutation SNP C C3N-00580_T 8463277 39091536 67952182 730 18865 LRFN5 0 . GRCh38 14 41891511 41891511 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.1647G>T p.Met549Ile p.M549I ENST00000298119 4/6 351 272 79 382 382 0 strelka-varscan-mutect LRFN5,missense_variant,p.Met549Ile,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; T ENST00000298119 Transcript missense_variant 2836/3723 1647/2160 549/719 M/I atG/atT COSM5066241,COSM5545248 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 tolerated(0.13) 4/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1333055470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 41891511 41891511 G T 1 0 0 0 0 1 0 0 0 8835 1290 45 2 2 LRFN5 14 41891511 Missense_Mutation SNP G C3N-00580_T 2799975 41891511 65152207 731 18866 LRFN5 0 . GRCh38 14 41891780 41891780 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1916T>A p.Val639Glu p.V639E ENST00000298119 4/6 338 263 75 423 423 0 strelka-varscan-mutect LRFN5,missense_variant,p.Val639Glu,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; A ENST00000298119 Transcript missense_variant 3105/3723 1916/2160 639/719 V/E gTg/gAg 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 tolerated_low_confidence(1) 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 41891780 41891780 T A 1 0 0 0 0 1 0 0 0 8835 1696 59 4 4 LRFN5 14 41891780 Missense_Mutation SNP T C3N-00580_T 269 41891780 65151938 732 18867 FAM179B 0 . GRCh38 14 45068565 45068565 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4891G>T p.Asp1631Tyr p.D1631Y ENST00000361462 18/20 257 191 66 228 228 0 strelka-varscan-mutect FAM179B,missense_variant,p.Asp1631Tyr,ENST00000361462,NM_001308120.1;FAM179B,missense_variant,p.Asp1578Tyr,ENST00000361577,NM_015091.2;FAM179B,missense_variant,p.Asp42Tyr,ENST00000556823,;FAM179B,3_prime_UTR_variant,,ENST00000557423,; T ENST00000361462 Transcript missense_variant 5074/6375 4891/5322 1631/1773 D/Y Gat/Tat 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 deleterious(0) 18/20 Gene3D:1.25.10.10,hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6,SMART_domains:SM01349,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 45068565 45068565 G T 1 0 0 0 0 1 0 0 0 5351 1174 41 2 2 FAM179B 14 45068565 Missense_Mutation SNP G C3N-00580_T 3176785 45068565 61975153 733 18868 PTGDR 0 . GRCh38 14 52268503 52268503 + Missense_Mutation SNP G G T rs201265894 C3N-00580_T C3N-00580_N G G c.689G>T p.Arg230Leu p.R230L ENST00000306051 1/2 237 188 49 184 184 0 strelka-varscan-mutect PTGDR,missense_variant,p.Arg230Leu,ENST00000306051,NM_000953.2;PTGDR,missense_variant,p.Arg230Leu,ENST00000553372,NM_001281469.1; T ENST00000306051 Transcript missense_variant 791/2942 689/1080 230/359 R/L cGg/cTg rs201265894,COSM3769460 1 1 PTGDR HGNC HGNC:9591 protein_coding YES CCDS9707.1 ENSP00000303424 Q13258 UPI000000D994 NM_000953.2 deleterious(0.03) 1/2 PROSITE_profiles:PS50262,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF14,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201265894 . 0 205 0 4 0 0 0 0 -20 0.9999546 1 1 1 0 T 3 4 61 52268503 52268503 G T 1 0 0 0 0 1 0 0 0 12894 1116 39 1 1 PTGDR 14 52268503 Missense_Mutation SNP G C3N-00580_T 7199938 52268503 54775215 734 18869 RTN1 0 . GRCh38 14 59727212 59727212 + Missense_Mutation SNP T T G C3N-00580_T C3N-00580_N T T c.1472A>C p.Lys491Thr p.K491T ENST00000267484 3/9 98 93 5 60 60 0 strelka-mutect RTN1,missense_variant,p.Lys491Thr,ENST00000267484,NM_021136.2;RTN1,missense_variant,p.Lys417Thr,ENST00000611068,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,; G ENST00000267484 Transcript missense_variant 1808/3435 1472/2331 491/776 K/T aAg/aCg COSM1264644 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 deleterious(0) 3/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.60843 0.9999999 1 1 1 0 G 3 3 61 59727212 59727212 T G 1 0 0 0 0 1 0 0 0 13985 1609 56 5 5 RTN1 14 59727212 Missense_Mutation SNP T C3N-00580_T 7458709 59727212 47316506 735 18870 SNAPC1 0 . GRCh38 14 61794970 61794970 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1094G>T p.Arg365Met p.R365M ENST00000216294 10/10 66 37 29 90 90 0 strelka-varscan-mutect SNAPC1,missense_variant,p.Arg365Met,ENST00000216294,NM_003082.3; T ENST00000216294 Transcript missense_variant 1198/2656 1094/1107 365/368 R/M aGg/aTg 1 1 SNAPC1 HGNC HGNC:11134 protein_coding YES CCDS9755.1 ENSP00000216294 Q16533 UPI0000000DEB NM_003082.3 deleterious(0) 10/10 hmmpanther:PTHR15131,hmmpanther:PTHR15131:SF3 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 61794970 61794970 G T 1 0 0 0 0 1 0 0 0 15155 1000 35 2 2 SNAPC1 14 61794970 Missense_Mutation SNP G C3N-00580_T 2067758 61794970 45248748 736 18871 KCNH5 0 . GRCh38 14 62707944 62707944 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.2531C>T p.Pro844Leu p.P844L ENST00000322893 11/11 357 273 84 221 221 0 strelka-varscan-mutect KCNH5,missense_variant,p.Pro844Leu,ENST00000322893,NM_139318.4;KCNH5,3_prime_UTR_variant,,ENST00000420622,NM_172375.2;KCNH5,downstream_gene_variant,,ENST00000394968,; A ENST00000322893 Transcript missense_variant 2800/11290 2531/2967 844/988 P/L cCc/cTc 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 tolerated_low_confidence(0.07) 11/11 hmmpanther:PTHR10217:SF533,hmmpanther:PTHR10217 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 62707944 62707944 G A 1 0 0 0 0 1 0 0 0 7951 1232 43 3 3 KCNH5 14 62707944 Missense_Mutation SNP G C3N-00580_T 912974 62707944 44335774 737 18872 SLC10A1 0 . GRCh38 14 69786253 69786253 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.411C>A p.= p.L137L ENST00000216540 2/5 441 342 99 518 518 0 strelka-varscan-mutect SLC10A1,synonymous_variant,p.=,ENST00000216540,NM_003049.3; T ENST00000216540 Transcript synonymous_variant 545/2049 411/1050 137/349 L ctC/ctA COSM5292853 1 -1 SLC10A1 HGNC HGNC:10905 protein_coding YES CCDS9797.1 ENSP00000216540 Q14973 UPI0000130576 NM_003049.3 2/5 Pfam_domain:PF01758,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF40,TIGRFAM_domain:TIGR00841,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS rs1299364646 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 69786253 69786253 G T 1 0 0 0 0 0 0 0 1 14638 1161 41 2 2 SLC10A1 14 69786253 Silent SNP G C3N-00580_T 7078309 69786253 37257465 738 18873 ADAM21 0 . GRCh38 14 70458790 70458790 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1291G>C p.Asp431His p.D431H ENST00000603540 2/2 462 355 107 461 461 0 strelka-varscan-mutect ADAM21,missense_variant,p.Asp431His,ENST00000603540,NM_003813.3;RP11-486O13.4,intron_variant,,ENST00000556646,; C ENST00000603540 Transcript missense_variant 1549/2658 1291/2169 431/722 D/H Gac/Cac 1 1 ADAM21 HGNC HGNC:200 protein_coding YES CCDS9804.1 ENSP00000474385 Q9UKJ8 UPI000013D756 NM_003813.3 deleterious(0.02) 2/2 PROSITE_profiles:PS50214,hmmpanther:PTHR11905:SF116,hmmpanther:PTHR11905,Pfam_domain:PF00200,SMART_domains:SM00050,Superfamily_domains:SSF57552 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 70458790 70458790 G C 1 0 0 0 0 1 0 0 0 287 942 33 4 4 ADAM21 14 70458790 Missense_Mutation SNP G C3N-00580_T 672537 70458790 36584928 739 18874 PCNX1 0 . GRCh38 14 71109476 71109476 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.6769G>C p.Glu2257Gln p.E2257Q ENST00000304743 35/36 201 144 57 144 144 0 strelka-varscan-mutect PCNX1,missense_variant,p.Glu2257Gln,ENST00000304743,NM_014982.2;PCNX1,missense_variant,p.Glu2146Gln,ENST00000439984,NM_001308160.1;PCNX1,missense_variant,p.Glu1244Gln,ENST00000554691,;PCNX1,missense_variant,p.Glu18Gln,ENST00000555780,;PCNX1,non_coding_transcript_exon_variant,,ENST00000556272,; C ENST00000304743 Transcript missense_variant 7215/12919 6769/7026 2257/2341 E/Q Gaa/Caa 1 1 PCNX1 HGNC HGNC:19740 protein_coding YES CCDS9806.1 ENSP00000304192 Q96RV3 UPI000013E9BB NM_014982.2 deleterious_low_confidence(0.01) 35/36 hmmpanther:PTHR12372:SF2,hmmpanther:PTHR12372 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 71109476 71109476 G C 1 0 0 0 0 1 0 0 0 11679 1175 41 4 4 PCNX1 14 71109476 Missense_Mutation SNP G C3N-00580_T 650686 71109476 35934242 740 18875 SIPA1L1 0 . GRCh38 14 71588265 71588265 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.393G>T p.Met131Ile p.M131I ENST00000555818 2/22 424 292 132 351 351 0 strelka-varscan-mutect SIPA1L1,missense_variant,p.Met131Ile,ENST00000555818,NM_015556.2,NM_001284247.1;SIPA1L1,missense_variant,p.Met131Ile,ENST00000358550,NM_001284246.1;SIPA1L1,missense_variant,p.Met131Ile,ENST00000381232,NM_001284245.1;SIPA1L1,downstream_gene_variant,,ENST00000557151,;SIPA1L1,downstream_gene_variant,,ENST00000555989,;SIPA1L1,downstream_gene_variant,,ENST00000554362,;SIPA1L1,downstream_gene_variant,,ENST00000555652,; T ENST00000555818 Transcript missense_variant 741/7831 393/5415 131/1804 M/I atG/atT 1 1 SIPA1L1 HGNC HGNC:20284 protein_coding YES CCDS9807.1 ENSP00000450832 O43166 UPI00000443CB NM_015556.2,NM_001284247.1 tolerated(0.28) 2/22 hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 71588265 71588265 G T 1 0 0 0 0 1 0 0 0 14592 1319 46 2 2 SIPA1L1 14 71588265 Missense_Mutation SNP G C3N-00580_T 478789 71588265 35455453 741 18876 YLPM1 0 . GRCh38 14 74780452 74780452 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.1158A>T p.= p.A386A ENST00000325680 3/21 143 112 31 127 127 0 strelka-varscan-mutect YLPM1,synonymous_variant,p.=,ENST00000325680,NM_019589.2;YLPM1,synonymous_variant,p.=,ENST00000552421,;YLPM1,upstream_gene_variant,,ENST00000549293,; T ENST00000325680 Transcript synonymous_variant 1282/7108 1158/6441 386/2146 A gcA/gcT 1 1 YLPM1 HGNC HGNC:17798 protein_coding YES CCDS45135.1 ENSP00000324463 P49750 UPI00006C1433 NM_019589.2 3/21 Low_complexity_(Seg):seg,hmmpanther:PTHR13413:SF0,hmmpanther:PTHR13413 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 74780452 74780452 A T 1 0 0 0 0 0 0 0 1 18048 175 7 4 4 YLPM1 14 74780452 Silent SNP A C3N-00580_T 3192187 74780452 32263266 742 18877 ESRRB 0 . GRCh38 14 76482701 76482701 + Silent SNP C C T C3N-00580_T C3N-00580_N C C c.729C>T p.= p.L243L ENST00000509242 5/9 318 228 90 328 328 0 strelka-varscan-mutect ESRRB,synonymous_variant,p.=,ENST00000509242,;ESRRB,synonymous_variant,p.=,ENST00000380887,NM_004452.3;ESRRB,synonymous_variant,p.=,ENST00000512784,;ESRRB,synonymous_variant,p.=,ENST00000556177,;ESRRB,downstream_gene_variant,,ENST00000507951,;ESRRB,synonymous_variant,p.=,ENST00000505752,; T ENST00000509242 Transcript synonymous_variant 937/2849 729/1527 243/508 L ctC/ctT COSM1587624,COSM958057 1 1 ESRRB HGNC HGNC:3473 protein_coding YES CCDS9850.2 ENSP00000422488 O95718 UPI000003157B 5/9 Gene3D:1.10.565.10,Pfam_domain:PF00104,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF23,Superfamily_domains:SSF48508 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 76482701 76482701 C T 1 0 0 0 0 0 0 0 1 5123 900 32 3 3 ESRRB 14 76482701 Silent SNP C C3N-00580_T 1702249 76482701 30561017 743 18878 TDP1 0 . GRCh38 14 90043080 90043080 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1764G>T p.Trp588Cys p.W588C ENST00000335725 17/17 592 426 166 594 593 1 strelka-varscan-mutect TDP1,missense_variant,p.Trp588Cys,ENST00000335725,NM_018319.3;TDP1,missense_variant,p.Trp588Cys,ENST00000393454,NM_001008744.1;TDP1,missense_variant,p.Gly552Val,ENST00000555880,;TDP1,3_prime_UTR_variant,,ENST00000393452,;TDP1,3_prime_UTR_variant,,ENST00000554976,;TDP1,3_prime_UTR_variant,,ENST00000545686,;TDP1,3_prime_UTR_variant,,ENST00000555178,; T ENST00000335725 Transcript missense_variant 2014/3702 1764/1827 588/608 W/C tgG/tgT 1 1 TDP1 HGNC HGNC:18884 protein_coding YES CCDS9888.1 ENSP00000337353 Q9NUW8 A0A024R6L5 UPI00000737ED NM_018319.3 deleterious(0) 17/17 Gene3D:3.30.870.20,hmmpanther:PTHR12415,hmmpanther:PTHR12415:SF0,Superfamily_domains:SSF56024 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 90043080 90043080 G T 1 0 0 0 0 1 0 0 0 16136 1183 41 2 2 TDP1 14 90043080 Missense_Mutation SNP G C3N-00580_T 13560379 90043080 17000638 744 18879 GPR68 0 . GRCh38 14 91234764 91234764 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.287T>C p.Val96Ala p.V96A ENST00000531499 2/2 206 165 41 261 261 0 strelka-varscan-mutect GPR68,missense_variant,p.Val96Ala,ENST00000531499,NM_003485.3;GPR68,missense_variant,p.Val96Ala,ENST00000535815,NM_001177676.1;GPR68,missense_variant,p.Val96Ala,ENST00000529102,;GPR68,downstream_gene_variant,,ENST00000529300,; G ENST00000531499 Transcript missense_variant 627/2859 287/1098 96/365 V/A gTg/gCg 1 -1 GPR68 HGNC HGNC:4519 protein_coding YES CCDS9894.2 ENSP00000434045 Q15743 UPI000005042A NM_003485.3 deleterious(0) 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24234:SF5,hmmpanther:PTHR24234,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01564 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 91234764 91234764 A G 1 0 0 0 0 1 0 0 0 6590 159 6 5 5 GPR68 14 91234764 Missense_Mutation SNP A C3N-00580_T 1191684 91234764 15808954 745 18880 SERPINA11 0 . GRCh38 14 94442648 94442648 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.1227C>G p.Ser409Arg p.S409R ENST00000334708 5/5 166 113 53 196 196 0 strelka-varscan-mutect SERPINA11,missense_variant,p.Ser409Arg,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; C ENST00000334708 Transcript missense_variant 1292/1476 1227/1269 409/422 S/R agC/agG 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 deleterious(0) 5/5 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS rs1321900897 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 94442648 94442648 G C 1 0 0 0 0 1 0 0 0 14364 962 34 4 4 SERPINA11 14 94442648 Missense_Mutation SNP G C3N-00580_T 3207884 94442648 12601070 746 18881 YY1 0 . GRCh38 14 100262452 100262452 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.828G>T p.= p.L276L ENST00000262238 2/5 304 240 64 303 302 1 strelka-varscan-mutect YY1,synonymous_variant,p.=,ENST00000262238,NM_003403.4;YY1,synonymous_variant,p.=,ENST00000554804,;YY1,synonymous_variant,p.=,ENST00000553625,;RP11-638I2.2,upstream_gene_variant,,ENST00000555212,; T ENST00000262238 Transcript synonymous_variant 1088/6697 828/1245 276/414 L ctG/ctT 1 1 YY1 HGNC HGNC:12856 protein_coding YES CCDS9957.1 ENSP00000262238 P25490 UPI00001378FC NM_003403.4 2/5 PIRSF_domain:PIRSF037113,hmmpanther:PTHR14003,hmmpanther:PTHR14003:SF10 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 100262452 100262452 G T 1 0 0 0 0 0 0 0 1 18068 1335 47 2 2 YY1 14 100262452 Silent SNP G C3N-00580_T 5819804 100262452 6781266 747 18882 DYNC1H1 0 . GRCh38 14 102034348 102034348 + Frame_Shift_Del DEL G G - rs143068719 C3N-00580_T C3N-00580_N G G c.10651delG p.Glu3551AsnfsTer30 p.E3551Nfs*30 ENST00000360184 56/78 630 450 180 786 786 0 sindel-varindel-pindel DYNC1H1,frameshift_variant,p.Glu3551AsnfsTer30,ENST00000360184,NM_001376.4;DYNC1H1,frameshift_variant,p.Glu27AsnfsTer30,ENST00000553423,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557551,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557242,;RP11-1017G21.4,downstream_gene_variant,,ENST00000553701,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000556791,;DYNC1H1,downstream_gene_variant,,ENST00000554854,;DYNC1H1,upstream_gene_variant,,ENST00000555800,; - ENST00000360184 Transcript frameshift_variant 10814/14333 10650/13941 3550/4646 T/X acG/ac rs143068719 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 56/78 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 102034348 102034348 G - 1 0 1 0 1 0 0 0 0 4665 1103 39 0 0 DYNC1H1 14 102034348 Frame_Shift_Del DEL G C3N-00580_T 1771896 102034348 5009370 748 18883 TNFAIP2 0 . GRCh38 14 103127118 103127118 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.349G>T p.Glu117Ter p.E117* ENST00000560869 3/12 18 10 8 36 36 0 strelka-varscan-mutect TNFAIP2,stop_gained,p.Glu117Ter,ENST00000560869,;TNFAIP2,stop_gained,p.Glu117Ter,ENST00000333007,NM_006291.2;TNFAIP2,upstream_gene_variant,,ENST00000560670,;TNFAIP2,downstream_gene_variant,,ENST00000558056,;LINC00677,upstream_gene_variant,,ENST00000558224,;LINC00677,upstream_gene_variant,,ENST00000560742,;TNFAIP2,intron_variant,,ENST00000559195,;TNFAIP2,intron_variant,,ENST00000559406,;TNFAIP2,intron_variant,,ENST00000560562,;TNFAIP2,upstream_gene_variant,,ENST00000560428,;TNFAIP2,upstream_gene_variant,,ENST00000561156,; T ENST00000560869 Transcript stop_gained 988/4683 349/1965 117/654 E/* Gag/Tag 1 1 TNFAIP2 HGNC HGNC:11895 protein_coding YES CCDS9979.1 ENSP00000452634 Q03169 UPI0000164A41 3/12 Low_complexity_(Seg):seg,hmmpanther:PTHR21292:SF4,hmmpanther:PTHR21292 HIGH SNV 5 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 103127118 103127118 G T 1 0 0 0 0 0 1 0 0 16747 1175 41 2 2 TNFAIP2 14 103127118 Nonsense_Mutation SNP G C3N-00580_T 1092770 103127118 3916600 749 18884 CEP170B 0 . GRCh38 14 104894336 104894336 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.4323C>G p.Ile1441Met p.I1441M ENST00000414716 17/19 340 262 78 478 478 0 strelka-varscan-mutect CEP170B,missense_variant,p.Ile1477Met,ENST00000453495,;CEP170B,missense_variant,p.Ile1441Met,ENST00000414716,NM_001112726.2;CEP170B,missense_variant,p.Ile1406Met,ENST00000556508,NM_015005.2;CEP170B,non_coding_transcript_exon_variant,,ENST00000251181,; G ENST00000414716 Transcript missense_variant 4551/6705 4323/4665 1441/1554 I/M atC/atG 1 1 CEP170B HGNC HGNC:20362 protein_coding YES CCDS45175.1 ENSP00000404151 Q9Y4F5 UPI00001FDCF7 NM_001112726.2 deleterious(0.04) 17/19 Pfam_domain:PF15308,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 104894336 104894336 C G 1 0 0 0 0 1 0 0 0 2965 816 29 4 4 CEP170B 14 104894336 Missense_Mutation SNP C C3N-00580_T 1767218 104894336 2149382 750 18885 CEP170B 0 . GRCh38 14 104894910 104894910 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.4617C>T p.= p.S1539S ENST00000414716 19/19 131 91 40 153 153 0 strelka-varscan-mutect CEP170B,synonymous_variant,p.=,ENST00000453495,;CEP170B,synonymous_variant,p.=,ENST00000414716,NM_001112726.2;CEP170B,synonymous_variant,p.=,ENST00000556508,NM_015005.2;CEP170B,non_coding_transcript_exon_variant,,ENST00000251181,; T ENST00000414716 Transcript synonymous_variant 4845/6705 4617/4665 1539/1554 S agC/agT 1 1 CEP170B HGNC HGNC:20362 protein_coding YES CCDS45175.1 ENSP00000404151 Q9Y4F5 UPI00001FDCF7 NM_001112726.2 19/19 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 61 104894910 104894910 C T 1 0 0 0 0 0 0 0 1 2965 738 26 3 3 CEP170B 14 104894910 Silent SNP C C3N-00580_T 574 104894910 2148808 751 18886 RP11-294C11.3 0 . GRCh38 15 21652484 21652484 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.550G>T p.Val184Phe p.V184F ENST00000623441 1/1 25 19 6 46 46 0 strelka-varscan-mutect RP11-294C11.3,missense_variant,p.Val184Phe,ENST00000623441,;RP11-294C11.3,missense_variant,p.Val79Phe,ENST00000629333,;RP11-983G14.1,non_coding_transcript_exon_variant,,ENST00000628444,; T ENST00000623441 Transcript missense_variant 641/1125 550/951 184/316 V/F Gtc/Ttc 1 1 RP11-294C11.3 Clone_based_vega_gene protein_coding YES ENSP00000485668 A0A096LPK9 UPI000514C5E0 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF97,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 47 161 2 0 0 0 0 0 -17.20961 1 1 1 1 0 T 3 4 61 21652484 21652484 G T 1 0 0 0 0 1 0 0 0 13727 1261 44 2 2 RP11-294C11.3 15 21652484 Missense_Mutation SNP G C3N-00580_T 21652484 80338705 752 18887 MAGEL2 0 . GRCh38 15 23647261 23647261 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.482A>T p.His161Leu p.H161L ENST00000532292 1/1 75 53 22 126 126 0 strelka-varscan-mutect MAGEL2,missense_variant,p.His161Leu,ENST00000532292,NM_019066.4; A ENST00000532292 Transcript missense_variant 581/4298 482/3750 161/1249 H/L cAt/cTt 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 tolerated_low_confidence(0.11) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 23647261 23647261 T A 1 0 0 0 0 1 0 0 0 9107 1464 51 4 4 MAGEL2 15 23647261 Missense_Mutation SNP T C3N-00580_T 1994777 23647261 78343928 753 18888 NPAP1 0 . GRCh38 15 24676611 24676611 + Frame_Shift_Del DEL T T - rs764952896 C3N-00580_T C3N-00580_N T T c.744delT p.Cys248TrpfsTer34 p.C248Wfs*34 ENST00000329468 1/1 105 73 32 142 142 0 sindel-varindel-pindel NPAP1,frameshift_variant,p.Cys248TrpfsTer34,ENST00000329468,NM_018958.2; - ENST00000329468 Transcript frameshift_variant 744/7526 744/3471 248/1156 C/X tgT/tg rs764952896 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229 HIGH 1 deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 24676611 24676611 T - 1 0 1 0 1 0 0 0 0 10609 1702 59 0 0 NPAP1 15 24676611 Frame_Shift_Del DEL T C3N-00580_T 1029350 24676611 77314578 754 18889 HERC2 0 . GRCh38 15 28233486 28233486 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.4427C>A p.Ser1476Ter p.S1476* ENST00000261609 29/93 157 144 13 183 183 0 varscan-mutect HERC2,stop_gained,p.Ser1476Ter,ENST00000261609,NM_004667.5;HERC2,upstream_gene_variant,,ENST00000569335,; T ENST00000261609 Transcript stop_gained 4536/15337 4427/14505 1476/4834 S/* tCa/tAa 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 29/93 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 28233486 28233486 G T 1 0 0 0 0 0 1 0 0 6942 1294 45 2 2 HERC2 15 28233486 Nonsense_Mutation SNP G C3N-00580_T 3556875 28233486 73757703 755 18890 ARHGAP11A 0 . GRCh38 15 32637811 32637811 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.3038A>T p.Gln1013Leu p.Q1013L ENST00000361627 12/12 62 43 19 67 67 0 strelka-varscan-mutect ARHGAP11A,missense_variant,p.Gln1013Leu,ENST00000361627,NM_014783.4;ARHGAP11A,missense_variant,p.Gln824Leu,ENST00000565905,NM_001286479.1;ARHGAP11A,missense_variant,p.Gln824Leu,ENST00000543522,NM_001286480.1;ARHGAP11A,downstream_gene_variant,,ENST00000567348,NM_199357.1;ARHGAP11A,downstream_gene_variant,,ENST00000563864,;SCG5,upstream_gene_variant,,ENST00000300175,NM_001144757.1;SCG5,upstream_gene_variant,,ENST00000413748,NM_003020.3;SCG5,upstream_gene_variant,,ENST00000494364,;SCG5,upstream_gene_variant,,ENST00000497208,;ARHGAP11A,downstream_gene_variant,,ENST00000562481,;ARHGAP11A,downstream_gene_variant,,ENST00000564918,; T ENST00000361627 Transcript missense_variant 3760/5898 3038/3072 1013/1023 Q/L cAa/cTa 1 1 ARHGAP11A HGNC HGNC:15783 protein_coding YES CCDS10028.1 ENSP00000355090 Q6P4F7 UPI0000071553 NM_014783.4 deleterious(0.01) 12/12 hmmpanther:PTHR15670:SF5,hmmpanther:PTHR15670 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 32637811 32637811 A T 1 0 0 0 0 1 0 0 0 987 130 5 4 4 ARHGAP11A 15 32637811 Missense_Mutation SNP A C3N-00580_T 4404325 32637811 69353378 756 18891 EXD1 0 . GRCh38 15 41184448 41184448 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1202A>T p.Glu401Val p.E401V ENST00000458580 12/12 161 147 14 263 263 0 strelka-varscan-mutect EXD1,missense_variant,p.Glu343Val,ENST00000314992,NM_152596.3;EXD1,missense_variant,p.Glu401Val,ENST00000458580,NM_001286441.1;EXD1,non_coding_transcript_exon_variant,,ENST00000558881,; A ENST00000458580 Transcript missense_variant 1468/2177 1202/1719 401/572 E/V gAg/gTg 1 -1 EXD1 HGNC HGNC:28507 protein_coding YES CCDS66738.1 ENSP00000415056 Q8NHP7 UPI000191512C NM_001286441.1 tolerated(0.09) 12/12 hmmpanther:PTHR12124,hmmpanther:PTHR12124:SF42 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -19.22772 0.9999998 1 1 1 0 A 3 1 61 41184448 41184448 T A 1 0 0 0 0 1 0 0 0 5164 1551 54 4 4 EXD1 15 41184448 Missense_Mutation SNP T C3N-00580_T 8546637 41184448 60806741 757 18892 CDAN1 0 . GRCh38 15 42735661 42735661 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.792G>T p.Gln264His p.Q264H ENST00000356231 4/28 260 148 112 381 381 0 strelka-varscan-mutect CDAN1,missense_variant,p.Gln264His,ENST00000356231,NM_138477.2;TTBK2,downstream_gene_variant,,ENST00000267890,NM_173500.3;CDAN1,downstream_gene_variant,,ENST00000563260,;CTD-2036P10.3,upstream_gene_variant,,ENST00000567456,;CDAN1,upstream_gene_variant,,ENST00000562465,; A ENST00000356231 Transcript missense_variant 816/4637 792/3684 264/1227 Q/H caG/caT 1 -1 CDAN1 HGNC HGNC:1713 protein_coding YES CCDS32209.1 ENSP00000348564 Q8IWY9 UPI0000229BCB NM_138477.2 tolerated(0.15) 4/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR28678 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 42735661 42735661 C A 1 0 0 0 0 1 0 0 0 2757 564 20 2 2 CDAN1 15 42735661 Missense_Mutation SNP C C3N-00580_T 1551213 42735661 59255528 758 18893 ATP8B4 0 . GRCh38 15 49866485 49866485 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.3028-1G>T p.X1010_splice ENST00000284509 81 48 33 111 111 0 strelka-varscan-mutect ATP8B4,splice_acceptor_variant,,ENST00000284509,NM_024837.3;ATP8B4,splice_acceptor_variant,,ENST00000559829,;ATP8B4,splice_acceptor_variant,,ENST00000558498,;ATP8B4,splice_acceptor_variant,,ENST00000560479,;ATP8B4,splice_acceptor_variant,,ENST00000559726,;ATP8B4,splice_acceptor_variant,,ENST00000558906,;ATP8B4,splice_acceptor_variant,,ENST00000557955,;ATP8B4,splice_acceptor_variant,,ENST00000558203,;ATP8B4,splice_acceptor_variant,,ENST00000560354,; A ENST00000284509 Transcript splice_acceptor_variant -/5676 3028/3579 1010/1192 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 25/27 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 49866485 49866485 C A 1 0 0 0 0 0 0 1 0 1350 927 32 2 2 ATP8B4 15 49866485 Splice_Site SNP C C3N-00580_T 7130824 49866485 52124704 759 18894 TRPM7 0 . GRCh38 15 50580909 50580909 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.4558-1G>T p.X1520_splice ENST00000313478 26 21 5 61 61 0 strelka-mutect TRPM7,splice_acceptor_variant,,ENST00000313478,NM_017672.5;TRPM7,splice_acceptor_variant,,ENST00000560955,NM_001301212.1;TRPM7,splice_acceptor_variant,,ENST00000561443,;TRPM7,splice_acceptor_variant,,ENST00000560849,;TRPM7,splice_acceptor_variant,,ENST00000558444,; A ENST00000313478 Transcript splice_acceptor_variant -/10400 4558/5598 1520/1865 1 -1 TRPM7 HGNC HGNC:17994 protein_coding YES CCDS42035.1 ENSP00000320239 Q96QT4 A0A024R5V1 UPI0000071CBA NM_017672.5 29/38 HIGH 1 SNV 1 1 PASS . . 0 193 14 2 0 0 0 0 -11.70693 0.9979671 1 1 1 0 A 5 1 61 50580909 50580909 C A 1 0 0 0 0 0 0 1 0 17097 695 24 2 2 TRPM7 15 50580909 Splice_Site SNP C C3N-00580_T 714424 50580909 51410280 760 18895 DMXL2 0 . GRCh38 15 51450265 51450265 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.8768G>T p.Gly2923Val p.G2923V ENST00000543779 42/43 413 242 171 447 447 0 strelka-varscan-mutect DMXL2,missense_variant,p.Gly2922Val,ENST00000251076,NM_015263.3;DMXL2,missense_variant,p.Gly2923Val,ENST00000543779,NM_001174116.1;DMXL2,missense_variant,p.Gly2286Val,ENST00000449909,NM_001174117.1;DMXL2,missense_variant,p.Gly1069Val,ENST00000560891,;DMXL2,3_prime_UTR_variant,,ENST00000559059,;RP11-707P17.1,intron_variant,,ENST00000561007,;DMXL2,non_coding_transcript_exon_variant,,ENST00000559769,;DMXL2,downstream_gene_variant,,ENST00000559868,; A ENST00000543779 Transcript missense_variant 8858/10400 8768/9114 2923/3037 G/V gGa/gTa 1 -1 DMXL2 HGNC HGNC:2938 protein_coding YES CCDS53946.1 ENSP00000441858 Q8TDJ6 UPI00001FE4C2 NM_001174116.1 deleterious(0) 42/43 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF11,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 51450265 51450265 C A 1 0 0 0 0 1 0 0 0 4404 855 30 2 2 DMXL2 15 51450265 Missense_Mutation SNP C C3N-00580_T 869356 51450265 50540924 761 18896 UNC13C 0 . GRCh38 15 54322054 54322054 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.4384C>A p.Gln1462Lys p.Q1462K ENST00000260323 13/32 138 100 38 206 206 0 strelka-varscan-mutect UNC13C,missense_variant,p.Gln1462Lys,ENST00000260323,NM_001080534.1;UNC13C,non_coding_transcript_exon_variant,,ENST00000561210,;HNRNPA1P74,upstream_gene_variant,,ENST00000560782,; A ENST00000260323 Transcript missense_variant 4384/12946 4384/6645 1462/2214 Q/K Cag/Aag 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 tolerated_low_confidence(0.24) 13/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 54322054 54322054 C A 1 0 0 0 0 1 0 0 0 17510 479 17 2 2 UNC13C 15 54322054 Missense_Mutation SNP C C3N-00580_T 2871789 54322054 47669135 762 18897 PRTG 0 . GRCh38 15 55627039 55627039 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2896G>T p.Val966Phe p.V966F ENST00000389286 17/20 138 128 10 164 164 0 strelka-varscan-mutect PRTG,missense_variant,p.Val966Phe,ENST00000389286,NM_173814.5; A ENST00000389286 Transcript missense_variant 2944/11967 2896/3453 966/1150 V/F Gtt/Ttt 1 -1 PRTG HGNC HGNC:26373 protein_coding YES CCDS42040.1 ENSP00000373937 Q2VWP7 UPI00001555A7 NM_173814.5 deleterious(0.02) 17/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF661,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 55627039 55627039 C A 1 0 0 0 0 1 0 0 0 12788 478 17 2 2 PRTG 15 55627039 Missense_Mutation SNP C C3N-00580_T 1304985 55627039 46364150 763 18898 LIPC 0 . GRCh38 15 58563503 58563503 + Splice_Site SNP A A T rs770068099 C3N-00580_T C3N-00580_N A A c.1170-2A>T p.X390_splice ENST00000299022 279 165 114 355 355 0 strelka-varscan-mutect LIPC,splice_acceptor_variant,,ENST00000414170,;LIPC,splice_acceptor_variant,,ENST00000299022,NM_000236.2;LIPC,splice_acceptor_variant,,ENST00000356113,;LIPC,splice_acceptor_variant,,ENST00000433326,;LIPC,splice_acceptor_variant,,ENST00000559845,; T ENST00000299022 Transcript splice_acceptor_variant -/2751 1170/1500 390/499 rs770068099 1 1 LIPC HGNC HGNC:6619 protein_coding YES CCDS10166.1 ENSP00000299022 P11150 UPI000013E54D NM_000236.2 7/8 HIGH 1 SNV 1 1 PASS rs770068099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 58563503 58563503 A T 1 0 0 0 0 0 0 1 0 8741 86 3 4 4 LIPC 15 58563503 Splice_Site SNP A C3N-00580_T 2936464 58563503 43427686 764 18899 MYO9A 0 . GRCh38 15 71898733 71898733 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3770G>T p.Arg1257Ile p.R1257I ENST00000356056 25/42 170 97 73 188 188 0 strelka-varscan-mutect MYO9A,missense_variant,p.Arg1257Ile,ENST00000356056,NM_006901.3;MYO9A,missense_variant,p.Arg1257Ile,ENST00000564571,;MYO9A,missense_variant,p.Arg1257Ile,ENST00000444904,;MYO9A,missense_variant,p.Arg877Ile,ENST00000566885,;MYO9A,missense_variant,p.Arg36Ile,ENST00000561618,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,upstream_gene_variant,,ENST00000568781,; A ENST00000356056 Transcript missense_variant 4243/12411 3770/7647 1257/2548 R/I aGa/aTa 1 -1 MYO9A HGNC HGNC:7608 protein_coding YES CCDS10239.1 ENSP00000348349 B2RTY4 UPI000013D213 NM_006901.3 deleterious_low_confidence(0) 25/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71898733 71898733 C A 1 0 0 0 0 1 0 0 0 10085 913 32 2 2 MYO9A 15 71898733 Missense_Mutation SNP C C3N-00580_T 13335230 71898733 30092456 765 18900 BBS4 0 . GRCh38 15 72712243 72712243 + Splice_Site SNP G G T novel C3N-00580_T C3N-00580_N G G c.157-1G>T p.X53_splice ENST00000268057 235 131 104 318 316 2 strelka-varscan-mutect BBS4,splice_acceptor_variant,,ENST00000268057,NM_033028.4;BBS4,splice_acceptor_variant,,ENST00000395205,NM_001252678.1;BBS4,splice_acceptor_variant,,ENST00000569338,;BBS4,splice_acceptor_variant,,ENST00000566829,;BBS4,splice_acceptor_variant,,ENST00000564239,;BBS4,upstream_gene_variant,,ENST00000569001,;BBS4,splice_acceptor_variant,,ENST00000566400,;BBS4,splice_acceptor_variant,,ENST00000567279,;BBS4,splice_acceptor_variant,,ENST00000562084,;BBS4,splice_acceptor_variant,,ENST00000561914,;BBS4,splice_acceptor_variant,,ENST00000565160,;BBS4,splice_acceptor_variant,,ENST00000569440,;BBS4,splice_acceptor_variant,,ENST00000566938,;BBS4,splice_acceptor_variant,,ENST00000563600,; T ENST00000268057 Transcript splice_acceptor_variant -/2490 157/1560 53/519 1 1 BBS4 HGNC HGNC:969 protein_coding YES CCDS10246.1 ENSP00000268057 Q96RK4 A0A0S2Z3A9 UPI000013D78E NM_033028.4 3/15 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 61 72712243 72712243 G T 1 0 0 0 0 0 0 1 0 1486 1014 35 2 2 BBS4 15 72712243 Splice_Site SNP G C3N-00580_T 813510 72712243 29278946 766 18901 LMAN1L 0 . GRCh38 15 74816443 74816443 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.347G>T p.Arg116Leu p.R116L ENST00000309664 3/14 23 11 12 44 44 0 strelka-varscan-mutect LMAN1L,missense_variant,p.Arg116Leu,ENST00000309664,NM_021819.2;LMAN1L,missense_variant,p.Arg116Leu,ENST00000379709,;LMAN1L,missense_variant,p.Arg72Leu,ENST00000562810,;LMAN1L,upstream_gene_variant,,ENST00000567848,;RP11-414J4.2,non_coding_transcript_exon_variant,,ENST00000488000,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000470711,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000568467,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000570147,;LMAN1L,intron_variant,,ENST00000456603,;RP11-414J4.2,upstream_gene_variant,,ENST00000564823,;LMAN1L,upstream_gene_variant,,ENST00000565585,; T ENST00000309664 Transcript missense_variant 486/1873 347/1581 116/526 R/L cGg/cTg COSM3672115 1 1 LMAN1L HGNC HGNC:6632 protein_coding YES CCDS10270.1 ENSP00000310431 Q9HAT1 UPI00001AEF1F NM_021819.2 tolerated(0.07) 3/14 Gene3D:2.60.120.200,Pfam_domain:PF03388,PROSITE_profiles:PS51328,hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF31,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS rs1366395705 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 74816443 74816443 G T 1 0 0 0 0 1 0 0 0 8761 1116 39 1 1 LMAN1L 15 74816443 Missense_Mutation SNP G C3N-00580_T 2104200 74816443 27174746 767 18902 SCAMP2 0 . GRCh38 15 74852086 74852086 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.326C>G p.Thr109Ser p.T109S ENST00000268099 4/9 55 33 22 114 114 0 strelka-varscan-mutect SCAMP2,missense_variant,p.Thr69Ser,ENST00000566480,;SCAMP2,missense_variant,p.Thr109Ser,ENST00000268099,NM_005697.3;SCAMP2,missense_variant,p.Thr152Ser,ENST00000564529,;SCAMP2,missense_variant,p.Thr86Ser,ENST00000562363,;SCAMP2,5_prime_UTR_variant,,ENST00000565345,;SCAMP2,missense_variant,p.Thr109Ser,ENST00000569904,;SCAMP2,non_coding_transcript_exon_variant,,ENST00000563829,;SCAMP2,non_coding_transcript_exon_variant,,ENST00000569251,;SCAMP2,non_coding_transcript_exon_variant,,ENST00000567638,;SCAMP2,non_coding_transcript_exon_variant,,ENST00000566557,;SCAMP2,intron_variant,,ENST00000563663,;SCAMP2,downstream_gene_variant,,ENST00000569124,; C ENST00000268099 Transcript missense_variant 436/2453 326/990 109/329 T/S aCt/aGt 1 -1 SCAMP2 HGNC HGNC:10564 protein_coding YES CCDS10271.1 ENSP00000268099 O15127 A0A140VK92 UPI00001355FD NM_005697.3 tolerated(0.85) 4/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10687,hmmpanther:PTHR10687:SF7 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 74852086 74852086 G C 1 0 0 0 0 1 0 0 0 14138 1029 36 4 4 SCAMP2 15 74852086 Missense_Mutation SNP G C3N-00580_T 35643 74852086 27139103 768 18903 CSPG4 0 . GRCh38 15 75689732 75689732 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1333G>T p.Ala445Ser p.A445S ENST00000308508 3/10 155 132 23 285 285 0 strelka-varscan-mutect CSPG4,missense_variant,p.Ala445Ser,ENST00000308508,NM_001897.4; A ENST00000308508 Transcript missense_variant 1426/8290 1333/6969 445/2322 A/S Gcc/Tcc 1 -1 CSPG4 HGNC HGNC:2466 protein_coding YES CCDS10284.1 ENSP00000312506 Q6UVK1 UPI00001AEEB6 NM_001897.4 deleterious(0) 3/10 hmmpanther:PTHR15036,hmmpanther:PTHR15036:SF16 MODERATE 1 SNV 1 1 PASS rs1386480849 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 75689732 75689732 C A 1 0 0 0 0 1 0 0 0 3761 797 28 2 2 CSPG4 15 75689732 Missense_Mutation SNP C C3N-00580_T 837646 75689732 26301457 769 18904 FES 0 . GRCh38 15 90887259 90887259 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.557A>G p.Tyr186Cys p.Y186C ENST00000328850 5/19 155 137 18 189 189 0 strelka-varscan-mutect FES,missense_variant,p.Tyr186Cys,ENST00000328850,NM_002005.3;FES,missense_variant,p.Tyr128Cys,ENST00000414248,NM_001143785.1;FES,missense_variant,p.Tyr128Cys,ENST00000394300,NM_001143783.1;FES,missense_variant,p.Tyr186Cys,ENST00000444422,NM_001143784.1;FES,missense_variant,p.Tyr128Cys,ENST00000394302,;FURIN,downstream_gene_variant,,ENST00000618099,NM_001289824.1;FURIN,downstream_gene_variant,,ENST00000268171,NM_002569.3;FURIN,downstream_gene_variant,,ENST00000610579,NM_001289823.1;FES,downstream_gene_variant,,ENST00000452243,;FES,downstream_gene_variant,,ENST00000559355,;FES,downstream_gene_variant,,ENST00000443697,;FES,downstream_gene_variant,,ENST00000416779,;FES,upstream_gene_variant,,ENST00000448367,;FES,missense_variant,p.Tyr186Cys,ENST00000464684,;FES,3_prime_UTR_variant,,ENST00000470152,;FES,non_coding_transcript_exon_variant,,ENST00000497945,;FES,upstream_gene_variant,,ENST00000496379,;FES,downstream_gene_variant,,ENST00000481665,;FES,upstream_gene_variant,,ENST00000494259,;FES,upstream_gene_variant,,ENST00000462476,; G ENST00000328850 Transcript missense_variant 699/2829 557/2469 186/822 Y/C tAt/tGt 1 1 FES HGNC HGNC:3657 protein_coding YES CCDS10365.1 ENSP00000331504 P07332 A0A024RC92 UPI0000001C30 NM_002005.3 deleterious(0) 5/19 PROSITE_profiles:PS51741,hmmpanther:PTHR24418:SF197,hmmpanther:PTHR24418,PIRSF_domain:PIRSF000632,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 90887259 90887259 A G 1 0 0 0 0 1 0 0 0 5683 449 16 5 5 FES 15 90887259 Missense_Mutation SNP A C3N-00580_T 15197527 90887259 11103930 770 18905 SNRPA1 0 . GRCh38 15 101292029 101292029 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.242A>T p.Glu81Val p.E81V ENST00000254193 3/9 188 176 12 311 311 0 varscan-mutect SNRPA1,missense_variant,p.Glu81Val,ENST00000254193,NM_003090.2;SNRPA1,missense_variant,p.Glu81Val,ENST00000626000,;SNRPA1,5_prime_UTR_variant,,ENST00000560496,;SNRPA1,upstream_gene_variant,,ENST00000559686,;RP11-299G20.2,upstream_gene_variant,,ENST00000558838,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560856,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560987,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000558020,;SNRPA1,intron_variant,,ENST00000394082,;SNRPA1,intron_variant,,ENST00000540017,;SNRPA1,missense_variant,p.Glu81Val,ENST00000559309,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000558036,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000558059,;SNRPA1,intron_variant,,ENST00000560383,;SNRPA1,upstream_gene_variant,,ENST00000560433,;SNRPA1,downstream_gene_variant,,ENST00000561187,; A ENST00000254193 Transcript missense_variant 315/1055 242/768 81/255 E/V gAg/gTg 1 -1 SNRPA1 HGNC HGNC:11152 protein_coding YES CCDS10391.1 ENSP00000254193 P09661 UPI000006DD72 NM_003090.2 deleterious(0.02) 3/9 PROSITE_profiles:PS51450,hmmpanther:PTHR10552,Gene3D:3.80.10.10,Pfam_domain:PF14580,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -15.41515 0.9999996 1 1 1 0 A 3 1 61 101292029 101292029 T A 1 0 0 0 0 1 0 0 0 15180 1551 54 4 4 SNRPA1 15 101292029 Missense_Mutation SNP T C3N-00580_T 10404770 101292029 699160 771 18906 SSTR5 0 . GRCh38 16 1078928 1078928 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.60C>T p.= p.A20A ENST00000293897 1/1 250 135 115 229 229 0 strelka-varscan-mutect SSTR5,synonymous_variant,p.=,ENST00000293897,NM_001172560.1,NM_001053.3;SSTR5-AS1,upstream_gene_variant,,ENST00000569832,;SSTR5-AS1,upstream_gene_variant,,ENST00000566499,;SSTR5-AS1,upstream_gene_variant,,ENST00000624643,; T ENST00000293897 Transcript synonymous_variant 148/1362 60/1095 20/364 A gcC/gcT 1 1 SSTR5 HGNC HGNC:11334 protein_coding YES CCDS10429.1 ENSP00000293897 P35346 UPI00000015DC NM_001172560.1,NM_001053.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF20 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 1078928 1078928 C T 1 0 0 0 0 0 0 0 1 15578 668 24 3 3 SSTR5 16 1078928 Silent SNP C C3N-00580_T 1078928 89259417 772 18907 PKD1 0 . GRCh38 16 2106431 2106431 + Missense_Mutation SNP C C G rs567983155 C3N-00580_T C3N-00580_N C C c.7456G>C p.Ala2486Pro p.A2486P ENST00000262304 18/46 228 207 21 277 277 0 varscan-mutect PKD1,missense_variant,p.Ala2486Pro,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Ala2486Pro,ENST00000423118,NM_000296.3;PKD1,upstream_gene_variant,,ENST00000567946,;PKD1,downstream_gene_variant,,ENST00000488185,;PKD1,downstream_gene_variant,,ENST00000483024,;PKD1,downstream_gene_variant,,ENST00000612014,;PKD1,non_coding_transcript_exon_variant,,ENST00000483558,;PKD1,upstream_gene_variant,,ENST00000561991,;PKD1,downstream_gene_variant,,ENST00000473780,;PKD1,upstream_gene_variant,,ENST00000475889,;PKD1,downstream_gene_variant,,ENST00000468674,;PKD1,upstream_gene_variant,,ENST00000564865,;PKD1,missense_variant,p.Ala715Pro,ENST00000487932,;PKD1,non_coding_transcript_exon_variant,,ENST00000486339,;PKD1,non_coding_transcript_exon_variant,,ENST00000496574,;PKD1,non_coding_transcript_exon_variant,,ENST00000483731,;PKD1,non_coding_transcript_exon_variant,,ENST00000415938,;PKD1,non_coding_transcript_exon_variant,,ENST00000565639,;PKD1,downstream_gene_variant,,ENST00000568591,;PKD1,upstream_gene_variant,,ENST00000471603,;PKD1,upstream_gene_variant,,ENST00000480227,;PKD1,upstream_gene_variant,,ENST00000562297,;PKD1,upstream_gene_variant,,ENST00000474088,;PKD1,downstream_gene_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000564890,; G ENST00000262304 Transcript missense_variant 7665/14138 7456/12912 2486/4303 A/P Gcc/Ccc rs567983155 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 deleterious(0.01) 18/46 Pfam_domain:PF02010,PROSITE_profiles:PS51111,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143,TIGRFAM_domain:TIGR00864 MODERATE 1 SNV 1 1 PASS rs567983155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 2106431 2106431 C G 1 0 0 0 0 1 0 0 0 12059 768 27 4 4 PKD1 16 2106431 Missense_Mutation SNP C C3N-00580_T 1027503 2106431 88231914 773 18908 PRSS21 0 . GRCh38 16 2821426 2821426 + Missense_Mutation SNP G G A rs766212468 C3N-00580_T C3N-00580_N G G c.766G>A p.Val256Met p.V256M ENST00000005995 6/6 368 341 27 473 473 0 strelka-varscan-mutect PRSS21,missense_variant,p.Val242Met,ENST00000450020,NM_144957.2;PRSS21,missense_variant,p.Val256Met,ENST00000005995,NM_144956.2,NM_006799.3;PRSS21,missense_variant,p.Val198Met,ENST00000574265,;PRSS21,3_prime_UTR_variant,,ENST00000574813,NM_001270452.1;PRSS21,intron_variant,,ENST00000575739,;PRSS21,downstream_gene_variant,,ENST00000577043,;PRSS21,downstream_gene_variant,,ENST00000570594,;PRSS21,downstream_gene_variant,,ENST00000575199,;PRSS21,downstream_gene_variant,,ENST00000570629,;PRSS21,downstream_gene_variant,,ENST00000571141,;EIF1P4,downstream_gene_variant,,ENST00000572664,; A ENST00000005995 Transcript missense_variant 808/1101 766/945 256/314 V/M Gtg/Atg rs766212468,COSM969505 1 1 PRSS21 HGNC HGNC:9485 protein_coding YES CCDS10478.1 ENSP00000005995 Q9Y6M0 UPI000004813E NM_144956.2,NM_006799.3 deleterious(0) 6/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF173,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs766212468 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 2821426 2821426 G A 1 0 0 0 0 1 0 0 0 12765 1145 40 1 1 PRSS21 16 2821426 Missense_Mutation SNP G C3N-00580_T 714995 2821426 87516919 774 18909 ZNF200 0 . GRCh38 16 3224034 3224034 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1046A>T p.Glu349Val p.E349V ENST00000431561 5/5 245 130 115 248 248 0 strelka-varscan-mutect ZNF200,missense_variant,p.Glu349Val,ENST00000431561,NM_003454.3;ZNF200,missense_variant,p.Glu349Val,ENST00000414144,NM_198088.2;ZNF200,missense_variant,p.Glu348Val,ENST00000396871,NM_001145446.1,NM_001145448.1;ZNF200,missense_variant,p.Glu348Val,ENST00000396868,NM_198087.2;ZNF200,missense_variant,p.Glu348Val,ENST00000396870,NM_001145447.1;ZNF200,missense_variant,p.Glu348Val,ENST00000575948,;AJ003147.9,intron_variant,,ENST00000576468,;ZNF200,non_coding_transcript_exon_variant,,ENST00000575285,; A ENST00000431561 Transcript missense_variant 1659/3348 1046/1188 349/395 E/V gAg/gTg 1 -1 ZNF200 HGNC HGNC:12993 protein_coding YES CCDS10497.1 ENSP00000395723 P98182 UPI00001D89D6 NM_003454.3 tolerated(0.18) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF156,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 3224034 3224034 T A 1 0 0 0 0 1 0 0 0 18339 1551 54 4 4 ZNF200 16 3224034 Missense_Mutation SNP T C3N-00580_T 402608 3224034 87114311 775 18910 MEFV 0 . GRCh38 16 3243870 3243870 + Missense_Mutation SNP C C A rs144122901 C3N-00580_T C3N-00580_N C C c.1782G>T p.Gln594His p.Q594H ENST00000219596 9/10 501 445 56 578 578 0 strelka-varscan-mutect MEFV,missense_variant,p.Gln594His,ENST00000219596,NM_000243.2;MEFV,missense_variant,p.Gln414His,ENST00000339854,;MEFV,missense_variant,p.Gly442Cys,ENST00000541159,NM_001198536.1;MEFV,missense_variant,p.Gln383His,ENST00000536379,;MEFV,3_prime_UTR_variant,,ENST00000542898,;MEFV,3_prime_UTR_variant,,ENST00000537682,;MEFV,3_prime_UTR_variant,,ENST00000538326,;MEFV,3_prime_UTR_variant,,ENST00000536980,;MEFV,3_prime_UTR_variant,,ENST00000570511,;MEFV,3_prime_UTR_variant,,ENST00000539145,;MEFV,3_prime_UTR_variant,,ENST00000576315,;MEFV,3_prime_UTR_variant,,ENST00000574583,;MEFV,3_prime_UTR_variant,,ENST00000572244,;MEFV,downstream_gene_variant,,ENST00000539154,; A ENST00000219596 Transcript missense_variant 1822/3499 1782/2346 594/781 Q/H caG/caT rs144122901 1 -1 MEFV HGNC HGNC:6998 protein_coding YES CCDS10498.1 ENSP00000219596 O15553 UPI000004C0CA NM_000243.2 deleterious(0.02) 9/10 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs144122901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 3243870 3243870 C A 1 0 0 0 0 1 0 0 0 9399 681 24 2 2 MEFV 16 3243870 Missense_Mutation SNP C C3N-00580_T 19836 3243870 87094475 776 18911 RBFOX1 0 . GRCh38 16 7518353 7518353 + Silent SNP G G A C3N-00580_T C3N-00580_N G G c.363G>A p.= p.A121A ENST00000422070 5/16 152 109 43 132 132 0 strelka-mutect RBFOX1,synonymous_variant,p.=,ENST00000550418,NM_018723.3;RBFOX1,synonymous_variant,p.=,ENST00000340209,;RBFOX1,synonymous_variant,p.=,ENST00000620507,;RBFOX1,synonymous_variant,p.=,ENST00000547372,;RBFOX1,synonymous_variant,p.=,ENST00000355637,NM_145893.2;RBFOX1,synonymous_variant,p.=,ENST00000311745,NM_145891.2;RBFOX1,synonymous_variant,p.=,ENST00000553186,NM_001142333.1;RBFOX1,synonymous_variant,p.=,ENST00000547605,;RBFOX1,synonymous_variant,p.=,ENST00000422070,NM_001308117.1;RBFOX1,synonymous_variant,p.=,ENST00000535565,;RBFOX1,synonymous_variant,p.=,ENST00000436368,NM_145892.2;RBFOX1,synonymous_variant,p.=,ENST00000547338,NM_001142334.1;RBFOX1,synonymous_variant,p.=,ENST00000552089,;RBFOX1,synonymous_variant,p.=,ENST00000551752,;RBFOX1,synonymous_variant,p.=,ENST00000570626,;RBFOX1,non_coding_transcript_exon_variant,,ENST00000569889,; A ENST00000422070 Transcript synonymous_variant 559/1684 363/1278 121/425 A gcG/gcA COSM4062893,COSM4062894,COSM4062895,COSM4062896 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 5/16 hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932 1,1,1,1 LOW 1 SNV 2 1,1,1,1 1 PASS rs1490574094 . 0 204 4 2 0 0 0 0 -20 0.9999952 1 1 1 0 A 2 1 61 7518353 7518353 G A 1 0 0 0 0 0 0 0 1 13271 1103 39 1 1 RBFOX1 16 7518353 Silent SNP G C3N-00580_T 4274483 7518353 82819992 777 18912 NOMO1 0 . GRCh38 16 14884457 14884457 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.3197C>T p.Ser1066Phe p.S1066F ENST00000287667 27/31 234 128 106 294 294 0 strelka-varscan-mutect NOMO1,missense_variant,p.Ser1066Phe,ENST00000287667,NM_014287.3;NOMO1,missense_variant,p.Ser1066Phe,ENST00000620755,;NOMO1,missense_variant,p.Ser899Phe,ENST00000610363,;NOMO1,upstream_gene_variant,,ENST00000565655,;NOMO1,upstream_gene_variant,,ENST00000566823,; T ENST00000287667 Transcript missense_variant 3368/4355 3197/3669 1066/1222 S/F tCc/tTc 1 1 NOMO1 HGNC HGNC:30060 protein_coding YES CCDS10556.1 ENSP00000287667 Q15155 UPI000013D37E NM_014287.3 deleterious(0.01) 27/31 hmmpanther:PTHR23303 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 14884457 14884457 C T 1 0 0 0 0 1 0 0 0 10575 855 30 3 3 NOMO1 16 14884457 Missense_Mutation SNP C C3N-00580_T 7366104 14884457 75453888 778 18913 NPIPA5 0 . GRCh38 16 15365289 15365289 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.839C>A p.Pro280His p.P280H ENST00000534094 7/7 175 89 86 193 192 1 strelka-varscan-mutect NPIPA5,missense_variant,p.Pro280His,ENST00000534094,;NPIPA5,intron_variant,,ENST00000360151,NM_001277325.1;NPIPA5,intron_variant,,ENST00000543801,;RP11-72I8.2,downstream_gene_variant,,ENST00000611162,; T ENST00000534094 Transcript missense_variant 839/954 839/954 280/317 P/H cCc/cAc 1 -1 NPIPA5 HGNC HGNC:41980 protein_coding ENSP00000435611 E9PJ88 UPI0001A5E893 deleterious_low_confidence(0) 7/7 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 15365289 15365289 G T 1 0 0 0 0 1 0 0 0 10634 1232 43 2 2 NPIPA5 16 15365289 Missense_Mutation SNP G C3N-00580_T 480832 15365289 74973056 779 18914 C16orf62 0 . GRCh38 16 19555551 19555551 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.89C>A p.Ala30Asp p.A30D ENST00000251143 1/31 388 343 45 404 403 1 strelka-varscan-mutect C16orf62,missense_variant,p.Ala30Asp,ENST00000251143,NM_020314.5;C16orf62,missense_variant,p.Ala30Asp,ENST00000438132,;C16orf62,missense_variant,p.Ala30Asp,ENST00000542263,NM_001300743.1;C16orf62,intron_variant,,ENST00000544670,;CCP110,downstream_gene_variant,,ENST00000396212,NM_001323572.1,NM_001323571.1,NM_014711.4;CCP110,downstream_gene_variant,,ENST00000381396,NM_001323569.1,NM_001199022.1;CCP110,downstream_gene_variant,,ENST00000396208,;C16orf62,upstream_gene_variant,,ENST00000417362,;C16orf62,upstream_gene_variant,,ENST00000513947,;C16orf62,upstream_gene_variant,,ENST00000567245,;C16orf62,missense_variant,p.Ala30Asp,ENST00000539322,;CCP110,downstream_gene_variant,,ENST00000562616,;CCP110,downstream_gene_variant,,ENST00000567451,;C16orf62,upstream_gene_variant,,ENST00000543460,;C16orf62,upstream_gene_variant,,ENST00000537186,; A ENST00000251143 Transcript missense_variant 137/3894 89/3159 30/1052 A/D gCt/gAt 1 1 C16orf62 HGNC HGNC:24641 protein_coding YES CCDS32397.2 ENSP00000251143 E7EWW0 UPI0001E1129C NM_020314.5 deleterious_low_confidence(0) 1/31 MODERATE 1 SNV 1 1 PASS rs1244614135 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 19555551 19555551 C A 1 0 0 0 0 1 0 0 0 1861 797 28 2 2 C16orf62 16 19555551 Missense_Mutation SNP C C3N-00580_T 4190262 19555551 70782794 780 18915 GP2 0 . GRCh38 16 20315988 20315988 + Missense_Mutation SNP C C A rs770032956 C3N-00580_T C3N-00580_N C C c.1478G>T p.Arg493Leu p.R493L ENST00000381362 10/12 301 165 136 397 396 1 strelka-varscan-mutect GP2,missense_variant,p.Arg490Leu,ENST00000302555,NM_001502.3;GP2,missense_variant,p.Arg493Leu,ENST00000381362,NM_001007240.2;GP2,missense_variant,p.Arg346Leu,ENST00000381360,NM_001007241.2;GP2,missense_variant,p.Arg343Leu,ENST00000341642,NM_001007242.2;GP2,downstream_gene_variant,,ENST00000572347,;GP2,downstream_gene_variant,,ENST00000575582,;GP2,downstream_gene_variant,,ENST00000572478,;GP2,downstream_gene_variant,,ENST00000573897,;GP2,downstream_gene_variant,,ENST00000574982,; A ENST00000381362 Transcript missense_variant 1555/2425 1478/1614 493/537 R/L cGg/cTg rs770032956 1 -1 GP2 HGNC HGNC:4441 protein_coding YES CCDS42128.1 ENSP00000370767 P55259 UPI000059D333 NM_001007240.2 tolerated(0.11) 10/12 hmmpanther:PTHR24044:SF284,hmmpanther:PTHR24044 MODERATE 1 SNV 1 1 PASS rs770032956 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 20315988 20315988 C A 1 0 0 0 0 1 0 0 0 6477 652 23 1 1 GP2 16 20315988 Missense_Mutation SNP C C3N-00580_T 760437 20315988 70022357 781 18916 UMOD 0 . GRCh38 16 20333335 20333335 + Silent SNP G G T rs766780246 C3N-00580_T C3N-00580_N G G c.2001C>A p.= p.T667T ENST00000396134 12/12 783 583 200 715 714 1 strelka-varscan-mutect UMOD,synonymous_variant,p.=,ENST00000302509,NM_001008389.2,NM_003361.3;UMOD,synonymous_variant,p.=,ENST00000396134,NM_001278614.1;UMOD,synonymous_variant,p.=,ENST00000396138,;UMOD,synonymous_variant,p.=,ENST00000570689,;UMOD,downstream_gene_variant,,ENST00000570331,; T ENST00000396134 Transcript synonymous_variant 2125/2408 2001/2022 667/673 T acC/acA rs766780246,COSM4870693,COSM968021 1 -1 UMOD HGNC HGNC:12559 protein_coding YES CCDS61876.1 ENSP00000379438 P07911 UPI000059D336 NM_001278614.1 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR24044:SF263,hmmpanther:PTHR24044 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs766780246 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 20333335 20333335 G T 1 0 0 0 0 0 0 0 1 17503 987 35 2 2 UMOD 16 20333335 Silent SNP G C3N-00580_T 17347 20333335 70005010 782 18917 ACSM2A 0 . GRCh38 16 20465643 20465643 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.304G>T p.Gly102Cys p.G102C ENST00000573854 3/14 398 341 57 456 455 1 strelka-varscan-mutect ACSM2A,missense_variant,p.Gly102Cys,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,missense_variant,p.Gly102Cys,ENST00000396104,;ACSM2A,missense_variant,p.Gly102Cys,ENST00000575690,;ACSM2A,missense_variant,p.Gly102Cys,ENST00000219054,;ACSM2A,missense_variant,p.Gly23Cys,ENST00000417235,NM_001308169.1;ACSM2A,missense_variant,p.Gly102Cys,ENST00000571894,;ACSM2A,missense_variant,p.Gly102Cys,ENST00000576361,;ACSM2A,missense_variant,p.Gly23Cys,ENST00000574251,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,missense_variant,p.Gly102Cys,ENST00000574692,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,; T ENST00000573854 Transcript missense_variant 418/2837 304/1734 102/577 G/C Ggc/Tgc 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 deleterious(0) 3/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 20465643 20465643 G T 1 0 0 0 0 1 0 0 0 225 1348 47 2 2 ACSM2A 16 20465643 Missense_Mutation SNP G C3N-00580_T 132308 20465643 69872702 783 18918 PLK1 0 . GRCh38 16 23681040 23681040 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.704G>T p.Trp235Leu p.W235L ENST00000300093 3/10 214 195 19 477 476 1 strelka-varscan-mutect PLK1,missense_variant,p.Trp235Leu,ENST00000300093,NM_005030.4;PLK1,5_prime_UTR_variant,,ENST00000567897,;PLK1,5_prime_UTR_variant,,ENST00000568568,;DCTN5,downstream_gene_variant,,ENST00000300087,NM_032486.3;PLK1,non_coding_transcript_exon_variant,,ENST00000564202,;PLK1,non_coding_transcript_exon_variant,,ENST00000562272,;PLK1,downstream_gene_variant,,ENST00000570220,;PLK1,upstream_gene_variant,,ENST00000562407,; T ENST00000300093 Transcript missense_variant 815/2227 704/1812 235/603 W/L tGg/tTg 1 1 PLK1 HGNC HGNC:9077 protein_coding YES CCDS10616.1 ENSP00000300093 P53350 UPI0000131BF9 NM_005030.4 deleterious(0) 3/10 PROSITE_profiles:PS50011,hmmpanther:PTHR24345,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 23681040 23681040 G T 1 0 0 0 0 1 0 0 0 12190 1357 47 2 2 PLK1 16 23681040 Missense_Mutation SNP G C3N-00580_T 3215397 23681040 66657305 784 18919 ERN2 0 . GRCh38 16 23713124 23713124 + Missense_Mutation SNP C C A rs571323575 C3N-00580_T C3N-00580_N C C c.208G>T p.Ala70Ser p.A70S ENST00000634482 1/22 173 74 99 193 193 0 strelka-varscan-mutect ERN2,missense_variant,p.Ala70Ser,ENST00000634482,NM_033266.3;ERN2,missense_variant,p.Ala22Ser,ENST00000256797,;ERN2,missense_variant,p.Ala22Ser,ENST00000457008,NM_001308220.1;CTD-2385L22.1,downstream_gene_variant,,ENST00000563611,;ERN2,missense_variant,p.Ala22Ser,ENST00000562562,;ERN2,missense_variant,p.Ala22Ser,ENST00000569903,; A ENST00000634482 Transcript missense_variant 377/3616 208/2925 70/974 A/S Gcg/Tcg rs571323575 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 tolerated_low_confidence(0.07) 1/22 Low_complexity_(Seg):seg,hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15 MODERATE 1 SNV 1 1 PASS rs571323575 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 23713124 23713124 C A 1 0 0 0 0 1 0 0 0 5096 739 26 2 2 ERN2 16 23713124 Missense_Mutation SNP C C3N-00580_T 32084 23713124 66625221 785 18920 PRKCB 0 . GRCh38 16 24092841 24092841 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.580C>A p.Pro194Thr p.P194T ENST00000303531 6/17 216 197 19 173 173 0 strelka-varscan-mutect PRKCB,missense_variant,p.Pro194Thr,ENST00000303531,NM_002738.6;PRKCB,missense_variant,p.Pro194Thr,ENST00000321728,NM_212535.2;PRKCB,missense_variant,p.Pro9Thr,ENST00000498739,;PRKCB,non_coding_transcript_exon_variant,,ENST00000482000,;PRKCB,non_coding_transcript_exon_variant,,ENST00000486868,; A ENST00000303531 Transcript missense_variant 732/7969 580/2022 194/673 P/T Ccc/Acc COSM3507901,COSM3507902,COSM3507903 1 1 PRKCB HGNC HGNC:9395 protein_coding YES CCDS10619.1 ENSP00000305355 P05771 UPI000002ACF9 NM_002738.6 deleterious(0.04) 6/17 Gene3D:2.60.40.150,Pfam_domain:PF00168,PIRSF_domain:PIRSF000550,Prints_domain:PR00360,PROSITE_profiles:PS50004,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF188,SMART_domains:SM00239,Superfamily_domains:SSF49562 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 24092841 24092841 C A 1 0 0 0 0 1 0 0 0 12641 855 30 2 2 PRKCB 16 24092841 Missense_Mutation SNP C C3N-00580_T 379717 24092841 66245504 786 18921 RBBP6 0 . GRCh38 16 24571961 24571961 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.4895C>T p.Thr1632Ile p.T1632I ENST00000319715 18/18 176 136 40 133 133 0 strelka-varscan-mutect RBBP6,missense_variant,p.Thr1632Ile,ENST00000319715,NM_006910.4;RBBP6,missense_variant,p.Thr1598Ile,ENST00000348022,NM_018703.3;RBBP6,missense_variant,p.Thr792Ile,ENST00000381039,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,; T ENST00000319715 Transcript missense_variant 5327/6229 4895/5379 1632/1792 T/I aCt/aTt 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 deleterious_low_confidence(0) 18/18 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 24571961 24571961 C T 1 0 0 0 0 1 0 0 0 13264 565 20 3 3 RBBP6 16 24571961 Missense_Mutation SNP C C3N-00580_T 479120 24571961 65766384 787 18922 IL4R 0 . GRCh38 16 27341170 27341170 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.171G>T p.Trp57Cys p.W57C ENST00000628578 2/2 118 69 49 86 86 0 strelka-varscan-mutect IL4R,missense_variant,p.Trp57Cys,ENST00000628578,;IL4R,intron_variant,,ENST00000395762,NM_000418.3;IL4R,intron_variant,,ENST00000543915,NM_001257997.1,NM_001257406.1;IL4R,intron_variant,,ENST00000563002,;IL4R,intron_variant,,ENST00000566117,;IL4R,intron_variant,,ENST00000562142,;IL4R,upstream_gene_variant,,ENST00000170630,NM_001257407.1;IL4R,upstream_gene_variant,,ENST00000562968,;IL4R,downstream_gene_variant,,ENST00000561742,;IL4R,missense_variant,p.Trp57Cys,ENST00000568746,;IL4R,missense_variant,p.Trp57Cys,ENST00000563926,;IL4R,intron_variant,,ENST00000563787,;IL4R,intron_variant,,ENST00000566318,;IL4R,intron_variant,,ENST00000561946,;IL4R,upstream_gene_variant,,ENST00000565696,; T ENST00000628578 Transcript missense_variant 171/201 171/201 57/66 W/C tgG/tgT 1 1 IL4R HGNC HGNC:6015 protein_coding ENSP00000486645 Q5FC08 UPI00004CA0C4 deleterious_low_confidence(0) 2/2 MODERATE SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 27341170 27341170 G T 1 0 0 0 0 1 0 0 0 7602 1241 43 2 2 IL4R 16 27341170 Missense_Mutation SNP G C3N-00580_T 2769209 27341170 62997175 788 18923 GTF3C1 0 . GRCh38 16 27485997 27485997 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.3858G>T p.Lys1286Asn p.K1286N ENST00000356183 24/37 89 58 31 96 96 0 strelka-varscan-mutect GTF3C1,missense_variant,p.Lys1286Asn,ENST00000356183,NM_001520.3;GTF3C1,missense_variant,p.Lys1286Asn,ENST00000561623,NM_001286242.1;GTF3C1,missense_variant,p.Lys55Asn,ENST00000568569,;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,splice_region_variant,,ENST00000570129,;GTF3C1,splice_region_variant,,ENST00000564664,;GTF3C1,upstream_gene_variant,,ENST00000566779,; A ENST00000356183 Transcript missense_variant,splice_region_variant 3874/7018 3858/6330 1286/2109 K/N aaG/aaT 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 deleterious(0) 24/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 61 27485997 27485997 C A 1 0 0 0 0 1 0 0 0 6753 695 24 2 2 GTF3C1 16 27485997 Missense_Mutation SNP C C3N-00580_T 144827 27485997 62852348 789 18924 KIAA0556 0 . GRCh38 16 27750121 27750121 + Frame_Shift_Del DEL G G - rs765345877 C3N-00580_T C3N-00580_N G G c.3164delG p.Gly1055AlafsTer18 p.G1055Afs*18 ENST00000261588 16/28 171 84 87 201 201 0 sindel-varindel-pindel KIAA0556,frameshift_variant,p.Gly1055AlafsTer18,ENST00000261588,NM_015202.2;KIAA0556,non_coding_transcript_exon_variant,,ENST00000573850,; - ENST00000261588 Transcript frameshift_variant 3180/6616 3161/4857 1054/1618 R/X cGg/cg rs765345877 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 16/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534,Pfam_domain:PF14652 HIGH 1 deletion 1 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 27750121 27750121 G - 1 0 1 0 1 0 0 0 0 8088 1116 39 0 0 KIAA0556 16 27750121 Frame_Shift_Del DEL G C3N-00580_T 264124 27750121 62588224 790 18925 NPIPB6 0 . GRCh38 16 28362784 28362784 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.39G>A p.= p.L13L ENST00000532254 1/7 562 457 105 668 668 0 strelka-varscan-mutect NPIPB6,synonymous_variant,p.=,ENST00000532254,NM_001282524.1;RP11-435I10.5,upstream_gene_variant,,ENST00000603787,; T ENST00000532254 Transcript synonymous_variant 725/2016 39/1278 13/425 L ctG/ctA 1 -1 NPIPB6 HGNC HGNC:37454 protein_coding YES CCDS61892.1 ENSP00000431871 E9PJ23 UPI000047D9DC NM_001282524.1 1/7 hmmpanther:PTHR15438,hmmpanther:PTHR15438:SF4 LOW 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 28362784 28362784 C T 1 0 0 0 0 0 0 0 1 10640 465 17 3 3 NPIPB6 16 28362784 Silent SNP C C3N-00580_T 612663 28362784 61975561 791 18926 TAOK2 0 . GRCh38 16 29981920 29981920 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.811A>T p.Thr271Ser p.T271S ENST00000308893 10/16 326 281 45 347 347 0 strelka-varscan-mutect TAOK2,missense_variant,p.Thr271Ser,ENST00000308893,NM_016151.3;TAOK2,missense_variant,p.Thr98Ser,ENST00000416441,;TAOK2,missense_variant,p.Thr271Ser,ENST00000279394,NM_004783.3;TAOK2,missense_variant,p.Thr271Ser,ENST00000543033,NM_001252043.1;TAOK2,upstream_gene_variant,,ENST00000566552,; T ENST00000308893 Transcript missense_variant 1854/5169 811/3708 271/1235 T/S Acc/Tcc 1 1 TAOK2 HGNC HGNC:16835 protein_coding YES CCDS10663.1 ENSP00000310094 Q9UL54 UPI000013EDDA NM_016151.3 tolerated(0.3) 10/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF188,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs970485759 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 29981920 29981920 A T 1 0 0 0 0 1 0 0 0 15947 43 2 4 4 TAOK2 16 29981920 Missense_Mutation SNP A C3N-00580_T 1619136 29981920 60356425 792 18927 ITGAL 0 . GRCh38 16 30483852 30483852 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.748G>T p.Gly250Trp p.G250W ENST00000356798 8/31 172 148 24 166 166 0 strelka-varscan-mutect ITGAL,missense_variant,p.Gly250Trp,ENST00000356798,NM_002209.2;ITGAL,missense_variant,p.Gly167Trp,ENST00000358164,NM_001114380.1;ITGAL,missense_variant,p.Gly167Trp,ENST00000564118,;ITGAL,intron_variant,,ENST00000433423,;ITGAL,downstream_gene_variant,,ENST00000569725,;RNU7-61P,upstream_gene_variant,,ENST00000515897,;RP11-297C4.2,intron_variant,,ENST00000569459,;RP11-297C4.3,upstream_gene_variant,,ENST00000562525,;ITGAL,non_coding_transcript_exon_variant,,ENST00000565348,;ITGAL,3_prime_UTR_variant,,ENST00000562857,;ITGAL,intron_variant,,ENST00000568926,;ITGAL,downstream_gene_variant,,ENST00000565864,;ITGAL,upstream_gene_variant,,ENST00000566149,; T ENST00000356798 Transcript missense_variant 928/5213 748/3513 250/1170 G/W Ggg/Tgg 1 1 ITGAL HGNC HGNC:6148 protein_coding YES CCDS32433.1 ENSP00000349252 P20701 UPI000013C4FF NM_002209.2 deleterious(0) 8/31 Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 30483852 30483852 G T 1 0 0 0 0 1 0 0 0 7793 1232 43 2 2 ITGAL 16 30483852 Missense_Mutation SNP G C3N-00580_T 501932 30483852 59854493 793 18928 ZNF689 0 . GRCh38 16 30605373 30605373 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.394G>T p.Gly132Cys p.G132C ENST00000287461 3/3 213 181 32 295 295 0 strelka-varscan-mutect ZNF689,missense_variant,p.Gly132Cys,ENST00000287461,NM_138447.2;RP11-146F11.5,intron_variant,,ENST00000563540,;ZNF689,non_coding_transcript_exon_variant,,ENST00000566673,;ZNF689,non_coding_transcript_exon_variant,,ENST00000563304,;ZNF689,non_coding_transcript_exon_variant,,ENST00000565440,;ZNF689,non_coding_transcript_exon_variant,,ENST00000564262,;ZNF689,non_coding_transcript_exon_variant,,ENST00000565710,; A ENST00000287461 Transcript missense_variant 732/3547 394/1503 132/500 G/C Ggc/Tgc 1 -1 ZNF689 HGNC HGNC:25173 protein_coding YES CCDS10686.1 ENSP00000287461 Q96CS4 UPI000006CDAD NM_138447.2 tolerated(0.12) 3/3 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF23,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1259511740 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 30605373 30605373 C A 1 0 0 0 0 1 0 0 0 18667 681 24 2 2 ZNF689 16 30605373 Missense_Mutation SNP C C3N-00580_T 121521 30605373 59732972 794 18929 ITGAX 0 . GRCh38 16 31359773 31359773 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.504C>A p.= p.A168A ENST00000562522 6/31 331 232 99 301 301 0 strelka-varscan-mutect ITGAX,synonymous_variant,p.=,ENST00000268296,NM_000887.4;ITGAX,synonymous_variant,p.=,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,upstream_gene_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;ITGAX,downstream_gene_variant,,ENST00000564308,;RP11-120K18.3,downstream_gene_variant,,ENST00000561830,; A ENST00000562522 Transcript synonymous_variant 537/3990 504/3510 168/1169 A gcC/gcA 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 6/31 Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 31359773 31359773 C A 1 0 0 0 0 0 0 0 1 7796 581 21 2 2 ITGAX 16 31359773 Silent SNP C C3N-00580_T 754400 31359773 58978572 795 18930 ITGAD 0 . GRCh38 16 31407776 31407776 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.869C>A p.Ala290Asp p.A290D ENST00000389202 9/30 262 168 94 217 217 0 strelka-varscan-mutect ITGAD,missense_variant,p.Ala290Asp,ENST00000389202,NM_001318185.1,NM_005353.2;RP11-120K18.2,downstream_gene_variant,,ENST00000567545,;ITGAD,non_coding_transcript_exon_variant,,ENST00000444228,; A ENST00000389202 Transcript missense_variant 918/3912 869/3486 290/1161 A/D gCt/gAt 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 deleterious(0.01) 9/30 Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 31407776 31407776 C A 1 0 0 0 0 1 0 0 0 7791 797 28 2 2 ITGAD 16 31407776 Missense_Mutation SNP C C3N-00580_T 48003 31407776 58930569 796 18931 ZNF267 0 . GRCh38 16 31914670 31914670 + Nonsense_Mutation SNP G G T rs751991210 C3N-00580_T C3N-00580_N G G c.421G>T p.Glu141Ter p.E141* ENST00000300870 4/4 170 147 23 129 129 0 strelka-varscan-mutect ZNF267,stop_gained,p.Glu141Ter,ENST00000300870,NM_003414.5;ZNF267,3_prime_UTR_variant,,ENST00000394846,;ZNF267,downstream_gene_variant,,ENST00000562971,;ZNF267,non_coding_transcript_exon_variant,,ENST00000575471,;ZNF267,downstream_gene_variant,,ENST00000566541,;ZNF267,downstream_gene_variant,,ENST00000561814,; T ENST00000300870 Transcript stop_gained 630/3317 421/2232 141/743 E/* Gaa/Taa rs751991210 1 1 ZNF267 HGNC HGNC:13060 protein_coding YES CCDS32440.1 ENSP00000300870 Q14586 UPI000045696F NM_003414.5 4/4 HIGH 1 SNV 1 1 PASS rs751991210 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 31914670 31914670 G T 1 0 0 0 0 0 1 0 0 18382 1291 45 2 2 ZNF267 16 31914670 Nonsense_Mutation SNP G C3N-00580_T 506894 31914670 58423675 797 18932 CBLN1 0 . GRCh38 16 49279449 49279449 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.537C>A p.= p.G179G ENST00000219197 3/3 551 331 220 516 516 0 strelka-varscan-mutect CBLN1,synonymous_variant,p.=,ENST00000219197,NM_004352.3;CBLN1,synonymous_variant,p.=,ENST00000536749,;CBLN1,3_prime_UTR_variant,,ENST00000564786,; T ENST00000219197 Transcript synonymous_variant 903/2435 537/582 179/193 G ggC/ggA 1 -1 CBLN1 HGNC HGNC:1543 protein_coding YES CCDS10736.1 ENSP00000219197 P23435 UPI0000127506 NM_004352.3 3/3 PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 49279449 49279449 G T 1 0 0 0 0 0 0 0 1 2405 958 34 2 2 CBLN1 16 49279449 Silent SNP G C3N-00580_T 17364779 49279449 41058896 798 18933 ZNF423 0 . GRCh38 16 49638847 49638847 + Nonsense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.305G>A p.Trp102Ter p.W102* ENST00000561648 5/9 107 80 27 101 101 0 strelka-varscan-mutect ZNF423,stop_gained,p.Trp102Ter,ENST00000561648,;ZNF423,stop_gained,p.Trp42Ter,ENST00000563137,;ZNF423,stop_gained,p.Trp102Ter,ENST00000262383,NM_015069.3;ZNF423,stop_gained,p.Trp42Ter,ENST00000562871,;ZNF423,stop_gained,p.Trp42Ter,ENST00000562520,NM_001271620.1;ZNF423,5_prime_UTR_variant,,ENST00000535559,;ZNF423,5_prime_UTR_variant,,ENST00000567169,; T ENST00000561648 Transcript stop_gained 606/7907 305/3855 102/1284 W/* tGg/tAg 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC 5/9 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 HIGH 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 49638847 49638847 C T 1 0 0 0 0 0 1 0 0 18470 595 21 3 3 ZNF423 16 49638847 Nonsense_Mutation SNP C C3N-00580_T 359398 49638847 40699498 799 18934 SALL1 0 . GRCh38 16 51139827 51139827 + Missense_Mutation SNP G G A rs267604571 C3N-00580_T C3N-00580_N G G c.2395C>T p.Pro799Ser p.P799S ENST00000251020 2/3 579 362 217 427 424 3 strelka-varscan-mutect SALL1,missense_variant,p.Pro702Ser,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Pro799Ser,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Pro702Ser,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 2429/5146 2395/3975 799/1324 P/S Ccc/Tcc rs267604571,COSM3510168 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.06) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs267604571 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 51139827 51139827 G A 1 0 0 0 0 1 0 0 0 14069 1232 43 3 3 SALL1 16 51139827 Missense_Mutation SNP G C3N-00580_T 1500980 51139827 39198518 800 18935 TOX3 0 . GRCh38 16 52439603 52439603 + Silent SNP C C T rs374335680 C3N-00580_T C3N-00580_N C C c.1353G>A p.= p.Q451Q ENST00000219746 7/7 304 188 116 256 256 0 strelka-varscan-mutect TOX3,synonymous_variant,p.=,ENST00000219746,NM_001080430.2;TOX3,synonymous_variant,p.=,ENST00000407228,NM_001146188.1;RP11-132F7.2,upstream_gene_variant,,ENST00000624321,;TOX3,non_coding_transcript_exon_variant,,ENST00000566696,; T ENST00000219746 Transcript synonymous_variant 1638/3233 1353/1731 451/576 Q caG/caA rs374335680 1 -1 TOX3 HGNC HGNC:11972 protein_coding YES CCDS54009.1 ENSP00000219746 O15405 UPI00001972E7 NM_001080430.2 7/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF220,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs374335680 . 0 10 0 0 173 27 0 0 -13.80777 0 0 1 0 0 T 2 4 61 52439603 52439603 C T 1 0 0 0 0 0 0 0 1 16857 796 28 3 3 TOX3 16 52439603 Silent SNP C C3N-00580_T 1299776 52439603 37898742 801 18936 MT1G 0 . GRCh38 16 56667261 56667261 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.145G>A p.Gly49Arg p.G49R ENST00000568675 2/2 490 306 184 348 348 0 strelka-varscan-mutect MT1G,missense_variant,p.Gly49Arg,ENST00000568675,;MT1G,intron_variant,,ENST00000444837,NM_005950.2;MT1G,intron_variant,,ENST00000379811,NM_001301267.1;MT1G,intron_variant,,ENST00000569500,;MT1H,upstream_gene_variant,,ENST00000569155,;MT1H,upstream_gene_variant,,ENST00000332374,NM_005951.2; T ENST00000568675 Transcript missense_variant 173/628 145/207 49/68 G/R Ggg/Agg 1 -1 MT1G HGNC HGNC:7399 protein_coding ENSP00000456835 H3BSS0 UPI00024670A3 tolerated_low_confidence(0.76) 2/2 Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 56667261 56667261 C T 1 0 0 0 0 1 0 0 0 9885 681 24 3 3 MT1G 16 56667261 Missense_Mutation SNP C C3N-00580_T 4227658 56667261 33671084 802 18937 CX3CL1 0 . GRCh38 16 57382619 57382619 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.781G>T p.Glu261Ter p.E261* ENST00000006053 3/3 226 164 62 201 201 0 strelka-varscan-mutect CX3CL1,stop_gained,p.Glu223Ter,ENST00000565912,;CX3CL1,stop_gained,p.Glu261Ter,ENST00000006053,NM_001304392.1,NM_002996.4;CX3CL1,stop_gained,p.Glu267Ter,ENST00000563383,;CX3CL1,downstream_gene_variant,,ENST00000564948,; T ENST00000006053 Transcript stop_gained 892/3321 781/1194 261/397 E/* Gag/Tag 1 1 CX3CL1 HGNC HGNC:10647 protein_coding YES CCDS10779.1 ENSP00000006053 P78423 A0N0N7 UPI0000040685 NM_001304392.1,NM_002996.4 3/3 hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF92 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 57382619 57382619 G T 1 0 0 0 0 0 1 0 0 3884 1175 41 2 2 CX3CL1 16 57382619 Nonsense_Mutation SNP G C3N-00580_T 715358 57382619 32955726 803 18938 CNOT1 0 . GRCh38 16 58539802 58539802 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.4958G>T p.Arg1653Leu p.R1653L ENST00000317147 35/49 194 147 47 161 161 0 strelka-varscan-mutect CNOT1,missense_variant,p.Arg1653Leu,ENST00000317147,NM_016284.4;CNOT1,missense_variant,p.Arg1648Leu,ENST00000569240,NM_001265612.1;CNOT1,missense_variant,p.Arg26Leu,ENST00000568917,;CNOT1,downstream_gene_variant,,ENST00000441024,NM_206999.2;CNOT1,downstream_gene_variant,,ENST00000567133,;CNOT1,missense_variant,p.Arg1648Leu,ENST00000567188,;CNOT1,non_coding_transcript_exon_variant,,ENST00000563283,;CNOT1,downstream_gene_variant,,ENST00000566240,; A ENST00000317147 Transcript missense_variant 5291/8471 4958/7131 1653/2376 R/L cGg/cTg 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 deleterious(0.05) 35/49 Low_complexity_(Seg):seg,hmmpanther:PTHR13162 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 58539802 58539802 C A 1 0 0 0 0 1 0 0 0 3396 652 23 1 1 CNOT1 16 58539802 Missense_Mutation SNP C C3N-00580_T 1157183 58539802 31798543 804 18939 CDH5 0 . GRCh38 16 66388373 66388373 + Silent SNP G G T rs755041783 C3N-00580_T C3N-00580_N G G c.549G>T p.= p.V183V ENST00000341529 4/12 276 222 54 323 322 1 strelka-varscan-mutect CDH5,synonymous_variant,p.=,ENST00000341529,NM_001795.3;CDH5,synonymous_variant,p.=,ENST00000614547,;CDH5,synonymous_variant,p.=,ENST00000563425,;CDH5,downstream_gene_variant,,ENST00000562048,;CDH5,downstream_gene_variant,,ENST00000568155,;CDH5,intron_variant,,ENST00000565334,; T ENST00000341529 Transcript synonymous_variant 697/4120 549/2355 183/784 V gtG/gtT rs755041783 1 1 CDH5 HGNC HGNC:1764 protein_coding YES CCDS10804.1 ENSP00000344115 P33151 UPI000016B272 NM_001795.3 4/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF89,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs755041783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 66388373 66388373 G T 1 0 0 0 0 0 0 0 1 2816 1335 47 2 2 CDH5 16 66388373 Silent SNP G C3N-00580_T 7848571 66388373 23949972 805 18940 HYDIN 0 . GRCh38 16 71129787 71129787 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1080G>T p.Glu360Asp p.E360D ENST00000393567 9/86 176 148 28 127 127 0 varscan-mutect HYDIN,missense_variant,p.Glu360Asp,ENST00000393567,NM_001270974.1;HYDIN,missense_variant,p.Glu360Asp,ENST00000321489,NM_017558.4;HYDIN,missense_variant,p.Glu387Asp,ENST00000538248,NM_001198542.1;HYDIN,missense_variant,p.Glu377Asp,ENST00000541601,NM_001198543.1;HYDIN,missense_variant,p.Glu377Asp,ENST00000288168,;HYDIN,downstream_gene_variant,,ENST00000538382,;HYDIN,missense_variant,p.Glu148Asp,ENST00000545230,;HYDIN,3_prime_UTR_variant,,ENST00000539447,;HYDIN,upstream_gene_variant,,ENST00000393552,;HYDIN,downstream_gene_variant,,ENST00000536785,; A ENST00000393567 Transcript missense_variant 1231/15719 1080/15366 360/5121 E/D gaG/gaT 1 -1 HYDIN HGNC HGNC:19368 protein_coding YES CCDS59269.1 ENSP00000377197 Q4G0P3 UPI0001FEF4F9 NM_001270974.1 tolerated(0.06) 9/86 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF16,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71129787 71129787 C A 1 0 0 0 0 1 0 0 0 7363 912 32 2 2 HYDIN 16 71129787 Missense_Mutation SNP C C3N-00580_T 4741414 71129787 19208558 806 18941 CALB2 0 . GRCh38 16 71385587 71385587 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.638G>T p.Gly213Val p.G213V ENST00000302628 10/11 225 136 89 212 211 1 strelka-varscan-mutect CALB2,missense_variant,p.Gly213Val,ENST00000302628,NM_001740.4;CALB2,missense_variant,p.Ala182Ser,ENST00000349553,NM_007088.3;CALB2,missense_variant,p.Gly142Val,ENST00000490520,;CALB2,intron_variant,,ENST00000562305,;CALB2,non_coding_transcript_exon_variant,,ENST00000467817,; T ENST00000302628 Transcript missense_variant 715/1466 638/816 213/271 G/V gGc/gTc 1 1 CALB2 HGNC HGNC:1435 protein_coding YES CCDS10899.1 ENSP00000307508 P22676 A0A140VK08 UPI000013E7FC NM_001740.4 deleterious(0) 10/11 Gene3D:1.10.238.10,Pfam_domain:PF13405,PROSITE_patterns:PS00018,PROSITE_profiles:PS50222,hmmpanther:PTHR19972,hmmpanther:PTHR19972:SF4,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 71385587 71385587 G T 1 0 0 0 0 1 0 0 0 2264 1203 42 2 2 CALB2 16 71385587 Missense_Mutation SNP G C3N-00580_T 255800 71385587 18952758 807 18942 ZNF23 0 . GRCh38 16 71450606 71450606 + Nonstop_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.252G>T p.Ter84TyrextTer602 p.*84Yext*602 ENST00000497160 6/7 72 38 34 65 65 0 strelka-varscan-mutect ZNF23,stop_lost,p.Ter84TyrextTer602,ENST00000497160,;ZNF23,stop_lost,p.Ter84TyrextTer602,ENST00000358700,;ZNF23,intron_variant,,ENST00000393539,NM_145911.2;ZNF23,intron_variant,,ENST00000357254,NM_001304492.1;ZNF23,intron_variant,,ENST00000564528,NM_001304493.1,NM_001304494.1;ZNF23,intron_variant,,ENST00000428724,;ZNF23,intron_variant,,ENST00000565718,;ZNF23,downstream_gene_variant,,ENST00000567340,;ZNF23,intron_variant,,ENST00000539742,;ZNF23,non_coding_transcript_exon_variant,,ENST00000576258,;AC010547.9,intron_variant,,ENST00000561908,; A ENST00000497160 Transcript stop_lost 497/2799 252/252 84/83 */Y taG/taT 1 -1 ZNF23 HGNC HGNC:13023 protein_coding ENSP00000456683 H0Y310 UPI0002467214 6/7 HIGH SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 71450606 71450606 C A 1 0 0 0 0 0 0 0 0 18360 808 28 2 2 ZNF23 16 71450606 Nonstop_Mutation SNP C C3N-00580_T 65019 71450606 18887739 808 18943 ZNF821 0 . GRCh38 16 71860062 71860062 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1195G>A p.Gly399Ser p.G399S ENST00000425432 8/8 122 74 48 87 87 0 strelka-varscan-mutect ZNF821,missense_variant,p.Gly399Ser,ENST00000425432,NM_001201552.1;ZNF821,missense_variant,p.Gly357Ser,ENST00000313565,NM_001201554.1;ZNF821,missense_variant,p.Gly399Ser,ENST00000565601,NM_001201553.1;ZNF821,missense_variant,p.Gly357Ser,ENST00000446827,NM_017530.2;ZNF821,missense_variant,p.Gly399Ser,ENST00000568666,;ZNF821,3_prime_UTR_variant,,ENST00000611294,NM_001201556.1;ZNF821,3_prime_UTR_variant,,ENST00000564134,;IST1,intron_variant,,ENST00000568581,;ATXN1L,downstream_gene_variant,,ENST00000427980,NM_001137675.3;ZNF821,downstream_gene_variant,,ENST00000562797,;ZNF821,downstream_gene_variant,,ENST00000565516,;ZNF821,downstream_gene_variant,,ENST00000568322,;ZNF821,downstream_gene_variant,,ENST00000565843,;RP11-417N10.4,non_coding_transcript_exon_variant,,ENST00000623505,;ATXN1L,intron_variant,,ENST00000569119,;ZNF821,downstream_gene_variant,,ENST00000564943,;ZNF821,3_prime_UTR_variant,,ENST00000568961,NM_001318238.1;ZNF821,3_prime_UTR_variant,,ENST00000566987,NM_001318239.1;ZNF821,3_prime_UTR_variant,,ENST00000562808,;ZNF821,downstream_gene_variant,,ENST00000563878,;ZNF821,downstream_gene_variant,,ENST00000562985,;ZNF821,downstream_gene_variant,,ENST00000563827,;ZNF821,downstream_gene_variant,,ENST00000569186,; T ENST00000425432 Transcript missense_variant 1618/2000 1195/1239 399/412 G/S Ggc/Agc 1 -1 ZNF821 HGNC HGNC:28043 protein_coding YES CCDS56006.1 ENSP00000398089 O75541 UPI0000EE78C4 NM_001201552.1 tolerated_low_confidence(0.21) 8/8 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 71860062 71860062 C T 1 0 0 0 0 1 0 0 0 18764 623 22 3 3 ZNF821 16 71860062 Missense_Mutation SNP C C3N-00580_T 409456 71860062 18478283 809 18944 PKD1L3 0 . GRCh38 16 71970065 71970065 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1994G>T p.Cys665Phe p.C665F ENST00000620267 13/30 323 205 118 308 308 0 strelka-varscan-mutect PKD1L3,missense_variant,p.Cys665Phe,ENST00000620267,NM_181536.1; A ENST00000620267 Transcript missense_variant 1994/5199 1994/5199 665/1732 C/F tGt/tTt 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 deleterious(0) 13/30 PROSITE_profiles:PS50221,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136,Pfam_domain:PF01825,SMART_domains:SM00303 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 71970065 71970065 C A 1 0 0 0 0 1 0 0 0 12061 478 17 2 2 PKD1L3 16 71970065 Missense_Mutation SNP C C3N-00580_T 110003 71970065 18368280 810 18945 KLHDC4 0 . GRCh38 16 87701653 87701653 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.862G>C p.Asp288His p.D288H ENST00000446344 1/1 62 38 24 92 92 0 strelka-varscan-mutect KLHDC4,missense_variant,p.Asp288His,ENST00000446344,;JPH3,downstream_gene_variant,,ENST00000284262,NM_020655.3;KLHDC4,non_coding_transcript_exon_variant,,ENST00000568346,;JPH3,downstream_gene_variant,,ENST00000563609,;JPH3,downstream_gene_variant,,ENST00000537256,;KLHDC4,downstream_gene_variant,,ENST00000568499,;KLHDC4,upstream_gene_variant,,ENST00000568444,;KLHDC4,3_prime_UTR_variant,,ENST00000567298,; G ENST00000446344 Transcript missense_variant 939/4444 862/876 288/291 D/H Gac/Cac 1 -1 KLHDC4 HGNC HGNC:25272 protein_coding ENSP00000392909 Q86VH3 UPI000018F332 1/1 MODERATE SNV 1 PASS rs1366235870 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 87701653 87701653 C G 1 0 0 0 0 1 0 0 0 8223 855 30 4 4 KLHDC4 16 87701653 Missense_Mutation SNP C C3N-00580_T 15731588 87701653 2636692 811 18946 ZNF469 0 . GRCh38 16 88436683 88436683 + Silent SNP C C G rs267604675 C3N-00580_T C3N-00580_N C C c.9129C>G p.= p.P3043P ENST00000437464 2/2 125 75 50 190 190 0 strelka-varscan-mutect ZNF469,synonymous_variant,p.=,ENST00000565624,;ZNF469,synonymous_variant,p.=,ENST00000437464,NM_001127464.2; G ENST00000437464 Transcript synonymous_variant 9129/13203 9129/11778 3043/3925 P ccC/ccG rs267604675 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 LOW 1 SNV 5 1 PASS rs267604675 . 0 205 2 2 0 0 0 0 -20 0.9999997 1 1 1 0 G 2 3 61 88436683 88436683 C G 1 0 0 0 0 0 0 0 1 18500 639 23 4 4 ZNF469 16 88436683 Silent SNP C C3N-00580_T 735030 88436683 1901662 812 18947 SPIRE2 0 . GRCh38 16 89856162 89856162 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1028A>T p.His343Leu p.H343L ENST00000378247 7/15 157 103 54 245 245 0 strelka-varscan-mutect SPIRE2,missense_variant,p.His343Leu,ENST00000378247,NM_032451.1;SPIRE2,missense_variant,p.His343Leu,ENST00000393062,;SPIRE2,3_prime_UTR_variant,,ENST00000566337,;SPIRE2,non_coding_transcript_exon_variant,,ENST00000569108,;SPIRE2,downstream_gene_variant,,ENST00000561883,; T ENST00000378247 Transcript missense_variant 1071/3235 1028/2145 343/714 H/L cAt/cTt 1 1 SPIRE2 HGNC HGNC:30623 protein_coding YES CCDS32516.1 ENSP00000367494 Q8WWL2 UPI00001C1FA8 NM_032451.1 deleterious(0) 7/15 PROSITE_profiles:PS51082,hmmpanther:PTHR21345,hmmpanther:PTHR21345:SF5 MODERATE 1 SNV 1 1 PASS rs1184028157 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 89856162 89856162 A T 1 0 0 0 0 1 0 0 0 15425 217 8 4 4 SPIRE2 16 89856162 Missense_Mutation SNP A C3N-00580_T 1419479 89856162 482183 813 18948 USP6 0 . GRCh38 17 5137706 5137706 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.881A>T p.Gln294Leu p.Q294L ENST00000574788 20/38 163 106 57 289 289 0 strelka-varscan-mutect USP6,missense_variant,p.Gln294Leu,ENST00000574788,NM_001304284.1;USP6,missense_variant,p.Gln294Leu,ENST00000250066,NM_004505.3;USP6,downstream_gene_variant,,ENST00000572429,;USP6,missense_variant,p.Gln294Leu,ENST00000575709,;USP6,missense_variant,p.Gln294Leu,ENST00000572949,;USP6,downstream_gene_variant,,ENST00000357482,; T ENST00000574788 Transcript missense_variant 3111/8464 881/4221 294/1406 Q/L cAg/cTg 1 1 USP6 HGNC HGNC:12629 protein_coding YES CCDS11069.2 ENSP00000460380 P35125 UPI000006226F NM_001304284.1 deleterious_low_confidence(0) 20/38 Pfam_domain:PF00566,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF233,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 5137706 5137706 A T 1 0 0 0 0 1 0 0 0 17629 188 7 4 4 USP6 17 5137706 Missense_Mutation SNP A C3N-00580_T 5137706 78119735 814 18949 NLRP1 0 . GRCh38 17 5530668 5530669 + Frame_Shift_Del DEL GG GG - novel C3N-00580_T C3N-00580_N GG GG c.3332_3333delCC p.Pro1111GlnfsTer15 p.P1111Qfs*15 ENST00000617618 13/18 228 138 90 344 344 0 sindel-varindel NLRP1,frameshift_variant,p.Pro1115GlnfsTer15,ENST00000262467,NM_001033053.2;NLRP1,frameshift_variant,p.Pro1111GlnfsTer15,ENST00000269280,NM_014922.4;NLRP1,frameshift_variant,p.Pro1111GlnfsTer15,ENST00000617618,NM_033004.3;NLRP1,frameshift_variant,p.Pro1081GlnfsTer15,ENST00000619223,NM_033006.3;NLRP1,frameshift_variant,p.Pro1111GlnfsTer15,ENST00000345221,;NLRP1,frameshift_variant,p.Pro1115GlnfsTer15,ENST00000613500,;NLRP1,frameshift_variant,p.Pro1111GlnfsTer15,ENST00000572272,;NLRP1,frameshift_variant,p.Pro1081GlnfsTer15,ENST00000354411,;NLRP1,frameshift_variant,p.Pro1081GlnfsTer15,ENST00000577119,NM_033007.3;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,frameshift_variant,p.Pro1115GlnfsTer15,ENST00000544378,;NLRP1,3_prime_UTR_variant,,ENST00000571451,; - ENST00000617618 Transcript frameshift_variant 3698-3699/4788 3332-3333/4422 1111/1473 P/X cCC/c 1 -1 NLRP1 HGNC HGNC:14374 protein_coding YES CCDS42246.1 ENSP00000478516 Q9C000 UPI0000038309 NM_033004.3 13/18 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF13,Pfam_domain:PF13553 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 5530668 5530668 GG - 1 0 1 0 1 0 0 0 0 10508 1335 47 0 0 NLRP1 17 5530668 Frame_Shift_Del DEL GG C3N-00580_T 392962 5530668 77726773 815 18950 WSCD1 0 . GRCh38 17 6120339 6120339 + Nonsense_Mutation SNP C C A rs148765035 C3N-00580_T C3N-00580_N C C c.1406C>A p.Ser469Ter p.S469* ENST00000574946 9/9 89 57 32 171 170 1 strelka-varscan-mutect WSCD1,stop_gained,p.Ser469Ter,ENST00000574946,;WSCD1,stop_gained,p.Ser469Ter,ENST00000317744,NM_015253.1;WSCD1,stop_gained,p.Ser469Ter,ENST00000539421,;WSCD1,stop_gained,p.Ser469Ter,ENST00000574232,;WSCD1,stop_gained,p.Ser353Ter,ENST00000573634,;WSCD1,3_prime_UTR_variant,,ENST00000571494,; A ENST00000574946 Transcript stop_gained 1796/5884 1406/1728 469/575 S/* tCg/tAg rs148765035,COSM3520476 1 1 WSCD1 HGNC HGNC:29060 protein_coding YES CCDS32538.1 ENSP00000460825 Q658N2 UPI0000197208 9/9 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF90,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 0,1 HIGH 1 SNV 2 0,1 1 PASS rs148765035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 6120339 6120339 C A 1 0 0 0 0 0 1 0 0 17963 893 31 1 1 WSCD1 17 6120339 Nonsense_Mutation SNP C C3N-00580_T 589671 6120339 77137102 816 18951 TP53 0 . GRCh38 17 7673806 7673806 + Missense_Mutation SNP C C A rs121912657 C3N-00580_T C3N-00580_N C C c.814G>T p.Val272Leu p.V272L ENST00000269305 8/11 597 381 216 946 945 1 strelka-varscan-mutect TP53,missense_variant,p.Val272Leu,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Val272Leu,ENST00000420246,;TP53,missense_variant,p.Val233Leu,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Val233Leu,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Val272Leu,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Val233Leu,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Val272Leu,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Val233Leu,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Val272Leu,ENST00000445888,;TP53,missense_variant,p.Val233Leu,ENST00000619485,;TP53,missense_variant,p.Val140Leu,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Val113Leu,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Val140Leu,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Val113Leu,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Val140Leu,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Val113Leu,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Val272Leu,ENST00000359597,;TP53,missense_variant,p.Val261Leu,ENST00000615910,;TP53,missense_variant,p.Val140Leu,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Val233Leu,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 1004/2579 814/1182 272/393 V/L Gtg/Ttg rs121912657,CM920676,TP53_g.13794G>T,TP53_g.13794del,TP53_g.13794G>C,TP53_g.13794G>A,COSM10859,COSM10891,COSM1177737,COSM13421,COSM1645249,COSM212313,COSM2744536,COSM2744537,COSM3388172,COSM3773300,COSM4271766,COSM45898,COSM99950 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 7673806 7673806 C A 1 0 0 0 0 1 0 0 0 16859 507 18 2 2 TP53 17 7673806 Missense_Mutation SNP C C3N-00580_T 1553467 7673806 75583635 817 18952 DNAH2 0 . GRCh38 17 7740426 7740426 + Silent SNP T T G novel C3N-00580_T C3N-00580_N T T c.1383T>G p.= p.R461R ENST00000572933 10/86 81 60 21 158 158 0 strelka-varscan-mutect DNAH2,synonymous_variant,p.=,ENST00000572933,NM_020877.3;DNAH2,synonymous_variant,p.=,ENST00000389173,;DNAH2,synonymous_variant,p.=,ENST00000570791,NM_001303270.1;DNAH2,upstream_gene_variant,,ENST00000575498,; G ENST00000572933 Transcript synonymous_variant 2843/14955 1383/13284 461/4427 R cgT/cgG 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 10/86 hmmpanther:PTHR10676:SF183,hmmpanther:PTHR10676,Pfam_domain:PF08385 LOW 1 SNV 1 1 PASS rs1170773744 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 7740426 7740426 T G 1 0 0 0 0 0 0 0 1 4417 1683 59 5 5 DNAH2 17 7740426 Silent SNP T C3N-00580_T 66620 7740426 75517015 818 18953 MFSD6L 0 . GRCh38 17 8798472 8798473 + Frame_Shift_Ins INS - - C rs34855885 C3N-00580_T C3N-00580_N - - c.648dupG p.Lys217GlufsTer20 p.K217Efs*20 ENST00000329805 1/1 39 35 4 76 76 0 sindel-pindel MFSD6L,frameshift_variant,p.Lys217GlufsTer20,ENST00000329805,NM_152599.3;PIK3R6,downstream_gene_variant,,ENST00000619866,NM_001010855.3,NM_001290211.1;PIK3R6,downstream_gene_variant,,ENST00000614407,;PIK3R6,downstream_gene_variant,,ENST00000611951,;PIK3R6,downstream_gene_variant,,ENST00000613555,; C ENST00000329805 Transcript frameshift_variant 877-878/2188 648-649/1761 216-217/586 -/X -/G rs34855885 1 -1 MFSD6L HGNC HGNC:26656 protein_coding YES CCDS11146.1 ENSP00000330051 Q8IWD5 UPI0000141B5F NM_152599.3 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR16172:SF22,hmmpanther:PTHR16172,Pfam_domain:PF12832 HIGH insertion 1 PASS . . 0 191 17 2 0 0 0 0 -8.841372 0.9854479 1 1 1 0 C 7 5 61 8798472 8798472 - C 1 0 1 1 0 0 0 0 0 9494 1792 62 0 0 MFSD6L 17 8798472 Frame_Shift_Ins INS - C3N-00580_T 1058046 8798472 74458969 819 18954 PIK3R5 0 . GRCh38 17 8888367 8888367 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1420C>A p.Gln474Lys p.Q474K ENST00000447110 10/19 92 63 29 146 146 0 strelka-varscan-mutect PIK3R5,missense_variant,p.Gln474Lys,ENST00000447110,NM_001142633.2;PIK3R5,missense_variant,p.Gln88Lys,ENST00000616147,NM_001251852.1;PIK3R5,missense_variant,p.Gln88Lys,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,missense_variant,p.Gln88Lys,ENST00000623421,NM_001251855.1;PIK3R5,missense_variant,p.Gln474Lys,ENST00000581552,NM_014308.3;PIK3R5,missense_variant,p.Gln474Lys,ENST00000584803,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,; T ENST00000447110 Transcript missense_variant 1550/4495 1420/2643 474/880 Q/K Cag/Aag 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 tolerated(1) 10/19 Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 8888367 8888367 G T 1 0 0 0 0 1 0 0 0 12017 1357 47 2 2 PIK3R5 17 8888367 Missense_Mutation SNP G C3N-00580_T 89895 8888367 74369074 820 18955 MYH4 0 . GRCh38 17 10460291 10460291 + Missense_Mutation SNP A A C novel C3N-00580_T C3N-00580_N A A c.1178T>G p.Leu393Arg p.L393R ENST00000255381 13/40 66 57 9 101 101 0 strelka-varscan-mutect MYH4,missense_variant,p.Leu393Arg,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; C ENST00000255381 Transcript missense_variant 1289/6016 1178/5820 393/1939 L/R cTg/cGg 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0) 13/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.91213 1 1 1 1 0 C 3 2 61 10460291 10460291 A C 1 0 0 0 0 1 0 0 0 10037 188 7 5 5 MYH4 17 10460291 Missense_Mutation SNP A C3N-00580_T 1571924 10460291 72797150 821 18956 ZNF18 0 . GRCh38 17 11990521 11990521 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.607G>T p.Glu203Ter p.E203* ENST00000322748 6/9 134 78 56 218 218 0 strelka-varscan-mutect ZNF18,stop_gained,p.Glu203Ter,ENST00000322748,NM_144680.3;ZNF18,stop_gained,p.Glu203Ter,ENST00000580306,NM_001303281.1;ZNF18,stop_gained,p.Glu203Ter,ENST00000454073,NM_001303282.1;ZNF18,stop_gained,p.Glu203Ter,ENST00000580613,;ZNF18,stop_gained,p.Glu27Ter,ENST00000582607,;ZNF18,stop_gained,p.Glu24Ter,ENST00000577671,;ZNF18,downstream_gene_variant,,ENST00000580903,; A ENST00000322748 Transcript stop_gained 1212/2767 607/1650 203/549 E/* Gag/Tag 1 -1 ZNF18 HGNC HGNC:12969 protein_coding YES CCDS32568.1 ENSP00000315664 P17022 UPI00000703B9 NM_144680.3 6/9 hmmpanther:PTHR10032:SF11,hmmpanther:PTHR10032 HIGH 1 SNV 2 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999886 1 1 1 0 A 4 1 61 11990521 11990521 C A 1 0 0 0 0 0 1 0 0 18327 864 30 2 2 ZNF18 17 11990521 Nonsense_Mutation SNP C C3N-00580_T 1530230 11990521 71266920 822 18957 WSB1 0 . GRCh38 17 27303525 27303525 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.368A>G p.Gln123Arg p.Q123R ENST00000262394 3/9 448 325 123 369 369 0 strelka-varscan-mutect WSB1,missense_variant,p.Gln123Arg,ENST00000262394,NM_015626.8;WSB1,missense_variant,p.Gln123Arg,ENST00000581185,;WSB1,missense_variant,p.Gln92Arg,ENST00000427287,;WSB1,missense_variant,p.Gln130Arg,ENST00000581440,;WSB1,intron_variant,,ENST00000579733,;WSB1,intron_variant,,ENST00000348811,NM_134265.2;WSB1,intron_variant,,ENST00000583193,;WSB1,intron_variant,,ENST00000584114,;WSB1,downstream_gene_variant,,ENST00000583742,;WSB1,downstream_gene_variant,,ENST00000578312,;WSB1,downstream_gene_variant,,ENST00000583786,;WSB1,non_coding_transcript_exon_variant,,ENST00000467843,;WSB1,non_coding_transcript_exon_variant,,ENST00000487603,;WSB1,non_coding_transcript_exon_variant,,ENST00000583096,;WSB1,non_coding_transcript_exon_variant,,ENST00000581089,;WSB1,intron_variant,,ENST00000582208,;WSB1,downstream_gene_variant,,ENST00000584354,; G ENST00000262394 Transcript missense_variant 684/5139 368/1266 123/421 Q/R cAg/cGg 1 1 WSB1 HGNC HGNC:19221 protein_coding YES CCDS11220.1 ENSP00000262394 Q9Y6I7 A0A024QZ51 UPI0000031568 NM_015626.8 tolerated(0.37) 3/9 hmmpanther:PTHR15622:SF12,hmmpanther:PTHR15622,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 27303525 27303525 A G 1 0 0 0 0 1 0 0 0 17961 188 7 5 5 WSB1 17 27303525 Missense_Mutation SNP A C3N-00580_T 15313004 27303525 55953916 823 18958 EFCAB5 0 . GRCh38 17 30080224 30080224 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.3180G>A p.= p.R1060R ENST00000394835 16/23 60 52 8 68 68 0 strelka-varscan-mutect EFCAB5,synonymous_variant,p.=,ENST00000394835,NM_198529.3;EFCAB5,synonymous_variant,p.=,ENST00000419434,;EFCAB5,intron_variant,,ENST00000588978,; A ENST00000394835 Transcript synonymous_variant 3372/5132 3180/4512 1060/1503 R agG/agA 1 1 EFCAB5 HGNC HGNC:24801 protein_coding YES CCDS11254.2 ENSP00000378312 A4FU69 UPI0000E59EF5 NM_198529.3 16/23 hmmpanther:PTHR31938,hmmpanther:PTHR31938:SF6,Superfamily_domains:SSF55781 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.60834 1 1 1 1 0 A 2 1 61 30080224 30080224 G A 1 0 0 0 0 0 0 0 1 4772 1223 43 3 3 EFCAB5 17 30080224 Silent SNP G C3N-00580_T 2776699 30080224 53177217 824 18959 TBC1D29 0 . GRCh38 17 30563292 30563292 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.320C>G p.Pro107Arg p.P107R ENST00000580161 6/6 590 464 126 566 566 0 strelka-varscan-mutect TBC1D29,missense_variant,p.Pro107Arg,ENST00000580161,;TBC1D29,missense_variant,p.Pro107Arg,ENST00000579181,NM_015594.2;TBC1D29,3_prime_UTR_variant,,ENST00000584297,;RP11-218M11.1,downstream_gene_variant,,ENST00000563063,;RP11-218M11.6,upstream_gene_variant,,ENST00000582125,;TBC1D29,non_coding_transcript_exon_variant,,ENST00000582511,;KRT17P3,downstream_gene_variant,,ENST00000420566,;RP11-271K11.1,downstream_gene_variant,,ENST00000578471,; G ENST00000580161 Transcript missense_variant 2817/3018 320/453 107/150 P/R cCc/cGc 1 1 TBC1D29 HGNC HGNC:24509 protein_coding YES CCDS32606.1 ENSP00000462799 Q9UFV1 UPI00000702F8 deleterious(0) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 30563292 30563292 C G 1 0 0 0 0 1 0 0 0 16018 623 22 4 4 TBC1D29 17 30563292 Missense_Mutation SNP C C3N-00580_T 483068 30563292 52694149 825 18960 SLFN14 0 . GRCh38 17 35557378 35557378 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.685C>A p.Pro229Thr p.P229T ENST00000415846 1/4 276 171 105 280 280 0 strelka-varscan-mutect SLFN14,missense_variant,p.Pro229Thr,ENST00000415846,NM_001129820.1;RP11-1094M14.14,downstream_gene_variant,,ENST00000591634,;RP11-1094M14.12,downstream_gene_variant,,ENST00000588445,; T ENST00000415846 Transcript missense_variant 721/2889 685/2739 229/912 P/T Cct/Act 1 -1 SLFN14 HGNC HGNC:32689 protein_coding YES CCDS45650.1 ENSP00000391101 P0C7P3 UPI000041A9FB NM_001129820.1 deleterious(0.01) 1/4 hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF30,Pfam_domain:PF04326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 35557378 35557378 G T 1 0 0 0 0 1 0 0 0 15026 1203 42 2 2 SLFN14 17 35557378 Missense_Mutation SNP G C3N-00580_T 4994086 35557378 47700063 826 18961 KRTAP4-11 0 . GRCh38 17 41118194 41118194 + Missense_Mutation SNP C C T rs750400835 C3N-00580_T C3N-00580_N C C c.122G>A p.Arg41His p.R41H ENST00000391413 1/1 399 338 61 406 406 0 strelka-varscan-mutect KRTAP4-11,missense_variant,p.Arg41His,ENST00000391413,NM_001322457.1,NM_033059.3;KRTAP4-12,downstream_gene_variant,,ENST00000394014,NM_031854.2; T ENST00000391413 Transcript missense_variant 167/1180 122/588 41/195 R/H cGc/cAc rs750400835,COSM3402868 1 -1 KRTAP4-11 HGNC HGNC:18911 protein_coding YES CCDS45675.1 ENSP00000375232 Q9BYQ6 UPI00001AFBF7 NM_001322457.1,NM_033059.3 tolerated(0.06) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262:SF1,hmmpanther:PTHR23262,Pfam_domain:PF13885 0,1 MODERATE 1 SNV 0,1 1 PASS rs750400835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 41118194 41118194 C T 1 0 0 0 0 1 0 0 0 8442 768 27 1 1 KRTAP4-11 17 41118194 Missense_Mutation SNP C C3N-00580_T 5560816 41118194 42139247 827 18962 KRTAP4-12 0 . GRCh38 17 41123570 41123570 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.553T>A p.Cys185Ser p.C185S ENST00000394014 1/1 256 199 57 212 211 1 strelka-varscan-mutect KRTAP4-12,missense_variant,p.Cys185Ser,ENST00000394014,NM_031854.2; T ENST00000394014 Transcript missense_variant 598/1077 553/606 185/201 C/S Tgt/Agt 1 -1 KRTAP4-12 HGNC HGNC:16776 protein_coding YES CCDS32649.1 ENSP00000377582 Q9BQ66 UPI0000072F19 NM_031854.2 deleterious(0.02) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 41123570 41123570 A T 1 0 0 0 0 1 0 0 0 8443 188 7 4 4 KRTAP4-12 17 41123570 Missense_Mutation SNP A C3N-00580_T 5376 41123570 42133871 828 18963 KRT13 0 . GRCh38 17 41505382 41505382 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.169G>T p.Ala57Ser p.A57S ENST00000246635 1/8 214 173 41 163 163 0 strelka-varscan-mutect KRT13,missense_variant,p.Ala57Ser,ENST00000246635,NM_153490.2;KRT13,missense_variant,p.Ala57Ser,ENST00000336861,NM_002274.3;KRT13,missense_variant,p.Ala57Ser,ENST00000587544,;KRT13,missense_variant,p.Ala57Ser,ENST00000587435,;KRT13,intron_variant,,ENST00000590425,;AC019349.5,downstream_gene_variant,,ENST00000411759,;KRT13,upstream_gene_variant,,ENST00000587118,;KRT13,upstream_gene_variant,,ENST00000475217,;KRT13,intron_variant,,ENST00000468313,;KRT13,intron_variant,,ENST00000464634,; A ENST00000246635 Transcript missense_variant 216/1699 169/1377 57/458 A/S Gct/Tct 1 -1 KRT13 HGNC HGNC:6415 protein_coding YES CCDS11396.1 ENSP00000246635 P13646 UPI000013CBF6 NM_153490.2 tolerated(0.75) 1/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF121,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1261980775 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 41505382 41505382 C A 1 0 0 0 0 1 0 0 0 8332 739 26 2 2 KRT13 17 41505382 Missense_Mutation SNP C C3N-00580_T 381812 41505382 41752059 829 18964 STAT5B 0 . GRCh38 17 42217279 42217279 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1261C>A p.Leu421Met p.L421M ENST00000293328 11/19 801 624 177 715 715 0 strelka-varscan-mutect STAT5B,missense_variant,p.Leu421Met,ENST00000293328,NM_012448.3;STAT5B,non_coding_transcript_exon_variant,,ENST00000481517,;STAT5B,non_coding_transcript_exon_variant,,ENST00000468496,;STAT5B,downstream_gene_variant,,ENST00000468312,; T ENST00000293328 Transcript missense_variant 1430/5103 1261/2364 421/787 L/M Ctg/Atg 1 -1 STAT5B HGNC HGNC:11367 protein_coding YES CCDS11423.1 ENSP00000293328 P51692 UPI000006F059 NM_012448.3 deleterious(0) 11/19 Gene3D:2.60.40.630,Pfam_domain:PF02864,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF39,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 42217279 42217279 G T 1 0 0 0 0 1 0 0 0 15645 1014 35 2 2 STAT5B 17 42217279 Missense_Mutation SNP G C3N-00580_T 711897 42217279 41040162 830 18965 STAT5B 0 . GRCh38 17 42219793 42219793 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.600G>T p.= p.R200R ENST00000293328 6/19 140 62 78 150 149 1 strelka-varscan-mutect STAT5B,synonymous_variant,p.=,ENST00000293328,NM_012448.3;STAT5B,downstream_gene_variant,,ENST00000415845,;STAT5B,non_coding_transcript_exon_variant,,ENST00000468312,;STAT5B,upstream_gene_variant,,ENST00000481517,;STAT5B,upstream_gene_variant,,ENST00000468496,; A ENST00000293328 Transcript synonymous_variant 769/5103 600/2364 200/787 R cgG/cgT 1 -1 STAT5B HGNC HGNC:11367 protein_coding YES CCDS11423.1 ENSP00000293328 P51692 UPI000006F059 NM_012448.3 6/19 Gene3D:1bg1A01,Pfam_domain:PF01017,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF39,Superfamily_domains:SSF47655 LOW 1 SNV 1 1 PASS rs1390762705 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 42219793 42219793 C A 1 0 0 0 0 0 0 0 1 15645 610 22 2 2 STAT5B 17 42219793 Silent SNP C C3N-00580_T 2514 42219793 41037648 831 18966 STAT3 0 . GRCh38 17 42325041 42325041 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1386G>T p.= p.V462V ENST00000264657 16/24 238 158 80 196 196 0 strelka-varscan-mutect STAT3,synonymous_variant,p.=,ENST00000264657,NM_139276.2;STAT3,synonymous_variant,p.=,ENST00000585517,NM_213662.1;STAT3,synonymous_variant,p.=,ENST00000588969,;STAT3,synonymous_variant,p.=,ENST00000404395,NM_003150.3;STAT3,synonymous_variant,p.=,ENST00000389272,;STAT3,non_coding_transcript_exon_variant,,ENST00000471989,;STAT3,non_coding_transcript_exon_variant,,ENST00000498330,;STAT3,downstream_gene_variant,,ENST00000478276,; A ENST00000264657 Transcript synonymous_variant 1699/5047 1386/2313 462/770 V gtG/gtT 1 -1 STAT3 HGNC HGNC:11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 UPI0000031047 NM_139276.2 16/24 hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF2,Pfam_domain:PF02864,Gene3D:2.60.40.630,Superfamily_domains:SSF49417 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 42325041 42325041 C A 1 0 0 0 0 0 0 0 1 15642 581 21 2 2 STAT3 17 42325041 Silent SNP C C3N-00580_T 105248 42325041 40932400 832 18967 CNTNAP1 0 . GRCh38 17 42685282 42685282 + Nonsense_Mutation SNP C C T rs752924771 C3N-00580_T C3N-00580_N C C c.577C>T p.Arg193Ter p.R193* ENST00000264638 5/24 409 275 134 447 447 0 strelka-varscan-mutect CNTNAP1,stop_gained,p.Arg193Ter,ENST00000264638,NM_003632.2;CCR10,upstream_gene_variant,,ENST00000591765,;CCR10,upstream_gene_variant,,ENST00000332438,NM_016602.2;CCR10,upstream_gene_variant,,ENST00000591568,;CTD-3193K9.3,intron_variant,,ENST00000592440,;CTD-3193K9.4,downstream_gene_variant,,ENST00000593139,;CNTNAP1,stop_gained,p.Arg193Ter,ENST00000591662,;CNTNAP1,upstream_gene_variant,,ENST00000586801,;CNTNAP1,upstream_gene_variant,,ENST00000585534,; T ENST00000264638 Transcript stop_gained 794/5276 577/4155 193/1384 R/* Cga/Tga rs752924771 1 1 CNTNAP1 HGNC HGNC:8011 protein_coding YES CCDS11436.1 ENSP00000264638 P78357 UPI00001285F6 NM_003632.2 5/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF4,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS rs752924771 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 42685282 42685282 C T 1 0 0 0 0 0 1 0 0 3427 644 23 1 1 CNTNAP1 17 42685282 Nonsense_Mutation SNP C C3N-00580_T 360241 42685282 40572159 833 18968 RPL27 0 . GRCh38 17 43002704 43002704 + Missense_Mutation SNP G G C rs765351338 C3N-00580_T C3N-00580_N G G c.283G>C p.Val95Leu p.V95L ENST00000589913 3/4 289 230 59 285 285 0 strelka-varscan-mutect RPL27,missense_variant,p.Val95Leu,ENST00000589913,;RPL27,missense_variant,p.Val95Leu,ENST00000589037,;RPL27,missense_variant,p.Val39Leu,ENST00000590864,;RPL27,missense_variant,p.Val95Leu,ENST00000253788,NM_000988.3;RPL27,missense_variant,p.Val103Leu,ENST00000586277,;IFI35,upstream_gene_variant,,ENST00000415816,;IFI35,upstream_gene_variant,,ENST00000438323,NM_005533.4;IFI35,upstream_gene_variant,,ENST00000536969,;RPL27,missense_variant,p.Cys38Ser,ENST00000588830,;RPL27,non_coding_transcript_exon_variant,,ENST00000593262,;IFI35,upstream_gene_variant,,ENST00000246911,;IFI35,upstream_gene_variant,,ENST00000396722,;RPL27,downstream_gene_variant,,ENST00000587478,; C ENST00000589913 Transcript missense_variant 557/697 283/411 95/136 V/L Gtc/Ctc rs765351338 1 1 RPL27 HGNC HGNC:10328 protein_coding YES CCDS11449.1 ENSP00000464813 P61353 A0A024R1V4 UPI00000002E0 tolerated(0.18) 3/4 hmmpanther:PTHR10497:SF1,hmmpanther:PTHR10497,Pfam_domain:PF01777,Gene3D:2.30.30.30,Superfamily_domains:SSF50104,PD009396 MODERATE 1 SNV 1 1 PASS rs765351338 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 43002704 43002704 G C 1 0 0 0 0 1 0 0 0 13827 1377 48 4 4 RPL27 17 43002704 Missense_Mutation SNP G C3N-00580_T 317422 43002704 40254737 834 18969 SLC4A1 0 . GRCh38 17 44257440 44257440 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.1536G>T p.= p.L512L ENST00000262418 13/20 475 358 117 438 438 0 strelka-varscan-mutect SLC4A1,synonymous_variant,p.=,ENST00000262418,NM_000342.3;SLC4A1,intron_variant,,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; A ENST00000262418 Transcript synonymous_variant 1692/4965 1536/2736 512/911 L ctG/ctT 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 13/20 Pfam_domain:PF00955,Prints_domain:PR01231,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,TIGRFAM_domain:TIGR00834,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 44257440 44257440 C A 1 0 0 0 0 0 0 0 1 14927 581 21 2 2 SLC4A1 17 44257440 Silent SNP C C3N-00580_T 1254736 44257440 39000001 835 18970 MEIOC 0 . GRCh38 17 44667438 44667438 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1527A>T p.Lys509Asn p.K509N ENST00000409122 5/8 73 55 18 92 92 0 strelka-varscan-mutect MEIOC,missense_variant,p.Lys509Asn,ENST00000409122,NM_001145080.2;MEIOC,missense_variant,p.Lys343Asn,ENST00000409464,;MEIOC,downstream_gene_variant,,ENST00000432494,;MEIOC,downstream_gene_variant,,ENST00000456912,;MEIOC,upstream_gene_variant,,ENST00000472403,; T ENST00000409122 Transcript missense_variant 1669/4604 1527/2859 509/952 K/N aaA/aaT 1 1 MEIOC HGNC HGNC:26670 protein_coding YES CCDS45703.2 ENSP00000386452 A2RUB1 UPI0001881A86 NM_001145080.2 deleterious(0) 5/8 hmmpanther:PTHR33861,hmmpanther:PTHR33861:SF3 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 44667438 44667438 A T 1 0 0 0 0 1 0 0 0 9410 69 3 4 4 MEIOC 17 44667438 Missense_Mutation SNP A C3N-00580_T 409998 44667438 38590003 836 18971 MEIOC 0 . GRCh38 17 44667977 44667977 + Missense_Mutation SNP C C A rs767292987 C3N-00580_T C3N-00580_N C C c.2066C>A p.Pro689His p.P689H ENST00000409122 5/8 179 140 39 166 166 0 strelka-varscan-mutect MEIOC,missense_variant,p.Pro689His,ENST00000409122,NM_001145080.2;MEIOC,missense_variant,p.Pro523His,ENST00000409464,;MEIOC,downstream_gene_variant,,ENST00000432494,;MEIOC,downstream_gene_variant,,ENST00000456912,;MEIOC,upstream_gene_variant,,ENST00000472403,; A ENST00000409122 Transcript missense_variant 2208/4604 2066/2859 689/952 P/H cCc/cAc rs767292987 1 1 MEIOC HGNC HGNC:26670 protein_coding YES CCDS45703.2 ENSP00000386452 A2RUB1 UPI0001881A86 NM_001145080.2 deleterious(0) 5/8 hmmpanther:PTHR33861,hmmpanther:PTHR33861:SF3 MODERATE 1 SNV 5 1 PASS rs767292987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 44667977 44667977 C A 1 0 0 0 0 1 0 0 0 9410 623 22 2 2 MEIOC 17 44667977 Missense_Mutation SNP C C3N-00580_T 539 44667977 38589464 837 18972 OSBPL7 0 . GRCh38 17 47808983 47808983 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.2178G>C p.Met726Ile p.M726I ENST00000007414 21/23 214 128 86 217 217 0 strelka-varscan-mutect OSBPL7,missense_variant,p.Met726Ile,ENST00000007414,NM_145798.2;OSBPL7,missense_variant,p.Met726Ile,ENST00000392507,;OSBPL7,3_prime_UTR_variant,,ENST00000613735,;OSBPL7,3_prime_UTR_variant,,ENST00000579728,;OSBPL7,non_coding_transcript_exon_variant,,ENST00000583167,;OSBPL7,intron_variant,,ENST00000578461,; G ENST00000007414 Transcript missense_variant 2370/3640 2178/2529 726/842 M/I atG/atC 1 -1 OSBPL7 HGNC HGNC:16387 protein_coding YES CCDS11515.1 ENSP00000007414 Q9BZF2 UPI0000130E98 NM_145798.2 deleterious(0.03) 21/23 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF85,Pfam_domain:PF01237,Superfamily_domains:0051579 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 47808983 47808983 C G 1 0 0 0 0 1 0 0 0 11348 710 25 4 4 OSBPL7 17 47808983 Missense_Mutation SNP C C3N-00580_T 3141006 47808983 35448458 838 18973 SCRN2 0 . GRCh38 17 47838637 47838637 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.832A>G p.Met278Val p.M278V ENST00000290216 6/8 265 184 81 286 286 0 strelka-varscan-mutect SCRN2,missense_variant,p.Met278Val,ENST00000407215,NM_001145023.1;SCRN2,missense_variant,p.Met286Val,ENST00000584123,;SCRN2,missense_variant,p.Met278Val,ENST00000290216,NM_138355.3;SCRN2,missense_variant,p.Met144Val,ENST00000584567,;LRRC46,downstream_gene_variant,,ENST00000269025,NM_033413.3;SCRN2,downstream_gene_variant,,ENST00000578323,;SCRN2,3_prime_UTR_variant,,ENST00000582459,;SCRN2,3_prime_UTR_variant,,ENST00000581645,;SCRN2,3_prime_UTR_variant,,ENST00000579856,;LRRC46,downstream_gene_variant,,ENST00000584580,;SCRN2,downstream_gene_variant,,ENST00000581546,;SCRN2,downstream_gene_variant,,ENST00000578840,;LRRC46,downstream_gene_variant,,ENST00000579971,;LRRC46,downstream_gene_variant,,ENST00000584809,;LRRC46,downstream_gene_variant,,ENST00000579742,;SCRN2,downstream_gene_variant,,ENST00000580428,;SCRN2,downstream_gene_variant,,ENST00000583090,;SCRN2,downstream_gene_variant,,ENST00000582656,; C ENST00000290216 Transcript missense_variant 958/1548 832/1278 278/425 M/V Atg/Gtg 1 -1 SCRN2 HGNC HGNC:30381 protein_coding YES CCDS11519.1 ENSP00000290216 Q96FV2 UPI000013DFCB NM_138355.3 tolerated(0.29) 6/8 hmmpanther:PTHR12994,hmmpanther:PTHR12994:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 47838637 47838637 T C 1 0 0 0 0 1 0 0 0 14209 1406 49 5 5 SCRN2 17 47838637 Missense_Mutation SNP T C3N-00580_T 29654 47838637 35418804 839 18974 PHOSPHO1 0 . GRCh38 17 49224420 49224420 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.705C>A p.= p.P235P ENST00000413580 3/3 161 111 50 147 147 0 strelka-varscan-mutect PHOSPHO1,synonymous_variant,p.=,ENST00000413580,NM_001143804.1;PHOSPHO1,synonymous_variant,p.=,ENST00000310544,NM_178500.3;PHOSPHO1,synonymous_variant,p.=,ENST00000514112,;ABI3,downstream_gene_variant,,ENST00000225941,NM_016428.2;ABI3,downstream_gene_variant,,ENST00000419580,NM_001135186.1;PHOSPHO1,downstream_gene_variant,,ENST00000511066,;ABI3,downstream_gene_variant,,ENST00000571035,;PHOSPHO1,downstream_gene_variant,,ENST00000503902,;ABI3,downstream_gene_variant,,ENST00000573347,;PHOSPHO1,downstream_gene_variant,,ENST00000512250,;PHOSPHO1,downstream_gene_variant,,ENST00000574638,; T ENST00000413580 Transcript synonymous_variant 1123/2173 705/879 235/292 P ccC/ccA 1 -1 PHOSPHO1 HGNC HGNC:16815 protein_coding YES CCDS45726.1 ENSP00000406909 Q8TCT1 UPI000189C296 NM_001143804.1 3/3 Gene3D:3.40.50.1000,Pfam_domain:PF06888,PIRSF_domain:PIRSF031051,hmmpanther:PTHR20889,hmmpanther:PTHR20889:SF2,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01488,TIGRFAM_domain:TIGR01489 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 49224420 49224420 G T 1 0 0 0 0 0 0 0 1 11944 1335 47 2 2 PHOSPHO1 17 49224420 Silent SNP G C3N-00580_T 1385783 49224420 34033021 840 18975 KIF2B 0 . GRCh38 17 53824481 53824481 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.1448T>C p.Leu483Pro p.L483P ENST00000268919 1/1 163 127 36 171 171 0 strelka-varscan-mutect KIF2B,missense_variant,p.Leu483Pro,ENST00000268919,NM_032559.4; C ENST00000268919 Transcript missense_variant 1581/2313 1448/2022 483/673 L/P cTg/cCg 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 deleterious(0) 1/1 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 53824481 53824481 T C 1 0 0 0 0 1 0 0 0 8163 1580 55 5 5 KIF2B 17 53824481 Missense_Mutation SNP T C3N-00580_T 4600061 53824481 29432960 841 18976 KIF2B 0 . GRCh38 17 53824904 53824904 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1871A>T p.Gln624Leu p.Q624L ENST00000268919 1/1 183 138 45 225 225 0 strelka-varscan-mutect KIF2B,missense_variant,p.Gln624Leu,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 2004/2313 1871/2022 624/673 Q/L cAg/cTg 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 tolerated(1) 1/1 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 53824904 53824904 A T 1 0 0 0 0 1 0 0 0 8163 188 7 4 4 KIF2B 17 53824904 Missense_Mutation SNP A C3N-00580_T 423 53824904 29432537 842 18977 RNFT1 0 . GRCh38 17 59953016 59953016 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.1269G>C p.Trp423Cys p.W423C ENST00000305783 9/9 186 111 75 148 148 0 strelka-varscan-mutect RNFT1,missense_variant,p.Trp423Cys,ENST00000305783,NM_016125.3;RP11-178C3.1,intron_variant,,ENST00000591035,;RPS6KB1,downstream_gene_variant,,ENST00000393021,NM_001272044.1;RPS6KB1,downstream_gene_variant,,ENST00000225577,NM_001272060.1,NM_003161.3;RPS6KB1,downstream_gene_variant,,ENST00000406116,NM_001272043.1;RPS6KB1,downstream_gene_variant,,ENST00000587061,;RNFT1,3_prime_UTR_variant,,ENST00000482446,;RNFT1,3_prime_UTR_variant,,ENST00000466544,;RNFT1,downstream_gene_variant,,ENST00000486103,;RNFT1,downstream_gene_variant,,ENST00000484257,; G ENST00000305783 Transcript missense_variant 1325/2101 1269/1308 423/435 W/C tgG/tgC 1 -1 RNFT1 HGNC HGNC:30206 protein_coding YES CCDS11622.2 ENSP00000304670 Q5M7Z0 UPI0000D4C2BF NM_016125.3 deleterious(0) 9/9 hmmpanther:PTHR15860,hmmpanther:PTHR15860:SF1,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 59953016 59953016 C G 1 0 0 0 0 1 0 0 0 13681 856 30 4 4 RNFT1 17 59953016 Missense_Mutation SNP C C3N-00580_T 6128112 59953016 23304425 843 18978 HELZ 0 . GRCh38 17 67107540 67107540 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.4870A>T p.Ser1624Cys p.S1624C ENST00000358691 31/33 433 327 106 434 434 0 strelka-varscan-mutect HELZ,missense_variant,p.Ser1624Cys,ENST00000358691,NM_014877.3;HELZ,missense_variant,p.Ser1625Cys,ENST00000580168,;HELZ,3_prime_UTR_variant,,ENST00000579953,; A ENST00000358691 Transcript missense_variant 5037/13810 4870/5829 1624/1942 S/C Agt/Tgt 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 deleterious_low_confidence(0.01) 31/33 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 67107540 67107540 T A 1 0 0 0 0 1 0 0 0 6931 1580 55 4 4 HELZ 17 67107540 Missense_Mutation SNP T C3N-00580_T 7154524 67107540 16149901 844 18979 ABCA10 0 . GRCh38 17 69152393 69152393 + Missense_Mutation SNP G G A rs771145174 C3N-00580_T C3N-00580_N G G c.4225C>T p.Arg1409Cys p.R1409C ENST00000269081 36/40 151 133 18 123 123 0 strelka-varscan-mutect ABCA10,missense_variant,p.Arg1409Cys,ENST00000269081,NM_080282.3;ABCA10,upstream_gene_variant,,ENST00000521538,;ABCA10,upstream_gene_variant,,ENST00000522787,;ABCA10,non_coding_transcript_exon_variant,,ENST00000519732,;ABCA10,3_prime_UTR_variant,,ENST00000522406,;ABCA10,3_prime_UTR_variant,,ENST00000518929,;ABCA10,3_prime_UTR_variant,,ENST00000523419,;ABCA10,upstream_gene_variant,,ENST00000524231,;ABCA10,upstream_gene_variant,,ENST00000588514,; A ENST00000269081 Transcript missense_variant 5135/6362 4225/4632 1409/1543 R/C Cgt/Tgt rs771145174 1 -1 ABCA10 HGNC HGNC:30 protein_coding YES CCDS11684.1 ENSP00000269081 Q8WWZ4 UPI000013D7F6 NM_080282.3 deleterious(0.01) 36/40 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF140,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs771145174 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 69152393 69152393 G A 1 0 0 0 0 1 0 0 0 33 1116 39 1 1 ABCA10 17 69152393 Missense_Mutation SNP G C3N-00580_T 2044853 69152393 14105048 845 18980 BTBD17 0 . GRCh38 17 74356697 74356697 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1397T>A p.Val466Asp p.V466D ENST00000375366 3/3 116 95 21 100 100 0 strelka-varscan-mutect BTBD17,missense_variant,p.Val466Asp,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000389916,NM_153209.3;KIF19,downstream_gene_variant,,ENST00000551294,; T ENST00000375366 Transcript missense_variant 1524/1805 1397/1437 466/478 V/D gTc/gAc 1 -1 BTBD17 HGNC HGNC:33758 protein_coding YES CCDS32719.1 ENSP00000364515 A6NE02 UPI00001D7961 NM_001080466.1 deleterious(0) 3/3 hmmpanther:PTHR24410:SF12,hmmpanther:PTHR24410 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 61 74356697 74356697 A T 1 0 0 0 0 1 0 0 0 1716 275 10 4 4 BTBD17 17 74356697 Missense_Mutation SNP A C3N-00580_T 5204304 74356697 8900744 846 18981 TMEM104 0 . GRCh38 17 74836677 74836677 + Missense_Mutation SNP C C G C3N-00580_T C3N-00580_N C C c.1481C>G p.Thr494Ser p.T494S ENST00000335464 10/10 77 56 21 59 59 0 strelka-varscan-mutect TMEM104,missense_variant,p.Thr494Ser,ENST00000335464,NM_017728.3;TMEM104,missense_variant,p.Thr494Ser,ENST00000582330,;TMEM104,intron_variant,,ENST00000417024,;TMEM104,intron_variant,,ENST00000582773,NM_001321264.1;TMEM104,upstream_gene_variant,,ENST00000584171,; G ENST00000335464 Transcript missense_variant 1643/4745 1481/1491 494/496 T/S aCc/aGc COSM5045991 1 1 TMEM104 HGNC HGNC:25984 protein_coding YES CCDS32723.1 ENSP00000334849 Q8NE00 A0A024R8L3 UPI00002001C9 NM_017728.3 tolerated_low_confidence(0.2) 10/10 hmmpanther:PTHR16189,hmmpanther:PTHR16189:SF0 1 MODERATE 1 SNV 1 1 1 PASS rs989352666 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 74836677 74836677 C G 1 0 0 0 0 1 0 0 0 16462 507 18 4 4 TMEM104 17 74836677 Missense_Mutation SNP C C3N-00580_T 479980 74836677 8420764 847 18982 USH1G 0 . GRCh38 17 74920224 74920224 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.612C>A p.= p.A204A ENST00000614341 2/3 428 271 157 310 310 0 strelka-varscan-mutect USH1G,synonymous_variant,p.=,ENST00000614341,NM_001282489.2,NM_173477.4;OTOP2,upstream_gene_variant,,ENST00000331427,NM_178160.2;OTOP2,upstream_gene_variant,,ENST00000580223,;USH1G,3_prime_UTR_variant,,ENST00000579243,;OTOP2,upstream_gene_variant,,ENST00000584711,; T ENST00000614341 Transcript synonymous_variant 795/3558 612/1386 204/461 A gcC/gcA 1 -1 USH1G HGNC HGNC:16356 protein_coding YES CCDS32725.1 ENSP00000480279 Q495M9 UPI00001BC010 NM_001282489.2,NM_173477.4 2/3 hmmpanther:PTHR24161:SF24,hmmpanther:PTHR24161 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 74920224 74920224 G T 1 0 0 0 0 0 0 0 1 17569 1335 47 2 2 USH1G 17 74920224 Silent SNP G C3N-00580_T 83547 74920224 8337217 848 18983 MGAT5B 0 . GRCh38 17 76882230 76882230 + Silent SNP A A T rs369390750 C3N-00580_T C3N-00580_N A A c.294A>T p.= p.A98A ENST00000428789 2/16 280 240 40 268 268 0 strelka-varscan-mutect MGAT5B,synonymous_variant,p.=,ENST00000569840,NM_001199172.1;MGAT5B,synonymous_variant,p.=,ENST00000301618,NM_144677.2;MGAT5B,synonymous_variant,p.=,ENST00000428789,NM_198955.1;MGAT5B,synonymous_variant,p.=,ENST00000565675,;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,synonymous_variant,p.=,ENST00000565043,; T ENST00000428789 Transcript synonymous_variant 397/4053 294/2406 98/801 A gcA/gcT rs369390750 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 2/16 hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 LOW 1 SNV 1 1 PASS rs369390750 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 76882230 76882230 A T 1 0 0 0 0 0 0 0 1 9510 146 6 4 4 MGAT5B 17 76882230 Silent SNP A C3N-00580_T 1962006 76882230 6375211 849 18984 MGAT5B 0 . GRCh38 17 76902612 76902612 + Silent SNP C C A rs750114361 C3N-00580_T C3N-00580_N C C c.420C>A p.= p.S140S ENST00000428789 3/16 299 196 103 314 314 0 strelka-varscan-mutect MGAT5B,synonymous_variant,p.=,ENST00000569840,NM_001199172.1;MGAT5B,synonymous_variant,p.=,ENST00000301618,NM_144677.2;MGAT5B,synonymous_variant,p.=,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,synonymous_variant,p.=,ENST00000565043,; A ENST00000428789 Transcript synonymous_variant 523/4053 420/2406 140/801 S tcC/tcA rs750114361 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 3/16 hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 LOW 1 SNV 1 1 PASS rs750114361 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 76902612 76902612 C A 1 0 0 0 0 0 0 0 1 9510 639 23 1 1 MGAT5B 17 76902612 Silent SNP C C3N-00580_T 20382 76902612 6354829 850 18985 DNAH17 0 . GRCh38 17 78496008 78496008 + Missense_Mutation SNP G G C rs768967388 C3N-00580_T C3N-00580_N G G c.5770C>G p.Arg1924Gly p.R1924G ENST00000389840 38/81 174 113 61 153 153 0 strelka-varscan-mutect DNAH17,missense_variant,p.Arg1924Gly,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Arg1919Gly,ENST00000585328,;DNAH17-AS1,intron_variant,,ENST00000591373,;DNAH17,upstream_gene_variant,,ENST00000586052,;DNAH17-AS1,upstream_gene_variant,,ENST00000598378,; C ENST00000389840 Transcript missense_variant 5895/13723 5770/13389 1924/4462 R/G Cgg/Ggg rs768967388,COSM264577,COSM3522931 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 38/81 Gene3D:3.40.50.300,Pfam_domain:PF12774,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284,Superfamily_domains:SSF52540 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs768967388 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 78496008 78496008 G C 1 0 0 0 0 1 0 0 0 4416 1057 37 4 4 DNAH17 17 78496008 Missense_Mutation SNP G C3N-00580_T 1593396 78496008 4761433 851 18986 LGALS3BP 0 . GRCh38 17 78972001 78972001 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1333G>T p.Asp445Tyr p.D445Y ENST00000262776 6/6 305 244 61 246 245 1 strelka-varscan-mutect LGALS3BP,missense_variant,p.Asp445Tyr,ENST00000262776,NM_005567.3;LGALS3BP,3_prime_UTR_variant,,ENST00000591778,;LGALS3BP,downstream_gene_variant,,ENST00000585407,;LGALS3BP,downstream_gene_variant,,ENST00000589775,;LGALS3BP,downstream_gene_variant,,ENST00000589527,;LGALS3BP,downstream_gene_variant,,ENST00000589906,;LGALS3BP,downstream_gene_variant,,ENST00000591274,;LGALS3BP,3_prime_UTR_variant,,ENST00000587251,;LGALS3BP,3_prime_UTR_variant,,ENST00000587311,;LGALS3BP,3_prime_UTR_variant,,ENST00000586720,;LGALS3BP,downstream_gene_variant,,ENST00000588198,;LGALS3BP,downstream_gene_variant,,ENST00000588587,;LGALS3BP,downstream_gene_variant,,ENST00000588508,;LGALS3BP,downstream_gene_variant,,ENST00000587310,;LGALS3BP,downstream_gene_variant,,ENST00000588899,;LGALS3BP,downstream_gene_variant,,ENST00000588990,;LGALS3BP,downstream_gene_variant,,ENST00000588205,;LGALS3BP,downstream_gene_variant,,ENST00000592255,;LGALS3BP,downstream_gene_variant,,ENST00000586300,; A ENST00000262776 Transcript missense_variant 1642/2405 1333/1758 445/585 D/Y Gat/Tat 1 -1 LGALS3BP HGNC HGNC:6564 protein_coding YES CCDS11759.1 ENSP00000262776 Q08380 A0A0S2Z3Y1 UPI000006E64A NM_005567.3 tolerated(0.06) 6/6 hmmpanther:PTHR24410,hmmpanther:PTHR24410:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 78972001 78972001 C A 1 0 0 0 0 1 0 0 0 8652 826 29 2 2 LGALS3BP 17 78972001 Missense_Mutation SNP C C3N-00580_T 475993 78972001 4285440 852 18987 OGFOD3 0 . GRCh38 17 82415559 82415559 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.143G>A p.Gly48Asp p.G48D ENST00000329197 2/10 476 381 95 402 402 0 strelka-varscan-mutect OGFOD3,missense_variant,p.Gly48Asp,ENST00000313056,NM_024648.2;OGFOD3,missense_variant,p.Gly48Asp,ENST00000329197,NM_175902.4;OGFOD3,5_prime_UTR_variant,,ENST00000577495,;HEXDC,upstream_gene_variant,,ENST00000337014,NM_173620.2;HEXDC,upstream_gene_variant,,ENST00000577944,;HEXDC,upstream_gene_variant,,ENST00000327949,;OGFOD3,upstream_gene_variant,,ENST00000583897,;HEXDC,upstream_gene_variant,,ENST00000580235,;Y_RNA,upstream_gene_variant,,ENST00000364369,;OGFOD3,non_coding_transcript_exon_variant,,ENST00000577606,;OGFOD3,missense_variant,p.Gly48Asp,ENST00000580445,;HEXDC,upstream_gene_variant,,ENST00000582315,;OGFOD3,upstream_gene_variant,,ENST00000579407,;HEXDC,upstream_gene_variant,,ENST00000583978,;HEXDC,upstream_gene_variant,,ENST00000581482,; T ENST00000329197 Transcript missense_variant 234/1652 143/996 48/331 G/D gGc/gAc 1 -1 OGFOD3 HGNC HGNC:26174 protein_coding YES CCDS11812.1 ENSP00000330075 Q6PK18 UPI00001AF029 NM_175902.4 tolerated(0.21) 2/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR14650,hmmpanther:PTHR14650:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 82415559 82415559 C T 1 0 0 0 0 1 0 0 0 10917 739 26 3 3 OGFOD3 17 82415559 Missense_Mutation SNP C C3N-00580_T 3443558 82415559 841882 853 18988 EMILIN2 0 . GRCh38 18 2892234 2892234 + Nonsense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2107G>T p.Glu703Ter p.E703* ENST00000254528 4/8 105 75 30 70 70 0 strelka-varscan-mutect EMILIN2,stop_gained,p.Glu703Ter,ENST00000254528,NM_032048.2; T ENST00000254528 Transcript stop_gained 2266/5910 2107/3162 703/1053 E/* Gag/Tag 1 1 EMILIN2 HGNC HGNC:19881 protein_coding YES CCDS11828.1 ENSP00000254528 Q9BXX0 UPI000013CE3E NM_032048.2 4/8 hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF5 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 2892234 2892234 G T 1 0 0 0 0 0 1 0 0 4937 1175 41 2 2 EMILIN2 18 2892234 Nonsense_Mutation SNP G C3N-00580_T 2892234 77481051 854 18989 MYL12A 0 . GRCh38 18 3254035 3254035 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.346G>T p.Asp116Tyr p.D116Y ENST00000580887 3/4 211 135 76 365 365 0 strelka-varscan-mutect MYL12A,missense_variant,p.Asp110Tyr,ENST00000217652,NM_006471.3;MYL12A,missense_variant,p.Asp110Tyr,ENST00000578611,NM_001303047.1;MYL12A,missense_variant,p.Asp110Tyr,ENST00000579226,NM_001303048.1;MYL12A,missense_variant,p.Asp110Tyr,ENST00000536605,;MYL12A,missense_variant,p.Asp116Tyr,ENST00000580887,NM_001303049.1;MYL12A,missense_variant,p.Asp110Tyr,ENST00000578562,;MYL12A,downstream_gene_variant,,ENST00000583449,;RP13-270P17.1,downstream_gene_variant,,ENST00000578800,;RP13-270P17.1,downstream_gene_variant,,ENST00000581905,;MYL12A,downstream_gene_variant,,ENST00000585090,;MYL12A,upstream_gene_variant,,ENST00000578038,;MYL12A,downstream_gene_variant,,ENST00000577510,;MYL12A,downstream_gene_variant,,ENST00000580353,; T ENST00000580887 Transcript missense_variant 394/899 346/534 116/177 D/Y Gat/Tat COSM438086 1 1 MYL12A HGNC HGNC:16701 protein_coding YES CCDS77145.1 ENSP00000464359 J3QRS3 UPI0000374C94 NM_001303049.1 deleterious(0) 3/4 PROSITE_profiles:PS50222,hmmpanther:PTHR23049,Pfam_domain:PF08976,Gene3D:1.10.238.10,SMART_domains:SM00054,Superfamily_domains:SSF47473 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 3254035 3254035 G T 1 0 0 0 0 1 0 0 0 10045 1290 45 2 2 MYL12A 18 3254035 Missense_Mutation SNP G C3N-00580_T 361801 3254035 77119250 855 18990 DLGAP1 0 . GRCh38 18 3502623 3502623 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.2594C>T p.Pro865Leu p.P865L ENST00000315677 12/13 173 106 67 147 147 0 strelka-varscan-mutect DLGAP1,missense_variant,p.Pro865Leu,ENST00000315677,NM_004746.3;DLGAP1,missense_variant,p.Pro581Leu,ENST00000400150,NM_001308390.1;DLGAP1,missense_variant,p.Pro587Leu,ENST00000515196,NM_001242763.1;DLGAP1,missense_variant,p.Pro563Leu,ENST00000400147,NM_001003809.2;DLGAP1,missense_variant,p.Pro571Leu,ENST00000400155,NM_001242764.1;DLGAP1,missense_variant,p.Pro555Leu,ENST00000400149,;DLGAP1,missense_variant,p.Pro865Leu,ENST00000581527,NM_001242761.1;DLGAP1,missense_variant,p.Pro573Leu,ENST00000539435,NM_001242766.1;DLGAP1,missense_variant,p.Pro549Leu,ENST00000534970,NM_001242762.1;DLGAP1,missense_variant,p.Pro571Leu,ENST00000581699,;DLGAP1,missense_variant,p.Pro563Leu,ENST00000400145,NM_001242765.1; A ENST00000315677 Transcript missense_variant 3190/6683 2594/2934 865/977 P/L cCc/cTc COSM269027,COSM5107189,COSM5107190,COSM5107191,COSM5107192 1 -1 DLGAP1 HGNC HGNC:2905 protein_coding YES CCDS11836.1 ENSP00000316377 O14490 UPI0000129490 NM_004746.3 deleterious(0.01) 12/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF7,Pfam_domain:PF03359 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs1443191460 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 3502623 3502623 G A 1 0 0 0 0 1 0 0 0 4366 1232 43 3 3 DLGAP1 18 3502623 Missense_Mutation SNP G C3N-00580_T 248588 3502623 76870662 856 18991 EPB41L3 0 . GRCh38 18 5397238 5397238 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.2661A>T p.= p.T887T ENST00000341928 18/23 273 169 104 312 312 0 strelka-varscan-mutect EPB41L3,synonymous_variant,p.=,ENST00000341928,NM_012307.3;EPB41L3,synonymous_variant,p.=,ENST00000342933,;EPB41L3,synonymous_variant,p.=,ENST00000400111,;EPB41L3,synonymous_variant,p.=,ENST00000544123,NM_001281533.1;EPB41L3,synonymous_variant,p.=,ENST00000540638,NM_001281534.1;EPB41L3,synonymous_variant,p.=,ENST00000545076,NM_001281535.1;EPB41L3,synonymous_variant,p.=,ENST00000578524,;EPB41L3,synonymous_variant,p.=,ENST00000581292,;EPB41L3,upstream_gene_variant,,ENST00000579951,;EPB41L3,downstream_gene_variant,,ENST00000579271,;EPB41L3,downstream_gene_variant,,ENST00000581387,;EPB41L3,downstream_gene_variant,,ENST00000580647,;EPB41L3,downstream_gene_variant,,ENST00000580316,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000542652,;EPB41L3,downstream_gene_variant,,ENST00000582729,;EPB41L3,3_prime_UTR_variant,,ENST00000637651,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578618,;EPB41L3,downstream_gene_variant,,ENST00000584055,;EPB41L3,downstream_gene_variant,,ENST00000578196,; A ENST00000341928 Transcript synonymous_variant 3002/4706 2661/3264 887/1087 T acA/acT 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 18/23 LOW 1 SNV 1 1 PASS rs1400765944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 5397238 5397238 T A 1 0 0 0 0 0 0 0 1 5001 1567 55 4 4 EPB41L3 18 5397238 Silent SNP T C3N-00580_T 1894615 5397238 74976047 857 18992 LAMA1 0 . GRCh38 18 7023222 7023222 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.2643C>A p.His881Gln p.H881Q ENST00000389658 19/63 514 368 146 427 427 0 strelka-varscan-mutect LAMA1,missense_variant,p.His881Gln,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; T ENST00000389658 Transcript missense_variant 2737/9657 2643/9228 881/3075 H/Q caC/caA COSM1325585 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0.01) 19/63 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 7023222 7023222 G T 1 0 0 0 0 1 0 0 0 8509 1020 36 2 2 LAMA1 18 7023222 Missense_Mutation SNP G C3N-00580_T 1625984 7023222 73350063 858 18993 LAMA1 0 . GRCh38 18 7024434 7024434 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2435A>T p.Asp812Val p.D812V ENST00000389658 18/63 392 279 113 368 368 0 strelka-varscan-mutect LAMA1,missense_variant,p.Asp812Val,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript missense_variant 2529/9657 2435/9228 812/3075 D/V gAt/gTt 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 tolerated(0.2) 18/63 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 7024434 7024434 T A 1 0 0 0 0 1 0 0 0 8509 1435 50 4 4 LAMA1 18 7024434 Missense_Mutation SNP T C3N-00580_T 1212 7024434 73348851 859 18994 TXNDC2 0 . GRCh38 18 9887773 9887773 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1294G>T p.Gly432Cys p.G432C ENST00000306084 2/2 160 108 52 160 160 0 strelka-varscan-mutect TXNDC2,missense_variant,p.Gly365Cys,ENST00000357775,NM_032243.5;TXNDC2,missense_variant,p.Gly417Cys,ENST00000611534,;TXNDC2,missense_variant,p.Gly432Cys,ENST00000306084,NM_001098529.1;TXNDC2,3_prime_UTR_variant,,ENST00000536353,;TXNDC2,downstream_gene_variant,,ENST00000584255,;TXNDC2,downstream_gene_variant,,ENST00000426718,; T ENST00000306084 Transcript missense_variant 1493/1873 1294/1662 432/553 G/C Ggt/Tgt 1 1 TXNDC2 HGNC HGNC:16470 protein_coding YES CCDS42414.1 ENSP00000304908 Q86VQ3 A0A140VJY8 UPI000013EAE7 NM_001098529.1 deleterious(0.02) 2/2 PROSITE_profiles:PS51352,hmmpanther:PTHR10438:SF107,hmmpanther:PTHR10438,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 9887773 9887773 G T 1 0 0 0 0 1 0 0 0 17313 1232 43 2 2 TXNDC2 18 9887773 Missense_Mutation SNP G C3N-00580_T 2863339 9887773 70485512 860 18995 GNAL 0 . GRCh38 18 11881082 11881082 + Missense_Mutation SNP G G T rs772266110 C3N-00580_T C3N-00580_N G G c.1324G>T p.Asp442Tyr p.D442Y ENST00000334049 12/12 195 161 34 182 182 0 strelka-varscan-mutect GNAL,missense_variant,p.Asp442Tyr,ENST00000334049,NM_182978.3;GNAL,missense_variant,p.Asp365Tyr,ENST00000423027,;GNAL,missense_variant,p.Asp365Tyr,ENST00000269162,NM_001142339.2;GNAL,missense_variant,p.Asp365Tyr,ENST00000535121,NM_001261443.1;GNAL,missense_variant,p.Asp158Tyr,ENST00000602628,NM_001261444.1;MPPE1,downstream_gene_variant,,ENST00000588072,NM_023075.5;MPPE1,downstream_gene_variant,,ENST00000317235,;MPPE1,downstream_gene_variant,,ENST00000344987,;MPPE1,downstream_gene_variant,,ENST00000309976,NM_001242904.1;MPPE1,downstream_gene_variant,,ENST00000592977,;MPPE1,downstream_gene_variant,,ENST00000587724,;MPPE1,downstream_gene_variant,,ENST00000592755,;MPPE1,downstream_gene_variant,,ENST00000592447,;MPPE1,downstream_gene_variant,,ENST00000496196,;MPPE1,downstream_gene_variant,,ENST00000317251,;MPPE1,downstream_gene_variant,,ENST00000592894,;MPPE1,downstream_gene_variant,,ENST00000592306,; T ENST00000334049 Transcript missense_variant 1932/6535 1324/1377 442/458 D/Y Gac/Tac rs772266110 1 1 GNAL HGNC HGNC:4388 protein_coding YES CCDS11851.1 ENSP00000334051 P38405 UPI000017DF81 NM_182978.3 deleterious(0.02) 12/12 hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF233,Gene3D:3.40.50.300,Pfam_domain:PF00503,SMART_domains:SM00275,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs772266110 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 11881082 11881082 G T 1 0 0 0 0 1 0 0 0 6387 1058 37 1 1 GNAL 18 11881082 Missense_Mutation SNP G C3N-00580_T 1993309 11881082 68492203 861 18996 ANKRD30B 0 . GRCh38 18 14748554 14748554 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.135T>A p.= p.A45A ENST00000358984 1/36 151 94 57 177 177 0 strelka-varscan-mutect ANKRD30B,synonymous_variant,p.=,ENST00000358984,NM_001145029.1;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,synonymous_variant,p.=,ENST00000580206,; A ENST00000358984 Transcript synonymous_variant 315/4359 135/4179 45/1392 A gcT/gcA 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 1/36 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 14748554 14748554 T A 1 0 0 0 0 0 0 0 1 762 1567 55 4 4 ANKRD30B 18 14748554 Silent SNP T C3N-00580_T 2867472 14748554 65624731 862 18997 GATA6 0 . GRCh38 18 22171709 22171709 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.565G>T p.Val189Leu p.V189L ENST00000269216 2/7 120 89 31 270 270 0 strelka-varscan-mutect GATA6,missense_variant,p.Val189Leu,ENST00000269216,NM_005257.5;GATA6,missense_variant,p.Val189Leu,ENST00000581694,;GATA6-AS1,upstream_gene_variant,,ENST00000583490,;GATA6-AS1,upstream_gene_variant,,ENST00000584373,;GATA6-AS1,upstream_gene_variant,,ENST00000579431,;GATA6-AS1,upstream_gene_variant,,ENST00000584201,;RP11-627G18.2,downstream_gene_variant,,ENST00000578504,; T ENST00000269216 Transcript missense_variant 842/3770 565/1788 189/595 V/L Gtg/Ttg 1 1 GATA6 HGNC HGNC:4174 protein_coding YES CCDS11872.1 ENSP00000269216 Q92908 UPI0000201AC8 NM_005257.5 deleterious(0.02) 2/7 Pfam_domain:PF05349,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF23 MODERATE 1 SNV 1 1 PASS rs1295009208 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 22171709 22171709 G T 1 0 0 0 0 1 0 0 0 6128 1145 40 1 1 GATA6 18 22171709 Missense_Mutation SNP G C3N-00580_T 7423155 22171709 58201576 863 18998 LAMA3 0 . GRCh38 18 23839827 23839827 + Silent SNP A A C C3N-00580_T C3N-00580_N A A c.3234A>C p.= p.A1078A ENST00000313654 27/75 949 615 334 797 795 2 strelka-varscan-mutect LAMA3,synonymous_variant,p.=,ENST00000313654,NM_198129.2;LAMA3,synonymous_variant,p.=,ENST00000399516,NM_001127717.2;LAMA3,downstream_gene_variant,,ENST00000592519,;LAMA3,downstream_gene_variant,,ENST00000591749,; C ENST00000313654 Transcript synonymous_variant 3475/10661 3234/10002 1078/3333 A gcA/gcC COSM4776026 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 27/75 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 23839827 23839827 A C 1 0 0 0 0 0 0 0 1 8511 204 8 5 5 LAMA3 18 23839827 Silent SNP A C3N-00580_T 1668118 23839827 56533458 864 18999 LAMA3 0 . GRCh38 18 23873213 23873213 + Nonsense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.169C>T p.Gln57Ter p.Q57* ENST00000269217 1/38 738 591 147 694 694 0 strelka-varscan-mutect LAMA3,stop_gained,p.Gln57Ter,ENST00000269217,NM_000227.4;LAMA3,stop_gained,p.Gln57Ter,ENST00000587184,NM_001127718.2;LAMA3,intron_variant,,ENST00000313654,NM_198129.2;LAMA3,intron_variant,,ENST00000399516,NM_001127717.2; T ENST00000269217 Transcript stop_gained,splice_region_variant 374/5671 169/5175 57/1724 Q/* Cag/Tag 1 1 LAMA3 HGNC HGNC:6483 protein_coding CCDS11880.1 ENSP00000269217 A0A0A6YYF2 UPI00000349C1 NM_000227.4 1/38 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 23873213 23873213 C T 1 0 0 0 0 0 1 0 0 8511 608 21 3 3 LAMA3 18 23873213 Nonsense_Mutation SNP C C3N-00580_T 33386 23873213 56500072 865 19000 IMPACT 0 . GRCh38 18 24428021 24428021 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.139G>A p.Asp47Asn p.D47N ENST00000284202 2/11 75 46 29 97 97 0 strelka-varscan-mutect IMPACT,missense_variant,p.Asp47Asn,ENST00000284202,NM_018439.3;IMPACT,missense_variant,p.Asp29Asn,ENST00000585067,;IMPACT,missense_variant,p.Asp47Asn,ENST00000578221,;Y_RNA,upstream_gene_variant,,ENST00000362766,;IMPACT,non_coding_transcript_exon_variant,,ENST00000580706,; A ENST00000284202 Transcript missense_variant 280/3792 139/963 47/320 D/N Gac/Aac 1 1 IMPACT HGNC HGNC:20387 protein_coding YES CCDS11886.1 ENSP00000284202 Q9P2X3 UPI000007006B NM_018439.3 tolerated(0.6) 2/11 Gene3D:3.10.110.10,Pfam_domain:PF05773,PROSITE_profiles:PS50908,hmmpanther:PTHR16301,hmmpanther:PTHR16301:SF6,SMART_domains:SM00591,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 24428021 24428021 G A 1 0 0 0 0 1 0 0 0 7626 1290 45 3 3 IMPACT 18 24428021 Missense_Mutation SNP G C3N-00580_T 554808 24428021 55945264 866 19001 CDH2 0 . GRCh38 18 27990218 27990218 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.1477G>A p.Glu493Lys p.E493K ENST00000269141 10/16 446 349 97 353 352 1 strelka-varscan-mutect CDH2,missense_variant,p.Glu493Lys,ENST00000269141,NM_001792.3;CDH2,missense_variant,p.Glu462Lys,ENST00000399380,NM_001308176.1; T ENST00000269141 Transcript missense_variant 1901/4332 1477/2721 493/906 E/K Gaa/Aaa 1 -1 CDH2 HGNC HGNC:1759 protein_coding YES CCDS11891.1 ENSP00000269141 P19022 A0A024RC42 UPI000013D7FD NM_001792.3 deleterious(0) 10/16 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF79,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 27990218 27990218 C T 1 0 0 0 0 1 0 0 0 2808 835 29 3 3 CDH2 18 27990218 Missense_Mutation SNP C C3N-00580_T 3562197 27990218 52383067 867 19002 DSG3 0 . GRCh38 18 31460883 31460883 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.735A>G p.= p.E245E ENST00000257189 7/16 131 91 40 222 222 0 strelka-varscan-mutect DSG3,synonymous_variant,p.=,ENST00000257189,NM_001944.2; G ENST00000257189 Transcript synonymous_variant 818/5525 735/3000 245/999 E gaA/gaG 1 1 DSG3 HGNC HGNC:3050 protein_coding YES CCDS11898.1 ENSP00000257189 P32926 UPI000013CF4B NM_001944.2 7/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF3,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 31460883 31460883 A G 1 0 0 0 0 0 0 0 1 4599 69 3 5 5 DSG3 18 31460883 Silent SNP A C3N-00580_T 3470665 31460883 48912402 868 19003 B4GALT6 0 . GRCh38 18 31626347 31626347 + Nonsense_Mutation SNP C C A rs779649111 C3N-00580_T C3N-00580_N C C c.937G>T p.Gly313Ter p.G313* ENST00000306851 8/9 139 123 16 132 131 1 strelka-varscan-mutect B4GALT6,stop_gained,p.Gly313Ter,ENST00000306851,NM_004775.3;B4GALT6,stop_gained,p.Gly274Ter,ENST00000237019,;B4GALT6,stop_gained,p.Gly274Ter,ENST00000383131,;B4GALT6,non_coding_transcript_exon_variant,,ENST00000578114,; A ENST00000306851 Transcript stop_gained 1234/3891 937/1149 313/382 G/* Gga/Tga rs779649111 1 -1 B4GALT6 HGNC HGNC:929 protein_coding YES CCDS11900.1 ENSP00000306459 Q9UBX8 UPI0000126721 NM_004775.3 8/9 hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF47,Pfam_domain:PF02709,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 HIGH 1 SNV 1 1 PASS rs779649111 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 31626347 31626347 C A 1 0 0 0 0 0 1 0 0 1431 632 22 2 2 B4GALT6 18 31626347 Nonsense_Mutation SNP C C3N-00580_T 165464 31626347 48746938 869 19004 B4GALT6 0 . GRCh38 18 31645375 31645375 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.451G>T p.Asp151Tyr p.D151Y ENST00000306851 4/9 231 151 80 320 320 0 strelka-varscan-mutect B4GALT6,missense_variant,p.Asp151Tyr,ENST00000306851,NM_004775.3;B4GALT6,missense_variant,p.Asp112Tyr,ENST00000237019,;B4GALT6,missense_variant,p.Asp151Tyr,ENST00000383131,;B4GALT6,intron_variant,,ENST00000578114,; A ENST00000306851 Transcript missense_variant 748/3891 451/1149 151/382 D/Y Gac/Tac 1 -1 B4GALT6 HGNC HGNC:929 protein_coding YES CCDS11900.1 ENSP00000306459 Q9UBX8 UPI0000126721 NM_004775.3 deleterious(0) 4/9 hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF47,Pfam_domain:PF13733,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 31645375 31645375 C A 1 0 0 0 0 1 0 0 0 1431 913 32 2 2 B4GALT6 18 31645375 Missense_Mutation SNP C C3N-00580_T 19028 31645375 48727910 870 19005 ASXL3 0 . GRCh38 18 33744665 33744665 + Missense_Mutation SNP G G T rs116363417 C3N-00580_T C3N-00580_N G G c.4817G>T p.Arg1606Leu p.R1606L ENST00000269197 12/12 306 213 93 263 263 0 strelka-varscan-mutect ASXL3,missense_variant,p.Arg1606Leu,ENST00000269197,NM_030632.1;ASXL3,downstream_gene_variant,,ENST00000592288,; T ENST00000269197 Transcript missense_variant 4872/11399 4817/6747 1606/2248 R/L cGg/cTg rs116363417 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 tolerated_low_confidence(0.05) 12/12 MODERATE 1 SNV 5 1 PASS rs116363417 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 33744665 33744665 G T 1 0 0 0 0 1 0 0 0 1216 1116 39 1 1 ASXL3 18 33744665 Missense_Mutation SNP G C3N-00580_T 2099290 33744665 46628620 871 19006 DTNA 0 . GRCh38 18 34794177 34794177 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.289C>A p.Pro97Thr p.P97T ENST00000598334 5/20 506 329 177 385 384 1 strelka-varscan-mutect DTNA,missense_variant,p.Pro97Thr,ENST00000283365,NM_032975.3;DTNA,missense_variant,p.Pro97Thr,ENST00000399121,NM_001198939.1;DTNA,missense_variant,p.Pro97Thr,ENST00000444659,NM_001390.4;DTNA,missense_variant,p.Pro97Thr,ENST00000595022,NM_001198940.1;DTNA,missense_variant,p.Pro97Thr,ENST00000348997,NM_032978.6,NM_001391.5;DTNA,missense_variant,p.Pro97Thr,ENST00000598334,NM_001198938.1;DTNA,missense_variant,p.Pro97Thr,ENST00000598142,;DTNA,missense_variant,p.Pro97Thr,ENST00000598774,NM_032979.4;DTNA,missense_variant,p.Pro97Thr,ENST00000399113,;DTNA,missense_variant,p.Pro97Thr,ENST00000597599,NM_001198941.1;DTNA,missense_variant,p.Pro97Thr,ENST00000315456,NM_001392.4;DTNA,missense_variant,p.Pro97Thr,ENST00000554864,NM_001128175.1;DTNA,missense_variant,p.Pro97Thr,ENST00000596745,NM_001198945.1;DTNA,missense_variant,p.Pro97Thr,ENST00000590598,;DTNA,missense_variant,p.Pro97Thr,ENST00000590412,;DTNA,missense_variant,p.Pro99Thr,ENST00000588949,;DTNA,non_coding_transcript_exon_variant,,ENST00000585446,; A ENST00000598334 Transcript missense_variant 615/3201 289/2175 97/724 P/T Cca/Aca 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 deleterious(0) 5/20 hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204,Pfam_domain:PF09068,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 34794177 34794177 C A 1 0 0 0 0 1 0 0 0 4611 739 26 2 2 DTNA 18 34794177 Missense_Mutation SNP C C3N-00580_T 1049512 34794177 45579108 872 19007 MAPRE2 0 . GRCh38 18 35097572 35097572 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.377A>G p.Lys126Arg p.K126R ENST00000300249 3/7 70 64 6 75 75 0 strelka-mutect MAPRE2,missense_variant,p.Lys114Arg,ENST00000436190,NM_001143827.2;MAPRE2,missense_variant,p.Lys126Arg,ENST00000300249,NM_014268.3;MAPRE2,missense_variant,p.Lys83Arg,ENST00000413393,NM_001143826.2;MAPRE2,missense_variant,p.Lys73Arg,ENST00000538170,NM_001256420.1;MAPRE2,missense_variant,p.Lys83Arg,ENST00000589699,;MAPRE2,missense_variant,p.Lys126Arg,ENST00000588910,;MAPRE2,missense_variant,p.Lys83Arg,ENST00000591734,;MAPRE2,missense_variant,p.Lys32Arg,ENST00000589180,;MAPRE2,missense_variant,p.Lys83Arg,ENST00000588349,;MAPRE2,downstream_gene_variant,,ENST00000587359,; G ENST00000300249 Transcript missense_variant 557/4265 377/984 126/327 K/R aAg/aGg 1 1 MAPRE2 HGNC HGNC:6891 protein_coding YES CCDS11910.1 ENSP00000300249 Q15555 A0A024RC33 UPI0000072407 NM_014268.3 deleterious(0.02) 3/7 PROSITE_profiles:PS50021,hmmpanther:PTHR10623:SF7,hmmpanther:PTHR10623,Gene3D:1.10.418.10,Pfam_domain:PF00307,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.62066 1 1 1 1 0 G 3 3 61 35097572 35097572 A G 1 0 0 0 0 1 0 0 0 9218 72 3 5 5 MAPRE2 18 35097572 Missense_Mutation SNP A C3N-00580_T 303395 35097572 45275713 873 19008 SYT4 0 . GRCh38 18 43273831 43273831 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.598C>A p.Pro200Thr p.P200T ENST00000255224 2/4 251 209 42 302 302 0 strelka-varscan-mutect SYT4,missense_variant,p.Pro200Thr,ENST00000255224,NM_020783.3;SYT4,missense_variant,p.Pro182Thr,ENST00000590752,;SYT4,intron_variant,,ENST00000596867,;SYT4,intron_variant,,ENST00000593720,;SYT4,intron_variant,,ENST00000586678,;SYT4,intron_variant,,ENST00000585604,;SYT4,upstream_gene_variant,,ENST00000589479,;SYT4,downstream_gene_variant,,ENST00000591820,; T ENST00000255224 Transcript missense_variant 967/4110 598/1278 200/425 P/T Cca/Aca COSM1711233,COSM1711234 1 -1 SYT4 HGNC HGNC:11512 protein_coding YES CCDS11922.1 ENSP00000255224 Q9H2B2 UPI000013669E NM_020783.3 deleterious(0) 2/4 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114,SMART_domains:SM00239,Superfamily_domains:SSF49562 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 43273831 43273831 G T 1 0 0 0 0 1 0 0 0 15870 1232 43 2 2 SYT4 18 43273831 Missense_Mutation SNP G C3N-00580_T 8176259 43273831 37099454 874 19009 LOXHD1 0 . GRCh38 18 46566305 46566305 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.2389C>T p.Arg797Cys p.R797C ENST00000536736 17/40 147 127 20 130 130 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Arg797Cys,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Arg797Cys,ENST00000441551,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; A ENST00000536736 Transcript missense_variant 2389/6848 2389/6636 797/2211 R/C Cgc/Tgc 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 deleterious(0.04) 17/40 Gene3D:2.60.60.20,PROSITE_profiles:PS50095,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE SNV 5 1 PASS rs920654744 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 46566305 46566305 G A 1 0 0 0 0 1 0 0 0 8801 1087 38 1 1 LOXHD1 18 46566305 Missense_Mutation SNP G C3N-00580_T 3292474 46566305 33806980 875 19010 TXNL1 0 . GRCh38 18 56624402 56624402 + Silent SNP T T C novel C3N-00580_T C3N-00580_N T T c.255A>G p.= p.K85K ENST00000217515 3/8 127 97 30 149 149 0 strelka-varscan-mutect TXNL1,synonymous_variant,p.=,ENST00000217515,NM_004786.2;TXNL1,synonymous_variant,p.=,ENST00000586262,;TXNL1,synonymous_variant,p.=,ENST00000590954,;TXNL1,synonymous_variant,p.=,ENST00000587613,;TXNL1,3_prime_UTR_variant,,ENST00000587807,; C ENST00000217515 Transcript synonymous_variant 460/6894 255/870 85/289 K aaA/aaG 1 -1 TXNL1 HGNC HGNC:12436 protein_coding YES CCDS11961.1 ENSP00000217515 O43396 V9HW51 UPI0000137838 NM_004786.2 3/8 hmmpanther:PTHR10438,hmmpanther:PTHR10438:SF284,Pfam_domain:PF00085,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 56624402 56624402 T C 1 0 0 0 0 0 0 0 1 17318 1606 56 5 5 TXNL1 18 56624402 Silent SNP T C3N-00580_T 10058097 56624402 23748883 876 19011 WDR7 0 . GRCh38 18 56757234 56757234 + Missense_Mutation SNP G G C rs368372292 C3N-00580_T C3N-00580_N G G c.2641G>C p.Gly881Arg p.G881R ENST00000254442 15/28 246 196 50 267 267 0 strelka-varscan-mutect WDR7,missense_variant,p.Gly881Arg,ENST00000254442,NM_015285.2;WDR7,missense_variant,p.Gly881Arg,ENST00000357574,NM_052834.2;WDR7,missense_variant,p.Gly206Arg,ENST00000615645,;WDR7,intron_variant,,ENST00000589935,;Y_RNA,upstream_gene_variant,,ENST00000384138,;WDR7,non_coding_transcript_exon_variant,,ENST00000585824,;WDR7,downstream_gene_variant,,ENST00000590557,;WDR7,downstream_gene_variant,,ENST00000587403,;WDR7,upstream_gene_variant,,ENST00000591524,; C ENST00000254442 Transcript missense_variant 2852/14083 2641/4473 881/1490 G/R Gga/Cga rs368372292 1 1 WDR7 HGNC HGNC:13490 protein_coding YES CCDS11962.1 ENSP00000254442 Q9Y4E6 UPI000013CE33 NM_015285.2 tolerated(0.27) 15/28 MODERATE 1 SNV 1 1 PASS rs368372292 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 56757234 56757234 G C 1 0 0 0 0 1 0 0 0 17876 1117 39 4 4 WDR7 18 56757234 Missense_Mutation SNP G C3N-00580_T 132832 56757234 23616051 877 19012 ALPK2 0 . GRCh38 18 58529200 58529200 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.5392C>A p.Pro1798Thr p.P1798T ENST00000361673 6/13 164 119 45 221 221 0 strelka-varscan-mutect ALPK2,missense_variant,p.Pro1798Thr,ENST00000361673,NM_052947.3;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; T ENST00000361673 Transcript missense_variant 5606/7303 5392/6513 1798/2170 P/T Cct/Act 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0) 6/13 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 58529200 58529200 G T 1 0 0 0 0 1 0 0 0 645 1232 43 2 2 ALPK2 18 58529200 Missense_Mutation SNP G C3N-00580_T 1771966 58529200 21844085 878 19013 TUBB4A 0 . GRCh38 19 6496214 6496214 + Silent SNP G G A rs767100230 C3N-00580_T C3N-00580_N G G c.285C>T p.= p.S95S ENST00000264071 4/4 73 53 20 99 99 0 strelka-varscan-mutect TUBB4A,missense_variant,p.Pro70Leu,ENST00000601152,;TUBB4A,missense_variant,p.Pro81Leu,ENST00000598006,;TUBB4A,synonymous_variant,p.=,ENST00000264071,NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1;TUBB4A,synonymous_variant,p.=,ENST00000597686,NM_001289127.1;TUBB4A,synonymous_variant,p.=,ENST00000598635,NM_001289123.1;TUBB4A,synonymous_variant,p.=,ENST00000596291,;TUBB4A,synonymous_variant,p.=,ENST00000601640,;TUBB4A,3_prime_UTR_variant,,ENST00000596926,;TUBB4A,intron_variant,,ENST00000594075,;TUBB4A,intron_variant,,ENST00000594276,;TUBB4A,intron_variant,,ENST00000600216,;CTD-2396E7.10,downstream_gene_variant,,ENST00000596027,;CTD-2396E7.9,downstream_gene_variant,,ENST00000599292,;TUBB4A,3_prime_UTR_variant,,ENST00000595324,;TUBB4A,3_prime_UTR_variant,,ENST00000594290,; A ENST00000264071 Transcript synonymous_variant 657/2552 285/1335 95/444 S tcC/tcT rs767100230,COSM5333908 1 -1 TUBB4A HGNC HGNC:20774 protein_coding YES CCDS12168.1 ENSP00000264071 P04350 UPI000005FC27 NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1 4/4 Gene3D:3.40.50.1440,Pfam_domain:PF00091,Prints_domain:PR01161,Prints_domain:PR01163,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF121,SMART_domains:SM00864,Superfamily_domains:SSF52490 0,1 LOW 1 SNV 1 0,1 1 PASS rs767100230 . 0 192 18 0 0 0 0 0 -20 0.9994792 1 1 1 0 A 2 1 61 6496214 6496214 G A 1 0 0 0 0 0 0 0 1 17268 1116 39 1 1 TUBB4A 19 6496214 Silent SNP G C3N-00580_T 6496214 52121402 879 19014 SH2D3A 0 . GRCh38 19 6760934 6760934 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.123G>T p.= p.G41G ENST00000245908 3/10 114 53 61 161 161 0 strelka-varscan-mutect SH2D3A,synonymous_variant,p.=,ENST00000245908,NM_005490.2;SH2D3A,synonymous_variant,p.=,ENST00000597687,;SH2D3A,intron_variant,,ENST00000437152,;SH2D3A,non_coding_transcript_exon_variant,,ENST00000599563,;SH2D3A,intron_variant,,ENST00000597254,;SH2D3A,non_coding_transcript_exon_variant,,ENST00000595369,;SH2D3A,non_coding_transcript_exon_variant,,ENST00000595681,; A ENST00000245908 Transcript synonymous_variant 393/2296 123/1731 41/576 G ggG/ggT 1 -1 SH2D3A HGNC HGNC:16885 protein_coding YES CCDS12173.1 ENSP00000245908 Q9BRG2 UPI000006FD60 NM_005490.2 3/10 PROSITE_profiles:PS50001,hmmpanther:PTHR14247,Pfam_domain:PF00017,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550,Prints_domain:PR00401 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 6760934 6760934 C A 1 0 0 0 0 0 0 0 1 14491 494 18 2 2 SH2D3A 19 6760934 Silent SNP C C3N-00580_T 264720 6760934 51856682 880 19015 FBN3 0 . GRCh38 19 8126606 8126606 + Splice_Site SNP C C A novel C3N-00580_T C3N-00580_N C C c.2417-1G>T p.X806_splice ENST00000600128 63 25 38 84 84 0 strelka-varscan-mutect FBN3,splice_acceptor_variant,,ENST00000600128,;FBN3,splice_acceptor_variant,,ENST00000270509,NM_032447.3;FBN3,splice_acceptor_variant,,ENST00000601739,NM_001321431.1; A ENST00000600128 Transcript splice_acceptor_variant -/9362 2417/8430 806/2809 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F 19/63 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 8126606 8126606 C A 1 0 0 0 0 0 0 1 0 5567 927 32 2 2 FBN3 19 8126606 Splice_Site SNP C C3N-00580_T 1365672 8126606 50491010 881 19016 MUC16 0 . GRCh38 19 8865600 8865600 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.42552T>C p.= p.D14184D ENST00000397910 75/84 43 19 24 124 124 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2;MUC16,synonymous_variant,p.=,ENST00000599436,;MUC16,intron_variant,,ENST00000596956,;MUC16,synonymous_variant,p.=,ENST00000601404,;MUC16,intron_variant,,ENST00000596768,; G ENST00000397910 Transcript synonymous_variant 42756/43816 42552/43524 14184/14507 D gaT/gaC 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 75/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Superfamily_domains:0047452 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 61 8865600 8865600 A G 1 0 0 0 0 0 0 0 1 9972 446 16 5 5 MUC16 19 8865600 Silent SNP A C3N-00580_T 738994 8865600 49752016 882 19017 MUC16 0 . GRCh38 19 8937817 8937817 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.33138C>A p.= p.V11046V ENST00000397910 5/84 204 170 34 266 266 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 33342/43816 33138/43524 11046/14507 V gtC/gtA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 8937817 8937817 G T 1 0 0 0 0 0 0 0 1 9972 1277 45 2 2 MUC16 19 8937817 Silent SNP G C3N-00580_T 72217 8937817 49679799 883 19018 MUC16 0 . GRCh38 19 8947235 8947235 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.29535C>G p.Ile9845Met p.I9845M ENST00000397910 3/84 170 100 70 190 190 0 strelka-varscan-mutect MUC16,missense_variant,p.Ile9845Met,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 29739/43816 29535/43524 9845/14507 I/M atC/atG 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 8947235 8947235 G C 1 0 0 0 0 1 0 0 0 9972 1280 45 4 4 MUC16 19 8947235 Missense_Mutation SNP G C3N-00580_T 9418 8947235 49670381 884 19019 ZNF699 0 . GRCh38 19 9295543 9295543 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1861G>T p.Gly621Trp p.G621W ENST00000591998 6/6 147 90 57 167 167 0 strelka-varscan-mutect ZNF699,missense_variant,p.Gly621Trp,ENST00000591998,;ZNF699,missense_variant,p.Gly621Trp,ENST00000308650,NM_198535.1;CTC-325H20.4,downstream_gene_variant,,ENST00000591336,; A ENST00000591998 Transcript missense_variant 2090/3358 1861/1929 621/642 G/W Ggg/Tgg 1 -1 ZNF699 HGNC HGNC:24750 protein_coding YES CCDS42495.1 ENSP00000467723 Q32M78 UPI00001D825F deleterious(0) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF132,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF13894,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 9295543 9295543 C A 1 0 0 0 0 1 0 0 0 18674 594 21 2 2 ZNF699 19 9295543 Missense_Mutation SNP C C3N-00580_T 348308 9295543 49322073 885 19020 ZNF844 0 . GRCh38 19 12075460 12075460 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.340G>A p.Gly114Ser p.G114S ENST00000439326 4/4 102 56 46 158 158 0 strelka-varscan-mutect ZNF844,missense_variant,p.Gly114Ser,ENST00000439326,NM_001136501.1;ZNF844,3_prime_UTR_variant,,ENST00000441304,;ZNF844,5_prime_UTR_variant,,ENST00000550826,; A ENST00000439326 Transcript missense_variant 515/6620 340/2001 114/666 G/S Ggt/Agt 1 1 ZNF844 HGNC HGNC:25932 protein_coding YES CCDS45985.1 ENSP00000392024 Q08AG5 UPI0000185F5D NM_001136501.1 tolerated(0.23) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF28,hmmpanther:PTHR24379,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 12075460 12075460 G A 1 0 0 0 0 1 0 0 0 18778 1232 43 3 3 ZNF844 19 12075460 Missense_Mutation SNP G C3N-00580_T 2779917 12075460 46542156 886 19021 ZNF136 0 . GRCh38 19 12187980 12187980 + Silent SNP A A G novel C3N-00580_T C3N-00580_N A A c.1602A>G p.= p.K534K ENST00000343979 4/4 31 23 8 15 15 0 strelka-varscan-mutect ZNF136,synonymous_variant,p.=,ENST00000343979,NM_003437.3;ZNF136,downstream_gene_variant,,ENST00000418338,;ZNF136,downstream_gene_variant,,ENST00000439995,;ZNF136,downstream_gene_variant,,ENST00000425827,;ZNF136,non_coding_transcript_exon_variant,,ENST00000464860,;ZNF136,downstream_gene_variant,,ENST00000476676,; G ENST00000343979 Transcript synonymous_variant 1742/3643 1602/1623 534/540 K aaA/aaG 1 1 ZNF136 HGNC HGNC:12920 protein_coding YES CCDS32916.1 ENSP00000344162 P52737 UPI0000000C7B NM_003437.3 4/4 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.98878 1 1 1 1 0 G 2 3 61 12187980 12187980 A G 1 0 0 0 0 0 0 0 1 18307 98 4 5 5 ZNF136 19 12187980 Silent SNP A C3N-00580_T 112520 12187980 46429636 887 19022 BEST2 0 . GRCh38 19 12755625 12755625 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.725T>A p.Ile242Asn p.I242N ENST00000549706 7/10 94 57 37 127 127 0 strelka-varscan-mutect BEST2,missense_variant,p.Ile242Asn,ENST00000549706,;BEST2,missense_variant,p.Ile242Asn,ENST00000553030,;BEST2,missense_variant,p.Ile242Asn,ENST00000042931,NM_017682.2;BEST2,upstream_gene_variant,,ENST00000552539,; A ENST00000549706 Transcript missense_variant 1049/2183 725/1530 242/509 I/N aTc/aAc 1 1 BEST2 HGNC HGNC:17107 protein_coding YES CCDS42506.1 ENSP00000448310 Q8NFU1 UPI000007395A deleterious(0) 7/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR10736,hmmpanther:PTHR10736:SF1,Pfam_domain:PF01062 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 12755625 12755625 T A 1 0 0 0 0 1 0 0 0 1553 1435 50 4 4 BEST2 19 12755625 Missense_Mutation SNP T C3N-00580_T 567645 12755625 45861991 888 19023 PALM3 0 . GRCh38 19 14054911 14054911 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.716A>T p.Glu239Val p.E239V ENST00000340790 6/6 111 98 13 172 172 0 strelka-varscan-mutect PALM3,missense_variant,p.Glu239Val,ENST00000340790,NM_001145028.1;PALM3,missense_variant,p.Glu188Val,ENST00000589048,;IL27RA,downstream_gene_variant,,ENST00000263379,NM_004843.3;PALM3,downstream_gene_variant,,ENST00000586368,; A ENST00000340790 Transcript missense_variant 716/2262 716/2022 239/673 E/V gAg/gTg 1 -1 PALM3 HGNC HGNC:33274 protein_coding YES CCDS46001.1 ENSP00000344996 A6NDB9 UPI0001662AC1 NM_001145028.1 deleterious(0) 6/6 hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF13,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 14054911 14054911 T A 1 0 0 0 0 1 0 0 0 11490 1551 54 4 4 PALM3 19 14054911 Missense_Mutation SNP T C3N-00580_T 1299286 14054911 44562705 889 19024 CLEC17A 0 . GRCh38 19 14594683 14594683 + Splice_Site SNP G G A novel C3N-00580_T C3N-00580_N G G c.361+1G>A p.X121_splice ENST00000417570 370 236 134 489 489 0 strelka-varscan-mutect CLEC17A,splice_donor_variant,,ENST00000547437,NM_207390.3;CLEC17A,splice_donor_variant,,ENST00000417570,NM_001204118.1;CLEC17A,splice_donor_variant,,ENST00000551730,;CLEC17A,splice_donor_variant,,ENST00000339847,; A ENST00000417570 Transcript splice_donor_variant -/1399 361/1137 121/378 1 1 CLEC17A HGNC HGNC:34520 protein_coding YES CCDS56087.1 ENSP00000393719 Q6ZS10 UPI0001747A7C NM_001204118.1 6/13 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 61 14594683 14594683 G A 1 0 0 0 0 0 0 1 0 3267 1275 44 3 3 CLEC17A 19 14594683 Splice_Site SNP G C3N-00580_T 539772 14594683 44022933 890 19025 WIZ 0 . GRCh38 19 15437094 15437094 + Missense_Mutation SNP G G A rs763355086 C3N-00580_T C3N-00580_N G G c.241C>T p.Arg81Cys p.R81C ENST00000263381 3/8 67 52 15 178 178 0 strelka-varscan-mutect WIZ,missense_variant,p.Arg81Cys,ENST00000263381,NM_021241.2;WIZ,missense_variant,p.Arg81Cys,ENST00000596159,;WIZ,upstream_gene_variant,,ENST00000599910,;WIZ,upstream_gene_variant,,ENST00000599686,;WIZ,non_coding_transcript_exon_variant,,ENST00000595214,; A ENST00000263381 Transcript missense_variant 455/5695 241/2385 81/794 R/C Cgc/Tgc rs763355086,COSM5566804,COSM5566805 1 -1 WIZ HGNC HGNC:30917 protein_coding YES CCDS42516.1 ENSP00000263381 O95785 UPI000041F888 NM_021241.2 deleterious(0.04) 3/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24396:SF20,hmmpanther:PTHR24396,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs763355086 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 15437094 15437094 G A 1 0 0 0 0 1 0 0 0 17931 1087 38 1 1 WIZ 19 15437094 Missense_Mutation SNP G C3N-00580_T 842411 15437094 43180522 891 19026 CYP4F3 0 . GRCh38 19 15658742 15658742 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1330C>A p.Arg444Ser p.R444S ENST00000221307 12/13 109 76 33 164 164 0 strelka-varscan-mutect CYP4F3,missense_variant,p.Arg444Ser,ENST00000221307,NM_000896.2;CYP4F3,missense_variant,p.Arg444Ser,ENST00000591058,NM_001199208.1;CYP4F3,missense_variant,p.Arg444Ser,ENST00000586182,NM_001199209.1;CYP4F3,missense_variant,p.Arg444Ser,ENST00000585846,;CYP4F3,missense_variant,p.Arg444Ser,ENST00000620621,;CYP4F3,upstream_gene_variant,,ENST00000588886,;CYP4F3,non_coding_transcript_exon_variant,,ENST00000592279,;CYP4F3,downstream_gene_variant,,ENST00000592424,; A ENST00000221307 Transcript missense_variant 1377/5050 1330/1563 444/520 R/S Cgc/Agc COSM3529780,COSM3529781 1 1 CYP4F3 HGNC HGNC:2646 protein_coding YES CCDS12332.1 ENSP00000221307 Q08477 A0A024R7J8 UPI0000052BE3 NM_000896.2 deleterious(0.02) 12/13 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF25,Superfamily_domains:SSF48264 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs964959320 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 15658742 15658742 C A 1 0 0 0 0 1 0 0 0 3993 884 31 1 1 CYP4F3 19 15658742 Missense_Mutation SNP C C3N-00580_T 221648 15658742 42958874 892 19027 SLC27A1 0 . GRCh38 19 17489107 17489107 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.986A>T p.Tyr329Phe p.Y329F ENST00000252595 6/12 161 84 77 161 161 0 strelka-varscan-mutect SLC27A1,missense_variant,p.Tyr329Phe,ENST00000252595,NM_198580.2;SLC27A1,missense_variant,p.Tyr150Phe,ENST00000598424,;CTD-3131K8.2,intron_variant,,ENST00000596643,;CTD-3131K8.2,downstream_gene_variant,,ENST00000598141,;SLC27A1,3_prime_UTR_variant,,ENST00000599380,;SLC27A1,3_prime_UTR_variant,,ENST00000600277,;SLC27A1,non_coding_transcript_exon_variant,,ENST00000593701,;SLC27A1,downstream_gene_variant,,ENST00000600297,; T ENST00000252595 Transcript missense_variant 1083/3594 986/1941 329/646 Y/F tAc/tTc 1 1 SLC27A1 HGNC HGNC:10995 protein_coding YES CCDS32953.1 ENSP00000252595 Q6PCB7 UPI0000038E7F NM_198580.2 tolerated(0.15) 6/12 hmmpanther:PTHR24096:SF148,hmmpanther:PTHR24096,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 17489107 17489107 A T 1 0 0 0 0 1 0 0 0 14795 391 14 4 4 SLC27A1 19 17489107 Missense_Mutation SNP A C3N-00580_T 1830365 17489107 41128509 893 19028 IL12RB1 0 . GRCh38 19 18082214 18082214 + Missense_Mutation SNP G G T rs865858530 C3N-00580_T C3N-00580_N G G c.175C>A p.Arg59Ser p.R59S ENST00000600835 4/18 506 429 77 632 632 0 strelka-varscan-mutect IL12RB1,missense_variant,p.Arg59Ser,ENST00000600835,NM_001290024.1;IL12RB1,missense_variant,p.Arg59Ser,ENST00000593993,NM_001290023.1,NM_005535.2;IL12RB1,missense_variant,p.Arg59Ser,ENST00000322153,NM_153701.2;IL12RB1,missense_variant,p.Arg59Ser,ENST00000598019,;IL12RB1,missense_variant,p.Arg63Ser,ENST00000430026,;IL12RB1,downstream_gene_variant,,ENST00000594176,;IL12RB1,downstream_gene_variant,,ENST00000597416,; T ENST00000600835 Transcript missense_variant 474/2901 175/1989 59/662 R/S Cgt/Agt rs865858530,COSM3530701,COSM3530702,COSM3530703 1 -1 IL12RB1 HGNC HGNC:5971 protein_coding YES CCDS54232.1 ENSP00000470788 P42701 UPI00000502CE NM_001290024.1 tolerated(0.83) 4/18 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF51,hmmpanther:PTHR23036 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs865858530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 18082214 18082214 G T 1 0 0 0 0 1 0 0 0 7534 1058 37 1 1 IL12RB1 19 18082214 Missense_Mutation SNP G C3N-00580_T 593107 18082214 40535402 894 19029 ZNF208 0 . GRCh38 19 21971698 21971698 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.3336C>A p.= p.P1112P ENST00000397126 4/4 213 111 102 247 246 1 strelka-varscan-mutect ZNF208,synonymous_variant,p.=,ENST00000397126,NM_007153.3;ZNF208,synonymous_variant,p.=,ENST00000609966,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,;AC003973.3,upstream_gene_variant,,ENST00000624863,; T ENST00000397126 Transcript synonymous_variant 3485/3992 3336/3843 1112/1280 P ccC/ccA 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 3 1 PASS rs991855213 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 21971698 21971698 G T 1 0 0 0 0 0 0 0 1 18343 987 35 2 2 ZNF208 19 21971698 Silent SNP G C3N-00580_T 3889484 21971698 36645918 895 19030 ZNF99 0 . GRCh38 19 22757583 22757583 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.2326C>A p.Leu776Ile p.L776I ENST00000596209 4/4 171 97 74 283 283 0 strelka-varscan-mutect ZNF99,missense_variant,p.Leu776Ile,ENST00000596209,NM_001080409.2;ZNF99,missense_variant,p.Leu685Ile,ENST00000397104,; T ENST00000596209 Transcript missense_variant 2417/7817 2326/2595 776/864 L/I Ctt/Att COSM1525003 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 deleterious(0.01) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 22757583 22757583 G T 1 0 0 0 0 1 0 0 0 18797 1000 35 2 2 ZNF99 19 22757583 Missense_Mutation SNP G C3N-00580_T 785885 22757583 35860033 896 19031 ZNF536 0 . GRCh38 19 30444062 30444062 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.500C>A p.Ala167Glu p.A167E ENST00000355537 2/5 273 140 133 317 317 0 strelka-varscan-mutect ZNF536,missense_variant,p.Ala167Glu,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Ala167Glu,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; A ENST00000355537 Transcript missense_variant 647/4945 500/3903 167/1300 A/E gCg/gAg COSM3532039 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 2/5 Gene3D:3.30.160.60,Pfam_domain:PF13909,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 30444062 30444062 C A 1 0 0 0 0 1 0 0 0 18547 768 27 1 1 ZNF536 19 30444062 Missense_Mutation SNP C C3N-00580_T 7686479 30444062 28173554 897 19032 ZNF536 0 . GRCh38 19 30445471 30445471 + Missense_Mutation SNP G G A C3N-00580_T C3N-00580_N G G c.1909G>A p.Gly637Ser p.G637S ENST00000355537 2/5 261 229 32 300 300 0 strelka-varscan-mutect ZNF536,missense_variant,p.Gly637Ser,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Gly637Ser,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; A ENST00000355537 Transcript missense_variant 2056/4945 1909/3903 637/1300 G/S Ggc/Agc COSM186389 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 2/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS rs1392485761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 30445471 30445471 G A 1 0 0 0 0 1 0 0 0 18547 1116 39 1 1 ZNF536 19 30445471 Missense_Mutation SNP G C3N-00580_T 1409 30445471 28172145 898 19033 SLC7A9 0 . GRCh38 19 32858461 32858461 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.956G>T p.Gly319Val p.G319V ENST00000023064 9/13 439 210 229 566 566 0 strelka-varscan-mutect SLC7A9,missense_variant,p.Gly319Val,ENST00000023064,NM_001243036.1,NM_001126335.1,NM_014270.4;SLC7A9,missense_variant,p.Gly319Val,ENST00000590341,;SLC7A9,missense_variant,p.Gly319Val,ENST00000587772,;RN7SKP22,downstream_gene_variant,,ENST00000365097,;SLC7A9,3_prime_UTR_variant,,ENST00000590465,;SLC7A9,3_prime_UTR_variant,,ENST00000592232,;SLC7A9,downstream_gene_variant,,ENST00000589659,; A ENST00000023064 Transcript missense_variant 1148/1761 956/1464 319/487 G/V gGg/gTg 1 -1 SLC7A9 HGNC HGNC:11067 protein_coding YES CCDS12425.1 ENSP00000023064 P82251 UPI0000037773 NM_001243036.1,NM_001126335.1,NM_014270.4 deleterious(0.03) 9/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785:SF354,hmmpanther:PTHR11785,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 32858461 32858461 C A 1 0 0 0 0 1 0 0 0 14988 623 22 2 2 SLC7A9 19 32858461 Missense_Mutation SNP C C3N-00580_T 2412990 32858461 25759155 899 19034 KIAA0355 0 . GRCh38 19 34320083 34320083 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.672G>T p.Glu224Asp p.E224D ENST00000299505 3/14 418 305 113 336 334 2 strelka-varscan-mutect KIAA0355,missense_variant,p.Glu224Asp,ENST00000299505,NM_014686.3;KIAA0355,downstream_gene_variant,,ENST00000588470,;KIAA0355,intron_variant,,ENST00000588338,; T ENST00000299505 Transcript missense_variant 1545/6717 672/3213 224/1070 E/D gaG/gaT 1 1 KIAA0355 HGNC HGNC:29016 protein_coding YES CCDS12436.1 ENSP00000299505 O15063 UPI000013E5AD NM_014686.3 tolerated(0.1) 3/14 hmmpanther:PTHR15703:SF3,hmmpanther:PTHR15703 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 34320083 34320083 G T 1 0 0 0 0 1 0 0 0 8082 991 35 2 2 KIAA0355 19 34320083 Missense_Mutation SNP G C3N-00580_T 1461622 34320083 24297533 900 19035 FFAR3 0 . GRCh38 19 35359435 35359435 + Missense_Mutation SNP T T A C3N-00580_T C3N-00580_N T T c.545T>A p.Leu182Gln p.L182Q ENST00000327809 2/2 1050 930 120 1290 1290 0 varscan-mutect FFAR3,missense_variant,p.Leu182Gln,ENST00000327809,NM_005304.3;FFAR3,missense_variant,p.Leu182Gln,ENST00000594310,; A ENST00000327809 Transcript missense_variant 746/1796 545/1041 182/346 L/Q cTg/cAg COSM5558800 1 1 FFAR3 HGNC HGNC:4499 protein_coding YES CCDS12459.1 ENSP00000328230 O14843 A0A0K0PUW7 UPI0000001C3F NM_005304.3 deleterious(0) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 35359435 35359435 T A 1 0 0 0 0 1 0 0 0 5692 1580 55 4 4 FFAR3 19 35359435 Missense_Mutation SNP T C3N-00580_T 1039352 35359435 23258181 901 19036 KMT2B 0 . GRCh38 19 35733371 35733371 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.6822G>T p.Gln2274His p.Q2274H ENST00000420124 28/37 210 87 123 277 277 0 strelka-varscan-mutect KMT2B,missense_variant,p.Gln2274His,ENST00000420124,NM_014727.2;KMT2B,non_coding_transcript_exon_variant,,ENST00000592092,;KMT2B,upstream_gene_variant,,ENST00000585476,;KMT2B,upstream_gene_variant,,ENST00000586308,; T ENST00000420124 Transcript missense_variant 6822/8469 6822/8148 2274/2715 Q/H caG/caT 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 tolerated(0.19) 28/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 35733371 35733371 G T 1 0 0 0 0 1 0 0 0 8296 991 35 2 2 KMT2B 19 35733371 Missense_Mutation SNP G C3N-00580_T 373936 35733371 22884245 902 19037 ZNF790 0 . GRCh38 19 36818556 36818556 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.1788C>T p.= p.N596N ENST00000356725 5/5 103 84 19 136 136 0 strelka-varscan-mutect ZNF790,synonymous_variant,p.=,ENST00000356725,NM_206894.3;ZNF790,synonymous_variant,p.=,ENST00000615484,NM_001242802.1;ZNF790,synonymous_variant,p.=,ENST00000614179,NM_001242801.1;ZNF790,synonymous_variant,p.=,ENST00000613249,NM_001242800.1;ZNF790,downstream_gene_variant,,ENST00000528994,;ZNF790,downstream_gene_variant,,ENST00000586323,;ZNF790,downstream_gene_variant,,ENST00000527645,;ZNF790,downstream_gene_variant,,ENST00000525288,;ZNF790-AS1,intron_variant,,ENST00000588906,;ZNF790-AS1,intron_variant,,ENST00000587278,; A ENST00000356725 Transcript synonymous_variant 1909/3037 1788/1911 596/636 N aaC/aaT 1 -1 ZNF790 HGNC HGNC:33114 protein_coding YES CCDS12496.1 ENSP00000349161 Q6PG37 UPI0000160EF0 NM_206894.3 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF224,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999956 1 1 1 0 A 2 1 61 36818556 36818556 G A 1 0 0 0 0 0 0 0 1 18747 1368 48 3 3 ZNF790 19 36818556 Silent SNP G C3N-00580_T 1085185 36818556 21799060 903 19038 ZNF527 0 . GRCh38 19 37388650 37388650 + Missense_Mutation SNP C C T novel C3N-00580_T C3N-00580_N C C c.601C>T p.Pro201Ser p.P201S ENST00000436120 5/5 99 69 30 113 113 0 strelka-varscan-mutect ZNF527,missense_variant,p.Pro201Ser,ENST00000436120,NM_032453.1;ZNF527,intron_variant,,ENST00000587349,;ZNF527,downstream_gene_variant,,ENST00000483919,;ZNF527,downstream_gene_variant,,ENST00000588911,;ZNF527,3_prime_UTR_variant,,ENST00000356178,;ZNF527,3_prime_UTR_variant,,ENST00000588512,; T ENST00000436120 Transcript missense_variant 708/2828 601/1830 201/609 P/S Ccc/Tcc 1 1 ZNF527 HGNC HGNC:29385 protein_coding YES CCDS42559.1 ENSP00000390179 Q8NB42 UPI00002021F5 NM_032453.1 tolerated(0.94) 5/5 MODERATE 1 SNV 4 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 37388650 37388650 C T 1 0 0 0 0 1 0 0 0 18541 623 22 3 3 ZNF527 19 37388650 Missense_Mutation SNP C C3N-00580_T 570094 37388650 21228966 904 19039 LGALS4 0 . GRCh38 19 38801806 38801806 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.930G>A p.= p.L310L ENST00000307751 10/10 218 109 109 328 327 1 strelka-varscan-mutect LGALS4,synonymous_variant,p.=,ENST00000307751,NM_006149.3;LGALS4,synonymous_variant,p.=,ENST00000600070,;RNU6-140P,upstream_gene_variant,,ENST00000384566,;LGALS4,downstream_gene_variant,,ENST00000597803,;LGALS4,3_prime_UTR_variant,,ENST00000595291,;LGALS4,downstream_gene_variant,,ENST00000595278,;LGALS4,downstream_gene_variant,,ENST00000597153,;LGALS4,downstream_gene_variant,,ENST00000596628,;LGALS4,downstream_gene_variant,,ENST00000595342,; T ENST00000307751 Transcript synonymous_variant 1408/1535 930/972 310/323 L ttG/ttA 1 -1 LGALS4 HGNC HGNC:6565 protein_coding YES CCDS12521.1 ENSP00000302100 P56470 Q6FHZ4 UPI0000001651 NM_006149.3 10/10 PROSITE_profiles:PS51304,hmmpanther:PTHR11346:SF32,hmmpanther:PTHR11346,Gene3D:2.60.120.200,Pfam_domain:PF00337,SMART_domains:SM00908,SMART_domains:SM00276,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 38801806 38801806 C T 1 0 0 0 0 0 0 0 1 8653 593 21 3 3 LGALS4 19 38801806 Silent SNP C C3N-00580_T 1413156 38801806 19815810 905 19040 FBL 0 . GRCh38 19 39840661 39840661 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.137G>T p.Gly46Val p.G46V ENST00000221801 2/9 204 152 52 218 218 0 strelka-varscan-mutect FBL,missense_variant,p.Gly46Val,ENST00000221801,NM_001436.3;FBL,missense_variant,p.Gly46Val,ENST00000594309,;FBL,missense_variant,p.Gly33Val,ENST00000598417,;FBL,missense_variant,p.Gly46Val,ENST00000599134,;FBL,intron_variant,,ENST00000601274,;FBL,intron_variant,,ENST00000597224,;FBL,intron_variant,,ENST00000597634,;FBL,upstream_gene_variant,,ENST00000595545,;FBL,upstream_gene_variant,,ENST00000626009,;FBL,upstream_gene_variant,,ENST00000593503,;FBL,non_coding_transcript_exon_variant,,ENST00000599159,;FBL,intron_variant,,ENST00000594443,; A ENST00000221801 Transcript missense_variant 251/1160 137/966 46/321 G/V gGa/gTa 1 -1 FBL HGNC HGNC:3599 protein_coding YES CCDS12545.1 ENSP00000221801 P22087 UPI000012A578 NM_001436.3 deleterious_low_confidence(0.01) 2/9 hmmpanther:PTHR10335,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39840661 39840661 C A 1 0 0 0 0 1 0 0 0 5558 855 30 2 2 FBL 19 39840661 Missense_Mutation SNP C C3N-00580_T 1038855 39840661 18776955 906 19041 FCGBP 0 . GRCh38 19 39872124 39872124 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.11703G>T p.Gln3901His p.Q3901H ENST00000616721 24/28 122 43 79 131 131 0 strelka-varscan-mutect FCGBP,missense_variant,p.Gln3901His,ENST00000616721,NM_003890.2; A ENST00000616721 Transcript missense_variant 11711/12787 11703/12615 3901/4204 Q/H caG/caT 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 tolerated(0.08) 24/28 Pfam_domain:PF08742,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF244,SMART_domains:SM00832 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39872124 39872124 C A 1 0 0 0 0 1 0 0 0 5641 680 24 2 2 FCGBP 19 39872124 Missense_Mutation SNP C C3N-00580_T 31463 39872124 18745492 907 19042 FCGBP 0 . GRCh38 19 39873508 39873508 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.10891G>T p.Ala3631Ser p.A3631S ENST00000616721 23/28 268 116 152 290 290 0 strelka-varscan-mutect FCGBP,missense_variant,p.Ala3631Ser,ENST00000616721,NM_003890.2; A ENST00000616721 Transcript missense_variant 10899/12787 10891/12615 3631/4204 A/S Gcc/Tcc 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 tolerated(1) 23/28 Pfam_domain:PF12714,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF244,SMART_domains:SM00215 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 39873508 39873508 C A 1 0 0 0 0 1 0 0 0 5641 797 28 2 2 FCGBP 19 39873508 Missense_Mutation SNP C C3N-00580_T 1384 39873508 18744108 908 19043 ZNF780B 0 . GRCh38 19 40036517 40036517 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.342G>T p.Glu114Asp p.E114D ENST00000434248 5/5 98 50 48 155 155 0 strelka-varscan-mutect ZNF780B,missense_variant,p.Glu114Asp,ENST00000434248,;ZNF780B,missense_variant,p.Glu114Asp,ENST00000617676,NM_001005851.2;ZNF780B,5_prime_UTR_variant,,ENST00000221355,;ZNF780B,downstream_gene_variant,,ENST00000598845,;ZNF780B,downstream_gene_variant,,ENST00000595995,; A ENST00000434248 Transcript missense_variant 408/8665 342/2502 114/833 E/D gaG/gaT 1 -1 ZNF780B HGNC HGNC:33109 protein_coding YES CCDS46077.1 ENSP00000391641 Q9Y6R6 A0A024R0P7 UPI000007137F tolerated(0.26) 5/5 hmmpanther:PTHR24377:SF203,hmmpanther:PTHR24377 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 40036517 40036517 C A 1 0 0 0 0 1 0 0 0 18736 680 24 2 2 ZNF780B 19 40036517 Missense_Mutation SNP C C3N-00580_T 163009 40036517 18581099 909 19044 SULT2B1 0 . GRCh38 19 48596811 48596811 + Missense_Mutation SNP G G A rs2302947 C3N-00580_T C3N-00580_N G G c.718G>A p.Val240Ile p.V240I ENST00000201586 6/7 190 170 20 329 329 0 strelka-varscan-mutect SULT2B1,missense_variant,p.Val225Ile,ENST00000323090,NM_004605.2;SULT2B1,missense_variant,p.Val240Ile,ENST00000201586,NM_177973.1;FAM83E,downstream_gene_variant,,ENST00000263266,NM_017708.3;SULT2B1,non_coding_transcript_exon_variant,,ENST00000594274,;SULT2B1,non_coding_transcript_exon_variant,,ENST00000597923,; A ENST00000201586 Transcript missense_variant 896/1295 718/1098 240/365 V/I Gtc/Atc rs2302947,COSM303321,COSM303322 1 1 SULT2B1 HGNC HGNC:11459 protein_coding YES CCDS12723.1 ENSP00000201586 O00204 UPI0000073F98 NM_177973.1 tolerated(0.1) 6/7 hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF9,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs2302947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 48596811 48596811 G A 1 0 0 0 0 1 0 0 0 15768 1145 40 1 1 SULT2B1 19 48596811 Missense_Mutation SNP G C3N-00580_T 8560294 48596811 10020805 910 19045 CGB2 0 . GRCh38 19 49033009 49033009 + Missense_Mutation SNP G G A novel C3N-00580_T C3N-00580_N G G c.280G>A p.Val94Met p.V94M ENST00000359342 3/3 93 33 60 150 150 0 strelka-varscan-mutect CGB2,missense_variant,p.Val82Met,ENST00000474913,NM_001319065.1;CGB2,missense_variant,p.Val94Met,ENST00000359342,NM_033378.1;CTB-60B18.6,intron_variant,,ENST00000591656,;CTB-60B18.6,intron_variant,,ENST00000604577,;CGB1,downstream_gene_variant,,ENST00000601167,;CGB1,downstream_gene_variant,,ENST00000301407,NM_033377.1;NTF6G,downstream_gene_variant,,ENST00000591094,; A ENST00000359342 Transcript missense_variant 398/627 280/492 94/163 V/M Gtg/Atg 1 1 CGB2 HGNC HGNC:16722 protein_coding YES CCDS12750.2 ENSP00000352295 H9KV56 UPI000059D759 NM_033378.1 deleterious(0) 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00007,hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF16,SMART_domains:SM00068,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS rs1463794919 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 49033009 49033009 G A 1 0 0 0 0 1 0 0 0 3055 1145 40 1 1 CGB2 19 49033009 Missense_Mutation SNP G C3N-00580_T 436198 49033009 9584607 911 19046 CGB1 0 . GRCh38 19 49036247 49036247 + Silent SNP C C A rs200371312 C3N-00580_T C3N-00580_N C C c.66G>T p.= p.P22P ENST00000301407 2/3 317 165 152 424 424 0 strelka-varscan-mutect CGB1,synonymous_variant,p.=,ENST00000601167,;CGB1,synonymous_variant,p.=,ENST00000301407,NM_033377.1;CTB-60B18.6,intron_variant,,ENST00000591656,;CTB-60B18.6,intron_variant,,ENST00000604577,;CGB2,downstream_gene_variant,,ENST00000474913,NM_001319065.1;CGB2,downstream_gene_variant,,ENST00000359342,NM_033378.1;NTF6B,downstream_gene_variant,,ENST00000591913,; A ENST00000301407 Transcript synonymous_variant 171/573 66/468 22/155 P ccG/ccT rs200371312,COSM1395173 1 -1 CGB1 HGNC HGNC:16721 protein_coding YES CCDS12751.2 ENSP00000301407 A6NKQ9 UPI0000EE7C13 NM_033377.1 2/3 hmmpanther:PTHR11515,hmmpanther:PTHR11515:SF16 0,1 LOW 1 SNV 1 0,1 1 PASS rs200371312 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 49036247 49036247 C A 1 0 0 0 0 0 0 0 1 3054 755 27 1 1 CGB1 19 49036247 Silent SNP C C3N-00580_T 3238 49036247 9581369 912 19047 CGB5 0 . GRCh38 19 49045262 49045262 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.466G>T p.Gly156Trp p.G156W ENST00000301408 3/3 66 29 37 56 56 0 strelka-varscan-mutect CGB5,missense_variant,p.Gly156Trp,ENST00000301408,NM_033043.1;CGB8,downstream_gene_variant,,ENST00000448456,NM_033183.2;CTB-60B18.15,downstream_gene_variant,,ENST00000596318,;CTB-60B18.17,downstream_gene_variant,,ENST00000593746,; T ENST00000301408 Transcript missense_variant 792/841 466/498 156/165 G/W Ggg/Tgg 1 1 CGB5 HGNC HGNC:16452 protein_coding YES CCDS12752.1 ENSP00000301408 P0DN86 A0A0F7RQP8 UPI0000035497 NM_033043.1 deleterious_low_confidence(0.01) 3/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1356275365 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 49045262 49045262 G T 1 0 0 0 0 1 0 0 0 3057 1232 43 2 2 CGB5 19 49045262 Missense_Mutation SNP G C3N-00580_T 9015 49045262 9572354 913 19048 KLK8 0 . GRCh38 19 51000233 51000233 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.391C>A p.His131Asn p.H131N ENST00000391806 4/6 65 46 19 68 67 1 strelka-varscan-mutect KLK8,missense_variant,p.His86Asn,ENST00000600767,NM_007196.3;KLK8,missense_variant,p.His131Asn,ENST00000391806,NM_144505.2;KLK8,missense_variant,p.His86Asn,ENST00000595238,;KLK8,5_prime_UTR_variant,,ENST00000291726,NM_001281431.1;KLK8,intron_variant,,ENST00000347619,NM_144506.2;KLK8,intron_variant,,ENST00000320838,NM_144507.2;KLK8,intron_variant,,ENST00000593490,;KLK9,downstream_gene_variant,,ENST00000594211,NM_012315.1;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK8,upstream_gene_variant,,ENST00000598195,;KLK8,synonymous_variant,p.=,ENST00000594669,;CTC-518B2.8,intron_variant,,ENST00000599166,;CTC-518B2.8,downstream_gene_variant,,ENST00000250366,;KLK9,downstream_gene_variant,,ENST00000544410,;KLK8,downstream_gene_variant,,ENST00000599710,;KLK8,upstream_gene_variant,,ENST00000594914,; T ENST00000391806 Transcript missense_variant 472/1051 391/918 131/305 H/N Cac/Aac 1 -1 KLK8 HGNC HGNC:6369 protein_coding YES CCDS42600.1 ENSP00000375682 O60259 UPI000002ACDB NM_144505.2 deleterious(0) 4/6 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF123,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 51000233 51000233 G T 1 0 0 0 0 1 0 0 0 8279 1348 47 2 2 KLK8 19 51000233 Missense_Mutation SNP G C3N-00580_T 1954971 51000233 7617383 914 19049 CEACAM18 0 . GRCh38 19 51480567 51480567 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.287G>T p.Arg96Ile p.R96I ENST00000396477 2/6 372 186 186 462 462 0 strelka-varscan-mutect CEACAM18,missense_variant,p.Arg96Ile,ENST00000396477,NM_001278392.1; T ENST00000396477 Transcript missense_variant 308/1476 287/1155 96/384 R/I aGa/aTa COSM4903578,COSM4903579 1 1 CEACAM18 HGNC HGNC:31949 protein_coding YES ENSP00000379738 A8MTB9 UPI0002C5E52C NM_001278392.1 tolerated(0.2) 2/6 Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 51480567 51480567 G T 1 0 0 0 0 1 0 0 0 2895 942 33 2 2 CEACAM18 19 51480567 Missense_Mutation SNP G C3N-00580_T 480334 51480567 7137049 915 19050 OSCAR 0 . GRCh38 19 54095744 54095744 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.795G>T p.Gln265His p.Q265H ENST00000611261 6/6 44 32 12 52 52 0 strelka-varscan-mutect OSCAR,missense_variant,p.Gln265His,ENST00000611261,NM_206818.2;OSCAR,missense_variant,p.Gln261His,ENST00000284648,NM_001282349.1;OSCAR,missense_variant,p.Gln250His,ENST00000616215,NM_001282350.1;OSCAR,missense_variant,p.Gln265His,ENST00000359649,;OSCAR,missense_variant,p.Gln250His,ENST00000391761,;OSCAR,intron_variant,,ENST00000617140,NM_130771.4;OSCAR,intron_variant,,ENST00000358375,NM_133169.4;OSCAR,intron_variant,,ENST00000351806,NM_133168.4;OSCAR,intron_variant,,ENST00000616447,;OSCAR,intron_variant,,ENST00000356532,;OSCAR,downstream_gene_variant,,ENST00000391760,; A ENST00000611261 Transcript missense_variant 987/2061 795/861 265/286 Q/H caG/caT 1 -1 OSCAR HGNC HGNC:29960 protein_coding YES CCDS12876.1 ENSP00000479089 A0A087WV17 UPI00034F23BB NM_206818.2 deleterious_low_confidence(0.05) 6/6 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 54095744 54095744 C A 1 0 0 0 0 1 0 0 0 11351 796 28 2 2 OSCAR 19 54095744 Missense_Mutation SNP C C3N-00580_T 2615177 54095744 4521872 916 19051 LENG1 0 . GRCh38 19 54159657 54159657 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.39C>A p.Asn13Lys p.N13K ENST00000222224 1/4 146 71 75 205 205 0 strelka-varscan-mutect LENG1,missense_variant,p.Asn13Lys,ENST00000222224,NM_024316.2;CNOT3,downstream_gene_variant,,ENST00000358389,;CNOT3,downstream_gene_variant,,ENST00000221232,NM_014516.3;CNOT3,downstream_gene_variant,,ENST00000447684,;TMC4,downstream_gene_variant,,ENST00000617472,NM_001145303.2;TMC4,downstream_gene_variant,,ENST00000619895,NM_144686.3;CNOT3,downstream_gene_variant,,ENST00000471126,;TMC4,downstream_gene_variant,,ENST00000476013,;TMC4,downstream_gene_variant,,ENST00000613492,;CNOT3,downstream_gene_variant,,ENST00000618939,;CNOT3,downstream_gene_variant,,ENST00000613073,;CNOT3,downstream_gene_variant,,ENST00000617930,;TMC4,downstream_gene_variant,,ENST00000613723,;TMC4,downstream_gene_variant,,ENST00000497518,;TMC4,downstream_gene_variant,,ENST00000615945,;TMC4,downstream_gene_variant,,ENST00000611183,;TMC4,downstream_gene_variant,,ENST00000495398,; T ENST00000222224 Transcript missense_variant 226/1542 39/795 13/264 N/K aaC/aaA 1 -1 LENG1 HGNC HGNC:15502 protein_coding YES CCDS12881.1 ENSP00000222224 Q96BZ8 UPI00034F2389 NM_024316.2 deleterious(0.01) 1/4 hmmpanther:PTHR22093,Pfam_domain:PF10197,SMART_domains:SM01083 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 54159657 54159657 G T 1 0 0 0 0 1 0 0 0 8631 1368 48 2 2 LENG1 19 54159657 Missense_Mutation SNP G C3N-00580_T 63913 54159657 4457959 917 19052 NLRP7 0 . GRCh38 19 54939759 54939759 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.1060G>T p.Ala354Ser p.A354S ENST00000588756 6/13 438 219 219 489 489 0 strelka-varscan-mutect NLRP7,missense_variant,p.Ala354Ser,ENST00000588756,;NLRP7,missense_variant,p.Ala354Ser,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Ala354Ser,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Ala354Ser,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Ala354Ser,ENST00000590030,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,downstream_gene_variant,,ENST00000587844,;NLRP7,missense_variant,p.Ala354Ser,ENST00000586379,; A ENST00000588756 Transcript missense_variant 1547/3826 1060/3114 354/1037 A/S Gcg/Tcg COSM1396432,COSM1396433,COSM5155907 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 tolerated(0.14) 6/13 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 54939759 54939759 C A 1 0 0 0 0 1 0 0 0 10520 768 27 1 1 NLRP7 19 54939759 Missense_Mutation SNP C C3N-00580_T 780102 54939759 3677857 918 19053 PTPRH 0 . GRCh38 19 55185656 55185656 + Nonsense_Mutation SNP C C A rs745624477 C3N-00580_T C3N-00580_N C C c.2908G>T p.Glu970Ter p.E970* ENST00000376350 18/20 124 61 63 173 173 0 strelka-varscan-mutect PTPRH,stop_gained,p.Glu970Ter,ENST00000376350,NM_002842.4;PTPRH,stop_gained,p.Glu792Ter,ENST00000263434,NM_001161440.2; A ENST00000376350 Transcript stop_gained 2931/3877 2908/3348 970/1115 E/* Gag/Tag rs745624477 1 -1 PTPRH HGNC HGNC:9672 protein_coding YES CCDS33110.1 ENSP00000365528 Q9HD43 UPI000052D443 NM_002842.4 18/20 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF297,hmmpanther:PTHR19134,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00194,Superfamily_domains:SSF52799 HIGH 1 SNV 1 1 PASS rs745624477 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 55185656 55185656 C A 1 0 0 0 0 0 1 0 0 12957 864 30 2 2 PTPRH 19 55185656 Nonsense_Mutation SNP C C3N-00580_T 245897 55185656 3431960 919 19054 PTPRH 0 . GRCh38 19 55187581 55187581 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2498G>T p.Ser833Ile p.S833I ENST00000376350 14/20 208 111 97 288 288 0 strelka-varscan-mutect PTPRH,missense_variant,p.Ser833Ile,ENST00000376350,NM_002842.4;PTPRH,missense_variant,p.Ser655Ile,ENST00000263434,NM_001161440.2; A ENST00000376350 Transcript missense_variant 2521/3877 2498/3348 833/1115 S/I aGc/aTc 1 -1 PTPRH HGNC HGNC:9672 protein_coding YES CCDS33110.1 ENSP00000365528 Q9HD43 UPI000052D443 NM_002842.4 tolerated(0.08) 14/20 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF297,hmmpanther:PTHR19134,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 55187581 55187581 C A 1 0 0 0 0 1 0 0 0 12957 797 28 2 2 PTPRH 19 55187581 Missense_Mutation SNP C C3N-00580_T 1925 55187581 3430035 920 19055 NLRP9 0 . GRCh38 19 55733449 55733449 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.382A>G p.Met128Val p.M128V ENST00000332836 2/9 116 51 65 181 181 0 strelka-varscan-mutect NLRP9,missense_variant,p.Met128Val,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Met128Val,ENST00000590200,;RN7SKP109,upstream_gene_variant,,ENST00000410592,; C ENST00000332836 Transcript missense_variant 410/3484 382/2976 128/991 M/V Atg/Gtg 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 tolerated(0.91) 2/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1192514526 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 55733449 55733449 T C 1 0 0 0 0 1 0 0 0 10522 1464 51 5 5 NLRP9 19 55733449 Missense_Mutation SNP T C3N-00580_T 545868 55733449 2884167 921 19056 CSNK2A1 0 . GRCh38 20 483999 483999 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1138G>T p.Gly380Trp p.G380W ENST00000217244 14/14 149 125 24 200 200 0 strelka-varscan-mutect CSNK2A1,missense_variant,p.Gly380Trp,ENST00000217244,NM_177559.2;CSNK2A1,missense_variant,p.Gly380Trp,ENST00000349736,NM_001895.3;CSNK2A1,missense_variant,p.Gly244Trp,ENST00000400217,NM_177560.2;CSNK2A1,intron_variant,,ENST00000400227,;CSNK2A1,intron_variant,,ENST00000619801,; A ENST00000217244 Transcript missense_variant 1514/4416 1138/1176 380/391 G/W Ggg/Tgg 1 -1 CSNK2A1 HGNC HGNC:2457 protein_coding YES CCDS13003.1 ENSP00000217244 P68400 UPI0000000CB5 NM_177559.2 deleterious_low_confidence(0) 14/14 hmmpanther:PTHR24054,hmmpanther:PTHR24054:SF28 MODERATE 1 SNV 1 1 PASS rs1397626830 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 483999 483999 C A 1 0 0 0 0 1 0 0 0 3757 594 21 2 2 CSNK2A1 20 483999 Missense_Mutation SNP C C3N-00580_T 483999 63960168 922 19057 RSPO4 0 . GRCh38 20 968115 968115 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.103T>A p.Cys35Ser p.C35S ENST00000217260 2/5 418 298 120 410 410 0 strelka-varscan-mutect RSPO4,missense_variant,p.Cys35Ser,ENST00000217260,NM_001029871.3;RSPO4,missense_variant,p.Cys35Ser,ENST00000400634,NM_001040007.2; T ENST00000217260 Transcript missense_variant 200/2707 103/705 35/234 C/S Tgc/Agc 1 -1 RSPO4 HGNC HGNC:16175 protein_coding YES CCDS42846.1 ENSP00000217260 Q2I0M5 UPI00001D8320 NM_001029871.3 deleterious(0) 2/5 hmmpanther:PTHR23275,hmmpanther:PTHR23275:SF51,Pfam_domain:PF15913,Gene3D:2.10.220.10,SMART_domains:SM00261 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 968115 968115 A T 1 0 0 0 0 1 0 0 0 13970 188 7 4 4 RSPO4 20 968115 Missense_Mutation SNP A C3N-00580_T 484116 968115 63476052 923 19058 SIRPG 0 . GRCh38 20 1635271 1635271 + Silent SNP G G T rs753213551 C3N-00580_T C3N-00580_N G G c.1077C>A p.= p.T359T ENST00000303415 4/6 103 76 27 93 93 0 strelka-varscan-mutect SIRPG,synonymous_variant,p.=,ENST00000381580,;SIRPG,synonymous_variant,p.=,ENST00000303415,NM_018556.3;SIRPG,intron_variant,,ENST00000381583,NM_001039508.1;SIRPG,intron_variant,,ENST00000344103,NM_080816.2;SIRPG,intron_variant,,ENST00000216927,;SIRPG-AS1,intron_variant,,ENST00000456177,;SIRPG-AS1,intron_variant,,ENST00000437384,;SIRPG,upstream_gene_variant,,ENST00000478145,;SIRPG,upstream_gene_variant,,ENST00000497407,; T ENST00000303415 Transcript synonymous_variant 1142/1716 1077/1164 359/387 T acC/acA rs753213551 1 -1 SIRPG HGNC HGNC:15757 protein_coding YES CCDS13020.2 ENSP00000305529 Q9P1W8 UPI00001AE5FD NM_018556.3 4/6 hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6 LOW 1 SNV 1 1 PASS rs753213551 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 61 1635271 1635271 G T 1 0 0 0 0 0 0 0 1 14599 1246 43 2 2 SIRPG 20 1635271 Silent SNP G C3N-00580_T 667156 1635271 62808896 924 19059 TGM3 0 . GRCh38 20 2325924 2325924 + Silent SNP G G A rs780274543 C3N-00580_T C3N-00580_N G G c.1059G>A p.= p.L353L ENST00000381458 8/13 270 187 83 271 271 0 strelka-varscan-mutect TGM3,synonymous_variant,p.=,ENST00000381458,NM_003245.3;TGM3,non_coding_transcript_exon_variant,,ENST00000463090,; A ENST00000381458 Transcript synonymous_variant 1122/2642 1059/2082 353/693 L ttG/ttA rs780274543 1 1 TGM3 HGNC HGNC:11779 protein_coding YES CCDS33435.1 ENSP00000370867 Q08188 UPI0000136CCC NM_003245.3 8/13 Gene3D:1ex0A02,Pfam_domain:PF01841,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF36,SMART_domains:SM00460,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS rs780274543 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 2325924 2325924 G A 1 0 0 0 0 0 0 0 1 16264 1339 47 3 3 TGM3 20 2325924 Silent SNP G C3N-00580_T 690653 2325924 62118243 925 19060 TMC2 0 . GRCh38 20 2558466 2558466 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.93G>T p.= p.L31L ENST00000358864 3/20 316 211 105 373 373 0 strelka-varscan-mutect TMC2,synonymous_variant,p.=,ENST00000358864,NM_080751.2; T ENST00000358864 Transcript synonymous_variant 108/3169 93/2721 31/906 L ctG/ctT 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 3/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 2558466 2558466 G T 1 0 0 0 0 0 0 0 1 16431 1335 47 2 2 TMC2 20 2558466 Silent SNP G C3N-00580_T 232542 2558466 61885701 926 19061 PROKR2 0 . GRCh38 20 5302556 5302556 + Silent SNP A A T rs763738276 C3N-00580_T C3N-00580_N A A c.639T>A p.= p.P213P ENST00000217270 2/2 790 510 280 639 639 0 strelka-varscan-mutect PROKR2,synonymous_variant,p.=,ENST00000217270,NM_144773.2; T ENST00000217270 Transcript synonymous_variant 639/1155 639/1155 213/384 P ccT/ccA rs763738276 1 -1 PROKR2 HGNC HGNC:15836 protein_coding YES CCDS13089.1 ENSP00000217270 Q8NFJ6 UPI000003BCC6 NM_144773.2 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF234,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs763738276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 5302556 5302556 A T 1 0 0 0 0 0 0 0 1 12686 175 7 4 4 PROKR2 20 5302556 Silent SNP A C3N-00580_T 2744090 5302556 59141611 927 19062 PCSK2 0 . GRCh38 20 17436722 17436722 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.724G>T p.Asp242Tyr p.D242Y ENST00000262545 8/12 115 63 52 92 92 0 strelka-varscan-mutect PCSK2,missense_variant,p.Asp242Tyr,ENST00000262545,NM_002594.4;PCSK2,missense_variant,p.Asp223Tyr,ENST00000377899,NM_001201528.1;PCSK2,missense_variant,p.Asp207Tyr,ENST00000536609,NM_001201529.2; T ENST00000262545 Transcript missense_variant 1039/4740 724/1917 242/638 D/Y Gac/Tac 1 1 PCSK2 HGNC HGNC:8744 protein_coding YES CCDS13125.1 ENSP00000262545 P16519 UPI0000000C6E NM_002594.4 deleterious(0) 8/12 Gene3D:3.40.50.200,Pfam_domain:PF00082,hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF11,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 61 17436722 17436722 G T 1 0 0 0 0 1 0 0 0 11689 1174 41 2 2 PCSK2 20 17436722 Missense_Mutation SNP G C3N-00580_T 12134166 17436722 47007445 928 19063 AL031664.1 0 . GRCh38 20 17508942 17508942 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.682G>T p.Gly228Cys p.G228C ENST00000377873 5/8 92 80 12 145 144 1 strelka-varscan-mutect BFSP1,missense_variant,p.Gly228Cys,ENST00000377873,NM_001195.4;BFSP1,missense_variant,p.Gly103Cys,ENST00000377868,NM_001161705.1,NM_001278607.1;AL031664.1,missense_variant,p.Gly89Cys,ENST00000536626,NM_001278606.1,NM_001278608.1;BFSP1,non_coding_transcript_exon_variant,,ENST00000492424,;BFSP1,downstream_gene_variant,,ENST00000473415,; A ENST00000377873 Transcript missense_variant 722/2207 682/1998 228/665 G/C Ggc/Tgc 1 -1 BFSP1 HGNC HGNC:1040 protein_coding YES CCDS13126.1 ENSP00000367104 Q12934 UPI00001268C7 NM_001195.4 tolerated(0.18) 5/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14069,hmmpanther:PTHR14069:SF0,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 17508942 17508942 C A 1 0 0 0 0 1 0 0 0 568 623 22 2 2 AL031664.1 20 17508942 Missense_Mutation SNP C C3N-00580_T 72220 17508942 46935225 929 19064 FAM182B 0 . GRCh38 20 25775005 25775005 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.315G>T p.Leu105Phe p.L105F ENST00000376403 3/3 510 430 80 459 458 1 strelka-varscan-mutect FAM182B,missense_variant,p.Leu105Phe,ENST00000376403,;FAM182B,missense_variant,p.Leu104Phe,ENST00000376404,;FAM182B,downstream_gene_variant,,ENST00000584071,;FAM182B,intron_variant,,ENST00000478164,;FAM182B,intron_variant,,ENST00000485279,;FAM182B,intron_variant,,ENST00000453481,;FAM182B,downstream_gene_variant,,ENST00000582267,;FAM182B,downstream_gene_variant,,ENST00000584356,; A ENST00000376403 Transcript missense_variant 694/1681 315/459 105/152 L/F ttG/ttT 1 -1 FAM182B HGNC HGNC:34503 protein_coding YES ENSP00000365585 Q5T319 UPI000047001E deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 25775005 25775005 C A 1 0 0 0 0 1 0 0 0 5356 477 17 2 2 FAM182B 20 25775005 Missense_Mutation SNP C C3N-00580_T 8266063 25775005 38669162 930 19065 COX4I2 0 . GRCh38 20 31639078 31639078 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.61A>G p.Met21Val p.M21V ENST00000376075 2/5 657 522 135 631 631 0 strelka-varscan-mutect COX4I2,missense_variant,p.Met21Val,ENST00000376075,NM_032609.2;COX4I2,non_coding_transcript_exon_variant,,ENST00000490030,; G ENST00000376075 Transcript missense_variant 136/693 61/516 21/171 M/V Atg/Gtg 1 1 COX4I2 HGNC HGNC:16232 protein_coding YES CCDS13187.1 ENSP00000365243 Q96KJ9 H6SG14 UPI000013CDC9 NM_032609.2 tolerated(0.47) 2/5 hmmpanther:PTHR10707,hmmpanther:PTHR10707:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 31639078 31639078 A G 1 0 0 0 0 1 0 0 0 3566 333 12 5 5 COX4I2 20 31639078 Missense_Mutation SNP A C3N-00580_T 5864073 31639078 32805089 931 19066 CCM2L 0 . GRCh38 20 32022750 32022750 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.1024T>A p.Tyr342Asn p.Y342N ENST00000262659 6/9 289 234 55 312 312 0 strelka-varscan-mutect CCM2L,missense_variant,p.Tyr342Asn,ENST00000262659,NM_080625.3;CCM2L,missense_variant,p.Tyr95Asn,ENST00000452892,; A ENST00000262659 Transcript missense_variant 1029/2523 1024/1302 342/433 Y/N Tac/Aac 1 1 CCM2L HGNC HGNC:16153 protein_coding YES CCDS13195.1 ENSP00000262659 Q9NUG4 UPI0000070921 NM_080625.3 deleterious(0) 6/9 hmmpanther:PTHR21642:SF2,hmmpanther:PTHR21642 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 32022750 32022750 T A 1 0 0 0 0 1 0 0 0 2607 1522 53 4 4 CCM2L 20 32022750 Missense_Mutation SNP T C3N-00580_T 383672 32022750 32421417 932 19067 SUN5 0 . GRCh38 20 32996329 32996329 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.420C>A p.Ser140Arg p.S140R ENST00000356173 7/13 132 96 36 112 112 0 strelka-varscan-mutect SUN5,missense_variant,p.Ser140Arg,ENST00000356173,NM_080675.3;SUN5,missense_variant,p.Ser115Arg,ENST00000375523,;SUN5,downstream_gene_variant,,ENST00000420875,;SUN5,downstream_gene_variant,,ENST00000375519,; T ENST00000356173 Transcript missense_variant 513/1254 420/1140 140/379 S/R agC/agA 1 -1 SUN5 HGNC HGNC:16252 protein_coding YES CCDS13209.1 ENSP00000348496 Q8TC36 UPI0000135D7C NM_080675.3 tolerated(0.33) 7/13 hmmpanther:PTHR12911,hmmpanther:PTHR12911:SF19 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 32996329 32996329 G T 1 0 0 0 0 1 0 0 0 15780 985 34 2 2 SUN5 20 32996329 Missense_Mutation SNP G C3N-00580_T 973579 32996329 31447838 933 19068 CHMP4B 0 . GRCh38 20 33848500 33848500 + Missense_Mutation SNP A A G novel C3N-00580_T C3N-00580_N A A c.224A>G p.Tyr75Cys p.Y75C ENST00000217402 2/5 591 558 33 560 560 0 varscan-mutect CHMP4B,missense_variant,p.Tyr75Cys,ENST00000217402,NM_176812.4; G ENST00000217402 Transcript missense_variant 389/1646 224/675 75/224 Y/C tAt/tGt 1 1 CHMP4B HGNC HGNC:16171 protein_coding YES CCDS13228.1 ENSP00000217402 Q9H444 UPI0000128625 NM_176812.4 deleterious(0.02) 2/5 hmmpanther:PTHR22761,hmmpanther:PTHR22761:SF4,Pfam_domain:PF03357 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 33848500 33848500 A G 1 0 0 0 0 1 0 0 0 3117 449 16 5 5 CHMP4B 20 33848500 Missense_Mutation SNP A C3N-00580_T 852171 33848500 30595667 934 19069 NDRG3 0 . GRCh38 20 36688684 36688684 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.194T>A p.Leu65His p.L65H ENST00000349004 4/16 186 128 58 160 160 0 strelka-varscan-mutect NDRG3,missense_variant,p.Leu65His,ENST00000373803,;NDRG3,missense_variant,p.Leu65His,ENST00000349004,NM_032013.3;NDRG3,missense_variant,p.Leu53His,ENST00000359675,NM_022477.3;NDRG3,missense_variant,p.Leu56His,ENST00000422536,;NDRG3,intron_variant,,ENST00000373773,; T ENST00000349004 Transcript missense_variant 276/2964 194/1128 65/375 L/H cTc/cAc 1 -1 NDRG3 HGNC HGNC:14462 protein_coding YES CCDS13285.1 ENSP00000345292 Q9UGV2 UPI000012FEDF NM_032013.3 deleterious(0) 4/16 hmmpanther:PTHR11034,hmmpanther:PTHR11034:SF20,Gene3D:3.40.50.1820,Pfam_domain:PF03096,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 36688684 36688684 A T 1 0 0 0 0 1 0 0 0 10274 318 11 4 4 NDRG3 20 36688684 Missense_Mutation SNP A C3N-00580_T 2840184 36688684 27755483 935 19070 PTPRT 0 . GRCh38 20 42199346 42199346 + Frame_Shift_Del DEL C C - novel C3N-00580_T C3N-00580_N C C c.2442delG p.Arg815GlyfsTer63 p.R815Gfs*63 ENST00000373198 17/32 171 132 39 193 193 0 sindel-varindel PTPRT,frameshift_variant,p.Arg815GlyfsTer63,ENST00000373198,NM_133170.3;PTPRT,frameshift_variant,p.Arg818GlyfsTer63,ENST00000373193,;PTPRT,frameshift_variant,p.Arg786GlyfsTer63,ENST00000373201,;PTPRT,frameshift_variant,p.Arg796GlyfsTer62,ENST00000373190,;PTPRT,frameshift_variant,p.Arg786GlyfsTer63,ENST00000373184,;PTPRT,frameshift_variant,p.Arg805GlyfsTer63,ENST00000356100,;PTPRT,frameshift_variant,p.Arg796GlyfsTer63,ENST00000373187,NM_007050.5;PTPRT,frameshift_variant,p.Arg414GlyfsTer63,ENST00000612229,;PTPRT,frameshift_variant,p.Arg431GlyfsTer63,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; - ENST00000373198 Transcript frameshift_variant 2678/12746 2442/4383 814/1460 Q/X caG/ca 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 17/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 42199346 42199346 C - 1 0 1 0 1 0 0 0 0 12967 912 32 0 0 PTPRT 20 42199346 Frame_Shift_Del DEL C C3N-00580_T 5510662 42199346 22244821 936 19071 R3HDML 0 . GRCh38 20 44341202 44341202 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.268G>T p.Asp90Tyr p.D90Y ENST00000217043 2/5 74 47 27 92 92 0 strelka-varscan-mutect R3HDML,missense_variant,p.Asp90Tyr,ENST00000217043,NM_178491.3;Y_RNA,upstream_gene_variant,,ENST00000364493,; T ENST00000217043 Transcript missense_variant 440/1377 268/762 90/253 D/Y Gac/Tac 1 1 R3HDML HGNC HGNC:16249 protein_coding YES CCDS13329.1 ENSP00000217043 Q9H3Y0 UPI00000422F8 NM_178491.3 deleterious(0) 2/5 Gene3D:3.40.33.10,Pfam_domain:PF00188,Prints_domain:PR00837,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF62,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS rs1344132303 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 44341202 44341202 G T 1 0 0 0 0 1 0 0 0 13047 1174 41 2 2 R3HDML 20 44341202 Missense_Mutation SNP G C3N-00580_T 2141856 44341202 20102965 937 19072 OCSTAMP 0 . GRCh38 20 46546121 46546121 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.253G>C p.Ala85Pro p.A85P ENST00000279028 2/3 580 443 137 563 563 0 strelka-varscan-mutect OCSTAMP,missense_variant,p.Ala85Pro,ENST00000279028,NM_080721.2; G ENST00000279028 Transcript missense_variant 267/2043 253/1701 85/566 A/P Gcc/Ccc 1 -1 OCSTAMP HGNC HGNC:16116 protein_coding YES CCDS54468.1 ENSP00000279028 Q9BR26 UPI00006C1A90 NM_080721.2 deleterious(0) 2/3 hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF3,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs1001843150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 46546121 46546121 C G 1 0 0 0 0 1 0 0 0 10901 710 25 4 4 OCSTAMP 20 46546121 Missense_Mutation SNP C C3N-00580_T 2204919 46546121 17898046 938 19073 TSHZ2 0 . GRCh38 20 53253667 53253667 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.209C>A p.Pro70Gln p.P70Q ENST00000371497 2/3 177 133 44 125 125 0 strelka-varscan-mutect TSHZ2,missense_variant,p.Pro70Gln,ENST00000371497,NM_173485.5;TSHZ2,missense_variant,p.Pro67Gln,ENST00000603338,NM_001193421.1;TSHZ2,missense_variant,p.Pro67Gln,ENST00000329613,;RP4-678D15.1,downstream_gene_variant,,ENST00000606932,;TSHZ2,upstream_gene_variant,,ENST00000605656,; A ENST00000371497 Transcript missense_variant 1096/12187 209/3105 70/1034 P/Q cCa/cAa 1 1 TSHZ2 HGNC HGNC:13010 protein_coding YES CCDS33490.1 ENSP00000360552 Q9NRE2 UPI0000206747 NM_173485.5 deleterious(0) 2/3 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF3 MODERATE 1 SNV 1 1 PASS rs1204884160 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 53253667 53253667 C A 1 0 0 0 0 1 0 0 0 17129 594 21 2 2 TSHZ2 20 53253667 Missense_Mutation SNP C C3N-00580_T 6707546 53253667 11190500 939 19074 PCK1 0 . GRCh38 20 57561531 57561531 + Silent SNP T T A novel C3N-00580_T C3N-00580_N T T c.120T>A p.= p.P40P ENST00000319441 2/10 397 294 103 388 388 0 strelka-varscan-mutect PCK1,synonymous_variant,p.=,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,non_coding_transcript_exon_variant,,ENST00000475833,;PCK1,upstream_gene_variant,,ENST00000498194,;PCK1,upstream_gene_variant,,ENST00000485958,;PCK1,upstream_gene_variant,,ENST00000470051,; A ENST00000319441 Transcript synonymous_variant 284/4341 120/1869 40/622 P ccT/ccA 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 2/10 HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,Gene3D:3.40.449.10,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF68923 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 57561531 57561531 T A 1 0 0 0 0 0 0 0 1 11669 1567 55 4 4 PCK1 20 57561531 Silent SNP T C3N-00580_T 4307864 57561531 6882636 940 19075 ZBP1 0 . GRCh38 20 57614951 57614951 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.438G>C p.Arg146Ser p.R146S ENST00000371173 4/8 318 209 109 356 356 0 strelka-varscan-mutect ZBP1,missense_variant,p.Arg146Ser,ENST00000371173,NM_001160417.1,NM_030776.2;ZBP1,missense_variant,p.Arg71Ser,ENST00000395822,NM_001160418.1;ZBP1,missense_variant,p.Arg146Ser,ENST00000541799,NM_001160419.2;ZBP1,upstream_gene_variant,,ENST00000453793,;ZBP1,non_coding_transcript_exon_variant,,ENST00000546110,;ZBP1,downstream_gene_variant,,ENST00000538947,;ZBP1,downstream_gene_variant,,ENST00000432548,;ZBP1,non_coding_transcript_exon_variant,,ENST00000461547,;ZBP1,non_coding_transcript_exon_variant,,ENST00000480037,; G ENST00000371173 Transcript missense_variant 616/2195 438/1290 146/429 R/S agG/agC 1 -1 ZBP1 HGNC HGNC:16176 protein_coding YES CCDS13461.1 ENSP00000360215 Q9H171 UPI000013CB5B NM_001160417.1,NM_030776.2 tolerated(0.64) 4/8 Gene3D:1.10.10.10,hmmpanther:PTHR14966,SMART_domains:SM00550,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 57614951 57614951 C G 1 0 0 0 0 1 0 0 0 18087 854 30 4 4 ZBP1 20 57614951 Missense_Mutation SNP C C3N-00580_T 53420 57614951 6829216 941 19076 ZNF831 0 . GRCh38 20 59192751 59192751 + Missense_Mutation SNP G G A rs773637126 C3N-00580_T C3N-00580_N G G c.1732G>A p.Ala578Thr p.A578T ENST00000637017 4/8 110 90 20 129 129 0 strelka-varscan-mutect ZNF831,missense_variant,p.Ala578Thr,ENST00000637017,;ZNF831,missense_variant,p.Ala578Thr,ENST00000371030,NM_178457.2; A ENST00000637017 Transcript missense_variant 3281/10953 1732/5034 578/1677 A/T Gcc/Acc rs773637126 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 tolerated(0.77) 4/8 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF52 MODERATE 1 SNV 1 PASS rs773637126 . 0 204 3 3 0 0 0 0 -20 0.9999439 1 1 1 0 A 3 1 61 59192751 59192751 G A 1 0 0 0 0 1 0 0 0 18770 1319 46 3 3 ZNF831 20 59192751 Missense_Mutation SNP G C3N-00580_T 1577800 59192751 5251416 942 19077 EDN3 0 . GRCh38 20 59301449 59301449 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.92G>T p.Arg31Leu p.R31L ENST00000337938 2/5 432 346 86 317 317 0 strelka-varscan-mutect EDN3,missense_variant,p.Arg31Leu,ENST00000311585,NM_207032.2;EDN3,missense_variant,p.Arg31Leu,ENST00000337938,NM_001302455.1,NM_207034.2;EDN3,missense_variant,p.Arg31Leu,ENST00000371028,;EDN3,missense_variant,p.Arg31Leu,ENST00000395654,NM_207033.2;EDN3,missense_variant,p.Arg31Leu,ENST00000371025,NM_001302456.1; T ENST00000337938 Transcript missense_variant 478/2636 92/717 31/238 R/L cGc/cTc 1 1 EDN3 HGNC HGNC:3178 protein_coding YES CCDS13477.1 ENSP00000337128 P14138 UPI000012A221 NM_001302455.1,NM_207034.2 tolerated(0.12) 2/5 hmmpanther:PTHR13874,hmmpanther:PTHR13874:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 59301449 59301449 G T 1 0 0 0 0 1 0 0 0 4746 1087 38 1 1 EDN3 20 59301449 Missense_Mutation SNP G C3N-00580_T 108698 59301449 5142718 943 19078 SYCP2 0 . GRCh38 20 59893192 59893192 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.1743C>T p.= p.L581L ENST00000357552 22/45 99 81 18 197 197 0 strelka-varscan-mutect SYCP2,synonymous_variant,p.=,ENST00000357552,;SYCP2,synonymous_variant,p.=,ENST00000371001,NM_014258.2;SYCP2,synonymous_variant,p.=,ENST00000446834,; A ENST00000357552 Transcript synonymous_variant 1969/5567 1743/4593 581/1530 L ctC/ctT 1 -1 SYCP2 HGNC HGNC:11490 protein_coding YES CCDS13482.1 ENSP00000350162 Q9BX26 UPI0000135683 22/45 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 59893192 59893192 G A 1 0 0 0 0 0 0 0 1 15822 1161 41 3 3 SYCP2 20 59893192 Silent SNP G C3N-00580_T 591743 59893192 4550975 944 19079 CDH4 0 . GRCh38 20 61844805 61844805 + Silent SNP G G A novel C3N-00580_T C3N-00580_N G G c.714G>A p.= p.E238E ENST00000614565 5/16 101 84 17 126 126 0 strelka-varscan-mutect CDH4,synonymous_variant,p.=,ENST00000614565,NM_001794.4;CDH4,synonymous_variant,p.=,ENST00000611855,;CDH4,synonymous_variant,p.=,ENST00000543233,NM_001252338.2,NM_001252339.2; A ENST00000614565 Transcript synonymous_variant 802/6513 714/2751 238/916 E gaG/gaA 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 5/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 61844805 61844805 G A 1 0 0 0 0 0 0 0 1 2815 991 35 3 3 CDH4 20 61844805 Silent SNP G C3N-00580_T 1951613 61844805 2599362 945 19080 HRH3 0 . GRCh38 20 62216855 62216855 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.489C>G p.= p.A163A ENST00000340177 3/3 164 113 51 172 172 0 strelka-varscan-mutect HRH3,synonymous_variant,p.=,ENST00000340177,NM_007232.2;HRH3,synonymous_variant,p.=,ENST00000317393,;HRH3,synonymous_variant,p.=,ENST00000611492,; C ENST00000340177 Transcript synonymous_variant 774/2659 489/1338 163/445 A gcC/gcG 1 -1 HRH3 HGNC HGNC:5184 protein_coding YES CCDS13493.1 ENSP00000342560 Q9Y5N1 UPI000012C6ED NM_007232.2 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF292,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 61 62216855 62216855 G C 1 0 0 0 0 0 0 0 1 7252 987 35 4 4 HRH3 20 62216855 Silent SNP G C3N-00580_T 372050 62216855 2227312 946 19081 OSBPL2 0 . GRCh38 20 62272252 62272252 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.386G>T p.Arg129Met p.R129M ENST00000313733 5/14 183 137 46 213 213 0 strelka-varscan-mutect OSBPL2,missense_variant,p.Arg129Met,ENST00000313733,NM_144498.2;OSBPL2,missense_variant,p.Arg117Met,ENST00000358053,NM_014835.3;OSBPL2,missense_variant,p.Arg37Met,ENST00000439951,NM_001278649.1;OSBPL2,missense_variant,p.Arg129Met,ENST00000622332,;OSBPL2,upstream_gene_variant,,ENST00000448156,;OSBPL2,upstream_gene_variant,,ENST00000618198,; T ENST00000313733 Transcript missense_variant 627/4009 386/1443 129/480 R/M aGg/aTg 1 1 OSBPL2 HGNC HGNC:15761 protein_coding YES CCDS13495.1 ENSP00000316649 Q9H1P3 UPI0000130E96 NM_144498.2 deleterious(0) 5/14 Superfamily_domains:0051579,Pfam_domain:PF01237,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF54 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 62272252 62272252 G T 1 0 0 0 0 1 0 0 0 11344 1000 35 2 2 OSBPL2 20 62272252 Missense_Mutation SNP G C3N-00580_T 55397 62272252 2171915 947 19082 LAMA5 0 . GRCh38 20 62311309 62311309 + Splice_Site SNP T T A novel C3N-00580_T C3N-00580_N T T c.9943-2A>T p.X3315_splice ENST00000252999 52 42 10 73 73 0 strelka-varscan-mutect LAMA5,splice_acceptor_variant,,ENST00000252999,NM_005560.4;ADRM1,downstream_gene_variant,,ENST00000491935,;ADRM1,downstream_gene_variant,,ENST00000253003,NM_007002.3,NM_175573.2;ADRM1,downstream_gene_variant,,ENST00000620230,NM_001281437.1,NM_001281438.1;ADRM1,downstream_gene_variant,,ENST00000462554,;RP11-157P1.4,upstream_gene_variant,,ENST00000414042,;LAMA5,upstream_gene_variant,,ENST00000492698,;ADRM1,downstream_gene_variant,,ENST00000465805,;LAMA5,splice_acceptor_variant,,ENST00000370691,;LAMA5,splice_acceptor_variant,,ENST00000462415,;LAMA5,upstream_gene_variant,,ENST00000495695,;LAMA5,downstream_gene_variant,,ENST00000491036,;LAMA5,downstream_gene_variant,,ENST00000471042,;LAMA5,downstream_gene_variant,,ENST00000468786,; A ENST00000252999 Transcript splice_acceptor_variant -/11426 9943/11088 3315/3695 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 72/79 HIGH 1 SNV 1 1 PASS rs1298371783 . 0 198 11 0 0 0 0 0 -19.99983 0.9999748 1 1 1 0 A 5 1 61 62311309 62311309 T A 1 0 0 0 0 0 0 1 0 8513 1594 55 4 4 LAMA5 20 62311309 Splice_Site SNP T C3N-00580_T 39057 62311309 2132858 948 19083 SLCO4A1 0 . GRCh38 20 62656646 62656646 + Silent SNP C C A rs781134379 C3N-00580_T C3N-00580_N C C c.192C>A p.= p.A64A ENST00000217159 2/12 326 263 63 364 364 0 strelka-varscan-mutect SLCO4A1,synonymous_variant,p.=,ENST00000217159,NM_016354.3;SLCO4A1,synonymous_variant,p.=,ENST00000370507,;RP11-93B14.10,upstream_gene_variant,,ENST00000620143,;SLCO4A1,synonymous_variant,p.=,ENST00000497209,; A ENST00000217159 Transcript synonymous_variant 397/2776 192/2169 64/722 A gcC/gcA rs781134379 1 1 SLCO4A1 HGNC HGNC:10953 protein_coding YES CCDS13501.1 ENSP00000217159 Q96BD0 UPI00000557C6 NM_016354.3 2/12 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF100 LOW 1 SNV 1 1 PASS rs781134379 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 62656646 62656646 C A 1 0 0 0 0 0 0 0 1 15016 639 23 1 1 SLCO4A1 20 62656646 Silent SNP C C3N-00580_T 345337 62656646 1787521 949 19084 KCNQ2 0 . GRCh38 20 63406667 63406667 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2596G>T p.Gly866Cys p.G866C ENST00000359125 17/17 173 106 67 198 197 1 strelka-varscan-mutect KCNQ2,missense_variant,p.Gly848Cys,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Gly866Cys,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Gly665Cys,ENST00000637193,;KCNQ2,missense_variant,p.Gly838Cys,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Gly835Cys,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Gly722Cys,ENST00000357249,;KCNQ2,intron_variant,,ENST00000370224,;KCNQ2,intron_variant,,ENST00000625514,;KCNQ2,intron_variant,,ENST00000629241,;KCNQ2,intron_variant,,ENST00000629676,;KCNQ2,downstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000637063,;KCNQ2,downstream_gene_variant,,ENST00000637338,;KCNQ2,downstream_gene_variant,,ENST00000637656,; A ENST00000359125 Transcript missense_variant 2723/3253 2596/2619 866/872 G/C Ggc/Tgc 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 tolerated_low_confidence(0.1) 17/17 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF6,Pfam_domain:PF11956 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 63406667 63406667 C A 1 0 0 0 0 1 0 0 0 7999 623 22 2 2 KCNQ2 20 63406667 Missense_Mutation SNP C C3N-00580_T 750021 63406667 1037500 950 19085 KCNQ2 0 . GRCh38 20 63407017 63407017 + Missense_Mutation SNP T T A novel C3N-00580_T C3N-00580_N T T c.2246A>T p.Glu749Val p.E749V ENST00000359125 17/17 68 38 30 83 83 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Glu731Val,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Glu749Val,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Glu548Val,ENST00000637193,;KCNQ2,missense_variant,p.Glu721Val,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Glu718Val,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Glu605Val,ENST00000357249,;KCNQ2,intron_variant,,ENST00000370224,;KCNQ2,intron_variant,,ENST00000625514,;KCNQ2,intron_variant,,ENST00000629241,;KCNQ2,intron_variant,,ENST00000629676,;KCNQ2,downstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000637063,;KCNQ2,downstream_gene_variant,,ENST00000637338,;KCNQ2,downstream_gene_variant,,ENST00000637656,; A ENST00000359125 Transcript missense_variant 2373/3253 2246/2619 749/872 E/V gAg/gTg 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious(0.05) 17/17 Pfam_domain:PF16642 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 63407017 63407017 T A 1 0 0 0 0 1 0 0 0 7999 1551 54 4 4 KCNQ2 20 63407017 Missense_Mutation SNP T C3N-00580_T 350 63407017 1037150 951 19086 PCMTD2 0 . GRCh38 20 64260260 64260260 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.295G>T p.Gly99Cys p.G99C ENST00000308824 2/6 127 101 26 134 134 0 strelka-varscan-mutect PCMTD2,missense_variant,p.Gly99Cys,ENST00000308824,NM_018257.2;PCMTD2,missense_variant,p.Gly99Cys,ENST00000369758,NM_001104925.1;PCMTD2,missense_variant,p.Gly99Cys,ENST00000299468,;PCMTD2,missense_variant,p.Gly99Cys,ENST00000609764,;PCMTD2,missense_variant,p.Gly99Cys,ENST00000610074,;PCMTD2,intron_variant,,ENST00000609372,;PCMTD2,downstream_gene_variant,,ENST00000610196,;PCMTD2,downstream_gene_variant,,ENST00000609297,;PCMTD2,missense_variant,p.Gly60Cys,ENST00000608844,; T ENST00000308824 Transcript missense_variant 422/3843 295/1086 99/361 G/C Ggc/Tgc 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 deleterious(0.01) 2/6 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2,Superfamily_domains:SSF53335 MODERATE 1 SNV 2 1 PASS . . 0 199 9 2 0 0 0 0 -20 0.9997503 1 1 1 0 T 3 4 61 64260260 64260260 G T 1 0 0 0 0 1 0 0 0 11675 1232 43 2 2 PCMTD2 20 64260260 Missense_Mutation SNP G C3N-00580_T 853243 64260260 183907 952 19087 HSPA13 0 . GRCh38 21 14373727 14373727 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1306G>T p.Val436Leu p.V436L ENST00000285667 5/5 333 156 177 287 287 0 strelka-varscan-mutect HSPA13,missense_variant,p.Val436Leu,ENST00000285667,NM_006948.4;HSPA13,downstream_gene_variant,,ENST00000478035,; A ENST00000285667 Transcript missense_variant 1374/3986 1306/1416 436/471 V/L Gta/Tta 1 -1 HSPA13 HGNC HGNC:11375 protein_coding YES CCDS13567.1 ENSP00000285667 P48723 A0A140VK72 UPI00001360C2 NM_006948.4 deleterious(0) 5/5 hmmpanther:PTHR19375:SF169,hmmpanther:PTHR19375,Pfam_domain:PF00012,Superfamily_domains:SSF53067,Prints_domain:PR00301 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 14373727 14373727 C A 1 0 0 0 0 1 0 0 0 7302 565 20 2 2 HSPA13 21 14373727 Missense_Mutation SNP C C3N-00580_T 14373727 32336256 953 19088 SYNJ1 0 . GRCh38 21 32727975 32727975 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.66G>T p.= p.G22G ENST00000433931 1/32 257 220 37 350 350 0 strelka-varscan-mutect SYNJ1,synonymous_variant,p.=,ENST00000382499,NM_203446.2;SYNJ1,synonymous_variant,p.=,ENST00000433931,NM_003895.3;SYNJ1,5_prime_UTR_variant,,ENST00000382491,;SYNJ1,upstream_gene_variant,,ENST00000357345,NM_001160302.1;SYNJ1,upstream_gene_variant,,ENST00000630077,NM_001160306.1;SYNJ1,upstream_gene_variant,,ENST00000429236,;SYNJ1,upstream_gene_variant,,ENST00000456084,;PAXBP1-AS1,upstream_gene_variant,,ENST00000440052,;PAXBP1-AS1,upstream_gene_variant,,ENST00000458479,;PAXBP1-AS1,upstream_gene_variant,,ENST00000455170,; A ENST00000433931 Transcript synonymous_variant 74/4852 66/4839 22/1612 G ggG/ggT 1 -1 SYNJ1 HGNC HGNC:11503 protein_coding YES CCDS33539.2 ENSP00000409667 J3KQV8 UPI0001A47572 NM_003895.3 1/32 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1427487040 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 32727975 32727975 C A 1 0 0 0 0 0 0 0 1 15846 842 30 2 2 SYNJ1 21 32727975 Silent SNP C C3N-00580_T 18354248 32727975 13982008 954 19089 DOPEY2 0 . GRCh38 21 36245588 36245588 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.3608A>T p.Gln1203Leu p.Q1203L ENST00000399151 19/37 172 78 94 167 165 2 strelka-varscan-mutect DOPEY2,missense_variant,p.Gln1203Leu,ENST00000399151,NM_001320714.1,NM_005128.3;DOPEY2,upstream_gene_variant,,ENST00000463668,; T ENST00000399151 Transcript missense_variant 3693/7685 3608/6897 1203/2298 Q/L cAg/cTg 1 1 DOPEY2 HGNC HGNC:1291 protein_coding YES CCDS13643.1 ENSP00000382104 Q9Y3R5 UPI000013D876 NM_001320714.1,NM_005128.3 deleterious(0) 19/37 hmmpanther:PTHR14042,hmmpanther:PTHR14042:SF23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 36245588 36245588 A T 1 0 0 0 0 1 0 0 0 4522 188 7 4 4 DOPEY2 21 36245588 Missense_Mutation SNP A C3N-00580_T 3517613 36245588 10464395 955 19090 DOPEY2 0 . GRCh38 21 36246408 36246408 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.4428G>T p.= p.L1476L ENST00000399151 19/37 238 113 125 264 264 0 strelka-varscan-mutect DOPEY2,synonymous_variant,p.=,ENST00000399151,NM_001320714.1,NM_005128.3;DOPEY2,non_coding_transcript_exon_variant,,ENST00000463668,; T ENST00000399151 Transcript synonymous_variant 4513/7685 4428/6897 1476/2298 L ctG/ctT 1 1 DOPEY2 HGNC HGNC:1291 protein_coding YES CCDS13643.1 ENSP00000382104 Q9Y3R5 UPI000013D876 NM_001320714.1,NM_005128.3 19/37 hmmpanther:PTHR14042,hmmpanther:PTHR14042:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 36246408 36246408 G T 1 0 0 0 0 0 0 0 1 4522 1277 45 2 2 DOPEY2 21 36246408 Silent SNP G C3N-00580_T 820 36246408 10463575 956 19091 KRTAP10-2 0 . GRCh38 21 44551122 44551122 + Missense_Mutation SNP C C A rs587678058 C3N-00580_T C3N-00580_N C C c.337G>T p.Val113Phe p.V113F ENST00000391621 1/1 885 423 462 1017 1016 1 strelka-varscan-mutect KRTAP10-2,missense_variant,p.Val113Phe,ENST00000391621,NM_198693.3;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,;KRTAP10-2,intron_variant,,ENST00000498210,; A ENST00000391621 Transcript missense_variant 384/1149 337/768 113/255 V/F Gtc/Ttc rs587678058 1 -1 KRTAP10-2 HGNC HGNC:22967 protein_coding YES CCDS42955.1 ENSP00000375479 P60368 UPI000021C438 NM_198693.3 deleterious(0) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF8,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs587678058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 44551122 44551122 C A 1 0 0 0 0 1 0 0 0 8392 536 19 1 1 KRTAP10-2 21 44551122 Missense_Mutation SNP C C3N-00580_T 8304714 44551122 2158861 957 19092 COL6A1 0 . GRCh38 21 45998120 45998120 + Splice_Site DEL G G - novel C3N-00580_T C3N-00580_N G G c.1526delG p.Gly509GlufsTer28 p.X509_splice ENST00000361866 458 231 227 586 586 0 sindel-varindel-pindel COL6A1,splice_acceptor_variant,p.Gly509GlufsTer28,ENST00000361866,NM_001848.2;COL6A1,splice_acceptor_variant,p.Gly509GlufsTer28,ENST00000612273,;COL6A1,upstream_gene_variant,,ENST00000498614,;COL6A1,upstream_gene_variant,,ENST00000486023,;COL6A1,upstream_gene_variant,,ENST00000463060,;COL6A1,upstream_gene_variant,,ENST00000466285,; - ENST00000361866 Transcript splice_acceptor_variant -/4238 1526/3087 509/1028 1 1 COL6A1 HGNC HGNC:2211 protein_coding YES CCDS13727.1 ENSP00000355180 P12109 UPI000019B179 NM_001848.2 22/34 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 61 45998120 45998120 G - 1 0 1 0 1 0 0 1 0 3488 1014 35 0 0 COL6A1 21 45998120 Splice_Site DEL G C3N-00580_T 1446998 45998120 711863 958 19093 FTCD 0 . GRCh38 21 46151569 46151569 + Missense_Mutation SNP C C A rs367906516 C3N-00580_T C3N-00580_N C C c.625G>T p.Gly209Trp p.G209W ENST00000291670 5/15 232 108 124 213 213 0 strelka-varscan-mutect FTCD,missense_variant,p.Gly209Trp,ENST00000397748,NM_001320412.1;FTCD,missense_variant,p.Gly209Trp,ENST00000291670,NM_006657.2;FTCD,missense_variant,p.Gly209Trp,ENST00000397746,NM_206965.1;FTCD,missense_variant,p.Gly209Trp,ENST00000397743,;FTCD-AS1,upstream_gene_variant,,ENST00000446649,;FTCD,non_coding_transcript_exon_variant,,ENST00000498355,;FTCD,upstream_gene_variant,,ENST00000480950,;FTCD,upstream_gene_variant,,ENST00000469240,; A ENST00000291670 Transcript missense_variant 669/1905 625/1626 209/541 G/W Ggg/Tgg rs367906516 1 -1 FTCD HGNC HGNC:3974 protein_coding YES CCDS13731.1 ENSP00000291670 O95954 UPI000012AC75 NM_006657.2 deleterious(0.01) 5/15 Gene3D:1qd1A02,Pfam_domain:PF02971,hmmpanther:PTHR12234,hmmpanther:PTHR12234:SF0,SMART_domains:SM01221,Superfamily_domains:SSF55116,TIGRFAM_domain:TIGR02024 MODERATE 1 SNV 1 1 PASS rs367906516 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 46151569 46151569 C A 1 0 0 0 0 1 0 0 0 5955 652 23 1 1 FTCD 21 46151569 Missense_Mutation SNP C C3N-00580_T 153449 46151569 558414 959 19094 CCT8L2 0 . GRCh38 22 16591174 16591174 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.1377T>A p.= p.A459A ENST00000359963 1/1 392 296 96 514 514 0 strelka-varscan-mutect CCT8L2,synonymous_variant,p.=,ENST00000359963,NM_014406.4;FABP5P11,downstream_gene_variant,,ENST00000430910,; T ENST00000359963 Transcript synonymous_variant 1637/2060 1377/1674 459/557 A gcT/gcA 1 -1 CCT8L2 HGNC HGNC:15553 protein_coding YES CCDS13738.1 ENSP00000353048 Q96SF2 UPI000006CF87 NM_014406.4 1/1 Gene3D:1.10.560.10,Pfam_domain:PF00118,hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF100,Superfamily_domains:SSF48592 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 16591174 16591174 A T 1 0 0 0 0 0 0 0 1 2662 175 7 4 4 CCT8L2 22 16591174 Silent SNP A C3N-00580_T 16591174 34227294 960 19095 CECR5 0 . GRCh38 22 17145081 17145081 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.480G>T p.= p.L160L ENST00000336737 4/8 316 251 65 418 417 1 strelka-varscan-mutect CECR5,synonymous_variant,p.=,ENST00000336737,NM_033070.2;CECR5,synonymous_variant,p.=,ENST00000155674,NM_017829.5;CECR5,intron_variant,,ENST00000399852,;CECR5,downstream_gene_variant,,ENST00000480451,;CECR5,downstream_gene_variant,,ENST00000463033,;CECR5,upstream_gene_variant,,ENST00000477157,;CECR5,upstream_gene_variant,,ENST00000486462,; A ENST00000336737 Transcript synonymous_variant 506/1799 480/1272 160/423 L ctG/ctT 1 -1 CECR5 HGNC HGNC:1843 protein_coding YES CCDS33595.1 ENSP00000337358 Q9BXW7 UPI000000D9E5 NM_033070.2 4/8 hmmpanther:PTHR14269,hmmpanther:PTHR14269:SF17,TIGRFAM_domain:TIGR01456,TIGRFAM_domain:TIGR01460 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 17145081 17145081 C A 1 0 0 0 0 0 0 0 1 2914 697 25 2 2 CECR5 22 17145081 Silent SNP C C3N-00580_T 553907 17145081 33673387 961 19096 MICAL3 0 . GRCh38 22 17841910 17841910 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.2713G>T p.Ala905Ser p.A905S ENST00000441493 20/32 517 389 128 502 502 0 strelka-varscan-mutect MICAL3,missense_variant,p.Ala905Ser,ENST00000441493,NM_015241.2;MICAL3,missense_variant,p.Ala933Ser,ENST00000414725,;MICAL3,missense_variant,p.Ala905Ser,ENST00000400561,NM_001122731.2;MICAL3,missense_variant,p.Ala905Ser,ENST00000383094,;MICAL3,3_prime_UTR_variant,,ENST00000495076,;MICAL3,non_coding_transcript_exon_variant,,ENST00000578905,; A ENST00000441493 Transcript missense_variant 3066/9445 2713/6009 905/2002 A/S Gca/Tca 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 deleterious_low_confidence(0.03) 20/32 MODERATE 1 SNV 5 1 PASS rs1415915530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 17841910 17841910 C A 1 0 0 0 0 1 0 0 0 9528 739 26 2 2 MICAL3 22 17841910 Missense_Mutation SNP C C3N-00580_T 696829 17841910 32976558 962 19097 C22orf29 0 . GRCh38 22 19851850 19851850 + Missense_Mutation SNP G G T rs547046193 C3N-00580_T C3N-00580_N G G c.412C>A p.Arg138Ser p.R138S ENST00000405640 2/2 294 263 31 331 331 0 strelka-varscan-mutect C22orf29,missense_variant,p.Arg138Ser,ENST00000405640,;C22orf29,missense_variant,p.Arg138Ser,ENST00000328554,NM_024627.5;C22orf29,missense_variant,p.Arg138Ser,ENST00000407472,;GNB1L,intron_variant,,ENST00000329517,NM_053004.2;GNB1L,intron_variant,,ENST00000403325,;GNB1L,intron_variant,,ENST00000405009,;GNB1L,intron_variant,,ENST00000453108,;C22orf29,downstream_gene_variant,,ENST00000416337,;C22orf29,intron_variant,,ENST00000484072,;GNB1L,intron_variant,,ENST00000460402,;GNB1L,intron_variant,,ENST00000481086,; T ENST00000405640 Transcript missense_variant 1081/6785 412/1095 138/364 R/S Cgt/Agt rs547046193 1 -1 C22orf29 HGNC HGNC:26112 protein_coding YES CCDS13769.1 ENSP00000384924 Q7L3V2 UPI0000207B8F tolerated(0.44) 2/2 Pfam_domain:PF16297,hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF4 MODERATE 1 SNV 1 1 PASS rs547046193 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 19851850 19851850 G T 1 0 0 0 0 1 0 0 0 2019 1116 39 1 1 C22orf29 22 19851850 Missense_Mutation SNP G C3N-00580_T 2009940 19851850 30966618 963 19098 PRAME 0 . GRCh38 22 22550305 22550305 + Missense_Mutation SNP C C T rs201783997 C3N-00580_T C3N-00580_N C C c.374G>A p.Arg125Gln p.R125Q ENST00000543184 4/5 120 72 48 157 156 1 strelka-varscan-mutect PRAME,missense_variant,p.Arg125Gln,ENST00000543184,NM_206953.2;PRAME,missense_variant,p.Arg125Gln,ENST00000398741,NM_206955.2;PRAME,missense_variant,p.Arg125Gln,ENST00000398743,NM_206954.2,NM_001291715.1,NM_006115.4;PRAME,missense_variant,p.Arg125Gln,ENST00000405655,NM_206956.2,NM_001291716.1;PRAME,missense_variant,p.Arg125Gln,ENST00000402697,;PRAME,missense_variant,p.Arg125Gln,ENST00000439106,;PRAME,missense_variant,p.Arg125Gln,ENST00000420709,;PRAME,missense_variant,p.Arg149Gln,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,non_coding_transcript_exon_variant,,ENST00000485532,;PRAME,non_coding_transcript_exon_variant,,ENST00000476336,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,; T ENST00000543184 Transcript missense_variant 1237/2758 374/1530 125/509 R/Q cGg/cAg rs201783997,COSM3390126,COSM3713625 1 -1 PRAME HGNC HGNC:9336 protein_coding YES CCDS13801.1 ENSP00000445675 P78395 A0A024R1E6 UPI0000000DDA NM_206953.2 tolerated(0.07) 4/5 hmmpanther:PTHR14224:SF4,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs201783997 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 22550305 22550305 C T 1 0 0 0 0 1 0 0 0 12553 652 23 1 1 PRAME 22 22550305 Missense_Mutation SNP C C3N-00580_T 2698455 22550305 28268163 964 19099 SUSD2 0 . GRCh38 22 24186346 24186346 + Nonsense_Mutation SNP G G T rs140483621 C3N-00580_T C3N-00580_N G G c.1573G>T p.Gly525Ter p.G525* ENST00000358321 10/15 230 193 37 334 334 0 strelka-varscan-mutect SUSD2,stop_gained,p.Gly525Ter,ENST00000358321,NM_019601.3;SUSD2,non_coding_transcript_exon_variant,,ENST00000463101,; T ENST00000358321 Transcript stop_gained 1834/3404 1573/2469 525/822 G/* Gga/Tga rs140483621 1 1 SUSD2 HGNC HGNC:30667 protein_coding YES CCDS13824.1 ENSP00000351075 Q9UGT4 A0A140VJW3 UPI000006CC92 NM_019601.3 10/15 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF43,SMART_domains:SM00216 HIGH 1 SNV 1 1 PASS rs140483621 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 61 24186346 24186346 G T 1 0 0 0 0 0 1 0 0 15793 1117 39 1 1 SUSD2 22 24186346 Nonsense_Mutation SNP G C3N-00580_T 1636041 24186346 26632122 965 19100 GUCD1 0 . GRCh38 22 24543098 24543098 + Nonsense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.799G>T p.Gly267Ter p.G267* ENST00000621833 6/6 207 176 31 248 248 0 strelka-varscan-mutect GUCD1,splice_acceptor_variant,,ENST00000435822,NM_001284255.1,NM_001284254.1;GUCD1,splice_acceptor_variant,,ENST00000404664,NM_001284252.1,NM_001284253.1;GUCD1,splice_acceptor_variant,,ENST00000447813,NM_001284257.1;GUCD1,stop_gained,p.Gly267Ter,ENST00000621833,NM_001284251.1;GUCD1,stop_gained,p.Gly211Ter,ENST00000407471,NM_031444.3;GUCD1,missense_variant,p.Arg130Met,ENST00000402766,NM_001284256.1;GUCD1,downstream_gene_variant,,ENST00000407973,;GUCD1,splice_acceptor_variant,,ENST00000493099,;GUCD1,intron_variant,,ENST00000490922,;GUCD1,downstream_gene_variant,,ENST00000490810,;GUCD1,splice_acceptor_variant,,ENST00000398245,;GUCD1,downstream_gene_variant,,ENST00000468170,;GUCD1,downstream_gene_variant,,ENST00000480272,; A ENST00000621833 Transcript stop_gained,splice_region_variant 909/3584 799/891 267/296 G/* Gga/Tga 1 -1 GUCD1 HGNC HGNC:14237 protein_coding YES CCDS74833.1 ENSP00000479370 A0A087WVD9 UPI00002327A0 NM_001284251.1 6/6 Pfam_domain:PF09778,hmmpanther:PTHR31400 HIGH 1 SNV 1 1 PASS rs1317907434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 61 24543098 24543098 C A 1 0 0 0 0 0 1 0 0 6774 695 24 2 2 GUCD1 22 24543098 Nonsense_Mutation SNP C C3N-00580_T 356752 24543098 26275370 966 19101 KIAA1671 0 . GRCh38 22 25039724 25039724 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.2594A>T p.Glu865Val p.E865V ENST00000358431 3/11 19 16 3 28 28 0 strelka-mutect KIAA1671,missense_variant,p.Glu865Val,ENST00000358431,NM_001145206.1;KIAA1671,missense_variant,p.Glu865Val,ENST00000406486,;KIAA1671,upstream_gene_variant,,ENST00000494730,;KIAA1671,upstream_gene_variant,,ENST00000461374,; T ENST00000358431 Transcript missense_variant 2620/10490 2594/5421 865/1806 E/V gAg/gTg 1 1 KIAA1671 HGNC HGNC:29345 protein_coding YES CCDS46676.1 ENSP00000351207 Q9BY89 UPI00002073DC NM_001145206.1 tolerated(0.12) 3/11 hmmpanther:PTHR22042,hmmpanther:PTHR22042:SF3 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.04043 1 1 1 1 0 T 3 4 61 25039724 25039724 A T 1 0 0 0 0 1 0 0 0 8125 304 11 4 4 KIAA1671 22 25039724 Missense_Mutation SNP A C3N-00580_T 496626 25039724 25778744 967 19102 SLC5A4 0 . GRCh38 22 32229246 32229246 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.1228T>A p.Tyr410Asn p.Y410N ENST00000266086 11/15 143 95 48 180 180 0 strelka-varscan-mutect SLC5A4,missense_variant,p.Tyr410Asn,ENST00000266086,NM_014227.2;RP1-90G24.10,intron_variant,,ENST00000434942,; T ENST00000266086 Transcript missense_variant 1240/2030 1228/1980 410/659 Y/N Tac/Aac 1 -1 SLC5A4 HGNC HGNC:11039 protein_coding YES CCDS13903.1 ENSP00000266086 Q9NY91 UPI00001359F4 NM_014227.2 deleterious(0) 11/15 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF112,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 32229246 32229246 A T 1 0 0 0 0 1 0 0 0 14950 420 15 4 4 SLC5A4 22 32229246 Missense_Mutation SNP A C3N-00580_T 7189522 32229246 18589222 968 19103 TEX33 0 . GRCh38 22 36999967 36999967 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.507T>A p.Asp169Glu p.D169E ENST00000405091 5/7 80 68 12 115 115 0 strelka-varscan-mutect TEX33,missense_variant,p.Asp169Glu,ENST00000405091,;TEX33,missense_variant,p.Asp84Glu,ENST00000402860,NM_178552.3;TEX33,missense_variant,p.Asp169Glu,ENST00000381821,NM_001163857.1;TEX33,missense_variant,p.Asp28Glu,ENST00000442538,; T ENST00000405091 Transcript missense_variant 759/1149 507/843 169/280 D/E gaT/gaA 1 -1 TEX33 HGNC HGNC:28568 protein_coding YES CCDS54524.1 ENSP00000386118 O43247 UPI000020767B tolerated(0.3) 5/7 Pfam_domain:PF15400,hmmpanther:PTHR31702 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 36999967 36999967 A T 1 0 0 0 0 1 0 0 0 16210 214 8 4 4 TEX33 22 36999967 Missense_Mutation SNP A C3N-00580_T 4770721 36999967 13818501 969 19104 ELFN2 0 . GRCh38 22 37373131 37373131 + Missense_Mutation SNP C C G C3N-00580_T C3N-00580_N C C c.2404G>C p.Glu802Gln p.E802Q ENST00000402918 3/3 95 61 34 145 145 0 strelka-varscan-mutect ELFN2,missense_variant,p.Glu802Gln,ENST00000402918,NM_052906.4;ELFN2,missense_variant,p.Glu802Gln,ENST00000613079,;ELFN2,intron_variant,,ENST00000430883,;ELFN2,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000451509,;ELFN2,downstream_gene_variant,,ENST00000424973,; G ENST00000402918 Transcript missense_variant 3190/8361 2404/2463 802/820 E/Q Gag/Cag COSM478940 1 -1 ELFN2 HGNC HGNC:29396 protein_coding YES CCDS33642.1 ENSP00000385277 Q5R3F8 UPI000004E87D NM_052906.4 deleterious(0) 3/3 hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367 1 MODERATE SNV 4 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 37373131 37373131 C G 1 0 0 0 0 1 0 0 0 4892 893 31 4 4 ELFN2 22 37373131 Missense_Mutation SNP C C3N-00580_T 373164 37373131 13445337 970 19105 ACO2 0 . GRCh38 22 41508030 41508030 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.413A>T p.Lys138Ile p.K138I ENST00000216254 3/18 112 92 20 185 185 0 strelka-varscan-mutect ACO2,missense_variant,p.Lys138Ile,ENST00000396512,;ACO2,missense_variant,p.Lys138Ile,ENST00000216254,NM_001098.2;ACO2,non_coding_transcript_exon_variant,,ENST00000471094,;ACO2,non_coding_transcript_exon_variant,,ENST00000478010,;ACO2,non_coding_transcript_exon_variant,,ENST00000482208,; T ENST00000216254 Transcript missense_variant 435/2741 413/2343 138/780 K/I aAa/aTa 1 1 ACO2 HGNC HGNC:118 protein_coding YES CCDS14017.1 ENSP00000216254 Q99798 UPI000003CA3B NM_001098.2 deleterious_low_confidence(0.04) 3/18 hmmpanther:PTHR11670,hmmpanther:PTHR11670:SF30,Pfam_domain:PF00330,TIGRFAM_domain:TIGR01340,Gene3D:3.30.499.10,Superfamily_domains:SSF53732 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 41508030 41508030 A T 1 0 0 0 0 1 0 0 0 188 14 1 4 4 ACO2 22 41508030 Missense_Mutation SNP A C3N-00580_T 4134899 41508030 9310438 971 19106 MEI1 0 . GRCh38 22 41784777 41784777 + Silent SNP G G C novel C3N-00580_T C3N-00580_N G G c.3339G>C p.= p.L1113L ENST00000401548 26/31 62 40 22 92 92 0 strelka-varscan-mutect MEI1,synonymous_variant,p.=,ENST00000401548,NM_152513.3;MEI1,synonymous_variant,p.=,ENST00000403492,;MEI1,non_coding_transcript_exon_variant,,ENST00000476893,;MEI1,intron_variant,,ENST00000487535,;MEI1,intron_variant,,ENST00000484966,;MEI1,downstream_gene_variant,,ENST00000462246,;MEI1,downstream_gene_variant,,ENST00000498456,;MEI1,downstream_gene_variant,,ENST00000462450,;MEI1,downstream_gene_variant,,ENST00000473736,; C ENST00000401548 Transcript synonymous_variant 3379/4020 3339/3825 1113/1274 L ctG/ctC 1 1 MEI1 HGNC HGNC:28613 protein_coding YES CCDS46718.1 ENSP00000384115 Q5TIA1 UPI00006E232C NM_152513.3 26/31 hmmpanther:PTHR12044,hmmpanther:PTHR12044:SF10 LOW 1 SNV 2 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 C 2 2 61 41784777 41784777 G C 1 0 0 0 0 0 0 0 1 9405 1335 47 4 4 MEI1 22 41784777 Silent SNP G C3N-00580_T 276747 41784777 9033691 972 19107 MPPED1 0 . GRCh38 22 43498255 43498255 + Frame_Shift_Del DEL G G - novel C3N-00580_T C3N-00580_N G G c.656delG p.Gly219AlafsTer21 p.G219Afs*21 ENST00000417669 5/7 100 86 14 170 170 0 sindel-varindel-pindel MPPED1,frameshift_variant,p.Gly219AlafsTer21,ENST00000417669,;MPPED1,frameshift_variant,p.Gly219AlafsTer21,ENST00000443721,NM_001044370.1; - ENST00000417669 Transcript frameshift_variant 1097/3657 653/981 218/326 W/X tGg/tg 1 1 MPPED1 HGNC HGNC:1306 protein_coding YES CCDS46723.1 ENSP00000388137 O15442 UPI000006DF41 5/7 Pfam_domain:PF00149,PIRSF_domain:PIRSF035808,hmmpanther:PTHR12905,hmmpanther:PTHR12905:SF12,Superfamily_domains:SSF56300 HIGH 1 deletion 5 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 61 43498255 43498255 G - 1 0 1 0 1 0 0 0 0 9707 1357 47 0 0 MPPED1 22 43498255 Frame_Shift_Del DEL G C3N-00580_T 1713478 43498255 7320213 973 19108 ARSF 0 . GRCh38 X 3112462 3112462 + Missense_Mutation SNP C C A rs772851609 C3N-00580_T C3N-00580_N C C c.1679C>A p.Thr560Lys p.T560K ENST00000381127 11/11 157 76 81 173 173 0 strelka-varscan-mutect ARSF,missense_variant,p.Thr560Lys,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,missense_variant,p.Thr560Lys,ENST00000359361,NM_004042.4;RP13-824C8.2,downstream_gene_variant,,ENST00000443851,; A ENST00000381127 Transcript missense_variant 1900/2164 1679/1773 560/590 T/K aCg/aAg rs772851609 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 deleterious(0) 11/11 hmmpanther:PTHR10342:SF220,hmmpanther:PTHR10342,Pfam_domain:PF14707,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS rs772851609 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 3112462 3112462 C A 1 0 0 0 0 1 0 0 0 1134 536 19 1 1 ARSF 23 3112462 Missense_Mutation SNP C C3N-00580_T 3112462 152928433 974 19109 MXRA5 0 . GRCh38 X 3317272 3317272 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.6409C>A p.Leu2137Met p.L2137M ENST00000217939 6/7 56 18 38 56 56 0 strelka-varscan-mutect MXRA5,missense_variant,p.Leu2137Met,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 6564/9793 6409/8487 2137/2828 L/M Ctg/Atg 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 6/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 3317272 3317272 G T 1 0 0 0 0 1 0 0 0 10002 962 34 2 2 MXRA5 23 3317272 Missense_Mutation SNP G C3N-00580_T 204810 3317272 152723623 975 19110 MXRA5 0 . GRCh38 X 3317878 3317878 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.5803G>T p.Gly1935Cys p.G1935C ENST00000217939 6/7 131 64 67 144 144 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gly1935Cys,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript missense_variant 5958/9793 5803/8487 1935/2828 G/C Ggc/Tgc COSM4704232,COSM4704233 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 6/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1470253715 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 3317878 3317878 C A 1 0 0 0 0 1 0 0 0 10002 652 23 1 1 MXRA5 23 3317878 Missense_Mutation SNP C C3N-00580_T 606 3317878 152723017 976 19111 MXRA5 0 . GRCh38 X 3321249 3321249 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.4436A>G p.Gln1479Arg p.Q1479R ENST00000217939 5/7 153 57 96 119 119 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gln1479Arg,ENST00000217939,NM_015419.3; C ENST00000217939 Transcript missense_variant 4591/9793 4436/8487 1479/2828 Q/R cAg/cGg 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.25) 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 3321249 3321249 T C 1 0 0 0 0 1 0 0 0 10002 1580 55 5 5 MXRA5 23 3321249 Missense_Mutation SNP T C3N-00580_T 3371 3321249 152719646 977 19112 MXRA5 0 . GRCh38 X 3324937 3324937 + Missense_Mutation SNP C C G rs762522596 C3N-00580_T C3N-00580_N C C c.748G>C p.Gly250Arg p.G250R ENST00000217939 5/7 32 17 15 23 23 0 strelka-varscan-mutect MXRA5,missense_variant,p.Gly250Arg,ENST00000217939,NM_015419.3; G ENST00000217939 Transcript missense_variant 903/9793 748/8487 250/2828 G/R Ggt/Cgt rs762522596,COSM312998,COSM312999 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,SMART_domains:SM00082 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs762522596 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 3324937 3324937 C G 1 0 0 0 0 1 0 0 0 10002 652 23 4 4 MXRA5 23 3324937 Missense_Mutation SNP C C3N-00580_T 3688 3324937 152715958 978 19113 DDX53 0 . GRCh38 X 23001458 23001458 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1401C>A p.Asn467Lys p.N467K ENST00000327968 1/1 67 20 47 75 75 0 strelka-varscan-mutect DDX53,missense_variant,p.Asn467Lys,ENST00000327968,NM_182699.3;PTCHD1-AS,intron_variant,,ENST00000455399,;PTCHD1-AS,intron_variant,,ENST00000608254,; A ENST00000327968 Transcript missense_variant 1498/3629 1401/1896 467/631 N/K aaC/aaA 1 1 DDX53 HGNC HGNC:20083 protein_coding YES CCDS35214.1 ENSP00000368667 Q86TM3 UPI0000199904 NM_182699.3 tolerated(1) 1/1 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF310,Superfamily_domains:SSF52540 MODERATE SNV 1 PASS rs1036606790 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 23001458 23001458 C A 1 0 0 0 0 1 0 0 0 4174 535 19 1 1 DDX53 23 23001458 Missense_Mutation SNP C C3N-00580_T 19676521 23001458 133039437 979 19114 ZFX 0 . GRCh38 X 24210515 24210515 + Silent SNP C C T novel C3N-00580_T C3N-00580_N C C c.1557C>T p.= p.H519H ENST00000379177 11/11 363 249 114 345 345 0 strelka-varscan-mutect ZFX,synonymous_variant,p.=,ENST00000379177,NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3;ZFX,synonymous_variant,p.=,ENST00000379188,;ZFX,synonymous_variant,p.=,ENST00000539115,NM_001178086.1;ZFX,synonymous_variant,p.=,ENST00000304543,;ZFX,synonymous_variant,p.=,ENST00000338565,;ZFX,downstream_gene_variant,,ENST00000459724,; T ENST00000379177 Transcript synonymous_variant 1984/7558 1557/2418 519/805 H caC/caT 1 1 ZFX HGNC HGNC:12869 protein_coding YES CCDS14211.1 ENSP00000368475 P17010 A0A024RC04 UPI000013C504 NM_001178095.1,NM_001178084.1,NM_001178085.1,NM_003410.3 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF222,hmmpanther:PTHR24387,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 24210515 24210515 C T 1 0 0 0 0 0 0 0 1 18239 477 17 3 3 ZFX 23 24210515 Silent SNP C C3N-00580_T 1209057 24210515 131830380 980 19115 PPP4R3CP 0 . GRCh38 X 27461079 27461079 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2218C>A p.Pro740Thr p.P740T ENST00000412172 1/1 216 82 134 276 276 0 strelka-varscan-mutect PPP4R3CP,missense_variant,p.Pro740Thr,ENST00000412172,; T ENST00000412172 Transcript missense_variant 2263/3131 2218/2499 740/832 P/T Cca/Aca 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 27461079 27461079 G T 1 0 0 0 0 1 0 0 0 12529 1203 42 2 2 PPP4R3CP 23 27461079 Missense_Mutation SNP G C3N-00580_T 3250564 27461079 128579816 981 19116 FAM47C 0 . GRCh38 X 37010869 37010869 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.2459G>T p.Gly820Val p.G820V ENST00000358047 1/1 238 160 78 224 224 0 strelka-varscan-mutect FAM47C,missense_variant,p.Gly820Val,ENST00000358047,NM_001013736.2; T ENST00000358047 Transcript missense_variant 2473/3270 2459/3108 820/1035 G/V gGa/gTa COSM5252580,COSM5252581 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 tolerated(0.28) 1/1 Pfam_domain:PF14642 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 37010869 37010869 G T 1 0 0 0 0 1 0 0 0 5449 1174 41 2 2 FAM47C 23 37010869 Missense_Mutation SNP G C3N-00580_T 9549790 37010869 119030026 982 19117 AKAP4 0 . GRCh38 X 50193913 50193913 + Missense_Mutation SNP G G T rs200204337 C3N-00580_T C3N-00580_N G G c.800C>A p.Ala267Glu p.A267E ENST00000358526 5/6 96 53 43 109 109 0 strelka-varscan-mutect AKAP4,missense_variant,p.Ala267Glu,ENST00000358526,NM_003886.2;AKAP4,missense_variant,p.Ala258Glu,ENST00000376064,NM_139289.1;AKAP4,intron_variant,,ENST00000448865,;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,; T ENST00000358526 Transcript missense_variant 924/2881 800/2565 267/854 A/E gCg/gAg rs200204337,COSM1161828 1 -1 AKAP4 HGNC HGNC:374 protein_coding YES CCDS14329.1 ENSP00000351327 Q5JQC9 UPI000013DA96 NM_003886.2 tolerated(0.75) 5/6 hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200204337 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 50193913 50193913 G T 1 0 0 0 0 1 0 0 0 537 1087 38 1 1 AKAP4 23 50193913 Missense_Mutation SNP G C3N-00580_T 13183044 50193913 105846982 983 19118 DGKK 0 . GRCh38 X 50403073 50403073 + Missense_Mutation SNP C C A novel C3N-00580_T C3N-00580_N C C c.1296G>T p.Trp432Cys p.W432C ENST00000611977 7/28 88 59 29 84 84 0 strelka-varscan-mutect DGKK,missense_variant,p.Trp432Cys,ENST00000611977,NM_001013742.3; A ENST00000611977 Transcript missense_variant 1356/7407 1296/3816 432/1271 W/C tgG/tgT 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 deleterious(0) 7/28 PROSITE_profiles:PS50081,hmmpanther:PTHR11255:SF33,hmmpanther:PTHR11255,Pfam_domain:PF00130,Gene3D:3.30.60.20,SMART_domains:SM00109,Superfamily_domains:SSF57889 MODERATE 1 SNV 1 1 PASS . . 0 204 3 2 0 0 0 0 -20 0.9999986 1 1 1 0 A 3 1 61 50403073 50403073 C A 1 0 0 0 0 1 0 0 0 4278 508 18 2 2 DGKK 23 50403073 Missense_Mutation SNP C C3N-00580_T 209160 50403073 105637822 984 19119 OGT 0 . GRCh38 X 71563228 71563228 + Silent SNP A A T novel C3N-00580_T C3N-00580_N A A c.2247A>T p.= p.P749P ENST00000373719 17/22 101 34 67 93 93 0 strelka-varscan-mutect OGT,synonymous_variant,p.=,ENST00000373719,NM_181672.2;OGT,synonymous_variant,p.=,ENST00000373701,NM_181673.2;OGT,non_coding_transcript_exon_variant,,ENST00000488174,;OGT,upstream_gene_variant,,ENST00000474633,; T ENST00000373719 Transcript synonymous_variant 2464/5461 2247/3141 749/1046 P ccA/ccT 1 1 OGT HGNC HGNC:8127 protein_coding YES CCDS14414.1 ENSP00000362824 O15294 UPI0000073C9F NM_181672.2 17/22 Pfam_domain:PF13844 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 71563228 71563228 A T 1 0 0 0 0 0 0 0 1 10922 175 7 4 4 OGT 23 71563228 Silent SNP A C3N-00580_T 21160155 71563228 84477667 985 19120 TBX22 0 . GRCh38 X 80023170 80023170 + Missense_Mutation SNP C C G novel C3N-00580_T C3N-00580_N C C c.286C>G p.Leu96Val p.L96V ENST00000373296 3/9 191 104 87 202 202 0 strelka-varscan-mutect TBX22,missense_variant,p.Leu96Val,ENST00000373296,NM_001109878.1,NM_001109879.1;TBX22,missense_variant,p.Leu96Val,ENST00000373294,NM_016954.2,NM_001303475.1;TBX22,non_coding_transcript_exon_variant,,ENST00000626877,;TBX22,missense_variant,p.Leu96Val,ENST00000626498,;TBX22,downstream_gene_variant,,ENST00000476373,; G ENST00000373296 Transcript missense_variant 420/2355 286/1563 96/520 L/V Ctt/Gtt 1 1 TBX22 HGNC HGNC:11600 protein_coding YES CCDS14445.1 ENSP00000362393 Q9Y458 UPI00001377ED NM_001109878.1,NM_001109879.1 deleterious(0.01) 3/9 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF116,Gene3D:1h6fA00,Pfam_domain:PF00907,SMART_domains:SM00425,Superfamily_domains:SSF49417 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 61 80023170 80023170 C G 1 0 0 0 0 1 0 0 0 16063 797 28 4 4 TBX22 23 80023170 Missense_Mutation SNP C C3N-00580_T 8459942 80023170 76017725 986 19121 PCDH19 0 . GRCh38 X 100406782 100406782 + Missense_Mutation SNP C C T C3N-00580_T C3N-00580_N C C c.1816G>A p.Asp606Asn p.D606N ENST00000373034 1/6 453 429 24 386 385 1 strelka-varscan-mutect PCDH19,missense_variant,p.Asp606Asn,ENST00000373034,NM_001184880.1;PCDH19,missense_variant,p.Asp606Asn,ENST00000255531,NM_001105243.1;PCDH19,missense_variant,p.Asp606Asn,ENST00000420881,NM_020766.2;PCDH19,upstream_gene_variant,,ENST00000636150,; T ENST00000373034 Transcript missense_variant 3492/9756 1816/3447 606/1148 D/N Gac/Aac COSM222440,COSM222441 1 -1 PCDH19 HGNC HGNC:14270 protein_coding YES CCDS55462.1 ENSP00000362125 Q8TAB3 UPI00001D7BCD NM_001184880.1 deleterious(0.02) 1/6 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF40,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 100406782 100406782 C T 1 0 0 0 0 1 0 0 0 11601 884 31 1 1 PCDH19 23 100406782 Missense_Mutation SNP C C3N-00580_T 20383612 100406782 55634113 987 19122 SRPX2 0 . GRCh38 X 100646360 100646360 + Missense_Mutation SNP T T C novel C3N-00580_T C3N-00580_N T T c.38T>C p.Leu13Pro p.L13P ENST00000373004 2/11 323 211 112 274 274 0 strelka-varscan-mutect SRPX2,missense_variant,p.Leu13Pro,ENST00000373004,NM_014467.2;SRPX2,non_coding_transcript_exon_variant,,ENST00000481988,; C ENST00000373004 Transcript missense_variant 466/2138 38/1398 13/465 L/P cTg/cCg 1 1 SRPX2 HGNC HGNC:30668 protein_coding YES CCDS14471.1 ENSP00000362095 O60687 UPI000006CCC6 NM_014467.2 deleterious(0) 2/11 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 61 100646360 100646360 T C 1 0 0 0 0 1 0 0 0 15526 1580 55 5 5 SRPX2 23 100646360 Missense_Mutation SNP T C3N-00580_T 239578 100646360 55394535 988 19123 MORF4L2 0 . GRCh38 X 103676716 103676716 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.312G>T p.= p.R104R ENST00000422154 4/4 79 52 27 79 79 0 strelka-varscan-mutect MORF4L2,synonymous_variant,p.=,ENST00000422154,NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1;MORF4L2,synonymous_variant,p.=,ENST00000433176,NM_001142421.1,NM_001142428.1,NM_001142419.1,NM_001142431.1,NM_001142422.1,NM_001142420.1,NM_001142427.1,NM_001142432.1;MORF4L2,synonymous_variant,p.=,ENST00000451301,NM_001142430.1,NM_001142426.1;MORF4L2,synonymous_variant,p.=,ENST00000441076,;MORF4L2,synonymous_variant,p.=,ENST00000360458,;MORF4L2,synonymous_variant,p.=,ENST00000434230,;MORF4L2,synonymous_variant,p.=,ENST00000442614,;MORF4L2,synonymous_variant,p.=,ENST00000418819,;MORF4L2,synonymous_variant,p.=,ENST00000423833,;MORF4L2,downstream_gene_variant,,ENST00000422355,;MORF4L2,non_coding_transcript_exon_variant,,ENST00000492116,;MORF4L2,downstream_gene_variant,,ENST00000474653,;MORF4L2,downstream_gene_variant,,ENST00000498064,;MORF4L2,downstream_gene_variant,,ENST00000467755,; A ENST00000422154 Transcript synonymous_variant 767/1983 312/867 104/288 R cgG/cgT 1 -1 MORF4L2 HGNC HGNC:16849 protein_coding YES CCDS14512.1 ENSP00000394417 Q15014 UPI000012F567 NM_001142418.1,NM_012286.2,NM_001142423.1,NM_001142424.1,NM_001142429.1,NM_001142425.1 4/4 Gene3D:1wgsA00,hmmpanther:PTHR10880,hmmpanther:PTHR10880:SF25 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 103676716 103676716 C A 1 0 0 0 0 0 0 0 1 9670 610 22 2 2 MORF4L2 23 103676716 Silent SNP C C3N-00580_T 3030356 103676716 52364179 989 19124 ESX1 0 . GRCh38 X 104254471 104254471 + Silent SNP C C A novel C3N-00580_T C3N-00580_N C C c.189G>T p.= p.T63T ENST00000372588 2/4 249 117 132 283 283 0 strelka-varscan-mutect ESX1,synonymous_variant,p.=,ENST00000372588,NM_153448.3; A ENST00000372588 Transcript synonymous_variant 273/1495 189/1221 63/406 T acG/acT 1 -1 ESX1 HGNC HGNC:14865 protein_coding YES CCDS14516.1 ENSP00000361669 Q8N693 UPI0000073D09 NM_153448.3 2/4 hmmpanther:PTHR24329:SF374,hmmpanther:PTHR24329 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 61 104254471 104254471 C A 1 0 0 0 0 0 0 0 1 5125 639 23 1 1 ESX1 23 104254471 Silent SNP C C3N-00580_T 577755 104254471 51786424 990 19125 MUM1L1 0 . GRCh38 X 106206983 106206983 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.1551G>T p.= p.L517L ENST00000337685 5/5 68 26 42 79 79 0 strelka-varscan-mutect MUM1L1,synonymous_variant,p.=,ENST00000337685,NM_152423.4;MUM1L1,synonymous_variant,p.=,ENST00000357175,NM_001171020.1;MUM1L1,synonymous_variant,p.=,ENST00000372552,; T ENST00000337685 Transcript synonymous_variant 2336/4308 1551/2091 517/696 L ctG/ctT 1 1 MUM1L1 HGNC HGNC:26583 protein_coding YES CCDS55469.1 ENSP00000338641 Q5H9M0 UPI0000212206 NM_152423.4 5/5 hmmpanther:PTHR31333,hmmpanther:PTHR31333:SF3 LOW 1 SNV 3 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 106206983 106206983 G T 1 0 0 0 0 0 0 0 1 9984 1306 46 2 2 MUM1L1 23 106206983 Silent SNP G C3N-00580_T 1952512 106206983 49833912 991 19126 DCAF12L1 0 . GRCh38 X 126552377 126552377 + Missense_Mutation SNP A A T novel C3N-00580_T C3N-00580_N A A c.232T>A p.Tyr78Asn p.Y78N ENST00000371126 1/2 115 52 63 106 106 0 strelka-varscan-mutect DCAF12L1,missense_variant,p.Tyr78Asn,ENST00000371126,NM_178470.4; T ENST00000371126 Transcript missense_variant 475/3382 232/1392 78/463 Y/N Tac/Aac 1 -1 DCAF12L1 HGNC HGNC:29395 protein_coding YES CCDS14610.1 ENSP00000360167 Q5VU92 UPI0000160112 NM_178470.4 tolerated(0.08) 1/2 hmmpanther:PTHR19860,hmmpanther:PTHR19860:SF9 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 126552377 126552377 A T 1 0 0 0 0 1 0 0 0 4065 420 15 4 4 DCAF12L1 23 126552377 Missense_Mutation SNP A C3N-00580_T 20345394 126552377 29488518 992 19127 PLAC1 0 . GRCh38 X 134566469 134566469 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.214C>A p.Gln72Lys p.Q72K ENST00000359237 3/3 158 62 96 103 103 0 strelka-varscan-mutect PLAC1,missense_variant,p.Gln72Lys,ENST00000359237,NM_021796.3;PLAC1,non_coding_transcript_exon_variant,,ENST00000476971,;PLAC1,downstream_gene_variant,,ENST00000473897,; T ENST00000359237 Transcript missense_variant 500/1131 214/639 72/212 Q/K Cag/Aag 1 -1 PLAC1 HGNC HGNC:9044 protein_coding YES CCDS14642.1 ENSP00000352173 Q9HBJ0 UPI0000070F9F NM_021796.3 tolerated(0.08) 3/3 hmmpanther:PTHR14380,hmmpanther:PTHR14380:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 134566469 134566469 G T 1 0 0 0 0 1 0 0 0 12108 1357 47 2 2 PLAC1 23 134566469 Missense_Mutation SNP G C3N-00580_T 8014092 134566469 21474426 993 19128 SLITRK2 0 . GRCh38 X 145822974 145822974 + Silent SNP G G T novel C3N-00580_T C3N-00580_N G G c.549G>T p.= p.L183L ENST00000370490 1/1 108 45 63 128 127 1 strelka-varscan-mutect SLITRK2,synonymous_variant,p.=,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,synonymous_variant,p.=,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript synonymous_variant 4804/7672 549/2538 183/845 L ctG/ctT 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 145822974 145822974 G T 1 0 0 0 0 0 0 0 1 15034 1277 45 2 2 SLITRK2 23 145822974 Silent SNP G C3N-00580_T 11256505 145822974 10217921 994 19129 SLITRK2 0 . GRCh38 X 145823907 145823907 + Silent SNP G G T rs781908643 C3N-00580_T C3N-00580_N G G c.1482G>T p.= p.T494T ENST00000370490 1/1 61 23 38 87 87 0 strelka-varscan-mutect SLITRK2,synonymous_variant,p.=,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,synonymous_variant,p.=,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript synonymous_variant 5737/7672 1482/2538 494/845 T acG/acT rs781908643 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 1/1 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 PASS rs781908643 . 0 202 5 3 0 0 0 0 -20 0.999981 1 1 1 0 T 2 4 61 145823907 145823907 G T 1 0 0 0 0 0 0 0 1 15034 1103 39 1 1 SLITRK2 23 145823907 Silent SNP G C3N-00580_T 933 145823907 10216988 995 19130 SLITRK2 0 . GRCh38 X 145824469 145824469 + Missense_Mutation SNP G G T C3N-00580_T C3N-00580_N G G c.2044G>T p.Gly682Cys p.G682C ENST00000370490 1/1 160 88 72 180 180 0 strelka-varscan-mutect SLITRK2,missense_variant,p.Gly682Cys,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,missense_variant,p.Gly682Cys,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; T ENST00000370490 Transcript missense_variant 6299/7672 2044/2538 682/845 G/C Ggc/Tgc COSM3233353,COSM375963,COSM5320877 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 deleterious(0) 1/1 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF36 1,1,1 MODERATE 1 SNV 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 145824469 145824469 G T 1 0 0 0 0 1 0 0 0 15034 1116 39 1 1 SLITRK2 23 145824469 Missense_Mutation SNP G C3N-00580_T 562 145824469 10216426 996 19131 MAGEA11 0 . GRCh38 X 149716605 149716605 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.1119G>T p.Gln373His p.Q373H ENST00000355220 5/5 222 57 165 107 107 0 strelka-varscan-mutect MAGEA11,missense_variant,p.Gln373His,ENST00000355220,NM_005366.4;MAGEA11,missense_variant,p.Gln344His,ENST00000333104,NM_001011544.1;MAGEA11,downstream_gene_variant,,ENST00000412632,;MAGEA11,non_coding_transcript_exon_variant,,ENST00000518694,; T ENST00000355220 Transcript missense_variant 1221/1864 1119/1290 373/429 Q/H caG/caT 1 1 MAGEA11 HGNC HGNC:6798 protein_coding YES CCDS48180.1 ENSP00000347358 P43364 UPI0000211BB0 NM_005366.4 deleterious(0) 5/5 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF71,Pfam_domain:PF01454,SMART_domains:SM01373 MODERATE 1 SNV 1 1 PASS rs782327063 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 149716605 149716605 G T 1 0 0 0 0 1 0 0 0 9081 991 35 2 2 MAGEA11 23 149716605 Missense_Mutation SNP G C3N-00580_T 3892136 149716605 6324290 997 19132 MAGEA12 0 . GRCh38 X 152736958 152736958 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.797C>A p.Pro266His p.P266H ENST00000393900 3/3 557 452 105 294 294 0 strelka-varscan-mutect MAGEA12,missense_variant,p.Pro266His,ENST00000393900,NM_001166386.3;MAGEA12,missense_variant,p.Pro266His,ENST00000393869,NM_001166387.3;MAGEA12,missense_variant,p.Pro266His,ENST00000357916,NM_005367.6;CSAG1,upstream_gene_variant,,ENST00000370291,;CSAG1,upstream_gene_variant,,ENST00000370287,NM_153478.2;CSAG1,upstream_gene_variant,,ENST00000452779,NM_001102576.2;CSAG4,intron_variant,,ENST00000361201,;CSAG1,upstream_gene_variant,,ENST00000361211,;CSAG4,upstream_gene_variant,,ENST00000583763,; A ENST00000393900 Transcript missense_variant 1151/1853 797/945 266/314 P/H cCt/cAt COSM5412246 1 1 MAGEA12 HGNC HGNC:6799 protein_coding YES CCDS76048.1 ENSP00000377478 P43365 Q6FHH8 UPI0000000C51 NM_001166386.3 deleterious(0.02) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF74,Pfam_domain:PF01454,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 152736958 152736958 C A 1 0 0 0 0 1 0 0 0 9082 681 24 2 2 MAGEA12 23 152736958 Missense_Mutation SNP C C3N-00580_T 3020353 152736958 3303937 998 19133 ATP2B3 0 . GRCh38 X 153553086 153553086 + Silent SNP G G T C3N-00580_T C3N-00580_N G G c.1875G>T p.= p.R625R ENST00000263519 11/20 181 127 54 86 86 0 strelka-varscan-mutect ATP2B3,synonymous_variant,p.=,ENST00000370186,;ATP2B3,synonymous_variant,p.=,ENST00000263519,NM_001001344.2;ATP2B3,synonymous_variant,p.=,ENST00000349466,;ATP2B3,synonymous_variant,p.=,ENST00000359149,NM_021949.3;ATP2B3,synonymous_variant,p.=,ENST00000393842,;ATP2B3,upstream_gene_variant,,ENST00000460549,; T ENST00000263519 Transcript synonymous_variant 2001/6420 1875/3663 625/1220 R cgG/cgT COSM5412271,COSM5412272,COSM5412273,COSM5412274 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 11/20 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Superfamily_domains:SSF81660 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 61 153553086 153553086 G T 1 0 0 0 0 0 0 0 1 1294 1219 43 2 2 ATP2B3 23 153553086 Silent SNP G C3N-00580_T 816128 153553086 2487809 999 19134 ATP2B3 0 . GRCh38 X 153556951 153556951 + Missense_Mutation SNP G G T novel C3N-00580_T C3N-00580_N G G c.2361G>T p.Gln787His p.Q787H ENST00000263519 14/20 432 80 352 305 305 0 strelka-varscan-mutect ATP2B3,missense_variant,p.Gln773His,ENST00000370186,;ATP2B3,missense_variant,p.Gln787His,ENST00000263519,NM_001001344.2;ATP2B3,missense_variant,p.Gln787His,ENST00000349466,;ATP2B3,missense_variant,p.Gln787His,ENST00000359149,NM_021949.3;ATP2B3,missense_variant,p.Gln773His,ENST00000393842,;ATP2B3,non_coding_transcript_exon_variant,,ENST00000460549,; T ENST00000263519 Transcript missense_variant 2487/6420 2361/3663 787/1220 Q/H caG/caT 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 deleterious(0) 14/20 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,TIGRFAM_domain:TIGR01494,Pfam_domain:PF08282,Superfamily_domains:SSF56784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 61 153556951 153556951 G T 1 0 0 0 0 1 0 0 0 1294 991 35 2 2 ATP2B3 23 153556951 Missense_Mutation SNP G C3N-00580_T 3865 153556951 2483944 1000 19135 L1CAM 0 . GRCh38 X 153872664 153872664 + Missense_Mutation SNP G G C novel C3N-00580_T C3N-00580_N G G c.125C>G p.Pro42Arg p.P42R ENST00000370060 4/29 587 419 168 326 326 0 strelka-varscan-mutect L1CAM,missense_variant,p.Pro42Arg,ENST00000370060,NM_001278116.1,NM_000425.4;L1CAM,missense_variant,p.Pro37Arg,ENST00000361981,NM_001143963.2;L1CAM,missense_variant,p.Pro37Arg,ENST00000370055,;L1CAM,missense_variant,p.Pro42Arg,ENST00000361699,NM_024003.3;L1CAM,missense_variant,p.Pro42Arg,ENST00000439496,;L1CAM,missense_variant,p.Pro42Arg,ENST00000458029,;L1CAM,missense_variant,p.Pro37Arg,ENST00000407935,;L1CAM,missense_variant,p.Pro37Arg,ENST00000420165,;L1CAM,upstream_gene_variant,,ENST00000455590,;L1CAM,non_coding_transcript_exon_variant,,ENST00000464967,;L1CAM,upstream_gene_variant,,ENST00000496122,;L1CAM,downstream_gene_variant,,ENST00000460553,;L1CAM,upstream_gene_variant,,ENST00000484652,; C ENST00000370060 Transcript missense_variant 315/5113 125/3774 42/1257 P/R cCa/cGa 1 -1 L1CAM HGNC HGNC:6470 protein_coding YES CCDS14733.1 ENSP00000359077 P32004 UPI0000126E89 NM_001278116.1,NM_000425.4 deleterious(0) 4/29 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF593,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9990393 1 1 1 0 C 3 2 61 153872664 153872664 G C 1 0 0 0 0 1 0 0 0 8489 1348 47 4 4 L1CAM 23 153872664 Missense_Mutation SNP G C3N-00580_T 315713 153872664 2168231 1001 19136 ARHGAP4 0 . GRCh38 X 153921713 153921713 + Missense_Mutation SNP C C A C3N-00580_T C3N-00580_N C C c.164G>T p.Arg55Leu p.R55L ENST00000370028 2/23 492 406 86 357 357 0 strelka-varscan-mutect ARHGAP4,missense_variant,p.Arg55Leu,ENST00000370028,NM_001164741.1;ARHGAP4,missense_variant,p.Arg55Leu,ENST00000350060,NM_001666.4;ARHGAP4,missense_variant,p.Arg55Leu,ENST00000370016,;ARHGAP4,missense_variant,p.Arg55Leu,ENST00000393721,;ARHGAP4,missense_variant,p.Arg32Leu,ENST00000461052,;ARHGAP4,missense_variant,p.Arg32Leu,ENST00000488269,;ARHGAP4,missense_variant,p.Arg32Leu,ENST00000442262,;ARHGAP4,missense_variant,p.Arg32Leu,ENST00000422091,;ARHGAP4,upstream_gene_variant,,ENST00000422918,;ARHGAP4,upstream_gene_variant,,ENST00000418750,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000470979,;ARHGAP4,missense_variant,p.Arg55Leu,ENST00000404127,;ARHGAP4,missense_variant,p.Arg55Leu,ENST00000420383,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000470209,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494302,;ARHGAP4,non_coding_transcript_exon_variant,,ENST00000494813,;ARHGAP4,upstream_gene_variant,,ENST00000460782,; A ENST00000370028 Transcript missense_variant 222/3372 164/2961 55/986 R/L cGc/cTc COSM5486785,COSM5486786 1 -1 ARHGAP4 HGNC HGNC:674 protein_coding YES CCDS55540.1 ENSP00000359045 P98171 UPI000019275E NM_001164741.1 deleterious(0) 2/23 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00611,PROSITE_profiles:PS51741,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF16,SMART_domains:SM00055,Superfamily_domains:SSF103657 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 61 153921713 153921713 C A 1 0 0 0 0 1 0 0 0 1011 768 27 1 1 ARHGAP4 23 153921713 Missense_Mutation SNP C C3N-00580_T 49049 153921713 2119182 1002 19137 CCDC27 0 . GRCh38 1 3766603 3766603 + Silent SNP C C G C3N-00704_T C3N-00704_N C C c.1521C>G p.= p.L507L ENST00000294600 9/12 191 166 25 229 229 0 strelka-varscan-mutect CCDC27,synonymous_variant,p.=,ENST00000294600,NM_152492.2;CCDC27,3_prime_UTR_variant,,ENST00000462521,; G ENST00000294600 Transcript synonymous_variant 1605/2176 1521/1971 507/656 L ctC/ctG COSM5629009 1 1 CCDC27 HGNC HGNC:26546 protein_coding YES CCDS50.1 ENSP00000294600 Q2M243 UPI000013E186 NM_152492.2 9/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18853:SF8,hmmpanther:PTHR18853 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 3766603 3766603 C G 1 0 0 0 0 0 0 0 1 2511 842 30 4 4 CCDC27 1 3766603 Silent SNP C C3N-00704_T 3766603 245189819 1 19138 PLEKHG5 0 . GRCh38 1 6469046 6469046 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.2482C>T p.His828Tyr p.H828Y ENST00000537245 20/22 289 247 42 382 382 0 strelka-varscan-mutect PLEKHG5,missense_variant,p.His826Tyr,ENST00000377748,NM_198681.3;PLEKHG5,missense_variant,p.His828Tyr,ENST00000537245,NM_001265592.1;PLEKHG5,missense_variant,p.His818Tyr,ENST00000535355,NM_001265593.1;PLEKHG5,missense_variant,p.His749Tyr,ENST00000340850,NM_001042664.1;PLEKHG5,missense_variant,p.His749Tyr,ENST00000400913,NM_001042665.1;PLEKHG5,missense_variant,p.His786Tyr,ENST00000377732,;PLEKHG5,missense_variant,p.His805Tyr,ENST00000400915,NM_001042663.1;PLEKHG5,missense_variant,p.His749Tyr,ENST00000377728,NM_020631.4;PLEKHG5,missense_variant,p.His826Tyr,ENST00000377740,;PLEKHG5,missense_variant,p.His749Tyr,ENST00000377725,NM_001265594.1;TNFRSF25,upstream_gene_variant,,ENST00000377782,NM_148965.1;TNFRSF25,upstream_gene_variant,,ENST00000356876,NM_003790.2;TNFRSF25,upstream_gene_variant,,ENST00000351959,NM_148966.1;TNFRSF25,upstream_gene_variant,,ENST00000348333,NM_148967.1;TNFRSF25,upstream_gene_variant,,ENST00000481401,;TNFRSF25,upstream_gene_variant,,ENST00000351748,NM_148970.1;TNFRSF25,upstream_gene_variant,,ENST00000461703,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000489097,;PLEKHG5,non_coding_transcript_exon_variant,,ENST00000487949,;TNFRSF25,upstream_gene_variant,,ENST00000513135,;TNFRSF25,upstream_gene_variant,,ENST00000485036,;TNFRSF25,upstream_gene_variant,,ENST00000480393,;TNFRSF25,upstream_gene_variant,,ENST00000414040,;TNFRSF25,upstream_gene_variant,,ENST00000510563,;TNFRSF25,upstream_gene_variant,,ENST00000502588,;TNFRSF25,upstream_gene_variant,,ENST00000502730,;TNFRSF25,upstream_gene_variant,,ENST00000469691,;TNFRSF25,upstream_gene_variant,,ENST00000453341,;TNFRSF25,upstream_gene_variant,,ENST00000515145,; A ENST00000537245 Transcript missense_variant 2547/4794 2482/3258 828/1085 H/Y Cac/Tac 1 -1 PLEKHG5 HGNC HGNC:29105 protein_coding YES CCDS57969.1 ENSP00000439625 O94827 UPI000206539E NM_001265592.1 deleterious(0.03) 20/22 hmmpanther:PTHR13217,hmmpanther:PTHR13217:SF9 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 6469046 6469046 G A 1 0 0 0 0 1 0 0 0 12166 1333 46 3 3 PLEKHG5 1 6469046 Missense_Mutation SNP G C3N-00704_T 2702443 6469046 242487376 2 19139 VPS13D 0 . GRCh38 1 12354202 12354202 + Silent SNP A A G novel C3N-00704_T C3N-00704_N A A c.9660A>G p.= p.T3220T ENST00000620676 47/70 160 138 22 182 182 0 strelka-varscan-mutect VPS13D,synonymous_variant,p.=,ENST00000620676,NM_015378.3;VPS13D,synonymous_variant,p.=,ENST00000613099,NM_018156.3;VPS13D,synonymous_variant,p.=,ENST00000011700,;VPS13D,downstream_gene_variant,,ENST00000469054,;VPS13D,non_coding_transcript_exon_variant,,ENST00000460333,; G ENST00000620676 Transcript synonymous_variant 9790/16320 9660/13167 3220/4388 T acA/acG 1 1 VPS13D HGNC HGNC:23595 protein_coding YES CCDS30588.1 ENSP00000478104 Q5THJ4 UPI0000451CA9 NM_015378.3 47/70 hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF104 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 12354202 12354202 A G 1 0 0 0 0 0 0 0 1 17739 204 8 5 5 VPS13D 1 12354202 Silent SNP A C3N-00704_T 5885156 12354202 236602220 3 19140 KAZN 0 . GRCh38 1 15104128 15104128 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1987G>C p.Gly663Arg p.G663R ENST00000376030 13/15 217 177 40 265 265 0 strelka-varscan-mutect KAZN,missense_variant,p.Gly751Arg,ENST00000636203,;KAZN,missense_variant,p.Gly663Arg,ENST00000376030,NM_201628.2; C ENST00000376030 Transcript missense_variant 2281/6030 1987/2328 663/775 G/R Ggg/Cgg 1 1 KAZN HGNC HGNC:29173 protein_coding YES CCDS152.2 ENSP00000365198 Q674X7 UPI0000E1E68A NM_201628.2 deleterious(0.03) 13/15 Pfam_domain:PF07647,hmmpanther:PTHR12776,hmmpanther:PTHR12776:SF1,SMART_domains:SM00454 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 15104128 15104128 G C 1 0 0 0 0 1 0 0 0 7907 1348 47 4 4 KAZN 1 15104128 Missense_Mutation SNP G C3N-00704_T 2749926 15104128 233852294 4 19141 CELA2A 0 . GRCh38 1 15467478 15467478 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.732C>A p.Asn244Lys p.N244K ENST00000359621 7/8 284 235 49 372 372 0 strelka-varscan-mutect CELA2A,missense_variant,p.Asn244Lys,ENST00000359621,NM_033440.2;CELA2B,non_coding_transcript_exon_variant,,ENST00000494280,;CELA2A,downstream_gene_variant,,ENST00000459653,; A ENST00000359621 Transcript missense_variant 757/919 732/810 244/269 N/K aaC/aaA 1 1 CELA2A HGNC HGNC:24609 protein_coding YES CCDS157.1 ENSP00000352639 P08217 UPI0000129E36 NM_033440.2 deleterious(0.01) 7/8 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24257,hmmpanther:PTHR24257:SF18,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs1480303890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 15467478 15467478 C A 1 0 0 0 0 1 0 0 0 2918 564 20 2 2 CELA2A 1 15467478 Missense_Mutation SNP C C3N-00704_T 363350 15467478 233488944 5 19142 CLCNKB 0 . GRCh38 1 16053702 16053702 + Missense_Mutation SNP G G T rs751162013 C3N-00704_T C3N-00704_N G G c.1686G>T p.Met562Ile p.M562I ENST00000375679 16/20 390 327 63 505 505 0 strelka-varscan-mutect CLCNKB,missense_variant,p.Met562Ile,ENST00000375679,NM_000085.4;CLCNKB,missense_variant,p.Met393Ile,ENST00000375667,NM_001165945.2;CLCNKB,missense_variant,p.Met51Ile,ENST00000431772,;CLCNKB,intron_variant,,ENST00000619181,;FAM131C,downstream_gene_variant,,ENST00000375662,NM_182623.2;FAM131C,downstream_gene_variant,,ENST00000494078,; T ENST00000375679 Transcript missense_variant 1797/2567 1686/2064 562/687 M/I atG/atT rs751162013 1 1 CLCNKB HGNC HGNC:2027 protein_coding YES CCDS168.1 ENSP00000364831 P51801 UPI000040E261 NM_000085.4 tolerated(0.23) 16/20 PROSITE_profiles:PS51371,hmmpanther:PTHR11689:SF95,hmmpanther:PTHR11689,Gene3D:3.10.580.10,Pfam_domain:PF00571,SMART_domains:SM00116,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS rs751162013 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 16053702 16053702 G T 1 0 0 0 0 1 0 0 0 3234 1319 46 2 2 CLCNKB 1 16053702 Missense_Mutation SNP G C3N-00704_T 586224 16053702 232902720 6 19143 PADI6 0 . GRCh38 1 17381135 17381135 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.524A>T p.Lys175Met p.K175M ENST00000619609 5/16 224 190 34 225 225 0 strelka-varscan-mutect PADI6,missense_variant,p.Lys175Met,ENST00000619609,NM_207421.4; T ENST00000619609 Transcript missense_variant 574/2396 524/2085 175/694 K/M aAg/aTg 1 1 PADI6 HGNC HGNC:20449 protein_coding YES CCDS72715.1 ENSP00000483125 Q6TGC4 UPI0000253BE7 NM_207421.4 tolerated(0.23) 5/16 hmmpanther:PTHR10837:SF4,hmmpanther:PTHR10837,PIRSF_domain:PIRSF001247,Pfam_domain:PF08527,Superfamily_domains:0044952,PD936484 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 17381135 17381135 A T 1 0 0 0 0 1 0 0 0 11459 72 3 4 4 PADI6 1 17381135 Missense_Mutation SNP A C3N-00704_T 1327433 17381135 231575287 7 19144 UBR4 0 . GRCh38 1 19199725 19199725 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.304G>T p.Ala102Ser p.A102S ENST00000375254 3/106 343 303 40 344 344 0 strelka-varscan-mutect UBR4,missense_variant,p.Ala102Ser,ENST00000375254,NM_020765.2; A ENST00000375254 Transcript missense_variant 332/15906 304/15552 102/5183 A/S Gca/Tca 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 tolerated(0.24) 3/106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 19199725 19199725 C A 1 0 0 0 0 1 0 0 0 17428 797 28 2 2 UBR4 1 19199725 Missense_Mutation SNP C C3N-00704_T 1818590 19199725 229756697 8 19145 ECE1 0 . GRCh38 1 21272871 21272871 + Silent SNP C C A rs763873947 C3N-00704_T C3N-00704_N C C c.321G>T p.= p.V107V ENST00000374893 4/19 489 407 82 578 578 0 strelka-varscan-mutect ECE1,synonymous_variant,p.=,ENST00000415912,NM_001113348.1;ECE1,synonymous_variant,p.=,ENST00000357071,NM_001113347.1;ECE1,synonymous_variant,p.=,ENST00000374893,NM_001397.2;ECE1,synonymous_variant,p.=,ENST00000264205,NM_001113349.1;ECE1,synonymous_variant,p.=,ENST00000436918,;ECE1,synonymous_variant,p.=,ENST00000527991,;ECE1,synonymous_variant,p.=,ENST00000481130,;ECE1,5_prime_UTR_variant,,ENST00000473505,;ECE1,non_coding_transcript_exon_variant,,ENST00000463334,;ECE1,non_coding_transcript_exon_variant,,ENST00000526194,; A ENST00000374893 Transcript synonymous_variant 396/2484 321/2313 107/770 V gtG/gtT rs763873947 1 -1 ECE1 HGNC HGNC:3146 protein_coding YES CCDS215.1 ENSP00000364028 P42892 A0A024RAF7 UPI0000129B5E NM_001397.2 4/19 hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF130,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS rs763873947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 21272871 21272871 C A 1 0 0 0 0 0 0 0 1 4715 813 29 2 2 ECE1 1 21272871 Silent SNP C C3N-00704_T 2073146 21272871 227683551 9 19146 TCEB3 0 . GRCh38 1 23754178 23754178 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1694G>T p.Gly565Val p.G565V ENST00000418390 6/11 315 259 56 335 335 0 strelka-varscan-mutect TCEB3,missense_variant,p.Gly565Val,ENST00000418390,;TCEB3,missense_variant,p.Gly565Val,ENST00000613537,NM_003198.2;TCEB3,missense_variant,p.Gly539Val,ENST00000609199,;TCEB3,downstream_gene_variant,,ENST00000487554,; T ENST00000418390 Transcript missense_variant 1965/5154 1694/2397 565/798 G/V gGt/gTt 1 1 TCEB3 HGNC HGNC:11620 protein_coding YES CCDS239.2 ENSP00000395574 Q14241 UPI000181BA17 deleterious(0) 6/11 hmmpanther:PTHR15141,hmmpanther:PTHR15141:SF46 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 23754178 23754178 G T 1 0 0 0 0 1 0 0 0 16088 1261 44 2 2 TCEB3 1 23754178 Missense_Mutation SNP G C3N-00704_T 2481307 23754178 225202244 10 19147 TRIM63 0 . GRCh38 1 26061198 26061198 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.469G>T p.Ala157Ser p.A157S ENST00000374272 3/9 160 137 23 189 188 1 strelka-varscan-mutect TRIM63,missense_variant,p.Ala157Ser,ENST00000374272,NM_032588.3;TRIM63,downstream_gene_variant,,ENST00000483052,; A ENST00000374272 Transcript missense_variant 608/1770 469/1062 157/353 A/S Gcc/Tcc COSM117486 1 -1 TRIM63 HGNC HGNC:16007 protein_coding YES CCDS273.1 ENSP00000363390 Q969Q1 UPI00000437F6 NM_032588.3 tolerated(0.19) 3/9 Gene3D:1freA00,PROSITE_profiles:PS50119,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF279,SMART_domains:SM00336,Superfamily_domains:SSF57845 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999979 1 1 1 0 A 3 1 62 26061198 26061198 C A 1 0 0 0 0 1 0 0 0 17030 739 26 2 2 TRIM63 1 26061198 Missense_Mutation SNP C C3N-00704_T 2307020 26061198 222895224 11 19148 WDTC1 0 . GRCh38 1 27303779 27303779 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1627G>T p.Ala543Ser p.A543S ENST00000319394 14/16 455 387 68 512 512 0 strelka-varscan-mutect WDTC1,missense_variant,p.Ala543Ser,ENST00000319394,NM_001276252.1;WDTC1,missense_variant,p.Ala542Ser,ENST00000361771,NM_015023.4;WDTC1,missense_variant,p.Ala543Ser,ENST00000447062,;WDTC1,non_coding_transcript_exon_variant,,ENST00000491239,;WDTC1,upstream_gene_variant,,ENST00000472249,; T ENST00000319394 Transcript missense_variant 2162/4819 1627/2034 543/677 A/S Gcc/Tcc 1 1 WDTC1 HGNC HGNC:29175 protein_coding YES CCDS60044.1 ENSP00000317971 Q8N5D0 UPI000004814E NM_001276252.1 deleterious(0.01) 14/16 Gene3D:2.130.10.10,Pfam_domain:PF00400,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF40,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 27303779 27303779 G T 1 0 0 0 0 1 0 0 0 17899 1203 42 2 2 WDTC1 1 27303779 Missense_Mutation SNP G C3N-00704_T 1242581 27303779 221652643 12 19149 C1orf216 0 . GRCh38 1 35716048 35716048 + Missense_Mutation SNP C C A rs781489022 C3N-00704_T C3N-00704_N C C c.274G>T p.Gly92Trp p.G92W ENST00000270815 2/2 269 226 43 301 301 0 strelka-varscan-mutect C1orf216,missense_variant,p.Gly92Trp,ENST00000270815,NM_152374.1;CLSPN,downstream_gene_variant,,ENST00000251195,;C1orf216,downstream_gene_variant,,ENST00000503824,;C1orf216,downstream_gene_variant,,ENST00000453178,; A ENST00000270815 Transcript missense_variant 1045/3218 274/690 92/229 G/W Ggg/Tgg rs781489022,COSM4856116 1 -1 C1orf216 HGNC HGNC:26800 protein_coding YES CCDS395.1 ENSP00000425166 Q8TAB5 UPI000006D838 NM_152374.1 deleterious(0) 2/2 Pfam_domain:PF15546,hmmpanther:PTHR35673,hmmpanther:PTHR35673:SF1,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781489022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 35716048 35716048 C A 1 0 0 0 0 1 0 0 0 1983 652 23 1 1 C1orf216 1 35716048 Missense_Mutation SNP C C3N-00704_T 8412269 35716048 213240374 13 19150 CLSPN 0 . GRCh38 1 35739196 35739196 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.3370G>A p.Asp1124Asn p.D1124N ENST00000318121 20/25 390 349 41 433 433 0 strelka-varscan-mutect CLSPN,missense_variant,p.Asp1124Asn,ENST00000251195,;CLSPN,missense_variant,p.Asp1124Asn,ENST00000318121,NM_022111.3;CLSPN,missense_variant,p.Asp1071Asn,ENST00000520551,;CLSPN,missense_variant,p.Asp1060Asn,ENST00000373220,NM_001190481.1;RP11-435D7.3,upstream_gene_variant,,ENST00000373226,;CLSPN,upstream_gene_variant,,ENST00000466308,; T ENST00000318121 Transcript missense_variant 3428/4169 3370/4020 1124/1339 D/N Gat/Aat 1 -1 CLSPN HGNC HGNC:19715 protein_coding YES CCDS396.1 ENSP00000312995 Q9HAW4 UPI0000161087 NM_022111.3 deleterious(0) 20/25 hmmpanther:PTHR14396:SF10,hmmpanther:PTHR14396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 35739196 35739196 C T 1 0 0 0 0 1 0 0 0 3332 826 29 3 3 CLSPN 1 35739196 Missense_Mutation SNP C C3N-00704_T 23148 35739196 213217226 14 19151 UTP11 0 . GRCh38 1 38018539 38018539 + Missense_Mutation SNP G G T rs143106814 C3N-00704_T C3N-00704_N G G c.304G>T p.Val102Phe p.V102F ENST00000373014 4/8 92 72 20 169 169 0 strelka-varscan-mutect UTP11,missense_variant,p.Val102Phe,ENST00000373014,NM_016037.3;UTP11,non_coding_transcript_exon_variant,,ENST00000488453,;UTP11,non_coding_transcript_exon_variant,,ENST00000483182,;UTP11,downstream_gene_variant,,ENST00000486563,; T ENST00000373014 Transcript missense_variant 365/2019 304/762 102/253 V/F Gtc/Ttc rs143106814,COSM909095 1 1 UTP11 HGNC HGNC:24329 protein_coding YES CCDS429.1 ENSP00000362105 Q9Y3A2 UPI000006FDFC NM_016037.3 deleterious(0.04) 4/8 Pfam_domain:PF03998,PIRSF_domain:PIRSF015952,hmmpanther:PTHR12838 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs143106814 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 38018539 38018539 G T 1 0 0 0 0 1 0 0 0 17637 1145 40 1 1 UTP11 1 38018539 Missense_Mutation SNP G C3N-00704_T 2279343 38018539 210937883 15 19152 COL9A2 0 . GRCh38 1 40312097 40312097 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.379G>T p.Val127Phe p.V127F ENST00000372748 8/32 285 244 41 279 279 0 strelka-varscan-mutect COL9A2,missense_variant,p.Val127Phe,ENST00000372748,NM_001852.3;COL9A2,missense_variant,p.Val116Phe,ENST00000417105,;COL9A2,missense_variant,p.Val56Phe,ENST00000372736,;COL9A2,downstream_gene_variant,,ENST00000490132,;COL9A2,downstream_gene_variant,,ENST00000495948,;COL9A2,non_coding_transcript_exon_variant,,ENST00000482722,;COL9A2,non_coding_transcript_exon_variant,,ENST00000488463,;COL9A2,non_coding_transcript_exon_variant,,ENST00000496215,;COL9A2,downstream_gene_variant,,ENST00000461118,; A ENST00000372748 Transcript missense_variant 476/2862 379/2070 127/689 V/F Gtt/Ttt 1 -1 COL9A2 HGNC HGNC:2218 protein_coding YES CCDS450.1 ENSP00000361834 Q14055 UPI0000126D47 NM_001852.3 tolerated(0.09) 8/32 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF513,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs1331964044 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 40312097 40312097 C A 1 0 0 0 0 1 0 0 0 3497 478 17 2 2 COL9A2 1 40312097 Missense_Mutation SNP C C3N-00704_T 2293558 40312097 208644325 16 19153 TRABD2B 0 . GRCh38 1 47994119 47994119 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.581C>A p.Ala194Asp p.A194D ENST00000606738 2/7 253 203 50 282 281 1 strelka-varscan-mutect TRABD2B,missense_variant,p.Ala194Asp,ENST00000606738,NM_001194986.1;TRABD2B,non_coding_transcript_exon_variant,,ENST00000435576,; T ENST00000606738 Transcript missense_variant 687/7034 581/1554 194/517 A/D gCt/gAt 1 -1 TRABD2B HGNC HGNC:44200 protein_coding YES CCDS58000.1 ENSP00000476820 A6NFA1 UPI00017BE8EF NM_001194986.1 deleterious(0) 2/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31120:SF8,hmmpanther:PTHR31120,Pfam_domain:PF01963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 47994119 47994119 G T 1 0 0 0 0 1 0 0 0 16918 971 34 2 2 TRABD2B 1 47994119 Missense_Mutation SNP G C3N-00704_T 7682022 47994119 200962303 17 19154 AGBL4 0 . GRCh38 1 49045646 49045646 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.532C>T p.Leu178Phe p.L178F ENST00000371839 5/14 288 242 46 319 318 1 strelka-varscan-mutect AGBL4,missense_variant,p.Leu24Phe,ENST00000416121,;AGBL4,missense_variant,p.Leu178Phe,ENST00000371839,NM_032785.3;AGBL4,missense_variant,p.Leu178Phe,ENST00000371836,;AGBL4,missense_variant,p.Leu178Phe,ENST00000371838,;RP11-141A19.1,upstream_gene_variant,,ENST00000456002,; A ENST00000371839 Transcript missense_variant 649/2947 532/1512 178/503 L/F Ctt/Ttt 1 -1 AGBL4 HGNC HGNC:25892 protein_coding YES CCDS44137.1 ENSP00000360905 Q5VU57 UPI00002042F9 NM_032785.3 deleterious(0) 5/14 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR12756,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 49045646 49045646 G A 1 0 0 0 0 1 0 0 0 454 1000 35 3 3 AGBL4 1 49045646 Missense_Mutation SNP G C3N-00704_T 1051527 49045646 199910776 18 19155 DMRTA2 0 . GRCh38 1 50419073 50419073 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1221G>T p.Gln407His p.Q407H ENST00000404795 3/3 75 59 16 79 79 0 strelka-varscan-mutect DMRTA2,missense_variant,p.Gln407His,ENST00000404795,NM_032110.2;DMRTA2,missense_variant,p.Gln407His,ENST00000418121,; A ENST00000404795 Transcript missense_variant 1614/3137 1221/1629 407/542 Q/H caG/caT 1 -1 DMRTA2 HGNC HGNC:13908 protein_coding YES CCDS44141.1 ENSP00000383909 Q96SC8 UPI00003D7962 NM_032110.2 tolerated_low_confidence(0.12) 3/3 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF76,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 50419073 50419073 C A 1 0 0 0 0 1 0 0 0 4396 680 24 2 2 DMRTA2 1 50419073 Missense_Mutation SNP C C3N-00704_T 1373427 50419073 198537349 19 19156 BSND 0 . GRCh38 1 54999349 54999349 + Nonsense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.163C>T p.Gln55Ter p.Q55* ENST00000371265 1/4 81 61 20 97 97 0 strelka-varscan-mutect BSND,stop_gained,p.Gln55Ter,ENST00000371265,NM_057176.2; T ENST00000371265 Transcript stop_gained 417/3472 163/963 55/320 Q/* Cag/Tag 1 1 BSND HGNC HGNC:16512 protein_coding YES CCDS602.1 ENSP00000360312 Q8WZ55 Q5VU50 UPI000006DC8D NM_057176.2 1/4 PD968187,Pfam_domain:PF15462,hmmpanther:PTHR28399,hmmpanther:PTHR28399:SF1 HIGH 1 SNV 1 1 PASS rs1486736339 . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 T 4 4 62 54999349 54999349 C T 1 0 0 0 0 0 1 0 0 1705 595 21 3 3 BSND 1 54999349 Nonsense_Mutation SNP C C3N-00704_T 4580276 54999349 193957073 20 19157 TM2D1 0 . GRCh38 1 61723784 61723784 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.167A>G p.Tyr56Cys p.Y56C ENST00000606498 2/7 45 39 6 147 147 0 strelka-varscan-mutect TM2D1,missense_variant,p.Tyr56Cys,ENST00000371177,;TM2D1,missense_variant,p.Tyr56Cys,ENST00000294613,;TM2D1,missense_variant,p.Tyr118Cys,ENST00000371180,;TM2D1,missense_variant,p.Tyr56Cys,ENST00000606498,NM_032027.2;TM2D1,splice_region_variant,,ENST00000371178,;TM2D1,intron_variant,,ENST00000488206,;TM2D1,intron_variant,,ENST00000468586,;TM2D1,intron_variant,,ENST00000496465,;TM2D1,intron_variant,,ENST00000494926,; C ENST00000606498 Transcript missense_variant,splice_region_variant 188/969 167/624 56/207 Y/C tAt/tGt 1 -1 TM2D1 HGNC HGNC:24142 protein_coding YES CCDS65554.1 ENSP00000475700 Q9BX74 UPI000006D36C NM_032027.2 deleterious(0) 2/7 hmmpanther:PTHR21016,hmmpanther:PTHR21016:SF1 MODERATE 1 SNV 5 1 PASS . . 0 176 29 5 0 0 0 0 -11.59831 0.7880733 0 1 1 0 C 3 2 62 61723784 61723784 T C 1 0 0 0 0 1 0 0 0 16408 1420 49 5 5 TM2D1 1 61723784 Missense_Mutation SNP T C3N-00704_T 6724435 61723784 187232638 21 19158 IL23R 0 . GRCh38 1 67219682 67219682 + Missense_Mutation SNP T T C C3N-00704_T C3N-00704_N T T c.907T>C p.Tyr303His p.Y303H ENST00000347310 7/11 483 405 78 665 665 0 strelka-varscan-mutect IL23R,missense_variant,p.Tyr303His,ENST00000347310,NM_144701.2;IL23R,missense_variant,p.Tyr100His,ENST00000637002,;IL23R,missense_variant,p.Tyr48His,ENST00000425614,;IL23R,5_prime_UTR_variant,,ENST00000395227,;C1orf141,intron_variant,,ENST00000371007,NM_001276351.1;C1orf141,intron_variant,,ENST00000448166,;IL23R,missense_variant,p.Tyr48His,ENST00000473881,; C ENST00000347310 Transcript missense_variant 1078/2912 907/1890 303/629 Y/H Tac/Cac COSM5659033 1 1 IL23R HGNC HGNC:19100 protein_coding YES CCDS637.1 ENSP00000321345 Q5VWK5 UPI000004CACD NM_144701.2 tolerated(0.27) 7/11 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF112,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 67219682 67219682 T C 1 0 0 0 0 1 0 0 0 7579 1638 57 5 5 IL23R 1 67219682 Missense_Mutation SNP T C3N-00704_T 5495898 67219682 181736740 22 19159 DEPDC1 0 . GRCh38 1 68482723 68482723 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1085C>G p.Thr362Ser p.T362S ENST00000456315 8/12 85 74 11 147 147 0 strelka-varscan-mutect DEPDC1,missense_variant,p.Thr362Ser,ENST00000456315,NM_001114120.2;DEPDC1,intron_variant,,ENST00000370966,NM_017779.5;DEPDC1,downstream_gene_variant,,ENST00000525124,;RP4-694A7.2,intron_variant,,ENST00000425820,;DEPDC1,missense_variant,p.Thr275Ser,ENST00000489862,;DEPDC1,upstream_gene_variant,,ENST00000488146,; C ENST00000456315 Transcript missense_variant 1200/5331 1085/2436 362/811 T/S aCt/aGt 1 -1 DEPDC1 HGNC HGNC:22949 protein_coding YES CCDS44159.1 ENSP00000412292 Q5TB30 UPI0000204557 NM_001114120.2 tolerated(0.84) 8/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 68482723 68482723 G C 1 0 0 0 0 1 0 0 0 4245 1029 36 4 4 DEPDC1 1 68482723 Missense_Mutation SNP G C3N-00704_T 1263041 68482723 180473699 23 19160 LRRC7 0 . GRCh38 1 70023145 70023145 + Missense_Mutation SNP C C T rs752772068 C3N-00704_T C3N-00704_N C C c.1451C>T p.Pro484Leu p.P484L ENST00000035383 15/25 29 25 4 24 24 0 strelka-mutect LRRC7,missense_variant,p.Pro489Leu,ENST00000310961,;LRRC7,missense_variant,p.Pro484Leu,ENST00000035383,NM_020794.2;LRRC7,intron_variant,,ENST00000415775,;RP11-181B18.1,intron_variant,,ENST00000414132,;RP11-181B18.1,upstream_gene_variant,,ENST00000425754,; T ENST00000035383 Transcript missense_variant 1481/5000 1451/4614 484/1537 P/L cCc/cTc rs752772068 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated(0.25) 15/25 MODERATE 1 SNV 1 1 PASS rs752772068 . 1 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 70023145 70023145 C T 1 0 0 0 0 1 0 0 0 8916 623 22 3 3 LRRC7 1 70023145 Missense_Mutation SNP C C3N-00704_T 1540422 70023145 178933277 24 19161 LRRC7 0 . GRCh38 1 70038591 70038591 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2653C>T p.Pro885Ser p.P885S ENST00000035383 19/25 255 211 44 298 298 0 strelka-varscan-mutect LRRC7,missense_variant,p.Pro890Ser,ENST00000310961,;LRRC7,missense_variant,p.Pro885Ser,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Pro169Ser,ENST00000415775,; T ENST00000035383 Transcript missense_variant 2683/5000 2653/4614 885/1537 P/S Cct/Tct 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated_low_confidence(0.22) 19/25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 70038591 70038591 C T 1 0 0 0 0 1 0 0 0 8916 507 18 3 3 LRRC7 1 70038591 Missense_Mutation SNP C C3N-00704_T 15446 70038591 178917831 25 19162 LRRC40 0 . GRCh38 1 70184784 70184784 + Splice_Site SNP C C T novel C3N-00704_T C3N-00704_N C C c.537+1G>A p.X179_splice ENST00000370952 46 42 4 170 170 0 strelka-varscan-mutect LRRC40,splice_donor_variant,,ENST00000370952,NM_017768.4;RN7SL242P,upstream_gene_variant,,ENST00000491451,; T ENST00000370952 Transcript splice_donor_variant -/2884 537/1809 179/602 1 -1 LRRC40 HGNC HGNC:26004 protein_coding YES CCDS646.1 ENSP00000359990 Q9H9A6 A0A140VJN3 UPI000004A0A0 NM_017768.4 4/14 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -10.54955 1 1 1 1 0 T 5 4 62 70184784 70184784 C T 1 0 0 0 0 0 0 1 0 8894 579 20 3 3 LRRC40 1 70184784 Splice_Site SNP C C3N-00704_T 146193 70184784 178771638 26 19163 SRSF11 0 . GRCh38 1 70232212 70232212 + Missense_Mutation SNP G G T rs759175040 C3N-00704_T C3N-00704_N G G c.102G>T p.Leu34Phe p.L34F ENST00000370949 1/10 258 222 36 375 373 2 strelka-varscan-mutect SRSF11,missense_variant,p.Leu34Phe,ENST00000370949,;SRSF11,intron_variant,,ENST00000370950,NM_004768.3;SRSF11,intron_variant,,ENST00000370951,NM_001190987.1;SRSF11,intron_variant,,ENST00000395136,;SRSF11,intron_variant,,ENST00000484162,;SRSF11,intron_variant,,ENST00000486667,;SRSF11,intron_variant,,ENST00000481648,;SRSF11,downstream_gene_variant,,ENST00000463116,;SRSF11,downstream_gene_variant,,ENST00000469170,;SRSF11,downstream_gene_variant,,ENST00000463877,;SRSF11,intron_variant,,ENST00000473950,;SRSF11,intron_variant,,ENST00000475204,; T ENST00000370949 Transcript missense_variant 665/3034 102/1275 34/424 L/F ttG/ttT rs759175040 1 1 SRSF11 HGNC HGNC:10782 protein_coding ENSP00000359987 Q5T757 UPI0000373D3B tolerated_low_confidence(0.17) 1/10 MODERATE SNV 1 1 PASS rs759175040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 70232212 70232212 G T 1 0 0 0 0 1 0 0 0 15537 1368 48 2 2 SRSF11 1 70232212 Missense_Mutation SNP G C3N-00704_T 47428 70232212 178724210 27 19164 LRRIQ3 0 . GRCh38 1 74041532 74041532 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1399G>T p.Ala467Ser p.A467S ENST00000354431 7/8 53 42 11 134 133 1 strelka-varscan-mutect LRRIQ3,missense_variant,p.Ala467Ser,ENST00000354431,NM_001105659.1;LRRIQ3,missense_variant,p.Ala467Ser,ENST00000395089,;LRRIQ3,intron_variant,,ENST00000417067,;LRRIQ3,intron_variant,,ENST00000415760,; A ENST00000354431 Transcript missense_variant 1591/2849 1399/1875 467/624 A/S Gct/Tct 1 -1 LRRIQ3 HGNC HGNC:28318 protein_coding YES CCDS41350.1 ENSP00000346414 A6PVS8 UPI000155D493 NM_001105659.1 tolerated(0.62) 7/8 MODERATE 1 SNV 5 1 PASS rs1177821357 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 74041532 74041532 C A 1 0 0 0 0 1 0 0 0 8936 710 25 2 2 LRRIQ3 1 74041532 Missense_Mutation SNP C C3N-00704_T 3809320 74041532 174914890 28 19165 PRKACB 0 . GRCh38 1 84185115 84185115 + Missense_Mutation SNP T T G novel C3N-00704_T C3N-00704_N T T c.493T>G p.Tyr165Asp p.Y165D ENST00000370685 5/10 41 33 8 105 105 0 strelka-varscan-mutect PRKACB,missense_variant,p.Tyr118Asp,ENST00000370689,NM_002731.3;PRKACB,missense_variant,p.Tyr165Asp,ENST00000370685,NM_182948.3;PRKACB,missense_variant,p.Tyr124Asp,ENST00000614872,NM_001242860.2;PRKACB,missense_variant,p.Tyr124Asp,ENST00000394838,;PRKACB,missense_variant,p.Tyr122Asp,ENST00000370682,NM_001242859.2;PRKACB,missense_variant,p.Tyr106Asp,ENST00000610703,NM_001242858.2;PRKACB,missense_variant,p.Tyr105Asp,ENST00000610457,NM_001242862.2;PRKACB,missense_variant,p.Tyr88Asp,ENST00000394839,NM_001242861.2;PRKACB,missense_variant,p.Tyr124Asp,ENST00000370680,NM_001300915.1;PRKACB,missense_variant,p.Tyr118Asp,ENST00000370688,NM_207578.2;PRKACB,missense_variant,p.Tyr125Asp,ENST00000446538,NM_001242857.2;PRKACB,missense_variant,p.Tyr121Asp,ENST00000450730,;PRKACB,missense_variant,p.Tyr106Asp,ENST00000370684,NM_001300917.1;PRKACB,missense_variant,p.Tyr113Asp,ENST00000413538,;PRKACB,missense_variant,p.Tyr105Asp,ENST00000417530,;PRKACB,missense_variant,p.Tyr114Asp,ENST00000432111,;PRKACB,missense_variant,p.Tyr122Asp,ENST00000436133,;PRKACB,non_coding_transcript_exon_variant,,ENST00000470673,;PRKACB,downstream_gene_variant,,ENST00000467507,; G ENST00000370685 Transcript missense_variant 584/4481 493/1197 165/398 Y/D Tac/Gac 1 1 PRKACB HGNC HGNC:9381 protein_coding YES CCDS693.1 ENSP00000359719 P22694 UPI00001A9CCB NM_182948.3 deleterious(0) 5/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24353,hmmpanther:PTHR24353:SF74,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.8501 1 1 1 1 0 G 3 3 62 84185115 84185115 T G 1 0 0 0 0 1 0 0 0 12631 1406 49 5 5 PRKACB 1 84185115 Missense_Mutation SNP T C3N-00704_T 10143583 84185115 164771307 29 19166 CLCA4 0 . GRCh38 1 86567495 86567495 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.1026C>A p.= p.S342S ENST00000370563 7/14 183 159 24 236 235 1 strelka-varscan-mutect CLCA4,synonymous_variant,p.=,ENST00000370563,NM_012128.3;RP4-651E10.4,downstream_gene_variant,,ENST00000456587,;CLCA4,upstream_gene_variant,,ENST00000496322,; A ENST00000370563 Transcript synonymous_variant 1068/3211 1026/2760 342/919 S tcC/tcA 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 7/14 PROSITE_profiles:PS50234,hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Gene3D:3.40.50.410,Pfam_domain:PF00092,Pfam_domain:PF08434,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 86567495 86567495 C A 1 0 0 0 0 0 0 0 1 3223 668 24 2 2 CLCA4 1 86567495 Silent SNP C C3N-00704_T 2382380 86567495 162388927 30 19167 ZNF644 0 . GRCh38 1 90938338 90938338 + Missense_Mutation SNP T T A C3N-00704_T C3N-00704_N T T c.3016A>T p.Thr1006Ser p.T1006S ENST00000337393 3/6 160 132 28 199 199 0 strelka-varscan-mutect ZNF644,missense_variant,p.Thr1006Ser,ENST00000337393,NM_201269.2;ZNF644,missense_variant,p.Thr1006Ser,ENST00000370440,;ZNF644,missense_variant,p.Thr578Ser,ENST00000621077,;ZNF644,intron_variant,,ENST00000347275,NM_016620.3;ZNF644,intron_variant,,ENST00000361321,NM_032186.4;ZNF644,intron_variant,,ENST00000467231,;ZNF644,upstream_gene_variant,,ENST00000479798,;ZNF644,downstream_gene_variant,,ENST00000498303,; A ENST00000337393 Transcript missense_variant 3299/5763 3016/3984 1006/1327 T/S Aca/Tca COSM913143 1 -1 ZNF644 HGNC HGNC:29222 protein_coding YES CCDS731.1 ENSP00000337008 Q9H582 UPI000004A010 NM_201269.2 tolerated(0.91) 3/6 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 90938338 90938338 T A 1 0 0 0 0 1 0 0 0 18633 1696 59 4 4 ZNF644 1 90938338 Missense_Mutation SNP T C3N-00704_T 4370843 90938338 158018084 31 19168 BRDT 0 . GRCh38 1 92005217 92005217 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2705C>A p.Ala902Asp p.A902D ENST00000399546 18/19 85 77 8 111 111 0 strelka-varscan-mutect BRDT,missense_variant,p.Ala825Asp,ENST00000370389,NM_001242810.2;BRDT,missense_variant,p.Ala898Asp,ENST00000362005,NM_001242805.2,NM_207189.3;BRDT,missense_variant,p.Ala902Asp,ENST00000399546,NM_001242806.2;BRDT,missense_variant,p.Ala852Asp,ENST00000394530,NM_001242808.2,NM_001242807.2;BRDT,missense_variant,p.Ala898Asp,ENST00000402388,NM_001726.4; A ENST00000399546 Transcript missense_variant 3054/3357 2705/2856 902/951 A/D gCt/gAt 1 1 BRDT HGNC HGNC:1105 protein_coding YES CCDS72820.1 ENSP00000387822 Q58F21 UPI000292A27D NM_001242806.2 tolerated(0.07) 18/19 MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -17.21187 1 1 1 1 0 A 3 1 62 92005217 92005217 C A 1 0 0 0 0 1 0 0 0 1678 797 28 2 2 BRDT 1 92005217 Missense_Mutation SNP C C3N-00704_T 1066879 92005217 156951205 32 19169 PLPPR5 0 . GRCh38 1 98953281 98953281 + Missense_Mutation SNP A A C novel C3N-00704_T C3N-00704_N A A c.410T>G p.Val137Gly p.V137G ENST00000263177 3/6 294 231 63 329 329 0 strelka-varscan-mutect PLPPR5,missense_variant,p.Val137Gly,ENST00000370188,NM_001010861.2;PLPPR5,missense_variant,p.Val137Gly,ENST00000263177,NM_001037317.1; C ENST00000263177 Transcript missense_variant 632/3288 410/966 137/321 V/G gTa/gGa 1 -1 PLPPR5 HGNC HGNC:31703 protein_coding YES CCDS30778.1 ENSP00000263177 Q32ZL2 UPI0000048D53 NM_001037317.1 deleterious(0.01) 3/6 Gene3D:1.20.144.10,Pfam_domain:PF01569,hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF17,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 98953281 98953281 A C 1 0 0 0 0 1 0 0 0 12213 391 14 5 5 PLPPR5 1 98953281 Missense_Mutation SNP A C3N-00704_T 6948064 98953281 150003141 33 19170 SASS6 0 . GRCh38 1 100107914 100107914 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.952A>T p.Asn318Tyr p.N318Y ENST00000287482 9/17 197 177 20 357 357 0 strelka-varscan-mutect SASS6,missense_variant,p.Asn318Tyr,ENST00000287482,NM_001304829.1,NM_194292.2;SASS6,non_coding_transcript_exon_variant,,ENST00000462159,; A ENST00000287482 Transcript missense_variant 1093/3880 952/1974 318/657 N/Y Aat/Tat 1 -1 SASS6 HGNC HGNC:25403 protein_coding YES CCDS764.1 ENSP00000287482 Q6UVJ0 UPI00001BDF30 NM_001304829.1,NM_194292.2 deleterious(0) 9/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF279 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 100107914 100107914 T A 1 0 0 0 0 1 0 0 0 14111 1754 61 4 4 SASS6 1 100107914 Missense_Mutation SNP T C3N-00704_T 1154633 100107914 148848508 34 19171 COL11A1 0 . GRCh38 1 102914766 102914766 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.3862G>T p.Gly1288Ter p.G1288* ENST00000370096 51/67 303 250 53 324 323 1 strelka-varscan-mutect COL11A1,stop_gained,p.Gly1300Ter,ENST00000358392,NM_080629.2;COL11A1,stop_gained,p.Gly1288Ter,ENST00000370096,NM_001854.3;COL11A1,stop_gained,p.Gly1249Ter,ENST00000353414,NM_001190709.1;COL11A1,stop_gained,p.Gly1172Ter,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; A ENST00000370096 Transcript stop_gained 4175/7286 3862/5421 1288/1806 G/* Gga/Tga 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 51/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 102914766 102914766 C A 1 0 0 0 0 0 1 0 0 3455 603 21 2 2 COL11A1 1 102914766 Nonsense_Mutation SNP C C3N-00704_T 2806852 102914766 146041656 35 19172 NTNG1 0 . GRCh38 1 107324414 107324414 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.379C>G p.Pro127Ala p.P127A ENST00000370068 3/8 370 303 67 431 431 0 strelka-varscan-mutect NTNG1,missense_variant,p.Pro127Ala,ENST00000370067,;NTNG1,missense_variant,p.Pro127Ala,ENST00000370068,;NTNG1,missense_variant,p.Pro127Ala,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Pro127Ala,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Pro127Ala,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Pro127Ala,ENST00000370065,;NTNG1,missense_variant,p.Pro127Ala,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; G ENST00000370068 Transcript missense_variant 1225/4034 379/1620 127/539 P/A Ccc/Gcc 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.60.120.260,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 107324414 107324414 C G 1 0 0 0 0 1 0 0 0 10769 855 30 4 4 NTNG1 1 107324414 Missense_Mutation SNP C C3N-00704_T 4409648 107324414 141632008 36 19173 VAV3 0 . GRCh38 1 107574172 107574172 + Missense_Mutation SNP C C T C3N-00704_T C3N-00704_N C C c.2377G>A p.Ala793Thr p.A793T ENST00000370056 26/27 141 123 18 121 121 0 strelka-varscan-mutect VAV3,missense_variant,p.Ala793Thr,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Ala821Thr,ENST00000527011,;VAV3,missense_variant,p.Ala233Thr,ENST00000415432,NM_001079874.1;VAV3,non_coding_transcript_exon_variant,,ENST00000343258,;VAV3,non_coding_transcript_exon_variant,,ENST00000525460,;VAV3,3_prime_UTR_variant,,ENST00000529413,; T ENST00000370056 Transcript missense_variant 2652/4990 2377/2544 793/847 A/T Gcc/Acc COSM1151780,COSM893319 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 deleterious(0.02) 26/27 PROSITE_profiles:PS50002,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00452 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 107574172 107574172 C T 1 0 0 0 0 1 0 0 0 17678 710 25 3 3 VAV3 1 107574172 Missense_Mutation SNP C C3N-00704_T 249758 107574172 141382250 37 19174 PRPF38B 0 . GRCh38 1 108699838 108699838 + Nonsense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.1459A>T p.Lys487Ter p.K487* ENST00000370025 6/6 114 90 24 138 138 0 strelka-varscan-mutect PRPF38B,stop_gained,p.Lys376Ter,ENST00000370021,;PRPF38B,stop_gained,p.Lys487Ter,ENST00000370025,NM_018061.2;PRPF38B,downstream_gene_variant,,ENST00000370022,;PRPF38B,downstream_gene_variant,,ENST00000467302,;PRPF38B,downstream_gene_variant,,ENST00000485810,; T ENST00000370025 Transcript stop_gained 1728/3693 1459/1641 487/546 K/* Aaa/Taa 1 1 PRPF38B HGNC HGNC:25512 protein_coding YES CCDS788.1 ENSP00000359042 Q5VTL8 UPI000013CF13 NM_018061.2 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR23142 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 108699838 108699838 A T 1 0 0 0 0 0 1 0 0 12704 15 1 4 4 PRPF38B 1 108699838 Nonsense_Mutation SNP A C3N-00704_T 1125666 108699838 140256584 38 19175 AKNAD1 0 . GRCh38 1 108834962 108834962 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1631C>A p.Pro544His p.P544H ENST00000370001 8/16 70 59 11 76 76 0 strelka-varscan-mutect AKNAD1,missense_variant,p.Pro544His,ENST00000370001,NM_152763.4;AKNAD1,missense_variant,p.Pro544His,ENST00000369995,;AKNAD1,missense_variant,p.Pro514His,ENST00000369994,;RP11-475E11.9,downstream_gene_variant,,ENST00000357393,;AKNAD1,missense_variant,p.Pro544His,ENST00000461774,;AKNAD1,intron_variant,,ENST00000474186,;AKNAD1,downstream_gene_variant,,ENST00000472781,;AKNAD1,upstream_gene_variant,,ENST00000603450,; T ENST00000370001 Transcript missense_variant 1900/3053 1631/2511 544/836 P/H cCc/cAc 1 -1 AKNAD1 HGNC HGNC:28398 protein_coding YES CCDS791.2 ENSP00000359018 Q5T1N1 UPI00004700A0 NM_152763.4 tolerated(0.6) 8/16 hmmpanther:PTHR21510,hmmpanther:PTHR21510:SF16 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 62 108834962 108834962 G T 1 0 0 0 0 1 0 0 0 548 1232 43 2 2 AKNAD1 1 108834962 Missense_Mutation SNP G C3N-00704_T 135124 108834962 140121460 39 19176 KCNA2 0 . GRCh38 1 110604391 110604391 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.392G>T p.Gly131Val p.G131V ENST00000633222 3/3 378 311 67 486 486 0 strelka-varscan-mutect KCNA2,missense_variant,p.Gly131Val,ENST00000633222,;KCNA2,missense_variant,p.Gly131Val,ENST00000485317,;KCNA2,missense_variant,p.Gly131Val,ENST00000316361,NM_004974.3;KCNA2,missense_variant,p.Gly131Val,ENST00000369770,NM_001204269.1;KCNA2,intron_variant,,ENST00000525120,; A ENST00000633222 Transcript missense_variant 1066/11877 392/1500 131/499 G/V gGc/gTc 1 -1 KCNA2 HGNC HGNC:6220 protein_coding YES CCDS827.1 ENSP00000487785 P16389 UPI00001279A1 deleterious(0) 3/3 Gene3D:3.30.710.10,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF23,SMART_domains:SM00225 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 110604391 110604391 C A 1 0 0 0 0 1 0 0 0 7919 739 26 2 2 KCNA2 1 110604391 Missense_Mutation SNP C C3N-00704_T 1769429 110604391 138352031 40 19177 HSD3B1 0 . GRCh38 1 119514530 119514530 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1007G>T p.Arg336Leu p.R336L ENST00000369413 4/4 265 232 33 283 282 1 strelka-varscan-mutect HSD3B1,missense_variant,p.Arg336Leu,ENST00000369413,NM_000862.2;HSD3B1,missense_variant,p.Arg336Leu,ENST00000528909,;HSD3B1,downstream_gene_variant,,ENST00000531340,;HSD3B1,downstream_gene_variant,,ENST00000492140,; T ENST00000369413 Transcript missense_variant 1152/1676 1007/1122 336/373 R/L cGa/cTa 1 1 HSD3B1 HGNC HGNC:5217 protein_coding YES CCDS903.1 ENSP00000358421 P14060 UPI0000036BD2 NM_000862.2 deleterious(0) 4/4 Gene3D:3.40.50.720,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF378,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs1224855842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 119514530 119514530 G T 1 0 0 0 0 1 0 0 0 7284 1058 37 1 1 HSD3B1 1 119514530 Missense_Mutation SNP G C3N-00704_T 8910139 119514530 129441892 41 19178 NBPF26 0 . GRCh38 1 120810379 120810379 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.1385C>T p.Pro462Leu p.P462L ENST00000620612 9/30 641 546 95 617 617 0 strelka-varscan-mutect NBPF26,missense_variant,p.Pro462Leu,ENST00000620612,;NBPF26,missense_variant,p.Pro200Leu,ENST00000617913,;NBPF26,missense_variant,p.Pro200Leu,ENST00000611287,;NBPF26,missense_variant,p.Pro165Leu,ENST00000615145,;NBPF26,5_prime_UTR_variant,,ENST00000619748,;NBPF26,intron_variant,,ENST00000615219,;NBPF26,intron_variant,,ENST00000611702,;NBPF26,upstream_gene_variant,,ENST00000609741,; T ENST00000620612 Transcript missense_variant 1614/4602 1385/4347 462/1448 P/L cCt/cTt 1 1 NBPF26 HGNC HGNC:49571 protein_coding YES ENSP00000481542 A0A087WY62 tolerated(0.18) 9/30 Pfam_domain:PF06758,PROSITE_profiles:PS51316,SMART_domains:SM01148 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 120810379 120810379 C T 1 0 0 0 0 1 0 0 0 10211 681 24 3 3 NBPF26 1 120810379 Missense_Mutation SNP C C3N-00704_T 1295849 120810379 128146043 42 19179 CERS2 0 . GRCh38 1 150968154 150968154 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.339G>T p.Gln113His p.Q113H ENST00000271688 4/11 216 195 21 244 244 0 strelka-varscan-mutect CERS2,missense_variant,p.Gln113His,ENST00000271688,NM_181746.3;CERS2,missense_variant,p.Gln113His,ENST00000368954,NM_022075.4;CERS2,missense_variant,p.Gln104His,ENST00000561294,;CERS2,missense_variant,p.Gln113His,ENST00000368949,;CERS2,missense_variant,p.Gln113His,ENST00000361419,;CERS2,missense_variant,p.Gln113His,ENST00000558062,;CERS2,missense_variant,p.Gln113His,ENST00000421609,;CERS2,missense_variant,p.Gln113His,ENST00000457392,;SETDB1,downstream_gene_variant,,ENST00000271640,NM_001145415.1;SETDB1,downstream_gene_variant,,ENST00000368969,NM_012432.3;SETDB1,downstream_gene_variant,,ENST00000498193,;CERS2,upstream_gene_variant,,ENST00000560793,;RP11-316M1.12,downstream_gene_variant,,ENST00000561111,;RP11-316M1.12,downstream_gene_variant,,ENST00000560481,;RP11-316M1.3,upstream_gene_variant,,ENST00000412838,;CERS2,non_coding_transcript_exon_variant,,ENST00000345896,;CERS2,non_coding_transcript_exon_variant,,ENST00000460664,;CERS2,non_coding_transcript_exon_variant,,ENST00000559020,;SETDB1,downstream_gene_variant,,ENST00000497314,;CERS2,upstream_gene_variant,,ENST00000482825,;SETDB1,downstream_gene_variant,,ENST00000533529,;CERS2,upstream_gene_variant,,ENST00000559660,; A ENST00000271688 Transcript missense_variant 765/2544 339/1143 113/380 Q/H caG/caT 1 -1 CERS2 HGNC HGNC:14076 protein_coding YES CCDS973.1 ENSP00000271688 Q96G23 UPI0000001237 NM_181746.3 deleterious(0.02) 4/11 PROSITE_profiles:PS50071,hmmpanther:PTHR12560:SF7,hmmpanther:PTHR12560,PIRSF_domain:PIRSF005225,Pfam_domain:PF00046,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 MODERATE SNV 5 1 PASS rs1480342063 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 150968154 150968154 C A 1 0 0 0 0 1 0 0 0 2996 680 24 2 2 CERS2 1 150968154 Missense_Mutation SNP C C3N-00704_T 30157775 150968154 97988268 43 19180 FLG 0 . GRCh38 1 152307387 152307387 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.7499G>T p.Arg2500Met p.R2500M ENST00000368799 3/3 525 456 69 571 570 1 strelka-varscan-mutect FLG,missense_variant,p.Arg2500Met,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript missense_variant 7535/12747 7499/12186 2500/4061 R/M aGg/aTg 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 152307387 152307387 C A 1 0 0 0 0 1 0 0 0 5784 681 24 2 2 FLG 1 152307387 Missense_Mutation SNP C C3N-00704_T 1339233 152307387 96649035 44 19181 KPRP 0 . GRCh38 1 152760359 152760359 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.771T>A p.= p.P257P ENST00000606109 1/1 282 236 46 288 288 0 strelka-varscan-mutect KPRP,synonymous_variant,p.=,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript synonymous_variant 799/2492 771/1740 257/579 P ccT/ccA 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 1/1 Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 152760359 152760359 T A 1 0 0 0 0 0 0 0 1 8316 1538 54 4 4 KPRP 1 152760359 Silent SNP T C3N-00704_T 452972 152760359 96196063 45 19182 IVL 0 . GRCh38 1 152910595 152910595 + Silent SNP G G T rs753903760 C3N-00704_T C3N-00704_N G G c.798G>T p.= p.L266L ENST00000368764 2/2 163 111 52 203 203 0 strelka-varscan-mutect IVL,synonymous_variant,p.=,ENST00000368764,NM_005547.2; T ENST00000368764 Transcript synonymous_variant 862/2153 798/1758 266/585 L ctG/ctT rs753903760 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 2/2 Pfam_domain:PF00904 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 152910595 152910595 G T 1 0 0 0 0 0 0 0 1 7835 1335 47 2 2 IVL 1 152910595 Silent SNP G C3N-00704_T 150236 152910595 96045827 46 19183 PGLYRP3 0 . GRCh38 1 153303917 153303917 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.469C>A p.Pro157Thr p.P157T ENST00000290722 4/7 208 184 24 176 176 0 strelka-varscan-mutect PGLYRP3,missense_variant,p.Pro157Thr,ENST00000290722,NM_052891.2; T ENST00000290722 Transcript missense_variant 522/1173 469/1026 157/341 P/T Cca/Aca 1 -1 PGLYRP3 HGNC HGNC:30014 protein_coding YES CCDS1035.1 ENSP00000290722 Q96LB9 UPI000006F12B NM_052891.2 deleterious(0) 4/7 hmmpanther:PTHR11022,hmmpanther:PTHR11022:SF12,Pfam_domain:PF01510,SMART_domains:SM00701,SMART_domains:SM00644,Superfamily_domains:SSF55846 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 153303917 153303917 G T 1 0 0 0 0 1 0 0 0 11884 1203 42 2 2 PGLYRP3 1 153303917 Missense_Mutation SNP G C3N-00704_T 393322 153303917 95652505 47 19184 GBA 0 . GRCh38 1 155239657 155239657 + Frame_Shift_Del DEL G G - rs759174705 C3N-00704_T C3N-00704_N G G c.413delC p.Pro138LeufsTer62 p.P138Lfs*62 ENST00000327247 5/12 564 377 187 532 532 0 sindel-varindel-pindel GBA,frameshift_variant,p.Pro138LeufsTer62,ENST00000327247,NM_001005741.2,NM_001005742.2;GBA,frameshift_variant,p.Pro138LeufsTer62,ENST00000368373,NM_000157.3;GBA,frameshift_variant,p.Pro51LeufsTer62,ENST00000428024,NM_001171811.1;GBA,intron_variant,,ENST00000427500,NM_001171812.1;GBA,non_coding_transcript_exon_variant,,ENST00000493842,;GBA,non_coding_transcript_exon_variant,,ENST00000473570,;GBA,non_coding_transcript_exon_variant,,ENST00000467918,;GBA,intron_variant,,ENST00000484489,;GBA,intron_variant,,ENST00000497670,;GBA,upstream_gene_variant,,ENST00000478472,;GBA,upstream_gene_variant,,ENST00000491081,;GBA,upstream_gene_variant,,ENST00000460156,;GBA,upstream_gene_variant,,ENST00000464536,;GBA,downstream_gene_variant,,ENST00000470104,; - ENST00000327247 Transcript frameshift_variant 646/2387 413/1611 138/536 P/X cCt/ct rs759174705,COSM252517,COSM252999 1 -1 GBA HGNC HGNC:4177 protein_coding YES CCDS1102.1 ENSP00000314508 P04062 A0A068F658 UPI0000073DCE NM_001005741.2,NM_001005742.2 5/12 hmmpanther:PTHR11069:SF9,hmmpanther:PTHR11069,Pfam_domain:PF02055,Gene3D:3.20.20.80,Superfamily_domains:SSF51445,Superfamily_domains:SSF51011 0,1,1 HIGH 1 deletion 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 155239657 155239657 G - 1 0 1 0 1 0 0 0 0 6138 1000 35 0 0 GBA 1 155239657 Frame_Shift_Del DEL G C3N-00704_T 1935740 155239657 93716765 48 19185 YY1AP1 0 . GRCh38 1 155676637 155676637 + Missense_Mutation SNP C C T rs763431851 C3N-00704_T C3N-00704_N C C c.649G>A p.Glu217Lys p.E217K ENST00000368339 4/10 630 596 34 535 535 0 strelka-varscan-mutect YY1AP1,missense_variant,p.Glu217Lys,ENST00000368339,NM_001198903.1;YY1AP1,missense_variant,p.Glu217Lys,ENST00000368340,NM_001198904.1;YY1AP1,missense_variant,p.Glu68Lys,ENST00000361831,NM_018253.3,NM_139121.2;YY1AP1,missense_variant,p.Glu68Lys,ENST00000407221,;YY1AP1,missense_variant,p.Glu68Lys,ENST00000359205,NM_001198899.1,NM_001198900.1;YY1AP1,missense_variant,p.Glu68Lys,ENST00000311573,;YY1AP1,missense_variant,p.Glu79Lys,ENST00000355499,NM_139119.2;YY1AP1,missense_variant,p.Glu79Lys,ENST00000404643,NM_001198905.1;YY1AP1,missense_variant,p.Glu145Lys,ENST00000295566,NM_001198906.1,NM_139118.2;YY1AP1,missense_variant,p.Glu79Lys,ENST00000368330,NM_001198901.1;YY1AP1,missense_variant,p.Glu79Lys,ENST00000347088,NM_001198902.1;YY1AP1,missense_variant,p.Glu217Lys,ENST00000405763,;YY1AP1,missense_variant,p.Glu68Lys,ENST00000443231,;YY1AP1,missense_variant,p.Glu79Lys,ENST00000454523,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000476093,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000493625,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000476027,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000466366,;YY1AP1,upstream_gene_variant,,ENST00000488784,;YY1AP1,upstream_gene_variant,,ENST00000477470,;YY1AP1,missense_variant,p.Glu79Lys,ENST00000361140,;YY1AP1,missense_variant,p.Glu79Lys,ENST00000354691,;YY1AP1,3_prime_UTR_variant,,ENST00000436865,;YY1AP1,non_coding_transcript_exon_variant,,ENST00000496324,; T ENST00000368339 Transcript missense_variant 841/3073 649/2667 217/888 E/K Gag/Aag rs763431851 1 -1 YY1AP1 HGNC HGNC:30935 protein_coding YES CCDS55645.1 ENSP00000357323 Q9H869 UPI0001AE792F NM_001198903.1 deleterious(0.01) 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR16088,hmmpanther:PTHR16088:SF9 MODERATE 1 SNV 2 1 PASS rs763431851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 155676637 155676637 C T 1 0 0 0 0 1 0 0 0 18069 922 32 3 3 YY1AP1 1 155676637 Missense_Mutation SNP C C3N-00704_T 436980 155676637 93279785 49 19186 NTRK1 0 . GRCh38 1 156866914 156866914 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.364C>A p.Leu122Ile p.L122I ENST00000524377 4/17 604 406 198 594 594 0 strelka-varscan-mutect NTRK1,missense_variant,p.Leu122Ile,ENST00000368196,NM_001012331.1;NTRK1,missense_variant,p.Leu92Ile,ENST00000392302,NM_001007792.1;NTRK1,missense_variant,p.Leu122Ile,ENST00000358660,;NTRK1,missense_variant,p.Leu122Ile,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,missense_variant,p.Leu92Ile,ENST00000497019,;NTRK1,non_coding_transcript_exon_variant,,ENST00000530298,;NTRK1,downstream_gene_variant,,ENST00000533630,; A ENST00000524377 Transcript missense_variant 405/2432 364/2391 122/796 L/I Ctc/Atc COSM4023441,COSM4023442 1 1 NTRK1 HGNC HGNC:8031 protein_coding YES CCDS1161.1 ENSP00000431418 P04629 UPI000013D5D3 NM_002529.3 deleterious(0.02) 4/17 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF370,Gene3D:3.80.10.10,Pfam_domain:PF13855,Superfamily_domains:SSF52058 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 156866914 156866914 C A 1 0 0 0 0 1 0 0 0 10772 927 32 2 2 NTRK1 1 156866914 Missense_Mutation SNP C C3N-00704_T 1190277 156866914 92089508 50 19187 CD1E 0 . GRCh38 1 158355948 158355948 + Missense_Mutation SNP G G T rs150649106 C3N-00704_T C3N-00704_N G G c.747G>T p.Gln249His p.Q249H ENST00000368167 4/6 203 171 32 207 207 0 strelka-varscan-mutect CD1E,missense_variant,p.Gln150His,ENST00000444681,NM_001185114.1;CD1E,missense_variant,p.Gln249His,ENST00000368160,NM_001042583.2;CD1E,missense_variant,p.Gln249His,ENST00000368161,NM_001042584.2;CD1E,missense_variant,p.Gln249His,ENST00000368167,NM_030893.3;CD1E,missense_variant,p.Gln60His,ENST00000368166,NM_001042586.2;CD1E,missense_variant,p.Gln159His,ENST00000368165,NM_001185107.1;CD1E,missense_variant,p.Gln19His,ENST00000368162,;CD1E,missense_variant,p.Gln60His,ENST00000368164,NM_001042587.2;CD1E,missense_variant,p.Gln159His,ENST00000368156,NM_001185115.1;CD1E,missense_variant,p.Gln60His,ENST00000452291,NM_001185112.1;CD1E,splice_region_variant,,ENST00000368163,NM_001042585.2;CD1E,splice_region_variant,,ENST00000368155,NM_001185108.1;CD1E,splice_region_variant,,ENST00000368154,NM_001185113.1;CD1E,splice_region_variant,,ENST00000368157,NM_001185110.1;CD1E,downstream_gene_variant,,ENST00000464822,; T ENST00000368167 Transcript missense_variant 986/1458 747/1167 249/388 Q/H caG/caT rs150649106,COSM107852 1 1 CD1E HGNC HGNC:1638 protein_coding YES CCDS41417.1 ENSP00000357149 P15812 UPI000046F8C2 NM_030893.3 deleterious(0.03) 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF146,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs150649106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 158355948 158355948 G T 1 0 0 0 0 1 0 0 0 2681 991 35 2 2 CD1E 1 158355948 Missense_Mutation SNP G C3N-00704_T 1489034 158355948 90600474 51 19188 OR10K1 0 . GRCh38 1 158466109 158466109 + Missense_Mutation SNP C C G rs527774086 C3N-00704_T C3N-00704_N C C c.548C>G p.Pro183Arg p.P183R ENST00000289451 1/1 162 143 19 175 175 0 strelka-varscan-mutect OR10K1,missense_variant,p.Pro183Arg,ENST00000289451,NM_001004473.1; G ENST00000289451 Transcript missense_variant 548/942 548/942 183/313 P/R cCt/cGt rs527774086,COSM4499710 1 1 OR10K1 HGNC HGNC:14693 protein_coding YES CCDS30897.1 ENSP00000289451 Q8NGX5 A0A126GV64 UPI0000041B19 NM_001004473.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF325,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 MODERATE 1 SNV 0,1 1 PASS rs527774086 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 158466109 158466109 C G 1 0 0 0 0 1 0 0 0 10990 681 24 4 4 OR10K1 1 158466109 Missense_Mutation SNP C C3N-00704_T 110161 158466109 90490313 52 19189 OR6P1 0 . GRCh38 1 158563484 158563484 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.121G>C p.Glu41Gln p.E41Q ENST00000334632 1/1 223 194 29 220 220 0 strelka-varscan-mutect OR6P1,missense_variant,p.Glu41Gln,ENST00000334632,NM_001160325.1; G ENST00000334632 Transcript missense_variant 121/954 121/954 41/317 E/Q Gag/Cag 1 -1 OR6P1 HGNC HGNC:15036 protein_coding YES CCDS53391.1 ENSP00000334721 Q8NGX9 A0A126GV72 UPI000004B1FF NM_001160325.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 158563484 158563484 C G 1 0 0 0 0 1 0 0 0 11277 864 30 4 4 OR6P1 1 158563484 Missense_Mutation SNP C C3N-00704_T 97375 158563484 90392938 53 19190 OR10Z1 0 . GRCh38 1 158607035 158607035 + Silent SNP C C A rs780817204 C3N-00704_T C3N-00704_N C C c.597C>A p.= p.I199I ENST00000361284 1/1 349 295 54 337 337 0 strelka-varscan-mutect OR10Z1,synonymous_variant,p.=,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000485680,; A ENST00000361284 Transcript synonymous_variant 597/942 597/942 199/313 I atC/atA rs780817204,COSM3476160 1 1 OR10Z1 HGNC HGNC:14996 protein_coding YES CCDS30901.1 ENSP00000354707 Q8NGY1 A0A126GV63 UPI000004CA23 NM_001004478.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 0,1 LOW SNV 0,1 1 PASS rs780817204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 158607035 158607035 C A 1 0 0 0 0 0 0 0 1 10999 903 32 2 2 OR10Z1 1 158607035 Silent SNP C C3N-00704_T 43551 158607035 90349387 54 19191 ITLN1 0 . GRCh38 1 160876690 160876690 + Missense_Mutation SNP C C A rs761780040 C3N-00704_T C3N-00704_N C C c.916G>T p.Ala306Ser p.A306S ENST00000326245 8/8 212 133 79 181 181 0 strelka-varscan-mutect ITLN1,missense_variant,p.Ala306Ser,ENST00000326245,NM_017625.2;ITLN1,downstream_gene_variant,,ENST00000487531,;ITLN1,downstream_gene_variant,,ENST00000464077,; A ENST00000326245 Transcript missense_variant 1032/1183 916/942 306/313 A/S Gca/Tca rs761780040 1 -1 ITLN1 HGNC HGNC:18259 protein_coding YES CCDS1211.1 ENSP00000323587 Q8WWA0 UPI0000032AA3 NM_017625.2 tolerated(0.54) 8/8 hmmpanther:PTHR16146,hmmpanther:PTHR16146:SF38 MODERATE 1 SNV 1 1 PASS rs761780040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 160876690 160876690 C A 1 0 0 0 0 1 0 0 0 7816 739 26 2 2 ITLN1 1 160876690 Missense_Mutation SNP C C3N-00704_T 2269655 160876690 88079732 55 19192 ADAMTS4 0 . GRCh38 1 161192108 161192108 + Missense_Mutation SNP C C A rs3134667 C3N-00704_T C3N-00704_N C C c.2044G>T p.Gly682Cys p.G682C ENST00000367996 8/9 226 143 83 212 212 0 strelka-varscan-mutect ADAMTS4,missense_variant,p.Gly682Cys,ENST00000367996,NM_005099.4;ADAMTS4,downstream_gene_variant,,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000479948,;ADAMTS4,downstream_gene_variant,,ENST00000478394,; A ENST00000367996 Transcript missense_variant 2473/9773 2044/2514 682/837 G/C Ggt/Tgt rs3134667 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 deleterious(0.01) 8/9 hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Prints_domain:PR01857 MODERATE 1 SNV 1 1 PASS rs3134667 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 161192108 161192108 C A 1 0 0 0 0 1 0 0 0 312 652 23 1 1 ADAMTS4 1 161192108 Missense_Mutation SNP C C3N-00704_T 315418 161192108 87764314 56 19193 ADAMTS4 0 . GRCh38 1 161193723 161193723 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.1652T>C p.Val551Ala p.V551A ENST00000367996 6/9 178 136 42 169 169 0 strelka-varscan-mutect ADAMTS4,missense_variant,p.Val551Ala,ENST00000367996,NM_005099.4;ADAMTS4,downstream_gene_variant,,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000496133,;NDUFS2,upstream_gene_variant,,ENST00000479948,;ADAMTS4,downstream_gene_variant,,ENST00000478394,; G ENST00000367996 Transcript missense_variant 2081/9773 1652/2514 551/837 V/A gTc/gCc 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 tolerated(0.21) 6/9 PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 206 0 0 3 0 0 0 -20 0.9851563 1 1 1 0 G 3 3 62 161193723 161193723 A G 1 0 0 0 0 1 0 0 0 312 275 10 5 5 ADAMTS4 1 161193723 Missense_Mutation SNP A C3N-00704_T 1615 161193723 87762699 57 19194 FCRLA 0 . GRCh38 1 161712163 161712163 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.798C>A p.= p.A266A ENST00000367959 5/6 172 114 58 152 152 0 strelka-varscan-mutect FCRLA,synonymous_variant,p.=,ENST00000367959,NM_001184866.1;FCRLA,synonymous_variant,p.=,ENST00000236938,NM_032738.3;FCRLA,synonymous_variant,p.=,ENST00000546024,NM_001184867.1;FCRLA,synonymous_variant,p.=,ENST00000367953,;FCRLA,synonymous_variant,p.=,ENST00000540521,NM_001184870.1;FCRLA,synonymous_variant,p.=,ENST00000367957,NM_001184872.1;FCRLA,synonymous_variant,p.=,ENST00000309691,;FCRLA,synonymous_variant,p.=,ENST00000294796,;FCRLA,intron_variant,,ENST00000367949,NM_001184873.1;FCRLA,intron_variant,,ENST00000350710,NM_001184871.1;FCRLA,intron_variant,,ENST00000349527,;FCRLA,intron_variant,,ENST00000367950,;FCRLA,non_coding_transcript_exon_variant,,ENST00000470841,;FCRLA,downstream_gene_variant,,ENST00000465403,; A ENST00000367959 Transcript synonymous_variant 1040/2362 798/1149 266/382 A gcC/gcA 1 1 FCRLA HGNC HGNC:18504 protein_coding YES CCDS53415.1 ENSP00000356936 Q7L513 UPI0001D3957E NM_001184866.1 5/6 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 161712163 161712163 C A 1 0 0 0 0 0 0 0 1 5662 581 21 2 2 FCRLA 1 161712163 Silent SNP C C3N-00704_T 518440 161712163 87244259 58 19195 FASLG 0 . GRCh38 1 172666015 172666015 + Silent SNP A A G novel C3N-00704_T C3N-00704_N A A c.845A>G p.= p.*282* ENST00000367721 4/4 159 122 37 164 164 0 strelka-varscan-mutect FASLG,stop_retained_variant,p.=,ENST00000367721,NM_000639.2;FASLG,3_prime_UTR_variant,,ENST00000340030,NM_001302746.1; G ENST00000367721 Transcript stop_retained_variant 1029/1888 845/846 282/281 * tAa/tGa 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 4/4 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 G 2 3 62 172666015 172666015 A G 1 0 0 0 0 0 0 0 1 5542 369 13 5 5 FASLG 1 172666015 Silent SNP A C3N-00704_T 10953852 172666015 76290407 59 19196 ANKRD45 0 . GRCh38 1 173659285 173659285 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.134C>G p.Thr45Arg p.T45R ENST00000333279 2/6 190 167 23 168 168 0 strelka-varscan-mutect ANKRD45,missense_variant,p.Thr45Arg,ENST00000333279,NM_198493.2;ANKRD45,non_coding_transcript_exon_variant,,ENST00000367712,; C ENST00000333279 Transcript missense_variant 195/1446 134/801 45/266 T/R aCa/aGa 1 -1 ANKRD45 HGNC HGNC:24786 protein_coding YES CCDS1309.1 ENSP00000331268 Q5TZF3 UPI000019851A NM_198493.2 tolerated(0.13) 2/6 hmmpanther:PTHR24180,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 173659285 173659285 G C 1 0 0 0 0 1 0 0 0 778 1377 48 4 4 ANKRD45 1 173659285 Missense_Mutation SNP G C3N-00704_T 993270 173659285 75297137 60 19197 FAM163A 0 . GRCh38 1 179813110 179813110 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.13A>T p.Thr5Ser p.T5S ENST00000341785 4/5 353 242 111 292 291 1 strelka-varscan-mutect FAM163A,missense_variant,p.Thr5Ser,ENST00000341785,NM_173509.2;RP11-12M5.3,downstream_gene_variant,,ENST00000415218,;RP11-12M5.3,downstream_gene_variant,,ENST00000453051,; T ENST00000341785 Transcript missense_variant 409/2909 13/504 5/167 T/S Acg/Tcg 1 1 FAM163A HGNC HGNC:28274 protein_coding YES CCDS1333.1 ENSP00000354891 Q96GL9 UPI000006ED82 NM_173509.2 deleterious(0.01) 4/5 Pfam_domain:PF15069,hmmpanther:PTHR31914,hmmpanther:PTHR31914:SF2,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1276100599 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 179813110 179813110 A T 1 0 0 0 0 1 0 0 0 5325 43 2 4 4 FAM163A 1 179813110 Missense_Mutation SNP A C3N-00704_T 6153825 179813110 69143312 61 19198 CAMSAP2 0 . GRCh38 1 200832239 200832239 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.718C>T p.Pro240Ser p.P240S ENST00000236925 6/18 127 94 33 129 129 0 strelka-varscan CAMSAP2,missense_variant,p.Pro229Ser,ENST00000358823,NM_203459.2;CAMSAP2,missense_variant,p.Pro240Ser,ENST00000236925,NM_001297707.1;CAMSAP2,missense_variant,p.Pro229Ser,ENST00000413307,NM_001297708.1;CAMSAP2,non_coding_transcript_exon_variant,,ENST00000532732,;CAMSAP2,upstream_gene_variant,,ENST00000447701,; T ENST00000236925 Transcript missense_variant 767/7161 718/4470 240/1489 P/S Cct/Tct 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 deleterious(0) 6/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1,Gene3D:1.10.418.10,Pfam_domain:PF11971,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 200832239 200832239 C T 1 0 0 0 0 1 0 0 0 2304 739 26 3 3 CAMSAP2 1 200832239 Missense_Mutation SNP C C3N-00704_T 21019129 200832239 48124183 62 19199 IGFN1 0 . GRCh38 1 201207702 201207702 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2809G>T p.Gly937Cys p.G937C ENST00000335211 12/24 227 213 14 206 206 0 strelka-varscan IGFN1,missense_variant,p.Gly937Cys,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,upstream_gene_variant,,ENST00000412892,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,downstream_gene_variant,,ENST00000444705,; T ENST00000335211 Transcript missense_variant 2939/11810 2809/11127 937/3708 G/C Ggt/Tgt 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0) 12/24 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF630 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 201207702 201207702 G T 1 0 0 0 0 1 0 0 0 7497 1000 35 2 2 IGFN1 1 201207702 Missense_Mutation SNP G C3N-00704_T 375463 201207702 47748720 63 19200 PLXNA2 0 . GRCh38 1 208027244 208027244 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.5684G>A p.= p.*1895* ENST00000367033 32/32 189 179 10 194 194 0 strelka-varscan PLXNA2,stop_retained_variant,p.=,ENST00000367033,NM_025179.3;PLXNA2,non_coding_transcript_exon_variant,,ENST00000483048,;PLXNA2,downstream_gene_variant,,ENST00000480053,; T ENST00000367033 Transcript stop_retained_variant 6442/11444 5684/5685 1895/1894 * tGa/tAa 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 32/32 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 208027244 208027244 C T 1 0 0 0 0 0 0 0 1 12226 837 29 3 3 PLXNA2 1 208027244 Silent SNP C C3N-00704_T 6819542 208027244 40929178 64 19201 USH2A 0 . GRCh38 1 215628823 215628824 + Frame_Shift_Ins INS - - T novel C3N-00704_T C3N-00704_N - - c.15509dupA p.Asn5170LysfsTer8 p.N5170Kfs*8 ENST00000307340 71/72 446 392 54 485 485 0 sindel-varindel-pindel USH2A,frameshift_variant,p.Asn5170LysfsTer8,ENST00000307340,NM_206933.2;SNORD116,downstream_gene_variant,,ENST00000365628,; T ENST00000307340 Transcript frameshift_variant 15896-15897/18883 15509-15510/15609 5170/5202 N/KX aac/aaAc 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 71/72 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 62 215628823 215628823 - T 1 0 1 1 0 0 0 0 0 17570 1368 48 0 0 USH2A 1 215628823 Frame_Shift_Ins INS - C3N-00704_T 7601579 215628823 33327599 65 19202 USH2A 0 . GRCh38 1 216190357 216190357 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.4262C>T p.Thr1421Ile p.T1421I ENST00000307340 20/72 301 264 37 344 344 0 strelka-varscan-mutect USH2A,missense_variant,p.Thr1421Ile,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Thr1421Ile,ENST00000366942,NM_007123.5;RP5-1099E6.3,upstream_gene_variant,,ENST00000420867,; A ENST00000307340 Transcript missense_variant 4649/18883 4262/15609 1421/5202 T/I aCt/aTt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.57) 20/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 216190357 216190357 G A 1 0 0 0 0 1 0 0 0 17570 1029 36 3 3 USH2A 1 216190357 Missense_Mutation SNP G C3N-00704_T 561534 216190357 32766065 66 19203 USH2A 0 . GRCh38 1 216418519 216418519 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.646G>C p.Val216Leu p.V216L ENST00000307340 3/72 162 143 19 279 279 0 strelka-varscan-mutect USH2A,missense_variant,p.Val216Leu,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Val216Leu,ENST00000366942,NM_007123.5; G ENST00000307340 Transcript missense_variant 1033/18883 646/15609 216/5202 V/L Gtg/Ctg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.33) 3/72 Gene3D:2.60.120.200,Pfam_domain:PF13385,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00560,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 216418519 216418519 C G 1 0 0 0 0 1 0 0 0 17570 492 17 4 4 USH2A 1 216418519 Missense_Mutation SNP C C3N-00704_T 228162 216418519 32537903 67 19204 MIA3 0 . GRCh38 1 222653313 222653313 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.4295A>G p.Asp1432Gly p.D1432G ENST00000344922 15/28 68 56 12 89 89 0 strelka-varscan-mutect MIA3,missense_variant,p.Asp1432Gly,ENST00000344922,NM_001324064.1,NM_198551.3;MIA3,missense_variant,p.Asp956Gly,ENST00000354906,;MIA3,missense_variant,p.Asp310Gly,ENST00000340535,NM_001300867.1;MIA3,intron_variant,,ENST00000344507,;MIA3,downstream_gene_variant,,ENST00000495210,;MIA3,downstream_gene_variant,,ENST00000467190,; G ENST00000344922 Transcript missense_variant 4320/8142 4295/5724 1432/1907 D/G gAt/gGt 1 1 MIA3 HGNC HGNC:24008 protein_coding YES CCDS41470.1 ENSP00000340900 Q5JRA6 UPI00001D75B3 NM_001324064.1,NM_198551.3 tolerated(0.08) 15/28 hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF37 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 222653313 222653313 A G 1 0 0 0 0 1 0 0 0 9522 333 12 5 5 MIA3 1 222653313 Missense_Mutation SNP A C3N-00704_T 6234794 222653313 26303109 68 19205 SDE2 0 . GRCh38 1 225999300 225999300 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.13G>C p.Ala5Pro p.A5P ENST00000272091 1/7 186 153 33 150 150 0 strelka-varscan-mutect SDE2,missense_variant,p.Ala5Pro,ENST00000272091,NM_152608.3; G ENST00000272091 Transcript missense_variant 32/3975 13/1356 5/451 A/P Gcg/Ccg 1 -1 SDE2 HGNC HGNC:26643 protein_coding YES CCDS41473.1 ENSP00000272091 Q6IQ49 UPI0000204007 NM_152608.3 deleterious_low_confidence(0.02) 1/7 hmmpanther:PTHR12786:SF1,hmmpanther:PTHR12786 MODERATE 1 SNV 1 1 PASS rs1291074316 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 225999300 225999300 C G 1 0 0 0 0 1 0 0 0 14231 768 27 4 4 SDE2 1 225999300 Missense_Mutation SNP C C3N-00704_T 3345987 225999300 22957122 69 19206 CDC42BPA 0 . GRCh38 1 227147395 227147395 + Silent SNP C C A C3N-00704_T C3N-00704_N C C c.858G>T p.= p.S286S ENST00000366769 7/36 180 130 50 163 163 0 varscan-mutect CDC42BPA,synonymous_variant,p.=,ENST00000366769,NM_003607.3;CDC42BPA,synonymous_variant,p.=,ENST00000366764,;CDC42BPA,synonymous_variant,p.=,ENST00000334218,;CDC42BPA,synonymous_variant,p.=,ENST00000366767,NM_014826.4;CDC42BPA,5_prime_UTR_variant,,ENST00000366766,; A ENST00000366769 Transcript synonymous_variant 2150/10855 858/5160 286/1719 S tcG/tcT COSM1339398,COSM1339399,COSM1339400,COSM4028788,COSM4028789 1 -1 CDC42BPA HGNC HGNC:1737 protein_coding YES CCDS1558.1 ENSP00000355731 Q5VT25 UPI000019097D NM_003607.3 7/36 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF31,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1,1,1,1 LOW 1 SNV 1 1,1,1,1,1 1 PASS rs1267392725 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 227147395 227147395 C A 1 0 0 0 0 0 0 0 1 2775 755 27 1 1 CDC42BPA 1 227147395 Silent SNP C C3N-00704_T 1148095 227147395 21809027 70 19207 OBSCN 0 . GRCh38 1 228279271 228279271 + Missense_Mutation SNP G G T rs761007386 C3N-00704_T C3N-00704_N G G c.8510G>T p.Arg2837Leu p.R2837L ENST00000570156 32/116 428 315 113 476 475 1 strelka-varscan-mutect OBSCN,missense_variant,p.Arg2837Leu,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Arg2837Leu,ENST00000366707,;OBSCN,missense_variant,p.Arg2408Leu,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Arg2408Leu,ENST00000636875,;OBSCN,missense_variant,p.Arg2408Leu,ENST00000284548,NM_052843.3;OBSCN,missense_variant,p.Arg256Leu,ENST00000366706,;OBSCN,upstream_gene_variant,,ENST00000483539,;RP5-1139B12.2,upstream_gene_variant,,ENST00000602517,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602529,;RP5-1139B12.3,upstream_gene_variant,,ENST00000602947,;OBSCN,upstream_gene_variant,,ENST00000366704,; T ENST00000570156 Transcript missense_variant 8584/26925 8510/26772 2837/8923 R/L cGg/cTg rs761007386 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.08) 32/116 Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs761007386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 228279271 228279271 G T 1 0 0 0 0 1 0 0 0 10889 1116 39 1 1 OBSCN 1 228279271 Missense_Mutation SNP G C3N-00704_T 1131876 228279271 20677151 71 19208 OR2AJ1 0 . GRCh38 1 247933966 247933966 + Silent SNP C C T rs535863153 C3N-00704_T C3N-00704_N C C c.198C>T p.= p.L66L ENST00000318244 1/1 190 160 30 222 222 0 strelka-varscan OR2AJ1,synonymous_variant,p.=,ENST00000318244,;CLK3P2,downstream_gene_variant,,ENST00000427566,; T ENST00000318244 Transcript synonymous_variant 198/987 198/987 66/328 L ctC/ctT rs535863153 1 1 OR2AJ1 HGNC HGNC:15001 protein_coding YES ENSP00000325078 Q8NGZ0 UPI0000061E5C 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF214,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 247933966 247933966 C T 1 0 0 0 0 0 0 0 1 11063 900 32 3 3 OR2AJ1 1 247933966 Silent SNP C C3N-00704_T 19654695 247933966 1022456 72 19209 OR2T3 0 . GRCh38 1 248473662 248473662 + Silent SNP C C A rs762426058 C3N-00704_T C3N-00704_N C C c.312C>A p.= p.I104I ENST00000359594 1/1 312 267 45 385 385 0 strelka-varscan OR2T3,synonymous_variant,p.=,ENST00000359594,NM_001005495.1; A ENST00000359594 Transcript synonymous_variant 312/957 312/957 104/318 I atC/atA rs762426058 1 1 OR2T3 HGNC HGNC:14727 protein_coding YES CCDS31117.1 ENSP00000352604 Q8NH03 A0A126GVW5 UPI00001D7CA5 NM_001005495.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF4,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 248473662 248473662 C A 1 0 0 0 0 0 0 0 1 11100 845 30 2 2 OR2T3 1 248473662 Silent SNP C C3N-00704_T 539696 248473662 482760 73 19210 TRAPPC12 0 . GRCh38 2 3388608 3388608 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.985G>T p.Gly329Cys p.G329C ENST00000324266 2/12 156 137 19 172 172 0 strelka-varscan-mutect TRAPPC12,missense_variant,p.Gly329Cys,ENST00000324266,NM_016030.5;TRAPPC12,missense_variant,p.Gly329Cys,ENST00000382110,NM_001321102.1;TRAPPC12,upstream_gene_variant,,ENST00000441983,;TRAPPC12,upstream_gene_variant,,ENST00000457845,;TRAPPC12,missense_variant,p.Gly162Cys,ENST00000411973,;TRAPPC12,non_coding_transcript_exon_variant,,ENST00000482645,; T ENST00000324266 Transcript missense_variant 1180/2508 985/2208 329/735 G/C Ggc/Tgc 1 1 TRAPPC12 HGNC HGNC:24284 protein_coding YES CCDS1652.1 ENSP00000324318 Q8WVT3 UPI000014132D NM_016030.5 deleterious(0) 2/12 hmmpanther:PTHR21581,hmmpanther:PTHR21581:SF6 MODERATE 1 SNV 1 1 PASS rs1211759477 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 3388608 3388608 G T 1 0 0 0 0 1 0 0 0 16942 1116 39 1 1 TRAPPC12 2 3388608 Missense_Mutation SNP G C3N-00704_T 3388608 238804921 74 19211 DDX1 0 . GRCh38 2 15607213 15607213 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.856G>C p.Ala286Pro p.A286P ENST00000381341 14/27 169 147 22 208 208 0 strelka-varscan-mutect DDX1,missense_variant,p.Ala286Pro,ENST00000381341,;DDX1,missense_variant,p.Ala286Pro,ENST00000233084,NM_004939.2;DDX1,missense_variant,p.Ala205Pro,ENST00000617198,;DDX1,missense_variant,p.Ala205Pro,ENST00000621973,; C ENST00000381341 Transcript missense_variant 1245/2817 856/2223 286/740 A/P Gct/Cct 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 deleterious(0.01) 14/27 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF307,hmmpanther:PTHR24031,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 15607213 15607213 G C 1 0 0 0 0 1 0 0 0 4145 1319 46 4 4 DDX1 2 15607213 Missense_Mutation SNP G C3N-00704_T 12218605 15607213 226586316 75 19212 TDRD15 0 . GRCh38 2 21140177 21140177 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2710G>T p.Ala904Ser p.A904S ENST00000405799 4/4 49 42 7 169 169 0 strelka-varscan-mutect TDRD15,missense_variant,p.Ala904Ser,ENST00000405799,;TDRD15,missense_variant,p.Ala904Ser,ENST00000622654,; T ENST00000405799 Transcript missense_variant 3040/6135 2710/5805 904/1934 A/S Gcc/Tcc 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 deleterious(0.04) 4/4 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 MODERATE 1 SNV 2 1 PASS rs1490288610 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 21140177 21140177 G T 1 0 0 0 0 1 0 0 0 16141 1319 46 2 2 TDRD15 2 21140177 Missense_Mutation SNP G C3N-00704_T 5532964 21140177 221053352 76 19213 CAD 0 . GRCh38 2 27242099 27242099 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.6072G>T p.= p.R2024R ENST00000264705 39/44 215 181 34 240 239 1 strelka-varscan-mutect CAD,synonymous_variant,p.=,ENST00000264705,NM_004341.3;CAD,synonymous_variant,p.=,ENST00000403525,NM_001306079.1;CAD,synonymous_variant,p.=,ENST00000428460,;CAD,downstream_gene_variant,,ENST00000456311,;CAD,downstream_gene_variant,,ENST00000458503,;CAD,downstream_gene_variant,,ENST00000491461,;CAD,downstream_gene_variant,,ENST00000487239,; T ENST00000264705 Transcript synonymous_variant 6234/7265 6072/6678 2024/2225 R cgG/cgT 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 39/44 Gene3D:3.40.50.1370,HAMAP:MF_00001,Pfam_domain:PF02729,Superfamily_domains:SSF53671,TIGRFAM_domain:TIGR00670 LOW 1 SNV 1 1 PASS rs1460981806 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 27242099 27242099 G T 1 0 0 0 0 0 0 0 1 2255 1190 42 2 2 CAD 2 27242099 Silent SNP G C3N-00704_T 6101922 27242099 214951430 77 19214 C2orf16 0 . GRCh38 2 27577591 27577591 + Nonsense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1019T>A p.Leu340Ter p.L340* ENST00000408964 1/1 315 267 48 341 341 0 strelka-varscan-mutect C2orf16,stop_gained,p.Leu340Ter,ENST00000408964,NM_032266.3; A ENST00000408964 Transcript stop_gained 1070/6199 1019/5955 340/1984 L/* tTa/tAa 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 1/1 hmmpanther:PTHR33888 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 27577591 27577591 T A 1 0 0 0 0 0 1 0 0 2032 1764 61 4 4 C2orf16 2 27577591 Nonsense_Mutation SNP T C3N-00704_T 335492 27577591 214615938 78 19215 PLB1 0 . GRCh38 2 28604738 28604738 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.2940C>T p.= p.N980N ENST00000327757 41/58 160 129 31 189 189 0 strelka-varscan-mutect PLB1,synonymous_variant,p.=,ENST00000422425,NM_001170585.1;PLB1,synonymous_variant,p.=,ENST00000327757,NM_153021.4;PLB1,synonymous_variant,p.=,ENST00000404858,;PLB1,synonymous_variant,p.=,ENST00000444257,;PLB1,intron_variant,,ENST00000411743,;PLB1,intron_variant,,ENST00000479065,; T ENST00000327757 Transcript synonymous_variant 2984/5107 2940/4377 980/1458 N aaC/aaT 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 41/58 Gene3D:3.40.50.1110,Pfam_domain:PF00657,hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31,Superfamily_domains:SSF52266 LOW 1 SNV 1 1 PASS rs1360944315 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 28604738 28604738 C T 1 0 0 0 0 0 0 0 1 12118 477 17 3 3 PLB1 2 28604738 Silent SNP C C3N-00704_T 1027147 28604738 213588791 79 19216 CAPN13 0 . GRCh38 2 30758134 30758134 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.778C>G p.Gln260Glu p.Q260E ENST00000295055 8/23 130 122 8 118 118 0 strelka-varscan-mutect CAPN13,missense_variant,p.Gln260Glu,ENST00000295055,NM_144575.2;CAPN13,non_coding_transcript_exon_variant,,ENST00000465960,;CAPN13,missense_variant,p.Gln260Glu,ENST00000458085,; C ENST00000295055 Transcript missense_variant 955/2683 778/2010 260/669 Q/E Caa/Gaa 1 -1 CAPN13 HGNC HGNC:16663 protein_coding YES CCDS46252.1 ENSP00000295055 Q6MZZ7 UPI00000463E5 NM_144575.2 tolerated(0.14) 8/23 Gene3D:3.90.70.10,Pfam_domain:PF00648,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF282,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -15.5191 1 1 1 1 0 C 3 2 62 30758134 30758134 G C 1 0 0 0 0 1 0 0 0 2318 1304 45 4 4 CAPN13 2 30758134 Missense_Mutation SNP G C3N-00704_T 2153396 30758134 211435395 80 19217 LTBP1 0 . GRCh38 2 33252737 33252737 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2060G>T p.Arg687Ile p.R687I ENST00000404816 11/34 165 143 22 126 126 0 strelka-varscan-mutect LTBP1,missense_variant,p.Arg687Ile,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Arg361Ile,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Arg361Ile,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Arg361Ile,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Arg361Ile,ENST00000402934,;LTBP1,missense_variant,p.Arg43Ile,ENST00000413303,;LTBP1,missense_variant,p.Arg4Ile,ENST00000468091,; T ENST00000404816 Transcript missense_variant 2413/6333 2060/5166 687/1721 R/I aGa/aTa 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0.01) 11/34 Gene3D:3.90.290.10,PROSITE_profiles:PS51364,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 33252737 33252737 G T 1 0 0 0 0 1 0 0 0 8979 942 33 2 2 LTBP1 2 33252737 Missense_Mutation SNP G C3N-00704_T 2494603 33252737 208940792 81 19218 HEATR5B 0 . GRCh38 2 37003594 37003594 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.4998A>T p.Gln1666His p.Q1666H ENST00000233099 31/36 182 147 35 224 224 0 strelka-varscan HEATR5B,missense_variant,p.Gln1666His,ENST00000233099,NM_019024.2;HEATR5B,downstream_gene_variant,,ENST00000471051,; A ENST00000233099 Transcript missense_variant 5094/6905 4998/6216 1666/2071 Q/H caA/caT 1 -1 HEATR5B HGNC HGNC:29273 protein_coding YES CCDS33181.1 ENSP00000233099 Q9P2D3 UPI0000160DCD NM_019024.2 deleterious(0.01) 31/36 hmmpanther:PTHR21663,hmmpanther:PTHR21663:SF2,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 37003594 37003594 T A 1 0 0 0 0 1 0 0 0 6914 1722 60 4 4 HEATR5B 2 37003594 Missense_Mutation SNP T C3N-00704_T 3750857 37003594 205189935 82 19219 OTX1 0 . GRCh38 2 63055964 63055964 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.713C>A p.Pro238His p.P238H ENST00000282549 5/5 361 315 46 427 425 2 strelka-varscan OTX1,missense_variant,p.Pro238His,ENST00000282549,NM_014562.3;OTX1,missense_variant,p.Pro238His,ENST00000366671,NM_001199770.1;OTX1,3_prime_UTR_variant,,ENST00000405984,;OTX1,downstream_gene_variant,,ENST00000484066,;OTX1,downstream_gene_variant,,ENST00000477348,;OTX1,downstream_gene_variant,,ENST00000476383,; A ENST00000282549 Transcript missense_variant 989/2861 713/1065 238/354 P/H cCc/cAc 1 1 OTX1 HGNC HGNC:8521 protein_coding YES CCDS1873.1 ENSP00000282549 P32242 UPI0000130F36 NM_014562.3 tolerated(0.05) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR24329:SF310,hmmpanther:PTHR24329,Pfam_domain:PF03529 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 63055964 63055964 C A 1 0 0 0 0 1 0 0 0 11390 623 22 2 2 OTX1 2 63055964 Missense_Mutation SNP C C3N-00704_T 26052370 63055964 179137565 83 19220 FBXO41 0 . GRCh38 2 73269478 73269478 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.153C>A p.= p.A51A ENST00000521871 2/13 174 123 51 138 138 0 strelka-varscan FBXO41,synonymous_variant,p.=,ENST00000521871,;FBXO41,synonymous_variant,p.=,ENST00000295133,NM_001080410.2;FBXO41,synonymous_variant,p.=,ENST00000520530,;FBXO41,downstream_gene_variant,,ENST00000520186,;FBXO41,upstream_gene_variant,,ENST00000519873,; T ENST00000521871 Transcript synonymous_variant 569/7336 153/2628 51/875 A gcC/gcA 1 -1 FBXO41 HGNC HGNC:29409 protein_coding YES CCDS46337.2 ENSP00000428646 Q8TF61 UPI0000D611B7 2/13 hmmpanther:PTHR15739,hmmpanther:PTHR15739:SF4,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 73269478 73269478 G T 1 0 0 0 0 0 0 0 1 5613 1103 39 1 1 FBXO41 2 73269478 Silent SNP G C3N-00704_T 10213514 73269478 168924051 84 19221 LRRTM4 0 . GRCh38 2 77518498 77518498 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.1371C>A p.= p.L457L ENST00000409093 3/4 139 116 23 165 165 0 strelka-varscan LRRTM4,synonymous_variant,p.=,ENST00000409088,NM_024993.4;LRRTM4,synonymous_variant,p.=,ENST00000409911,;LRRTM4,synonymous_variant,p.=,ENST00000409282,NM_001282928.1;LRRTM4,synonymous_variant,p.=,ENST00000409093,NM_001282924.1;LRRTM4,synonymous_variant,p.=,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; T ENST00000409093 Transcript synonymous_variant 1708/2247 1371/1773 457/590 L ctC/ctA 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 77518498 77518498 G T 1 0 0 0 0 0 0 0 1 8948 1161 41 2 2 LRRTM4 2 77518498 Silent SNP G C3N-00704_T 4249020 77518498 164675031 85 19222 CNNM3 0 . GRCh38 2 96816409 96816420 + In_Frame_Del DEL GGGCGCGGGTTG GGGCGCGGGTTG - novel C3N-00704_T C3N-00704_N GGGCGCGGGTTG GGGCGCGGGTTG c.134_145delGCGCGGGTTGGG p.Gly45_Trp48del p.G45_W48del ENST00000305510 1/8 43 35 8 64 64 0 sindel-varindel-pindel CNNM3,inframe_deletion,p.Gly45_Trp48del,ENST00000305510,NM_017623.4;CNNM3,inframe_deletion,p.Gly45_Trp48del,ENST00000377060,NM_199078.2;CNNM4,downstream_gene_variant,,ENST00000377075,NM_020184.3;RP11-353K11.1,upstream_gene_variant,,ENST00000608609,; - ENST00000305510 Transcript inframe_deletion 160-171/3447 132-143/2124 44-48/707 AGAGW/A gcGGGCGCGGGTTGg/gcg 1 1 CNNM3 HGNC HGNC:104 protein_coding YES CCDS2025.1 ENSP00000305449 Q8NE01 UPI000006CEA7 NM_017623.4 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF27 MODERATE 1 deletion 1 2 1 PASS . . 0 202 7 0 0 0 0 0 -19.48283 0.9999997 1 1 1 0 - 7 5 62 96816409 96816409 GGGCGCGGGTTG - 1 0 1 0 1 0 0 0 0 3394 1103 39 0 0 CNNM3 2 96816409 In_Frame_Del DEL GGGCGCGGGTTG C3N-00704_T 19297911 96816409 145377120 86 19223 IL1RL2 0 . GRCh38 2 102192013 102192013 + Missense_Mutation SNP T T G C3N-00704_T C3N-00704_N T T c.382T>G p.Leu128Val p.L128V ENST00000264257 4/12 95 85 10 263 262 1 strelka-varscan IL1RL2,missense_variant,p.Leu128Val,ENST00000264257,NM_003854.2;IL1RL2,missense_variant,p.Leu128Val,ENST00000421464,;IL1RL2,intron_variant,,ENST00000441515,;IL1RL2,intron_variant,,ENST00000481806,; G ENST00000264257 Transcript missense_variant 508/2615 382/1728 128/575 L/V Tta/Gta COSM4924469 1 1 IL1RL2 HGNC HGNC:5999 protein_coding YES CCDS2056.1 ENSP00000264257 Q9HB29 UPI000013D4ED NM_003854.2 tolerated(0.58) 4/12 Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF9 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 102192013 102192013 T G 1 0 0 0 0 1 0 0 0 7567 1838 64 5 5 IL1RL2 2 102192013 Missense_Mutation SNP T C3N-00704_T 5375604 102192013 140001516 87 19224 IL18R1 0 . GRCh38 2 102367955 102367955 + Missense_Mutation SNP G G T rs370305765 C3N-00704_T C3N-00704_N G G c.189G>T p.Gln63His p.Q63H ENST00000409599 4/12 459 379 80 467 467 0 strelka-varscan IL18R1,missense_variant,p.Gln63His,ENST00000409599,;IL18R1,missense_variant,p.Gln63His,ENST00000233957,NM_003855.3,NM_001282399.1;IL18R1,missense_variant,p.Gln63His,ENST00000410040,;IL18R1,missense_variant,p.Gln63His,ENST00000334376,; T ENST00000409599 Transcript missense_variant 545/3854 189/1626 63/541 Q/H caG/caT rs370305765 1 1 IL18R1 HGNC HGNC:5988 protein_coding YES CCDS2060.1 ENSP00000387211 Q13478 UPI000012D871 tolerated(0.84) 4/12 hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF6,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 102367955 102367955 G T 1 0 0 0 0 1 0 0 0 7555 991 35 2 2 IL18R1 2 102367955 Missense_Mutation SNP G C3N-00704_T 175942 102367955 139825574 88 19225 POU3F3 0 . GRCh38 2 104855625 104855625 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.115G>A p.Gly39Ser p.G39S ENST00000361360 1/1 28 19 9 24 24 0 strelka-varscan POU3F3,missense_variant,p.Gly39Ser,ENST00000361360,NM_006236.1;LINC01158,upstream_gene_variant,,ENST00000413121,;RP11-13J10.1,intron_variant,,ENST00000598623,;LINC01158,upstream_gene_variant,,ENST00000458253,;LINC01158,upstream_gene_variant,,ENST00000454729,;LINC01158,upstream_gene_variant,,ENST00000443988,;LINC01158,upstream_gene_variant,,ENST00000447876,; A ENST00000361360 Transcript missense_variant 115/3064 115/1503 39/500 G/S Ggc/Agc 1 1 POU3F3 HGNC HGNC:9216 protein_coding YES CCDS33265.1 ENSP00000355001 P20264 UPI0000131D87 NM_006236.1 deleterious_low_confidence(0) 1/1 PIRSF_domain:PIRSF002629,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF73,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 16 192 2 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 62 104855625 104855625 G A 1 0 0 0 0 1 0 0 0 12392 1116 39 1 1 POU3F3 2 104855625 Missense_Mutation SNP G C3N-00704_T 2487670 104855625 137337904 89 19226 UXS1 0 . GRCh38 2 106104811 106104811 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.906G>T p.Arg302Ser p.R302S ENST00000283148 11/15 288 253 35 296 296 0 strelka-varscan UXS1,missense_variant,p.Arg302Ser,ENST00000283148,NM_001253875.1;UXS1,missense_variant,p.Arg129Ser,ENST00000409032,NM_001253876.1;UXS1,missense_variant,p.Arg297Ser,ENST00000409501,NM_025076.4;UXS1,missense_variant,p.Arg129Ser,ENST00000416298,;UXS1,missense_variant,p.Arg141Ser,ENST00000441952,;UXS1,non_coding_transcript_exon_variant,,ENST00000470053,;UXS1,upstream_gene_variant,,ENST00000497604,; A ENST00000283148 Transcript missense_variant 1004/2099 906/1278 302/425 R/S agG/agT 1 -1 UXS1 HGNC HGNC:17729 protein_coding YES CCDS58721.1 ENSP00000283148 Q8NBZ7 UPI000003CA36 NM_001253875.1 deleterious(0.02) 11/15 hmmpanther:PTHR10366:SF399,hmmpanther:PTHR10366,Pfam_domain:PF16363,Gene3D:3.90.25.10,Superfamily_domains:SSF51735 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 106104811 106104811 C A 1 0 0 0 0 1 0 0 0 17654 622 22 2 2 UXS1 2 106104811 Missense_Mutation SNP C C3N-00704_T 1249186 106104811 136088718 90 19227 TFCP2L1 0 . GRCh38 2 121242443 121242443 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.684G>T p.Lys228Asn p.K228N ENST00000263707 7/15 205 179 26 328 328 0 strelka-varscan TFCP2L1,missense_variant,p.Lys228Asn,ENST00000263707,NM_014553.2; A ENST00000263707 Transcript missense_variant 782/9292 684/1440 228/479 K/N aaG/aaT 1 -1 TFCP2L1 HGNC HGNC:17925 protein_coding YES CCDS2134.1 ENSP00000263707 Q9NZI6 UPI0000072817 NM_014553.2 deleterious(0) 7/15 Pfam_domain:PF04516,hmmpanther:PTHR11037,hmmpanther:PTHR11037:SF18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 121242443 121242443 C A 1 0 0 0 0 1 0 0 0 16229 912 32 2 2 TFCP2L1 2 121242443 Missense_Mutation SNP C C3N-00704_T 15137632 121242443 120951086 91 19228 CNTNAP5 0 . GRCh38 2 124221806 124221806 + Missense_Mutation SNP G G A C3N-00704_T C3N-00704_N G G c.184G>A p.Val62Ile p.V62I ENST00000431078 2/24 171 151 20 180 180 0 strelka-varscan CNTNAP5,missense_variant,p.Val62Ile,ENST00000431078,NM_130773.3;CNTNAP5,non_coding_transcript_exon_variant,,ENST00000470921,; A ENST00000431078 Transcript missense_variant 548/5284 184/3921 62/1306 V/I Gtt/Att COSM1006060 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0.05) 2/24 PROSITE_profiles:PS50022,Gene3D:2.60.120.260,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 124221806 124221806 G A 1 0 0 0 0 1 0 0 0 3432 1043 36 3 3 CNTNAP5 2 124221806 Missense_Mutation SNP G C3N-00704_T 2979363 124221806 117971723 92 19229 MAP3K19 0 . GRCh38 2 134998895 134998895 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.417G>T p.= p.R139R ENST00000392915 8/13 308 262 46 413 412 1 strelka-varscan MAP3K19,synonymous_variant,p.=,ENST00000392915,;MAP3K19,synonymous_variant,p.=,ENST00000375845,NM_025052.4;MAP3K19,synonymous_variant,p.=,ENST00000637841,;MAP3K19,synonymous_variant,p.=,ENST00000392917,NM_001282883.1;MAP3K19,synonymous_variant,p.=,ENST00000375844,NM_001018046.2;MAP3K19,synonymous_variant,p.=,ENST00000392918,NM_001018047.2;MAP3K19,intron_variant,,ENST00000358371,NM_001018044.2;MAP3K19,non_coding_transcript_exon_variant,,ENST00000638025,;MAP3K19,downstream_gene_variant,,ENST00000425952,;MAP3K19,non_coding_transcript_exon_variant,,ENST00000468155,; A ENST00000392915 Transcript synonymous_variant 1101/5030 417/3987 139/1328 R cgG/cgT 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 8/13 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 134998895 134998895 C A 1 0 0 0 0 0 0 0 1 9172 726 26 2 2 MAP3K19 2 134998895 Silent SNP C C3N-00704_T 10777089 134998895 107194634 93 19230 R3HDM1 0 . GRCh38 2 135675433 135675433 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.2152G>C p.Gly718Arg p.G718R ENST00000409606 19/26 138 113 25 158 158 0 strelka-varscan R3HDM1,missense_variant,p.Gly717Arg,ENST00000264160,NM_015361.3;R3HDM1,missense_variant,p.Gly662Arg,ENST00000410054,NM_001282800.1;R3HDM1,missense_variant,p.Gly589Arg,ENST00000628915,;R3HDM1,missense_variant,p.Gly589Arg,ENST00000409478,NM_001282799.1;R3HDM1,missense_variant,p.Gly718Arg,ENST00000409606,NM_001282798.1;R3HDM1,missense_variant,p.Gly441Arg,ENST00000429703,;R3HDM1,missense_variant,p.Gly13Arg,ENST00000445855,; C ENST00000409606 Transcript missense_variant 2471/3673 2152/3303 718/1100 G/R Gga/Cga 1 1 R3HDM1 HGNC HGNC:9757 protein_coding YES CCDS63025.1 ENSP00000387010 Q15032 UPI0001881805 NM_001282798.1 deleterious(0) 19/26 hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF12 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 135675433 135675433 G C 1 0 0 0 0 1 0 0 0 13044 1349 47 4 4 R3HDM1 2 135675433 Missense_Mutation SNP G C3N-00704_T 676538 135675433 106518096 94 19231 LRP1B 0 . GRCh38 2 140485465 140485465 + Silent SNP G G T rs759752435 C3N-00704_T C3N-00704_N G G c.9303C>A p.= p.L3101L ENST00000389484 59/91 148 126 22 200 200 0 strelka-varscan LRP1B,synonymous_variant,p.=,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript synonymous_variant 10275/16535 9303/13800 3101/4599 L ctC/ctA rs759752435,COSM4826976 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 59/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Pfam_domain:PF16472,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 62 140485465 140485465 G T 1 0 0 0 0 0 0 0 1 8850 929 33 2 2 LRP1B 2 140485465 Silent SNP G C3N-00704_T 4810032 140485465 101708064 95 19232 LRP1B 0 . GRCh38 2 140716811 140716811 + Missense_Mutation SNP C C A rs759977926 C3N-00704_T C3N-00704_N C C c.5764G>T p.Asp1922Tyr p.D1922Y ENST00000389484 36/91 61 53 8 106 106 0 strelka-varscan LRP1B,missense_variant,p.Asp1922Tyr,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 6736/16535 5764/13800 1922/4599 D/Y Gat/Tat rs759977926 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 36/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.42204 1 1 1 1 0 A 3 1 62 140716811 140716811 C A 1 0 0 0 0 1 0 0 0 8850 840 29 2 2 LRP1B 2 140716811 Missense_Mutation SNP C C3N-00704_T 231346 140716811 101476718 96 19233 RIF1 0 . GRCh38 2 151420239 151420239 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.553G>T p.Ala185Ser p.A185S ENST00000243326 6/35 154 131 23 174 173 1 strelka-varscan RIF1,missense_variant,p.Ala185Ser,ENST00000243326,;RIF1,missense_variant,p.Ala185Ser,ENST00000453091,NM_001177663.1;RIF1,missense_variant,p.Ala185Ser,ENST00000430328,NM_001177665.1;RIF1,missense_variant,p.Ala185Ser,ENST00000444746,NM_018151.4;RIF1,missense_variant,p.Ala185Ser,ENST00000428287,NM_001177664.1;RIF1,missense_variant,p.Ala177Ser,ENST00000414861,;RIF1,non_coding_transcript_exon_variant,,ENST00000498041,;RIF1,non_coding_transcript_exon_variant,,ENST00000494333,; T ENST00000243326 Transcript missense_variant 1036/15003 553/7419 185/2472 A/S Gca/Tca 1 1 RIF1 HGNC HGNC:23207 protein_coding YES CCDS2194.1 ENSP00000243326 Q5UIP0 UPI000023729F deleterious(0.05) 6/35 hmmpanther:PTHR22928,Pfam_domain:PF12231,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 151420239 151420239 G T 1 0 0 0 0 1 0 0 0 13533 1203 42 2 2 RIF1 2 151420239 Missense_Mutation SNP G C3N-00704_T 10703428 151420239 90773290 97 19234 SCN1A 0 . GRCh38 2 166036507 166036507 + Frame_Shift_Del DEL C C - C3N-00704_T C3N-00704_N C C c.2970delG p.Leu990PhefsTer3 p.L990Ffs*3 ENST00000303395 18/28 84 74 10 147 147 0 sindel-varindel-pindel SCN1A,frameshift_variant,p.Leu979PhefsTer3,ENST00000635776,;SCN1A,frameshift_variant,p.Leu979PhefsTer3,ENST00000637988,;SCN1A,frameshift_variant,p.Leu990PhefsTer3,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,frameshift_variant,p.Leu979PhefsTer3,ENST00000635750,;SCN1A,frameshift_variant,p.Leu990PhefsTer3,ENST00000423058,;SCN1A,frameshift_variant,p.Leu979PhefsTer3,ENST00000375405,NM_006920.4;SCN1A,frameshift_variant,p.Leu962PhefsTer3,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;AC010127.3,downstream_gene_variant,,ENST00000597623,;SCN1A,3_prime_UTR_variant,,ENST00000636194,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,;SCN1A,upstream_gene_variant,,ENST00000637038,;SCN1A,downstream_gene_variant,,ENST00000636759,; - ENST00000303395 Transcript frameshift_variant 3388/8533 2970/6030 990/2009 L/X ttG/tt CM087897 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 18/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix HIGH 1 deletion 5 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.99183 1 1 1 1 0 - 7 5 62 166036507 166036507 C - 1 0 1 0 1 0 0 0 0 14183 709 25 0 0 SCN1A 2 166036507 Frame_Shift_Del DEL C C3N-00704_T 14616268 166036507 76157022 98 19235 SCN7A 0 . GRCh38 2 166405857 166405857 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.4772G>T p.Arg1591Met p.R1591M ENST00000409855 25/25 210 171 39 278 277 1 strelka-varscan SCN7A,missense_variant,p.Arg1591Met,ENST00000619410,;SCN7A,missense_variant,p.Arg1591Met,ENST00000621965,;SCN7A,missense_variant,p.Arg1591Met,ENST00000409855,NM_002976.3;SCN7A,3_prime_UTR_variant,,ENST00000424326,; A ENST00000409855 Transcript missense_variant 4899/7183 4772/5049 1591/1682 R/M aGg/aTg 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0) 25/25 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 166405857 166405857 C A 1 0 0 0 0 1 0 0 0 14192 681 24 2 2 SCN7A 2 166405857 Missense_Mutation SNP C C3N-00704_T 369350 166405857 75787672 99 19236 XIRP2 0 . GRCh38 2 167244871 167244871 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.3479G>A p.Gly1160Glu p.G1160E ENST00000409195 9/11 157 135 22 192 192 0 strelka-varscan XIRP2,missense_variant,p.Gly1160Glu,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Gly938Glu,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Gly985Glu,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 3568/12675 3479/10650 1160/3549 G/E gGg/gAg 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 tolerated(0.12) 9/11 PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 167244871 167244871 G A 1 0 0 0 0 1 0 0 0 17989 1232 43 3 3 XIRP2 2 167244871 Missense_Mutation SNP G C3N-00704_T 839014 167244871 74948658 100 19237 XIRP2 0 . GRCh38 2 167247470 167247470 + Silent SNP A A T novel C3N-00704_T C3N-00704_N A A c.6078A>T p.= p.V2026V ENST00000409195 9/11 221 189 32 338 338 0 strelka-varscan XIRP2,synonymous_variant,p.=,ENST00000409195,NM_152381.5;XIRP2,synonymous_variant,p.=,ENST00000409273,NM_001199144.1;XIRP2,synonymous_variant,p.=,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; T ENST00000409195 Transcript synonymous_variant 6167/12675 6078/10650 2026/3549 V gtA/gtT 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 167247470 167247470 A T 1 0 0 0 0 0 0 0 1 17989 349 13 4 4 XIRP2 2 167247470 Silent SNP A C3N-00704_T 2599 167247470 74946059 101 19238 MYO3B 0 . GRCh38 2 170404373 170404373 + Frame_Shift_Del DEL C C - novel C3N-00704_T C3N-00704_N C C c.2407delC p.Gln803LysfsTer62 p.Q803Kfs*62 ENST00000408978 20/35 120 106 14 134 134 0 sindel-pindel MYO3B,frameshift_variant,p.Gln803LysfsTer62,ENST00000408978,NM_138995.4;MYO3B,frameshift_variant,p.Gln803LysfsTer62,ENST00000409044,NM_001083615.3;MYO3B,frameshift_variant,p.Gln812LysfsTer62,ENST00000484338,;AC012594.1,intron_variant,,ENST00000625968,;MYO3B,non_coding_transcript_exon_variant,,ENST00000602629,;MYO3B,non_coding_transcript_exon_variant,,ENST00000438642,;MYO3B,upstream_gene_variant,,ENST00000469359,;MYO3B,frameshift_variant,p.Gln803LysfsTer62,ENST00000317935,;MYO3B,non_coding_transcript_exon_variant,,ENST00000409940,; - ENST00000408978 Transcript frameshift_variant 2547/5529 2404/4026 802/1341 P/X Ccc/cc 1 1 MYO3B HGNC HGNC:15576 protein_coding YES CCDS42773.1 ENSP00000386213 Q8WXR4 UPI000020907B NM_138995.4 20/35 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF476,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 deletion 1 3 1 PASS . . 0 206 2 2 0 0 0 0 -19.97685 0.9999968 1 1 1 0 - 7 5 62 170404373 170404373 C - 1 0 1 0 1 0 0 0 0 10078 855 30 0 0 MYO3B 2 170404373 Frame_Shift_Del DEL C C3N-00704_T 3156903 170404373 71789156 102 19239 RAPGEF4 0 . GRCh38 2 172967263 172967263 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.823G>T p.Asp275Tyr p.D275Y ENST00000397081 10/31 55 46 9 71 71 0 strelka-varscan RAPGEF4,missense_variant,p.Asp275Tyr,ENST00000397081,NM_007023.3;RAPGEF4,missense_variant,p.Asp131Tyr,ENST00000397087,NM_001100397.1;RAPGEF4,missense_variant,p.Asp275Tyr,ENST00000409036,;RAPGEF4,missense_variant,p.Asp122Tyr,ENST00000540783,NM_001282899.1;RAPGEF4,missense_variant,p.Asp104Tyr,ENST00000538974,NM_001282900.1;RAPGEF4,missense_variant,p.Asp55Tyr,ENST00000535187,NM_001282901.1;RAPGEF4,splice_region_variant,,ENST00000473043,;RAPGEF4,splice_region_variant,,ENST00000466030,;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000459852,;RAPGEF4,downstream_gene_variant,,ENST00000473003,;RAPGEF4,splice_region_variant,,ENST00000473182,; T ENST00000397081 Transcript missense_variant,splice_region_variant 966/4299 823/3036 275/1011 D/Y Gac/Tac 1 1 RAPGEF4 HGNC HGNC:16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 UPI000006D4C7 NM_007023.3 deleterious(0.02) 10/31 Gene3D:1.10.10.10,Pfam_domain:PF00610,PROSITE_profiles:PS50186,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,SMART_domains:SM00049,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.97263 1 1 1 1 0 T 3 4 62 172967263 172967263 G T 1 0 0 0 0 1 0 0 0 13205 1188 41 2 2 RAPGEF4 2 172967263 Missense_Mutation SNP G C3N-00704_T 2562890 172967263 69226266 103 19240 ZNF804A 0 . GRCh38 2 184936198 184936198 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.802C>A p.Leu268Ile p.L268I ENST00000302277 4/4 179 150 29 233 233 0 strelka-varscan ZNF804A,missense_variant,p.Leu268Ile,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Leu183Ile,ENST00000613975,; A ENST00000302277 Transcript missense_variant 1396/4690 802/3630 268/1209 L/I Ctt/Att 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.21) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 184936198 184936198 C A 1 0 0 0 0 1 0 0 0 18755 797 28 2 2 ZNF804A 2 184936198 Missense_Mutation SNP C C3N-00704_T 11968935 184936198 57257331 104 19241 CALCRL 0 . GRCh38 2 187380562 187380562 + Missense_Mutation SNP A A T rs764002527 C3N-00704_T C3N-00704_N A A c.313T>A p.Cys105Ser p.C105S ENST00000409998 8/16 114 95 19 170 170 0 strelka-varscan CALCRL,missense_variant,p.Cys105Ser,ENST00000409998,;CALCRL,missense_variant,p.Cys105Ser,ENST00000392370,NM_005795.5;CALCRL,missense_variant,p.Cys105Ser,ENST00000410068,NM_001271751.1;CALCRL,downstream_gene_variant,,ENST00000447403,;CALCRL,downstream_gene_variant,,ENST00000410102,;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; T ENST00000409998 Transcript missense_variant 1095/5223 313/1386 105/461 C/S Tgt/Agt rs764002527 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF deleterious(0) 8/16 PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF67,Pfam_domain:PF02793,SMART_domains:SM00008,Superfamily_domains:SSF111418 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 187380562 187380562 A T 1 0 0 0 0 1 0 0 0 2270 188 7 4 4 CALCRL 2 187380562 Missense_Mutation SNP A C3N-00704_T 2444364 187380562 54812967 105 19242 HIBCH 0 . GRCh38 2 190290423 190290423 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.367A>G p.Met123Val p.M123V ENST00000359678 5/14 179 140 39 423 423 0 strelka-varscan HIBCH,missense_variant,p.Met123Val,ENST00000392332,NM_198047.2;HIBCH,missense_variant,p.Met123Val,ENST00000359678,NM_014362.3;HIBCH,missense_variant,p.Met177Val,ENST00000409934,;HIBCH,missense_variant,p.Met22Val,ENST00000392333,; C ENST00000359678 Transcript missense_variant 662/1939 367/1161 123/386 M/V Atg/Gtg 1 -1 HIBCH HGNC HGNC:4908 protein_coding YES CCDS2304.1 ENSP00000352706 Q6NVY1 A0A140VJL0 UPI000013F16E NM_014362.3 tolerated(0.42) 5/14 Gene3D:3.90.226.10,Pfam_domain:PF16113,hmmpanther:PTHR11941,hmmpanther:PTHR11941:SF53,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 190290423 190290423 T C 1 0 0 0 0 1 0 0 0 6984 1406 49 5 5 HIBCH 2 190290423 Missense_Mutation SNP T C3N-00704_T 2909861 190290423 51903106 106 19243 DNAH7 0 . GRCh38 2 195910047 195910047 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.4084G>T p.Ala1362Ser p.A1362S ENST00000312428 25/65 114 91 23 151 151 0 strelka-varscan DNAH7,missense_variant,p.Ala1362Ser,ENST00000312428,NM_018897.2;DNAH7,upstream_gene_variant,,ENST00000475293,; A ENST00000312428 Transcript missense_variant 4185/12394 4084/12075 1362/4024 A/S Gct/Tct 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.03) 25/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12774,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 195910047 195910047 C A 1 0 0 0 0 1 0 0 0 4421 739 26 2 2 DNAH7 2 195910047 Missense_Mutation SNP C C3N-00704_T 5619624 195910047 46283482 107 19244 C2orf80 0 . GRCh38 2 208189961 208189961 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.62C>A p.Ser21Tyr p.S21Y ENST00000451346 1/7 262 222 40 284 284 0 strelka-varscan C2orf80,missense_variant,p.Ser21Tyr,ENST00000451346,;C2orf80,5_prime_UTR_variant,,ENST00000341287,NM_001099334.2;C2orf80,5_prime_UTR_variant,,ENST00000449053,;C2orf80,upstream_gene_variant,,ENST00000453017,;C2orf80,upstream_gene_variant,,ENST00000423952,; T ENST00000451346 Transcript missense_variant 64/979 62/525 21/174 S/Y tCt/tAt 1 -1 C2orf80 HGNC HGNC:34352 protein_coding ENSP00000405393 C9J2L1 UPI000198C640 deleterious_low_confidence(0.02) 1/7 hmmpanther:PTHR36296 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 208189961 208189961 G T 1 0 0 0 0 1 0 0 0 2051 956 33 2 2 C2orf80 2 208189961 Missense_Mutation SNP G C3N-00704_T 12279914 208189961 34003568 108 19245 UNC80 0 . GRCh38 2 209970905 209970905 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.8006C>G p.Pro2669Arg p.P2669R ENST00000439458 53/64 180 162 18 189 189 0 strelka-varscan UNC80,missense_variant,p.Pro2669Arg,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Pro2664Arg,ENST00000272845,NM_182587.3;UNC80,missense_variant,p.Pro195Arg,ENST00000333907,;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,;UNC80,downstream_gene_variant,,ENST00000489023,; G ENST00000439458 Transcript missense_variant 8086/13562 8006/9777 2669/3258 P/R cCa/cGa 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious(0) 53/64 Low_complexity_(Seg):seg,hmmpanther:PTHR31781:SF1,hmmpanther:PTHR31781 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 209970905 209970905 C G 1 0 0 0 0 1 0 0 0 17521 594 21 4 4 UNC80 2 209970905 Missense_Mutation SNP C C3N-00704_T 1780944 209970905 32222624 109 19246 ABCA12 0 . GRCh38 2 214989380 214989380 + Missense_Mutation SNP C C T C3N-00704_T C3N-00704_N C C c.3778G>A p.Asp1260Asn p.D1260N ENST00000272895 26/53 335 293 42 401 401 0 strelka-varscan ABCA12,missense_variant,p.Asp1260Asn,ENST00000272895,NM_173076.2;ABCA12,missense_variant,p.Asp942Asn,ENST00000389661,NM_015657.3; T ENST00000272895 Transcript missense_variant 3998/9100 3778/7788 1260/2595 D/N Gac/Aac COSM4806636,COSM4806637 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 deleterious(0) 26/53 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF29,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 214989380 214989380 C T 1 0 0 0 0 1 0 0 0 34 826 29 3 3 ABCA12 2 214989380 Missense_Mutation SNP C C3N-00704_T 5018475 214989380 27204149 110 19247 TNS1 0 . GRCh38 2 217885077 217885077 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.829G>A p.Gly277Arg p.G277R ENST00000171887 14/33 298 245 53 299 299 0 strelka-varscan TNS1,missense_variant,p.Gly277Arg,ENST00000171887,NM_022648.4;TNS1,missense_variant,p.Gly277Arg,ENST00000611415,;TNS1,missense_variant,p.Gly277Arg,ENST00000419504,;TNS1,missense_variant,p.Gly277Arg,ENST00000430930,NM_001308023.1;TNS1,missense_variant,p.Gly402Arg,ENST00000446903,;TNS1,missense_variant,p.Gly308Arg,ENST00000310858,;TNS1,missense_variant,p.Gly345Arg,ENST00000413554,;TNS1,missense_variant,p.Gly53Arg,ENST00000453356,;TNS1,5_prime_UTR_variant,,ENST00000615025,;TNS1,non_coding_transcript_exon_variant,,ENST00000479185,; T ENST00000171887 Transcript missense_variant 1282/10331 829/5208 277/1735 G/R Ggg/Agg 1 -1 TNS1 HGNC HGNC:11973 protein_coding YES CCDS2407.1 ENSP00000171887 Q9HBL0 UPI0000456EEB NM_022648.4 tolerated(0.08) 14/33 Gene3D:1d5rA02,Pfam_domain:PF10409,PROSITE_profiles:PS51182,hmmpanther:PTHR12305,hmmpanther:PTHR12305:SF40,SMART_domains:SM01326,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 217885077 217885077 C T 1 0 0 0 0 1 0 0 0 16816 623 22 3 3 TNS1 2 217885077 Missense_Mutation SNP C C3N-00704_T 2895697 217885077 24308452 111 19248 DOCK10 0 . GRCh38 2 224864996 224864996 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1349C>G p.Ala450Gly p.A450G ENST00000258390 12/56 490 412 78 520 520 0 strelka-varscan-mutect DOCK10,missense_variant,p.Ala444Gly,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Ala450Gly,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,; C ENST00000258390 Transcript missense_variant 1417/7260 1349/6561 450/2186 A/G gCt/gGt 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 tolerated(0.33) 12/56 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 224864996 224864996 G C 1 0 0 0 0 1 0 0 0 4500 971 34 4 4 DOCK10 2 224864996 Missense_Mutation SNP G C3N-00704_T 6979919 224864996 17328533 112 19249 DOCK10 0 . GRCh38 2 224865051 224865051 + Missense_Mutation SNP G G C rs754969484 C3N-00704_T C3N-00704_N G G c.1294C>G p.Leu432Val p.L432V ENST00000258390 12/56 301 244 57 334 334 0 strelka-varscan-mutect DOCK10,missense_variant,p.Leu426Val,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Leu432Val,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,; C ENST00000258390 Transcript missense_variant 1362/7260 1294/6561 432/2186 L/V Ctc/Gtc rs754969484 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 tolerated(1) 12/56 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS rs754969484 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 224865051 224865051 G C 1 0 0 0 0 1 0 0 0 4500 1000 35 4 4 DOCK10 2 224865051 Missense_Mutation SNP G C3N-00704_T 55 224865051 17328478 113 19250 COL4A4 0 . GRCh38 2 227118722 227118722 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.412A>G p.Met138Val p.M138V ENST00000396625 7/48 365 299 66 364 364 0 strelka-varscan-mutect COL4A4,missense_variant,p.Met138Val,ENST00000396625,NM_000092.4; C ENST00000396625 Transcript missense_variant 620/9895 412/5073 138/1690 M/V Atg/Gtg 1 -1 COL4A4 HGNC HGNC:2206 protein_coding YES CCDS42828.1 ENSP00000379866 P53420 UPI000013D987 NM_000092.4 tolerated(0.16) 7/48 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF533,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 227118722 227118722 T C 1 0 0 0 0 1 0 0 0 3482 1406 49 5 5 COL4A4 2 227118722 Missense_Mutation SNP T C3N-00704_T 2253671 227118722 15074807 114 19251 GPR55 0 . GRCh38 2 230910836 230910836 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.127C>A p.His43Asn p.H43N ENST00000392040 2/2 208 160 48 271 271 0 strelka-varscan-mutect GPR55,missense_variant,p.His43Asn,ENST00000392040,NM_005683.3;GPR55,missense_variant,p.His43Asn,ENST00000622008,;GPR55,missense_variant,p.His43Asn,ENST00000392039,;GPR55,missense_variant,p.His43Asn,ENST00000438398,;AC012507.4,downstream_gene_variant,,ENST00000454890,;GPR55,missense_variant,p.His43Asn,ENST00000444078,; T ENST00000392040 Transcript missense_variant 320/3828 127/960 43/319 H/N Cat/Aat 1 -1 GPR55 HGNC HGNC:4511 protein_coding YES CCDS2480.1 ENSP00000375894 Q9Y2T6 A8K858 UPI000006D64F NM_005683.3 tolerated(0.31) 2/2 Gene3D:1.20.1070.10,PROSITE_profiles:PS50262,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF56,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 230910836 230910836 G T 1 0 0 0 0 1 0 0 0 6584 1348 47 2 2 GPR55 2 230910836 Missense_Mutation SNP G C3N-00704_T 3792114 230910836 11282693 115 19252 NGEF 0 . GRCh38 2 232891400 232891400 + Silent SNP G G T C3N-00704_T C3N-00704_N G G c.1230C>A p.= p.I410I ENST00000264051 8/15 204 172 32 231 231 0 strelka-varscan-mutect NGEF,synonymous_variant,p.=,ENST00000264051,NM_019850.2;NGEF,synonymous_variant,p.=,ENST00000373552,NM_001114090.1;NGEF,synonymous_variant,p.=,ENST00000416114,;NGEF,downstream_gene_variant,,ENST00000409079,;NGEF,upstream_gene_variant,,ENST00000424488,;NGEF,downstream_gene_variant,,ENST00000420650,;NGEF,upstream_gene_variant,,ENST00000461944,; T ENST00000264051 Transcript synonymous_variant 1509/3215 1230/2133 410/710 I atC/atA COSM5066145,COSM5066146,COSM5066147 1 -1 NGEF HGNC HGNC:7807 protein_coding YES CCDS2500.1 ENSP00000264051 Q8N5V2 UPI000013D4AE NM_019850.2 8/15 PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 232891400 232891400 G T 1 0 0 0 0 0 0 0 1 10430 1164 41 2 2 NGEF 2 232891400 Silent SNP G C3N-00704_T 1980564 232891400 9302129 116 19253 SH3BP4 0 . GRCh38 2 235040932 235040932 + Frame_Shift_Del DEL G G - rs748959328 C3N-00704_T C3N-00704_N G G c.164delG p.Gly55GlufsTer6 p.G55Efs*6 ENST00000409212 4/6 107 88 19 138 138 0 sindel-varindel-pindel SH3BP4,frameshift_variant,p.Gly55GlufsTer6,ENST00000409212,;SH3BP4,frameshift_variant,p.Gly55GlufsTer6,ENST00000392011,NM_014521.2;SH3BP4,frameshift_variant,p.Gly55GlufsTer6,ENST00000344528,;SH3BP4,frameshift_variant,p.Gly55GlufsTer6,ENST00000446904,;SH3BP4,frameshift_variant,p.Gly55GlufsTer6,ENST00000416021,;SH3BP4,frameshift_variant,p.Gly55GlufsTer?,ENST00000444916,;SH3BP4,frameshift_variant,p.Gly55GlufsTer?,ENST00000454947,; - ENST00000409212 Transcript frameshift_variant 670/5231 163/2892 55/963 G/X Gga/ga rs748959328 1 1 SH3BP4 HGNC HGNC:10826 protein_coding YES CCDS2513.1 ENSP00000386862 Q9P0V3 UPI000006DA47 4/6 PROSITE_profiles:PS50002,hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF3,Superfamily_domains:SSF50044 HIGH 1 deletion 5 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999717 1 1 1 0 - 7 5 62 235040932 235040932 G - 1 0 1 0 1 0 0 0 0 14504 1117 39 0 0 SH3BP4 2 235040932 Frame_Shift_Del DEL G C3N-00704_T 2149532 235040932 7152597 117 19254 IQCA1 0 . GRCh38 2 236497360 236497360 + Missense_Mutation SNP C C A rs369386783 C3N-00704_T C3N-00704_N C C c.160G>T p.Val54Leu p.V54L ENST00000431676 2/19 374 326 48 425 424 1 strelka-varscan-mutect IQCA1,missense_variant,p.Val47Leu,ENST00000409907,NM_024726.4;IQCA1,missense_variant,p.Val47Leu,ENST00000309507,NM_001270584.1;IQCA1,missense_variant,p.Val54Leu,ENST00000431676,NM_001270585.1;IQCA1,missense_variant,p.Val66Leu,ENST00000418802,;IQCA1,missense_variant,p.Val47Leu,ENST00000254653,; A ENST00000431676 Transcript missense_variant 195/3069 160/2493 54/830 V/L Gta/Tta rs369386783 1 -1 IQCA1 HGNC HGNC:26195 protein_coding YES CCDS74677.1 ENSP00000407213 A0A0A0MSY6 UPI0001AE77A0 NM_001270585.1 tolerated(0.47) 2/19 hmmpanther:PTHR14690,hmmpanther:PTHR14690:SF8 MODERATE 1 SNV 2 1 PASS rs369386783 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 236497360 236497360 C A 1 0 0 0 0 1 0 0 0 7705 536 19 1 1 IQCA1 2 236497360 Missense_Mutation SNP C C3N-00704_T 1456428 236497360 5696169 118 19255 KLHL30 0 . GRCh38 2 238149072 238149072 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1405C>A p.Leu469Met p.L469M ENST00000409223 7/8 281 245 36 353 353 0 strelka-varscan-mutect KLHL30,missense_variant,p.Leu469Met,ENST00000409223,NM_198582.3;KLHL30-AS1,downstream_gene_variant,,ENST00000623136,; A ENST00000409223 Transcript missense_variant 1512/3726 1405/1737 469/578 L/M Ctg/Atg 1 1 KLHL30 HGNC HGNC:24770 protein_coding YES CCDS46555.2 ENSP00000386389 Q0D2K2 UPI00001D7DA5 NM_198582.3 tolerated(0.09) 7/8 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF9 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 238149072 238149072 C A 1 0 0 0 0 1 0 0 0 8249 564 20 2 2 KLHL30 2 238149072 Missense_Mutation SNP C C3N-00704_T 1651712 238149072 4044457 119 19256 CROCC2 0 . GRCh38 2 240963768 240963768 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.3306G>T p.Lys1102Asn p.K1102N ENST00000443866 21/32 110 92 18 120 120 0 strelka-varscan-mutect CROCC2,missense_variant,p.Lys1102Asn,ENST00000443866,;AC104809.4,intron_variant,,ENST00000418218,;AC104809.4,upstream_gene_variant,,ENST00000457369,;AC104809.4,upstream_gene_variant,,ENST00000438506,; T ENST00000443866 Transcript missense_variant 3490/5382 3306/4968 1102/1655 K/N aaG/aaT 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A deleterious(0) 21/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS rs1269688872 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 240963768 240963768 G T 1 0 0 0 0 1 0 0 0 3695 1014 35 2 2 CROCC2 2 240963768 Missense_Mutation SNP G C3N-00704_T 2814696 240963768 1229761 120 19257 CHL1 0 . GRCh38 3 361753 361753 + Missense_Mutation SNP G G A C3N-00704_T C3N-00704_N G G c.1361G>A p.Gly454Glu p.G454E ENST00000256509 13/28 155 122 33 212 212 0 strelka-varscan-mutect CHL1,missense_variant,p.Gly454Glu,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Gly454Glu,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Gly438Glu,ENST00000397491,NM_001253387.1;CHL1-AS1,downstream_gene_variant,,ENST00000417612,;CHL1-AS1,downstream_gene_variant,,ENST00000608098,;CHL1,non_coding_transcript_exon_variant,,ENST00000471332,;CHL1,3_prime_UTR_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant 2003/8023 1361/3675 454/1224 G/E gGg/gAg COSM1179800 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 deleterious(0.02) 13/28 Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS rs1459767123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 361753 361753 G A 1 0 0 0 0 1 0 0 0 3108 1232 43 3 3 CHL1 3 361753 Missense_Mutation SNP G C3N-00704_T 361753 197933806 121 19258 ARPC4-TTLL3 0 . GRCh38 3 9825836 9825836 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.1191C>A p.= p.V397V ENST00000426895 8/13 367 302 65 516 516 0 strelka-varscan-mutect TTLL3,synonymous_variant,p.=,ENST00000383827,;TTLL3,synonymous_variant,p.=,ENST00000455274,;TTLL3,synonymous_variant,p.=,ENST00000426895,NM_001025930.3;ARPC4-TTLL3,synonymous_variant,p.=,ENST00000397256,NM_001198793.1;TTLL3,synonymous_variant,p.=,ENST00000430793,;TTLL3,synonymous_variant,p.=,ENST00000443148,;TTLL3,synonymous_variant,p.=,ENST00000310252,;TTLL3,synonymous_variant,p.=,ENST00000452823,;TTLL3,upstream_gene_variant,,ENST00000471058,;TTLL3,upstream_gene_variant,,ENST00000466245,;TTLL3,missense_variant,p.Pro116Thr,ENST00000430390,;TTLL3,synonymous_variant,p.=,ENST00000473661,;TTLL3,synonymous_variant,p.=,ENST00000438141,;TTLL3,3_prime_UTR_variant,,ENST00000427220,;TTLL3,non_coding_transcript_exon_variant,,ENST00000496526,;TTLL3,non_coding_transcript_exon_variant,,ENST00000483051,;TTLL3,non_coding_transcript_exon_variant,,ENST00000492440,;TTLL3,non_coding_transcript_exon_variant,,ENST00000482269,;TTLL3,intron_variant,,ENST00000431204,;TTLL3,downstream_gene_variant,,ENST00000602338,; A ENST00000426895 Transcript synonymous_variant 1210/2767 1191/2748 397/915 V gtC/gtA 1 1 TTLL3 HGNC HGNC:24483 protein_coding YES CCDS43048.2 ENSP00000392549 J3KQB2 UPI0001B79456 NM_001025930.3 8/13 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51221,Pfam_domain:PF03133 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 9825836 9825836 C A 1 0 0 0 0 0 0 0 1 1116 842 30 2 2 ARPC4-TTLL3 3 9825836 Silent SNP C C3N-00704_T 9464083 9825836 188469723 122 19259 XIRP1 0 . GRCh38 3 39189258 39189258 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.188C>A p.Pro63His p.P63H ENST00000340369 2/2 116 85 31 202 202 0 strelka-varscan-mutect XIRP1,missense_variant,p.Pro63His,ENST00000340369,NM_194293.2;XIRP1,missense_variant,p.Pro63His,ENST00000396251,NM_001198621.2;XIRP1,intron_variant,,ENST00000421646,; T ENST00000340369 Transcript missense_variant 417/6460 188/5532 63/1843 P/H cCt/cAt 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 deleterious(0) 2/2 hmmpanther:PTHR22591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 39189258 39189258 G T 1 0 0 0 0 1 0 0 0 17988 1000 35 2 2 XIRP1 3 39189258 Missense_Mutation SNP G C3N-00704_T 29363422 39189258 159106301 123 19260 CACNA2D2 0 . GRCh38 3 50384212 50384212 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.636G>T p.= p.T212T ENST00000479441 6/39 124 90 34 187 187 0 strelka-varscan-mutect CACNA2D2,synonymous_variant,p.=,ENST00000266039,NM_001005505.2;CACNA2D2,synonymous_variant,p.=,ENST00000423994,;CACNA2D2,synonymous_variant,p.=,ENST00000429770,;CACNA2D2,synonymous_variant,p.=,ENST00000360963,NM_001291101.1;CACNA2D2,synonymous_variant,p.=,ENST00000424201,NM_006030.3;CACNA2D2,synonymous_variant,p.=,ENST00000479441,NM_001174051.2; A ENST00000479441 Transcript synonymous_variant 636/3453 636/3453 212/1150 T acG/acT 1 -1 CACNA2D2 HGNC HGNC:1400 protein_coding YES CCDS54588.1 ENSP00000418081 Q9NY47 UPI0000E5A6AF NM_001174051.2 6/39 Pfam_domain:PF08399,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF7 LOW 1 SNV 1 1 PASS rs1335792927 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 50384212 50384212 C A 1 0 0 0 0 0 0 0 1 2237 639 23 1 1 CACNA2D2 3 50384212 Silent SNP C C3N-00704_T 11194954 50384212 147911347 124 19261 STAB1 0 . GRCh38 3 52518581 52518581 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.4855C>A p.Pro1619Thr p.P1619T ENST00000321725 47/69 227 186 41 390 390 0 strelka-varscan-mutect STAB1,missense_variant,p.Pro1619Thr,ENST00000321725,NM_015136.2;STAB1,upstream_gene_variant,,ENST00000469989,;STAB1,non_coding_transcript_exon_variant,,ENST00000461325,;STAB1,upstream_gene_variant,,ENST00000481626,;STAB1,upstream_gene_variant,,ENST00000462741,;STAB1,upstream_gene_variant,,ENST00000462681,; A ENST00000321725 Transcript missense_variant 4931/7928 4855/7713 1619/2570 P/T Ccg/Acg 1 1 STAB1 HGNC HGNC:18628 protein_coding YES CCDS33768.1 ENSP00000312946 Q9NY15 UPI0000140C12 NM_015136.2 deleterious(0) 47/69 Gene3D:2.30.180.10,Pfam_domain:PF02469,PROSITE_profiles:PS50213,hmmpanther:PTHR24038,hmmpanther:PTHR24038:SF2,SMART_domains:SM00554,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS rs1164265974 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 52518581 52518581 C A 1 0 0 0 0 1 0 0 0 15615 739 26 2 2 STAB1 3 52518581 Missense_Mutation SNP C C3N-00704_T 2134369 52518581 145776978 125 19262 ERC2 0 . GRCh38 3 56010550 56010550 + Missense_Mutation SNP C C T C3N-00704_T C3N-00704_N C C c.1819G>A p.Asp607Asn p.D607N ENST00000288221 9/18 90 77 13 116 116 0 strelka-varscan-mutect ERC2,missense_variant,p.Asp607Asn,ENST00000288221,NM_015576.1;ERC2,missense_variant,p.Asp607Asn,ENST00000612797,;ERC2,missense_variant,p.Asp246Asn,ENST00000492584,;ERC2,missense_variant,p.Asp607Asn,ENST00000460849,; T ENST00000288221 Transcript missense_variant 2075/6138 1819/2874 607/957 D/N Gat/Aat COSM3596513,COSM3596514 1 -1 ERC2 HGNC HGNC:31922 protein_coding YES CCDS46851.1 ENSP00000288221 O15083 UPI00001C1572 NM_015576.1 deleterious(0.01) 9/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10174,hmmpanther:PTHR18861,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 56010550 56010550 C T 1 0 0 0 0 1 0 0 0 5060 913 32 3 3 ERC2 3 56010550 Missense_Mutation SNP C C3N-00704_T 3491969 56010550 142285009 126 19263 CADPS 0 . GRCh38 3 62403086 62403086 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.3877G>T p.Val1293Leu p.V1293L ENST00000383710 29/30 116 92 24 124 124 0 strelka-varscan-mutect CADPS,missense_variant,p.Val1293Leu,ENST00000383710,NM_003716.3;CADPS,missense_variant,p.Val1284Leu,ENST00000612439,;CADPS,missense_variant,p.Val1214Leu,ENST00000357948,NM_183393.2;CADPS,missense_variant,p.Val1254Leu,ENST00000283269,NM_183394.2;CADPS,missense_variant,p.Val285Leu,ENST00000473635,;CADPS,missense_variant,p.Val162Leu,ENST00000613879,;CADPS,downstream_gene_variant,,ENST00000466621,;CADPS,non_coding_transcript_exon_variant,,ENST00000474560,;CADPS,non_coding_transcript_exon_variant,,ENST00000486172,; A ENST00000383710 Transcript missense_variant 4227/5471 3877/4062 1293/1353 V/L Gta/Tta 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 deleterious(0.03) 29/30 hmmpanther:PTHR12166:SF6,hmmpanther:PTHR12166 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 62403086 62403086 C A 1 0 0 0 0 1 0 0 0 2260 521 18 2 2 CADPS 3 62403086 Missense_Mutation SNP C C3N-00704_T 6392536 62403086 135892473 127 19264 PDZRN3 0 . GRCh38 3 73624388 73624388 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.438C>A p.Cys146Ter p.C146* ENST00000263666 1/10 71 54 17 55 55 0 strelka-varscan-mutect PDZRN3,stop_gained,p.Cys146Ter,ENST00000263666,NM_015009.2;PDZRN3,stop_gained,p.Cys146Ter,ENST00000308537,;PDZRN3-AS1,intron_variant,,ENST00000478988,;PDZRN3-AS1,intron_variant,,ENST00000608743,;PDZRN3-AS1,intron_variant,,ENST00000608304,;PDZRN3-AS1,intron_variant,,ENST00000619517,;CTD-2006M22.2,upstream_gene_variant,,ENST00000625169,; T ENST00000263666 Transcript stop_gained 553/4248 438/3201 146/1066 C/* tgC/tgA 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 1/10 Superfamily_domains:SSF49599 HIGH 1 SNV 1 1 PASS rs1301415586 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 73624388 73624388 G T 1 0 0 0 0 0 1 0 0 11797 1079 38 1 1 PDZRN3 3 73624388 Nonsense_Mutation SNP G C3N-00704_T 11221302 73624388 124671171 128 19265 OR5H1 0 . GRCh38 3 98133131 98133131 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.434T>C p.Leu145Ser p.L145S ENST00000354565 1/1 197 169 28 332 332 0 strelka-varscan-mutect OR5H1,missense_variant,p.Leu145Ser,ENST00000354565,NM_001005338.1;RP11-343D2.11,intron_variant,,ENST00000508964,; C ENST00000354565 Transcript missense_variant 434/942 434/942 145/313 L/S tTa/tCa 1 1 OR5H1 HGNC HGNC:8346 protein_coding YES CCDS33797.1 ENSP00000346575 A6NKK0 A0A126GW79 UPI0000197652 NM_001005338.1 tolerated(0.08) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF135,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs1467908282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 98133131 98133131 T C 1 0 0 0 0 1 0 0 0 11229 1764 61 5 5 OR5H1 3 98133131 Missense_Mutation SNP T C3N-00704_T 24508743 98133131 100162428 129 19266 OR5H15 0 . GRCh38 3 98169005 98169005 + Silent SNP T T C novel C3N-00704_T C3N-00704_N T T c.306T>C p.= p.F102F ENST00000356526 1/1 297 233 64 402 402 0 strelka-varscan-mutect OR5H15,synonymous_variant,p.=,ENST00000356526,NM_001005515.1;OR5H15,synonymous_variant,p.=,ENST00000615035,; C ENST00000356526 Transcript synonymous_variant 306/942 306/942 102/313 F ttT/ttC 1 1 OR5H15 HGNC HGNC:31287 protein_coding YES CCDS33799.1 ENSP00000373195 A6NDH6 UPI00001606CE NM_001005515.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF325,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 62 98169005 98169005 T C 1 0 0 0 0 0 0 0 1 11231 1838 64 5 5 OR5H15 3 98169005 Silent SNP T C3N-00704_T 35874 98169005 100126554 130 19267 CLDND1 0 . GRCh38 3 98516840 98516840 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.650G>T p.Gly217Val p.G217V ENST00000394181 6/6 292 245 47 293 293 0 strelka-varscan-mutect CLDND1,missense_variant,p.Gly194Val,ENST00000503004,;CLDND1,missense_variant,p.Gly194Val,ENST00000394180,NM_019895.2;CLDND1,missense_variant,p.Gly217Val,ENST00000394181,NM_001040182.1;CLDND1,missense_variant,p.Gly194Val,ENST00000341181,NM_001040183.1,NM_001040181.1,NM_001040199.1;CLDND1,missense_variant,p.Gly194Val,ENST00000394185,;CLDND1,missense_variant,p.Gly194Val,ENST00000510545,;CLDND1,missense_variant,p.Gly194Val,ENST00000514537,;CLDND1,missense_variant,p.Gly194Val,ENST00000513287,;CLDND1,missense_variant,p.Gly194Val,ENST00000508902,;CLDND1,missense_variant,p.Gly172Val,ENST00000511667,;CLDND1,missense_variant,p.Gly194Val,ENST00000502299,;CLDND1,missense_variant,p.Gly194Val,ENST00000513452,;CLDND1,missense_variant,p.Gly99Val,ENST00000511081,NM_001040200.1;CLDND1,missense_variant,p.Gly79Val,ENST00000512147,;CLDND1,missense_variant,p.Gly79Val,ENST00000510541,;CLDND1,missense_variant,p.Gly50Val,ENST00000513873,;CLDND1,intron_variant,,ENST00000507874,;CLDND1,intron_variant,,ENST00000506885,;CLDND1,intron_variant,,ENST00000502288,;CLDND1,downstream_gene_variant,,ENST00000507944,;CLDND1,downstream_gene_variant,,ENST00000508659,;CLDND1,downstream_gene_variant,,ENST00000515620,;CLDND1,downstream_gene_variant,,ENST00000508071,;CLDND1,downstream_gene_variant,,ENST00000503621,;CLDND1,downstream_gene_variant,,ENST00000506575,;CLDND1,non_coding_transcript_exon_variant,,ENST00000508503,;CLDND1,non_coding_transcript_exon_variant,,ENST00000507411,;CLDND1,non_coding_transcript_exon_variant,,ENST00000506927,;CLDND1,downstream_gene_variant,,ENST00000502980,;CLDND1,downstream_gene_variant,,ENST00000513988,;CPOX,downstream_gene_variant,,ENST00000512905,;CLDND1,downstream_gene_variant,,ENST00000503799,; A ENST00000394181 Transcript missense_variant 813/2170 650/831 217/276 G/V gGa/gTa 1 -1 CLDND1 HGNC HGNC:1322 protein_coding YES CCDS46877.1 ENSP00000377735 A0A0R4J2F2 UPI0000469E7B NM_001040182.1 deleterious(0.01) 6/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR14347,hmmpanther:PTHR14347:SF3,Pfam_domain:PF13903 MODERATE 1 SNV 1 1 PASS rs1244290647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 98516840 98516840 C A 1 0 0 0 0 1 0 0 0 3259 855 30 2 2 CLDND1 3 98516840 Missense_Mutation SNP C C3N-00704_T 347835 98516840 99778719 131 19268 CCDC54 0 . GRCh38 3 107378477 107378477 + Missense_Mutation SNP C C A rs367560807 C3N-00704_T C3N-00704_N C C c.890C>A p.Thr297Asn p.T297N ENST00000261058 1/1 261 225 36 291 291 0 strelka-varscan-mutect CCDC54,missense_variant,p.Thr297Asn,ENST00000261058,NM_032600.2;RP11-446H18.5,intron_variant,,ENST00000599431,;RP11-446H18.5,intron_variant,,ENST00000595232,;RP11-446H18.5,intron_variant,,ENST00000593837,; A ENST00000261058 Transcript missense_variant 1284/1444 890/987 297/328 T/N aCt/aAt rs367560807 1 1 CCDC54 HGNC HGNC:30703 protein_coding YES CCDS2949.1 ENSP00000261058 Q8NEL0 A0A140VJF9 UPI000006EB42 NM_032600.2 deleterious(0.03) 1/1 hmmpanther:PTHR37880 MODERATE 1 SNV 1 PASS rs367560807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 107378477 107378477 C A 1 0 0 0 0 1 0 0 0 2528 565 20 2 2 CCDC54 3 107378477 Missense_Mutation SNP C C3N-00704_T 8861637 107378477 90917082 132 19269 PHLDB2 0 . GRCh38 3 111920405 111920405 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.1987G>T p.Gly663Cys p.G663C ENST00000431670 5/18 73 55 18 136 136 0 strelka-varscan-mutect PHLDB2,missense_variant,p.Gly663Cys,ENST00000431670,NM_001134438.1;PHLDB2,missense_variant,p.Gly663Cys,ENST00000412622,NM_145753.2;PHLDB2,missense_variant,p.Gly690Cys,ENST00000393923,NM_001134437.1;PHLDB2,missense_variant,p.Gly663Cys,ENST00000393925,NM_001134439.1;PHLDB2,missense_variant,p.Gly663Cys,ENST00000481953,;PHLDB2,missense_variant,p.Gly249Cys,ENST00000495180,;PHLDB2,missense_variant,p.Gly663Cys,ENST00000498699,;PHLDB2,downstream_gene_variant,,ENST00000477695,; T ENST00000431670 Transcript missense_variant 2398/6127 1987/3762 663/1253 G/C Ggt/Tgt COSM1670419,COSM1670420,COSM1670421 1 1 PHLDB2 HGNC HGNC:29573 protein_coding YES CCDS46886.1 ENSP00000405405 Q86SQ0 UPI0000457152 NM_001134438.1 deleterious(0.01) 5/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF21 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 111920405 111920405 G T 1 0 0 0 0 1 0 0 0 11940 1348 47 2 2 PHLDB2 3 111920405 Missense_Mutation SNP G C3N-00704_T 4541928 111920405 86375154 133 19270 IGSF11 0 . GRCh38 3 118902719 118902719 + Missense_Mutation SNP G G T rs770373736 C3N-00704_T C3N-00704_N G G c.1097C>A p.Pro366Gln p.P366Q ENST00000393775 7/7 234 193 41 253 253 0 strelka-varscan-mutect IGSF11,missense_variant,p.Pro365Gln,ENST00000425327,NM_152538.2;IGSF11,missense_variant,p.Pro366Gln,ENST00000393775,NM_001015887.1;IGSF11,missense_variant,p.Pro342Gln,ENST00000489689,;IGSF11,missense_variant,p.Pro365Gln,ENST00000354673,;IGSF11,missense_variant,p.Pro341Gln,ENST00000441144,;IGSF11,missense_variant,p.Pro338Gln,ENST00000491903,; T ENST00000393775 Transcript missense_variant 1403/3495 1097/1296 366/431 P/Q cCg/cAg rs770373736 1 -1 IGSF11 HGNC HGNC:16669 protein_coding YES CCDS46891.1 ENSP00000377370 Q5DX21 UPI000013D9B3 NM_001015887.1 deleterious(0.01) 7/7 hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF74 MODERATE 1 SNV 1 1 PASS rs770373736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 118902719 118902719 G T 1 0 0 0 0 1 0 0 0 7505 1116 39 1 1 IGSF11 3 118902719 Missense_Mutation SNP G C3N-00704_T 6982314 118902719 79392840 134 19271 PARP14 0 . GRCh38 3 122720308 122720308 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.4861G>A p.Glu1621Lys p.E1621K ENST00000474629 15/17 293 246 47 356 356 0 strelka-varscan-mutect PARP14,missense_variant,p.Glu1621Lys,ENST00000474629,NM_017554.2;PARP14,non_coding_transcript_exon_variant,,ENST00000475640,;PARP14,missense_variant,p.Glu1462Lys,ENST00000460683,;PARP14,non_coding_transcript_exon_variant,,ENST00000474669,; A ENST00000474629 Transcript missense_variant 5127/7915 4861/5406 1621/1801 E/K Gag/Aag 1 1 PARP14 HGNC HGNC:29232 protein_coding YES CCDS46894.1 ENSP00000418194 Q460N5 UPI00015A20AB NM_017554.2 tolerated(0.46) 15/17 PROSITE_profiles:PS51059,hmmpanther:PTHR14453:SF65,hmmpanther:PTHR14453,Gene3D:3.90.228.10,Superfamily_domains:SSF56399 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 122720308 122720308 G A 1 0 0 0 0 1 0 0 0 11538 1175 41 3 3 PARP14 3 122720308 Missense_Mutation SNP G C3N-00704_T 3817589 122720308 75575251 135 19272 KALRN 0 . GRCh38 3 124326076 124326076 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.1183C>A p.Gln395Lys p.Q395K ENST00000240874 7/34 147 120 27 172 172 0 strelka-varscan-mutect KALRN,missense_variant,p.Gln395Lys,ENST00000360013,NM_001024660.3;KALRN,missense_variant,p.Gln373Lys,ENST00000354186,;KALRN,missense_variant,p.Gln395Lys,ENST00000240874,NM_003947.4;KALRN,missense_variant,p.Gln395Lys,ENST00000460856,NM_001322989.1;KALRN,non_coding_transcript_exon_variant,,ENST00000498499,; A ENST00000240874 Transcript missense_variant 1340/6537 1183/4992 395/1663 Q/K Cag/Aag COSM1693359,COSM1693360 1 1 KALRN HGNC HGNC:4814 protein_coding YES CCDS3027.1 ENSP00000240874 O60229 UPI000012C095 NM_003947.4 tolerated(0.4) 7/34 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,SMART_domains:SM00150,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 124326076 124326076 C A 1 0 0 0 0 1 0 0 0 7884 595 21 2 2 KALRN 3 124326076 Missense_Mutation SNP C C3N-00704_T 1605768 124326076 73969483 136 19273 PLXNA1 0 . GRCh38 3 127022164 127022164 + Missense_Mutation SNP G G T rs752299650 C3N-00704_T C3N-00704_N G G c.4118G>T p.Arg1373Leu p.R1373L ENST00000393409 21/31 313 268 45 375 375 0 strelka-varscan-mutect PLXNA1,missense_variant,p.Arg1373Leu,ENST00000393409,NM_032242.3;PLXNA1,upstream_gene_variant,,ENST00000503234,; T ENST00000393409 Transcript missense_variant 4118/9066 4118/5691 1373/1896 R/L cGc/cTc rs752299650 1 1 PLXNA1 HGNC HGNC:9099 protein_coding YES CCDS33847.2 ENSP00000377061 Q9UIW2 UPI00001A7983 NM_032242.3 deleterious(0.01) 21/31 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF35,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS rs752299650 . 0 204 0 3 3 0 0 0 -19.55422 0.882513 1 1 1 0 T 3 4 62 127022164 127022164 G T 1 0 0 0 0 1 0 0 0 12225 1087 38 1 1 PLXNA1 3 127022164 Missense_Mutation SNP G C3N-00704_T 2696088 127022164 71273395 137 19274 COL6A5 0 . GRCh38 3 130455586 130455586 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.6698G>T p.Ser2233Ile p.S2233I ENST00000265379 38/43 203 171 32 337 336 1 strelka-varscan-mutect COL6A5,missense_variant,p.Ser2233Ile,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Ser489Ile,ENST00000512836,;COL6A5,missense_variant,p.Ser72Ile,ENST00000512482,;COL6A5,missense_variant,p.Ser180Ile,ENST00000373157,;COL6A5,missense_variant,p.Ser2237Ile,ENST00000312481,; T ENST00000265379 Transcript missense_variant 7192/9214 6698/7836 2233/2611 S/I aGc/aTc 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0) 38/43 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 130455586 130455586 G T 1 0 0 0 0 1 0 0 0 3491 971 34 2 2 COL6A5 3 130455586 Missense_Mutation SNP G C3N-00704_T 3433422 130455586 67839973 138 19275 PRR23C 0 . GRCh38 3 139044415 139044423 + In_Frame_Del DEL AGGGCACAG AGGGCACAG - novel C3N-00704_T C3N-00704_N AGGGCACAG AGGGCACAG c.198_206delCTGTGCCCT p.Cys67_Leu69del p.C67_L69del ENST00000413199 1/1 99 76 23 152 152 0 sindel-varindel PRR23C,inframe_deletion,p.Cys67_Leu69del,ENST00000413199,NM_001134657.1;MRPS22,intron_variant,,ENST00000495075,; - ENST00000413199 Transcript inframe_deletion 470-478/2791 198-206/789 66-69/262 GCAL/G ggCTGTGCCCTg/ggg 1 -1 PRR23C HGNC HGNC:37173 protein_coding YES CCDS46924.1 ENSP00000396648 Q6ZRP0 UPI00001C0F48 NM_001134657.1 1/1 hmmpanther:PTHR31813:SF6,hmmpanther:PTHR31813,Pfam_domain:PF10630 MODERATE deletion 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 139044415 139044415 AGGGCACAG - 1 0 1 0 1 0 0 0 0 12731 188 7 0 0 PRR23C 3 139044415 In_Frame_Del DEL AGGGCACAG C3N-00704_T 8588829 139044415 59251144 139 19276 TRPC1 0 . GRCh38 3 142784992 142784992 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1249G>A p.Gly417Arg p.G417R ENST00000476941 7/13 106 81 25 175 175 0 strelka-varscan-mutect TRPC1,missense_variant,p.Gly383Arg,ENST00000273482,;TRPC1,missense_variant,p.Gly383Arg,ENST00000612385,NM_003304.4;TRPC1,missense_variant,p.Gly417Arg,ENST00000476941,NM_001251845.1;TRPC1,non_coding_transcript_exon_variant,,ENST00000480101,; A ENST00000476941 Transcript missense_variant 1735/3061 1249/2382 417/793 G/R Ggg/Agg 1 1 TRPC1 HGNC HGNC:12333 protein_coding YES CCDS58856.1 ENSP00000419313 P48995 UPI00001374A4 NM_001251845.1 deleterious(0) 7/13 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF56,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 142784992 142784992 G A 1 0 0 0 0 1 0 0 0 17083 1232 43 3 3 TRPC1 3 142784992 Missense_Mutation SNP G C3N-00704_T 3740577 142784992 55510567 140 19277 ERICH6 0 . GRCh38 3 150678519 150678519 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.1147T>A p.Ser383Thr p.S383T ENST00000295910 10/14 96 88 8 229 229 0 strelka-varscan-mutect ERICH6,missense_variant,p.Ser383Thr,ENST00000295910,NM_152394.4;ERICH6,missense_variant,p.Ser237Thr,ENST00000491361,NM_001308234.1;ERICH6,non_coding_transcript_exon_variant,,ENST00000491716,; T ENST00000295910 Transcript missense_variant 1200/2052 1147/1992 383/663 S/T Tct/Act 1 -1 ERICH6 HGNC HGNC:28602 protein_coding YES CCDS3151.2 ENSP00000295910 Q7L0X2 UPI000023281A NM_152394.4 deleterious(0) 10/14 hmmpanther:PTHR23093 MODERATE 1 SNV 1 1 PASS rs1171429668 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 150678519 150678519 A T 1 0 0 0 0 1 0 0 0 5086 246 9 4 4 ERICH6 3 150678519 Missense_Mutation SNP A C3N-00704_T 7893527 150678519 47617040 141 19278 ZBBX 0 . GRCh38 3 167372844 167372844 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.58C>A p.Leu20Ile p.L20I ENST00000455345 3/21 46 37 9 143 143 0 strelka-varscan-mutect ZBBX,missense_variant,p.Leu20Ile,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Leu20Ile,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Leu20Ile,ENST00000307529,;ZBBX,missense_variant,p.Leu20Ile,ENST00000474464,;ZBBX,5_prime_UTR_variant,,ENST00000392767,;ZBBX,5_prime_UTR_variant,,ENST00000392764,NM_001199202.1;ZBBX,5_prime_UTR_variant,,ENST00000485651,;ZBBX,intron_variant,,ENST00000469220,;ZBBX,non_coding_transcript_exon_variant,,ENST00000473888,; T ENST00000455345 Transcript missense_variant 342/3185 58/2520 20/839 L/I Cta/Ata 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 deleterious(0) 3/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -17.57804 1 1 1 1 0 T 3 4 62 167372844 167372844 G T 1 0 0 0 0 1 0 0 0 18078 962 34 2 2 ZBBX 3 167372844 Missense_Mutation SNP G C3N-00704_T 16694325 167372844 30922715 142 19279 SERPINI2 0 . GRCh38 3 167465597 167465597 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.585C>A p.Phe195Leu p.F195L ENST00000616363 5/10 131 112 19 226 226 0 strelka-varscan-mutect SERPINI2,missense_variant,p.Phe185Leu,ENST00000476257,;SERPINI2,missense_variant,p.Phe195Leu,ENST00000616363,NM_001012303.2;SERPINI2,missense_variant,p.Phe185Leu,ENST00000264677,NM_006217.4;SERPINI2,missense_variant,p.Phe185Leu,ENST00000461846,;SERPINI2,missense_variant,p.Phe185Leu,ENST00000471111,;SERPINI2,missense_variant,p.Phe185Leu,ENST00000466903,;SERPINI2,downstream_gene_variant,,ENST00000467583,;SERPINI2,downstream_gene_variant,,ENST00000465031,; T ENST00000616363 Transcript missense_variant 786/1769 585/1248 195/415 F/L ttC/ttA 1 -1 SERPINI2 HGNC HGNC:8945 protein_coding YES CCDS75047.1 ENSP00000481699 A0A0C4DGW9 UPI00004CEC5E NM_001012303.2 deleterious(0) 5/10 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF51,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 167465597 167465597 G T 1 0 0 0 0 1 0 0 0 14395 1281 45 2 2 SERPINI2 3 167465597 Missense_Mutation SNP G C3N-00704_T 92753 167465597 30829962 143 19280 ECT2 0 . GRCh38 3 172805759 172805759 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2135G>T p.Gly712Val p.G712V ENST00000392692 21/25 220 178 42 185 184 1 strelka-varscan-mutect ECT2,missense_variant,p.Gly681Val,ENST00000540509,NM_001258316.1;ECT2,missense_variant,p.Gly680Val,ENST00000417960,;ECT2,missense_variant,p.Gly712Val,ENST00000392692,NM_001258315.1;ECT2,missense_variant,p.Gly681Val,ENST00000232458,NM_018098.5;ECT2,missense_variant,p.Gly681Val,ENST00000441497,;ECT2,missense_variant,p.Gly52Val,ENST00000437296,;ECT2,non_coding_transcript_exon_variant,,ENST00000460860,;ECT2,upstream_gene_variant,,ENST00000486027,; T ENST00000392692 Transcript missense_variant 2311/4158 2135/2745 712/914 G/V gGc/gTc 1 1 ECT2 HGNC HGNC:3155 protein_coding YES CCDS58860.1 ENSP00000376457 Q9H8V3 UPI00003DFD0A NM_001258315.1 tolerated(0.05) 21/25 Gene3D:2.30.29.30,hmmpanther:PTHR16777,hmmpanther:PTHR16777:SF2,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 172805759 172805759 G T 1 0 0 0 0 1 0 0 0 4729 1203 42 2 2 ECT2 3 172805759 Missense_Mutation SNP G C3N-00704_T 5340162 172805759 25489800 144 19281 NAALADL2 0 . GRCh38 3 175097118 175097118 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.372C>A p.His124Gln p.H124Q ENST00000454872 2/14 337 270 67 383 383 0 strelka-varscan-mutect NAALADL2,missense_variant,p.His124Gln,ENST00000454872,NM_207015.2;NAALADL2,missense_variant,p.His107Gln,ENST00000434257,;NAALADL2-AS3,intron_variant,,ENST00000453180,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000473253,;NAALADL2,non_coding_transcript_exon_variant,,ENST00000485853,;NAALADL2-AS3,intron_variant,,ENST00000436929,; A ENST00000454872 Transcript missense_variant 500/9865 372/2388 124/795 H/Q caC/caA COSM4115373 1 1 NAALADL2 HGNC HGNC:23219 protein_coding YES CCDS46960.1 ENSP00000404705 Q58DX5 UPI0000161608 NM_207015.2 tolerated(0.5) 2/14 hmmpanther:PTHR10404:SF32,hmmpanther:PTHR10404 1 MODERATE 1 SNV 1 1 1 PASS rs993923083 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 175097118 175097118 C A 1 0 0 0 0 1 0 0 0 10134 535 19 1 1 NAALADL2 3 175097118 Missense_Mutation SNP C C3N-00704_T 2291359 175097118 23198441 145 19282 MUC4 0 . GRCh38 3 195779869 195779869 + Missense_Mutation SNP G G C C3N-00704_T C3N-00704_N G G c.11711C>G p.Pro3904Arg p.P3904R ENST00000463781 2/25 220 148 72 241 241 0 strelka-varscan-mutect MUC4,missense_variant,p.Pro3904Arg,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Pro3904Arg,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Pro3904Arg,ENST00000478156,;MUC4,missense_variant,p.Pro3904Arg,ENST00000466475,;MUC4,missense_variant,p.Pro3904Arg,ENST00000477756,;MUC4,missense_variant,p.Pro3904Arg,ENST00000477086,;MUC4,missense_variant,p.Pro3904Arg,ENST00000480843,;MUC4,missense_variant,p.Pro3904Arg,ENST00000462323,;MUC4,missense_variant,p.Pro3904Arg,ENST00000470451,;MUC4,missense_variant,p.Pro3904Arg,ENST00000479406,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,; C ENST00000463781 Transcript missense_variant 12171/17110 11711/16239 3904/5412 P/R cCt/cGt COSM4595468 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 tolerated_low_confidence(0.08) 2/25 1 MODERATE 1 SNV 5 1 1 PASS rs878968946 . 0 197 12 0 0 0 0 0 -20 0.9999811 1 1 1 0 C 3 2 62 195779869 195779869 G C 1 0 0 0 0 1 0 0 0 9977 1000 35 4 4 MUC4 3 195779869 Missense_Mutation SNP G C3N-00704_T 20682751 195779869 2515690 146 19283 SH3BP2 0 . GRCh38 4 2830029 2830029 + Nonsense_Mutation SNP G G T rs375094936 C3N-00704_T C3N-00704_N G G c.1294G>T p.Gly432Ter p.G432* ENST00000503393 8/13 151 124 27 186 185 1 strelka-varscan-mutect SH3BP2,stop_gained,p.Gly375Ter,ENST00000356331,NM_003023.4;SH3BP2,stop_gained,p.Gly403Ter,ENST00000442312,NM_001145855.1;SH3BP2,stop_gained,p.Gly432Ter,ENST00000503393,NM_001145856.1;SH3BP2,stop_gained,p.Gly375Ter,ENST00000511747,;SH3BP2,stop_gained,p.Gly375Ter,ENST00000435136,;SH3BP2,stop_gained,p.Gly375Ter,ENST00000452765,NM_001122681.1;SH3BP2,downstream_gene_variant,,ENST00000508385,;SH3BP2,downstream_gene_variant,,ENST00000502260,;SH3BP2,downstream_gene_variant,,ENST00000512014,;SH3BP2,downstream_gene_variant,,ENST00000513095,;SH3BP2,downstream_gene_variant,,ENST00000504294,;SH3BP2,downstream_gene_variant,,ENST00000503219,;SH3BP2,downstream_gene_variant,,ENST00000515183,;SH3BP2,stop_gained,p.Gly79Ter,ENST00000513069,;SH3BP2,3_prime_UTR_variant,,ENST00000515737,;SH3BP2,non_coding_transcript_exon_variant,,ENST00000510204,;SH3BP2,non_coding_transcript_exon_variant,,ENST00000515802,;SH3BP2,intron_variant,,ENST00000504450,;SH3BP2,downstream_gene_variant,,ENST00000509677,;SH3BP2,downstream_gene_variant,,ENST00000511185,;SH3BP2,downstream_gene_variant,,ENST00000511663,;SH3BP2,downstream_gene_variant,,ENST00000505941,;SH3BP2,downstream_gene_variant,,ENST00000513020,; T ENST00000503393 Transcript stop_gained 1333/9158 1294/1857 432/618 G/* Gga/Tga rs375094936 1 1 SH3BP2 HGNC HGNC:10825 protein_coding YES CCDS54716.1 ENSP00000422168 P78314 UPI00019638E3 NM_001145856.1 8/13 hmmpanther:PTHR15126:SF4,hmmpanther:PTHR15126 HIGH 1 SNV 1 1 PASS rs375094936 . 0 206 0 3 0 0 0 0 -20 0.9999954 1 1 1 0 T 4 4 62 2830029 2830029 G T 1 0 0 0 0 0 1 0 0 14503 1117 39 1 1 SH3BP2 4 2830029 Nonsense_Mutation SNP G C3N-00704_T 2830029 187384526 147 19284 EVC 0 . GRCh38 4 5801971 5801971 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2326G>T p.Val776Leu p.V776L ENST00000264956 16/21 476 421 55 571 571 0 strelka-varscan-mutect EVC,missense_variant,p.Val776Leu,ENST00000264956,NM_001306090.1,NM_153717.2;CRMP1,intron_variant,,ENST00000506216,;EVC,downstream_gene_variant,,ENST00000515113,;EVC,downstream_gene_variant,,ENST00000506240,; T ENST00000264956 Transcript missense_variant 2510/6431 2326/2979 776/992 V/L Gtg/Ttg 1 1 EVC HGNC HGNC:3497 protein_coding YES CCDS3383.1 ENSP00000264956 P57679 UPI000012A2A5 NM_001306090.1,NM_153717.2 deleterious(0.03) 16/21 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 5801971 5801971 G T 1 0 0 0 0 1 0 0 0 5152 1029 36 2 2 EVC 4 5801971 Missense_Mutation SNP G C3N-00704_T 2971942 5801971 184412584 148 19285 C4orf50 0 . GRCh38 4 5959584 5959584 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.4318C>A p.Leu1440Met p.L1440M ENST00000531445 12/12 147 120 27 141 141 0 strelka-varscan-mutect C4orf50,missense_variant,p.Leu1440Met,ENST00000531445,;C4orf50,missense_variant,p.Leu208Met,ENST00000324058,; T ENST00000531445 Transcript missense_variant 4394/6860 4318/4527 1440/1508 L/M Ctg/Atg 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 tolerated(0.2) 12/12 hmmpanther:PTHR36866,Pfam_domain:PF15030 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 5959584 5959584 G T 1 0 0 0 0 1 0 0 0 2089 991 35 2 2 C4orf50 4 5959584 Missense_Mutation SNP G C3N-00704_T 157613 5959584 184254971 149 19286 MAN2B2 0 . GRCh38 4 6610951 6610951 + Silent SNP G G T rs147196628 C3N-00704_T C3N-00704_N G G c.2331G>T p.= p.R777R ENST00000285599 14/19 176 147 29 224 224 0 strelka-varscan-mutect MAN2B2,synonymous_variant,p.=,ENST00000505907,;MAN2B2,synonymous_variant,p.=,ENST00000285599,NM_015274.2;MAN2B2,synonymous_variant,p.=,ENST00000504248,NM_001292038.1;MAN2B2,downstream_gene_variant,,ENST00000504960,; T ENST00000285599 Transcript synonymous_variant 2367/5143 2331/3030 777/1009 R cgG/cgT rs147196628 1 1 MAN2B2 HGNC HGNC:29623 protein_coding YES CCDS33951.1 ENSP00000285599 Q9Y2E5 UPI000004BF05 NM_015274.2 14/19 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF28,Gene3D:2.70.98.30,Pfam_domain:PF07748,Superfamily_domains:SSF74650 LOW 1 SNV 1 1 PASS rs147196628 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 6610951 6610951 G T 1 0 0 0 0 0 0 0 1 9138 1219 43 2 2 MAN2B2 4 6610951 Silent SNP G C3N-00704_T 651367 6610951 183603604 150 19287 ZNF518B 0 . GRCh38 4 10445653 10445653 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.676G>A p.Ala226Thr p.A226T ENST00000326756 3/3 112 101 11 162 162 0 strelka-varscan-mutect ZNF518B,missense_variant,p.Ala226Thr,ENST00000326756,NM_053042.2;ZNF518B,downstream_gene_variant,,ENST00000507515,; T ENST00000326756 Transcript missense_variant 1115/6894 676/3225 226/1074 A/T Gcc/Acc 1 -1 ZNF518B HGNC HGNC:29365 protein_coding YES CCDS33960.1 ENSP00000317614 Q9C0D4 UPI0000160B97 NM_053042.2 tolerated(0.44) 3/3 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF188 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 10445653 10445653 C T 1 0 0 0 0 1 0 0 0 18535 710 25 3 3 ZNF518B 4 10445653 Missense_Mutation SNP C C3N-00704_T 3834702 10445653 179768902 151 19288 GABRA2 0 . GRCh38 4 46250453 46250453 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1211C>T p.Pro404Leu p.P404L ENST00000510861 10/10 385 307 78 369 369 0 strelka-varscan-mutect GABRA2,missense_variant,p.Pro404Leu,ENST00000510861,;GABRA2,missense_variant,p.Pro404Leu,ENST00000514090,;GABRA2,missense_variant,p.Pro404Leu,ENST00000356504,NM_001114175.1;GABRA2,missense_variant,p.Pro380Leu,ENST00000540012,NM_001286827.1;GABRA2,missense_variant,p.Pro404Leu,ENST00000381620,NM_000807.2;GABRA2,missense_variant,p.Pro464Leu,ENST00000507069,;GABRA2,3_prime_UTR_variant,,ENST00000630416,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;GABRA2,3_prime_UTR_variant,,ENST00000513005,; A ENST00000510861 Transcript missense_variant 1385/3411 1211/1356 404/451 P/L cCa/cTa 1 -1 GABRA2 HGNC HGNC:4076 protein_coding YES CCDS3471.1 ENSP00000421828 P47869 A0A024R9X6 UPI000013DC88 tolerated(0.14) 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF218,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR01615 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 46250453 46250453 G A 1 0 0 0 0 1 0 0 0 6032 1348 47 3 3 GABRA2 4 46250453 Missense_Mutation SNP G C3N-00704_T 35804800 46250453 143964102 152 19289 GABRA2 0 . GRCh38 4 46305655 46305655 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.616G>C p.Val206Leu p.V206L ENST00000510861 7/10 145 122 23 240 240 0 strelka-varscan-mutect GABRA2,missense_variant,p.Val206Leu,ENST00000510861,;GABRA2,missense_variant,p.Val206Leu,ENST00000514090,;GABRA2,missense_variant,p.Val206Leu,ENST00000356504,NM_001114175.1;GABRA2,missense_variant,p.Val122Leu,ENST00000540012,NM_001286827.1;GABRA2,missense_variant,p.Val206Leu,ENST00000381620,NM_000807.2;GABRA2,missense_variant,p.Val206Leu,ENST00000515082,;GABRA2,missense_variant,p.Val206Leu,ENST00000507069,;GABRA2,3_prime_UTR_variant,,ENST00000630416,;GABRA2,intron_variant,,ENST00000510233,;GABRA2,intron_variant,,ENST00000513005,;GABRA2,upstream_gene_variant,,ENST00000514236,;GABRA2,downstream_gene_variant,,ENST00000514193,; G ENST00000510861 Transcript missense_variant 790/3411 616/1356 206/451 V/L Gta/Cta 1 -1 GABRA2 HGNC HGNC:4076 protein_coding YES CCDS3471.1 ENSP00000421828 P47869 A0A024R9X6 UPI000013DC88 deleterious(0.04) 7/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF218,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932,Prints_domain:PR01079 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 46305655 46305655 C G 1 0 0 0 0 1 0 0 0 6032 565 20 4 4 GABRA2 4 46305655 Missense_Mutation SNP C C3N-00704_T 55202 46305655 143908900 153 19290 KIAA1211 0 . GRCh38 4 56298240 56298240 + Missense_Mutation SNP G G T rs763160970 C3N-00704_T C3N-00704_N G G c.11G>T p.Arg4Leu p.R4L ENST00000504228 2/9 120 101 19 101 101 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Arg4Leu,ENST00000504228,;KIAA1211,missense_variant,p.Arg4Leu,ENST00000264229,NM_020722.1;KIAA1211,missense_variant,p.Arg4Leu,ENST00000636006,;KIAA1211,missense_variant,p.Arg4Leu,ENST00000629263,;KIAA1211,5_prime_UTR_variant,,ENST00000541073,;KIAA1211,non_coding_transcript_exon_variant,,ENST00000503618,; T ENST00000504228 Transcript missense_variant 116/4628 11/3702 4/1233 R/L cGg/cTg rs763160970 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 deleterious(0) 2/9 MODERATE 1 SNV 5 1 PASS rs763160970 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 56298240 56298240 G T 1 0 0 0 0 1 0 0 0 8107 1116 39 1 1 KIAA1211 4 56298240 Missense_Mutation SNP G C3N-00704_T 9992585 56298240 133916315 154 19291 UGT2B4 0 . GRCh38 4 69486692 69486692 + Missense_Mutation SNP A A G rs532930350 C3N-00704_T C3N-00704_N A A c.1007T>C p.Leu336Pro p.L336P ENST00000305107 4/6 72 61 11 180 180 0 strelka-varscan-mutect UGT2B4,missense_variant,p.Leu336Pro,ENST00000305107,NM_021139.2;UGT2B4,missense_variant,p.Leu336Pro,ENST00000512583,NM_001297615.1;UGT2B4,non_coding_transcript_exon_variant,,ENST00000506580,;UGT2B4,non_coding_transcript_exon_variant,,ENST00000502655,;UGT2B4,downstream_gene_variant,,ENST00000503836,; G ENST00000305107 Transcript missense_variant 1054/2103 1007/1587 336/528 L/P cTg/cCg rs532930350 1 -1 UGT2B4 HGNC HGNC:12553 protein_coding YES CCDS43234.1 ENSP00000305221 P06133 UPI000000087F NM_021139.2 deleterious(0) 4/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF198,Pfam_domain:PF00201,Gene3D:3.40.50.2000,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 69486692 69486692 A G 1 0 0 0 0 1 0 0 0 17485 202 7 5 5 UGT2B4 4 69486692 Missense_Mutation SNP A C3N-00704_T 13188452 69486692 120727863 155 19292 SULT1E1 0 . GRCh38 4 69849558 69849558 + Silent SNP G G T C3N-00704_T C3N-00704_N G G c.375C>A p.= p.I125I ENST00000226444 5/8 75 61 14 119 119 0 strelka-varscan-mutect SULT1E1,synonymous_variant,p.=,ENST00000226444,NM_005420.2;SULT1E1,non_coding_transcript_exon_variant,,ENST00000504002,;SULT1E1,upstream_gene_variant,,ENST00000506796,; T ENST00000226444 Transcript synonymous_variant 488/1780 375/885 125/294 I atC/atA COSM373155,COSM4398217 1 -1 SULT1E1 HGNC HGNC:11377 protein_coding YES CCDS3531.1 ENSP00000226444 P49888 Q53X91 UPI00000623C8 NM_005420.2 5/8 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF53,Superfamily_domains:SSF52540 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 69849558 69849558 G T 1 0 0 0 0 0 0 0 1 15766 956 33 2 2 SULT1E1 4 69849558 Silent SNP G C3N-00704_T 362866 69849558 120364997 156 19293 SDAD1 0 . GRCh38 4 75971375 75971375 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.795G>T p.Lys265Asn p.K265N ENST00000356260 9/22 125 104 21 161 161 0 strelka-mutect SDAD1,missense_variant,p.Lys265Asn,ENST00000356260,NM_001288984.1,NM_018115.3;SDAD1,missense_variant,p.Lys228Asn,ENST00000395711,NM_001288983.1;SDAD1,non_coding_transcript_exon_variant,,ENST00000513089,;SDAD1,non_coding_transcript_exon_variant,,ENST00000507396,;SDAD1,downstream_gene_variant,,ENST00000515836,;SDAD1,3_prime_UTR_variant,,ENST00000395710,;SDAD1,downstream_gene_variant,,ENST00000503411,; A ENST00000356260 Transcript missense_variant 914/3017 795/2064 265/687 K/N aaG/aaT 1 -1 SDAD1 HGNC HGNC:25537 protein_coding YES CCDS3573.2 ENSP00000348596 Q9NVU7 UPI000020B02A NM_001288984.1,NM_018115.3 tolerated(0.05) 9/22 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12730:SF0,hmmpanther:PTHR12730,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1231557205 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 75971375 75971375 C A 1 0 0 0 0 1 0 0 0 14222 680 24 2 2 SDAD1 4 75971375 Missense_Mutation SNP C C3N-00704_T 6121817 75971375 114243180 157 19294 FRAS1 0 . GRCh38 4 78337693 78337693 + Missense_Mutation SNP G G T rs749090827 C3N-00704_T C3N-00704_N G G c.2298G>T p.Arg766Ser p.R766S ENST00000512123 20/74 118 101 17 130 129 1 strelka-varscan FRAS1,missense_variant,p.Arg766Ser,ENST00000512123,NM_025074.6;FRAS1,missense_variant,p.Arg766Ser,ENST00000325942,NM_001166133.1;FRAS1,missense_variant,p.Arg609Ser,ENST00000508900,;FRAS1,intron_variant,,ENST00000264899,; T ENST00000512123 Transcript missense_variant 2738/15624 2298/12039 766/4012 R/S agG/agT rs749090827 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 tolerated(0.23) 20/74 Gene3D:2.10.220.10,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29,SMART_domains:SM00181,SMART_domains:SM00261 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 78337693 78337693 G T 1 0 0 0 0 1 0 0 0 5908 1194 42 2 2 FRAS1 4 78337693 Missense_Mutation SNP G C3N-00704_T 2366318 78337693 111876862 158 19295 UNC5C 0 . GRCh38 4 95170272 95170272 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2512G>A p.Gly838Arg p.G838R ENST00000453304 15/16 239 203 36 252 251 1 strelka-varscan UNC5C,missense_variant,p.Gly838Arg,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Gly797Arg,ENST00000610318,; T ENST00000453304 Transcript missense_variant 2861/9875 2512/2796 838/931 G/R Ggg/Agg 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 deleterious(0.01) 15/16 Gene3D:1.10.533.10,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,SMART_domains:SM00005 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 95170272 95170272 C T 1 0 0 0 0 1 0 0 0 17517 623 22 3 3 UNC5C 4 95170272 Missense_Mutation SNP C C3N-00704_T 16832579 95170272 95044283 159 19296 STPG2 0 . GRCh38 4 97559110 97559110 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1328A>T p.Gln443Leu p.Q443L ENST00000295268 11/11 82 67 15 175 175 0 strelka-varscan STPG2,missense_variant,p.Gln443Leu,ENST00000295268,NM_174952.2;STPG2,intron_variant,,ENST00000522676,;RP11-681L8.1,intron_variant,,ENST00000518105,;RP11-681L8.1,intron_variant,,ENST00000521680,;STPG2,intron_variant,,ENST00000506482,; A ENST00000295268 Transcript missense_variant 1418/1652 1328/1380 443/459 Q/L cAg/cTg 1 -1 STPG2 HGNC HGNC:28712 protein_coding YES CCDS3645.1 ENSP00000295268 Q8N412 UPI00000734EC NM_174952.2 tolerated(0.06) 11/11 hmmpanther:PTHR21580,hmmpanther:PTHR21580:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 97559110 97559110 T A 1 0 0 0 0 1 0 0 0 15700 1580 55 4 4 STPG2 4 97559110 Missense_Mutation SNP T C3N-00704_T 2388838 97559110 92655445 160 19297 RP11-766F14.2 0 . GRCh38 4 99653946 99653946 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.703G>T p.Glu235Ter p.E235* ENST00000511828 1/2 221 178 43 231 231 0 strelka-varscan RP11-766F14.2,stop_gained,p.Glu235Ter,ENST00000511828,; A ENST00000511828 Transcript stop_gained 703/10086 703/5382 235/1793 E/* Gaa/Taa 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE 1/2 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 99653946 99653946 C A 1 0 0 0 0 0 1 0 0 13762 835 29 2 2 RP11-766F14.2 4 99653946 Nonsense_Mutation SNP C C3N-00704_T 2094836 99653946 90560609 161 19298 PPP3CA 0 . GRCh38 4 101040487 101040487 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.1236G>T p.= p.V412V ENST00000394854 11/14 132 107 25 149 149 0 strelka-varscan PPP3CA,synonymous_variant,p.=,ENST00000394854,NM_000944.4;PPP3CA,synonymous_variant,p.=,ENST00000323055,NM_001130692.1;PPP3CA,synonymous_variant,p.=,ENST00000512215,;PPP3CA,synonymous_variant,p.=,ENST00000394853,NM_001130691.1;PPP3CA,synonymous_variant,p.=,ENST00000507176,; A ENST00000394854 Transcript synonymous_variant 1920/4685 1236/1566 412/521 V gtG/gtT 1 -1 PPP3CA HGNC HGNC:9314 protein_coding YES CCDS34037.1 ENSP00000378323 Q08209 A0A0S2Z4C6 UPI0000110660 NM_000944.4 11/14 hmmpanther:PTHR11668:SF261,hmmpanther:PTHR11668,Superfamily_domains:SSF56300 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 101040487 101040487 C A 1 0 0 0 0 0 0 0 1 12519 724 25 2 2 PPP3CA 4 101040487 Silent SNP C C3N-00704_T 1386541 101040487 89174068 162 19299 SEC24B 0 . GRCh38 4 109463160 109463160 + Silent SNP A A T novel C3N-00704_T C3N-00704_N A A c.486A>T p.= p.L162L ENST00000504968 3/25 209 167 42 274 274 0 strelka-varscan SEC24B,synonymous_variant,p.=,ENST00000265175,NM_001318085.1,NM_006323.3;SEC24B,synonymous_variant,p.=,ENST00000504968,NM_001300813.1;SEC24B,synonymous_variant,p.=,ENST00000399100,NM_001042734.2; T ENST00000504968 Transcript synonymous_variant 584/4066 486/3897 162/1298 L ctA/ctT 1 1 SEC24B HGNC HGNC:10704 protein_coding YES CCDS75179.1 ENSP00000428564 O95487 UPI000189A7A7 NM_001300813.1 3/25 hmmpanther:PTHR13803:SF7,hmmpanther:PTHR13803 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 109463160 109463160 A T 1 0 0 0 0 0 0 0 1 14272 407 15 4 4 SEC24B 4 109463160 Silent SNP A C3N-00704_T 8422673 109463160 80751395 163 19300 ZGRF1 0 . GRCh38 4 112548303 112548303 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.5424G>T p.= p.L1808L ENST00000505019 23/28 172 153 19 218 218 0 strelka-varscan ZGRF1,synonymous_variant,p.=,ENST00000505019,NM_018392.4;ZGRF1,synonymous_variant,p.=,ENST00000445203,;ZGRF1,intron_variant,,ENST00000612287,;RP11-402J6.1,downstream_gene_variant,,ENST00000504009,;ZGRF1,non_coding_transcript_exon_variant,,ENST00000506675,;ZGRF1,intron_variant,,ENST00000445413,; A ENST00000505019 Transcript synonymous_variant 5550/6652 5424/6315 1808/2104 L ctG/ctT 1 -1 ZGRF1 HGNC HGNC:25654 protein_coding YES CCDS3700.2 ENSP00000424737 Q86YA3 UPI0000EE2F8F NM_018392.4 23/28 Gene3D:3.40.50.300,Pfam_domain:PF13086,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF325,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 112548303 112548303 C A 1 0 0 0 0 0 0 0 1 18253 581 21 2 2 ZGRF1 4 112548303 Silent SNP C C3N-00704_T 3085143 112548303 77666252 164 19301 ANK2 0 . GRCh38 4 113278523 113278523 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.1846C>G p.Leu616Val p.L616V ENST00000357077 17/46 432 368 64 399 398 1 strelka-varscan ANK2,missense_variant,p.Leu616Val,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Leu616Val,ENST00000264366,;ANK2,missense_variant,p.Leu595Val,ENST00000506722,NM_001127493.1;ANK2,missense_variant,p.Leu616Val,ENST00000394537,NM_020977.3;ANK2,missense_variant,p.Leu631Val,ENST00000504454,;ANK2,missense_variant,p.Leu588Val,ENST00000634436,;ANK2,missense_variant,p.Leu595Val,ENST00000503271,;ANK2,intron_variant,,ENST00000503423,; G ENST00000357077 Transcript missense_variant 1899/14196 1846/11874 616/3957 L/V Ctg/Gtg 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious(0.03) 17/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 113278523 113278523 C G 1 0 0 0 0 1 0 0 0 721 564 20 4 4 ANK2 4 113278523 Missense_Mutation SNP C C3N-00704_T 730220 113278523 76936032 165 19302 ANK2 0 . GRCh38 4 113278535 113278535 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1858G>T p.Ala620Ser p.A620S ENST00000357077 17/46 408 352 56 387 387 0 strelka-varscan ANK2,missense_variant,p.Ala620Ser,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala620Ser,ENST00000264366,;ANK2,missense_variant,p.Ala599Ser,ENST00000506722,NM_001127493.1;ANK2,missense_variant,p.Ala620Ser,ENST00000394537,NM_020977.3;ANK2,missense_variant,p.Ala635Ser,ENST00000504454,;ANK2,missense_variant,p.Ala592Ser,ENST00000634436,;ANK2,missense_variant,p.Ala599Ser,ENST00000503271,;ANK2,intron_variant,,ENST00000503423,; T ENST00000357077 Transcript missense_variant 1911/14196 1858/11874 620/3957 A/S Gct/Tct 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious(0.02) 17/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 113278535 113278535 G T 1 0 0 0 0 1 0 0 0 721 1319 46 2 2 ANK2 4 113278535 Missense_Mutation SNP G C3N-00704_T 12 113278535 76936020 166 19303 ANK2 0 . GRCh38 4 113356135 113356135 + Missense_Mutation SNP G G T rs780131495 C3N-00704_T C3N-00704_N G G c.7517G>T p.Arg2506Leu p.R2506L ENST00000357077 38/46 224 181 43 295 295 0 strelka-varscan ANK2,missense_variant,p.Arg2506Leu,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Arg2473Leu,ENST00000264366,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; T ENST00000357077 Transcript missense_variant 7570/14196 7517/11874 2506/3957 R/L cGg/cTg rs780131495 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious_low_confidence(0.02) 38/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 113356135 113356135 G T 1 0 0 0 0 1 0 0 0 721 1116 39 1 1 ANK2 4 113356135 Missense_Mutation SNP G C3N-00704_T 77600 113356135 76858420 167 19304 NDST3 0 . GRCh38 4 118224493 118224493 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.1542C>G p.Ile514Met p.I514M ENST00000296499 7/14 71 51 20 77 77 0 strelka-varscan NDST3,missense_variant,p.Ile514Met,ENST00000296499,NM_004784.2; G ENST00000296499 Transcript missense_variant,splice_region_variant 1945/5961 1542/2622 514/873 I/M atC/atG 1 1 NDST3 HGNC HGNC:7682 protein_coding YES CCDS3708.1 ENSP00000296499 O95803 UPI0000071C44 NM_004784.2 deleterious(0.03) 7/14 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF29 MODERATE 1 SNV 1 1 PASS . . 0 176 31 3 0 0 0 0 -20 0.9545044 0 1 1 0 G 3 3 62 118224493 118224493 C G 1 0 0 0 0 1 0 0 0 10278 840 29 4 4 NDST3 4 118224493 Missense_Mutation SNP C C3N-00704_T 4868358 118224493 71990062 168 19305 DCLK2 0 . GRCh38 4 150102493 150102493 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.437G>T p.Cys146Phe p.C146F ENST00000302176 2/17 121 102 19 154 154 0 strelka-varscan DCLK2,missense_variant,p.Cys146Phe,ENST00000296550,NM_001040260.3;DCLK2,missense_variant,p.Cys146Phe,ENST00000302176,NM_001040261.4;DCLK2,missense_variant,p.Cys146Phe,ENST00000506325,;DCLK2,missense_variant,p.Cys146Phe,ENST00000635524,;DCLK2,missense_variant,p.Cys146Phe,ENST00000411937,; T ENST00000302176 Transcript missense_variant 437/3543 437/2352 146/783 C/F tGt/tTt 1 1 DCLK2 HGNC HGNC:19002 protein_coding YES CCDS47142.2 ENSP00000303887 Q8N568 UPI0000D615C9 NM_001040261.4 deleterious(0) 2/17 PROSITE_profiles:PS50309,hmmpanther:PTHR24347:SF122,hmmpanther:PTHR24347,Pfam_domain:PF03607,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 150102493 150102493 G T 1 0 0 0 0 1 0 0 0 4094 1377 48 2 2 DCLK2 4 150102493 Missense_Mutation SNP G C3N-00704_T 31878000 150102493 40112062 169 19306 FHDC1 0 . GRCh38 4 152975789 152975789 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2498C>T p.Pro833Leu p.P833L ENST00000511601 12/12 16 12 4 33 33 0 strelka-varscan FHDC1,missense_variant,p.Pro833Leu,ENST00000511601,;FHDC1,missense_variant,p.Pro833Leu,ENST00000260008,NM_033393.2; T ENST00000511601 Transcript missense_variant 2686/6583 2498/3432 833/1143 P/L cCt/cTt 1 1 FHDC1 HGNC HGNC:29363 protein_coding YES CCDS34081.1 ENSP00000427567 Q9C0D6 UPI00001D7673 deleterious(0.05) 12/12 MODERATE 1 SNV 5 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 152975789 152975789 C T 1 0 0 0 0 1 0 0 0 5741 681 24 3 3 FHDC1 4 152975789 Missense_Mutation SNP C C3N-00704_T 2873296 152975789 37238766 170 19307 GRIA2 0 . GRCh38 4 157335725 157335725 + Missense_Mutation SNP C C A rs761885028 C3N-00704_T C3N-00704_N C C c.1321C>A p.Arg441Ser p.R441S ENST00000296526 10/16 334 278 56 317 316 1 strelka-varscan GRIA2,missense_variant,p.Arg441Ser,ENST00000296526,NM_000826.3;GRIA2,missense_variant,p.Arg394Ser,ENST00000393815,NM_001083620.1;GRIA2,missense_variant,p.Arg441Ser,ENST00000264426,NM_001083619.1;GRIA2,missense_variant,p.Arg394Ser,ENST00000507898,;GRIA2,missense_variant,p.Arg394Ser,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; A ENST00000296526 Transcript missense_variant 1646/5621 1321/2652 441/883 R/S Cgc/Agc rs761885028,COSM1428249,COSM1428250 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 tolerated(0.09) 10/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,SMART_domains:SM00079,SMART_domains:SM00918,Superfamily_domains:SSF53850 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 157335725 157335725 C A 1 0 0 0 0 1 0 0 0 6648 768 27 1 1 GRIA2 4 157335725 Missense_Mutation SNP C C3N-00704_T 4359936 157335725 32878830 171 19308 TLL1 0 . GRCh38 4 166055165 166055165 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.1614T>A p.= p.G538G ENST00000061240 13/21 121 103 18 159 159 0 strelka-varscan TLL1,synonymous_variant,p.=,ENST00000061240,NM_012464.4;TLL1,synonymous_variant,p.=,ENST00000507499,;RNA5SP170,upstream_gene_variant,,ENST00000517150,;TLL1,3_prime_UTR_variant,,ENST00000509505,; A ENST00000061240 Transcript synonymous_variant 2261/6708 1614/3042 538/1013 G ggT/ggA 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 13/21 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 166055165 166055165 T A 1 0 0 0 0 0 0 0 1 16391 1712 60 4 4 TLL1 4 166055165 Silent SNP T C3N-00704_T 8719440 166055165 24159390 172 19309 DDX60 0 . GRCh38 4 168248249 168248249 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.3902C>G p.Pro1301Arg p.P1301R ENST00000393743 29/38 101 87 14 121 121 0 strelka-varscan DDX60,missense_variant,p.Pro1301Arg,ENST00000393743,NM_017631.5;DDX60,downstream_gene_variant,,ENST00000505393,; C ENST00000393743 Transcript missense_variant 4194/6071 3902/5139 1301/1712 P/R cCt/cGt 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 deleterious(0) 29/38 PROSITE_profiles:PS51194,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 168248249 168248249 G C 1 0 0 0 0 1 0 0 0 4181 1000 35 4 4 DDX60 4 168248249 Missense_Mutation SNP G C3N-00704_T 2193084 168248249 21966306 173 19310 CEP44 0 . GRCh38 4 174310051 174310051 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.880A>G p.Lys294Glu p.K294E ENST00000457424 8/11 66 56 10 157 157 0 strelka-varscan CEP44,missense_variant,p.Lys294Glu,ENST00000503780,NM_001040157.2;CEP44,missense_variant,p.Lys294Glu,ENST00000296519,;CEP44,missense_variant,p.Lys294Glu,ENST00000457424,NM_001145314.1;CEP44,missense_variant,p.Lys294Glu,ENST00000426172,;CEP44,downstream_gene_variant,,ENST00000515299,;CEP44,missense_variant,p.Lys294Glu,ENST00000396791,;CEP44,non_coding_transcript_exon_variant,,ENST00000508483,; G ENST00000457424 Transcript missense_variant 1185/3290 880/1200 294/399 K/E Aaa/Gaa 1 1 CEP44 HGNC HGNC:29356 protein_coding YES CCDS47163.1 ENSP00000389427 Q9C0F1 UPI000014031D NM_001145314.1 deleterious(0) 8/11 hmmpanther:PTHR31477:SF1,hmmpanther:PTHR31477 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 174310051 174310051 A G 1 0 0 0 0 1 0 0 0 2974 376 13 5 5 CEP44 4 174310051 Missense_Mutation SNP A C3N-00704_T 6061802 174310051 15904504 174 19311 ADAM29 0 . GRCh38 4 174977477 174977477 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1952C>A p.Pro651His p.P651H ENST00000615367 6/6 132 100 32 167 167 0 strelka-varscan ADAM29,missense_variant,p.Pro651His,ENST00000615367,NM_001278125.1;ADAM29,missense_variant,p.Pro651His,ENST00000359240,NM_014269.4,NM_001278126.1;ADAM29,missense_variant,p.Pro651His,ENST00000445694,NM_001130703.1;ADAM29,missense_variant,p.Pro651His,ENST00000404450,NM_001130704.1;ADAM29,missense_variant,p.Pro651His,ENST00000514159,NM_001130705.1;ADAM29,missense_variant,p.Pro651His,ENST00000618444,NM_001278127.1;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000505141,;ADAM29,downstream_gene_variant,,ENST00000502940,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,; A ENST00000615367 Transcript missense_variant 2683/3386 1952/2463 651/820 P/H cCc/cAc 1 1 ADAM29 HGNC HGNC:207 protein_coding YES CCDS3823.1 ENSP00000484862 Q9UKF5 A0A140VJD8 UPI000013E9DE NM_001278125.1 deleterious(0) 6/6 hmmpanther:PTHR11905:SF34,hmmpanther:PTHR11905 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 174977477 174977477 C A 1 0 0 0 0 1 0 0 0 291 623 22 2 2 ADAM29 4 174977477 Missense_Mutation SNP C C3N-00704_T 667426 174977477 15237078 175 19312 FAT1 0 . GRCh38 4 186598094 186598094 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.12135A>T p.= p.I4045I ENST00000441802 23/27 181 129 52 163 163 0 strelka-varscan FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,;FAT1,upstream_gene_variant,,ENST00000512772,;FAT1,upstream_gene_variant,,ENST00000507105,;FAT1,upstream_gene_variant,,ENST00000509927,;FAT1,non_coding_transcript_exon_variant,,ENST00000512347,;FAT1,non_coding_transcript_exon_variant,,ENST00000507662,;FAT1,upstream_gene_variant,,ENST00000500085,;FAT1,upstream_gene_variant,,ENST00000509537,;FAT1,downstream_gene_variant,,ENST00000503253,; A ENST00000441802 Transcript synonymous_variant 12345/14786 12135/13767 4045/4588 I atA/atT 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 23/27 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 186598094 186598094 T A 1 0 0 0 0 0 0 0 1 5549 1512 53 4 4 FAT1 4 186598094 Silent SNP T C3N-00704_T 11620617 186598094 3616461 176 19313 CLPTM1L 0 . GRCh38 5 1318422 1318422 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1564G>T p.Glu522Ter p.E522* ENST00000320895 17/17 330 299 31 267 267 0 strelka-varscan-mutect CLPTM1L,stop_gained,p.Glu522Ter,ENST00000320895,NM_030782.3;CLPTM1L,stop_gained,p.Glu353Ter,ENST00000630539,;CLPTM1L,stop_gained,p.Glu353Ter,ENST00000507807,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000506641,;CLPTM1L,downstream_gene_variant,,ENST00000507195,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503042,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000503534,;CLPTM1L,non_coding_transcript_exon_variant,,ENST00000515719,;CLPTM1L,downstream_gene_variant,,ENST00000511268,;CLPTM1L,downstream_gene_variant,,ENST00000503151,;CLPTM1L,downstream_gene_variant,,ENST00000505914,;CLPTM1L,downstream_gene_variant,,ENST00000505605,;CLPTM1L,downstream_gene_variant,,ENST00000512451,; A ENST00000320895 Transcript stop_gained 1822/2500 1564/1617 522/538 E/* Gag/Tag 1 -1 CLPTM1L HGNC HGNC:24308 protein_coding YES CCDS3862.1 ENSP00000313854 Q96KA5 UPI00000707DF NM_030782.3 17/17 hmmpanther:PTHR21347:SF1,hmmpanther:PTHR21347 HIGH 1 SNV 1 1 PASS rs939527654 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 1318422 1318422 C A 1 0 0 0 0 0 1 0 0 3327 893 31 1 1 CLPTM1L 5 1318422 Nonsense_Mutation SNP C C3N-00704_T 1318422 180219837 177 19314 IRX1 0 . GRCh38 5 3599984 3599984 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1036C>A p.Pro346Thr p.P346T ENST00000302006 2/4 67 60 7 59 59 0 strelka-varscan-mutect IRX1,missense_variant,p.Pro346Thr,ENST00000302006,NM_024337.3;CTD-2012M11.3,non_coding_transcript_exon_variant,,ENST00000559410,; A ENST00000302006 Transcript missense_variant 1088/1858 1036/1443 346/480 P/T Ccc/Acc 1 1 IRX1 HGNC HGNC:14358 protein_coding YES CCDS34132.1 ENSP00000305244 P78414 UPI00001B6455 NM_024337.3 tolerated(0.14) 2/4 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -15.99946 1 1 1 1 0 A 3 1 62 3599984 3599984 C A 1 0 0 0 0 1 0 0 0 7751 739 26 2 2 IRX1 5 3599984 Missense_Mutation SNP C C3N-00704_T 2281562 3599984 177938275 178 19315 ADCY2 0 . GRCh38 5 7706791 7706791 + Missense_Mutation SNP T T A C3N-00704_T C3N-00704_N T T c.1157T>A p.Val386Glu p.V386E ENST00000338316 8/25 329 290 39 304 304 0 strelka-varscan-mutect ADCY2,missense_variant,p.Val386Glu,ENST00000338316,NM_020546.2;RP11-711G10.1,downstream_gene_variant,,ENST00000514105,; A ENST00000338316 Transcript missense_variant 1246/6575 1157/3276 386/1091 V/E gTg/gAg COSM1647830,COSM739189 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0) 8/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,PROSITE_profiles:PS50125,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 7706791 7706791 T A 1 0 0 0 0 1 0 0 0 338 1696 59 4 4 ADCY2 5 7706791 Missense_Mutation SNP T C3N-00704_T 4106807 7706791 173831468 179 19316 ANKRD33B 0 . GRCh38 5 10650046 10650046 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1418C>A p.Ala473Asp p.A473D ENST00000296657 4/4 177 110 67 143 143 0 strelka-varscan-mutect ANKRD33B,missense_variant,p.Ala473Asp,ENST00000296657,NM_001164440.1;ANKRD33B,downstream_gene_variant,,ENST00000504806,;RP11-54F2.1,downstream_gene_variant,,ENST00000508690,; A ENST00000296657 Transcript missense_variant 1418/9188 1418/1485 473/494 A/D gCc/gAc 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 tolerated(0.26) 4/4 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 10650046 10650046 C A 1 0 0 0 0 1 0 0 0 766 739 26 2 2 ANKRD33B 5 10650046 Missense_Mutation SNP C C3N-00704_T 2943255 10650046 170888213 180 19317 CTNND2 0 . GRCh38 5 10973518 10973518 + Missense_Mutation SNP G G T rs377404994 C3N-00704_T C3N-00704_N G G c.3613C>A p.Arg1205Ser p.R1205S ENST00000304623 22/22 120 104 16 112 112 0 strelka-varscan-mutect CTNND2,missense_variant,p.Arg1205Ser,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Arg1114Ser,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Arg868Ser,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Arg300Ser,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,downstream_gene_variant,,ENST00000506324,;CTNND2,3_prime_UTR_variant,,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 3803/5481 3613/3678 1205/1225 R/S Cgt/Agt rs377404994 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0) 22/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS rs377404994 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 10973518 10973518 G T 1 0 0 0 0 1 0 0 0 3829 1116 39 1 1 CTNND2 5 10973518 Missense_Mutation SNP G C3N-00704_T 323472 10973518 170564741 181 19318 PRDM9 0 . GRCh38 5 23527256 23527256 + Missense_Mutation SNP G G T rs368347213 C3N-00704_T C3N-00704_N G G c.2168G>T p.Arg723Met p.R723M ENST00000296682 11/11 330 293 37 296 296 0 varscan-mutect PRDM9,missense_variant,p.Arg723Met,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; T ENST00000296682 Transcript missense_variant 2350/3691 2168/2685 723/894 R/M aGg/aTg rs368347213 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 tolerated(0.08) 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR16515:SF10,hmmpanther:PTHR16515,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs368347213 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 23527256 23527256 G T 1 0 0 0 0 1 0 0 0 12595 1000 35 2 2 PRDM9 5 23527256 Missense_Mutation SNP G C3N-00704_T 12553738 23527256 158011003 182 19319 CDH9 0 . GRCh38 5 26885808 26885808 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1688C>A p.Thr563Asn p.T563N ENST00000231021 11/12 315 260 55 340 340 0 strelka-varscan-mutect CDH9,missense_variant,p.Thr563Asn,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505020,; T ENST00000231021 Transcript missense_variant 1861/3079 1688/2370 563/789 T/N aCc/aAc 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0.02) 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 26885808 26885808 G T 1 0 0 0 0 1 0 0 0 2820 1261 44 2 2 CDH9 5 26885808 Missense_Mutation SNP G C3N-00704_T 3358552 26885808 154652451 183 19320 CAPSL 0 . GRCh38 5 35921019 35921019 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.102G>T p.= p.L34L ENST00000397367 2/5 242 163 79 226 225 1 strelka-varscan-mutect CAPSL,synonymous_variant,p.=,ENST00000397367,NM_144647.3;CAPSL,synonymous_variant,p.=,ENST00000397366,NM_001042625.1;CAPSL,synonymous_variant,p.=,ENST00000513623,;CAPSL,synonymous_variant,p.=,ENST00000514524,; A ENST00000397367 Transcript synonymous_variant 229/1004 102/627 34/208 L ctG/ctT 1 -1 CAPSL HGNC HGNC:28375 protein_coding YES CCDS3912.2 ENSP00000380524 Q8WWF8 UPI0000149B20 NM_144647.3 2/5 hmmpanther:PTHR10891,hmmpanther:PTHR10891:SF551 LOW 1 SNV 1 1 PASS rs878903625 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 35921019 35921019 C A 1 0 0 0 0 0 0 0 1 2334 581 21 2 2 CAPSL 5 35921019 Silent SNP C C3N-00704_T 9035211 35921019 145617240 184 19321 FYB 0 . GRCh38 5 39202601 39202601 + Missense_Mutation SNP C C A rs766831131 C3N-00704_T C3N-00704_N C C c.390G>T p.Leu130Phe p.L130F ENST00000512982 2/19 489 331 158 420 418 2 strelka-varscan-mutect FYB,missense_variant,p.Leu120Phe,ENST00000351578,NM_199335.3;FYB,missense_variant,p.Leu120Phe,ENST00000505428,NM_001465.4;FYB,missense_variant,p.Leu130Phe,ENST00000512982,NM_001243093.1;FYB,missense_variant,p.Leu120Phe,ENST00000515010,;FYB,missense_variant,p.Leu120Phe,ENST00000510188,;FYB,downstream_gene_variant,,ENST00000506557,;FYB,downstream_gene_variant,,ENST00000504542,;FYB,downstream_gene_variant,,ENST00000509072,;FYB,downstream_gene_variant,,ENST00000512138,; A ENST00000512982 Transcript missense_variant 476/2747 390/2520 130/839 L/F ttG/ttT rs766831131 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 tolerated(0.66) 2/19 hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF13 MODERATE 1 SNV 2 1 PASS rs766831131 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 39202601 39202601 C A 1 0 0 0 0 1 0 0 0 5995 709 25 2 2 FYB 5 39202601 Missense_Mutation SNP C C3N-00704_T 3281582 39202601 142335658 185 19322 C9 0 . GRCh38 5 39306741 39306741 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1292G>T p.Gly431Val p.G431V ENST00000263408 9/11 231 206 25 331 331 0 strelka-varscan-mutect C9,missense_variant,p.Gly431Val,ENST00000263408,NM_001737.3; A ENST00000263408 Transcript missense_variant 1388/2713 1292/1680 431/559 G/V gGt/gTt 1 -1 C9 HGNC HGNC:1358 protein_coding YES CCDS3929.1 ENSP00000263408 P02748 UPI0000001065 NM_001737.3 deleterious(0) 9/11 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF362,hmmpanther:PTHR19325,Pfam_domain:PF01823,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 39306741 39306741 C A 1 0 0 0 0 1 0 0 0 2169 507 18 2 2 C9 5 39306741 Missense_Mutation SNP C C3N-00704_T 104140 39306741 142231518 186 19323 C9 0 . GRCh38 5 39331680 39331680 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.611A>T p.Tyr204Phe p.Y204F ENST00000263408 5/11 591 422 169 582 582 0 strelka-varscan-mutect C9,missense_variant,p.Tyr204Phe,ENST00000263408,NM_001737.3;C9,non_coding_transcript_exon_variant,,ENST00000509186,;C9,downstream_gene_variant,,ENST00000483232,; A ENST00000263408 Transcript missense_variant 707/2713 611/1680 204/559 Y/F tAt/tTt 1 -1 C9 HGNC HGNC:1358 protein_coding YES CCDS3929.1 ENSP00000263408 P02748 UPI0000001065 NM_001737.3 tolerated(0.15) 5/11 PROSITE_profiles:PS51412,hmmpanther:PTHR19325:SF362,hmmpanther:PTHR19325 MODERATE 1 SNV 1 1 PASS rs1348472463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 39331680 39331680 T A 1 0 0 0 0 1 0 0 0 2169 1420 49 4 4 C9 5 39331680 Missense_Mutation SNP T C3N-00704_T 24939 39331680 142206579 187 19324 C6 0 . GRCh38 5 41176514 41176514 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1129C>G p.Leu377Val p.L377V ENST00000263413 8/18 242 166 76 235 235 0 strelka-varscan-mutect C6,missense_variant,p.Leu377Val,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Leu377Val,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000475349,;C6,upstream_gene_variant,,ENST00000473450,; C ENST00000263413 Transcript missense_variant 1394/3661 1129/2805 377/934 L/V Ctt/Gtt 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 tolerated(0.08) 8/18 PROSITE_profiles:PS51412,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Pfam_domain:PF01823,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 41176514 41176514 G C 1 0 0 0 0 1 0 0 0 2111 1000 35 4 4 C6 5 41176514 Missense_Mutation SNP G C3N-00704_T 1844834 41176514 140361745 188 19325 PLCXD3 0 . GRCh38 5 41382004 41382004 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.634A>T p.Met212Leu p.M212L ENST00000377801 2/3 239 214 25 182 182 0 strelka-varscan-mutect PLCXD3,missense_variant,p.Met212Leu,ENST00000377801,;PLCXD3,missense_variant,p.Met212Leu,ENST00000328457,NM_001005473.2; A ENST00000377801 Transcript missense_variant 709/7704 634/966 212/321 M/L Atg/Ttg 1 -1 PLCXD3 HGNC HGNC:31822 protein_coding YES CCDS34150.1 ENSP00000367032 Q63HM9 UPI0000049DBB deleterious(0.04) 2/3 Gene3D:3.20.20.190,hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF33,Superfamily_domains:SSF51695 MODERATE 1 SNV 2 1 PASS rs1423161865 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 41382004 41382004 T A 1 0 0 0 0 1 0 0 0 12137 1435 50 4 4 PLCXD3 5 41382004 Missense_Mutation SNP T C3N-00704_T 205490 41382004 140156255 189 19326 ARL15 0 . GRCh38 5 54113359 54113359 + Missense_Mutation SNP C C A rs375592157 C3N-00704_T C3N-00704_N C C c.305G>T p.Gly102Val p.G102V ENST00000504924 4/5 244 203 41 318 318 0 strelka-varscan-mutect ARL15,missense_variant,p.Gly102Val,ENST00000504924,NM_019087.2;ARL15,missense_variant,p.Gly102Val,ENST00000620747,;ARL15,missense_variant,p.Gly102Val,ENST00000507646,;ARL15,5_prime_UTR_variant,,ENST00000502271,;ARL15,non_coding_transcript_exon_variant,,ENST00000510591,;ARL15,non_coding_transcript_exon_variant,,ENST00000505630,; A ENST00000504924 Transcript missense_variant 399/2486 305/615 102/204 G/V gGg/gTg rs375592157 1 -1 ARL15 HGNC HGNC:25945 protein_coding YES CCDS54850.1 ENSP00000433427 Q9NXU5 UPI000006D66A NM_019087.2 deleterious(0) 4/5 Gene3D:3.40.50.300,Pfam_domain:PF00025,Prints_domain:PR00328,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF192,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs375592157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 54113359 54113359 C A 1 0 0 0 0 1 0 0 0 1070 623 22 2 2 ARL15 5 54113359 Missense_Mutation SNP C C3N-00704_T 12731355 54113359 127424900 190 19327 MAP3K1 0 . GRCh38 5 56882625 56882625 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.3425C>T p.Ser1142Leu p.S1142L ENST00000399503 14/20 204 178 26 267 267 0 strelka-varscan-mutect MAP3K1,missense_variant,p.Ser1142Leu,ENST00000399503,NM_005921.1;MAP3K1,upstream_gene_variant,,ENST00000469188,; T ENST00000399503 Transcript missense_variant 3425/7011 3425/4539 1142/1512 S/L tCa/tTa 1 1 MAP3K1 HGNC HGNC:6848 protein_coding YES CCDS43318.1 ENSP00000382423 Q13233 UPI000015153B NM_005921.1 deleterious(0) 14/20 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 56882625 56882625 C T 1 0 0 0 0 1 0 0 0 9165 838 29 3 3 MAP3K1 5 56882625 Missense_Mutation SNP C C3N-00704_T 2769266 56882625 124655634 191 19328 LRRC70 0 . GRCh38 5 62580150 62580150 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.712A>T p.Asn238Tyr p.N238Y ENST00000334994 2/2 203 178 25 371 371 0 strelka-varscan-mutect LRRC70,missense_variant,p.Asn238Tyr,ENST00000334994,NM_181506.4;IPO11,intron_variant,,ENST00000325324,NM_016338.4;IPO11,intron_variant,,ENST00000409296,NM_001134779.1;IPO11,intron_variant,,ENST00000511713,;IPO11,intron_variant,,ENST00000409534,;LRRC70,intron_variant,,ENST00000491184,;LRRC70,intron_variant,,ENST00000448151,;IPO11,intron_variant,,ENST00000511133,;IPO11,intron_variant,,ENST00000424533,;IPO11,intron_variant,,ENST00000413749,;RP11-95I19.1,upstream_gene_variant,,ENST00000469402,; T ENST00000334994 Transcript missense_variant 951/2249 712/1869 238/622 N/Y Aat/Tat 1 1 LRRC70 HGNC HGNC:35155 protein_coding YES CCDS47218.1 ENSP00000399441 Q7Z2Q7 UPI000004C632 NM_181506.4 deleterious(0) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF113,hmmpanther:PTHR24373,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 62580150 62580150 A T 1 0 0 0 0 1 0 0 0 8917 362 13 4 4 LRRC70 5 62580150 Missense_Mutation SNP A C3N-00704_T 5697525 62580150 118958109 192 19329 ENC1 0 . GRCh38 5 74635952 74635952 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.534C>T p.= p.T178T ENST00000618628 3/4 247 205 42 283 283 0 strelka-varscan-mutect ENC1,synonymous_variant,p.=,ENST00000618628,NM_001256574.1;ENC1,synonymous_variant,p.=,ENST00000302351,NM_003633.3,NM_001256575.1;ENC1,synonymous_variant,p.=,ENST00000510316,NM_001256576.1;ENC1,synonymous_variant,p.=,ENST00000537006,;HEXB,upstream_gene_variant,,ENST00000511181,NM_001292004.1;ENC1,downstream_gene_variant,,ENST00000508331,;ENC1,downstream_gene_variant,,ENST00000509127,;ENC1,upstream_gene_variant,,ENST00000509284,; A ENST00000618628 Transcript synonymous_variant 1802/5657 534/1770 178/589 T acC/acT 1 -1 ENC1 HGNC HGNC:3345 protein_coding YES CCDS4021.1 ENSP00000479101 O14682 Q53XS2 UPI0000129EBB NM_001256574.1 3/4 hmmpanther:PTHR24410:SF5,hmmpanther:PTHR24410,PIRSF_domain:PIRSF037037,Pfam_domain:PF07707,SMART_domains:SM00875 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 74635952 74635952 G A 1 0 0 0 0 0 0 0 1 4955 1335 47 3 3 ENC1 5 74635952 Silent SNP G C3N-00704_T 12055802 74635952 106902307 193 19330 F2R 0 . GRCh38 5 76733464 76733464 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1239T>A p.Ser413Arg p.S413R ENST00000319211 2/2 121 99 22 146 146 0 strelka-varscan-mutect F2R,missense_variant,p.Ser413Arg,ENST00000319211,NM_001992.3; A ENST00000319211 Transcript missense_variant 1504/3821 1239/1278 413/425 S/R agT/agA 1 1 F2R HGNC HGNC:3537 protein_coding YES CCDS4032.1 ENSP00000321326 P25116 A0A024RAP7 UPI0000131312 NM_001992.3 deleterious(0) 2/2 hmmpanther:PTHR24232:SF20,hmmpanther:PTHR24232,Prints_domain:PR00908 MODERATE 1 SNV 1 1 PASS rs1355823262 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 76733464 76733464 T A 1 0 0 0 0 1 0 0 0 5211 1635 57 4 4 F2R 5 76733464 Missense_Mutation SNP T C3N-00704_T 2097512 76733464 104804795 194 19331 CHD1 0 . GRCh38 5 98897277 98897277 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1409C>T p.Pro470Leu p.P470L ENST00000614616 11/36 162 142 20 304 304 0 strelka-varscan-mutect CHD1,missense_variant,p.Pro470Leu,ENST00000614616,;CHD1,missense_variant,p.Pro470Leu,ENST00000284049,NM_001270.2; A ENST00000614616 Transcript missense_variant 1976/8095 1409/5133 470/1710 P/L cCa/cTa 1 -1 CHD1 HGNC HGNC:1915 protein_coding YES CCDS34204.1 ENSP00000483667 O14646 UPI000013DD75 deleterious(0.02) 11/36 hmmpanther:PTHR10799:SF535,hmmpanther:PTHR10799,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 98897277 98897277 G A 1 0 0 0 0 1 0 0 0 3082 1348 47 3 3 CHD1 5 98897277 Missense_Mutation SNP G C3N-00704_T 22163813 98897277 82640982 195 19332 TSSK1B 0 . GRCh38 5 113433783 113433783 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1057A>T p.Thr353Ser p.T353S ENST00000390666 1/1 94 81 13 106 106 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Thr353Ser,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; A ENST00000390666 Transcript missense_variant 1249/2478 1057/1104 353/367 T/S Aca/Tca 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 tolerated_low_confidence(0.63) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 113433783 113433783 T A 1 0 0 0 0 1 0 0 0 17176 1667 58 4 4 TSSK1B 5 113433783 Missense_Mutation SNP T C3N-00704_T 14536506 113433783 68104476 196 19333 SEMA6A 0 . GRCh38 5 116447392 116447392 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2365C>A p.Arg789Ser p.R789S ENST00000257414 20/20 188 161 27 222 222 0 strelka-varscan-mutect SEMA6A,missense_variant,p.Arg772Ser,ENST00000343348,NM_020796.4;SEMA6A,missense_variant,p.Arg789Ser,ENST00000257414,NM_001300780.1;SEMA6A,missense_variant,p.Arg199Ser,ENST00000513137,;SEMA6A,missense_variant,p.Arg772Ser,ENST00000510263,;SEMA6A,missense_variant,p.Arg287Ser,ENST00000515129,;SEMA6A,missense_variant,p.Arg151Ser,ENST00000503865,;SEMA6A-AS1,upstream_gene_variant,,ENST00000508424,;SEMA6A-AS1,upstream_gene_variant,,ENST00000514214,;SEMA6A-AS1,upstream_gene_variant,,ENST00000508640,;SEMA6A-AS1,upstream_gene_variant,,ENST00000510682,;SEMA6A-AS1,upstream_gene_variant,,ENST00000512128,;SEMA6A,downstream_gene_variant,,ENST00000506114,; T ENST00000257414 Transcript missense_variant 2614/4256 2365/3144 789/1047 R/S Cgc/Agc 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 tolerated(0.43) 20/20 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 116447392 116447392 G T 1 0 0 0 0 1 0 0 0 14315 1116 39 1 1 SEMA6A 5 116447392 Missense_Mutation SNP G C3N-00704_T 3013609 116447392 65090867 197 19334 SEMA6A 0 . GRCh38 5 116504874 116504874 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.71C>A p.Ser24Tyr p.S24Y ENST00000257414 2/20 219 188 31 192 192 0 strelka-varscan-mutect SEMA6A,missense_variant,p.Ser24Tyr,ENST00000343348,NM_020796.4;SEMA6A,missense_variant,p.Ser24Tyr,ENST00000257414,NM_001300780.1;SEMA6A,missense_variant,p.Ser24Tyr,ENST00000510263,;SEMA6A,missense_variant,p.Ser24Tyr,ENST00000515009,;SEMA6A,missense_variant,p.Ser24Tyr,ENST00000509665,;SEMA6A-AS1,intron_variant,,ENST00000510682,;SEMA6A,upstream_gene_variant,,ENST00000503962,; T ENST00000257414 Transcript missense_variant 320/4256 71/3144 24/1047 S/Y tCt/tAt 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 tolerated(0.07) 2/20 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12 MODERATE 1 SNV 1 1 PASS rs1248369822 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 116504874 116504874 G T 1 0 0 0 0 1 0 0 0 14315 942 33 2 2 SEMA6A 5 116504874 Missense_Mutation SNP G C3N-00704_T 57482 116504874 65033385 198 19335 SEPT8 0 . GRCh38 5 132765429 132765429 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.131G>T p.Ser44Ile p.S44I ENST00000378719 2/10 221 195 26 276 276 0 strelka-varscan-mutect SEPT8,missense_variant,p.Ser44Ile,ENST00000296873,NM_001300799.1,NM_015146.1;SEPT8,missense_variant,p.Ser44Ile,ENST00000620483,;SEPT8,missense_variant,p.Ser44Ile,ENST00000378706,;SEPT8,missense_variant,p.Ser44Ile,ENST00000378719,NM_001098811.1;SEPT8,missense_variant,p.Ser44Ile,ENST00000378701,NM_001300798.1;SEPT8,missense_variant,p.Ser44Ile,ENST00000458488,NM_001098812.1;SEPT8,missense_variant,p.Ser44Ile,ENST00000378721,;SEPT8,5_prime_UTR_variant,,ENST00000448933,NM_001098813.1;SEPT8,5_prime_UTR_variant,,ENST00000378699,;SEPT8,5_prime_UTR_variant,,ENST00000453480,;SEPT8,5_prime_UTR_variant,,ENST00000414594,;SEPT8,5_prime_UTR_variant,,ENST00000371493,;SEPT8,non_coding_transcript_exon_variant,,ENST00000371478,;SEPT8,non_coding_transcript_exon_variant,,ENST00000492490,;SEPT8,upstream_gene_variant,,ENST00000481030,;SEPT8,non_coding_transcript_exon_variant,,ENST00000481794,; A ENST00000378719 Transcript missense_variant 369/2889 131/1452 44/483 S/I aGc/aTc 1 -1 SEPT8 HGNC HGNC:16511 protein_coding YES CCDS43358.1 ENSP00000367991 Q92599 UPI00001C1E27 NM_001098811.1 tolerated(0.17) 2/10 Gene3D:3.40.50.300,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF54,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 132765429 132765429 C A 1 0 0 0 0 1 0 0 0 14346 797 28 2 2 SEPT8 5 132765429 Missense_Mutation SNP C C3N-00704_T 16260555 132765429 48772830 199 19336 IK 0 . GRCh38 5 140659066 140659066 + Nonsense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.1078C>T p.Arg360Ter p.R360* ENST00000417647 12/20 404 349 55 484 484 0 strelka-varscan-mutect IK,stop_gained,p.Arg360Ter,ENST00000417647,NM_006083.3;IK,stop_gained,p.Arg45Ter,ENST00000610522,;IK,downstream_gene_variant,,ENST00000508301,;IK,downstream_gene_variant,,ENST00000502899,;IK,non_coding_transcript_exon_variant,,ENST00000515015,;IK,upstream_gene_variant,,ENST00000515592,; T ENST00000417647 Transcript stop_gained 1217/1962 1078/1674 360/557 R/* Cga/Tga 1 1 IK HGNC HGNC:5958 protein_coding YES CCDS47280.1 ENSP00000396301 Q13123 UPI0000378337 NM_006083.3 12/20 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12765:SF5,hmmpanther:PTHR12765 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 140659066 140659066 C T 1 0 0 0 0 0 1 0 0 7516 760 27 1 1 IK 5 140659066 Nonsense_Mutation SNP C C3N-00704_T 7893637 140659066 40879193 200 19337 PCDHA4 0 . GRCh38 5 140808457 140808457 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1270G>T p.Val424Leu p.V424L ENST00000530339 1/4 480 385 95 643 643 0 strelka-varscan-mutect PCDHA4,missense_variant,p.Val424Leu,ENST00000618834,NM_031500.2;PCDHA4,missense_variant,p.Val424Leu,ENST00000530339,NM_018907.3;PCDHA4,missense_variant,p.Val424Leu,ENST00000512229,;PCDHA4,missense_variant,p.Val423Leu,ENST00000378125,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,downstream_gene_variant,,ENST00000532566,NM_031497.1;PCDHA2,downstream_gene_variant,,ENST00000520672,NM_031496.1;AC005609.16,intron_variant,,ENST00000624712,; T ENST00000530339 Transcript missense_variant 1270/5251 1270/2844 424/947 V/L Gtg/Ttg 1 1 PCDHA4 HGNC HGNC:8670 protein_coding YES CCDS54916.1 ENSP00000435300 Q9UN74 UPI00001273CC NM_018907.3 tolerated_low_confidence(0.1) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF82,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 140808457 140808457 G T 1 0 0 0 0 1 0 0 0 11613 1261 44 2 2 PCDHA4 5 140808457 Missense_Mutation SNP G C3N-00704_T 149391 140808457 40729802 201 19338 PCDHA7 0 . GRCh38 5 140836643 140836643 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.2260A>T p.Arg754Trp p.R754W ENST00000525929 1/4 141 116 25 164 164 0 strelka-varscan-mutect PCDHA7,missense_variant,p.Arg754Trp,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Arg754Trp,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA8,upstream_gene_variant,,ENST00000531613,NM_018911.2;PCDHA8,upstream_gene_variant,,ENST00000378123,NM_031856.1; T ENST00000525929 Transcript missense_variant 2260/5221 2260/2814 754/937 R/W Agg/Tgg 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 deleterious_low_confidence(0) 1/4 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 140836643 140836643 A T 1 0 0 0 0 1 0 0 0 11616 295 11 4 4 PCDHA7 5 140836643 Missense_Mutation SNP A C3N-00704_T 28186 140836643 40701616 202 19339 PCDHB7 0 . GRCh38 5 141175019 141175019 + Silent SNP C C A rs782564883 C3N-00704_T C3N-00704_N C C c.2184C>A p.= p.G728G ENST00000231137 1/1 267 229 38 401 401 0 strelka-varscan-mutect PCDHB7,synonymous_variant,p.=,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; A ENST00000231137 Transcript synonymous_variant 2401/3765 2184/2382 728/793 G ggC/ggA rs782564883 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69 LOW SNV 1 PASS rs782564883 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 141175019 141175019 C A 1 0 0 0 0 0 0 0 1 11634 726 26 2 2 PCDHB7 5 141175019 Silent SNP C C3N-00704_T 338376 141175019 40363240 203 19340 PCDHB9 0 . GRCh38 5 141189059 141189059 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1741G>T p.Glu581Ter p.E581* ENST00000316105 1/1 514 448 66 793 793 0 varscan-mutect PCDHB9,stop_gained,p.Glu581Ter,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; T ENST00000316105 Transcript stop_gained 1933/4415 1741/2394 581/797 E/* Gag/Tag 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 141189059 141189059 G T 1 0 0 0 0 0 1 0 0 11636 1059 37 1 1 PCDHB9 5 141189059 Nonsense_Mutation SNP G C3N-00704_T 14040 141189059 40349200 204 19341 PCDHGA4 0 . GRCh38 5 141356893 141356893 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.1786C>T p.Pro596Ser p.P596S ENST00000571252 1/4 288 251 37 375 374 1 strelka-varscan-mutect PCDHGA4,missense_variant,p.Pro596Ser,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Pro596Ser,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 1869/4778 1786/2889 596/962 P/S Ccc/Tcc 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 141356893 141356893 C T 1 0 0 0 0 1 0 0 0 11643 623 22 3 3 PCDHGA4 5 141356893 Missense_Mutation SNP C C3N-00704_T 167834 141356893 40181366 205 19342 PCDHGA8 0 . GRCh38 5 141394587 141394588 + Frame_Shift_Ins INS - - T novel C3N-00704_T C3N-00704_N - - c.1775dupT p.Ala593GlyfsTer74 p.A593Gfs*74 ENST00000398604 1/4 380 311 69 637 637 0 sindel-varindel-pindel PCDHGA8,frameshift_variant,p.Ala593GlyfsTer74,ENST00000610569,NM_014004.2;PCDHGA8,frameshift_variant,p.Ala593GlyfsTer74,ENST00000398604,NM_032088.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB4,downstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB5,upstream_gene_variant,,ENST00000617380,NM_018925.2;PCDHGB5,upstream_gene_variant,,ENST00000621169,NM_032099.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398604 Transcript frameshift_variant 1774-1775/4605 1774-1775/2799 592/932 V/VX gtg/gTtg 1 1 PCDHGA8 HGNC HGNC:8706 protein_coding YES CCDS47291.1 ENSP00000381605 Q9Y5G5 UPI000006FC06 NM_032088.1 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF72,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 62 141394587 141394587 - T 1 0 1 1 0 0 0 0 0 11647 1261 44 0 0 PCDHGA8 5 141394587 Frame_Shift_Ins INS - C3N-00704_T 37694 141394587 40143672 206 19343 LARS 0 . GRCh38 5 146171979 146171979 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.225G>T p.= p.G75G ENST00000394434 4/32 176 150 26 270 270 0 strelka-varscan-mutect LARS,synonymous_variant,p.=,ENST00000394434,NM_001317965.1,NM_020117.9;LARS,synonymous_variant,p.=,ENST00000510191,;LARS,synonymous_variant,p.=,ENST00000618084,;LARS,5_prime_UTR_variant,,ENST00000274562,;LARS,non_coding_transcript_exon_variant,,ENST00000511505,;LARS,non_coding_transcript_exon_variant,,ENST00000503654,;LARS,intron_variant,,ENST00000505223,;LARS,downstream_gene_variant,,ENST00000506436,; A ENST00000394434 Transcript synonymous_variant 392/4766 225/3531 75/1176 G ggG/ggT 1 -1 LARS HGNC HGNC:6512 protein_coding YES CCDS34265.1 ENSP00000377954 Q9P2J5 UPI0000037316 NM_001317965.1,NM_020117.9 4/32 hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF51,Pfam_domain:PF00133,Gene3D:3.40.50.620,TIGRFAM_domain:TIGR00395,Superfamily_domains:SSF52374 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 146171979 146171979 C A 1 0 0 0 0 0 0 0 1 8545 494 18 2 2 LARS 5 146171979 Silent SNP C C3N-00704_T 4777392 146171979 35366280 207 19344 PPP2R2B 0 . GRCh38 5 146691160 146691160 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.613C>G p.Leu205Val p.L205V ENST00000394414 5/10 182 152 30 220 220 0 strelka-mutect PPP2R2B,missense_variant,p.Leu139Val,ENST00000394409,;PPP2R2B,missense_variant,p.Leu128Val,ENST00000453001,NM_001271948.1;PPP2R2B,missense_variant,p.Leu205Val,ENST00000394414,NM_181674.2;PPP2R2B,missense_variant,p.Leu139Val,ENST00000394411,NM_181675.3;PPP2R2B,missense_variant,p.Leu128Val,ENST00000508545,NM_181678.2;PPP2R2B,missense_variant,p.Leu145Val,ENST00000504198,NM_001271899.1,NM_181677.2;PPP2R2B,missense_variant,p.Leu142Val,ENST00000336640,NM_181676.2;PPP2R2B,missense_variant,p.Leu197Val,ENST00000394413,NM_001271900.1;PPP2R2B,non_coding_transcript_exon_variant,,ENST00000530902,;PPP2R2B,intron_variant,,ENST00000522831,;PPP2R2B,3_prime_UTR_variant,,ENST00000512639,;PPP2R2B,downstream_gene_variant,,ENST00000528601,; C ENST00000394414 Transcript missense_variant 902/2262 613/1530 205/509 L/V Ctc/Gtc 1 -1 PPP2R2B HGNC HGNC:9305 protein_coding YES CCDS4284.2 ENSP00000377936 Q00005 UPI00005A7962 NM_181674.2 tolerated(0.17) 5/10 hmmpanther:PTHR11871,hmmpanther:PTHR11871:SF1,PIRSF_domain:PIRSF037309 MODERATE 1 SNV 1 1 PASS rs1254691315 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 146691160 146691160 G C 1 0 0 0 0 1 0 0 0 12508 971 34 4 4 PPP2R2B 5 146691160 Missense_Mutation SNP G C3N-00704_T 519181 146691160 34847099 208 19345 FBXO38 0 . GRCh38 5 148404729 148404729 + Missense_Mutation SNP C C T rs768270226 C3N-00704_T C3N-00704_N C C c.637C>T p.Leu213Phe p.L213F ENST00000394370 6/22 81 67 14 181 181 0 strelka-varscan-mutect FBXO38,missense_variant,p.Leu213Phe,ENST00000340253,;FBXO38,missense_variant,p.Leu213Phe,ENST00000394370,NM_030793.4;FBXO38,missense_variant,p.Leu213Phe,ENST00000296701,NM_001271723.1;FBXO38,missense_variant,p.Leu213Phe,ENST00000513826,;FBXO38,non_coding_transcript_exon_variant,,ENST00000509699,;FBXO38,intron_variant,,ENST00000511080,;FBXO38,downstream_gene_variant,,ENST00000503613,;FBXO38,downstream_gene_variant,,ENST00000521160,;FBXO38,non_coding_transcript_exon_variant,,ENST00000502571,;FBXO38,downstream_gene_variant,,ENST00000508326,;FBXO38,downstream_gene_variant,,ENST00000502629,; T ENST00000394370 Transcript missense_variant 738/4132 637/3342 213/1113 L/F Ctt/Ttt rs768270226 1 1 FBXO38 HGNC HGNC:28844 protein_coding YES CCDS43384.1 ENSP00000377895 Q6PIJ6 UPI000034ECEB NM_030793.4 deleterious(0) 6/22 hmmpanther:PTHR14753,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs768270226 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 148404729 148404729 C T 1 0 0 0 0 1 0 0 0 5609 681 24 3 3 FBXO38 5 148404729 Missense_Mutation SNP C C3N-00704_T 1713569 148404729 33133530 209 19346 SH3TC2 0 . GRCh38 5 149004756 149004756 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.3822C>T p.= p.S1274S ENST00000515425 17/17 218 182 36 248 248 0 strelka-varscan-mutect SH3TC2,synonymous_variant,p.=,ENST00000515425,NM_024577.3;SH3TC2,synonymous_variant,p.=,ENST00000512049,;SH3TC2,synonymous_variant,p.=,ENST00000502274,;SH3TC2,intron_variant,,ENST00000515229,;SH3TC2,intron_variant,,ENST00000510350,;SH3TC2,3_prime_UTR_variant,,ENST00000323829,;SH3TC2,3_prime_UTR_variant,,ENST00000504517,;SH3TC2,3_prime_UTR_variant,,ENST00000510779,;SH3TC2,intron_variant,,ENST00000504690,; A ENST00000515425 Transcript synonymous_variant 3924/4059 3822/3867 1274/1288 S tcC/tcT 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 17/17 hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 149004756 149004756 G A 1 0 0 0 0 0 0 0 1 14521 987 35 3 3 SH3TC2 5 149004756 Silent SNP G C3N-00704_T 600027 149004756 32533503 210 19347 PDE6A 0 . GRCh38 5 149944253 149944253 + Missense_Mutation SNP C C A rs757733655 C3N-00704_T C3N-00704_N C C c.421G>T p.Val141Leu p.V141L ENST00000255266 1/22 311 249 62 390 388 2 strelka-varscan-mutect PDE6A,missense_variant,p.Val141Leu,ENST00000255266,NM_000440.2;PDE6A,missense_variant,p.Val141Leu,ENST00000613228,;PDE6A,missense_variant,p.Val141Leu,ENST00000617647,;Y_RNA,upstream_gene_variant,,ENST00000363464,;PDE6A,non_coding_transcript_exon_variant,,ENST00000508173,; A ENST00000255266 Transcript missense_variant 541/5642 421/2583 141/860 V/L Gtg/Ttg rs757733655 1 -1 PDE6A HGNC HGNC:8785 protein_coding YES CCDS4299.1 ENSP00000255266 P16499 UPI000013CE9F NM_000440.2 deleterious(0.05) 1/22 hmmpanther:PTHR11347:SF115,hmmpanther:PTHR11347,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS rs757733655 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 149944253 149944253 C A 1 0 0 0 0 1 0 0 0 11733 536 19 1 1 PDE6A 5 149944253 Missense_Mutation SNP C C3N-00704_T 939497 149944253 31594006 211 19348 SLC36A1 0 . GRCh38 5 151479450 151479450 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1120G>T p.Val374Leu p.V374L ENST00000243389 10/11 183 148 35 201 201 0 strelka-varscan-mutect SLC36A1,missense_variant,p.Val374Leu,ENST00000243389,NM_078483.2;SLC36A1,missense_variant,p.Val374Leu,ENST00000520701,;SLC36A1,missense_variant,p.Val374Leu,ENST00000521925,;SLC36A1,missense_variant,p.Val374Leu,ENST00000616007,;SLC36A1,missense_variant,p.Val133Leu,ENST00000517628,;RNA5SP197,upstream_gene_variant,,ENST00000363357,;SLC36A1,3_prime_UTR_variant,,ENST00000522185,; T ENST00000243389 Transcript missense_variant 1343/5781 1120/1431 374/476 V/L Gtg/Ttg 1 1 SLC36A1 HGNC HGNC:18761 protein_coding YES CCDS4316.1 ENSP00000243389 Q7Z2H8 UPI00001A9D3C NM_078483.2 tolerated(0.31) 10/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF188 MODERATE 1 SNV 1 1 PASS rs1053544056 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 151479450 151479450 G T 1 0 0 0 0 1 0 0 0 14871 1261 44 2 2 SLC36A1 5 151479450 Missense_Mutation SNP G C3N-00704_T 1535197 151479450 30058809 212 19349 GLRA1 0 . GRCh38 5 151892371 151892371 + Missense_Mutation SNP G G T rs267600494 C3N-00704_T C3N-00704_N G G c.124C>A p.Leu42Met p.L42M ENST00000455880 2/9 381 325 56 399 399 0 strelka-varscan-mutect GLRA1,missense_variant,p.Leu42Met,ENST00000274576,NM_000171.3,NM_001292000.1;GLRA1,missense_variant,p.Leu42Met,ENST00000455880,NM_001146040.1;GLRA1,non_coding_transcript_exon_variant,,ENST00000471351,;GLRA1,intron_variant,,ENST00000462581,; T ENST00000455880 Transcript missense_variant 411/1707 124/1374 42/457 L/M Ctg/Atg rs267600494 1 -1 GLRA1 HGNC HGNC:4326 protein_coding YES CCDS54942.1 ENSP00000411593 P23415 UPI0000DA6BF2 NM_001146040.1 deleterious(0.03) 2/9 hmmpanther:PTHR18945:SF213,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR01673 MODERATE 1 SNV 1 1 PASS rs267600494 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 151892371 151892371 G T 1 0 0 0 0 1 0 0 0 6333 991 35 2 2 GLRA1 5 151892371 Missense_Mutation SNP G C3N-00704_T 412921 151892371 29645888 213 19350 ITK 0 . GRCh38 5 157181104 157181104 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.127G>C p.Asp43His p.D43H ENST00000422843 1/17 394 316 78 457 457 0 strelka-varscan-mutect ITK,missense_variant,p.Asp43His,ENST00000422843,NM_005546.3;ITK,intron_variant,,ENST00000521769,;ITK,non_coding_transcript_exon_variant,,ENST00000522616,;ITK,missense_variant,p.Asp43His,ENST00000517779,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,non_coding_transcript_exon_variant,,ENST00000520555,; C ENST00000422843 Transcript missense_variant 279/4528 127/1863 43/620 D/H Gat/Cat 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 tolerated(0.56) 1/17 PROSITE_profiles:PS50003,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 157181104 157181104 G C 1 0 0 0 0 1 0 0 0 7815 942 33 4 4 ITK 5 157181104 Missense_Mutation SNP G C3N-00704_T 5288733 157181104 24357155 214 19351 ITK 0 . GRCh38 5 157248904 157248904 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1688G>A p.Ser563Asn p.S563N ENST00000422843 16/17 613 500 113 618 618 0 strelka-varscan-mutect ITK,missense_variant,p.Ser563Asn,ENST00000422843,NM_005546.3;ITK,non_coding_transcript_exon_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,downstream_gene_variant,,ENST00000523926,;ITK,downstream_gene_variant,,ENST00000520173,; A ENST00000422843 Transcript missense_variant 1840/4528 1688/1863 563/620 S/N aGc/aAc 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 tolerated(0.57) 16/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 157248904 157248904 G A 1 0 0 0 0 1 0 0 0 7815 971 34 3 3 ITK 5 157248904 Missense_Mutation SNP G C3N-00704_T 67800 157248904 24289355 215 19352 C1QTNF2 0 . GRCh38 5 160349709 160349709 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.452G>A p.Gly151Asp p.G151D ENST00000393975 3/3 62 38 24 80 80 0 strelka-varscan-mutect C1QTNF2,missense_variant,p.Gly151Asp,ENST00000393975,NM_031908.4;CCNJL,upstream_gene_variant,,ENST00000521643,; T ENST00000393975 Transcript missense_variant 456/2414 452/993 151/330 G/D gGc/gAc 1 -1 C1QTNF2 HGNC HGNC:14325 protein_coding YES CCDS4351.2 ENSP00000377545 Q9BXJ5 UPI0000D4B9D3 NM_031908.4 deleterious(0) 3/3 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF607,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 160349709 160349709 C T 1 0 0 0 0 1 0 0 0 1941 739 26 3 3 C1QTNF2 5 160349709 Missense_Mutation SNP C C3N-00704_T 3100805 160349709 21188550 216 19353 GABRA6 0 . GRCh38 5 161689651 161689651 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.545G>T p.Ser182Ile p.S182I ENST00000274545 6/9 67 58 9 167 167 0 strelka-varscan-mutect GABRA6,missense_variant,p.Ser172Ile,ENST00000523217,;GABRA6,missense_variant,p.Ser182Ile,ENST00000274545,NM_000811.2;GABRA6,missense_variant,p.Ser122Ile,ENST00000520000,;GABRA6,missense_variant,p.Ser102Ile,ENST00000523691,;GABRA6,missense_variant,p.Ser129Ile,ENST00000517823,;RP11-348M17.2,upstream_gene_variant,,ENST00000521984,;GABRA6,downstream_gene_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,non_coding_transcript_exon_variant,,ENST00000521520,;GABRA6,downstream_gene_variant,,ENST00000524220,; T ENST00000274545 Transcript missense_variant 978/2128 545/1362 182/453 S/I aGt/aTt 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 deleterious(0) 6/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS rs774441339 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 161689651 161689651 G T 1 0 0 0 0 1 0 0 0 6036 1029 36 2 2 GABRA6 5 161689651 Missense_Mutation SNP G C3N-00704_T 1339942 161689651 19848608 217 19354 TENM2 0 . GRCh38 5 168244702 168244702 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.5803T>C p.Ser1935Pro p.S1935P ENST00000518659 26/29 25 16 9 14 14 0 strelka-varscan-mutect TENM2,missense_variant,p.Ser1814Pro,ENST00000519204,;TENM2,missense_variant,p.Ser1935Pro,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Ser1696Pro,ENST00000520394,;TENM2,downstream_gene_variant,,ENST00000517941,; C ENST00000518659 Transcript missense_variant 5842/8550 5803/8325 1935/2774 S/P Tcc/Ccc 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 26/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 MODERATE 1 SNV 5 1 PASS . . 9 199 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 168244702 168244702 T C 1 0 0 0 0 1 0 0 0 16172 1551 54 5 5 TENM2 5 168244702 Missense_Mutation SNP T C3N-00704_T 6555051 168244702 13293557 218 19355 DOCK2 0 . GRCh38 5 169714158 169714158 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.1790G>T p.Arg597Leu p.R597L ENST00000256935 18/52 85 72 13 82 82 0 strelka-varscan-mutect DOCK2,missense_variant,p.Arg597Leu,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Arg89Leu,ENST00000520908,;DOCK2,missense_variant,p.Arg115Leu,ENST00000540750,;DOCK2,upstream_gene_variant,,ENST00000520836,;DOCK2,missense_variant,p.Arg597Leu,ENST00000524185,; T ENST00000256935 Transcript missense_variant 1870/6097 1790/5493 597/1830 R/L cGg/cTg COSM4531469 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0) 18/52 Low_complexity_(Seg):seg,PROSITE_profiles:PS51650,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF14429 1 MODERATE 1 SNV 1 1 1 PASS rs1384088682 . 0 202 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 62 169714158 169714158 G T 1 0 0 0 0 1 0 0 0 4502 1116 39 1 1 DOCK2 5 169714158 Missense_Mutation SNP G C3N-00704_T 1469456 169714158 11824101 219 19356 DOCK2 0 . GRCh38 5 170041118 170041118 + Silent SNP G G T rs560979452 C3N-00704_T C3N-00704_N G G c.3729G>T p.= p.T1243T ENST00000256935 37/52 295 257 38 291 291 0 strelka-varscan-mutect DOCK2,synonymous_variant,p.=,ENST00000256935,NM_004946.2;DOCK2,synonymous_variant,p.=,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000518056,; T ENST00000256935 Transcript synonymous_variant 3809/6097 3729/5493 1243/1830 T acG/acT rs560979452 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 37/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF06920,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs560979452 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 170041118 170041118 G T 1 0 0 0 0 0 0 0 1 4502 1074 38 1 1 DOCK2 5 170041118 Silent SNP G C3N-00704_T 326960 170041118 11497141 220 19357 GPRIN1 0 . GRCh38 5 176597065 176597065 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2770G>A p.Val924Ile p.V924I ENST00000303991 2/2 122 104 18 141 141 0 strelka-varscan-mutect GPRIN1,missense_variant,p.Val924Ile,ENST00000303991,NM_052899.2;CDHR2,downstream_gene_variant,,ENST00000510636,NM_001171976.1;CDHR2,downstream_gene_variant,,ENST00000261944,NM_017675.4;CDHR2,downstream_gene_variant,,ENST00000506348,; T ENST00000303991 Transcript missense_variant 2948/4211 2770/3027 924/1008 V/I Gta/Ata 1 -1 GPRIN1 HGNC HGNC:24835 protein_coding YES CCDS4405.1 ENSP00000305839 Q7Z2K8 UPI0000246D49 NM_052899.2 deleterious(0) 2/2 hmmpanther:PTHR12239:SF37,hmmpanther:PTHR12239,Pfam_domain:PF15235 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 176597065 176597065 C T 1 0 0 0 0 1 0 0 0 6608 507 18 3 3 GPRIN1 5 176597065 Missense_Mutation SNP C C3N-00704_T 6555947 176597065 4941194 221 19358 HK3 0 . GRCh38 5 176881398 176881398 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.2531T>A p.Val844Glu p.V844E ENST00000292432 18/19 250 210 40 335 335 0 strelka-varscan-mutect HK3,missense_variant,p.Val844Glu,ENST00000292432,NM_002115.2;UNC5A,downstream_gene_variant,,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000514058,;HK3,non_coding_transcript_exon_variant,,ENST00000506834,;HK3,non_coding_transcript_exon_variant,,ENST00000514666,; T ENST00000292432 Transcript missense_variant 2623/3066 2531/2772 844/923 V/E gTa/gAa 1 -1 HK3 HGNC HGNC:4925 protein_coding YES CCDS4407.1 ENSP00000292432 P52790 A0A024R7R1 UPI000006E237 NM_002115.2 deleterious(0) 18/19 PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF1,Gene3D:3.40.367.20,Pfam_domain:PF03727,Superfamily_domains:SSF53067,Prints_domain:PR00475 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 176881398 176881398 A T 1 0 0 0 0 1 0 0 0 7081 391 14 4 4 HK3 5 176881398 Missense_Mutation SNP A C3N-00704_T 284333 176881398 4656861 222 19359 RMND5B 0 . GRCh38 5 178147592 178147592 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.920A>G p.Gln307Arg p.Q307R ENST00000515098 10/12 247 208 39 262 262 0 strelka-varscan-mutect RMND5B,missense_variant,p.Gln307Arg,ENST00000515098,NM_001288794.1;RMND5B,missense_variant,p.Gln307Arg,ENST00000313386,NM_022762.4;RMND5B,missense_variant,p.Gln294Arg,ENST00000542098,NM_001288795.1;NHP2,downstream_gene_variant,,ENST00000274606,NM_017838.3;RMND5B,downstream_gene_variant,,ENST00000507457,;RMND5B,downstream_gene_variant,,ENST00000502814,;NHP2,downstream_gene_variant,,ENST00000314397,NM_001034833.1;RMND5B,downstream_gene_variant,,ENST00000508647,;NHP2,downstream_gene_variant,,ENST00000502263,;NHP2,downstream_gene_variant,,ENST00000511078,;NHP2,downstream_gene_variant,,ENST00000514354,;RMND5B,non_coding_transcript_exon_variant,,ENST00000513162,;RMND5B,non_coding_transcript_exon_variant,,ENST00000515360,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507937,;RMND5B,non_coding_transcript_exon_variant,,ENST00000507575,;RMND5B,downstream_gene_variant,,ENST00000512663,;RMND5B,downstream_gene_variant,,ENST00000512811,; G ENST00000515098 Transcript missense_variant 1271/4066 920/1182 307/393 Q/R cAg/cGg 1 1 RMND5B HGNC HGNC:26181 protein_coding YES CCDS4431.1 ENSP00000420875 Q96G75 UPI0000037C23 NM_001288794.1 deleterious(0.01) 10/12 hmmpanther:PTHR12170:SF6,hmmpanther:PTHR12170 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 178147592 178147592 A G 1 0 0 0 0 1 0 0 0 13577 188 7 5 5 RMND5B 5 178147592 Missense_Mutation SNP A C3N-00704_T 1266194 178147592 3390667 223 19360 FOXF2 0 . GRCh38 6 1390450 1390450 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.503C>A p.Pro168His p.P168H ENST00000259806 1/2 532 430 102 649 649 0 strelka-varscan-mutect FOXF2,missense_variant,p.Pro168His,ENST00000259806,NM_001452.1;MIR6720,upstream_gene_variant,,ENST00000611664,; A ENST00000259806 Transcript missense_variant 617/2187 503/1335 168/444 P/H cCc/cAc 1 1 FOXF2 HGNC HGNC:3810 protein_coding YES CCDS4472.1 ENSP00000259806 Q12947 UPI000012ADD6 NM_001452.1 deleterious(0) 1/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF224,Gene3D:1.10.10.10,Pfam_domain:PF00250,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS rs1173749640 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 1390450 1390450 C A 1 0 0 0 0 1 0 0 0 5868 623 22 2 2 FOXF2 6 1390450 Missense_Mutation SNP C C3N-00704_T 1390450 169415529 224 19361 F13A1 0 . GRCh38 6 6197327 6197327 + Splice_Site SNP C C A novel C3N-00704_T C3N-00704_N C C c.1113-1G>T p.X371_splice ENST00000264870 572 465 107 624 623 1 strelka-varscan-mutect F13A1,splice_acceptor_variant,,ENST00000264870,NM_000129.3; A ENST00000264870 Transcript splice_acceptor_variant -/3999 1113/2199 371/732 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 8/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 62 6197327 6197327 C A 1 0 0 0 0 0 0 1 0 5208 695 24 2 2 F13A1 6 6197327 Splice_Site SNP C C3N-00704_T 4806877 6197327 164608652 225 19362 DSP 0 . GRCh38 6 7584991 7584991 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.7729G>T p.Val2577Phe p.V2577F ENST00000379802 24/24 438 345 93 514 514 0 strelka-varscan-mutect DSP,missense_variant,p.Val2577Phe,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Val1978Phe,ENST00000418664,NM_001008844.1; T ENST00000379802 Transcript missense_variant 8070/9796 7729/8616 2577/2871 V/F Gtc/Ttc 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 tolerated(0.51) 24/24 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 7584991 7584991 G T 1 0 0 0 0 1 0 0 0 4602 1377 48 2 2 DSP 6 7584991 Missense_Mutation SNP G C3N-00704_T 1387664 7584991 163220988 226 19363 CAP2 0 . GRCh38 6 17507703 17507703 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.507G>T p.Arg169Ser p.R169S ENST00000229922 6/13 173 155 18 188 186 2 strelka-varscan-mutect CAP2,missense_variant,p.Arg169Ser,ENST00000229922,NM_006366.2;CAP2,missense_variant,p.Arg143Ser,ENST00000378990,;CAP2,intron_variant,,ENST00000616440,;CAP2,intron_variant,,ENST00000611958,;CAP2,intron_variant,,ENST00000489374,;CAP2,intron_variant,,ENST00000465994,;CAP2,intron_variant,,ENST00000493172,;CAP2,missense_variant,p.Arg143Ser,ENST00000479291,;CAP2,3_prime_UTR_variant,,ENST00000476263,; T ENST00000229922 Transcript missense_variant 1039/3316 507/1434 169/477 R/S agG/agT 1 1 CAP2 HGNC HGNC:20039 protein_coding YES CCDS4539.1 ENSP00000229922 P40123 UPI0000126EC6 NM_006366.2 deleterious(0) 6/13 Superfamily_domains:0043456,Pfam_domain:PF01213,hmmpanther:PTHR10652,hmmpanther:PTHR10652:SF2 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 17507703 17507703 G T 1 0 0 0 0 1 0 0 0 2312 1223 43 2 2 CAP2 6 17507703 Missense_Mutation SNP G C3N-00704_T 9922712 17507703 153298276 227 19364 SLC17A4 0 . GRCh38 6 25773513 25773513 + Missense_Mutation SNP G G T rs774010672 C3N-00704_T C3N-00704_N G G c.826G>T p.Asp276Tyr p.D276Y ENST00000377905 8/12 74 55 19 87 87 0 strelka-varscan-mutect SLC17A4,missense_variant,p.Asp222Tyr,ENST00000439485,NM_001286121.1;SLC17A4,missense_variant,p.Asp276Tyr,ENST00000377905,NM_005495.2;SLC17A4,missense_variant,p.Asp46Tyr,ENST00000397076,; T ENST00000377905 Transcript missense_variant,splice_region_variant 945/3616 826/1494 276/497 D/Y Gac/Tac rs774010672 1 1 SLC17A4 HGNC HGNC:10932 protein_coding YES CCDS4564.1 ENSP00000367137 Q9Y2C5 A0A024R013 UPI0000073585 NM_005495.2 tolerated(1) 8/12 Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF284,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs774010672 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 25773513 25773513 G T 1 0 0 0 0 1 0 0 0 14684 1188 41 2 2 SLC17A4 6 25773513 Missense_Mutation SNP G C3N-00704_T 8265810 25773513 145032466 228 19365 GPX5 0 . GRCh38 6 28531816 28531816 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.280C>A p.Leu94Ile p.L94I ENST00000412168 3/5 204 166 38 249 247 2 strelka-varscan-mutect GPX5,missense_variant,p.Leu94Ile,ENST00000412168,NM_001509.2;GPX5,intron_variant,,ENST00000469384,NM_003996.3;GPX5,non_coding_transcript_exon_variant,,ENST00000442674,;GPX5,intron_variant,,ENST00000483784,;GPX6,upstream_gene_variant,,ENST00000483058,; A ENST00000412168 Transcript missense_variant 369/1540 280/666 94/221 L/I Cta/Ata 1 1 GPX5 HGNC HGNC:4557 protein_coding YES CCDS4652.1 ENSP00000392398 O75715 V9HWN8 UPI0000031FD7 NM_001509.2 deleterious(0.02) 3/5 Gene3D:3.40.30.10,Pfam_domain:PF00255,PIRSF_domain:PIRSF000303,Prints_domain:PR01011,PROSITE_profiles:PS51355,hmmpanther:PTHR11592,hmmpanther:PTHR11592:SF29,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 28531816 28531816 C A 1 0 0 0 0 1 0 0 0 6622 912 32 2 2 GPX5 6 28531816 Missense_Mutation SNP C C3N-00704_T 2758303 28531816 142274163 229 19366 ZBED9 0 . GRCh38 6 28575040 28575040 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1665A>T p.Lys555Asn p.K555N ENST00000452236 3/4 280 212 68 435 435 0 strelka-varscan-mutect ZBED9,missense_variant,p.Lys555Asn,ENST00000452236,NM_052923.1;ZBED9,downstream_gene_variant,,ENST00000530247,; A ENST00000452236 Transcript missense_variant 2283/4877 1665/3978 555/1325 K/N aaA/aaT 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 tolerated_low_confidence(0.11) 3/4 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 28575040 28575040 T A 1 0 0 0 0 1 0 0 0 18086 1606 56 4 4 ZBED9 6 28575040 Missense_Mutation SNP T C3N-00704_T 43224 28575040 142230939 230 19367 TRIM10 0 . GRCh38 6 30158548 30158548 + Missense_Mutation SNP G G T rs760939998 C3N-00704_T C3N-00704_N G G c.607C>A p.Leu203Ile p.L203I ENST00000449742 3/7 361 286 75 514 514 0 strelka-varscan-mutect TRIM10,missense_variant,p.Leu203Ile,ENST00000449742,NM_006778.3;TRIM10,missense_variant,p.Leu203Ile,ENST00000376704,NM_052828.2;TRIM15,upstream_gene_variant,,ENST00000619857,;TRIM15,upstream_gene_variant,,ENST00000376694,NM_033229.2; T ENST00000449742 Transcript missense_variant 683/3546 607/1446 203/481 L/I Ctc/Atc rs760939998 1 -1 TRIM10 HGNC HGNC:10072 protein_coding YES CCDS34375.1 ENSP00000397073 Q9UDY6 UPI000000D736 NM_006778.3 deleterious(0.02) 3/7 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF329 MODERATE 1 SNV 1 1 PASS rs760939998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 30158548 30158548 G T 1 0 0 0 0 1 0 0 0 16975 1000 35 2 2 TRIM10 6 30158548 Missense_Mutation SNP G C3N-00704_T 1583508 30158548 140647431 231 19368 NOTCH4 0 . GRCh38 6 32195871 32195871 + Missense_Mutation SNP G G A rs764118051 C3N-00704_T C3N-00704_N G G c.5578C>T p.Arg1860Cys p.R1860C ENST00000375023 30/30 190 154 36 221 221 0 strelka-varscan-mutect NOTCH4,missense_variant,p.Arg1860Cys,ENST00000375023,NM_004557.3;GPSM3,upstream_gene_variant,,ENST00000375040,NM_001276501.1;GPSM3,upstream_gene_variant,,ENST00000487761,;GPSM3,upstream_gene_variant,,ENST00000375043,NM_022107.1;GPSM3,upstream_gene_variant,,ENST00000619085,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000474612,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000491215,;GPSM3,upstream_gene_variant,,ENST00000472768,; A ENST00000375023 Transcript missense_variant 5717/6745 5578/6012 1860/2003 R/C Cgc/Tgc rs764118051 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0) 30/30 hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF64 MODERATE 1 SNV 1 1 PASS rs764118051 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 32195871 32195871 G A 1 0 0 0 0 1 0 0 0 10596 1087 38 1 1 NOTCH4 6 32195871 Missense_Mutation SNP G C3N-00704_T 2037323 32195871 138610108 232 19369 ITPR3 0 . GRCh38 6 33676810 33676810 + Missense_Mutation SNP G G T rs756112186 C3N-00704_T C3N-00704_N G G c.3325G>T p.Val1109Leu p.V1109L ENST00000374316 27/59 168 135 33 236 236 0 strelka-varscan-mutect ITPR3,missense_variant,p.Val1109Leu,ENST00000374316,;ITPR3,missense_variant,p.Val1109Leu,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript missense_variant 4385/9870 3325/8016 1109/2671 V/L Gtg/Ttg rs756112186,COSM1672312,COSM1672313 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 tolerated(0.1) 27/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs756112186 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 33676810 33676810 G T 1 0 0 0 0 1 0 0 0 7828 1261 44 2 2 ITPR3 6 33676810 Missense_Mutation SNP G C3N-00704_T 1480939 33676810 137129169 233 19370 CMTR1 0 . GRCh38 6 37458678 37458678 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.844G>T p.Gly282Cys p.G282C ENST00000373451 9/24 386 313 73 457 457 0 strelka-varscan-mutect CMTR1,missense_variant,p.Gly282Cys,ENST00000373451,NM_015050.2;CMTR1,missense_variant,p.Gly226Cys,ENST00000455891,;CMTR1,upstream_gene_variant,,ENST00000493656,; T ENST00000373451 Transcript missense_variant 1008/4033 844/2508 282/835 G/C Ggc/Tgc 1 1 CMTR1 HGNC HGNC:21077 protein_coding YES CCDS4835.1 ENSP00000362550 Q8N1G2 UPI00000700C2 NM_015050.2 deleterious(0) 9/24 PROSITE_profiles:PS51613,hmmpanther:PTHR16121:SF0,hmmpanther:PTHR16121,Gene3D:3.40.50.150,Pfam_domain:PF01728,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 37458678 37458678 G T 1 0 0 0 0 1 0 0 0 3366 1348 47 2 2 CMTR1 6 37458678 Missense_Mutation SNP G C3N-00704_T 3781868 37458678 133347301 234 19371 CAPN11 0 . GRCh38 6 44176921 44176921 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.1160A>G p.Lys387Arg p.K387R ENST00000398776 11/23 244 204 40 316 316 0 strelka-varscan-mutect CAPN11,missense_variant,p.Lys387Arg,ENST00000398776,NM_007058.3;CAPN11,downstream_gene_variant,,ENST00000532171,;CAPN11,non_coding_transcript_exon_variant,,ENST00000524554,;CAPN11,non_coding_transcript_exon_variant,,ENST00000533604,; G ENST00000398776 Transcript missense_variant 1198/2728 1160/2220 387/739 K/R aAg/aGg 1 1 CAPN11 HGNC HGNC:1478 protein_coding YES CCDS47436.1 ENSP00000381758 Q9UMQ6 UPI00000383D5 NM_007058.3 tolerated(0.37) 11/23 hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF322 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 44176921 44176921 A G 1 0 0 0 0 1 0 0 0 2316 72 3 5 5 CAPN11 6 44176921 Missense_Mutation SNP A C3N-00704_T 6718243 44176921 126629058 235 19372 PGK2 0 . GRCh38 6 49786195 49786195 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.993A>T p.= p.A331A ENST00000304801 1/1 389 327 62 429 428 1 strelka-varscan-mutect PGK2,synonymous_variant,p.=,ENST00000304801,NM_138733.4; A ENST00000304801 Transcript synonymous_variant 1113/1657 993/1254 331/417 A gcA/gcT 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 49786195 49786195 T A 1 0 0 0 0 0 0 0 1 11880 1799 63 4 4 PGK2 6 49786195 Silent SNP T C3N-00704_T 5609274 49786195 121019784 236 19373 FAM83B 0 . GRCh38 6 54940432 54940432 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.1461C>A p.= p.T487T ENST00000306858 5/5 200 169 31 206 206 0 strelka-varscan-mutect FAM83B,synonymous_variant,p.=,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; A ENST00000306858 Transcript synonymous_variant 1577/3167 1461/3036 487/1011 T acC/acA 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 LOW 1 SNV 1 1 PASS rs1029940353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 54940432 54940432 C A 1 0 0 0 0 0 0 0 1 5492 581 21 2 2 FAM83B 6 54940432 Silent SNP C C3N-00704_T 5154237 54940432 115865547 237 19374 FAM83B 0 . GRCh38 6 54941218 54941218 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2247G>T p.Glu749Asp p.E749D ENST00000306858 5/5 151 131 20 272 272 0 strelka-varscan-mutect FAM83B,missense_variant,p.Glu749Asp,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; T ENST00000306858 Transcript missense_variant 2363/3167 2247/3036 749/1011 E/D gaG/gaT 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 tolerated(0.08) 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 54941218 54941218 G T 1 0 0 0 0 1 0 0 0 5492 991 35 2 2 FAM83B 6 54941218 Missense_Mutation SNP G C3N-00704_T 786 54941218 115864761 238 19375 DST 0 . GRCh38 6 56642095 56642095 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.1366A>G p.Lys456Glu p.K456E ENST00000312431 14/95 101 87 14 252 252 0 strelka-varscan-mutect DST,missense_variant,p.Lys416Glu,ENST00000361203,;DST,missense_variant,p.Lys416Glu,ENST00000421834,NM_183380.3;DST,missense_variant,p.Lys456Glu,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Lys416Glu,ENST00000370788,;DST,missense_variant,p.Lys90Glu,ENST00000244364,NM_015548.4;DST,missense_variant,p.Lys90Glu,ENST00000439203,;DST,missense_variant,p.Lys90Glu,ENST00000370765,NM_001723.5;DST,missense_variant,p.Lys456Glu,ENST00000520645,;DST,missense_variant,p.Lys90Glu,ENST00000518935,;DST,missense_variant,p.Lys594Glu,ENST00000449297,;DST,non_coding_transcript_exon_variant,,ENST00000521104,;DST,non_coding_transcript_exon_variant,,ENST00000523967,;DST,downstream_gene_variant,,ENST00000518828,; C ENST00000312431 Transcript missense_variant 1492/17756 1366/16614 456/5537 K/E Aaa/Gaa 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 deleterious(0.04) 14/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 56642095 56642095 T C 1 0 0 0 0 1 0 0 0 4604 1763 61 5 5 DST 6 56642095 Missense_Mutation SNP T C3N-00704_T 1700877 56642095 114163884 239 19376 ADGRB3 0 . GRCh38 6 69332969 69332969 + Missense_Mutation SNP G G A C3N-00704_T C3N-00704_N G G c.3149G>A p.Arg1050Lys p.R1050K ENST00000370598 24/32 107 89 18 177 176 1 strelka-varscan-mutect ADGRB3,missense_variant,p.Arg1050Lys,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Arg1050Lys,ENST00000546190,;ADGRB3,missense_variant,p.Arg256Lys,ENST00000238918,; A ENST00000370598 Transcript missense_variant 3970/6010 3149/4569 1050/1522 R/K aGa/aAa COSM93946 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 tolerated(1) 24/32 PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF40,Pfam_domain:PF00002 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 69332969 69332969 G A 1 0 0 0 0 1 0 0 0 357 942 33 3 3 ADGRB3 6 69332969 Missense_Mutation SNP G C3N-00704_T 12690874 69332969 101473010 240 19377 SNAP91 0 . GRCh38 6 83580534 83580534 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.2215T>A p.Ser739Thr p.S739T ENST00000439399 24/30 107 85 22 171 171 0 strelka-varscan-mutect SNAP91,missense_variant,p.Ser734Thr,ENST00000521485,;SNAP91,missense_variant,p.Ser739Thr,ENST00000439399,NM_014841.2;SNAP91,missense_variant,p.Ser739Thr,ENST00000369694,NM_001242792.1;SNAP91,missense_variant,p.Ser734Thr,ENST00000195649,NM_001256718.1;SNAP91,missense_variant,p.Ser739Thr,ENST00000521743,;SNAP91,missense_variant,p.Ser709Thr,ENST00000520302,NM_001256717.1,NM_001242793.1;SNAP91,missense_variant,p.Ser432Thr,ENST00000520213,NM_001242794.1;SNAP91,missense_variant,p.Ser552Thr,ENST00000521931,;SNAP91,missense_variant,p.Ser80Thr,ENST00000523448,;SNAP91,upstream_gene_variant,,ENST00000519133,;SNAP91,3_prime_UTR_variant,,ENST00000518312,;SNAP91,3_prime_UTR_variant,,ENST00000521616,; T ENST00000439399 Transcript missense_variant 2532/4452 2215/2724 739/907 S/T Tca/Aca 1 -1 SNAP91 HGNC HGNC:14986 protein_coding YES CCDS47455.1 ENSP00000400459 O60641 UPI0000124FB3 NM_014841.2 tolerated(0.46) 24/30 Low_complexity_(Seg):seg,hmmpanther:PTHR22951,hmmpanther:PTHR22951:SF4 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 83580534 83580534 A T 1 0 0 0 0 1 0 0 0 15154 304 11 4 4 SNAP91 6 83580534 Missense_Mutation SNP A C3N-00704_T 14247565 83580534 87225445 241 19378 GABRR2 0 . GRCh38 6 89267788 89267788 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.627C>A p.Tyr209Ter p.Y209* ENST00000402938 6/9 85 57 28 145 145 0 strelka-varscan-mutect GABRR2,stop_gained,p.Tyr209Ter,ENST00000402938,NM_002043.3;GABRR2,downstream_gene_variant,,ENST00000602808,;GABRR2,non_coding_transcript_exon_variant,,ENST00000602432,; T ENST00000402938 Transcript stop_gained 761/1682 627/1398 209/465 Y/* taC/taA 1 -1 GABRR2 HGNC HGNC:4091 protein_coding YES CCDS5020.3 ENSP00000386029 P28476 UPI000012B0DB NM_002043.3 6/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF197,TIGRFAM_domain:TIGR00860 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 89267788 89267788 G T 1 0 0 0 0 0 1 0 0 6048 1024 36 2 2 GABRR2 6 89267788 Nonsense_Mutation SNP G C3N-00704_T 5687254 89267788 81538191 242 19379 PRDM13 0 . GRCh38 6 99613597 99613597 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.962G>T p.Gly321Val p.G321V ENST00000369215 4/4 93 71 22 125 125 0 strelka-varscan-mutect PRDM13,missense_variant,p.Gly321Val,ENST00000369215,NM_021620.3;PRDM13,3_prime_UTR_variant,,ENST00000369214,; T ENST00000369215 Transcript missense_variant 1267/2429 962/2124 321/707 G/V gGa/gTa 1 1 PRDM13 HGNC HGNC:13998 protein_coding YES CCDS43487.1 ENSP00000358217 Q9H4Q3 UPI000047099D NM_021620.3 deleterious_low_confidence(0.01) 4/4 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 99613597 99613597 G T 1 0 0 0 0 1 0 0 0 12585 1174 41 2 2 PRDM13 6 99613597 Missense_Mutation SNP G C3N-00704_T 10345809 99613597 71192382 243 19380 OSTM1 0 . GRCh38 6 108049276 108049276 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.926A>T p.Gln309Leu p.Q309L ENST00000193322 5/6 198 164 34 393 393 0 strelka-varscan-mutect OSTM1,missense_variant,p.Gln309Leu,ENST00000193322,NM_014028.3;OSTM1,missense_variant,p.Gln162Leu,ENST00000440575,;OSTM1,non_coding_transcript_exon_variant,,ENST00000472669,;OSTM1,non_coding_transcript_exon_variant,,ENST00000477774,; A ENST00000193322 Transcript missense_variant 1012/4467 926/1005 309/334 Q/L cAa/cTa 1 -1 OSTM1 HGNC HGNC:21652 protein_coding YES CCDS5062.1 ENSP00000193322 Q86WC4 UPI00000472C4 NM_014028.3 deleterious(0) 5/6 Pfam_domain:PF09777,hmmpanther:PTHR15644 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 108049276 108049276 T A 1 0 0 0 0 1 0 0 0 11365 1812 63 4 4 OSTM1 6 108049276 Missense_Mutation SNP T C3N-00704_T 8435679 108049276 62756703 244 19381 RNF217 0 . GRCh38 6 124963111 124963127 + Frame_Shift_Del DEL TGGGGCTCCGCCAGTGT TGGGGCTCCGCCAGTGT - novel C3N-00704_T C3N-00704_N TGGGGCTCCGCCAGTGT TGGGGCTCCGCCAGTGT c.569_585delGGGCTCCGCCAGTGTTG p.Gly190GlufsTer116 p.G190Efs*116 ENST00000521654 1/6 86 68 18 128 128 0 sindel-varindel-pindel RNF217,frameshift_variant,p.Gly190GlufsTer116,ENST00000521654,NM_001286398.1;RNF217,5_prime_UTR_variant,,ENST00000560949,;RNF217-AS1,upstream_gene_variant,,ENST00000439075,;RNF217,upstream_gene_variant,,ENST00000519971,;RNF217,upstream_gene_variant,,ENST00000519565,; - ENST00000521654 Transcript frameshift_variant 567-583/11325 567-583/1629 189-195/542 PGAPPVL/PX ccTGGGGCTCCGCCAGTGTtg/cctg 1 1 RNF217 HGNC HGNC:21487 protein_coding YES CCDS69191.1 ENSP00000428698 Q8TC41 UPI00022F843E NM_001286398.1 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR11685:SF113,hmmpanther:PTHR11685 HIGH deletion 2 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 124963111 124963111 TGGGGCTCCGCCAGTGT - 1 0 1 0 1 0 0 0 0 13660 1567 55 0 0 RNF217 6 124963111 Frame_Shift_Del DEL TGGGGCTCCGCCAGTGT C3N-00704_T 16913835 124963111 45842868 245 19382 TAAR1 0 . GRCh38 6 132645741 132645741 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.263G>C p.Cys88Ser p.C88S ENST00000275216 1/1 257 215 42 381 381 0 strelka-varscan-mutect TAAR1,missense_variant,p.Cys88Ser,ENST00000275216,NM_138327.1; G ENST00000275216 Transcript missense_variant 263/1020 263/1020 88/339 C/S tGt/tCt 1 -1 TAAR1 HGNC HGNC:17734 protein_coding YES CCDS5158.1 ENSP00000275216 Q96RJ0 UPI000000D874 NM_138327.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF220,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01830 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 132645741 132645741 C G 1 0 0 0 0 1 0 0 0 15885 478 17 4 4 TAAR1 6 132645741 Missense_Mutation SNP C C3N-00704_T 7682630 132645741 38160238 246 19383 STXBP5 0 . GRCh38 6 147373739 147373739 + Frame_Shift_Del DEL G G - novel C3N-00704_T C3N-00704_N G G c.3092delG p.Gly1031ValfsTer7 p.G1031Vfs*7 ENST00000321680 26/28 78 63 15 174 174 0 sindel-varindel-pindel STXBP5,frameshift_variant,p.Gly995ValfsTer7,ENST00000367481,NM_139244.4;STXBP5,frameshift_variant,p.Gly1031ValfsTer7,ENST00000321680,NM_001127715.2;STXBP5,frameshift_variant,p.Gly978ValfsTer7,ENST00000367480,; - ENST00000321680 Transcript frameshift_variant 3090/3456 3090/3456 1030/1151 L/X ttG/tt 1 1 STXBP5 HGNC HGNC:19665 protein_coding YES CCDS47499.1 ENSP00000321826 Q5T5C0 UPI0000199FE0 NM_001127715.2 26/28 hmmpanther:PTHR10241,hmmpanther:PTHR10241:SF22 HIGH 1 deletion 5 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 147373739 147373739 G - 1 0 1 0 1 0 0 0 0 15740 1339 47 0 0 STXBP5 6 147373739 Frame_Shift_Del DEL G C3N-00704_T 14727998 147373739 23432240 247 19384 SYNE1 0 . GRCh38 6 152331656 152331656 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.13029G>T p.Leu4343Phe p.L4343F ENST00000367255 78/146 552 425 127 737 737 0 strelka-varscan-mutect SYNE1,missense_variant,p.Leu4343Phe,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Leu4272Phe,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Leu4191Phe,ENST00000341594,;SYNE1,5_prime_UTR_variant,,ENST00000448038,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,;SYNE1,downstream_gene_variant,,ENST00000471834,; A ENST00000367255 Transcript missense_variant 13631/27748 13029/26394 4343/8797 L/F ttG/ttT 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 78/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 152331656 152331656 C A 1 0 0 0 0 1 0 0 0 15837 593 21 2 2 SYNE1 6 152331656 Missense_Mutation SNP C C3N-00704_T 4957917 152331656 18474323 248 19385 TCP1 0 . GRCh38 6 159781097 159781097 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.811A>T p.Thr271Ser p.T271S ENST00000321394 8/12 62 42 20 95 95 0 strelka-varscan-mutect TCP1,missense_variant,p.Thr271Ser,ENST00000321394,NM_030752.2;TCP1,missense_variant,p.Thr116Ser,ENST00000392168,NM_001008897.1;TCP1,missense_variant,p.Thr271Ser,ENST00000420894,;TCP1,missense_variant,p.Thr47Ser,ENST00000544255,;TCP1,missense_variant,p.Thr69Ser,ENST00000539756,;ACAT2,downstream_gene_variant,,ENST00000367048,NM_005891.2;TCP1,downstream_gene_variant,,ENST00000539948,;TCP1,downstream_gene_variant,,ENST00000537390,;TCP1,downstream_gene_variant,,ENST00000538128,;TCP1,downstream_gene_variant,,ENST00000536394,;SNORA29,downstream_gene_variant,,ENST00000384183,;SNORA20,upstream_gene_variant,,ENST00000384662,;ACAT2,downstream_gene_variant,,ENST00000472052,;TCP1,downstream_gene_variant,,ENST00000543532,;TCP1,non_coding_transcript_exon_variant,,ENST00000536807,;TCP1,downstream_gene_variant,,ENST00000538530,;TCP1,downstream_gene_variant,,ENST00000545764,;TCP1,downstream_gene_variant,,ENST00000467544,;TCP1,upstream_gene_variant,,ENST00000546204,;TCP1,downstream_gene_variant,,ENST00000543517,; A ENST00000321394 Transcript missense_variant 1092/2499 811/1671 271/556 T/S Acc/Tcc 1 -1 TCP1 HGNC HGNC:11655 protein_coding YES CCDS5269.1 ENSP00000317334 P17987 UPI0000136AEA NM_030752.2 tolerated(0.06) 8/12 hmmpanther:PTHR11353,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02340,Gene3D:3.50.7.10,Superfamily_domains:SSF52029 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 159781097 159781097 T A 1 0 0 0 0 1 0 0 0 16116 1696 59 4 4 TCP1 6 159781097 Missense_Mutation SNP T C3N-00704_T 7449441 159781097 11024882 249 19386 PDE10A 0 . GRCh38 6 165379299 165379299 + Missense_Mutation SNP C C A rs772091396 C3N-00704_T C3N-00704_N C C c.1880G>T p.Arg627Leu p.R627L ENST00000539869 18/22 235 196 39 332 332 0 strelka-varscan-mutect PDE10A,missense_variant,p.Arg617Leu,ENST00000366882,NM_006661.3;PDE10A,missense_variant,p.Arg627Leu,ENST00000539869,NM_001130690.2; A ENST00000539869 Transcript missense_variant 1936/4401 1880/2370 627/789 R/L cGc/cTc rs772091396,COSM5357472,COSM5357473 1 -1 PDE10A HGNC HGNC:8772 protein_coding YES CCDS47513.1 ENSP00000438284 Q9Y233 UPI000006F80E NM_001130690.2 deleterious(0.01) 18/22 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF111,SMART_domains:SM00471,Superfamily_domains:SSF109604 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs772091396 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 165379299 165379299 C A 1 0 0 0 0 1 0 0 0 11718 768 27 1 1 PDE10A 6 165379299 Missense_Mutation SNP C C3N-00704_T 5598202 165379299 5426680 250 19387 WDR27 0 . GRCh38 6 169643758 169643758 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1686G>T p.Leu562Phe p.L562F ENST00000448612 17/26 113 96 17 160 159 1 strelka-varscan-mutect WDR27,missense_variant,p.Leu562Phe,ENST00000448612,NM_182552.4;WDR27,missense_variant,p.Leu435Phe,ENST00000423258,NM_001202550.1;WDR27,downstream_gene_variant,,ENST00000441385,;WDR27,non_coding_transcript_exon_variant,,ENST00000546525,;WDR27,non_coding_transcript_exon_variant,,ENST00000479310,; A ENST00000448612 Transcript missense_variant 1796/3178 1686/2688 562/895 L/F ttG/ttT 1 -1 WDR27 HGNC HGNC:21248 protein_coding YES CCDS47520.2 ENSP00000416289 A2RRH5 UPI00015E06AF NM_182552.4 deleterious(0.03) 17/26 PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF410,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 169643758 169643758 C A 1 0 0 0 0 1 0 0 0 17844 593 21 2 2 WDR27 6 169643758 Missense_Mutation SNP C C3N-00704_T 4264459 169643758 1162221 251 19388 DGKB 0 . GRCh38 7 14178064 14178064 + Missense_Mutation SNP C C A rs781698994 C3N-00704_T C3N-00704_N C C c.2213G>T p.Arg738Leu p.R738L ENST00000403951 24/26 116 95 21 140 140 0 strelka-varscan-mutect DGKB,missense_variant,p.Arg738Leu,ENST00000403951,;DGKB,missense_variant,p.Arg738Leu,ENST00000399322,NM_004080.2;DGKB,missense_variant,p.Arg737Leu,ENST00000402815,;DGKB,missense_variant,p.Arg730Leu,ENST00000407950,;DGKB,missense_variant,p.Arg738Leu,ENST00000406247,NM_145695.2;DGKB,non_coding_transcript_exon_variant,,ENST00000493142,; A ENST00000403951 Transcript missense_variant 2633/6917 2213/2415 738/804 R/L cGg/cTg rs781698994 1 -1 DGKB HGNC HGNC:2850 protein_coding YES CCDS47547.1 ENSP00000385780 Q9Y6T7 UPI0000033B9B tolerated(0.1) 24/26 hmmpanther:PTHR11255:SF32,hmmpanther:PTHR11255,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331 MODERATE 1 SNV 5 1 PASS rs781698994 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 14178064 14178064 C A 1 0 0 0 0 1 0 0 0 4272 652 23 1 1 DGKB 7 14178064 Missense_Mutation SNP C C3N-00704_T 14178064 145167909 252 19389 ABCB5 0 . GRCh38 7 20643239 20643239 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.370C>A p.Gln124Lys p.Q124K ENST00000404938 6/28 152 129 23 151 150 1 strelka-varscan-mutect ABCB5,missense_variant,p.Gln124Lys,ENST00000404938,NM_001163941.1;ABCB5,upstream_gene_variant,,ENST00000258738,NM_178559.5;ABCB5,upstream_gene_variant,,ENST00000443026,NM_001163942.1;ABCB5,upstream_gene_variant,,ENST00000406935,NM_001163993.2;ABCB5,upstream_gene_variant,,ENST00000477094,;AC002486.3,upstream_gene_variant,,ENST00000435098,; A ENST00000404938 Transcript missense_variant 1022/5811 370/3774 124/1257 Q/K Cag/Aag 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 deleterious(0.01) 6/28 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 20643239 20643239 C A 1 0 0 0 0 1 0 0 0 48 479 17 2 2 ABCB5 7 20643239 Missense_Mutation SNP C C3N-00704_T 6465175 20643239 138702734 253 19390 NPC1L1 0 . GRCh38 7 44540162 44540162 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.235C>A p.Pro79Thr p.P79T ENST00000289547 2/20 300 270 30 403 403 0 strelka-varscan-mutect NPC1L1,missense_variant,p.Pro79Thr,ENST00000289547,NM_013389.2;NPC1L1,missense_variant,p.Pro79Thr,ENST00000546276,;NPC1L1,missense_variant,p.Pro79Thr,ENST00000381160,NM_001101648.1;NPC1L1,missense_variant,p.Pro79Thr,ENST00000423141,NM_001300967.1; T ENST00000289547 Transcript missense_variant 291/5048 235/4080 79/1359 P/T Ccc/Acc 1 -1 NPC1L1 HGNC HGNC:7898 protein_coding YES CCDS5491.1 ENSP00000289547 Q9UHC9 UPI000013DF88 NM_013389.2 deleterious(0) 2/20 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF89,Pfam_domain:PF16414 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 44540162 44540162 G T 1 0 0 0 0 1 0 0 0 10619 1232 43 2 2 NPC1L1 7 44540162 Missense_Mutation SNP G C3N-00704_T 23896923 44540162 114805811 254 19391 CALN1 0 . GRCh38 7 71810489 71810489 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.505G>C p.Asp169His p.D169H ENST00000395275 6/7 84 66 18 99 99 0 strelka-varscan-mutect CALN1,missense_variant,p.Asp169His,ENST00000395275,NM_031468.3;CALN1,missense_variant,p.Asp127His,ENST00000329008,NM_001017440.2;CALN1,missense_variant,p.Asp127His,ENST00000395276,;CALN1,missense_variant,p.Asp3His,ENST00000405452,;CALN1,missense_variant,p.Asp127His,ENST00000431984,; G ENST00000395275 Transcript missense_variant 894/9459 505/786 169/261 D/H Gac/Cac 1 -1 CALN1 HGNC HGNC:13248 protein_coding YES CCDS47603.1 ENSP00000378690 Q9BXU9 UPI0000D4B903 NM_031468.3 deleterious(0) 6/7 hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF51,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 71810489 71810489 C G 1 0 0 0 0 1 0 0 0 2282 840 29 4 4 CALN1 7 71810489 Missense_Mutation SNP C C3N-00704_T 27270327 71810489 87535484 255 19392 POM121 0 . GRCh38 7 72942328 72942328 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1540G>T p.Gly514Trp p.G514W ENST00000395270 14/16 244 202 42 308 308 0 strelka-varscan-mutect POM121,missense_variant,p.Gly514Trp,ENST00000395270,NM_001257190.2;POM121,missense_variant,p.Gly514Trp,ENST00000627934,NM_172020.4;POM121,missense_variant,p.Gly514Trp,ENST00000358357,;POM121,missense_variant,p.Gly779Trp,ENST00000434423,;POM121,missense_variant,p.Gly514Trp,ENST00000446813,; T ENST00000395270 Transcript missense_variant 2581/7011 1540/3000 514/999 G/W Ggg/Tgg 1 1 POM121 HGNC HGNC:19702 protein_coding YES CCDS59059.1 ENSP00000378687 Q96HA1 UPI000013DA6B NM_001257190.2 deleterious(0) 14/16 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 72942328 72942328 G T 1 0 0 0 0 1 0 0 0 12350 1232 43 2 2 POM121 7 72942328 Missense_Mutation SNP G C3N-00704_T 1131839 72942328 86403645 256 19393 FGL2 0 . GRCh38 7 77199446 77199446 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.348A>T p.Leu116Phe p.L116F ENST00000248598 1/2 246 210 36 322 321 1 strelka-varscan FGL2,missense_variant,p.Leu116Phe,ENST00000248598,NM_006682.2;FGL2,missense_variant,p.Leu116Phe,ENST00000637771,;CCDC146,intron_variant,,ENST00000285871,NM_020879.2;CCDC146,intron_variant,,ENST00000415750,;RP11-467H10.2,downstream_gene_variant,,ENST00000459742,; A ENST00000248598 Transcript missense_variant 381/4261 348/1320 116/439 L/F ttA/ttT 1 -1 FGL2 HGNC HGNC:3696 protein_coding YES CCDS5591.1 ENSP00000248598 Q14314 A4D1B8 UPI000012A724 NM_006682.2 deleterious(0.05) 1/2 hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF189 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 77199446 77199446 T A 1 0 0 0 0 1 0 0 0 5737 1635 57 4 4 FGL2 7 77199446 Missense_Mutation SNP T C3N-00704_T 4257118 77199446 82146527 257 19394 HGF 0 . GRCh38 7 81720764 81720764 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.1252A>G p.Asn418Asp p.N418D ENST00000222390 10/18 168 150 18 327 327 0 strelka-varscan HGF,missense_variant,p.Asn418Asp,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Asn413Asp,ENST00000457544,NM_001010932.1; C ENST00000222390 Transcript missense_variant 1479/5989 1252/2187 418/728 N/D Aac/Gac 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 tolerated(0.06) 10/18 PROSITE_profiles:PS50070,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 81720764 81720764 T C 1 0 0 0 0 1 0 0 0 6969 1783 62 5 5 HGF 7 81720764 Missense_Mutation SNP T C3N-00704_T 4521318 81720764 77625209 258 19395 SAMD9 0 . GRCh38 7 93102647 93102647 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.3451G>A p.Ala1151Thr p.A1151T ENST00000379958 3/3 277 238 39 570 570 0 strelka-varscan SAMD9,missense_variant,p.Ala1151Thr,ENST00000379958,NM_017654.3;SAMD9,missense_variant,p.Ala1151Thr,ENST00000620985,NM_001193307.1;SAMD9,missense_variant,p.Ala1151Thr,ENST00000446617,; T ENST00000379958 Transcript missense_variant 3721/6852 3451/4770 1151/1589 A/T Gct/Act 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 tolerated(0.62) 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 93102647 93102647 C T 1 0 0 0 0 1 0 0 0 14086 710 25 3 3 SAMD9 7 93102647 Missense_Mutation SNP C C3N-00704_T 11381883 93102647 66243326 259 19396 SAMD9 0 . GRCh38 7 93103835 93103835 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.2263A>T p.Arg755Trp p.R755W ENST00000379958 3/3 307 267 40 394 394 0 strelka-varscan SAMD9,missense_variant,p.Arg755Trp,ENST00000379958,NM_017654.3;SAMD9,missense_variant,p.Arg755Trp,ENST00000620985,NM_001193307.1;SAMD9,missense_variant,p.Arg755Trp,ENST00000446617,; A ENST00000379958 Transcript missense_variant 2533/6852 2263/4770 755/1589 R/W Agg/Tgg 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 deleterious(0) 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 93103835 93103835 T A 1 0 0 0 0 1 0 0 0 14086 1608 56 4 4 SAMD9 7 93103835 Missense_Mutation SNP T C3N-00704_T 1188 93103835 66242138 260 19397 SAMD9 0 . GRCh38 7 93103870 93103870 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2228G>T p.Gly743Val p.G743V ENST00000379958 3/3 251 205 46 280 280 0 strelka-varscan SAMD9,missense_variant,p.Gly743Val,ENST00000379958,NM_017654.3;SAMD9,missense_variant,p.Gly743Val,ENST00000620985,NM_001193307.1;SAMD9,missense_variant,p.Gly743Val,ENST00000446617,; A ENST00000379958 Transcript missense_variant 2498/6852 2228/4770 743/1589 G/V gGa/gTa 1 -1 SAMD9 HGNC HGNC:1348 protein_coding YES CCDS34680.1 ENSP00000369292 Q5K651 UPI0000038BC6 NM_017654.3 deleterious(0) 3/3 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF17,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 93103870 93103870 C A 1 0 0 0 0 1 0 0 0 14086 855 30 2 2 SAMD9 7 93103870 Missense_Mutation SNP C C3N-00704_T 35 93103870 66242103 261 19398 CALCR 0 . GRCh38 7 93438119 93438119 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.973C>A p.Leu325Met p.L325M ENST00000359558 13/16 288 240 48 324 324 0 strelka-varscan CALCR,missense_variant,p.Leu325Met,ENST00000359558,NM_001164737.1;CALCR,missense_variant,p.Leu307Met,ENST00000421592,;CALCR,missense_variant,p.Leu291Met,ENST00000394441,NM_001164738.1;CALCR,missense_variant,p.Leu291Met,ENST00000426151,NM_001742.3;CALCR,3_prime_UTR_variant,,ENST00000360249,;CALCR,3_prime_UTR_variant,,ENST00000423724,;CALCR,3_prime_UTR_variant,,ENST00000415529,; T ENST00000359558 Transcript missense_variant 1273/3696 973/1527 325/508 L/M Ctg/Atg 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 tolerated(0.56) 13/16 PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 93438119 93438119 G T 1 0 0 0 0 1 0 0 0 2269 962 34 2 2 CALCR 7 93438119 Missense_Mutation SNP G C3N-00704_T 334249 93438119 65907854 262 19399 SHFM1 0 . GRCh38 7 96486392 96486392 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.38C>A p.Ala13Asp p.A13D ENST00000615352 2/3 339 272 67 362 362 0 strelka-varscan SHFM1,missense_variant,p.Ala13Asp,ENST00000356686,NM_001201450.1;SHFM1,missense_variant,p.Ala13Asp,ENST00000615352,NM_001201451.1;SHFM1,non_coding_transcript_exon_variant,,ENST00000493858,;SHFM1,non_coding_transcript_exon_variant,,ENST00000611360,;SHFM1,3_prime_UTR_variant,,ENST00000613919,;SHFM1,3_prime_UTR_variant,,ENST00000617133,;SHFM1,3_prime_UTR_variant,,ENST00000618105,;SHFM1,3_prime_UTR_variant,,ENST00000466986,;SHFM1,3_prime_UTR_variant,,ENST00000619259,; T ENST00000615352 Transcript missense_variant 85/2637 38/357 13/118 A/D gCt/gAt 1 -1 SHFM1 HGNC HGNC:10845 protein_coding YES CCDS75638.1 ENSP00000481021 B7ZVW6 UPI000189A9A3 NM_001201451.1 deleterious_low_confidence(0.01) 2/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 96486392 96486392 G T 1 0 0 0 0 1 0 0 0 14538 971 34 2 2 SHFM1 7 96486392 Missense_Mutation SNP G C3N-00704_T 3048273 96486392 62859581 263 19400 TMEM130 0 . GRCh38 7 98855297 98855297 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.746G>T p.Gly249Val p.G249V ENST00000416379 5/8 92 76 16 93 93 0 strelka-varscan TMEM130,missense_variant,p.Gly165Val,ENST00000450876,;TMEM130,missense_variant,p.Gly249Val,ENST00000339375,NM_152913.2;TMEM130,missense_variant,p.Gly249Val,ENST00000416379,NM_001134450.1;TMEM130,missense_variant,p.Gly147Val,ENST00000345589,NM_001134451.1;TMEM130,non_coding_transcript_exon_variant,,ENST00000461092,;TMEM130,downstream_gene_variant,,ENST00000486839,; A ENST00000416379 Transcript missense_variant 751/2881 746/1308 249/435 G/V gGg/gTg 1 -1 TMEM130 HGNC HGNC:25429 protein_coding YES CCDS47650.1 ENSP00000413163 Q8N3G9 UPI000006EF2E NM_001134450.1 deleterious(0.01) 5/8 hmmpanther:PTHR11861:SF10,hmmpanther:PTHR11861 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999953 1 1 1 0 A 3 1 62 98855297 98855297 C A 1 0 0 0 0 1 0 0 0 16487 623 22 2 2 TMEM130 7 98855297 Missense_Mutation SNP C C3N-00704_T 2368905 98855297 60490676 264 19401 MUC17 0 . GRCh38 7 101033703 101033703 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2287G>T p.Glu763Ter p.E763* ENST00000306151 3/13 96 76 20 123 122 1 strelka-varscan MUC17,stop_gained,p.Glu763Ter,ENST00000306151,NM_001040105.1;MUC17,stop_gained,p.Glu763Ter,ENST00000379439,; T ENST00000306151 Transcript stop_gained 2351/14247 2287/13482 763/4493 E/* Gag/Tag 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 101033703 101033703 G T 1 0 0 0 0 0 1 0 0 9973 1291 45 2 2 MUC17 7 101033703 Nonsense_Mutation SNP G C3N-00704_T 2178406 101033703 58312270 265 19402 RELN 0 . GRCh38 7 103682180 103682180 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1225G>T p.Val409Leu p.V409L ENST00000428762 11/65 517 461 56 549 549 0 strelka-varscan RELN,missense_variant,p.Val409Leu,ENST00000424685,;RELN,missense_variant,p.Val409Leu,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Val409Leu,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 1385/11571 1225/10383 409/3460 V/L Gta/Tta 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.25) 11/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 103682180 103682180 C A 1 0 0 0 0 1 0 0 0 13390 478 17 2 2 RELN 7 103682180 Missense_Mutation SNP C C3N-00704_T 2648477 103682180 55663793 266 19403 CDHR3 0 . GRCh38 7 105981010 105981010 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.292C>T p.Pro98Ser p.P98S ENST00000317716 3/19 163 135 28 220 220 0 strelka-varscan CDHR3,missense_variant,p.Pro98Ser,ENST00000317716,NM_152750.4;CDHR3,missense_variant,p.Pro10Ser,ENST00000478080,NM_001301161.1;CDHR3,non_coding_transcript_exon_variant,,ENST00000470188,;CDHR3,non_coding_transcript_exon_variant,,ENST00000461766,;CDHR3,missense_variant,p.Pro98Ser,ENST00000496633,;CDHR3,missense_variant,p.Pro10Ser,ENST00000488386,; T ENST00000317716 Transcript missense_variant 372/3813 292/2658 98/885 P/S Cca/Tca 1 1 CDHR3 HGNC HGNC:26308 protein_coding YES CCDS47684.1 ENSP00000325954 Q6ZTQ4 UPI00001C0C6E NM_152750.4 deleterious(0.01) 3/19 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF336,Gene3D:2.60.40.60,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 105981010 105981010 C T 1 0 0 0 0 1 0 0 0 2823 507 18 3 3 CDHR3 7 105981010 Missense_Mutation SNP C C3N-00704_T 2298830 105981010 53364963 267 19404 SLC26A4 0 . GRCh38 7 107674240 107674240 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.492C>A p.= p.S164S ENST00000265715 5/21 256 229 27 353 353 0 strelka-varscan SLC26A4,synonymous_variant,p.=,ENST00000265715,NM_000441.1;SLC26A4,downstream_gene_variant,,ENST00000440056,; A ENST00000265715 Transcript synonymous_variant 716/4930 492/2343 164/780 S tcC/tcA 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 5/21 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF33,TIGRFAM_domain:TIGR00815 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 107674240 107674240 C A 1 0 0 0 0 0 0 0 1 14789 581 21 2 2 SLC26A4 7 107674240 Silent SNP C C3N-00704_T 1693230 107674240 51671733 268 19405 LAMB1 0 . GRCh38 7 107986282 107986282 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.505G>T p.Asp169Tyr p.D169Y ENST00000222399 6/34 184 165 19 191 191 0 strelka-varscan LAMB1,missense_variant,p.Asp193Tyr,ENST00000393561,;LAMB1,missense_variant,p.Asp169Tyr,ENST00000222399,NM_002291.2;LAMB1,missense_variant,p.Asp169Tyr,ENST00000393560,; A ENST00000222399 Transcript missense_variant 736/5725 505/5361 169/1786 D/Y Gac/Tac 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 deleterious(0) 6/34 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF233,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 62 107986282 107986282 C A 1 0 0 0 0 1 0 0 0 8514 826 29 2 2 LAMB1 7 107986282 Missense_Mutation SNP C C3N-00704_T 312042 107986282 51359691 269 19406 PPP1R3A 0 . GRCh38 7 113878346 113878346 + Missense_Mutation SNP A A T rs370279511 C3N-00704_T C3N-00704_N A A c.2746T>A p.Phe916Ile p.F916I ENST00000284601 4/4 129 111 18 273 273 0 strelka-varscan PPP1R3A,missense_variant,p.Phe916Ile,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; T ENST00000284601 Transcript missense_variant 2815/4384 2746/3369 916/1122 F/I Ttt/Att rs370279511 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 tolerated(0.54) 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 113878346 113878346 A T 1 0 0 0 0 1 0 0 0 12492 14 1 4 4 PPP1R3A 7 113878346 Missense_Mutation SNP A C3N-00704_T 5892064 113878346 45467627 270 19407 PPP1R3A 0 . GRCh38 7 113918830 113918830 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.167C>A p.Thr56Asn p.T56N ENST00000284601 1/4 218 184 34 290 290 0 strelka-varscan PPP1R3A,missense_variant,p.Thr56Asn,ENST00000284601,NM_002711.3;PPP1R3A,intron_variant,,ENST00000449795,;PPP1R3A,missense_variant,p.Thr56Asn,ENST00000284602,; T ENST00000284601 Transcript missense_variant 236/4384 167/3369 56/1122 T/N aCc/aAc 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 tolerated(0.08) 1/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 113918830 113918830 G T 1 0 0 0 0 1 0 0 0 12492 1261 44 2 2 PPP1R3A 7 113918830 Missense_Mutation SNP G C3N-00704_T 40484 113918830 45427143 271 19408 WNT2 0 . GRCh38 7 117297834 117297834 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.631G>T p.Val211Leu p.V211L ENST00000265441 4/5 136 122 14 128 128 0 strelka-varscan WNT2,missense_variant,p.Val211Leu,ENST00000265441,NM_003391.2;WNT2,missense_variant,p.Gly118Val,ENST00000491214,;AC002465.2,upstream_gene_variant,,ENST00000436097,;WNT2,3_prime_UTR_variant,,ENST00000449446,; A ENST00000265441 Transcript missense_variant 931/2907 631/1083 211/360 V/L Gtg/Ttg 1 -1 WNT2 HGNC HGNC:12780 protein_coding YES CCDS5771.1 ENSP00000265441 P09544 UPI0000051044 NM_003391.2 deleterious(0) 4/5 hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF86,PROSITE_patterns:PS00246,Pfam_domain:PF00110,SMART_domains:SM00097,Prints_domain:PR01349 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 117297834 117297834 C A 1 0 0 0 0 1 0 0 0 17942 507 18 2 2 WNT2 7 117297834 Missense_Mutation SNP C C3N-00704_T 3379004 117297834 42048139 272 19409 CCDC136 0 . GRCh38 7 128812753 128812753 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2587G>T p.Val863Leu p.V863L ENST00000297788 14/18 373 334 39 413 413 0 strelka-varscan CCDC136,missense_variant,p.Val863Leu,ENST00000297788,NM_022742.4;CCDC136,missense_variant,p.Val740Leu,ENST00000494552,;CCDC136,missense_variant,p.Val454Leu,ENST00000464672,;CCDC136,intron_variant,,ENST00000487361,;CCDC136,intron_variant,,ENST00000464832,;CCDC136,intron_variant,,ENST00000378685,NM_001201372.1;CCDC136,upstream_gene_variant,,ENST00000471729,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,intron_variant,,ENST00000528772,;CCDC136,downstream_gene_variant,,ENST00000485832,;CCDC136,downstream_gene_variant,,ENST00000460941,; T ENST00000297788 Transcript missense_variant 2954/4169 2587/3465 863/1154 V/L Gtg/Ttg 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 tolerated(0.13) 14/18 hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 128812753 128812753 G T 1 0 0 0 0 1 0 0 0 2459 1261 44 2 2 CCDC136 7 128812753 Missense_Mutation SNP G C3N-00704_T 11514919 128812753 30533220 273 19410 FLNC 0 . GRCh38 7 128854861 128854861 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.7084G>C p.Glu2362Gln p.E2362Q ENST00000325888 42/48 595 527 68 667 667 0 strelka-varscan FLNC,missense_variant,p.Glu2362Gln,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Glu2329Gln,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; C ENST00000325888 Transcript missense_variant 7345/9188 7084/8178 2362/2725 E/Q Gag/Cag 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.23) 42/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 128854861 128854861 G C 1 0 0 0 0 1 0 0 0 5791 1291 45 4 4 FLNC 7 128854861 Missense_Mutation SNP G C3N-00704_T 42108 128854861 30491112 274 19411 FLNC 0 . GRCh38 7 128857328 128857328 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.7772A>T p.Lys2591Met p.K2591M ENST00000325888 46/48 167 144 23 211 211 0 strelka-varscan FLNC,missense_variant,p.Lys2591Met,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Lys2558Met,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; T ENST00000325888 Transcript missense_variant 8033/9188 7772/8178 2591/2725 K/M aAg/aTg 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 deleterious(0.01) 46/48 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 128857328 128857328 A T 1 0 0 0 0 1 0 0 0 5791 72 3 4 4 FLNC 7 128857328 Missense_Mutation SNP A C3N-00704_T 2467 128857328 30488645 275 19412 FAM180A 0 . GRCh38 7 135734076 135734076 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.421C>A p.His141Asn p.H141N ENST00000338588 3/4 265 247 18 267 267 0 strelka-varscan FAM180A,missense_variant,p.His141Asn,ENST00000338588,NM_205855.3;FAM180A,missense_variant,p.His141Asn,ENST00000415751,;SLC13A4,upstream_gene_variant,,ENST00000378428,;SLC13A4,upstream_gene_variant,,ENST00000422620,;FAM180A,intron_variant,,ENST00000435869,;FAM180A,missense_variant,p.His141Asn,ENST00000444083,; T ENST00000338588 Transcript missense_variant 687/1800 421/522 141/173 H/N Cac/Aac 1 -1 FAM180A HGNC HGNC:33773 protein_coding YES CCDS5841.1 ENSP00000342336 Q6UWF9 UPI0000035A01 NM_205855.3 tolerated(0.54) 3/4 hmmpanther:PTHR34034,hmmpanther:PTHR34034:SF2,Pfam_domain:PF15173 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 135734076 135734076 G T 1 0 0 0 0 1 0 0 0 5352 1348 47 2 2 FAM180A 7 135734076 Missense_Mutation SNP G C3N-00704_T 6876748 135734076 23611897 276 19413 KIAA1549 0 . GRCh38 7 138917958 138917958 + Silent SNP T T A rs771673550 C3N-00704_T C3N-00704_N T T c.1668A>T p.= p.A556A ENST00000422774 2/20 126 115 11 148 148 0 strelka-varscan KIAA1549,synonymous_variant,p.=,ENST00000440172,NM_020910.2;KIAA1549,synonymous_variant,p.=,ENST00000422774,NM_001164665.1; A ENST00000422774 Transcript synonymous_variant 1717/6283 1668/5853 556/1950 A gcA/gcT rs771673550 1 -1 KIAA1549 HGNC HGNC:22219 protein_coding YES CCDS56513.1 ENSP00000416040 Q9HCM3 UPI0001837EBD NM_001164665.1 2/20 hmmpanther:PTHR21590:SF4,hmmpanther:PTHR21590 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 138917958 138917958 T A 1 0 0 0 0 0 0 0 1 8120 1451 51 4 4 KIAA1549 7 138917958 Silent SNP T C3N-00704_T 3183882 138917958 20428015 277 19414 TPK1 0 . GRCh38 7 144548569 144548569 + Nonsense_Mutation SNP C C A rs767663147 C3N-00704_T C3N-00704_N C C c.535G>T p.Glu179Ter p.E179* ENST00000360057 8/9 299 223 76 309 309 0 strelka-varscan TPK1,stop_gained,p.Glu179Ter,ENST00000360057,NM_022445.3;TPK1,stop_gained,p.Glu130Ter,ENST00000378099,NM_001042482.1;TPK1,stop_gained,p.Glu125Ter,ENST00000538212,;TPK1,non_coding_transcript_exon_variant,,ENST00000547966,;TPK1,non_coding_transcript_exon_variant,,ENST00000551062,;TPK1,3_prime_UTR_variant,,ENST00000482940,;TPK1,3_prime_UTR_variant,,ENST00000378098,; A ENST00000360057 Transcript stop_gained 638/2439 535/732 179/243 E/* Gag/Tag rs767663147,COSM5553639,COSM5553640 1 -1 TPK1 HGNC HGNC:17358 protein_coding YES CCDS5888.1 ENSP00000353165 Q9H3S4 A0A090N8Y0 UPI000004FD50 NM_022445.3 8/9 hmmpanther:PTHR13622,Pfam_domain:PF04265,PIRSF_domain:PIRSF031057,TIGRFAM_domain:TIGR01378,Gene3D:2.60.120.320,SMART_domains:SM00983,Superfamily_domains:SSF63862 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 144548569 144548569 C A 1 0 0 0 0 0 1 0 0 16885 864 30 2 2 TPK1 7 144548569 Nonsense_Mutation SNP C C3N-00704_T 5630611 144548569 14797404 278 19415 CNTNAP2 0 . GRCh38 7 146839844 146839844 + Silent SNP G G A rs748217915 C3N-00704_T C3N-00704_N G G c.342G>A p.= p.R114R ENST00000361727 3/24 281 238 43 351 351 0 strelka-varscan CNTNAP2,synonymous_variant,p.=,ENST00000361727,NM_014141.5;CNTNAP2,synonymous_variant,p.=,ENST00000625365,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; A ENST00000361727 Transcript synonymous_variant 860/9896 342/3996 114/1331 R cgG/cgA rs748217915 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 3/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,SMART_domains:SM00231,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 146839844 146839844 G A 1 0 0 0 0 0 0 0 1 3428 1161 41 3 3 CNTNAP2 7 146839844 Silent SNP G C3N-00704_T 2291275 146839844 12506129 279 19416 CNTNAP2 0 . GRCh38 7 147132284 147132284 + Missense_Mutation SNP C C A rs757993314 C3N-00704_T C3N-00704_N C C c.1123C>A p.Pro375Thr p.P375T ENST00000361727 8/24 281 234 47 316 315 1 strelka-varscan CNTNAP2,missense_variant,p.Pro375Thr,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; A ENST00000361727 Transcript missense_variant 1641/9896 1123/3996 375/1331 P/T Cct/Act rs757993314 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 8/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 147132284 147132284 C A 1 0 0 0 0 1 0 0 0 3428 739 26 2 2 CNTNAP2 7 147132284 Missense_Mutation SNP C C3N-00704_T 292440 147132284 12213689 280 19417 SSPO 0 . GRCh38 7 149787437 149787437 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.3451G>T p.Asp1151Tyr p.D1151Y ENST00000378016 23/107 118 106 12 123 123 0 strelka-varscan SSPO,missense_variant,p.Asp1151Tyr,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000486824,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,;SSPO,downstream_gene_variant,,ENST00000493502,; T ENST00000378016 Transcript missense_variant 3451/15589 3451/15453 1151/5150 D/Y Gat/Tat 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 23/107 Pfam_domain:PF00094,SMART_domains:SM00216,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 149787437 149787437 G T 1 0 0 0 0 1 0 0 0 15566 1290 45 2 2 SSPO 7 149787437 Missense_Mutation SNP G C3N-00704_T 2655153 149787437 9558536 281 19418 SSPO 0 . GRCh38 7 149804062 149804062 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.8289G>T p.Gln2763His p.Q2763H ENST00000378016 55/107 372 325 47 396 395 1 strelka-varscan SSPO,missense_variant,p.Gln2763His,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000475488,; T ENST00000378016 Transcript missense_variant 8289/15589 8289/15453 2763/5150 Q/H caG/caT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0.01) 55/107 Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895,PROSITE_profiles:PS50092 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 149804062 149804062 G T 1 0 0 0 0 1 0 0 0 15566 991 35 2 2 SSPO 7 149804062 Missense_Mutation SNP G C3N-00704_T 16625 149804062 9541911 282 19419 GIMAP6 0 . GRCh38 7 150628018 150628018 + Silent SNP G G T rs151245597 C3N-00704_T C3N-00704_N G G c.790C>A p.= p.R264R ENST00000618759 3/3 347 305 42 403 403 0 strelka-varscan GIMAP6,synonymous_variant,p.=,ENST00000618759,NM_001244072.1;GIMAP6,synonymous_variant,p.=,ENST00000328902,NM_024711.5;GIMAP6,3_prime_UTR_variant,,ENST00000493969,NM_001244071.1; T ENST00000618759 Transcript synonymous_variant 1270/3910 790/1089 264/362 R Cgg/Agg rs151245597 1 -1 GIMAP6 HGNC HGNC:21918 protein_coding YES CCDS75676.1 ENSP00000479580 B4DH95 UPI00017A6DF2 NM_001244072.1 3/3 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF51,hmmpanther:PTHR10903,Pfam_domain:PF04548,Gene3D:3.40.50.300 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 150628018 150628018 G T 1 0 0 0 0 0 0 0 1 6263 1144 40 1 1 GIMAP6 7 150628018 Silent SNP G C3N-00704_T 823956 150628018 8717955 283 19420 BLACE 0 . GRCh38 7 155357912 155357912 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.268C>A p.Pro90Thr p.P90T ENST00000378120 6/6 238 161 77 319 319 0 strelka-varscan BLACE,missense_variant,p.Pro90Thr,ENST00000378120,;BLACE,missense_variant,p.Pro90Thr,ENST00000616210,; T ENST00000378120 Transcript missense_variant 1529/2456 268/540 90/179 P/T Ccc/Acc 1 -1 BLACE HGNC HGNC:20484 protein_coding YES ENSP00000367360 A4D250 UPI00002522B3 6/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 155357912 155357912 G T 1 0 0 0 0 1 0 0 0 1593 1232 43 2 2 BLACE 7 155357912 Missense_Mutation SNP G C3N-00704_T 4729894 155357912 3988061 284 19421 RP1L1 0 . GRCh38 8 10623061 10623061 + Silent SNP A A T novel C3N-00704_T C3N-00704_N A A c.141T>A p.= p.A47A ENST00000382483 2/4 220 167 53 313 313 0 strelka-varscan-mutect RP1L1,synonymous_variant,p.=,ENST00000382483,NM_178857.5;RP1L1,non_coding_transcript_exon_variant,,ENST00000329335,; T ENST00000382483 Transcript synonymous_variant 365/7973 141/7203 47/2400 A gcT/gcA 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 2/4 Gene3D:1mfwA00,PROSITE_profiles:PS50309,hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3,SMART_domains:SM00537,Superfamily_domains:SSF89837 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 10623061 10623061 A T 1 0 0 0 0 0 0 0 1 13773 175 7 4 4 RP1L1 8 10623061 Silent SNP A C3N-00704_T 10623061 134515575 285 19422 PIWIL2 0 . GRCh38 8 22315112 22315112 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2175G>T p.Leu725Phe p.L725F ENST00000356766 18/23 99 92 7 133 133 0 strelka-varscan-mutect PIWIL2,missense_variant,p.Leu725Phe,ENST00000356766,NM_018068.3;PIWIL2,missense_variant,p.Leu725Phe,ENST00000521356,;PIWIL2,missense_variant,p.Leu725Phe,ENST00000454009,NM_001135721.1;PIWIL2,missense_variant,p.Leu725Phe,ENST00000611073,; T ENST00000356766 Transcript missense_variant 2323/5128 2175/2922 725/973 L/F ttG/ttT 1 1 PIWIL2 HGNC HGNC:17644 protein_coding YES CCDS6029.1 ENSP00000349208 Q8TC59 W0HK13 UPI000006E98E NM_018068.3 deleterious(0) 18/23 Gene3D:3.40.50.2300,Pfam_domain:PF02171,PROSITE_profiles:PS50822,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF47,SMART_domains:SM00950,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -11.0411 0.9999997 1 1 1 0 T 3 4 62 22315112 22315112 G T 1 0 0 0 0 1 0 0 0 12054 1339 47 2 2 PIWIL2 8 22315112 Missense_Mutation SNP G C3N-00704_T 11692051 22315112 122823524 286 19423 NUGGC 0 . GRCh38 8 28047614 28047614 + Splice_Site SNP T T A novel C3N-00704_T C3N-00704_N T T c.1207-2A>T p.X403_splice ENST00000413272 137 111 26 158 158 0 strelka-varscan NUGGC,splice_acceptor_variant,,ENST00000413272,NM_001010906.1; A ENST00000413272 Transcript splice_acceptor_variant -/3887 1207/2391 403/796 1 -1 NUGGC HGNC HGNC:33550 protein_coding YES CCDS47833.1 ENSP00000408697 Q68CJ6 UPI0000237454 NM_001010906.1 10/18 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 62 28047614 28047614 T A 1 0 0 0 0 0 0 1 0 10814 1594 55 4 4 NUGGC 8 28047614 Splice_Site SNP T C3N-00704_T 5732502 28047614 117091022 287 19424 KCNU1 0 . GRCh38 8 36806339 36806339 + Missense_Mutation SNP C C A rs757612843 C3N-00704_T C3N-00704_N C C c.539C>A p.Pro180Gln p.P180Q ENST00000399881 5/27 81 71 10 147 147 0 strelka-varscan KCNU1,missense_variant,p.Pro180Gln,ENST00000399881,NM_001031836.2;KCNU1,missense_variant,p.Pro180Gln,ENST00000523973,;KCNU1,missense_variant,p.Pro180Gln,ENST00000522372,;KCNU1,3_prime_UTR_variant,,ENST00000522417,; A ENST00000399881 Transcript missense_variant 576/3695 539/3450 180/1149 P/Q cCa/cAa rs757612843 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 deleterious(0) 5/27 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF23,Gene3D:1.10.287.70,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 36806339 36806339 C A 1 0 0 0 0 1 0 0 0 8009 594 21 2 2 KCNU1 8 36806339 Missense_Mutation SNP C C3N-00704_T 8758725 36806339 108332297 288 19425 PRKDC 0 . GRCh38 8 47820718 47820718 + Splice_Site SNP C C A novel C3N-00704_T C3N-00704_N C C c.9336+1G>T p.X3112_splice ENST00000314191 73 42 31 89 89 0 strelka-varscan PRKDC,splice_donor_variant,,ENST00000314191,NM_006904.6;PRKDC,splice_donor_variant,,ENST00000338368,NM_001081640.1; A ENST00000314191 Transcript splice_donor_variant -/13509 9336/12387 3112/4128 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 66/85 HIGH 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 5 1 62 47820718 47820718 C A 1 0 0 0 0 0 0 1 0 12654 521 18 2 2 PRKDC 8 47820718 Splice_Site SNP C C3N-00704_T 11014379 47820718 97317918 289 19426 RP1 0 . GRCh38 8 54720240 54720240 + Missense_Mutation SNP G G T rs770924118 C3N-00704_T C3N-00704_N G G c.2422G>T p.Gly808Trp p.G808W ENST00000637698 15/29 283 192 91 317 317 0 strelka-varscan RP1,missense_variant,p.Gly808Trp,ENST00000637698,;RP1,missense_variant,p.Gly775Trp,ENST00000636932,; T ENST00000637698 Transcript missense_variant 2570/6177 2422/4251 808/1416 G/W Ggg/Tgg rs770924118 1 1 RP1 HGNC HGNC:10263 protein_coding ENSP00000490104 deleterious(0) 15/29 Gene3D:2.80.10.50,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 54720240 54720240 G T 1 0 0 0 0 1 0 0 0 13709 1348 47 2 2 RP1 8 54720240 Missense_Mutation SNP G C3N-00704_T 6899522 54720240 90418396 290 19427 TRIM55 0 . GRCh38 8 66127304 66127304 + Silent SNP A A G novel C3N-00704_T C3N-00704_N A A c.36A>G p.= p.K12K ENST00000315962 1/10 196 131 65 218 218 0 strelka-varscan-mutect TRIM55,synonymous_variant,p.=,ENST00000315962,NM_184085.1;TRIM55,synonymous_variant,p.=,ENST00000353317,NM_184086.1;TRIM55,synonymous_variant,p.=,ENST00000276573,NM_033058.2;TRIM55,synonymous_variant,p.=,ENST00000350034,NM_184087.1; G ENST00000315962 Transcript synonymous_variant 409/2914 36/1647 12/548 K aaA/aaG 1 1 TRIM55 HGNC HGNC:14215 protein_coding YES CCDS6184.1 ENSP00000323913 Q9BYV6 UPI00001CE3B7 NM_184085.1 1/10 Gene3D:3.30.40.10 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 66127304 66127304 A G 1 0 0 0 0 0 0 0 1 17022 69 3 5 5 TRIM55 8 66127304 Silent SNP A C3N-00704_T 11407064 66127304 79011332 291 19428 C8orf44 0 . GRCh38 8 66677815 66677815 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.107G>A p.Gly36Asp p.G36D ENST00000519561 2/3 142 122 20 141 141 0 strelka-varscan-mutect C8orf44,missense_variant,p.Gly36Asp,ENST00000519561,NM_019607.2;C8orf44,missense_variant,p.Gly36Asp,ENST00000390159,;C8orf44,missense_variant,p.Gly36Asp,ENST00000521889,;C8orf44-SGK3,intron_variant,,ENST00000519289,NM_001204173.1;AC090154.1,upstream_gene_variant,,ENST00000623055,;C8orf44-SGK3,intron_variant,,ENST00000520044,;C8orf44,intron_variant,,ENST00000521113,;C8orf44,upstream_gene_variant,,ENST00000518860,; A ENST00000519561 Transcript missense_variant 258/1835 107/480 36/159 G/D gGc/gAc 1 1 C8orf44 HGNC HGNC:25646 protein_coding YES CCDS6193.1 ENSP00000428002 Q96CB5 A0A024R7W3 UPI0000071799 NM_019607.2 deleterious_low_confidence(0.03) 2/3 hmmpanther:PTHR22878 MODERATE 1 SNV 1 1 PASS rs1300001346 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 66677815 66677815 G A 1 0 0 0 0 1 0 0 0 2158 1203 42 3 3 C8orf44 8 66677815 Missense_Mutation SNP G C3N-00704_T 550511 66677815 78460821 292 19429 ARFGEF1 0 . GRCh38 8 67253493 67253493 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2656G>T p.Glu886Ter p.E886* ENST00000262215 18/39 64 58 6 132 132 0 strelka-varscan-mutect ARFGEF1,stop_gained,p.Glu886Ter,ENST00000262215,NM_006421.4;ARFGEF1,stop_gained,p.Glu365Ter,ENST00000520381,; A ENST00000262215 Transcript stop_gained 3046/7225 2656/5550 886/1849 E/* Gaa/Taa 1 -1 ARFGEF1 HGNC HGNC:15772 protein_coding YES CCDS6199.1 ENSP00000262215 Q9Y6D6 A0A024R7X0 UPI000013D275 NM_006421.4 18/39 Gene3D:1.10.1000.11 HIGH 1 SNV 1 1 PASS . . 0 204 4 0 0 0 0 0 -13.89947 1 1 1 1 0 A 4 1 62 67253493 67253493 C A 1 0 0 0 0 0 1 0 0 975 922 32 2 2 ARFGEF1 8 67253493 Nonsense_Mutation SNP C C3N-00704_T 575678 67253493 77885143 293 19430 ZFHX4 0 . GRCh38 8 76855344 76855344 + Missense_Mutation SNP C C A rs372591784 C3N-00704_T C3N-00704_N C C c.8423C>A p.Thr2808Lys p.T2808K ENST00000521891 10/11 275 206 69 244 244 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Thr2808Lys,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Thr2782Lys,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript missense_variant 8871/14019 8423/10851 2808/3616 T/K aCg/aAg rs372591784,COSM751704 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs372591784 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 76855344 76855344 C A 1 0 0 0 0 1 0 0 0 18213 536 19 1 1 ZFHX4 8 76855344 Missense_Mutation SNP C C3N-00704_T 9601851 76855344 68283292 294 19431 CNBD1 0 . GRCh38 8 87236967 87236967 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.626C>A p.Pro209His p.P209H ENST00000518476 6/11 91 57 34 129 129 0 strelka-varscan-mutect CNBD1,missense_variant,p.Pro209His,ENST00000518476,NM_173538.2;CNBD1,missense_variant,p.Pro65His,ENST00000620844,;CNBD1,non_coding_transcript_exon_variant,,ENST00000522427,;CNBD1,non_coding_transcript_exon_variant,,ENST00000522105,; A ENST00000518476 Transcript missense_variant 677/1594 626/1311 209/436 P/H cCt/cAt 1 1 CNBD1 HGNC HGNC:26663 protein_coding YES CCDS55259.1 ENSP00000430073 Q8NA66 UPI000006EA68 NM_173538.2 deleterious(0) 6/11 hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF142,Gene3D:2.60.120.10,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS rs1398916303 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 87236967 87236967 C A 1 0 0 0 0 1 0 0 0 3369 681 24 2 2 CNBD1 8 87236967 Missense_Mutation SNP C C3N-00704_T 10381623 87236967 57901669 295 19432 CNBD1 0 . GRCh38 8 87284796 87284796 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.890G>C p.Gly297Ala p.G297A ENST00000518476 7/11 129 85 44 123 123 0 strelka-varscan-mutect CNBD1,missense_variant,p.Gly297Ala,ENST00000518476,NM_173538.2;CNBD1,missense_variant,p.Gly153Ala,ENST00000620844,;CNBD1,upstream_gene_variant,,ENST00000523299,;CNBD1,downstream_gene_variant,,ENST00000522427,; C ENST00000518476 Transcript missense_variant 941/1594 890/1311 297/436 G/A gGa/gCa 1 1 CNBD1 HGNC HGNC:26663 protein_coding YES CCDS55259.1 ENSP00000430073 Q8NA66 UPI000006EA68 NM_173538.2 tolerated(0.08) 7/11 hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF142,Gene3D:2.60.120.10,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS rs1401217594 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 87284796 87284796 G C 1 0 0 0 0 1 0 0 0 3369 1174 41 4 4 CNBD1 8 87284796 Missense_Mutation SNP G C3N-00704_T 47829 87284796 57853840 296 19433 SNX31 0 . GRCh38 8 100600396 100600396 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.727C>G p.Gln243Glu p.Q243E ENST00000311812 9/14 255 178 77 323 323 0 strelka-varscan-mutect SNX31,missense_variant,p.Gln243Glu,ENST00000311812,NM_152628.3;SNX31,missense_variant,p.Gln144Glu,ENST00000428383,;SNX31,upstream_gene_variant,,ENST00000519521,; C ENST00000311812 Transcript missense_variant 878/2457 727/1323 243/440 Q/E Cag/Gag 1 -1 SNX31 HGNC HGNC:28605 protein_coding YES CCDS6288.1 ENSP00000312368 Q8N9S9 UPI000004A790 NM_152628.3 deleterious(0.01) 9/14 hmmpanther:PTHR12431,hmmpanther:PTHR12431:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 100600396 100600396 G C 1 0 0 0 0 1 0 0 0 15222 1386 48 4 4 SNX31 8 100600396 Missense_Mutation SNP G C3N-00704_T 13315600 100600396 44538240 297 19434 DCAF13 0 . GRCh38 8 103427288 103427288 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.552G>T p.Met184Ile p.M184I ENST00000521971 4/4 62 40 22 82 82 0 strelka-varscan-mutect DCAF13,missense_variant,p.Met184Ile,ENST00000521971,;DCAF13,missense_variant,p.Met220Ile,ENST00000519682,;DCAF13,3_prime_UTR_variant,,ENST00000618975,;DCAF13,intron_variant,,ENST00000297579,NM_015420.6;DCAF13,intron_variant,,ENST00000616836,;DCAF13,intron_variant,,ENST00000612750,;DCAF13,intron_variant,,ENST00000521999,;DCAF13,non_coding_transcript_exon_variant,,ENST00000518554,; T ENST00000521971 Transcript missense_variant 620/2049 552/558 184/185 M/I atG/atT 1 1 DCAF13 HGNC HGNC:24535 protein_coding ENSP00000430883 E5RHM4 UPI0004620AB6 4/4 MODERATE SNV 5 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999926 1 1 1 0 T 3 4 62 103427288 103427288 G T 1 0 0 0 0 1 0 0 0 4067 1348 47 2 2 DCAF13 8 103427288 Missense_Mutation SNP G C3N-00704_T 2826892 103427288 41711348 298 19435 RIMS2 0 . GRCh38 8 104013564 104013564 + Missense_Mutation SNP G G T rs542594833 C3N-00704_T C3N-00704_N G G c.3167G>T p.Arg1056Met p.R1056M ENST00000504942 18/24 255 213 42 251 251 0 strelka-varscan-mutect RIMS2,missense_variant,p.Arg870Met,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Arg1056Met,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Arg998Met,ENST00000626043,;RIMS2,missense_variant,p.Arg870Met,ENST00000408894,;RIMS2,missense_variant,p.Arg895Met,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Arg1066Met,ENST00000632716,;RIMS2,intron_variant,,ENST00000436393,; T ENST00000504942 Transcript missense_variant 3306/4228 3167/4050 1056/1349 R/M aGg/aTg rs542594833 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0.01) 18/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS rs542594833 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 104013564 104013564 G T 1 0 0 0 0 1 0 0 0 13543 1000 35 2 2 RIMS2 8 104013564 Missense_Mutation SNP G C3N-00704_T 586276 104013564 41125072 299 19436 ABRA 0 . GRCh38 8 106769590 106769590 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.601G>A p.Glu201Lys p.E201K ENST00000311955 1/2 244 211 33 259 259 0 strelka-varscan-mutect ABRA,missense_variant,p.Glu201Lys,ENST00000311955,NM_139166.4; T ENST00000311955 Transcript missense_variant 656/2755 601/1146 201/381 E/K Gag/Aag 1 -1 ABRA HGNC HGNC:30655 protein_coding YES CCDS6305.1 ENSP00000311436 Q8N0Z2 UPI000006F0DE NM_139166.4 tolerated(0.1) 1/2 hmmpanther:PTHR22739,hmmpanther:PTHR22739:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 106769590 106769590 C T 1 0 0 0 0 1 0 0 0 109 835 29 3 3 ABRA 8 106769590 Missense_Mutation SNP C C3N-00704_T 2756026 106769590 38369046 300 19437 EIF3E 0 . GRCh38 8 108248673 108248673 + Silent SNP G G A C3N-00704_T C3N-00704_N G G c.30C>T p.= p.I10I ENST00000220849 1/13 233 204 29 214 214 0 strelka-varscan-mutect EIF3E,synonymous_variant,p.=,ENST00000220849,NM_001568.2;EIF3E,synonymous_variant,p.=,ENST00000521440,;EIF3E,synonymous_variant,p.=,ENST00000519627,;EIF3E,5_prime_UTR_variant,,ENST00000519030,;EIF3E,5_prime_UTR_variant,,ENST00000518345,;EIF3E,upstream_gene_variant,,ENST00000521297,;EIF3E,intron_variant,,ENST00000518634,;EIF3E,synonymous_variant,p.=,ENST00000522445,;EIF3E,synonymous_variant,p.=,ENST00000518100,;EIF3E,synonymous_variant,p.=,ENST00000522887,;EIF3E,non_coding_transcript_exon_variant,,ENST00000518442,; A ENST00000220849 Transcript synonymous_variant 93/1543 30/1338 10/445 I atC/atT COSM219636,COSM3271560,COSM453840 1 -1 EIF3E HGNC HGNC:3277 protein_coding YES CCDS6308.1 ENSP00000220849 P60228 UPI0000000C92 NM_001568.2 1/13 HAMAP:MF_03004,Pfam_domain:PF09440,PIRSF_domain:PIRSF016255,hmmpanther:PTHR10317,hmmpanther:PTHR10317:SF1,SMART_domains:SM01186 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 62 108248673 108248673 G A 1 0 0 0 0 0 0 0 1 4849 1048 37 1 1 EIF3E 8 108248673 Silent SNP G C3N-00704_T 1479083 108248673 36889963 301 19438 CSMD3 0 . GRCh38 8 112636932 112636933 + Frame_Shift_Ins INS - - T novel C3N-00704_T C3N-00704_N - - c.3599_3600insA p.Gly1201TrpfsTer2 p.G1201Wfs*2 ENST00000297405 22/71 615 555 60 508 508 0 sindel-varindel-pindel CSMD3,frameshift_variant,p.Gly1201TrpfsTer2,ENST00000297405,NM_198123.1;CSMD3,frameshift_variant,p.Gly1161TrpfsTer2,ENST00000343508,NM_198124.1;CSMD3,frameshift_variant,p.Gly1097TrpfsTer2,ENST00000455883,NM_052900.2;CSMD3,frameshift_variant,p.Gly541TrpfsTer2,ENST00000339701,; T ENST00000297405 Transcript frameshift_variant 3844-3845/13212 3599-3600/11124 1200/3707 I/IX att/atAt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 22/71 PROSITE_profiles:PS50923,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 62 112636932 112636932 - T 1 0 1 1 0 0 0 0 0 3747 126 5 0 0 CSMD3 8 112636932 Frame_Shift_Ins INS - C3N-00704_T 4388259 112636932 32501704 302 19439 COLEC10 0 . GRCh38 8 119067418 119067418 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.137C>A p.Pro46Gln p.P46Q ENST00000332843 1/6 233 206 27 159 159 0 strelka-varscan-mutect COLEC10,missense_variant,p.Pro46Gln,ENST00000332843,NM_006438.3;RP11-278I4.2,intron_variant,,ENST00000518362,;COLEC10,intron_variant,,ENST00000521788,; A ENST00000332843 Transcript missense_variant 178/1266 137/834 46/277 P/Q cCa/cAa 1 1 COLEC10 HGNC HGNC:2220 protein_coding YES CCDS6327.1 ENSP00000332723 Q9Y6Z7 A0A024R9J3 UPI00001B01DD NM_006438.3 deleterious(0) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF20,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 119067418 119067418 C A 1 0 0 0 0 1 0 0 0 3500 594 21 2 2 COLEC10 8 119067418 Missense_Mutation SNP C C3N-00704_T 6430486 119067418 26071218 303 19440 ADCY8 0 . GRCh38 8 130867900 130867900 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2156C>A p.Ala719Glu p.A719E ENST00000286355 9/18 145 96 49 192 191 1 strelka-varscan-mutect ADCY8,missense_variant,p.Ala719Glu,ENST00000286355,NM_001115.2;ADCY8,intron_variant,,ENST00000377928,; T ENST00000286355 Transcript missense_variant 4249/5938 2156/3756 719/1251 A/E gCa/gAa 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 deleterious(0) 9/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 MODERATE 1 SNV 1 1 PASS rs1023661733 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 130867900 130867900 G T 1 0 0 0 0 1 0 0 0 344 1319 46 2 2 ADCY8 8 130867900 Missense_Mutation SNP G C3N-00704_T 11800482 130867900 14270736 304 19441 LRRC6 0 . GRCh38 8 132611357 132611357 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.981G>T p.Met327Ile p.M327I ENST00000620350 9/12 115 79 36 131 131 0 strelka-varscan-mutect LRRC6,missense_variant,p.Met327Ile,ENST00000620350,NM_012472.4;LRRC6,missense_variant,p.Met327Ile,ENST00000618342,;LRRC6,missense_variant,p.Met327Ile,ENST00000519595,;LRRC6,missense_variant,p.Met327Ile,ENST00000518642,;LRRC6,missense_variant,p.Met327Ile,ENST00000250173,;LRRC6,missense_variant,p.Met67Ile,ENST00000522789,;LRRC6,missense_variant,p.Met49Ile,ENST00000519085,;LRRC6,non_coding_transcript_exon_variant,,ENST00000522597,; A ENST00000620350 Transcript missense_variant 1105/1878 981/1401 327/466 M/I atG/atT COSM749300 1 -1 LRRC6 HGNC HGNC:16725 protein_coding YES CCDS6365.1 ENSP00000484634 Q86X45 UPI000000DBC5 NM_012472.4 deleterious(0.01) 9/12 PROSITE_profiles:PS51203 1 MODERATE 1 SNV 1 1 1 PASS rs1480173229 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 132611357 132611357 C A 1 0 0 0 0 1 0 0 0 8911 594 21 2 2 LRRC6 8 132611357 Missense_Mutation SNP C C3N-00704_T 1743457 132611357 12527279 305 19442 FAM135B 0 . GRCh38 8 138152738 138152738 + Missense_Mutation SNP C C A rs752946476 C3N-00704_T C3N-00704_N C C c.1737G>T p.Arg579Ser p.R579S ENST00000395297 13/20 280 168 112 273 270 3 strelka-varscan-mutect FAM135B,missense_variant,p.Arg579Ser,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Arg579Ser,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 1908/6962 1737/4221 579/1406 R/S agG/agT rs752946476,COSM4530890,COSM4530891,COSM5688597,COSM5688598 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.64) 13/20 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs752946476 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 138152738 138152738 C A 1 0 0 0 0 1 0 0 0 5299 854 30 2 2 FAM135B 8 138152738 Missense_Mutation SNP C C3N-00704_T 5541381 138152738 6985898 306 19443 FAM135B 0 . GRCh38 8 138367941 138367941 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.43C>A p.His15Asn p.H15N ENST00000395297 2/20 136 94 42 167 167 0 strelka-varscan-mutect FAM135B,missense_variant,p.His15Asn,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.His15Asn,ENST00000520380,;FAM135B,missense_variant,p.His15Asn,ENST00000160713,;FAM135B,non_coding_transcript_exon_variant,,ENST00000517849,;FAM135B,missense_variant,p.His15Asn,ENST00000482951,;FAM135B,missense_variant,p.His15Asn,ENST00000276737,; T ENST00000395297 Transcript missense_variant 214/6962 43/4221 15/1406 H/N Cat/Aat COSM604305,COSM604306 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.19) 2/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 138367941 138367941 G T 1 0 0 0 0 1 0 0 0 5299 1377 48 2 2 FAM135B 8 138367941 Missense_Mutation SNP G C3N-00704_T 215203 138367941 6770695 307 19444 ADGRB1 0 . GRCh38 8 142464651 142464651 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.453C>A p.= p.P151P ENST00000517894 2/31 179 147 32 196 196 0 strelka-varscan-mutect ADGRB1,synonymous_variant,p.=,ENST00000517894,;ADGRB1,synonymous_variant,p.=,ENST00000323289,NM_001702.2;ADGRB1,synonymous_variant,p.=,ENST00000521208,; A ENST00000517894 Transcript synonymous_variant 1347/6241 453/4755 151/1584 P ccC/ccA 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 2/31 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 142464651 142464651 C A 1 0 0 0 0 0 0 0 1 355 610 22 2 2 ADGRB1 8 142464651 Silent SNP C C3N-00704_T 4096710 142464651 2673985 308 19445 ADCK5 0 . GRCh38 8 144392265 144392265 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1187C>A p.Ala396Asp p.A396D ENST00000308860 12/15 102 88 14 113 113 0 strelka-varscan-mutect ADCK5,missense_variant,p.Ala396Asp,ENST00000308860,NM_174922.4;CPSF1,downstream_gene_variant,,ENST00000616140,NM_013291.2;CPSF1,downstream_gene_variant,,ENST00000620219,;CPSF1,downstream_gene_variant,,ENST00000531727,;CPSF1,downstream_gene_variant,,ENST00000532935,;CPSF1,downstream_gene_variant,,ENST00000401314,;ADCK5,downstream_gene_variant,,ENST00000526231,;ADCK5,downstream_gene_variant,,ENST00000534714,;ADCK5,3_prime_UTR_variant,,ENST00000529654,;ADCK5,downstream_gene_variant,,ENST00000533715,;CPSF1,downstream_gene_variant,,ENST00000531480,;CPSF1,downstream_gene_variant,,ENST00000526271,;ADCK5,downstream_gene_variant,,ENST00000526833,;CPSF1,downstream_gene_variant,,ENST00000527827,;CPSF1,downstream_gene_variant,,ENST00000532725,;ADCK5,downstream_gene_variant,,ENST00000532190,;CPSF1,downstream_gene_variant,,ENST00000529288,;CPSF1,downstream_gene_variant,,ENST00000531042,; A ENST00000308860 Transcript missense_variant 1231/1949 1187/1743 396/580 A/D gCc/gAc 1 1 ADCK5 HGNC HGNC:21738 protein_coding YES CCDS34965.2 ENSP00000310547 Q3MIX3 UPI00005B7249 NM_174922.4 deleterious(0.04) 12/15 hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF59,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 200 8 2 0 0 0 0 -19.99811 0.9996778 1 1 1 0 A 3 1 62 144392265 144392265 C A 1 0 0 0 0 1 0 0 0 335 739 26 2 2 ADCK5 8 144392265 Missense_Mutation SNP C C3N-00704_T 1927614 144392265 746371 309 19446 ARHGAP39 0 . GRCh38 8 144548115 144548115 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.971T>A p.Ile324Asn p.I324N ENST00000377307 4/11 51 45 6 55 55 0 strelka-varscan-mutect ARHGAP39,missense_variant,p.Ile324Asn,ENST00000276826,NM_001308208.1,NM_001308207.1;ARHGAP39,missense_variant,p.Ile324Asn,ENST00000377307,NM_025251.1;ARHGAP39,upstream_gene_variant,,ENST00000528810,; T ENST00000377307 Transcript missense_variant 1056/4673 971/3345 324/1114 I/N aTc/aAc 1 -1 ARHGAP39 HGNC HGNC:29351 protein_coding YES CCDS34971.1 ENSP00000366522 Q9C0H5 UPI000021015B NM_025251.1 deleterious(0) 4/11 hmmpanther:PTHR23177,hmmpanther:PTHR23177:SF9 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -14.51394 1 1 1 1 0 T 3 4 62 144548115 144548115 A T 1 0 0 0 0 1 0 0 0 1010 333 12 4 4 ARHGAP39 8 144548115 Missense_Mutation SNP A C3N-00704_T 155850 144548115 590521 310 19447 DOCK8 0 . GRCh38 9 434937 434937 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.5041G>T p.Asp1681Tyr p.D1681Y ENST00000432829 39/48 340 276 64 387 387 0 strelka-varscan-mutect DOCK8,missense_variant,p.Asp1681Tyr,ENST00000432829,NM_203447.3;DOCK8,missense_variant,p.Asp1613Tyr,ENST00000453981,NM_001193536.1;DOCK8,missense_variant,p.Asp1581Tyr,ENST00000469391,NM_001190458.1;DOCK8,missense_variant,p.Asp1148Tyr,ENST00000382329,;DOCK8,non_coding_transcript_exon_variant,,ENST00000495184,; T ENST00000432829 Transcript missense_variant 5153/7452 5041/6300 1681/2099 D/Y Gac/Tac COSM1319592,COSM1319593 1 1 DOCK8 HGNC HGNC:19191 protein_coding YES CCDS6440.2 ENSP00000394888 Q8NF50 UPI0000E0B9E5 NM_203447.3 deleterious(0) 39/48 PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF74,Pfam_domain:PF06920 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 434937 434937 G T 1 0 0 0 0 1 0 0 0 4508 1174 41 2 2 DOCK8 9 434937 Missense_Mutation SNP G C3N-00704_T 434937 137959780 311 19448 KANK1 0 . GRCh38 9 713397 713397 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.2631G>A p.Met877Ile p.M877I ENST00000619269 4/13 103 96 7 112 112 0 strelka-varscan-mutect KANK1,missense_variant,p.Met877Ile,ENST00000619269,NM_001256877.1;KANK1,missense_variant,p.Met877Ile,ENST00000382303,NM_001256876.1;KANK1,missense_variant,p.Met719Ile,ENST00000382293,NM_153186.4;KANK1,missense_variant,p.Met877Ile,ENST00000382297,NM_015158.3;KANK1,non_coding_transcript_exon_variant,,ENST00000489369,;KANK1,non_coding_transcript_exon_variant,,ENST00000354485,; A ENST00000619269 Transcript missense_variant 3389/5688 2631/4059 877/1352 M/I atG/atA 1 1 KANK1 HGNC HGNC:19309 protein_coding YES CCDS34976.1 ENSP00000477725 Q14678 UPI00001AF26E NM_001256877.1 tolerated(0.07) 4/13 hmmpanther:PTHR24168,hmmpanther:PTHR24168:SF19 MODERATE 1 SNV 5 1 PASS rs1014868984 . 0 204 5 0 0 0 0 0 -14.2494 1 1 1 1 0 A 3 1 62 713397 713397 G A 1 0 0 0 0 1 0 0 0 7885 1290 45 3 3 KANK1 9 713397 Missense_Mutation SNP G C3N-00704_T 278460 713397 137681320 312 19449 UHRF2 0 . GRCh38 9 6460791 6460791 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.863G>T p.Gly288Val p.G288V ENST00000276893 4/16 61 47 14 123 123 0 strelka-varscan-mutect UHRF2,missense_variant,p.Gly288Val,ENST00000276893,NM_152896.2;UHRF2,missense_variant,p.Gly65Val,ENST00000450508,;UHRF2,downstream_gene_variant,,ENST00000481049,;UHRF2,missense_variant,p.Gly288Val,ENST00000468435,;UHRF2,splice_region_variant,,ENST00000484159,; T ENST00000276893 Transcript missense_variant,splice_region_variant 1031/3452 863/2409 288/802 G/V gGg/gTg 1 1 UHRF2 HGNC HGNC:12557 protein_coding YES CCDS6469.1 ENSP00000276893 Q96PU4 UPI000006E524 NM_152896.2 deleterious(0) 4/16 hmmpanther:PTHR14140:SF3,hmmpanther:PTHR14140,Pfam_domain:PF12148,Gene3D:2.30.30.30 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999927 1 1 1 0 T 3 4 62 6460791 6460791 G T 1 0 0 0 0 1 0 0 0 17494 1246 43 2 2 UHRF2 9 6460791 Missense_Mutation SNP G C3N-00704_T 5747394 6460791 131933926 313 19450 AL513412.1 0 . GRCh38 9 6990415 6990415 + Splice_Site SNP G G C novel C3N-00704_T C3N-00704_N G G c.1678-1G>C p.X560_splice ENST00000381309 290 248 42 324 324 0 strelka-varscan-mutect KDM4C,splice_acceptor_variant,,ENST00000381309,NM_015061.3,NM_001304340.1,NM_001304339.1;KDM4C,splice_acceptor_variant,,ENST00000381306,;RP11-146B14.1,splice_acceptor_variant,,ENST00000536108,;KDM4C,splice_acceptor_variant,,ENST00000543771,NM_001146695.1;KDM4C,splice_acceptor_variant,,ENST00000428870,;AL513412.1,splice_acceptor_variant,,ENST00000535193,NM_001146696.1;KDM4C,downstream_gene_variant,,ENST00000494570,;KDM4C,splice_acceptor_variant,,ENST00000438023,; C ENST00000381309 Transcript splice_acceptor_variant -/4655 1678/3171 560/1056 1 1 KDM4C HGNC HGNC:17071 protein_coding YES CCDS6471.1 ENSP00000370710 Q9H3R0 UPI0000367602 NM_015061.3,NM_001304340.1,NM_001304339.1 11/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 62 6990415 6990415 G C 1 0 0 0 0 0 0 1 0 581 956 33 4 4 AL513412.1 9 6990415 Splice_Site SNP G C3N-00704_T 529624 6990415 131404302 314 19451 SNAPC3 0 . GRCh38 9 15423052 15423052 + Frame_Shift_Del DEL C C - novel C3N-00704_T C3N-00704_N C C c.174delC p.Asp60ThrfsTer4 p.D60Tfs*4 ENST00000380821 1/9 51 46 5 70 70 0 varindel-pindel SNAPC3,frameshift_variant,p.Asp60ThrfsTer4,ENST00000380821,NM_001039697.1;SNAPC3,frameshift_variant,p.Asp60ThrfsTer4,ENST00000610884,;SNAPC3,frameshift_variant,p.Asp60ThrfsTer4,ENST00000421710,;SNAPC3,upstream_gene_variant,,ENST00000461041,;SNAPC3,frameshift_variant,p.Asp60ThrfsTer4,ENST00000467062,;SNAPC3,frameshift_variant,p.Asp60ThrfsTer4,ENST00000490969,; - ENST00000380821 Transcript frameshift_variant 349/5680 173/1236 58/411 A/X gCc/gc 1 1 SNAPC3 HGNC HGNC:11136 protein_coding YES CCDS6478.1 ENSP00000370200 Q92966 UPI0000135B24 NM_001039697.1 1/9 hmmpanther:PTHR13421,hmmpanther:PTHR13421:SF16 HIGH 1 deletion 1 1 1 PASS . . 0 202 8 0 0 0 0 0 -12.12751 0.9999953 1 1 1 0 - 7 5 62 15423052 15423052 C - 1 0 1 0 1 0 0 0 0 15157 739 26 0 0 SNAPC3 9 15423052 Frame_Shift_Del DEL C C3N-00704_T 8432637 15423052 122971665 315 19452 CCDC171 0 . GRCh38 9 15784638 15784638 + Nonsense_Mutation SNP G G T rs761945690 C3N-00704_T C3N-00704_N G G c.3211G>T p.Glu1071Ter p.E1071* ENST00000380701 21/26 146 121 25 185 185 0 strelka-varscan-mutect CCDC171,stop_gained,p.Glu1071Ter,ENST00000380701,NM_173550.2;CCDC171,stop_gained,p.Glu311Ter,ENST00000449575,;CCDC171,stop_gained,p.Glu125Ter,ENST00000432954,; T ENST00000380701 Transcript stop_gained 3539/6512 3211/3981 1071/1326 E/* Gaa/Taa rs761945690 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 21/26 Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS rs761945690 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 15784638 15784638 G T 1 0 0 0 0 0 1 0 0 2488 1291 45 2 2 CCDC171 9 15784638 Nonsense_Mutation SNP G C3N-00704_T 361586 15784638 122610079 316 19453 FAM205A 0 . GRCh38 9 34725296 34725296 + Missense_Mutation SNP G G T rs562140350 C3N-00704_T C3N-00704_N G G c.1944C>A p.Asn648Lys p.N648K ENST00000378788 4/4 71 66 5 106 106 0 varscan-mutect FAM205A,missense_variant,p.Asn648Lys,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript missense_variant 1984/4225 1944/4008 648/1335 N/K aaC/aaA rs562140350 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 tolerated(0.69) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859 MODERATE 1 SNV 2 1 PASS rs562140350 . 0 199 8 3 0 0 0 0 -8.861142 0.9953964 1 1 1 0 T 3 4 62 34725296 34725296 G T 1 0 0 0 0 1 0 0 0 5386 1136 40 1 1 FAM205A 9 34725296 Missense_Mutation SNP G C3N-00704_T 18940658 34725296 103669421 317 19454 FAM214B 0 . GRCh38 9 35106851 35106851 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.935G>A p.Gly312Glu p.G312E ENST00000378561 3/8 191 174 17 188 188 0 strelka-varscan-mutect FAM214B,missense_variant,p.Gly312Glu,ENST00000378561,;FAM214B,missense_variant,p.Gly312Glu,ENST00000603301,NM_001317991.1;FAM214B,missense_variant,p.Gly312Glu,ENST00000378557,;FAM214B,missense_variant,p.Gly312Glu,ENST00000322813,NM_025182.2;FAM214B,missense_variant,p.Gly312Glu,ENST00000605244,;FAM214B,missense_variant,p.Gly312Glu,ENST00000488109,;FAM214B,missense_variant,p.Gly7Glu,ENST00000378566,;STOML2,upstream_gene_variant,,ENST00000452248,NM_001287031.1;STOML2,upstream_gene_variant,,ENST00000619795,NM_001287033.1;STOML2,upstream_gene_variant,,ENST00000356493,NM_013442.2,NM_001287032.1;FAM214B,downstream_gene_variant,,ENST00000605392,;FAM214B,downstream_gene_variant,,ENST00000605104,;STOML2,upstream_gene_variant,,ENST00000487490,; T ENST00000378561 Transcript missense_variant 3991/5771 935/1617 312/538 G/E gGa/gAa 1 -1 FAM214B HGNC HGNC:25666 protein_coding YES CCDS6578.1 ENSP00000367823 Q7L5A3 UPI0000169E3E deleterious(0.04) 3/8 Low_complexity_(Seg):seg,hmmpanther:PTHR13199:SF12,hmmpanther:PTHR13199 MODERATE 1 SNV 1 1 PASS rs1439347183 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 35106851 35106851 C T 1 0 0 0 0 1 0 0 0 5403 855 30 3 3 FAM214B 9 35106851 Missense_Mutation SNP C C3N-00704_T 381555 35106851 103287866 318 19455 NPR2 0 . GRCh38 9 35800138 35800138 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1104G>T p.Met368Ile p.M368I ENST00000342694 4/22 469 386 83 551 549 2 strelka-varscan-mutect NPR2,missense_variant,p.Met368Ile,ENST00000342694,NM_003995.3;NPR2,non_coding_transcript_exon_variant,,ENST00000464810,; T ENST00000342694 Transcript missense_variant 1359/3686 1104/3144 368/1047 M/I atG/atT 1 1 NPR2 HGNC HGNC:7944 protein_coding YES CCDS6590.1 ENSP00000341083 P20594 UPI0000125B42 NM_003995.3 deleterious(0.01) 4/22 hmmpanther:PTHR11920:SF305,hmmpanther:PTHR11920,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 35800138 35800138 G T 1 0 0 0 0 1 0 0 0 10651 1319 46 2 2 NPR2 9 35800138 Missense_Mutation SNP G C3N-00704_T 693287 35800138 102594579 319 19456 TMEM8B 0 . GRCh38 9 35846026 35846026 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.331G>T p.Val111Leu p.V111L ENST00000377988 7/13 280 240 40 312 312 0 strelka-varscan-mutect TMEM8B,missense_variant,p.Val111Leu,ENST00000377988,NM_001042590.2;TMEM8B,missense_variant,p.Val111Leu,ENST00000377991,NM_001042589.2;TMEM8B,missense_variant,p.Val111Leu,ENST00000377996,;TMEM8B,missense_variant,p.Val111Leu,ENST00000439587,NM_016446.3;TMEM8B,non_coding_transcript_exon_variant,,ENST00000473947,;TMEM8B,non_coding_transcript_exon_variant,,ENST00000490199,;TMEM8B,downstream_gene_variant,,ENST00000472010,;TMEM8B,downstream_gene_variant,,ENST00000464519,; T ENST00000377988 Transcript missense_variant 1637/3731 331/1419 111/472 V/L Gtg/Ttg 1 1 TMEM8B HGNC HGNC:21427 protein_coding YES CCDS43800.1 ENSP00000367227 A6NDV4 UPI00002113B9 NM_001042590.2 tolerated(0.27) 7/13 hmmpanther:PTHR14319,hmmpanther:PTHR14319:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 35846026 35846026 G T 1 0 0 0 0 1 0 0 0 16692 1261 44 2 2 TMEM8B 9 35846026 Missense_Mutation SNP G C3N-00704_T 45888 35846026 102548691 320 19457 CNTNAP3 0 . GRCh38 9 39078395 39078395 + Silent SNP A A C novel C3N-00704_T C3N-00704_N A A c.3735T>G p.= p.A1245A ENST00000297668 23/24 938 882 56 1244 1244 0 varscan-mutect CNTNAP3,synonymous_variant,p.=,ENST00000297668,NM_033655.3;CNTNAP3,synonymous_variant,p.=,ENST00000377656,;CNTNAP3,non_coding_transcript_exon_variant,,ENST00000493965,;CNTNAP3,downstream_gene_variant,,ENST00000477002,; C ENST00000297668 Transcript synonymous_variant 3809/5064 3735/3867 1245/1288 A gcT/gcG 1 -1 CNTNAP3 HGNC HGNC:13834 protein_coding YES CCDS6616.1 ENSP00000297668 Q9BZ76 UPI000013E43B NM_033655.3 23/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs1260778277 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 62 39078395 39078395 A C 1 0 0 0 0 0 0 0 1 3429 175 7 5 5 CNTNAP3 9 39078395 Silent SNP A C3N-00704_T 3232369 39078395 99316322 321 19458 CNTNAP3B 0 . GRCh38 9 41964612 41964612 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1682A>T p.Glu561Val p.E561V ENST00000377561 11/24 63 58 5 58 58 0 varscan-mutect CNTNAP3B,missense_variant,p.Glu561Val,ENST00000612828,;CNTNAP3B,missense_variant,p.Glu561Val,ENST00000377561,NM_001201380.2;CNTNAP3B,missense_variant,p.Glu561Val,ENST00000341990,;CNTNAP3B,intron_variant,,ENST00000617422,;CNTNAP3B,upstream_gene_variant,,ENST00000491438,;CNTNAP3B,non_coding_transcript_exon_variant,,ENST00000618777,;CNTNAP3B,intron_variant,,ENST00000619138,;CNTNAP3B,intron_variant,,ENST00000479351,; A ENST00000377561 Transcript missense_variant 2075/5379 1682/3867 561/1288 E/V gAg/gTg 1 -1 CNTNAP3B HGNC HGNC:32035 protein_coding YES CCDS75836.1 ENSP00000478671 A0A087WUH3 UPI00043788D3 NM_001201380.2 tolerated(0.1) 11/24 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF605,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -9.348304 0.9999927 1 1 1 0 A 3 1 62 41964612 41964612 T A 1 0 0 0 0 1 0 0 0 3430 1551 54 4 4 CNTNAP3B 9 41964612 Missense_Mutation SNP T C3N-00704_T 2886217 41964612 96430105 322 19459 SPATA31A7 0 . GRCh38 9 61192505 61192505 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.419A>T p.Glu140Val p.E140V ENST00000619167 4/4 468 381 87 550 550 0 strelka-varscan-mutect SPATA31A7,missense_variant,p.Glu140Val,ENST00000619167,NM_015667.2;RP11-101E5.6,downstream_gene_variant,,ENST00000611332,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000618860,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000619140,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000622751,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000376458,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000614013,;SPATA31A7,non_coding_transcript_exon_variant,,ENST00000611017,;SPATA31A7,intron_variant,,ENST00000621711,;SPATA31A7,downstream_gene_variant,,ENST00000622899,; T ENST00000619167 Transcript missense_variant 481/4256 419/4044 140/1347 E/V gAg/gTg 1 1 SPATA31A7 HGNC HGNC:32007 protein_coding YES CCDS75838.1 ENSP00000484807 Q8IWB4 UPI0000457748 NM_015667.2 deleterious(0) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF22,Pfam_domain:PF15371 MODERATE 1 SNV 1 1 PASS . . 4 205 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 61192505 61192505 A T 1 0 0 0 0 1 0 0 0 15346 304 11 4 4 SPATA31A7 9 61192505 Missense_Mutation SNP A C3N-00704_T 19227893 61192505 77202212 323 19460 ANKRD20A4 0 . GRCh38 9 64411514 64411514 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2228G>T p.Trp743Leu p.W743L ENST00000357336 15/15 266 233 33 471 471 0 varscan-mutect ANKRD20A4,missense_variant,p.Trp743Leu,ENST00000357336,NM_001098805.1; T ENST00000357336 Transcript missense_variant 2509/4137 2228/2472 743/823 W/L tGg/tTg 1 1 ANKRD20A4 HGNC HGNC:31982 protein_coding YES CCDS43828.1 ENSP00000349891 Q4UJ75 UPI000051917A NM_001098805.1 tolerated(1) 15/15 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF1 MODERATE 1 SNV 1 1 PASS rs1195604654 . 16 192 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 64411514 64411514 G T 1 0 0 0 0 1 0 0 0 753 1357 47 2 2 ANKRD20A4 9 64411514 Missense_Mutation SNP G C3N-00704_T 3219009 64411514 73983203 324 19461 GDA 0 . GRCh38 9 72223163 72223163 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.650C>A p.Ser217Tyr p.S217Y ENST00000238018 7/16 195 160 35 204 204 0 strelka-varscan-mutect GDA,missense_variant,p.Ser143Tyr,ENST00000545168,NM_001242507.2,NM_001242506.2;GDA,missense_variant,p.Ser217Tyr,ENST00000358399,NM_004293.4;GDA,missense_variant,p.Ser217Tyr,ENST00000238018,NM_001242505.2;GDA,missense_variant,p.Ser83Tyr,ENST00000414671,;GDA,intron_variant,,ENST00000376986,;GDA,upstream_gene_variant,,ENST00000436438,;GDA,non_coding_transcript_exon_variant,,ENST00000477618,;GDA,missense_variant,p.Ser217Tyr,ENST00000475764,;GDA,upstream_gene_variant,,ENST00000489618,; A ENST00000238018 Transcript missense_variant 859/2074 650/1416 217/471 S/Y tCc/tAc 1 1 GDA HGNC HGNC:4212 protein_coding YES CCDS56576.1 ENSP00000238018 Q9Y2T3 UPI000015828B NM_001242505.2 deleterious(0) 7/16 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11271,hmmpanther:PTHR11271:SF6,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02967 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 72223163 72223163 C A 1 0 0 0 0 1 0 0 0 6178 855 30 2 2 GDA 9 72223163 Missense_Mutation SNP C C3N-00704_T 7811649 72223163 66171554 325 19462 PRUNE2 0 . GRCh38 9 76826656 76826656 + Silent SNP C C A C3N-00704_T C3N-00704_N C C c.585G>T p.= p.L195L ENST00000376718 5/19 113 104 9 144 144 0 strelka-varscan-mutect PRUNE2,synonymous_variant,p.=,ENST00000376718,NM_015225.2;PRUNE2,synonymous_variant,p.=,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,synonymous_variant,p.=,ENST00000376713,;PRUNE2,5_prime_UTR_variant,,ENST00000428286,;PRUNE2,non_coding_transcript_exon_variant,,ENST00000492157,; A ENST00000376718 Transcript synonymous_variant 709/12584 585/9267 195/3088 L ctG/ctT COSM3780090,COSM3780091 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 5/19 Low_complexity_(Seg):seg,Gene3D:1wpnA00,Superfamily_domains:SSF64182 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 197 11 2 0 0 0 0 -13.54026 0.9963785 1 1 1 0 A 2 1 62 76826656 76826656 C A 1 0 0 0 0 0 0 0 1 12791 581 21 2 2 PRUNE2 9 76826656 Silent SNP C C3N-00704_T 4603493 76826656 61568061 326 19463 SPATA31E1 0 . GRCh38 9 87887107 87887107 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.2620A>G p.Thr874Ala p.T874A ENST00000325643 4/4 170 137 33 197 197 0 strelka-varscan-mutect SPATA31E1,missense_variant,p.Thr874Ala,ENST00000325643,NM_178828.4; G ENST00000325643 Transcript missense_variant 2686/4478 2620/4338 874/1445 T/A Acc/Gcc 1 1 SPATA31E1 HGNC HGNC:26672 protein_coding YES CCDS6676.1 ENSP00000322640 Q6ZUB1 UPI000036764A NM_178828.4 tolerated(0.91) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF19 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 87887107 87887107 A G 1 0 0 0 0 1 0 0 0 15350 159 6 5 5 SPATA31E1 9 87887107 Missense_Mutation SNP A C3N-00704_T 11060451 87887107 50507610 327 19464 SHC3 0 . GRCh38 9 89038164 89038164 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1485A>T p.Gln495His p.Q495H ENST00000375835 11/12 363 301 62 469 469 0 strelka-varscan-mutect SHC3,missense_variant,p.Gln495His,ENST00000375835,NM_016848.5;SHC3,missense_variant,p.Gln43His,ENST00000375831,; A ENST00000375835 Transcript missense_variant 1792/9768 1485/1785 495/594 Q/H caA/caT 1 -1 SHC3 HGNC HGNC:18181 protein_coding YES CCDS6681.1 ENSP00000364995 Q92529 UPI0000073E1F NM_016848.5 deleterious(0.03) 11/12 hmmpanther:PTHR10337:SF4,hmmpanther:PTHR10337,Gene3D:3.30.505.10,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 89038164 89038164 T A 1 0 0 0 0 1 0 0 0 14531 1606 56 4 4 SHC3 9 89038164 Missense_Mutation SNP T C3N-00704_T 1151057 89038164 49356553 328 19465 IPPK 0 . GRCh38 9 92648150 92648150 + Splice_Site SNP T T A novel C3N-00704_T C3N-00704_N T T c.415-2A>T p.X139_splice ENST00000287996 160 131 29 182 182 0 strelka-varscan-mutect IPPK,splice_acceptor_variant,,ENST00000287996,NM_022755.5; A ENST00000287996 Transcript splice_acceptor_variant -/4401 415/1476 139/491 1 -1 IPPK HGNC HGNC:14645 protein_coding YES CCDS6699.1 ENSP00000287996 Q9H8X2 UPI000006EBCA NM_022755.5 5/12 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999957 1 1 1 0 A 5 1 62 92648150 92648150 T A 1 0 0 0 0 0 0 1 0 7704 1594 55 4 4 IPPK 9 92648150 Splice_Site SNP T C3N-00704_T 3609986 92648150 45746567 329 19466 WNK2 0 . GRCh38 9 93289477 93289477 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.4834C>T p.Pro1612Ser p.P1612S ENST00000297954 20/30 139 108 31 154 154 0 strelka-mutect WNK2,missense_variant,p.Pro1571Ser,ENST00000432730,;WNK2,missense_variant,p.Pro1612Ser,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Pro1575Ser,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Pro1179Ser,ENST00000411624,;WNK2,missense_variant,p.Pro372Ser,ENST00000448251,;WNK2,missense_variant,p.Pro98Ser,ENST00000453718,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000474009,;WNK2,upstream_gene_variant,,ENST00000479696,; T ENST00000297954 Transcript missense_variant 4834/7138 4834/6894 1612/2297 P/S Cct/Tct 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0) 20/30 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF10 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 93289477 93289477 C T 1 0 0 0 0 1 0 0 0 17934 623 22 3 3 WNK2 9 93289477 Missense_Mutation SNP C C3N-00704_T 641327 93289477 45105240 330 19467 KIAA0368 0 . GRCh38 9 111371799 111371799 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.5093A>T p.Gln1698Leu p.Q1698L ENST00000259335 44/51 328 283 45 318 318 0 strelka-varscan-mutect KIAA0368,missense_variant,p.Gln1698Leu,ENST00000259335,NM_001080398.1;KIAA0368,missense_variant,p.Gln1520Leu,ENST00000338205,;KIAA0368,upstream_gene_variant,,ENST00000374383,;KIAA0368,upstream_gene_variant,,ENST00000465499,; A ENST00000259335 Transcript missense_variant 5093/7391 5093/6054 1698/2017 Q/L cAg/cTg 1 -1 KIAA0368 HGNC HGNC:29020 protein_coding YES CCDS48006.1 ENSP00000259335 J3KN16 UPI0000DD7F7A NM_001080398.1 tolerated(0.25) 44/51 hmmpanther:PTHR23346,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 111371799 111371799 T A 1 0 0 0 0 1 0 0 0 8083 1580 55 4 4 KIAA0368 9 111371799 Missense_Mutation SNP T C3N-00704_T 18082322 111371799 27022918 331 19468 FKBP15 0 . GRCh38 9 113186257 113186257 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1490A>T p.His497Leu p.H497L ENST00000238256 15/28 128 105 23 160 160 0 strelka-varscan-mutect FKBP15,missense_variant,p.His522Leu,ENST00000446284,;FKBP15,missense_variant,p.His497Leu,ENST00000238256,NM_015258.1;FKBP15,downstream_gene_variant,,ENST00000414250,;FKBP15,non_coding_transcript_exon_variant,,ENST00000489645,; A ENST00000238256 Transcript missense_variant 1608/4336 1490/3660 497/1219 H/L cAt/cTt 1 -1 FKBP15 HGNC HGNC:23397 protein_coding YES CCDS48007.1 ENSP00000238256 Q5T1M5 UPI000022D996 NM_015258.1 tolerated(0.12) 15/28 hmmpanther:PTHR18937:SF256,hmmpanther:PTHR18937 MODERATE 1 SNV 1 1 PASS rs1243252279 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 113186257 113186257 T A 1 0 0 0 0 1 0 0 0 5768 1464 51 4 4 FKBP15 9 113186257 Missense_Mutation SNP T C3N-00704_T 1814458 113186257 25208460 332 19469 PAPPA 0 . GRCh38 9 116187483 116187483 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.745T>A p.Tyr249Asn p.Y249N ENST00000328252 2/22 143 121 22 175 175 0 strelka-varscan-mutect PAPPA,missense_variant,p.Tyr249Asn,ENST00000328252,NM_002581.3; A ENST00000328252 Transcript missense_variant 1114/10959 745/4884 249/1627 Y/N Tac/Aac 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 2/22 Gene3D:2.60.120.200,Pfam_domain:PF13385,SMART_domains:SM00560,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 116187483 116187483 T A 1 0 0 0 0 1 0 0 0 11512 1522 53 4 4 PAPPA 9 116187483 Missense_Mutation SNP T C3N-00704_T 3001226 116187483 22207234 333 19470 FBXW2 0 . GRCh38 9 120788074 120788075 + Frame_Shift_Ins INS - - G novel C3N-00704_T C3N-00704_N - - c.184dupC p.Leu62ProfsTer24 p.L62Pfs*24 ENST00000608872 3/8 353 311 42 429 429 0 sindel-varindel FBXW2,frameshift_variant,p.Leu62ProfsTer24,ENST00000608872,NM_012164.3;FBXW2,5_prime_UTR_variant,,ENST00000453291,;FBXW2,non_coding_transcript_exon_variant,,ENST00000474117,;FBXW2,non_coding_transcript_exon_variant,,ENST00000476481,; G ENST00000608872 Transcript frameshift_variant 372-373/9138 184-185/1365 62/454 L/PX ctg/cCtg 1 -1 FBXW2 HGNC HGNC:13608 protein_coding YES CCDS43872.1 ENSP00000476369 Q9UKT8 UPI000006FE3A NM_012164.3 3/8 Low_complexity_(Seg):seg,PROSITE_profiles:PS50181,hmmpanther:PTHR22844:SF166,hmmpanther:PTHR22844,Gene3D:1.20.1280.50,Pfam_domain:PF12937,SMART_domains:SM00256,Superfamily_domains:SSF81383 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 62 120788074 120788074 - G 1 0 1 1 0 0 0 0 0 5629 188 7 0 0 FBXW2 9 120788074 Frame_Shift_Ins INS - C3N-00704_T 4600591 120788074 17606643 334 19471 GAPVD1 0 . GRCh38 9 125337042 125337042 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2534C>T p.Pro845Leu p.P845L ENST00000394105 15/27 216 178 38 224 224 0 strelka-varscan-mutect GAPVD1,missense_variant,p.Pro818Leu,ENST00000470056,;GAPVD1,missense_variant,p.Pro818Leu,ENST00000394104,;GAPVD1,missense_variant,p.Pro818Leu,ENST00000297933,NM_001282680.1;GAPVD1,missense_variant,p.Pro818Leu,ENST00000495955,NM_001282679.1;GAPVD1,missense_variant,p.Pro845Leu,ENST00000394105,NM_015635.3;GAPVD1,missense_variant,p.Pro797Leu,ENST00000394083,;GAPVD1,missense_variant,p.Pro797Leu,ENST00000312123,NM_001282681.1;GAPVD1,missense_variant,p.Pro818Leu,ENST00000467750,;GAPVD1,missense_variant,p.Pro655Leu,ENST00000436712,;GAPVD1,3_prime_UTR_variant,,ENST00000265956,;GAPVD1,intron_variant,,ENST00000431329,;GAPVD1,upstream_gene_variant,,ENST00000469498,;GAPVD1,3_prime_UTR_variant,,ENST00000497580,;GAPVD1,non_coding_transcript_exon_variant,,ENST00000479511,; T ENST00000394105 Transcript missense_variant 2694/5207 2534/4464 845/1487 P/L cCt/cTt 1 1 GAPVD1 HGNC HGNC:23375 protein_coding YES CCDS35138.1 ENSP00000377665 Q14C86 A0A024R8A2 UPI00001D76F1 NM_015635.3 deleterious_low_confidence(0) 15/27 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 125337042 125337042 C T 1 0 0 0 0 1 0 0 0 6107 681 24 3 3 GAPVD1 9 125337042 Missense_Mutation SNP C C3N-00704_T 4548968 125337042 13057675 335 19472 FAM129B 0 . GRCh38 9 127531700 127531700 + Missense_Mutation SNP C C T rs773683224 C3N-00704_T C3N-00704_N C C c.134G>A p.Arg45His p.R45H ENST00000373312 2/14 176 146 30 214 214 0 strelka-varscan-mutect FAM129B,missense_variant,p.Arg45His,ENST00000373312,NM_022833.3;FAM129B,missense_variant,p.Arg32His,ENST00000373314,NM_001035534.2;FAM129B,non_coding_transcript_exon_variant,,ENST00000468379,;FAM129B,intron_variant,,ENST00000484348,;FAM129B,intron_variant,,ENST00000478917,;FAM129B,upstream_gene_variant,,ENST00000476091,; T ENST00000373312 Transcript missense_variant 348/3957 134/2241 45/746 R/H cGc/cAc rs773683224,COSM292749,COSM4872723 1 -1 FAM129B HGNC HGNC:25282 protein_coding YES CCDS35145.1 ENSP00000362409 Q96TA1 UPI00001592F0 NM_022833.3 tolerated(0.05) 2/14 hmmpanther:PTHR14392:SF2,hmmpanther:PTHR14392 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs773683224 . 0 206 0 4 0 0 0 0 -20 0.9999364 1 1 1 0 T 3 4 62 127531700 127531700 C T 1 0 0 0 0 1 0 0 0 5287 768 27 1 1 FAM129B 9 127531700 Missense_Mutation SNP C C3N-00704_T 2194658 127531700 10863017 336 19473 ENG 0 . GRCh38 9 127854349 127854349 + Missense_Mutation SNP G G T rs139334561 C3N-00704_T C3N-00704_N G G c.7C>A p.Arg3Ser p.R3S ENST00000373203 1/15 183 164 19 217 217 0 strelka-varscan-mutect ENG,missense_variant,p.Arg3Ser,ENST00000344849,NM_000118.3;ENG,missense_variant,p.Arg3Ser,ENST00000373203,NM_001114753.2; T ENST00000373203 Transcript missense_variant 408/3048 7/1977 3/658 R/S Cgc/Agc rs139334561 1 -1 ENG HGNC HGNC:3349 protein_coding YES CCDS48029.1 ENSP00000362299 P17813 A0A024R878 UPI0000129E00 NM_001114753.2 deleterious(0.01) 1/15 PROSITE_profiles:PS51257,hmmpanther:PTHR14002,hmmpanther:PTHR14002:SF1,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs139334561 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 127854349 127854349 G T 1 0 0 0 0 1 0 0 0 4960 1116 39 1 1 ENG 9 127854349 Missense_Mutation SNP G C3N-00704_T 322649 127854349 10540368 337 19474 PRRC2B 0 . GRCh38 9 131475581 131475581 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.3452G>T p.Arg1151Met p.R1151M ENST00000357304 15/31 91 78 13 101 101 0 strelka-varscan-mutect PRRC2B,missense_variant,p.Arg1151Met,ENST00000357304,NM_013318.3;PRRC2B,intron_variant,,ENST00000405995,;PRRC2B,upstream_gene_variant,,ENST00000451855,;PRRC2B,downstream_gene_variant,,ENST00000422467,;PRRC2B,downstream_gene_variant,,ENST00000456307,; T ENST00000357304 Transcript missense_variant 3507/11042 3452/6690 1151/2229 R/M aGg/aTg 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 deleterious(0) 15/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS rs1282788368 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 131475581 131475581 G T 1 0 0 0 0 1 0 0 0 12749 1000 35 2 2 PRRC2B 9 131475581 Missense_Mutation SNP G C3N-00704_T 3621232 131475581 6919136 338 19475 SETX 0 . GRCh38 9 132264682 132264682 + Missense_Mutation SNP G G A C3N-00704_T C3N-00704_N G G c.7591C>T p.Pro2531Ser p.P2531S ENST00000224140 26/26 669 595 74 817 817 0 strelka-varscan-mutect SETX,missense_variant,p.Pro2531Ser,ENST00000224140,NM_015046.5;SETX,missense_variant,p.Pro802Ser,ENST00000436441,;SETX,non_coding_transcript_exon_variant,,ENST00000477049,; A ENST00000224140 Transcript missense_variant 7774/11100 7591/8034 2531/2677 P/S Cct/Tct COSM3375147,COSM3375148 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 tolerated(0.23) 26/26 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF377 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1451963911 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 132264682 132264682 G A 1 0 0 0 0 1 0 0 0 14420 1174 41 3 3 SETX 9 132264682 Missense_Mutation SNP G C3N-00704_T 789101 132264682 6130035 339 19476 SETX 0 . GRCh38 9 132278242 132278242 + Missense_Mutation SNP C C A rs780449068 C3N-00704_T C3N-00704_N C C c.6670G>T p.Gly2224Cys p.G2224C ENST00000224140 21/26 262 224 38 409 409 0 strelka-mutect SETX,missense_variant,p.Gly2224Cys,ENST00000224140,NM_015046.5;SETX,missense_variant,p.Gly466Cys,ENST00000436441,;SETX,upstream_gene_variant,,ENST00000477049,;SETX,downstream_gene_variant,,ENST00000474172,;SETX,upstream_gene_variant,,ENST00000464133,; A ENST00000224140 Transcript missense_variant 6853/11100 6670/8034 2224/2677 G/C Ggc/Tgc rs780449068 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 deleterious(0) 21/26 Gene3D:3.40.50.300,hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF377,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs780449068 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 132278242 132278242 C A 1 0 0 0 0 1 0 0 0 14420 594 21 2 2 SETX 9 132278242 Missense_Mutation SNP C C3N-00704_T 13560 132278242 6116475 340 19477 GFI1B 0 . GRCh38 9 132988334 132988334 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.376A>T p.Met126Leu p.M126L ENST00000339463 8/11 402 364 38 526 526 0 strelka-varscan-mutect GFI1B,missense_variant,p.Met126Leu,ENST00000339463,NM_004188.5;GFI1B,missense_variant,p.Met126Leu,ENST00000636137,;GFI1B,missense_variant,p.Met126Leu,ENST00000372122,;GFI1B,missense_variant,p.Met126Leu,ENST00000636263,;GFI1B,missense_variant,p.Met126Leu,ENST00000372123,NM_001135031.1; T ENST00000339463 Transcript missense_variant 1195/2449 376/993 126/330 M/L Atg/Ttg 1 1 GFI1B HGNC HGNC:4238 protein_coding YES CCDS6957.1 ENSP00000344782 Q5VTD9 UPI000013E4EE NM_004188.5 tolerated(0.54) 8/11 MODERATE 1 SNV 1 1 PASS rs1274965157 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 132988334 132988334 A T 1 0 0 0 0 1 0 0 0 6214 217 8 4 4 GFI1B 9 132988334 Missense_Mutation SNP A C3N-00704_T 710092 132988334 5406383 341 19478 FAM163B 0 . GRCh38 9 133580139 133580139 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.85C>A p.= p.R29R ENST00000356873 1/2 174 145 29 209 209 0 strelka-mutect FAM163B,synonymous_variant,p.=,ENST00000356873,NM_001080515.2;FAM163B,synonymous_variant,p.=,ENST00000496132,;ADAMTSL2,downstream_gene_variant,,ENST00000393061,;ADAMTSL2,downstream_gene_variant,,ENST00000354484,NM_001145320.1;ADAMTSL2,downstream_gene_variant,,ENST00000393060,NM_014694.3; T ENST00000356873 Transcript synonymous_variant 108/1131 85/501 29/166 R Cgg/Agg 1 -1 FAM163B HGNC HGNC:33277 protein_coding YES CCDS35171.1 ENSP00000349336 P0C2L3 UPI00004577D5 NM_001080515.2 1/2 hmmpanther:PTHR31396,Pfam_domain:PF15069 LOW 1 SNV 1 1 PASS rs1269042210 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 133580139 133580139 G T 1 0 0 0 0 0 0 0 1 5326 1115 39 1 1 FAM163B 9 133580139 Silent SNP G C3N-00704_T 591805 133580139 4814578 342 19479 COL5A1 0 . GRCh38 9 134780120 134780120 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.2404G>A p.Gly802Ser p.G802S ENST00000371817 28/66 415 374 41 500 500 0 strelka-varscan-mutect COL5A1,missense_variant,p.Gly802Ser,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly802Ser,ENST00000618395,NM_001278074.1; A ENST00000371817 Transcript missense_variant 2818/8471 2404/5517 802/1838 G/S Ggt/Agt 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0) 28/66 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 134780120 134780120 G A 1 0 0 0 0 1 0 0 0 3485 1348 47 3 3 COL5A1 9 134780120 Missense_Mutation SNP G C3N-00704_T 1199981 134780120 3614597 343 19480 FCN1 0 . GRCh38 9 134913607 134913607 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.314C>A p.Ala105Asp p.A105D ENST00000371806 5/9 54 43 11 52 52 0 strelka-varscan-mutect FCN1,missense_variant,p.Ala105Asp,ENST00000616356,;FCN1,missense_variant,p.Ala105Asp,ENST00000371806,NM_002003.3; T ENST00000371806 Transcript missense_variant 406/1286 314/981 105/326 A/D gCt/gAt COSM5531157 1 -1 FCN1 HGNC HGNC:3623 protein_coding YES CCDS6985.1 ENSP00000360871 O00602 UPI000012A5A7 NM_002003.3 tolerated(0.17) 5/9 hmmpanther:PTHR19143:SF165,hmmpanther:PTHR19143,Pfam_domain:PF01391 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 134913607 134913607 G T 1 0 0 0 0 1 0 0 0 5654 971 34 2 2 FCN1 9 134913607 Missense_Mutation SNP G C3N-00704_T 133487 134913607 3481110 344 19481 TRAF2 0 . GRCh38 9 136908117 136908117 + Silent SNP G G T rs533013634 C3N-00704_T C3N-00704_N G G c.414G>T p.= p.A138A ENST00000247668 5/11 190 155 35 202 202 0 strelka-varscan-mutect TRAF2,synonymous_variant,p.=,ENST00000247668,NM_021138.3;TRAF2,synonymous_variant,p.=,ENST00000429509,;TRAF2,synonymous_variant,p.=,ENST00000419057,;TRAF2,non_coding_transcript_exon_variant,,ENST00000482854,;TRAF2,non_coding_transcript_exon_variant,,ENST00000474950,;TRAF2,upstream_gene_variant,,ENST00000469701,; T ENST00000247668 Transcript synonymous_variant 466/2264 414/1506 138/501 A gcG/gcT rs533013634,COSM753085 1 1 TRAF2 HGNC HGNC:12032 protein_coding YES CCDS7013.1 ENSP00000247668 Q12933 A0A024R8H5 UPI0000001612 NM_021138.3 5/11 PIRSF_domain:PIRSF015614,PROSITE_profiles:PS50145,hmmpanther:PTHR10131,hmmpanther:PTHR10131:SF21 0,1 LOW 1 SNV 1 0,1 1 PASS rs533013634 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 136908117 136908117 G T 1 0 0 0 0 0 0 0 1 16921 1132 40 1 1 TRAF2 9 136908117 Silent SNP G C3N-00704_T 1994510 136908117 1486600 345 19482 AKR1C2 0 . GRCh38 10 5003806 5003806 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.30G>T p.= p.L10L ENST00000380753 1/9 239 208 31 240 240 0 varscan-mutect AKR1C2,synonymous_variant,p.=,ENST00000380753,NM_205845.2,NM_001354.5;AKR1C2,synonymous_variant,p.=,ENST00000421196,;AKR1C2,synonymous_variant,p.=,ENST00000455190,NM_001135241.2;AKR1C2,synonymous_variant,p.=,ENST00000604507,;U8,upstream_gene_variant,,ENST00000459141,;AKR1C2,non_coding_transcript_exon_variant,,ENST00000604184,;AKR1C2,downstream_gene_variant,,ENST00000604428,;AKR1C2,downstream_gene_variant,,ENST00000604711,;AKR1C2,non_coding_transcript_exon_variant,,ENST00000460124,; A ENST00000380753 Transcript synonymous_variant 218/3756 30/972 10/323 L ctG/ctT 1 -1 AKR1C2 HGNC HGNC:385 protein_coding YES CCDS7062.1 ENSP00000370129 P52895 UPI0000111D9F NM_205845.2,NM_001354.5 1/9 hmmpanther:PTHR11732:SF153,hmmpanther:PTHR11732,PIRSF_domain:PIRSF000097,Gene3D:3.20.20.100,Superfamily_domains:SSF51430 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 5003806 5003806 C A 1 0 0 0 0 0 0 0 1 554 813 29 2 2 AKR1C2 10 5003806 Silent SNP C C3N-00704_T 5003806 128793616 346 19483 CREM 0 . GRCh38 10 35188347 35188347 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.557C>G p.Thr186Arg p.T186R ENST00000345491 6/8 178 145 33 160 159 1 strelka-varscan-mutect CREM,missense_variant,p.Thr186Arg,ENST00000345491,NM_181571.2;CREM,missense_variant,p.Thr156Arg,ENST00000361599,NM_182771.1,NM_182772.1;CREM,missense_variant,p.Thr131Arg,ENST00000342105,NM_182770.2,NM_182769.2;CREM,missense_variant,p.Thr219Arg,ENST00000429130,;CREM,missense_variant,p.Thr24Arg,ENST00000463314,NM_001267567.1;CREM,missense_variant,p.Thr186Arg,ENST00000479070,;CREM,missense_variant,p.Thr186Arg,ENST00000337656,NM_183011.1;CREM,missense_variant,p.Thr156Arg,ENST00000395887,NM_001267564.1;CREM,missense_variant,p.Thr65Arg,ENST00000494479,;CREM,missense_variant,p.Thr65Arg,ENST00000495301,;CREM,intron_variant,,ENST00000439705,;CREM,intron_variant,,ENST00000374721,;CREM,intron_variant,,ENST00000374728,NM_183060.2;CREM,intron_variant,,ENST00000348787,;CREM,intron_variant,,ENST00000354759,NM_183013.2;CREM,intron_variant,,ENST00000460270,;CREM,intron_variant,,ENST00000474362,;CREM,intron_variant,,ENST00000374734,NM_183012.1;CREM,intron_variant,,ENST00000484283,;CREM,intron_variant,,ENST00000487132,;CREM,intron_variant,,ENST00000463960,;CREM,downstream_gene_variant,,ENST00000427847,;CREM,non_coding_transcript_exon_variant,,ENST00000374711,;CREM,intron_variant,,ENST00000461968,;CREM,intron_variant,,ENST00000466251,;CREM,3_prime_UTR_variant,,ENST00000495960,;CREM,intron_variant,,ENST00000490460,;CREM,intron_variant,,ENST00000464475,; G ENST00000345491 Transcript missense_variant 719/2220 557/903 186/300 T/R aCa/aGa 1 1 CREM HGNC HGNC:2352 protein_coding YES CCDS7180.1 ENSP00000265372 Q03060 UPI00001BDF4F NM_181571.2 tolerated(0.07) 6/8 hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF97 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 35188347 35188347 C G 1 0 0 0 0 1 0 0 0 3669 478 17 4 4 CREM 10 35188347 Missense_Mutation SNP C C3N-00704_T 30184541 35188347 98609075 347 19484 ZNF248 0 . GRCh38 10 37833086 37833086 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.269A>T p.Glu90Val p.E90V ENST00000395867 6/6 48 37 11 93 93 0 strelka-varscan-mutect ZNF248,missense_variant,p.Glu90Val,ENST00000395867,NM_021045.2;ZNF248,missense_variant,p.Glu90Val,ENST00000357328,NM_001267597.1;ZNF248,missense_variant,p.Glu90Val,ENST00000611278,NM_001267605.1,NM_001267606.1;ZNF248,missense_variant,p.Glu90Val,ENST00000374648,;ZNF248,missense_variant,p.Glu90Val,ENST00000395873,;AL135791.1,missense_variant,p.Glu90Val,ENST00000615949,NM_001267607.1;ZNF248,downstream_gene_variant,,ENST00000395874,;ZNF248,non_coding_transcript_exon_variant,,ENST00000494133,;ZNF248,missense_variant,p.Glu90Val,ENST00000485560,; A ENST00000395867 Transcript missense_variant 820/5141 269/1740 90/579 E/V gAg/gTg 1 -1 ZNF248 HGNC HGNC:13041 protein_coding YES CCDS7194.1 ENSP00000379208 Q8NDW4 A2RUI7 UPI000006CF12 NM_021045.2 deleterious(0.03) 6/6 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF68 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 37833086 37833086 T A 1 0 0 0 0 1 0 0 0 18369 1551 54 4 4 ZNF248 10 37833086 Missense_Mutation SNP T C3N-00704_T 2644739 37833086 95964336 348 19485 ZNF33B 0 . GRCh38 10 42592886 42592886 + Silent SNP C C A rs149979023 C3N-00704_T C3N-00704_N C C c.2064G>T p.= p.T688T ENST00000359467 5/5 272 233 39 348 348 0 strelka-varscan-mutect ZNF33B,synonymous_variant,p.=,ENST00000359467,NM_001305036.1,NM_001305033.1,NM_006955.1;ZNF33B,synonymous_variant,p.=,ENST00000613419,;ZNF33B,intron_variant,,ENST00000465206,;ZNF33B,intron_variant,,ENST00000462075,;ZNF33B,intron_variant,,ENST00000486187,; A ENST00000359467 Transcript synonymous_variant 2179/5958 2064/2337 688/778 T acG/acT rs149979023,COSM684341 1 -1 ZNF33B HGNC HGNC:13097 protein_coding YES CCDS7198.1 ENSP00000352444 Q06732 UPI000007257B NM_001305036.1,NM_001305033.1,NM_006955.1 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF204,Superfamily_domains:SSF57667 0,1 LOW 1 SNV 1 0,1 1 PASS rs149979023 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 42592886 42592886 C A 1 0 0 0 0 0 0 0 1 18427 639 23 1 1 ZNF33B 10 42592886 Silent SNP C C3N-00704_T 4759800 42592886 91204536 349 19486 ANTXRL 0 . GRCh38 10 46287287 46287287 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.25C>A p.Pro9Thr p.P9T ENST00000620264 1/17 174 143 31 197 197 0 strelka-varscan-mutect ANTXRL,missense_variant,p.Pro9Thr,ENST00000620264,NM_001278688.2;ANTXRL,missense_variant,p.Pro9Thr,ENST00000622632,;ANTXRL,intron_variant,,ENST00000619553,;ANTXRL,intron_variant,,ENST00000617088,; A ENST00000620264 Transcript missense_variant 290/2206 25/1896 9/631 P/T Ccc/Acc 1 1 ANTXRL HGNC HGNC:27277 protein_coding YES CCDS60524.1 ENSP00000480615 A6NF34 UPI00015B6A6A NM_001278688.2 deleterious_low_confidence(0) 1/17 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR16059,hmmpanther:PTHR16059:SF10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 46287287 46287287 C A 1 0 0 0 0 1 0 0 0 820 739 26 2 2 ANTXRL 10 46287287 Missense_Mutation SNP C C3N-00704_T 3694401 46287287 87510135 350 19487 RBP3 0 . GRCh38 10 47353493 47353493 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.3223G>A p.Asp1075Asn p.D1075N ENST00000584701 2/4 322 274 48 406 406 0 strelka-varscan-mutect RBP3,missense_variant,p.Asp1075Asn,ENST00000584701,NM_002900.2; A ENST00000584701 Transcript missense_variant 3337/4276 3223/3744 1075/1247 D/N Gat/Aat 1 1 RBP3 HGNC HGNC:9921 protein_coding YES CCDS73119.1 ENSP00000463151 P10745 UPI000012D87A NM_002900.2 tolerated(0.15) 2/4 Gene3D:3.90.226.10,Pfam_domain:PF03572,hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF3,SMART_domains:SM00245,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 47353493 47353493 G A 1 0 0 0 0 1 0 0 0 13325 1174 41 3 3 RBP3 10 47353493 Missense_Mutation SNP G C3N-00704_T 1066206 47353493 86443929 351 19488 WDFY4 0 . GRCh38 10 48830737 48830737 + Nonsense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.6378G>A p.Trp2126Ter p.W2126* ENST00000325239 37/61 147 130 17 157 157 0 strelka-varscan-mutect WDFY4,stop_gained,p.Trp2126Ter,ENST00000325239,NM_020945.1;WDFY4,stop_gained,p.Trp213Ter,ENST00000265453,; A ENST00000325239 Transcript stop_gained 6378/9555 6378/9555 2126/3184 W/* tgG/tgA 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 37/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 HIGH 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 48830737 48830737 G A 1 0 0 0 0 0 1 0 0 17831 1212 42 3 3 WDFY4 10 48830737 Nonsense_Mutation SNP G C3N-00704_T 1477244 48830737 84966685 352 19489 ERCC6 0 . GRCh38 10 49532735 49532735 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.230G>T p.Arg77Leu p.R77L ENST00000355832 2/21 267 224 43 345 345 0 strelka-varscan-mutect ERCC6,missense_variant,p.Arg77Leu,ENST00000355832,NM_000124.3;ERCC6,missense_variant,p.Arg77Leu,ENST00000515869,NM_001277059.1;ERCC6,missense_variant,p.Arg77Leu,ENST00000447839,NM_001277058.1;ERCC6,missense_variant,p.Arg77Leu,ENST00000462247,;ERCC6,upstream_gene_variant,,ENST00000479652,; A ENST00000355832 Transcript missense_variant 309/8008 230/4482 77/1493 R/L cGa/cTa 1 -1 ERCC6 HGNC HGNC:3438 protein_coding YES CCDS7229.1 ENSP00000348089 Q03468 UPI000000D8DA NM_000124.3 deleterious(0) 2/21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 49532735 49532735 C A 1 0 0 0 0 1 0 0 0 5066 884 31 1 1 ERCC6 10 49532735 Missense_Mutation SNP C C3N-00704_T 701998 49532735 84264687 353 19490 OGDHL 0 . GRCh38 10 49756812 49756812 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.339C>A p.Asp113Glu p.D113E ENST00000374103 3/23 103 86 17 105 105 0 strelka-varscan-mutect OGDHL,missense_variant,p.Asp113Glu,ENST00000374103,NM_018245.2;OGDHL,intron_variant,,ENST00000419399,NM_001143996.1;OGDHL,intron_variant,,ENST00000432695,NM_001143997.1;OGDHL,non_coding_transcript_exon_variant,,ENST00000471460,; T ENST00000374103 Transcript missense_variant 425/3704 339/3033 113/1010 D/E gaC/gaA 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 tolerated(0.16) 3/23 PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 49756812 49756812 G T 1 0 0 0 0 1 0 0 0 10914 1252 44 2 2 OGDHL 10 49756812 Missense_Mutation SNP G C3N-00704_T 224077 49756812 84040610 354 19491 IPMK 0 . GRCh38 10 58196659 58196659 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.668A>T p.Lys223Ile p.K223I ENST00000373935 6/6 51 37 14 109 109 0 strelka-varscan-mutect IPMK,missense_variant,p.Lys223Ile,ENST00000373935,NM_152230.4; A ENST00000373935 Transcript missense_variant 991/6133 668/1251 223/416 K/I aAa/aTa 1 -1 IPMK HGNC HGNC:20739 protein_coding YES CCDS7250.1 ENSP00000363046 Q8NFU5 UPI000006FB8E NM_152230.4 deleterious(0.01) 6/6 hmmpanther:PTHR12400:SF51,hmmpanther:PTHR12400,Pfam_domain:PF03770,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 58196659 58196659 T A 1 0 0 0 0 1 0 0 0 7695 1841 64 4 4 IPMK 10 58196659 Missense_Mutation SNP T C3N-00704_T 8439847 58196659 75600763 355 19492 FAM13C 0 . GRCh38 10 59352473 59352473 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.121G>A p.Asp41Asn p.D41N ENST00000618804 3/14 166 137 29 199 199 0 varscan-mutect FAM13C,missense_variant,p.Asp41Asn,ENST00000621119,;FAM13C,missense_variant,p.Asp41Asn,ENST00000614220,;FAM13C,missense_variant,p.Asp41Asn,ENST00000618804,NM_198215.3;FAM13C,missense_variant,p.Asp41Asn,ENST00000611933,NM_001001971.2;FAM13C,missense_variant,p.Asp41Asn,ENST00000435852,;FAM13C,missense_variant,p.Asp41Asn,ENST00000422313,;FAM13C,splice_region_variant,,ENST00000618427,NM_001166698.1;FAM13C,splice_region_variant,,ENST00000468840,NM_001143773.1;FAM13C,splice_region_variant,,ENST00000503444,;FAM13C,splice_region_variant,,ENST00000512919,;FAM13C,splice_region_variant,,ENST00000470220,;FAM13C,upstream_gene_variant,,ENST00000507862,;FAM13C,splice_region_variant,,ENST00000622363,;FAM13C,splice_region_variant,,ENST00000619059,; T ENST00000618804 Transcript missense_variant,splice_region_variant 211/3333 121/1758 41/585 D/N Gat/Aat 1 -1 FAM13C HGNC HGNC:19371 protein_coding YES CCDS7255.1 ENSP00000481854 Q8NE31 UPI00001AEA18 NM_198215.3 deleterious_low_confidence(0) 3/14 hmmpanther:PTHR15904:SF19,hmmpanther:PTHR15904 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 59352473 59352473 C T 1 0 0 0 0 1 0 0 0 5303 927 32 3 3 FAM13C 10 59352473 Missense_Mutation SNP C C3N-00704_T 1155814 59352473 74444949 356 19493 CDH23 0 . GRCh38 10 71740927 71740927 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.4609G>T p.Gly1537Ter p.G1537* ENST00000224721 37/70 252 205 47 273 272 1 strelka-varscan-mutect CDH23,stop_gained,p.Gly1537Ter,ENST00000224721,NM_022124.5;CDH23,stop_gained,p.Gly1532Ter,ENST00000622827,;C10orf105,upstream_gene_variant,,ENST00000398786,NM_001168390.1;CDH23,non_coding_transcript_exon_variant,,ENST00000398792,; T ENST00000224721 Transcript stop_gained 4999/11139 4609/10080 1537/3359 G/* Gga/Tga 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 37/70 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,Superfamily_domains:SSF49313 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 71740927 71740927 G T 1 0 0 0 0 0 1 0 0 2811 1349 47 2 2 CDH23 10 71740927 Nonsense_Mutation SNP G C3N-00704_T 12388454 71740927 62056495 357 19494 SFTPD 0 . GRCh38 10 79938077 79938077 + Silent SNP T T C novel C3N-00704_T C3N-00704_N T T c.903A>G p.= p.Q301Q ENST00000372292 8/8 242 196 46 311 311 0 strelka-varscan-mutect SFTPD,synonymous_variant,p.=,ENST00000372292,NM_003019.4;SFTPD,downstream_gene_variant,,ENST00000444384,;MBL1P,intron_variant,,ENST00000421889,; C ENST00000372292 Transcript synonymous_variant 944/1281 903/1128 301/375 Q caA/caG 1 -1 SFTPD HGNC HGNC:10803 protein_coding YES CCDS7362.1 ENSP00000361366 P35247 UPI000013CEE7 NM_003019.4 8/8 PROSITE_profiles:PS50041,hmmpanther:PTHR24024:SF15,hmmpanther:PTHR24024,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 62 79938077 79938077 T C 1 0 0 0 0 0 0 0 1 14453 1722 60 5 5 SFTPD 10 79938077 Silent SNP T C3N-00704_T 8197150 79938077 53859345 358 19495 GRID1 0 . GRCh38 10 85647284 85647284 + Missense_Mutation SNP G G T rs771133372 C3N-00704_T C3N-00704_N G G c.2111C>A p.Thr704Lys p.T704K ENST00000327946 13/16 240 209 31 318 318 0 strelka-varscan-mutect GRID1,missense_variant,p.Thr704Lys,ENST00000327946,NM_017551.2;RP11-93H12.4,non_coding_transcript_exon_variant,,ENST00000474115,;RN7SKP238,downstream_gene_variant,,ENST00000516483,;GRID1,missense_variant,p.Thr704Lys,ENST00000464741,; T ENST00000327946 Transcript missense_variant 2197/5834 2111/3030 704/1009 T/K aCg/aAg rs771133372 1 -1 GRID1 HGNC HGNC:4575 protein_coding YES CCDS31236.1 ENSP00000330148 Q9ULK0 UPI00001D8051 NM_017551.2 deleterious(0.03) 13/16 Gene3D:1.10.287.70,Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 2 1 PASS rs771133372 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 85647284 85647284 G T 1 0 0 0 0 1 0 0 0 6651 1145 40 1 1 GRID1 10 85647284 Missense_Mutation SNP G C3N-00704_T 5709207 85647284 48150138 359 19496 PPP1R3C 0 . GRCh38 10 91630640 91630640 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.241G>T p.Ala81Ser p.A81S ENST00000238994 2/2 108 92 16 161 159 2 strelka-varscan-mutect PPP1R3C,missense_variant,p.Ala81Ser,ENST00000238994,NM_005398.5; A ENST00000238994 Transcript missense_variant 326/2524 241/954 81/317 A/S Gcc/Tcc 1 -1 PPP1R3C HGNC HGNC:9293 protein_coding YES CCDS7416.1 ENSP00000238994 Q9UQK1 UPI000006EFF1 NM_005398.5 tolerated(0.38) 2/2 PIRSF_domain:PIRSF038207,PIRSF_domain:PIRSF500813,hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF15 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 91630640 91630640 C A 1 0 0 0 0 1 0 0 0 12494 797 28 2 2 PPP1R3C 10 91630640 Missense_Mutation SNP C C3N-00704_T 5983356 91630640 42166782 360 19497 PLCE1 0 . GRCh38 10 94132433 94132433 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1466G>T p.Gly489Val p.G489V ENST00000371380 2/32 282 250 32 334 334 0 strelka-varscan-mutect PLCE1,missense_variant,p.Gly489Val,ENST00000371380,NM_016341.3,NM_001288989.1;PLCE1,missense_variant,p.Gly181Val,ENST00000371375,;PLCE1,missense_variant,p.Gly181Val,ENST00000371385,NM_001165979.2; T ENST00000371380 Transcript missense_variant 1701/12024 1466/6909 489/2302 G/V gGa/gTa 1 1 PLCE1 HGNC HGNC:17175 protein_coding YES CCDS41552.1 ENSP00000360431 Q9P212 UPI00001F93EE NM_016341.3,NM_001288989.1 deleterious_low_confidence(0) 2/32 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs951540403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 94132433 94132433 G T 1 0 0 0 0 1 0 0 0 12128 1174 41 2 2 PLCE1 10 94132433 Missense_Mutation SNP G C3N-00704_T 2501793 94132433 39664989 361 19498 TLL2 0 . GRCh38 10 96446151 96446151 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.304G>T p.Ala102Ser p.A102S ENST00000357947 3/21 215 187 28 252 252 0 strelka-varscan-mutect TLL2,missense_variant,p.Ala102Ser,ENST00000357947,NM_012465.3;TLL2,non_coding_transcript_exon_variant,,ENST00000469598,; A ENST00000357947 Transcript missense_variant 530/6756 304/3048 102/1015 A/S Gca/Tca 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 tolerated(0.82) 3/21 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF638,PIRSF_domain:PIRSF001199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 96446151 96446151 C A 1 0 0 0 0 1 0 0 0 16392 739 26 2 2 TLL2 10 96446151 Missense_Mutation SNP C C3N-00704_T 2313718 96446151 37351271 362 19499 SORCS3 0 . GRCh38 10 105200117 105200117 + Splice_Site SNP G G T rs760373074 C3N-00704_T C3N-00704_N G G c.2127+1G>T p.X709_splice ENST00000369701 129 110 19 134 134 0 strelka-varscan-mutect SORCS3,splice_donor_variant,,ENST00000369701,NM_014978.2;SORCS3,splice_donor_variant,,ENST00000369699,;SORCS3,intron_variant,,ENST00000393176,; T ENST00000369701 Transcript splice_donor_variant -/5757 2127/3669 709/1222 rs760373074 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 15/26 HIGH 1 SNV 1 1 PASS rs760373074 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 62 105200117 105200117 G T 1 0 0 0 0 0 0 1 0 15254 1275 44 2 2 SORCS3 10 105200117 Splice_Site SNP G C3N-00704_T 8753966 105200117 28597305 363 19500 SORCS3 0 . GRCh38 10 105247217 105247217 + Splice_Site SNP A A T C3N-00704_T C3N-00704_N A A c.2993-2A>T p.X998_splice ENST00000369701 49 42 7 65 65 0 strelka-mutect SORCS3,splice_acceptor_variant,,ENST00000369701,NM_014978.2;SORCS3,splice_acceptor_variant,,ENST00000369699,; T ENST00000369701 Transcript splice_acceptor_variant -/5757 2993/3669 998/1222 COSM5370054,COSM5575182 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 21/26 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -17.13085 1 1 1 1 0 T 5 4 62 105247217 105247217 A T 1 0 0 0 0 0 0 1 0 15254 202 7 4 4 SORCS3 10 105247217 Splice_Site SNP A C3N-00704_T 47100 105247217 28550205 364 19501 SORCS3 0 . GRCh38 10 105247253 105247253 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.3027T>A p.= p.P1009P ENST00000369701 22/27 89 74 15 113 113 0 strelka-varscan-mutect SORCS3,synonymous_variant,p.=,ENST00000369701,NM_014978.2;SORCS3,synonymous_variant,p.=,ENST00000369699,; A ENST00000369701 Transcript synonymous_variant 3254/5757 3027/3669 1009/1222 P ccT/ccA 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 22/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 105247253 105247253 T A 1 0 0 0 0 0 0 0 1 15254 1509 53 4 4 SORCS3 10 105247253 Silent SNP T C3N-00704_T 36 105247253 28550169 365 19502 RBM20 0 . GRCh38 10 110781235 110781235 + Missense_Mutation SNP A A C C3N-00704_T C3N-00704_N A A c.626A>C p.Gln209Pro p.Q209P ENST00000369519 2/14 289 245 44 361 361 0 strelka-varscan-mutect RBM20,missense_variant,p.Gln209Pro,ENST00000369519,NM_001134363.2; C ENST00000369519 Transcript missense_variant 684/7233 626/3684 209/1227 Q/P cAg/cCg COSM4807509 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 deleterious(0) 2/14 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 110781235 110781235 A C 1 0 0 0 0 1 0 0 0 13287 188 7 5 5 RBM20 10 110781235 Missense_Mutation SNP A C3N-00704_T 5533982 110781235 23016187 366 19503 PNLIPRP1 0 . GRCh38 10 116591794 116591794 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.73C>A p.Leu25Ile p.L25I ENST00000528052 3/13 152 128 24 165 165 0 strelka-varscan-mutect PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000528052,NM_001303135.1;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000358834,NM_006229.3;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000534537,;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000531984,;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000530319,;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000527980,;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000471549,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000480870,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525157,;PNLIPRP1,upstream_gene_variant,,ENST00000510125,;PNLIPRP1,missense_variant,p.Leu25Ile,ENST00000497792,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000482159,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000484402,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000529584,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000530626,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000470678,;PNLIPRP1,upstream_gene_variant,,ENST00000482833,; A ENST00000528052 Transcript missense_variant 144/1533 73/1404 25/467 L/I Ctc/Atc 1 1 PNLIPRP1 HGNC HGNC:9156 protein_coding YES CCDS7595.1 ENSP00000433933 P54315 UPI000012E6AA NM_001303135.1 tolerated(0.13) 3/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Prints_domain:PR00823,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF108,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 116591794 116591794 C A 1 0 0 0 0 1 0 0 0 12258 681 24 2 2 PNLIPRP1 10 116591794 Missense_Mutation SNP C C3N-00704_T 5810559 116591794 17205628 367 19504 TACC2 0 . GRCh38 10 122227998 122227998 + Missense_Mutation SNP C C A rs150511831 C3N-00704_T C3N-00704_N C C c.7886C>A p.Ala2629Glu p.A2629E ENST00000369005 14/23 104 84 20 131 131 0 strelka-varscan-mutect TACC2,missense_variant,p.Ala2629Glu,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Ala2629Glu,ENST00000334433,;TACC2,missense_variant,p.Ala2633Glu,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Ala2633Glu,ENST00000453444,;TACC2,missense_variant,p.Ala2584Glu,ENST00000515603,NM_001291876.1;TACC2,missense_variant,p.Ala775Glu,ENST00000513429,NM_206861.2;TACC2,missense_variant,p.Ala707Glu,ENST00000360561,NM_206860.2;TACC2,missense_variant,p.Ala719Glu,ENST00000368999,;TACC2,missense_variant,p.Ala775Glu,ENST00000358010,;TACC2,missense_variant,p.Ala329Glu,ENST00000369000,;TACC2,missense_variant,p.Ala333Glu,ENST00000369001,NM_001291879.1;TACC2,missense_variant,p.Ala719Glu,ENST00000369004,NM_001291878.1;TACC2,missense_variant,p.Ala707Glu,ENST00000260733,NM_006997.3;TACC2,missense_variant,p.Ala364Glu,ENST00000496913,;TACC2,downstream_gene_variant,,ENST00000514539,;TACC2,downstream_gene_variant,,ENST00000508411,;TACC2,non_coding_transcript_exon_variant,,ENST00000368997,;TACC2,downstream_gene_variant,,ENST00000440764,; A ENST00000369005 Transcript missense_variant 8226/9673 7886/8847 2629/2948 A/E gCg/gAg rs150511831 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious(0.01) 14/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS rs150511831 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 122227998 122227998 C A 1 0 0 0 0 1 0 0 0 15898 768 27 1 1 TACC2 10 122227998 Missense_Mutation SNP C C3N-00704_T 5636204 122227998 11569424 368 19505 CTBP2 0 . GRCh38 10 125026750 125026750 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.1010G>A p.Gly337Asp p.G337D ENST00000309035 1/9 227 183 44 331 331 0 strelka-varscan-mutect CTBP2,missense_variant,p.Gly337Asp,ENST00000309035,NM_022802.2;CTBP2,intron_variant,,ENST00000337195,NM_001329.2;CTBP2,intron_variant,,ENST00000411419,NM_001083914.1;CTBP2,intron_variant,,ENST00000494626,NM_001290214.1;CTBP2,intron_variant,,ENST00000531469,NM_001290215.1;CTBP2,intron_variant,,ENST00000460976,;CTBP2,intron_variant,,ENST00000493552,; T ENST00000309035 Transcript missense_variant 1141/3669 1010/2958 337/985 G/D gGc/gAc 1 -1 CTBP2 HGNC HGNC:2495 protein_coding YES CCDS7644.1 ENSP00000311825 P56545 UPI000013EE11 NM_022802.2 deleterious_low_confidence(0) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 125026750 125026750 C T 1 0 0 0 0 1 0 0 0 3804 739 26 3 3 CTBP2 10 125026750 Missense_Mutation SNP C C3N-00704_T 2798752 125026750 8770672 369 19506 TCERG1L 0 . GRCh38 10 131134424 131134424 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1214C>A p.Ser405Tyr p.S405Y ENST00000368642 8/12 211 176 35 260 260 0 strelka-varscan-mutect TCERG1L,missense_variant,p.Ser405Tyr,ENST00000368642,NM_174937.3;TCERG1L,non_coding_transcript_exon_variant,,ENST00000483040,; T ENST00000368642 Transcript missense_variant 1300/2618 1214/1761 405/586 S/Y tCt/tAt 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 deleterious(0.01) 8/12 hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 131134424 131134424 G T 1 0 0 0 0 1 0 0 0 16093 942 33 2 2 TCERG1L 10 131134424 Missense_Mutation SNP G C3N-00704_T 6107674 131134424 2662998 370 19507 ADGRA1 0 . GRCh38 10 133129304 133129304 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.1476C>A p.= p.A492A ENST00000392607 7/7 155 130 25 203 203 0 strelka-varscan-mutect ADGRA1,synonymous_variant,p.=,ENST00000607359,;ADGRA1,synonymous_variant,p.=,ENST00000392607,NM_001083909.2;ADGRA1,synonymous_variant,p.=,ENST00000392606,NM_001291085.1; A ENST00000392607 Transcript synonymous_variant 1912/4283 1476/1683 492/560 A gcC/gcA 1 1 ADGRA1 HGNC HGNC:13838 protein_coding YES CCDS41580.1 ENSP00000376384 Q86SQ6 UPI00003D41AD NM_001083909.2 7/7 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 133129304 133129304 C A 1 0 0 0 0 0 0 0 1 352 610 22 2 2 ADGRA1 10 133129304 Silent SNP C C3N-00704_T 1994880 133129304 668118 371 19508 CYP2E1 0 . GRCh38 10 133527509 133527509 + Silent SNP G G T rs137875795 C3N-00704_T C3N-00704_N G G c.114G>T p.= p.P38P ENST00000463117 3/11 135 124 11 155 155 0 strelka-varscan-mutect CYP2E1,missense_variant,p.Ala5Ser,ENST00000421586,;CYP2E1,missense_variant,p.Ala5Ser,ENST00000418356,;CYP2E1,synonymous_variant,p.=,ENST00000463117,;CYP2E1,synonymous_variant,p.=,ENST00000252945,NM_000773.3;CYP2E1,synonymous_variant,p.=,ENST00000541261,;RP11-108K14.12,non_coding_transcript_exon_variant,,ENST00000622716,;CYP2E1,non_coding_transcript_exon_variant,,ENST00000477500,;CYP2E1,upstream_gene_variant,,ENST00000480558,;CYP2E1,synonymous_variant,p.=,ENST00000541080,;CYP2E1,upstream_gene_variant,,ENST00000368520,;SCART1,downstream_gene_variant,,ENST00000488261,; T ENST00000463117 Transcript synonymous_variant 386/1912 114/1482 38/493 P ccG/ccT rs137875795 1 1 CYP2E1 HGNC HGNC:2631 protein_coding YES CCDS7686.1 ENSP00000440689 P05181 UPI0000128291 3/11 Low_complexity_(Seg):seg,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF19,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 5 1 PASS rs137875795 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 133527509 133527509 G T 1 0 0 0 0 0 0 0 1 3973 1074 38 1 1 CYP2E1 10 133527509 Silent SNP G C3N-00704_T 398205 133527509 269913 372 19509 RIC8A 0 . GRCh38 11 212685 212685 + Missense_Mutation SNP G G T rs367798950 C3N-00704_T C3N-00704_N G G c.1154G>T p.Arg385Leu p.R385L ENST00000325207 7/10 326 274 52 378 378 0 strelka-varscan-mutect RIC8A,missense_variant,p.Arg379Leu,ENST00000526104,NM_001286134.1;RIC8A,missense_variant,p.Arg385Leu,ENST00000325207,NM_021932.5;RIC8A,missense_variant,p.Arg373Leu,ENST00000527696,;RIC8A,missense_variant,p.Arg274Leu,ENST00000527728,;SIRT3,downstream_gene_variant,,ENST00000382743,NM_012239.5;SIRT3,downstream_gene_variant,,ENST00000525319,;SIRT3,downstream_gene_variant,,ENST00000524564,;SIRT3,downstream_gene_variant,,ENST00000532956,;SIRT3,downstream_gene_variant,,ENST00000529382,NM_001017524.2;RIC8A,upstream_gene_variant,,ENST00000524854,;RIC8A,downstream_gene_variant,,ENST00000527468,;RIC8A,downstream_gene_variant,,ENST00000530889,;RIC8A,downstream_gene_variant,,ENST00000528357,;RIC8A,upstream_gene_variant,,ENST00000529275,;RIC8A,downstream_gene_variant,,ENST00000626818,;RIC8A,downstream_gene_variant,,ENST00000611346,;RIC8A,upstream_gene_variant,,ENST00000531541,;RIC8A,non_coding_transcript_exon_variant,,ENST00000530149,;RIC8A,non_coding_transcript_exon_variant,,ENST00000532241,;SIRT3,downstream_gene_variant,,ENST00000529937,;SIRT3,downstream_gene_variant,,ENST00000532837,;RIC8A,downstream_gene_variant,,ENST00000526982,;RIC8A,downstream_gene_variant,,ENST00000527039,;RIC8A,upstream_gene_variant,,ENST00000526557,;RIC8A,downstream_gene_variant,,ENST00000532373,; T ENST00000325207 Transcript missense_variant 1479/2702 1154/1614 385/537 R/L cGc/cTc rs367798950,COSM2112354 1 1 RIC8A HGNC HGNC:29550 protein_coding YES CCDS7690.1 ENSP00000325941 Q9NPQ8 UPI0000037C19 NM_021932.5 deleterious(0) 7/10 hmmpanther:PTHR12425:SF4,hmmpanther:PTHR12425,Gene3D:1.25.10.10,Pfam_domain:PF10165,Superfamily_domains:SSF48371,Prints_domain:PR01802 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367798950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 212685 212685 G T 1 0 0 0 0 1 0 0 0 13529 1087 38 1 1 RIC8A 11 212685 Missense_Mutation SNP G C3N-00704_T 212685 134873937 373 19510 PHRF1 0 . GRCh38 11 606497 606497 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1510G>T p.Asp504Tyr p.D504Y ENST00000264555 13/18 169 141 28 228 228 0 strelka-varscan-mutect PHRF1,missense_variant,p.Asp504Tyr,ENST00000264555,NM_001286581.1;PHRF1,missense_variant,p.Asp503Tyr,ENST00000416188,NM_020901.3;PHRF1,missense_variant,p.Asp502Tyr,ENST00000413872,NM_001286582.1;PHRF1,missense_variant,p.Asp500Tyr,ENST00000533464,NM_001286583.1;PHRF1,missense_variant,p.Asp504Tyr,ENST00000534320,;PHRF1,non_coding_transcript_exon_variant,,ENST00000532550,; T ENST00000264555 Transcript missense_variant 1638/5523 1510/4950 504/1649 D/Y Gac/Tac 1 1 PHRF1 HGNC HGNC:24351 protein_coding YES CCDS65988.1 ENSP00000264555 Q9P1Y6 A0A024RCA1 UPI000041A715 NM_001286581.1 deleterious(0) 13/18 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 606497 606497 G T 1 0 0 0 0 1 0 0 0 11949 1290 45 2 2 PHRF1 11 606497 Missense_Mutation SNP G C3N-00704_T 393812 606497 134480125 374 19511 MRGPRE 0 . GRCh38 11 3228224 3228224 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.576G>T p.Met192Ile p.M192I ENST00000389832 2/2 81 69 12 140 140 0 strelka-mutect MRGPRE,missense_variant,p.Met192Ile,ENST00000389832,NM_001039165.2;AC109309.4,intron_variant,,ENST00000418995,; A ENST00000389832 Transcript missense_variant 883/1409 576/939 192/312 M/I atG/atT 1 -1 MRGPRE HGNC HGNC:30694 protein_coding YES CCDS41603.2 ENSP00000374482 Q86SM8 W4VSQ4 UPI000015F138 NM_001039165.2 deleterious(0.04) 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF26,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR02111 MODERATE 1 SNV 2 1 PASS rs957686838 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 3228224 3228224 C A 1 0 0 0 0 1 0 0 0 9730 478 17 2 2 MRGPRE 11 3228224 Missense_Mutation SNP C C3N-00704_T 2621727 3228224 131858398 375 19512 OR52J3 0 . GRCh38 11 5047405 5047405 + Missense_Mutation SNP G G T rs377359439 C3N-00704_T C3N-00704_N G G c.880G>T p.Gly294Trp p.G294W ENST00000380370 1/1 91 76 15 123 123 0 strelka-varscan-mutect OR52J3,missense_variant,p.Gly294Trp,ENST00000380370,NM_001001916.2; T ENST00000380370 Transcript missense_variant 880/936 880/936 294/311 G/W Ggg/Tgg rs377359439 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs377359439 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 5047405 5047405 G T 1 0 0 0 0 1 0 0 0 11195 1348 47 2 2 OR52J3 11 5047405 Missense_Mutation SNP G C3N-00704_T 1819181 5047405 130039217 376 19513 HBB 0 . GRCh38 11 5225720 5225720 + Missense_Mutation SNP C C A rs35017910 C3N-00704_T C3N-00704_N C C c.322G>T p.Gly108Cys p.G108C ENST00000335295 3/3 475 406 69 614 613 1 strelka-varscan-mutect HBB,missense_variant,p.Gly108Cys,ENST00000335295,NM_000518.4;HBB,downstream_gene_variant,,ENST00000380315,;CoTC_ribozyme,upstream_gene_variant,,ENST00000408104,;HBB,3_prime_UTR_variant,,ENST00000633227,;HBB,non_coding_transcript_exon_variant,,ENST00000475226,;HBB,downstream_gene_variant,,ENST00000485743,; A ENST00000335295 Transcript missense_variant 372/628 322/444 108/147 G/C Ggc/Tgc rs35017910,HbVar.478 1 -1 HBB HGNC HGNC:4827 protein_coding YES CCDS7753.1 ENSP00000333994 P68871 D9YZU5 UPI00000015C9 NM_000518.4 deleterious(0.02) 3/3 Gene3D:1.10.490.10,Pfam_domain:PF00042,PROSITE_profiles:PS01033,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF50,Superfamily_domains:SSF46458 other 108833557997 MODERATE 1 SNV 1 1 PASS rs35017910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 5225720 5225720 C A 1 0 0 0 0 1 0 0 0 6864 623 22 2 2 HBB 11 5225720 Missense_Mutation SNP C C3N-00704_T 178315 5225720 129860902 377 19514 HBB 0 . GRCh38 11 5226935 5226935 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.87G>A p.= p.L29L ENST00000335295 1/3 546 456 90 644 644 0 strelka-varscan-mutect HBB,synonymous_variant,p.=,ENST00000335295,NM_000518.4;HBB,synonymous_variant,p.=,ENST00000380315,;CoTC_ribozyme,upstream_gene_variant,,ENST00000408104,;HBB,non_coding_transcript_exon_variant,,ENST00000485743,;HBB,intron_variant,,ENST00000633227,;HBB,upstream_gene_variant,,ENST00000475226,; T ENST00000335295 Transcript synonymous_variant 137/628 87/444 29/147 L ctG/ctA 1 -1 HBB HGNC HGNC:4827 protein_coding YES CCDS7753.1 ENSP00000333994 P68871 D9YZU5 UPI00000015C9 NM_000518.4 1/3 Gene3D:1.10.490.10,Pfam_domain:PF00042,PROSITE_profiles:PS01033,hmmpanther:PTHR11442,hmmpanther:PTHR11442:SF50,Superfamily_domains:SSF46458 LOW 1 SNV 1 1 PASS rs1191121382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 5226935 5226935 C T 1 0 0 0 0 0 0 0 1 6864 608 21 3 3 HBB 11 5226935 Silent SNP C C3N-00704_T 1215 5226935 129859687 378 19515 OR51B5 0 . GRCh38 11 5343147 5343147 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.378C>A p.Asn126Lys p.N126K ENST00000300773 1/1 91 82 9 144 144 0 strelka-mutect OR51B5,missense_variant,p.Asn126Lys,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300773 Transcript missense_variant 378/939 378/939 126/312 N/K aaC/aaA 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 tolerated(0.06) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 5343147 5343147 G T 1 0 0 0 0 1 0 0 0 11165 1252 44 2 2 OR51B5 11 5343147 Missense_Mutation SNP G C3N-00704_T 116212 5343147 129743475 379 19516 OR52N5 0 . GRCh38 11 5777911 5777911 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.724G>T p.Ala242Ser p.A242S ENST00000317093 1/1 149 107 42 179 179 0 strelka-varscan-mutect OR52N5,missense_variant,p.Ala242Ser,ENST00000317093,NM_001001922.2;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000317093 Transcript missense_variant 757/1034 724/975 242/324 A/S Gct/Tct 1 -1 OR52N5 HGNC HGNC:15231 protein_coding YES CCDS31397.1 ENSP00000322866 Q8NH56 A0A126GVK9 UPI0000041BF9 NM_001001922.2 deleterious(0.02) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF18,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 10 196 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 5777911 5777911 C A 1 0 0 0 0 1 0 0 0 11203 710 25 2 2 OR52N5 11 5777911 Missense_Mutation SNP C C3N-00704_T 434764 5777911 129308711 380 19517 ABCC8 0 . GRCh38 11 17428572 17428572 + Missense_Mutation SNP T T G novel C3N-00704_T C3N-00704_N T T c.1916A>C p.Gln639Pro p.Q639P ENST00000302539 13/39 160 133 27 192 192 0 strelka-varscan-mutect ABCC8,missense_variant,p.Gln639Pro,ENST00000302539,NM_001287174.1;ABCC8,missense_variant,p.Gln639Pro,ENST00000389817,NM_000352.4;ABCC8,downstream_gene_variant,,ENST00000528202,;ABCC8,missense_variant,p.Gln629Pro,ENST00000527905,;ABCC8,downstream_gene_variant,,ENST00000532728,;ABCC8,downstream_gene_variant,,ENST00000635881,;ABCC8,upstream_gene_variant,,ENST00000531911,;ABCC8,downstream_gene_variant,,ENST00000526002,; G ENST00000302539 Transcript missense_variant 1985/4923 1916/4749 639/1582 Q/P cAg/cCg 1 -1 ABCC8 HGNC HGNC:59 protein_coding YES CCDS73264.1 ENSP00000303960 Q09428 UPI00015DFF64 NM_001287174.1 tolerated(0.26) 13/39 Prints_domain:PR01093 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 17428572 17428572 T G 1 0 0 0 0 1 0 0 0 62 1580 55 5 5 ABCC8 11 17428572 Missense_Mutation SNP T C3N-00704_T 11650661 17428572 117658050 381 19518 KCNC1 0 . GRCh38 11 17736263 17736263 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.261C>A p.Tyr87Ter p.Y87* ENST00000265969 1/4 354 298 56 446 446 0 strelka-varscan-mutect KCNC1,stop_gained,p.Tyr87Ter,ENST00000379472,NM_004976.4;KCNC1,stop_gained,p.Tyr87Ter,ENST00000265969,NM_001112741.1; A ENST00000265969 Transcript stop_gained 1452/3887 261/1758 87/585 Y/* taC/taA 1 1 KCNC1 HGNC HGNC:6233 protein_coding YES CCDS44547.1 ENSP00000265969 P48547 UPI0000E2291F NM_001112741.1 1/4 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,Pfam_domain:PF02214,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 17736263 17736263 C A 1 0 0 0 0 0 1 0 0 7930 547 19 1 1 KCNC1 11 17736263 Nonsense_Mutation SNP C C3N-00704_T 307691 17736263 117350359 382 19519 NELL1 0 . GRCh38 11 21573316 21573316 + Missense_Mutation SNP C C G rs759298291 C3N-00704_T C3N-00704_N C C c.2373C>G p.Ile791Met p.I791M ENST00000298925 20/21 425 382 43 437 437 0 strelka-varscan-mutect NELL1,missense_variant,p.Ile791Met,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Ile706Met,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Ile763Met,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Ile716Met,ENST00000532434,NM_201551.2;NELL1,non_coding_transcript_exon_variant,,ENST00000529218,; G ENST00000298925 Transcript missense_variant 2526/3329 2373/2517 791/838 I/M atC/atG rs759298291 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 deleterious(0.02) 20/21 hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2 MODERATE 1 SNV 2 1 PASS rs759298291 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 21573316 21573316 C G 1 0 0 0 0 1 0 0 0 10364 816 29 4 4 NELL1 11 21573316 Missense_Mutation SNP C C3N-00704_T 3837053 21573316 113513306 383 19520 PAX6 0 . GRCh38 11 31801664 31801664 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.296G>T p.Ser99Ile p.S99I ENST00000419022 7/14 693 555 138 854 852 2 strelka-varscan-mutect PAX6,missense_variant,p.Ser99Ile,ENST00000419022,NM_001310158.1,NM_001310161.1,NM_001258462.1;PAX6,missense_variant,p.Ser99Ile,ENST00000606377,NM_001310161.1,NM_001258463.1;PAX6,missense_variant,p.Ser99Ile,ENST00000379129,;PAX6,missense_variant,p.Ser99Ile,ENST00000379107,;PAX6,missense_variant,p.Ser85Ile,ENST00000379132,NM_001127612.1;PAX6,missense_variant,p.Ser85Ile,ENST00000379123,NM_001258464.1,NM_000280.4;PAX6,missense_variant,p.Ser85Ile,ENST00000379109,;PAX6,missense_variant,p.Ser99Ile,ENST00000379115,NM_001604.5;PAX6,missense_variant,p.Ser85Ile,ENST00000241001,;PAX6,missense_variant,p.Ser85Ile,ENST00000379111,NM_001258465.1;PAX6,intron_variant,,ENST00000455099,;PAX6,downstream_gene_variant,,ENST00000525535,;PAX6,downstream_gene_variant,,ENST00000524853,;PAX6,downstream_gene_variant,,ENST00000423822,;PAX6,downstream_gene_variant,,ENST00000438681,;PAX6,non_coding_transcript_exon_variant,,ENST00000471303,;PAX6,non_coding_transcript_exon_variant,,ENST00000481563,;PAX6,non_coding_transcript_exon_variant,,ENST00000530714,;PAX6,non_coding_transcript_exon_variant,,ENST00000534353,;PAX6,downstream_gene_variant,,ENST00000533156,;PAX6,upstream_gene_variant,,ENST00000531910,;PAX6,upstream_gene_variant,,ENST00000530373,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000534390,;PAX6,intron_variant,,ENST00000464174,;PAX6,downstream_gene_variant,,ENST00000532175,;PAX6,downstream_gene_variant,,ENST00000527769,; A ENST00000419022 Transcript missense_variant 765/6922 296/1311 99/436 S/I aGc/aTc 1 -1 PAX6 HGNC HGNC:8620 protein_coding YES CCDS31452.1 ENSP00000404100 P26367 F1T0F8 UPI000002B0A0 NM_001310158.1,NM_001310161.1,NM_001258462.1 tolerated(0.08) 7/14 Gene3D:1.10.10.10,Pfam_domain:PF00292,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294,SMART_domains:SM00351,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 31801664 31801664 C A 1 0 0 0 0 1 0 0 0 11568 797 28 2 2 PAX6 11 31801664 Missense_Mutation SNP C C3N-00704_T 10228348 31801664 103284958 384 19521 C1QTNF4 0 . GRCh38 11 47590179 47590179 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.632G>A p.Gly211Asp p.G211D ENST00000302514 2/2 88 77 11 111 111 0 strelka-varscan-mutect C1QTNF4,missense_variant,p.Gly211Asp,ENST00000302514,NM_031909.2;C1QTNF4,intron_variant,,ENST00000530097,;FAM180B,downstream_gene_variant,,ENST00000538490,NM_001164379.1; T ENST00000302514 Transcript missense_variant 1149/1664 632/990 211/329 G/D gGc/gAc 1 -1 C1QTNF4 HGNC HGNC:14346 protein_coding YES CCDS7942.1 ENSP00000302274 Q9BXJ3 UPI00000746B6 NM_031909.2 deleterious(0) 2/2 Gene3D:2.60.120.40,Pfam_domain:PF00386,PROSITE_profiles:PS50871,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF551,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99986 1 1 1 1 0 T 3 4 62 47590179 47590179 C T 1 0 0 0 0 1 0 0 0 1943 739 26 3 3 C1QTNF4 11 47590179 Missense_Mutation SNP C C3N-00704_T 15788515 47590179 87496443 385 19522 OR4C3 0 . GRCh38 11 48325401 48325401 + Missense_Mutation SNP C C A rs140275122 C3N-00704_T C3N-00704_N C C c.461C>A p.Pro154His p.P154H ENST00000319856 1/1 109 82 27 172 172 0 strelka-varscan-mutect OR4C3,missense_variant,p.Pro154His,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.Pro17His,ENST00000611380,; A ENST00000319856 Transcript missense_variant 482/1036 461/990 154/329 P/H cCc/cAc rs140275122 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs140275122 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 48325401 48325401 C A 1 0 0 0 0 1 0 0 0 11126 623 22 2 2 OR4C3 11 48325401 Missense_Mutation SNP C C3N-00704_T 735222 48325401 86761221 386 19523 TRIM49B 0 . GRCh38 11 49037644 49037644 + Nonsense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.1026C>G p.Tyr342Ter p.Y342* ENST00000622138 8/8 381 315 66 436 436 0 strelka-varscan-mutect TRIM49B,stop_gained,p.Tyr342Ter,ENST00000622138,;TRIM49B,stop_gained,p.Tyr342Ter,ENST00000332682,NM_001206626.1; G ENST00000622138 Transcript stop_gained 1355/2162 1026/1359 342/452 Y/* taC/taG 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 HIGH 1 SNV 5 1 PASS rs1468850389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 62 49037644 49037644 C G 1 0 0 0 0 0 1 0 0 17015 576 20 4 4 TRIM49B 11 49037644 Nonsense_Mutation SNP C C3N-00704_T 712243 49037644 86048978 387 19524 FOLH1 0 . GRCh38 11 49146916 49146916 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.2093A>T p.Asn698Ile p.N698I ENST00000256999 19/19 112 88 24 107 107 0 strelka-varscan-mutect FOLH1,missense_variant,p.Asn683Ile,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Asn698Ile,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Asn667Ile,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Asn390Ile,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Asn652Ile,ENST00000533034,NM_001193472.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,; A ENST00000256999 Transcript missense_variant 2354/2635 2093/2253 698/750 N/I aAc/aTc 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 19/19 Gene3D:3kasA03,Pfam_domain:PF04253,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF47672 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 49146916 49146916 T A 1 0 0 0 0 1 0 0 0 5840 1725 60 4 4 FOLH1 11 49146916 Missense_Mutation SNP T C3N-00704_T 109272 49146916 85939706 388 19525 OR4C13 0 . GRCh38 11 49952581 49952581 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.159G>T p.= p.L53L ENST00000555099 1/1 289 226 63 275 275 0 strelka-varscan-mutect OR4C13,synonymous_variant,p.=,ENST00000555099,NM_001001955.2; T ENST00000555099 Transcript synonymous_variant 191/1029 159/930 53/309 L ctG/ctT 1 1 OR4C13 HGNC HGNC:15169 protein_coding YES CCDS31495.1 ENSP00000452277 Q8NGP0 UPI000013F7D1 NM_001001955.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF60,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 49952581 49952581 G T 1 0 0 0 0 0 0 0 1 11124 1277 45 2 2 OR4C13 11 49952581 Silent SNP G C3N-00704_T 805665 49952581 85134041 389 19526 OR4C46 0 . GRCh38 11 54603919 54603919 + Missense_Mutation SNP A A G C3N-00704_T C3N-00704_N A A c.80T>C p.Val27Ala p.V27A ENST00000328188 1/1 259 210 49 288 288 0 strelka-varscan-mutect OR4C46,missense_variant,p.Val27Ala,ENST00000328188,NM_001004703.1; G ENST00000328188 Transcript missense_variant 80/930 80/930 27/309 V/A gTt/gCt COSM4033492 1 -1 OR4C46 HGNC HGNC:31271 protein_coding YES CCDS73288.1 ENSP00000329056 A6NHA9 UPI000013F6F8 NM_001004703.1 tolerated_low_confidence(0.43) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26451:SF284,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS rs1346328521 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 54603919 54603919 A G 1 0 0 0 0 1 0 0 0 11127 43 2 5 5 OR4C46 11 54603919 Missense_Mutation SNP A C3N-00704_T 4651338 54603919 80482703 390 19527 OR5L2 0 . GRCh38 11 55827582 55827582 + Missense_Mutation SNP C C A rs536857563 C3N-00704_T C3N-00704_N C C c.364C>A p.Arg122Ser p.R122S ENST00000378397 1/1 199 163 36 241 241 0 strelka-varscan-mutect OR5L2,missense_variant,p.Arg122Ser,ENST00000378397,NM_001004739.1; A ENST00000378397 Transcript missense_variant 364/936 364/936 122/311 R/S Cgc/Agc rs536857563,COSM1628056 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 0,1 1 PASS rs536857563 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 55827582 55827582 C A 1 0 0 0 0 1 0 0 0 11240 652 23 1 1 OR5L2 11 55827582 Missense_Mutation SNP C C3N-00704_T 1223663 55827582 79259040 391 19528 OR5W2 0 . GRCh38 11 55913801 55913801 + Missense_Mutation SNP C C A rs202102548 C3N-00704_T C3N-00704_N C C c.782G>T p.Arg261Leu p.R261L ENST00000344514 1/1 225 204 21 255 255 0 strelka-varscan-mutect OR5W2,missense_variant,p.Arg261Leu,ENST00000344514,NM_001001960.1; A ENST00000344514 Transcript missense_variant 782/933 782/933 261/310 R/L cGg/cTg rs202102548,COSM218332 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs202102548 . 0 208 0 0 0 0 0 2 -7.036533 0 0 1 0 0 A 3 1 62 55913801 55913801 C A 1 0 0 0 0 1 0 0 0 11253 652 23 1 1 OR5W2 11 55913801 Missense_Mutation SNP C C3N-00704_T 86219 55913801 79172821 392 19529 OR8H1 0 . GRCh38 11 56290914 56290914 + Missense_Mutation SNP C C T rs191885508 C3N-00704_T C3N-00704_N C C c.149G>A p.Arg50His p.R50H ENST00000313022 1/1 232 209 23 258 258 0 strelka-varscan-mutect OR8H1,missense_variant,p.Arg50His,ENST00000313022,NM_001005199.1;OR8H1,missense_variant,p.Arg46His,ENST00000610894,; T ENST00000313022 Transcript missense_variant 177/1038 149/936 50/311 R/H cGc/cAc rs191885508,COSM1298174,COSM5675086 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 tolerated(0.23) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs191885508 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 56290914 56290914 C T 1 0 0 0 0 1 0 0 0 11305 768 27 1 1 OR8H1 11 56290914 Missense_Mutation SNP C C3N-00704_T 377113 56290914 78795708 393 19530 OR8J1 0 . GRCh38 11 56360720 56360720 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.474G>A p.= p.V158V ENST00000303039 1/1 85 73 12 117 117 0 strelka-mutect OR8J1,synonymous_variant,p.=,ENST00000303039,NM_001005205.2;RPL5P29,downstream_gene_variant,,ENST00000482972,; A ENST00000303039 Transcript synonymous_variant 506/1074 474/951 158/316 V gtG/gtA 1 1 OR8J1 HGNC HGNC:14855 protein_coding YES CCDS31529.1 ENSP00000304060 Q8NGP2 UPI000004BE58 NM_001005205.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF317,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs1386315339 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 56360720 56360720 G A 1 0 0 0 0 0 0 0 1 11309 1335 47 3 3 OR8J1 11 56360720 Silent SNP G C3N-00704_T 69806 56360720 78725902 394 19531 OR8U1 0 . GRCh38 11 56376295 56376295 + Silent SNP C C T C3N-00704_T C3N-00704_N C C c.672C>T p.= p.A224A ENST00000302270 1/1 261 201 60 266 266 0 strelka-varscan-mutect OR8U1,synonymous_variant,p.=,ENST00000302270,NM_001005204.1; T ENST00000302270 Transcript synonymous_variant 672/930 672/930 224/309 A gcC/gcT COSM5658134 1 1 OR8U1 HGNC HGNC:19611 protein_coding YES CCDS41647.1 ENSP00000304188 Q8NH10 UPI0000061EEF NM_001005204.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF360,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 56376295 56376295 C T 1 0 0 0 0 0 0 0 1 11314 581 21 3 3 OR8U1 11 56376295 Silent SNP C C3N-00704_T 15575 56376295 78710327 395 19532 OR10W1 0 . GRCh38 11 58267375 58267375 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.484G>T p.Ala162Ser p.A162S ENST00000395079 1/1 136 108 28 143 143 0 strelka-varscan-mutect OR10W1,missense_variant,p.Ala162Ser,ENST00000395079,NM_207374.3; A ENST00000395079 Transcript missense_variant 886/1469 484/918 162/305 A/S Gct/Tct 1 -1 OR10W1 HGNC HGNC:15139 protein_coding YES CCDS7968.1 ENSP00000378516 Q8NGF6 UPI000004B229 NM_207374.3 tolerated(0.87) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF165,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1015816300 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 58267375 58267375 C A 1 0 0 0 0 1 0 0 0 10998 739 26 2 2 OR10W1 11 58267375 Missense_Mutation SNP C C3N-00704_T 1891080 58267375 76819247 396 19533 OR10V1 0 . GRCh38 11 59712919 59712919 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.927C>A p.Phe309Leu p.F309L ENST00000307552 1/1 77 62 15 90 90 0 strelka-varscan-mutect OR10V1,missense_variant,p.Phe309Leu,ENST00000307552,NM_001005324.1; T ENST00000307552 Transcript missense_variant 946/1042 927/930 309/309 F/L ttC/ttA 1 -1 OR10V1 HGNC HGNC:15136 protein_coding YES CCDS31565.1 ENSP00000302199 Q8NGI7 UPI0000061EC8 NM_001005324.1 deleterious(0.02) 1/1 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 59712919 59712919 G T 1 0 0 0 0 1 0 0 0 10997 933 33 2 2 OR10V1 11 59712919 Missense_Mutation SNP G C3N-00704_T 1445544 59712919 75373703 397 19534 MS4A14 0 . GRCh38 11 60415605 60415605 + Missense_Mutation SNP T T A rs746461684 C3N-00704_T C3N-00704_N T T c.736T>A p.Ser246Thr p.S246T ENST00000531783 6/6 119 98 21 194 194 0 strelka-varscan-mutect MS4A14,missense_variant,p.Ser229Thr,ENST00000395001,NM_001261827.1;MS4A14,missense_variant,p.Ser213Thr,ENST00000300187,NM_032597.4;MS4A14,missense_variant,p.Ser246Thr,ENST00000531783,NM_001261828.1;MS4A14,missense_variant,p.Ser196Thr,ENST00000395005,NM_001079692.2;MS4A14,missense_variant,p.Ser101Thr,ENST00000531787,;MS4A14,3_prime_UTR_variant,,ENST00000530662,;MS4A14,3_prime_UTR_variant,,ENST00000527841,;MS4A14,3_prime_UTR_variant,,ENST00000525397,; A ENST00000531783 Transcript missense_variant 827/2910 736/2139 246/712 S/T Tct/Act rs746461684 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 tolerated(0.47) 6/6 MODERATE 1 SNV 5 1 PASS rs746461684 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 60415605 60415605 T A 1 0 0 0 0 1 0 0 0 9835 1551 54 4 4 MS4A14 11 60415605 Missense_Mutation SNP T C3N-00704_T 702686 60415605 74671017 398 19535 PLCB3 0 . GRCh38 11 64251696 64251696 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.47C>A p.Pro16His p.P16H ENST00000540288 1/32 118 102 16 112 112 0 strelka-varscan-mutect PLCB3,missense_variant,p.Pro16His,ENST00000540288,NM_001316314.1,NM_000932.2;PLCB3,missense_variant,p.Pro16His,ENST00000279230,;PLCB3,missense_variant,p.Pro16His,ENST00000325234,NM_001184883.1;PPP1R14B,upstream_gene_variant,,ENST00000309318,NM_138689.2;RP11-783K16.13,upstream_gene_variant,,ENST00000545800,;RP11-783K16.5,downstream_gene_variant,,ENST00000538355,;RP11-783K16.5,downstream_gene_variant,,ENST00000544553,; A ENST00000540288 Transcript missense_variant 150/4469 47/3705 16/1234 P/H cCc/cAc 1 1 PLCB3 HGNC HGNC:9056 protein_coding YES CCDS8064.1 ENSP00000443631 Q01970 UPI0000131AFF NM_001316314.1,NM_000932.2 deleterious(0.03) 1/32 hmmpanther:PTHR10336:SF11,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000956,Gene3D:2.30.29.30 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 64251696 64251696 C A 1 0 0 0 0 1 0 0 0 12123 623 22 2 2 PLCB3 11 64251696 Missense_Mutation SNP C C3N-00704_T 3836091 64251696 70834926 399 19536 ATG2A 0 . GRCh38 11 64900936 64900937 + Frame_Shift_Del DEL GG GG - novel C3N-00704_T C3N-00704_N GG GG c.4275_4276delCC p.Leu1426ArgfsTer121 p.L1426Rfs*121 ENST00000377264 30/41 135 114 21 199 199 0 sindel-varindel-pindel ATG2A,frameshift_variant,p.Leu1426ArgfsTer121,ENST00000377264,NM_015104.2;ATG2A,frameshift_variant,p.Leu1230ArgfsTer121,ENST00000418259,;ATG2A,intron_variant,,ENST00000421419,;MIR6750,upstream_gene_variant,,ENST00000617817,;MIR6749,downstream_gene_variant,,ENST00000617008,;ATG2A,upstream_gene_variant,,ENST00000472525,; - ENST00000377264 Transcript frameshift_variant 4388-4389/6357 4275-4276/5817 1425-1426/1938 SL/SX tcCCtc/tctc 1 -1 ATG2A HGNC HGNC:29028 protein_coding YES CCDS31602.1 ENSP00000366475 Q2TAZ0 UPI00001C1F21 NM_015104.2 30/41 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF21 HIGH 1 deletion 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 64900936 64900936 GG - 1 0 1 0 1 0 0 0 0 1245 1000 35 0 0 ATG2A 11 64900936 Frame_Shift_Del DEL GG C3N-00704_T 649240 64900936 70185686 400 19537 CARNS1 0 . GRCh38 11 67418816 67418816 + Missense_Mutation SNP C C A rs61744660 C3N-00704_T C3N-00704_N C C c.425C>A p.Pro142Gln p.P142Q ENST00000445895 4/9 106 89 17 129 129 0 strelka-varscan-mutect CARNS1,missense_variant,p.Pro142Gln,ENST00000445895,NM_001166222.1;CARNS1,missense_variant,p.Pro19Gln,ENST00000307823,NM_020811.1;CARNS1,missense_variant,p.Pro142Gln,ENST00000531040,;PPP1CA,intron_variant,,ENST00000542876,;PPP1CA,intron_variant,,ENST00000546202,;CARNS1,downstream_gene_variant,,ENST00000529925,;CARNS1,downstream_gene_variant,,ENST00000525907,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531388,;CARNS1,non_coding_transcript_exon_variant,,ENST00000531958,; A ENST00000445895 Transcript missense_variant 539/3971 425/2853 142/950 P/Q cCg/cAg rs61744660 1 1 CARNS1 HGNC HGNC:29268 protein_coding YES CCDS53667.1 ENSP00000389009 A5YM72 UPI0001B99E02 NM_001166222.1 deleterious(0.01) 4/9 MODERATE 1 SNV 5 1 PASS rs61744660 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 67418816 67418816 C A 1 0 0 0 0 1 0 0 0 2355 652 23 1 1 CARNS1 11 67418816 Missense_Mutation SNP C C3N-00704_T 2517880 67418816 67667806 401 19538 ANO1 0 . GRCh38 11 70132026 70132026 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.1205A>G p.His402Arg p.H402R ENST00000355303 11/26 198 168 30 246 246 0 strelka-varscan-mutect ANO1,missense_variant,p.His402Arg,ENST00000355303,NM_018043.5;ANO1,missense_variant,p.His137Arg,ENST00000531349,;ANO1,missense_variant,p.His286Arg,ENST00000530676,;ANO1,missense_variant,p.His374Arg,ENST00000316296,;ANO1,missense_variant,p.His267Arg,ENST00000530480,;RP11-805J14.3,intron_variant,,ENST00000530525,; G ENST00000355303 Transcript missense_variant 1510/4790 1205/2961 402/986 H/R cAc/cGc 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 deleterious(0.01) 11/26 Pfam_domain:PF04547,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 70132026 70132026 A G 1 0 0 0 0 1 0 0 0 802 159 6 5 5 ANO1 11 70132026 Missense_Mutation SNP A C3N-00704_T 2713210 70132026 64954596 402 19539 KRTAP5-8 0 . GRCh38 11 71538128 71538128 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.73G>T p.Gly25Cys p.G25C ENST00000398534 1/1 354 270 84 473 473 0 strelka-varscan-mutect KRTAP5-8,missense_variant,p.Gly25Cys,ENST00000398534,NM_021046.2; T ENST00000398534 Transcript missense_variant 104/1183 73/564 25/187 G/C Ggc/Tgc 1 1 KRTAP5-8 HGNC HGNC:23603 protein_coding YES CCDS41683.1 ENSP00000420723 O75690 UPI000013ECDA NM_021046.2 deleterious_low_confidence(0.01) 1/1 hmmpanther:PTHR23262,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 71538128 71538128 G T 1 0 0 0 0 1 0 0 0 8462 1348 47 2 2 KRTAP5-8 11 71538128 Missense_Mutation SNP G C3N-00704_T 1406102 71538128 63548494 403 19540 MYO7A 0 . GRCh38 11 77211206 77211206 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.6106C>G p.Gln2036Glu p.Q2036E ENST00000409709 45/49 132 103 29 164 164 0 strelka-varscan-mutect MYO7A,missense_variant,p.Gln2036Glu,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Gln1998Glu,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Gln1987Glu,ENST00000409619,;MYO7A,missense_variant,p.Gln1178Glu,ENST00000458169,;MYO7A,non_coding_transcript_exon_variant,,ENST00000605744,;MYO7A,intron_variant,,ENST00000526863,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,;MYO7A,upstream_gene_variant,,ENST00000481532,; G ENST00000409709 Transcript missense_variant 6378/7462 6106/6648 2036/2215 Q/E Cag/Gag 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.38) 45/49 PROSITE_profiles:PS50057,Gene3D:1.20.80.10,Pfam_domain:PF00373,SMART_domains:SM00295,Superfamily_domains:SSF47031 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 77211206 77211206 C G 1 0 0 0 0 1 0 0 0 10083 711 25 4 4 MYO7A 11 77211206 Missense_Mutation SNP C C3N-00704_T 5673078 77211206 57875416 404 19541 RSF1 0 . GRCh38 11 77675086 77675086 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.3512A>T p.Tyr1171Phe p.Y1171F ENST00000308488 14/16 127 101 26 143 143 0 strelka-varscan-mutect RSF1,missense_variant,p.Tyr1171Phe,ENST00000308488,NM_016578.3;RSF1,missense_variant,p.Tyr919Phe,ENST00000480887,;RSF1,downstream_gene_variant,,ENST00000531026,;RSF1,non_coding_transcript_exon_variant,,ENST00000529470,; A ENST00000308488 Transcript missense_variant 3815/11550 3512/4326 1171/1441 Y/F tAt/tTt 1 -1 RSF1 HGNC HGNC:18118 protein_coding YES CCDS8253.1 ENSP00000311513 Q96T23 UPI00001FB001 NM_016578.3 tolerated(0.09) 14/16 hmmpanther:PTHR10615:SF113,hmmpanther:PTHR10615 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 77675086 77675086 T A 1 0 0 0 0 1 0 0 0 13955 1406 49 4 4 RSF1 11 77675086 Missense_Mutation SNP T C3N-00704_T 463880 77675086 57411536 405 19542 DLG2 0 . GRCh38 11 83541739 83541739 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2060G>T p.Arg687Met p.R687M ENST00000376104 20/28 162 140 22 153 152 1 strelka-varscan-mutect DLG2,missense_variant,p.Arg582Met,ENST00000398309,NM_001364.3;DLG2,missense_variant,p.Arg621Met,ENST00000280241,NM_001206769.1;DLG2,missense_variant,p.Arg64Met,ENST00000426717,NM_001142702.1;DLG2,missense_variant,p.Arg687Met,ENST00000376104,NM_001142699.1;DLG2,missense_variant,p.Arg479Met,ENST00000418306,NM_001142700.1;DLG2,missense_variant,p.Arg549Met,ENST00000531015,;DLG2,missense_variant,p.Arg582Met,ENST00000532653,NM_001300983.1;DLG2,missense_variant,p.Arg582Met,ENST00000524982,;DLG2,missense_variant,p.Arg521Met,ENST00000330014,;DLG2,missense_variant,p.Arg64Met,ENST00000404783,;DLG2,missense_variant,p.Arg64Met,ENST00000420775,;DLG2,missense_variant,p.Arg64Met,ENST00000398304,;DLG2,missense_variant,p.Arg91Met,ENST00000530800,;DLG2,missense_variant,p.Arg64Met,ENST00000529399,;DLG2,missense_variant,p.Arg64Met,ENST00000524601,;DLG2,missense_variant,p.Arg93Met,ENST00000434967,; A ENST00000376104 Transcript missense_variant 2372/5139 2060/2928 687/975 R/M aGg/aTg 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 deleterious(0) 20/28 PROSITE_profiles:PS50002,hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119,PIRSF_domain:PIRSF001741,Pfam_domain:PF07653,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 83541739 83541739 C A 1 0 0 0 0 1 0 0 0 4362 681 24 2 2 DLG2 11 83541739 Missense_Mutation SNP C C3N-00704_T 5866653 83541739 51544883 406 19543 CEP295 0 . GRCh38 11 93698772 93698772 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.3860G>T p.Gly1287Val p.G1287V ENST00000325212 15/30 141 120 21 224 224 0 strelka-varscan-mutect CEP295,missense_variant,p.Gly1287Val,ENST00000325212,NM_033395.1;CEP295,intron_variant,,ENST00000531700,;CEP295,upstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000531877,;CEP295,downstream_gene_variant,,ENST00000531622,; T ENST00000325212 Transcript missense_variant 4022/8057 3860/7806 1287/2601 G/V gGt/gTt 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 tolerated(0.1) 15/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25 MODERATE 1 SNV 2 1 PASS rs1485420875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 93698772 93698772 G T 1 0 0 0 0 1 0 0 0 2970 1261 44 2 2 CEP295 11 93698772 Missense_Mutation SNP G C3N-00704_T 10157033 93698772 41387850 407 19544 FDX1 0 . GRCh38 11 110456951 110456951 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.344G>T p.Cys115Phe p.C115F ENST00000260270 3/4 138 99 39 163 163 0 strelka-varscan-mutect FDX1,missense_variant,p.Cys115Phe,ENST00000260270,NM_004109.4; T ENST00000260270 Transcript missense_variant 582/3206 344/555 115/184 C/F tGt/tTt 1 1 FDX1 HGNC HGNC:3638 protein_coding YES CCDS8344.1 ENSP00000260270 P10109 UPI0000125630 NM_004109.4 deleterious(0) 3/4 PROSITE_profiles:PS51085,hmmpanther:PTHR23426,hmmpanther:PTHR23426:SF26,PROSITE_patterns:PS00814,Gene3D:3.10.20.30,Pfam_domain:PF00111,Superfamily_domains:SSF54292,Prints_domain:PR00355 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 110456951 110456951 G T 1 0 0 0 0 1 0 0 0 5667 1377 48 2 2 FDX1 11 110456951 Missense_Mutation SNP G C3N-00704_T 16758179 110456951 24629671 408 19545 NCAM1 0 . GRCh38 11 113235102 113235102 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.1841C>A p.Ala614Glu p.A614E ENST00000619839 15/21 198 165 33 200 200 0 strelka-varscan-mutect NCAM1,missense_variant,p.Ala614Glu,ENST00000615285,;NCAM1,missense_variant,p.Ala588Glu,ENST00000615112,;NCAM1,missense_variant,p.Ala578Glu,ENST00000618266,;NCAM1,missense_variant,p.Ala588Glu,ENST00000316851,NM_181351.4;NCAM1,missense_variant,p.Ala578Glu,ENST00000621518,;NCAM1,missense_variant,p.Ala578Glu,ENST00000621128,NM_001242608.1;NCAM1,missense_variant,p.Ala614Glu,ENST00000619839,NM_001242607.1;NCAM1,missense_variant,p.Ala578Glu,ENST00000531044,NM_000615.6;NCAM1,missense_variant,p.Ala578Glu,ENST00000621850,NM_001076682.3;NCAM1,missense_variant,p.Ala578Glu,ENST00000401611,;NCAM1,missense_variant,p.Ala88Glu,ENST00000533073,;NCAM1,missense_variant,p.Ala123Glu,ENST00000526322,;NCAM1,missense_variant,p.Ala81Glu,ENST00000528590,;NCAM1,missense_variant,p.Ala144Glu,ENST00000530543,;NCAM1,intron_variant,,ENST00000620046,;NCAM1,downstream_gene_variant,,ENST00000613217,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,missense_variant,p.Ala88Glu,ENST00000531817,;NCAM1,non_coding_transcript_exon_variant,,ENST00000525355,;NCAM1,downstream_gene_variant,,ENST00000534046,; A ENST00000619839 Transcript missense_variant 2179/2993 1841/2655 614/884 A/E gCg/gAg COSM1127907,COSM1127908,COSM1127910,COSM4017881 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 deleterious(0) 15/21 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 113235102 113235102 C A 1 0 0 0 0 1 0 0 0 10218 768 27 1 1 NCAM1 11 113235102 Missense_Mutation SNP C C3N-00704_T 2778151 113235102 21851520 409 19546 HTR3A 0 . GRCh38 11 113986534 113986534 + Missense_Mutation SNP G G A rs373069618 C3N-00704_T C3N-00704_N G G c.740G>A p.Arg247Gln p.R247Q ENST00000355556 7/8 312 266 46 366 366 0 strelka-varscan-mutect HTR3A,missense_variant,p.Arg241Gln,ENST00000504030,;HTR3A,missense_variant,p.Arg247Gln,ENST00000355556,NM_213621.3;HTR3A,missense_variant,p.Arg247Gln,ENST00000375498,NM_000869.5;HTR3A,missense_variant,p.Arg241Gln,ENST00000506841,;HTR3A,missense_variant,p.Arg226Gln,ENST00000299961,NM_001161772.2;HTR3A,synonymous_variant,p.=,ENST00000510849,;HTR3A,non_coding_transcript_exon_variant,,ENST00000502622,; A ENST00000355556 Transcript missense_variant 973/2331 740/1551 247/516 R/Q cGg/cAg rs373069618,COSM3443606 1 1 HTR3A HGNC HGNC:5297 protein_coding YES CCDS8366.2 ENSP00000347754 P46098 UPI000013F7F1 NM_213621.3 deleterious(0) 7/8 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF52,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs373069618 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 113986534 113986534 G A 1 0 0 0 0 1 0 0 0 7340 1116 39 1 1 HTR3A 11 113986534 Missense_Mutation SNP G C3N-00704_T 751432 113986534 21100088 410 19547 ARHGEF12 0 . GRCh38 11 120448267 120448267 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1656G>A p.Met552Ile p.M552I ENST00000397843 20/41 189 155 34 189 189 0 strelka-varscan-mutect ARHGEF12,missense_variant,p.Met552Ile,ENST00000397843,NM_015313.2;ARHGEF12,missense_variant,p.Met449Ile,ENST00000532993,NM_001301084.1;ARHGEF12,missense_variant,p.Met533Ile,ENST00000356641,NM_001198665.1;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000529970,;ARHGEF12,non_coding_transcript_exon_variant,,ENST00000528225,;ARHGEF12,upstream_gene_variant,,ENST00000525222,;ARHGEF12,upstream_gene_variant,,ENST00000532823,;ARHGEF12,downstream_gene_variant,,ENST00000525960,; A ENST00000397843 Transcript missense_variant 1822/9660 1656/4635 552/1544 M/I atG/atA 1 1 ARHGEF12 HGNC HGNC:14193 protein_coding YES CCDS41727.1 ENSP00000380942 Q9NZN5 UPI00000708ED NM_015313.2 deleterious(0) 20/41 hmmpanther:PTHR12673:SF126,hmmpanther:PTHR12673,Pfam_domain:PF09128,Superfamily_domains:SSF48097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 120448267 120448267 G A 1 0 0 0 0 1 0 0 0 1027 1290 45 3 3 ARHGEF12 11 120448267 Missense_Mutation SNP G C3N-00704_T 6461733 120448267 14638355 411 19548 SORL1 0 . GRCh38 11 121452521 121452521 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.190G>T p.Gly64Trp p.G64W ENST00000260197 1/48 89 73 16 84 84 0 strelka-varscan-mutect SORL1,missense_variant,p.Gly64Trp,ENST00000260197,NM_003105.5;RP11-730K11.1,intron_variant,,ENST00000501964,;RP11-730K11.1,intron_variant,,ENST00000529160,;SORL1,non_coding_transcript_exon_variant,,ENST00000532451,; T ENST00000260197 Transcript missense_variant 319/10904 190/6645 64/2214 G/W Ggg/Tgg 1 1 SORL1 HGNC HGNC:11185 protein_coding YES CCDS8436.1 ENSP00000260197 Q92673 UPI000013D0B1 NM_003105.5 tolerated_low_confidence(0.07) 1/48 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF20,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 121452521 121452521 G T 1 0 0 0 0 1 0 0 0 15256 1116 39 1 1 SORL1 11 121452521 Missense_Mutation SNP G C3N-00704_T 1004254 121452521 13634101 412 19549 PDE3A 0 . GRCh38 12 20653983 20653983 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2962C>T p.Pro988Ser p.P988S ENST00000359062 15/16 207 155 52 292 292 0 strelka-varscan-mutect PDE3A,missense_variant,p.Pro988Ser,ENST00000359062,NM_000921.4,NM_001244683.1;PDE3A,non_coding_transcript_exon_variant,,ENST00000544307,; T ENST00000359062 Transcript missense_variant 3002/7576 2962/3426 988/1141 P/S Ccc/Tcc 1 1 PDE3A HGNC HGNC:8778 protein_coding YES CCDS31754.1 ENSP00000351957 Q14432 UPI000014175F NM_000921.4,NM_001244683.1 deleterious(0) 15/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF104,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 20653983 20653983 C T 1 0 0 0 0 1 0 0 0 11725 623 22 3 3 PDE3A 12 20653983 Missense_Mutation SNP C C3N-00704_T 20653983 112621326 413 19550 SLCO1A2 0 . GRCh38 12 21274468 21274468 + Splice_Site SNP C C A novel C3N-00704_T C3N-00704_N C C c.1793+1G>T p.X598_splice ENST00000307378 110 90 20 164 164 0 strelka-varscan-mutect SLCO1A2,splice_donor_variant,,ENST00000307378,NM_021094.3,NM_134431.3;SLCO1A2,splice_donor_variant,,ENST00000458504,;SLCO1A2,splice_donor_variant,,ENST00000544290,;SLCO1A2,splice_donor_variant,,ENST00000544020,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,;SLCO1A2,downstream_gene_variant,,ENST00000463718,; A ENST00000307378 Transcript splice_donor_variant -/7682 1793/2013 598/670 1 -1 SLCO1A2 HGNC HGNC:10956 protein_coding YES CCDS8686.1 ENSP00000305974 P46721 A0A024RAT5 UPI0000037575 NM_021094.3,NM_134431.3 15/15 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 62 21274468 21274468 C A 1 0 0 0 0 0 0 1 0 15008 521 18 2 2 SLCO1A2 12 21274468 Splice_Site SNP C C3N-00704_T 620485 21274468 112000841 414 19551 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-00704_T C3N-00704_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 272 192 80 422 422 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-00704_T 3970883 25245351 108029958 415 19552 ENDOU 0 . GRCh38 12 47711663 47711663 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1085C>A p.Ser362Tyr p.S362Y ENST00000422538 9/10 143 93 50 224 224 0 strelka-varscan-mutect ENDOU,missense_variant,p.Ser362Tyr,ENST00000422538,NM_001172439.1;ENDOU,missense_variant,p.Ser321Tyr,ENST00000229003,NM_006025.3;ENDOU,missense_variant,p.Ser299Tyr,ENST00000545824,NM_001172440.1;RP1-197B17.3,intron_variant,,ENST00000547799,;ENDOU,downstream_gene_variant,,ENST00000551186,; T ENST00000422538 Transcript missense_variant 1208/2413 1085/1233 362/410 S/Y tCc/tAc 1 -1 ENDOU HGNC HGNC:14369 protein_coding YES CCDS53785.1 ENSP00000397679 P21128 UPI00001FC0AE NM_001172439.1 deleterious(0) 9/10 hmmpanther:PTHR12439,hmmpanther:PTHR12439:SF9,Pfam_domain:PF09412,Superfamily_domains:SSF142877 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 47711663 47711663 G T 1 0 0 0 0 1 0 0 0 4958 1174 41 2 2 ENDOU 12 47711663 Missense_Mutation SNP G C3N-00704_T 22466312 47711663 85563646 416 19553 PPFIA2 0 . GRCh38 12 81341125 81341125 + Silent SNP G G C novel C3N-00704_T C3N-00704_N G G c.2346C>G p.= p.L782L ENST00000549396 20/33 175 152 23 187 187 0 strelka-varscan-mutect PPFIA2,synonymous_variant,p.=,ENST00000333447,NM_001220478.2;PPFIA2,synonymous_variant,p.=,ENST00000550584,NM_001220473.2;PPFIA2,synonymous_variant,p.=,ENST00000549396,NM_003625.4;PPFIA2,synonymous_variant,p.=,ENST00000549325,NM_001220474.2;PPFIA2,synonymous_variant,p.=,ENST00000548586,NM_001220476.2;PPFIA2,synonymous_variant,p.=,ENST00000552948,NM_001220475.2;PPFIA2,synonymous_variant,p.=,ENST00000407050,NM_001220477.2;PPFIA2,synonymous_variant,p.=,ENST00000550359,NM_001282536.1;PPFIA2,synonymous_variant,p.=,ENST00000443686,;PPFIA2,synonymous_variant,p.=,ENST00000541570,NM_001220479.2;PPFIA2,5_prime_UTR_variant,,ENST00000541017,NM_001220480.2;PPFIA2,upstream_gene_variant,,ENST00000551147,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000549917,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000549344,; C ENST00000549396 Transcript synonymous_variant 2507/5363 2346/3774 782/1257 L ctC/ctG 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 20/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 62 81341125 81341125 G C 1 0 0 0 0 0 0 0 1 12419 1277 45 4 4 PPFIA2 12 81341125 Silent SNP G C3N-00704_T 33629462 81341125 51934184 417 19554 DEPDC4 0 . GRCh38 12 100263577 100263577 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.474C>A p.Tyr158Ter p.Y158* ENST00000416321 2/5 60 38 22 119 119 0 strelka-varscan-mutect DEPDC4,stop_gained,p.Tyr158Ter,ENST00000550587,;DEPDC4,stop_gained,p.Tyr158Ter,ENST00000416321,NM_152317.2;DEPDC4,stop_gained,p.Tyr151Ter,ENST00000551642,NM_001319310.1;DEPDC4,stop_gained,p.Tyr91Ter,ENST00000549249,;SCYL2,upstream_gene_variant,,ENST00000360820,NM_001317784.1,NM_017988.4;SCYL2,upstream_gene_variant,,ENST00000635101,;SCYL2,upstream_gene_variant,,ENST00000549687,;SCYL2,upstream_gene_variant,,ENST00000548392,;DEPDC4,upstream_gene_variant,,ENST00000548313,;SCYL2,upstream_gene_variant,,ENST00000550067,;DEPDC4,stop_gained,p.Tyr158Ter,ENST00000378244,;DEPDC4,intron_variant,,ENST00000299185,;DEPDC4,intron_variant,,ENST00000549341,; T ENST00000416321 Transcript stop_gained 477/1155 474/885 158/294 Y/* taC/taA 1 -1 DEPDC4 HGNC HGNC:22952 protein_coding YES CCDS9075.1 ENSP00000396234 Q8N2C3 A0A024RBI9 UPI0000071E6F NM_152317.2 2/5 PROSITE_profiles:PS50186,hmmpanther:PTHR16206:SF10,hmmpanther:PTHR16206,Gene3D:1.10.10.10,Pfam_domain:PF00610,SMART_domains:SM00049,Superfamily_domains:SSF46785 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 100263577 100263577 G T 1 0 0 0 0 0 1 0 0 4247 1372 48 2 2 DEPDC4 12 100263577 Nonsense_Mutation SNP G C3N-00704_T 18922452 100263577 33011732 418 19555 CORO1C 0 . GRCh38 12 108662158 108662158 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.478G>A p.Val160Ile p.V160I ENST00000420959 4/11 135 109 26 202 202 0 strelka-varscan-mutect CORO1C,missense_variant,p.Val160Ile,ENST00000420959,NM_001105237.2;CORO1C,missense_variant,p.Val107Ile,ENST00000261401,NM_014325.3;CORO1C,missense_variant,p.Val107Ile,ENST00000541050,NM_001276471.1;CORO1C,missense_variant,p.Val113Ile,ENST00000549772,;CORO1C,missense_variant,p.Val2Ile,ENST00000421578,;CORO1C,missense_variant,p.Val107Ile,ENST00000546571,;CORO1C,missense_variant,p.Val2Ile,ENST00000552871,;CORO1C,missense_variant,p.Val107Ile,ENST00000551044,;CORO1C,missense_variant,p.Val107Ile,ENST00000547294,;CORO1C,missense_variant,p.Val107Ile,ENST00000550032,;CORO1C,missense_variant,p.Val107Ile,ENST00000551550,;CORO1C,intron_variant,,ENST00000549384,;CORO1C,upstream_gene_variant,,ENST00000552030,;CORO1C,missense_variant,p.Val107Ile,ENST00000550542,;CORO1C,splice_region_variant,,ENST00000547170,;CORO1C,upstream_gene_variant,,ENST00000547361,; T ENST00000420959 Transcript missense_variant,splice_region_variant 527/3921 478/1584 160/527 V/I Gta/Ata 1 -1 CORO1C HGNC HGNC:2254 protein_coding YES CCDS61236.1 ENSP00000394496 Q9ULV4 UPI00015BFD0B NM_001105237.2 tolerated(0.5) 4/11 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 108662158 108662158 C T 1 0 0 0 0 1 0 0 0 3549 521 18 3 3 CORO1C 12 108662158 Missense_Mutation SNP C C3N-00704_T 8398581 108662158 24613151 419 19556 SDSL 0 . GRCh38 12 113428132 113428132 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.150G>T p.= p.R50R ENST00000403593 2/8 195 151 44 276 275 1 strelka-varscan-mutect SDSL,synonymous_variant,p.=,ENST00000403593,NM_001304993.1;SDSL,synonymous_variant,p.=,ENST00000345635,NM_138432.3;SDSL,intron_variant,,ENST00000553248,;SDSL,upstream_gene_variant,,ENST00000546672,;SDS,upstream_gene_variant,,ENST00000547342,;SDSL,downstream_gene_variant,,ENST00000547802,; T ENST00000403593 Transcript synonymous_variant 412/1449 150/990 50/329 R cgG/cgT 1 1 SDSL HGNC HGNC:30404 protein_coding YES CCDS9170.1 ENSP00000385790 Q96GA7 A0A024RBL2 UPI0000072263 NM_001304993.1 2/8 hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF99,PROSITE_patterns:PS00165,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 113428132 113428132 G T 1 0 0 0 0 0 0 0 1 14252 1219 43 2 2 SDSL 12 113428132 Silent SNP G C3N-00704_T 4765974 113428132 19847177 420 19557 TMEM132C 0 . GRCh38 12 128697367 128697367 + Silent SNP C C A rs562181064 C3N-00704_T C3N-00704_N C C c.2073C>A p.= p.A691A ENST00000435159 8/9 74 52 22 86 86 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript synonymous_variant 2073/4947 2073/3327 691/1108 A gcC/gcA rs562181064,COSM2227790,COSM2227791 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs562181064 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 62 128697367 128697367 C A 1 0 0 0 0 0 0 0 1 16491 639 23 1 1 TMEM132C 12 128697367 Silent SNP C C3N-00704_T 15269235 128697367 4577942 421 19558 TMEM132C 0 . GRCh38 12 128705245 128705245 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.2277G>A p.= p.V759V ENST00000435159 9/9 155 120 35 196 196 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript synonymous_variant 2277/4947 2277/3327 759/1108 V gtG/gtA 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 128705245 128705245 G A 1 0 0 0 0 0 0 0 1 16491 1335 47 3 3 TMEM132C 12 128705245 Silent SNP G C3N-00704_T 7878 128705245 4570064 422 19559 ATP12A 0 . GRCh38 13 24691229 24691229 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1065G>T p.Glu355Asp p.E355D ENST00000218548 8/23 72 59 13 92 92 0 strelka-varscan-mutect ATP12A,missense_variant,p.Glu349Asp,ENST00000381946,NM_001676.5;ATP12A,missense_variant,p.Glu355Asp,ENST00000218548,NM_001185085.1; T ENST00000218548 Transcript missense_variant 1398/3732 1065/3138 355/1045 E/D gaG/gaT 1 1 ATP12A HGNC HGNC:13816 protein_coding YES CCDS53858.1 ENSP00000218548 P54707 UPI000006D1DE NM_001185085.1 deleterious(0.03) 8/23 hmmpanther:PTHR24093:SF282,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01494,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01106,Superfamily_domains:0049473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 24691229 24691229 G T 1 0 0 0 0 1 0 0 0 1274 991 35 2 2 ATP12A 13 24691229 Missense_Mutation SNP G C3N-00704_T 24691229 89673099 423 19560 TRPC4 0 . GRCh38 13 37637433 37637433 + Missense_Mutation SNP G G T rs374449501 C3N-00704_T C3N-00704_N G G c.2419C>A p.Leu807Met p.L807M ENST00000625583 10/10 132 109 23 148 148 0 strelka-varscan-mutect TRPC4,missense_variant,p.Leu802Met,ENST00000379705,NM_016179.2;TRPC4,missense_variant,p.Leu807Met,ENST00000625583,NM_003306.1;TRPC4,missense_variant,p.Leu629Met,ENST00000338947,NM_001135958.1;TRPC4,missense_variant,p.Leu629Met,ENST00000379679,;TRPC4,intron_variant,,ENST00000358477,NM_001135955.1;TRPC4,intron_variant,,ENST00000355779,NM_001135957.1;TRPC4,intron_variant,,ENST00000379673,NM_001135956.1;TRPC4,intron_variant,,ENST00000426868,;TRPC4,3_prime_UTR_variant,,ENST00000488717,; T ENST00000625583 Transcript missense_variant 2419/3009 2419/2949 807/982 L/M Ctg/Atg rs374449501,COSM696628,COSM696629 1 -1 TRPC4 HGNC HGNC:12336 protein_coding YES CCDS45037.1 ENSP00000486109 Q9UBN4 UPI000006E5BE NM_003306.1 tolerated_low_confidence(0.44) 10/10 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF25,Prints_domain:PR01645 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs374449501 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 37637433 37637433 G T 1 0 0 0 0 1 0 0 0 17085 991 35 2 2 TRPC4 13 37637433 Missense_Mutation SNP G C3N-00704_T 12946204 37637433 76726895 424 19561 VWA8 0 . GRCh38 13 41868420 41868420 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1138G>T p.Glu380Ter p.E380* ENST00000379310 10/45 208 183 25 332 332 0 strelka-varscan-mutect VWA8,stop_gained,p.Glu380Ter,ENST00000379310,NM_015058.1;VWA8,stop_gained,p.Glu380Ter,ENST00000281496,NM_001009814.1;VWA8,upstream_gene_variant,,ENST00000379302,; A ENST00000379310 Transcript stop_gained 1207/7147 1138/5718 380/1905 E/* Gag/Tag 1 -1 VWA8 HGNC HGNC:29071 protein_coding YES CCDS41881.1 ENSP00000368612 A3KMH1 UPI00001606AC NM_015058.1 10/45 hmmpanther:PTHR21610 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 41868420 41868420 C A 1 0 0 0 0 0 1 0 0 17800 922 32 2 2 VWA8 13 41868420 Nonsense_Mutation SNP C C3N-00704_T 4230987 41868420 72495908 425 19562 VWA8 0 . GRCh38 13 41907696 41907696 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.373G>T p.Glu125Ter p.E125* ENST00000379310 4/45 249 201 48 230 230 0 strelka-varscan-mutect VWA8,stop_gained,p.Glu125Ter,ENST00000379310,NM_015058.1;VWA8,stop_gained,p.Glu125Ter,ENST00000281496,NM_001009814.1;RNU6-74P,downstream_gene_variant,,ENST00000384235,; A ENST00000379310 Transcript stop_gained,splice_region_variant 442/7147 373/5718 125/1905 E/* Gag/Tag 1 -1 VWA8 HGNC HGNC:29071 protein_coding YES CCDS41881.1 ENSP00000368612 A3KMH1 UPI00001606AC NM_015058.1 4/45 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR21610,Superfamily_domains:SSF52540 HIGH 1 SNV 2 1 PASS rs1442109682 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 41907696 41907696 C A 1 0 0 0 0 0 1 0 0 17800 869 30 2 2 VWA8 13 41907696 Nonsense_Mutation SNP C C3N-00704_T 39276 41907696 72456632 426 19563 EPSTI1 0 . GRCh38 13 42900319 42900319 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.839A>T p.Glu280Val p.E280V ENST00000313640 10/13 245 199 46 304 304 0 strelka-varscan-mutect EPSTI1,missense_variant,p.Glu280Val,ENST00000313640,NM_001002264.2;EPSTI1,missense_variant,p.Glu269Val,ENST00000313624,NM_033255.3;EPSTI1,missense_variant,p.Glu280Val,ENST00000398762,;EPSTI1,non_coding_transcript_exon_variant,,ENST00000535677,;EPSTI1,non_coding_transcript_exon_variant,,ENST00000540470,; A ENST00000313640 Transcript missense_variant 904/3160 839/1233 280/410 E/V gAa/gTa 1 -1 EPSTI1 HGNC HGNC:16465 protein_coding YES CCDS31964.1 ENSP00000318982 Q96J88 UPI0000074657 NM_001002264.2 deleterious(0) 10/13 hmmpanther:PTHR22529:SF1,hmmpanther:PTHR22529 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 42900319 42900319 T A 1 0 0 0 0 1 0 0 0 5046 1783 62 4 4 EPSTI1 13 42900319 Missense_Mutation SNP T C3N-00704_T 992623 42900319 71464009 427 19564 SUCLA2 0 . GRCh38 13 47968646 47968646 + Missense_Mutation SNP C C A rs397515462 C3N-00704_T C3N-00704_N C C c.751G>T p.Asp251Tyr p.D251Y ENST00000378654 6/11 204 176 28 348 347 1 strelka-varscan-mutect SUCLA2,missense_variant,p.Asp251Tyr,ENST00000378654,NM_003850.2;SUCLA2,missense_variant,p.Asp181Tyr,ENST00000434484,;SUCLA2,missense_variant,p.Asp103Tyr,ENST00000433022,;SUCLA2,missense_variant,p.Asp76Tyr,ENST00000634878,;SUCLA2,3_prime_UTR_variant,,ENST00000497202,; A ENST00000378654 Transcript missense_variant 836/2192 751/1392 251/463 D/Y Gat/Tat rs397515462 1 -1 SUCLA2 HGNC HGNC:11448 protein_coding YES CCDS9406.1 ENSP00000367923 Q9P2R7 E5KS60 UPI000013CFEB NM_003850.2 deleterious(0) 6/11 Gene3D:3.30.470.20,HAMAP:MF_00558,Pfam_domain:PF08442,PIRSF_domain:PIRSF001554,PROSITE_profiles:PS50975,hmmpanther:PTHR11815,hmmpanther:PTHR11815:SF1,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01016 pathogenic MODERATE 1 SNV 1 1 1 PASS rs397515462 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 47968646 47968646 C A 1 0 0 0 0 1 0 0 0 15747 884 31 1 1 SUCLA2 13 47968646 Missense_Mutation SNP C C3N-00704_T 5068327 47968646 66395682 428 19565 NALCN 0 . GRCh38 13 101068824 101068824 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.4201C>A p.Gln1401Lys p.Q1401K ENST00000251127 38/44 75 66 9 95 95 0 strelka-mutect NALCN,missense_variant,p.Gln1401Lys,ENST00000251127,NM_052867.2; T ENST00000251127 Transcript missense_variant 4283/6818 4201/5217 1401/1738 Q/K Cag/Aag 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 tolerated(0.25) 38/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.56667 1 1 1 1 0 T 3 4 62 101068824 101068824 G T 1 0 0 0 0 1 0 0 0 10155 1304 45 2 2 NALCN 13 101068824 Missense_Mutation SNP G C3N-00704_T 53100178 101068824 13295504 429 19566 FAM155A 0 . GRCh38 13 107866176 107866176 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.421G>T p.Gly141Cys p.G141C ENST00000375915 1/3 74 64 10 94 94 0 strelka-varscan-mutect FAM155A,missense_variant,p.Gly141Cys,ENST00000375915,NM_001080396.2;RP11-346C4.3,upstream_gene_variant,,ENST00000622038,; A ENST00000375915 Transcript missense_variant 560/8503 421/1377 141/458 G/C Ggc/Tgc 1 -1 FAM155A HGNC HGNC:33877 protein_coding YES CCDS32006.1 ENSP00000365080 B1AL88 UPI000045882C NM_001080396.2 tolerated_low_confidence(0.16) 1/3 hmmpanther:PTHR15819,hmmpanther:PTHR15819:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99431 0.9999999 1 1 1 0 A 3 1 62 107866176 107866176 C A 1 0 0 0 0 1 0 0 0 5313 652 23 1 1 FAM155A 13 107866176 Missense_Mutation SNP C C3N-00704_T 6797352 107866176 6498152 430 19567 MYO16 0 . GRCh38 13 109179598 109179598 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.5380A>T p.Thr1794Ser p.T1794S ENST00000457511 34/35 136 116 20 184 184 0 strelka-varscan-mutect MYO16,missense_variant,p.Thr1794Ser,ENST00000457511,NM_001198950.1;MYO16,missense_variant,p.Thr1772Ser,ENST00000356711,NM_015011.1;MYO16,missense_variant,p.Thr1772Ser,ENST00000357550,;MYO16-AS1,intron_variant,,ENST00000439299,; T ENST00000457511 Transcript missense_variant 6002/7436 5380/5643 1794/1880 T/S Aca/Tca 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 tolerated_low_confidence(1) 34/35 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 62 109179598 109179598 A T 1 0 0 0 0 1 0 0 0 10065 275 10 4 4 MYO16 13 109179598 Missense_Mutation SNP A C3N-00704_T 1313422 109179598 5184730 431 19568 COL4A1 0 . GRCh38 13 110201476 110201476 + Missense_Mutation SNP G G T rs771204034 C3N-00704_T C3N-00704_N G G c.1046C>A p.Pro349His p.P349H ENST00000375820 19/52 246 205 41 322 322 0 strelka-varscan-mutect COL4A1,missense_variant,p.Pro349His,ENST00000375820,NM_001845.5;COL4A1,missense_variant,p.Pro349His,ENST00000543140,NM_001303110.1; T ENST00000375820 Transcript missense_variant 1168/6532 1046/5010 349/1669 P/H cCt/cAt rs771204034 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0.02) 19/52 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs771204034 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 110201476 110201476 G T 1 0 0 0 0 1 0 0 0 3478 1000 35 2 2 COL4A1 13 110201476 Missense_Mutation SNP G C3N-00704_T 1021878 110201476 4162852 432 19569 COL4A1 0 . GRCh38 13 110212610 110212610 + Silent SNP C C A rs748783113 C3N-00704_T C3N-00704_N C C c.288G>T p.= p.P96P ENST00000375820 5/52 306 255 51 359 358 1 strelka-varscan-mutect COL4A1,synonymous_variant,p.=,ENST00000375820,NM_001845.5;COL4A1,synonymous_variant,p.=,ENST00000543140,NM_001303110.1;COL4A1,synonymous_variant,p.=,ENST00000615732,; A ENST00000375820 Transcript synonymous_variant 410/6532 288/5010 96/1669 P ccG/ccT rs748783113 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 5/52 Pfam_domain:PF01391,Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543 LOW 1 SNV 1 1 PASS rs748783113 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 110212610 110212610 C A 1 0 0 0 0 0 0 0 1 3478 639 23 1 1 COL4A1 13 110212610 Silent SNP C C3N-00704_T 11134 110212610 4151718 433 19570 OR11H2 0 . GRCh38 14 19713025 19713025 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.892C>A p.Pro298Thr p.P298T ENST00000556246 1/1 353 323 30 502 502 0 varscan-mutect OR11H2,missense_variant,p.Pro298Thr,ENST00000556246,NM_001197287.1; T ENST00000556246 Transcript missense_variant 896/985 892/981 298/326 P/T Cca/Aca 1 -1 OR11H2 HGNC HGNC:14716 protein_coding YES CCDS76655.1 ENSP00000485150 Q8NH07 UPI0000061EAC NM_001197287.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF201,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1471645703 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 19713025 19713025 G T 1 0 0 0 0 1 0 0 0 11004 1232 43 2 2 OR11H2 14 19713025 Missense_Mutation SNP G C3N-00704_T 19713025 87330693 434 19571 OR4N2 0 . GRCh38 14 19827616 19827616 + Silent SNP A A T C3N-00704_T C3N-00704_N A A c.168A>T p.= p.T56T ENST00000315947 1/1 292 275 17 396 396 0 varscan-mutect OR4N2,synonymous_variant,p.=,ENST00000315947,NM_001004723.2;OR4N2,synonymous_variant,p.=,ENST00000557677,;OR4N2,downstream_gene_variant,,ENST00000557414,; T ENST00000315947 Transcript synonymous_variant 168/924 168/924 56/307 T acA/acT COSM5070113 1 1 OR4N2 HGNC HGNC:14742 protein_coding YES CCDS32022.1 ENSP00000319601 Q8NGD1 A0A126GVT2 UPI000004A5DF NM_001004723.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF439,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 19827616 19827616 A T 1 0 0 0 0 0 0 0 1 11153 175 7 4 4 OR4N2 14 19827616 Silent SNP A C3N-00704_T 114591 19827616 87216102 435 19572 OR4K2 0 . GRCh38 14 19876930 19876930 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.663C>A p.= p.V221V ENST00000298642 1/1 655 620 35 923 923 0 strelka-varscan-mutect OR4K2,synonymous_variant,p.=,ENST00000298642,NM_001005501.1; A ENST00000298642 Transcript synonymous_variant 699/1078 663/945 221/314 V gtC/gtA 1 1 OR4K2 HGNC HGNC:14728 protein_coding YES CCDS32023.1 ENSP00000298642 Q8NGD2 A0A126GVP5 UPI0000041B4D NM_001005501.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF260,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs997624085 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 19876930 19876930 C A 1 0 0 0 0 0 0 0 1 11149 842 30 2 2 OR4K2 14 19876930 Silent SNP C C3N-00704_T 49314 19876930 87166788 436 19573 70 2 OR4K2 0 . GRCh38 14 19876931 19876931 + Missense_Mutation SNP C C A rs771348325 C3N-00704_T C3N-00704_N C C c.664C>A p.Leu222Met p.L222M ENST00000298642 1/1 663 623 40 936 936 0 strelka-varscan-mutect OR4K2,missense_variant,p.Leu222Met,ENST00000298642,NM_001005501.1; A ENST00000298642 Transcript missense_variant 700/1078 664/945 222/314 L/M Ctg/Atg rs771348325 1 1 OR4K2 HGNC HGNC:14728 protein_coding YES CCDS32023.1 ENSP00000298642 Q8NGD2 A0A126GVP5 UPI0000041B4D NM_001005501.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF260,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs771348325 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 19876931 19876931 C A 1 0 0 0 0 1 0 0 0 11149 680 24 2 2 OR4K2 14 19876931 Missense_Mutation SNP C C3N-00704_T 1 19876931 87166787 437 19574 70 2 OR4N5 0 . GRCh38 14 20144293 20144293 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.558G>C p.Lys186Asn p.K186N ENST00000333629 1/1 212 172 40 267 267 0 strelka-varscan-mutect OR4N5,missense_variant,p.Lys186Asn,ENST00000333629,NM_001004724.1;PSMB7P1,upstream_gene_variant,,ENST00000556349,; C ENST00000333629 Transcript missense_variant 558/927 558/927 186/308 K/N aaG/aaC 1 1 OR4N5 HGNC HGNC:15358 protein_coding YES CCDS32031.1 ENSP00000332110 Q8IXE1 A0A126GVN4 UPI0000041C40 NM_001004724.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF40,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 20144293 20144293 G C 1 0 0 0 0 1 0 0 0 11155 962 34 4 4 OR4N5 14 20144293 Missense_Mutation SNP G C3N-00704_T 267362 20144293 86899425 438 19575 RNASE13 0 . GRCh38 14 21034090 21034090 + Missense_Mutation SNP C C A rs745935764 C3N-00704_T C3N-00704_N C C c.199G>T p.Asp67Tyr p.D67Y ENST00000382951 2/2 244 210 34 308 308 0 strelka-varscan-mutect RNASE13,missense_variant,p.Asp67Tyr,ENST00000382951,NM_001012264.3;NDRG2,intron_variant,,ENST00000403829,NM_001282211.1;NDRG2,intron_variant,,ENST00000555026,;TPPP2,intron_variant,,ENST00000472458,;TPPP2,intron_variant,,ENST00000555751,;TPPP2,intron_variant,,ENST00000481535,;TPPP2,downstream_gene_variant,,ENST00000321760,NM_173846.4;TPPP2,downstream_gene_variant,,ENST00000530140,;TPPP2,downstream_gene_variant,,ENST00000460647,;AL161668.5,downstream_gene_variant,,ENST00000533984,;AL161668.5,downstream_gene_variant,,ENST00000532213,;RP11-998D10.1,downstream_gene_variant,,ENST00000531638,;TPPP2,intron_variant,,ENST00000495665,;TPPP2,intron_variant,,ENST00000529496,;TPPP2,downstream_gene_variant,,ENST00000534434,;TPPP2,downstream_gene_variant,,ENST00000533755,;TPPP2,downstream_gene_variant,,ENST00000525425,;TPPP2,downstream_gene_variant,,ENST00000532060,; A ENST00000382951 Transcript missense_variant 337/1607 199/471 67/156 D/Y Gat/Tat rs745935764 1 -1 RNASE13 HGNC HGNC:25285 protein_coding YES CCDS32039.1 ENSP00000372410 Q5GAN3 V9HW52 UPI00001FCFB5 NM_001012264.3 tolerated(1) 2/2 Gene3D:3.10.130.10,PD000535,Pfam_domain:PF00074,hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF11,Superfamily_domains:SSF54076 MODERATE 1 SNV 1 1 PASS rs745935764 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 21034090 21034090 C A 1 0 0 0 0 1 0 0 0 13582 913 32 2 2 RNASE13 14 21034090 Missense_Mutation SNP C C3N-00704_T 889797 21034090 86009628 439 19576 IPO4 0 . GRCh38 14 24187772 24187772 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.303C>T p.= p.A101A ENST00000354464 5/30 161 130 31 211 211 0 strelka-varscan-mutect IPO4,synonymous_variant,p.=,ENST00000354464,NM_024658.3;RP11-468E2.2,intron_variant,,ENST00000625289,;RP11-468E2.1,downstream_gene_variant,,ENST00000530611,;TM9SF1,downstream_gene_variant,,ENST00000261789,NM_006405.6;TM9SF1,downstream_gene_variant,,ENST00000528669,;TM9SF1,downstream_gene_variant,,ENST00000396854,NM_001014842.2;TM9SF1,downstream_gene_variant,,ENST00000524835,NM_001289006.1;IPO4,upstream_gene_variant,,ENST00000561462,;IPO4,upstream_gene_variant,,ENST00000558233,;TM9SF1,downstream_gene_variant,,ENST00000528895,;TM9SF1,downstream_gene_variant,,ENST00000530563,;TM9SF1,downstream_gene_variant,,ENST00000532632,;IPO4,missense_variant,p.Pro91Ser,ENST00000558046,;IPO4,synonymous_variant,p.=,ENST00000560155,;RP11-468E2.2,3_prime_UTR_variant,,ENST00000561419,;IPO4,3_prime_UTR_variant,,ENST00000558780,;IPO4,non_coding_transcript_exon_variant,,ENST00000561090,;IPO4,non_coding_transcript_exon_variant,,ENST00000560798,;IPO4,non_coding_transcript_exon_variant,,ENST00000559588,;IPO4,non_coding_transcript_exon_variant,,ENST00000561199,;IPO4,non_coding_transcript_exon_variant,,ENST00000558193,;IPO4,non_coding_transcript_exon_variant,,ENST00000558718,;IPO4,non_coding_transcript_exon_variant,,ENST00000559635,;IPO4,intron_variant,,ENST00000559253,;TM9SF1,downstream_gene_variant,,ENST00000529332,;TM9SF1,downstream_gene_variant,,ENST00000531406,;IPO4,upstream_gene_variant,,ENST00000560935,;IPO4,upstream_gene_variant,,ENST00000561379,;IPO4,downstream_gene_variant,,ENST00000560222,;IPO4,downstream_gene_variant,,ENST00000560315,;IPO4,downstream_gene_variant,,ENST00000561034,;IPO4,downstream_gene_variant,,ENST00000557996,; A ENST00000354464 Transcript synonymous_variant 480/3646 303/3246 101/1081 A gcC/gcT 1 -1 IPO4 HGNC HGNC:19426 protein_coding YES CCDS9616.1 ENSP00000346453 Q8TEX9 UPI000013CCB3 NM_024658.3 5/30 Gene3D:1.25.10.10,hmmpanther:PTHR10527,hmmpanther:PTHR10527:SF6,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs1426242676 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 24187772 24187772 G A 1 0 0 0 0 0 0 0 1 7698 1219 43 3 3 IPO4 14 24187772 Silent SNP G C3N-00704_T 3153682 24187772 82855946 440 19577 NOP9 0 . GRCh38 14 24302283 24302283 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1002G>T p.Gln334His p.Q334H ENST00000267425 5/10 196 168 28 173 173 0 strelka-varscan-mutect NOP9,missense_variant,p.Gln334His,ENST00000267425,NM_174913.2;NOP9,missense_variant,p.Gln334His,ENST00000396802,NM_001286367.1;CIDEB,downstream_gene_variant,,ENST00000336557,NM_001318807.1;CIDEB,downstream_gene_variant,,ENST00000258807,NM_014430.2;CIDEB,downstream_gene_variant,,ENST00000554411,;DHRS1,upstream_gene_variant,,ENST00000288111,NM_001136050.2;DHRS1,upstream_gene_variant,,ENST00000396813,NM_138452.2;LTB4R2,upstream_gene_variant,,ENST00000527924,;NOP9,upstream_gene_variant,,ENST00000557362,;CIDEB,downstream_gene_variant,,ENST00000556756,;DHRS1,upstream_gene_variant,,ENST00000559483,;DHRS1,upstream_gene_variant,,ENST00000561273,;DHRS1,upstream_gene_variant,,ENST00000558340,;DHRS1,upstream_gene_variant,,ENST00000558114,;DHRS1,upstream_gene_variant,,ENST00000560991,; T ENST00000267425 Transcript missense_variant 1095/6033 1002/1911 334/636 Q/H caG/caT 1 1 NOP9 HGNC HGNC:19826 protein_coding YES CCDS9624.1 ENSP00000267425 Q86U38 UPI000000CBCF NM_174913.2 tolerated(0.06) 5/10 Gene3D:1.25.10.10,hmmpanther:PTHR13102,hmmpanther:PTHR13102:SF0,Low_complexity_(Seg):seg,SMART_domains:SM00025,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1332639713 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 24302283 24302283 G T 1 0 0 0 0 1 0 0 0 10585 991 35 2 2 NOP9 14 24302283 Missense_Mutation SNP G C3N-00704_T 114511 24302283 82741435 441 19578 LRFN5 0 . GRCh38 14 41891258 41891258 + Missense_Mutation SNP C C G rs767752963 C3N-00704_T C3N-00704_N C C c.1394C>G p.Pro465Arg p.P465R ENST00000298119 4/6 208 169 39 336 336 0 strelka-mutect LRFN5,missense_variant,p.Pro465Arg,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; G ENST00000298119 Transcript missense_variant 2583/3723 1394/2160 465/719 P/R cCt/cGt rs767752963 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0) 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs767752963 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 41891258 41891258 C G 1 0 0 0 0 1 0 0 0 8835 681 24 4 4 LRFN5 14 41891258 Missense_Mutation SNP C C3N-00704_T 17588975 41891258 65152460 442 19579 MDGA2 0 . GRCh38 14 47035281 47035281 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1342C>G p.Gln448Glu p.Q448E ENST00000399232 8/17 146 89 57 159 159 0 strelka-varscan-mutect MDGA2,missense_variant,p.Gln318Glu,ENST00000426342,;MDGA2,missense_variant,p.Gln448Glu,ENST00000399232,NM_001113498.2;MDGA2,missense_variant,p.Gln219Glu,ENST00000357362,NM_182830.4;MDGA2,missense_variant,p.Gln223Glu,ENST00000554762,;MDGA2,splice_region_variant,,ENST00000557238,; C ENST00000399232 Transcript missense_variant 1707/5075 1342/2871 448/956 Q/E Cag/Gag 1 -1 MDGA2 HGNC HGNC:19835 protein_coding YES CCDS45098.3 ENSP00000382178 Q7Z553 UPI00001C14FF NM_001113498.2 tolerated(0.47) 8/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF62,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 47035281 47035281 G C 1 0 0 0 0 1 0 0 0 9345 1386 48 4 4 MDGA2 14 47035281 Missense_Mutation SNP G C3N-00704_T 5144023 47035281 60008437 443 19580 L2HGDH 0 . GRCh38 14 50247059 50247059 + Nonstop_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.1391A>T p.Ter464LeuextTer10 p.*464Lext*10 ENST00000267436 10/10 159 115 44 175 175 0 strelka-varscan-mutect L2HGDH,stop_lost,p.Ter464LeuextTer10,ENST00000267436,NM_024884.2;L2HGDH,stop_lost,p.Ter464LeuextTer16,ENST00000421284,;L2HGDH,intron_variant,,ENST00000261699,; A ENST00000267436 Transcript stop_lost 1789/6414 1391/1392 464/463 */L tAa/tTa 1 -1 L2HGDH HGNC HGNC:20499 protein_coding YES CCDS9698.1 ENSP00000267436 Q9H9P8 UPI0000048F63 NM_024884.2 10/10 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 50247059 50247059 T A 1 0 0 0 0 0 0 0 0 8491 1761 61 4 4 L2HGDH 14 50247059 Nonstop_Mutation SNP T C3N-00704_T 3211778 50247059 56796659 444 19581 C14orf39 0 . GRCh38 14 60455005 60455005 + Missense_Mutation SNP T T A C3N-00704_T C3N-00704_N T T c.1499A>T p.Asp500Val p.D500V ENST00000321731 16/18 35 21 14 78 77 1 strelka-varscan-mutect C14orf39,missense_variant,p.Asp500Val,ENST00000321731,NM_174978.2;C14orf39,missense_variant,p.Asp16Val,ENST00000498565,;C14orf39,3_prime_UTR_variant,,ENST00000557138,; A ENST00000321731 Transcript missense_variant 1659/2813 1499/1764 500/587 D/V gAt/gTt COSM4666857 1 -1 C14orf39 HGNC HGNC:19849 protein_coding YES CCDS9746.1 ENSP00000324920 Q8N1H7 UPI0000140C15 NM_174978.2 deleterious(0) 16/18 hmmpanther:PTHR35449,Pfam_domain:PF15676 1 MODERATE 1 SNV 1 1 1 PASS . . 2 202 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 60455005 60455005 T A 1 0 0 0 0 1 0 0 0 1839 1449 50 4 4 C14orf39 14 60455005 Missense_Mutation SNP T C3N-00704_T 10207946 60455005 46588713 445 19582 SLC38A6 0 . GRCh38 14 61052356 61052356 + Missense_Mutation SNP T T G novel C3N-00704_T C3N-00704_N T T c.1298T>G p.Val433Gly p.V433G ENST00000267488 16/16 79 72 7 210 210 0 strelka-mutect SLC38A6,missense_variant,p.Val433Gly,ENST00000267488,NM_153811.2;SLC38A6,missense_variant,p.Val206Gly,ENST00000529212,;SLC38A6,intron_variant,,ENST00000354886,NM_001172702.1;SLC38A6,intron_variant,,ENST00000451406,;SLC38A6,3_prime_UTR_variant,,ENST00000525723,;SLC38A6,3_prime_UTR_variant,,ENST00000491344,;SLC38A6,3_prime_UTR_variant,,ENST00000527591,;SLC38A6,non_coding_transcript_exon_variant,,ENST00000556938,;SLC38A6,non_coding_transcript_exon_variant,,ENST00000554498,;SLC38A6,intron_variant,,ENST00000529345,;SLC38A6,intron_variant,,ENST00000526539,; G ENST00000267488 Transcript missense_variant 1414/1688 1298/1371 433/456 V/G gTt/gGt 1 1 SLC38A6 HGNC HGNC:19863 protein_coding CCDS9751.1 ENSP00000267488 Q8IZM9 UPI000013D755 NM_153811.2 deleterious(0.05) 16/16 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF72,Transmembrane_helices:TMhelix MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 61052356 61052356 T G 1 0 0 0 0 1 0 0 0 14886 1725 60 5 5 SLC38A6 14 61052356 Missense_Mutation SNP T C3N-00704_T 597351 61052356 45991362 446 19583 FLRT2 0 . GRCh38 14 85621985 85621985 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.471G>T p.Glu157Asp p.E157D ENST00000330753 2/2 52 44 8 77 77 0 strelka-varscan-mutect FLRT2,missense_variant,p.Glu157Asp,ENST00000330753,NM_013231.4;FLRT2,missense_variant,p.Glu157Asp,ENST00000554746,;FLRT2,upstream_gene_variant,,ENST00000553650,; T ENST00000330753 Transcript missense_variant 1238/33679 471/1983 157/660 E/D gaG/gaT 1 1 FLRT2 HGNC HGNC:3761 protein_coding YES CCDS9877.1 ENSP00000332879 O43155 UPI0000049E10 NM_013231.4 tolerated(1) 2/2 hmmpanther:PTHR24369:SF23,hmmpanther:PTHR24369,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -18.8182 0.9999996 1 1 1 0 T 3 4 62 85621985 85621985 G T 1 0 0 0 0 1 0 0 0 5795 991 35 2 2 FLRT2 14 85621985 Missense_Mutation SNP G C3N-00704_T 24569629 85621985 21421733 447 19584 UNC79 0 . GRCh38 14 93612842 93612842 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.3269C>A p.Pro1090Gln p.P1090Q ENST00000256339 27/50 220 176 44 233 233 0 strelka-varscan-mutect UNC79,missense_variant,p.Pro1289Gln,ENST00000553484,;UNC79,missense_variant,p.Pro1267Gln,ENST00000555664,;UNC79,missense_variant,p.Pro1090Gln,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Pro1267Gln,ENST00000393151,;UNC79,missense_variant,p.Pro1090Gln,ENST00000621021,; A ENST00000256339 Transcript missense_variant 3924/8400 3269/7377 1090/2458 P/Q cCa/cAa 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated(0.08) 27/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999965 1 1 1 0 A 3 1 62 93612842 93612842 C A 1 0 0 0 0 1 0 0 0 17520 594 21 2 2 UNC79 14 93612842 Missense_Mutation SNP C C3N-00704_T 7990857 93612842 13430876 448 19585 IFI27L1 0 . GRCh38 14 94100769 94100769 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.59G>T p.Gly20Val p.G20V ENST00000555523 3/5 382 305 77 385 383 2 strelka-varscan-mutect IFI27L1,missense_variant,p.Gly19Val,ENST00000556381,;IFI27L1,missense_variant,p.Gly20Val,ENST00000555523,NM_206949.2;IFI27L1,missense_variant,p.Gly20Val,ENST00000393115,NM_145249.2;IFI27L1,missense_variant,p.Arg42Ser,ENST00000553664,;IFI27L1,missense_variant,p.Gly19Val,ENST00000555341,;IFI27L1,missense_variant,p.Gly19Val,ENST00000554166,;IFI27L1,missense_variant,p.Gly20Val,ENST00000557066,;IFI27L1,missense_variant,p.Gly20Val,ENST00000554562,;IFI27L1,missense_variant,p.Gly20Val,ENST00000557218,;IFI27L1,intron_variant,,ENST00000554544,;IFI27,upstream_gene_variant,,ENST00000614204,;IFI27L1,intron_variant,,ENST00000553350,;IFI27L1,non_coding_transcript_exon_variant,,ENST00000557600,; T ENST00000555523 Transcript missense_variant,splice_region_variant 278/680 59/315 20/104 G/V gGa/gTa 1 1 IFI27L1 HGNC HGNC:19754 protein_coding YES CCDS9919.1 ENSP00000451851 Q96BM0 UPI000012A3C8 NM_206949.2 deleterious(0.01) 3/5 Pfam_domain:PF06140,hmmpanther:PTHR16932,hmmpanther:PTHR16932:SF22,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 94100769 94100769 G T 1 0 0 0 0 1 0 0 0 7414 1188 41 2 2 IFI27L1 14 94100769 Missense_Mutation SNP G C3N-00704_T 487927 94100769 12942949 449 19586 IFI27L2 0 . GRCh38 14 94128555 94128555 + Missense_Mutation SNP C C T rs777656704 C3N-00704_T C3N-00704_N C C c.158G>A p.Gly53Asp p.G53D ENST00000238609 3/4 251 209 42 274 274 0 strelka-varscan-mutect IFI27L2,missense_variant,p.Gly28Asp,ENST00000556727,;IFI27L2,missense_variant,p.Gly53Asp,ENST00000238609,NM_032036.2;IFI27L2,non_coding_transcript_exon_variant,,ENST00000556552,;IFI27L2,non_coding_transcript_exon_variant,,ENST00000554909,;IFI27L2,non_coding_transcript_exon_variant,,ENST00000555558,;IFI27L2,intron_variant,,ENST00000553601,; T ENST00000238609 Transcript missense_variant 258/511 158/393 53/130 G/D gGt/gAt rs777656704,COSM4923132 1 -1 IFI27L2 HGNC HGNC:19753 protein_coding YES CCDS9920.1 ENSP00000238609 Q9H2X8 UPI0000049526 NM_032036.2 deleterious(0) 3/4 hmmpanther:PTHR16932,hmmpanther:PTHR16932:SF2,Pfam_domain:PF06140 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777656704 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 94128555 94128555 C T 1 0 0 0 0 1 0 0 0 7415 507 18 3 3 IFI27L2 14 94128555 Missense_Mutation SNP C C3N-00704_T 27786 94128555 12915163 450 19587 PPP4R4 0 . GRCh38 14 94256524 94256524 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.1930C>G p.Leu644Val p.L644V ENST00000304338 17/25 99 94 5 169 169 0 strelka-varscan PPP4R4,missense_variant,p.Leu644Val,ENST00000304338,NM_058237.1; G ENST00000304338 Transcript missense_variant 2084/3868 1930/2622 644/873 L/V Cta/Gta 1 1 PPP4R4 HGNC HGNC:23788 protein_coding YES CCDS9921.1 ENSP00000305924 Q6NUP7 UPI000016223B NM_058237.1 deleterious(0.03) 17/25 Gene3D:1.25.10.10,hmmpanther:PTHR21467,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 94256524 94256524 C G 1 0 0 0 0 1 0 0 0 12530 912 32 4 4 PPP4R4 14 94256524 Missense_Mutation SNP C C3N-00704_T 127969 94256524 12787194 451 19588 TCL1A 0 . GRCh38 14 95714053 95714053 + Missense_Mutation SNP G G T rs772465102 C3N-00704_T C3N-00704_N G G c.14C>A p.Pro5Gln p.P5Q ENST00000402399 1/4 137 115 22 161 161 0 strelka-varscan-mutect TCL1A,missense_variant,p.Pro5Gln,ENST00000402399,NM_021966.2;TCL1A,missense_variant,p.Pro5Gln,ENST00000554012,NM_001098725.1;TCL1A,missense_variant,p.Pro5Gln,ENST00000556450,;TCL1A,missense_variant,p.Pro5Gln,ENST00000555202,;TCL1A,upstream_gene_variant,,ENST00000557043,;RP11-164H13.1,intron_variant,,ENST00000553445,;RP11-164H13.1,intron_variant,,ENST00000547644,;RP11-164H13.1,upstream_gene_variant,,ENST00000556386,;TCL1A,missense_variant,p.Pro5Gln,ENST00000554119,;TCL1A,missense_variant,p.Pro5Gln,ENST00000556156,;TCL1A,missense_variant,p.Pro5Gln,ENST00000555886,;TCL1A,upstream_gene_variant,,ENST00000553467,; T ENST00000402399 Transcript missense_variant 144/1395 14/345 5/114 P/Q cCg/cAg rs772465102 1 -1 TCL1A HGNC HGNC:11648 protein_coding YES CCDS9941.1 ENSP00000385036 P56279 A0A024R6G5 UPI00000413AD NM_021966.2 tolerated(0.23) 1/4 Gene3D:2.40.15.10,Pfam_domain:PF01840,hmmpanther:PTHR14060,hmmpanther:PTHR14060:SF4 MODERATE 1 SNV 1 1 PASS rs772465102 . 0 207 0 3 0 0 0 0 -20 0.9999945 1 1 1 0 T 3 4 62 95714053 95714053 G T 1 0 0 0 0 1 0 0 0 16111 1116 39 1 1 TCL1A 14 95714053 Missense_Mutation SNP G C3N-00704_T 1457529 95714053 11329665 452 19589 SLC25A47 0 . GRCh38 14 100328751 100328751 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.353T>A p.Val118Glu p.V118E ENST00000361529 5/6 620 452 168 693 693 0 strelka-varscan-mutect SLC25A47,missense_variant,p.Val118Glu,ENST00000361529,NM_207117.2;SLC25A47,5_prime_UTR_variant,,ENST00000557052,; A ENST00000361529 Transcript missense_variant 431/1738 353/927 118/308 V/E gTg/gAg 1 1 SLC25A47 HGNC HGNC:20115 protein_coding YES CCDS9959.1 ENSP00000354886 Q6Q0C1 A0A024R6H7 UPI000004ABFB NM_207117.2 deleterious(0) 5/6 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF224,hmmpanther:PTHR24089,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588,Prints_domain:PR00926 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 100328751 100328751 T A 1 0 0 0 0 1 0 0 0 14777 1696 59 4 4 SLC25A47 14 100328751 Missense_Mutation SNP T C3N-00704_T 4614698 100328751 6714967 453 19590 RTL1 0 . GRCh38 14 100881633 100881633 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.3156C>A p.= p.A1052A ENST00000534062 1/1 157 135 22 214 214 0 strelka-varscan-mutect RTL1,synonymous_variant,p.=,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,upstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; T ENST00000534062 Transcript synonymous_variant 3215/4193 3156/4077 1052/1358 A gcC/gcA 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 1/1 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF9 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 100881633 100881633 G T 1 0 0 0 0 0 0 0 1 13984 1335 47 2 2 RTL1 14 100881633 Silent SNP G C3N-00704_T 552882 100881633 6162085 454 19591 BAG5 0 . GRCh38 14 103559853 103559853 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1435C>G p.Leu479Val p.L479V ENST00000337322 2/2 129 120 9 133 133 0 strelka-varscan-mutect BAG5,missense_variant,p.Leu438Val,ENST00000445922,NM_004873.3;BAG5,missense_variant,p.Leu438Val,ENST00000299204,NM_001015048.2;BAG5,missense_variant,p.Leu479Val,ENST00000337322,NM_001015049.2;APOPT1,upstream_gene_variant,,ENST00000409074,NM_032374.4,NM_001302652.1;RP11-73M18.2,upstream_gene_variant,,ENST00000472726,;APOPT1,upstream_gene_variant,,ENST00000477116,;BAG5,downstream_gene_variant,,ENST00000557666,;APOPT1,upstream_gene_variant,,ENST00000556253,NM_001302653.1;APOPT1,upstream_gene_variant,,ENST00000476323,;APOPT1,upstream_gene_variant,,ENST00000473127,;APOPT1,upstream_gene_variant,,ENST00000495778,NM_001302654.1;APOPT1,upstream_gene_variant,,ENST00000440963,;KLC1,upstream_gene_variant,,ENST00000557172,;APOPT1,upstream_gene_variant,,ENST00000492189,;RP11-894P9.2,intron_variant,,ENST00000556332,;APOPT1,upstream_gene_variant,,ENST00000497901,;APOPT1,upstream_gene_variant,,ENST00000458117,;APOPT1,upstream_gene_variant,,ENST00000489117,;APOPT1,upstream_gene_variant,,ENST00000554625,; C ENST00000337322 Transcript missense_variant 1726/1960 1435/1467 479/488 L/V Ctc/Gtc 1 -1 BAG5 HGNC HGNC:941 protein_coding YES CCDS41995.1 ENSP00000338814 Q9UL15 UPI00001FDC93 NM_001015049.2 deleterious(0) 2/2 PROSITE_profiles:PS51035,hmmpanther:PTHR12329,hmmpanther:PTHR12329:SF2,Pfam_domain:PF02179,Gene3D:1.20.58.120,SMART_domains:SM00264,Superfamily_domains:SSF63491 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 103559853 103559853 G C 1 0 0 0 0 1 0 0 0 1448 942 33 4 4 BAG5 14 103559853 Missense_Mutation SNP G C3N-00704_T 2678220 103559853 3483865 455 19592 BAG5 0 . GRCh38 14 103560355 103560355 + Silent SNP C C G novel C3N-00704_T C3N-00704_N C C c.933G>C p.= p.L311L ENST00000337322 2/2 192 171 21 243 243 0 strelka-varscan-mutect BAG5,synonymous_variant,p.=,ENST00000445922,NM_004873.3;BAG5,synonymous_variant,p.=,ENST00000299204,NM_001015048.2;BAG5,synonymous_variant,p.=,ENST00000337322,NM_001015049.2;APOPT1,upstream_gene_variant,,ENST00000409074,NM_032374.4,NM_001302652.1;RP11-73M18.2,upstream_gene_variant,,ENST00000472726,;APOPT1,upstream_gene_variant,,ENST00000477116,;BAG5,downstream_gene_variant,,ENST00000557666,;APOPT1,upstream_gene_variant,,ENST00000556253,NM_001302653.1;APOPT1,upstream_gene_variant,,ENST00000476323,;APOPT1,upstream_gene_variant,,ENST00000473127,;APOPT1,upstream_gene_variant,,ENST00000495778,NM_001302654.1;APOPT1,upstream_gene_variant,,ENST00000440963,;KLC1,upstream_gene_variant,,ENST00000557172,;APOPT1,upstream_gene_variant,,ENST00000492189,;RP11-894P9.2,intron_variant,,ENST00000556332,;APOPT1,upstream_gene_variant,,ENST00000497901,;APOPT1,upstream_gene_variant,,ENST00000458117,;APOPT1,upstream_gene_variant,,ENST00000489117,;APOPT1,upstream_gene_variant,,ENST00000554625,; G ENST00000337322 Transcript synonymous_variant 1224/1960 933/1467 311/488 L ctG/ctC 1 -1 BAG5 HGNC HGNC:941 protein_coding YES CCDS41995.1 ENSP00000338814 Q9UL15 UPI00001FDC93 NM_001015049.2 2/2 hmmpanther:PTHR12329,hmmpanther:PTHR12329:SF2,Gene3D:1.20.58.120,Superfamily_domains:SSF63491 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 103560355 103560355 C G 1 0 0 0 0 0 0 0 1 1448 813 29 4 4 BAG5 14 103560355 Silent SNP C C3N-00704_T 502 103560355 3483363 456 19593 BAG5 0 . GRCh38 14 103561122 103561122 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.166G>A p.Glu56Lys p.E56K ENST00000337322 2/2 103 93 10 150 149 1 strelka-varscan-mutect BAG5,missense_variant,p.Glu15Lys,ENST00000445922,NM_004873.3;BAG5,missense_variant,p.Glu15Lys,ENST00000299204,NM_001015048.2;BAG5,missense_variant,p.Glu56Lys,ENST00000337322,NM_001015049.2;BAG5,missense_variant,p.Glu15Lys,ENST00000557666,;APOPT1,upstream_gene_variant,,ENST00000409074,NM_032374.4,NM_001302652.1;RP11-73M18.2,upstream_gene_variant,,ENST00000472726,;APOPT1,upstream_gene_variant,,ENST00000477116,;APOPT1,upstream_gene_variant,,ENST00000556253,NM_001302653.1;APOPT1,upstream_gene_variant,,ENST00000476323,;APOPT1,upstream_gene_variant,,ENST00000473127,;APOPT1,upstream_gene_variant,,ENST00000495778,NM_001302654.1;APOPT1,upstream_gene_variant,,ENST00000440963,;KLC1,upstream_gene_variant,,ENST00000557172,;APOPT1,upstream_gene_variant,,ENST00000492189,;RP11-894P9.2,intron_variant,,ENST00000556332,;APOPT1,upstream_gene_variant,,ENST00000497901,;APOPT1,upstream_gene_variant,,ENST00000458117,;APOPT1,upstream_gene_variant,,ENST00000489117,;APOPT1,upstream_gene_variant,,ENST00000554625,; T ENST00000337322 Transcript missense_variant 457/1960 166/1467 56/488 E/K Gaa/Aaa 1 -1 BAG5 HGNC HGNC:941 protein_coding YES CCDS41995.1 ENSP00000338814 Q9UL15 UPI00001FDC93 NM_001015049.2 deleterious(0.01) 2/2 PROSITE_profiles:PS51035,hmmpanther:PTHR12329,hmmpanther:PTHR12329:SF2,Pfam_domain:PF02179,Gene3D:1.20.58.120,SMART_domains:SM00264,Superfamily_domains:SSF63491 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 103561122 103561122 C T 1 0 0 0 0 1 0 0 0 1448 864 30 3 3 BAG5 14 103561122 Missense_Mutation SNP C C3N-00704_T 767 103561122 3482596 457 19594 AHNAK2 0 . GRCh38 14 104950244 104950244 + Frame_Shift_Del DEL C C - novel C3N-00704_T C3N-00704_N C C c.5207delG p.Gly1736AlafsTer14 p.G1736Afs*14 ENST00000333244 7/7 401 316 85 743 743 0 sindel-varindel-pindel AHNAK2,frameshift_variant,p.Gly1736AlafsTer14,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; - ENST00000333244 Transcript frameshift_variant 5327/18254 5207/17388 1736/5795 G/X gGc/gc 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 7/7 hmmpanther:PTHR23348:SF37,hmmpanther:PTHR23348 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 104950244 104950244 C - 1 0 1 0 1 0 0 0 0 492 739 26 0 0 AHNAK2 14 104950244 Frame_Shift_Del DEL C C3N-00704_T 1389122 104950244 2093474 458 19595 NPAP1 0 . GRCh38 15 24676936 24676936 + Missense_Mutation SNP C C A rs780241835 C3N-00704_T C3N-00704_N C C c.1069C>A p.Leu357Ile p.L357I ENST00000329468 1/1 120 95 25 178 178 0 strelka-varscan-mutect NPAP1,missense_variant,p.Leu357Ile,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1069/7526 1069/3471 357/1156 L/I Ctc/Atc rs780241835 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 deleterious(0.04) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15,Pfam_domain:PF15229 MODERATE 1 SNV 1 PASS rs780241835 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 24676936 24676936 C A 1 0 0 0 0 1 0 0 0 10609 797 28 2 2 NPAP1 15 24676936 Missense_Mutation SNP C C3N-00704_T 24676936 77314253 459 19596 AC124312.1 0 . GRCh38 15 25092136 25092136 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.242C>A p.Thr81Lys p.T81K ENST00000623624 1/1 179 138 41 255 255 0 strelka-varscan-mutect AC124312.1,missense_variant,p.Thr81Lys,ENST00000623624,;RP11-701H24.4,downstream_gene_variant,,ENST00000567527,;SNORD116-22,downstream_gene_variant,,ENST00000384430,;SNORD116-21,downstream_gene_variant,,ENST00000384507,;SNORD116-20,downstream_gene_variant,,ENST00000384529,;SNORD116-24,upstream_gene_variant,,ENST00000384549,;SNORD116-23,downstream_gene_variant,,ENST00000384645,;SNHG14,intron_variant,,ENST00000546682,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,intron_variant,,ENST00000553108,; T ENST00000623624 Transcript missense_variant 242/418 242/417 81/138 T/K aCa/aAa 1 -1 AC124312.1 Clone_based_ensembl_gene protein_coding YES ENSP00000485422 A0A0B4J2H5 UPI000006F2CD 1/1 MODERATE SNV 1 PASS rs948827199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 25092136 25092136 G T 1 0 0 0 0 1 0 0 0 141 1377 48 2 2 AC124312.1 15 25092136 Missense_Mutation SNP G C3N-00704_T 415200 25092136 76899053 460 19597 GABRB3 0 . GRCh38 15 26547886 26547886 + Silent SNP G G T rs754147659 C3N-00704_T C3N-00704_N G G c.1329C>A p.= p.T443T ENST00000311550 9/9 243 189 54 416 416 0 strelka-varscan-mutect GABRB3,synonymous_variant,p.=,ENST00000541819,;GABRB3,synonymous_variant,p.=,ENST00000622697,NM_001278631.1;GABRB3,synonymous_variant,p.=,ENST00000311550,NM_000814.5;GABRB3,synonymous_variant,p.=,ENST00000628124,NM_001191320.1;GABRB3,synonymous_variant,p.=,ENST00000636466,;GABRB3,synonymous_variant,p.=,ENST00000299267,NM_021912.4;GABRB3,synonymous_variant,p.=,ENST00000638099,;GABRB3,synonymous_variant,p.=,ENST00000400188,NM_001191321.2;GABRB3,synonymous_variant,p.=,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,downstream_gene_variant,,ENST00000637293,;GABRB3,3_prime_UTR_variant,,ENST00000635994,;GABRB3,3_prime_UTR_variant,,ENST00000555632,; T ENST00000311550 Transcript synonymous_variant 1441/5781 1329/1422 443/473 T acC/acA rs754147659 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 9/9 hmmpanther:PTHR18945:SF571,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Superfamily_domains:SSF90112,Prints_domain:PR01160 LOW 1 SNV 1 1 PASS rs754147659 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 26547886 26547886 G T 1 0 0 0 0 0 0 0 1 6039 1103 39 1 1 GABRB3 15 26547886 Silent SNP G C3N-00704_T 1455750 26547886 75443303 461 19598 GABRA5 0 . GRCh38 15 26940019 26940019 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.819C>A p.= p.I273I ENST00000335625 9/11 241 180 61 362 361 1 strelka-varscan-mutect GABRA5,synonymous_variant,p.=,ENST00000335625,NM_000810.3;GABRA5,synonymous_variant,p.=,ENST00000400081,NM_001165037.1;GABRA5,synonymous_variant,p.=,ENST00000355395,;GABRB3,upstream_gene_variant,,ENST00000541819,;GABRA5,downstream_gene_variant,,ENST00000555182,; A ENST00000335625 Transcript synonymous_variant 1707/3251 819/1389 273/462 I atC/atA 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 9/11 Gene3D:1.20.58.390,Pfam_domain:PF02932,Prints_domain:PR00253,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 26940019 26940019 C A 1 0 0 0 0 0 0 0 1 6035 903 32 2 2 GABRA5 15 26940019 Silent SNP C C3N-00704_T 392133 26940019 75051170 462 19599 OTUD7A 0 . GRCh38 15 31483952 31483952 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2123G>T p.Arg708Leu p.R708L ENST00000307050 11/11 33 24 9 33 33 0 strelka-varscan-mutect OTUD7A,missense_variant,p.Arg708Leu,ENST00000307050,NM_130901.1; A ENST00000307050 Transcript missense_variant 2216/10770 2123/2781 708/926 R/L cGc/cTc 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 tolerated_low_confidence(0.32) 11/11 hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 31483952 31483952 C A 1 0 0 0 0 1 0 0 0 11387 768 27 1 1 OTUD7A 15 31483952 Missense_Mutation SNP C C3N-00704_T 4543933 31483952 70507237 463 19600 RYR3 0 . GRCh38 15 33810581 33810582 + Frame_Shift_Ins INS - - T novel C3N-00704_T C3N-00704_N - - c.10131dupT p.Gly3378TrpfsTer23 p.G3378Wfs*23 ENST00000634891 71/104 198 161 37 362 362 0 sindel-varindel-pindel RYR3,frameshift_variant,p.Gly3378TrpfsTer23,ENST00000634891,NM_001036.4;RYR3,frameshift_variant,p.Gly3378TrpfsTer23,ENST00000622037,;RYR3,frameshift_variant,p.Gly3373TrpfsTer23,ENST00000415757,NM_001243996.2;RYR3,frameshift_variant,p.Gly3377TrpfsTer23,ENST00000389232,;RYR3,frameshift_variant,p.Gly3372TrpfsTer23,ENST00000634418,;RYR3,upstream_gene_variant,,ENST00000638085,;RYR3,upstream_gene_variant,,ENST00000637201,;RYR3,upstream_gene_variant,,ENST00000638038,;RYR3,3_prime_UTR_variant,,ENST00000635790,; T ENST00000634891 Transcript frameshift_variant 10230-10231/15591 10129-10130/14613 3377/4870 I/IX att/aTtt 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 71/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 HIGH 1 insertion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 62 33810581 33810581 - T 1 0 1 1 0 0 0 0 0 14030 217 8 0 0 RYR3 15 33810581 Frame_Shift_Ins INS - C3N-00704_T 2326629 33810581 68180608 464 19601 MGA 0 . GRCh38 15 41742699 41742699 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.4739C>G p.Pro1580Arg p.P1580R ENST00000219905 15/24 195 152 43 244 244 0 strelka-varscan-mutect MGA,missense_variant,p.Pro1580Arg,ENST00000219905,NM_001164273.1;MGA,missense_variant,p.Pro1580Arg,ENST00000570161,;MGA,missense_variant,p.Pro228Arg,ENST00000564190,;MGA,intron_variant,,ENST00000566586,;MGA,intron_variant,,ENST00000545763,NM_001080541.2; G ENST00000219905 Transcript missense_variant 4920/12042 4739/9198 1580/3065 P/R cCt/cGt 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 deleterious(0) 15/24 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 41742699 41742699 C G 1 0 0 0 0 1 0 0 0 9498 681 24 4 4 MGA 15 41742699 Missense_Mutation SNP C C3N-00704_T 7932118 41742699 60248490 465 19602 ATP8B4 0 . GRCh38 15 49931132 49931132 + Missense_Mutation SNP C C G novel C3N-00704_T C3N-00704_N C C c.1629G>C p.Arg543Ser p.R543S ENST00000284509 16/28 50 39 11 55 55 0 strelka-varscan-mutect ATP8B4,missense_variant,p.Arg543Ser,ENST00000284509,NM_024837.3;ATP8B4,missense_variant,p.Arg543Ser,ENST00000559829,;ATP8B4,missense_variant,p.Arg543Ser,ENST00000557955,;ATP8B4,missense_variant,p.Arg35Ser,ENST00000558458,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,; G ENST00000284509 Transcript missense_variant 1771/5676 1629/3579 543/1192 R/S agG/agC 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 deleterious(0) 16/28 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF80,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Pfam_domain:PF13246,Superfamily_domains:SSF81660 MODERATE 1 SNV 5 1 PASS rs1013618309 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 49931132 49931132 C G 1 0 0 0 0 1 0 0 0 1350 854 30 4 4 ATP8B4 15 49931132 Missense_Mutation SNP C C3N-00704_T 8188433 49931132 52060057 466 19603 AQP9 0 . GRCh38 15 58138625 58138625 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.60C>T p.= p.S20S ENST00000219919 1/6 159 132 27 238 238 0 strelka-varscan-mutect AQP9,synonymous_variant,p.=,ENST00000219919,NM_020980.3;AQP9,synonymous_variant,p.=,ENST00000536493,;ALDH1A2,5_prime_UTR_variant,,ENST00000557967,;ALDH1A2,intron_variant,,ENST00000558231,;AQP9,intron_variant,,ENST00000558772,;ALDH1A2,intron_variant,,ENST00000558239,;AQP9,non_coding_transcript_exon_variant,,ENST00000559443,;ALDH1A2,intron_variant,,ENST00000560863,;ALDH1A2,intron_variant,,ENST00000558073,;ALDH1A2,intron_variant,,ENST00000560122,;ALDH1A2,intron_variant,,ENST00000559297,;ALDH1A2,intron_variant,,ENST00000558504,; T ENST00000219919 Transcript synonymous_variant 430/3034 60/888 20/295 S agC/agT 1 1 AQP9 HGNC HGNC:643 protein_coding YES CCDS10165.1 ENSP00000219919 O43315 UPI000013C796 NM_020980.3 1/6 hmmpanther:PTHR19139:SF149,hmmpanther:PTHR19139,Gene3D:1.20.1080.10,Pfam_domain:PF00230,Prints_domain:PR02021 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 58138625 58138625 C T 1 0 0 0 0 0 0 0 1 956 709 25 3 3 AQP9 15 58138625 Silent SNP C C3N-00704_T 8207493 58138625 43852564 467 19604 C15orf61 0 . GRCh38 15 67521303 67521303 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.55C>T p.Pro19Ser p.P19S ENST00000342683 1/2 60 56 4 92 92 0 varscan-mutect C15orf61,missense_variant,p.Pro19Ser,ENST00000342683,NM_001143936.1;C15orf61,upstream_gene_variant,,ENST00000557807,;IQCH-AS1,intron_variant,,ENST00000559298,;IQCH-AS1,intron_variant,,ENST00000561232,;IQCH-AS1,upstream_gene_variant,,ENST00000559285,;IQCH-AS1,upstream_gene_variant,,ENST00000559702,;C15orf61,upstream_gene_variant,,ENST00000560041,;C15orf61,upstream_gene_variant,,ENST00000560547,; T ENST00000342683 Transcript missense_variant 236/4253 55/474 19/157 P/S Ccg/Tcg 1 1 C15orf61 HGNC HGNC:34453 protein_coding YES CCDS45289.1 ENSP00000342254 A6NNL5 UPI0000039EE4 NM_001143936.1 tolerated_low_confidence(0.3) 1/2 hmmpanther:PTHR34651,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -10.09091 1 1 1 1 0 T 3 4 62 67521303 67521303 C T 1 0 0 0 0 1 0 0 0 1851 739 26 3 3 C15orf61 15 67521303 Missense_Mutation SNP C C3N-00704_T 9382678 67521303 34469886 468 19605 UACA 0 . GRCh38 15 70668678 70668678 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2006G>A p.Arg669Lys p.R669K ENST00000322954 16/19 205 153 52 320 320 0 strelka-varscan-mutect UACA,missense_variant,p.Arg669Lys,ENST00000322954,NM_018003.2;UACA,missense_variant,p.Arg656Lys,ENST00000379983,NM_001008224.1;UACA,missense_variant,p.Arg654Lys,ENST00000560441,;UACA,missense_variant,p.Arg560Lys,ENST00000539319,;UACA,downstream_gene_variant,,ENST00000558758,;UACA,upstream_gene_variant,,ENST00000560831,;UACA,downstream_gene_variant,,ENST00000559290,;UACA,downstream_gene_variant,,ENST00000560523,;UACA,downstream_gene_variant,,ENST00000558308,; T ENST00000322954 Transcript missense_variant 2192/6939 2006/4251 669/1416 R/K aGa/aAa 1 -1 UACA HGNC HGNC:15947 protein_coding YES CCDS10235.1 ENSP00000314556 Q9BZF9 UPI000006DCF3 NM_018003.2 tolerated(0.12) 16/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF23 MODERATE 1 SNV 1 1 PASS rs1217943474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 70668678 70668678 C T 1 0 0 0 0 1 0 0 0 17343 913 32 3 3 UACA 15 70668678 Missense_Mutation SNP C C3N-00704_T 3147375 70668678 31322511 469 19606 CELF6 0 . GRCh38 15 72289637 72289637 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.737A>T p.Tyr246Phe p.Y246F ENST00000287202 6/13 67 51 16 109 109 0 strelka-varscan-mutect CELF6,missense_variant,p.Tyr246Phe,ENST00000287202,NM_052840.4;CELF6,missense_variant,p.Tyr133Phe,ENST00000395258,;CELF6,missense_variant,p.Tyr131Phe,ENST00000543764,NM_001172685.1;CELF6,missense_variant,p.Tyr246Phe,ENST00000567083,NM_001172684.1;RP11-106M3.3,intron_variant,,ENST00000570175,;RP11-106M3.5,missense_variant,p.Tyr246Phe,ENST00000569547,;RP11-106M3.2,3_prime_UTR_variant,,ENST00000379915,;CELF6,3_prime_UTR_variant,,ENST00000437872,; A ENST00000287202 Transcript missense_variant 992/3345 737/1446 246/481 Y/F tAc/tTc 1 -1 CELF6 HGNC HGNC:14059 protein_coding YES CCDS10242.1 ENSP00000287202 Q96J87 UPI000006F0AA NM_052840.4 tolerated(0.1) 6/13 MODERATE 1 SNV 1 1 PASS rs1453964755 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 72289637 72289637 T A 1 0 0 0 0 1 0 0 0 2927 1638 57 4 4 CELF6 15 72289637 Missense_Mutation SNP T C3N-00704_T 1620959 72289637 29701552 470 19607 RAB40C 0 . GRCh38 16 626045 626045 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.489C>T p.= p.V163V ENST00000535977 6/7 343 299 44 392 392 0 strelka-varscan-mutect RAB40C,synonymous_variant,p.=,ENST00000535977,NM_001172663.1;RAB40C,synonymous_variant,p.=,ENST00000248139,NM_021168.4;RAB40C,synonymous_variant,p.=,ENST00000539661,NM_001172664.1;RAB40C,synonymous_variant,p.=,ENST00000538492,NM_001172665.1,NM_001172666.1;RAB40C,synonymous_variant,p.=,ENST00000564703,;RAB40C,synonymous_variant,p.=,ENST00000566290,;RAB40C,synonymous_variant,p.=,ENST00000563109,;RAB40C,synonymous_variant,p.=,ENST00000568586,;WFIKKN1,upstream_gene_variant,,ENST00000319070,NM_053284.2;RAB40C,downstream_gene_variant,,ENST00000569575,;RAB40C,3_prime_UTR_variant,,ENST00000565511,;RAB40C,non_coding_transcript_exon_variant,,ENST00000561781,;WFIKKN1,upstream_gene_variant,,ENST00000573440,;RAB40C,downstream_gene_variant,,ENST00000509637,; T ENST00000535977 Transcript synonymous_variant 711/2717 489/846 163/281 V gtC/gtT 1 1 RAB40C HGNC HGNC:18285 protein_coding YES CCDS10413.1 ENSP00000438492 Q96S21 UPI0000133002 NM_001172663.1 6/7 PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF365,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 626045 626045 C T 1 0 0 0 0 0 0 0 1 13101 813 29 3 3 RAB40C 16 626045 Silent SNP C C3N-00704_T 626045 89712300 471 19608 WDR24 0 . GRCh38 16 689505 689505 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.136C>A p.Arg46Ser p.R46S ENST00000293883 1/9 395 334 61 469 467 2 strelka-varscan-mutect WDR24,missense_variant,p.Arg46Ser,ENST00000293883,NM_032259.3;WDR24,missense_variant,p.Arg108Ser,ENST00000248142,;FBXL16,downstream_gene_variant,,ENST00000397621,NM_153350.3;FBXL16,downstream_gene_variant,,ENST00000324361,;FBXL16,downstream_gene_variant,,ENST00000562563,;LA16c-313D11.12,non_coding_transcript_exon_variant,,ENST00000566927,;LA16c-313D11.12,non_coding_transcript_exon_variant,,ENST00000575305,;FBXL16,downstream_gene_variant,,ENST00000562648,;JMJD8,upstream_gene_variant,,ENST00000567120,;WDR24,upstream_gene_variant,,ENST00000567014,; T ENST00000293883 Transcript missense_variant 896/3245 136/2373 46/790 R/S Cgt/Agt 1 -1 WDR24 HGNC HGNC:20852 protein_coding YES CCDS10420.1 ENSP00000293883 Q96S15 UPI0000037D32 NM_032259.3 deleterious(0) 1/9 hmmpanther:PTHR22850:SF131,hmmpanther:PTHR22850,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 689505 689505 G T 1 0 0 0 0 1 0 0 0 17841 1116 39 1 1 WDR24 16 689505 Missense_Mutation SNP G C3N-00704_T 63460 689505 89648840 472 19609 CHTF18 0 . GRCh38 16 796780 796780 + Silent SNP G G C rs374658777 C3N-00704_T C3N-00704_N G G c.2520G>C p.= p.T840T ENST00000262315 19/22 219 181 38 242 242 0 strelka-varscan-mutect CHTF18,synonymous_variant,p.=,ENST00000631357,;CHTF18,synonymous_variant,p.=,ENST00000455171,;CHTF18,synonymous_variant,p.=,ENST00000262315,NM_022092.2;CHTF18,synonymous_variant,p.=,ENST00000317063,;GNG13,downstream_gene_variant,,ENST00000248150,NM_016541.2;CHTF18,downstream_gene_variant,,ENST00000461268,;CHTF18,downstream_gene_variant,,ENST00000493715,;CHTF18,upstream_gene_variant,,ENST00000564940,;CHTF18,non_coding_transcript_exon_variant,,ENST00000471202,;CHTF18,non_coding_transcript_exon_variant,,ENST00000464728,;CHTF18,non_coding_transcript_exon_variant,,ENST00000498439,;CHTF18,downstream_gene_variant,,ENST00000440239,;CHTF18,downstream_gene_variant,,ENST00000569270,;CHTF18,downstream_gene_variant,,ENST00000567620,;CHTF18,downstream_gene_variant,,ENST00000565787,; C ENST00000262315 Transcript synonymous_variant 2583/3090 2520/2928 840/975 T acG/acC rs374658777,COSM974413 1 1 CHTF18 HGNC HGNC:18435 protein_coding YES CCDS45371.1 ENSP00000262315 Q8WVB6 UPI00000710D2 NM_022092.2 19/22 hmmpanther:PTHR23389:SF3,hmmpanther:PTHR23389 0,1 LOW 1 SNV 1 0,1 1 PASS rs374658777 . 0 206 0 3 0 0 0 0 -20 0.9999951 1 1 1 0 C 2 2 62 796780 796780 G C 1 0 0 0 0 0 0 0 1 3174 1045 37 4 4 CHTF18 16 796780 Silent SNP G C3N-00704_T 107275 796780 89541565 473 19610 TPSB2 0 . GRCh38 16 1229719 1229719 + Missense_Mutation SNP T T A rs755831769 C3N-00704_T C3N-00704_N T T c.80A>T p.Gln27Leu p.Q27L ENST00000606293 3/6 77 69 8 77 77 0 varscan-mutect TPSB2,missense_variant,p.Gln34Leu,ENST00000612142,;TPSB2,missense_variant,p.Gln27Leu,ENST00000606293,NM_024164.5;TPSG1,upstream_gene_variant,,ENST00000234798,NM_012467.3;TPSB2,missense_variant,p.Gln27Leu,ENST00000611196,;TPSG1,upstream_gene_variant,,ENST00000564684,; A ENST00000606293 Transcript missense_variant 103/1165 80/828 27/275 Q/L cAg/cTg rs755831769 1 -1 TPSB2 HGNC HGNC:14120 protein_coding YES ENSP00000482743 P20231 A0A140VJT7 UPI0000169899 NM_024164.5 deleterious(0.02) 3/6 hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF178,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs755831769 . 0 207 3 0 0 0 0 0 -17.60936 1 1 1 1 0 A 3 1 62 1229719 1229719 T A 1 0 0 0 0 1 0 0 0 16905 1580 55 4 4 TPSB2 16 1229719 Missense_Mutation SNP T C3N-00704_T 432939 1229719 89108626 474 19611 SLC9A3R2 0 . GRCh38 16 2037830 2037830 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.860G>A p.Gly287Asp p.G287D ENST00000424542 7/7 113 92 21 128 128 0 strelka-varscan-mutect SLC9A3R2,missense_variant,p.Gly287Asp,ENST00000424542,NM_001130012.2;SLC9A3R2,missense_variant,p.Gly176Asp,ENST00000566198,NM_001252073.1,NM_001252076.1;SLC9A3R2,missense_variant,p.Gly181Asp,ENST00000563587,;SLC9A3R2,missense_variant,p.Gly174Asp,ENST00000565855,NM_001252075.1;SLC9A3R2,3_prime_UTR_variant,,ENST00000561844,;SLC9A3R2,intron_variant,,ENST00000432365,NM_004785.5;NTHL1,downstream_gene_variant,,ENST00000219066,NM_002528.5;NTHL1,downstream_gene_variant,,ENST00000566380,;SLC9A3R2,downstream_gene_variant,,ENST00000567504,;SLC9A3R2,downstream_gene_variant,,ENST00000565086,;NTHL1,downstream_gene_variant,,ENST00000562951,;SLC9A3R2,non_coding_transcript_exon_variant,,ENST00000564033,;NTHL1,downstream_gene_variant,,ENST00000561841,;NTHL1,downstream_gene_variant,,ENST00000568513,;NTHL1,downstream_gene_variant,,ENST00000565406,;NTHL1,downstream_gene_variant,,ENST00000567727,;NTHL1,downstream_gene_variant,,ENST00000561862,; A ENST00000424542 Transcript missense_variant 998/2194 860/1014 287/337 G/D gGc/gAc 1 1 SLC9A3R2 HGNC HGNC:11076 protein_coding YES CCDS45382.1 ENSP00000408005 Q15599 UPI0000070578 NM_001130012.2 tolerated(0.51) 7/7 hmmpanther:PTHR14191:SF4,hmmpanther:PTHR14191,PIRSF_domain:PIRSF037866,Pfam_domain:PF09007 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 2037830 2037830 G A 1 0 0 0 0 1 0 0 0 14997 1217 42 3 3 SLC9A3R2 16 2037830 Missense_Mutation SNP G C3N-00704_T 808111 2037830 88300515 475 19612 IL32 0 . GRCh38 16 3069213 3069213 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.563A>T p.Gln188Leu p.Q188L ENST00000534507 6/6 418 379 39 555 554 1 varscan-mutect IL32,missense_variant,p.Gln142Leu,ENST00000525643,;IL32,missense_variant,p.Gln142Leu,ENST00000526464,;IL32,missense_variant,p.Gln188Leu,ENST00000534507,;IL32,missense_variant,p.Gln142Leu,ENST00000325568,NM_001012718.1,NM_004221.4;IL32,missense_variant,p.Gln188Leu,ENST00000396890,;IL32,missense_variant,p.Gln122Leu,ENST00000008180,NM_001012634.1;IL32,missense_variant,p.Gln122Leu,ENST00000613483,;IL32,missense_variant,p.Gln188Leu,ENST00000548476,;IL32,missense_variant,p.Gln142Leu,ENST00000528163,NM_001012631.1;IL32,missense_variant,p.Gln142Leu,ENST00000440815,;IL32,missense_variant,p.Gln142Leu,ENST00000444393,;IL32,missense_variant,p.Gln133Leu,ENST00000382213,NM_001012636.1;IL32,missense_variant,p.Gln142Leu,ENST00000533097,;IL32,missense_variant,p.Gln133Leu,ENST00000548652,;IL32,missense_variant,p.Gln188Leu,ENST00000548807,;IL32,missense_variant,p.Gln179Leu,ENST00000551513,;IL32,missense_variant,p.Gln122Leu,ENST00000530890,NM_001012635.1;IL32,missense_variant,p.Gln142Leu,ENST00000529550,;IL32,missense_variant,p.Gln132Leu,ENST00000531965,;IL32,missense_variant,p.Gln142Leu,ENST00000552664,NM_001012632.1;IL32,missense_variant,p.Gln166Leu,ENST00000552936,;IL32,missense_variant,p.Gln142Leu,ENST00000530538,;IL32,missense_variant,p.Gln122Leu,ENST00000529699,;IL32,missense_variant,p.Gln122Leu,ENST00000552356,;IL32,missense_variant,p.Gln113Leu,ENST00000525228,;IL32,missense_variant,p.Gln102Leu,ENST00000548246,;IL32,intron_variant,,ENST00000525377,;IL32,intron_variant,,ENST00000396887,NM_001012633.1;IL32,intron_variant,,ENST00000551122,;IL32,intron_variant,,ENST00000549213,;RNU1-125P,upstream_gene_variant,,ENST00000516752,;IL32,non_coding_transcript_exon_variant,,ENST00000525003,;IL32,intron_variant,,ENST00000528652,;IL32,downstream_gene_variant,,ENST00000532247,;IL32,downstream_gene_variant,,ENST00000532086,;IL32,downstream_gene_variant,,ENST00000534748,; T ENST00000534507 Transcript missense_variant 774/1112 563/705 188/234 Q/L cAg/cTg 1 1 IL32 HGNC HGNC:16830 protein_coding YES CCDS76811.1 ENSP00000431775 P24001 UPI0000070836 deleterious(0.01) 6/6 Pfam_domain:PF15225 MODERATE 1 SNV 2 1 PASS rs779733588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 3069213 3069213 A T 1 0 0 0 0 1 0 0 0 7591 188 7 4 4 IL32 16 3069213 Missense_Mutation SNP A C3N-00704_T 1031383 3069213 87269132 476 19613 71 2 IL32 0 . GRCh38 16 3069215 3069215 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.565G>A p.Ala189Thr p.A189T ENST00000534507 6/6 422 382 40 560 559 1 varscan-mutect IL32,missense_variant,p.Ala143Thr,ENST00000525643,;IL32,missense_variant,p.Ala143Thr,ENST00000526464,;IL32,missense_variant,p.Ala189Thr,ENST00000534507,;IL32,missense_variant,p.Ala143Thr,ENST00000325568,NM_001012718.1,NM_004221.4;IL32,missense_variant,p.Ala189Thr,ENST00000396890,;IL32,missense_variant,p.Ala123Thr,ENST00000008180,NM_001012634.1;IL32,missense_variant,p.Ala123Thr,ENST00000613483,;IL32,missense_variant,p.Ala189Thr,ENST00000548476,;IL32,missense_variant,p.Ala143Thr,ENST00000528163,NM_001012631.1;IL32,missense_variant,p.Ala143Thr,ENST00000440815,;IL32,missense_variant,p.Ala143Thr,ENST00000444393,;IL32,missense_variant,p.Ala134Thr,ENST00000382213,NM_001012636.1;IL32,missense_variant,p.Ala143Thr,ENST00000533097,;IL32,missense_variant,p.Ala134Thr,ENST00000548652,;IL32,missense_variant,p.Ala189Thr,ENST00000548807,;IL32,missense_variant,p.Ala180Thr,ENST00000551513,;IL32,missense_variant,p.Ala123Thr,ENST00000530890,NM_001012635.1;IL32,missense_variant,p.Ala143Thr,ENST00000529550,;IL32,missense_variant,p.Ala133Thr,ENST00000531965,;IL32,missense_variant,p.Ala143Thr,ENST00000552664,NM_001012632.1;IL32,missense_variant,p.Ala167Thr,ENST00000552936,;IL32,missense_variant,p.Ala143Thr,ENST00000530538,;IL32,missense_variant,p.Ala123Thr,ENST00000529699,;IL32,missense_variant,p.Ala123Thr,ENST00000552356,;IL32,missense_variant,p.Ala114Thr,ENST00000525228,;IL32,missense_variant,p.Ala103Thr,ENST00000548246,;IL32,intron_variant,,ENST00000525377,;IL32,intron_variant,,ENST00000396887,NM_001012633.1;IL32,intron_variant,,ENST00000551122,;IL32,intron_variant,,ENST00000549213,;RNU1-125P,upstream_gene_variant,,ENST00000516752,;IL32,non_coding_transcript_exon_variant,,ENST00000525003,;IL32,intron_variant,,ENST00000528652,;IL32,downstream_gene_variant,,ENST00000532247,;IL32,downstream_gene_variant,,ENST00000532086,;IL32,downstream_gene_variant,,ENST00000534748,; A ENST00000534507 Transcript missense_variant 776/1112 565/705 189/234 A/T Gcc/Acc 1 1 IL32 HGNC HGNC:16830 protein_coding YES CCDS76811.1 ENSP00000431775 P24001 UPI0000070836 tolerated(0.34) 6/6 Pfam_domain:PF15225 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 3069215 3069215 G A 1 0 0 0 0 1 0 0 0 7591 1203 42 3 3 IL32 16 3069215 Missense_Mutation SNP G C3N-00704_T 2 3069215 87269130 477 19614 71 2 SLX4 0 . GRCh38 16 3597992 3597992 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1171G>T p.Asp391Tyr p.D391Y ENST00000294008 6/15 556 468 88 691 691 0 strelka-varscan-mutect SLX4,missense_variant,p.Asp391Tyr,ENST00000294008,NM_032444.2;SLX4,non_coding_transcript_exon_variant,,ENST00000466154,;SLX4,downstream_gene_variant,,ENST00000486524,; A ENST00000294008 Transcript missense_variant 1812/7307 1171/5505 391/1834 D/Y Gat/Tat 1 -1 SLX4 HGNC HGNC:23845 protein_coding YES CCDS10506.2 ENSP00000294008 Q8IY92 UPI000050D2C5 NM_032444.2 deleterious(0.01) 6/15 hmmpanther:PTHR21541,hmmpanther:PTHR21541:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 3597992 3597992 C A 1 0 0 0 0 1 0 0 0 15048 826 29 2 2 SLX4 16 3597992 Missense_Mutation SNP C C3N-00704_T 528777 3597992 86740353 478 19615 PDXDC1 0 . GRCh38 16 15032907 15032907 + Missense_Mutation SNP G G A rs141392697 C3N-00704_T C3N-00704_N G G c.1618G>A p.Glu540Lys p.E540K ENST00000396410 18/23 155 137 18 233 232 1 strelka-varscan-mutect PDXDC1,missense_variant,p.Glu540Lys,ENST00000396410,NM_001324019.1,NM_015027.3;PDXDC1,missense_variant,p.Glu449Lys,ENST00000450288,NM_001285448.1;PDXDC1,missense_variant,p.Glu513Lys,ENST00000569715,NM_001285444.1;PDXDC1,missense_variant,p.Glu558Lys,ENST00000563679,NM_001285447.1;PDXDC1,missense_variant,p.Glu512Lys,ENST00000627450,NM_001285445.1;PDXDC1,intron_variant,,ENST00000535621,NM_001324020.1,NM_001285449.1;PDXDC1,downstream_gene_variant,,ENST00000455313,NM_001285450.1;NTAN1,downstream_gene_variant,,ENST00000287706,NM_173474.3;NTAN1,downstream_gene_variant,,ENST00000624579,NM_001270766.1;NTAN1,downstream_gene_variant,,ENST00000622833,NM_001270767.1;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,;PDXDC1,intron_variant,,ENST00000562119,;PDXDC1,downstream_gene_variant,,ENST00000566633,;NTAN1,downstream_gene_variant,,ENST00000566542,;NTAN1,downstream_gene_variant,,ENST00000565187,;PDXDC1,upstream_gene_variant,,ENST00000565986,; A ENST00000396410 Transcript missense_variant 1715/4521 1618/2367 540/788 E/K Gaa/Aaa rs141392697,COSM967316 1 1 PDXDC1 HGNC HGNC:28995 protein_coding YES CCDS32393.1 ENSP00000379691 Q6P996 UPI000004A864 NM_001324019.1,NM_015027.3 deleterious(0.01) 18/23 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs141392697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 15032907 15032907 G A 1 0 0 0 0 1 0 0 0 11784 1059 37 1 1 PDXDC1 16 15032907 Missense_Mutation SNP G C3N-00704_T 11434915 15032907 75305438 479 19616 XYLT1 0 . GRCh38 16 17141276 17141276 + Silent SNP G G T rs143737358 C3N-00704_T C3N-00704_N G G c.1464C>A p.= p.A488A ENST00000261381 7/12 242 199 43 237 237 0 strelka-varscan-mutect XYLT1,synonymous_variant,p.=,ENST00000261381,NM_022166.3;CTD-2576D5.4,downstream_gene_variant,,ENST00000567344,; T ENST00000261381 Transcript synonymous_variant 1549/9891 1464/2880 488/959 A gcC/gcA rs143737358 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 7/12 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF91,Pfam_domain:PF02485 LOW 1 SNV 1 1 PASS rs143737358 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 17141276 17141276 G T 1 0 0 0 0 0 0 0 1 18022 1103 39 1 1 XYLT1 16 17141276 Silent SNP G C3N-00704_T 2108369 17141276 73197069 480 19617 ACSM2A 0 . GRCh38 16 20475665 20475665 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.990T>A p.His330Gln p.H330Q ENST00000573854 8/14 236 188 48 237 237 0 strelka-varscan-mutect ACSM2A,missense_variant,p.His330Gln,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,missense_variant,p.His330Gln,ENST00000396104,;ACSM2A,missense_variant,p.His330Gln,ENST00000575690,;ACSM2A,missense_variant,p.His330Gln,ENST00000219054,;ACSM2A,missense_variant,p.His251Gln,ENST00000417235,NM_001308169.1;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,downstream_gene_variant,,ENST00000572921,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000572843,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,;ACSM2A,upstream_gene_variant,,ENST00000576101,;ACSM2A,downstream_gene_variant,,ENST00000574692,; A ENST00000573854 Transcript missense_variant 1104/2837 990/1734 330/577 H/Q caT/caA 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 deleterious(0.04) 8/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 20475665 20475665 T A 1 0 0 0 0 1 0 0 0 225 1432 50 4 4 ACSM2A 16 20475665 Missense_Mutation SNP T C3N-00704_T 3334389 20475665 69862680 481 19618 ACSM2B 0 . GRCh38 16 20555384 20555384 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.481G>T p.Asp161Tyr p.D161Y ENST00000329697 4/14 272 210 62 270 270 0 strelka-varscan-mutect ACSM2B,missense_variant,p.Asp161Tyr,ENST00000329697,NM_001105069.1;ACSM2B,missense_variant,p.Asp161Tyr,ENST00000414188,;ACSM2B,missense_variant,p.Asp161Tyr,ENST00000565232,;ACSM2B,missense_variant,p.Asp161Tyr,ENST00000567001,NM_182617.3;ACSM2B,missense_variant,p.Asp82Tyr,ENST00000565322,;ACSM2B,upstream_gene_variant,,ENST00000567288,;ACSM2B,upstream_gene_variant,,ENST00000569163,;ACSM2B,downstream_gene_variant,,ENST00000566384,;ACSM2B,downstream_gene_variant,,ENST00000569344,;ACSM2B,downstream_gene_variant,,ENST00000568882,;ACSM2B,missense_variant,p.Asp161Tyr,ENST00000569327,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,; A ENST00000329697 Transcript missense_variant 650/2935 481/1734 161/577 D/Y Gat/Tat COSM3507002,COSM4898945 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 deleterious(0) 4/14 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF188,Superfamily_domains:SSF56801 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 20555384 20555384 C A 1 0 0 0 0 1 0 0 0 226 855 30 2 2 ACSM2B 16 20555384 Missense_Mutation SNP C C3N-00704_T 79719 20555384 69782961 482 19619 HS3ST2 0 . GRCh38 16 22814632 22814632 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.22C>T p.Arg8Cys p.R8C ENST00000261374 1/2 159 139 20 152 152 0 strelka-varscan-mutect HS3ST2,missense_variant,p.Arg8Cys,ENST00000261374,NM_006043.1;CTC-591M7.1,upstream_gene_variant,,ENST00000636354,;CTC-591M7.1,upstream_gene_variant,,ENST00000636266,;HS3ST2,missense_variant,p.Arg8Cys,ENST00000473392,; T ENST00000261374 Transcript missense_variant 456/2314 22/1104 8/367 R/C Cgc/Tgc 1 1 HS3ST2 HGNC HGNC:5195 protein_coding YES CCDS10606.1 ENSP00000261374 Q9Y278 UPI000004C63A NM_006043.1 deleterious_low_confidence(0) 1/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS51257,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 22814632 22814632 C T 1 0 0 0 0 1 0 0 0 7258 652 23 1 1 HS3ST2 16 22814632 Missense_Mutation SNP C C3N-00704_T 2259248 22814632 67523713 483 19620 RBBP6 0 . GRCh38 16 24571765 24571765 + Nonsense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.4699A>T p.Lys1567Ter p.K1567* ENST00000319715 18/18 93 75 18 258 258 0 strelka-varscan-mutect RBBP6,stop_gained,p.Lys1567Ter,ENST00000319715,NM_006910.4;RBBP6,stop_gained,p.Lys1533Ter,ENST00000348022,NM_018703.3;RBBP6,stop_gained,p.Lys727Ter,ENST00000381039,;RBBP6,downstream_gene_variant,,ENST00000564314,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,; T ENST00000319715 Transcript stop_gained 5131/6229 4699/5379 1567/1792 K/* Aag/Tag 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 18/18 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 24571765 24571765 A T 1 0 0 0 0 0 1 0 0 13264 363 13 4 4 RBBP6 16 24571765 Nonsense_Mutation SNP A C3N-00704_T 1757133 24571765 65766580 484 19621 IL4R 0 . GRCh38 16 27363019 27363019 + Missense_Mutation SNP G G T rs201672347 C3N-00704_T C3N-00704_N G G c.1667G>T p.Arg556Leu p.R556L ENST00000395762 11/11 292 240 52 322 322 0 strelka-varscan-mutect IL4R,missense_variant,p.Arg556Leu,ENST00000395762,NM_000418.3;IL4R,missense_variant,p.Arg556Leu,ENST00000543915,NM_001257997.1,NM_001257406.1;IL4R,missense_variant,p.Arg541Leu,ENST00000170630,NM_001257407.1;IL4R,intron_variant,,ENST00000565352,;IL4R,downstream_gene_variant,,ENST00000565179,;IL4R,downstream_gene_variant,,ENST00000565915,;IL4R,3_prime_UTR_variant,,ENST00000568746,;IL4R,downstream_gene_variant,,ENST00000563886,; T ENST00000395762 Transcript missense_variant 1926/3685 1667/2478 556/825 R/L cGa/cTa rs201672347,COSM3508179 1 1 IL4R HGNC HGNC:6015 protein_coding YES CCDS10629.1 ENSP00000379111 P24394 UPI0000044371 NM_000418.3 tolerated(0.29) 11/11 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF32 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201672347 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 27363019 27363019 G T 1 0 0 0 0 1 0 0 0 7602 1058 37 1 1 IL4R 16 27363019 Missense_Mutation SNP G C3N-00704_T 2791254 27363019 62975326 485 19622 GSG1L 0 . GRCh38 16 27828839 27828839 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.780G>T p.= p.R260R ENST00000447459 5/7 176 139 37 262 260 2 strelka-varscan-mutect GSG1L,synonymous_variant,p.=,ENST00000447459,NM_001109763.1;GSG1L,synonymous_variant,p.=,ENST00000395724,;GSG1L,synonymous_variant,p.=,ENST00000380897,NM_144675.2;GSG1L,synonymous_variant,p.=,ENST00000569166,;GSG1L,3_prime_UTR_variant,,ENST00000562611,; A ENST00000447459 Transcript synonymous_variant 865/4916 780/996 260/331 R cgG/cgT 1 -1 GSG1L HGNC HGNC:28283 protein_coding YES CCDS45450.1 ENSP00000394954 Q6UXU4 UPI0000EE765B NM_001109763.1 5/7 hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF35 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 27828839 27828839 C A 1 0 0 0 0 0 0 0 1 6704 610 22 2 2 GSG1L 16 27828839 Silent SNP C C3N-00704_T 465820 27828839 62509506 486 19623 SETD1A 0 . GRCh38 16 30983985 30983985 + Silent SNP C C T C3N-00704_T C3N-00704_N C C c.5086C>T p.= p.L1696L ENST00000262519 19/19 143 117 26 156 156 0 strelka-varscan-mutect SETD1A,synonymous_variant,p.=,ENST00000262519,NM_014712.2;HSD3B7,upstream_gene_variant,,ENST00000262520,NM_001142777.1,NM_001142778.1;HSD3B7,upstream_gene_variant,,ENST00000297679,NM_025193.3;HSD3B7,upstream_gene_variant,,ENST00000562932,;HSD3B7,upstream_gene_variant,,ENST00000574447,;RP11-1072A3.3,downstream_gene_variant,,ENST00000624286,; T ENST00000262519 Transcript synonymous_variant 5772/6903 5086/5124 1696/1707 L Ctg/Ttg COSM970053 1 1 SETD1A HGNC HGNC:29010 protein_coding YES CCDS32435.1 ENSP00000262519 O15047 UPI00001C1FA9 NM_014712.2 19/19 Gene3D:2.170.270.10,PROSITE_profiles:PS50868,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF295,SMART_domains:SM00508,Superfamily_domains:SSF82199 1 LOW 1 SNV 1 1 1 PASS rs1219140788 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 30983985 30983985 C T 1 0 0 0 0 0 0 0 1 14407 912 32 3 3 SETD1A 16 30983985 Silent SNP C C3N-00704_T 3155146 30983985 59354360 487 19624 TRIM72 0 . GRCh38 16 31224545 31224545 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1224G>C p.Arg408Ser p.R408S ENST00000322122 7/7 59 47 12 86 86 0 strelka-varscan-mutect TRIM72,missense_variant,p.Arg408Ser,ENST00000322122,NM_001008274.3;TRIM72,intron_variant,,ENST00000613872,; C ENST00000322122 Transcript missense_variant 1508/8500 1224/1434 408/477 R/S agG/agC 1 1 TRIM72 HGNC HGNC:32671 protein_coding YES CCDS32437.1 ENSP00000312675 Q6ZMU5 UPI00001FFF74 NM_001008274.3 tolerated(0.71) 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF11,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 31224545 31224545 G C 1 0 0 0 0 1 0 0 0 17041 1194 42 4 4 TRIM72 16 31224545 Missense_Mutation SNP G C3N-00704_T 240560 31224545 59113800 488 19625 ITGAM 0 . GRCh38 16 31278020 31278020 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1267G>A p.Ala423Thr p.A423T ENST00000544665 12/30 149 125 24 249 248 1 strelka-varscan-mutect ITGAM,missense_variant,p.Ala423Thr,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Ala423Thr,ENST00000287497,NM_000632.3;ITGAM,intron_variant,,ENST00000567031,;ITGAM,downstream_gene_variant,,ENST00000570242,; A ENST00000544665 Transcript missense_variant 1338/4718 1267/3462 423/1153 A/T Gca/Aca 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0.02) 12/30 Gene3D:3nigC00,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 62 31278020 31278020 G A 1 0 0 0 0 1 0 0 0 7794 1203 42 3 3 ITGAM 16 31278020 Missense_Mutation SNP G C3N-00704_T 53475 31278020 59060325 489 19626 MYLK3 0 . GRCh38 16 46738069 46738069 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.643G>T p.Asp215Tyr p.D215Y ENST00000394809 3/13 78 69 9 82 82 0 strelka-varscan-mutect MYLK3,missense_variant,p.Asp215Tyr,ENST00000394809,NM_182493.2;MYLK3,intron_variant,,ENST00000536476,NM_001308301.1;MYLK3,non_coding_transcript_exon_variant,,ENST00000569810,;MYLK3,non_coding_transcript_exon_variant,,ENST00000564731,; A ENST00000394809 Transcript missense_variant 759/6911 643/2460 215/819 D/Y Gac/Tac 1 -1 MYLK3 HGNC HGNC:29826 protein_coding YES CCDS10723.2 ENSP00000378288 Q32MK0 UPI000059D380 NM_182493.2 deleterious(0) 3/13 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.44645 1 1 1 1 0 A 3 1 62 46738069 46738069 C A 1 0 0 0 0 1 0 0 0 10058 826 29 2 2 MYLK3 16 46738069 Missense_Mutation SNP C C3N-00704_T 15460049 46738069 43600276 490 19627 CBLN1 0 . GRCh38 16 49281372 49281372 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.94G>T p.Gly32Cys p.G32C ENST00000219197 1/3 256 232 24 190 190 0 strelka-varscan-mutect CBLN1,missense_variant,p.Gly32Cys,ENST00000219197,NM_004352.3;CBLN1,missense_variant,p.Gly32Cys,ENST00000536749,;CBLN1,missense_variant,p.Gly32Cys,ENST00000564786,; A ENST00000219197 Transcript missense_variant 460/2435 94/582 32/193 G/C Ggc/Tgc COSM2833419 1 -1 CBLN1 HGNC HGNC:1543 protein_coding YES CCDS10736.1 ENSP00000219197 P23435 UPI0000127506 NM_004352.3 deleterious(0) 1/3 hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 49281372 49281372 C A 1 0 0 0 0 1 0 0 0 2405 623 22 2 2 CBLN1 16 49281372 Missense_Mutation SNP C C3N-00704_T 2543303 49281372 41056973 491 19628 CHD9 0 . GRCh38 16 53235184 53235184 + Splice_Site SNP G G C novel C3N-00704_T C3N-00704_N G G c.2512-1G>C p.X838_splice ENST00000447540 84 77 7 107 107 0 strelka-varscan-mutect CHD9,splice_acceptor_variant,,ENST00000566029,NM_025134.4;CHD9,splice_acceptor_variant,,ENST00000447540,NM_001308319.1;CHD9,splice_acceptor_variant,,ENST00000564845,;CHD9,splice_acceptor_variant,,ENST00000398510,;CHD9,splice_acceptor_variant,,ENST00000615216,;CHD9,splice_acceptor_variant,,ENST00000565803,;CHD9,intron_variant,,ENST00000622617,;CHD9,splice_acceptor_variant,,ENST00000564255,;CHD9,non_coding_transcript_exon_variant,,ENST00000219084,;CHD9,non_coding_transcript_exon_variant,,ENST00000569225,; C ENST00000447540 Transcript splice_acceptor_variant -/11509 2512/8694 838/2897 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 10/38 HIGH 1 SNV 5 1 PASS rs1232857631 . 0 203 6 0 0 0 0 0 -14.89142 0.9999998 1 1 1 0 C 5 2 62 53235184 53235184 G C 1 0 0 0 0 0 0 1 0 3091 1014 35 4 4 CHD9 16 53235184 Splice_Site SNP G C3N-00704_T 3953812 53235184 37103161 492 19629 CCDC102A 0 . GRCh38 16 57528675 57528675 + Missense_Mutation SNP T T C rs765543276 C3N-00704_T C3N-00704_N T T c.503A>G p.Asp168Gly p.D168G ENST00000258214 2/9 78 71 7 65 65 0 strelka-varscan-mutect CCDC102A,missense_variant,p.Asp168Gly,ENST00000258214,NM_033212.3; C ENST00000258214 Transcript missense_variant 750/2463 503/1653 168/550 D/G gAc/gGc rs765543276 1 -1 CCDC102A HGNC HGNC:28097 protein_coding YES CCDS10784.1 ENSP00000258214 Q96A19 UPI000013CFBA NM_033212.3 tolerated(0.49) 2/9 MODERATE 1 SNV 1 1 PASS rs765543276 . 1 207 2 0 0 0 0 0 -15.63213 1 1 1 1 0 C 3 2 62 57528675 57528675 T C 1 0 0 0 0 1 0 0 0 2434 1667 58 5 5 CCDC102A 16 57528675 Missense_Mutation SNP T C3N-00704_T 4293491 57528675 32809670 493 19630 ADGRG5 0 . GRCh38 16 57574931 57574931 + Missense_Mutation SNP G G T rs780881181 C3N-00704_T C3N-00704_N G G c.1325G>T p.Arg442Leu p.R442L ENST00000340339 11/12 268 224 44 206 206 0 strelka-varscan-mutect ADGRG5,missense_variant,p.Arg442Leu,ENST00000340339,NM_153837.2;ADGRG5,missense_variant,p.Arg442Leu,ENST00000349457,NM_001304376.1;ADGRG5,non_coding_transcript_exon_variant,,ENST00000394361,;ADGRG5,non_coding_transcript_exon_variant,,ENST00000569839,;ADGRG5,non_coding_transcript_exon_variant,,ENST00000564607,; T ENST00000340339 Transcript missense_variant 1848/3767 1325/1587 442/528 R/L cGg/cTg rs780881181,COSM3818153 1 1 ADGRG5 HGNC HGNC:19010 protein_coding YES CCDS10785.1 ENSP00000342981 Q8IZF4 A0A024R6S3 UPI0000039944 NM_153837.2 deleterious(0) 11/12 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF326,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780881181 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 57574931 57574931 G T 1 0 0 0 0 1 0 0 0 372 1116 39 1 1 ADGRG5 16 57574931 Missense_Mutation SNP G C3N-00704_T 46256 57574931 32763414 494 19631 KIFC3 0 . GRCh38 16 57765551 57765551 + Missense_Mutation SNP C C A rs372355077 C3N-00704_T C3N-00704_N C C c.1420G>T p.Asp474Tyr p.D474Y ENST00000379655 11/19 380 344 36 278 278 0 strelka-varscan-mutect KIFC3,missense_variant,p.Asp474Tyr,ENST00000379655,NM_005550.3;KIFC3,missense_variant,p.Asp474Tyr,ENST00000445690,NM_001318710.1,NM_001130100.1;KIFC3,missense_variant,p.Asp335Tyr,ENST00000465878,NM_001318715.1;KIFC3,missense_variant,p.Asp335Tyr,ENST00000562903,;KIFC3,missense_variant,p.Asp335Tyr,ENST00000421376,NM_001130099.1;KIFC3,missense_variant,p.Asp496Tyr,ENST00000541240,;KIFC3,missense_variant,p.Asp335Tyr,ENST00000543930,;KIFC3,missense_variant,p.Asp372Tyr,ENST00000540079,;KIFC3,upstream_gene_variant,,ENST00000565270,;KIFC3,upstream_gene_variant,,ENST00000565397,;KIFC3,non_coding_transcript_exon_variant,,ENST00000563266,;KIFC3,missense_variant,p.Asp335Tyr,ENST00000564136,;KIFC3,upstream_gene_variant,,ENST00000565753,; A ENST00000379655 Transcript missense_variant 1678/3427 1420/2502 474/833 D/Y Gac/Tac rs372355077 1 -1 KIFC3 HGNC HGNC:6326 protein_coding YES CCDS10789.2 ENSP00000368976 Q9BVG8 UPI000059D399 NM_005550.3 deleterious(0) 11/19 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF387,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs372355077 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 57765551 57765551 C A 1 0 0 0 0 1 0 0 0 8179 884 31 1 1 KIFC3 16 57765551 Missense_Mutation SNP C C3N-00704_T 190620 57765551 32572794 495 19632 TANGO6 0 . GRCh38 16 68919129 68919129 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.2037C>T p.= p.S679S ENST00000261778 12/18 145 112 33 171 171 0 strelka-varscan-mutect TANGO6,synonymous_variant,p.=,ENST00000261778,NM_024562.1;TANGO6,3_prime_UTR_variant,,ENST00000561856,; T ENST00000261778 Transcript synonymous_variant 2049/4816 2037/3285 679/1094 S agC/agT 1 1 TANGO6 HGNC HGNC:25749 protein_coding YES CCDS45516.1 ENSP00000261778 Q9C0B7 UPI00001FF4A8 NM_024562.1 12/18 Gene3D:1.25.10.10,hmmpanther:PTHR20959,hmmpanther:PTHR20959:SF1,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 68919129 68919129 C T 1 0 0 0 0 0 0 0 1 15944 738 26 3 3 TANGO6 16 68919129 Silent SNP C C3N-00704_T 11153578 68919129 21419216 496 19633 CMTR2 0 . GRCh38 16 71284705 71284705 + Nonsense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1216C>T p.Gln406Ter p.Q406* ENST00000338099 3/3 87 63 24 173 173 0 strelka-varscan-mutect CMTR2,stop_gained,p.Gln406Ter,ENST00000338099,;CMTR2,stop_gained,p.Gln406Ter,ENST00000434935,NM_001324377.1,NM_018348.5,NM_001099642.1;CMTR2,downstream_gene_variant,,ENST00000565850,;CMTR2,downstream_gene_variant,,ENST00000568910,;CMTR2,downstream_gene_variant,,ENST00000563876,;CMTR2,downstream_gene_variant,,ENST00000564183,;CMTR2,downstream_gene_variant,,ENST00000567610,;CMTR2,downstream_gene_variant,,ENST00000564690,; A ENST00000338099 Transcript stop_gained 1553/4869 1216/2313 406/770 Q/* Caa/Taa 1 -1 CMTR2 HGNC HGNC:25635 protein_coding YES CCDS10898.1 ENSP00000337512 Q8IYT2 UPI000006EA8B 3/3 hmmpanther:PTHR16121,hmmpanther:PTHR16121:SF2 HIGH 1 SNV 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 71284705 71284705 G A 1 0 0 0 0 0 1 0 0 3367 1328 46 3 3 CMTR2 16 71284705 Nonsense_Mutation SNP G C3N-00704_T 2365576 71284705 19053640 497 19634 PHLPP2 0 . GRCh38 16 71658748 71658748 + Missense_Mutation SNP T T A C3N-00704_T C3N-00704_N T T c.2053A>T p.Thr685Ser p.T685S ENST00000568954 14/19 185 149 36 318 318 0 strelka-varscan-mutect PHLPP2,missense_variant,p.Thr618Ser,ENST00000393524,NM_001289003.1;PHLPP2,missense_variant,p.Thr685Ser,ENST00000568954,NM_015020.3;PHLPP2,missense_variant,p.Thr720Ser,ENST00000567016,;RP11-432I5.6,intron_variant,,ENST00000567077,;PHLPP2,missense_variant,p.Thr423Ser,ENST00000568004,;PHLPP2,missense_variant,p.Thr48Ser,ENST00000564884,; A ENST00000568954 Transcript missense_variant 2432/8317 2053/3972 685/1323 T/S Aca/Tca COSM4871764,COSM973349 1 -1 PHLPP2 HGNC HGNC:29149 protein_coding YES CCDS32479.1 ENSP00000457991 Q6ZVD8 UPI0000229F5A NM_015020.3 tolerated(0.24) 14/19 PROSITE_profiles:PS51450,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 71658748 71658748 T A 1 0 0 0 0 1 0 0 0 11943 1696 59 4 4 PHLPP2 16 71658748 Missense_Mutation SNP T C3N-00704_T 374043 71658748 18679597 498 19635 SMG6 0 . GRCh38 17 2300403 2300403 + Frame_Shift_Del DEL C C - novel C3N-00704_T C3N-00704_N C C c.350delG p.Gly117AspfsTer16 p.G117Dfs*16 ENST00000263073 2/19 177 129 48 250 250 0 sindel-varindel-pindel SMG6,frameshift_variant,p.Gly117AspfsTer16,ENST00000263073,NM_017575.4;SRR,upstream_gene_variant,,ENST00000344595,NM_021947.2;SRR,upstream_gene_variant,,ENST00000576848,;SRR,upstream_gene_variant,,ENST00000574987,;SRR,upstream_gene_variant,,ENST00000575840,;SRR,upstream_gene_variant,,ENST00000576620,;SRR,upstream_gene_variant,,ENST00000572709,; - ENST00000263073 Transcript frameshift_variant 401/5960 350/4260 117/1419 G/X gGa/ga 1 -1 SMG6 HGNC HGNC:17809 protein_coding YES CCDS11016.1 ENSP00000263073 Q86US8 UPI00002005C8 NM_017575.4 2/19 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 2300403 2300403 C - 1 0 1 0 1 0 0 0 0 15091 855 30 0 0 SMG6 17 2300403 Frame_Shift_Del DEL C C3N-00704_T 2300403 80957038 499 19636 SPNS3 0 . GRCh38 17 4453143 4453143 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1051G>T p.Ala351Ser p.A351S ENST00000355530 8/12 139 111 28 198 198 0 strelka-varscan-mutect SPNS3,missense_variant,p.Ala351Ser,ENST00000355530,NM_182538.4;SPNS3,non_coding_transcript_exon_variant,,ENST00000576069,;SPNS3,3_prime_UTR_variant,,ENST00000575194,NM_001320449.1;SPNS3,downstream_gene_variant,,ENST00000575185,;SPNS3,downstream_gene_variant,,ENST00000572078,; T ENST00000355530 Transcript missense_variant 1331/2133 1051/1539 351/512 A/S Gcc/Tcc 1 1 SPNS3 HGNC HGNC:28433 protein_coding YES CCDS11045.1 ENSP00000347721 Q6ZMD2 UPI00001971EC NM_182538.4 tolerated(0.48) 8/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF3,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 4453143 4453143 G T 1 0 0 0 0 1 0 0 0 15429 1319 46 2 2 SPNS3 17 4453143 Missense_Mutation SNP G C3N-00704_T 2152740 4453143 78804298 500 19637 GP1BA 0 . GRCh38 17 4933077 4933077 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.473G>T p.Gly158Val p.G158V ENST00000329125 2/2 181 141 40 268 268 0 strelka-varscan-mutect GP1BA,missense_variant,p.Gly158Val,ENST00000329125,NM_000173.6;GP1BA,missense_variant,p.Gly158Val,ENST00000611961,;SLC25A11,downstream_gene_variant,,ENST00000225665,NM_003562.4;SLC25A11,downstream_gene_variant,,ENST00000544061,NM_001165418.1;SLC25A11,downstream_gene_variant,,ENST00000576951,NM_001165417.1;SLC25A11,downstream_gene_variant,,ENST00000574710,; T ENST00000329125 Transcript missense_variant 548/2501 473/1959 158/652 G/V gGg/gTg 1 1 GP1BA HGNC HGNC:4439 protein_coding YES CCDS54068.1 ENSP00000329380 P07359 UPI0001CB792B NM_000173.6 deleterious(0.01) 2/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR24369:SF61,hmmpanther:PTHR24369,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00364,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs1443315792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 4933077 4933077 G T 1 0 0 0 0 1 0 0 0 6476 1232 43 2 2 GP1BA 17 4933077 Missense_Mutation SNP G C3N-00704_T 479934 4933077 78324364 501 19638 TP53 0 . GRCh38 17 7674238 7674238 + Missense_Mutation SNP C C A rs121912655 C3N-00704_T C3N-00704_N C C c.725G>T p.Cys242Phe p.C242F ENST00000269305 7/11 291 216 75 344 344 0 strelka-varscan-mutect TP53,missense_variant,p.Cys242Phe,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Cys242Phe,ENST00000420246,;TP53,missense_variant,p.Cys203Phe,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Cys203Phe,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Cys242Phe,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Cys203Phe,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Cys242Phe,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Cys203Phe,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Cys242Phe,ENST00000445888,;TP53,missense_variant,p.Cys203Phe,ENST00000619485,;TP53,missense_variant,p.Cys110Phe,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Cys83Phe,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Cys110Phe,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Cys83Phe,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Cys110Phe,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Cys83Phe,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Cys242Phe,ENST00000359597,;TP53,missense_variant,p.Cys231Phe,ENST00000615910,;TP53,missense_variant,p.Cys242Phe,ENST00000413465,;TP53,missense_variant,p.Cys110Phe,ENST00000509690,;TP53,missense_variant,p.Cys149Phe,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Cys203Phe,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 915/2579 725/1182 242/393 C/F tGc/tTc rs121912655,CM910618,TP53_g.13362G>A,TP53_g.13362G>T,TP53_g.13362G>C,COSM10646,COSM10810,COSM11133,COSM129834,COSM129835,COSM129836,COSM1610838,COSM1610839,COSM1610840,COSM1646852,COSM251396,COSM251397,COSM251398,COSM2744611,COSM2744612,COSM3378347,COSM3403262,COSM3717642 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 7674238 7674238 C A 1 0 0 0 0 1 0 0 0 16859 710 25 2 2 TP53 17 7674238 Missense_Mutation SNP C C3N-00704_T 2741161 7674238 75583203 502 19639 PER1 0 . GRCh38 17 8147791 8147791 + Missense_Mutation SNP G G A rs778073764 C3N-00704_T C3N-00704_N G G c.1271C>T p.Pro424Leu p.P424L ENST00000317276 11/23 173 130 43 276 276 0 strelka-varscan-mutect PER1,missense_variant,p.Pro424Leu,ENST00000317276,NM_002616.2;PER1,missense_variant,p.Pro404Leu,ENST00000581082,;PER1,missense_variant,p.Pro408Leu,ENST00000354903,;PER1,downstream_gene_variant,,ENST00000577253,;PER1,downstream_gene_variant,,ENST00000584202,;PER1,downstream_gene_variant,,ENST00000581703,;PER1,upstream_gene_variant,,ENST00000583559,;RP11-599B13.6,downstream_gene_variant,,ENST00000498285,;PER1,upstream_gene_variant,,ENST00000614952,;PER1,upstream_gene_variant,,ENST00000578089,;PER1,missense_variant,p.Pro424Leu,ENST00000582719,;PER1,missense_variant,p.Pro424Leu,ENST00000581395,;PER1,non_coding_transcript_exon_variant,,ENST00000578223,;PER1,non_coding_transcript_exon_variant,,ENST00000579203,;PER1,downstream_gene_variant,,ENST00000579065,;PER1,upstream_gene_variant,,ENST00000585095,;PER1,upstream_gene_variant,,ENST00000577424,;PER1,upstream_gene_variant,,ENST00000578950,;PER1,upstream_gene_variant,,ENST00000579098,; A ENST00000317276 Transcript missense_variant 1509/4707 1271/3873 424/1290 P/L cCt/cTt rs778073764 1 -1 PER1 HGNC HGNC:8845 protein_coding YES CCDS11131.1 ENSP00000314420 O15534 UPI000013FFF5 NM_002616.2 deleterious(0) 11/23 hmmpanther:PTHR11269:SF8,hmmpanther:PTHR11269,Gene3D:3.30.450.20,Pfam_domain:PF08447,Superfamily_domains:SSF55785 MODERATE 1 SNV 1 1 PASS rs778073764 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 8147791 8147791 G A 1 0 0 0 0 1 0 0 0 11817 1000 35 3 3 PER1 17 8147791 Missense_Mutation SNP G C3N-00704_T 473553 8147791 75109650 503 19640 MYH1 0 . GRCh38 17 10512690 10512690 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.999G>T p.Met333Ile p.M333I ENST00000226207 11/40 174 131 43 239 239 0 strelka-varscan-mutect MYH1,missense_variant,p.Met333Ile,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 1094/6024 999/5820 333/1939 M/I atG/atT 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 tolerated(0.19) 11/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 205 0 3 2 0 0 0 -20 0.9888603 1 1 1 0 A 3 1 62 10512690 10512690 C A 1 0 0 0 0 1 0 0 0 10029 594 21 2 2 MYH1 17 10512690 Missense_Mutation SNP C C3N-00704_T 2364899 10512690 72744751 504 19641 MYH3 0 . GRCh38 17 10639446 10639446 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.2954G>A p.Gly985Glu p.G985E ENST00000583535 24/41 205 163 42 370 370 0 strelka-varscan-mutect MYH3,missense_variant,p.Gly985Glu,ENST00000583535,NM_002470.3; T ENST00000583535 Transcript missense_variant 3042/6037 2954/5823 985/1940 G/E gGg/gAg 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 tolerated(0.1) 24/41 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF427,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 10639446 10639446 C T 1 0 0 0 0 1 0 0 0 10036 623 22 3 3 MYH3 17 10639446 Missense_Mutation SNP C C3N-00704_T 126756 10639446 72617995 505 19642 TBC1D28 0 . GRCh38 17 18637870 18637870 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.491G>T p.Gly164Val p.G164V ENST00000345096 8/9 307 250 57 455 453 2 strelka-varscan-mutect TBC1D28,missense_variant,p.Gly164Val,ENST00000345096,;TBC1D28,missense_variant,p.Gly164Val,ENST00000405044,NM_001039397.2;TBC1D28,downstream_gene_variant,,ENST00000575220,;TBC1D28,downstream_gene_variant,,ENST00000572213,;TBC1D28,downstream_gene_variant,,ENST00000573652,;TBC1D28,downstream_gene_variant,,ENST00000575211,;TBC1D28,downstream_gene_variant,,ENST00000575570,;TBC1D28,downstream_gene_variant,,ENST00000579178,;TBC1D28,downstream_gene_variant,,ENST00000575970,;TBC1D28,downstream_gene_variant,,ENST00000570881,;RP11-815I9.3,downstream_gene_variant,,ENST00000571884,; A ENST00000345096 Transcript missense_variant 1191/2789 491/633 164/210 G/V gGa/gTa 1 -1 TBC1D28 HGNC HGNC:26858 protein_coding YES CCDS42273.1 ENSP00000339973 Q2M2D7 UPI0000251DA5 deleterious(0) 8/9 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF322,Pfam_domain:PF00566,Gene3D:2qq8A02,Superfamily_domains:SSF47923 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 18637870 18637870 C A 1 0 0 0 0 1 0 0 0 16017 855 30 2 2 TBC1D28 17 18637870 Missense_Mutation SNP C C3N-00704_T 7998424 18637870 64619571 506 19643 MAP2K3 0 . GRCh38 17 21298461 21298461 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.98C>A p.Pro33Gln p.P33Q ENST00000342679 2/12 447 413 34 675 674 1 strelka-varscan-mutect MAP2K3,missense_variant,p.Pro33Gln,ENST00000342679,NM_145109.2;MAP2K3,missense_variant,p.Pro4Gln,ENST00000361818,NM_002756.4;MAP2K3,missense_variant,p.Pro4Gln,ENST00000613338,;MAP2K3,missense_variant,p.Pro4Gln,ENST00000316920,;MAP2K3,missense_variant,p.Pro4Gln,ENST00000526076,;MAP2K3,downstream_gene_variant,,ENST00000529517,;MAP2K3,downstream_gene_variant,,ENST00000627447,;MAP2K3,missense_variant,p.Pro33Gln,ENST00000496046,;MAP2K3,3_prime_UTR_variant,,ENST00000395491,NM_001316332.1;MAP2K3,3_prime_UTR_variant,,ENST00000479129,;MAP2K3,non_coding_transcript_exon_variant,,ENST00000583508,;MAP2K3,downstream_gene_variant,,ENST00000483928,; A ENST00000342679 Transcript missense_variant 347/2303 98/1044 33/347 P/Q cCa/cAa COSM2798817,COSM382006,COSM5368129 1 1 MAP2K3 HGNC HGNC:6843 protein_coding YES CCDS11217.1 ENSP00000345083 P46734 Q6FI23 UPI000012F48C NM_145109.2 tolerated(0.43) 2/12 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF191,Low_complexity_(Seg):seg 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1391649195 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 21298461 21298461 C A 1 0 0 0 0 1 0 0 0 9160 594 21 2 2 MAP2K3 17 21298461 Missense_Mutation SNP C C3N-00704_T 2660591 21298461 61958980 507 19644 TMEM132E 0 . GRCh38 17 34637675 34637675 + Missense_Mutation SNP G G T rs748031574 C3N-00704_T C3N-00704_N G G c.2398G>T p.Gly800Cys p.G800C ENST00000321639 10/10 105 81 24 138 138 0 strelka-varscan-mutect TMEM132E,missense_variant,p.Gly890Cys,ENST00000631683,NM_001304438.1;TMEM132E,missense_variant,p.Gly800Cys,ENST00000321639,;TMEM132E,downstream_gene_variant,,ENST00000577271,; T ENST00000321639 Transcript missense_variant 2726/4369 2398/2955 800/984 G/C Ggc/Tgc rs748031574 1 1 TMEM132E HGNC HGNC:26991 protein_coding YES ENSP00000316532 Q6IEE7 UPI000035960F deleterious(0) 10/10 Pfam_domain:PF15706,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF7 MODERATE 1 SNV 5 1 PASS rs748031574 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 34637675 34637675 G T 1 0 0 0 0 1 0 0 0 16493 1116 39 1 1 TMEM132E 17 34637675 Missense_Mutation SNP G C3N-00704_T 13339214 34637675 48619766 508 19645 CCL3 0 . GRCh38 17 36090024 36090024 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.35T>A p.Leu12His p.L12H ENST00000613922 1/3 370 338 32 514 514 0 strelka-varscan-mutect CCL3,missense_variant,p.Leu12His,ENST00000613922,NM_002983.2;AC069363.1,non_coding_transcript_exon_variant,,ENST00000616926,;AC069363.1,downstream_gene_variant,,ENST00000620056,;AC069363.1,downstream_gene_variant,,ENST00000615750,;CCL3,non_coding_transcript_exon_variant,,ENST00000614051,;CCL3,non_coding_transcript_exon_variant,,ENST00000613928,; T ENST00000613922 Transcript missense_variant 118/778 35/279 12/92 L/H cTc/cAc 1 -1 CCL3 HGNC HGNC:10627 protein_coding YES CCDS11307.1 ENSP00000477908 P10147 UPI00001362C9 NM_002983.2 deleterious(0) 1/3 hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF94,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 36090024 36090024 A T 1 0 0 0 0 1 0 0 0 2599 304 11 4 4 CCL3 17 36090024 Missense_Mutation SNP A C3N-00704_T 1452349 36090024 47167417 509 19646 ARHGAP23 0 . GRCh38 17 38500596 38500596 + Splice_Site SNP G G A novel C3N-00704_T C3N-00704_N G G c.3416-1G>A p.X1139_splice ENST00000622683 196 164 32 250 250 0 strelka-varscan-mutect ARHGAP23,splice_acceptor_variant,,ENST00000622683,NM_001199417.1;ARHGAP23,splice_acceptor_variant,,ENST00000620417,;ARHGAP23,splice_acceptor_variant,,ENST00000614693,;ARHGAP23,splice_acceptor_variant,,ENST00000620329,;ARHGAP23,non_coding_transcript_exon_variant,,ENST00000618325,; A ENST00000622683 Transcript splice_acceptor_variant -/5964 3416/4476 1139/1491 1 1 ARHGAP23 HGNC HGNC:29293 protein_coding YES CCDS56027.1 ENSP00000481862 Q9P227 UPI0000F3BE51 NM_001199417.1 22/23 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 62 38500596 38500596 G A 1 0 0 0 0 0 0 1 0 997 956 33 3 3 ARHGAP23 17 38500596 Splice_Site SNP G C3N-00704_T 2410572 38500596 44756845 510 19647 KRT16 0 . GRCh38 17 41609941 41609941 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.1416C>T p.= p.S472S ENST00000301653 8/8 414 335 79 559 559 0 strelka-varscan-mutect KRT16,synonymous_variant,p.=,ENST00000301653,NM_005557.3;KRT16,downstream_gene_variant,,ENST00000593067,;KRT16,downstream_gene_variant,,ENST00000590990,;KRT16,downstream_gene_variant,,ENST00000588319,; A ENST00000301653 Transcript synonymous_variant 1481/1644 1416/1422 472/473 S agC/agT 1 -1 KRT16 HGNC HGNC:6423 protein_coding YES CCDS11401.1 ENSP00000301653 P08779 UPI0000001C7B NM_005557.3 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105 LOW 1 SNV 1 1 PASS rs1295536283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 41609941 41609941 G A 1 0 0 0 0 0 0 0 1 8335 962 34 3 3 KRT16 17 41609941 Silent SNP G C3N-00704_T 3109345 41609941 41647500 511 19648 HAP1 0 . GRCh38 17 41724870 41724870 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1691G>T p.Gly564Val p.G564V ENST00000347901 11/11 216 166 50 276 276 0 strelka-varscan-mutect HAP1,missense_variant,p.Gly539Val,ENST00000393939,NM_001079871.1;HAP1,missense_variant,p.Gly616Val,ENST00000310778,;HAP1,missense_variant,p.Gly564Val,ENST00000347901,NM_177977.2;HAP1,missense_variant,p.Gly547Val,ENST00000341193,NM_001079870.1;HAP1,missense_variant,p.Gly71Val,ENST00000458656,;HAP1,intron_variant,,ENST00000442364,;HAP1,intron_variant,,ENST00000455021,; A ENST00000347901 Transcript missense_variant 1701/3931 1691/1860 564/619 G/V gGc/gTc 1 -1 HAP1 HGNC HGNC:4812 protein_coding YES CCDS11406.1 ENSP00000334002 P54257 UPI000024700D NM_177977.2 deleterious_low_confidence(0) 11/11 hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF14 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 41724870 41724870 C A 1 0 0 0 0 1 0 0 0 6839 739 26 2 2 HAP1 17 41724870 Missense_Mutation SNP C C3N-00704_T 114929 41724870 41532571 512 19649 ANKFN1 0 . GRCh38 17 56457348 56457348 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1408C>A p.His470Asn p.H470N ENST00000318698 12/17 38 28 10 104 104 0 strelka-varscan-mutect ANKFN1,missense_variant,p.His470Asn,ENST00000566473,;ANKFN1,missense_variant,p.His470Asn,ENST00000318698,NM_153228.2;ANKFN1,non_coding_transcript_exon_variant,,ENST00000572321,; A ENST00000318698 Transcript missense_variant 1443/2426 1408/2292 470/763 H/N Cac/Aac 1 1 ANKFN1 HGNC HGNC:26766 protein_coding YES CCDS32686.1 ENSP00000321627 Q8N957 UPI000049DE57 NM_153228.2 deleterious(0.02) 12/17 hmmpanther:PTHR21437,hmmpanther:PTHR21437:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 56457348 56457348 C A 1 0 0 0 0 1 0 0 0 727 826 29 2 2 ANKFN1 17 56457348 Missense_Mutation SNP C C3N-00704_T 14732478 56457348 26800093 513 19650 OR4D1 0 . GRCh38 17 58155315 58155315 + Silent SNP G G A novel C3N-00704_T C3N-00704_N G G c.162G>A p.= p.R54R ENST00000268912 1/1 157 139 18 237 237 0 strelka-varscan-mutect OR4D1,synonymous_variant,p.=,ENST00000268912,NM_012374.1;MSX2P1,upstream_gene_variant,,ENST00000584100,; A ENST00000268912 Transcript synonymous_variant 183/1024 162/933 54/310 R cgG/cgA 1 1 OR4D1 HGNC HGNC:8293 protein_coding YES CCDS42365.1 ENSP00000365451 Q15615 UPI0000041E8C NM_012374.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF310,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 58155315 58155315 G A 1 0 0 0 0 0 0 0 1 11130 1190 42 3 3 OR4D1 17 58155315 Silent SNP G C3N-00704_T 1697967 58155315 25102126 514 19651 TANC2 0 . GRCh38 17 63389500 63389500 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2785G>T p.Gly929Trp p.G929W ENST00000424789 15/25 473 421 52 478 478 0 strelka-varscan-mutect TANC2,missense_variant,p.Gly929Trp,ENST00000424789,NM_025185.3;TANC2,missense_variant,p.Gly858Trp,ENST00000583356,;TANC2,missense_variant,p.Gly929Trp,ENST00000389520,;TANC2,missense_variant,p.Gly30Trp,ENST00000613171,;AC015923.1,intron_variant,,ENST00000431604,;RP11-269G24.3,downstream_gene_variant,,ENST00000583552,;TANC2,non_coding_transcript_exon_variant,,ENST00000583545,;TANC2,non_coding_transcript_exon_variant,,ENST00000581143,;RP11-269G24.7,upstream_gene_variant,,ENST00000606610,; T ENST00000424789 Transcript missense_variant 2789/11721 2785/5973 929/1990 G/W Ggg/Tgg 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 deleterious(0) 15/25 Gene3D:1.25.40.20,Pfam_domain:PF12796,Prints_domain:PR01415,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 63389500 63389500 G T 1 0 0 0 0 1 0 0 0 15942 1000 35 2 2 TANC2 17 63389500 Missense_Mutation SNP G C3N-00704_T 5234185 63389500 19867941 515 19652 ABCA8 0 . GRCh38 17 68917412 68917412 + Missense_Mutation SNP G G T rs145869753 C3N-00704_T C3N-00704_N G G c.2087C>A p.Ala696Glu p.A696E ENST00000586539 17/40 116 100 16 201 201 0 strelka-varscan-mutect ABCA8,missense_variant,p.Ala696Glu,ENST00000430352,NM_001288986.1;ABCA8,missense_variant,p.Ala656Glu,ENST00000269080,NM_007168.3;ABCA8,missense_variant,p.Ala696Glu,ENST00000586539,NM_001288985.1;ABCA8,3_prime_UTR_variant,,ENST00000615593,;ABCA8,missense_variant,p.Ala344Glu,ENST00000589533,;ABCA8,non_coding_transcript_exon_variant,,ENST00000541225,;ABCA8,downstream_gene_variant,,ENST00000587206,; T ENST00000586539 Transcript missense_variant 2276/5088 2087/4866 696/1621 A/E gCg/gAg rs145869753,COSM1640784,COSM3421831 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 deleterious(0.01) 17/40 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs145869753 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 68917412 68917412 G T 1 0 0 0 0 1 0 0 0 42 1087 38 1 1 ABCA8 17 68917412 Missense_Mutation SNP G C3N-00704_T 5527912 68917412 14340029 516 19653 TMEM94 0 . GRCh38 17 75492507 75492507 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1630G>T p.Ala544Ser p.A544S ENST00000314256 15/32 77 59 18 94 94 0 strelka-varscan-mutect TMEM94,missense_variant,p.Ala544Ser,ENST00000314256,NM_001321149.1,NM_014738.4;TMEM94,missense_variant,p.Ala554Ser,ENST00000375248,;TMEM94,missense_variant,p.Ala195Ser,ENST00000579208,;TMEM94,missense_variant,p.Ala93Ser,ENST00000578853,;TMEM94,missense_variant,p.Ala172Ser,ENST00000580918,;TMEM94,upstream_gene_variant,,ENST00000577247,;TMEM94,upstream_gene_variant,,ENST00000584694,;TMEM94,downstream_gene_variant,,ENST00000581252,;TMEM94,downstream_gene_variant,,ENST00000583795,;TMEM94,downstream_gene_variant,,ENST00000580416,;TMEM94,3_prime_UTR_variant,,ENST00000582843,;TMEM94,non_coding_transcript_exon_variant,,ENST00000585105,;TMEM94,non_coding_transcript_exon_variant,,ENST00000581085,;TMEM94,non_coding_transcript_exon_variant,,ENST00000583071,;TMEM94,non_coding_transcript_exon_variant,,ENST00000583296,;TMEM94,upstream_gene_variant,,ENST00000579898,;TMEM94,downstream_gene_variant,,ENST00000579241,;TMEM94,upstream_gene_variant,,ENST00000581453,;TMEM94,upstream_gene_variant,,ENST00000581867,;TMEM94,upstream_gene_variant,,ENST00000578624,;TMEM94,upstream_gene_variant,,ENST00000581723,;TMEM94,downstream_gene_variant,,ENST00000579707,;TMEM94,downstream_gene_variant,,ENST00000580441,;TMEM94,downstream_gene_variant,,ENST00000584383,;TMEM94,downstream_gene_variant,,ENST00000580849,; T ENST00000314256 Transcript missense_variant 2024/5213 1630/4071 544/1356 A/S Gca/Tca 1 1 TMEM94 HGNC HGNC:28983 protein_coding YES CCDS32732.1 ENSP00000313885 Q12767 A0A024R8S6 UPI0000139439 NM_001321149.1,NM_014738.4 deleterious(0.02) 15/32 hmmpanther:PTHR13219,hmmpanther:PTHR13219:SF6 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.999993 1 1 1 0 T 3 4 62 75492507 75492507 G T 1 0 0 0 0 1 0 0 0 16697 971 34 2 2 TMEM94 17 75492507 Missense_Mutation SNP G C3N-00704_T 6575095 75492507 7764934 517 19654 MGAT5B 0 . GRCh38 17 76872832 76872832 + Missense_Mutation SNP G G A rs569753276 C3N-00704_T C3N-00704_N G G c.83G>A p.Arg28His p.R28H ENST00000428789 1/16 422 381 41 615 615 0 strelka-varscan-mutect MGAT5B,missense_variant,p.Arg28His,ENST00000428789,NM_198955.1;MGAT5B,intron_variant,,ENST00000569840,NM_001199172.1;MGAT5B,intron_variant,,ENST00000301618,NM_144677.2;MGAT5B,intron_variant,,ENST00000565675,;MGAT5B,intron_variant,,ENST00000374998,;MGAT5B,missense_variant,p.Arg28His,ENST00000565043,; A ENST00000428789 Transcript missense_variant 186/4053 83/2406 28/801 R/H cGc/cAc rs569753276 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 tolerated_low_confidence(0.08) 1/16 hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs569753276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 76872832 76872832 G A 1 0 0 0 0 1 0 0 0 9510 1087 38 1 1 MGAT5B 17 76872832 Missense_Mutation SNP G C3N-00704_T 1380325 76872832 6384609 518 19655 SEC14L1 0 . GRCh38 17 77196254 77196254 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.762G>T p.= p.L254L ENST00000392476 10/20 168 155 13 207 207 0 strelka-varscan-mutect SEC14L1,synonymous_variant,p.=,ENST00000436233,NM_001143999.1,NM_003003.3,NM_001143998.1;SEC14L1,synonymous_variant,p.=,ENST00000430767,NM_001204410.1;SEC14L1,synonymous_variant,p.=,ENST00000392476,NM_001204408.1;SEC14L1,synonymous_variant,p.=,ENST00000443798,NM_001039573.2;SEC14L1,synonymous_variant,p.=,ENST00000591437,;SEC14L1,synonymous_variant,p.=,ENST00000585618,;SEC14L1,synonymous_variant,p.=,ENST00000431431,NM_001144001.1;SEC14L1,synonymous_variant,p.=,ENST00000589827,;SEC14L1,downstream_gene_variant,,ENST00000588616,;SEC14L1,downstream_gene_variant,,ENST00000589202,;SEC14L1,downstream_gene_variant,,ENST00000590483,;SEC14L1,downstream_gene_variant,,ENST00000586390,;SEC14L1,downstream_gene_variant,,ENST00000591786,;CYCSP40,downstream_gene_variant,,ENST00000575927,; T ENST00000392476 Transcript synonymous_variant 1321/2957 762/2160 254/719 L ctG/ctT 1 1 SEC14L1 HGNC HGNC:10698 protein_coding YES CCDS42385.1 ENSP00000376268 Q92503 UPI00006AB82A NM_001204408.1 10/20 Gene3D:3.40.525.10,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF51,Superfamily_domains:SSF46938 LOW 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -17.51895 0.9999997 1 1 1 0 T 2 4 62 77196254 77196254 G T 1 0 0 0 0 0 0 0 1 14257 1306 46 2 2 SEC14L1 17 77196254 Silent SNP G C3N-00704_T 323422 77196254 6061187 519 19656 PIEZO2 0 . GRCh38 18 10857065 10857065 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.639G>T p.Glu213Asp p.E213D ENST00000503781 6/52 366 293 73 476 475 1 strelka-varscan-mutect PIEZO2,missense_variant,p.Glu162Asp,ENST00000383408,;PIEZO2,missense_variant,p.Glu213Asp,ENST00000302079,;PIEZO2,missense_variant,p.Glu213Asp,ENST00000580640,;PIEZO2,missense_variant,p.Glu213Asp,ENST00000503781,NM_022068.3;PIEZO2,upstream_gene_variant,,ENST00000579112,;PIEZO2,non_coding_transcript_exon_variant,,ENST00000579899,;PIEZO2,missense_variant,p.Glu213Asp,ENST00000582913,; A ENST00000503781 Transcript missense_variant 639/8259 639/8259 213/2752 E/D gaG/gaT 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0.02) 6/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS rs1424044033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 10857065 10857065 C A 1 0 0 0 0 1 0 0 0 11975 564 20 2 2 PIEZO2 18 10857065 Missense_Mutation SNP C C3N-00704_T 10857065 69516220 520 19657 ROCK1 0 . GRCh38 18 21042595 21042595 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.790G>T p.Val264Phe p.V264F ENST00000399799 7/33 135 100 35 234 234 0 strelka-varscan-mutect ROCK1,missense_variant,p.Val264Phe,ENST00000399799,NM_005406.2;ROCK1,missense_variant,p.Val264Phe,ENST00000635540,;ROCK1,downstream_gene_variant,,ENST00000582445,; A ENST00000399799 Transcript missense_variant 1731/9484 790/4065 264/1354 V/F Gtt/Ttt 1 -1 ROCK1 HGNC HGNC:10251 protein_coding YES CCDS11870.2 ENSP00000382697 Q13464 UPI000006F0A4 NM_005406.2 deleterious(0) 7/33 PROSITE_profiles:PS50011,hmmpanther:PTHR22988:SF33,hmmpanther:PTHR22988,Gene3D:1.10.510.10,PIRSF_domain:PIRSF037568,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 21042595 21042595 C A 1 0 0 0 0 1 0 0 0 13695 507 18 2 2 ROCK1 18 21042595 Missense_Mutation SNP C C3N-00704_T 10185530 21042595 59330690 521 19658 KLHL14 0 . GRCh38 18 32741995 32741995 + Silent SNP C C G rs369873078 C3N-00704_T C3N-00704_N C C c.1002G>C p.= p.P334P ENST00000359358 3/9 175 136 39 250 250 0 strelka-varscan-mutect KLHL14,synonymous_variant,p.=,ENST00000359358,NM_020805.1;KLHL14,synonymous_variant,p.=,ENST00000358095,; G ENST00000359358 Transcript synonymous_variant 1441/4312 1002/1887 334/628 P ccG/ccC rs369873078 1 -1 KLHL14 HGNC HGNC:29266 protein_coding YES CCDS32813.1 ENSP00000352314 Q9P2G3 UPI00001C1FF2 NM_020805.1 3/9 Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60,Low_complexity_(Seg):seg,SMART_domains:SM00612 LOW 1 SNV 1 1 PASS rs369873078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 32741995 32741995 C G 1 0 0 0 0 0 0 0 1 8234 639 23 4 4 KLHL14 18 32741995 Silent SNP C C3N-00704_T 11699400 32741995 47631290 522 19659 CDH7 0 . GRCh38 18 65814555 65814555 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.576C>T p.= p.V192V ENST00000397968 4/12 267 216 51 316 316 0 strelka-varscan-mutect CDH7,synonymous_variant,p.=,ENST00000397968,NM_004361.2;CDH7,synonymous_variant,p.=,ENST00000536984,NM_001317214.1;CDH7,synonymous_variant,p.=,ENST00000323011,NM_033646.1; T ENST00000397968 Transcript synonymous_variant 1002/12231 576/2358 192/785 V gtC/gtT 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 4/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 65814555 65814555 C T 1 0 0 0 0 0 0 0 1 2818 900 32 3 3 CDH7 18 65814555 Silent SNP C C3N-00704_T 33072560 65814555 14558730 523 19660 CDH7 0 . GRCh38 18 65844061 65844061 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1231G>T p.Val411Leu p.V411L ENST00000397968 7/12 212 177 35 317 317 0 strelka-varscan-mutect CDH7,missense_variant,p.Val411Leu,ENST00000397968,NM_004361.2;CDH7,missense_variant,p.Val411Leu,ENST00000536984,NM_001317214.1;CDH7,missense_variant,p.Val411Leu,ENST00000323011,NM_033646.1; T ENST00000397968 Transcript missense_variant 1657/12231 1231/2358 411/785 V/L Gtg/Ttg 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 deleterious(0.04) 7/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 65844061 65844061 G T 1 0 0 0 0 1 0 0 0 2818 1391 48 2 2 CDH7 18 65844061 Missense_Mutation SNP G C3N-00704_T 29506 65844061 14529224 524 19661 ZNF236 0 . GRCh38 18 76880206 76880206 + Missense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.1078A>T p.Ile360Phe p.I360F ENST00000320610 8/31 245 201 44 361 361 0 strelka-varscan-mutect ZNF236,missense_variant,p.Ile358Phe,ENST00000253159,NM_007345.3;ZNF236,missense_variant,p.Ile360Phe,ENST00000320610,NM_001306089.1;ZNF236,missense_variant,p.Ile358Phe,ENST00000579322,;ZNF236,downstream_gene_variant,,ENST00000583095,;ZNF236,missense_variant,p.Ile358Phe,ENST00000543926,;ZNF236,upstream_gene_variant,,ENST00000583488,;RP11-162A12.3,downstream_gene_variant,,ENST00000583058,; T ENST00000320610 Transcript missense_variant 1079/7124 1078/5544 360/1847 I/F Atc/Ttc 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 deleterious(0.05) 8/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 76880206 76880206 A T 1 0 0 0 0 1 0 0 0 18366 217 8 4 4 ZNF236 18 76880206 Missense_Mutation SNP A C3N-00704_T 11036145 76880206 3493079 525 19662 MED16 0 . GRCh38 19 873481 873481 + Missense_Mutation SNP C C A rs757761207 C3N-00704_T C3N-00704_N C C c.1873G>T p.Val625Leu p.V625L ENST00000325464 11/16 102 83 19 152 152 0 strelka-varscan-mutect MED16,missense_variant,p.Val625Leu,ENST00000395808,;MED16,missense_variant,p.Val625Leu,ENST00000312090,;MED16,missense_variant,p.Val625Leu,ENST00000325464,NM_005481.2;MED16,missense_variant,p.Val625Leu,ENST00000589119,;MED16,missense_variant,p.Val379Leu,ENST00000607471,;MED16,intron_variant,,ENST00000269814,;MED16,intron_variant,,ENST00000616387,;MED16,intron_variant,,ENST00000617672,;MED16,downstream_gene_variant,,ENST00000592943,;MED16,downstream_gene_variant,,ENST00000586017,;MED16,downstream_gene_variant,,ENST00000606828,;MED16,upstream_gene_variant,,ENST00000621073,;MED16,missense_variant,p.Val625Leu,ENST00000606248,; A ENST00000325464 Transcript missense_variant 2024/2922 1873/2634 625/877 V/L Gtg/Ttg rs757761207 1 -1 MED16 HGNC HGNC:17556 protein_coding YES CCDS12047.1 ENSP00000325612 Q9Y2X0 UPI0000141671 NM_005481.2 tolerated(0.07) 11/16 Pfam_domain:PF11635,hmmpanther:PTHR13224,hmmpanther:PTHR13224:SF6 MODERATE 1 SNV 5 1 PASS rs757761207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 873481 873481 C A 1 0 0 0 0 1 0 0 0 9373 536 19 1 1 MED16 19 873481 Missense_Mutation SNP C C3N-00704_T 873481 57744135 526 19663 DOT1L 0 . GRCh38 19 2214489 2214489 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1816G>T p.Glu606Ter p.E606* ENST00000398665 19/28 136 97 39 208 208 0 strelka-varscan-mutect DOT1L,stop_gained,p.Glu606Ter,ENST00000398665,NM_032482.2;DOT1L,stop_gained,p.Glu70Ter,ENST00000586024,;AC004490.1,non_coding_transcript_exon_variant,,ENST00000585593,;DOT1L,non_coding_transcript_exon_variant,,ENST00000608122,;DOT1L,non_coding_transcript_exon_variant,,ENST00000591498,;DOT1L,upstream_gene_variant,,ENST00000482433,; T ENST00000398665 Transcript stop_gained 1852/7436 1816/4614 606/1537 E/* Gag/Tag 1 1 DOT1L HGNC HGNC:24948 protein_coding YES CCDS42460.1 ENSP00000381657 Q8TEK3 UPI000002A839 NM_032482.2 19/28 hmmpanther:PTHR21451,hmmpanther:PTHR21451:SF0,PIRSF_domain:PIRSF037123 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 2214489 2214489 G T 1 0 0 0 0 0 1 0 0 4523 1175 41 2 2 DOT1L 19 2214489 Nonsense_Mutation SNP G C3N-00704_T 1341008 2214489 56403127 527 19664 CCDC94 0 . GRCh38 19 4251093 4251093 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.192G>T p.Gln64His p.Q64H ENST00000262962 3/8 235 174 61 286 285 1 strelka-varscan-mutect CCDC94,missense_variant,p.Gln64His,ENST00000262962,NM_018074.4;CCDC94,missense_variant,p.Gln29His,ENST00000596496,;AC005578.3,upstream_gene_variant,,ENST00000622962,; T ENST00000262962 Transcript missense_variant 260/1434 192/972 64/323 Q/H caG/caT 1 1 CCDC94 HGNC HGNC:25518 protein_coding YES CCDS12124.1 ENSP00000262962 Q9BW85 UPI000006CF6B NM_018074.4 deleterious(0) 3/8 Pfam_domain:PF04502,hmmpanther:PTHR12111,hmmpanther:PTHR12111:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 4251093 4251093 G T 1 0 0 0 0 1 0 0 0 2571 933 33 2 2 CCDC94 19 4251093 Missense_Mutation SNP G C3N-00704_T 2036604 4251093 54366523 528 19665 SEMA6B 0 . GRCh38 19 4552528 4552528 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.883C>A p.Pro295Thr p.P295T ENST00000586582 10/17 219 173 46 349 349 0 strelka-varscan-mutect SEMA6B,missense_variant,p.Pro295Thr,ENST00000586582,NM_032108.3;SEMA6B,missense_variant,p.Pro295Thr,ENST00000586965,; T ENST00000586582 Transcript missense_variant 1194/3986 883/2667 295/888 P/T Ccc/Acc 1 -1 SEMA6B HGNC HGNC:10739 protein_coding YES CCDS12131.1 ENSP00000467290 Q9H3T3 UPI000004BA6B NM_032108.3 deleterious(0.01) 10/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 4552528 4552528 G T 1 0 0 0 0 1 0 0 0 14316 1261 44 2 2 SEMA6B 19 4552528 Missense_Mutation SNP G C3N-00704_T 301435 4552528 54065088 529 19666 ADAMTS10 0 . GRCh38 19 8586381 8586381 + Nonsense_Mutation SNP A A C novel C3N-00704_T C3N-00704_N A A c.2493T>G p.Tyr831Ter p.Y831* ENST00000270328 20/25 242 192 50 344 343 1 strelka-varscan-mutect ADAMTS10,stop_gained,p.Tyr831Ter,ENST00000270328,;ADAMTS10,stop_gained,p.Tyr831Ter,ENST00000597188,NM_030957.3;ADAMTS10,stop_gained,p.Tyr318Ter,ENST00000595838,NM_001282352.1;AC130469.2,downstream_gene_variant,,ENST00000597256,;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,;ADAMTS10,downstream_gene_variant,,ENST00000603221,;ADAMTS10,downstream_gene_variant,,ENST00000593826,;ADAMTS10,downstream_gene_variant,,ENST00000596911,;ADAMTS10,downstream_gene_variant,,ENST00000596236,; C ENST00000270328 Transcript stop_gained 2724/4194 2493/3312 831/1103 Y/* taT/taG 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 20/25 Gene3D:2.20.100.10,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26,SMART_domains:SM00209,Superfamily_domains:SSF82895 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 62 8586381 8586381 A C 1 0 0 0 0 0 1 0 0 300 224 8 5 5 ADAMTS10 19 8586381 Nonsense_Mutation SNP A C3N-00704_T 4033853 8586381 50031235 530 19667 MUC16 0 . GRCh38 19 8958269 8958269 + Silent SNP A A G novel C3N-00704_T C3N-00704_N A A c.18501T>C p.= p.L6167L ENST00000397910 3/84 130 90 40 171 171 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; G ENST00000397910 Transcript synonymous_variant 18705/43816 18501/43524 6167/14507 L ctT/ctC 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 8958269 8958269 A G 1 0 0 0 0 0 0 0 1 9972 117 5 5 5 MUC16 19 8958269 Silent SNP A C3N-00704_T 371888 8958269 49659347 531 19668 MUC16 0 . GRCh38 19 8965457 8965457 + Silent SNP T T A novel C3N-00704_T C3N-00704_N T T c.11313A>T p.= p.P3771P ENST00000397910 3/84 100 74 26 123 123 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript synonymous_variant 11517/43816 11313/43524 3771/14507 P ccA/ccT 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 8965457 8965457 T A 1 0 0 0 0 0 0 0 1 9972 1567 55 4 4 MUC16 19 8965457 Silent SNP T C3N-00704_T 7188 8965457 49652159 532 19669 OR7E24 0 . GRCh38 19 9251566 9251566 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.523C>A p.Gln175Lys p.Q175K ENST00000456448 1/1 154 124 30 255 255 0 strelka-varscan-mutect OR7E24,missense_variant,p.Gln175Lys,ENST00000456448,NM_001079935.1; A ENST00000456448 Transcript missense_variant 637/1550 523/1020 175/339 Q/K Cag/Aag COSM1286907 1 1 OR7E24 HGNC HGNC:8396 protein_coding YES CCDS45955.1 ENSP00000387523 Q6IFN5 UPI00003B2886 NM_001079935.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF173,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS rs1290162377 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 9251566 9251566 C A 1 0 0 0 0 1 0 0 0 11291 595 21 2 2 OR7E24 19 9251566 Missense_Mutation SNP C C3N-00704_T 286109 9251566 49366050 533 19670 ZNF564 0 . GRCh38 19 12528604 12528604 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.96G>A p.= p.V32V ENST00000339282 2/4 158 126 32 213 213 0 strelka-varscan-mutect ZNF564,synonymous_variant,p.=,ENST00000339282,NM_144976.3;ZNF564,5_prime_UTR_variant,,ENST00000596193,;CTD-2192J16.17,intron_variant,,ENST00000428311,;CTD-2192J16.21,downstream_gene_variant,,ENST00000601420,;CTD-2192J16.20,3_prime_UTR_variant,,ENST00000593682,;ZNF564,3_prime_UTR_variant,,ENST00000427105,; T ENST00000339282 Transcript synonymous_variant 293/2935 96/1662 32/553 V gtG/gtA 1 -1 ZNF564 HGNC HGNC:31106 protein_coding YES CCDS42505.1 ENSP00000340004 Q8TBZ8 UPI0000051C17 NM_144976.3 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF10,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 12528604 12528604 C T 1 0 0 0 0 0 0 0 1 18569 813 29 3 3 ZNF564 19 12528604 Silent SNP C C3N-00704_T 3277038 12528604 46089012 534 19671 HOOK2 0 . GRCh38 19 12771397 12771397 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.600G>T p.Gln200His p.Q200H ENST00000397668 8/23 178 141 37 233 233 0 strelka-varscan-mutect HOOK2,missense_variant,p.Gln200His,ENST00000264827,NM_001100176.1;HOOK2,missense_variant,p.Gln200His,ENST00000397668,NM_013312.2;HOOK2,missense_variant,p.Gln127His,ENST00000589400,;HOOK2,missense_variant,p.Gln127His,ENST00000592079,;HOOK2,missense_variant,p.Gln127His,ENST00000590839,;HOOK2,missense_variant,p.Gln127His,ENST00000588052,;HOOK2,downstream_gene_variant,,ENST00000587178,;HOOK2,intron_variant,,ENST00000589965,;HOOK2,downstream_gene_variant,,ENST00000587964,;HOOK2,downstream_gene_variant,,ENST00000589765,;HOOK2,splice_region_variant,,ENST00000586284,;HOOK2,splice_region_variant,,ENST00000586719,;HOOK2,intron_variant,,ENST00000586188,;HOOK2,upstream_gene_variant,,ENST00000592259,;HOOK2,downstream_gene_variant,,ENST00000592808,;HOOK2,downstream_gene_variant,,ENST00000591251,;HOOK2,downstream_gene_variant,,ENST00000589134,;HOOK2,upstream_gene_variant,,ENST00000591839,;HOOK2,downstream_gene_variant,,ENST00000591641,;HOOK2,upstream_gene_variant,,ENST00000589398,;HOOK2,downstream_gene_variant,,ENST00000593143,;HOOK2,downstream_gene_variant,,ENST00000592512,; A ENST00000397668 Transcript missense_variant,splice_region_variant 674/2513 600/2160 200/719 Q/H caG/caT 1 -1 HOOK2 HGNC HGNC:19885 protein_coding YES CCDS42508.1 ENSP00000380785 Q96ED9 UPI00003D0BC0 NM_013312.2 deleterious(0) 8/23 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05622,hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF37 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 12771397 12771397 C A 1 0 0 0 0 1 0 0 0 7177 695 24 2 2 HOOK2 19 12771397 Missense_Mutation SNP C C3N-00704_T 242793 12771397 45846219 535 19672 B3GNT3 0 . GRCh38 19 17811964 17811964 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.961G>T p.Gly321Cys p.G321C ENST00000318683 3/3 304 262 42 324 322 2 strelka-varscan-mutect B3GNT3,missense_variant,p.Gly321Cys,ENST00000318683,NM_014256.3;B3GNT3,missense_variant,p.Gly321Cys,ENST00000595387,;INSL3,downstream_gene_variant,,ENST00000379695,NM_001265587.1;B3GNT3,downstream_gene_variant,,ENST00000599265,;INSL3,downstream_gene_variant,,ENST00000598577,;INSL3,downstream_gene_variant,,ENST00000317306,NM_005543.3;B3GNT3,downstream_gene_variant,,ENST00000600777,; T ENST00000318683 Transcript missense_variant 1108/2226 961/1119 321/372 G/C Ggc/Tgc 1 1 B3GNT3 HGNC HGNC:13528 protein_coding YES CCDS12364.1 ENSP00000321874 Q9Y2A9 UPI000007021E NM_014256.3 deleterious(0) 3/3 hmmpanther:PTHR11214:SF23,hmmpanther:PTHR11214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 17811964 17811964 G T 1 0 0 0 0 1 0 0 0 1414 1348 47 2 2 B3GNT3 19 17811964 Missense_Mutation SNP G C3N-00704_T 5040567 17811964 40805652 536 19673 NCAN 0 . GRCh38 19 19226499 19226499 + Silent SNP G G C rs771429364 C3N-00704_T C3N-00704_N G G c.1086G>C p.= p.T362T ENST00000252575 7/15 54 50 4 43 43 0 strelka-mutect NCAN,synonymous_variant,p.=,ENST00000252575,NM_004386.2;NCAN,upstream_gene_variant,,ENST00000590187,; C ENST00000252575 Transcript synonymous_variant 1185/6387 1086/3966 362/1321 T acG/acC rs771429364 1 1 NCAN HGNC HGNC:2465 protein_coding YES CCDS12397.1 ENSP00000252575 O14594 A0A024R7M3 UPI000013CD70 NM_004386.2 7/15 hmmpanther:PTHR22804:SF24,hmmpanther:PTHR22804,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs771429364 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 62 19226499 19226499 G C 1 0 0 0 0 0 0 0 1 10220 1132 40 4 4 NCAN 19 19226499 Silent SNP G C3N-00704_T 1414535 19226499 39391117 537 19674 ZNF676 0 . GRCh38 19 22181200 22181200 + Nonsense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.517G>T p.Glu173Ter p.E173* ENST00000397121 3/3 94 82 12 222 222 0 strelka-varscan-mutect ZNF676,stop_gained,p.Glu173Ter,ENST00000397121,NM_001001411.2; A ENST00000397121 Transcript stop_gained 835/2944 517/1767 173/588 E/* Gaa/Taa 1 -1 ZNF676 HGNC HGNC:20429 protein_coding YES CCDS42539.1 ENSP00000380310 Q8N7Q3 UPI00002376EC NM_001001411.2 3/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 22181200 22181200 C A 1 0 0 0 0 0 1 0 0 18656 922 32 2 2 ZNF676 19 22181200 Nonsense_Mutation SNP C C3N-00704_T 2954701 22181200 36436416 538 19675 ZNF729 0 . GRCh38 19 22315681 22315681 + Missense_Mutation SNP T T A novel C3N-00704_T C3N-00704_N T T c.2264T>A p.Leu755His p.L755H ENST00000601693 4/4 155 132 23 363 363 0 strelka-varscan-mutect ZNF729,missense_variant,p.Leu755His,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript missense_variant 2382/3877 2264/3759 755/1252 L/H cTt/cAt 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 22315681 22315681 T A 1 0 0 0 0 1 0 0 0 18703 1609 56 4 4 ZNF729 19 22315681 Missense_Mutation SNP T C3N-00704_T 134481 22315681 36301935 539 19676 ZNF536 0 . GRCh38 19 30444095 30444095 + Missense_Mutation SNP G G A C3N-00704_T C3N-00704_N G G c.533G>A p.Arg178Gln p.R178Q ENST00000355537 2/5 201 152 49 297 297 0 strelka-mutect ZNF536,missense_variant,p.Arg178Gln,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Arg178Gln,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; A ENST00000355537 Transcript missense_variant 680/4945 533/3903 178/1300 R/Q cGg/cAg COSM5273204 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 2/5 Gene3D:3.30.160.60,Pfam_domain:PF13909,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 30444095 30444095 G A 1 0 0 0 0 1 0 0 0 18547 1116 39 1 1 ZNF536 19 30444095 Missense_Mutation SNP G C3N-00704_T 8128414 30444095 28173521 540 19677 ARHGAP33 0 . GRCh38 19 35778309 35778309 + Silent SNP C C T rs755736461 C3N-00704_T C3N-00704_N C C c.219C>T p.= p.P73P ENST00000314737 4/21 238 190 48 286 286 0 strelka-varscan-mutect ARHGAP33,synonymous_variant,p.=,ENST00000314737,NM_052948.3;ARHGAP33,synonymous_variant,p.=,ENST00000007510,;ARHGAP33,5_prime_UTR_variant,,ENST00000378944,NM_001172630.1;ARHGAP33,upstream_gene_variant,,ENST00000587447,;ARHGAP33,upstream_gene_variant,,ENST00000588248,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000221905,;ARHGAP33,non_coding_transcript_exon_variant,,ENST00000589133,;ARHGAP33,upstream_gene_variant,,ENST00000591438,;ARHGAP33,synonymous_variant,p.=,ENST00000590893,;ARHGAP33,upstream_gene_variant,,ENST00000601474,;ARHGAP33,upstream_gene_variant,,ENST00000586918,; T ENST00000314737 Transcript synonymous_variant 303/3858 219/3381 73/1126 P ccC/ccT rs755736461 1 1 ARHGAP33 HGNC HGNC:23085 protein_coding YES CCDS12477.1 ENSP00000320038 O14559 UPI000013F8F9 NM_052948.3 4/21 hmmpanther:PTHR15729:SF11,hmmpanther:PTHR15729 LOW 1 SNV 2 1 PASS rs755736461 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 35778309 35778309 C T 1 0 0 0 0 0 0 0 1 1007 581 21 3 3 ARHGAP33 19 35778309 Silent SNP C C3N-00704_T 5334214 35778309 22839307 541 19678 ZNF607 0 . GRCh38 19 37699080 37699080 + Nonsense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.1051C>T p.Gln351Ter p.Q351* ENST00000355202 5/5 144 134 10 217 217 0 strelka-varscan-mutect ZNF607,stop_gained,p.Gln351Ter,ENST00000355202,NM_032689.4;ZNF607,stop_gained,p.Gln350Ter,ENST00000395835,NM_001172677.1;ZNF607,downstream_gene_variant,,ENST00000591664,;ZNF607,downstream_gene_variant,,ENST00000590670,;CTD-2528L19.4,intron_variant,,ENST00000586606,;CTD-2528L19.4,intron_variant,,ENST00000585547,;CTD-2528L19.4,intron_variant,,ENST00000591114,;ZNF607,downstream_gene_variant,,ENST00000586559,; A ENST00000355202 Transcript stop_gained 1647/4364 1051/2091 351/696 Q/* Caa/Taa 1 -1 ZNF607 HGNC HGNC:28192 protein_coding YES CCDS33006.1 ENSP00000347338 Q96SK3 UPI000040BC07 NM_032689.4 5/5 Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 62 37699080 37699080 G A 1 0 0 0 0 0 1 0 0 18608 1299 45 3 3 ZNF607 19 37699080 Nonsense_Mutation SNP G C3N-00704_T 1920771 37699080 20918536 542 19679 FBL 0 . GRCh38 19 39840436 39840436 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.261G>T p.Met87Ile p.M87I ENST00000221801 3/9 204 149 55 251 251 0 strelka-varscan-mutect FBL,missense_variant,p.Met87Ile,ENST00000221801,NM_001436.3;FBL,missense_variant,p.Met2Ile,ENST00000595545,;FBL,missense_variant,p.Met63Ile,ENST00000601274,;FBL,missense_variant,p.Met25Ile,ENST00000597224,;FBL,missense_variant,p.Met50Ile,ENST00000597634,;FBL,missense_variant,p.Met86Ile,ENST00000594309,;FBL,missense_variant,p.Met74Ile,ENST00000598417,;FBL,missense_variant,p.Met74Ile,ENST00000599134,;FBL,missense_variant,p.Met27Ile,ENST00000626009,;FBL,upstream_gene_variant,,ENST00000593503,;FBL,missense_variant,p.Met30Ile,ENST00000594443,;FBL,non_coding_transcript_exon_variant,,ENST00000599159,; A ENST00000221801 Transcript missense_variant 375/1160 261/966 87/321 M/I atG/atT 1 -1 FBL HGNC HGNC:3599 protein_coding YES CCDS12545.1 ENSP00000221801 P22087 UPI000012A578 NM_001436.3 tolerated(0.95) 3/9 Gene3D:3.30.200.20,hmmpanther:PTHR10335,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 39840436 39840436 C A 1 0 0 0 0 1 0 0 0 5558 594 21 2 2 FBL 19 39840436 Missense_Mutation SNP C C3N-00704_T 2141356 39840436 18777180 543 19680 PSG4 0 . GRCh38 19 43194575 43194575 + Missense_Mutation SNP G G T rs769133726 C3N-00704_T C3N-00704_N G G c.1008C>A p.Ser336Arg p.S336R ENST00000405312 5/6 96 75 21 139 139 0 strelka-varscan-mutect PSG4,missense_variant,p.Ser336Arg,ENST00000405312,NM_002780.4;PSG4,missense_variant,p.Ser243Arg,ENST00000433626,NM_001276495.1;PSG4,missense_variant,p.Ser243Arg,ENST00000244295,NM_213633.2;PSG4,missense_variant,p.Ser214Arg,ENST00000596907,;PSG4,missense_variant,p.Ser128Arg,ENST00000597374,;PSG4,missense_variant,p.Ser222Arg,ENST00000599746,;PSG4,missense_variant,p.Ser121Arg,ENST00000599391,;PSG4,downstream_gene_variant,,ENST00000451895,;PSG4,downstream_gene_variant,,ENST00000599371,;PSG4,downstream_gene_variant,,ENST00000600572,;PSG4,3_prime_UTR_variant,,ENST00000601041,;PSG4,non_coding_transcript_exon_variant,,ENST00000490769,;PSG4,non_coding_transcript_exon_variant,,ENST00000597349,;PSG4,downstream_gene_variant,,ENST00000595949,;PSG4,downstream_gene_variant,,ENST00000495316,;PSG4,downstream_gene_variant,,ENST00000596199,; T ENST00000405312 Transcript missense_variant 1246/2168 1008/1260 336/419 S/R agC/agA rs769133726 1 -1 PSG4 HGNC HGNC:9521 protein_coding YES CCDS46093.1 ENSP00000384770 Q00888 UPI000034ECBA NM_002780.4 tolerated(0.77) 5/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13895,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs769133726 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 43194575 43194575 G T 1 0 0 0 0 1 0 0 0 12808 1310 46 2 2 PSG4 19 43194575 Missense_Mutation SNP G C3N-00704_T 3354139 43194575 15423041 544 19681 IRGC 0 . GRCh38 19 43719268 43719268 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.710C>A p.Pro237His p.P237H ENST00000244314 2/2 73 52 21 109 108 1 strelka-varscan-mutect IRGC,missense_variant,p.Pro237His,ENST00000244314,NM_019612.3;IRGC,missense_variant,p.Pro274His,ENST00000596627,; A ENST00000244314 Transcript missense_variant 909/1662 710/1392 237/463 P/H cCc/cAc 1 1 IRGC HGNC HGNC:28835 protein_coding YES CCDS12629.1 ENSP00000244314 Q6NXR0 J7NNX4 UPI000011DFC0 NM_019612.3 deleterious(0.01) 2/2 Pfam_domain:PF05049,hmmpanther:PTHR32341,hmmpanther:PTHR32341:SF7,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 62 43719268 43719268 C A 1 0 0 0 0 1 0 0 0 7745 623 22 2 2 IRGC 19 43719268 Missense_Mutation SNP C C3N-00704_T 524693 43719268 14898348 545 19682 RASIP1 0 . GRCh38 19 48721870 48721870 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.2676G>T p.= p.R892R ENST00000222145 11/12 94 87 7 108 108 0 strelka-varscan-mutect RASIP1,synonymous_variant,p.=,ENST00000222145,NM_017805.2;MAMSTR,upstream_gene_variant,,ENST00000318083,NM_001130915.1;MAMSTR,upstream_gene_variant,,ENST00000356751,NM_182574.2;MAMSTR,upstream_gene_variant,,ENST00000594582,NM_001297753.1;MAMSTR,upstream_gene_variant,,ENST00000599703,;RASIP1,downstream_gene_variant,,ENST00000599291,;RASIP1,non_coding_transcript_exon_variant,,ENST00000601530,; A ENST00000222145 Transcript synonymous_variant 2881/3308 2676/2892 892/963 R cgG/cgT 1 -1 RASIP1 HGNC HGNC:24716 protein_coding YES CCDS12731.1 ENSP00000222145 Q5U651 UPI000020283D NM_017805.2 11/12 PROSITE_profiles:PS51126,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF4 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.79392 1 1 1 1 0 A 2 1 62 48721870 48721870 C A 1 0 0 0 0 0 0 0 1 13239 610 22 2 2 RASIP1 19 48721870 Silent SNP C C3N-00704_T 5002602 48721870 9895746 546 19683 TRPM4 0 . GRCh38 19 49196732 49196732 + Nonsense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.2503G>T p.Gly835Ter p.G835* ENST00000252826 17/25 136 108 28 200 200 0 strelka-varscan-mutect TRPM4,stop_gained,p.Gly835Ter,ENST00000252826,NM_017636.3;TRPM4,intron_variant,,ENST00000427978,NM_001195227.1;TRPM4,3_prime_UTR_variant,,ENST00000595519,NM_001321283.1;TRPM4,3_prime_UTR_variant,,ENST00000598502,NM_001321282.1;TRPM4,3_prime_UTR_variant,,ENST00000598697,NM_001321285.1;TRPM4,non_coding_transcript_exon_variant,,ENST00000596338,;TRPM4,non_coding_transcript_exon_variant,,ENST00000595071,;TRPM4,downstream_gene_variant,,ENST00000595882,; T ENST00000252826 Transcript stop_gained 2629/4109 2503/3645 835/1214 G/* Gga/Tga 1 1 TRPM4 HGNC HGNC:17993 protein_coding YES CCDS33073.1 ENSP00000252826 Q8TD43 UPI0000070598 NM_017636.3 17/25 Low_complexity_(Seg):seg,hmmpanther:PTHR13800:SF6,hmmpanther:PTHR13800,Pfam_domain:PF00520 HIGH 1 SNV 1 1 PASS rs1343094946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 49196732 49196732 G T 1 0 0 0 0 0 1 0 0 17094 1117 39 1 1 TRPM4 19 49196732 Nonsense_Mutation SNP G C3N-00704_T 474862 49196732 9420884 547 19684 SLC6A16 0 . GRCh38 19 49308916 49308916 + Missense_Mutation SNP C C A rs765379330 C3N-00704_T C3N-00704_N C C c.1189G>T p.Gly397Cys p.G397C ENST00000335875 7/12 167 150 17 245 244 1 strelka-varscan-mutect SLC6A16,missense_variant,p.Gly397Cys,ENST00000454748,;SLC6A16,missense_variant,p.Gly397Cys,ENST00000335875,NM_014037.2;SLC6A16,missense_variant,p.Gly13Cys,ENST00000594180,;SLC6A16,intron_variant,,ENST00000598828,;SLC6A16,intron_variant,,ENST00000597969,;SLC6A16,intron_variant,,ENST00000594917,;MIR4324,upstream_gene_variant,,ENST00000584846,;SLC6A16,intron_variant,,ENST00000598221,; A ENST00000335875 Transcript missense_variant 1431/2938 1189/2211 397/736 G/C Ggc/Tgc rs765379330 1 -1 SLC6A16 HGNC HGNC:13622 protein_coding YES CCDS42590.1 ENSP00000338627 Q9GZN6 UPI00001305CE NM_014037.2 deleterious(0) 7/12 PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF113,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 5 1 PASS rs765379330 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 49308916 49308916 C A 1 0 0 0 0 1 0 0 0 14962 623 22 2 2 SLC6A16 19 49308916 Missense_Mutation SNP C C3N-00704_T 112184 49308916 9308700 548 19685 SHANK1 0 . GRCh38 19 50702492 50702492 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.1722C>A p.= p.S574S ENST00000293441 11/23 129 119 10 126 126 0 strelka-varscan-mutect SHANK1,synonymous_variant,p.=,ENST00000293441,NM_016148.2;SHANK1,synonymous_variant,p.=,ENST00000391814,;SHANK1,synonymous_variant,p.=,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000461154,; T ENST00000293441 Transcript synonymous_variant 1741/6643 1722/6486 574/2161 S tcC/tcA 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 11/23 PROSITE_profiles:PS50002,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.2245 1 1 1 1 0 T 2 4 62 50702492 50702492 G T 1 0 0 0 0 0 0 0 1 14523 1219 43 2 2 SHANK1 19 50702492 Silent SNP G C3N-00704_T 1393576 50702492 7915124 549 19686 ZNF534 0 . GRCh38 19 52438532 52438532 + Nonsense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.1111G>T p.Glu371Ter p.E371* ENST00000332323 4/4 115 102 13 150 149 1 strelka-varscan-mutect ZNF534,stop_gained,p.Glu371Ter,ENST00000332323,NM_001143939.1;ZNF534,stop_gained,p.Glu358Ter,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; T ENST00000332323 Transcript stop_gained 1172/2086 1111/2025 371/674 E/* Gaa/Taa COSM5390579 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 HIGH 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.6224 0.9999999 1 1 1 0 T 4 4 62 52438532 52438532 G T 1 0 0 0 0 0 1 0 0 18546 1291 45 2 2 ZNF534 19 52438532 Nonsense_Mutation SNP G C3N-00704_T 1736040 52438532 6179084 550 19687 LAIR1 0 . GRCh38 19 54355402 54355402 + Missense_Mutation SNP C C A C3N-00704_T C3N-00704_N C C c.730G>T p.Gly244Trp p.G244W ENST00000391742 10/10 81 58 23 90 90 0 strelka-varscan-mutect LAIR1,missense_variant,p.Gly244Trp,ENST00000391742,NM_002287.5;LAIR1,missense_variant,p.Gly226Trp,ENST00000391743,NM_001289026.2,NM_001289027.2;LAIR1,missense_variant,p.Gly243Trp,ENST00000434277,NM_001289025.2;LAIR1,missense_variant,p.Gly227Trp,ENST00000348231,NM_021706.4;LAIR1,missense_variant,p.Gly226Trp,ENST00000474878,NM_001289023.2;LAIR1,downstream_gene_variant,,ENST00000622064,;LAIR1,non_coding_transcript_exon_variant,,ENST00000440716,;LAIR1,downstream_gene_variant,,ENST00000463489,;LAIR1,downstream_gene_variant,,ENST00000468656,;LAIR1,3_prime_UTR_variant,,ENST00000391741,;LAIR1,non_coding_transcript_exon_variant,,ENST00000475389,;LAIR1,non_coding_transcript_exon_variant,,ENST00000467269,;LAIR1,non_coding_transcript_exon_variant,,ENST00000498511,;LAIR1,downstream_gene_variant,,ENST00000460312,;LAIR1,downstream_gene_variant,,ENST00000418556,;LAIR1,downstream_gene_variant,,ENST00000436513,;LAIR1,downstream_gene_variant,,ENST00000420483,; A ENST00000391742 Transcript missense_variant 883/4901 730/864 244/287 G/W Ggg/Tgg COSM5251483 1 -1 LAIR1 HGNC HGNC:6477 protein_coding YES CCDS12891.1 ENSP00000375622 Q6GTX8 UPI00034F23B9 NM_002287.5 deleterious(0) 10/10 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF122 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 54355402 54355402 C A 1 0 0 0 0 1 0 0 0 8506 681 24 2 2 LAIR1 19 54355402 Missense_Mutation SNP C C3N-00704_T 1916870 54355402 4262214 551 19688 LILRA1 0 . GRCh38 19 54596353 54596353 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.1123T>C p.Tyr375His p.Y375H ENST00000251372 7/10 501 462 39 635 635 0 strelka-varscan-mutect LILRA1,missense_variant,p.Tyr375His,ENST00000251372,NM_006863.3;LILRA1,missense_variant,p.Tyr375His,ENST00000618665,;LILRA1,intron_variant,,ENST00000453777,NM_001278318.1;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,non_coding_transcript_exon_variant,,ENST00000495417,;LILRA1,non_coding_transcript_exon_variant,,ENST00000477255,; C ENST00000251372 Transcript missense_variant 1305/1910 1123/1470 375/489 Y/H Tat/Cat 1 1 LILRA1 HGNC HGNC:6602 protein_coding YES CCDS12901.1 ENSP00000251372 O75019 UPI0000034C00 NM_006863.3 deleterious(0.03) 7/10 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 54596353 54596353 T C 1 0 0 0 0 1 0 0 0 8693 1406 49 5 5 LILRA1 19 54596353 Missense_Mutation SNP T C3N-00704_T 240951 54596353 4021263 552 19689 NLRP9 0 . GRCh38 19 55715107 55715107 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.2449G>T p.Ala817Ser p.A817S ENST00000332836 6/9 103 81 22 150 150 0 strelka-varscan-mutect NLRP9,missense_variant,p.Ala817Ser,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Ala817Ser,ENST00000590200,; A ENST00000332836 Transcript missense_variant 2477/3484 2449/2976 817/991 A/S Gca/Tca 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 tolerated(0.75) 6/9 hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 55715107 55715107 C A 1 0 0 0 0 1 0 0 0 10522 739 26 2 2 NLRP9 19 55715107 Missense_Mutation SNP C C3N-00704_T 1118754 55715107 2902509 553 19690 AURKC 0 . GRCh38 19 57232064 57232064 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.136G>T p.Gly46Trp p.G46W ENST00000302804 3/7 422 339 83 496 495 1 strelka-varscan-mutect AURKC,missense_variant,p.Gly12Trp,ENST00000448930,;AURKC,missense_variant,p.Gly46Trp,ENST00000302804,NM_001015878.1;AURKC,missense_variant,p.Gly12Trp,ENST00000598785,NM_003160.2;AURKC,missense_variant,p.Gly27Trp,ENST00000415300,NM_001015879.1;AURKC,missense_variant,p.Gly43Trp,ENST00000599062,;AURKC,upstream_gene_variant,,ENST00000594599,;AURKC,missense_variant,p.Gly12Trp,ENST00000596375,;AURKC,3_prime_UTR_variant,,ENST00000601799,; T ENST00000302804 Transcript missense_variant 322/1247 136/930 46/309 G/W Ggg/Tgg COSM1245846,COSM1245847 1 1 AURKC HGNC HGNC:11391 protein_coding YES CCDS33128.1 ENSP00000302898 Q9UQB9 UPI000013610A NM_001015878.1 deleterious(0) 3/7 Gene3D:3.30.200.20,Pfam_domain:PF00069,PIRSF_domain:PIRSF000654,PROSITE_profiles:PS50011,hmmpanther:PTHR24350,hmmpanther:PTHR24350:SF3,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 57232064 57232064 G T 1 0 0 0 0 1 0 0 0 1380 1116 39 1 1 AURKC 19 57232064 Missense_Mutation SNP G C3N-00704_T 1516957 57232064 1385552 554 19691 SIRPD 0 . GRCh38 20 1552016 1552016 + Silent SNP C C G novel C3N-00704_T C3N-00704_N C C c.453G>C p.= p.V151V ENST00000567028 3/3 102 72 30 160 160 0 strelka-varscan-mutect RP4-576H24.4,missense_variant,p.Cys156Ser,ENST00000564763,;SIRPD,synonymous_variant,p.=,ENST00000381623,NM_178460.2;SIRPD,synonymous_variant,p.=,ENST00000381621,;RP4-576H24.4,synonymous_variant,p.=,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPD,upstream_gene_variant,,ENST00000429387,;RP4-576H24.2,non_coding_transcript_exon_variant,,ENST00000453770,; G ENST00000567028 Transcript synonymous_variant 490/568 453/531 151/177 V gtG/gtC 1 -1 RP4-576H24.4 Clone_based_vega_gene protein_coding YES ENSP00000454437 H3BML4 UPI0002466C6D 3/3 hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12 LOW SNV 4 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 1552016 1552016 C G 1 0 0 0 0 0 0 0 1 14598 697 25 4 4 SIRPD 20 1552016 Silent SNP C C3N-00704_T 1552016 62892151 555 19692 TMEM239 0 . GRCh38 20 2816410 2816410 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.76C>A p.Pro26Thr p.P26T ENST00000361033 1/2 167 138 29 261 261 0 strelka-varscan-mutect TMEM239,missense_variant,p.Pro26Thr,ENST00000361033,NM_001318207.1;TMEM239,5_prime_UTR_variant,,ENST00000380585,NM_001167670.1;RP5-860F19.8,intron_variant,,ENST00000380593,;C20orf141,downstream_gene_variant,,ENST00000380589,NM_080739.2;C20orf141,downstream_gene_variant,,ENST00000603872,NM_001256538.1; A ENST00000361033 Transcript missense_variant 109/3892 76/588 26/195 P/T Cca/Aca 1 1 TMEM239 HGNC HGNC:40044 protein_coding ENSP00000354312 Q8WW34 UPI00001C0BF4 NM_001318207.1 deleterious_low_confidence(0.03) 1/2 hmmpanther:PTHR37356:SF1,hmmpanther:PTHR37356 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 2816410 2816410 C A 1 0 0 0 0 1 0 0 0 16599 637 22 2 2 TMEM239 20 2816410 Missense_Mutation SNP C C3N-00704_T 1264394 2816410 61627757 556 19693 PAX1 0 . GRCh38 20 21706926 21706926 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.775C>A p.Pro259Thr p.P259T ENST00000398485 2/5 86 70 16 187 187 0 strelka-varscan-mutect PAX1,missense_variant,p.Pro259Thr,ENST00000613128,NM_001257096.1;PAX1,missense_variant,p.Pro259Thr,ENST00000398485,NM_006192.4;PAX1,missense_variant,p.Pro235Thr,ENST00000444366,;RP5-1065O2.4,upstream_gene_variant,,ENST00000624692,;PAX1,non_coding_transcript_exon_variant,,ENST00000460221,;PAX1,upstream_gene_variant,,ENST00000485038,; A ENST00000398485 Transcript missense_variant 829/2838 775/1605 259/534 P/T Ccc/Acc 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious(0.02) 2/5 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF262 MODERATE SNV 5 1 PASS rs1277587661 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 21706926 21706926 C A 1 0 0 0 0 1 0 0 0 11563 855 30 2 2 PAX1 20 21706926 Missense_Mutation SNP C C3N-00704_T 18890516 21706926 42737241 557 19694 DEFB118 0 . GRCh38 20 31372963 31372963 + Silent SNP C C T novel C3N-00704_T C3N-00704_N C C c.165C>T p.= p.C55C ENST00000253381 2/2 312 250 62 470 470 0 strelka-varscan-mutect DEFB118,synonymous_variant,p.=,ENST00000253381,NM_054112.2;DEFB119,downstream_gene_variant,,ENST00000339144,;DEFB119,downstream_gene_variant,,ENST00000376321,NM_153289.3;SNORA40,upstream_gene_variant,,ENST00000390832,;DEFB119,downstream_gene_variant,,ENST00000492344,; T ENST00000253381 Transcript synonymous_variant 198/1158 165/372 55/123 C tgC/tgT 1 1 DEFB118 HGNC HGNC:16196 protein_coding YES CCDS13177.1 ENSP00000253381 Q96PH6 UPI0000128D91 NM_054112.2 2/2 PD866254,Pfam_domain:PF13841,hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 31372963 31372963 C T 1 0 0 0 0 0 0 0 1 4209 718 25 3 3 DEFB118 20 31372963 Silent SNP C C3N-00704_T 9666037 31372963 33071204 558 19695 NDRG3 0 . GRCh38 20 36688757 36688757 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.121G>T p.Val41Leu p.V41L ENST00000349004 4/16 120 101 19 201 201 0 strelka-varscan-mutect NDRG3,missense_variant,p.Val41Leu,ENST00000373803,;NDRG3,missense_variant,p.Val41Leu,ENST00000349004,NM_032013.3;NDRG3,missense_variant,p.Val29Leu,ENST00000359675,NM_022477.3;NDRG3,missense_variant,p.Val32Leu,ENST00000422536,;NDRG3,intron_variant,,ENST00000373773,; A ENST00000349004 Transcript missense_variant 203/2964 121/1128 41/375 V/L Gtg/Ttg 1 -1 NDRG3 HGNC HGNC:14462 protein_coding YES CCDS13285.1 ENSP00000345292 Q9UGV2 UPI000012FEDF NM_032013.3 tolerated(0.77) 4/16 hmmpanther:PTHR11034,hmmpanther:PTHR11034:SF20,Gene3D:3.40.50.1820,Pfam_domain:PF03096,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs1444622744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 36688757 36688757 C A 1 0 0 0 0 1 0 0 0 10274 478 17 2 2 NDRG3 20 36688757 Missense_Mutation SNP C C3N-00704_T 5315794 36688757 27755410 559 19696 RPN2 0 . GRCh38 20 37207347 37207347 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.765G>T p.= p.V255V ENST00000237530 7/17 337 253 84 511 511 0 strelka-varscan-mutect RPN2,synonymous_variant,p.=,ENST00000237530,NM_001324303.1,NM_002951.3;RPN2,synonymous_variant,p.=,ENST00000373622,NM_001135771.1;RPN2,synonymous_variant,p.=,ENST00000373632,;RPN2,synonymous_variant,p.=,ENST00000456102,;RPN2,synonymous_variant,p.=,ENST00000462163,; T ENST00000237530 Transcript synonymous_variant 1076/2515 765/1896 255/631 V gtG/gtT 1 1 RPN2 HGNC HGNC:10382 protein_coding YES CCDS13291.1 ENSP00000237530 P04844 UPI0000000C52 NM_001324303.1,NM_002951.3 7/17 Pfam_domain:PF05817,hmmpanther:PTHR12640,hmmpanther:PTHR12640:SF0,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 37207347 37207347 G T 1 0 0 0 0 0 0 0 1 13861 1335 47 2 2 RPN2 20 37207347 Silent SNP G C3N-00704_T 518590 37207347 27236820 560 19697 LBP 0 . GRCh38 20 38364033 38364033 + Silent SNP G G T rs753960229 C3N-00704_T C3N-00704_N G G c.711G>T p.= p.R237R ENST00000217407 7/15 216 159 57 274 274 0 strelka-varscan-mutect LBP,synonymous_variant,p.=,ENST00000217407,NM_004139.4; T ENST00000217407 Transcript synonymous_variant 872/1961 711/1446 237/481 R cgG/cgT rs753960229 1 1 LBP HGNC HGNC:6517 protein_coding YES CCDS13304.1 ENSP00000217407 P18428 UPI000013C728 NM_004139.4 7/15 hmmpanther:PTHR10504:SF66,hmmpanther:PTHR10504,PIRSF_domain:PIRSF002417,Gene3D:1ewfA02,SMART_domains:SM00328,Superfamily_domains:SSF55394 LOW 1 SNV 1 1 PASS rs753960229 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 38364033 38364033 G T 1 0 0 0 0 0 0 0 1 8557 1219 43 2 2 LBP 20 38364033 Silent SNP G C3N-00704_T 1156686 38364033 26080134 561 19698 PTPRT 0 . GRCh38 20 42199349 42199349 + Silent SNP G G T rs780918827 C3N-00704_T C3N-00704_N G G c.2439C>A p.= p.A813A ENST00000373198 17/32 100 74 26 168 168 0 strelka-varscan-mutect PTPRT,synonymous_variant,p.=,ENST00000373198,NM_133170.3;PTPRT,synonymous_variant,p.=,ENST00000373193,;PTPRT,synonymous_variant,p.=,ENST00000373201,;PTPRT,synonymous_variant,p.=,ENST00000373190,;PTPRT,synonymous_variant,p.=,ENST00000373184,;PTPRT,synonymous_variant,p.=,ENST00000356100,;PTPRT,synonymous_variant,p.=,ENST00000373187,NM_007050.5;PTPRT,synonymous_variant,p.=,ENST00000612229,;PTPRT,synonymous_variant,p.=,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript synonymous_variant 2675/12746 2439/4383 813/1460 A gcC/gcA rs780918827 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 17/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 LOW 1 SNV 2 1 PASS rs780918827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 42199349 42199349 G T 1 0 0 0 0 0 0 0 1 12967 1219 43 2 2 PTPRT 20 42199349 Silent SNP G C3N-00704_T 3835316 42199349 22244818 562 19699 BMP7 0 . GRCh38 20 57202483 57202483 + Missense_Mutation SNP G G T rs112344257 C3N-00704_T C3N-00704_N G G c.752C>A p.Thr251Lys p.T251K ENST00000395863 3/7 365 278 87 405 405 0 strelka-varscan-mutect BMP7,missense_variant,p.Thr251Lys,ENST00000395863,NM_001719.2;BMP7,missense_variant,p.Thr251Lys,ENST00000450594,;BMP7,missense_variant,p.Thr251Lys,ENST00000395864,;BMP7,missense_variant,p.Thr173Lys,ENST00000433911,;BMP7,non_coding_transcript_exon_variant,,ENST00000460817,;BMP7,non_coding_transcript_exon_variant,,ENST00000530870,;BMP7,non_coding_transcript_exon_variant,,ENST00000524700,; T ENST00000395863 Transcript missense_variant 1258/4013 752/1296 251/431 T/K aCg/aAg rs112344257,COSM3991798 1 -1 BMP7 HGNC HGNC:1074 protein_coding YES CCDS13455.1 ENSP00000379204 P18075 A8K571 UPI00000349AD NM_001719.2 deleterious(0) 3/7 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF135 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs112344257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 57202483 57202483 G T 1 0 0 0 0 1 0 0 0 1620 1145 40 1 1 BMP7 20 57202483 Missense_Mutation SNP G C3N-00704_T 15003134 57202483 7241684 563 19700 SPO11 0 . GRCh38 20 57343450 57343450 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.1181G>T p.Gly394Val p.G394V ENST00000371263 13/13 52 47 5 156 156 0 strelka-varscan-mutect SPO11,missense_variant,p.Gly394Val,ENST00000371263,NM_012444.2;SPO11,missense_variant,p.Gly356Val,ENST00000345868,NM_198265.1;SPO11,missense_variant,p.Gly352Val,ENST00000371260,;SPO11,downstream_gene_variant,,ENST00000418127,;SPO11,3_prime_UTR_variant,,ENST00000494972,; T ENST00000371263 Transcript missense_variant 1290/1834 1181/1191 394/396 G/V gGa/gTa 1 1 SPO11 HGNC HGNC:11250 protein_coding YES CCDS13456.1 ENSP00000360310 Q9Y5K1 UPI0000135E5E NM_012444.2 tolerated(0.09) 13/13 hmmpanther:PTHR10848,Gene3D:3.40.1360.10,Superfamily_domains:0036260,Prints_domain:PR01551 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 57343450 57343450 G T 1 0 0 0 0 1 0 0 0 15430 1174 41 2 2 SPO11 20 57343450 Missense_Mutation SNP G C3N-00704_T 140967 57343450 7100717 564 19701 CTCFL 0 . GRCh38 20 57523968 57523968 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.238C>G p.Leu80Val p.L80V ENST00000423479 2/12 235 214 21 351 351 0 strelka-varscan-mutect CTCFL,missense_variant,p.Leu80Val,ENST00000608263,NM_001269041.1;CTCFL,missense_variant,p.Leu80Val,ENST00000429804,NM_001269046.1;CTCFL,missense_variant,p.Leu80Val,ENST00000609232,NM_080618.3;CTCFL,missense_variant,p.Leu80Val,ENST00000243914,;CTCFL,missense_variant,p.Leu80Val,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,missense_variant,p.Leu80Val,ENST00000422869,NM_001269047.1;CTCFL,missense_variant,p.Leu80Val,ENST00000432255,NM_001269048.1;CTCFL,missense_variant,p.Leu80Val,ENST00000608425,NM_001269045.1;CTCFL,missense_variant,p.Leu80Val,ENST00000608440,NM_001269044.1;CTCFL,missense_variant,p.Leu80Val,ENST00000423479,NM_001269043.1;CTCFL,missense_variant,p.Leu80Val,ENST00000608158,NM_001269052.1;CTCFL,missense_variant,p.Leu80Val,ENST00000481655,NM_001269051.1;CTCFL,intron_variant,,ENST00000539382,NM_001269050.1;CTCFL,intron_variant,,ENST00000433949,NM_001269049.1;CTCFL,intron_variant,,ENST00000608903,NM_001269055.1;CTCFL,intron_variant,,ENST00000502686,NM_001269054.1;CTCFL,intron_variant,,ENST00000608858,;CTCFL,missense_variant,p.Leu80Val,ENST00000426658,;CTCFL,missense_variant,p.Leu80Val,ENST00000422109,;CTCFL,missense_variant,p.Leu80Val,ENST00000608720,;CTCFL,non_coding_transcript_exon_variant,,ENST00000607923,;CTCFL,intron_variant,,ENST00000608108,; C ENST00000423479 Transcript missense_variant 329/2478 238/2103 80/700 L/V Ctg/Gtg 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 tolerated(0.08) 2/12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 57523968 57523968 G C 1 0 0 0 0 1 0 0 0 3808 991 35 4 4 CTCFL 20 57523968 Missense_Mutation SNP G C3N-00704_T 180518 57523968 6920199 565 19702 HRH3 0 . GRCh38 20 62219930 62219930 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.41G>T p.Gly14Val p.G14V ENST00000340177 1/3 51 40 11 73 73 0 strelka-varscan-mutect HRH3,missense_variant,p.Gly14Val,ENST00000340177,NM_007232.2;HRH3,missense_variant,p.Gly14Val,ENST00000317393,;HRH3,missense_variant,p.Gly14Val,ENST00000611492,; A ENST00000340177 Transcript missense_variant 326/2659 41/1338 14/445 G/V gGg/gTg 1 -1 HRH3 HGNC HGNC:5184 protein_coding YES CCDS13493.1 ENSP00000342560 Q9Y5N1 UPI000012C6ED NM_007232.2 tolerated(0.09) 1/3 Prints_domain:PR01471,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF292,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 62219930 62219930 C A 1 0 0 0 0 1 0 0 0 7252 623 22 2 2 HRH3 20 62219930 Missense_Mutation SNP C C3N-00704_T 4695962 62219930 2224237 566 19703 SAMSN1 0 . GRCh38 21 14512456 14512456 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.601C>A p.Gln201Lys p.Q201K ENST00000285670 5/9 193 158 35 198 198 0 strelka-varscan-mutect SAMSN1,missense_variant,p.Gln201Lys,ENST00000285670,NM_001256370.1;SAMSN1,missense_variant,p.Gln64Lys,ENST00000619120,NM_001286523.1;SAMSN1,missense_variant,p.Gln133Lys,ENST00000400566,NM_022136.4;SAMSN1,intron_variant,,ENST00000400564,; T ENST00000285670 Transcript missense_variant 776/2185 601/1326 201/441 Q/K Cag/Aag COSM4100831,COSM4100832 1 -1 SAMSN1 HGNC HGNC:10528 protein_coding YES CCDS58786.1 ENSP00000285670 Q9NSI8 UPI000013DDFD NM_001256370.1 tolerated(0.25) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR12301,hmmpanther:PTHR12301:SF4,Pfam_domain:PF12485 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 14512456 14512456 G T 1 0 0 0 0 1 0 0 0 14090 1386 48 2 2 SAMSN1 21 14512456 Missense_Mutation SNP G C3N-00704_T 14512456 32197527 567 19704 DSCAM 0 . GRCh38 21 40075189 40075189 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.4736C>T p.Ser1579Leu p.S1579L ENST00000400454 27/33 161 129 32 192 192 0 strelka-varscan-mutect DSCAM,missense_variant,p.Ser1579Leu,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Ser1414Leu,ENST00000617870,;DSCAM,missense_variant,p.Ser1331Leu,ENST00000404019,; A ENST00000400454 Transcript missense_variant 5214/8552 4736/6039 1579/2012 S/L tCa/tTa 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 tolerated(0.07) 27/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 40075189 40075189 G A 1 0 0 0 0 1 0 0 0 4589 1294 45 3 3 DSCAM 21 40075189 Missense_Mutation SNP G C3N-00704_T 25562733 40075189 6634794 568 19705 TSPEAR 0 . GRCh38 21 44527291 44527291 + Splice_Site SNP C C A novel C3N-00704_T C3N-00704_N C C c.1149+1G>T p.X383_splice ENST00000323084 188 154 34 254 254 0 strelka-varscan-mutect TSPEAR,splice_donor_variant,,ENST00000614657,NM_001272037.1;TSPEAR,splice_donor_variant,,ENST00000323084,NM_144991.2;TSPEAR,splice_donor_variant,,ENST00000613245,;TSPEAR,splice_donor_variant,,ENST00000397916,;TSPEAR-AS2,downstream_gene_variant,,ENST00000465978,; A ENST00000323084 Transcript splice_donor_variant -/3967 1149/2010 383/669 1 -1 TSPEAR HGNC HGNC:1268 protein_coding YES CCDS13712.1 ENSP00000321987 Q8WU66 UPI0000137746 NM_144991.2 7/11 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 62 44527291 44527291 C A 1 0 0 0 0 0 0 1 0 17160 753 26 2 2 TSPEAR 21 44527291 Splice_Site SNP C C3N-00704_T 4452102 44527291 2182692 569 19706 ITGB2 0 . GRCh38 21 44889429 44889429 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1724G>T p.Cys575Phe p.C575F ENST00000397850 14/17 354 291 63 416 415 1 strelka-varscan-mutect ITGB2,missense_variant,p.Cys575Phe,ENST00000397850,;ITGB2,missense_variant,p.Cys575Phe,ENST00000302347,NM_001303238.1,NM_000211.4;ITGB2,missense_variant,p.Cys575Phe,ENST00000355153,NM_001127491.2;ITGB2,missense_variant,p.Cys575Phe,ENST00000397857,;ITGB2,missense_variant,p.Cys575Phe,ENST00000397852,;ITGB2,missense_variant,p.Cys518Phe,ENST00000397854,;ITGB2,3_prime_UTR_variant,,ENST00000523323,;ITGB2,non_coding_transcript_exon_variant,,ENST00000498666,;ITGB2,non_coding_transcript_exon_variant,,ENST00000475170,;ITGB2,upstream_gene_variant,,ENST00000479202,; A ENST00000397850 Transcript missense_variant 2177/3178 1724/2310 575/769 C/F tGc/tTc 1 -1 ITGB2 HGNC HGNC:6155 protein_coding YES CCDS13716.1 ENSP00000380948 P05107 UPI0000000C70 deleterious(0) 14/17 Gene3D:2.10.25.10,PIRSF_domain:PIRSF002512,hmmpanther:PTHR10082,hmmpanther:PTHR10082:SF15,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS rs1378618759 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 44889429 44889429 C A 1 0 0 0 0 1 0 0 0 7800 710 25 2 2 ITGB2 21 44889429 Missense_Mutation SNP C C3N-00704_T 362138 44889429 1820554 570 19707 PCNT 0 . GRCh38 21 46399737 46399737 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.4732G>C p.Val1578Leu p.V1578L ENST00000359568 25/47 346 298 48 520 520 0 strelka-varscan-mutect PCNT,missense_variant,p.Val1578Leu,ENST00000359568,NM_006031.5;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,; C ENST00000359568 Transcript missense_variant 4839/10560 4732/10011 1578/3336 V/L Gtg/Ctg 1 1 PCNT HGNC HGNC:16068 protein_coding YES CCDS33592.1 ENSP00000352572 O95613 UPI00001AEB88 NM_006031.5 tolerated(0.27) 25/47 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 46399737 46399737 G C 1 0 0 0 0 1 0 0 0 11678 1029 36 4 4 PCNT 21 46399737 Missense_Mutation SNP G C3N-00704_T 1510308 46399737 310246 571 19708 OR11H1 0 . GRCh38 22 15528714 15528714 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.556C>A p.Pro186Thr p.P186T ENST00000252835 1/1 197 175 22 313 313 0 varscan-mutect OR11H1,missense_variant,p.Pro186Thr,ENST00000252835,NM_001005239.1; A ENST00000252835 Transcript missense_variant 557/982 556/981 186/326 P/T Cca/Aca 1 1 OR11H1 HGNC HGNC:15404 protein_coding YES CCDS74807.1 ENSP00000252835 Q8NG94 UPI000004B1CF NM_001005239.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 15528714 15528714 C A 1 0 0 0 0 1 0 0 0 11002 623 22 2 2 OR11H1 22 15528714 Missense_Mutation SNP C C3N-00704_T 15528714 35289754 572 19709 ZNF74 0 . GRCh38 22 20406322 20406322 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.1289G>T p.Arg430Leu p.R430L ENST00000611540 6/6 128 96 32 163 163 0 strelka-varscan-mutect ZNF74,missense_variant,p.Arg430Leu,ENST00000611540,NM_001256524.1;ZNF74,missense_variant,p.Arg430Leu,ENST00000400451,NM_001256525.1,NM_003426.3;ZNF74,missense_variant,p.Arg398Leu,ENST00000405993,;ZNF74,3_prime_UTR_variant,,ENST00000403682,NM_001256523.1;ZNF74,3_prime_UTR_variant,,ENST00000357502,;ZNF74,downstream_gene_variant,,ENST00000420626,;ZNF74,3_prime_UTR_variant,,ENST00000437275,;ZNF74,non_coding_transcript_exon_variant,,ENST00000476678,;ZNF74,non_coding_transcript_exon_variant,,ENST00000493734,; T ENST00000611540 Transcript missense_variant 1575/3714 1289/1935 430/644 R/L cGc/cTc COSM4609952 1 1 ZNF74 HGNC HGNC:13144 protein_coding YES CCDS42982.1 ENSP00000483077 Q16587 UPI000020710C NM_001256524.1 tolerated(0.74) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF336,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 20406322 20406322 G T 1 0 0 0 0 1 0 0 0 18710 1087 38 1 1 ZNF74 22 20406322 Missense_Mutation SNP G C3N-00704_T 4877608 20406322 30412146 573 19710 SCARF2 0 . GRCh38 22 20431084 20431084 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.788G>T p.Gly263Val p.G263V ENST00000623402 4/11 74 63 11 122 122 0 strelka-varscan-mutect SCARF2,missense_variant,p.Gly263Val,ENST00000623402,NM_153334.6;SCARF2,missense_variant,p.Gly263Val,ENST00000622235,NM_182895.4;XXbac-B562F10.12,intron_variant,,ENST00000429594,;SCARF2,upstream_gene_variant,,ENST00000494535,; A ENST00000623402 Transcript missense_variant 860/3248 788/2616 263/871 G/V gGc/gTc 1 -1 SCARF2 HGNC HGNC:19869 protein_coding YES CCDS13779.2 ENSP00000485276 A0A096LNX8 UPI0000EE7ADB NM_153334.6 deleterious(0) 4/11 Gene3D:2gy5A03,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF5,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -19.99996 0.9999979 1 1 1 0 A 3 1 62 20431084 20431084 C A 1 0 0 0 0 1 0 0 0 14150 739 26 2 2 SCARF2 22 20431084 Missense_Mutation SNP C C3N-00704_T 24762 20431084 30387384 574 19711 CABIN1 0 . GRCh38 22 24050926 24050926 + Missense_Mutation SNP G G T rs773327324 C3N-00704_T C3N-00704_N G G c.758G>T p.Arg253Leu p.R253L ENST00000398319 8/37 443 362 81 558 557 1 strelka-varscan-mutect CABIN1,missense_variant,p.Arg253Leu,ENST00000398319,NM_001199281.1;CABIN1,missense_variant,p.Arg253Leu,ENST00000263119,NM_012295.3;CABIN1,missense_variant,p.Arg208Leu,ENST00000445422,;CABIN1,missense_variant,p.Arg208Leu,ENST00000454754,;CABIN1,intron_variant,,ENST00000617531,NM_001201429.1;CABIN1,intron_variant,,ENST00000405822,;CABIN1,upstream_gene_variant,,ENST00000474981,; T ENST00000398319 Transcript missense_variant 1143/7480 758/6663 253/2220 R/L cGg/cTg rs773327324,COSM4417046 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 tolerated(0.11) 8/37 hmmpanther:PTHR15502,hmmpanther:PTHR15502:SF7 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773327324 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 24050926 24050926 G T 1 0 0 0 0 1 0 0 0 2214 1116 39 1 1 CABIN1 22 24050926 Missense_Mutation SNP G C3N-00704_T 3619842 24050926 26767542 575 19712 RFPL3S 0 . GRCh38 22 32360319 32360319 + Silent SNP C C A novel C3N-00704_T C3N-00704_N C C c.441C>A p.= p.V147V ENST00000249007 2/2 175 146 29 266 265 1 strelka-varscan-mutect RFPL3,synonymous_variant,p.=,ENST00000249007,NM_001098535.1;RFPL3,synonymous_variant,p.=,ENST00000397468,NM_006604.2;RFPL3S,synonymous_variant,p.=,ENST00000621921,;RFPL3S,3_prime_UTR_variant,,ENST00000400234,;RFPL3S,3_prime_UTR_variant,,ENST00000382084,;RFPL3S,downstream_gene_variant,,ENST00000577714,;RFPL3S,downstream_gene_variant,,ENST00000382086,;RFPL3-AS1_1,upstream_gene_variant,,ENST00000617561,;RFPL3S,downstream_gene_variant,,ENST00000461833,;IGLCOR22-2,upstream_gene_variant,,ENST00000605398,; A ENST00000249007 Transcript synonymous_variant 646/1488 441/954 147/317 V gtC/gtA 1 1 RFPL3 HGNC HGNC:9980 protein_coding YES CCDS43011.1 ENSP00000249007 O75679 UPI000013CC68 NM_001098535.1 2/2 Pfam_domain:PF13765,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF225,SMART_domains:SM00589,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 62 32360319 32360319 C A 1 0 0 0 0 0 0 0 1 13427 842 30 2 2 RFPL3S 22 32360319 Silent SNP C C3N-00704_T 8309393 32360319 18458149 576 19713 FOXRED2 0 . GRCh38 22 36498055 36498055 + Missense_Mutation SNP C C A rs202223816 C3N-00704_T C3N-00704_N C C c.1318G>T p.Val440Leu p.V440L ENST00000397224 6/9 168 137 31 238 238 0 strelka-varscan-mutect FOXRED2,missense_variant,p.Val440Leu,ENST00000397224,NM_001102371.1;FOXRED2,missense_variant,p.Val440Leu,ENST00000216187,NM_024955.5;FOXRED2,missense_variant,p.Val440Leu,ENST00000397223,;FOXRED2,non_coding_transcript_exon_variant,,ENST00000366463,; A ENST00000397224 Transcript missense_variant 1412/4967 1318/2055 440/684 V/L Gtg/Ttg rs202223816 1 -1 FOXRED2 HGNC HGNC:26264 protein_coding YES CCDS13929.1 ENSP00000380401 Q8IWF2 UPI00000744FA NM_001102371.1 tolerated(0.15) 6/9 hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF53 MODERATE 1 SNV 1 1 PASS rs202223816 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 36498055 36498055 C A 1 0 0 0 0 1 0 0 0 5899 536 19 1 1 FOXRED2 22 36498055 Missense_Mutation SNP C C3N-00704_T 4137736 36498055 14320413 577 19714 KCNJ4 0 . GRCh38 22 38427950 38427950 + Silent SNP G G T novel C3N-00704_T C3N-00704_N G G c.183C>A p.= p.I61I ENST00000303592 2/2 103 91 12 152 152 0 strelka-varscan-mutect KCNJ4,synonymous_variant,p.=,ENST00000303592,NM_152868.2,NM_004981.1;RP3-434P1.6,downstream_gene_variant,,ENST00000433230,; T ENST00000303592 Transcript synonymous_variant 442/2065 183/1338 61/445 I atC/atA 1 -1 KCNJ4 HGNC HGNC:6265 protein_coding YES CCDS13971.1 ENSP00000306497 P48050 A0A024R1L8 UPI000012D89B NM_152868.2,NM_004981.1 2/2 hmmpanther:PTHR11767:SF53,hmmpanther:PTHR11767,Gene3D:1.10.287.70,PIRSF_domain:PIRSF005465,Pfam_domain:PF01007,Superfamily_domains:SSF81324,Prints_domain:PR01320,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 62 38427950 38427950 G T 1 0 0 0 0 0 0 0 1 7970 932 33 2 2 KCNJ4 22 38427950 Silent SNP G C3N-00704_T 1929895 38427950 12390518 578 19715 CACNA1I 0 . GRCh38 22 39677390 39677390 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.4904C>A p.Ala1635Asp p.A1635D ENST00000402142 30/37 121 102 19 113 113 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Ala1635Asp,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Ala1600Asp,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Ala1635Asp,ENST00000401624,;CACNA1I,missense_variant,p.Ala1600Asp,ENST00000407673,; A ENST00000402142 Transcript missense_variant 4904/10004 4904/6672 1635/2223 A/D gCt/gAt 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0) 30/37 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 62 39677390 39677390 C A 1 0 0 0 0 1 0 0 0 2234 797 28 2 2 CACNA1I 22 39677390 Missense_Mutation SNP C C3N-00704_T 1249440 39677390 11141078 579 19716 MPPED1 0 . GRCh38 22 43502677 43502677 + Missense_Mutation SNP G G T rs371051285 C3N-00704_T C3N-00704_N G G c.782G>T p.Arg261Leu p.R261L ENST00000417669 6/7 201 158 43 305 304 1 strelka-varscan-mutect MPPED1,missense_variant,p.Arg261Leu,ENST00000417669,;MPPED1,missense_variant,p.Arg261Leu,ENST00000443721,NM_001044370.1; T ENST00000417669 Transcript missense_variant 1226/3657 782/981 261/326 R/L cGg/cTg rs371051285 1 1 MPPED1 HGNC HGNC:1306 protein_coding YES CCDS46723.1 ENSP00000388137 O15442 UPI000006DF41 tolerated(0.1) 6/7 Gene3D:3.60.21.10,Pfam_domain:PF00149,PIRSF_domain:PIRSF035808,hmmpanther:PTHR12905,hmmpanther:PTHR12905:SF12,Superfamily_domains:SSF56300 MODERATE 1 SNV 5 1 PASS rs371051285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 43502677 43502677 G T 1 0 0 0 0 1 0 0 0 9707 1116 39 1 1 MPPED1 22 43502677 Missense_Mutation SNP G C3N-00704_T 3825287 43502677 7315791 580 19717 SHANK3 0 . GRCh38 22 50720750 50720750 + Missense_Mutation SNP A A G novel C3N-00704_T C3N-00704_N A A c.2914A>G p.Ser972Gly p.S972G ENST00000262795 24/25 132 113 19 88 88 0 strelka-varscan-mutect SHANK3,missense_variant,p.Ser972Gly,ENST00000262795,;SHANK3,missense_variant,p.Ser966Gly,ENST00000445220,NM_033517.1;SHANK3,non_coding_transcript_exon_variant,,ENST00000414786,; G ENST00000262795 Transcript missense_variant 2914/7091 2914/5193 972/1730 S/G Agc/Ggc 1 1 SHANK3 HGNC HGNC:14294 protein_coding YES ENSP00000489147 A0A0U1RQS4 UPI00071AFB18 tolerated(0.32) 24/25 hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 50720750 50720750 A G 1 0 0 0 0 1 0 0 0 14525 188 7 5 5 SHANK3 22 50720750 Missense_Mutation SNP A C3N-00704_T 7218073 50720750 97718 581 19718 ARSF 0 . GRCh38 X 3084419 3084419 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.583C>A p.Leu195Ile p.L195I ENST00000381127 6/11 389 353 36 567 567 0 strelka-varscan-mutect ARSF,missense_variant,p.Leu195Ile,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,missense_variant,p.Leu195Ile,ENST00000359361,NM_004042.4; A ENST00000381127 Transcript missense_variant 804/2164 583/1773 195/590 L/I Cta/Ata 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 tolerated(0.88) 6/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF220,Pfam_domain:PF00884,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 3084419 3084419 C A 1 0 0 0 0 1 0 0 0 1134 796 28 2 2 ARSF 23 3084419 Missense_Mutation SNP C C3N-00704_T 3084419 152956476 582 19719 MXRA5 0 . GRCh38 X 3324225 3324225 + Missense_Mutation SNP C C T rs745868713 C3N-00704_T C3N-00704_N C C c.1460G>A p.Arg487Lys p.R487K ENST00000217939 5/7 76 64 12 124 124 0 strelka-varscan-mutect MXRA5,missense_variant,p.Arg487Lys,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 1615/9793 1460/8487 487/2828 R/K aGa/aAa rs745868713 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.41) 5/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs745868713 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 3324225 3324225 C T 1 0 0 0 0 1 0 0 0 10002 913 32 3 3 MXRA5 23 3324225 Missense_Mutation SNP C C3N-00704_T 239806 3324225 152716670 583 19720 FANCB 0 . GRCh38 X 14844890 14844890 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1893G>T p.Lys631Asn p.K631N ENST00000398334 8/10 55 51 4 149 149 0 strelka-varscan-mutect FANCB,missense_variant,p.Lys631Asn,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Lys631Asn,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Lys631Asn,ENST00000452869,; A ENST00000398334 Transcript missense_variant 2161/3008 1893/2580 631/859 K/N aaG/aaT 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 tolerated(0.14) 8/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS . . 1 203 6 0 0 0 0 0 -9.98048 0.9999997 1 1 1 0 A 3 1 62 14844890 14844890 C A 1 0 0 0 0 1 0 0 0 5522 564 20 2 2 FANCB 23 14844890 Missense_Mutation SNP C C3N-00704_T 11520665 14844890 141196005 584 19721 ADGRG2 0 . GRCh38 X 18990896 18990896 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.3022C>T p.Arg1008Trp p.R1008W ENST00000379869 29/29 113 103 10 136 136 0 varscan-mutect ADGRG2,missense_variant,p.Arg992Trp,ENST00000379878,NM_001184833.1;ADGRG2,missense_variant,p.Arg984Trp,ENST00000379876,NM_001184835.1,NM_001184836.1;ADGRG2,missense_variant,p.Arg1008Trp,ENST00000379869,NM_001079858.2;ADGRG2,missense_variant,p.Arg986Trp,ENST00000360279,NM_001079860.2;ADGRG2,missense_variant,p.Arg957Trp,ENST00000379873,NM_001184834.1;ADGRG2,missense_variant,p.Arg978Trp,ENST00000357544,NM_001184837.1;ADGRG2,missense_variant,p.Arg1005Trp,ENST00000357991,NM_005756.3;ADGRG2,missense_variant,p.Arg994Trp,ENST00000356606,NM_001079859.2;ADGRG2,missense_variant,p.Arg889Trp,ENST00000354791,;ADGRG2,missense_variant,p.Arg889Trp,ENST00000340581,; A ENST00000379869 Transcript missense_variant 3186/4768 3022/3054 1008/1017 R/W Cgg/Tgg 1 -1 ADGRG2 HGNC HGNC:4516 protein_coding YES CCDS43923.1 ENSP00000369198 Q8IZP9 UPI000021246C NM_001079858.2 deleterious_low_confidence(0) 29/29 MODERATE 1 SNV 1 1 PASS rs1373623454 . 0 208 2 0 0 0 0 0 -19.80754 1 1 1 1 0 A 3 1 62 18990896 18990896 G A 1 0 0 0 0 1 0 0 0 369 1086 38 1 1 ADGRG2 23 18990896 Missense_Mutation SNP G C3N-00704_T 4146006 18990896 137049999 585 19722 PCYT1B 0 . GRCh38 X 24672613 24672613 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.20G>A p.Cys7Tyr p.C7Y ENST00000379145 1/8 149 136 13 249 249 0 strelka-varscan-mutect PCYT1B,missense_variant,p.Cys7Tyr,ENST00000379145,NM_001163264.1; T ENST00000379145 Transcript missense_variant 65/5307 20/1056 7/351 C/Y tGc/tAc 1 -1 PCYT1B HGNC HGNC:8755 protein_coding CCDS55392.1 ENSP00000368440 Q9Y5K3 UPI00002124D9 NM_001163264.1 tolerated_low_confidence(1) 1/8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 24672613 24672613 C T 1 0 0 0 0 1 0 0 0 11699 710 25 3 3 PCYT1B 23 24672613 Missense_Mutation SNP C C3N-00704_T 5681717 24672613 131368282 586 19723 PPP4R3CP 0 . GRCh38 X 27461692 27461692 + Missense_Mutation SNP G G C novel C3N-00704_T C3N-00704_N G G c.1605C>G p.Asn535Lys p.N535K ENST00000412172 1/1 74 68 6 233 233 0 strelka-varscan-mutect PPP4R3CP,missense_variant,p.Asn535Lys,ENST00000412172,; C ENST00000412172 Transcript missense_variant 1650/3131 1605/2499 535/832 N/K aaC/aaG 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 27461692 27461692 G C 1 0 0 0 0 1 0 0 0 12529 1368 48 4 4 PPP4R3CP 23 27461692 Missense_Mutation SNP G C3N-00704_T 2789079 27461692 128579203 587 19724 MAGEB1 0 . GRCh38 X 30251524 30251524 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1031C>A p.Ser344Tyr p.S344Y ENST00000378981 4/4 53 48 5 126 126 0 strelka-varscan-mutect MAGEB1,missense_variant,p.Ser344Tyr,ENST00000378981,NM_002363.4;MAGEB1,missense_variant,p.Ser344Tyr,ENST00000397550,NM_177415.2;MAGEB1,missense_variant,p.Ser344Tyr,ENST00000397548,NM_177404.2; A ENST00000378981 Transcript missense_variant 1352/1866 1031/1044 344/347 S/Y tCc/tAc 1 1 MAGEB1 HGNC HGNC:6808 protein_coding YES CCDS14222.1 ENSP00000368264 P43366 UPI000012F053 NM_002363.4 deleterious(0) 4/4 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF52,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -12.08291 0.9999988 1 1 1 0 A 3 1 62 30251524 30251524 C A 1 0 0 0 0 1 0 0 0 9087 855 30 2 2 MAGEB1 23 30251524 Missense_Mutation SNP C C3N-00704_T 2789832 30251524 125789371 588 19725 DMD 0 . GRCh38 X 32441261 32441261 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.3840G>T p.Lys1280Asn p.K1280N ENST00000357033 28/79 121 98 23 246 246 0 strelka-varscan-mutect DMD,missense_variant,p.Lys1280Asn,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Lys1276Asn,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Lys1280Asn,ENST00000620040,;DMD,missense_variant,p.Lys1276Asn,ENST00000619831,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000488902,; A ENST00000357033 Transcript missense_variant 4047/13956 3840/11058 1280/3685 K/N aaG/aaT 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 tolerated(0.36) 28/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 32441261 32441261 C A 1 0 0 0 0 1 0 0 0 4387 564 20 2 2 DMD 23 32441261 Missense_Mutation SNP C C3N-00704_T 2189737 32441261 123599634 589 19726 CFAP47 0 . GRCh38 X 36353592 36353592 + Missense_Mutation SNP G G T rs781868486 C3N-00704_T C3N-00704_N G G c.8762G>T p.Gly2921Val p.G2921V ENST00000378653 60/64 117 105 12 302 302 0 strelka-varscan-mutect CFAP47,missense_variant,p.Gly2921Val,ENST00000378653,NM_001304548.1; T ENST00000378653 Transcript missense_variant 8828/9943 8762/9564 2921/3187 G/V gGt/gTt rs781868486,COSM5431869,COSM5431870 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 tolerated(0.18) 60/64 hmmpanther:PTHR23053 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs781868486 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 36353592 36353592 G T 1 0 0 0 0 1 0 0 0 3022 1261 44 2 2 CFAP47 23 36353592 Missense_Mutation SNP G C3N-00704_T 3912331 36353592 119687303 590 19727 OTUD6A 0 . GRCh38 X 70062642 70062642 + Nonsense_Mutation SNP A A T novel C3N-00704_T C3N-00704_N A A c.118A>T p.Lys40Ter p.K40* ENST00000338352 1/1 233 186 47 331 331 0 strelka-varscan-mutect OTUD6A,stop_gained,p.Lys40Ter,ENST00000338352,NM_207320.2; T ENST00000338352 Transcript stop_gained 152/1689 118/867 40/288 K/* Aaa/Taa 1 1 OTUD6A HGNC HGNC:32312 protein_coding YES CCDS14395.1 ENSP00000339389 Q7L8S5 UPI00000712B7 NM_207320.2 1/1 hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF13 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 62 70062642 70062642 A T 1 0 0 0 0 0 1 0 0 11385 247 9 4 4 OTUD6A 23 70062642 Nonsense_Mutation SNP A C3N-00704_T 33709050 70062642 85978253 591 19728 ZNF711 0 . GRCh38 X 85271492 85271492 + Missense_Mutation SNP G G T C3N-00704_T C3N-00704_N G G c.1950G>T p.Arg650Ser p.R650S ENST00000373165 9/9 272 220 52 430 430 0 strelka-varscan-mutect ZNF711,missense_variant,p.Arg696Ser,ENST00000360700,;ZNF711,missense_variant,p.Arg650Ser,ENST00000373165,NM_021998.4;ZNF711,missense_variant,p.Arg650Ser,ENST00000276123,; T ENST00000373165 Transcript missense_variant 2256/4124 1950/2286 650/761 R/S agG/agT COSM4111378,COSM4111379 1 1 ZNF711 HGNC HGNC:13128 protein_coding YES CCDS35344.1 ENSP00000362260 Q9Y462 UPI0000212114 NM_021998.4 deleterious(0) 9/9 PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF1,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1385831814 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 85271492 85271492 G T 1 0 0 0 0 1 0 0 0 18691 1194 42 2 2 ZNF711 23 85271492 Missense_Mutation SNP G C3N-00704_T 15208850 85271492 70769403 592 19729 CHM 0 . GRCh38 X 85901127 85901127 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.1306G>T p.Asp436Tyr p.D436Y ENST00000357749 10/15 162 133 29 183 183 0 strelka-varscan-mutect CHM,missense_variant,p.Asp436Tyr,ENST00000357749,NM_001320959.1,NM_000390.2;MIR361,downstream_gene_variant,,ENST00000362181,;CHM,intron_variant,,ENST00000467744,; A ENST00000357749 Transcript missense_variant 1336/5442 1306/1962 436/653 D/Y Gac/Tac 1 -1 CHM HGNC HGNC:1940 protein_coding YES CCDS14454.1 ENSP00000350386 P24386 UPI0000049C8C NM_001320959.1,NM_000390.2 deleterious(0) 10/15 hmmpanther:PTHR11787:SF12,hmmpanther:PTHR11787,Gene3D:3.50.50.60,Pfam_domain:PF00996,PIRSF_domain:PIRSF016550,Superfamily_domains:SSF51905,Prints_domain:PR00893 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 85901127 85901127 C A 1 0 0 0 0 1 0 0 0 3109 855 30 2 2 CHM 23 85901127 Missense_Mutation SNP C C3N-00704_T 629635 85901127 70139768 593 19730 TGIF2LX 0 . GRCh38 X 89922117 89922117 + Frame_Shift_Del DEL C C - novel C3N-00704_T C3N-00704_N C C c.34delC p.Gln12LysfsTer175 p.Q12Kfs*175 ENST00000561129 1/1 427 347 80 681 681 0 sindel-varindel-pindel TGIF2LX,frameshift_variant,p.Gln12LysfsTer175,ENST00000561129,;TGIF2LX,frameshift_variant,p.Gln12LysfsTer175,ENST00000283891,NM_138960.3; - ENST00000561129 Transcript frameshift_variant 162/928 32/726 11/241 T/X aCc/ac 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 1/1 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 62 89922117 89922117 C - 1 0 1 0 1 0 0 0 0 16260 507 18 0 0 TGIF2LX 23 89922117 Frame_Shift_Del DEL C C3N-00704_T 4020990 89922117 66118778 594 19731 TGIF2LX 0 . GRCh38 X 89922444 89922444 + Missense_Mutation SNP C C A novel C3N-00704_T C3N-00704_N C C c.359C>A p.Pro120His p.P120H ENST00000561129 1/1 377 285 92 603 602 1 strelka-varscan-mutect TGIF2LX,missense_variant,p.Pro120His,ENST00000561129,;TGIF2LX,missense_variant,p.Pro120His,ENST00000283891,NM_138960.3; A ENST00000561129 Transcript missense_variant 489/928 359/726 120/241 P/H cCc/cAc 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 deleterious(0) 1/1 hmmpanther:PTHR11850:SF16,hmmpanther:PTHR11850 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 89922444 89922444 C A 1 0 0 0 0 1 0 0 0 16260 623 22 2 2 TGIF2LX 23 89922444 Missense_Mutation SNP C C3N-00704_T 327 89922444 66118451 595 19732 COL4A5 0 . GRCh38 X 108687535 108687535 + Missense_Mutation SNP G G T rs104886280 C3N-00704_T C3N-00704_N G G c.4369G>T p.Gly1457Cys p.G1457C ENST00000328300 49/53 257 194 63 374 374 0 strelka-varscan-mutect COL4A5,missense_variant,p.Gly1457Cys,ENST00000328300,NM_033380.2;COL4A5,missense_variant,p.Gly1451Cys,ENST00000361603,NM_000495.4;COL4A5,missense_variant,p.Gly56Cys,ENST00000515658,;COL4A5,downstream_gene_variant,,ENST00000489230,; T ENST00000328300 Transcript missense_variant 4613/6483 4369/5076 1457/1691 G/C Ggt/Tgt rs104886280,CM970368 1 1 COL4A5 HGNC HGNC:2207 protein_coding YES CCDS35366.1 ENSP00000331902 P29400 UPI000002A538 NM_033380.2 deleterious(0.02) 49/53 Low_complexity_(Seg):seg,hmmpanther:PTHR24023:SF543,hmmpanther:PTHR24023,Pfam_domain:PF01391 pathogenic 9195222 MODERATE 1 SNV 1 1,1 1 PASS rs104886280 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 108687535 108687535 G T 1 0 0 0 0 1 0 0 0 3483 1000 35 2 2 COL4A5 23 108687535 Missense_Mutation SNP G C3N-00704_T 18765091 108687535 47353360 596 19733 DCX 0 . GRCh38 X 111410865 111410865 + Missense_Mutation SNP C C T rs779227493 C3N-00704_T C3N-00704_N C C c.110G>A p.Cys37Tyr p.C37Y ENST00000338081 1/7 328 262 66 472 472 0 strelka-varscan-mutect DCX,missense_variant,p.Cys37Tyr,ENST00000338081,NM_000555.3;DCX,5_prime_UTR_variant,,ENST00000358070,;DCX,5_prime_UTR_variant,,ENST00000496551,;DCX,intron_variant,,ENST00000636035,NM_001195553.1;DCX,intron_variant,,ENST00000371993,NM_178153.2,NM_178151.2;DCX,intron_variant,,ENST00000635795,NM_178152.2;DCX,intron_variant,,ENST00000637570,;DCX,intron_variant,,ENST00000356220,;DCX,intron_variant,,ENST00000488120,;DCX,intron_variant,,ENST00000637453,;DCX,intron_variant,,ENST00000468911,;DCX,upstream_gene_variant,,ENST00000636381,; T ENST00000338081 Transcript missense_variant 282/9402 110/1326 37/441 C/Y tGt/tAt rs779227493 1 -1 DCX HGNC HGNC:2714 protein_coding YES CCDS14556.1 ENSP00000337697 A0A140LJL1 UPI000013D33F NM_000555.3 deleterious_low_confidence(0) 1/7 MODERATE 1 SNV 1 1 PASS rs779227493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 111410865 111410865 C T 1 0 0 0 0 1 0 0 0 4121 478 17 3 3 DCX 23 111410865 Missense_Mutation SNP C C3N-00704_T 2723330 111410865 44630030 597 19734 ZCCHC16 0 . GRCh38 X 112454981 112454981 + Missense_Mutation SNP C C T novel C3N-00704_T C3N-00704_N C C c.253C>T p.Leu85Phe p.L85F ENST00000340433 1/1 103 81 22 170 170 0 strelka-varscan-mutect ZCCHC16,missense_variant,p.Leu85Phe,ENST00000340433,NM_001004308.2; T ENST00000340433 Transcript missense_variant 482/2613 253/933 85/310 L/F Ctc/Ttc 1 1 ZCCHC16 HGNC HGNC:25214 protein_coding YES CCDS35369.1 ENSP00000340590 Q6ZR62 UPI00001975B5 NM_001004308.2 tolerated(0.3) 1/1 hmmpanther:PTHR15503:SF8,hmmpanther:PTHR15503 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 112454981 112454981 C T 1 0 0 0 0 1 0 0 0 18159 913 32 3 3 ZCCHC16 23 112454981 Missense_Mutation SNP C C3N-00704_T 1044116 112454981 43585914 598 19735 PLS3 0 . GRCh38 X 115636939 115636939 + Silent SNP G G T rs782019404 C3N-00704_T C3N-00704_N G G c.852G>T p.= p.S284S ENST00000355899 8/16 113 90 23 208 207 1 strelka-varscan-mutect PLS3,synonymous_variant,p.=,ENST00000355899,NM_005032.6;PLS3,synonymous_variant,p.=,ENST00000420625,;PLS3,synonymous_variant,p.=,ENST00000539310,NM_001172335.2,NM_001136025.4,NM_001282338.1;PLS3,synonymous_variant,p.=,ENST00000289290,NM_001282337.1;PLS3,upstream_gene_variant,,ENST00000497870,;PLS3,downstream_gene_variant,,ENST00000473026,;PLS3,3_prime_UTR_variant,,ENST00000481823,;PLS3,upstream_gene_variant,,ENST00000466150,; T ENST00000355899 Transcript synonymous_variant 939/3280 852/1893 284/630 S tcG/tcT rs782019404 1 1 PLS3 HGNC HGNC:9091 protein_coding YES CCDS14568.1 ENSP00000348163 P13797 UPI000000D962 NM_005032.6 8/16 PROSITE_profiles:PS50021,hmmpanther:PTHR19961,hmmpanther:PTHR19961:SF32,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS rs782019404 . 0 187 19 4 0 0 0 0 -20 0.9778537 0 1 1 0 T 2 4 62 115636939 115636939 G T 1 0 0 0 0 0 0 0 1 12216 1103 39 1 1 PLS3 23 115636939 Silent SNP G C3N-00704_T 3181958 115636939 40403956 599 19736 UBE2A 0 . GRCh38 X 119581583 119581583 + Missense_Mutation SNP G G A novel C3N-00704_T C3N-00704_N G G c.228G>A p.Met76Ile p.M76I ENST00000371558 4/6 73 59 14 230 229 1 strelka-varscan-mutect UBE2A,start_lost,p.Met1?,ENST00000630695,;UBE2A,missense_variant,p.Met76Ile,ENST00000371558,NM_003336.3;UBE2A,missense_variant,p.Met76Ile,ENST00000631185,;UBE2A,missense_variant,p.Met43Ile,ENST00000628549,NM_001282161.1;UBE2A,missense_variant,p.Met76Ile,ENST00000346330,;UBE2A,intron_variant,,ENST00000625938,NM_181762.2;UBE2A,3_prime_UTR_variant,,ENST00000629303,;UBE2A,non_coding_transcript_exon_variant,,ENST00000371569,;UBE2A,upstream_gene_variant,,ENST00000628734,; A ENST00000371558 Transcript missense_variant 473/1874 228/459 76/152 M/I atG/atA 1 1 UBE2A HGNC HGNC:12472 protein_coding YES CCDS14580.1 ENSP00000360613 P49459 UPI00000043A0 NM_003336.3 tolerated(0.26) 4/6 Gene3D:3.10.110.10,Pfam_domain:PF00179,PROSITE_profiles:PS50127,hmmpanther:PTHR24067,hmmpanther:PTHR24067:SF92,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 62 119581583 119581583 G A 1 0 0 0 0 1 0 0 0 17366 1377 48 3 3 UBE2A 23 119581583 Missense_Mutation SNP G C3N-00704_T 3944644 119581583 36459312 600 19737 MAGEC2 0 . GRCh38 X 142203439 142203439 + Missense_Mutation SNP C C G C3N-00704_T C3N-00704_N C C c.549G>C p.Lys183Asn p.K183N ENST00000247452 3/3 138 108 30 202 202 0 strelka-varscan-mutect MAGEC2,missense_variant,p.Lys183Asn,ENST00000247452,NM_016249.3; G ENST00000247452 Transcript missense_variant 897/1991 549/1122 183/373 K/N aaG/aaC COSM3800438 1 -1 MAGEC2 HGNC HGNC:13574 protein_coding YES CCDS14678.1 ENSP00000354660 Q9UBF1 UPI000012F059 NM_016249.3 deleterious(0.05) 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF29,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 62 142203439 142203439 C G 1 0 0 0 0 1 0 0 0 9099 912 32 4 4 MAGEC2 23 142203439 Missense_Mutation SNP C C3N-00704_T 22621856 142203439 13837456 601 19738 MAMLD1 0 . GRCh38 X 150470315 150470315 + Missense_Mutation SNP G G T novel C3N-00704_T C3N-00704_N G G c.667G>T p.Gly223Cys p.G223C ENST00000432680 3/5 90 76 14 162 162 0 strelka-varscan-mutect MAMLD1,missense_variant,p.Gly248Cys,ENST00000370401,;MAMLD1,missense_variant,p.Gly248Cys,ENST00000262858,NM_005491.4;MAMLD1,missense_variant,p.Gly223Cys,ENST00000426613,NM_001177466.2;MAMLD1,missense_variant,p.Gly223Cys,ENST00000432680,NM_001177465.2;MAMLD1,downstream_gene_variant,,ENST00000358892,;MAMLD1,downstream_gene_variant,,ENST00000468306,; T ENST00000432680 Transcript missense_variant 842/3224 667/2997 223/998 G/C Ggc/Tgc 1 1 MAMLD1 HGNC HGNC:2568 protein_coding YES CCDS55526.1 ENSP00000414517 Q13495 UPI00017A6EBC NM_001177465.2 deleterious(0) 3/5 hmmpanther:PTHR15275,hmmpanther:PTHR15275:SF0 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 62 150470315 150470315 G T 1 0 0 0 0 1 0 0 0 9129 1348 47 2 2 MAMLD1 23 150470315 Missense_Mutation SNP G C3N-00704_T 8266876 150470315 5570580 602 19739 PASD1 0 . GRCh38 X 151672493 151672493 + Missense_Mutation SNP T T C novel C3N-00704_T C3N-00704_N T T c.1748T>C p.Val583Ala p.V583A ENST00000370357 14/16 461 378 83 604 604 0 strelka-varscan-mutect PASD1,missense_variant,p.Val583Ala,ENST00000370357,NM_173493.2;PASD1,non_coding_transcript_exon_variant,,ENST00000464219,;RP11-45D17.1,downstream_gene_variant,,ENST00000413236,; C ENST00000370357 Transcript missense_variant 1993/3163 1748/2322 583/773 V/A gTg/gCg 1 1 PASD1 HGNC HGNC:20686 protein_coding YES CCDS35431.1 ENSP00000359382 Q8IV76 UPI0000074686 NM_173493.2 tolerated(0.13) 14/16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 62 151672493 151672493 T C 1 0 0 0 0 1 0 0 0 11552 1696 59 5 5 PASD1 23 151672493 Missense_Mutation SNP T C3N-00704_T 1202178 151672493 4368402 603 19740 PLXNB3 0 . GRCh38 X 153767100 153767100 + Silent SNP T T G novel C3N-00704_T C3N-00704_N T T c.342T>G p.= p.P114P ENST00000538966 4/37 156 91 65 222 222 0 strelka-varscan-mutect PLXNB3,synonymous_variant,p.=,ENST00000538966,NM_001163257.1;PLXNB3,synonymous_variant,p.=,ENST00000361971,NM_005393.2;U52111.14,upstream_gene_variant,,ENST00000434284,;U52111.14,upstream_gene_variant,,ENST00000416854,; G ENST00000538966 Transcript synonymous_variant 613/6377 342/5799 114/1932 P ccT/ccG 1 1 PLXNB3 HGNC HGNC:9105 protein_coding YES CCDS55536.1 ENSP00000442736 Q9ULL4 UPI0001AFF680 NM_001163257.1 4/37 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF33,SMART_domains:SM00630,Superfamily_domains:SSF101912 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 62 153767100 153767100 T G 1 0 0 0 0 0 0 0 1 12231 1567 55 5 5 PLXNB3 23 153767100 Silent SNP T C3N-00704_T 2094607 153767100 2273795 604 19741 NPHP4 0 . GRCh38 1 5879533 5879533 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.2708G>A p.Gly903Glu p.G903E ENST00000622020 20/20 212 193 19 180 180 0 strelka-varscan-mutect NPHP4,missense_variant,p.Gly903Glu,ENST00000622020,;NPHP4,intron_variant,,ENST00000378156,NM_001291594.1,NM_001291593.1,NM_015102.4;NPHP4,intron_variant,,ENST00000478423,;NPHP4,missense_variant,p.Gly903Glu,ENST00000489180,;NPHP4,intron_variant,,ENST00000378169,;NPHP4,intron_variant,,ENST00000470763,;NPHP4,upstream_gene_variant,,ENST00000506941,; T ENST00000622020 Transcript missense_variant 2976/3004 2708/2736 903/911 G/E gGa/gAa 1 -1 NPHP4 HGNC HGNC:19104 protein_coding ENSP00000481831 O75161 UPI0000074519 tolerated_low_confidence(0.09) 20/20 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 5879533 5879533 C T 1 0 0 0 0 1 0 0 0 10629 855 30 3 3 NPHP4 1 5879533 Missense_Mutation SNP C C3N-00737_T 5879533 243076889 1 19742 TMEM82 0 . GRCh38 1 15742601 15742601 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.42C>T p.= p.L14L ENST00000375782 1/6 109 97 12 118 118 0 strelka-varscan-mutect TMEM82,synonymous_variant,p.=,ENST00000375782,NM_001013641.2;SLC25A34,downstream_gene_variant,,ENST00000294454,NM_207348.2;RP11-169K16.4,intron_variant,,ENST00000418525,;TMEM82,non_coding_transcript_exon_variant,,ENST00000465575,;SLC25A34,downstream_gene_variant,,ENST00000489568,;SLC25A34,downstream_gene_variant,,ENST00000465495,; T ENST00000375782 Transcript synonymous_variant 180/1520 42/1032 14/343 L ctC/ctT 1 1 TMEM82 HGNC HGNC:32350 protein_coding YES CCDS30608.1 ENSP00000364938 A0PJX8 UPI0000458A15 NM_001013641.2 1/6 Pfam_domain:PF15816,hmmpanther:PTHR35257,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 204 4 0 0 0 0 0 -19.99998 1 1 1 1 0 T 2 4 63 15742601 15742601 C T 1 0 0 0 0 0 0 0 1 16683 842 30 3 3 TMEM82 1 15742601 Silent SNP C C3N-00737_T 9863068 15742601 233213821 2 19743 WNT4 0 . GRCh38 1 22142881 22142881 + Silent SNP G G T novel C3N-00737_T C3N-00737_N G G c.42C>A p.= p.V14V ENST00000290167 1/5 182 154 28 88 88 0 strelka-varscan-mutect WNT4,synonymous_variant,p.=,ENST00000290167,NM_030761.4;WNT4,intron_variant,,ENST00000441048,; T ENST00000290167 Transcript synonymous_variant 86/3845 42/1056 14/351 V gtC/gtA 1 -1 WNT4 HGNC HGNC:12783 protein_coding YES CCDS223.1 ENSP00000290167 P56705 UPI0000048EC6 NM_030761.4 1/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR12027:SF101,hmmpanther:PTHR12027 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 22142881 22142881 G T 1 0 0 0 0 0 0 0 1 17946 929 33 2 2 WNT4 1 22142881 Silent SNP G C3N-00737_T 6400280 22142881 226813541 3 19744 ADGRB2 0 . GRCh38 1 31733138 31733138 + Missense_Mutation SNP G G A C3N-00737_T C3N-00737_N G G c.3458C>T p.Ser1153Leu p.S1153L ENST00000373655 26/33 107 101 6 126 126 0 strelka-varscan-mutect ADGRB2,missense_variant,p.Ser1153Leu,ENST00000373658,;ADGRB2,missense_variant,p.Ser1153Leu,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Ser1053Leu,ENST00000398542,;ADGRB2,missense_variant,p.Ser1120Leu,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Ser1068Leu,ENST00000398556,;ADGRB2,missense_variant,p.Ser1086Leu,ENST00000398547,;ADGRB2,missense_variant,p.Ser1141Leu,ENST00000398538,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000465256,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000530999,; A ENST00000373655 Transcript missense_variant 3800/5400 3458/4755 1153/1584 S/L tCa/tTa COSM4851018 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 deleterious(0) 26/33 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF41,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249 1 MODERATE 1 SNV 1 1 1 PASS rs1283190767 . 0 207 3 0 0 0 0 0 -12.43813 1 1 1 1 0 A 3 1 63 31733138 31733138 G A 1 0 0 0 0 1 0 0 0 356 1304 45 3 3 ADGRB2 1 31733138 Missense_Mutation SNP G C3N-00737_T 9590257 31733138 217223284 4 19745 ZMYM4 0 . GRCh38 1 35414052 35414052 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.4029G>C p.Leu1343Phe p.L1343F ENST00000314607 27/30 171 155 16 219 219 0 strelka-varscan-mutect ZMYM4,missense_variant,p.Leu1343Phe,ENST00000314607,NM_005095.2;ZMYM4,missense_variant,p.Leu1002Phe,ENST00000457946,; C ENST00000314607 Transcript missense_variant 4109/6994 4029/4647 1343/1548 L/F ttG/ttC 1 1 ZMYM4 HGNC HGNC:13055 protein_coding YES CCDS389.1 ENSP00000322915 Q5VZL5 UPI0000203EE6 NM_005095.2 deleterious(0) 27/30 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF10 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 35414052 35414052 G C 1 0 0 0 0 1 0 0 0 18282 1281 45 4 4 ZMYM4 1 35414052 Missense_Mutation SNP G C3N-00737_T 3680914 35414052 213542370 5 19746 CFAP57 0 . GRCh38 1 43198642 43198642 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.1424G>A p.Gly475Glu p.G475E ENST00000610710 8/24 280 257 23 246 246 0 strelka-varscan-mutect CFAP57,missense_variant,p.Gly475Glu,ENST00000372492,;CFAP57,missense_variant,p.Gly475Glu,ENST00000610710,NM_001195831.2;CFAP57,missense_variant,p.Gly475Glu,ENST00000528956,NM_001167965.1,NM_152498.3;RNA5SP46,downstream_gene_variant,,ENST00000362370,;EBNA1BP2,intron_variant,,ENST00000461557,;EBNA1BP2,intron_variant,,ENST00000474566,;EBNA1BP2,intron_variant,,ENST00000466927,;CFAP57,3_prime_UTR_variant,,ENST00000533339,; A ENST00000610710 Transcript missense_variant 1570/4162 1424/3852 475/1283 G/E gGa/gAa 1 1 CFAP57 HGNC HGNC:26485 protein_coding YES CCDS72768.1 ENSP00000479773 A0A087WVY5 UPI000223C368 NM_001195831.2 deleterious(0.02) 8/24 Gene3D:2.130.10.10,hmmpanther:PTHR32215,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 43198642 43198642 G A 1 0 0 0 0 1 0 0 0 3026 1188 41 3 3 CFAP57 1 43198642 Missense_Mutation SNP G C3N-00737_T 7784590 43198642 205757780 6 19747 ZZZ3 0 . GRCh38 1 77565727 77565727 + Silent SNP T T C rs750092524 C3N-00737_T C3N-00737_N T T c.2625A>G p.= p.S875S ENST00000370801 15/15 173 156 17 198 198 0 strelka-varscan-mutect ZZZ3,synonymous_variant,p.=,ENST00000370801,NM_015534.4;ZZZ3,synonymous_variant,p.=,ENST00000370798,NM_001308237.1;ZZZ3,non_coding_transcript_exon_variant,,ENST00000476275,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000481346,; C ENST00000370801 Transcript synonymous_variant 3101/4328 2625/2712 875/903 S tcA/tcG rs750092524 1 -1 ZZZ3 HGNC HGNC:24523 protein_coding YES CCDS677.1 ENSP00000359837 Q8IYH5 UPI0000074256 NM_015534.4 15/15 hmmpanther:PTHR22705 LOW 1 SNV 1 1 PASS rs750092524 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 77565727 77565727 T C 1 0 0 0 0 0 0 0 1 18860 1567 55 5 5 ZZZ3 1 77565727 Silent SNP T C3N-00737_T 34367085 77565727 171390695 7 19748 COL11A1 0 . GRCh38 1 102965505 102965505 + Silent SNP C C A C3N-00737_T C3N-00737_N C C c.2898G>T p.= p.G966G ENST00000370096 38/67 361 331 30 312 310 2 strelka-varscan-mutect COL11A1,synonymous_variant,p.=,ENST00000358392,NM_080629.2;COL11A1,synonymous_variant,p.=,ENST00000370096,NM_001854.3;COL11A1,synonymous_variant,p.=,ENST00000353414,NM_001190709.1;COL11A1,synonymous_variant,p.=,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,;COL11A1,upstream_gene_variant,,ENST00000465209,; A ENST00000370096 Transcript synonymous_variant 3211/7286 2898/5421 966/1806 G ggG/ggT COSM5461894,COSM5461895 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 38/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 102965505 102965505 C A 1 0 0 0 0 0 0 0 1 3455 610 22 2 2 COL11A1 1 102965505 Silent SNP C C3N-00737_T 25399778 102965505 145990917 8 19749 HIST2H3D 0 . GRCh38 1 149813655 149813655 + Silent SNP G G A rs781922786 C3N-00737_T C3N-00737_N G G c.27C>T p.= p.R9R ENST00000331491 1/1 314 212 102 233 233 0 strelka-varscan-mutect HIST2H3D,synonymous_variant,p.=,ENST00000331491,NM_001123375.2;HIST2H2BF,upstream_gene_variant,,ENST00000369167,NM_001024599.4;HIST2H2BF,upstream_gene_variant,,ENST00000545683,NM_001161334.1;HIST2H2BF,upstream_gene_variant,,ENST00000469483,;HIST2H2BF,upstream_gene_variant,,ENST00000420462,;HIST2H2BF,upstream_gene_variant,,ENST00000620458,; A ENST00000331491 Transcript synonymous_variant 27/411 27/411 9/136 R cgC/cgT rs781922786 1 -1 HIST2H3D HGNC HGNC:25311 protein_coding YES CCDS41388.1 ENSP00000333277 Q71DI3 UPI0000000586 NM_001123375.2 1/1 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,Superfamily_domains:SSF47113,Prints_domain:PR00622 LOW SNV 1 PASS rs781922786 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 149813655 149813655 G A 1 0 0 0 0 0 0 0 1 7069 1306 46 3 3 HIST2H3D 1 149813655 Silent SNP G C3N-00737_T 46848150 149813655 99142767 9 19750 SETDB1 0 . GRCh38 1 150964348 150964348 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.3860G>C p.Arg1287Thr p.R1287T ENST00000271640 22/22 331 300 31 246 246 0 strelka-varscan-mutect SETDB1,missense_variant,p.Arg1287Thr,ENST00000271640,NM_001145415.1;SETDB1,missense_variant,p.Arg1286Thr,ENST00000368969,NM_012432.3;CERS2,missense_variant,p.Ser368Cys,ENST00000561294,;SETDB1,downstream_gene_variant,,ENST00000498193,;CERS2,downstream_gene_variant,,ENST00000271688,NM_181746.3;CERS2,downstream_gene_variant,,ENST00000368954,NM_022075.4;CERS2,downstream_gene_variant,,ENST00000560793,;CERS2,downstream_gene_variant,,ENST00000368949,;CERS2,downstream_gene_variant,,ENST00000361419,;CERS2,downstream_gene_variant,,ENST00000558062,;CERS2,downstream_gene_variant,,ENST00000421609,;CERS2,downstream_gene_variant,,ENST00000457392,;RP11-316M1.12,upstream_gene_variant,,ENST00000561111,;RP11-316M1.12,upstream_gene_variant,,ENST00000560481,;CERS2,downstream_gene_variant,,ENST00000345896,;SETDB1,downstream_gene_variant,,ENST00000459773,;SETDB1,non_coding_transcript_exon_variant,,ENST00000497314,;CERS2,non_coding_transcript_exon_variant,,ENST00000482825,;CERS2,downstream_gene_variant,,ENST00000460664,;CERS2,downstream_gene_variant,,ENST00000559020,;SETDB1,downstream_gene_variant,,ENST00000528749,;SETDB1,downstream_gene_variant,,ENST00000533529,;CERS2,downstream_gene_variant,,ENST00000559660,; C ENST00000271640 Transcript missense_variant 4050/4437 3860/3876 1287/1291 R/T aGa/aCa 1 1 SETDB1 HGNC HGNC:10761 protein_coding YES CCDS44217.1 ENSP00000271640 Q15047 UPI0000135897 NM_001145415.1 deleterious(0) 22/22 Gene3D:2.170.270.10,PROSITE_profiles:PS50868,PROSITE_profiles:PS51573 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 150964348 150964348 G C 1 0 0 0 0 1 0 0 0 14416 942 33 4 4 SETDB1 1 150964348 Missense_Mutation SNP G C3N-00737_T 1150693 150964348 97992074 10 19751 FLAD1 0 . GRCh38 1 154988038 154988038 + Silent SNP A A G novel C3N-00737_T C3N-00737_N A A c.9A>G p.= p.P3P ENST00000368431 3/3 122 111 11 100 100 0 strelka-varscan-mutect FLAD1,synonymous_variant,p.=,ENST00000368431,NM_001184892.1;FLAD1,intron_variant,,ENST00000368433,;FLAD1,intron_variant,,ENST00000292180,NM_025207.4;FLAD1,intron_variant,,ENST00000368432,NM_001184891.1;FLAD1,intron_variant,,ENST00000315144,NM_201398.2;FLAD1,upstream_gene_variant,,ENST00000295530,;FLAD1,upstream_gene_variant,,ENST00000368428,;FLAD1,non_coding_transcript_exon_variant,,ENST00000492620,;FLAD1,intron_variant,,ENST00000487371,;FLAD1,upstream_gene_variant,,ENST00000489992,;FLAD1,upstream_gene_variant,,ENST00000477609,;FLAD1,upstream_gene_variant,,ENST00000481758,; G ENST00000368431 Transcript synonymous_variant 829/1803 9/885 3/294 P ccA/ccG 1 1 FLAD1 HGNC HGNC:24671 protein_coding CCDS53372.1 ENSP00000357416 Q8NFF5 UPI0000072FC0 NM_001184892.1 3/3 LOW SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.9816 0.9999987 1 1 1 0 G 2 3 63 154988038 154988038 A G 1 0 0 0 0 0 0 0 1 5782 204 8 5 5 FLAD1 1 154988038 Silent SNP A C3N-00737_T 4023690 154988038 93968384 11 19752 72 2 FLAD1 0 . GRCh38 1 154988043 154988043 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.14C>G p.Ser5Cys p.S5C ENST00000368431 3/3 131 119 12 107 107 0 strelka-varscan-mutect FLAD1,missense_variant,p.Ser5Cys,ENST00000368431,NM_001184892.1;FLAD1,intron_variant,,ENST00000368433,;FLAD1,intron_variant,,ENST00000292180,NM_025207.4;FLAD1,intron_variant,,ENST00000368432,NM_001184891.1;FLAD1,intron_variant,,ENST00000315144,NM_201398.2;FLAD1,upstream_gene_variant,,ENST00000295530,;FLAD1,upstream_gene_variant,,ENST00000368428,;FLAD1,non_coding_transcript_exon_variant,,ENST00000492620,;FLAD1,intron_variant,,ENST00000487371,;FLAD1,upstream_gene_variant,,ENST00000489992,;FLAD1,upstream_gene_variant,,ENST00000477609,;FLAD1,upstream_gene_variant,,ENST00000481758,; G ENST00000368431 Transcript missense_variant 834/1803 14/885 5/294 S/C tCt/tGt 1 1 FLAD1 HGNC HGNC:24671 protein_coding CCDS53372.1 ENSP00000357416 Q8NFF5 UPI0000072FC0 NM_001184892.1 deleterious_low_confidence(0.01) 3/3 MODERATE SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.99958 0.9999988 1 1 1 0 G 3 3 63 154988043 154988043 C G 1 0 0 0 0 1 0 0 0 5782 913 32 4 4 FLAD1 1 154988043 Missense_Mutation SNP C C3N-00737_T 5 154988043 93968379 12 19753 72 2 IQGAP3 0 . GRCh38 1 156563595 156563595 + Missense_Mutation SNP C C A rs200795481 C3N-00737_T C3N-00737_N C C c.577G>T p.Gly193Trp p.G193W ENST00000361170 7/38 249 160 89 134 134 0 strelka-varscan-mutect IQGAP3,missense_variant,p.Gly193Trp,ENST00000361170,NM_178229.4;IQGAP3,missense_variant,p.Gly150Trp,ENST00000491900,; A ENST00000361170 Transcript missense_variant 588/5988 577/4896 193/1631 G/W Ggg/Tgg rs200795481,COSM1983754 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 deleterious(0) 7/38 hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200795481 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 156563595 156563595 C A 1 0 0 0 0 1 0 0 0 7722 652 23 1 1 IQGAP3 1 156563595 Missense_Mutation SNP C C3N-00737_T 1575552 156563595 92392827 13 19754 CD84 0 . GRCh38 1 160548295 160548295 + Silent SNP A A G novel C3N-00737_T C3N-00737_N A A c.999T>C p.= p.S333S ENST00000311224 8/8 395 366 29 246 246 0 strelka-varscan-mutect CD84,synonymous_variant,p.=,ENST00000368054,NM_003874.3;CD84,synonymous_variant,p.=,ENST00000534968,NM_001184882.1;CD84,synonymous_variant,p.=,ENST00000311224,NM_001184879.1;CD84,synonymous_variant,p.=,ENST00000368048,;CD84,3_prime_UTR_variant,,ENST00000368051,NM_001184881.1;RP11-528G1.2,intron_variant,,ENST00000446952,;CD84,non_coding_transcript_exon_variant,,ENST00000466767,;CD84,downstream_gene_variant,,ENST00000360056,; G ENST00000311224 Transcript synonymous_variant 1066/1116 999/1038 333/345 S agT/agC 1 -1 CD84 HGNC HGNC:1704 protein_coding YES CCDS53396.1 ENSP00000312367 Q9UIB8 UPI0000071B5F NM_001184879.1 8/8 hmmpanther:PTHR12080:SF50,hmmpanther:PTHR12080 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 160548295 160548295 A G 1 0 0 0 0 0 0 0 1 2746 388 14 5 5 CD84 1 160548295 Silent SNP A C3N-00737_T 3984700 160548295 88408127 14 19755 CD48 0 . GRCh38 1 160685007 160685007 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.265C>A p.Pro89Thr p.P89T ENST00000613788 2/3 411 365 46 288 287 1 strelka-varscan-mutect CD48,missense_variant,p.Pro89Thr,ENST00000368045,;CD48,missense_variant,p.Pro89Thr,ENST00000613788,NM_001256030.1;CD48,missense_variant,p.Pro89Thr,ENST00000368046,NM_001778.3;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000628340,;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000598917,;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000630436,;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000621431,;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000626085,;RP11-404F10.2,non_coding_transcript_exon_variant,,ENST00000627996,;RP11-404F10.2,intron_variant,,ENST00000627799,;RP11-404F10.2,downstream_gene_variant,,ENST00000443928,;RP11-404F10.2,downstream_gene_variant,,ENST00000627180,;RP11-404F10.2,downstream_gene_variant,,ENST00000588034,; T ENST00000613788 Transcript missense_variant 333/1500 265/759 89/252 P/T Cct/Act 1 -1 CD48 HGNC HGNC:1683 protein_coding YES CCDS72955.1 ENSP00000484431 A0A087X1S7 UPI00024336A1 NM_001256030.1 tolerated(0.57) 2/3 hmmpanther:PTHR12080:SF47,hmmpanther:PTHR12080,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 160685007 160685007 G T 1 0 0 0 0 1 0 0 0 2724 1174 41 2 2 CD48 1 160685007 Missense_Mutation SNP G C3N-00737_T 136712 160685007 88271415 15 19756 HSD17B7 0 . GRCh38 1 162799766 162799766 + Silent SNP C C G novel C3N-00737_T C3N-00737_N C C c.471C>G p.= p.L157L ENST00000254521 5/9 157 138 19 146 145 1 varscan-mutect HSD17B7,synonymous_variant,p.=,ENST00000254521,NM_016371.3;HSD17B7,downstream_gene_variant,,ENST00000367913,NM_001304513.1,NM_001304512.1;HSD17B7,non_coding_transcript_exon_variant,,ENST00000485405,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000463037,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000484251,;HSD17B7,3_prime_UTR_variant,,ENST00000466176,;HSD17B7,non_coding_transcript_exon_variant,,ENST00000494450,;HSD17B7,upstream_gene_variant,,ENST00000488656,;HSD17B7,upstream_gene_variant,,ENST00000470195,; G ENST00000254521 Transcript synonymous_variant 526/1190 471/1026 157/341 L ctC/ctG 1 1 HSD17B7 HGNC HGNC:5215 protein_coding YES CCDS1242.1 ENSP00000254521 P56937 A0A024R913 UPI000004C64C NM_016371.3 5/9 hmmpanther:PTHR24322:SF339,hmmpanther:PTHR24322,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 162799766 162799766 C G 1 0 0 0 0 0 0 0 1 7282 900 32 4 4 HSD17B7 1 162799766 Silent SNP C C3N-00737_T 2114759 162799766 86156656 16 19757 FASLG 0 . GRCh38 1 172664379 172664379 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.440C>G p.Ala147Gly p.A147G ENST00000367721 3/4 568 508 60 417 417 0 strelka-varscan-mutect FASLG,missense_variant,p.Ala147Gly,ENST00000367721,NM_000639.2;FASLG,3_prime_UTR_variant,,ENST00000340030,NM_001302746.1; G ENST00000367721 Transcript missense_variant 624/1888 440/846 147/281 A/G gCc/gGc 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 deleterious(0.01) 3/4 Gene3D:2.60.120.40,Prints_domain:PR01681,PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF33,SMART_domains:SM00207,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 172664379 172664379 C G 1 0 0 0 0 1 0 0 0 5542 739 26 4 4 FASLG 1 172664379 Missense_Mutation SNP C C3N-00737_T 9864613 172664379 76292043 17 19758 ASPM 0 . GRCh38 1 197117787 197117787 + Splice_Site SNP A A T novel C3N-00737_T C3N-00737_N A A c.4065+2T>A p.X1355_splice ENST00000367409 189 157 32 225 225 0 strelka-varscan-mutect ASPM,splice_donor_variant,,ENST00000367409,NM_018136.4;ASPM,splice_donor_variant,,ENST00000294732,NM_001206846.1;ASPM,splice_donor_variant,,ENST00000367408,;ASPM,intron_variant,,ENST00000612785,; T ENST00000367409 Transcript splice_donor_variant -/10887 4065/10434 1355/3477 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 17/27 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 63 197117787 197117787 A T 1 0 0 0 0 0 0 1 0 1203 405 14 4 4 ASPM 1 197117787 Splice_Site SNP A C3N-00737_T 24453408 197117787 51838635 18 19759 KIF21B 0 . GRCh38 1 200990706 200990706 + Missense_Mutation SNP T T C novel C3N-00737_T C3N-00737_N T T c.2705A>G p.Lys902Arg p.K902R ENST00000422435 19/35 142 105 37 127 127 0 strelka-varscan-mutect KIF21B,missense_variant,p.Lys902Arg,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Lys902Arg,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Lys902Arg,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Lys902Arg,ENST00000360529,NM_001252103.1; C ENST00000422435 Transcript missense_variant 3022/5519 2705/4914 902/1637 K/R aAg/aGg 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 tolerated(0.19) 19/35 hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 200990706 200990706 T C 1 0 0 0 0 1 0 0 0 8154 1609 56 5 5 KIF21B 1 200990706 Missense_Mutation SNP T C3N-00737_T 3872919 200990706 47965716 19 19760 KDM5B 0 . GRCh38 1 202740711 202740711 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.3047G>C p.Arg1016Thr p.R1016T ENST00000367265 20/27 166 124 42 118 118 0 strelka-varscan-mutect KDM5B,missense_variant,p.Arg1016Thr,ENST00000367265,NM_006618.3;KDM5B,missense_variant,p.Arg1052Thr,ENST00000367264,;KDM5B,missense_variant,p.Arg858Thr,ENST00000235790,;KDM5B,upstream_gene_variant,,ENST00000472822,; G ENST00000367265 Transcript missense_variant 4212/10345 3047/4635 1016/1544 R/T aGa/aCa 1 -1 KDM5B HGNC HGNC:18039 protein_coding YES CCDS30974.1 ENSP00000356234 Q9UGL1 UPI0000032AA2 NM_006618.3 deleterious(0) 20/27 Pfam_domain:PF08429,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 202740711 202740711 C G 1 0 0 0 0 1 0 0 0 8052 913 32 4 4 KDM5B 1 202740711 Missense_Mutation SNP C C3N-00737_T 1750005 202740711 46215711 20 19761 URB2 0 . GRCh38 1 229635251 229635251 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.638C>G p.Ser213Cys p.S213C ENST00000258243 4/10 173 142 31 184 184 0 strelka-varscan URB2,missense_variant,p.Ser213Cys,ENST00000258243,NM_001314021.1,NM_014777.2; G ENST00000258243 Transcript missense_variant 774/5613 638/4575 213/1524 S/C tCt/tGt 1 1 URB2 HGNC HGNC:28967 protein_coding YES CCDS31052.1 ENSP00000258243 Q14146 UPI000013CFBD NM_001314021.1,NM_014777.2 deleterious(0.02) 4/10 hmmpanther:PTHR15682 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 229635251 229635251 C G 1 0 0 0 0 1 0 0 0 17555 913 32 4 4 URB2 1 229635251 Missense_Mutation SNP C C3N-00737_T 26894540 229635251 19321171 21 19762 TPO 0 . GRCh38 2 1484746 1484746 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.1489A>G p.Ile497Val p.I497V ENST00000345913 9/17 426 358 68 435 435 0 strelka-varscan-mutect TPO,missense_variant,p.Ile426Val,ENST00000422464,;TPO,missense_variant,p.Ile497Val,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Ile497Val,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Ile497Val,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Ile497Val,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Ile324Val,ENST00000382198,NM_175722.3;TPO,missense_variant,p.Ile29Val,ENST00000446278,;TPO,missense_variant,p.Ile28Val,ENST00000469607,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,non_coding_transcript_exon_variant,,ENST00000462973,; G ENST00000345913 Transcript missense_variant 1580/3145 1489/2802 497/933 I/V Atc/Gtc 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 tolerated(0.38) 9/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS rs1288889178 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 1484746 1484746 A G 1 0 0 0 0 1 0 0 0 16891 333 12 5 5 TPO 2 1484746 Missense_Mutation SNP A C3N-00737_T 1484746 240708783 22 19763 PDIA6 0 . GRCh38 2 10793142 10793142 + Missense_Mutation SNP T T A novel C3N-00737_T C3N-00737_N T T c.563A>T p.Lys188Met p.K188M ENST00000404371 7/15 274 250 24 224 223 1 strelka-varscan-mutect PDIA6,missense_variant,p.Lys188Met,ENST00000404371,NM_001282704.1;PDIA6,missense_variant,p.Lys141Met,ENST00000381611,NM_001282706.1;PDIA6,missense_variant,p.Lys133Met,ENST00000540494,NM_001282707.1;PDIA6,missense_variant,p.Lys188Met,ENST00000617249,;PDIA6,missense_variant,p.Lys136Met,ENST00000272227,NM_005742.3;PDIA6,missense_variant,p.Lys184Met,ENST00000404824,NM_001282705.1;PDIA6,downstream_gene_variant,,ENST00000489662,; A ENST00000404371 Transcript missense_variant 901/2682 563/1479 188/492 K/M aAg/aTg 1 -1 PDIA6 HGNC HGNC:30168 protein_coding YES CCDS62854.1 ENSP00000385385 Q15084 UPI000022BCCE NM_001282704.1 deleterious(0.02) 7/15 hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF38 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 10793142 10793142 T A 1 0 0 0 0 1 0 0 0 11760 1609 56 4 4 PDIA6 2 10793142 Missense_Mutation SNP T C3N-00737_T 9308396 10793142 231400387 23 19764 RAD51AP2 0 . GRCh38 2 17515694 17515694 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.2722G>C p.Glu908Gln p.E908Q ENST00000399080 1/3 107 92 15 173 173 0 strelka-varscan-mutect RAD51AP2,missense_variant,p.Glu908Gln,ENST00000399080,NM_001321233.1,NM_001099218.2; G ENST00000399080 Transcript missense_variant 2746/3724 2722/3480 908/1159 E/Q Gaa/Caa 1 -1 RAD51AP2 HGNC HGNC:34417 protein_coding YES CCDS42656.1 ENSP00000382030 Q09MP3 UPI0000418FD4 NM_001321233.1,NM_001099218.2 deleterious(0.01) 1/3 hmmpanther:PTHR15361,hmmpanther:PTHR15361:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 17515694 17515694 C G 1 0 0 0 0 1 0 0 0 13148 922 32 4 4 RAD51AP2 2 17515694 Missense_Mutation SNP C C3N-00737_T 6722552 17515694 224677835 24 19765 RAD51AP2 0 . GRCh38 2 17515757 17515757 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.2659G>A p.Glu887Lys p.E887K ENST00000399080 1/3 82 71 11 147 147 0 strelka-varscan-mutect RAD51AP2,missense_variant,p.Glu887Lys,ENST00000399080,NM_001321233.1,NM_001099218.2; T ENST00000399080 Transcript missense_variant 2683/3724 2659/3480 887/1159 E/K Gaa/Aaa 1 -1 RAD51AP2 HGNC HGNC:34417 protein_coding YES CCDS42656.1 ENSP00000382030 Q09MP3 UPI0000418FD4 NM_001321233.1,NM_001099218.2 deleterious(0.05) 1/3 hmmpanther:PTHR15361,hmmpanther:PTHR15361:SF6 MODERATE 1 SNV 1 1 PASS rs1184690643 . 0 207 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 63 17515757 17515757 C T 1 0 0 0 0 1 0 0 0 13148 922 32 3 3 RAD51AP2 2 17515757 Missense_Mutation SNP C C3N-00737_T 63 17515757 224677772 25 19766 TTC27 0 . GRCh38 2 32787038 32787038 + Nonsense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.1887G>A p.Trp629Ter p.W629* ENST00000317907 16/20 242 202 40 184 184 0 strelka-varscan TTC27,stop_gained,p.Trp629Ter,ENST00000317907,NM_017735.4,NM_001193509.1;TTC27,3_prime_UTR_variant,,ENST00000428527,;TTC27,3_prime_UTR_variant,,ENST00000433416,; A ENST00000317907 Transcript stop_gained 2118/2876 1887/2532 629/843 W/* tgG/tgA 1 1 TTC27 HGNC HGNC:25986 protein_coding YES CCDS33176.1 ENSP00000313953 Q6P3X3 UPI0000208226 NM_017735.4,NM_001193509.1 16/20 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR16193,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 63 32787038 32787038 G A 1 0 0 0 0 0 1 0 0 17203 1212 42 3 3 TTC27 2 32787038 Nonsense_Mutation SNP G C3N-00737_T 15271281 32787038 209406491 26 19767 NAT8 0 . GRCh38 2 73641044 73641044 + Missense_Mutation SNP C C A C3N-00737_T C3N-00737_N C C c.585G>T p.Lys195Asn p.K195N ENST00000272425 2/2 254 225 29 247 246 1 strelka-varscan NAT8,missense_variant,p.Lys195Asn,ENST00000272425,NM_003960.3;ALMS1P1,upstream_gene_variant,,ENST00000450720,; A ENST00000272425 Transcript missense_variant 735/947 585/684 195/227 K/N aaG/aaT COSM4095660 1 -1 NAT8 HGNC HGNC:18069 protein_coding YES CCDS1926.1 ENSP00000272425 Q9UHE5 UPI00000707D4 NM_003960.3 deleterious(0.02) 2/2 Gene3D:3.40.630.30,PROSITE_profiles:PS51186,hmmpanther:PTHR13947,hmmpanther:PTHR13947:SF14,Superfamily_domains:SSF55729 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 73641044 73641044 C A 1 0 0 0 0 1 0 0 0 10188 912 32 2 2 NAT8 2 73641044 Missense_Mutation SNP C C3N-00737_T 40854006 73641044 168552485 27 19768 DCTN1 0 . GRCh38 2 74369446 74369446 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.1438G>C p.Glu480Gln p.E480Q ENST00000361874 14/32 380 319 61 334 334 0 strelka-varscan DCTN1,missense_variant,p.Glu480Gln,ENST00000361874,NM_004082.4;DCTN1,missense_variant,p.Glu463Gln,ENST00000628224,;DCTN1,missense_variant,p.Glu473Gln,ENST00000394003,NM_001190837.1;DCTN1,missense_variant,p.Glu443Gln,ENST00000409240,NM_001190836.1;DCTN1,missense_variant,p.Glu463Gln,ENST00000409868,;DCTN1,missense_variant,p.Glu346Gln,ENST00000633691,NM_023019.3;DCTN1,missense_variant,p.Glu346Gln,ENST00000409438,NM_001135041.2;DCTN1,missense_variant,p.Glu460Gln,ENST00000409567,NM_001135040.2;DCTN1,downstream_gene_variant,,ENST00000458655,;DCTN1,upstream_gene_variant,,ENST00000495643,;DCTN1,downstream_gene_variant,,ENST00000463583,;DCTN1,upstream_gene_variant,,ENST00000497666,;DCTN1,missense_variant,p.Glu443Gln,ENST00000434055,;DCTN1,non_coding_transcript_exon_variant,,ENST00000466110,;DCTN1,upstream_gene_variant,,ENST00000491465,;DCTN1,downstream_gene_variant,,ENST00000477966,;DCTN1,downstream_gene_variant,,ENST00000470351,;DCTN1,upstream_gene_variant,,ENST00000495895,;DCTN1,downstream_gene_variant,,ENST00000462813,; G ENST00000361874 Transcript missense_variant 1756/4500 1438/3837 480/1278 E/Q Gag/Cag 1 -1 DCTN1 HGNC HGNC:2711 protein_coding YES CCDS1939.1 ENSP00000354791 Q14203 UPI0000129A25 NM_004082.4 tolerated(0.07) 14/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF40 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 74369446 74369446 C G 1 0 0 0 0 1 0 0 0 4109 835 29 4 4 DCTN1 2 74369446 Missense_Mutation SNP C C3N-00737_T 728402 74369446 167824083 28 19769 MAP3K2 0 . GRCh38 2 127338963 127338963 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.92G>A p.Arg31Lys p.R31K ENST00000409947 3/17 213 169 44 243 243 0 strelka-varscan MAP3K2,missense_variant,p.Arg31Lys,ENST00000409947,;MAP3K2,missense_variant,p.Arg31Lys,ENST00000344908,NM_006609.4;MAP3K2,missense_variant,p.Arg31Lys,ENST00000409179,; T ENST00000409947 Transcript missense_variant 375/10992 92/1860 31/619 R/K aGa/aAa 1 -1 MAP3K2 HGNC HGNC:6854 protein_coding YES CCDS46404.1 ENSP00000387246 Q9Y2U5 A0A024RAH0 UPI0000208C78 tolerated(0.99) 3/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 127338963 127338963 C T 1 0 0 0 0 1 0 0 0 9173 913 32 3 3 MAP3K2 2 127338963 Missense_Mutation SNP C C3N-00737_T 52969517 127338963 114854566 29 19770 LRP1B 0 . GRCh38 2 140541014 140541014 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.7472G>T p.Cys2491Phe p.C2491F ENST00000389484 45/91 175 141 34 206 206 0 strelka-varscan LRP1B,missense_variant,p.Cys2491Phe,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 8444/16535 7472/13800 2491/4599 C/F tGc/tTc 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 45/91 Gene3D:2.10.25.10,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 140541014 140541014 C A 1 0 0 0 0 1 0 0 0 8850 710 25 2 2 LRP1B 2 140541014 Missense_Mutation SNP C C3N-00737_T 13202051 140541014 101652515 30 19771 SCN1A 0 . GRCh38 2 165992141 165992141 + Missense_Mutation SNP T T G novel C3N-00737_T C3N-00737_N T T c.5134A>C p.Asn1712His p.N1712H ENST00000303395 28/28 354 280 74 350 350 0 strelka-varscan-mutect SCN1A,missense_variant,p.Asn1701His,ENST00000637988,;SCN1A,missense_variant,p.Asn1712His,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Asn1701His,ENST00000635750,;SCN1A,missense_variant,p.Asn1712His,ENST00000423058,;SCN1A,missense_variant,p.Asn1701His,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Asn1684His,ENST00000409050,NM_001165964.1;SCN1A,3_prime_UTR_variant,,ENST00000635776,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000597623,;AC010127.3,intron_variant,,ENST00000630226,;SCN1A,3_prime_UTR_variant,,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000637038,;SCN1A,downstream_gene_variant,,ENST00000625916,;SCN1A,downstream_gene_variant,,ENST00000473295,; G ENST00000303395 Transcript missense_variant 5552/8533 5134/6030 1712/2009 N/H Aac/Cac 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 deleterious(0) 28/28 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 165992141 165992141 T G 1 0 0 0 0 1 0 0 0 14183 1812 63 5 5 SCN1A 2 165992141 Missense_Mutation SNP T C3N-00737_T 25451127 165992141 76201388 31 19772 DNAH7 0 . GRCh38 2 195808864 195808864 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.9901G>C p.Glu3301Gln p.E3301Q ENST00000312428 53/65 130 96 34 154 154 0 strelka-varscan-mutect DNAH7,missense_variant,p.Glu3301Gln,ENST00000312428,NM_018897.2; G ENST00000312428 Transcript missense_variant 10002/12394 9901/12075 3301/4024 E/Q Gag/Cag 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 tolerated(0.2) 53/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 195808864 195808864 C G 1 0 0 0 0 1 0 0 0 4421 835 29 4 4 DNAH7 2 195808864 Missense_Mutation SNP C C3N-00737_T 29816723 195808864 46384665 32 19773 ZDBF2 0 . GRCh38 2 206311580 206311580 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.7052A>G p.Asn2351Ser p.N2351S ENST00000374423 5/5 30 24 6 24 24 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Asn2351Ser,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Asn2349Ser,ENST00000611847,NM_001285549.1; G ENST00000374423 Transcript missense_variant 7438/10286 7052/7065 2351/2354 N/S aAt/aGt 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.15) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.61025 1 1 1 1 0 G 3 3 63 206311580 206311580 A G 1 0 0 0 0 1 0 0 0 18174 101 4 5 5 ZDBF2 2 206311580 Missense_Mutation SNP A C3N-00737_T 10502716 206311580 35881949 33 19774 ADAM23 0 . GRCh38 2 206609929 206609929 + Silent SNP C C G novel C3N-00737_T C3N-00737_N C C c.2379C>G p.= p.L793L ENST00000264377 25/26 222 166 56 237 237 0 strelka-varscan-mutect ADAM23,synonymous_variant,p.=,ENST00000264377,NM_003812.3;ADAM23,intron_variant,,ENST00000374415,;ADAM23,intron_variant,,ENST00000444281,;AC010731.2,upstream_gene_variant,,ENST00000415275,; G ENST00000264377 Transcript synonymous_variant 2707/6330 2379/2499 793/832 L ctC/ctG 1 1 ADAM23 HGNC HGNC:202 protein_coding YES CCDS2369.1 ENSP00000264377 O75077 A0A024R3W8 UPI0000044543 NM_003812.3 25/26 Low_complexity_(Seg):seg,hmmpanther:PTHR11905:SF13,hmmpanther:PTHR11905 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 206609929 206609929 C G 1 0 0 0 0 0 0 0 1 289 813 29 4 4 ADAM23 2 206609929 Silent SNP C C3N-00737_T 298349 206609929 35583600 34 19775 EPHA4 0 . GRCh38 2 221430045 221430045 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.2603G>A p.Arg868Lys p.R868K ENST00000281821 15/18 309 234 75 265 265 0 strelka-varscan-mutect EPHA4,missense_variant,p.Arg868Lys,ENST00000281821,NM_001304536.1,NM_001304537.1,NM_004438.4;EPHA4,missense_variant,p.Arg868Lys,ENST00000409854,;EPHA4,missense_variant,p.Arg868Lys,ENST00000409938,;EPHA4,upstream_gene_variant,,ENST00000469354,;EPHA4,upstream_gene_variant,,ENST00000472696,;EPHA4,intron_variant,,ENST00000424339,; T ENST00000281821 Transcript missense_variant 2645/6346 2603/2961 868/986 R/K aGg/aAg 1 -1 EPHA4 HGNC HGNC:3388 protein_coding YES CCDS2447.1 ENSP00000281821 P54764 A0A024R452 UPI000012A077 NM_001304536.1,NM_001304537.1,NM_004438.4 deleterious(0) 15/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF337,hmmpanther:PTHR24416,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Gene3D:1.10.510.10,SMART_domains:SM00220,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 221430045 221430045 C T 1 0 0 0 0 1 0 0 0 5016 681 24 3 3 EPHA4 2 221430045 Missense_Mutation SNP C C3N-00737_T 14820116 221430045 20763484 35 19776 COL6A3 0 . GRCh38 2 237345187 237345187 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.7119C>T p.= p.S2373S ENST00000295550 33/44 486 365 121 468 467 1 strelka-varscan-mutect COL6A3,synonymous_variant,p.=,ENST00000295550,NM_004369.3;COL6A3,synonymous_variant,p.=,ENST00000353578,NM_057167.3;COL6A3,synonymous_variant,p.=,ENST00000409809,;COL6A3,synonymous_variant,p.=,ENST00000472056,NM_057166.4;COL6A3,synonymous_variant,p.=,ENST00000347401,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;COL6A3,upstream_gene_variant,,ENST00000468792,; A ENST00000295550 Transcript synonymous_variant 7572/10749 7119/9534 2373/3177 S tcC/tcT 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 33/44 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 237345187 237345187 G A 1 0 0 0 0 0 0 0 1 3490 1335 47 3 3 COL6A3 2 237345187 Silent SNP G C3N-00737_T 15915142 237345187 4848342 36 19777 TATDN2 0 . GRCh38 3 10260410 10260410 + Missense_Mutation SNP C C G rs370249364 C3N-00737_T C3N-00737_N C C c.688C>G p.Pro230Ala p.P230A ENST00000287652 3/8 491 366 125 467 467 0 strelka-varscan-mutect TATDN2,missense_variant,p.Pro230Ala,ENST00000287652,NM_014760.3;TATDN2,missense_variant,p.Pro230Ala,ENST00000448281,;RP11-438J1.1,missense_variant,p.Pro173Ala,ENST00000437082,;RP11-438J1.1,3_prime_UTR_variant,,ENST00000450534,; G ENST00000287652 Transcript missense_variant 1739/5342 688/2286 230/761 P/A Cca/Gca rs370249364 1 1 TATDN2 HGNC HGNC:28988 protein_coding YES CCDS33698.1 ENSP00000287652 Q93075 A0A024R2F3 UPI000013DEC1 NM_014760.3 tolerated(0.26) 3/8 MODERATE 1 SNV 1 1 PASS rs370249364 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 10260410 10260410 C G 1 0 0 0 0 1 0 0 0 15991 507 18 4 4 TATDN2 3 10260410 Missense_Mutation SNP C C3N-00737_T 10260410 188035149 37 19778 TRIM71 0 . GRCh38 3 32818458 32818458 + Silent SNP T T G novel C3N-00737_T C3N-00737_N T T c.378T>G p.= p.T126T ENST00000383763 1/4 390 349 41 320 316 4 strelka-varscan-mutect TRIM71,synonymous_variant,p.=,ENST00000383763,NM_001039111.1; G ENST00000383763 Transcript synonymous_variant 441/8685 378/2607 126/868 T acT/acG 1 1 TRIM71 HGNC HGNC:32669 protein_coding YES CCDS43060.1 ENSP00000373272 Q2Q1W2 UPI000067CB89 NM_001039111.1 1/4 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF359 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 32818458 32818458 T G 1 0 0 0 0 0 0 0 1 17040 1567 55 5 5 TRIM71 3 32818458 Silent SNP T C3N-00737_T 22558048 32818458 165477101 38 19779 LMOD3 0 . GRCh38 3 69118791 69118792 + Frame_Shift_Ins INS - - T novel C3N-00737_T C3N-00737_N - - c.1563_1564insA p.Pro522ThrfsTer30 p.P522Tfs*30 ENST00000420581 2/3 198 180 18 161 160 1 varindel-pindel LMOD3,frameshift_variant,p.Pro522ThrfsTer30,ENST00000420581,;LMOD3,frameshift_variant,p.Pro522ThrfsTer30,ENST00000475434,;LMOD3,frameshift_variant,p.Pro522ThrfsTer30,ENST00000489031,NM_001304418.1,NM_198271.4; T ENST00000420581 Transcript frameshift_variant 1743-1744/4086 1563-1564/1683 521-522/560 -/X -/A 1 -1 LMOD3 HGNC HGNC:6649 protein_coding YES CCDS46862.1 ENSP00000414670 Q0VAK6 UPI00001612AC 2/3 hmmpanther:PTHR10901:SF3,hmmpanther:PTHR10901 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 63 69118791 69118791 - T 1 0 1 1 0 0 0 0 0 8785 1203 42 0 0 LMOD3 3 69118791 Frame_Shift_Ins INS - C3N-00737_T 36300333 69118791 129176768 39 19780 OR5H2 0 . GRCh38 3 98283180 98283180 + Missense_Mutation SNP C C T C3N-00737_T C3N-00737_N C C c.293C>T p.Ser98Phe p.S98F ENST00000355273 1/1 379 330 49 359 358 1 strelka-varscan-mutect OR5H2,missense_variant,p.Ser98Phe,ENST00000355273,NM_001005482.1;RP11-325B23.2,intron_variant,,ENST00000508616,; T ENST00000355273 Transcript missense_variant 293/945 293/945 98/314 S/F tCt/tTt COSM1049177 1 1 OR5H2 HGNC HGNC:14752 protein_coding YES CCDS33801.1 ENSP00000347418 Q8NGV7 UPI0000041B67 NM_001005482.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF231,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 98283180 98283180 C T 1 0 0 0 0 1 0 0 0 11232 913 32 3 3 OR5H2 3 98283180 Missense_Mutation SNP C C3N-00737_T 29164389 98283180 100012379 40 19781 GPR156 0 . GRCh38 3 120167238 120167238 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.2239G>A p.Glu747Lys p.E747K ENST00000464295 10/10 249 224 25 192 190 2 strelka-varscan-mutect GPR156,missense_variant,p.Glu747Lys,ENST00000464295,;GPR156,missense_variant,p.Glu747Lys,ENST00000315843,NM_153002.2;GPR156,missense_variant,p.Glu743Lys,ENST00000461057,NM_001168271.1;GPR156,3_prime_UTR_variant,,ENST00000495912,; T ENST00000464295 Transcript missense_variant 2685/4442 2239/2445 747/814 E/K Gag/Aag 1 -1 GPR156 HGNC HGNC:20844 protein_coding YES CCDS2997.1 ENSP00000417261 Q8NFN8 UPI000004731C deleterious(0.04) 10/10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 120167238 120167238 C T 1 0 0 0 0 1 0 0 0 6547 835 29 3 3 GPR156 3 120167238 Missense_Mutation SNP C C3N-00737_T 21884058 120167238 78128321 41 19782 GPR156 0 . GRCh38 3 120243723 120243723 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.150G>T p.Leu50Phe p.L50F ENST00000464295 3/10 305 235 70 242 241 1 strelka-varscan-mutect GPR156,missense_variant,p.Leu50Phe,ENST00000464295,;GPR156,missense_variant,p.Leu50Phe,ENST00000315843,NM_153002.2;GPR156,missense_variant,p.Leu50Phe,ENST00000461057,NM_001168271.1;GPR156,missense_variant,p.Leu50Phe,ENST00000495912,;GPR156,non_coding_transcript_exon_variant,,ENST00000481907,; A ENST00000464295 Transcript missense_variant 596/4442 150/2445 50/814 L/F ttG/ttT 1 -1 GPR156 HGNC HGNC:20844 protein_coding YES CCDS2997.1 ENSP00000417261 Q8NFN8 UPI000004731C deleterious(0.01) 3/10 Prints_domain:PR01176,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF20,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 120243723 120243723 C A 1 0 0 0 0 1 0 0 0 6547 593 21 2 2 GPR156 3 120243723 Missense_Mutation SNP C C3N-00737_T 76485 120243723 78051836 42 19783 HSPBAP1 0 . GRCh38 3 122741042 122741042 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.897G>C p.Glu299Asp p.E299D ENST00000306103 7/8 413 349 64 310 310 0 strelka-varscan-mutect HSPBAP1,missense_variant,p.Glu299Asp,ENST00000306103,NM_024610.5;HSPBAP1,non_coding_transcript_exon_variant,,ENST00000471534,; G ENST00000306103 Transcript missense_variant 1041/1953 897/1467 299/488 E/D gaG/gaC 1 -1 HSPBAP1 HGNC HGNC:16389 protein_coding YES CCDS3017.1 ENSP00000302562 Q96EW2 UPI00000715E9 NM_024610.5 tolerated(0.21) 7/8 hmmpanther:PTHR12461,hmmpanther:PTHR12461:SF43,Superfamily_domains:SSF51197,Prints_domain:PR01886 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 122741042 122741042 C G 1 0 0 0 0 1 0 0 0 7322 912 32 4 4 HSPBAP1 3 122741042 Missense_Mutation SNP C C3N-00737_T 2497319 122741042 75554517 43 19784 IFT122 0 . GRCh38 3 129481668 129481668 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.1780A>G p.Ile594Val p.I594V ENST00000296266 15/31 453 409 44 296 296 0 varscan-mutect IFT122,missense_variant,p.Ile393Val,ENST00000431818,NM_001280545.1;IFT122,missense_variant,p.Ile594Val,ENST00000296266,NM_052985.3;IFT122,missense_variant,p.Ile334Val,ENST00000440957,NM_001280546.1;IFT122,missense_variant,p.Ile543Val,ENST00000348417,NM_052989.2;IFT122,missense_variant,p.Ile484Val,ENST00000347300,NM_018262.3;IFT122,missense_variant,p.Ile535Val,ENST00000507564,NM_001280541.1;IFT122,missense_variant,p.Ile432Val,ENST00000349441,NM_052990.2;IFT122,missense_variant,p.Ile437Val,ENST00000504021,;IFT122,missense_variant,p.Ile58Val,ENST00000509522,;IFT122,downstream_gene_variant,,ENST00000515783,;IFT122,downstream_gene_variant,,ENST00000512157,;IFT122,3_prime_UTR_variant,,ENST00000512220,;IFT122,non_coding_transcript_exon_variant,,ENST00000506507,;IFT122,non_coding_transcript_exon_variant,,ENST00000513891,;IFT122,non_coding_transcript_exon_variant,,ENST00000448668,;IFT122,non_coding_transcript_exon_variant,,ENST00000512814,;IFT122,downstream_gene_variant,,ENST00000508654,; G ENST00000296266 Transcript missense_variant 1972/4151 1780/3879 594/1292 I/V Atc/Gtc 1 1 IFT122 HGNC HGNC:13556 protein_coding YES CCDS3060.1 ENSP00000296266 Q9HBG6 UPI0000141042 NM_052985.3 tolerated(0.17) 15/31 Gene3D:2.130.10.10,hmmpanther:PTHR12764,hmmpanther:PTHR12764:SF4,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 129481668 129481668 A G 1 0 0 0 0 1 0 0 0 7459 217 8 5 5 IFT122 3 129481668 Missense_Mutation SNP A C3N-00737_T 6740626 129481668 68813891 44 19785 TMCC1 0 . GRCh38 3 129670728 129670728 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.1113G>C p.Glu371Asp p.E371D ENST00000393238 4/6 266 221 45 234 234 0 strelka-varscan-mutect TMCC1,missense_variant,p.Glu371Asp,ENST00000393238,NM_001017395.3;TMCC1,missense_variant,p.Glu47Asp,ENST00000432054,;TMCC1,missense_variant,p.Glu257Asp,ENST00000426664,NM_001128224.2;TMCC1,downstream_gene_variant,,ENST00000505616,; G ENST00000393238 Transcript missense_variant 1454/5992 1113/1962 371/653 E/D gaG/gaC 1 -1 TMCC1 HGNC HGNC:29116 protein_coding YES CCDS33855.1 ENSP00000376930 O94876 UPI0000197B80 NM_001017395.3 tolerated(0.08) 4/6 Pfam_domain:PF10267,hmmpanther:PTHR17613,hmmpanther:PTHR17613:SF11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 129670728 129670728 C G 1 0 0 0 0 1 0 0 0 16438 912 32 4 4 TMCC1 3 129670728 Missense_Mutation SNP C C3N-00737_T 189060 129670728 68624831 45 19786 RASA2 0 . GRCh38 3 141512189 141512189 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.160C>A p.Leu54Ile p.L54I ENST00000286364 2/24 289 248 41 270 269 1 strelka-varscan-mutect RASA2,missense_variant,p.Leu54Ile,ENST00000286364,NM_001303246.1,NM_001303245.1,NM_006506.3;RASA2,missense_variant,p.Leu54Ile,ENST00000452898,;RASA2,synonymous_variant,p.=,ENST00000515549,; A ENST00000286364 Transcript missense_variant 195/5614 160/2550 54/849 L/I Ctt/Att 1 1 RASA2 HGNC HGNC:9872 protein_coding YES CCDS3117.1 ENSP00000286364 Q15283 UPI00001351F5 NM_001303246.1,NM_001303245.1,NM_006506.3 tolerated(0.41) 2/24 PROSITE_profiles:PS50004,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF21,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 141512189 141512189 C A 1 0 0 0 0 1 0 0 0 13220 913 32 2 2 RASA2 3 141512189 Missense_Mutation SNP C C3N-00737_T 11841461 141512189 56783370 46 19787 GRK7 0 . GRCh38 3 141778405 141778405 + Missense_Mutation SNP G G T C3N-00737_T C3N-00737_N G G c.121G>T p.Gly41Trp p.G41W ENST00000264952 1/4 328 303 25 170 170 0 strelka-varscan-mutect GRK7,missense_variant,p.Gly41Trp,ENST00000264952,NM_139209.2; T ENST00000264952 Transcript missense_variant 258/3239 121/1662 41/553 G/W Ggg/Tgg COSM3781094 1 1 GRK7 HGNC HGNC:17031 protein_coding YES CCDS3120.1 ENSP00000264952 Q8WTQ7 UPI000004244D NM_139209.2 deleterious(0.01) 1/4 hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF12,Superfamily_domains:SSF48097 1 MODERATE 1 SNV 1 1 1 PASS rs1475883464 . 0 208 0 2 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 63 141778405 141778405 G T 1 0 0 0 0 1 0 0 0 6677 1116 39 1 1 GRK7 3 141778405 Missense_Mutation SNP G C3N-00737_T 266216 141778405 56517154 47 19788 ATR 0 . GRCh38 3 142453145 142453145 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.7744G>C p.Glu2582Gln p.E2582Q ENST00000350721 46/47 348 309 39 253 253 0 strelka-varscan-mutect ATR,missense_variant,p.Glu2582Gln,ENST00000350721,NM_001184.3;ATR,missense_variant,p.Glu429Gln,ENST00000513291,;ATR,missense_variant,p.Glu66Gln,ENST00000504521,;ATR,missense_variant,p.Glu8Gln,ENST00000515810,;ATR,non_coding_transcript_exon_variant,,ENST00000511016,;RP11-383G6.4,downstream_gene_variant,,ENST00000481134,; G ENST00000350721 Transcript missense_variant 7866/8249 7744/7935 2582/2644 E/Q Gaa/Caa 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious(0) 46/47 Gene3D:1.10.1070.11,PROSITE_profiles:PS50290,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69,SMART_domains:SM00146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 142453145 142453145 C G 1 0 0 0 0 1 0 0 0 1356 922 32 4 4 ATR 3 142453145 Missense_Mutation SNP C C3N-00737_T 674740 142453145 55842414 48 19789 SUCNR1 0 . GRCh38 3 151881319 151881319 + Missense_Mutation SNP G G T rs770883727 C3N-00737_T C3N-00737_N G G c.776G>T p.Arg259Leu p.R259L ENST00000362032 3/3 357 284 73 265 265 0 strelka-varscan-mutect SUCNR1,missense_variant,p.Arg259Leu,ENST00000362032,NM_033050.4;AADACL2-AS1,intron_variant,,ENST00000483843,;AADACL2-AS1,intron_variant,,ENST00000475855,; T ENST00000362032 Transcript missense_variant 881/4181 776/1005 259/334 R/L cGc/cTc rs770883727 1 1 SUCNR1 HGNC HGNC:4542 protein_coding YES CCDS3162.1 ENSP00000355156 Q9BXA5 UPI0000072507 NM_033050.4 deleterious(0) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF14,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs770883727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 151881319 151881319 G T 1 0 0 0 0 1 0 0 0 15750 1087 38 1 1 SUCNR1 3 151881319 Missense_Mutation SNP G C3N-00737_T 9428174 151881319 46414240 49 19790 PLCH1 0 . GRCh38 3 155482773 155482773 + Missense_Mutation SNP C C A rs74737650 C3N-00737_T C3N-00737_N C C c.3277G>T p.Asp1093Tyr p.D1093Y ENST00000340059 23/23 434 373 61 332 332 0 strelka-varscan-mutect PLCH1,missense_variant,p.Asp1055Tyr,ENST00000460012,;PLCH1,missense_variant,p.Asp1093Tyr,ENST00000340059,NM_001130960.1;PLCH1,missense_variant,p.Asp1055Tyr,ENST00000334686,NM_014996.2;PLCH1,3_prime_UTR_variant,,ENST00000447496,NM_001130961.1;PLCH1,intron_variant,,ENST00000494598,;PLCH1-AS2,upstream_gene_variant,,ENST00000472913,; A ENST00000340059 Transcript missense_variant 3277/6168 3277/5082 1093/1693 D/Y Gat/Tat rs74737650 1 -1 PLCH1 HGNC HGNC:29185 protein_coding YES CCDS46939.1 ENSP00000345988 Q4KWH8 UPI00001D800E NM_001130960.1 deleterious_low_confidence(0) 23/23 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF51 MODERATE 1 SNV 1 1 PASS rs74737650 . 0 172 0 0 0 0 0 38 -3.866648 0 0 1 0 0 A 3 1 63 155482773 155482773 C A 1 0 0 0 0 1 0 0 0 12131 884 31 1 1 PLCH1 3 155482773 Missense_Mutation SNP C C3N-00737_T 3601454 155482773 42812786 50 19791 MFN1 0 . GRCh38 3 179378422 179378422 + Nonsense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.1411C>T p.Gln471Ter p.Q471* ENST00000471841 13/18 85 73 12 95 95 0 strelka-varscan-mutect MFN1,stop_gained,p.Gln471Ter,ENST00000471841,NM_033540.2;MFN1,stop_gained,p.Gln471Ter,ENST00000263969,;MFN1,intron_variant,,ENST00000474903,;MFN1,3_prime_UTR_variant,,ENST00000357390,;MFN1,non_coding_transcript_exon_variant,,ENST00000480636,;MFN1,non_coding_transcript_exon_variant,,ENST00000482661,;MFN1,downstream_gene_variant,,ENST00000466287,; T ENST00000471841 Transcript stop_gained 1537/5224 1411/2226 471/741 Q/* Cag/Tag 1 1 MFN1 HGNC HGNC:18262 protein_coding YES CCDS3228.1 ENSP00000420617 A0A0C4DFN1 UPI0000074528 NM_033540.2 13/18 hmmpanther:PTHR10465,hmmpanther:PTHR10465:SF2 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 63 179378422 179378422 C T 1 0 0 0 0 0 1 0 0 9475 827 29 3 3 MFN1 3 179378422 Nonsense_Mutation SNP C C3N-00737_T 23895649 179378422 18917137 51 19792 EIF2B5 0 . GRCh38 3 184142594 184142594 + Missense_Mutation SNP A A T novel C3N-00737_T C3N-00737_N A A c.1537A>T p.Asn513Tyr p.N513Y ENST00000273783 10/16 628 576 52 462 462 0 strelka-varscan EIF2B5,missense_variant,p.Asn513Tyr,ENST00000273783,NM_003907.2;EIF2B5,non_coding_transcript_exon_variant,,ENST00000492773,;EIF2B5,downstream_gene_variant,,ENST00000498831,;EIF2B5,downstream_gene_variant,,ENST00000479833,;EIF2B5,3_prime_UTR_variant,,ENST00000432982,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000481054,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000491144,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000465218,;EIF2B5,non_coding_transcript_exon_variant,,ENST00000479250,;EIF2B5,downstream_gene_variant,,ENST00000491008,;EIF2B5,downstream_gene_variant,,ENST00000468748,;EIF2B5,downstream_gene_variant,,ENST00000493740,;EIF2B5,upstream_gene_variant,,ENST00000492226,;EIF2B5,upstream_gene_variant,,ENST00000484154,; T ENST00000273783 Transcript missense_variant 1659/2655 1537/2166 513/721 N/Y Aat/Tat 1 1 EIF2B5 HGNC HGNC:3261 protein_coding YES CCDS3252.1 ENSP00000273783 Q13144 UPI000013D9CF NM_003907.2 tolerated(0.05) 10/16 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 184142594 184142594 A T 1 0 0 0 0 1 0 0 0 4840 246 9 4 4 EIF2B5 3 184142594 Missense_Mutation SNP A C3N-00737_T 4764172 184142594 14152965 52 19793 EIF4G1 0 . GRCh38 3 184324303 184324303 + Nonsense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.2596G>T p.Glu866Ter p.E866* ENST00000424196 16/32 721 568 153 574 573 1 strelka-varscan EIF4G1,stop_gained,p.Glu860Ter,ENST00000342981,NM_182917.4;EIF4G1,stop_gained,p.Glu866Ter,ENST00000424196,;EIF4G1,stop_gained,p.Glu819Ter,ENST00000414031,NM_001291157.1;EIF4G1,stop_gained,p.Glu859Ter,ENST00000346169,NM_198241.2;EIF4G1,stop_gained,p.Glu866Ter,ENST00000352767,NM_001194947.1;EIF4G1,stop_gained,p.Glu772Ter,ENST00000392537,NM_198244.2;EIF4G1,stop_gained,p.Glu866Ter,ENST00000382330,NM_001194946.1;EIF4G1,stop_gained,p.Glu773Ter,ENST00000427845,;EIF4G1,stop_gained,p.Glu664Ter,ENST00000434061,NM_004953.4;EIF4G1,stop_gained,p.Glu695Ter,ENST00000350481,NM_198242.2;EIF4G1,stop_gained,p.Glu820Ter,ENST00000411531,;EIF4G1,stop_gained,p.Glu663Ter,ENST00000435046,;EIF4G1,stop_gained,p.Glu696Ter,ENST00000441154,;EIF4G1,stop_gained,p.Glu800Ter,ENST00000426123,;EIF4G1,stop_gained,p.Glu867Ter,ENST00000421110,;EIF4G1,stop_gained,p.Glu695Ter,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;EIF4G1,downstream_gene_variant,,ENST00000427141,;EIF4G1,downstream_gene_variant,,ENST00000456033,;EIF4G1,upstream_gene_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000440448,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000428387,;SNORD66,upstream_gene_variant,,ENST00000390856,;EIF4G1,3_prime_UTR_variant,,ENST00000442406,;EIF4G1,3_prime_UTR_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,upstream_gene_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000493299,;EIF4G1,upstream_gene_variant,,ENST00000482303,; T ENST00000424196 Transcript stop_gained 2985/5653 2596/4821 866/1606 E/* Gag/Tag 1 1 EIF4G1 HGNC HGNC:3296 protein_coding YES CCDS54687.1 ENSP00000416255 Q04637 UPI00015E0966 16/32 Gene3D:1.25.40.180,Pfam_domain:PF02854,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF10,Low_complexity_(Seg):seg,SMART_domains:SM00543,Superfamily_domains:SSF48371 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 63 184324303 184324303 G T 1 0 0 0 0 0 1 0 0 4870 1291 45 2 2 EIF4G1 3 184324303 Nonsense_Mutation SNP G C3N-00737_T 181709 184324303 13971256 53 19794 MB21D2 0 . GRCh38 3 192798744 192798744 + Missense_Mutation SNP A A C novel C3N-00737_T C3N-00737_N A A c.1118T>G p.Met373Arg p.M373R ENST00000392452 2/2 180 146 34 156 156 0 strelka-varscan MB21D2,missense_variant,p.Met373Arg,ENST00000392452,NM_178496.3; C ENST00000392452 Transcript missense_variant 1439/3368 1118/1476 373/491 M/R aTg/aGg 1 -1 MB21D2 HGNC HGNC:30438 protein_coding YES CCDS3302.2 ENSP00000376246 Q8IYB1 UPI000013FAFE NM_178496.3 tolerated(0.07) 2/2 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF47,Pfam_domain:PF03281,SMART_domains:SM01265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 192798744 192798744 A C 1 0 0 0 0 1 0 0 0 9270 217 8 5 5 MB21D2 3 192798744 Missense_Mutation SNP A C3N-00737_T 8474441 192798744 5496815 54 19795 CEP135 0 . GRCh38 4 56011816 56011816 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.2633A>G p.Asp878Gly p.D878G ENST00000257287 21/26 71 59 12 81 81 0 strelka-varscan-mutect CEP135,missense_variant,p.Asp878Gly,ENST00000257287,NM_025009.4;CEP135,non_coding_transcript_exon_variant,,ENST00000506202,; G ENST00000257287 Transcript missense_variant 2757/5562 2633/3423 878/1140 D/G gAt/gGt 1 1 CEP135 HGNC HGNC:29086 protein_coding YES CCDS33986.1 ENSP00000257287 Q66GS9 UPI00003CE420 NM_025009.4 tolerated(0.07) 21/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF18 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 56011816 56011816 A G 1 0 0 0 0 1 0 0 0 2960 333 12 5 5 CEP135 4 56011816 Missense_Mutation SNP A C3N-00737_T 56011816 134202739 55 19796 ANK2 0 . GRCh38 4 113277887 113277887 + Silent SNP G G T novel C3N-00737_T C3N-00737_N G G c.1734G>T p.= p.V578V ENST00000357077 16/46 440 383 57 480 480 0 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000506722,NM_001127493.1;ANK2,synonymous_variant,p.=,ENST00000394537,NM_020977.3;ANK2,synonymous_variant,p.=,ENST00000504454,;ANK2,synonymous_variant,p.=,ENST00000503423,;ANK2,synonymous_variant,p.=,ENST00000634436,;ANK2,synonymous_variant,p.=,ENST00000503271,; T ENST00000357077 Transcript synonymous_variant 1787/14196 1734/11874 578/3957 V gtG/gtT 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 16/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 113277887 113277887 G T 1 0 0 0 0 0 0 0 1 721 1335 47 2 2 ANK2 4 113277887 Silent SNP G C3N-00737_T 57266071 113277887 76936668 56 19797 FAT4 0 . GRCh38 4 125491001 125491001 + Missense_Mutation SNP G G A C3N-00737_T C3N-00737_N G G c.14179G>A p.Asp4727Asn p.D4727N ENST00000394329 17/17 419 381 38 313 313 0 strelka-varscan-mutect FAT4,missense_variant,p.Asp4727Asn,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Asp2968Asn,ENST00000335110,; A ENST00000394329 Transcript missense_variant 14192/16123 14179/14946 4727/4981 D/N Gat/Aat COSM3917146,COSM3917147 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.02) 17/17 hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 125491001 125491001 G A 1 0 0 0 0 1 0 0 0 5552 1174 41 3 3 FAT4 4 125491001 Missense_Mutation SNP G C3N-00737_T 12213114 125491001 64723554 57 19798 INTU 0 . GRCh38 4 127705735 127705735 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.1711C>T p.Leu571Phe p.L571F ENST00000335251 11/16 614 566 48 457 456 1 strelka-varscan-mutect INTU,missense_variant,p.Leu571Phe,ENST00000335251,NM_015693.3;INTU,missense_variant,p.Leu85Phe,ENST00000506283,;INTU,non_coding_transcript_exon_variant,,ENST00000512995,;INTU,3_prime_UTR_variant,,ENST00000503626,;INTU,3_prime_UTR_variant,,ENST00000503952,;INTU,upstream_gene_variant,,ENST00000510766,; T ENST00000335251 Transcript missense_variant 1814/13233 1711/2829 571/942 L/F Ctc/Ttc 1 1 INTU HGNC HGNC:29239 protein_coding YES CCDS34061.1 ENSP00000334003 Q9ULD6 UPI00001C1E05 NM_015693.3 tolerated(0.23) 11/16 hmmpanther:PTHR21082:SF4,hmmpanther:PTHR21082 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 127705735 127705735 C T 1 0 0 0 0 1 0 0 0 7689 681 24 3 3 INTU 4 127705735 Missense_Mutation SNP C C3N-00737_T 2214734 127705735 62508820 58 19799 NEIL3 0 . GRCh38 4 177310062 177310062 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.109G>C p.Gly37Arg p.G37R ENST00000264596 1/10 143 129 14 110 110 0 strelka-varscan-mutect NEIL3,missense_variant,p.Gly37Arg,ENST00000264596,NM_018248.2;NEIL3,missense_variant,p.Gly37Arg,ENST00000513321,; C ENST00000264596 Transcript missense_variant 227/2408 109/1818 37/605 G/R Ggc/Cgc 1 1 NEIL3 HGNC HGNC:24573 protein_coding YES CCDS3828.1 ENSP00000264596 Q8TAT5 UPI000013D53D NM_018248.2 tolerated(0.23) 1/10 PROSITE_profiles:PS51068,hmmpanther:PTHR22993,hmmpanther:PTHR22993:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 177310062 177310062 G C 1 0 0 0 0 1 0 0 0 10348 1232 43 4 4 NEIL3 4 177310062 Missense_Mutation SNP G C3N-00737_T 49604327 177310062 12904493 59 19800 TERT 0 . GRCh38 5 1294370 1294370 + Silent SNP C C G novel C3N-00737_T C3N-00737_N C C c.516G>C p.= p.G172G ENST00000310581 2/16 337 308 29 246 245 1 strelka-varscan-mutect TERT,synonymous_variant,p.=,ENST00000310581,NM_198253.2;TERT,synonymous_variant,p.=,ENST00000334602,NM_001193376.1;TERT,synonymous_variant,p.=,ENST00000508104,;TERT,downstream_gene_variant,,ENST00000522877,;TERT,synonymous_variant,p.=,ENST00000460137,; G ENST00000310581 Transcript synonymous_variant 574/4018 516/3399 172/1132 G ggG/ggC 1 -1 TERT HGNC HGNC:11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 UPI0000031309 NM_198253.2 2/16 hmmpanther:PTHR12066,hmmpanther:PTHR12066:SF0 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 1294370 1294370 C G 1 0 0 0 0 0 0 0 1 16183 726 26 4 4 TERT 5 1294370 Silent SNP C C3N-00737_T 1294370 180243889 60 19801 PDE8B 0 . GRCh38 5 77419777 77419777 + Missense_Mutation SNP C C G C3N-00737_T C3N-00737_N C C c.2140C>G p.Arg714Gly p.R714G ENST00000264917 19/22 510 456 54 444 444 0 strelka-varscan-mutect PDE8B,missense_variant,p.Arg714Gly,ENST00000264917,NM_003719.3;PDE8B,missense_variant,p.Arg179Gly,ENST00000505283,;PDE8B,missense_variant,p.Arg667Gly,ENST00000340978,NM_001029854.2;PDE8B,missense_variant,p.Arg617Gly,ENST00000346042,NM_001029851.2;PDE8B,missense_variant,p.Arg694Gly,ENST00000342343,NM_001029853.2;PDE8B,missense_variant,p.Arg659Gly,ENST00000333194,NM_001029852.2; G ENST00000264917 Transcript missense_variant 2185/5956 2140/2658 714/885 R/G Cga/Gga COSM1220036 1 1 PDE8B HGNC HGNC:8794 protein_coding YES CCDS4037.1 ENSP00000264917 O95263 UPI0000001BBE NM_003719.3 deleterious(0) 19/22 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF98,SMART_domains:SM00471,Superfamily_domains:SSF109604 1 MODERATE 1 SNV 1 1 1 PASS rs1346301868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 77419777 77419777 C G 1 0 0 0 0 1 0 0 0 11742 876 31 4 4 PDE8B 5 77419777 Missense_Mutation SNP C C3N-00737_T 76125407 77419777 104118482 61 19802 PCDHA11 0 . GRCh38 5 140869794 140869794 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.691C>A p.Gln231Lys p.Q231K ENST00000398640 1/4 167 119 48 196 196 0 strelka-varscan-mutect PCDHA11,missense_variant,p.Gln231Lys,ENST00000398640,NM_018902.4;PCDHA11,missense_variant,p.Gln231Lys,ENST00000616325,NM_031861.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA10,downstream_gene_variant,,ENST00000562220,NM_031859.2;PCDHA11,upstream_gene_variant,,ENST00000617408,;AC005609.20,upstream_gene_variant,,ENST00000625071,; A ENST00000398640 Transcript missense_variant 1549/6115 691/2850 231/949 Q/K Caa/Aaa 1 1 PCDHA11 HGNC HGNC:8665 protein_coding YES CCDS47284.1 ENSP00000381636 Q9Y5I1 UPI00001273D4 NM_018902.4 tolerated_low_confidence(0.22) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF68,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 140869794 140869794 C A 1 0 0 0 0 1 0 0 0 11608 595 21 2 2 PCDHA11 5 140869794 Missense_Mutation SNP C C3N-00737_T 63450017 140869794 40668465 62 19803 PCDHB12 0 . GRCh38 5 141208978 141208978 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.71C>A p.Ser24Tyr p.S24Y ENST00000239450 1/1 50 39 11 65 65 0 strelka-varscan-mutect PCDHB12,missense_variant,p.Ser24Tyr,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Ser24Tyr,ENST00000622978,;PCDHB12,intron_variant,,ENST00000624949,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239450 Transcript missense_variant 260/3853 71/2388 24/795 S/Y tCt/tAt 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 tolerated_low_confidence(0.32) 1/1 hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999814 1 1 1 0 A 3 1 63 141208978 141208978 C A 1 0 0 0 0 1 0 0 0 11624 913 32 2 2 PCDHB12 5 141208978 Missense_Mutation SNP C C3N-00737_T 339184 141208978 40329281 63 19804 PCDHGB5 0 . GRCh38 5 141400077 141400077 + Silent SNP C C G novel C3N-00737_T C3N-00737_N C C c.1950C>G p.= p.L650L ENST00000617380 1/4 237 189 48 240 240 0 strelka-varscan-mutect PCDHGB5,synonymous_variant,p.=,ENST00000617380,NM_018925.2;PCDHGB5,synonymous_variant,p.=,ENST00000621169,NM_032099.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGA8,downstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA9,upstream_gene_variant,,ENST00000573521,NM_018921.2;PCDHGA9,upstream_gene_variant,,ENST00000616887,NM_032089.1;PCDHGA3,intron_variant,,ENST00000612467,; G ENST00000617380 Transcript synonymous_variant 1950/4578 1950/2772 650/923 L ctC/ctG 1 1 PCDHGB5 HGNC HGNC:8712 protein_coding YES CCDS75339.1 ENSP00000478258 Q9Y5G0 UPI000007279C NM_018925.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF126,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 141400077 141400077 C G 1 0 0 0 0 0 0 0 1 11653 900 32 4 4 PCDHGB5 5 141400077 Silent SNP C C3N-00737_T 191099 141400077 40138182 64 19805 CCHCR1 0 . GRCh38 6 31150159 31150159 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.1269G>A p.= p.L423L ENST00000396268 8/18 344 314 30 254 254 0 strelka-varscan-mutect CCHCR1,synonymous_variant,p.=,ENST00000396268,NM_001105564.1;CCHCR1,synonymous_variant,p.=,ENST00000376266,NM_019052.3;CCHCR1,synonymous_variant,p.=,ENST00000451521,NM_001105563.1;CCHCR1,synonymous_variant,p.=,ENST00000396263,;CCHCR1,downstream_gene_variant,,ENST00000426967,;CCHCR1,downstream_gene_variant,,ENST00000448162,;CCHCR1,downstream_gene_variant,,ENST00000455279,;CCHCR1,downstream_gene_variant,,ENST00000448141,;CCHCR1,downstream_gene_variant,,ENST00000502557,;CCHCR1,downstream_gene_variant,,ENST00000507829,;CCHCR1,downstream_gene_variant,,ENST00000507751,;CCHCR1,downstream_gene_variant,,ENST00000503420,;CCHCR1,downstream_gene_variant,,ENST00000508683,;CCHCR1,downstream_gene_variant,,ENST00000503934,;CCHCR1,downstream_gene_variant,,ENST00000507226,;CCHCR1,downstream_gene_variant,,ENST00000513222,;CCHCR1,downstream_gene_variant,,ENST00000428174,;CCHCR1,intron_variant,,ENST00000480060,;CCHCR1,non_coding_transcript_exon_variant,,ENST00000509552,;CCHCR1,upstream_gene_variant,,ENST00000467553,;CCHCR1,downstream_gene_variant,,ENST00000508852,;CCHCR1,downstream_gene_variant,,ENST00000507459,;CCHCR1,downstream_gene_variant,,ENST00000512418,;CCHCR1,downstream_gene_variant,,ENST00000505392,;CCHCR1,downstream_gene_variant,,ENST00000464012,; T ENST00000396268 Transcript synonymous_variant 1458/2958 1269/2616 423/871 L ctG/ctA 1 -1 CCHCR1 HGNC HGNC:13930 protein_coding YES CCDS43445.1 ENSP00000379566 Q8TD31 UPI0000E5ACDF NM_001105564.1 8/18 Pfam_domain:PF07111,hmmpanther:PTHR23161,hmmpanther:PTHR23161:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 31150159 31150159 C T 1 0 0 0 0 0 0 0 1 2575 813 29 3 3 CCHCR1 6 31150159 Silent SNP C C3N-00737_T 31150159 139655820 65 19806 HSPA1L 0 . GRCh38 6 31811399 31811399 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.574C>G p.Gln192Glu p.Q192E ENST00000375654 2/2 403 361 42 402 402 0 strelka-varscan-mutect HSPA1L,missense_variant,p.Gln192Glu,ENST00000375654,NM_005527.3;HSPA1A,upstream_gene_variant,,ENST00000375651,NM_005345.5;HSPA1A,upstream_gene_variant,,ENST00000608703,;LSM2,upstream_gene_variant,,ENST00000375661,NM_021177.4;LSM2,upstream_gene_variant,,ENST00000491421,;LSM2,upstream_gene_variant,,ENST00000477182,;LSM2,upstream_gene_variant,,ENST00000493387,;LSM2,upstream_gene_variant,,ENST00000470086,;LSM2,upstream_gene_variant,,ENST00000470083,;LSM2,upstream_gene_variant,,ENST00000475835,; C ENST00000375654 Transcript missense_variant 764/2544 574/1926 192/641 Q/E Caa/Gaa 1 -1 HSPA1L HGNC HGNC:5234 protein_coding YES CCDS34413.1 ENSP00000364805 P34931 UPI000012CC97 NM_005527.3 tolerated_low_confidence(0.54) 2/2 hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF236,Pfam_domain:PF00012,Gene3D:3.30.420.40 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 31811399 31811399 G C 1 0 0 0 0 1 0 0 0 7306 1299 45 4 4 HSPA1L 6 31811399 Missense_Mutation SNP G C3N-00737_T 661240 31811399 138994580 66 19807 TNXB 0 . GRCh38 6 32058109 32058109 + Missense_Mutation SNP C C G rs767643312 C3N-00737_T C3N-00737_N C C c.7774G>C p.Gly2592Arg p.G2592R ENST00000375244 22/44 120 94 26 71 71 0 strelka-varscan-mutect TNXB,missense_variant,p.Gly2592Arg,ENST00000375244,NM_019105.6;TNXB,missense_variant,p.Gly312Arg,ENST00000611016,; G ENST00000375244 Transcript missense_variant 7976/13132 7774/12735 2592/4244 G/R Ggc/Cgc rs767643312,COSM4735233,COSM4735234 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 deleterious(0) 22/44 PROSITE_profiles:PS50853,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs767643312 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 32058109 32058109 C G 1 0 0 0 0 1 0 0 0 16820 652 23 4 4 TNXB 6 32058109 Missense_Mutation SNP C C3N-00737_T 246710 32058109 138747870 67 19808 TMEM217 0 . GRCh38 6 37218959 37218959 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.72G>A p.Met24Ile p.M24I ENST00000336655 2/4 201 177 24 190 190 0 strelka-varscan-mutect TMEM217,missense_variant,p.Met24Ile,ENST00000336655,NM_145316.3;TMEM217,missense_variant,p.Met24Ile,ENST00000356757,NM_001286401.1;TMEM217,intron_variant,,ENST00000497775,;TMEM217,intron_variant,,ENST00000478262,;TMEM217,upstream_gene_variant,,ENST00000482580,;TMEM217,non_coding_transcript_exon_variant,,ENST00000357219,; T ENST00000336655 Transcript missense_variant 112/1546 72/690 24/229 M/I atG/atA 1 -1 TMEM217 HGNC HGNC:21238 protein_coding YES CCDS4831.1 ENSP00000338164 Q8N7C4 UPI0000071695 NM_145316.3 tolerated(0.24) 2/4 Pfam_domain:PF15049,hmmpanther:PTHR34928,hmmpanther:PTHR34928:SF2,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 37218959 37218959 C T 1 0 0 0 0 1 0 0 0 16581 594 21 3 3 TMEM217 6 37218959 Missense_Mutation SNP C C3N-00737_T 5160850 37218959 133587020 68 19809 KCNK16 0 . GRCh38 6 39322530 39322530 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.11C>A p.Ala4Asp p.A4D ENST00000425054 1/5 100 76 24 99 99 0 strelka-varscan-mutect KCNK16,missense_variant,p.Ala4Asp,ENST00000425054,NM_001135105.1;KCNK16,missense_variant,p.Ala4Asp,ENST00000373229,NM_032115.3;KCNK16,missense_variant,p.Ala4Asp,ENST00000437525,NM_001135106.1;KCNK16,missense_variant,p.Ala4Asp,ENST00000373227,NM_001135107.1;KCNK16,intron_variant,,ENST00000507712,; T ENST00000425054 Transcript missense_variant 11/1272 11/969 4/322 A/D gCt/gAt 1 -1 KCNK16 HGNC HGNC:14464 protein_coding YES CCDS47421.1 ENSP00000391498 Q96T55 UPI00006838F1 NM_001135105.1 deleterious_low_confidence(0) 1/5 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF104 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 63 39322530 39322530 G T 1 0 0 0 0 1 0 0 0 7980 971 34 2 2 KCNK16 6 39322530 Missense_Mutation SNP G C3N-00737_T 2103571 39322530 131483449 69 19810 LAMA2 0 . GRCh38 6 129383186 129383186 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.5024C>A p.Ala1675Glu p.A1675E ENST00000421865 35/65 545 432 113 370 370 0 strelka-varscan LAMA2,missense_variant,p.Ala1675Glu,ENST00000618192,;LAMA2,missense_variant,p.Ala1675Glu,ENST00000617695,;LAMA2,missense_variant,p.Ala1675Glu,ENST00000421865,NM_001079823.1,NM_000426.3; A ENST00000421865 Transcript missense_variant 5073/9640 5024/9369 1675/3122 A/E gCa/gAa 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 deleterious(0) 35/65 PD936484,Pfam_domain:PF06008 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 129383186 129383186 C A 1 0 0 0 0 1 0 0 0 8510 710 25 2 2 LAMA2 6 129383186 Missense_Mutation SNP C C3N-00737_T 90060656 129383186 41422793 70 19811 PLAGL1 0 . GRCh38 6 143942192 143942192 + Silent SNP T T C novel C3N-00737_T C3N-00737_N T T c.624A>G p.= p.S208S ENST00000360537 5/5 442 404 38 403 403 0 strelka-varscan PLAGL1,synonymous_variant,p.=,ENST00000360537,NM_001289042.1,NM_001289044.1;PLAGL1,synonymous_variant,p.=,ENST00000354765,NM_001080954.1,NM_001289046.1;PLAGL1,synonymous_variant,p.=,ENST00000416623,NM_001289047.1;PLAGL1,synonymous_variant,p.=,ENST00000625622,NM_006718.3,NM_001080953.1,NM_001080952.1,NM_001289048.1,NM_001289049.1,NM_001289045.1;PLAGL1,synonymous_variant,p.=,ENST00000444202,NM_001289043.1,NM_001080951.1;PLAGL1,synonymous_variant,p.=,ENST00000367571,;PLAGL1,synonymous_variant,p.=,ENST00000437412,NM_001289040.1,NM_001289039.1,NM_001289037.1,NM_001080955.1,NM_001289038.1;PLAGL1,synonymous_variant,p.=,ENST00000367572,;PLAGL1,synonymous_variant,p.=,ENST00000417959,NM_002656.3,NM_001289041.1,NM_001080956.1;PLAGL1,5_prime_UTR_variant,,ENST00000392307,;ZC2HC1B,downstream_gene_variant,,ENST00000237275,NM_001013623.2;PLAGL1,downstream_gene_variant,,ENST00000629195,;PLAGL1,downstream_gene_variant,,ENST00000626294,;PLAGL1,downstream_gene_variant,,ENST00000627449,;PLAGL1,downstream_gene_variant,,ENST00000626462,;PLAGL1,downstream_gene_variant,,ENST00000628651,;PLAGL1,downstream_gene_variant,,ENST00000626373,;ZC2HC1B,downstream_gene_variant,,ENST00000539295,;RP3-468K18.7,downstream_gene_variant,,ENST00000454207,; C ENST00000360537 Transcript synonymous_variant 2538/4430 624/1392 208/463 S tcA/tcG 1 -1 PLAGL1 HGNC HGNC:9046 protein_coding YES CCDS5202.1 ENSP00000353734 Q9UM63 UPI000006F274 NM_001289042.1,NM_001289044.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF227,Gene3D:3.30.160.60 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 143942192 143942192 T C 1 0 0 0 0 0 0 0 1 12113 1683 59 5 5 PLAGL1 6 143942192 Silent SNP T C3N-00737_T 14559006 143942192 26863787 71 19812 SYNE1 0 . GRCh38 6 152325254 152325254 + Missense_Mutation SNP C C G rs374861508 C3N-00737_T C3N-00737_N C C c.15487G>C p.Glu5163Gln p.E5163Q ENST00000367255 81/146 534 479 55 441 441 0 strelka-varscan SYNE1,missense_variant,p.Glu5163Gln,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Glu5092Gln,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Glu4839Gln,ENST00000341594,;SYNE1,5_prime_UTR_variant,,ENST00000448038,;SYNE1,non_coding_transcript_exon_variant,,ENST00000490135,; G ENST00000367255 Transcript missense_variant 16089/27748 15487/26394 5163/8797 E/Q Gag/Cag rs374861508 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 81/146 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 152325254 152325254 C G 1 0 0 0 0 1 0 0 0 15837 835 29 4 4 SYNE1 6 152325254 Missense_Mutation SNP C C3N-00737_T 8383062 152325254 18480725 72 19813 TIAM2 0 . GRCh38 6 155144683 155144683 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.1708G>T p.Ala570Ser p.A570S ENST00000461783 8/29 193 169 24 149 149 0 strelka-varscan TIAM2,missense_variant,p.Ala570Ser,ENST00000461783,;TIAM2,missense_variant,p.Ala570Ser,ENST00000318981,NM_012454.3;TIAM2,missense_variant,p.Ala570Ser,ENST00000360366,;TIAM2,missense_variant,p.Ala570Ser,ENST00000529824,;TIAM2,missense_variant,p.Ala570Ser,ENST00000528535,;TIAM2,upstream_gene_variant,,ENST00000528391,;TIAM2,upstream_gene_variant,,ENST00000456877,; T ENST00000461783 Transcript missense_variant 2981/6981 1708/5106 570/1701 A/S Gca/Tca 1 1 TIAM2 HGNC HGNC:11806 protein_coding YES CCDS34558.1 ENSP00000437188 Q8IVF5 UPI00004DF8BE deleterious(0.03) 8/29 PROSITE_profiles:PS50003,hmmpanther:PTHR22826:SF118,hmmpanther:PTHR22826,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 155144683 155144683 G T 1 0 0 0 0 1 0 0 0 16325 1319 46 2 2 TIAM2 6 155144683 Missense_Mutation SNP G C3N-00737_T 2819429 155144683 15661296 73 19814 AVL9 0 . GRCh38 7 32551393 32551393 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.432G>C p.Glu144Asp p.E144D ENST00000318709 5/16 158 135 23 189 189 0 strelka-varscan AVL9,missense_variant,p.Glu144Asp,ENST00000318709,NM_015060.2;AVL9,missense_variant,p.Glu75Asp,ENST00000446718,;AVL9,missense_variant,p.Glu144Asp,ENST00000409301,;AVL9,non_coding_transcript_exon_variant,,ENST00000485228,; C ENST00000318709 Transcript missense_variant 653/6982 432/1947 144/648 E/D gaG/gaC 1 1 AVL9 HGNC HGNC:28994 protein_coding YES CCDS34613.1 ENSP00000315568 Q8NBF6 A0A024RA36 UPI0000049D97 NM_015060.2 deleterious(0.01) 5/16 hmmpanther:PTHR31017,Pfam_domain:PF09794 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 32551393 32551393 G C 1 0 0 0 0 1 0 0 0 1384 933 33 4 4 AVL9 7 32551393 Missense_Mutation SNP G C3N-00737_T 32551393 126794580 74 19815 VWC2 0 . GRCh38 7 49776101 49776101 + Silent SNP C C A novel C3N-00737_T C3N-00737_N C C c.666C>A p.= p.G222G ENST00000340652 2/4 85 77 8 95 95 0 strelka-varscan VWC2,synonymous_variant,p.=,ENST00000340652,NM_198570.3; A ENST00000340652 Transcript synonymous_variant 1222/11299 666/978 222/325 G ggC/ggA 1 1 VWC2 HGNC HGNC:30200 protein_coding YES CCDS5508.1 ENSP00000341819 Q2TAL6 UPI00002373A5 NM_198570.3 2/4 PROSITE_profiles:PS50184,hmmpanther:PTHR11339,Pfam_domain:PF00093,Gene3D:2.10.70.10,SMART_domains:SM00214,Superfamily_domains:SSF57603 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -16.91119 0.9999998 1 1 1 0 A 2 1 63 49776101 49776101 C A 1 0 0 0 0 0 0 0 1 17802 697 25 2 2 VWC2 7 49776101 Silent SNP C C3N-00737_T 17224708 49776101 109569872 75 19816 BAZ1B 0 . GRCh38 7 73477845 73477845 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.1616C>T p.Ser539Phe p.S539F ENST00000339594 7/20 262 223 39 289 289 0 strelka-varscan-mutect BAZ1B,missense_variant,p.Ser539Phe,ENST00000339594,NM_032408.3;BAZ1B,missense_variant,p.Ser539Phe,ENST00000404251,; A ENST00000339594 Transcript missense_variant 1955/6102 1616/4452 539/1483 S/F tCt/tTt 1 -1 BAZ1B HGNC HGNC:961 protein_coding YES CCDS5549.1 ENSP00000342434 Q9UIG0 UPI0000126731 NM_032408.3 deleterious(0) 7/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF145 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 73477845 73477845 G A 1 0 0 0 0 1 0 0 0 1475 942 33 3 3 BAZ1B 7 73477845 Missense_Mutation SNP G C3N-00737_T 23701744 73477845 85868128 76 19817 SPDYE5 0 . GRCh38 7 75501401 75501401 + Silent SNP C C G rs781999748 C3N-00737_T C3N-00737_N C C c.795C>G p.= p.S265S ENST00000625065 6/8 408 362 46 409 408 1 varscan-mutect SPDYE5,synonymous_variant,p.=,ENST00000624640,NM_001099435.2;SPDYE5,synonymous_variant,p.=,ENST00000625065,;SPDYE5,synonymous_variant,p.=,ENST00000455862,;PMS2P3,downstream_gene_variant,,ENST00000529061,; G ENST00000625065 Transcript synonymous_variant 1218/1700 795/1209 265/402 S tcC/tcG rs781999748 1 1 SPDYE5 HGNC HGNC:35464 protein_coding YES CCDS78241.1 ENSP00000485398 A0A096LPK5 UPI000387D8EA 6/8 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF15,Pfam_domain:PF11357 LOW 1 SNV 5 1 PASS rs781999748 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 75501401 75501401 C G 1 0 0 0 0 0 0 0 1 15381 581 21 4 4 SPDYE5 7 75501401 Silent SNP C C3N-00737_T 2023556 75501401 83844572 77 19818 ABCB1 0 . GRCh38 7 87505993 87505993 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.3540G>A p.= p.Q1180Q ENST00000622132 27/28 431 332 99 322 322 0 strelka-varscan-mutect ABCB1,synonymous_variant,p.=,ENST00000622132,;ABCB1,synonymous_variant,p.=,ENST00000265724,NM_000927.4;ABCB1,synonymous_variant,p.=,ENST00000543898,;ABCB1,non_coding_transcript_exon_variant,,ENST00000488737,;ABCB1,non_coding_transcript_exon_variant,,ENST00000475929,;ABCB1,non_coding_transcript_exon_variant,,ENST00000491360,; T ENST00000622132 Transcript synonymous_variant 3865/4778 3540/3843 1180/1280 Q caG/caA 1 -1 ABCB1 HGNC HGNC:40 protein_coding YES CCDS5608.1 ENSP00000478255 P08183 A4D1D2 UPI000013D66C 27/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_patterns:PS00211,PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF241,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 87505993 87505993 C T 1 0 0 0 0 0 0 0 1 44 912 32 3 3 ABCB1 7 87505993 Silent SNP C C3N-00737_T 12004592 87505993 71839980 78 19819 CFAP69 0 . GRCh38 7 90277096 90277096 + Silent SNP G G A C3N-00737_T C3N-00737_N G G c.1008G>A p.= p.L336L ENST00000389297 10/23 93 82 11 157 157 0 strelka-varscan-mutect CFAP69,synonymous_variant,p.=,ENST00000389297,NM_001039706.2;CFAP69,synonymous_variant,p.=,ENST00000497910,NM_001160138.1;CFAP69,intron_variant,,ENST00000457170,;CFAP69,upstream_gene_variant,,ENST00000449577,;CFAP69,downstream_gene_variant,,ENST00000418199,;CFAP69,downstream_gene_variant,,ENST00000463311,;CFAP69,3_prime_UTR_variant,,ENST00000451029,;CFAP69,3_prime_UTR_variant,,ENST00000427396,;CFAP69,non_coding_transcript_exon_variant,,ENST00000475031,;CFAP69,upstream_gene_variant,,ENST00000491886,; A ENST00000389297 Transcript synonymous_variant 1259/3902 1008/2826 336/941 L ttG/ttA COSM4825015,COSM4825016 1 1 CFAP69 HGNC HGNC:26107 protein_coding YES CCDS43613.2 ENSP00000373948 A5D8W1 UPI000066DA29 NM_001039706.2 10/23 hmmpanther:PTHR14716:SF0,hmmpanther:PTHR14716,Superfamily_domains:SSF48371 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 90277096 90277096 G A 1 0 0 0 0 0 0 0 1 3030 1281 45 3 3 CFAP69 7 90277096 Silent SNP G C3N-00737_T 2771103 90277096 69068877 79 19820 ANKIB1 0 . GRCh38 7 92343054 92343054 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.818G>C p.Trp273Ser p.W273S ENST00000265742 6/20 445 393 52 326 326 0 strelka-varscan-mutect ANKIB1,missense_variant,p.Trp273Ser,ENST00000265742,NM_019004.1;ANKIB1,3_prime_UTR_variant,,ENST00000439883,;ANKIB1,upstream_gene_variant,,ENST00000413588,; C ENST00000265742 Transcript missense_variant 1194/6081 818/3270 273/1089 W/S tGg/tCg 1 1 ANKIB1 HGNC HGNC:22215 protein_coding YES CCDS47639.1 ENSP00000265742 Q9P2G1 UPI00001C1E7C NM_019004.1 deleterious(0) 6/20 hmmpanther:PTHR11685,hmmpanther:PTHR11685:SF95 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 92343054 92343054 G C 1 0 0 0 0 1 0 0 0 731 1357 47 4 4 ANKIB1 7 92343054 Missense_Mutation SNP G C3N-00737_T 2065958 92343054 67002919 80 19821 CADPS2 0 . GRCh38 7 122360822 122360822 + Splice_Site SNP T T G novel C3N-00737_T C3N-00737_N T T c.3472-2A>C p.X1158_splice ENST00000449022 107 89 18 162 162 0 strelka-varscan-mutect CADPS2,splice_acceptor_variant,,ENST00000615869,;CADPS2,splice_acceptor_variant,,ENST00000313070,NM_001167940.1;CADPS2,splice_acceptor_variant,,ENST00000334010,;CADPS2,splice_acceptor_variant,,ENST00000412584,NM_001009571.3;CADPS2,splice_acceptor_variant,,ENST00000449022,NM_017954.10;CADPS2,splice_acceptor_variant,,ENST00000397721,;CADPS2,splice_acceptor_variant,,ENST00000462699,;RP5-1101C3.1,intron_variant,,ENST00000602012,;RP5-1101C3.1,intron_variant,,ENST00000591140,;RP5-1101C3.1,intron_variant,,ENST00000625850,;RP5-1101C3.1,intron_variant,,ENST00000628132,;RP5-1101C3.1,intron_variant,,ENST00000602199,;RP5-1101C3.1,intron_variant,,ENST00000628268,;RP5-1101C3.1,intron_variant,,ENST00000593910,;RP5-1101C3.1,intron_variant,,ENST00000626052,;RP5-1101C3.1,intron_variant,,ENST00000626740,;RP5-1101C3.1,intron_variant,,ENST00000630897,;RP5-1101C3.1,intron_variant,,ENST00000626092,;RP5-1101C3.1,intron_variant,,ENST00000482375,;RP5-1101C3.1,intron_variant,,ENST00000630777,;RP5-1101C3.1,intron_variant,,ENST00000631248,;RP5-1101C3.1,intron_variant,,ENST00000627005,; G ENST00000449022 Transcript splice_acceptor_variant -/4073 3472/3891 1158/1296 1 -1 CADPS2 HGNC HGNC:16018 protein_coding YES CCDS55158.1 ENSP00000398481 Q86UW7 UPI0000668808 NM_017954.10 26/29 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 63 122360822 122360822 T G 1 0 0 0 0 0 0 1 0 2261 1623 56 5 5 CADPS2 7 122360822 Splice_Site SNP T C3N-00737_T 30017768 122360822 36985151 81 19822 SLC13A1 0 . GRCh38 7 123115545 123115545 + Silent SNP A A G novel C3N-00737_T C3N-00737_N A A c.1761T>C p.= p.P587P ENST00000194130 15/15 173 157 16 167 166 1 strelka-mutect SLC13A1,synonymous_variant,p.=,ENST00000194130,NM_022444.3;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; G ENST00000194130 Transcript synonymous_variant 1801/3815 1761/1788 587/595 P ccT/ccC 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 15/15 hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 123115545 123115545 A G 1 0 0 0 0 0 0 0 1 14656 175 7 5 5 SLC13A1 7 123115545 Silent SNP A C3N-00737_T 754723 123115545 36230428 82 19823 CPA4 0 . GRCh38 7 130299310 130299310 + Missense_Mutation SNP T T A novel C3N-00737_T C3N-00737_N T T c.191T>A p.Val64Glu p.V64E ENST00000222482 3/11 242 229 13 218 218 0 strelka-varscan-mutect CPA4,missense_variant,p.Val64Glu,ENST00000222482,NM_016352.3;CPA4,missense_variant,p.Val64Glu,ENST00000445470,NM_001163446.1;CPA4,missense_variant,p.Val64Glu,ENST00000473956,;CPA4,missense_variant,p.Val64Glu,ENST00000492072,;CPA4,5_prime_UTR_variant,,ENST00000486598,;CPA4,intron_variant,,ENST00000493259,;CPA4,non_coding_transcript_exon_variant,,ENST00000470542,;CPA4,non_coding_transcript_exon_variant,,ENST00000474254,;CPA4,non_coding_transcript_exon_variant,,ENST00000490117,;CPA4,non_coding_transcript_exon_variant,,ENST00000497388,; A ENST00000222482 Transcript missense_variant 219/2797 191/1266 64/421 V/E gTg/gAg 1 1 CPA4 HGNC HGNC:15740 protein_coding YES CCDS5818.1 ENSP00000222482 Q9UI42 A4D1M3 UPI0000048F00 NM_016352.3 deleterious(0) 3/11 Gene3D:3.30.70.340,Pfam_domain:PF02244,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF50,Superfamily_domains:SSF54897 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 130299310 130299310 T A 1 0 0 0 0 1 0 0 0 3586 1696 59 4 4 CPA4 7 130299310 Missense_Mutation SNP T C3N-00737_T 7183765 130299310 29046663 83 19824 ELP3 0 . GRCh38 8 28132290 28132290 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.792G>A p.= p.V264V ENST00000256398 9/15 218 201 17 176 175 1 strelka-varscan-mutect ELP3,synonymous_variant,p.=,ENST00000256398,NM_018091.5;ELP3,synonymous_variant,p.=,ENST00000521015,NM_001284222.1;ELP3,synonymous_variant,p.=,ENST00000380353,NM_001284226.1;ELP3,synonymous_variant,p.=,ENST00000537665,NM_001284225.1,NM_001284224.1;ELP3,synonymous_variant,p.=,ENST00000524103,NM_001284220.1;ELP3,non_coding_transcript_exon_variant,,ENST00000520110,;ELP3,3_prime_UTR_variant,,ENST00000518112,;ELP3,3_prime_UTR_variant,,ENST00000519261,;ELP3,3_prime_UTR_variant,,ENST00000523687,;ELP3,non_coding_transcript_exon_variant,,ENST00000520011,; A ENST00000256398 Transcript synonymous_variant 1169/3452 792/1644 264/547 V gtG/gtA 1 1 ELP3 HGNC HGNC:20696 protein_coding YES CCDS6065.1 ENSP00000256398 Q9H9T3 UPI000006F0B5 NM_018091.5 9/15 hmmpanther:PTHR11135,PIRSF_domain:PIRSF005669,TIGRFAM_domain:TIGR01211,Gene3D:2qgqB01,Pfam_domain:PF04055,SMART_domains:SM00729,Superfamily_domains:SSF102114 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 28132290 28132290 G A 1 0 0 0 0 0 0 0 1 4915 1277 45 3 3 ELP3 8 28132290 Silent SNP G C3N-00737_T 28132290 117006346 84 19825 DKK4 0 . GRCh38 8 42374854 42374854 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.322G>A p.Asp108Asn p.D108N ENST00000220812 3/4 424 385 39 292 292 0 strelka-varscan-mutect DKK4,missense_variant,p.Asp108Asn,ENST00000220812,NM_014420.2;POLB,downstream_gene_variant,,ENST00000265421,NM_002690.2;POLB,downstream_gene_variant,,ENST00000521290,;POLB,downstream_gene_variant,,ENST00000521492,;POLB,downstream_gene_variant,,ENST00000518579,;POLB,downstream_gene_variant,,ENST00000517393,;POLB,downstream_gene_variant,,ENST00000522610,;POLB,downstream_gene_variant,,ENST00000524208,;POLB,downstream_gene_variant,,ENST00000521418,; T ENST00000220812 Transcript missense_variant 509/894 322/675 108/224 D/N Gat/Aat 1 -1 DKK4 HGNC HGNC:2894 protein_coding YES CCDS6130.1 ENSP00000220812 Q9UBT3 UPI0000051057 NM_014420.2 tolerated(0.18) 3/4 hmmpanther:PTHR12113,hmmpanther:PTHR12113:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 42374854 42374854 C T 1 0 0 0 0 1 0 0 0 4353 913 32 3 3 DKK4 8 42374854 Missense_Mutation SNP C C3N-00737_T 14242564 42374854 102763782 85 19826 MCM4 0 . GRCh38 8 47974836 47974836 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.2239G>C p.Val747Leu p.V747L ENST00000262105 14/16 341 289 52 275 275 0 strelka-varscan-mutect MCM4,missense_variant,p.Val747Leu,ENST00000262105,NM_005914.3;MCM4,missense_variant,p.Val747Leu,ENST00000523944,NM_182746.2;MCM4,downstream_gene_variant,,ENST00000520637,;RNU6-519P,upstream_gene_variant,,ENST00000410590,;MCM4,downstream_gene_variant,,ENST00000518680,;MCM4,3_prime_UTR_variant,,ENST00000518382,;MCM4,non_coding_transcript_exon_variant,,ENST00000521261,;MCM4,upstream_gene_variant,,ENST00000521151,;MCM4,downstream_gene_variant,,ENST00000517709,;MCM4,downstream_gene_variant,,ENST00000519470,;MCM4,downstream_gene_variant,,ENST00000523853,; C ENST00000262105 Transcript missense_variant 2448/4183 2239/2592 747/863 V/L Gta/Cta 1 1 MCM4 HGNC HGNC:6947 protein_coding YES CCDS6143.1 ENSP00000262105 P33991 UPI000013D25C NM_005914.3 tolerated(0.08) 14/16 Gene3D:3.40.50.300,Pfam_domain:PF00493,hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF66,SMART_domains:SM00350,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 47974836 47974836 G C 1 0 0 0 0 1 0 0 0 9321 1029 36 4 4 MCM4 8 47974836 Missense_Mutation SNP G C3N-00737_T 5599982 47974836 97163800 86 19827 BHLHE22 0 . GRCh38 8 64581181 64581181 + Nonsense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.391G>T p.Glu131Ter p.E131* ENST00000321870 1/1 43 38 5 50 50 0 strelka-mutect BHLHE22,stop_gained,p.Glu131Ter,ENST00000321870,NM_152414.4;RP11-21C4.1,intron_variant,,ENST00000517909,;RP11-21C4.1,upstream_gene_variant,,ENST00000520834,; T ENST00000321870 Transcript stop_gained 815/3262 391/1146 131/381 E/* Gaa/Taa 1 1 BHLHE22 HGNC HGNC:11963 protein_coding YES CCDS6179.1 ENSP00000318799 Q8NFJ8 UPI0000070A3C NM_152414.4 1/1 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF52 HIGH SNV 1 PASS . . 0 208 2 0 0 0 0 0 -13.18659 1 1 1 1 0 T 4 4 63 64581181 64581181 G T 1 0 0 0 0 0 1 0 0 1569 1059 37 1 1 BHLHE22 8 64581181 Nonsense_Mutation SNP G C3N-00737_T 16606345 64581181 80557455 87 19828 TMEM67 0 . GRCh38 8 93759972 93759972 + Missense_Mutation SNP T T C novel C3N-00737_T C3N-00737_N T T c.142T>C p.Tyr48His p.Y48H ENST00000409623 4/29 116 87 29 85 85 0 strelka-varscan-mutect TMEM67,missense_variant,p.Tyr48His,ENST00000409623,NM_001142301.1;TMEM67,intron_variant,,ENST00000453321,NM_153704.5;TMEM67,intron_variant,,ENST00000452276,;TMEM67,intron_variant,,ENST00000518319,;TMEM67,intron_variant,,ENST00000453906,;TMEM67,intron_variant,,ENST00000521517,;TMEM67,intron_variant,,ENST00000498673,;TMEM67,intron_variant,,ENST00000323130,;TMEM67,intron_variant,,ENST00000474944,;TMEM67,intron_variant,,ENST00000455946,;TMEM67,intron_variant,,ENST00000521222,;TMEM67,intron_variant,,ENST00000521065,;TMEM67,downstream_gene_variant,,ENST00000481620,;TMEM67,downstream_gene_variant,,ENST00000475305,; C ENST00000409623 Transcript missense_variant 344/3255 142/2745 48/914 Y/H Tac/Cac 1 1 TMEM67 HGNC HGNC:28396 protein_coding CCDS47893.1 ENSP00000386966 Q5HYA8 UPI0000EE3237 NM_001142301.1 tolerated_low_confidence(0.52) 4/29 MODERATE SNV 2 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 C 3 2 63 93759972 93759972 T C 1 0 0 0 0 1 0 0 0 16671 1638 57 5 5 TMEM67 8 93759972 Missense_Mutation SNP T C3N-00737_T 29178791 93759972 51378664 88 19829 DPY19L4 0 . GRCh38 8 94781094 94781094 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.1643G>A p.Arg548Lys p.R548K ENST00000414645 16/19 122 112 10 135 135 0 varscan-mutect DPY19L4,missense_variant,p.Arg548Lys,ENST00000414645,NM_181787.2;DPY19L4,intron_variant,,ENST00000522669,; A ENST00000414645 Transcript missense_variant 1742/6197 1643/2172 548/723 R/K aGa/aAa 1 1 DPY19L4 HGNC HGNC:27829 protein_coding YES CCDS34924.1 ENSP00000389630 Q7Z388 A0A024R9F2 UPI00001A9D7A NM_181787.2 tolerated(0.67) 16/19 hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.5248 1 1 1 1 0 A 3 1 63 94781094 94781094 G A 1 0 0 0 0 1 0 0 0 4558 942 33 3 3 DPY19L4 8 94781094 Missense_Mutation SNP G C3N-00737_T 1021122 94781094 50357542 89 19830 SPAG1 0 . GRCh38 8 100240693 100240693 + Silent SNP G G C novel C3N-00737_T C3N-00737_N G G c.2571G>C p.= p.L857L ENST00000388798 18/19 179 157 22 201 201 0 strelka-varscan-mutect SPAG1,synonymous_variant,p.=,ENST00000388798,NM_003114.4;SPAG1,synonymous_variant,p.=,ENST00000251809,NM_172218.2;SPAG1,non_coding_transcript_exon_variant,,ENST00000519409,;SPAG1,downstream_gene_variant,,ENST00000519424,; C ENST00000388798 Transcript synonymous_variant 2762/3852 2571/2781 857/926 L ctG/ctC 1 1 SPAG1 HGNC HGNC:11212 protein_coding YES CCDS34930.1 ENSP00000373450 Q07617 UPI000016783D NM_003114.4 18/19 Pfam_domain:PF13877 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999971 1 1 1 0 C 2 2 63 100240693 100240693 G C 1 0 0 0 0 0 0 0 1 15306 1277 45 4 4 SPAG1 8 100240693 Silent SNP G C3N-00737_T 5459599 100240693 44897943 90 19831 FRMPD1 0 . GRCh38 9 37745466 37745466 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.3434C>T p.Ser1145Leu p.S1145L ENST00000539465 16/16 300 263 37 321 321 0 strelka-varscan-mutect FRMPD1,missense_variant,p.Ser1145Leu,ENST00000539465,;FRMPD1,missense_variant,p.Ser1145Leu,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; T ENST00000539465 Transcript missense_variant 4027/5465 3434/4737 1145/1578 S/L tCa/tTa 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC tolerated_low_confidence(0.33) 16/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 37745466 37745466 C T 1 0 0 0 0 1 0 0 0 5927 838 29 3 3 FRMPD1 9 37745466 Missense_Mutation SNP C C3N-00737_T 37745466 100649251 91 19832 TMEM245 0 . GRCh38 9 109087332 109087332 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.1161C>T p.= p.L387L ENST00000374586 6/18 127 92 35 110 109 1 varscan-mutect TMEM245,synonymous_variant,p.=,ENST00000374586,NM_032012.3;TMEM245,upstream_gene_variant,,ENST00000413712,;TMEM245,synonymous_variant,p.=,ENST00000491854,; A ENST00000374586 Transcript synonymous_variant 1193/7980 1161/2640 387/879 L ctC/ctT 1 -1 TMEM245 HGNC HGNC:1363 protein_coding YES CCDS43858.1 ENSP00000363714 Q9H330 UPI000013C833 NM_032012.3 6/18 hmmpanther:PTHR21716:SF4,hmmpanther:PTHR21716 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 109087332 109087332 G A 1 0 0 0 0 0 0 0 1 16605 1277 45 3 3 TMEM245 9 109087332 Silent SNP G C3N-00737_T 71341866 109087332 29307385 92 19833 SFMBT2 0 . GRCh38 10 7172576 7172576 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.2070G>A p.= p.R690R ENST00000397167 18/21 255 193 62 237 237 0 strelka-varscan-mutect SFMBT2,synonymous_variant,p.=,ENST00000397167,NM_001029880.2;SFMBT2,synonymous_variant,p.=,ENST00000361972,NM_001018039.1; T ENST00000397167 Transcript synonymous_variant 2263/8024 2070/2685 690/894 R agG/agA 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 18/21 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 7172576 7172576 C T 1 0 0 0 0 0 0 0 1 14436 738 26 3 3 SFMBT2 10 7172576 Silent SNP C C3N-00737_T 7172576 126624846 93 19834 ZNF33A 0 . GRCh38 10 38054644 38054644 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.574G>A p.Gly192Arg p.G192R ENST00000307441 6/6 149 136 13 219 218 1 varscan-mutect ZNF33A,missense_variant,p.Gly192Arg,ENST00000307441,NM_001324175.1,NM_001324177.1,NM_001324178.1,NM_001278173.1;ZNF33A,missense_variant,p.Gly62Arg,ENST00000374618,NM_001324175.1,NM_001324177.1,NM_001324176.1,NM_001278176.1,NM_001278179.1,NM_001278178.1,NM_001278171.1,NM_001278174.1,NM_001278175.1;ZNF33A,missense_variant,p.Gly173Arg,ENST00000458705,NM_006974.2;ZNF33A,missense_variant,p.Gly174Arg,ENST00000432900,NM_001278177.1,NM_006954.1;ZNF33A,missense_variant,p.Gly180Arg,ENST00000628825,NM_001278170.1;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,; A ENST00000307441 Transcript missense_variant 777/6196 574/2490 192/829 G/R Ggg/Agg 1 1 ZNF33A HGNC HGNC:13096 protein_coding YES CCDS73088.1 ENSP00000304268 A0A0A0MR11 UPI00032969BB NM_001324175.1,NM_001324177.1,NM_001324178.1,NM_001278173.1 tolerated(0.1) 6/6 MODERATE 1 SNV 4 1 PASS . . 0 206 2 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 63 38054644 38054644 G A 1 0 0 0 0 1 0 0 0 18426 1348 47 3 3 ZNF33A 10 38054644 Missense_Mutation SNP G C3N-00737_T 30882068 38054644 95742778 94 19835 PCDH15 0 . GRCh38 10 53809166 53809166 + Silent SNP T T C novel C3N-00737_T C3N-00737_N T T c.4899A>G p.= p.S1633S ENST00000613657 37/37 490 373 117 460 460 0 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000613657,NM_001142769.1;PCDH15,synonymous_variant,p.=,ENST00000395445,;PCDH15,synonymous_variant,p.=,ENST00000612394,;PCDH15,synonymous_variant,p.=,ENST00000395446,;PCDH15,synonymous_variant,p.=,ENST00000395440,;PCDH15,synonymous_variant,p.=,ENST00000395442,;PCDH15,3_prime_UTR_variant,,ENST00000617271,NM_001142770.1;PCDH15,3_prime_UTR_variant,,ENST00000395438,;PCDH15,3_prime_UTR_variant,,ENST00000409834,;PCDH15,3_prime_UTR_variant,,ENST00000615043,;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,3_prime_UTR_variant,,ENST00000414367,;PCDH15,intron_variant,,ENST00000476074,; C ENST00000613657 Transcript synonymous_variant 5294/6329 4899/5373 1633/1790 S tcA/tcG 1 -1 PCDH15 HGNC HGNC:14674 protein_coding CCDS73138.1 ENSP00000482794 A0A087WZN9 UPI0001884905 NM_001142769.1 37/37 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Low_complexity_(Seg):seg LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 53809166 53809166 T C 1 0 0 0 0 0 0 0 1 11598 1567 55 5 5 PCDH15 10 53809166 Silent SNP T C3N-00737_T 15754522 53809166 79988256 95 19836 IFIT3 0 . GRCh38 10 89339175 89339175 + Missense_Mutation SNP T T A novel C3N-00737_T C3N-00737_N T T c.520T>A p.Ser174Thr p.S174T ENST00000371818 2/2 126 108 18 142 142 0 strelka-varscan-mutect IFIT3,missense_variant,p.Ser174Thr,ENST00000371818,NM_001549.5;IFIT3,missense_variant,p.Ser174Thr,ENST00000371811,NM_001031683.3;LIPA,intron_variant,,ENST00000371837,;LIPA,intron_variant,,ENST00000282673,;LIPA,intron_variant,,ENST00000487618,;LIPA,intron_variant,,ENST00000463623,;LIPA,intron_variant,,ENST00000489359,; A ENST00000371818 Transcript missense_variant 700/2496 520/1473 174/490 S/T Tct/Act 1 1 IFIT3 HGNC HGNC:5411 protein_coding YES CCDS7402.1 ENSP00000360883 O14879 Q5T765 UPI000012D3E5 NM_001549.5 tolerated(0.22) 2/2 Gene3D:1.25.40.10,PROSITE_profiles:PS50293,hmmpanther:PTHR10271,hmmpanther:PTHR10271:SF3,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 89339175 89339175 T A 1 0 0 0 0 1 0 0 0 7424 1551 54 4 4 IFIT3 10 89339175 Missense_Mutation SNP T C3N-00737_T 35530009 89339175 44458247 96 19837 PDCD11 0 . GRCh38 10 103441902 103441902 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.4634C>G p.Ser1545Cys p.S1545C ENST00000369797 31/36 232 194 38 201 201 0 strelka-varscan-mutect PDCD11,missense_variant,p.Ser1545Cys,ENST00000369797,NM_014976.1;CALHM2,downstream_gene_variant,,ENST00000260743,NM_015916.4;CALHM2,downstream_gene_variant,,ENST00000369788,;PDCD11,upstream_gene_variant,,ENST00000478543,; G ENST00000369797 Transcript missense_variant 4728/6453 4634/5616 1545/1871 S/C tCt/tGt 1 1 PDCD11 HGNC HGNC:13408 protein_coding YES CCDS31276.1 ENSP00000358812 Q14690 UPI00001C1ED1 NM_014976.1 deleterious(0) 31/36 hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF10 MODERATE 1 SNV 1 1 PASS rs1483740559 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 103441902 103441902 C G 1 0 0 0 0 1 0 0 0 11705 913 32 4 4 PDCD11 10 103441902 Missense_Mutation SNP C C3N-00737_T 14102727 103441902 30355520 97 19838 EIF3A 0 . GRCh38 10 119073852 119073852 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.135G>C p.Lys45Asn p.K45N ENST00000369144 2/22 139 121 18 137 137 0 strelka-varscan-mutect EIF3A,missense_variant,p.Lys45Asn,ENST00000369144,NM_003750.2;EIF3A,missense_variant,p.Lys45Asn,ENST00000541549,; G ENST00000369144 Transcript missense_variant 263/6646 135/4149 45/1382 K/N aaG/aaC 1 -1 EIF3A HGNC HGNC:3271 protein_coding YES CCDS7608.1 ENSP00000358140 Q14152 UPI000012D311 NM_003750.2 deleterious(0.03) 2/22 HAMAP:MF_03000,hmmpanther:PTHR14005 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 119073852 119073852 C G 1 0 0 0 0 1 0 0 0 4846 912 32 4 4 EIF3A 10 119073852 Missense_Mutation SNP C C3N-00737_T 15631950 119073852 14723570 98 19839 CHST15 0 . GRCh38 10 124044733 124044733 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.733G>T p.Gly245Trp p.G245W ENST00000435907 3/8 123 110 13 92 92 0 strelka-varscan-mutect CHST15,missense_variant,p.Gly245Trp,ENST00000435907,NM_001270764.1;CHST15,missense_variant,p.Gly245Trp,ENST00000346248,NM_015892.4;CHST15,missense_variant,p.Gly245Trp,ENST00000628426,NM_001270765.1,NM_014863.3;CHST15,downstream_gene_variant,,ENST00000462406,; A ENST00000435907 Transcript missense_variant 1384/4820 733/1686 245/561 G/W Ggg/Tgg 1 -1 CHST15 HGNC HGNC:18137 protein_coding YES CCDS7638.1 ENSP00000402394 Q7LFX5 UPI000004D06B NM_001270764.1 deleterious(0) 3/8 hmmpanther:PTHR15723,hmmpanther:PTHR15723:SF0,Gene3D:3.40.50.300 MODERATE 1 SNV 1 1 PASS rs878912191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 124044733 124044733 C A 1 0 0 0 0 1 0 0 0 3163 652 23 1 1 CHST15 10 124044733 Missense_Mutation SNP C C3N-00737_T 4970881 124044733 9752689 99 19840 PTDSS2 0 . GRCh38 11 490475 490475 + Missense_Mutation SNP G G A rs762215454 C3N-00737_T C3N-00737_N G G c.1357G>A p.Asp453Asn p.D453N ENST00000308020 12/12 424 377 47 336 336 0 strelka-varscan-mutect PTDSS2,missense_variant,p.Asp453Asn,ENST00000308020,NM_030783.1;RNH1,downstream_gene_variant,,ENST00000534797,;RNH1,downstream_gene_variant,,ENST00000397615,NM_203383.1,NM_002939.3;RNH1,downstream_gene_variant,,ENST00000354420,NM_203387.2;RNH1,downstream_gene_variant,,ENST00000397614,NM_203385.1;RNH1,downstream_gene_variant,,ENST00000533410,NM_203386.2;RNH1,downstream_gene_variant,,ENST00000356187,NM_203389.2;RNH1,downstream_gene_variant,,ENST00000438658,NM_203384.1;RNH1,downstream_gene_variant,,ENST00000397604,NM_203388.2;RNH1,downstream_gene_variant,,ENST00000529768,;PTDSS2,downstream_gene_variant,,ENST00000532614,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000526878,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000531411,;PTDSS2,non_coding_transcript_exon_variant,,ENST00000530029,;RNH1,downstream_gene_variant,,ENST00000525522,;RNH1,downstream_gene_variant,,ENST00000525701,;PTDSS2,downstream_gene_variant,,ENST00000531520,;PTDSS2,downstream_gene_variant,,ENST00000527325,;RNH1,downstream_gene_variant,,ENST00000524464,; A ENST00000308020 Transcript missense_variant 1533/2445 1357/1464 453/487 D/N Gac/Aac rs762215454 1 1 PTDSS2 HGNC HGNC:15463 protein_coding YES CCDS7696.1 ENSP00000308258 Q9BVG9 A0A024RC97 UPI000004124C NM_030783.1 deleterious(0.03) 12/12 hmmpanther:PTHR15362,hmmpanther:PTHR15362:SF12 MODERATE 1 SNV 1 1 PASS rs762215454 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 490475 490475 G A 1 0 0 0 0 1 0 0 0 12890 1290 45 3 3 PTDSS2 11 490475 Missense_Mutation SNP G C3N-00737_T 490475 134596147 100 19841 OR10A2 0 . GRCh38 11 6870459 6870459 + Silent SNP C C A C3N-00737_T C3N-00737_N C C c.705C>A p.= p.V235V ENST00000307322 1/1 205 177 28 238 237 1 strelka-varscan-mutect OR10A2,synonymous_variant,p.=,ENST00000307322,NM_001004460.1;RP11-413N10.3,intron_variant,,ENST00000637205,; A ENST00000307322 Transcript synonymous_variant 767/1053 705/912 235/303 V gtC/gtA COSM5436306 1 1 OR10A2 HGNC HGNC:8161 protein_coding YES CCDS31415.1 ENSP00000303862 Q9H208 UPI000015F21C NM_001004460.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 6870459 6870459 C A 1 0 0 0 0 0 0 0 1 10966 900 32 2 2 OR10A2 11 6870459 Silent SNP C C3N-00737_T 6379984 6870459 128216163 101 19842 RNF141 0 . GRCh38 11 10514995 10514995 + Nonsense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.614C>G p.Ser205Ter p.S205* ENST00000265981 6/6 216 201 15 206 206 0 strelka-varscan-mutect RNF141,stop_gained,p.Ser205Ter,ENST00000265981,NM_016422.3;RNF141,downstream_gene_variant,,ENST00000528665,;RNF141,downstream_gene_variant,,ENST00000533412,;RNF141,non_coding_transcript_exon_variant,,ENST00000534281,; C ENST00000265981 Transcript stop_gained 757/4074 614/693 205/230 S/* tCa/tGa 1 -1 RNF141 HGNC HGNC:21159 protein_coding YES CCDS7803.1 ENSP00000265981 Q8WVD5 UPI000006DA5A NM_016422.3 6/6 hmmpanther:PTHR12109 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 63 10514995 10514995 G C 1 0 0 0 0 0 1 0 0 13622 1294 45 4 4 RNF141 11 10514995 Nonsense_Mutation SNP G C3N-00737_T 3644536 10514995 124571627 102 19843 ACCSL 0 . GRCh38 11 44048040 44048040 + Missense_Mutation SNP A A T novel C3N-00737_T C3N-00737_N A A c.4A>T p.Ser2Cys p.S2C ENST00000378832 1/14 88 76 12 100 100 0 strelka-varscan-mutect ACCSL,missense_variant,p.Ser2Cys,ENST00000378832,NM_001031854.2;ACCSL,missense_variant,p.Ser2Cys,ENST00000527145,; T ENST00000378832 Transcript missense_variant 60/1820 4/1707 2/568 S/C Agt/Tgt 1 1 ACCSL HGNC HGNC:34391 protein_coding YES CCDS41636.1 ENSP00000368109 Q4AC99 UPI000023785D NM_001031854.2 deleterious_low_confidence(0) 1/14 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 63 44048040 44048040 A T 1 0 0 0 0 1 0 0 0 172 304 11 4 4 ACCSL 11 44048040 Missense_Mutation SNP A C3N-00737_T 33533045 44048040 91038582 103 19844 ARHGAP1 0 . GRCh38 11 46679413 46679413 + Silent SNP G G A rs773769674 C3N-00737_T C3N-00737_N G G c.1083C>T p.= p.P361P ENST00000311956 12/13 240 212 28 211 211 0 strelka-varscan-mutect ARHGAP1,synonymous_variant,p.=,ENST00000311956,NM_004308.3;ARHGAP1,synonymous_variant,p.=,ENST00000528837,;ATG13,downstream_gene_variant,,ENST00000359513,NM_001205120.1,NM_001142673.2;ATG13,downstream_gene_variant,,ENST00000526508,;ATG13,downstream_gene_variant,,ENST00000524625,NM_014741.4;ARHGAP1,downstream_gene_variant,,ENST00000525488,;ATG13,downstream_gene_variant,,ENST00000526485,;ARHGAP1,non_coding_transcript_exon_variant,,ENST00000526423,; A ENST00000311956 Transcript synonymous_variant 1181/3375 1083/1320 361/439 P ccC/ccT rs773769674,COSM1353979 1 -1 ARHGAP1 HGNC HGNC:673 protein_coding YES CCDS7922.1 ENSP00000310491 Q07960 UPI0000040691 NM_004308.3 12/13 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF28,SMART_domains:SM00324,Superfamily_domains:SSF48350 0,1 LOW 1 SNV 1 0,1 1 PASS rs773769674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 46679413 46679413 G A 1 0 0 0 0 0 0 0 1 985 1103 39 1 1 ARHGAP1 11 46679413 Silent SNP G C3N-00737_T 2631373 46679413 88407209 104 19845 OR4S2 0 . GRCh38 11 55651381 55651381 + Silent SNP C C T C3N-00737_T C3N-00737_N C C c.478C>T p.= p.L160L ENST00000312422 1/1 92 73 19 95 95 0 strelka-varscan-mutect OR4S2,synonymous_variant,p.=,ENST00000312422,NM_001004059.2; T ENST00000312422 Transcript synonymous_variant 478/936 478/936 160/311 L Ctg/Ttg COSM3448943 1 1 OR4S2 HGNC HGNC:15183 protein_coding YES CCDS31505.1 ENSP00000310337 Q8NH73 A0A126GVG1 UPI00001D77D2 NM_001004059.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 23 185 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 55651381 55651381 C T 1 0 0 0 0 0 0 0 1 11159 912 32 3 3 OR4S2 11 55651381 Silent SNP C C3N-00737_T 8971968 55651381 79435241 105 19846 OR5T3 0 . GRCh38 11 56252769 56252769 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.570A>G p.Ile190Met p.I190M ENST00000303059 1/1 260 234 26 327 326 1 varscan-mutect OR5T3,missense_variant,p.Ile190Met,ENST00000303059,NM_001004747.1; G ENST00000303059 Transcript missense_variant 570/1023 570/1023 190/340 I/M atA/atG 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs915824479 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 56252769 56252769 A G 1 0 0 0 0 1 0 0 0 11251 410 15 5 5 OR5T3 11 56252769 Missense_Mutation SNP A C3N-00737_T 601388 56252769 78833853 106 19847 OR5T3 0 . GRCh38 11 56253050 56253050 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.851C>A p.Thr284Lys p.T284K ENST00000303059 1/1 187 163 24 188 188 0 strelka-varscan-mutect OR5T3,missense_variant,p.Thr284Lys,ENST00000303059,NM_001004747.1; A ENST00000303059 Transcript missense_variant 851/1023 851/1023 284/340 T/K aCa/aAa 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1411723444 . 0 205 2 3 0 0 0 0 -20 0.9999461 1 1 1 0 A 3 1 63 56253050 56253050 C A 1 0 0 0 0 1 0 0 0 11251 478 17 2 2 OR5T3 11 56253050 Missense_Mutation SNP C C3N-00737_T 281 56253050 78833572 107 19848 SYTL2 0 . GRCh38 11 85734040 85734040 + Missense_Mutation SNP G G A rs753365696 C3N-00737_T C3N-00737_N G G c.1289C>T p.Ala430Val p.A430V ENST00000316356 7/19 307 283 24 294 294 0 strelka-varscan-mutect SYTL2,missense_variant,p.Ala430Val,ENST00000634661,;SYTL2,missense_variant,p.Ala429Val,ENST00000389960,NM_032943.4;SYTL2,missense_variant,p.Ala430Val,ENST00000316356,;SYTL2,missense_variant,p.Ala430Val,ENST00000359152,NM_001162953.2;SYTL2,missense_variant,p.Ala429Val,ENST00000528231,NM_001162951.2;SYTL2,missense_variant,p.Ala381Val,ENST00000527523,NM_001289608.1;SYTL2,missense_variant,p.Ala429Val,ENST00000524452,;SYTL2,non_coding_transcript_exon_variant,,ENST00000438197,; A ENST00000316356 Transcript missense_variant 1854/4293 1289/2808 430/935 A/V gCa/gTa rs753365696 1 -1 SYTL2 HGNC HGNC:15585 protein_coding YES CCDS53689.1 ENSP00000318803 Q9HCH5 UPI0001917079 tolerated(0.36) 7/19 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF10 MODERATE 1 SNV 5 1 PASS rs753365696 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 85734040 85734040 G A 1 0 0 0 0 1 0 0 0 15877 1319 46 3 3 SYTL2 11 85734040 Missense_Mutation SNP G C3N-00737_T 29480990 85734040 49352582 108 19849 CD3G 0 . GRCh38 11 118349775 118349775 + Missense_Mutation SNP G G C rs749951677 C3N-00737_T C3N-00737_N G G c.112G>C p.Glu38Gln p.E38Q ENST00000532917 3/7 401 363 38 375 375 0 strelka-varscan-mutect CD3G,missense_variant,p.Glu38Gln,ENST00000532917,NM_000073.2;CD3G,5_prime_UTR_variant,,ENST00000392883,;CD3G,non_coding_transcript_exon_variant,,ENST00000532903,;CD3G,non_coding_transcript_exon_variant,,ENST00000528540,;CD3G,3_prime_UTR_variant,,ENST00000292144,;CD3G,non_coding_transcript_exon_variant,,ENST00000533462,;CD3G,non_coding_transcript_exon_variant,,ENST00000527777,; C ENST00000532917 Transcript missense_variant 180/2678 112/549 38/182 E/Q Gaa/Caa rs749951677 1 1 CD3G HGNC HGNC:1675 protein_coding YES CCDS8395.1 ENSP00000431445 P09693 B0YIY5 UPI000012735F NM_000073.2 tolerated(0.41) 3/7 hmmpanther:PTHR10570,hmmpanther:PTHR10570:SF8,Gene3D:2.60.40.10,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 118349775 118349775 G C 1 0 0 0 0 1 0 0 0 2717 943 33 4 4 CD3G 11 118349775 Missense_Mutation SNP G C3N-00737_T 32615735 118349775 16736847 109 19850 EI24 0 . GRCh38 11 125575332 125575332 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.112G>C p.Glu38Gln p.E38Q ENST00000278903 3/11 193 171 22 171 171 0 strelka-varscan-mutect EI24,missense_variant,p.Glu38Gln,ENST00000278903,NM_004879.4;EI24,missense_variant,p.Glu38Gln,ENST00000620753,;EI24,missense_variant,p.Glu38Gln,ENST00000527235,;EI24,missense_variant,p.Glu24Gln,ENST00000534546,NM_001290135.1;EI24,missense_variant,p.Glu38Gln,ENST00000524723,;EI24,missense_variant,p.Glu38Gln,ENST00000527842,;EI24,missense_variant,p.Glu38Gln,ENST00000527131,;EI24,missense_variant,p.Glu24Gln,ENST00000527520,;EI24,5_prime_UTR_variant,,ENST00000618552,;EI24,intron_variant,,ENST00000615917,;EI24,downstream_gene_variant,,ENST00000529812,;RNU6-1156P,downstream_gene_variant,,ENST00000410365,;STT3A-AS1,intron_variant,,ENST00000530526,;EI24,missense_variant,p.Glu22Asp,ENST00000531636,;EI24,non_coding_transcript_exon_variant,,ENST00000529765,; C ENST00000278903 Transcript missense_variant 540/2455 112/1023 38/340 E/Q Gag/Cag 1 1 EI24 HGNC HGNC:13276 protein_coding YES CCDS73410.1 ENSP00000278903 O14681 A0A024R3I8 UPI000006CFDB NM_004879.4 tolerated(0.18) 3/11 Low_complexity_(Seg):seg,hmmpanther:PTHR21389:SF0,hmmpanther:PTHR21389 MODERATE 1 SNV 1 1 PASS rs961210908 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 125575332 125575332 G C 1 0 0 0 0 1 0 0 0 4821 943 33 4 4 EI24 11 125575332 Missense_Mutation SNP G C3N-00737_T 7225557 125575332 9511290 110 19851 SRPRA 0 . GRCh38 11 126264474 126264474 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.1591C>T p.= p.L531L ENST00000332118 12/14 226 202 24 211 211 0 strelka-varscan-mutect SRPRA,synonymous_variant,p.=,ENST00000332118,NM_003139.3;SRPRA,synonymous_variant,p.=,ENST00000532259,NM_001177842.1;FAM118B,downstream_gene_variant,,ENST00000533050,NM_024556.3;FOXRED1,upstream_gene_variant,,ENST00000263578,NM_017547.3;FAM118B,downstream_gene_variant,,ENST00000627851,;FOXRED1,upstream_gene_variant,,ENST00000532125,;FAM118B,downstream_gene_variant,,ENST00000360194,;FAM118B,downstream_gene_variant,,ENST00000528985,;FAM118B,downstream_gene_variant,,ENST00000529731,;FOXRED1,upstream_gene_variant,,ENST00000534011,;FOXRED1,upstream_gene_variant,,ENST00000533839,;SRPRA,downstream_gene_variant,,ENST00000530680,;FOXRED1,upstream_gene_variant,,ENST00000526366,;SRPRA,non_coding_transcript_exon_variant,,ENST00000532268,;FAM118B,downstream_gene_variant,,ENST00000531935,;FOXRED1,upstream_gene_variant,,ENST00000527004,;FOXRED1,upstream_gene_variant,,ENST00000525770,;FOXRED1,upstream_gene_variant,,ENST00000525083,;FOXRED1,upstream_gene_variant,,ENST00000532101,;FOXRED1,upstream_gene_variant,,ENST00000524751,;SRPRA,downstream_gene_variant,,ENST00000528744,;SRPRA,downstream_gene_variant,,ENST00000527817,;FOXRED1,upstream_gene_variant,,ENST00000526525,;FOXRED1,upstream_gene_variant,,ENST00000529802,;SRPRA,downstream_gene_variant,,ENST00000531104,; A ENST00000332118 Transcript synonymous_variant 1746/3069 1591/1917 531/638 L Ctg/Ttg 1 -1 SRPRA HGNC HGNC:11307 protein_coding YES CCDS31717.1 ENSP00000328023 P08240 UPI0000135F5A NM_003139.3 12/14 hmmpanther:PTHR11564,Gene3D:3.40.50.300,Pfam_domain:PF00448,SMART_domains:SM00962,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 126264474 126264474 G A 1 0 0 0 0 0 0 0 1 15523 933 33 3 3 SRPRA 11 126264474 Silent SNP G C3N-00737_T 689142 126264474 8822148 111 19852 ARHGAP32 0 . GRCh38 11 128973232 128973232 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.3232G>T p.Ala1078Ser p.A1078S ENST00000310343 21/22 444 414 30 416 414 2 strelka-varscan-mutect ARHGAP32,missense_variant,p.Ala1078Ser,ENST00000310343,NM_001142685.1;ARHGAP32,missense_variant,p.Ala729Ser,ENST00000392657,NM_014715.3;ARHGAP32,missense_variant,p.Ala729Ser,ENST00000527272,;ARHGAP32,3_prime_UTR_variant,,ENST00000524655,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000526162,; A ENST00000310343 Transcript missense_variant 3232/10111 3232/6264 1078/2087 A/S Gct/Tct 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 deleterious_low_confidence(0.03) 21/22 hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 128973232 128973232 C A 1 0 0 0 0 1 0 0 0 1006 739 26 2 2 ARHGAP32 11 128973232 Missense_Mutation SNP C C3N-00737_T 2708758 128973232 6113390 112 19853 FGF6 0 . GRCh38 12 4445405 4445405 + Missense_Mutation SNP T T A novel C3N-00737_T C3N-00737_N T T c.166A>T p.Thr56Ser p.T56S ENST00000228837 1/3 283 246 37 263 263 0 strelka-varscan-mutect FGF6,missense_variant,p.Thr56Ser,ENST00000228837,NM_020996.2;FGF6,upstream_gene_variant,,ENST00000543077,; A ENST00000228837 Transcript missense_variant 210/743 166/627 56/208 T/S Acc/Tcc 1 -1 FGF6 HGNC HGNC:3684 protein_coding YES CCDS8527.1 ENSP00000228837 P10767 UPI00000411BF NM_020996.2 tolerated(0.63) 1/3 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF25 MODERATE 1 SNV 1 1 PASS rs1321896007 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 4445405 4445405 T A 1 0 0 0 0 1 0 0 0 5720 1696 59 4 4 FGF6 12 4445405 Missense_Mutation SNP T C3N-00737_T 4445405 128829904 113 19854 ABCC9 0 . GRCh38 12 21815891 21815891 + Missense_Mutation SNP G G T C3N-00737_T C3N-00737_N G G c.3895C>A p.Pro1299Thr p.P1299T ENST00000261200 32/38 380 342 38 349 348 1 strelka-varscan-mutect ABCC9,missense_variant,p.Pro1299Thr,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Pro1299Thr,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Pro926Thr,ENST00000544039,; T ENST00000261200 Transcript missense_variant,splice_region_variant 3895/8293 3895/4650 1299/1549 P/T Cct/Act COSM3459275,COSM3459276 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 tolerated(0.08) 32/38 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF173 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 21815891 21815891 G T 1 0 0 0 0 1 0 0 0 63 1188 41 2 2 ABCC9 12 21815891 Missense_Mutation SNP G C3N-00737_T 17370486 21815891 111459418 114 19855 BLOC1S1 0 . GRCh38 12 55716068 55716068 + Missense_Mutation SNP G G C rs545542768 C3N-00737_T C3N-00737_N G G c.17G>C p.Arg6Pro p.R6P ENST00000550412 1/4 101 75 26 115 115 0 strelka-varscan-mutect RP11-644F5.10,missense_variant,p.Arg6Pro,ENST00000550412,;BLOC1S1,missense_variant,p.Arg6Pro,ENST00000549147,;BLOC1S1,missense_variant,p.Arg6Pro,ENST00000548925,NM_001487.3;ITGA7,upstream_gene_variant,,ENST00000452168,NM_001144997.1;RDH5,upstream_gene_variant,,ENST00000257895,NM_002905.3,NM_001199771.1;RDH5,upstream_gene_variant,,ENST00000548082,;RDH5,upstream_gene_variant,,ENST00000547072,;BLOC1S1,upstream_gene_variant,,ENST00000547076,;ITGA7,upstream_gene_variant,,ENST00000557257,;BLOC1S1,upstream_gene_variant,,ENST00000551926,;RDH5,upstream_gene_variant,,ENST00000552930,;BLOC1S1,upstream_gene_variant,,ENST00000548556,;RP11-644F5.10,upstream_gene_variant,,ENST00000549424,;RDH5,upstream_gene_variant,,ENST00000553160,;RP11-644F5.10,missense_variant,p.Arg6Pro,ENST00000551946,;RDH5,upstream_gene_variant,,ENST00000550608,;ITGA7,upstream_gene_variant,,ENST00000553276,;RDH5,upstream_gene_variant,,ENST00000548486,;RP11-644F5.10,upstream_gene_variant,,ENST00000257899,;RDH5,upstream_gene_variant,,ENST00000553187,;ITGA7,upstream_gene_variant,,ENST00000555687,;ITGA7,upstream_gene_variant,,ENST00000553737,;ITGA7,upstream_gene_variant,,ENST00000555809,;RDH5,upstream_gene_variant,,ENST00000547301,;ITGA7,upstream_gene_variant,,ENST00000553893,;ITGA7,upstream_gene_variant,,ENST00000556273,;ITGA7,upstream_gene_variant,,ENST00000554724,;ITGA7,upstream_gene_variant,,ENST00000556371,;BLOC1S1,upstream_gene_variant,,ENST00000553100,; C ENST00000550412 Transcript missense_variant 33/3382 17/369 6/122 R/P cGa/cCa rs545542768 1 1 RP11-644F5.10 Clone_based_vega_gene protein_coding YES ENSP00000447650 F8W036 UPI0000D46D68 tolerated_low_confidence(0.07) 1/4 hmmpanther:PTHR13073,hmmpanther:PTHR13073:SF1,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS rs545542768 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 55716068 55716068 G C 1 0 0 0 0 1 0 0 0 1600 1058 37 4 4 BLOC1S1 12 55716068 Missense_Mutation SNP G C3N-00737_T 33900177 55716068 77559241 115 19856 BLOC1S1 0 . GRCh38 12 55716174 55716174 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.123G>A p.= p.Q41Q ENST00000550412 1/4 250 180 70 237 237 0 strelka-varscan-mutect RP11-644F5.10,synonymous_variant,p.=,ENST00000550412,;BLOC1S1,synonymous_variant,p.=,ENST00000549147,;BLOC1S1,synonymous_variant,p.=,ENST00000548925,NM_001487.3;ITGA7,upstream_gene_variant,,ENST00000452168,NM_001144997.1;RDH5,upstream_gene_variant,,ENST00000257895,NM_002905.3,NM_001199771.1;RDH5,upstream_gene_variant,,ENST00000548082,;RDH5,upstream_gene_variant,,ENST00000547072,;BLOC1S1,upstream_gene_variant,,ENST00000547076,;ITGA7,upstream_gene_variant,,ENST00000557257,;BLOC1S1,upstream_gene_variant,,ENST00000551926,;RDH5,upstream_gene_variant,,ENST00000552930,;BLOC1S1,upstream_gene_variant,,ENST00000548556,;RP11-644F5.10,upstream_gene_variant,,ENST00000549424,;RDH5,upstream_gene_variant,,ENST00000553160,;RP11-644F5.10,synonymous_variant,p.=,ENST00000551946,;RP11-644F5.10,synonymous_variant,p.=,ENST00000257899,;BLOC1S1,synonymous_variant,p.=,ENST00000553100,;RDH5,upstream_gene_variant,,ENST00000550608,;ITGA7,upstream_gene_variant,,ENST00000553276,;RDH5,upstream_gene_variant,,ENST00000548486,;RDH5,upstream_gene_variant,,ENST00000553187,;ITGA7,upstream_gene_variant,,ENST00000555687,;ITGA7,upstream_gene_variant,,ENST00000553737,;ITGA7,upstream_gene_variant,,ENST00000555809,;RDH5,upstream_gene_variant,,ENST00000547301,;ITGA7,upstream_gene_variant,,ENST00000553893,;ITGA7,upstream_gene_variant,,ENST00000556273,;ITGA7,upstream_gene_variant,,ENST00000554724,;ITGA7,upstream_gene_variant,,ENST00000556371,; A ENST00000550412 Transcript synonymous_variant 139/3382 123/369 41/122 Q caG/caA 1 1 RP11-644F5.10 Clone_based_vega_gene protein_coding YES ENSP00000447650 F8W036 UPI0000D46D68 1/4 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06320,hmmpanther:PTHR13073,hmmpanther:PTHR13073:SF1,Low_complexity_(Seg):seg LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 55716174 55716174 G A 1 0 0 0 0 0 0 0 1 1600 933 33 3 3 BLOC1S1 12 55716174 Silent SNP G C3N-00737_T 106 55716174 77559135 116 19857 ERBB3 0 . GRCh38 12 56101609 56101609 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.3583G>C p.Glu1195Gln p.E1195Q ENST00000267101 28/28 464 374 90 381 381 0 strelka-varscan-mutect ERBB3,missense_variant,p.Glu1195Gln,ENST00000267101,NM_001982.3;ERBB3,missense_variant,p.Glu1136Gln,ENST00000415288,;ERBB3,missense_variant,p.Glu315Gln,ENST00000549832,;ERBB3,missense_variant,p.Glu436Gln,ENST00000553131,;ERBB3,missense_variant,p.Glu502Gln,ENST00000550070,;RP11-603J24.9,intron_variant,,ENST00000548861,;PA2G4,upstream_gene_variant,,ENST00000303305,NM_006191.2;PA2G4,upstream_gene_variant,,ENST00000552766,;PA2G4,upstream_gene_variant,,ENST00000551061,;PA2G4,upstream_gene_variant,,ENST00000553057,;RP11-603J24.17,downstream_gene_variant,,ENST00000548595,;ERBB3,3_prime_UTR_variant,,ENST00000551085,;ERBB3,3_prime_UTR_variant,,ENST00000551242,;ERBB3,downstream_gene_variant,,ENST00000550869,;ERBB3,downstream_gene_variant,,ENST00000548709,;ERBB3,downstream_gene_variant,,ENST00000552691,; C ENST00000267101 Transcript missense_variant 4023/5919 3583/4029 1195/1342 E/Q Gag/Cag 1 1 ERBB3 HGNC HGNC:3431 protein_coding YES CCDS31833.1 ENSP00000267101 P21860 UPI000012A113 NM_001982.3 tolerated(0.26) 28/28 PIRSF_domain:PIRSF000619,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 56101609 56101609 G C 1 0 0 0 0 1 0 0 0 5056 1291 45 4 4 ERBB3 12 56101609 Missense_Mutation SNP G C3N-00737_T 385435 56101609 77173700 117 19858 RB1 0 . GRCh38 13 48362958 48362958 + Splice_Site SNP G G A C3N-00737_T C3N-00737_N G G c.861+1G>A p.X287_splice ENST00000267163 204 156 48 188 188 0 strelka-varscan-mutect RB1,splice_donor_variant,,ENST00000267163,NM_000321.2;RB1,downstream_gene_variant,,ENST00000525036,;RB1,downstream_gene_variant,,ENST00000467505,; A ENST00000267163 Transcript splice_donor_variant -/4840 861/2787 287/928 CS0910389,COSM1514097,COSM1514098,COSM4169364,COSM4169365 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 8/26 0,1,1,1,1 HIGH 1 SNV 1 1,1,1,1,1 1 PASS rs1064795296 . 0 206 0 3 0 0 0 0 -20 0.9999973 1 1 1 0 A 5 1 63 48362958 48362958 G A 1 0 0 0 0 0 0 1 0 13259 1275 44 3 3 RB1 13 48362958 Splice_Site SNP G C3N-00737_T 48362958 66001370 118 19859 NALCN 0 . GRCh38 13 101089902 101089902 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.3334C>A p.Leu1112Ile p.L1112I ENST00000251127 29/44 364 296 68 334 333 1 strelka-varscan-mutect NALCN,missense_variant,p.Leu1112Ile,ENST00000251127,NM_052867.2; T ENST00000251127 Transcript missense_variant 3416/6818 3334/5217 1112/1738 L/I Ctc/Atc 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 deleterious(0) 29/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 101089902 101089902 G T 1 0 0 0 0 1 0 0 0 10155 942 33 2 2 NALCN 13 101089902 Missense_Mutation SNP G C3N-00737_T 52726944 101089902 13274426 119 19860 COL4A2 0 . GRCh38 13 110450378 110450378 + Silent SNP C C T rs757264758 C3N-00737_T C3N-00737_N C C c.1263C>T p.= p.Y421Y ENST00000360467 20/48 292 218 74 216 216 0 strelka-varscan-mutect COL4A2,synonymous_variant,p.=,ENST00000360467,NM_001846.2; T ENST00000360467 Transcript synonymous_variant 1569/6281 1263/5139 421/1712 Y taC/taT rs757264758,COSM4673812 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 20/48 0,1 LOW 1 SNV 5 0,1 1 PASS rs757264758 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 110450378 110450378 C T 1 0 0 0 0 0 0 0 1 3479 547 19 1 1 COL4A2 13 110450378 Silent SNP C C3N-00737_T 9360476 110450378 3913950 120 19861 STRN3 0 . GRCh38 14 30905540 30905540 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.1907C>T p.Ser636Leu p.S636L ENST00000357479 15/18 379 224 155 309 309 0 strelka-varscan-mutect STRN3,missense_variant,p.Ser552Leu,ENST00000355683,NM_014574.3;STRN3,missense_variant,p.Ser636Leu,ENST00000357479,NM_001083893.1;STRN3,3_prime_UTR_variant,,ENST00000555358,;STRN3,non_coding_transcript_exon_variant,,ENST00000554124,; A ENST00000357479 Transcript missense_variant 2104/2799 1907/2394 636/797 S/L tCa/tTa 1 -1 STRN3 HGNC HGNC:15720 protein_coding YES CCDS41938.1 ENSP00000350071 Q13033 UPI0000F734B1 NM_001083893.1 deleterious(0) 15/18 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR15653,hmmpanther:PTHR15653:SF3,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 30905540 30905540 G A 1 0 0 0 0 1 0 0 0 15713 1294 45 3 3 STRN3 14 30905540 Missense_Mutation SNP G C3N-00737_T 30905540 76138178 121 19862 RTN1 0 . GRCh38 14 59746198 59746198 + Silent SNP G G C novel C3N-00737_T C3N-00737_N G G c.525C>G p.= p.S175S ENST00000267484 2/9 117 84 33 122 122 0 strelka-varscan-mutect RTN1,synonymous_variant,p.=,ENST00000267484,NM_021136.2;RTN1,synonymous_variant,p.=,ENST00000611068,; C ENST00000267484 Transcript synonymous_variant 861/3435 525/2331 175/776 S tcC/tcG 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 2/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 59746198 59746198 G C 1 0 0 0 0 0 0 0 1 13985 1335 47 4 4 RTN1 14 59746198 Silent SNP G C3N-00737_T 28840658 59746198 47297520 122 19863 HERC2 0 . GRCh38 15 28274412 28274412 + Nonsense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.679G>T p.Glu227Ter p.E227* ENST00000261609 7/93 144 121 23 122 122 0 strelka-varscan-mutect HERC2,stop_gained,p.Glu227Ter,ENST00000261609,NM_004667.5;HERC2,3_prime_UTR_variant,,ENST00000564734,;HERC2,upstream_gene_variant,,ENST00000563670,; A ENST00000261609 Transcript stop_gained 788/15337 679/14505 227/4834 E/* Gag/Tag 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 7/93 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF325 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 63 28274412 28274412 C A 1 0 0 0 0 0 1 0 0 6942 864 30 2 2 HERC2 15 28274412 Nonsense_Mutation SNP C C3N-00737_T 28274412 73716777 123 19864 MAPKBP1 0 . GRCh38 15 41813641 41813641 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.858C>G p.Ile286Met p.I286M ENST00000456763 10/32 198 171 27 163 163 0 strelka-varscan-mutect MAPKBP1,missense_variant,p.Ile280Met,ENST00000457542,NM_014994.2;MAPKBP1,missense_variant,p.Ile286Met,ENST00000456763,NM_001128608.1;MAPKBP1,missense_variant,p.Ile280Met,ENST00000514566,NM_001265611.1;MAPKBP1,downstream_gene_variant,,ENST00000510535,;MAPKBP1,downstream_gene_variant,,ENST00000627631,;MAPKBP1,downstream_gene_variant,,ENST00000507762,;MAPKBP1,missense_variant,p.Ile280Met,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000502292,;MAPKBP1,downstream_gene_variant,,ENST00000515164,;MAPKBP1,upstream_gene_variant,,ENST00000503526,;MAPKBP1,downstream_gene_variant,,ENST00000507147,; G ENST00000456763 Transcript missense_variant 1054/7158 858/4545 286/1514 I/M atC/atG 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 deleterious(0.01) 10/32 hmmpanther:PTHR22847:SF432,hmmpanther:PTHR22847,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 41813641 41813641 C G 1 0 0 0 0 1 0 0 0 9216 903 32 4 4 MAPKBP1 15 41813641 Missense_Mutation SNP C C3N-00737_T 13539229 41813641 60177548 124 19865 MAPKBP1 0 . GRCh38 15 41813706 41813706 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.923C>G p.Ser308Cys p.S308C ENST00000456763 10/32 151 132 19 141 141 0 strelka-varscan-mutect MAPKBP1,missense_variant,p.Ser302Cys,ENST00000457542,NM_014994.2;MAPKBP1,missense_variant,p.Ser308Cys,ENST00000456763,NM_001128608.1;MAPKBP1,missense_variant,p.Ser302Cys,ENST00000514566,NM_001265611.1;MAPKBP1,downstream_gene_variant,,ENST00000510535,;MAPKBP1,downstream_gene_variant,,ENST00000627631,;MAPKBP1,downstream_gene_variant,,ENST00000507762,;MAPKBP1,missense_variant,p.Ser302Cys,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000502292,;MAPKBP1,downstream_gene_variant,,ENST00000515164,;MAPKBP1,upstream_gene_variant,,ENST00000503526,;MAPKBP1,downstream_gene_variant,,ENST00000507147,; G ENST00000456763 Transcript missense_variant 1119/7158 923/4545 308/1514 S/C tCt/tGt 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 tolerated(0.19) 10/32 hmmpanther:PTHR22847:SF432,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 41813706 41813706 C G 1 0 0 0 0 1 0 0 0 9216 913 32 4 4 MAPKBP1 15 41813706 Missense_Mutation SNP C C3N-00737_T 65 41813706 60177483 125 19866 CILP 0 . GRCh38 15 65198482 65198482 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.1804G>A p.Glu602Lys p.E602K ENST00000261883 9/9 311 248 63 273 273 0 strelka-varscan-mutect CILP,missense_variant,p.Glu602Lys,ENST00000261883,NM_003613.3; T ENST00000261883 Transcript missense_variant 1971/5695 1804/3555 602/1184 E/K Gag/Aag 1 -1 CILP HGNC HGNC:1980 protein_coding YES CCDS10203.1 ENSP00000261883 O75339 UPI000013D21B NM_003613.3 tolerated(0.18) 9/9 hmmpanther:PTHR15031 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 65198482 65198482 C T 1 0 0 0 0 1 0 0 0 3191 864 30 3 3 CILP 15 65198482 Missense_Mutation SNP C C3N-00737_T 23384776 65198482 36792707 126 19867 SMAD3 0 . GRCh38 15 67138083 67138083 + Silent SNP A A G novel C3N-00737_T C3N-00737_N A A c.57A>G p.= p.K19K ENST00000439724 1/9 260 233 27 200 200 0 strelka-varscan-mutect SMAD3,synonymous_variant,p.=,ENST00000439724,NM_001145103.1;SMAD3,intron_variant,,ENST00000327367,NM_005902.3;SMAD3,intron_variant,,ENST00000540846,NM_001145102.1;SMAD3,intron_variant,,ENST00000558894,;SMAD3,intron_variant,,ENST00000559092,;SMAD3,intron_variant,,ENST00000559460,;SMAD3,intron_variant,,ENST00000560175,;SMAD3,upstream_gene_variant,,ENST00000558739,;RP11-342M21.2,downstream_gene_variant,,ENST00000558463,;SMAD3,intron_variant,,ENST00000559937,; G ENST00000439724 Transcript synonymous_variant 83/1530 57/1146 19/381 K aaA/aaG 1 1 SMAD3 HGNC HGNC:6769 protein_coding CCDS45288.1 ENSP00000401133 P84022 UPI0001915047 NM_001145103.1 1/9 PROSITE_profiles:PS51075,SMART_domains:SM00523 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 67138083 67138083 A G 1 0 0 0 0 0 0 0 1 15052 69 3 5 5 SMAD3 15 67138083 Silent SNP A C3N-00737_T 1939601 67138083 34853106 127 19868 UACA 0 . GRCh38 15 70668887 70668887 + Silent SNP T T C novel C3N-00737_T C3N-00737_N T T c.1797A>G p.= p.E599E ENST00000322954 16/19 233 187 46 242 241 1 strelka-varscan-mutect UACA,synonymous_variant,p.=,ENST00000322954,NM_018003.2;UACA,synonymous_variant,p.=,ENST00000379983,NM_001008224.1;UACA,synonymous_variant,p.=,ENST00000560441,;UACA,synonymous_variant,p.=,ENST00000539319,;UACA,downstream_gene_variant,,ENST00000558758,;UACA,upstream_gene_variant,,ENST00000560831,;UACA,downstream_gene_variant,,ENST00000559290,;UACA,downstream_gene_variant,,ENST00000560523,;UACA,downstream_gene_variant,,ENST00000558308,; C ENST00000322954 Transcript synonymous_variant 1983/6939 1797/4251 599/1416 E gaA/gaG 1 -1 UACA HGNC HGNC:15947 protein_coding YES CCDS10235.1 ENSP00000314556 Q9BZF9 UPI000006DCF3 NM_018003.2 16/19 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 70668887 70668887 T C 1 0 0 0 0 0 0 0 1 17343 1838 64 5 5 UACA 15 70668887 Silent SNP T C3N-00737_T 3530804 70668887 31322302 128 19869 PEAK1 0 . GRCh38 15 77179964 77179964 + Missense_Mutation SNP C C T C3N-00737_T C3N-00737_N C C c.1963G>A p.Glu655Lys p.E655K ENST00000560626 4/7 339 305 34 389 388 1 strelka-varscan-mutect PEAK1,missense_variant,p.Glu655Lys,ENST00000560626,;PEAK1,missense_variant,p.Glu655Lys,ENST00000312493,NM_024776.3;PEAK1,missense_variant,p.Glu655Lys,ENST00000558305,;PEAK1,missense_variant,p.Glu655Lys,ENST00000564328,;PEAK1,downstream_gene_variant,,ENST00000565820,;PEAK1,upstream_gene_variant,,ENST00000559791,;PEAK1,downstream_gene_variant,,ENST00000567808,;PEAK1,upstream_gene_variant,,ENST00000560854,; T ENST00000560626 Transcript missense_variant 2439/19217 1963/5241 655/1746 E/K Gaa/Aaa COSM1374715,COSM1374716 1 -1 PEAK1 HGNC HGNC:29431 protein_coding YES CCDS42062.1 ENSP00000452796 Q9H792 UPI00002378D0 tolerated(0.32) 4/7 hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 173 0 6 30 0 0 0 -10.24968 0 0 1 0 0 T 3 4 63 77179964 77179964 C T 1 0 0 0 0 1 0 0 0 11800 864 30 3 3 PEAK1 15 77179964 Missense_Mutation SNP C C3N-00737_T 6511077 77179964 24811225 129 19870 BNC1 0 . GRCh38 15 83264609 83264609 + Missense_Mutation SNP C C A rs772576851 C3N-00737_T C3N-00737_N C C c.642G>T p.Arg214Ser p.R214S ENST00000345382 4/5 218 170 48 236 235 1 strelka-varscan-mutect BNC1,missense_variant,p.Arg214Ser,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Arg207Ser,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; A ENST00000345382 Transcript missense_variant 728/4610 642/2985 214/994 R/S agG/agT rs772576851,COSM5522197 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0.02) 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772576851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 83264609 83264609 C A 1 0 0 0 0 1 0 0 0 1630 854 30 2 2 BNC1 15 83264609 Missense_Mutation SNP C C3N-00737_T 6084645 83264609 18726580 130 19871 IQGAP1 0 . GRCh38 15 90477217 90477217 + Nonsense_Mutation SNP C C T rs371671746 C3N-00737_T C3N-00737_N C C c.3091C>T p.Gln1031Ter p.Q1031* ENST00000268182 25/38 163 145 18 158 158 0 strelka-varscan-mutect IQGAP1,stop_gained,p.Gln1031Ter,ENST00000268182,NM_003870.3;IQGAP1,stop_gained,p.Gln459Ter,ENST00000560738,;IQGAP1,downstream_gene_variant,,ENST00000560373,;IQGAP1,downstream_gene_variant,,ENST00000560020,;IQGAP1,stop_gained,p.Gln1031Ter,ENST00000633485,;IQGAP1,downstream_gene_variant,,ENST00000558003,;IQGAP1,downstream_gene_variant,,ENST00000560733,; T ENST00000268182 Transcript stop_gained 3215/7233 3091/4974 1031/1657 Q/* Caa/Taa rs371671746,COSM1254909 1 1 IQGAP1 HGNC HGNC:6110 protein_coding YES CCDS10362.1 ENSP00000268182 P46940 A0A024RC65 UPI000012D863 NM_003870.3 25/38 PROSITE_profiles:PS50018,hmmpanther:PTHR14149:SF15,hmmpanther:PTHR14149,Gene3D:1.10.506.10,Pfam_domain:PF00616,SMART_domains:SM00323,Superfamily_domains:SSF48350 0,1 HIGH 1 SNV 1 0,1 1 PASS rs371671746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 63 90477217 90477217 C T 1 0 0 0 0 0 1 0 0 7720 595 21 3 3 IQGAP1 15 90477217 Nonsense_Mutation SNP C C3N-00737_T 7212608 90477217 11513972 131 19872 ITPRIPL2 0 . GRCh38 16 19115580 19115580 + Silent SNP C C G novel C3N-00737_T C3N-00737_N C C c.1119C>G p.= p.L373L ENST00000381440 1/1 76 59 17 110 110 0 strelka-varscan-mutect ITPRIPL2,synonymous_variant,p.=,ENST00000381440,NM_001034841.3;ITPRIPL2,3_prime_UTR_variant,,ENST00000566735,;RP11-626G11.6,upstream_gene_variant,,ENST00000617407,;RP11-626G11.3,downstream_gene_variant,,ENST00000567236,;CTD-2349B8.1,intron_variant,,ENST00000564808,;CTD-2349B8.1,intron_variant,,ENST00000568526,; G ENST00000381440 Transcript synonymous_variant 1198/7247 1119/1608 373/535 L ctC/ctG 1 1 ITPRIPL2 HGNC HGNC:27257 protein_coding YES CCDS32395.1 ENSP00000370849 Q3MIP1 UPI000023760C NM_001034841.3 1/1 Pfam_domain:PF03281,Prints_domain:PR02107,hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF9,SMART_domains:SM01265 LOW SNV 1 PASS rs1056011073 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 63 19115580 19115580 C G 1 0 0 0 0 0 0 0 1 7831 813 29 4 4 ITPRIPL2 16 19115580 Silent SNP C C3N-00737_T 19115580 71222765 132 19873 TNRC6A 0 . GRCh38 16 24777160 24777160 + Missense_Mutation SNP C C G rs201072103 C3N-00737_T C3N-00737_N C C c.391C>G p.Arg131Gly p.R131G ENST00000395799 5/25 549 456 93 498 498 0 strelka-varscan-mutect TNRC6A,missense_variant,p.Arg131Gly,ENST00000395799,NM_014494.2;TNRC6A,missense_variant,p.Arg131Gly,ENST00000315183,;TNRC6A,downstream_gene_variant,,ENST00000562829,;TNRC6A,upstream_gene_variant,,ENST00000491718,; G ENST00000395799 Transcript missense_variant 520/8438 391/5889 131/1962 R/G Cgg/Ggg rs201072103,COSM3280413 1 1 TNRC6A HGNC HGNC:11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 UPI000059D33E NM_014494.2 deleterious(0) 5/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs201072103 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 24777160 24777160 C G 1 0 0 0 0 1 0 0 0 16813 875 31 4 4 TNRC6A 16 24777160 Missense_Mutation SNP C C3N-00737_T 5661580 24777160 65561185 133 19874 GTF3C1 0 . GRCh38 16 27492640 27492640 + Missense_Mutation SNP C C T C3N-00737_T C3N-00737_N C C c.2950G>A p.Glu984Lys p.E984K ENST00000356183 18/37 272 226 46 224 224 0 strelka-varscan-mutect GTF3C1,missense_variant,p.Glu984Lys,ENST00000356183,NM_001520.3;GTF3C1,missense_variant,p.Glu984Lys,ENST00000561623,NM_001286242.1;GTF3C1,intron_variant,,ENST00000569653,;GTF3C1,upstream_gene_variant,,ENST00000568569,;GTF3C1,upstream_gene_variant,,ENST00000564664,; T ENST00000356183 Transcript missense_variant 2966/7018 2950/6330 984/2109 E/K Gaa/Aaa COSM4541149,COSM702819 1 -1 GTF3C1 HGNC HGNC:4664 protein_coding YES CCDS32414.1 ENSP00000348510 Q12789 UPI00001FF123 NM_001520.3 deleterious(0) 18/37 hmmpanther:PTHR15180,hmmpanther:PTHR15180:SF1 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 27492640 27492640 C T 1 0 0 0 0 1 0 0 0 6753 864 30 3 3 GTF3C1 16 27492640 Missense_Mutation SNP C C3N-00737_T 2715480 27492640 62845705 134 19875 RBL2 0 . GRCh38 16 53434675 53434675 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.119C>G p.Ser40Trp p.S40W ENST00000262133 1/22 232 202 30 148 148 0 strelka-varscan-mutect RBL2,missense_variant,p.Ser40Trp,ENST00000262133,NM_001323611.1,NM_005611.3;RBL2,intron_variant,,ENST00000567964,;RBL2,upstream_gene_variant,,ENST00000544405,; G ENST00000262133 Transcript missense_variant 256/4906 119/3420 40/1139 S/W tCg/tGg 1 1 RBL2 HGNC HGNC:9894 protein_coding YES CCDS10748.1 ENSP00000262133 Q08999 UPI000013D264 NM_001323611.1,NM_005611.3 deleterious(0.01) 1/22 Low_complexity_(Seg):seg,hmmpanther:PTHR13742:SF8,hmmpanther:PTHR13742 MODERATE 1 SNV 1 1 PASS rs1280372152 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 63 53434675 53434675 C G 1 0 0 0 0 1 0 0 0 13276 893 31 4 4 RBL2 16 53434675 Missense_Mutation SNP C C3N-00737_T 25942035 53434675 36903670 135 19876 1 14 2 2 12 C 6.51802e-05 RBL2 0 . GRCh38 16 53434686 53434686 + Nonsense_Mutation SNP C C T rs763967250 C3N-00737_T C3N-00737_N C C c.130C>T p.Gln44Ter p.Q44* ENST00000262133 1/22 249 219 30 158 158 0 strelka-varscan-mutect RBL2,stop_gained,p.Gln44Ter,ENST00000262133,NM_001323611.1,NM_005611.3;RBL2,intron_variant,,ENST00000567964,;RBL2,upstream_gene_variant,,ENST00000544405,; T ENST00000262133 Transcript stop_gained 267/4906 130/3420 44/1139 Q/* Cag/Tag rs763967250 1 1 RBL2 HGNC HGNC:9894 protein_coding YES CCDS10748.1 ENSP00000262133 Q08999 UPI000013D264 NM_001323611.1,NM_005611.3 1/22 hmmpanther:PTHR13742:SF8,hmmpanther:PTHR13742 HIGH 1 SNV 1 1 PASS rs763967250 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 63 53434686 53434686 C T 1 0 0 0 0 0 1 0 0 13276 827 29 3 3 RBL2 16 53434686 Nonsense_Mutation SNP C C3N-00737_T 11 53434686 36903659 136 19877 1 14 2 2 12 C 6.51802e-05 TP53 0 . GRCh38 17 7675076 7675076 + Missense_Mutation SNP T T C C3N-00737_T C3N-00737_N T T c.536A>G p.His179Arg p.H179R ENST00000269305 5/11 362 276 86 382 382 0 strelka-varscan-mutect TP53,missense_variant,p.His179Arg,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.His179Arg,ENST00000420246,;TP53,missense_variant,p.His140Arg,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.His140Arg,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.His179Arg,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.His140Arg,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.His179Arg,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.His140Arg,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.His179Arg,ENST00000445888,;TP53,missense_variant,p.His140Arg,ENST00000619485,;TP53,missense_variant,p.His47Arg,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.His20Arg,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.His47Arg,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.His20Arg,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.His47Arg,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.His20Arg,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.His179Arg,ENST00000359597,;TP53,missense_variant,p.His168Arg,ENST00000615910,;TP53,missense_variant,p.His179Arg,ENST00000413465,;TP53,missense_variant,p.His47Arg,ENST00000509690,;TP53,missense_variant,p.His86Arg,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.His140Arg,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 726/2579 536/1182 179/393 H/R cAt/cGt TP53_g.12524A>G,TP53_g.12524A>C,TP53_g.12524del,TP53_g.12524A>T,COSM10889,COSM129844,COSM129845,COSM129846,COSM129847,COSM1645241,COSM1731642,COSM214222,COSM214223,COSM214224,COSM214225,COSM3396280,COSM3980298,COSM43635,COSM44218,COSM44627 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1057519991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 63 7675076 7675076 T C 1 0 0 0 0 1 0 0 0 16859 1464 51 5 5 TP53 17 7675076 Missense_Mutation SNP T C3N-00737_T 7675076 75582365 137 19878 KDM6B 0 . GRCh38 17 7852506 7852506 + Nonsense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.4480C>T p.Gln1494Ter p.Q1494* ENST00000254846 20/22 631 595 36 580 580 0 strelka-varscan-mutect KDM6B,stop_gained,p.Gln1494Ter,ENST00000254846,NM_001080424.1;KDM6B,stop_gained,p.Gln1494Ter,ENST00000448097,;KDM6B,downstream_gene_variant,,ENST00000570632,;NAA38,downstream_gene_variant,,ENST00000333775,NM_032356.3;TMEM88,upstream_gene_variant,,ENST00000301599,NM_203411.1;NAA38,downstream_gene_variant,,ENST00000575771,;NAA38,downstream_gene_variant,,ENST00000576861,;NAA38,downstream_gene_variant,,ENST00000575071,;NAA38,downstream_gene_variant,,ENST00000575208,;TMEM88,upstream_gene_variant,,ENST00000574668,NM_001319941.1;NAA38,downstream_gene_variant,,ENST00000576384,; T ENST00000254846 Transcript stop_gained 4869/6713 4480/5049 1494/1682 Q/* Cag/Tag 1 1 KDM6B HGNC HGNC:29012 protein_coding YES CCDS32552.1 ENSP00000254846 O15054 UPI00006C175B NM_001080424.1 20/22 PROSITE_profiles:PS51184,hmmpanther:PTHR14017:SF5,hmmpanther:PTHR14017,SMART_domains:SM00558,Superfamily_domains:SSF51197 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 63 7852506 7852506 C T 1 0 0 0 0 0 1 0 0 8056 595 21 3 3 KDM6B 17 7852506 Nonsense_Mutation SNP C C3N-00737_T 177430 7852506 75404935 138 19879 KRT38 0 . GRCh38 17 41438147 41438147 + Missense_Mutation SNP C C G rs370561631 C3N-00737_T C3N-00737_N C C c.1187G>C p.Arg396Pro p.R396P ENST00000246646 6/7 217 199 18 219 219 0 strelka-varscan-mutect KRT38,missense_variant,p.Arg396Pro,ENST00000246646,NM_006771.3; G ENST00000246646 Transcript missense_variant 1187/2337 1187/1371 396/456 R/P cGg/cCg rs370561631 1 -1 KRT38 HGNC HGNC:6456 protein_coding YES CCDS11392.1 ENSP00000246646 O76015 UPI000013CBF9 NM_006771.3 deleterious(0) 6/7 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF166,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs370561631 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 41438147 41438147 C G 1 0 0 0 0 1 0 0 0 8357 652 23 4 4 KRT38 17 41438147 Missense_Mutation SNP C C3N-00737_T 33585641 41438147 41819294 139 19880 ITGA2B 0 . GRCh38 17 44389455 44389455 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.19C>T p.Pro7Ser p.P7S ENST00000262407 1/30 343 281 62 299 299 0 strelka-varscan-mutect ITGA2B,missense_variant,p.Pro7Ser,ENST00000262407,NM_000419.3;ITGA2B,upstream_gene_variant,,ENST00000592226,;ITGA2B,upstream_gene_variant,,ENST00000589645,;ITGA2B,upstream_gene_variant,,ENST00000591990,;ITGA2B,upstream_gene_variant,,ENST00000592944,;ITGA2B,upstream_gene_variant,,ENST00000592253,;ITGA2B,upstream_gene_variant,,ENST00000592075,; A ENST00000262407 Transcript missense_variant 51/3333 19/3120 7/1039 P/S Cca/Tca 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 tolerated_low_confidence(0.29) 1/30 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 44389455 44389455 G A 1 0 0 0 0 1 0 0 0 7783 1174 41 3 3 ITGA2B 17 44389455 Missense_Mutation SNP G C3N-00737_T 2951308 44389455 38867986 140 19881 CRHR1 0 . GRCh38 17 45830459 45830459 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.73G>T p.Val25Leu p.V25L ENST00000634540 9/15 100 92 8 98 97 1 strelka-varscan-mutect CRHR1,missense_variant,p.Val25Leu,ENST00000634540,NM_001256299.2,NM_001303018.1;CRHR1,missense_variant,p.Val229Leu,ENST00000293493,;CRHR1,missense_variant,p.Val200Leu,ENST00000314537,NM_004382.4;CRHR1,missense_variant,p.Val99Leu,ENST00000339069,NM_001303016.1,NM_001303020.1;CRHR1,missense_variant,p.Val229Leu,ENST00000398285,NM_001145146.1;CRHR1,missense_variant,p.Cys131Phe,ENST00000619154,;CRHR1,missense_variant,p.Val200Leu,ENST00000577353,NM_001145148.1;CRHR1,missense_variant,p.Val160Leu,ENST00000352855,NM_001145147.1;CRHR1,upstream_gene_variant,,ENST00000580876,;MAPT-AS1,intron_variant,,ENST00000634876,;CRHR1,3_prime_UTR_variant,,ENST00000347197,;CRHR1,non_coding_transcript_exon_variant,,ENST00000582766,;CRHR1,non_coding_transcript_exon_variant,,ENST00000581479,;CRHR1,intron_variant,,ENST00000583888,;CRHR1,upstream_gene_variant,,ENST00000535778,;CRHR1,downstream_gene_variant,,ENST00000580955,; T ENST00000634540 Transcript missense_variant 983/2695 73/723 25/240 V/L Gtg/Ttg 1 1 CRHR1 EntrezGene HGNC:2357 protein_coding YES ENSP00000488912 A0A024R9X9 UPI0000D4A34F NM_001256299.2,NM_001303018.1 tolerated(1) 9/15 Pfam_domain:PF00002,Prints_domain:PR00249,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF175,Superfamily_domains:SSF81321 MODERATE SNV 2 1 PASS . . 0 201 6 3 0 0 0 0 -12.33907 0.9984746 1 1 1 0 T 3 4 63 45830459 45830459 G T 1 0 0 0 0 1 0 0 0 3672 1377 48 2 2 CRHR1 17 45830459 Missense_Mutation SNP G C3N-00737_T 1441004 45830459 37426982 141 19882 SPAG9 0 . GRCh38 17 51041517 51041517 + Missense_Mutation SNP G G C novel C3N-00737_T C3N-00737_N G G c.725C>G p.Ser242Cys p.S242C ENST00000262013 5/30 152 128 24 119 119 0 strelka-varscan-mutect SPAG9,missense_variant,p.Ser242Cys,ENST00000262013,NM_001130528.2;SPAG9,missense_variant,p.Ser242Cys,ENST00000618113,;SPAG9,missense_variant,p.Ser99Cys,ENST00000510283,NM_001251971.1;SPAG9,missense_variant,p.Ser242Cys,ENST00000357122,NM_003971.5;SPAG9,missense_variant,p.Ser242Cys,ENST00000505279,NM_001130527.2;SPAG9,missense_variant,p.Ser99Cys,ENST00000510855,;RP11-481C4.1,upstream_gene_variant,,ENST00000509833,;SPAG9,upstream_gene_variant,,ENST00000576492,;SPAG9,non_coding_transcript_exon_variant,,ENST00000514613,;SPAG9,non_coding_transcript_exon_variant,,ENST00000505173,;SPAG9,non_coding_transcript_exon_variant,,ENST00000511987,;SPAG9,non_coding_transcript_exon_variant,,ENST00000502329,; C ENST00000262013 Transcript missense_variant 934/8273 725/3966 242/1321 S/C tCt/tGt 1 -1 SPAG9 HGNC HGNC:14524 protein_coding YES CCDS45740.1 ENSP00000262013 O60271 UPI0000D60DF7 NM_001130528.2 tolerated(0.06) 5/30 hmmpanther:PTHR13886:SF2,hmmpanther:PTHR13886 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999846 1 1 1 0 C 3 2 63 51041517 51041517 G C 1 0 0 0 0 1 0 0 0 15316 942 33 4 4 SPAG9 17 51041517 Missense_Mutation SNP G C3N-00737_T 5211058 51041517 32215924 142 19883 BRIP1 0 . GRCh38 17 61801358 61801358 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.1035G>A p.= p.K345K ENST00000259008 8/20 661 586 75 566 566 0 strelka-varscan-mutect BRIP1,synonymous_variant,p.=,ENST00000259008,NM_032043.2;BRIP1,synonymous_variant,p.=,ENST00000577598,; T ENST00000259008 Transcript synonymous_variant 1303/6048 1035/3750 345/1249 K aaG/aaA 1 -1 BRIP1 HGNC HGNC:20473 protein_coding YES CCDS11631.1 ENSP00000259008 Q9BX63 A0A024QZ45 UPI000013D01F NM_032043.2 8/20 PROSITE_profiles:PS51193,hmmpanther:PTHR11472:SF6,hmmpanther:PTHR11472,TIGRFAM_domain:TIGR00604,Pfam_domain:PF06733,SMART_domains:SM00488,SMART_domains:SM00487 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 61801358 61801358 C T 1 0 0 0 0 0 0 0 1 1688 912 32 3 3 BRIP1 17 61801358 Silent SNP C C3N-00737_T 10759841 61801358 21456083 143 19884 TRIM47 0 . GRCh38 17 75878418 75878418 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.131G>A p.Gly44Glu p.G44E ENST00000254816 1/6 88 78 10 47 47 0 strelka-varscan-mutect TRIM47,missense_variant,p.Gly44Glu,ENST00000254816,NM_033452.2;TRIM65,downstream_gene_variant,,ENST00000591668,;TRIM47,upstream_gene_variant,,ENST00000586495,;TRIM47,upstream_gene_variant,,ENST00000585333,;TRIM65,downstream_gene_variant,,ENST00000592642,;RP11-552F3.9,non_coding_transcript_exon_variant,,ENST00000586076,;TRIM47,upstream_gene_variant,,ENST00000587339,;TRIM47,upstream_gene_variant,,ENST00000592942,;TRIM47,upstream_gene_variant,,ENST00000587774,;TRIM47,upstream_gene_variant,,ENST00000593089,; T ENST00000254816 Transcript missense_variant 158/2266 131/1917 44/638 G/E gGa/gAa 1 -1 TRIM47 HGNC HGNC:19020 protein_coding YES CCDS32737.1 ENSP00000254816 Q96LD4 UPI000013CE62 NM_033452.2 deleterious(0.03) 1/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF328,Gene3D:3.30.40.10,Pfam_domain:PF15227,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.98616 1 1 1 1 0 T 3 4 63 75878418 75878418 C T 1 0 0 0 0 1 0 0 0 17012 855 30 3 3 TRIM47 17 75878418 Missense_Mutation SNP C C3N-00737_T 14077060 75878418 7379023 144 19885 PIEZO2 0 . GRCh38 18 10691277 10691277 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.6958G>A p.Gly2320Arg p.G2320R ENST00000503781 44/52 262 247 15 197 197 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Gly2271Arg,ENST00000383408,;PIEZO2,missense_variant,p.Gly2320Arg,ENST00000302079,;PIEZO2,missense_variant,p.Gly2345Arg,ENST00000580640,;PIEZO2,missense_variant,p.Gly2320Arg,ENST00000503781,NM_022068.3;PIEZO2,missense_variant,p.Gly277Arg,ENST00000538948,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; T ENST00000503781 Transcript missense_variant 6958/8259 6958/8259 2320/2752 G/R Ggg/Agg 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 44/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 10691277 10691277 C T 1 0 0 0 0 1 0 0 0 11975 623 22 3 3 PIEZO2 18 10691277 Missense_Mutation SNP C C3N-00737_T 10691277 69682008 145 19886 TRAPPC8 0 . GRCh38 18 31916279 31916279 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.610G>A p.Glu204Lys p.E204K ENST00000283351 4/29 90 85 5 113 113 0 varscan-mutect TRAPPC8,missense_variant,p.Glu204Lys,ENST00000283351,NM_014939.3;TRAPPC8,missense_variant,p.Glu150Lys,ENST00000582539,;TRAPPC8,missense_variant,p.Glu204Lys,ENST00000582513,;TRAPPC8,missense_variant,p.Glu179Lys,ENST00000578658,;TRAPPC8,missense_variant,p.Glu204Lys,ENST00000580104,; T ENST00000283351 Transcript missense_variant 946/6226 610/4308 204/1435 E/K Gaa/Aaa 1 -1 TRAPPC8 HGNC HGNC:29169 protein_coding YES CCDS11901.1 ENSP00000283351 Q9Y2L5 UPI0000052E22 NM_014939.3 deleterious(0.01) 4/29 hmmpanther:PTHR12975:SF6,hmmpanther:PTHR12975,Pfam_domain:PF12739 MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -10.48862 0.999701 1 1 1 0 T 3 4 63 31916279 31916279 C T 1 0 0 0 0 1 0 0 0 16953 835 29 3 3 TRAPPC8 18 31916279 Missense_Mutation SNP C C3N-00737_T 21225002 31916279 48457006 146 19887 ASXL3 0 . GRCh38 18 33738812 33738812 + Missense_Mutation SNP C C T rs866757981 C3N-00737_T C3N-00737_N C C c.1408C>T p.His470Tyr p.H470Y ENST00000269197 11/12 267 241 26 272 272 0 strelka-varscan-mutect ASXL3,missense_variant,p.His470Tyr,ENST00000269197,NM_030632.1;ASXL3,3_prime_UTR_variant,,ENST00000592288,; T ENST00000269197 Transcript missense_variant 1463/11399 1408/6747 470/2248 H/Y Cat/Tat rs866757981,COSM3525421,COSM3525422 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 tolerated_low_confidence(0.06) 11/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF18 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs866757981 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 33738812 33738812 C T 1 0 0 0 0 1 0 0 0 1216 826 29 3 3 ASXL3 18 33738812 Missense_Mutation SNP C C3N-00737_T 1822533 33738812 46634473 147 19888 LOXHD1 0 . GRCh38 18 46485084 46485084 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.2784G>T p.Glu928Asp p.E928D ENST00000300591 21/24 130 117 13 150 150 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Glu1977Asp,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Glu1833Asp,ENST00000441551,;LOXHD1,missense_variant,p.Glu928Asp,ENST00000300591,NM_001145472.2;LOXHD1,missense_variant,p.Glu866Asp,ENST00000582408,;LOXHD1,missense_variant,p.Glu832Asp,ENST00000579038,NM_001308013.1;LOXHD1,missense_variant,p.Glu278Asp,ENST00000398686,NM_001145473.2;LOXHD1,missense_variant,p.Glu278Asp,ENST00000398705,NM_001173129.1; A ENST00000300591 Transcript missense_variant 3198/3970 2784/3345 928/1114 E/D gaG/gaT 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 tolerated(0.12) 21/24 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,Superfamily_domains:SSF49723 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.04414 0.9999998 1 1 1 0 A 3 1 63 46485084 46485084 C A 1 0 0 0 0 1 0 0 0 8801 680 24 2 2 LOXHD1 18 46485084 Missense_Mutation SNP C C3N-00737_T 12746272 46485084 33888201 148 19889 VPS4B 0 . GRCh38 18 63397254 63397254 + Splice_Site SNP C C G novel C3N-00737_T C3N-00737_N C C c.873-1G>C p.X291_splice ENST00000238497 92 80 12 111 111 0 strelka-varscan-mutect VPS4B,splice_acceptor_variant,,ENST00000238497,NM_004869.3;VPS4B,downstream_gene_variant,,ENST00000591383,;VPS4B,upstream_gene_variant,,ENST00000588323,;VPS4B,splice_acceptor_variant,,ENST00000591475,;VPS4B,splice_acceptor_variant,,ENST00000589604,;VPS4B,splice_acceptor_variant,,ENST00000588059,; G ENST00000238497 Transcript splice_acceptor_variant -/3324 873/1335 291/444 1 -1 VPS4B HGNC HGNC:10895 protein_coding YES CCDS11983.1 ENSP00000238497 O75351 A0A024R2C5 UPI0000073CAF NM_004869.3 8/10 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 63 63397254 63397254 C G 1 0 0 0 0 0 0 1 0 17759 927 32 4 4 VPS4B 18 63397254 Splice_Site SNP C C3N-00737_T 16912170 63397254 16976031 149 19890 OR7D4 0 . GRCh38 19 9214759 9214759 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.79C>T p.Leu27Phe p.L27F ENST00000308682 1/1 179 137 42 188 188 0 strelka-varscan-mutect OR7D4,missense_variant,p.Leu27Phe,ENST00000308682,NM_001005191.2; A ENST00000308682 Transcript missense_variant 113/1022 79/939 27/312 L/F Ctc/Ttc 1 -1 OR7D4 HGNC HGNC:8380 protein_coding YES CCDS32901.1 ENSP00000310488 Q8NG98 A0A126GVR1 UPI00000472B5 NM_001005191.2 tolerated(0.1) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF371,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 9214759 9214759 G A 1 0 0 0 0 1 0 0 0 11290 1000 35 3 3 OR7D4 19 9214759 Missense_Mutation SNP G C3N-00737_T 9214759 49402857 150 19891 IL27RA 0 . GRCh38 19 14039506 14039506 + Splice_Site SNP A A T novel C3N-00737_T C3N-00737_N A A c.219-2A>T p.X73_splice ENST00000263379 55 40 15 79 79 0 strelka-varscan-mutect IL27RA,splice_acceptor_variant,,ENST00000263379,NM_004843.3; T ENST00000263379 Transcript splice_acceptor_variant -/2962 219/1911 73/636 1 1 IL27RA HGNC HGNC:17290 protein_coding YES CCDS12303.1 ENSP00000263379 Q6UWB1 UPI0000039E1F NM_004843.3 2/13 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 63 14039506 14039506 A T 1 0 0 0 0 0 0 1 0 7584 202 7 4 4 IL27RA 19 14039506 Splice_Site SNP A C3N-00737_T 4824747 14039506 44578110 151 19892 SLC35E1 0 . GRCh38 19 16553793 16553793 + Silent SNP G G C novel C3N-00737_T C3N-00737_N G G c.1119C>G p.= p.L373L ENST00000595753 6/6 103 96 7 98 98 0 strelka-varscan-mutect SLC35E1,synonymous_variant,p.=,ENST00000595753,NM_024881.4;SLC35E1,synonymous_variant,p.=,ENST00000436553,;SLC35E1,downstream_gene_variant,,ENST00000421082,;CTD-3222D19.11,downstream_gene_variant,,ENST00000597357,;SLC35E1,non_coding_transcript_exon_variant,,ENST00000600356,;SLC35E1,upstream_gene_variant,,ENST00000593812,;SLC35E1,downstream_gene_variant,,ENST00000470077,;SLC35E1,upstream_gene_variant,,ENST00000596387,;SLC35E1,3_prime_UTR_variant,,ENST00000409648,;CTD-3222D19.2,3_prime_UTR_variant,,ENST00000409035,;SLC35E1,downstream_gene_variant,,ENST00000469055,; C ENST00000595753 Transcript synonymous_variant 1137/5099 1119/1233 373/410 L ctC/ctG 1 -1 SLC35E1 HGNC HGNC:20803 protein_coding YES CCDS12346.2 ENSP00000470652 Q96K37 A0A024R7G7 UPI000004D338 NM_024881.4 6/6 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF54 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.64734 1 1 1 1 0 C 2 2 63 16553793 16553793 G C 1 0 0 0 0 0 0 0 1 14854 929 33 4 4 SLC35E1 19 16553793 Silent SNP G C3N-00737_T 2514287 16553793 42063823 152 19893 JAK3 0 . GRCh38 19 17831377 17831377 + Silent SNP G G A novel C3N-00737_T C3N-00737_N G G c.2829C>T p.= p.R943R ENST00000458235 21/24 225 200 25 189 189 0 strelka-varscan-mutect JAK3,synonymous_variant,p.=,ENST00000458235,NM_000215.3;JAK3,synonymous_variant,p.=,ENST00000527670,;JAK3,synonymous_variant,p.=,ENST00000534444,;JAK3,intron_variant,,ENST00000527031,; A ENST00000458235 Transcript synonymous_variant 2929/5432 2829/3375 943/1124 R cgC/cgT 1 -1 JAK3 HGNC HGNC:6193 protein_coding YES CCDS12366.1 ENSP00000391676 P52333 A0A024R7M7 UPI0000071146 NM_000215.3 21/24 PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF233,hmmpanther:PTHR24418,PIRSF_domain:PIRSF000636,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 LOW 1 SNV 5 1 PASS rs1315172619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 17831377 17831377 G A 1 0 0 0 0 0 0 0 1 7852 1190 42 3 3 JAK3 19 17831377 Silent SNP G C3N-00737_T 1277584 17831377 40786239 153 19894 DPY19L3 0 . GRCh38 19 32439876 32439876 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.821C>T p.Thr274Ile p.T274I ENST00000342179 8/19 361 277 84 298 297 1 strelka-varscan-mutect DPY19L3,missense_variant,p.Thr274Ile,ENST00000342179,NM_207325.2;DPY19L3,missense_variant,p.Thr274Ile,ENST00000392250,NM_001172774.1;DPY19L3,missense_variant,p.Thr274Ile,ENST00000586987,;DPY19L3,downstream_gene_variant,,ENST00000586427,;DPY19L3,missense_variant,p.Thr41Ile,ENST00000588648,;DPY19L3,non_coding_transcript_exon_variant,,ENST00000585597,; T ENST00000342179 Transcript missense_variant 1036/6015 821/2151 274/716 T/I aCa/aTa 1 1 DPY19L3 HGNC HGNC:27120 protein_coding YES CCDS12422.1 ENSP00000344937 Q6ZPD9 UPI00001C10BE NM_207325.2 tolerated(0.48) 8/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF4,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 32439876 32439876 C T 1 0 0 0 0 1 0 0 0 4557 478 17 3 3 DPY19L3 19 32439876 Missense_Mutation SNP C C3N-00737_T 14608499 32439876 26177740 154 19895 SELV 0 . GRCh38 19 39515444 39515444 + Missense_Mutation SNP C C G rs375570045 C3N-00737_T C3N-00737_N C C c.232C>G p.Leu78Val p.L78V ENST00000335426 1/6 502 433 69 489 489 0 strelka-varscan-mutect SELV,missense_variant,p.Leu78Val,ENST00000335426,NM_182704.1;SELV,missense_variant,p.Leu78Val,ENST00000622070,;SELV,missense_variant,p.Leu78Val,ENST00000423711,;SELV,upstream_gene_variant,,ENST00000597876,;SELV,upstream_gene_variant,,ENST00000600586,; G ENST00000335426 Transcript missense_variant 332/1704 232/1041 78/346 L/V Ctg/Gtg rs375570045,COSM1742013 1 1 SELV EntrezGene protein_coding YES CCDS54266.1 ENSP00000333956 UPI00001B2974 NM_182704.1 tolerated(0.44) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR15124,hmmpanther:PTHR15124:SF17,Prints_domain:PR01217 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs375570045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 39515444 39515444 C G 1 0 0 0 0 1 0 0 0 14299 912 32 4 4 SELV 19 39515444 Missense_Mutation SNP C C3N-00737_T 7075568 39515444 19102172 155 19896 C19orf47 0 . GRCh38 19 40336137 40336137 + Silent SNP G G C novel C3N-00737_T C3N-00737_N G G c.306C>G p.= p.L102L ENST00000582783 4/9 283 247 36 274 274 0 strelka-varscan-mutect C19orf47,synonymous_variant,p.=,ENST00000582783,NM_001256441.1,NM_001256440.1;C19orf47,synonymous_variant,p.=,ENST00000392035,;C19orf47,synonymous_variant,p.=,ENST00000580606,;C19orf47,synonymous_variant,p.=,ENST00000582006,;Y_RNA,downstream_gene_variant,,ENST00000384551,;C19orf47,synonymous_variant,p.=,ENST00000357884,;C19orf47,synonymous_variant,p.=,ENST00000580977,; C ENST00000582783 Transcript synonymous_variant 319/3628 306/1269 102/422 L ctC/ctG 1 -1 C19orf47 HGNC HGNC:26723 protein_coding YES CCDS58662.1 ENSP00000463159 Q8N9M1 UPI000006FE9B NM_001256441.1,NM_001256440.1 4/9 hmmpanther:PTHR21359,hmmpanther:PTHR21359:SF1,Gene3D:1.10.150.50,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 40336137 40336137 G C 1 0 0 0 0 0 0 0 1 1913 1277 45 4 4 C19orf47 19 40336137 Silent SNP G C3N-00737_T 820693 40336137 18281479 156 19897 FBXO46 0 . GRCh38 19 45712912 45712912 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.584C>T p.Thr195Ile p.T195I ENST00000317683 2/2 103 91 12 94 94 0 strelka-varscan-mutect FBXO46,missense_variant,p.Thr195Ile,ENST00000317683,NM_001080469.1;FBXO46,downstream_gene_variant,,ENST00000586899,;FBXO46,downstream_gene_variant,,ENST00000591686,;AC007191.4,downstream_gene_variant,,ENST00000623179,; A ENST00000317683 Transcript missense_variant 718/3001 584/1812 195/603 T/I aCc/aTc 1 -1 FBXO46 HGNC HGNC:25069 protein_coding YES CCDS46116.1 ENSP00000410007 Q6PJ61 UPI00002026A5 NM_001080469.1 tolerated(0.09) 2/2 hmmpanther:PTHR16271,hmmpanther:PTHR16271:SF10 MODERATE 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 63 45712912 45712912 G A 1 0 0 0 0 1 0 0 0 5618 1261 44 3 3 FBXO46 19 45712912 Missense_Mutation SNP G C3N-00737_T 5376775 45712912 12904704 157 19898 DBP 0 . GRCh38 19 48636980 48636980 + Silent SNP C C A novel C3N-00737_T C3N-00737_N C C c.15G>T p.= p.V5V ENST00000222122 1/4 54 50 4 42 42 0 strelka-mutect DBP,synonymous_variant,p.=,ENST00000222122,NM_001352.4;DBP,synonymous_variant,p.=,ENST00000601104,;CA11,downstream_gene_variant,,ENST00000084798,NM_001217.3;DBP,upstream_gene_variant,,ENST00000593500,;DBP,upstream_gene_variant,,ENST00000599385,;CA11,downstream_gene_variant,,ENST00000596080,;SEC1P,upstream_gene_variant,,ENST00000430145,;SEC1P,upstream_gene_variant,,ENST00000474419,;SEC1P,upstream_gene_variant,,ENST00000483163,;DBP,non_coding_transcript_exon_variant,,ENST00000594723,;CA11,downstream_gene_variant,,ENST00000599267,;CA11,downstream_gene_variant,,ENST00000594088,; A ENST00000222122 Transcript synonymous_variant 459/2229 15/978 5/325 V gtG/gtT 1 -1 DBP HGNC HGNC:2697 protein_coding YES CCDS12728.1 ENSP00000222122 Q10586 UPI0000000CC1 NM_001352.4 1/4 hmmpanther:PTHR11988,hmmpanther:PTHR11988:SF7 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.49786 1 1 1 1 0 A 2 1 63 48636980 48636980 C A 1 0 0 0 0 0 0 0 1 4056 813 29 2 2 DBP 19 48636980 Silent SNP C C3N-00737_T 2924068 48636980 9980636 158 19899 ZNF611 0 . GRCh38 19 52706838 52706838 + Missense_Mutation SNP C C G C3N-00737_T C3N-00737_N C C c.217G>C p.Glu73Gln p.E73Q ENST00000543227 6/6 114 91 23 144 144 0 strelka-mutect ZNF611,missense_variant,p.Glu73Gln,ENST00000543227,NM_001161499.1;ZNF611,missense_variant,p.Glu73Gln,ENST00000540744,NM_001161500.1;ZNF611,missense_variant,p.Glu4Gln,ENST00000453741,NM_001161501.1;ZNF611,missense_variant,p.Glu4Gln,ENST00000602162,;ZNF611,missense_variant,p.Glu73Gln,ENST00000319783,NM_030972.3;ZNF611,missense_variant,p.Glu4Gln,ENST00000595798,;ZNF611,missense_variant,p.Gly55Ala,ENST00000600943,;ZNF611,missense_variant,p.Glu4Gln,ENST00000601643,;ZNF611,3_prime_UTR_variant,,ENST00000596702,;ZNF611,downstream_gene_variant,,ENST00000602046,;ZNF611,3_prime_UTR_variant,,ENST00000595001,;ZNF611,3_prime_UTR_variant,,ENST00000601249,;ZNF611,3_prime_UTR_variant,,ENST00000597343,;ZNF611,3_prime_UTR_variant,,ENST00000598639,;ZNF611,3_prime_UTR_variant,,ENST00000598723,; G ENST00000543227 Transcript missense_variant 492/4517 217/2118 73/705 E/Q Gag/Cag COSM5637662 1 -1 ZNF611 HGNC HGNC:28766 protein_coding YES CCDS12855.1 ENSP00000437616 Q8N823 UPI00001406C1 NM_001161499.1 tolerated(0.11) 6/6 PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF375,SMART_domains:SM00349 1 MODERATE 1 SNV 4 1 1 PASS rs746667686 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 52706838 52706838 C G 1 0 0 0 0 1 0 0 0 18612 864 30 4 4 ZNF611 19 52706838 Missense_Mutation SNP C C3N-00737_T 4069858 52706838 5910778 159 19900 LILRB4 0 . GRCh38 19 54664460 54664460 + Missense_Mutation SNP T T G rs201118199 C3N-00737_T C3N-00737_N T T c.630T>G p.Ser210Arg p.S210R ENST00000391736 6/14 106 96 10 93 92 1 strelka-varscan-mutect LILRB4,missense_variant,p.Ser210Arg,ENST00000391736,NM_001278426.3;LILRB4,missense_variant,p.Ser210Arg,ENST00000430952,NM_001278427.3;LILRB4,missense_variant,p.Ser210Arg,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,missense_variant,p.Ser210Arg,ENST00000391734,;LILRB4,missense_variant,p.Ser210Arg,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000470943,; G ENST00000391736 Transcript missense_variant 945/4002 630/1347 210/448 S/R agT/agG rs201118199 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 deleterious(0) 6/14 PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs201118199 . 0 208 2 0 0 0 0 0 -19.89612 1 1 1 1 0 G 3 3 63 54664460 54664460 T G 1 0 0 0 0 1 0 0 0 8701 1693 59 5 5 LILRB4 19 54664460 Missense_Mutation SNP T C3N-00737_T 1957622 54664460 3953156 160 19901 FCAR 0 . GRCh38 19 54885408 54885408 + Missense_Mutation SNP G G A novel C3N-00737_T C3N-00737_N G G c.244G>A p.Asp82Asn p.D82N ENST00000355524 3/5 565 472 93 378 376 2 strelka-varscan-mutect FCAR,missense_variant,p.Asp82Asn,ENST00000355524,NM_002000.3;FCAR,missense_variant,p.Asp82Asn,ENST00000469767,;FCAR,missense_variant,p.Asp82Asn,ENST00000391725,NM_133269.3;FCAR,missense_variant,p.Asp70Asn,ENST00000359272,NM_133272.3;FCAR,missense_variant,p.Asp70Asn,ENST00000391724,NM_133278.3;FCAR,missense_variant,p.Asp70Asn,ENST00000391723,NM_133274.3;FCAR,missense_variant,p.Asp70Asn,ENST00000391726,NM_133273.3;FCAR,missense_variant,p.Asp82Asn,ENST00000345937,NM_133271.3;FCAR,intron_variant,,ENST00000353758,NM_133277.3;FCAR,non_coding_transcript_exon_variant,,ENST00000482092,;FCAR,non_coding_transcript_exon_variant,,ENST00000471750,;FCAR,non_coding_transcript_exon_variant,,ENST00000472634,;FCAR,missense_variant,p.Asp70Asn,ENST00000488066,; A ENST00000355524 Transcript missense_variant 254/1483 244/864 82/287 D/N Gat/Aat 1 1 FCAR HGNC HGNC:3608 protein_coding YES CCDS12907.1 ENSP00000347714 P24071 UPI000011B429 NM_002000.3 tolerated(0.44) 3/5 Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF4,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 54885408 54885408 G A 1 0 0 0 0 1 0 0 0 5636 1290 45 3 3 FCAR 19 54885408 Missense_Mutation SNP G C3N-00737_T 220948 54885408 3732208 161 19902 GP6 0 . GRCh38 19 55014766 55014766 + Silent SNP C C T novel C3N-00737_T C3N-00737_N C C c.1179G>A p.= p.E393E ENST00000310373 8/8 395 314 81 295 294 1 strelka-varscan-mutect GP6,synonymous_variant,p.=,ENST00000310373,NM_001083899.2;GP6,3_prime_UTR_variant,,ENST00000417454,NM_016363.5;GP6,3_prime_UTR_variant,,ENST00000333884,NM_001256017.2;CTC-550B14.7,intron_variant,,ENST00000593060,;CTC-550B14.7,intron_variant,,ENST00000586845,;GP6,non_coding_transcript_exon_variant,,ENST00000465648,; T ENST00000310373 Transcript synonymous_variant 1207/2268 1179/1863 393/620 E gaG/gaA 1 -1 GP6 HGNC HGNC:14388 protein_coding YES CCDS42626.1 ENSP00000308782 Q9HCN6 UPI000013C631 NM_001083899.2 8/8 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 55014766 55014766 C T 1 0 0 0 0 0 0 0 1 6479 796 28 3 3 GP6 19 55014766 Silent SNP C C3N-00737_T 129358 55014766 3602850 162 19903 TMEM150B 0 . GRCh38 19 55312867 55312867 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.694C>A p.Gln232Lys p.Q232K ENST00000326652 8/8 106 90 16 77 77 0 strelka-varscan-mutect TMEM150B,missense_variant,p.Gln232Lys,ENST00000326652,NM_001085488.2,NM_001282011.1;BRSK1,downstream_gene_variant,,ENST00000309383,NM_032430.1;BRSK1,downstream_gene_variant,,ENST00000590333,;BRSK1,downstream_gene_variant,,ENST00000326848,;TMEM150B,downstream_gene_variant,,ENST00000591570,;TMEM150B,downstream_gene_variant,,ENST00000585918,;CTD-2105E13.14,upstream_gene_variant,,ENST00000596786,;TMEM150B,3_prime_UTR_variant,,ENST00000586609,;TMEM150B,3_prime_UTR_variant,,ENST00000592603,;TMEM150B,downstream_gene_variant,,ENST00000592731,; T ENST00000326652 Transcript missense_variant 877/943 694/702 232/233 Q/K Cag/Aag 1 -1 TMEM150B HGNC HGNC:34415 protein_coding YES CCDS42629.1 ENSP00000320757 A6NC51 UPI00001AF4D4 NM_001085488.2,NM_001282011.1 tolerated_low_confidence(0.2) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 55312867 55312867 G T 1 0 0 0 0 1 0 0 0 16510 1357 47 2 2 TMEM150B 19 55312867 Missense_Mutation SNP G C3N-00737_T 298101 55312867 3304749 163 19904 NLRP8 0 . GRCh38 19 55954840 55954840 + Missense_Mutation SNP A A T novel C3N-00737_T C3N-00737_N A A c.782A>T p.Glu261Val p.E261V ENST00000291971 3/10 288 230 58 271 271 0 strelka-varscan-mutect NLRP8,missense_variant,p.Glu261Val,ENST00000291971,NM_176811.2;NLRP8,missense_variant,p.Glu261Val,ENST00000590542,; T ENST00000291971 Transcript missense_variant 853/3934 782/3147 261/1048 E/V gAg/gTg 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 deleterious(0.04) 3/10 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF54,Pfam_domain:PF05729,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 55954840 55954840 A T 1 0 0 0 0 1 0 0 0 10521 304 11 4 4 NLRP8 19 55954840 Missense_Mutation SNP A C3N-00737_T 641973 55954840 2662776 164 19905 ZSCAN5CP 0 . GRCh38 19 56209111 56209111 + Missense_Mutation SNP C C A rs745624946 C3N-00737_T C3N-00737_N C C c.1402C>A p.His468Asn p.H468N ENST00000534327 5/5 253 194 59 206 206 0 strelka-varscan-mutect ZSCAN5CP,missense_variant,p.His468Asn,ENST00000534327,;ZSCAN5CP,missense_variant,p.His468Asn,ENST00000376267,; A ENST00000534327 Transcript missense_variant 1551/1892 1402/1491 468/496 H/N Cac/Aac rs745624946 1 1 ZSCAN5CP HGNC HGNC:34294 protein_coding YES ENSP00000435234 A6NGD5 UPI000041AA91 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF223,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs745624946 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 56209111 56209111 C A 1 0 0 0 0 1 0 0 0 18839 594 21 2 2 ZSCAN5CP 19 56209111 Missense_Mutation SNP C C3N-00737_T 254271 56209111 2408505 165 19906 ZNF583 0 . GRCh38 19 56424258 56424258 + Missense_Mutation SNP C C A novel C3N-00737_T C3N-00737_N C C c.1600C>A p.His534Asn p.H534N ENST00000333201 5/5 240 223 17 204 204 0 strelka-varscan-mutect ZNF583,missense_variant,p.His534Asn,ENST00000333201,NM_152478.2,NM_001159861.1;ZNF583,missense_variant,p.His534Asn,ENST00000291598,NM_001159860.1;ZNF583,downstream_gene_variant,,ENST00000391778,;ZNF583,downstream_gene_variant,,ENST00000537943,;ZNF583,intron_variant,,ENST00000585612,; A ENST00000333201 Transcript missense_variant 1810/4916 1600/1710 534/569 H/N Cat/Aat 1 1 ZNF583 HGNC HGNC:26427 protein_coding YES CCDS12943.1 ENSP00000388502 Q96ND8 UPI000013E700 NM_152478.2,NM_001159861.1 tolerated(0.16) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF211,hmmpanther:PTHR24387,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 56424258 56424258 C A 1 0 0 0 0 1 0 0 0 18589 478 17 2 2 ZNF583 19 56424258 Missense_Mutation SNP C C3N-00737_T 215147 56424258 2193358 166 19907 TBC1D20 0 . GRCh38 20 440269 440269 + Missense_Mutation SNP C C A C3N-00737_T C3N-00737_N C C c.747G>T p.Met249Ile p.M249I ENST00000354200 6/8 227 191 36 164 163 1 strelka-varscan-mutect TBC1D20,missense_variant,p.Met249Ile,ENST00000354200,NM_144628.3;TBC1D20,non_coding_transcript_exon_variant,,ENST00000461188,;TBC1D20,non_coding_transcript_exon_variant,,ENST00000494633,;TBC1D20,missense_variant,p.Met249Ile,ENST00000461304,; A ENST00000354200 Transcript missense_variant 895/4466 747/1212 249/403 M/I atG/atT COSM3770807 1 -1 TBC1D20 HGNC HGNC:16133 protein_coding YES CCDS13002.1 ENSP00000346139 Q96BZ9 UPI000006D549 NM_144628.3 deleterious(0) 6/8 Pfam_domain:PF00566,hmmpanther:PTHR20913,hmmpanther:PTHR20913:SF10,SMART_domains:SM00164,Superfamily_domains:SSF47923,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 63 440269 440269 C A 1 0 0 0 0 1 0 0 0 16009 710 25 2 2 TBC1D20 20 440269 Missense_Mutation SNP C C3N-00737_T 440269 64003898 167 19908 CNBD2 0 . GRCh38 20 35972734 35972734 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.157C>T p.His53Tyr p.H53Y ENST00000349339 2/12 306 233 73 255 255 0 strelka-varscan-mutect CNBD2,missense_variant,p.His53Tyr,ENST00000489667,NM_001304367.1;CNBD2,missense_variant,p.His53Tyr,ENST00000373973,;CNBD2,missense_variant,p.His53Tyr,ENST00000349339,NM_080834.3;CNBD2,missense_variant,p.His53Tyr,ENST00000538900,NM_001207076.2;CNBD2,missense_variant,p.His112Tyr,ENST00000622112,;CNBD2,missense_variant,p.His53Tyr,ENST00000463258,; T ENST00000349339 Transcript missense_variant 313/1927 157/1719 53/572 H/Y Cac/Tac 1 1 CNBD2 HGNC HGNC:16145 protein_coding YES CCDS13270.1 ENSP00000340954 Q96M20 UPI0000367038 NM_080834.3 tolerated(0.24) 2/12 hmmpanther:PTHR23011:SF15,hmmpanther:PTHR23011 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 35972734 35972734 C T 1 0 0 0 0 1 0 0 0 3370 826 29 3 3 CNBD2 20 35972734 Missense_Mutation SNP C C3N-00737_T 35532465 35972734 28471433 168 19909 CTCFL 0 . GRCh38 20 57512664 57512664 + Silent SNP G G C rs751239769 C3N-00737_T C3N-00737_N G G c.1419C>G p.= p.L473L ENST00000423479 8/12 276 256 20 215 215 0 strelka-varscan-mutect CTCFL,synonymous_variant,p.=,ENST00000608263,NM_001269041.1;CTCFL,synonymous_variant,p.=,ENST00000429804,NM_001269046.1;CTCFL,synonymous_variant,p.=,ENST00000609232,NM_080618.3;CTCFL,synonymous_variant,p.=,ENST00000243914,;CTCFL,synonymous_variant,p.=,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,synonymous_variant,p.=,ENST00000422869,NM_001269047.1;CTCFL,synonymous_variant,p.=,ENST00000608425,NM_001269045.1;CTCFL,synonymous_variant,p.=,ENST00000608440,NM_001269044.1;CTCFL,synonymous_variant,p.=,ENST00000423479,NM_001269043.1;CTCFL,synonymous_variant,p.=,ENST00000539382,NM_001269050.1;CTCFL,synonymous_variant,p.=,ENST00000433949,NM_001269049.1;CTCFL,synonymous_variant,p.=,ENST00000608903,NM_001269055.1;CTCFL,synonymous_variant,p.=,ENST00000502686,NM_001269054.1;CTCFL,intron_variant,,ENST00000432255,NM_001269048.1;CTCFL,downstream_gene_variant,,ENST00000608858,;CTCFL,3_prime_UTR_variant,,ENST00000426658,;CTCFL,intron_variant,,ENST00000422109,;CTCFL,downstream_gene_variant,,ENST00000607923,;CTCFL,downstream_gene_variant,,ENST00000608720,;CTCFL,downstream_gene_variant,,ENST00000608108,; C ENST00000423479 Transcript synonymous_variant 1510/2478 1419/2103 473/700 L ctC/ctG rs751239769 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 8/12 PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF96,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs751239769 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 63 57512664 57512664 G C 1 0 0 0 0 0 0 0 1 3808 1277 45 4 4 CTCFL 20 57512664 Silent SNP G C3N-00737_T 21539930 57512664 6931503 169 19910 GAB4 0 . GRCh38 22 16970163 16970163 + Silent SNP G G A C3N-00737_T C3N-00737_N G G c.717C>T p.= p.A239A ENST00000400588 4/10 291 263 28 222 221 1 varscan-mutect GAB4,synonymous_variant,p.=,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,intron_variant,,ENST00000523144,;GAB4,upstream_gene_variant,,ENST00000520505,;GAB4,intron_variant,,ENST00000465611,; A ENST00000400588 Transcript synonymous_variant 825/2630 717/1725 239/574 A gcC/gcT COSM3379255 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 4/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20 1 LOW 1 SNV 1 1 1 PASS rs1441617680 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 63 16970163 16970163 G A 1 0 0 0 0 0 0 0 1 6022 1219 43 3 3 GAB4 22 16970163 Silent SNP G C3N-00737_T 16970163 33848305 170 19911 TRMT2A 0 . GRCh38 22 20113504 20113504 + Missense_Mutation SNP C C G novel C3N-00737_T C3N-00737_N C C c.1360G>C p.Val454Leu p.V454L ENST00000252136 9/12 245 198 47 185 185 0 strelka-varscan-mutect TRMT2A,missense_variant,p.Val454Leu,ENST00000252136,NM_022727.5,NM_182984.4;TRMT2A,missense_variant,p.Val454Leu,ENST00000403707,;TRMT2A,missense_variant,p.Val454Leu,ENST00000404751,NM_001257994.1;TRMT2A,missense_variant,p.Val472Leu,ENST00000439169,;TRMT2A,missense_variant,p.Val2Leu,ENST00000444845,;TRMT2A,missense_variant,p.Gly43Ala,ENST00000444256,;DGCR8,downstream_gene_variant,,ENST00000351989,NM_022720.6;DGCR8,downstream_gene_variant,,ENST00000383024,NM_001190326.1;DGCR8,downstream_gene_variant,,ENST00000407755,;RANBP1,upstream_gene_variant,,ENST00000430524,NM_001278639.1;RANBP1,upstream_gene_variant,,ENST00000402752,NM_001278640.1;RANBP1,upstream_gene_variant,,ENST00000418705,NM_001278641.1;RANBP1,upstream_gene_variant,,ENST00000331821,NM_002882.3;RANBP1,upstream_gene_variant,,ENST00000423859,;RANBP1,upstream_gene_variant,,ENST00000432879,;RANBP1,upstream_gene_variant,,ENST00000416427,;RANBP1,upstream_gene_variant,,ENST00000411892,;TRMT2A,downstream_gene_variant,,ENST00000445045,;RANBP1,upstream_gene_variant,,ENST00000421656,;MIR6816,downstream_gene_variant,,ENST00000620368,;AC006547.8,upstream_gene_variant,,ENST00000412713,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000492988,;RANBP1,upstream_gene_variant,,ENST00000467920,;TRMT2A,downstream_gene_variant,,ENST00000488335,;TRMT2A,downstream_gene_variant,,ENST00000480460,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000494820,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000487668,;TRMT2A,non_coding_transcript_exon_variant,,ENST00000471040,;DGCR8,downstream_gene_variant,,ENST00000495826,;DGCR8,downstream_gene_variant,,ENST00000498171,;DGCR8,downstream_gene_variant,,ENST00000475941,;RANBP1,upstream_gene_variant,,ENST00000435265,;TRMT2A,downstream_gene_variant,,ENST00000494641,;TRMT2A,downstream_gene_variant,,ENST00000468917,;TRMT2A,downstream_gene_variant,,ENST00000464535,;TRMT2A,upstream_gene_variant,,ENST00000480339,;TRMT2A,downstream_gene_variant,,ENST00000463710,;RANBP1,upstream_gene_variant,,ENST00000488484,;TRMT2A,upstream_gene_variant,,ENST00000487378,;TRMT2A,downstream_gene_variant,,ENST00000459644,;DGCR8,downstream_gene_variant,,ENST00000485802,; G ENST00000252136 Transcript missense_variant 1749/2964 1360/1878 454/625 V/L Gta/Cta 1 -1 TRMT2A HGNC HGNC:24974 protein_coding YES CCDS13774.1 ENSP00000252136 Q8IZ69 UPI00001BBFC5 NM_022727.5,NM_182984.4 deleterious(0.01) 9/12 PROSITE_profiles:PS51687,hmmpanther:PTHR11061:SF24,hmmpanther:PTHR11061,Gene3D:3.40.50.150,Pfam_domain:PF05958,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS rs1194700864 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 20113504 20113504 C G 1 0 0 0 0 1 0 0 0 17069 521 18 4 4 TRMT2A 22 20113504 Missense_Mutation SNP C C3N-00737_T 3143341 20113504 30704964 171 19912 ZNF280B 0 . GRCh38 22 22489110 22489110 + Missense_Mutation SNP C C T novel C3N-00737_T C3N-00737_N C C c.289G>A p.Glu97Lys p.E97K ENST00000626650 4/4 255 214 41 265 264 1 strelka-varscan-mutect ZNF280B,missense_variant,p.Glu97Lys,ENST00000626650,NM_080764.3;ZNF280B,missense_variant,p.Glu97Lys,ENST00000613655,;ZNF280B,missense_variant,p.Glu97Lys,ENST00000619852,; T ENST00000626650 Transcript missense_variant 1032/5721 289/1632 97/543 E/K Gaa/Aaa 1 -1 ZNF280B HGNC HGNC:23022 protein_coding YES CCDS13799.1 ENSP00000485750 A0A0D9SEJ8 UPI000000D980 NM_080764.3 tolerated(0.77) 4/4 Pfam_domain:PF13836 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 22489110 22489110 C T 1 0 0 0 0 1 0 0 0 18391 922 32 3 3 ZNF280B 22 22489110 Missense_Mutation SNP C C3N-00737_T 2375606 22489110 28329358 172 19913 SGSM1 0 . GRCh38 22 24868777 24868777 + Missense_Mutation SNP A A G novel C3N-00737_T C3N-00737_N A A c.1213A>G p.Thr405Ala p.T405A ENST00000400359 12/26 237 183 54 228 228 0 strelka-varscan-mutect SGSM1,missense_variant,p.Thr405Ala,ENST00000400358,NM_001098497.2;SGSM1,missense_variant,p.Thr405Ala,ENST00000610372,NM_133454.3,NM_001098498.2;SGSM1,missense_variant,p.Thr405Ala,ENST00000400359,NM_001039948.3;SGSM1,non_coding_transcript_exon_variant,,ENST00000473458,;SGSM1,non_coding_transcript_exon_variant,,ENST00000480523,; G ENST00000400359 Transcript missense_variant 1220/4317 1213/3447 405/1148 T/A Aca/Gca 1 1 SGSM1 HGNC HGNC:29410 protein_coding YES CCDS46674.1 ENSP00000383212 Q2NKQ1 UPI00006EB130 NM_001039948.3 tolerated(0.75) 12/26 hmmpanther:PTHR22957:SF187,hmmpanther:PTHR22957 MODERATE 1 SNV 5 1 PASS rs1005672841 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 63 24868777 24868777 A G 1 0 0 0 0 1 0 0 0 14480 159 6 5 5 SGSM1 22 24868777 Missense_Mutation SNP A C3N-00737_T 2379667 24868777 25949691 173 19914 SEZ6L 0 . GRCh38 22 26292887 26292887 + Silent SNP G G T rs368342681 C3N-00737_T C3N-00737_N G G c.576G>T p.= p.A192A ENST00000248933 2/17 262 191 71 226 226 0 strelka-varscan-mutect SEZ6L,synonymous_variant,p.=,ENST00000529632,NM_001184775.1;SEZ6L,synonymous_variant,p.=,ENST00000360929,NM_001184776.1;SEZ6L,synonymous_variant,p.=,ENST00000404234,NM_001184773.1;SEZ6L,synonymous_variant,p.=,ENST00000248933,NM_021115.4;SEZ6L,synonymous_variant,p.=,ENST00000629590,NM_001184774.1;SEZ6L,synonymous_variant,p.=,ENST00000343706,NM_001184777.1;SEZ6L,5_prime_UTR_variant,,ENST00000402979,;SEZ6L,5_prime_UTR_variant,,ENST00000403121,; T ENST00000248933 Transcript synonymous_variant 671/3248 576/3075 192/1024 A gcG/gcT rs368342681,COSM300387 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 2/17 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81 0,1 LOW 1 SNV 1 0,1 1 PASS rs368342681 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 26292887 26292887 G T 1 0 0 0 0 0 0 0 1 14422 1103 39 1 1 SEZ6L 22 26292887 Silent SNP G C3N-00737_T 1424110 26292887 24525581 174 19915 AP1B1 0 . GRCh38 22 29356617 29356617 + Splice_Site SNP C C G novel C3N-00737_T C3N-00737_N C C c.526-1G>C p.X176_splice ENST00000357586 89 82 7 74 74 0 strelka-varscan-mutect AP1B1,splice_acceptor_variant,,ENST00000357586,NM_001127.3;AP1B1,splice_acceptor_variant,,ENST00000432560,NM_145730.2;AP1B1,splice_acceptor_variant,,ENST00000317368,NM_001166019.1;AP1B1,splice_acceptor_variant,,ENST00000405198,;AP1B1,splice_acceptor_variant,,ENST00000402502,;AP1B1,splice_acceptor_variant,,ENST00000415447,;AP1B1,splice_acceptor_variant,,ENST00000421126,;AP1B1,upstream_gene_variant,,ENST00000415756,;AP1B1,downstream_gene_variant,,ENST00000473606,; G ENST00000357586 Transcript splice_acceptor_variant -/4176 526/2850 176/949 1 -1 AP1B1 HGNC HGNC:554 protein_coding YES CCDS13855.1 ENSP00000350199 Q10567 UPI0000124FE1 NM_001127.3 5/22 HIGH 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -14.68633 0.9999997 1 1 1 0 G 5 3 63 29356617 29356617 C G 1 0 0 0 0 0 0 1 0 847 695 24 4 4 AP1B1 22 29356617 Splice_Site SNP C C3N-00737_T 3063730 29356617 21461851 175 19916 LARGE1 0 . GRCh38 22 33650583 33650583 + Missense_Mutation SNP G G T C3N-00737_T C3N-00737_N G G c.192C>A p.Ser64Arg p.S64R ENST00000354992 4/16 143 126 17 137 137 0 strelka-varscan-mutect LARGE1,missense_variant,p.Ser64Arg,ENST00000354992,NM_004737.4;LARGE1,missense_variant,p.Ser64Arg,ENST00000397394,NM_133642.3;LARGE1,missense_variant,p.Ser64Arg,ENST00000402320,;LARGE1,missense_variant,p.Ser64Arg,ENST00000413114,;LARGE1,missense_variant,p.Ser64Arg,ENST00000434071,;LARGE1,missense_variant,p.Ser64Arg,ENST00000430220,;LARGE1,downstream_gene_variant,,ENST00000423375,;LARGE1,downstream_gene_variant,,ENST00000432776,;LARGE1,non_coding_transcript_exon_variant,,ENST00000462606,;LARGE1,non_coding_transcript_exon_variant,,ENST00000494763,; T ENST00000354992 Transcript missense_variant 764/4409 192/2271 64/756 S/R agC/agA COSM4427160 1 -1 LARGE1 HGNC HGNC:6511 protein_coding YES CCDS13912.1 ENSP00000347088 O95461 X5DR28 UPI000012E200 NM_004737.4 tolerated_low_confidence(0.24) 4/16 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 33650583 33650583 G T 1 0 0 0 0 1 0 0 0 8537 1194 42 2 2 LARGE1 22 33650583 Missense_Mutation SNP G C3N-00737_T 4293966 33650583 17167885 176 19917 ADGRG2 0 . GRCh38 X 19013724 19013724 + Missense_Mutation SNP G G A C3N-00737_T C3N-00737_N G G c.1061C>T p.Ala354Val p.A354V ENST00000379869 16/29 99 90 9 55 55 0 strelka-mutect ADGRG2,missense_variant,p.Ala338Val,ENST00000379878,NM_001184833.1;ADGRG2,missense_variant,p.Ala330Val,ENST00000379876,NM_001184835.1,NM_001184836.1;ADGRG2,missense_variant,p.Ala354Val,ENST00000379869,NM_001079858.2;ADGRG2,missense_variant,p.Ala332Val,ENST00000360279,NM_001079860.2;ADGRG2,missense_variant,p.Ala354Val,ENST00000379873,NM_001184834.1;ADGRG2,missense_variant,p.Ala324Val,ENST00000357544,NM_001184837.1;ADGRG2,missense_variant,p.Ala351Val,ENST00000357991,NM_005756.3;ADGRG2,missense_variant,p.Ala340Val,ENST00000356606,NM_001079859.2;ADGRG2,missense_variant,p.Ala324Val,ENST00000354791,;ADGRG2,missense_variant,p.Ala324Val,ENST00000340581,; A ENST00000379869 Transcript missense_variant 1225/4768 1061/3054 354/1017 A/V gCg/gTg COSM4108495 1 -1 ADGRG2 HGNC HGNC:4516 protein_coding YES CCDS43923.1 ENSP00000369198 Q8IZP9 UPI000021246C NM_001079858.2 tolerated(0.71) 16/29 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF264 1 MODERATE 1 SNV 1 1 1 PASS rs1254226753 . 0 203 7 0 0 0 0 0 -18.26626 0.9999987 1 1 1 0 A 3 1 63 19013724 19013724 G A 1 0 0 0 0 1 0 0 0 369 1087 38 1 1 ADGRG2 23 19013724 Missense_Mutation SNP G C3N-00737_T 19013724 137027171 177 19918 GAGE2A 0 . GRCh38 X 49591300 49591300 + Missense_Mutation SNP G G T novel C3N-00737_T C3N-00737_N G G c.185G>T p.Gly62Val p.G62V ENST00000362097 3/5 872 742 130 462 462 0 strelka-varscan-mutect GAGE2A,missense_variant,p.Gly62Val,ENST00000362097,NM_001472.2,NM_012196.1,NM_001127212.1;GAGE1,intron_variant,,ENST00000610680,NM_001098405.2,NM_001127200.2;GAGE12H,downstream_gene_variant,,ENST00000381722,NM_001098410.1; T ENST00000362097 Transcript missense_variant 268/528 185/351 62/116 G/V gGa/gTa 1 1 GAGE2A HGNC HGNC:4099 protein_coding YES CCDS48114.1 ENSP00000355421 Q6NT46 UPI00001AF5C0 NM_001472.2,NM_012196.1,NM_001127212.1 deleterious(0.02) 3/5 Pfam_domain:PF05831,hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF6,SMART_domains:SM01379 MODERATE 1 SNV 1 1 PASS . . 70 140 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 49591300 49591300 G T 1 0 0 0 0 1 0 0 0 6062 1174 41 2 2 GAGE2A 23 49591300 Missense_Mutation SNP G C3N-00737_T 30577576 49591300 106449595 178 19919 BMP15 0 . GRCh38 X 50911076 50911076 + Missense_Mutation SNP T T A novel C3N-00737_T C3N-00737_N T T c.293T>A p.Val98Glu p.V98E ENST00000252677 1/2 172 73 99 132 131 1 strelka-varscan-mutect BMP15,missense_variant,p.Val98Glu,ENST00000252677,NM_005448.2; A ENST00000252677 Transcript missense_variant 293/1179 293/1179 98/392 V/E gTg/gAg 1 1 BMP15 HGNC HGNC:1068 protein_coding YES CCDS14334.1 ENSP00000252677 O95972 UPI000013CD7C NM_005448.2 deleterious(0) 1/2 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 50911076 50911076 T A 1 0 0 0 0 1 0 0 0 1613 1696 59 4 4 BMP15 23 50911076 Missense_Mutation SNP T C3N-00737_T 1319776 50911076 105129819 179 19920 TBX22 0 . GRCh38 X 80028021 80028021 + Nonsense_Mutation SNP C C A C3N-00737_T C3N-00737_N C C c.894C>A p.Tyr298Ter p.Y298* ENST00000373296 8/9 227 195 32 233 233 0 strelka-varscan-mutect TBX22,stop_gained,p.Tyr298Ter,ENST00000373296,NM_001109878.1,NM_001109879.1;TBX22,stop_gained,p.Tyr298Ter,ENST00000373294,NM_016954.2,NM_001303475.1;TBX22,non_coding_transcript_exon_variant,,ENST00000626877,;TBX22,3_prime_UTR_variant,,ENST00000626498,; A ENST00000373296 Transcript stop_gained 1028/2355 894/1563 298/520 Y/* taC/taA COSM5234032 1 1 TBX22 HGNC HGNC:11600 protein_coding YES CCDS14445.1 ENSP00000362393 Q9Y458 UPI00001377ED NM_001109878.1,NM_001109879.1 8/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF116 1 HIGH 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 63 80028021 80028021 C A 1 0 0 0 0 0 1 0 0 16063 518 18 2 2 TBX22 23 80028021 Nonsense_Mutation SNP C C3N-00737_T 29116945 80028021 76012874 180 19921 KIAA1210 0 . GRCh38 X 119089476 119089476 + Missense_Mutation SNP G G A C3N-00737_T C3N-00737_N G G c.1754C>T p.Ser585Leu p.S585L ENST00000402510 11/14 217 186 31 146 146 0 strelka-varscan-mutect KIAA1210,missense_variant,p.Ser585Leu,ENST00000402510,NM_020721.1; A ENST00000402510 Transcript missense_variant 1754/7824 1754/5130 585/1709 S/L tCg/tTg COSM4376961,COSM4376962 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 deleterious(0.04) 11/14 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs934680222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 119089476 119089476 G A 1 0 0 0 0 1 0 0 0 8106 1059 37 1 1 KIAA1210 23 119089476 Missense_Mutation SNP G C3N-00737_T 39061455 119089476 36951419 181 19922 XPNPEP2 0 . GRCh38 X 129754520 129754520 + Missense_Mutation SNP A A T novel C3N-00737_T C3N-00737_N A A c.1156A>T p.Asn386Tyr p.N386Y ENST00000371106 12/21 175 150 25 108 108 0 strelka-varscan-mutect XPNPEP2,missense_variant,p.Asn386Tyr,ENST00000371106,NM_003399.5; T ENST00000371106 Transcript missense_variant 1348/3270 1156/2025 386/674 N/Y Aac/Tac 1 1 XPNPEP2 HGNC HGNC:12823 protein_coding YES CCDS14613.1 ENSP00000360147 O43895 UPI000013901A NM_003399.5 deleterious(0.02) 12/21 hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF98,Gene3D:3.90.230.10,Pfam_domain:PF00557,Superfamily_domains:SSF55920 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 63 129754520 129754520 A T 1 0 0 0 0 1 0 0 0 18002 246 9 4 4 XPNPEP2 23 129754520 Missense_Mutation SNP A C3N-00737_T 10665044 129754520 26286375 182 19923 ADGRG4 0 . GRCh38 X 136344971 136344971 + Missense_Mutation SNP C C A C3N-00737_T C3N-00737_N C C c.1265C>A p.Ser422Tyr p.S422Y ENST00000394143 6/26 93 58 35 96 96 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Ser422Tyr,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Ser422Tyr,ENST00000370652,;ADGRG4,missense_variant,p.Ser217Tyr,ENST00000394141,; A ENST00000394143 Transcript missense_variant 1556/9931 1265/9243 422/3080 S/Y tCc/tAc COSM230834 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0.04) 6/26 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 63 136344971 136344971 C A 1 0 0 0 0 1 0 0 0 371 855 30 2 2 ADGRG4 23 136344971 Missense_Mutation SNP C C3N-00737_T 6590451 136344971 19695924 183 19924 F8 0 . GRCh38 X 154904057 154904057 + Silent SNP A A T novel C3N-00737_T C3N-00737_N A A c.5847T>A p.= p.P1949P ENST00000360256 18/26 156 129 27 132 132 0 strelka-varscan-mutect F8,synonymous_variant,p.=,ENST00000360256,NM_000132.3;EEF1A1P31,downstream_gene_variant,,ENST00000415978,; T ENST00000360256 Transcript synonymous_variant 6048/9059 5847/7056 1949/2351 P ccT/ccA 1 -1 F8 HGNC HGNC:3546 protein_coding YES CCDS35457.1 ENSP00000353393 P00451 UPI000012A416 NM_000132.3 18/26 Gene3D:2.60.40.420,Pfam_domain:PF07731,PIRSF_domain:PIRSF000354,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF50,Superfamily_domains:SSF49503 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 63 154904057 154904057 A T 1 0 0 0 0 0 0 0 1 5218 175 7 4 4 F8 23 154904057 Silent SNP A C3N-00737_T 18559086 154904057 1136838 184 19925 PRAMEF10 0 . GRCh38 1 12893205 12893205 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.1136T>A p.Leu379His p.L379H ENST00000235347 4/4 269 249 20 374 373 1 varscan-mutect PRAMEF10,missense_variant,p.Leu379His,ENST00000235347,NM_001039361.4; T ENST00000235347 Transcript missense_variant 1216/1525 1136/1425 379/474 L/H cTc/cAc 1 -1 PRAMEF10 HGNC HGNC:27997 protein_coding YES CCDS41255.1 ENSP00000235347 O60809 UPI000442CF00 NM_001039361.4 deleterious(0) 4/4 hmmpanther:PTHR14224:SF28,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 12893205 12893205 A T 1 0 0 0 0 1 0 0 0 12555 304 11 4 4 PRAMEF10 1 12893205 Missense_Mutation SNP A C3N-00738_T 12893205 236063217 1 19926 HSPG2 0 . GRCh38 1 21855666 21855666 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.5711G>T p.Gly1904Val p.G1904V ENST00000374695 46/97 365 331 34 448 446 2 strelka-varscan-mutect HSPG2,missense_variant,p.Gly1904Val,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,upstream_gene_variant,,ENST00000493940,; A ENST00000374695 Transcript missense_variant 5791/14327 5711/13176 1904/4391 G/V gGc/gTc 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 deleterious(0) 46/97 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 21855666 21855666 C A 1 0 0 0 0 1 0 0 0 7326 739 26 2 2 HSPG2 1 21855666 Missense_Mutation SNP C C3N-00738_T 8962461 21855666 227100756 2 19927 ADGRB2 0 . GRCh38 1 31741377 31741377 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.1790T>A p.Leu597Gln p.L597Q ENST00000373655 11/33 160 150 10 187 186 1 strelka-varscan-mutect ADGRB2,missense_variant,p.Leu597Gln,ENST00000373658,;ADGRB2,missense_variant,p.Leu597Gln,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Leu530Gln,ENST00000398542,;ADGRB2,missense_variant,p.Leu597Gln,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Leu545Gln,ENST00000398556,;ADGRB2,missense_variant,p.Leu530Gln,ENST00000398547,;ADGRB2,missense_variant,p.Leu585Gln,ENST00000398538,;ADGRB2,missense_variant,p.Leu535Gln,ENST00000420125,;ADGRB2,downstream_gene_variant,,ENST00000533175,;ADGRB2,intron_variant,,ENST00000530134,;ADGRB2,downstream_gene_variant,,ENST00000468430,;ADGRB2,upstream_gene_variant,,ENST00000465256,;ADGRB2,upstream_gene_variant,,ENST00000466109,; T ENST00000373655 Transcript missense_variant 2132/5400 1790/4755 597/1584 L/Q cTg/cAg 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 tolerated(0.38) 11/33 hmmpanther:PTHR12011:SF41,hmmpanther:PTHR12011 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 31741377 31741377 A T 1 0 0 0 0 1 0 0 0 356 202 7 4 4 ADGRB2 1 31741377 Missense_Mutation SNP A C3N-00738_T 9885711 31741377 217215045 3 19928 RAD54L 0 . GRCh38 1 46278146 46278146 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.2108T>A p.Leu703Gln p.L703Q ENST00000371975 18/18 435 405 30 558 557 1 strelka-varscan-mutect RAD54L,missense_variant,p.Leu703Gln,ENST00000371975,NM_003579.3;RAD54L,missense_variant,p.Leu703Gln,ENST00000442598,NM_001142548.1;RAD54L,missense_variant,p.Leu277Gln,ENST00000488942,;LRRC41,3_prime_UTR_variant,,ENST00000617190,;LRRC41,intron_variant,,ENST00000496156,;LRRC41,downstream_gene_variant,,ENST00000343304,NM_006369.4;LRRC41,downstream_gene_variant,,ENST00000615587,;LRRC41,downstream_gene_variant,,ENST00000617760,;LRRC41,downstream_gene_variant,,ENST00000472710,;RAD54L,downstream_gene_variant,,ENST00000459678,;RAD54L,downstream_gene_variant,,ENST00000476687,; A ENST00000371975 Transcript missense_variant 2782/3108 2108/2244 703/747 L/Q cTg/cAg 1 1 RAD54L HGNC HGNC:9826 protein_coding YES CCDS532.1 ENSP00000361043 Q92698 UPI0000378007 NM_003579.3 deleterious(0.04) 18/18 Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1384711289 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 46278146 46278146 T A 1 0 0 0 0 1 0 0 0 13154 1580 55 4 4 RAD54L 1 46278146 Missense_Mutation SNP T C3N-00738_T 14536769 46278146 202678276 4 19929 CC2D1B 0 . GRCh38 1 52362604 52362625 + Frame_Shift_Del DEL TGCCCCTTGGGTGCTGGCTTCT TGCCCCTTGGGTGCTGGCTTCT - novel C3N-00738_T C3N-00738_N TGCCCCTTGGGTGCTGGCTTCT TGCCCCTTGGGTGCTGGCTTCT c.191_212delAGAAGCCAGCACCCAAGGGGCA p.Lys64ArgfsTer36 p.K64Rfs*36 ENST00000371586 3/24 181 166 15 203 203 0 sindel-varindel-pindel CC2D1B,frameshift_variant,p.Lys64ArgfsTer36,ENST00000371586,NM_032449.2;CC2D1B,frameshift_variant,p.Lys64ArgfsTer36,ENST00000284376,;CC2D1B,upstream_gene_variant,,ENST00000438021,;CC2D1B,upstream_gene_variant,,ENST00000450942,;CC2D1B,upstream_gene_variant,,ENST00000460261,;CC2D1B,splice_region_variant,,ENST00000491136,; - ENST00000371586 Transcript frameshift_variant,splice_region_variant 330-351/5642 191-212/2577 64-71/858 KKPAPKGQ/X aAGAAGCCAGCACCCAAGGGGCAg/ag 1 -1 CC2D1B HGNC HGNC:29386 protein_coding YES CCDS30714.1 ENSP00000360642 Q5T0F9 UPI00001609B7 NM_032449.2 3/24 hmmpanther:PTHR13076,hmmpanther:PTHR13076:SF5 HIGH 1 deletion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 64 52362604 52362604 TGCCCCTTGGGTGCTGGCTTCT - 1 0 1 0 1 0 0 0 0 2428 1594 55 0 0 CC2D1B 1 52362604 Frame_Shift_Del DEL TGCCCCTTGGGTGCTGGCTTCT C3N-00738_T 6084458 52362604 196593818 5 19930 CTH 0 . GRCh38 1 70411462 70411462 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.47A>T p.Gln16Leu p.Q16L ENST00000370938 1/12 478 434 44 499 499 0 strelka-varscan-mutect CTH,missense_variant,p.Gln16Leu,ENST00000411986,NM_001190463.1;CTH,missense_variant,p.Gln16Leu,ENST00000370938,NM_001902.5;CTH,missense_variant,p.Gln16Leu,ENST00000346806,NM_153742.4;CTH,non_coding_transcript_exon_variant,,ENST00000464926,; T ENST00000370938 Transcript missense_variant 191/1805 47/1218 16/405 Q/L cAa/cTa 1 1 CTH HGNC HGNC:2501 protein_coding YES CCDS650.1 ENSP00000359976 P32929 UPI00001275DE NM_001902.5 tolerated(0.16) 1/12 Gene3D:3.40.640.10,PIRSF_domain:PIRSF001434,hmmpanther:PTHR11808,hmmpanther:PTHR11808:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 70411462 70411462 A T 1 0 0 0 0 1 0 0 0 3817 130 5 4 4 CTH 1 70411462 Missense_Mutation SNP A C3N-00738_T 18048858 70411462 178544960 6 19931 EPS8L3 0 . GRCh38 1 109757842 109757842 + Missense_Mutation SNP A A C rs760225779 C3N-00738_T C3N-00738_N A A c.857T>G p.Ile286Ser p.I286S ENST00000369805 10/19 340 307 33 375 374 1 strelka-varscan-mutect EPS8L3,missense_variant,p.Ile286Ser,ENST00000369805,NM_139053.2;EPS8L3,missense_variant,p.Ile285Ser,ENST00000361852,NM_001319952.1,NM_024526.3;EPS8L3,missense_variant,p.Ile285Ser,ENST00000361965,NM_133181.3;RP4-735C1.4,intron_variant,,ENST00000431955,;GSTM5,intron_variant,,ENST00000429410,;EPS8L3,downstream_gene_variant,,ENST00000494151,;EPS8L3,downstream_gene_variant,,ENST00000477568,;EPS8L3,3_prime_UTR_variant,,ENST00000472325,; C ENST00000369805 Transcript missense_variant 1087/2325 857/1785 286/594 I/S aTt/aGt rs760225779 1 -1 EPS8L3 HGNC HGNC:21297 protein_coding YES CCDS815.1 ENSP00000358820 Q8TE67 UPI00001613C9 NM_139053.2 deleterious(0.01) 10/19 hmmpanther:PTHR12287:SF22,hmmpanther:PTHR12287 MODERATE 1 SNV 1 1 PASS rs760225779 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 109757842 109757842 A C 1 0 0 0 0 1 0 0 0 5045 101 4 5 5 EPS8L3 1 109757842 Missense_Mutation SNP A C3N-00738_T 39346380 109757842 139198580 7 19932 PIAS3 0 . GRCh38 1 145856627 145856627 + Missense_Mutation SNP T T C rs781818284 C3N-00738_T C3N-00738_N T T c.404A>G p.Tyr135Cys p.Y135C ENST00000393045 2/14 48 44 4 86 86 0 strelka-varscan-mutect PIAS3,missense_variant,p.Tyr135Cys,ENST00000393045,NM_006099.3;PIAS3,missense_variant,p.Tyr100Cys,ENST00000369298,;PIAS3,missense_variant,p.Tyr126Cys,ENST00000393046,;PIAS3,downstream_gene_variant,,ENST00000463514,;PIAS3,non_coding_transcript_exon_variant,,ENST00000369299,;PIAS3,non_coding_transcript_exon_variant,,ENST00000498436,;PIAS3,non_coding_transcript_exon_variant,,ENST00000484423,;PIAS3,upstream_gene_variant,,ENST00000475261,; C ENST00000393045 Transcript missense_variant 494/2901 404/1887 135/628 Y/C tAt/tGt rs781818284,COSM3369256 1 -1 PIAS3 HGNC HGNC:16861 protein_coding YES CCDS72866.1 ENSP00000376765 Q9Y6X2 UPI0000150636 NM_006099.3 deleterious(0) 2/14 PROSITE_profiles:PS51466,hmmpanther:PTHR10782,hmmpanther:PTHR10782:SF10,Pfam_domain:PF14324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781818284 . 0 204 5 0 0 0 0 0 -10.35885 1 1 1 1 0 C 3 2 64 145856627 145856627 T C 1 0 0 0 0 1 0 0 0 11967 1406 49 5 5 PIAS3 1 145856627 Missense_Mutation SNP T C3N-00738_T 36098785 145856627 103099795 8 19933 SV2A 0 . GRCh38 1 149913804 149913804 + Missense_Mutation SNP G G T rs781957523 C3N-00738_T C3N-00738_N G G c.37C>A p.Arg13Ser p.R13S ENST00000369146 2/13 77 71 6 87 87 0 strelka-varscan-mutect SV2A,missense_variant,p.Arg13Ser,ENST00000369146,NM_014849.4;SV2A,missense_variant,p.Arg13Ser,ENST00000369145,; T ENST00000369146 Transcript missense_variant 528/4416 37/2229 13/742 R/S Cgt/Agt rs781957523 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 deleterious_low_confidence(0.01) 2/13 TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 1 1 PASS rs781957523 . 0 203 7 0 0 0 0 0 -13.08218 0.9999982 1 1 1 0 T 3 4 64 149913804 149913804 G T 1 0 0 0 0 1 0 0 0 15801 1116 39 1 1 SV2A 1 149913804 Missense_Mutation SNP G C3N-00738_T 4057177 149913804 99042618 9 19934 TDRKH 0 . GRCh38 1 151776241 151776241 + Missense_Mutation SNP C C G novel C3N-00738_T C3N-00738_N C C c.1072G>C p.Asp358His p.D358H ENST00000368822 8/14 100 92 8 106 106 0 strelka-varscan-mutect TDRKH,missense_variant,p.Asp358His,ENST00000368822,;TDRKH,missense_variant,p.Asp358His,ENST00000368824,NM_001083965.1;TDRKH,missense_variant,p.Asp358His,ENST00000458431,NM_001083963.1;TDRKH,missense_variant,p.Asp354His,ENST00000368823,;TDRKH,missense_variant,p.Asp313His,ENST00000368825,NM_001083964.1;TDRKH,missense_variant,p.Asp358His,ENST00000368827,NM_006862.3;TDRKH,missense_variant,p.Asp358His,ENST00000440583,;OAZ3,downstream_gene_variant,,ENST00000479764,;OAZ3,downstream_gene_variant,,ENST00000400999,NM_016178.2;OAZ3,downstream_gene_variant,,ENST00000321531,NM_001134939.1;OAZ3,downstream_gene_variant,,ENST00000627780,;OAZ3,downstream_gene_variant,,ENST00000635322,;OAZ3,downstream_gene_variant,,ENST00000453029,NM_001301371.1;TDRKH,downstream_gene_variant,,ENST00000526378,;OAZ3,downstream_gene_variant,,ENST00000635374,;OAZ3,downstream_gene_variant,,ENST00000582415,;TDRKH,downstream_gene_variant,,ENST00000484421,;TDRKH,3_prime_UTR_variant,,ENST00000525790,;TDRKH,3_prime_UTR_variant,,ENST00000526413,;TDRKH,downstream_gene_variant,,ENST00000486986,;TDRKH,downstream_gene_variant,,ENST00000494725,;TDRKH,downstream_gene_variant,,ENST00000530202,; G ENST00000368822 Transcript missense_variant 1706/3093 1072/1686 358/561 D/H Gac/Cac 1 -1 TDRKH HGNC HGNC:11713 protein_coding YES CCDS41394.1 ENSP00000357812 Q9Y2W6 UPI0000204267 deleterious(0) 8/14 PROSITE_profiles:PS50304,hmmpanther:PTHR22948,Gene3D:2.30.30.140,Pfam_domain:PF00567,SMART_domains:SM00333,Superfamily_domains:SSF63748 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -12.51519 0.9999928 1 1 1 0 G 3 3 64 151776241 151776241 C G 1 0 0 0 0 1 0 0 0 16147 913 32 4 4 TDRKH 1 151776241 Missense_Mutation SNP C C3N-00738_T 1862437 151776241 97180181 10 19935 LINGO4 0 . GRCh38 1 151801970 151801970 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.735C>A p.Asp245Glu p.D245E ENST00000368820 2/2 147 133 14 200 200 0 strelka-varscan-mutect LINGO4,missense_variant,p.Asp245Glu,ENST00000368820,NM_001004432.3;RORC,downstream_gene_variant,,ENST00000356728,NM_001001523.1;RORC,downstream_gene_variant,,ENST00000318247,NM_005060.3;RP11-98D18.17,downstream_gene_variant,,ENST00000601909,;RORC,downstream_gene_variant,,ENST00000480719,; T ENST00000368820 Transcript missense_variant 1673/3379 735/1782 245/593 D/E gaC/gaA 1 -1 LINGO4 HGNC HGNC:31814 protein_coding YES CCDS30855.1 ENSP00000357810 Q6UY18 UPI000019993B NM_001004432.3 tolerated(0.68) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF156,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.54469 0.9999838 1 1 1 0 T 3 4 64 151801970 151801970 G T 1 0 0 0 0 1 0 0 0 8738 1252 44 2 2 LINGO4 1 151801970 Missense_Mutation SNP G C3N-00738_T 25729 151801970 97154452 11 19936 FLG2 0 . GRCh38 1 152351449 152351449 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.6337G>A p.Val2113Met p.V2113M ENST00000388718 3/3 378 347 31 412 411 1 varscan-mutect FLG2,missense_variant,p.Val2113Met,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 6410/9124 6337/7176 2113/2391 V/M Gtg/Atg 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 tolerated(0.07) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 152351449 152351449 C T 1 0 0 0 0 1 0 0 0 5785 565 20 3 3 FLG2 1 152351449 Missense_Mutation SNP C C3N-00738_T 549479 152351449 96604973 12 19937 UBAP2L 0 . GRCh38 1 154268921 154268921 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.3135G>A p.= p.Q1045Q ENST00000428931 26/27 261 243 18 255 254 1 strelka-varscan-mutect UBAP2L,synonymous_variant,p.=,ENST00000271877,NM_001287816.1;UBAP2L,synonymous_variant,p.=,ENST00000428931,NM_014847.3;UBAP2L,synonymous_variant,p.=,ENST00000361546,;UBAP2L,synonymous_variant,p.=,ENST00000433615,;UBAP2L,synonymous_variant,p.=,ENST00000428595,;HAX1,upstream_gene_variant,,ENST00000328703,NM_006118.3;HAX1,upstream_gene_variant,,ENST00000483970,;HAX1,upstream_gene_variant,,ENST00000457918,NM_001018837.1;HAX1,upstream_gene_variant,,ENST00000435087,;HAX1,upstream_gene_variant,,ENST00000532105,;UBAP2L,non_coding_transcript_exon_variant,,ENST00000484819,;UBAP2L,non_coding_transcript_exon_variant,,ENST00000493867,;HAX1,upstream_gene_variant,,ENST00000531435,;HAX1,upstream_gene_variant,,ENST00000471326,;HAX1,upstream_gene_variant,,ENST00000477780,;HAX1,upstream_gene_variant,,ENST00000447768,;HAX1,upstream_gene_variant,,ENST00000492550,;HAX1,upstream_gene_variant,,ENST00000459914,; A ENST00000428931 Transcript synonymous_variant 3302/3988 3135/3264 1045/1087 Q caG/caA 1 1 UBAP2L HGNC HGNC:29877 protein_coding YES CCDS1063.1 ENSP00000389445 Q14157 UPI000013E257 NM_014847.3 26/27 hmmpanther:PTHR16308,hmmpanther:PTHR16308:SF18 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 154268921 154268921 G A 1 0 0 0 0 0 0 0 1 17360 933 33 3 3 UBAP2L 1 154268921 Silent SNP G C3N-00738_T 1917472 154268921 94687501 13 19938 AQP10 0 . GRCh38 1 154323751 154323751 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.652G>T p.Asp218Tyr p.D218Y ENST00000324978 5/6 298 276 22 319 319 0 strelka-varscan-mutect AQP10,missense_variant,p.Asp218Tyr,ENST00000484864,;AQP10,missense_variant,p.Asp218Tyr,ENST00000324978,NM_080429.2;ATP8B2,upstream_gene_variant,,ENST00000368489,NM_020452.3;ATP8B2,upstream_gene_variant,,ENST00000368487,NM_001005855.1;AQP10,non_coding_transcript_exon_variant,,ENST00000355197,;ATP8B2,upstream_gene_variant,,ENST00000368490,; T ENST00000324978 Transcript missense_variant 692/1791 652/906 218/301 D/Y Gac/Tac 1 1 AQP10 HGNC HGNC:16029 protein_coding YES CCDS1065.1 ENSP00000318355 Q96PS8 UPI000007028A NM_080429.2 deleterious(0) 5/6 hmmpanther:PTHR19139:SF138,hmmpanther:PTHR19139,TIGRFAM_domain:TIGR00861,Pfam_domain:PF00230,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 154323751 154323751 G T 1 0 0 0 0 1 0 0 0 945 1174 41 2 2 AQP10 1 154323751 Missense_Mutation SNP G C3N-00738_T 54830 154323751 94632671 14 19939 CCT3 0 . GRCh38 1 156311187 156311187 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.1164A>G p.= p.E388E ENST00000295688 12/14 125 106 19 204 204 0 strelka-varscan-mutect CCT3,synonymous_variant,p.=,ENST00000295688,NM_005998.4;CCT3,synonymous_variant,p.=,ENST00000472765,;CCT3,synonymous_variant,p.=,ENST00000368259,NM_001008800.2;CCT3,intron_variant,,ENST00000368261,;CCT3,3_prime_UTR_variant,,ENST00000368262,;CCT3,3_prime_UTR_variant,,ENST00000368258,; C ENST00000295688 Transcript synonymous_variant 1445/2150 1164/1638 388/545 E gaA/gaG 1 -1 CCT3 HGNC HGNC:1616 protein_coding YES CCDS1140.2 ENSP00000295688 P49368 UPI000040EEFE NM_005998.4 12/14 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF63,Gene3D:3.30.260.10,TIGRFAM_domain:TIGR02344,Pfam_domain:PF00118,Superfamily_domains:SSF54849,Prints_domain:PR00304 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 156311187 156311187 T C 1 0 0 0 0 0 0 0 1 2655 1722 60 5 5 CCT3 1 156311187 Silent SNP T C3N-00738_T 1987436 156311187 92645235 15 19940 FCRL2 0 . GRCh38 1 157770660 157770660 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.59T>A p.Leu20Gln p.L20Q ENST00000361516 3/12 130 104 26 174 174 0 strelka-varscan-mutect FCRL2,missense_variant,p.Leu20Gln,ENST00000361516,NM_030764.3;FCRL2,missense_variant,p.Leu20Gln,ENST00000368181,;FCRL2,upstream_gene_variant,,ENST00000469986,;FCRL2,non_coding_transcript_exon_variant,,ENST00000462774,;FCRL2,upstream_gene_variant,,ENST00000368178,; T ENST00000361516 Transcript missense_variant 108/2579 59/1527 20/508 L/Q cTg/cAg 1 -1 FCRL2 HGNC HGNC:14875 protein_coding YES CCDS1168.1 ENSP00000355157 Q96LA5 UPI000006E1F3 NM_030764.3 deleterious(0) 3/12 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF61,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 157770660 157770660 A T 1 0 0 0 0 1 0 0 0 5658 188 7 4 4 FCRL2 1 157770660 Missense_Mutation SNP A C3N-00738_T 1459473 157770660 91185762 16 19941 OR10Z1 0 . GRCh38 1 158606526 158606526 + Missense_Mutation SNP T T A C3N-00738_T C3N-00738_N T T c.88T>A p.Leu30Met p.L30M ENST00000361284 1/1 275 234 41 316 316 0 strelka-varscan-mutect OR10Z1,missense_variant,p.Leu30Met,ENST00000361284,NM_001004478.1;SPTA1,downstream_gene_variant,,ENST00000368147,NM_003126.2;SPTA1,downstream_gene_variant,,ENST00000485680,; A ENST00000361284 Transcript missense_variant 88/942 88/942 30/313 L/M Ttg/Atg COSM3399845 1 1 OR10Z1 HGNC HGNC:14996 protein_coding YES CCDS30901.1 ENSP00000354707 Q8NGY1 A0A126GV63 UPI000004CA23 NM_001004478.1 tolerated(0.09) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF49,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 158606526 158606526 T A 1 0 0 0 0 1 0 0 0 10999 1606 56 4 4 OR10Z1 1 158606526 Missense_Mutation SNP T C3N-00738_T 835866 158606526 90349896 17 19942 SPTA1 0 . GRCh38 1 158634641 158634641 + Nonsense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.5467C>T p.Gln1823Ter p.Q1823* ENST00000368147 39/52 540 482 58 573 573 0 strelka-varscan-mutect SPTA1,stop_gained,p.Gln1823Ter,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,;SPTA1,downstream_gene_variant,,ENST00000465741,; A ENST00000368147 Transcript stop_gained 5648/7999 5467/7260 1823/2419 Q/* Caa/Taa 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 39/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 158634641 158634641 G A 1 0 0 0 0 0 1 0 0 15472 1328 46 3 3 SPTA1 1 158634641 Nonsense_Mutation SNP G C3N-00738_T 28115 158634641 90321781 18 19943 ACKR1 0 . GRCh38 1 159205822 159205822 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.389T>C p.Leu130Pro p.L130P ENST00000368121 1/1 94 88 6 129 129 0 strelka-varscan-mutect ACKR1,missense_variant,p.Leu128Pro,ENST00000537147,;ACKR1,missense_variant,p.Leu128Pro,ENST00000368122,NM_002036.3;ACKR1,missense_variant,p.Leu130Pro,ENST00000368121,NM_001122951.2;ACKR1,missense_variant,p.Leu130Pro,ENST00000435307,;CADM3,downstream_gene_variant,,ENST00000368125,NM_001127173.1;CADM3,downstream_gene_variant,,ENST00000368124,NM_021189.3;CADM3-AS1,intron_variant,,ENST00000609696,;CADM3-AS1,upstream_gene_variant,,ENST00000415675,; C ENST00000368121 Transcript missense_variant 564/1240 389/1017 130/338 L/P cTg/cCg 1 1 ACKR1 HGNC HGNC:4035 protein_coding YES CCDS44252.1 ENSP00000357103 Q16570 Q5Y7A1 UPI000013E1B0 NM_001122951.2 deleterious(0) 1/1 hmmpanther:PTHR14181,Prints_domain:PR01559 MODERATE SNV 1 PASS . . 0 205 4 0 0 0 0 0 -12.71023 1 1 1 1 0 C 3 2 64 159205822 159205822 T C 1 0 0 0 0 1 0 0 0 181 1580 55 5 5 ACKR1 1 159205822 Missense_Mutation SNP T C3N-00738_T 571181 159205822 89750600 19 19944 F5 0 . GRCh38 1 169541840 169541840 + Nonsense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.3250C>T p.Gln1084Ter p.Q1084* ENST00000367797 13/25 191 173 18 316 315 1 strelka-varscan-mutect F5,stop_gained,p.Gln1089Ter,ENST00000367796,;F5,stop_gained,p.Gln1084Ter,ENST00000367797,NM_000130.4; A ENST00000367797 Transcript stop_gained 3452/7024 3250/6675 1084/2224 Q/* Cag/Tag 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 13/25 PIRSF_domain:PIRSF000354 HIGH 1 SNV 1 1 PASS rs1359808137 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 169541840 169541840 G A 1 0 0 0 0 0 1 0 0 5216 1299 45 3 3 F5 1 169541840 Nonsense_Mutation SNP G C3N-00738_T 10336018 169541840 79414582 20 19945 TNN 0 . GRCh38 1 175080268 175080268 + Missense_Mutation SNP C C A C3N-00738_T C3N-00738_N C C c.890C>A p.Pro297His p.P297H ENST00000239462 4/19 396 367 29 446 445 1 strelka-varscan-mutect TNN,missense_variant,p.Pro297His,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Pro297His,ENST00000621086,;TNN,missense_variant,p.Pro297His,ENST00000622870,; A ENST00000239462 Transcript missense_variant 1003/5008 890/3900 297/1299 P/H cCc/cAc COSM3863591 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 deleterious(0) 4/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 2 1 1 PASS rs1249138784 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 175080268 175080268 C A 1 0 0 0 0 1 0 0 0 16796 623 22 2 2 TNN 1 175080268 Missense_Mutation SNP C C3N-00738_T 5538428 175080268 73876154 21 19946 BRINP2 0 . GRCh38 1 177255930 177255930 + Missense_Mutation SNP G G T rs770338219 C3N-00738_T C3N-00738_N G G c.281G>T p.Arg94Leu p.R94L ENST00000361539 3/8 143 134 9 164 164 0 strelka-varscan-mutect BRINP2,missense_variant,p.Arg94Leu,ENST00000361539,NM_021165.3;BRINP2,upstream_gene_variant,,ENST00000478325,;BRINP2,upstream_gene_variant,,ENST00000460161,; T ENST00000361539 Transcript missense_variant 593/3558 281/2352 94/783 R/L cGt/cTt rs770338219 1 1 BRINP2 HGNC HGNC:13746 protein_coding YES CCDS1320.1 ENSP00000354481 Q9C0B6 UPI000006DF55 NM_021165.3 deleterious(0) 3/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF8,Pfam_domain:PF01823,SMART_domains:SM00457 MODERATE 1 SNV 1 1 PASS rs770338219 . 0 205 5 0 0 0 0 0 -16.79082 1 1 1 1 0 T 3 4 64 177255930 177255930 G T 1 0 0 0 0 1 0 0 0 1686 1145 40 1 1 BRINP2 1 177255930 Missense_Mutation SNP G C3N-00738_T 2175662 177255930 71700492 22 19947 HMCN1 0 . GRCh38 1 186122995 186122995 + Missense_Mutation SNP G G C C3N-00738_T C3N-00738_N G G c.12274G>C p.Val4092Leu p.V4092L ENST00000271588 81/107 362 332 30 424 423 1 strelka-varscan-mutect HMCN1,missense_variant,p.Val4092Leu,ENST00000271588,NM_031935.2; C ENST00000271588 Transcript missense_variant 12503/18208 12274/16908 4092/5635 V/L Gtg/Ctg COSM1160881 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.27) 81/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 186122995 186122995 G C 1 0 0 0 0 1 0 0 0 7111 1377 48 4 4 HMCN1 1 186122995 Missense_Mutation SNP G C3N-00738_T 8867065 186122995 62833427 23 19948 KCNT2 0 . GRCh38 1 196285699 196285699 + Silent SNP C C A novel C3N-00738_T C3N-00738_N C C c.2655G>T p.= p.G885G ENST00000294725 23/28 332 293 39 343 343 0 strelka-varscan-mutect KCNT2,synonymous_variant,p.=,ENST00000367433,NM_001287819.1;KCNT2,synonymous_variant,p.=,ENST00000294725,NM_198503.3;KCNT2,synonymous_variant,p.=,ENST00000609185,NM_001287820.1;KCNT2,3_prime_UTR_variant,,ENST00000451324,;KCNT2,non_coding_transcript_exon_variant,,ENST00000498426,;KCNT2,non_coding_transcript_exon_variant,,ENST00000610076,; A ENST00000294725 Transcript synonymous_variant 3571/4409 2655/3408 885/1135 G ggG/ggT 1 -1 KCNT2 HGNC HGNC:18866 protein_coding YES CCDS1384.1 ENSP00000294725 Q6UVM3 A9LNM6 UPI00001E0966 NM_198503.3 23/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF9 LOW 1 SNV 1 1 PASS rs1300255005 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 196285699 196285699 C A 1 0 0 0 0 0 0 0 1 8008 842 30 2 2 KCNT2 1 196285699 Silent SNP C C3N-00738_T 10162704 196285699 52670723 24 19949 GPR25 0 . GRCh38 1 200873824 200873824 + Silent SNP C C T novel C3N-00738_T C3N-00738_N C C c.787C>T p.= p.L263L ENST00000304244 1/1 245 225 20 265 265 0 strelka-varscan-mutect GPR25,synonymous_variant,p.=,ENST00000304244,NM_005298.3; T ENST00000304244 Transcript synonymous_variant 870/1224 787/1086 263/361 L Ctg/Ttg 1 1 GPR25 HGNC HGNC:4480 protein_coding YES CCDS1405.1 ENSP00000301917 O00155 UPI000013E957 NM_005298.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF9,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 200873824 200873824 C T 1 0 0 0 0 0 0 0 1 6567 680 24 3 3 GPR25 1 200873824 Silent SNP C C3N-00738_T 4588125 200873824 48082598 25 19950 OR2AK2 0 . GRCh38 1 247965446 247965446 + Missense_Mutation SNP A A T C3N-00738_T C3N-00738_N A A c.115A>T p.Asn39Tyr p.N39Y ENST00000366480 1/1 207 184 23 241 240 1 strelka-varscan-mutect OR2AK2,missense_variant,p.Asn39Tyr,ENST00000366480,NM_001004491.1; T ENST00000366480 Transcript missense_variant 214/1107 115/1008 39/335 N/Y Aac/Tac COSM4030647 1 1 OR2AK2 HGNC HGNC:19569 protein_coding YES CCDS31102.1 ENSP00000355436 Q8NG84 UPI00003B2873 NM_001004491.1 deleterious(0.02) 1/1 hmmpanther:PTHR26453:SF299,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 247965446 247965446 A T 1 0 0 0 0 1 0 0 0 11064 14 1 4 4 OR2AK2 1 247965446 Missense_Mutation SNP A C3N-00738_T 47091622 247965446 990976 26 19951 ALLC 0 . GRCh38 2 3683028 3683028 + Silent SNP C C G rs756013424 C3N-00738_T C3N-00738_N C C c.465C>G p.= p.V155V ENST00000252505 7/12 259 240 19 256 255 1 strelka-varscan-mutect ALLC,synonymous_variant,p.=,ENST00000252505,NM_018436.3;GAPDHP48,downstream_gene_variant,,ENST00000436626,; G ENST00000252505 Transcript synonymous_variant 627/1446 465/1176 155/391 V gtC/gtG rs756013424 1 1 ALLC HGNC HGNC:17377 protein_coding YES CCDS46223.1 ENSP00000252505 B4DY77 UPI000050BBEF NM_018436.3 7/12 hmmpanther:PTHR12045,TIGRFAM_domain:TIGR02961,PIRSF_domain:PIRSF016516,Pfam_domain:PF03561,Gene3D:2.60.120.260,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS rs756013424 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 3683028 3683028 C G 1 0 0 0 0 0 0 0 1 634 813 29 4 4 ALLC 2 3683028 Silent SNP C C3N-00738_T 3683028 238510501 27 19952 PLB1 0 . GRCh38 2 28541762 28541762 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.830C>A p.Thr277Asn p.T277N ENST00000327757 13/58 293 260 33 294 294 0 strelka-varscan-mutect PLB1,missense_variant,p.Thr288Asn,ENST00000422425,NM_001170585.1;PLB1,missense_variant,p.Thr277Asn,ENST00000327757,NM_153021.4;PLB1,missense_variant,p.Thr287Asn,ENST00000404858,;PLB1,downstream_gene_variant,,ENST00000416713,; A ENST00000327757 Transcript missense_variant 874/5107 830/4377 277/1458 T/N aCc/aAc 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 deleterious(0.01) 13/58 hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31 MODERATE 1 SNV 1 1 PASS rs1202413678 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 28541762 28541762 C A 1 0 0 0 0 1 0 0 0 12118 507 18 2 2 PLB1 2 28541762 Missense_Mutation SNP C C3N-00738_T 24858734 28541762 213651767 28 19953 PSME4 0 . GRCh38 2 53932075 53932075 + Missense_Mutation SNP C C A rs775712608 C3N-00738_T C3N-00738_N C C c.1076G>T p.Arg359Leu p.R359L ENST00000404125 10/47 101 93 8 163 163 0 strelka-varscan-mutect PSME4,missense_variant,p.Arg359Leu,ENST00000404125,NM_014614.2;PSME4,downstream_gene_variant,,ENST00000481518,;PSME4,missense_variant,p.Arg359Leu,ENST00000389993,;PSME4,non_coding_transcript_exon_variant,,ENST00000475694,; A ENST00000404125 Transcript missense_variant 1132/7099 1076/5532 359/1843 R/L cGg/cTg rs775712608 1 -1 PSME4 HGNC HGNC:20635 protein_coding YES CCDS33197.2 ENSP00000384211 Q14997 UPI0000F3BE4A NM_014614.2 deleterious(0.01) 10/47 Pfam_domain:PF16507,hmmpanther:PTHR32170,hmmpanther:PTHR32170:SF3,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs775712608 . 0 206 3 0 0 0 0 0 -16.52139 1 1 1 1 0 A 3 1 64 53932075 53932075 C A 1 0 0 0 0 1 0 0 0 12860 652 23 1 1 PSME4 2 53932075 Missense_Mutation SNP C C3N-00738_T 25390313 53932075 188261454 29 19954 RFX8 0 . GRCh38 2 101402643 101402643 + Missense_Mutation SNP C C A rs746630582,rs758513252 C3N-00738_T C3N-00738_N C C c.1038G>T p.Met346Ile p.M346I ENST00000428343 11/12 295 269 26 365 362 3 strelka-varscan-mutect RFX8,missense_variant,p.Met346Ile,ENST00000428343,NM_001145664.1;RFX8,3_prime_UTR_variant,,ENST00000481179,; A ENST00000428343 Transcript missense_variant 1158/1686 1038/1422 346/473 M/I atG/atT rs746630582,rs758513252 1 -1 RFX8 HGNC HGNC:37253 protein_coding YES CCDS46376.1 ENSP00000401536 Q6ZV50 UPI0001AE76D5 NM_001145664.1 tolerated(0.29) 11/12 hmmpanther:PTHR12619:SF24,hmmpanther:PTHR12619 MODERATE 1 SNV 2 1 PASS rs758513252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 101402643 101402643 C A 1 0 0 0 0 1 0 0 0 13443 710 25 2 2 RFX8 2 101402643 Missense_Mutation SNP C C3N-00738_T 47470568 101402643 140790886 30 19955 SMPD4 0 . GRCh38 2 130153765 130153765 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.1947C>T p.= p.D649D ENST00000409031 17/20 295 267 28 393 393 0 varscan-mutect SMPD4,synonymous_variant,p.=,ENST00000409031,NM_017951.4;SMPD4,synonymous_variant,p.=,ENST00000351288,NM_017751.4;SMPD4,synonymous_variant,p.=,ENST00000431183,NM_001171083.2;SMPD4,synonymous_variant,p.=,ENST00000439886,;SMPD4,synonymous_variant,p.=,ENST00000457039,;SMPD4,synonymous_variant,p.=,ENST00000449159,;SMPD4,downstream_gene_variant,,ENST00000430682,;SMPD4,downstream_gene_variant,,ENST00000451542,;SMPD4,downstream_gene_variant,,ENST00000473720,;SMPD4,downstream_gene_variant,,ENST00000455548,;SMPD4,3_prime_UTR_variant,,ENST00000412570,;SMPD4,3_prime_UTR_variant,,ENST00000454468,;SMPD4,3_prime_UTR_variant,,ENST00000433118,;SMPD4,non_coding_transcript_exon_variant,,ENST00000482171,;SMPD4,non_coding_transcript_exon_variant,,ENST00000491128,;SMPD4,non_coding_transcript_exon_variant,,ENST00000491319,;SMPD4,downstream_gene_variant,,ENST00000435455,;SMPD4,downstream_gene_variant,,ENST00000461187,;SMPD4,downstream_gene_variant,,ENST00000439029,; A ENST00000409031 Transcript synonymous_variant 3096/4896 1947/2601 649/866 D gaC/gaT 1 -1 SMPD4 HGNC HGNC:32949 protein_coding YES CCDS42751.1 ENSP00000386531 B1PBA3 UPI000036FC5A NM_017951.4 17/20 Pfam_domain:PF14724,hmmpanther:PTHR12988,hmmpanther:PTHR12988:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 130153765 130153765 G A 1 0 0 0 0 0 0 0 1 15128 1368 48 3 3 SMPD4 2 130153765 Silent SNP G C3N-00738_T 28751122 130153765 112039764 31 19956 SLC4A10 0 . GRCh38 2 161904176 161904176 + Missense_Mutation SNP A A C novel C3N-00738_T C3N-00738_N A A c.1615A>C p.Ile539Leu p.I539L ENST00000446997 13/27 105 99 6 128 128 0 strelka-varscan-mutect SLC4A10,missense_variant,p.Ile520Leu,ENST00000375514,NM_001178016.1;SLC4A10,missense_variant,p.Ile509Leu,ENST00000415876,NM_022058.3;SLC4A10,missense_variant,p.Ile539Leu,ENST00000446997,NM_001178015.1;SLC4A10,missense_variant,p.Ile509Leu,ENST00000272716,;SLC4A10,missense_variant,p.Ile539Leu,ENST00000421911,;SLC4A10,downstream_gene_variant,,ENST00000493021,;SLC4A10,splice_region_variant,,ENST00000446228,; C ENST00000446997 Transcript missense_variant,splice_region_variant 1708/5551 1615/3357 539/1118 I/L Ata/Cta 1 1 SLC4A10 HGNC HGNC:13811 protein_coding YES CCDS54411.1 ENSP00000393066 Q6U841 UPI00001D4707 NM_001178015.1 tolerated(0.36) 13/27 hmmpanther:PTHR11453:SF32,hmmpanther:PTHR11453,Pfam_domain:PF00955,TIGRFAM_domain:TIGR00834 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.67194 1 1 1 1 0 C 3 2 64 161904176 161904176 A C 1 0 0 0 0 1 0 0 0 14928 463 16 5 5 SLC4A10 2 161904176 Missense_Mutation SNP A C3N-00738_T 31750411 161904176 80289353 32 19957 SP3 0 . GRCh38 2 173956150 173956151 + Frame_Shift_Ins INS - - AA novel C3N-00738_T C3N-00738_N - - c.361_362insTT p.Asp121ValfsTer7 p.D121Vfs*7 ENST00000310015 4/7 110 102 8 190 190 0 sindel-pindel SP3,frameshift_variant,p.Asp121ValfsTer7,ENST00000310015,NM_003111.4,NM_001172712.1;SP3,frameshift_variant,p.Asp53ValfsTer7,ENST00000418194,NM_001017371.4;SP3,frameshift_variant,p.Asp78ValfsTer7,ENST00000416195,;SP3,non_coding_transcript_exon_variant,,ENST00000483084,;SP3,non_coding_transcript_exon_variant,,ENST00000462904,;SP3,non_coding_transcript_exon_variant,,ENST00000490182,; AA ENST00000310015 Transcript frameshift_variant 892-893/6359 361-362/2346 121/781 D/VX gat/gTTat 1 -1 SP3 HGNC HGNC:11208 protein_coding YES CCDS2254.1 ENSP00000310301 Q02447 UPI000019B3E0 NM_003111.4,NM_001172712.1 4/7 hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF3 HIGH 1 insertion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 AA 7 5 64 173956150 173956150 - AA 1 0 1 1 0 0 0 0 0 15291 1435 50 0 0 SP3 2 173956150 Frame_Shift_Ins INS - C3N-00738_T 12051974 173956150 68237379 33 19958 TTN 0 . GRCh38 2 178756265 178756265 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.11211C>T p.= p.D3737D ENST00000589042 46/363 116 105 11 169 168 1 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000591111,;TTN,intron_variant,,ENST00000615779,NM_001256850.1;TTN,intron_variant,,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000360870,NM_133379.4;TTN,intron_variant,,ENST00000634225,;TTN-AS1,splice_acceptor_variant,,ENST00000578746,;TTN-AS1,splice_acceptor_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000627661,;TTN-AS1,upstream_gene_variant,,ENST00000610005,; A ENST00000589042 Transcript synonymous_variant 11436/109224 11211/107976 3737/35991 D gaC/gaT 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 46/363 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 178756265 178756265 G A 1 0 0 0 0 0 0 0 1 17245 1020 36 3 3 TTN 2 178756265 Silent SNP G C3N-00738_T 4800115 178756265 63437264 34 19959 FAM117B 0 . GRCh38 2 202765506 202765506 + Silent SNP C C T novel C3N-00738_T C3N-00738_N C C c.1512C>T p.= p.F504F ENST00000392238 8/8 223 200 23 313 313 0 strelka-varscan-mutect FAM117B,synonymous_variant,p.=,ENST00000392238,NM_173511.3; T ENST00000392238 Transcript synonymous_variant 1512/5763 1512/1770 504/589 F ttC/ttT 1 1 FAM117B HGNC HGNC:14440 protein_coding YES CCDS33362.2 ENSP00000376071 Q6P1L5 UPI00015B3B88 NM_173511.3 8/8 Pfam_domain:PF15388,hmmpanther:PTHR14972,hmmpanther:PTHR14972:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 202765506 202765506 C T 1 0 0 0 0 0 0 0 1 5269 825 29 3 3 FAM117B 2 202765506 Silent SNP C C3N-00738_T 24009241 202765506 39428023 35 19960 FASTKD2 0 . GRCh38 2 206770187 206770187 + Nonsense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.874G>T p.Gly292Ter p.G292* ENST00000236980 3/12 413 373 40 519 519 0 strelka-varscan-mutect FASTKD2,stop_gained,p.Gly292Ter,ENST00000236980,NM_014929.3;FASTKD2,stop_gained,p.Gly292Ter,ENST00000402774,NM_001136193.1,NM_001136194.1;FASTKD2,stop_gained,p.Gly292Ter,ENST00000403094,;MDH1B,upstream_gene_variant,,ENST00000374412,NM_001039845.2;MDH1B,upstream_gene_variant,,ENST00000454776,NM_001282940.1;MDH1B,upstream_gene_variant,,ENST00000449792,;FASTKD2,downstream_gene_variant,,ENST00000418289,;FASTKD2,non_coding_transcript_exon_variant,,ENST00000487777,;MDH1B,upstream_gene_variant,,ENST00000432911,;MDH1B,upstream_gene_variant,,ENST00000436472,;MDH1B,upstream_gene_variant,,ENST00000471988,; T ENST00000236980 Transcript stop_gained 1222/3188 874/2133 292/710 G/* Gga/Tga 1 1 FASTKD2 HGNC HGNC:29160 protein_coding YES CCDS2371.1 ENSP00000236980 Q9NYY8 A0A024R419 UPI0000073E9F NM_014929.3 3/12 hmmpanther:PTHR21228,hmmpanther:PTHR21228:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 64 206770187 206770187 G T 1 0 0 0 0 0 1 0 0 5546 1233 43 2 2 FASTKD2 2 206770187 Nonsense_Mutation SNP G C3N-00738_T 4004681 206770187 35423342 36 19961 DOCK10 0 . GRCh38 2 224778190 224778190 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.5750A>T p.Tyr1917Phe p.Y1917F ENST00000258390 51/56 251 227 24 273 273 0 strelka-varscan-mutect DOCK10,missense_variant,p.Tyr1911Phe,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Tyr1917Phe,ENST00000258390,NM_014689.2;DOCK10,missense_variant,p.Tyr67Phe,ENST00000535663,; A ENST00000258390 Transcript missense_variant 5818/7260 5750/6561 1917/2186 Y/F tAt/tTt 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 deleterious(0.03) 51/56 Pfam_domain:PF06920,PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS rs1422304992 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 224778190 224778190 T A 1 0 0 0 0 1 0 0 0 4500 1406 49 4 4 DOCK10 2 224778190 Missense_Mutation SNP T C3N-00738_T 18008003 224778190 17415339 37 19962 NEU2 0 . GRCh38 2 233034586 233034586 + Silent SNP C C T rs540432557 C3N-00738_T C3N-00738_N C C c.672C>T p.= p.V224V ENST00000233840 2/2 111 97 14 149 149 0 strelka-varscan-mutect NEU2,synonymous_variant,p.=,ENST00000233840,NM_005383.2; T ENST00000233840 Transcript synonymous_variant 672/1143 672/1143 224/380 V gtC/gtT rs540432557,COSM1259015 1 1 NEU2 HGNC HGNC:7759 protein_coding YES CCDS2501.1 ENSP00000233840 Q9Y3R4 UPI000013C98F NM_005383.2 2/2 hmmpanther:PTHR10628:SF6,hmmpanther:PTHR10628,Gene3D:2.120.10.10,Pfam_domain:PF13088,Superfamily_domains:SSF50939 0,1 LOW 1 SNV 1 0,1 1 PASS rs540432557 . 0 206 0 3 0 0 0 0 -19.98949 0.9999905 1 1 1 0 T 2 4 64 233034586 233034586 C T 1 0 0 0 0 0 0 0 1 10377 871 31 1 1 NEU2 2 233034586 Silent SNP C C3N-00738_T 8256396 233034586 9158943 38 19963 GBX2 0 . GRCh38 2 236167776 236167776 + Missense_Mutation SNP G G C novel C3N-00738_T C3N-00738_N G G c.196C>G p.Pro66Ala p.P66A ENST00000306318 1/2 103 94 9 88 88 0 strelka-varscan-mutect GBX2,missense_variant,p.Pro66Ala,ENST00000306318,NM_001485.3;GBX2,missense_variant,p.Pro66Ala,ENST00000551105,NM_001301687.1;AC079135.1,intron_variant,,ENST00000483218,;AC079135.1,intron_variant,,ENST00000415226,;GBX2,upstream_gene_variant,,ENST00000465889,; C ENST00000306318 Transcript missense_variant 594/2123 196/1047 66/348 P/A Ccc/Gcc 1 -1 GBX2 HGNC HGNC:4186 protein_coding YES CCDS2515.1 ENSP00000302251 P52951 UPI000012B273 NM_001485.3 tolerated(0.78) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24334,hmmpanther:PTHR24334:SF3 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.33121 1 1 1 1 0 C 3 2 64 236167776 236167776 G C 1 0 0 0 0 1 0 0 0 6151 1203 42 4 4 GBX2 2 236167776 Missense_Mutation SNP G C3N-00738_T 3133190 236167776 6025753 39 19964 MLH1 0 . GRCh38 3 37020358 37020358 + Missense_Mutation SNP G G C novel C3N-00738_T C3N-00738_N G G c.933G>C p.Lys311Asn p.K311N ENST00000231790 11/19 264 246 18 304 304 0 strelka-varscan-mutect MLH1,missense_variant,p.Lys311Asn,ENST00000231790,NM_000249.3;MLH1,missense_variant,p.Lys70Asn,ENST00000458205,NM_001258274.1;MLH1,missense_variant,p.Lys70Asn,ENST00000536378,NM_001258273.1;MLH1,missense_variant,p.Lys213Asn,ENST00000435176,NM_001167617.1;MLH1,missense_variant,p.Lys70Asn,ENST00000539477,NM_001167619.1;MLH1,missense_variant,p.Lys70Asn,ENST00000455445,NM_001167618.1;MLH1,missense_variant,p.Lys303Asn,ENST00000456676,NM_001258271.1;MLH1,missense_variant,p.Lys70Asn,ENST00000441265,;MLH1,3_prime_UTR_variant,,ENST00000447829,;MLH1,intron_variant,,ENST00000413212,;MLH1,intron_variant,,ENST00000458009,;RPL29P11,upstream_gene_variant,,ENST00000494408,; C ENST00000231790 Transcript missense_variant 1149/2752 933/2271 311/756 K/N aaG/aaC 1 1 MLH1 HGNC HGNC:7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 UPI0000000C7E NM_000249.3 deleterious(0) 11/19 Gene3D:3.30.230.10,Pfam_domain:PF01119,hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF40,SMART_domains:SM01340,Superfamily_domains:SSF54211,TIGRFAM_domain:TIGR00585 MODERATE 1 SNV 1 1 PASS rs876660775 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 37020358 37020358 G C 1 0 0 0 0 1 0 0 0 9584 962 34 4 4 MLH1 3 37020358 Missense_Mutation SNP G C3N-00738_T 37020358 161275201 40 19965 EXOG 0 . GRCh38 3 38497713 38497713 + Missense_Mutation SNP C C G novel C3N-00738_T C3N-00738_N C C c.248C>G p.Ser83Cys p.S83C ENST00000287675 2/6 220 197 23 269 269 0 strelka-varscan-mutect EXOG,missense_variant,p.Ser83Cys,ENST00000287675,NM_005107.3;EXOG,missense_variant,p.Ser46Cys,ENST00000453767,;EXOG,intron_variant,,ENST00000422077,NM_001145464.1;ACVR2B,downstream_gene_variant,,ENST00000352511,NM_001106.3;EXOG,downstream_gene_variant,,ENST00000630638,;EXOG,missense_variant,p.Ser83Cys,ENST00000457367,;EXOG,missense_variant,p.Ser83Cys,ENST00000431472,;EXOG,3_prime_UTR_variant,,ENST00000447573,;EXOG,3_prime_UTR_variant,,ENST00000443942,;EXOG,non_coding_transcript_exon_variant,,ENST00000489813,;EXOG,intron_variant,,ENST00000474071,;EXOG,intron_variant,,ENST00000436414,;EXOG,intron_variant,,ENST00000454803,;EXOG,intron_variant,,ENST00000412107,;EXOG,intron_variant,,ENST00000438992,;EXOG,intron_variant,,ENST00000450732,;EXOG,intron_variant,,ENST00000470291,;EXOG,upstream_gene_variant,,ENST00000483749,; G ENST00000287675 Transcript missense_variant 344/2792 248/1107 83/368 S/C tCt/tGt 1 1 EXOG HGNC HGNC:3347 protein_coding YES CCDS2680.1 ENSP00000287675 Q9Y2C4 UPI00001AEB05 NM_005107.3 tolerated(0.1) 2/6 Gene3D:1g8tA00,Pfam_domain:PF01223,hmmpanther:PTHR13966,SMART_domains:SM00477,SMART_domains:SM00892,Superfamily_domains:SSF54060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 38497713 38497713 C G 1 0 0 0 0 1 0 0 0 5180 913 32 4 4 EXOG 3 38497713 Missense_Mutation SNP C C3N-00738_T 1477355 38497713 159797846 41 19966 RTP3 0 . GRCh38 3 46498128 46498128 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.66G>T p.Trp22Cys p.W22C ENST00000296142 1/2 284 247 37 349 349 0 strelka-varscan-mutect RTP3,missense_variant,p.Trp22Cys,ENST00000296142,NM_031440.1; T ENST00000296142 Transcript missense_variant 638/1321 66/699 22/232 W/C tgG/tgT 1 1 RTP3 HGNC HGNC:15572 protein_coding YES CCDS2740.1 ENSP00000296142 Q9BQQ7 UPI000005033A NM_031440.1 tolerated(0.07) 1/2 hmmpanther:PTHR14402,hmmpanther:PTHR14402:SF9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 46498128 46498128 G T 1 0 0 0 0 1 0 0 0 13995 1212 42 2 2 RTP3 3 46498128 Missense_Mutation SNP G C3N-00738_T 8000415 46498128 151797431 42 19967 CELSR3 0 . GRCh38 3 48651419 48651419 + Silent SNP A A G novel C3N-00738_T C3N-00738_N A A c.6126T>C p.= p.C2042C ENST00000164024 14/35 226 213 13 181 181 0 strelka-varscan-mutect CELSR3,synonymous_variant,p.=,ENST00000164024,NM_001407.2; G ENST00000164024 Transcript synonymous_variant 6407/11956 6126/9939 2042/3312 C tgT/tgC 1 -1 CELSR3 HGNC HGNC:3230 protein_coding YES CCDS2775.1 ENSP00000164024 Q9NYQ7 UPI00001AE5A6 NM_001407.2 14/35 Gene3D:2gy5A03,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF38 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 48651419 48651419 A G 1 0 0 0 0 0 0 0 1 2930 157 6 5 5 CELSR3 3 48651419 Silent SNP A C3N-00738_T 2153291 48651419 149644140 43 19968 ABI3BP 0 . GRCh38 3 100864020 100864020 + Silent SNP A A G novel C3N-00738_T C3N-00738_N A A c.1141T>C p.= p.L381L ENST00000471714 12/67 263 242 21 269 269 0 strelka-varscan-mutect ABI3BP,synonymous_variant,p.=,ENST00000471714,;ABI3BP,synonymous_variant,p.=,ENST00000495063,;ABI3BP,synonymous_variant,p.=,ENST00000483129,;ABI3BP,intron_variant,,ENST00000284322,NM_015429.3;ABI3BP,intron_variant,,ENST00000533855,;ABI3BP,intron_variant,,ENST00000528305,;ABI3BP,upstream_gene_variant,,ENST00000459682,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000475896,; G ENST00000471714 Transcript synonymous_variant 1251/6783 1141/5334 381/1777 L Ttg/Ctg 1 -1 ABI3BP HGNC HGNC:17265 protein_coding ENSP00000420524 D3YTG3 UPI00004225FE 12/67 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF10 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 100864020 100864020 A G 1 0 0 0 0 0 0 0 1 101 98 4 5 5 ABI3BP 3 100864020 Silent SNP A C3N-00738_T 52212601 100864020 97431539 44 19969 ATP6V1A 0 . GRCh38 3 113795093 113795093 + Missense_Mutation SNP G G T rs777475410 C3N-00738_T C3N-00738_N G G c.1115G>T p.Ser372Ile p.S372I ENST00000273398 10/15 146 137 9 234 234 0 strelka-varscan-mutect ATP6V1A,missense_variant,p.Ser372Ile,ENST00000273398,NM_001690.3;ATP6V1A,3_prime_UTR_variant,,ENST00000470455,; T ENST00000273398 Transcript missense_variant 1223/4591 1115/1854 372/617 S/I aGt/aTt rs777475410 1 1 ATP6V1A HGNC HGNC:851 protein_coding YES CCDS2976.1 ENSP00000273398 P38606 UPI000013809A NM_001690.3 deleterious(0.01) 10/15 HAMAP:MF_00309,hmmpanther:PTHR15184,hmmpanther:PTHR15184:SF51,TIGRFAM_domain:TIGR01042,Pfam_domain:PF00006,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs777475410 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 113795093 113795093 G T 1 0 0 0 0 1 0 0 0 1330 1043 36 2 2 ATP6V1A 3 113795093 Missense_Mutation SNP G C3N-00738_T 12931073 113795093 84500466 45 19970 WDR49 0 . GRCh38 3 167500264 167500264 + Frame_Shift_Del DEL C C - C3N-00738_T C3N-00738_N C C c.1864delG p.Glu622SerfsTer5 p.E622Sfs*5 ENST00000308378 14/15 210 190 20 283 283 0 sindel-varindel WDR49,frameshift_variant,p.Glu622SerfsTer5,ENST00000308378,NM_178824.3;WDR49,frameshift_variant,p.Glu599SerfsTer5,ENST00000472600,;WDR49,intron_variant,,ENST00000479765,;WDR49,non_coding_transcript_exon_variant,,ENST00000476376,; - ENST00000308378 Transcript frameshift_variant 2170/2594 1864/2094 622/697 E/X Gag/ag COSM1693745,COSM1693746 1 -1 WDR49 HGNC HGNC:26587 protein_coding YES CCDS3201.1 ENSP00000311343 Q8IV35 UPI00000746AD NM_178824.3 14/15 1,1 HIGH 1 deletion 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 64 167500264 167500264 C - 1 0 1 0 1 0 0 0 0 17862 922 32 0 0 WDR49 3 167500264 Frame_Shift_Del DEL C C3N-00738_T 53705171 167500264 30795295 46 19971 RUBCN 0 . GRCh38 3 197705127 197705128 + Frame_Shift_Ins INS - - C novel C3N-00738_T C3N-00738_N - - c.267dupG p.Trp90ValfsTer25 p.W90Vfs*25 ENST00000296343 3/20 417 381 36 464 464 0 varindel-pindel RUBCN,frameshift_variant,p.Trp30ValfsTer25,ENST00000273582,NM_001145642.3;RUBCN,frameshift_variant,p.Trp69ValfsTer25,ENST00000413360,;RUBCN,frameshift_variant,p.Trp90ValfsTer25,ENST00000296343,NM_014687.2;RUBCN,frameshift_variant,p.Trp90ValfsTer25,ENST00000449205,;RUBCN,5_prime_UTR_variant,,ENST00000474214,;RUBCN,upstream_gene_variant,,ENST00000415452,;RUBCN,upstream_gene_variant,,ENST00000447048,;RUBCN,non_coding_transcript_exon_variant,,ENST00000467303,; C ENST00000296343 Transcript frameshift_variant 267-268/2919 267-268/2919 89-90/972 -/X -/G 1 -1 RUBCN HGNC HGNC:28991 protein_coding YES CCDS43195.1 ENSP00000296343 Q92622 UPI00001C1DE4 NM_014687.2 3/20 PROSITE_profiles:PS50826,hmmpanther:PTHR12326:SF11,hmmpanther:PTHR12326,Pfam_domain:PF02759,Superfamily_domains:0052343 HIGH 1 insertion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 64 197705127 197705127 - C 1 0 1 1 0 0 0 0 0 13999 159 6 0 0 RUBCN 3 197705127 Frame_Shift_Ins INS - C3N-00738_T 30204863 197705127 590432 47 19972 ZNF595 0 . GRCh38 4 86691 86691 + Missense_Mutation SNP A A G novel C3N-00738_T C3N-00738_N A A c.1187A>G p.Tyr396Cys p.Y396C ENST00000610261 4/4 180 161 19 230 230 0 strelka-varscan-mutect ZNF595,missense_variant,p.Tyr396Cys,ENST00000610261,NM_182524.3;ZNF595,missense_variant,p.Tyr364Cys,ENST00000609518,NM_001286052.1;ZNF595,missense_variant,p.Tyr213Cys,ENST00000608255,NM_001286053.1,NM_001286054.1; G ENST00000610261 Transcript missense_variant 1391/2911 1187/1947 396/648 Y/C tAc/tGc 1 1 ZNF595 HGNC HGNC:27196 protein_coding YES CCDS75075.1 ENSP00000477392 Q7Z3I0 UPI00001A9D0D NM_182524.3 deleterious(0.02) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF303,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 86691 86691 A G 1 0 0 0 0 1 0 0 0 18600 391 14 5 5 ZNF595 4 86691 Missense_Mutation SNP A C3N-00738_T 86691 190127864 48 19973 AFAP1 0 . GRCh38 4 7819173 7819173 + Splice_Site SNP T T A rs762771077 C3N-00738_T C3N-00738_N T T c.727-2A>T p.X243_splice ENST00000420658 88 81 7 52 52 0 strelka-mutect AFAP1,splice_acceptor_variant,,ENST00000420658,NM_001134647.1;AFAP1,splice_acceptor_variant,,ENST00000358461,NM_198595.2;AFAP1,splice_acceptor_variant,,ENST00000360265,;AFAP1,splice_acceptor_variant,,ENST00000382543,;AFAP1,upstream_gene_variant,,ENST00000614385,; A ENST00000420658 Transcript splice_acceptor_variant -/7768 727/2445 243/814 rs762771077 1 -1 AFAP1 HGNC HGNC:24017 protein_coding YES CCDS47010.1 ENSP00000410689 Q8N556 UPI000048041E NM_001134647.1 6/17 HIGH 1 SNV 2 1 PASS rs762771077 . 0 202 8 0 0 0 0 0 -14.60144 0.9999927 1 1 1 0 A 5 1 64 7819173 7819173 T A 1 0 0 0 0 0 0 1 0 430 1536 53 4 4 AFAP1 4 7819173 Splice_Site SNP T C3N-00738_T 7732482 7819173 182395382 49 19974 HTRA3 0 . GRCh38 4 8291439 8291439 + Missense_Mutation SNP G G T rs774347163 C3N-00738_T C3N-00738_N G G c.778G>T p.Gly260Cys p.G260C ENST00000307358 4/9 340 312 28 324 324 0 strelka-varscan-mutect HTRA3,missense_variant,p.Gly260Cys,ENST00000307358,NM_053044.4;HTRA3,missense_variant,p.Gly260Cys,ENST00000382512,NM_001297559.1; T ENST00000307358 Transcript missense_variant 982/2541 778/1362 260/453 G/C Ggc/Tgc rs774347163 1 1 HTRA3 HGNC HGNC:30406 protein_coding YES CCDS3400.1 ENSP00000303766 P83110 UPI0000001647 NM_053044.4 deleterious(0) 4/9 hmmpanther:PTHR22939:SF14,hmmpanther:PTHR22939,Gene3D:2.40.10.10,Pfam_domain:PF13365,Superfamily_domains:SSF50494,Prints_domain:PR00834 MODERATE 1 SNV 1 1 PASS rs774347163 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 8291439 8291439 G T 1 0 0 0 0 1 0 0 0 7351 1116 39 1 1 HTRA3 4 8291439 Missense_Mutation SNP G C3N-00738_T 472266 8291439 181923116 50 19975 PACRGL 0 . GRCh38 4 20709772 20709772 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.365A>T p.Glu122Val p.E122V ENST00000503585 5/9 174 154 20 206 206 0 strelka-varscan-mutect PACRGL,missense_variant,p.Glu122Val,ENST00000360916,NM_145048.3;PACRGL,missense_variant,p.Glu122Val,ENST00000295290,;PACRGL,missense_variant,p.Glu122Val,ENST00000503585,NM_001258345.1;PACRGL,missense_variant,p.Glu122Val,ENST00000507634,;PACRGL,missense_variant,p.Glu170Val,ENST00000510051,;PACRGL,missense_variant,p.Glu122Val,ENST00000513590,;PACRGL,missense_variant,p.Glu122Val,ENST00000514485,;PACRGL,missense_variant,p.Glu122Val,ENST00000509469,;PACRGL,missense_variant,p.Glu54Val,ENST00000506457,;PACRGL,intron_variant,,ENST00000513459,NM_001317849.1;PACRGL,intron_variant,,ENST00000444671,NM_001130727.1;PACRGL,intron_variant,,ENST00000502374,NM_001258346.1;PACRGL,intron_variant,,ENST00000502938,;PACRGL,intron_variant,,ENST00000511089,;PACRGL,intron_variant,,ENST00000514292,;PACRGL,intron_variant,,ENST00000513861,;PACRGL,intron_variant,,ENST00000515339,;PACRGL,downstream_gene_variant,,ENST00000506745,;PACRGL,downstream_gene_variant,,ENST00000504630,;PACRGL,downstream_gene_variant,,ENST00000514663,;PACRGL,missense_variant,p.Glu122Val,ENST00000471979,;PACRGL,missense_variant,p.Glu122Val,ENST00000467997,;PACRGL,missense_variant,p.Glu122Val,ENST00000506702,;PACRGL,splice_region_variant,,ENST00000506951,;PACRGL,intron_variant,,ENST00000508952,;PACRGL,intron_variant,,ENST00000503747,;PACRGL,upstream_gene_variant,,ENST00000506648,;PACRGL,upstream_gene_variant,,ENST00000506552,; T ENST00000503585 Transcript missense_variant,splice_region_variant 756/1582 365/747 122/248 E/V gAg/gTg 1 1 PACRGL HGNC HGNC:28442 protein_coding YES CCDS58895.1 ENSP00000423881 Q8N7B6 UPI00001405F2 NM_001258345.1 deleterious(0) 5/9 Pfam_domain:PF10274,hmmpanther:PTHR21207,hmmpanther:PTHR21207:SF5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 20709772 20709772 A T 1 0 0 0 0 1 0 0 0 11449 318 11 4 4 PACRGL 4 20709772 Missense_Mutation SNP A C3N-00738_T 12418333 20709772 169504783 51 19976 ADGRA3 0 . GRCh38 4 22387705 22387705 + Nonstop_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.3966A>T p.Ter1322TyrextTer6 p.*1322Yext*6 ENST00000334304 19/19 69 58 11 105 105 0 strelka-varscan-mutect ADGRA3,stop_lost,p.Ter1322TyrextTer6,ENST00000334304,NM_145290.3;ADGRA3,downstream_gene_variant,,ENST00000282943,;ADGRA3,downstream_gene_variant,,ENST00000504617,;ADGRA3,non_coding_transcript_exon_variant,,ENST00000499527,;ADGRA3,intron_variant,,ENST00000511051,; A ENST00000334304 Transcript stop_lost 4236/4566 3966/3966 1322/1321 */Y taA/taT 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 19/19 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 22387705 22387705 T A 1 0 0 0 0 0 0 0 0 354 1732 60 4 4 ADGRA3 4 22387705 Nonstop_Mutation SNP T C3N-00738_T 1677933 22387705 167826850 52 19977 UBA6 0 . GRCh38 4 67670587 67670587 + Silent SNP G G A rs764833296 C3N-00738_T C3N-00738_N G G c.552C>T p.= p.I184I ENST00000322244 8/33 235 211 24 308 307 1 strelka-varscan-mutect UBA6,synonymous_variant,p.=,ENST00000322244,NM_018227.5;UBA6,synonymous_variant,p.=,ENST00000420827,;UBA6,non_coding_transcript_exon_variant,,ENST00000429659,; A ENST00000322244 Transcript synonymous_variant 612/9564 552/3159 184/1052 I atC/atT rs764833296 1 -1 UBA6 HGNC HGNC:25581 protein_coding YES CCDS3516.1 ENSP00000313454 A0AVT1 A0A024RDB0 UPI000004A4F7 NM_018227.5 8/33 hmmpanther:PTHR10953:SF141,hmmpanther:PTHR10953,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR01408,Pfam_domain:PF00899,Superfamily_domains:SSF69572 LOW 1 SNV 1 1 PASS rs764833296 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 67670587 67670587 G A 1 0 0 0 0 0 0 0 1 17351 1304 45 3 3 UBA6 4 67670587 Silent SNP G C3N-00738_T 45282882 67670587 122543968 53 19978 PPP3CA 0 . GRCh38 4 101026017 101026017 + Nonsense_Mutation SNP C C A rs775976578 C3N-00738_T C3N-00738_N C C c.1414G>T p.Glu472Ter p.E472* ENST00000394854 14/14 127 114 13 122 122 0 strelka-varscan-mutect PPP3CA,stop_gained,p.Glu472Ter,ENST00000394854,NM_000944.4;PPP3CA,stop_gained,p.Glu420Ter,ENST00000323055,NM_001130692.1;PPP3CA,stop_gained,p.Glu240Ter,ENST00000512215,;PPP3CA,stop_gained,p.Glu462Ter,ENST00000394853,NM_001130691.1;PPP3CA,stop_gained,p.Glu374Ter,ENST00000507176,; A ENST00000394854 Transcript stop_gained 2098/4685 1414/1566 472/521 E/* Gaa/Taa rs775976578,COSM5615336 1 -1 PPP3CA HGNC HGNC:9314 protein_coding YES CCDS34037.1 ENSP00000378323 Q08209 A0A0S2Z4C6 UPI0000110660 NM_000944.4 14/14 Superfamily_domains:SSF56300 0,1 HIGH 1 SNV 1 0,1 1 PASS rs775976578 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 101026017 101026017 C A 1 0 0 0 0 0 1 0 0 12519 864 30 2 2 PPP3CA 4 101026017 Nonsense_Mutation SNP C C3N-00738_T 33355430 101026017 89188538 54 19979 NPNT 0 . GRCh38 4 105937053 105937053 + Missense_Mutation SNP T T G novel C3N-00738_T C3N-00738_N T T c.400T>G p.Cys134Gly p.C134G ENST00000427316 5/13 204 186 18 271 270 1 strelka-varscan-mutect NPNT,missense_variant,p.Cys104Gly,ENST00000379987,NM_001033047.2;NPNT,missense_variant,p.Cys104Gly,ENST00000305572,;NPNT,missense_variant,p.Cys134Gly,ENST00000427316,NM_001184691.1;NPNT,missense_variant,p.Cys121Gly,ENST00000453617,NM_001184690.1;NPNT,missense_variant,p.Cys104Gly,ENST00000514622,NM_001184692.1;NPNT,missense_variant,p.Cys134Gly,ENST00000506666,NM_001184693.1;NPNT,missense_variant,p.Cys151Gly,ENST00000503451,;NPNT,missense_variant,p.Cys81Gly,ENST00000514837,;NPNT,5_prime_UTR_variant,,ENST00000504304,;RP11-710F7.2,upstream_gene_variant,,ENST00000512514,;NPNT,non_coding_transcript_exon_variant,,ENST00000513430,;NPNT,non_coding_transcript_exon_variant,,ENST00000505821,;NPNT,non_coding_transcript_exon_variant,,ENST00000506056,; G ENST00000427316 Transcript missense_variant 612/2481 400/1788 134/595 C/G Tgc/Ggc 1 1 NPNT HGNC HGNC:27405 protein_coding YES CCDS54785.1 ENSP00000389252 Q6UXI9 UPI0001AE758D NM_001184691.1 deleterious(0) 5/13 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24050,hmmpanther:PTHR24050:SF19,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 105937053 105937053 T G 1 0 0 0 0 1 0 0 0 10646 1696 59 5 5 NPNT 4 105937053 Missense_Mutation SNP T C3N-00738_T 4911036 105937053 84277502 55 19980 FSTL5 0 . GRCh38 4 161386173 161386173 + Silent SNP A A T novel C3N-00738_T C3N-00738_N A A c.2118T>A p.= p.L706L ENST00000306100 16/16 302 275 27 397 397 0 strelka-varscan-mutect FSTL5,synonymous_variant,p.=,ENST00000306100,NM_020116.4;FSTL5,synonymous_variant,p.=,ENST00000379164,NM_001128427.2;FSTL5,synonymous_variant,p.=,ENST00000427802,NM_001128428.2;RP11-234O6.2,non_coding_transcript_exon_variant,,ENST00000508189,; T ENST00000306100 Transcript synonymous_variant 2555/4831 2118/2544 706/847 L ctT/ctA 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 16/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Gene3D:2.130.10.10,Superfamily_domains:0047643 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 161386173 161386173 A T 1 0 0 0 0 0 0 0 1 5954 117 5 4 4 FSTL5 4 161386173 Silent SNP A C3N-00738_T 55449120 161386173 28828382 56 19981 MARCH1 0 . GRCh38 4 163585888 163585888 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.284C>A p.Thr95Lys p.T95K ENST00000503008 6/8 89 77 12 105 104 1 strelka-varscan-mutect MARCH1,missense_variant,p.Thr95Lys,ENST00000503008,NM_001166373.1;MARCH1,missense_variant,p.Thr95Lys,ENST00000274056,;MARCH1,missense_variant,p.Thr351Lys,ENST00000514618,;MARCH1,missense_variant,p.Thr78Lys,ENST00000339875,NM_017923.3;MARCH1,missense_variant,p.Thr95Lys,ENST00000507270,;MARCH1,missense_variant,p.Thr78Lys,ENST00000510786,;MARCH1,non_coding_transcript_exon_variant,,ENST00000512214,;MARCH1,non_coding_transcript_exon_variant,,ENST00000505517,; T ENST00000503008 Transcript missense_variant 1261/5877 284/870 95/289 T/K aCa/aAa 1 -1 MARCH1 HGNC HGNC:26077 protein_coding YES CCDS54814.1 ENSP00000427223 Q8TCQ1 UPI0000037BB3 NM_001166373.1 deleterious(0.03) 6/8 PROSITE_profiles:PS51292,hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF53,Pfam_domain:PF12906,Gene3D:3.30.40.10,SMART_domains:SM00744,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 163585888 163585888 G T 1 0 0 0 0 1 0 0 0 9223 1377 48 2 2 MARCH1 4 163585888 Missense_Mutation SNP G C3N-00738_T 2199715 163585888 26628667 57 19982 DDX60 0 . GRCh38 4 168293919 168293919 + Silent SNP T T G novel C3N-00738_T C3N-00738_N T T c.750A>C p.= p.T250T ENST00000393743 7/38 137 125 12 166 166 0 strelka-varscan-mutect DDX60,synonymous_variant,p.=,ENST00000393743,NM_017631.5; G ENST00000393743 Transcript synonymous_variant 1042/6071 750/5139 250/1712 T acA/acC 1 -1 DDX60 HGNC HGNC:25942 protein_coding YES CCDS34097.1 ENSP00000377344 Q8IY21 UPI000020B6AB NM_017631.5 7/38 LOW 1 SNV 1 1 PASS rs1173273630 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 168293919 168293919 T G 1 0 0 0 0 0 0 0 1 4181 1683 59 5 5 DDX60 4 168293919 Silent SNP T C3N-00738_T 4708031 168293919 21920636 58 19983 KLKB1 0 . GRCh38 4 186257329 186257329 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.1689T>C p.= p.C563C ENST00000264690 14/15 207 182 25 294 294 0 strelka-varscan-mutect KLKB1,synonymous_variant,p.=,ENST00000264690,NM_000892.3;KLKB1,synonymous_variant,p.=,ENST00000511608,;KLKB1,intron_variant,,ENST00000513864,NM_001318394.1;KLKB1,non_coding_transcript_exon_variant,,ENST00000511406,; C ENST00000264690 Transcript synonymous_variant 1876/2363 1689/1917 563/638 C tgT/tgC 1 1 KLKB1 HGNC HGNC:6371 protein_coding YES CCDS34120.1 ENSP00000264690 P03952 UPI000050EC06 NM_000892.3 14/15 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF121,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 186257329 186257329 T C 1 0 0 0 0 0 0 0 1 8281 1702 59 5 5 KLKB1 4 186257329 Silent SNP T C3N-00738_T 17963410 186257329 3957226 59 19984 ICE1 0 . GRCh38 5 5463495 5463495 + Silent SNP C C T novel C3N-00738_T C3N-00738_N C C c.4161C>T p.= p.N1387N ENST00000296564 13/19 202 189 13 255 254 1 strelka-varscan-mutect ICE1,synonymous_variant,p.=,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript synonymous_variant 4383/7927 4161/6801 1387/2266 N aaC/aaT 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 5463495 5463495 C T 1 0 0 0 0 0 0 0 1 7384 564 20 3 3 ICE1 5 5463495 Silent SNP C C3N-00738_T 5463495 176074764 60 19985 ADAMTS12 0 . GRCh38 5 33658183 33658183 + Splice_Site DEL C C - novel C3N-00738_T C3N-00738_N C C c.1190+1delG p.X397_splice ENST00000504830 83 68 15 105 105 0 sindel-varindel-pindel ADAMTS12,splice_donor_variant,,ENST00000504830,NM_030955.2;ADAMTS12,splice_donor_variant,,ENST00000352040,;ADAMTS12,splice_donor_variant,,ENST00000504582,; - ENST00000504830 Transcript splice_donor_variant -/8774 1190/4785 397/1594 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 7/23 HIGH 1 deletion 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 64 33658183 33658183 C - 1 0 1 0 1 0 0 1 0 301 521 18 0 0 ADAMTS12 5 33658183 Splice_Site DEL C C3N-00738_T 28194688 33658183 147880076 61 19986 RNF180 0 . GRCh38 5 64217413 64217413 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.1244T>A p.Leu415His p.L415H ENST00000296615 5/5 59 51 8 58 58 0 strelka-varscan-mutect RNF180,missense_variant,p.Leu415His,ENST00000296615,NM_178532.3;RNF180,intron_variant,,ENST00000389100,NM_001113561.1;RNF180,downstream_gene_variant,,ENST00000504296,; A ENST00000296615 Transcript missense_variant 1354/1727 1244/1251 415/416 L/H cTt/cAt 1 1 RNF180 HGNC HGNC:27752 protein_coding CCDS34169.1 ENSP00000296615 Q86T96 UPI000006D6E2 NM_178532.3 deleterious_low_confidence(0) 5/5 MODERATE SNV 1 1 PASS rs982796912 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 64217413 64217413 T A 1 0 0 0 0 1 0 0 0 13641 1609 56 4 4 RNF180 5 64217413 Missense_Mutation SNP T C3N-00738_T 30559230 64217413 117320846 62 19987 ANKDD1B 0 . GRCh38 5 75663410 75663410 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.1112T>A p.Leu371Gln p.L371Q ENST00000601380 11/14 197 174 23 282 282 0 strelka-varscan-mutect ANKDD1B,missense_variant,p.Leu371Gln,ENST00000601380,NM_001276713.1;ANKDD1B,non_coding_transcript_exon_variant,,ENST00000506596,;ANKDD1B,non_coding_transcript_exon_variant,,ENST00000504514,;ANKDD1B,downstream_gene_variant,,ENST00000594319,; A ENST00000601380 Transcript missense_variant 1288/2569 1112/1587 371/528 L/Q cTg/cAg 1 1 ANKDD1B HGNC HGNC:32525 protein_coding YES CCDS64180.1 ENSP00000471417 A6NHY2 UPI0002A4709F NM_001276713.1 deleterious(0) 11/14 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR24125,hmmpanther:PTHR24125:SF1,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 75663410 75663410 T A 1 0 0 0 0 1 0 0 0 725 1580 55 4 4 ANKDD1B 5 75663410 Missense_Mutation SNP T C3N-00738_T 11445997 75663410 105874849 63 19988 ANKRD34B 0 . GRCh38 5 80558701 80558701 + Missense_Mutation SNP C C A C3N-00738_T C3N-00738_N C C c.1319G>T p.Ser440Ile p.S440I ENST00000338682 5/5 201 178 23 283 283 0 strelka-varscan-mutect ANKRD34B,missense_variant,p.Ser440Ile,ENST00000338682,NM_001004441.2;ANKRD34B,downstream_gene_variant,,ENST00000508916,; A ENST00000338682 Transcript missense_variant 1992/3938 1319/1545 440/514 S/I aGt/aTt COSM1754345 1 -1 ANKRD34B HGNC HGNC:33736 protein_coding YES CCDS34194.1 ENSP00000339802 A5PLL1 UPI00003672FA NM_001004441.2 tolerated(0.1) 5/5 hmmpanther:PTHR24156,hmmpanther:PTHR24156:SF1 1 MODERATE 1 SNV 1 1 1 PASS rs1250730901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 80558701 80558701 C A 1 0 0 0 0 1 0 0 0 768 565 20 2 2 ANKRD34B 5 80558701 Missense_Mutation SNP C C3N-00738_T 4895291 80558701 100979558 64 19989 NEUROG1 0 . GRCh38 5 135535290 135535290 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.401T>A p.Leu134Gln p.L134Q ENST00000314744 1/1 279 255 24 363 363 0 strelka-varscan-mutect NEUROG1,missense_variant,p.Leu134Gln,ENST00000314744,NM_006161.2; T ENST00000314744 Transcript missense_variant 660/1668 401/714 134/237 L/Q cTg/cAg 1 -1 NEUROG1 HGNC HGNC:7764 protein_coding YES CCDS4187.1 ENSP00000317580 Q92886 F1T0H3 UPI0000072868 NM_006161.2 deleterious(0) 1/1 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF92,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 135535290 135535290 A T 1 0 0 0 0 1 0 0 0 10389 188 7 4 4 NEUROG1 5 135535290 Missense_Mutation SNP A C3N-00738_T 54976589 135535290 46002969 65 19990 PCDHA1 0 . GRCh38 5 140788301 140788301 + Missense_Mutation SNP G G C novel C3N-00738_T C3N-00738_N G G c.2011G>C p.Glu671Gln p.E671Q ENST00000504120 1/4 245 228 17 354 354 0 strelka-varscan-mutect PCDHA1,missense_variant,p.Glu671Gln,ENST00000504120,NM_018900.3;PCDHA1,missense_variant,p.Glu671Gln,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; C ENST00000504120 Transcript missense_variant 2011/5263 2011/2853 671/950 E/Q Gag/Cag 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 140788301 140788301 G C 1 0 0 0 0 1 0 0 0 11606 1175 41 4 4 PCDHA1 5 140788301 Missense_Mutation SNP G C3N-00738_T 5253011 140788301 40749958 66 19991 NSD1 0 . GRCh38 5 177210753 177210753 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.2354C>T p.Pro785Leu p.P785L ENST00000439151 5/23 241 214 27 406 406 0 strelka-varscan-mutect NSD1,missense_variant,p.Pro785Leu,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Pro516Leu,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Pro516Leu,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENST00000439151 Transcript missense_variant 2399/12892 2354/8091 785/2696 P/L cCc/cTc 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.21) 5/23 MODERATE 1 SNV 1 1 PASS rs1190163166 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 177210753 177210753 C T 1 0 0 0 0 1 0 0 0 10728 623 22 3 3 NSD1 5 177210753 Missense_Mutation SNP C C3N-00738_T 36422452 177210753 4327506 67 19992 NSD1 0 . GRCh38 5 177269802 177269802 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.5504A>T p.Lys1835Ile p.K1835I ENST00000439151 16/23 84 75 9 158 157 1 strelka-varscan-mutect NSD1,missense_variant,p.Lys1835Ile,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Lys1566Ile,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Lys1566Ile,ENST00000347982,;NSD1,missense_variant,p.Lys49Ile,ENST00000503056,;NSD1,missense_variant,p.Lys49Ile,ENST00000515735,;NSD1,downstream_gene_variant,,ENST00000504457,;NSD1,downstream_gene_variant,,ENST00000508029,;NSD1,downstream_gene_variant,,ENST00000505395,;PRMT1P1,upstream_gene_variant,,ENST00000604252,;CTD-2301A4.3,downstream_gene_variant,,ENST00000460608,; T ENST00000439151 Transcript missense_variant 5549/12892 5504/8091 1835/2696 K/I aAa/aTa 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 deleterious(0.01) 16/23 Gene3D:2.30.30.160,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00855,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 177269802 177269802 A T 1 0 0 0 0 1 0 0 0 10728 28 1 4 4 NSD1 5 177269802 Missense_Mutation SNP A C3N-00738_T 59049 177269802 4268457 68 19993 NKAPL 0 . GRCh38 6 28260429 28260429 + Missense_Mutation SNP G G A C3N-00738_T C3N-00738_N G G c.1058G>A p.Arg353Gln p.R353Q ENST00000343684 1/1 250 234 16 310 310 0 strelka-varscan-mutect NKAPL,missense_variant,p.Arg353Gln,ENST00000343684,NM_001007531.2; A ENST00000343684 Transcript missense_variant 1110/1639 1058/1209 353/402 R/Q cGa/cAa COSM3861162 1 1 NKAPL HGNC HGNC:21584 protein_coding YES CCDS34353.1 ENSP00000345716 Q5M9Q1 UPI0000072A86 NM_001007531.2 deleterious(0) 1/1 Pfam_domain:PF06047,hmmpanther:PTHR13087,hmmpanther:PTHR13087:SF3 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 28260429 28260429 G A 1 0 0 0 0 1 0 0 0 10475 1058 37 1 1 NKAPL 6 28260429 Missense_Mutation SNP G C3N-00738_T 28260429 142545550 69 19994 PSMB9 0 . GRCh38 6 32858014 32858014 + Silent SNP G G T novel C3N-00738_T C3N-00738_N G G c.270G>T p.= p.L90L ENST00000374859 4/6 167 158 9 174 174 0 strelka-mutect PSMB9,synonymous_variant,p.=,ENST00000395330,;PSMB9,synonymous_variant,p.=,ENST00000374859,NM_002800.4;PSMB9,synonymous_variant,p.=,ENST00000414474,;TAP1,upstream_gene_variant,,ENST00000354258,NM_000593.5,NM_001292022.1;PSMB9,non_coding_transcript_exon_variant,,ENST00000464863,;PSMB9,non_coding_transcript_exon_variant,,ENST00000467593,; T ENST00000374859 Transcript synonymous_variant 339/782 270/660 90/219 L ctG/ctT 1 1 PSMB9 HGNC HGNC:9546 protein_coding YES CCDS4759.1 ENSP00000363993 P28065 UPI00001325CD NM_002800.4 4/6 Gene3D:3.60.20.10,Pfam_domain:PF00227,PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF50,Superfamily_domains:SSF56235 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -11.68621 0.9999459 1 1 1 0 T 2 4 64 32858014 32858014 G T 1 0 0 0 0 0 0 0 1 12835 1335 47 2 2 PSMB9 6 32858014 Silent SNP G C3N-00738_T 4597585 32858014 137947965 70 19995 ADGRF1 0 . GRCh38 6 47005823 47005823 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.2586A>G p.= p.T862T ENST00000371253 13/15 136 119 17 171 171 0 strelka-varscan-mutect ADGRF1,synonymous_variant,p.=,ENST00000371253,NM_153840.3;ADGRF1,synonymous_variant,p.=,ENST00000283297,;ADGRF1,non_coding_transcript_exon_variant,,ENST00000449332,;ADGRF1,non_coding_transcript_exon_variant,,ENST00000419892,;ADGRF1,upstream_gene_variant,,ENST00000477858,; C ENST00000371253 Transcript synonymous_variant 2802/5468 2586/2733 862/910 T acA/acG 1 -1 ADGRF1 HGNC HGNC:18990 protein_coding YES CCDS34471.1 ENSP00000360299 Q5T601 UPI00000474ED NM_153840.3 13/15 Prints_domain:PR01695,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF310 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 47005823 47005823 T C 1 0 0 0 0 0 0 0 1 363 1567 55 5 5 ADGRF1 6 47005823 Silent SNP T C3N-00738_T 14147809 47005823 123800156 71 19996 PKHD1 0 . GRCh38 6 51911898 51911898 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.6391A>T p.Thr2131Ser p.T2131S ENST00000371117 39/67 299 281 18 382 382 0 strelka-varscan-mutect PKHD1,missense_variant,p.Thr2131Ser,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Thr2131Ser,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 6667/16282 6391/12225 2131/4074 T/S Act/Tct 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.03) 39/67 MODERATE 1 SNV 1 1 PASS rs1191383685 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 51911898 51911898 T A 1 0 0 0 0 1 0 0 0 12067 1696 59 4 4 PKHD1 6 51911898 Missense_Mutation SNP T C3N-00738_T 4906075 51911898 118894081 72 19997 FIG4 0 . GRCh38 6 109715169 109715169 + Missense_Mutation SNP A A G novel C3N-00738_T C3N-00738_N A A c.158A>G p.Asp53Gly p.D53G ENST00000230124 2/23 237 224 13 264 264 0 strelka-mutect FIG4,missense_variant,p.Asp53Gly,ENST00000230124,NM_014845.5;FIG4,missense_variant,p.Asp32Gly,ENST00000454215,;FIG4,upstream_gene_variant,,ENST00000368941,; G ENST00000230124 Transcript missense_variant 282/3011 158/2724 53/907 D/G gAt/gGt 1 1 FIG4 HGNC HGNC:16873 protein_coding YES CCDS5078.1 ENSP00000230124 Q92562 UPI000000D9A3 NM_014845.5 deleterious(0.01) 2/23 hmmpanther:PTHR11200:SF9,hmmpanther:PTHR11200 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 109715169 109715169 A G 1 0 0 0 0 1 0 0 0 5753 333 12 5 5 FIG4 6 109715169 Missense_Mutation SNP A C3N-00738_T 57803271 109715169 61090810 73 19998 STX11 0 . GRCh38 6 144186854 144186854 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.227T>A p.Met76Lys p.M76K ENST00000367568 2/2 343 325 18 426 425 1 strelka-varscan STX11,missense_variant,p.Met76Lys,ENST00000367568,NM_003764.3; A ENST00000367568 Transcript missense_variant 410/1926 227/864 76/287 M/K aTg/aAg 1 1 STX11 HGNC HGNC:11429 protein_coding YES CCDS5205.1 ENSP00000356540 O75558 UPI0000001C25 NM_003764.3 deleterious(0.03) 2/2 Gene3D:1.20.58.70,Pfam_domain:PF00804,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF30,SMART_domains:SM00503,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 144186854 144186854 T A 1 0 0 0 0 1 0 0 0 15721 1464 51 4 4 STX11 6 144186854 Missense_Mutation SNP T C3N-00738_T 34471685 144186854 26619125 74 19999 INTS1 0 . GRCh38 7 1495472 1495472 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.1793C>T p.Pro598Leu p.P598L ENST00000404767 13/48 124 113 11 136 136 0 strelka-varscan-mutect INTS1,missense_variant,p.Pro598Leu,ENST00000404767,NM_001080453.2;INTS1,non_coding_transcript_exon_variant,,ENST00000496988,;INTS1,downstream_gene_variant,,ENST00000493531,;INTS1,upstream_gene_variant,,ENST00000468115,; A ENST00000404767 Transcript missense_variant 1879/6959 1793/6573 598/2190 P/L cCc/cTc 1 -1 INTS1 HGNC HGNC:24555 protein_coding YES CCDS47526.1 ENSP00000385722 Q8N201 UPI0000D7211C NM_001080453.2 deleterious(0.01) 13/48 hmmpanther:PTHR21224:SF1,hmmpanther:PTHR21224 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99348 1 1 1 1 0 A 3 1 64 1495472 1495472 G A 1 0 0 0 0 1 0 0 0 7677 1232 43 3 3 INTS1 7 1495472 Missense_Mutation SNP G C3N-00738_T 1495472 157850501 75 20000 THSD7A 0 . GRCh38 7 11543008 11543008 + Missense_Mutation SNP C C A C3N-00738_T C3N-00738_N C C c.1563G>T p.Trp521Cys p.W521C ENST00000423059 5/28 189 172 17 238 237 1 strelka-varscan-mutect THSD7A,missense_variant,p.Trp521Cys,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Trp521Cys,ENST00000617773,;THSD7A,non_coding_transcript_exon_variant,,ENST00000497575,; A ENST00000423059 Transcript missense_variant 1815/10663 1563/4974 521/1657 W/C tgG/tgT COSM364717 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 deleterious(0) 5/28 PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,Gene3D:2.20.100.10,SMART_domains:SM00209 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 11543008 11543008 C A 1 0 0 0 0 1 0 0 0 16313 624 22 2 2 THSD7A 7 11543008 Missense_Mutation SNP C C3N-00738_T 10047536 11543008 147802965 76 20001 AGMO 0 . GRCh38 7 15418607 15418607 + Missense_Mutation SNP G G T C3N-00738_T C3N-00738_N G G c.560C>A p.Ala187Asp p.A187D ENST00000342526 5/13 171 156 15 228 228 0 strelka-varscan-mutect AGMO,missense_variant,p.Ala187Asp,ENST00000342526,NM_001004320.1; T ENST00000342526 Transcript missense_variant 730/2475 560/1338 187/445 A/D gCt/gAt COSM745776 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 deleterious(0.01) 5/13 Pfam_domain:PF04116,hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.86637 0.9999998 1 1 1 0 T 3 4 64 15418607 15418607 G T 1 0 0 0 0 1 0 0 0 463 971 34 2 2 AGMO 7 15418607 Missense_Mutation SNP G C3N-00738_T 3875599 15418607 143927366 77 20002 DFNA5 0 . GRCh38 7 24719069 24719069 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.554G>A p.Gly185Asp p.G185D ENST00000342947 4/10 353 333 20 406 406 0 strelka-varscan-mutect DFNA5,missense_variant,p.Gly185Asp,ENST00000342947,NM_004403.2;DFNA5,missense_variant,p.Gly21Asp,ENST00000419307,NM_001127454.1;DFNA5,missense_variant,p.Gly21Asp,ENST00000409970,;DFNA5,missense_variant,p.Gly185Asp,ENST00000409775,NM_001127453.1;DFNA5,missense_variant,p.Gly10Asp,ENST00000446822,;DFNA5,downstream_gene_variant,,ENST00000414428,;DFNA5,upstream_gene_variant,,ENST00000415480,;DFNA5,non_coding_transcript_exon_variant,,ENST00000559637,;DFNA5,missense_variant,p.Gly108Asp,ENST00000411476,;DFNA5,non_coding_transcript_exon_variant,,ENST00000493723,; T ENST00000342947 Transcript missense_variant 980/2590 554/1491 185/496 G/D gGc/gAc 1 -1 DFNA5 HGNC HGNC:2810 protein_coding YES CCDS5389.1 ENSP00000339587 O60443 A0A024RA58 UPI00001291FC NM_004403.2 deleterious(0.01) 4/10 Pfam_domain:PF04598,hmmpanther:PTHR15207,hmmpanther:PTHR15207:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 24719069 24719069 C T 1 0 0 0 0 1 0 0 0 4262 739 26 3 3 DFNA5 7 24719069 Missense_Mutation SNP C C3N-00738_T 9300462 24719069 134626904 78 20003 NPSR1 0 . GRCh38 7 34827495 34827495 + Silent SNP C C A novel C3N-00738_T C3N-00738_N C C c.573C>A p.= p.S191S ENST00000381539 5/10 490 455 35 480 479 1 strelka-varscan-mutect NPSR1,synonymous_variant,p.=,ENST00000360581,NM_207172.1;NPSR1,synonymous_variant,p.=,ENST00000359791,NM_207173.1;NPSR1,synonymous_variant,p.=,ENST00000531252,NM_001300933.1;NPSR1,synonymous_variant,p.=,ENST00000381542,NM_001300934.1;NPSR1,synonymous_variant,p.=,ENST00000381539,NM_001300935.1;NPSR1-AS1,intron_variant,,ENST00000436945,;NPSR1-AS1,intron_variant,,ENST00000431669,;NPSR1,missense_variant,p.Gln157Lys,ENST00000381544,;NPSR1,3_prime_UTR_variant,,ENST00000396095,; A ENST00000381539 Transcript synonymous_variant 577/1233 573/1173 191/390 S tcC/tcA 1 1 NPSR1 HGNC HGNC:23631 protein_coding YES CCDS75579.1 ENSP00000370950 Q6W5P4 UPI00004F9C01 NM_001300935.1 5/10 PROSITE_profiles:PS50262,hmmpanther:PTHR24244,hmmpanther:PTHR24244:SF2,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 34827495 34827495 C A 1 0 0 0 0 0 0 0 1 10656 581 21 2 2 NPSR1 7 34827495 Silent SNP C C3N-00738_T 10108426 34827495 124518478 79 20004 ZNF804B 0 . GRCh38 7 89336871 89336871 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.3889G>T p.Gly1297Cys p.G1297C ENST00000333190 4/4 253 226 27 349 349 0 strelka-varscan-mutect ZNF804B,missense_variant,p.Gly1297Cys,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Gly1214Cys,ENST00000611114,; T ENST00000333190 Transcript missense_variant 4498/4659 3889/4050 1297/1349 G/C Ggt/Tgt 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 deleterious(0.03) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS rs960852950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 89336871 89336871 G T 1 0 0 0 0 1 0 0 0 18756 1348 47 2 2 ZNF804B 7 89336871 Missense_Mutation SNP G C3N-00738_T 54509376 89336871 70009102 80 20005 OR2A14 0 . GRCh38 7 144129262 144129262 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.150G>A p.= p.L50L ENST00000408899 1/1 232 203 29 256 256 0 strelka-varscan-mutect OR2A14,synonymous_variant,p.=,ENST00000408899,NM_001001659.1;OR2A14,intron_variant,,ENST00000627593,; A ENST00000408899 Transcript synonymous_variant 205/1012 150/933 50/310 L ctG/ctA 1 1 OR2A14 HGNC HGNC:15084 protein_coding YES CCDS43672.1 ENSP00000386137 Q96R47 A0A126GVB0 UPI0000061E6E NM_001001659.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF27,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 144129262 144129262 G A 1 0 0 0 0 0 0 0 1 11053 1335 47 3 3 OR2A14 7 144129262 Silent SNP G C3N-00738_T 54792391 144129262 15216711 81 20006 CNTNAP2 0 . GRCh38 7 147132452 147132452 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.1291G>T p.Val431Leu p.V431L ENST00000361727 8/24 340 301 39 473 473 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Val431Leu,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; T ENST00000361727 Transcript missense_variant 1809/9896 1291/3996 431/1331 V/L Gtg/Ttg 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(1) 8/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1300358055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 147132452 147132452 G T 1 0 0 0 0 1 0 0 0 3428 1029 36 2 2 CNTNAP2 7 147132452 Missense_Mutation SNP G C3N-00738_T 3003190 147132452 12213521 82 20007 CSMD1 0 . GRCh38 8 3343382 3343382 + Silent SNP C C G novel C3N-00738_T C3N-00738_N C C c.3546G>C p.= p.L1182L ENST00000520002 24/71 191 181 10 257 257 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; G ENST00000520002 Transcript synonymous_variant 4102/11740 3546/10698 1182/3565 L ctG/ctC 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 24/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 5 1 PASS rs1341958896 . 0 208 0 2 0 0 0 0 -12.60052 0.9999993 1 1 1 0 G 2 3 64 3343382 3343382 C G 1 0 0 0 0 0 0 0 1 3745 813 29 4 4 CSMD1 8 3343382 Silent SNP C C3N-00738_T 3343382 141795254 83 20008 DLC1 0 . GRCh38 8 13499151 13499151 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.921A>G p.= p.P307P ENST00000276297 2/18 279 249 30 289 289 0 strelka-varscan-mutect DLC1,synonymous_variant,p.=,ENST00000276297,NM_182643.2;DLC1,synonymous_variant,p.=,ENST00000511869,NM_024767.3;DLC1,synonymous_variant,p.=,ENST00000316609,;DLC1,synonymous_variant,p.=,ENST00000517868,;DLC1,downstream_gene_variant,,ENST00000631382,;DLC1,downstream_gene_variant,,ENST00000517333,; C ENST00000276297 Transcript synonymous_variant 1331/7447 921/4587 307/1528 P ccA/ccG 1 -1 DLC1 HGNC HGNC:2897 protein_coding YES CCDS5989.1 ENSP00000276297 Q96QB1 UPI0000210275 NM_182643.2 2/18 hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 13499151 13499151 T C 1 0 0 0 0 0 0 0 1 4356 1683 59 5 5 DLC1 8 13499151 Silent SNP T C3N-00738_T 10155769 13499151 131639485 84 20009 PLAG1 0 . GRCh38 8 56166373 56166374 + Frame_Shift_Del DEL GG GG - novel C3N-00738_T C3N-00738_N GG GG c.1372_1373delCC p.Pro458ThrfsTer74 p.P458Tfs*74 ENST00000316981 5/5 109 103 6 145 144 1 varindel-pindel PLAG1,frameshift_variant,p.Pro458ThrfsTer74,ENST00000316981,NM_002655.2;PLAG1,frameshift_variant,p.Pro458ThrfsTer?,ENST00000429357,NM_001114634.1;PLAG1,frameshift_variant,p.Pro376ThrfsTer74,ENST00000423799,NM_001114635.1;PLAG1,non_coding_transcript_exon_variant,,ENST00000522009,; - ENST00000316981 Transcript frameshift_variant 1852-1853/7322 1372-1373/1503 458/500 P/X CCa/a 1 -1 PLAG1 HGNC HGNC:9045 protein_coding YES CCDS6165.1 ENSP00000325546 Q6DJT9 A0A024R7Z0 UPI000013FF2F NM_002655.2 5/5 Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 151 0 0 0 0 0 59 -5.386197 0 0 1 0 0 - 7 5 64 56166373 56166373 GG - 1 0 1 0 1 0 0 0 0 12112 1348 47 0 0 PLAG1 8 56166373 Frame_Shift_Del DEL GG C3N-00738_T 42667222 56166373 88972263 85 20010 NSMAF 0 . GRCh38 8 58597902 58597902 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.1679T>A p.Val560Glu p.V560E ENST00000427130 20/31 159 142 17 166 165 1 strelka-varscan-mutect NSMAF,missense_variant,p.Val529Glu,ENST00000038176,NM_003580.3;NSMAF,missense_variant,p.Val560Glu,ENST00000427130,NM_001144772.1;NSMAF,splice_region_variant,,ENST00000523982,;NSMAF,downstream_gene_variant,,ENST00000519858,;NSMAF,upstream_gene_variant,,ENST00000523177,;NSMAF,splice_region_variant,,ENST00000523106,;NSMAF,splice_region_variant,,ENST00000519227,;NSMAF,upstream_gene_variant,,ENST00000519166,;NSMAF,upstream_gene_variant,,ENST00000524148,;NSMAF,upstream_gene_variant,,ENST00000519174,; T ENST00000427130 Transcript missense_variant,splice_region_variant 1867/3371 1679/2847 560/948 V/E gTa/gAa 1 -1 NSMAF HGNC HGNC:8017 protein_coding YES CCDS47864.1 ENSP00000411012 Q92636 UPI000192950C NM_001144772.1 deleterious(0) 20/31 PROSITE_profiles:PS50197,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF53,Gene3D:1t77A02,Pfam_domain:PF02138,SMART_domains:SM01026,Superfamily_domains:SSF81837 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -19.99997 0.9999999 1 1 1 0 T 3 4 64 58597902 58597902 A T 1 0 0 0 0 1 0 0 0 10734 405 14 4 4 NSMAF 8 58597902 Missense_Mutation SNP A C3N-00738_T 2431529 58597902 86540734 86 20011 MMP16 0 . GRCh38 8 88118775 88118775 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.796C>A p.Pro266Thr p.P266T ENST00000286614 5/10 221 198 23 247 247 0 strelka-varscan-mutect MMP16,missense_variant,p.Pro266Thr,ENST00000286614,NM_005941.4;MMP16,non_coding_transcript_exon_variant,,ENST00000544227,; T ENST00000286614 Transcript missense_variant 1078/11558 796/1824 266/607 P/T Cca/Aca 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 deleterious(0) 5/10 hmmpanther:PTHR10201:SF26,hmmpanther:PTHR10201,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00413,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 88118775 88118775 G T 1 0 0 0 0 1 0 0 0 9618 1174 41 2 2 MMP16 8 88118775 Missense_Mutation SNP G C3N-00738_T 29520873 88118775 57019861 87 20012 CSMD3 0 . GRCh38 8 112247070 112247070 + Missense_Mutation SNP C C A rs750171856 C3N-00738_T C3N-00738_N C C c.10172G>T p.Arg3391Leu p.R3391L ENST00000297405 64/71 279 256 23 347 347 0 strelka-varscan-mutect CSMD3,missense_variant,p.Arg3391Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Arg3351Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Arg3222Leu,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Arg2661Leu,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000534172,; A ENST00000297405 Transcript missense_variant 10417/13212 10172/11124 3391/3707 R/L cGc/cTc rs750171856,COSM1150875,COSM1330369,COSM1330370,COSM748709 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.02) 64/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs750171856 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 112247070 112247070 C A 1 0 0 0 0 1 0 0 0 3747 768 27 1 1 CSMD3 8 112247070 Missense_Mutation SNP C C3N-00738_T 24128295 112247070 32891566 88 20013 GLI4 0 . GRCh38 8 143276603 143276603 + Silent SNP C C T novel C3N-00738_T C3N-00738_N C C c.930C>T p.= p.L310L ENST00000340042 4/4 209 198 11 229 229 0 strelka-varscan-mutect GLI4,synonymous_variant,p.=,ENST00000340042,NM_138465.3;GLI4,synonymous_variant,p.=,ENST00000523522,;RP13-582O9.6,downstream_gene_variant,,ENST00000522452,;GLI4,downstream_gene_variant,,ENST00000521682,;GLI4,downstream_gene_variant,,ENST00000344692,;GLI4,downstream_gene_variant,,ENST00000517468,;GLI4,downstream_gene_variant,,ENST00000517530,;GLI4,downstream_gene_variant,,ENST00000520021,;MINCR,downstream_gene_variant,,ENST00000523031,;MINCR,downstream_gene_variant,,ENST00000517411,;MINCR,downstream_gene_variant,,ENST00000524335,;MINCR,downstream_gene_variant,,ENST00000521207,;MINCR,downstream_gene_variant,,ENST00000518073,;MINCR,downstream_gene_variant,,ENST00000519852,;GLI4,non_coding_transcript_exon_variant,,ENST00000523812,;GLI4,downstream_gene_variant,,ENST00000519876,;GLI4,downstream_gene_variant,,ENST00000522479,;GLI4,downstream_gene_variant,,ENST00000522033,; T ENST00000340042 Transcript synonymous_variant 1015/1341 930/1131 310/376 L ctC/ctT 1 1 GLI4 HGNC HGNC:4320 protein_coding YES CCDS6398.1 ENSP00000345024 P10075 UPI0000070432 NM_138465.3 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF122,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 143276603 143276603 C T 1 0 0 0 0 0 0 0 1 6318 813 29 3 3 GLI4 8 143276603 Silent SNP C C3N-00738_T 31029533 143276603 1862033 89 20014 C9orf129 0 . GRCh38 9 93335621 93335621 + Missense_Mutation SNP C C A rs756990522 C3N-00738_T C3N-00738_N C C c.118G>T p.Gly40Cys p.G40C ENST00000375419 3/5 88 80 8 146 146 0 varscan-mutect C9orf129,missense_variant,p.Gly40Cys,ENST00000375419,NM_001098808.1; A ENST00000375419 Transcript missense_variant 482/1154 118/591 40/196 G/C Ggt/Tgt rs756990522 1 -1 C9orf129 HGNC HGNC:31116 protein_coding YES CCDS43850.1 ENSP00000364568 Q5T035 UPI000047014B NM_001098808.1 deleterious_low_confidence(0) 3/5 hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs756990522 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 93335621 93335621 C A 1 0 0 0 0 1 0 0 0 2172 623 22 2 2 C9orf129 9 93335621 Missense_Mutation SNP C C3N-00738_T 93335621 45059096 90 20015 PTCHD3 0 . GRCh38 10 27413415 27413415 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.836A>G p.Asn279Ser p.N279S ENST00000438700 1/4 315 296 19 436 436 0 strelka-varscan-mutect PTCHD3,missense_variant,p.Asn279Ser,ENST00000438700,NM_001034842.3;PTCHD3,missense_variant,p.Asn279Ser,ENST00000622555,; C ENST00000438700 Transcript missense_variant 954/2529 836/2304 279/767 N/S aAc/aGc 1 -1 PTCHD3 HGNC HGNC:24776 protein_coding YES CCDS31173.1 ENSP00000417658 Q3KNS1 UPI000004E892 NM_001034842.3 tolerated(0.2) 1/4 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF60 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 27413415 27413415 T C 1 0 0 0 0 1 0 0 0 12886 1725 60 5 5 PTCHD3 10 27413415 Missense_Mutation SNP T C3N-00738_T 27413415 106384007 91 20016 SLIT1 0 . GRCh38 10 97021331 97021331 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.2665G>A p.Gly889Ser p.G889S ENST00000266058 26/37 199 188 11 205 205 0 strelka-varscan-mutect SLIT1,missense_variant,p.Gly889Ser,ENST00000266058,NM_003061.2;SLIT1,missense_variant,p.Gly889Ser,ENST00000371070,; T ENST00000266058 Transcript missense_variant 2911/7925 2665/4605 889/1534 G/S Ggc/Agc 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 deleterious(0) 26/37 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,SMART_domains:SM00082 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 97021331 97021331 C T 1 0 0 0 0 1 0 0 0 15030 623 22 3 3 SLIT1 10 97021331 Missense_Mutation SNP C C3N-00738_T 69607916 97021331 36776091 92 20017 NLRP6 0 . GRCh38 11 281780 281780 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.2046G>A p.= p.A682A ENST00000312165 4/8 81 70 11 99 99 0 strelka-varscan-mutect NLRP6,synonymous_variant,p.=,ENST00000534750,NM_001276700.1;NLRP6,synonymous_variant,p.=,ENST00000312165,NM_138329.2;NLRP6,downstream_gene_variant,,ENST00000527946,; A ENST00000312165 Transcript synonymous_variant 2046/2679 2046/2679 682/892 A gcG/gcA 1 1 NLRP6 HGNC HGNC:22944 protein_coding YES CCDS7693.1 ENSP00000309767 P59044 UPI00001AEFE1 NM_138329.2 4/8 Gene3D:3.80.10.10 LOW 1 SNV 1 1 PASS rs1226772781 . 0 206 4 0 0 0 0 0 -19.99994 1 1 1 1 0 A 2 1 64 281780 281780 G A 1 0 0 0 0 0 0 0 1 10519 1074 38 1 1 NLRP6 11 281780 Silent SNP G C3N-00738_T 281780 134804842 93 20018 B4GALNT4 0 . GRCh38 11 379463 379463 + Missense_Mutation SNP C C G novel C3N-00738_T C3N-00738_N C C c.2250C>G p.Asp750Glu p.D750E ENST00000329962 15/20 115 104 11 123 122 1 strelka-varscan-mutect B4GALNT4,missense_variant,p.Asp750Glu,ENST00000329962,NM_178537.4;B4GALNT4,upstream_gene_variant,,ENST00000534778,;B4GALNT4,upstream_gene_variant,,ENST00000526584,;B4GALNT4,downstream_gene_variant,,ENST00000524443,; G ENST00000329962 Transcript missense_variant 2250/3444 2250/3120 750/1039 D/E gaC/gaG 1 1 B4GALNT4 HGNC HGNC:26315 protein_coding YES CCDS7694.1 ENSP00000328277 Q76KP1 UPI00002326B6 NM_178537.4 deleterious(0) 15/20 Pfam_domain:PF05679,hmmpanther:PTHR12369,hmmpanther:PTHR12369:SF9 MODERATE 1 SNV 1 1 PASS rs946166688 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 379463 379463 C G 1 0 0 0 0 1 0 0 0 1425 564 20 4 4 B4GALNT4 11 379463 Missense_Mutation SNP C C3N-00738_T 97683 379463 134707159 94 20019 OR52D1 0 . GRCh38 11 5489243 5489243 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.537C>A p.His179Gln p.H179Q ENST00000322641 1/1 228 208 20 308 308 0 strelka-varscan-mutect OR52D1,missense_variant,p.His179Gln,ENST00000322641,NM_001005163.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000322641 Transcript missense_variant 559/1065 537/957 179/318 H/Q caC/caA 1 1 OR52D1 HGNC HGNC:15212 protein_coding YES CCDS31384.1 ENSP00000326232 Q9H346 A0A126GVG9 UPI0000041DD3 NM_001005163.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF75,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 5489243 5489243 C A 1 0 0 0 0 1 0 0 0 11186 477 17 2 2 OR52D1 11 5489243 Missense_Mutation SNP C C3N-00738_T 5109780 5489243 129597379 95 20020 OR56B4 0 . GRCh38 11 6108123 6108123 + Missense_Mutation SNP C C G novel C3N-00738_T C3N-00738_N C C c.345C>G p.Cys115Trp p.C115W ENST00000316529 1/1 285 256 29 372 372 0 strelka-varscan-mutect OR56B4,missense_variant,p.Cys115Trp,ENST00000316529,NM_001005181.2;RP11-290F24.3,downstream_gene_variant,,ENST00000529961,; G ENST00000316529 Transcript missense_variant 440/1152 345/960 115/319 C/W tgC/tgG 1 1 OR56B4 HGNC HGNC:15248 protein_coding YES CCDS31406.1 ENSP00000321196 Q8NH76 UPI000004B214 NM_001005181.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF142,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs1487684441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 6108123 6108123 C G 1 0 0 0 0 1 0 0 0 11210 718 25 4 4 OR56B4 11 6108123 Missense_Mutation SNP C C3N-00738_T 618880 6108123 128978499 96 20021 NUCB2 0 . GRCh38 11 17311210 17311210 + Silent SNP A A G novel C3N-00738_T C3N-00738_N A A c.687A>G p.= p.L229L ENST00000529010 8/14 125 110 15 208 208 0 strelka-mutect NUCB2,synonymous_variant,p.=,ENST00000529010,NM_005013.2;NUCB2,synonymous_variant,p.=,ENST00000323688,;NUCB2,synonymous_variant,p.=,ENST00000622082,;NUCB2,synonymous_variant,p.=,ENST00000458064,;NUCB2,synonymous_variant,p.=,ENST00000527580,;NUCB2,downstream_gene_variant,,ENST00000530527,;NUCB2,downstream_gene_variant,,ENST00000529313,;NUCB2,upstream_gene_variant,,ENST00000527735,;NUCB2,synonymous_variant,p.=,ENST00000533773,;NUCB2,upstream_gene_variant,,ENST00000531242,; G ENST00000529010 Transcript synonymous_variant 906/2274 687/1263 229/420 L ctA/ctG 1 1 NUCB2 HGNC HGNC:8044 protein_coding YES CCDS41623.1 ENSP00000436455 V9HW75 UPI000012FE2C NM_005013.2 8/14 Gene3D:1.10.238.10,hmmpanther:PTHR19237,hmmpanther:PTHR19237:SF22 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 17311210 17311210 A G 1 0 0 0 0 0 0 0 1 10785 349 13 5 5 NUCB2 11 17311210 Silent SNP A C3N-00738_T 11203087 17311210 117775412 97 20022 MPEG1 0 . GRCh38 11 59211292 59211292 + Missense_Mutation SNP G G A rs199736754 C3N-00738_T C3N-00738_N G G c.1574C>T p.Ala525Val p.A525V ENST00000361050 1/1 199 182 17 249 249 0 strelka-varscan-mutect MPEG1,missense_variant,p.Ala525Val,ENST00000361050,NM_001039396.1;DTX4,downstream_gene_variant,,ENST00000227451,NM_015177.1;RN7SL42P,downstream_gene_variant,,ENST00000579786,; A ENST00000361050 Transcript missense_variant 1660/4442 1574/2151 525/716 A/V gCg/gTg rs199736754,COSM928993 1 -1 MPEG1 HGNC HGNC:29619 protein_coding YES CCDS41650.1 ENSP00000354335 Q2M385 UPI0000049D9F NM_001039396.1 deleterious(0.02) 1/1 hmmpanther:PTHR31463,hmmpanther:PTHR31463:SF4 0,1 MODERATE SNV 0,1 1 PASS rs199736754 . 0 205 0 0 4 0 0 0 -6.120969 0.7216481 1 1 1 0 A 3 1 64 59211292 59211292 G A 1 0 0 0 0 1 0 0 0 9688 1087 38 1 1 MPEG1 11 59211292 Missense_Mutation SNP G C3N-00738_T 41900082 59211292 75875330 98 20023 ATL3 0 . GRCh38 11 63644228 63644228 + Missense_Mutation SNP G G C rs554468070 C3N-00738_T C3N-00738_N G G c.652C>G p.Pro218Ala p.P218A ENST00000398868 7/13 278 253 25 311 311 0 strelka-varscan-mutect ATL3,missense_variant,p.Pro218Ala,ENST00000398868,NM_015459.4;ATL3,missense_variant,p.Pro200Ala,ENST00000538786,NM_001290048.1;RP11-697H9.2,intron_variant,,ENST00000540307,; C ENST00000398868 Transcript missense_variant 929/7135 652/1626 218/541 P/A Cct/Gct rs554468070 1 -1 ATL3 HGNC HGNC:24526 protein_coding YES CCDS41663.1 ENSP00000381844 Q6DD88 UPI0000071A21 NM_015459.4 tolerated(0.07) 7/13 PROSITE_profiles:PS51715,hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF32,Pfam_domain:PF02263,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs554468070 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 63644228 63644228 G C 1 0 0 0 0 1 0 0 0 1260 1232 43 4 4 ATL3 11 63644228 Missense_Mutation SNP G C3N-00738_T 4432936 63644228 71442394 99 20024 ATG16L2 0 . GRCh38 11 72828481 72828481 + Frame_Shift_Del DEL G G - rs775912740 C3N-00738_T C3N-00738_N G G c.1595delG p.Arg532LeufsTer76 p.R532Lfs*76 ENST00000321297 15/18 172 154 18 184 184 0 sindel-varindel-pindel ATG16L2,frameshift_variant,p.Arg532LeufsTer76,ENST00000321297,NM_033388.1;ATG16L2,frameshift_variant,p.Cys148ValfsTer39,ENST00000534905,;ATG16L2,frameshift_variant,p.Arg363LeufsTer76,ENST00000541367,;ATG16L2,frameshift_variant,p.Arg363LeufsTer42,ENST00000538973,;ATG16L2,frameshift_variant,p.Arg310LeufsTer76,ENST00000540222,;ATG16L2,downstream_gene_variant,,ENST00000535830,;ATG16L2,downstream_gene_variant,,ENST00000541554,;ATG16L2,3_prime_UTR_variant,,ENST00000544490,;ATG16L2,3_prime_UTR_variant,,ENST00000435507,NM_001318766.1;ATG16L2,non_coding_transcript_exon_variant,,ENST00000536995,;ATG16L2,non_coding_transcript_exon_variant,,ENST00000439504,;ATG16L2,downstream_gene_variant,,ENST00000542908,;ATG16L2,downstream_gene_variant,,ENST00000537212,;ATG16L2,downstream_gene_variant,,ENST00000537837,;ATG16L2,downstream_gene_variant,,ENST00000542481,;ATG16L2,downstream_gene_variant,,ENST00000541999,; - ENST00000321297 Transcript frameshift_variant 1733/2243 1595/1860 532/619 R/X cGt/ct rs775912740,COSM4757323 1 1 ATG16L2 HGNC HGNC:25464 protein_coding YES CCDS31634.1 ENSP00000326340 Q8NAA4 UPI0000140B06 NM_033388.1 15/18 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR19878,hmmpanther:PTHR19878:SF7,Superfamily_domains:SSF50978 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 64 72828481 72828481 G - 1 0 1 0 1 0 0 0 0 1244 1145 40 0 0 ATG16L2 11 72828481 Frame_Shift_Del DEL G C3N-00738_T 9184253 72828481 62258141 100 20025 MYO7A 0 . GRCh38 11 77175440 77175440 + Silent SNP A A T novel C3N-00738_T C3N-00738_N A A c.2163A>T p.= p.I721I ENST00000409709 18/49 232 220 12 194 194 0 strelka-mutect MYO7A,synonymous_variant,p.=,ENST00000409709,NM_000260.3;MYO7A,synonymous_variant,p.=,ENST00000458637,NM_001127180.1;MYO7A,synonymous_variant,p.=,ENST00000409619,;MYO7A,synonymous_variant,p.=,ENST00000409893,NM_001127179.2;MYO7A,synonymous_variant,p.=,ENST00000620575,;MYO7A,upstream_gene_variant,,ENST00000458169,;MYO7A,upstream_gene_variant,,ENST00000481328,; T ENST00000409709 Transcript synonymous_variant 2435/7462 2163/6648 721/2215 I atA/atT 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 18/49 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF369,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 77175440 77175440 A T 1 0 0 0 0 0 0 0 1 10083 410 15 4 4 MYO7A 11 77175440 Silent SNP A C3N-00738_T 4346959 77175440 57911182 101 20026 RDX 0 . GRCh38 11 110232005 110232005 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.1616G>T p.Arg539Ile p.R539I ENST00000405097 14/16 393 353 40 469 469 0 strelka-varscan-mutect RDX,splice_acceptor_variant,,ENST00000530301,NM_001260496.1;RDX,missense_variant,p.Arg539Ile,ENST00000343115,NM_002906.3;RDX,missense_variant,p.Arg403Ile,ENST00000544551,NM_001260494.1;RDX,missense_variant,p.Arg539Ile,ENST00000405097,NM_001260492.1;RDX,missense_variant,p.Arg539Ile,ENST00000528498,NM_001260493.1;RDX,missense_variant,p.Arg192Ile,ENST00000528900,NM_001260495.1;RDX,non_coding_transcript_exon_variant,,ENST00000530085,;RDX,missense_variant,p.Arg539Ile,ENST00000530749,;RDX,3_prime_UTR_variant,,ENST00000530131,;RDX,non_coding_transcript_exon_variant,,ENST00000527537,;RDX,non_coding_transcript_exon_variant,,ENST00000532461,;RDX,non_coding_transcript_exon_variant,,ENST00000533961,; A ENST00000405097 Transcript missense_variant 1926/2761 1616/1815 539/604 R/I aGa/aTa 1 -1 RDX HGNC HGNC:9944 protein_coding YES CCDS58174.1 ENSP00000384136 P35241 UPI0000EE3914 NM_001260492.1 deleterious(0.01) 14/16 Superfamily_domains:0036951,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00769,PIRSF_domain:PIRSF002305,Prints_domain:PR00661,hmmpanther:PTHR23281,hmmpanther:PTHR23281:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 110232005 110232005 C A 1 0 0 0 0 1 0 0 0 13367 927 32 2 2 RDX 11 110232005 Missense_Mutation SNP C C3N-00738_T 33056565 110232005 24854617 102 20027 CACNA1C 0 . GRCh38 12 2677731 2677731 + Splice_Site SNP A A T novel C3N-00738_T C3N-00738_N A A c.5101-2A>T p.X1701_splice ENST00000347598 115 106 9 137 137 0 strelka-varscan-mutect CACNA1C,splice_acceptor_variant,,ENST00000399655,NM_000719.6;CACNA1C,splice_acceptor_variant,,ENST00000399634,NM_001167625.1;CACNA1C,splice_acceptor_variant,,ENST00000406454,;CACNA1C,splice_acceptor_variant,,ENST00000399617,NM_001167624.2;CACNA1C,splice_acceptor_variant,,ENST00000399603,NM_001167623.1;CACNA1C,splice_acceptor_variant,,ENST00000335762,;CACNA1C,splice_acceptor_variant,,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,splice_acceptor_variant,,ENST00000344100,NM_001129829.1;CACNA1C,splice_acceptor_variant,,ENST00000327702,NM_001129830.2;CACNA1C,splice_acceptor_variant,,ENST00000399638,NM_001129831.1;CACNA1C,splice_acceptor_variant,,ENST00000399606,NM_001129832.1;CACNA1C,splice_acceptor_variant,,ENST00000399621,NM_001129834.1;CACNA1C,splice_acceptor_variant,,ENST00000399637,NM_001129835.1;CACNA1C,splice_acceptor_variant,,ENST00000402845,NM_001129833.1;CACNA1C,splice_acceptor_variant,,ENST00000399629,NM_001129836.1;CACNA1C,splice_acceptor_variant,,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,splice_acceptor_variant,,ENST00000399595,NM_001129837.1;CACNA1C,splice_acceptor_variant,,ENST00000399649,NM_001129839.1;CACNA1C,splice_acceptor_variant,,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,splice_acceptor_variant,,ENST00000399601,NM_001129843.1;CACNA1C,splice_acceptor_variant,,ENST00000399641,NM_001129840.1;CACNA1C,splice_acceptor_variant,,ENST00000399644,NM_001129841.1;CACNA1C,splice_acceptor_variant,,ENST00000616390,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000501371,;CACNA1C,splice_acceptor_variant,,ENST00000465934,; T ENST00000347598 Transcript splice_acceptor_variant -/6655 5101/6561 1701/2186 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 42/48 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.14539 1 1 1 1 0 T 5 4 64 2677731 2677731 A T 1 0 0 0 0 0 0 1 0 2228 202 7 4 4 CACNA1C 12 2677731 Splice_Site SNP A C3N-00738_T 2677731 130597578 103 20028 FGF23 0 . GRCh38 12 4379542 4379542 + Missense_Mutation SNP C C G novel C3N-00738_T C3N-00738_N C C c.41G>C p.Cys14Ser p.C14S ENST00000237837 1/3 264 241 23 380 380 0 strelka-varscan-mutect FGF23,missense_variant,p.Cys14Ser,ENST00000237837,NM_020638.2; G ENST00000237837 Transcript missense_variant 187/3018 41/756 14/251 C/S tGc/tCc 1 -1 FGF23 HGNC HGNC:3680 protein_coding YES CCDS8526.1 ENSP00000237837 Q9GZV9 UPI000003ED58 NM_020638.2 tolerated(0.14) 1/3 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF69,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1366675674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 4379542 4379542 C G 1 0 0 0 0 1 0 0 0 5716 710 25 4 4 FGF23 12 4379542 Missense_Mutation SNP C C3N-00738_T 1701811 4379542 128895767 104 20029 SCN8A 0 . GRCh38 12 51762643 51762643 + Silent SNP G G T C3N-00738_T C3N-00738_N G G c.2511G>T p.= p.V837V ENST00000354534 15/27 202 184 18 276 276 0 strelka-varscan-mutect SCN8A,synonymous_variant,p.=,ENST00000354534,NM_014191.3;SCN8A,synonymous_variant,p.=,ENST00000545061,NM_001177984.2;SCN8A,synonymous_variant,p.=,ENST00000599343,;SCN8A,synonymous_variant,p.=,ENST00000627620,;SCN8A,synonymous_variant,p.=,ENST00000355133,;SCN8A,synonymous_variant,p.=,ENST00000636945,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,non_coding_transcript_exon_variant,,ENST00000550891,; T ENST00000354534 Transcript synonymous_variant 2689/11556 2511/5943 837/1980 V gtG/gtT COSM5682753,COSM5682754 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 15/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037,Gene3D:1.20.120.350,Pfam_domain:PF00520,Superfamily_domains:SSF81324 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 51762643 51762643 G T 1 0 0 0 0 0 0 0 1 14193 1335 47 2 2 SCN8A 12 51762643 Silent SNP G C3N-00738_T 47383101 51762643 81512666 105 20030 HOXC12 0 . GRCh38 12 53955132 53955132 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.203A>T p.Tyr68Phe p.Y68F ENST00000243103 1/2 365 340 25 373 373 0 strelka-varscan-mutect HOXC12,missense_variant,p.Tyr68Phe,ENST00000243103,NM_173860.1; T ENST00000243103 Transcript missense_variant 299/3335 203/849 68/282 Y/F tAc/tTc 1 1 HOXC12 HGNC HGNC:5124 protein_coding YES CCDS8866.1 ENSP00000243103 P31275 UPI000012CF7E NM_173860.1 tolerated(0.16) 1/2 hmmpanther:PTHR24326:SF164,hmmpanther:PTHR24326 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 53955132 53955132 A T 1 0 0 0 0 1 0 0 0 7205 391 14 4 4 HOXC12 12 53955132 Missense_Mutation SNP A C3N-00738_T 2192489 53955132 79320177 106 20031 IRAK3 0 . GRCh38 12 66245211 66245211 + Silent SNP G G A novel C3N-00738_T C3N-00738_N G G c.1263G>A p.= p.L421L ENST00000261233 11/12 267 244 23 352 352 0 strelka-varscan-mutect IRAK3,synonymous_variant,p.=,ENST00000261233,NM_007199.2;IRAK3,synonymous_variant,p.=,ENST00000457197,NM_001142523.1; A ENST00000261233 Transcript synonymous_variant 1684/8663 1263/1791 421/596 L ttG/ttA 1 1 IRAK3 HGNC HGNC:17020 protein_coding YES CCDS8975.1 ENSP00000261233 Q9Y616 UPI000013D14A NM_007199.2 11/12 PROSITE_profiles:PS50011,hmmpanther:PTHR24419:SF7,hmmpanther:PTHR24419,Pfam_domain:PF00069,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 66245211 66245211 G A 1 0 0 0 0 0 0 0 1 7730 1339 47 3 3 IRAK3 12 66245211 Silent SNP G C3N-00738_T 12290079 66245211 67030098 107 20032 CEP290 0 . GRCh38 12 88131194 88131194 + Nonsense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.466G>T p.Glu156Ter p.E156* ENST00000552810 7/54 104 98 6 130 130 0 strelka-varscan-mutect CEP290,stop_gained,p.Glu156Ter,ENST00000552810,NM_025114.3;CEP290,stop_gained,p.Glu156Ter,ENST00000309041,;CEP290,stop_gained,p.Glu156Ter,ENST00000397838,;CEP290,intron_variant,,ENST00000550962,;CEP290,upstream_gene_variant,,ENST00000604024,;CEP290,downstream_gene_variant,,ENST00000552770,;CEP290,stop_gained,p.Glu122Ter,ENST00000547926,; A ENST00000552810 Transcript stop_gained 810/7948 466/7440 156/2479 E/* Gaa/Taa 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 7/54 Low_complexity_(Seg):seg,hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879,Coiled-coils_(Ncoils):Coil HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -9.435793 0.9999854 1 1 1 0 A 4 1 64 88131194 88131194 C A 1 0 0 0 0 0 1 0 0 2969 922 32 2 2 CEP290 12 88131194 Nonsense_Mutation SNP C C3N-00738_T 21885983 88131194 45144115 108 20033 NDUFA12 0 . GRCh38 12 94971592 94971592 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.286G>T p.Asp96Tyr p.D96Y ENST00000327772 4/4 384 340 44 530 528 2 strelka-varscan-mutect NDUFA12,missense_variant,p.Asp96Tyr,ENST00000327772,NM_018838.4;NDUFA12,3_prime_UTR_variant,,ENST00000547986,NM_001258338.1;NDUFA12,intron_variant,,ENST00000547157,;NDUFA12,non_coding_transcript_exon_variant,,ENST00000550187,;NDUFA12,3_prime_UTR_variant,,ENST00000546788,;NDUFA12,3_prime_UTR_variant,,ENST00000551991,;NDUFA12,non_coding_transcript_exon_variant,,ENST00000538372,;NDUFA12,intron_variant,,ENST00000552205,; A ENST00000327772 Transcript missense_variant 376/635 286/438 96/145 D/Y Gat/Tat 1 -1 NDUFA12 HGNC HGNC:23987 protein_coding YES CCDS9050.1 ENSP00000330737 Q9UI09 UPI000012FC31 NM_018838.4 deleterious(0.03) 4/4 Pfam_domain:PF05071,hmmpanther:PTHR12910,hmmpanther:PTHR12910:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 94971592 94971592 C A 1 0 0 0 0 1 0 0 0 10283 826 29 2 2 NDUFA12 12 94971592 Missense_Mutation SNP C C3N-00738_T 6840398 94971592 38303717 109 20034 UHRF1BP1L 0 . GRCh38 12 100037696 100037696 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.4335A>G p.= p.A1445A ENST00000279907 21/21 154 145 9 220 220 0 varscan-mutect UHRF1BP1L,synonymous_variant,p.=,ENST00000279907,NM_015054.1;UHRF1BP1L,synonymous_variant,p.=,ENST00000545232,;UHRF1BP1L,intron_variant,,ENST00000548712,;RP11-135F9.3,upstream_gene_variant,,ENST00000623268,; C ENST00000279907 Transcript synonymous_variant 4548/5168 4335/4395 1445/1464 A gcA/gcG 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 21/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 100037696 100037696 T C 1 0 0 0 0 0 0 0 1 17493 1567 55 5 5 UHRF1BP1L 12 100037696 Silent SNP T C3N-00738_T 5066104 100037696 33237613 110 20035 HIP1R 0 . GRCh38 12 122860450 122860450 + Missense_Mutation SNP G G C C3N-00738_T C3N-00738_N G G c.2587G>C p.Ala863Pro p.A863P ENST00000253083 27/32 179 165 14 220 220 0 strelka-varscan-mutect HIP1R,missense_variant,p.Ala863Pro,ENST00000253083,NM_003959.2;HIP1R,intron_variant,,ENST00000535012,;VPS37B,downstream_gene_variant,,ENST00000267202,NM_024667.2;RP11-463O12.3,upstream_gene_variant,,ENST00000537827,;HIP1R,upstream_gene_variant,,ENST00000537322,;HIP1R,non_coding_transcript_exon_variant,,ENST00000536617,;HIP1R,non_coding_transcript_exon_variant,,ENST00000538236,;HIP1R,downstream_gene_variant,,ENST00000535831,;HIP1R,downstream_gene_variant,,ENST00000452196,;HIP1R,downstream_gene_variant,,ENST00000536847,;HIP1R,downstream_gene_variant,,ENST00000541712,; C ENST00000253083 Transcript missense_variant 2712/4539 2587/3207 863/1068 A/P Gcc/Ccc COSM1561795 1 1 HIP1R HGNC HGNC:18415 protein_coding YES CCDS31922.1 ENSP00000253083 O75146 UPI000012C72C NM_003959.2 deleterious(0) 27/32 Gene3D:1r0dB00,PD011820,Pfam_domain:PF01608,PROSITE_profiles:PS50945,hmmpanther:PTHR10407,hmmpanther:PTHR10407:SF10,SMART_domains:SM00307,Superfamily_domains:SSF109885 1 MODERATE 1 SNV 1 1 1 PASS rs1362881983 . 0 208 0 2 0 0 0 0 -18.59636 0.9999997 1 1 1 0 C 3 2 64 122860450 122860450 G C 1 0 0 0 0 1 0 0 0 7003 1087 38 4 4 HIP1R 12 122860450 Missense_Mutation SNP G C3N-00738_T 22822754 122860450 10414859 111 20036 MPHOSPH9 0 . GRCh38 12 123156862 123156862 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.3497C>T p.Ser1166Leu p.S1166L ENST00000606320 24/24 151 141 10 170 170 0 strelka-varscan-mutect MPHOSPH9,missense_variant,p.Ser1166Leu,ENST00000606320,NM_022782.3;MPHOSPH9,missense_variant,p.Ser1136Leu,ENST00000541076,;MPHOSPH9,intron_variant,,ENST00000541603,;RP11-546D6.3,upstream_gene_variant,,ENST00000625082,;MPHOSPH9,upstream_gene_variant,,ENST00000544217,;MPHOSPH9,3_prime_UTR_variant,,ENST00000545556,;MPHOSPH9,3_prime_UTR_variant,,ENST00000302373,;MPHOSPH9,3_prime_UTR_variant,,ENST00000606704,;MPHOSPH9,non_coding_transcript_exon_variant,,ENST00000545974,;MPHOSPH9,downstream_gene_variant,,ENST00000539024,;MPHOSPH9,downstream_gene_variant,,ENST00000536198,; A ENST00000606320 Transcript missense_variant 3704/6351 3497/3552 1166/1183 S/L tCa/tTa 1 -1 MPHOSPH9 HGNC HGNC:7215 protein_coding YES CCDS9243.2 ENSP00000475489 Q99550 UPI00001FB90F NM_022782.3 tolerated(0.07) 24/24 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14926,hmmpanther:PTHR14926:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 123156862 123156862 G A 1 0 0 0 0 1 0 0 0 9693 1294 45 3 3 MPHOSPH9 12 123156862 Missense_Mutation SNP G C3N-00738_T 296412 123156862 10118447 112 20037 NCOR2 0 . GRCh38 12 124327439 124327439 + Nonsense_Mutation SNP C C A rs373620221 C3N-00738_T C3N-00738_N C C c.7153G>T p.Gly2385Ter p.G2385* ENST00000405201 45/47 100 94 6 144 144 0 strelka-varscan-mutect NCOR2,stop_gained,p.Gly2385Ter,ENST00000405201,NM_006312.5;NCOR2,stop_gained,p.Gly2375Ter,ENST00000429285,NM_001206654.1;NCOR2,stop_gained,p.Gly1950Ter,ENST00000356219,;NCOR2,stop_gained,p.Gly1933Ter,ENST00000404121,;NCOR2,stop_gained,p.Gly50Ter,ENST00000413172,;NCOR2,intron_variant,,ENST00000404621,NM_001077261.3;NCOR2,intron_variant,,ENST00000418829,;NCOR2,downstream_gene_variant,,ENST00000440337,;NCOR2,non_coding_transcript_exon_variant,,ENST00000464377,;NCOR2,intron_variant,,ENST00000443451,;NCOR2,downstream_gene_variant,,ENST00000461081,; A ENST00000405201 Transcript stop_gained 7154/8533 7153/7545 2385/2514 G/* Gga/Tga rs373620221 1 -1 NCOR2 HGNC HGNC:7673 protein_coding YES CCDS41858.2 ENSP00000384018 C9JFD3 UPI000013D737 NM_006312.5 45/47 hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF21 HIGH 1 SNV 1 1 PASS rs373620221 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 124327439 124327439 C A 1 0 0 0 0 0 1 0 0 10255 661 23 1 1 NCOR2 12 124327439 Nonsense_Mutation SNP C C3N-00738_T 1170577 124327439 8947870 113 20038 SLC15A4 0 . GRCh38 12 128814787 128814787 + Missense_Mutation SNP C C G rs199661368 C3N-00738_T C3N-00738_N C C c.830G>C p.Arg277Pro p.R277P ENST00000266771 2/8 95 87 8 163 163 0 strelka-varscan-mutect SLC15A4,missense_variant,p.Arg277Pro,ENST00000266771,NM_145648.3;SLC15A4,5_prime_UTR_variant,,ENST00000614634,;SLC15A4,non_coding_transcript_exon_variant,,ENST00000539703,;RP11-21K12.2,upstream_gene_variant,,ENST00000623017,;SLC15A4,downstream_gene_variant,,ENST00000535272,;SLC15A4,missense_variant,p.Arg223Pro,ENST00000376744,;SLC15A4,missense_variant,p.Arg137Pro,ENST00000376740,;SLC15A4,non_coding_transcript_exon_variant,,ENST00000366292,;SLC15A4,upstream_gene_variant,,ENST00000544112,; G ENST00000266771 Transcript missense_variant 870/2779 830/1734 277/577 R/P cGc/cCc rs199661368,COSM936911 1 -1 SLC15A4 HGNC HGNC:23090 protein_coding YES CCDS9264.1 ENSP00000266771 Q8N697 UPI000006F120 NM_145648.3 tolerated(0.06) 2/8 hmmpanther:PTHR11654,hmmpanther:PTHR11654:SF80,Pfam_domain:PF00854 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199661368 . 0 203 5 2 0 0 0 0 -12.7163 0.9998736 1 1 1 0 G 3 3 64 128814787 128814787 C G 1 0 0 0 0 1 0 0 0 14666 768 27 4 4 SLC15A4 12 128814787 Missense_Mutation SNP C C3N-00738_T 4487348 128814787 4460522 114 20039 ANHX 0 . GRCh38 12 133231620 133231620 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.274C>A p.Gln92Lys p.Q92K ENST00000545940 2/8 215 199 16 234 233 1 strelka-varscan-mutect ANHX,missense_variant,p.Gln92Lys,ENST00000545940,;ANHX,missense_variant,p.Gln92Lys,ENST00000419717,NM_001191054.1; T ENST00000545940 Transcript missense_variant 2013/3452 274/1140 92/379 Q/K Cag/Aag 1 -1 ANHX HGNC HGNC:40024 protein_coding YES CCDS53855.1 ENSP00000439513 E9PGG2 UPI0001AE6BD3 tolerated(0.88) 2/8 hmmpanther:PTHR10390,hmmpanther:PTHR10390:SF34,Pfam_domain:PF16878 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 133231620 133231620 G T 1 0 0 0 0 1 0 0 0 719 1357 47 2 2 ANHX 12 133231620 Missense_Mutation SNP G C3N-00738_T 4416833 133231620 43689 115 20040 STOML3 0 . GRCh38 13 38972532 38972532 + Missense_Mutation SNP A A C novel C3N-00738_T C3N-00738_N A A c.292T>G p.Cys98Gly p.C98G ENST00000379631 4/7 182 161 21 217 216 1 strelka-varscan-mutect STOML3,missense_variant,p.Cys98Gly,ENST00000379631,NM_145286.2;STOML3,missense_variant,p.Cys89Gly,ENST00000423210,NM_001144033.1; C ENST00000379631 Transcript missense_variant 637/2121 292/876 98/291 C/G Tgc/Ggc 1 -1 STOML3 HGNC HGNC:19420 protein_coding YES CCDS9367.1 ENSP00000368952 Q8TAV4 UPI000003615B NM_145286.2 deleterious(0.01) 4/7 Superfamily_domains:0050593,Pfam_domain:PF01145,hmmpanther:PTHR10264,hmmpanther:PTHR10264:SF49,SMART_domains:SM00244 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 38972532 38972532 A C 1 0 0 0 0 1 0 0 0 15694 130 5 5 5 STOML3 13 38972532 Missense_Mutation SNP A C3N-00738_T 38972532 75391796 116 20041 GPALPP1 0 . GRCh38 13 45006255 45006255 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.275G>T p.Gly92Val p.G92V ENST00000379151 3/8 243 225 18 233 233 0 strelka-varscan GPALPP1,missense_variant,p.Gly90Val,ENST00000361121,;GPALPP1,missense_variant,p.Gly92Val,ENST00000379151,NM_018559.2;GPALPP1,5_prime_UTR_variant,,ENST00000357537,;RP11-321C24.1,intron_variant,,ENST00000437748,;RN7SL49P,downstream_gene_variant,,ENST00000581392,;GPALPP1,downstream_gene_variant,,ENST00000479068,;GPALPP1,missense_variant,p.Gly92Val,ENST00000497558,; T ENST00000379151 Transcript missense_variant 378/1393 275/1023 92/340 G/V gGa/gTa 1 1 GPALPP1 HGNC HGNC:20298 protein_coding YES CCDS9394.1 ENSP00000368447 Q8IXQ4 A0A024RDS7 UPI000007435F NM_018559.2 deleterious(0.02) 3/8 hmmpanther:PTHR15606 MODERATE 1 SNV 1 1 PASS . . 0 200 0 3 7 0 0 0 -5.245206 0.1030722 1 1 0 0 T 3 4 64 45006255 45006255 G T 1 0 0 0 0 1 0 0 0 6483 1174 41 2 2 GPALPP1 13 45006255 Missense_Mutation SNP G C3N-00738_T 6033723 45006255 69358073 117 20042 PCDH17 0 . GRCh38 13 57633990 57633990 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.1444C>A p.His482Asn p.H482N ENST00000377918 1/4 360 328 32 490 490 0 strelka-varscan-mutect PCDH17,missense_variant,p.His482Asn,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,upstream_gene_variant,,ENST00000610846,;PCDH17,missense_variant,p.His482Asn,ENST00000484979,; A ENST00000377918 Transcript missense_variant 2179/8232 1444/3480 482/1159 H/N Cac/Aac 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.19) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 57633990 57633990 C A 1 0 0 0 0 1 0 0 0 11599 710 25 2 2 PCDH17 13 57633990 Missense_Mutation SNP C C3N-00738_T 12627735 57633990 56730338 118 20043 SLITRK1 0 . GRCh38 13 83879642 83879642 + Silent SNP C C A novel C3N-00738_T C3N-00738_N C C c.1866G>T p.= p.P622P ENST00000377084 1/1 199 178 21 324 323 1 strelka-varscan-mutect SLITRK1,synonymous_variant,p.=,ENST00000377084,NM_052910.2,NM_001281503.1; A ENST00000377084 Transcript synonymous_variant 2752/5189 1866/2091 622/696 P ccG/ccT 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 1/1 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs891710476 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 83879642 83879642 C A 1 0 0 0 0 0 0 0 1 15033 639 23 1 1 SLITRK1 13 83879642 Silent SNP C C3N-00738_T 26245652 83879642 30484686 119 20044 DOCK9 0 . GRCh38 13 98880595 98880595 + Silent SNP C C A rs749743956 C3N-00738_T C3N-00738_N C C c.2823G>T p.= p.T941T ENST00000376460 26/57 332 312 20 392 392 0 strelka-varscan-mutect DOCK9,synonymous_variant,p.=,ENST00000448493,;DOCK9,synonymous_variant,p.=,ENST00000442173,;DOCK9,synonymous_variant,p.=,ENST00000376460,NM_001130048.1,NM_015296.2;DOCK9,synonymous_variant,p.=,ENST00000427887,NM_001130049.1;DOCK9,synonymous_variant,p.=,ENST00000627024,NM_001130050.1;DOCK9,synonymous_variant,p.=,ENST00000339416,;DOCK9,3_prime_UTR_variant,,ENST00000630992,; A ENST00000376460 Transcript synonymous_variant 2904/7549 2823/6207 941/2068 T acG/acT rs749743956,COSM4419781,COSM4419782,COSM4419783,COSM4419784,COSM4419785 1 -1 DOCK9 HGNC HGNC:14132 protein_coding YES CCDS45062.1 ENSP00000365643 Q9BZ29 UPI000046FD7F NM_001130048.1,NM_015296.2 26/57 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF77 0,1,1,1,1,1 LOW 1 SNV 5 0,1,1,1,1,1 1 PASS rs749743956 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 98880595 98880595 C A 1 0 0 0 0 0 0 0 1 4509 871 31 1 1 DOCK9 13 98880595 Silent SNP C C3N-00738_T 15000953 98880595 15483733 120 20045 COL4A1 0 . GRCh38 13 110175297 110175297 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.3119C>T p.Pro1040Leu p.P1040L ENST00000375820 37/52 471 435 36 573 572 1 strelka-varscan-mutect COL4A1,missense_variant,p.Pro1040Leu,ENST00000375820,NM_001845.5; A ENST00000375820 Transcript missense_variant 3241/6532 3119/5010 1040/1669 P/L cCt/cTt 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0.03) 37/52 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 110175297 110175297 G A 1 0 0 0 0 1 0 0 0 3478 1000 35 3 3 COL4A1 13 110175297 Missense_Mutation SNP G C3N-00738_T 11294702 110175297 4189031 121 20046 PCID2 0 . GRCh38 13 113200479 113200479 + Missense_Mutation SNP C C T rs776910105 C3N-00738_T C3N-00738_N C C c.74G>A p.Cys25Tyr p.C25Y ENST00000622406 2/15 315 288 27 355 355 0 strelka-varscan-mutect PCID2,missense_variant,p.Cys23Tyr,ENST00000375457,NM_001320660.1,NM_001258213.1;PCID2,missense_variant,p.Cys25Tyr,ENST00000622406,NM_001258212.1;PCID2,missense_variant,p.Cys25Tyr,ENST00000337344,NM_001127202.2;PCID2,missense_variant,p.Cys25Tyr,ENST00000246505,;PCID2,missense_variant,p.Cys25Tyr,ENST00000375479,NM_001127203.2,NM_018386.3;PCID2,missense_variant,p.Cys23Tyr,ENST00000375459,;PCID2,missense_variant,p.Cys25Tyr,ENST00000375477,;PCID2,non_coding_transcript_exon_variant,,ENST00000484641,;PCID2,non_coding_transcript_exon_variant,,ENST00000475433,;PCID2,non_coding_transcript_exon_variant,,ENST00000480971,;PCID2,non_coding_transcript_exon_variant,,ENST00000491548,;PCID2,non_coding_transcript_exon_variant,,ENST00000462853,; T ENST00000622406 Transcript missense_variant 155/1937 74/1362 25/453 C/Y tGt/tAt rs776910105 1 -1 PCID2 HGNC HGNC:25653 protein_coding YES CCDS58302.1 ENSP00000479494 Q5JVF3 A0A024RE04 UPI00001AEF24 NM_001258212.1 deleterious(0.04) 2/15 hmmpanther:PTHR12732,hmmpanther:PTHR12732:SF0 MODERATE 1 SNV 5 1 PASS rs776910105 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 113200479 113200479 C T 1 0 0 0 0 1 0 0 0 11667 478 17 3 3 PCID2 13 113200479 Missense_Mutation SNP C C3N-00738_T 3025182 113200479 1163849 122 20047 UPF3A 0 . GRCh38 13 114301883 114301883 + Missense_Mutation SNP G G T C3N-00738_T C3N-00738_N G G c.1160G>T p.Arg387Ile p.R387I ENST00000375299 9/10 140 128 12 175 175 0 varscan-mutect UPF3A,missense_variant,p.Arg387Ile,ENST00000375299,NM_023011.3;UPF3A,missense_variant,p.Arg354Ile,ENST00000351487,NM_080687.2;UPF3A,non_coding_transcript_exon_variant,,ENST00000475218,;UPF3A,intron_variant,,ENST00000480362,;UPF3A,downstream_gene_variant,,ENST00000493727,;UPF3A,downstream_gene_variant,,ENST00000474056,;CLCP2,upstream_gene_variant,,ENST00000392050,; T ENST00000375299 Transcript missense_variant 1216/2387 1160/1431 387/476 R/I aGa/aTa COSM4801234 1 1 UPF3A HGNC HGNC:20332 protein_coding YES CCDS9543.1 ENSP00000364448 Q9H1J1 UPI0000072FCB NM_023011.3 deleterious(0) 9/10 hmmpanther:PTHR13112,hmmpanther:PTHR13112:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 114301883 114301883 G T 1 0 0 0 0 1 0 0 0 17531 942 33 2 2 UPF3A 13 114301883 Missense_Mutation SNP G C3N-00738_T 1101404 114301883 62445 123 20048 ARHGEF40 0 . GRCh38 14 21087103 21087103 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.4241G>A p.Arg1414Lys p.R1414K ENST00000298694 20/24 141 127 14 145 145 0 strelka-varscan-mutect ARHGEF40,missense_variant,p.Arg1414Lys,ENST00000298694,NM_001278530.1,NM_001278529.1,NM_018071.4;ZNF219,downstream_gene_variant,,ENST00000360947,NM_016423.2;ZNF219,downstream_gene_variant,,ENST00000451119,NM_001102454.1;ZNF219,downstream_gene_variant,,ENST00000421093,NM_001101672.1;ARHGEF40,splice_region_variant,,ENST00000553709,;ARHGEF40,splice_region_variant,,ENST00000556399,;ARHGEF40,non_coding_transcript_exon_variant,,ENST00000554514,;ARHGEF40,downstream_gene_variant,,ENST00000555232,;ARHGEF40,upstream_gene_variant,,ENST00000557498,; A ENST00000298694 Transcript missense_variant,splice_region_variant 4368/5919 4241/4560 1414/1519 R/K aGa/aAa 1 1 ARHGEF40 HGNC HGNC:25516 protein_coding YES CCDS32041.1 ENSP00000298694 Q8TER5 UPI00001FCFB7 NM_001278530.1,NM_001278529.1,NM_018071.4 deleterious(0.01) 20/24 Low_complexity_(Seg):seg,hmmpanther:PTHR22826:SF143,hmmpanther:PTHR22826 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 21087103 21087103 G A 1 0 0 0 0 1 0 0 0 1044 956 33 3 3 ARHGEF40 14 21087103 Missense_Mutation SNP G C3N-00738_T 21087103 85956615 124 20049 PELI2 0 . GRCh38 14 56296635 56296635 + Silent SNP C C G rs72720080 C3N-00738_T C3N-00738_N C C c.732C>G p.= p.S244S ENST00000267460 6/6 114 103 11 103 103 0 strelka-varscan-mutect PELI2,synonymous_variant,p.=,ENST00000267460,NM_021255.2; G ENST00000267460 Transcript synonymous_variant 1018/5909 732/1263 244/420 S tcC/tcG rs72720080 1 1 PELI2 HGNC HGNC:8828 protein_coding YES CCDS9726.1 ENSP00000267460 Q9HAT8 UPI0000062262 NM_021255.2 6/6 hmmpanther:PTHR12098,Pfam_domain:PF04710,PIRSF_domain:PIRSF038886 LOW 1 SNV 1 1 PASS rs72720080 . 0 197 12 0 0 0 0 0 -19.9863 0.9997963 1 1 1 0 G 2 3 64 56296635 56296635 C G 1 0 0 0 0 0 0 0 1 11810 610 22 4 4 PELI2 14 56296635 Silent SNP C C3N-00738_T 35209532 56296635 50747083 125 20050 PPM1A 0 . GRCh38 14 60245885 60245885 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.38C>T p.Thr13Ile p.T13I ENST00000325642 1/6 124 113 11 117 117 0 strelka-varscan-mutect PPM1A,missense_variant,p.Thr13Ile,ENST00000325642,NM_177952.2;PPM1A,upstream_gene_variant,,ENST00000395076,NM_021003.4;PPM1A,upstream_gene_variant,,ENST00000325658,NM_177951.2;PPM1A,upstream_gene_variant,,ENST00000525399,;PPM1A,upstream_gene_variant,,ENST00000528241,;CTD-2184C24.2,intron_variant,,ENST00000529171,;CTD-2184C24.2,upstream_gene_variant,,ENST00000532515,;CTD-2184C24.2,upstream_gene_variant,,ENST00000553269,;CTD-2184C24.2,upstream_gene_variant,,ENST00000553775,;PPM1A,missense_variant,p.Thr13Ile,ENST00000532036,;PPM1A,missense_variant,p.Thr13Ile,ENST00000531143,; T ENST00000325642 Transcript missense_variant 134/1713 38/1368 13/455 T/I aCa/aTa 1 1 PPM1A HGNC HGNC:9275 protein_coding YES CCDS45120.1 ENSP00000327255 P35813 UPI0000E01530 NM_177952.2 1/6 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -19.98707 1 1 1 1 0 T 3 4 64 60245885 60245885 C T 1 0 0 0 0 1 0 0 0 12445 478 17 3 3 PPM1A 14 60245885 Missense_Mutation SNP C C3N-00738_T 3949250 60245885 46797833 126 20051 PROX2 0 . GRCh38 14 74858415 74858415 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.1405G>A p.Asp469Asn p.D469N ENST00000556489 2/4 76 70 6 106 106 0 strelka-varscan-mutect PROX2,missense_variant,p.Asp469Asn,ENST00000556489,NM_001243007.1;YLPM1,3_prime_UTR_variant,,ENST00000554107,;PROX2,intron_variant,,ENST00000556084,NM_001080408.2;YLPM1,downstream_gene_variant,,ENST00000553381,; T ENST00000556489 Transcript missense_variant 1405/3878 1405/1779 469/592 D/N Gat/Aat 1 -1 PROX2 HGNC HGNC:26715 protein_coding YES CCDS73663.1 ENSP00000451223 G3V3G0 UPI0002190191 NM_001243007.1 deleterious(0) 2/4 hmmpanther:PTHR12198,Pfam_domain:PF05044,Gene3D:1mijA00,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1199930390 . 0 205 4 0 0 0 0 0 -13.36568 1 1 1 1 0 T 3 4 64 74858415 74858415 C T 1 0 0 0 0 1 0 0 0 12697 826 29 3 3 PROX2 14 74858415 Missense_Mutation SNP C C3N-00738_T 14612530 74858415 32185303 127 20052 FAM181A 0 . GRCh38 14 93928839 93928839 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.740C>A p.Ser247Tyr p.S247Y ENST00000267594 3/3 436 403 33 417 417 0 strelka-varscan-mutect FAM181A,missense_variant,p.Ser247Tyr,ENST00000267594,NM_138344.4;FAM181A,missense_variant,p.Ser185Tyr,ENST00000557000,NM_001207072.1;FAM181A,missense_variant,p.Ser185Tyr,ENST00000556222,NM_001207074.1,NM_001207073.1;FAM181A,missense_variant,p.Ser185Tyr,ENST00000557719,NM_001207071.1;FAM181A,missense_variant,p.Ser185Tyr,ENST00000554404,;FAM181A-AS1,upstream_gene_variant,,ENST00000554742,;FAM181A-AS1,upstream_gene_variant,,ENST00000554538,;FAM181A-AS1,upstream_gene_variant,,ENST00000556290,;FAM181A-AS1,upstream_gene_variant,,ENST00000555732,; A ENST00000267594 Transcript missense_variant 1047/1816 740/1065 247/354 S/Y tCc/tAc 1 1 FAM181A HGNC HGNC:20491 protein_coding YES CCDS9914.1 ENSP00000267594 Q8N9Y4 UPI00004567C0 NM_138344.4 deleterious(0.04) 3/3 Pfam_domain:PF15238,hmmpanther:PTHR33766,hmmpanther:PTHR33766:SF1 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 93928839 93928839 C A 1 0 0 0 0 1 0 0 0 5354 855 30 2 2 FAM181A 14 93928839 Missense_Mutation SNP C C3N-00738_T 19070424 93928839 13114879 128 20053 SERPINA6 0 . GRCh38 14 94309848 94309848 + Frame_Shift_Del DEL C C - rs778913169 C3N-00738_T C3N-00738_N C C c.772delG p.Val258TrpfsTer16 p.V258Wfs*16 ENST00000341584 3/5 484 448 36 500 500 0 varindel-pindel SERPINA6,frameshift_variant,p.Val258TrpfsTer16,ENST00000341584,NM_001756.3;SERPINA6,downstream_gene_variant,,ENST00000557225,;SERPINA6,3_prime_UTR_variant,,ENST00000555056,; - ENST00000341584 Transcript frameshift_variant 919/1534 772/1218 258/405 V/X Gtg/tg rs778913169,COSM4053225,COSM4053226 1 -1 SERPINA6 HGNC HGNC:1540 protein_coding YES CCDS9924.1 ENSP00000342850 P08185 UPI0000127182 NM_001756.3 3/5 hmmpanther:PTHR11461:SF34,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574,Prints_domain:PR00780 0,1,1 HIGH 1 deletion 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 64 94309848 94309848 C - 1 0 1 0 1 0 0 0 0 14369 536 19 0 0 SERPINA6 14 94309848 Frame_Shift_Del DEL C C3N-00738_T 381009 94309848 12733870 129 20054 WDR72 0 . GRCh38 15 53702346 53702346 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.1357C>A p.Pro453Thr p.P453T ENST00000396328 12/20 197 180 17 269 269 0 strelka-varscan-mutect WDR72,missense_variant,p.Pro453Thr,ENST00000396328,;WDR72,missense_variant,p.Pro450Thr,ENST00000557913,;WDR72,missense_variant,p.Pro453Thr,ENST00000360509,NM_182758.3;WDR72,missense_variant,p.Pro463Thr,ENST00000559418,;WDR72,missense_variant,p.Pro453Thr,ENST00000560036,; T ENST00000396328 Transcript missense_variant 1597/7507 1357/3309 453/1102 P/T Cct/Act 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D deleterious(0.01) 12/20 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF408,SMART_domains:SM00320 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 53702346 53702346 G T 1 0 0 0 0 1 0 0 0 17878 1232 43 2 2 WDR72 15 53702346 Missense_Mutation SNP G C3N-00738_T 53702346 48288843 130 20055 PTPN9 0 . GRCh38 15 75523244 75523244 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.299A>G p.Asn100Ser p.N100S ENST00000618819 4/13 169 144 25 172 172 0 strelka-varscan-mutect PTPN9,missense_variant,p.Asn100Ser,ENST00000618819,NM_002833.3;PTPN9,missense_variant,p.Asn90Ser,ENST00000306726,;PTPN9,missense_variant,p.Asn23Ser,ENST00000561731,;CTD-2323K18.1,downstream_gene_variant,,ENST00000568707,;CTD-2323K18.1,downstream_gene_variant,,ENST00000565138,;CTD-2323K18.1,downstream_gene_variant,,ENST00000567875,;CTD-2323K18.1,downstream_gene_variant,,ENST00000566032,; C ENST00000618819 Transcript missense_variant,splice_region_variant 812/7813 299/1782 100/593 N/S aAt/aGt 1 -1 PTPN9 HGNC HGNC:9661 protein_coding YES CCDS10280.1 ENSP00000482732 P43378 UPI0000000CAC NM_002833.3 tolerated(0.61) 4/13 PROSITE_profiles:PS50191,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF326,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 75523244 75523244 T C 1 0 0 0 0 1 0 0 0 12948 1507 52 5 5 PTPN9 15 75523244 Missense_Mutation SNP T C3N-00738_T 21820898 75523244 26467945 131 20056 ADAMTS17 0 . GRCh38 15 100133241 100133241 + Silent SNP C C G rs762724843 C3N-00738_T C3N-00738_N C C c.1548G>C p.= p.L516L ENST00000268070 11/22 218 205 13 256 256 0 strelka-mutect ADAMTS17,synonymous_variant,p.=,ENST00000268070,NM_139057.2;RP11-90E5.1,downstream_gene_variant,,ENST00000560128,;ADAMTS17,non_coding_transcript_exon_variant,,ENST00000378898,; G ENST00000268070 Transcript synonymous_variant 1654/6207 1548/3288 516/1095 L ctG/ctC rs762724843 1 -1 ADAMTS17 HGNC HGNC:17109 protein_coding YES CCDS10383.1 ENSP00000268070 Q8TE56 UPI00001AE929 NM_139057.2 11/22 hmmpanther:PTHR13723:SF151,hmmpanther:PTHR13723,SMART_domains:SM00608 LOW 1 SNV 1 1 PASS rs762724843 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 64 100133241 100133241 C G 1 0 0 0 0 0 0 0 1 306 581 21 4 4 ADAMTS17 15 100133241 Silent SNP C C3N-00738_T 24609997 100133241 1857948 132 20057 CHSY1 0 . GRCh38 15 101178928 101178928 + Missense_Mutation SNP C C G C3N-00738_T C3N-00738_N C C c.869G>C p.Arg290Thr p.R290T ENST00000254190 3/3 221 199 22 211 211 0 strelka-varscan-mutect CHSY1,missense_variant,p.Arg290Thr,ENST00000254190,NM_014918.4;CHSY1,non_coding_transcript_exon_variant,,ENST00000543813,;CHSY1,non_coding_transcript_exon_variant,,ENST00000561414,;CHSY1,non_coding_transcript_exon_variant,,ENST00000560766,; G ENST00000254190 Transcript missense_variant 1345/4550 869/2409 290/802 R/T aGa/aCa COSM459079 1 -1 CHSY1 HGNC HGNC:17198 protein_coding YES CCDS10390.1 ENSP00000254190 Q86X52 UPI000000DB6C NM_014918.4 tolerated(0.25) 3/3 hmmpanther:PTHR12369:SF16,hmmpanther:PTHR12369,Pfam_domain:PF05679,Superfamily_domains:SSF53448 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 101178928 101178928 C G 1 0 0 0 0 1 0 0 0 3172 913 32 4 4 CHSY1 15 101178928 Missense_Mutation SNP C C3N-00738_T 1045687 101178928 812261 133 20058 SRRM2 0 . GRCh38 16 2766275 2766275 + Frame_Shift_Del DEL C C - C3N-00738_T C3N-00738_N C C c.5750delC p.Pro1917GlnfsTer2 p.P1917Qfs*2 ENST00000301740 11/15 179 164 15 238 237 1 varindel-pindel SRRM2,frameshift_variant,p.Pro1917GlnfsTer2,ENST00000301740,NM_016333.3;SRRM2,intron_variant,,ENST00000630499,;SRRM2,downstream_gene_variant,,ENST00000576924,;SRRM2,downstream_gene_variant,,ENST00000571378,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,upstream_gene_variant,,ENST00000570539,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,upstream_gene_variant,,ENST00000574866,;SRRM2,downstream_gene_variant,,ENST00000576674,;SRRM2,upstream_gene_variant,,ENST00000574331,;SRRM2,upstream_gene_variant,,ENST00000576878,;SRRM2,downstream_gene_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,upstream_gene_variant,,ENST00000573311,;SRRM2,upstream_gene_variant,,ENST00000570705,;SRRM2,upstream_gene_variant,,ENST00000571041,;SRRM2,upstream_gene_variant,,ENST00000573692,; - ENST00000301740 Transcript frameshift_variant 6296/9353 5747/8259 1916/2752 S/X tCc/tc COSM4789454 1 1 SRRM2 HGNC HGNC:16639 protein_coding YES CCDS32373.1 ENSP00000301740 Q9UQ35 A0A140VK53 UPI000049DDFC NM_016333.3 11/15 Low_complexity_(Seg):seg 1 HIGH 1 deletion 1 3 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.75611 0.9999998 1 1 1 0 - 7 5 64 2766275 2766275 C - 1 0 1 0 1 0 0 0 0 15530 855 30 0 0 SRRM2 16 2766275 Frame_Shift_Del DEL C C3N-00738_T 2766275 87572070 134 20059 CREBBP 0 . GRCh38 16 3770778 3770778 + Frame_Shift_Del DEL G G - novel C3N-00738_T C3N-00738_N G G c.2672delC p.Pro891LeufsTer36 p.P891Lfs*36 ENST00000262367 14/31 302 273 29 419 419 0 sindel-varindel-pindel CREBBP,frameshift_variant,p.Pro891LeufsTer36,ENST00000262367,NM_004380.2;CREBBP,frameshift_variant,p.Pro853LeufsTer36,ENST00000382070,NM_001079846.1;CREBBP,frameshift_variant,p.Pro426LeufsTer36,ENST00000570939,;CREBBP,downstream_gene_variant,,ENST00000572134,;CREBBP,downstream_gene_variant,,ENST00000571826,;CREBBP,upstream_gene_variant,,ENST00000573672,;CREBBP,downstream_gene_variant,,ENST00000575237,; - ENST00000262367 Transcript frameshift_variant 3482/10803 2672/7329 891/2442 P/X cCt/ct 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 14/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 64 3770778 3770778 G - 1 0 1 0 1 0 0 0 0 3661 1000 35 0 0 CREBBP 16 3770778 Frame_Shift_Del DEL G C3N-00738_T 1004503 3770778 86567567 135 20060 METTL22 0 . GRCh38 16 8629073 8629073 + Silent SNP G G A C3N-00738_T C3N-00738_N G G c.477G>A p.= p.E159E ENST00000381920 3/11 136 124 12 177 177 0 strelka-varscan-mutect METTL22,synonymous_variant,p.=,ENST00000381920,NM_024109.2;METTL22,synonymous_variant,p.=,ENST00000561758,;METTL22,downstream_gene_variant,,ENST00000563958,;METTL22,downstream_gene_variant,,ENST00000564554,;METTL22,upstream_gene_variant,,ENST00000568967,;METTL22,downstream_gene_variant,,ENST00000563037,;METTL22,synonymous_variant,p.=,ENST00000163678,;METTL22,3_prime_UTR_variant,,ENST00000567295,; A ENST00000381920 Transcript synonymous_variant 735/4984 477/1215 159/404 E gaG/gaA COSM3999970 1 1 METTL22 HGNC HGNC:28368 protein_coding YES CCDS10533.2 ENSP00000371345 Q9BUU2 UPI00001FED9D NM_024109.2 3/11 hmmpanther:PTHR23108:SF0,hmmpanther:PTHR23108 1 LOW 1 SNV 5 1 1 PASS rs1386322649 . 0 206 3 0 0 0 0 0 -19.9997 1 1 1 1 0 A 2 1 64 8629073 8629073 G A 1 0 0 0 0 0 0 0 1 9448 991 35 3 3 METTL22 16 8629073 Silent SNP G C3N-00738_T 4858295 8629073 81709272 136 20061 QPRT 0 . GRCh38 16 29694772 29694772 + Missense_Mutation SNP C C T C3N-00738_T C3N-00738_N C C c.122C>T p.Pro41Leu p.P41L ENST00000395384 2/4 94 84 10 93 93 0 strelka-varscan-mutect QPRT,missense_variant,p.Pro41Leu,ENST00000395384,NM_014298.3;AC009133.22,missense_variant,p.Pro41Leu,ENST00000449759,;QPRT,intron_variant,,ENST00000562473,;QPRT,intron_variant,,ENST00000219771,;QPRT,upstream_gene_variant,,ENST00000564967,; T ENST00000395384 Transcript missense_variant 283/2343 122/894 41/297 P/L cCc/cTc COSM3888360 1 1 QPRT HGNC HGNC:9755 protein_coding YES CCDS10651.1 ENSP00000378782 Q15274 UPI000013C78C NM_014298.3 tolerated(0.25) 2/4 hmmpanther:PTHR32179,PIRSF_domain:PIRSF006250,TIGRFAM_domain:TIGR00078,Pfam_domain:PF02749,Gene3D:3.90.1170.20,Superfamily_domains:SSF54675 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.94397 1 1 1 1 0 T 3 4 64 29694772 29694772 C T 1 0 0 0 0 1 0 0 0 13031 623 22 3 3 QPRT 16 29694772 Missense_Mutation SNP C C3N-00738_T 21065699 29694772 60643573 137 20062 ABCC11 0 . GRCh38 16 48214992 48214992 + Nonsense_Mutation SNP G G T rs377586143 C3N-00738_T C3N-00738_N G G c.1137C>A p.Cys379Ter p.C379* ENST00000394747 8/29 178 154 24 227 227 0 strelka-varscan-mutect ABCC11,stop_gained,p.Cys379Ter,ENST00000394747,NM_033151.3;ABCC11,stop_gained,p.Cys379Ter,ENST00000356608,;ABCC11,stop_gained,p.Cys379Ter,ENST00000394748,NM_032583.3;ABCC11,stop_gained,p.Cys379Ter,ENST00000353782,NM_145186.2;ABCC11,downstream_gene_variant,,ENST00000565487,;ABCC11,non_coding_transcript_exon_variant,,ENST00000567385,; T ENST00000394747 Transcript stop_gained 1487/4862 1137/4149 379/1382 C/* tgC/tgA rs377586143,COSM1378038 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 8/29 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 0,1 HIGH 1 SNV 1 0,1 1 PASS rs377586143 . 0 206 0 3 0 0 0 0 -20 0.9999918 1 1 1 0 T 4 4 64 48214992 48214992 G T 1 0 0 0 0 0 1 0 0 55 1079 38 1 1 ABCC11 16 48214992 Nonsense_Mutation SNP G C3N-00738_T 18520220 48214992 42123353 138 20063 CNGB1 0 . GRCh38 16 57901369 57901369 + Missense_Mutation SNP C C A rs768408396 C3N-00738_T C3N-00738_N C C c.2959G>T p.Asp987Tyr p.D987Y ENST00000251102 29/33 532 471 61 528 527 1 strelka-varscan-mutect CNGB1,missense_variant,p.Asp987Tyr,ENST00000251102,NM_001297.4;CNGB1,missense_variant,p.Asp981Tyr,ENST00000564448,NM_001286130.1;CNGB1,missense_variant,p.Asp3Tyr,ENST00000565942,;CNGB1,non_coding_transcript_exon_variant,,ENST00000569643,; A ENST00000251102 Transcript missense_variant 3020/5641 2959/3756 987/1251 D/Y Gac/Tac rs768408396 1 -1 CNGB1 HGNC HGNC:2151 protein_coding YES CCDS42169.1 ENSP00000251102 Q14028 UPI000013CCDF NM_001297.4 deleterious(0) 29/33 PROSITE_profiles:PS50042,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF386,Gene3D:2.60.120.10,Pfam_domain:PF00027,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS rs768408396 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 57901369 57901369 C A 1 0 0 0 0 1 0 0 0 3380 884 31 1 1 CNGB1 16 57901369 Missense_Mutation SNP C C3N-00738_T 9686377 57901369 32436976 139 20064 CES2 0 . GRCh38 16 66943968 66943968 + Silent SNP G G C rs763130930 C3N-00738_T C3N-00738_N G G c.1815G>C p.= p.A605A ENST00000317091 12/12 73 66 7 58 58 0 strelka-mutect CES2,synonymous_variant,p.=,ENST00000317091,NM_003869.5;CES2,synonymous_variant,p.=,ENST00000417689,NM_198061.2;CES2,downstream_gene_variant,,ENST00000561697,;CES2,downstream_gene_variant,,ENST00000564420,;RP11-361L15.4,intron_variant,,ENST00000566869,;RP11-361L15.3,downstream_gene_variant,,ENST00000623356,;CES2,3_prime_UTR_variant,,ENST00000568470,;CES2,non_coding_transcript_exon_variant,,ENST00000563988,;CES2,downstream_gene_variant,,ENST00000568347,;CES2,downstream_gene_variant,,ENST00000561843,;CES2,downstream_gene_variant,,ENST00000567128,; C ENST00000317091 Transcript synonymous_variant 2799/3927 1815/1872 605/623 A gcG/gcC rs763130930,COSM379107 1 1 CES2 HGNC HGNC:1864 protein_coding YES CCDS10825.1 ENSP00000317842 A0A024R6X1 UPI0000074733 NM_003869.5 12/12 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF149,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 0,1 LOW 1 SNV 1 0,1 1 PASS rs763130930 . 0 196 13 0 0 0 0 0 -15.0556 0.9996144 1 1 1 0 C 2 2 64 66943968 66943968 G C 1 0 0 0 0 0 0 0 1 3002 1074 38 4 4 CES2 16 66943968 Silent SNP G C3N-00738_T 9042599 66943968 23394377 140 20065 OR1G1 0 . GRCh38 17 3127223 3127223 + Missense_Mutation SNP A A C novel C3N-00738_T C3N-00738_N A A c.329T>G p.Leu110Arg p.L110R ENST00000328890 1/1 323 289 34 396 395 1 strelka-varscan-mutect OR1G1,missense_variant,p.Leu110Arg,ENST00000328890,NM_003555.1; C ENST00000328890 Transcript missense_variant 359/998 329/942 110/313 L/R cTg/cGg 1 -1 OR1G1 HGNC HGNC:8204 protein_coding YES CCDS11020.1 ENSP00000331545 P47890 A0A126GW57 UPI0000041B68 NM_003555.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 3127223 3127223 A C 1 0 0 0 0 1 0 0 0 11035 188 7 5 5 OR1G1 17 3127223 Missense_Mutation SNP A C3N-00738_T 3127223 80130218 141 20066 ARRB2 0 . GRCh38 17 4720247 4720247 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.1012G>A p.Gly338Arg p.G338R ENST00000412477 12/15 248 227 21 296 296 0 strelka-varscan-mutect ARRB2,missense_variant,p.Gly317Arg,ENST00000269260,NM_001257330.1,NM_004313.3;ARRB2,missense_variant,p.Gly338Arg,ENST00000412477,NM_001257328.1;ARRB2,missense_variant,p.Gly302Arg,ENST00000346341,NM_001257331.1;ARRB2,missense_variant,p.Gly125Arg,ENST00000572457,;ARRB2,missense_variant,p.Gly125Arg,ENST00000571206,;ARRB2,missense_variant,p.Gly273Glu,ENST00000575877,NM_001257329.1;ARRB2,missense_variant,p.Gly125Arg,ENST00000574954,;ARRB2,missense_variant,p.Gly302Arg,ENST00000381488,NM_199004.1;ARRB2,downstream_gene_variant,,ENST00000571428,;ARRB2,downstream_gene_variant,,ENST00000570718,;ARRB2,downstream_gene_variant,,ENST00000570739,;ARRB2,3_prime_UTR_variant,,ENST00000576235,;ARRB2,downstream_gene_variant,,ENST00000571791,;ARRB2,downstream_gene_variant,,ENST00000574502,;ARRB2,downstream_gene_variant,,ENST00000573886,;ARRB2,downstream_gene_variant,,ENST00000577054,;ARRB2,downstream_gene_variant,,ENST00000575131,;ARRB2,downstream_gene_variant,,ENST00000572782,;ARRB2,downstream_gene_variant,,ENST00000574888,;ARRB2,downstream_gene_variant,,ENST00000572497,; A ENST00000412477 Transcript missense_variant 1041/1779 1012/1293 338/430 G/R Gga/Aga 1 1 ARRB2 HGNC HGNC:712 protein_coding YES CCDS58504.1 ENSP00000403701 P32121 UPI0001AE6690 NM_001257328.1 deleterious(0) 12/15 Gene3D:1g4mB02,Pfam_domain:PF02752,hmmpanther:PTHR11792,hmmpanther:PTHR11792:SF20,SMART_domains:SM01017,Superfamily_domains:SSF81296 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 4720247 4720247 G A 1 0 0 0 0 1 0 0 0 1124 1233 43 3 3 ARRB2 17 4720247 Missense_Mutation SNP G C3N-00738_T 1593024 4720247 78537194 142 20067 MINK1 0 . GRCh38 17 4878317 4878317 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.58G>T p.Asp20Tyr p.D20Y ENST00000355280 2/32 134 122 12 164 164 0 strelka-varscan-mutect MINK1,missense_variant,p.Asp20Tyr,ENST00000355280,NM_153827.4,NM_015716.4;MINK1,missense_variant,p.Asp20Tyr,ENST00000347992,NM_170663.4;MINK1,missense_variant,p.Asp20Tyr,ENST00000453408,NM_001024937.3;RN7SL784P,upstream_gene_variant,,ENST00000577319,;MINK1,missense_variant,p.Lys58Asn,ENST00000574453,NM_001321236.1;MINK1,missense_variant,p.Asp8Tyr,ENST00000577021,;MINK1,splice_region_variant,,ENST00000572330,; T ENST00000355280 Transcript missense_variant,splice_region_variant 254/4961 58/3999 20/1332 D/Y Gac/Tac 1 1 MINK1 HGNC HGNC:17565 protein_coding YES CCDS45588.1 ENSP00000347427 Q8N4C8 UPI00001678BB NM_153827.4,NM_015716.4 deleterious_low_confidence(0) 2/32 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF196,Gene3D:3.30.200.20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 4878317 4878317 G T 1 0 0 0 0 1 0 0 0 9551 1188 41 2 2 MINK1 17 4878317 Missense_Mutation SNP G C3N-00738_T 158070 4878317 78379124 143 20068 AIPL1 0 . GRCh38 17 6426687 6426687 + Nonsense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.712C>T p.Gln238Ter p.Q238* ENST00000381129 5/6 350 325 25 419 418 1 strelka-varscan-mutect AIPL1,stop_gained,p.Gln238Ter,ENST00000381129,NM_014336.4;AIPL1,stop_gained,p.Gln175Ter,ENST00000250087,NM_001033054.2;AIPL1,stop_gained,p.Gln238Ter,ENST00000575265,;AIPL1,stop_gained,p.Gln226Ter,ENST00000574506,NM_001285399.2,NM_001285402.1;AIPL1,stop_gained,p.Gln230Ter,ENST00000571740,NM_001285403.2;AIPL1,stop_gained,p.Gln216Ter,ENST00000570466,NM_001285400.2;AIPL1,stop_gained,p.Gln178Ter,ENST00000576307,NM_001033055.2;AIPL1,splice_region_variant,,ENST00000576776,NM_001285401.2;AIPL1,intron_variant,,ENST00000570584,;AIPL1,downstream_gene_variant,,ENST00000574913,;AIPL1,3_prime_UTR_variant,,ENST00000381128,; A ENST00000381129 Transcript stop_gained 793/2959 712/1155 238/384 Q/* Cag/Tag 1 -1 AIPL1 HGNC HGNC:359 protein_coding YES CCDS11075.1 ENSP00000370521 Q9NZN9 F1T0B6 UPI0000125741 NM_014336.4 5/6 Gene3D:1.25.40.10,PROSITE_profiles:PS50293,hmmpanther:PTHR11242,hmmpanther:PTHR11242:SF2,Superfamily_domains:SSF48452 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 64 6426687 6426687 G A 1 0 0 0 0 0 1 0 0 513 1362 47 3 3 AIPL1 17 6426687 Nonsense_Mutation SNP G C3N-00738_T 1548370 6426687 76830754 144 20069 SHMT1 0 . GRCh38 17 18340212 18340212 + Silent SNP C C A rs758391400 C3N-00738_T C3N-00738_N C C c.645G>T p.= p.R215R ENST00000316694 7/12 738 660 78 742 740 2 strelka-varscan-mutect SHMT1,synonymous_variant,p.=,ENST00000316694,NM_004169.4;SHMT1,synonymous_variant,p.=,ENST00000352886,NM_001281786.1;SHMT1,synonymous_variant,p.=,ENST00000354098,NM_148918.2;SHMT1,downstream_gene_variant,,ENST00000617912,;SHMT1,3_prime_UTR_variant,,ENST00000580002,;SHMT1,non_coding_transcript_exon_variant,,ENST00000395684,;SHMT1,downstream_gene_variant,,ENST00000579558,; A ENST00000316694 Transcript synonymous_variant 780/2464 645/1452 215/483 R cgG/cgT rs758391400 1 -1 SHMT1 HGNC HGNC:10850 protein_coding YES CCDS11196.1 ENSP00000318868 P34896 UPI0000001C71 NM_004169.4 7/12 HAMAP:MF_00051,hmmpanther:PTHR11680:SF14,hmmpanther:PTHR11680,Pfam_domain:PF00464,PIRSF_domain:PIRSF000412,Gene3D:3.40.640.10,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS rs758391400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 18340212 18340212 C A 1 0 0 0 0 0 0 0 1 14548 842 30 2 2 SHMT1 17 18340212 Silent SNP C C3N-00738_T 11913525 18340212 64917229 145 20070 KRTAP4-8 0 . GRCh38 17 41097830 41097830 + Nonsense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.255C>A p.Cys85Ter p.C85* ENST00000333822 1/1 389 360 29 474 473 1 varscan-mutect KRTAP4-8,stop_gained,p.Cys85Ter,ENST00000333822,NM_031960.2;KRTAP4-8,splice_region_variant,,ENST00000318329,;KRTAP4-7,intron_variant,,ENST00000612231,;KRTAP4-16,downstream_gene_variant,,ENST00000440582,; T ENST00000333822 Transcript stop_gained 312/1161 255/558 85/185 C/* tgC/tgA 1 -1 KRTAP4-8 HGNC HGNC:17230 protein_coding YES CCDS45674.1 ENSP00000328444 Q9BYQ9 UPI0000366BFD NM_031960.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF67,Pfam_domain:PF13885 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 64 41097830 41097830 G T 1 0 0 0 0 0 1 0 0 8451 1195 42 2 2 KRTAP4-8 17 41097830 Nonsense_Mutation SNP G C3N-00738_T 22757618 41097830 42159611 146 20071 SOST 0 . GRCh38 17 43755408 43755408 + Silent SNP G G T novel C3N-00738_T C3N-00738_N G G c.576C>A p.= p.G192G ENST00000301691 2/2 223 194 29 230 230 0 strelka-varscan-mutect SOST,synonymous_variant,p.=,ENST00000301691,NM_025237.2; T ENST00000301691 Transcript synonymous_variant 623/2300 576/642 192/213 G ggC/ggA 1 -1 SOST HGNC HGNC:13771 protein_coding YES CCDS11468.1 ENSP00000301691 Q9BQB4 UPI0000035BBE NM_025237.2 2/2 Pfam_domain:PF05463,hmmpanther:PTHR14903,hmmpanther:PTHR14903:SF4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 43755408 43755408 G T 1 0 0 0 0 0 0 0 1 15260 1190 42 2 2 SOST 17 43755408 Silent SNP G C3N-00738_T 2657578 43755408 39502033 147 20072 CD300LG 0 . GRCh38 17 43848861 43848861 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.347A>T p.Glu116Val p.E116V ENST00000317310 2/7 124 111 13 195 195 0 strelka-varscan-mutect CD300LG,missense_variant,p.Glu116Val,ENST00000317310,NM_145273.3;CD300LG,missense_variant,p.Glu116Val,ENST00000588884,;CD300LG,missense_variant,p.Glu116Val,ENST00000539718,NM_001168322.1;CD300LG,missense_variant,p.Glu116Val,ENST00000377203,NM_001168323.1;CD300LG,missense_variant,p.Glu116Val,ENST00000293396,NM_001168324.1;CD300LG,missense_variant,p.Glu116Val,ENST00000586233,; T ENST00000317310 Transcript missense_variant 388/2758 347/999 116/332 E/V gAg/gTg 1 1 CD300LG HGNC HGNC:30455 protein_coding YES CCDS11470.1 ENSP00000321005 Q6UXG3 UPI000013E104 NM_145273.3 deleterious(0) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR11860:SF22,hmmpanther:PTHR11860,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 43848861 43848861 A T 1 0 0 0 0 1 0 0 0 2706 304 11 4 4 CD300LG 17 43848861 Missense_Mutation SNP A C3N-00738_T 93453 43848861 39408580 148 20073 GPATCH8 0 . GRCh38 17 44398532 44398532 + Frame_Shift_Del DEL G G - C3N-00738_T C3N-00738_N G G c.3545delC p.Pro1182GlnfsTer22 p.P1182Qfs*22 ENST00000591680 8/8 36 31 5 68 68 0 sindel-varindel-pindel GPATCH8,frameshift_variant,p.Pro1182GlnfsTer22,ENST00000591680,NM_001304939.1,NM_001002909.3;GPATCH8,downstream_gene_variant,,ENST00000585614,;GPATCH8,3_prime_UTR_variant,,ENST00000587228,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000335500,;GPATCH8,non_coding_transcript_exon_variant,,ENST00000635257,;GPATCH8,downstream_gene_variant,,ENST00000590041,; - ENST00000591680 Transcript frameshift_variant 3576/4692 3545/4509 1182/1502 P/X cCa/ca COSM5561399 1 -1 GPATCH8 HGNC HGNC:29066 protein_coding YES CCDS32666.1 ENSP00000467556 Q9UKJ3 UPI0000237985 NM_001304939.1,NM_001002909.3 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR17614:SF11,hmmpanther:PTHR17614 1 HIGH 1 deletion 2 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.26841 1 1 1 1 0 - 7 5 64 44398532 44398532 G - 1 0 1 0 1 0 0 0 0 6495 1348 47 0 0 GPATCH8 17 44398532 Frame_Shift_Del DEL G C3N-00738_T 549671 44398532 38858909 149 20074 TTLL6 0 . GRCh38 17 48786187 48786187 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.1738G>A p.Ala580Thr p.A580T ENST00000393382 12/16 200 186 14 186 186 0 strelka-varscan-mutect TTLL6,missense_variant,p.Ala580Thr,ENST00000393382,NM_001130918.1;TTLL6,missense_variant,p.Ala273Thr,ENST00000433608,NM_173623.3;TTLL6,3_prime_UTR_variant,,ENST00000376681,;TTLL6,3_prime_UTR_variant,,ENST00000416950,;TTLL6,non_coding_transcript_exon_variant,,ENST00000490027,;TTLL6,downstream_gene_variant,,ENST00000424018,; T ENST00000393382 Transcript missense_variant 1880/3551 1738/2676 580/891 A/T Gcc/Acc 1 -1 TTLL6 HGNC HGNC:26664 protein_coding YES CCDS45724.1 ENSP00000377043 Q8N841 UPI00017BCE80 NM_001130918.1 tolerated(0.65) 12/16 Low_complexity_(Seg):seg,hmmpanther:PTHR12241:SF96,hmmpanther:PTHR12241 MODERATE 1 SNV 2 1 PASS rs1026875124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 48786187 48786187 C T 1 0 0 0 0 1 0 0 0 17242 739 26 3 3 TTLL6 17 48786187 Missense_Mutation SNP C C3N-00738_T 4387655 48786187 34471254 150 20075 ZNF652 0 . GRCh38 17 49317129 49317129 + Frame_Shift_Del DEL G G - rs759904071 C3N-00738_T C3N-00738_N G G c.597delC p.Ala200GlnfsTer18 p.A200Qfs*18 ENST00000362063 2/6 206 184 22 321 321 0 sindel-varindel-pindel ZNF652,frameshift_variant,p.Ala200GlnfsTer18,ENST00000362063,NM_014897.2;ZNF652,frameshift_variant,p.Ala200GlnfsTer18,ENST00000430262,NM_001145365.1;ZNF652,intron_variant,,ENST00000508237,; - ENST00000362063 Transcript frameshift_variant 916/5988 597/1821 199/606 A/X gcC/gc rs759904071 1 -1 ZNF652 HGNC HGNC:29147 protein_coding YES CCDS32677.1 ENSP00000354686 Q9Y2D9 UPI000006D93D NM_014897.2 2/6 Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 64 49317129 49317129 G - 1 0 1 0 1 0 0 0 0 18638 1103 39 0 0 ZNF652 17 49317129 Frame_Shift_Del DEL G C3N-00738_T 530942 49317129 33940312 151 20076 MPO 0 . GRCh38 17 58271861 58271861 + Silent SNP G G A rs569034063 C3N-00738_T C3N-00738_N G G c.1824C>T p.= p.L608L ENST00000225275 11/12 209 193 16 269 269 0 strelka-varscan-mutect MPO,synonymous_variant,p.=,ENST00000225275,NM_000250.1;MPO,intron_variant,,ENST00000577220,;LPO,downstream_gene_variant,,ENST00000262290,NM_006151.2;LPO,downstream_gene_variant,,ENST00000421678,NM_001160102.1;LPO,downstream_gene_variant,,ENST00000582328,;LPO,downstream_gene_variant,,ENST00000543544,;MPO,downstream_gene_variant,,ENST00000578493,;LPO,downstream_gene_variant,,ENST00000580890,;LPO,downstream_gene_variant,,ENST00000389576,; A ENST00000225275 Transcript synonymous_variant 2001/3215 1824/2238 608/745 L ctC/ctT rs569034063 1 -1 MPO HGNC HGNC:7218 protein_coding YES CCDS11604.1 ENSP00000225275 P05164 UPI0000131634 NM_000250.1 11/12 PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 LOW 1 SNV 1 1 PASS rs569034063 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 58271861 58271861 G A 1 0 0 0 0 0 0 0 1 9698 1161 41 3 3 MPO 17 58271861 Silent SNP G C3N-00738_T 8954732 58271861 24985580 152 20077 TRIM37 0 . GRCh38 17 59031925 59031925 + Missense_Mutation SNP C C A rs112762655 C3N-00738_T C3N-00738_N C C c.1919G>T p.Arg640Leu p.R640L ENST00000262294 18/24 163 151 12 240 240 0 strelka-varscan-mutect TRIM37,missense_variant,p.Arg640Leu,ENST00000262294,NM_015294.3;TRIM37,missense_variant,p.Arg640Leu,ENST00000393066,NM_001005207.2;TRIM37,missense_variant,p.Arg606Leu,ENST00000393065,;TRIM37,3_prime_UTR_variant,,ENST00000577554,NM_001320990.1; A ENST00000262294 Transcript missense_variant 2179/4330 1919/2895 640/964 R/L cGc/cTc rs112762655 1 -1 TRIM37 HGNC HGNC:7523 protein_coding YES CCDS32694.1 ENSP00000262294 O94972 UPI0000167B57 NM_015294.3 deleterious_low_confidence(0) 18/24 MODERATE 1 SNV 1 1 PASS rs112762655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 59031925 59031925 C A 1 0 0 0 0 1 0 0 0 17000 768 27 1 1 TRIM37 17 59031925 Missense_Mutation SNP C C3N-00738_T 760064 59031925 24225516 153 20078 BAHCC1 0 . GRCh38 17 81447443 81447443 + Nonsense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.3664G>T p.Glu1222Ter p.E1222* ENST00000584436 12/29 117 108 9 164 164 0 strelka-varscan-mutect BAHCC1,stop_gained,p.Glu1222Ter,ENST00000584436,NM_001291324.1;BAHCC1,stop_gained,p.Glu1191Ter,ENST00000307745,;MIR3186,downstream_gene_variant,,ENST00000577404,;BAHCC1,downstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript stop_gained 4031/10801 3664/7920 1222/2639 E/* Gag/Tag 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 12/29 Low_complexity_(Seg):seg,hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 64 81447443 81447443 G T 1 0 0 0 0 0 1 0 0 1451 1175 41 2 2 BAHCC1 17 81447443 Nonsense_Mutation SNP G C3N-00738_T 22415518 81447443 1809998 154 20079 CABLES1 0 . GRCh38 18 23214010 23214010 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.1044T>C p.= p.C348C ENST00000256925 4/10 148 136 12 181 181 0 strelka-varscan-mutect CABLES1,synonymous_variant,p.=,ENST00000256925,NM_001100619.2;CABLES1,synonymous_variant,p.=,ENST00000420687,NM_138375.2;CABLES1,synonymous_variant,p.=,ENST00000400473,NM_001256438.1;CABLES1,synonymous_variant,p.=,ENST00000582882,;TMEM241,intron_variant,,ENST00000584625,;TMEM241,intron_variant,,ENST00000578790,;CABLES1,intron_variant,,ENST00000585061,;CABLES1,synonymous_variant,p.=,ENST00000579963,;TMEM241,intron_variant,,ENST00000581444,; C ENST00000256925 Transcript synonymous_variant 1044/5002 1044/1902 348/633 C tgT/tgC 1 1 CABLES1 HGNC HGNC:25097 protein_coding YES CCDS42417.1 ENSP00000256925 Q8TDN4 A7K6Y5 UPI00004C2CAA NM_001100619.2 4/10 hmmpanther:PTHR22896:SF1,hmmpanther:PTHR22896 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.5838 0.9999773 1 1 1 0 C 2 2 64 23214010 23214010 T C 1 0 0 0 0 0 0 0 1 2215 1644 57 5 5 CABLES1 18 23214010 Silent SNP T C3N-00738_T 23214010 57159275 155 20080 RNF125 0 . GRCh38 18 32042268 32042268 + Silent SNP A A T novel C3N-00738_T C3N-00738_N A A c.408A>T p.= p.A136A ENST00000217740 3/6 209 182 27 284 284 0 strelka-varscan-mutect RNF125,synonymous_variant,p.=,ENST00000217740,NM_017831.3;RNF125,non_coding_transcript_exon_variant,,ENST00000583384,;RP11-53I6.2,non_coding_transcript_exon_variant,,ENST00000583184,;RNF125,non_coding_transcript_exon_variant,,ENST00000583814,;RNF125,non_coding_transcript_exon_variant,,ENST00000580863,;RNF125,intron_variant,,ENST00000580209,; T ENST00000217740 Transcript synonymous_variant 900/6020 408/699 136/232 A gcA/gcT 1 1 RNF125 HGNC HGNC:21150 protein_coding YES CCDS11902.1 ENSP00000217740 Q96EQ8 UPI000013C731 NM_017831.3 3/6 hmmpanther:PTHR23327,hmmpanther:PTHR23327:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 32042268 32042268 A T 1 0 0 0 0 0 0 0 1 13612 202 7 4 4 RNF125 18 32042268 Silent SNP A C3N-00738_T 8828258 32042268 48331017 156 20081 NOL4 0 . GRCh38 18 33957418 33957418 + Missense_Mutation SNP G G C rs767337796 C3N-00738_T C3N-00738_N G G c.1336C>G p.Arg446Gly p.R446G ENST00000261592 8/11 191 177 14 229 229 0 strelka-varscan-mutect NOL4,missense_variant,p.Arg446Gly,ENST00000261592,NM_003787.4;NOL4,missense_variant,p.Arg372Gly,ENST00000538587,NM_001198547.1;NOL4,missense_variant,p.Arg161Gly,ENST00000535384,NM_001198549.1;NOL4,intron_variant,,ENST00000589544,NM_001198548.1;NOL4,intron_variant,,ENST00000590712,NM_001198546.1;NOL4,intron_variant,,ENST00000586553,;NOL4,intron_variant,,ENST00000586314,; C ENST00000261592 Transcript missense_variant 1634/3957 1336/1917 446/638 R/G Cga/Gga rs767337796 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 deleterious(0) 8/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 MODERATE 1 SNV 1 1 PASS rs767337796 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 33957418 33957418 G C 1 0 0 0 0 1 0 0 0 10567 1095 38 4 4 NOL4 18 33957418 Missense_Mutation SNP G C3N-00738_T 1915150 33957418 46415867 157 20082 MAPK4 0 . GRCh38 18 50729363 50729363 + Missense_Mutation SNP G G T rs781183183 C3N-00738_T C3N-00738_N G G c.1273G>T p.Gly425Trp p.G425W ENST00000400384 6/6 89 81 8 99 98 1 strelka-mutect MAPK4,missense_variant,p.Gly425Trp,ENST00000400384,NM_002747.3;MAPK4,missense_variant,p.Gly214Trp,ENST00000540640,NM_001292039.1;MAPK4,3_prime_UTR_variant,,ENST00000592595,NM_001292040.1; T ENST00000400384 Transcript missense_variant 2309/4770 1273/1764 425/587 G/W Ggg/Tgg rs781183183 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 deleterious_low_confidence(0) 6/6 MODERATE 1 SNV 1 1 PASS rs781183183 . 0 205 5 0 0 0 0 0 -16.80567 1 1 1 1 0 T 3 4 64 50729363 50729363 G T 1 0 0 0 0 1 0 0 0 9204 1116 39 1 1 MAPK4 18 50729363 Missense_Mutation SNP G C3N-00738_T 16771945 50729363 29643922 158 20083 CDH20 0 . GRCh38 18 61503027 61503027 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.736G>T p.Asp246Tyr p.D246Y ENST00000262717 5/12 155 139 16 171 171 0 strelka-varscan-mutect CDH20,missense_variant,p.Asp246Tyr,ENST00000262717,;CDH20,missense_variant,p.Asp246Tyr,ENST00000536675,NM_031891.2;CDH20,missense_variant,p.Asp246Tyr,ENST00000538374,; T ENST00000262717 Transcript missense_variant 1134/3882 736/2406 246/801 D/Y Gac/Tac 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D deleterious(0) 5/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 61503027 61503027 G T 1 0 0 0 0 1 0 0 0 2809 1174 41 2 2 CDH20 18 61503027 Missense_Mutation SNP G C3N-00738_T 10773664 61503027 18870258 159 20084 SERPINB10 0 . GRCh38 18 63915646 63915646 + Missense_Mutation SNP G G T rs375113713 C3N-00738_T C3N-00738_N G G c.136G>T p.Ala46Ser p.A46S ENST00000238508 2/8 122 115 7 136 136 0 strelka-varscan-mutect SERPINB10,missense_variant,p.Ala46Ser,ENST00000238508,;SERPINB10,missense_variant,p.Ala46Ser,ENST00000619595,NM_005024.1;SERPINB10,missense_variant,p.Ala259Ser,ENST00000397996,;SERPINB10,missense_variant,p.Ala232Ser,ENST00000418725,; T ENST00000238508 Transcript missense_variant 195/2122 136/1194 46/397 A/S Gcc/Tcc rs375113713,COSM4072964 1 1 SERPINB10 HGNC HGNC:8942 protein_coding YES CCDS11990.1 ENSP00000238508 P48595 UPI000013558E tolerated(0.13) 2/8 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF175,SMART_domains:SM00093,Superfamily_domains:SSF56574 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs375113713 . 0 197 8 4 0 0 0 0 -10.02343 0.9803976 1 1 1 0 T 3 4 64 63915646 63915646 G T 1 0 0 0 0 1 0 0 0 14373 1087 38 1 1 SERPINB10 18 63915646 Missense_Mutation SNP G C3N-00738_T 2412619 63915646 16457639 160 20085 TSHZ1 0 . GRCh38 18 75287098 75287098 + Missense_Mutation SNP G G C novel C3N-00738_T C3N-00738_N G G c.1691G>C p.Ser564Thr p.S564T ENST00000580243 2/2 177 161 16 201 201 0 strelka-varscan-mutect TSHZ1,missense_variant,p.Ser519Thr,ENST00000322038,NM_005786.5;TSHZ1,missense_variant,p.Ser564Thr,ENST00000580243,NM_001308210.1;TSHZ1,downstream_gene_variant,,ENST00000560918,;TSHZ1,downstream_gene_variant,,ENST00000560661,;TSHZ1,non_coding_transcript_exon_variant,,ENST00000584217,; C ENST00000580243 Transcript missense_variant 2039/3582 1691/3234 564/1077 S/T aGc/aCc 1 1 TSHZ1 HGNC HGNC:10669 protein_coding YES CCDS77199.1 ENSP00000464391 Q6ZSZ6 UPI0000201D5A NM_001308210.1 deleterious(0) 2/2 hmmpanther:PTHR12487:SF6,hmmpanther:PTHR12487 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 75287098 75287098 G C 1 0 0 0 0 1 0 0 0 17128 971 34 4 4 TSHZ1 18 75287098 Missense_Mutation SNP G C3N-00738_T 11371452 75287098 5086187 161 20086 AP3D1 0 . GRCh38 19 2117228 2117228 + Missense_Mutation SNP G G A novel C3N-00738_T C3N-00738_N G G c.1853C>T p.Pro618Leu p.P618L ENST00000355272 16/32 54 46 8 56 56 0 strelka-varscan-mutect AP3D1,missense_variant,p.Pro618Leu,ENST00000355272,NM_001261826.1;AP3D1,missense_variant,p.Pro618Leu,ENST00000345016,NM_003938.6;AP3D1,non_coding_transcript_exon_variant,,ENST00000591631,;AP3D1,non_coding_transcript_exon_variant,,ENST00000586177,;AP3D1,upstream_gene_variant,,ENST00000585652,;AP3D1,upstream_gene_variant,,ENST00000589223,;AP3D1,downstream_gene_variant,,ENST00000590683,;AP3D1,upstream_gene_variant,,ENST00000592488,; A ENST00000355272 Transcript missense_variant 2060/5034 1853/3648 618/1215 P/L cCc/cTc 1 -1 AP3D1 HGNC HGNC:568 protein_coding YES CCDS58638.1 ENSP00000347416 O14617 UPI0000202F99 NM_001261826.1 deleterious(0.01) 16/32 hmmpanther:PTHR22781,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037092,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -18.89894 1 1 1 1 0 A 3 1 64 2117228 2117228 G A 1 0 0 0 0 1 0 0 0 862 1232 43 3 3 AP3D1 19 2117228 Missense_Mutation SNP G C3N-00738_T 2117228 56500388 162 20087 DNM2 0 . GRCh38 19 10829186 10829186 + Missense_Mutation SNP G G T rs774897265 C3N-00738_T C3N-00738_N G G c.2209G>T p.Gly737Cys p.G737C ENST00000389253 19/21 516 471 45 610 609 1 strelka-varscan-mutect DNM2,missense_variant,p.Gly733Cys,ENST00000359692,NM_004945.3;DNM2,missense_variant,p.Gly737Cys,ENST00000389253,NM_001005361.2;DNM2,missense_variant,p.Gly737Cys,ENST00000355667,NM_001005360.2;DNM2,missense_variant,p.Gly733Cys,ENST00000408974,NM_001005362.2;DNM2,missense_variant,p.Gly737Cys,ENST00000585892,NM_001190716.1;DNM2,missense_variant,p.Gly26Cys,ENST00000589106,;TMED1,downstream_gene_variant,,ENST00000214869,NM_006858.3;TMED1,downstream_gene_variant,,ENST00000591695,;TMED1,downstream_gene_variant,,ENST00000586835,;TMED1,downstream_gene_variant,,ENST00000589638,;TMED1,downstream_gene_variant,,ENST00000588289,;DNM2,upstream_gene_variant,,ENST00000591818,;MIR6793,downstream_gene_variant,,ENST00000612376,;DNM2,non_coding_transcript_exon_variant,,ENST00000590806,;DNM2,non_coding_transcript_exon_variant,,ENST00000593203,;DNM2,downstream_gene_variant,,ENST00000590787,;TMED1,downstream_gene_variant,,ENST00000591157,;TMED1,downstream_gene_variant,,ENST00000588259,; T ENST00000389253 Transcript missense_variant 2321/3581 2209/2613 737/870 G/C Ggt/Tgt rs774897265 1 1 DNM2 HGNC HGNC:2974 protein_coding YES CCDS45969.1 ENSP00000373905 P50570 UPI000049A626 NM_001005361.2 deleterious(0) 19/21 Pfam_domain:PF02212,PROSITE_profiles:PS51388,hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF23,SMART_domains:SM00302 MODERATE SNV 5 1 PASS rs774897265 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 10829186 10829186 G T 1 0 0 0 0 1 0 0 0 4485 1116 39 1 1 DNM2 19 10829186 Missense_Mutation SNP G C3N-00738_T 8711958 10829186 47788430 163 20088 ZNF490 0 . GRCh38 19 12583538 12583538 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.181G>T p.Asp61Tyr p.D61Y ENST00000311437 3/5 95 85 10 143 143 0 strelka-varscan-mutect ZNF490,missense_variant,p.Asp61Tyr,ENST00000311437,NM_020714.2;ZNF490,missense_variant,p.Asp8Tyr,ENST00000440366,;ZNF490,non_coding_transcript_exon_variant,,ENST00000465656,;ZNF490,3_prime_UTR_variant,,ENST00000414906,;CTD-2192J16.20,upstream_gene_variant,,ENST00000593682,; A ENST00000311437 Transcript missense_variant 304/4237 181/1590 61/529 D/Y Gat/Tat 1 -1 ZNF490 HGNC HGNC:23705 protein_coding YES CCDS12272.1 ENSP00000311521 Q9ULM2 UPI0000001C6F NM_020714.2 deleterious(0) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF16,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 12583538 12583538 C A 1 0 0 0 0 1 0 0 0 18514 855 30 2 2 ZNF490 19 12583538 Missense_Mutation SNP C C3N-00738_T 1754352 12583538 46034078 164 20089 KCNN4 0 . GRCh38 19 43776620 43776620 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.176T>A p.Phe59Tyr p.F59Y ENST00000262888 2/9 161 151 10 191 191 0 strelka-varscan-mutect KCNN4,missense_variant,p.Phe59Tyr,ENST00000262888,NM_002250.2;KCNN4,5_prime_UTR_variant,,ENST00000615047,;KCNN4,non_coding_transcript_exon_variant,,ENST00000599107,;KCNN4,intron_variant,,ENST00000599720,;KCNN4,upstream_gene_variant,,ENST00000601549,;KCNN4,upstream_gene_variant,,ENST00000600408,; T ENST00000262888 Transcript missense_variant 572/2240 176/1284 59/427 F/Y tTc/tAc 1 -1 KCNN4 HGNC HGNC:6293 protein_coding YES CCDS12630.1 ENSP00000262888 O15554 UPI0000000DF3 NM_002250.2 tolerated(0.22) 2/9 Pfam_domain:PF03530,hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF41,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 43776620 43776620 A T 1 0 0 0 0 1 0 0 0 7997 246 9 4 4 KCNN4 19 43776620 Missense_Mutation SNP A C3N-00738_T 31193082 43776620 14840996 165 20090 ZNF841 0 . GRCh38 19 52067158 52067158 + Missense_Mutation SNP A A G novel C3N-00738_T C3N-00738_N A A c.724T>C p.Phe242Leu p.F242L ENST00000594295 6/6 101 93 8 171 171 0 strelka-varscan-mutect ZNF841,missense_variant,p.Phe242Leu,ENST00000594295,NM_001136499.1;ZNF841,missense_variant,p.Phe126Leu,ENST00000426391,NM_001321349.1;ZNF841,missense_variant,p.Phe242Leu,ENST00000389534,;ZNF841,missense_variant,p.Phe138Leu,ENST00000601738,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,; G ENST00000594295 Transcript missense_variant 1127/3819 724/2775 242/924 F/L Ttt/Ctt 1 -1 ZNF841 HGNC HGNC:27611 protein_coding YES CCDS46161.1 ENSP00000470746 Q6ZN19 UPI00001D818B NM_001136499.1 tolerated(0.16) 6/6 Superfamily_domains:SSF57667 MODERATE SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 52067158 52067158 A G 1 0 0 0 0 1 0 0 0 18776 14 1 5 5 ZNF841 19 52067158 Missense_Mutation SNP A C3N-00738_T 8290538 52067158 6550458 166 20091 ZNF329 0 . GRCh38 19 58128995 58128995 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.509G>A p.Arg170Lys p.R170K ENST00000597186 5/5 100 93 7 156 156 0 strelka-varscan-mutect ZNF329,missense_variant,p.Arg170Lys,ENST00000597186,;ZNF329,missense_variant,p.Arg170Lys,ENST00000598312,NM_024620.3;ZNF329,missense_variant,p.Arg170Lys,ENST00000358067,;ZNF329,downstream_gene_variant,,ENST00000601887,;ZNF329,missense_variant,p.Arg170Lys,ENST00000500161,; T ENST00000597186 Transcript missense_variant 1187/3930 509/1626 170/541 R/K aGa/aAa 1 -1 ZNF329 HGNC HGNC:14209 protein_coding YES CCDS12972.1 ENSP00000470323 Q86UD4 A0A024R4Q4 UPI0000246E79 tolerated(0.36) 5/5 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF118 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -14.57544 1 1 1 1 0 T 3 4 64 58128995 58128995 C T 1 0 0 0 0 1 0 0 0 18419 913 32 3 3 ZNF329 19 58128995 Missense_Mutation SNP C C3N-00738_T 6061837 58128995 488621 167 20092 CENPB 0 . GRCh38 20 3786335 3786335 + Missense_Mutation SNP C C A novel C3N-00738_T C3N-00738_N C C c.149G>T p.Arg50Leu p.R50L ENST00000379751 1/1 178 159 19 207 207 0 strelka-varscan-mutect CENPB,missense_variant,p.Arg50Leu,ENST00000379751,NM_001810.5;CDC25B,upstream_gene_variant,,ENST00000344256,NM_001287516.1,NM_001287517.1;CDC25B,upstream_gene_variant,,ENST00000379598,NM_001287518.1;SPEF1,upstream_gene_variant,,ENST00000379756,NM_015417.4;SPEF1,upstream_gene_variant,,ENST00000463490,;SPEF1,upstream_gene_variant,,ENST00000471499,; A ENST00000379751 Transcript missense_variant 356/2840 149/1800 50/599 R/L cGc/cTc 1 -1 CENPB HGNC HGNC:1852 protein_coding YES CCDS13064.1 ENSP00000369075 P07199 UPI00001274F8 NM_001810.5 tolerated(0.21) 1/1 Gene3D:1.10.10.60,Pfam_domain:PF04218,PROSITE_profiles:PS50960,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF194,Superfamily_domains:SSF46689 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 3786335 3786335 C A 1 0 0 0 0 1 0 0 0 2935 768 27 1 1 CENPB 20 3786335 Missense_Mutation SNP C C3N-00738_T 3786335 60657832 168 20093 PTPRT 0 . GRCh38 20 42677973 42677973 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.1046A>G p.His349Arg p.H349R ENST00000373198 7/32 366 331 35 428 428 0 strelka-varscan-mutect PTPRT,missense_variant,p.His349Arg,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.His349Arg,ENST00000373193,;PTPRT,missense_variant,p.His349Arg,ENST00000373201,;PTPRT,missense_variant,p.His349Arg,ENST00000373190,;PTPRT,missense_variant,p.His349Arg,ENST00000373184,;PTPRT,missense_variant,p.His349Arg,ENST00000356100,;PTPRT,missense_variant,p.His349Arg,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.His278Arg,ENST00000620410,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; C ENST00000373198 Transcript missense_variant 1282/12746 1046/4383 349/1460 H/R cAt/cGt 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 7/32 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 42677973 42677973 T C 1 0 0 0 0 1 0 0 0 12967 1464 51 5 5 PTPRT 20 42677973 Missense_Mutation SNP T C3N-00738_T 38891638 42677973 21766194 169 20094 DBNDD2 0 . GRCh38 20 45408886 45408886 + Silent SNP A A T novel C3N-00738_T C3N-00738_N A A c.531A>T p.= p.A177A ENST00000372710 2/3 444 405 39 481 481 0 strelka-varscan-mutect DBNDD2,synonymous_variant,p.=,ENST00000372712,;DBNDD2,synonymous_variant,p.=,ENST00000372720,NM_018478.3;DBNDD2,synonymous_variant,p.=,ENST00000372710,NM_001048225.2;DBNDD2,synonymous_variant,p.=,ENST00000443296,NM_001048226.2;DBNDD2,synonymous_variant,p.=,ENST00000372717,NM_001048224.2;DBNDD2,synonymous_variant,p.=,ENST00000372722,NM_001048222.2;DBNDD2,synonymous_variant,p.=,ENST00000372723,NM_001048221.2;DBNDD2,synonymous_variant,p.=,ENST00000360981,NM_001197139.1,NM_001048223.2;DBNDD2,synonymous_variant,p.=,ENST00000357275,NM_001197140.1;SYS1-DBNDD2,non_coding_transcript_exon_variant,,ENST00000475242,;TP53TG5,upstream_gene_variant,,ENST00000494455,;TP53TG5,upstream_gene_variant,,ENST00000488588,;TP53TG5,upstream_gene_variant,,ENST00000468375,;SYS1-DBNDD2,3_prime_UTR_variant,,ENST00000419593,;SYS1-DBNDD2,3_prime_UTR_variant,,ENST00000452133,;SYS1-DBNDD2,3_prime_UTR_variant,,ENST00000458187,; T ENST00000372710 Transcript synonymous_variant 686/1417 531/792 177/263 A gcA/gcT 1 1 DBNDD2 HGNC HGNC:15881 protein_coding YES CCDS56194.1 ENSP00000361795 Q9BQY9 UPI00004708B3 NM_001048225.2 2/3 hmmpanther:PTHR16294,hmmpanther:PTHR16294:SF7,Pfam_domain:PF04440 LOW 1 SNV 1 1 PASS rs1008218432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 45408886 45408886 A T 1 0 0 0 0 0 0 0 1 4054 175 7 4 4 DBNDD2 20 45408886 Silent SNP A C3N-00738_T 2730913 45408886 19035281 170 20095 ZSWIM1 0 . GRCh38 20 45883845 45883845 + Missense_Mutation SNP C C T rs551866738 C3N-00738_T C3N-00738_N C C c.1253C>T p.Thr418Met p.T418M ENST00000372523 2/2 139 130 9 190 190 0 strelka-varscan-mutect ZSWIM1,missense_variant,p.Thr418Met,ENST00000372523,NM_080603.4;ZSWIM1,missense_variant,p.Thr418Met,ENST00000372520,;ZSWIM3,downstream_gene_variant,,ENST00000255152,NM_080752.3;NEURL2,downstream_gene_variant,,ENST00000372518,NM_080749.3;SPATA25,downstream_gene_variant,,ENST00000372519,NM_080608.3;NEURL2,downstream_gene_variant,,ENST00000545238,; T ENST00000372523 Transcript missense_variant 1348/2769 1253/1458 418/485 T/M aCg/aTg rs551866738 1 1 ZSWIM1 HGNC HGNC:16155 protein_coding YES CCDS13382.2 ENSP00000361601 Q9BR11 UPI0000470896 NM_080603.4 tolerated(0.09) 2/2 hmmpanther:PTHR31569,hmmpanther:PTHR31569:SF0 MODERATE SNV 2 1 PASS rs551866738 . 0 207 0 3 0 0 0 0 -12.4692 0.9999635 1 1 1 0 T 3 4 64 45883845 45883845 C T 1 0 0 0 0 1 0 0 0 18841 536 19 1 1 ZSWIM1 20 45883845 Missense_Mutation SNP C C3N-00738_T 474959 45883845 18560322 171 20096 CBLN4 0 . GRCh38 20 55998731 55998731 + Missense_Mutation SNP T T G novel C3N-00738_T C3N-00738_N T T c.432A>C p.Lys144Asn p.K144N ENST00000064571 3/3 303 270 33 348 348 0 strelka-mutect CBLN4,missense_variant,p.Lys144Asn,ENST00000064571,NM_080617.5; G ENST00000064571 Transcript missense_variant 1733/3024 432/606 144/201 K/N aaA/aaC 1 -1 CBLN4 HGNC HGNC:16231 protein_coding YES CCDS13448.1 ENSP00000064571 Q9NTU7 UPI0000046135 NM_080617.5 tolerated(0.33) 3/3 Gene3D:2.60.120.40,Pfam_domain:PF00386,PROSITE_profiles:PS50871,hmmpanther:PTHR22923,hmmpanther:PTHR22923:SF3,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 64 55998731 55998731 T G 1 0 0 0 0 1 0 0 0 2408 1722 60 5 5 CBLN4 20 55998731 Missense_Mutation SNP T C3N-00738_T 10114886 55998731 8445436 172 20097 CSTF1 0 . GRCh38 20 56397829 56397829 + Silent SNP C C T novel C3N-00738_T C3N-00738_N C C c.633C>T p.= p.F211F ENST00000217109 4/6 185 167 18 229 229 0 strelka-varscan-mutect CSTF1,synonymous_variant,p.=,ENST00000217109,NM_001033521.1,NM_001324.2,NM_001033522.1;CSTF1,synonymous_variant,p.=,ENST00000415828,;CSTF1,synonymous_variant,p.=,ENST00000452950,;CSTF1,downstream_gene_variant,,ENST00000428552,;CSTF1,downstream_gene_variant,,ENST00000613138,;CSTF1,3_prime_UTR_variant,,ENST00000493039,;CSTF1,3_prime_UTR_variant,,ENST00000490539,;CSTF1,downstream_gene_variant,,ENST00000498689,; T ENST00000217109 Transcript synonymous_variant 985/4290 633/1296 211/431 F ttC/ttT 1 1 CSTF1 HGNC HGNC:2483 protein_coding YES CCDS13452.1 ENSP00000217109 Q05048 UPI0000000C1E NM_001033521.1,NM_001324.2,NM_001033522.1 4/6 PROSITE_profiles:PS50294,hmmpanther:PTHR22840,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 64 56397829 56397829 C T 1 0 0 0 0 0 0 0 1 3783 825 29 3 3 CSTF1 20 56397829 Silent SNP C C3N-00738_T 399098 56397829 8046338 173 20098 COL20A1 0 . GRCh38 20 63310473 63310473 + Silent SNP C C A rs751998432 C3N-00738_T C3N-00738_N C C c.1356C>A p.= p.G452G ENST00000358894 11/36 178 158 20 186 186 0 strelka-varscan-mutect COL20A1,synonymous_variant,p.=,ENST00000422202,;COL20A1,synonymous_variant,p.=,ENST00000358894,NM_020882.2;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,; A ENST00000358894 Transcript synonymous_variant 1456/4172 1356/3855 452/1284 G ggC/ggA rs751998432 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 11/36 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,Low_complexity_(Seg):seg,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs751998432 . 0 206 0 4 0 0 0 0 -20 0.9998554 1 1 1 0 A 2 1 64 63310473 63310473 C A 1 0 0 0 0 0 0 0 1 3467 755 27 1 1 COL20A1 20 63310473 Silent SNP C C3N-00738_T 6912644 63310473 1133694 174 20099 EEF1A2 0 . GRCh38 20 63493171 63493171 + Silent SNP C C A novel C3N-00738_T C3N-00738_N C C c.738G>T p.= p.L246L ENST00000217182 5/8 116 108 8 120 120 0 strelka-varscan-mutect EEF1A2,synonymous_variant,p.=,ENST00000217182,NM_001958.3;EEF1A2,synonymous_variant,p.=,ENST00000298049,; A ENST00000217182 Transcript synonymous_variant 1067/2006 738/1392 246/463 L ctG/ctT 1 -1 EEF1A2 HGNC HGNC:3192 protein_coding YES CCDS13522.1 ENSP00000217182 Q05639 UPI0000000136 NM_001958.3 5/8 HAMAP:MF_00118_A,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF104,Gene3D:2.40.30.10,TIGRFAM_domain:TIGR00483,Superfamily_domains:SSF52540,Superfamily_domains:SSF50447 LOW 1 SNV 1 1 PASS rs1333751988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 63493171 63493171 C A 1 0 0 0 0 0 0 0 1 4753 697 25 2 2 EEF1A2 20 63493171 Silent SNP C C3N-00738_T 182698 63493171 950996 175 20100 MICAL3 0 . GRCh38 22 17818243 17818243 + Missense_Mutation SNP C C G rs766517694 C3N-00738_T C3N-00738_N C C c.4418G>C p.Arg1473Pro p.R1473P ENST00000441493 26/32 72 64 8 102 102 0 strelka-mutect MICAL3,missense_variant,p.Arg1473Pro,ENST00000441493,NM_015241.2;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,; G ENST00000441493 Transcript missense_variant 4771/9445 4418/6009 1473/2002 R/P cGg/cCg rs766517694 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 deleterious_low_confidence(0.02) 26/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF239 MODERATE 1 SNV 5 1 PASS rs766517694 . 0 203 7 0 0 0 0 0 -17.51358 0.9999992 1 1 1 0 G 3 3 64 17818243 17818243 C G 1 0 0 0 0 1 0 0 0 9528 652 23 4 4 MICAL3 22 17818243 Missense_Mutation SNP C C3N-00738_T 17818243 33000225 176 20101 KCTD17 0 . GRCh38 22 37056364 37056364 + Missense_Mutation SNP C C A rs747167411 C3N-00738_T C3N-00738_N C C c.364C>A p.Arg122Ser p.R122S ENST00000403888 3/9 135 125 10 134 134 0 strelka-varscan-mutect KCTD17,missense_variant,p.Arg122Ser,ENST00000403888,NM_001282684.1;KCTD17,missense_variant,p.Arg122Ser,ENST00000402077,NM_024681.3;KCTD17,missense_variant,p.Arg122Ser,ENST00000610767,NM_001282686.1;KCTD17,missense_variant,p.Arg77Ser,ENST00000456470,NM_001282685.1;KCTD17,downstream_gene_variant,,ENST00000431531,;RN7SKP214,upstream_gene_variant,,ENST00000364208,;KCTD17,missense_variant,p.Arg85Ser,ENST00000421900,;KCTD17,non_coding_transcript_exon_variant,,ENST00000478231,;KCTD17,non_coding_transcript_exon_variant,,ENST00000483389,;KCTD17,upstream_gene_variant,,ENST00000462640,; A ENST00000403888 Transcript missense_variant 365/1763 364/966 122/321 R/S Cgc/Agc rs747167411,COSM5564279,COSM5564280 1 1 KCTD17 HGNC HGNC:25705 protein_coding YES CCDS74854.1 ENSP00000385096 Q8N5Z5 UPI0001610FBA NM_001282684.1 tolerated(0.06) 3/9 hmmpanther:PTHR14958:SF24,hmmpanther:PTHR14958,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs747167411 . 0 205 2 3 0 0 0 0 -14.05864 0.9998355 1 1 1 0 A 3 1 64 37056364 37056364 C A 1 0 0 0 0 1 0 0 0 8021 652 23 1 1 KCTD17 22 37056364 Missense_Mutation SNP C C3N-00738_T 19238121 37056364 13762104 177 20102 FAM9A 0 . GRCh38 X 8795339 8795339 + Silent SNP T T C novel C3N-00738_T C3N-00738_N T T c.570A>G p.= p.E190E ENST00000543214 7/10 195 181 14 202 202 0 strelka-varscan-mutect FAM9A,synonymous_variant,p.=,ENST00000543214,NM_001171186.1;FAM9A,synonymous_variant,p.=,ENST00000381003,NM_174951.3; C ENST00000543214 Transcript synonymous_variant 706/1544 570/999 190/332 E gaA/gaG 1 -1 FAM9A HGNC HGNC:18403 protein_coding YES CCDS14131.1 ENSP00000440163 Q8IZU1 UPI000012A418 NM_001171186.1 7/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs1348258464 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 64 8795339 8795339 T C 1 0 0 0 0 0 0 0 1 5517 1606 56 5 5 FAM9A 23 8795339 Silent SNP T C3N-00738_T 8795339 147245556 178 20103 NHS 0 . GRCh38 X 17725631 17725631 + Silent SNP C C A C3N-00738_T C3N-00738_N C C c.1462C>A p.= p.R488R ENST00000380060 6/8 196 181 15 280 279 1 strelka-varscan-mutect NHS,synonymous_variant,p.=,ENST00000615422,;NHS,synonymous_variant,p.=,ENST00000380060,NM_198270.3,NM_001291867.1;NHS,synonymous_variant,p.=,ENST00000398097,NM_001136024.3;NHS,synonymous_variant,p.=,ENST00000617601,NM_001291868.1;NHS,downstream_gene_variant,,ENST00000485305,; A ENST00000380060 Transcript synonymous_variant 1800/8761 1462/4893 488/1630 R Cgg/Agg COSM5412384,COSM5412385 1 1 NHS HGNC HGNC:7820 protein_coding YES CCDS14181.1 ENSP00000369400 Q6T4R5 UPI00001DFBF3 NM_198270.3,NM_001291867.1 6/8 Pfam_domain:PF15273,hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF5 1,1 LOW 1 SNV 1 1,1 1 PASS rs965999976 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 17725631 17725631 C A 1 0 0 0 0 0 0 0 1 10443 643 23 1 1 NHS 23 17725631 Silent SNP C C3N-00738_T 8930292 17725631 138315264 179 20104 YY2 0 . GRCh38 X 21856835 21856835 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.351G>T p.Gln117His p.Q117H ENST00000429584 1/1 206 188 18 262 262 0 strelka-varscan-mutect YY2,missense_variant,p.Gln117His,ENST00000429584,NM_206923.3;MBTPS2,intron_variant,,ENST00000365779,;MBTPS2,intron_variant,,ENST00000379484,NM_015884.3;MBTPS2,non_coding_transcript_exon_variant,,ENST00000465888,; T ENST00000429584 Transcript missense_variant 849/2741 351/1119 117/372 Q/H caG/caT 1 1 YY2 HGNC HGNC:31684 protein_coding YES CCDS14202.1 ENSP00000389381 O15391 UPI000006CE0D NM_206923.3 deleterious(0) 1/1 hmmpanther:PTHR14003,hmmpanther:PTHR14003:SF9,PIRSF_domain:PIRSF037113 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 21856835 21856835 G T 1 0 0 0 0 1 0 0 0 18070 933 33 2 2 YY2 23 21856835 Missense_Mutation SNP G C3N-00738_T 4131204 21856835 134184060 180 20105 LANCL3 0 . GRCh38 X 37572023 37572023 + Silent SNP C C A novel C3N-00738_T C3N-00738_N C C c.153C>A p.= p.A51A ENST00000378619 1/5 113 98 15 143 143 0 strelka-varscan-mutect LANCL3,synonymous_variant,p.=,ENST00000378621,NM_198511.2;LANCL3,synonymous_variant,p.=,ENST00000378619,NM_001170331.1;LANCL3,synonymous_variant,p.=,ENST00000614025,;RP5-972B16.2,intron_variant,,ENST00000465127,; A ENST00000378619 Transcript synonymous_variant 372/3063 153/1263 51/420 A gcC/gcA 1 1 LANCL3 HGNC HGNC:24767 protein_coding YES CCDS55398.1 ENSP00000367882 Q6ZV70 UPI000059DAED NM_001170331.1 1/5 hmmpanther:PTHR12736,hmmpanther:PTHR12736:SF12,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 37572023 37572023 C A 1 0 0 0 0 0 0 0 1 8532 610 22 2 2 LANCL3 23 37572023 Silent SNP C C3N-00738_T 15715188 37572023 118468872 181 20106 DGKK 0 . GRCh38 X 50376083 50376083 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.3355A>G p.Ile1119Val p.I1119V ENST00000611977 24/28 250 235 15 238 238 0 strelka-varscan-mutect DGKK,missense_variant,p.Ile1119Val,ENST00000611977,NM_001013742.3; C ENST00000611977 Transcript missense_variant 3415/7407 3355/3816 1119/1271 I/V Ata/Gta 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 tolerated(1) 24/28 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF33 MODERATE 1 SNV 1 1 PASS . . 0 202 6 0 0 0 0 0 -19.99999 0.9999995 1 1 1 0 C 3 2 64 50376083 50376083 T C 1 0 0 0 0 1 0 0 0 4278 1406 49 5 5 DGKK 23 50376083 Missense_Mutation SNP T C3N-00738_T 12804060 50376083 105664812 182 20107 DGKK 0 . GRCh38 X 50380012 50380012 + Missense_Mutation SNP T T C novel C3N-00738_T C3N-00738_N T T c.2723A>G p.Tyr908Cys p.Y908C ENST00000611977 19/28 226 209 17 274 274 0 strelka-mutect DGKK,missense_variant,p.Tyr908Cys,ENST00000611977,NM_001013742.3; C ENST00000611977 Transcript missense_variant 2783/7407 2723/3816 908/1271 Y/C tAc/tGc 1 -1 DGKK HGNC HGNC:32395 protein_coding YES CCDS75980.1 ENSP00000477515 Q5KSL6 UPI00004BA922 NM_001013742.3 tolerated(0.06) 19/28 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF33,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 50380012 50380012 T C 1 0 0 0 0 1 0 0 0 4278 1638 57 5 5 DGKK 23 50380012 Missense_Mutation SNP T C3N-00738_T 3929 50380012 105660883 183 20108 TAF1 0 . GRCh38 X 71378926 71378926 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.1315G>T p.Gly439Trp p.G439W ENST00000423759 8/39 315 279 36 364 364 0 strelka-varscan-mutect TAF1,missense_variant,p.Gly439Trp,ENST00000423759,NM_001286074.1;TAF1,missense_variant,p.Gly418Trp,ENST00000373790,NM_138923.3;TAF1,missense_variant,p.Gly439Trp,ENST00000276072,NM_004606.4;TAF1,downstream_gene_variant,,ENST00000483365,; T ENST00000423759 Transcript missense_variant 1391/7722 1315/5688 439/1895 G/W Ggg/Tgg 1 1 TAF1 HGNC HGNC:11535 protein_coding YES CCDS69783.1 ENSP00000406549 P21675 UPI000171708A NM_001286074.1 deleterious(0) 8/39 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 71378926 71378926 G T 1 0 0 0 0 1 0 0 0 15909 1348 47 2 2 TAF1 23 71378926 Missense_Mutation SNP G C3N-00738_T 20998914 71378926 84661969 184 20109 PGK1 0 . GRCh38 X 78113824 78113824 + Missense_Mutation SNP G G C novel C3N-00738_T C3N-00738_N G G c.197G>C p.Arg66Pro p.R66P ENST00000373316 3/11 361 333 28 496 495 1 strelka-varscan-mutect PGK1,missense_variant,p.Arg66Pro,ENST00000373316,NM_000291.3;PGK1,non_coding_transcript_exon_variant,,ENST00000491291,;PGK1,non_coding_transcript_exon_variant,,ENST00000477335,; C ENST00000373316 Transcript missense_variant 364/4887 197/1254 66/417 R/P cGg/cCg 1 1 PGK1 HGNC HGNC:8896 protein_coding YES CCDS14438.1 ENSP00000362413 P00558 V9HWF4 UPI00000727EE NM_000291.3 deleterious(0.01) 3/11 Gene3D:3.40.50.1260,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF12,Superfamily_domains:SSF53748 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 64 78113824 78113824 G C 1 0 0 0 0 1 0 0 0 11879 1116 39 4 4 PGK1 23 78113824 Missense_Mutation SNP G C3N-00738_T 6734898 78113824 77927071 185 20110 PABPC5 0 . GRCh38 X 91435929 91435929 + Missense_Mutation SNP G G T C3N-00738_T C3N-00738_N G G c.352G>T p.Asp118Tyr p.D118Y ENST00000312600 2/2 267 245 22 376 376 0 strelka-varscan-mutect PABPC5,missense_variant,p.Asp118Tyr,ENST00000312600,NM_080832.2;PABPC5,intron_variant,,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; T ENST00000312600 Transcript missense_variant 566/3221 352/1149 118/382 D/Y Gac/Tac COSM262716 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 deleterious(0) 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF407,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01628 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 91435929 91435929 G T 1 0 0 0 0 1 0 0 0 11445 942 33 2 2 PABPC5 23 91435929 Missense_Mutation SNP G C3N-00738_T 13322105 91435929 64604966 186 20111 PABPC5 0 . GRCh38 X 91436553 91436553 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.976G>T p.Gly326Trp p.G326W ENST00000312600 2/2 311 279 32 390 389 1 strelka-varscan-mutect PABPC5,missense_variant,p.Gly326Trp,ENST00000312600,NM_080832.2;PABPC5,missense_variant,p.Gly162Trp,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; T ENST00000312600 Transcript missense_variant 1190/3221 976/1149 326/382 G/W Ggg/Tgg 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 deleterious(0) 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF407,SMART_domains:SM00360,SMART_domains:SM00361,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01628 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 91436553 91436553 G T 1 0 0 0 0 1 0 0 0 11445 1348 47 2 2 PABPC5 23 91436553 Missense_Mutation SNP G C3N-00738_T 624 91436553 64604342 187 20112 PCDH19 0 . GRCh38 X 100406932 100406932 + Missense_Mutation SNP C C T novel C3N-00738_T C3N-00738_N C C c.1666G>A p.Val556Ile p.V556I ENST00000373034 1/6 441 404 37 570 570 0 strelka-varscan-mutect PCDH19,missense_variant,p.Val556Ile,ENST00000373034,NM_001184880.1;PCDH19,missense_variant,p.Val556Ile,ENST00000255531,NM_001105243.1;PCDH19,missense_variant,p.Val556Ile,ENST00000420881,NM_020766.2;PCDH19,upstream_gene_variant,,ENST00000636150,; T ENST00000373034 Transcript missense_variant 3342/9756 1666/3447 556/1148 V/I Gtc/Atc 1 -1 PCDH19 HGNC HGNC:14270 protein_coding YES CCDS55462.1 ENSP00000362125 Q8TAB3 UPI00001D7BCD NM_001184880.1 tolerated(0.19) 1/6 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF40,hmmpanther:PTHR24028,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 100406932 100406932 C T 1 0 0 0 0 1 0 0 0 11601 536 19 1 1 PCDH19 23 100406932 Missense_Mutation SNP C C3N-00738_T 8970379 100406932 55633963 188 20113 ARMCX4 0 . GRCh38 X 101489060 101489060 + Missense_Mutation SNP A A T novel C3N-00738_T C3N-00738_N A A c.471A>T p.Lys157Asn p.K157N ENST00000423738 2/2 167 151 16 226 225 1 strelka-varscan-mutect ARMCX4,missense_variant,p.Lys157Asn,ENST00000423738,NM_001256155.2;ARMCX4,missense_variant,p.Lys261Asn,ENST00000433011,;ARMCX4,missense_variant,p.Lys261Asn,ENST00000452188,;ARMCX4,missense_variant,p.Lys249Asn,ENST00000354842,;ARMCX4,missense_variant,p.Lys249Asn,ENST00000455331,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,; T ENST00000423738 Transcript missense_variant 673/7424 471/6873 157/2290 K/N aaA/aaT 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 tolerated(0.39) 2/2 hmmpanther:PTHR15712,hmmpanther:PTHR15712:SF21 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 101489060 101489060 A T 1 0 0 0 0 1 0 0 0 1102 11 1 4 4 ARMCX4 23 101489060 Missense_Mutation SNP A C3N-00738_T 1082128 101489060 54551835 189 20114 KIAA1210 0 . GRCh38 X 119089117 119089117 + Missense_Mutation SNP G G T rs199571562 C3N-00738_T C3N-00738_N G G c.2113C>A p.Gln705Lys p.Q705K ENST00000402510 11/14 246 228 18 395 395 0 strelka-varscan-mutect KIAA1210,missense_variant,p.Gln705Lys,ENST00000402510,NM_020721.1; T ENST00000402510 Transcript missense_variant 2113/7824 2113/5130 705/1709 Q/K Caa/Aaa rs199571562 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 tolerated(0.28) 11/14 MODERATE 1 SNV 5 1 PASS rs199571562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 119089117 119089117 G T 1 0 0 0 0 1 0 0 0 8106 1299 45 2 2 KIAA1210 23 119089117 Missense_Mutation SNP G C3N-00738_T 17600057 119089117 36951778 190 20115 TENM1 0 . GRCh38 X 124523441 124523441 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.2956C>A p.Pro986Thr p.P986T ENST00000422452 17/32 345 315 30 394 394 0 strelka-varscan-mutect TENM1,missense_variant,p.Pro986Thr,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Pro986Thr,ENST00000371130,NM_014253.3; T ENST00000422452 Transcript missense_variant 3020/12891 2956/8199 986/2732 P/T Cct/Act 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 17/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 64 124523441 124523441 G T 1 0 0 0 0 1 0 0 0 16171 1232 43 2 2 TENM1 23 124523441 Missense_Mutation SNP G C3N-00738_T 5434324 124523441 31517454 191 20116 PRRG3 0 . GRCh38 X 151700816 151700816 + Missense_Mutation SNP G G T novel C3N-00738_T C3N-00738_N G G c.479G>T p.Gly160Val p.G160V ENST00000370353 4/4 42 33 9 50 50 0 strelka-varscan-mutect PRRG3,missense_variant,p.Gly160Val,ENST00000370353,;PRRG3,missense_variant,p.Gly160Val,ENST00000538575,NM_024082.3;PRRG3,intron_variant,,ENST00000448324,;PRRG3,downstream_gene_variant,,ENST00000370354,;PRRG3,downstream_gene_variant,,ENST00000448726,; T ENST00000370353 Transcript missense_variant 869/5977 479/696 160/231 G/V gGg/gTg 1 1 PRRG3 HGNC HGNC:30798 protein_coding YES CCDS14699.1 ENSP00000359378 Q9BZD7 UPI00004578A5 deleterious(0.03) 4/4 hmmpanther:PTHR24251:SF12,hmmpanther:PTHR24251 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99923 1 1 1 1 0 T 3 4 64 151700816 151700816 G T 1 0 0 0 0 1 0 0 0 12753 1232 43 2 2 PRRG3 23 151700816 Missense_Mutation SNP G C3N-00738_T 27177375 151700816 4340079 192 20117 MAGEA4 0 . GRCh38 X 151923805 151923805 + Silent SNP C C A rs759371757 C3N-00738_T C3N-00738_N C C c.141C>A p.= p.V47V ENST00000360243 3/3 126 109 17 171 171 0 strelka-varscan-mutect MAGEA4,synonymous_variant,p.=,ENST00000360243,NM_001011550.1;MAGEA4,synonymous_variant,p.=,ENST00000370335,;MAGEA4,synonymous_variant,p.=,ENST00000370340,;MAGEA4,synonymous_variant,p.=,ENST00000393921,;MAGEA4,synonymous_variant,p.=,ENST00000276344,NM_001011548.1;MAGEA4,synonymous_variant,p.=,ENST00000393920,NM_002362.4,NM_001011549.1;MAGEA4,synonymous_variant,p.=,ENST00000416020,;MAGEA4,synonymous_variant,p.=,ENST00000431971,;MAGEA4,synonymous_variant,p.=,ENST00000441865,;MAGEA4,synonymous_variant,p.=,ENST00000457310,;MAGEA4,synonymous_variant,p.=,ENST00000430273,;MAGEA4,synonymous_variant,p.=,ENST00000425182,;MAGEA4,synonymous_variant,p.=,ENST00000448295,;MAGEA4,synonymous_variant,p.=,ENST00000431963,; A ENST00000360243 Transcript synonymous_variant 408/1773 141/954 47/317 V gtC/gtA rs759371757 1 1 MAGEA4 HGNC HGNC:6802 protein_coding YES CCDS14702.1 ENSP00000353379 P43358 A0A024RC12 UPI000013EA1F NM_001011550.1 3/3 hmmpanther:PTHR11736:SF48,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS rs759371757 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 64 151923805 151923805 C A 1 0 0 0 0 0 0 0 1 9084 842 30 2 2 MAGEA4 23 151923805 Silent SNP C C3N-00738_T 222989 151923805 4117090 193 20118 GABRE 0 . GRCh38 X 151962502 151962502 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.484A>T p.Arg162Trp p.R162W ENST00000370328 4/9 266 245 21 315 315 0 strelka-varscan-mutect GABRE,missense_variant,p.Arg162Trp,ENST00000370328,NM_004961.3;GABRE,upstream_gene_variant,,ENST00000385020,;GABRE,upstream_gene_variant,,ENST00000384889,;GABRE,upstream_gene_variant,,ENST00000462018,;GABRE,3_prime_UTR_variant,,ENST00000441219,;GABRE,non_coding_transcript_exon_variant,,ENST00000476016,;GABRE,non_coding_transcript_exon_variant,,ENST00000474932,;GABRE,upstream_gene_variant,,ENST00000486255,; A ENST00000370328 Transcript missense_variant 538/3152 484/1521 162/506 R/W Agg/Tgg 1 -1 GABRE HGNC HGNC:4085 protein_coding YES CCDS14703.1 ENSP00000359353 P78334 UPI00000307E6 NM_004961.3 deleterious(0) 4/9 hmmpanther:PTHR18945:SF397,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 151962502 151962502 T A 1 0 0 0 0 1 0 0 0 6041 1550 54 4 4 GABRE 23 151962502 Missense_Mutation SNP T C3N-00738_T 38697 151962502 4078393 194 20119 AVPR2 0 . GRCh38 X 153905943 153905943 + Missense_Mutation SNP T T A novel C3N-00738_T C3N-00738_N T T c.437T>A p.Leu146Gln p.L146Q ENST00000358927 3/4 616 554 62 686 686 0 strelka-varscan-mutect AVPR2,missense_variant,p.Leu146Gln,ENST00000358927,;AVPR2,missense_variant,p.Leu146Gln,ENST00000337474,NM_000054.4;AVPR2,missense_variant,p.Leu146Gln,ENST00000370049,NM_001146151.1;AVPR2,missense_variant,p.Leu146Gln,ENST00000430697,;ARHGAP4,downstream_gene_variant,,ENST00000370028,NM_001164741.1;ARHGAP4,downstream_gene_variant,,ENST00000350060,NM_001666.4;ARHGAP4,downstream_gene_variant,,ENST00000370016,;ARHGAP4,downstream_gene_variant,,ENST00000393721,;ARHGAP4,downstream_gene_variant,,ENST00000442172,;ARHGAP4,downstream_gene_variant,,ENST00000454164,;ARHGAP4,downstream_gene_variant,,ENST00000467421,;AVPR2,intron_variant,,ENST00000434679,;L1CAM,intron_variant,,ENST00000464967,;ARHGAP4,downstream_gene_variant,,ENST00000404127,;ARHGAP4,downstream_gene_variant,,ENST00000470209,;ARHGAP4,downstream_gene_variant,,ENST00000420383,;ARHGAP4,downstream_gene_variant,,ENST00000494302,;ARHGAP4,downstream_gene_variant,,ENST00000494397,;ARHGAP4,downstream_gene_variant,,ENST00000466928,;ARHGAP4,downstream_gene_variant,,ENST00000461739,; A ENST00000358927 Transcript missense_variant 646/1763 437/1116 146/371 L/Q cTg/cAg 1 1 AVPR2 HGNC HGNC:897 protein_coding YES CCDS14735.1 ENSP00000351805 P30518 UPI000005043B tolerated(0.51) 3/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF20,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00898 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 64 153905943 153905943 T A 1 0 0 0 0 1 0 0 0 1389 1580 55 4 4 AVPR2 23 153905943 Missense_Mutation SNP T C3N-00738_T 1943441 153905943 2134952 195 20120 MECP2 0 . GRCh38 X 154032319 154032319 + Missense_Mutation SNP G G T rs782601477 C3N-00738_T C3N-00738_N G G c.301C>A p.Arg101Ser p.R101S ENST00000453960 2/3 140 124 16 182 182 0 strelka-varscan-mutect MECP2,missense_variant,p.Arg89Ser,ENST00000303391,NM_004992.3;MECP2,missense_variant,p.Arg101Ser,ENST00000453960,NM_001110792.1;MECP2,missense_variant,p.Arg89Ser,ENST00000628176,;MECP2,missense_variant,p.Arg101Ser,ENST00000407218,;MECP2,missense_variant,p.Arg85Ser,ENST00000622433,;MECP2,missense_variant,p.Arg85Ser,ENST00000611468,;MECP2,downstream_gene_variant,,ENST00000415944,;MECP2,downstream_gene_variant,,ENST00000630151,;MECP2,upstream_gene_variant,,ENST00000637917,;MECP2,downstream_gene_variant,,ENST00000460227,;MECP2,downstream_gene_variant,,ENST00000488293,;MECP2,downstream_gene_variant,,ENST00000463644,;MECP2,downstream_gene_variant,,ENST00000626422,;MECP2,downstream_gene_variant,,ENST00000631210,;MECP2,downstream_gene_variant,,ENST00000625300,;MECP2,downstream_gene_variant,,ENST00000496908,;MECP2,downstream_gene_variant,,ENST00000637533,;MECP2,downstream_gene_variant,,ENST00000637791,;MECP2,3_prime_UTR_variant,,ENST00000369957,;MECP2,non_coding_transcript_exon_variant,,ENST00000486506,;MECP2,downstream_gene_variant,,ENST00000481807,; T ENST00000453960 Transcript missense_variant 400/1729 301/1497 101/498 R/S Cgt/Agt rs782601477 1 -1 MECP2 HGNC HGNC:6990 protein_coding YES CCDS48193.1 ENSP00000395535 P51608 A0A140VKC4 UPI0000253F1B NM_001110792.1 deleterious(0) 2/3 hmmpanther:PTHR15074,hmmpanther:PTHR15074:SF4,Gene3D:3.30.890.10,PIRSF_domain:PIRSF038006,Superfamily_domains:SSF54171 MODERATE 1 SNV 1 1 PASS rs782601477 . 0 203 7 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 64 154032319 154032319 G T 1 0 0 0 0 1 0 0 0 9362 1116 39 1 1 MECP2 23 154032319 Missense_Mutation SNP G C3N-00738_T 126376 154032319 2008576 196 20121 SLC2A5 0 . GRCh38 1 9040077 9040077 + Silent SNP C C T novel C3N-00959_T C3N-00959_N C C c.684G>A p.= p.A228A ENST00000377424 6/12 48 39 9 71 71 0 strelka-varscan-mutect SLC2A5,synonymous_variant,p.=,ENST00000377424,NM_003039.2;SLC2A5,downstream_gene_variant,,ENST00000377414,NM_001135585.1;SLC2A5,downstream_gene_variant,,ENST00000486632,;SLC2A5,downstream_gene_variant,,ENST00000474145,;SLC2A5,downstream_gene_variant,,ENST00000479813,;SLC2A5,downstream_gene_variant,,ENST00000487835,;SLC2A5,downstream_gene_variant,,ENST00000484798,;SLC2A5,upstream_gene_variant,,ENST00000487492,; T ENST00000377424 Transcript synonymous_variant 864/4165 684/1506 228/501 A gcG/gcA 1 -1 SLC2A5 HGNC HGNC:11010 protein_coding YES CCDS99.1 ENSP00000366641 P22732 UPI00000532AC NM_003039.2 6/12 PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF32,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00879,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99027 1 1 1 1 0 T 2 4 65 9040077 9040077 C T 1 0 0 0 0 0 0 0 1 14818 639 23 1 1 SLC2A5 1 9040077 Silent SNP C C3N-00959_T 9040077 239916345 1 20122 PADI4 0 . GRCh38 1 17354575 17354575 + Missense_Mutation SNP G G A novel C3N-00959_T C3N-00959_N G G c.1198G>A p.Gly400Ser p.G400S ENST00000375448 11/16 156 136 20 216 216 0 strelka-varscan-mutect PADI4,missense_variant,p.Gly400Ser,ENST00000375448,NM_012387.2;PADI4,non_coding_transcript_exon_variant,,ENST00000487048,;PADI4,non_coding_transcript_exon_variant,,ENST00000467001,; A ENST00000375448 Transcript missense_variant 1224/2267 1198/1992 400/663 G/S Ggt/Agt 1 1 PADI4 HGNC HGNC:18368 protein_coding YES CCDS180.1 ENSP00000364597 Q9UM07 UPI000013DFF1 NM_012387.2 tolerated(0.86) 11/16 Pfam_domain:PF03068,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF3,Superfamily_domains:SSF55909 MODERATE 1 SNV 1 1 PASS rs1168147339 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 17354575 17354575 G A 1 0 0 0 0 1 0 0 0 11458 1232 43 3 3 PADI4 1 17354575 Missense_Mutation SNP G C3N-00959_T 8314498 17354575 231601847 2 20123 DNM3 0 . GRCh38 1 172032421 172032421 + Silent SNP T T G novel C3N-00959_T C3N-00959_N T T c.609T>G p.= p.V203V ENST00000627582 5/21 131 96 35 158 158 0 strelka-varscan-mutect DNM3,synonymous_variant,p.=,ENST00000627582,NM_015569.4;DNM3,synonymous_variant,p.=,ENST00000367731,NM_001136127.2;DNM3,synonymous_variant,p.=,ENST00000520906,;DNM3,synonymous_variant,p.=,ENST00000355305,;DNM3,synonymous_variant,p.=,ENST00000367733,NM_001278252.1;DNM3,synonymous_variant,p.=,ENST00000523513,; G ENST00000627582 Transcript synonymous_variant 766/7625 609/2592 203/863 V gtT/gtG 1 1 DNM3 HGNC HGNC:29125 protein_coding YES CCDS53431.1 ENSP00000486701 Q9UQ16 UPI0000251D91 NM_015569.4 5/21 Gene3D:3.40.50.300,Pfam_domain:PF00350,Prints_domain:PR00195,PROSITE_profiles:PS51718,hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF54,SMART_domains:SM00053,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 65 172032421 172032421 T G 1 0 0 0 0 0 0 0 1 4486 1741 61 5 5 DNM3 1 172032421 Silent SNP T C3N-00959_T 154677846 172032421 76924001 3 20124 KCNK3 0 . GRCh38 2 26727708 26727717 + Frame_Shift_Del DEL TTCTGCATGT TTCTGCATGT - novel C3N-00959_T C3N-00959_N TTCTGCATGT TTCTGCATGT c.326_335delTCTGCATGTT p.Phe109SerfsTer25 p.F109Sfs*25 ENST00000302909 2/2 27 23 4 19 19 0 sindel-pindel KCNK3,frameshift_variant,p.Phe109SerfsTer25,ENST00000302909,NM_002246.2;KCNK3,5_prime_UTR_variant,,ENST00000620977,; - ENST00000302909 Transcript frameshift_variant 450-459/6162 325-334/1185 109-112/394 FCMF/X TTCTGCATGTtc/tc 1 1 KCNK3 HGNC HGNC:6278 protein_coding YES CCDS1727.1 ENSP00000306275 O14649 UPI00000422B1 NM_002246.2 2/2 Gene3D:1.10.287.70,Pfam_domain:PF07885,PIRSF_domain:PIRSF038061,Prints_domain:PR01333,hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF138,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 1 PASS . . 2 206 2 0 0 0 0 0 -12.03705 1 1 1 1 0 - 7 5 65 26727708 26727708 TTCTGCATGT - 1 0 1 0 1 0 0 0 0 7984 1725 60 0 0 KCNK3 2 26727708 Frame_Shift_Del DEL TTCTGCATGT C3N-00959_T 26727708 215465821 4 20125 CLHC1 0 . GRCh38 2 55175835 55175835 + Silent SNP A A G novel C3N-00959_T C3N-00959_N A A c.1716T>C p.= p.S572S ENST00000401408 13/13 171 117 54 149 149 0 strelka-varscan-mutect CLHC1,synonymous_variant,p.=,ENST00000401408,NM_152385.2;CLHC1,synonymous_variant,p.=,ENST00000407122,;CLHC1,synonymous_variant,p.=,ENST00000406076,NM_001135598.1;CLHC1,non_coding_transcript_exon_variant,,ENST00000494539,;CLHC1,downstream_gene_variant,,ENST00000487320,;CLHC1,3_prime_UTR_variant,,ENST00000428621,;CLHC1,downstream_gene_variant,,ENST00000411884,; G ENST00000401408 Transcript synonymous_variant 2062/2248 1716/1761 572/586 S tcT/tcC 1 -1 CLHC1 HGNC HGNC:26453 protein_coding YES CCDS33201.1 ENSP00000384869 Q8NHS4 UPI00004DEC65 NM_152385.2 13/13 PIRSF_domain:PIRSF037469,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF11 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 65 55175835 55175835 A G 1 0 0 0 0 0 0 0 1 3293 175 7 5 5 CLHC1 2 55175835 Silent SNP A C3N-00959_T 28448127 55175835 187017694 5 20126 KANSL3 0 . GRCh38 2 96610787 96610787 + Missense_Mutation SNP G G A novel C3N-00959_T C3N-00959_N G G c.1258C>T p.Arg420Trp p.R420W ENST00000431828 11/21 210 196 14 185 185 0 strelka-varscan-mutect KANSL3,missense_variant,p.Arg420Trp,ENST00000431828,NM_001115016.2;KANSL3,downstream_gene_variant,,ENST00000448075,;KANSL3,non_coding_transcript_exon_variant,,ENST00000487070,;KANSL3,downstream_gene_variant,,ENST00000464738,;KANSL3,missense_variant,p.Arg420Trp,ENST00000420155,;KANSL3,3_prime_UTR_variant,,ENST00000354204,;KANSL3,3_prime_UTR_variant,,ENST00000447759,;KANSL3,3_prime_UTR_variant,,ENST00000597150,;KANSL3,3_prime_UTR_variant,,ENST00000444759,;KANSL3,3_prime_UTR_variant,,ENST00000425656,;KANSL3,3_prime_UTR_variant,,ENST00000452268,;KANSL3,non_coding_transcript_exon_variant,,ENST00000488907,;KANSL3,upstream_gene_variant,,ENST00000476534,;KANSL3,downstream_gene_variant,,ENST00000451819,;KANSL3,downstream_gene_variant,,ENST00000418735,;KANSL3,downstream_gene_variant,,ENST00000416138,; A ENST00000431828 Transcript missense_variant 1335/5153 1258/2637 420/878 R/W Cgg/Tgg 1 -1 KANSL3 HGNC HGNC:25473 protein_coding YES CCDS46361.1 ENSP00000396749 Q9P2N6 UPI0000207C82 NM_001115016.2 deleterious(0.01) 11/21 hmmpanther:PTHR13136,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 96610787 96610787 G A 1 0 0 0 0 1 0 0 0 7892 1115 39 1 1 KANSL3 2 96610787 Missense_Mutation SNP G C3N-00959_T 41434952 96610787 145582742 6 20127 TTN 0 . GRCh38 2 178740294 178740295 + Frame_Shift_Ins INS - - T novel C3N-00959_T C3N-00959_N - - c.12938dupA p.Asn4313LysfsTer11 p.N4313Kfs*11 ENST00000589042 48/363 140 125 15 141 141 0 sindel-varindel-pindel TTN,frameshift_variant,p.Asn4313LysfsTer11,ENST00000589042,NM_001267550.2;TTN,frameshift_variant,p.Asn3996LysfsTer11,ENST00000591111,;TTN,frameshift_variant,p.Asn3996LysfsTer11,ENST00000615779,NM_001256850.1;TTN,frameshift_variant,p.Asn3950LysfsTer11,ENST00000460472,NM_003319.4;TTN,frameshift_variant,p.Asn4142LysfsTer11,ENST00000342175,NM_133437.4;TTN,frameshift_variant,p.Asn4075LysfsTer11,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000342992,NM_133378.4;TTN,downstream_gene_variant,,ENST00000360870,NM_133379.4;TTN-AS1,intron_variant,,ENST00000582847,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000627661,;TTN-AS1,intron_variant,,ENST00000590773,;TTN-AS1,intron_variant,,ENST00000631319,;TTN-AS1,upstream_gene_variant,,ENST00000578746,;TTN-AS1,downstream_gene_variant,,ENST00000625480,; T ENST00000589042 Transcript frameshift_variant 13163-13164/109224 12938-12939/107976 4313/35991 N/KX aat/aaAt 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 48/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 HIGH 1 insertion 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 65 178740294 178740294 - T 1 0 1 1 0 0 0 0 0 17245 214 8 0 0 TTN 2 178740294 Frame_Shift_Ins INS - C3N-00959_T 82129507 178740294 63453235 7 20128 MROH2A 0 . GRCh38 2 233798806 233798806 + Missense_Mutation SNP G G T novel C3N-00959_T C3N-00959_N G G c.1294G>T p.Ala432Ser p.A432S ENST00000610772 12/42 187 155 32 188 188 0 strelka-varscan-mutect MROH2A,missense_variant,p.Ala429Ser,ENST00000389758,;MROH2A,missense_variant,p.Ala432Ser,ENST00000610772,NM_001287395.1;MROH2A,downstream_gene_variant,,ENST00000480634,;MROH2A,non_coding_transcript_exon_variant,,ENST00000477506,; T ENST00000610772 Transcript missense_variant 1387/5324 1294/5067 432/1688 A/S Gct/Tct 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 tolerated(0.19) 12/42 Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 233798806 233798806 G T 1 0 0 0 0 1 0 0 0 9744 1203 42 2 2 MROH2A 2 233798806 Missense_Mutation SNP G C3N-00959_T 55058512 233798806 8394723 8 20129 SETD2 0 . GRCh38 3 47101479 47101479 + Missense_Mutation SNP T T C C3N-00959_T C3N-00959_N T T c.4994A>G p.Asp1665Gly p.D1665G ENST00000409792 8/21 91 86 5 157 157 0 strelka-varscan-mutect SETD2,missense_variant,p.Asp1665Gly,ENST00000409792,NM_014159.6;SETD2,missense_variant,p.Asp1299Gly,ENST00000445387,;SETD2,3_prime_UTR_variant,,ENST00000330022,;SETD2,3_prime_UTR_variant,,ENST00000431180,;SETD2,upstream_gene_variant,,ENST00000484689,; C ENST00000409792 Transcript missense_variant 5037/8142 4994/7695 1665/2564 D/G gAc/gGc COSM1660292,COSM1660293 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 deleterious(0) 8/21 PROSITE_profiles:PS50280,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF344,Gene3D:2.170.270.10,Pfam_domain:PF00856,SMART_domains:SM00317,Superfamily_domains:SSF82199 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -8.401963 0.9999994 1 1 1 0 C 3 2 65 47101479 47101479 T C 1 0 0 0 0 1 0 0 0 14409 1667 58 5 5 SETD2 3 47101479 Missense_Mutation SNP T C3N-00959_T 47101479 151194080 9 20130 SETD2 0 . GRCh38 3 47123840 47123841 + Frame_Shift_Ins INS - - T novel C3N-00959_T C3N-00959_N - - c.795dupA p.His266ThrfsTer8 p.H266Tfs*8 ENST00000409792 3/21 69 57 12 65 65 0 sindel-varindel-pindel SETD2,frameshift_variant,p.His266ThrfsTer8,ENST00000409792,NM_014159.6;SETD2,frameshift_variant,p.His222ThrfsTer8,ENST00000412450,;SETD2,frameshift_variant,p.His138ThrfsTer8,ENST00000330022,;SETD2,upstream_gene_variant,,ENST00000431180,;SETD2,upstream_gene_variant,,ENST00000445387,; T ENST00000409792 Transcript frameshift_variant 838-839/8142 795-796/7695 265-266/2564 -/X -/A 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 3/21 hmmpanther:PTHR22884:SF344,hmmpanther:PTHR22884 HIGH 1 insertion 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 65 47123840 47123840 - T 1 0 1 1 0 0 0 0 0 14409 1377 48 0 0 SETD2 3 47123840 Frame_Shift_Ins INS - C3N-00959_T 22361 47123840 151171719 10 20131 SMARCC1 0 . GRCh38 3 47675573 47675573 + Missense_Mutation SNP G G T novel C3N-00959_T C3N-00959_N G G c.1741C>A p.Gln581Lys p.Q581K ENST00000254480 18/28 143 117 26 169 169 0 strelka-varscan-mutect SMARCC1,missense_variant,p.Gln581Lys,ENST00000254480,NM_003074.3;SMARCC1,non_coding_transcript_exon_variant,,ENST00000425518,;SMARCC1,downstream_gene_variant,,ENST00000462198,;SMARCC1,non_coding_transcript_exon_variant,,ENST00000483847,;SMARCC1,downstream_gene_variant,,ENST00000485737,; T ENST00000254480 Transcript missense_variant 1861/6375 1741/3318 581/1105 Q/K Cag/Aag 1 -1 SMARCC1 HGNC HGNC:11104 protein_coding YES CCDS2758.1 ENSP00000254480 Q92922 UPI000013CE3B NM_003074.3 tolerated(0.14) 18/28 hmmpanther:PTHR12802,hmmpanther:PTHR12802:SF9 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 47675573 47675573 G T 1 0 0 0 0 1 0 0 0 15068 1386 48 2 2 SMARCC1 3 47675573 Missense_Mutation SNP G C3N-00959_T 551733 47675573 150619986 11 20132 UBE2QL1 0 . GRCh38 5 6491343 6491343 + Silent SNP C C T C3N-00959_T C3N-00959_N C C c.480C>T p.= p.D160D ENST00000399816 2/2 37 32 5 74 74 0 strelka-mutect UBE2QL1,synonymous_variant,p.=,ENST00000399816,NM_001145161.2; T ENST00000399816 Transcript synonymous_variant 751/4317 480/486 160/161 D gaC/gaT COSM165369 1 1 UBE2QL1 HGNC HGNC:37269 protein_coding YES CCDS47189.1 ENSP00000382713 A1L167 UPI000020BF29 NM_001145161.2 2/2 hmmpanther:PTHR24068:SF72,hmmpanther:PTHR24068 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -13.416 1 1 1 1 0 T 2 4 65 6491343 6491343 C T 1 0 0 0 0 0 0 0 1 17393 535 19 1 1 UBE2QL1 5 6491343 Silent SNP C C3N-00959_T 6491343 175046916 12 20133 PDZD2 0 . GRCh38 5 31799331 31799331 + Missense_Mutation SNP A A G novel C3N-00959_T C3N-00959_N A A c.83A>G p.Asp28Gly p.D28G ENST00000438447 2/25 127 113 14 117 117 0 strelka-varscan-mutect PDZD2,missense_variant,p.Asp28Gly,ENST00000438447,NM_178140.2;PDZD2,downstream_gene_variant,,ENST00000513910,;PDZD2,non_coding_transcript_exon_variant,,ENST00000502824,; G ENST00000438447 Transcript missense_variant 471/11704 83/8520 28/2839 D/G gAt/gGt 1 1 PDZD2 HGNC HGNC:18486 protein_coding YES CCDS34137.1 ENSP00000402033 O15018 A0A024RE15 UPI000069648B NM_178140.2 deleterious(0.04) 2/25 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 65 31799331 31799331 A G 1 0 0 0 0 1 0 0 0 11789 333 12 5 5 PDZD2 5 31799331 Missense_Mutation SNP A C3N-00959_T 25307988 31799331 149738928 13 20134 TENM2 0 . GRCh38 5 168118478 168118478 + Missense_Mutation SNP G G T novel C3N-00959_T C3N-00959_N G G c.2000G>T p.Cys667Phe p.C667F ENST00000518659 10/29 28 25 3 30 30 0 strelka-mutect TENM2,missense_variant,p.Cys546Phe,ENST00000519204,;TENM2,missense_variant,p.Cys667Phe,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Cys435Phe,ENST00000520394,;CTB-178M22.1,intron_variant,,ENST00000517408,; T ENST00000518659 Transcript missense_variant 2039/8550 2000/8325 667/2774 C/F tGt/tTt 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 10/29 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Gene3D:2.10.25.10,SMART_domains:SM00181,PD936484 MODERATE SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -9.478102 1 1 1 1 0 T 3 4 65 168118478 168118478 G T 1 0 0 0 0 1 0 0 0 16172 1377 48 2 2 TENM2 5 168118478 Missense_Mutation SNP G C3N-00959_T 136319147 168118478 13419781 14 20135 UNC5CL 0 . GRCh38 6 41031708 41031708 + Silent SNP G G A novel C3N-00959_T C3N-00959_N G G c.1092C>T p.= p.I364I ENST00000244565 6/9 149 124 25 232 232 0 strelka-varscan-mutect UNC5CL,synonymous_variant,p.=,ENST00000244565,NM_173561.2;UNC5CL,synonymous_variant,p.=,ENST00000373164,;UNC5CL,intron_variant,,ENST00000470102,;OARD1,downstream_gene_variant,,ENST00000482853,; A ENST00000244565 Transcript synonymous_variant 1209/3136 1092/1557 364/518 I atC/atT 1 -1 UNC5CL HGNC HGNC:21203 protein_coding YES CCDS4847.1 ENSP00000244565 Q8IV45 H8YHX0 UPI00001609DB NM_173561.2 6/9 hmmpanther:PTHR12582 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 65 41031708 41031708 G A 1 0 0 0 0 0 0 0 1 17518 1280 45 3 3 UNC5CL 6 41031708 Silent SNP G C3N-00959_T 41031708 129774271 15 20136 ZNF800 0 . GRCh38 7 127386088 127386090 + In_Frame_Del DEL AAT AAT - novel C3N-00959_T C3N-00959_N AAT AAT c.127_129delATT p.Ile43del p.I43del ENST00000393313 3/6 124 101 23 153 153 0 sindel-varindel-pindel ZNF800,inframe_deletion,p.Ile43del,ENST00000393313,;ZNF800,inframe_deletion,p.Ile43del,ENST00000265827,NM_176814.4;ZNF800,inframe_deletion,p.Ile43del,ENST00000393312,;ZNF800,inframe_deletion,p.Ile43del,ENST00000619291,;ZNF800,inframe_deletion,p.Ile43del,ENST00000434602,;ZNF800,inframe_deletion,p.Ile43del,ENST00000436992,;ZNF800,inframe_deletion,p.Ile43del,ENST00000439506,; - ENST00000393313 Transcript inframe_deletion 719-721/4358 127-129/1995 43/664 I/- ATT/- 1 -1 ZNF800 HGNC HGNC:27267 protein_coding YES CCDS5795.1 ENSP00000376989 Q2TB10 UPI000020FA03 3/6 hmmpanther:PTHR21020 MODERATE 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 65 127386088 127386088 AAT - 1 0 1 0 1 0 0 0 0 18754 242 9 0 0 ZNF800 7 127386088 In_Frame_Del DEL AAT C3N-00959_T 127386088 31959885 16 20137 COL22A1 0 . GRCh38 8 138607943 138607943 + Missense_Mutation SNP C C T C3N-00959_T C3N-00959_N C C c.4025G>A p.Gly1342Glu p.G1342E ENST00000303045 57/65 140 116 24 172 172 0 strelka-varscan-mutect COL22A1,missense_variant,p.Gly1342Glu,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Gly1035Glu,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,;COL22A1,non_coding_transcript_exon_variant,,ENST00000487854,; T ENST00000303045 Transcript missense_variant 4472/6346 4025/4881 1342/1626 G/E gGa/gAa COSM1096550 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 deleterious(0) 57/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 138607943 138607943 C T 1 0 0 0 0 1 0 0 0 3469 855 30 3 3 COL22A1 8 138607943 Missense_Mutation SNP C C3N-00959_T 138607943 6530693 17 20138 BNC2 0 . GRCh38 9 16435571 16435571 + Missense_Mutation SNP G G A novel C3N-00959_T C3N-00959_N G G c.2623C>T p.Arg875Cys p.R875C ENST00000380672 6/7 305 278 27 398 398 0 strelka-varscan-mutect BNC2,missense_variant,p.Arg875Cys,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Arg701Cys,ENST00000545497,;BNC2,missense_variant,p.Arg832Cys,ENST00000418777,;BNC2,missense_variant,p.Arg808Cys,ENST00000380667,;BNC2,missense_variant,p.Arg268Cys,ENST00000411752,;BNC2,downstream_gene_variant,,ENST00000380666,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,missense_variant,p.Arg875Cys,ENST00000484726,; A ENST00000380672 Transcript missense_variant 2681/12844 2623/3300 875/1099 R/C Cgc/Tgc 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 deleterious(0) 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021,SMART_domains:SM00355 MODERATE 1 SNV 2 1 PASS rs1290133928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 16435571 16435571 G A 1 0 0 0 0 1 0 0 0 1631 1058 37 1 1 BNC2 9 16435571 Missense_Mutation SNP G C3N-00959_T 16435571 121959146 18 20139 OLFM1 0 . GRCh38 9 135119534 135119534 + Missense_Mutation SNP C C T rs747137531 C3N-00959_T C3N-00959_N C C c.814C>T p.Arg272Cys p.R272C ENST00000371793 6/6 57 49 8 83 83 0 strelka-varscan-mutect OLFM1,missense_variant,p.Arg254Cys,ENST00000252854,NM_014279.4;OLFM1,missense_variant,p.Arg245Cys,ENST00000371796,NM_001282612.1;OLFM1,missense_variant,p.Arg272Cys,ENST00000371793,NM_001282611.1;OLFM1,missense_variant,p.Arg169Cys,ENST00000539877,;OLFM1,missense_variant,p.Pro96Leu,ENST00000545657,;OLFM1,non_coding_transcript_exon_variant,,ENST00000483042,; T ENST00000371793 Transcript missense_variant 1065/2444 814/1458 272/485 R/C Cgc/Tgc rs747137531,COSM4933017 1 1 OLFM1 HGNC HGNC:17187 protein_coding YES CCDS65184.1 ENSP00000360858 Q99784 UPI000013DB05 NM_001282611.1 deleterious(0) 6/6 PROSITE_profiles:PS51132,hmmpanther:PTHR23192:SF34,hmmpanther:PTHR23192,Pfam_domain:PF02191,SMART_domains:SM00284 0,1 MODERATE 1 SNV 3 0,1 1 PASS rs747137531 . 0 204 6 0 0 0 0 0 -18.52125 0.9999999 1 1 1 0 T 3 4 65 135119534 135119534 C T 1 0 0 0 0 1 0 0 0 10927 652 23 1 1 OLFM1 9 135119534 Missense_Mutation SNP C C3N-00959_T 118683963 135119534 3275183 19 20140 OLR1 0 . GRCh38 12 10160397 10160397 + Missense_Mutation SNP G G T novel C3N-00959_T C3N-00959_N G G c.630C>A p.Asn210Lys p.N210K ENST00000309539 5/6 194 158 36 248 248 0 strelka-varscan-mutect OLR1,missense_variant,p.Asn210Lys,ENST00000309539,NM_002543.3;OLR1,missense_variant,p.Pro164Thr,ENST00000432556,NM_001172632.1;OLR1,missense_variant,p.Pro60Thr,ENST00000543993,;OLR1,missense_variant,p.Asn157Lys,ENST00000539518,;OLR1,missense_variant,p.Asn106Lys,ENST00000538745,;OLR1,intron_variant,,ENST00000545927,NM_001172633.1;OLR1,intron_variant,,ENST00000544577,;OLR1,downstream_gene_variant,,ENST00000339968,;OLR1,downstream_gene_variant,,ENST00000538873,;OLR1,downstream_gene_variant,,ENST00000543414,;OLR1,non_coding_transcript_exon_variant,,ENST00000536989,; T ENST00000309539 Transcript missense_variant 691/2462 630/822 210/273 N/K aaC/aaA 1 -1 OLR1 HGNC HGNC:8133 protein_coding YES CCDS8618.1 ENSP00000309124 P78380 A0A024RAU0 UPI000004A917 NM_002543.3 tolerated(1) 5/6 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF146,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 10160397 10160397 G T 1 0 0 0 0 1 0 0 0 10938 1261 44 2 2 OLR1 12 10160397 Missense_Mutation SNP G C3N-00959_T 10160397 123114912 20 20141 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C A rs121913529 C3N-00959_T C3N-00959_N C C c.35G>T p.Gly12Val p.G12V ENST00000256078 2/6 295 246 49 337 337 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Val,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Val,ENST00000556131,;KRAS,missense_variant,p.Gly12Val,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Val,ENST00000557334,; A ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/V gGt/gTt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 25245350 25245350 C A 1 0 0 0 0 1 0 0 0 8318 507 18 2 2 KRAS 12 25245350 Missense_Mutation SNP C C3N-00959_T 15084953 25245350 108029959 21 20142 LTBP2 0 . GRCh38 14 74532493 74532493 + Silent SNP G G T novel C3N-00959_T C3N-00959_N G G c.1920C>A p.= p.T640T ENST00000261978 10/36 558 465 93 656 656 0 strelka-varscan-mutect LTBP2,synonymous_variant,p.=,ENST00000261978,NM_000428.2;LTBP2,synonymous_variant,p.=,ENST00000556690,;LTBP2,downstream_gene_variant,,ENST00000557425,;LTBP2,synonymous_variant,p.=,ENST00000553939,; T ENST00000261978 Transcript synonymous_variant 2307/8567 1920/5466 640/1821 T acC/acA 1 -1 LTBP2 HGNC HGNC:6715 protein_coding YES CCDS9831.1 ENSP00000261978 Q14767 UPI000013D239 NM_000428.2 10/36 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS00010,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF49,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 1 1 PASS rs1276655725 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 65 74532493 74532493 G T 1 0 0 0 0 0 0 0 1 8980 1335 47 2 2 LTBP2 14 74532493 Silent SNP G C3N-00959_T 74532493 32511225 22 20143 CDAN1 0 . GRCh38 15 42730692 42730692 + Missense_Mutation SNP G G A novel C3N-00959_T C3N-00959_N G G c.2080C>T p.Pro694Ser p.P694S ENST00000356231 14/28 268 235 33 364 364 0 strelka-varscan-mutect CDAN1,missense_variant,p.Pro694Ser,ENST00000356231,NM_138477.2;CTD-2036P10.6,downstream_gene_variant,,ENST00000617465,;CDAN1,missense_variant,p.Pro25Ser,ENST00000562465,; A ENST00000356231 Transcript missense_variant 2104/4637 2080/3684 694/1227 P/S Ccc/Tcc 1 -1 CDAN1 HGNC HGNC:1713 protein_coding YES CCDS32209.1 ENSP00000348564 Q8IWY9 UPI0000229BCB NM_138477.2 deleterious(0) 14/28 hmmpanther:PTHR28678 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 42730692 42730692 G A 1 0 0 0 0 1 0 0 0 2757 1203 42 3 3 CDAN1 15 42730692 Missense_Mutation SNP G C3N-00959_T 42730692 59260497 23 20144 ALOX12B 0 . GRCh38 17 8080705 8080705 + Silent SNP G G A rs763119821 C3N-00959_T C3N-00959_N G G c.603C>T p.= p.R201R ENST00000319144 5/15 339 273 66 458 458 0 strelka-varscan-mutect ALOX12B,synonymous_variant,p.=,ENST00000319144,NM_001139.2;AC129492.6,non_coding_transcript_exon_variant,,ENST00000399413,;ALOX12B,upstream_gene_variant,,ENST00000577351,;ALOX12B,upstream_gene_variant,,ENST00000583276,;ALOX12B,upstream_gene_variant,,ENST00000584116,; A ENST00000319144 Transcript synonymous_variant 864/2502 603/2106 201/701 R cgC/cgT rs763119821 1 -1 ALOX12B HGNC HGNC:430 protein_coding YES CCDS11129.1 ENSP00000315167 O75342 UPI000000D996 NM_001139.2 5/15 PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF40,Superfamily_domains:SSF48484 LOW 1 SNV 1 1 PASS rs763119821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 65 8080705 8080705 G A 1 0 0 0 0 0 0 0 1 637 958 34 3 3 ALOX12B 17 8080705 Silent SNP G C3N-00959_T 8080705 75176736 24 20145 ERBB2 0 . GRCh38 17 39716353 39716353 + Silent SNP T T G novel C3N-00959_T C3N-00959_N T T c.1566T>G p.= p.G522G ENST00000269571 13/27 36 24 12 86 86 0 strelka-varscan-mutect ERBB2,synonymous_variant,p.=,ENST00000584601,NM_001005862.2;ERBB2,synonymous_variant,p.=,ENST00000406381,;ERBB2,synonymous_variant,p.=,ENST00000269571,NM_004448.3;ERBB2,synonymous_variant,p.=,ENST00000541774,NM_001289936.1;ERBB2,synonymous_variant,p.=,ENST00000584450,NM_001289937.1;ERBB2,synonymous_variant,p.=,ENST00000445658,;ERBB2,synonymous_variant,p.=,ENST00000578199,NM_001289938.1;ERBB2,upstream_gene_variant,,ENST00000580074,;ERBB2,upstream_gene_variant,,ENST00000582818,;ERBB2,downstream_gene_variant,,ENST00000578502,;ERBB2,3_prime_UTR_variant,,ENST00000578373,;ERBB2,non_coding_transcript_exon_variant,,ENST00000583038,;ERBB2,non_coding_transcript_exon_variant,,ENST00000582788,;ERBB2,downstream_gene_variant,,ENST00000584908,;ERBB2,downstream_gene_variant,,ENST00000582648,;ERBB2,upstream_gene_variant,,ENST00000578630,;ERBB2,upstream_gene_variant,,ENST00000584684,; G ENST00000269571 Transcript synonymous_variant 1725/4545 1566/3768 522/1255 G ggT/ggG 1 1 ERBB2 HGNC HGNC:3430 protein_coding YES CCDS32642.1 ENSP00000269571 P04626 X5DNK3 UPI000003F55F NM_004448.3 13/27 hmmpanther:PTHR24416:SF137,hmmpanther:PTHR24416,Gene3D:2.10.220.10,Pfam_domain:PF14843,PIRSF_domain:PIRSF000619,SMART_domains:SM00261,Superfamily_domains:SSF57184,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 65 39716353 39716353 T G 1 0 0 0 0 0 0 0 1 5055 1654 58 5 5 ERBB2 17 39716353 Silent SNP T C3N-00959_T 31635648 39716353 43541088 25 20146 CCBE1 0 . GRCh38 18 59466792 59466792 + Missense_Mutation SNP C C T rs368065685 C3N-00959_T C3N-00959_N C C c.500G>A p.Arg167Gln p.R167Q ENST00000439986 5/11 406 344 62 464 463 1 strelka-varscan-mutect CCBE1,missense_variant,p.Arg167Gln,ENST00000439986,NM_133459.3;CCBE1,missense_variant,p.Arg97Gln,ENST00000398179,;CCBE1,5_prime_UTR_variant,,ENST00000589419,;RP11-27G24.3,downstream_gene_variant,,ENST00000589242,; T ENST00000439986 Transcript missense_variant 538/6227 500/1221 167/406 R/Q cGg/cAg rs368065685,COSM1389378,COSM5281125 1 -1 CCBE1 HGNC HGNC:29426 protein_coding YES CCDS32838.1 ENSP00000404464 Q6UXH8 UPI000004C616 NM_133459.3 tolerated(0.23) 5/11 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24034,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs368065685 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 59466792 59466792 C T 1 0 0 0 0 1 0 0 0 2433 652 23 1 1 CCBE1 18 59466792 Missense_Mutation SNP C C3N-00959_T 59466792 20906493 26 20147 LRP3 0 . GRCh38 19 33205593 33205593 + Missense_Mutation SNP C C T novel C3N-00959_T C3N-00959_N C C c.823C>T p.Arg275Cys p.R275C ENST00000253193 5/7 119 94 25 151 151 0 strelka-varscan-mutect LRP3,missense_variant,p.Arg275Cys,ENST00000253193,NM_002333.3;SLC7A10,downstream_gene_variant,,ENST00000253188,NM_019849.2;LRP3,downstream_gene_variant,,ENST00000592484,;CTD-2540B15.13,upstream_gene_variant,,ENST00000609744,;LRP3,non_coding_transcript_exon_variant,,ENST00000590278,;SLC7A10,downstream_gene_variant,,ENST00000590036,;SLC7A10,downstream_gene_variant,,ENST00000590490,;LRP3,downstream_gene_variant,,ENST00000590275,; T ENST00000253193 Transcript missense_variant 1025/3807 823/2313 275/770 R/C Cgc/Tgc 1 1 LRP3 HGNC HGNC:6695 protein_coding YES CCDS12430.1 ENSP00000253193 O75074 UPI0000047A9C NM_002333.3 tolerated(0.05) 5/7 PROSITE_profiles:PS01180,hmmpanther:PTHR10529:SF226,hmmpanther:PTHR10529,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs1457666753 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 65 33205593 33205593 C T 1 0 0 0 0 1 0 0 0 8853 884 31 1 1 LRP3 19 33205593 Missense_Mutation SNP C C3N-00959_T 33205593 25412023 27 20148 RYR1 0 . GRCh38 19 38525407 38525407 + Missense_Mutation SNP G G A rs376389988 C3N-00959_T C3N-00959_N G G c.10531G>A p.Val3511Met p.V3511M ENST00000359596 71/106 520 420 100 574 574 0 strelka-varscan-mutect RYR1,missense_variant,p.Val3506Met,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Val3511Met,ENST00000359596,NM_000540.2;RYR1,missense_variant,p.Val447Met,ENST00000599547,;RYR1,upstream_gene_variant,,ENST00000601514,;AC067969.1,downstream_gene_variant,,ENST00000597015,;RYR1,3_prime_UTR_variant,,ENST00000594335,;RYR1,downstream_gene_variant,,ENST00000600337,; A ENST00000359596 Transcript missense_variant 10531/15117 10531/15117 3511/5038 V/M Gtg/Atg rs376389988,COSM314956 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0) 71/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 0,1 MODERATE SNV 5 0,1 1 PASS rs376389988 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 65 38525407 38525407 G A 1 0 0 0 0 1 0 0 0 14028 1145 40 1 1 RYR1 19 38525407 Missense_Mutation SNP G C3N-00959_T 5319814 38525407 20092209 28 20149 CAMTA1 0 . GRCh38 1 7732559 7732559 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.3026G>T p.Gly1009Val p.G1009V ENST00000303635 12/23 98 75 23 129 128 1 strelka-varscan-mutect CAMTA1,missense_variant,p.Gly1009Val,ENST00000303635,NM_015215.3;CAMTA1,upstream_gene_variant,,ENST00000495233,; T ENST00000303635 Transcript missense_variant 3233/8444 3026/5022 1009/1673 G/V gGa/gTa 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 tolerated(0.13) 12/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 7732559 7732559 G T 1 0 0 0 0 1 0 0 0 2306 1174 41 2 2 CAMTA1 1 7732559 Missense_Mutation SNP G C3N-01016_T 7732559 241223863 1 20150 PRAMEF11 0 . GRCh38 1 12828765 12828765 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.25C>A p.Pro9Thr p.P9T ENST00000619922 2/4 321 253 68 315 313 2 strelka-varscan-mutect PRAMEF11,missense_variant,p.Pro9Thr,ENST00000619922,NM_001146344.2; T ENST00000619922 Transcript missense_variant 96/1845 25/1437 9/478 P/T Ccc/Acc 1 -1 PRAMEF11 HGNC HGNC:14086 protein_coding YES CCDS53268.2 ENSP00000480027 A0A087WW85 UPI0003EAF149 NM_001146344.2 deleterious(0.01) 2/4 hmmpanther:PTHR14224:SF19,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 12828765 12828765 G T 1 0 0 0 0 1 0 0 0 12556 1261 44 2 2 PRAMEF11 1 12828765 Missense_Mutation SNP G C3N-01016_T 5096206 12828765 236127657 2 20151 UBR4 0 . GRCh38 1 19179203 19179203 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2202G>T p.Gln734His p.Q734H ENST00000375254 18/106 71 57 14 69 69 0 strelka-varscan-mutect UBR4,missense_variant,p.Gln734His,ENST00000375254,NM_020765.2;UBR4,upstream_gene_variant,,ENST00000419533,; A ENST00000375254 Transcript missense_variant 2230/15906 2202/15552 734/5183 Q/H caG/caT 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 tolerated(1) 18/106 hmmpanther:PTHR21725 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 19179203 19179203 C A 1 0 0 0 0 1 0 0 0 17428 796 28 2 2 UBR4 1 19179203 Missense_Mutation SNP C C3N-01016_T 6350438 19179203 229777219 3 20152 EIF4G3 0 . GRCh38 1 20864593 20864593 + Silent SNP T T C novel C3N-01016_T C3N-01016_N T T c.2829A>G p.= p.E943E ENST00000400422 20/35 228 178 50 332 332 0 strelka-varscan-mutect EIF4G3,synonymous_variant,p.=,ENST00000602326,NM_001198802.1;EIF4G3,synonymous_variant,p.=,ENST00000264211,NM_003760.4;EIF4G3,synonymous_variant,p.=,ENST00000400422,NM_001198801.1;EIF4G3,synonymous_variant,p.=,ENST00000374935,;EIF4G3,synonymous_variant,p.=,ENST00000634879,; C ENST00000400422 Transcript synonymous_variant 3410/5762 2829/4866 943/1621 E gaA/gaG 1 -1 EIF4G3 HGNC HGNC:3298 protein_coding YES CCDS72723.1 ENSP00000383274 A0A0A0MSA7 UPI0000D4C1EC NM_001198801.1 20/35 Gene3D:1.25.40.180,Pfam_domain:PF02854,hmmpanther:PTHR23253,hmmpanther:PTHR23253:SF23,SMART_domains:SM00543,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 66 20864593 20864593 T C 1 0 0 0 0 0 0 0 1 4871 1606 56 5 5 EIF4G3 1 20864593 Silent SNP T C3N-01016_T 1685390 20864593 228091829 4 20153 COL16A1 0 . GRCh38 1 31661705 31661705 + Splice_Site SNP C C A rs774492040 C3N-01016_T C3N-01016_N C C c.3682-1G>T p.X1228_splice ENST00000373672 124 96 28 155 155 0 strelka-varscan-mutect COL16A1,splice_acceptor_variant,,ENST00000373672,NM_001856.3;COL16A1,splice_acceptor_variant,,ENST00000440437,;RP11-73M7.6,downstream_gene_variant,,ENST00000610043,;RP11-73M7.6,downstream_gene_variant,,ENST00000591929,;RP11-73M7.6,downstream_gene_variant,,ENST00000585413,;RP11-73M7.6,downstream_gene_variant,,ENST00000609549,;RP11-73M7.6,downstream_gene_variant,,ENST00000609033,;RP11-73M7.6,downstream_gene_variant,,ENST00000589462,;RP11-73M7.6,downstream_gene_variant,,ENST00000609625,;RP11-73M7.6,downstream_gene_variant,,ENST00000607926,;RP11-73M7.6,downstream_gene_variant,,ENST00000623786,;RP11-73M7.6,downstream_gene_variant,,ENST00000587445,;RP11-73M7.6,downstream_gene_variant,,ENST00000585660,;RP11-73M7.6,downstream_gene_variant,,ENST00000610216,;RP11-73M7.6,downstream_gene_variant,,ENST00000623791,;RP11-73M7.6,downstream_gene_variant,,ENST00000609373,;RP11-73M7.6,downstream_gene_variant,,ENST00000608246,;RP11-73M7.6,downstream_gene_variant,,ENST00000593188,;RP11-73M7.6,downstream_gene_variant,,ENST00000623425,;RP11-73M7.6,downstream_gene_variant,,ENST00000608888,;RP11-73M7.6,downstream_gene_variant,,ENST00000624388,;RP11-73M7.6,downstream_gene_variant,,ENST00000608332,;RP11-73M7.6,downstream_gene_variant,,ENST00000591592,;RP11-73M7.6,downstream_gene_variant,,ENST00000609338,;RP11-73M7.6,downstream_gene_variant,,ENST00000588288,;RP11-73M7.6,downstream_gene_variant,,ENST00000445166,;COL16A1,non_coding_transcript_exon_variant,,ENST00000466829,;COL16A1,downstream_gene_variant,,ENST00000468459,;COL16A1,splice_acceptor_variant,,ENST00000488128,;COL16A1,splice_acceptor_variant,,ENST00000488897,;COL16A1,splice_acceptor_variant,,ENST00000470799,;COL16A1,splice_acceptor_variant,,ENST00000482910,; A ENST00000373672 Transcript splice_acceptor_variant -/5736 3682/4815 1228/1604 rs774492040 1 -1 COL16A1 HGNC HGNC:2193 protein_coding YES CCDS41297.1 ENSP00000362776 Q07092 UPI0000203DD1 NM_001856.3 58/70 HIGH 1 SNV 5 1 PASS rs774492040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 66 31661705 31661705 C A 1 0 0 0 0 0 0 1 0 3461 695 24 2 2 COL16A1 1 31661705 Splice_Site SNP C C3N-01016_T 10797112 31661705 217294717 5 20154 NT5C1A 0 . GRCh38 1 39659252 39659252 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.976T>A p.Phe326Ile p.F326I ENST00000235628 6/6 669 156 513 199 198 1 strelka-varscan-mutect NT5C1A,missense_variant,p.Phe326Ile,ENST00000235628,NM_032526.2; T ENST00000235628 Transcript missense_variant 976/1107 976/1107 326/368 F/I Ttc/Atc 1 -1 NT5C1A HGNC HGNC:17819 protein_coding YES CCDS440.1 ENSP00000235628 Q9BXI3 UPI000004978A NM_032526.2 deleterious(0) 6/6 Pfam_domain:PF06189,hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 39659252 39659252 A T 1 0 0 0 0 1 0 0 0 10748 72 3 4 4 NT5C1A 1 39659252 Missense_Mutation SNP A C3N-01016_T 7997547 39659252 209297170 6 20155 FAM183A 0 . GRCh38 1 43156224 43156224 + Missense_Mutation SNP G G A novel C3N-01016_T C3N-01016_N G G c.316G>A p.Asp106Asn p.D106N ENST00000335282 4/4 518 482 36 218 218 0 strelka-varscan-mutect FAM183A,missense_variant,p.Asp78Asn,ENST00000410048,;FAM183A,missense_variant,p.Asp106Asn,ENST00000335282,NM_001101376.2;FAM183A,missense_variant,p.Asp122Asn,ENST00000409396,;FAM183A,non_coding_transcript_exon_variant,,ENST00000409337,;FAM183A,3_prime_UTR_variant,,ENST00000410025,;FAM183A,non_coding_transcript_exon_variant,,ENST00000481753,; A ENST00000335282 Transcript missense_variant 316/488 316/405 106/134 D/N Gac/Aac 1 1 FAM183A HGNC HGNC:34347 protein_coding YES CCDS44126.1 ENSP00000334415 A6NL82 UPI00015D7728 NM_001101376.2 deleterious(0) 4/4 Pfam_domain:PF14886,hmmpanther:PTHR33865,hmmpanther:PTHR33865:SF2 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 66 43156224 43156224 G A 1 0 0 0 0 1 0 0 0 5357 1290 45 3 3 FAM183A 1 43156224 Missense_Mutation SNP G C3N-01016_T 3496972 43156224 205800198 7 20156 MROH7 0 . GRCh38 1 54653231 54653231 + Missense_Mutation SNP G G T rs751192948 C3N-01016_T C3N-01016_N G G c.305G>T p.Gly102Val p.G102V ENST00000421030 3/24 320 177 143 252 252 0 strelka-varscan-mutect MROH7,missense_variant,p.Gly102Val,ENST00000421030,NM_001039464.3;MROH7,missense_variant,p.Gly102Val,ENST00000339553,;MROH7,missense_variant,p.Gly102Val,ENST00000395690,;MROH7,intron_variant,,ENST00000409996,NM_001291332.1;MROH7,non_coding_transcript_exon_variant,,ENST00000472987,;MROH7,intron_variant,,ENST00000478097,;MROH7-TTC4,missense_variant,p.Gly102Val,ENST00000425300,;MROH7-TTC4,missense_variant,p.Gly102Val,ENST00000414150,;MROH7-TTC4,missense_variant,p.Gly102Val,ENST00000606515,;MROH7,missense_variant,p.Gly102Val,ENST00000413188,;MROH7,missense_variant,p.Gly102Val,ENST00000422659,;MROH7,missense_variant,p.Gly102Val,ENST00000440047,;MROH7,missense_variant,p.Gly102Val,ENST00000438846,;MROH7,upstream_gene_variant,,ENST00000440217,; T ENST00000421030 Transcript missense_variant 590/4329 305/3972 102/1323 G/V gGt/gTt rs751192948 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 tolerated_low_confidence(0.43) 3/24 MODERATE 1 SNV 2 1 PASS rs751192948 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 54653231 54653231 G T 1 0 0 0 0 1 0 0 0 9747 1261 44 2 2 MROH7 1 54653231 Missense_Mutation SNP G C3N-01016_T 11497007 54653231 194303191 8 20157 USP1 0 . GRCh38 1 62445253 62445253 + Missense_Mutation SNP T T G novel C3N-01016_T C3N-01016_N T T c.1073T>G p.Leu358Arg p.L358R ENST00000339950 6/9 112 39 73 54 54 0 strelka-varscan-mutect USP1,missense_variant,p.Leu358Arg,ENST00000339950,NM_003368.4;USP1,missense_variant,p.Leu358Arg,ENST00000371146,NM_001017415.1,NM_001017416.1;USP1,downstream_gene_variant,,ENST00000452143,;USP1,downstream_gene_variant,,ENST00000442679,; G ENST00000339950 Transcript missense_variant 1888/3996 1073/2358 358/785 L/R cTg/cGg 1 1 USP1 HGNC HGNC:12607 protein_coding YES CCDS621.1 ENSP00000343526 O94782 UPI00001379D4 NM_003368.4 deleterious(0) 6/9 Pfam_domain:PF00443,PROSITE_profiles:PS50235 MODERATE 1 SNV 1 1 PASS rs35765018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 62445253 62445253 T G 1 0 0 0 0 1 0 0 0 17574 1580 55 5 5 USP1 1 62445253 Missense_Mutation SNP T C3N-01016_T 7792022 62445253 186511169 9 20158 SGIP1 0 . GRCh38 1 66733841 66733841 + Silent SNP C C A C3N-01016_T C3N-01016_N C C c.1992C>A p.= p.P664P ENST00000371037 21/25 84 69 15 84 84 0 strelka-varscan-mutect SGIP1,synonymous_variant,p.=,ENST00000371037,NM_032291.2;SGIP1,synonymous_variant,p.=,ENST00000371039,NM_001308203.1;SGIP1,synonymous_variant,p.=,ENST00000237247,;SGIP1,synonymous_variant,p.=,ENST00000435165,; A ENST00000371037 Transcript synonymous_variant 2069/7768 1992/2487 664/828 P ccC/ccA COSM1646189,COSM682346,COSM682347 1 1 SGIP1 HGNC HGNC:25412 protein_coding YES CCDS30744.1 ENSP00000360076 Q9BQI5 UPI000045891B NM_032291.2 21/25 Pfam_domain:PF10291,PROSITE_profiles:PS51072,hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF8 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 66733841 66733841 C A 1 0 0 0 0 0 0 0 1 14466 610 22 2 2 SGIP1 1 66733841 Silent SNP C C3N-01016_T 4288588 66733841 182222581 10 20159 LRRC7 0 . GRCh38 1 70053101 70053101 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.4072C>G p.Pro1358Ala p.P1358A ENST00000035383 21/25 126 107 19 149 149 0 strelka-varscan-mutect LRRC7,missense_variant,p.Pro1316Ala,ENST00000310961,;LRRC7,missense_variant,p.Pro1358Ala,ENST00000035383,NM_020794.2;LRRC7,missense_variant,p.Pro642Ala,ENST00000415775,; G ENST00000035383 Transcript missense_variant 4102/5000 4072/4614 1358/1537 P/A Cca/Gca 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious(0.05) 21/25 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 70053101 70053101 C G 1 0 0 0 0 1 0 0 0 8916 855 30 4 4 LRRC7 1 70053101 Missense_Mutation SNP C C3N-01016_T 3319260 70053101 178903321 11 20160 HFM1 0 . GRCh38 1 91378146 91378146 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.1274T>C p.Leu425Pro p.L425P ENST00000370425 11/39 171 92 79 123 123 0 strelka-varscan-mutect HFM1,missense_variant,p.Leu425Pro,ENST00000370425,NM_001017975.4;HFM1,downstream_gene_variant,,ENST00000448819,;HFM1,non_coding_transcript_exon_variant,,ENST00000481900,;HFM1,non_coding_transcript_exon_variant,,ENST00000488023,; G ENST00000370425 Transcript missense_variant 1373/4931 1274/4308 425/1435 L/P cTt/cCt 1 -1 HFM1 HGNC HGNC:20193 protein_coding YES CCDS30769.2 ENSP00000359454 A2PYH4 UPI0000F51F79 NM_001017975.4 deleterious(0) 11/39 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 91378146 91378146 A G 1 0 0 0 0 1 0 0 0 6967 72 3 5 5 HFM1 1 91378146 Missense_Mutation SNP A C3N-01016_T 21325045 91378146 157578276 12 20161 COL11A1 0 . GRCh38 1 102965512 102965512 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2891G>T p.Gly964Val p.G964V ENST00000370096 38/67 270 216 54 360 360 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly976Val,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly964Val,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly925Val,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly848Val,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,;COL11A1,upstream_gene_variant,,ENST00000465209,; A ENST00000370096 Transcript missense_variant 3204/7286 2891/5421 964/1806 G/V gGg/gTg 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 38/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 102965512 102965512 C A 1 0 0 0 0 1 0 0 0 3455 623 22 2 2 COL11A1 1 102965512 Missense_Mutation SNP C C3N-01016_T 11587366 102965512 145990910 13 20162 AMPD1 0 . GRCh38 1 114679585 114679585 + Nonsense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.990C>A p.Cys330Ter p.C330* ENST00000520113 7/16 338 214 124 346 346 0 strelka-varscan-mutect AMPD1,stop_gained,p.Cys326Ter,ENST00000369538,NM_001172626.1;AMPD1,stop_gained,p.Cys330Ter,ENST00000520113,NM_000036.2;AMPD1,3_prime_UTR_variant,,ENST00000637080,;AMPD1,downstream_gene_variant,,ENST00000485564,; T ENST00000520113 Transcript stop_gained 1006/2375 990/2343 330/780 C/* tgC/tgA 1 -1 AMPD1 HGNC HGNC:468 protein_coding YES CCDS876.2 ENSP00000430075 P23109 UPI0000470A27 NM_000036.2 7/16 Gene3D:3.20.20.140,Pfam_domain:PF00962,PIRSF_domain:PIRSF001251,hmmpanther:PTHR11359,hmmpanther:PTHR11359:SF1,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR01429 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 114679585 114679585 G T 1 0 0 0 0 0 1 0 0 683 1311 46 2 2 AMPD1 1 114679585 Nonsense_Mutation SNP G C3N-01016_T 11714073 114679585 134276837 14 20163 NBPF15 0 . GRCh38 1 144426319 144426319 + Nonsense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1397C>A p.Ser466Ter p.S466* ENST00000577412 17/21 175 133 42 122 121 1 strelka-varscan-mutect NBPF15,stop_gained,p.Ser466Ter,ENST00000577412,NM_001170755.2;NBPF15,stop_gained,p.Ser466Ter,ENST00000488031,;NBPF15,stop_gained,p.Ser466Ter,ENST00000581897,NM_173638.4;NBPF15,non_coding_transcript_exon_variant,,ENST00000584793,; T ENST00000577412 Transcript stop_gained 2464/4707 1397/2013 466/670 S/* tCa/tAa 1 -1 NBPF15 HGNC HGNC:28791 protein_coding YES CCDS72852.1 ENSP00000462600 Q8N660 UPI000013D89F NM_001170755.2 17/21 Pfam_domain:PF06758,PROSITE_profiles:PS51316,hmmpanther:PTHR14199,hmmpanther:PTHR14199:SF20,SMART_domains:SM01148 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 144426319 144426319 G T 1 0 0 0 0 0 1 0 0 10208 1294 45 2 2 NBPF15 1 144426319 Nonsense_Mutation SNP G C3N-01016_T 29746734 144426319 104530103 15 20164 FAM72D 0 . GRCh38 1 145103129 145103129 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.353C>A p.Thr118Lys p.T118K ENST00000400889 3/4 79 51 28 51 51 0 strelka-varscan-mutect FAM72D,missense_variant,p.Thr118Lys,ENST00000400889,NM_207418.2; A ENST00000400889 Transcript missense_variant,splice_region_variant 1201/2397 353/450 118/149 T/K aCa/aAa 1 1 FAM72D HGNC HGNC:33593 protein_coding YES CCDS72855.1 ENSP00000383682 Q6L9T8 UPI0000252280 NM_207418.2 tolerated(0.18) 3/4 Pfam_domain:PF14976,hmmpanther:PTHR31841 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 66 145103129 145103129 C A 1 0 0 0 0 1 0 0 0 5482 492 17 2 2 FAM72D 1 145103129 Missense_Mutation SNP C C3N-01016_T 676810 145103129 103853293 16 20165 SV2A 0 . GRCh38 1 149913707 149913707 + Nonsense_Mutation SNP G G T rs782071934 C3N-01016_T C3N-01016_N G G c.134C>A p.Ser45Ter p.S45* ENST00000369146 2/13 255 165 90 198 198 0 strelka-varscan-mutect SV2A,stop_gained,p.Ser45Ter,ENST00000369146,NM_014849.4;SV2A,stop_gained,p.Ser45Ter,ENST00000369145,; T ENST00000369146 Transcript stop_gained 625/4416 134/2229 45/742 S/* tCg/tAg rs782071934,COSM137782 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 2/13 Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR01299 0,1 HIGH 1 SNV 1 0,1 1 PASS rs782071934 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 149913707 149913707 G T 1 0 0 0 0 0 1 0 0 15801 1059 37 1 1 SV2A 1 149913707 Nonsense_Mutation SNP G C3N-01016_T 4810578 149913707 99042715 17 20166 TUFT1 0 . GRCh38 1 151562122 151562122 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.92A>T p.Gln31Leu p.Q31L ENST00000368849 2/13 135 121 14 103 103 0 strelka-varscan-mutect TUFT1,missense_variant,p.Gln31Leu,ENST00000368849,NM_020127.2,NM_001301317.1;TUFT1,intron_variant,,ENST00000368848,NM_001126337.1;TUFT1,intron_variant,,ENST00000392712,;TUFT1,intron_variant,,ENST00000353024,;RP11-74C1.4,downstream_gene_variant,,ENST00000434112,;TUFT1,non_coding_transcript_exon_variant,,ENST00000498606,;TUFT1,upstream_gene_variant,,ENST00000461859,;TUFT1,upstream_gene_variant,,ENST00000490156,;RP11-74C1.2,downstream_gene_variant,,ENST00000452587,; T ENST00000368849 Transcript missense_variant 154/3111 92/1173 31/390 Q/L cAg/cTg 1 1 TUFT1 HGNC HGNC:12422 protein_coding YES CCDS1000.1 ENSP00000357842 Q9NNX1 UPI0000037BFA NM_020127.2,NM_001301317.1 deleterious(0.02) 2/13 hmmpanther:PTHR23171:SF4,hmmpanther:PTHR23171 MODERATE 1 SNV 1 1 PASS rs1048610386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 151562122 151562122 A T 1 0 0 0 0 1 0 0 0 17282 188 7 4 4 TUFT1 1 151562122 Missense_Mutation SNP A C3N-01016_T 1648415 151562122 97394300 18 20167 FLG 0 . GRCh38 1 152308041 152308041 + Missense_Mutation SNP G G T rs750002465 C3N-01016_T C3N-01016_N G G c.6845C>A p.Pro2282His p.P2282H ENST00000368799 3/3 1053 780 273 661 658 3 strelka-varscan-mutect FLG,missense_variant,p.Pro2282His,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 6881/12747 6845/12186 2282/4061 P/H cCc/cAc rs750002465 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.01) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS rs750002465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 152308041 152308041 G T 1 0 0 0 0 1 0 0 0 5784 1232 43 2 2 FLG 1 152308041 Missense_Mutation SNP G C3N-01016_T 745919 152308041 96648381 19 20168 LCE1A 0 . GRCh38 1 152827514 152827514 + Silent SNP C C T novel C3N-01016_T C3N-01016_N C C c.42C>T p.= p.P14P ENST00000335123 1/1 124 72 52 109 109 0 strelka-varscan-mutect LCE1A,synonymous_variant,p.=,ENST00000335123,NM_178348.2; T ENST00000335123 Transcript synonymous_variant 42/422 42/333 14/110 P ccC/ccT 1 1 LCE1A HGNC HGNC:29459 protein_coding YES CCDS1028.1 ENSP00000334869 Q5T7P2 UPI0000192766 NM_178348.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23263,Prints_domain:PR00021 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 152827514 152827514 C T 1 0 0 0 0 0 0 0 1 8564 581 21 3 3 LCE1A 1 152827514 Silent SNP C C3N-01016_T 519473 152827514 96128908 20 20169 LOR 0 . GRCh38 1 153261381 153261383 + In_Frame_Del DEL CTC CTC - novel C3N-01016_T C3N-01016_N CTC CTC c.436_438delTCC p.Ser146del p.S146del ENST00000368742 2/2 218 186 32 159 159 0 sindel-varindel-pindel LOR,inframe_deletion,p.Ser146del,ENST00000368742,NM_000427.2; - ENST00000368742 Transcript inframe_deletion 489-491/1230 432-434/939 144-145/312 FS/F ttCTCc/ttc 1 1 LOR HGNC HGNC:6663 protein_coding YES CCDS30870.1 ENSP00000357731 P23490 UPI0000470BBD NM_000427.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR39228,Pfam_domain:PF15847,Prints_domain:PR01228 MODERATE 1 deletion 1 4 1 PASS . . 0 201 0 8 0 0 0 0 -20 0.9900432 1 1 1 0 - 7 5 66 153261381 153261381 CTC - 1 0 1 0 1 0 0 0 0 8799 912 32 0 0 LOR 1 153261381 In_Frame_Del DEL CTC C3N-01016_T 433867 153261381 95695041 21 20170 TDRD10 0 . GRCh38 1 154544431 154544431 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.711G>A p.= p.Q237Q ENST00000368480 10/12 233 219 14 171 171 0 strelka-mutect TDRD10,synonymous_variant,p.=,ENST00000368482,NM_182499.3;TDRD10,synonymous_variant,p.=,ENST00000368480,NM_001098475.1;UBE2Q1,downstream_gene_variant,,ENST00000292211,NM_017582.6;TDRD10,non_coding_transcript_exon_variant,,ENST00000479937,;TDRD10,non_coding_transcript_exon_variant,,ENST00000462871,;TDRD10,intron_variant,,ENST00000468714,; A ENST00000368480 Transcript synonymous_variant 796/1776 711/1101 237/366 Q caG/caA 1 1 TDRD10 HGNC HGNC:25316 protein_coding YES CCDS41406.1 ENSP00000357465 Q5VZ19 UPI0001533DB6 NM_001098475.1 10/12 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF12,Gene3D:2.30.30.140,Pfam_domain:PF00567,Superfamily_domains:SSF63748 LOW SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -16.90886 0.9999995 1 1 1 0 A 2 1 66 154544431 154544431 G A 1 0 0 0 0 0 0 0 1 16139 962 34 3 3 TDRD10 1 154544431 Silent SNP G C3N-01016_T 1283050 154544431 94411991 22 20171 ADAM15 0 . GRCh38 1 155054438 155054438 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.544A>T p.Ser182Cys p.S182C ENST00000356955 6/23 94 66 28 65 65 0 strelka-varscan-mutect ADAM15,missense_variant,p.Ser182Cys,ENST00000356955,NM_207197.2;ADAM15,missense_variant,p.Ser182Cys,ENST00000449910,NM_207196.2;ADAM15,missense_variant,p.Ser182Cys,ENST00000355956,NM_207194.2;ADAM15,missense_variant,p.Ser182Cys,ENST00000359280,NM_207195.2;ADAM15,missense_variant,p.Ser182Cys,ENST00000368412,NM_001261465.1;ADAM15,missense_variant,p.Ser182Cys,ENST00000271836,NM_003815.4;ADAM15,missense_variant,p.Ser182Cys,ENST00000360674,NM_207191.2;ADAM15,missense_variant,p.Ser192Cys,ENST00000531455,NM_001261464.1;ADAM15,missense_variant,p.Ser166Cys,ENST00000447332,NM_001261466.1;ADAM15,intron_variant,,ENST00000368413,;DCST1,downstream_gene_variant,,ENST00000295542,NM_152494.3;DCST1,downstream_gene_variant,,ENST00000423025,NM_001143687.2;ADAM15,non_coding_transcript_exon_variant,,ENST00000472434,;ADAM15,non_coding_transcript_exon_variant,,ENST00000473905,;ADAM15,non_coding_transcript_exon_variant,,ENST00000487956,;ADAM15,non_coding_transcript_exon_variant,,ENST00000480331,;ADAM15,upstream_gene_variant,,ENST00000461234,;ADAM15,upstream_gene_variant,,ENST00000474709,;ADAM15,downstream_gene_variant,,ENST00000485346,;ADAM15,downstream_gene_variant,,ENST00000531831,;ADAM15,downstream_gene_variant,,ENST00000533732,;ADAM15,downstream_gene_variant,,ENST00000531703,;ADAM15,upstream_gene_variant,,ENST00000462116,;ADAM15,upstream_gene_variant,,ENST00000470779,;ADAM15,downstream_gene_variant,,ENST00000477533,;ADAM15,missense_variant,p.Ser182Cys,ENST00000526491,;ADAM15,missense_variant,p.Ser182Cys,ENST00000529473,;ADAM15,non_coding_transcript_exon_variant,,ENST00000527418,;ADAM15,non_coding_transcript_exon_variant,,ENST00000461564,;ADAM15,upstream_gene_variant,,ENST00000498481,;ADAM15,upstream_gene_variant,,ENST00000534019,;ADAM15,upstream_gene_variant,,ENST00000525020,; T ENST00000356955 Transcript missense_variant 645/2949 544/2592 182/863 S/C Agc/Tgc 1 1 ADAM15 HGNC HGNC:193 protein_coding YES CCDS1087.1 ENSP00000349436 Q13444 UPI000035CC78 NM_207197.2 deleterious(0.01) 6/23 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF130 MODERATE 1 SNV 1 1 PASS rs1253110550 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 155054438 155054438 A T 1 0 0 0 0 1 0 0 0 281 304 11 4 4 ADAM15 1 155054438 Missense_Mutation SNP A C3N-01016_T 510007 155054438 93901984 23 20172 INSRR 0 . GRCh38 1 156858588 156858588 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.34T>A p.Cys12Ser p.C12S ENST00000368195 1/22 307 197 110 293 293 0 strelka-varscan-mutect INSRR,missense_variant,p.Cys12Ser,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,upstream_gene_variant,,ENST00000368196,NM_001012331.1;NTRK1,upstream_gene_variant,,ENST00000358660,;NTRK1,upstream_gene_variant,,ENST00000524377,NM_002529.3;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,;NTRK1,upstream_gene_variant,,ENST00000533630,; T ENST00000368195 Transcript missense_variant 431/5101 34/3894 12/1297 C/S Tgc/Agc 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 tolerated(0.32) 1/22 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24416:SF338,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620 MODERATE SNV 2 1 PASS rs1312207505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 156858588 156858588 A T 1 0 0 0 0 1 0 0 0 7676 217 8 4 4 INSRR 1 156858588 Missense_Mutation SNP A C3N-01016_T 1804150 156858588 92097834 24 20173 LRRC71 0 . GRCh38 1 156932014 156932014 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1428C>A p.His476Gln p.H476Q ENST00000337428 13/15 271 185 86 179 179 0 strelka-varscan-mutect LRRC71,missense_variant,p.His476Gln,ENST00000337428,NM_144702.2;ARHGEF11,downstream_gene_variant,,ENST00000368194,NM_198236.2;ARHGEF11,downstream_gene_variant,,ENST00000361409,NM_014784.3;MIR765,downstream_gene_variant,,ENST00000390226,;LRRC71,non_coding_transcript_exon_variant,,ENST00000490146,;LRRC71,intron_variant,,ENST00000476550,;ARHGEF11,downstream_gene_variant,,ENST00000487682,;ARHGEF11,downstream_gene_variant,,ENST00000492592,;LRRC71,upstream_gene_variant,,ENST00000472465,; A ENST00000337428 Transcript missense_variant 1582/1959 1428/1680 476/559 H/Q caC/caA 1 1 LRRC71 HGNC HGNC:26556 protein_coding YES CCDS44249.1 ENSP00000336661 Q8N4P6 UPI00000719B9 NM_144702.2 deleterious(0.01) 13/15 Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF147,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 156932014 156932014 C A 1 0 0 0 0 1 0 0 0 8918 506 18 2 2 LRRC71 1 156932014 Missense_Mutation SNP C C3N-01016_T 73426 156932014 92024408 25 20174 FCRL4 0 . GRCh38 1 157587402 157587402 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.721A>T p.Ser241Cys p.S241C ENST00000271532 5/12 605 459 146 435 435 0 strelka-varscan-mutect FCRL4,missense_variant,p.Ser241Cys,ENST00000271532,NM_031282.2;FCRL4,non_coding_transcript_exon_variant,,ENST00000448509,; A ENST00000271532 Transcript missense_variant 857/3459 721/1548 241/515 S/C Agc/Tgc 1 -1 FCRL4 HGNC HGNC:18507 protein_coding YES CCDS1166.1 ENSP00000271532 Q96PJ5 UPI000006E26B NM_031282.2 deleterious(0) 5/12 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF59,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 157587402 157587402 T A 1 0 0 0 0 1 0 0 0 5659 1551 54 4 4 FCRL4 1 157587402 Missense_Mutation SNP T C3N-01016_T 655388 157587402 91369020 26 20175 KIRREL 0 . GRCh38 1 158091430 158091430 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1345G>T p.Gly449Cys p.G449C ENST00000359209 11/15 353 268 85 233 233 0 strelka-varscan-mutect KIRREL,missense_variant,p.Gly349Cys,ENST00000368173,NM_001286349.1;KIRREL,missense_variant,p.Gly263Cys,ENST00000368172,;KIRREL,missense_variant,p.Gly285Cys,ENST00000360089,;KIRREL,missense_variant,p.Gly449Cys,ENST00000359209,NM_018240.6; T ENST00000359209 Transcript missense_variant 1412/2874 1345/2274 449/757 G/C Ggc/Tgc 1 1 KIRREL HGNC HGNC:15734 protein_coding YES CCDS1172.2 ENSP00000352138 Q96J84 UPI0000443FBD NM_018240.6 deleterious(0) 11/15 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF14,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 158091430 158091430 G T 1 0 0 0 0 1 0 0 0 8188 1000 35 2 2 KIRREL 1 158091430 Missense_Mutation SNP G C3N-01016_T 504028 158091430 90864992 27 20176 LY9 0 . GRCh38 1 160823781 160823781 + Silent SNP A A G novel C3N-01016_T C3N-01016_N A A c.1815A>G p.= p.Q605Q ENST00000263285 8/10 145 106 39 53 53 0 strelka-varscan-mutect LY9,synonymous_variant,p.=,ENST00000368037,NM_001261456.1;LY9,synonymous_variant,p.=,ENST00000263285,NM_002348.3;LY9,synonymous_variant,p.=,ENST00000392203,NM_001261457.1;LY9,synonymous_variant,p.=,ENST00000368035,; G ENST00000263285 Transcript synonymous_variant 1845/2443 1815/1968 605/655 Q caA/caG 1 1 LY9 HGNC HGNC:6730 protein_coding YES CCDS30916.1 ENSP00000263285 Q9HBG7 UPI00001416AF NM_002348.3 8/10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 66 160823781 160823781 A G 1 0 0 0 0 0 0 0 1 9012 69 3 5 5 LY9 1 160823781 Silent SNP A C3N-01016_T 2732351 160823781 88132641 28 20177 UHMK1 0 . GRCh38 1 162500912 162500912 + Splice_Site SNP G G T novel C3N-01016_T C3N-01016_N G G c.562-1G>T p.X188_splice ENST00000489294 94 72 22 58 58 0 strelka-varscan-mutect UHMK1,splice_acceptor_variant,,ENST00000489294,NM_175866.4;UHMK1,splice_acceptor_variant,,ENST00000538489,NM_144624.2;UHMK1,splice_acceptor_variant,,ENST00000545294,NM_001184763.1;UHMK1,non_coding_transcript_exon_variant,,ENST00000282169,; T ENST00000489294 Transcript splice_acceptor_variant -/8478 562/1260 188/419 1 1 UHMK1 HGNC HGNC:19683 protein_coding YES CCDS1239.1 ENSP00000420270 Q8TAS1 UPI000000DCCA NM_175866.4 2/7 HIGH 1 SNV 1 1 PASS . . 0 192 17 0 0 0 0 0 -20 0.9995129 1 1 1 0 T 5 4 66 162500912 162500912 G T 1 0 0 0 0 0 0 1 0 17490 1014 35 2 2 UHMK1 1 162500912 Splice_Site SNP G C3N-01016_T 1677131 162500912 86455510 29 20178 DUSP27 0 . GRCh38 1 167126935 167126935 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.1804A>T p.Ser602Cys p.S602C ENST00000361200 6/6 77 47 30 43 43 0 strelka-varscan-mutect DUSP27,missense_variant,p.Ser602Cys,ENST00000361200,;DUSP27,missense_variant,p.Ser602Cys,ENST00000443333,NM_001080426.1;DUSP27,missense_variant,p.Ser602Cys,ENST00000271385,;GPA33,intron_variant,,ENST00000632571,;DUSP27,intron_variant,,ENST00000485151,; T ENST00000361200 Transcript missense_variant 1970/4164 1804/3477 602/1158 S/C Agt/Tgt 1 1 DUSP27 HGNC HGNC:25034 protein_coding YES CCDS30932.1 ENSP00000354483 Q5VZP5 UPI000040DFF5 deleterious(0) 6/6 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 167126935 167126935 A T 1 0 0 0 0 1 0 0 0 4646 188 7 4 4 DUSP27 1 167126935 Missense_Mutation SNP A C3N-01016_T 4626023 167126935 81829487 30 20179 ADCY10 0 . GRCh38 1 167856221 167856221 + Missense_Mutation SNP G G C C3N-01016_T C3N-01016_N G G c.2115C>G p.Ile705Met p.I705M ENST00000367851 17/33 213 165 48 135 135 0 strelka-varscan-mutect ADCY10,missense_variant,p.Ile613Met,ENST00000367848,NM_001297772.1;ADCY10,missense_variant,p.Ile705Met,ENST00000367851,NM_018417.5;ADCY10,missense_variant,p.Ile552Met,ENST00000545172,NM_001167749.2; C ENST00000367851 Transcript missense_variant 2300/5051 2115/4833 705/1610 I/M atC/atG COSM349841 1 -1 ADCY10 HGNC HGNC:21285 protein_coding YES CCDS1265.1 ENSP00000356825 Q96PN6 A0A0K0K1J8 UPI0000204D00 NM_018417.5 deleterious(0.04) 17/33 hmmpanther:PTHR16305,hmmpanther:PTHR16305:SF32,PIRSF_domain:PIRSF011131 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 167856221 167856221 G C 1 0 0 0 0 1 0 0 0 337 932 33 4 4 ADCY10 1 167856221 Missense_Mutation SNP G C3N-01016_T 729286 167856221 81100201 31 20180 F5 0 . GRCh38 1 169515559 169515559 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.6413C>A p.Thr2138Lys p.T2138K ENST00000367797 24/25 472 357 115 277 277 0 strelka-varscan-mutect F5,missense_variant,p.Thr2143Lys,ENST00000367796,;F5,missense_variant,p.Thr2138Lys,ENST00000367797,NM_000130.4;F5,non_coding_transcript_exon_variant,,ENST00000495481,; T ENST00000367797 Transcript missense_variant 6615/7024 6413/6675 2138/2224 T/K aCa/aAa 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 deleterious(0) 24/25 Low_complexity_(Seg):seg,PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,PROSITE_patterns:PS01285,Gene3D:2.60.120.260,PIRSF_domain:PIRSF000354,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 169515559 169515559 G T 1 0 0 0 0 1 0 0 0 5216 1377 48 2 2 F5 1 169515559 Missense_Mutation SNP G C3N-01016_T 1659338 169515559 79440863 32 20181 PRRX1 0 . GRCh38 1 170726383 170726383 + Missense_Mutation SNP G G C rs766027745 C3N-01016_T C3N-01016_N G G c.581G>C p.Gly194Ala p.G194A ENST00000239461 3/4 233 176 57 130 130 0 strelka-varscan-mutect PRRX1,missense_variant,p.Gly194Ala,ENST00000239461,NM_022716.3;PRRX1,missense_variant,p.Gly194Ala,ENST00000497230,;PRRX1,missense_variant,p.Gly194Ala,ENST00000367760,NM_006902.4;PRRX1,non_coding_transcript_exon_variant,,ENST00000476867,;PRRX1,non_coding_transcript_exon_variant,,ENST00000495280,;PRRX1,upstream_gene_variant,,ENST00000496573,;PRRX1,upstream_gene_variant,,ENST00000485529,; C ENST00000239461 Transcript missense_variant 894/4284 581/738 194/245 G/A gGg/gCg rs766027745,COSM3478168,COSM3478169 1 1 PRRX1 HGNC HGNC:9142 protein_coding YES CCDS1290.1 ENSP00000239461 P54821 UPI0000131D11 NM_022716.3 tolerated(0.39) 3/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF335 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766027745 . 0 204 0 5 0 0 0 0 -20 0.9998148 1 1 1 0 C 3 2 66 170726383 170726383 G C 1 0 0 0 0 1 0 0 0 12759 1232 43 4 4 PRRX1 1 170726383 Missense_Mutation SNP G C3N-01016_T 1210824 170726383 78230039 33 20182 ABL2 0 . GRCh38 1 179108005 179108005 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.3262G>T p.Ala1088Ser p.A1088S ENST00000502732 12/12 294 230 64 254 251 3 strelka-varscan-mutect ABL2,missense_variant,p.Ala1088Ser,ENST00000502732,NM_007314.3;ABL2,missense_variant,p.Ala970Ser,ENST00000344730,NM_001136000.2;ABL2,missense_variant,p.Ala1073Ser,ENST00000512653,NM_005158.4;ABL2,missense_variant,p.Ala1067Ser,ENST00000367623,NM_001168236.1;ABL2,missense_variant,p.Ala985Ser,ENST00000511413,NM_001168237.1;ABL2,missense_variant,p.Ala964Ser,ENST00000507173,NM_001168238.1;ABL2,missense_variant,p.Ala949Ser,ENST00000504405,NM_001168239.1;ABL2,downstream_gene_variant,,ENST00000392043,NM_001136001.1; A ENST00000502732 Transcript missense_variant 3466/12144 3262/3549 1088/1182 A/S Gcc/Tcc 1 -1 ABL2 HGNC HGNC:77 protein_coding YES CCDS30947.1 ENSP00000427562 P42684 UPI0000125140 NM_007314.3 deleterious_low_confidence(0.01) 12/12 Gene3D:1.20.120.330,Pfam_domain:PF08919,SMART_domains:SM00808 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 179108005 179108005 C A 1 0 0 0 0 1 0 0 0 103 739 26 2 2 ABL2 1 179108005 Missense_Mutation SNP C C3N-01016_T 8381622 179108005 69848417 34 20183 PPFIA4 0 . GRCh38 1 203053806 203053806 + Missense_Mutation SNP C C A rs769099610 C3N-01016_T C3N-01016_N C C c.1643C>A p.Pro548His p.P548H ENST00000447715 19/35 352 242 110 322 321 1 strelka-varscan PPFIA4,missense_variant,p.Pro548His,ENST00000447715,;PPFIA4,synonymous_variant,p.=,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,synonymous_variant,p.=,ENST00000295706,;PPFIA4,synonymous_variant,p.=,ENST00000272198,;PPFIA4,synonymous_variant,p.=,ENST00000599966,;PPFIA4,synonymous_variant,p.=,ENST00000600426,;PPFIA4,synonymous_variant,p.=,ENST00000599514,;PPFIA4,non_coding_transcript_exon_variant,,ENST00000600447,; A ENST00000447715 Transcript missense_variant 2084/6349 1643/3558 548/1185 P/H cCt/cAt rs769099610 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 deleterious(0.03) 19/35 hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 203053806 203053806 C A 1 0 0 0 0 1 0 0 0 12421 668 24 2 2 PPFIA4 1 203053806 Missense_Mutation SNP C C3N-01016_T 23945801 203053806 45902616 35 20184 USH2A 0 . GRCh38 1 215965445 215965445 + Missense_Mutation SNP C C A rs754075911 C3N-01016_T C3N-01016_N C C c.6992G>T p.Gly2331Val p.G2331V ENST00000307340 37/72 275 190 85 215 213 2 strelka-varscan USH2A,missense_variant,p.Gly2331Val,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 7379/18883 6992/15609 2331/5202 G/V gGa/gTa rs754075911 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 37/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 215965445 215965445 C A 1 0 0 0 0 1 0 0 0 17570 855 30 2 2 USH2A 1 215965445 Missense_Mutation SNP C C3N-01016_T 12911639 215965445 32990977 36 20185 DNAH14 0 . GRCh38 1 225240783 225240783 + Nonsense_Mutation SNP A A T rs773162310 C3N-01016_T C3N-01016_N A A c.6643A>T p.Lys2215Ter p.K2215* ENST00000430092 42/84 270 195 75 130 130 0 strelka-varscan DNAH14,stop_gained,p.Lys2215Ter,ENST00000430092,NM_001373.1;DNAH14,stop_gained,p.Lys2215Ter,ENST00000439375,;DNAH14,stop_gained,p.Lys1810Ter,ENST00000445597,;DNAH14,upstream_gene_variant,,ENST00000327794,; T ENST00000430092 Transcript stop_gained 6858/13763 6643/13548 2215/4515 K/* Aaa/Taa rs773162310 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 42/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 225240783 225240783 A T 1 0 0 0 0 0 1 0 0 4415 131 5 4 4 DNAH14 1 225240783 Nonsense_Mutation SNP A C3N-01016_T 9275338 225240783 23715639 37 20186 MAP10 0 . GRCh38 1 232807606 232807606 + Silent SNP C C T novel C3N-01016_T C3N-01016_N C C c.2583C>T p.= p.T861T ENST00000418460 1/1 181 112 69 86 86 0 strelka-varscan-mutect MAP10,synonymous_variant,p.=,ENST00000418460,NM_019090.2; T ENST00000418460 Transcript synonymous_variant 2715/3516 2583/3144 861/1047 T acC/acT 1 1 MAP10 HGNC HGNC:29265 protein_coding YES CCDS44334.1 ENSP00000403208 Q9P2G4 UPI0000418F25 NM_019090.2 1/1 Pfam_domain:PF14925,hmmpanther:PTHR21831,hmmpanther:PTHR21831:SF2 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 232807606 232807606 C T 1 0 0 0 0 0 0 0 1 9149 581 21 3 3 MAP10 1 232807606 Silent SNP C C3N-01016_T 7566823 232807606 16148816 38 20187 RYR2 0 . GRCh38 1 237503461 237503461 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.2569C>A p.Leu857Met p.L857M ENST00000366574 22/105 225 174 51 154 154 0 strelka-varscan-mutect RYR2,missense_variant,p.Leu857Met,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu841Met,ENST00000360064,; A ENST00000366574 Transcript missense_variant 2886/16562 2569/14904 857/4967 L/M Ctg/Atg COSM323164,COSM3485708 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.05) 22/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 237503461 237503461 C A 1 0 0 0 0 1 0 0 0 14029 680 24 2 2 RYR2 1 237503461 Missense_Mutation SNP C C3N-01016_T 4695855 237503461 11452961 39 20188 RYR2 0 . GRCh38 1 237783934 237783934 + Silent SNP G G A C3N-01016_T C3N-01016_N G G c.12222G>A p.= p.E4074E ENST00000366574 90/105 409 375 34 304 304 0 strelka-varscan-mutect RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript synonymous_variant 12539/16562 12222/14904 4074/4967 E gaG/gaA COSM2048972,COSM4234605 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 90/105 Gene3D:1.10.238.10,Pfam_domain:PF13833,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Superfamily_domains:SSF47473 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 237783934 237783934 G A 1 0 0 0 0 0 0 0 1 14029 933 33 3 3 RYR2 1 237783934 Silent SNP G C3N-01016_T 280473 237783934 11172488 40 20189 RYR2 0 . GRCh38 1 237791480 237791480 + Missense_Mutation SNP G G T rs397516510 C3N-01016_T C3N-01016_N G G c.13528G>T p.Ala4510Ser p.A4510S ENST00000366574 93/105 166 128 38 101 101 0 strelka-varscan-mutect RYR2,missense_variant,p.Ala4510Ser,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Ala4493Ser,ENST00000360064,;RYR2,upstream_gene_variant,,ENST00000608590,; T ENST00000366574 Transcript missense_variant 13845/16562 13528/14904 4510/4967 A/S Gca/Tca rs397516510,CM043079,COSM259084,COSM5071048 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.03) 93/105 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Transmembrane_helices:TMhelix uncertain_significance,likely_pathogenic,pathogenic 0,0,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs397516510 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 237791480 237791480 G T 1 0 0 0 0 1 0 0 0 14029 1087 38 1 1 RYR2 1 237791480 Missense_Mutation SNP G C3N-01016_T 7546 237791480 11164942 41 20190 RGS7 0 . GRCh38 1 240813714 240813714 + Missense_Mutation SNP G G T rs751557145 C3N-01016_T C3N-01016_N G G c.860C>A p.Thr287Lys p.T287K ENST00000366565 13/18 366 339 27 285 285 0 strelka-varscan-mutect RGS7,missense_variant,p.Thr287Lys,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Thr287Lys,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Thr287Lys,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Thr234Lys,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Thr118Lys,ENST00000440928,; T ENST00000366565 Transcript missense_variant 1242/2494 860/1464 287/487 T/K aCg/aAg rs751557145,COSM1146246,COSM1646109,COSM679748 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 tolerated(0.28) 13/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26,Pfam_domain:PF00631,Gene3D:4.10.260.10,SMART_domains:SM00224,SMART_domains:SM01224,Superfamily_domains:SSF48670 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs751557145 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 240813714 240813714 G T 1 0 0 0 0 1 0 0 0 13481 1145 40 1 1 RGS7 1 240813714 Missense_Mutation SNP G C3N-01016_T 3022234 240813714 8142708 42 20191 KMO 0 . GRCh38 1 241592019 241592019 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.1327C>T p.His443Tyr p.H443Y ENST00000366559 15/15 422 302 120 364 364 0 strelka-varscan-mutect KMO,missense_variant,p.His443Tyr,ENST00000366559,NM_003679.4;KMO,missense_variant,p.His409Tyr,ENST00000366557,;KMO,missense_variant,p.His430Tyr,ENST00000366558,;KMO,missense_variant,p.His129Tyr,ENST00000366555,;OPN3,downstream_gene_variant,,ENST00000366554,NM_014322.2;OPN3,non_coding_transcript_exon_variant,,ENST00000462265,;OPN3,downstream_gene_variant,,ENST00000463155,;OPN3,downstream_gene_variant,,ENST00000469376,;OPN3,downstream_gene_variant,,ENST00000490673,;OPN3,downstream_gene_variant,,ENST00000478849,; T ENST00000366559 Transcript missense_variant 1638/5261 1327/1461 443/486 H/Y Cac/Tac 1 1 KMO HGNC HGNC:6381 protein_coding YES CCDS1618.1 ENSP00000355517 O15229 UPI000045632A NM_003679.4 tolerated(0.87) 15/15 HAMAP:MF_01971,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 241592019 241592019 C T 1 0 0 0 0 1 0 0 0 8294 478 17 3 3 KMO 1 241592019 Missense_Mutation SNP C C3N-01016_T 778305 241592019 7364403 43 20192 AKT3 0 . GRCh38 1 243573029 243573029 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.716G>T p.Arg239Ile p.R239I ENST00000263826 8/13 139 85 54 108 108 0 strelka-varscan-mutect AKT3,missense_variant,p.Arg239Ile,ENST00000263826,NM_005465.4;AKT3,missense_variant,p.Arg239Ile,ENST00000366539,;AKT3,missense_variant,p.Arg239Ile,ENST00000336199,NM_181690.2;AKT3,missense_variant,p.Arg239Ile,ENST00000366540,NM_001206729.1; A ENST00000263826 Transcript missense_variant 828/7081 716/1440 239/479 R/I aGa/aTa 1 -1 AKT3 HGNC HGNC:393 protein_coding YES CCDS31077.1 ENSP00000263826 Q9Y243 UPI00000335E8 NM_005465.4 deleterious(0) 8/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF190,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999991 1 1 1 0 A 3 1 66 243573029 243573029 C A 1 0 0 0 0 1 0 0 0 564 913 32 2 2 AKT3 1 243573029 Missense_Mutation SNP C C3N-01016_T 1981010 243573029 5383393 44 20193 OR1C1 0 . GRCh38 1 247758221 247758221 + Missense_Mutation SNP G G T rs866016097 C3N-01016_T C3N-01016_N G G c.186C>A p.Phe62Leu p.F62L ENST00000408896 1/1 267 172 95 195 195 0 strelka-varscan-mutect OR1C1,missense_variant,p.Phe62Leu,ENST00000408896,NM_012353.2; T ENST00000408896 Transcript missense_variant 186/945 186/945 62/314 F/L ttC/ttA rs866016097,COSM2232445 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 0,1 1 PASS rs866016097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 247758221 247758221 G T 1 0 0 0 0 1 0 0 0 11029 1165 41 2 2 OR1C1 1 247758221 Missense_Mutation SNP G C3N-01016_T 4185192 247758221 1198201 45 20194 OR2AJ1 0 . GRCh38 1 247933903 247933903 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.135G>T p.Met45Ile p.M45I ENST00000318244 1/1 97 87 10 74 74 0 strelka-varscan-mutect OR2AJ1,missense_variant,p.Met45Ile,ENST00000318244,;CLK3P2,downstream_gene_variant,,ENST00000427566,; T ENST00000318244 Transcript missense_variant 135/987 135/987 45/328 M/I atG/atT 1 1 OR2AJ1 HGNC HGNC:15001 protein_coding YES ENSP00000325078 Q8NGZ0 UPI0000061E5C tolerated(0.07) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF214,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1047799203 . 0 207 3 0 0 0 0 0 -19.94014 1 1 1 1 0 T 3 4 66 247933903 247933903 G T 1 0 0 0 0 1 0 0 0 11063 1290 45 2 2 OR2AJ1 1 247933903 Missense_Mutation SNP G C3N-01016_T 175682 247933903 1022519 46 20195 OR2M3 0 . GRCh38 1 248203825 248203825 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.758G>T p.Gly253Val p.G253V ENST00000456743 1/1 540 369 171 461 459 2 strelka-varscan-mutect OR2M3,missense_variant,p.Gly253Val,ENST00000456743,NM_001004689.1; T ENST00000456743 Transcript missense_variant 758/939 758/939 253/312 G/V gGa/gTa COSM2233250 1 1 OR2M3 HGNC HGNC:8269 protein_coding YES CCDS31107.1 ENSP00000389625 Q8NG83 A0A126GV67 UPI000004B234 NM_001004689.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 248203825 248203825 G T 1 0 0 0 0 1 0 0 0 11089 1174 41 2 2 OR2M3 1 248203825 Missense_Mutation SNP G C3N-01016_T 269922 248203825 752597 47 20196 OR2T12 0 . GRCh38 1 248295134 248295134 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.445C>G p.Leu149Val p.L149V ENST00000317996 1/1 466 351 115 376 375 1 strelka-varscan-mutect OR2T12,missense_variant,p.Leu149Val,ENST00000317996,NM_001004692.1; C ENST00000317996 Transcript missense_variant 445/963 445/963 149/320 L/V Ctg/Gtg 1 -1 OR2T12 HGNC HGNC:19592 protein_coding YES CCDS31110.1 ENSP00000324583 Q8NG77 UPI000004B235 NM_001004692.1 tolerated(0.15) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 248295134 248295134 G C 1 0 0 0 0 1 0 0 0 11096 991 35 4 4 OR2T12 1 248295134 Missense_Mutation SNP G C3N-01016_T 91309 248295134 661288 48 20197 OR2T6 0 . GRCh38 1 248387762 248387762 + Missense_Mutation SNP G G T rs749687401 C3N-01016_T C3N-01016_N G G c.154G>T p.Asp52Tyr p.D52Y ENST00000355728 1/1 125 78 47 115 115 0 strelka-varscan-mutect OR2T6,missense_variant,p.Asp52Tyr,ENST00000355728,NM_001005471.1; T ENST00000355728 Transcript missense_variant 154/927 154/927 52/308 D/Y Gac/Tac rs749687401,COSM246233 1 1 OR2T6 HGNC HGNC:15018 protein_coding YES CCDS31114.1 ENSP00000347965 Q8NHC8 UPI0000199147 NM_001005471.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF57,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs749687401 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 248387762 248387762 G T 1 0 0 0 0 1 0 0 0 11106 942 33 2 2 OR2T6 1 248387762 Missense_Mutation SNP G C3N-01016_T 92628 248387762 568660 49 20198 LYPD8 0 . GRCh38 1 248739782 248739782 + Silent SNP C C A novel C3N-01016_T C3N-01016_N C C c.543G>T p.= p.L181L ENST00000590317 7/7 445 270 175 381 381 0 strelka-varscan-mutect LYPD8,synonymous_variant,p.=,ENST00000590317,NM_001291283.1,NM_001085474.1;XX-CR54.1,intron_variant,,ENST00000611154,;LYPD8,intron_variant,,ENST00000566597,; A ENST00000590317 Transcript synonymous_variant 775/1142 543/714 181/237 L ctG/ctT 1 -1 LYPD8 HGNC HGNC:44208 protein_coding YES CCDS73059.1 ENSP00000466070 Q6UX82 UPI00017648F2 NM_001291283.1,NM_001085474.1 7/7 hmmpanther:PTHR20914,hmmpanther:PTHR20914:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 248739782 248739782 C A 1 0 0 0 0 0 0 0 1 9027 465 17 2 2 LYPD8 1 248739782 Silent SNP C C3N-01016_T 352020 248739782 216640 50 20199 EMILIN1 0 . GRCh38 2 27082897 27082897 + Silent SNP C C T C3N-01016_T C3N-01016_N C C c.1326C>T p.= p.A442A ENST00000380320 4/8 91 64 27 85 84 1 strelka-varscan-mutect EMILIN1,synonymous_variant,p.=,ENST00000380320,NM_007046.3;KHK,upstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,upstream_gene_variant,,ENST00000260598,NM_006488.2;EMILIN1,upstream_gene_variant,,ENST00000433140,;KHK,upstream_gene_variant,,ENST00000429697,;KHK,upstream_gene_variant,,ENST00000490823,; T ENST00000380320 Transcript synonymous_variant 1825/3943 1326/3051 442/1016 A gcC/gcT COSM1718733 1 1 EMILIN1 HGNC HGNC:19880 protein_coding YES CCDS1733.1 ENSP00000369677 A0A0C4DFX3 UPI0000073B0E NM_007046.3 4/8 1 LOW 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 27082897 27082897 C T 1 0 0 0 0 0 0 0 1 4936 610 22 3 3 EMILIN1 2 27082897 Silent SNP C C3N-01016_T 27082897 215110632 51 20200 FSHR 0 . GRCh38 2 49068275 49068275 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.168C>A p.= p.T56T ENST00000406846 2/10 381 294 87 396 396 0 strelka-varscan-mutect FSHR,synonymous_variant,p.=,ENST00000406846,NM_000145.3;FSHR,synonymous_variant,p.=,ENST00000304421,NM_181446.2;FSHR,synonymous_variant,p.=,ENST00000454032,;RP11-460M2.1,intron_variant,,ENST00000634588,;FSHR,synonymous_variant,p.=,ENST00000419927,; T ENST00000406846 Transcript synonymous_variant 288/2784 168/2088 56/695 T acC/acA 1 -1 FSHR HGNC HGNC:3969 protein_coding YES CCDS1843.1 ENSP00000384708 UPI000013E97A NM_000145.3 2/10 Gene3D:3.80.10.10,Prints_domain:PR01143,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF5,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 49068275 49068275 G T 1 0 0 0 0 0 0 0 1 5947 1335 47 2 2 FSHR 2 49068275 Silent SNP G C3N-01016_T 21985378 49068275 193125254 52 20201 USP34 0 . GRCh38 2 61284887 61284887 + Missense_Mutation SNP T T C novel C3N-01016_T C3N-01016_N T T c.4820A>G p.Asn1607Ser p.N1607S ENST00000398571 35/80 158 113 45 96 96 0 strelka-varscan-mutect USP34,missense_variant,p.Asn1607Ser,ENST00000398571,NM_014709.3;USP34,upstream_gene_variant,,ENST00000453734,;USP34,intron_variant,,ENST00000472706,;USP34,upstream_gene_variant,,ENST00000484179,;USP34,upstream_gene_variant,,ENST00000494867,; C ENST00000398571 Transcript missense_variant 4897/11357 4820/10641 1607/3546 N/S aAt/aGt 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 tolerated(0.51) 35/80 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF97 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 61284887 61284887 T C 1 0 0 0 0 1 0 0 0 17607 1493 52 5 5 USP34 2 61284887 Missense_Mutation SNP T C3N-01016_T 12216612 61284887 180908642 53 20202 USP34 0 . GRCh38 2 61348431 61348431 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1724G>T p.Gly575Val p.G575V ENST00000398571 15/80 218 157 61 129 129 0 strelka-varscan-mutect USP34,missense_variant,p.Gly575Val,ENST00000398571,NM_014709.3;USP34,upstream_gene_variant,,ENST00000460004,;USP34,3_prime_UTR_variant,,ENST00000453133,; A ENST00000398571 Transcript missense_variant 1801/11357 1724/10641 575/3546 G/V gGa/gTa 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 deleterious_low_confidence(0.04) 15/80 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 61348431 61348431 C A 1 0 0 0 0 1 0 0 0 17607 855 30 2 2 USP34 2 61348431 Missense_Mutation SNP C C3N-01016_T 63544 61348431 180845098 54 20203 LGALSL 0 . GRCh38 2 64456419 64456419 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.329A>T p.Gln110Leu p.Q110L ENST00000238875 4/5 123 90 33 85 85 0 strelka-varscan-mutect LGALSL,missense_variant,p.Gln110Leu,ENST00000238875,NM_014181.2;LGALSL,missense_variant,p.Gln110Leu,ENST00000464281,;LGALSL,intron_variant,,ENST00000409537,;AC008074.3,upstream_gene_variant,,ENST00000441630,;LGALSL,3_prime_UTR_variant,,ENST00000420552,;LGALSL,3_prime_UTR_variant,,ENST00000462737,; T ENST00000238875 Transcript missense_variant 783/3926 329/519 110/172 Q/L cAg/cTg 1 1 LGALSL HGNC HGNC:25012 protein_coding YES CCDS1877.1 ENSP00000238875 Q3ZCW2 UPI000013CA5E NM_014181.2 deleterious(0) 4/5 PROSITE_profiles:PS51304,hmmpanther:PTHR11346:SF98,hmmpanther:PTHR11346,Gene3D:2.60.120.200,Pfam_domain:PF00337,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 64456419 64456419 A T 1 0 0 0 0 1 0 0 0 8660 188 7 4 4 LGALSL 2 64456419 Missense_Mutation SNP A C3N-01016_T 3107988 64456419 177737110 55 20204 DYSF 0 . GRCh38 2 71574201 71574201 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.3232A>T p.Arg1078Trp p.R1078W ENST00000410020 30/56 126 95 31 109 109 0 strelka-varscan-mutect DYSF,missense_variant,p.Arg1060Trp,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Arg1077Trp,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Arg1091Trp,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Arg1060Trp,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Arg1077Trp,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Arg1078Trp,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Arg1092Trp,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Arg1061Trp,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Arg1078Trp,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Arg1047Trp,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Arg1061Trp,ENST00000394120,NM_001130455.1;DYSF,upstream_gene_variant,,ENST00000479049,;DYSF,upstream_gene_variant,,ENST00000475076,;DYSF,downstream_gene_variant,,ENST00000461565,; T ENST00000410020 Transcript missense_variant 3373/6657 3232/6360 1078/2119 R/W Agg/Tgg 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0.02) 30/56 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 71574201 71574201 A T 1 0 0 0 0 1 0 0 0 4683 202 7 4 4 DYSF 2 71574201 Missense_Mutation SNP A C3N-01016_T 7117782 71574201 170619328 56 20205 ALMS1 0 . GRCh38 2 73448095 73448095 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1568G>T p.Ser523Ile p.S523I ENST00000613296 8/23 231 174 57 157 157 0 strelka-varscan-mutect ALMS1,missense_variant,p.Ser523Ile,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Ser481Ile,ENST00000484298,;ALMS1,missense_variant,p.Ser523Ile,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; T ENST00000613296 Transcript missense_variant 1679/12925 1568/12507 523/4168 S/I aGt/aTt 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 deleterious_low_confidence(0.02) 8/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS rs797045226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 73448095 73448095 G T 1 0 0 0 0 1 0 0 0 635 1029 36 2 2 ALMS1 2 73448095 Missense_Mutation SNP G C3N-01016_T 1873894 73448095 168745434 57 20206 SMYD1 0 . GRCh38 2 88110499 88110499 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.1460A>G p.His487Arg p.H487R ENST00000419482 10/10 68 45 23 63 63 0 strelka-varscan-mutect SMYD1,missense_variant,p.His487Arg,ENST00000419482,NM_198274.3;SMYD1,missense_variant,p.His474Arg,ENST00000444564,;SMYD1,intron_variant,,ENST00000438570,; G ENST00000419482 Transcript missense_variant 1545/4433 1460/1473 487/490 H/R cAc/cGc 1 1 SMYD1 HGNC HGNC:20986 protein_coding YES CCDS33240.1 ENSP00000393453 Q8NB12 A0A0A6YYB2 UPI000006EB68 NM_198274.3 tolerated_low_confidence(0.28) 10/10 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 88110499 88110499 A G 1 0 0 0 0 1 0 0 0 15142 159 6 5 5 SMYD1 2 88110499 Missense_Mutation SNP A C3N-01016_T 14662404 88110499 154083030 58 20207 ZAP70 0 . GRCh38 2 97737630 97737630 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.1447T>A p.Ser483Thr p.S483T ENST00000264972 11/14 285 231 54 291 291 0 strelka-varscan-mutect ZAP70,missense_variant,p.Ser483Thr,ENST00000264972,NM_001079.3;ZAP70,missense_variant,p.Ser176Thr,ENST00000451498,NM_207519.1;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000487283,;ZAP70,non_coding_transcript_exon_variant,,ENST00000495754,;ZAP70,downstream_gene_variant,,ENST00000483781,;ZAP70,upstream_gene_variant,,ENST00000489250,;ZAP70,downstream_gene_variant,,ENST00000498836,; A ENST00000264972 Transcript missense_variant 1662/2437 1447/1860 483/619 S/T Tcc/Acc 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 deleterious(0) 11/14 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000604,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 97737630 97737630 T A 1 0 0 0 0 1 0 0 0 18075 1551 54 4 4 ZAP70 2 97737630 Missense_Mutation SNP T C3N-01016_T 9627131 97737630 144455899 59 20208 TMEM131 0 . GRCh38 2 97805448 97805448 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2212G>T p.Ala738Ser p.A738S ENST00000186436 21/41 146 89 57 159 159 0 strelka-varscan-mutect TMEM131,missense_variant,p.Ala738Ser,ENST00000186436,NM_015348.1; A ENST00000186436 Transcript missense_variant 2441/6640 2212/5652 738/1883 A/S Gca/Tca 1 -1 TMEM131 HGNC HGNC:30366 protein_coding YES CCDS46368.1 ENSP00000186436 Q92545 UPI00006C0498 NM_015348.1 deleterious(0.02) 21/41 hmmpanther:PTHR22050:SF1,hmmpanther:PTHR22050 MODERATE 1 SNV 5 1 PASS . . 0 205 0 5 0 0 0 0 -20 0.9999246 1 1 1 0 A 3 1 66 97805448 97805448 C A 1 0 0 0 0 1 0 0 0 16488 724 25 2 2 TMEM131 2 97805448 Missense_Mutation SNP C C3N-01016_T 67818 97805448 144388081 60 20209 POLR1B 0 . GRCh38 2 112559415 112559415 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.1567A>T p.Thr523Ser p.T523S ENST00000541869 10/16 427 351 76 489 489 0 strelka-varscan-mutect POLR1B,missense_variant,p.Thr523Ser,ENST00000541869,NM_001282772.1;POLR1B,missense_variant,p.Thr274Ser,ENST00000537335,NM_001282776.1;POLR1B,missense_variant,p.Thr485Ser,ENST00000263331,NM_019014.5;POLR1B,missense_variant,p.Thr429Ser,ENST00000417433,NM_001137604.2,NM_001282779.1,NM_001282777.1;POLR1B,intron_variant,,ENST00000409894,NM_001282774.1;POLR1B,upstream_gene_variant,,ENST00000458012,;POLR1B,downstream_gene_variant,,ENST00000498054,;POLR1B,3_prime_UTR_variant,,ENST00000333990,;POLR1B,intron_variant,,ENST00000448770,;POLR1B,upstream_gene_variant,,ENST00000484574,; T ENST00000541869 Transcript missense_variant 1683/5059 1567/3522 523/1173 T/S Aca/Tca 1 1 POLR1B HGNC HGNC:20454 protein_coding YES CCDS62988.1 ENSP00000444136 Q9H9Y6 UPI0002065A70 NM_001282772.1 tolerated(0.22) 10/16 Gene3D:2a6hC02,Pfam_domain:PF04565,hmmpanther:PTHR20856,hmmpanther:PTHR20856:SF5,Superfamily_domains:SSF64484 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 112559415 112559415 A T 1 0 0 0 0 1 0 0 0 12320 159 6 4 4 POLR1B 2 112559415 Missense_Mutation SNP A C3N-01016_T 14753967 112559415 129634114 61 20210 HS6ST1 0 . GRCh38 2 128268703 128268703 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.695G>T p.Gly232Val p.G232V ENST00000259241 2/2 553 470 83 498 497 1 strelka-varscan-mutect HS6ST1,missense_variant,p.Gly232Val,ENST00000259241,NM_004807.2;HS6ST1,non_coding_transcript_exon_variant,,ENST00000463963,;HS6ST1,intron_variant,,ENST00000469019,; A ENST00000259241 Transcript missense_variant 709/3932 695/1236 232/411 G/V gGc/gTc 1 -1 HS6ST1 HGNC HGNC:5201 protein_coding YES CCDS42748.1 ENSP00000259241 O60243 UPI0000D61231 NM_004807.2 deleterious(0) 2/2 hmmpanther:PTHR12812:SF1,hmmpanther:PTHR12812,Pfam_domain:PF03567,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 128268703 128268703 C A 1 0 0 0 0 1 0 0 0 7264 739 26 2 2 HS6ST1 2 128268703 Missense_Mutation SNP C C3N-01016_T 15709288 128268703 113924826 62 20211 CCDC74A 0 . GRCh38 2 131531662 131531663 + Splice_Site INS - - T novel C3N-01016_T C3N-01016_N - - c.545-2_545-1insT p.X182_splice ENST00000295171 73 33 40 65 65 0 sindel-varindel-pindel CCDC74A,splice_acceptor_variant,,ENST00000295171,NM_138770.2,NM_001258304.1;CCDC74A,splice_acceptor_variant,,ENST00000467992,NM_001258305.1;CCDC74A,splice_acceptor_variant,,ENST00000409856,NM_001258306.1;CCDC74A,splice_acceptor_variant,,ENST00000434330,;CCDC74A,downstream_gene_variant,,ENST00000478665,;CCDC74A,downstream_gene_variant,,ENST00000465939,;CCDC74A,downstream_gene_variant,,ENST00000454549,;CCDC74A,downstream_gene_variant,,ENST00000468650,;MED15P4,downstream_gene_variant,,ENST00000417579,; T ENST00000295171 Transcript splice_acceptor_variant -/1543 545/1137 182/378 1 1 CCDC74A HGNC HGNC:25197 protein_coding YES CCDS2167.1 ENSP00000295171 Q96AQ1 UPI000006E43A NM_138770.2,NM_001258304.1 3/7 HIGH 1 insertion 1 1 PASS . . 19 187 4 0 0 0 0 0 -20 1 1 1 1 0 T 8 5 66 131531662 131531662 - T 1 0 1 1 0 0 0 1 0 2547 86 3 0 0 CCDC74A 2 131531662 Splice_Site INS - C3N-01016_T 3262959 131531662 110661867 63 20212 ZRANB3 0 . GRCh38 2 135504408 135504408 + Missense_Mutation SNP A A C novel C3N-01016_T C3N-01016_N A A c.82T>G p.Phe28Val p.F28V ENST00000264159 2/21 217 156 61 200 200 0 strelka-varscan-mutect ZRANB3,missense_variant,p.Phe28Val,ENST00000401392,NM_001286568.1;ZRANB3,missense_variant,p.Phe28Val,ENST00000264159,NM_032143.3;ZRANB3,5_prime_UTR_variant,,ENST00000536680,NM_001286569.1;ZRANB3,intron_variant,,ENST00000452187,;ZRANB3,missense_variant,p.Phe28Val,ENST00000403017,;ZRANB3,non_coding_transcript_exon_variant,,ENST00000492193,; C ENST00000264159 Transcript missense_variant 199/4046 82/3240 28/1079 F/V Ttt/Gtt 1 -1 ZRANB3 HGNC HGNC:25249 protein_coding YES CCDS46419.1 ENSP00000264159 Q5FWF4 UPI0000509F0C NM_032143.3 tolerated(0.25) 2/21 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF731,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 135504408 135504408 A C 1 0 0 0 0 1 0 0 0 18817 14 1 5 5 ZRANB3 2 135504408 Missense_Mutation SNP A C3N-01016_T 3972746 135504408 106689121 64 20213 LRP1B 0 . GRCh38 2 140526258 140526258 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.7855G>T p.Ala2619Ser p.A2619S ENST00000389484 48/91 181 142 39 211 210 1 strelka-varscan-mutect LRP1B,missense_variant,p.Ala2619Ser,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript missense_variant 8827/16535 7855/13800 2619/4599 A/S Gct/Tct 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.03) 48/91 PROSITE_profiles:PS50068,PROSITE_patterns:PS01209,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 140526258 140526258 C A 1 0 0 0 0 1 0 0 0 8850 710 25 2 2 LRP1B 2 140526258 Missense_Mutation SNP C C3N-01016_T 5021850 140526258 101667271 65 20214 NEB 0 . GRCh38 2 151506241 151506241 + Silent SNP A A G novel C3N-01016_T C3N-01016_N A A c.23679T>C p.= p.D7893D ENST00000618972 165/183 96 77 19 97 97 0 strelka-varscan-mutect NEB,synonymous_variant,p.=,ENST00000618972,NM_001271208.1;NEB,synonymous_variant,p.=,ENST00000397345,NM_001164508.1;NEB,synonymous_variant,p.=,ENST00000427231,NM_001164507.1;NEB,synonymous_variant,p.=,ENST00000603639,;NEB,synonymous_variant,p.=,ENST00000604864,;NEB,synonymous_variant,p.=,ENST00000409198,NM_004543.4;NEB,synonymous_variant,p.=,ENST00000172853,;NEB,synonymous_variant,p.=,ENST00000413693,;NEB,synonymous_variant,p.=,ENST00000397337,;NEB,synonymous_variant,p.=,ENST00000434685,;NEB,synonymous_variant,p.=,ENST00000421461,;NEB,synonymous_variant,p.=,ENST00000424585,;RIF1,non_coding_transcript_exon_variant,,ENST00000467762,;NEB,non_coding_transcript_exon_variant,,ENST00000498015,;RIF1,3_prime_UTR_variant,,ENST00000454583,; G ENST00000618972 Transcript synonymous_variant 23882/26307 23679/25683 7893/8560 D gaT/gaC 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 165/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,Pfam_domain:PF00880,SMART_domains:SM00227 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 66 151506241 151506241 A G 1 0 0 0 0 0 0 0 1 10326 214 8 5 5 NEB 2 151506241 Silent SNP A C3N-01016_T 10979983 151506241 90687288 66 20215 NEB 0 . GRCh38 2 151619696 151619696 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.10627G>T p.Asp3543Tyr p.D3543Y ENST00000618972 73/183 194 113 81 177 177 0 strelka-varscan-mutect NEB,missense_variant,p.Asp3543Tyr,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Asp3543Tyr,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Asp3543Tyr,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Asp3543Tyr,ENST00000603639,;NEB,missense_variant,p.Asp3543Tyr,ENST00000604864,;NEB,missense_variant,p.Asp3300Tyr,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Asp3300Tyr,ENST00000172853,;NEB,upstream_gene_variant,,ENST00000486320,; A ENST00000618972 Transcript missense_variant 10830/26307 10627/25683 3543/8560 D/Y Gac/Tac 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 deleterious(0) 73/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,Pfam_domain:PF00880,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 151619696 151619696 C A 1 0 0 0 0 1 0 0 0 10326 826 29 2 2 NEB 2 151619696 Missense_Mutation SNP C C3N-01016_T 113455 151619696 90573833 67 20216 XIRP2 0 . GRCh38 2 167245989 167245989 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.4597C>A p.Pro1533Thr p.P1533T ENST00000409195 9/11 150 100 50 122 122 0 strelka-varscan-mutect XIRP2,missense_variant,p.Pro1533Thr,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Pro1311Thr,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Pro1358Thr,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 4686/12675 4597/10650 1533/3549 P/T Cca/Aca 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0) 9/11 Pfam_domain:PF08043,PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 167245989 167245989 C A 1 0 0 0 0 1 0 0 0 17989 507 18 2 2 XIRP2 2 167245989 Missense_Mutation SNP C C3N-01016_T 15626293 167245989 74947540 68 20217 PPIG 0 . GRCh38 2 169637130 169637130 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1872G>T p.Arg624Ser p.R624S ENST00000260970 14/14 130 112 18 111 111 0 strelka-varscan-mutect PPIG,missense_variant,p.Arg624Ser,ENST00000260970,NM_004792.2;PPIG,missense_variant,p.Arg609Ser,ENST00000409714,;PPIG,missense_variant,p.Arg624Ser,ENST00000448752,;PPIG,downstream_gene_variant,,ENST00000462903,;PPIG,downstream_gene_variant,,ENST00000433207,;PPIG,downstream_gene_variant,,ENST00000482772,;PPIG,downstream_gene_variant,,ENST00000466142,; T ENST00000260970 Transcript missense_variant 2092/6368 1872/2265 624/754 R/S agG/agT 1 1 PPIG HGNC HGNC:14650 protein_coding YES CCDS2235.1 ENSP00000260970 Q13427 UPI000013D124 NM_004792.2 tolerated_low_confidence(0.33) 14/14 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 169637130 169637130 G T 1 0 0 0 0 1 0 0 0 12435 1165 41 2 2 PPIG 2 169637130 Missense_Mutation SNP G C3N-01016_T 2391141 169637130 72556399 69 20218 RAPGEF4 0 . GRCh38 2 172961180 172961180 + Missense_Mutation SNP G G A rs373393896 C3N-01016_T C3N-01016_N G G c.650G>A p.Arg217Gln p.R217Q ENST00000397081 8/31 122 89 33 119 119 0 strelka-varscan-mutect RAPGEF4,missense_variant,p.Arg217Gln,ENST00000397081,NM_007023.3;RAPGEF4,missense_variant,p.Arg73Gln,ENST00000397087,NM_001100397.1;RAPGEF4,missense_variant,p.Arg217Gln,ENST00000409036,;RAPGEF4,missense_variant,p.Arg64Gln,ENST00000540783,NM_001282899.1;RAPGEF4,missense_variant,p.Arg46Gln,ENST00000538974,NM_001282900.1;RAPGEF4,5_prime_UTR_variant,,ENST00000535187,NM_001282901.1;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000473043,;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000473003,;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000466030,;RAPGEF4,upstream_gene_variant,,ENST00000473182,; A ENST00000397081 Transcript missense_variant 793/4299 650/3036 217/1011 R/Q cGa/cAa rs373393896,COSM1009618 1 1 RAPGEF4 HGNC HGNC:16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 UPI000006D4C7 NM_007023.3 tolerated(0.4) 8/31 Gene3D:1.10.10.10,PROSITE_profiles:PS50186,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,SMART_domains:SM00049,Superfamily_domains:SSF46785 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373393896 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 172961180 172961180 G A 1 0 0 0 0 1 0 0 0 13205 1058 37 1 1 RAPGEF4 2 172961180 Missense_Mutation SNP G C3N-01016_T 3324050 172961180 69232349 70 20219 TTN 0 . GRCh38 2 178559772 178559772 + Missense_Mutation SNP A A C novel C3N-01016_T C3N-01016_N A A c.86360T>G p.Leu28787Trp p.L28787W ENST00000589042 326/363 52 31 21 29 29 0 strelka-varscan-mutect TTN,missense_variant,p.Leu28787Trp,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu27146Trp,ENST00000591111,;TTN,missense_variant,p.Leu27146Trp,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu26219Trp,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Leu19722Trp,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Leu19914Trp,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Leu19847Trp,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,downstream_gene_variant,,ENST00000624360,; C ENST00000589042 Transcript missense_variant 86585/109224 86360/107976 28787/35991 L/W tTg/tGg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs1237283720 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 178559772 178559772 A C 1 0 0 0 0 1 0 0 0 17245 131 5 5 5 TTN 2 178559772 Missense_Mutation SNP A C3N-01016_T 5598592 178559772 63633757 71 20220 COL3A1 0 . GRCh38 2 188984860 188984860 + Silent SNP T T A novel C3N-01016_T C3N-01016_N T T c.180T>A p.= p.V60V ENST00000304636 2/51 385 288 97 359 359 0 strelka-varscan-mutect COL3A1,synonymous_variant,p.=,ENST00000304636,NM_000090.3;COL3A1,synonymous_variant,p.=,ENST00000317840,;COL3A1,non_coding_transcript_exon_variant,,ENST00000470167,; A ENST00000304636 Transcript synonymous_variant 350/5543 180/4401 60/1466 V gtT/gtA 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 2/51 PROSITE_profiles:PS50184,PROSITE_patterns:PS01208,Pfam_domain:PF00093,Gene3D:2.10.70.10,SMART_domains:SM00214,Superfamily_domains:SSF57603 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 188984860 188984860 T A 1 0 0 0 0 0 0 0 1 3477 1770 62 4 4 COL3A1 2 188984860 Silent SNP T C3N-01016_T 10425088 188984860 53208669 72 20221 COL3A1 0 . GRCh38 2 189008040 189008040 + Silent SNP T T G novel C3N-01016_T C3N-01016_N T T c.3423T>G p.= p.P1141P ENST00000304636 47/51 453 333 120 450 450 0 strelka-varscan-mutect COL3A1,synonymous_variant,p.=,ENST00000304636,NM_000090.3;COL3A1,intron_variant,,ENST00000317840,;COL3A1,upstream_gene_variant,,ENST00000487010,;COL3A1,downstream_gene_variant,,ENST00000467886,; G ENST00000304636 Transcript synonymous_variant 3593/5543 3423/4401 1141/1466 P ccT/ccG 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 47/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 66 189008040 189008040 T G 1 0 0 0 0 0 0 0 1 3477 1594 55 5 5 COL3A1 2 189008040 Silent SNP T C3N-01016_T 23180 189008040 53185489 73 20222 SUMO1 0 . GRCh38 2 202207309 202207309 + Nonsense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.250G>T p.Glu84Ter p.E84* ENST00000392246 5/5 260 171 89 143 143 0 strelka-varscan-mutect SUMO1,stop_gained,p.Glu84Ter,ENST00000392246,NM_003352.4;SUMO1,stop_gained,p.Glu129Ter,ENST00000409368,;SUMO1,stop_gained,p.Glu84Ter,ENST00000392245,NM_001005781.1;SUMO1,stop_gained,p.Glu59Ter,ENST00000392244,NM_001005782.1;SUMO1,stop_gained,p.Glu45Ter,ENST00000409498,;SUMO1,stop_gained,p.Glu60Ter,ENST00000409712,;SUMO1,stop_gained,p.Glu45Ter,ENST00000409205,;SUMO1,3_prime_UTR_variant,,ENST00000409181,;KIAA2012,downstream_gene_variant,,ENST00000498697,;SUMO1,non_coding_transcript_exon_variant,,ENST00000469034,;SUMO1,3_prime_UTR_variant,,ENST00000409627,; A ENST00000392246 Transcript stop_gained 407/1536 250/306 84/101 E/* Gaa/Taa 1 -1 SUMO1 HGNC HGNC:12502 protein_coding YES CCDS2352.1 ENSP00000376077 P63165 A0A024R3Z2 UPI0000001227 NM_003352.4 5/5 PROSITE_profiles:PS50053,hmmpanther:PTHR10562,Gene3D:3.10.20.90,Pfam_domain:PF11976,SMART_domains:SM00213,Superfamily_domains:SSF54236 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 202207309 202207309 C A 1 0 0 0 0 0 1 0 0 15773 864 30 2 2 SUMO1 2 202207309 Nonsense_Mutation SNP C C3N-01016_T 13199269 202207309 39986220 74 20223 MAP2 0 . GRCh38 2 209695274 209695274 + Missense_Mutation SNP A A G C3N-01016_T C3N-01016_N A A c.3104A>G p.Glu1035Gly p.E1035G ENST00000360351 7/15 113 90 23 76 76 0 strelka-varscan-mutect MAP2,missense_variant,p.Glu1035Gly,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Glu1031Gly,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; G ENST00000360351 Transcript missense_variant 3610/9711 3104/5484 1035/1827 E/G gAa/gGa COSM5287313 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0.04) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 209695274 209695274 A G 1 0 0 0 0 1 0 0 0 9157 246 9 5 5 MAP2 2 209695274 Missense_Mutation SNP A C3N-01016_T 7487965 209695274 32498255 75 20224 CXCR2 0 . GRCh38 2 218135385 218135385 + Missense_Mutation SNP C C A rs200413041 C3N-01016_T C3N-01016_N C C c.584C>A p.Ala195Asp p.A195D ENST00000318507 3/3 229 154 75 154 154 0 strelka-varscan-mutect CXCR2,missense_variant,p.Ala195Asp,ENST00000318507,NM_001168298.1,NM_001557.3;CXCR2,missense_variant,p.Ala195Asp,ENST00000453237,;CXCR2,downstream_gene_variant,,ENST00000428565,;CXCR2,downstream_gene_variant,,ENST00000454148,;CXCR2,downstream_gene_variant,,ENST00000415392,;CXCR2,downstream_gene_variant,,ENST00000449014,;CXCR2,downstream_gene_variant,,ENST00000418878,; A ENST00000318507 Transcript missense_variant 1011/2879 584/1083 195/360 A/D gCc/gAc rs200413041,COSM3043209 1 1 CXCR2 HGNC HGNC:6027 protein_coding YES CCDS2408.1 ENSP00000319635 P25025 Q53PC4 UPI000004358A NM_001168298.1,NM_001557.3 deleterious(0.01) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF632,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200413041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 218135385 218135385 C A 1 0 0 0 0 1 0 0 0 3902 739 26 2 2 CXCR2 2 218135385 Missense_Mutation SNP C C3N-01016_T 8440111 218135385 24058144 76 20225 PTPRN 0 . GRCh38 2 219301626 219301626 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.1088T>A p.Leu363Gln p.L363Q ENST00000295718 7/23 108 94 14 129 129 0 strelka-varscan-mutect PTPRN,missense_variant,p.Leu363Gln,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Leu363Gln,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Leu273Gln,ENST00000423636,NM_001199764.1;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,upstream_gene_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,; T ENST00000295718 Transcript missense_variant 1329/3784 1088/2940 363/979 L/Q cTg/cAg 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 tolerated(0.18) 7/23 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 219301626 219301626 A T 1 0 0 0 0 1 0 0 0 12961 188 7 4 4 PTPRN 2 219301626 Missense_Mutation SNP A C3N-01016_T 1166241 219301626 22891903 77 20226 OBSL1 0 . GRCh38 2 219567526 219567526 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1584G>T p.Lys528Asn p.K528N ENST00000404537 4/21 136 128 8 130 130 0 strelka-varscan-mutect OBSL1,missense_variant,p.Lys528Asn,ENST00000404537,NM_015311.2;OBSL1,missense_variant,p.Lys528Asn,ENST00000603926,NM_001173431.1;OBSL1,missense_variant,p.Lys528Asn,ENST00000373876,;OBSL1,missense_variant,p.Lys528Asn,ENST00000373873,NM_001173408.1;OBSL1,missense_variant,p.Lys115Asn,ENST00000289656,;INHA,upstream_gene_variant,,ENST00000243786,NM_002191.3;INHA,upstream_gene_variant,,ENST00000489456,;OBSL1,downstream_gene_variant,,ENST00000491370,;OBSL1,downstream_gene_variant,,ENST00000465589,;OBSL1,non_coding_transcript_exon_variant,,ENST00000465149,;OBSL1,upstream_gene_variant,,ENST00000462385,; A ENST00000404537 Transcript missense_variant 1641/5841 1584/5691 528/1896 K/N aaG/aaT 1 -1 OBSL1 HGNC HGNC:29092 protein_coding YES CCDS46520.1 ENSP00000385636 O75147 UPI0000E07EA0 NM_015311.2 tolerated(0.1) 4/21 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Superfamily_domains:SSF48726,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1424872527 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 219567526 219567526 C A 1 0 0 0 0 1 0 0 0 10890 680 24 2 2 OBSL1 2 219567526 Missense_Mutation SNP C C3N-01016_T 265900 219567526 22626003 78 20227 SPHKAP 0 . GRCh38 2 228017612 228017612 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.3242C>G p.Ser1081Cys p.S1081C ENST00000392056 7/12 126 78 48 148 148 0 strelka-varscan-mutect SPHKAP,missense_variant,p.Ser1081Cys,ENST00000392056,NM_001142644.1;SPHKAP,missense_variant,p.Ser1081Cys,ENST00000344657,NM_030623.3; C ENST00000392056 Transcript missense_variant 3289/6917 3242/5103 1081/1700 S/C tCc/tGc 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 deleterious(0) 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 228017612 228017612 G C 1 0 0 0 0 1 0 0 0 15399 1174 41 4 4 SPHKAP 2 228017612 Missense_Mutation SNP G C3N-01016_T 8450086 228017612 14175917 79 20228 GBX2 0 . GRCh38 2 236166178 236166178 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.783G>T p.Glu261Asp p.E261D ENST00000306318 2/2 189 125 64 211 211 0 strelka-varscan-mutect GBX2,missense_variant,p.Glu261Asp,ENST00000306318,NM_001485.3;GBX2,3_prime_UTR_variant,,ENST00000551105,NM_001301687.1;AC079135.1,upstream_gene_variant,,ENST00000483218,;AC079135.1,upstream_gene_variant,,ENST00000415226,;GBX2,non_coding_transcript_exon_variant,,ENST00000465889,; A ENST00000306318 Transcript missense_variant 1181/2123 783/1047 261/348 E/D gaG/gaT 1 -1 GBX2 HGNC HGNC:4186 protein_coding YES CCDS2515.1 ENSP00000302251 P52951 UPI000012B273 NM_001485.3 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24334,hmmpanther:PTHR24334:SF3,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1177420598 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 236166178 236166178 C A 1 0 0 0 0 1 0 0 0 6151 796 28 2 2 GBX2 2 236166178 Missense_Mutation SNP C C3N-01016_T 8148566 236166178 6027351 80 20229 BTD 0 . GRCh38 3 15644571 15644571 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.721A>T p.Arg241Trp p.R241W ENST00000437172 6/6 325 192 133 342 342 0 strelka-varscan-mutect BTD,missense_variant,p.Arg219Trp,ENST00000383778,NM_001281725.1;BTD,missense_variant,p.Arg241Trp,ENST00000437172,NM_001281724.1;BTD,missense_variant,p.Arg239Trp,ENST00000303498,NM_000060.3;BTD,missense_variant,p.Arg241Trp,ENST00000449107,NM_001281723.1;BTD,missense_variant,p.Arg219Trp,ENST00000436193,;BTD,downstream_gene_variant,,ENST00000482824,; T ENST00000437172 Transcript missense_variant 953/2097 721/1638 241/545 R/W Agg/Tgg 1 1 BTD HGNC HGNC:1122 protein_coding YES CCDS63564.1 ENSP00000400995 P43251 UPI00017A7026 NM_001281724.1 deleterious(0) 6/6 Gene3D:3.60.110.10,Pfam_domain:PF00795,PIRSF_domain:PIRSF011861,PROSITE_profiles:PS50263,hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF17,Superfamily_domains:SSF56317 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 15644571 15644571 A T 1 0 0 0 0 1 0 0 0 1726 179 7 4 4 BTD 3 15644571 Missense_Mutation SNP A C3N-01016_T 15644571 182650988 81 20230 ALS2CL 0 . GRCh38 3 46678265 46678265 + Missense_Mutation SNP C C A rs774616995 C3N-01016_T C3N-01016_N C C c.1751G>T p.Cys584Phe p.C584F ENST00000318962 16/26 45 29 16 42 42 0 strelka-varscan-mutect ALS2CL,missense_variant,p.Cys584Phe,ENST00000318962,NM_147129.3;ALS2CL,missense_variant,p.Cys584Phe,ENST00000415953,NM_001190707.1;ALS2CL,upstream_gene_variant,,ENST00000383742,NM_182775.2;ALS2CL,upstream_gene_variant,,ENST00000473484,;ALS2CL,3_prime_UTR_variant,,ENST00000423707,;ALS2CL,3_prime_UTR_variant,,ENST00000434140,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000450172,;ALS2CL,non_coding_transcript_exon_variant,,ENST00000431015,;ALS2CL,upstream_gene_variant,,ENST00000486301,;ALS2CL,upstream_gene_variant,,ENST00000498817,; A ENST00000318962 Transcript missense_variant 1835/4741 1751/2862 584/953 C/F tGc/tTc rs774616995 1 -1 ALS2CL HGNC HGNC:20605 protein_coding YES CCDS2743.1 ENSP00000313670 Q60I27 A0A024R2U1 UPI00001B5641 NM_147129.3 tolerated(0.07) 16/26 hmmpanther:PTHR23084,hmmpanther:PTHR23084:SF164 MODERATE 1 SNV 1 1 PASS rs774616995 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 46678265 46678265 C A 1 0 0 0 0 1 0 0 0 651 710 25 2 2 ALS2CL 3 46678265 Missense_Mutation SNP C C3N-01016_T 31033694 46678265 151617294 82 20231 CACNA2D3 0 . GRCh38 3 54871614 54871614 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1702G>T p.Asp568Tyr p.D568Y ENST00000474759 18/38 63 51 12 110 110 0 strelka-varscan-mutect CACNA2D3,missense_variant,p.Asp568Tyr,ENST00000474759,NM_018398.2;CACNA2D3,missense_variant,p.Asp568Tyr,ENST00000288197,;CACNA2D3,missense_variant,p.Asp568Tyr,ENST00000415676,;CACNA2D3,missense_variant,p.Asp474Tyr,ENST00000490478,;CACNA2D3,missense_variant,p.Asp468Tyr,ENST00000620722,;CACNA2D3-AS1,downstream_gene_variant,,ENST00000471265,;CACNA2D3,missense_variant,p.Asp468Tyr,ENST00000471363,;CACNA2D3,missense_variant,p.Asp474Tyr,ENST00000477024,;CACNA2D3,3_prime_UTR_variant,,ENST00000468658,; T ENST00000474759 Transcript missense_variant 1750/3675 1702/3276 568/1091 D/Y Gat/Tat 1 1 CACNA2D3 HGNC HGNC:15460 protein_coding YES CCDS54598.1 ENSP00000419101 Q8IZS8 UPI000004A7BF NM_018398.2 deleterious(0) 18/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF25 MODERATE 1 SNV 1 1 PASS rs1422207990 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 54871614 54871614 G T 1 0 0 0 0 1 0 0 0 2238 942 33 2 2 CACNA2D3 3 54871614 Missense_Mutation SNP G C3N-01016_T 8193349 54871614 143423945 83 20232 RETNLB 0 . GRCh38 3 108755798 108755798 + Missense_Mutation SNP G G T rs148724960 C3N-01016_T C3N-01016_N G G c.316C>A p.Arg106Ser p.R106S ENST00000295755 3/3 95 52 43 127 127 0 strelka-varscan-mutect RETNLB,missense_variant,p.Arg106Ser,ENST00000295755,NM_032579.2;RETNLB,intron_variant,,ENST00000482939,; T ENST00000295755 Transcript missense_variant 515/676 316/336 106/111 R/S Cgc/Agc rs148724960 1 -1 RETNLB HGNC HGNC:20388 protein_coding YES CCDS2953.1 ENSP00000295755 Q9BQ08 UPI00000015BE NM_032579.2 deleterious(0) 3/3 Pfam_domain:PF06954,hmmpanther:PTHR21101,hmmpanther:PTHR21101:SF13,Superfamily_domains:SSF111423 MODERATE 1 SNV 1 1 PASS rs148724960 . 0 204 4 2 0 0 0 0 -20 0.9999981 1 1 1 0 T 3 4 66 108755798 108755798 G T 1 0 0 0 0 1 0 0 0 13408 1116 39 1 1 RETNLB 3 108755798 Missense_Mutation SNP G C3N-01016_T 53884184 108755798 89539761 84 20233 PARP14 0 . GRCh38 3 122701633 122701633 + Nonsense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.3079A>T p.Lys1027Ter p.K1027* ENST00000474629 6/17 45 26 19 35 35 0 strelka-varscan-mutect PARP14,stop_gained,p.Lys1027Ter,ENST00000474629,NM_017554.2;PARP14,stop_gained,p.Lys868Ter,ENST00000460683,;PARP14,splice_region_variant,,ENST00000474669,; T ENST00000474629 Transcript stop_gained,splice_region_variant 3345/7915 3079/5406 1027/1801 K/* Aag/Tag 1 1 PARP14 HGNC HGNC:29232 protein_coding YES CCDS46894.1 ENSP00000418194 Q460N5 UPI00015A20AB NM_017554.2 6/17 PROSITE_profiles:PS51154,hmmpanther:PTHR14453:SF65,hmmpanther:PTHR14453,Gene3D:3.40.220.10,SMART_domains:SM00506,Superfamily_domains:SSF52949 HIGH 1 SNV 2 1 PASS rs1231106782 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 122701633 122701633 A T 1 0 0 0 0 0 1 0 0 11538 376 13 4 4 PARP14 3 122701633 Nonsense_Mutation SNP A C3N-01016_T 13945835 122701633 75593926 85 20234 COL6A6 0 . GRCh38 3 130565384 130565385 + Frame_Shift_Ins INS - - A novel C3N-01016_T C3N-01016_N - - c.1053dupA p.Ala352SerfsTer3 p.A352Sfs*3 ENST00000358511 3/36 288 268 20 275 275 0 varindel-pindel COL6A6,frameshift_variant,p.Ala352SerfsTer3,ENST00000358511,NM_001102608.1; A ENST00000358511 Transcript frameshift_variant 1083-1084/9581 1052-1053/6792 351/2263 A/AX gca/gcAa 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 3/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 HIGH 1 insertion 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 66 130565384 130565384 - A 1 0 1 1 0 0 0 0 0 3492 710 25 0 0 COL6A6 3 130565384 Frame_Shift_Ins INS - C3N-01016_T 7863751 130565384 67730175 86 20235 TOPBP1 0 . GRCh38 3 133628592 133628592 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.2662A>T p.Ser888Cys p.S888C ENST00000260810 15/28 146 83 63 141 141 0 strelka-varscan-mutect TOPBP1,missense_variant,p.Ser888Cys,ENST00000260810,NM_007027.3;TOPBP1,non_coding_transcript_exon_variant,,ENST00000506779,;TOPBP1,upstream_gene_variant,,ENST00000513818,; A ENST00000260810 Transcript missense_variant 2794/5378 2662/4569 888/1522 S/C Agc/Tgc 1 -1 TOPBP1 HGNC HGNC:17008 protein_coding YES CCDS46919.1 ENSP00000260810 Q92547 UPI000020A292 NM_007027.3 deleterious(0) 15/28 hmmpanther:PTHR13561:SF32,hmmpanther:PTHR13561 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 133628592 133628592 T A 1 0 0 0 0 1 0 0 0 16846 1580 55 4 4 TOPBP1 3 133628592 Missense_Mutation SNP T C3N-01016_T 3063208 133628592 64666967 87 20236 ATR 0 . GRCh38 3 142555929 142555929 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.2289C>G p.Cys763Trp p.C763W ENST00000350721 10/47 102 41 61 77 77 0 strelka-varscan-mutect ATR,missense_variant,p.Cys763Trp,ENST00000350721,NM_001184.3;ATR,downstream_gene_variant,,ENST00000515149,;ATR,downstream_gene_variant,,ENST00000507148,;ATR,downstream_gene_variant,,ENST00000515863,; C ENST00000350721 Transcript missense_variant 2411/8249 2289/7935 763/2644 C/W tgC/tgG 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious(0.01) 10/47 Gene3D:1.25.10.10,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1362094246 . 0 205 2 3 0 0 0 0 -20 0.9999973 1 1 1 0 C 3 2 66 142555929 142555929 G C 1 0 0 0 0 1 0 0 0 1356 1311 46 4 4 ATR 3 142555929 Missense_Mutation SNP G C3N-01016_T 8927337 142555929 55739630 88 20237 PLSCR5 0 . GRCh38 3 146589761 146589761 + Silent SNP T T G rs377510646 C3N-01016_T C3N-01016_N T T c.669A>C p.= p.S223S ENST00000443512 6/8 145 86 59 96 96 0 strelka-varscan-mutect PLSCR5,synonymous_variant,p.=,ENST00000443512,NM_001085420.1;PLSCR5,synonymous_variant,p.=,ENST00000492200,;PLSCR5,synonymous_variant,p.=,ENST00000482567,;PLSCR5-AS1,non_coding_transcript_exon_variant,,ENST00000473817,; G ENST00000443512 Transcript synonymous_variant 1673/1969 669/816 223/271 S tcA/tcC rs377510646 1 -1 PLSCR5 HGNC HGNC:19952 protein_coding YES CCDS46931.1 ENSP00000390111 A0PG75 UPI0000425F34 NM_001085420.1 6/8 Pfam_domain:PF03803,hmmpanther:PTHR23248,hmmpanther:PTHR23248:SF25,Superfamily_domains:SSF54518 LOW 1 SNV 1 1 PASS rs377510646 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 66 146589761 146589761 T G 1 0 0 0 0 0 0 0 1 12220 1567 55 5 5 PLSCR5 3 146589761 Silent SNP T C3N-01016_T 4033832 146589761 51705798 89 20238 PEX5L 0 . GRCh38 3 179887684 179887684 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.299C>A p.Ser100Tyr p.S100Y ENST00000467460 4/15 127 90 37 125 125 0 strelka-varscan-mutect PEX5L,missense_variant,p.Ser100Tyr,ENST00000467460,NM_016559.2;PEX5L,missense_variant,p.Ser57Tyr,ENST00000392649,;PEX5L,missense_variant,p.Ser65Tyr,ENST00000485199,NM_001256752.1;PEX5L,missense_variant,p.Ser98Tyr,ENST00000263962,NM_001256750.1;PEX5L,missense_variant,p.Ser57Tyr,ENST00000476138,NM_001256754.1;PEX5L,missense_variant,p.Ser41Tyr,ENST00000472994,NM_001256753.1;PEX5L,missense_variant,p.Ser76Tyr,ENST00000465751,NM_001256751.1;PEX5L,missense_variant,p.Ser57Tyr,ENST00000464614,NM_001256755.1;PEX5L,missense_variant,p.Ser124Tyr,ENST00000463761,;PEX5L,missense_variant,p.Ser89Tyr,ENST00000469198,;PEX5L,5_prime_UTR_variant,,ENST00000468741,NM_001256756.1;PEX5L,5_prime_UTR_variant,,ENST00000491640,;PEX5L,5_prime_UTR_variant,,ENST00000496721,;PEX5L,non_coding_transcript_exon_variant,,ENST00000467440,;PEX5L,non_coding_transcript_exon_variant,,ENST00000487198,; T ENST00000467460 Transcript missense_variant 630/9082 299/1881 100/626 S/Y tCc/tAc 1 -1 PEX5L HGNC HGNC:30024 protein_coding YES CCDS3236.1 ENSP00000419975 Q8IYB4 UPI0000049CE2 NM_016559.2 deleterious_low_confidence(0) 4/15 hmmpanther:PTHR10130,hmmpanther:PTHR10130:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 179887684 179887684 G T 1 0 0 0 0 1 0 0 0 11839 1174 41 2 2 PEX5L 3 179887684 Missense_Mutation SNP G C3N-01016_T 33297923 179887684 18407875 90 20239 YEATS2 0 . GRCh38 3 183721956 183721956 + Silent SNP A A T novel C3N-01016_T C3N-01016_N A A c.357A>T p.= p.P119P ENST00000305135 5/31 273 157 116 246 246 0 strelka-varscan-mutect YEATS2,synonymous_variant,p.=,ENST00000305135,NM_018023.4; T ENST00000305135 Transcript synonymous_variant 552/6506 357/4269 119/1422 P ccA/ccT 1 1 YEATS2 HGNC HGNC:25489 protein_coding YES CCDS43175.1 ENSP00000306983 Q9ULM3 UPI00001BB2B9 NM_018023.4 5/31 hmmpanther:PTHR23195:SF7,hmmpanther:PTHR23195 LOW 1 SNV 1 1 PASS rs1327233759 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 183721956 183721956 A T 1 0 0 0 0 0 0 0 1 18034 204 8 4 4 YEATS2 3 183721956 Silent SNP A C3N-01016_T 3834272 183721956 14573603 91 20240 POLR2H 0 . GRCh38 3 184368219 184368219 + Missense_Mutation SNP G G T rs780161088 C3N-01016_T C3N-01016_N G G c.442G>T p.Gly148Trp p.G148W ENST00000429568 5/5 97 51 46 125 125 0 strelka-varscan-mutect POLR2H,missense_variant,p.Gln126His,ENST00000456318,NM_006232.3;POLR2H,missense_variant,p.Gln98His,ENST00000430783,NM_001278714.1;POLR2H,missense_variant,p.Gln90His,ENST00000438240,NM_001278700.1;POLR2H,missense_variant,p.Gly148Trp,ENST00000429568,NM_001278698.1;POLR2H,missense_variant,p.Gln126His,ENST00000455712,;POLR2H,missense_variant,p.Gln62His,ENST00000443489,NM_001278715.1;POLR2H,missense_variant,p.Gln90His,ENST00000452961,NM_001278699.1;THPO,downstream_gene_variant,,ENST00000204615,NM_000460.3,NM_001289998.1,NM_001290028.1;THPO,downstream_gene_variant,,ENST00000445696,NM_001177598.2,NM_001290022.1,NM_001177597.2,NM_001290026.1;THPO,downstream_gene_variant,,ENST00000421442,NM_001289997.1,NM_001290027.1;POLR2H,downstream_gene_variant,,ENST00000412877,;POLR2H,downstream_gene_variant,,ENST00000460083,;THPO,downstream_gene_variant,,ENST00000477594,;POLR2H,non_coding_transcript_exon_variant,,ENST00000488213,;POLR2H,non_coding_transcript_exon_variant,,ENST00000476003,;POLR2H,non_coding_transcript_exon_variant,,ENST00000489043,;POLR2H,downstream_gene_variant,,ENST00000490958,; T ENST00000429568 Transcript missense_variant 501/878 442/528 148/175 G/W Ggg/Tgg rs780161088,COSM4613097 1 1 POLR2H HGNC HGNC:9195 protein_coding YES CCDS63859.1 ENSP00000415536 P52434 UPI000198CBDF NM_001278698.1 deleterious_low_confidence(0) 5/5 0,1 MODERATE SNV 2 0,1 1 PASS rs780161088 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 184368219 184368219 G T 1 0 0 0 0 1 0 0 0 12331 1000 35 2 2 POLR2H 3 184368219 Missense_Mutation SNP G C3N-01016_T 646263 184368219 13927340 92 20241 RUBCN 0 . GRCh38 3 197683403 197683403 + Silent SNP C C A rs765574552 C3N-01016_T C3N-01016_N C C c.1884G>T p.= p.A628A ENST00000296343 13/20 233 167 66 299 298 1 strelka-varscan-mutect RUBCN,synonymous_variant,p.=,ENST00000273582,NM_001145642.3;RUBCN,synonymous_variant,p.=,ENST00000413360,;RUBCN,synonymous_variant,p.=,ENST00000296343,NM_014687.2;RUBCN,synonymous_variant,p.=,ENST00000415452,;RUBCN,non_coding_transcript_exon_variant,,ENST00000471364,; A ENST00000296343 Transcript synonymous_variant 1884/2919 1884/2919 628/972 A gcG/gcT rs765574552 1 -1 RUBCN HGNC HGNC:28991 protein_coding YES CCDS43195.1 ENSP00000296343 Q92622 UPI00001C1DE4 NM_014687.2 13/20 hmmpanther:PTHR12326:SF11,hmmpanther:PTHR12326 LOW 1 SNV 2 1 PASS rs765574552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 197683403 197683403 C A 1 0 0 0 0 0 0 0 1 13999 639 23 1 1 RUBCN 3 197683403 Silent SNP C C3N-01016_T 13315184 197683403 612156 93 20242 EVC 0 . GRCh38 4 5753918 5753918 + Silent SNP G G T rs775819388 C3N-01016_T C3N-01016_N G G c.1449G>T p.= p.P483P ENST00000264956 10/21 439 301 138 449 448 1 strelka-varscan-mutect EVC,synonymous_variant,p.=,ENST00000264956,NM_001306090.1,NM_153717.2;EVC,synonymous_variant,p.=,ENST00000509451,NM_001306092.1;EVC,non_coding_transcript_exon_variant,,ENST00000514919,;CRMP1,intron_variant,,ENST00000506216,; T ENST00000264956 Transcript synonymous_variant 1633/6431 1449/2979 483/992 P ccG/ccT rs775819388,COSM3302184 1 1 EVC HGNC HGNC:3497 protein_coding YES CCDS3383.1 ENSP00000264956 P57679 UPI000012A2A5 NM_001306090.1,NM_153717.2 10/21 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF13 0,1 LOW 1 SNV 1 0,1 1 PASS rs775819388 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 5753918 5753918 G T 1 0 0 0 0 0 0 0 1 5152 1103 39 1 1 EVC 4 5753918 Silent SNP G C3N-01016_T 5753918 184460637 94 20243 BOD1L1 0 . GRCh38 4 13614714 13614714 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.656G>T p.Arg219Met p.R219M ENST00000040738 4/26 332 231 101 324 324 0 strelka-varscan-mutect BOD1L1,missense_variant,p.Arg219Met,ENST00000040738,NM_148894.2;BOD1L1,3_prime_UTR_variant,,ENST00000482713,; A ENST00000040738 Transcript missense_variant 792/10565 656/9156 219/3051 R/M aGg/aTg 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 deleterious(0) 4/26 Low_complexity_(Seg):seg,hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 MODERATE 1 SNV 2 1 PASS rs1475187596 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 13614714 13614714 C A 1 0 0 0 0 1 0 0 0 1639 681 24 2 2 BOD1L1 4 13614714 Missense_Mutation SNP C C3N-01016_T 7860796 13614714 176599841 95 20244 ADAMTS3 0 . GRCh38 4 72323098 72323098 + Splice_Site SNP C C A novel C3N-01016_T C3N-01016_N C C c.862-1G>T p.X288_splice ENST00000286657 128 73 55 135 134 1 strelka-varscan ADAMTS3,splice_acceptor_variant,,ENST00000286657,;ADAMTS3,splice_acceptor_variant,,ENST00000622135,NM_014243.2;RP11-373J21.1,non_coding_transcript_exon_variant,,ENST00000503918,; A ENST00000286657 Transcript splice_acceptor_variant -/6409 862/3618 288/1205 1 -1 ADAMTS3 HGNC HGNC:219 protein_coding YES CCDS3553.1 ENSP00000286657 O15072 UPI00001AEAEA 5/21 HIGH 1 SNV 1 1 PASS . . 0 191 14 5 0 0 0 0 -20 0.995667 1 1 1 0 A 5 1 66 72323098 72323098 C A 1 0 0 0 0 0 0 1 0 311 695 24 2 2 ADAMTS3 4 72323098 Splice_Site SNP C C3N-01016_T 58708384 72323098 117891457 96 20245 CENPE 0 . GRCh38 4 103196205 103196205 + Missense_Mutation SNP T T C novel C3N-01016_T C3N-01016_N T T c.196A>G p.Ile66Val p.I66V ENST00000265148 3/49 150 122 28 122 122 0 strelka-varscan-mutect CENPE,missense_variant,p.Ile66Val,ENST00000265148,NM_001813.2;CENPE,missense_variant,p.Ile66Val,ENST00000611174,;CENPE,missense_variant,p.Ile66Val,ENST00000380026,NM_001286734.1;CENPE,missense_variant,p.Ile66Val,ENST00000503705,;CENPE,missense_variant,p.Ile66Val,ENST00000514974,; C ENST00000265148 Transcript missense_variant 286/8612 196/8106 66/2701 I/V Ata/Gta 1 -1 CENPE HGNC HGNC:1856 protein_coding YES CCDS34042.1 ENSP00000265148 Q02224 UPI000020B28A NM_001813.2 tolerated(0.37) 3/49 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF459,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 103196205 103196205 T C 1 0 0 0 0 1 0 0 0 2938 1493 52 5 5 CENPE 4 103196205 Missense_Mutation SNP T C3N-01016_T 30873107 103196205 87018350 97 20246 ANK2 0 . GRCh38 4 113341899 113341899 + Nonsense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.4105A>T p.Arg1369Ter p.R1369* ENST00000357077 33/46 241 189 52 274 274 0 strelka-varscan-mutect ANK2,stop_gained,p.Arg1369Ter,ENST00000357077,NM_001148.4;ANK2,stop_gained,p.Arg1336Ter,ENST00000264366,;ANK2,stop_gained,p.Arg1360Ter,ENST00000506722,NM_001127493.1;ANK2,stop_gained,p.Arg1369Ter,ENST00000394537,NM_020977.3;ANK2,stop_gained,p.Arg1384Ter,ENST00000504454,;ANK2,stop_gained,p.Arg382Ter,ENST00000514960,;ANK2,stop_gained,p.Arg1282Ter,ENST00000503423,;ANK2,stop_gained,p.Arg545Ter,ENST00000509550,;ANK2,stop_gained,p.Arg21Ter,ENST00000510275,;ANK2,stop_gained,p.Arg64Ter,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504887,; T ENST00000357077 Transcript stop_gained 4158/14196 4105/11874 1369/3957 R/* Aga/Tga 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 33/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 113341899 113341899 A T 1 0 0 0 0 0 1 0 0 721 180 7 4 4 ANK2 4 113341899 Nonsense_Mutation SNP A C3N-01016_T 10145694 113341899 76872656 98 20247 ANK2 0 . GRCh38 4 113357290 113357290 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.8672C>A p.Pro2891His p.P2891H ENST00000357077 38/46 574 338 236 663 662 1 strelka-varscan-mutect ANK2,missense_variant,p.Pro2891His,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Pro2858His,ENST00000264366,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,upstream_gene_variant,,ENST00000505342,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript missense_variant 8725/14196 8672/11874 2891/3957 P/H cCc/cAc COSM4511392 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(0.27) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 113357290 113357290 C A 1 0 0 0 0 1 0 0 0 721 623 22 2 2 ANK2 4 113357290 Missense_Mutation SNP C C3N-01016_T 15391 113357290 76857265 99 20248 RAPGEF2 0 . GRCh38 4 159356147 159356147 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.4463C>T p.Thr1488Ile p.T1488I ENST00000264431 23/24 111 58 53 113 113 0 strelka-varscan-mutect RAPGEF2,missense_variant,p.Thr1488Ile,ENST00000264431,NM_014247.2;RAPGEF2,downstream_gene_variant,,ENST00000505026,;RAPGEF2,downstream_gene_variant,,ENST00000510253,;RAPGEF2,downstream_gene_variant,,ENST00000509891,; T ENST00000264431 Transcript missense_variant 4882/6949 4463/4500 1488/1499 T/I aCc/aTc 1 1 RAPGEF2 HGNC HGNC:16854 protein_coding YES CCDS43277.1 ENSP00000264431 Q9Y4G8 UPI0000033783 NM_014247.2 deleterious_low_confidence(0.02) 23/24 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 159356147 159356147 C T 1 0 0 0 0 1 0 0 0 13203 507 18 3 3 RAPGEF2 4 159356147 Missense_Mutation SNP C C3N-01016_T 45998857 159356147 30858408 100 20249 CTNND2 0 . GRCh38 5 11397065 11397065 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.578C>G p.Thr193Arg p.T193R ENST00000304623 6/22 144 90 54 134 134 0 strelka-mutect CTNND2,missense_variant,p.Thr193Arg,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Thr102Arg,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Thr102Arg,ENST00000513598,;CTNND2,intron_variant,,ENST00000503622,NM_001288716.1;CTNND2,intron_variant,,ENST00000502551,;CTNND2,downstream_gene_variant,,ENST00000508761,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,intron_variant,,ENST00000511278,;CTNND2,missense_variant,p.Thr193Arg,ENST00000504499,;CTNND2,intron_variant,,ENST00000513588,; C ENST00000304623 Transcript missense_variant 768/5481 578/3678 193/1225 T/R aCa/aGa 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.38) 6/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 11397065 11397065 G C 1 0 0 0 0 1 0 0 0 3829 1377 48 4 4 CTNND2 5 11397065 Missense_Mutation SNP G C3N-01016_T 11397065 170141194 101 20250 DNAH5 0 . GRCh38 5 13714475 13714475 + Missense_Mutation SNP C C A rs376585054 C3N-01016_T C3N-01016_N C C c.13055G>T p.Arg4352Leu p.R4352L ENST00000265104 75/79 445 277 168 403 402 1 strelka-varscan-mutect DNAH5,missense_variant,p.Arg4352Leu,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript missense_variant 13160/15633 13055/13875 4352/4624 R/L cGg/cTg rs376585054,COSM1541856 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 75/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF03028 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs376585054 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 13714475 13714475 C A 1 0 0 0 0 1 0 0 0 4419 652 23 1 1 DNAH5 5 13714475 Missense_Mutation SNP C C3N-01016_T 2317410 13714475 167823784 102 20251 CDH10 0 . GRCh38 5 24511393 24511393 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.936C>A p.Asp312Glu p.D312E ENST00000264463 6/12 159 125 34 140 140 0 strelka-varscan-mutect CDH10,missense_variant,p.Asp312Glu,ENST00000264463,NM_006727.3;CDH10,missense_variant,p.Asp312Glu,ENST00000510477,; T ENST00000264463 Transcript missense_variant 1444/3438 936/2367 312/788 D/E gaC/gaA COSM4670773 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 tolerated(0.22) 6/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS rs1021736142 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 24511393 24511393 G T 1 0 0 0 0 1 0 0 0 2799 1136 40 1 1 CDH10 5 24511393 Missense_Mutation SNP G C3N-01016_T 10796918 24511393 157026866 103 20252 CDH9 0 . GRCh38 5 26915653 26915653 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.500G>T p.Ser167Ile p.S167I ENST00000231021 3/12 119 96 23 97 97 0 strelka-varscan-mutect CDH9,missense_variant,p.Ser167Ile,ENST00000231021,NM_016279.3;CDH9,downstream_gene_variant,,ENST00000513289,;CDH9,downstream_gene_variant,,ENST00000511822,;CDH9,non_coding_transcript_exon_variant,,ENST00000505045,; A ENST00000231021 Transcript missense_variant 673/3079 500/2370 167/789 S/I aGt/aTt COSM5065700 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0.02) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 1 MODERATE 1 SNV 1 1 1 PASS rs1359344852 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 26915653 26915653 C A 1 0 0 0 0 1 0 0 0 2820 565 20 2 2 CDH9 5 26915653 Missense_Mutation SNP C C3N-01016_T 2404260 26915653 154622606 104 20253 ZFR 0 . GRCh38 5 32379159 32379159 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.2791G>T p.Asp931Tyr p.D931Y ENST00000265069 17/20 268 191 77 268 268 0 strelka-varscan-mutect ZFR,missense_variant,p.Asp931Tyr,ENST00000265069,NM_016107.3;ZFR,non_coding_transcript_exon_variant,,ENST00000510369,;ZFR,3_prime_UTR_variant,,ENST00000507465,;ZFR,non_coding_transcript_exon_variant,,ENST00000514356,; A ENST00000265069 Transcript missense_variant 2894/4738 2791/3225 931/1074 D/Y Gac/Tac COSM3744838 1 -1 ZFR HGNC HGNC:17277 protein_coding YES CCDS34139.1 ENSP00000265069 Q96KR1 UPI00001BBB38 NM_016107.3 deleterious(0) 17/20 PROSITE_profiles:PS51703,hmmpanther:PTHR10910:SF87,hmmpanther:PTHR10910,Pfam_domain:PF07528,SMART_domains:SM00572 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 32379159 32379159 C A 1 0 0 0 0 1 0 0 0 18237 913 32 2 2 ZFR 5 32379159 Missense_Mutation SNP C C3N-01016_T 5463506 32379159 149159100 105 20254 CDC20B 0 . GRCh38 5 55119847 55119847 + Silent SNP C C A C3N-01016_T C3N-01016_N C C c.1413G>T p.= p.V471V ENST00000381375 11/12 221 187 34 235 235 0 strelka-varscan-mutect CDC20B,synonymous_variant,p.=,ENST00000296733,NM_152623.2;CDC20B,synonymous_variant,p.=,ENST00000381375,NM_001170402.1;CDC20B,synonymous_variant,p.=,ENST00000322374,NM_001145734.2;CDC20B,3_prime_UTR_variant,,ENST00000513180,; A ENST00000381375 Transcript synonymous_variant 1559/2591 1413/1560 471/519 V gtG/gtT COSM3855593,COSM3855594 1 -1 CDC20B HGNC HGNC:24222 protein_coding YES CCDS54852.1 ENSP00000370781 Q86Y33 UPI0000D61625 NM_001170402.1 11/12 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF4,Superfamily_domains:SSF50978 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 55119847 55119847 C A 1 0 0 0 0 0 0 0 1 2763 813 29 2 2 CDC20B 5 55119847 Silent SNP C C3N-01016_T 22740688 55119847 126418412 106 20255 CCDC125 0 . GRCh38 5 69320327 69320327 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.214G>A p.Ala72Thr p.A72T ENST00000396496 2/12 256 213 43 226 226 0 strelka-varscan-mutect CCDC125,missense_variant,p.Ala72Thr,ENST00000396496,NM_176816.4;CCDC125,missense_variant,p.Ala72Thr,ENST00000396499,;CCDC125,missense_variant,p.Ala72Thr,ENST00000383374,NM_001297696.1;CCDC125,5_prime_UTR_variant,,ENST00000511257,NM_001297697.1;CCDC125,non_coding_transcript_exon_variant,,ENST00000460090,;CCDC125,non_coding_transcript_exon_variant,,ENST00000513172,;CCDC125,non_coding_transcript_exon_variant,,ENST00000512045,; T ENST00000396496 Transcript missense_variant 322/4198 214/1536 72/511 A/T Gcg/Acg 1 -1 CCDC125 HGNC HGNC:28924 protein_coding YES CCDS4000.1 ENSP00000379754 Q86Z20 UPI00004572F8 NM_176816.4 tolerated(0.22) 2/12 hmmpanther:PTHR28616 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 69320327 69320327 C T 1 0 0 0 0 1 0 0 0 2453 797 28 3 3 CCDC125 5 69320327 Missense_Mutation SNP C C3N-01016_T 14200480 69320327 112217932 107 20256 MARVELD2 0 . GRCh38 5 69419629 69419629 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.244G>T p.Val82Phe p.V82F ENST00000325631 2/7 117 96 21 70 70 0 strelka-varscan-mutect MARVELD2,missense_variant,p.Val82Phe,ENST00000454295,NM_001244734.1;MARVELD2,missense_variant,p.Val82Phe,ENST00000325631,NM_001038603.2;MARVELD2,missense_variant,p.Val82Phe,ENST00000512803,;MARVELD2,missense_variant,p.Val82Phe,ENST00000413223,;MARVELD2,missense_variant,p.Val82Phe,ENST00000436532,;MARVELD2,missense_variant,p.Val82Phe,ENST00000515844,;RAD17,downstream_gene_variant,,ENST00000509734,;RAD17,downstream_gene_variant,,ENST00000305138,NM_002873.1;RAD17,downstream_gene_variant,,ENST00000354868,NM_133338.2;RAD17,downstream_gene_variant,,ENST00000616683,NM_001278622.1;RAD17,downstream_gene_variant,,ENST00000361732,NM_133343.1;RAD17,downstream_gene_variant,,ENST00000354312,NM_133342.2;RAD17,downstream_gene_variant,,ENST00000345306,NM_133344.2;RAD17,downstream_gene_variant,,ENST00000358030,NM_133340.2; T ENST00000325631 Transcript missense_variant 318/2153 244/1677 82/558 V/F Gtc/Ttc 1 1 MARVELD2 HGNC HGNC:26401 protein_coding YES CCDS34175.1 ENSP00000323264 Q8N4S9 UPI00001416EB NM_001038603.2 deleterious(0.03) 2/7 hmmpanther:PTHR23288,hmmpanther:PTHR23288:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 69419629 69419629 G T 1 0 0 0 0 1 0 0 0 9244 1377 48 2 2 MARVELD2 5 69419629 Missense_Mutation SNP G C3N-01016_T 99302 69419629 112118630 108 20257 ARHGEF28 0 . GRCh38 5 73753136 73753136 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.409G>T p.Val137Leu p.V137L ENST00000545377 4/37 39 35 4 28 28 0 strelka-mutect ARHGEF28,missense_variant,p.Val137Leu,ENST00000545377,NM_001080479.2;ARHGEF28,missense_variant,p.Val137Leu,ENST00000513042,NM_001177693.1;ARHGEF28,missense_variant,p.Val137Leu,ENST00000426542,;ARHGEF28,missense_variant,p.Val137Leu,ENST00000437974,;ARHGEF28,missense_variant,p.Val137Leu,ENST00000296794,;ARHGEF28,downstream_gene_variant,,ENST00000509848,; T ENST00000545377 Transcript missense_variant 585/6351 409/5196 137/1731 V/L Gtg/Ttg COSM3975622,COSM3975623 1 1 ARHGEF28 HGNC HGNC:30322 protein_coding YES CCDS47231.2 ENSP00000441913 Q8N1W1 UPI00004DF58E NM_001080479.2 tolerated(0.1) 4/37 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF133 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1476513959 . 0 207 3 0 0 0 0 0 -11.03953 1 1 1 1 0 T 3 4 66 73753136 73753136 G T 1 0 0 0 0 1 0 0 0 1036 1145 40 1 1 ARHGEF28 5 73753136 Missense_Mutation SNP G C3N-01016_T 4333507 73753136 107785123 109 20258 RHOBTB3 0 . GRCh38 5 95788791 95788791 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1653G>T p.Trp551Cys p.W551C ENST00000379982 11/12 314 244 70 271 271 0 strelka-varscan-mutect RHOBTB3,missense_variant,p.Trp551Cys,ENST00000379982,NM_014899.3;RHOBTB3,missense_variant,p.Trp133Cys,ENST00000510313,;RHOBTB3,missense_variant,p.Trp182Cys,ENST00000504179,;RHOBTB3,missense_variant,p.Trp54Cys,ENST00000503737,;GLRX,intron_variant,,ENST00000508780,;RHOBTB3,upstream_gene_variant,,ENST00000513091,;RHOBTB3,upstream_gene_variant,,ENST00000514198,;GLRX,intron_variant,,ENST00000507605,;RHOBTB3,non_coding_transcript_exon_variant,,ENST00000511558,;RHOBTB3,downstream_gene_variant,,ENST00000507186,; T ENST00000379982 Transcript missense_variant 2161/5537 1653/1836 551/611 W/C tgG/tgT 1 1 RHOBTB3 HGNC HGNC:18757 protein_coding YES CCDS4077.1 ENSP00000369318 O94955 UPI0000367303 NM_014899.3 deleterious(0) 11/12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 95788791 95788791 G T 1 0 0 0 0 1 0 0 0 13508 1212 42 2 2 RHOBTB3 5 95788791 Missense_Mutation SNP G C3N-01016_T 22035655 95788791 85749468 110 20259 CAMK4 0 . GRCh38 5 111446710 111446711 + Frame_Shift_Ins INS - - A novel C3N-01016_T C3N-01016_N - - c.485dupA p.His162GlnfsTer3 p.H162Qfs*3 ENST00000282356 6/11 96 67 29 149 149 0 sindel-varindel CAMK4,frameshift_variant,p.His162GlnfsTer3,ENST00000282356,NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4;CAMK4,frameshift_variant,p.His162GlnfsTer3,ENST00000512453,;CAMK4,non_coding_transcript_exon_variant,,ENST00000505763,;CAMK4,non_coding_transcript_exon_variant,,ENST00000502916,;CAMK4,3_prime_UTR_variant,,ENST00000515231,;CAMK4,3_prime_UTR_variant,,ENST00000514007,;CAMK4,3_prime_UTR_variant,,ENST00000504544,; A ENST00000282356 Transcript frameshift_variant 882-883/12240 484-485/1422 162/473 H/QX cat/cAat 1 1 CAMK4 HGNC HGNC:1464 protein_coding YES CCDS4103.1 ENSP00000282356 Q16566 UPI000000128E NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4 6/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24349,hmmpanther:PTHR24349:SF152,PROSITE_patterns:PS00108,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 insertion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 66 111446710 111446710 - A 1 0 1 1 0 0 0 0 0 2296 594 21 0 0 CAMK4 5 111446710 Frame_Shift_Ins INS - C3N-01016_T 15657919 111446710 70091549 111 20260 TSSK1B 0 . GRCh38 5 113434563 113434563 + Missense_Mutation SNP C C T rs373083902 C3N-01016_T C3N-01016_N C C c.277G>A p.Ala93Thr p.A93T ENST00000390666 1/1 157 121 36 151 150 1 strelka-varscan-mutect TSSK1B,missense_variant,p.Ala93Thr,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; T ENST00000390666 Transcript missense_variant 469/2478 277/1104 93/367 A/T Gcg/Acg rs373083902,COSM268098,COSM268099 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 deleterious(0) 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 MODERATE SNV 0,1,1 1 PASS rs373083902 . 0 204 3 3 0 0 0 0 -20 0.9999642 1 1 1 0 T 3 4 66 113434563 113434563 C T 1 0 0 0 0 1 0 0 0 17176 768 27 1 1 TSSK1B 5 113434563 Missense_Mutation SNP C C3N-01016_T 1987853 113434563 68103696 112 20261 TSSK1B 0 . GRCh38 5 113434830 113434830 + Missense_Mutation SNP C C A rs200485378 C3N-01016_T C3N-01016_N C C c.10G>T p.Ala4Ser p.A4S ENST00000390666 1/1 60 45 15 53 53 0 strelka-varscan-mutect TSSK1B,missense_variant,p.Ala4Ser,ENST00000390666,NM_032028.3;MCC,intron_variant,,ENST00000408903,NM_001085377.1;CTD-2201G3.1,non_coding_transcript_exon_variant,,ENST00000416046,;CTD-2201G3.1,upstream_gene_variant,,ENST00000510381,; A ENST00000390666 Transcript missense_variant 202/2478 10/1104 4/367 A/S Gct/Tct rs200485378,COSM2991430,COSM2991431 1 -1 TSSK1B HGNC HGNC:14968 protein_coding YES CCDS4112.1 ENSP00000375081 Q9BXA7 A0ZT98 UPI000003C96E NM_032028.3 tolerated(0.12) 1/1 hmmpanther:PTHR24343:SF76,hmmpanther:PTHR24343 0,1,1 MODERATE SNV 0,1,1 1 PASS rs200485378 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 113434830 113434830 C A 1 0 0 0 0 1 0 0 0 17176 768 27 1 1 TSSK1B 5 113434830 Missense_Mutation SNP C C3N-01016_T 267 113434830 68103429 113 20262 LVRN 0 . GRCh38 5 115962968 115962968 + Silent SNP C C T rs756915267 C3N-01016_T C3N-01016_N C C c.351C>T p.= p.P117P ENST00000357872 1/20 178 144 34 164 164 0 strelka-varscan-mutect LVRN,synonymous_variant,p.=,ENST00000357872,NM_173800.4;LVRN,synonymous_variant,p.=,ENST00000395528,;LVRN,synonymous_variant,p.=,ENST00000504467,; T ENST00000357872 Transcript synonymous_variant 475/4581 351/2973 117/990 P ccC/ccT rs756915267 1 1 LVRN HGNC HGNC:26904 protein_coding YES CCDS4124.1 ENSP00000350541 Q6Q4G3 A0A0A6YYA2 UPI0000457329 NM_173800.4 1/20 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF31,Pfam_domain:PF01433,Superfamily_domains:0038696 LOW 1 SNV 1 1 PASS rs756915267 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 115962968 115962968 C T 1 0 0 0 0 0 0 0 1 8998 639 23 1 1 LVRN 5 115962968 Silent SNP C C3N-01016_T 2528138 115962968 65575291 114 20263 FBN2 0 . GRCh38 5 128263496 128263496 + Silent SNP A A G novel C3N-01016_T C3N-01016_N A A c.8121T>C p.= p.N2707N ENST00000508053 69/71 383 303 80 412 411 1 strelka-varscan-mutect FBN2,synonymous_variant,p.=,ENST00000508053,;FBN2,synonymous_variant,p.=,ENST00000262464,NM_001999.3;FBN2,synonymous_variant,p.=,ENST00000619499,; G ENST00000508053 Transcript synonymous_variant 9096/11132 8121/8739 2707/2912 N aaT/aaC 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 69/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 66 128263496 128263496 A G 1 0 0 0 0 0 0 0 1 5566 98 4 5 5 FBN2 5 128263496 Silent SNP A C3N-01016_T 12300528 128263496 53274763 115 20264 DCANP1 0 . GRCh38 5 135446730 135446730 + Nonsense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.379G>T p.Gly127Ter p.G127* ENST00000503143 1/1 136 113 23 129 129 0 strelka-varscan-mutect DCANP1,stop_gained,p.Gly127Ter,ENST00000503143,NM_130848.2;TIFAB,3_prime_UTR_variant,,ENST00000537858,NM_001099221.1;CTB-138E5.1,upstream_gene_variant,,ENST00000510230,; A ENST00000503143 Transcript stop_gained 619/3135 379/735 127/244 G/* Gga/Tga 1 -1 DCANP1 HGNC HGNC:24459 protein_coding YES CCDS4186.1 ENSP00000421871 Q8TF63 UPI000006FF8B NM_130848.2 1/1 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 135446730 135446730 C A 1 0 0 0 0 0 1 0 0 4081 632 22 2 2 DCANP1 5 135446730 Nonsense_Mutation SNP C C3N-01016_T 7183234 135446730 46091529 116 20265 PCDHB4 0 . GRCh38 5 141124174 141124174 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.2176G>T p.Val726Leu p.V726L ENST00000194152 1/1 363 292 71 369 368 1 strelka-varscan-mutect PCDHB4,missense_variant,p.Val726Leu,ENST00000194152,NM_018938.3;AC005754.8,downstream_gene_variant,,ENST00000606030,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB4,downstream_gene_variant,,ENST00000623478,; T ENST00000194152 Transcript missense_variant 2376/3825 2176/2388 726/795 V/L Gtg/Ttg 1 1 PCDHB4 HGNC HGNC:8689 protein_coding YES CCDS4246.1 ENSP00000194152 Q9Y5E5 UPI00001273DF NM_018938.3 deleterious_low_confidence(0.05) 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF55 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 141124174 141124174 G T 1 0 0 0 0 1 0 0 0 11631 1261 44 2 2 PCDHB4 5 141124174 Missense_Mutation SNP G C3N-01016_T 5677444 141124174 40414085 117 20266 PCDHB6 0 . GRCh38 5 141151281 141151281 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1024G>T p.Ala342Ser p.A342S ENST00000231136 1/1 166 134 32 159 159 0 strelka-varscan-mutect PCDHB6,missense_variant,p.Ala342Ser,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Ala206Ser,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; T ENST00000231136 Transcript missense_variant 1260/3266 1024/2385 342/794 A/S Gcc/Tcc 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 tolerated_low_confidence(0.13) 1/1 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 PASS rs782430920 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 141151281 141151281 G T 1 0 0 0 0 1 0 0 0 11633 1319 46 2 2 PCDHB6 5 141151281 Missense_Mutation SNP G C3N-01016_T 27107 141151281 40386978 118 20267 PCDHB8 0 . GRCh38 5 141178916 141178916 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.882G>T p.Lys294Asn p.K294N ENST00000239444 1/1 286 265 21 227 227 0 strelka-varscan-mutect PCDHB8,missense_variant,p.Lys294Asn,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; T ENST00000239444 Transcript missense_variant 1127/2740 882/2406 294/801 K/N aaG/aaT COSM3610750 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 deleterious_low_confidence(0.04) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 141178916 141178916 G T 1 0 0 0 0 1 0 0 0 11635 991 35 2 2 PCDHB8 5 141178916 Missense_Mutation SNP G C3N-01016_T 27635 141178916 40359343 119 20268 PCDHGA7 0 . GRCh38 5 141383344 141383344 + Frame_Shift_Del DEL G G - novel C3N-01016_T C3N-01016_N G G c.448delG p.Val150PhefsTer5 p.V150Ffs*5 ENST00000518325 1/4 256 218 38 248 248 0 sindel-varindel PCDHGA7,frameshift_variant,p.Val150PhefsTer5,ENST00000518325,NM_018920.3;PCDHGA7,frameshift_variant,p.Val150PhefsTer5,ENST00000617050,NM_032087.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,downstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGB4,upstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB4,upstream_gene_variant,,ENST00000519479,NM_003736.2;PCDHGA3,intron_variant,,ENST00000612467,; - ENST00000518325 Transcript frameshift_variant 445/4605 445/2799 149/932 G/X Ggg/gg 1 1 PCDHGA7 HGNC HGNC:8705 protein_coding YES CCDS54927.1 ENSP00000430024 Q9Y5G6 UPI000007146F NM_018920.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,Superfamily_domains:SSF49313 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 66 141383344 141383344 G - 1 0 1 0 1 0 0 0 0 11646 1348 47 0 0 PCDHGA7 5 141383344 Frame_Shift_Del DEL G C3N-01016_T 204428 141383344 40154915 120 20269 PCDH1 0 . GRCh38 5 141864104 141864104 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2227G>T p.Asp743Tyr p.D743Y ENST00000287008 3/5 71 60 11 44 44 0 strelka-varscan-mutect PCDH1,missense_variant,p.Asp743Tyr,ENST00000287008,NM_032420.3;PCDH1,missense_variant,p.Asp743Tyr,ENST00000394536,NM_001278613.1,NM_002587.4;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,downstream_gene_variant,,ENST00000514773,;PCDH1,non_coding_transcript_exon_variant,,ENST00000357517,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,downstream_gene_variant,,ENST00000505937,; A ENST00000287008 Transcript missense_variant 2375/4793 2227/3714 743/1237 D/Y Gac/Tac 1 -1 PCDH1 HGNC HGNC:8655 protein_coding YES CCDS4267.1 ENSP00000287008 Q08174 UPI000016158F NM_032420.3 deleterious(0) 3/5 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF326,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -19.99999 1 1 1 1 0 A 3 1 66 141864104 141864104 C A 1 0 0 0 0 1 0 0 0 11593 855 30 2 2 PCDH1 5 141864104 Missense_Mutation SNP C C3N-01016_T 480760 141864104 39674155 121 20270 SPINK5 0 . GRCh38 5 148095822 148095822 + Missense_Mutation SNP C C A rs200808369 C3N-01016_T C3N-01016_N C C c.799C>A p.Gln267Lys p.Q267K ENST00000359874 10/34 251 188 63 201 201 0 strelka-varscan-mutect SPINK5,missense_variant,p.Gln267Lys,ENST00000359874,NM_001127698.1;SPINK5,missense_variant,p.Gln267Lys,ENST00000256084,NM_006846.3;SPINK5,missense_variant,p.Gln267Lys,ENST00000398454,NM_001127699.1;SPINK5,missense_variant,p.Gln248Lys,ENST00000508733,;SPINK5,non_coding_transcript_exon_variant,,ENST00000476608,;SPINK5,non_coding_transcript_exon_variant,,ENST00000481286,;SPINK5,3_prime_UTR_variant,,ENST00000476697,;SPINK5,non_coding_transcript_exon_variant,,ENST00000507988,; A ENST00000359874 Transcript missense_variant 872/3656 799/3285 267/1094 Q/K Cag/Aag rs200808369 1 1 SPINK5 HGNC HGNC:15464 protein_coding YES CCDS47300.1 ENSP00000352936 Q9NQ38 UPI000020CF25 NM_001127698.1 tolerated(0.98) 10/34 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51465,Gene3D:1.10.1890.10,Pfam_domain:PF07648,SMART_domains:SM00280,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS rs200808369 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 148095822 148095822 C A 1 0 0 0 0 1 0 0 0 15415 724 25 2 2 SPINK5 5 148095822 Missense_Mutation SNP C C3N-01016_T 6231718 148095822 33442437 122 20271 PPARGC1B 0 . GRCh38 5 149836490 149836490 + Missense_Mutation SNP G G T rs755834462 C3N-01016_T C3N-01016_N G G c.2035G>T p.Ala679Ser p.A679S ENST00000309241 8/12 252 229 23 245 245 0 strelka-varscan-mutect PPARGC1B,missense_variant,p.Ala679Ser,ENST00000309241,NM_133263.3;PPARGC1B,missense_variant,p.Ala679Ser,ENST00000394320,;PPARGC1B,missense_variant,p.Ala615Ser,ENST00000403750,NM_001172699.1;PPARGC1B,missense_variant,p.Ala640Ser,ENST00000360453,NM_001172698.1;PPARGC1B,missense_variant,p.Ala366Ser,ENST00000434684,; T ENST00000309241 Transcript missense_variant 2067/10568 2035/3072 679/1023 A/S Gct/Tct rs755834462 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 tolerated(0.11) 8/12 hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 MODERATE 1 SNV 1 1 PASS rs755834462 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 149836490 149836490 G T 1 0 0 0 0 1 0 0 0 12410 1203 42 2 2 PPARGC1B 5 149836490 Missense_Mutation SNP G C3N-01016_T 1740668 149836490 31701769 123 20272 PPARGC1B 0 . GRCh38 5 149836551 149836551 + Missense_Mutation SNP G G T rs747080012 C3N-01016_T C3N-01016_N G G c.2096G>T p.Arg699Leu p.R699L ENST00000309241 8/12 375 284 91 441 441 0 strelka-varscan-mutect PPARGC1B,missense_variant,p.Arg699Leu,ENST00000309241,NM_133263.3;PPARGC1B,missense_variant,p.Arg699Leu,ENST00000394320,;PPARGC1B,missense_variant,p.Arg635Leu,ENST00000403750,NM_001172699.1;PPARGC1B,missense_variant,p.Arg660Leu,ENST00000360453,NM_001172698.1;PPARGC1B,missense_variant,p.Arg386Leu,ENST00000434684,; T ENST00000309241 Transcript missense_variant 2128/10568 2096/3072 699/1023 R/L cGa/cTa rs747080012 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 tolerated(0.07) 8/12 hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 MODERATE 1 SNV 1 1 PASS rs747080012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 149836551 149836551 G T 1 0 0 0 0 1 0 0 0 12410 1058 37 1 1 PPARGC1B 5 149836551 Missense_Mutation SNP G C3N-01016_T 61 149836551 31701708 124 20273 PDE6A 0 . GRCh38 5 149896486 149896486 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.1490A>T p.Asp497Val p.D497V ENST00000255266 12/22 257 207 50 233 233 0 strelka-varscan-mutect PDE6A,missense_variant,p.Asp497Val,ENST00000255266,NM_000440.2;PDE6A,missense_variant,p.Asp416Val,ENST00000613228,;PDE6A,missense_variant,p.Asp416Val,ENST00000617647,;PDE6A,non_coding_transcript_exon_variant,,ENST00000508173,; A ENST00000255266 Transcript missense_variant 1610/5642 1490/2583 497/860 D/V gAt/gTt 1 -1 PDE6A HGNC HGNC:8785 protein_coding YES CCDS4299.1 ENSP00000255266 P16499 UPI000013CE9F NM_000440.2 tolerated(0.08) 12/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF115,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 149896486 149896486 T A 1 0 0 0 0 1 0 0 0 11733 1435 50 4 4 PDE6A 5 149896486 Missense_Mutation SNP T C3N-01016_T 59935 149896486 31641773 125 20274 FAM71B 0 . GRCh38 5 157162977 157162977 + Nonsense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.1288G>T p.Glu430Ter p.E430* ENST00000302938 2/2 271 227 44 287 287 0 strelka-varscan-mutect FAM71B,stop_gained,p.Glu430Ter,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; A ENST00000302938 Transcript stop_gained 1384/2515 1288/1818 430/605 E/* Gaa/Taa COSM3613089 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 157162977 157162977 C A 1 0 0 0 0 0 1 0 0 5472 864 30 2 2 FAM71B 5 157162977 Nonsense_Mutation SNP C C3N-01016_T 7266491 157162977 24375282 126 20275 SLU7 0 . GRCh38 5 160415206 160415206 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.89G>T p.Arg30Ile p.R30I ENST00000297151 2/16 137 106 31 174 174 0 strelka-varscan-mutect SLU7,missense_variant,p.Arg30Ile,ENST00000297151,NM_006425.4;SLU7,missense_variant,p.Arg30Ile,ENST00000520664,;SLU7,missense_variant,p.Arg30Ile,ENST00000519349,;SLU7,missense_variant,p.Arg30Ile,ENST00000521826,;SLU7,non_coding_transcript_exon_variant,,ENST00000518268,;SLU7,non_coding_transcript_exon_variant,,ENST00000521190,; A ENST00000297151 Transcript missense_variant 477/3793 89/1761 30/586 R/I aGa/aTa COSM4889509 1 -1 SLU7 HGNC HGNC:16939 protein_coding YES CCDS4352.1 ENSP00000297151 O95391 UPI000013E3CE NM_006425.4 deleterious(0) 2/16 hmmpanther:PTHR12942,hmmpanther:PTHR12942:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 160415206 160415206 C A 1 0 0 0 0 1 0 0 0 15044 913 32 2 2 SLU7 5 160415206 Missense_Mutation SNP C C3N-01016_T 3252229 160415206 21123053 127 20276 ATP10B 0 . GRCh38 5 160632314 160632314 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1435C>A p.Gln479Lys p.Q479K ENST00000327245 13/26 234 185 49 212 212 0 strelka-varscan-mutect ATP10B,missense_variant,p.Gln479Lys,ENST00000327245,NM_025153.2;ATP10B,missense_variant,p.Gln87Lys,ENST00000520108,;CTC-348L5.1,intron_variant,,ENST00000523598,;ATP10B,downstream_gene_variant,,ENST00000326831,;ATP10B,downstream_gene_variant,,ENST00000517802,;ATP10B,downstream_gene_variant,,ENST00000521033,; T ENST00000327245 Transcript missense_variant 2282/7566 1435/4386 479/1461 Q/K Caa/Aaa 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 tolerated(1) 13/26 hmmpanther:PTHR24092:SF79,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 160632314 160632314 G T 1 0 0 0 0 1 0 0 0 1269 1357 47 2 2 ATP10B 5 160632314 Missense_Mutation SNP G C3N-01016_T 217108 160632314 20905945 128 20277 FAM196B 0 . GRCh38 5 169883693 169883693 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.206A>T p.Gln69Leu p.Q69L ENST00000377365 2/4 53 43 10 56 56 0 strelka-varscan-mutect FAM196B,missense_variant,p.Gln69Leu,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; A ENST00000377365 Transcript missense_variant 1588/2999 206/1608 69/535 Q/L cAa/cTa 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 deleterious(0.01) 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 MODERATE SNV 2 1 PASS . . 0 199 11 0 0 0 0 0 -19.99979 0.9999749 1 1 1 0 A 3 1 66 169883693 169883693 T A 1 0 0 0 0 1 0 0 0 5374 1812 63 4 4 FAM196B 5 169883693 Missense_Mutation SNP T C3N-01016_T 9251379 169883693 11654566 129 20278 SIRT5 0 . GRCh38 6 13596970 13596970 + Nonsense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.571G>T p.Glu191Ter p.E191* ENST00000606117 7/10 160 105 55 185 185 0 strelka-varscan-mutect SIRT5,stop_gained,p.Glu83Ter,ENST00000397350,NM_001242827.1;SIRT5,stop_gained,p.Glu191Ter,ENST00000606117,NM_012241.4;SIRT5,stop_gained,p.Glu191Ter,ENST00000379262,NM_031244.3;SIRT5,intron_variant,,ENST00000359782,NM_001193267.2;SIRT5,3_prime_UTR_variant,,ENST00000379250,; T ENST00000606117 Transcript stop_gained 867/3922 571/933 191/310 E/* Gaa/Taa 1 1 SIRT5 HGNC HGNC:14933 protein_coding YES CCDS4526.1 ENSP00000476228 Q9NXA8 A0A024R012 UPI0000073EB3 NM_012241.4 7/10 Gene3D:3.30.1600.10,HAMAP:MF_01121,Pfam_domain:PF02146,PROSITE_profiles:PS50305,hmmpanther:PTHR11085,hmmpanther:PTHR11085:SF24,Superfamily_domains:SSF52467 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 13596970 13596970 G T 1 0 0 0 0 0 1 0 0 14604 943 33 2 2 SIRT5 6 13596970 Nonsense_Mutation SNP G C3N-01016_T 13596970 157209009 130 20279 GPX6 0 . GRCh38 6 28504416 28504416 + Nonsense_Mutation SNP C C T C3N-01016_T C3N-01016_N C C c.542G>A p.Trp181Ter p.W181* ENST00000361902 5/5 367 306 61 395 395 0 strelka-varscan-mutect GPX6,stop_gained,p.Trp181Ter,ENST00000361902,NM_182701.1;GPX6,stop_gained,p.Trp180Ter,ENST00000612264,;GPX6,missense_variant,p.Gly148Arg,ENST00000474923,;GPX6,downstream_gene_variant,,ENST00000483058,; T ENST00000361902 Transcript stop_gained 592/1712 542/666 181/221 W/* tGg/tAg COSM3623754 1 -1 GPX6 HGNC HGNC:4558 protein_coding YES CCDS43432.1 ENSP00000354581 P59796 UPI00001B2975 NM_182701.1 5/5 Gene3D:3.40.30.10,PIRSF_domain:PIRSF000303,Prints_domain:PR01011,PROSITE_profiles:PS51355,hmmpanther:PTHR11592,hmmpanther:PTHR11592:SF15,Superfamily_domains:SSF52833 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 28504416 28504416 C T 1 0 0 0 0 0 1 0 0 6623 604 21 3 3 GPX6 6 28504416 Nonsense_Mutation SNP C C3N-01016_T 14907446 28504416 142301563 131 20280 TNXB 0 . GRCh38 6 32061433 32061433 + Missense_Mutation SNP G G A rs752650618 C3N-01016_T C3N-01016_N G G c.7456C>T p.Arg2486Trp p.R2486W ENST00000375244 21/44 196 167 29 148 147 1 strelka-varscan-mutect TNXB,missense_variant,p.Arg2486Trp,ENST00000375244,NM_019105.6;TNXB,missense_variant,p.Arg206Trp,ENST00000611016,;TNXB,downstream_gene_variant,,ENST00000613214,; A ENST00000375244 Transcript missense_variant 7658/13132 7456/12735 2486/4244 R/W Cgg/Tgg rs752650618,COSM3347950,COSM3347951 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 deleterious(0) 21/44 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs752650618 . 0 201 8 0 0 0 0 0 -20 0.9999979 1 1 1 0 A 3 1 66 32061433 32061433 G A 1 0 0 0 0 1 0 0 0 16820 1086 38 1 1 TNXB 6 32061433 Missense_Mutation SNP G C3N-01016_T 3557017 32061433 138744546 132 20281 TNXB 0 . GRCh38 6 32067939 32067939 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.6266C>A p.Ala2089Asp p.A2089D ENST00000375244 18/44 217 169 48 166 166 0 strelka-varscan-mutect TNXB,missense_variant,p.Ala2089Asp,ENST00000375244,NM_019105.6;TNXB,3_prime_UTR_variant,,ENST00000613214,; T ENST00000375244 Transcript missense_variant 6468/13132 6266/12735 2089/4244 A/D gCc/gAc 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 tolerated(0.07) 18/44 Low_complexity_(Seg):seg,Gene3D:2.60.40.10 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 32067939 32067939 G T 1 0 0 0 0 1 0 0 0 16820 1203 42 2 2 TNXB 6 32067939 Missense_Mutation SNP G C3N-01016_T 6506 32067939 138738040 133 20282 MDGA1 0 . GRCh38 6 37650214 37650214 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1504G>C p.Glu502Gln p.E502Q ENST00000434837 8/17 133 87 46 93 93 0 strelka-varscan-mutect MDGA1,missense_variant,p.Glu502Gln,ENST00000434837,NM_153487.3;MDGA1,missense_variant,p.Glu502Gln,ENST00000505425,;MDGA1,upstream_gene_variant,,ENST00000418178,;MDGA1,upstream_gene_variant,,ENST00000510077,;MDGA1,non_coding_transcript_exon_variant,,ENST00000478143,;MDGA1,upstream_gene_variant,,ENST00000502298,; G ENST00000434837 Transcript missense_variant 2683/10736 1504/2868 502/955 E/Q Gag/Cag 1 -1 MDGA1 HGNC HGNC:19267 protein_coding YES CCDS47417.1 ENSP00000402584 Q8NFP4 UPI0000071D28 NM_153487.3 tolerated(0.58) 8/17 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF66,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 37650214 37650214 C G 1 0 0 0 0 1 0 0 0 9344 864 30 4 4 MDGA1 6 37650214 Missense_Mutation SNP C C3N-01016_T 5582275 37650214 133155765 134 20283 BTBD9 0 . GRCh38 6 38597942 38597942 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.153G>T p.Arg51Ser p.R51S ENST00000481247 2/11 143 109 34 129 129 0 strelka-varscan-mutect BTBD9,missense_variant,p.Arg51Ser,ENST00000481247,NM_052893.1,NM_001099272.1;BTBD9,missense_variant,p.Arg51Ser,ENST00000403056,;BTBD9,missense_variant,p.Arg51Ser,ENST00000498633,;BTBD9,5_prime_UTR_variant,,ENST00000497373,;BTBD9,upstream_gene_variant,,ENST00000314100,NM_152733.2;BTBD9,upstream_gene_variant,,ENST00000419706,NM_001172418.1;BTBD9,upstream_gene_variant,,ENST00000408958,;BTBD9,upstream_gene_variant,,ENST00000328403,; A ENST00000481247 Transcript missense_variant 305/8525 153/1839 51/612 R/S agG/agT 1 -1 BTBD9 HGNC HGNC:21228 protein_coding YES CCDS47418.1 ENSP00000418751 Q96Q07 UPI00001C040E NM_052893.1,NM_001099272.1 deleterious(0) 2/11 PROSITE_profiles:PS50097,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF79,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 5 1 PASS rs1477598121 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 38597942 38597942 C A 1 0 0 0 0 1 0 0 0 1724 622 22 2 2 BTBD9 6 38597942 Missense_Mutation SNP C C3N-01016_T 947728 38597942 132208037 135 20284 TNFRSF21 0 . GRCh38 6 47286107 47286107 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.585G>C p.Gln195His p.Q195H ENST00000296861 2/6 504 421 83 440 440 0 strelka-varscan-mutect TNFRSF21,missense_variant,p.Gln195His,ENST00000296861,NM_014452.4; G ENST00000296861 Transcript missense_variant 979/3595 585/1968 195/655 Q/H caG/caC 1 -1 TNFRSF21 HGNC HGNC:13469 protein_coding YES CCDS4921.1 ENSP00000296861 O75509 A0A024RD71 UPI000004680F NM_014452.4 tolerated(0.52) 2/6 hmmpanther:PTHR23097:SF127,hmmpanther:PTHR23097,Pfam_domain:PF00020,SMART_domains:SM00208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 47286107 47286107 C G 1 0 0 0 0 1 0 0 0 16769 912 32 4 4 TNFRSF21 6 47286107 Missense_Mutation SNP C C3N-01016_T 8688165 47286107 123519872 136 20285 ADGRB3 0 . GRCh38 6 68638859 68638859 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.184C>A p.Pro62Thr p.P62T ENST00000370598 3/32 224 192 32 165 165 0 strelka-varscan-mutect ADGRB3,missense_variant,p.Pro62Thr,ENST00000370598,NM_001704.2;ADGRB3,missense_variant,p.Pro62Thr,ENST00000546190,;RP3-525N10.2,upstream_gene_variant,,ENST00000604392,;RP3-525N10.2,upstream_gene_variant,,ENST00000603261,;RP3-525N10.2,upstream_gene_variant,,ENST00000419979,; A ENST00000370598 Transcript missense_variant 1005/6010 184/4569 62/1522 P/T Cca/Aca 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 deleterious(0) 3/32 PROSITE_profiles:PS01180,Prints_domain:PR01694 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 68638859 68638859 C A 1 0 0 0 0 1 0 0 0 357 855 30 2 2 ADGRB3 6 68638859 Missense_Mutation SNP C C3N-01016_T 21352752 68638859 102167120 137 20286 BCKDHB 0 . GRCh38 6 80171298 80171298 + Missense_Mutation SNP G G A rs779760508 C3N-01016_T C3N-01016_N G G c.650G>A p.Ser217Asn p.S217N ENST00000320393 6/10 288 246 42 204 204 0 strelka-varscan-mutect BCKDHB,missense_variant,p.Ser217Asn,ENST00000320393,NM_001318975.1,NM_183050.2;BCKDHB,missense_variant,p.Ser217Asn,ENST00000356489,NM_000056.3;BCKDHB,downstream_gene_variant,,ENST00000369760,; A ENST00000320393 Transcript missense_variant 697/3692 650/1179 217/392 S/N aGc/aAc rs779760508 1 1 BCKDHB HGNC HGNC:987 protein_coding YES CCDS4994.1 ENSP00000318351 P21953 A0A140VKB3 UPI0000001C97 NM_001318975.1,NM_183050.2 tolerated(0.24) 6/10 Gene3D:3.40.50.970,Pfam_domain:PF02779,hmmpanther:PTHR11624,hmmpanther:PTHR11624:SF21,SMART_domains:SM00861,Superfamily_domains:SSF52518 MODERATE 1 SNV 1 1 PASS rs779760508 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 80171298 80171298 G A 1 0 0 0 0 1 0 0 0 1507 971 34 3 3 BCKDHB 6 80171298 Missense_Mutation SNP G C3N-01016_T 11532439 80171298 90634681 138 20287 SYNCRIP 0 . GRCh38 6 85615090 85615090 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1538G>C p.Gly513Ala p.G513A ENST00000369622 11/11 197 158 39 175 175 0 strelka-varscan-mutect SYNCRIP,missense_variant,p.Gly415Ala,ENST00000616122,NM_001253771.1,NM_001159673.1;SYNCRIP,missense_variant,p.Gly513Ala,ENST00000355238,NM_001159676.1,NM_001159674.1,NM_001159677.1;SYNCRIP,missense_variant,p.Gly513Ala,ENST00000369622,NM_006372.4,NM_001159675.1;RP11-321N4.5,missense_variant,p.Gly49Ala,ENST00000503906,; G ENST00000369622 Transcript missense_variant 2039/3023 1538/1872 513/623 G/A gGg/gCg 1 -1 SYNCRIP HGNC HGNC:16918 protein_coding YES CCDS5005.1 ENSP00000358635 O60506 UPI000013CF84 NM_006372.4,NM_001159675.1 deleterious(0.03) 11/11 Low_complexity_(Seg):seg,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF440,TIGRFAM_domain:TIGR01648 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 85615090 85615090 C G 1 0 0 0 0 1 0 0 0 15834 623 22 4 4 SYNCRIP 6 85615090 Missense_Mutation SNP C C3N-01016_T 5443792 85615090 85190889 139 20288 FUT9 0 . GRCh38 6 96204040 96204040 + Silent SNP C C A novel C3N-01016_T C3N-01016_N C C c.885C>A p.= p.P295P ENST00000302103 3/3 53 46 7 33 33 0 strelka-varscan-mutect FUT9,synonymous_variant,p.=,ENST00000302103,NM_006581.3; A ENST00000302103 Transcript synonymous_variant 1211/12783 885/1080 295/359 P ccC/ccA 1 1 FUT9 HGNC HGNC:4020 protein_coding YES CCDS5033.1 ENSP00000302599 Q9Y231 UPI000013E792 NM_006581.3 3/3 Pfam_domain:PF00852,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF10,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -16.6236 1 1 1 1 0 A 2 1 66 96204040 96204040 C A 1 0 0 0 0 0 0 0 1 5983 581 21 2 2 FUT9 6 96204040 Silent SNP C C3N-01016_T 10588950 96204040 74601939 140 20289 KLHL32 0 . GRCh38 6 97114009 97114009 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.854G>T p.Arg285Leu p.R285L ENST00000369261 7/11 271 239 32 236 236 0 strelka-varscan-mutect KLHL32,missense_variant,p.Arg249Leu,ENST00000536676,NM_001286250.1;KLHL32,missense_variant,p.Arg285Leu,ENST00000369261,NM_001323260.1,NM_052904.3;KLHL32,missense_variant,p.Arg216Leu,ENST00000539200,NM_001286251.1;KLHL32,3_prime_UTR_variant,,ENST00000447886,;KLHL32,intron_variant,,ENST00000544166,;KLHL32,intron_variant,,ENST00000620278,NM_001286254.1;KLHL32,intron_variant,,ENST00000369254,; T ENST00000369261 Transcript missense_variant 1217/3698 854/1863 285/620 R/L cGa/cTa COSM3179130 1 1 KLHL32 HGNC HGNC:21221 protein_coding YES CCDS5038.1 ENSP00000358265 Q96NJ5 UPI000020DFAB NM_001323260.1,NM_052904.3 deleterious(0) 7/11 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF65 1 MODERATE 1 SNV 2 1 1 PASS rs1198441138 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 97114009 97114009 G T 1 0 0 0 0 1 0 0 0 8251 1058 37 1 1 KLHL32 6 97114009 Missense_Mutation SNP G C3N-01016_T 909969 97114009 73691970 141 20290 GPRC6A 0 . GRCh38 6 116800622 116800622 + Missense_Mutation SNP G G A novel C3N-01016_T C3N-01016_N G G c.1510C>T p.Pro504Ser p.P504S ENST00000310357 4/6 226 152 74 198 198 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Pro504Ser,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Pro329Ser,ENST00000530250,NM_001286354.1;GPRC6A,intron_variant,,ENST00000368549,NM_001286355.1; A ENST00000310357 Transcript missense_variant 1532/2860 1510/2781 504/926 P/S Cca/Tca 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated(0.71) 4/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 116800622 116800622 G A 1 0 0 0 0 1 0 0 0 6607 1232 43 3 3 GPRC6A 6 116800622 Missense_Mutation SNP G C3N-01016_T 19686613 116800622 54005357 142 20291 CLVS2 0 . GRCh38 6 123011047 123011047 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.452C>A p.Pro151His p.P151H ENST00000275162 3/6 149 102 47 156 156 0 strelka-varscan-mutect CLVS2,missense_variant,p.Pro151His,ENST00000275162,NM_001010852.3;CLVS2,missense_variant,p.Pro5His,ENST00000368438,; A ENST00000275162 Transcript missense_variant 1787/11485 452/984 151/327 P/H cCt/cAt COSM3620102,COSM3620103 1 1 CLVS2 HGNC HGNC:23046 protein_coding YES CCDS34525.1 ENSP00000275162 Q5SYC1 UPI000013DA49 NM_001010852.3 tolerated(0.06) 3/6 PROSITE_profiles:PS50191,hmmpanther:PTHR10174,hmmpanther:PTHR10174:SF73,Pfam_domain:PF00650,Gene3D:3.40.525.10,SMART_domains:SM00516,Superfamily_domains:SSF52087 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 66 123011047 123011047 C A 1 0 0 0 0 1 0 0 0 3345 681 24 2 2 CLVS2 6 123011047 Missense_Mutation SNP C C3N-01016_T 6210425 123011047 47794932 143 20292 TXLNB 0 . GRCh38 6 139270489 139270489 + Nonsense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.654C>A p.Cys218Ter p.C218* ENST00000358430 4/10 193 122 71 152 152 0 strelka-varscan-mutect TXLNB,stop_gained,p.Cys218Ter,ENST00000358430,NM_153235.3;RP11-445F6.2,upstream_gene_variant,,ENST00000441249,;RP1-225E12.3,non_coding_transcript_exon_variant,,ENST00000616537,;RP1-225E12.3,non_coding_transcript_exon_variant,,ENST00000621913,;RP1-225E12.3,non_coding_transcript_exon_variant,,ENST00000612486,; T ENST00000358430 Transcript stop_gained 887/4753 654/2055 218/684 C/* tgC/tgA 1 -1 TXLNB HGNC HGNC:21617 protein_coding YES CCDS34545.1 ENSP00000351206 Q8N3L3 UPI0000072983 NM_153235.3 4/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16127,hmmpanther:PTHR16127:SF10,Pfam_domain:PF09728 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 139270489 139270489 G T 1 0 0 0 0 0 1 0 0 17304 1195 42 2 2 TXLNB 6 139270489 Nonsense_Mutation SNP G C3N-01016_T 16259442 139270489 31535490 144 20293 SYNE1 0 . GRCh38 6 152472413 152472413 + Missense_Mutation SNP C C G rs764265403 C3N-01016_T C3N-01016_N C C c.1351G>C p.Asp451His p.D451H ENST00000367255 15/146 252 221 31 207 207 0 strelka-mutect SYNE1,missense_variant,p.Asp451His,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Asp458His,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Asp441His,ENST00000341594,;SYNE1,missense_variant,p.Asp441His,ENST00000367248,;SYNE1,missense_variant,p.Asp451His,ENST00000367253,;SYNE1,missense_variant,p.Asp451His,ENST00000413186,;SYNE1,missense_variant,p.Asp434His,ENST00000537750,;SYNE1,missense_variant,p.Asp451His,ENST00000466159,;SYNE1,missense_variant,p.Asp18His,ENST00000495090,;SYNE1,splice_region_variant,,ENST00000535896,;SYNE1,upstream_gene_variant,,ENST00000481502,;SYNE1,missense_variant,p.Asp17His,ENST00000474655,;SYNE1,splice_region_variant,,ENST00000461872,;SYNE1,non_coding_transcript_exon_variant,,ENST00000468937,; G ENST00000367255 Transcript missense_variant,splice_region_variant 1953/27748 1351/26394 451/8797 D/H Gat/Cat rs764265403 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 15/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267 MODERATE 1 SNV 1 1 PASS rs764265403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 152472413 152472413 C G 1 0 0 0 0 1 0 0 0 15837 869 30 4 4 SYNE1 6 152472413 Missense_Mutation SNP C C3N-01016_T 13201924 152472413 18333566 145 20294 PLG 0 . GRCh38 6 160731082 160731082 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.1288G>C p.Asp430His p.D430H ENST00000308192 11/19 195 154 41 170 170 0 strelka-varscan-mutect PLG,missense_variant,p.Asp430His,ENST00000308192,NM_000301.3;PLG,non_coding_transcript_exon_variant,,ENST00000297289,;PLG,non_coding_transcript_exon_variant,,ENST00000493435,; C ENST00000308192 Transcript missense_variant 1351/2741 1288/2433 430/810 D/H Gat/Cat 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 deleterious(0) 11/19 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001150,Prints_domain:PR00018,PROSITE_patterns:PS00021,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 160731082 160731082 G C 1 0 0 0 0 1 0 0 0 12181 942 33 4 4 PLG 6 160731082 Missense_Mutation SNP G C3N-01016_T 8258669 160731082 10074897 146 20295 GET4 0 . GRCh38 7 893909 893909 + Missense_Mutation SNP G G A rs764382449 C3N-01016_T C3N-01016_N G G c.833G>A p.Arg278His p.R278H ENST00000265857 8/9 110 92 18 79 79 0 strelka-varscan-mutect GET4,missense_variant,p.Arg225His,ENST00000407192,;GET4,missense_variant,p.Arg278His,ENST00000265857,NM_015949.2;ADAP1,downstream_gene_variant,,ENST00000265846,NM_006869.3;ADAP1,downstream_gene_variant,,ENST00000539900,NM_001284308.1;ADAP1,downstream_gene_variant,,ENST00000611167,NM_001284309.1;ADAP1,downstream_gene_variant,,ENST00000449296,NM_001284310.1;ADAP1,downstream_gene_variant,,ENST00000446141,;ADAP1,downstream_gene_variant,,ENST00000617043,NM_001284311.1;GET4,downstream_gene_variant,,ENST00000412734,;GET4,downstream_gene_variant,,ENST00000426056,;SUN1,3_prime_UTR_variant,,ENST00000457861,;GET4,non_coding_transcript_exon_variant,,ENST00000464468,;ADAP1,downstream_gene_variant,,ENST00000495809,;ADAP1,downstream_gene_variant,,ENST00000478000,;COX19,downstream_gene_variant,,ENST00000457254,;GET4,downstream_gene_variant,,ENST00000483469,; A ENST00000265857 Transcript missense_variant 927/2090 833/984 278/327 R/H cGc/cAc rs764382449 1 1 GET4 HGNC HGNC:21690 protein_coding YES CCDS5317.1 ENSP00000265857 Q7L5D6 UPI00001AE543 NM_015949.2 deleterious(0) 8/9 hmmpanther:PTHR12875:SF0,hmmpanther:PTHR12875,Pfam_domain:PF04190 MODERATE 1 SNV 1 1 PASS rs764382449 . 0 187 20 3 0 0 0 0 -20 0.9772685 0 1 1 0 A 3 1 66 893909 893909 G A 1 0 0 0 0 1 0 0 0 6210 1087 38 1 1 GET4 7 893909 Missense_Mutation SNP G C3N-01016_T 893909 158452064 147 20296 CYP2W1 0 . GRCh38 7 987377 987377 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.989T>A p.Leu330Gln p.L330Q ENST00000308919 7/9 86 62 24 90 90 0 strelka-varscan-mutect CYP2W1,missense_variant,p.Leu274Gln,ENST00000340150,;CYP2W1,missense_variant,p.Leu330Gln,ENST00000308919,NM_017781.2;CYP2W1,missense_variant,p.Leu104Gln,ENST00000415893,;CYP2W1,non_coding_transcript_exon_variant,,ENST00000468456,;CYP2W1,downstream_gene_variant,,ENST00000462453,; A ENST00000308919 Transcript missense_variant 1002/2304 989/1473 330/490 L/Q cTg/cAg 1 1 CYP2W1 HGNC HGNC:20243 protein_coding YES CCDS5319.2 ENSP00000310149 Q8TAV3 UPI000013C59A NM_017781.2 deleterious(0) 7/9 hmmpanther:PTHR24300:SF183,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 987377 987377 T A 1 0 0 0 0 1 0 0 0 3979 1580 55 4 4 CYP2W1 7 987377 Missense_Mutation SNP T C3N-01016_T 93468 987377 158358596 148 20297 SDK1 0 . GRCh38 7 4114100 4114100 + Missense_Mutation SNP C C T rs758661396 C3N-01016_T C3N-01016_N C C c.3649C>T p.Arg1217Cys p.R1217C ENST00000404826 25/45 489 362 127 404 404 0 strelka-varscan-mutect SDK1,missense_variant,p.Arg1217Cys,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Arg1217Cys,ENST00000615806,;SDK1,missense_variant,p.Arg1217Cys,ENST00000389531,; T ENST00000404826 Transcript missense_variant 3788/10397 3649/6642 1217/2213 R/C Cgc/Tgc rs758661396,COSM272023 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0.04) 25/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs758661396 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 4114100 4114100 C T 1 0 0 0 0 1 0 0 0 14243 768 27 1 1 SDK1 7 4114100 Missense_Mutation SNP C C3N-01016_T 3126723 4114100 155231873 149 20298 RADIL 0 . GRCh38 7 4799678 4799678 + Missense_Mutation SNP C C A rs766532873 C3N-01016_T C3N-01016_N C C c.3074G>T p.Arg1025Leu p.R1025L ENST00000399583 14/15 115 82 33 109 109 0 strelka-varscan-mutect RADIL,missense_variant,p.Arg1025Leu,ENST00000399583,NM_018059.4;RADIL,3_prime_UTR_variant,,ENST00000445392,;RADIL,non_coding_transcript_exon_variant,,ENST00000473130,;RADIL,non_coding_transcript_exon_variant,,ENST00000472999,; A ENST00000399583 Transcript missense_variant 3262/3689 3074/3228 1025/1075 R/L cGt/cTt rs766532873 1 -1 RADIL HGNC HGNC:22226 protein_coding YES CCDS43544.1 ENSP00000382492 Q96JH8 UPI0000E0A787 NM_018059.4 deleterious(0) 14/15 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR16027,hmmpanther:PTHR16027:SF3,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS rs766532873 . 0 201 3 5 0 0 0 0 -20 0.9995056 1 1 1 0 A 3 1 66 4799678 4799678 C A 1 0 0 0 0 1 0 0 0 13158 536 19 1 1 RADIL 7 4799678 Missense_Mutation SNP C C3N-01016_T 685578 4799678 154546295 150 20299 PCLO 0 . GRCh38 7 82950136 82950136 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.10452G>T p.Met3484Ile p.M3484I ENST00000333891 6/25 241 206 35 247 247 0 strelka-varscan PCLO,missense_variant,p.Met3484Ile,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Met3484Ile,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Met204Ile,ENST00000437081,; A ENST00000333891 Transcript missense_variant 10790/20329 10452/15429 3484/5142 M/I atG/atT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.4) 6/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 82950136 82950136 C A 1 0 0 0 0 1 0 0 0 11671 710 25 2 2 PCLO 7 82950136 Missense_Mutation SNP C C3N-01016_T 78150458 82950136 76395837 151 20300 AKAP9 0 . GRCh38 7 91994659 91994659 + Silent SNP C C T novel C3N-01016_T C3N-01016_N C C c.615C>T p.= p.G205G ENST00000356239 6/50 183 148 35 63 63 0 strelka-varscan AKAP9,synonymous_variant,p.=,ENST00000356239,NM_005751.4,NM_147185.2;AKAP9,synonymous_variant,p.=,ENST00000359028,;AKAP9,synonymous_variant,p.=,ENST00000358100,;AKAP9,synonymous_variant,p.=,ENST00000619023,;AKAP9,synonymous_variant,p.=,ENST00000394564,;AKAP9,synonymous_variant,p.=,ENST00000438114,;AKAP9,non_coding_transcript_exon_variant,,ENST00000493453,; T ENST00000356239 Transcript synonymous_variant 848/12471 615/11724 205/3907 G ggC/ggT 1 1 AKAP9 HGNC HGNC:379 protein_coding YES CCDS5622.1 ENSP00000348573 Q99996 UPI000002A38D NM_005751.4,NM_147185.2 6/50 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 91994659 91994659 C T 1 0 0 0 0 0 0 0 1 543 697 25 3 3 AKAP9 7 91994659 Silent SNP C C3N-01016_T 9044523 91994659 67351314 152 20301 FOXP2 0 . GRCh38 7 114658217 114658217 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1493G>T p.Gly498Val p.G498V ENST00000408937 12/18 285 222 63 318 318 0 strelka-varscan FOXP2,missense_variant,p.Gly498Val,ENST00000408937,NM_148898.3;FOXP2,missense_variant,p.Gly490Val,ENST00000403559,NM_148900.3;FOXP2,missense_variant,p.Gly470Val,ENST00000635534,;FOXP2,missense_variant,p.Gly456Val,ENST00000634411,;FOXP2,missense_variant,p.Gly473Val,ENST00000393494,;FOXP2,missense_variant,p.Gly473Val,ENST00000350908,NM_001172766.2,NM_014491.3;FOXP2,missense_variant,p.Gly452Val,ENST00000393498,;FOXP2,missense_variant,p.Gly474Val,ENST00000635638,;FOXP2,missense_variant,p.Gly381Val,ENST00000393489,;FOXP2,missense_variant,p.Gly453Val,ENST00000634623,;FOXP2,intron_variant,,ENST00000393491,;FOXP2,downstream_gene_variant,,ENST00000390668,NM_001172767.2;FOXP2,downstream_gene_variant,,ENST00000360232,NM_148899.3;MIR3666,downstream_gene_variant,,ENST00000607845,;FOXP2,upstream_gene_variant,,ENST00000634664,;FOXP2,3_prime_UTR_variant,,ENST00000441290,;FOXP2,3_prime_UTR_variant,,ENST00000635109,;FOXP2,intron_variant,,ENST00000412402,; T ENST00000408937 Transcript missense_variant 1867/6443 1493/2223 498/740 G/V gGa/gTa 1 1 FOXP2 HGNC HGNC:13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 X5D2H2 UPI000007412B NM_148898.3 deleterious(0) 12/18 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF202 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 114658217 114658217 G T 1 0 0 0 0 1 0 0 0 5892 1174 41 2 2 FOXP2 7 114658217 Missense_Mutation SNP G C3N-01016_T 22663558 114658217 44687756 153 20302 CCDC136 0 . GRCh38 7 128805825 128805825 + Missense_Mutation SNP A A C novel C3N-01016_T C3N-01016_N A A c.1013A>C p.Gln338Pro p.Q338P ENST00000297788 7/18 283 227 56 344 343 1 strelka-varscan CCDC136,missense_variant,p.Gln338Pro,ENST00000297788,NM_022742.4;CCDC136,missense_variant,p.Gln215Pro,ENST00000494552,;CCDC136,missense_variant,p.Gln338Pro,ENST00000487361,;CCDC136,missense_variant,p.Gln388Pro,ENST00000464832,;CCDC136,missense_variant,p.Gln376Pro,ENST00000378685,NM_001201372.1;CCDC136,upstream_gene_variant,,ENST00000464672,;CCDC136,downstream_gene_variant,,ENST00000485998,;CCDC136,non_coding_transcript_exon_variant,,ENST00000480137,;CCDC136,upstream_gene_variant,,ENST00000485832,;CCDC136,upstream_gene_variant,,ENST00000528772,;CCDC136,upstream_gene_variant,,ENST00000460941,; C ENST00000297788 Transcript missense_variant 1380/4169 1013/3465 338/1154 Q/P cAg/cCg 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 deleterious(0) 7/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 128805825 128805825 A C 1 0 0 0 0 1 0 0 0 2459 188 7 5 5 CCDC136 7 128805825 Missense_Mutation SNP A C3N-01016_T 14147608 128805825 30540148 154 20303 FLNC 0 . GRCh38 7 128855288 128855288 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.7225C>A p.Arg2409Ser p.R2409S ENST00000325888 43/48 327 257 70 355 355 0 strelka-varscan FLNC,missense_variant,p.Arg2409Ser,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Arg2376Ser,ENST00000346177,NM_001127487.1;RP11-309L24.2,intron_variant,,ENST00000469965,; A ENST00000325888 Transcript missense_variant 7486/9188 7225/8178 2409/2725 R/S Cgc/Agc 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.6) 43/48 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 128855288 128855288 C A 1 0 0 0 0 1 0 0 0 5791 884 31 1 1 FLNC 7 128855288 Missense_Mutation SNP C C3N-01016_T 49463 128855288 30490685 155 20304 PLXNA4 0 . GRCh38 7 132211144 132211144 + Splice_Site SNP C C A C3N-01016_T C3N-01016_N C C c.2098-1G>T p.X700_splice ENST00000359827 115 93 22 95 95 0 strelka-varscan PLXNA4,splice_acceptor_variant,,ENST00000359827,;PLXNA4,splice_acceptor_variant,,ENST00000321063,NM_020911.1; A ENST00000359827 Transcript splice_acceptor_variant -/13786 2098/5685 700/1894 COSM1448121,COSM1448122,COSM4449353,COSM4449354 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 9/31 1,1,1,1 HIGH 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 66 132211144 132211144 C A 1 0 0 0 0 0 0 1 0 12228 695 24 2 2 PLXNA4 7 132211144 Splice_Site SNP C C3N-01016_T 3355856 132211144 27134829 156 20305 SVOPL 0 . GRCh38 7 138630093 138630093 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.819G>T p.Leu273Phe p.L273F ENST00000419765 9/15 138 114 24 125 125 0 strelka-varscan SVOPL,missense_variant,p.Leu153Phe,ENST00000421622,;SVOPL,missense_variant,p.Leu273Phe,ENST00000419765,NM_001139456.1;SVOPL,missense_variant,p.Leu121Phe,ENST00000436657,NM_174959.3;SVOPL,missense_variant,p.Leu121Phe,ENST00000288513,;SNORA40,upstream_gene_variant,,ENST00000516379,;SVOPL,upstream_gene_variant,,ENST00000463557,;SVOPL,missense_variant,p.Leu26Phe,ENST00000441685,;SVOPL,upstream_gene_variant,,ENST00000478865,; A ENST00000419765 Transcript missense_variant 853/1523 819/1479 273/492 L/F ttG/ttT 1 -1 SVOPL HGNC HGNC:27034 protein_coding YES CCDS47721.1 ENSP00000405482 Q8N434 UPI0001565476 NM_001139456.1 tolerated(0.71) 9/15 Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF168,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 138630093 138630093 C A 1 0 0 0 0 1 0 0 0 15809 593 21 2 2 SVOPL 7 138630093 Missense_Mutation SNP C C3N-01016_T 6418949 138630093 20715880 157 20306 CLEC5A 0 . GRCh38 7 141930193 141930193 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.478A>T p.Asn160Tyr p.N160Y ENST00000546910 7/7 158 133 25 198 198 0 strelka-varscan CLEC5A,missense_variant,p.Asn160Tyr,ENST00000546910,NM_013252.2;CLEC5A,missense_variant,p.Asn137Tyr,ENST00000551012,NM_001301167.1;CLEC5A,missense_variant,p.Asn56Tyr,ENST00000439991,;MGAM,intron_variant,,ENST00000465654,;CLEC5A,downstream_gene_variant,,ENST00000438351,;MGAM,intron_variant,,ENST00000497554,;CLEC5A,downstream_gene_variant,,ENST00000470595,;CLEC5A,3_prime_UTR_variant,,ENST00000418498,;CLEC5A,downstream_gene_variant,,ENST00000481301,; A ENST00000546910 Transcript missense_variant 675/3511 478/567 160/188 N/Y Aac/Tac 1 -1 CLEC5A HGNC HGNC:2054 protein_coding YES CCDS5870.1 ENSP00000449999 Q9NY25 A4D1U7 UPI0000071CCD NM_013252.2 deleterious(0) 7/7 Low_complexity_(Seg):seg,PROSITE_profiles:PS50041,hmmpanther:PTHR22800:SF177,hmmpanther:PTHR22800,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 141930193 141930193 T A 1 0 0 0 0 1 0 0 0 3287 1812 63 4 4 CLEC5A 7 141930193 Missense_Mutation SNP T C3N-01016_T 3300100 141930193 17415780 158 20307 OR2A25 0 . GRCh38 7 144074607 144074607 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.388C>G p.Arg130Gly p.R130G ENST00000408898 1/1 350 286 64 403 403 0 strelka-varscan OR2A25,missense_variant,p.Arg130Gly,ENST00000408898,NM_001004488.1;OR2A41P,upstream_gene_variant,,ENST00000473586,; G ENST00000408898 Transcript missense_variant 426/1014 388/933 130/310 R/G Cga/Gga 1 1 OR2A25 HGNC HGNC:19562 protein_coding YES CCDS43669.1 ENSP00000386167 A4D2G3 A0A126GVV5 UPI00002373C5 NM_001004488.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF146,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 144074607 144074607 C G 1 0 0 0 0 1 0 0 0 11055 644 23 4 4 OR2A25 7 144074607 Missense_Mutation SNP C C3N-01016_T 2144414 144074607 15271366 159 20308 GIMAP8 0 . GRCh38 7 150474201 150474201 + Missense_Mutation SNP G G A C3N-01016_T C3N-01016_N G G c.872G>A p.Arg291Lys p.R291K ENST00000307271 4/5 261 206 55 319 319 0 strelka-varscan GIMAP8,missense_variant,p.Arg291Lys,ENST00000307271,NM_175571.3; A ENST00000307271 Transcript missense_variant 1446/4184 872/1998 291/665 R/K aGa/aAa COSM3260612 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 deleterious(0.04) 4/5 PROSITE_profiles:PS51720,Gene3D:3.40.50.300,Pfam_domain:PF04548,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 150474201 150474201 G A 1 0 0 0 0 1 0 0 0 6265 942 33 3 3 GIMAP8 7 150474201 Missense_Mutation SNP G C3N-01016_T 6399594 150474201 8871772 160 20309 ADAM7 0 . GRCh38 8 24441133 24441133 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.25A>G p.Met9Val p.M9V ENST00000175238 1/22 182 149 33 136 136 0 strelka-varscan-mutect ADAM7,missense_variant,p.Met9Val,ENST00000175238,NM_003817.3;ADAM7,missense_variant,p.Met9Val,ENST00000380789,;ADAM7,missense_variant,p.Met9Val,ENST00000441335,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,; G ENST00000175238 Transcript missense_variant 108/3367 25/2265 9/754 M/V Atg/Gtg 1 1 ADAM7 HGNC HGNC:214 protein_coding YES CCDS6045.1 ENSP00000175238 Q9H2U9 UPI000013C5CC NM_003817.3 tolerated(0.21) 1/22 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 24441133 24441133 A G 1 0 0 0 0 1 0 0 0 295 333 12 5 5 ADAM7 8 24441133 Missense_Mutation SNP A C3N-01016_T 24441133 120697503 161 20310 CDCA2 0 . GRCh38 8 25506843 25506843 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.2177G>T p.Ser726Ile p.S726I ENST00000330560 15/15 208 164 44 187 187 0 strelka-varscan-mutect CDCA2,missense_variant,p.Ser726Ile,ENST00000330560,NM_001317907.1,NM_152562.2;CDCA2,missense_variant,p.Ser711Ile,ENST00000380665,NM_001317906.1;CDCA2,non_coding_transcript_exon_variant,,ENST00000521098,; T ENST00000330560 Transcript missense_variant 2654/3731 2177/3072 726/1023 S/I aGt/aTt 1 1 CDCA2 HGNC HGNC:14623 protein_coding YES CCDS6049.1 ENSP00000328228 Q69YH5 UPI000013DF9A NM_001317907.1,NM_152562.2 tolerated(0.16) 15/15 hmmpanther:PTHR21603:SF16,hmmpanther:PTHR21603 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 25506843 25506843 G T 1 0 0 0 0 1 0 0 0 2789 1029 36 2 2 CDCA2 8 25506843 Missense_Mutation SNP G C3N-01016_T 1065710 25506843 119631793 162 20311 UNC5D 0 . GRCh38 8 35790539 35790539 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2838C>A p.Asn946Lys p.N946K ENST00000404895 17/17 271 198 73 244 244 0 strelka-varscan UNC5D,missense_variant,p.Asn877Lys,ENST00000287272,;UNC5D,missense_variant,p.Asn941Lys,ENST00000453357,;UNC5D,missense_variant,p.Asn951Lys,ENST00000416672,;UNC5D,missense_variant,p.Asn946Lys,ENST00000404895,NM_080872.2;UNC5D,missense_variant,p.Asn879Lys,ENST00000420357,;UNC5D,missense_variant,p.Asn522Lys,ENST00000449677,; A ENST00000404895 Transcript missense_variant 3166/3252 2838/2862 946/953 N/K aaC/aaA 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 tolerated_low_confidence(0.2) 17/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 35790539 35790539 C A 1 0 0 0 0 1 0 0 0 17519 564 20 2 2 UNC5D 8 35790539 Missense_Mutation SNP C C3N-01016_T 10283696 35790539 109348097 163 20312 WHSC1L1 0 . GRCh38 8 38275670 38275670 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.4285C>G p.Gln1429Glu p.Q1429E ENST00000317025 24/24 153 108 45 165 164 1 strelka-varscan WHSC1L1,missense_variant,p.Gln1429Glu,ENST00000317025,NM_023034.1;WHSC1L1,missense_variant,p.Gln1380Glu,ENST00000433384,;WHSC1L1,missense_variant,p.Gln1418Glu,ENST00000527502,;RP11-513D5.5,upstream_gene_variant,,ENST00000529325,;DDHD2,downstream_gene_variant,,ENST00000529872,;DDHD2,downstream_gene_variant,,ENST00000526071,;WHSC1L1,non_coding_transcript_exon_variant,,ENST00000528828,; C ENST00000317025 Transcript missense_variant 4803/10776 4285/4314 1429/1437 Q/E Caa/Gaa 1 -1 WHSC1L1 HGNC HGNC:12767 protein_coding YES CCDS43729.1 ENSP00000313983 Q9BZ95 UPI000006F297 NM_023034.1 tolerated_low_confidence(0.1) 24/24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 38275670 38275670 G C 1 0 0 0 0 1 0 0 0 17921 1386 48 4 4 WHSC1L1 8 38275670 Missense_Mutation SNP G C3N-01016_T 2485131 38275670 106862966 164 20313 SOX17 0 . GRCh38 8 54459215 54459215 + Missense_Mutation SNP C C G rs765170070 C3N-01016_T C3N-01016_N C C c.465C>G p.Phe155Leu p.F155L ENST00000297316 2/2 124 101 23 103 103 0 strelka-varscan SOX17,missense_variant,p.Phe155Leu,ENST00000297316,NM_022454.3; G ENST00000297316 Transcript missense_variant 669/2342 465/1245 155/414 F/L ttC/ttG rs765170070 1 1 SOX17 HGNC HGNC:18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 UPI00001362B7 NM_022454.3 tolerated(0.27) 2/2 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF216 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 54459215 54459215 C G 1 0 0 0 0 1 0 0 0 15273 854 30 4 4 SOX17 8 54459215 Missense_Mutation SNP C C3N-01016_T 16183545 54459215 90679421 165 20314 CSPP1 0 . GRCh38 8 67103056 67103056 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.970G>T p.Gly324Trp p.G324W ENST00000262210 7/29 150 126 24 111 111 0 strelka-varscan CSPP1,missense_variant,p.Gly324Trp,ENST00000262210,NM_024790.6;CSPP1,missense_variant,p.Gly30Trp,ENST00000519668,NM_001291339.1;RNA5SP268,downstream_gene_variant,,ENST00000516828,;CSPP1,missense_variant,p.Gly323Trp,ENST00000519163,; T ENST00000262210 Transcript missense_variant 1001/4367 970/3666 324/1221 G/W Ggg/Tgg COSM4641281 1 1 CSPP1 HGNC HGNC:26193 protein_coding YES CCDS43744.1 ENSP00000262210 Q1MSJ5 UPI00005A95D7 NM_024790.6 deleterious(0.02) 7/29 hmmpanther:PTHR21616 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 67103056 67103056 G T 1 0 0 0 0 1 0 0 0 3763 1000 35 2 2 CSPP1 8 67103056 Missense_Mutation SNP G C3N-01016_T 12643841 67103056 78035580 166 20315 MSC 0 . GRCh38 8 71843848 71843848 + Missense_Mutation SNP C C G C3N-01016_T C3N-01016_N C C c.331G>C p.Ala111Pro p.A111P ENST00000325509 1/2 201 153 48 204 204 0 strelka-varscan MSC,missense_variant,p.Ala111Pro,ENST00000325509,NM_005098.3;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000521467,;MSC-AS1,upstream_gene_variant,,ENST00000457356,;MSC-AS1,upstream_gene_variant,,ENST00000518916,;MSC-AS1,upstream_gene_variant,,ENST00000519751,;MSC,upstream_gene_variant,,ENST00000518440,;MSC,upstream_gene_variant,,ENST00000521739,; G ENST00000325509 Transcript missense_variant 621/2023 331/621 111/206 A/P Gcg/Ccg COSM3432550,COSM5548415 1 -1 MSC HGNC HGNC:7321 protein_coding YES CCDS43746.1 ENSP00000321445 O60682 UPI000012FA29 NM_005098.3 deleterious(0) 1/2 Low_complexity_(Seg):seg,PROSITE_profiles:PS50888,hmmpanther:PTHR23349:SF62,hmmpanther:PTHR23349,Gene3D:4.10.280.10,Pfam_domain:PF00010,Superfamily_domains:SSF47459 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 71843848 71843848 C G 1 0 0 0 0 1 0 0 0 9851 768 27 4 4 MSC 8 71843848 Missense_Mutation SNP C C3N-01016_T 4740792 71843848 73294788 167 20316 TRPA1 0 . GRCh38 8 72026046 72026046 + Nonsense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.2965A>T p.Lys989Ter p.K989* ENST00000262209 25/27 308 249 59 262 262 0 strelka-varscan TRPA1,stop_gained,p.Lys989Ter,ENST00000262209,NM_007332.2;TRPA1,stop_gained,p.Lys841Ter,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,upstream_gene_variant,,ENST00000512290,;TRPA1,upstream_gene_variant,,ENST00000520596,; A ENST00000262209 Transcript stop_gained 3173/5223 2965/3360 989/1119 K/* Aag/Tag 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 25/27 hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 72026046 72026046 T A 1 0 0 0 0 0 1 0 0 17082 1792 62 4 4 TRPA1 8 72026046 Nonsense_Mutation SNP T C3N-01016_T 182198 72026046 73112590 168 20317 JPH1 0 . GRCh38 8 74315610 74315610 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.390G>C p.Gln130His p.Q130H ENST00000342232 2/6 136 104 32 88 88 0 strelka-varscan JPH1,missense_variant,p.Gln130His,ENST00000342232,NM_020647.2;JPH1,missense_variant,p.Gly9Arg,ENST00000519947,; G ENST00000342232 Transcript missense_variant 431/4378 390/1986 130/661 Q/H caG/caC 1 -1 JPH1 HGNC HGNC:14201 protein_coding YES CCDS6217.1 ENSP00000344488 Q9HDC5 UPI000012DAC0 NM_020647.2 deleterious(0.02) 2/6 hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF6,PIRSF_domain:PIRSF037387,Gene3D:1h3iA01,Pfam_domain:PF02493,SMART_domains:SM00698,Superfamily_domains:0038399 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 74315610 74315610 C G 1 0 0 0 0 1 0 0 0 7872 680 24 4 4 JPH1 8 74315610 Missense_Mutation SNP C C3N-01016_T 2289564 74315610 70823026 169 20318 SLC26A7 0 . GRCh38 8 91352919 91352919 + Missense_Mutation SNP A A G C3N-01016_T C3N-01016_N A A c.1237A>G p.Ile413Val p.I413V ENST00000309536 11/19 265 233 32 89 89 0 strelka-varscan SLC26A7,missense_variant,p.Ile413Val,ENST00000276609,NM_052832.3;SLC26A7,missense_variant,p.Ile413Val,ENST00000617233,;SLC26A7,missense_variant,p.Ile112Val,ENST00000617078,NM_001282357.1;SLC26A7,missense_variant,p.Ile413Val,ENST00000523719,NM_001282356.1;SLC26A7,missense_variant,p.Ile413Val,ENST00000309536,NM_134266.1;SLC26A7,non_coding_transcript_exon_variant,,ENST00000520249,;SLC26A7,upstream_gene_variant,,ENST00000517930,;SLC26A7,3_prime_UTR_variant,,ENST00000522181,; G ENST00000309536 Transcript missense_variant 1457/2656 1237/1992 413/663 I/V Att/Gtt COSM5216773,COSM5216774 1 1 SLC26A7 HGNC HGNC:14467 protein_coding YES CCDS6255.1 ENSP00000309504 Q8TE54 UPI0000046B1C NM_134266.1 tolerated(0.95) 11/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR11814:SF75,hmmpanther:PTHR11814,Pfam_domain:PF00916 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 91352919 91352919 A G 1 0 0 0 0 1 0 0 0 14792 449 16 5 5 SLC26A7 8 91352919 Missense_Mutation SNP A C3N-01016_T 17037309 91352919 53785717 170 20319 PKHD1L1 0 . GRCh38 8 109489972 109489972 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.9901G>T p.Val3301Leu p.V3301L ENST00000378402 60/78 291 269 22 149 149 0 strelka-varscan PKHD1L1,missense_variant,p.Val3301Leu,ENST00000378402,NM_177531.4;PKHD1L1,missense_variant,p.Val229Leu,ENST00000526472,; T ENST00000378402 Transcript missense_variant 10005/13076 9901/12732 3301/4243 V/L Gtg/Ttg COSM5040362 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 60/78 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF330,SMART_domains:SM00710,Superfamily_domains:SSF51126 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 109489972 109489972 G T 1 0 0 0 0 1 0 0 0 12068 1377 48 2 2 PKHD1L1 8 109489972 Missense_Mutation SNP G C3N-01016_T 18137053 109489972 35648664 171 20320 KCNK9 0 . GRCh38 8 139618380 139618380 + Nonsense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.1003G>T p.Glu335Ter p.E335* ENST00000520439 2/2 823 448 375 729 727 2 strelka-varscan KCNK9,stop_gained,p.Glu335Ter,ENST00000520439,NM_001282534.1;KCNK9,stop_gained,p.Glu335Ter,ENST00000303015,;KCNK9,upstream_gene_variant,,ENST00000523477,;KCNK9,upstream_gene_variant,,ENST00000519923,;KCNK9,stop_gained,p.Glu335Ter,ENST00000522317,; A ENST00000520439 Transcript stop_gained 1067/1441 1003/1125 335/374 E/* Gag/Tag COSM3645689,COSM3645690 1 -1 KCNK9 HGNC HGNC:6283 protein_coding YES CCDS6377.1 ENSP00000430676 Q9NPC2 A0A024R9H3 UPI000000D8AC NM_001282534.1 2/2 hmmpanther:PTHR11003:SF75,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061,Prints_domain:PR01585 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 139618380 139618380 C A 1 0 0 0 0 0 1 0 0 7989 893 31 1 1 KCNK9 8 139618380 Nonsense_Mutation SNP C C3N-01016_T 30128408 139618380 5520256 172 20321 LY6H 0 . GRCh38 8 143158256 143158256 + Silent SNP C C A rs759590027 C3N-01016_T C3N-01016_N C C c.480G>T p.= p.G160G ENST00000414417 5/5 187 86 101 127 127 0 strelka-varscan LY6H,synonymous_variant,p.=,ENST00000414417,NM_001130478.1;LY6H,synonymous_variant,p.=,ENST00000615409,;LY6H,synonymous_variant,p.=,ENST00000342752,NM_001135655.1;LY6H,synonymous_variant,p.=,ENST00000430474,NM_002347.4;LY6H,non_coding_transcript_exon_variant,,ENST00000479685,; A ENST00000414417 Transcript synonymous_variant 714/1056 480/486 160/161 G ggG/ggT rs759590027,COSM5289859,COSM5289860 1 -1 LY6H HGNC HGNC:6728 protein_coding YES CCDS47926.1 ENSP00000399485 O94772 UPI00005A7901 NM_001130478.1 5/5 hmmpanther:PTHR32217,hmmpanther:PTHR32217:SF5,Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 143158256 143158256 C A 1 0 0 0 0 0 0 0 1 9008 726 26 2 2 LY6H 8 143158256 Silent SNP C C3N-01016_T 3539876 143158256 1980380 173 20322 CCDC166 0 . GRCh38 8 143707753 143707753 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.357C>T p.= p.R119R ENST00000542437 1/2 216 181 35 125 125 0 strelka-varscan CCDC166,synonymous_variant,p.=,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; A ENST00000542437 Transcript synonymous_variant 357/1320 357/1320 119/439 R cgC/cgT 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 1/2 Pfam_domain:PF14988,hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 143707753 143707753 G A 1 0 0 0 0 0 0 0 1 2482 1074 38 1 1 CCDC166 8 143707753 Silent SNP G C3N-01016_T 549497 143707753 1430883 174 20323 PLEC 0 . GRCh38 8 143920719 143920719 + Silent SNP C C A rs782591966 C3N-01016_T C3N-01016_N C C c.9513G>T p.= p.A3171A ENST00000322810 32/32 815 644 171 637 636 1 strelka-varscan PLEC,synonymous_variant,p.=,ENST00000322810,NM_201380.3;PLEC,synonymous_variant,p.=,ENST00000345136,NM_201384.2;PLEC,synonymous_variant,p.=,ENST00000436759,NM_000445.4;PLEC,synonymous_variant,p.=,ENST00000354958,NM_201379.2;PLEC,synonymous_variant,p.=,ENST00000354589,NM_201382.3;PLEC,synonymous_variant,p.=,ENST00000357649,NM_201383.2;PLEC,synonymous_variant,p.=,ENST00000356346,NM_201378.3;PLEC,synonymous_variant,p.=,ENST00000398774,NM_201381.2;PLEC,synonymous_variant,p.=,ENST00000527096,;PLEC,downstream_gene_variant,,ENST00000527303,; A ENST00000322810 Transcript synonymous_variant 9683/15249 9513/14055 3171/4684 A gcG/gcT rs782591966,COSM1684155,COSM1684156,COSM1684157,COSM1684158 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 32/32 Gene3D:3.90.1290.10,Pfam_domain:PF00681,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247,SMART_domains:SM00250,Superfamily_domains:SSF75399 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 143920719 143920719 C A 1 0 0 0 0 0 0 0 1 12145 639 23 1 1 PLEC 8 143920719 Silent SNP C C3N-01016_T 212966 143920719 1217917 175 20324 SPATC1 0 . GRCh38 8 144012542 144012542 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.27G>A p.= p.G9G ENST00000377470 1/5 337 299 38 193 193 0 strelka-varscan SPATC1,synonymous_variant,p.=,ENST00000377470,NM_198572.2;SPATC1,synonymous_variant,p.=,ENST00000447830,NM_001134374.1;PARP10,5_prime_UTR_variant,,ENST00000530478,; A ENST00000377470 Transcript synonymous_variant 129/2007 27/1776 9/591 G ggG/ggA 1 1 SPATC1 HGNC HGNC:30510 protein_coding YES CCDS6413.2 ENSP00000366690 Q76KD6 UPI00001D8243 NM_198572.2 1/5 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15058,hmmpanther:PTHR22192,hmmpanther:PTHR22192:SF16 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 144012542 144012542 G A 1 0 0 0 0 0 0 0 1 15362 1190 42 3 3 SPATC1 8 144012542 Silent SNP G C3N-01016_T 91823 144012542 1126094 176 20325 GLDC 0 . GRCh38 9 6620246 6620246 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.408G>T p.Met136Ile p.M136I ENST00000321612 3/25 466 409 57 405 405 0 strelka-varscan-mutect GLDC,missense_variant,p.Met136Ile,ENST00000321612,NM_000170.2; A ENST00000321612 Transcript missense_variant 559/3767 408/3063 136/1020 M/I atG/atT 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0.02) 3/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Gene3D:3.40.640.10,Pfam_domain:PF02347,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 6620246 6620246 C A 1 0 0 0 0 1 0 0 0 6311 594 21 2 2 GLDC 9 6620246 Missense_Mutation SNP C C3N-01016_T 6620246 131774471 177 20326 CCDC171 0 . GRCh38 9 15744322 15744322 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.2099A>T p.Glu700Val p.E700V ENST00000380701 17/26 92 79 13 94 94 0 strelka-varscan-mutect CCDC171,missense_variant,p.Glu700Val,ENST00000380701,NM_173550.2;CCDC171,upstream_gene_variant,,ENST00000449575,; T ENST00000380701 Transcript missense_variant 2427/6512 2099/3981 700/1326 E/V gAg/gTg 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 deleterious(0) 17/26 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 MODERATE 1 SNV 1 1 PASS rs1392743601 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 15744322 15744322 A T 1 0 0 0 0 1 0 0 0 2488 304 11 4 4 CCDC171 9 15744322 Missense_Mutation SNP A C3N-01016_T 9124076 15744322 122650395 178 20327 ADAMTSL1 0 . GRCh38 9 18777714 18777714 + Missense_Mutation SNP G G A rs767012703 C3N-01016_T C3N-01016_N G G c.3485G>A p.Arg1162His p.R1162H ENST00000380548 19/29 103 81 22 121 121 0 strelka-varscan-mutect ADAMTSL1,missense_variant,p.Arg1162His,ENST00000380548,NM_001040272.5;ADAMTSL1,non_coding_transcript_exon_variant,,ENST00000380559,; A ENST00000380548 Transcript missense_variant 3824/8030 3485/5289 1162/1762 R/H cGc/cAc rs767012703,COSM1283286 1 1 ADAMTSL1 HGNC HGNC:14632 protein_coding YES CCDS47954.1 ENSP00000369921 Q8N6G6 UPI000004FD83 NM_001040272.5 deleterious(0) 19/29 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs767012703 . 0 198 12 0 0 0 0 0 -20 0.999959 1 1 1 0 A 3 1 66 18777714 18777714 G A 1 0 0 0 0 1 0 0 0 318 1087 38 1 1 ADAMTSL1 9 18777714 Missense_Mutation SNP G C3N-01016_T 3033392 18777714 119617003 179 20328 FOCAD 0 . GRCh38 9 20881878 20881878 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.2325G>T p.Glu775Asp p.E775D ENST00000380249 22/46 170 150 20 156 156 0 strelka-varscan-mutect FOCAD,missense_variant,p.Glu775Asp,ENST00000380249,NM_017794.4;FOCAD,missense_variant,p.Glu775Asp,ENST00000338382,;FOCAD,missense_variant,p.Glu211Asp,ENST00000605086,;FOCAD,non_coding_transcript_exon_variant,,ENST00000605852,;FOCAD,upstream_gene_variant,,ENST00000603552,; T ENST00000380249 Transcript missense_variant 2689/6096 2325/5406 775/1801 E/D gaG/gaT 1 1 FOCAD HGNC HGNC:23377 protein_coding YES CCDS34993.1 ENSP00000369599 Q5VW36 UPI0000EE4244 NM_017794.4 deleterious(0.04) 22/46 hmmpanther:PTHR16212,hmmpanther:PTHR16212:SF4,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 20881878 20881878 G T 1 0 0 0 0 1 0 0 0 5839 991 35 2 2 FOCAD 9 20881878 Missense_Mutation SNP G C3N-01016_T 2104164 20881878 117512839 180 20329 TAF1L 0 . GRCh38 9 32630304 32630304 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.5276T>A p.Val1759Asp p.V1759D ENST00000242310 1/1 436 289 147 452 452 0 strelka-varscan-mutect TAF1L,missense_variant,p.Val1759Asp,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; T ENST00000242310 Transcript missense_variant 5366/6216 5276/5481 1759/1826 V/D gTc/gAc 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious_low_confidence(0) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 32630304 32630304 A T 1 0 0 0 0 1 0 0 0 15919 275 10 4 4 TAF1L 9 32630304 Missense_Mutation SNP A C3N-01016_T 11748426 32630304 105764413 181 20330 DNAI1 0 . GRCh38 9 34506681 34506681 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1130C>G p.Pro377Arg p.P377R ENST00000614641 13/20 394 336 58 343 343 0 strelka-varscan-mutect DNAI1,missense_variant,p.Pro377Arg,ENST00000614641,NM_001281428.1;DNAI1,missense_variant,p.Pro373Arg,ENST00000242317,NM_012144.3;DNAI1,missense_variant,p.Pro19Arg,ENST00000470169,; G ENST00000614641 Transcript missense_variant 1384/2598 1130/2112 377/703 P/R cCc/cGc 1 1 DNAI1 HGNC HGNC:2954 protein_coding YES CCDS75829.1 ENSP00000480538 A0A087WWV9 UPI000382F365 NM_001281428.1 deleterious(0) 13/20 Gene3D:2.130.10.10,hmmpanther:PTHR12442,hmmpanther:PTHR12442:SF11,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 34506681 34506681 C G 1 0 0 0 0 1 0 0 0 4424 623 22 4 4 DNAI1 9 34506681 Missense_Mutation SNP C C3N-01016_T 1876377 34506681 103888036 182 20331 UNC13B 0 . GRCh38 9 35399163 35399163 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.3830T>A p.Leu1277His p.L1277H ENST00000378495 33/39 174 157 17 158 158 0 strelka-varscan-mutect UNC13B,missense_variant,p.Leu4026His,ENST00000635942,;UNC13B,missense_variant,p.Leu1657His,ENST00000636694,;UNC13B,missense_variant,p.Leu864His,ENST00000617908,;UNC13B,missense_variant,p.Leu1277His,ENST00000619578,;UNC13B,missense_variant,p.Leu1277His,ENST00000378495,NM_006377.3;UNC13B,missense_variant,p.Leu1289His,ENST00000396787,;UNC13B,missense_variant,p.Leu864His,ENST00000378496,;UNC13B,missense_variant,p.Leu188His,ENST00000481299,;UNC13B,splice_region_variant,,ENST00000637271,;UNC13B,splice_region_variant,,ENST00000634487,; A ENST00000378495 Transcript missense_variant,splice_region_variant 4052/6303 3830/4776 1277/1591 L/H cTc/cAc 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 deleterious(0) 33/39 Pfam_domain:PF10540,PROSITE_profiles:PS51259,hmmpanther:PTHR10480 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 35399163 35399163 T A 1 0 0 0 0 1 0 0 0 17509 1565 54 4 4 UNC13B 9 35399163 Missense_Mutation SNP T C3N-01016_T 892482 35399163 102995554 183 20332 SPATA31A6 0 . GRCh38 9 42186352 42186352 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.650C>A p.Ser217Tyr p.S217Y ENST00000332857 4/4 92 67 25 40 40 0 strelka-varscan SPATA31A6,missense_variant,p.Ser217Tyr,ENST00000332857,NM_001145196.1;SPATA31A6,non_coding_transcript_exon_variant,,ENST00000496386,; A ENST00000332857 Transcript missense_variant 679/4209 650/4032 217/1343 S/Y tCt/tAt 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(1) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 MODERATE 1 SNV 5 1 PASS . . 2 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 42186352 42186352 C A 1 0 0 0 0 1 0 0 0 15345 913 32 2 2 SPATA31A6 9 42186352 Missense_Mutation SNP C C3N-01016_T 6787189 42186352 96208365 184 20333 SPATA31A7 0 . GRCh38 9 61193418 61193418 + Frame_Shift_Del DEL T T - novel C3N-01016_T C3N-01016_N T T c.1334delT p.Phe445SerfsTer73 p.F445Sfs*73 ENST00000619167 4/4 54 39 15 25 25 0 sindel-varindel-pindel SPATA31A7,frameshift_variant,p.Phe445SerfsTer73,ENST00000619167,NM_015667.2;RP11-101E5.6,downstream_gene_variant,,ENST00000611332,;SPATA31A7,intron_variant,,ENST00000621711,;SPATA31A7,downstream_gene_variant,,ENST00000618860,;SPATA31A7,downstream_gene_variant,,ENST00000619140,;SPATA31A7,downstream_gene_variant,,ENST00000622899,;SPATA31A7,downstream_gene_variant,,ENST00000622751,;SPATA31A7,downstream_gene_variant,,ENST00000376458,;SPATA31A7,downstream_gene_variant,,ENST00000614013,;SPATA31A7,downstream_gene_variant,,ENST00000611017,; - ENST00000619167 Transcript frameshift_variant 1394/4256 1332/4044 444/1347 P/X ccT/cc 1 1 SPATA31A7 HGNC HGNC:32007 protein_coding YES CCDS75838.1 ENSP00000484807 Q8IWB4 UPI0000457748 NM_015667.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF22,Pfam_domain:PF14650 HIGH 1 deletion 1 2 1 PASS . . 28 175 7 0 0 0 0 0 -20 0.9999994 1 1 1 0 - 7 5 66 61193418 61193418 T - 1 0 1 0 1 0 0 0 0 15346 1596 56 0 0 SPATA31A7 9 61193418 Frame_Shift_Del DEL T C3N-01016_T 19007066 61193418 77201299 185 20334 TRMO 0 . GRCh38 9 97910032 97910032 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.994G>C p.Ala332Pro p.A332P ENST00000375119 4/5 63 37 26 30 30 0 strelka-varscan-mutect TRMO,missense_variant,p.Ala186Pro,ENST00000375118,;TRMO,missense_variant,p.Ala332Pro,ENST00000375119,NM_016481.4;TRMO,3_prime_UTR_variant,,ENST00000611338,;TRMO,downstream_gene_variant,,ENST00000375117,;TRMO,downstream_gene_variant,,ENST00000455506,;TRMO,non_coding_transcript_exon_variant,,ENST00000478126,;TRMO,downstream_gene_variant,,ENST00000471580,; G ENST00000375119 Transcript missense_variant 1071/1647 994/1326 332/441 A/P Gct/Cct 1 -1 TRMO HGNC HGNC:30967 protein_coding YES CCDS6730.1 ENSP00000364260 Q9BU70 UPI000013D057 NM_016481.4 tolerated(0.42) 4/5 hmmpanther:PTHR12818:SF0,hmmpanther:PTHR12818,Superfamily_domains:0051066 MODERATE 1 SNV 1 1 PASS rs1156379710 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 97910032 97910032 C G 1 0 0 0 0 1 0 0 0 17059 739 26 4 4 TRMO 9 97910032 Missense_Mutation SNP C C3N-01016_T 36716614 97910032 40484685 186 20335 GABBR2 0 . GRCh38 9 98290633 98290633 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.2777G>C p.Arg926Pro p.R926P ENST00000259455 19/19 30 25 5 24 24 0 strelka-varscan-mutect GABBR2,missense_variant,p.Arg926Pro,ENST00000259455,NM_005458.7;GABBR2,downstream_gene_variant,,ENST00000637410,; G ENST00000259455 Transcript missense_variant 3237/5788 2777/2826 926/941 R/P cGc/cCc 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 deleterious_low_confidence(0) 19/19 Prints_domain:PR01178,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF40 MODERATE 1 SNV 1 1 PASS rs771637982 . 0 204 6 0 0 0 0 0 -13.68633 1 1 1 1 0 G 3 3 66 98290633 98290633 C G 1 0 0 0 0 1 0 0 0 6027 768 27 4 4 GABBR2 9 98290633 Missense_Mutation SNP C C3N-01016_T 380601 98290633 40104084 187 20336 OR1L8 0 . GRCh38 9 122567729 122567729 + Missense_Mutation SNP G G A rs372497222 C3N-01016_T C3N-01016_N G G c.749C>T p.Thr250Met p.T250M ENST00000304865 1/1 101 79 22 112 112 0 strelka-varscan-mutect OR1L8,missense_variant,p.Thr250Met,ENST00000304865,NM_001004454.1; A ENST00000304865 Transcript missense_variant 749/930 749/930 250/309 T/M aCg/aTg rs372497222 1 -1 OR1L8 HGNC HGNC:15110 protein_coding YES CCDS35124.1 ENSP00000306607 Q8NGR8 A0A126GVC5 UPI0000041CB7 NM_001004454.1 tolerated(0.09) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF277,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs372497222 . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 122567729 122567729 G A 1 0 0 0 0 1 0 0 0 11045 1145 40 1 1 OR1L8 9 122567729 Missense_Mutation SNP G C3N-01016_T 24277096 122567729 15826988 188 20337 ADAMTSL2 0 . GRCh38 9 133538382 133538382 + Silent SNP C C A novel C3N-01016_T C3N-01016_N C C c.267C>A p.= p.T89T ENST00000354484 4/19 337 196 141 362 362 0 strelka-varscan-mutect ADAMTSL2,synonymous_variant,p.=,ENST00000393061,;ADAMTSL2,synonymous_variant,p.=,ENST00000354484,NM_001145320.1;ADAMTSL2,synonymous_variant,p.=,ENST00000393060,NM_014694.3; A ENST00000354484 Transcript synonymous_variant 824/4068 267/2856 89/951 T acC/acA 1 1 ADAMTSL2 HGNC HGNC:14631 protein_coding YES CCDS6976.1 ENSP00000346478 Q86TH1 UPI000018CEA2 NM_001145320.1 4/19 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF147,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS rs1307914195 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 133538382 133538382 C A 1 0 0 0 0 0 0 0 1 319 668 24 2 2 ADAMTSL2 9 133538382 Silent SNP C C3N-01016_T 10970653 133538382 4856335 189 20338 KCNT1 0 . GRCh38 9 135779385 135779385 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2756C>A p.Thr919Lys p.T919K ENST00000371757 24/31 156 84 72 207 207 0 strelka-varscan-mutect KCNT1,missense_variant,p.Thr874Lys,ENST00000628528,NM_001272003.1;KCNT1,missense_variant,p.Thr886Lys,ENST00000263604,;KCNT1,missense_variant,p.Thr919Lys,ENST00000371757,NM_020822.2;KCNT1,missense_variant,p.Thr900Lys,ENST00000631073,;KCNT1,missense_variant,p.Thr919Lys,ENST00000487664,;KCNT1,missense_variant,p.Thr880Lys,ENST00000486577,;KCNT1,missense_variant,p.Thr898Lys,ENST00000490355,;KCNT1,missense_variant,p.Thr900Lys,ENST00000488444,;KCNT1,missense_variant,p.Thr900Lys,ENST00000491806,;KCNT1,missense_variant,p.Thr864Lys,ENST00000630792,;KCNT1,3_prime_UTR_variant,,ENST00000460750,;KCNT1,3_prime_UTR_variant,,ENST00000631193,;KCNT1,non_coding_transcript_exon_variant,,ENST00000490363,; A ENST00000371757 Transcript missense_variant 2823/4717 2756/3708 919/1235 T/K aCg/aAg 1 1 KCNT1 HGNC HGNC:18865 protein_coding YES CCDS35175.2 ENSP00000360822 Q5JUK3 UPI000192C42B NM_020822.2 deleterious(0) 24/31 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF14 MODERATE 1 SNV 1 1 PASS rs1213818774 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 135779385 135779385 C A 1 0 0 0 0 1 0 0 0 8007 536 19 1 1 KCNT1 9 135779385 Missense_Mutation SNP C C3N-01016_T 2241003 135779385 2615332 190 20339 NSMF 0 . GRCh38 9 137458499 137458499 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.122G>T p.Arg41Leu p.R41L ENST00000371475 2/16 295 166 129 389 388 1 strelka-varscan-mutect NSMF,missense_variant,p.Arg41Leu,ENST00000371475,NM_001130969.1;NSMF,missense_variant,p.Arg41Leu,ENST00000265663,NM_015537.4;NSMF,missense_variant,p.Arg41Leu,ENST00000437259,NM_001130970.1;NSMF,missense_variant,p.Arg41Leu,ENST00000371474,NM_001130971.1;NSMF,missense_variant,p.Arg41Leu,ENST00000371473,NM_001178064.1;NSMF,missense_variant,p.Arg41Leu,ENST00000371472,;PNPLA7,downstream_gene_variant,,ENST00000406427,NM_001098537.2;PNPLA7,downstream_gene_variant,,ENST00000277531,NM_152286.4;NSMF,upstream_gene_variant,,ENST00000339554,;PNPLA7,downstream_gene_variant,,ENST00000492278,;PNPLA7,downstream_gene_variant,,ENST00000469998,;PNPLA7,downstream_gene_variant,,ENST00000487228,;NSMF,upstream_gene_variant,,ENST00000371482,;NSMF,upstream_gene_variant,,ENST00000484316,;NSMF,upstream_gene_variant,,ENST00000371468,; A ENST00000371475 Transcript missense_variant 354/3646 122/1593 41/530 R/L cGc/cTc 1 -1 NSMF HGNC HGNC:29843 protein_coding YES CCDS48069.1 ENSP00000360530 Q6X4W1 UPI000035198D NM_001130969.1 deleterious_low_confidence(0) 2/16 hmmpanther:PTHR32061 MODERATE 1 SNV 1 1 PASS rs989048174 . 0 208 0 0 2 0 0 0 -20 0.9995479 1 1 1 0 A 3 1 66 137458499 137458499 C A 1 0 0 0 0 1 0 0 0 10739 768 27 1 1 NSMF 9 137458499 Missense_Mutation SNP C C3N-01016_T 1679114 137458499 936218 191 20340 CACNA1B 0 . GRCh38 9 137917400 137917400 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.935C>T p.Thr312Ile p.T312I ENST00000371372 6/47 93 74 19 123 123 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Thr312Ile,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Thr312Ile,ENST00000371363,;CACNA1B,missense_variant,p.Thr312Ile,ENST00000371355,;CACNA1B,missense_variant,p.Thr312Ile,ENST00000371357,;CACNA1B,missense_variant,p.Thr312Ile,ENST00000277549,;CACNA1B,missense_variant,p.Thr312Ile,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 1080/9790 935/7020 312/2339 T/I aCc/aTc 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 deleterious(0) 6/47 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 137917400 137917400 C T 1 0 0 0 0 1 0 0 0 2227 507 18 3 3 CACNA1B 9 137917400 Missense_Mutation SNP C C3N-01016_T 458901 137917400 477317 192 20341 TUBAL3 0 . GRCh38 10 5394224 5394224 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.634G>T p.Asp212Tyr p.D212Y ENST00000380419 4/4 189 167 22 181 181 0 strelka-varscan-mutect TUBAL3,missense_variant,p.Asp212Tyr,ENST00000380419,NM_024803.2;TUBAL3,missense_variant,p.Asp172Tyr,ENST00000479328,NM_001171864.1; A ENST00000380419 Transcript missense_variant 672/1798 634/1341 212/446 D/Y Gac/Tac 1 -1 TUBAL3 HGNC HGNC:23534 protein_coding YES CCDS7066.2 ENSP00000369784 A6NHL2 UPI00000497AE NM_024803.2 deleterious_low_confidence(0) 4/4 hmmpanther:PTHR11588:SF130,hmmpanther:PTHR11588,Pfam_domain:PF00091,Gene3D:3.40.50.1440,SMART_domains:SM00864,Superfamily_domains:SSF52490,Prints_domain:PR01161 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 5394224 5394224 C A 1 0 0 0 0 1 0 0 0 17262 855 30 2 2 TUBAL3 10 5394224 Missense_Mutation SNP C C3N-01016_T 5394224 128403198 193 20342 CREM 0 . GRCh38 10 35167757 35167757 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.32G>T p.Arg11Met p.R11M ENST00000361599 1/6 157 136 21 156 155 1 strelka-varscan-mutect CREM,missense_variant,p.Arg11Met,ENST00000361599,NM_182771.1,NM_182772.1;CREM,missense_variant,p.Arg11Met,ENST00000395887,NM_001267564.1;CREM,missense_variant,p.Arg11Met,ENST00000484283,;CREM,intron_variant,,ENST00000439705,;CREM,intron_variant,,ENST00000345491,NM_181571.2;CREM,intron_variant,,ENST00000374721,;CREM,intron_variant,,ENST00000374728,NM_183060.2;CREM,intron_variant,,ENST00000348787,;CREM,intron_variant,,ENST00000354759,NM_183013.2;CREM,intron_variant,,ENST00000429130,;CREM,intron_variant,,ENST00000460270,;CREM,intron_variant,,ENST00000374726,NM_001881.3;CREM,intron_variant,,ENST00000474362,;CREM,intron_variant,,ENST00000479070,;CREM,intron_variant,,ENST00000337656,NM_183011.1;CREM,intron_variant,,ENST00000489321,;CREM,intron_variant,,ENST00000374734,NM_183012.1;CREM,intron_variant,,ENST00000487132,;CREM,intron_variant,,ENST00000427847,;CREM,non_coding_transcript_exon_variant,,ENST00000497686,;CREM,intron_variant,,ENST00000489388,;CREM,intron_variant,,ENST00000461968,;CREM,intron_variant,,ENST00000496019,;CREM,intron_variant,,ENST00000466251,;CREM,intron_variant,,ENST00000490460,;CREM,intron_variant,,ENST00000495960,;CREM,intron_variant,,ENST00000464475,;CREM,intron_variant,,ENST00000482633,; T ENST00000361599 Transcript missense_variant 242/2170 32/813 11/270 R/M aGg/aTg 1 1 CREM HGNC HGNC:2352 protein_coding CCDS7185.1 ENSP00000354593 Q03060 UPI00001BDF5B NM_182771.1,NM_182772.1 deleterious_low_confidence(0) 1/6 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 35167757 35167757 G T 1 0 0 0 0 1 0 0 0 3669 1000 35 2 2 CREM 10 35167757 Missense_Mutation SNP G C3N-01016_T 29773533 35167757 98629665 194 20343 ZNF33B 0 . GRCh38 10 42594168 42594168 + Missense_Mutation SNP G G A novel C3N-01016_T C3N-01016_N G G c.782C>T p.Ser261Phe p.S261F ENST00000359467 5/5 198 175 23 113 113 0 strelka-varscan-mutect ZNF33B,missense_variant,p.Ser261Phe,ENST00000359467,NM_001305036.1,NM_001305033.1,NM_006955.1;ZNF33B,missense_variant,p.Ser261Phe,ENST00000613419,;ZNF33B,intron_variant,,ENST00000465206,;ZNF33B,intron_variant,,ENST00000462075,;ZNF33B,intron_variant,,ENST00000486187,; A ENST00000359467 Transcript missense_variant 897/5958 782/2337 261/778 S/F tCc/tTc 1 -1 ZNF33B HGNC HGNC:13097 protein_coding YES CCDS7198.1 ENSP00000352444 Q06732 UPI000007257B NM_001305036.1,NM_001305033.1,NM_006955.1 tolerated(0.2) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 42594168 42594168 G A 1 0 0 0 0 1 0 0 0 18427 1174 41 3 3 ZNF33B 10 42594168 Missense_Mutation SNP G C3N-01016_T 7426411 42594168 91203254 195 20344 PCDH15 0 . GRCh38 10 54023095 54023095 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.2338G>T p.Val780Leu p.V780L ENST00000373957 20/35 496 433 63 383 383 0 strelka-varscan-mutect PCDH15,missense_variant,p.Val780Leu,ENST00000614895,;PCDH15,missense_variant,p.Val775Leu,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Val775Leu,ENST00000414778,;PCDH15,missense_variant,p.Val780Leu,ENST00000617051,;PCDH15,missense_variant,p.Val780Leu,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Val775Leu,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Val775Leu,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Val753Leu,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Val738Leu,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Val775Leu,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Val704Leu,ENST00000622048,;PCDH15,missense_variant,p.Val704Leu,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Val775Leu,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Val787Leu,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Val782Leu,ENST00000395445,;PCDH15,missense_variant,p.Val775Leu,ENST00000616114,;PCDH15,missense_variant,p.Val775Leu,ENST00000395438,;PCDH15,missense_variant,p.Val787Leu,ENST00000612394,;PCDH15,missense_variant,p.Val780Leu,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Val386Leu,ENST00000409834,;PCDH15,missense_variant,p.Val775Leu,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript missense_variant 2733/7032 2338/5889 780/1962 V/L Gtg/Ttg COSM2147349,COSM2147350,COSM2147351,COSM2147352 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.06) 20/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 54023095 54023095 C A 1 0 0 0 0 1 0 0 0 11598 565 20 2 2 PCDH15 10 54023095 Missense_Mutation SNP C C3N-01016_T 11428927 54023095 79774327 196 20345 DYDC2 0 . GRCh38 10 80366711 80366711 + Silent SNP C C T novel C3N-01016_T C3N-01016_N C C c.336C>T p.= p.S112S ENST00000372198 4/4 219 88 131 159 159 0 strelka-varscan-mutect DYDC2,synonymous_variant,p.=,ENST00000372199,;DYDC2,synonymous_variant,p.=,ENST00000372197,;DYDC2,synonymous_variant,p.=,ENST00000256039,NM_032372.5;DYDC2,synonymous_variant,p.=,ENST00000372198,NM_001270042.1;DYDC2,synonymous_variant,p.=,ENST00000616870,NM_001270041.1;DYDC2,synonymous_variant,p.=,ENST00000444807,;DYDC2,synonymous_variant,p.=,ENST00000411538,; T ENST00000372198 Transcript synonymous_variant 374/1736 336/576 112/191 S tcC/tcT 1 1 DYDC2 HGNC HGNC:23468 protein_coding YES CCDS58088.1 ENSP00000361272 A0A0A0MRQ7 UPI000046FF92 NM_001270042.1 4/4 hmmpanther:PTHR23356:SF3,hmmpanther:PTHR23356 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 80366711 80366711 C T 1 0 0 0 0 0 0 0 1 4662 581 21 3 3 DYDC2 10 80366711 Silent SNP C C3N-01016_T 26343616 80366711 53430711 197 20346 AL365273.1 0 . GRCh38 10 95847655 95847655 + Silent SNP C C A novel C3N-01016_T C3N-01016_N C C c.1059C>A p.= p.S353S ENST00000371207 7/10 349 288 61 260 260 0 strelka-varscan-mutect ENTPD1,synonymous_variant,p.=,ENST00000453258,NM_001098175.1;ENTPD1,synonymous_variant,p.=,ENST00000371205,NM_001164179.1,NM_001776.5;ENTPD1,synonymous_variant,p.=,ENST00000371207,NM_001164178.1;ENTPD1,synonymous_variant,p.=,ENST00000543964,NM_001164181.1;AL365273.1,synonymous_variant,p.=,ENST00000539125,NM_001164182.1,NM_001164183.1;ENTPD1-AS1,intron_variant,,ENST00000416301,;RP11-429G19.3,intron_variant,,ENST00000433113,;ENTPD1,downstream_gene_variant,,ENST00000490659,;ENTPD1,downstream_gene_variant,,ENST00000494070,;ENTPD1,downstream_gene_variant,,ENST00000635677,;ENTPD1,downstream_gene_variant,,ENST00000422161,;ENTPD1,3_prime_UTR_variant,,ENST00000635076,;ENTPD1,downstream_gene_variant,,ENST00000371206,;ENTPD1,downstream_gene_variant,,ENST00000483213,; A ENST00000371207 Transcript synonymous_variant 1122/1903 1059/1569 353/522 S tcC/tcA 1 1 ENTPD1 HGNC HGNC:3363 protein_coding YES CCDS53556.1 ENSP00000360250 P49961 UPI0000EE3B3A NM_001164178.1 7/10 hmmpanther:PTHR11782,hmmpanther:PTHR11782:SF32,Pfam_domain:PF01150 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 95847655 95847655 C A 1 0 0 0 0 0 0 0 1 578 610 22 2 2 AL365273.1 10 95847655 Silent SNP C C3N-01016_T 15480944 95847655 37949767 198 20347 HPSE2 0 . GRCh38 10 99144390 99144390 + Missense_Mutation SNP C C A rs767173222 C3N-01016_T C3N-01016_N C C c.458G>T p.Arg153Leu p.R153L ENST00000370552 3/12 174 80 94 124 124 0 strelka-varscan-mutect HPSE2,missense_variant,p.Arg153Leu,ENST00000370552,NM_021828.4;HPSE2,missense_variant,p.Arg153Leu,ENST00000370549,NM_001166244.1;HPSE2,missense_variant,p.Arg153Leu,ENST00000370546,NM_001166246.1;HPSE2,intron_variant,,ENST00000628193,NM_001166245.1; A ENST00000370552 Transcript missense_variant 518/2295 458/1779 153/592 R/L cGa/cTa rs767173222 1 -1 HPSE2 HGNC HGNC:18374 protein_coding YES CCDS7477.1 ENSP00000359583 Q8WWQ2 UPI00001AEEC0 NM_021828.4 tolerated(0.18) 3/12 MODERATE 1 SNV 1 1 PASS rs767173222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 99144390 99144390 C A 1 0 0 0 0 1 0 0 0 7240 884 31 1 1 HPSE2 10 99144390 Missense_Mutation SNP C C3N-01016_T 3296735 99144390 34653032 199 20348 LBX1 0 . GRCh38 10 101228687 101228687 + Missense_Mutation SNP G G T rs770184475 C3N-01016_T C3N-01016_N G G c.129C>A p.Asn43Lys p.N43K ENST00000370193 1/2 428 276 152 397 397 0 strelka-varscan-mutect LBX1,missense_variant,p.Asn43Lys,ENST00000370193,NM_006562.4;LBX1-AS1,upstream_gene_variant,,ENST00000454527,;LBX1-AS1,upstream_gene_variant,,ENST00000546988,;LBX1-AS1,upstream_gene_variant,,ENST00000547077,; T ENST00000370193 Transcript missense_variant 1108/2900 129/846 43/281 N/K aaC/aaA rs770184475 1 -1 LBX1 HGNC HGNC:16960 protein_coding YES CCDS31270.1 ENSP00000359212 P52954 UPI00001F95A1 NM_006562.4 deleterious(0.04) 1/2 hmmpanther:PTHR24336,hmmpanther:PTHR24336:SF9 MODERATE 1 SNV 1 1 PASS rs770184475 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 101228687 101228687 G T 1 0 0 0 0 1 0 0 0 8559 1368 48 2 2 LBX1 10 101228687 Missense_Mutation SNP G C3N-01016_T 2084297 101228687 32568735 200 20349 VWA2 0 . GRCh38 10 114285963 114285963 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.1022G>C p.Arg341Thr p.R341T ENST00000392982 11/14 90 43 47 46 46 0 strelka-varscan-mutect VWA2,missense_variant,p.Arg341Thr,ENST00000392982,NM_001272046.1;VWA2,missense_variant,p.Arg37Thr,ENST00000603594,;CTB-1144G6.6,upstream_gene_variant,,ENST00000622689,;VWA2,non_coding_transcript_exon_variant,,ENST00000298715,; C ENST00000392982 Transcript missense_variant 1272/2794 1022/2268 341/755 R/T aGg/aCg 1 1 VWA2 HGNC HGNC:24709 protein_coding YES CCDS7589.2 ENSP00000376708 Q5GFL6 UPI00004C7AA3 NM_001272046.1 tolerated(0.47) 11/14 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF117,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs1476870062 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 114285963 114285963 G C 1 0 0 0 0 1 0 0 0 17793 1000 35 4 4 VWA2 10 114285963 Missense_Mutation SNP G C3N-01016_T 13057276 114285963 19511459 201 20350 VAX1 0 . GRCh38 10 117136500 117136500 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.401C>A p.Ala134Asp p.A134D ENST00000369206 2/3 256 144 112 243 243 0 strelka-varscan-mutect VAX1,missense_variant,p.Ala134Asp,ENST00000277905,NM_199131.2;VAX1,missense_variant,p.Ala134Asp,ENST00000369206,NM_001112704.1; T ENST00000369206 Transcript missense_variant 401/1723 401/1005 134/334 A/D gCc/gAc 1 -1 VAX1 HGNC HGNC:12660 protein_coding YES CCDS44483.1 ENSP00000358207 Q5SQQ9 UPI000013DB43 NM_001112704.1 deleterious(0) 2/3 Gene3D:1.10.10.60,Pfam_domain:PF00046,Prints_domain:PR00031,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF32,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 117136500 117136500 G T 1 0 0 0 0 1 0 0 0 17679 1203 42 2 2 VAX1 10 117136500 Missense_Mutation SNP G C3N-01016_T 2850537 117136500 16660922 202 20351 CFAP46 0 . GRCh38 10 132920178 132920178 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.1611C>A p.= p.S537S ENST00000368586 14/58 90 49 41 65 65 0 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2;CFAP46,upstream_gene_variant,,ENST00000486104,; T ENST00000368586 Transcript synonymous_variant 1712/8278 1611/8148 537/2715 S tcC/tcA 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 14/58 hmmpanther:PTHR15977,hmmpanther:PTHR15977:SF15 LOW 1 SNV 5 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 66 132920178 132920178 G T 1 0 0 0 0 0 0 0 1 3021 1362 47 2 2 CFAP46 10 132920178 Silent SNP G C3N-01016_T 15783678 132920178 877244 203 20352 ECHS1 0 . GRCh38 10 133368979 133368979 + Missense_Mutation SNP T T A rs759771909 C3N-01016_T C3N-01016_N T T c.458A>T p.Tyr153Phe p.Y153F ENST00000368547 4/8 155 76 79 150 150 0 strelka-varscan-mutect ECHS1,missense_variant,p.Tyr153Phe,ENST00000368547,NM_004092.3;MIR3944,downstream_gene_variant,,ENST00000581277,; A ENST00000368547 Transcript missense_variant 814/1617 458/873 153/290 Y/F tAt/tTt rs759771909 1 -1 ECHS1 HGNC HGNC:3151 protein_coding YES CCDS7681.1 ENSP00000357535 P30084 UPI000013CC49 NM_004092.3 tolerated(0.08) 4/8 hmmpanther:PTHR11941:SF54,hmmpanther:PTHR11941,Pfam_domain:PF00378,Gene3D:3.90.226.10,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS rs759771909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 133368979 133368979 T A 1 0 0 0 0 1 0 0 0 4722 1406 49 4 4 ECHS1 10 133368979 Missense_Mutation SNP T C3N-01016_T 448801 133368979 428443 204 20353 DEAF1 0 . GRCh38 11 644606 644606 + Missense_Mutation SNP C C T C3N-01016_T C3N-01016_N C C c.1642G>A p.Val548Ile p.V548I ENST00000382409 12/12 417 390 27 489 488 1 strelka-varscan-mutect DEAF1,missense_variant,p.Val548Ile,ENST00000382409,NM_021008.3;DRD4,downstream_gene_variant,,ENST00000176183,NM_000797.3;DEAF1,non_coding_transcript_exon_variant,,ENST00000527658,;DRD4,downstream_gene_variant,,ENST00000528733,;DEAF1,3_prime_UTR_variant,,ENST00000527170,; T ENST00000382409 Transcript missense_variant 2127/2500 1642/1698 548/565 V/I Gtc/Atc COSM5373217 1 -1 DEAF1 HGNC HGNC:14677 protein_coding YES CCDS31327.1 ENSP00000371846 O75398 UPI00001290E6 NM_021008.3 tolerated(0.07) 12/12 hmmpanther:PTHR10237 1 MODERATE 1 SNV 1 1 1 PASS rs1472386316 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 644606 644606 C T 1 0 0 0 0 1 0 0 0 4183 536 19 1 1 DEAF1 11 644606 Missense_Mutation SNP C C3N-01016_T 644606 134442016 205 20354 ART1 0 . GRCh38 11 3659831 3659831 + Silent SNP C C A C3N-01016_T C3N-01016_N C C c.312C>A p.= p.S104S ENST00000250693 3/5 100 57 43 83 83 0 strelka-varscan-mutect ART1,synonymous_variant,p.=,ENST00000250693,NM_004314.2;Y_RNA,downstream_gene_variant,,ENST00000364409,;ART1,downstream_gene_variant,,ENST00000529556,; A ENST00000250693 Transcript synonymous_variant 413/1312 312/984 104/327 S tcC/tcA COSM5273157 1 1 ART1 HGNC HGNC:723 protein_coding YES CCDS7744.1 ENSP00000250693 P52961 UPI000013CCC8 NM_004314.2 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR10339,hmmpanther:PTHR10339:SF19,Pfam_domain:PF01129,Gene3D:3.90.176.10,Superfamily_domains:SSF56399 1 LOW 1 SNV 1 1 1 PASS rs1421320555 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 3659831 3659831 C A 1 0 0 0 0 0 0 0 1 1140 610 22 2 2 ART1 11 3659831 Silent SNP C C3N-01016_T 3015225 3659831 131426791 206 20355 OR52M1 0 . GRCh38 11 4545777 4545777 + Missense_Mutation SNP G G T rs747410605 C3N-01016_T C3N-01016_N G G c.587G>T p.Arg196Met p.R196M ENST00000360213 1/1 113 102 11 141 141 0 strelka-varscan-mutect OR52M1,missense_variant,p.Arg196Met,ENST00000360213,NM_001004137.1; T ENST00000360213 Transcript missense_variant 587/954 587/954 196/317 R/M aGg/aTg rs747410605 1 1 OR52M1 HGNC HGNC:15225 protein_coding YES CCDS31353.1 ENSP00000353343 Q8NGK5 UPI0000041C62 NM_001004137.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF136,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs747410605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 4545777 4545777 G T 1 0 0 0 0 1 0 0 0 11199 1000 35 2 2 OR52M1 11 4545777 Missense_Mutation SNP G C3N-01016_T 885946 4545777 130540845 207 20356 OR51L1 0 . GRCh38 11 4999081 4999081 + Silent SNP C C T C3N-01016_T C3N-01016_N C C c.99C>T p.= p.F33F ENST00000321543 1/1 152 94 58 157 157 0 strelka-varscan-mutect OR51L1,synonymous_variant,p.=,ENST00000321543,NM_001004755.1; T ENST00000321543 Transcript synonymous_variant 99/948 99/948 33/315 F ttC/ttT COSM3448393 1 1 OR51L1 HGNC HGNC:14759 protein_coding YES CCDS31369.1 ENSP00000322156 Q8NGJ5 A0A126GVJ8 UPI0000041B76 NM_001004755.1 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF37,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 4999081 4999081 C T 1 0 0 0 0 0 0 0 1 11176 912 32 3 3 OR51L1 11 4999081 Silent SNP C C3N-01016_T 453304 4999081 130087541 208 20357 OR52A5 0 . GRCh38 11 5132555 5132555 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.88G>T p.Gly30Trp p.G30W ENST00000307388 1/1 114 107 7 109 108 1 strelka-mutect OR52A5,missense_variant,p.Gly30Trp,ENST00000307388,NM_001005160.2; A ENST00000307388 Transcript missense_variant 88/951 88/951 30/316 G/W Ggg/Tgg COSM3935491 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -10.55622 0.9999995 1 1 1 0 A 3 1 66 5132555 5132555 C A 1 0 0 0 0 1 0 0 0 11183 594 21 2 2 OR52A5 11 5132555 Missense_Mutation SNP C C3N-01016_T 133474 5132555 129954067 209 20358 OR10A5 0 . GRCh38 11 6846470 6846470 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.788C>A p.Pro263His p.P263H ENST00000299454 1/1 171 102 69 146 146 0 strelka-varscan-mutect OR10A5,missense_variant,p.Pro263His,ENST00000299454,NM_178168.1;RP11-413N10.3,intron_variant,,ENST00000637205,;RP11-560B16.5,upstream_gene_variant,,ENST00000530632,; A ENST00000299454 Transcript missense_variant 819/1054 788/954 263/317 P/H cCt/cAt 1 1 OR10A5 HGNC HGNC:15131 protein_coding YES CCDS7773.1 ENSP00000299454 Q9H207 A0A126GWR0 UPI000004C155 NM_178168.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 6846470 6846470 C A 1 0 0 0 0 1 0 0 0 10969 681 24 2 2 OR10A5 11 6846470 Missense_Mutation SNP C C3N-01016_T 1713915 6846470 128240152 210 20359 OLFML1 0 . GRCh38 11 7488411 7488411 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.414T>A p.Asn138Lys p.N138K ENST00000329293 2/3 120 104 16 97 97 0 strelka-varscan-mutect OLFML1,missense_variant,p.Asn138Lys,ENST00000329293,NM_198474.3;OLFML1,missense_variant,p.Asn138Lys,ENST00000530135,;OLFML1,intron_variant,,ENST00000528758,;OLFML1,downstream_gene_variant,,ENST00000534244,;CTD-2516F10.2,intron_variant,,ENST00000622955,;CTD-2516F10.2,intron_variant,,ENST00000530201,;OLFML1,non_coding_transcript_exon_variant,,ENST00000528308,; A ENST00000329293 Transcript missense_variant 808/2792 414/1209 138/402 N/K aaT/aaA 1 1 OLFML1 HGNC HGNC:24473 protein_coding YES CCDS7779.1 ENSP00000332511 Q6UWY5 UPI0000161991 NM_198474.3 tolerated(0.08) 2/3 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 7488411 7488411 T A 1 0 0 0 0 1 0 0 0 10931 1478 51 4 4 OLFML1 11 7488411 Missense_Mutation SNP T C3N-01016_T 641941 7488411 127598211 211 20360 OTOG 0 . GRCh38 11 17633711 17633711 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.7140G>C p.Gln2380His p.Q2380H ENST00000399391 42/55 46 33 13 55 55 0 strelka-varscan-mutect OTOG,missense_variant,p.Gln2368His,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Gln2380His,ENST00000399391,NM_001277269.1;OTOG,missense_variant,p.Gln1386His,ENST00000342528,; C ENST00000399391 Transcript missense_variant 7140/8778 7140/8778 2380/2925 Q/H caG/caC 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 42/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 17633711 17633711 G C 1 0 0 0 0 1 0 0 0 11370 991 35 4 4 OTOG 11 17633711 Missense_Mutation SNP G C3N-01016_T 10145300 17633711 117452911 212 20361 MRGPRX4 0 . GRCh38 11 18173436 18173436 + Silent SNP T T A rs552161707 C3N-01016_T C3N-01016_N T T c.180T>A p.= p.A60A ENST00000314254 1/1 125 84 41 153 153 0 strelka-varscan-mutect MRGPRX4,synonymous_variant,p.=,ENST00000314254,NM_054032.3;MRGPRX4,synonymous_variant,p.=,ENST00000618161,;RP11-113D6.6,intron_variant,,ENST00000527671,; A ENST00000314254 Transcript synonymous_variant 600/1444 180/969 60/322 A gcT/gcA rs552161707 1 1 MRGPRX4 HGNC HGNC:17617 protein_coding YES CCDS7831.1 ENSP00000314042 Q96LA9 UPI0000061F60 NM_054032.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF23,hmmpanther:PTHR11334,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR02108 LOW SNV 1 PASS rs552161707 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 18173436 18173436 T A 1 0 0 0 0 0 0 0 1 9736 1567 55 4 4 MRGPRX4 11 18173436 Silent SNP T C3N-01016_T 539725 18173436 116913186 213 20362 KIAA1549L 0 . GRCh38 11 33591293 33591293 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.3732G>T p.Glu1244Asp p.E1244D ENST00000321505 11/20 217 203 14 240 240 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Glu1244Asp,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Glu642Asp,ENST00000526400,;KIAA1549L,intron_variant,,ENST00000265654,; T ENST00000321505 Transcript missense_variant 3912/11678 3732/5550 1244/1849 E/D gaG/gaT 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 tolerated(0.82) 11/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3,Pfam_domain:PF12877 MODERATE 1 SNV 1 1 PASS rs1333032923 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 33591293 33591293 G T 1 0 0 0 0 1 0 0 0 8121 991 35 2 2 KIAA1549L 11 33591293 Missense_Mutation SNP G C3N-01016_T 15417857 33591293 101495329 214 20363 RAG1 0 . GRCh38 11 36575018 36575018 + Missense_Mutation SNP G G A novel C3N-01016_T C3N-01016_N G G c.1714G>A p.Asp572Asn p.D572N ENST00000299440 2/2 314 192 122 233 233 0 strelka-varscan-mutect RAG1,missense_variant,p.Asp572Asn,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Asp572Asn,ENST00000534663,; A ENST00000299440 Transcript missense_variant 1826/6564 1714/3132 572/1043 D/N Gac/Aac 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 deleterious_low_confidence(0) 2/2 Pfam_domain:PF12940,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 36575018 36575018 G A 1 0 0 0 0 1 0 0 0 13164 1174 41 3 3 RAG1 11 36575018 Missense_Mutation SNP G C3N-01016_T 2983725 36575018 98511604 215 20364 PACSIN3 0 . GRCh38 11 47178903 47178903 + Missense_Mutation SNP C C A rs753955865 C3N-01016_T C3N-01016_N C C c.1028G>T p.Gly343Val p.G343V ENST00000539589 9/11 193 176 17 185 184 1 strelka-varscan-mutect PACSIN3,missense_variant,p.Gly343Val,ENST00000539589,NM_001184975.1;PACSIN3,missense_variant,p.Gly343Val,ENST00000298838,NM_016223.4,NM_001184974.1;PACSIN3,missense_variant,p.Gly343Val,ENST00000528462,;PACSIN3,missense_variant,p.Gly66Val,ENST00000533686,;ARFGAP2,upstream_gene_variant,,ENST00000524782,NM_032389.4;ARFGAP2,upstream_gene_variant,,ENST00000426335,NM_001242832.1;ARFGAP2,upstream_gene_variant,,ENST00000627920,;ARFGAP2,upstream_gene_variant,,ENST00000525398,;PACSIN3,downstream_gene_variant,,ENST00000530513,;PACSIN3,downstream_gene_variant,,ENST00000528201,;ARFGAP2,upstream_gene_variant,,ENST00000527927,;ARFGAP2,upstream_gene_variant,,ENST00000525314,;ARFGAP2,upstream_gene_variant,,ENST00000528444,;PACSIN3,downstream_gene_variant,,ENST00000525725,;PACSIN3,downstream_gene_variant,,ENST00000531226,;PACSIN3,downstream_gene_variant,,ENST00000530405,;PACSIN3,downstream_gene_variant,,ENST00000524509,;ARFGAP2,upstream_gene_variant,,ENST00000530596,;ARFGAP2,upstream_gene_variant,,ENST00000526342,;ARFGAP2,upstream_gene_variant,,ENST00000629231,;MIR6745,downstream_gene_variant,,ENST00000612694,;ARFGAP2,upstream_gene_variant,,ENST00000395449,;ARFGAP2,upstream_gene_variant,,ENST00000531750,;ARFGAP2,upstream_gene_variant,,ENST00000533939,;ARFGAP2,upstream_gene_variant,,ENST00000529599,;PACSIN3,3_prime_UTR_variant,,ENST00000532457,;ARFGAP2,upstream_gene_variant,,ENST00000526185,;ARFGAP2,upstream_gene_variant,,ENST00000533243,;ARFGAP2,upstream_gene_variant,,ENST00000524727,;ARFGAP2,upstream_gene_variant,,ENST00000527097,;ARFGAP2,upstream_gene_variant,,ENST00000532478,;ARFGAP2,upstream_gene_variant,,ENST00000529455,;ARFGAP2,upstream_gene_variant,,ENST00000532438,;ARFGAP2,upstream_gene_variant,,ENST00000528041,;ARFGAP2,upstream_gene_variant,,ENST00000529439,;ARFGAP2,upstream_gene_variant,,ENST00000528708,;ARFGAP2,upstream_gene_variant,,ENST00000524586,;ARFGAP2,upstream_gene_variant,,ENST00000528072,;ARFGAP2,upstream_gene_variant,,ENST00000530794,; A ENST00000539589 Transcript missense_variant 1371/2009 1028/1275 343/424 G/V gGg/gTg rs753955865 1 -1 PACSIN3 HGNC HGNC:8572 protein_coding YES CCDS31481.1 ENSP00000440945 Q9UKS6 UPI0000034CB1 NM_001184975.1 tolerated(0.48) 9/11 hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF18,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS rs753955865 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 47178903 47178903 C A 1 0 0 0 0 1 0 0 0 11454 623 22 2 2 PACSIN3 11 47178903 Missense_Mutation SNP C C3N-01016_T 10603885 47178903 87907719 216 20365 OR4B1 0 . GRCh38 11 48217728 48217728 + Missense_Mutation SNP G G T rs763310670 C3N-01016_T C3N-01016_N G G c.919G>T p.Gly307Trp p.G307W ENST00000309562 1/1 55 47 8 46 46 0 strelka-varscan-mutect OR4B1,missense_variant,p.Gly307Trp,ENST00000309562,NM_001005470.1; T ENST00000309562 Transcript missense_variant 937/971 919/930 307/309 G/W Ggg/Tgg rs763310670 1 1 OR4B1 HGNC HGNC:8290 protein_coding YES CCDS31485.1 ENSP00000311605 Q8NGF8 A0A126GVH6 UPI0000041BD9 NM_001005470.1 deleterious(0) 1/1 MODERATE 1 SNV 1 PASS rs763310670 . 0 201 8 0 0 0 0 0 -18.54265 0.9999979 1 1 1 0 T 3 4 66 48217728 48217728 G T 1 0 0 0 0 1 0 0 0 11121 1000 35 2 2 OR4B1 11 48217728 Missense_Mutation SNP G C3N-01016_T 1038825 48217728 86868894 217 20366 OR4A5 0 . GRCh38 11 54706924 54706924 + Missense_Mutation SNP G G T rs376153513 C3N-01016_T C3N-01016_N G G c.40G>T p.Gly14Cys p.G14C ENST00000319760 1/1 94 52 42 85 85 0 strelka-varscan-mutect OR4A5,missense_variant,p.Gly14Cys,ENST00000319760,NM_001005272.3; T ENST00000319760 Transcript missense_variant 40/948 40/948 14/315 G/C Ggc/Tgc rs376153513,COSM322299 1 1 OR4A5 HGNC HGNC:15162 protein_coding YES CCDS73289.1 ENSP00000367664 Q8NH83 A0A126GWJ2 UPI0000041D58 NM_001005272.3 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF306,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs376153513 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 54706924 54706924 G T 1 0 0 0 0 1 0 0 0 11120 1232 43 2 2 OR4A5 11 54706924 Missense_Mutation SNP G C3N-01016_T 6489196 54706924 80379698 218 20367 OR4C15 0 . GRCh38 11 55554960 55554960 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.654G>A p.= p.Q218Q ENST00000314644 1/1 193 120 73 188 188 0 strelka-varscan-mutect OR4C15,synonymous_variant,p.=,ENST00000314644,NM_001001920.1; A ENST00000314644 Transcript synonymous_variant 654/1113 654/1113 218/370 Q caG/caA 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF14,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1467610630 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 55554960 55554960 G A 1 0 0 0 0 0 0 0 1 11125 962 34 3 3 OR4C15 11 55554960 Silent SNP G C3N-01016_T 848036 55554960 79531662 219 20368 OR4P4 0 . GRCh38 11 55638716 55638716 + Missense_Mutation SNP G G T rs143338269 C3N-01016_T C3N-01016_N G G c.359G>T p.Arg120Leu p.R120L ENST00000314612 1/1 124 58 66 145 145 0 strelka-varscan-mutect OR4P4,missense_variant,p.Arg120Leu,ENST00000314612,NM_001004124.2; T ENST00000314612 Transcript missense_variant 359/939 359/939 120/312 R/L cGc/cTc rs143338269,COSM3670791 1 1 OR4P4 HGNC HGNC:15180 protein_coding YES CCDS31504.1 ENSP00000324831 Q8NGL7 UPI0000061E8A NM_001004124.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF386,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs143338269 . 23 183 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 55638716 55638716 G T 1 0 0 0 0 1 0 0 0 11156 1087 38 1 1 OR4P4 11 55638716 Missense_Mutation SNP G C3N-01016_T 83756 55638716 79447906 220 20369 OR5D18 0 . GRCh38 11 55820432 55820432 + Missense_Mutation SNP C C T C3N-01016_T C3N-01016_N C C c.803C>T p.Ser268Phe p.S268F ENST00000333976 1/1 156 125 31 188 188 0 strelka-varscan-mutect OR5D18,missense_variant,p.Ser268Phe,ENST00000333976,NM_001001952.1; T ENST00000333976 Transcript missense_variant 803/942 803/942 268/313 S/F tCc/tTc COSM3449041,COSM3791565 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 55820432 55820432 C T 1 0 0 0 0 1 0 0 0 11227 855 30 3 3 OR5D18 11 55820432 Missense_Mutation SNP C C3N-01016_T 181716 55820432 79266190 221 20370 OR5M11 0 . GRCh38 11 56542363 56542363 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.895G>T p.Ala299Ser p.A299S ENST00000528616 1/1 41 27 14 30 30 0 strelka-varscan-mutect OR5M11,missense_variant,p.Ala299Ser,ENST00000528616,NM_001005245.1; A ENST00000528616 Transcript missense_variant 895/918 895/918 299/305 A/S Gcc/Tcc 1 -1 OR5M11 HGNC HGNC:15291 protein_coding YES CCDS53629.1 ENSP00000432417 Q96RB7 A0A126GVL9 UPI00000405CF NM_001005245.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF97,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.999992 1 1 1 0 A 3 1 66 56542363 56542363 C A 1 0 0 0 0 1 0 0 0 11243 739 26 2 2 OR5M11 11 56542363 Missense_Mutation SNP C C3N-01016_T 721931 56542363 78544259 222 20371 MS4A8 0 . GRCh38 11 60715026 60715026 + Silent SNP T T A rs368354928 C3N-01016_T C3N-01016_N T T c.540T>A p.= p.P180P ENST00000300226 6/7 223 140 83 233 233 0 strelka-varscan-mutect MS4A8,missense_variant,p.Trp163Arg,ENST00000529752,;MS4A8,synonymous_variant,p.=,ENST00000300226,NM_031457.1;MS4A8,downstream_gene_variant,,ENST00000525458,; A ENST00000300226 Transcript synonymous_variant 743/1353 540/753 180/250 P ccT/ccA rs368354928 1 1 MS4A8 HGNC HGNC:13380 protein_coding YES CCDS7990.1 ENSP00000300226 Q9BY19 UPI0000047F97 NM_031457.1 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR23320:SF56,hmmpanther:PTHR23320 LOW 1 SNV 1 1 PASS rs368354928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 60715026 60715026 T A 1 0 0 0 0 0 0 0 1 9846 1594 55 4 4 MS4A8 11 60715026 Silent SNP T C3N-01016_T 4172663 60715026 74371596 223 20372 CHRM1 0 . GRCh38 11 62910008 62910008 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.1093C>A p.= p.R365R ENST00000306960 2/2 184 107 77 182 182 0 strelka-varscan-mutect CHRM1,synonymous_variant,p.=,ENST00000306960,NM_000738.2;CHRM1,synonymous_variant,p.=,ENST00000543973,;CHRM1,downstream_gene_variant,,ENST00000536524,;AP000438.2,intron_variant,,ENST00000543624,; T ENST00000306960 Transcript synonymous_variant 1635/2964 1093/1383 365/460 R Cgg/Agg 1 -1 CHRM1 HGNC HGNC:1950 protein_coding YES CCDS8040.1 ENSP00000306490 P11229 Q53XZ3 UPI00001252AB NM_000738.2 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF283,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS rs1158763845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 62910008 62910008 G T 1 0 0 0 0 0 0 0 1 3136 1057 37 1 1 CHRM1 11 62910008 Silent SNP G C3N-01016_T 2194982 62910008 72176614 224 20373 RTN3 0 . GRCh38 11 63720450 63720451 + Frame_Shift_Ins INS - - C novel C3N-01016_T C3N-01016_N - - c.1952dupC p.Glu652ArgfsTer13 p.E652Rfs*13 ENST00000377819 3/9 81 62 19 59 59 0 sindel-varindel-pindel RTN3,frameshift_variant,p.Glu652ArgfsTer13,ENST00000377819,NM_001265589.1;RTN3,frameshift_variant,p.Glu633ArgfsTer13,ENST00000339997,NM_201428.2;RTN3,frameshift_variant,p.Glu540ArgfsTer13,ENST00000540798,NM_001265590.1;RTN3,intron_variant,,ENST00000356000,NM_201429.2;RTN3,intron_variant,,ENST00000537981,NM_006054.3;RTN3,intron_variant,,ENST00000341307,NM_201430.2;RTN3,intron_variant,,ENST00000354497,NM_001265591.1;RTN3,intron_variant,,ENST00000542238,;RTN3,downstream_gene_variant,,ENST00000545432,;RTN3,downstream_gene_variant,,ENST00000543552,;RTN3,intron_variant,,ENST00000536011,;RTN3,intron_variant,,ENST00000543123,; C ENST00000377819 Transcript frameshift_variant 2102-2103/4937 1948-1949/3099 650/1032 S/SX tcc/tCcc 1 1 RTN3 HGNC HGNC:10469 protein_coding YES CCDS58141.1 ENSP00000367050 O95197 UPI00004546A2 NM_001265589.1 3/9 hmmpanther:PTHR10994,hmmpanther:PTHR10994:SF1 HIGH 1 insertion 1 4 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 66 63720450 63720450 - C 1 0 1 1 0 0 0 0 0 13987 1551 54 0 0 RTN3 11 63720450 Frame_Shift_Ins INS - C3N-01016_T 810442 63720450 71366172 225 20374 RIN1 0 . GRCh38 11 66334679 66334679 + Missense_Mutation SNP C C A rs745661610 C3N-01016_T C3N-01016_N C C c.1120G>T p.Asp374Tyr p.D374Y ENST00000311320 6/10 651 255 396 508 508 0 strelka-varscan-mutect RIN1,missense_variant,p.Asp374Tyr,ENST00000311320,NM_004292.2;RIN1,missense_variant,p.Asp269Tyr,ENST00000530056,;BRMS1,downstream_gene_variant,,ENST00000359957,NM_015399.3;BRMS1,downstream_gene_variant,,ENST00000425825,NM_001024957.1;BRMS1,downstream_gene_variant,,ENST00000524699,;BRMS1,downstream_gene_variant,,ENST00000530756,;RIN1,downstream_gene_variant,,ENST00000627248,;RP11-867G23.12,non_coding_transcript_exon_variant,,ENST00000526655,;RIN1,upstream_gene_variant,,ENST00000524804,;RIN1,3_prime_UTR_variant,,ENST00000530745,;RIN1,3_prime_UTR_variant,,ENST00000534824,;RIN1,non_coding_transcript_exon_variant,,ENST00000526246,;BRMS1,downstream_gene_variant,,ENST00000530238,;BRMS1,downstream_gene_variant,,ENST00000527375,;RIN1,downstream_gene_variant,,ENST00000528006,; A ENST00000311320 Transcript missense_variant 1247/2693 1120/2352 374/783 D/Y Gac/Tac rs745661610 1 -1 RIN1 HGNC HGNC:18749 protein_coding YES CCDS31614.1 ENSP00000310406 Q13671 A0A0S2Z4U0 UPI000013F14D NM_004292.2 deleterious(0) 6/10 hmmpanther:PTHR23101,hmmpanther:PTHR23101:SF62 MODERATE 1 SNV 1 1 PASS rs745661610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 66334679 66334679 C A 1 0 0 0 0 1 0 0 0 13545 855 30 2 2 RIN1 11 66334679 Missense_Mutation SNP C C3N-01016_T 2614229 66334679 68751943 226 20375 CTSF 0 . GRCh38 11 66566169 66566169 + Splice_Site SNP T T G novel C3N-01016_T C3N-01016_N T T c.722-2A>C p.X241_splice ENST00000310325 159 60 99 110 110 0 strelka-varscan-mutect CTSF,splice_acceptor_variant,,ENST00000310325,NM_003793.3;CTSF,splice_acceptor_variant,,ENST00000524994,;ACTN3,downstream_gene_variant,,ENST00000502692,NM_001258371.2;ACTN3,downstream_gene_variant,,ENST00000513398,NM_001104.3;CTSF,downstream_gene_variant,,ENST00000526010,;CTSF,downstream_gene_variant,,ENST00000533168,;CTSF,downstream_gene_variant,,ENST00000529561,;CTSF,splice_acceptor_variant,,ENST00000527141,;CTSF,upstream_gene_variant,,ENST00000525733,;CTSF,upstream_gene_variant,,ENST00000529199,;CTSF,upstream_gene_variant,,ENST00000530565,; G ENST00000310325 Transcript splice_acceptor_variant -/2035 722/1455 241/484 1 -1 CTSF HGNC HGNC:2531 protein_coding YES CCDS8144.1 ENSP00000310832 Q9UBX1 UPI0000001657 NM_003793.3 5/12 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 66 66566169 66566169 T G 1 0 0 0 0 0 0 1 0 3843 1594 55 5 5 CTSF 11 66566169 Splice_Site SNP T C3N-01016_T 231490 66566169 68520453 227 20376 FOLR1 0 . GRCh38 11 72195299 72195299 + Missense_Mutation SNP G G T rs779015471 C3N-01016_T C3N-01016_N G G c.197G>T p.Cys66Phe p.C66F ENST00000393679 3/5 573 216 357 400 399 1 strelka-varscan-mutect FOLR1,missense_variant,p.Cys66Phe,ENST00000393679,;FOLR1,missense_variant,p.Cys66Phe,ENST00000312293,NM_016725.2;FOLR1,missense_variant,p.Cys66Phe,ENST00000393681,NM_016724.2;FOLR1,missense_variant,p.Cys66Phe,ENST00000393676,NM_000802.3,NM_016729.2;RP11-807H22.7,intron_variant,,ENST00000378140,; T ENST00000393679 Transcript missense_variant 633/1331 197/774 66/257 C/F tGt/tTt rs779015471 1 1 FOLR1 HGNC HGNC:3791 protein_coding YES CCDS8211.1 ENSP00000377284 P15328 A0A024R5H1 UPI0000000C4C deleterious(0.02) 3/5 hmmpanther:PTHR10517:SF15,hmmpanther:PTHR10517,Pfam_domain:PF03024 MODERATE 1 SNV 1 1 PASS rs779015471 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 72195299 72195299 G T 1 0 0 0 0 1 0 0 0 5841 1377 48 2 2 FOLR1 11 72195299 Missense_Mutation SNP G C3N-01016_T 5629130 72195299 62891323 228 20377 SLCO2B1 0 . GRCh38 11 75193474 75193474 + Silent SNP C C A C3N-01016_T C3N-01016_N C C c.1332C>A p.= p.A444A ENST00000289575 9/14 95 31 64 52 52 0 strelka-varscan-mutect SLCO2B1,synonymous_variant,p.=,ENST00000289575,NM_007256.4;SLCO2B1,synonymous_variant,p.=,ENST00000454962,;SLCO2B1,synonymous_variant,p.=,ENST00000532236,;SLCO2B1,synonymous_variant,p.=,ENST00000428359,NM_001145211.2;SLCO2B1,synonymous_variant,p.=,ENST00000525650,NM_001145212.2;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000531756,;SLCO2B1,upstream_gene_variant,,ENST00000530012,;SLCO2B1,upstream_gene_variant,,ENST00000528108,; A ENST00000289575 Transcript synonymous_variant 1727/4494 1332/2130 444/709 A gcC/gcA COSM3870209 1 1 SLCO2B1 HGNC HGNC:10962 protein_coding YES CCDS8235.1 ENSP00000289575 A0A024R5I4 UPI000000D99A NM_007256.4 9/14 Gene3D:1.20.1250.20,Pfam_domain:PF03137,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF87,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 75193474 75193474 C A 1 0 0 0 0 0 0 0 1 15014 610 22 2 2 SLCO2B1 11 75193474 Silent SNP C C3N-01016_T 2998175 75193474 59893148 229 20378 MOGAT2 0 . GRCh38 11 75728874 75728874 + Nonsense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.735T>A p.Tyr245Ter p.Y245* ENST00000198801 5/6 465 177 288 342 342 0 strelka-varscan-mutect MOGAT2,stop_gained,p.Tyr163Ter,ENST00000526712,;MOGAT2,stop_gained,p.Tyr245Ter,ENST00000198801,NM_025098.2;MOGAT2,upstream_gene_variant,,ENST00000624180,;MOGAT2,3_prime_UTR_variant,,ENST00000525093,; A ENST00000198801 Transcript stop_gained 805/1404 735/1005 245/334 Y/* taT/taA 1 1 MOGAT2 HGNC HGNC:23248 protein_coding YES CCDS8240.1 ENSP00000198801 Q3SYC2 UPI000000D839 NM_025098.2 5/6 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF5 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 75728874 75728874 T A 1 0 0 0 0 0 1 0 0 9658 1413 49 4 4 MOGAT2 11 75728874 Nonsense_Mutation SNP T C3N-01016_T 535400 75728874 59357748 230 20379 FAT3 0 . GRCh38 11 92890632 92890632 + Missense_Mutation SNP G G T rs142403035 C3N-01016_T C3N-01016_N G G c.12839G>T p.Gly4280Val p.G4280V ENST00000525166 27/27 171 96 75 185 185 0 strelka-varscan-mutect FAT3,missense_variant,p.Gly4398Val,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Gly4280Val,ENST00000525166,;FAT3,missense_variant,p.Gly733Val,ENST00000533797,;FAT3,non_coding_transcript_exon_variant,,ENST00000489716,;FAT3,downstream_gene_variant,,ENST00000469900,; T ENST00000525166 Transcript missense_variant 12861/18699 12839/13320 4280/4439 G/V gGt/gTt rs142403035,COSM4601798,COSM4601799,COSM4601800 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0) 27/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs142403035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 92890632 92890632 G T 1 0 0 0 0 1 0 0 0 5551 1261 44 2 2 FAT3 11 92890632 Missense_Mutation SNP G C3N-01016_T 17161758 92890632 42195990 231 20380 CEP126 0 . GRCh38 11 101981943 101981943 + Missense_Mutation SNP G G A rs766595119 C3N-01016_T C3N-01016_N G G c.3013G>A p.Gly1005Ser p.G1005S ENST00000263468 8/11 126 81 45 53 53 0 strelka-varscan-mutect CEP126,missense_variant,p.Gly1005Ser,ENST00000263468,NM_020802.3;CEP126,missense_variant,p.Gly39Ser,ENST00000532077,;CEP126,3_prime_UTR_variant,,ENST00000532529,; A ENST00000263468 Transcript missense_variant 3283/7039 3013/3354 1005/1117 G/S Ggt/Agt rs766595119 1 1 CEP126 HGNC HGNC:29264 protein_coding YES CCDS31658.1 ENSP00000263468 Q9P2H0 UPI0004433B8D NM_020802.3 tolerated(0.09) 8/11 hmmpanther:PTHR31191:SF4,hmmpanther:PTHR31191,Pfam_domain:PF15352 MODERATE 1 SNV 1 1 PASS rs766595119 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 101981943 101981943 G A 1 0 0 0 0 1 0 0 0 2957 1232 43 3 3 CEP126 11 101981943 Missense_Mutation SNP G C3N-01016_T 9091311 101981943 33104679 232 20381 CACNA1C 0 . GRCh38 12 2593318 2593318 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2636C>A p.Ala879Glu p.A879E ENST00000347598 19/49 127 100 27 213 213 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Ala879Glu,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000406454,;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Ala904Glu,ENST00000335762,;CACNA1C,missense_variant,p.Ala879Glu,ENST00000480911,;CACNA1C,missense_variant,p.Ala879Glu,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Ala879Glu,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Ala879Glu,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Ala158Glu,ENST00000465278,; A ENST00000347598 Transcript missense_variant 2636/6655 2636/6561 879/2186 A/E gCg/gAg 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious(0) 19/49 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 MODERATE 1 SNV 1 1 PASS rs1199713333 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 2593318 2593318 C A 1 0 0 0 0 1 0 0 0 2228 768 27 1 1 CACNA1C 12 2593318 Missense_Mutation SNP C C3N-01016_T 2593318 130681991 233 20382 CACNA1C 0 . GRCh38 12 2690921 2690921 + Missense_Mutation SNP G G T C3N-01016_T C3N-01016_N G G c.6283G>T p.Gly2095Trp p.G2095W ENST00000347598 49/49 53 35 18 64 64 0 strelka-varscan-mutect CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399655,NM_000719.6;CACNA1C,missense_variant,p.Gly2118Trp,ENST00000399634,NM_001167625.1;CACNA1C,missense_variant,p.Gly2118Trp,ENST00000406454,;CACNA1C,missense_variant,p.Gly2082Trp,ENST00000399617,NM_001167624.2;CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399603,NM_001167623.1;CACNA1C,missense_variant,p.Gly2072Trp,ENST00000335762,;CACNA1C,missense_variant,p.Gly2095Trp,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,missense_variant,p.Gly2088Trp,ENST00000344100,NM_001129829.1;CACNA1C,missense_variant,p.Gly2082Trp,ENST00000327702,NM_001129830.2;CACNA1C,missense_variant,p.Gly2075Trp,ENST00000399638,NM_001129831.1;CACNA1C,missense_variant,p.Gly2067Trp,ENST00000399606,NM_001129832.1;CACNA1C,missense_variant,p.Gly2066Trp,ENST00000399621,NM_001129834.1;CACNA1C,missense_variant,p.Gly2066Trp,ENST00000399637,NM_001129835.1;CACNA1C,missense_variant,p.Gly2066Trp,ENST00000402845,NM_001129833.1;CACNA1C,missense_variant,p.Gly2064Trp,ENST00000399629,NM_001129836.1;CACNA1C,missense_variant,p.Gly2055Trp,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,missense_variant,p.Gly2055Trp,ENST00000399595,NM_001129837.1;CACNA1C,missense_variant,p.Gly2053Trp,ENST00000399649,NM_001129839.1;CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399601,NM_001129843.1;CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399641,NM_001129840.1;CACNA1C,missense_variant,p.Gly2047Trp,ENST00000399644,NM_001129841.1;CACNA1C,missense_variant,p.Gly738Trp,ENST00000616390,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000501371,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000544517,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000541673,;RP11-885B4.1,downstream_gene_variant,,ENST00000636122,; T ENST00000347598 Transcript missense_variant 6283/6655 6283/6561 2095/2186 G/W Ggg/Tgg COSM5157884,COSM5157885,COSM5157886,COSM5157887,COSM5157888,COSM5157889 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 deleterious_low_confidence(0) 49/49 Pfam_domain:PF16885 1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 2690921 2690921 G T 1 0 0 0 0 1 0 0 0 2228 1232 43 2 2 CACNA1C 12 2690921 Missense_Mutation SNP G C3N-01016_T 97603 2690921 130584388 234 20383 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C T rs121913530 C3N-01016_T C3N-01016_N C C c.34G>A p.Gly12Ser p.G12S ENST00000256078 2/6 461 280 181 313 313 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Ser,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Ser,ENST00000556131,;KRAS,missense_variant,p.Gly12Ser,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Ser,ENST00000557334,; T ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/S Ggt/Agt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.03) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 25245351 25245351 C T 1 0 0 0 0 1 0 0 0 8318 594 21 3 3 KRAS 12 25245351 Missense_Mutation SNP C C3N-01016_T 22554430 25245351 108029958 235 20384 CCDC91 0 . GRCh38 12 28306853 28306853 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.379G>T p.Ala127Ser p.A127S ENST00000545336 8/16 310 285 25 169 169 0 strelka-varscan-mutect CCDC91,missense_variant,p.Ala127Ser,ENST00000545336,;CCDC91,missense_variant,p.Ala127Ser,ENST00000539107,;CCDC91,missense_variant,p.Ala127Ser,ENST00000381259,NM_018318.3;CCDC91,intron_variant,,ENST00000536154,;CCDC91,intron_variant,,ENST00000540794,;CCDC91,downstream_gene_variant,,ENST00000543534,;CCDC91,downstream_gene_variant,,ENST00000538586,;CCDC91,non_coding_transcript_exon_variant,,ENST00000540401,;CCDC91,non_coding_transcript_exon_variant,,ENST00000539904,;CCDC91,non_coding_transcript_exon_variant,,ENST00000544649,;CCDC91,missense_variant,p.Ala127Ser,ENST00000543809,;CCDC91,missense_variant,p.Ala127Ser,ENST00000545737,;CCDC91,missense_variant,p.Ala127Ser,ENST00000536442,;CCDC91,3_prime_UTR_variant,,ENST00000535520,; T ENST00000545336 Transcript missense_variant 798/2738 379/1326 127/441 A/S Gcc/Tcc 1 1 CCDC91 HGNC HGNC:24855 protein_coding YES CCDS8716.1 ENSP00000438040 Q7Z6B0 A0A024RAW6 UPI00001AEE23 tolerated(0.19) 8/16 hmmpanther:PTHR35072 MODERATE 1 SNV 5 1 PASS rs1396625177 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 28306853 28306853 G T 1 0 0 0 0 1 0 0 0 2568 971 34 2 2 CCDC91 12 28306853 Missense_Mutation SNP G C3N-01016_T 3061502 28306853 104968456 236 20385 PRPH 0 . GRCh38 12 49295660 49295660 + Missense_Mutation SNP G G A novel C3N-01016_T C3N-01016_N G G c.460G>A p.Glu154Lys p.E154K ENST00000257860 1/9 175 155 20 119 119 0 strelka-varscan-mutect PRPH,missense_variant,p.Glu154Lys,ENST00000257860,NM_006262.3;PRPH,missense_variant,p.Glu41Lys,ENST00000451891,;PRPH,upstream_gene_variant,,ENST00000532332,;RP11-161H23.9,non_coding_transcript_exon_variant,,ENST00000553259,;PRPH,downstream_gene_variant,,ENST00000551194,;PRPH,upstream_gene_variant,,ENST00000533401,;PRPH,upstream_gene_variant,,ENST00000530631,;PRPH,upstream_gene_variant,,ENST00000537252,; A ENST00000257860 Transcript missense_variant 1959/3245 460/1413 154/470 E/K Gag/Aag 1 1 PRPH HGNC HGNC:9461 protein_coding YES CCDS8783.1 ENSP00000257860 P41219 UPI000013CF92 NM_006262.3 deleterious(0.03) 1/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF29,Low_complexity_(Seg):seg,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 49295660 49295660 G A 1 0 0 0 0 1 0 0 0 12712 943 33 3 3 PRPH 12 49295660 Missense_Mutation SNP G C3N-01016_T 20988807 49295660 83979649 237 20386 SCN8A 0 . GRCh38 12 51721672 51721672 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1762C>G p.His588Asp p.H588D ENST00000354534 12/27 310 237 73 319 319 0 strelka-varscan-mutect SCN8A,missense_variant,p.His588Asp,ENST00000354534,NM_014191.3;SCN8A,missense_variant,p.His588Asp,ENST00000545061,NM_001177984.2;SCN8A,missense_variant,p.His588Asp,ENST00000599343,;SCN8A,missense_variant,p.His588Asp,ENST00000627620,;SCN8A,missense_variant,p.His588Asp,ENST00000355133,;SCN8A,missense_variant,p.His438Asp,ENST00000551216,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,non_coding_transcript_exon_variant,,ENST00000550891,; G ENST00000354534 Transcript missense_variant 1940/11556 1762/5943 588/1980 H/D Cac/Gac 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 deleterious(0.02) 12/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037,Pfam_domain:PF11933 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 51721672 51721672 C G 1 0 0 0 0 1 0 0 0 14193 710 25 4 4 SCN8A 12 51721672 Missense_Mutation SNP C C3N-01016_T 2426012 51721672 81553637 238 20387 ANKRD52 0 . GRCh38 12 56254189 56254189 + Nonsense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.784G>T p.Gly262Ter p.G262* ENST00000267116 8/28 485 420 65 387 387 0 strelka-varscan-mutect ANKRD52,stop_gained,p.Gly262Ter,ENST00000267116,NM_173595.3;ANKRD52,downstream_gene_variant,,ENST00000551023,;ANKRD52,non_coding_transcript_exon_variant,,ENST00000548081,; A ENST00000267116 Transcript stop_gained 906/8688 784/3231 262/1076 G/* Gga/Tga COSM1245072 1 -1 ANKRD52 HGNC HGNC:26614 protein_coding YES CCDS44920.1 ENSP00000267116 Q8NB46 UPI0000237861 NM_173595.3 8/28 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24158:SF17,hmmpanther:PTHR24158,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 56254189 56254189 C A 1 0 0 0 0 0 1 0 0 782 661 23 1 1 ANKRD52 12 56254189 Nonsense_Mutation SNP C C3N-01016_T 4532517 56254189 77021120 239 20388 RAB21 0 . GRCh38 12 71755196 71755196 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.67G>T p.Val23Leu p.V23L ENST00000261263 1/7 158 114 44 158 158 0 strelka-varscan-mutect RAB21,missense_variant,p.Val23Leu,ENST00000261263,NM_014999.2; T ENST00000261263 Transcript missense_variant 323/15546 67/678 23/225 V/L Gtg/Ttg 1 1 RAB21 HGNC HGNC:18263 protein_coding YES CCDS9003.1 ENSP00000261263 Q9UL25 A0A024RBA9 UPI000013315D NM_014999.2 deleterious(0.02) 1/7 PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF509,Gene3D:3.40.50.300,Pfam_domain:PF00071,TIGRFAM_domain:TIGR00231,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00173,Superfamily_domains:SSF52540,Prints_domain:PR00449 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 71755196 71755196 G T 1 0 0 0 0 1 0 0 0 13066 1261 44 2 2 RAB21 12 71755196 Missense_Mutation SNP G C3N-01016_T 15501007 71755196 61520113 240 20389 PTPRQ 0 . GRCh38 12 80673271 80673271 + Silent SNP G G C novel C3N-01016_T C3N-01016_N G G c.6705G>C p.= p.L2235L ENST00000614701 43/45 236 174 62 136 136 0 strelka-varscan-mutect PTPRQ,synonymous_variant,p.=,ENST00000614701,NM_001145026.1;PTPRQ,synonymous_variant,p.=,ENST00000616559,; C ENST00000614701 Transcript synonymous_variant 6883/8289 6705/6900 2235/2299 L ctG/ctC 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 43/45 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 66 80673271 80673271 G C 1 0 0 0 0 0 0 0 1 12964 1277 45 4 4 PTPRQ 12 80673271 Silent SNP G C3N-01016_T 8918075 80673271 52602038 241 20390 PPFIA2 0 . GRCh38 12 81341184 81341184 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.2287C>A p.= p.R763R ENST00000549396 20/33 160 139 21 119 119 0 strelka-varscan-mutect PPFIA2,synonymous_variant,p.=,ENST00000333447,NM_001220478.2;PPFIA2,synonymous_variant,p.=,ENST00000550584,NM_001220473.2;PPFIA2,synonymous_variant,p.=,ENST00000549396,NM_003625.4;PPFIA2,synonymous_variant,p.=,ENST00000549325,NM_001220474.2;PPFIA2,synonymous_variant,p.=,ENST00000548586,NM_001220476.2;PPFIA2,synonymous_variant,p.=,ENST00000552948,NM_001220475.2;PPFIA2,synonymous_variant,p.=,ENST00000407050,NM_001220477.2;PPFIA2,synonymous_variant,p.=,ENST00000550359,NM_001282536.1;PPFIA2,synonymous_variant,p.=,ENST00000443686,;PPFIA2,synonymous_variant,p.=,ENST00000541570,NM_001220479.2;PPFIA2,5_prime_UTR_variant,,ENST00000541017,NM_001220480.2;PPFIA2,upstream_gene_variant,,ENST00000551147,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000549917,;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,;PPFIA2,non_coding_transcript_exon_variant,,ENST00000549344,; T ENST00000549396 Transcript synonymous_variant 2448/5363 2287/3774 763/1257 R Cga/Aga 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 20/33 hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 LOW 1 SNV 1 1 PASS rs945544638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 81341184 81341184 G T 1 0 0 0 0 0 0 0 1 12419 1066 37 1 1 PPFIA2 12 81341184 Silent SNP G C3N-01016_T 667913 81341184 51934125 242 20391 BTBD11 0 . GRCh38 12 107543958 107543958 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1309C>G p.His437Asp p.H437D ENST00000280758 3/17 162 117 45 121 121 0 strelka-varscan-mutect BTBD11,missense_variant,p.His437Asp,ENST00000280758,NM_001018072.1;BTBD11,missense_variant,p.His437Asp,ENST00000490090,;BTBD11,missense_variant,p.His437Asp,ENST00000420571,;BTBD11,missense_variant,p.His71Asp,ENST00000415943,;BTBD11,missense_variant,p.His68Asp,ENST00000550706,; G ENST00000280758 Transcript missense_variant 1837/5767 1309/3315 437/1104 H/D Cat/Gat 1 1 BTBD11 HGNC HGNC:23844 protein_coding YES CCDS31893.1 ENSP00000280758 A6QL63 UPI000051901E NM_001018072.1 deleterious(0) 3/17 MODERATE 1 SNV 5 1 PASS rs1432004253 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 107543958 107543958 C G 1 0 0 0 0 1 0 0 0 1714 710 25 4 4 BTBD11 12 107543958 Missense_Mutation SNP C C3N-01016_T 26202774 107543958 25731351 243 20392 SDSL 0 . GRCh38 12 113438067 113438067 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.978G>T p.= p.L326L ENST00000403593 8/8 91 54 37 81 81 0 strelka-varscan-mutect SDSL,synonymous_variant,p.=,ENST00000403593,NM_001304993.1;SDSL,synonymous_variant,p.=,ENST00000345635,NM_138432.3;SDSL,synonymous_variant,p.=,ENST00000546672,;SDSL,downstream_gene_variant,,ENST00000553248,;SDSL,downstream_gene_variant,,ENST00000551760,; T ENST00000403593 Transcript synonymous_variant 1240/1449 978/990 326/329 L ctG/ctT 1 1 SDSL HGNC HGNC:30404 protein_coding YES CCDS9170.1 ENSP00000385790 Q96GA7 A0A024RBL2 UPI0000072263 NM_001304993.1 8/8 hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF99 LOW 1 SNV 1 1 PASS rs959821103 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 113438067 113438067 G T 1 0 0 0 0 0 0 0 1 14252 1335 47 2 2 SDSL 12 113438067 Silent SNP G C3N-01016_T 5894109 113438067 19837242 244 20393 NOS1 0 . GRCh38 12 117286149 117286149 + Silent SNP C C A C3N-01016_T C3N-01016_N C C c.1245G>T p.= p.R415R ENST00000618760 6/30 237 160 77 214 213 1 strelka-varscan-mutect NOS1,synonymous_variant,p.=,ENST00000618760,NM_001204218.1;NOS1,synonymous_variant,p.=,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,synonymous_variant,p.=,ENST00000338101,;NOS1,synonymous_variant,p.=,ENST00000344089,; A ENST00000618760 Transcript synonymous_variant 1956/12283 1245/4407 415/1468 R cgG/cgT COSM4523978 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 6/30 Pfam_domain:PF02898,Gene3D:3.90.340.10,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 117286149 117286149 C A 1 0 0 0 0 0 0 0 1 10586 842 30 2 2 NOS1 12 117286149 Silent SNP C C3N-01016_T 3848082 117286149 15989160 245 20394 SETD1B 0 . GRCh38 12 121827607 121827607 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.5297C>T p.Thr1766Ile p.T1766I ENST00000542440 15/18 178 132 46 158 158 0 strelka-varscan-mutect SETD1B,missense_variant,p.Thr1766Ile,ENST00000542440,NM_015048.1;SETD1B,missense_variant,p.Thr1809Ile,ENST00000604567,;SETD1B,missense_variant,p.Thr1809Ile,ENST00000619791,;SETD1B,missense_variant,p.Thr1766Ile,ENST00000267197,; T ENST00000542440 Transcript missense_variant 5365/8185 5297/5772 1766/1923 T/I aCt/aTt 1 1 SETD1B HGNC HGNC:29187 protein_coding YES CCDS53838.1 ENSP00000442924 Q9UPS6 UPI00006C12ED NM_015048.1 tolerated(0.05) 15/18 Pfam_domain:PF11764,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF296,SMART_domains:SM01291 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 121827607 121827607 C T 1 0 0 0 0 1 0 0 0 14408 565 20 3 3 SETD1B 12 121827607 Missense_Mutation SNP C C3N-01016_T 4541458 121827607 11447702 246 20395 RIMBP2 0 . GRCh38 12 130451218 130451218 + Missense_Mutation SNP C C T rs370254266 C3N-01016_T C3N-01016_N C C c.430G>A p.Ala144Thr p.A144T ENST00000261655 5/19 142 126 16 148 148 0 strelka-varscan-mutect RIMBP2,missense_variant,p.Ala144Thr,ENST00000261655,NM_015347.4;RIMBP2,missense_variant,p.Ala52Thr,ENST00000535703,; T ENST00000261655 Transcript missense_variant 594/6321 430/3159 144/1052 A/T Gca/Aca rs370254266,COSM1360103 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 tolerated(0.22) 5/19 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs370254266 . 0 206 0 3 0 0 0 0 -19.99974 0.9999881 1 1 1 0 T 3 4 66 130451218 130451218 C T 1 0 0 0 0 1 0 0 0 13538 768 27 1 1 RIMBP2 12 130451218 Missense_Mutation SNP C C3N-01016_T 8623611 130451218 2824091 247 20396 SGCG 0 . GRCh38 13 23279388 23279388 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.415C>A p.Gln139Lys p.Q139K ENST00000218867 5/8 395 232 163 370 370 0 strelka-varscan-mutect SGCG,missense_variant,p.Gln139Lys,ENST00000218867,NM_000231.2; A ENST00000218867 Transcript missense_variant 539/1624 415/876 139/291 Q/K Cag/Aag 1 1 SGCG HGNC HGNC:10809 protein_coding YES CCDS9299.1 ENSP00000218867 Q13326 UPI000013C76D NM_000231.2 tolerated(0.78) 5/8 hmmpanther:PTHR12939,hmmpanther:PTHR12939:SF4,Pfam_domain:PF04790 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 23279388 23279388 C A 1 0 0 0 0 1 0 0 0 14463 479 17 2 2 SGCG 13 23279388 Missense_Mutation SNP C C3N-01016_T 23279388 91084940 248 20397 NBEA 0 . GRCh38 13 35550526 35550526 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.6635T>A p.Ile2212Lys p.I2212K ENST00000400445 42/58 159 95 64 167 167 0 strelka-varscan-mutect NBEA,missense_variant,p.Ile2212Lys,ENST00000400445,NM_015678.4;NBEA,missense_variant,p.Ile2213Lys,ENST00000310336,;NBEA,missense_variant,p.Ile2212Lys,ENST00000629018,;NBEA,missense_variant,p.Ile2209Lys,ENST00000379939,;NBEA,missense_variant,p.Ile5Lys,ENST00000537702,NM_001204197.1; A ENST00000400445 Transcript missense_variant 7169/11119 6635/8841 2212/2946 I/K aTa/aAa 1 1 NBEA HGNC HGNC:7648 protein_coding YES CCDS45026.1 ENSP00000383295 Q8NFP9 UPI00004FF92F NM_015678.4 deleterious(0) 42/58 Gene3D:1t77A01,Pfam_domain:PF14844,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF62,Superfamily_domains:SSF50729 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 35550526 35550526 T A 1 0 0 0 0 1 0 0 0 10198 1406 49 4 4 NBEA 13 35550526 Missense_Mutation SNP T C3N-01016_T 12271138 35550526 78813802 249 20398 CSNK1A1L 0 . GRCh38 13 37104443 37104443 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.814C>A p.Pro272Thr p.P272T ENST00000379800 1/1 368 208 160 336 333 3 strelka-varscan-mutect CSNK1A1L,missense_variant,p.Pro272Thr,ENST00000379800,NM_145203.5; T ENST00000379800 Transcript missense_variant 1222/2406 814/1014 272/337 P/T Cca/Aca 1 -1 CSNK1A1L HGNC HGNC:20289 protein_coding YES CCDS9363.1 ENSP00000369126 Q8N752 UPI000003C95C NM_145203.5 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50011,hmmpanther:PTHR11909:SF139,hmmpanther:PTHR11909,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 37104443 37104443 G T 1 0 0 0 0 1 0 0 0 3751 1232 43 2 2 CSNK1A1L 13 37104443 Missense_Mutation SNP G C3N-01016_T 1553917 37104443 77259885 250 20399 PCDH17 0 . GRCh38 13 57666785 57666785 + Missense_Mutation SNP G G T rs572132103 C3N-01016_T C3N-01016_N G G c.2749G>T p.Ala917Ser p.A917S ENST00000377918 3/4 99 50 49 69 69 0 strelka-varscan-mutect PCDH17,missense_variant,p.Ala917Ser,ENST00000377918,NM_001040429.2;PCDH17,missense_variant,p.Ala304Ser,ENST00000612954,;PCDH17,missense_variant,p.Ala95Ser,ENST00000615375,;PCDH17,3_prime_UTR_variant,,ENST00000484979,; T ENST00000377918 Transcript missense_variant 3484/8232 2749/3480 917/1159 A/S Gca/Tca rs572132103 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.07) 3/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41 MODERATE 1 SNV 1 1 PASS rs572132103 . 0 199 10 0 0 0 0 0 -20 0.9999983 1 1 1 0 T 3 4 66 57666785 57666785 G T 1 0 0 0 0 1 0 0 0 11599 1203 42 2 2 PCDH17 13 57666785 Missense_Mutation SNP G C3N-01016_T 20562342 57666785 56697543 251 20400 COL4A2 0 . GRCh38 13 110457353 110457353 + Silent SNP T T C novel C3N-01016_T C3N-01016_N T T c.1350T>C p.= p.F450F ENST00000360467 21/48 457 255 202 560 560 0 strelka-varscan-mutect COL4A2,synonymous_variant,p.=,ENST00000360467,NM_001846.2;COL4A2,upstream_gene_variant,,ENST00000617564,;COL4A2-AS2,non_coding_transcript_exon_variant,,ENST00000458403,;COL4A2,upstream_gene_variant,,ENST00000478681,; C ENST00000360467 Transcript synonymous_variant 1656/6281 1350/5139 450/1712 F ttT/ttC 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 21/48 Low_complexity_(Seg):seg,Pfam_domain:PF01391 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 66 110457353 110457353 T C 1 0 0 0 0 0 0 0 1 3479 1809 63 5 5 COL4A2 13 110457353 Silent SNP T C3N-01016_T 52790568 110457353 3906975 252 20401 OR11H6 0 . GRCh38 14 20224259 20224259 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.550C>A p.Leu184Ile p.L184I ENST00000315519 1/1 231 201 30 218 218 0 strelka-varscan-mutect OR11H6,missense_variant,p.Leu184Ile,ENST00000315519,NM_001004480.1; A ENST00000315519 Transcript missense_variant 628/1174 550/993 184/330 L/I Ctt/Att COSM2152869 1 1 OR11H6 HGNC HGNC:15349 protein_coding YES CCDS32033.1 ENSP00000319071 Q8NGC7 A0A126GVP4 UPI000004B1F1 NM_001004480.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF90,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs946398048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 20224259 20224259 C A 1 0 0 0 0 1 0 0 0 11006 565 20 2 2 OR11H6 14 20224259 Missense_Mutation SNP C C3N-01016_T 20224259 86819459 253 20402 TEP1 0 . GRCh38 14 20408389 20408389 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.51G>T p.Leu17Phe p.L17F ENST00000262715 2/55 167 134 33 160 160 0 strelka-varscan-mutect TEP1,missense_variant,p.Leu17Phe,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Leu17Phe,ENST00000556935,;TEP1,missense_variant,p.Leu17Phe,ENST00000556549,;TEP1,missense_variant,p.Leu17Phe,ENST00000555727,;TEP1,upstream_gene_variant,,ENST00000557627,; A ENST00000262715 Transcript missense_variant 92/10695 51/7884 17/2627 L/F ttG/ttT 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 deleterious_low_confidence(0.01) 2/55 PROSITE_profiles:PS51226,Pfam_domain:PF05386 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 20408389 20408389 C A 1 0 0 0 0 1 0 0 0 16175 593 21 2 2 TEP1 14 20408389 Missense_Mutation SNP C C3N-01016_T 184130 20408389 86635329 254 20403 CHMP4A 0 . GRCh38 14 24210467 24210467 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.491A>T p.Glu164Val p.E164V ENST00000530611 5/10 181 97 84 143 143 0 strelka-varscan-mutect RP11-468E2.1,missense_variant,p.Glu164Val,ENST00000530611,;CHMP4A,missense_variant,p.Glu207Val,ENST00000347519,NM_014169.3;CHMP4A,missense_variant,p.Glu59Val,ENST00000530996,;CHMP4A,missense_variant,p.Glu164Val,ENST00000609024,;CHMP4A,missense_variant,p.Glu174Val,ENST00000533011,;TSSK4,downstream_gene_variant,,ENST00000339917,NM_001184739.1;TSSK4,downstream_gene_variant,,ENST00000287913,NM_174944.3;TSSK4,downstream_gene_variant,,ENST00000556621,NM_001308067.1;MDP1,downstream_gene_variant,,ENST00000288087,NM_001199822.1,NM_138476.3;TSSK4,downstream_gene_variant,,ENST00000553766,;TSSK4,downstream_gene_variant,,ENST00000555092,;NEDD8-MDP1,downstream_gene_variant,,ENST00000534348,NM_001199823.1;MDP1,downstream_gene_variant,,ENST00000396833,NM_001199821.1;TSSK4,downstream_gene_variant,,ENST00000428351,;CHMP4A,non_coding_transcript_exon_variant,,ENST00000542700,;NEDD8-MDP1,downstream_gene_variant,,ENST00000604306,;CHMP4A,downstream_gene_variant,,ENST00000531158,;MDP1,downstream_gene_variant,,ENST00000532557,;MDP1,downstream_gene_variant,,ENST00000525696,;CHMP4A,3_prime_UTR_variant,,ENST00000533523,;AL136419.6,non_coding_transcript_exon_variant,,ENST00000565988,;CHMP4A,non_coding_transcript_exon_variant,,ENST00000524955,;AL136419.6,downstream_gene_variant,,ENST00000528804,;TSSK4,downstream_gene_variant,,ENST00000554420,;MDP1,downstream_gene_variant,,ENST00000530222,;NEDD8-MDP1,downstream_gene_variant,,ENST00000605847,;MDP1,downstream_gene_variant,,ENST00000466422,;CHMP4A,downstream_gene_variant,,ENST00000552620,;MDP1,downstream_gene_variant,,ENST00000532742,;MDP1,downstream_gene_variant,,ENST00000533536,;CHMP4A,downstream_gene_variant,,ENST00000527154,;MDP1,downstream_gene_variant,,ENST00000528849,;MDP1,downstream_gene_variant,,ENST00000531553,;NEDD8-MDP1,downstream_gene_variant,,ENST00000530579,;CHMP4A,downstream_gene_variant,,ENST00000534106,; A ENST00000530611 Transcript missense_variant 525/2740 491/2448 164/815 E/V gAg/gTg 1 -1 RP11-468E2.1 Clone_based_vega_gene protein_coding YES ENSP00000433967 E9PSI1 UPI0001F77BE7 deleterious_low_confidence(0) 5/10 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF03357 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 24210467 24210467 T A 1 0 0 0 0 1 0 0 0 3116 1551 54 4 4 CHMP4A 14 24210467 Missense_Mutation SNP T C3N-01016_T 3802078 24210467 82833251 255 20404 NFATC4 0 . GRCh38 14 24370257 24370257 + Missense_Mutation SNP C C T rs755808600 C3N-01016_T C3N-01016_N C C c.1048C>T p.Arg350Cys p.R350C ENST00000413692 3/10 132 68 64 91 91 0 strelka-varscan-mutect NFATC4,missense_variant,p.Arg350Cys,ENST00000413692,NM_001136022.2;NFATC4,missense_variant,p.Arg319Cys,ENST00000539237,;NFATC4,missense_variant,p.Arg217Cys,ENST00000557451,;NFATC4,missense_variant,p.Arg275Cys,ENST00000422617,NM_001288802.1;NFATC4,missense_variant,p.Arg300Cys,ENST00000424781,;NFATC4,missense_variant,p.Arg287Cys,ENST00000553708,;NFATC4,missense_variant,p.Arg287Cys,ENST00000250373,NM_001320043.1,NM_004554.4;NFATC4,missense_variant,p.Arg275Cys,ENST00000555453,;NFATC4,missense_variant,p.Arg287Cys,ENST00000554050,NM_001198965.1;NFATC4,missense_variant,p.Arg217Cys,ENST00000554344,;NFATC4,missense_variant,p.Arg319Cys,ENST00000556279,;NFATC4,missense_variant,p.Arg350Cys,ENST00000554591,NM_001198967.2;NFATC4,missense_variant,p.Arg300Cys,ENST00000555590,;NFATC4,missense_variant,p.Arg217Cys,ENST00000553879,NM_001198966.2;NFATC4,missense_variant,p.Arg217Cys,ENST00000554661,;NFATC4,missense_variant,p.Arg319Cys,ENST00000553469,;NFATC4,missense_variant,p.Arg275Cys,ENST00000556169,;NFATC4,missense_variant,p.Arg300Cys,ENST00000554966,;NFATC4,intron_variant,,ENST00000554779,;NFATC4,upstream_gene_variant,,ENST00000555167,;NFATC4,upstream_gene_variant,,ENST00000555393,;NFATC4,upstream_gene_variant,,ENST00000556759,;NFATC4,upstream_gene_variant,,ENST00000555802,;NFATC4,upstream_gene_variant,,ENST00000554473,;NFATC4,downstream_gene_variant,,ENST00000557674,;NFATC4,upstream_gene_variant,,ENST00000557767,;NFATC4,downstream_gene_variant,,ENST00000554903,;NFATC4,non_coding_transcript_exon_variant,,ENST00000440487,;NFATC4,non_coding_transcript_exon_variant,,ENST00000554655,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556302,;NFATC4,non_coding_transcript_exon_variant,,ENST00000556957,;NFATC4,intron_variant,,ENST00000557028,; T ENST00000413692 Transcript missense_variant 1192/5700 1048/2895 350/964 R/C Cgt/Tgt rs755808600,COSM1140497,COSM5253336,COSM5253337,COSM552879 1 1 NFATC4 HGNC HGNC:7778 protein_coding YES CCDS45089.1 ENSP00000388910 Q14934 UPI00017BD050 NM_001136022.2 deleterious(0) 3/10 Low_complexity_(Seg):seg,hmmpanther:PTHR12533:SF11,hmmpanther:PTHR12533 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs755808600 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 24370257 24370257 C T 1 0 0 0 0 1 0 0 0 10402 652 23 1 1 NFATC4 14 24370257 Missense_Mutation SNP C C3N-01016_T 159790 24370257 82673461 256 20405 PRKD1 0 . GRCh38 14 29597689 29597689 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.2236A>T p.Thr746Ser p.T746S ENST00000331968 16/18 318 277 41 231 231 0 strelka-varscan-mutect PRKD1,missense_variant,p.Thr746Ser,ENST00000331968,NM_002742.2;PRKD1,missense_variant,p.Thr746Ser,ENST00000616995,;PRKD1,missense_variant,p.Thr754Ser,ENST00000415220,;PRKD1,upstream_gene_variant,,ENST00000490795,; A ENST00000331968 Transcript missense_variant 2466/3726 2236/2739 746/912 T/S Acc/Tcc 1 -1 PRKD1 HGNC HGNC:9407 protein_coding YES CCDS9637.1 ENSP00000333568 Q15139 UPI0000456761 NM_002742.2 deleterious(0.02) 16/18 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000552,PROSITE_profiles:PS50011,hmmpanther:PTHR22968,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 29597689 29597689 T A 1 0 0 0 0 1 0 0 0 12651 1638 57 4 4 PRKD1 14 29597689 Missense_Mutation SNP T C3N-01016_T 5227432 29597689 77446029 257 20406 LRFN5 0 . GRCh38 14 41886917 41886917 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.292C>A p.Leu98Ile p.L98I ENST00000298119 3/6 372 171 201 190 189 1 strelka-varscan-mutect LRFN5,missense_variant,p.Leu98Ile,ENST00000554171,;LRFN5,missense_variant,p.Leu98Ile,ENST00000298119,NM_152447.3;LRFN5,missense_variant,p.Leu98Ile,ENST00000554120,; A ENST00000298119 Transcript missense_variant 1481/3723 292/2160 98/719 L/I Cta/Ata 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 deleterious(0) 3/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,Pfam_domain:PF13306,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 41886917 41886917 C A 1 0 0 0 0 1 0 0 0 8835 680 24 2 2 LRFN5 14 41886917 Missense_Mutation SNP C C3N-01016_T 12289228 41886917 65156801 258 20407 DACT1 0 . GRCh38 14 58646216 58646216 + Silent SNP C C A rs750523668 C3N-01016_T C3N-01016_N C C c.1593C>A p.= p.P531P ENST00000335867 4/4 280 172 108 249 249 0 strelka-varscan-mutect DACT1,synonymous_variant,p.=,ENST00000395153,NM_001079520.1;DACT1,synonymous_variant,p.=,ENST00000541264,;DACT1,synonymous_variant,p.=,ENST00000335867,NM_016651.5;DACT1,synonymous_variant,p.=,ENST00000556859,;DACT1,downstream_gene_variant,,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,; A ENST00000335867 Transcript synonymous_variant 1617/2571 1593/2511 531/836 P ccC/ccA rs750523668 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 4/4 hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268 LOW 1 SNV 2 1 PASS rs750523668 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 58646216 58646216 C A 1 0 0 0 0 0 0 0 1 4023 639 23 1 1 DACT1 14 58646216 Silent SNP C C3N-01016_T 16759299 58646216 48397502 259 20408 SYT16 0 . GRCh38 14 62075288 62075288 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.890G>T p.Arg297Met p.R297M ENST00000568344 3/6 301 249 52 316 316 0 strelka-varscan-mutect SYT16,missense_variant,p.Arg297Met,ENST00000568344,NM_031914.2;SYT16,missense_variant,p.Arg187Met,ENST00000636133,;SYT16,upstream_gene_variant,,ENST00000430451,;RP11-355I22.5,intron_variant,,ENST00000553990,;SYT16,missense_variant,p.Arg297Met,ENST00000555409,; T ENST00000568344 Transcript missense_variant 1087/13978 890/1938 297/645 R/M aGg/aTg 1 1 SYT16 HGNC HGNC:23142 protein_coding YES CCDS45121.1 ENSP00000478637 Q17RD7 UPI0000EE1AC0 NM_031914.2 tolerated(0.06) 3/6 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 62075288 62075288 G T 1 0 0 0 0 1 0 0 0 15866 1000 35 2 2 SYT16 14 62075288 Missense_Mutation SNP G C3N-01016_T 3429072 62075288 44968430 260 20409 MAP3K9 0 . GRCh38 14 70733132 70733132 + Missense_Mutation SNP T T C rs755568141 C3N-01016_T C3N-01016_N T T c.2279A>G p.His760Arg p.H760R ENST00000555993 12/13 167 102 65 127 127 0 strelka-varscan-mutect MAP3K9,missense_variant,p.His746Arg,ENST00000554752,NM_001284230.1;MAP3K9,missense_variant,p.His522Arg,ENST00000611979,NM_001284231.1;MAP3K9,missense_variant,p.His760Arg,ENST00000555993,NM_033141.3;MAP3K9,missense_variant,p.His723Arg,ENST00000381250,;MAP3K9,missense_variant,p.His479Arg,ENST00000553414,NM_001284232.1;MAP3K9,missense_variant,p.His474Arg,ENST00000554146,; C ENST00000555993 Transcript missense_variant 2642/4449 2279/3357 760/1118 H/R cAc/cGc rs755568141 1 -1 MAP3K9 HGNC HGNC:6861 protein_coding YES CCDS32112.1 ENSP00000451263 P80192 UPI00001D7B5C NM_033141.3 tolerated(1) 12/13 PIRSF_domain:PIRSF000556 MODERATE 1 SNV 1 1 PASS rs755568141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 70733132 70733132 T C 1 0 0 0 0 1 0 0 0 9181 1696 59 5 5 MAP3K9 14 70733132 Missense_Mutation SNP T C3N-01016_T 8657844 70733132 36310586 261 20410 CHGA 0 . GRCh38 14 92924211 92924211 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.59C>A p.Pro20His p.P20H ENST00000216492 2/8 222 183 39 251 251 0 strelka-varscan-mutect CHGA,missense_variant,p.Pro20His,ENST00000216492,NM_001275.3;CHGA,missense_variant,p.Pro20His,ENST00000334654,NM_001301690.1;CHGA,intron_variant,,ENST00000553866,;CHGA,missense_variant,p.Pro20His,ENST00000556076,;CHGA,upstream_gene_variant,,ENST00000556098,; A ENST00000216492 Transcript missense_variant 339/2063 59/1374 20/457 P/H cCt/cAt 1 1 CHGA HGNC HGNC:1929 protein_coding YES CCDS9906.1 ENSP00000216492 P10645 UPI000013C6F3 NM_001275.3 deleterious(0) 2/8 hmmpanther:PTHR10583 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 92924211 92924211 C A 1 0 0 0 0 1 0 0 0 3097 681 24 2 2 CHGA 14 92924211 Missense_Mutation SNP C C3N-01016_T 22191079 92924211 14119507 262 20411 SERPINA12 0 . GRCh38 14 94497787 94497787 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.611T>C p.Leu204Pro p.L204P ENST00000341228 3/6 98 62 36 78 78 0 strelka-varscan-mutect SERPINA12,missense_variant,p.Leu204Pro,ENST00000341228,NM_173850.3;SERPINA12,missense_variant,p.Leu204Pro,ENST00000556881,NM_001304461.1; G ENST00000341228 Transcript missense_variant 1407/2061 611/1245 204/414 L/P cTt/cCt 1 -1 SERPINA12 HGNC HGNC:18359 protein_coding YES CCDS9926.1 ENSP00000342109 Q8IW75 UPI000000D86C NM_173850.3 deleterious(0) 3/6 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF157,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 94497787 94497787 A G 1 0 0 0 0 1 0 0 0 14365 72 3 5 5 SERPINA12 14 94497787 Missense_Mutation SNP A C3N-01016_T 1573576 94497787 12545931 263 20412 KIF26A 0 . GRCh38 14 104152097 104152097 + Missense_Mutation SNP G G C rs369169884 C3N-01016_T C3N-01016_N G G c.371G>C p.Arg124Pro p.R124P ENST00000423312 3/15 605 407 198 616 614 2 strelka-varscan-mutect KIF26A,missense_variant,p.Arg124Pro,ENST00000423312,NM_015656.1;KIF26A,5_prime_UTR_variant,,ENST00000315264,; C ENST00000423312 Transcript missense_variant 371/5649 371/5649 124/1882 R/P cGc/cCc rs369169884 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 deleterious(0) 3/15 MODERATE 1 SNV 5 1 PASS rs369169884 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 104152097 104152097 G C 1 0 0 0 0 1 0 0 0 8159 1087 38 4 4 KIF26A 14 104152097 Missense_Mutation SNP G C3N-01016_T 9654310 104152097 2891621 264 20413 AHNAK2 0 . GRCh38 14 104952337 104952337 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.3114G>T p.Gln1038His p.Q1038H ENST00000333244 7/7 433 375 58 394 394 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Gln1038His,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,downstream_gene_variant,,ENST00000555544,; A ENST00000333244 Transcript missense_variant 3234/18254 3114/17388 1038/5795 Q/H caG/caT 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.16) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 104952337 104952337 C A 1 0 0 0 0 1 0 0 0 492 680 24 2 2 AHNAK2 14 104952337 Missense_Mutation SNP C C3N-01016_T 800240 104952337 2091381 265 20414 MAGEL2 0 . GRCh38 15 23647144 23647144 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.599C>A p.Ala200Asp p.A200D ENST00000532292 1/1 95 72 23 54 54 0 strelka-varscan-mutect MAGEL2,missense_variant,p.Ala200Asp,ENST00000532292,NM_019066.4; T ENST00000532292 Transcript missense_variant 698/4298 599/3750 200/1249 A/D gCt/gAt 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 23647144 23647144 G T 1 0 0 0 0 1 0 0 0 9107 971 34 2 2 MAGEL2 15 23647144 Missense_Mutation SNP G C3N-01016_T 23647144 78344045 266 20415 GOLGA8Q 0 . GRCh38 15 30561909 30561909 + Nonsense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.1487T>A p.Leu496Ter p.L496* ENST00000562783 17/19 33 25 8 19 19 0 varscan-mutect GOLGA8Q,stop_gained,p.Leu496Ter,ENST00000562783,;RN7SL796P,downstream_gene_variant,,ENST00000613991,;GOLGA8Q,downstream_gene_variant,,ENST00000565941,; A ENST00000562783 Transcript stop_gained 1487/1899 1487/1899 496/632 L/* tTa/tAa 1 1 GOLGA8Q HGNC HGNC:44408 protein_coding YES ENSP00000457904 H3BV12 UPI0000DD8290 17/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 HIGH 1 SNV 5 1 PASS . . 34 173 3 0 0 0 0 0 -19.96929 1 1 1 1 0 A 4 1 66 30561909 30561909 T A 1 0 0 0 0 0 1 0 0 6456 1764 61 4 4 GOLGA8Q 15 30561909 Nonsense_Mutation SNP T C3N-01016_T 6914765 30561909 71429280 267 20416 RYR3 0 . GRCh38 15 33539377 33539377 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.461C>G p.Pro154Arg p.P154R ENST00000634891 6/104 195 125 70 197 197 0 strelka-varscan-mutect RYR3,missense_variant,p.Pro154Arg,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Pro154Arg,ENST00000622037,;RYR3,missense_variant,p.Pro154Arg,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Pro154Arg,ENST00000389232,;RYR3,missense_variant,p.Pro154Arg,ENST00000634418,;RYR3,downstream_gene_variant,,ENST00000635875,; G ENST00000634891 Transcript missense_variant 562/15591 461/14613 154/4870 P/R cCt/cGt 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 6/104 Gene3D:2.80.10.50,Pfam_domain:PF08709,PROSITE_profiles:PS50919,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,SMART_domains:SM00472,Superfamily_domains:SSF82109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 33539377 33539377 C G 1 0 0 0 0 1 0 0 0 14030 681 24 4 4 RYR3 15 33539377 Missense_Mutation SNP C C3N-01016_T 2977468 33539377 68451812 268 20417 BAHD1 0 . GRCh38 15 40463931 40463931 + Missense_Mutation SNP G G A C3N-01016_T C3N-01016_N G G c.1886G>A p.Arg629Gln p.R629Q ENST00000416165 4/7 248 220 28 286 286 0 strelka-varscan-mutect BAHD1,missense_variant,p.Arg628Gln,ENST00000561234,NM_001301132.1;BAHD1,missense_variant,p.Arg629Gln,ENST00000416165,NM_014952.4;BAHD1,missense_variant,p.Arg629Gln,ENST00000560846,;RP11-64K12.8,downstream_gene_variant,,ENST00000559730,;BAHD1,upstream_gene_variant,,ENST00000561464,; A ENST00000416165 Transcript missense_variant 1957/4526 1886/2343 629/780 R/Q cGg/cAg COSM309421 1 1 BAHD1 HGNC HGNC:29153 protein_coding YES CCDS10058.1 ENSP00000396976 Q8TBE0 A0A024R9K2 UPI000013D778 NM_014952.4 deleterious(0.01) 4/7 PROSITE_profiles:PS51038,hmmpanther:PTHR12505,Pfam_domain:PF01426,SMART_domains:SM00439 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 2 0 0 0 -11.17805 0.9947243 1 1 1 0 A 3 1 66 40463931 40463931 G A 1 0 0 0 0 1 0 0 0 1452 1116 39 1 1 BAHD1 15 40463931 Missense_Mutation SNP G C3N-01016_T 6924554 40463931 61527258 269 20418 ISLR 0 . GRCh38 15 74176058 74176058 + Silent SNP C C A rs576140565 C3N-01016_T C3N-01016_N C C c.1200C>A p.= p.V400V ENST00000249842 2/2 75 51 24 83 83 0 strelka-varscan-mutect ISLR,synonymous_variant,p.=,ENST00000249842,NM_005545.3;ISLR,synonymous_variant,p.=,ENST00000395118,NM_201526.1;STRA6,downstream_gene_variant,,ENST00000323940,NM_001142617.1;STRA6,downstream_gene_variant,,ENST00000616000,NM_001142618.1;STRA6,downstream_gene_variant,,ENST00000395105,NM_022369.3;STRA6,downstream_gene_variant,,ENST00000423167,NM_001142619.1;STRA6,downstream_gene_variant,,ENST00000416286,;STRA6,downstream_gene_variant,,ENST00000449139,;STRA6,downstream_gene_variant,,ENST00000535552,NM_001199040.1;STRA6,downstream_gene_variant,,ENST00000563965,NM_001199042.1;STRA6,downstream_gene_variant,,ENST00000574278,NM_001199041.1;STRA6,downstream_gene_variant,,ENST00000572785,;ISLR,downstream_gene_variant,,ENST00000560862,;ISLR,downstream_gene_variant,,ENST00000559510,;RP11-665J16.1,intron_variant,,ENST00000561647,;STRA6,downstream_gene_variant,,ENST00000574439,;STRA6,downstream_gene_variant,,ENST00000545137,; A ENST00000249842 Transcript synonymous_variant 1557/2371 1200/1287 400/428 V gtC/gtA rs576140565 1 1 ISLR HGNC HGNC:6133 protein_coding YES CCDS10260.1 ENSP00000249842 O14498 A0A146E5L3 UPI0000049E09 NM_005545.3 2/2 hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF14 LOW 1 SNV 1 1 PASS rs576140565 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 74176058 74176058 C A 1 0 0 0 0 0 0 0 1 7765 871 31 1 1 ISLR 15 74176058 Silent SNP C C3N-01016_T 33712127 74176058 27815131 270 20419 MEX3B 0 . GRCh38 15 82045573 82045573 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.133G>T p.Gly45Trp p.G45W ENST00000329713 1/2 338 283 55 290 290 0 strelka-varscan-mutect MEX3B,missense_variant,p.Gly45Trp,ENST00000558133,;MEX3B,missense_variant,p.Gly45Trp,ENST00000329713,NM_032246.4; A ENST00000329713 Transcript missense_variant 569/3528 133/1710 45/569 G/W Ggg/Tgg 1 -1 MEX3B HGNC HGNC:25297 protein_coding YES CCDS10319.1 ENSP00000329918 Q6ZN04 UPI00001982CC NM_032246.4 deleterious(0) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23285,hmmpanther:PTHR23285:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 82045573 82045573 C A 1 0 0 0 0 1 0 0 0 9463 623 22 2 2 MEX3B 15 82045573 Missense_Mutation SNP C C3N-01016_T 7869515 82045573 19945616 271 20420 NTRK3 0 . GRCh38 15 88183474 88183474 + Silent SNP T T A novel C3N-01016_T C3N-01016_N T T c.339A>T p.= p.S113S ENST00000360948 5/20 404 342 62 434 434 0 strelka-varscan-mutect NTRK3,synonymous_variant,p.=,ENST00000394480,NM_002530.3;NTRK3,synonymous_variant,p.=,ENST00000558676,;NTRK3,synonymous_variant,p.=,ENST00000317501,;NTRK3,synonymous_variant,p.=,ENST00000360948,NM_001012338.2;NTRK3,synonymous_variant,p.=,ENST00000357724,;NTRK3,synonymous_variant,p.=,ENST00000355254,NM_001243101.1;NTRK3,synonymous_variant,p.=,ENST00000626019,;NTRK3,synonymous_variant,p.=,ENST00000629765,;NTRK3,synonymous_variant,p.=,ENST00000557856,;NTRK3,synonymous_variant,p.=,ENST00000542733,NM_001320135.1;NTRK3,synonymous_variant,p.=,ENST00000540489,NM_001007156.2;NTRK3,synonymous_variant,p.=,ENST00000559188,; A ENST00000360948 Transcript synonymous_variant 645/3004 339/2520 113/839 S tcA/tcT 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 5/20 Gene3D:3.80.10.10,Pfam_domain:PF13855,Prints_domain:PR01939,Superfamily_domains:SSF52058 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 88183474 88183474 T A 1 0 0 0 0 0 0 0 1 10774 1567 55 4 4 NTRK3 15 88183474 Silent SNP T C3N-01016_T 6137901 88183474 13807715 272 20421 ACAN 0 . GRCh38 15 88843585 88843585 + Missense_Mutation SNP G G A rs766293702 C3N-01016_T C3N-01016_N G G c.988G>A p.Val330Met p.V330M ENST00000439576 6/18 88 71 17 89 89 0 strelka-varscan-mutect ACAN,missense_variant,p.Val330Met,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Val330Met,ENST00000617301,;ACAN,missense_variant,p.Val330Met,ENST00000559004,;ACAN,missense_variant,p.Val330Met,ENST00000561243,;ACAN,missense_variant,p.Val330Met,ENST00000352105,NM_001135.3;ACAN,missense_variant,p.Val330Met,ENST00000558207,; A ENST00000439576 Transcript missense_variant 1362/8840 988/7593 330/2530 V/M Gtg/Atg rs766293702,COSM4426762,COSM4426763 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0.03) 6/18 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs766293702 . 0 201 9 0 0 0 0 0 -20 0.9999962 1 1 1 0 A 3 1 66 88843585 88843585 G A 1 0 0 0 0 1 0 0 0 160 1145 40 1 1 ACAN 15 88843585 Missense_Mutation SNP G C3N-01016_T 660111 88843585 13147604 273 20422 CIITA 0 . GRCh38 16 10907215 10907215 + Nonsense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.1726C>T p.Gln576Ter p.Q576* ENST00000618327 11/20 778 729 49 601 601 0 strelka-varscan-mutect CIITA,stop_gained,p.Gln575Ter,ENST00000324288,NM_000246.3;CIITA,stop_gained,p.Gln576Ter,ENST00000618327,NM_001286402.1;CIITA,intron_variant,,ENST00000618207,;CIITA,intron_variant,,ENST00000381835,NM_001286403.1;CIITA,intron_variant,,ENST00000537380,;CIITA,non_coding_transcript_exon_variant,,ENST00000570546,;CIITA,non_coding_transcript_exon_variant,,ENST00000573309,;CIITA,downstream_gene_variant,,ENST00000571186,; T ENST00000618327 Transcript stop_gained 1859/4657 1726/3396 576/1131 Q/* Cag/Tag 1 1 CIITA HGNC HGNC:7067 protein_coding YES CCDS73826.1 ENSP00000485010 A0A087X2I7 UPI0003C0C509 NM_001286402.1 11/20 Pfam_domain:PF05729,PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF104,Superfamily_domains:SSF52540 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 10907215 10907215 C T 1 0 0 0 0 0 1 0 0 3190 595 21 3 3 CIITA 16 10907215 Nonsense_Mutation SNP C C3N-01016_T 10907215 79431130 274 20423 MYH11 0 . GRCh38 16 15837919 15837919 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.334G>T p.Gly112Trp p.G112W ENST00000396324 2/42 222 147 75 261 260 1 strelka-varscan-mutect MYH11,missense_variant,p.Gly112Trp,ENST00000452625,NM_001040113.1;MYH11,missense_variant,p.Gly112Trp,ENST00000396324,NM_001040114.1;MYH11,missense_variant,p.Gly112Trp,ENST00000576790,NM_022844.2;MYH11,missense_variant,p.Gly112Trp,ENST00000300036,NM_002474.2;MYH11,non_coding_transcript_exon_variant,,ENST00000571505,; A ENST00000396324 Transcript missense_variant 422/6847 334/5940 112/1979 G/W Ggg/Tgg 1 -1 MYH11 HGNC HGNC:7569 protein_coding YES CCDS45423.1 ENSP00000379616 P35749 UPI00005B7237 NM_001040114.1 deleterious(0) 2/42 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF335,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 15837919 15837919 C A 1 0 0 0 0 1 0 0 0 10031 681 24 2 2 MYH11 16 15837919 Missense_Mutation SNP C C3N-01016_T 4930704 15837919 74500426 275 20424 GPR139 0 . GRCh38 16 20032000 20032000 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.797T>A p.Met266Lys p.M266K ENST00000570682 2/2 258 244 14 287 287 0 strelka-varscan-mutect GPR139,missense_variant,p.Met266Lys,ENST00000570682,NM_001002911.2;GPR139,3_prime_UTR_variant,,ENST00000326571,; T ENST00000570682 Transcript missense_variant 1098/1613 797/1062 266/353 M/K aTg/aAg 1 -1 GPR139 HGNC HGNC:19995 protein_coding YES CCDS32398.1 ENSP00000458791 Q6DWJ6 A0A142CHG1 UPI000004C566 NM_001002911.2 deleterious(0) 2/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF49,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs1159032666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 20032000 20032000 A T 1 0 0 0 0 1 0 0 0 6534 217 8 4 4 GPR139 16 20032000 Missense_Mutation SNP A C3N-01016_T 4194081 20032000 70306345 276 20425 PDILT 0 . GRCh38 16 20376163 20376163 + Silent SNP G G T rs139247719 C3N-01016_T C3N-01016_N G G c.448C>A p.= p.R150R ENST00000302451 4/12 168 102 66 199 199 0 strelka-varscan-mutect PDILT,synonymous_variant,p.=,ENST00000302451,NM_174924.1; T ENST00000302451 Transcript synonymous_variant 697/2153 448/1755 150/584 R Cga/Aga rs139247719,COSM1478596 1 -1 PDILT HGNC HGNC:27338 protein_coding YES CCDS10584.1 ENSP00000305465 Q8N807 UPI000000DAC6 NM_174924.1 4/12 hmmpanther:PTHR18929:SF58,hmmpanther:PTHR18929,Pfam_domain:PF00085,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 0,1 LOW 1 SNV 1 0,1 1 PASS rs139247719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 20376163 20376163 G T 1 0 0 0 0 0 0 0 1 11762 1153 40 1 1 PDILT 16 20376163 Silent SNP G C3N-01016_T 344163 20376163 69962182 277 20426 ARHGAP17 0 . GRCh38 16 24964308 24964308 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.462G>T p.Arg154Ser p.R154S ENST00000289968 7/20 102 90 12 84 84 0 strelka-mutect ARHGAP17,missense_variant,p.Arg154Ser,ENST00000289968,NM_001006634.2;ARHGAP17,missense_variant,p.Arg154Ser,ENST00000303665,NM_018054.5;ARHGAP17,missense_variant,p.Arg153Ser,ENST00000455311,;ARHGAP17,downstream_gene_variant,,ENST00000573449,;ARHGAP17,splice_region_variant,,ENST00000575975,;ARHGAP17,splice_region_variant,,ENST00000571480,;ARHGAP17,splice_region_variant,,ENST00000573625,;ARHGAP17,splice_region_variant,,ENST00000571575,;ARHGAP17,upstream_gene_variant,,ENST00000575656,;ARHGAP17,downstream_gene_variant,,ENST00000575447,; A ENST00000289968 Transcript missense_variant,splice_region_variant 532/3461 462/2646 154/881 R/S agG/agT 1 -1 ARHGAP17 HGNC HGNC:18239 protein_coding YES CCDS32409.1 ENSP00000289968 Q68EM7 UPI00000433FD NM_001006634.2 deleterious(0.01) 7/20 Gene3D:1.20.1270.60,Pfam_domain:PF03114,PROSITE_profiles:PS51021,hmmpanther:PTHR14130,hmmpanther:PTHR14130:SF3,SMART_domains:SM00721,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 24964308 24964308 C A 1 0 0 0 0 1 0 0 0 991 521 18 2 2 ARHGAP17 16 24964308 Missense_Mutation SNP C C3N-01016_T 4588145 24964308 65374037 278 20427 TBX6 0 . GRCh38 16 30086384 30086384 + Silent SNP A A T rs373496540 C3N-01016_T C3N-01016_N A A c.1152T>A p.= p.A384A ENST00000395224 9/9 89 70 19 57 57 0 strelka-mutect TBX6,synonymous_variant,p.=,ENST00000395224,NM_004608.3;TBX6,synonymous_variant,p.=,ENST00000279386,;TBX6,synonymous_variant,p.=,ENST00000627355,;TBX6,downstream_gene_variant,,ENST00000553607,;PPP4C,downstream_gene_variant,,ENST00000279387,NM_001303503.1,NM_002720.2,NM_001303507.1,NM_001303506.1;PPP4C,downstream_gene_variant,,ENST00000561610,;PPP4C,downstream_gene_variant,,ENST00000627746,;PPP4C,downstream_gene_variant,,ENST00000562664,NM_001303504.1;PPP4C,downstream_gene_variant,,ENST00000562222,;TBX6,3_prime_UTR_variant,,ENST00000567664,;PPP4C,downstream_gene_variant,,ENST00000566749,;PPP4C,downstream_gene_variant,,ENST00000563200,;PPP4C,downstream_gene_variant,,ENST00000564966,;PPP4C,downstream_gene_variant,,ENST00000568810,;PPP4C,downstream_gene_variant,,ENST00000567040,;PPP4C,downstream_gene_variant,,ENST00000563732,;PPP4C,downstream_gene_variant,,ENST00000563597,;PPP4C,downstream_gene_variant,,ENST00000567828,;PPP4C,downstream_gene_variant,,ENST00000567642,; T ENST00000395224 Transcript synonymous_variant 1212/1803 1152/1311 384/436 A gcT/gcA rs373496540 1 -1 TBX6 HGNC HGNC:11605 protein_coding YES CCDS10670.1 ENSP00000378650 O95947 UPI000013DBC7 NM_004608.3 9/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF100 LOW 1 SNV 1 1 PASS rs373496540 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 66 30086384 30086384 A T 1 0 0 0 0 0 0 0 1 16066 175 7 4 4 TBX6 16 30086384 Silent SNP A C3N-01016_T 5122076 30086384 60251961 279 20428 ITGAL 0 . GRCh38 16 30481509 30481509 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.647A>G p.Asp216Gly p.D216G ENST00000356798 7/31 323 200 123 307 307 0 strelka-varscan-mutect ITGAL,missense_variant,p.Asp216Gly,ENST00000356798,NM_002209.2;ITGAL,missense_variant,p.Asp133Gly,ENST00000358164,NM_001114380.1;ITGAL,missense_variant,p.Asp133Gly,ENST00000564118,;ITGAL,intron_variant,,ENST00000433423,;ITGAL,downstream_gene_variant,,ENST00000569725,;RNU7-61P,downstream_gene_variant,,ENST00000515897,;RP11-297C4.2,intron_variant,,ENST00000569459,;RP11-297C4.3,upstream_gene_variant,,ENST00000562525,;ITGAL,intron_variant,,ENST00000565348,;ITGAL,3_prime_UTR_variant,,ENST00000562857,;ITGAL,intron_variant,,ENST00000568926,;ITGAL,downstream_gene_variant,,ENST00000565864,;ITGAL,upstream_gene_variant,,ENST00000566149,; G ENST00000356798 Transcript missense_variant 827/5213 647/3513 216/1170 D/G gAc/gGc 1 1 ITGAL HGNC HGNC:6148 protein_coding YES CCDS32433.1 ENSP00000349252 P20701 UPI000013C4FF NM_002209.2 deleterious(0.02) 7/31 Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 30481509 30481509 A G 1 0 0 0 0 1 0 0 0 7793 275 10 5 5 ITGAL 16 30481509 Missense_Mutation SNP A C3N-01016_T 395125 30481509 59856836 280 20429 TRIM72 0 . GRCh38 16 31224562 31224562 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1241G>T p.Gly414Val p.G414V ENST00000322122 7/7 85 46 39 65 65 0 strelka-varscan-mutect TRIM72,missense_variant,p.Gly414Val,ENST00000322122,NM_001008274.3;TRIM72,intron_variant,,ENST00000613872,; T ENST00000322122 Transcript missense_variant 1525/8500 1241/1434 414/477 G/V gGc/gTc 1 1 TRIM72 HGNC HGNC:32671 protein_coding YES CCDS32437.1 ENSP00000312675 Q6ZMU5 UPI00001FFF74 NM_001008274.3 deleterious(0) 7/7 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF11,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 2 1 PASS rs1393209259 . 0 199 11 0 0 0 0 0 -20 0.9999955 1 1 1 0 T 3 4 66 31224562 31224562 G T 1 0 0 0 0 1 0 0 0 17041 1203 42 2 2 TRIM72 16 31224562 Missense_Mutation SNP G C3N-01016_T 743053 31224562 59113783 281 20430 ITGAM 0 . GRCh38 16 31275698 31275698 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1008G>T p.Glu336Asp p.E336D ENST00000544665 9/30 154 94 60 97 97 0 strelka-varscan-mutect ITGAM,missense_variant,p.Glu336Asp,ENST00000544665,NM_001145808.1;ITGAM,missense_variant,p.Glu336Asp,ENST00000287497,NM_000632.3;ITGAM,missense_variant,p.Glu36Asp,ENST00000567031,;ITGAM,downstream_gene_variant,,ENST00000570242,; T ENST00000544665 Transcript missense_variant,splice_region_variant 1079/4718 1008/3462 336/1153 E/D gaG/gaT 1 1 ITGAM HGNC HGNC:6149 protein_coding YES CCDS54004.1 ENSP00000441691 P11215 UPI000004B26A NM_001145808.1 deleterious(0) 9/30 Gene3D:3nigC00,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF76,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS rs1399415217 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 31275698 31275698 G T 1 0 0 0 0 1 0 0 0 7794 1014 35 2 2 ITGAM 16 31275698 Missense_Mutation SNP G C3N-01016_T 51136 31275698 59062647 282 20431 MYLK3 0 . GRCh38 16 46712667 46712667 + Nonsense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2095G>T p.Gly699Ter p.G699* ENST00000394809 10/13 53 34 19 46 46 0 strelka-varscan-mutect MYLK3,stop_gained,p.Gly699Ter,ENST00000394809,NM_182493.2;MYLK3,stop_gained,p.Gly358Ter,ENST00000536476,NM_001308301.1;MYLK3,upstream_gene_variant,,ENST00000562104,;MYLK3,upstream_gene_variant,,ENST00000565182,; A ENST00000394809 Transcript stop_gained 2211/6911 2095/2460 699/819 G/* Gga/Tga 1 -1 MYLK3 HGNC HGNC:29826 protein_coding YES CCDS10723.2 ENSP00000378288 Q32MK0 UPI000059D380 NM_182493.2 10/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24347:SF45,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS rs1263790395 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 46712667 46712667 C A 1 0 0 0 0 0 1 0 0 10058 632 22 2 2 MYLK3 16 46712667 Nonsense_Mutation SNP C C3N-01016_T 15436969 46712667 43625678 283 20432 CHST6 0 . GRCh38 16 75479150 75479150 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.679G>T p.Gly227Cys p.G227C ENST00000332272 3/3 377 317 60 315 315 0 strelka-varscan-mutect CHST6,missense_variant,p.Gly227Cys,ENST00000332272,NM_021615.4;CHST6,missense_variant,p.Gly227Cys,ENST00000390664,;RP11-77K12.4,intron_variant,,ENST00000530512,; A ENST00000332272 Transcript missense_variant 859/7957 679/1188 227/395 G/C Ggc/Tgc COSM1679276 1 -1 CHST6 HGNC HGNC:6938 protein_coding YES CCDS10918.1 ENSP00000328983 Q9GZX3 UPI00000467C8 NM_021615.4 deleterious(0.01) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF13,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 3 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 75479150 75479150 C A 1 0 0 0 0 1 0 0 0 3168 623 22 2 2 CHST6 16 75479150 Missense_Mutation SNP C C3N-01016_T 28766483 75479150 14859195 284 20433 CNTNAP4 0 . GRCh38 16 76355436 76355436 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.315G>C p.Trp105Cys p.W105C ENST00000611870 3/24 167 114 53 193 193 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Trp105Cys,ENST00000307431,;CNTNAP4,missense_variant,p.Trp105Cys,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Trp105Cys,ENST00000377504,;CNTNAP4,missense_variant,p.Trp108Cys,ENST00000476707,;CNTNAP4,missense_variant,p.Trp105Cys,ENST00000622250,;CNTNAP4,missense_variant,p.Trp80Cys,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000463177,;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; C ENST00000611870 Transcript missense_variant 700/4867 315/3927 105/1308 W/C tgG/tgC 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0) 3/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00231,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 76355436 76355436 G C 1 0 0 0 0 1 0 0 0 3431 1241 43 4 4 CNTNAP4 16 76355436 Missense_Mutation SNP G C3N-01016_T 876286 76355436 13982909 285 20434 ADAMTS18 0 . GRCh38 16 77319872 77319872 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.2509A>T p.Thr837Ser p.T837S ENST00000282849 16/23 392 260 132 363 363 0 strelka-varscan-mutect ADAMTS18,missense_variant,p.Thr837Ser,ENST00000282849,NM_001326358.1,NM_199355.2;ADAMTS18,non_coding_transcript_exon_variant,,ENST00000568393,; A ENST00000282849 Transcript missense_variant 2928/5913 2509/3666 837/1221 T/S Aca/Tca 1 -1 ADAMTS18 HGNC HGNC:17110 protein_coding YES CCDS10926.1 ENSP00000282849 Q8TE60 UPI0000233610 NM_001326358.1,NM_199355.2 deleterious(0) 16/23 hmmpanther:PTHR13723:SF167,hmmpanther:PTHR13723,Pfam_domain:PF05986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 77319872 77319872 T A 1 0 0 0 0 1 0 0 0 307 1696 59 4 4 ADAMTS18 16 77319872 Missense_Mutation SNP T C3N-01016_T 964436 77319872 13018473 286 20435 ZNF469 0 . GRCh38 16 88434432 88434432 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.6878G>T p.Arg2293Met p.R2293M ENST00000437464 2/2 261 186 75 207 207 0 strelka-varscan-mutect ZNF469,missense_variant,p.Arg2321Met,ENST00000565624,;ZNF469,missense_variant,p.Arg2293Met,ENST00000437464,NM_001127464.2; T ENST00000437464 Transcript missense_variant 6878/13203 6878/11778 2293/3925 R/M aGg/aTg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.05) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 88434432 88434432 G T 1 0 0 0 0 1 0 0 0 18500 1000 35 2 2 ZNF469 16 88434432 Missense_Mutation SNP G C3N-01016_T 11114560 88434432 1903913 287 20436 GALNS 0 . GRCh38 16 88842826 88842826 + Nonsense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.124G>T p.Gly42Ter p.G42* ENST00000268695 2/14 128 114 14 109 109 0 strelka-varscan-mutect GALNS,stop_gained,p.Gly42Ter,ENST00000268695,NM_000512.4;GALNS,intron_variant,,ENST00000562831,;GALNS,non_coding_transcript_exon_variant,,ENST00000565364,;GALNS,upstream_gene_variant,,ENST00000562931,;GALNS,upstream_gene_variant,,ENST00000561812,;GALNS,3_prime_UTR_variant,,ENST00000568613,;GALNS,non_coding_transcript_exon_variant,,ENST00000562593,;GALNS,intron_variant,,ENST00000567525,;GALNS,upstream_gene_variant,,ENST00000567779,;GALNS,upstream_gene_variant,,ENST00000566563,; A ENST00000268695 Transcript stop_gained 213/2363 124/1569 42/522 G/* Gga/Tga 1 -1 GALNS HGNC HGNC:4122 protein_coding YES CCDS10970.1 ENSP00000268695 P34059 UPI000012AF92 NM_000512.4 2/14 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF198,Low_complexity_(Seg):seg,Superfamily_domains:SSF53649 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 88842826 88842826 C A 1 0 0 0 0 0 1 0 0 6074 637 22 2 2 GALNS 16 88842826 Nonsense_Mutation SNP C C3N-01016_T 408394 88842826 1495519 288 20437 NLRP1 0 . GRCh38 17 5559089 5559089 + Missense_Mutation SNP C C T rs138756363 C3N-01016_T C3N-01016_N C C c.1607G>A p.Arg536Gln p.R536Q ENST00000617618 5/18 238 178 60 275 275 0 strelka-varscan-mutect NLRP1,missense_variant,p.Arg536Gln,ENST00000262467,NM_001033053.2;NLRP1,missense_variant,p.Arg536Gln,ENST00000269280,NM_014922.4;NLRP1,missense_variant,p.Arg536Gln,ENST00000617618,NM_033004.3;NLRP1,missense_variant,p.Arg536Gln,ENST00000619223,NM_033006.3;NLRP1,missense_variant,p.Arg536Gln,ENST00000345221,;NLRP1,missense_variant,p.Arg536Gln,ENST00000613500,;NLRP1,missense_variant,p.Arg536Gln,ENST00000572272,;NLRP1,missense_variant,p.Arg536Gln,ENST00000354411,;NLRP1,missense_variant,p.Arg536Gln,ENST00000577119,NM_033007.3;NLRP1,non_coding_transcript_exon_variant,,ENST00000571307,;NLRP1,missense_variant,p.Arg536Gln,ENST00000571451,;NLRP1,missense_variant,p.Arg536Gln,ENST00000544378,; T ENST00000617618 Transcript missense_variant 1973/4788 1607/4422 536/1473 R/Q cGg/cAg rs138756363,COSM1610510,COSM1610511,COSM1610512 1 -1 NLRP1 HGNC HGNC:14374 protein_coding YES CCDS42246.1 ENSP00000478516 Q9C000 UPI0000038309 NM_033004.3 tolerated(1) 5/18 Low_complexity_(Seg):seg,PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF13,hmmpanther:PTHR24106 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs138756363 . 0 208 0 0 2 0 0 0 -20 0.998793 1 1 1 0 T 3 4 66 5559089 5559089 C T 1 0 0 0 0 1 0 0 0 10508 652 23 1 1 NLRP1 17 5559089 Missense_Mutation SNP C C3N-01016_T 5559089 77698352 289 20438 SLC13A5 0 . GRCh38 17 6687583 6687583 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.1521C>T p.= p.A507A ENST00000433363 11/12 155 116 39 180 180 0 strelka-varscan-mutect SLC13A5,synonymous_variant,p.=,ENST00000433363,NM_177550.4;SLC13A5,synonymous_variant,p.=,ENST00000293800,NM_001284509.1;SLC13A5,synonymous_variant,p.=,ENST00000381074,NM_001284510.1;SLC13A5,synonymous_variant,p.=,ENST00000570687,;SLC13A5,intron_variant,,ENST00000573648,NM_001143838.2;C17orf100,intron_variant,,ENST00000635042,;C17orf100,downstream_gene_variant,,ENST00000634977,;CTC-281F24.3,intron_variant,,ENST00000634558,;CTC-281F24.3,intron_variant,,ENST00000634823,;SLC13A5,downstream_gene_variant,,ENST00000572727,;SLC13A5,non_coding_transcript_exon_variant,,ENST00000574580,; A ENST00000433363 Transcript synonymous_variant 1755/3435 1521/1707 507/568 A gcC/gcT 1 -1 SLC13A5 HGNC HGNC:23089 protein_coding YES CCDS11079.1 ENSP00000406220 Q86YT5 UPI000000D834 NM_177550.4 11/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF82,hmmpanther:PTHR10283,PROSITE_patterns:PS01271,Pfam_domain:PF00939 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 6687583 6687583 G A 1 0 0 0 0 0 0 0 1 14660 1335 47 3 3 SLC13A5 17 6687583 Silent SNP G C3N-01016_T 1128494 6687583 76569858 290 20439 MYH13 0 . GRCh38 17 10309364 10309364 + Missense_Mutation SNP C C A rs747286137 C3N-01016_T C3N-01016_N C C c.5039G>T p.Arg1680Leu p.R1680L ENST00000418404 34/41 190 155 35 208 208 0 strelka-varscan-mutect MYH13,missense_variant,p.Arg1680Leu,ENST00000418404,;MYH13,missense_variant,p.Arg1680Leu,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Arg1680Leu,ENST00000621918,;RP11-401O9.4,intron_variant,,ENST00000609088,; A ENST00000418404 Transcript missense_variant 5203/6296 5039/5817 1680/1938 R/L cGc/cTc rs747286137,COSM1216153,COSM1216154 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0) 34/41 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,Superfamily_domains:SSF90257 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs747286137 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 10309364 10309364 C A 1 0 0 0 0 1 0 0 0 10032 768 27 1 1 MYH13 17 10309364 Missense_Mutation SNP C C3N-01016_T 3621781 10309364 72948077 291 20440 MYH3 0 . GRCh38 17 10635796 10635796 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.3914G>T p.Ser1305Ile p.S1305I ENST00000583535 29/41 462 358 104 528 528 0 strelka-varscan-mutect MYH3,missense_variant,p.Ser1305Ile,ENST00000583535,NM_002470.3; A ENST00000583535 Transcript missense_variant 4002/6037 3914/5823 1305/1940 S/I aGc/aTc 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 tolerated(0.12) 29/41 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE 1 SNV 5 1 PASS rs1272813611 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 10635796 10635796 C A 1 0 0 0 0 1 0 0 0 10036 797 28 2 2 MYH3 17 10635796 Missense_Mutation SNP C C3N-01016_T 326432 10635796 72621645 292 20441 DNAH9 0 . GRCh38 17 11891945 11891945 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.11281C>A p.Gln3761Lys p.Q3761K ENST00000262442 58/69 104 83 21 126 126 0 strelka-varscan-mutect DNAH9,missense_variant,p.Gln3761Lys,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Gln3761Lys,ENST00000454412,;DNAH9,missense_variant,p.Gln73Lys,ENST00000608377,NM_004662.2;DNAH9,splice_region_variant,,ENST00000396001,;DNAH9,splice_region_variant,,ENST00000581682,; A ENST00000262442 Transcript missense_variant,splice_region_variant 11349/13750 11281/13461 3761/4486 Q/K Cag/Aag 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0.01) 58/69 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 11891945 11891945 C A 1 0 0 0 0 1 0 0 0 4423 840 29 2 2 DNAH9 17 11891945 Missense_Mutation SNP C C3N-01016_T 1256149 11891945 71365496 293 20442 TRPV2 0 . GRCh38 17 16431851 16431851 + Splice_Site SNP G G T rs780683461 C3N-01016_T C3N-01016_N G G c.1654+1G>T p.X552_splice ENST00000338560 169 134 35 203 203 0 strelka-varscan-mutect TRPV2,splice_donor_variant,,ENST00000338560,NM_016113.4;TRPV2,intron_variant,,ENST00000577277,;TRPV2,upstream_gene_variant,,ENST00000581560,;TRPV2,upstream_gene_variant,,ENST00000580788,;TRPV2,upstream_gene_variant,,ENST00000577865,;TRPV2,intron_variant,,ENST00000583241,;TRPV2,upstream_gene_variant,,ENST00000475513,;TRPV2,upstream_gene_variant,,ENST00000493434,;AC093484.4,downstream_gene_variant,,ENST00000441875,; T ENST00000338560 Transcript splice_donor_variant -/2808 1654/2295 552/764 rs780683461 1 1 TRPV2 HGNC HGNC:18082 protein_coding YES CCDS32576.1 ENSP00000342222 Q9Y5S1 UPI0000032F4E NM_016113.4 11/14 HIGH 1 SNV 1 1 PASS rs780683461 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 66 16431851 16431851 G T 1 0 0 0 0 0 0 1 0 17102 1275 44 2 2 TRPV2 17 16431851 Splice_Site SNP G C3N-01016_T 4539906 16431851 66825590 294 20443 PEMT 0 . GRCh38 17 17512563 17512563 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.412G>T p.Val138Phe p.V138F ENST00000255389 4/7 68 49 19 76 76 0 strelka-varscan-mutect PEMT,missense_variant,p.Val138Phe,ENST00000395781,NM_001267552.1;PEMT,missense_variant,p.Val138Phe,ENST00000255389,NM_148172.2,NM_001267551.1;PEMT,missense_variant,p.Val101Phe,ENST00000395783,NM_007169.2;PEMT,missense_variant,p.Val116Phe,ENST00000435340,;PEMT,missense_variant,p.Val101Phe,ENST00000395782,NM_148173.1;RP11-524F11.1,downstream_gene_variant,,ENST00000582325,;PEMT,non_coding_transcript_exon_variant,,ENST00000484838,;PEMT,non_coding_transcript_exon_variant,,ENST00000490392,;PEMT,non_coding_transcript_exon_variant,,ENST00000421096,;PEMT,non_coding_transcript_exon_variant,,ENST00000472446,;PEMT,3_prime_UTR_variant,,ENST00000461404,;PEMT,intron_variant,,ENST00000580147,; A ENST00000255389 Transcript missense_variant 486/1013 412/711 138/236 V/F Gtc/Ttc 1 -1 PEMT HGNC HGNC:8830 protein_coding YES CCDS11186.1 ENSP00000255389 Q9UBM1 UPI000013FE53 NM_148172.2,NM_001267551.1 tolerated(0.31) 4/7 Pfam_domain:PF04191,PIRSF_domain:PIRSF005444,PROSITE_profiles:PS51599,hmmpanther:PTHR15458,hmmpanther:PTHR15458:SF5,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1336774178 . 0 200 8 2 0 0 0 0 -20 0.9999167 1 1 1 0 A 3 1 66 17512563 17512563 C A 1 0 0 0 0 1 0 0 0 11814 536 19 1 1 PEMT 17 17512563 Missense_Mutation SNP C C3N-01016_T 1080712 17512563 65744878 295 20444 OMG 0 . GRCh38 17 31295443 31295443 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.889C>G p.Gln297Glu p.Q297E ENST00000247271 2/2 566 468 98 496 496 0 strelka-varscan-mutect OMG,missense_variant,p.Gln297Glu,ENST00000247271,NM_002544.4;NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;OMG,intron_variant,,ENST00000580156,;OMG,non_coding_transcript_exon_variant,,ENST00000582029,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,; C ENST00000247271 Transcript missense_variant 1151/1947 889/1323 297/440 Q/E Caa/Gaa 1 -1 OMG HGNC HGNC:8135 protein_coding YES CCDS11265.1 ENSP00000247271 P23515 UPI0000130CE1 NM_002544.4 tolerated(1) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 31295443 31295443 G C 1 0 0 0 0 1 0 0 0 10941 1299 45 4 4 OMG 17 31295443 Missense_Mutation SNP G C3N-01016_T 13782880 31295443 51961998 296 20445 SLFN14 0 . GRCh38 17 35557512 35557512 + Missense_Mutation SNP C C A rs780550066 C3N-01016_T C3N-01016_N C C c.551G>T p.Arg184Met p.R184M ENST00000415846 1/4 245 209 36 156 156 0 strelka-varscan-mutect SLFN14,missense_variant,p.Arg184Met,ENST00000415846,NM_001129820.1;RP11-1094M14.14,downstream_gene_variant,,ENST00000591634,;RP11-1094M14.12,downstream_gene_variant,,ENST00000588445,; A ENST00000415846 Transcript missense_variant 587/2889 551/2739 184/912 R/M aGg/aTg rs780550066 1 -1 SLFN14 HGNC HGNC:32689 protein_coding YES CCDS45650.1 ENSP00000391101 P0C7P3 UPI000041A9FB NM_001129820.1 deleterious(0.02) 1/4 hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF30 MODERATE 1 SNV 1 1 PASS rs780550066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 35557512 35557512 C A 1 0 0 0 0 1 0 0 0 15026 681 24 2 2 SLFN14 17 35557512 Missense_Mutation SNP C C3N-01016_T 4262069 35557512 47699929 297 20446 TADA2A 0 . GRCh38 17 37426962 37426962 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.145G>C p.Gly49Arg p.G49R ENST00000615182 4/16 196 137 59 102 101 1 strelka-varscan-mutect TADA2A,missense_variant,p.Gly49Arg,ENST00000615182,NM_001166105.2;TADA2A,missense_variant,p.Gly49Arg,ENST00000612272,NM_001488.4;TADA2A,missense_variant,p.Gly49Arg,ENST00000620367,NM_001291918.1,NM_133439.3;TADA2A,missense_variant,p.Gly49Arg,ENST00000614112,;TADA2A,5_prime_UTR_variant,,ENST00000621780,;TADA2A,intron_variant,,ENST00000615328,;TADA2A,downstream_gene_variant,,ENST00000618662,;TADA2A,missense_variant,p.Gly49Arg,ENST00000620628,;TADA2A,missense_variant,p.Gly49Arg,ENST00000614122,;TADA2A,non_coding_transcript_exon_variant,,ENST00000610834,;TADA2A,intron_variant,,ENST00000620838,; C ENST00000615182 Transcript missense_variant 318/4253 145/1332 49/443 G/R Ggc/Cgc 1 1 TADA2A HGNC HGNC:11531 protein_coding YES CCDS11319.1 ENSP00000481091 A0A024R0Y4 UPI00001254E3 NM_001166105.2 deleterious(0) 4/16 PIRSF_domain:PIRSF025024,hmmpanther:PTHR12374,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 37426962 37426962 G C 1 0 0 0 0 1 0 0 0 15906 1000 35 4 4 TADA2A 17 37426962 Missense_Mutation SNP G C3N-01016_T 1869450 37426962 45830479 298 20447 ARHGAP23 0 . GRCh38 17 38510151 38510151 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.3655G>T p.Gly1219Cys p.G1219C ENST00000622683 24/24 20 11 9 27 27 0 strelka-varscan-mutect ARHGAP23,missense_variant,p.Gly1219Cys,ENST00000622683,NM_001199417.1;ARHGAP23,downstream_gene_variant,,ENST00000620417,;ARHGAP23,downstream_gene_variant,,ENST00000620329,;ARHGAP23,downstream_gene_variant,,ENST00000618325,; T ENST00000622683 Transcript missense_variant 3723/5964 3655/4476 1219/1491 G/C Ggc/Tgc 1 1 ARHGAP23 HGNC HGNC:29293 protein_coding YES CCDS56027.1 ENSP00000481862 Q9P227 UPI0000F3BE51 NM_001199417.1 deleterious(0.02) 24/24 hmmpanther:PTHR23175:SF5,hmmpanther:PTHR23175 MODERATE 1 SNV 5 1 PASS . . 3 204 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 38510151 38510151 G T 1 0 0 0 0 1 0 0 0 997 1348 47 2 2 ARHGAP23 17 38510151 Missense_Mutation SNP G C3N-01016_T 1083189 38510151 44747290 299 20448 KRTAP9-2 0 . GRCh38 17 41226674 41226674 + Missense_Mutation SNP C C A rs760736540 C3N-01016_T C3N-01016_N C C c.20C>A p.Pro7His p.P7H ENST00000377721 1/1 145 108 37 127 127 0 strelka-varscan-mutect KRTAP9-2,missense_variant,p.Pro7His,ENST00000377721,NM_031961.2; A ENST00000377721 Transcript missense_variant 27/1005 20/525 7/174 P/H cCt/cAt rs760736540 1 1 KRTAP9-2 HGNC HGNC:16926 protein_coding YES CCDS32651.1 ENSP00000366950 Q9BYQ4 UPI000013CE13 NM_031961.2 deleterious(0) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF56,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs760736540 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 41226674 41226674 C A 1 0 0 0 0 1 0 0 0 8470 681 24 2 2 KRTAP9-2 17 41226674 Missense_Mutation SNP C C3N-01016_T 2716523 41226674 42030767 300 20449 PTRF 0 . GRCh38 17 42404796 42404796 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1064G>T p.Arg355Leu p.R355L ENST00000357037 2/2 161 112 49 132 132 0 strelka-varscan-mutect PTRF,missense_variant,p.Arg355Leu,ENST00000357037,NM_012232.5; A ENST00000357037 Transcript missense_variant 1484/3828 1064/1173 355/390 R/L cGc/cTc 1 -1 PTRF HGNC HGNC:9688 protein_coding YES CCDS11425.1 ENSP00000349541 Q6NZI2 UPI00001AF3C2 NM_012232.5 tolerated(0.32) 2/2 hmmpanther:PTHR15240,hmmpanther:PTHR15240:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 42404796 42404796 C A 1 0 0 0 0 1 0 0 0 12970 768 27 1 1 PTRF 17 42404796 Missense_Mutation SNP C C3N-01016_T 1178122 42404796 40852645 301 20450 MEOX1 0 . GRCh38 17 43661416 43661416 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.119C>A p.Pro40His p.P40H ENST00000318579 1/3 169 130 39 179 179 0 strelka-varscan-mutect MEOX1,missense_variant,p.Pro40His,ENST00000318579,NM_004527.3;MEOX1,missense_variant,p.Pro40His,ENST00000329168,NM_013999.3;MEOX1,missense_variant,p.Pro11Thr,ENST00000549132,;MEOX1,intron_variant,,ENST00000393661,NM_001040002.1; T ENST00000318579 Transcript missense_variant 539/2707 119/765 40/254 P/H cCc/cAc 1 -1 MEOX1 HGNC HGNC:7013 protein_coding YES CCDS11466.1 ENSP00000321684 P50221 UPI000012F410 NM_004527.3 tolerated(0.13) 1/3 hmmpanther:PTHR24328:SF8,hmmpanther:PTHR24328 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 43661416 43661416 G T 1 0 0 0 0 1 0 0 0 9418 1232 43 2 2 MEOX1 17 43661416 Missense_Mutation SNP G C3N-01016_T 1256620 43661416 39596025 302 20451 PLEKHM1 0 . GRCh38 17 45475246 45475246 + Silent SNP T T A rs766416067 C3N-01016_T C3N-01016_N T T c.777A>T p.= p.S259S ENST00000430334 4/12 516 413 103 489 489 0 strelka-varscan-mutect PLEKHM1,synonymous_variant,p.=,ENST00000430334,NM_014798.2;PLEKHM1,synonymous_variant,p.=,ENST00000584420,;PLEKHM1,downstream_gene_variant,,ENST00000589780,;PLEKHM1,downstream_gene_variant,,ENST00000636800,;PLEKHM1,intron_variant,,ENST00000582119,;PLEKHM1,downstream_gene_variant,,ENST00000586562,;PLEKHM1,synonymous_variant,p.=,ENST00000581448,;PLEKHM1,3_prime_UTR_variant,,ENST00000579197,;PLEKHM1,3_prime_UTR_variant,,ENST00000446609,;PLEKHM1,downstream_gene_variant,,ENST00000581932,;PLEKHM1,downstream_gene_variant,,ENST00000586084,; A ENST00000430334 Transcript synonymous_variant 911/5263 777/3171 259/1056 S tcA/tcT rs766416067 1 -1 PLEKHM1 HGNC HGNC:29017 protein_coding YES CCDS32671.1 ENSP00000389913 Q9Y4G2 UPI00001C1FC4 NM_014798.2 4/12 Low_complexity_(Seg):seg,hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF5 LOW 1 SNV 1 1 PASS rs766416067 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 45475246 45475246 T A 1 0 0 0 0 0 0 0 1 12173 1451 51 4 4 PLEKHM1 17 45475246 Silent SNP T C3N-01016_T 1813830 45475246 37782195 303 20452 MRPL10 0 . GRCh38 17 47824279 47824279 + Missense_Mutation SNP T T C novel C3N-01016_T C3N-01016_N T T c.742A>G p.Arg248Gly p.R248G ENST00000290208 5/5 206 169 37 228 227 1 strelka-varscan-mutect MRPL10,missense_variant,p.Arg248Gly,ENST00000290208,;MRPL10,missense_variant,p.Arg238Gly,ENST00000351111,NM_145255.3;MRPL10,missense_variant,p.Arg248Gly,ENST00000414011,NM_148887.2;OSBPL7,upstream_gene_variant,,ENST00000007414,NM_145798.2;OSBPL7,upstream_gene_variant,,ENST00000392507,;OSBPL7,upstream_gene_variant,,ENST00000613735,;MRPL10,3_prime_UTR_variant,,ENST00000421763,;OSBPL7,upstream_gene_variant,,ENST00000579728,;OSBPL7,upstream_gene_variant,,ENST00000580140,;OSBPL7,upstream_gene_variant,,ENST00000580226,;OSBPL7,upstream_gene_variant,,ENST00000585051,;MRPL10,downstream_gene_variant,,ENST00000423147,;MRPL10,downstream_gene_variant,,ENST00000480901,;MRPL10,downstream_gene_variant,,ENST00000466016,; C ENST00000290208 Transcript missense_variant 1195/2013 742/816 248/271 R/G Aga/Gga 1 -1 MRPL10 HGNC HGNC:14055 protein_coding YES CCDS11517.1 ENSP00000290208 Q7Z7H8 UPI000013DFCA deleterious(0) 5/5 hmmpanther:PTHR11560:SF8,hmmpanther:PTHR11560,Superfamily_domains:0053665 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 47824279 47824279 T C 1 0 0 0 0 1 0 0 0 9750 1588 55 5 5 MRPL10 17 47824279 Missense_Mutation SNP T C3N-01016_T 2349033 47824279 35433162 304 20453 PPP1R9B 0 . GRCh38 17 50150101 50150101 + Missense_Mutation SNP G G A rs539885092 C3N-01016_T C3N-01016_N G G c.413C>T p.Pro138Leu p.P138L ENST00000612501 1/10 81 53 28 54 54 0 strelka-varscan-mutect PPP1R9B,missense_variant,p.Pro138Leu,ENST00000612501,NM_032595.4;AC002401.1,downstream_gene_variant,,ENST00000451776,;PPP1R9B,upstream_gene_variant,,ENST00000513579,; A ENST00000612501 Transcript missense_variant 530/4167 413/2454 138/817 P/L cCg/cTg rs539885092 1 -1 PPP1R9B HGNC HGNC:9298 protein_coding YES CCDS74102.1 ENSP00000478767 D3DTX6 UPI00005AE42D NM_032595.4 tolerated(0.31) 1/10 hmmpanther:PTHR16154,hmmpanther:PTHR16154:SF24,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs539885092 . 0 201 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 66 50150101 50150101 G A 1 0 0 0 0 1 0 0 0 12502 1116 39 1 1 PPP1R9B 17 50150101 Missense_Mutation SNP G C3N-01016_T 2325822 50150101 33107340 305 20454 DGKE 0 . GRCh38 17 56856518 56856518 + Missense_Mutation SNP A A G novel C3N-01016_T C3N-01016_N A A c.1105A>G p.Thr369Ala p.T369A ENST00000284061 8/12 97 67 30 77 77 0 strelka-varscan-mutect DGKE,missense_variant,p.Thr369Ala,ENST00000284061,NM_003647.2;DGKE,missense_variant,p.Thr313Ala,ENST00000572944,; G ENST00000284061 Transcript missense_variant 1285/8660 1105/1704 369/567 T/A Aca/Gca 1 1 DGKE HGNC HGNC:2852 protein_coding YES CCDS11590.1 ENSP00000284061 P52429 A1L4Q0 UPI000012DD1F NM_003647.2 tolerated(0.49) 8/12 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF45,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 56856518 56856518 A G 1 0 0 0 0 1 0 0 0 4274 159 6 5 5 DGKE 17 56856518 Missense_Mutation SNP A C3N-01016_T 6706417 56856518 26400923 306 20455 ACE 0 . GRCh38 17 63488655 63488655 + Silent SNP G G A rs747443207 C3N-01016_T C3N-01016_N G G c.2313G>A p.= p.T771T ENST00000290866 16/25 303 218 85 271 270 1 strelka-mutect ACE,synonymous_variant,p.=,ENST00000428043,;ACE,synonymous_variant,p.=,ENST00000290866,NM_000789.3;ACE,synonymous_variant,p.=,ENST00000290863,NM_152830.2;ACE,synonymous_variant,p.=,ENST00000413513,NM_001178057.1;ACE,synonymous_variant,p.=,ENST00000582761,;ACE,upstream_gene_variant,,ENST00000577418,;CTD-2501B8.1,synonymous_variant,p.=,ENST00000577647,;ACE,3_prime_UTR_variant,,ENST00000579314,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,3_prime_UTR_variant,,ENST00000582005,;ACE,3_prime_UTR_variant,,ENST00000579204,;ACE,non_coding_transcript_exon_variant,,ENST00000584865,;ACE,downstream_gene_variant,,ENST00000582678,;ACE,upstream_gene_variant,,ENST00000583645,;ACE,downstream_gene_variant,,ENST00000579726,; A ENST00000290866 Transcript synonymous_variant 2337/4959 2313/3921 771/1306 T acG/acA rs747443207,COSM5526153,COSM5526154,COSM5526155,COSM5526156 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 16/25 hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS rs747443207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 63488655 63488655 G A 1 0 0 0 0 0 0 0 1 174 1045 37 1 1 ACE 17 63488655 Silent SNP G C3N-01016_T 6632137 63488655 19768786 307 20456 SCN4A 0 . GRCh38 17 63963804 63963804 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.1474G>A p.Glu492Lys p.E492K ENST00000435607 10/24 86 76 10 100 100 0 strelka-varscan-mutect SCN4A,missense_variant,p.Glu492Lys,ENST00000435607,NM_000334.4;SCN4A,missense_variant,p.Glu492Lys,ENST00000578147,;SCN4A,upstream_gene_variant,,ENST00000581514,; T ENST00000435607 Transcript missense_variant 1551/7805 1474/5511 492/1836 E/K Gaa/Aaa 1 -1 SCN4A HGNC HGNC:10591 protein_coding YES CCDS45761.1 ENSP00000396320 P35499 UPI0000201254 NM_000334.4 tolerated(0.39) 10/24 Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF223,Prints_domain:PR01665 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 63963804 63963804 C T 1 0 0 0 0 1 0 0 0 14189 864 30 3 3 SCN4A 17 63963804 Missense_Mutation SNP C C3N-01016_T 475149 63963804 19293637 308 20457 PSMD12 0 . GRCh38 17 67357398 67357398 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.202G>T p.Val68Phe p.V68F ENST00000356126 3/11 185 146 39 169 169 0 strelka-varscan-mutect PSMD12,missense_variant,p.Val68Phe,ENST00000356126,NM_002816.3;PSMD12,missense_variant,p.Val48Phe,ENST00000357146,NM_174871.2;PSMD12,non_coding_transcript_exon_variant,,ENST00000581618,;PSMD12,3_prime_UTR_variant,,ENST00000584008,;PSMD12,3_prime_UTR_variant,,ENST00000579365,;PSMD12,non_coding_transcript_exon_variant,,ENST00000584289,;PSMD12,non_coding_transcript_exon_variant,,ENST00000578015,; A ENST00000356126 Transcript missense_variant 310/4406 202/1371 68/456 V/F Gtt/Ttt 1 -1 PSMD12 HGNC HGNC:9557 protein_coding YES CCDS11669.1 ENSP00000348442 O00232 A0A0S2Z489 UPI0000132792 NM_002816.3 deleterious(0) 3/11 hmmpanther:PTHR10855,hmmpanther:PTHR10855:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 67357398 67357398 C A 1 0 0 0 0 1 0 0 0 12846 565 20 2 2 PSMD12 17 67357398 Missense_Mutation SNP C C3N-01016_T 3393594 67357398 15900043 309 20458 ABCA6 0 . GRCh38 17 69136128 69136128 + Nonsense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.424G>T p.Gly142Ter p.G142* ENST00000284425 4/39 142 111 31 59 59 0 strelka-varscan-mutect ABCA6,stop_gained,p.Gly142Ter,ENST00000284425,NM_080284.2;ABCA6,stop_gained,p.Gly142Ter,ENST00000590645,; A ENST00000284425 Transcript stop_gained 599/5300 424/4854 142/1617 G/* Gga/Tga 1 -1 ABCA6 HGNC HGNC:36 protein_coding YES CCDS11683.1 ENSP00000284425 Q8N139 UPI000013DD9D NM_080284.2 4/39 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF13 HIGH 1 SNV 1 1 PASS rs1485620410 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 66 69136128 69136128 C A 1 0 0 0 0 0 1 0 0 40 632 22 2 2 ABCA6 17 69136128 Nonsense_Mutation SNP C C3N-01016_T 1778730 69136128 14121313 310 20459 SDK2 0 . GRCh38 17 73395261 73395261 + Silent SNP G G T rs779642580 C3N-01016_T C3N-01016_N G G c.3486C>A p.= p.I1162I ENST00000392650 25/45 345 273 72 350 350 0 strelka-varscan-mutect SDK2,synonymous_variant,p.=,ENST00000392650,NM_001144952.1;SDK2,synonymous_variant,p.=,ENST00000424778,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; T ENST00000392650 Transcript synonymous_variant 3487/10723 3486/6519 1162/2172 I atC/atA rs779642580,COSM1303285,COSM4810920 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 25/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs779642580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 73395261 73395261 G T 1 0 0 0 0 0 0 0 1 14244 1048 37 1 1 SDK2 17 73395261 Silent SNP G C3N-01016_T 4259133 73395261 9862180 311 20460 CARD14 0 . GRCh38 17 80189841 80189841 + Missense_Mutation SNP G G T rs771413361 C3N-01016_T C3N-01016_N G G c.932G>T p.Arg311Leu p.R311L ENST00000573882 8/23 99 83 16 136 136 0 strelka-varscan-mutect CARD14,missense_variant,p.Arg311Leu,ENST00000573882,;CARD14,missense_variant,p.Arg311Leu,ENST00000344227,NM_024110.4;CARD14,missense_variant,p.Arg311Leu,ENST00000570421,NM_001257970.1;CARD14,non_coding_transcript_exon_variant,,ENST00000573754,;CARD14,upstream_gene_variant,,ENST00000574148,;CARD14,missense_variant,p.Arg311Leu,ENST00000575500,;CARD14,missense_variant,p.Arg108Leu,ENST00000571450,;CARD14,non_coding_transcript_exon_variant,,ENST00000571861,;CARD14,upstream_gene_variant,,ENST00000575666,;CARD14,downstream_gene_variant,,ENST00000572838,; T ENST00000573882 Transcript missense_variant 1468/4537 932/3015 311/1004 R/L cGg/cTg rs771413361 1 1 CARD14 HGNC HGNC:16446 protein_coding YES CCDS11768.1 ENSP00000458715 Q9BXL6 UPI000013D81B deleterious(0.01) 8/23 Low_complexity_(Seg):seg,hmmpanther:PTHR14559:SF1,hmmpanther:PTHR14559,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS rs771413361 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 80189841 80189841 G T 1 0 0 0 0 1 0 0 0 2341 1116 39 1 1 CARD14 17 80189841 Missense_Mutation SNP G C3N-01016_T 6794580 80189841 3067600 312 20461 MYOM1 0 . GRCh38 18 3100171 3100171 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.3715C>A p.His1239Asn p.H1239N ENST00000356443 25/38 205 172 33 179 179 0 strelka-varscan-mutect MYOM1,missense_variant,p.His1239Asn,ENST00000356443,NM_003803.3;MYOM1,missense_variant,p.His1143Asn,ENST00000261606,NM_019856.1;MYOM1,missense_variant,p.His1006Asn,ENST00000400569,; T ENST00000356443 Transcript missense_variant 4049/5847 3715/5058 1239/1685 H/N Cac/Aac 1 -1 MYOM1 HGNC HGNC:7613 protein_coding YES CCDS45824.1 ENSP00000348821 P52179 UPI000022A657 NM_003803.3 tolerated(0.22) 25/38 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 3100171 3100171 G T 1 0 0 0 0 1 0 0 0 10092 1377 48 2 2 MYOM1 18 3100171 Missense_Mutation SNP G C3N-01016_T 3100171 77273114 313 20462 LOXHD1 0 . GRCh38 18 46485144 46485144 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2724G>T p.Glu908Asp p.E908D ENST00000300591 21/24 72 46 26 98 98 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Glu1957Asp,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Glu1813Asp,ENST00000441551,;LOXHD1,missense_variant,p.Glu908Asp,ENST00000300591,NM_001145472.2;LOXHD1,missense_variant,p.Glu846Asp,ENST00000582408,;LOXHD1,missense_variant,p.Glu812Asp,ENST00000579038,NM_001308013.1;LOXHD1,missense_variant,p.Glu258Asp,ENST00000398686,NM_001145473.2;LOXHD1,missense_variant,p.Glu258Asp,ENST00000398705,NM_001173129.1; A ENST00000300591 Transcript missense_variant 3138/3970 2724/3345 908/1114 E/D gaG/gaT 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding YES CCDS45861.1 ENSP00000300591 Q8IVV2 UPI0000456B8D NM_001145472.2 tolerated(0.06) 21/24 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,Superfamily_domains:SSF49723 MODERATE 1 SNV 1 1 PASS rs1192453516 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 66 46485144 46485144 C A 1 0 0 0 0 1 0 0 0 8801 912 32 2 2 LOXHD1 18 46485144 Missense_Mutation SNP C C3N-01016_T 43384973 46485144 33888141 314 20463 PHLPP1 0 . GRCh38 18 62903052 62903052 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.2533G>T p.Asp845Tyr p.D845Y ENST00000262719 7/17 267 218 49 304 304 0 strelka-varscan-mutect PHLPP1,missense_variant,p.Asp845Tyr,ENST00000262719,NM_194449.3;PHLPP1,upstream_gene_variant,,ENST00000591386,;PHLPP1,upstream_gene_variant,,ENST00000591106,; T ENST00000262719 Transcript missense_variant 2767/6390 2533/5154 845/1717 D/Y Gat/Tat 1 1 PHLPP1 HGNC HGNC:20610 protein_coding YES CCDS45881.2 ENSP00000262719 O60346 UPI000051AE2E NM_194449.3 deleterious(0) 7/17 Gene3D:3.80.10.10,Pfam_domain:PF13516,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF252,SMART_domains:SM00369,Superfamily_domains:SSF52058,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs1351664436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 62903052 62903052 G T 1 0 0 0 0 1 0 0 0 11942 1290 45 2 2 PHLPP1 18 62903052 Missense_Mutation SNP G C3N-01016_T 16417908 62903052 17470233 315 20464 HCN2 0 . GRCh38 19 616352 616352 + Missense_Mutation SNP C C T novel C3N-01016_T C3N-01016_N C C c.2548C>T p.Pro850Ser p.P850S ENST00000251287 8/8 63 38 25 56 56 0 strelka-varscan-mutect HCN2,missense_variant,p.Pro850Ser,ENST00000251287,NM_001194.3;POLRMT,downstream_gene_variant,,ENST00000588649,NM_005035.3;POLRMT,downstream_gene_variant,,ENST00000590336,;POLRMT,downstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000589961,;POLRMT,downstream_gene_variant,,ENST00000592633,; T ENST00000251287 Transcript missense_variant 2601/3408 2548/2670 850/889 P/S Ccc/Tcc 1 1 HCN2 HGNC HGNC:4846 protein_coding YES CCDS12035.1 ENSP00000251287 Q9UL51 UPI000013CCF6 NM_001194.3 tolerated_low_confidence(0.06) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF372 MODERATE 1 SNV 1 1 PASS rs1294418727 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 616352 616352 C T 1 0 0 0 0 1 0 0 0 6884 739 26 3 3 HCN2 19 616352 Missense_Mutation SNP C C3N-01016_T 616352 58001264 316 20465 STK11 0 . GRCh38 19 1220494 1220494 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.586G>C p.Gly196Arg p.G196R ENST00000326873 4/10 78 38 40 82 82 0 strelka-varscan-mutect STK11,missense_variant,p.Gly196Arg,ENST00000586243,;STK11,missense_variant,p.Gly196Arg,ENST00000326873,NM_000455.4;STK11,missense_variant,p.Gly138Arg,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; C ENST00000326873 Transcript missense_variant 1036/2611 586/1302 196/433 G/R Ggc/Cgc 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 4/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 C 3 2 66 1220494 1220494 G C 1 0 0 0 0 1 0 0 0 15664 1232 43 4 4 STK11 19 1220494 Missense_Mutation SNP G C3N-01016_T 604142 1220494 57397122 317 20466 NMRK2 0 . GRCh38 19 3937248 3937248 + Missense_Mutation SNP C C A rs756000055 C3N-01016_T C3N-01016_N C C c.141C>A p.Asp47Glu p.D47E ENST00000616156 4/8 226 140 86 236 235 1 strelka-varscan-mutect NMRK2,missense_variant,p.Asp47Glu,ENST00000616156,NM_001289117.1;NMRK2,missense_variant,p.Asp42Glu,ENST00000168977,NM_170678.2;NMRK2,missense_variant,p.Asp47Glu,ENST00000593949,;NMRK2,missense_variant,p.Asp33Glu,ENST00000599576,;NMRK2,missense_variant,p.Asp18Glu,ENST00000597889,; A ENST00000616156 Transcript missense_variant 431/1139 141/708 47/235 D/E gaC/gaA rs756000055 1 1 NMRK2 HGNC HGNC:17871 protein_coding YES CCDS74259.1 ENSP00000480091 Q9NPI5 UPI000189A7D7 NM_001289117.1 deleterious(0.02) 4/8 Gene3D:3.40.50.300,Pfam_domain:PF13238,hmmpanther:PTHR23404,hmmpanther:PTHR23404:SF7,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs756000055 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 3937248 3937248 C A 1 0 0 0 0 1 0 0 0 10542 506 18 2 2 NMRK2 19 3937248 Missense_Mutation SNP C C3N-01016_T 2716754 3937248 54680368 318 20467 DPP9 0 . GRCh38 19 4694762 4694762 + Missense_Mutation SNP C C A rs182103254 C3N-01016_T C3N-01016_N C C c.1415G>T p.Arg472Leu p.R472L ENST00000262960 13/22 186 117 69 305 305 0 strelka-varscan-mutect DPP9,missense_variant,p.Arg472Leu,ENST00000262960,NM_139159.4;DPP9,missense_variant,p.Arg443Leu,ENST00000594671,;DPP9,missense_variant,p.Arg443Leu,ENST00000598800,;DPP9,missense_variant,p.Arg472Leu,ENST00000597849,;DPP9,upstream_gene_variant,,ENST00000595327,;DPP9,3_prime_UTR_variant,,ENST00000599163,;DPP9,non_coding_transcript_exon_variant,,ENST00000597145,;DPP9,non_coding_transcript_exon_variant,,ENST00000601764,;DPP9,non_coding_transcript_exon_variant,,ENST00000599998,;DPP9,upstream_gene_variant,,ENST00000597253,; A ENST00000262960 Transcript missense_variant 1693/4295 1415/2679 472/892 R/L cGc/cTc rs182103254 1 -1 DPP9 HGNC HGNC:18648 protein_coding YES CCDS45928.1 ENSP00000262960 Q86TI2 UPI000004DB00 NM_139159.4 tolerated(0.08) 13/22 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF109,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS rs182103254 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 4694762 4694762 C A 1 0 0 0 0 1 0 0 0 4548 768 27 1 1 DPP9 19 4694762 Missense_Mutation SNP C C3N-01016_T 757514 4694762 53922854 319 20468 ADGRE3 0 . GRCh38 19 14668763 14668763 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.115A>T p.Arg39Trp p.R39W ENST00000595472 2/2 118 71 47 120 120 0 strelka-varscan-mutect ADGRE3,missense_variant,p.Arg39Trp,ENST00000595472,;ADGRE3,intron_variant,,ENST00000344373,NM_001289158.1;ADGRE3,intron_variant,,ENST00000253673,NM_032571.4;ADGRE3,intron_variant,,ENST00000599900,;ADGRE3,intron_variant,,ENST00000443157,NM_001289159.1; A ENST00000595472 Transcript missense_variant 343/486 115/174 39/57 R/W Agg/Tgg 1 -1 ADGRE3 HGNC HGNC:23647 protein_coding ENSP00000469965 M0QYN7 UPI0002A474AE deleterious_low_confidence(0.03) 2/2 MODERATE SNV 3 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 14668763 14668763 T A 1 0 0 0 0 1 0 0 0 361 1608 56 4 4 ADGRE3 19 14668763 Missense_Mutation SNP T C3N-01016_T 9974001 14668763 43948853 320 20469 ZNF66 0 . GRCh38 19 20806138 20806138 + Nonsense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.538A>T p.Lys180Ter p.K180* ENST00000344519 4/4 73 62 11 60 60 0 strelka-mutect ZNF66,stop_gained,p.Lys180Ter,ENST00000344519,; T ENST00000344519 Transcript stop_gained 561/1745 538/1722 180/573 K/* Aaa/Taa 1 1 ZNF66 HGNC HGNC:13135 protein_coding YES ENSP00000461425 Q6ZN08 UPI00025A2C0A 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 66 20806138 20806138 A T 1 0 0 0 0 0 1 0 0 18643 131 5 4 4 ZNF66 19 20806138 Nonsense_Mutation SNP A C3N-01016_T 6137375 20806138 37811478 321 20470 ZNF729 0 . GRCh38 19 22315953 22315953 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.2536C>A p.His846Asn p.H846N ENST00000601693 4/4 402 280 122 212 212 0 strelka-varscan-mutect ZNF729,missense_variant,p.His846Asn,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript missense_variant 2654/3877 2536/3759 846/1252 H/N Cat/Aat 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 22315953 22315953 C A 1 0 0 0 0 1 0 0 0 18703 826 29 2 2 ZNF729 19 22315953 Missense_Mutation SNP C C3N-01016_T 1509815 22315953 36301663 322 20471 ZNF98 0 . GRCh38 19 22402864 22402864 + Missense_Mutation SNP C C A C3N-01016_T C3N-01016_N C C c.178G>T p.Asp60Tyr p.D60Y ENST00000357774 3/4 69 51 18 80 80 0 strelka-mutect ZNF98,missense_variant,p.Asp60Tyr,ENST00000357774,NM_001098626.1;ZNF98,missense_variant,p.Asp19Tyr,ENST00000593657,;ZNF98,missense_variant,p.Asp60Tyr,ENST00000601553,;ZNF98,downstream_gene_variant,,ENST00000593802,; A ENST00000357774 Transcript missense_variant 300/2338 178/1719 60/572 D/Y Gac/Tac COSM1271946,COSM1271947 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 deleterious(0.03) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,SMART_domains:SM00349,Superfamily_domains:0044637 1,1 MODERATE 1 SNV 3 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 22402864 22402864 C A 1 0 0 0 0 1 0 0 0 18796 913 32 2 2 ZNF98 19 22402864 Missense_Mutation SNP C C3N-01016_T 86911 22402864 36214752 323 20472 ZNF492 0 . GRCh38 19 22665086 22665086 + Missense_Mutation SNP G G A C3N-01016_T C3N-01016_N G G c.1417G>A p.Gly473Arg p.G473R ENST00000456783 4/4 142 89 53 102 102 0 strelka-varscan-mutect ZNF492,missense_variant,p.Gly473Arg,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; A ENST00000456783 Transcript missense_variant 1661/4245 1417/1596 473/531 G/R Gga/Aga COSM223983 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.05) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS rs745700525 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 22665086 22665086 G A 1 0 0 0 0 1 0 0 0 18516 1349 47 3 3 ZNF492 19 22665086 Missense_Mutation SNP G C3N-01016_T 262222 22665086 35952530 324 20473 TSHZ3 0 . GRCh38 19 31278146 31278146 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.1647C>G p.Ser549Arg p.S549R ENST00000240587 2/2 196 118 78 192 192 0 strelka-varscan-mutect TSHZ3,missense_variant,p.Ser549Arg,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; C ENST00000240587 Transcript missense_variant 1975/5176 1647/3246 549/1081 S/R agC/agG 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 31278146 31278146 G C 1 0 0 0 0 1 0 0 0 17130 1310 46 4 4 TSHZ3 19 31278146 Missense_Mutation SNP G C3N-01016_T 8613060 31278146 27339470 325 20474 UPK1A 0 . GRCh38 19 35668534 35668534 + Silent SNP A A T novel C3N-01016_T C3N-01016_N A A c.165A>T p.= p.S55S ENST00000616789 3/9 408 246 162 400 400 0 strelka-varscan-mutect UPK1A,synonymous_variant,p.=,ENST00000616789,NM_001281443.1;UPK1A,synonymous_variant,p.=,ENST00000617999,NM_007000.3;UPK1A,synonymous_variant,p.=,ENST00000222275,;UPK1A,synonymous_variant,p.=,ENST00000379013,;UPK1A-AS1,non_coding_transcript_exon_variant,,ENST00000443196,; T ENST00000616789 Transcript synonymous_variant 192/1366 165/822 55/273 S tcA/tcT 1 1 UPK1A HGNC HGNC:12577 protein_coding YES CCDS62640.1 ENSP00000478942 O00322 UPI00005C40C1 NM_001281443.1 3/9 Pfam_domain:PF00335,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF25 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 35668534 35668534 A T 1 0 0 0 0 0 0 0 1 17533 175 7 4 4 UPK1A 19 35668534 Silent SNP A C3N-01016_T 4390388 35668534 22949082 326 20475 ZFP82 0 . GRCh38 19 36393157 36393157 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.1183G>C p.Glu395Gln p.E395Q ENST00000392161 5/5 180 157 23 116 116 0 strelka-varscan-mutect ZFP82,missense_variant,p.Glu395Gln,ENST00000392161,NM_133466.2;ZFP82,intron_variant,,ENST00000445543,;ZFP82,non_coding_transcript_exon_variant,,ENST00000590993,; G ENST00000392161 Transcript missense_variant 1426/2623 1183/1599 395/532 E/Q Gaa/Caa 1 -1 ZFP82 HGNC HGNC:28682 protein_coding YES CCDS12493.1 ENSP00000431265 Q8N141 D3Y299 UPI0000071159 NM_133466.2 deleterious(0.04) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF252,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1292048626 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 36393157 36393157 C G 1 0 0 0 0 1 0 0 0 18230 893 31 4 4 ZFP82 19 36393157 Missense_Mutation SNP C C3N-01016_T 724623 36393157 22224459 327 20476 RASGRP4 0 . GRCh38 19 38420184 38420184 + Silent SNP G G A C3N-01016_T C3N-01016_N G G c.456C>T p.= p.T152T ENST00000615439 5/17 123 71 52 153 153 0 strelka-varscan-mutect RASGRP4,synonymous_variant,p.=,ENST00000618320,;RASGRP4,synonymous_variant,p.=,ENST00000615439,NM_170604.2;RASGRP4,synonymous_variant,p.=,ENST00000454404,NM_001146205.1;RASGRP4,synonymous_variant,p.=,ENST00000586305,NM_001146202.1;RASGRP4,synonymous_variant,p.=,ENST00000587753,NM_001146204.1;RASGRP4,synonymous_variant,p.=,ENST00000614135,;RASGRP4,synonymous_variant,p.=,ENST00000433821,NM_001146203.1;RASGRP4,synonymous_variant,p.=,ENST00000617966,;RASGRP4,synonymous_variant,p.=,ENST00000293062,NM_001146207.1;RASGRP4,synonymous_variant,p.=,ENST00000622174,;RASGRP4,synonymous_variant,p.=,ENST00000426920,NM_001146206.1;RASGRP4,synonymous_variant,p.=,ENST00000587738,;RASGRP4,synonymous_variant,p.=,ENST00000589358,;RASGRP4,synonymous_variant,p.=,ENST00000589474,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000615340,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,upstream_gene_variant,,ENST00000588708,; A ENST00000615439 Transcript synonymous_variant 670/3217 456/2022 152/673 T acC/acT COSM1481006,COSM5538038 1 -1 RASGRP4 HGNC HGNC:18958 protein_coding YES CCDS46068.1 ENSP00000479844 Q8TDF6 UPI0000050F40 NM_170604.2 5/17 PROSITE_profiles:PS50212,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF157,Gene3D:2ii0A01,Superfamily_domains:0041591 1,1 LOW 1 SNV 1 1,1 1 PASS rs1048545329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 38420184 38420184 G A 1 0 0 0 0 0 0 0 1 13238 1103 39 1 1 RASGRP4 19 38420184 Silent SNP G C3N-01016_T 2027027 38420184 20197432 328 20477 LRFN1 0 . GRCh38 19 39308317 39308317 + Missense_Mutation SNP G G C C3N-01016_T C3N-01016_N G G c.1632C>G p.Ile544Met p.I544M ENST00000248668 2/2 281 252 29 283 283 0 strelka-varscan-mutect LRFN1,missense_variant,p.Ile544Met,ENST00000248668,NM_020862.1; C ENST00000248668 Transcript missense_variant 1632/3381 1632/2316 544/771 I/M atC/atG COSM5309579,COSM5309580 1 -1 LRFN1 HGNC HGNC:29290 protein_coding YES CCDS46071.1 ENSP00000248668 Q9P244 UPI00001A5C55 NM_020862.1 deleterious(0) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF34,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 39308317 39308317 G C 1 0 0 0 0 1 0 0 0 8831 1048 37 4 4 LRFN1 19 39308317 Missense_Mutation SNP G C3N-01016_T 888133 39308317 19309299 329 20478 AKT2 0 . GRCh38 19 40240079 40240079 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.605G>T p.Arg202Leu p.R202L ENST00000392038 7/14 544 484 60 507 507 0 strelka-varscan-mutect AKT2,missense_variant,p.Arg202Leu,ENST00000392038,NM_001626.5;AKT2,missense_variant,p.Arg202Leu,ENST00000424901,;AKT2,missense_variant,p.Arg140Leu,ENST00000579047,NM_001243027.2,NM_001243028.2;AKT2,missense_variant,p.Arg202Leu,ENST00000311278,;AKT2,intron_variant,,ENST00000578615,;AKT2,intron_variant,,ENST00000578310,;AKT2,downstream_gene_variant,,ENST00000416362,;AKT2,downstream_gene_variant,,ENST00000441941,;AKT2,downstream_gene_variant,,ENST00000423127,;AKT2,downstream_gene_variant,,ENST00000392037,;AKT2,downstream_gene_variant,,ENST00000486368,;AKT2,downstream_gene_variant,,ENST00000596634,;AKT2,downstream_gene_variant,,ENST00000456441,;AKT2,downstream_gene_variant,,ENST00000452077,;AKT2,downstream_gene_variant,,ENST00000583859,;AKT2,downstream_gene_variant,,ENST00000578123,;AKT2,downstream_gene_variant,,ENST00000358335,;AKT2,upstream_gene_variant,,ENST00000476247,;AKT2,upstream_gene_variant,,ENST00000497948,;AKT2,non_coding_transcript_exon_variant,,ENST00000391845,;AKT2,non_coding_transcript_exon_variant,,ENST00000480878,;AKT2,upstream_gene_variant,,ENST00000486647,;AKT2,missense_variant,p.Gly117Trp,ENST00000601166,;AKT2,3_prime_UTR_variant,,ENST00000391844,;AKT2,3_prime_UTR_variant,,ENST00000584288,;AKT2,3_prime_UTR_variant,,ENST00000492463,;AKT2,3_prime_UTR_variant,,ENST00000491778,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,non_coding_transcript_exon_variant,,ENST00000537834,;AKT2,upstream_gene_variant,,ENST00000483166,;AKT2,downstream_gene_variant,,ENST00000578975,;AKT2,upstream_gene_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000487537,;AKT2,upstream_gene_variant,,ENST00000489375,;AKT2,upstream_gene_variant,,ENST00000580878,;AKT2,upstream_gene_variant,,ENST00000579345,;AKT2,upstream_gene_variant,,ENST00000578282,; A ENST00000392038 Transcript missense_variant 904/5300 605/1446 202/481 R/L cGg/cTg 1 -1 AKT2 HGNC HGNC:392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 UPI0000049EDB NM_001626.5 deleterious(0.02) 7/14 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF176,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 40240079 40240079 C A 1 0 0 0 0 1 0 0 0 563 652 23 1 1 AKT2 19 40240079 Missense_Mutation SNP C C3N-01016_T 931762 40240079 18377537 330 20479 PNMAL1 0 . GRCh38 19 46470040 46470040 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.996C>T p.= p.A332A ENST00000313683 2/3 69 27 42 44 44 0 strelka-varscan-mutect PNMAL1,synonymous_variant,p.=,ENST00000313683,NM_018215.3;PNMAL1,synonymous_variant,p.=,ENST00000438932,NM_001103149.1;PNMAL1,intron_variant,,ENST00000602246,; A ENST00000313683 Transcript synonymous_variant 1302/3689 996/1320 332/439 A gcC/gcT 1 -1 PNMAL1 HGNC HGNC:25578 protein_coding YES CCDS33059.1 ENSP00000318131 Q86V59 UPI0000231C97 NM_018215.3 2/3 hmmpanther:PTHR23095:SF21,hmmpanther:PTHR23095,Pfam_domain:PF14893 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 66 46470040 46470040 G A 1 0 0 0 0 0 0 0 1 12265 987 35 3 3 PNMAL1 19 46470040 Silent SNP G C3N-01016_T 6229961 46470040 12147576 331 20480 SYNGR4 0 . GRCh38 19 48365890 48365890 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.48G>A p.= p.V16V ENST00000344846 2/5 267 149 118 280 280 0 strelka-varscan-mutect SYNGR4,synonymous_variant,p.=,ENST00000344846,NM_012451.3;TMEM143,upstream_gene_variant,,ENST00000293261,NM_001303539.1,NM_018273.3;TMEM143,upstream_gene_variant,,ENST00000435956,NM_001303538.1;TMEM143,upstream_gene_variant,,ENST00000377431,NM_001303540.1;TMEM143,upstream_gene_variant,,ENST00000601522,;TMEM143,upstream_gene_variant,,ENST00000598926,;TMEM143,upstream_gene_variant,,ENST00000598012,;TMEM143,upstream_gene_variant,,ENST00000598258,;TMEM143,upstream_gene_variant,,ENST00000595720,;TMEM143,upstream_gene_variant,,ENST00000601332,;TMEM143,upstream_gene_variant,,ENST00000597370,;TMEM143,upstream_gene_variant,,ENST00000593914,;TMEM143,upstream_gene_variant,,ENST00000599220,; A ENST00000344846 Transcript synonymous_variant 298/1000 48/705 16/234 V gtG/gtA 1 1 SYNGR4 HGNC HGNC:11502 protein_coding YES CCDS12717.1 ENSP00000344041 O95473 A0A140VKF5 UPI000013C7EB NM_012451.3 2/5 hmmpanther:PTHR10838:SF22,hmmpanther:PTHR10838,PIRSF_domain:PIRSF011282 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 48365890 48365890 G A 1 0 0 0 0 0 0 0 1 15845 1306 46 3 3 SYNGR4 19 48365890 Silent SNP G C3N-01016_T 1895850 48365890 10251726 332 20481 CD37 0 . GRCh38 19 49337218 49337218 + Silent SNP C C T novel C3N-01016_T C3N-01016_N C C c.339C>T p.= p.A113A ENST00000323906 4/8 179 94 85 179 178 1 strelka-varscan-mutect CD37,synonymous_variant,p.=,ENST00000535669,;CD37,synonymous_variant,p.=,ENST00000598095,;CD37,synonymous_variant,p.=,ENST00000323906,NM_001774.2;CD37,synonymous_variant,p.=,ENST00000426897,NM_001040031.1;CD37,synonymous_variant,p.=,ENST00000594743,;TEAD2,downstream_gene_variant,,ENST00000377214,;TEAD2,downstream_gene_variant,,ENST00000598810,NM_001256661.1;TEAD2,downstream_gene_variant,,ENST00000601519,NM_001256659.1,NM_001256658.1;TEAD2,downstream_gene_variant,,ENST00000311227,NM_003598.1;TEAD2,downstream_gene_variant,,ENST00000593945,NM_001256660.1;TEAD2,downstream_gene_variant,,ENST00000539846,NM_001256662.1;CD37,downstream_gene_variant,,ENST00000595660,;CD37,downstream_gene_variant,,ENST00000597602,;CTC-301O7.4,intron_variant,,ENST00000358234,;CTC-301O7.4,intron_variant,,ENST00000602554,;CD37,non_coding_transcript_exon_variant,,ENST00000596426,;CD37,non_coding_transcript_exon_variant,,ENST00000597033,;CD37,upstream_gene_variant,,ENST00000600121,;CD37,missense_variant,p.Pro112Leu,ENST00000595725,;CD37,synonymous_variant,p.=,ENST00000391859,;CD37,non_coding_transcript_exon_variant,,ENST00000597852,;CD37,non_coding_transcript_exon_variant,,ENST00000593512,;CD37,non_coding_transcript_exon_variant,,ENST00000598134,; T ENST00000323906 Transcript synonymous_variant 480/1265 339/846 113/281 A gcC/gcT 1 1 CD37 HGNC HGNC:1666 protein_coding YES CCDS12760.1 ENSP00000325708 P11049 UPI0000127350 NM_001774.2 4/8 Superfamily_domains:0037997,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF263 LOW 1 SNV 1 1 PASS rs1282377025 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 49337218 49337218 C T 1 0 0 0 0 0 0 0 1 2712 637 22 3 3 CD37 19 49337218 Silent SNP C C3N-01016_T 971328 49337218 9280398 333 20482 ALDH16A1 0 . GRCh38 19 49463852 49463852 + Splice_Site SNP A A G novel C3N-01016_T C3N-01016_N A A c.1099-2A>G p.X367_splice ENST00000293350 72 38 34 72 72 0 strelka-varscan-mutect ALDH16A1,splice_acceptor_variant,,ENST00000293350,NM_153329.3;ALDH16A1,splice_acceptor_variant,,ENST00000455361,NM_001145396.1;ALDH16A1,splice_acceptor_variant,,ENST00000540132,;ALDH16A1,downstream_gene_variant,,ENST00000598015,;ALDH16A1,splice_acceptor_variant,,ENST00000599652,;ALDH16A1,splice_acceptor_variant,,ENST00000593417,;CTD-3148I10.9,splice_acceptor_variant,,ENST00000599536,;ALDH16A1,upstream_gene_variant,,ENST00000600265,;ALDH16A1,upstream_gene_variant,,ENST00000594549,; G ENST00000293350 Transcript splice_acceptor_variant -/3153 1099/2409 367/802 1 1 ALDH16A1 HGNC HGNC:28114 protein_coding YES CCDS12766.1 ENSP00000293350 Q8IZ83 UPI000013E0FF NM_153329.3 8/16 HIGH 1 SNV 1 1 PASS rs1194117017 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 66 49463852 49463852 A G 1 0 0 0 0 0 0 1 0 588 434 15 5 5 ALDH16A1 19 49463852 Splice_Site SNP A C3N-01016_T 126634 49463852 9153764 334 20483 LILRB5 0 . GRCh38 19 54256158 54256158 + Missense_Mutation SNP G G C C3N-01016_T C3N-01016_N G G c.540C>G p.Phe180Leu p.F180L ENST00000449561 4/13 97 92 5 129 129 0 strelka-varscan-mutect LILRB5,missense_variant,p.Phe180Leu,ENST00000316219,NM_006840.4;LILRB5,missense_variant,p.Phe180Leu,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,intron_variant,,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000615654,;LILRB5,intron_variant,,ENST00000621581,; C ENST00000449561 Transcript missense_variant 611/2137 540/1776 180/591 F/L ttC/ttG COSM4499356 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 tolerated(0.06) 4/13 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS rs1332838508 . 0 208 2 0 0 0 0 0 -11.03315 1 1 1 1 0 C 3 2 66 54256158 54256158 G C 1 0 0 0 0 1 0 0 0 8702 1165 41 4 4 LILRB5 19 54256158 Missense_Mutation SNP G C3N-01016_T 4792306 54256158 4361458 335 20484 LILRB5 0 . GRCh38 19 54256666 54256666 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.178C>T p.= p.L60L ENST00000449561 3/13 342 320 22 327 326 1 strelka-varscan-mutect LILRB5,synonymous_variant,p.=,ENST00000316219,NM_006840.4;LILRB5,synonymous_variant,p.=,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,synonymous_variant,p.=,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000621581,;LILRB5,intron_variant,,ENST00000615654,; A ENST00000449561 Transcript synonymous_variant 249/2137 178/1776 60/591 L Ctg/Ttg 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 3/13 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs950462921 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 54256666 54256666 G A 1 0 0 0 0 0 0 0 1 8702 933 33 3 3 LILRB5 19 54256666 Silent SNP G C3N-01016_T 508 54256666 4360950 336 20485 PTPRH 0 . GRCh38 19 55185865 55185865 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.2898C>T p.= p.L966L ENST00000376350 17/20 165 80 85 190 190 0 strelka-varscan-mutect PTPRH,synonymous_variant,p.=,ENST00000376350,NM_002842.4;PTPRH,synonymous_variant,p.=,ENST00000263434,NM_001161440.2; A ENST00000376350 Transcript synonymous_variant 2921/3877 2898/3348 966/1115 L ctC/ctT 1 -1 PTPRH HGNC HGNC:9672 protein_coding YES CCDS33110.1 ENSP00000365528 Q9HD43 UPI000052D443 NM_002842.4 17/20 Low_complexity_(Seg):seg,PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF297,hmmpanther:PTHR19134,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00194,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 55185865 55185865 G A 1 0 0 0 0 0 0 0 1 12957 1188 41 3 3 PTPRH 19 55185865 Silent SNP G C3N-01016_T 929199 55185865 3431751 337 20486 NLRP8 0 . GRCh38 19 55955206 55955206 + Frame_Shift_Del DEL C C - rs775679678 C3N-01016_T C3N-01016_N C C c.1149delC p.Met384TrpfsTer23 p.M384Wfs*23 ENST00000291971 3/10 137 71 66 155 155 0 sindel-varindel-pindel NLRP8,frameshift_variant,p.Met384TrpfsTer23,ENST00000291971,NM_176811.2;NLRP8,frameshift_variant,p.Met384TrpfsTer23,ENST00000590542,; - ENST00000291971 Transcript frameshift_variant 1219/3934 1148/3147 383/1048 A/X gCc/gc rs775679678 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 3/10 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF54 HIGH 1 deletion 2 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 66 55955206 55955206 C - 1 0 1 0 1 0 0 0 0 10521 739 26 0 0 NLRP8 19 55955206 Frame_Shift_Del DEL C C3N-01016_T 769341 55955206 2662410 338 20487 ZNF135 0 . GRCh38 19 58066945 58066945 + Missense_Mutation SNP C C G rs746765542 C3N-01016_T C3N-01016_N C C c.533C>G p.Thr178Arg p.T178R ENST00000401053 4/4 242 148 94 223 223 0 strelka-varscan-mutect ZNF135,missense_variant,p.Thr112Arg,ENST00000506786,NM_001289402.1;ZNF135,missense_variant,p.Thr178Arg,ENST00000401053,NM_001164529.1,NM_007134.1;ZNF135,missense_variant,p.Thr154Arg,ENST00000313434,NM_001289401.1;ZNF135,missense_variant,p.Thr166Arg,ENST00000511556,NM_003436.3;ZNF135,missense_variant,p.Thr166Arg,ENST00000359978,NM_001164530.1;RN7SL526P,upstream_gene_variant,,ENST00000469492,;ZNF135,intron_variant,,ENST00000515535,; G ENST00000401053 Transcript missense_variant 536/3346 533/2049 178/682 T/R aCg/aGg rs746765542,COSM2156527,COSM2156528,COSM714103,COSM714104 1 1 ZNF135 HGNC HGNC:12919 protein_coding YES CCDS54329.1 ENSP00000441410 P52742 UPI0001B3CB2A NM_001164529.1,NM_007134.1 tolerated(0.06) 4/4 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs746765542 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 58066945 58066945 C G 1 0 0 0 0 1 0 0 0 18306 536 19 4 4 ZNF135 19 58066945 Missense_Mutation SNP C C3N-01016_T 2111739 58066945 550671 339 20488 SIRPG 0 . GRCh38 20 1649182 1649182 + Missense_Mutation SNP C C T rs527643862 C3N-01016_T C3N-01016_N C C c.300G>A p.Met100Ile p.M100I ENST00000303415 2/6 462 313 149 352 352 0 strelka-varscan-mutect SIRPG,missense_variant,p.Met67Ile,ENST00000381580,;SIRPG,missense_variant,p.Met100Ile,ENST00000303415,NM_018556.3;SIRPG,missense_variant,p.Met100Ile,ENST00000381583,NM_001039508.1;SIRPG,missense_variant,p.Met100Ile,ENST00000344103,NM_080816.2;SIRPG,missense_variant,p.Met100Ile,ENST00000216927,;SIRPG-AS1,downstream_gene_variant,,ENST00000456177,; T ENST00000303415 Transcript missense_variant 365/1716 300/1164 100/387 M/I atG/atA rs527643862,COSM4541471 1 -1 SIRPG HGNC HGNC:15757 protein_coding YES CCDS13020.2 ENSP00000305529 Q9P1W8 UPI00001AE5FD NM_018556.3 tolerated(0.06) 2/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs527643862 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 1649182 1649182 C T 1 0 0 0 0 1 0 0 0 14599 594 21 3 3 SIRPG 20 1649182 Missense_Mutation SNP C C3N-01016_T 1649182 62794985 340 20489 TMC2 0 . GRCh38 20 2613204 2613204 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.1754G>T p.Arg585Met p.R585M ENST00000358864 14/20 170 124 46 94 94 0 strelka-varscan-mutect TMC2,missense_variant,p.Arg585Met,ENST00000358864,NM_080751.2;TMC2,non_coding_transcript_exon_variant,,ENST00000496948,; T ENST00000358864 Transcript missense_variant 1769/3169 1754/2721 585/906 R/M aGg/aTg 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 deleterious(0) 14/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17,Pfam_domain:PF07810 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 2613204 2613204 G T 1 0 0 0 0 1 0 0 0 16431 1000 35 2 2 TMC2 20 2613204 Missense_Mutation SNP G C3N-01016_T 964022 2613204 61830963 341 20490 ADAM33 0 . GRCh38 20 3677076 3677076 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.245A>T p.Glu82Val p.E82V ENST00000356518 3/22 198 175 23 167 167 0 strelka-varscan-mutect ADAM33,missense_variant,p.Glu82Val,ENST00000356518,NM_025220.3;ADAM33,missense_variant,p.Glu82Val,ENST00000379861,NM_001282447.1;ADAM33,missense_variant,p.Glu82Val,ENST00000350009,NM_153202.2;ADAM33,missense_variant,p.Glu82Val,ENST00000619289,;ADAM33,missense_variant,p.Glu82Val,ENST00000617732,;ADAM33,upstream_gene_variant,,ENST00000466620,; A ENST00000356518 Transcript missense_variant 487/3677 245/2442 82/813 E/V gAg/gTg 1 -1 ADAM33 HGNC HGNC:15478 protein_coding YES CCDS13058.1 ENSP00000348912 Q9BZ11 UPI0000048F2A NM_025220.3 deleterious(0.01) 3/22 Low_complexity_(Seg):seg,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF38,Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 3677076 3677076 T A 1 0 0 0 0 1 0 0 0 294 1551 54 4 4 ADAM33 20 3677076 Missense_Mutation SNP T C3N-01016_T 1063872 3677076 60767091 342 20491 PLCB1 0 . GRCh38 20 8628422 8628422 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.375A>T p.Glu125Asp p.E125D ENST00000338037 4/32 216 156 60 147 147 0 strelka-varscan-mutect PLCB1,missense_variant,p.Glu125Asp,ENST00000378641,NM_182734.2;PLCB1,missense_variant,p.Glu125Asp,ENST00000338037,NM_015192.3;PLCB1,missense_variant,p.Glu45Asp,ENST00000612075,;PLCB1,missense_variant,p.Glu45Asp,ENST00000617005,;PLCB1,missense_variant,p.Glu24Asp,ENST00000637919,;PLCB1,missense_variant,p.Glu125Asp,ENST00000378637,;PLCB1,missense_variant,p.Glu24Asp,ENST00000625874,;PLCB1,missense_variant,p.Glu125Asp,ENST00000629992,;PLCB1,missense_variant,p.Glu24Asp,ENST00000626966,;PLCB1,missense_variant,p.Glu125Asp,ENST00000404098,;PLCB1,missense_variant,p.Glu24Asp,ENST00000630495,;PLCB1,non_coding_transcript_exon_variant,,ENST00000635830,;PLCB1,non_coding_transcript_exon_variant,,ENST00000636825,;PLCB1,non_coding_transcript_exon_variant,,ENST00000628900,;PLCB1,downstream_gene_variant,,ENST00000635850,;PLCB1,downstream_gene_variant,,ENST00000636784,;PLCB1,downstream_gene_variant,,ENST00000637000,;PLCB1,missense_variant,p.Glu125Asp,ENST00000636319,;PLCB1,non_coding_transcript_exon_variant,,ENST00000626161,;PLCB1,non_coding_transcript_exon_variant,,ENST00000626114,; T ENST00000338037 Transcript missense_variant 762/7092 375/3651 125/1216 E/D gaA/gaT 1 1 PLCB1 HGNC HGNC:15917 protein_coding YES CCDS13102.1 ENSP00000338185 Q9NQ66 UPI0000131A8F NM_015192.3 tolerated(1) 4/32 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF12,PIRSF_domain:PIRSF000956,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 8628422 8628422 A T 1 0 0 0 0 1 0 0 0 12121 69 3 4 4 PLCB1 20 8628422 Missense_Mutation SNP A C3N-01016_T 4951346 8628422 55815745 343 20492 PCSK2 0 . GRCh38 20 17360577 17360577 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.442G>T p.Val148Leu p.V148L ENST00000262545 4/12 225 151 74 175 175 0 strelka-varscan-mutect PCSK2,missense_variant,p.Val148Leu,ENST00000262545,NM_002594.4;PCSK2,missense_variant,p.Val129Leu,ENST00000377899,NM_001201528.1;PCSK2,missense_variant,p.Val113Leu,ENST00000536609,NM_001201529.2;PCSK2,non_coding_transcript_exon_variant,,ENST00000470007,; T ENST00000262545 Transcript missense_variant 757/4740 442/1917 148/638 V/L Gtg/Ttg 1 1 PCSK2 HGNC HGNC:8744 protein_coding YES CCDS13125.1 ENSP00000262545 P16519 UPI0000000C6E NM_002594.4 deleterious(0) 4/12 Gene3D:3.40.50.200,hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF11,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 17360577 17360577 G T 1 0 0 0 0 1 0 0 0 11689 1377 48 2 2 PCSK2 20 17360577 Missense_Mutation SNP G C3N-01016_T 8732155 17360577 47083590 344 20493 PTPRT 0 . GRCh38 20 42085743 42085743 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.4014C>A p.= p.I1338I ENST00000373198 29/32 208 148 60 195 195 0 strelka-varscan-mutect PTPRT,synonymous_variant,p.=,ENST00000373198,NM_133170.3;PTPRT,synonymous_variant,p.=,ENST00000373193,;PTPRT,synonymous_variant,p.=,ENST00000373201,;PTPRT,synonymous_variant,p.=,ENST00000373190,;PTPRT,synonymous_variant,p.=,ENST00000373184,;PTPRT,synonymous_variant,p.=,ENST00000356100,;PTPRT,synonymous_variant,p.=,ENST00000373187,NM_007050.5;PTPRT,synonymous_variant,p.=,ENST00000612229,;PTPRT,synonymous_variant,p.=,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript synonymous_variant 4250/12746 4014/4383 1338/1460 I atC/atA 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 29/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,SMART_domains:SM00194,Superfamily_domains:SSF52799 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 42085743 42085743 G T 1 0 0 0 0 0 0 0 1 12967 932 33 2 2 PTPRT 20 42085743 Silent SNP G C3N-01016_T 24725166 42085743 22358424 345 20494 ZMYND8 0 . GRCh38 20 47238808 47238808 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.2615A>T p.Gln872Leu p.Q872L ENST00000471951 15/23 159 135 24 106 106 0 strelka-mutect ZMYND8,missense_variant,p.Gln852Leu,ENST00000355972,NM_001281773.2;ZMYND8,missense_variant,p.Gln852Leu,ENST00000396281,NM_001281772.2;ZMYND8,missense_variant,p.Gln852Leu,ENST00000446994,;ZMYND8,missense_variant,p.Gln852Leu,ENST00000311275,;ZMYND8,missense_variant,p.Gln879Leu,ENST00000536340,;ZMYND8,missense_variant,p.Gln872Leu,ENST00000471951,NM_001281775.2,NM_001281776.2;ZMYND8,missense_variant,p.Gln800Leu,ENST00000540497,NM_001281781.2,NM_001281784.2;ZMYND8,intron_variant,,ENST00000372023,NM_001281779.2,NM_001281780.2;ZMYND8,intron_variant,,ENST00000611941,;ZMYND8,intron_variant,,ENST00000360911,NM_183048.3,NM_001281778.2;ZMYND8,intron_variant,,ENST00000262975,NM_001281774.2;ZMYND8,intron_variant,,ENST00000619049,;ZMYND8,intron_variant,,ENST00000352431,NM_012408.5,NM_001281783.2;ZMYND8,intron_variant,,ENST00000458360,NM_001281771.2;ZMYND8,intron_variant,,ENST00000467200,;ZMYND8,intron_variant,,ENST00000461685,NM_001281777.2,NM_183047.3;ZMYND8,intron_variant,,ENST00000617418,NM_001281782.2;ZMYND8,non_coding_transcript_exon_variant,,ENST00000468376,; A ENST00000471951 Transcript missense_variant 2642/4053 2615/3705 872/1234 Q/L cAg/cTg 1 -1 ZMYND8 HGNC HGNC:9397 protein_coding YES CCDS63306.1 ENSP00000420095 Q9ULU4 UPI0000695D9A NM_001281775.2,NM_001281776.2 tolerated_low_confidence(0.1) 15/23 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999938 1 1 1 0 A 3 1 66 47238808 47238808 T A 1 0 0 0 0 1 0 0 0 18290 1580 55 4 4 ZMYND8 20 47238808 Missense_Mutation SNP T C3N-01016_T 5153065 47238808 17205359 346 20495 SALL4 0 . GRCh38 20 51791459 51791459 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1024G>T p.Val342Leu p.V342L ENST00000217086 2/4 215 186 29 142 142 0 strelka-varscan-mutect SALL4,missense_variant,p.Val342Leu,ENST00000217086,NM_020436.3;SALL4,missense_variant,p.Val342Leu,ENST00000395997,;SALL4,intron_variant,,ENST00000371539,;SALL4,downstream_gene_variant,,ENST00000483130,;SALL4,downstream_gene_variant,,ENST00000481363,; A ENST00000217086 Transcript missense_variant 1136/5208 1024/3162 342/1053 V/L Gtg/Ttg 1 -1 SALL4 HGNC HGNC:15924 protein_coding YES CCDS13438.1 ENSP00000217086 Q9UJQ4 UPI0000135527 NM_020436.3 tolerated(0.12) 2/4 hmmpanther:PTHR23233:SF19,hmmpanther:PTHR23233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 51791459 51791459 C A 1 0 0 0 0 1 0 0 0 14072 507 18 2 2 SALL4 20 51791459 Missense_Mutation SNP C C3N-01016_T 4552651 51791459 12652708 347 20496 TAF4 0 . GRCh38 20 62065637 62065637 + Silent SNP G G A novel C3N-01016_T C3N-01016_N G G c.174C>T p.= p.L58L ENST00000252996 1/15 37 20 17 14 14 0 strelka-varscan-mutect TAF4,synonymous_variant,p.=,ENST00000252996,NM_003185.3;RP11-11M20.4,upstream_gene_variant,,ENST00000635124,;MIR3195,downstream_gene_variant,,ENST00000585001,;TAF4,upstream_gene_variant,,ENST00000608887,; A ENST00000252996 Transcript synonymous_variant 174/4628 174/3258 58/1085 L ctC/ctT 1 -1 TAF4 HGNC HGNC:11537 protein_coding YES CCDS33500.1 ENSP00000252996 O00268 UPI000020630A NM_003185.3 1/15 hmmpanther:PTHR15138:SF18,hmmpanther:PTHR15138 LOW 1 SNV 1 1 PASS . . 23 186 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 62065637 62065637 G A 1 0 0 0 0 0 0 0 1 15922 1045 37 1 1 TAF4 20 62065637 Silent SNP G C3N-01016_T 10274178 62065637 2378530 348 20497 CABLES2 0 . GRCh38 20 62393440 62393440 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.880G>C p.Gly294Arg p.G294R ENST00000279101 6/10 56 36 20 56 56 0 strelka-varscan-mutect CABLES2,missense_variant,p.Gly294Arg,ENST00000279101,NM_031215.2;CABLES2,missense_variant,p.Gly88Arg,ENST00000453274,;RPS21,downstream_gene_variant,,ENST00000370562,;RPS21,downstream_gene_variant,,ENST00000450116,;RPS21,downstream_gene_variant,,ENST00000343986,NM_001024.3;RPS21,downstream_gene_variant,,ENST00000492356,; G ENST00000279101 Transcript missense_variant,splice_region_variant 889/3785 880/1437 294/478 G/R Ggg/Cgg 1 -1 CABLES2 HGNC HGNC:16143 protein_coding YES CCDS33503.1 ENSP00000279101 Q9BTV7 UPI00001AEA34 NM_031215.2 deleterious(0.01) 6/10 hmmpanther:PTHR22896,hmmpanther:PTHR22896:SF3 MODERATE SNV 5 1 PASS . . 1 203 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 62393440 62393440 C G 1 0 0 0 0 1 0 0 0 2216 695 24 4 4 CABLES2 20 62393440 Missense_Mutation SNP C C3N-01016_T 327803 62393440 2050727 349 20498 KRTAP10-2 0 . GRCh38 21 44550889 44550889 + Silent SNP A A G rs76021731 C3N-01016_T C3N-01016_N A A c.570T>C p.= p.P190P ENST00000391621 1/1 114 103 11 178 175 3 varscan-mutect KRTAP10-2,synonymous_variant,p.=,ENST00000391621,NM_198693.3;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,;KRTAP10-2,intron_variant,,ENST00000498210,; G ENST00000391621 Transcript synonymous_variant 617/1149 570/768 190/255 P ccT/ccC rs76021731 1 -1 KRTAP10-2 HGNC HGNC:22967 protein_coding YES CCDS42955.1 ENSP00000375479 P60368 UPI000021C438 NM_198693.3 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF8,Low_complexity_(Seg):seg LOW SNV 1 PASS rs76021731 . 0 113 0 0 0 0 0 97 -3.032754 0 0 1 0 0 G 2 3 66 44550889 44550889 A G 1 0 0 0 0 0 0 0 1 8392 175 7 5 5 KRTAP10-2 21 44550889 Silent SNP A C3N-01016_T 44550889 2159094 350 20499 CLTCL1 0 . GRCh38 22 19210458 19210458 + Silent SNP C C T C3N-01016_T C3N-01016_N C C c.3117G>A p.= p.R1039R ENST00000427926 20/33 171 124 47 212 212 0 strelka-varscan-mutect CLTCL1,synonymous_variant,p.=,ENST00000427926,NM_007098.3;CLTCL1,synonymous_variant,p.=,ENST00000621271,NM_001835.3;CLTCL1,upstream_gene_variant,,ENST00000622493,;CLTCL1,upstream_gene_variant,,ENST00000617926,;CLTCL1,synonymous_variant,p.=,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,upstream_gene_variant,,ENST00000611723,; T ENST00000427926 Transcript synonymous_variant 3190/5513 3117/4923 1039/1640 R cgG/cgA COSM369314 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 20/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 19210458 19210458 C T 1 0 0 0 0 0 0 0 1 3339 610 22 3 3 CLTCL1 22 19210458 Silent SNP C C3N-01016_T 19210458 31608010 351 20500 MYO18B 0 . GRCh38 22 25950378 25950378 + Missense_Mutation SNP C C G novel C3N-01016_T C3N-01016_N C C c.5760C>G p.Asp1920Glu p.D1920E ENST00000335473 37/44 116 92 24 98 98 0 strelka-varscan-mutect MYO18B,missense_variant,p.Asp1920Glu,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Asp1921Glu,ENST00000407587,;MYO18B,missense_variant,p.Asp1920Glu,ENST00000536101,;MYO18B,upstream_gene_variant,,ENST00000543971,;MYO18B,upstream_gene_variant,,ENST00000539544,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; G ENST00000335473 Transcript missense_variant 6010/8565 5760/7704 1920/2567 D/E gaC/gaG 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated(0.08) 37/44 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 25950378 25950378 C G 1 0 0 0 0 1 0 0 0 10067 477 17 4 4 MYO18B 22 25950378 Missense_Mutation SNP C C3N-01016_T 6739920 25950378 24868090 352 20501 RFPL1 0 . GRCh38 22 29441707 29441707 + Missense_Mutation SNP A A T novel C3N-01016_T C3N-01016_N A A c.539A>T p.His180Leu p.H180L ENST00000354373 2/2 252 203 49 242 242 0 strelka-varscan-mutect RFPL1,missense_variant,p.His180Leu,ENST00000354373,NM_021026.2;RFPL1S,non_coding_transcript_exon_variant,,ENST00000461286,;RFPL1S,upstream_gene_variant,,ENST00000539579,;AC000041.10,downstream_gene_variant,,ENST00000619824,; T ENST00000354373 Transcript missense_variant 748/1496 539/954 180/317 H/L cAc/cTc 1 1 RFPL1 HGNC HGNC:9977 protein_coding YES CCDS13857.2 ENSP00000346342 O75677 UPI000013CC65 NM_021026.2 deleterious(0) 2/2 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF225,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 29441707 29441707 A T 1 0 0 0 0 1 0 0 0 13424 159 6 4 4 RFPL1 22 29441707 Missense_Mutation SNP A C3N-01016_T 3491329 29441707 21376761 353 20502 DEPDC5 0 . GRCh38 22 31876220 31876220 + Missense_Mutation SNP G G T rs746114133 C3N-01016_T C3N-01016_N G G c.3760G>T p.Gly1254Cys p.G1254C ENST00000400246 37/43 141 125 16 150 150 0 strelka-varscan-mutect DEPDC5,missense_variant,p.Gly1254Cys,ENST00000400246,NM_001242896.1;DEPDC5,missense_variant,p.Gly1223Cys,ENST00000400249,;DEPDC5,missense_variant,p.Gly1245Cys,ENST00000382112,NM_001136029.2;DEPDC5,missense_variant,p.Gly1223Cys,ENST00000400248,NM_014662.4;DEPDC5,missense_variant,p.Gly1254Cys,ENST00000382111,;DEPDC5,missense_variant,p.Gly1154Cys,ENST00000535622,NM_001242897.1;DEPDC5,missense_variant,p.Gly630Cys,ENST00000433147,;DEPDC5,downstream_gene_variant,,ENST00000494060,;DEPDC5,non_coding_transcript_exon_variant,,ENST00000479261,;DEPDC5,intron_variant,,ENST00000448753,; T ENST00000400246 Transcript missense_variant 3962/5551 3760/4812 1254/1603 G/C Ggc/Tgc rs746114133 1 1 DEPDC5 HGNC HGNC:18423 protein_coding YES CCDS74849.1 ENSP00000383105 O75140 UPI000192C426 NM_001242896.1 deleterious(0) 37/43 PROSITE_profiles:PS50186,hmmpanther:PTHR13179,Gene3D:1.10.10.10,Pfam_domain:PF00610,SMART_domains:SM00049,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS rs746114133 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 31876220 31876220 G T 1 0 0 0 0 1 0 0 0 4248 1116 39 1 1 DEPDC5 22 31876220 Missense_Mutation SNP G C3N-01016_T 2434513 31876220 18942248 354 20503 FBXO7 0 . GRCh38 22 32479069 32479069 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.211G>T p.Gly71Trp p.G71W ENST00000266087 2/9 326 260 66 346 346 0 strelka-varscan-mutect FBXO7,missense_variant,p.Gly71Trp,ENST00000266087,NM_012179.3;FBXO7,5_prime_UTR_variant,,ENST00000397426,NM_001257990.1;FBXO7,5_prime_UTR_variant,,ENST00000444207,;FBXO7,intron_variant,,ENST00000452138,NM_001033024.1;FBXO7,non_coding_transcript_exon_variant,,ENST00000465418,;FBXO7,intron_variant,,ENST00000492535,;FBXO7,intron_variant,,ENST00000425028,;FBXO7,intron_variant,,ENST00000420700,; T ENST00000266087 Transcript missense_variant 538/2195 211/1569 71/522 G/W Ggg/Tgg 1 1 FBXO7 HGNC HGNC:13586 protein_coding YES CCDS13907.1 ENSP00000266087 Q9Y3I1 UPI000012A587 NM_012179.3 deleterious(0) 2/9 hmmpanther:PTHR15537,hmmpanther:PTHR15537:SF2,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 32479069 32479069 G T 1 0 0 0 0 1 0 0 0 5623 1348 47 2 2 FBXO7 22 32479069 Missense_Mutation SNP G C3N-01016_T 602849 32479069 18339399 355 20504 CSF2RA 0 . GRCh38 X 1288590 1288590 + Missense_Mutation SNP C C G rs76312561 C3N-01016_T C3N-01016_N C C c.291C>G p.His97Gln p.H97Q ENST00000417535 5/14 590 436 154 592 592 0 strelka-varscan-mutect CSF2RA,missense_variant,p.His97Gln,ENST00000381524,;CSF2RA,missense_variant,p.His97Gln,ENST00000417535,NM_001161530.1;CSF2RA,missense_variant,p.His97Gln,ENST00000432318,NM_001161529.1;CSF2RA,missense_variant,p.His97Gln,ENST00000381529,NM_006140.4,NM_172245.2;CSF2RA,missense_variant,p.His97Gln,ENST00000355432,NM_172246.2;CSF2RA,missense_variant,p.His97Gln,ENST00000381509,NM_001161531.1;CSF2RA,missense_variant,p.His97Gln,ENST00000355805,NM_172249.2;CSF2RA,missense_variant,p.His97Gln,ENST00000381500,NM_172247.2;CSF2RA,missense_variant,p.His97Gln,ENST00000412290,;CSF2RA,5_prime_UTR_variant,,ENST00000501036,NM_001161532.1;CSF2RA,intron_variant,,ENST00000494969,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000493312,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000477940,;CSF2RA,upstream_gene_variant,,ENST00000475259,;CSF2RA,upstream_gene_variant,,ENST00000478256,;CSF2RA,missense_variant,p.His97Gln,ENST00000486791,; G ENST00000417535 Transcript missense_variant 485/1955 291/1305 97/434 H/Q caC/caG rs76312561 1 1 CSF2RA HGNC HGNC:2435 protein_coding YES CCDS55359.1 ENSP00000394227 P15509 UPI000159C3E4 NM_001161530.1 tolerated(0.58) 5/14 hmmpanther:PTHR23036:SF94,hmmpanther:PTHR23036 MODERATE 1 SNV 5 1 PASS rs76312561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 66 1288590 1288590 C G 1 0 0 0 0 1 0 0 0 3735 535 19 4 4 CSF2RA 23 1288590 Missense_Mutation SNP C C3N-01016_T 1288590 154752305 356 20505 PPP4R3CP 0 . GRCh38 X 27462722 27462722 + Missense_Mutation SNP T T A novel C3N-01016_T C3N-01016_N T T c.575A>T p.His192Leu p.H192L ENST00000412172 1/1 128 99 29 94 94 0 strelka-varscan-mutect PPP4R3CP,missense_variant,p.His192Leu,ENST00000412172,; A ENST00000412172 Transcript missense_variant 620/3131 575/2499 192/832 H/L cAc/cTc 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 Pfam_domain:PF04802,hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 27462722 27462722 T A 1 0 0 0 0 1 0 0 0 12529 1696 59 4 4 PPP4R3CP 23 27462722 Missense_Mutation SNP T C3N-01016_T 26174132 27462722 128578173 357 20506 BMP15 0 . GRCh38 X 50916586 50916586 + Silent SNP T T A novel C3N-01016_T C3N-01016_N T T c.1158T>A p.= p.A386A ENST00000252677 2/2 219 159 60 212 212 0 strelka-varscan-mutect BMP15,synonymous_variant,p.=,ENST00000252677,NM_005448.2; A ENST00000252677 Transcript synonymous_variant 1158/1179 1158/1179 386/392 A gcT/gcA 1 1 BMP15 HGNC HGNC:1068 protein_coding YES CCDS14334.1 ENSP00000252677 O95972 UPI000013CD7C NM_005448.2 2/2 Gene3D:2.10.90.10,Pfam_domain:PF00019,Prints_domain:PR00669,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF22,SMART_domains:SM00204,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 50916586 50916586 T A 1 0 0 0 0 0 0 0 1 1613 1567 55 4 4 BMP15 23 50916586 Silent SNP T C3N-01016_T 23453864 50916586 105124309 358 20507 ITIH6 0 . GRCh38 X 54758149 54758149 + Missense_Mutation SNP C C A novel C3N-01016_T C3N-01016_N C C c.1925G>T p.Gly642Val p.G642V ENST00000218436 8/13 166 69 97 91 91 0 strelka-varscan-mutect ITIH6,missense_variant,p.Gly642Val,ENST00000218436,NM_198510.2; A ENST00000218436 Transcript missense_variant 1955/4968 1925/3942 642/1313 G/V gGc/gTc 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 deleterious(0.01) 8/13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 66 54758149 54758149 C A 1 0 0 0 0 1 0 0 0 7814 739 26 2 2 ITIH6 23 54758149 Missense_Mutation SNP C C3N-01016_T 3841563 54758149 101282746 359 20508 MAGED2 0 . GRCh38 X 54813513 54813513 + Missense_Mutation SNP G G A C3N-01016_T C3N-01016_N G G c.1234G>A p.Val412Met p.V412M ENST00000375068 10/13 77 46 31 74 74 0 strelka-varscan-mutect MAGED2,missense_variant,p.Val412Met,ENST00000375068,NM_177433.2;MAGED2,missense_variant,p.Val394Met,ENST00000347546,;MAGED2,missense_variant,p.Val412Met,ENST00000375053,;MAGED2,missense_variant,p.Val412Met,ENST00000375058,NM_014599.5;MAGED2,missense_variant,p.Val412Met,ENST00000396224,NM_201222.2;MAGED2,missense_variant,p.Val412Met,ENST00000218439,;MAGED2,missense_variant,p.Val327Met,ENST00000627068,;MAGED2,missense_variant,p.Val327Met,ENST00000375060,;SNORA11,upstream_gene_variant,,ENST00000408789,;MAGED2,downstream_gene_variant,,ENST00000497484,;MAGED2,downstream_gene_variant,,ENST00000485483,;MAGED2,downstream_gene_variant,,ENST00000463787,;MAGED2,downstream_gene_variant,,ENST00000487463,;MAGED2,downstream_gene_variant,,ENST00000487482,; A ENST00000375068 Transcript missense_variant 1467/2189 1234/1821 412/606 V/M Gtg/Atg COSM5279952 1 1 MAGED2 HGNC HGNC:16353 protein_coding YES CCDS14362.1 ENSP00000364209 Q9UNF1 A0A024R9Y7 UPI000000123B NM_177433.2 deleterious(0.03) 10/13 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF11,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 6 3 0 0 0 0 -20 0.9999262 1 1 1 0 A 3 1 66 54813513 54813513 G A 1 0 0 0 0 1 0 0 0 9102 1145 40 1 1 MAGED2 23 54813513 Missense_Mutation SNP G C3N-01016_T 55364 54813513 101227382 360 20509 CHM 0 . GRCh38 X 85956278 85956278 + Silent SNP T T A novel C3N-01016_T C3N-01016_N T T c.1041A>T p.= p.T347T ENST00000357749 8/15 234 120 114 202 202 0 strelka-varscan-mutect CHM,synonymous_variant,p.=,ENST00000357749,NM_001320959.1,NM_000390.2;CHM,intron_variant,,ENST00000467744,; A ENST00000357749 Transcript synonymous_variant 1071/5442 1041/1962 347/653 T acA/acT 1 -1 CHM HGNC HGNC:1940 protein_coding YES CCDS14454.1 ENSP00000350386 P24386 UPI0000049C8C NM_001320959.1,NM_000390.2 8/15 hmmpanther:PTHR11787:SF12,hmmpanther:PTHR11787,Pfam_domain:PF00996,Gene3D:3.30.519.10,PIRSF_domain:PIRSF016550,Superfamily_domains:SSF51905 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 66 85956278 85956278 T A 1 0 0 0 0 0 0 0 1 3109 1567 55 4 4 CHM 23 85956278 Silent SNP T C3N-01016_T 31142765 85956278 70084617 361 20510 TCEAL2 0 . GRCh38 X 102127483 102127483 + Missense_Mutation SNP G G A C3N-01016_T C3N-01016_N G G c.653G>A p.Arg218Gln p.R218Q ENST00000372780 3/3 24 16 8 15 15 0 strelka-varscan-mutect TCEAL2,missense_variant,p.Arg218Gln,ENST00000372780,NM_080390.3;TCEAL2,missense_variant,p.Arg218Gln,ENST00000329035,;TCEAL2,downstream_gene_variant,,ENST00000476749,; A ENST00000372780 Transcript missense_variant 872/1100 653/684 218/227 R/Q cGa/cAa COSM1228700 1 1 TCEAL2 HGNC HGNC:29818 protein_coding YES CCDS14496.1 ENSP00000361866 Q9H3H9 UPI00000709E1 NM_080390.3 tolerated(1) 3/3 hmmpanther:PTHR14754,hmmpanther:PTHR14754:SF15 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99875 1 1 1 1 0 A 3 1 66 102127483 102127483 G A 1 0 0 0 0 1 0 0 0 16078 1058 37 1 1 TCEAL2 23 102127483 Missense_Mutation SNP G C3N-01016_T 16171205 102127483 53913412 362 20511 ADGRG4 0 . GRCh38 X 136346976 136346976 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.3270G>T p.Glu1090Asp p.E1090D ENST00000394143 6/26 147 68 79 138 138 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Glu1090Asp,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Glu1090Asp,ENST00000370652,;ADGRG4,missense_variant,p.Glu885Asp,ENST00000394141,; T ENST00000394143 Transcript missense_variant 3561/9931 3270/9243 1090/3080 E/D gaG/gaT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 6/26 MODERATE 1 SNV 1 1 PASS rs957548002 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 66 136346976 136346976 G T 1 0 0 0 0 1 0 0 0 371 991 35 2 2 ADGRG4 23 136346976 Missense_Mutation SNP G C3N-01016_T 34219493 136346976 19693919 363 20512 ADGRG4 0 . GRCh38 X 136347189 136347189 + Silent SNP G G T novel C3N-01016_T C3N-01016_N G G c.3483G>T p.= p.V1161V ENST00000394143 6/26 159 74 85 111 111 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; T ENST00000394143 Transcript synonymous_variant 3774/9931 3483/9243 1161/3080 V gtG/gtT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 6/26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 66 136347189 136347189 G T 1 0 0 0 0 0 0 0 1 371 1277 45 2 2 ADGRG4 23 136347189 Silent SNP G C3N-01016_T 213 136347189 19693706 364 20513 HSFX2 0 . GRCh38 X 149594565 149594565 + Missense_Mutation SNP G G C novel C3N-01016_T C3N-01016_N G G c.136C>G p.Pro46Ala p.P46A ENST00000598963 1/2 67 46 21 59 59 0 strelka-varscan-mutect HSFX2,missense_variant,p.Pro46Ala,ENST00000598963,NM_001164415.2;TMEM185A,downstream_gene_variant,,ENST00000600449,NM_032508.3;TMEM185A,downstream_gene_variant,,ENST00000611119,NM_001174092.2;TMEM185A,downstream_gene_variant,,ENST00000613273,;TMEM185A,downstream_gene_variant,,ENST00000502858,;TMEM185A,downstream_gene_variant,,ENST00000616857,;TMEM185A,downstream_gene_variant,,ENST00000612022,; C ENST00000598963 Transcript missense_variant 152/1365 136/1272 46/423 P/A Cct/Gct 1 -1 HSFX2 HGNC HGNC:32701 protein_coding YES CCDS48179.1 ENSP00000469223 Q9UBD0 A0A140VK21 UPI000007033B NM_001164415.2 tolerated(0.8) 1/2 hmmpanther:PTHR10015,hmmpanther:PTHR10015:SF163 MODERATE 1 SNV 1 1 PASS . . 25 183 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 66 149594565 149594565 G C 1 0 0 0 0 1 0 0 0 7295 1232 43 4 4 HSFX2 23 149594565 Missense_Mutation SNP G C3N-01016_T 13247376 149594565 6446330 365 20514 ATP2B3 0 . GRCh38 X 153560832 153560832 + Missense_Mutation SNP G G T novel C3N-01016_T C3N-01016_N G G c.2996G>T p.Gly999Val p.G999V ENST00000263519 17/20 259 105 154 222 222 0 strelka-varscan-mutect ATP2B3,missense_variant,p.Gly985Val,ENST00000370186,;ATP2B3,missense_variant,p.Gly999Val,ENST00000263519,NM_001001344.2;ATP2B3,missense_variant,p.Gly999Val,ENST00000349466,;ATP2B3,missense_variant,p.Gly999Val,ENST00000359149,NM_021949.3;ATP2B3,missense_variant,p.Gly985Val,ENST00000393842,;ATP2B3,downstream_gene_variant,,ENST00000460549,; T ENST00000263519 Transcript missense_variant 3122/6420 2996/3663 999/1220 G/V gGc/gTc 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 deleterious(0) 17/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00689,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 66 153560832 153560832 G T 1 0 0 0 0 1 0 0 0 1294 1203 42 2 2 ATP2B3 23 153560832 Missense_Mutation SNP G C3N-01016_T 3966267 153560832 2480063 366 20515 KIF2C 0 . GRCh38 1 44760648 44760648 + Silent SNP G G A novel C3N-01021_T C3N-01021_N G G c.1629G>A p.= p.K543K ENST00000372224 16/21 383 352 31 344 344 0 strelka-varscan-mutect KIF2C,synonymous_variant,p.=,ENST00000372217,NM_001297657.1,NM_001297656.1;KIF2C,synonymous_variant,p.=,ENST00000372224,NM_006845.3,NM_001297655.1;KIF2C,synonymous_variant,p.=,ENST00000423289,;KIF2C,downstream_gene_variant,,ENST00000452259,;KIF2C,downstream_gene_variant,,ENST00000455186,;RP11-269F19.2,intron_variant,,ENST00000428791,;RP11-269F19.2,intron_variant,,ENST00000440985,;KIF2C,downstream_gene_variant,,ENST00000493027,;KIF2C,upstream_gene_variant,,ENST00000472235,; A ENST00000372224 Transcript synonymous_variant 1742/2879 1629/2178 543/725 K aaG/aaA 1 1 KIF2C HGNC HGNC:6393 protein_coding YES CCDS512.1 ENSP00000361298 Q99661 A0A140VKF1 UPI000012DDAD NM_006845.3,NM_001297655.1 16/21 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF454,hmmpanther:PTHR24115,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 67 44760648 44760648 G A 1 0 0 0 0 0 0 0 1 8164 962 34 3 3 KIF2C 1 44760648 Silent SNP G C3N-01021_T 44760648 204195774 1 20516 MOV10 0 . GRCh38 1 112694587 112694587 + Missense_Mutation SNP C C T novel C3N-01021_T C3N-01021_N C C c.1430C>T p.Ala477Val p.A477V ENST00000413052 9/21 74 47 27 112 112 0 strelka-mutect MOV10,missense_variant,p.Ala421Val,ENST00000369644,NM_001286072.1;MOV10,missense_variant,p.Ala477Val,ENST00000413052,NM_020963.4;MOV10,missense_variant,p.Ala477Val,ENST00000369645,NM_001321324.1,NM_001130079.2;MOV10,missense_variant,p.Ala477Val,ENST00000357443,;RP11-426L16.3,non_coding_transcript_exon_variant,,ENST00000421943,;MOV10,non_coding_transcript_exon_variant,,ENST00000468624,;MOV10,non_coding_transcript_exon_variant,,ENST00000496577,;MOV10,upstream_gene_variant,,ENST00000490413,;MOV10,upstream_gene_variant,,ENST00000488160,;MOV10,upstream_gene_variant,,ENST00000471160,;MOV10,downstream_gene_variant,,ENST00000479858,;MOV10,upstream_gene_variant,,ENST00000482545,;MOV10,upstream_gene_variant,,ENST00000481711,; T ENST00000413052 Transcript missense_variant 1820/3641 1430/3012 477/1003 A/V gCa/gTa 1 1 MOV10 HGNC HGNC:7200 protein_coding YES CCDS853.1 ENSP00000399797 Q9HCE1 UPI000012FA84 NM_020963.4 tolerated(0.25) 9/21 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF322 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 112694587 112694587 C T 1 0 0 0 0 1 0 0 0 9680 710 25 3 3 MOV10 1 112694587 Missense_Mutation SNP C C3N-01021_T 67933939 112694587 136261835 2 20517 SNX27 0 . GRCh38 1 151683395 151683395 + Missense_Mutation SNP G G A C3N-01021_T C3N-01021_N G G c.1189G>A p.Glu397Lys p.E397K ENST00000368843 8/12 279 189 90 224 224 0 strelka-varscan SNX27,missense_variant,p.Glu397Lys,ENST00000368843,NM_030918.5;SNX27,missense_variant,p.Glu397Lys,ENST00000458013,;SNX27,missense_variant,p.Glu304Lys,ENST00000368838,;SNX27,3_prime_UTR_variant,,ENST00000368841,; A ENST00000368843 Transcript missense_variant 1309/7197 1189/1587 397/528 E/K Gaa/Aaa COSM895881 1 1 SNX27 HGNC HGNC:20073 protein_coding YES CCDS1001.1 ENSP00000357836 Q96L92 UPI00001A962E NM_030918.5 tolerated(0.14) 8/12 hmmpanther:PTHR12431,hmmpanther:PTHR12431:SF17 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 151683395 151683395 G A 1 0 0 0 0 1 0 0 0 15218 943 33 3 3 SNX27 1 151683395 Missense_Mutation SNP G C3N-01021_T 38988808 151683395 97273027 3 20518 FLG 0 . GRCh38 1 152313790 152313790 + Missense_Mutation SNP G G T rs371936330 C3N-01021_T C3N-01021_N G G c.1096C>A p.Arg366Ser p.R366S ENST00000368799 3/3 649 595 54 678 677 1 strelka-varscan FLG,missense_variant,p.Arg366Ser,ENST00000368799,NM_002016.1;FLG-AS1,non_coding_transcript_exon_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 1132/12747 1096/12186 366/4061 R/S Cgt/Agt rs371936330 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.06) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 152313790 152313790 G T 1 0 0 0 0 1 0 0 0 5784 1058 37 1 1 FLG 1 152313790 Missense_Mutation SNP G C3N-01021_T 630395 152313790 96642632 4 20519 CRNN 0 . GRCh38 1 152410078 152410078 + Missense_Mutation SNP C C T C3N-01021_T C3N-01021_N C C c.1004G>A p.Arg335Lys p.R335K ENST00000271835 3/3 353 305 48 302 301 1 strelka-varscan CRNN,missense_variant,p.Arg335Lys,ENST00000271835,NM_016190.2;FLG-AS1,intron_variant,,ENST00000411804,;FLG-AS1,downstream_gene_variant,,ENST00000628475,; T ENST00000271835 Transcript missense_variant 1067/1902 1004/1488 335/495 R/K aGg/aAg COSM3862784 1 -1 CRNN HGNC HGNC:1230 protein_coding YES CCDS1010.1 ENSP00000271835 Q9UBG3 UPI000006E106 NM_016190.2 tolerated(0.25) 3/3 hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF26 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 152410078 152410078 C T 1 0 0 0 0 1 0 0 0 3693 681 24 3 3 CRNN 1 152410078 Missense_Mutation SNP C C3N-01021_T 96288 152410078 96546344 5 20520 HADHB 0 . GRCh38 2 26254274 26254274 + Missense_Mutation SNP C C G rs866708381 C3N-01021_T C3N-01021_N C C c.20C>G p.Pro7Arg p.P7R ENST00000317799 2/16 428 360 68 448 448 0 strelka-varscan HADHB,missense_variant,p.Pro7Arg,ENST00000537713,NM_001281512.1;HADHB,missense_variant,p.Pro7Arg,ENST00000317799,NM_000183.2;HADHB,missense_variant,p.Pro7Arg,ENST00000405867,;HADHB,missense_variant,p.Pro7Arg,ENST00000425035,;HADHB,missense_variant,p.Pro7Arg,ENST00000412805,;HADHB,missense_variant,p.Pro7Arg,ENST00000448743,;HADHB,non_coding_transcript_exon_variant,,ENST00000479347,; G ENST00000317799 Transcript missense_variant 124/2044 20/1425 7/474 P/R cCc/cGc rs866708381 1 1 HADHB HGNC HGNC:4803 protein_coding YES CCDS1722.1 ENSP00000325136 P55084 UPI0000129B6F NM_000183.2 tolerated_low_confidence(0.12) 2/16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 67 26254274 26254274 C G 1 0 0 0 0 1 0 0 0 6830 623 22 4 4 HADHB 2 26254274 Missense_Mutation SNP C C3N-01021_T 26254274 215939255 6 20521 DHX57 0 . GRCh38 2 38826551 38826551 + Frame_Shift_Del DEL G G - rs576995265 C3N-01021_T C3N-01021_N G G c.2778delC p.Tyr927MetfsTer8 p.Y927Mfs*8 ENST00000457308 15/24 146 127 19 175 175 0 sindel-varindel-pindel DHX57,frameshift_variant,p.Tyr927MetfsTer8,ENST00000457308,NM_198963.1;DHX57,frameshift_variant,p.Tyr251MetfsTer8,ENST00000452978,;DHX57,3_prime_UTR_variant,,ENST00000620517,;DHX57,non_coding_transcript_exon_variant,,ENST00000622155,; - ENST00000457308 Transcript frameshift_variant 2906/4859 2778/4161 926/1386 V/X gtC/gt rs576995265 1 -1 DHX57 HGNC HGNC:20086 protein_coding YES CCDS1800.1 ENSP00000405111 Q6P158 UPI0000231C8C NM_198963.1 15/24 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF145,SMART_domains:SM00490,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 67 38826551 38826551 G - 1 0 1 0 1 0 0 0 0 4317 929 33 0 0 DHX57 2 38826551 Frame_Shift_Del DEL G C3N-01021_T 12572277 38826551 203366978 7 20522 DNAH6 0 . GRCh38 2 84548336 84548336 + Missense_Mutation SNP A A T novel C3N-01021_T C3N-01021_N A A c.1235A>T p.Glu412Val p.E412V ENST00000389394 8/77 246 227 19 263 263 0 strelka-varscan-mutect DNAH6,missense_variant,p.Glu412Val,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Glu412Val,ENST00000237449,;DNAH6,downstream_gene_variant,,ENST00000468661,;DNAH6,non_coding_transcript_exon_variant,,ENST00000476689,;DNAH6,non_coding_transcript_exon_variant,,ENST00000494025,; T ENST00000389394 Transcript missense_variant 1372/12795 1235/12477 412/4158 E/V gAg/gTg 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 tolerated(0.07) 8/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 84548336 84548336 A T 1 0 0 0 0 1 0 0 0 4420 304 11 4 4 DNAH6 2 84548336 Missense_Mutation SNP A C3N-01021_T 45721785 84548336 157645193 8 20523 SPC25 0 . GRCh38 2 168871484 168871484 + Missense_Mutation SNP A A G novel C3N-01021_T C3N-01021_N A A c.622T>C p.Ser208Pro p.S208P ENST00000282074 7/7 166 141 25 217 217 0 strelka-varscan-mutect SPC25,missense_variant,p.Ser208Pro,ENST00000282074,NM_020675.3;SPC25,intron_variant,,ENST00000479309,; G ENST00000282074 Transcript missense_variant 764/1354 622/675 208/224 S/P Tca/Cca 1 -1 SPC25 HGNC HGNC:24031 protein_coding YES CCDS2229.1 ENSP00000282074 Q9HBM1 UPI000006D2C9 NM_020675.3 tolerated(0.05) 7/7 hmmpanther:PTHR14281:SF0,hmmpanther:PTHR14281,Pfam_domain:PF08234 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 67 168871484 168871484 A G 1 0 0 0 0 1 0 0 0 15368 246 9 5 5 SPC25 2 168871484 Missense_Mutation SNP A C3N-01021_T 84323148 168871484 73322045 9 20524 FASTKD1 0 . GRCh38 2 169540078 169540078 + Missense_Mutation SNP A A C rs755078934 C3N-01021_T C3N-01021_N A A c.1918T>G p.Leu640Val p.L640V ENST00000453153 10/15 156 132 24 133 133 0 strelka-varscan-mutect FASTKD1,missense_variant,p.Leu640Val,ENST00000453153,NM_024622.4;FASTKD1,missense_variant,p.Leu640Val,ENST00000453929,NM_001281476.1;FASTKD1,non_coding_transcript_exon_variant,,ENST00000495505,;FASTKD1,non_coding_transcript_exon_variant,,ENST00000490590,;FASTKD1,upstream_gene_variant,,ENST00000488516,; C ENST00000453153 Transcript missense_variant 2265/2967 1918/2544 640/847 L/V Tta/Gta rs755078934 1 -1 FASTKD1 HGNC HGNC:26150 protein_coding YES CCDS33318.1 ENSP00000400513 Q53R41 UPI000050BC4D NM_024622.4 deleterious(0) 10/15 hmmpanther:PTHR21228:SF29,hmmpanther:PTHR21228,Pfam_domain:PF06743 MODERATE 1 SNV 1 1 PASS rs755078934 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 67 169540078 169540078 A C 1 0 0 0 0 1 0 0 0 5545 69 3 5 5 FASTKD1 2 169540078 Missense_Mutation SNP A C3N-01021_T 668594 169540078 72653451 10 20525 PID1 0 . GRCh38 2 229025926 229025926 + Missense_Mutation SNP C C A novel C3N-01021_T C3N-01021_N C C c.453G>T p.Glu151Asp p.E151D ENST00000392054 4/4 292 254 38 324 323 1 strelka-varscan PID1,missense_variant,p.Glu151Asp,ENST00000392054,NM_017933.4;PID1,missense_variant,p.Glu120Asp,ENST00000392055,NM_001100818.1;PID1,missense_variant,p.Glu71Asp,ENST00000409462,;PID1,missense_variant,p.Glu153Asp,ENST00000354069,;PID1,intron_variant,,ENST00000482518,;PID1,downstream_gene_variant,,ENST00000534952,; A ENST00000392054 Transcript missense_variant 793/2745 453/747 151/248 E/D gaG/gaT 1 -1 PID1 HGNC HGNC:26084 protein_coding YES CCDS2471.1 ENSP00000375907 Q7Z2X4 UPI00001C0AF7 NM_017933.4 tolerated(0.17) 4/4 hmmpanther:PTHR16265:SF1,hmmpanther:PTHR16265,Pfam_domain:PF14719,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 229025926 229025926 C A 1 0 0 0 0 1 0 0 0 11972 680 24 2 2 PID1 2 229025926 Missense_Mutation SNP C C3N-01021_T 59485848 229025926 13167603 11 20526 RTP2 0 . GRCh38 3 187698972 187698972 + Silent SNP G G A novel C3N-01021_T C3N-01021_N G G c.204C>T p.= p.A68A ENST00000358241 2/2 33 27 6 54 54 0 strelka-varscan-mutect RTP2,synonymous_variant,p.=,ENST00000358241,NM_001004312.2;RP11-211G3.3,upstream_gene_variant,,ENST00000449623,;RP11-211G3.3,upstream_gene_variant,,ENST00000437407,; A ENST00000358241 Transcript synonymous_variant 633/1346 204/678 68/225 A gcC/gcT 1 -1 RTP2 HGNC HGNC:32486 protein_coding YES CCDS33911.1 ENSP00000350976 Q5QGT7 UPI00001D801A NM_001004312.2 2/2 hmmpanther:PTHR14402:SF18,hmmpanther:PTHR14402,Pfam_domain:PF13695,SMART_domains:SM01328 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.12455 1 1 1 1 0 A 2 1 67 187698972 187698972 G A 1 0 0 0 0 0 0 0 1 13994 1219 43 3 3 RTP2 3 187698972 Silent SNP G C3N-01021_T 187698972 10596587 12 20527 ENPEP 0 . GRCh38 4 110561463 110561463 + Missense_Mutation SNP C C A novel C3N-01021_T C3N-01021_N C C c.2779C>A p.Gln927Lys p.Q927K ENST00000265162 20/20 348 330 18 355 355 0 strelka-varscan ENPEP,missense_variant,p.Gln927Lys,ENST00000265162,NM_001977.3;ENPEP,non_coding_transcript_exon_variant,,ENST00000504100,; A ENST00000265162 Transcript missense_variant 3121/6943 2779/2874 927/957 Q/K Caa/Aaa 1 1 ENPEP HGNC HGNC:3355 protein_coding YES CCDS3691.1 ENSP00000265162 Q07075 UPI000013D5C6 NM_001977.3 deleterious(0.02) 20/20 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF188 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 110561463 110561463 C A 1 0 0 0 0 1 0 0 0 4973 479 17 2 2 ENPEP 4 110561463 Missense_Mutation SNP C C3N-01021_T 110561463 79653092 13 20528 EGFR 0 . GRCh38 7 55174015 55174015 + Missense_Mutation SNP G G C rs121913428 C3N-01021_T C3N-01021_N G G c.2156G>C p.Gly719Ala p.G719A ENST00000275493 18/28 362 283 79 415 415 0 strelka-varscan-mutect EGFR,missense_variant,p.Gly719Ala,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Gly674Ala,ENST00000454757,;EGFR,missense_variant,p.Gly674Ala,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1; C ENST00000275493 Transcript missense_variant 2333/9821 2156/3633 719/1210 G/A gGc/gCc rs121913428,COSM18425,COSM20848,COSM6239 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 18/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913428 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 67 55174015 55174015 G C 1 0 0 0 0 1 0 0 0 4803 1203 42 4 4 EGFR 7 55174015 Missense_Mutation SNP G C3N-01021_T 55174015 104171958 14 20529 EGFR 0 . GRCh38 7 55191831 55191831 + Missense_Mutation SNP T T A rs121913444 C3N-01021_T C3N-01021_N T T c.2582T>A p.Leu861Gln p.L861Q ENST00000275493 21/28 561 457 104 624 624 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu861Gln,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu816Gln,ENST00000454757,;EGFR,missense_variant,p.Leu816Gln,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; A ENST00000275493 Transcript missense_variant 2759/9821 2582/3633 861/1210 L/Q cTg/cAg rs121913444,COSM12374,COSM6213 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 uncertain_significance,drug_response 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs121913444 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 55191831 55191831 T A 1 0 0 0 0 1 0 0 0 4803 1580 55 4 4 EGFR 7 55191831 Missense_Mutation SNP T C3N-01021_T 17816 55191831 104154142 15 20530 EPHA1 0 . GRCh38 7 143397330 143397330 + Missense_Mutation SNP C C A rs555587376 C3N-01021_T C3N-01021_N C C c.1745G>T p.Arg582Leu p.R582L ENST00000275815 10/18 101 87 14 125 125 0 strelka-varscan-mutect EPHA1,missense_variant,p.Arg582Leu,ENST00000275815,NM_005232.4;EPHA1,non_coding_transcript_exon_variant,,ENST00000488068,;EPHA1,downstream_gene_variant,,ENST00000497891,;EPHA1,upstream_gene_variant,,ENST00000494989,;EPHA1,upstream_gene_variant,,ENST00000465208,;EPHA1,downstream_gene_variant,,ENST00000479459,; A ENST00000275815 Transcript missense_variant 1832/3363 1745/2931 582/976 R/L cGt/cTt rs555587376 1 -1 EPHA1 HGNC HGNC:3385 protein_coding YES CCDS5884.1 ENSP00000275815 P21709 UPI000013DA82 NM_005232.4 tolerated(0.12) 10/18 Low_complexity_(Seg):seg,hmmpanther:PTHR24416:SF28,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Pfam_domain:PF14575 MODERATE 1 SNV 1 1 PASS rs555587376 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 67 143397330 143397330 C A 1 0 0 0 0 1 0 0 0 5012 536 19 1 1 EPHA1 7 143397330 Missense_Mutation SNP C C3N-01021_T 88205499 143397330 15948643 16 20531 OR2A12 0 . GRCh38 7 144095706 144095706 + Missense_Mutation SNP C C T rs770997909 C3N-01021_T C3N-01021_N C C c.599C>T p.Ala200Val p.A200V ENST00000408949 1/1 417 341 76 469 469 0 strelka-varscan-mutect OR2A12,missense_variant,p.Ala200Val,ENST00000408949,NM_001004135.1; T ENST00000408949 Transcript missense_variant 659/1046 599/933 200/310 A/V gCg/gTg rs770997909,COSM41029 1 1 OR2A12 HGNC HGNC:15082 protein_coding YES CCDS43670.1 ENSP00000386174 Q8NGT7 A4D2G4 UPI0000061E6F NM_001004135.1 tolerated(0.36) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF50,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs770997909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 144095706 144095706 C T 1 0 0 0 0 1 0 0 0 11052 768 27 1 1 OR2A12 7 144095706 Missense_Mutation SNP C C3N-01021_T 698376 144095706 15250267 17 20532 ITGA8 0 . GRCh38 10 15608279 15608279 + Missense_Mutation SNP C C G novel C3N-01021_T C3N-01021_N C C c.1565G>C p.Arg522Thr p.R522T ENST00000378076 16/30 170 161 9 146 146 0 strelka-varscan-mutect ITGA8,missense_variant,p.Arg522Thr,ENST00000378076,NM_003638.2,NM_001291494.1;ITGA8,upstream_gene_variant,,ENST00000477064,;ITGA8,downstream_gene_variant,,ENST00000468882,; G ENST00000378076 Transcript missense_variant 1919/6755 1565/3192 522/1063 R/T aGa/aCa 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 tolerated(0.25) 16/30 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs1424172876 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 67 15608279 15608279 C G 1 0 0 0 0 1 0 0 0 7789 913 32 4 4 ITGA8 10 15608279 Missense_Mutation SNP C C3N-01021_T 15608279 118189143 18 20533 MAP6 0 . GRCh38 11 75668263 75668263 + Missense_Mutation SNP G G T novel C3N-01021_T C3N-01021_N G G c.107C>A p.Ala36Asp p.A36D ENST00000304771 1/4 185 173 12 208 208 0 strelka-varscan-mutect MAP6,missense_variant,p.Ala36Asp,ENST00000434603,NM_207577.1;MAP6,missense_variant,p.Ala36Asp,ENST00000304771,NM_033063.1;MAP6,intron_variant,,ENST00000526740,; T ENST00000304771 Transcript missense_variant 858/3334 107/2442 36/813 A/D gCc/gAc 1 -1 MAP6 HGNC HGNC:6868 protein_coding YES CCDS31641.1 ENSP00000307093 Q96JE9 UPI0000251E6A NM_033063.1 deleterious(0.04) 1/4 hmmpanther:PTHR14759,hmmpanther:PTHR14759:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -15.50489 0.9999996 1 1 1 0 T 3 4 67 75668263 75668263 G T 1 0 0 0 0 1 0 0 0 9188 1203 42 2 2 MAP6 11 75668263 Missense_Mutation SNP G C3N-01021_T 75668263 59418359 19 20534 SALL2 0 . GRCh38 14 21523598 21523598 + Silent SNP G G A C3N-01021_T C3N-01021_N G G c.2130C>T p.= p.V710V ENST00000614342 2/2 215 163 52 215 215 0 strelka-varscan-mutect SALL2,synonymous_variant,p.=,ENST00000614342,NM_005407.2;SALL2,synonymous_variant,p.=,ENST00000450879,NM_001291447.1;SALL2,synonymous_variant,p.=,ENST00000546363,NM_001291446.1;SALL2,intron_variant,,ENST00000613414,;SALL2,intron_variant,,ENST00000611430,;SALL2,downstream_gene_variant,,ENST00000537235,;SALL2,downstream_gene_variant,,ENST00000541965,;AE000658.22,downstream_gene_variant,,ENST00000535893,; A ENST00000614342 Transcript synonymous_variant 2425/4942 2130/3024 710/1007 V gtC/gtT COSM432843 1 -1 SALL2 HGNC HGNC:10526 protein_coding YES CCDS32045.1 ENSP00000483562 Q9Y467 UPI0000135524 NM_005407.2 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF15,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF12874,SMART_domains:SM00355 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 67 21523598 21523598 G A 1 0 0 0 0 0 0 0 1 14070 1161 41 3 3 SALL2 14 21523598 Silent SNP G C3N-01021_T 21523598 85520120 20 20535 SPTBN5 0 . GRCh38 15 41887267 41887267 + Nonsense_Mutation SNP G G T novel C3N-01021_T C3N-01021_N G G c.834C>A p.Tyr278Ter p.Y278* ENST00000320955 6/68 380 339 41 439 438 1 strelka-varscan-mutect SPTBN5,stop_gained,p.Tyr278Ter,ENST00000320955,NM_016642.3; T ENST00000320955 Transcript stop_gained 1062/11725 834/11025 278/3674 Y/* taC/taA 1 -1 SPTBN5 HGNC HGNC:15680 protein_coding YES CCDS61599.1 ENSP00000317790 Q9NRC6 UPI0000E59BE4 NM_016642.3 6/68 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF265,Gene3D:1.10.418.10,Pfam_domain:PF00307,Superfamily_domains:SSF47576 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 67 41887267 41887267 G T 1 0 0 0 0 0 1 0 0 15478 1256 44 2 2 SPTBN5 15 41887267 Nonsense_Mutation SNP G C3N-01021_T 41887267 60103922 21 20536 RBFOX1 0 . GRCh38 16 7709077 7709077 + Silent SNP C C T rs148909710 C3N-01021_T C3N-01021_N C C c.1146C>T p.= p.A382A ENST00000422070 15/16 270 239 31 290 290 0 strelka-varscan-mutect RBFOX1,missense_variant,p.Pro400Leu,ENST00000547372,;RBFOX1,missense_variant,p.Pro378Leu,ENST00000355637,NM_145893.2;RBFOX1,missense_variant,p.Pro314Leu,ENST00000535565,;RBFOX1,missense_variant,p.Pro374Leu,ENST00000552089,;RBFOX1,missense_variant,p.Pro57Leu,ENST00000567470,;RBFOX1,synonymous_variant,p.=,ENST00000550418,NM_018723.3;RBFOX1,synonymous_variant,p.=,ENST00000340209,;RBFOX1,synonymous_variant,p.=,ENST00000620507,;RBFOX1,synonymous_variant,p.=,ENST00000311745,NM_145891.2;RBFOX1,synonymous_variant,p.=,ENST00000553186,NM_001142333.1;RBFOX1,synonymous_variant,p.=,ENST00000422070,NM_001308117.1;RBFOX1,synonymous_variant,p.=,ENST00000436368,NM_145892.2;RBFOX1,synonymous_variant,p.=,ENST00000547338,NM_001142334.1;RBFOX1,non_coding_transcript_exon_variant,,ENST00000570188,; T ENST00000422070 Transcript synonymous_variant 1342/1684 1146/1278 382/425 A gcC/gcT rs148909710,COSM973908,COSM973909 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 15/16 hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932,Pfam_domain:PF12414 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs148909710 . 0 207 0 3 0 0 0 0 -20 0.999989 1 1 1 0 T 2 4 67 7709077 7709077 C T 1 0 0 0 0 0 0 0 1 13271 652 23 1 1 RBFOX1 16 7709077 Silent SNP C C3N-01021_T 7709077 82629268 22 20537 CBLN1 0 . GRCh38 16 49281346 49281346 + Silent SNP G G A C3N-01021_T C3N-01021_N G G c.120C>T p.= p.S40S ENST00000219197 1/3 213 145 68 195 195 0 strelka-varscan-mutect CBLN1,synonymous_variant,p.=,ENST00000219197,NM_004352.3;CBLN1,synonymous_variant,p.=,ENST00000536749,;CBLN1,synonymous_variant,p.=,ENST00000564786,; A ENST00000219197 Transcript synonymous_variant 486/2435 120/582 40/193 S tcC/tcT COSM3509915 1 -1 CBLN1 HGNC HGNC:1543 protein_coding YES CCDS10736.1 ENSP00000219197 P23435 UPI0000127506 NM_004352.3 1/3 hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 67 49281346 49281346 G A 1 0 0 0 0 0 0 0 1 2405 1335 47 3 3 CBLN1 16 49281346 Silent SNP G C3N-01021_T 41572269 49281346 41056999 23 20538 RAD51C 0 . GRCh38 17 58703235 58703235 + Missense_Mutation SNP T T G novel C3N-01021_T C3N-01021_N T T c.611T>G p.Ile204Ser p.I204S ENST00000337432 4/9 320 253 67 273 273 0 strelka-varscan-mutect RAD51C,missense_variant,p.Ile204Ser,ENST00000337432,NM_058216.2;RAD51C,missense_variant,p.Ile204Ser,ENST00000583539,;RAD51C,missense_variant,p.Ile84Ser,ENST00000413590,;RAD51C,missense_variant,p.Ile87Ser,ENST00000461271,;RAD51C,missense_variant,p.Ile136Ser,ENST00000425173,;RAD51C,downstream_gene_variant,,ENST00000622327,;RAD51C,non_coding_transcript_exon_variant,,ENST00000487921,;RAD51C,3_prime_UTR_variant,,ENST00000475762,;RAD51C,3_prime_UTR_variant,,ENST00000487525,;RAD51C,3_prime_UTR_variant,,ENST00000482007,;RAD51C,3_prime_UTR_variant,,ENST00000584617,; G ENST00000337432 Transcript missense_variant 682/2591 611/1131 204/376 I/S aTt/aGt 1 1 RAD51C HGNC HGNC:9820 protein_coding YES CCDS11611.1 ENSP00000336701 O43502 UPI0000133007 NM_058216.2 deleterious(0) 4/9 PROSITE_profiles:PS50162,hmmpanther:PTHR22942:SF14,hmmpanther:PTHR22942,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005856,Pfam_domain:PF08423,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 67 58703235 58703235 T G 1 0 0 0 0 1 0 0 0 13150 1493 52 5 5 RAD51C 17 58703235 Missense_Mutation SNP T C3N-01021_T 58703235 24554206 24 20539 IMPACT 0 . GRCh38 18 24430356 24430356 + Missense_Mutation SNP T T A novel C3N-01021_T C3N-01021_N T T c.253T>A p.Leu85Ile p.L85I ENST00000284202 4/11 182 154 28 186 186 0 strelka-varscan-mutect IMPACT,missense_variant,p.Leu85Ile,ENST00000284202,NM_018439.3;IMPACT,missense_variant,p.Leu67Ile,ENST00000585067,;IMPACT,missense_variant,p.Leu85Ile,ENST00000578221,;Y_RNA,downstream_gene_variant,,ENST00000362766,;IMPACT,non_coding_transcript_exon_variant,,ENST00000580706,; A ENST00000284202 Transcript missense_variant 394/3792 253/963 85/320 L/I Tta/Ata 1 1 IMPACT HGNC HGNC:20387 protein_coding YES CCDS11886.1 ENSP00000284202 Q9P2X3 UPI000007006B NM_018439.3 tolerated(0.08) 4/11 Gene3D:3.10.110.10,Pfam_domain:PF05773,PROSITE_profiles:PS50908,hmmpanther:PTHR16301,hmmpanther:PTHR16301:SF6,SMART_domains:SM00591,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 24430356 24430356 T A 1 0 0 0 0 1 0 0 0 7626 1838 64 4 4 IMPACT 18 24430356 Missense_Mutation SNP T C3N-01021_T 24430356 55942929 25 20540 MUC16 0 . GRCh38 19 8966376 8966376 + Missense_Mutation SNP G G A novel C3N-01021_T C3N-01021_N G G c.10394C>T p.Pro3465Leu p.P3465L ENST00000397910 3/84 434 369 65 420 420 0 strelka-varscan-mutect MUC16,missense_variant,p.Pro3465Leu,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 10598/43816 10394/43524 3465/14507 P/L cCc/cTc 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 67 8966376 8966376 G A 1 0 0 0 0 1 0 0 0 9972 1232 43 3 3 MUC16 19 8966376 Missense_Mutation SNP G C3N-01021_T 8966376 49651240 26 20541 ATP4A 0 . GRCh38 19 35560573 35560573 + Missense_Mutation SNP C C T rs781628677 C3N-01021_T C3N-01021_N C C c.577G>A p.Ala193Thr p.A193T ENST00000262623 6/22 201 169 32 177 177 0 strelka-varscan-mutect ATP4A,missense_variant,p.Ala193Thr,ENST00000262623,NM_000704.2;ATP4A,upstream_gene_variant,,ENST00000592131,;ATP4A,upstream_gene_variant,,ENST00000592767,;ATP4A,downstream_gene_variant,,ENST00000590916,; T ENST00000262623 Transcript missense_variant 606/3709 577/3108 193/1035 A/T Gct/Act rs781628677,COSM4752759 1 -1 ATP4A HGNC HGNC:819 protein_coding YES CCDS12467.1 ENSP00000262623 P20648 UPI000016A49B NM_000704.2 tolerated(0.12) 6/22 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF251,Pfam_domain:PF00122,TIGRFAM_domain:TIGR01106,Gene3D:2.70.150.10,Superfamily_domains:0049471 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781628677 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 67 35560573 35560573 C T 1 0 0 0 0 1 0 0 0 1298 768 27 1 1 ATP4A 19 35560573 Missense_Mutation SNP C C3N-01021_T 26594197 35560573 23057043 27 20542 CCDC8 0 . GRCh38 19 46411370 46411371 + Frame_Shift_Del DEL GG GG - novel C3N-01021_T C3N-01021_N GG GG c.1440_1441delCC p.Phe480LeufsTer50 p.F480Lfs*50 ENST00000307522 1/1 329 300 29 368 368 0 sindel-varindel-pindel CCDC8,frameshift_variant,p.Phe480LeufsTer50,ENST00000307522,NM_032040.4; - ENST00000307522 Transcript frameshift_variant 2214-2215/3213 1440-1441/1617 480-481/538 FQ/LX ttCCag/ttag 1 -1 CCDC8 HGNC HGNC:25367 protein_coding YES CCDS12685.1 ENSP00000303158 Q9H0W5 UPI00000730F2 NM_032040.4 1/1 hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF2 HIGH 1 deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 67 46411370 46411370 GG - 1 0 1 0 1 0 0 0 0 2551 1357 47 0 0 CCDC8 19 46411370 Frame_Shift_Del DEL GG C3N-01021_T 10850797 46411370 12206246 28 20543 CDH4 0 . GRCh38 20 61844676 61844676 + Silent SNP C C T rs374076466 C3N-01021_T C3N-01021_N C C c.585C>T p.= p.S195S ENST00000614565 5/16 69 55 14 90 90 0 strelka-varscan-mutect CDH4,synonymous_variant,p.=,ENST00000614565,NM_001794.4;CDH4,synonymous_variant,p.=,ENST00000611855,;CDH4,synonymous_variant,p.=,ENST00000543233,NM_001252338.2,NM_001252339.2; T ENST00000614565 Transcript synonymous_variant 673/6513 585/2751 195/916 S tcC/tcT rs374076466,COSM5336643 1 1 CDH4 HGNC HGNC:1763 protein_coding YES CCDS13488.1 ENSP00000484928 P55283 UPI000015FE86 NM_001794.4 5/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF81,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 LOW 1 SNV 1 0,1 1 PASS rs374076466 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 67 61844676 61844676 C T 1 0 0 0 0 0 0 0 1 2815 639 23 1 1 CDH4 20 61844676 Silent SNP C C3N-01021_T 61844676 2599491 29 20544 EPHA8 0 . GRCh38 1 22601693 22601693 + Silent SNP C C G C3N-01023_T C3N-01023_N C C c.2970C>G p.= p.T990T ENST00000166244 17/17 332 286 46 286 285 1 strelka-varscan-mutect EPHA8,synonymous_variant,p.=,ENST00000166244,NM_020526.3; G ENST00000166244 Transcript synonymous_variant 3042/4943 2970/3018 990/1005 T acC/acG COSM3667475 1 1 EPHA8 HGNC HGNC:3391 protein_coding YES CCDS225.1 ENSP00000166244 P29322 UPI000012A07B NM_020526.3 17/17 PROSITE_profiles:PS50105,hmmpanther:PTHR24416:SF339,hmmpanther:PTHR24416,Pfam_domain:PF00536,Gene3D:1.10.150.50,PIRSF_domain:PIRSF000666,SMART_domains:SM00454,Superfamily_domains:SSF47769 1 LOW 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 68 22601693 22601693 C G 1 0 0 0 0 0 0 0 1 5020 581 21 4 4 EPHA8 1 22601693 Silent SNP C C3N-01023_T 22601693 226354729 1 20545 PAQR7 0 . GRCh38 1 25863624 25863624 + Silent SNP G G A rs376473466 C3N-01023_T C3N-01023_N G G c.216C>T p.= p.A72A ENST00000374296 2/2 166 140 26 130 130 0 strelka-varscan-mutect PAQR7,synonymous_variant,p.=,ENST00000374296,NM_178422.5;AUNIP,upstream_gene_variant,,ENST00000374298,NM_024037.2;AUNIP,upstream_gene_variant,,ENST00000538789,NM_001287490.1;RP1-125I3.2,downstream_gene_variant,,ENST00000455431,; A ENST00000374296 Transcript synonymous_variant 883/3297 216/1041 72/346 A gcC/gcT rs376473466,COSM51607 1 -1 PAQR7 HGNC HGNC:23146 protein_coding YES CCDS267.1 ENSP00000363414 Q86WK9 UPI000000D789 NM_178422.5 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR20855:SF41,hmmpanther:PTHR20855,Pfam_domain:PF03006 0,1 LOW 1 SNV 1 0,1 1 PASS rs376473466 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 25863624 25863624 G A 1 0 0 0 0 0 0 0 1 11520 1103 39 1 1 PAQR7 1 25863624 Silent SNP G C3N-01023_T 3261931 25863624 223092798 2 20546 AGBL4 0 . GRCh38 1 48534256 48534256 + Silent SNP G G T novel C3N-01023_T C3N-01023_N G G c.1429C>A p.= p.R477R ENST00000371839 14/14 162 131 31 114 114 0 strelka-varscan-mutect AGBL4,synonymous_variant,p.=,ENST00000371839,NM_032785.3;AGBL4,synonymous_variant,p.=,ENST00000334103,; T ENST00000371839 Transcript synonymous_variant 1546/2947 1429/1512 477/503 R Cgg/Agg 1 -1 AGBL4 HGNC HGNC:25892 protein_coding YES CCDS44137.1 ENSP00000360905 Q5VU57 UPI00002042F9 NM_032785.3 14/14 hmmpanther:PTHR12756 LOW 1 SNV 2 1 PASS rs947029939 . 0 206 0 4 0 0 0 0 -20 0.9999492 1 1 1 0 T 2 4 68 48534256 48534256 G T 1 0 0 0 0 0 0 0 1 454 1086 38 1 1 AGBL4 1 48534256 Silent SNP G C3N-01023_T 22670632 48534256 200422166 3 20547 BTBD8 0 . GRCh38 1 92080639 92080639 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.68A>T p.Lys23Met p.K23M ENST00000342818 1/9 256 217 39 226 226 0 strelka-varscan-mutect BTBD8,missense_variant,p.Lys23Met,ENST00000636805,;BTBD8,missense_variant,p.Lys23Met,ENST00000342818,NM_183242.3;BTBD8,missense_variant,p.Lys23Met,ENST00000635934,;BTBD8,non_coding_transcript_exon_variant,,ENST00000370382,; T ENST00000342818 Transcript missense_variant 304/1412 68/1137 23/378 K/M aAg/aTg 1 1 BTBD8 HGNC HGNC:21019 protein_coding YES CCDS737.1 ENSP00000343686 Q5XKL5 UPI000014114A NM_183242.3 deleterious(0) 1/9 hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF34 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 92080639 92080639 A T 1 0 0 0 0 1 0 0 0 1723 72 3 4 4 BTBD8 1 92080639 Missense_Mutation SNP A C3N-01023_T 43546383 92080639 156875783 4 20548 TRMT13 0 . GRCh38 1 100148292 100148292 + Missense_Mutation SNP A A G novel C3N-01023_T C3N-01023_N A A c.1216A>G p.Arg406Gly p.R406G ENST00000370141 10/11 115 93 22 90 90 0 strelka-varscan-mutect TRMT13,missense_variant,p.Arg406Gly,ENST00000370141,NM_019083.2;LRRC39,downstream_gene_variant,,ENST00000620882,;LRRC39,downstream_gene_variant,,ENST00000342895,NM_001256387.1;LRRC39,downstream_gene_variant,,ENST00000370138,NM_001256385.1;LRRC39,downstream_gene_variant,,ENST00000370137,NM_001256386.1,NM_144620.3;TRMT13,downstream_gene_variant,,ENST00000493651,;TRMT13,downstream_gene_variant,,ENST00000482437,; G ENST00000370141 Transcript missense_variant 1222/3129 1216/1446 406/481 R/G Aga/Gga 1 1 TRMT13 HGNC HGNC:25502 protein_coding YES CCDS765.1 ENSP00000359160 Q9NUP7 UPI000013CAE6 NM_019083.2 tolerated(0.17) 10/11 hmmpanther:PTHR12998:SF0,hmmpanther:PTHR12998,Pfam_domain:PF05206 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 100148292 100148292 A G 1 0 0 0 0 1 0 0 0 17067 180 7 5 5 TRMT13 1 100148292 Missense_Mutation SNP A C3N-01023_T 8067653 100148292 148808130 5 20549 VAV3 0 . GRCh38 1 107964749 107964749 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.121G>T p.Val41Phe p.V41F ENST00000370056 1/27 254 240 14 219 218 1 strelka-varscan-mutect VAV3,missense_variant,p.Val41Phe,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Val41Phe,ENST00000527011,;VAV3,missense_variant,p.Val36Phe,ENST00000490388,;VAV3-AS1,intron_variant,,ENST00000438318,;VAV3,upstream_gene_variant,,ENST00000469325,;VAV3,upstream_gene_variant,,ENST00000530671,; A ENST00000370056 Transcript missense_variant 396/4990 121/2544 41/847 V/F Gtc/Ttc 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 deleterious(0) 1/27 PROSITE_profiles:PS50021,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Pfam_domain:PF11971,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576,Prints_domain:PR00888 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 107964749 107964749 C A 1 0 0 0 0 1 0 0 0 17678 565 20 2 2 VAV3 1 107964749 Missense_Mutation SNP C C3N-01023_T 7816457 107964749 140991673 6 20550 PPM1J 0 . GRCh38 1 112715098 112715098 + Silent SNP G G T novel C3N-01023_T C3N-01023_N G G c.204C>A p.= p.S68S ENST00000309276 1/10 150 127 23 122 122 0 strelka-varscan-mutect PPM1J,synonymous_variant,p.=,ENST00000309276,NM_005167.5;PPM1J,5_prime_UTR_variant,,ENST00000464951,;RP11-426L16.10,upstream_gene_variant,,ENST00000606505,;RP11-426L16.10,upstream_gene_variant,,ENST00000605933,;RP11-426L16.9,upstream_gene_variant,,ENST00000566195,;RP11-426L16.10,upstream_gene_variant,,ENST00000471038,;PPM1J,synonymous_variant,p.=,ENST00000471106,;PPM1J,synonymous_variant,p.=,ENST00000482367,;PPM1J,non_coding_transcript_exon_variant,,ENST00000486709,;RP11-426L16.10,upstream_gene_variant,,ENST00000607158,;RP11-426L16.10,upstream_gene_variant,,ENST00000606954,; T ENST00000309276 Transcript synonymous_variant 380/1863 204/1518 68/505 S tcC/tcA 1 -1 PPM1J HGNC HGNC:20785 protein_coding YES CCDS855.2 ENSP00000308926 Q5JR12 UPI000013EE69 NM_005167.5 1/10 hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF305 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 112715098 112715098 G T 1 0 0 0 0 0 0 0 1 12452 1335 47 2 2 PPM1J 1 112715098 Silent SNP G C3N-01023_T 4750349 112715098 136241324 7 20551 TBX15 0 . GRCh38 1 118885240 118885240 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.983C>A p.Pro328His p.P328H ENST00000207157 8/8 497 426 71 437 437 0 strelka-varscan-mutect TBX15,missense_variant,p.Pro434His,ENST00000369429,;TBX15,missense_variant,p.Pro328His,ENST00000207157,NM_152380.2;TBX15,missense_variant,p.Pro162His,ENST00000449873,; T ENST00000207157 Transcript missense_variant 1298/3492 983/1491 328/496 P/H cCc/cAc 1 -1 TBX15 HGNC HGNC:11594 protein_coding YES CCDS30816.1 ENSP00000207157 Q96SF7 UPI000046D38E NM_152380.2 tolerated(0.06) 8/8 hmmpanther:PTHR11267:SF98,hmmpanther:PTHR11267 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 118885240 118885240 G T 1 0 0 0 0 1 0 0 0 16057 1232 43 2 2 TBX15 1 118885240 Missense_Mutation SNP G C3N-01023_T 6170142 118885240 130071182 8 20552 FLG2 0 . GRCh38 1 152357544 152357544 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.242T>A p.Leu81Gln p.L81Q ENST00000388718 3/3 422 383 39 203 203 0 strelka-varscan-mutect FLG2,missense_variant,p.Leu81Gln,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 315/9124 242/7176 81/2391 L/Q cTg/cAg 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious(0) 3/3 PROSITE_profiles:PS50222,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 152357544 152357544 A T 1 0 0 0 0 1 0 0 0 5785 188 7 4 4 FLG2 1 152357544 Missense_Mutation SNP A C3N-01023_T 33472304 152357544 96598878 9 20553 TPM3 0 . GRCh38 1 154191968 154191968 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.51G>T p.Glu17Asp p.E17D ENST00000368530 1/10 733 667 66 451 450 1 strelka-varscan-mutect TPM3,missense_variant,p.Glu17Asp,ENST00000368530,NM_152263.3;TPM3,missense_variant,p.Glu17Asp,ENST00000271850,;TPM3,missense_variant,p.Glu17Asp,ENST00000515609,;MIR190B,downstream_gene_variant,,ENST00000401119,;TPM3,upstream_gene_variant,,ENST00000466010,; A ENST00000368530 Transcript missense_variant 244/1523 51/858 17/285 E/D gaG/gaT 1 -1 TPM3 HGNC HGNC:12012 protein_coding YES CCDS41403.1 ENSP00000357516 P06753 UPI000013D90D NM_152263.3 tolerated(0.28) 1/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19269:SF38,hmmpanther:PTHR19269,Gene3D:1.20.5.340,Superfamily_domains:SSF57997 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 154191968 154191968 C A 1 0 0 0 0 1 0 0 0 16888 912 32 2 2 TPM3 1 154191968 Missense_Mutation SNP C C3N-01023_T 1834424 154191968 94764454 10 20554 RHBG 0 . GRCh38 1 156382156 156382156 + Missense_Mutation SNP G G T rs756230851 C3N-01023_T C3N-01023_N G G c.1067G>T p.Gly356Val p.G356V ENST00000537040 7/10 191 169 22 124 123 1 strelka-varscan-mutect RHBG,missense_variant,p.Gly356Val,ENST00000537040,NM_001256395.1,NM_020407.4,NM_001256396.1;RHBG,non_coding_transcript_exon_variant,,ENST00000494874,;RHBG,3_prime_UTR_variant,,ENST00000620376,;RHBG,3_prime_UTR_variant,,ENST00000451864,;RHBG,3_prime_UTR_variant,,ENST00000613460,;RHBG,3_prime_UTR_variant,,ENST00000612897,;RHBG,non_coding_transcript_exon_variant,,ENST00000618120,;RHBG,upstream_gene_variant,,ENST00000622297,; T ENST00000537040 Transcript missense_variant 1105/1789 1067/1377 356/458 G/V gGg/gTg rs756230851 1 1 RHBG HGNC HGNC:14572 protein_coding YES ENSP00000441197 Q9H310 UPI000004F267 NM_001256395.1,NM_020407.4,NM_001256396.1 deleterious(0) 7/10 Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,Prints_domain:PR00342,hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF42,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs756230851 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 156382156 156382156 G T 1 0 0 0 0 1 0 0 0 13496 1232 43 2 2 RHBG 1 156382156 Missense_Mutation SNP G C3N-01023_T 2190188 156382156 92574266 11 20555 SPTA1 0 . GRCh38 1 158644361 158644361 + Missense_Mutation SNP C C A C3N-01023_T C3N-01023_N C C c.4230G>T p.Trp1410Cys p.W1410C ENST00000368147 30/52 496 449 47 260 260 0 strelka-varscan-mutect SPTA1,missense_variant,p.Trp1410Cys,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000465741,; A ENST00000368147 Transcript missense_variant 4411/7999 4230/7260 1410/2419 W/C tgG/tgT COSM4605342 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 30/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 158644361 158644361 C A 1 0 0 0 0 1 0 0 0 15472 856 30 2 2 SPTA1 1 158644361 Missense_Mutation SNP C C3N-01023_T 2262205 158644361 90312061 12 20556 VSIG8 0 . GRCh38 1 159855995 159855995 + Missense_Mutation SNP C C T rs199554966 C3N-01023_T C3N-01023_N C C c.859G>A p.Val287Ile p.V287I ENST00000368100 6/7 454 306 148 204 204 0 strelka-varscan-mutect VSIG8,missense_variant,p.Val287Ile,ENST00000368100,NM_001013661.1;C1orf204,upstream_gene_variant,,ENST00000368102,NM_001134233.1;C1orf204,upstream_gene_variant,,ENST00000621242,;SNORD64,upstream_gene_variant,,ENST00000390859,;C1orf204,upstream_gene_variant,,ENST00000491974,;RP11-190A12.7,downstream_gene_variant,,ENST00000537167,;RP11-190A12.7,downstream_gene_variant,,ENST00000536764,;RP11-190A12.7,downstream_gene_variant,,ENST00000543372,;RP11-190A12.7,downstream_gene_variant,,ENST00000544342,;RP11-190A12.7,downstream_gene_variant,,ENST00000536779,; T ENST00000368100 Transcript missense_variant 995/1818 859/1245 287/414 V/I Gtc/Atc rs199554966 1 -1 VSIG8 HGNC HGNC:32063 protein_coding YES CCDS30913.1 ENSP00000357080 Q5VU13 UPI0000458A8F NM_001013661.1 tolerated(0.7) 6/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR12231:SF142,hmmpanther:PTHR12231 MODERATE 1 SNV 1 1 PASS rs199554966 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 159855995 159855995 C T 1 0 0 0 0 1 0 0 0 17777 536 19 1 1 VSIG8 1 159855995 Missense_Mutation SNP C C3N-01023_T 1211634 159855995 89100427 13 20557 DHX9 0 . GRCh38 1 182887219 182887219 + Missense_Mutation SNP G G T C3N-01023_T C3N-01023_N G G c.3598G>T p.Gly1200Cys p.G1200C ENST00000367549 28/28 637 391 246 376 376 0 strelka-varscan-mutect DHX9,missense_variant,p.Gly1200Cys,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000485081,;DHX9,non_coding_transcript_exon_variant,,ENST00000473076,; T ENST00000367549 Transcript missense_variant 3708/4240 3598/3813 1200/1270 G/C Ggt/Tgt COSM5160935 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 tolerated(0.13) 28/28 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 182887219 182887219 G T 1 0 0 0 0 1 0 0 0 4320 1348 47 2 2 DHX9 1 182887219 Missense_Mutation SNP G C3N-01023_T 23031224 182887219 66069203 14 20558 NMNAT2 0 . GRCh38 1 183278615 183278615 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.589C>A p.Leu197Met p.L197M ENST00000287713 8/11 344 315 29 183 183 0 strelka-varscan-mutect NMNAT2,missense_variant,p.Leu197Met,ENST00000287713,NM_015039.3;NMNAT2,missense_variant,p.Leu192Met,ENST00000294868,NM_170706.3;NMNAT2,non_coding_transcript_exon_variant,,ENST00000464047,;NMNAT2,downstream_gene_variant,,ENST00000473046,; T ENST00000287713 Transcript missense_variant 924/5663 589/924 197/307 L/M Ctg/Atg 1 -1 NMNAT2 HGNC HGNC:16789 protein_coding YES CCDS1353.1 ENSP00000287713 Q9BZQ4 UPI00000706AB NM_015039.3 deleterious(0) 8/11 Gene3D:3.40.50.620,Pfam_domain:PF01467,hmmpanther:PTHR12039,hmmpanther:PTHR12039:SF2,Low_complexity_(Seg):seg,Superfamily_domains:SSF52374 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 183278615 183278615 G T 1 0 0 0 0 1 0 0 0 10538 962 34 2 2 NMNAT2 1 183278615 Missense_Mutation SNP G C3N-01023_T 391396 183278615 65677807 15 20559 PTPN7 0 . GRCh38 1 202158224 202158224 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.515C>A p.Pro172His p.P172H ENST00000309017 3/10 337 308 29 190 190 0 strelka-mutect PTPN7,missense_variant,p.Pro172His,ENST00000309017,NM_002832.3;PTPN7,missense_variant,p.Pro106His,ENST00000367279,NM_080588.2;PTPN7,missense_variant,p.Pro148His,ENST00000477554,NM_001199797.1;PTPN7,missense_variant,p.Pro67His,ENST00000467283,;PTPN7,missense_variant,p.Pro67His,ENST00000492451,;PTPN7,missense_variant,p.Pro67His,ENST00000486116,;PTPN7,missense_variant,p.Pro46His,ENST00000476061,;PTPN7,missense_variant,p.Pro67His,ENST00000464870,;PTPN7,missense_variant,p.Pro67His,ENST00000629151,;PTPN7,synonymous_variant,p.=,ENST00000435759,;PTPN7,intron_variant,,ENST00000477625,;PTPN7,non_coding_transcript_exon_variant,,ENST00000492977,;PTPN7,intron_variant,,ENST00000479092,;PTPN7,missense_variant,p.Pro67His,ENST00000495688,;PTPN7,missense_variant,p.Pro67His,ENST00000462815,;PTPN7,synonymous_variant,p.=,ENST00000496197,;PTPN7,non_coding_transcript_exon_variant,,ENST00000491584,;PTPN7,intron_variant,,ENST00000480836,;PTPN7,downstream_gene_variant,,ENST00000468385,; T ENST00000309017 Transcript missense_variant 1289/3765 515/1398 172/465 P/H cCc/cAc 1 -1 PTPN7 HGNC HGNC:9659 protein_coding YES CCDS1423.2 ENSP00000309116 P35236 UPI00004701F6 NM_002832.3 deleterious(0) 3/10 hmmpanther:PTHR19134:SF41,hmmpanther:PTHR19134,Prints_domain:PR01778 MODERATE 1 SNV 1 1 PASS rs1444845146 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 202158224 202158224 G T 1 0 0 0 0 1 0 0 0 12947 1232 43 2 2 PTPN7 1 202158224 Missense_Mutation SNP G C3N-01023_T 18879609 202158224 46798198 16 20560 MARK1 0 . GRCh38 1 220631092 220631092 + Missense_Mutation SNP T T C novel C3N-01023_T C3N-01023_N T T c.967T>C p.Tyr323His p.Y323H ENST00000611084 10/18 218 198 20 144 144 0 strelka-varscan-mutect MARK1,missense_variant,p.Tyr323His,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Tyr323His,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Tyr301His,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Tyr323His,ENST00000366917,NM_018650.4;HDAC1P2,downstream_gene_variant,,ENST00000602936,;HDAC1P2,downstream_gene_variant,,ENST00000453661,; C ENST00000611084 Transcript missense_variant 1607/5321 967/2391 323/796 Y/H Tat/Cat 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 tolerated(0.15) 10/18 hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 220631092 220631092 T C 1 0 0 0 0 1 0 0 0 9237 1406 49 5 5 MARK1 1 220631092 Missense_Mutation SNP T C3N-01023_T 18472868 220631092 28325330 17 20561 RYR2 0 . GRCh38 1 237795288 237795288 + Splice_Site SNP G G T novel C3N-01023_T C3N-01023_N G G c.13914-1G>T p.X4638_splice ENST00000366574 91 64 27 78 78 0 strelka-varscan-mutect RYR2,splice_acceptor_variant,,ENST00000366574,NM_001035.2;RYR2,splice_acceptor_variant,,ENST00000360064,;RYR2,splice_acceptor_variant,,ENST00000608590,;RYR2,upstream_gene_variant,,ENST00000466626,; T ENST00000366574 Transcript splice_acceptor_variant -/16562 13914/14904 4638/4967 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 95/104 HIGH 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999896 1 1 1 0 T 5 4 68 237795288 237795288 G T 1 0 0 0 0 0 0 1 0 14029 1014 35 2 2 RYR2 1 237795288 Splice_Site SNP G C3N-01023_T 17164196 237795288 11161134 18 20562 TPO 0 . GRCh38 2 1493888 1493888 + Missense_Mutation SNP G G T C3N-01023_T C3N-01023_N G G c.1855G>T p.Ala619Ser p.A619S ENST00000345913 11/17 503 420 83 300 300 0 strelka-varscan-mutect TPO,missense_variant,p.Ala548Ser,ENST00000422464,;TPO,missense_variant,p.Ala619Ser,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Ala619Ser,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Ala562Ser,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Ala619Ser,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Ala446Ser,ENST00000382198,NM_175722.3;TPO,missense_variant,p.Ala94Ser,ENST00000446278,;TPO,missense_variant,p.Ala93Ser,ENST00000469607,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,non_coding_transcript_exon_variant,,ENST00000462973,; T ENST00000345913 Transcript missense_variant 1946/3145 1855/2802 619/933 A/S Gcc/Tcc COSM5133334,COSM5133335 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 tolerated(0.07) 11/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 1493888 1493888 G T 1 0 0 0 0 1 0 0 0 16891 1203 42 2 2 TPO 2 1493888 Missense_Mutation SNP G C3N-01023_T 1493888 240699641 19 20563 OTOF 0 . GRCh38 2 26460103 26460103 + Silent SNP G G T rs753228900 C3N-01023_T C3N-01023_N G G c.5916C>A p.= p.L1972L ENST00000272371 46/47 269 207 62 157 157 0 strelka-varscan-mutect OTOF,synonymous_variant,p.=,ENST00000272371,NM_194248.2;OTOF,synonymous_variant,p.=,ENST00000402415,NM_194322.2;OTOF,synonymous_variant,p.=,ENST00000338581,NM_004802.3;OTOF,intron_variant,,ENST00000403946,NM_001287489.1;OTOF,intron_variant,,ENST00000339598,NM_194323.2;DRC1,downstream_gene_variant,,ENST00000288710,NM_145038.3;OTOF,downstream_gene_variant,,ENST00000464574,; T ENST00000272371 Transcript synonymous_variant 6043/7156 5916/5994 1972/1997 L ctC/ctA rs753228900 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 46/47 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Pfam_domain:PF16165 LOW 1 SNV 1 1 PASS rs753228900 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 26460103 26460103 G T 1 0 0 0 0 0 0 0 1 11369 1161 41 2 2 OTOF 2 26460103 Silent SNP G C3N-01023_T 24966215 26460103 215733426 20 20564 PPM1B 0 . GRCh38 2 44230498 44230498 + Missense_Mutation SNP A A G novel C3N-01023_T C3N-01023_N A A c.1220A>G p.Tyr407Cys p.Y407C ENST00000282412 6/6 475 373 102 270 270 0 strelka-varscan-mutect PPM1B,missense_variant,p.Tyr407Cys,ENST00000282412,NM_002706.5;PPM1B,missense_variant,p.Tyr120Cys,ENST00000345249,NM_177969.3;PPM1B,3_prime_UTR_variant,,ENST00000409432,NM_001033557.2;PPM1B,intron_variant,,ENST00000378551,NM_177968.3;PPM1B,intron_variant,,ENST00000378540,;PPM1B,intron_variant,,ENST00000459690,;PPM1B,intron_variant,,ENST00000487286,; G ENST00000282412 Transcript missense_variant 1632/2606 1220/1440 407/479 Y/C tAc/tGc 1 1 PPM1B HGNC HGNC:9276 protein_coding YES CCDS1817.1 ENSP00000282412 O75688 UPI0000130FE7 NM_002706.5 deleterious_low_confidence(0) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 44230498 44230498 A G 1 0 0 0 0 1 0 0 0 12446 391 14 5 5 PPM1B 2 44230498 Missense_Mutation SNP A C3N-01023_T 17770395 44230498 197963031 21 20565 EML6 0 . GRCh38 2 54962631 54962631 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.5077C>A p.Leu1693Met p.L1693M ENST00000356458 35/41 140 108 32 118 118 0 strelka-varscan-mutect EML6,missense_variant,p.Leu1693Met,ENST00000356458,NM_001039753.2;EML6,non_coding_transcript_exon_variant,,ENST00000490828,;EML6,downstream_gene_variant,,ENST00000481376,;EML6,upstream_gene_variant,,ENST00000488611,;EML6,upstream_gene_variant,,ENST00000472965,; A ENST00000356458 Transcript missense_variant 5597/8320 5077/5877 1693/1958 L/M Ctg/Atg 1 1 EML6 HGNC HGNC:35412 protein_coding YES CCDS46286.1 ENSP00000348842 Q6ZMW3 UPI00006C0432 NM_001039753.2 deleterious(0) 35/41 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF8,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 54962631 54962631 C A 1 0 0 0 0 1 0 0 0 4944 680 24 2 2 EML6 2 54962631 Missense_Mutation SNP C C3N-01023_T 10732133 54962631 187230898 22 20566 EXOC6B 0 . GRCh38 2 72179355 72179355 + Missense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.2416A>T p.Ile806Phe p.I806F ENST00000272427 22/22 122 98 24 79 79 0 strelka-varscan-mutect EXOC6B,missense_variant,p.Ile806Phe,ENST00000272427,NM_001321729.1,NM_001321734.1,NM_015189.1;EXOC6B,missense_variant,p.Ile810Phe,ENST00000634650,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000490919,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000471335,;EXOC6B,non_coding_transcript_exon_variant,,ENST00000492257,; A ENST00000272427 Transcript missense_variant 2547/5918 2416/2436 806/811 I/F Atc/Ttc 1 -1 EXOC6B HGNC HGNC:17085 protein_coding YES CCDS46333.1 ENSP00000272427 Q9Y2D4 UPI000046995C NM_001321729.1,NM_001321734.1,NM_015189.1 deleterious(0.01) 22/22 hmmpanther:PTHR12702:SF3,hmmpanther:PTHR12702,PIRSF_domain:PIRSF025007 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 72179355 72179355 T A 1 0 0 0 0 1 0 0 0 5177 1464 51 4 4 EXOC6B 2 72179355 Missense_Mutation SNP T C3N-01023_T 17216724 72179355 170014174 23 20567 ALMS1 0 . GRCh38 2 73600830 73600830 + Missense_Mutation SNP G G C rs61741524 C3N-01023_T C3N-01023_N G G c.11821G>C p.Gly3941Arg p.G3941R ENST00000613296 18/23 226 174 52 186 186 0 strelka-varscan-mutect ALMS1,missense_variant,p.Gly3941Arg,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Gly3899Arg,ENST00000484298,;ALMS1,upstream_gene_variant,,ENST00000464408,;ALMS1,upstream_gene_variant,,ENST00000490821,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,; C ENST00000613296 Transcript missense_variant 11932/12925 11821/12507 3941/4168 G/R Ggt/Cgt rs61741524 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 tolerated(0.17) 18/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 benign MODERATE 1 SNV 1 1 1 PASS rs61741524 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 73600830 73600830 G C 1 0 0 0 0 1 0 0 0 635 1116 39 4 4 ALMS1 2 73600830 Missense_Mutation SNP G C3N-01023_T 1421475 73600830 168592699 24 20568 LRRTM1 0 . GRCh38 2 80302923 80302923 + Silent SNP G G T rs756293616 C3N-01023_T C3N-01023_N G G c.897C>A p.= p.I299I ENST00000295057 2/2 223 165 58 132 132 0 strelka-varscan-mutect LRRTM1,synonymous_variant,p.=,ENST00000295057,;LRRTM1,synonymous_variant,p.=,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.=,ENST00000433224,;LRRTM1,synonymous_variant,p.=,ENST00000417012,; T ENST00000295057 Transcript synonymous_variant 1554/2599 897/1569 299/522 I atC/atA rs756293616 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs756293616 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 80302923 80302923 G T 1 0 0 0 0 0 0 0 1 8945 1164 41 2 2 LRRTM1 2 80302923 Silent SNP G C3N-01023_T 6702093 80302923 161890606 25 20569 CCDC150 0 . GRCh38 2 196656990 196656990 + Nonsense_Mutation SNP G G T rs755378315 C3N-01023_T C3N-01023_N G G c.430G>T p.Glu144Ter p.E144* ENST00000389175 4/28 203 158 45 123 123 0 strelka-varscan-mutect CCDC150,stop_gained,p.Glu144Ter,ENST00000389175,NM_001080539.1;CCDC150,non_coding_transcript_exon_variant,,ENST00000495513,;CCDC150,intron_variant,,ENST00000498512,;CCDC150,non_coding_transcript_exon_variant,,ENST00000471546,;CCDC150,non_coding_transcript_exon_variant,,ENST00000471033,;CCDC150,intron_variant,,ENST00000431807,; T ENST00000389175 Transcript stop_gained 565/3685 430/3306 144/1101 E/* Gaa/Taa rs755378315 1 1 CCDC150 HGNC HGNC:26834 protein_coding YES CCDS46478.1 ENSP00000373827 Q8NCX0 UPI0000DD7A7C NM_001080539.1 4/28 hmmpanther:PTHR35352 HIGH 1 SNV 5 1 PASS rs755378315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 196656990 196656990 G T 1 0 0 0 0 0 1 0 0 2471 1175 41 2 2 CCDC150 2 196656990 Nonsense_Mutation SNP G C3N-01023_T 116354067 196656990 45536539 26 20570 TRAK2 0 . GRCh38 2 201380678 201380678 + Silent SNP A A T novel C3N-01023_T C3N-01023_N A A c.2610T>A p.= p.S870S ENST00000332624 16/16 526 481 45 327 327 0 strelka-varscan-mutect TRAK2,synonymous_variant,p.=,ENST00000332624,NM_015049.2; T ENST00000332624 Transcript synonymous_variant 3039/6510 2610/2745 870/914 S tcT/tcA 1 -1 TRAK2 HGNC HGNC:13206 protein_coding YES CCDS2347.1 ENSP00000328875 O60296 UPI0000125022 NM_015049.2 16/16 hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 201380678 201380678 A T 1 0 0 0 0 0 0 0 1 16933 175 7 4 4 TRAK2 2 201380678 Silent SNP A C3N-01023_T 4723688 201380678 40812851 27 20571 CUL3 0 . GRCh38 2 224514725 224514725 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.426G>T p.Leu142Phe p.L142F ENST00000264414 4/16 131 98 33 92 92 0 strelka-varscan-mutect CUL3,missense_variant,p.Leu142Phe,ENST00000264414,NM_003590.4;CUL3,missense_variant,p.Leu76Phe,ENST00000344951,NM_001257197.1;CUL3,missense_variant,p.Leu118Phe,ENST00000409777,;CUL3,missense_variant,p.Leu118Phe,ENST00000409096,NM_001257198.1;CUL3,missense_variant,p.Leu163Phe,ENST00000436172,;CUL3,non_coding_transcript_exon_variant,,ENST00000541548,;CUL3,3_prime_UTR_variant,,ENST00000432260,;CUL3,upstream_gene_variant,,ENST00000484081,; A ENST00000264414 Transcript missense_variant 765/6741 426/2307 142/768 L/F ttG/ttT 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 deleterious(0) 4/16 hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.20.1310.10,Superfamily_domains:SSF74788 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 224514725 224514725 C A 1 0 0 0 0 1 0 0 0 3866 593 21 2 2 CUL3 2 224514725 Missense_Mutation SNP C C3N-01023_T 23134047 224514725 17678804 28 20572 OXTR 0 . GRCh38 3 8753148 8753148 + Silent SNP C C A rs189691866 C3N-01023_T C3N-01023_N C C c.999G>T p.= p.T333T ENST00000316793 4/4 377 350 27 253 253 0 strelka-varscan-mutect OXTR,synonymous_variant,p.=,ENST00000316793,NM_000916.3;CAV3,intron_variant,,ENST00000472766,; A ENST00000316793 Transcript synonymous_variant 1624/4364 999/1170 333/389 T acG/acT rs189691866,COSM3597831 1 -1 OXTR HGNC HGNC:8529 protein_coding YES CCDS2570.1 ENSP00000324270 P30559 B2R9L7 UPI000013FEA9 NM_000916.3 4/4 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF19,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 1 0,1 1 PASS rs189691866 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 8753148 8753148 C A 1 0 0 0 0 0 0 0 1 11411 639 23 1 1 OXTR 3 8753148 Silent SNP C C3N-01023_T 8753148 189542411 29 20573 SCN5A 0 . GRCh38 3 38550767 38550767 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.5605G>T p.Asp1869Tyr p.D1869Y ENST00000413689 28/28 379 331 48 281 281 0 strelka-varscan-mutect SCN5A,missense_variant,p.Asp1869Tyr,ENST00000413689,NM_001099404.1;SCN5A,missense_variant,p.Asp1869Tyr,ENST00000333535,NM_198056.2;SCN5A,missense_variant,p.Asp1851Tyr,ENST00000425664,NM_001099405.1;SCN5A,missense_variant,p.Asp1868Tyr,ENST00000423572,NM_000335.4;SCN5A,missense_variant,p.Asp1815Tyr,ENST00000451551,NM_001160161.1;SCN5A,missense_variant,p.Asp1851Tyr,ENST00000414099,;SCN5A,missense_variant,p.Asp1836Tyr,ENST00000455624,NM_001160160.1;SCN5A,missense_variant,p.Asp1815Tyr,ENST00000450102,;SCN5A,missense_variant,p.Asp1815Tyr,ENST00000449557,;SCN5A,downstream_gene_variant,,ENST00000464652,; A ENST00000413689 Transcript missense_variant 5799/8504 5605/6051 1869/2016 D/Y Gac/Tac 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 deleterious(0) 28/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 38550767 38550767 C A 1 0 0 0 0 1 0 0 0 14191 855 30 2 2 SCN5A 3 38550767 Missense_Mutation SNP C C3N-01023_T 29797619 38550767 159744792 30 20574 ZNF502 0 . GRCh38 3 44721688 44721688 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.871G>T p.Gly291Cys p.G291C ENST00000296091 4/4 113 103 10 77 77 0 strelka-varscan-mutect ZNF502,missense_variant,p.Gly291Cys,ENST00000296091,NM_001134440.1,NM_001282880.1,NM_033210.4;ZNF502,missense_variant,p.Gly291Cys,ENST00000449836,NM_001134441.1,NM_001134442.1;ZNF502,missense_variant,p.Gly291Cys,ENST00000436624,;ZNF502,downstream_gene_variant,,ENST00000411443,; T ENST00000296091 Transcript missense_variant 1127/3270 871/1635 291/544 G/C Ggt/Tgt 1 1 ZNF502 HGNC HGNC:23718 protein_coding YES CCDS2719.1 ENSP00000296091 Q8TBZ5 A0A024R2Z2 UPI0000072CFB NM_001134440.1,NM_001282880.1,NM_033210.4 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF133,hmmpanther:PTHR24384,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.73603 1 1 1 1 0 T 3 4 68 44721688 44721688 G T 1 0 0 0 0 1 0 0 0 18522 1348 47 2 2 ZNF502 3 44721688 Missense_Mutation SNP G C3N-01023_T 6170921 44721688 153573871 31 20575 UQCRC1 0 . GRCh38 3 48600497 48600497 + Missense_Mutation SNP C C A rs561584985 C3N-01023_T C3N-01023_N C C c.1198G>T p.Val400Leu p.V400L ENST00000203407 10/13 201 151 50 139 139 0 strelka-varscan-mutect UQCRC1,missense_variant,p.Val400Leu,ENST00000203407,NM_003365.2;UQCRC1,3_prime_UTR_variant,,ENST00000415995,;UQCRC1,non_coding_transcript_exon_variant,,ENST00000480561,;UQCRC1,non_coding_transcript_exon_variant,,ENST00000471189,;UQCRC1,non_coding_transcript_exon_variant,,ENST00000460105,;UQCRC1,downstream_gene_variant,,ENST00000467690,;UQCRC1,downstream_gene_variant,,ENST00000412343,;UQCRC1,downstream_gene_variant,,ENST00000463708,;UQCRC1,downstream_gene_variant,,ENST00000472438,; A ENST00000203407 Transcript missense_variant 1615/1985 1198/1443 400/480 V/L Gta/Tta rs561584985 1 -1 UQCRC1 HGNC HGNC:12585 protein_coding YES CCDS2774.1 ENSP00000203407 P31930 UPI000006DFD4 NM_003365.2 tolerated(1) 10/13 hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF116,Gene3D:3.30.830.10,Superfamily_domains:SSF63411 MODERATE 1 SNV 1 1 PASS rs561584985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 48600497 48600497 C A 1 0 0 0 0 1 0 0 0 17547 507 18 2 2 UQCRC1 3 48600497 Missense_Mutation SNP C C3N-01023_T 3878809 48600497 149695062 32 20576 ROBO1 0 . GRCh38 3 78636050 78636050 + Silent SNP G G C novel C3N-01023_T C3N-01023_N G G c.3096C>G p.= p.L1032L ENST00000464233 23/31 148 113 35 126 126 0 strelka-varscan-mutect ROBO1,synonymous_variant,p.=,ENST00000436010,;ROBO1,synonymous_variant,p.=,ENST00000618833,;ROBO1,synonymous_variant,p.=,ENST00000618846,;ROBO1,synonymous_variant,p.=,ENST00000464233,NM_002941.3;ROBO1,synonymous_variant,p.=,ENST00000495273,NM_133631.3;ROBO1,intron_variant,,ENST00000467549,NM_001145845.1;ROBO1,upstream_gene_variant,,ENST00000472273,;ROBO1,non_coding_transcript_exon_variant,,ENST00000498428,; C ENST00000464233 Transcript synonymous_variant 3210/6742 3096/4956 1032/1651 L ctC/ctG 1 -1 ROBO1 HGNC HGNC:10249 protein_coding YES CCDS54611.1 ENSP00000420321 Q9Y6N7 UPI00000713D9 NM_002941.3 23/31 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF107 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 68 78636050 78636050 G C 1 0 0 0 0 0 0 0 1 13691 1161 41 4 4 ROBO1 3 78636050 Silent SNP G C3N-01023_T 30035553 78636050 119659509 33 20577 ZIC1 0 . GRCh38 3 147413466 147413466 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1259G>T p.Ser420Ile p.S420I ENST00000282928 3/3 176 126 50 159 159 0 strelka-varscan-mutect ZIC1,missense_variant,p.Ser420Ile,ENST00000282928,NM_003412.3;ZIC1,missense_variant,p.Ser109Ile,ENST00000488404,;ZIC1,intron_variant,,ENST00000472523,; T ENST00000282928 Transcript missense_variant 1988/5241 1259/1344 420/447 S/I aGc/aTc 1 1 ZIC1 HGNC HGNC:12872 protein_coding YES CCDS3136.1 ENSP00000282928 Q15915 UPI000013DD09 NM_003412.3 tolerated(0.08) 3/3 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 147413466 147413466 G T 1 0 0 0 0 1 0 0 0 18257 971 34 2 2 ZIC1 3 147413466 Missense_Mutation SNP G C3N-01023_T 68777416 147413466 50882093 34 20578 MME 0 . GRCh38 3 155144418 155144418 + Silent SNP T T A novel C3N-01023_T C3N-01023_N T T c.1377T>A p.= p.T459T ENST00000460393 14/23 373 259 114 267 267 0 strelka-varscan-mutect MME,synonymous_variant,p.=,ENST00000460393,NM_000902.3;MME,synonymous_variant,p.=,ENST00000615825,NM_007287.2,NM_007289.2;MME,synonymous_variant,p.=,ENST00000462745,NM_007288.2;MME,synonymous_variant,p.=,ENST00000492661,;MME,synonymous_variant,p.=,ENST00000493237,;MME,synonymous_variant,p.=,ENST00000360490,; A ENST00000460393 Transcript synonymous_variant 1497/5622 1377/2253 459/750 T acT/acA 1 1 MME HGNC HGNC:7154 protein_coding YES CCDS3172.1 ENSP00000418525 P08473 UPI0000033C41 NM_000902.3 14/23 hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF114,Gene3D:3.40.390.10,Pfam_domain:PF05649,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 155144418 155144418 T A 1 0 0 0 0 0 0 0 1 9608 1596 56 4 4 MME 3 155144418 Silent SNP T C3N-01023_T 7730952 155144418 43151141 35 20579 YIPF7 0 . GRCh38 4 44635922 44635922 + Missense_Mutation SNP C C G C3N-01023_T C3N-01023_N C C c.352G>C p.Glu118Gln p.E118Q ENST00000332990 3/6 91 82 9 68 68 0 strelka-varscan-mutect YIPF7,missense_variant,p.Glu94Gln,ENST00000415895,;YIPF7,missense_variant,p.Glu118Gln,ENST00000332990,NM_182592.2;YIPF7,non_coding_transcript_exon_variant,,ENST00000510035,;YIPF7,intron_variant,,ENST00000502794,; G ENST00000332990 Transcript missense_variant,splice_region_variant 369/937 352/843 118/280 E/Q Gaa/Caa COSM4741855 1 -1 YIPF7 HGNC HGNC:26825 protein_coding YES CCDS54766.1 ENSP00000332772 Q8N8F6 UPI00015347BF NM_182592.2 deleterious(0.01) 3/6 hmmpanther:PTHR21236,hmmpanther:PTHR21236:SF5 1 MODERATE 1 SNV 5 1 1 PASS rs1472993599 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 44635922 44635922 C G 1 0 0 0 0 1 0 0 0 18045 927 32 4 4 YIPF7 4 44635922 Missense_Mutation SNP C C3N-01023_T 44635922 145578633 36 20580 KIAA1211 0 . GRCh38 4 56316230 56316230 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.2728C>T p.Arg910Trp p.R910W ENST00000504228 6/9 231 206 25 137 137 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Arg910Trp,ENST00000504228,;KIAA1211,missense_variant,p.Arg903Trp,ENST00000541073,;KIAA1211,missense_variant,p.Arg910Trp,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,;MRPL22P1,downstream_gene_variant,,ENST00000505398,; T ENST00000504228 Transcript missense_variant 2833/4628 2728/3702 910/1233 R/W Cgg/Tgg 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 deleterious(0) 6/9 MODERATE 1 SNV 5 1 PASS rs1003914517 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 56316230 56316230 C T 1 0 0 0 0 1 0 0 0 8107 759 27 1 1 KIAA1211 4 56316230 Missense_Mutation SNP C C3N-01023_T 11680308 56316230 133898325 37 20581 ADGRL3 0 . GRCh38 4 62070580 62070580 + Missense_Mutation SNP T T G novel C3N-01023_T C3N-01023_N T T c.4082T>G p.Leu1361Trp p.L1361W ENST00000514591 25/25 347 298 49 230 230 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Leu1361Trp,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Leu1472Trp,ENST00000506720,;ADGRL3,missense_variant,p.Leu1463Trp,ENST00000506746,;ADGRL3,missense_variant,p.Leu1420Trp,ENST00000507625,;ADGRL3,missense_variant,p.Leu1404Trp,ENST00000508946,;ADGRL3,missense_variant,p.Leu1395Trp,ENST00000514996,;ADGRL3,missense_variant,p.Leu810Trp,ENST00000502815,;ADGRL3,3_prime_UTR_variant,,ENST00000512091,NM_001322246.1;ADGRL3,3_prime_UTR_variant,,ENST00000509896,;ADGRL3,3_prime_UTR_variant,,ENST00000511324,;ADGRL3,3_prime_UTR_variant,,ENST00000508693,;ADGRL3,3_prime_UTR_variant,,ENST00000507164,;ADGRL3,3_prime_UTR_variant,,ENST00000506700,;ADGRL3,3_prime_UTR_variant,,ENST00000504896,;ADGRL3,3_prime_UTR_variant,,ENST00000514157,;ADGRL3-AS1,downstream_gene_variant,,ENST00000506704,;ADGRL3-AS1,downstream_gene_variant,,ENST00000504135,;ADGRL3-AS1,downstream_gene_variant,,ENST00000509461,; G ENST00000514591 Transcript missense_variant 4411/6297 4082/4410 1361/1469 L/W tTg/tGg 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious_low_confidence(0.01) 25/25 Pfam_domain:PF02354 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 62070580 62070580 T G 1 0 0 0 0 1 0 0 0 377 1821 63 5 5 ADGRL3 4 62070580 Missense_Mutation SNP T C3N-01023_T 5754350 62070580 128143975 38 20582 ANKRD17 0 . GRCh38 4 73142271 73142271 + Silent SNP A A G C3N-01023_T C3N-01023_N A A c.2200T>C p.= p.L734L ENST00000358602 13/34 97 82 15 92 92 0 strelka-varscan-mutect ANKRD17,synonymous_variant,p.=,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,synonymous_variant,p.=,ENST00000558247,;ANKRD17,synonymous_variant,p.=,ENST00000509867,NM_001286771.1;ANKRD17,synonymous_variant,p.=,ENST00000330838,NM_198889.1;ANKRD17,intron_variant,,ENST00000561029,;ANKRD17,non_coding_transcript_exon_variant,,ENST00000514252,; G ENST00000358602 Transcript synonymous_variant 2317/10784 2200/7812 734/2603 L Tta/Cta COSM1619042 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 13/34 PROSITE_profiles:PS50297,hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1 1 LOW 1 SNV 5 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 68 73142271 73142271 A G 1 0 0 0 0 0 0 0 1 747 40 2 5 5 ANKRD17 4 73142271 Silent SNP A C3N-01023_T 11071691 73142271 117072284 39 20583 ALPK1 0 . GRCh38 4 112431577 112431577 + Missense_Mutation SNP A A G novel C3N-01023_T C3N-01023_N A A c.2030A>G p.His677Arg p.H677R ENST00000458497 11/16 312 286 26 266 266 0 strelka-varscan-mutect ALPK1,missense_variant,p.His677Arg,ENST00000458497,NM_025144.3,NM_001102406.1;ALPK1,missense_variant,p.His599Arg,ENST00000504176,NM_001253884.1;ALPK1,missense_variant,p.His677Arg,ENST00000177648,;ALPK1,downstream_gene_variant,,ENST00000508589,;ALPK1,3_prime_UTR_variant,,ENST00000509722,;ALPK1,non_coding_transcript_exon_variant,,ENST00000504745,;ALPK1,intron_variant,,ENST00000505127,;ALPK1,downstream_gene_variant,,ENST00000512847,; G ENST00000458497 Transcript missense_variant 2309/5410 2030/3735 677/1244 H/R cAt/cGt 1 1 ALPK1 HGNC HGNC:20917 protein_coding YES CCDS3697.1 ENSP00000398048 Q96QP1 UPI000045725F NM_025144.3,NM_001102406.1 tolerated(0.5) 11/16 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 112431577 112431577 A G 1 0 0 0 0 1 0 0 0 644 217 8 5 5 ALPK1 4 112431577 Missense_Mutation SNP A C3N-01023_T 39289306 112431577 77782978 40 20584 LARP1B 0 . GRCh38 4 128091052 128091052 + Missense_Mutation SNP T T C novel C3N-01023_T C3N-01023_N T T c.410T>C p.Val137Ala p.V137A ENST00000326639 6/20 286 249 37 305 305 0 strelka-varscan-mutect LARP1B,missense_variant,p.Val137Ala,ENST00000326639,NM_018078.3;LARP1B,missense_variant,p.Val137Ala,ENST00000512292,NM_178043.2;LARP1B,missense_variant,p.Val137Ala,ENST00000432347,NM_032239.3;LARP1B,missense_variant,p.Val137Ala,ENST00000394288,NM_001278604.1;LARP1B,missense_variant,p.Val90Ala,ENST00000508819,;LARP1B,missense_variant,p.Val106Ala,ENST00000507377,; C ENST00000326639 Transcript missense_variant 621/4891 410/2745 137/914 V/A gTg/gCg 1 1 LARP1B HGNC HGNC:24704 protein_coding YES CCDS3738.1 ENSP00000321997 Q659C4 UPI0000190831 NM_018078.3 deleterious(0) 6/20 hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF50,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 128091052 128091052 T C 1 0 0 0 0 1 0 0 0 8540 1696 59 5 5 LARP1B 4 128091052 Missense_Mutation SNP T C3N-01023_T 15659475 128091052 62123503 41 20585 WWC2 0 . GRCh38 4 183280776 183280776 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.2563G>T p.Asp855Tyr p.D855Y ENST00000403733 17/23 179 154 25 178 177 1 strelka-mutect WWC2,missense_variant,p.Asp855Tyr,ENST00000403733,NM_024949.5;WWC2,missense_variant,p.Asp855Tyr,ENST00000448232,;WWC2,missense_variant,p.Asp537Tyr,ENST00000504005,;WWC2,missense_variant,p.Asp806Tyr,ENST00000513834,;WWC2,upstream_gene_variant,,ENST00000508747,;WWC2,splice_region_variant,,ENST00000427431,;WWC2,splice_region_variant,,ENST00000438543,;WWC2,splice_region_variant,,ENST00000515284,; T ENST00000403733 Transcript missense_variant,splice_region_variant 2762/8826 2563/3579 855/1192 D/Y Gat/Tat 1 1 WWC2 HGNC HGNC:24148 protein_coding YES CCDS34109.2 ENSP00000384222 Q6AWC2 UPI000022C4C2 NM_024949.5 deleterious(0) 17/23 hmmpanther:PTHR14791:SF26,hmmpanther:PTHR14791 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 183280776 183280776 G T 1 0 0 0 0 1 0 0 0 17970 1188 41 2 2 WWC2 4 183280776 Missense_Mutation SNP G C3N-01023_T 55189724 183280776 6933779 42 20586 MARCH6 0 . GRCh38 5 10386997 10386997 + Missense_Mutation SNP G G A novel C3N-01023_T C3N-01023_N G G c.338G>A p.Arg113His p.R113H ENST00000274140 5/26 233 208 25 143 143 0 strelka-varscan-mutect MARCH6,missense_variant,p.Arg113His,ENST00000274140,NM_005885.3;MARCH6,missense_variant,p.Arg65His,ENST00000449913,NM_001270660.1;MARCH6,missense_variant,p.Arg8His,ENST00000503788,NM_001270661.1;MARCH6,non_coding_transcript_exon_variant,,ENST00000507863,;MARCH6,non_coding_transcript_exon_variant,,ENST00000510872,;MARCH6,non_coding_transcript_exon_variant,,ENST00000511802,;MARCH6,non_coding_transcript_exon_variant,,ENST00000506131,;MARCH6,intron_variant,,ENST00000502795,; A ENST00000274140 Transcript missense_variant 470/9569 338/2733 113/910 R/H cGc/cAc 1 1 MARCH6 HGNC HGNC:30550 protein_coding YES CCDS34135.1 ENSP00000274140 O60337 UPI00001B94D6 NM_005885.3 deleterious(0) 5/26 Transmembrane_helices:TMhelix,hmmpanther:PTHR13145 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9998353 1 1 1 0 A 3 1 68 10386997 10386997 G A 1 0 0 0 0 1 0 0 0 9230 1101 38 1 1 MARCH6 5 10386997 Missense_Mutation SNP G C3N-01023_T 10386997 171151262 43 20587 DROSHA 0 . GRCh38 5 31422862 31422862 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.3344G>T p.Gly1115Val p.G1115V ENST00000511367 28/35 171 133 38 147 147 0 strelka-varscan-mutect DROSHA,missense_variant,p.Gly1115Val,ENST00000511367,NM_013235.4;DROSHA,missense_variant,p.Gly1115Val,ENST00000344624,;DROSHA,missense_variant,p.Gly1078Val,ENST00000442743,;DROSHA,missense_variant,p.Gly1078Val,ENST00000513349,NM_001100412.1;DROSHA,non_coding_transcript_exon_variant,,ENST00000510178,;DROSHA,non_coding_transcript_exon_variant,,ENST00000511778,;DROSHA,non_coding_transcript_exon_variant,,ENST00000504133,; A ENST00000511367 Transcript missense_variant 3589/5305 3344/4125 1115/1374 G/V gGa/gTa 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 deleterious(0) 28/35 Gene3D:1.10.1520.10,HAMAP:MF_00104,PROSITE_profiles:PS50142,hmmpanther:PTHR11207,Superfamily_domains:SSF69065 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 31422862 31422862 C A 1 0 0 0 0 1 0 0 0 4584 855 30 2 2 DROSHA 5 31422862 Missense_Mutation SNP C C3N-01023_T 21035865 31422862 150115397 44 20588 TTC23L 0 . GRCh38 5 34863034 34863034 + Silent SNP G G T novel C3N-01023_T C3N-01023_N G G c.516G>T p.= p.V172V ENST00000505624 5/11 190 148 42 149 148 1 strelka-varscan-mutect TTC23L,synonymous_variant,p.=,ENST00000505624,NM_144725.3;TTC23L,synonymous_variant,p.=,ENST00000610313,;TTC23L,non_coding_transcript_exon_variant,,ENST00000514080,;TTC23L,downstream_gene_variant,,ENST00000506758,;TTC23L,downstream_gene_variant,,ENST00000502782,;TTC23L,synonymous_variant,p.=,ENST00000502674,;TTC23L,3_prime_UTR_variant,,ENST00000508722,;CTD-2517O10.5,upstream_gene_variant,,ENST00000515352,; T ENST00000505624 Transcript synonymous_variant 619/1353 516/1086 172/361 V gtG/gtT 1 1 TTC23L HGNC HGNC:26355 protein_coding YES CCDS54840.1 ENSP00000422188 Q6PF05 UPI000013F897 NM_144725.3 5/11 Gene3D:1.25.40.10,hmmpanther:PTHR14485,hmmpanther:PTHR14485:SF4,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 34863034 34863034 G T 1 0 0 0 0 0 0 0 1 17199 1335 47 2 2 TTC23L 5 34863034 Silent SNP G C3N-01023_T 3440172 34863034 146675225 45 20589 HCN1 0 . GRCh38 5 45262527 45262527 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.2067G>T p.Gln689His p.Q689H ENST00000303230 8/8 234 211 23 172 172 0 strelka-mutect HCN1,missense_variant,p.Gln689His,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; A ENST00000303230 Transcript missense_variant 2308/9885 2067/2673 689/890 Q/H caG/caT 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 tolerated_low_confidence(0.08) 8/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 45262527 45262527 C A 1 0 0 0 0 1 0 0 0 6883 796 28 2 2 HCN1 5 45262527 Missense_Mutation SNP C C3N-01023_T 10399493 45262527 136275732 46 20590 CEP120 0 . GRCh38 5 123377461 123377461 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.2271G>T p.Arg757Ser p.R757S ENST00000306467 16/20 252 191 61 186 186 0 strelka-varscan-mutect CEP120,missense_variant,p.Arg757Ser,ENST00000306467,;CEP120,missense_variant,p.Arg757Ser,ENST00000328236,NM_153223.3;CEP120,missense_variant,p.Arg731Ser,ENST00000306481,NM_001166226.1;CEP120,missense_variant,p.Arg731Ser,ENST00000508442,;CEP120,3_prime_UTR_variant,,ENST00000508138,;CEP120,3_prime_UTR_variant,,ENST00000513565,; A ENST00000306467 Transcript missense_variant 2576/4900 2271/2961 757/986 R/S agG/agT 1 -1 CEP120 HGNC HGNC:26690 protein_coding YES CCDS4134.2 ENSP00000303058 Q8N960 UPI0000D79C73 deleterious(0.03) 16/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21574 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 123377461 123377461 C A 1 0 0 0 0 1 0 0 0 2956 622 22 2 2 CEP120 5 123377461 Missense_Mutation SNP C C3N-01023_T 78114934 123377461 58160798 47 20591 PPARGC1B 0 . GRCh38 5 149820444 149820444 + Silent SNP C C A rs368304290 C3N-01023_T C3N-01023_N C C c.90C>A p.= p.S30S ENST00000309241 2/12 121 95 26 59 59 0 strelka-varscan-mutect PPARGC1B,synonymous_variant,p.=,ENST00000309241,NM_133263.3;PPARGC1B,synonymous_variant,p.=,ENST00000394320,;PPARGC1B,synonymous_variant,p.=,ENST00000403750,NM_001172699.1;PPARGC1B,synonymous_variant,p.=,ENST00000360453,NM_001172698.1;PPARGC1B,downstream_gene_variant,,ENST00000461780,; A ENST00000309241 Transcript synonymous_variant 122/10568 90/3072 30/1023 S tcC/tcA rs368304290 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 2/12 hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 LOW 1 SNV 1 1 PASS rs368304290 . 0 197 13 0 0 0 0 0 -20 0.9999228 1 1 1 0 A 2 1 68 149820444 149820444 C A 1 0 0 0 0 0 0 0 1 12410 639 23 1 1 PPARGC1B 5 149820444 Silent SNP C C3N-01023_T 26442983 149820444 31717815 48 20592 GPX5 0 . GRCh38 6 28529568 28529568 + Missense_Mutation SNP G G T rs376708612 C3N-01023_T C3N-01023_N G G c.205G>T p.Val69Leu p.V69L ENST00000412168 2/5 129 109 20 100 100 0 strelka-varscan-mutect GPX5,missense_variant,p.Val69Leu,ENST00000412168,NM_001509.2;GPX5,missense_variant,p.Val69Leu,ENST00000469384,NM_003996.3;GPX5,non_coding_transcript_exon_variant,,ENST00000442674,;GPX5,non_coding_transcript_exon_variant,,ENST00000483784,;GPX6,upstream_gene_variant,,ENST00000483058,; T ENST00000412168 Transcript missense_variant 294/1540 205/666 69/221 V/L Gtg/Ttg rs376708612 1 1 GPX5 HGNC HGNC:4557 protein_coding YES CCDS4652.1 ENSP00000392398 O75715 V9HWN8 UPI0000031FD7 NM_001509.2 deleterious(0.01) 2/5 Gene3D:3.40.30.10,Pfam_domain:PF00255,PIRSF_domain:PIRSF000303,Prints_domain:PR01011,PROSITE_patterns:PS00460,PROSITE_profiles:PS51355,hmmpanther:PTHR11592,hmmpanther:PTHR11592:SF29,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS rs376708612 . 0 207 0 3 0 0 0 0 -20 0.9999941 1 1 1 0 T 3 4 68 28529568 28529568 G T 1 0 0 0 0 1 0 0 0 6622 1145 40 1 1 GPX5 6 28529568 Missense_Mutation SNP G C3N-01023_T 28529568 142276411 49 20593 MDC1 0 . GRCh38 6 30712261 30712261 + Nonsense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.1681A>T p.Lys561Ter p.K561* ENST00000376406 5/15 148 122 26 81 81 0 strelka-varscan-mutect MDC1,stop_gained,p.Lys561Ter,ENST00000376406,NM_014641.2;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000613547,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;MDC1,upstream_gene_variant,,ENST00000492462,; A ENST00000376406 Transcript stop_gained 2329/7576 1681/6270 561/2089 K/* Aag/Tag 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 5/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 HIGH SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 68 30712261 30712261 T A 1 0 0 0 0 0 1 0 0 9341 1850 64 4 4 MDC1 6 30712261 Nonsense_Mutation SNP T C3N-01023_T 2182693 30712261 140093718 50 20594 KIFC1 0 . GRCh38 6 33403485 33403485 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.305G>C p.Gly102Ala p.G102A ENST00000428849 5/11 297 279 18 225 225 0 strelka-varscan-mutect KIFC1,missense_variant,p.Gly102Ala,ENST00000428849,NM_002263.3;KIFC1,missense_variant,p.Gly143Ala,ENST00000450504,;KIFC1,upstream_gene_variant,,ENST00000494554,;KIFC1,splice_region_variant,,ENST00000486695,;RPL12P1,upstream_gene_variant,,ENST00000374520,; C ENST00000428849 Transcript missense_variant,splice_region_variant 755/2706 305/2022 102/673 G/A gGg/gCg 1 1 KIFC1 HGNC HGNC:6389 protein_coding YES CCDS34430.1 ENSP00000393963 Q9BW19 A0A024RCS7 UPI000012DDB8 NM_002263.3 tolerated(1) 5/11 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF443 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 33403485 33403485 G C 1 0 0 0 0 1 0 0 0 8177 1246 43 4 4 KIFC1 6 33403485 Missense_Mutation SNP G C3N-01023_T 2691224 33403485 137402494 51 20595 ZNF318 0 . GRCh38 6 43355494 43355494 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.1840C>G p.Arg614Gly p.R614G ENST00000361428 4/10 296 253 43 224 224 0 strelka-varscan-mutect ZNF318,missense_variant,p.Arg614Gly,ENST00000361428,NM_014345.2;ZNF318,missense_variant,p.Arg614Gly,ENST00000605935,; C ENST00000361428 Transcript missense_variant 1918/8006 1840/6840 614/2279 R/G Cgc/Ggc 1 -1 ZNF318 HGNC HGNC:13578 protein_coding YES CCDS4895.2 ENSP00000354964 Q5VUA4 UPI000049E044 NM_014345.2 deleterious(0) 4/10 hmmpanther:PTHR15577:SF2,hmmpanther:PTHR15577 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 43355494 43355494 G C 1 0 0 0 0 1 0 0 0 18411 1145 40 4 4 ZNF318 6 43355494 Missense_Mutation SNP G C3N-01023_T 9952009 43355494 127450485 52 20596 PKHD1 0 . GRCh38 6 51791261 51791261 + Silent SNP G G T novel C3N-01023_T C3N-01023_N G G c.8415C>A p.= p.V2805V ENST00000371117 53/67 574 484 90 386 386 0 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; T ENST00000371117 Transcript synonymous_variant 8691/16282 8415/12225 2805/4074 V gtC/gtA 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 53/67 PROSITE_profiles:PS51484,Pfam_domain:PF10162,SMART_domains:SM01225 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 51791261 51791261 G T 1 0 0 0 0 0 0 0 1 12067 1277 45 2 2 PKHD1 6 51791261 Silent SNP G C3N-01023_T 8435767 51791261 119014718 53 20597 RFX6 0 . GRCh38 6 116927402 116927402 + Missense_Mutation SNP C C A rs563217936 C3N-01023_T C3N-01023_N C C c.2261C>A p.Pro754Gln p.P754Q ENST00000332958 17/19 89 78 11 66 66 0 strelka-varscan-mutect RFX6,missense_variant,p.Pro754Gln,ENST00000332958,NM_173560.3;RFX6,downstream_gene_variant,,ENST00000487683,; A ENST00000332958 Transcript missense_variant 2277/3460 2261/2787 754/928 P/Q cCg/cAg rs563217936,COSM3928052 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 tolerated_low_confidence(0.11) 17/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs563217936 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 116927402 116927402 C A 1 0 0 0 0 1 0 0 0 13441 652 23 1 1 RFX6 6 116927402 Missense_Mutation SNP C C3N-01023_T 65136141 116927402 53878577 54 20598 PNLDC1 0 . GRCh38 6 159801125 159801125 + Missense_Mutation SNP G G C C3N-01023_T C3N-01023_N G G c.147G>C p.Leu49Phe p.L49F ENST00000392167 3/19 167 153 14 159 159 0 strelka-varscan-mutect PNLDC1,missense_variant,p.Leu38Phe,ENST00000610273,NM_173516.2;PNLDC1,missense_variant,p.Leu49Phe,ENST00000392167,NM_001271862.1;MRPL18,downstream_gene_variant,,ENST00000367034,NM_014161.3;PNLDC1,non_coding_transcript_exon_variant,,ENST00000609334,;MRPL18,downstream_gene_variant,,ENST00000480842,;MRPL18,downstream_gene_variant,,ENST00000476826,;MRPL18,downstream_gene_variant,,ENST00000479638,;PNLDC1,3_prime_UTR_variant,,ENST00000275275,;PNLDC1,3_prime_UTR_variant,,ENST00000610041,;PNLDC1,intron_variant,,ENST00000610048,; C ENST00000392167 Transcript missense_variant 181/1816 147/1596 49/531 L/F ttG/ttC COSM3745037 1 1 PNLDC1 HGNC HGNC:21185 protein_coding YES CCDS5271.2 ENSP00000376007 Q8NA58 UPI000006E4CF NM_001271862.1 deleterious(0.03) 3/19 Gene3D:3.30.420.10,Pfam_domain:PF04857,hmmpanther:PTHR15092,hmmpanther:PTHR15092:SF29,Superfamily_domains:SSF53098 1 MODERATE SNV 2 1 1 PASS . . 0 203 0 5 2 0 0 0 -5.756938 0.8301957 1 1 1 0 C 3 2 68 159801125 159801125 G C 1 0 0 0 0 1 0 0 0 12256 1310 46 4 4 PNLDC1 6 159801125 Missense_Mutation SNP G C3N-01023_T 42873723 159801125 11004854 55 20599 73 2 PNLDC1 0 . GRCh38 6 159801128 159801128 + Silent SNP A A T rs765610792 C3N-01023_T C3N-01023_N A A c.150A>T p.= p.P50P ENST00000392167 3/19 168 154 14 171 171 0 strelka-varscan-mutect PNLDC1,synonymous_variant,p.=,ENST00000610273,NM_173516.2;PNLDC1,synonymous_variant,p.=,ENST00000392167,NM_001271862.1;MRPL18,downstream_gene_variant,,ENST00000367034,NM_014161.3;PNLDC1,non_coding_transcript_exon_variant,,ENST00000609334,;MRPL18,downstream_gene_variant,,ENST00000480842,;MRPL18,downstream_gene_variant,,ENST00000476826,;MRPL18,downstream_gene_variant,,ENST00000479638,;PNLDC1,3_prime_UTR_variant,,ENST00000275275,;PNLDC1,3_prime_UTR_variant,,ENST00000610041,;PNLDC1,intron_variant,,ENST00000610048,; T ENST00000392167 Transcript synonymous_variant 184/1816 150/1596 50/531 P ccA/ccT rs765610792 1 1 PNLDC1 HGNC HGNC:21185 protein_coding YES CCDS5271.2 ENSP00000376007 Q8NA58 UPI000006E4CF NM_001271862.1 3/19 Gene3D:3.30.420.10,Pfam_domain:PF04857,hmmpanther:PTHR15092,hmmpanther:PTHR15092:SF29,Superfamily_domains:SSF53098 LOW SNV 2 1 PASS rs765610792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 159801128 159801128 A T 1 0 0 0 0 0 0 0 1 12256 204 8 4 4 PNLDC1 6 159801128 Silent SNP A C3N-01023_T 3 159801128 11004851 56 20600 73 2 HDAC9 0 . GRCh38 7 18727619 18727619 + Missense_Mutation SNP C C A C3N-01023_T C3N-01023_N C C c.1771C>A p.Arg591Ser p.R591S ENST00000441542 12/25 150 105 45 133 132 1 strelka-varscan-mutect HDAC9,missense_variant,p.Arg588Ser,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Arg547Ser,ENST00000401921,;HDAC9,missense_variant,p.Arg591Ser,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Arg588Ser,ENST00000432645,NM_058176.2;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; A ENST00000441542 Transcript missense_variant 1771/3210 1771/3210 591/1069 R/S Cgc/Agc COSM4640787,COSM4640788 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 tolerated(0.17) 12/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,PIRSF_domain:PIRSF037911 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 18727619 18727619 C A 1 0 0 0 0 1 0 0 0 6901 768 27 1 1 HDAC9 7 18727619 Missense_Mutation SNP C C3N-01023_T 18727619 140618354 57 20601 POM121L12 0 . GRCh38 7 53036150 53036150 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.479C>A p.Pro160His p.P160H ENST00000408890 1/1 198 148 50 99 99 0 strelka-varscan-mutect POM121L12,missense_variant,p.Pro160His,ENST00000408890,NM_182595.3; A ENST00000408890 Transcript missense_variant 509/1283 479/891 160/296 P/H cCc/cAc 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.54) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 53036150 53036150 C A 1 0 0 0 0 1 0 0 0 12352 623 22 2 2 POM121L12 7 53036150 Missense_Mutation SNP C C3N-01023_T 34308531 53036150 106309823 58 20602 CHCHD2 0 . GRCh38 7 56104442 56104442 + Silent SNP T T A novel C3N-01023_T C3N-01023_N T T c.84A>T p.= p.P28P ENST00000395422 2/4 136 92 44 94 94 0 strelka-mutect CHCHD2,synonymous_variant,p.=,ENST00000395422,NM_001320327.1,NM_016139.2;CHCHD2,non_coding_transcript_exon_variant,,ENST00000473095,; A ENST00000395422 Transcript synonymous_variant 247/901 84/456 28/151 P ccA/ccT 1 -1 CHCHD2 HGNC HGNC:21645 protein_coding YES CCDS5526.1 ENSP00000378812 Q9Y6H1 UPI0000073DC7 NM_001320327.1,NM_016139.2 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR13523:SF3,hmmpanther:PTHR13523 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 56104442 56104442 T A 1 0 0 0 0 0 0 0 1 3076 1567 55 4 4 CHCHD2 7 56104442 Silent SNP T C3N-01023_T 3068292 56104442 103241531 59 20603 DMTF1 0 . GRCh38 7 87195122 87195122 + Silent SNP T T C novel C3N-01023_T C3N-01023_N T T c.2265T>C p.= p.D755D ENST00000394703 20/20 117 92 25 86 86 0 strelka-varscan-mutect DMTF1,missense_variant,p.Ile175Thr,ENST00000454008,;DMTF1,synonymous_variant,p.=,ENST00000394703,NM_021145.3;DMTF1,synonymous_variant,p.=,ENST00000331242,NM_001142327.1;DMTF1,synonymous_variant,p.=,ENST00000413276,;DMTF1,synonymous_variant,p.=,ENST00000432937,NM_001142326.1;TMEM243,downstream_gene_variant,,ENST00000433078,;TMEM243,downstream_gene_variant,,ENST00000257637,NM_024315.2;TMEM243,downstream_gene_variant,,ENST00000423734,;DMTF1,downstream_gene_variant,,ENST00000582204,;TMEM243,downstream_gene_variant,,ENST00000481425,;TMEM243,downstream_gene_variant,,ENST00000465976,;DMTF1,3_prime_UTR_variant,,ENST00000412139,;DMTF1,3_prime_UTR_variant,,ENST00000447863,;DMTF1,3_prime_UTR_variant,,ENST00000579677,;DMTF1,3_prime_UTR_variant,,ENST00000425406,;DMTF1,3_prime_UTR_variant,,ENST00000547146,;DMTF1,3_prime_UTR_variant,,ENST00000579850,;DMTF1,non_coding_transcript_exon_variant,,ENST00000488352,;DMTF1,non_coding_transcript_exon_variant,,ENST00000580010,;DMTF1,downstream_gene_variant,,ENST00000480982,;DMTF1,downstream_gene_variant,,ENST00000584619,;TMEM243,downstream_gene_variant,,ENST00000474074,;TMEM243,downstream_gene_variant,,ENST00000492231,;DMTF1,downstream_gene_variant,,ENST00000580803,; C ENST00000394703 Transcript synonymous_variant 2828/4038 2265/2283 755/760 D gaT/gaC 1 1 DMTF1 HGNC HGNC:14603 protein_coding YES CCDS5601.1 ENSP00000378193 Q9Y222 UPI000006FB78 NM_021145.3 20/20 hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF672 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 68 87195122 87195122 T C 1 0 0 0 0 0 0 0 1 4400 1490 52 5 5 DMTF1 7 87195122 Silent SNP T C3N-01023_T 31090680 87195122 72150851 60 20604 C7orf62 0 . GRCh38 7 88794463 88794463 + Silent SNP A A G novel C3N-01023_T C3N-01023_N A A c.480T>C p.= p.D160D ENST00000297203 2/2 205 180 25 184 184 0 strelka-varscan-mutect C7orf62,synonymous_variant,p.=,ENST00000297203,NM_152706.3;ZNF804B,intron_variant,,ENST00000333190,NM_181646.3; G ENST00000297203 Transcript synonymous_variant 666/1023 480/762 160/253 D gaT/gaC 1 -1 C7orf62 HGNC HGNC:22402 protein_coding YES CCDS34678.1 ENSP00000297203 Q8TBZ9 UPI000005034C NM_152706.3 2/2 hmmpanther:PTHR34035,hmmpanther:PTHR34035:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 68 88794463 88794463 A G 1 0 0 0 0 0 0 0 1 2146 214 8 5 5 C7orf62 7 88794463 Silent SNP A C3N-01023_T 1599341 88794463 70551510 61 20605 PTPRZ1 0 . GRCh38 7 122012713 122012713 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.3667C>A p.His1223Asn p.H1223N ENST00000393386 12/30 227 194 33 155 153 2 strelka-varscan-mutect PTPRZ1,missense_variant,p.His1223Asn,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,intron_variant,,ENST00000449182,NM_001206839.1;PTPRZ1,intron_variant,,ENST00000483028,; A ENST00000393386 Transcript missense_variant 4078/8175 3667/6948 1223/2315 H/N Cat/Aat 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious_low_confidence(0.05) 12/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 122012713 122012713 C A 1 0 0 0 0 1 0 0 0 12969 710 25 2 2 PTPRZ1 7 122012713 Missense_Mutation SNP C C3N-01023_T 33218250 122012713 37333260 62 20606 CCDC136 0 . GRCh38 7 128794394 128794394 + Silent SNP A A G novel C3N-01023_T C3N-01023_N A A c.63A>G p.= p.E21E ENST00000297788 2/18 217 205 12 129 128 1 varscan-mutect CCDC136,synonymous_variant,p.=,ENST00000297788,NM_022742.4;CCDC136,synonymous_variant,p.=,ENST00000487361,;CCDC136,synonymous_variant,p.=,ENST00000464832,;CCDC136,synonymous_variant,p.=,ENST00000378685,NM_001201372.1;CCDC136,synonymous_variant,p.=,ENST00000485998,;CCDC136,synonymous_variant,p.=,ENST00000459946,;CCDC136,synonymous_variant,p.=,ENST00000488925,;CCDC136,downstream_gene_variant,,ENST00000472049,; G ENST00000297788 Transcript synonymous_variant 430/4169 63/3465 21/1154 E gaA/gaG 1 1 CCDC136 HGNC HGNC:22225 protein_coding YES CCDS47704.1 ENSP00000297788 Q96JN2 UPI0000E445DE NM_022742.4 2/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF26,Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS rs768765556 . 0 206 0 3 0 0 0 0 -14.4433 0.9999465 1 1 1 0 G 2 3 68 128794394 128794394 A G 1 0 0 0 0 0 0 0 1 2459 69 3 5 5 CCDC136 7 128794394 Silent SNP A C3N-01023_T 6781681 128794394 30551579 63 20607 FLNC 0 . GRCh38 7 128835552 128835552 + Silent SNP C C A novel C3N-01023_T C3N-01023_N C C c.579C>A p.= p.A193A ENST00000325888 2/48 220 169 51 126 126 0 strelka-varscan-mutect FLNC,synonymous_variant,p.=,ENST00000325888,NM_001458.4;FLNC,synonymous_variant,p.=,ENST00000346177,NM_001127487.1; A ENST00000325888 Transcript synonymous_variant 840/9188 579/8178 193/2725 A gcC/gcA 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 2/48 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 128835552 128835552 C A 1 0 0 0 0 0 0 0 1 5791 610 22 2 2 FLNC 7 128835552 Silent SNP C C3N-01023_T 41158 128835552 30510421 64 20608 AKR1D1 0 . GRCh38 7 138107561 138107561 + Missense_Mutation SNP G G T rs765314823 C3N-01023_T C3N-01023_N G G c.836G>T p.Arg279Met p.R279M ENST00000242375 7/9 395 354 41 260 260 0 strelka-varscan-mutect AKR1D1,missense_variant,p.Arg279Met,ENST00000242375,NM_005989.3;AKR1D1,missense_variant,p.Arg238Met,ENST00000411726,NM_001190906.1;AKR1D1,missense_variant,p.Arg279Met,ENST00000432161,NM_001190907.1;AKR1D1,non_coding_transcript_exon_variant,,ENST00000468877,; T ENST00000242375 Transcript missense_variant 878/2347 836/981 279/326 R/M aGg/aTg rs765314823,COSM3633839 1 1 AKR1D1 HGNC HGNC:388 protein_coding YES CCDS5846.1 ENSP00000242375 P51857 UPI0000125764 NM_005989.3 deleterious(0.01) 7/9 Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,PROSITE_patterns:PS00063,hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF211,Superfamily_domains:SSF51430 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs765314823 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 138107561 138107561 G T 1 0 0 0 0 1 0 0 0 557 1000 35 2 2 AKR1D1 7 138107561 Missense_Mutation SNP G C3N-01023_T 9272009 138107561 21238412 65 20609 BRAF 0 . GRCh38 7 140808042 140808042 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.629G>T p.Trp210Leu p.W210L ENST00000288602 5/18 278 194 84 238 237 1 strelka-varscan-mutect BRAF,missense_variant,p.Trp210Leu,ENST00000288602,NM_004333.4;BRAF,3_prime_UTR_variant,,ENST00000497784,; A ENST00000288602 Transcript missense_variant 690/2480 629/2301 210/766 W/L tGg/tTg 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious(0) 5/18 Gene3D:3.10.20.90,Pfam_domain:PF02196,PROSITE_profiles:PS50898,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF43,SMART_domains:SM00455,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 140808042 140808042 C A 1 0 0 0 0 1 0 0 0 1665 595 21 2 2 BRAF 7 140808042 Missense_Mutation SNP C C3N-01023_T 2700481 140808042 18537931 66 20610 TRPV6 0 . GRCh38 7 142873540 142873540 + Missense_Mutation SNP C C A rs771971978 C3N-01023_T C3N-01023_N C C c.1816G>T p.Ala606Ser p.A606S ENST00000359396 13/15 532 484 48 376 375 1 strelka-varscan-mutect TRPV6,missense_variant,p.Ala606Ser,ENST00000359396,NM_018646.5;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;TRPV6,downstream_gene_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000619250,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; A ENST00000359396 Transcript missense_variant 1942/2928 1816/2298 606/765 A/S Gcc/Tcc rs771971978 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 tolerated(0.18) 13/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,Transmembrane_helices:TMhelix,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520 MODERATE 1 SNV 1 1 PASS rs771971978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 142873540 142873540 C A 1 0 0 0 0 1 0 0 0 17106 768 27 1 1 TRPV6 7 142873540 Missense_Mutation SNP C C3N-01023_T 2065498 142873540 16472433 67 20611 TAS2R40 0 . GRCh38 7 143222241 143222241 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.163A>T p.Thr55Ser p.T55S ENST00000408947 1/1 276 175 101 180 180 0 strelka-varscan-mutect TAS2R40,missense_variant,p.Thr55Ser,ENST00000408947,NM_176882.1;RP11-556I13.2,non_coding_transcript_exon_variant,,ENST00000595842,;RP11-556I13.1,downstream_gene_variant,,ENST00000624211,; T ENST00000408947 Transcript missense_variant 205/1043 163/972 55/323 T/S Act/Tct 1 1 TAS2R40 HGNC HGNC:18885 protein_coding YES CCDS43662.1 ENSP00000386210 P59535 UPI000000D7CA NM_176882.1 tolerated(0.26) 1/1 hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF59,Pfam_domain:PF05296,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 143222241 143222241 A T 1 0 0 0 0 1 0 0 0 15977 159 6 4 4 TAS2R40 7 143222241 Missense_Mutation SNP A C3N-01023_T 348701 143222241 16123732 68 20612 OR2A42 0 . GRCh38 7 144232806 144232806 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.38T>A p.Leu13Gln p.L13Q ENST00000391496 1/1 73 66 7 44 44 0 varscan-mutect OR2A42,missense_variant,p.Leu13Gln,ENST00000391496,NM_001001802.2;RP4-545C24.1,intron_variant,,ENST00000498693,;RP4-545C24.1,intron_variant,,ENST00000464929,;RP4-545C24.1,intron_variant,,ENST00000460955,;RP4-545C24.1,intron_variant,,ENST00000493248,;RP4-545C24.1,intron_variant,,ENST00000489077,;RP4-545C24.1,intron_variant,,ENST00000477797,;RP4-545C24.1,downstream_gene_variant,,ENST00000480074,; T ENST00000391496 Transcript missense_variant 38/933 38/933 13/310 L/Q cTa/cAa 1 -1 OR2A42 HGNC HGNC:31230 protein_coding YES CCDS56515.1 ENSP00000375334 Q8NGT9 UPI0000041DF3 NM_001001802.2 deleterious(0) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF115,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 144232806 144232806 A T 1 0 0 0 0 1 0 0 0 11057 420 15 4 4 OR2A42 7 144232806 Missense_Mutation SNP A C3N-01023_T 1010565 144232806 15113167 69 20613 EN2 0 . GRCh38 7 155458967 155458967 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.590C>T p.Ser197Leu p.S197L ENST00000297375 1/2 275 249 26 189 189 0 strelka-varscan-mutect EN2,missense_variant,p.Ser197Leu,ENST00000297375,NM_001427.3;AC008060.8,upstream_gene_variant,,ENST00000419225,; T ENST00000297375 Transcript missense_variant 839/3395 590/1002 197/333 S/L tCg/tTg 1 1 EN2 HGNC HGNC:3343 protein_coding YES CCDS5940.1 ENSP00000297375 P19622 UPI000012CA05 NM_001427.3 deleterious(0.01) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24341:SF5,hmmpanther:PTHR24341 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 155458967 155458967 C T 1 0 0 0 0 1 0 0 0 4952 893 31 1 1 EN2 7 155458967 Missense_Mutation SNP C C3N-01023_T 11226161 155458967 3887006 70 20614 XPO7 0 . GRCh38 8 21969530 21969530 + Silent SNP A A G C3N-01023_T C3N-01023_N A A c.213A>G p.= p.V71V ENST00000252512 3/28 347 319 28 270 270 0 strelka-varscan-mutect XPO7,synonymous_variant,p.=,ENST00000252512,NM_015024.4;XPO7,synonymous_variant,p.=,ENST00000433566,;XPO7,synonymous_variant,p.=,ENST00000521303,;XPO7,non_coding_transcript_exon_variant,,ENST00000518017,;XPO7,downstream_gene_variant,,ENST00000520754,;XPO7,non_coding_transcript_exon_variant,,ENST00000519769,; G ENST00000252512 Transcript synonymous_variant 313/4861 213/3264 71/1087 V gtA/gtG COSM1623847 1 1 XPO7 HGNC HGNC:14108 protein_coding YES CCDS47818.1 ENSP00000252512 Q9UIA9 UPI0000134559 NM_015024.4 3/28 PROSITE_profiles:PS50166,hmmpanther:PTHR12596,hmmpanther:PTHR12596:SF11,Pfam_domain:PF03810,SMART_domains:SM00913,Superfamily_domains:SSF48371 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 68 21969530 21969530 A G 1 0 0 0 0 0 0 0 1 18008 436 16 5 5 XPO7 8 21969530 Silent SNP A C3N-01023_T 21969530 123169106 71 20615 LOXL2 0 . GRCh38 8 23341052 23341052 + Missense_Mutation SNP C C G rs143787010 C3N-01023_T C3N-01023_N C C c.683G>C p.Arg228Pro p.R228P ENST00000389131 4/14 506 448 58 352 352 0 strelka-varscan-mutect LOXL2,missense_variant,p.Arg228Pro,ENST00000389131,NM_002318.2;LOXL2,intron_variant,,ENST00000523833,;RP11-177H13.2,non_coding_transcript_exon_variant,,ENST00000519692,;LOXL2,missense_variant,p.Arg42Pro,ENST00000518878,;RP11-177H13.2,non_coding_transcript_exon_variant,,ENST00000517420,; G ENST00000389131 Transcript missense_variant 1053/3549 683/2325 228/774 R/P cGc/cCc rs143787010 1 -1 LOXL2 HGNC HGNC:6666 protein_coding YES CCDS34864.1 ENSP00000373783 Q9Y4K0 UPI000012E7AB NM_002318.2 deleterious(0) 4/14 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_patterns:PS00420,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF318,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS rs143787010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 23341052 23341052 C G 1 0 0 0 0 1 0 0 0 8803 768 27 4 4 LOXL2 8 23341052 Missense_Mutation SNP C C3N-01023_T 1371522 23341052 121797584 72 20616 TRIM35 0 . GRCh38 8 27287623 27287623 + Missense_Mutation SNP C C G novel C3N-01023_T C3N-01023_N C C c.1409G>C p.Arg470Pro p.R470P ENST00000305364 6/6 202 143 59 124 124 0 strelka-varscan-mutect TRIM35,missense_variant,p.Arg470Pro,ENST00000305364,NM_171982.4;TRIM35,intron_variant,,ENST00000521283,;TRIM35,downstream_gene_variant,,ENST00000521253,NM_001304495.1; G ENST00000305364 Transcript missense_variant 1493/4229 1409/1482 470/493 R/P cGg/cCg 1 -1 TRIM35 HGNC HGNC:16285 protein_coding YES CCDS6056.2 ENSP00000301924 Q9UPQ4 UPI00001649FB NM_171982.4 tolerated(0.56) 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103:SF404,hmmpanther:PTHR24103,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1337467786 . 0 207 0 3 0 0 0 0 -20 0.9999983 1 1 1 0 G 3 3 68 27287623 27287623 C G 1 0 0 0 0 1 0 0 0 16998 652 23 4 4 TRIM35 8 27287623 Missense_Mutation SNP C C3N-01023_T 3946571 27287623 117851013 73 20617 HTRA4 0 . GRCh38 8 38978124 38978124 + Missense_Mutation SNP G G A C3N-01023_T C3N-01023_N G G c.943G>A p.Val315Ile p.V315I ENST00000302495 4/9 122 108 14 86 86 0 strelka-varscan-mutect HTRA4,missense_variant,p.Val315Ile,ENST00000302495,NM_153692.3;PLEKHA2,downstream_gene_variant,,ENST00000617275,NM_021623.1; A ENST00000302495 Transcript missense_variant 1043/2095 943/1431 315/476 V/I Gtc/Atc COSM1239105 1 1 HTRA4 HGNC HGNC:26909 protein_coding YES CCDS6110.1 ENSP00000305919 P83105 UPI0000001BEC NM_153692.3 tolerated(1) 4/9 hmmpanther:PTHR22939,hmmpanther:PTHR22939:SF105,Gene3D:2.40.10.10,Pfam_domain:PF13365,Superfamily_domains:SSF50494,Prints_domain:PR00834 1 MODERATE 1 SNV 1 1 1 PASS rs1056292241 . 0 202 8 0 0 0 0 0 -20 0.9999966 1 1 1 0 A 3 1 68 38978124 38978124 G A 1 0 0 0 0 1 0 0 0 7352 1145 40 1 1 HTRA4 8 38978124 Missense_Mutation SNP G C3N-01023_T 11690501 38978124 106160512 74 20618 ADAM18 0 . GRCh38 8 39637313 39637313 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.638A>T p.Gln213Leu p.Q213L ENST00000265707 8/20 74 63 11 81 81 0 strelka-varscan-mutect ADAM18,missense_variant,p.Gln213Leu,ENST00000265707,NM_014237.2;ADAM18,intron_variant,,ENST00000379866,NM_001320313.1;ADAM18,3_prime_UTR_variant,,ENST00000520087,; T ENST00000265707 Transcript missense_variant 683/2388 638/2220 213/739 Q/L cAg/cTg 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 tolerated(0.05) 8/20 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 39637313 39637313 A T 1 0 0 0 0 1 0 0 0 283 188 7 4 4 ADAM18 8 39637313 Missense_Mutation SNP A C3N-01023_T 659189 39637313 105501323 75 20619 CYP7A1 0 . GRCh38 8 58494514 58494514 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1031C>A p.Pro344Gln p.P344Q ENST00000301645 4/6 387 302 85 310 310 0 strelka-varscan-mutect CYP7A1,missense_variant,p.Pro344Gln,ENST00000301645,NM_000780.3; T ENST00000301645 Transcript missense_variant 1169/2950 1031/1515 344/504 P/Q cCa/cAa 1 -1 CYP7A1 HGNC HGNC:2651 protein_coding YES CCDS6171.1 ENSP00000301645 P22680 UPI0000128214 NM_000780.3 deleterious(0.04) 4/6 hmmpanther:PTHR24304,hmmpanther:PTHR24304:SF1,Pfam_domain:PF00067,PIRSF_domain:PIRSF000047,Gene3D:1.10.630.10,PIRSF_domain:PIRSF500625,Superfamily_domains:SSF48264,Prints_domain:PR00465 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 58494514 58494514 G T 1 0 0 0 0 1 0 0 0 3999 1348 47 2 2 CYP7A1 8 58494514 Missense_Mutation SNP G C3N-01023_T 18857201 58494514 86644122 76 20620 TRIM55 0 . GRCh38 8 66174475 66174475 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1529G>T p.Gly510Val p.G510V ENST00000315962 10/10 254 189 65 240 240 0 strelka-varscan-mutect TRIM55,missense_variant,p.Gly510Val,ENST00000315962,NM_184085.1;TRIM55,missense_variant,p.Gly414Val,ENST00000353317,NM_184086.1;TRIM55,missense_variant,p.Trp539Cys,ENST00000276573,NM_033058.2;TRIM55,missense_variant,p.Gly203Val,ENST00000350034,NM_184087.1;CRH,downstream_gene_variant,,ENST00000276571,NM_000756.2;TRIM55,non_coding_transcript_exon_variant,,ENST00000517647,; T ENST00000315962 Transcript missense_variant 1902/2914 1529/1647 510/548 G/V gGa/gTa 1 1 TRIM55 HGNC HGNC:14215 protein_coding YES CCDS6184.1 ENSP00000323913 Q9BYV6 UPI00001CE3B7 NM_184085.1 deleterious_low_confidence(0.01) 10/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 66174475 66174475 G T 1 0 0 0 0 1 0 0 0 17022 1188 41 2 2 TRIM55 8 66174475 Missense_Mutation SNP G C3N-01023_T 7679961 66174475 78964161 77 20621 FREM1 0 . GRCh38 9 14868890 14868890 + Missense_Mutation SNP G G T rs758674491 C3N-01023_T C3N-01023_N G G c.88C>A p.Arg30Ser p.R30S ENST00000422223 3/38 167 121 46 109 108 1 strelka-varscan-mutect FREM1,missense_variant,p.Arg30Ser,ENST00000422223,NM_144966.5;FREM1,missense_variant,p.Arg30Ser,ENST00000380880,;FREM1,missense_variant,p.Arg30Ser,ENST00000380875,; T ENST00000422223 Transcript missense_variant 904/10086 88/6540 30/2179 R/S Cgc/Agc rs758674491,COSM1554447,COSM4685579 1 -1 FREM1 HGNC HGNC:23399 protein_coding YES CCDS47952.1 ENSP00000412940 Q5H8C1 UPI000057A218 NM_144966.5 tolerated(0.68) 3/38 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF24 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs758674491 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 14868890 14868890 G T 1 0 0 0 0 1 0 0 0 5911 1116 39 1 1 FREM1 9 14868890 Missense_Mutation SNP G C3N-01023_T 14868890 123525827 78 20622 FRMPD1 0 . GRCh38 9 37740797 37740797 + Missense_Mutation SNP C C G rs767267038 C3N-01023_T C3N-01023_N C C c.2269C>G p.His757Asp p.H757D ENST00000539465 15/16 215 193 22 132 132 0 strelka-varscan-mutect FRMPD1,missense_variant,p.His757Asp,ENST00000539465,;FRMPD1,missense_variant,p.His757Asp,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; G ENST00000539465 Transcript missense_variant 2862/5465 2269/4737 757/1578 H/D Cac/Gac rs767267038 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC tolerated(0.56) 15/16 MODERATE 1 SNV 1 1 PASS rs767267038 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 37740797 37740797 C G 1 0 0 0 0 1 0 0 0 5927 710 25 4 4 FRMPD1 9 37740797 Missense_Mutation SNP C C3N-01023_T 22871907 37740797 100653920 79 20623 SPATA31A6 0 . GRCh38 9 42183691 42183691 + Nonsense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.4G>T p.Glu2Ter p.E2* ENST00000332857 1/4 114 69 45 83 83 0 strelka-varscan-mutect SPATA31A6,stop_gained,p.Glu2Ter,ENST00000332857,NM_001145196.1;SPATA31A6,upstream_gene_variant,,ENST00000496386,; T ENST00000332857 Transcript stop_gained 33/4209 4/4032 2/1343 E/* Gag/Tag 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 1/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 HIGH 1 SNV 5 1 PASS . . 10 200 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 42183691 42183691 G T 1 0 0 0 0 0 1 0 0 15345 1175 41 2 2 SPATA31A6 9 42183691 Nonsense_Mutation SNP G C3N-01023_T 4442894 42183691 96211026 80 20624 ZCCHC6 0 . GRCh38 9 86322979 86322979 + Missense_Mutation SNP T T G novel C3N-01023_T C3N-01023_N T T c.2771A>C p.Asn924Thr p.N924T ENST00000375963 13/27 149 130 19 129 129 0 strelka-varscan-mutect ZCCHC6,missense_variant,p.Asn213Thr,ENST00000277141,;ZCCHC6,missense_variant,p.Asn924Thr,ENST00000375963,NM_024617.3,NM_001185059.1;ZCCHC6,missense_variant,p.Asn801Thr,ENST00000375960,NM_001185074.1;ZCCHC6,upstream_gene_variant,,ENST00000375957,;ZCCHC6,downstream_gene_variant,,ENST00000469004,; G ENST00000375963 Transcript missense_variant 2944/5379 2771/4488 924/1495 N/T aAt/aCt 1 -1 ZCCHC6 HGNC HGNC:25817 protein_coding YES CCDS35057.1 ENSP00000365130 Q5VYS8 UPI00004588F6 NM_024617.3,NM_001185059.1 tolerated(0.06) 13/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 86322979 86322979 T G 1 0 0 0 0 1 0 0 0 18167 1493 52 5 5 ZCCHC6 9 86322979 Missense_Mutation SNP T C3N-01023_T 44139288 86322979 52071738 81 20625 OR13D1 0 . GRCh38 9 104695009 104695009 + Missense_Mutation SNP G G C rs149708960 C3N-01023_T C3N-01023_N G G c.588G>C p.Met196Ile p.M196I ENST00000318763 1/1 308 274 34 257 257 0 strelka-varscan-mutect OR13D1,missense_variant,p.Met196Ile,ENST00000318763,NM_001004484.1; C ENST00000318763 Transcript missense_variant 588/1041 588/1041 196/346 M/I atG/atC rs149708960,COSM3652587 1 1 OR13D1 HGNC HGNC:14695 protein_coding YES CCDS35094.1 ENSP00000317357 Q8NGV5 UPI0000061E68 NM_001004484.1 tolerated(0.23) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF268,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs149708960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 104695009 104695009 G C 1 0 0 0 0 1 0 0 0 11016 1290 45 4 4 OR13D1 9 104695009 Missense_Mutation SNP G C3N-01023_T 18372030 104695009 33699708 82 20626 SVEP1 0 . GRCh38 9 110408111 110408111 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.7489G>A p.Glu2497Lys p.E2497K ENST00000374469 38/48 342 289 53 243 243 0 strelka-varscan-mutect SVEP1,missense_variant,p.Glu2500Lys,ENST00000401783,;SVEP1,missense_variant,p.Glu2497Lys,ENST00000374469,NM_153366.3; T ENST00000374469 Transcript missense_variant 7684/12194 7489/10716 2497/3571 E/K Gag/Aag 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 tolerated(0.22) 38/48 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 110408111 110408111 C T 1 0 0 0 0 1 0 0 0 15805 835 29 3 3 SVEP1 9 110408111 Missense_Mutation SNP C C3N-01023_T 5713102 110408111 27986606 83 20627 TLR4 0 . GRCh38 9 117713300 117713300 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1172G>T p.Cys391Phe p.C391F ENST00000355622 3/3 397 306 91 257 257 0 strelka-varscan-mutect TLR4,missense_variant,p.Cys391Phe,ENST00000355622,NM_138554.4;TLR4,missense_variant,p.Cys351Phe,ENST00000394487,NM_003266.3;TLR4,non_coding_transcript_exon_variant,,ENST00000472304,;TLR4,downstream_gene_variant,,ENST00000490685,; T ENST00000355622 Transcript missense_variant 1273/4844 1172/2520 391/839 C/F tGt/tTt 1 1 TLR4 HGNC HGNC:11850 protein_coding YES CCDS6818.1 ENSP00000363089 O00206 UPI0000137057 NM_138554.4 deleterious(0.01) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF230,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 117713300 117713300 G T 1 0 0 0 0 1 0 0 0 16399 1377 48 2 2 TLR4 9 117713300 Missense_Mutation SNP G C3N-01023_T 7305189 117713300 20681417 84 20628 FAM208B 0 . GRCh38 10 5730604 5730604 + Missense_Mutation SNP C C T rs748092041 C3N-01023_T C3N-01023_N C C c.605C>T p.Pro202Leu p.P202L ENST00000328090 11/21 163 139 24 153 153 0 strelka-varscan-mutect FAM208B,missense_variant,p.Pro202Leu,ENST00000328090,NM_001321784.1,NM_001321783.1,NM_017782.4;FAM208B,upstream_gene_variant,,ENST00000380270,;RP11-336A10.2,intron_variant,,ENST00000411512,;FAM208B,non_coding_transcript_exon_variant,,ENST00000532080,; T ENST00000328090 Transcript missense_variant 1230/8626 605/7293 202/2430 P/L cCa/cTa rs748092041 1 1 FAM208B HGNC HGNC:23484 protein_coding YES CCDS41485.1 ENSP00000328426 Q5VWN6 UPI00004589BB NM_001321784.1,NM_001321783.1,NM_017782.4 tolerated(0.39) 11/21 hmmpanther:PTHR16207,hmmpanther:PTHR16207:SF10 MODERATE 1 SNV 1 1 PASS rs748092041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 5730604 5730604 C T 1 0 0 0 0 1 0 0 0 5390 594 21 3 3 FAM208B 10 5730604 Missense_Mutation SNP C C3N-01023_T 5730604 128066818 85 20629 SFMBT2 0 . GRCh38 10 7197620 7197620 + Silent SNP G G A novel C3N-01023_T C3N-01023_N G G c.1626C>T p.= p.Y542Y ENST00000397167 15/21 202 187 15 176 176 0 strelka-varscan-mutect SFMBT2,synonymous_variant,p.=,ENST00000397167,NM_001029880.2;SFMBT2,synonymous_variant,p.=,ENST00000361972,NM_001018039.1; A ENST00000397167 Transcript synonymous_variant 1819/8024 1626/2685 542/894 Y taC/taT 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 15/21 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Pfam_domain:PF12140 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 7197620 7197620 G A 1 0 0 0 0 0 0 0 1 14436 1256 44 3 3 SFMBT2 10 7197620 Silent SNP G C3N-01023_T 1467016 7197620 126599802 86 20630 ANKRD30A 0 . GRCh38 10 37219382 37219382 + Missense_Mutation SNP C C T C3N-01023_T C3N-01023_N C C c.3502C>T p.His1168Tyr p.H1168Y ENST00000361713 34/36 224 177 47 153 153 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.His1287Tyr,ENST00000374660,;ANKRD30A,missense_variant,p.His1224Tyr,ENST00000611781,;ANKRD30A,missense_variant,p.His1168Tyr,ENST00000602533,;ANKRD30A,missense_variant,p.His1168Tyr,ENST00000361713,NM_052997.2; T ENST00000361713 Transcript missense_variant 3601/4405 3502/4026 1168/1341 H/Y Cac/Tac COSM3437657,COSM3437658 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 deleterious(0.03) 34/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF14915 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 37219382 37219382 C T 1 0 0 0 0 1 0 0 0 761 594 21 3 3 ANKRD30A 10 37219382 Missense_Mutation SNP C C3N-01023_T 30021762 37219382 96578040 87 20631 ADO 0 . GRCh38 10 62805188 62805188 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.129G>C p.Met43Ile p.M43I ENST00000373783 1/1 149 130 19 94 94 0 strelka-varscan-mutect ADO,missense_variant,p.Met43Ile,ENST00000373783,NM_032804.5;RP11-436D10.3,intron_variant,,ENST00000425290,; C ENST00000373783 Transcript missense_variant 332/3627 129/813 43/270 M/I atG/atC 1 1 ADO HGNC HGNC:23506 protein_coding YES CCDS7266.2 ENSP00000362888 Q96SZ5 UPI00001F8D78 NM_032804.5 tolerated_low_confidence(0.26) 1/1 Superfamily_domains:SSF51182 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 62805188 62805188 G C 1 0 0 0 0 1 0 0 0 400 1319 46 4 4 ADO 10 62805188 Missense_Mutation SNP G C3N-01023_T 25585806 62805188 70992234 88 20632 DNA2 0 . GRCh38 10 68445033 68445033 + Missense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.1108A>T p.Ser370Cys p.S370C ENST00000358410 8/21 188 136 52 149 149 0 strelka-varscan-mutect DNA2,missense_variant,p.Ser370Cys,ENST00000358410,NM_001080449.2;DNA2,missense_variant,p.Ser370Cys,ENST00000551118,;DNA2,missense_variant,p.Ser370Cys,ENST00000399180,;DNA2,missense_variant,p.Ser370Cys,ENST00000399179,;DNA2,upstream_gene_variant,,ENST00000478029,; A ENST00000358410 Transcript missense_variant 1159/4208 1108/3183 370/1060 S/C Agc/Tgc 1 -1 DNA2 HGNC HGNC:2939 protein_coding YES CCDS44415.2 ENSP00000351185 P51530 UPI00001C1EDB NM_001080449.2 tolerated(0.16) 8/21 hmmpanther:PTHR10887:SF14,hmmpanther:PTHR10887 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 68445033 68445033 T A 1 0 0 0 0 1 0 0 0 4405 1522 53 4 4 DNA2 10 68445033 Missense_Mutation SNP T C3N-01023_T 5639845 68445033 65352389 89 20633 KCNMA1 0 . GRCh38 10 76891603 76891603 + Silent SNP G G A novel C3N-01023_T C3N-01023_N G G c.3264C>T p.= p.T1088T ENST00000286628 26/28 585 478 107 384 384 0 strelka-varscan-mutect KCNMA1,synonymous_variant,p.=,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,synonymous_variant,p.=,ENST00000286627,NM_002247.3;KCNMA1,synonymous_variant,p.=,ENST00000286628,NM_001161352.1;KCNMA1,synonymous_variant,p.=,ENST00000354353,;KCNMA1,synonymous_variant,p.=,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,synonymous_variant,p.=,ENST00000372443,;KCNMA1,synonymous_variant,p.=,ENST00000372440,NM_001014797.2;KCNMA1,synonymous_variant,p.=,ENST00000404771,;KCNMA1,synonymous_variant,p.=,ENST00000457953,;KCNMA1,synonymous_variant,p.=,ENST00000626620,NM_001161353.1;KCNMA1,synonymous_variant,p.=,ENST00000372437,;KCNMA1,synonymous_variant,p.=,ENST00000372421,;KCNMA1,synonymous_variant,p.=,ENST00000372408,;KCNMA1,synonymous_variant,p.=,ENST00000372403,;KCNMA1,synonymous_variant,p.=,ENST00000404857,NM_001271518.1;KCNMA1,synonymous_variant,p.=,ENST00000434208,;KCNMA1-AS1,non_coding_transcript_exon_variant,,ENST00000609102,;KCNMA1-AS1,intron_variant,,ENST00000429850,;KCNMA1-AS1,intron_variant,,ENST00000426234,;KCNMA1-AS1,intron_variant,,ENST00000458661,;KCNMA1-AS1,intron_variant,,ENST00000595702,;KCNMA1,upstream_gene_variant,,ENST00000468471,; A ENST00000286628 Transcript synonymous_variant 3264/6100 3264/3711 1088/1236 T acC/acT 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 26/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 76891603 76891603 G A 1 0 0 0 0 0 0 0 1 7990 1219 43 3 3 KCNMA1 10 76891603 Silent SNP G C3N-01023_T 8446570 76891603 56905819 90 20634 LIPF 0 . GRCh38 10 88675659 88675659 + Splice_Site SNP T T C novel C3N-01023_T C3N-01023_N T T c.918+2T>C p.X306_splice ENST00000394375 141 128 13 113 113 0 strelka-varscan-mutect LIPF,splice_donor_variant,,ENST00000394375,NM_001198829.1;LIPF,splice_donor_variant,,ENST00000238983,NM_004190.3;LIPF,splice_donor_variant,,ENST00000355843,NM_001198830.1;LIPF,splice_donor_variant,,ENST00000608620,NM_001198828.1;LIPF,splice_donor_variant,,ENST00000496797,; C ENST00000394375 Transcript splice_donor_variant -/1470 918/1227 306/408 1 1 LIPF HGNC HGNC:6622 protein_coding YES CCDS55718.1 ENSP00000377900 P07098 UPI0001E92A2A NM_001198829.1 9/10 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 68 88675659 88675659 T C 1 0 0 0 0 0 0 1 0 8743 1652 57 5 5 LIPF 10 88675659 Splice_Site SNP T C3N-01023_T 11784056 88675659 45121763 91 20635 SORCS3 0 . GRCh38 10 105223208 105223208 + Missense_Mutation SNP G G T rs746806515 C3N-01023_T C3N-01023_N G G c.2827G>T p.Gly943Trp p.G943W ENST00000369701 20/27 105 87 18 72 72 0 strelka-varscan-mutect SORCS3,missense_variant,p.Gly943Trp,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Gly943Trp,ENST00000369699,; T ENST00000369701 Transcript missense_variant 3054/5757 2827/3669 943/1222 G/W Ggg/Tgg rs746806515,COSM1345688 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0.01) 20/27 Gene3D:2.60.40.670,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Superfamily_domains:SSF49299 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746806515 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 105223208 105223208 G T 1 0 0 0 0 1 0 0 0 15254 1232 43 2 2 SORCS3 10 105223208 Missense_Mutation SNP G C3N-01023_T 16547549 105223208 28574214 92 20636 SHOC2 0 . GRCh38 10 111007541 111007541 + Nonsense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.1172T>A p.Leu391Ter p.L391* ENST00000369452 6/9 413 368 45 318 318 0 strelka-varscan-mutect SHOC2,stop_gained,p.Leu391Ter,ENST00000369452,NM_001324336.1,NM_001324337.1,NM_007373.3;SHOC2,stop_gained,p.Leu345Ter,ENST00000265277,NM_001269039.1;SHOC2,stop_gained,p.Leu181Ter,ENST00000451838,;SHOC2,non_coding_transcript_exon_variant,,ENST00000489390,; A ENST00000369452 Transcript stop_gained 1517/3943 1172/1749 391/582 L/* tTa/tAa 1 1 SHOC2 HGNC HGNC:15454 protein_coding YES CCDS7568.1 ENSP00000358464 Q9UQ13 UPI0000135954 NM_001324336.1,NM_001324337.1,NM_007373.3 6/9 PROSITE_profiles:PS51450,Gene3D:3.80.10.10,Superfamily_domains:SSF52058,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 68 111007541 111007541 T A 1 0 0 0 0 0 1 0 0 14550 1764 61 4 4 SHOC2 10 111007541 Nonsense_Mutation SNP T C3N-01023_T 5784333 111007541 22789881 93 20637 TOLLIP 0 . GRCh38 11 1290388 1290388 + Missense_Mutation SNP C C A rs143130045 C3N-01023_T C3N-01023_N C C c.205G>T p.Gly69Cys p.G69C ENST00000317204 3/6 101 83 18 84 84 0 strelka-varscan-mutect TOLLIP,missense_variant,p.Gly69Cys,ENST00000317204,NM_001318512.1,NM_019009.3;TOLLIP,missense_variant,p.Gly41Cys,ENST00000263646,;TOLLIP,missense_variant,p.Gly19Cys,ENST00000530541,;TOLLIP,5_prime_UTR_variant,,ENST00000527886,NM_001318514.1;TOLLIP,intron_variant,,ENST00000525159,NM_001318516.1;TOLLIP,intron_variant,,ENST00000527938,;TOLLIP,non_coding_transcript_exon_variant,,ENST00000528719,;TOLLIP,downstream_gene_variant,,ENST00000527638,;TOLLIP,missense_variant,p.Gly19Cys,ENST00000530506,;TOLLIP,non_coding_transcript_exon_variant,,ENST00000527746,;TOLLIP,downstream_gene_variant,,ENST00000532551,; A ENST00000317204 Transcript missense_variant 329/3617 205/825 69/274 G/C Ggc/Tgc rs143130045,COSM687237 1 -1 TOLLIP HGNC HGNC:16476 protein_coding YES CCDS7723.1 ENSP00000314733 Q9H0E2 Q6FIE9 UPI0000035D9F NM_001318512.1,NM_019009.3 deleterious(0) 3/6 hmmpanther:PTHR16461:SF5,hmmpanther:PTHR16461,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs143130045 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 1290388 1290388 C A 1 0 0 0 0 1 0 0 0 16824 652 23 1 1 TOLLIP 11 1290388 Missense_Mutation SNP C C3N-01023_T 1290388 133796234 94 20638 DBX1 0 . GRCh38 11 20156520 20156520 + Silent SNP G G A novel C3N-01023_T C3N-01023_N G G c.726C>T p.= p.R242R ENST00000524983 4/4 431 367 64 346 346 0 strelka-varscan-mutect DBX1,synonymous_variant,p.=,ENST00000524983,NM_001029865.2; A ENST00000524983 Transcript synonymous_variant 1015/1380 726/1032 242/343 R cgC/cgT 1 -1 DBX1 HGNC HGNC:33185 protein_coding YES ENSP00000436881 A6NMT0 UPI000013C8B1 NM_001029865.2 4/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF6,SMART_domains:SM00389 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 20156520 20156520 G A 1 0 0 0 0 0 0 0 1 4059 1074 38 1 1 DBX1 11 20156520 Silent SNP G C3N-01023_T 18866132 20156520 114930102 95 20639 KIAA1549L 0 . GRCh38 11 33542625 33542625 + Silent SNP G G T rs58783133 C3N-01023_T C3N-01023_N G G c.171G>T p.= p.P57P ENST00000321505 1/20 144 120 24 103 103 0 strelka-varscan-mutect KIAA1549L,synonymous_variant,p.=,ENST00000321505,NM_012194.2;KIAA1549L,synonymous_variant,p.=,ENST00000265654,;KIAA1549L,intron_variant,,ENST00000526400,; T ENST00000321505 Transcript synonymous_variant 351/11678 171/5550 57/1849 P ccG/ccT rs58783133 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 1/20 Low_complexity_(Seg):seg,hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3 LOW 1 SNV 1 1 PASS rs58783133 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 68 33542625 33542625 G T 1 0 0 0 0 0 0 0 1 8121 1132 40 1 1 KIAA1549L 11 33542625 Silent SNP G C3N-01023_T 13386105 33542625 101543997 96 20640 CHST1 0 . GRCh38 11 45650192 45650192 + Silent SNP G G A C3N-01023_T C3N-01023_N G G c.732C>T p.= p.S244S ENST00000308064 4/4 180 154 26 124 124 0 strelka-varscan-mutect CHST1,synonymous_variant,p.=,ENST00000308064,NM_003654.5;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,upstream_gene_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,; A ENST00000308064 Transcript synonymous_variant 1403/2718 732/1236 244/411 S agC/agT COSM1492521 1 -1 CHST1 HGNC HGNC:1969 protein_coding YES CCDS7913.1 ENSP00000309270 O43916 UPI0000073EA0 NM_003654.5 4/4 hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF36,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS rs1006152663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 45650192 45650192 G A 1 0 0 0 0 0 0 0 1 3157 1078 38 1 1 CHST1 11 45650192 Silent SNP G C3N-01023_T 12107567 45650192 89436430 97 20641 OR5W2 0 . GRCh38 11 55914180 55914180 + Missense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.403A>T p.Asn135Tyr p.N135Y ENST00000344514 1/1 106 91 15 99 99 0 strelka-varscan-mutect OR5W2,missense_variant,p.Asn135Tyr,ENST00000344514,NM_001001960.1; A ENST00000344514 Transcript missense_variant 403/933 403/933 135/310 N/Y Aac/Tac 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 55914180 55914180 T A 1 0 0 0 0 1 0 0 0 11253 1812 63 4 4 OR5W2 11 55914180 Missense_Mutation SNP T C3N-01023_T 10263988 55914180 79172442 98 20642 OR5B12 0 . GRCh38 11 58439830 58439830 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.322G>A p.Ala108Thr p.A108T ENST00000302572 1/1 373 320 53 340 340 0 strelka-varscan-mutect OR5B12,missense_variant,p.Ala108Thr,ENST00000302572,NM_001004733.2; T ENST00000302572 Transcript missense_variant 344/1054 322/945 108/314 A/T Gca/Aca 1 -1 OR5B12 HGNC HGNC:15432 protein_coding YES CCDS31551.1 ENSP00000306657 Q96R08 UPI00000015B2 NM_001004733.2 tolerated_low_confidence(0.21) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF15,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 58439830 58439830 C T 1 0 0 0 0 1 0 0 0 11219 710 25 3 3 OR5B12 11 58439830 Missense_Mutation SNP C C3N-01023_T 2525650 58439830 76646792 99 20643 TRIM77 0 . GRCh38 11 89710453 89710453 + Missense_Mutation SNP G G C rs545633553 C3N-01023_T C3N-01023_N G G c.155G>C p.Cys52Ser p.C52S ENST00000398290 1/6 162 146 16 128 128 0 strelka-varscan-mutect TRIM77,missense_variant,p.Cys52Ser,ENST00000398290,NM_001146162.1,NM_001271942.1;TRIM77,upstream_gene_variant,,ENST00000534392,; C ENST00000398290 Transcript missense_variant 155/1353 155/1353 52/450 C/S tGc/tCc rs545633553 1 1 TRIM77 HGNC HGNC:34228 protein_coding YES CCDS60929.1 ENSP00000474003 I1YAP6 UPI00001607F2 NM_001146162.1,NM_001271942.1 deleterious(0) 1/6 PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF353,Pfam_domain:PF00097,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS rs545633553 . 0 207 0 2 0 0 0 0 -19.99831 0.9999998 1 1 1 0 C 3 2 68 89710453 89710453 G C 1 0 0 0 0 1 0 0 0 17044 1319 46 4 4 TRIM77 11 89710453 Missense_Mutation SNP G C3N-01023_T 31270623 89710453 45376169 100 20644 ATM 0 . GRCh38 11 108317487 108317487 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.6313A>T p.Arg2105Trp p.R2105W ENST00000278616 43/63 413 347 66 310 308 2 strelka-varscan-mutect ATM,missense_variant,p.Arg2105Trp,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Arg2105Trp,ENST00000452508,;C11orf65,intron_variant,,ENST00000525729,;ATM,downstream_gene_variant,,ENST00000532765,;ATM,non_coding_transcript_exon_variant,,ENST00000524792,;ATM,non_coding_transcript_exon_variant,,ENST00000533690,;ATM,downstream_gene_variant,,ENST00000529588,; T ENST00000278616 Transcript missense_variant 6698/13147 6313/9171 2105/3056 R/W Agg/Tgg 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 deleterious(0) 43/63 PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF72,hmmpanther:PTHR11139,Pfam_domain:PF02259 MODERATE 1 SNV 5 1 PASS rs879253983 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 108317487 108317487 A T 1 0 0 0 0 1 0 0 0 1261 295 11 4 4 ATM 11 108317487 Missense_Mutation SNP A C3N-01023_T 18607034 108317487 26769135 101 20645 ARHGAP20 0 . GRCh38 11 110579819 110579819 + Missense_Mutation SNP C C A rs776441588 C3N-01023_T C3N-01023_N C C c.3127G>T p.Ala1043Ser p.A1043S ENST00000260283 16/16 183 139 44 115 114 1 strelka-varscan-mutect ARHGAP20,missense_variant,p.Ala1043Ser,ENST00000260283,NM_020809.3;ARHGAP20,missense_variant,p.Ala1020Ser,ENST00000524756,NM_001258415.1;ARHGAP20,missense_variant,p.Ala1017Ser,ENST00000533353,NM_001258416.1;ARHGAP20,missense_variant,p.Ala1007Ser,ENST00000527598,NM_001258418.1;ARHGAP20,missense_variant,p.Ala1007Ser,ENST00000528829,NM_001258417.1;ARHGAP20,missense_variant,p.Ala586Ser,ENST00000529591,; A ENST00000260283 Transcript missense_variant 3412/6189 3127/3576 1043/1191 A/S Gcc/Tcc rs776441588 1 -1 ARHGAP20 HGNC HGNC:18357 protein_coding YES CCDS31673.1 ENSP00000260283 Q9P2F6 UPI000013D0BA NM_020809.3 tolerated(0.32) 16/16 hmmpanther:PTHR23179,hmmpanther:PTHR23179:SF28 MODERATE 1 SNV 1 1 PASS rs776441588 . 0 207 0 3 0 0 0 0 -20 0.9999976 1 1 1 0 A 3 1 68 110579819 110579819 C A 1 0 0 0 0 1 0 0 0 994 739 26 2 2 ARHGAP20 11 110579819 Missense_Mutation SNP C C3N-01023_T 2262332 110579819 24506803 102 20646 C11orf63 0 . GRCh38 11 122904087 122904087 + Silent SNP G G A C3N-01023_T C3N-01023_N G G c.507G>A p.= p.T169T ENST00000227349 3/9 347 299 48 257 257 0 strelka-varscan-mutect C11orf63,synonymous_variant,p.=,ENST00000227349,NM_024806.3;C11orf63,synonymous_variant,p.=,ENST00000531316,;C11orf63,synonymous_variant,p.=,ENST00000307257,NM_199124.2; A ENST00000227349 Transcript synonymous_variant 1041/3147 507/2337 169/778 T acG/acA COSM924127 1 1 C11orf63 HGNC HGNC:26288 protein_coding YES CCDS8438.1 ENSP00000227349 Q6NUN7 UPI00001FA5AB NM_024806.3 3/9 hmmpanther:PTHR14726,hmmpanther:PTHR14726:SF1 1 LOW 1 SNV 1 1 1 PASS rs992412552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 122904087 122904087 G A 1 0 0 0 0 0 0 0 1 1790 1132 40 1 1 C11orf63 11 122904087 Silent SNP G C3N-01023_T 12324268 122904087 12182535 103 20647 GRAMD1B 0 . GRCh38 11 123608765 123608765 + Silent SNP C C A novel C3N-01023_T C3N-01023_N C C c.1212C>A p.= p.P404P ENST00000456860 12/21 135 122 13 98 98 0 strelka-varscan-mutect GRAMD1B,synonymous_variant,p.=,ENST00000529750,NM_020716.2;GRAMD1B,synonymous_variant,p.=,ENST00000529432,NM_001286564.1;GRAMD1B,synonymous_variant,p.=,ENST00000638157,;GRAMD1B,synonymous_variant,p.=,ENST00000635736,;GRAMD1B,synonymous_variant,p.=,ENST00000456860,NM_001286563.1;GRAMD1B,synonymous_variant,p.=,ENST00000638086,;GRAMD1B,synonymous_variant,p.=,ENST00000322282,;GRAMD1B,synonymous_variant,p.=,ENST00000450171,;GRAMD1B,synonymous_variant,p.=,ENST00000534764,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,upstream_gene_variant,,ENST00000525945,; A ENST00000456860 Transcript synonymous_variant 1725/2805 1212/2238 404/745 P ccC/ccA 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 12/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319,Pfam_domain:PF16016 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 123608765 123608765 C A 1 0 0 0 0 0 0 0 1 6627 668 24 2 2 GRAMD1B 11 123608765 Silent SNP C C3N-01023_T 704678 123608765 11477857 104 20648 NTM 0 . GRCh38 11 132146495 132146495 + Silent SNP G G A C3N-01023_T C3N-01023_N G G c.381G>A p.= p.R127R ENST00000425719 2/8 166 149 17 127 127 0 strelka-varscan-mutect NTM,synonymous_variant,p.=,ENST00000374786,NM_016522.2;NTM,synonymous_variant,p.=,ENST00000374791,NM_001048209.1;NTM,synonymous_variant,p.=,ENST00000425719,NM_001144058.1;NTM,synonymous_variant,p.=,ENST00000374784,NM_001144059.1;NTM,synonymous_variant,p.=,ENST00000550167,;NTM,5_prime_UTR_variant,,ENST00000427481,;NTM,5_prime_UTR_variant,,ENST00000539799,;NTM,non_coding_transcript_exon_variant,,ENST00000467255,;NTM,intron_variant,,ENST00000498764,;NTM,non_coding_transcript_exon_variant,,ENST00000479431,; A ENST00000425719 Transcript synonymous_variant 401/1607 381/1068 127/355 R agG/agA COSM5372080,COSM5372081,COSM5372082,COSM5372083 1 1 NTM HGNC HGNC:17941 protein_coding YES CCDS44777.1 ENSP00000396722 Q9P121 UPI00001A58B9 NM_001144058.1 2/8 hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF116,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 132146495 132146495 G A 1 0 0 0 0 0 0 0 1 10763 1223 43 3 3 NTM 11 132146495 Silent SNP G C3N-01023_T 8537730 132146495 2940127 105 20649 B3GAT1 0 . GRCh38 11 134383811 134383811 + Missense_Mutation SNP G G T C3N-01023_T C3N-01023_N G G c.490C>A p.Pro164Thr p.P164T ENST00000524765 3/6 197 179 18 144 144 0 strelka-varscan-mutect B3GAT1,missense_variant,p.Pro164Thr,ENST00000524765,;B3GAT1,missense_variant,p.Pro164Thr,ENST00000312527,NM_054025.2;B3GAT1,missense_variant,p.Pro164Thr,ENST00000392580,NM_018644.3;B3GAT1,downstream_gene_variant,,ENST00000531510,;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531778,; T ENST00000524765 Transcript missense_variant 5035/5737 490/1005 164/334 P/T Ccg/Acg COSM3445561,COSM3445562 1 -1 B3GAT1 HGNC HGNC:921 protein_coding YES CCDS8500.1 ENSP00000433847 Q9P2W7 UPI0000073281 deleterious(0) 3/6 Gene3D:3.90.550.10,Pfam_domain:PF03360,hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF21,Superfamily_domains:SSF53448 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1229449843 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 134383811 134383811 G T 1 0 0 0 0 1 0 0 0 1409 1232 43 2 2 B3GAT1 11 134383811 Missense_Mutation SNP G C3N-01023_T 2237316 134383811 702811 106 20650 CLSTN3 0 . GRCh38 12 7142970 7142970 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1642G>T p.Ala548Ser p.A548S ENST00000266546 11/18 222 203 19 154 154 0 varscan-mutect CLSTN3,missense_variant,p.Ala560Ser,ENST00000537408,;CLSTN3,missense_variant,p.Ala548Ser,ENST00000266546,NM_014718.3;CLSTN3,non_coding_transcript_exon_variant,,ENST00000544584,;CLSTN3,downstream_gene_variant,,ENST00000535668,;CLSTN3,upstream_gene_variant,,ENST00000541770,; T ENST00000266546 Transcript missense_variant 2092/4185 1642/2871 548/956 A/S Gca/Tca 1 1 CLSTN3 HGNC HGNC:18371 protein_coding YES CCDS8575.1 ENSP00000266546 Q9BQT9 UPI0000049E7C NM_014718.3 tolerated(0.07) 11/18 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF5,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 7142970 7142970 G T 1 0 0 0 0 1 0 0 0 3335 1319 46 2 2 CLSTN3 12 7142970 Missense_Mutation SNP G C3N-01023_T 7142970 126132339 107 20651 PTPRO 0 . GRCh38 12 15516927 15516927 + Missense_Mutation SNP G G A C3N-01023_T C3N-01023_N G G c.1750G>A p.Ala584Thr p.A584T ENST00000281171 9/27 314 269 45 245 244 1 strelka-varscan-mutect PTPRO,missense_variant,p.Ala584Thr,ENST00000281171,NM_030667.2;PTPRO,missense_variant,p.Ala584Thr,ENST00000348962,NM_002848.3;PTPRO,missense_variant,p.Ala584Thr,ENST00000543886,; A ENST00000281171 Transcript missense_variant 2080/5301 1750/3651 584/1216 A/T Gca/Aca COSM5273172 1 1 PTPRO HGNC HGNC:9678 protein_coding YES CCDS8675.1 ENSP00000281171 Q16827 UPI000013DC62 NM_030667.2 tolerated(0.08) 9/27 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF315,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 15516927 15516927 G A 1 0 0 0 0 1 0 0 0 12963 971 34 3 3 PTPRO 12 15516927 Missense_Mutation SNP G C3N-01023_T 8373957 15516927 117758382 108 20652 BCAT1 0 . GRCh38 12 24881316 24881316 + Silent SNP C C T novel C3N-01023_T C3N-01023_N C C c.411G>A p.= p.V137V ENST00000539282 4/11 205 151 54 145 145 0 strelka-varscan-mutect BCAT1,synonymous_variant,p.=,ENST00000261192,NM_005504.6;BCAT1,synonymous_variant,p.=,ENST00000538118,NM_001178094.1;BCAT1,synonymous_variant,p.=,ENST00000539282,NM_001178093.1;BCAT1,synonymous_variant,p.=,ENST00000546285,;BCAT1,intron_variant,,ENST00000342945,NM_001178092.1;BCAT1,intron_variant,,ENST00000539780,NM_001178091.1;BCAT1,non_coding_transcript_exon_variant,,ENST00000544418,;BCAT1,synonymous_variant,p.=,ENST00000612790,; T ENST00000539282 Transcript synonymous_variant 498/1811 411/1197 137/398 V gtG/gtA 1 -1 BCAT1 HGNC HGNC:976 protein_coding YES CCDS53761.1 ENSP00000443459 P54687 UPI0001D27F89 NM_001178093.1 4/11 hmmpanther:PTHR11825,hmmpanther:PTHR11825:SF51,Gene3D:3.30.470.10,TIGRFAM_domain:TIGR01123,Pfam_domain:PF01063,PIRSF_domain:PIRSF006468,Superfamily_domains:SSF56752 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 24881316 24881316 C T 1 0 0 0 0 0 0 0 1 1501 813 29 3 3 BCAT1 12 24881316 Silent SNP C C3N-01023_T 9364389 24881316 108393993 109 20653 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-01023_T C3N-01023_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 366 273 93 286 284 2 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-01023_T 364035 25245351 108029958 110 20654 KIAA1551 0 . GRCh38 12 31981611 31981611 + Missense_Mutation SNP G G C rs139948313 C3N-01023_T C3N-01023_N G G c.656G>C p.Arg219Pro p.R219P ENST00000312561 4/6 398 319 79 296 296 0 strelka-varscan-mutect KIAA1551,missense_variant,p.Arg219Pro,ENST00000312561,NM_018169.3;KIAA1551,missense_variant,p.Arg219Pro,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,; C ENST00000312561 Transcript missense_variant 1070/6230 656/5244 219/1747 R/P cGt/cCt rs139948313 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 tolerated(0.28) 4/6 hmmpanther:PTHR21604 MODERATE 1 SNV 1 1 PASS rs139948313 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 31981611 31981611 G C 1 0 0 0 0 1 0 0 0 8122 1145 40 4 4 KIAA1551 12 31981611 Missense_Mutation SNP G C3N-01023_T 6736260 31981611 101293698 111 20655 PKP2 0 . GRCh38 12 32843223 32843223 + Missense_Mutation SNP C C A rs369518480 C3N-01023_T C3N-01023_N C C c.1469G>T p.Arg490Leu p.R490L ENST00000070846 6/14 97 69 28 73 73 0 strelka-varscan-mutect PKP2,missense_variant,p.Arg490Leu,ENST00000070846,NM_004572.3;PKP2,intron_variant,,ENST00000340811,NM_001005242.2; A ENST00000070846 Transcript missense_variant 1494/4241 1469/2646 490/881 R/L cGg/cTg rs369518480 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 tolerated_low_confidence(0.65) 6/14 MODERATE 1 SNV 1 1 PASS rs369518480 . 0 199 8 3 0 0 0 0 -20 0.9996792 1 1 1 0 A 3 1 68 32843223 32843223 C A 1 0 0 0 0 1 0 0 0 12081 652 23 1 1 PKP2 12 32843223 Missense_Mutation SNP C C3N-01023_T 861612 32843223 100432086 112 20656 KRT6B 0 . GRCh38 12 52451635 52451635 + Silent SNP G G T C3N-01023_T C3N-01023_N G G c.444C>A p.= p.L148L ENST00000252252 1/9 357 316 41 234 234 0 varscan-mutect KRT6B,synonymous_variant,p.=,ENST00000252252,NM_005555.3; T ENST00000252252 Transcript synonymous_variant 492/2282 444/1695 148/564 L ctC/ctA COSM403660 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 1/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Pfam_domain:PF16208 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 52451635 52451635 G T 1 0 0 0 0 0 0 0 1 8363 1277 45 2 2 KRT6B 12 52451635 Silent SNP G C3N-01023_T 19608412 52451635 80823674 113 20657 DPY19L2 0 . GRCh38 12 63560604 63560604 + Missense_Mutation SNP G G T rs199856082 C3N-01023_T C3N-01023_N G G c.2185C>A p.Pro729Thr p.P729T ENST00000324472 22/22 371 310 61 316 315 1 strelka-varscan-mutect DPY19L2,missense_variant,p.Pro729Thr,ENST00000324472,NM_173812.4;DPY19L2,3_prime_UTR_variant,,ENST00000439061,;DPY19L2,non_coding_transcript_exon_variant,,ENST00000413230,;DPY19L2,non_coding_transcript_exon_variant,,ENST00000541911,; T ENST00000324472 Transcript missense_variant 2369/4060 2185/2277 729/758 P/T Cct/Act rs199856082 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 tolerated(0.58) 22/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6 MODERATE 1 SNV 1 1 PASS rs199856082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 63560604 63560604 G T 1 0 0 0 0 1 0 0 0 4556 1232 43 2 2 DPY19L2 12 63560604 Missense_Mutation SNP G C3N-01023_T 11108969 63560604 69714705 114 20658 POC1B 0 . GRCh38 12 89492006 89492006 + Missense_Mutation SNP C C A rs749740287 C3N-01023_T C3N-01023_N C C c.382G>T p.Val128Leu p.V128L ENST00000313546 4/12 183 152 31 111 111 0 strelka-varscan-mutect POC1B,missense_variant,p.Val128Leu,ENST00000313546,NM_172240.2;POC1B,missense_variant,p.Val86Leu,ENST00000549035,NM_001199777.1;POC1B,5_prime_UTR_variant,,ENST00000393179,;POC1B,5_prime_UTR_variant,,ENST00000549504,;POC1B,3_prime_UTR_variant,,ENST00000547496,;POC1B,3_prime_UTR_variant,,ENST00000548715,;POC1B,3_prime_UTR_variant,,ENST00000547274,;POC1B,non_coding_transcript_exon_variant,,ENST00000539190,;POC1B,non_coding_transcript_exon_variant,,ENST00000552563,;POC1B,downstream_gene_variant,,ENST00000546830,; A ENST00000313546 Transcript missense_variant 511/3001 382/1437 128/478 V/L Gta/Tta rs749740287 1 -1 POC1B HGNC HGNC:30836 protein_coding YES CCDS31869.1 ENSP00000323302 Q8TC44 A0MNP0 UPI000006E6B9 NM_172240.2 tolerated(0.34) 4/12 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320 MODERATE 1 SNV 1 1 PASS rs749740287 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 89492006 89492006 C A 1 0 0 0 0 1 0 0 0 12285 565 20 2 2 POC1B 12 89492006 Missense_Mutation SNP C C3N-01023_T 25931402 89492006 43783303 115 20659 KSR2 0 . GRCh38 12 117667571 117667571 + Silent SNP C C A rs370976488 C3N-01023_T C3N-01023_N C C c.987G>T p.= p.P329P ENST00000425217 5/20 184 143 41 115 115 0 strelka-varscan-mutect KSR2,synonymous_variant,p.=,ENST00000339824,;KSR2,synonymous_variant,p.=,ENST00000425217,NM_173598.4;KSR2,non_coding_transcript_exon_variant,,ENST00000545002,; A ENST00000425217 Transcript synonymous_variant 1042/17008 987/2766 329/921 P ccG/ccT rs370976488 1 -1 KSR2 HGNC HGNC:18610 protein_coding YES CCDS61250.1 ENSP00000389715 E9PB13 UPI000164FA1C NM_173598.4 5/20 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS rs370976488 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 117667571 117667571 C A 1 0 0 0 0 0 0 0 1 8481 755 27 1 1 KSR2 12 117667571 Silent SNP C C3N-01023_T 28175565 117667571 15607738 116 20660 ZNF84 0 . GRCh38 12 133048004 133048004 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.65G>C p.Trp22Ser p.W22S ENST00000327668 3/5 204 148 56 151 151 0 strelka-varscan-mutect ZNF84,missense_variant,p.Trp22Ser,ENST00000327668,NM_001289972.1;ZNF84,missense_variant,p.Trp22Ser,ENST00000392319,NM_001289971.1,NM_001127372.2,NM_003428.5;ZNF84,missense_variant,p.Trp22Ser,ENST00000543758,;ZNF84,missense_variant,p.Trp22Ser,ENST00000539354,;ZNF84,missense_variant,p.Trp22Ser,ENST00000540031,;ZNF84,missense_variant,p.Trp22Ser,ENST00000535439,;ZNF84,missense_variant,p.Trp22Ser,ENST00000543310,;ZNF84,missense_variant,p.Trp22Ser,ENST00000438628,;ZNF84,missense_variant,p.Trp22Ser,ENST00000536123,;ZNF84,missense_variant,p.Trp22Ser,ENST00000542874,;ZNF84,non_coding_transcript_exon_variant,,ENST00000543124,;ZNF84,non_coding_transcript_exon_variant,,ENST00000542358,;ZNF84,non_coding_transcript_exon_variant,,ENST00000539686,;ZNF84,non_coding_transcript_exon_variant,,ENST00000539098,;ZNF84,non_coding_transcript_exon_variant,,ENST00000441040,; C ENST00000327668 Transcript missense_variant 645/7162 65/2217 22/738 W/S tGg/tCg 1 1 ZNF84 HGNC HGNC:13159 protein_coding YES CCDS31940.1 ENSP00000331465 P51523 UPI000016AACC NM_001289972.1 deleterious(0) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF146,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 133048004 133048004 G C 1 0 0 0 0 1 0 0 0 18775 1357 47 4 4 ZNF84 12 133048004 Missense_Mutation SNP G C3N-01023_T 15380433 133048004 227305 117 20661 ALG11 0 . GRCh38 13 52019100 52019100 + Missense_Mutation SNP G G A novel C3N-01023_T C3N-01023_N G G c.232G>A p.Gly78Arg p.G78R ENST00000521508 2/4 282 222 60 180 180 0 strelka-varscan-mutect ALG11,missense_variant,p.Gly78Arg,ENST00000521508,NM_001004127.2;ALG11,intron_variant,,ENST00000523764,;ALG11,downstream_gene_variant,,ENST00000616513,;ALG11,upstream_gene_variant,,ENST00000519151,; A ENST00000521508 Transcript missense_variant 237/2558 232/1479 78/492 G/R Gga/Aga 1 1 ALG11 HGNC HGNC:32456 protein_coding YES CCDS31977.1 ENSP00000430236 Q2TAA5 UPI000044C60E NM_001004127.2 deleterious(0) 2/4 hmmpanther:PTHR12526,hmmpanther:PTHR12526:SF315,Pfam_domain:PF15924,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 52019100 52019100 G A 1 0 0 0 0 1 0 0 0 613 1001 35 3 3 ALG11 13 52019100 Missense_Mutation SNP G C3N-01023_T 52019100 62345228 118 20662 KCTD12 0 . GRCh38 13 76885580 76885580 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.569C>A p.Ala190Glu p.A190E ENST00000377474 1/1 129 109 20 95 95 0 strelka-mutect KCTD12,missense_variant,p.Ala190Glu,ENST00000377474,NM_138444.3;AC000403.4,upstream_gene_variant,,ENST00000613696,; T ENST00000377474 Transcript missense_variant 811/6225 569/978 190/325 A/E gCg/gAg 1 -1 KCTD12 HGNC HGNC:14678 protein_coding YES CCDS9455.1 ENSP00000366694 Q96CX2 A0A140VJM4 UPI0000073DDF NM_138444.3 tolerated(0.17) 1/1 hmmpanther:PTHR14499:SF29,hmmpanther:PTHR14499 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 76885580 76885580 G T 1 0 0 0 0 1 0 0 0 8016 1087 38 1 1 KCTD12 13 76885580 Missense_Mutation SNP G C3N-01023_T 24866480 76885580 37478748 119 20663 GPC5 0 . GRCh38 13 92144881 92144881 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1453G>T p.Gly485Cys p.G485C ENST00000377067 7/8 106 89 17 119 118 1 strelka-varscan-mutect GPC5,missense_variant,p.Gly485Cys,ENST00000377067,NM_004466.5; T ENST00000377067 Transcript missense_variant 1893/2957 1453/1719 485/572 G/C Ggc/Tgc 1 1 GPC5 HGNC HGNC:4453 protein_coding YES CCDS9468.1 ENSP00000366267 P78333 UPI0000001C85 NM_004466.5 deleterious(0) 7/8 hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF12,Pfam_domain:PF01153 MODERATE 1 SNV 1 1 PASS rs951460621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 92144881 92144881 G T 1 0 0 0 0 1 0 0 0 6503 1232 43 2 2 GPC5 13 92144881 Missense_Mutation SNP G C3N-01023_T 15259301 92144881 22219447 120 20664 GPC6 0 . GRCh38 13 93227570 93227570 + Silent SNP T T G novel C3N-01023_T C3N-01023_N T T c.114T>G p.= p.G38G ENST00000377047 1/9 214 198 16 138 138 0 strelka-varscan-mutect GPC6,synonymous_variant,p.=,ENST00000377047,NM_005708.3;RP11-632L2.2,upstream_gene_variant,,ENST00000610286,; G ENST00000377047 Transcript synonymous_variant 729/6467 114/1668 38/555 G ggT/ggG 1 1 GPC6 HGNC HGNC:4454 protein_coding YES CCDS9469.1 ENSP00000366246 Q9Y625 UPI0000032F5B NM_005708.3 1/9 Pfam_domain:PF01153,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF31 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 68 93227570 93227570 T G 1 0 0 0 0 0 0 0 1 6504 1683 59 5 5 GPC6 13 93227570 Silent SNP T C3N-01023_T 1082689 93227570 21136758 121 20665 OR4K1 0 . GRCh38 14 19935899 19935899 + Missense_Mutation SNP C C A rs777615482 C3N-01023_T C3N-01023_N C C c.233C>A p.Thr78Asn p.T78N ENST00000285600 1/1 374 350 24 289 288 1 strelka-varscan-mutect OR4K1,missense_variant,p.Thr78Asn,ENST00000285600,NM_001004063.2; A ENST00000285600 Transcript missense_variant 292/1076 233/936 78/311 T/N aCc/aAc rs777615482 1 1 OR4K1 HGNC HGNC:14726 protein_coding YES CCDS32025.1 ENSP00000285600 Q8NGD4 UPI0000041B4A NM_001004063.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF182,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs777615482 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 19935899 19935899 C A 1 0 0 0 0 1 0 0 0 11144 507 18 2 2 OR4K1 14 19935899 Missense_Mutation SNP C C3N-01023_T 19935899 87107819 122 20666 JPH4 0 . GRCh38 14 23571185 23571185 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.1546G>T p.Asp516Tyr p.D516Y ENST00000397118 6/7 235 211 24 130 130 0 strelka-varscan-mutect JPH4,missense_variant,p.Asp516Tyr,ENST00000397118,NM_032452.2;JPH4,missense_variant,p.Asp516Tyr,ENST00000356300,NM_001146028.1;JPH4,missense_variant,p.Asp517Tyr,ENST00000622501,;JPH4,missense_variant,p.Asp181Tyr,ENST00000544177,;AP1G2,upstream_gene_variant,,ENST00000308724,NM_001282475.1;AP1G2,upstream_gene_variant,,ENST00000397120,NM_001282474.1,NM_003917.4;AP1G2,upstream_gene_variant,,ENST00000557189,;AP1G2,upstream_gene_variant,,ENST00000556843,;RP11-66N24.3,downstream_gene_variant,,ENST00000555968,;AP1G2,upstream_gene_variant,,ENST00000556277,;AP1G2,upstream_gene_variant,,ENST00000460049,;AP1G2,upstream_gene_variant,,ENST00000465445,;AP1G2,upstream_gene_variant,,ENST00000535852,;JPH4,downstream_gene_variant,,ENST00000553505,;AP1G2,upstream_gene_variant,,ENST00000556743,;AP1G2,upstream_gene_variant,,ENST00000553629,;AP1G2,upstream_gene_variant,,ENST00000557619,;AP1G2,upstream_gene_variant,,ENST00000555896,;AP1G2,upstream_gene_variant,,ENST00000554069,;AP1G2,upstream_gene_variant,,ENST00000556943,;AP1G2,upstream_gene_variant,,ENST00000557482,;AP1G2,upstream_gene_variant,,ENST00000553756,;AP1G2,upstream_gene_variant,,ENST00000554312,;AP1G2,upstream_gene_variant,,ENST00000553685,;AP1G2,upstream_gene_variant,,ENST00000554816,; A ENST00000397118 Transcript missense_variant 2449/4386 1546/1887 516/628 D/Y Gat/Tat 1 -1 JPH4 HGNC HGNC:20156 protein_coding YES CCDS9603.1 ENSP00000380307 Q96JJ6 UPI00001C1F68 NM_032452.2 deleterious(0.01) 6/7 hmmpanther:PTHR23085,hmmpanther:PTHR23085:SF14,PIRSF_domain:PIRSF037387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 23571185 23571185 C A 1 0 0 0 0 1 0 0 0 7875 855 30 2 2 JPH4 14 23571185 Missense_Mutation SNP C C3N-01023_T 3635286 23571185 83472533 123 20667 KLHDC1 0 . GRCh38 14 49728947 49728947 + Nonsense_Mutation SNP C C T rs767154456 C3N-01023_T C3N-01023_N C C c.589C>T p.Arg197Ter p.R197* ENST00000359332 7/13 316 284 32 228 227 1 strelka-varscan-mutect KLHDC1,stop_gained,p.Arg197Ter,ENST00000359332,NM_172193.2;KLHDC1,stop_gained,p.Arg68Ter,ENST00000557128,;KLHDC1,synonymous_variant,p.=,ENST00000553274,;KLHDC1,non_coding_transcript_exon_variant,,ENST00000554512,;KLHDC1,3_prime_UTR_variant,,ENST00000555704,;KLHDC1,3_prime_UTR_variant,,ENST00000556392,; T ENST00000359332 Transcript stop_gained 679/2691 589/1221 197/406 R/* Cga/Tga rs767154456 1 1 KLHDC1 HGNC HGNC:19836 protein_coding YES CCDS9692.1 ENSP00000352282 Q8N7A1 UPI0000072D4D NM_172193.2 7/13 hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF317,Gene3D:1zgkA00,Pfam_domain:PF13418,Superfamily_domains:0052715 HIGH 1 SNV 1 1 PASS rs767154456 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 49728947 49728947 C T 1 0 0 0 0 0 1 0 0 8219 528 19 1 1 KLHDC1 14 49728947 Nonsense_Mutation SNP C C3N-01023_T 26157762 49728947 57314771 124 20668 VRTN 0 . GRCh38 14 74358326 74358326 + Missense_Mutation SNP G G A novel C3N-01023_T C3N-01023_N G G c.1543G>A p.Ala515Thr p.A515T ENST00000256362 2/2 77 56 21 69 69 0 strelka-varscan-mutect VRTN,missense_variant,p.Ala515Thr,ENST00000256362,NM_018228.2;VRTN,downstream_gene_variant,,ENST00000557177,; A ENST00000256362 Transcript missense_variant 1784/3466 1543/2109 515/702 A/T Gcc/Acc 1 1 VRTN HGNC HGNC:20223 protein_coding YES CCDS9830.1 ENSP00000256362 Q9H8Y1 UPI00000737D5 NM_018228.2 deleterious(0) 2/2 hmmpanther:PTHR16081,hmmpanther:PTHR16081:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 68 74358326 74358326 G A 1 0 0 0 0 1 0 0 0 17771 1319 46 3 3 VRTN 14 74358326 Missense_Mutation SNP G C3N-01023_T 24629379 74358326 32685392 125 20669 SLC25A47 0 . GRCh38 14 100329435 100329435 + Missense_Mutation SNP C C A rs754918242 C3N-01023_T C3N-01023_N C C c.717C>A p.Asp239Glu p.D239E ENST00000361529 6/6 180 114 66 141 141 0 strelka-varscan-mutect SLC25A47,missense_variant,p.Asp239Glu,ENST00000361529,NM_207117.2;SLC25A47,missense_variant,p.Asp93Glu,ENST00000557052,;WARS,downstream_gene_variant,,ENST00000355338,NM_173701.1;WARS,downstream_gene_variant,,ENST00000392882,NM_004184.3;WARS,downstream_gene_variant,,ENST00000344102,NM_213646.1;WARS,downstream_gene_variant,,ENST00000358655,NM_213645.1;RP11-638I2.8,upstream_gene_variant,,ENST00000557226,; A ENST00000361529 Transcript missense_variant 795/1738 717/927 239/308 D/E gaC/gaA rs754918242 1 1 SLC25A47 HGNC HGNC:20115 protein_coding YES CCDS9959.1 ENSP00000354886 Q6Q0C1 A0A024R6H7 UPI000004ABFB NM_207117.2 deleterious(0) 6/6 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF224,hmmpanther:PTHR24089,Pfam_domain:PF00153,Gene3D:1okcA00,Superfamily_domains:0048588,Prints_domain:PR00926 MODERATE 1 SNV 1 1 PASS rs754918242 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 100329435 100329435 C A 1 0 0 0 0 1 0 0 0 14777 535 19 1 1 SLC25A47 14 100329435 Missense_Mutation SNP C C3N-01023_T 25971109 100329435 6714283 126 20670 POTEB3 0 . GRCh38 15 21422128 21422128 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.1189C>A p.Gln397Lys p.Q397K ENST00000611217 7/11 228 210 18 178 178 0 varscan-mutect POTEB3,missense_variant,p.Gln397Lys,ENST00000611217,NM_207355.3;POTEB3,intron_variant,,ENST00000624267,;POTEB3,downstream_gene_variant,,ENST00000612601,; T ENST00000611217 Transcript missense_variant 1237/1813 1189/1746 397/581 Q/K Cag/Aag 1 -1 POTEB3 HGNC HGNC:51240 protein_coding YES CCDS73690.1 ENSP00000483103 A0JP26,Q6S5H4 UPI0000197FCA NM_207355.3 tolerated(0.06) 7/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38 MODERATE 1 SNV 1 1 PASS rs1227898734 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 21422128 21422128 G T 1 0 0 0 0 1 0 0 0 12375 1357 47 2 2 POTEB3 15 21422128 Missense_Mutation SNP G C3N-01023_T 21422128 80569061 127 20671 STARD9 0 . GRCh38 15 42684463 42684463 + Missense_Mutation SNP G G T rs542925209 C3N-01023_T C3N-01023_N G G c.2885G>T p.Arg962Met p.R962M ENST00000290607 23/33 134 110 24 104 104 0 strelka-varscan-mutect STARD9,missense_variant,p.Arg962Met,ENST00000290607,NM_020759.2;STARD9,downstream_gene_variant,,ENST00000569419,;STARD9,downstream_gene_variant,,ENST00000562139,; T ENST00000290607 Transcript missense_variant 2942/15567 2885/14103 962/4700 R/M aGg/aTg rs542925209 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 deleterious(0.04) 23/33 MODERATE 1 SNV 5 1 PASS rs542925209 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 42684463 42684463 G T 1 0 0 0 0 1 0 0 0 15639 1000 35 2 2 STARD9 15 42684463 Missense_Mutation SNP G C3N-01023_T 21262335 42684463 59306726 128 20672 DUOX1 0 . GRCh38 15 45152463 45152463 + Missense_Mutation SNP A A C novel C3N-01023_T C3N-01023_N A A c.3371A>C p.Asp1124Ala p.D1124A ENST00000321429 26/35 281 224 57 223 223 0 strelka-varscan-mutect DUOX1,missense_variant,p.Asp1124Ala,ENST00000321429,NM_017434.4;DUOX1,missense_variant,p.Asp1124Ala,ENST00000389037,NM_175940.2;DUOX1,missense_variant,p.Asp770Ala,ENST00000561166,;CTD-2651B20.1,downstream_gene_variant,,ENST00000558039,;DUOX1,upstream_gene_variant,,ENST00000559221,;DUOX1,3_prime_UTR_variant,,ENST00000561220,;DUOX1,non_coding_transcript_exon_variant,,ENST00000557893,;DUOX1,non_coding_transcript_exon_variant,,ENST00000559716,;DUOX1,downstream_gene_variant,,ENST00000558446,;DUOX1,downstream_gene_variant,,ENST00000559219,;DUOX1,upstream_gene_variant,,ENST00000558744,; C ENST00000321429 Transcript missense_variant 3778/5738 3371/4656 1124/1551 D/A gAc/gCc 1 1 DUOX1 HGNC HGNC:3062 protein_coding YES CCDS32221.1 ENSP00000317997 Q9NRD9 UPI000006E50E NM_017434.4 deleterious(0.01) 26/35 hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF75,Pfam_domain:PF01794 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 45152463 45152463 A C 1 0 0 0 0 1 0 0 0 4622 275 10 5 5 DUOX1 15 45152463 Missense_Mutation SNP A C3N-01023_T 2468000 45152463 56838726 129 20673 ALDH1A2 0 . GRCh38 15 57960770 57960770 + Missense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.1484T>A p.Met495Lys p.M495K ENST00000249750 12/13 268 230 38 273 273 0 strelka-varscan-mutect ALDH1A2,missense_variant,p.Met495Lys,ENST00000249750,NM_003888.3;ALDH1A2,missense_variant,p.Met474Lys,ENST00000537372,NM_001206897.1;ALDH1A2,missense_variant,p.Met457Lys,ENST00000347587,NM_170696.2;ALDH1A2,missense_variant,p.Met466Lys,ENST00000558231,;ALDH1A2,missense_variant,p.Met399Lys,ENST00000559517,NM_170697.2;ALDH1A2,splice_region_variant,,ENST00000560312,;ALDH1A2,splice_region_variant,,ENST00000430119,; T ENST00000249750 Transcript missense_variant,splice_region_variant 2252/4098 1484/1557 495/518 M/K aTg/aAg 1 -1 ALDH1A2 HGNC HGNC:15472 protein_coding YES CCDS10163.1 ENSP00000249750 O94788 UPI00001678B4 NM_003888.3 tolerated(0.13) 12/13 hmmpanther:PTHR11699:SF102,hmmpanther:PTHR11699,Pfam_domain:PF00171,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 57960770 57960770 A T 1 0 0 0 0 1 0 0 0 591 231 8 4 4 ALDH1A2 15 57960770 Missense_Mutation SNP A C3N-01023_T 12808307 57960770 44030419 130 20674 PRSS22 0 . GRCh38 16 2853161 2853161 + Missense_Mutation SNP C C A C3N-01023_T C3N-01023_N C C c.886G>T p.Gly296Trp p.G296W ENST00000161006 6/6 369 271 98 165 165 0 strelka-varscan-mutect PRSS22,missense_variant,p.Gly296Trp,ENST00000161006,NM_022119.3;PRSS22,missense_variant,p.Gly186Trp,ENST00000571228,;LA16c-325D7.1,upstream_gene_variant,,ENST00000577140,;PRSS22,downstream_gene_variant,,ENST00000574768,;PRSS22,downstream_gene_variant,,ENST00000577177,;PRSS22,non_coding_transcript_exon_variant,,ENST00000575164,;PRSS22,downstream_gene_variant,,ENST00000576381,;PRSS22,downstream_gene_variant,,ENST00000570950,;PRSS22,downstream_gene_variant,,ENST00000572061,; A ENST00000161006 Transcript missense_variant 952/1386 886/954 296/317 G/W Ggg/Tgg COSM5520818 1 -1 PRSS22 HGNC HGNC:14368 protein_coding YES CCDS10481.1 ENSP00000161006 Q9GZN4 UPI0000126AFA NM_022119.3 deleterious(0) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR24253:SF6,hmmpanther:PTHR24253 1 MODERATE 1 SNV 1 1 1 PASS rs1303026628 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 2853161 2853161 C A 1 0 0 0 0 1 0 0 0 12766 652 23 1 1 PRSS22 16 2853161 Missense_Mutation SNP C C3N-01023_T 2853161 87485184 131 20675 XYLT1 0 . GRCh38 16 17108936 17108936 + Missense_Mutation SNP C C A rs769620977 C3N-01023_T C3N-01023_N C C c.2639G>T p.Ser880Ile p.S880I ENST00000261381 12/12 69 52 17 40 40 0 strelka-varscan-mutect XYLT1,missense_variant,p.Ser880Ile,ENST00000261381,NM_022166.3; A ENST00000261381 Transcript missense_variant 2724/9891 2639/2880 880/959 S/I aGc/aTc rs769620977 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 deleterious(0.02) 12/12 hmmpanther:PTHR19297:SF91,hmmpanther:PTHR19297 MODERATE 1 SNV 1 1 PASS rs769620977 . 0 202 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 68 17108936 17108936 C A 1 0 0 0 0 1 0 0 0 18022 797 28 2 2 XYLT1 16 17108936 Missense_Mutation SNP C C3N-01023_T 14255775 17108936 73229409 132 20676 DNAH3 0 . GRCh38 16 20963581 20963581 + Missense_Mutation SNP G G T rs767592950 C3N-01023_T C3N-01023_N G G c.10303C>A p.Leu3435Met p.L3435M ENST00000261383 53/62 343 254 89 273 272 1 strelka-varscan-mutect DNAH3,missense_variant,p.Leu3435Met,ENST00000261383,NM_017539.2; T ENST00000261383 Transcript missense_variant 10303/12394 10303/12351 3435/4116 L/M Ctg/Atg rs767592950 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 deleterious(0.01) 53/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS rs767592950 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 20963581 20963581 G T 1 0 0 0 0 1 0 0 0 4418 991 35 2 2 DNAH3 16 20963581 Missense_Mutation SNP G C3N-01023_T 3854645 20963581 69374764 133 20677 ITGAD 0 . GRCh38 16 31423926 31423926 + Nonsense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.3127A>T p.Lys1043Ter p.K1043* ENST00000389202 27/30 240 217 23 167 167 0 strelka-varscan-mutect ITGAD,stop_gained,p.Lys1043Ter,ENST00000389202,NM_001318185.1,NM_005353.2;COX6A2,downstream_gene_variant,,ENST00000287490,NM_005205.3;RP11-452L6.8,upstream_gene_variant,,ENST00000615068,;ITGAD,upstream_gene_variant,,ENST00000567308,;COX6A2,downstream_gene_variant,,ENST00000565462,; T ENST00000389202 Transcript stop_gained 3176/3912 3127/3486 1043/1161 K/* Aag/Tag 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 27/30 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,Superfamily_domains:SSF69179 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 31423926 31423926 A T 1 0 0 0 0 0 1 0 0 7791 247 9 4 4 ITGAD 16 31423926 Nonsense_Mutation SNP A C3N-01023_T 10460345 31423926 58914419 134 20678 CBLN1 0 . GRCh38 16 49279466 49279466 + Nonsense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.520G>T p.Gly174Ter p.G174* ENST00000219197 3/3 367 316 51 292 290 2 strelka-varscan-mutect CBLN1,stop_gained,p.Gly174Ter,ENST00000219197,NM_004352.3;CBLN1,stop_gained,p.Gly174Ter,ENST00000536749,;CBLN1,3_prime_UTR_variant,,ENST00000564786,; A ENST00000219197 Transcript stop_gained 886/2435 520/582 174/193 G/* Gga/Tga 1 -1 CBLN1 HGNC HGNC:1543 protein_coding YES CCDS10736.1 ENSP00000219197 P23435 UPI0000127506 NM_004352.3 3/3 PROSITE_profiles:PS50871,hmmpanther:PTHR22923:SF5,hmmpanther:PTHR22923,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 68 49279466 49279466 C A 1 0 0 0 0 0 1 0 0 2405 632 22 2 2 CBLN1 16 49279466 Nonsense_Mutation SNP C C3N-01023_T 17855540 49279466 41058879 135 20679 ZNF423 0 . GRCh38 16 49638045 49638045 + Missense_Mutation SNP G G T rs369662414 C3N-01023_T C3N-01023_N G G c.1107C>A p.Ser369Arg p.S369R ENST00000561648 5/9 331 275 56 245 244 1 strelka-varscan-mutect ZNF423,missense_variant,p.Ser369Arg,ENST00000561648,;ZNF423,missense_variant,p.Ser309Arg,ENST00000563137,;ZNF423,missense_variant,p.Ser369Arg,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Ser309Arg,ENST00000562871,;ZNF423,missense_variant,p.Ser252Arg,ENST00000535559,;ZNF423,missense_variant,p.Ser309Arg,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Ser252Arg,ENST00000567169,; T ENST00000561648 Transcript missense_variant 1408/7907 1107/3855 369/1284 S/R agC/agA rs369662414 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC deleterious(0) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 MODERATE 1 SNV 5 1 PASS rs369662414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 49638045 49638045 G T 1 0 0 0 0 1 0 0 0 18470 1078 38 1 1 ZNF423 16 49638045 Missense_Mutation SNP G C3N-01023_T 358579 49638045 40700300 136 20680 SALL1 0 . GRCh38 16 51138911 51138911 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.3311C>A p.Pro1104His p.P1104H ENST00000251020 2/3 555 481 74 402 402 0 strelka-varscan-mutect SALL1,missense_variant,p.Pro1007His,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Pro1104His,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Pro1007His,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; T ENST00000251020 Transcript missense_variant 3345/5146 3311/3975 1104/1324 P/H cCc/cAc 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0.03) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 51138911 51138911 G T 1 0 0 0 0 1 0 0 0 14069 1232 43 2 2 SALL1 16 51138911 Missense_Mutation SNP G C3N-01023_T 1500866 51138911 39199434 137 20681 TERF2 0 . GRCh38 16 69384615 69384615 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.571G>T p.Val191Leu p.V191L ENST00000254942 3/10 237 181 56 164 164 0 strelka-varscan-mutect TERF2,missense_variant,p.Val191Leu,ENST00000254942,NM_005652.4;TERF2,missense_variant,p.Val191Leu,ENST00000567296,;TERF2,missense_variant,p.Val70Leu,ENST00000566750,;TERF2,missense_variant,p.Val28Leu,ENST00000566257,;TERF2,missense_variant,p.Val46Leu,ENST00000567841,;TERF2,missense_variant,p.Val13Leu,ENST00000569542,;TERF2,non_coding_transcript_exon_variant,,ENST00000569611,;TERF2,3_prime_UTR_variant,,ENST00000569280,; A ENST00000254942 Transcript missense_variant 588/2983 571/1629 191/542 V/L Gtg/Ttg 1 -1 TERF2 HGNC HGNC:11729 protein_coding YES CCDS10879.2 ENSP00000254942 Q15554 UPI0000EE5A05 NM_005652.4 tolerated(0.25) 3/10 hmmpanther:PTHR21717:SF13,hmmpanther:PTHR21717,Pfam_domain:PF08558,Gene3D:1.25.40.210,Superfamily_domains:SSF63600,PD014243 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 69384615 69384615 C A 1 0 0 0 0 1 0 0 0 16181 565 20 2 2 TERF2 16 69384615 Missense_Mutation SNP C C3N-01023_T 18245704 69384615 20953730 138 20682 CNTNAP4 0 . GRCh38 16 76535666 76535666 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.2877G>T p.Arg959Ser p.R959S ENST00000611870 18/24 381 295 86 243 243 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Arg959Ser,ENST00000307431,;CNTNAP4,missense_variant,p.Arg959Ser,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Arg911Ser,ENST00000377504,;CNTNAP4,missense_variant,p.Arg962Ser,ENST00000476707,;CNTNAP4,missense_variant,p.Arg911Ser,ENST00000622250,;CNTNAP4,missense_variant,p.Arg886Ser,ENST00000478060,NM_138994.3; T ENST00000611870 Transcript missense_variant 3262/4867 2877/3927 959/1308 R/S agG/agT 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 tolerated(0.13) 18/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50026,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 76535666 76535666 G T 1 0 0 0 0 1 0 0 0 3431 1223 43 2 2 CNTNAP4 16 76535666 Missense_Mutation SNP G C3N-01023_T 7151051 76535666 13802679 139 20683 CNTNAP4 0 . GRCh38 16 76558563 76558563 + Missense_Mutation SNP G G T rs372665319 C3N-01023_T C3N-01023_N G G c.3807G>T p.Arg1269Ser p.R1269S ENST00000611870 24/24 151 136 15 138 138 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Arg1269Ser,ENST00000307431,;CNTNAP4,missense_variant,p.Arg1269Ser,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Arg1221Ser,ENST00000377504,;CNTNAP4,missense_variant,p.Arg1272Ser,ENST00000476707,;CNTNAP4,missense_variant,p.Arg1221Ser,ENST00000622250,;CNTNAP4,missense_variant,p.Arg1196Ser,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000619533,;RP11-58C22.1,intron_variant,,ENST00000563764,; T ENST00000611870 Transcript missense_variant 4192/4867 3807/3927 1269/1308 R/S agG/agT rs372665319,COSM5643531,COSM5643532,COSM5681691,COSM5681692 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 tolerated(0.57) 24/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs372665319 . 0 207 0 3 0 0 0 0 -19.96992 0.9999852 1 1 1 0 T 3 4 68 76558563 76558563 G T 1 0 0 0 0 1 0 0 0 3431 1252 44 2 2 CNTNAP4 16 76558563 Missense_Mutation SNP G C3N-01023_T 22897 76558563 13779782 140 20684 MYH13 0 . GRCh38 17 10315797 10315797 + Silent SNP G G T C3N-01023_T C3N-01023_N G G c.3880C>A p.= p.R1294R ENST00000418404 28/41 190 130 60 157 157 0 strelka-varscan-mutect MYH13,synonymous_variant,p.=,ENST00000418404,;MYH13,synonymous_variant,p.=,ENST00000252172,NM_003802.2;MYH13,synonymous_variant,p.=,ENST00000621918,;RP11-401O9.4,intron_variant,,ENST00000609088,;RP11-401O9.3,upstream_gene_variant,,ENST00000577743,; T ENST00000418404 Transcript synonymous_variant 4044/6296 3880/5817 1294/1938 R Cga/Aga COSM4605249,COSM4605250 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA 28/41 Pfam_domain:PF01576,Superfamily_domains:SSF90257 1,1 LOW SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 10315797 10315797 G T 1 0 0 0 0 0 0 0 1 10032 1124 39 1 1 MYH13 17 10315797 Silent SNP G C3N-01023_T 10315797 72941644 141 20685 CDC6 0 . GRCh38 17 40291315 40291318 + Frame_Shift_Del DEL TGTG TGTG - novel C3N-01023_T C3N-01023_N TGTG TGTG c.438_441delTGTG p.Cys146Ter p.C146* ENST00000209728 3/12 245 212 33 215 215 0 sindel-varindel-pindel CDC6,frameshift_variant,p.Cys146Ter,ENST00000209728,NM_001254.3;CDC6,frameshift_variant,p.Cys146Ter,ENST00000580824,;CDC6,downstream_gene_variant,,ENST00000473555,;CDC6,downstream_gene_variant,,ENST00000577249,;CDC6,upstream_gene_variant,,ENST00000582402,; - ENST00000209728 Transcript frameshift_variant 907-910/4810 436-439/1683 146-147/560 CV/X TGTGtg/tg 1 1 CDC6 HGNC HGNC:1744 protein_coding YES CCDS11365.1 ENSP00000209728 Q99741 A0A024R1S2 UPI0000073C6C NM_001254.3 3/12 hmmpanther:PTHR10763:SF26,hmmpanther:PTHR10763,PIRSF_domain:PIRSF001767 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 68 40291315 40291315 TGTG - 1 0 1 0 1 0 0 0 0 2786 1464 51 0 0 CDC6 17 40291315 Frame_Shift_Del DEL TGTG C3N-01023_T 29975518 40291315 42966126 142 20686 KRTAP4-6 0 . GRCh38 17 41140291 41140291 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.197G>A p.Cys66Tyr p.C66Y ENST00000345847 1/1 436 384 52 284 283 1 strelka-varscan-mutect KRTAP4-6,missense_variant,p.Cys66Tyr,ENST00000345847,NM_030976.1; T ENST00000345847 Transcript missense_variant 197/1055 197/618 66/205 C/Y tGt/tAt 1 -1 KRTAP4-6 HGNC HGNC:18909 protein_coding YES CCDS54125.1 ENSP00000328270 Q9BYQ5 UPI00006C17B9 NM_030976.1 deleterious(0.04) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF60,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 41140291 41140291 C T 1 0 0 0 0 1 0 0 0 8449 478 17 3 3 KRTAP4-6 17 41140291 Missense_Mutation SNP C C3N-01023_T 848976 41140291 42117150 143 20687 ABCA10 0 . GRCh38 17 69152184 69152184 + Splice_Site SNP C C A novel C3N-01023_T C3N-01023_N C C c.4257-1G>T p.X1419_splice ENST00000269081 83 74 9 58 58 0 strelka-varscan-mutect ABCA10,splice_acceptor_variant,,ENST00000269081,NM_080282.3;ABCA10,upstream_gene_variant,,ENST00000521538,;ABCA10,upstream_gene_variant,,ENST00000522787,;ABCA10,splice_acceptor_variant,,ENST00000519732,;ABCA10,splice_acceptor_variant,,ENST00000522406,;ABCA10,splice_acceptor_variant,,ENST00000518929,;ABCA10,splice_acceptor_variant,,ENST00000523419,;ABCA10,upstream_gene_variant,,ENST00000524231,;ABCA10,upstream_gene_variant,,ENST00000588514,; A ENST00000269081 Transcript splice_acceptor_variant -/6362 4257/4632 1419/1543 1 -1 ABCA10 HGNC HGNC:30 protein_coding YES CCDS11684.1 ENSP00000269081 Q8WWZ4 UPI000013D7F6 NM_080282.3 36/39 HIGH 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -18.91855 0.9999877 1 1 1 0 A 5 1 68 69152184 69152184 C A 1 0 0 0 0 0 0 1 0 33 695 24 2 2 ABCA10 17 69152184 Splice_Site SNP C C3N-01023_T 28011893 69152184 14105257 144 20688 CELF4 0 . GRCh38 18 37270785 37270785 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.1082G>T p.Gly361Val p.G361V ENST00000420428 8/13 356 325 31 224 224 0 strelka-varscan-mutect CELF4,missense_variant,p.Gly361Val,ENST00000420428,NM_020180.3;CELF4,missense_variant,p.Gly360Val,ENST00000591287,;CELF4,missense_variant,p.Gly351Val,ENST00000334919,NM_001025089.1;CELF4,missense_variant,p.Gly54Val,ENST00000588591,;CELF4,missense_variant,p.Gly46Val,ENST00000586009,;CELF4,missense_variant,p.Gly360Val,ENST00000603232,NM_001025087.1;CELF4,missense_variant,p.Gly359Val,ENST00000361795,NM_001025088.1;CELF4,missense_variant,p.Gly359Val,ENST00000601019,;CELF4,missense_variant,p.Gly361Val,ENST00000591282,;CELF4,missense_variant,p.Gly350Val,ENST00000588597,;CELF4,missense_variant,p.Gly50Val,ENST00000589386,;CELF4,missense_variant,p.Gly50Val,ENST00000593271,;CELF4,missense_variant,p.Gly50Val,ENST00000587657,;CELF4,downstream_gene_variant,,ENST00000601392,;CELF4,downstream_gene_variant,,ENST00000587819,;CELF4,downstream_gene_variant,,ENST00000589229,;CELF4,downstream_gene_variant,,ENST00000587924,;RP11-797E24.3,upstream_gene_variant,,ENST00000586610,;RP11-797E24.3,upstream_gene_variant,,ENST00000588766,;CELF4,non_coding_transcript_exon_variant,,ENST00000587074,;CELF4,3_prime_UTR_variant,,ENST00000590112,;CELF4,non_coding_transcript_exon_variant,,ENST00000591421,; A ENST00000420428 Transcript missense_variant 1478/4052 1082/1461 361/486 G/V gGc/gTc 1 -1 CELF4 HGNC HGNC:14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 UPI00000726FC NM_020180.3 deleterious(0) 8/13 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 37270785 37270785 C A 1 0 0 0 0 1 0 0 0 2925 739 26 2 2 CELF4 18 37270785 Missense_Mutation SNP C C3N-01023_T 37270785 43102500 145 20689 CDH20 0 . GRCh38 18 61528105 61528105 + Missense_Mutation SNP C C A rs777679557 C3N-01023_T C3N-01023_N C C c.1156C>A p.Pro386Thr p.P386T ENST00000262717 7/12 578 443 135 370 370 0 strelka-varscan-mutect CDH20,missense_variant,p.Pro386Thr,ENST00000262717,;CDH20,missense_variant,p.Pro386Thr,ENST00000536675,NM_031891.2;CDH20,missense_variant,p.Pro386Thr,ENST00000538374,; A ENST00000262717 Transcript missense_variant 1554/3882 1156/2406 386/801 P/T Ccc/Acc rs777679557,COSM5505943 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D deleterious(0) 7/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs777679557 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 61528105 61528105 C A 1 0 0 0 0 1 0 0 0 2809 739 26 2 2 CDH20 18 61528105 Missense_Mutation SNP C C3N-01023_T 24257320 61528105 18845180 146 20690 PIGN 0 . GRCh38 18 62157207 62157207 + Missense_Mutation SNP C C T rs200756305 C3N-01023_T C3N-01023_N C C c.364G>A p.Glu122Lys p.E122K ENST00000357637 6/31 167 156 11 134 134 0 strelka-mutect PIGN,missense_variant,p.Glu122Lys,ENST00000357637,NM_176787.4;PIGN,missense_variant,p.Glu122Lys,ENST00000400334,NM_012327.5;PIGN,missense_variant,p.Glu122Lys,ENST00000589720,;PIGN,missense_variant,p.Glu122Lys,ENST00000585923,;PIGN,missense_variant,p.Glu45Lys,ENST00000588748,;PIGN,missense_variant,p.Glu45Lys,ENST00000591238,;PIGN,missense_variant,p.Glu86Lys,ENST00000590765,;PIGN,missense_variant,p.Glu45Lys,ENST00000585458,;PIGN,missense_variant,p.Glu27Lys,ENST00000589098,;PIGN,downstream_gene_variant,,ENST00000587134,;PIGN,downstream_gene_variant,,ENST00000585344,;PIGN,downstream_gene_variant,,ENST00000588571,;PIGN,downstream_gene_variant,,ENST00000589339,;PIGN,downstream_gene_variant,,ENST00000585926,;PIGN,upstream_gene_variant,,ENST00000592803,; T ENST00000357637 Transcript missense_variant 780/5501 364/2796 122/931 E/K Gag/Aag rs200756305 1 -1 PIGN HGNC HGNC:8967 protein_coding YES CCDS45879.1 ENSP00000350263 O95427 A0A024R2C3 UPI0000070A47 NM_176787.4 deleterious(0) 6/31 Gene3D:3.40.720.10,hmmpanther:PTHR12250,Superfamily_domains:SSF53649 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs200756305 . 0 208 0 2 0 0 0 0 -14.63464 0.9999996 1 1 1 0 T 3 4 68 62157207 62157207 C T 1 0 0 0 0 1 0 0 0 11987 922 32 3 3 PIGN 18 62157207 Missense_Mutation SNP C C3N-01023_T 629102 62157207 18216078 147 20691 CDH7 0 . GRCh38 18 65880847 65880847 + Nonsense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.2311C>T p.Arg771Ter p.R771* ENST00000397968 12/12 177 152 25 137 137 0 strelka-varscan-mutect CDH7,stop_gained,p.Arg771Ter,ENST00000397968,NM_004361.2;CDH7,stop_gained,p.Arg771Ter,ENST00000323011,NM_033646.1; T ENST00000397968 Transcript stop_gained 2737/12231 2311/2358 771/785 R/* Cga/Tga 1 1 CDH7 HGNC HGNC:1766 protein_coding YES CCDS11993.1 ENSP00000381058 Q9ULB5 UPI000013D269 NM_004361.2 12/12 Gene3D:4.10.900.10,Pfam_domain:PF01049,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF91 HIGH 1 SNV 1 1 PASS rs1454134664 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 65880847 65880847 C T 1 0 0 0 0 0 1 0 0 2818 528 19 1 1 CDH7 18 65880847 Nonsense_Mutation SNP C C3N-01023_T 3723640 65880847 14492438 148 20692 ELANE 0 . GRCh38 19 856036 856036 + Missense_Mutation SNP G G T rs780046041 C3N-01023_T C3N-01023_N G G c.676G>T p.Gly226Trp p.G226W ENST00000590230 6/6 407 340 67 306 306 0 strelka-varscan-mutect ELANE,missense_variant,p.Gly226Trp,ENST00000590230,;ELANE,missense_variant,p.Gly226Trp,ENST00000263621,NM_001972.2;CFD,upstream_gene_variant,,ENST00000327726,NM_001317335.1,NM_001928.2;CFD,upstream_gene_variant,,ENST00000592860,; T ENST00000590230 Transcript missense_variant 817/1028 676/804 226/267 G/W Ggg/Tgg rs780046041,CM078497 1 1 ELANE HGNC HGNC:3309 protein_coding YES CCDS12045.1 ENSP00000466090 P08246 UPI0000129E6B deleterious(0) 6/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24257,hmmpanther:PTHR24257:SF16,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE SNV 5 0,1 1 PASS rs780046041 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 856036 856036 G T 1 0 0 0 0 1 0 0 0 4881 1000 35 2 2 ELANE 19 856036 Missense_Mutation SNP G C3N-01023_T 856036 57761580 149 20693 SBNO2 0 . GRCh38 19 1117463 1117463 + Missense_Mutation SNP C C A rs771547650 C3N-01023_T C3N-01023_N C C c.1564G>T p.Asp522Tyr p.D522Y ENST00000361757 15/32 166 139 27 130 129 1 strelka-varscan-mutect SBNO2,missense_variant,p.Asp522Tyr,ENST00000361757,NM_014963.2;SBNO2,missense_variant,p.Asp512Tyr,ENST00000587024,;SBNO2,missense_variant,p.Asp465Tyr,ENST00000438103,NM_001100122.1;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222,;SBNO2,non_coding_transcript_exon_variant,,ENST00000590446,; A ENST00000361757 Transcript missense_variant 1802/4923 1564/4101 522/1366 D/Y Gac/Tac rs771547650 1 -1 SBNO2 HGNC HGNC:29158 protein_coding YES CCDS45894.1 ENSP00000354733 Q9Y2G9 UPI0000140680 NM_014963.2 deleterious(0) 15/32 hmmpanther:PTHR12706,hmmpanther:PTHR12706:SF5 MODERATE 1 SNV 1 1 PASS rs771547650 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 1117463 1117463 C A 1 0 0 0 0 1 0 0 0 14128 884 31 1 1 SBNO2 19 1117463 Missense_Mutation SNP C C3N-01023_T 261427 1117463 57500153 150 20694 STK11 0 . GRCh38 19 1207133 1207134 + Frame_Shift_Ins INS - - TGAGGGC novel C3N-01023_T C3N-01023_N - - c.220_221insTGAGGGC p.Arg74MetfsTer91 p.R74Mfs*91 ENST00000326873 1/10 246 154 92 200 200 0 sindel-varindel STK11,frameshift_variant,p.Arg74MetfsTer91,ENST00000586243,;STK11,frameshift_variant,p.Arg74MetfsTer91,ENST00000326873,NM_000455.4;STK11,frameshift_variant,p.Arg74MetfsTer33,ENST00000585851,;STK11,intron_variant,,ENST00000585748,;STK11,frameshift_variant,p.Arg74MetfsTer?,ENST00000593219,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;HMGB2P1,downstream_gene_variant,,ENST00000591146,; TGAGGGC ENST00000326873 Transcript frameshift_variant 670-671/2611 220-221/1302 74/433 R/MRAX agg/aTGAGGGCgg 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 1/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_patterns:PS00107,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 TGAGGGC 7 5 68 1207133 1207133 - TGAGGGC 1 0 1 1 0 0 0 0 0 15664 179 7 0 0 STK11 19 1207133 Frame_Shift_Ins INS - C3N-01023_T 89670 1207133 57410483 151 20695 RFX2 0 . GRCh38 19 6001849 6001849 + Missense_Mutation SNP C C A rs753304252 C3N-01023_T C3N-01023_N C C c.1825G>T p.Ala609Ser p.A609S ENST00000303657 15/18 71 66 5 85 85 0 strelka-varscan-mutect RFX2,missense_variant,p.Ala609Ser,ENST00000303657,NM_000635.3;RFX2,missense_variant,p.Ala609Ser,ENST00000359161,;RFX2,missense_variant,p.Ala584Ser,ENST00000592546,NM_134433.2;RFX2,downstream_gene_variant,,ENST00000589340,;CTC-232P5.1,intron_variant,,ENST00000587836,;RFX2,upstream_gene_variant,,ENST00000590778,; A ENST00000303657 Transcript missense_variant 1975/3993 1825/2172 609/723 A/S Gcc/Tcc rs753304252 1 -1 RFX2 HGNC HGNC:9983 protein_coding YES CCDS12157.1 ENSP00000306335 P48378 UPI000013D4B1 NM_000635.3 deleterious(0.01) 15/18 hmmpanther:PTHR12619:SF17,hmmpanther:PTHR12619 MODERATE 1 SNV 1 1 PASS rs753304252 . 0 197 12 0 0 0 0 0 -11.07381 0.9996148 1 1 1 0 A 3 1 68 6001849 6001849 C A 1 0 0 0 0 1 0 0 0 13437 768 27 1 1 RFX2 19 6001849 Missense_Mutation SNP C C3N-01023_T 4794716 6001849 52615767 152 20696 ACER1 0 . GRCh38 19 6312412 6312412 + Missense_Mutation SNP C C A rs373391912 C3N-01023_T C3N-01023_N C C c.181G>T p.Val61Phe p.V61F ENST00000301452 2/6 217 184 33 195 195 0 strelka-varscan-mutect ACER1,missense_variant,p.Val61Phe,ENST00000301452,NM_133492.2; A ENST00000301452 Transcript missense_variant 259/1445 181/795 61/264 V/F Gtt/Ttt rs373391912 1 -1 ACER1 HGNC HGNC:18356 protein_coding YES CCDS12161.1 ENSP00000301452 Q8TDN7 UPI000003FD52 NM_133492.2 tolerated(0.63) 2/6 Pfam_domain:PF05875,hmmpanther:PTHR12956,hmmpanther:PTHR12956:SF18,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs373391912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 6312412 6312412 C A 1 0 0 0 0 1 0 0 0 176 536 19 1 1 ACER1 19 6312412 Missense_Mutation SNP C C3N-01023_T 310563 6312412 52305204 153 20697 MUC16 0 . GRCh38 19 8980915 8980915 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.224C>G p.Thr75Ser p.T75S ENST00000397910 1/84 140 113 27 142 142 0 strelka-varscan-mutect MUC16,missense_variant,p.Thr75Ser,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 428/43816 224/43524 75/14507 T/S aCc/aGc 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 8980915 8980915 G C 1 0 0 0 0 1 0 0 0 9972 1261 44 4 4 MUC16 19 8980915 Missense_Mutation SNP G C3N-01023_T 2668503 8980915 49636701 154 20698 ZNF208 0 . GRCh38 19 21972847 21972847 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.2187C>A p.Ser729Arg p.S729R ENST00000397126 4/4 245 200 45 214 214 0 strelka-varscan-mutect ZNF208,missense_variant,p.Ser729Arg,ENST00000397126,NM_007153.3;ZNF208,missense_variant,p.Ser629Arg,ENST00000609966,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,;AC003973.3,upstream_gene_variant,,ENST00000624863,; T ENST00000397126 Transcript missense_variant 2336/3992 2187/3843 729/1280 S/R agC/agA 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 21972847 21972847 G T 1 0 0 0 0 1 0 0 0 18343 962 34 2 2 ZNF208 19 21972847 Missense_Mutation SNP G C3N-01023_T 12991932 21972847 36644769 155 20699 ZNF676 0 . GRCh38 19 22180694 22180694 + Missense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.1023A>T p.Glu341Asp p.E341D ENST00000397121 3/3 314 281 33 285 285 0 varscan-mutect ZNF676,missense_variant,p.Glu341Asp,ENST00000397121,NM_001001411.2; A ENST00000397121 Transcript missense_variant 1341/2944 1023/1767 341/588 E/D gaA/gaT 1 -1 ZNF676 HGNC HGNC:20429 protein_coding YES CCDS42539.1 ENSP00000380310 Q8N7Q3 UPI00002376EC NM_001001411.2 deleterious(0.03) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF112,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 22180694 22180694 T A 1 0 0 0 0 1 0 0 0 18656 1490 52 4 4 ZNF676 19 22180694 Missense_Mutation SNP T C3N-01023_T 207847 22180694 36436922 156 20700 USF2 0 . GRCh38 19 35279098 35279098 + Silent SNP T T A novel C3N-01023_T C3N-01023_N T T c.969T>A p.= p.G323G ENST00000594064 9/9 112 77 35 75 75 0 strelka-varscan-mutect USF2,synonymous_variant,p.=,ENST00000594064,;USF2,intron_variant,,ENST00000222305,NM_003367.2;USF2,intron_variant,,ENST00000595068,;USF2,intron_variant,,ENST00000343550,NM_207291.1;USF2,intron_variant,,ENST00000599471,;USF2,intron_variant,,ENST00000379134,;USF2,intron_variant,,ENST00000599625,;HAMP,upstream_gene_variant,,ENST00000598398,;HAMP,upstream_gene_variant,,ENST00000222304,NM_021175.2;USF2,downstream_gene_variant,,ENST00000596380,;USF2,intron_variant,,ENST00000600341,;USF2,intron_variant,,ENST00000594264,;USF2,intron_variant,,ENST00000607959,;USF2,intron_variant,,ENST00000600898,;HAMP,upstream_gene_variant,,ENST00000593580,;USF2,downstream_gene_variant,,ENST00000597671,; A ENST00000594064 Transcript synonymous_variant 969/1179 969/1050 323/349 G ggT/ggA 1 1 USF2 HGNC HGNC:12594 protein_coding ENSP00000471511 B4DLJ1 UPI00017A7577 9/9 Low_complexity_(Seg):seg LOW SNV 2 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999986 1 1 1 0 A 2 1 68 35279098 35279098 T A 1 0 0 0 0 0 0 0 1 17566 1654 58 4 4 USF2 19 35279098 Silent SNP T C3N-01023_T 13098404 35279098 23338518 157 20701 UBOX5 0 . GRCh38 20 3121659 3121659 + Missense_Mutation SNP C C A rs779690705 C3N-01023_T C3N-01023_N C C c.980G>T p.Arg327Leu p.R327L ENST00000217173 3/5 368 318 50 300 299 1 strelka-varscan-mutect UBOX5,missense_variant,p.Arg327Leu,ENST00000217173,NM_001267584.1,NM_014948.3;UBOX5,missense_variant,p.Arg327Leu,ENST00000348031,NM_199415.2;UBOX5,downstream_gene_variant,,ENST00000449731,;UBOX5-AS1,intron_variant,,ENST00000446537,;UBOX5-AS1,downstream_gene_variant,,ENST00000454019,; A ENST00000217173 Transcript missense_variant 1452/4631 980/1626 327/541 R/L cGg/cTg rs779690705 1 -1 UBOX5 HGNC HGNC:17777 protein_coding YES CCDS13046.1 ENSP00000217173 O94941 UPI0000137935 NM_001267584.1,NM_014948.3 deleterious(0) 3/5 PROSITE_profiles:PS51698,hmmpanther:PTHR13492:SF2,hmmpanther:PTHR13492,Pfam_domain:PF04564,Gene3D:3.30.40.10,SMART_domains:SM00504,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs779690705 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 3121659 3121659 C A 1 0 0 0 0 1 0 0 0 17418 652 23 1 1 UBOX5 20 3121659 Missense_Mutation SNP C C3N-01023_T 3121659 61322508 158 20702 PTPRT 0 . GRCh38 20 42315731 42315731 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.2131G>T p.Ala711Ser p.A711S ENST00000373198 12/32 139 122 17 94 94 0 strelka-varscan-mutect PTPRT,missense_variant,p.Ala711Ser,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Ala711Ser,ENST00000373193,;PTPRT,missense_variant,p.Ala711Ser,ENST00000373201,;PTPRT,missense_variant,p.Ala711Ser,ENST00000373190,;PTPRT,missense_variant,p.Ala711Ser,ENST00000373184,;PTPRT,missense_variant,p.Ala711Ser,ENST00000356100,;PTPRT,missense_variant,p.Ala711Ser,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Ala329Ser,ENST00000612229,;PTPRT,missense_variant,p.Ala327Ser,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 2367/12746 2131/4383 711/1460 A/S Gcc/Tcc 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 tolerated(0.37) 12/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 MODERATE 1 SNV 2 1 PASS rs1329010453 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 42315731 42315731 C A 1 0 0 0 0 1 0 0 0 12967 797 28 2 2 PTPRT 20 42315731 Missense_Mutation SNP C C3N-01023_T 39194072 42315731 22128436 159 20703 ZMYND8 0 . GRCh38 20 47298845 47298845 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.337G>T p.Val113Phe p.V113F ENST00000471951 4/23 637 422 215 371 371 0 strelka-varscan-mutect ZMYND8,missense_variant,p.Val93Phe,ENST00000355972,NM_001281773.2;ZMYND8,missense_variant,p.Val93Phe,ENST00000396281,NM_001281772.2;ZMYND8,missense_variant,p.Val93Phe,ENST00000446994,;ZMYND8,missense_variant,p.Val93Phe,ENST00000311275,;ZMYND8,missense_variant,p.Val120Phe,ENST00000536340,;ZMYND8,missense_variant,p.Val68Phe,ENST00000372023,NM_001281779.2,NM_001281780.2;ZMYND8,missense_variant,p.Val93Phe,ENST00000611941,;ZMYND8,missense_variant,p.Val88Phe,ENST00000360911,NM_183048.3,NM_001281778.2;ZMYND8,missense_variant,p.Val93Phe,ENST00000262975,NM_001281774.2;ZMYND8,missense_variant,p.Val113Phe,ENST00000471951,NM_001281775.2,NM_001281776.2;ZMYND8,missense_variant,p.Val68Phe,ENST00000619049,;ZMYND8,missense_variant,p.Val113Phe,ENST00000352431,NM_012408.5,NM_001281783.2;ZMYND8,missense_variant,p.Val88Phe,ENST00000458360,NM_001281771.2;ZMYND8,missense_variant,p.Val20Phe,ENST00000467200,;ZMYND8,missense_variant,p.Val113Phe,ENST00000461685,NM_001281777.2,NM_183047.3;ZMYND8,missense_variant,p.Val88Phe,ENST00000617418,NM_001281782.2;ZMYND8,missense_variant,p.Val88Phe,ENST00000540497,NM_001281781.2,NM_001281784.2;ZMYND8,missense_variant,p.Val68Phe,ENST00000435836,;ZMYND8,non_coding_transcript_exon_variant,,ENST00000468376,; A ENST00000471951 Transcript missense_variant 364/4053 337/3705 113/1234 V/F Gtt/Ttt 1 -1 ZMYND8 HGNC HGNC:9397 protein_coding YES CCDS63306.1 ENSP00000420095 Q9ULU4 UPI0000695D9A NM_001281775.2,NM_001281776.2 deleterious(0.01) 4/23 Gene3D:3.30.40.10,PROSITE_patterns:PS01359,PROSITE_profiles:PS50016,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF13,SMART_domains:SM00249,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 47298845 47298845 C A 1 0 0 0 0 1 0 0 0 18290 507 18 2 2 ZMYND8 20 47298845 Missense_Mutation SNP C C3N-01023_T 4983114 47298845 17145322 160 20704 SLC9A8 0 . GRCh38 20 49855497 49855497 + Missense_Mutation SNP A A G rs200096437 C3N-01023_T C3N-01023_N A A c.677A>G p.Asn226Ser p.N226S ENST00000417961 8/16 310 269 41 177 177 0 strelka-varscan-mutect SLC9A8,missense_variant,p.Asn226Ser,ENST00000417961,NM_001260491.1;SLC9A8,missense_variant,p.Asn210Ser,ENST00000361573,NM_015266.2; G ENST00000417961 Transcript missense_variant 887/6309 677/1794 226/597 N/S aAt/aGt rs200096437,COSM3389824,COSM3389825 1 1 SLC9A8 HGNC HGNC:20728 protein_coding YES CCDS58774.1 ENSP00000416418 Q9Y2E8 UPI00017A7E08 NM_001260491.1 tolerated(0.29) 8/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF122,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs200096437 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 49855497 49855497 A G 1 0 0 0 0 1 0 0 0 15002 101 4 5 5 SLC9A8 20 49855497 Missense_Mutation SNP A C3N-01023_T 2556652 49855497 14588670 161 20705 NTSR1 0 . GRCh38 20 62758279 62758279 + Silent SNP C C A rs765205667 C3N-01023_T C3N-01023_N C C c.930C>A p.= p.I310I ENST00000370501 3/4 156 95 61 99 99 0 strelka-varscan-mutect NTSR1,synonymous_variant,p.=,ENST00000370501,NM_002531.2;NTSR1,non_coding_transcript_exon_variant,,ENST00000482259,; A ENST00000370501 Transcript synonymous_variant 1301/4132 930/1257 310/418 I atC/atA rs765205667,COSM5535751 1 1 NTSR1 HGNC HGNC:8039 protein_coding YES CCDS13502.1 ENSP00000359532 P30989 UPI000013D6CF NM_002531.2 3/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF9,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW 1 SNV 1 0,1 1 PASS rs765205667 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 68 62758279 62758279 C A 1 0 0 0 0 0 0 0 1 10776 874 31 1 1 NTSR1 20 62758279 Silent SNP C C3N-01023_T 12902782 62758279 1685888 162 20706 ITSN1 0 . GRCh38 21 33817413 33817413 + Missense_Mutation SNP C C G novel C3N-01023_T C3N-01023_N C C c.2895C>G p.Ile965Met p.I965M ENST00000399338 21/21 440 371 69 336 336 0 strelka-varscan-mutect ITSN1,missense_variant,p.Ile965Met,ENST00000399338,;ITSN1,missense_variant,p.Ile205Met,ENST00000440794,;ITSN1,intron_variant,,ENST00000381318,NM_003024.2;ITSN1,intron_variant,,ENST00000381285,;ITSN1,intron_variant,,ENST00000399367,;ITSN1,intron_variant,,ENST00000381291,NM_001001132.1;ITSN1,intron_variant,,ENST00000399352,;ITSN1,intron_variant,,ENST00000399349,;ITSN1,intron_variant,,ENST00000399355,;ITSN1,intron_variant,,ENST00000399353,;ITSN1,intron_variant,,ENST00000379960,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,upstream_gene_variant,,ENST00000428240,;ITSN1,3_prime_UTR_variant,,ENST00000419241,;ITSN1,upstream_gene_variant,,ENST00000487427,;ITSN1,downstream_gene_variant,,ENST00000465143,;ITSN1,upstream_gene_variant,,ENST00000437126,; G ENST00000399338 Transcript missense_variant 2914/3115 2895/3063 965/1020 I/M atC/atG 1 1 ITSN1 HGNC HGNC:6183 protein_coding ENSP00000382275 Q15811 UPI0001AE629E 21/21 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 33817413 33817413 C G 1 0 0 0 0 1 0 0 0 7832 903 32 4 4 ITSN1 21 33817413 Missense_Mutation SNP C C3N-01023_T 33817413 12892570 163 20707 LRRC74B 0 . GRCh38 22 21047896 21047896 + Missense_Mutation SNP C C G novel C3N-01023_T C3N-01023_N C C c.295C>G p.Leu99Val p.L99V ENST00000442047 3/9 160 128 32 126 125 1 strelka-varscan-mutect LRRC74B,missense_variant,p.Leu99Val,ENST00000442047,NM_001291006.1;AC002472.11,downstream_gene_variant,,ENST00000450652,;P2RX6P,upstream_gene_variant,,ENST00000439119,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000497328,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000473769,;P2RX6P,upstream_gene_variant,,ENST00000450626,; G ENST00000442047 Transcript missense_variant 295/1179 295/1179 99/392 L/V Ctg/Gtg 1 1 LRRC74B HGNC HGNC:34301 protein_coding YES CCDS77654.1 ENSP00000394078 Q6ZQY2 UPI000436DF24 NM_001291006.1 deleterious(0) 3/9 Gene3D:3.80.10.10,hmmpanther:PTHR24114,hmmpanther:PTHR24114:SF21,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 68 21047896 21047896 C G 1 0 0 0 0 1 0 0 0 8922 912 32 4 4 LRRC74B 22 21047896 Missense_Mutation SNP C C3N-01023_T 21047896 29770572 164 20708 GAS2L1 0 . GRCh38 22 29308489 29308489 + Silent SNP G G T novel C3N-01023_T C3N-01023_N G G c.384G>T p.= p.V128V ENST00000618518 1/5 117 102 15 105 105 0 strelka-varscan-mutect GAS2L1,synonymous_variant,p.=,ENST00000618518,;GAS2L1,synonymous_variant,p.=,ENST00000616432,;GAS2L1,synonymous_variant,p.=,ENST00000621062,NM_006478.4;GAS2L1,synonymous_variant,p.=,ENST00000611648,NM_152236.2;GAS2L1,synonymous_variant,p.=,ENST00000610653,;GAS2L1,synonymous_variant,p.=,ENST00000406549,NM_001278730.1;GAS2L1,synonymous_variant,p.=,ENST00000416823,;GAS2L1,synonymous_variant,p.=,ENST00000428622,;RASL10A,downstream_gene_variant,,ENST00000401450,;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.4;GAS2L1,upstream_gene_variant,,ENST00000491016,;GAS2L1,downstream_gene_variant,,ENST00000487341,; T ENST00000618518 Transcript synonymous_variant 1432/3382 384/2046 128/681 V gtG/gtT 1 1 GAS2L1 HGNC HGNC:16955 protein_coding YES CCDS74840.1 ENSP00000481012 A0A5E8 UPI0000073BD7 1/5 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF296,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW SNV 2 1 PASS rs1281435641 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 68 29308489 29308489 G T 1 0 0 0 0 0 0 0 1 6116 1306 46 2 2 GAS2L1 22 29308489 Silent SNP G C3N-01023_T 8260593 29308489 21509979 165 20709 GAS2L1 0 . GRCh38 22 29312426 29312426 + Missense_Mutation SNP C C T novel C3N-01023_T C3N-01023_N C C c.1975C>T p.Pro659Ser p.P659S ENST00000618518 5/5 27 22 5 11 11 0 strelka-mutect GAS2L1,missense_variant,p.Pro659Ser,ENST00000618518,;GAS2L1,missense_variant,p.Pro659Ser,ENST00000616432,;GAS2L1,missense_variant,p.Pro659Ser,ENST00000621062,NM_006478.4;GAS2L1,missense_variant,p.Pro659Ser,ENST00000611648,NM_152236.2;GAS2L1,missense_variant,p.Pro432Ser,ENST00000406549,NM_001278730.1;GAS2L1,downstream_gene_variant,,ENST00000610653,;RASL10A,downstream_gene_variant,,ENST00000401450,;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.4;GAS2L1,downstream_gene_variant,,ENST00000416823,;GAS2L1,downstream_gene_variant,,ENST00000428622,;AC002059.10,downstream_gene_variant,,ENST00000608014,;RASL10A,downstream_gene_variant,,ENST00000608559,;RASL10A,downstream_gene_variant,,ENST00000474590,;GAS2L1,downstream_gene_variant,,ENST00000491016,;GAS2L1,downstream_gene_variant,,ENST00000487341,; T ENST00000618518 Transcript missense_variant 3023/3382 1975/2046 659/681 P/S Ccc/Tcc 1 1 GAS2L1 HGNC HGNC:16955 protein_coding YES CCDS74840.1 ENSP00000481012 A0A5E8 UPI0000073BD7 deleterious_low_confidence(0) 5/5 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF296,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 1 206 3 0 0 0 0 0 -14.27725 1 1 1 1 0 T 3 4 68 29312426 29312426 C T 1 0 0 0 0 1 0 0 0 6116 507 18 3 3 GAS2L1 22 29312426 Missense_Mutation SNP C C3N-01023_T 3937 29312426 21506042 166 20710 SFI1 0 . GRCh38 22 31546876 31546876 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.354G>T p.Gln118His p.Q118H ENST00000400288 5/33 74 55 19 108 108 0 strelka-varscan-mutect SFI1,missense_variant,p.Gln94His,ENST00000540643,NM_001258325.1;SFI1,missense_variant,p.Gln118His,ENST00000432498,NM_014775.3;SFI1,missense_variant,p.Gln118His,ENST00000400288,NM_001007467.2;SFI1,missense_variant,p.Gln36His,ENST00000400289,NM_001258326.1,NM_001258327.1;SFI1,missense_variant,p.Gln36His,ENST00000443011,;SFI1,intron_variant,,ENST00000450787,;SFI1,missense_variant,p.Gln118His,ENST00000524296,;SFI1,non_coding_transcript_exon_variant,,ENST00000382162,;SFI1,non_coding_transcript_exon_variant,,ENST00000486708,; T ENST00000400288 Transcript missense_variant 459/4002 354/3729 118/1242 Q/H caG/caT 1 1 SFI1 HGNC HGNC:29064 protein_coding YES CCDS43004.1 ENSP00000383145 A8K8P3 UPI00004703B1 NM_001007467.2 deleterious(0.02) 5/33 hmmpanther:PTHR22028,hmmpanther:PTHR22028:SF4 MODERATE 1 SNV 2 1 PASS rs1189767324 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 31546876 31546876 G T 1 0 0 0 0 1 0 0 0 14434 962 34 2 2 SFI1 22 31546876 Missense_Mutation SNP G C3N-01023_T 2234450 31546876 19271592 167 20711 CACNG2 0 . GRCh38 22 36564743 36564743 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.580G>T p.Gly194Trp p.G194W ENST00000300105 4/4 690 582 108 516 515 1 strelka-varscan-mutect CACNG2,missense_variant,p.Gly194Trp,ENST00000300105,NM_006078.3;RP5-1119A7.17,upstream_gene_variant,,ENST00000562756,; A ENST00000300105 Transcript missense_variant 1562/2384 580/972 194/323 G/W Ggg/Tgg 1 -1 CACNG2 HGNC HGNC:1406 protein_coding YES CCDS13931.1 ENSP00000300105 Q9Y698 UPI00001272AC NM_006078.3 deleterious(0) 4/4 Pfam_domain:PF00822,Prints_domain:PR01792,hmmpanther:PTHR12107,hmmpanther:PTHR12107:SF1,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 36564743 36564743 C A 1 0 0 0 0 1 0 0 0 2245 652 23 1 1 CACNG2 22 36564743 Missense_Mutation SNP C C3N-01023_T 5017867 36564743 14253725 168 20712 PICK1 0 . GRCh38 22 38070867 38070867 + Nonsense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.469G>T p.Glu157Ter p.E157* ENST00000404072 7/13 428 366 62 334 334 0 strelka-varscan-mutect PICK1,stop_gained,p.Glu157Ter,ENST00000404072,NM_001039584.1,NM_001039583.1;PICK1,stop_gained,p.Glu157Ter,ENST00000356976,NM_012407.3;PICK1,stop_gained,p.Glu157Ter,ENST00000424694,;PICK1,downstream_gene_variant,,ENST00000435166,;PICK1,downstream_gene_variant,,ENST00000437453,;RP5-1039K5.13,intron_variant,,ENST00000445483,;PICK1,non_coding_transcript_exon_variant,,ENST00000468288,;PICK1,3_prime_UTR_variant,,ENST00000432756,;PICK1,3_prime_UTR_variant,,ENST00000426258,;PICK1,non_coding_transcript_exon_variant,,ENST00000484021,;PICK1,non_coding_transcript_exon_variant,,ENST00000494434,;PICK1,non_coding_transcript_exon_variant,,ENST00000472724,;PICK1,downstream_gene_variant,,ENST00000466374,; T ENST00000404072 Transcript stop_gained 816/2164 469/1248 157/415 E/* Gag/Tag 1 1 PICK1 HGNC HGNC:9394 protein_coding YES CCDS13965.1 ENSP00000385205 Q9NRD5 A0A024R1J5 UPI0000131A98 NM_001039584.1,NM_001039583.1 7/13 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50870,hmmpanther:PTHR12141:SF1,hmmpanther:PTHR12141,Pfam_domain:PF06456,Gene3D:1.20.1270.60,SMART_domains:SM01015,Superfamily_domains:SSF103657 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 38070867 38070867 G T 1 0 0 0 0 0 1 0 0 11971 1175 41 2 2 PICK1 22 38070867 Nonsense_Mutation SNP G C3N-01023_T 1506124 38070867 12747601 169 20713 TCF20 0 . GRCh38 22 42211614 42211614 + Missense_Mutation SNP T T A novel C3N-01023_T C3N-01023_N T T c.3692A>T p.Lys1231Ile p.K1231I ENST00000359486 1/5 275 232 43 220 219 1 strelka-varscan-mutect TCF20,missense_variant,p.Lys1231Ile,ENST00000359486,NM_005650.2;TCF20,missense_variant,p.Lys1231Ile,ENST00000335626,NM_181492.2;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,; A ENST00000359486 Transcript missense_variant 3829/7410 3692/5883 1231/1960 K/I aAa/aTa 1 -1 TCF20 HGNC HGNC:11631 protein_coding YES CCDS14033.1 ENSP00000352463 Q9UGU0 W5ZR30 UPI00001A95D9 NM_005650.2 deleterious_low_confidence(0) 1/5 hmmpanther:PTHR14955,hmmpanther:PTHR14955:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 42211614 42211614 T A 1 0 0 0 0 1 0 0 0 16097 1841 64 4 4 TCF20 22 42211614 Missense_Mutation SNP T C3N-01023_T 4140747 42211614 8606854 170 20714 KIAA0930 0 . GRCh38 22 45203872 45203872 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.645G>T p.Glu215Asp p.E215D ENST00000251993 6/10 210 172 38 186 186 0 strelka-mutect KIAA0930,missense_variant,p.Glu210Asp,ENST00000336156,NM_001009880.1;KIAA0930,missense_variant,p.Glu215Asp,ENST00000251993,NM_015264.1;KIAA0930,missense_variant,p.Glu176Asp,ENST00000391627,;KIAA0930,missense_variant,p.Glu95Asp,ENST00000423262,;KIAA0930,downstream_gene_variant,,ENST00000424508,;KIAA0930,downstream_gene_variant,,ENST00000414854,;MIR1249,upstream_gene_variant,,ENST00000408671,;KIAA0930,upstream_gene_variant,,ENST00000474515,;KIAA0930,upstream_gene_variant,,ENST00000493003,;KIAA0930,downstream_gene_variant,,ENST00000486640,;KIAA0930,3_prime_UTR_variant,,ENST00000440039,;KIAA0930,non_coding_transcript_exon_variant,,ENST00000488038,;KIAA0930,upstream_gene_variant,,ENST00000498418,;KIAA0930,downstream_gene_variant,,ENST00000417906,; A ENST00000251993 Transcript missense_variant 790/2723 645/1230 215/409 E/D gaG/gaT 1 -1 KIAA0930 HGNC HGNC:1314 protein_coding YES CCDS33666.1 ENSP00000251993 Q6ICG6 UPI00001C0A16 NM_015264.1 tolerated(0.37) 6/10 Pfam_domain:PF09741,hmmpanther:PTHR21477,hmmpanther:PTHR21477:SF13 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 45203872 45203872 C A 1 0 0 0 0 1 0 0 0 8096 680 24 2 2 KIAA0930 22 45203872 Missense_Mutation SNP C C3N-01023_T 2992258 45203872 5614596 171 20715 GTSE1 0 . GRCh38 22 46328713 46328713 + Nonsense_Mutation SNP A A T novel C3N-01023_T C3N-01023_N A A c.1750A>T p.Arg584Ter p.R584* ENST00000454366 10/12 111 89 22 105 105 0 strelka-varscan-mutect GTSE1,stop_gained,p.Arg584Ter,ENST00000454366,NM_016426.6;TRMU,upstream_gene_variant,,ENST00000476901,;TRMU,upstream_gene_variant,,ENST00000486620,;GTSE1,non_coding_transcript_exon_variant,,ENST00000479645,;GTSE1,downstream_gene_variant,,ENST00000466510,;GTSE1,upstream_gene_variant,,ENST00000491863,; T ENST00000454366 Transcript stop_gained 1962/3112 1750/2220 584/739 R/* Aga/Tga 1 1 GTSE1 HGNC HGNC:13698 protein_coding YES CCDS14074.2 ENSP00000415430 Q9NYZ3 UPI000021D19B NM_016426.6 10/12 hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 68 46328713 46328713 A T 1 0 0 0 0 0 1 0 0 6766 180 7 4 4 GTSE1 22 46328713 Nonsense_Mutation SNP A C3N-01023_T 1124841 46328713 4489755 172 20716 FRMPD4 0 . GRCh38 X 12717590 12717590 + Missense_Mutation SNP C C A novel C3N-01023_T C3N-01023_N C C c.2764C>A p.Leu922Met p.L922M ENST00000380682 16/17 126 61 65 103 103 0 strelka-varscan-mutect FRMPD4,missense_variant,p.Leu922Met,ENST00000380682,NM_014728.3;FRMPD4,missense_variant,p.Leu882Met,ENST00000616992,; A ENST00000380682 Transcript missense_variant 3270/8465 2764/3969 922/1322 L/M Ctg/Atg 1 1 FRMPD4 HGNC HGNC:29007 protein_coding YES CCDS35201.1 ENSP00000370057 Q14CM0 UPI00001C2066 NM_014728.3 tolerated(0.3) 16/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 68 12717590 12717590 C A 1 0 0 0 0 1 0 0 0 5930 564 20 2 2 FRMPD4 23 12717590 Missense_Mutation SNP C C3N-01023_T 12717590 143323305 173 20717 CAPN6 0 . GRCh38 X 111251072 111251072 + Missense_Mutation SNP G G C novel C3N-01023_T C3N-01023_N G G c.1003C>G p.His335Asp p.H335D ENST00000324068 8/13 115 67 48 70 70 0 strelka-varscan-mutect CAPN6,missense_variant,p.His335Asp,ENST00000324068,NM_014289.3; C ENST00000324068 Transcript missense_variant 1171/3568 1003/1926 335/641 H/D Cac/Gac 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 deleterious(0.02) 8/13 PROSITE_profiles:PS50203,hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183,Pfam_domain:PF00648,Gene3D:3.90.70.10,SMART_domains:SM00230,Superfamily_domains:SSF54001,Prints_domain:PR00704 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 68 111251072 111251072 G C 1 0 0 0 0 1 0 0 0 2324 1290 45 4 4 CAPN6 23 111251072 Missense_Mutation SNP G C3N-01023_T 98533482 111251072 44789823 174 20718 ZCCHC16 0 . GRCh38 X 112455545 112455545 + Missense_Mutation SNP C C T rs745929651 C3N-01023_T C3N-01023_N C C c.817C>T p.Arg273Cys p.R273C ENST00000340433 1/1 133 86 47 92 92 0 strelka-varscan-mutect ZCCHC16,missense_variant,p.Arg273Cys,ENST00000340433,NM_001004308.2; T ENST00000340433 Transcript missense_variant 1046/2613 817/933 273/310 R/C Cgc/Tgc rs745929651,COSM4791449 1 1 ZCCHC16 HGNC HGNC:25214 protein_coding YES CCDS35369.1 ENSP00000340590 Q6ZR62 UPI00001975B5 NM_001004308.2 deleterious(0.02) 1/1 hmmpanther:PTHR15503:SF8,hmmpanther:PTHR15503,Superfamily_domains:SSF57756 0,1 MODERATE 1 SNV 0,1 1 PASS rs745929651 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 112455545 112455545 C T 1 0 0 0 0 1 0 0 0 18159 652 23 1 1 ZCCHC16 23 112455545 Missense_Mutation SNP C C3N-01023_T 1204473 112455545 43585350 175 20719 SLITRK4 0 . GRCh38 X 143630250 143630250 + Missense_Mutation SNP G G T novel C3N-01023_T C3N-01023_N G G c.859C>A p.Pro287Thr p.P287T ENST00000596188 2/2 130 70 60 106 104 2 strelka-varscan-mutect SLITRK4,missense_variant,p.Pro287Thr,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.Pro287Thr,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.Pro287Thr,ENST00000356928,NM_001184749.2; T ENST00000596188 Transcript missense_variant 1085/8545 859/2514 287/837 P/T Ccc/Acc 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 tolerated(0.08) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 68 143630250 143630250 G T 1 0 0 0 0 1 0 0 0 15036 1174 41 2 2 SLITRK4 23 143630250 Missense_Mutation SNP G C3N-01023_T 31174705 143630250 12410645 176 20720 ESPN 0 . GRCh38 1 6428310 6428310 + Missense_Mutation SNP G G A rs755009690,rs780647660 C3N-01024_T C3N-01024_N G G c.379G>A p.Gly127Ser p.G127S ENST00000377828 2/13 279 233 46 214 214 0 strelka-varscan-mutect ESPN,missense_variant,p.Gly127Ser,ENST00000636330,;ESPN,missense_variant,p.Gly127Ser,ENST00000377828,NM_031475.2;HES2,upstream_gene_variant,,ENST00000377837,;MIR4252,downstream_gene_variant,,ENST00000585139,; A ENST00000377828 Transcript missense_variant 547/3531 379/2565 127/854 G/S Ggc/Agc rs755009690,rs780647660 1 1 ESPN HGNC HGNC:13281 protein_coding YES CCDS70.1 ENSP00000367059 B1AK53 UPI000013D2B6 NM_031475.2 deleterious(0.01) 2/13 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24153:SF14,hmmpanther:PTHR24153,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs780647660 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 6428310 6428310 G A 1 0 0 0 0 1 0 0 0 5116 1348 47 3 3 ESPN 1 6428310 Missense_Mutation SNP G C3N-01024_T 6428310 242528112 1 20721 KHDRBS1 0 . GRCh38 1 32014139 32014139 + Silent SNP A A G novel C3N-01024_T C3N-01024_N A A c.144A>G p.= p.G48G ENST00000327300 1/9 56 49 7 41 41 0 strelka-varscan-mutect KHDRBS1,synonymous_variant,p.=,ENST00000327300,NM_006559.2;KHDRBS1,synonymous_variant,p.=,ENST00000492989,NM_001271878.1;KHDRBS1,non_coding_transcript_exon_variant,,ENST00000307714,;KHDRBS1,upstream_gene_variant,,ENST00000484270,; G ENST00000327300 Transcript synonymous_variant 311/2757 144/1332 48/443 G ggA/ggG 1 1 KHDRBS1 HGNC HGNC:18116 protein_coding YES CCDS350.1 ENSP00000313829 Q07666 UPI0000073DA7 NM_006559.2 1/9 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -16.34477 0.9999999 1 1 1 0 G 2 3 69 32014139 32014139 A G 1 0 0 0 0 0 0 0 1 8067 291 11 5 5 KHDRBS1 1 32014139 Silent SNP A C3N-01024_T 25585829 32014139 216942283 2 20722 SAMD13 0 . GRCh38 1 84349720 84349720 + Silent SNP C C T rs374324643 C3N-01024_T C3N-01024_N C C c.297C>T p.= p.Y99Y ENST00000370673 4/4 173 128 45 177 176 1 strelka-varscan-mutect SAMD13,synonymous_variant,p.=,ENST00000370673,NM_001010971.2;SAMD13,synonymous_variant,p.=,ENST00000370668,NM_001134664.1;SAMD13,synonymous_variant,p.=,ENST00000370669,;SAMD13,synonymous_variant,p.=,ENST00000394834,NM_001134663.1;SAMD13,synonymous_variant,p.=,ENST00000370671,;SAMD13,synonymous_variant,p.=,ENST00000370670,;SAMD13,intron_variant,,ENST00000454967,;RP11-376N17.4,non_coding_transcript_exon_variant,,ENST00000505585,;RP11-376N17.4,non_coding_transcript_exon_variant,,ENST00000506295,;RP11-376N17.4,downstream_gene_variant,,ENST00000510918,; T ENST00000370673 Transcript synonymous_variant 489/1567 297/351 99/116 Y taC/taT rs374324643,COSM5626016,COSM5626017 1 1 SAMD13 HGNC HGNC:24582 protein_coding YES CCDS30760.1 ENSP00000359707 Q5VXD3 UPI00001A83BF NM_001010971.2 4/4 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF19,Pfam_domain:PF00536,Gene3D:1.10.150.50,Superfamily_domains:SSF47769 0,1,1 LOW SNV 2 0,1,1 1 PASS rs374324643 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 84349720 84349720 C T 1 0 0 0 0 0 0 0 1 14077 547 19 1 1 SAMD13 1 84349720 Silent SNP C C3N-01024_T 52335581 84349720 164606702 3 20723 OR10J5 0 . GRCh38 1 159535643 159535643 + Missense_Mutation SNP C C A rs138439831 C3N-01024_T C3N-01024_N C C c.365G>T p.Arg122Leu p.R122L ENST00000334857 1/1 339 215 124 230 229 1 strelka-varscan-mutect OR10J5,missense_variant,p.Arg122Leu,ENST00000334857,NM_001004469.1; A ENST00000334857 Transcript missense_variant 365/930 365/930 122/309 R/L cGc/cTc rs138439831,COSM424287 1 -1 OR10J5 HGNC HGNC:14993 protein_coding YES CCDS30910.1 ENSP00000334441 Q8NHC4 A0A126GV70 UPI0000041E4E NM_001004469.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF115,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs138439831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 159535643 159535643 C A 1 0 0 0 0 1 0 0 0 10989 768 27 1 1 OR10J5 1 159535643 Missense_Mutation SNP C C3N-01024_T 75185923 159535643 89420779 4 20724 CACNA1E 0 . GRCh38 1 181756068 181756068 + Missense_Mutation SNP G G A rs574530214 C3N-01024_T C3N-01024_N G G c.4102G>A p.Val1368Ile p.V1368I ENST00000367573 29/48 177 157 20 90 90 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Val1349Ile,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Val1368Ile,ENST00000621551,;CACNA1E,missense_variant,p.Val1368Ile,ENST00000367567,;CACNA1E,missense_variant,p.Val1349Ile,ENST00000358338,;CACNA1E,missense_variant,p.Val1368Ile,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Val1368Ile,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Val1367Ile,ENST00000357570,;CACNA1E,missense_variant,p.Val1349Ile,ENST00000360108,; A ENST00000367573 Transcript missense_variant 4102/7067 4102/6942 1368/2313 V/I Gtc/Atc rs574530214,COSM1138861,COSM5000056,COSM5000057,COSM5164455,COSM531332 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0.02) 29/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Superfamily_domains:SSF81324 0,1,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1,1 1 PASS rs574530214 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 181756068 181756068 G A 1 0 0 0 0 1 0 0 0 2230 1145 40 1 1 CACNA1E 1 181756068 Missense_Mutation SNP G C3N-01024_T 22220425 181756068 67200354 5 20725 EFEMP1 0 . GRCh38 2 55917668 55917668 + Nonsense_Mutation SNP G G A novel C3N-01024_T C3N-01024_N G G c.514C>T p.Gln172Ter p.Q172* ENST00000394555 4/11 381 322 59 306 306 0 strelka-varscan-mutect EFEMP1,stop_gained,p.Gln172Ter,ENST00000394555,NM_001039348.2,NM_001039349.2;EFEMP1,stop_gained,p.Gln172Ter,ENST00000355426,;EFEMP1,stop_gained,p.Gln39Ter,ENST00000634374,;EFEMP1,stop_gained,p.Gln172Ter,ENST00000438672,;EFEMP1,downstream_gene_variant,,ENST00000439193,;EFEMP1,downstream_gene_variant,,ENST00000440439,;EFEMP1,downstream_gene_variant,,ENST00000429909,;EFEMP1,downstream_gene_variant,,ENST00000452337,;EFEMP1,downstream_gene_variant,,ENST00000421664,;EFEMP1,downstream_gene_variant,,ENST00000424207,;EFEMP1,downstream_gene_variant,,ENST00000497698,;EFEMP1,downstream_gene_variant,,ENST00000452161,;EFEMP1,3_prime_UTR_variant,,ENST00000635671,;EFEMP1,downstream_gene_variant,,ENST00000480016,; A ENST00000394555 Transcript stop_gained 950/3024 514/1482 172/493 Q/* Caa/Taa 1 -1 EFEMP1 HGNC HGNC:3218 protein_coding YES CCDS1857.1 ENSP00000378058 Q12805 A0A0S2Z4F1 UPI0000000C12 NM_001039348.2,NM_001039349.2 4/11 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF310,Gene3D:2.10.25.10,Superfamily_domains:SSF57196 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 69 55917668 55917668 G A 1 0 0 0 0 0 1 0 0 4778 1362 47 3 3 EFEMP1 2 55917668 Nonsense_Mutation SNP G C3N-01024_T 55917668 186275861 6 20726 CCDC85A 0 . GRCh38 2 56192886 56192886 + Missense_Mutation SNP C C T rs746024337 C3N-01024_T C3N-01024_N C C c.686C>T p.Ala229Val p.A229V ENST00000407595 2/6 114 76 38 95 95 0 strelka-varscan-mutect CCDC85A,missense_variant,p.Ala229Val,ENST00000407595,NM_001080433.1;RP11-482H16.1,intron_variant,,ENST00000607540,; T ENST00000407595 Transcript missense_variant 1188/3982 686/1662 229/553 A/V gCg/gTg rs746024337,COSM5437249 1 1 CCDC85A HGNC HGNC:29400 protein_coding YES CCDS46290.1 ENSP00000384040 Q96PX6 UPI00001C1DC1 NM_001080433.1 tolerated(0.24) 2/6 hmmpanther:PTHR13546,hmmpanther:PTHR13546:SF16 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746024337 . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 69 56192886 56192886 C T 1 0 0 0 0 1 0 0 0 2557 768 27 1 1 CCDC85A 2 56192886 Missense_Mutation SNP C C3N-01024_T 275218 56192886 186000643 7 20727 CTNNA2 0 . GRCh38 2 79909678 79909678 + Missense_Mutation SNP G G A C3N-01024_T C3N-01024_N G G c.937G>A p.Gly313Ser p.G313S ENST00000402739 6/18 193 168 25 116 116 0 strelka-varscan-mutect CTNNA2,missense_variant,p.Gly313Ser,ENST00000466387,;CTNNA2,missense_variant,p.Gly313Ser,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Gly313Ser,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Gly313Ser,ENST00000629316,NM_001164883.1; A ENST00000402739 Transcript missense_variant 942/3684 937/2862 313/953 G/S Ggc/Agc COSM3000741,COSM4315443 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0.01) 6/18 Pfam_domain:PF01044,Prints_domain:PR00805,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 79909678 79909678 G A 1 0 0 0 0 1 0 0 0 3822 1116 39 1 1 CTNNA2 2 79909678 Missense_Mutation SNP G C3N-01024_T 23716792 79909678 162283851 8 20728 ZNF804A 0 . GRCh38 2 184935947 184935947 + Missense_Mutation SNP C C T C3N-01024_T C3N-01024_N C C c.551C>T p.Ala184Val p.A184V ENST00000302277 4/4 189 160 29 172 172 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Ala184Val,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Ala99Val,ENST00000613975,; T ENST00000302277 Transcript missense_variant 1145/4690 551/3630 184/1209 A/V gCt/gTt COSM1641745 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.05) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 1 MODERATE 1 SNV 1 1 1 PASS rs1254650215 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 184935947 184935947 C T 1 0 0 0 0 1 0 0 0 18755 797 28 3 3 ZNF804A 2 184935947 Missense_Mutation SNP C C3N-01024_T 105026269 184935947 57257582 9 20729 DTX3L 0 . GRCh38 3 122568611 122568611 + Silent SNP G G T novel C3N-01024_T C3N-01024_N G G c.522G>T p.= p.V174V ENST00000296161 3/5 302 247 55 256 256 0 strelka-varscan-mutect DTX3L,synonymous_variant,p.=,ENST00000296161,NM_138287.3;DTX3L,intron_variant,,ENST00000383661,;PARP9,upstream_gene_variant,,ENST00000462315,NM_001146106.1;PARP9,upstream_gene_variant,,ENST00000360356,NM_001146102.1,NM_031458.2;PARP9,upstream_gene_variant,,ENST00000477522,NM_001146103.1,NM_001146105.1;PARP9,upstream_gene_variant,,ENST00000471785,NM_001146104.1;PARP9,upstream_gene_variant,,ENST00000492382,;PARP9,upstream_gene_variant,,ENST00000466126,; T ENST00000296161 Transcript synonymous_variant 711/5868 522/2223 174/740 V gtG/gtT 1 1 DTX3L HGNC HGNC:30323 protein_coding YES CCDS3015.1 ENSP00000296161 Q8TDB6 UPI000000D9D0 NM_138287.3 3/5 hmmpanther:PTHR12622:SF23,hmmpanther:PTHR12622 LOW 1 SNV 1 1 PASS rs1256045116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 122568611 122568611 G T 1 0 0 0 0 0 0 0 1 4619 1364 48 2 2 DTX3L 3 122568611 Silent SNP G C3N-01024_T 122568611 75726948 10 20730 MED12L 0 . GRCh38 3 151387913 151387914 + Frame_Shift_Ins INS - - A novel C3N-01024_T C3N-01024_N - - c.5087_5088insA p.Asp1697GlyfsTer37 p.D1697Gfs*37 ENST00000474524 35/43 294 270 24 231 231 0 sindel-varindel-pindel MED12L,frameshift_variant,p.Asp1697GlyfsTer37,ENST00000474524,NM_053002.5;MED12L,frameshift_variant,p.Asp1557GlyfsTer37,ENST00000273432,;P2RY12,upstream_gene_variant,,ENST00000302632,NM_176876.2,NM_022788.4; A ENST00000474524 Transcript frameshift_variant 5125-5126/10744 5087-5088/6438 1696/2145 V/VX gtg/gtAg 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 35/43 hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 69 151387913 151387913 - A 1 0 1 1 0 0 0 0 0 9368 1696 59 0 0 MED12L 3 151387913 Frame_Shift_Ins INS - C3N-01024_T 28819302 151387913 46907646 11 20731 ZNF639 0 . GRCh38 3 179333320 179333324 + Frame_Shift_Del DEL CAGTC CAGTC - novel C3N-01024_T C3N-01024_N CAGTC CAGTC c.356_360delCAGTC p.Ser119Ter p.S119* ENST00000326361 7/7 132 94 38 144 144 0 sindel-varindel-pindel ZNF639,frameshift_variant,p.Ser119Ter,ENST00000326361,NM_016331.2;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000496856,NM_001303426.1,NM_001303425.1;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000484866,;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000621687,;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000491818,;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000466264,;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000481587,;ZNF639,frameshift_variant,p.Ser119Ter,ENST00000494234,;ZNF639,non_coding_transcript_exon_variant,,ENST00000466663,;ZNF639,downstream_gene_variant,,ENST00000483460,; - ENST00000326361 Transcript frameshift_variant 801-805/6064 356-360/1458 119-120/485 SV/X tCAGTC/t 1 1 ZNF639 HGNC HGNC:30950 protein_coding YES CCDS3227.1 ENSP00000325634 Q9UID6 UPI000003EA4C NM_016331.2 7/7 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF35 HIGH 1 deletion 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 69 179333320 179333320 CAGTC - 1 0 1 0 1 0 0 0 0 18631 838 29 0 0 ZNF639 3 179333320 Frame_Shift_Del DEL CAGTC C3N-01024_T 27945407 179333320 18962239 12 20732 HTR3E 0 . GRCh38 3 184106317 184106317 + Missense_Mutation SNP C C T rs763844964 C3N-01024_T C3N-01024_N C C c.1193C>T p.Pro398Leu p.P398L ENST00000440596 6/7 267 184 83 141 141 0 strelka-varscan-mutect HTR3E,missense_variant,p.Pro372Leu,ENST00000415389,NM_001256613.1;HTR3E,missense_variant,p.Pro387Leu,ENST00000335304,NM_182589.2;HTR3E,missense_variant,p.Pro398Leu,ENST00000440596,NM_001256614.1;HTR3E,missense_variant,p.Pro372Leu,ENST00000436361,NM_198314.2;HTR3E,missense_variant,p.Pro357Leu,ENST00000425359,NM_198313.2;HTR3E,downstream_gene_variant,,ENST00000431041,;HTR3E-AS1,upstream_gene_variant,,ENST00000431427,; T ENST00000440596 Transcript missense_variant 1193/1449 1193/1449 398/482 P/L cCg/cTg rs763844964 1 1 HTR3E HGNC HGNC:24005 protein_coding YES CCDS58871.1 ENSP00000406050 A5X5Y0 UPI000198CB5D NM_001256614.1 tolerated(0.56) 6/7 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF378,Pfam_domain:PF02932,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS rs763844964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 184106317 184106317 C T 1 0 0 0 0 1 0 0 0 7344 652 23 1 1 HTR3E 3 184106317 Missense_Mutation SNP C C3N-01024_T 4772997 184106317 14189242 13 20733 FRAS1 0 . GRCh38 4 78278693 78278693 + Silent SNP T T G novel C3N-01024_T C3N-01024_N T T c.1020T>G p.= p.P340P ENST00000512123 10/74 253 194 59 180 180 0 strelka-varscan-mutect FRAS1,synonymous_variant,p.=,ENST00000512123,NM_025074.6;FRAS1,synonymous_variant,p.=,ENST00000325942,NM_001166133.1;FRAS1,synonymous_variant,p.=,ENST00000502446,;FRAS1,synonymous_variant,p.=,ENST00000508900,;FRAS1,intron_variant,,ENST00000264899,; G ENST00000512123 Transcript synonymous_variant 1460/15624 1020/12039 340/4012 P ccT/ccG 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 10/74 Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29,SMART_domains:SM00214,Superfamily_domains:SSF57603 LOW 1 SNV 5 1 PASS rs1307155890 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 69 78278693 78278693 T G 1 0 0 0 0 0 0 0 1 5908 1567 55 5 5 FRAS1 4 78278693 Silent SNP T C3N-01024_T 78278693 111935862 14 20734 MAPK10 0 . GRCh38 4 86067926 86067926 + Nonsense_Mutation SNP G G A novel C3N-01024_T C3N-01024_N G G c.832C>T p.Gln278Ter p.Q278* ENST00000359221 10/14 105 69 36 85 85 0 strelka-varscan-mutect MAPK10,stop_gained,p.Gln133Ter,ENST00000395161,;MAPK10,stop_gained,p.Gln240Ter,ENST00000395169,NM_138980.2;MAPK10,stop_gained,p.Gln240Ter,ENST00000395166,;MAPK10,stop_gained,p.Gln278Ter,ENST00000359221,NM_138982.2;MAPK10,stop_gained,p.Gln133Ter,ENST00000449047,;MAPK10,stop_gained,p.Gln278Ter,ENST00000361569,NM_002753.3;MAPK10,stop_gained,p.Gln133Ter,ENST00000395160,NM_138981.2;MAPK10,stop_gained,p.Gln133Ter,ENST00000395157,;MAPK10,stop_gained,p.Gln191Ter,ENST00000515400,;MAPK10,non_coding_transcript_exon_variant,,ENST00000489368,;MAPK10,3_prime_UTR_variant,,ENST00000310816,;MAPK10,non_coding_transcript_exon_variant,,ENST00000508262,; A ENST00000359221 Transcript stop_gained 1359/2672 832/1395 278/464 Q/* Caa/Taa 1 -1 MAPK10 HGNC HGNC:6872 protein_coding YES CCDS34026.1 ENSP00000352157 P53779 UPI0000049042 NM_138982.2 10/14 Gene3D:1.10.510.10,Pfam_domain:PF00069,Prints_domain:PR01772,PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF162,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 69 86067926 86067926 G A 1 0 0 0 0 0 1 0 0 9196 1386 48 3 3 MAPK10 4 86067926 Nonsense_Mutation SNP G C3N-01024_T 7789233 86067926 104146629 15 20735 TRIML1 0 . GRCh38 4 188142441 188142441 + Missense_Mutation SNP A A G novel C3N-01024_T C3N-01024_N A A c.694A>G p.Ile232Val p.I232V ENST00000332517 3/6 392 301 91 191 191 0 strelka-varscan-mutect TRIML1,missense_variant,p.Ile232Val,ENST00000332517,NM_178556.3;RP11-366H4.3,intron_variant,,ENST00000501322,;TRIML1,upstream_gene_variant,,ENST00000507581,;TRIML1,upstream_gene_variant,,ENST00000512233,; G ENST00000332517 Transcript missense_variant 834/1797 694/1407 232/468 I/V Att/Gtt 1 1 TRIML1 HGNC HGNC:26698 protein_coding YES CCDS3851.1 ENSP00000327738 Q8N9V2 UPI000006FC8A NM_178556.3 tolerated(0.69) 3/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 69 188142441 188142441 A G 1 0 0 0 0 1 0 0 0 17047 333 12 5 5 TRIML1 4 188142441 Missense_Mutation SNP A C3N-01024_T 102074515 188142441 2072114 16 20736 EGFLAM 0 . GRCh38 5 38406138 38406138 + Missense_Mutation SNP C C T rs750333897 C3N-01024_T C3N-01024_N C C c.725C>T p.Ala242Val p.A242V ENST00000354891 7/23 382 276 106 232 232 0 strelka-varscan-mutect EGFLAM,missense_variant,p.Ala242Val,ENST00000322350,NM_152403.3;EGFLAM,missense_variant,p.Ala242Val,ENST00000354891,NM_001205301.1;EGFLAM,missense_variant,p.Ala8Val,ENST00000336740,NM_182798.2;EGFLAM,intron_variant,,ENST00000397202,;EGFLAM-AS2,upstream_gene_variant,,ENST00000514377,;EGFLAM-AS2,upstream_gene_variant,,ENST00000512603,; T ENST00000354891 Transcript missense_variant 1071/3963 725/3054 242/1017 A/V gCg/gTg rs750333897,COSM1734436,COSM1734437,COSM84899 1 1 EGFLAM HGNC HGNC:26810 protein_coding YES CCDS56363.1 ENSP00000346964 Q63HQ2 UPI000022C806 NM_001205301.1 tolerated_low_confidence(0.57) 7/23 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs750333897 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 38406138 38406138 C T 1 0 0 0 0 1 0 0 0 4802 768 27 1 1 EGFLAM 5 38406138 Missense_Mutation SNP C C3N-01024_T 38406138 143132121 17 20737 CAMK4 0 . GRCh38 5 111478433 111478435 + In_Frame_Del DEL AGG AGG - novel C3N-01024_T C3N-01024_N AGG AGG c.756_758delGAG p.Arg253del p.R253del ENST00000282356 9/11 154 128 26 169 169 0 sindel-varindel-pindel CAMK4,inframe_deletion,p.Arg253del,ENST00000282356,NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4;CAMK4,inframe_deletion,p.Arg253del,ENST00000512453,;CAMK4,upstream_gene_variant,,ENST00000512890,;CAMK4,upstream_gene_variant,,ENST00000510858,;CAMK4,3_prime_UTR_variant,,ENST00000515231,;CAMK4,3_prime_UTR_variant,,ENST00000514007,;CAMK4,upstream_gene_variant,,ENST00000509645,; - ENST00000282356 Transcript inframe_deletion 1152-1154/12240 754-756/1422 252/473 R/- AGG/- 1 1 CAMK4 HGNC HGNC:1464 protein_coding YES CCDS4103.1 ENSP00000282356 Q16566 UPI000000128E NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4 9/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24349,hmmpanther:PTHR24349:SF152,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 69 111478433 111478433 AGG - 1 0 1 0 1 0 0 0 0 2296 179 7 0 0 CAMK4 5 111478433 In_Frame_Del DEL AGG C3N-01024_T 73072295 111478433 70059826 18 20738 DMXL1 0 . GRCh38 5 119150369 119150369 + Silent SNP T T C novel C3N-01024_T C3N-01024_N T T c.4542T>C p.= p.D1514D ENST00000539542 18/44 173 122 51 126 126 0 strelka-varscan-mutect DMXL1,synonymous_variant,p.=,ENST00000539542,NM_001290321.2;DMXL1,synonymous_variant,p.=,ENST00000311085,NM_001290322.2,NM_005509.5;MIR5706,upstream_gene_variant,,ENST00000579841,;DMXL1,downstream_gene_variant,,ENST00000512281,; C ENST00000539542 Transcript synonymous_variant 4723/11236 4542/9147 1514/3048 D gaT/gaC 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 18/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12,Pfam_domain:PF12234 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 69 119150369 119150369 T C 1 0 0 0 0 0 0 0 1 4403 1403 49 5 5 DMXL1 5 119150369 Silent SNP T C3N-01024_T 7671936 119150369 62387890 19 20739 PCDHA1 0 . GRCh38 5 140786989 140786989 + Silent SNP C C T C3N-01024_T C3N-01024_N C C c.699C>T p.= p.L233L ENST00000504120 1/4 161 131 30 113 113 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,synonymous_variant,p.=,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; T ENST00000504120 Transcript synonymous_variant 699/5263 699/2853 233/950 L ctC/ctT COSM3776242,COSM3776243 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 1,1 LOW 1 SNV 1 1,1 1 PASS rs1230076426 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 140786989 140786989 C T 1 0 0 0 0 0 0 0 1 11606 871 31 1 1 PCDHA1 5 140786989 Silent SNP C C3N-01024_T 21636620 140786989 40751270 20 20740 PCDHB7 0 . GRCh38 5 141174701 141174701 + Silent SNP C C T rs782289543 C3N-01024_T C3N-01024_N C C c.1866C>T p.= p.G622G ENST00000231137 1/1 1573 1410 163 1001 1000 1 strelka-varscan-mutect PCDHB7,synonymous_variant,p.=,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; T ENST00000231137 Transcript synonymous_variant 2083/3765 1866/2382 622/793 G ggC/ggT rs782289543,COSM736059 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 LOW SNV 0,1 1 PASS rs782289543 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 141174701 141174701 C T 1 0 0 0 0 0 0 0 1 11634 755 27 1 1 PCDHB7 5 141174701 Silent SNP C C3N-01024_T 387712 141174701 40363558 21 20741 PCDHGB4 0 . GRCh38 5 141388864 141388864 + Missense_Mutation SNP C C T rs748559328 C3N-01024_T C3N-01024_N C C c.980C>T p.Ala327Val p.A327V ENST00000519479 1/4 307 216 91 204 204 0 strelka-varscan-mutect PCDHGB4,missense_variant,p.Ala327Val,ENST00000615384,NM_032098.1;PCDHGB4,missense_variant,p.Ala327Val,ENST00000519479,NM_003736.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000519479 Transcript missense_variant 980/4578 980/2772 327/923 A/V gCg/gTg rs748559328,COSM388169 1 1 PCDHGB4 HGNC HGNC:8711 protein_coding YES CCDS54928.1 ENSP00000428288 Q9UN71 UPI000006F773 NM_003736.2 deleterious(0.04) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF117,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748559328 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 141388864 141388864 C T 1 0 0 0 0 1 0 0 0 11652 768 27 1 1 PCDHGB4 5 141388864 Missense_Mutation SNP C C3N-01024_T 214163 141388864 40149395 22 20742 RANBP17 0 . GRCh38 5 171240941 171240941 + Silent SNP G G T novel C3N-01024_T C3N-01024_N G G c.2436G>T p.= p.L812L ENST00000523189 23/28 153 107 46 120 120 0 strelka-varscan-mutect RANBP17,synonymous_variant,p.=,ENST00000523189,NM_022897.4;RANBP17,synonymous_variant,p.=,ENST00000616486,;RANBP17,non_coding_transcript_exon_variant,,ENST00000521759,;RANBP17,upstream_gene_variant,,ENST00000521834,;RANBP17,3_prime_UTR_variant,,ENST00000522066,;RANBP17,3_prime_UTR_variant,,ENST00000519949,;RANBP17,3_prime_UTR_variant,,ENST00000522533,;RANBP17,3_prime_UTR_variant,,ENST00000389118,;RANBP17,3_prime_UTR_variant,,ENST00000519256,; T ENST00000523189 Transcript synonymous_variant 2600/4588 2436/3267 812/1088 L ctG/ctT 1 1 RANBP17 HGNC HGNC:14428 protein_coding YES CCDS34287.1 ENSP00000427975 Q9H2T7 Q546R4 UPI000000107C NM_022897.4 23/28 hmmpanther:PTHR12596,hmmpanther:PTHR12596:SF8,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 171240941 171240941 G T 1 0 0 0 0 0 0 0 1 13186 1364 48 2 2 RANBP17 5 171240941 Silent SNP G C3N-01024_T 29852077 171240941 10297318 23 20743 TCP1 0 . GRCh38 6 159783945 159783945 + Missense_Mutation SNP G G C novel C3N-01024_T C3N-01024_N G G c.793C>G p.Gln265Glu p.Q265E ENST00000321394 7/12 149 116 33 111 111 0 strelka-varscan-mutect TCP1,missense_variant,p.Gln265Glu,ENST00000321394,NM_030752.2;TCP1,missense_variant,p.Gln110Glu,ENST00000392168,NM_001008897.1;TCP1,missense_variant,p.Gln265Glu,ENST00000420894,;TCP1,missense_variant,p.Gln41Glu,ENST00000544255,;TCP1,missense_variant,p.Gln63Glu,ENST00000539756,;ACAT2,downstream_gene_variant,,ENST00000367048,NM_005891.2;TCP1,downstream_gene_variant,,ENST00000539948,;TCP1,downstream_gene_variant,,ENST00000537390,;TCP1,downstream_gene_variant,,ENST00000538128,;TCP1,downstream_gene_variant,,ENST00000536394,;SNORA29,downstream_gene_variant,,ENST00000384183,;SNORA20,upstream_gene_variant,,ENST00000384662,;ACAT2,downstream_gene_variant,,ENST00000472052,;TCP1,downstream_gene_variant,,ENST00000546023,;TCP1,downstream_gene_variant,,ENST00000543532,;TCP1,non_coding_transcript_exon_variant,,ENST00000536807,;TCP1,downstream_gene_variant,,ENST00000538530,;TCP1,downstream_gene_variant,,ENST00000545764,;TCP1,downstream_gene_variant,,ENST00000467544,;TCP1,downstream_gene_variant,,ENST00000536607,;TCP1,upstream_gene_variant,,ENST00000546204,;TCP1,downstream_gene_variant,,ENST00000543517,; C ENST00000321394 Transcript missense_variant 1074/2499 793/1671 265/556 Q/E Cag/Gag 1 -1 TCP1 HGNC HGNC:11655 protein_coding YES CCDS5269.1 ENSP00000317334 P17987 UPI0000136AEA NM_030752.2 tolerated(0.36) 7/12 hmmpanther:PTHR11353,Pfam_domain:PF00118,TIGRFAM_domain:TIGR02340,Gene3D:3.50.7.10,Superfamily_domains:SSF52029 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 69 159783945 159783945 G C 1 0 0 0 0 1 0 0 0 16116 1391 48 4 4 TCP1 6 159783945 Missense_Mutation SNP G C3N-01024_T 159783945 11022034 24 20744 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-01024_T C3N-01024_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 439 334 105 383 383 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 69 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-01024_T 55174772 104171201 25 20745 SLC26A3 0 . GRCh38 7 107774795 107774795 + Silent SNP G G A novel C3N-01024_T C3N-01024_N G G c.1755C>T p.= p.G585G ENST00000340010 16/21 600 446 154 395 395 0 strelka-varscan-mutect SLC26A3,synonymous_variant,p.=,ENST00000340010,NM_000111.2;SLC26A3,3_prime_UTR_variant,,ENST00000379083,;SLC26A3,downstream_gene_variant,,ENST00000469651,; A ENST00000340010 Transcript synonymous_variant 1940/2863 1755/2295 585/764 G ggC/ggT 1 -1 SLC26A3 HGNC HGNC:3018 protein_coding YES CCDS5748.1 ENSP00000345873 P40879 UPI000000128C NM_000111.2 16/21 Pfam_domain:PF01740,PROSITE_profiles:PS50801,TIGRFAM_domain:TIGR00815 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 69 107774795 107774795 G A 1 0 0 0 0 0 0 0 1 14788 958 34 3 3 SLC26A3 7 107774795 Silent SNP G C3N-01024_T 52600023 107774795 51571178 26 20746 ADAM32 0 . GRCh38 8 39165117 39165117 + Missense_Mutation SNP G G C novel C3N-01024_T C3N-01024_N G G c.754G>C p.Asp252His p.D252H ENST00000379907 9/25 149 140 9 138 138 0 strelka-varscan-mutect ADAM32,missense_variant,p.Asp252His,ENST00000379907,NM_145004.5;ADAM32,missense_variant,p.Asp259His,ENST00000437682,NM_001313994.1;ADAM32,missense_variant,p.Asp252His,ENST00000519315,;ADAM32,downstream_gene_variant,,ENST00000399831,;ADAM32,downstream_gene_variant,,ENST00000522506,;ADAM32,non_coding_transcript_exon_variant,,ENST00000518259,; C ENST00000379907 Transcript missense_variant 881/2601 754/2364 252/787 D/H Gat/Cat 1 1 ADAM32 HGNC HGNC:15479 protein_coding YES CCDS47846.1 ENSP00000369238 Q8TC27 UPI000013F62F NM_145004.5 deleterious(0.02) 9/25 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF24,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 69 39165117 39165117 G C 1 0 0 0 0 1 0 0 0 293 942 33 4 4 ADAM32 8 39165117 Missense_Mutation SNP G C3N-01024_T 39165117 105973519 27 20747 MCM4 0 . GRCh38 8 47966294 47966294 + Silent SNP C C A rs750729954 C3N-01024_T C3N-01024_N C C c.940C>A p.= p.R314R ENST00000262105 8/16 253 223 30 184 184 0 strelka-varscan-mutect MCM4,synonymous_variant,p.=,ENST00000262105,NM_005914.3;MCM4,synonymous_variant,p.=,ENST00000523944,NM_182746.2;MCM4,intron_variant,,ENST00000520637,;MCM4,downstream_gene_variant,,ENST00000519170,;MCM4,downstream_gene_variant,,ENST00000518221,;MCM4,upstream_gene_variant,,ENST00000518680,;MCM4,non_coding_transcript_exon_variant,,ENST00000519138,;MCM4,upstream_gene_variant,,ENST00000517709,;MCM4,downstream_gene_variant,,ENST00000520934,;MCM4,downstream_gene_variant,,ENST00000524086,;MCM4,downstream_gene_variant,,ENST00000520994,;MCM4,upstream_gene_variant,,ENST00000519470,; A ENST00000262105 Transcript synonymous_variant 1149/4183 940/2592 314/863 R Cgg/Agg rs750729954 1 1 MCM4 HGNC HGNC:6947 protein_coding YES CCDS6143.1 ENSP00000262105 P33991 UPI000013D25C NM_005914.3 8/16 Gene3D:2.20.28.10,hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF66,SMART_domains:SM00350,Superfamily_domains:SSF50249 LOW 1 SNV 1 1 PASS rs750729954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 69 47966294 47966294 C A 1 0 0 0 0 0 0 0 1 9321 643 23 1 1 MCM4 8 47966294 Silent SNP C C3N-01024_T 8801177 47966294 97172342 28 20748 CSMD3 0 . GRCh38 8 112319923 112319923 + Silent SNP C C T rs781779613 C3N-01024_T C3N-01024_N C C c.7224G>A p.= p.T2408T ENST00000297405 46/71 454 256 198 287 287 0 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000492692,; T ENST00000297405 Transcript synonymous_variant 7469/13212 7224/11124 2408/3707 T acG/acA rs781779613,COSM3884865,COSM3884866 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 46/71 PROSITE_profiles:PS50923,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs781779613 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 112319923 112319923 C T 1 0 0 0 0 0 0 0 1 3747 639 23 1 1 CSMD3 8 112319923 Silent SNP C C3N-01024_T 64353629 112319923 32818713 29 20749 TRPM3 0 . GRCh38 9 70618887 70618887 + Missense_Mutation SNP G G A rs747610777 C3N-01024_T C3N-01024_N G G c.2302C>T p.Arg768Cys p.R768C ENST00000377110 16/25 139 130 9 130 130 0 strelka-varscan-mutect TRPM3,missense_variant,p.Arg768Cys,ENST00000377110,NM_001007471.2;TRPM3,missense_variant,p.Arg630Cys,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,missense_variant,p.Arg627Cys,ENST00000377105,NM_024971.5;TRPM3,missense_variant,p.Arg772Cys,ENST00000357533,;TRPM3,missense_variant,p.Arg640Cys,ENST00000396292,NM_206946.3;TRPM3,missense_variant,p.Arg630Cys,ENST00000358082,;TRPM3,missense_variant,p.Arg615Cys,ENST00000396285,NM_020952.4;TRPM3,missense_variant,p.Arg627Cys,ENST00000408909,;TRPM3,missense_variant,p.Arg617Cys,ENST00000396280,NM_206945.3;TRPM3,missense_variant,p.Arg768Cys,ENST00000377111,; A ENST00000377110 Transcript missense_variant 2546/12258 2302/5124 768/1707 R/C Cgc/Tgc rs747610777,COSM3907828,COSM3907829,COSM3907830,COSM3907831 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 deleterious(0) 16/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs747610777 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 70618887 70618887 G A 1 0 0 0 0 1 0 0 0 17093 1087 38 1 1 TRPM3 9 70618887 Missense_Mutation SNP G C3N-01024_T 70618887 67775830 30 20750 MMS19 0 . GRCh38 10 97470777 97470777 + Missense_Mutation SNP C C T novel C3N-01024_T C3N-01024_N C C c.769G>A p.Glu257Lys p.E257K ENST00000438925 9/31 133 76 57 98 98 0 strelka-varscan-mutect MMS19,missense_variant,p.Glu257Lys,ENST00000438925,NM_022362.4,NM_001289404.1;MMS19,missense_variant,p.Glu214Lys,ENST00000355839,NM_001289403.1;MMS19,missense_variant,p.Glu257Lys,ENST00000370782,NM_001289405.1;MMS19,missense_variant,p.Glu257Lys,ENST00000327238,;MMS19,missense_variant,p.Glu248Lys,ENST00000437002,;MMS19,upstream_gene_variant,,ENST00000434538,;MMS19,downstream_gene_variant,,ENST00000422685,;MMS19,splice_region_variant,,ENST00000483626,;MMS19,splice_region_variant,,ENST00000415383,;MMS19,splice_region_variant,,ENST00000441194,;MMS19,upstream_gene_variant,,ENST00000434392,; T ENST00000438925 Transcript missense_variant,splice_region_variant 1105/3797 769/3093 257/1030 E/K Gag/Aag 1 -1 MMS19 HGNC HGNC:13824 protein_coding YES CCDS7464.1 ENSP00000412698 Q96T76 UPI000013DDF7 NM_022362.4,NM_001289404.1 deleterious(0.03) 9/31 hmmpanther:PTHR12891,Gene3D:1.25.10.10,Pfam_domain:PF14500 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 97470777 97470777 C T 1 0 0 0 0 1 0 0 0 9635 840 29 3 3 MMS19 10 97470777 Missense_Mutation SNP C C3N-01024_T 97470777 36326645 31 20751 EIF3A 0 . GRCh38 10 119058251 119058251 + Nonsense_Mutation SNP G G T novel C3N-01024_T C3N-01024_N G G c.1682C>A p.Ser561Ter p.S561* ENST00000369144 12/22 224 192 32 216 216 0 strelka-varscan-mutect EIF3A,stop_gained,p.Ser561Ter,ENST00000369144,NM_003750.2;EIF3A,stop_gained,p.Ser561Ter,ENST00000541549,;SNORA19,downstream_gene_variant,,ENST00000410656,;SNORA19,downstream_gene_variant,,ENST00000384737,;EIF3A,non_coding_transcript_exon_variant,,ENST00000462527,; T ENST00000369144 Transcript stop_gained 1810/6646 1682/4149 561/1382 S/* tCa/tAa 1 -1 EIF3A HGNC HGNC:3271 protein_coding YES CCDS7608.1 ENSP00000358140 Q14152 UPI000012D311 NM_003750.2 12/22 Coiled-coils_(Ncoils):Coil,HAMAP:MF_03000,hmmpanther:PTHR14005 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 69 119058251 119058251 G T 1 0 0 0 0 0 1 0 0 4846 1294 45 2 2 EIF3A 10 119058251 Nonsense_Mutation SNP G C3N-01024_T 21587474 119058251 14739171 32 20752 OR51B5 0 . GRCh38 11 5343272 5343272 + Missense_Mutation SNP G G T C3N-01024_T C3N-01024_N G G c.253C>A p.Leu85Met p.L85M ENST00000300773 1/1 161 115 46 144 143 1 strelka-varscan-mutect OR51B5,missense_variant,p.Leu85Met,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300773 Transcript missense_variant 253/939 253/939 85/312 L/M Ctg/Atg COSM3448640 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 tolerated(0.12) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS rs1218953607 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 5343272 5343272 G T 1 0 0 0 0 1 0 0 0 11165 962 34 2 2 OR51B5 11 5343272 Missense_Mutation SNP G C3N-01024_T 5343272 129743350 33 20753 DBX1 0 . GRCh38 11 20160158 20160158 + Missense_Mutation SNP C C T novel C3N-01024_T C3N-01024_N C C c.167G>A p.Arg56His p.R56H ENST00000524983 1/4 134 125 9 141 141 0 strelka-varscan-mutect DBX1,missense_variant,p.Arg56His,ENST00000524983,NM_001029865.2; T ENST00000524983 Transcript missense_variant 456/1380 167/1032 56/343 R/H cGc/cAc 1 -1 DBX1 HGNC HGNC:33185 protein_coding YES ENSP00000436881 A6NMT0 UPI000013C8B1 NM_001029865.2 deleterious(0) 1/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF6 MODERATE 1 SNV 5 1 PASS rs1298541244 . 0 206 4 0 0 0 0 0 -17.17357 1 1 1 1 0 T 3 4 69 20160158 20160158 C T 1 0 0 0 0 1 0 0 0 4059 768 27 1 1 DBX1 11 20160158 Missense_Mutation SNP C C3N-01024_T 14816886 20160158 114926464 34 20754 KCNA4 0 . GRCh38 11 30012093 30012093 + Missense_Mutation SNP G G T C3N-01024_T C3N-01024_N G G c.586C>A p.Gln196Lys p.Q196K ENST00000328224 2/2 336 231 105 262 262 0 strelka-varscan-mutect KCNA4,missense_variant,p.Gln196Lys,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; T ENST00000328224 Transcript missense_variant 1820/4172 586/1962 196/653 Q/K Cag/Aag COSM4751935 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 deleterious(0.04) 2/2 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 30012093 30012093 G T 1 0 0 0 0 1 0 0 0 7921 1357 47 2 2 KCNA4 11 30012093 Missense_Mutation SNP G C3N-01024_T 9851935 30012093 105074529 35 20755 TP53I11 0 . GRCh38 11 44935608 44935608 + Missense_Mutation SNP C C A novel C3N-01024_T C3N-01024_N C C c.389G>T p.Arg130Leu p.R130L ENST00000533940 9/10 345 242 103 226 226 0 strelka-varscan-mutect TP53I11,missense_variant,p.Arg130Leu,ENST00000533940,NM_001258320.1;TP53I11,missense_variant,p.Arg130Leu,ENST00000308212,NM_001318386.1,NM_001258321.1;TP53I11,missense_variant,p.Arg130Leu,ENST00000616990,NM_001258324.1,NM_001258322.1;TP53I11,missense_variant,p.Arg130Leu,ENST00000395648,NM_001318384.1,NM_001258323.1;TP53I11,missense_variant,p.Arg130Leu,ENST00000525680,NM_006034.3;TP53I11,missense_variant,p.Arg130Leu,ENST00000528473,;TP53I11,missense_variant,p.Arg78Leu,ENST00000528290,;TSPAN18,downstream_gene_variant,,ENST00000340160,NM_130783.4;TSPAN18,downstream_gene_variant,,ENST00000520358,;TSPAN18,downstream_gene_variant,,ENST00000518429,;TP53I11,downstream_gene_variant,,ENST00000531928,;TP53I11,downstream_gene_variant,,ENST00000533443,;TP53I11,downstream_gene_variant,,ENST00000530035,;TP53I11,downstream_gene_variant,,ENST00000533937,;TP53I11,downstream_gene_variant,,ENST00000525683,;TP53I11,downstream_gene_variant,,ENST00000527685,;TP53I11,downstream_gene_variant,,ENST00000525138,;TP53I11,downstream_gene_variant,,ENST00000627720,;TP53I11,non_coding_transcript_exon_variant,,ENST00000533955,;TP53I11,downstream_gene_variant,,ENST00000531130,;TP53I11,3_prime_UTR_variant,,ENST00000532253,;TP53I11,non_coding_transcript_exon_variant,,ENST00000524774,;TP53I11,intron_variant,,ENST00000354556,;TP53I11,downstream_gene_variant,,ENST00000532921,;TP53I11,downstream_gene_variant,,ENST00000525145,;TP53I11,downstream_gene_variant,,ENST00000525667,; A ENST00000533940 Transcript missense_variant 994/3703 389/570 130/189 R/L cGa/cTa 1 -1 TP53I11 HGNC HGNC:16842 protein_coding YES CCDS7911.1 ENSP00000436152 O14683 UPI00001BB8BA NM_001258320.1 deleterious(0) 9/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR31584,hmmpanther:PTHR31584:SF1,Pfam_domain:PF14936 MODERATE 1 SNV 1 1 PASS rs897730445 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 44935608 44935608 C A 1 0 0 0 0 1 0 0 0 16863 884 31 1 1 TP53I11 11 44935608 Missense_Mutation SNP C C3N-01024_T 14923515 44935608 90151014 36 20756 OR4S2 0 . GRCh38 11 55651675 55651675 + Missense_Mutation SNP C C T rs188197652 C3N-01024_T C3N-01024_N C C c.772C>T p.Arg258Cys p.R258C ENST00000312422 1/1 101 43 58 101 101 0 strelka-varscan-mutect OR4S2,missense_variant,p.Arg258Cys,ENST00000312422,NM_001004059.2; T ENST00000312422 Transcript missense_variant 772/936 772/936 258/311 R/C Cgc/Tgc rs188197652,COSM3397787 1 1 OR4S2 HGNC HGNC:15183 protein_coding YES CCDS31505.1 ENSP00000310337 Q8NH73 A0A126GVG1 UPI00001D77D2 NM_001004059.2 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs188197652 . 23 182 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 55651675 55651675 C T 1 0 0 0 0 1 0 0 0 11159 768 27 1 1 OR4S2 11 55651675 Missense_Mutation SNP C C3N-01024_T 10716067 55651675 79434947 37 20757 PATE4 0 . GRCh38 11 125833381 125833381 + Missense_Mutation SNP C C A novel C3N-01024_T C3N-01024_N C C c.22C>A p.Leu8Ile p.L8I ENST00000457514 1/3 200 141 59 83 83 0 strelka-varscan-mutect PATE4,missense_variant,p.Leu8Ile,ENST00000457514,NM_001144874.1;PATE4,missense_variant,p.Leu8Ile,ENST00000534411,;PATE4,non_coding_transcript_exon_variant,,ENST00000525411,; A ENST00000457514 Transcript missense_variant 66/1983 22/297 8/98 L/I Ctc/Atc 1 1 PATE4 HGNC HGNC:35427 protein_coding YES CCDS44765.1 ENSP00000411439 P0C8F1 UPI0000251F10 NM_001144874.1 tolerated(0.11) 1/3 hmmpanther:PTHR17571,hmmpanther:PTHR17571:SF37,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 125833381 125833381 C A 1 0 0 0 0 1 0 0 0 11557 797 28 2 2 PATE4 11 125833381 Missense_Mutation SNP C C3N-01024_T 70181706 125833381 9253241 38 20758 DBX2 0 . GRCh38 12 45036046 45036046 + Missense_Mutation SNP G G A rs781083157 C3N-01024_T C3N-01024_N G G c.472C>T p.Arg158Cys p.R158C ENST00000332700 2/4 209 153 56 98 98 0 strelka-varscan-mutect DBX2,missense_variant,p.Arg158Cys,ENST00000332700,NM_001004329.2; A ENST00000332700 Transcript missense_variant 644/2806 472/1020 158/339 R/C Cgc/Tgc rs781083157,COSM5467940 1 -1 DBX2 HGNC HGNC:33186 protein_coding YES CCDS31781.1 ENSP00000331470 Q6ZNG2 UPI000041A784 NM_001004329.2 deleterious(0.03) 2/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs781083157 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 45036046 45036046 G A 1 0 0 0 0 1 0 0 0 4060 1087 38 1 1 DBX2 12 45036046 Missense_Mutation SNP G C3N-01024_T 45036046 88239263 39 20759 KMT2D 0 . GRCh38 12 49032442 49032442 + Missense_Mutation SNP G G C C3N-01024_T C3N-01024_N G G c.12263C>G p.Ser4088Cys p.S4088C ENST00000301067 39/54 328 293 35 205 205 0 strelka-varscan-mutect KMT2D,missense_variant,p.Ser4088Cys,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000552391,; C ENST00000301067 Transcript missense_variant 12263/19419 12263/16614 4088/5537 S/C tCt/tGt COSM5534591,COSM5534592 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 deleterious_low_confidence(0.03) 39/54 Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 69 49032442 49032442 G C 1 0 0 0 0 1 0 0 0 8298 942 33 4 4 KMT2D 12 49032442 Missense_Mutation SNP G C3N-01024_T 3996396 49032442 84242867 40 20760 ACACB 0 . GRCh38 12 109139861 109139861 + Missense_Mutation SNP G G T novel C3N-01024_T C3N-01024_N G G c.456G>T p.Lys152Asn p.K152N ENST00000338432 2/53 177 149 28 121 121 0 strelka-varscan-mutect ACACB,missense_variant,p.Lys152Asn,ENST00000338432,;ACACB,missense_variant,p.Lys152Asn,ENST00000377848,NM_001093.3;ACACB,missense_variant,p.Lys127Asn,ENST00000539864,;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,upstream_gene_variant,,ENST00000546328,; T ENST00000338432 Transcript missense_variant 575/9360 456/7377 152/2458 K/N aaG/aaT 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB tolerated_low_confidence(0.14) 2/53 hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF94 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 109139861 109139861 G T 1 0 0 0 0 1 0 0 0 150 933 33 2 2 ACACB 12 109139861 Missense_Mutation SNP G C3N-01024_T 60107419 109139861 24135448 41 20761 PEBP1 0 . GRCh38 12 118144747 118144747 + Nonsense_Mutation SNP C C T novel C3N-01024_T C3N-01024_N C C c.508C>T p.Gln170Ter p.Q170* ENST00000261313 4/4 621 422 199 378 378 0 strelka-varscan-mutect PEBP1,stop_gained,p.Gln170Ter,ENST00000261313,NM_002567.2;PEBP1,non_coding_transcript_exon_variant,,ENST00000542939,; T ENST00000261313 Transcript stop_gained 860/1697 508/564 170/187 Q/* Cag/Tag 1 1 PEBP1 HGNC HGNC:8630 protein_coding YES CCDS9187.1 ENSP00000261313 P30086 D9IAI1 UPI00000015F1 NM_002567.2 4/4 Gene3D:3.90.280.10,hmmpanther:PTHR11362,hmmpanther:PTHR11362:SF8,Superfamily_domains:SSF49777 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 69 118144747 118144747 C T 1 0 0 0 0 0 1 0 0 11802 595 21 3 3 PEBP1 12 118144747 Nonsense_Mutation SNP C C3N-01024_T 9004886 118144747 15130562 42 20762 DIS3 0 . GRCh38 13 72772200 72772200 + Missense_Mutation SNP C C T C3N-01024_T C3N-01024_N C C c.1462G>A p.Asp488Asn p.D488N ENST00000377767 10/21 206 165 41 157 157 0 strelka-varscan-mutect DIS3,missense_variant,p.Asp488Asn,ENST00000377767,NM_014953.4;DIS3,missense_variant,p.Asp458Asn,ENST00000377780,NM_001128226.2;DIS3,missense_variant,p.Asp326Asn,ENST00000545453,;DIS3,missense_variant,p.Asp488Asn,ENST00000490646,; T ENST00000377767 Transcript missense_variant 1563/10604 1462/2877 488/958 D/N Gat/Aat COSM158635,COSM3955721 1 -1 DIS3 HGNC HGNC:20604 protein_coding YES CCDS9447.1 ENSP00000366997 Q9Y2L1 UPI0000141B79 NM_014953.4 deleterious(0) 10/21 hmmpanther:PTHR23355,hmmpanther:PTHR23355:SF35,Pfam_domain:PF00773,SMART_domains:SM00955,Superfamily_domains:SSF50249 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 72772200 72772200 C T 1 0 0 0 0 1 0 0 0 4341 884 31 1 1 DIS3 13 72772200 Missense_Mutation SNP C C3N-01024_T 72772200 41592128 43 20763 PAX9 0 . GRCh38 14 36663175 36663175 + Missense_Mutation SNP C C T novel C3N-01024_T C3N-01024_N C C c.283C>T p.Pro95Ser p.P95S ENST00000361487 2/4 925 324 601 333 333 0 strelka-varscan-mutect PAX9,missense_variant,p.Pro95Ser,ENST00000361487,;PAX9,missense_variant,p.Pro95Ser,ENST00000402703,NM_006194.3;PAX9,5_prime_UTR_variant,,ENST00000554201,;RP11-964E11.2,upstream_gene_variant,,ENST00000555107,;PAX9,upstream_gene_variant,,ENST00000557107,;PAX9,downstream_gene_variant,,ENST00000553267,;PAX9,downstream_gene_variant,,ENST00000555639,; T ENST00000361487 Transcript missense_variant 508/4514 283/1026 95/341 P/S Ccc/Tcc 1 1 PAX9 HGNC HGNC:8623 protein_coding YES CCDS9662.1 ENSP00000355245 P55771 Q2L4T1 UPI0000131377 deleterious(0.01) 2/4 PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF297,Pfam_domain:PF00292,Gene3D:1.10.10.10,SMART_domains:SM00351,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 36663175 36663175 C T 1 0 0 0 0 1 0 0 0 11571 623 22 3 3 PAX9 14 36663175 Missense_Mutation SNP C C3N-01024_T 36663175 70380543 44 20764 OTUD7A 0 . GRCh38 15 31484306 31484306 + Nonsense_Mutation SNP G G T novel C3N-01024_T C3N-01024_N G G c.1769C>A p.Ser590Ter p.S590* ENST00000307050 11/11 187 154 33 137 137 0 strelka-varscan-mutect OTUD7A,stop_gained,p.Ser590Ter,ENST00000307050,NM_130901.1; T ENST00000307050 Transcript stop_gained 1862/10770 1769/2781 590/926 S/* tCg/tAg 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 11/11 Low_complexity_(Seg):seg,hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367 HIGH 1 SNV 1 1 PASS rs1473335284 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 69 31484306 31484306 G T 1 0 0 0 0 0 1 0 0 11387 1059 37 1 1 OTUD7A 15 31484306 Nonsense_Mutation SNP G C3N-01024_T 31484306 70506883 45 20765 AQR 0 . GRCh38 15 34897560 34897560 + Missense_Mutation SNP G G A rs201758262 C3N-01024_T C3N-01024_N G G c.2389C>T p.Arg797Cys p.R797C ENST00000156471 21/35 344 279 65 277 276 1 strelka-mutect AQR,missense_variant,p.Arg797Cys,ENST00000156471,NM_014691.2;AQR,splice_region_variant,,ENST00000543879,; A ENST00000156471 Transcript missense_variant,splice_region_variant 2615/9694 2389/4458 797/1485 R/C Cgt/Tgt rs201758262 1 -1 AQR HGNC HGNC:29513 protein_coding YES CCDS42013.1 ENSP00000156471 O60306 A0A024R9L1 UPI00001C1F85 NM_014691.2 deleterious(0) 21/35 hmmpanther:PTHR10887:SF5,hmmpanther:PTHR10887,Pfam_domain:PF16399,PIRSF_domain:PIRSF038901,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs201758262 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 34897560 34897560 G A 1 0 0 0 0 1 0 0 0 957 1159 40 1 1 AQR 15 34897560 Missense_Mutation SNP G C3N-01024_T 3413254 34897560 67093629 46 20766 MYO9A 0 . GRCh38 15 71899863 71899863 + Silent SNP C C T novel C3N-01024_T C3N-01024_N C C c.3294G>A p.= p.R1098R ENST00000356056 24/42 415 284 131 259 259 0 strelka-varscan-mutect MYO9A,synonymous_variant,p.=,ENST00000356056,NM_006901.3;MYO9A,synonymous_variant,p.=,ENST00000564571,;MYO9A,synonymous_variant,p.=,ENST00000444904,;MYO9A,synonymous_variant,p.=,ENST00000566885,;MYO9A,upstream_gene_variant,,ENST00000561618,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,downstream_gene_variant,,ENST00000566744,;MYO9A,upstream_gene_variant,,ENST00000568781,; T ENST00000356056 Transcript synonymous_variant 3767/12411 3294/7647 1098/2548 R cgG/cgA 1 -1 MYO9A HGNC HGNC:7608 protein_coding YES CCDS10239.1 ENSP00000348349 B2RTY4 UPI000013D213 NM_006901.3 24/42 PROSITE_profiles:PS50096,hmmpanther:PTHR13140:SF9,hmmpanther:PTHR13140,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 71899863 71899863 C T 1 0 0 0 0 0 0 0 1 10085 610 22 3 3 MYO9A 15 71899863 Silent SNP C C3N-01024_T 37002303 71899863 30091326 47 20767 FAM169B 0 . GRCh38 15 98439694 98439694 + Silent SNP C C A novel C3N-01024_T C3N-01024_N C C c.516G>T p.= p.V172V ENST00000332908 5/5 262 187 75 215 215 0 strelka-varscan-mutect FAM169B,synonymous_variant,p.=,ENST00000332908,NM_182562.2;FAM169B,non_coding_transcript_exon_variant,,ENST00000558256,;FAM169B,downstream_gene_variant,,ENST00000636796,; A ENST00000332908 Transcript synonymous_variant 516/579 516/579 172/192 V gtG/gtT 1 -1 FAM169B HGNC HGNC:26835 protein_coding YES CCDS45360.1 ENSP00000332615 Q8N8A8 A0A0A0MR76 UPI0000199E5A NM_182562.2 5/5 LOW 1 SNV 2 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9990396 1 1 1 0 A 2 1 69 98439694 98439694 C A 1 0 0 0 0 0 0 0 1 5334 581 21 2 2 FAM169B 15 98439694 Silent SNP C C3N-01024_T 26539831 98439694 3551495 48 20768 CARMIL2 0 . GRCh38 16 67648411 67648411 + Missense_Mutation SNP G G A C3N-01024_T C3N-01024_N G G c.1348G>A p.Ala450Thr p.A450T ENST00000334583 15/38 163 106 57 115 115 0 strelka-varscan-mutect CARMIL2,missense_variant,p.Ala450Thr,ENST00000334583,NM_001013838.1;CARMIL2,missense_variant,p.Ala414Thr,ENST00000545661,NM_001317026.1;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602321,;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602742,;CARMIL2,downstream_gene_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602931,;CARMIL2,upstream_gene_variant,,ENST00000602924,;CARMIL2,downstream_gene_variant,,ENST00000602467,; A ENST00000334583 Transcript missense_variant 1676/4687 1348/4308 450/1435 A/T Gcg/Acg COSM403700,COSM403701 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 tolerated(0.08) 15/38 hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF32,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 69 67648411 67648411 G A 1 0 0 0 0 1 0 0 0 2352 1087 38 1 1 CARMIL2 16 67648411 Missense_Mutation SNP G C3N-01024_T 67648411 22689934 49 20769 CMTR2 0 . GRCh38 16 71285409 71285409 + Missense_Mutation SNP G G A rs145097675 C3N-01024_T C3N-01024_N G G c.512C>T p.Ala171Val p.A171V ENST00000338099 3/3 214 194 20 197 196 1 strelka-varscan-mutect CMTR2,missense_variant,p.Ala171Val,ENST00000338099,;CMTR2,missense_variant,p.Ala171Val,ENST00000434935,NM_001324377.1,NM_018348.5,NM_001099642.1;CMTR2,downstream_gene_variant,,ENST00000565850,;CMTR2,downstream_gene_variant,,ENST00000568910,;CMTR2,downstream_gene_variant,,ENST00000563876,;CMTR2,downstream_gene_variant,,ENST00000564183,;CMTR2,downstream_gene_variant,,ENST00000567610,;CMTR2,downstream_gene_variant,,ENST00000564690,; A ENST00000338099 Transcript missense_variant 849/4869 512/2313 171/770 A/V gCg/gTg rs145097675,COSM973265 1 -1 CMTR2 HGNC HGNC:25635 protein_coding YES CCDS10898.1 ENSP00000337512 Q8IYT2 UPI000006EA8B deleterious(0) 3/3 PROSITE_profiles:PS51614,hmmpanther:PTHR16121,hmmpanther:PTHR16121:SF2,Gene3D:3.40.50.150,Pfam_domain:PF01728,Superfamily_domains:SSF53335 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs145097675 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 71285409 71285409 G A 1 0 0 0 0 1 0 0 0 3367 1087 38 1 1 CMTR2 16 71285409 Missense_Mutation SNP G C3N-01024_T 3636998 71285409 19052936 50 20770 TP53 0 . GRCh38 17 7674878 7674878 + Missense_Mutation SNP A A C C3N-01024_T C3N-01024_N A A c.653T>G p.Val218Gly p.V218G ENST00000269305 6/11 423 238 185 330 329 1 strelka-varscan-mutect TP53,missense_variant,p.Val218Gly,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Val218Gly,ENST00000420246,;TP53,missense_variant,p.Val179Gly,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Val179Gly,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Val218Gly,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Val179Gly,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Val218Gly,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Val179Gly,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Val218Gly,ENST00000445888,;TP53,missense_variant,p.Val179Gly,ENST00000619485,;TP53,missense_variant,p.Val86Gly,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Val59Gly,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Val86Gly,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Val59Gly,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Val86Gly,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Val59Gly,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Val218Gly,ENST00000359597,;TP53,missense_variant,p.Val207Gly,ENST00000615910,;TP53,missense_variant,p.Val218Gly,ENST00000413465,;TP53,missense_variant,p.Val86Gly,ENST00000509690,;TP53,missense_variant,p.Val125Gly,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Val179Gly,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 843/2579 653/1182 218/393 V/G gTg/gGg TP53_g.12722T>C,TP53_g.12722T>G,TP53_g.12722T>A,COSM44198,COSM44317,COSM44930 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,1,1,1 MODERATE 1 SNV 1 0,0,0,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 69 7674878 7674878 A C 1 0 0 0 0 1 0 0 0 16859 159 6 5 5 TP53 17 7674878 Missense_Mutation SNP A C3N-01024_T 7674878 75582563 51 20771 KRTAP4-12 0 . GRCh38 17 41123699 41123699 + Missense_Mutation SNP G G A rs146088137 C3N-01024_T C3N-01024_N G G c.424C>T p.Arg142Cys p.R142C ENST00000394014 1/1 528 392 136 313 313 0 strelka-varscan-mutect KRTAP4-12,missense_variant,p.Arg142Cys,ENST00000394014,NM_031854.2; A ENST00000394014 Transcript missense_variant 469/1077 424/606 142/201 R/C Cgc/Tgc rs146088137 1 -1 KRTAP4-12 HGNC HGNC:16776 protein_coding YES CCDS32649.1 ENSP00000377582 Q9BQ66 UPI0000072F19 NM_031854.2 deleterious(0.03) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs146088137 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 41123699 41123699 G A 1 0 0 0 0 1 0 0 0 8443 1116 39 1 1 KRTAP4-12 17 41123699 Missense_Mutation SNP G C3N-01024_T 33448821 41123699 42133742 52 20772 KAT7 0 . GRCh38 17 49821671 49821671 + Silent SNP C C T novel C3N-01024_T C3N-01024_N C C c.1267C>T p.= p.L423L ENST00000259021 11/15 305 217 88 196 196 0 strelka-varscan-mutect KAT7,synonymous_variant,p.=,ENST00000259021,NM_007067.4;KAT7,synonymous_variant,p.=,ENST00000435742,;KAT7,synonymous_variant,p.=,ENST00000424009,NM_001199155.1;KAT7,synonymous_variant,p.=,ENST00000454930,NM_001199156.1;KAT7,synonymous_variant,p.=,ENST00000509773,NM_001199157.1;KAT7,synonymous_variant,p.=,ENST00000510819,NM_001199158.1;KAT7,non_coding_transcript_exon_variant,,ENST00000513980,;KAT7,non_coding_transcript_exon_variant,,ENST00000512616,;KAT7,non_coding_transcript_exon_variant,,ENST00000513171,;KAT7,non_coding_transcript_exon_variant,,ENST00000514540,;KAT7,non_coding_transcript_exon_variant,,ENST00000508594,;KAT7,upstream_gene_variant,,ENST00000503101,;KAT7,non_coding_transcript_exon_variant,,ENST00000509794,;KAT7,upstream_gene_variant,,ENST00000503635,;KAT7,upstream_gene_variant,,ENST00000510426,;KAT7,upstream_gene_variant,,ENST00000513075,; T ENST00000259021 Transcript synonymous_variant 1547/9644 1267/1836 423/611 L Ctg/Ttg 1 1 KAT7 HGNC HGNC:17016 protein_coding YES CCDS11554.1 ENSP00000259021 O95251 UPI000006D3D5 NM_007067.4 11/15 PROSITE_profiles:PS51726,hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF111,Pfam_domain:PF01853,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 49821671 49821671 C T 1 0 0 0 0 0 0 0 1 7900 680 24 3 3 KAT7 17 49821671 Silent SNP C C3N-01024_T 8697972 49821671 33435770 53 20773 PIEZO2 0 . GRCh38 18 10696283 10696283 + Missense_Mutation SNP G G C novel C3N-01024_T C3N-01024_N G G c.6642C>G p.His2214Gln p.H2214Q ENST00000503781 43/52 181 93 88 187 187 0 strelka-varscan-mutect PIEZO2,missense_variant,p.His2165Gln,ENST00000383408,;PIEZO2,missense_variant,p.His2214Gln,ENST00000302079,;PIEZO2,missense_variant,p.His2239Gln,ENST00000580640,;PIEZO2,missense_variant,p.His2214Gln,ENST00000503781,NM_022068.3;PIEZO2,missense_variant,p.His171Gln,ENST00000538948,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; C ENST00000503781 Transcript missense_variant 6642/8259 6642/8259 2214/2752 H/Q caC/caG 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0) 43/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 69 10696283 10696283 G C 1 0 0 0 0 1 0 0 0 11975 1043 36 4 4 PIEZO2 18 10696283 Missense_Mutation SNP G C3N-01024_T 10696283 69677002 54 20774 MAST1 0 . GRCh38 19 12843535 12843535 + Silent SNP C C T rs201497430 C3N-01024_T C3N-01024_N C C c.255C>T p.= p.D85D ENST00000251472 4/26 112 95 17 85 84 1 strelka-varscan-mutect MAST1,synonymous_variant,p.=,ENST00000251472,NM_014975.2;MAST1,synonymous_variant,p.=,ENST00000591495,;MAST1,synonymous_variant,p.=,ENST00000588379,;MAST1,upstream_gene_variant,,ENST00000590204,;HOOK2,intron_variant,,ENST00000589765,;MAST1,intron_variant,,ENST00000590883,;MAST1,upstream_gene_variant,,ENST00000592713,; T ENST00000251472 Transcript synonymous_variant 294/4833 255/4713 85/1570 D gaC/gaT rs201497430,COSM1304046,COSM1304047 1 1 MAST1 HGNC HGNC:19034 protein_coding YES CCDS32921.1 ENSP00000251472 Q9Y2H9 UPI000004A042 NM_014975.2 4/26 hmmpanther:PTHR24356:SF150,hmmpanther:PTHR24356,Pfam_domain:PF08926 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs201497430 . 0 197 8 5 0 0 0 0 -20 0.9928823 1 1 1 0 T 2 4 69 12843535 12843535 C T 1 0 0 0 0 0 0 0 1 9250 535 19 1 1 MAST1 19 12843535 Silent SNP C C3N-01024_T 12843535 45774081 55 20775 ZNF730 0 . GRCh38 19 23145706 23145706 + Missense_Mutation SNP G G T novel C3N-01024_T C3N-01024_N G G c.662G>T p.Arg221Ile p.R221I ENST00000597761 4/4 150 112 38 172 172 0 strelka-varscan-mutect ZNF730,missense_variant,p.Arg221Ile,ENST00000597761,NM_001277403.1;ZNF730,downstream_gene_variant,,ENST00000599195,; T ENST00000597761 Transcript missense_variant 861/2374 662/1512 221/503 R/I aGa/aTa 1 1 ZNF730 HGNC HGNC:32470 protein_coding YES CCDS59371.1 ENSP00000472959 Q6ZMV8 UPI000035E7F4 NM_001277403.1 tolerated(0.4) 4/4 Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 69 23145706 23145706 G T 1 0 0 0 0 1 0 0 0 18704 942 33 2 2 ZNF730 19 23145706 Missense_Mutation SNP G C3N-01024_T 10302171 23145706 35471910 56 20776 ZNF181 0 . GRCh38 19 34741548 34741548 + Missense_Mutation SNP C C A novel C3N-01024_T C3N-01024_N C C c.1167C>A p.Ser389Arg p.S389R ENST00000492450 4/4 173 147 26 213 213 0 strelka-varscan-mutect ZNF181,missense_variant,p.Ser389Arg,ENST00000492450,NM_001029997.3;ZNF181,missense_variant,p.Ser433Arg,ENST00000392232,;ZNF181,missense_variant,p.Ser388Arg,ENST00000459757,NM_001145665.1;ZNF181,downstream_gene_variant,,ENST00000595708,;ZNF181,downstream_gene_variant,,ENST00000599244,;ZNF181,downstream_gene_variant,,ENST00000593781,;ZNF181,non_coding_transcript_exon_variant,,ENST00000448715,; A ENST00000492450 Transcript missense_variant 1256/5086 1167/1716 389/571 S/R agC/agA 1 1 ZNF181 HGNC HGNC:12971 protein_coding YES CCDS32990.2 ENSP00000420727 Q2M3W8 UPI000020207A NM_001029997.3 tolerated(0.99) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 69 34741548 34741548 C A 1 0 0 0 0 1 0 0 0 18329 796 28 2 2 ZNF181 19 34741548 Missense_Mutation SNP C C3N-01024_T 11595842 34741548 23876068 57 20777 SYCP2 0 . GRCh38 20 59892131 59892131 + Silent SNP C C T C3N-01024_T C3N-01024_N C C c.2223G>A p.= p.K741K ENST00000357552 24/45 228 182 46 192 192 0 strelka-varscan-mutect SYCP2,synonymous_variant,p.=,ENST00000357552,;SYCP2,synonymous_variant,p.=,ENST00000371001,NM_014258.2;SYCP2,synonymous_variant,p.=,ENST00000446834,; T ENST00000357552 Transcript synonymous_variant 2449/5567 2223/4593 741/1530 K aaG/aaA COSM1228090 1 -1 SYCP2 HGNC HGNC:11490 protein_coding YES CCDS13482.1 ENSP00000350162 Q9BX26 UPI0000135683 24/45 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 69 59892131 59892131 C T 1 0 0 0 0 0 0 0 1 15822 912 32 3 3 SYCP2 20 59892131 Silent SNP C C3N-01024_T 59892131 4552036 58 20778 NLRP2B 0 . GRCh38 X 57680149 57680149 + Missense_Mutation SNP C C G novel C3N-01024_T C3N-01024_N C C c.112G>C p.Glu38Gln p.E38Q ENST00000434992 1/1 36 29 7 33 33 0 strelka-varscan-mutect NLRP2B,missense_variant,p.Glu38Gln,ENST00000434992,NM_001319967.1; G ENST00000434992 Transcript missense_variant 112/3194 112/138 38/45 E/Q Gag/Cag 1 -1 NLRP2B HGNC HGNC:29887 protein_coding YES ENSP00000488995 P0DMW2 UPI00061CDBEB NM_001319967.1 deleterious_low_confidence(0.04) 1/1 hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 PASS . . 9 199 2 0 0 0 0 0 -18.43376 1 1 1 1 0 G 3 3 69 57680149 57680149 C G 1 0 0 0 0 1 0 0 0 10515 835 29 4 4 NLRP2B 23 57680149 Missense_Mutation SNP C C3N-01024_T 57680149 98360746 59 20779 MED12 0 . GRCh38 X 71140759 71140759 + Nonsense_Mutation SNP C C T novel C3N-01024_T C3N-01024_N C C c.6169C>T p.Gln2057Ter p.Q2057* ENST00000374080 42/45 298 190 108 341 341 0 strelka-varscan-mutect MED12,stop_gained,p.Gln1907Ter,ENST00000333646,;MED12,stop_gained,p.Gln2056Ter,ENST00000374102,;MED12,stop_gained,p.Gln2057Ter,ENST00000374080,NM_005120.2;NLGN3,upstream_gene_variant,,ENST00000374051,NM_018977.3;NLGN3,upstream_gene_variant,,ENST00000536169,NM_001166660.1;NLGN3,upstream_gene_variant,,ENST00000612180,NM_001321276.1;NLGN3,upstream_gene_variant,,ENST00000358741,NM_181303.1;NLGN3,upstream_gene_variant,,ENST00000395855,;MED12,downstream_gene_variant,,ENST00000444034,; T ENST00000374080 Transcript stop_gained 6201/6795 6169/6534 2057/2177 Q/* Cag/Tag 1 1 MED12 HGNC HGNC:11957 protein_coding YES CCDS43970.1 ENSP00000363193 Q93074 UPI00004257E2 NM_005120.2 42/45 Gene3D:1.25.10.10,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF24,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 69 71140759 71140759 C T 1 0 0 0 0 0 1 0 0 9367 479 17 3 3 MED12 23 71140759 Nonsense_Mutation SNP C C3N-01024_T 13460610 71140759 84900136 60 20780 ADGRG4 0 . GRCh38 X 136416452 136416452 + Splice_Site SNP A A G novel C3N-01024_T C3N-01024_N A A c.9206-2A>G p.X3069_splice ENST00000394143 235 223 12 161 161 0 strelka-varscan-mutect ADGRG4,splice_acceptor_variant,,ENST00000394143,NM_153834.3;ADGRG4,splice_acceptor_variant,,ENST00000370652,;ADGRG4,splice_acceptor_variant,,ENST00000394141,; G ENST00000394143 Transcript splice_acceptor_variant -/9931 9206/9243 3069/3080 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 25/25 HIGH 1 SNV 1 1 PASS . . 0 205 3 0 0 0 0 0 -19.71254 1 1 1 1 0 G 5 3 69 136416452 136416452 A G 1 0 0 0 0 0 0 1 0 371 202 7 5 5 ADGRG4 23 136416452 Splice_Site SNP A C3N-01024_T 65275693 136416452 19624443 61 20781 AGRN 0 . GRCh38 1 1051335 1051335 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.5336C>G p.Ala1779Gly p.A1779G ENST00000379370 31/36 204 147 57 173 173 0 strelka-varscan-mutect AGRN,missense_variant,p.Ala1645Gly,ENST00000620552,NM_001305275.1;AGRN,missense_variant,p.Ala1779Gly,ENST00000379370,NM_198576.3;AGRN,missense_variant,p.Ala82Gly,ENST00000419249,;RP11-54O7.14,upstream_gene_variant,,ENST00000418300,;AGRN,upstream_gene_variant,,ENST00000461111,;AGRN,downstream_gene_variant,,ENST00000492947,;AGRN,downstream_gene_variant,,ENST00000479707,;AGRN,downstream_gene_variant,,ENST00000466223,;AGRN,downstream_gene_variant,,ENST00000478677,; G ENST00000379370 Transcript missense_variant 5386/7323 5336/6138 1779/2045 A/G gCc/gGc 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 tolerated(0.3) 31/36 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 1051335 1051335 C G 1 0 0 0 0 1 0 0 0 476 739 26 4 4 AGRN 1 1051335 Missense_Mutation SNP C C3N-01030_T 1051335 247905087 1 20782 ATAD3C 0 . GRCh38 1 1455881 1455881 + Missense_Mutation SNP G G T rs535257873 C3N-01030_T C3N-01030_N G G c.529G>T p.Gly177Trp p.G177W ENST00000378785 6/12 232 211 21 218 217 1 varscan-mutect ATAD3C,missense_variant,p.Gly177Trp,ENST00000378785,NM_001039211.2;ATAD3C,missense_variant,p.Gly125Trp,ENST00000475091,; T ENST00000378785 Transcript missense_variant 1524/3859 529/1236 177/411 G/W Ggg/Tgg rs535257873 1 1 ATAD3C HGNC HGNC:32151 protein_coding YES CCDS44039.1 ENSP00000368062 Q5T2N8 UPI00001619C0 NM_001039211.2 deleterious(0) 6/12 hmmpanther:PTHR23075:SF5,hmmpanther:PTHR23075,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS rs535257873 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 1455881 1455881 G T 1 0 0 0 0 1 0 0 0 1223 1116 39 1 1 ATAD3C 1 1455881 Missense_Mutation SNP G C3N-01030_T 404546 1455881 247500541 2 20783 TMEM201 0 . GRCh38 1 9609843 9609843 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1397C>T p.Ser466Phe p.S466F ENST00000340381 8/11 133 117 16 153 153 0 strelka-mutect TMEM201,missense_variant,p.Ser466Phe,ENST00000340381,NM_001130924.2;TMEM201,intron_variant,,ENST00000416541,;TMEM201,downstream_gene_variant,,ENST00000340305,NM_001010866.3;TMEM201,downstream_gene_variant,,ENST00000510900,;TMEM201,missense_variant,p.Ser23Phe,ENST00000508400,; T ENST00000340381 Transcript missense_variant 1406/3776 1397/2001 466/666 S/F tCc/tTc 1 1 TMEM201 HGNC HGNC:33719 protein_coding YES CCDS44055.2 ENSP00000344503 Q5SNT2 UPI000022B297 NM_001130924.2 deleterious(0) 8/11 hmmpanther:PTHR28646 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 9609843 9609843 C T 1 0 0 0 0 1 0 0 0 16565 869 30 3 3 TMEM201 1 9609843 Missense_Mutation SNP C C3N-01030_T 8153962 9609843 239346579 3 20784 KIF1B 0 . GRCh38 1 10304578 10304578 + Silent SNP G G C novel C3N-01030_T C3N-01030_N G G c.3393G>C p.= p.V1131V ENST00000377093 21/21 127 113 14 155 155 0 strelka-varscan-mutect KIF1B,synonymous_variant,p.=,ENST00000377093,NM_183416.3;KIF1B,synonymous_variant,p.=,ENST00000377083,;KIF1B,intron_variant,,ENST00000377086,;KIF1B,intron_variant,,ENST00000377081,;KIF1B,intron_variant,,ENST00000620295,;KIF1B,intron_variant,,ENST00000622724,;KIF1B,intron_variant,,ENST00000263934,NM_015074.3;RN7SL731P,upstream_gene_variant,,ENST00000584329,; C ENST00000377093 Transcript synonymous_variant 3546/7565 3393/3462 1131/1153 V gtG/gtC 1 1 KIF1B HGNC HGNC:16636 protein_coding CCDS112.1 ENSP00000366297 O60333 UPI0000140CB8 NM_183416.3 21/21 hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF322 LOW SNV 1 1 PASS rs1186469668 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 10304578 10304578 G C 1 0 0 0 0 0 0 0 1 8148 1277 45 4 4 KIF1B 1 10304578 Silent SNP G C3N-01030_T 694735 10304578 238651844 4 20785 CORT 0 . GRCh38 1 10451464 10451464 + Frame_Shift_Del DEL G G - rs201158337 C3N-01030_T C3N-01030_N G G c.366delG p.Leu124SerfsTer2 p.L124Sfs*2 ENST00000400900 5/5 192 162 30 161 161 0 sindel-varindel-pindel APITD1-CORT,frameshift_variant,p.Leu124SerfsTer2,ENST00000400900,NM_198544.3;APITD1-CORT,frameshift_variant,p.Leu103SerfsTer2,ENST00000602296,NM_001243768.1;CORT,frameshift_variant,p.Leu65SerfsTer2,ENST00000377049,NM_001302.4;APITD1-CORT,3_prime_UTR_variant,,ENST00000470413,NM_199006.2;APITD1-CORT,3_prime_UTR_variant,,ENST00000465026,;APITD1-CORT,downstream_gene_variant,,ENST00000602787,NM_001270517.1; - ENST00000400900 Transcript frameshift_variant 780/1469 364/495 122/164 G/X Ggg/gg rs201158337 1 1 APITD1-CORT HGNC HGNC:38843 protein_coding YES CCDS114.1 ENSP00000383692 UPI000007101C NM_198544.3 5/5 hmmpanther:PTHR22980,hmmpanther:PTHR22980:SF4 HIGH deletion 2 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999942 1 1 1 0 - 7 5 70 10451464 10451464 G - 1 0 1 0 1 0 0 0 0 3554 1116 39 0 0 CORT 1 10451464 Frame_Shift_Del DEL G C3N-01030_T 146886 10451464 238504958 5 20786 MTHFR 0 . GRCh38 1 11801318 11801318 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.318G>T p.Glu106Asp p.E106D ENST00000376592 2/11 365 285 80 345 345 0 strelka-varscan-mutect MTHFR,missense_variant,p.Glu106Asp,ENST00000376592,;MTHFR,missense_variant,p.Glu147Asp,ENST00000376583,;MTHFR,missense_variant,p.Glu106Asp,ENST00000376590,NM_005957.4;MTHFR,missense_variant,p.Glu147Asp,ENST00000376585,;MTHFR,missense_variant,p.Glu106Asp,ENST00000418034,;CLCN6,upstream_gene_variant,,ENST00000312413,NM_001256959.1;CLCN6,upstream_gene_variant,,ENST00000346436,NM_001286.3;CLCN6,upstream_gene_variant,,ENST00000376496,;MTHFR,downstream_gene_variant,,ENST00000423400,;MTHFR,downstream_gene_variant,,ENST00000376486,;MTHFR,downstream_gene_variant,,ENST00000431243,;CLCN6,upstream_gene_variant,,ENST00000376497,;MTHFR,downstream_gene_variant,,ENST00000413656,;CLCN6,upstream_gene_variant,,ENST00000376492,;CLCN6,upstream_gene_variant,,ENST00000376490,;CLCN6,upstream_gene_variant,,ENST00000376491,; A ENST00000376592 Transcript missense_variant 447/7057 318/1971 106/656 E/D gaG/gaT 1 -1 MTHFR HGNC HGNC:7436 protein_coding YES CCDS137.1 ENSP00000365777 P42898 UPI0000141098 tolerated(0.21) 2/11 Gene3D:3.20.20.220,Pfam_domain:PF02219,Superfamily_domains:SSF51730,TIGRFAM_domain:TIGR00677 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 11801318 11801318 C A 1 0 0 0 0 1 0 0 0 9920 912 32 2 2 MTHFR 1 11801318 Missense_Mutation SNP C C3N-01030_T 1349854 11801318 237155104 6 20787 HNRNPCL1 0 . GRCh38 1 12847545 12847545 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.745G>A p.Glu249Lys p.E249K ENST00000317869 2/2 523 460 63 519 519 0 strelka-varscan-mutect HNRNPCL1,missense_variant,p.Glu249Lys,ENST00000317869,NM_001013631.2; T ENST00000317869 Transcript missense_variant 971/1108 745/882 249/293 E/K Gag/Aag 1 -1 HNRNPCL1 HGNC HGNC:29295 protein_coding YES CCDS30591.1 ENSP00000365370 O60812 UPI0000134525 NM_001013631.2 tolerated(0.05) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR13968:SF17,hmmpanther:PTHR13968,PIRSF_domain:PIRSF037992 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 12847545 12847545 C T 1 0 0 0 0 1 0 0 0 7154 835 29 3 3 HNRNPCL1 1 12847545 Missense_Mutation SNP C C3N-01030_T 1046227 12847545 236108877 7 20788 PRAMEF10 0 . GRCh38 1 12893220 12893220 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1121G>A p.Ser374Asn p.S374N ENST00000235347 4/4 295 272 23 336 336 0 varscan-mutect PRAMEF10,missense_variant,p.Ser374Asn,ENST00000235347,NM_001039361.4; T ENST00000235347 Transcript missense_variant 1201/1525 1121/1425 374/474 S/N aGc/aAc 1 -1 PRAMEF10 HGNC HGNC:27997 protein_coding YES CCDS41255.1 ENSP00000235347 O60809 UPI000442CF00 NM_001039361.4 deleterious(0.03) 4/4 hmmpanther:PTHR14224:SF28,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 12893220 12893220 C T 1 0 0 0 0 1 0 0 0 12555 797 28 3 3 PRAMEF10 1 12893220 Missense_Mutation SNP C C3N-01030_T 45675 12893220 236063202 8 20789 74 2 PRAMEF10 0 . GRCh38 1 12893230 12893230 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1111C>A p.Pro371Thr p.P371T ENST00000235347 4/4 264 243 21 304 303 1 varscan-mutect PRAMEF10,missense_variant,p.Pro371Thr,ENST00000235347,NM_001039361.4; T ENST00000235347 Transcript missense_variant 1191/1525 1111/1425 371/474 P/T Cct/Act 1 -1 PRAMEF10 HGNC HGNC:27997 protein_coding YES CCDS41255.1 ENSP00000235347 O60809 UPI000442CF00 NM_001039361.4 deleterious(0) 4/4 hmmpanther:PTHR14224:SF28,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 12893230 12893230 G T 1 0 0 0 0 1 0 0 0 12555 1203 42 2 2 PRAMEF10 1 12893230 Missense_Mutation SNP G C3N-01030_T 10 12893230 236063192 9 20790 74 2 SPATA21 0 . GRCh38 1 16409146 16409146 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.645G>A p.= p.E215E ENST00000335496 7/13 260 224 36 225 225 0 strelka-varscan-mutect SPATA21,synonymous_variant,p.=,ENST00000335496,NM_198546.1;SPATA21,synonymous_variant,p.=,ENST00000540400,;SPATA21,non_coding_transcript_exon_variant,,ENST00000466212,; T ENST00000335496 Transcript synonymous_variant 1128/2015 645/1410 215/469 E gaG/gaA 1 -1 SPATA21 HGNC HGNC:28026 protein_coding YES CCDS172.1 ENSP00000335612 Q7Z572 UPI00001B4B16 NM_198546.1 7/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10891:SF596,hmmpanther:PTHR10891,Gene3D:1.10.238.10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 16409146 16409146 C T 1 0 0 0 0 0 0 0 1 15337 680 24 3 3 SPATA21 1 16409146 Silent SNP C C3N-01030_T 3515916 16409146 232547276 10 20791 EPHA8 0 . GRCh38 1 22589005 22589005 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1114G>T p.Ala372Ser p.A372S ENST00000166244 5/17 245 180 65 172 172 0 strelka-varscan-mutect EPHA8,missense_variant,p.Ala372Ser,ENST00000166244,NM_020526.3;EPHA8,missense_variant,p.Ala372Ser,ENST00000374644,NM_001006943.1; T ENST00000166244 Transcript missense_variant 1186/4943 1114/3018 372/1005 A/S Gca/Tca 1 1 EPHA8 HGNC HGNC:3391 protein_coding YES CCDS225.1 ENSP00000166244 P29322 UPI000012A07B NM_020526.3 tolerated(0.47) 5/17 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF339,hmmpanther:PTHR24416,Pfam_domain:PF00041,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS rs1250156610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 22589005 22589005 G T 1 0 0 0 0 1 0 0 0 5020 1203 42 2 2 EPHA8 1 22589005 Missense_Mutation SNP G C3N-01030_T 6179859 22589005 226367417 11 20792 AIM1L 0 . GRCh38 1 26345911 26345911 + Silent SNP A A G rs748928358 C3N-01030_T C3N-01030_N A A c.747T>C p.= p.P249P ENST00000308182 2/20 84 72 12 92 92 0 strelka-varscan-mutect AIM1L,synonymous_variant,p.=,ENST00000308182,NM_001039775.3;AIM1L,synonymous_variant,p.=,ENST00000475866,;AIM1L,upstream_gene_variant,,ENST00000527815,;AIM1L,intron_variant,,ENST00000374207,; G ENST00000308182 Transcript synonymous_variant 897/5245 747/4986 249/1661 P ccT/ccC rs748928358 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 2/20 LOW 1 SNV 5 1 PASS rs748928358 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 26345911 26345911 A G 1 0 0 0 0 0 0 0 1 508 175 7 5 5 AIM1L 1 26345911 Silent SNP A C3N-01030_T 3756906 26345911 222610511 12 20793 MAP3K6 0 . GRCh38 1 27360715 27360715 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2044C>T p.Arg682Trp p.R682W ENST00000493901 16/30 141 124 17 110 109 1 strelka-mutect MAP3K6,missense_variant,p.Arg674Trp,ENST00000374040,NM_001297609.1;MAP3K6,missense_variant,p.Arg682Trp,ENST00000493901,NM_004672.4;MAP3K6,missense_variant,p.Arg682Trp,ENST00000357582,;MAP3K6,missense_variant,p.Arg406Trp,ENST00000472410,;MAP3K6,upstream_gene_variant,,ENST00000486046,;MAP3K6,upstream_gene_variant,,ENST00000470890,;MAP3K6,upstream_gene_variant,,ENST00000476509,;MAP3K6,upstream_gene_variant,,ENST00000495230,; A ENST00000493901 Transcript missense_variant 2284/4309 2044/3867 682/1288 R/W Cgg/Tgg 1 -1 MAP3K6 HGNC HGNC:6858 protein_coding YES CCDS299.1 ENSP00000419591 O95382 UPI0000205587 NM_004672.4 deleterious(0) 16/30 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF391,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs888314478 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 27360715 27360715 G A 1 0 0 0 0 1 0 0 0 9177 1086 38 1 1 MAP3K6 1 27360715 Missense_Mutation SNP G C3N-01030_T 1014804 27360715 221595707 13 20794 FCN3 0 . GRCh38 1 27374386 27374386 + Missense_Mutation SNP G G C rs376437282 C3N-01030_T C3N-01030_N G G c.157C>G p.Pro53Ala p.P53A ENST00000270879 2/8 93 65 28 91 91 0 strelka-varscan-mutect FCN3,missense_variant,p.Pro53Ala,ENST00000270879,NM_003665.2;FCN3,missense_variant,p.Pro53Ala,ENST00000354982,NM_173452.1;CD164L2,downstream_gene_variant,,ENST00000374027,NM_207397.3;CD164L2,downstream_gene_variant,,ENST00000374030,;FCN3,non_coding_transcript_exon_variant,,ENST00000481748,;FCN3,upstream_gene_variant,,ENST00000498393,; C ENST00000270879 Transcript missense_variant 163/1030 157/900 53/299 P/A Cct/Gct rs376437282 1 -1 FCN3 HGNC HGNC:3625 protein_coding YES CCDS300.1 ENSP00000270879 O75636 UPI00000343FF NM_003665.2 tolerated(0.15) 2/8 Low_complexity_(Seg):seg,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF215 MODERATE 1 SNV 1 1 PASS rs376437282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 27374386 27374386 G C 1 0 0 0 0 1 0 0 0 5656 1174 41 4 4 FCN3 1 27374386 Missense_Mutation SNP G C3N-01030_T 13671 27374386 221582036 14 20795 IFI6 0 . GRCh38 1 27668226 27668226 + Missense_Mutation SNP C C A rs758060629 C3N-01030_T C3N-01030_N C C c.322G>T p.Gly108Trp p.G108W ENST00000339145 4/5 76 55 21 56 56 0 strelka-varscan-mutect IFI6,missense_variant,p.Gly100Trp,ENST00000361157,NM_002038.3;IFI6,missense_variant,p.Gly104Trp,ENST00000362020,NM_022872.2;IFI6,missense_variant,p.Gly108Trp,ENST00000339145,NM_022873.2;RP11-288L9.4,upstream_gene_variant,,ENST00000625232,;RP11-288L9.4,upstream_gene_variant,,ENST00000628586,;RP11-288L9.4,upstream_gene_variant,,ENST00000629895,;RP11-288L9.4,upstream_gene_variant,,ENST00000430683,;RP11-288L9.4,upstream_gene_variant,,ENST00000628584,;RP11-288L9.4,upstream_gene_variant,,ENST00000626608,; A ENST00000339145 Transcript missense_variant,splice_region_variant 410/822 322/417 108/138 G/W Ggg/Tgg rs758060629,COSM534760 1 -1 IFI6 HGNC HGNC:4054 protein_coding YES CCDS308.1 ENSP00000342513 P09912 UPI000002ABE5 NM_022873.2 deleterious(0) 4/5 Pfam_domain:PF06140,hmmpanther:PTHR16932,hmmpanther:PTHR16932:SF25 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs758060629 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 70 27668226 27668226 C A 1 0 0 0 0 1 0 0 0 7419 666 23 1 1 IFI6 1 27668226 Missense_Mutation SNP C C3N-01030_T 293840 27668226 221288196 15 20796 C1orf94 0 . GRCh38 1 34197361 34197361 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.457G>T p.Gly153Trp p.G153W ENST00000488417 2/7 155 136 19 133 133 0 strelka-varscan-mutect C1orf94,missense_variant,p.Gly153Trp,ENST00000488417,NM_001134734.1;C1orf94,5_prime_UTR_variant,,ENST00000373374,NM_032884.4; T ENST00000488417 Transcript missense_variant 577/2287 457/1797 153/598 G/W Ggg/Tgg 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 tolerated(0.06) 2/7 hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 34197361 34197361 G T 1 0 0 0 0 1 0 0 0 2000 1232 43 2 2 C1orf94 1 34197361 Missense_Mutation SNP G C3N-01030_T 6529135 34197361 214759061 16 20797 MRPS15 0 . GRCh38 1 36455846 36455846 + Missense_Mutation SNP C C G rs776496972 C3N-01030_T C3N-01030_N C C c.716G>C p.Arg239Pro p.R239P ENST00000373116 8/8 245 214 31 245 245 0 strelka-varscan-mutect MRPS15,missense_variant,p.Arg239Pro,ENST00000373116,NM_031280.3;MRPS15,non_coding_transcript_exon_variant,,ENST00000488606,;MRPS15,non_coding_transcript_exon_variant,,ENST00000462067,;MRPS15,non_coding_transcript_exon_variant,,ENST00000477040,; G ENST00000373116 Transcript missense_variant 878/1006 716/774 239/257 R/P cGg/cCg rs776496972,COSM4007495 1 -1 MRPS15 HGNC HGNC:14504 protein_coding YES CCDS411.1 ENSP00000362208 P82914 UPI0000135287 NM_031280.3 deleterious(0.04) 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776496972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 36455846 36455846 C G 1 0 0 0 0 1 0 0 0 9802 652 23 4 4 MRPS15 1 36455846 Missense_Mutation SNP C C3N-01030_T 2258485 36455846 212500576 17 20798 SMAP2 0 . GRCh38 1 40408721 40408721 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.306G>T p.= p.R102R ENST00000372718 3/10 139 114 25 142 142 0 strelka-varscan-mutect SMAP2,synonymous_variant,p.=,ENST00000372718,NM_022733.2;SMAP2,synonymous_variant,p.=,ENST00000614549,NM_001198979.1;SMAP2,synonymous_variant,p.=,ENST00000539317,NM_001198980.1;SMAP2,synonymous_variant,p.=,ENST00000372708,NM_001198978.1;SMAP2,synonymous_variant,p.=,ENST00000435168,; T ENST00000372718 Transcript synonymous_variant 730/2939 306/1290 102/429 R cgG/cgT 1 1 SMAP2 HGNC HGNC:25082 protein_coding YES CCDS451.1 ENSP00000361803 Q8WU79 UPI000006DD04 NM_022733.2 3/10 Pfam_domain:PF01412,PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF29,SMART_domains:SM00105,Superfamily_domains:SSF57863 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 40408721 40408721 G T 1 0 0 0 0 0 0 0 1 15060 1190 42 2 2 SMAP2 1 40408721 Silent SNP G C3N-01030_T 3952875 40408721 208547701 18 20799 HIVEP3 0 . GRCh38 1 41513043 41513043 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.6178G>T p.Asp2060Tyr p.D2060Y ENST00000372583 8/9 97 70 27 108 108 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Asp2060Tyr,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Asp2060Tyr,ENST00000372583,NM_024503.4;HIVEP3,non_coding_transcript_exon_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 7064/12193 6178/7221 2060/2406 D/Y Gac/Tac 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious_low_confidence(0.01) 8/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS rs1179896477 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 41513043 41513043 C A 1 0 0 0 0 1 0 0 0 7077 884 31 1 1 HIVEP3 1 41513043 Missense_Mutation SNP C C3N-01030_T 1104322 41513043 207443379 19 20800 STIL 0 . GRCh38 1 47269788 47269788 + Missense_Mutation SNP G G A rs867802549 C3N-01030_T C3N-01030_N G G c.2462C>T p.Ser821Phe p.S821F ENST00000371877 14/17 177 156 21 268 268 0 strelka-varscan-mutect STIL,missense_variant,p.Ser821Phe,ENST00000360380,NM_001282936.1,NM_003035.2;STIL,missense_variant,p.Ser774Phe,ENST00000337817,NM_001282939.1,NM_001282938.1;STIL,missense_variant,p.Ser821Phe,ENST00000371877,NM_001048166.1;STIL,missense_variant,p.Ser821Phe,ENST00000396221,NM_001282937.1;STIL,missense_variant,p.Ser774Phe,ENST00000447475,;STIL,missense_variant,p.Ser161Phe,ENST00000436811,;STIL,non_coding_transcript_exon_variant,,ENST00000418131,; A ENST00000371877 Transcript missense_variant 2610/5009 2462/3867 821/1288 S/F tCc/tTc rs867802549,COSM3490535 1 -1 STIL HGNC HGNC:10879 protein_coding YES CCDS41329.1 ENSP00000360944 Q15468 UPI00002042D5 NM_001048166.1 deleterious(0) 14/17 hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs867802549 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 47269788 47269788 G A 1 0 0 0 0 1 0 0 0 15659 1174 41 3 3 STIL 1 47269788 Missense_Mutation SNP G C3N-01030_T 5756745 47269788 201686634 20 20801 ORC1 0 . GRCh38 1 52373325 52373325 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.2442C>T p.= p.P814P ENST00000371568 17/17 192 148 44 214 214 0 strelka-varscan-mutect ORC1,synonymous_variant,p.=,ENST00000371568,NM_004153.3,NM_001190818.1,NM_001190819.1;ORC1,synonymous_variant,p.=,ENST00000371566,;PLA2G12AP1,downstream_gene_variant,,ENST00000497678,; A ENST00000371568 Transcript synonymous_variant 2661/3157 2442/2586 814/861 P ccC/ccT 1 -1 ORC1 HGNC HGNC:8487 protein_coding YES CCDS566.1 ENSP00000360623 Q13415 UPI000013D2FB NM_004153.3,NM_001190818.1,NM_001190819.1 17/17 Gene3D:1.10.10.10,Pfam_domain:PF09079,hmmpanther:PTHR10763,hmmpanther:PTHR10763:SF23,SMART_domains:SM01074 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 52373325 52373325 G A 1 0 0 0 0 0 0 0 1 11327 1335 47 3 3 ORC1 1 52373325 Silent SNP G C3N-01030_T 5103537 52373325 196583097 21 20802 C1orf168 0 . GRCh38 1 56751063 56751063 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1368C>A p.= p.A456A ENST00000343433 9/20 104 94 10 135 135 0 strelka-varscan-mutect C1orf168,synonymous_variant,p.=,ENST00000343433,NM_001004303.4;C1orf168,non_coding_transcript_exon_variant,,ENST00000484327,;C1orf168,non_coding_transcript_exon_variant,,ENST00000493000,; T ENST00000343433 Transcript synonymous_variant 1449/3135 1368/2187 456/728 A gcC/gcA 1 -1 C1orf168 HGNC HGNC:27295 protein_coding YES CCDS30729.1 ENSP00000345972 Q5VWT5 UPI000022AE5B NM_001004303.4 9/20 hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 56751063 56751063 G T 1 0 0 0 0 0 0 0 1 1973 1335 47 2 2 C1orf168 1 56751063 Silent SNP G C3N-01030_T 4377738 56751063 192205359 22 20803 OMA1 0 . GRCh38 1 58534193 58534193 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.868G>T p.Val290Phe p.V290F ENST00000371226 4/9 157 138 19 230 230 0 strelka-varscan-mutect OMA1,missense_variant,p.Val132Phe,ENST00000421528,;OMA1,missense_variant,p.Val290Phe,ENST00000371226,NM_145243.4;OMA1,missense_variant,p.Val290Phe,ENST00000456980,;OMA1,downstream_gene_variant,,ENST00000419242,;OMA1,downstream_gene_variant,,ENST00000426139,;OMA1,downstream_gene_variant,,ENST00000453710,;OMA1,downstream_gene_variant,,ENST00000482274,;OMA1,non_coding_transcript_exon_variant,,ENST00000467063,;DAB1,intron_variant,,ENST00000485760,;OMA1,upstream_gene_variant,,ENST00000476933,;OMA1,upstream_gene_variant,,ENST00000467509,; A ENST00000371226 Transcript missense_variant 982/1935 868/1575 290/524 V/F Gtt/Ttt 1 -1 OMA1 HGNC HGNC:29661 protein_coding YES CCDS608.1 ENSP00000360270 Q96E52 UPI000006D0C6 NM_145243.4 deleterious(0) 4/9 hmmpanther:PTHR22726,hmmpanther:PTHR22726:SF1,Gene3D:3cqbA01,Pfam_domain:PF01435 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 58534193 58534193 C A 1 0 0 0 0 1 0 0 0 10939 507 18 2 2 OMA1 1 58534193 Missense_Mutation SNP C C3N-01030_T 1783130 58534193 190422229 23 20804 RPE65 0 . GRCh38 1 68431477 68431477 + Missense_Mutation SNP G G C rs369142161 C3N-01030_T C3N-01030_N G G c.1237C>G p.Arg413Gly p.R413G ENST00000262340 11/14 392 341 51 454 453 1 strelka-varscan-mutect RPE65,missense_variant,p.Arg413Gly,ENST00000262340,NM_000329.2; C ENST00000262340 Transcript missense_variant 1291/2610 1237/1602 413/533 R/G Cgt/Ggt rs369142161 1 -1 RPE65 HGNC HGNC:10294 protein_coding YES CCDS643.1 ENSP00000262340 Q16518 UPI000004346C NM_000329.2 tolerated(0.32) 11/14 Pfam_domain:PF03055,hmmpanther:PTHR10543,hmmpanther:PTHR10543:SF43 MODERATE 1 SNV 1 1 PASS rs369142161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 68431477 68431477 G C 1 0 0 0 0 1 0 0 0 13796 1058 37 4 4 RPE65 1 68431477 Missense_Mutation SNP G C3N-01030_T 9897284 68431477 180524945 24 20805 LRRC7 0 . GRCh38 1 70016532 70016532 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1204C>A p.Gln402Lys p.Q402K ENST00000035383 12/25 42 30 12 68 68 0 strelka-varscan-mutect LRRC7,missense_variant,p.Gln407Lys,ENST00000310961,;LRRC7,missense_variant,p.Gln402Lys,ENST00000035383,NM_020794.2;LRRC7,splice_region_variant,,ENST00000415775,;RP11-181B18.1,intron_variant,,ENST00000414132,;RP11-181B18.1,downstream_gene_variant,,ENST00000425754,; A ENST00000035383 Transcript missense_variant,splice_region_variant 1234/5000 1204/4614 402/1537 Q/K Cag/Aag 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 deleterious(0) 12/25 PROSITE_profiles:PS51450,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 70016532 70016532 C A 1 0 0 0 0 1 0 0 0 8916 840 29 2 2 LRRC7 1 70016532 Missense_Mutation SNP C C3N-01030_T 1585055 70016532 178939890 25 20806 FPGT 0 . GRCh38 1 74198303 74198303 + Nonsense_Mutation SNP G G T rs755449906 C3N-01030_T C3N-01030_N G G c.64G>T p.Glu22Ter p.E22* ENST00000557284 1/27 116 104 12 104 104 0 strelka-mutect FPGT-TNNI3K,stop_gained,p.Glu9Ter,ENST00000370895,;FPGT,stop_gained,p.Glu22Ter,ENST00000370898,NM_003838.4;FPGT-TNNI3K,stop_gained,p.Glu22Ter,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,stop_gained,p.Glu9Ter,ENST00000370899,NM_001199327.1;FPGT,stop_gained,p.Glu9Ter,ENST00000534056,NM_001199328.2;FPGT,stop_gained,p.Glu9Ter,ENST00000370894,NM_001199329.2;FPGT-TNNI3K,stop_gained,p.Glu9Ter,ENST00000370893,;FPGT,stop_gained,p.Glu22Ter,ENST00000467578,;FPGT,stop_gained,p.Glu9Ter,ENST00000482102,;FPGT-TNNI3K,stop_gained,p.Glu9Ter,ENST00000534632,;LRRIQ3,upstream_gene_variant,,ENST00000354431,NM_001105659.1;LRRIQ3,upstream_gene_variant,,ENST00000370911,;LRRIQ3,upstream_gene_variant,,ENST00000370909,;FPGT,upstream_gene_variant,,ENST00000472069,;FPGT,non_coding_transcript_exon_variant,,ENST00000524915,;FPGT-TNNI3K,non_coding_transcript_exon_variant,,ENST00000533006,;FPGT,stop_gained,p.Glu9Ter,ENST00000529485,;LRRIQ3,upstream_gene_variant,,ENST00000415760,;LRRIQ3,upstream_gene_variant,,ENST00000463724,; T ENST00000557284 Transcript stop_gained 69/2855 64/2850 22/949 E/* Gaa/Taa rs755449906,COSM4538791 1 1 FPGT-TNNI3K HGNC HGNC:42952 protein_coding YES CCDS44161.2 ENSP00000450895 V9GXZ4 UPI0001EECC26 NM_001112808.2 1/27 0,1 HIGH SNV 2 0,1 1 PASS rs755449906 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 74198303 74198303 G T 1 0 0 0 0 0 1 0 0 5903 1175 41 2 2 FPGT 1 74198303 Nonsense_Mutation SNP G C3N-01030_T 4181771 74198303 174758119 26 20807 ST6GALNAC5 0 . GRCh38 1 76868697 76868697 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.216G>A p.= p.A72A ENST00000477717 2/5 133 124 9 108 108 0 strelka-varscan-mutect ST6GALNAC5,synonymous_variant,p.=,ENST00000477717,NM_030965.1;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000496845,;ST6GALNAC5,non_coding_transcript_exon_variant,,ENST00000480428,;ST6GALNAC5,synonymous_variant,p.=,ENST00000318803,; A ENST00000477717 Transcript synonymous_variant 451/3751 216/1011 72/336 A gcG/gcA 1 1 ST6GALNAC5 HGNC HGNC:19342 protein_coding YES CCDS673.1 ENSP00000417583 Q9BVH7 UPI0000001C9F NM_030965.1 2/5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 76868697 76868697 G A 1 0 0 0 0 0 0 0 1 15605 1103 39 1 1 ST6GALNAC5 1 76868697 Silent SNP G C3N-01030_T 2670394 76868697 172087725 27 20808 LPAR3 0 . GRCh38 1 84865990 84865991 + Frame_Shift_Ins INS - - T novel C3N-01030_T C3N-01030_N - - c.130dupA p.Ile44AsnfsTer5 p.I44Nfs*5 ENST00000440886 1/2 186 159 27 217 215 2 sindel-varindel-pindel LPAR3,frameshift_variant,p.Ile44AsnfsTer5,ENST00000440886,;LPAR3,frameshift_variant,p.Ile44AsnfsTer5,ENST00000370611,NM_012152.2;LPAR3,non_coding_transcript_exon_variant,,ENST00000491034,; T ENST00000440886 Transcript frameshift_variant 169-170/3345 130-131/1062 44/353 I/NX att/aAtt 1 -1 LPAR3 HGNC HGNC:14298 protein_coding YES CCDS700.1 ENSP00000395389 Q9UBY5 UPI000003CAC0 1/2 Gene3D:1.20.1070.10,Prints_domain:PR00237,Prints_domain:PR01560,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF21,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 70 84865990 84865990 - T 1 0 1 1 0 0 0 0 0 8809 101 4 0 0 LPAR3 1 84865990 Frame_Shift_Ins INS - C3N-01030_T 7997293 84865990 164090432 28 20809 ZNHIT6 0 . GRCh38 1 85706442 85706442 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.722G>T p.Ser241Ile p.S241I ENST00000370574 2/10 102 74 28 183 183 0 strelka-varscan-mutect ZNHIT6,missense_variant,p.Ser202Ile,ENST00000431532,NM_001170670.1;ZNHIT6,missense_variant,p.Ser241Ile,ENST00000370574,NM_017953.3; A ENST00000370574 Transcript missense_variant,splice_region_variant 856/2797 722/1413 241/470 S/I aGt/aTt 1 -1 ZNHIT6 HGNC HGNC:26089 protein_coding YES CCDS707.1 ENSP00000359606 Q9NWK9 UPI000006D8D2 NM_017953.3 deleterious(0) 2/10 Pfam_domain:PF04438,PROSITE_profiles:PS51083,hmmpanther:PTHR13483,hmmpanther:PTHR13483:SF6,Superfamily_domains:SSF144232 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 85706442 85706442 C A 1 0 0 0 0 1 0 0 0 18802 695 24 2 2 ZNHIT6 1 85706442 Missense_Mutation SNP C C3N-01030_T 840452 85706442 163249980 29 20810 TGFBR3 0 . GRCh38 1 91758666 91758666 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.331G>T p.Val111Leu p.V111L ENST00000212355 4/17 296 254 42 359 359 0 strelka-varscan-mutect TGFBR3,missense_variant,p.Val111Leu,ENST00000212355,NM_003243.4;TGFBR3,missense_variant,p.Val111Leu,ENST00000370399,NM_001195684.1;TGFBR3,missense_variant,p.Val111Leu,ENST00000525962,;TGFBR3,missense_variant,p.Val111Leu,ENST00000465892,NM_001195683.1;TGFBR3,non_coding_transcript_exon_variant,,ENST00000468996,;TGFBR3,3_prime_UTR_variant,,ENST00000533089,;TGFBR3,3_prime_UTR_variant,,ENST00000532540,; A ENST00000212355 Transcript missense_variant 846/6465 331/2556 111/851 V/L Gtg/Ttg 1 -1 TGFBR3 HGNC HGNC:11774 protein_coding YES CCDS30770.1 ENSP00000212355 Q03167 UPI000049D997 NM_003243.4 tolerated(0.13) 4/17 hmmpanther:PTHR14002:SF7,hmmpanther:PTHR14002 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 91758666 91758666 C A 1 0 0 0 0 1 0 0 0 16256 507 18 2 2 TGFBR3 1 91758666 Missense_Mutation SNP C C3N-01030_T 6052224 91758666 157197756 30 20811 SETSIP 0 . GRCh38 1 92074610 92074610 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.832delG p.Asp278MetfsTer? p.D278Mfs*? ENST00000596516 1/1 40 32 8 52 52 0 sindel-varindel-pindel SETSIP,frameshift_variant,p.Asp278MetfsTer?,ENST00000596516,NM_001287737.1;SETSIP,frameshift_variant,p.Asp268MetfsTer?,ENST00000485873,; - ENST00000596516 Transcript frameshift_variant 832/909 832/909 278/302 D/X Gat/at 1 -1 SETSIP HGNC HGNC:42937 protein_coding YES CCDS72821.1 ENSP00000480946 P0DME0 UPI000016114F NM_001287737.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11875:SF74,hmmpanther:PTHR11875 HIGH 1 deletion 1 PASS . . 0 200 9 0 0 0 0 0 -19.60927 0.9999963 1 1 1 0 - 7 5 70 92074610 92074610 C - 1 0 1 0 1 0 0 0 0 14419 855 30 0 0 SETSIP 1 92074610 Frame_Shift_Del DEL C C3N-01030_T 315944 92074610 156881812 31 20812 F3 0 . GRCh38 1 94532359 94532359 + Missense_Mutation SNP G G C rs760826348 C3N-01030_T C3N-01030_N G G c.713C>G p.Pro238Arg p.P238R ENST00000334047 5/6 159 140 19 153 153 0 strelka-varscan-mutect F3,missense_variant,p.Pro238Arg,ENST00000334047,NM_001993.4;F3,intron_variant,,ENST00000370207,NM_001178096.1;F3,downstream_gene_variant,,ENST00000480356,;F3,downstream_gene_variant,,ENST00000478217,; C ENST00000334047 Transcript missense_variant 877/2287 713/888 238/295 P/R cCg/cGg rs760826348,COSM1320828 1 -1 F3 HGNC HGNC:3541 protein_coding YES CCDS750.1 ENSP00000334145 P13726 UPI000002CD0D NM_001993.4 tolerated(0.53) 5/6 Gene3D:2.60.40.10,Pfam_domain:PF09294,PIRSF_domain:PIRSF002498,hmmpanther:PTHR20859,hmmpanther:PTHR20859:SF22,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760826348 . 0 207 0 3 0 0 0 0 -20 0.9999899 1 1 1 0 C 3 2 70 94532359 94532359 G C 1 0 0 0 0 1 0 0 0 5215 1116 39 4 4 F3 1 94532359 Missense_Mutation SNP G C3N-01030_T 2457749 94532359 154424063 32 20813 DBT 0 . GRCh38 1 100230736 100230736 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.430A>G p.Lys144Glu p.K144E ENST00000370132 4/11 79 70 9 152 152 0 strelka-varscan-mutect DBT,missense_variant,p.Lys144Glu,ENST00000370132,NM_001918.3;DBT,missense_variant,p.Lys144Glu,ENST00000370131,; C ENST00000370132 Transcript missense_variant 444/10799 430/1449 144/482 K/E Aaa/Gaa 1 -1 DBT HGNC HGNC:2698 protein_coding YES CCDS767.1 ENSP00000359151 P11182 UPI000013D0E7 NM_001918.3 tolerated(0.78) 4/11 hmmpanther:PTHR23151,hmmpanther:PTHR23151:SF71,Superfamily_domains:SSF51230 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 100230736 100230736 T C 1 0 0 0 0 1 0 0 0 4058 1855 64 5 5 DBT 1 100230736 Missense_Mutation SNP T C3N-01030_T 5698377 100230736 148725686 33 20814 SLC30A7 0 . GRCh38 1 100896296 100896296 + Nonsense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.34A>T p.Lys12Ter p.K12* ENST00000370112 1/12 250 221 29 207 207 0 strelka-varscan-mutect SLC30A7,stop_gained,p.Lys12Ter,ENST00000370112,NM_001144884.1,NM_133496.4;SLC30A7,stop_gained,p.Lys12Ter,ENST00000357650,;EXTL2,upstream_gene_variant,,ENST00000370114,NM_001261440.1,NM_001033025.2;EXTL2,upstream_gene_variant,,ENST00000535414,NM_001261442.1;EXTL2,upstream_gene_variant,,ENST00000370113,NM_001439.3;EXTL2,upstream_gene_variant,,ENST00000450240,NM_001261441.1;EXTL2,upstream_gene_variant,,ENST00000416479,;RP4-549L20.3,downstream_gene_variant,,ENST00000609247,;EXTL2,upstream_gene_variant,,ENST00000480774,;EXTL2,upstream_gene_variant,,ENST00000494907,; T ENST00000370112 Transcript stop_gained 221/7898 34/1131 12/376 K/* Aaa/Taa 1 1 SLC30A7 HGNC HGNC:19306 protein_coding YES CCDS776.1 ENSP00000359130 Q8NEW0 UPI0000050F45 NM_001144884.1,NM_133496.4 1/12 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 100896296 100896296 A T 1 0 0 0 0 0 1 0 0 14830 131 5 4 4 SLC30A7 1 100896296 Nonsense_Mutation SNP A C3N-01030_T 665560 100896296 148060126 34 20815 COL11A1 0 . GRCh38 1 102935086 102935086 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3466G>T p.Gly1156Ter p.G1156* ENST00000370096 45/67 209 190 19 286 284 2 strelka-varscan-mutect COL11A1,stop_gained,p.Gly1168Ter,ENST00000358392,NM_080629.2;COL11A1,stop_gained,p.Gly1156Ter,ENST00000370096,NM_001854.3;COL11A1,stop_gained,p.Gly1117Ter,ENST00000353414,NM_001190709.1;COL11A1,stop_gained,p.Gly1040Ter,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; A ENST00000370096 Transcript stop_gained 3779/7286 3466/5421 1156/1806 G/* Gga/Tga 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 45/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 102935086 102935086 C A 1 0 0 0 0 0 1 0 0 3455 690 24 2 2 COL11A1 1 102935086 Nonsense_Mutation SNP C C3N-01030_T 2038790 102935086 146021336 35 20816 COL11A1 0 . GRCh38 1 102946921 102946921 + Silent SNP A A T novel C3N-01030_T C3N-01030_N A A c.3204T>A p.= p.A1068A ENST00000370096 42/67 274 187 87 303 303 0 strelka-varscan-mutect COL11A1,synonymous_variant,p.=,ENST00000358392,NM_080629.2;COL11A1,synonymous_variant,p.=,ENST00000370096,NM_001854.3;COL11A1,synonymous_variant,p.=,ENST00000353414,NM_001190709.1;COL11A1,synonymous_variant,p.=,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; T ENST00000370096 Transcript synonymous_variant 3517/7286 3204/5421 1068/1806 A gcT/gcA 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 42/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 102946921 102946921 A T 1 0 0 0 0 0 0 0 1 3455 175 7 4 4 COL11A1 1 102946921 Silent SNP A C3N-01030_T 11835 102946921 146009501 36 20817 COL11A1 0 . GRCh38 1 103074655 103074655 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.614T>A p.Val205Asp p.V205D ENST00000370096 4/67 164 132 32 204 204 0 strelka-varscan-mutect COL11A1,missense_variant,p.Val205Asp,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Val205Asp,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Val205Asp,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Val205Asp,ENST00000512756,NM_080630.3;COL11A1,missense_variant,p.Val205Asp,ENST00000427239,;COL11A1,missense_variant,p.Val132Asp,ENST00000447608,; T ENST00000370096 Transcript missense_variant 927/7286 614/5421 205/1806 V/D gTt/gAt 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 4/67 Gene3D:2.60.120.200,SMART_domains:SM00210,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 103074655 103074655 A T 1 0 0 0 0 1 0 0 0 3455 43 2 4 4 COL11A1 1 103074655 Missense_Mutation SNP A C3N-01030_T 127734 103074655 145881767 37 20818 AMY2B 0 . GRCh38 1 103572236 103572236 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.295A>T p.Thr99Ser p.T99S ENST00000361355 4/12 84 59 25 134 134 0 strelka-varscan-mutect AMY2B,missense_variant,p.Thr99Ser,ENST00000361355,NM_020978.4;AMY2B,missense_variant,p.Thr99Ser,ENST00000610648,;AMY2B,downstream_gene_variant,,ENST00000453959,;AMY2B,downstream_gene_variant,,ENST00000435302,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,missense_variant,p.Thr99Ser,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,; T ENST00000361355 Transcript missense_variant 911/2181 295/1536 99/511 T/S Act/Tct 1 1 AMY2B HGNC HGNC:478 protein_coding YES CCDS782.1 ENSP00000354610 P19961 UPI0000000CB1 NM_020978.4 tolerated(0.37) 4/12 hmmpanther:PTHR10357:SF105,hmmpanther:PTHR10357,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 103572236 103572236 A T 1 0 0 0 0 1 0 0 0 692 275 10 4 4 AMY2B 1 103572236 Missense_Mutation SNP A C3N-01030_T 497581 103572236 145384186 38 20819 SLC16A1 0 . GRCh38 1 112913995 112913995 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1399A>T p.Ser467Cys p.S467C ENST00000538576 5/5 307 233 74 365 365 0 strelka-varscan-mutect SLC16A1,missense_variant,p.Ser467Cys,ENST00000538576,NM_001166496.1;SLC16A1,missense_variant,p.Ser467Cys,ENST00000369626,NM_003051.3;SLC16A1,downstream_gene_variant,,ENST00000458229,;SLC16A1,downstream_gene_variant,,ENST00000443580,;SLC16A1,downstream_gene_variant,,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,; A ENST00000538576 Transcript missense_variant 2231/4374 1399/1503 467/500 S/C Agt/Tgt 1 -1 SLC16A1 HGNC HGNC:10922 protein_coding YES CCDS858.1 ENSP00000441065 P53985 A0A024R0H1 UPI00000012F5 NM_001166496.1 deleterious(0.04) 5/5 hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF24 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 112913995 112913995 T A 1 0 0 0 0 1 0 0 0 14668 1580 55 4 4 SLC16A1 1 112913995 Missense_Mutation SNP T C3N-01030_T 9341759 112913995 136042427 39 20820 CASQ2 0 . GRCh38 1 115738322 115738322 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.434C>A p.Pro145Gln p.P145Q ENST00000261448 4/11 272 228 44 282 279 3 strelka-varscan-mutect CASQ2,missense_variant,p.Pro145Gln,ENST00000261448,NM_001232.3; T ENST00000261448 Transcript missense_variant 674/2674 434/1200 145/399 P/Q cCa/cAa 1 -1 CASQ2 HGNC HGNC:1513 protein_coding YES CCDS884.1 ENSP00000261448 O14958 UPI0000126F16 NM_001232.3 deleterious(0) 4/11 Gene3D:3.40.30.10,Pfam_domain:PF01216,hmmpanther:PTHR10033,hmmpanther:PTHR10033:SF15,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 115738322 115738322 G T 1 0 0 0 0 1 0 0 0 2380 1348 47 2 2 CASQ2 1 115738322 Missense_Mutation SNP G C3N-01030_T 2824327 115738322 133218100 40 20821 PTGFRN 0 . GRCh38 1 116961665 116961665 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1636G>T p.Glu546Ter p.E546* ENST00000393203 5/9 57 51 6 86 86 0 strelka-varscan-mutect PTGFRN,stop_gained,p.Glu546Ter,ENST00000393203,NM_020440.3;RNA5SP55,downstream_gene_variant,,ENST00000516701,; T ENST00000393203 Transcript stop_gained 1783/6178 1636/2640 546/879 E/* Gaa/Taa 1 1 PTGFRN HGNC HGNC:9601 protein_coding YES CCDS890.1 ENSP00000376899 Q9P2B2 UPI000012ABC4 NM_020440.3 5/9 Gene3D:2.60.40.10,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF3 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -14.26144 1 1 1 1 0 T 4 4 70 116961665 116961665 G T 1 0 0 0 0 0 1 0 0 12906 956 33 2 2 PTGFRN 1 116961665 Nonsense_Mutation SNP G C3N-01030_T 1223343 116961665 131994757 41 20822 HSD3B2 0 . GRCh38 1 119422010 119422010 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.509G>T p.Gly170Val p.G170V ENST00000543831 4/4 376 334 42 413 413 0 strelka-varscan-mutect HSD3B2,missense_variant,p.Gly170Val,ENST00000543831,NM_001166120.1;HSD3B2,missense_variant,p.Gly170Val,ENST00000369416,NM_000198.3;HSD3B2,missense_variant,p.Gly170Val,ENST00000433745,;HSD3B2,non_coding_transcript_exon_variant,,ENST00000448448,;HSD3B2,downstream_gene_variant,,ENST00000471656,;HSD3B2,downstream_gene_variant,,ENST00000443865,; T ENST00000543831 Transcript missense_variant 758/1783 509/1119 170/372 G/V gGg/gTg 1 1 HSD3B2 HGNC HGNC:5218 protein_coding YES CCDS902.1 ENSP00000445122 P26439 A0A024R0F9 UPI0000001C6C NM_001166120.1 deleterious(0) 4/4 Gene3D:3.40.50.720,Pfam_domain:PF01073,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF444,Superfamily_domains:SSF51735 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 119422010 119422010 G T 1 0 0 0 0 1 0 0 0 7285 1232 43 2 2 HSD3B2 1 119422010 Missense_Mutation SNP G C3N-01030_T 2460345 119422010 129534412 42 20823 ZNF697 0 . GRCh38 1 119623322 119623322 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1021G>T p.Ala341Ser p.A341S ENST00000421812 3/3 66 52 14 54 54 0 strelka-varscan-mutect ZNF697,missense_variant,p.Ala341Ser,ENST00000421812,NM_001080470.1; A ENST00000421812 Transcript missense_variant 1141/5041 1021/1638 341/545 A/S Gcg/Tcg 1 -1 ZNF697 HGNC HGNC:32034 protein_coding YES CCDS44202.1 ENSP00000396857 Q5TEC3 UPI0000DD78D7 NM_001080470.1 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF233,Low_complexity_(Seg):seg MODERATE 1 SNV 3 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 119623322 119623322 C A 1 0 0 0 0 1 0 0 0 18673 739 26 2 2 ZNF697 1 119623322 Missense_Mutation SNP C C3N-01030_T 201312 119623322 129333100 43 20824 ADAM30 0 . GRCh38 1 119895433 119895433 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.904A>T p.Asn302Tyr p.N302Y ENST00000369400 1/1 122 101 21 145 145 0 strelka-varscan-mutect ADAM30,missense_variant,p.Asn302Tyr,ENST00000369400,NM_021794.3; A ENST00000369400 Transcript missense_variant 1063/2963 904/2373 302/790 N/Y Aat/Tat 1 -1 ADAM30 HGNC HGNC:208 protein_coding YES CCDS907.1 ENSP00000358407 Q9UKF2 UPI000004C638 NM_021794.3 tolerated(0.05) 1/1 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF148,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 119895433 119895433 T A 1 0 0 0 0 1 0 0 0 292 1754 61 4 4 ADAM30 1 119895433 Missense_Mutation SNP T C3N-01030_T 272111 119895433 129060989 44 20825 SEC22B 0 . GRCh38 1 120163236 120163236 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.320C>T p.Ser107Phe p.S107F ENST00000578049 3/5 37 27 10 29 29 0 strelka-varscan-mutect SEC22B,missense_variant,p.Ser107Phe,ENST00000578049,NM_004892.5;SEC22B,upstream_gene_variant,,ENST00000618538,; A ENST00000578049 Transcript missense_variant 454/6922 320/648 107/215 S/F tCc/tTc 1 -1 SEC22B HGNC HGNC:10700 protein_coding YES ENSP00000463393 O75396 UPI0000022D17 NM_004892.5 deleterious(0.01) 3/5 PROSITE_profiles:PS50859,hmmpanther:PTHR21136,hmmpanther:PTHR21136:SF96,Pfam_domain:PF13774,Gene3D:3.30.450.50,SMART_domains:SM01270,Superfamily_domains:SSF64356 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 120163236 120163236 G A 1 0 0 0 0 1 0 0 0 14266 1174 41 3 3 SEC22B 1 120163236 Missense_Mutation SNP G C3N-01030_T 267803 120163236 128793186 45 20826 CHD1L 0 . GRCh38 1 147252662 147252662 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.167G>T p.Trp56Leu p.W56L ENST00000369258 2/23 214 186 28 117 117 0 strelka-varscan-mutect CHD1L,missense_variant,p.Trp56Leu,ENST00000369258,NM_004284.4;CHD1L,5_prime_UTR_variant,,ENST00000431239,NM_024568.2,NM_001256336.1;CHD1L,intron_variant,,ENST00000361293,NM_001256337.1;CHD1L,intron_variant,,ENST00000369259,NM_001256338.1;RP11-337C18.10,downstream_gene_variant,,ENST00000606856,;CHD1L,missense_variant,p.Trp56Leu,ENST00000622533,;CHD1L,missense_variant,p.Trp56Leu,ENST00000467213,;CHD1L,non_coding_transcript_exon_variant,,ENST00000492728,;CHD1L,intron_variant,,ENST00000488864,; T ENST00000369258 Transcript missense_variant 187/2967 167/2694 56/897 W/L tGg/tTg 1 1 CHD1L HGNC HGNC:1916 protein_coding YES CCDS927.1 ENSP00000358262 Q86WJ1 UPI000000D7F1 NM_004284.4 deleterious(0) 2/23 Gene3D:3.40.50.300,hmmpanther:PTHR10799,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 147252662 147252662 G T 1 0 0 0 0 1 0 0 0 3083 1357 47 2 2 CHD1L 1 147252662 Missense_Mutation SNP G C3N-01030_T 27089426 147252662 101703760 46 20827 ACP6 0 . GRCh38 1 147654321 147654321 + Missense_Mutation SNP C C A rs782463000 C3N-01030_T C3N-01030_N C C c.653G>T p.Arg218Leu p.R218L ENST00000583509 6/10 213 163 50 156 156 0 strelka-varscan-mutect ACP6,missense_variant,p.Arg218Leu,ENST00000583509,NM_016361.4;ACP6,missense_variant,p.Arg46Leu,ENST00000609196,;ACP6,missense_variant,p.Arg175Leu,ENST00000392988,;ACP6,missense_variant,p.Arg218Leu,ENST00000487562,;ACP6,missense_variant,p.Arg113Leu,ENST00000611629,;ACP6,downstream_gene_variant,,ENST00000493129,;ACP6,3_prime_UTR_variant,,ENST00000620634,;ACP6,non_coding_transcript_exon_variant,,ENST00000613673,;ACP6,non_coding_transcript_exon_variant,,ENST00000614551,;ACP6,upstream_gene_variant,,ENST00000460583,; A ENST00000583509 Transcript missense_variant 1101/6923 653/1287 218/428 R/L cGg/cTg rs782463000,COSM5353165,COSM5353166 1 -1 ACP6 HGNC HGNC:29609 protein_coding YES CCDS928.1 ENSP00000463574 X5D289 UPI000003F07E NM_016361.4 tolerated(0.22) 6/10 hmmpanther:PTHR11567,hmmpanther:PTHR11567:SF123,Gene3D:3.40.50.1240,Pfam_domain:PF00328,Superfamily_domains:SSF53254 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782463000 . 0 206 0 4 0 0 0 0 -20 0.9999658 1 1 1 0 A 3 1 70 147654321 147654321 C A 1 0 0 0 0 1 0 0 0 207 666 23 1 1 ACP6 1 147654321 Missense_Mutation SNP C C3N-01030_T 401659 147654321 101302101 47 20828 GPR89B 0 . GRCh38 1 147968894 147968894 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.747G>T p.Gln249His p.Q249H ENST00000314163 9/14 195 109 86 172 170 2 strelka-varscan-mutect GPR89B,missense_variant,p.Gln249His,ENST00000314163,NM_016334.3;GPR89B,downstream_gene_variant,,ENST00000468618,;GPR89B,splice_acceptor_variant,,ENST00000488603,;GPR89B,splice_acceptor_variant,,ENST00000461786,;GPR89B,3_prime_UTR_variant,,ENST00000488165,;GPR89B,3_prime_UTR_variant,,ENST00000491975,;GPR89B,non_coding_transcript_exon_variant,,ENST00000478307,;GPR89B,upstream_gene_variant,,ENST00000490955,; T ENST00000314163 Transcript missense_variant 891/1934 747/1368 249/455 Q/H caG/caT 1 1 GPR89B HGNC HGNC:13840 protein_coding YES CCDS930.1 ENSP00000358233 P0CG08 X5D7G6 UPI00000389CC NM_016334.3 tolerated(0.18) 9/14 hmmpanther:PTHR15948 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 147968894 147968894 G T 1 0 0 0 0 1 0 0 0 6600 991 35 2 2 GPR89B 1 147968894 Missense_Mutation SNP G C3N-01030_T 314573 147968894 100987528 48 20829 FLG 0 . GRCh38 1 152306361 152306361 + Missense_Mutation SNP C C A rs556196419 C3N-01030_T C3N-01030_N C C c.8525G>T p.Arg2842Leu p.R2842L ENST00000368799 3/3 1383 1150 233 813 813 0 strelka-varscan FLG,missense_variant,p.Arg2842Leu,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; A ENST00000368799 Transcript missense_variant 8561/12747 8525/12186 2842/4061 R/L cGt/cTt rs556196419,COSM5292325 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.11) 3/3 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 152306361 152306361 C A 1 0 0 0 0 1 0 0 0 5784 536 19 1 1 FLG 1 152306361 Missense_Mutation SNP C C3N-01030_T 4337467 152306361 96650061 49 20830 FLG2 0 . GRCh38 1 152353676 152353676 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.4110C>A p.His1370Gln p.H1370Q ENST00000388718 3/3 268 149 119 173 172 1 strelka-varscan FLG2,missense_variant,p.His1370Gln,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 4183/9124 4110/7176 1370/2391 H/Q caC/caA 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious(0.01) 3/3 hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 152353676 152353676 G T 1 0 0 0 0 1 0 0 0 5785 1368 48 2 2 FLG2 1 152353676 Missense_Mutation SNP G C3N-01030_T 47315 152353676 96602746 50 20831 PGLYRP3 0 . GRCh38 1 153307102 153307102 + Missense_Mutation SNP G G A rs771297602 C3N-01030_T C3N-01030_N G G c.221C>T p.Ser74Phe p.S74F ENST00000290722 2/7 374 314 60 191 191 0 strelka-varscan PGLYRP3,missense_variant,p.Ser74Phe,ENST00000290722,NM_052891.2; A ENST00000290722 Transcript missense_variant 274/1173 221/1026 74/341 S/F tCc/tTc rs771297602,COSM230880 1 -1 PGLYRP3 HGNC HGNC:30014 protein_coding YES CCDS1035.1 ENSP00000290722 Q96LB9 UPI000006F12B NM_052891.2 deleterious(0.03) 2/7 hmmpanther:PTHR11022,hmmpanther:PTHR11022:SF12,Gene3D:3.40.80.10,Pfam_domain:PF01510,SMART_domains:SM00701,SMART_domains:SM00644,Superfamily_domains:SSF55846 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 153307102 153307102 G A 1 0 0 0 0 1 0 0 0 11884 1174 41 3 3 PGLYRP3 1 153307102 Missense_Mutation SNP G C3N-01030_T 953426 153307102 95649320 51 20832 S100A7A 0 . GRCh38 1 153419308 153419308 + Silent SNP G G A rs368556174 C3N-01030_T C3N-01030_N G G c.305G>A p.= p.*102* ENST00000368729 3/3 115 105 10 94 94 0 strelka-varscan S100A7A,stop_retained_variant,p.=,ENST00000368729,NM_176823.3;S100A7A,stop_retained_variant,p.=,ENST00000329256,;S100A7A,stop_retained_variant,p.=,ENST00000368728,; A ENST00000368729 Transcript stop_retained_variant 362/4279 305/306 102/101 * tGa/tAa rs368556174 1 1 S100A7A HGNC HGNC:21657 protein_coding YES CCDS30872.1 ENSP00000357718 Q86SG5 UPI000000D89D NM_176823.3 3/3 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.77471 1 1 1 1 0 A 2 1 70 153419308 153419308 G A 1 0 0 0 0 0 0 0 1 14043 1285 45 3 3 S100A7A 1 153419308 Silent SNP G C3N-01030_T 112206 153419308 95537114 52 20833 RUSC1 0 . GRCh38 1 155326617 155326617 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1899C>G p.Phe633Leu p.F633L ENST00000368352 8/10 120 110 10 61 61 0 strelka-varscan RUSC1,missense_variant,p.Phe633Leu,ENST00000368352,NM_001105203.1;RUSC1,missense_variant,p.Phe223Leu,ENST00000368347,NM_001105205.1;RUSC1,missense_variant,p.Phe164Leu,ENST00000292254,NM_001278230.1;RUSC1,missense_variant,p.Phe164Leu,ENST00000368349,NM_001278229.1,NM_014328.4,NM_001278227.1,NM_001278228.1;RUSC1,missense_variant,p.Phe164Leu,ENST00000497930,;RUSC1,missense_variant,p.Phe164Leu,ENST00000489860,;RUSC1,missense_variant,p.Phe54Leu,ENST00000485924,;RUSC1,5_prime_UTR_variant,,ENST00000490373,;RUSC1,intron_variant,,ENST00000368354,NM_001105204.1;RUSC1,intron_variant,,ENST00000471876,;RUSC1,intron_variant,,ENST00000479924,;RUSC1-AS1,upstream_gene_variant,,ENST00000450199,;RUSC1-AS1,upstream_gene_variant,,ENST00000443642,;RUSC1,3_prime_UTR_variant,,ENST00000468764,;RUSC1,non_coding_transcript_exon_variant,,ENST00000462780,;RUSC1,non_coding_transcript_exon_variant,,ENST00000492536,;RUSC1,non_coding_transcript_exon_variant,,ENST00000467820,;RUSC1,non_coding_transcript_exon_variant,,ENST00000473331,; G ENST00000368352 Transcript missense_variant 2050/3403 1899/2709 633/902 F/L ttC/ttG 1 1 RUSC1 HGNC HGNC:17153 protein_coding YES CCDS41410.1 ENSP00000357336 Q9BVN2 UPI000046FDA5 NM_001105203.1 tolerated(0.61) 8/10 PROSITE_profiles:PS50826,hmmpanther:PTHR15591,Pfam_domain:PF02759,SMART_domains:SM00593,Superfamily_domains:0052343 MODERATE SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.42617 1 1 1 1 0 G 3 3 70 155326617 155326617 C G 1 0 0 0 0 1 0 0 0 14011 912 32 4 4 RUSC1 1 155326617 Missense_Mutation SNP C C3N-01030_T 1907309 155326617 93629805 53 20834 FCRL5 0 . GRCh38 1 157524277 157524277 + Splice_Site SNP A A T novel C3N-01030_T C3N-01030_N A A c.2239+2T>A p.X747_splice ENST00000361835 153 78 75 124 124 0 strelka-varscan FCRL5,splice_donor_variant,,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,synonymous_variant,p.=,ENST00000368190,;FCRL5,splice_donor_variant,,ENST00000497286,;FCRL5,upstream_gene_variant,,ENST00000461387,; T ENST00000361835 Transcript splice_donor_variant -/5390 2239/2934 747/977 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 10/16 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 70 157524277 157524277 A T 1 0 0 0 0 0 0 1 0 5660 173 6 4 4 FCRL5 1 157524277 Splice_Site SNP A C3N-01030_T 2197660 157524277 91432145 54 20835 SLAMF8 0 . GRCh38 1 159832991 159832991 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.483C>A p.= p.T161T ENST00000289707 3/5 502 431 71 300 300 0 strelka-varscan SLAMF8,synonymous_variant,p.=,ENST00000289707,NM_020125.2;SLAMF8,synonymous_variant,p.=,ENST00000368104,;C1orf204,downstream_gene_variant,,ENST00000368102,NM_001134233.1;C1orf204,downstream_gene_variant,,ENST00000621242,;SLAMF8,non_coding_transcript_exon_variant,,ENST00000471286,;C1orf204,downstream_gene_variant,,ENST00000491974,;SLAMF8,upstream_gene_variant,,ENST00000497141,; A ENST00000289707 Transcript synonymous_variant 632/2996 483/858 161/285 T acC/acA 1 1 SLAMF8 HGNC HGNC:21391 protein_coding YES CCDS1188.1 ENSP00000289707 Q9P0V8 UPI000003E841 NM_020125.2 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF55,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 159832991 159832991 C A 1 0 0 0 0 0 0 0 1 14635 668 24 2 2 SLAMF8 1 159832991 Silent SNP C C3N-01030_T 2308714 159832991 89123431 55 20836 SLAMF1 0 . GRCh38 1 160634642 160634642 + Missense_Mutation SNP G G T rs753033265 C3N-01030_T C3N-01030_N G G c.671C>A p.Pro224Gln p.P224Q ENST00000302035 3/7 96 52 44 57 57 0 strelka-varscan SLAMF1,missense_variant,p.Pro224Gln,ENST00000302035,NM_003037.3;SLAMF1,missense_variant,p.Pro224Gln,ENST00000538290,;SLAMF1,intron_variant,,ENST00000235739,;SLAMF1,downstream_gene_variant,,ENST00000494463,; T ENST00000302035 Transcript missense_variant 1021/4006 671/1008 224/335 P/Q cCg/cAg rs753033265,COSM530069 1 -1 SLAMF1 HGNC HGNC:10903 protein_coding YES CCDS1207.1 ENSP00000306190 Q13291 UPI0000047630 NM_003037.3 deleterious(0.02) 3/7 hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF49 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 160634642 160634642 G T 1 0 0 0 0 1 0 0 0 14632 1116 39 1 1 SLAMF1 1 160634642 Missense_Mutation SNP G C3N-01030_T 801651 160634642 88321780 56 20837 ILDR2 0 . GRCh38 1 166921204 166921204 + Silent SNP G G T C3N-01030_T C3N-01030_N G G c.1387C>A p.= p.R463R ENST00000271417 9/10 127 109 18 83 83 0 strelka-varscan ILDR2,synonymous_variant,p.=,ENST00000271417,NM_199351.2;ILDR2,synonymous_variant,p.=,ENST00000529071,;ILDR2,synonymous_variant,p.=,ENST00000528703,;ILDR2,synonymous_variant,p.=,ENST00000526687,;ILDR2,synonymous_variant,p.=,ENST00000525740,;ILDR2,intron_variant,,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; T ENST00000271417 Transcript synonymous_variant 1443/13140 1387/1920 463/639 R Cgg/Agg COSM4692395 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 9/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0,Low_complexity_(Seg):seg 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 166921204 166921204 G T 1 0 0 0 0 0 0 0 1 7613 1086 38 1 1 ILDR2 1 166921204 Silent SNP G C3N-01030_T 6286562 166921204 82035218 57 20838 ADCY10 0 . GRCh38 1 167883511 167883511 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.946G>T p.Asp316Tyr p.D316Y ENST00000367851 9/33 444 267 177 321 320 1 strelka-varscan ADCY10,missense_variant,p.Asp224Tyr,ENST00000367848,NM_001297772.1;ADCY10,missense_variant,p.Asp316Tyr,ENST00000367851,NM_018417.5;ADCY10,missense_variant,p.Asp163Tyr,ENST00000545172,NM_001167749.2; A ENST00000367851 Transcript missense_variant 1131/5051 946/4833 316/1610 D/Y Gat/Tat 1 -1 ADCY10 HGNC HGNC:21285 protein_coding YES CCDS1265.1 ENSP00000356825 Q96PN6 A0A0K0K1J8 UPI0000204D00 NM_018417.5 deleterious(0) 9/33 hmmpanther:PTHR16305,hmmpanther:PTHR16305:SF32,Pfam_domain:PF00211,PIRSF_domain:PIRSF011131,Gene3D:3.30.70.1230,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 167883511 167883511 C A 1 0 0 0 0 1 0 0 0 337 855 30 2 2 ADCY10 1 167883511 Missense_Mutation SNP C C3N-01030_T 962307 167883511 81072911 58 20839 TBX19 0 . GRCh38 1 168312772 168312772 + Missense_Mutation SNP G G C rs778358146 C3N-01030_T C3N-01030_N G G c.1117G>C p.Val373Leu p.V373L ENST00000367821 8/8 519 307 212 289 289 0 strelka-varscan TBX19,missense_variant,p.Val373Leu,ENST00000367821,NM_005149.2;TBX19,missense_variant,p.Val243Leu,ENST00000431969,;TBX19,missense_variant,p.Val206Leu,ENST00000441464,;TBX19,non_coding_transcript_exon_variant,,ENST00000465440,;RP5-1059H15.1,upstream_gene_variant,,ENST00000636624,; C ENST00000367821 Transcript missense_variant 1168/2822 1117/1347 373/448 V/L Gtg/Ctg rs778358146 1 1 TBX19 HGNC HGNC:11596 protein_coding YES CCDS1272.1 ENSP00000356795 O60806 UPI000003176C NM_005149.2 tolerated(0.27) 8/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF114 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 168312772 168312772 G C 1 0 0 0 0 1 0 0 0 16059 1261 44 4 4 TBX19 1 168312772 Missense_Mutation SNP G C3N-01030_T 429261 168312772 80643650 59 20840 PRRC2C 0 . GRCh38 1 171557940 171557940 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.5822A>T p.Gln1941Leu p.Q1941L ENST00000338920 19/34 156 78 78 120 120 0 strelka-varscan PRRC2C,missense_variant,p.Gln1943Leu,ENST00000367742,;PRRC2C,missense_variant,p.Gln1941Leu,ENST00000338920,NM_015172.3;PRRC2C,missense_variant,p.Gln1941Leu,ENST00000426496,;PRRC2C,missense_variant,p.Gln489Leu,ENST00000495585,; T ENST00000338920 Transcript missense_variant 6059/10355 5822/8454 1941/2817 Q/L cAg/cTg 1 1 PRRC2C HGNC HGNC:24903 protein_coding YES CCDS1296.2 ENSP00000343629 Q9Y520 UPI0000E265EC NM_015172.3 deleterious_low_confidence(0) 19/34 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 171557940 171557940 A T 1 0 0 0 0 1 0 0 0 12750 188 7 4 4 PRRC2C 1 171557940 Missense_Mutation SNP A C3N-01030_T 3245168 171557940 77398482 60 20841 SLC9C2 0 . GRCh38 1 173554758 173554758 + Silent SNP C C A C3N-01030_T C3N-01030_N C C c.1272G>T p.= p.V424V ENST00000367714 11/28 115 103 12 124 123 1 strelka-varscan-mutect SLC9C2,synonymous_variant,p.=,ENST00000367714,NM_178527.3;RP3-436N22.3,upstream_gene_variant,,ENST00000431459,;SLC9C2,intron_variant,,ENST00000466087,; A ENST00000367714 Transcript synonymous_variant 1695/4428 1272/3375 424/1124 V gtG/gtT COSM5495348 1 -1 SLC9C2 HGNC HGNC:28664 protein_coding YES CCDS1308.1 ENSP00000356687 Q5TAH2 UPI0000197379 NM_178527.3 11/28 Transmembrane_helices:TMhelix,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF91 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 173554758 173554758 C A 1 0 0 0 0 0 0 0 1 15007 813 29 2 2 SLC9C2 1 173554758 Silent SNP C C3N-01030_T 1996818 173554758 75401664 61 20842 RC3H1 0 . GRCh38 1 173980853 173980853 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.925G>A p.Gly309Arg p.G309R ENST00000367696 6/20 237 135 102 185 185 0 strelka-varscan-mutect RC3H1,missense_variant,p.Gly309Arg,ENST00000367696,;RC3H1,missense_variant,p.Gly309Arg,ENST00000258349,NM_001300850.1,NM_172071.3;RC3H1,missense_variant,p.Gly309Arg,ENST00000367694,NM_001300851.1,NM_001300852.1;RC3H1,downstream_gene_variant,,ENST00000484867,; T ENST00000367696 Transcript missense_variant 1277/11261 925/3402 309/1133 G/R Gga/Aga 1 -1 RC3H1 HGNC HGNC:29434 protein_coding YES CCDS30940.1 ENSP00000356669 Q5TC82 UPI00001D7DA8 deleterious(0) 6/20 hmmpanther:PTHR13139:SF6,hmmpanther:PTHR13139 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 173980853 173980853 C T 1 0 0 0 0 1 0 0 0 13335 603 21 3 3 RC3H1 1 173980853 Missense_Mutation SNP C C3N-01030_T 426095 173980853 74975569 62 20843 TNN 0 . GRCh38 1 175144466 175144466 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.3675C>T p.= p.A1225A ENST00000239462 18/19 270 227 43 175 175 0 strelka-varscan-mutect TNN,synonymous_variant,p.=,ENST00000239462,NM_022093.1;TNN,synonymous_variant,p.=,ENST00000621086,;TNN,synonymous_variant,p.=,ENST00000622870,; T ENST00000239462 Transcript synonymous_variant 3788/5008 3675/3900 1225/1299 A gcC/gcT 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 18/19 PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Pfam_domain:PF00147,Gene3D:4.10.530.10,SMART_domains:SM00186,Superfamily_domains:SSF56496 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 175144466 175144466 C T 1 0 0 0 0 0 0 0 1 16796 610 22 3 3 TNN 1 175144466 Silent SNP C C3N-01030_T 1163613 175144466 73811956 63 20844 ASTN1 0 . GRCh38 1 176958395 176958395 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.1686A>T p.= p.S562S ENST00000361833 10/23 282 261 21 225 225 0 strelka-varscan-mutect ASTN1,synonymous_variant,p.=,ENST00000361833,NM_004319.2;ASTN1,synonymous_variant,p.=,ENST00000367657,NM_001286164.1;ASTN1,synonymous_variant,p.=,ENST00000424564,NM_207108.2;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,; A ENST00000361833 Transcript synonymous_variant 1700/7116 1686/3885 562/1294 S tcA/tcT 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 10/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 176958395 176958395 T A 1 0 0 0 0 0 0 0 1 1211 1567 55 4 4 ASTN1 1 176958395 Silent SNP T C3N-01030_T 1813929 176958395 71998027 64 20845 CACNA1E 0 . GRCh38 1 181752229 181752229 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3818C>A p.Pro1273His p.P1273H ENST00000367573 27/48 277 157 120 175 175 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Pro1254His,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Pro1273His,ENST00000621551,;CACNA1E,missense_variant,p.Pro1273His,ENST00000367567,;CACNA1E,missense_variant,p.Pro1254His,ENST00000358338,;CACNA1E,missense_variant,p.Pro1273His,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Pro1273His,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Pro1272His,ENST00000357570,;CACNA1E,missense_variant,p.Pro1254His,ENST00000360108,; A ENST00000367573 Transcript missense_variant 3818/7067 3818/6942 1273/2313 P/H cCc/cAc 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0) 27/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 181752229 181752229 C A 1 0 0 0 0 1 0 0 0 2230 623 22 2 2 CACNA1E 1 181752229 Missense_Mutation SNP C C3N-01030_T 4793834 181752229 67204193 65 20846 COLGALT2 0 . GRCh38 1 183969350 183969350 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.751C>A p.Leu251Met p.L251M ENST00000361927 5/12 159 90 69 146 146 0 strelka-varscan-mutect COLGALT2,missense_variant,p.Leu251Met,ENST00000361927,NM_001303420.1,NM_015101.3,NM_001303421.1;COLGALT2,upstream_gene_variant,,ENST00000367520,; T ENST00000361927 Transcript missense_variant 1123/5177 751/1881 251/626 L/M Ctg/Atg 1 -1 COLGALT2 HGNC HGNC:16790 protein_coding YES CCDS1360.1 ENSP00000354960 Q8IYK4 UPI000007423A NM_001303420.1,NM_015101.3,NM_001303421.1 deleterious(0.01) 5/12 hmmpanther:PTHR10730,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 183969350 183969350 G T 1 0 0 0 0 1 0 0 0 3504 962 34 2 2 COLGALT2 1 183969350 Missense_Mutation SNP G C3N-01030_T 2217121 183969350 64987072 66 20847 BRINP3 0 . GRCh38 1 190160688 190160688 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.1164C>T p.= p.L388L ENST00000367462 7/8 160 137 23 158 158 0 strelka-varscan-mutect BRINP3,synonymous_variant,p.=,ENST00000367462,NM_199051.1; A ENST00000367462 Transcript synonymous_variant 1649/3142 1164/2301 388/766 L ctC/ctT 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 7/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 190160688 190160688 G A 1 0 0 0 0 0 0 0 1 1687 1277 45 3 3 BRINP3 1 190160688 Silent SNP G C3N-01030_T 6191338 190160688 58795734 67 20848 KIF21B 0 . GRCh38 1 201004417 201004417 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.939G>T p.Gln313His p.Q313H ENST00000422435 7/35 283 259 24 175 175 0 strelka-varscan KIF21B,missense_variant,p.Gln313His,ENST00000332129,NM_017596.3;KIF21B,missense_variant,p.Gln313His,ENST00000422435,NM_001252100.1;KIF21B,missense_variant,p.Gln313His,ENST00000461742,NM_001252102.1;KIF21B,missense_variant,p.Gln313His,ENST00000360529,NM_001252103.1;KIF21B,non_coding_transcript_exon_variant,,ENST00000534043,; A ENST00000422435 Transcript missense_variant 1256/5519 939/4914 313/1637 Q/H caG/caT 1 -1 KIF21B HGNC HGNC:29442 protein_coding YES CCDS58056.1 ENSP00000411831 O75037 UPI0000153E7C NM_001252100.1 deleterious(0.02) 7/35 PROSITE_profiles:PS50067,hmmpanther:PTHR24115:SF335,hmmpanther:PTHR24115,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 201004417 201004417 C A 1 0 0 0 0 1 0 0 0 8154 912 32 2 2 KIF21B 1 201004417 Missense_Mutation SNP C C3N-01030_T 10843729 201004417 47952005 68 20849 IGFN1 0 . GRCh38 1 201213081 201213081 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.8191delG p.Glu2731SerfsTer11 p.E2731Sfs*11 ENST00000335211 12/24 233 120 113 187 187 0 sindel-varindel-pindel IGFN1,frameshift_variant,p.Glu2731SerfsTer11,ENST00000335211,NM_001164586.1;IGFN1,frameshift_variant,p.Glu149SerfsTer11,ENST00000412892,;IGFN1,intron_variant,,ENST00000295591,;IGFN1,intron_variant,,ENST00000437879,;IGFN1,upstream_gene_variant,,ENST00000473483,; - ENST00000335211 Transcript frameshift_variant 8318/11810 8188/11127 2730/3708 G/X Ggg/gg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 12/24 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF630 HIGH 1 deletion 5 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 201213081 201213081 G - 1 0 1 0 1 0 0 0 0 7497 1348 47 0 0 IGFN1 1 201213081 Frame_Shift_Del DEL G C3N-01030_T 208664 201213081 47743341 69 20850 ZC3H11A 0 . GRCh38 1 203847456 203847456 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1315G>A p.Glu439Lys p.E439K ENST00000545588 12/17 477 421 56 399 399 0 strelka-varscan ZC3H11A,missense_variant,p.Glu439Lys,ENST00000545588,;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000332127,NM_001319239.1;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000367210,;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000367214,;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000367212,NM_014827.4;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000453771,;ZC3H11A,upstream_gene_variant,,ENST00000488411,;ZC3H11A,missense_variant,p.Glu439Lys,ENST00000495527,; A ENST00000545588 Transcript missense_variant 5142/7979 1315/2433 439/810 E/K Gaa/Aaa 1 1 ZC3H11A HGNC HGNC:29093 protein_coding YES CCDS30978.1 ENSP00000438527 O75152 UPI000006F3FD deleterious(0.01) 12/17 hmmpanther:PTHR15725,hmmpanther:PTHR15725:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 203847456 203847456 G A 1 0 0 0 0 1 0 0 0 18134 1291 45 3 3 ZC3H11A 1 203847456 Missense_Mutation SNP G C3N-01030_T 2634375 203847456 45108966 70 20851 LRRN2 0 . GRCh38 1 204619198 204619198 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.795C>G p.Phe265Leu p.F265L ENST00000367175 1/1 289 259 30 232 232 0 strelka-varscan LRRN2,missense_variant,p.Phe265Leu,ENST00000367175,;LRRN2,missense_variant,p.Phe265Leu,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Phe265Leu,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; C ENST00000367175 Transcript missense_variant 3008/5036 795/2142 265/713 F/L ttC/ttG 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC deleterious(0) 1/1 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF162,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 204619198 204619198 G C 1 0 0 0 0 1 0 0 0 8941 1165 41 4 4 LRRN2 1 204619198 Missense_Mutation SNP G C3N-01030_T 771742 204619198 44337224 71 20852 NFASC 0 . GRCh38 1 204954239 204954239 + Silent SNP G G T rs748244825 C3N-01030_T C3N-01030_N G G c.267G>T p.= p.R89R ENST00000339876 6/30 416 376 40 233 232 1 strelka-varscan NFASC,synonymous_variant,p.=,ENST00000339876,NM_001005388.2;NFASC,synonymous_variant,p.=,ENST00000401399,;NFASC,synonymous_variant,p.=,ENST00000539706,NM_001160332.1;NFASC,synonymous_variant,p.=,ENST00000360049,NM_015090.3;NFASC,synonymous_variant,p.=,ENST00000404076,;NFASC,synonymous_variant,p.=,ENST00000404907,;NFASC,synonymous_variant,p.=,ENST00000430393,NM_001160331.1;NFASC,synonymous_variant,p.=,ENST00000367173,;NFASC,synonymous_variant,p.=,ENST00000513543,;NFASC,synonymous_variant,p.=,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,synonymous_variant,p.=,ENST00000505079,;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,upstream_gene_variant,,ENST00000504149,;NFASC,synonymous_variant,p.=,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000514644,;NFASC,upstream_gene_variant,,ENST00000512826,; T ENST00000339876 Transcript synonymous_variant 595/10333 267/3723 89/1240 R cgG/cgT rs748244825 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 6/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 204954239 204954239 G T 1 0 0 0 0 0 0 0 1 10396 1219 43 2 2 NFASC 1 204954239 Silent SNP G C3N-01030_T 335041 204954239 44002183 72 20853 SLC45A3 0 . GRCh38 1 205661968 205661968 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1117C>T p.His373Tyr p.H373Y ENST00000367145 4/5 319 292 27 190 189 1 strelka-varscan SLC45A3,missense_variant,p.His373Tyr,ENST00000367145,NM_033102.2;SLC45A3,non_coding_transcript_exon_variant,,ENST00000460934,; A ENST00000367145 Transcript missense_variant 1413/3341 1117/1662 373/553 H/Y Cac/Tac 1 -1 SLC45A3 HGNC HGNC:8642 protein_coding YES CCDS1458.1 ENSP00000356113 Q96JT2 UPI0000039836 NM_033102.2 deleterious(0.01) 4/5 Gene3D:1.20.1250.20,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF37,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 205661968 205661968 G A 1 0 0 0 0 1 0 0 0 14919 1348 47 3 3 SLC45A3 1 205661968 Missense_Mutation SNP G C3N-01030_T 707729 205661968 43294454 73 20854 75 2 SLC45A3 0 . GRCh38 1 205661970 205661970 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1115C>T p.Ser372Phe p.S372F ENST00000367145 4/5 321 293 28 189 189 0 strelka-varscan SLC45A3,missense_variant,p.Ser372Phe,ENST00000367145,NM_033102.2;SLC45A3,non_coding_transcript_exon_variant,,ENST00000460934,; A ENST00000367145 Transcript missense_variant 1411/3341 1115/1662 372/553 S/F tCc/tTc 1 -1 SLC45A3 HGNC HGNC:8642 protein_coding YES CCDS1458.1 ENSP00000356113 Q96JT2 UPI0000039836 NM_033102.2 deleterious(0.04) 4/5 Gene3D:1.20.1250.20,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF37,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 205661970 205661970 G A 1 0 0 0 0 1 0 0 0 14919 1174 41 3 3 SLC45A3 1 205661970 Missense_Mutation SNP G C3N-01030_T 2 205661970 43294452 74 20855 75 2 PLXNA2 0 . GRCh38 1 208096063 208096063 + Nonsense_Mutation SNP C C A rs866521000 C3N-01030_T C3N-01030_N C C c.1948G>T p.Glu650Ter p.E650* ENST00000367033 8/32 267 145 122 208 208 0 strelka-varscan PLXNA2,stop_gained,p.Glu650Ter,ENST00000367033,NM_025179.3; A ENST00000367033 Transcript stop_gained 2706/11444 1948/5685 650/1894 E/* Gag/Tag rs866521000 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 8/32 hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 208096063 208096063 C A 1 0 0 0 0 0 1 0 0 12226 893 31 1 1 PLXNA2 1 208096063 Nonsense_Mutation SNP C C3N-01030_T 2434093 208096063 40860359 75 20856 LAMB3 0 . GRCh38 1 209625992 209625992 + Silent SNP C C A rs753960912 C3N-01030_T C3N-01030_N C C c.1632G>T p.= p.P544P ENST00000391911 13/22 138 59 79 97 97 0 strelka-varscan LAMB3,synonymous_variant,p.=,ENST00000391911,NM_001017402.1;LAMB3,synonymous_variant,p.=,ENST00000356082,NM_000228.2;LAMB3,synonymous_variant,p.=,ENST00000367030,NM_001127641.1;LAMB3,upstream_gene_variant,,ENST00000583107,; A ENST00000391911 Transcript synonymous_variant 2022/4305 1632/3519 544/1172 P ccG/ccT rs753960912 1 -1 LAMB3 HGNC HGNC:6490 protein_coding YES CCDS1487.1 ENSP00000375778 Q13751 A0A0S2Z3R6 UPI000012E76F NM_001017402.1 13/22 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF268,hmmpanther:PTHR10574,Pfam_domain:PF00053,Gene3D:2.10.25.10,SMART_domains:SM00180,Superfamily_domains:SSF57196,Prints_domain:PR00011 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 209625992 209625992 C A 1 0 0 0 0 0 0 0 1 8516 639 23 1 1 LAMB3 1 209625992 Silent SNP C C3N-01030_T 1529929 209625992 39330430 76 20857 FAM71A 0 . GRCh38 1 212625202 212625202 + Missense_Mutation SNP A A C novel C3N-01030_T C3N-01030_N A A c.325A>C p.Lys109Gln p.K109Q ENST00000294829 1/1 289 272 17 183 183 0 strelka-varscan FAM71A,missense_variant,p.Lys109Gln,ENST00000294829,NM_153606.3;ATF3,downstream_gene_variant,,ENST00000341491,NM_001674.3;ATF3,downstream_gene_variant,,ENST00000613954,NM_001206488.2,NM_001206484.2;ATF3,downstream_gene_variant,,ENST00000366987,NM_001030287.3;RP11-338C15.5,intron_variant,,ENST00000427949,;ATF3,downstream_gene_variant,,ENST00000492118,; C ENST00000294829 Transcript missense_variant 729/2305 325/1785 109/594 K/Q Aaa/Caa 1 1 FAM71A HGNC HGNC:26541 protein_coding YES CCDS1507.1 ENSP00000294829 Q8IYT1 UPI000013E1C2 NM_153606.3 deleterious(0.03) 1/1 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF9,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 212625202 212625202 A C 1 0 0 0 0 1 0 0 0 5471 15 1 5 5 FAM71A 1 212625202 Missense_Mutation SNP A C3N-01030_T 2999210 212625202 36331220 77 20858 USH2A 0 . GRCh38 1 215628964 215628964 + Silent SNP G G T rs142939648 C3N-01030_T C3N-01030_N G G c.15369C>A p.= p.V5123V ENST00000307340 71/72 327 164 163 251 251 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;SNORD116,downstream_gene_variant,,ENST00000365628,; T ENST00000307340 Transcript synonymous_variant 15756/18883 15369/15609 5123/5202 V gtC/gtA rs142939648 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 71/72 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 215628964 215628964 G T 1 0 0 0 0 0 0 0 1 17570 1161 41 2 2 USH2A 1 215628964 Silent SNP G C3N-01030_T 3003762 215628964 33327458 78 20859 USH2A 0 . GRCh38 1 215728055 215728055 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.12041C>A p.Pro4014His p.P4014H ENST00000307340 61/72 326 301 25 250 250 0 strelka-varscan USH2A,missense_variant,p.Pro4014His,ENST00000307340,NM_206933.2; T ENST00000307340 Transcript missense_variant 12428/18883 12041/15609 4014/5202 P/H cCt/cAt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.17) 61/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 215728055 215728055 G T 1 0 0 0 0 1 0 0 0 17570 1000 35 2 2 USH2A 1 215728055 Missense_Mutation SNP G C3N-01030_T 99091 215728055 33228367 79 20860 GPATCH2 0 . GRCh38 1 217611006 217611006 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.901G>T p.Val301Phe p.V301F ENST00000366935 4/10 190 111 79 178 178 0 strelka-varscan GPATCH2,missense_variant,p.Val301Phe,ENST00000366935,NM_018040.3;GPATCH2,missense_variant,p.Val301Phe,ENST00000366934,NM_001297754.1;GPATCH2,upstream_gene_variant,,ENST00000470014,;GPATCH2,upstream_gene_variant,,ENST00000485274,; A ENST00000366935 Transcript missense_variant 1012/5851 901/1587 301/528 V/F Gtt/Ttt 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 tolerated(0.08) 4/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 217611006 217611006 C A 1 0 0 0 0 1 0 0 0 6491 565 20 2 2 GPATCH2 1 217611006 Missense_Mutation SNP C C3N-01030_T 1882951 217611006 31345416 80 20861 GPATCH2 0 . GRCh38 1 217614187 217614187 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.789C>T p.= p.L263L ENST00000366935 3/10 111 99 12 97 97 0 strelka-varscan GPATCH2,synonymous_variant,p.=,ENST00000366935,NM_018040.3;GPATCH2,synonymous_variant,p.=,ENST00000366934,NM_001297754.1;GPATCH2,upstream_gene_variant,,ENST00000470014,;GPATCH2,upstream_gene_variant,,ENST00000485274,; A ENST00000366935 Transcript synonymous_variant 900/5851 789/1587 263/528 L ctC/ctT 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 3/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -19.99997 1 1 1 1 0 A 2 1 70 217614187 217614187 G A 1 0 0 0 0 0 0 0 1 6491 1277 45 3 3 GPATCH2 1 217614187 Silent SNP G C3N-01030_T 3181 217614187 31342235 81 20862 SPATA17 0 . GRCh38 1 217683283 217683283 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.317G>T p.Arg106Met p.R106M ENST00000366933 5/11 140 81 59 162 162 0 strelka-varscan SPATA17,missense_variant,p.Arg106Met,ENST00000366933,NM_138796.3;SPATA17,3_prime_UTR_variant,,ENST00000470448,; T ENST00000366933 Transcript missense_variant 372/5818 317/1086 106/361 R/M aGg/aTg 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 tolerated(0.1) 5/11 Pfam_domain:PF00612,PROSITE_profiles:PS50096,hmmpanther:PTHR22706,SMART_domains:SM00015,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 217683283 217683283 G T 1 0 0 0 0 1 0 0 0 15332 1000 35 2 2 SPATA17 1 217683283 Missense_Mutation SNP G C3N-01030_T 69096 217683283 31273139 82 20863 EPRS 0 . GRCh38 1 219997046 219997046 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.2478G>T p.= p.L826L ENST00000366923 18/32 114 96 18 136 136 0 strelka-varscan EPRS,synonymous_variant,p.=,ENST00000366923,NM_004446.2;EPRS,synonymous_variant,p.=,ENST00000609181,;EPRS,downstream_gene_variant,,ENST00000477030,;EPRS,downstream_gene_variant,,ENST00000464052,; A ENST00000366923 Transcript synonymous_variant 2748/5014 2478/4539 826/1512 L ctG/ctT 1 -1 EPRS HGNC HGNC:3418 protein_coding YES CCDS31027.1 ENSP00000355890 P07814 UPI0000205E8C NM_004446.2 18/32 Gene3D:1.10.287.10,Pfam_domain:PF00458,PROSITE_profiles:PS51185,SMART_domains:SM00991,Superfamily_domains:SSF47060 LOW 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9999232 1 1 1 0 A 2 1 70 219997046 219997046 C A 1 0 0 0 0 0 0 0 1 5039 465 17 2 2 EPRS 1 219997046 Silent SNP C C3N-01030_T 2313763 219997046 28959376 83 20864 MARK1 0 . GRCh38 1 220661907 220661907 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2132G>T p.Ser711Ile p.S711I ENST00000611084 18/18 198 182 16 214 214 0 strelka-varscan MARK1,missense_variant,p.Ser711Ile,ENST00000611084,NM_001286124.1;MARK1,missense_variant,p.Ser695Ile,ENST00000402574,NM_001286126.1;MARK1,missense_variant,p.Ser673Ile,ENST00000366918,NM_001286128.1;MARK1,missense_variant,p.Ser710Ile,ENST00000366917,NM_018650.4; T ENST00000611084 Transcript missense_variant 2772/5321 2132/2391 711/796 S/I aGt/aTt 1 1 MARK1 HGNC HGNC:6896 protein_coding YES CCDS73033.1 ENSP00000483424 A0A087X0I6 UPI0000E592B1 NM_001286124.1 deleterious(0) 18/18 hmmpanther:PTHR24346,hmmpanther:PTHR24346:SF21,Gene3D:3.30.310.80,Superfamily_domains:SSF103243 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 220661907 220661907 G T 1 0 0 0 0 1 0 0 0 9237 1029 36 2 2 MARK1 1 220661907 Missense_Mutation SNP G C3N-01030_T 664861 220661907 28294515 84 20865 CNIH3 0 . GRCh38 1 224730542 224730542 + Silent SNP G G C C3N-01030_T C3N-01030_N G G c.279G>C p.= p.L93L ENST00000272133 4/6 190 164 26 116 116 0 strelka-varscan CNIH3,synonymous_variant,p.=,ENST00000272133,NM_152495.1;RP11-3L21.2,non_coding_transcript_exon_variant,,ENST00000431691,;CNIH3,non_coding_transcript_exon_variant,,ENST00000498382,;CNIH3,non_coding_transcript_exon_variant,,ENST00000478120,;CNIH3,non_coding_transcript_exon_variant,,ENST00000481095,; C ENST00000272133 Transcript synonymous_variant 1161/2558 279/483 93/160 L ctG/ctC COSM4846406 1 1 CNIH3 HGNC HGNC:26802 protein_coding YES CCDS1544.1 ENSP00000272133 Q8TBE1 UPI0000003FD7 NM_152495.1 4/6 Pfam_domain:PF03311,hmmpanther:PTHR12290,hmmpanther:PTHR12290:SF12,SMART_domains:SM01398,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 224730542 224730542 G C 1 0 0 0 0 0 0 0 1 3384 1277 45 4 4 CNIH3 1 224730542 Silent SNP G C3N-01030_T 4068635 224730542 24225880 85 20866 ENAH 0 . GRCh38 1 225505019 225505019 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1573G>A p.Asp525Asn p.D525N ENST00000366844 12/15 123 85 38 151 151 0 strelka-varscan ENAH,missense_variant,p.Asp525Asn,ENST00000366844,NM_001008493.1;ENAH,intron_variant,,ENST00000635051,;ENAH,intron_variant,,ENST00000366843,NM_018212.4;ENAH,intron_variant,,ENST00000483952,;ENAH,non_coding_transcript_exon_variant,,ENST00000358675,;ENAH,upstream_gene_variant,,ENST00000498108,; T ENST00000366844 Transcript missense_variant 2025/13168 1573/1776 525/591 D/N Gac/Aac 1 -1 ENAH HGNC HGNC:18271 protein_coding YES CCDS31041.1 ENSP00000355809 Q8N8S7 UPI0000203FDB NM_001008493.1 tolerated_low_confidence(0.11) 12/15 hmmpanther:PTHR11202:SF1,hmmpanther:PTHR11202 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 70 225505019 225505019 C T 1 0 0 0 0 1 0 0 0 4953 826 29 3 3 ENAH 1 225505019 Missense_Mutation SNP C C3N-01030_T 774477 225505019 23451403 86 20867 WNT9A 0 . GRCh38 1 227921926 227921926 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.690G>T p.Trp230Cys p.W230C ENST00000272164 4/4 201 179 22 145 145 0 strelka-varscan WNT9A,missense_variant,p.Trp230Cys,ENST00000272164,NM_003395.2; A ENST00000272164 Transcript missense_variant 701/3971 690/1098 230/365 W/C tgG/tgT 1 -1 WNT9A HGNC HGNC:12778 protein_coding YES CCDS31045.1 ENSP00000272164 O14904 D9ZGG3 UPI000005104B NM_003395.2 deleterious(0) 4/4 Pfam_domain:PF00110,Prints_domain:PR01349,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF75,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 227921926 227921926 C A 1 0 0 0 0 1 0 0 0 17954 740 26 2 2 WNT9A 1 227921926 Missense_Mutation SNP C C3N-01030_T 2416907 227921926 21034496 87 20868 OBSCN 0 . GRCh38 1 228276009 228276009 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.7328C>A p.Ala2443Asp p.A2443D ENST00000570156 25/116 123 109 14 78 78 0 strelka-varscan OBSCN,missense_variant,p.Ala2443Asp,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Ala2443Asp,ENST00000366707,;OBSCN,missense_variant,p.Ala2068Asp,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Ala2068Asp,ENST00000636875,;OBSCN,missense_variant,p.Ala2068Asp,ENST00000284548,NM_052843.3;OBSCN,upstream_gene_variant,,ENST00000483539,;OBSCN,upstream_gene_variant,,ENST00000366706,;RP5-1139B12.3,non_coding_transcript_exon_variant,,ENST00000602529,;RP5-1139B12.3,non_coding_transcript_exon_variant,,ENST00000602947,;RP5-1139B12.2,upstream_gene_variant,,ENST00000602517,;OBSCN,upstream_gene_variant,,ENST00000366704,; A ENST00000570156 Transcript missense_variant 7402/26925 7328/26772 2443/8923 A/D gCc/gAc 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.07) 25/116 PROSITE_profiles:PS50835,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 228276009 228276009 C A 1 0 0 0 0 1 0 0 0 10889 739 26 2 2 OBSCN 1 228276009 Missense_Mutation SNP C C3N-01030_T 354083 228276009 20680413 88 20869 OBSCN 0 . GRCh38 1 228294879 228294879 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.12782A>G p.Glu4261Gly p.E4261G ENST00000570156 48/116 372 332 40 274 274 0 strelka-varscan OBSCN,missense_variant,p.Glu4261Gly,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Glu4261Gly,ENST00000366707,;OBSCN,missense_variant,p.Glu3832Gly,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Glu3832Gly,ENST00000636875,;OBSCN,missense_variant,p.Glu3832Gly,ENST00000284548,NM_052843.3;OBSCN,missense_variant,p.Glu1108Gly,ENST00000483539,;RP5-1139B12.4,downstream_gene_variant,,ENST00000602778,;OBSCN,upstream_gene_variant,,ENST00000602685,;OBSCN,non_coding_transcript_exon_variant,,ENST00000494839,; G ENST00000570156 Transcript missense_variant 12856/26925 12782/26772 4261/8923 E/G gAg/gGg 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 48/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF708,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 228294879 228294879 A G 1 0 0 0 0 1 0 0 0 10889 304 11 5 5 OBSCN 1 228294879 Missense_Mutation SNP A C3N-01030_T 18870 228294879 20661543 89 20870 TRIM17 0 . GRCh38 1 228414960 228414960 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.113C>A p.Ala38Asp p.A38D ENST00000366697 1/6 207 109 98 152 152 0 strelka-varscan TRIM17,missense_variant,p.Ala38Asp,ENST00000366697,;TRIM17,missense_variant,p.Ala38Asp,ENST00000366698,NM_016102.3;TRIM17,missense_variant,p.Ala38Asp,ENST00000456946,NM_001134855.1;TRIM17,missense_variant,p.Ala38Asp,ENST00000295033,NM_001024940.2;TRIM17,missense_variant,p.Ala11Asp,ENST00000479800,;TRIM17,missense_variant,p.Ala38Asp,ENST00000355586,;TRIM17,missense_variant,p.Ala11Asp,ENST00000457345,;TRIM17,missense_variant,p.Ala38Asp,ENST00000520264,; T ENST00000366697 Transcript missense_variant 1070/2652 113/1434 38/477 A/D gCc/gAc COSM1997165,COSM1997166 1 -1 TRIM17 HGNC HGNC:13430 protein_coding YES CCDS1571.1 ENSP00000355658 Q9Y577 A0A024R3T1 UPI000000163B tolerated(0.26) 1/6 Gene3D:3.30.40.10,Pfam_domain:PF15227,PROSITE_patterns:PS00518,PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF397,SMART_domains:SM00184,Superfamily_domains:SSF57850 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 228414960 228414960 G T 1 0 0 0 0 1 0 0 0 16982 1203 42 2 2 TRIM17 1 228414960 Missense_Mutation SNP G C3N-01030_T 120081 228414960 20541462 90 20871 AGT 0 . GRCh38 1 230710425 230710425 + Silent SNP G G C novel C3N-01030_T C3N-01030_N G G c.426C>G p.= p.T142T ENST00000366667 2/5 880 779 101 542 542 0 strelka-varscan AGT,synonymous_variant,p.=,ENST00000366667,NM_000029.3;RP11-99J16__A.2,downstream_gene_variant,,ENST00000412344,; C ENST00000366667 Transcript synonymous_variant 641/2291 426/1458 142/485 T acC/acG 1 -1 AGT HGNC HGNC:333 protein_coding YES CCDS1585.1 ENSP00000355627 P01019 B0ZBE2 UPI0000125B13 NM_000029.3 2/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF13,Pfam_domain:PF00079,Gene3D:3.30.497.10,SMART_domains:SM00093,Superfamily_domains:SSF56574,Prints_domain:PR00654 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 230710425 230710425 G C 1 0 0 0 0 0 0 0 1 478 1219 43 4 4 AGT 1 230710425 Silent SNP G C3N-01030_T 2295465 230710425 18245997 91 20872 C1orf198 0 . GRCh38 1 230868289 230868289 + Missense_Mutation SNP A A C novel C3N-01030_T C3N-01030_N A A c.224T>G p.Val75Gly p.V75G ENST00000366663 1/4 117 56 61 85 85 0 strelka-varscan C1orf198,missense_variant,p.Val75Gly,ENST00000366663,NM_032800.2;C1orf198,missense_variant,p.Val37Gly,ENST00000470540,NM_001136494.1;C1orf198,missense_variant,p.Val32Gly,ENST00000522201,;C1orf198,intron_variant,,ENST00000427697,;C1orf198,downstream_gene_variant,,ENST00000521263,; C ENST00000366663 Transcript missense_variant 365/3858 224/984 75/327 V/G gTg/gGg 1 -1 C1orf198 HGNC HGNC:25900 protein_coding YES CCDS1587.1 ENSP00000355623 Q9H425 A0A024R3S1 UPI000006F49A NM_032800.2 tolerated(0.06) 1/4 Pfam_domain:PF15797,hmmpanther:PTHR34394 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 230868289 230868289 A C 1 0 0 0 0 1 0 0 0 1979 159 6 5 5 C1orf198 1 230868289 Missense_Mutation SNP A C3N-01030_T 157864 230868289 18088133 92 20873 RYR2 0 . GRCh38 1 237589930 237589930 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.3736G>T p.Asp1246Tyr p.D1246Y ENST00000366574 30/105 312 188 124 293 293 0 strelka-varscan RYR2,missense_variant,p.Asp1246Tyr,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp1230Tyr,ENST00000360064,; T ENST00000366574 Transcript missense_variant 4053/16562 3736/14904 1246/4967 D/Y Gat/Tat 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 30/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 237589930 237589930 G T 1 0 0 0 0 1 0 0 0 14029 1174 41 2 2 RYR2 1 237589930 Missense_Mutation SNP G C3N-01030_T 6721641 237589930 11366492 93 20874 RYR2 0 . GRCh38 1 237654303 237654303 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.7854G>C p.Trp2618Cys p.W2618C ENST00000366574 52/105 201 107 94 153 153 0 strelka-varscan RYR2,missense_variant,p.Trp2618Cys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Trp2602Cys,ENST00000360064,; C ENST00000366574 Transcript missense_variant 8171/16562 7854/14904 2618/4967 W/C tgG/tgC COSM4608262,COSM4608263 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.02) 52/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 237654303 237654303 G C 1 0 0 0 0 1 0 0 0 14029 1183 41 4 4 RYR2 1 237654303 Missense_Mutation SNP G C3N-01030_T 64373 237654303 11302119 94 20875 KMO 0 . GRCh38 1 241568618 241568618 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.928G>T p.Val310Leu p.V310L ENST00000366559 10/15 201 185 16 141 141 0 strelka-varscan KMO,missense_variant,p.Val310Leu,ENST00000366559,NM_003679.4;KMO,missense_variant,p.Val310Leu,ENST00000366557,;KMO,missense_variant,p.Val310Leu,ENST00000366558,;KMO,upstream_gene_variant,,ENST00000366555,;KMO,non_coding_transcript_exon_variant,,ENST00000431245,;KMO,downstream_gene_variant,,ENST00000477907,; T ENST00000366559 Transcript missense_variant 1239/5261 928/1461 310/486 V/L Gtg/Ttg 1 1 KMO HGNC HGNC:6381 protein_coding YES CCDS1618.1 ENSP00000355517 O15229 UPI000045632A NM_003679.4 deleterious(0) 10/15 Gene3D:3.50.50.60,HAMAP:MF_01971,Pfam_domain:PF01494,Prints_domain:PR00420,hmmpanther:PTHR13789,hmmpanther:PTHR13789:SF205,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 241568618 241568618 G T 1 0 0 0 0 1 0 0 0 8294 1029 36 2 2 KMO 1 241568618 Missense_Mutation SNP G C3N-01030_T 3914315 241568618 7387804 95 20876 OR14K1 0 . GRCh38 1 247738939 247738939 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.325G>T p.Glu109Ter p.E109* ENST00000283225 1/1 465 429 36 343 343 0 strelka-varscan OR14K1,stop_gained,p.Glu109Ter,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; T ENST00000283225 Transcript stop_gained 325/945 325/945 109/314 E/* Gag/Tag 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 247738939 247738939 G T 1 0 0 0 0 0 1 0 0 11026 943 33 2 2 OR14K1 1 247738939 Nonsense_Mutation SNP G C3N-01030_T 6170321 247738939 1217483 96 20877 TRIM58 0 . GRCh38 1 247867860 247867860 + Silent SNP C C T C3N-01030_T C3N-01030_N C C c.763C>T p.= p.L255L ENST00000366481 4/6 334 313 21 230 230 0 strelka-varscan TRIM58,synonymous_variant,p.=,ENST00000366481,NM_015431.3; T ENST00000366481 Transcript synonymous_variant 811/3225 763/1461 255/486 L Ctg/Ttg COSM5271583 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 4/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 247867860 247867860 C T 1 0 0 0 0 0 0 0 1 17024 680 24 3 3 TRIM58 1 247867860 Silent SNP C C3N-01030_T 128921 247867860 1088562 97 20878 OR2T8 0 . GRCh38 1 247921126 247921126 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.109C>A p.Leu37Met p.L37M ENST00000319968 1/1 90 56 34 67 67 0 strelka-varscan OR2T8,missense_variant,p.Leu37Met,ENST00000319968,NM_001005522.1; A ENST00000319968 Transcript missense_variant 109/939 109/939 37/312 L/M Ctg/Atg COSM363138 1 1 OR2T8 HGNC HGNC:15020 protein_coding YES CCDS31100.1 ENSP00000326225 A6NH00 UPI00001999E3 NM_001005522.1 tolerated(0.06) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 247921126 247921126 C A 1 0 0 0 0 1 0 0 0 11107 680 24 2 2 OR2T8 1 247921126 Missense_Mutation SNP C C3N-01030_T 53266 247921126 1035296 98 20879 SH3BP5L 0 . GRCh38 1 248814584 248814584 + Silent SNP C C A rs756594510 C3N-01030_T C3N-01030_N C C c.402G>T p.= p.A134A ENST00000366472 5/7 298 142 156 166 166 0 strelka-varscan SH3BP5L,synonymous_variant,p.=,ENST00000366472,NM_030645.1;SH3BP5L,non_coding_transcript_exon_variant,,ENST00000475978,;SH3BP5L,upstream_gene_variant,,ENST00000484202,;SH3BP5L,downstream_gene_variant,,ENST00000494837,; A ENST00000366472 Transcript synonymous_variant 1632/3861 402/1182 134/393 A gcG/gcT rs756594510,COSM4030811,COSM4030812 1 -1 SH3BP5L HGNC HGNC:29360 protein_coding YES CCDS31126.1 ENSP00000355428 Q7L8J4 A0A024R0T2 UPI000003F53A NM_030645.1 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR19423,hmmpanther:PTHR19423:SF8,Pfam_domain:PF05276 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 248814584 248814584 C A 1 0 0 0 0 0 0 0 1 14506 755 27 1 1 SH3BP5L 1 248814584 Silent SNP C C3N-01030_T 893458 248814584 141838 99 20880 GREB1 0 . GRCh38 2 11625254 11625254 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.4248C>A p.Asp1416Glu p.D1416E ENST00000381486 24/33 221 163 58 228 228 0 strelka-varscan-mutect GREB1,missense_variant,p.Asp1416Glu,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Asp1416Glu,ENST00000234142,;GREB1,missense_variant,p.Asp414Glu,ENST00000396123,; A ENST00000381486 Transcript missense_variant 4548/8484 4248/5850 1416/1949 D/E gaC/gaA 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 tolerated(0.06) 24/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS rs992519368 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 11625254 11625254 C A 1 0 0 0 0 1 0 0 0 6639 506 18 2 2 GREB1 2 11625254 Missense_Mutation SNP C C3N-01030_T 11625254 230568275 100 20881 APOB 0 . GRCh38 2 21005708 21005708 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.11160C>A p.= p.S3720S ENST00000233242 26/29 192 151 41 218 218 0 strelka-varscan APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; T ENST00000233242 Transcript synonymous_variant 11288/14121 11160/13692 3720/4563 S tcC/tcA 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 21005708 21005708 G T 1 0 0 0 0 0 0 0 1 907 1335 47 2 2 APOB 2 21005708 Silent SNP G C3N-01030_T 9380454 21005708 221187821 101 20882 APOB 0 . GRCh38 2 21009203 21009203 + Silent SNP A A T rs774919897 C3N-01030_T C3N-01030_N A A c.7665T>A p.= p.T2555T ENST00000233242 26/29 299 226 73 297 296 1 strelka-varscan APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript synonymous_variant 7793/14121 7665/13692 2555/4563 T acT/acA rs774919897 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 21009203 21009203 A T 1 0 0 0 0 0 0 0 1 907 291 11 4 4 APOB 2 21009203 Silent SNP A C3N-01030_T 3495 21009203 221184326 102 20883 ATAD2B 0 . GRCh38 2 23823354 23823354 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.2035A>T p.Ile679Leu p.I679L ENST00000238789 16/28 335 251 84 302 302 0 strelka-varscan ATAD2B,missense_variant,p.Ile679Leu,ENST00000238789,NM_017552.3,NM_001242338.2;ATAD2B,upstream_gene_variant,,ENST00000381024,;ATAD2B,downstream_gene_variant,,ENST00000458510,;ATAD2B,non_coding_transcript_exon_variant,,ENST00000474583,; A ENST00000238789 Transcript missense_variant 2379/8103 2035/4377 679/1458 I/L Ata/Tta 1 -1 ATAD2B HGNC HGNC:29230 protein_coding YES CCDS46227.1 ENSP00000238789 Q9ULI0 UPI00006C056C NM_017552.3,NM_001242338.2 tolerated(0.43) 16/28 hmmpanther:PTHR23069:SF5,hmmpanther:PTHR23069 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 23823354 23823354 T A 1 0 0 0 0 1 0 0 0 1220 1464 51 4 4 ATAD2B 2 23823354 Missense_Mutation SNP T C3N-01030_T 2814151 23823354 218370175 103 20884 EMILIN1 0 . GRCh38 2 27080946 27080946 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.505G>T p.Gly169Ter p.G169* ENST00000380320 3/8 73 54 19 51 51 0 strelka-varscan EMILIN1,stop_gained,p.Gly169Ter,ENST00000380320,NM_007046.3;EMILIN1,upstream_gene_variant,,ENST00000433140,; T ENST00000380320 Transcript stop_gained 1004/3943 505/3051 169/1016 G/* Gga/Tga 1 1 EMILIN1 HGNC HGNC:19880 protein_coding YES CCDS1733.1 ENSP00000369677 A0A0C4DFX3 UPI0000073B0E NM_007046.3 3/8 Low_complexity_(Seg):seg,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF1 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 27080946 27080946 G T 1 0 0 0 0 0 1 0 0 4936 1233 43 2 2 EMILIN1 2 27080946 Nonsense_Mutation SNP G C3N-01030_T 3257592 27080946 215112583 104 20885 C2orf71 0 . GRCh38 2 29071110 29071110 + Missense_Mutation SNP G G A rs543584326 C3N-01030_T C3N-01030_N G G c.3152C>T p.Pro1051Leu p.P1051L ENST00000331664 1/2 62 50 12 77 77 0 strelka-varscan C2orf71,missense_variant,p.Pro1051Leu,ENST00000331664,NM_001029883.2; A ENST00000331664 Transcript missense_variant 3152/7044 3152/3867 1051/1288 P/L cCg/cTg rs543584326,COSM1198731 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.18) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 70 29071110 29071110 G A 1 0 0 0 0 1 0 0 0 2045 1116 39 1 1 C2orf71 2 29071110 Missense_Mutation SNP G C3N-01030_T 1990164 29071110 213122419 105 20886 HEATR5B 0 . GRCh38 2 37070235 37070235 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.922A>T p.Thr308Ser p.T308S ENST00000233099 7/36 105 82 23 92 92 0 strelka-varscan HEATR5B,missense_variant,p.Thr308Ser,ENST00000233099,NM_019024.2;HEATR5B,downstream_gene_variant,,ENST00000478810,; A ENST00000233099 Transcript missense_variant 1018/6905 922/6216 308/2071 T/S Acg/Tcg 1 -1 HEATR5B HGNC HGNC:29273 protein_coding YES CCDS33181.1 ENSP00000233099 Q9P2D3 UPI0000160DCD NM_019024.2 tolerated(0.06) 7/36 Gene3D:1.25.10.10,hmmpanther:PTHR21663,hmmpanther:PTHR21663:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 37070235 37070235 T A 1 0 0 0 0 1 0 0 0 6914 1652 57 4 4 HEATR5B 2 37070235 Missense_Mutation SNP T C3N-01030_T 7999125 37070235 205123294 106 20887 MAP4K3 0 . GRCh38 2 39272283 39272283 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.1973G>T p.Arg658Met p.R658M ENST00000263881 26/34 107 74 33 144 144 0 strelka-varscan MAP4K3,missense_variant,p.Arg658Met,ENST00000263881,NM_003618.3;MAP4K3,missense_variant,p.Arg637Met,ENST00000341681,NM_001270425.1;MAP4K3,missense_variant,p.Arg574Met,ENST00000437545,;MAP4K3,non_coding_transcript_exon_variant,,ENST00000495648,;MAP4K3,upstream_gene_variant,,ENST00000475457,; A ENST00000263881 Transcript missense_variant,splice_region_variant 2298/4362 1973/2685 658/894 R/M aGg/aTg COSM3581531 1 -1 MAP4K3 HGNC HGNC:6865 protein_coding YES CCDS1803.1 ENSP00000263881 Q8IVH8 UPI00000747E6 NM_003618.3 deleterious(0) 26/34 PROSITE_profiles:PS50219,PIRSF_domain:PIRSF038172,Pfam_domain:PF00780,SMART_domains:SM00036 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 39272283 39272283 C A 1 0 0 0 0 1 0 0 0 9185 695 24 2 2 MAP4K3 2 39272283 Missense_Mutation SNP C C3N-01030_T 2202048 39272283 202921246 107 20888 NRXN1 0 . GRCh38 2 50236835 50236835 + Missense_Mutation SNP C C A rs753212939 C3N-01030_T C3N-01030_N C C c.3620G>T p.Arg1207Leu p.R1207L ENST00000404971 19/24 379 283 96 345 344 1 strelka-varscan NRXN1,missense_variant,p.Arg1167Leu,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Arg1159Leu,ENST00000625672,;NRXN1,missense_variant,p.Arg1207Leu,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Arg1167Leu,ENST00000401669,;NRXN1,missense_variant,p.Arg1155Leu,ENST00000405472,;NRXN1,missense_variant,p.Arg1159Leu,ENST00000630543,;NRXN1,missense_variant,p.Arg132Leu,ENST00000342183,NM_138735.2;NRXN1,missense_variant,p.Arg132Leu,ENST00000401710,;NRXN1,missense_variant,p.Arg132Leu,ENST00000628364,;NRXN1,missense_variant,p.Arg210Leu,ENST00000625320,;NRXN1,5_prime_UTR_variant,,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636736,;NRXN1,downstream_gene_variant,,ENST00000636818,;NRXN1,missense_variant,p.Arg885Leu,ENST00000331040,;NRXN1,missense_variant,p.Arg93Leu,ENST00000637906,; A ENST00000404971 Transcript missense_variant 4960/7578 3620/4644 1207/1547 R/L cGa/cTa rs753212939,COSM1142629,COSM1217867,COSM1217868,COSM1217869,COSM1217870,COSM5234606,COSM575416,COSM575417,COSM575418 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.03) 19/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 0,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 50236835 50236835 C A 1 0 0 0 0 1 0 0 0 10724 884 31 1 1 NRXN1 2 50236835 Missense_Mutation SNP C C3N-01030_T 10964552 50236835 191956694 108 20889 SPTBN1 0 . GRCh38 2 54618084 54618084 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.654C>T p.= p.D218D ENST00000356805 7/36 72 53 19 57 57 0 strelka-varscan SPTBN1,synonymous_variant,p.=,ENST00000615901,;SPTBN1,synonymous_variant,p.=,ENST00000333896,NM_178313.2;SPTBN1,synonymous_variant,p.=,ENST00000356805,NM_003128.2;SPTBN1,synonymous_variant,p.=,ENST00000389980,; T ENST00000356805 Transcript synonymous_variant 935/8482 654/7095 218/2364 D gaC/gaT 1 1 SPTBN1 HGNC HGNC:11275 protein_coding YES CCDS33198.1 ENSP00000349259 Q01082 B2ZZ89 UPI0000DBEE4B NM_003128.2 7/36 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF325,PIRSF_domain:PIRSF002297,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 54618084 54618084 C T 1 0 0 0 0 0 0 0 1 15475 506 18 3 3 SPTBN1 2 54618084 Silent SNP C C3N-01030_T 4381249 54618084 187575445 109 20890 ARHGAP25 0 . GRCh38 2 68807403 68807403 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.597C>A p.Phe199Leu p.F199L ENST00000409202 5/11 344 262 82 276 275 1 strelka-varscan ARHGAP25,missense_variant,p.Phe199Leu,ENST00000409202,NM_001007231.2;ARHGAP25,missense_variant,p.Phe192Leu,ENST00000409220,NM_001166276.1;ARHGAP25,missense_variant,p.Phe191Leu,ENST00000409030,NM_014882.2;ARHGAP25,missense_variant,p.Phe159Leu,ENST00000467265,NM_001166277.1;ARHGAP25,missense_variant,p.Phe58Leu,ENST00000497259,;ARHGAP25,missense_variant,p.Phe192Leu,ENST00000497079,;ARHGAP25,non_coding_transcript_exon_variant,,ENST00000456116,;ARHGAP25,non_coding_transcript_exon_variant,,ENST00000485700,;ARHGAP25,missense_variant,p.Phe173Leu,ENST00000463483,;ARHGAP25,missense_variant,p.Ser131Tyr,ENST00000488795,;ARHGAP25,3_prime_UTR_variant,,ENST00000473986,; A ENST00000409202 Transcript missense_variant 962/2945 597/1941 199/646 F/L ttC/ttA 1 1 ARHGAP25 HGNC HGNC:28951 protein_coding YES CCDS33214.2 ENSP00000386911 P42331 UPI0000251EDD NM_001007231.2 deleterious(0) 5/11 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF20,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 68807403 68807403 C A 1 0 0 0 0 1 0 0 0 999 854 30 2 2 ARHGAP25 2 68807403 Missense_Mutation SNP C C3N-01030_T 14189319 68807403 173386126 110 20891 CLEC4F 0 . GRCh38 2 70809282 70809282 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.1759C>G p.Leu587Val p.L587V ENST00000272367 7/7 138 104 34 127 127 0 strelka-varscan CLEC4F,missense_variant,p.Leu587Val,ENST00000272367,NM_001258027.1,NM_173535.2;CLEC4F,intron_variant,,ENST00000426626,;AC007395.4,downstream_gene_variant,,ENST00000451333,; C ENST00000272367 Transcript missense_variant 1836/2475 1759/1770 587/589 L/V Ctc/Gtc COSM5183316 1 -1 CLEC4F HGNC HGNC:25357 protein_coding YES CCDS1910.1 ENSP00000272367 Q8N1N0 UPI0000376BCC NM_001258027.1,NM_173535.2 deleterious_low_confidence(0.02) 7/7 SMART_domains:SM00034 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 70809282 70809282 G C 1 0 0 0 0 1 0 0 0 3284 1000 35 4 4 CLEC4F 2 70809282 Missense_Mutation SNP G C3N-01030_T 2001879 70809282 171384247 111 20892 LRRTM4 0 . GRCh38 2 77518741 77518741 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1128A>T p.Gln376His p.Q376H ENST00000409093 3/4 209 158 51 190 190 0 strelka-varscan LRRTM4,missense_variant,p.Gln376His,ENST00000409088,NM_024993.4;LRRTM4,missense_variant,p.Gln377His,ENST00000409911,;LRRTM4,missense_variant,p.Gln377His,ENST00000409282,NM_001282928.1;LRRTM4,missense_variant,p.Gln376His,ENST00000409093,NM_001282924.1;LRRTM4,missense_variant,p.Gln376His,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; A ENST00000409093 Transcript missense_variant 1465/2247 1128/1773 376/590 Q/H caA/caT 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 tolerated(0.11) 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 77518741 77518741 T A 1 0 0 0 0 1 0 0 0 8948 1838 64 4 4 LRRTM4 2 77518741 Missense_Mutation SNP T C3N-01030_T 6709459 77518741 164674788 112 20893 REG1A 0 . GRCh38 2 79121572 79121572 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.75C>A p.= p.A25A ENST00000233735 3/6 256 194 62 236 236 0 strelka-varscan REG1A,synonymous_variant,p.=,ENST00000233735,NM_002909.4;REG1A,non_coding_transcript_exon_variant,,ENST00000488524,;REG1A,non_coding_transcript_exon_variant,,ENST00000485184,;REG1A,non_coding_transcript_exon_variant,,ENST00000461579,; A ENST00000233735 Transcript synonymous_variant 178/808 75/501 25/166 A gcC/gcA 1 1 REG1A HGNC HGNC:9951 protein_coding YES CCDS1964.1 ENSP00000233735 P05451 UPI000012E72D NM_002909.4 3/6 hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF55 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 79121572 79121572 C A 1 0 0 0 0 0 0 0 1 13380 610 22 2 2 REG1A 2 79121572 Silent SNP C C3N-01030_T 1602831 79121572 163071957 113 20894 LRRTM1 0 . GRCh38 2 80303613 80303613 + Silent SNP G G T rs778753800 C3N-01030_T C3N-01030_N G G c.207C>A p.= p.G69G ENST00000295057 2/2 116 84 32 101 101 0 strelka-varscan LRRTM1,synonymous_variant,p.=,ENST00000295057,;LRRTM1,synonymous_variant,p.=,ENST00000409148,NM_178839.4;LRRTM1,synonymous_variant,p.=,ENST00000416268,;LRRTM1,synonymous_variant,p.=,ENST00000452811,;LRRTM1,synonymous_variant,p.=,ENST00000415098,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.=,ENST00000433224,;LRRTM1,synonymous_variant,p.=,ENST00000417012,; T ENST00000295057 Transcript synonymous_variant 864/2599 207/1569 69/522 G ggC/ggA rs778753800 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 80303613 80303613 G T 1 0 0 0 0 0 0 0 1 8945 958 34 2 2 LRRTM1 2 80303613 Silent SNP G C3N-01030_T 1182041 80303613 161889916 114 20895 SUCLG1 0 . GRCh38 2 84441284 84441284 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.494C>A p.Thr165Lys p.T165K ENST00000393868 4/9 446 332 114 380 380 0 strelka-varscan SUCLG1,missense_variant,p.Thr165Lys,ENST00000393868,NM_003849.3;SUCLG1,non_coding_transcript_exon_variant,,ENST00000491642,;SUCLG1,non_coding_transcript_exon_variant,,ENST00000483605,;SUCLG1,non_coding_transcript_exon_variant,,ENST00000430989,;SUCLG1,upstream_gene_variant,,ENST00000488234,;SUCLG1,3_prime_UTR_variant,,ENST00000442240,; T ENST00000393868 Transcript missense_variant 705/1475 494/1041 165/346 T/K aCa/aAa 1 -1 SUCLG1 HGNC HGNC:11449 protein_coding YES CCDS1967.2 ENSP00000377446 P53597 UPI000014BF59 NM_003849.3 deleterious(0) 4/9 hmmpanther:PTHR11117,TIGRFAM_domain:TIGR01019,PIRSF_domain:PIRSF001553,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 84441284 84441284 G T 1 0 0 0 0 1 0 0 0 15748 1377 48 2 2 SUCLG1 2 84441284 Missense_Mutation SNP G C3N-01030_T 4137671 84441284 157752245 115 20896 ANKRD36C 0 . GRCh38 2 95855803 95855803 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.4458A>T p.Arg1486Ser p.R1486S ENST00000456556 63/67 398 298 100 453 452 1 strelka-varscan ANKRD36C,missense_variant,p.Arg1486Ser,ENST00000456556,;ANKRD36C,downstream_gene_variant,,ENST00000295246,;ANKRD36C,upstream_gene_variant,,ENST00000612359,;ANKRD36C,non_coding_transcript_exon_variant,,ENST00000488721,;ANKRD36C,downstream_gene_variant,,ENST00000531153,;ANKRD36C,downstream_gene_variant,,ENST00000534304,; A ENST00000456556 Transcript missense_variant 4543/5428 4458/5337 1486/1778 R/S agA/agT 1 -1 ANKRD36C HGNC HGNC:32946 protein_coding YES ENSP00000403302 Q5JPF3 UPI00016620F5 tolerated(0.11) 63/67 hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF1,Pfam_domain:PF14915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 95855803 95855803 T A 1 0 0 0 0 1 0 0 0 773 1548 54 4 4 ANKRD36C 2 95855803 Missense_Mutation SNP T C3N-01030_T 11414519 95855803 146337726 116 20897 VWA3B 0 . GRCh38 2 98218029 98218029 + Splice_Site SNP G G T novel C3N-01030_T C3N-01030_N G G c.2019+1G>T p.X673_splice ENST00000477737 66 48 18 90 89 1 strelka-varscan VWA3B,splice_donor_variant,,ENST00000477737,NM_144992.4;VWA3B,splice_donor_variant,,ENST00000473149,;VWA3B,downstream_gene_variant,,ENST00000489968,;VWA3B,splice_donor_variant,,ENST00000432242,;VWA3B,splice_donor_variant,,ENST00000409460,;VWA3B,splice_donor_variant,,ENST00000416277,;VWA3B,splice_donor_variant,,ENST00000495571,;VWA3B,splice_donor_variant,,ENST00000433678,;VWA3B,splice_donor_variant,,ENST00000489630,;VWA3B,splice_donor_variant,,ENST00000448638,;VWA3B,downstream_gene_variant,,ENST00000422503,; T ENST00000477737 Transcript splice_donor_variant -/4454 2019/3885 673/1294 1 1 VWA3B HGNC HGNC:28385 protein_coding YES CCDS42718.1 ENSP00000417955 Q502W6 UPI0000E9B173 NM_144992.4 14/27 HIGH 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 5 4 70 98218029 98218029 G T 1 0 0 0 0 0 0 1 0 17795 1275 44 2 2 VWA3B 2 98218029 Splice_Site SNP G C3N-01030_T 2362226 98218029 143975500 117 20898 TBC1D8 0 . GRCh38 2 101033744 101033744 + Missense_Mutation SNP G G C rs776533987 C3N-01030_T C3N-01030_N G G c.1573C>G p.Leu525Val p.L525V ENST00000376840 10/20 87 72 15 108 108 0 strelka-varscan TBC1D8,missense_variant,p.Leu540Val,ENST00000409318,;TBC1D8,missense_variant,p.Leu525Val,ENST00000376840,NM_001102426.1;TBC1D8,upstream_gene_variant,,ENST00000481317,;TBC1D8,upstream_gene_variant,,ENST00000473937,;TBC1D8,upstream_gene_variant,,ENST00000485875,; C ENST00000376840 Transcript missense_variant 1573/3627 1573/3423 525/1140 L/V Ctt/Gtt rs776533987 1 -1 TBC1D8 HGNC HGNC:17791 protein_coding YES CCDS46375.1 ENSP00000366036 O95759 UPI00015ADD19 NM_001102426.1 deleterious(0.02) 10/20 Gene3D:2qq8A02,Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF260,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 101033744 101033744 G C 1 0 0 0 0 1 0 0 0 16030 942 33 4 4 TBC1D8 2 101033744 Missense_Mutation SNP G C3N-01030_T 2815715 101033744 141159785 118 20899 MAP4K4 0 . GRCh38 2 101877119 101877119 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.3025G>T p.Gly1009Cys p.G1009C ENST00000350878 25/31 154 129 25 197 196 1 strelka-varscan MAP4K4,missense_variant,p.Gly1009Cys,ENST00000350878,NM_145686.3;MAP4K4,missense_variant,p.Gly971Cys,ENST00000324219,NM_001242560.1;MAP4K4,missense_variant,p.Gly1056Cys,ENST00000625522,;MAP4K4,missense_variant,p.Gly893Cys,ENST00000350198,;MAP4K4,missense_variant,p.Gly890Cys,ENST00000413150,;MAP4K4,missense_variant,p.Gly723Cys,ENST00000302217,;MAP4K4,missense_variant,p.Gly1008Cys,ENST00000425019,;MAP4K4,missense_variant,p.Gly906Cys,ENST00000417294,;MAP4K4,missense_variant,p.Gly774Cys,ENST00000456652,;MAP4K4,missense_variant,p.Gly893Cys,ENST00000634702,NM_004834.4,NM_145687.3;MAP4K4,missense_variant,p.Gly975Cys,ENST00000347699,NM_001242559.1;MAP4K4,missense_variant,p.Gly792Cys,ENST00000421882,;MAP4K4,missense_variant,p.Gly780Cys,ENST00000627726,; T ENST00000350878 Transcript missense_variant 3403/7640 3025/3822 1009/1273 G/C Ggc/Tgc 1 1 MAP4K4 HGNC HGNC:6866 protein_coding YES CCDS74546.1 ENSP00000343658 E7ESS2 UPI0000EE6D9F NM_145686.3 deleterious_low_confidence(0.01) 25/31 Pfam_domain:PF00780,PROSITE_profiles:PS50219,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 101877119 101877119 G T 1 0 0 0 0 1 0 0 0 9186 1232 43 2 2 MAP4K4 2 101877119 Missense_Mutation SNP G C3N-01030_T 843375 101877119 140316410 119 20900 CNTNAP5 0 . GRCh38 2 124869753 124869753 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.3424A>G p.Lys1142Glu p.K1142E ENST00000431078 21/24 119 102 17 137 137 0 strelka-varscan-mutect CNTNAP5,missense_variant,p.Lys1142Glu,ENST00000431078,NM_130773.3; G ENST00000431078 Transcript missense_variant 3788/5284 3424/3921 1142/1306 K/E Aaa/Gaa 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0) 21/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 124869753 124869753 A G 1 0 0 0 0 1 0 0 0 3432 131 5 5 5 CNTNAP5 2 124869753 Missense_Mutation SNP A C3N-01030_T 22992634 124869753 117323776 120 20901 CYP27C1 0 . GRCh38 2 127193278 127193278 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.818A>T p.His273Leu p.H273L ENST00000335247 7/8 223 180 43 234 234 0 strelka-varscan-mutect CYP27C1,missense_variant,p.His273Leu,ENST00000335247,NM_001001665.3;CYP27C1,missense_variant,p.His273Leu,ENST00000409327,; A ENST00000335247 Transcript missense_variant 949/4401 818/1119 273/372 H/L cAc/cTc 1 -1 CYP27C1 HGNC HGNC:33480 protein_coding YES CCDS33285.1 ENSP00000334128 Q4G0S4 A0A024RAI7 UPI00001995F8 NM_001001665.3 deleterious(0) 7/8 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF9,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 127193278 127193278 T A 1 0 0 0 0 1 0 0 0 3963 1696 59 4 4 CYP27C1 2 127193278 Missense_Mutation SNP T C3N-01030_T 2323525 127193278 115000251 121 20902 CYP27C1 0 . GRCh38 2 127193819 127193819 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.768G>T p.= p.L256L ENST00000335247 6/8 201 166 35 170 168 2 strelka-varscan-mutect CYP27C1,synonymous_variant,p.=,ENST00000335247,NM_001001665.3;CYP27C1,synonymous_variant,p.=,ENST00000409327,; A ENST00000335247 Transcript synonymous_variant 899/4401 768/1119 256/372 L ctG/ctT 1 -1 CYP27C1 HGNC HGNC:33480 protein_coding YES CCDS33285.1 ENSP00000334128 Q4G0S4 A0A024RAI7 UPI00001995F8 NM_001001665.3 6/8 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF9,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 127193819 127193819 C A 1 0 0 0 0 0 0 0 1 3963 581 21 2 2 CYP27C1 2 127193819 Silent SNP C C3N-01030_T 541 127193819 114999710 122 20903 POTEE 0 . GRCh38 2 131253076 131253076 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1755C>A p.Asp585Glu p.D585E ENST00000356920 13/15 64 52 12 84 84 0 strelka-varscan-mutect POTEE,missense_variant,p.Asp585Glu,ENST00000356920,NM_001083538.1;POTEE,missense_variant,p.Asp462Glu,ENST00000613282,;POTEE,3_prime_UTR_variant,,ENST00000626191,;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,3_prime_UTR_variant,,ENST00000358087,;POTEE,3_prime_UTR_variant,,ENST00000514256,; A ENST00000356920 Transcript missense_variant 2091/4159 1755/3228 585/1075 D/E gaC/gaA 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 tolerated_low_confidence(0.21) 13/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 131253076 131253076 C A 1 0 0 0 0 1 0 0 0 12378 477 17 2 2 POTEE 2 131253076 Missense_Mutation SNP C C3N-01030_T 4059257 131253076 110940453 123 20904 MZT2A 0 . GRCh38 2 131484089 131484089 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.449G>T p.Gly150Val p.G150V ENST00000309451 3/3 110 89 21 98 98 0 strelka-varscan-mutect MZT2A,missense_variant,p.Gly150Val,ENST00000309451,NM_001085365.1;TUBA3D,downstream_gene_variant,,ENST00000321253,NM_080386.3;MZT2A,non_coding_transcript_exon_variant,,ENST00000410036,;TUBA3D,downstream_gene_variant,,ENST00000409047,;MZT2A,downstream_gene_variant,,ENST00000488586,;MZT2A,intron_variant,,ENST00000445782,;MZT2A,intron_variant,,ENST00000427024,; A ENST00000309451 Transcript missense_variant 495/624 449/477 150/158 G/V gGg/gTg 1 -1 MZT2A HGNC HGNC:33187 protein_coding YES CCDS42758.1 ENSP00000311500 Q6P582 UPI0000421BEF NM_001085365.1 tolerated_low_confidence(0.06) 3/3 hmmpanther:PTHR28578,hmmpanther:PTHR28578:SF1 MODERATE 1 SNV 1 1 PASS rs1264352916 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 131484089 131484089 C A 1 0 0 0 0 1 0 0 0 10111 623 22 2 2 MZT2A 2 131484089 Missense_Mutation SNP C C3N-01030_T 231013 131484089 110709440 124 20905 ZRANB3 0 . GRCh38 2 135265551 135265551 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1522G>C p.Glu508Gln p.E508Q ENST00000264159 12/21 89 68 21 126 126 0 strelka-varscan-mutect ZRANB3,missense_variant,p.Glu54Gln,ENST00000536680,NM_001286569.1;ZRANB3,missense_variant,p.Glu508Gln,ENST00000401392,NM_001286568.1;ZRANB3,missense_variant,p.Glu508Gln,ENST00000264159,NM_032143.3;ZRANB3,downstream_gene_variant,,ENST00000452187,;ZRANB3,3_prime_UTR_variant,,ENST00000403017,; G ENST00000264159 Transcript missense_variant 1639/4046 1522/3240 508/1079 E/Q Gaa/Caa 1 -1 ZRANB3 HGNC HGNC:25249 protein_coding YES CCDS46419.1 ENSP00000264159 Q5FWF4 UPI0000509F0C NM_032143.3 deleterious(0.01) 12/21 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF731 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 135265551 135265551 C G 1 0 0 0 0 1 0 0 0 18817 864 30 4 4 ZRANB3 2 135265551 Missense_Mutation SNP C C3N-01030_T 3781462 135265551 106927978 125 20906 LRP1B 0 . GRCh38 2 140502968 140502968 + Frame_Shift_Del DEL C C - C3N-01030_T C3N-01030_N C C c.8657delG p.Ser2886MetfsTer42 p.S2886Mfs*42 ENST00000389484 54/91 78 62 16 118 118 0 sindel-varindel-pindel LRP1B,frameshift_variant,p.Ser2886MetfsTer42,ENST00000389484,NM_018557.2; - ENST00000389484 Transcript frameshift_variant 9629/16535 8657/13800 2886/4599 S/X aGt/at COSM3894873 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 54/91 SMART_domains:SM00192 1 HIGH 1 deletion 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 140502968 140502968 C - 1 0 1 0 1 0 0 0 0 8850 579 20 0 0 LRP1B 2 140502968 Frame_Shift_Del DEL C C3N-01030_T 5237417 140502968 101690561 126 20907 GALNT13 0 . GRCh38 2 154242748 154242748 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.529G>A p.Val177Ile p.V177I ENST00000409237 4/12 178 148 30 235 235 0 strelka-mutect GALNT13,missense_variant,p.Val177Ile,ENST00000392825,NM_052917.3;GALNT13,missense_variant,p.Val177Ile,ENST00000409237,NM_001301627.1;GALNT13,3_prime_UTR_variant,,ENST00000431076,; A ENST00000409237 Transcript missense_variant 529/2591 529/1686 177/561 V/I Gta/Ata 1 1 GALNT13 HGNC HGNC:23242 protein_coding YES CCDS77472.1 ENSP00000387239 Q8IUC8 UPI0000E4465D NM_001301627.1 tolerated(0.09) 4/12 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF47,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 154242748 154242748 G A 1 0 0 0 0 1 0 0 0 6079 1029 36 3 3 GALNT13 2 154242748 Missense_Mutation SNP G C3N-01030_T 13739780 154242748 87950781 127 20908 GALNT13 0 . GRCh38 2 154409046 154409046 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.1361delG p.Gly454ValfsTer38 p.G454Vfs*38 ENST00000409237 9/12 202 148 54 331 331 0 sindel-varindel-pindel GALNT13,frameshift_variant,p.Gly454ValfsTer38,ENST00000392825,NM_052917.3;GALNT13,frameshift_variant,p.Gly454ValfsTer38,ENST00000409237,NM_001301627.1;GALNT13,frameshift_variant,p.Gly13ValfsTer83,ENST00000422126,;GALNT13,intron_variant,,ENST00000450838,;GALNT13,non_coding_transcript_exon_variant,,ENST00000487047,;GALNT13,3_prime_UTR_variant,,ENST00000431076,; - ENST00000409237 Transcript frameshift_variant 1359/2591 1359/1686 453/561 V/X gtG/gt 1 1 GALNT13 HGNC HGNC:23242 protein_coding YES CCDS77472.1 ENSP00000387239 Q8IUC8 UPI0000E4465D NM_001301627.1 9/12 Gene3D:2.80.10.50,Pfam_domain:PF00652,PROSITE_profiles:PS50231,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF47,SMART_domains:SM00458,Superfamily_domains:SSF50370 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 154409046 154409046 G - 1 0 1 0 1 0 0 0 0 6079 1335 47 0 0 GALNT13 2 154409046 Frame_Shift_Del DEL G C3N-01030_T 166298 154409046 87784483 128 20909 LY75 0 . GRCh38 2 159890335 159890335 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.680G>T p.Gly227Val p.G227V ENST00000263636 4/35 234 197 37 303 301 2 strelka-varscan-mutect LY75,missense_variant,p.Gly227Val,ENST00000263636,NM_002349.3;LY75-CD302,missense_variant,p.Gly227Val,ENST00000504764,NM_001198759.1;LY75-CD302,missense_variant,p.Gly227Val,ENST00000505052,NM_001198760.1;LY75,non_coding_transcript_exon_variant,,ENST00000484559,; A ENST00000263636 Transcript missense_variant 708/6886 680/5169 227/1722 G/V gGa/gTa 1 -1 LY75 HGNC HGNC:6729 protein_coding YES CCDS2211.1 ENSP00000263636 O60449 UPI00001AE885 NM_002349.3 deleterious(0.01) 4/35 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF65,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 159890335 159890335 C A 1 0 0 0 0 1 0 0 0 9010 855 30 2 2 LY75 2 159890335 Missense_Mutation SNP C C3N-01030_T 5481289 159890335 82303194 129 20910 UBR3 0 . GRCh38 2 170007180 170007180 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.4220G>T p.Gly1407Val p.G1407V ENST00000418381 28/39 146 111 35 154 154 0 strelka-varscan-mutect UBR3,missense_variant,p.Gly1407Val,ENST00000272793,;UBR3,missense_variant,p.Gly1407Val,ENST00000418381,NM_172070.3;UBR3,missense_variant,p.Gly465Val,ENST00000392632,;UBR3,missense_variant,p.Gly78Val,ENST00000439681,;UBR3,3_prime_UTR_variant,,ENST00000430321,;UBR3,upstream_gene_variant,,ENST00000444475,; T ENST00000418381 Transcript missense_variant 4220/7951 4220/5667 1407/1888 G/V gGa/gTa 1 1 UBR3 HGNC HGNC:30467 protein_coding YES CCDS2238.2 ENSP00000396068 Q6ZT12 UPI00015FA088 NM_172070.3 tolerated(0.27) 28/39 hmmpanther:PTHR21497 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 170007180 170007180 G T 1 0 0 0 0 1 0 0 0 17427 1174 41 2 2 UBR3 2 170007180 Missense_Mutation SNP G C3N-01030_T 10116845 170007180 72186349 130 20911 DLX1 0 . GRCh38 2 172085968 172085968 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.291C>A p.= p.A97A ENST00000361725 1/3 79 58 21 76 76 0 strelka-varscan-mutect DLX1,synonymous_variant,p.=,ENST00000361725,NM_178120.4;DLX1,synonymous_variant,p.=,ENST00000341900,NM_001038493.1;DLX1,synonymous_variant,p.=,ENST00000361609,;DLX1,synonymous_variant,p.=,ENST00000469444,;METAP1D,downstream_gene_variant,,ENST00000315796,NM_199227.1;DLX1,upstream_gene_variant,,ENST00000550686,;DLX1,non_coding_transcript_exon_variant,,ENST00000409492,;DLX1,upstream_gene_variant,,ENST00000475989,; A ENST00000361725 Transcript synonymous_variant 743/2640 291/768 97/255 A gcC/gcA 1 1 DLX1 HGNC HGNC:2914 protein_coding YES CCDS2247.2 ENSP00000354478 P56177 X5D2F9 UPI0000185FE8 NM_178120.4 1/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF33 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 172085968 172085968 C A 1 0 0 0 0 0 0 0 1 4377 610 22 2 2 DLX1 2 172085968 Silent SNP C C3N-01030_T 2078788 172085968 70107561 131 20912 PDE11A 0 . GRCh38 2 177817896 177817896 + Missense_Mutation SNP C C A rs775354403 C3N-01030_T C3N-01030_N C C c.1606G>T p.Gly536Trp p.G536W ENST00000286063 8/20 200 164 36 293 291 2 strelka-varscan-mutect PDE11A,missense_variant,p.Gly536Trp,ENST00000286063,NM_016953.3;PDE11A,missense_variant,p.Gly286Trp,ENST00000358450,NM_001077197.1;PDE11A,missense_variant,p.Gly178Trp,ENST00000409504,NM_001077358.1;PDE11A,missense_variant,p.Gly92Trp,ENST00000389683,NM_001077196.1;PDE11A,missense_variant,p.Gly175Trp,ENST00000433879,;PDE11A,non_coding_transcript_exon_variant,,ENST00000497003,;PDE11A,non_coding_transcript_exon_variant,,ENST00000492761,; A ENST00000286063 Transcript missense_variant 1924/9275 1606/2802 536/933 G/W Ggg/Tgg rs775354403 1 -1 PDE11A HGNC HGNC:8773 protein_coding YES CCDS33334.1 ENSP00000286063 Q9HCR9 UPI00001402C1 NM_016953.3 deleterious(0) 8/20 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF130,Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS rs775354403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 177817896 177817896 C A 1 0 0 0 0 1 0 0 0 11719 594 21 2 2 PDE11A 2 177817896 Missense_Mutation SNP C C3N-01030_T 5731928 177817896 64375633 132 20913 TTN 0 . GRCh38 2 178553748 178553748 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.89257C>A p.Leu29753Ile p.L29753I ENST00000589042 334/363 77 59 18 72 72 0 strelka-varscan-mutect TTN,missense_variant,p.Leu29753Ile,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu28112Ile,ENST00000591111,;TTN,missense_variant,p.Leu28112Ile,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu27185Ile,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Leu20688Ile,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Leu20880Ile,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Leu20813Ile,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; T ENST00000589042 Transcript missense_variant 89482/109224 89257/107976 29753/35991 L/I Ctt/Att COSM3709116,COSM3709117,COSM3709118,COSM3709119 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 334/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1,1 MODERATE SNV 5 1,1,1,1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 178553748 178553748 G T 1 0 0 0 0 1 0 0 0 17245 1000 35 2 2 TTN 2 178553748 Missense_Mutation SNP G C3N-01030_T 735852 178553748 63639781 133 20914 TTN 0 . GRCh38 2 178636499 178636499 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.41228T>A p.Leu13743Gln p.L13743Q ENST00000589042 225/363 201 166 35 205 205 0 strelka-varscan-mutect TTN,missense_variant,p.Leu13743Gln,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Leu12102Gln,ENST00000591111,;TTN,missense_variant,p.Leu12102Gln,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Leu11175Gln,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Leu4678Gln,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Leu4870Gln,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Leu4803Gln,ENST00000359218,NM_133432.3;TTN,downstream_gene_variant,,ENST00000414766,;TTN,downstream_gene_variant,,ENST00000446966,;TTN,downstream_gene_variant,,ENST00000426232,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000626954,;TTN-AS1,upstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000418062,;TTN-AS1,downstream_gene_variant,,ENST00000628296,; T ENST00000589042 Transcript missense_variant 41453/109224 41228/107976 13743/35991 L/Q cTg/cAg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 225/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 178636499 178636499 A T 1 0 0 0 0 1 0 0 0 17245 188 7 4 4 TTN 2 178636499 Missense_Mutation SNP A C3N-01030_T 82751 178636499 63557030 134 20915 TTN 0 . GRCh38 2 178706513 178706513 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.29361G>A p.= p.Q9787Q ENST00000589042 102/363 146 120 26 148 148 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,upstream_gene_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript synonymous_variant 29586/109224 29361/107976 9787/35991 Q caG/caA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 102/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 178706513 178706513 C T 1 0 0 0 0 0 0 0 1 17245 680 24 3 3 TTN 2 178706513 Silent SNP C C3N-01030_T 70014 178706513 63487016 135 20916 PLCL1 0 . GRCh38 2 198101347 198101347 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2982G>T p.Gln994His p.Q994H ENST00000428675 4/6 120 101 19 143 143 0 strelka-varscan-mutect PLCL1,missense_variant,p.Gln917His,ENST00000437704,;PLCL1,missense_variant,p.Gln994His,ENST00000428675,NM_006226.3;PLCL1,missense_variant,p.Gln920His,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript missense_variant 3380/5125 2982/3288 994/1095 Q/H caG/caT 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 tolerated(0.5) 4/6 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102 MODERATE 1 SNV 1 1 PASS rs1332018043 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 198101347 198101347 G T 1 0 0 0 0 1 0 0 0 12133 1020 36 2 2 PLCL1 2 198101347 Missense_Mutation SNP G C3N-01030_T 19394834 198101347 44092182 136 20917 MPP4 0 . GRCh38 2 201692920 201692920 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.189G>A p.= p.Q63Q ENST00000409474 3/22 197 167 30 160 160 0 strelka-varscan-mutect MPP4,synonymous_variant,p.=,ENST00000409474,NM_033066.2;MPP4,synonymous_variant,p.=,ENST00000359962,;MPP4,synonymous_variant,p.=,ENST00000620095,;MPP4,synonymous_variant,p.=,ENST00000315506,;MPP4,synonymous_variant,p.=,ENST00000428900,;MPP4,synonymous_variant,p.=,ENST00000396886,;MPP4,synonymous_variant,p.=,ENST00000409143,;MPP4,synonymous_variant,p.=,ENST00000447335,;MPP4,synonymous_variant,p.=,ENST00000602867,;MPP4,synonymous_variant,p.=,ENST00000409818,;MPP4,non_coding_transcript_exon_variant,,ENST00000486212,;MPP4,non_coding_transcript_exon_variant,,ENST00000483841,; T ENST00000409474 Transcript synonymous_variant 397/2462 189/1914 63/637 Q caG/caA 1 -1 MPP4 HGNC HGNC:13680 protein_coding YES CCDS46491.1 ENSP00000387278 Q96JB8 UPI000050A341 NM_033066.2 3/22 PROSITE_profiles:PS51022,hmmpanther:PTHR23122,hmmpanther:PTHR23122:SF34,SMART_domains:SM00569 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 201692920 201692920 C T 1 0 0 0 0 0 0 0 1 9702 680 24 3 3 MPP4 2 201692920 Silent SNP C C3N-01030_T 3591573 201692920 40500609 137 20918 ERBB4 0 . GRCh38 2 211422043 211422043 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2928G>T p.Arg976Ser p.R976S ENST00000342788 24/28 218 177 41 296 296 0 strelka-varscan-mutect ERBB4,missense_variant,p.Arg976Ser,ENST00000342788,NM_005235.2;ERBB4,missense_variant,p.Arg976Ser,ENST00000436443,NM_001042599.1;ERBB4,missense_variant,p.Arg950Ser,ENST00000402597,; A ENST00000342788 Transcript missense_variant 3239/12136 2928/3927 976/1308 R/S agG/agT 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 deleterious(0.05) 24/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF90,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000619,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 211422043 211422043 C A 1 0 0 0 0 1 0 0 0 5057 854 30 2 2 ERBB4 2 211422043 Missense_Mutation SNP C C3N-01030_T 9729123 211422043 30771486 138 20919 ERBB4 0 . GRCh38 2 211624045 211624045 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.2080-1G>T p.X694_splice ENST00000342788 260 239 21 288 288 0 strelka-varscan-mutect ERBB4,splice_acceptor_variant,,ENST00000342788,NM_005235.2;ERBB4,splice_acceptor_variant,,ENST00000436443,NM_001042599.1;ERBB4,splice_acceptor_variant,,ENST00000402597,;ERBB4,splice_acceptor_variant,,ENST00000260943,;ERBB4,splice_acceptor_variant,,ENST00000484594,; A ENST00000342788 Transcript splice_acceptor_variant -/12136 2080/3927 694/1308 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 17/27 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 211624045 211624045 C A 1 0 0 0 0 0 0 1 0 5057 579 20 2 2 ERBB4 2 211624045 Splice_Site SNP C C3N-01030_T 202002 211624045 30569484 139 20920 CUL3 0 . GRCh38 2 224513640 224513640 + Splice_Site SNP T T A C3N-01030_T C3N-01030_N T T c.540-2A>T p.X180_splice ENST00000264414 95 72 23 122 121 1 strelka-varscan-mutect CUL3,splice_acceptor_variant,,ENST00000264414,NM_003590.4;CUL3,splice_acceptor_variant,,ENST00000344951,NM_001257197.1;CUL3,splice_acceptor_variant,,ENST00000409777,;CUL3,splice_acceptor_variant,,ENST00000409096,NM_001257198.1;CUL3,downstream_gene_variant,,ENST00000436172,;CUL3,splice_acceptor_variant,,ENST00000541548,;CUL3,splice_acceptor_variant,,ENST00000432260,;CUL3,upstream_gene_variant,,ENST00000484081,; A ENST00000264414 Transcript splice_acceptor_variant -/6741 540/2307 180/768 COSM720511 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 4/15 1 HIGH 1 SNV 1 1 1 PASS . . 0 195 7 6 2 0 0 0 -17.06524 0.9024275 1 1 1 0 A 5 1 70 224513640 224513640 T A 1 0 0 0 0 0 0 1 0 3866 1594 55 4 4 CUL3 2 224513640 Splice_Site SNP T C3N-01030_T 12889595 224513640 17679889 140 20921 COL4A3 0 . GRCh38 2 227283795 227283795 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.2685C>A p.= p.G895G ENST00000396578 33/52 252 196 56 271 268 3 strelka-varscan-mutect COL4A3,synonymous_variant,p.=,ENST00000396578,NM_000091.4;AC097662.2,intron_variant,,ENST00000439598,;AC097662.2,intron_variant,,ENST00000396588,;AC097662.2,intron_variant,,ENST00000433324,;COL4A3,upstream_gene_variant,,ENST00000487633,; A ENST00000396578 Transcript synonymous_variant 2847/8097 2685/5013 895/1670 G ggC/ggA 1 1 COL4A3 HGNC HGNC:2204 protein_coding YES CCDS42829.1 ENSP00000379823 Q01955 UPI000013E9F3 NM_000091.4 33/52 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF598,Pfam_domain:PF01391,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 227283795 227283795 C A 1 0 0 0 0 0 0 0 1 3480 784 28 2 2 COL4A3 2 227283795 Silent SNP C C3N-01030_T 2770155 227283795 14909734 141 20922 EFHD1 0 . GRCh38 2 232662850 232662850 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.351G>A p.= p.L117L ENST00000264059 2/4 154 146 8 135 135 0 strelka-varscan-mutect EFHD1,synonymous_variant,p.=,ENST00000264059,NM_025202.3;EFHD1,synonymous_variant,p.=,ENST00000409708,;EFHD1,synonymous_variant,p.=,ENST00000410095,;EFHD1,synonymous_variant,p.=,ENST00000611312,;EFHD1,synonymous_variant,p.=,ENST00000409613,NM_001243252.1;EFHD1,synonymous_variant,p.=,ENST00000427698,;EFHD1,3_prime_UTR_variant,,ENST00000442845,; A ENST00000264059 Transcript synonymous_variant 828/2259 351/720 117/239 L ctG/ctA 1 1 EFHD1 HGNC HGNC:29556 protein_coding YES CCDS2497.1 ENSP00000264059 Q9BUP0 UPI00001362A7 NM_025202.3 2/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50222,hmmpanther:PTHR13025:SF5,hmmpanther:PTHR13025,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 232662850 232662850 G A 1 0 0 0 0 0 0 0 1 4783 1277 45 3 3 EFHD1 2 232662850 Silent SNP G C3N-01030_T 5379055 232662850 9530679 142 20923 SAG 0 . GRCh38 2 233335053 233335053 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.898G>T p.Asp300Tyr p.D300Y ENST00000409110 11/16 122 91 31 117 117 0 strelka-varscan-mutect SAG,missense_variant,p.Asp300Tyr,ENST00000409110,NM_000541.4;SAG,non_coding_transcript_exon_variant,,ENST00000476500,;SAG,non_coding_transcript_exon_variant,,ENST00000469222,;SAG,non_coding_transcript_exon_variant,,ENST00000471884,;SAG,non_coding_transcript_exon_variant,,ENST00000412969,;SAG,non_coding_transcript_exon_variant,,ENST00000483231,;SAG,non_coding_transcript_exon_variant,,ENST00000473771,;SAG,upstream_gene_variant,,ENST00000474220,; T ENST00000409110 Transcript missense_variant 1128/1591 898/1218 300/405 D/Y Gat/Tat 1 1 SAG HGNC HGNC:10521 protein_coding YES CCDS46545.1 ENSP00000386444 P10523 UPI000013CD8D NM_000541.4 deleterious(0) 11/16 hmmpanther:PTHR11792:SF15,hmmpanther:PTHR11792,Gene3D:1g4mB02,Pfam_domain:PF02752,SMART_domains:SM01017,Superfamily_domains:SSF81296,Prints_domain:PR00309 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 233335053 233335053 G T 1 0 0 0 0 1 0 0 0 14067 1174 41 2 2 SAG 2 233335053 Missense_Mutation SNP G C3N-01030_T 672203 233335053 8858476 143 20924 UGT1A3 0 . GRCh38 2 233729318 233729318 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.192G>A p.= p.E64E ENST00000482026 1/5 148 123 25 144 144 0 strelka-varscan-mutect UGT1A3,synonymous_variant,p.=,ENST00000482026,NM_019093.2;UGT1A6,intron_variant,,ENST00000305139,NM_001072.3;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A4,intron_variant,,ENST00000373409,NM_007120.2;UGT1A5,intron_variant,,ENST00000373414,NM_019078.1;UGT1A7,intron_variant,,ENST00000373426,NM_019077.2;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,NM_205862.1;UGT1A6,intron_variant,,ENST00000406651,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,intron_variant,,ENST00000478062,;UGT1A4,intron_variant,,ENST00000450233,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,; A ENST00000482026 Transcript synonymous_variant 211/2364 192/1605 64/534 E gaG/gaA 1 1 UGT1A3 HGNC HGNC:12535 protein_coding YES CCDS2509.1 ENSP00000418532 P35503 Q5DT01 UPI0000001045 NM_019093.2 1/5 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF173,Pfam_domain:PF00201,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 233729318 233729318 G A 1 0 0 0 0 0 0 0 1 17471 991 35 3 3 UGT1A3 2 233729318 Silent SNP G C3N-01030_T 394265 233729318 8464211 144 20925 HJURP 0 . GRCh38 2 233841451 233841451 + Silent SNP C C G novel C3N-01030_T C3N-01030_N C C c.1329G>C p.= p.R443R ENST00000411486 8/9 297 227 70 297 297 0 strelka-varscan-mutect HJURP,synonymous_variant,p.=,ENST00000411486,NM_018410.4;HJURP,synonymous_variant,p.=,ENST00000432087,NM_001282962.1;HJURP,synonymous_variant,p.=,ENST00000441687,NM_001282963.1;HJURP,synonymous_variant,p.=,ENST00000414924,;HJURP,downstream_gene_variant,,ENST00000454020,;HJURP,downstream_gene_variant,,ENST00000434039,;HJURP,upstream_gene_variant,,ENST00000433484,;HJURP,downstream_gene_variant,,ENST00000453122,;HJURP,downstream_gene_variant,,ENST00000373395,; G ENST00000411486 Transcript synonymous_variant 1395/3187 1329/2247 443/748 R cgG/cgC 1 -1 HJURP HGNC HGNC:25444 protein_coding YES CCDS33406.1 ENSP00000414109 Q8NCD3 UPI000013CB29 NM_018410.4 8/9 hmmpanther:PTHR15992,hmmpanther:PTHR15992:SF5,Pfam_domain:PF12347 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 233841451 233841451 C G 1 0 0 0 0 0 0 0 1 7078 610 22 4 4 HJURP 2 233841451 Silent SNP C C3N-01030_T 112133 233841451 8352078 145 20926 COL6A3 0 . GRCh38 2 237334789 237334789 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.9066C>A p.= p.L3022L ENST00000295550 41/44 283 233 50 267 267 0 strelka-varscan-mutect COL6A3,synonymous_variant,p.=,ENST00000295550,NM_004369.3;COL6A3,synonymous_variant,p.=,ENST00000353578,NM_057167.3;COL6A3,synonymous_variant,p.=,ENST00000409809,;COL6A3,synonymous_variant,p.=,ENST00000472056,NM_057166.4;COL6A3,synonymous_variant,p.=,ENST00000347401,;COL6A3,upstream_gene_variant,,ENST00000473258,;COL6A3,upstream_gene_variant,,ENST00000493608,;COL6A3,non_coding_transcript_exon_variant,,ENST00000491769,;COL6A3,downstream_gene_variant,,ENST00000468792,; T ENST00000295550 Transcript synonymous_variant 9519/10749 9066/9534 3022/3177 L ctC/ctA 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 41/44 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 237334789 237334789 G T 1 0 0 0 0 0 0 0 1 3490 1277 45 2 2 COL6A3 2 237334789 Silent SNP G C3N-01030_T 3493338 237334789 4858740 146 20927 UBE2F 0 . GRCh38 2 237987965 237987965 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.121G>T p.Val41Phe p.V41F ENST00000612130 3/10 53 38 15 91 91 0 strelka-varscan-mutect UBE2F,missense_variant,p.Val41Phe,ENST00000612130,NM_001278305.1;UBE2F,missense_variant,p.Val41Phe,ENST00000272930,NM_080678.2;UBE2F,missense_variant,p.Val41Phe,ENST00000409332,;UBE2F,missense_variant,p.Val17Phe,ENST00000409953,NM_001278306.1;UBE2F,missense_variant,p.Val41Phe,ENST00000409633,NM_001278308.1;UBE2F,missense_variant,p.Val41Phe,ENST00000434655,;UBE2F,missense_variant,p.Val41Phe,ENST00000448502,;UBE2F,intron_variant,,ENST00000414443,NM_001278307.1;UBE2F,intron_variant,,ENST00000416292,;UBE2F,intron_variant,,ENST00000434137,;UBE2F-SCLY,missense_variant,p.Val41Phe,ENST00000449891,;UBE2F,missense_variant,p.Val41Phe,ENST00000441728,;UBE2F-SCLY,missense_variant,p.Val41Phe,ENST00000449191,;UBE2F,missense_variant,p.Val41Phe,ENST00000439338,;UBE2F,missense_variant,p.Val17Phe,ENST00000445676,;UBE2F,missense_variant,p.Val41Phe,ENST00000433241,;UBE2F,missense_variant,p.Val41Phe,ENST00000455999,;UBE2F,missense_variant,p.Val41Phe,ENST00000433568,;UBE2F,missense_variant,p.Val41Phe,ENST00000439780,;UBE2F,splice_region_variant,,ENST00000454786,;UBE2F,splice_region_variant,,ENST00000417231,;UBE2F,splice_region_variant,,ENST00000440223,; T ENST00000612130 Transcript missense_variant,splice_region_variant 254/2135 121/558 41/185 V/F Gtt/Ttt 1 1 UBE2F HGNC HGNC:12480 protein_coding YES CCDS2523.1 ENSP00000478474 Q969M7 UPI000007332C NM_001278305.1 deleterious(0.03) 3/10 PROSITE_profiles:PS50127,hmmpanther:PTHR24067:SF152,hmmpanther:PTHR24067,Gene3D:3.10.110.10,Pfam_domain:PF00179,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 237987965 237987965 G T 1 0 0 0 0 1 0 0 0 17376 1275 44 2 2 UBE2F 2 237987965 Missense_Mutation SNP G C3N-01030_T 653176 237987965 4205564 147 20928 AQP12B 0 . GRCh38 2 240682457 240682457 + Silent SNP G G T rs780283546 C3N-01030_T C3N-01030_N G G c.381C>A p.= p.T127T ENST00000407834 1/3 169 133 36 156 155 1 strelka-varscan-mutect AQP12B,synonymous_variant,p.=,ENST00000407834,NM_001102467.1;AQP12B,synonymous_variant,p.=,ENST00000621682,;AC011298.2,upstream_gene_variant,,ENST00000407635,;AQP12B,upstream_gene_variant,,ENST00000459806,;AQP12B,missense_variant,p.Pro31Thr,ENST00000414322,;AQP12B,missense_variant,p.Pro31Thr,ENST00000413999,;AQP12B,missense_variant,p.Pro31Thr,ENST00000452886,; T ENST00000407834 Transcript synonymous_variant 444/1094 381/924 127/307 T acC/acA rs780283546 1 -1 AQP12B HGNC HGNC:6096 protein_coding YES CCDS46560.1 ENSP00000384894 A6NM10 UPI0000F705B9 NM_001102467.1 1/3 hmmpanther:PTHR21191:SF8,hmmpanther:PTHR21191,PIRSF_domain:PIRSF017529,Pfam_domain:PF00230,Gene3D:1.20.1080.10,Superfamily_domains:SSF81338,Prints_domain:PR02025 LOW 1 SNV 1 1 PASS rs780283546 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 240682457 240682457 G T 1 0 0 0 0 0 0 0 1 948 1219 43 2 2 AQP12B 2 240682457 Silent SNP G C3N-01030_T 2694492 240682457 1511072 148 20929 KIF1A 0 . GRCh38 2 240720936 240720936 + Silent SNP G G T rs368124753 C3N-01030_T C3N-01030_N G G c.4846C>A p.= p.R1616R ENST00000498729 45/49 51 42 9 43 43 0 strelka-varscan-mutect KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,downstream_gene_variant,,ENST00000404283,;KIF1A,downstream_gene_variant,,ENST00000431776,;KIF1A,non_coding_transcript_exon_variant,,ENST00000460788,;KIF1A,non_coding_transcript_exon_variant,,ENST00000492812,;KIF1A,non_coding_transcript_exon_variant,,ENST00000465813,;KIF1A,upstream_gene_variant,,ENST00000488776,; T ENST00000498729 Transcript synonymous_variant 5093/9223 4846/5376 1616/1791 R Cgg/Agg rs368124753,COSM1018761,COSM3782163 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 45/49 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs368124753 . 0 206 4 0 0 0 0 0 -19.98758 1 1 1 1 0 T 2 4 70 240720936 240720936 G T 1 0 0 0 0 0 0 0 1 8147 1086 38 1 1 KIF1A 2 240720936 Silent SNP G C3N-01030_T 38479 240720936 1472593 149 20930 NEU4 0 . GRCh38 2 241815084 241815084 + Missense_Mutation SNP G G T rs766104247 C3N-01030_T C3N-01030_N G G c.433G>T p.Ala145Ser p.A145S ENST00000325935 3/4 92 73 19 73 73 0 strelka-varscan-mutect NEU4,missense_variant,p.Ala132Ser,ENST00000391969,NM_001167602.2;NEU4,missense_variant,p.Ala144Ser,ENST00000404257,NM_080741.3;NEU4,missense_variant,p.Ala145Ser,ENST00000325935,NM_001167599.2;NEU4,missense_variant,p.Ala132Ser,ENST00000407683,NM_001167601.2,NM_001167600.2;NEU4,missense_variant,p.Ala132Ser,ENST00000405370,;NEU4,missense_variant,p.Ala132Ser,ENST00000420288,;NEU4,missense_variant,p.Ala132Ser,ENST00000423583,;NEU4,intron_variant,,ENST00000415936,;NEU4,intron_variant,,ENST00000426032,;NEU4,downstream_gene_variant,,ENST00000428592,;NEU4,downstream_gene_variant,,ENST00000435894,;NEU4,downstream_gene_variant,,ENST00000435934,;AC114730.3,upstream_gene_variant,,ENST00000413820,;AC114730.3,upstream_gene_variant,,ENST00000420272,;AC114730.3,upstream_gene_variant,,ENST00000439270,;NEU4,missense_variant,p.Ala132Ser,ENST00000435855,;NEU4,non_coding_transcript_exon_variant,,ENST00000618597,;NEU4,downstream_gene_variant,,ENST00000488997,;NEU4,downstream_gene_variant,,ENST00000476542,;NEU4,downstream_gene_variant,,ENST00000494678,; T ENST00000325935 Transcript missense_variant 862/2288 433/1494 145/497 A/S Gcc/Tcc rs766104247 1 1 NEU4 HGNC HGNC:21328 protein_coding YES CCDS54441.1 ENSP00000320318 Q8WWR8 UPI0000EE378E NM_001167599.2 tolerated(0.21) 3/4 Gene3D:2.120.10.10,Pfam_domain:PF13088,hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF22,Superfamily_domains:SSF50939 MODERATE 1 SNV 1 1 PASS rs766104247 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 241815084 241815084 G T 1 0 0 0 0 1 0 0 0 10379 1087 38 1 1 NEU4 2 241815084 Missense_Mutation SNP G C3N-01030_T 1094148 241815084 378445 150 20931 PDCD1 0 . GRCh38 2 241852301 241852301 + Silent SNP G G T rs770113678 C3N-01030_T C3N-01030_N G G c.489C>A p.= p.A163A ENST00000334409 3/5 63 52 11 68 68 0 strelka-varscan-mutect PDCD1,synonymous_variant,p.=,ENST00000334409,NM_005018.2;PDCD1,intron_variant,,ENST00000343705,;PDCD1,3_prime_UTR_variant,,ENST00000418831,; T ENST00000334409 Transcript synonymous_variant 559/2114 489/867 163/288 A gcC/gcA rs770113678 1 -1 PDCD1 HGNC HGNC:8760 protein_coding YES CCDS33428.1 ENSP00000335062 Q15116 A0A0M3M0G7 UPI0000061E11 NM_005018.2 3/5 hmmpanther:PTHR15264 LOW 1 SNV 1 1 PASS rs770113678 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 241852301 241852301 G T 1 0 0 0 0 0 0 0 1 11703 1103 39 1 1 PDCD1 2 241852301 Silent SNP G C3N-01030_T 37217 241852301 341228 151 20932 CNTN6 0 . GRCh38 3 1352404 1352404 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1445C>A p.Thr482Lys p.T482K ENST00000446702 12/23 81 66 15 79 79 0 strelka-varscan-mutect CNTN6,missense_variant,p.Thr482Lys,ENST00000446702,;CNTN6,missense_variant,p.Thr482Lys,ENST00000350110,NM_014461.3,NM_001289080.1,NM_001289081.1;CNTN6,3_prime_UTR_variant,,ENST00000397479,; A ENST00000446702 Transcript missense_variant 2072/4513 1445/3087 482/1028 T/K aCa/aAa 1 1 CNTN6 HGNC HGNC:2176 protein_coding YES CCDS2557.1 ENSP00000407822 Q9UQ52 A0A024R2C7 UPI0000072430 tolerated(0.47) 12/23 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF52,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999888 1 1 1 0 A 3 1 70 1352404 1352404 C A 1 0 0 0 0 1 0 0 0 3426 478 17 2 2 CNTN6 3 1352404 Missense_Mutation SNP C C3N-01030_T 1352404 196943155 152 20933 GRM7 0 . GRCh38 3 6861821 6861821 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.433G>C p.Val145Leu p.V145L ENST00000357716 1/10 207 163 44 170 170 0 strelka-varscan-mutect GRM7,missense_variant,p.Val145Leu,ENST00000486284,NM_181874.2;GRM7,missense_variant,p.Val145Leu,ENST00000357716,NM_000844.3;GRM7,missense_variant,p.Val145Leu,ENST00000389336,;GRM7,intron_variant,,ENST00000448328,;GRM7,missense_variant,p.Val145Leu,ENST00000467425,;GRM7,missense_variant,p.Val145Leu,ENST00000440923,;GRM7,missense_variant,p.Val145Leu,ENST00000389335,;GRM7,intron_variant,,ENST00000443259,;GRM7,upstream_gene_variant,,ENST00000435689,; C ENST00000357716 Transcript missense_variant 707/4127 433/2748 145/915 V/L Gtc/Ctc COSM1253836 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 tolerated(0.29) 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 1 MODERATE 1 SNV 1 1 1 PASS rs1055345234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 6861821 6861821 G C 1 0 0 0 0 1 0 0 0 6684 1145 40 4 4 GRM7 3 6861821 Missense_Mutation SNP G C3N-01030_T 5509417 6861821 191433738 153 20934 FANCD2 0 . GRCh38 3 10094362 10094362 + Frame_Shift_Del DEL G G - rs147205530 C3N-01030_T C3N-01030_N G G c.3963+1delG ENST00000287647 40/43 410 314 96 431 431 0 sindel-varindel-pindel FANCD2,frameshift_variant,,ENST00000287647,NM_033084.3;FANCD2,frameshift_variant,,ENST00000419585,NM_001319984.1;FANCD2,frameshift_variant,,ENST00000383807,NM_001018115.1;FANCD2OS,intron_variant,,ENST00000524279,NM_173472.1;FANCD2,intron_variant,,ENST00000470028,;FANCD2OS,intron_variant,,ENST00000436517,;FANCD2OS,intron_variant,,ENST00000431315,;FANCD2,splice_region_variant,,ENST00000421731,; - ENST00000287647 Transcript frameshift_variant,splice_region_variant 4055/5219 3962/4416 1321/1471 R/X cGg/cg rs147205530,COSM215886 1 1 FANCD2 HGNC HGNC:3585 protein_coding YES CCDS2595.1 ENSP00000287647 Q9BXW9 UPI000006F678 NM_033084.3 40/43 hmmpanther:PTHR32086,Pfam_domain:PF14631 0,1 HIGH 1 deletion 1 2 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 10094362 10094362 G - 1 0 1 0 1 0 0 0 0 5524 1130 39 0 0 FANCD2 3 10094362 Frame_Shift_Del DEL G C3N-01030_T 3232541 10094362 188201197 154 20935 ATP2B2 0 . GRCh38 3 10342782 10342782 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.2887delC p.Ala964ProfsTer41 p.A964Pfs*41 ENST00000360273 19/23 326 252 74 281 281 0 sindel-varindel-pindel ATP2B2,frameshift_variant,p.Ala919ProfsTer41,ENST00000397077,;ATP2B2,frameshift_variant,p.Ala964ProfsTer41,ENST00000360273,NM_001001331.2;ATP2B2,frameshift_variant,p.Ala919ProfsTer41,ENST00000383800,NM_001683.3;ATP2B2,frameshift_variant,p.Ala964ProfsTer41,ENST00000352432,;ATP2B2,frameshift_variant,p.Ala820ProfsTer41,ENST00000452124,;ATP2B2,frameshift_variant,p.Ala919ProfsTer41,ENST00000460129,; - ENST00000360273 Transcript frameshift_variant 3326/8962 2887/3732 963/1243 L/X Ctt/tt 1 -1 ATP2B2 HGNC HGNC:815 protein_coding YES CCDS33701.1 ENSP00000353414 Q01814 A0A024R2K6 UPI00001261EF NM_001001331.2 19/23 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,TIGRFAM_domain:TIGR01517,Transmembrane_helices:TMhelix HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 10342782 10342782 G - 1 0 1 0 1 0 0 0 0 1293 971 34 0 0 ATP2B2 3 10342782 Frame_Shift_Del DEL G C3N-01030_T 248420 10342782 187952777 155 20936 FBLN2 0 . GRCh38 3 13637648 13637648 + Missense_Mutation SNP C C T rs200284680 C3N-01030_T C3N-01030_N C C c.3425C>T p.Thr1142Met p.T1142M ENST00000404922 18/18 137 98 39 120 120 0 strelka-varscan-mutect FBLN2,missense_variant,p.Thr1142Met,ENST00000404922,NM_001004019.1;FBLN2,missense_variant,p.Thr1142Met,ENST00000492059,NM_001165035.1;FBLN2,missense_variant,p.Thr1095Met,ENST00000295760,NM_001998.2;FBLN2,intron_variant,,ENST00000295761,;FBLN2,intron_variant,,ENST00000421373,; T ENST00000404922 Transcript missense_variant 3544/4318 3425/3696 1142/1231 T/M aCg/aTg rs200284680 1 1 FBLN2 HGNC HGNC:3601 protein_coding YES CCDS46761.1 ENSP00000384169 P98095 UPI000042B0C1 NM_001004019.1 deleterious(0) 18/18 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF303 MODERATE 1 SNV 5 1 PASS rs200284680 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 13637648 13637648 C T 1 0 0 0 0 1 0 0 0 5562 536 19 1 1 FBLN2 3 13637648 Missense_Mutation SNP C C3N-01030_T 3294866 13637648 184657911 156 20937 TGFBR2 0 . GRCh38 3 30644911 30644911 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.334G>T p.Val112Leu p.V112L ENST00000359013 3/8 267 206 61 305 305 0 strelka-varscan-mutect TGFBR2,missense_variant,p.Val87Leu,ENST00000295754,NM_003242.5;TGFBR2,missense_variant,p.Val112Leu,ENST00000359013,NM_001024847.2; T ENST00000359013 Transcript missense_variant 617/4605 334/1779 112/592 V/L Gta/Tta 1 1 TGFBR2 HGNC HGNC:11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 tolerated(0.11) 3/8 hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PIRSF_domain:PIRSF037393,Gene3D:2.10.60.10,Pfam_domain:PF08917,Superfamily_domains:SSF57302 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 30644911 30644911 G T 1 0 0 0 0 1 0 0 0 16255 1391 48 2 2 TGFBR2 3 30644911 Missense_Mutation SNP G C3N-01030_T 17007263 30644911 167650648 157 20938 OSBPL10 0 . GRCh38 3 31733332 31733332 + Silent SNP T T A rs546090839 C3N-01030_T C3N-01030_N T T c.1020A>T p.= p.S340S ENST00000396556 6/12 165 130 35 162 162 0 strelka-varscan-mutect OSBPL10,synonymous_variant,p.=,ENST00000429492,;OSBPL10,synonymous_variant,p.=,ENST00000396556,NM_017784.4;OSBPL10,synonymous_variant,p.=,ENST00000438237,NM_001174060.1;OSBPL10,synonymous_variant,p.=,ENST00000428241,;OSBPL10,non_coding_transcript_exon_variant,,ENST00000467647,; A ENST00000396556 Transcript synonymous_variant 1143/6600 1020/2295 340/764 S tcA/tcT rs546090839 1 -1 OSBPL10 HGNC HGNC:16395 protein_coding YES CCDS2651.1 ENSP00000379804 Q9BXB5 UPI0000130E9B NM_017784.4 6/12 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF47 LOW 1 SNV 1 1 PASS rs546090839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 31733332 31733332 T A 1 0 0 0 0 0 0 0 1 11341 1567 55 4 4 OSBPL10 3 31733332 Silent SNP T C3N-01030_T 1088421 31733332 166562227 158 20939 MYRIP 0 . GRCh38 3 40209858 40209858 + Missense_Mutation SNP C C T rs201954262 C3N-01030_T C3N-01030_N C C c.1670C>T p.Ser557Leu p.S557L ENST00000302541 11/17 110 90 20 110 110 0 strelka-varscan-mutect MYRIP,missense_variant,p.Ser557Leu,ENST00000302541,NM_015460.3;MYRIP,missense_variant,p.Ser468Leu,ENST00000396217,NM_001284425.1;MYRIP,missense_variant,p.Ser370Leu,ENST00000539167,NM_001284426.1;MYRIP,missense_variant,p.Ser557Leu,ENST00000425621,NM_001284424.1;MYRIP,missense_variant,p.Ser557Leu,ENST00000444716,NM_001284423.1;EIF1B-AS1,intron_variant,,ENST00000625390,;RN7SL411P,downstream_gene_variant,,ENST00000585204,;MYRIP,non_coding_transcript_exon_variant,,ENST00000459828,;MYRIP,missense_variant,p.Ser557Leu,ENST00000458292,;MYRIP,3_prime_UTR_variant,,ENST00000458441,; T ENST00000302541 Transcript missense_variant 2012/5077 1670/2580 557/859 S/L tCg/tTg rs201954262 1 1 MYRIP HGNC HGNC:19156 protein_coding YES CCDS2689.1 ENSP00000301972 Q8NFW9 UPI0000074787 NM_015460.3 tolerated(0.66) 11/17 Pfam_domain:PF04698,hmmpanther:PTHR14555,hmmpanther:PTHR14555:SF6 MODERATE 1 SNV 1 1 PASS rs201954262 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 40209858 40209858 C T 1 0 0 0 0 1 0 0 0 10103 898 31 1 1 MYRIP 3 40209858 Missense_Mutation SNP C C3N-01030_T 8476526 40209858 158085701 159 20940 CCK 0 . GRCh38 3 42258151 42258151 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.295G>A p.Gly99Ser p.G99S ENST00000396169 5/5 173 134 39 151 151 0 strelka-varscan-mutect CCK,missense_variant,p.Gly99Ser,ENST00000396169,NM_000729.4;CCK,missense_variant,p.Gly99Ser,ENST00000334681,;CCK,missense_variant,p.Gly99Ser,ENST00000434608,NM_001174138.1;CCK,downstream_gene_variant,,ENST00000484359,; T ENST00000396169 Transcript missense_variant 1201/1527 295/348 99/115 G/S Ggc/Agc COSM5481815 1 -1 CCK HGNC HGNC:1569 protein_coding YES CCDS2696.1 ENSP00000379472 P06307 Q6FG82 UPI00001272C3 NM_000729.4 deleterious(0) 5/5 Pfam_domain:PF00918,PROSITE_patterns:PS00259,hmmpanther:PTHR10786,SMART_domains:SM00029 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 42258151 42258151 C T 1 0 0 0 0 1 0 0 0 2577 623 22 3 3 CCK 3 42258151 Missense_Mutation SNP C C3N-01030_T 2048293 42258151 156037408 160 20941 ZNF445 0 . GRCh38 3 44449562 44449562 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.882G>T p.= p.L294L ENST00000396077 7/8 282 233 49 221 221 0 strelka-varscan-mutect ZNF445,synonymous_variant,p.=,ENST00000396077,NM_181489.5;ZNF445,synonymous_variant,p.=,ENST00000425708,;ZNF445,downstream_gene_variant,,ENST00000617032,;ZNF445,downstream_gene_variant,,ENST00000460529,; A ENST00000396077 Transcript synonymous_variant 1230/18299 882/3096 294/1031 L ctG/ctT 1 -1 ZNF445 HGNC HGNC:21018 protein_coding YES CCDS2713.1 ENSP00000379387 P59923 UPI000019AD12 NM_181489.5 7/8 PROSITE_profiles:PS50805,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF214 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 44449562 44449562 C A 1 0 0 0 0 0 0 0 1 18489 813 29 2 2 ZNF445 3 44449562 Silent SNP C C3N-01030_T 2191411 44449562 153845997 161 20942 PTH1R 0 . GRCh38 3 46903317 46903317 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1443G>T p.= p.L481L ENST00000313049 14/14 251 192 59 167 167 0 strelka-varscan-mutect PTH1R,synonymous_variant,p.=,ENST00000313049,;PTH1R,synonymous_variant,p.=,ENST00000449590,NM_000316.2;PTH1R,synonymous_variant,p.=,ENST00000418619,;PTH1R,synonymous_variant,p.=,ENST00000430002,NM_001184744.1;PTH1R,synonymous_variant,p.=,ENST00000427125,;PTH1R,synonymous_variant,p.=,ENST00000422115,;PTH1R,downstream_gene_variant,,ENST00000490109,;PTH1R,3_prime_UTR_variant,,ENST00000428220,; T ENST00000313049 Transcript synonymous_variant 1646/2123 1443/1782 481/593 L ctG/ctT 1 1 PTH1R HGNC HGNC:9608 protein_coding YES CCDS2747.1 ENSP00000321999 Q03431 A0A024R2Z8 UPI000005041F 14/14 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF24,Prints_domain:PR00393 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 46903317 46903317 G T 1 0 0 0 0 0 0 0 1 12914 1335 47 2 2 PTH1R 3 46903317 Silent SNP G C3N-01030_T 2453755 46903317 151392242 162 20943 NBEAL2 0 . GRCh38 3 46998195 46998195 + Silent SNP C C A rs373998295 C3N-01030_T C3N-01030_N C C c.3087C>A p.= p.L1029L ENST00000450053 21/54 276 225 51 258 257 1 strelka-varscan-mutect NBEAL2,synonymous_variant,p.=,ENST00000450053,NM_015175.2;NBEAL2,synonymous_variant,p.=,ENST00000416683,;NBEAL2,upstream_gene_variant,,ENST00000443829,;NBEAL2,upstream_gene_variant,,ENST00000475689,; A ENST00000450053 Transcript synonymous_variant 3266/8827 3087/8265 1029/2754 L ctC/ctA rs373998295 1 1 NBEAL2 HGNC HGNC:31928 protein_coding YES CCDS46817.1 ENSP00000415034 Q6ZNJ1 UPI000022C020 NM_015175.2 21/54 Low_complexity_(Seg):seg,hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF50,Pfam_domain:PF15787 LOW 1 SNV 2 1 PASS rs373998295 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 46998195 46998195 C A 1 0 0 0 0 0 0 0 1 10200 900 32 2 2 NBEAL2 3 46998195 Silent SNP C C3N-01030_T 94878 46998195 151297364 163 20944 CADPS 0 . GRCh38 3 62645793 62645793 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.1254C>G p.Ile418Met p.I418M ENST00000383710 6/30 237 194 43 257 257 0 strelka-varscan-mutect CADPS,missense_variant,p.Ile418Met,ENST00000383710,NM_003716.3;CADPS,missense_variant,p.Ile418Met,ENST00000612439,;CADPS,missense_variant,p.Ile418Met,ENST00000357948,NM_183393.2;CADPS,missense_variant,p.Ile418Met,ENST00000283269,NM_183394.2;CADPS,missense_variant,p.Ile418Met,ENST00000490353,; C ENST00000383710 Transcript missense_variant 1604/5471 1254/4062 418/1353 I/M atC/atG COSM1047970,COSM1047971 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 tolerated(0.07) 6/30 hmmpanther:PTHR12166:SF6,hmmpanther:PTHR12166 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1434547440 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 62645793 62645793 G C 1 0 0 0 0 1 0 0 0 2260 1048 37 4 4 CADPS 3 62645793 Missense_Mutation SNP G C3N-01030_T 15647598 62645793 135649766 164 20945 SNTN 0 . GRCh38 3 63675606 63675606 + Silent SNP T T C novel C3N-01030_T C3N-01030_N T T c.330T>C p.= p.L110L ENST00000496807 4/4 199 161 38 253 253 0 strelka-varscan-mutect SNTN,synonymous_variant,p.=,ENST00000496807,; C ENST00000496807 Transcript synonymous_variant 332/3746 330/348 110/115 L ctT/ctC 1 1 SNTN HGNC HGNC:33706 protein_coding ENSP00000419971 C9JXY5 UPI00004A25CC 4/4 LOW 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 63675606 63675606 T C 1 0 0 0 0 0 0 0 1 15196 1741 61 5 5 SNTN 3 63675606 Silent SNP T C3N-01030_T 1029813 63675606 134619953 165 20946 OR5H2 0 . GRCh38 3 98283137 98283137 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.252delC p.Met86CysfsTer11 p.M86Cfs*11 ENST00000355273 1/1 214 161 53 273 273 0 sindel-varindel-pindel OR5H2,frameshift_variant,p.Met86CysfsTer11,ENST00000355273,NM_001005482.1;RP11-325B23.2,intron_variant,,ENST00000508616,; - ENST00000355273 Transcript frameshift_variant 250/945 250/945 84/314 P/X Ccc/cc 1 1 OR5H2 HGNC HGNC:14752 protein_coding YES CCDS33801.1 ENSP00000347418 Q8NGV7 UPI0000041B67 NM_001005482.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF231,Superfamily_domains:SSF81321 HIGH deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 98283137 98283137 C - 1 0 1 0 1 0 0 0 0 11232 855 30 0 0 OR5H2 3 98283137 Frame_Shift_Del DEL C C3N-01030_T 34607531 98283137 100012422 166 20947 NFKBIZ 0 . GRCh38 3 101852164 101852164 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.369C>A p.= p.L123L ENST00000326172 2/12 212 172 40 203 203 0 strelka-varscan-mutect NFKBIZ,synonymous_variant,p.=,ENST00000326172,NM_031419.3;NFKBIZ,synonymous_variant,p.=,ENST00000394054,NM_001005474.2;NFKBIZ,synonymous_variant,p.=,ENST00000326151,;NFKBIZ,synonymous_variant,p.=,ENST00000483180,;NFKBIZ,synonymous_variant,p.=,ENST00000491281,;NFKBIZ,downstream_gene_variant,,ENST00000461724,;NFKBIZ,upstream_gene_variant,,ENST00000477601,;NFKBIZ,non_coding_transcript_exon_variant,,ENST00000486444,;NFKBIZ,upstream_gene_variant,,ENST00000495089,;NFKBIZ,upstream_gene_variant,,ENST00000465476,; A ENST00000326172 Transcript synonymous_variant 484/3923 369/2157 123/718 L ctC/ctA 1 1 NFKBIZ HGNC HGNC:29805 protein_coding YES CCDS2946.1 ENSP00000325663 Q9BYH8 UPI000006FBB1 NM_031419.3 2/12 hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 101852164 101852164 C A 1 0 0 0 0 0 0 0 1 10419 842 30 2 2 NFKBIZ 3 101852164 Silent SNP C C3N-01030_T 3569027 101852164 96443395 167 20948 NFKBIZ 0 . GRCh38 3 101853477 101853481 + Frame_Shift_Del DEL CCAGT CCAGT - novel C3N-01030_T C3N-01030_N CCAGT CCAGT c.953_957delAGTCC p.Gln318ProfsTer4 p.Q318Pfs*4 ENST00000326172 5/12 189 137 52 180 179 1 sindel-varindel-pindel NFKBIZ,frameshift_variant,p.Gln318ProfsTer4,ENST00000326172,NM_031419.3;NFKBIZ,frameshift_variant,p.Gln218ProfsTer4,ENST00000394054,NM_001005474.2;NFKBIZ,frameshift_variant,p.Gln218ProfsTer4,ENST00000483180,;NFKBIZ,intron_variant,,ENST00000326151,;NFKBIZ,downstream_gene_variant,,ENST00000461724,;NFKBIZ,downstream_gene_variant,,ENST00000491281,;NFKBIZ,upstream_gene_variant,,ENST00000477601,;NFKBIZ,upstream_gene_variant,,ENST00000495089,;NFKBIZ,upstream_gene_variant,,ENST00000465476,;NFKBIZ,downstream_gene_variant,,ENST00000486444,;NFKBIZ,upstream_gene_variant,,ENST00000495719,; - ENST00000326172 Transcript frameshift_variant 1066-1070/3923 951-955/2157 317-319/718 PQS/PX ccCCAGTcc/cccc 1 1 NFKBIZ HGNC HGNC:29805 protein_coding YES CCDS2946.1 ENSP00000325663 Q9BYH8 UPI000006FBB1 NM_031419.3 5/12 hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF5 HIGH 1 deletion 1 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 101853477 101853477 CCAGT - 1 0 1 0 1 0 0 0 0 10419 610 22 0 0 NFKBIZ 3 101853477 Frame_Shift_Del DEL CCAGT C3N-01030_T 1313 101853477 96442082 168 20949 POLQ 0 . GRCh38 3 121489234 121489234 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3697G>T p.Val1233Phe p.V1233F ENST00000264233 16/30 88 67 21 151 151 0 strelka-varscan-mutect POLQ,missense_variant,p.Val1368Phe,ENST00000621776,;POLQ,missense_variant,p.Val1233Phe,ENST00000264233,NM_199420.3;RPL7AP11,upstream_gene_variant,,ENST00000486538,; A ENST00000264233 Transcript missense_variant 3826/8775 3697/7773 1233/2590 V/F Gtt/Ttt 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious_low_confidence(0.04) 16/30 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 121489234 121489234 C A 1 0 0 0 0 1 0 0 0 12318 478 17 2 2 POLQ 3 121489234 Missense_Mutation SNP C C3N-01030_T 19635757 121489234 76806325 169 20950 ADCY5 0 . GRCh38 3 123296194 123296194 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.2953G>A p.Ala985Thr p.A985T ENST00000462833 17/21 124 95 29 105 105 0 strelka-varscan ADCY5,missense_variant,p.Ala985Thr,ENST00000462833,NM_183357.2;ADCY5,missense_variant,p.Ala643Thr,ENST00000491190,;ADCY5,missense_variant,p.Ala635Thr,ENST00000309879,NM_001199642.1;ADCY5,downstream_gene_variant,,ENST00000466617,;ADCY5,downstream_gene_variant,,ENST00000468683,;ADCY5,downstream_gene_variant,,ENST00000474577,; T ENST00000462833 Transcript missense_variant 4166/7311 2953/3786 985/1261 A/T Gca/Aca 1 -1 ADCY5 HGNC HGNC:236 protein_coding YES CCDS3022.1 ENSP00000419361 O95622 UPI000015E262 NM_183357.2 tolerated(0.17) 17/21 PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF332,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 123296194 123296194 C T 1 0 0 0 0 1 0 0 0 341 739 26 3 3 ADCY5 3 123296194 Missense_Mutation SNP C C3N-01030_T 1806960 123296194 74999365 170 20951 KALRN 0 . GRCh38 3 124264644 124264644 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.404G>T p.Trp135Leu p.W135L ENST00000240874 4/34 157 131 26 144 144 0 strelka-varscan KALRN,missense_variant,p.Trp135Leu,ENST00000360013,NM_001024660.3;KALRN,missense_variant,p.Trp113Leu,ENST00000354186,;KALRN,missense_variant,p.Trp135Leu,ENST00000240874,NM_003947.4;KALRN,missense_variant,p.Trp135Leu,ENST00000460856,NM_001322989.1;KALRN,missense_variant,p.Trp163Leu,ENST00000448253,;KALRN,upstream_gene_variant,,ENST00000498499,; T ENST00000240874 Transcript missense_variant 561/6537 404/4992 135/1663 W/L tGg/tTg 1 1 KALRN HGNC HGNC:4814 protein_coding YES CCDS3027.1 ENSP00000240874 O60229 UPI000012C095 NM_003947.4 deleterious(0) 4/34 Gene3D:3.40.525.10,Pfam_domain:PF00650,PROSITE_profiles:PS50191,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 70 124264644 124264644 G T 1 0 0 0 0 1 0 0 0 7884 1357 47 2 2 KALRN 3 124264644 Missense_Mutation SNP G C3N-01030_T 968450 124264644 74030915 171 20952 UMPS 0 . GRCh38 3 124731509 124731509 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.160G>T p.Gly54Ter p.G54* ENST00000628619 2/2 74 55 19 50 50 0 strelka-varscan UMPS,stop_gained,p.Gly54Ter,ENST00000628619,;UMPS,intron_variant,,ENST00000232607,NM_000373.3;MIR544B,upstream_gene_variant,,ENST00000582372,;UMPS,stop_gained,p.Gly54Ter,ENST00000467167,;UMPS,stop_gained,p.Gly54Ter,ENST00000460034,;UMPS,intron_variant,,ENST00000479719,;UMPS,intron_variant,,ENST00000462091,;UMPS,intron_variant,,ENST00000474588,;UMPS,intron_variant,,ENST00000497791,;RP11-71H17.1,downstream_gene_variant,,ENST00000475510,; T ENST00000628619 Transcript stop_gained 187/228 160/201 54/66 G/* Gga/Tga 1 1 UMPS HGNC HGNC:12563 protein_coding ENSP00000486143 F2Z303 UPI0000412984 2/2 Gene3D:3.40.50.2020,hmmpanther:PTHR19278,hmmpanther:PTHR19278:SF9,Superfamily_domains:SSF53271 HIGH SNV 5 1 PASS . . 0 197 11 2 0 0 0 0 -20 0.9996025 1 1 1 0 T 4 4 70 124731509 124731509 G T 1 0 0 0 0 0 1 0 0 17505 1246 43 2 2 UMPS 3 124731509 Nonsense_Mutation SNP G C3N-01030_T 466865 124731509 73564050 172 20953 CFAP100 0 . GRCh38 3 126419706 126419706 + Silent SNP G G A rs757315451 C3N-01030_T C3N-01030_N G G c.801G>A p.= p.S267S ENST00000352312 9/17 211 169 42 190 190 0 strelka-varscan CFAP100,synonymous_variant,p.=,ENST00000352312,NM_182628.2;CFAP100,synonymous_variant,p.=,ENST00000505024,;CFAP100,upstream_gene_variant,,ENST00000507830,;CFAP100,downstream_gene_variant,,ENST00000533201,;CFAP100,downstream_gene_variant,,ENST00000503905,; A ENST00000352312 Transcript synonymous_variant 900/2086 801/1836 267/611 S tcG/tcA rs757315451,COSM1037730 1 1 CFAP100 HGNC HGNC:26842 protein_coding YES CCDS3037.1 ENSP00000344749 Q494V2 UPI000013E315 NM_182628.2 9/17 hmmpanther:PTHR21683:SF5,hmmpanther:PTHR21683,Pfam_domain:PF13863 0,1 LOW 1 SNV 2 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 126419706 126419706 G A 1 0 0 0 0 0 0 0 1 3010 1074 38 1 1 CFAP100 3 126419706 Silent SNP G C3N-01030_T 1688197 126419706 71875853 173 20954 ZIC1 0 . GRCh38 3 147411004 147411004 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.892G>T p.Gly298Cys p.G298C ENST00000282928 1/3 235 189 46 211 211 0 strelka-varscan ZIC1,missense_variant,p.Gly298Cys,ENST00000282928,NM_003412.3;ZIC1,intron_variant,,ENST00000488404,;ZIC4,upstream_gene_variant,,ENST00000383075,NM_032153.5;ZIC4,upstream_gene_variant,,ENST00000462748,;ZIC4,upstream_gene_variant,,ENST00000491672,NM_001243256.1;ZIC4,upstream_gene_variant,,ENST00000463250,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,upstream_gene_variant,,ENST00000464144,; T ENST00000282928 Transcript missense_variant 1621/5241 892/1344 298/447 G/C Ggc/Tgc 1 1 ZIC1 HGNC HGNC:12872 protein_coding YES CCDS3136.1 ENSP00000282928 Q15915 UPI000013DD09 NM_003412.3 deleterious(0) 1/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF26,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 147411004 147411004 G T 1 0 0 0 0 1 0 0 0 18257 1232 43 2 2 ZIC1 3 147411004 Missense_Mutation SNP G C3N-01030_T 20991298 147411004 50884555 174 20955 CPA3 0 . GRCh38 3 148883758 148883758 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.924G>T p.Gln308His p.Q308H ENST00000296046 9/11 243 190 53 299 298 1 strelka-varscan CPA3,missense_variant,p.Gln308His,ENST00000296046,NM_001870.2;RP11-680B3.2,intron_variant,,ENST00000488190,;CPA3,non_coding_transcript_exon_variant,,ENST00000477926,; T ENST00000296046 Transcript missense_variant 976/1795 924/1254 308/417 Q/H caG/caT 1 1 CPA3 HGNC HGNC:2298 protein_coding YES CCDS3138.1 ENSP00000296046 P15088 UPI000013E2F4 NM_001870.2 deleterious(0) 9/11 Gene3D:3.40.630.10,Pfam_domain:PF00246,Prints_domain:PR00765,PROSITE_patterns:PS00133,hmmpanther:PTHR11705,hmmpanther:PTHR11705:SF65,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 148883758 148883758 G T 1 0 0 0 0 1 0 0 0 3585 933 33 2 2 CPA3 3 148883758 Missense_Mutation SNP G C3N-01030_T 1472754 148883758 49411801 175 20956 ERICH6 0 . GRCh38 3 150682268 150682268 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.832C>A p.Leu278Ile p.L278I ENST00000295910 7/14 176 142 34 200 198 2 strelka-varscan ERICH6,missense_variant,p.Leu278Ile,ENST00000295910,NM_152394.4;ERICH6,missense_variant,p.Leu132Ile,ENST00000491361,NM_001308234.1;ERICH6,downstream_gene_variant,,ENST00000474463,;ERICH6,non_coding_transcript_exon_variant,,ENST00000491716,; T ENST00000295910 Transcript missense_variant 885/2052 832/1992 278/663 L/I Cta/Ata 1 -1 ERICH6 HGNC HGNC:28602 protein_coding YES CCDS3151.2 ENSP00000295910 Q7L0X2 UPI000023281A NM_152394.4 deleterious(0.04) 7/14 hmmpanther:PTHR23093 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 150682268 150682268 G T 1 0 0 0 0 1 0 0 0 5086 933 33 2 2 ERICH6 3 150682268 Missense_Mutation SNP G C3N-01030_T 1798510 150682268 47613291 176 20957 MLF1 0 . GRCh38 3 158598207 158598207 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.500G>A p.Gly167Glu p.G167E ENST00000392822 5/8 106 82 24 136 136 0 strelka-varscan MLF1,missense_variant,p.Gly126Glu,ENST00000619577,;MLF1,missense_variant,p.Gly111Glu,ENST00000359117,NM_001130156.2;MLF1,missense_variant,p.Gly136Glu,ENST00000355893,NM_022443.4;MLF1,missense_variant,p.Gly167Glu,ENST00000392822,NM_001195432.1;MLF1,missense_variant,p.Gly126Glu,ENST00000478894,;MLF1,missense_variant,p.Gly126Glu,ENST00000471745,NM_001195434.1;MLF1,missense_variant,p.Gly111Glu,ENST00000484955,NM_001130157.2;MLF1,missense_variant,p.Gly111Glu,ENST00000482628,;MLF1,missense_variant,p.Gly62Glu,ENST00000491767,;MLF1,missense_variant,p.Gly126Glu,ENST00000477042,;MLF1,missense_variant,p.Gly91Glu,ENST00000498592,;MLF1,missense_variant,p.Gly151Glu,ENST00000466246,;MLF1,intron_variant,,ENST00000618075,;MLF1,intron_variant,,ENST00000469452,NM_001195433.1;MLF1,splice_region_variant,,ENST00000497004,;MLF1,splice_region_variant,,ENST00000495452,;MLF1,downstream_gene_variant,,ENST00000487838,; A ENST00000392822 Transcript missense_variant,splice_region_variant 500/2157 500/900 167/299 G/E gGa/gAa 1 1 MLF1 HGNC HGNC:7125 protein_coding YES CCDS56286.1 ENSP00000376568 P58340 UPI000007134A NM_001195432.1 deleterious(0) 5/8 hmmpanther:PTHR13105,hmmpanther:PTHR13105:SF3,Pfam_domain:PF10248 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 158598207 158598207 G A 1 0 0 0 0 1 0 0 0 9582 1188 41 3 3 MLF1 3 158598207 Missense_Mutation SNP G C3N-01030_T 7915939 158598207 39697352 177 20958 SLITRK3 0 . GRCh38 3 165188974 165188974 + Silent SNP T T G novel C3N-01030_T C3N-01030_N T T c.1857A>C p.= p.P619P ENST00000475390 2/2 183 131 52 182 182 0 strelka-varscan SLITRK3,synonymous_variant,p.=,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,synonymous_variant,p.=,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; G ENST00000475390 Transcript synonymous_variant 2301/4555 1857/2934 619/977 P ccA/ccC 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 165188974 165188974 T G 1 0 0 0 0 0 0 0 1 15035 1567 55 5 5 SLITRK3 3 165188974 Silent SNP T C3N-01030_T 6590767 165188974 33106585 178 20959 ATP11B 0 . GRCh38 3 182897352 182897352 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.3098G>T p.Trp1033Leu p.W1033L ENST00000323116 27/30 114 95 19 187 187 0 strelka-varscan ATP11B,missense_variant,p.Trp1033Leu,ENST00000323116,NM_014616.2;ATP11B,missense_variant,p.Trp834Leu,ENST00000498086,;ATP11B,missense_variant,p.Trp18Leu,ENST00000491699,;ATP11B,downstream_gene_variant,,ENST00000482070,;ATP11B,upstream_gene_variant,,ENST00000484691,;ATP11B,upstream_gene_variant,,ENST00000475636,;ATP11B,3_prime_UTR_variant,,ENST00000466758,;ATP11B,non_coding_transcript_exon_variant,,ENST00000490303,; T ENST00000323116 Transcript missense_variant 3358/7325 3098/3534 1033/1177 W/L tGg/tTg 1 1 ATP11B HGNC HGNC:13553 protein_coding YES CCDS33896.1 ENSP00000321195 Q9Y2G3 UPI000004124E NM_014616.2 tolerated(0.12) 27/30 Superfamily_domains:0049473,Pfam_domain:PF16212,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF57,TIGRFAM_domain:TIGR01652,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 182897352 182897352 G T 1 0 0 0 0 1 0 0 0 1272 1357 47 2 2 ATP11B 3 182897352 Missense_Mutation SNP G C3N-01030_T 17708378 182897352 15398207 179 20960 ABCC5 0 . GRCh38 3 183953249 183953249 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.2504A>T p.Glu835Val p.E835V ENST00000334444 18/30 94 69 25 92 92 0 strelka-varscan ABCC5,missense_variant,p.Glu835Val,ENST00000334444,NM_005688.2;ABCC5,missense_variant,p.Glu835Val,ENST00000265586,;ABCC5,3_prime_UTR_variant,,ENST00000437205,NM_001320032.1; A ENST00000334444 Transcript missense_variant 2745/5921 2504/4314 835/1437 E/V gAg/gTg 1 -1 ABCC5 HGNC HGNC:56 protein_coding YES CCDS43176.1 ENSP00000333926 O15440 UPI000004A33C NM_005688.2 tolerated(0.11) 18/30 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF196 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 183953249 183953249 T A 1 0 0 0 0 1 0 0 0 60 1551 54 4 4 ABCC5 3 183953249 Missense_Mutation SNP T C3N-01030_T 1055897 183953249 14342310 180 20961 POLR2H 0 . GRCh38 3 184368273 184368273 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.496G>A p.Asp166Asn p.D166N ENST00000429568 5/5 63 53 10 73 73 0 strelka-varscan POLR2H,missense_variant,p.Asp166Asn,ENST00000429568,NM_001278698.1;POLR2H,synonymous_variant,p.=,ENST00000456318,NM_006232.3;POLR2H,synonymous_variant,p.=,ENST00000430783,NM_001278714.1;POLR2H,synonymous_variant,p.=,ENST00000438240,NM_001278700.1;POLR2H,synonymous_variant,p.=,ENST00000455712,;POLR2H,synonymous_variant,p.=,ENST00000443489,NM_001278715.1;POLR2H,synonymous_variant,p.=,ENST00000452961,NM_001278699.1;THPO,downstream_gene_variant,,ENST00000204615,NM_000460.3,NM_001289998.1,NM_001290028.1;THPO,downstream_gene_variant,,ENST00000445696,NM_001177598.2,NM_001290022.1,NM_001177597.2,NM_001290026.1;THPO,downstream_gene_variant,,ENST00000421442,NM_001289997.1,NM_001290027.1;POLR2H,downstream_gene_variant,,ENST00000412877,;THPO,downstream_gene_variant,,ENST00000477594,;POLR2H,non_coding_transcript_exon_variant,,ENST00000488213,;POLR2H,non_coding_transcript_exon_variant,,ENST00000476003,;POLR2H,downstream_gene_variant,,ENST00000490958,;POLR2H,downstream_gene_variant,,ENST00000489043,; A ENST00000429568 Transcript missense_variant 555/878 496/528 166/175 D/N Gat/Aat 1 1 POLR2H HGNC HGNC:9195 protein_coding YES CCDS63859.1 ENSP00000415536 P52434 UPI000198CBDF NM_001278698.1 deleterious_low_confidence(0) 5/5 MODERATE SNV 2 1 PASS . . 0 200 9 0 0 0 0 0 -19.99868 0.9999941 1 1 1 0 A 3 1 70 184368273 184368273 G A 1 0 0 0 0 1 0 0 0 12331 1290 45 3 3 POLR2H 3 184368273 Missense_Mutation SNP G C3N-01030_T 415024 184368273 13927286 181 20962 VPS8 0 . GRCh38 3 184849999 184849999 + Nonsense_Mutation SNP G G T rs748940907 C3N-01030_T C3N-01030_N G G c.730G>T p.Gly244Ter p.G244* ENST00000625842 10/48 128 85 43 170 170 0 strelka-varscan VPS8,stop_gained,p.Gly244Ter,ENST00000287546,;VPS8,stop_gained,p.Gly242Ter,ENST00000436792,NM_015303.3;VPS8,stop_gained,p.Gly244Ter,ENST00000625842,NM_001009921.2;VPS8,stop_gained,p.Gly242Ter,ENST00000446204,;VPS8,downstream_gene_variant,,ENST00000422105,;VPS8,non_coding_transcript_exon_variant,,ENST00000452666,;VPS8,non_coding_transcript_exon_variant,,ENST00000469713,;VPS8,non_coding_transcript_exon_variant,,ENST00000465818,;VPS8,downstream_gene_variant,,ENST00000469479,; T ENST00000625842 Transcript stop_gained 837/4969 730/4287 244/1428 G/* Gga/Tga rs748940907 1 1 VPS8 HGNC HGNC:29122 protein_coding YES CCDS46971.1 ENSP00000487164 Q8N3P4 UPI0000160BDC NM_001009921.2 10/48 hmmpanther:PTHR22847:SF425,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Superfamily_domains:SSF50978,Superfamily_domains:SSF50969 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 184849999 184849999 G T 1 0 0 0 0 0 1 0 0 17766 1001 35 2 2 VPS8 3 184849999 Nonsense_Mutation SNP G C3N-01030_T 481726 184849999 13445560 182 20963 ACAP2 0 . GRCh38 3 195297276 195297276 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1401G>T p.Met467Ile p.M467I ENST00000326793 16/23 79 59 20 138 137 1 strelka-varscan ACAP2,missense_variant,p.Met467Ile,ENST00000326793,NM_012287.5;ACAP2,missense_variant,p.Met466Ile,ENST00000618471,;ACAP2,missense_variant,p.Met474Ile,ENST00000635383,;ACAP2,missense_variant,p.Met26Ile,ENST00000450200,;ACAP2,downstream_gene_variant,,ENST00000439758,;ACAP2,non_coding_transcript_exon_variant,,ENST00000475905,;ACAP2,non_coding_transcript_exon_variant,,ENST00000484296,; A ENST00000326793 Transcript missense_variant 1632/7160 1401/2337 467/778 M/I atG/atT 1 -1 ACAP2 HGNC HGNC:16469 protein_coding YES CCDS33924.1 ENSP00000324287 Q15057 UPI0000141A1A NM_012287.5 deleterious(0) 16/23 PROSITE_profiles:PS50115,hmmpanther:PTHR23180:SF241,hmmpanther:PTHR23180,Pfam_domain:PF01412,SMART_domains:SM00105,Superfamily_domains:SSF57863,Prints_domain:PR00405 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 195297276 195297276 C A 1 0 0 0 0 1 0 0 0 162 492 17 2 2 ACAP2 3 195297276 Missense_Mutation SNP C C3N-01030_T 10447277 195297276 2998283 183 20964 MUC4 0 . GRCh38 3 195771666 195771666 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.13228A>G p.Thr4410Ala p.T4410A ENST00000463781 5/25 109 80 29 103 103 0 strelka-varscan MUC4,missense_variant,p.Thr4410Ala,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Thr4410Ala,ENST00000475231,;MUC4,missense_variant,p.Thr174Ala,ENST00000346145,NM_004532.5;MUC4,missense_variant,p.Thr123Ala,ENST00000349607,NM_138297.4;MUC4,upstream_gene_variant,,ENST00000486425,;MUC4,missense_variant,p.Thr4410Ala,ENST00000478156,;MUC4,missense_variant,p.Thr4410Ala,ENST00000477756,;MUC4,missense_variant,p.Thr4410Ala,ENST00000480843,;MUC4,synonymous_variant,p.=,ENST00000466475,;MUC4,synonymous_variant,p.=,ENST00000477086,;MUC4,synonymous_variant,p.=,ENST00000462323,;MUC4,synonymous_variant,p.=,ENST00000470451,;MUC4,synonymous_variant,p.=,ENST00000479406,;MUC4,synonymous_variant,p.=,ENST00000448861,;MUC4,synonymous_variant,p.=,ENST00000308466,;MUC4,synonymous_variant,p.=,ENST00000339251,;MUC4,synonymous_variant,p.=,ENST00000415455,;MUC4,synonymous_variant,p.=,ENST00000392407,; C ENST00000463781 Transcript missense_variant 13688/17110 13228/16239 4410/5412 T/A Acc/Gcc 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 deleterious_low_confidence(0.01) 5/25 PROSITE_profiles:PS51220,hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF42,SMART_domains:SM00539 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 195771666 195771666 T C 1 0 0 0 0 1 0 0 0 9977 1667 58 5 5 MUC4 3 195771666 Missense_Mutation SNP T C3N-01030_T 474390 195771666 2523893 184 20965 LRCH3 0 . GRCh38 3 197871348 197871348 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.2016G>A p.= p.V672V ENST00000334859 19/19 118 98 20 108 108 0 strelka-varscan LRCH3,synonymous_variant,p.=,ENST00000438796,;LRCH3,synonymous_variant,p.=,ENST00000428136,;LRCH3,synonymous_variant,p.=,ENST00000425562,;LRCH3,synonymous_variant,p.=,ENST00000414675,;LRCH3,synonymous_variant,p.=,ENST00000334859,NM_032773.3;LRCH3,synonymous_variant,p.=,ENST00000441090,;LRCH3,synonymous_variant,p.=,ENST00000433298,;LRCH3,synonymous_variant,p.=,ENST00000452660,;LRCH3,non_coding_transcript_exon_variant,,ENST00000471667,;LRCH3,non_coding_transcript_exon_variant,,ENST00000483442,;LRCH3,non_coding_transcript_exon_variant,,ENST00000473177,;LRCH3,upstream_gene_variant,,ENST00000466054,;LRCH3,downstream_gene_variant,,ENST00000461674,;LRCH3,upstream_gene_variant,,ENST00000476664,; A ENST00000334859 Transcript synonymous_variant 2021/2258 2016/2139 672/712 V gtG/gtA 1 1 LRCH3 HGNC HGNC:28637 protein_coding YES CCDS3330.1 ENSP00000334375 Q96II8 UPI000006E903 NM_032773.3 19/19 Gene3D:1.10.418.10,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 197871348 197871348 G A 1 0 0 0 0 0 0 0 1 8828 1364 48 3 3 LRCH3 3 197871348 Silent SNP G C3N-01030_T 2099682 197871348 424211 185 20966 LMLN 0 . GRCh38 3 197980347 197980347 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.571G>T p.Gly191Cys p.G191C ENST00000420910 6/17 112 83 29 90 90 0 strelka-varscan LMLN,missense_variant,p.Gly191Cys,ENST00000330198,NM_033029.3;LMLN,missense_variant,p.Gly191Cys,ENST00000420910,NM_001136049.2;LMLN,missense_variant,p.Gly139Cys,ENST00000482695,;LMLN,missense_variant,p.Gly139Cys,ENST00000332636,;LMLN,missense_variant,p.Gly119Cys,ENST00000419117,;LMLN,non_coding_transcript_exon_variant,,ENST00000451139,;LMLN,non_coding_transcript_exon_variant,,ENST00000473676,;LMLN,non_coding_transcript_exon_variant,,ENST00000482837,; T ENST00000420910 Transcript missense_variant 571/2423 571/2079 191/692 G/C Ggt/Tgt 1 1 LMLN HGNC HGNC:15991 protein_coding YES CCDS46988.1 ENSP00000410926 Q96KR4 UPI000192C367 NM_001136049.2 deleterious(0.03) 6/17 hmmpanther:PTHR10942,hmmpanther:PTHR10942:SF0,Gene3D:1lmlA01,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 197980347 197980347 G T 1 0 0 0 0 1 0 0 0 8771 1232 43 2 2 LMLN 3 197980347 Missense_Mutation SNP G C3N-01030_T 108999 197980347 315212 186 20967 USP17L17 0 . GRCh38 4 9243944 9243944 + Silent SNP T T C novel C3N-01030_T C3N-01030_N T T c.66T>C p.= p.S22S ENST00000511568 1/1 201 188 13 158 158 0 varscan-mutect USP17L17,synonymous_variant,p.=,ENST00000614762,;USP17L17,synonymous_variant,p.=,ENST00000511568,NM_001256857.1;USP17L18,upstream_gene_variant,,ENST00000619296,;USP17L18,upstream_gene_variant,,ENST00000504209,NM_001256859.1;USP17L16P,downstream_gene_variant,,ENST00000507155,; C ENST00000511568 Transcript synonymous_variant 66/1593 66/1593 22/530 S tcT/tcC 1 1 USP17L17 HGNC HGNC:44445 protein_coding YES CCDS59458.1 ENSP00000422621 D6RBQ6 UPI0000160391 NM_001256857.1 1/1 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 9243944 9243944 T C 1 0 0 0 0 0 0 0 1 17584 1596 56 5 5 USP17L17 4 9243944 Silent SNP T C3N-01030_T 9243944 180970611 187 20968 PROM1 0 . GRCh38 4 16023392 16023392 + Nonsense_Mutation SNP C C A rs752543587 C3N-01030_T C3N-01030_N C C c.718G>T p.Gly240Ter p.G240* ENST00000510224 8/28 136 105 31 119 119 0 strelka-varscan-mutect PROM1,stop_gained,p.Gly231Ter,ENST00000505450,NM_001145848.1;PROM1,stop_gained,p.Gly231Ter,ENST00000508167,NM_001145847.1;PROM1,stop_gained,p.Gly240Ter,ENST00000510224,;PROM1,stop_gained,p.Gly240Ter,ENST00000447510,NM_006017.2;PROM1,stop_gained,p.Gly240Ter,ENST00000540805,NM_001145849.1,NM_001145851.1;PROM1,stop_gained,p.Gly240Ter,ENST00000539194,NM_001145850.1,NM_001145852.1;PROM1,non_coding_transcript_exon_variant,,ENST00000502943,;PROM1,3_prime_UTR_variant,,ENST00000511153,; A ENST00000510224 Transcript stop_gained 967/4006 718/2598 240/865 G/* Gga/Tga rs752543587 1 -1 PROM1 HGNC HGNC:9454 protein_coding YES CCDS47029.1 ENSP00000426809 O43490 UPI000004ECD6 8/28 hmmpanther:PTHR22730,hmmpanther:PTHR22730:SF3,Pfam_domain:PF05478 HIGH 1 SNV 5 1 PASS rs752543587 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 16023392 16023392 C A 1 0 0 0 0 0 1 0 0 12687 661 23 1 1 PROM1 4 16023392 Nonsense_Mutation SNP C C3N-01030_T 6779448 16023392 174191163 188 20969 ARAP2 0 . GRCh38 4 36210534 36210534 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1343G>T p.Arg448Met p.R448M ENST00000303965 6/33 196 155 41 214 212 2 strelka-varscan-mutect ARAP2,missense_variant,p.Arg448Met,ENST00000303965,NM_015230.3;ARAP2,5_prime_UTR_variant,,ENST00000511416,;ARAP2,non_coding_transcript_exon_variant,,ENST00000508066,; A ENST00000303965 Transcript missense_variant 1833/7514 1343/5115 448/1704 R/M aGg/aTg 1 -1 ARAP2 HGNC HGNC:16924 protein_coding YES CCDS3441.1 ENSP00000302895 Q8WZ64 UPI000013E917 NM_015230.3 tolerated(0.26) 6/33 hmmpanther:PTHR23180:SF263,hmmpanther:PTHR23180 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 36210534 36210534 C A 1 0 0 0 0 1 0 0 0 961 681 24 2 2 ARAP2 4 36210534 Missense_Mutation SNP C C3N-01030_T 20187142 36210534 154004021 189 20970 TLR1 0 . GRCh38 4 38796824 38796824 + Missense_Mutation SNP C C T rs138709743 C3N-01030_T C3N-01030_N C C c.2008G>A p.Glu670Lys p.E670K ENST00000308979 4/4 231 168 63 255 255 0 strelka-varscan-mutect TLR1,missense_variant,p.Glu670Lys,ENST00000308979,NM_003263.3;TLR1,missense_variant,p.Glu670Lys,ENST00000502213,;TLR1,downstream_gene_variant,,ENST00000505940,;TLR1,downstream_gene_variant,,ENST00000508364,;TLR1,downstream_gene_variant,,ENST00000515861,;TLR1,downstream_gene_variant,,ENST00000506146,;TLR1,intron_variant,,ENST00000505744,;TLR1,upstream_gene_variant,,ENST00000510552,;TLR1,downstream_gene_variant,,ENST00000509754,;TLR1,downstream_gene_variant,,ENST00000508535,; T ENST00000308979 Transcript missense_variant 2282/2849 2008/2361 670/786 E/K Gag/Aag rs138709743,COSM110527 1 -1 TLR1 HGNC HGNC:11847 protein_coding YES CCDS33973.1 ENSP00000354932 Q15399 UPI000013EDFA NM_003263.3 deleterious(0) 4/4 Gene3D:3.40.50.10140,Pfam_domain:PF01582,PIRSF_domain:PIRSF037595,PROSITE_profiles:PS50104,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF261,SMART_domains:SM00255,Superfamily_domains:SSF52200 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs138709743 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 38796824 38796824 C T 1 0 0 0 0 1 0 0 0 16395 835 29 3 3 TLR1 4 38796824 Missense_Mutation SNP C C3N-01030_T 2586290 38796824 151417731 190 20971 N4BP2 0 . GRCh38 4 40103033 40103033 + Silent SNP A A T rs540805933 C3N-01030_T C3N-01030_N A A c.1188A>T p.= p.T396T ENST00000261435 4/18 270 202 68 277 277 0 strelka-varscan-mutect N4BP2,synonymous_variant,p.=,ENST00000261435,NM_018177.4;N4BP2,synonymous_variant,p.=,ENST00000513269,;N4BP2,downstream_gene_variant,,ENST00000515550,;N4BP2,3_prime_UTR_variant,,ENST00000511480,NM_001318359.1; T ENST00000261435 Transcript synonymous_variant 1604/9744 1188/5313 396/1770 T acA/acT rs540805933 1 1 N4BP2 HGNC HGNC:29851 protein_coding YES CCDS3457.1 ENSP00000261435 Q86UW6 UPI00001A962C NM_018177.4 4/18 hmmpanther:PTHR13308,hmmpanther:PTHR13308:SF21 LOW 1 SNV 5 1 PASS rs540805933 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 40103033 40103033 A T 1 0 0 0 0 0 0 0 1 10114 204 8 4 4 N4BP2 4 40103033 Silent SNP A C3N-01030_T 1306209 40103033 150111522 191 20972 GABRA4 0 . GRCh38 4 46977567 46977567 + Missense_Mutation SNP G G T rs775500790 C3N-01030_T C3N-01030_N G G c.337C>A p.Pro113Thr p.P113T ENST00000264318 4/9 136 102 34 188 187 1 strelka-varscan-mutect GABRA4,missense_variant,p.Pro113Thr,ENST00000264318,NM_000809.3,NM_001204266.1;GABRA4,3_prime_UTR_variant,,ENST00000508560,;GABRA4,3_prime_UTR_variant,,ENST00000511523,;GABRA4,3_prime_UTR_variant,,ENST00000502874,; T ENST00000264318 Transcript missense_variant 1320/11973 337/1665 113/554 P/T Ccc/Acc rs775500790 1 -1 GABRA4 HGNC HGNC:4078 protein_coding YES CCDS3473.1 ENSP00000264318 P48169 X5D7F5 UPI0000074200 NM_000809.3,NM_001204266.1 tolerated(0.17) 4/9 hmmpanther:PTHR18945:SF393,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR01079 MODERATE 1 SNV 1 1 PASS rs775500790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 46977567 46977567 G T 1 0 0 0 0 1 0 0 0 6034 1232 43 2 2 GABRA4 4 46977567 Missense_Mutation SNP G C3N-01030_T 6874534 46977567 143236988 192 20973 CORIN 0 . GRCh38 4 47623666 47623666 + Frame_Shift_Del DEL C C - rs762631726 C3N-01030_T C3N-01030_N C C c.2445delG p.Trp815CysfsTer25 p.W815Cfs*25 ENST00000273857 19/22 206 169 37 209 209 0 sindel-varindel-pindel CORIN,frameshift_variant,p.Trp815CysfsTer25,ENST00000273857,NM_006587.3;CORIN,frameshift_variant,p.Trp711CysfsTer25,ENST00000610355,NM_001278585.1;CORIN,frameshift_variant,p.Trp676CysfsTer25,ENST00000508498,;CORIN,frameshift_variant,p.Trp748CysfsTer25,ENST00000502252,;CORIN,frameshift_variant,p.Trp778CysfsTer25,ENST00000505909,;CORIN,non_coding_transcript_exon_variant,,ENST00000515827,; - ENST00000273857 Transcript frameshift_variant 2445/4852 2445/3129 815/1042 W/X tgG/tg rs762631726,COSM1429878 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 19/22 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF036376,PROSITE_profiles:PS50240,hmmpanther:PTHR24270,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 47623666 47623666 C - 1 0 1 0 1 0 0 0 0 3546 740 26 0 0 CORIN 4 47623666 Frame_Shift_Del DEL C C3N-01030_T 646099 47623666 142590889 193 20974 KIAA1211 0 . GRCh38 4 56315487 56315487 + Missense_Mutation SNP C C G C3N-01030_T C3N-01030_N C C c.1985C>G p.Ala662Gly p.A662G ENST00000504228 6/9 234 165 69 196 196 0 strelka-varscan-mutect KIAA1211,missense_variant,p.Ala662Gly,ENST00000504228,;KIAA1211,missense_variant,p.Ala655Gly,ENST00000541073,;KIAA1211,missense_variant,p.Ala662Gly,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; G ENST00000504228 Transcript missense_variant 2090/4628 1985/3702 662/1233 A/G gCg/gGg COSM325616,COSM4993811 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 tolerated(0.42) 6/9 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 56315487 56315487 C G 1 0 0 0 0 1 0 0 0 8107 768 27 4 4 KIAA1211 4 56315487 Missense_Mutation SNP C C3N-01030_T 8691821 56315487 133899068 194 20975 KIAA1211 0 . GRCh38 4 56316277 56316277 + Silent SNP C C T rs776614182 C3N-01030_T C3N-01030_N C C c.2775C>T p.= p.S925S ENST00000504228 6/9 145 107 38 114 114 0 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,;MRPL22P1,downstream_gene_variant,,ENST00000505398,; T ENST00000504228 Transcript synonymous_variant 2880/4628 2775/3702 925/1233 S agC/agT rs776614182 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 LOW 1 SNV 5 1 PASS rs776614182 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 56316277 56316277 C T 1 0 0 0 0 0 0 0 1 8107 709 25 3 3 KIAA1211 4 56316277 Silent SNP C C3N-01030_T 790 56316277 133898278 195 20976 KIAA1211 0 . GRCh38 4 56316295 56316295 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.2793G>T p.= p.V931V ENST00000504228 6/9 144 111 33 108 107 1 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,;MRPL22P1,downstream_gene_variant,,ENST00000505398,; T ENST00000504228 Transcript synonymous_variant 2898/4628 2793/3702 931/1233 V gtG/gtT 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 6/9 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 56316295 56316295 G T 1 0 0 0 0 0 0 0 1 8107 1335 47 2 2 KIAA1211 4 56316295 Silent SNP G C3N-01030_T 18 56316295 133898260 196 20977 ADGRL3 0 . GRCh38 4 61813809 61813809 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.1196G>T p.Gly399Val p.G399V ENST00000514591 8/25 176 132 44 257 257 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Gly399Val,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.Gly399Val,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Gly467Val,ENST00000509896,;ADGRL3,missense_variant,p.Gly467Val,ENST00000511324,;ADGRL3,missense_variant,p.Gly467Val,ENST00000508693,;ADGRL3,missense_variant,p.Gly467Val,ENST00000507164,;ADGRL3,missense_variant,p.Gly467Val,ENST00000506720,;ADGRL3,missense_variant,p.Gly467Val,ENST00000506746,;ADGRL3,missense_variant,p.Gly467Val,ENST00000507625,;ADGRL3,missense_variant,p.Gly399Val,ENST00000506700,;ADGRL3,missense_variant,p.Gly399Val,ENST00000504896,;ADGRL3,missense_variant,p.Gly399Val,ENST00000514157,;ADGRL3,missense_variant,p.Gly399Val,ENST00000508946,;ADGRL3,missense_variant,p.Gly399Val,ENST00000514996,; T ENST00000514591 Transcript missense_variant,splice_region_variant 1525/6297 1196/4410 399/1469 G/V gGg/gTg COSM4959706,COSM4959707,COSM4959708,COSM4959709 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0.04) 8/25 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 61813809 61813809 G T 1 0 0 0 0 1 0 0 0 377 1246 43 2 2 ADGRL3 4 61813809 Missense_Mutation SNP G C3N-01030_T 5497514 61813809 128400746 197 20978 ADGRL3 0 . GRCh38 4 61947008 61947008 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.2310C>A p.= p.S770S ENST00000514591 15/25 247 189 58 337 336 1 strelka-varscan-mutect ADGRL3,synonymous_variant,p.=,ENST00000512091,NM_001322246.1;ADGRL3,synonymous_variant,p.=,ENST00000514591,NM_015236.4;ADGRL3,synonymous_variant,p.=,ENST00000509896,;ADGRL3,synonymous_variant,p.=,ENST00000511324,;ADGRL3,synonymous_variant,p.=,ENST00000508693,;ADGRL3,synonymous_variant,p.=,ENST00000507164,;ADGRL3,synonymous_variant,p.=,ENST00000506720,;ADGRL3,synonymous_variant,p.=,ENST00000506746,;ADGRL3,synonymous_variant,p.=,ENST00000507625,;ADGRL3,synonymous_variant,p.=,ENST00000506700,;ADGRL3,synonymous_variant,p.=,ENST00000504896,;ADGRL3,synonymous_variant,p.=,ENST00000514157,;ADGRL3,synonymous_variant,p.=,ENST00000508946,;ADGRL3,synonymous_variant,p.=,ENST00000514996,;ADGRL3,synonymous_variant,p.=,ENST00000502815,;ADGRL3,non_coding_transcript_exon_variant,,ENST00000508078,; A ENST00000514591 Transcript synonymous_variant 2639/6297 2310/4410 770/1469 S tcC/tcA 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 15/25 hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF16489 LOW 1 SNV 5 1 PASS rs1243411031 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 61947008 61947008 C A 1 0 0 0 0 0 0 0 1 377 581 21 2 2 ADGRL3 4 61947008 Silent SNP C C3N-01030_T 133199 61947008 128267547 198 20979 YTHDC1 0 . GRCh38 4 68320206 68320206 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.1602-1G>T p.X534_splice ENST00000344157 105 83 22 131 131 0 strelka-varscan-mutect YTHDC1,splice_acceptor_variant,,ENST00000344157,NM_001031732.2;YTHDC1,splice_acceptor_variant,,ENST00000355665,NM_133370.2;YTHDC1,splice_acceptor_variant,,ENST00000579690,;YTHDC1,upstream_gene_variant,,ENST00000507529,;YTHDC1,downstream_gene_variant,,ENST00000506175,; A ENST00000344157 Transcript splice_acceptor_variant -/6232 1602/2184 534/727 1 -1 YTHDC1 HGNC HGNC:30626 protein_coding YES CCDS33992.1 ENSP00000339245 Q96MU7 UPI000020B86D NM_001031732.2 11/16 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 68320206 68320206 C A 1 0 0 0 0 0 0 1 0 18057 695 24 2 2 YTHDC1 4 68320206 Splice_Site SNP C C3N-01030_T 6373198 68320206 121894349 199 20980 SULT1E1 0 . GRCh38 4 69847746 69847746 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.543G>T p.Lys181Asn p.K181N ENST00000226444 6/8 98 85 13 169 169 0 strelka-varscan-mutect SULT1E1,missense_variant,p.Lys181Asn,ENST00000226444,NM_005420.2;SULT1E1,missense_variant,p.Lys14Asn,ENST00000506796,;SULT1E1,downstream_gene_variant,,ENST00000504002,; A ENST00000226444 Transcript missense_variant 656/1780 543/885 181/294 K/N aaG/aaT 1 -1 SULT1E1 HGNC HGNC:11377 protein_coding YES CCDS3531.1 ENSP00000226444 P49888 Q53X91 UPI00000623C8 NM_005420.2 tolerated(0.16) 6/8 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF53,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1298507007 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 69847746 69847746 C A 1 0 0 0 0 1 0 0 0 15766 680 24 2 2 SULT1E1 4 69847746 Missense_Mutation SNP C C3N-01030_T 1527540 69847746 120366809 200 20981 AMBN 0 . GRCh38 4 70603280 70603280 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.669G>T p.Leu223Phe p.L223F ENST00000322937 10/13 152 121 31 192 191 1 strelka-varscan-mutect AMBN,missense_variant,p.Leu223Phe,ENST00000322937,NM_016519.5;AMBN,missense_variant,p.Leu222Phe,ENST00000613447,;AMBN,missense_variant,p.Leu208Phe,ENST00000449493,; T ENST00000322937 Transcript missense_variant 772/2005 669/1344 223/447 L/F ttG/ttT 1 1 AMBN HGNC HGNC:452 protein_coding YES CCDS3543.1 ENSP00000313809 Q9NP70 Q546D7 UPI000000DCCB NM_016519.5 tolerated(0.28) 10/13 hmmpanther:PTHR14115,hmmpanther:PTHR14115:SF0,Pfam_domain:PF05111,SMART_domains:SM00817 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 70603280 70603280 G T 1 0 0 0 0 1 0 0 0 659 1281 45 2 2 AMBN 4 70603280 Missense_Mutation SNP G C3N-01030_T 755534 70603280 119611275 201 20982 CXCL13 0 . GRCh38 4 77607769 77607769 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.131C>A p.Pro44His p.P44H ENST00000286758 3/5 184 144 40 236 236 0 strelka-varscan-mutect CXCL13,missense_variant,p.Pro44His,ENST00000286758,NM_006419.2;CXCL13,non_coding_transcript_exon_variant,,ENST00000506590,; A ENST00000286758 Transcript missense_variant 209/1203 131/330 44/109 P/H cCt/cAt 1 1 CXCL13 HGNC HGNC:10639 protein_coding YES CCDS3582.1 ENSP00000286758 O43927 Q53X90 UPI0000000CC9 NM_006419.2 tolerated(0.46) 3/5 Gene3D:2.40.50.40,Pfam_domain:PF00048,PROSITE_patterns:PS00471,hmmpanther:PTHR10179,hmmpanther:PTHR10179:SF27,SMART_domains:SM00199,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 77607769 77607769 C A 1 0 0 0 0 1 0 0 0 3891 681 24 2 2 CXCL13 4 77607769 Missense_Mutation SNP C C3N-01030_T 7004489 77607769 112606786 202 20983 GPRIN3 0 . GRCh38 4 89248011 89248011 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2100G>T p.Leu700Phe p.L700F ENST00000609438 2/2 170 127 43 162 162 0 strelka-varscan-mutect GPRIN3,missense_variant,p.Leu700Phe,ENST00000609438,NM_198281.2;GPRIN3,missense_variant,p.Leu700Phe,ENST00000333209,; A ENST00000609438 Transcript missense_variant 2619/14244 2100/2331 700/776 L/F ttG/ttT 1 -1 GPRIN3 HGNC HGNC:27733 protein_coding YES CCDS34030.1 ENSP00000476603 Q6ZVF9 UPI00001C1E20 NM_198281.2 deleterious(0) 2/2 hmmpanther:PTHR15718:SF6,hmmpanther:PTHR15718,Pfam_domain:PF15235 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 89248011 89248011 C A 1 0 0 0 0 1 0 0 0 6610 593 21 2 2 GPRIN3 4 89248011 Missense_Mutation SNP C C3N-01030_T 11640242 89248011 100966544 203 20984 GRID2 0 . GRCh38 4 93515371 93515371 + Nonsense_Mutation SNP C C A rs757924739 C3N-01030_T C3N-01030_N C C c.2153C>A p.Ser718Ter p.S718* ENST00000282020 13/16 125 96 29 112 112 0 strelka-varscan-mutect GRID2,stop_gained,p.Ser718Ter,ENST00000282020,NM_001510.3;GRID2,stop_gained,p.Ser637Ter,ENST00000611049,;GRID2,stop_gained,p.Ser623Ter,ENST00000510992,NM_001286838.1; A ENST00000282020 Transcript stop_gained 3188/6117 2153/3024 718/1007 S/* tCg/tAg rs757924739,COSM1130992 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 13/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 0,1 HIGH 1 SNV 1 0,1 1 PASS rs757924739 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 93515371 93515371 C A 1 0 0 0 0 0 1 0 0 6652 893 31 1 1 GRID2 4 93515371 Nonsense_Mutation SNP C C3N-01030_T 4267360 93515371 96699184 204 20985 RAP1GDS1 0 . GRCh38 4 98293477 98293477 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.77G>T p.Gly26Val p.G26V ENST00000339360 2/15 115 86 29 158 157 1 strelka-varscan-mutect RAP1GDS1,missense_variant,p.Gly25Val,ENST00000408927,NM_001100427.1;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000453712,NM_021159.4;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000339360,NM_001100426.1;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000380158,NM_001100428.1;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000408900,NM_001100429.1;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000264572,NM_001100430.1;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000514122,;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000508213,;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000511212,;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000509011,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000512857,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000515187,;RAP1GDS1,missense_variant,p.Gly26Val,ENST00000503667,;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000508490,;RAP1GDS1,missense_variant,p.Gly25Val,ENST00000510870,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000511379,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000505378,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000507303,; T ENST00000339360 Transcript missense_variant 125/2092 77/1827 26/608 G/V gGa/gTa 1 1 RAP1GDS1 HGNC HGNC:9859 protein_coding YES CCDS47105.1 ENSP00000340454 P52306 UPI000004A01F NM_001100426.1 tolerated(0.22) 2/15 hmmpanther:PTHR10957,hmmpanther:PTHR10957:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 98293477 98293477 G T 1 0 0 0 0 1 0 0 0 13198 1174 41 2 2 RAP1GDS1 4 98293477 Missense_Mutation SNP G C3N-01030_T 4778106 98293477 91921078 205 20986 RP11-766F14.2 0 . GRCh38 4 99651485 99651485 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3164G>T p.Gly1055Val p.G1055V ENST00000511828 1/2 226 172 54 197 197 0 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Gly1055Val,ENST00000511828,; A ENST00000511828 Transcript missense_variant 3164/10086 3164/5382 1055/1793 G/V gGt/gTt 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE deleterious(0.04) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 99651485 99651485 C A 1 0 0 0 0 1 0 0 0 13762 507 18 2 2 RP11-766F14.2 4 99651485 Missense_Mutation SNP C C3N-01030_T 1358008 99651485 90563070 206 20987 TACR3 0 . GRCh38 4 103589921 103589921 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1159C>A p.Leu387Ile p.L387I ENST00000304883 5/5 377 295 82 338 338 0 strelka-varscan-mutect TACR3,missense_variant,p.Leu387Ile,ENST00000304883,NM_001059.2;RP11-297P16.3,intron_variant,,ENST00000502936,;RP11-297P16.3,intron_variant,,ENST00000512401,; T ENST00000304883 Transcript missense_variant 1300/5190 1159/1398 387/465 L/I Ctc/Atc 1 -1 TACR3 HGNC HGNC:11528 protein_coding YES CCDS3664.1 ENSP00000303325 P29371 UPI0000050413 NM_001059.2 deleterious(0.01) 5/5 Prints_domain:PR01026,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF46 MODERATE 1 SNV 1 1 PASS rs1353918699 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 103589921 103589921 G T 1 0 0 0 0 1 0 0 0 15903 971 34 2 2 TACR3 4 103589921 Missense_Mutation SNP G C3N-01030_T 3938436 103589921 86624634 207 20988 ANK2 0 . GRCh38 4 113358380 113358380 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.9762C>A p.= p.V3254V ENST00000357077 38/46 133 97 36 173 173 0 strelka-varscan-mutect ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript synonymous_variant 9815/14196 9762/11874 3254/3957 V gtC/gtA 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 113358380 113358380 C A 1 0 0 0 0 0 0 0 1 721 842 30 2 2 ANK2 4 113358380 Silent SNP C C3N-01030_T 9768459 113358380 76856175 208 20989 BBS7 0 . GRCh38 4 121859009 121859009 + Missense_Mutation SNP C C A rs377607757 C3N-01030_T C3N-01030_N C C c.511G>T p.Val171Leu p.V171L ENST00000264499 5/19 218 155 63 235 235 0 strelka-varscan-mutect BBS7,missense_variant,p.Val171Leu,ENST00000264499,NM_176824.2;BBS7,missense_variant,p.Val171Leu,ENST00000506636,NM_018190.3;BBS7,non_coding_transcript_exon_variant,,ENST00000505692,;BBS7,non_coding_transcript_exon_variant,,ENST00000508536,;BBS7,downstream_gene_variant,,ENST00000502444,; A ENST00000264499 Transcript missense_variant 695/3752 511/2148 171/715 V/L Gtg/Ttg rs377607757 1 -1 BBS7 HGNC HGNC:18758 protein_coding YES CCDS3724.1 ENSP00000264499 Q8IWZ6 UPI00001684D7 NM_176824.2 tolerated(0.1) 5/19 hmmpanther:PTHR16074,hmmpanther:PTHR16074:SF4,PIRSF_domain:PIRSF011091,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs377607757 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 121859009 121859009 C A 1 0 0 0 0 1 0 0 0 1488 565 20 2 2 BBS7 4 121859009 Missense_Mutation SNP C C3N-01030_T 8500629 121859009 68355546 209 20990 PCDH10 0 . GRCh38 4 133151349 133151349 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.1210delC p.Arg404AlafsTer28 p.R404Afs*28 ENST00000264360 1/5 229 168 61 178 178 0 sindel-varindel-pindel PCDH10,frameshift_variant,p.Arg404AlafsTer28,ENST00000264360,NM_032961.2;PCDH10,frameshift_variant,p.Arg404AlafsTer28,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; - ENST00000264360 Transcript frameshift_variant 2035/8489 1209/3123 403/1040 F/X ttC/tt 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 1/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 133151349 133151349 C - 1 0 1 0 1 0 0 0 0 11594 854 30 0 0 PCDH10 4 133151349 Frame_Shift_Del DEL C C3N-01030_T 11292340 133151349 57063206 210 20991 FGG 0 . GRCh38 4 154606975 154606975 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.859G>T p.Asp287Tyr p.D287Y ENST00000336098 8/9 33 25 8 47 47 0 strelka-varscan-mutect FGG,missense_variant,p.Asp287Tyr,ENST00000404648,NM_000509.4;FGG,missense_variant,p.Asp287Tyr,ENST00000336098,NM_021870.2;FGG,missense_variant,p.Asp295Tyr,ENST00000407946,;FGG,missense_variant,p.Asp295Tyr,ENST00000405164,;FGG,downstream_gene_variant,,ENST00000443553,;FGG,downstream_gene_variant,,ENST00000393846,;FGG,non_coding_transcript_exon_variant,,ENST00000492082,;FGG,non_coding_transcript_exon_variant,,ENST00000465913,;FGG,downstream_gene_variant,,ENST00000473393,;FGG,downstream_gene_variant,,ENST00000465336,;FGG,downstream_gene_variant,,ENST00000464532,;FGG,downstream_gene_variant,,ENST00000484695,; A ENST00000336098 Transcript missense_variant 898/1659 859/1362 287/453 D/Y Gac/Tac 1 -1 FGG HGNC HGNC:3694 protein_coding YES CCDS3788.1 ENSP00000336829 P02679 UPI000012A78D NM_021870.2 tolerated(0.27) 8/9 Gene3D:3.90.215.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF22,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.94997 1 1 1 1 0 A 3 1 70 154606975 154606975 C A 1 0 0 0 0 1 0 0 0 5734 913 32 2 2 FGG 4 154606975 Missense_Mutation SNP C C3N-01030_T 21455626 154606975 35607580 211 20992 NPY1R 0 . GRCh38 4 163325606 163325606 + Silent SNP A A T novel C3N-01030_T C3N-01030_N A A c.852T>A p.= p.T284T ENST00000296533 3/3 220 164 56 208 208 0 strelka-varscan-mutect NPY1R,synonymous_variant,p.=,ENST00000296533,NM_000909.5;NPY1R,synonymous_variant,p.=,ENST00000509586,;NPY1R,synonymous_variant,p.=,ENST00000504391,;NPY1R,downstream_gene_variant,,ENST00000515701,;NPY1R,downstream_gene_variant,,ENST00000511901,;NPY1R,downstream_gene_variant,,ENST00000512819,;NPY1R,downstream_gene_variant,,ENST00000504790,; T ENST00000296533 Transcript synonymous_variant 1384/3029 852/1155 284/384 T acT/acA 1 -1 NPY1R HGNC HGNC:7956 protein_coding YES CCDS34089.1 ENSP00000354652 P25929 UPI000002D509 NM_000909.5 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF222,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 163325606 163325606 A T 1 0 0 0 0 0 0 0 1 10663 175 7 4 4 NPY1R 4 163325606 Silent SNP A C3N-01030_T 8718631 163325606 26888949 212 20993 SPOCK3 0 . GRCh38 4 166737590 166737590 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.1018C>T p.= p.L340L ENST00000357154 11/12 89 66 23 78 78 0 strelka-varscan-mutect SPOCK3,synonymous_variant,p.=,ENST00000421836,NM_001204352.1;SPOCK3,synonymous_variant,p.=,ENST00000357154,NM_016950.2;SPOCK3,synonymous_variant,p.=,ENST00000506886,;SPOCK3,synonymous_variant,p.=,ENST00000357545,NM_001040159.1;SPOCK3,synonymous_variant,p.=,ENST00000511531,;SPOCK3,synonymous_variant,p.=,ENST00000504953,;SPOCK3,synonymous_variant,p.=,ENST00000541354,NM_001204355.1,NM_001204353.1;SPOCK3,synonymous_variant,p.=,ENST00000502330,;SPOCK3,synonymous_variant,p.=,ENST00000535728,NM_001204354.1;SPOCK3,synonymous_variant,p.=,ENST00000510741,NM_001204356.1;SPOCK3,synonymous_variant,p.=,ENST00000511269,;SPOCK3,synonymous_variant,p.=,ENST00000512681,NM_001251967.1;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,; A ENST00000357154 Transcript synonymous_variant 1156/2986 1018/1311 340/436 L Ctg/Ttg 1 -1 SPOCK3 HGNC HGNC:13565 protein_coding YES CCDS54817.1 ENSP00000349677 Q9BQ16 UPI000004BA60 NM_016950.2 11/12 PROSITE_profiles:PS51162,hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF10,PROSITE_patterns:PS00484,Gene3D:4.10.800.10,Pfam_domain:PF00086,SMART_domains:SM00211,Superfamily_domains:SSF57610 LOW 1 SNV 5 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999716 1 1 1 0 A 2 1 70 166737590 166737590 G A 1 0 0 0 0 0 0 0 1 15434 991 35 3 3 SPOCK3 4 166737590 Silent SNP G C3N-01030_T 3411984 166737590 23476965 213 20994 DDX60L 0 . GRCh38 4 168432529 168432529 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1442C>A p.Ser481Tyr p.S481Y ENST00000260184 12/38 136 102 34 196 195 1 strelka-varscan-mutect DDX60L,missense_variant,p.Ser481Tyr,ENST00000511577,;DDX60L,missense_variant,p.Ser481Tyr,ENST00000260184,NM_001012967.2;DDX60L,missense_variant,p.Ser481Tyr,ENST00000505890,NM_001291510.1;DDX60L,missense_variant,p.Ser209Tyr,ENST00000505863,; T ENST00000260184 Transcript missense_variant 1663/6754 1442/5121 481/1706 S/Y tCt/tAt 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 tolerated(0.09) 12/38 MODERATE 1 SNV 5 1 PASS rs932190730 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 168432529 168432529 G T 1 0 0 0 0 1 0 0 0 4182 942 33 2 2 DDX60L 4 168432529 Missense_Mutation SNP G C3N-01030_T 1694939 168432529 21782026 214 20995 PALLD 0 . GRCh38 4 168512221 168512222 + Frame_Shift_Ins INS - - A novel C3N-01030_T C3N-01030_N - - c.718dupA p.Arg240LysfsTer54 p.R240Kfs*54 ENST00000505667 2/22 77 59 18 76 76 0 sindel-varindel-pindel PALLD,frameshift_variant,p.Arg240LysfsTer54,ENST00000261509,NM_016081.3;PALLD,frameshift_variant,p.Arg240LysfsTer54,ENST00000505667,NM_001166108.1;PALLD,frameshift_variant,p.Arg219LysfsTer54,ENST00000508898,;PALLD,downstream_gene_variant,,ENST00000511948,;DDX60L,intron_variant,,ENST00000512958,;DDX60L,intron_variant,,ENST00000505150,; A ENST00000505667 Transcript frameshift_variant 890-891/3637 717-718/3372 239-240/1123 -/X -/A 1 1 PALLD HGNC HGNC:17068 protein_coding YES CCDS54818.1 ENSP00000425556 Q8WX93 UPI000189A85C NM_001166108.1 2/22 HIGH 1 insertion 1 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999974 1 1 1 0 A 7 5 70 168512221 168512221 - A 1 0 1 1 0 0 0 0 0 11487 581 21 0 0 PALLD 4 168512221 Frame_Shift_Ins INS - C3N-01030_T 79692 168512221 21702334 215 20996 HAND2 0 . GRCh38 4 173528981 173528981 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.309C>T p.= p.T103T ENST00000359562 1/2 169 160 9 137 137 0 strelka-mutect HAND2,synonymous_variant,p.=,ENST00000359562,NM_021973.2;HAND2,synonymous_variant,p.=,ENST00000621866,;HAND2-AS1,intron_variant,,ENST00000512099,;HAND2-AS1,intron_variant,,ENST00000515310,;HAND2-AS1,upstream_gene_variant,,ENST00000502896,;HAND2-AS1,upstream_gene_variant,,ENST00000507062,;HAND2-AS1,upstream_gene_variant,,ENST00000510339,;HAND2-AS1,upstream_gene_variant,,ENST00000515350,;HAND2-AS1,upstream_gene_variant,,ENST00000507571,;HAND2-AS1,upstream_gene_variant,,ENST00000508534,;HAND2-AS1,upstream_gene_variant,,ENST00000503198,;HAND2-AS1,upstream_gene_variant,,ENST00000616485,;HAND2-AS1,upstream_gene_variant,,ENST00000503474,;HAND2-AS1,upstream_gene_variant,,ENST00000502334,;HAND2-AS1,upstream_gene_variant,,ENST00000514673,;HAND2-AS1,upstream_gene_variant,,ENST00000508887,;HAND2-AS1,upstream_gene_variant,,ENST00000515376,;HAND2-AS1,upstream_gene_variant,,ENST00000514431,;HAND2-AS1,upstream_gene_variant,,ENST00000512246,;HAND2-AS1,upstream_gene_variant,,ENST00000505621,;HAND2-AS1,upstream_gene_variant,,ENST00000507322,;HAND2-AS1,upstream_gene_variant,,ENST00000504740,;HAND2-AS1,upstream_gene_variant,,ENST00000515741,;HAND2-AS1,upstream_gene_variant,,ENST00000515345,;HAND2-AS1,upstream_gene_variant,,ENST00000504429,;HAND2-AS1,upstream_gene_variant,,ENST00000509640,;HAND2-AS1,upstream_gene_variant,,ENST00000509866,;HAND2-AS1,upstream_gene_variant,,ENST00000510268,;HAND2-AS1,upstream_gene_variant,,ENST00000511728,;HAND2-AS1,upstream_gene_variant,,ENST00000512929,;HAND2-AS1,upstream_gene_variant,,ENST00000507636,;HAND2-AS1,upstream_gene_variant,,ENST00000510221,;HAND2-AS1,upstream_gene_variant,,ENST00000511196,;HAND2-AS1,upstream_gene_variant,,ENST00000512209,;HAND2-AS1,upstream_gene_variant,,ENST00000512943,;HAND2-AS1,upstream_gene_variant,,ENST00000505032,;HAND2-AS1,upstream_gene_variant,,ENST00000503309,;HAND2-AS1,upstream_gene_variant,,ENST00000505817,;HAND2-AS1,upstream_gene_variant,,ENST00000502941,;HAND2,non_coding_transcript_exon_variant,,ENST00000505300,;HAND2,upstream_gene_variant,,ENST00000503024,; A ENST00000359562 Transcript synonymous_variant 1249/2780 309/654 103/217 T acC/acT 1 -1 HAND2 HGNC HGNC:4808 protein_coding YES CCDS3819.1 ENSP00000352565 P61296 UPI0000003FE8 NM_021973.2 1/2 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR23349,hmmpanther:PTHR23349:SF41,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 173528981 173528981 G A 1 0 0 0 0 0 0 0 1 6836 1130 39 1 1 HAND2 4 173528981 Silent SNP G C3N-01030_T 5016760 173528981 16685574 216 20997 TENM3 0 . GRCh38 4 182754599 182754599 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.4232C>A p.Ser1411Tyr p.S1411Y ENST00000511685 22/28 153 109 44 137 137 0 strelka-varscan-mutect TENM3,missense_variant,p.Ser1411Tyr,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,; A ENST00000511685 Transcript missense_variant 4355/10896 4232/8100 1411/2699 S/Y tCc/tAc 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 deleterious(0) 22/28 Gene3D:2.120.10.30,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10,Superfamily_domains:SSF101898 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 182754599 182754599 C A 1 0 0 0 0 1 0 0 0 16173 855 30 2 2 TENM3 4 182754599 Missense_Mutation SNP C C3N-01030_T 9225618 182754599 7459956 217 20998 SLC9A3 0 . GRCh38 5 474885 474885 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2499C>A p.His833Gln p.H833Q ENST00000264938 16/17 106 90 16 69 69 0 strelka-varscan-mutect SLC9A3,missense_variant,p.His833Gln,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.His824Gln,ENST00000514375,NM_001284351.1;CTD-2228K2.7,intron_variant,,ENST00000607286,;PP7080,upstream_gene_variant,,ENST00000342584,;PP7080,upstream_gene_variant,,ENST00000510604,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606288,;PP7080,upstream_gene_variant,,ENST00000510714,;PP7080,upstream_gene_variant,,ENST00000502511,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606319,;CTD-2228K2.7,upstream_gene_variant,,ENST00000607005,;EXOC3,downstream_gene_variant,,ENST00000509294,;EXOC3,downstream_gene_variant,,ENST00000515601,;EXOC3,downstream_gene_variant,,ENST00000503889,;CTD-2228K2.7,upstream_gene_variant,,ENST00000534918,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606074,;CTD-2228K2.7,upstream_gene_variant,,ENST00000606107,;SLC9A3,downstream_gene_variant,,ENST00000507407,; T ENST00000264938 Transcript missense_variant,splice_region_variant 2509/2584 2499/2505 833/834 H/Q caC/caA 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 deleterious_low_confidence(0.04) 16/17 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 474885 474885 G T 1 0 0 0 0 1 0 0 0 14995 1391 48 2 2 SLC9A3 5 474885 Missense_Mutation SNP G C3N-01030_T 474885 181063374 218 20999 SLC6A3 0 . GRCh38 5 1414710 1414710 + Silent SNP G G A rs201605046 C3N-01030_T C3N-01030_N G G c.1137C>T p.= p.I379I ENST00000270349 8/15 542 477 65 342 342 0 strelka-varscan-mutect SLC6A3,synonymous_variant,p.=,ENST00000270349,NM_001044.4;SLC6A3,downstream_gene_variant,,ENST00000511750,; A ENST00000270349 Transcript synonymous_variant 1265/3936 1137/1863 379/620 I atC/atT rs201605046 1 -1 SLC6A3 HGNC HGNC:11049 protein_coding YES CCDS3863.1 ENSP00000270349 Q01959 UPI000013548F NM_001044.4 8/15 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF38,Pfam_domain:PF00209,Superfamily_domains:0053687 LOW 1 SNV 1 1 PASS rs201605046 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 1414710 1414710 G A 1 0 0 0 0 0 0 0 1 14968 1048 37 1 1 SLC6A3 5 1414710 Silent SNP G C3N-01030_T 939825 1414710 180123549 219 21000 LPCAT1 0 . GRCh38 5 1494775 1494775 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.418G>A p.Asp140Asn p.D140N ENST00000283415 3/14 413 336 77 210 210 0 strelka-varscan-mutect LPCAT1,missense_variant,p.Asp140Asn,ENST00000283415,NM_024830.3;LPCAT1,non_coding_transcript_exon_variant,,ENST00000514484,;LPCAT1,missense_variant,p.Asp140Asn,ENST00000475622,;LPCAT1,non_coding_transcript_exon_variant,,ENST00000513757,;LPCAT1,non_coding_transcript_exon_variant,,ENST00000507282,; T ENST00000283415 Transcript missense_variant 551/3966 418/1605 140/534 D/N Gac/Aac COSM1671486 1 -1 LPCAT1 HGNC HGNC:25718 protein_coding YES CCDS3864.1 ENSP00000283415 Q8NF37 UPI000004771C NM_024830.3 deleterious(0) 3/14 hmmpanther:PTHR23063:SF11,hmmpanther:PTHR23063,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 1494775 1494775 C T 1 0 0 0 0 1 0 0 0 8813 884 31 1 1 LPCAT1 5 1494775 Missense_Mutation SNP C C3N-01030_T 80065 1494775 180043484 220 21001 ICE1 0 . GRCh38 5 5464885 5464885 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.5551G>T p.Asp1851Tyr p.D1851Y ENST00000296564 13/19 261 234 27 228 227 1 strelka-varscan-mutect ICE1,missense_variant,p.Asp1851Tyr,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 5773/7927 5551/6801 1851/2266 D/Y Gac/Tac 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0) 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 5464885 5464885 G T 1 0 0 0 0 1 0 0 0 7384 1174 41 2 2 ICE1 5 5464885 Missense_Mutation SNP G C3N-01030_T 3970110 5464885 176073374 221 21002 ADCY2 0 . GRCh38 5 7690823 7690823 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.853delC p.Arg285GlyfsTer5 p.R285Gfs*5 ENST00000338316 5/25 73 54 19 62 62 0 sindel-varindel-pindel ADCY2,frameshift_variant,p.Arg285GlyfsTer5,ENST00000338316,NM_020546.2;ADCY2,frameshift_variant,p.Arg74GlyfsTer5,ENST00000515681,;ADCY2,non_coding_transcript_exon_variant,,ENST00000513693,; - ENST00000338316 Transcript frameshift_variant 942/6575 853/3276 285/1091 R/X Cgg/gg 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 5/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 HIGH 1 deletion 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 70 7690823 7690823 C - 1 0 1 0 1 0 0 0 0 338 759 27 0 0 ADCY2 5 7690823 Frame_Shift_Del DEL C C3N-01030_T 2225938 7690823 173847436 222 21003 DNAH5 0 . GRCh38 5 13716639 13716639 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.12757G>T p.Gly4253Cys p.G4253C ENST00000265104 74/79 427 220 207 404 403 1 strelka-varscan-mutect DNAH5,missense_variant,p.Gly4253Cys,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript missense_variant 12862/15633 12757/13875 4253/4624 G/C Ggc/Tgc 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 74/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 13716639 13716639 C A 1 0 0 0 0 1 0 0 0 4419 681 24 2 2 DNAH5 5 13716639 Missense_Mutation SNP C C3N-01030_T 6025816 13716639 167821620 223 21004 PRDM9 0 . GRCh38 5 23524343 23524343 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.960C>A p.Asn320Lys p.N320K ENST00000296682 10/11 396 308 88 378 377 1 strelka-varscan PRDM9,missense_variant,p.Asn320Lys,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Asn261Lys,ENST00000635252,; A ENST00000296682 Transcript missense_variant 1142/3691 960/2685 320/894 N/K aaC/aaA 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0) 10/11 PROSITE_profiles:PS50280,hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Pfam_domain:PF00856,Gene3D:2.170.270.10,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 23524343 23524343 C A 1 0 0 0 0 1 0 0 0 12595 564 20 2 2 PRDM9 5 23524343 Missense_Mutation SNP C C3N-01030_T 9807704 23524343 158013916 224 21005 GOLPH3 0 . GRCh38 5 32126347 32126347 + Silent SNP A A T novel C3N-01030_T C3N-01030_N A A c.762T>A p.= p.A254A ENST00000265070 4/4 354 334 20 239 238 1 strelka-varscan GOLPH3,synonymous_variant,p.=,ENST00000265070,NM_022130.3;CTD-2152M20.2,upstream_gene_variant,,ENST00000503441,;GOLPH3,downstream_gene_variant,,ENST00000512668,;GOLPH3,downstream_gene_variant,,ENST00000503610,; T ENST00000265070 Transcript synonymous_variant 1078/2721 762/897 254/298 A gcT/gcA 1 -1 GOLPH3 HGNC HGNC:15452 protein_coding YES CCDS3896.1 ENSP00000265070 Q9H4A6 UPI000006EEF4 NM_022130.3 4/4 hmmpanther:PTHR12704:SF3,hmmpanther:PTHR12704,Pfam_domain:PF05719,Gene3D:2zihB00 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 32126347 32126347 A T 1 0 0 0 0 0 0 0 1 6462 291 11 4 4 GOLPH3 5 32126347 Silent SNP A C3N-01030_T 8602004 32126347 149411912 225 21006 SLC45A2 0 . GRCh38 5 33963696 33963696 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.883G>T p.Glu295Ter p.E295* ENST00000296589 3/7 319 291 28 294 294 0 strelka-varscan SLC45A2,stop_gained,p.Glu295Ter,ENST00000382102,NM_001012509.3;SLC45A2,stop_gained,p.Glu295Ter,ENST00000296589,NM_016180.4;SLC45A2,stop_gained,p.Glu120Ter,ENST00000510600,;SLC45A2,intron_variant,,ENST00000509381,NM_001297417.2;SLC45A2,non_coding_transcript_exon_variant,,ENST00000505056,; A ENST00000296589 Transcript stop_gained 1030/1772 883/1593 295/530 E/* Gaa/Taa 1 -1 SLC45A2 HGNC HGNC:16472 protein_coding YES CCDS3901.1 ENSP00000296589 Q9UMX9 A0A076YIB8 UPI00001AEC19 NM_016180.4 3/7 hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF34 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 33963696 33963696 C A 1 0 0 0 0 0 1 0 0 14918 840 29 2 2 SLC45A2 5 33963696 Nonsense_Mutation SNP C C3N-01030_T 1837349 33963696 147574563 226 21007 SPEF2 0 . GRCh38 5 35776268 35776268 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.4090C>A p.Gln1364Lys p.Q1364K ENST00000356031 29/37 73 68 5 96 96 0 strelka-varscan SPEF2,missense_variant,p.Gln1364Lys,ENST00000637569,;SPEF2,missense_variant,p.Gln1359Lys,ENST00000440995,;SPEF2,missense_variant,p.Gln1364Lys,ENST00000356031,NM_024867.3;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,missense_variant,p.Gln15Lys,ENST00000506526,;SPEF2,missense_variant,p.Gln55Lys,ENST00000637061,;SPEF2,upstream_gene_variant,,ENST00000513078,; A ENST00000356031 Transcript missense_variant 4244/5681 4090/5469 1364/1822 Q/K Caa/Aaa COSM4155810 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 tolerated(0.98) 29/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0 1 MODERATE 1 SNV 2 1 1 PASS . . 0 204 5 0 0 0 0 0 -11.3808 1 1 1 1 0 A 3 1 70 35776268 35776268 C A 1 0 0 0 0 1 0 0 0 15386 711 25 2 2 SPEF2 5 35776268 Missense_Mutation SNP C C3N-01030_T 1812572 35776268 145761991 227 21008 UGT3A1 0 . GRCh38 5 35965626 35965626 + Silent SNP C C T C3N-01030_T C3N-01030_N C C c.603G>A p.= p.V201V ENST00000274278 4/7 396 354 42 302 302 0 strelka-varscan UGT3A1,synonymous_variant,p.=,ENST00000274278,NM_152404.3;UGT3A1,synonymous_variant,p.=,ENST00000625798,NM_001171873.1;UGT3A1,synonymous_variant,p.=,ENST00000503189,;UGT3A1,synonymous_variant,p.=,ENST00000507113,;UGT3A1,synonymous_variant,p.=,ENST00000333811,;UGT3A1,intron_variant,,ENST00000513233,;UGT3A1,3_prime_UTR_variant,,ENST00000515801,; T ENST00000274278 Transcript synonymous_variant 961/5122 603/1572 201/523 V gtG/gtA COSM3615828,COSM3615829 1 -1 UGT3A1 HGNC HGNC:26625 protein_coding YES CCDS3913.1 ENSP00000274278 Q6NUS8 A8K444 UPI000003C38B NM_152404.3 4/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF208,Pfam_domain:PF00201,Superfamily_domains:SSF53756 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 35965626 35965626 C T 1 0 0 0 0 0 0 0 1 17487 813 29 3 3 UGT3A1 5 35965626 Silent SNP C C3N-01030_T 189358 35965626 145572633 228 21009 C5orf42 0 . GRCh38 5 37157744 37157744 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.7883C>T p.Pro2628Leu p.P2628L ENST00000425232 40/52 266 211 55 234 234 0 strelka-varscan C5orf42,missense_variant,p.Pro2628Leu,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Pro2628Leu,ENST00000508244,;C5orf42,missense_variant,p.Pro1694Leu,ENST00000514429,;C5orf42,missense_variant,p.Pro337Leu,ENST00000511824,;C5orf42,non_coding_transcript_exon_variant,,ENST00000511210,;C5orf42,upstream_gene_variant,,ENST00000508405,;C5orf42,missense_variant,p.Pro1650Leu,ENST00000509849,;C5orf42,non_coding_transcript_exon_variant,,ENST00000509957,;C5orf42,non_coding_transcript_exon_variant,,ENST00000515380,;C5orf42,non_coding_transcript_exon_variant,,ENST00000510830,; A ENST00000425232 Transcript missense_variant 8114/11199 7883/9594 2628/3197 P/L cCa/cTa 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0.03) 40/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 37157744 37157744 G A 1 0 0 0 0 1 0 0 0 2100 1348 47 3 3 C5orf42 5 37157744 Missense_Mutation SNP G C3N-01030_T 1192118 37157744 144380515 229 21010 C5orf42 0 . GRCh38 5 37183581 37183581 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.4600A>T p.Thr1534Ser p.T1534S ENST00000425232 26/52 174 150 24 195 195 0 strelka-varscan C5orf42,missense_variant,p.Thr1534Ser,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Thr1534Ser,ENST00000508244,;C5orf42,missense_variant,p.Thr582Ser,ENST00000514429,;C5orf42,missense_variant,p.Thr539Ser,ENST00000509849,; A ENST00000425232 Transcript missense_variant 4831/11199 4600/9594 1534/3197 T/S Aca/Tca 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 tolerated(0.52) 26/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 37183581 37183581 T A 1 0 0 0 0 1 0 0 0 2100 1638 57 4 4 C5orf42 5 37183581 Missense_Mutation SNP T C3N-01030_T 25837 37183581 144354678 230 21011 LIFR 0 . GRCh38 5 38502772 38502772 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1465A>T p.Asn489Tyr p.N489Y ENST00000263409 11/20 165 129 36 165 165 0 strelka-varscan LIFR,missense_variant,p.Asn489Tyr,ENST00000263409,NM_002310.5;LIFR,missense_variant,p.Asn489Tyr,ENST00000453190,NM_001127671.1;LIFR,non_coding_transcript_exon_variant,,ENST00000503088,;LIFR,upstream_gene_variant,,ENST00000506003,; A ENST00000263409 Transcript missense_variant 1628/10089 1465/3294 489/1097 N/Y Aat/Tat 1 -1 LIFR HGNC HGNC:6597 protein_coding YES CCDS3927.1 ENSP00000263409 P42702 UPI000004CAC2 NM_002310.5 tolerated(0.42) 11/20 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF105,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 38502772 38502772 T A 1 0 0 0 0 1 0 0 0 8689 1841 64 4 4 LIFR 5 38502772 Missense_Mutation SNP T C3N-01030_T 1319191 38502772 143035487 231 21012 HMGCS1 0 . GRCh38 5 43297158 43297158 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.583G>T p.Gly195Trp p.G195W ENST00000325110 5/11 75 54 21 84 84 0 strelka-varscan HMGCS1,missense_variant,p.Gly195Trp,ENST00000325110,NM_001098272.2;HMGCS1,missense_variant,p.Gly195Trp,ENST00000433297,NM_002130.7;HMGCS1,downstream_gene_variant,,ENST00000511774,;HMGCS1,downstream_gene_variant,,ENST00000507004,;HMGCS1,downstream_gene_variant,,ENST00000507293,;HMGCS1,upstream_gene_variant,,ENST00000508319,;HMGCS1,upstream_gene_variant,,ENST00000514610,; A ENST00000325110 Transcript missense_variant 790/3506 583/1563 195/520 G/W Ggg/Tgg 1 -1 HMGCS1 HGNC HGNC:5007 protein_coding YES CCDS34154.1 ENSP00000322706 Q01581 A0A024R059 UPI000012C9BC NM_001098272.2 deleterious(0) 5/11 Gene3D:3.40.47.10,Pfam_domain:PF08540,hmmpanther:PTHR11877,hmmpanther:PTHR11877:SF12,Superfamily_domains:SSF53901,TIGRFAM_domain:TIGR01833 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 70 43297158 43297158 C A 1 0 0 0 0 1 0 0 0 7124 594 21 2 2 HMGCS1 5 43297158 Missense_Mutation SNP C C3N-01030_T 4794386 43297158 138241101 232 21013 KIF2A 0 . GRCh38 5 62385559 62385559 + Missense_Mutation SNP G G T rs780774764 C3N-01030_T C3N-01030_N G G c.2225G>T p.Arg742Leu p.R742L ENST00000407818 21/21 151 112 39 163 163 0 strelka-varscan KIF2A,missense_variant,p.Arg684Leu,ENST00000381103,NM_001243952.1;KIF2A,missense_variant,p.Arg704Leu,ENST00000401507,NM_001243953.1,NM_004520.4;KIF2A,missense_variant,p.Arg742Leu,ENST00000407818,NM_001098511.2;KIF2A,missense_variant,p.Arg658Leu,ENST00000506857,;DIMT1,downstream_gene_variant,,ENST00000199320,NM_014473.2;KIF2A,intron_variant,,ENST00000509663,;DIMT1,downstream_gene_variant,,ENST00000514605,; T ENST00000407818 Transcript missense_variant 2246/2315 2225/2235 742/744 R/L cGt/cTt rs780774764 1 1 KIF2A HGNC HGNC:6318 protein_coding YES CCDS47216.1 ENSP00000385000 O00139 UPI0001533DB2 NM_001098511.2 deleterious(0) 21/21 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 62385559 62385559 G T 1 0 0 0 0 1 0 0 0 8162 1145 40 1 1 KIF2A 5 62385559 Missense_Mutation SNP G C3N-01030_T 19088401 62385559 119152700 233 21014 RNF180 0 . GRCh38 5 64369613 64369613 + Splice_Site SNP A A T novel C3N-01030_T C3N-01030_N A A c.1580-2A>T p.X527_splice ENST00000389100 45 39 6 73 73 0 strelka-varscan RNF180,splice_acceptor_variant,,ENST00000389100,NM_001113561.1; T ENST00000389100 Transcript splice_acceptor_variant -/4906 1580/1779 527/592 1 1 RNF180 HGNC HGNC:27752 protein_coding YES CCDS47219.1 ENSP00000373752 Q86T96 UPI0000141201 NM_001113561.1 7/7 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.83033 0.9999999 1 1 1 0 T 5 4 70 64369613 64369613 A T 1 0 0 0 0 0 0 1 0 13641 434 15 4 4 RNF180 5 64369613 Splice_Site SNP A C3N-01030_T 1984054 64369613 117168646 234 21015 SV2C 0 . GRCh38 5 76131888 76131888 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.138C>A p.Tyr46Ter p.Y46* ENST00000502798 2/13 143 130 13 152 152 0 strelka-varscan-mutect SV2C,stop_gained,p.Tyr46Ter,ENST00000502798,NM_014979.3;SV2C,stop_gained,p.Tyr46Ter,ENST00000322285,NM_001297716.1; A ENST00000502798 Transcript stop_gained 580/11035 138/2184 46/727 Y/* taC/taA 1 1 SV2C HGNC HGNC:30670 protein_coding YES CCDS43331.1 ENSP00000423541 Q496J9 UPI000011DDBB NM_014979.3 2/13 TIGRFAM_domain:TIGR01299 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 76131888 76131888 C A 1 0 0 0 0 0 1 0 0 15803 489 17 2 2 SV2C 5 76131888 Nonsense_Mutation SNP C C3N-01030_T 11762275 76131888 105406371 235 21016 VCAN 0 . GRCh38 5 83519951 83519951 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1645G>T p.Gly549Ter p.G549* ENST00000265077 7/15 368 322 46 481 481 0 strelka-varscan-mutect VCAN,stop_gained,p.Gly549Ter,ENST00000265077,NM_004385.4;VCAN,stop_gained,p.Gly549Ter,ENST00000342785,NM_001164098.1;VCAN,stop_gained,p.Gly501Ter,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; T ENST00000265077 Transcript stop_gained 2210/12625 1645/10191 549/3396 G/* Gga/Tga 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 7/15 HIGH 1 SNV 1 1 PASS rs1220156241 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 83519951 83519951 G T 1 0 0 0 0 0 1 0 0 17683 1349 47 2 2 VCAN 5 83519951 Nonsense_Mutation SNP G C3N-01030_T 7388063 83519951 98018308 236 21017 VCAN 0 . GRCh38 5 83537519 83537519 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.4516T>A p.Phe1506Ile p.F1506I ENST00000265077 8/15 230 204 26 251 251 0 strelka-varscan-mutect VCAN,missense_variant,p.Phe1506Ile,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Phe519Ile,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Phe519Ile,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 5081/12625 4516/10191 1506/3396 F/I Ttc/Atc 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.18) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 83537519 83537519 T A 1 0 0 0 0 1 0 0 0 17683 1493 52 4 4 VCAN 5 83537519 Missense_Mutation SNP T C3N-01030_T 17568 83537519 98000740 237 21018 VCAN 0 . GRCh38 5 83542094 83542094 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.9091C>A p.Gln3031Lys p.Q3031K ENST00000265077 8/15 66 40 26 73 73 0 strelka-varscan-mutect VCAN,missense_variant,p.Gln3031Lys,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Gln2044Lys,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,non_coding_transcript_exon_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 9656/12625 9091/10191 3031/3396 Q/K Cag/Aag COSM5690783 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.71) 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 83542094 83542094 C A 1 0 0 0 0 1 0 0 0 17683 479 17 2 2 VCAN 5 83542094 Missense_Mutation SNP C C3N-01030_T 4575 83542094 97996165 238 21019 VCAN 0 . GRCh38 5 83545564 83545564 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.9293G>T p.Cys3098Phe p.C3098F ENST00000265077 9/15 382 334 48 379 379 0 strelka-varscan-mutect VCAN,missense_variant,p.Cys3098Phe,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Cys2111Phe,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Cys1344Phe,ENST00000342785,NM_001164098.1;VCAN,missense_variant,p.Cys1296Phe,ENST00000512590,;VCAN,missense_variant,p.Cys357Phe,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,non_coding_transcript_exon_variant,,ENST00000507162,; T ENST00000265077 Transcript missense_variant 9858/12625 9293/10191 3098/3396 C/F tGc/tTc COSM1070946 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 deleterious(0) 9/15 PROSITE_profiles:PS50026,hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804,Pfam_domain:PF00008,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 83545564 83545564 G T 1 0 0 0 0 1 0 0 0 17683 1319 46 2 2 VCAN 5 83545564 Missense_Mutation SNP G C3N-01030_T 3470 83545564 97992695 239 21020 POU5F2 0 . GRCh38 5 93740719 93740719 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.845G>T p.Gly282Val p.G282V ENST00000606183 1/1 155 111 44 164 164 0 strelka-varscan-mutect POU5F2,missense_variant,p.Gly282Val,ENST00000606183,NM_153216.1;FAM172A,intron_variant,,ENST00000395965,NM_032042.5;FAM172A,intron_variant,,ENST00000505869,NM_001163418.1;FAM172A,intron_variant,,ENST00000509163,NM_001163417.1;FAM172A,intron_variant,,ENST00000509739,;RP11-185E12.2,upstream_gene_variant,,ENST00000606528,;FAM172A,intron_variant,,ENST00000502503,; A ENST00000606183 Transcript missense_variant 919/8418 845/987 282/328 G/V gGg/gTg 1 -1 POU5F2 HGNC HGNC:26367 protein_coding YES CCDS59489.1 ENSP00000489796 Q8N7G0 UPI0000135E4C NM_153216.1 deleterious(0) 1/1 hmmpanther:PTHR11636:SF14,hmmpanther:PTHR11636 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 93740719 93740719 C A 1 0 0 0 0 1 0 0 0 12399 623 22 2 2 POU5F2 5 93740719 Missense_Mutation SNP C C3N-01030_T 10195155 93740719 87797540 240 21021 KIAA0825 0 . GRCh38 5 94477133 94477133 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1205A>T p.Glu402Val p.E402V ENST00000513200 6/20 99 87 12 188 188 0 strelka-varscan-mutect KIAA0825,missense_variant,p.Glu402Val,ENST00000513200,NM_001145678.1;KIAA0825,non_coding_transcript_exon_variant,,ENST00000504117,; A ENST00000513200 Transcript missense_variant 1278/4942 1205/3828 402/1275 E/V gAg/gTg 1 -1 KIAA0825 HGNC HGNC:28532 protein_coding ENSP00000424618 A0A088AWM3 UPI0001D3B505 NM_001145678.1 deleterious(0.01) 6/20 hmmpanther:PTHR33960:SF1,hmmpanther:PTHR33960 MODERATE SNV 5 1 PASS rs1261394819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 94477133 94477133 T A 1 0 0 0 0 1 0 0 0 8091 1551 54 4 4 KIAA0825 5 94477133 Missense_Mutation SNP T C3N-01030_T 736414 94477133 87061126 241 21022 APC 0 . GRCh38 5 112838434 112838434 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.2840G>C p.Cys947Ser p.C947S ENST00000257430 16/16 206 169 37 290 290 0 strelka-varscan-mutect APC,missense_variant,p.Cys947Ser,ENST00000257430,NM_000038.5;APC,missense_variant,p.Cys947Ser,ENST00000508376,NM_001127510.2;APC,missense_variant,p.Cys947Ser,ENST00000512211,;APC,missense_variant,p.Cys929Ser,ENST00000507379,NM_001127511.2;APC,downstream_gene_variant,,ENST00000504915,;APC,3_prime_UTR_variant,,ENST00000508624,;APC,3_prime_UTR_variant,,ENST00000502371,;CTC-554D6.1,intron_variant,,ENST00000520401,; C ENST00000257430 Transcript missense_variant 2896/10701 2840/8532 947/2843 C/S tGt/tCt CD011087,CD104010,CM080073,COSM327126 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 tolerated(0.53) 16/16 Pfam_domain:PF16629,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 0,0,0,1 MODERATE SNV 5 1,1,1,1 1 PASS rs997271472 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 112838434 112838434 G C 1 0 0 0 0 1 0 0 0 883 1377 48 4 4 APC 5 112838434 Missense_Mutation SNP G C3N-01030_T 18361301 112838434 68699825 242 21023 FBN2 0 . GRCh38 5 128272103 128272103 + Missense_Mutation SNP T T C C3N-01030_T C3N-01030_N T T c.7856A>G p.Asp2619Gly p.D2619G ENST00000508053 68/71 235 170 65 267 267 0 strelka-varscan FBN2,missense_variant,p.Asp2619Gly,ENST00000508053,;FBN2,missense_variant,p.Asp2619Gly,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Asp2618Gly,ENST00000619499,; C ENST00000508053 Transcript missense_variant 8831/11132 7856/8739 2619/2912 D/G gAt/gGt COSM5334297,COSM5334298 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.07) 68/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57184 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 128272103 128272103 T C 1 0 0 0 0 1 0 0 0 5566 1435 50 5 5 FBN2 5 128272103 Missense_Mutation SNP T C3N-01030_T 15433669 128272103 53266156 243 21024 RAD50 0 . GRCh38 5 132640748 132640748 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.3695A>T p.Glu1232Val p.E1232V ENST00000378823 24/25 476 443 33 497 497 0 strelka-varscan RAD50,missense_variant,p.Glu1232Val,ENST00000378823,NM_005732.3;RAD50,missense_variant,p.Glu111Val,ENST00000455677,;TH2LCRR,intron_variant,,ENST00000435042,;TH2LCRR,intron_variant,,ENST00000457489,;TH2LCRR,intron_variant,,ENST00000458509,;TH2LCRR,intron_variant,,ENST00000417516,;RAD50,3_prime_UTR_variant,,ENST00000533482,; T ENST00000378823 Transcript missense_variant 4082/8306 3695/3939 1232/1312 E/V gAg/gTg 1 1 RAD50 HGNC HGNC:9816 protein_coding YES CCDS34233.1 ENSP00000368100 Q92878 UPI000006E9ED NM_005732.3 deleterious(0.04) 24/25 Gene3D:3.40.50.300,Pfam_domain:PF13558,hmmpanther:PTHR18867,hmmpanther:PTHR18867:SF12,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 132640748 132640748 A T 1 0 0 0 0 1 0 0 0 13145 304 11 4 4 RAD50 5 132640748 Missense_Mutation SNP A C3N-01030_T 4368645 132640748 48897511 244 21025 NEUROG1 0 . GRCh38 5 135535414 135535414 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.277C>A p.= p.R93R ENST00000314744 1/1 152 133 19 134 134 0 strelka-varscan NEUROG1,synonymous_variant,p.=,ENST00000314744,NM_006161.2; T ENST00000314744 Transcript synonymous_variant 536/1668 277/714 93/237 R Cgg/Agg 1 -1 NEUROG1 HGNC HGNC:7764 protein_coding YES CCDS4187.1 ENSP00000317580 Q92886 F1T0H3 UPI0000072868 NM_006161.2 1/1 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF92,Superfamily_domains:SSF47459 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 135535414 135535414 G T 1 0 0 0 0 0 0 0 1 10389 1115 39 1 1 NEUROG1 5 135535414 Silent SNP G C3N-01030_T 2894666 135535414 46002845 245 21026 TRPC7 0 . GRCh38 5 136251811 136251811 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1417C>A p.Leu473Met p.L473M ENST00000513104 6/12 231 204 27 258 257 1 strelka-varscan TRPC7,missense_variant,p.Leu473Met,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Leu418Met,ENST00000502753,;TRPC7,missense_variant,p.Leu412Met,ENST00000378459,NM_001167577.1;TRPC7,missense_variant,p.Leu357Met,ENST00000352189,NM_001167576.1;TRPC7,3_prime_UTR_variant,,ENST00000503275,;TRPC7,3_prime_UTR_variant,,ENST00000514963,; T ENST00000513104 Transcript missense_variant 1700/2987 1417/2589 473/862 L/M Ctg/Atg 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 tolerated(0.23) 6/12 Pfam_domain:PF00520,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 136251811 136251811 G T 1 0 0 0 0 1 0 0 0 17090 991 35 2 2 TRPC7 5 136251811 Missense_Mutation SNP G C3N-01030_T 716397 136251811 45286448 246 21027 PCDHA2 0 . GRCh38 5 140797296 140797296 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.2332C>G p.Gln778Glu p.Q778E ENST00000526136 1/4 374 297 77 347 347 0 strelka-varscan PCDHA2,missense_variant,p.Gln778Glu,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Gln778Glu,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Gln778Glu,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,upstream_gene_variant,,ENST00000522353,NM_018906.2;PCDHA3,upstream_gene_variant,,ENST00000532566,NM_031497.1;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; G ENST00000526136 Transcript missense_variant 2332/5254 2332/2847 778/948 Q/E Caa/Gaa 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 tolerated_low_confidence(0.07) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 140797296 140797296 C G 1 0 0 0 0 1 0 0 0 11611 827 29 4 4 PCDHA2 5 140797296 Missense_Mutation SNP C C3N-01030_T 4545485 140797296 40740963 247 21028 PCDHB14 0 . GRCh38 5 141225629 141225629 + Silent SNP C C T rs782228717 C3N-01030_T C3N-01030_N C C c.2124C>T p.= p.F708F ENST00000239449 1/1 359 275 84 344 344 0 strelka-varscan PCDHB14,synonymous_variant,p.=,ENST00000239449,NM_018934.3;PCDHB14,synonymous_variant,p.=,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; T ENST00000239449 Transcript synonymous_variant 2698/4828 2124/2397 708/798 F ttC/ttT rs782228717,COSM3610943 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix 0,1 LOW SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 141225629 141225629 C T 1 0 0 0 0 0 0 0 1 11626 883 31 1 1 PCDHB14 5 141225629 Silent SNP C C3N-01030_T 428333 141225629 40312630 248 21029 SH3TC2 0 . GRCh38 5 149007003 149007003 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.3553G>C p.Ala1185Pro p.A1185P ENST00000515425 16/17 455 342 113 455 455 0 strelka-varscan SH3TC2,missense_variant,p.Ala1185Pro,ENST00000515425,NM_024577.3;SH3TC2,missense_variant,p.Ala1178Pro,ENST00000512049,;SH3TC2,missense_variant,p.Ala47Pro,ENST00000502274,;SH3TC2,non_coding_transcript_exon_variant,,ENST00000515229,;SH3TC2,non_coding_transcript_exon_variant,,ENST00000510350,;SH3TC2,missense_variant,p.Ala1185Pro,ENST00000504690,;SH3TC2,3_prime_UTR_variant,,ENST00000323829,;SH3TC2,3_prime_UTR_variant,,ENST00000504517,;SH3TC2,3_prime_UTR_variant,,ENST00000510779,; G ENST00000515425 Transcript missense_variant 3655/4059 3553/3867 1185/1288 A/P Gct/Cct 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 deleterious(0) 16/17 Gene3D:1.25.40.10,hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF2,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 149007003 149007003 C G 1 0 0 0 0 1 0 0 0 14521 739 26 4 4 SH3TC2 5 149007003 Missense_Mutation SNP C C3N-01030_T 7781374 149007003 32531256 249 21030 SH3TC2 0 . GRCh38 5 149012582 149012582 + Splice_Site SNP A A G novel C3N-01030_T C3N-01030_N A A c.3204+2T>C p.X1068_splice ENST00000515425 262 203 59 279 279 0 strelka-varscan SH3TC2,splice_donor_variant,,ENST00000515425,NM_024577.3;SH3TC2,splice_donor_variant,,ENST00000512049,;SH3TC2,upstream_gene_variant,,ENST00000502274,;SH3TC2,upstream_gene_variant,,ENST00000515229,;SH3TC2,splice_donor_variant,,ENST00000323829,;SH3TC2,splice_donor_variant,,ENST00000504690,;SH3TC2,splice_donor_variant,,ENST00000504517,;SH3TC2,splice_donor_variant,,ENST00000510779,; G ENST00000515425 Transcript splice_donor_variant -/4059 3204/3867 1068/1288 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 13/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 70 149012582 149012582 A G 1 0 0 0 0 0 0 1 0 14521 405 14 5 5 SH3TC2 5 149012582 Splice_Site SNP A C3N-01030_T 5579 149012582 32525677 250 21031 ARHGEF37 0 . GRCh38 5 149627254 149627254 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1643G>T p.Trp548Leu p.W548L ENST00000333677 11/13 91 75 16 86 85 1 strelka-varscan ARHGEF37,missense_variant,p.Trp548Leu,ENST00000333677,NM_001001669.2;ARHGEF37,non_coding_transcript_exon_variant,,ENST00000509831,; T ENST00000333677 Transcript missense_variant 1806/4968 1643/2028 548/675 W/L tGg/tTg 1 1 ARHGEF37 HGNC HGNC:34430 protein_coding YES CCDS43385.1 ENSP00000328083 A1IGU5 UPI00001D7F04 NM_001001669.2 deleterious(0) 11/13 hmmpanther:PTHR22834,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 2 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 149627254 149627254 G T 1 0 0 0 0 1 0 0 0 1040 1357 47 2 2 ARHGEF37 5 149627254 Missense_Mutation SNP G C3N-01030_T 614672 149627254 31911005 251 21032 HMGXB3 0 . GRCh38 5 150004949 150004949 + Nonsense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.97A>T p.Lys33Ter p.K33* ENST00000502717 2/20 136 103 33 194 194 0 strelka-varscan HMGXB3,stop_gained,p.Lys279Ter,ENST00000613459,;HMGXB3,stop_gained,p.Lys33Ter,ENST00000503427,;HMGXB3,stop_gained,p.Lys33Ter,ENST00000502717,NM_014983.2;TIGD6,upstream_gene_variant,,ENST00000296736,NM_030953.3;TIGD6,upstream_gene_variant,,ENST00000515406,NM_001243253.1;TIGD6,upstream_gene_variant,,ENST00000532987,; T ENST00000502717 Transcript stop_gained 561/4974 97/3879 33/1292 K/* Aaa/Taa 1 1 HMGXB3 HGNC HGNC:28982 protein_coding YES CCDS54935.1 ENSP00000421917 Q12766 UPI00001C1E29 NM_014983.2 2/20 Low_complexity_(Seg):seg,hmmpanther:PTHR17609:SF2,hmmpanther:PTHR17609,Superfamily_domains:SSF47095 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 150004949 150004949 A T 1 0 0 0 0 0 1 0 0 7131 247 9 4 4 HMGXB3 5 150004949 Nonsense_Mutation SNP A C3N-01030_T 377695 150004949 31533310 252 21033 CSF1R 0 . GRCh38 5 150070200 150070200 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1301G>A p.Cys434Tyr p.C434Y ENST00000286301 9/22 105 79 26 83 83 0 strelka-varscan CSF1R,missense_variant,p.Cys434Tyr,ENST00000286301,NM_001288705.1,NM_005211.3;CSF1R,downstream_gene_variant,,ENST00000543093,;CSF1R,upstream_gene_variant,,ENST00000515239,;CSF1R,missense_variant,p.Cys434Tyr,ENST00000504875,;CSF1R,upstream_gene_variant,,ENST00000513609,; T ENST00000286301 Transcript missense_variant 1593/3989 1301/2919 434/972 C/Y tGc/tAc 1 -1 CSF1R HGNC HGNC:2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 UPI000004984A NM_001288705.1,NM_005211.3 deleterious(0) 9/22 PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF47,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000615,Pfam_domain:PF13927,Gene3D:2.60.40.10,PIRSF_domain:PIRSF500947,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 70 150070200 150070200 C T 1 0 0 0 0 1 0 0 0 3733 710 25 3 3 CSF1R 5 150070200 Missense_Mutation SNP C C3N-01030_T 65251 150070200 31468059 253 21034 ARSI 0 . GRCh38 5 150298100 150298100 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.824G>T p.Arg275Leu p.R275L ENST00000328668 2/2 235 170 65 190 190 0 strelka-varscan ARSI,missense_variant,p.Arg275Leu,ENST00000328668,NM_001012301.2;ARSI,missense_variant,p.Arg132Leu,ENST00000515301,;ARSI,downstream_gene_variant,,ENST00000509146,; A ENST00000328668 Transcript missense_variant 1404/3161 824/1710 275/569 R/L cGc/cTc 1 -1 ARSI HGNC HGNC:32521 protein_coding YES CCDS34275.1 ENSP00000333395 Q5FYB1 UPI000003FD83 NM_001012301.2 tolerated(0.09) 2/2 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF68,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 150298100 150298100 C A 1 0 0 0 0 1 0 0 0 1137 768 27 1 1 ARSI 5 150298100 Missense_Mutation SNP C C3N-01030_T 227900 150298100 31240159 254 21035 ARSI 0 . GRCh38 5 150298298 150298298 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.626C>T p.Thr209Ile p.T209I ENST00000328668 2/2 216 162 54 201 201 0 strelka-varscan ARSI,missense_variant,p.Thr209Ile,ENST00000328668,NM_001012301.2;ARSI,missense_variant,p.Thr66Ile,ENST00000515301,;ARSI,missense_variant,p.Thr66Ile,ENST00000509146,; A ENST00000328668 Transcript missense_variant 1206/3161 626/1710 209/569 T/I aCt/aTt 1 -1 ARSI HGNC HGNC:32521 protein_coding YES CCDS34275.1 ENSP00000333395 Q5FYB1 UPI000003FD83 NM_001012301.2 deleterious(0) 2/2 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF68,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 150298298 150298298 G A 1 0 0 0 0 1 0 0 0 1137 1029 36 3 3 ARSI 5 150298298 Missense_Mutation SNP G C3N-01030_T 198 150298298 31239961 255 21036 GABRA6 0 . GRCh38 5 161689717 161689717 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.611G>T p.Ser204Ile p.S204I ENST00000274545 6/9 114 89 25 202 202 0 strelka-varscan GABRA6,missense_variant,p.Ser194Ile,ENST00000523217,;GABRA6,missense_variant,p.Ser204Ile,ENST00000274545,NM_000811.2;GABRA6,missense_variant,p.Ser144Ile,ENST00000520000,;GABRA6,missense_variant,p.Ser124Ile,ENST00000523691,;GABRA6,missense_variant,p.Ser151Ile,ENST00000517823,;RP11-348M17.2,upstream_gene_variant,,ENST00000521984,;GABRA6,downstream_gene_variant,,ENST00000522269,;GABRA6,downstream_gene_variant,,ENST00000518888,;GABRA6,non_coding_transcript_exon_variant,,ENST00000521520,;GABRA6,downstream_gene_variant,,ENST00000524220,; T ENST00000274545 Transcript missense_variant 1044/2128 611/1362 204/453 S/I aGc/aTc 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 deleterious(0) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR01079 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 161689717 161689717 G T 1 0 0 0 0 1 0 0 0 6036 971 34 2 2 GABRA6 5 161689717 Missense_Mutation SNP G C3N-01030_T 11391419 161689717 19848542 256 21037 GABRA6 0 . GRCh38 5 161701666 161701666 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1255C>A p.Gln419Lys p.Q419K ENST00000274545 9/9 309 253 56 337 337 0 strelka-varscan GABRA6,missense_variant,p.Gln409Lys,ENST00000523217,;GABRA6,missense_variant,p.Gln419Lys,ENST00000274545,NM_000811.2;GABRA6,non_coding_transcript_exon_variant,,ENST00000521520,; A ENST00000274545 Transcript missense_variant 1688/2128 1255/1362 419/453 Q/K Cag/Aag 1 1 GABRA6 HGNC HGNC:4080 protein_coding YES CCDS4356.1 ENSP00000274545 Q16445 UPI000013DA14 NM_000811.2 tolerated(1) 9/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF335,Gene3D:1.20.58.390,Superfamily_domains:SSF90112,Prints_domain:PR01079 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 161701666 161701666 C A 1 0 0 0 0 1 0 0 0 6036 595 21 2 2 GABRA6 5 161701666 Missense_Mutation SNP C C3N-01030_T 11949 161701666 19836593 257 21038 GABRA1 0 . GRCh38 5 161897321 161897321 + Nonsense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1270A>T p.Arg424Ter p.R424* ENST00000393943 10/10 209 155 54 244 244 0 strelka-varscan GABRA1,stop_gained,p.Arg424Ter,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,stop_gained,p.Arg424Ter,ENST00000428797,NM_001127643.1;GABRA1,stop_gained,p.Arg439Ter,ENST00000638159,;GABRA1,stop_gained,p.Arg424Ter,ENST00000437025,NM_001127645.1;GABRA1,stop_gained,p.Arg424Ter,ENST00000638112,;GABRA1,stop_gained,p.Arg424Ter,ENST00000636573,;GABRA1,stop_gained,p.Arg424Ter,ENST00000023897,NM_000806.5;GABRA1,stop_gained,p.Arg424Ter,ENST00000637827,;GABRA1,stop_gained,p.Arg424Ter,ENST00000635880,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,; T ENST00000393943 Transcript stop_gained 2053/4686 1270/1371 424/456 R/* Aga/Tga 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 10/10 Gene3D:1.20.58.390,Prints_domain:PR00253,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,Superfamily_domains:SSF90112,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 161897321 161897321 A T 1 0 0 0 0 0 1 0 0 6031 64 3 4 4 GABRA1 5 161897321 Nonsense_Mutation SNP A C3N-01030_T 195655 161897321 19640938 258 21039 TENM2 0 . GRCh38 5 167375272 167375272 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.301G>T p.Gly101Trp p.G101W ENST00000518659 2/29 329 261 68 303 302 1 strelka-varscan TENM2,missense_variant,p.Gly101Trp,ENST00000518659,NM_001122679.1; T ENST00000518659 Transcript missense_variant 340/8550 301/8325 101/2774 G/W Ggg/Tgg 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious_low_confidence(0) 2/29 PROSITE_profiles:PS51361,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Pfam_domain:PF06484 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 167375272 167375272 G T 1 0 0 0 0 1 0 0 0 16172 1232 43 2 2 TENM2 5 167375272 Missense_Mutation SNP G C3N-01030_T 5477951 167375272 14162987 259 21040 TENM2 0 . GRCh38 5 168162641 168162641 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2453G>A p.Gly818Glu p.G818E ENST00000518659 13/29 132 115 17 120 119 1 strelka-varscan TENM2,missense_variant,p.Gly697Glu,ENST00000519204,;TENM2,missense_variant,p.Gly818Glu,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Gly586Glu,ENST00000520394,;CTB-178M22.1,intron_variant,,ENST00000517408,;TENM2,upstream_gene_variant,,ENST00000521126,; A ENST00000518659 Transcript missense_variant 2492/8550 2453/8325 818/2774 G/E gGg/gAg 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 13/29 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2gy5A03,SMART_domains:SM00179,SMART_domains:SM00181 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 168162641 168162641 G A 1 0 0 0 0 1 0 0 0 16172 1232 43 3 3 TENM2 5 168162641 Missense_Mutation SNP G C3N-01030_T 787369 168162641 13375618 260 21041 SLIT3 0 . GRCh38 5 168666668 168666668 + Missense_Mutation SNP A A T rs201812377 C3N-01030_T C3N-01030_N A A c.4379T>A p.Val1460Glu p.V1460E ENST00000332966 36/36 168 125 43 150 150 0 strelka-varscan SLIT3,missense_variant,p.Val1453Glu,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Val1323Glu,ENST00000404867,;SLIT3,missense_variant,p.Val1460Glu,ENST00000332966,NM_001271946.1;CTC-558O2.2,non_coding_transcript_exon_variant,,ENST00000520041,; T ENST00000332966 Transcript missense_variant 4452/4895 4379/4593 1460/1530 V/E gTa/gAa rs201812377 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 tolerated(0.48) 36/36 PROSITE_profiles:PS01225 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 168666668 168666668 A T 1 0 0 0 0 1 0 0 0 15032 391 14 4 4 SLIT3 5 168666668 Missense_Mutation SNP A C3N-01030_T 504027 168666668 12871591 261 21042 SLIT3 0 . GRCh38 5 168806526 168806526 + Silent SNP C C A rs367972639 C3N-01030_T C3N-01030_N C C c.855G>T p.= p.T285T ENST00000332966 9/36 206 170 36 164 164 0 strelka-varscan SLIT3,synonymous_variant,p.=,ENST00000519560,NM_003062.3;SLIT3,synonymous_variant,p.=,ENST00000404867,;SLIT3,synonymous_variant,p.=,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000518140,;SLIT3,non_coding_transcript_exon_variant,,ENST00000521150,; A ENST00000332966 Transcript synonymous_variant 928/4895 855/4593 285/1530 T acG/acT rs367972639,COSM1435904,COSM4942178,COSM4942179 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 9/36 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,Gene3D:3.80.10.10,Pfam_domain:PF01462,SMART_domains:SM00013 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 168806526 168806526 C A 1 0 0 0 0 0 0 0 1 15032 523 19 1 1 SLIT3 5 168806526 Silent SNP C C3N-01030_T 139858 168806526 12731733 262 21043 SLIT3 0 . GRCh38 5 169251398 169251398 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.259C>A p.Leu87Ile p.L87I ENST00000332966 2/36 99 81 18 111 111 0 strelka-varscan SLIT3,missense_variant,p.Leu87Ile,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Leu87Ile,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000521130,;SLIT3,non_coding_transcript_exon_variant,,ENST00000518140,; T ENST00000332966 Transcript missense_variant 332/4895 259/4593 87/1530 L/I Ctc/Atc 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 deleterious(0.01) 2/36 PROSITE_profiles:PS51450,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 169251398 169251398 G T 1 0 0 0 0 1 0 0 0 15032 1000 35 2 2 SLIT3 5 169251398 Missense_Mutation SNP G C3N-01030_T 444872 169251398 12286861 263 21044 SH3PXD2B 0 . GRCh38 5 172362735 172362735 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.562G>T p.Gly188Cys p.G188C ENST00000311601 7/13 318 236 82 263 262 1 strelka-varscan SH3PXD2B,missense_variant,p.Gly188Cys,ENST00000311601,NM_001017995.2;SH3PXD2B,missense_variant,p.Gly174Cys,ENST00000636523,;SH3PXD2B,missense_variant,p.Gly188Cys,ENST00000519643,NM_001308175.1; A ENST00000311601 Transcript missense_variant,splice_region_variant 733/7777 562/2736 188/911 G/C Ggt/Tgt 1 -1 SH3PXD2B HGNC HGNC:29242 protein_coding YES CCDS34291.1 ENSP00000309714 A1X283 UPI000020C12E NM_001017995.2 deleterious(0) 7/13 Gene3D:2.30.30.40,Pfam_domain:PF00018,PROSITE_profiles:PS50002,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF8,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 172362735 172362735 C A 1 0 0 0 0 1 0 0 0 14516 695 24 2 2 SH3PXD2B 5 172362735 Missense_Mutation SNP C C3N-01030_T 3111337 172362735 9175524 264 21045 UNC5A 0 . GRCh38 5 176870438 176870438 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.790C>A p.Arg264Ser p.R264S ENST00000329542 6/15 110 89 21 88 88 0 strelka-varscan UNC5A,missense_variant,p.Arg264Ser,ENST00000329542,NM_133369.2;UNC5A,missense_variant,p.Arg286Ser,ENST00000509580,;UNC5A,3_prime_UTR_variant,,ENST00000513890,; A ENST00000329542 Transcript missense_variant 1064/3812 790/2529 264/842 R/S Cgt/Agt 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 deleterious(0) 6/15 PROSITE_profiles:PS50092,hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 176870438 176870438 C A 1 0 0 0 0 1 0 0 0 17515 652 23 1 1 UNC5A 5 176870438 Missense_Mutation SNP C C3N-01030_T 4507703 176870438 4667821 265 21046 UNC5A 0 . GRCh38 5 176879427 176879427 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2302G>T p.Asp768Tyr p.D768Y ENST00000329542 14/15 132 110 22 79 79 0 strelka-varscan UNC5A,missense_variant,p.Asp768Tyr,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000292432,NM_002115.2;HK3,downstream_gene_variant,,ENST00000514058,;HK3,downstream_gene_variant,,ENST00000506834,;HK3,downstream_gene_variant,,ENST00000514666,; T ENST00000329542 Transcript missense_variant 2576/3812 2302/2529 768/842 D/Y Gac/Tac 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 deleterious(0) 14/15 hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582,Pfam_domain:PF00531,Gene3D:1.10.533.10,SMART_domains:SM00005,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 176879427 176879427 G T 1 0 0 0 0 1 0 0 0 17515 1174 41 2 2 UNC5A 5 176879427 Missense_Mutation SNP G C3N-01030_T 8989 176879427 4658832 266 21047 HK3 0 . GRCh38 5 176881519 176881519 + Missense_Mutation SNP G G C rs746886792 C3N-01030_T C3N-01030_N G G c.2410C>G p.Arg804Gly p.R804G ENST00000292432 18/19 94 75 19 71 71 0 strelka-varscan HK3,missense_variant,p.Arg804Gly,ENST00000292432,NM_002115.2;UNC5A,downstream_gene_variant,,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000514058,;HK3,non_coding_transcript_exon_variant,,ENST00000506834,;HK3,non_coding_transcript_exon_variant,,ENST00000514666,; C ENST00000292432 Transcript missense_variant 2502/3066 2410/2772 804/923 R/G Cgg/Ggg rs746886792 1 -1 HK3 HGNC HGNC:4925 protein_coding YES CCDS4407.1 ENSP00000292432 P52790 A0A024R7R1 UPI000006E237 NM_002115.2 tolerated(0.38) 18/19 PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF1,Gene3D:3.40.367.20,Pfam_domain:PF03727,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 201 5 4 0 0 0 0 -20 0.9993818 1 1 1 0 C 3 2 70 176881519 176881519 G C 1 0 0 0 0 1 0 0 0 7081 1086 38 4 4 HK3 5 176881519 Missense_Mutation SNP G C3N-01030_T 2092 176881519 4656740 267 21048 COL23A1 0 . GRCh38 5 178256929 178256929 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.775-1G>T p.X259_splice ENST00000390654 105 73 32 75 75 0 strelka-varscan COL23A1,splice_acceptor_variant,,ENST00000390654,NM_173465.3;COL23A1,splice_acceptor_variant,,ENST00000407622,; A ENST00000390654 Transcript splice_acceptor_variant -/3061 775/1623 259/540 1 -1 COL23A1 HGNC HGNC:22990 protein_coding YES CCDS4436.1 ENSP00000375069 Q86Y22 UPI0000062274 NM_173465.3 13/28 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 178256929 178256929 C A 1 0 0 0 0 0 0 1 0 3470 695 24 2 2 COL23A1 5 178256929 Splice_Site SNP C C3N-01030_T 1375410 178256929 3281330 268 21049 MAK 0 . GRCh38 6 10803753 10803754 + Frame_Shift_Del DEL AA AA - novel C3N-01030_T C3N-01030_N AA AA c.629_630delTT p.Phe210Ter p.F210* ENST00000354489 7/15 223 197 26 295 295 0 sindel-varindel-pindel MAK,frameshift_variant,p.Phe210Ter,ENST00000313243,;MAK,frameshift_variant,p.Phe210Ter,ENST00000354489,NM_001242957.1;MAK,frameshift_variant,p.Phe210Ter,ENST00000474039,NM_005906.4;MAK,frameshift_variant,p.Phe210Ter,ENST00000536370,NM_001242385.1;MAK,frameshift_variant,p.Phe210Ter,ENST00000538030,;TMEM14B,intron_variant,,ENST00000489137,;TMEM14B,intron_variant,,ENST00000463448,;RP11-637O19.3,intron_variant,,ENST00000480294,;TMEM14B,intron_variant,,ENST00000473166,;TMEM14B,intron_variant,,ENST00000460341,;TMEM14B,intron_variant,,ENST00000463100,;TMEM14B,intron_variant,,ENST00000467229,;TMEM14B,downstream_gene_variant,,ENST00000473807,;TMEM14B,downstream_gene_variant,,ENST00000478732,; - ENST00000354489 Transcript frameshift_variant 911-912/3941 629-630/1947 210/648 F/X tTT/t 1 -1 MAK HGNC HGNC:6816 protein_coding YES CCDS75399.1 ENSP00000346484 P20794 UPI000217CBBA NM_001242957.1 7/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF194,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 10803753 10803753 AA - 1 0 1 0 1 0 0 0 0 9116 359 13 0 0 MAK 6 10803753 Frame_Shift_Del DEL AA C3N-01030_T 10803753 160002226 269 21050 ZBED9 0 . GRCh38 6 28576136 28576136 + Missense_Mutation SNP C C A rs746884939 C3N-01030_T C3N-01030_N C C c.569G>T p.Gly190Val p.G190V ENST00000452236 3/4 15 11 4 34 34 0 strelka-varscan ZBED9,missense_variant,p.Gly190Val,ENST00000452236,NM_052923.1;ZBED9,splice_region_variant,,ENST00000530247,; A ENST00000452236 Transcript missense_variant,splice_region_variant 1187/4877 569/3978 190/1325 G/V gGg/gTg rs746884939 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 deleterious_low_confidence(0) 3/4 MODERATE 1 SNV 1 1 PASS . . 1 202 7 0 0 0 0 0 -12.84082 0.9999999 1 1 1 0 A 3 1 70 28576136 28576136 C A 1 0 0 0 0 1 0 0 0 18086 637 22 2 2 ZBED9 6 28576136 Missense_Mutation SNP C C3N-01030_T 17772383 28576136 142229843 270 21051 AGPAT1 0 . GRCh38 6 32171296 32171296 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.200+1G>T p.X67_splice ENST00000395499 224 109 115 162 162 0 strelka-varscan AGPAT1,splice_donor_variant,,ENST00000395499,;AGPAT1,splice_donor_variant,,ENST00000375107,NM_006411.3;AGPAT1,splice_donor_variant,,ENST00000395497,;AGPAT1,splice_donor_variant,,ENST00000395496,;AGPAT1,splice_donor_variant,,ENST00000336984,NM_032741.4;AGPAT1,splice_donor_variant,,ENST00000375104,;EGFL8,downstream_gene_variant,,ENST00000395512,;EGFL8,downstream_gene_variant,,ENST00000333845,NM_030652.3;EGFL8,downstream_gene_variant,,ENST00000432129,;AGPAT1,upstream_gene_variant,,ENST00000617181,;AGPAT1,splice_donor_variant,,ENST00000490711,;AGPAT1,non_coding_transcript_exon_variant,,ENST00000476663,;PPT2-EGFL8,downstream_gene_variant,,ENST00000453656,;EGFL8,downstream_gene_variant,,ENST00000489721,;PPT2-EGFL8,3_prime_UTR_variant,,ENST00000422437,;PPT2-EGFL8,downstream_gene_variant,,ENST00000428388,;EGFL8,downstream_gene_variant,,ENST00000466239,;PPT2-EGFL8,downstream_gene_variant,,ENST00000583227,;PPT2-EGFL8,downstream_gene_variant,,ENST00000421600,;EGFL8,downstream_gene_variant,,ENST00000482938,; A ENST00000395499 Transcript splice_donor_variant -/2496 200/852 67/283 1 -1 AGPAT1 HGNC HGNC:324 protein_coding YES CCDS4744.1 ENSP00000378877 Q99943 A0A024RCV5 UPI0000131BD2 2/6 HIGH SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 32171296 32171296 C A 1 0 0 0 0 0 0 1 0 468 579 20 2 2 AGPAT1 6 32171296 Splice_Site SNP C C3N-01030_T 3595160 32171296 138634683 271 21052 BRPF3 0 . GRCh38 6 36209786 36209786 + Splice_Site SNP G G T novel C3N-01030_T C3N-01030_N G G c.1738-1G>T p.X580_splice ENST00000357641 97 73 24 112 112 0 strelka-varscan-mutect BRPF3,splice_acceptor_variant,,ENST00000357641,NM_015695.2;BRPF3,splice_acceptor_variant,,ENST00000339717,;BRPF3,splice_acceptor_variant,,ENST00000534694,;BRPF3,splice_acceptor_variant,,ENST00000534400,;BRPF3,downstream_gene_variant,,ENST00000527657,;BRPF3,splice_acceptor_variant,,ENST00000441123,;BRPF3,splice_acceptor_variant,,ENST00000449261,;BRPF3,splice_acceptor_variant,,ENST00000532330,;BRPF3,upstream_gene_variant,,ENST00000441730,;BRPF3,upstream_gene_variant,,ENST00000532538,; T ENST00000357641 Transcript splice_acceptor_variant -/6052 1738/3618 580/1205 1 1 BRPF3 HGNC HGNC:14256 protein_coding YES CCDS34437.1 ENSP00000350267 Q9ULD4 UPI00001C1E4C NM_015695.2 4/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 70 36209786 36209786 G T 1 0 0 0 0 0 0 1 0 1695 1014 35 2 2 BRPF3 6 36209786 Splice_Site SNP G C3N-01030_T 4038490 36209786 134596193 272 21053 TREML1 0 . GRCh38 6 41153762 41153762 + Silent SNP G G T C3N-01030_T C3N-01030_N G G c.372C>A p.= p.P124P ENST00000426005 2/6 66 57 9 75 75 0 strelka-varscan-mutect TREML1,synonymous_variant,p.=,ENST00000373127,NM_001271807.1;TREML1,synonymous_variant,p.=,ENST00000426005,NM_178174.3;TREML1,intron_variant,,ENST00000437044,NM_001271808.1;TREM2,downstream_gene_variant,,ENST00000373113,NM_018965.3;TREM2,downstream_gene_variant,,ENST00000373122,;TREM2,downstream_gene_variant,,ENST00000338469,NM_001271821.1;TREML1,upstream_gene_variant,,ENST00000590581,; T ENST00000426005 Transcript synonymous_variant 416/981 372/936 124/311 P ccC/ccA COSM4916895 1 -1 TREML1 HGNC HGNC:20434 protein_coding YES CCDS4851.1 ENSP00000402855 Q86YW5 UPI0000074451 NM_178174.3 2/6 hmmpanther:PTHR11860,hmmpanther:PTHR11860:SF37,Gene3D:2.60.40.10 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.8067 1 1 1 1 0 T 2 4 70 41153762 41153762 G T 1 0 0 0 0 0 0 0 1 16961 1246 43 2 2 TREML1 6 41153762 Silent SNP G C3N-01030_T 4943976 41153762 129652217 273 21054 FRS3 0 . GRCh38 6 41775587 41775587 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.85G>A p.Glu29Lys p.E29K ENST00000373018 4/7 428 397 31 266 266 0 strelka-varscan-mutect FRS3,missense_variant,p.Glu29Lys,ENST00000373018,NM_006653.4;FRS3,missense_variant,p.Glu29Lys,ENST00000259748,;FRS3,missense_variant,p.Glu53Lys,ENST00000426290,;FRS3,missense_variant,p.Glu29Lys,ENST00000422888,;FRS3,downstream_gene_variant,,ENST00000466420,;PRICKLE4,upstream_gene_variant,,ENST00000456057,; T ENST00000373018 Transcript missense_variant 337/2174 85/1479 29/492 E/K Gag/Aag COSM5672332 1 -1 FRS3 HGNC HGNC:16970 protein_coding YES CCDS4860.1 ENSP00000362109 O43559 A0A140VJJ7 UPI0000073ACA NM_006653.4 deleterious(0.01) 4/7 Gene3D:2.30.29.30,Pfam_domain:PF02174,PROSITE_profiles:PS51064,hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF39,SMART_domains:SM00310,SMART_domains:SM01244,Superfamily_domains:SSF50729 1 MODERATE 1 SNV 3 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 41775587 41775587 C T 1 0 0 0 0 1 0 0 0 5934 835 29 3 3 FRS3 6 41775587 Missense_Mutation SNP C C3N-01030_T 621825 41775587 129030392 274 21055 TCTE1 0 . GRCh38 6 44286187 44286187 + Missense_Mutation SNP G G T rs577201749 C3N-01030_T C3N-01030_N G G c.623C>A p.Pro208Gln p.P208Q ENST00000371505 3/5 106 79 27 76 76 0 strelka-varscan-mutect TCTE1,missense_variant,p.Pro208Gln,ENST00000371505,NM_182539.3;TCTE1,missense_variant,p.Pro55Gln,ENST00000371504,;TMEM151B,intron_variant,,ENST00000438774,;RP11-444E17.6,intron_variant,,ENST00000505802,; T ENST00000371505 Transcript missense_variant 746/3067 623/1506 208/501 P/Q cCg/cAg rs577201749 1 -1 TCTE1 HGNC HGNC:11693 protein_coding YES CCDS4910.1 ENSP00000360560 Q5JU00 UPI0000160BC0 NM_182539.3 tolerated(0.51) 3/5 hmmpanther:PTHR24107:SF2,hmmpanther:PTHR24107 MODERATE 1 SNV 1 1 PASS rs577201749 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 44286187 44286187 G T 1 0 0 0 0 1 0 0 0 16125 1116 39 1 1 TCTE1 6 44286187 Missense_Mutation SNP G C3N-01030_T 2510600 44286187 126519792 275 21056 ADGRF2 0 . GRCh38 6 47681632 47681632 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1073A>T p.Asn358Ile p.N358I ENST00000296862 6/6 156 119 37 158 158 0 strelka-varscan-mutect ADGRF2,missense_variant,p.Asn290Ile,ENST00000398742,NM_153839.6;ADGRF2,missense_variant,p.Asn290Ile,ENST00000507065,;ADGRF2,missense_variant,p.Asn358Ile,ENST00000296862,;ADGRF4,upstream_gene_variant,,ENST00000371220,;ADGRF2,missense_variant,p.Asn290Ile,ENST00000467205,; T ENST00000296862 Transcript missense_variant 1073/2127 1073/2127 358/708 N/I aAt/aTt 1 1 ADGRF2 HGNC HGNC:18991 protein_coding YES ENSP00000296862 Q8IZF7 UPI000007411C deleterious(0.01) 6/6 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF54 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 47681632 47681632 A T 1 0 0 0 0 1 0 0 0 364 101 4 4 4 ADGRF2 6 47681632 Missense_Mutation SNP A C3N-01030_T 3395445 47681632 123124347 276 21057 PTCHD4 0 . GRCh38 6 47879530 47879530 + Silent SNP C C T rs752591947 C3N-01030_T C3N-01030_N C C c.1314G>A p.= p.T438T ENST00000339488 3/3 165 150 15 216 216 0 strelka-varscan-mutect PTCHD4,synonymous_variant,p.=,ENST00000339488,NM_001013732.3; T ENST00000339488 Transcript synonymous_variant 1348/2850 1314/2541 438/846 T acG/acA rs752591947,COSM1444978 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 3/3 Pfam_domain:PF02460 0,1 LOW 1 SNV 2 0,1 1 PASS rs752591947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 47879530 47879530 C T 1 0 0 0 0 0 0 0 1 12887 871 31 1 1 PTCHD4 6 47879530 Silent SNP C C3N-01030_T 197898 47879530 122926449 277 21058 PKHD1 0 . GRCh38 6 51934251 51934251 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.5980G>T p.Gly1994Ter p.G1994* ENST00000371117 37/67 337 243 94 296 296 0 strelka-varscan-mutect PKHD1,stop_gained,p.Gly1994Ter,ENST00000371117,NM_138694.3;PKHD1,stop_gained,p.Gly1994Ter,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript stop_gained 6256/16282 5980/12225 1994/4074 G/* Gga/Tga 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 37/67 PROSITE_profiles:PS51484,Pfam_domain:PF10162,SMART_domains:SM01225 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 51934251 51934251 C A 1 0 0 0 0 0 1 0 0 12067 603 21 2 2 PKHD1 6 51934251 Nonsense_Mutation SNP C C3N-01030_T 4054721 51934251 118871728 278 21059 ICK 0 . GRCh38 6 53012174 53012174 + Missense_Mutation SNP C C A rs752349756 C3N-01030_T C3N-01030_N C C c.1206G>T p.Arg402Ser p.R402S ENST00000356971 11/15 338 266 72 385 384 1 strelka-varscan-mutect ICK,missense_variant,p.Arg402Ser,ENST00000356971,NM_016513.4;ICK,missense_variant,p.Arg402Ser,ENST00000350082,NM_014920.3; A ENST00000356971 Transcript missense_variant 1696/6227 1206/1899 402/632 R/S agG/agT rs752349756 1 -1 ICK HGNC HGNC:21219 protein_coding YES CCDS4949.1 ENSP00000349458 Q9UPZ9 A0A024RD59 UPI0000073DE8 NM_016513.4 deleterious(0.02) 11/15 MODERATE 1 SNV 2 1 PASS rs752349756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 53012174 53012174 C A 1 0 0 0 0 1 0 0 0 7386 854 30 2 2 ICK 6 53012174 Missense_Mutation SNP C C3N-01030_T 1077923 53012174 117793805 279 21060 GCLC 0 . GRCh38 6 53500142 53500142 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1605C>G p.Ile535Met p.I535M ENST00000229416 15/16 339 263 76 309 309 0 strelka-varscan-mutect GCLC,missense_variant,p.Ile535Met,ENST00000229416,NM_001498.3;GCLC,missense_variant,p.Ile497Met,ENST00000616923,NM_001197115.1;RP1-27K12.4,upstream_gene_variant,,ENST00000508884,;GCLC,non_coding_transcript_exon_variant,,ENST00000509541,;GCLC,non_coding_transcript_exon_variant,,ENST00000515580,;GCLC,non_coding_transcript_exon_variant,,ENST00000510837,;GCLC,downstream_gene_variant,,ENST00000504353,; C ENST00000229416 Transcript missense_variant 2089/3813 1605/1914 535/637 I/M atC/atG 1 -1 GCLC HGNC HGNC:4311 protein_coding YES CCDS4952.1 ENSP00000229416 P48506 Q14TF0 UPI000000D970 NM_001498.3 tolerated(0.11) 15/16 hmmpanther:PTHR11164,Pfam_domain:PF03074,Superfamily_domains:SSF55931 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 53500142 53500142 G C 1 0 0 0 0 1 0 0 0 6165 1164 41 4 4 GCLC 6 53500142 Missense_Mutation SNP G C3N-01030_T 487968 53500142 117305837 280 21061 MLIP 0 . GRCh38 6 54124710 54124710 + Missense_Mutation SNP G G T rs778436086 C3N-01030_T C3N-01030_N G G c.490G>T p.Gly164Trp p.G164W ENST00000502396 3/14 148 111 37 123 123 0 strelka-varscan-mutect MLIP,missense_variant,p.Gly153Trp,ENST00000514921,NM_001281746.1;MLIP,missense_variant,p.Gly164Trp,ENST00000502396,NM_001281747.1;MLIP,missense_variant,p.Gly153Trp,ENST00000274897,NM_138569.2;MLIP,missense_variant,p.Gly112Trp,ENST00000503951,;MLIP,missense_variant,p.Gly101Trp,ENST00000370877,;MLIP,missense_variant,p.Gly91Trp,ENST00000370876,;MLIP,missense_variant,p.Gly101Trp,ENST00000509997,;MLIP,missense_variant,p.Gly154Trp,ENST00000514433,;MLIP,missense_variant,p.Gly35Trp,ENST00000447836,;MLIP,missense_variant,p.Gly35Trp,ENST00000511678,;MLIP,downstream_gene_variant,,ENST00000505762,;MLIP,downstream_gene_variant,,ENST00000460844,;MLIP,non_coding_transcript_exon_variant,,ENST00000511744,; T ENST00000502396 Transcript missense_variant 522/3102 490/2982 164/993 G/W Ggg/Tgg rs778436086 1 1 MLIP HGNC HGNC:21355 protein_coding YES CCDS64449.1 ENSP00000426290 Q5VWP3 UPI0001D3BBBE NM_001281747.1 deleterious(0) 3/14 hmmpanther:PTHR31514,hmmpanther:PTHR31514:SF1,Pfam_domain:PF15274 MODERATE 1 SNV 2 1 PASS rs778436086 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 54124710 54124710 G T 1 0 0 0 0 1 0 0 0 9586 1232 43 2 2 MLIP 6 54124710 Missense_Mutation SNP G C3N-01030_T 624568 54124710 116681269 281 21062 EYS 0 . GRCh38 6 64081940 64081940 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.6487T>A p.Phe2163Ile p.F2163I ENST00000370621 32/44 81 60 21 142 142 0 strelka-varscan-mutect EYS,missense_variant,p.Phe2163Ile,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Phe2163Ile,ENST00000370621,NM_001292009.1; T ENST00000370621 Transcript missense_variant 7014/10485 6487/9498 2163/3165 F/I Ttt/Att 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.28) 32/44 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 64081940 64081940 A T 1 0 0 0 0 1 0 0 0 5200 43 2 4 4 EYS 6 64081940 Missense_Mutation SNP A C3N-01030_T 9957230 64081940 106724039 282 21063 EYS 0 . GRCh38 6 64822686 64822686 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.3129C>A p.= p.A1043A ENST00000370621 20/44 158 118 40 232 232 0 strelka-varscan-mutect EYS,synonymous_variant,p.=,ENST00000503581,NM_001142800.1;EYS,synonymous_variant,p.=,ENST00000370621,NM_001292009.1; T ENST00000370621 Transcript synonymous_variant 3656/10485 3129/9498 1043/3165 A gcC/gcA 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 20/44 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS rs911291244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 64822686 64822686 G T 1 0 0 0 0 0 0 0 1 5200 1335 47 2 2 EYS 6 64822686 Silent SNP G C3N-01030_T 740746 64822686 105983293 283 21064 MRAP2 0 . GRCh38 6 84055392 84055392 + Missense_Mutation SNP A A T rs754918660 C3N-01030_T C3N-01030_N A A c.74A>T p.Tyr25Phe p.Y25F ENST00000257776 2/4 109 71 38 180 180 0 strelka-varscan-mutect MRAP2,missense_variant,p.Tyr25Phe,ENST00000257776,NM_138409.2; T ENST00000257776 Transcript missense_variant 209/2153 74/618 25/205 Y/F tAt/tTt rs754918660 1 1 MRAP2 HGNC HGNC:21232 protein_coding YES CCDS5001.1 ENSP00000257776 Q96G30 UPI0000074376 NM_138409.2 tolerated(0.05) 2/4 hmmpanther:PTHR28675:SF1,hmmpanther:PTHR28675,Pfam_domain:PF15183,PD396861 MODERATE 1 SNV 1 1 PASS rs754918660 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 84055392 84055392 A T 1 0 0 0 0 1 0 0 0 9720 449 16 4 4 MRAP2 6 84055392 Missense_Mutation SNP A C3N-01030_T 19232706 84055392 86750587 284 21065 EPHA7 0 . GRCh38 6 93410757 93410757 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.576C>A p.Cys192Ter p.C192* ENST00000369303 3/17 137 94 43 179 178 1 strelka-varscan-mutect EPHA7,stop_gained,p.Cys192Ter,ENST00000369303,NM_001288629.1,NM_004440.3;EPHA7,stop_gained,p.Cys192Ter,ENST00000369297,NM_001288630.1; T ENST00000369303 Transcript stop_gained 761/6588 576/2997 192/998 C/* tgC/tgA 1 -1 EPHA7 HGNC HGNC:3390 protein_coding YES CCDS5031.1 ENSP00000358309 Q15375 UPI0000044771 NM_001288629.1,NM_004440.3 3/17 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_patterns:PS00790,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF377,SMART_domains:SM00615,Superfamily_domains:SSF49785 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 93410757 93410757 G T 1 0 0 0 0 0 1 0 0 5019 1311 46 2 2 EPHA7 6 93410757 Nonsense_Mutation SNP G C3N-01030_T 9355365 93410757 77395222 285 21066 SIM1 0 . GRCh38 6 100390787 100390787 + Silent SNP G G T C3N-01030_T C3N-01030_N G G c.1875C>A p.= p.A625A ENST00000369208 12/12 213 168 45 282 282 0 strelka-varscan-mutect SIM1,synonymous_variant,p.=,ENST00000369208,;SIM1,synonymous_variant,p.=,ENST00000262901,NM_005068.2;SIM1,downstream_gene_variant,,ENST00000505753,; T ENST00000369208 Transcript synonymous_variant 2658/8430 1875/2301 625/766 A gcC/gcA COSM3941430 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 12/12 Pfam_domain:PF06621,PROSITE_profiles:PS51302,hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29 1 LOW 1 SNV 1 1 1 PASS rs1180910746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 100390787 100390787 G T 1 0 0 0 0 0 0 0 1 14586 1335 47 2 2 SIM1 6 100390787 Silent SNP G C3N-01030_T 6980030 100390787 70415192 286 21067 GRIK2 0 . GRCh38 6 101889697 101889697 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.1582G>T p.Asp528Tyr p.D528Y ENST00000421544 11/16 166 117 49 204 204 0 strelka-varscan-mutect GRIK2,missense_variant,p.Asp528Tyr,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Asp528Tyr,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Asp528Tyr,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Asp490Tyr,ENST00000318991,;GRIK2,missense_variant,p.Asp490Tyr,ENST00000369137,;GRIK2,missense_variant,p.Asp490Tyr,ENST00000369134,;GRIK2,missense_variant,p.Asp127Tyr,ENST00000436862,; T ENST00000421544 Transcript missense_variant 2072/4789 1582/2727 528/908 D/Y Gac/Tac COSM1236041,COSM1236042,COSM212929,COSM212930,COSM3715286 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 deleterious(0) 11/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,SMART_domains:SM00079,Superfamily_domains:SSF53850 1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs1402876014 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 101889697 101889697 G T 1 0 0 0 0 1 0 0 0 6656 1058 37 1 1 GRIK2 6 101889697 Missense_Mutation SNP G C3N-01030_T 1498910 101889697 68916282 287 21068 MAN1A1 0 . GRCh38 6 119189793 119189793 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1417C>T p.His473Tyr p.H473Y ENST00000368468 10/13 194 138 56 216 216 0 strelka-varscan-mutect MAN1A1,missense_variant,p.His473Tyr,ENST00000368468,NM_005907.3; A ENST00000368468 Transcript missense_variant 1859/5014 1417/1962 473/653 H/Y Cac/Tac 1 -1 MAN1A1 HGNC HGNC:6821 protein_coding YES CCDS5122.1 ENSP00000357453 P33908 UPI000013D632 NM_005907.3 deleterious(0) 10/13 hmmpanther:PTHR11742:SF31,hmmpanther:PTHR11742,Pfam_domain:PF01532,Gene3D:1.50.10.50,Superfamily_domains:SSF48225,Prints_domain:PR00747 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 119189793 119189793 G A 1 0 0 0 0 1 0 0 0 9131 1348 47 3 3 MAN1A1 6 119189793 Missense_Mutation SNP G C3N-01030_T 17300096 119189793 51616186 288 21069 ARHGAP18 0 . GRCh38 6 129638543 129638543 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.403G>T p.Val135Leu p.V135L ENST00000368149 3/15 178 123 55 215 214 1 strelka-varscan-mutect ARHGAP18,missense_variant,p.Val135Leu,ENST00000368149,NM_033515.2; A ENST00000368149 Transcript missense_variant 492/4462 403/1992 135/663 V/L Gtg/Ttg 1 -1 ARHGAP18 HGNC HGNC:21035 protein_coding YES CCDS34535.1 ENSP00000357131 Q8N392 UPI000020E208 NM_033515.2 tolerated(0.16) 3/15 hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 129638543 129638543 C A 1 0 0 0 0 1 0 0 0 992 478 17 2 2 ARHGAP18 6 129638543 Missense_Mutation SNP C C3N-01030_T 10448750 129638543 41167436 289 21070 SDK1 0 . GRCh38 7 4130097 4130097 + Missense_Mutation SNP G G T rs768078718 C3N-01030_T C3N-01030_N G G c.4129G>T p.Ala1377Ser p.A1377S ENST00000404826 27/45 71 61 10 54 54 0 strelka-varscan-mutect SDK1,missense_variant,p.Ala1377Ser,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Ala1377Ser,ENST00000615806,;SDK1,missense_variant,p.Ala1377Ser,ENST00000389531,;SDK1,splice_region_variant,,ENST00000476701,; T ENST00000404826 Transcript missense_variant,splice_region_variant 4268/10397 4129/6642 1377/2213 A/S Gcc/Tcc rs768078718 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 tolerated(0.11) 27/45 hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs768078718 . 0 201 9 0 0 0 0 0 -19.99471 0.9999928 1 1 1 0 T 3 4 70 4130097 4130097 G T 1 0 0 0 0 1 0 0 0 14243 1362 47 2 2 SDK1 7 4130097 Missense_Mutation SNP G C3N-01030_T 4130097 155215876 290 21071 THSD7A 0 . GRCh38 7 11460706 11460706 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2561G>T p.Ser854Ile p.S854I ENST00000423059 11/28 228 143 85 154 154 0 strelka-varscan-mutect THSD7A,missense_variant,p.Ser854Ile,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Ser854Ile,ENST00000617773,;AC004538.3,intron_variant,,ENST00000445839,;THSD7A,intron_variant,,ENST00000497575,; A ENST00000423059 Transcript missense_variant 2813/10663 2561/4974 854/1657 S/I aGc/aTc 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 tolerated(0.4) 11/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 11460706 11460706 C A 1 0 0 0 0 1 0 0 0 16313 797 28 2 2 THSD7A 7 11460706 Missense_Mutation SNP C C3N-01030_T 7330609 11460706 147885267 291 21072 AHR 0 . GRCh38 7 17339541 17339541 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1716C>G p.Phe572Leu p.F572L ENST00000242057 10/11 153 111 42 147 147 0 strelka-varscan-mutect AHR,missense_variant,p.Phe572Leu,ENST00000242057,NM_001621.4;RP11-507K12.1,missense_variant,p.Phe562Leu,ENST00000637807,;AHR,downstream_gene_variant,,ENST00000492120,;AHR,downstream_gene_variant,,ENST00000481944,;AHR,missense_variant,p.Phe572Leu,ENST00000463496,; G ENST00000242057 Transcript missense_variant 2359/6276 1716/2547 572/848 F/L ttC/ttG 1 1 AHR HGNC HGNC:348 protein_coding YES CCDS5366.1 ENSP00000242057 P35869 A0A024R9Z8 UPI0000125727 NM_001621.4 tolerated(0.9) 10/11 hmmpanther:PTHR10649:SF9,hmmpanther:PTHR10649 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 17339541 17339541 C G 1 0 0 0 0 1 0 0 0 493 825 29 4 4 AHR 7 17339541 Missense_Mutation SNP C C3N-01030_T 5878835 17339541 142006432 292 21073 ABCB5 0 . GRCh38 7 20753404 20753404 + Silent SNP C C G rs148088276 C3N-01030_T C3N-01030_N C C c.3474C>G p.= p.G1158G ENST00000404938 27/28 171 146 25 164 164 0 strelka-varscan-mutect ABCB5,synonymous_variant,p.=,ENST00000404938,NM_001163941.1;ABCB5,synonymous_variant,p.=,ENST00000258738,NM_178559.5;ABCB5,intron_variant,,ENST00000441315,; G ENST00000404938 Transcript synonymous_variant 4126/5811 3474/3774 1158/1257 G ggC/ggG rs148088276 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 27/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_patterns:PS00211,PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF217,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs148088276 . 0 205 0 3 0 0 0 2 -3.407825 0 0 1 0 0 G 2 3 70 20753404 20753404 C G 1 0 0 0 0 0 0 0 1 48 755 27 4 4 ABCB5 7 20753404 Silent SNP C C3N-01030_T 3413863 20753404 138592569 293 21074 DNAH11 0 . GRCh38 7 21599979 21599979 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2860G>A p.Glu954Lys p.E954K ENST00000409508 15/82 168 153 15 155 155 0 strelka-varscan-mutect DNAH11,missense_variant,p.Glu954Lys,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.Glu954Lys,ENST00000328843,;DNAH11,missense_variant,p.Glu954Lys,ENST00000620169,; A ENST00000409508 Transcript missense_variant 2891/14167 2860/13551 954/4516 E/K Gag/Aag 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 tolerated(0.1) 15/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 21599979 21599979 G A 1 0 0 0 0 1 0 0 0 4413 1291 45 3 3 DNAH11 7 21599979 Missense_Mutation SNP G C3N-01030_T 846575 21599979 137745994 294 21075 TRA2A 0 . GRCh38 7 23521786 23521786 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.91G>T p.Glu31Ter p.E31* ENST00000297071 2/8 282 236 46 246 246 0 strelka-varscan-mutect TRA2A,stop_gained,p.Glu31Ter,ENST00000297071,NM_013293.4;TRA2A,5_prime_UTR_variant,,ENST00000392502,NM_001282759.1;TRA2A,5_prime_UTR_variant,,ENST00000538367,NM_001282757.1;TRA2A,5_prime_UTR_variant,,ENST00000621813,NM_001282758.1;TRA2A,non_coding_transcript_exon_variant,,ENST00000474586,;TRA2A,non_coding_transcript_exon_variant,,ENST00000490942,;TRA2A,missense_variant,p.Gly57Val,ENST00000448549,;TRA2A,non_coding_transcript_exon_variant,,ENST00000494255,; A ENST00000297071 Transcript stop_gained 308/1845 91/849 31/282 E/* Gag/Tag 1 -1 TRA2A HGNC HGNC:16645 protein_coding YES CCDS5383.1 ENSP00000297071 Q13595 Q549U1 UPI00001372AB NM_013293.4 2/8 Low_complexity_(Seg):seg,hmmpanther:PTHR15241:SF3,hmmpanther:PTHR15241 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 23521786 23521786 C A 1 0 0 0 0 0 1 0 0 16914 864 30 2 2 TRA2A 7 23521786 Nonsense_Mutation SNP C C3N-01030_T 1921807 23521786 135824187 295 21076 HOXA10 0 . GRCh38 7 27172165 27172165 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.967A>G p.Lys323Glu p.K323E ENST00000283921 2/2 374 307 67 267 267 0 strelka-varscan-mutect HOXA10,missense_variant,p.Lys323Glu,ENST00000283921,NM_018951.3;HOXA10,missense_variant,p.Gln201Arg,ENST00000613671,;HOXA10,missense_variant,p.Lys7Glu,ENST00000396344,;HOXA10-HOXA9,intron_variant,,ENST00000470747,;HOXA9,upstream_gene_variant,,ENST00000384852,;HOXA10-AS,downstream_gene_variant,,ENST00000519935,;HOXA10-AS,downstream_gene_variant,,ENST00000523790,;HOXA10-AS,downstream_gene_variant,,ENST00000519694,;HOXA10,non_coding_transcript_exon_variant,,ENST00000521421,;HOXA10,non_coding_transcript_exon_variant,,ENST00000524368,;HOXA10,non_coding_transcript_exon_variant,,ENST00000519593,;HOXA9,intron_variant,,ENST00000465941,;HOXA9,upstream_gene_variant,,ENST00000497089,;HOXA9,upstream_gene_variant,,ENST00000487384,;HOXA9,upstream_gene_variant,,ENST00000489695,; C ENST00000283921 Transcript missense_variant 967/2541 967/1233 323/410 K/E Aaa/Gaa 1 -1 HOXA10 HGNC HGNC:5100 protein_coding YES CCDS5410.2 ENSP00000283921 P31260 UPI0000EE42DA NM_018951.3 deleterious(0) 2/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 27172165 27172165 T C 1 0 0 0 0 1 0 0 0 7183 1821 63 5 5 HOXA10 7 27172165 Missense_Mutation SNP T C3N-01030_T 3650379 27172165 132173808 296 21077 PDE1C 0 . GRCh38 7 31824946 31824946 + Missense_Mutation SNP T T G novel C3N-01030_T C3N-01030_N T T c.1507A>C p.Thr503Pro p.T503P ENST00000396193 14/19 141 117 24 157 157 0 strelka-varscan-mutect PDE1C,missense_variant,p.Thr443Pro,ENST00000396184,NM_001322057.1,NM_001322056.1,NM_001322059.1,NM_005020.3;PDE1C,missense_variant,p.Thr503Pro,ENST00000396193,NM_001191058.2;PDE1C,missense_variant,p.Thr443Pro,ENST00000396191,NM_001191057.2;PDE1C,missense_variant,p.Thr443Pro,ENST00000321453,NM_001191059.2;PDE1C,missense_variant,p.Thr443Pro,ENST00000396182,NM_001191056.2;PDE1C,upstream_gene_variant,,ENST00000479980,; G ENST00000396193 Transcript missense_variant 2101/5109 1507/2310 503/769 T/P Acg/Ccg 1 -1 PDE1C HGNC HGNC:8776 protein_coding YES CCDS55100.1 ENSP00000379496 A0A0A0MS69 UPI00043788D1 NM_001191058.2 deleterious(0.03) 14/19 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Superfamily_domains:SSF109604 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 31824946 31824946 T G 1 0 0 0 0 1 0 0 0 11723 1638 57 5 5 PDE1C 7 31824946 Missense_Mutation SNP T C3N-01030_T 4652781 31824946 127521027 297 21078 VPS41 0 . GRCh38 7 38763485 38763485 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1392C>A p.= p.I464I ENST00000310301 17/29 102 87 15 193 193 0 strelka-mutect VPS41,synonymous_variant,p.=,ENST00000310301,NM_014396.3;VPS41,synonymous_variant,p.=,ENST00000395969,NM_080631.3;VPS41,non_coding_transcript_exon_variant,,ENST00000462429,; T ENST00000310301 Transcript synonymous_variant 1447/5903 1392/2565 464/854 I atC/atA 1 -1 VPS41 HGNC HGNC:12713 protein_coding YES CCDS5457.1 ENSP00000309457 P49754 UPI000000DAB7 NM_014396.3 17/29 hmmpanther:PTHR12616,PIRSF_domain:PIRSF028921 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 38763485 38763485 G T 1 0 0 0 0 0 0 0 1 17756 932 33 2 2 VPS41 7 38763485 Silent SNP G C3N-01030_T 6938539 38763485 120582488 298 21079 CDK13 0 . GRCh38 7 40094615 40094615 + Nonsense_Mutation SNP C C T rs751226317 C3N-01030_T C3N-01030_N C C c.4174C>T p.Gln1392Ter p.Q1392* ENST00000181839 14/14 100 81 19 107 107 0 strelka-varscan-mutect CDK13,stop_gained,p.Gln1392Ter,ENST00000181839,NM_003718.4;CDK13,stop_gained,p.Gln1332Ter,ENST00000340829,NM_031267.3;CDK13,downstream_gene_variant,,ENST00000611390,;CDK13,non_coding_transcript_exon_variant,,ENST00000465643,;CDK13,downstream_gene_variant,,ENST00000478563,; T ENST00000181839 Transcript stop_gained 4779/7298 4174/4539 1392/1512 Q/* Cag/Tag rs751226317 1 1 CDK13 HGNC HGNC:1733 protein_coding YES CCDS5461.1 ENSP00000181839 Q14004 A0A024RA85 UPI000013C5E3 NM_003718.4 14/14 HIGH 1 SNV 1 1 PASS rs751226317 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 40094615 40094615 C T 1 0 0 0 0 0 1 0 0 2833 827 29 3 3 CDK13 7 40094615 Nonsense_Mutation SNP C C3N-01030_T 1331130 40094615 119251358 299 21080 INHBA 0 . GRCh38 7 41689857 41689857 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.1074A>T p.= p.I358I ENST00000242208 3/3 128 99 29 128 128 0 strelka-varscan-mutect INHBA,synonymous_variant,p.=,ENST00000242208,NM_002192.2;INHBA,synonymous_variant,p.=,ENST00000638023,;INHBA,synonymous_variant,p.=,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript synonymous_variant 1321/6064 1074/1281 358/426 I atA/atT 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 3/3 PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00019,Gene3D:2.10.90.10,SMART_domains:SM00204,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 41689857 41689857 T A 1 0 0 0 0 0 0 0 1 7643 1512 53 4 4 INHBA 7 41689857 Silent SNP T C3N-01030_T 1595242 41689857 117656116 300 21081 CAMK2B 0 . GRCh38 7 44228798 44228798 + Frame_Shift_Del DEL G G - rs555460132 C3N-01030_T C3N-01030_N G G c.1466delC p.Pro489ArgfsTer9 p.P489Rfs*9 ENST00000395749 19/24 26 18 8 19 19 0 sindel-varindel CAMK2B,frameshift_variant,p.Pro489ArgfsTer9,ENST00000395749,NM_001220.4;CAMK2B,intron_variant,,ENST00000457475,NM_172079.2;CAMK2B,intron_variant,,ENST00000350811,NM_001293170.1;CAMK2B,intron_variant,,ENST00000440254,NM_172078.2;CAMK2B,intron_variant,,ENST00000358707,NM_172081.2;CAMK2B,intron_variant,,ENST00000258682,NM_172080.2;CAMK2B,intron_variant,,ENST00000353625,NM_172083.2;CAMK2B,intron_variant,,ENST00000347193,NM_172082.2;CAMK2B,intron_variant,,ENST00000395747,;CAMK2B,intron_variant,,ENST00000346990,NM_172084.2;CAMK2B,intron_variant,,ENST00000433930,;CAMK2B,upstream_gene_variant,,ENST00000425809,;CAMK2B,splice_region_variant,,ENST00000489429,;CAMK2B,intron_variant,,ENST00000497584,;CAMK2B,intron_variant,,ENST00000523845,;CAMK2B,intron_variant,,ENST00000353185,; - ENST00000395749 Transcript frameshift_variant,splice_region_variant 1543/4447 1466/2001 489/666 P/X cCg/cg rs555460132,COSM20487 1 -1 CAMK2B HGNC HGNC:1461 protein_coding YES CCDS5483.1 ENSP00000379098 Q13554 A4D2J9 UPI0000164A3E NM_001220.4 19/24 Low_complexity_(Seg):seg 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 206 4 0 0 0 0 0 -19.9962 1 1 1 1 0 - 7 5 70 44228798 44228798 G - 1 0 1 0 1 0 0 0 0 2291 1130 39 0 0 CAMK2B 7 44228798 Frame_Shift_Del DEL G C3N-01030_T 2538941 44228798 115117175 301 21082 ZNF716 0 . GRCh38 7 57469709 57469709 + Silent SNP C C A rs782437065 C3N-01030_T C3N-01030_N C C c.1248C>A p.= p.A416A ENST00000420713 4/4 166 132 34 260 260 0 strelka-varscan-mutect ZNF716,synonymous_variant,p.=,ENST00000420713,NM_001159279.1; A ENST00000420713 Transcript synonymous_variant 1360/5197 1248/1488 416/495 A gcC/gcA rs782437065 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 4 1 PASS rs782437065 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 57469709 57469709 C A 1 0 0 0 0 0 0 0 1 18694 668 24 2 2 ZNF716 7 57469709 Silent SNP C C3N-01030_T 13240911 57469709 101876264 302 21083 ZNF716 0 . GRCh38 7 57469842 57469842 + Missense_Mutation SNP G G A C3N-01030_T C3N-01030_N G G c.1381G>A p.Glu461Lys p.E461K ENST00000420713 4/4 147 126 21 174 174 0 strelka-varscan-mutect ZNF716,missense_variant,p.Glu461Lys,ENST00000420713,NM_001159279.1; A ENST00000420713 Transcript missense_variant 1493/5197 1381/1488 461/495 E/K Gag/Aag COSM3923867,COSM3923868 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 deleterious(0.03) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 4 1,1 1 PASS rs1192695901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 57469842 57469842 G A 1 0 0 0 0 1 0 0 0 18694 943 33 3 3 ZNF716 7 57469842 Missense_Mutation SNP G C3N-01030_T 133 57469842 101876131 303 21084 CALN1 0 . GRCh38 7 72106264 72106264 + Missense_Mutation SNP C C A rs753498969 C3N-01030_T C3N-01030_N C C c.275G>T p.Arg92Leu p.R92L ENST00000395275 4/7 114 72 42 124 124 0 strelka-varscan-mutect CALN1,missense_variant,p.Arg92Leu,ENST00000395275,NM_031468.3;CALN1,missense_variant,p.Arg50Leu,ENST00000329008,NM_001017440.2;CALN1,missense_variant,p.Arg50Leu,ENST00000395276,;CALN1,missense_variant,p.Arg50Leu,ENST00000431984,;CALN1,missense_variant,p.Arg50Leu,ENST00000446128,;ABCF2P2,downstream_gene_variant,,ENST00000450549,; A ENST00000395275 Transcript missense_variant 664/9459 275/786 92/261 R/L cGg/cTg rs753498969,COSM362543,COSM3882180,COSM3882181 1 -1 CALN1 HGNC HGNC:13248 protein_coding YES CCDS47603.1 ENSP00000378690 Q9BXU9 UPI0000D4B903 NM_031468.3 deleterious(0) 4/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF51,PROSITE_patterns:PS00018,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs753498969 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 72106264 72106264 C A 1 0 0 0 0 1 0 0 0 2282 652 23 1 1 CALN1 7 72106264 Missense_Mutation SNP C C3N-01030_T 14636422 72106264 87239709 304 21085 BAZ1B 0 . GRCh38 7 73477235 73477235 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.2226A>T p.= p.S742S ENST00000339594 7/20 214 157 57 260 260 0 strelka-varscan-mutect BAZ1B,synonymous_variant,p.=,ENST00000339594,NM_032408.3;BAZ1B,synonymous_variant,p.=,ENST00000404251,; A ENST00000339594 Transcript synonymous_variant 2565/6102 2226/4452 742/1483 S tcA/tcT 1 -1 BAZ1B HGNC HGNC:961 protein_coding YES CCDS5549.1 ENSP00000342434 Q9UIG0 UPI0000126731 NM_032408.3 7/20 Low_complexity_(Seg):seg,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF145,Pfam_domain:PF15612 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 73477235 73477235 T A 1 0 0 0 0 0 0 0 1 1475 1567 55 4 4 BAZ1B 7 73477235 Silent SNP T C3N-01030_T 1370971 73477235 85868738 305 21086 TBL2 0 . GRCh38 7 73573461 73573461 + Missense_Mutation SNP C C A rs373168324 C3N-01030_T C3N-01030_N C C c.457G>T p.Val153Phe p.V153F ENST00000305632 4/7 86 59 27 113 113 0 strelka-varscan-mutect TBL2,missense_variant,p.Val153Phe,ENST00000305632,NM_012453.2;TBL2,missense_variant,p.Val153Phe,ENST00000610724,;TBL2,missense_variant,p.Val117Phe,ENST00000432538,;TBL2,missense_variant,p.Val58Phe,ENST00000479892,;TBL2,non_coding_transcript_exon_variant,,ENST00000459913,;TBL2,non_coding_transcript_exon_variant,,ENST00000452475,;TBL2,non_coding_transcript_exon_variant,,ENST00000465279,;TBL2,non_coding_transcript_exon_variant,,ENST00000476136,;TBL2,downstream_gene_variant,,ENST00000468669,;TBL2,missense_variant,p.Arg145Leu,ENST00000450285,;TBL2,3_prime_UTR_variant,,ENST00000424598,;TBL2,3_prime_UTR_variant,,ENST00000417008,;TBL2,3_prime_UTR_variant,,ENST00000433464,;TBL2,3_prime_UTR_variant,,ENST00000426966,;TBL2,3_prime_UTR_variant,,ENST00000435792,;TBL2,3_prime_UTR_variant,,ENST00000437521,;TBL2,3_prime_UTR_variant,,ENST00000452125,;TBL2,upstream_gene_variant,,ENST00000488915,;TBL2,downstream_gene_variant,,ENST00000458466,;TBL2,downstream_gene_variant,,ENST00000469518,;TBL2,downstream_gene_variant,,ENST00000496056,;TBL2,upstream_gene_variant,,ENST00000495885,; A ENST00000305632 Transcript missense_variant 699/3161 457/1344 153/447 V/F Gtc/Ttc rs373168324 1 -1 TBL2 HGNC HGNC:11586 protein_coding YES CCDS5551.1 ENSP00000307260 Q9Y4P3 UPI0000048EF4 NM_012453.2 deleterious(0.01) 4/7 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF358,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs373168324 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 73573461 73573461 C A 1 0 0 0 0 1 0 0 0 16047 536 19 1 1 TBL2 7 73573461 Missense_Mutation SNP C C3N-01030_T 96226 73573461 85772512 306 21087 NCF1 0 . GRCh38 7 74779327 74779327 + Silent SNP G G T rs371075194 C3N-01030_T C3N-01030_N G G c.300G>T p.= p.T100T ENST00000289473 4/11 293 212 81 269 269 0 strelka-varscan-mutect NCF1,synonymous_variant,p.=,ENST00000289473,NM_000265.5;NCF1,synonymous_variant,p.=,ENST00000433458,;NCF1,synonymous_variant,p.=,ENST00000442021,;NCF1,non_coding_transcript_exon_variant,,ENST00000443956,;NCF1,non_coding_transcript_exon_variant,,ENST00000438106,;NCF1,missense_variant,p.Arg51Leu,ENST00000464878,;NCF1,non_coding_transcript_exon_variant,,ENST00000398421,;NCF1,non_coding_transcript_exon_variant,,ENST00000449343,;NCF1,intron_variant,,ENST00000455062,;NCF1,upstream_gene_variant,,ENST00000488197,;NCF1,upstream_gene_variant,,ENST00000486097,; T ENST00000289473 Transcript synonymous_variant 370/1396 300/1173 100/390 T acG/acT rs371075194 1 1 NCF1 HGNC HGNC:7660 protein_coding YES CCDS34657.1 ENSP00000289473 P14598 UPI000013E46E NM_000265.5 4/11 PROSITE_profiles:PS50195,hmmpanther:PTHR15706,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268 LOW 1 SNV 1 1 PASS rs371075194 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 74779327 74779327 G T 1 0 0 0 0 0 0 0 1 10234 1074 38 1 1 NCF1 7 74779327 Silent SNP G C3N-01030_T 1205866 74779327 84566646 307 21088 PCLO 0 . GRCh38 7 82760745 82760745 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.15182A>G p.Gln5061Arg p.Q5061R ENST00000333891 24/25 68 51 17 107 107 0 strelka-varscan-mutect PCLO,missense_variant,p.Gln5061Arg,ENST00000333891,NM_033026.5; C ENST00000333891 Transcript missense_variant 15520/20329 15182/15429 5061/5142 Q/R cAa/cGa 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0) 24/25 PROSITE_profiles:PS50004,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 82760745 82760745 T C 1 0 0 0 0 1 0 0 0 11671 1812 63 5 5 PCLO 7 82760745 Missense_Mutation SNP T C3N-01030_T 7981418 82760745 76585228 308 21089 STEAP2 0 . GRCh38 7 90232409 90232409 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1258G>C p.Glu420Gln p.E420Q ENST00000394621 6/6 103 86 17 166 166 0 strelka-varscan-mutect STEAP2,missense_variant,p.Glu420Gln,ENST00000394621,NM_001244944.1;STEAP2,missense_variant,p.Glu420Gln,ENST00000287908,NM_152999.3;STEAP2,missense_variant,p.Glu420Gln,ENST00000394622,NM_001040665.1;STEAP2,missense_variant,p.Glu420Gln,ENST00000394626,NM_001244945.1;STEAP2,missense_variant,p.Glu420Gln,ENST00000394629,NM_001040666.1;STEAP2,intron_variant,,ENST00000394632,NM_001244946.1;STEAP2,intron_variant,,ENST00000402625,; C ENST00000394621 Transcript missense_variant 1764/7033 1258/1473 420/490 E/Q Gag/Cag 1 1 STEAP2 HGNC HGNC:17885 protein_coding YES CCDS5615.1 ENSP00000378119 Q8NFT2 UPI000013DEE0 NM_001244944.1 tolerated(0.5) 6/6 hmmpanther:PTHR14239:SF6,hmmpanther:PTHR14239 MODERATE 1 SNV 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 70 90232409 90232409 G C 1 0 0 0 0 1 0 0 0 15655 1291 45 4 4 STEAP2 7 90232409 Missense_Mutation SNP G C3N-01030_T 7471664 90232409 69113564 309 21090 BHLHA15 0 . GRCh38 7 98212798 98212798 + Silent SNP G G T rs754943764 C3N-01030_T C3N-01030_N G G c.489G>T p.= p.A163A ENST00000609256 2/2 210 174 36 121 121 0 strelka-varscan-mutect BHLHA15,synonymous_variant,p.=,ENST00000609256,;BHLHA15,synonymous_variant,p.=,ENST00000314018,NM_177455.3;LMTK2,downstream_gene_variant,,ENST00000297293,NM_014916.3;TECPR1,downstream_gene_variant,,ENST00000447648,NM_015395.2;TECPR1,downstream_gene_variant,,ENST00000462511,;TECPR1,downstream_gene_variant,,ENST00000490842,;TECPR1,downstream_gene_variant,,ENST00000463402,;TECPR1,downstream_gene_variant,,ENST00000485716,; T ENST00000609256 Transcript synonymous_variant 615/796 489/570 163/189 A gcG/gcT rs754943764 1 1 BHLHA15 HGNC HGNC:22265 protein_coding YES CCDS5655.1 ENSP00000476312 Q7RTS1 UPI000013F6EA 2/2 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF85 LOW SNV 3 1 PASS rs754943764 . 0 207 0 3 0 0 0 0 -20 0.9999952 1 1 1 0 T 2 4 70 98212798 98212798 G T 1 0 0 0 0 0 0 0 1 1567 1132 40 1 1 BHLHA15 7 98212798 Silent SNP G C3N-01030_T 7980389 98212798 61133175 310 21091 GAL3ST4 0 . GRCh38 7 100160846 100160846 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.543G>A p.= p.K181K ENST00000360039 4/4 290 200 90 200 199 1 strelka-varscan-mutect GAL3ST4,missense_variant,p.Ser80Asn,ENST00000423751,;GAL3ST4,missense_variant,p.Ser80Asn,ENST00000411994,;GAL3ST4,missense_variant,p.Ser80Asn,ENST00000498000,;GAL3ST4,synonymous_variant,p.=,ENST00000360039,NM_024637.4;GAL3ST4,synonymous_variant,p.=,ENST00000413800,;C7orf43,upstream_gene_variant,,ENST00000316937,NM_018275.4;C7orf43,upstream_gene_variant,,ENST00000456769,NM_001303470.1;C7orf43,upstream_gene_variant,,ENST00000457641,;LAMTOR4,downstream_gene_variant,,ENST00000490633,;C7orf43,upstream_gene_variant,,ENST00000584344,;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000495882,;C7orf43,upstream_gene_variant,,ENST00000419037,;C7orf43,upstream_gene_variant,,ENST00000448720,;C7orf43,upstream_gene_variant,,ENST00000419841,;C7orf43,upstream_gene_variant,,ENST00000394035,;C7orf43,upstream_gene_variant,,ENST00000498638,;C7orf43,upstream_gene_variant,,ENST00000472061,; T ENST00000360039 Transcript synonymous_variant 936/2537 543/1461 181/486 K aaG/aaA 1 -1 GAL3ST4 HGNC HGNC:24145 protein_coding YES CCDS5688.1 ENSP00000353142 Q96RP7 UPI0000070C68 NM_024637.4 4/4 hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF57,Pfam_domain:PF06990,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 100160846 100160846 C T 1 0 0 0 0 0 0 0 1 6068 565 20 3 3 GAL3ST4 7 100160846 Silent SNP C C3N-01030_T 1948048 100160846 59185127 311 21092 SPDYE3 0 . GRCh38 7 100319970 100319970 + Missense_Mutation SNP G G A rs781753979 C3N-01030_T C3N-01030_N G G c.1630G>A p.Asp544Asn p.D544N ENST00000332397 10/11 490 413 77 369 369 0 strelka-varscan-mutect SPDYE3,missense_variant,p.Asp544Asn,ENST00000332397,NM_001004351.4;SPDYE3,non_coding_transcript_exon_variant,,ENST00000380765,;PMS2P1,downstream_gene_variant,,ENST00000431037,; A ENST00000332397 Transcript missense_variant 1814/3185 1630/1650 544/549 D/N Gat/Aat rs781753979,COSM164554,COSM3268132 1 1 SPDYE3 HGNC HGNC:35462 protein_coding YES CCDS47658.2 ENSP00000329565 A6NKU9 UPI00004193B6 NM_001004351.4 deleterious(0.04) 10/11 Pfam_domain:PF11357,hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF13 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs781753979 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 100319970 100319970 G A 1 0 0 0 0 1 0 0 0 15379 942 33 3 3 SPDYE3 7 100319970 Missense_Mutation SNP G C3N-01030_T 159124 100319970 59026003 312 21093 ZAN 0 . GRCh38 7 100752342 100752342 + Missense_Mutation SNP C C A rs545019910 C3N-01030_T C3N-01030_N C C c.2237C>A p.Thr746Asn p.T746N ENST00000613979 14/48 327 275 52 267 266 1 strelka-varscan-mutect ZAN,missense_variant,p.Thr746Asn,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Thr746Asn,ENST00000618565,;ZAN,missense_variant,p.Thr746Asn,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Thr746Asn,ENST00000546292,;ZAN,missense_variant,p.Thr746Asn,ENST00000542585,;ZAN,missense_variant,p.Thr746Asn,ENST00000538115,;ZAN,missense_variant,p.Thr746Asn,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; A ENST00000613979 Transcript missense_variant 2402/8669 2237/8439 746/2812 T/N aCc/aAc rs545019910 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 deleterious(0.01) 14/48 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs545019910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 100752342 100752342 C A 1 0 0 0 0 1 0 0 0 18074 507 18 2 2 ZAN 7 100752342 Missense_Mutation SNP C C3N-01030_T 432372 100752342 58593631 313 21094 MUC12 0 . GRCh38 7 101014068 101014068 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.15794G>T p.Arg5265Leu p.R5265L ENST00000536621 9/12 41 20 21 37 37 0 strelka-varscan-mutect MUC12,missense_variant,p.Arg5408Leu,ENST00000379442,;MUC12,missense_variant,p.Arg5265Leu,ENST00000536621,NM_001164462.1;RP11-395B7.4,downstream_gene_variant,,ENST00000441882,;RP11-395B7.4,downstream_gene_variant,,ENST00000448513,;MUC12,upstream_gene_variant,,ENST00000467414,;MUC12,upstream_gene_variant,,ENST00000473098,;MUC12,missense_variant,p.Arg82Leu,ENST00000305119,;MUC12,upstream_gene_variant,,ENST00000474482,; T ENST00000536621 Transcript missense_variant 15794/16321 15794/16008 5265/5335 R/L cGg/cTg 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 tolerated(0.52) 9/12 MODERATE SNV 5 1 PASS rs1041951745 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 101014068 101014068 G T 1 0 0 0 0 1 0 0 0 9969 1116 39 1 1 MUC12 7 101014068 Missense_Mutation SNP G C3N-01030_T 261726 101014068 58331905 314 21095 MUC12 0 . GRCh38 7 101015684 101015684 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.15870C>G p.Ile5290Met p.I5290M ENST00000536621 10/12 249 209 40 179 179 0 strelka-varscan-mutect MUC12,missense_variant,p.Ile5433Met,ENST00000379442,;MUC12,missense_variant,p.Ile5290Met,ENST00000536621,NM_001164462.1;MUC17,upstream_gene_variant,,ENST00000306151,NM_001040105.1;RP11-395B7.4,intron_variant,,ENST00000441882,;RP11-395B7.4,intron_variant,,ENST00000448513,;MUC12,upstream_gene_variant,,ENST00000467414,;MUC12,upstream_gene_variant,,ENST00000473098,;MUC12,intron_variant,,ENST00000305119,;MUC17,upstream_gene_variant,,ENST00000379439,;MUC12,upstream_gene_variant,,ENST00000474482,; G ENST00000536621 Transcript missense_variant 15870/16321 15870/16008 5290/5335 I/M atC/atG 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 deleterious(0.01) 10/12 MODERATE SNV 5 1 PASS rs1227427844 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 101015684 101015684 C G 1 0 0 0 0 1 0 0 0 9969 903 32 4 4 MUC12 7 101015684 Missense_Mutation SNP C C3N-01030_T 1616 101015684 58330289 315 21096 MUC17 0 . GRCh38 7 101039080 101039080 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.7664C>A p.Ser2555Tyr p.S2555Y ENST00000306151 3/13 136 104 32 112 112 0 strelka-varscan-mutect MUC17,missense_variant,p.Ser2555Tyr,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ser2555Tyr,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; A ENST00000306151 Transcript missense_variant 7728/14247 7664/13482 2555/4493 S/Y tCt/tAt 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 101039080 101039080 C A 1 0 0 0 0 1 0 0 0 9973 913 32 2 2 MUC17 7 101039080 Missense_Mutation SNP C C3N-01030_T 23396 101039080 58306893 316 21097 RELN 0 . GRCh38 7 103553552 103553552 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.5981C>A p.Ser1994Ter p.S1994* ENST00000428762 40/65 320 269 51 335 335 0 strelka-varscan-mutect RELN,stop_gained,p.Ser1994Ter,ENST00000424685,;RELN,stop_gained,p.Ser1994Ter,ENST00000428762,NM_005045.3;RELN,stop_gained,p.Ser1994Ter,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript stop_gained 6141/11571 5981/10383 1994/3460 S/* tCa/tAa 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 40/65 hmmpanther:PTHR11841 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 103553552 103553552 G T 1 0 0 0 0 0 1 0 0 13390 1294 45 2 2 RELN 7 103553552 Nonsense_Mutation SNP G C3N-01030_T 2514472 103553552 55792421 317 21098 KMT2E 0 . GRCh38 7 105105893 105105893 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.2486C>T p.Ser829Leu p.S829L ENST00000311117 19/27 133 119 14 114 114 0 strelka-mutect KMT2E,missense_variant,p.Ser829Leu,ENST00000311117,NM_182931.2;KMT2E,missense_variant,p.Ser829Leu,ENST00000257745,NM_018682.3;KMT2E,downstream_gene_variant,,ENST00000622386,;KMT2E,downstream_gene_variant,,ENST00000479838,;KMT2E,upstream_gene_variant,,ENST00000473063,;CTB-152G17.6,upstream_gene_variant,,ENST00000607968,;SRPK2,downstream_gene_variant,,ENST00000493638,;KMT2E,missense_variant,p.Ser829Leu,ENST00000334884,;KMT2E,upstream_gene_variant,,ENST00000478079,; T ENST00000311117 Transcript missense_variant 3031/6874 2486/5577 829/1858 S/L tCa/tTa 1 1 KMT2E HGNC HGNC:18541 protein_coding YES CCDS34723.1 ENSP00000312379 Q8IZD2 UPI0000074133 NM_182931.2 deleterious_low_confidence(0.02) 19/27 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 105105893 105105893 C T 1 0 0 0 0 1 0 0 0 8299 838 29 3 3 KMT2E 7 105105893 Missense_Mutation SNP C C3N-01030_T 1552341 105105893 54240080 318 21099 LAMB1 0 . GRCh38 7 107986240 107986240 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.547A>G p.Lys183Glu p.K183E ENST00000222399 6/34 156 90 66 148 148 0 strelka-varscan-mutect LAMB1,missense_variant,p.Lys207Glu,ENST00000393561,;LAMB1,missense_variant,p.Lys183Glu,ENST00000222399,NM_002291.2;LAMB1,missense_variant,p.Lys183Glu,ENST00000393560,; C ENST00000222399 Transcript missense_variant 778/5725 547/5361 183/1786 K/E Aaa/Gaa 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 tolerated(0.1) 6/34 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF233,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 107986240 107986240 T C 1 0 0 0 0 1 0 0 0 8514 1792 62 5 5 LAMB1 7 107986240 Missense_Mutation SNP T C3N-01030_T 2880347 107986240 51359733 319 21100 SLC13A1 0 . GRCh38 7 123115622 123115622 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1684G>T p.Val562Phe p.V562F ENST00000194130 15/15 215 141 74 166 166 0 strelka-varscan-mutect SLC13A1,missense_variant,p.Val562Phe,ENST00000194130,NM_022444.3;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; A ENST00000194130 Transcript missense_variant 1724/3815 1684/1788 562/595 V/F Gtt/Ttt 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 deleterious(0) 15/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283,Pfam_domain:PF00939 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 123115622 123115622 C A 1 0 0 0 0 1 0 0 0 14656 478 17 2 2 SLC13A1 7 123115622 Missense_Mutation SNP C C3N-01030_T 15129382 123115622 36230351 320 21101 SLC13A1 0 . GRCh38 7 123123183 123123183 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1293G>T p.Met431Ile p.M431I ENST00000194130 12/15 256 215 41 285 284 1 strelka-varscan-mutect SLC13A1,missense_variant,p.Met431Ile,ENST00000194130,NM_022444.3;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; A ENST00000194130 Transcript missense_variant 1333/3815 1293/1788 431/595 M/I atG/atT 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 deleterious(0.02) 12/15 hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283,Pfam_domain:PF00939 MODERATE 1 SNV 1 1 PASS rs1421250230 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 123123183 123123183 C A 1 0 0 0 0 1 0 0 0 14656 710 25 2 2 SLC13A1 7 123123183 Missense_Mutation SNP C C3N-01030_T 7561 123123183 36222790 321 21102 WASL 0 . GRCh38 7 123692615 123692615 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1079C>A p.Pro360Gln p.P360Q ENST00000223023 9/11 79 63 16 56 56 0 strelka-varscan-mutect WASL,missense_variant,p.Pro360Gln,ENST00000223023,NM_003941.3; T ENST00000223023 Transcript missense_variant 1412/4435 1079/1518 360/505 P/Q cCa/cAa 1 -1 WASL HGNC HGNC:12735 protein_coding YES CCDS34743.1 ENSP00000223023 O00401 UPI000013C821 NM_003941.3 tolerated(0.35) 9/11 hmmpanther:PTHR23202,hmmpanther:PTHR23202:SF33,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 123692615 123692615 G T 1 0 0 0 0 1 0 0 0 17816 1348 47 2 2 WASL 7 123692615 Missense_Mutation SNP G C3N-01030_T 569432 123692615 35653358 322 21103 GRM8 0 . GRCh38 7 126769948 126769948 + Missense_Mutation SNP G G T rs376815449 C3N-01030_T C3N-01030_N G G c.1274C>A p.Pro425His p.P425H ENST00000339582 7/11 248 209 39 217 217 0 strelka-varscan-mutect GRM8,missense_variant,p.Pro425His,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Pro425His,ENST00000358373,NM_001127323.1;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,non_coding_transcript_exon_variant,,ENST00000448250,;GRM8,missense_variant,p.Pro425His,ENST00000472701,;GRM8,missense_variant,p.Pro425His,ENST00000341617,; T ENST00000339582 Transcript missense_variant 2083/4057 1274/2727 425/908 P/H cCt/cAt rs376815449,COSM325455,COSM325456 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious(0.01) 7/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs376815449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 126769948 126769948 G T 1 0 0 0 0 1 0 0 0 6685 1000 35 2 2 GRM8 7 126769948 Missense_Mutation SNP G C3N-01030_T 3077333 126769948 32576025 323 21104 PAX4 0 . GRCh38 7 127614515 127614515 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.379C>A p.Gln127Lys p.Q127K ENST00000341640 3/9 567 464 103 356 356 0 strelka-varscan-mutect PAX4,missense_variant,p.Gln127Lys,ENST00000341640,NM_006193.2;PAX4,missense_variant,p.Gln125Lys,ENST00000463946,;PAX4,missense_variant,p.Gln125Lys,ENST00000611453,;PAX4,missense_variant,p.Gln127Lys,ENST00000378740,;PAX4,missense_variant,p.Gln135Lys,ENST00000338516,;PAX4,missense_variant,p.Gln125Lys,ENST00000483494,;PAX4,non_coding_transcript_exon_variant,,ENST00000477423,; T ENST00000341640 Transcript missense_variant 585/2010 379/1032 127/343 Q/K Cag/Aag 1 -1 PAX4 HGNC HGNC:8618 protein_coding YES CCDS5797.1 ENSP00000339906 O43316 UPI000013C824 NM_006193.2 tolerated(0.37) 3/9 hmmpanther:PTHR24329:SF14,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS rs886061969 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 127614515 127614515 G T 1 0 0 0 0 1 0 0 0 11566 1357 47 2 2 PAX4 7 127614515 Missense_Mutation SNP G C3N-01030_T 844567 127614515 31731458 324 21105 NRF1 0 . GRCh38 7 129710464 129710464 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.856C>G p.Gln286Glu p.Q286E ENST00000353868 7/12 411 260 151 313 313 0 strelka-varscan-mutect NRF1,missense_variant,p.Gln286Glu,ENST00000353868,;NRF1,missense_variant,p.Gln286Glu,ENST00000393232,NM_005011.4,NM_001293164.1;NRF1,missense_variant,p.Gln286Glu,ENST00000393230,NM_001040110.1;NRF1,missense_variant,p.Gln286Glu,ENST00000311967,NM_001293163.1;NRF1,missense_variant,p.Gln286Glu,ENST00000223190,;NRF1,downstream_gene_variant,,ENST00000454688,; G ENST00000353868 Transcript missense_variant 956/3568 856/1569 286/522 Q/E Caa/Gaa 1 1 NRF1 HGNC HGNC:7996 protein_coding YES CCDS78273.1 ENSP00000342351 Q16656 A0A024R774 UPI0000072ED3 tolerated(0.77) 7/12 Low_complexity_(Seg):seg,hmmpanther:PTHR20338,Gene3D:3.40.50.740 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 129710464 129710464 C G 1 0 0 0 0 1 0 0 0 10704 711 25 4 4 NRF1 7 129710464 Missense_Mutation SNP C C3N-01030_T 2095949 129710464 29635509 325 21106 PLXNA4 0 . GRCh38 7 132508429 132508429 + Missense_Mutation SNP C C G C3N-01030_T C3N-01030_N C C c.265G>C p.Asp89His p.D89H ENST00000359827 2/32 362 285 77 224 224 0 strelka-varscan-mutect PLXNA4,missense_variant,p.Asp89His,ENST00000359827,;PLXNA4,missense_variant,p.Asp89His,ENST00000321063,NM_020911.1;PLXNA4,missense_variant,p.Asp89His,ENST00000423507,NM_001105543.1;PLXNA4,missense_variant,p.Asp89His,ENST00000378539,NM_181775.3; G ENST00000359827 Transcript missense_variant 1228/13786 265/5685 89/1894 D/H Gac/Cac COSM1150567,COSM72232,COSM744481,COSM744482,COSM744483 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B tolerated(0.13) 2/32 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,SMART_domains:SM00630,Superfamily_domains:SSF101912 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs1355011226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 132508429 132508429 C G 1 0 0 0 0 1 0 0 0 12228 855 30 4 4 PLXNA4 7 132508429 Missense_Mutation SNP C C3N-01030_T 2797965 132508429 26837544 326 21107 FAM180A 0 . GRCh38 7 135734045 135734045 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.452C>A p.Ser151Tyr p.S151Y ENST00000338588 3/4 197 163 34 124 124 0 strelka-varscan-mutect FAM180A,missense_variant,p.Ser151Tyr,ENST00000338588,NM_205855.3;FAM180A,missense_variant,p.Ser151Tyr,ENST00000415751,;SLC13A4,upstream_gene_variant,,ENST00000378428,;SLC13A4,upstream_gene_variant,,ENST00000422620,;FAM180A,intron_variant,,ENST00000435869,;FAM180A,missense_variant,p.Ser151Tyr,ENST00000444083,; T ENST00000338588 Transcript missense_variant 718/1800 452/522 151/173 S/Y tCc/tAc 1 -1 FAM180A HGNC HGNC:33773 protein_coding YES CCDS5841.1 ENSP00000342336 Q6UWF9 UPI0000035A01 NM_205855.3 deleterious(0) 3/4 hmmpanther:PTHR34034,hmmpanther:PTHR34034:SF2,Pfam_domain:PF15173 MODERATE 1 SNV 1 1 PASS rs1412266948 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 135734045 135734045 G T 1 0 0 0 0 1 0 0 0 5352 1174 41 2 2 FAM180A 7 135734045 Missense_Mutation SNP G C3N-01030_T 3225616 135734045 23611928 327 21108 FAM180A 0 . GRCh38 7 135737101 135737101 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.175G>T p.Glu59Ter p.E59* ENST00000338588 2/4 231 201 30 174 173 1 strelka-varscan-mutect FAM180A,stop_gained,p.Glu59Ter,ENST00000338588,NM_205855.3;FAM180A,stop_gained,p.Glu59Ter,ENST00000415751,;FAM180A,splice_region_variant,,ENST00000435869,;FAM180A,stop_gained,p.Glu59Ter,ENST00000444083,; A ENST00000338588 Transcript stop_gained,splice_region_variant 441/1800 175/522 59/173 E/* Gag/Tag 1 -1 FAM180A HGNC HGNC:33773 protein_coding YES CCDS5841.1 ENSP00000342336 Q6UWF9 UPI0000035A01 NM_205855.3 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR34034,hmmpanther:PTHR34034:SF2,Pfam_domain:PF15173 HIGH 1 SNV 1 1 PASS rs890848627 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 135737101 135737101 C A 1 0 0 0 0 0 1 0 0 5352 898 31 1 1 FAM180A 7 135737101 Nonsense_Mutation SNP C C3N-01030_T 3056 135737101 23608872 328 21109 SVOPL 0 . GRCh38 7 138628242 138628242 + Missense_Mutation SNP C C T rs200942722 C3N-01030_T C3N-01030_N C C c.985G>A p.Glu329Lys p.E329K ENST00000419765 10/15 508 435 73 323 323 0 strelka-varscan-mutect SVOPL,missense_variant,p.Glu209Lys,ENST00000421622,;SVOPL,missense_variant,p.Glu329Lys,ENST00000419765,NM_001139456.1;SVOPL,missense_variant,p.Glu177Lys,ENST00000436657,NM_174959.3;SVOPL,missense_variant,p.Glu177Lys,ENST00000288513,;SNORA40,upstream_gene_variant,,ENST00000516379,;SVOPL,upstream_gene_variant,,ENST00000463557,;SVOPL,missense_variant,p.Glu82Lys,ENST00000441685,;SVOPL,upstream_gene_variant,,ENST00000478865,; T ENST00000419765 Transcript missense_variant 1019/1523 985/1479 329/492 E/K Gag/Aag rs200942722,COSM5539898,COSM5539899 1 -1 SVOPL HGNC HGNC:27034 protein_coding YES CCDS47721.1 ENSP00000405482 Q8N434 UPI0001565476 NM_001139456.1 tolerated(0.3) 10/15 Gene3D:1.20.1250.20,PROSITE_profiles:PS50850,Superfamily_domains:SSF103473 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs200942722 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 138628242 138628242 C T 1 0 0 0 0 1 0 0 0 15809 864 30 3 3 SVOPL 7 138628242 Missense_Mutation SNP C C3N-01030_T 2891141 138628242 20717731 329 21110 PRSS37 0 . GRCh38 7 141837189 141837189 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.490delC p.Gln164LysfsTer15 p.Q164Kfs*15 ENST00000350549 4/5 94 57 37 105 105 0 sindel-varindel-pindel PRSS37,frameshift_variant,p.Gln164LysfsTer15,ENST00000350549,NM_001008270.2,NM_001171951.1;PRSS37,frameshift_variant,p.Gln164LysfsTer15,ENST00000438520,;PRSS37,3_prime_UTR_variant,,ENST00000419085,;PRSS37,3_prime_UTR_variant,,ENST00000452758,; - ENST00000350549 Transcript frameshift_variant 862/1189 490/708 164/235 Q/X Caa/aa 1 -1 PRSS37 HGNC HGNC:29211 protein_coding YES CCDS34764.1 ENSP00000297767 A4D1T9 UPI000004223A NM_001008270.2,NM_001171951.1 4/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF244,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 HIGH 1 deletion 1 1 PASS . . 0 201 3 6 0 0 0 0 -20 0.9992559 1 1 1 0 - 7 5 70 141837189 141837189 G - 1 0 1 0 1 0 0 0 0 12773 1357 47 0 0 PRSS37 7 141837189 Frame_Shift_Del DEL G C3N-01030_T 3208947 141837189 17508784 330 21111 FAM131B 0 . GRCh38 7 143356676 143356676 + Silent SNP C C G rs774486508 C3N-01030_T C3N-01030_N C C c.957G>C p.= p.R319R ENST00000443739 7/7 428 354 74 247 247 0 strelka-varscan-mutect FAM131B,synonymous_variant,p.=,ENST00000409408,;FAM131B,synonymous_variant,p.=,ENST00000443739,NM_001031690.2,NM_001278297.1;FAM131B,synonymous_variant,p.=,ENST00000409346,;FAM131B,synonymous_variant,p.=,ENST00000409578,;FAM131B,synonymous_variant,p.=,ENST00000409222,NM_014690.4;CLCN1,downstream_gene_variant,,ENST00000343257,NM_000083.2;FAM131B,3_prime_UTR_variant,,ENST00000410085,;FAM131B,downstream_gene_variant,,ENST00000519161,;FAM131B,downstream_gene_variant,,ENST00000521347,;FAM131B,downstream_gene_variant,,ENST00000519279,; G ENST00000443739 Transcript synonymous_variant 1106/4382 957/1083 319/360 R cgG/cgC rs774486508 1 -1 FAM131B HGNC HGNC:22202 protein_coding YES CCDS47734.1 ENSP00000410603 Q86XD5 UPI0001633639 NM_001031690.2,NM_001278297.1 7/7 hmmpanther:PTHR15736,hmmpanther:PTHR15736:SF9,Pfam_domain:PF15010 LOW 1 SNV 1 1 PASS rs774486508 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 143356676 143356676 C G 1 0 0 0 0 0 0 0 1 5290 610 22 4 4 FAM131B 7 143356676 Silent SNP C C3N-01030_T 1519487 143356676 15989297 331 21112 EZH2 0 . GRCh38 7 148815513 148815513 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.1539G>A p.= p.L513L ENST00000320356 13/20 230 195 35 188 188 0 strelka-varscan-mutect EZH2,synonymous_variant,p.=,ENST00000320356,NM_004456.4;EZH2,synonymous_variant,p.=,ENST00000460911,NM_001203247.1;EZH2,synonymous_variant,p.=,ENST00000476773,NM_001203249.1;EZH2,synonymous_variant,p.=,ENST00000478654,;EZH2,synonymous_variant,p.=,ENST00000350995,NM_152998.2;EZH2,synonymous_variant,p.=,ENST00000483967,NM_001203248.1;EZH2,3_prime_UTR_variant,,ENST00000492143,;EZH2,downstream_gene_variant,,ENST00000498186,;EZH2,downstream_gene_variant,,ENST00000483012,;EZH2,upstream_gene_variant,,ENST00000469631,; T ENST00000320356 Transcript synonymous_variant 1661/2639 1539/2256 513/751 L ctG/ctA 1 -1 EZH2 HGNC HGNC:3527 protein_coding YES CCDS5891.1 ENSP00000320147 Q15910 A0A090N8E9 UPI000006D77C NM_004456.4 13/20 PROSITE_profiles:PS51633,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF287,Gene3D:2.170.270.10 LOW 1 SNV 1 1 PASS . . 0 195 0 10 4 0 0 0 -16.77703 0.3793758 1 1 0 0 T 2 4 70 148815513 148815513 C T 1 0 0 0 0 0 0 0 1 5202 813 29 3 3 EZH2 7 148815513 Silent SNP C C3N-01030_T 5458837 148815513 10530460 332 21113 PDIA4 0 . GRCh38 7 149004042 149004042 + Missense_Mutation SNP C C A rs374338308 C3N-01030_T C3N-01030_N C C c.1690G>T p.Val564Leu p.V564L ENST00000286091 10/10 234 167 67 148 147 1 strelka-varscan-mutect PDIA4,missense_variant,p.Val564Leu,ENST00000286091,NM_004911.4;PDIA4,downstream_gene_variant,,ENST00000466592,; A ENST00000286091 Transcript missense_variant 1923/2903 1690/1938 564/645 V/L Gtg/Ttg rs374338308 1 -1 PDIA4 HGNC HGNC:30167 protein_coding YES CCDS5893.1 ENSP00000286091 P13667 A0A090N8Y2 UPI000004062C NM_004911.4 tolerated(0.22) 10/10 PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF110,PROSITE_patterns:PS00194,Pfam_domain:PF00085,TIGRFAM_domain:TIGR01130,TIGRFAM_domain:TIGR01126,PIRSF_domain:PIRSF036862,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS rs374338308 . 0 205 0 4 0 0 0 0 -20 0.9999757 1 1 1 0 A 3 1 70 149004042 149004042 C A 1 0 0 0 0 1 0 0 0 11758 536 19 1 1 PDIA4 7 149004042 Missense_Mutation SNP C C3N-01030_T 188529 149004042 10341931 333 21114 SSPO 0 . GRCh38 7 149783211 149783211 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2184G>T p.Gln728His p.Q728H ENST00000378016 15/107 598 483 115 311 311 0 strelka-varscan-mutect SSPO,missense_variant,p.Gln728His,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000475488,;SSPO,upstream_gene_variant,,ENST00000493502,; T ENST00000378016 Transcript missense_variant 2184/15589 2184/15453 728/5150 Q/H caG/caT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0.04) 15/107 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 149783211 149783211 G T 1 0 0 0 0 1 0 0 0 15566 991 35 2 2 SSPO 7 149783211 Missense_Mutation SNP G C3N-01030_T 779169 149783211 9562762 334 21115 KCNH2 0 . GRCh38 7 150951637 150951637 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.1756C>A p.Leu586Met p.L586M ENST00000262186 7/15 378 306 72 248 248 0 strelka-varscan-mutect KCNH2,missense_variant,p.Leu586Met,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Leu246Met,ENST00000330883,NM_172057.2;KCNH2,missense_variant,p.Leu470Met,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; T ENST00000262186 Transcript missense_variant 2158/4286 1756/3480 586/1159 L/M Ctg/Atg CM122154 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0) 7/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 150951637 150951637 G T 1 0 0 0 0 1 0 0 0 7948 962 34 2 2 KCNH2 7 150951637 Missense_Mutation SNP G C3N-01030_T 1168426 150951637 8394336 335 21116 ABCF2 0 . GRCh38 7 151223755 151223755 + Silent SNP C C G novel C3N-01030_T C3N-01030_N C C c.645G>C p.= p.L215L ENST00000222388 5/16 101 78 23 78 78 0 strelka-varscan-mutect ABCF2,synonymous_variant,p.=,ENST00000287844,NM_007189.2;ABCF2,synonymous_variant,p.=,ENST00000222388,NM_005692.4;ABCF2,synonymous_variant,p.=,ENST00000468073,;ABCF2,synonymous_variant,p.=,ENST00000441774,;ABCF2,upstream_gene_variant,,ENST00000473874,;ABCF2,downstream_gene_variant,,ENST00000477252,; G ENST00000222388 Transcript synonymous_variant 691/2185 645/1905 215/634 L ctG/ctC 1 -1 ABCF2 HGNC HGNC:71 protein_coding YES CCDS5922.1 ENSP00000222388 Q9UG63 A0A090N7Y2 UPI000004C4C9 NM_005692.4 5/16 PROSITE_profiles:PS50893,hmmpanther:PTHR19211,hmmpanther:PTHR19211:SF15,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 151223755 151223755 C G 1 0 0 0 0 0 0 0 1 70 581 21 4 4 ABCF2 7 151223755 Silent SNP C C3N-01030_T 272118 151223755 8122218 336 21117 RBM33 0 . GRCh38 7 155745310 155745310 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.2687C>T p.Ser896Phe p.S896F ENST00000401878 14/18 457 409 48 416 416 0 strelka-varscan-mutect RBM33,missense_variant,p.Ser896Phe,ENST00000401878,NM_053043.2;RBM33,missense_variant,p.Ser668Phe,ENST00000392761,;RBM33,upstream_gene_variant,,ENST00000341148,;RBM33,upstream_gene_variant,,ENST00000438356,;RBM33,3_prime_UTR_variant,,ENST00000307403,; T ENST00000401878 Transcript missense_variant 2885/10149 2687/3513 896/1170 S/F tCc/tTc 1 1 RBM33 HGNC HGNC:27223 protein_coding YES CCDS5941.2 ENSP00000384160 Q96EV2 UPI00015743D7 NM_053043.2 tolerated(0.09) 14/18 hmmpanther:PTHR22014,hmmpanther:PTHR22014:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 155745310 155745310 C T 1 0 0 0 0 1 0 0 0 13296 855 30 3 3 RBM33 7 155745310 Missense_Mutation SNP C C3N-01030_T 4521555 155745310 3600663 337 21118 PTPRN2 0 . GRCh38 7 158138402 158138402 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1024G>T p.Gly342Cys p.G342C ENST00000389418 7/23 539 345 194 300 300 0 strelka-varscan-mutect PTPRN2,missense_variant,p.Gly342Cys,ENST00000389413,NM_130843.2;PTPRN2,missense_variant,p.Gly304Cys,ENST00000409483,NM_001308267.1;PTPRN2,missense_variant,p.Gly342Cys,ENST00000389418,NM_001308268.1,NM_002847.3;PTPRN2,missense_variant,p.Gly325Cys,ENST00000389416,NM_130842.2;PTPRN2,missense_variant,p.Gly251Cys,ENST00000404321,; A ENST00000389418 Transcript missense_variant 1034/4706 1024/3048 342/1015 G/C Ggc/Tgc 1 -1 PTPRN2 HGNC HGNC:9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 UPI000002E7C7 NM_001308268.1,NM_002847.3 tolerated(0.07) 7/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 158138402 158138402 C A 1 0 0 0 0 1 0 0 0 12962 681 24 2 2 PTPRN2 7 158138402 Missense_Mutation SNP C C3N-01030_T 2393092 158138402 1207571 338 21119 MYOM2 0 . GRCh38 8 2090168 2090168 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1805C>A p.Pro602His p.P602H ENST00000262113 15/37 107 93 14 89 89 0 strelka-varscan-mutect MYOM2,missense_variant,p.Pro602His,ENST00000262113,NM_003970.3;MYOM2,missense_variant,p.Pro27His,ENST00000523438,;MYOM2,non_coding_transcript_exon_variant,,ENST00000518803,;MYOM2,downstream_gene_variant,,ENST00000519518,; A ENST00000262113 Transcript missense_variant 1946/5014 1805/4398 602/1465 P/H cCc/cAc 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 deleterious(0) 15/37 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 2090168 2090168 C A 1 0 0 0 0 1 0 0 0 10093 623 22 2 2 MYOM2 8 2090168 Missense_Mutation SNP C C3N-01030_T 2090168 143048468 339 21120 CSMD1 0 . GRCh38 8 3029362 3029362 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.7815C>A p.= p.A2605A ENST00000520002 52/71 113 103 10 105 105 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000519623,; T ENST00000520002 Transcript synonymous_variant 8371/11740 7815/10698 2605/3565 A gcC/gcA 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 52/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 3029362 3029362 G T 1 0 0 0 0 0 0 0 1 3745 1335 47 2 2 CSMD1 8 3029362 Silent SNP G C3N-01030_T 939194 3029362 142109274 340 21121 CSMD1 0 . GRCh38 8 3284218 3284218 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.4082C>A p.Thr1361Asn p.T1361N ENST00000520002 27/71 299 212 87 270 270 0 strelka-varscan-mutect CSMD1,missense_variant,p.Thr1222Asn,ENST00000537824,;CSMD1,missense_variant,p.Thr841Asn,ENST00000335551,;CSMD1,missense_variant,p.Thr1361Asn,ENST00000520002,;CSMD1,missense_variant,p.Thr1361Asn,ENST00000602557,;CSMD1,missense_variant,p.Thr1360Asn,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Thr1361Asn,ENST00000400186,;CSMD1,missense_variant,p.Thr1361Asn,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000521646,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; T ENST00000520002 Transcript missense_variant 4638/11740 4082/10698 1361/3565 T/N aCc/aAc 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 27/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 3284218 3284218 G T 1 0 0 0 0 1 0 0 0 3745 1261 44 2 2 CSMD1 8 3284218 Missense_Mutation SNP G C3N-01030_T 254856 3284218 141854418 341 21122 CSMD1 0 . GRCh38 8 3348145 3348145 + Silent SNP A A G novel C3N-01030_T C3N-01030_N A A c.3324T>C p.= p.S1108S ENST00000520002 23/71 148 133 15 187 187 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; G ENST00000520002 Transcript synonymous_variant 3880/11740 3324/10698 1108/3565 S agT/agC 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 23/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 3348145 3348145 A G 1 0 0 0 0 0 0 0 1 3745 156 6 5 5 CSMD1 8 3348145 Silent SNP A C3N-01030_T 63927 3348145 141790491 342 21123 CSMD1 0 . GRCh38 8 3387624 3387624 + Silent SNP G G C C3N-01030_T C3N-01030_N G G c.2655C>G p.= p.R885R ENST00000520002 19/71 126 101 25 126 126 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; C ENST00000520002 Transcript synonymous_variant 3211/11740 2655/10698 885/3565 R cgC/cgG COSM3432362,COSM3432363,COSM3432364 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 19/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 3387624 3387624 G C 1 0 0 0 0 0 0 0 1 3745 1190 42 4 4 CSMD1 8 3387624 Silent SNP G C3N-01030_T 39479 3387624 141751012 343 21124 RP1L1 0 . GRCh38 8 10611081 10611081 + Missense_Mutation SNP G G T rs750020905 C3N-01030_T C3N-01030_N G G c.3017C>A p.Pro1006Gln p.P1006Q ENST00000382483 4/4 146 131 15 106 106 0 strelka-varscan-mutect RP1L1,missense_variant,p.Pro1006Gln,ENST00000382483,NM_178857.5; T ENST00000382483 Transcript missense_variant 3241/7973 3017/7203 1006/2400 P/Q cCa/cAa rs750020905 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 tolerated(0.11) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 MODERATE 1 SNV 1 1 PASS rs750020905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 10611081 10611081 G T 1 0 0 0 0 1 0 0 0 13773 1348 47 2 2 RP1L1 8 10611081 Missense_Mutation SNP G C3N-01030_T 7223457 10611081 134527555 344 21125 C8orf74 0 . GRCh38 8 10697783 10697783 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.426G>T p.= p.L142L ENST00000304519 3/4 129 104 25 135 134 1 strelka-varscan-mutect C8orf74,synonymous_variant,p.=,ENST00000304519,NM_001040032.1;C8orf74,downstream_gene_variant,,ENST00000521818,;RP1L1,intron_variant,,ENST00000329335,;C8orf74,3_prime_UTR_variant,,ENST00000523289,; T ENST00000304519 Transcript synonymous_variant 455/1036 426/885 142/294 L ctG/ctT 1 1 C8orf74 HGNC HGNC:32296 protein_coding YES CCDS47800.1 ENSP00000307129 Q6P047 UPI00001D82A9 NM_001040032.1 3/4 hmmpanther:PTHR28457,hmmpanther:PTHR28457:SF2 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 10697783 10697783 G T 1 0 0 0 0 0 0 0 1 2163 1335 47 2 2 C8orf74 8 10697783 Silent SNP G C3N-01030_T 86702 10697783 134440853 345 21126 UNC5D 0 . GRCh38 8 35684744 35684744 + Frame_Shift_Del DEL G G - C3N-01030_T C3N-01030_N G G c.914delG p.Cys305PhefsTer43 p.C305Ffs*43 ENST00000404895 6/17 53 35 18 55 55 0 sindel-varindel-pindel UNC5D,frameshift_variant,p.Cys300PhefsTer43,ENST00000453357,;UNC5D,frameshift_variant,p.Cys305PhefsTer43,ENST00000416672,;UNC5D,frameshift_variant,p.Cys305PhefsTer43,ENST00000404895,NM_080872.2;UNC5D,intron_variant,,ENST00000287272,;UNC5D,intron_variant,,ENST00000420357,;UNC5D,non_coding_transcript_exon_variant,,ENST00000474634,; - ENST00000404895 Transcript frameshift_variant 1242/3252 914/2862 305/953 C/X tGt/tt COSM216107 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 6/17 PROSITE_profiles:PS50092,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5,SMART_domains:SM00209 1 HIGH 1 deletion 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 35684744 35684744 G - 1 0 1 0 1 0 0 0 0 17519 1391 48 0 0 UNC5D 8 35684744 Frame_Shift_Del DEL G C3N-01030_T 24986961 35684744 109453892 346 21127 ADAM18 0 . GRCh38 8 39637657 39637657 + Silent SNP C C A rs141094631 C3N-01030_T C3N-01030_N C C c.781C>A p.= p.R261R ENST00000265707 9/20 93 71 22 139 139 0 strelka-varscan-mutect ADAM18,synonymous_variant,p.=,ENST00000265707,NM_014237.2;ADAM18,synonymous_variant,p.=,ENST00000379866,NM_001320313.1;ADAM18,3_prime_UTR_variant,,ENST00000520087,; A ENST00000265707 Transcript synonymous_variant 826/2388 781/2220 261/739 R Cgg/Agg rs141094631,COSM1099750 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 9/20 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,Superfamily_domains:SSF55486 0,1 LOW 1 SNV 1 0,1 1 PASS rs141094631 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 39637657 39637657 C A 1 0 0 0 0 0 0 0 1 283 527 19 1 1 ADAM18 8 39637657 Silent SNP C C3N-01030_T 3952913 39637657 105500979 347 21128 ADAM18 0 . GRCh38 8 39645397 39645397 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.969T>A p.= p.L323L ENST00000265707 11/20 111 73 38 190 189 1 strelka-varscan-mutect ADAM18,synonymous_variant,p.=,ENST00000265707,NM_014237.2;ADAM18,synonymous_variant,p.=,ENST00000379866,NM_001320313.1;ADAM18,3_prime_UTR_variant,,ENST00000520087,; A ENST00000265707 Transcript synonymous_variant 1014/2388 969/2220 323/739 L ctT/ctA 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 11/20 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 39645397 39645397 T A 1 0 0 0 0 0 0 0 1 283 1741 61 4 4 ADAM18 8 39645397 Silent SNP T C3N-01030_T 7740 39645397 105493239 348 21129 SLC20A2 0 . GRCh38 8 42465802 42465802 + Silent SNP C C A C3N-01030_T C3N-01030_N C C c.405G>T p.= p.V135V ENST00000342228 3/11 129 93 36 145 145 0 strelka-mutect SLC20A2,synonymous_variant,p.=,ENST00000342228,NM_006749.4;SLC20A2,synonymous_variant,p.=,ENST00000520262,NM_001257180.1;SLC20A2,synonymous_variant,p.=,ENST00000520179,NM_001257181.1;SLC20A2,upstream_gene_variant,,ENST00000518660,;SLC20A2,3_prime_UTR_variant,,ENST00000524211,; A ENST00000342228 Transcript synonymous_variant 775/3657 405/1959 135/652 V gtG/gtT COSM3900300 1 -1 SLC20A2 HGNC HGNC:10947 protein_coding YES CCDS6132.1 ENSP00000340465 Q08357 UPI000006DC58 NM_006749.4 3/11 hmmpanther:PTHR11101,hmmpanther:PTHR11101:SF15,Pfam_domain:PF01384 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 42465802 42465802 C A 1 0 0 0 0 0 0 0 1 14705 697 25 2 2 SLC20A2 8 42465802 Silent SNP C C3N-01030_T 2820405 42465802 102672834 349 21130 HOOK3 0 . GRCh38 8 42974106 42974106 + Splice_Site SNP G G T novel C3N-01030_T C3N-01030_N G G c.1234-1G>T p.X412_splice ENST00000307602 58 39 19 75 75 0 strelka-varscan-mutect HOOK3,splice_acceptor_variant,,ENST00000307602,NM_032410.3;HOOK3,splice_acceptor_variant,,ENST00000527306,;HOOK3,upstream_gene_variant,,ENST00000526882,; T ENST00000307602 Transcript splice_acceptor_variant -/14398 1234/2157 412/718 1 1 HOOK3 HGNC HGNC:23576 protein_coding YES CCDS6139.1 ENSP00000305699 Q86VS8 UPI000006DD7B NM_032410.3 12/21 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 70 42974106 42974106 G T 1 0 0 0 0 0 0 1 0 7178 956 33 2 2 HOOK3 8 42974106 Splice_Site SNP G C3N-01030_T 508304 42974106 102164530 350 21131 C8orf22 0 . GRCh38 8 49074136 49074136 + Missense_Mutation SNP G G C rs538898821 C3N-01030_T C3N-01030_N G G c.133G>C p.Gly45Arg p.G45R ENST00000303202 3/5 155 88 67 157 157 0 strelka-varscan-mutect C8orf22,missense_variant,p.Gly45Arg,ENST00000303202,NM_001256598.1;C8orf22,missense_variant,p.Gly45Arg,ENST00000399653,NM_001007176.4;C8orf22,missense_variant,p.Gly45Arg,ENST00000517663,NM_001256596.1;C8orf22,missense_variant,p.Gly45Arg,ENST00000522267,NM_001256597.1; C ENST00000303202 Transcript missense_variant,splice_region_variant 306/1499 133/255 45/84 G/R Ggg/Cgg rs538898821,COSM4900592,COSM4900593 1 1 C8orf22 HGNC HGNC:31745 protein_coding YES CCDS59101.1 ENSP00000304926 Q8WWR9 UPI0000070316 NM_001256598.1 deleterious(0) 3/5 hmmpanther:PTHR14572:SF1,hmmpanther:PTHR14572,Pfam_domain:PF15060,Prints_domain:PR02071 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs538898821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 49074136 49074136 G C 1 0 0 0 0 1 0 0 0 2153 1014 35 4 4 C8orf22 8 49074136 Missense_Mutation SNP G C3N-01030_T 6100030 49074136 96064500 351 21132 OPRK1 0 . GRCh38 8 53250829 53250829 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.209T>C p.Phe70Ser p.F70S ENST00000265572 2/4 198 186 12 148 148 0 strelka-varscan-mutect OPRK1,missense_variant,p.Phe70Ser,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,missense_variant,p.Phe56Ser,ENST00000613482,;OPRK1,missense_variant,p.Phe70Ser,ENST00000520287,;OPRK1,5_prime_UTR_variant,,ENST00000612786,NM_001282904.1;OPRK1,missense_variant,p.Phe70Ser,ENST00000522508,; G ENST00000265572 Transcript missense_variant 507/5014 209/1143 70/380 F/S tTc/tCc 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 deleterious(0.02) 2/4 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF1,Low_complexity_(Seg):seg,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 53250829 53250829 A G 1 0 0 0 0 1 0 0 0 10961 246 9 5 5 OPRK1 8 53250829 Missense_Mutation SNP A C3N-01030_T 4176693 53250829 91887807 352 21133 SOX17 0 . GRCh38 8 54459602 54459602 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.852G>T p.= p.P284P ENST00000297316 2/2 283 238 45 169 169 0 strelka-varscan-mutect SOX17,synonymous_variant,p.=,ENST00000297316,NM_022454.3; T ENST00000297316 Transcript synonymous_variant 1056/2342 852/1245 284/414 P ccG/ccT 1 1 SOX17 HGNC HGNC:18122 protein_coding YES CCDS6159.1 ENSP00000297316 Q9H6I2 UPI00001362B7 NM_022454.3 2/2 PROSITE_profiles:PS51516,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF216 LOW 1 SNV 1 1 PASS rs1441052427 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 70 54459602 54459602 G T 1 0 0 0 0 0 0 0 1 15273 1103 39 1 1 SOX17 8 54459602 Silent SNP G C3N-01030_T 1208773 54459602 90679034 353 21134 CHD7 0 . GRCh38 8 60853216 60853216 + Missense_Mutation SNP A A C novel C3N-01030_T C3N-01030_N A A c.6491A>C p.Asp2164Ala p.D2164A ENST00000423902 31/38 279 257 22 174 174 0 strelka-varscan-mutect CHD7,missense_variant,p.Asp2164Ala,ENST00000423902,NM_017780.3;CHD7,intron_variant,,ENST00000524602,;CHD7,upstream_gene_variant,,ENST00000529472,;CHD7,downstream_gene_variant,,ENST00000527921,;CHD7,upstream_gene_variant,,ENST00000531695,; C ENST00000423902 Transcript missense_variant 6970/11568 6491/8994 2164/2997 D/A gAt/gCt 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 tolerated(0.17) 31/38 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 60853216 60853216 A C 1 0 0 0 0 1 0 0 0 3089 333 12 5 5 CHD7 8 60853216 Missense_Mutation SNP A C3N-01030_T 6393614 60853216 84285420 354 21135 ZFHX4 0 . GRCh38 8 76854918 76854918 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.7997G>T p.Arg2666Leu p.R2666L ENST00000521891 10/11 140 122 18 95 95 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Arg2666Leu,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Arg2640Leu,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; T ENST00000521891 Transcript missense_variant 8445/14019 7997/10851 2666/3616 R/L cGg/cTg 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00389 MODERATE 1 SNV 5 1 PASS rs1037499412 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 76854918 76854918 G T 1 0 0 0 0 1 0 0 0 18213 1116 39 1 1 ZFHX4 8 76854918 Missense_Mutation SNP G C3N-01030_T 16001702 76854918 68283718 355 21136 WWP1 0 . GRCh38 8 86448276 86448276 + Nonsense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2127G>A p.Trp709Ter p.W709* ENST00000517970 19/25 81 75 6 107 107 0 varscan-mutect WWP1,stop_gained,p.Trp709Ter,ENST00000517970,NM_007013.3;WWP1,stop_gained,p.Trp709Ter,ENST00000265428,;WWP1,stop_gained,p.Trp210Ter,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,; A ENST00000517970 Transcript stop_gained 2434/4686 2127/2769 709/922 W/* tgG/tgA 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 19/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -13.4697 1 1 1 1 0 A 4 1 70 86448276 86448276 G A 1 0 0 0 0 0 1 0 0 17973 1188 41 3 3 WWP1 8 86448276 Nonsense_Mutation SNP G C3N-01030_T 9593358 86448276 58690360 356 21137 RUNX1T1 0 . GRCh38 8 91986931 91986931 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1210C>G p.Leu404Val p.L404V ENST00000436581 8/12 252 133 119 256 256 0 strelka-varscan-mutect RUNX1T1,missense_variant,p.Leu345Val,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.Leu345Val,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.Leu345Val,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.Leu345Val,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.Leu404Val,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.Leu318Val,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.Leu325Val,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.Leu345Val,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.Leu318Val,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.Leu318Val,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.Leu308Val,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.Leu308Val,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.Leu356Val,ENST00000520724,NM_001198634.1;RUNX1T1,missense_variant,p.Leu45Val,ENST00000521751,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,3_prime_UTR_variant,,ENST00000518361,;RUNX1T1,downstream_gene_variant,,ENST00000520047,; C ENST00000436581 Transcript missense_variant 1397/7454 1210/1992 404/663 L/V Cta/Gta 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 deleterious(0.02) 8/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379,Pfam_domain:PF08788 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 91986931 91986931 G C 1 0 0 0 0 1 0 0 0 14008 1020 36 4 4 RUNX1T1 8 91986931 Missense_Mutation SNP G C3N-01030_T 5538655 91986931 53151705 357 21138 GDF6 0 . GRCh38 8 96144742 96144742 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1189C>T p.Pro397Ser p.P397S ENST00000287020 2/2 652 528 124 377 376 1 strelka-varscan-mutect GDF6,missense_variant,p.Pro397Ser,ENST00000287020,NM_001001557.2;GDF6,missense_variant,p.Ala313Val,ENST00000621429,;GDF6,intron_variant,,ENST00000620978,;KB-1043D8.8,upstream_gene_variant,,ENST00000602571,; A ENST00000287020 Transcript missense_variant 1289/3701 1189/1368 397/455 P/S Ccc/Tcc 1 -1 GDF6 HGNC HGNC:4221 protein_coding YES CCDS34926.1 ENSP00000287020 Q6KF10 A0A0S2A5D6 UPI0000047253 NM_001001557.2 deleterious(0) 2/2 Gene3D:2.10.90.10,Pfam_domain:PF00019,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF43,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 96144742 96144742 G A 1 0 0 0 0 1 0 0 0 6190 1203 42 3 3 GDF6 8 96144742 Missense_Mutation SNP G C3N-01030_T 4157811 96144742 48993894 358 21139 TSPYL5 0 . GRCh38 8 97277172 97277172 + Missense_Mutation SNP G G A C3N-01030_T C3N-01030_N G G c.673C>T p.Arg225Trp p.R225W ENST00000322128 1/1 325 293 32 219 219 0 strelka-varscan-mutect TSPYL5,missense_variant,p.Arg225Trp,ENST00000322128,NM_033512.2; A ENST00000322128 Transcript missense_variant 793/4491 673/1254 225/417 R/W Cgg/Tgg COSM4828540 1 -1 TSPYL5 HGNC HGNC:29367 protein_coding YES CCDS34927.1 ENSP00000322802 Q86VY4 UPI0000210364 NM_033512.2 deleterious(0) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF30,Superfamily_domains:SSF143113 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 97277172 97277172 G A 1 0 0 0 0 1 0 0 0 17169 1057 37 1 1 TSPYL5 8 97277172 Missense_Mutation SNP G C3N-01030_T 1132430 97277172 47861464 359 21140 VPS13B 0 . GRCh38 8 99818461 99818461 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.8447C>T p.Ser2816Leu p.S2816L ENST00000358544 46/62 396 360 36 283 283 0 strelka-varscan-mutect VPS13B,missense_variant,p.Ser2816Leu,ENST00000358544,NM_017890.4;VPS13B,missense_variant,p.Ser2791Leu,ENST00000357162,NM_152564.4; T ENST00000358544 Transcript missense_variant 8558/14094 8447/12069 2816/4022 S/L tCa/tTa 1 1 VPS13B HGNC HGNC:2183 protein_coding YES CCDS6280.1 ENSP00000351346 Q7Z7G8 UPI00001D2D35 NM_017890.4 deleterious(0.04) 46/62 hmmpanther:PTHR12517,hmmpanther:PTHR12517:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 99818461 99818461 C T 1 0 0 0 0 1 0 0 0 17737 838 29 3 3 VPS13B 8 99818461 Missense_Mutation SNP C C3N-01030_T 2541289 99818461 45320175 360 21141 RIMS2 0 . GRCh38 8 103886187 103886187 + Missense_Mutation SNP G G T rs747622094 C3N-01030_T C3N-01030_N G G c.1588G>T p.Asp530Tyr p.D530Y ENST00000504942 4/24 167 81 86 129 128 1 strelka-varscan-mutect RIMS2,missense_variant,p.Asp338Tyr,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Asp308Tyr,ENST00000436393,;RIMS2,missense_variant,p.Asp530Tyr,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Asp472Tyr,ENST00000626043,;RIMS2,missense_variant,p.Asp338Tyr,ENST00000408894,;RIMS2,missense_variant,p.Asp338Tyr,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Asp534Tyr,ENST00000632716,;RIMS2,missense_variant,p.Asp338Tyr,ENST00000515551,; T ENST00000504942 Transcript missense_variant 1727/4228 1588/4050 530/1349 D/Y Gat/Tat rs747622094 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs747622094 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 103886187 103886187 G T 1 0 0 0 0 1 0 0 0 13543 1290 45 2 2 RIMS2 8 103886187 Missense_Mutation SNP G C3N-01030_T 4067726 103886187 41252449 361 21142 KCNV1 0 . GRCh38 8 109972358 109972358 + Silent SNP C C A rs866022506 C3N-01030_T C3N-01030_N C C c.891G>T p.= p.G297G ENST00000524391 3/4 179 92 87 151 150 1 strelka-varscan-mutect KCNV1,synonymous_variant,p.=,ENST00000524391,;KCNV1,synonymous_variant,p.=,ENST00000297404,NM_014379.2;RP11-696P8.2,upstream_gene_variant,,ENST00000530667,; A ENST00000524391 Transcript synonymous_variant 1924/6979 891/1503 297/500 G ggG/ggT rs866022506 1 -1 KCNV1 HGNC HGNC:18861 protein_coding YES CCDS6314.1 ENSP00000435954 Q6PIU1 UPI0000073DA5 3/4 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF38,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS rs866022506 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 109972358 109972358 C A 1 0 0 0 0 0 0 0 1 8010 842 30 2 2 KCNV1 8 109972358 Silent SNP C C3N-01030_T 6086171 109972358 35166278 362 21143 CSMD3 0 . GRCh38 8 112638849 112638849 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3373G>T p.Glu1125Ter p.E1125* ENST00000297405 21/71 261 234 27 225 225 0 strelka-varscan-mutect CSMD3,stop_gained,p.Glu1125Ter,ENST00000297405,NM_198123.1;CSMD3,stop_gained,p.Glu1085Ter,ENST00000343508,NM_198124.1;CSMD3,stop_gained,p.Glu1021Ter,ENST00000455883,NM_052900.2;CSMD3,stop_gained,p.Glu465Ter,ENST00000339701,;MIR2053,upstream_gene_variant,,ENST00000459295,; A ENST00000297405 Transcript stop_gained 3618/13212 3373/11124 1125/3707 E/* Gag/Tag 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 21/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 112638849 112638849 C A 1 0 0 0 0 0 1 0 0 3747 922 32 2 2 CSMD3 8 112638849 Nonsense_Mutation SNP C C3N-01030_T 2666491 112638849 32499787 363 21144 PHF20L1 0 . GRCh38 8 132839496 132839496 + Missense_Mutation SNP G G T rs774205944 C3N-01030_T C3N-01030_N G G c.2301G>T p.Lys767Asn p.K767N ENST00000395386 18/21 222 201 21 188 188 0 strelka-varscan-mutect PHF20L1,missense_variant,p.Lys767Asn,ENST00000395386,NM_016018.4;PHF20L1,missense_variant,p.Lys742Asn,ENST00000395390,;PHF20L1,missense_variant,p.Lys767Asn,ENST00000622263,;PHF20L1,missense_variant,p.Lys741Asn,ENST00000220847,NM_001277196.1;AF230666.2,intron_variant,,ENST00000608375,;AF230666.2,intron_variant,,ENST00000429151,;PHF20L1,3_prime_UTR_variant,,ENST00000460236,;PHF20L1,upstream_gene_variant,,ENST00000477051,;PHF20L1,downstream_gene_variant,,ENST00000493126,; T ENST00000395386 Transcript missense_variant 2600/6237 2301/3054 767/1017 K/N aaG/aaT rs774205944,COSM268087,COSM5103274 1 1 PHF20L1 HGNC HGNC:24280 protein_coding YES CCDS6367.2 ENSP00000378784 A8MW92 UPI0000DBD7AF NM_016018.4 deleterious(0) 18/21 hmmpanther:PTHR15856:SF26,hmmpanther:PTHR15856 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs774205944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 132839496 132839496 G T 1 0 0 0 0 1 0 0 0 11918 933 33 2 2 PHF20L1 8 132839496 Missense_Mutation SNP G C3N-01030_T 20200647 132839496 12299140 364 21145 ADGRB1 0 . GRCh38 8 142464535 142464535 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.337A>G p.Thr113Ala p.T113A ENST00000517894 2/31 118 53 65 95 95 0 strelka-varscan-mutect ADGRB1,missense_variant,p.Thr113Ala,ENST00000517894,;ADGRB1,missense_variant,p.Thr113Ala,ENST00000323289,NM_001702.2;ADGRB1,missense_variant,p.Thr113Ala,ENST00000521208,; G ENST00000517894 Transcript missense_variant 1231/6241 337/4755 113/1584 T/A Acc/Gcc 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 deleterious(0.03) 2/31 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 142464535 142464535 A G 1 0 0 0 0 1 0 0 0 355 159 6 5 5 ADGRB1 8 142464535 Missense_Mutation SNP A C3N-01030_T 9625039 142464535 2674101 365 21146 EPPK1 0 . GRCh38 8 143867899 143867899 + Silent SNP G G T rs184979586 C3N-01030_T C3N-01030_N G G c.5355C>A p.= p.R1785R ENST00000615648 2/2 260 242 18 166 166 0 strelka-varscan-mutect EPPK1,synonymous_variant,p.=,ENST00000615648,NM_031308.3;EPPK1,synonymous_variant,p.=,ENST00000568225,; T ENST00000615648 Transcript synonymous_variant 5427/16002 5355/15267 1785/5088 R cgC/cgA rs184979586 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 2/2 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF252 LOW 1 SNV 5 1 PASS rs184979586 . 0 208 0 2 0 0 0 0 -19.99173 0.9999997 1 1 1 0 T 2 4 70 143867899 143867899 G T 1 0 0 0 0 0 0 0 1 5038 1074 38 1 1 EPPK1 8 143867899 Silent SNP G C3N-01030_T 1403364 143867899 1270737 366 21147 WDR97 0 . GRCh38 8 144107801 144107801 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.51G>T p.= p.S17S ENST00000323662 1/24 383 355 28 257 257 0 strelka-varscan-mutect WDR97,synonymous_variant,p.=,ENST00000323662,;SHARPIN,upstream_gene_variant,,ENST00000398712,NM_030974.3;MAF1,downstream_gene_variant,,ENST00000534585,;MAF1,downstream_gene_variant,,ENST00000322428,NM_032272.4;MAF1,downstream_gene_variant,,ENST00000532522,;MAF1,downstream_gene_variant,,ENST00000527058,;MAF1,downstream_gene_variant,,ENST00000527572,;MAF1,downstream_gene_variant,,ENST00000534811,;SHARPIN,intron_variant,,ENST00000533184,;WDR97,upstream_gene_variant,,ENST00000533108,;SHARPIN,upstream_gene_variant,,ENST00000533948,;SHARPIN,upstream_gene_variant,,ENST00000534242,;WDR97,synonymous_variant,p.=,ENST00000534167,;WDR97,upstream_gene_variant,,ENST00000528691,;WDR97,upstream_gene_variant,,ENST00000525150,;WDR97,upstream_gene_variant,,ENST00000529209,;SHARPIN,upstream_gene_variant,,ENST00000359551,;SHARPIN,upstream_gene_variant,,ENST00000534435,;SHARPIN,upstream_gene_variant,,ENST00000531375,; T ENST00000323662 Transcript synonymous_variant 76/6916 51/4869 17/1622 S tcG/tcT 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 1/24 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF497 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 144107801 144107801 G T 1 0 0 0 0 0 0 0 1 17897 1103 39 1 1 WDR97 8 144107801 Silent SNP G C3N-01030_T 239902 144107801 1030835 367 21148 CBWD1 0 . GRCh38 9 156515 156515 + Nonsense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.541G>T p.Glu181Ter p.E181* ENST00000377400 7/15 156 127 29 257 257 0 strelka-varscan-mutect CBWD1,stop_gained,p.Glu181Ter,ENST00000377447,;CBWD1,stop_gained,p.Glu181Ter,ENST00000377400,;CBWD1,stop_gained,p.Glu145Ter,ENST00000314367,NM_001145355.1;CBWD1,stop_gained,p.Glu181Ter,ENST00000356521,NM_018491.3;CBWD1,stop_gained,p.Glu181Ter,ENST00000382447,NM_001145356.1;CBWD1,stop_gained,p.Glu181Ter,ENST00000613508,;CBWD1,non_coding_transcript_exon_variant,,ENST00000495302,;CBWD1,non_coding_transcript_exon_variant,,ENST00000487575,;CBWD1,non_coding_transcript_exon_variant,,ENST00000498044,;CBWD1,downstream_gene_variant,,ENST00000431099,;CBWD1,3_prime_UTR_variant,,ENST00000618061,;CBWD1,3_prime_UTR_variant,,ENST00000612045,;CBWD1,3_prime_UTR_variant,,ENST00000616944,;CBWD1,3_prime_UTR_variant,,ENST00000465014,;CBWD1,3_prime_UTR_variant,,ENST00000613355,;CBWD1,3_prime_UTR_variant,,ENST00000619157,;CBWD1,3_prime_UTR_variant,,ENST00000618361,;CBWD1,3_prime_UTR_variant,,ENST00000489272,;CBWD1,3_prime_UTR_variant,,ENST00000616803,;CBWD1,non_coding_transcript_exon_variant,,ENST00000613988,;CBWD1,non_coding_transcript_exon_variant,,ENST00000620292,; A ENST00000377400 Transcript stop_gained 719/1792 541/1188 181/395 E/* Gag/Tag COSM455707,COSM4815793,COSM4815794 1 -1 CBWD1 HGNC HGNC:17134 protein_coding YES CCDS6438.1 ENSP00000366617 Q9BRT8 UPI000006EFDF 7/15 hmmpanther:PTHR13748:SF38,hmmpanther:PTHR13748,Pfam_domain:PF02492,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 156515 156515 C A 1 0 0 0 0 0 1 0 0 2412 922 32 2 2 CBWD1 9 156515 Nonsense_Mutation SNP C C3N-01030_T 156515 138238202 368 21149 PUM3 0 . GRCh38 9 2828674 2828674 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.956+1G>T p.X319_splice ENST00000397885 104 74 30 148 148 0 strelka-varscan-mutect PUM3,splice_donor_variant,,ENST00000397885,NM_014878.4;PUM3,non_coding_transcript_exon_variant,,ENST00000469168,; A ENST00000397885 Transcript splice_donor_variant -/2321 956/1947 319/648 1 -1 PUM3 HGNC HGNC:29676 protein_coding YES CCDS6448.2 ENSP00000380982 Q15397 UPI000013D67E NM_014878.4 9/17 HIGH 1 SNV 1 1 PASS rs1377185761 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 2828674 2828674 C A 1 0 0 0 0 0 0 1 0 12984 579 20 2 2 PUM3 9 2828674 Splice_Site SNP C C3N-01030_T 2672159 2828674 135566043 369 21150 KIAA2026 0 . GRCh38 9 6007420 6007420 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.368G>T p.Gly123Val p.G123V ENST00000399933 1/8 69 51 18 66 66 0 strelka-varscan-mutect KIAA2026,missense_variant,p.Gly123Val,ENST00000399933,NM_001017969.2;KIAA2026,missense_variant,p.Gly123Val,ENST00000381461,;KIAA2026,missense_variant,p.Gly123Val,ENST00000513355,;RANBP6,downstream_gene_variant,,ENST00000259569,NM_012416.3;MIR4665,upstream_gene_variant,,ENST00000581132,; A ENST00000399933 Transcript missense_variant 368/6988 368/6312 123/2103 G/V gGc/gTc 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 tolerated_low_confidence(0.71) 1/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3,Gene3D:1.20.920.10 MODERATE 1 SNV 5 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999941 1 1 1 0 A 3 1 70 6007420 6007420 C A 1 0 0 0 0 1 0 0 0 8134 739 26 2 2 KIAA2026 9 6007420 Missense_Mutation SNP C C3N-01030_T 3178746 6007420 132387297 370 21151 ELAVL2 0 . GRCh38 9 23762095 23762095 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.140C>A p.Pro47His p.P47H ENST00000397312 2/7 192 143 49 235 235 0 strelka-varscan-mutect ELAVL2,missense_variant,p.Pro47His,ENST00000397312,NM_004432.3;ELAVL2,missense_variant,p.Pro47His,ENST00000544538,;ELAVL2,missense_variant,p.Pro47His,ENST00000223951,NM_001171197.1,NM_001171195.1;ELAVL2,missense_variant,p.Pro76His,ENST00000380110,;ELAVL2,missense_variant,p.Pro47His,ENST00000380117,;ELAVL2,missense_variant,p.Pro47His,ENST00000440102,;ELAVL2,downstream_gene_variant,,ENST00000462649,; T ENST00000397312 Transcript missense_variant 415/3805 140/1080 47/359 P/H cCt/cAt 1 -1 ELAVL2 HGNC HGNC:3313 protein_coding YES CCDS6515.1 ENSP00000380479 Q12926 UPI000013C83F NM_004432.3 deleterious(0) 2/7 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF351,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01661,SMART_domains:SM00360,Superfamily_domains:SSF54928,Prints_domain:PR00961 MODERATE 1 SNV 1 1 PASS rs1442587497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 23762095 23762095 G T 1 0 0 0 0 1 0 0 0 4883 1000 35 2 2 ELAVL2 9 23762095 Missense_Mutation SNP G C3N-01030_T 17754675 23762095 114632622 371 21152 ACO1 0 . GRCh38 9 32448916 32448916 + Silent SNP C C A rs776083510 C3N-01030_T C3N-01030_N C C c.2391C>A p.= p.A797A ENST00000309951 20/21 248 202 46 230 229 1 strelka-varscan-mutect ACO1,synonymous_variant,p.=,ENST00000309951,NM_002197.2;ACO1,synonymous_variant,p.=,ENST00000541043,NM_001278352.1;ACO1,synonymous_variant,p.=,ENST00000379923,; A ENST00000309951 Transcript synonymous_variant 2529/7466 2391/2670 797/889 A gcC/gcA rs776083510,COSM1108152,COSM1108154 1 1 ACO1 HGNC HGNC:117 protein_coding YES CCDS6525.1 ENSP00000309477 P21399 V9HWB7 UPI000012D87E NM_002197.2 20/21 hmmpanther:PTHR11670:SF32,hmmpanther:PTHR11670,Pfam_domain:PF00694,Gene3D:3.20.19.10,TIGRFAM_domain:TIGR01341,Superfamily_domains:SSF52016 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs776083510 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 32448916 32448916 C A 1 0 0 0 0 0 0 0 1 187 639 23 1 1 ACO1 9 32448916 Silent SNP C C3N-01030_T 8686821 32448916 105945801 372 21153 C9orf24 0 . GRCh38 9 34382805 34382805 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.345C>A p.Tyr115Ter p.Y115* ENST00000297623 3/7 247 213 34 214 214 0 strelka-varscan-mutect C9orf24,stop_gained,p.Tyr115Ter,ENST00000297623,NM_032596.3;C9orf24,stop_gained,p.Tyr81Ter,ENST00000444429,;C9orf24,upstream_gene_variant,,ENST00000379133,NM_147168.1;C9orf24,upstream_gene_variant,,ENST00000379124,;C9orf24,upstream_gene_variant,,ENST00000379127,NM_001252195.1;C9orf24,upstream_gene_variant,,ENST00000379126,NM_147169.2;C9orf24,upstream_gene_variant,,ENST00000481295,; T ENST00000297623 Transcript stop_gained 544/1151 345/789 115/262 Y/* taC/taA 1 -1 C9orf24 HGNC HGNC:19919 protein_coding YES CCDS6554.1 ENSP00000297623 Q8NCR6 UPI000006E5B3 NM_032596.3 3/7 Pfam_domain:PF15181,hmmpanther:PTHR35664,hmmpanther:PTHR35664:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 34382805 34382805 G T 1 0 0 0 0 0 1 0 0 2180 1372 48 2 2 C9orf24 9 34382805 Nonsense_Mutation SNP G C3N-01030_T 1933889 34382805 104011912 373 21154 UNC13B 0 . GRCh38 9 35381132 35381132 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2161G>T p.Ala721Ser p.A721S ENST00000378495 18/39 129 95 34 142 142 0 strelka-varscan-mutect UNC13B,missense_variant,p.Ala3470Ser,ENST00000635942,;UNC13B,missense_variant,p.Ala1101Ser,ENST00000636694,;UNC13B,missense_variant,p.Ala308Ser,ENST00000617908,;UNC13B,missense_variant,p.Ala721Ser,ENST00000619578,;UNC13B,missense_variant,p.Ala721Ser,ENST00000378495,NM_006377.3;UNC13B,missense_variant,p.Ala733Ser,ENST00000396787,;UNC13B,missense_variant,p.Ala308Ser,ENST00000378496,;UNC13B,non_coding_transcript_exon_variant,,ENST00000637271,;UNC13B,3_prime_UTR_variant,,ENST00000634487,; T ENST00000378495 Transcript missense_variant 2383/6303 2161/4776 721/1591 A/S Gct/Tct 1 1 UNC13B HGNC HGNC:12566 protein_coding YES CCDS6579.1 ENSP00000367756 O14795 UPI0000211336 NM_006377.3 deleterious(0.02) 18/39 Gene3D:2.60.40.150,hmmpanther:PTHR10480,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 35381132 35381132 G T 1 0 0 0 0 1 0 0 0 17509 1203 42 2 2 UNC13B 9 35381132 Missense_Mutation SNP G C3N-01030_T 998327 35381132 103013585 374 21155 CA9 0 . GRCh38 9 35676079 35676079 + Missense_Mutation SNP C C A rs771400520 C3N-01030_T C3N-01030_N C C c.620C>A p.Pro207His p.P207H ENST00000378357 4/11 187 162 25 159 159 0 strelka-varscan-mutect CA9,missense_variant,p.Pro207His,ENST00000378357,NM_001216.2;CA9,missense_variant,p.Pro207His,ENST00000617161,;RN7SL22P,downstream_gene_variant,,ENST00000471800,;CA9,upstream_gene_variant,,ENST00000493245,;CA9,upstream_gene_variant,,ENST00000485665,;ARHGEF39,upstream_gene_variant,,ENST00000490638,; A ENST00000378357 Transcript missense_variant 724/1618 620/1380 207/459 P/H cCt/cAt rs771400520 1 1 CA9 HGNC HGNC:1383 protein_coding YES CCDS6585.1 ENSP00000367608 Q16790 A0A0S2Z3D0 UPI000013E02C NM_001216.2 deleterious(0) 4/11 Gene3D:3.10.200.10,Pfam_domain:PF00194,PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF18,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS rs771400520 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 35676079 35676079 C A 1 0 0 0 0 1 0 0 0 2210 681 24 2 2 CA9 9 35676079 Missense_Mutation SNP C C3N-01030_T 294947 35676079 102718638 375 21156 SPATA31A1 0 . GRCh38 9 39360715 39360715 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2992G>A p.Gly998Arg p.G998R ENST00000377647 4/4 471 355 116 549 549 0 strelka-varscan-mutect SPATA31A1,missense_variant,p.Gly998Arg,ENST00000377647,NM_001085452.2;RP11-347J14.4,non_coding_transcript_exon_variant,,ENST00000615174,;SPATA31A1,downstream_gene_variant,,ENST00000473440,; A ENST00000377647 Transcript missense_variant 3012/4256 2992/4086 998/1361 G/R Ggg/Agg 1 1 SPATA31A1 HGNC HGNC:23394 protein_coding YES CCDS43808.2 ENSP00000366875 A0A0R4J2F1 UPI0001AE6DFD NM_001085452.2 tolerated(0.83) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS rs1240994635 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 39360715 39360715 G A 1 0 0 0 0 1 0 0 0 15343 1000 35 3 3 SPATA31A1 9 39360715 Missense_Mutation SNP G C3N-01030_T 3684636 39360715 99034002 376 21157 SPATA31A3 0 . GRCh38 9 66988662 66988662 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1836C>A p.= p.G612G ENST00000428649 4/4 336 259 77 351 351 0 strelka-varscan-mutect SPATA31A3,synonymous_variant,p.=,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; T ENST00000428649 Transcript synonymous_variant 1898/4256 1836/4044 612/1347 G ggC/ggA 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 4/4 Pfam_domain:PF14650,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 LOW 1 SNV 1 1 PASS rs1294389865 . 34 175 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 66988662 66988662 G T 1 0 0 0 0 0 0 0 1 15344 1306 46 2 2 SPATA31A3 9 66988662 Silent SNP G C3N-01030_T 27627947 66988662 71406055 377 21158 PGM5 0 . GRCh38 9 68392462 68392462 + Missense_Mutation SNP G G T rs782775578 C3N-01030_T C3N-01030_N G G c.1032G>T p.Met344Ile p.M344I ENST00000396396 6/11 162 143 19 125 125 0 varscan-mutect PGM5,missense_variant,p.Met344Ile,ENST00000396396,NM_021965.3;PGM5,missense_variant,p.Met344Ile,ENST00000396392,;PGM5,downstream_gene_variant,,ENST00000431583,;RP11-88I18.2,downstream_gene_variant,,ENST00000590767,;RP11-88I18.2,downstream_gene_variant,,ENST00000629161,;RP11-88I18.2,downstream_gene_variant,,ENST00000629181,;PGM5,non_coding_transcript_exon_variant,,ENST00000604870,;PGM5,upstream_gene_variant,,ENST00000587852,; T ENST00000396396 Transcript missense_variant 1261/3338 1032/1704 344/567 M/I atG/atT rs782775578 1 1 PGM5 HGNC HGNC:8908 protein_coding YES CCDS6622.2 ENSP00000379678 Q15124 UPI0000210ABF NM_021965.3 tolerated(0.1) 6/11 Gene3D:3.40.120.10,Pfam_domain:PF02880,hmmpanther:PTHR22573,hmmpanther:PTHR22573:SF27,Superfamily_domains:SSF53738 MODERATE 1 SNV 2 1 PASS rs782775578 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 70 68392462 68392462 G T 1 0 0 0 0 1 0 0 0 11890 1348 47 2 2 PGM5 9 68392462 Missense_Mutation SNP G C3N-01030_T 1403800 68392462 70002255 378 21159 ALDH1A1 0 . GRCh38 9 72930938 72930938 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.253A>G p.Arg85Gly p.R85G ENST00000297785 3/13 216 169 47 221 221 0 strelka-varscan-mutect ALDH1A1,missense_variant,p.Arg85Gly,ENST00000297785,NM_000689.4;ALDH1A1,missense_variant,p.Arg85Gly,ENST00000376939,;ALDH1A1,missense_variant,p.Arg85Gly,ENST00000419959,;ALDH1A1,missense_variant,p.Arg85Gly,ENST00000446946,;ALDH1A1,non_coding_transcript_exon_variant,,ENST00000482210,;ALDH1A1,non_coding_transcript_exon_variant,,ENST00000493113,; C ENST00000297785 Transcript missense_variant 308/2107 253/1506 85/501 R/G Agg/Ggg 1 -1 ALDH1A1 HGNC HGNC:402 protein_coding YES CCDS6644.1 ENSP00000297785 P00352 V9HW83 UPI0000000DC0 NM_000689.4 deleterious(0) 3/13 Gene3D:3.40.605.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF140,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 72930938 72930938 T C 1 0 0 0 0 1 0 0 0 590 1550 54 5 5 ALDH1A1 9 72930938 Missense_Mutation SNP T C3N-01030_T 4538476 72930938 65463779 379 21160 C9orf40 0 . GRCh38 9 74952595 74952595 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.17delC p.Ala6GlyfsTer5 p.A6Gfs*5 ENST00000376854 1/2 129 97 32 105 105 0 sindel-varindel-pindel C9orf40,frameshift_variant,p.Ala6GlyfsTer5,ENST00000376854,NM_017998.2;C9orf41-AS1,upstream_gene_variant,,ENST00000455609,; - ENST00000376854 Transcript frameshift_variant 292/2327 17/585 6/194 A/X gCg/gg 1 -1 C9orf40 HGNC HGNC:23433 protein_coding YES CCDS6648.1 ENSP00000366050 Q8IXQ3 UPI0000074360 NM_017998.2 1/2 PD309264,hmmpanther:PTHR16003,hmmpanther:PTHR16003:SF3 HIGH 1 deletion 1 1 PASS . . 0 203 2 5 0 0 0 0 -20 0.9995765 1 1 1 0 - 7 5 70 74952595 74952595 G - 1 0 1 0 1 0 0 0 0 2182 1087 38 0 0 C9orf40 9 74952595 Frame_Shift_Del DEL G C3N-01030_T 2021657 74952595 63442122 380 21161 PRUNE2 0 . GRCh38 9 76707478 76707478 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.4796T>A p.Val1599Glu p.V1599E ENST00000376718 8/19 123 92 31 156 155 1 strelka-varscan-mutect PRUNE2,missense_variant,p.Val1599Glu,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Val1240Glu,ENST00000428286,;PRUNE2,missense_variant,p.Val1599Glu,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,missense_variant,p.Val921Glu,ENST00000426088,;PRUNE2,upstream_gene_variant,,ENST00000480674,; T ENST00000376718 Transcript missense_variant 4920/12584 4796/9267 1599/3088 V/E gTg/gAg 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 tolerated(0.24) 8/19 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 76707478 76707478 A T 1 0 0 0 0 1 0 0 0 12791 159 6 4 4 PRUNE2 9 76707478 Missense_Mutation SNP A C3N-01030_T 1754883 76707478 61687239 381 21162 AGTPBP1 0 . GRCh38 9 85575445 85575445 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.3529G>A p.Glu1177Lys p.E1177K ENST00000337006 24/25 210 186 24 268 268 0 strelka-varscan-mutect AGTPBP1,missense_variant,p.Glu1177Lys,ENST00000337006,NM_001286715.1;AGTPBP1,missense_variant,p.Glu1125Lys,ENST00000357081,;AGTPBP1,missense_variant,p.Glu1137Lys,ENST00000628899,NM_001286717.1;AGTPBP1,missense_variant,p.Glu1085Lys,ENST00000376083,NM_015239.2;AGTPBP1,non_coding_transcript_exon_variant,,ENST00000489265,; T ENST00000337006 Transcript missense_variant 3596/4473 3529/3837 1177/1278 E/K Gag/Aag COSM422328,COSM4811627 1 -1 AGTPBP1 HGNC HGNC:17258 protein_coding YES CCDS75854.1 ENSP00000338512 J3KNS1 UPI000387D56E NM_001286715.1 deleterious(0) 24/25 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF24,Superfamily_domains:SSF53187 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 85575445 85575445 C T 1 0 0 0 0 1 0 0 0 479 922 32 3 3 AGTPBP1 9 85575445 Missense_Mutation SNP C C3N-01030_T 8867967 85575445 52819272 382 21163 ECM2 0 . GRCh38 9 92505588 92505588 + Missense_Mutation SNP C C T rs763096769 C3N-01030_T C3N-01030_N C C c.1409G>A p.Arg470His p.R470H ENST00000344604 7/10 147 112 35 205 205 0 strelka-varscan-mutect ECM2,missense_variant,p.Arg470His,ENST00000344604,NM_001197295.1,NM_001393.3;ECM2,missense_variant,p.Arg448His,ENST00000444490,NM_001197296.1;CENPP,intron_variant,,ENST00000375587,NM_001012267.2; T ENST00000344604 Transcript missense_variant 1559/3253 1409/2100 470/699 R/H cGt/cAt rs763096769,COSM3908895,COSM3908896 1 -1 ECM2 HGNC HGNC:3154 protein_coding YES CCDS6698.1 ENSP00000344758 O94769 UPI0000129B80 NM_001197295.1,NM_001393.3 deleterious(0.02) 7/10 Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF134,SMART_domains:SM00369,Superfamily_domains:SSF52047 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs763096769 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 92505588 92505588 C T 1 0 0 0 0 1 0 0 0 4726 536 19 1 1 ECM2 9 92505588 Missense_Mutation SNP C C3N-01030_T 6930143 92505588 45889129 383 21164 WNK2 0 . GRCh38 9 93234827 93234827 + Silent SNP G G T rs550073972 C3N-01030_T C3N-01030_N G G c.1095G>T p.= p.A365A ENST00000297954 4/30 80 63 17 76 76 0 strelka-varscan-mutect WNK2,synonymous_variant,p.=,ENST00000432730,;WNK2,synonymous_variant,p.=,ENST00000297954,NM_001282394.1;WNK2,synonymous_variant,p.=,ENST00000395477,NM_006648.3;WNK2,synonymous_variant,p.=,ENST00000448039,;WNK2,5_prime_UTR_variant,,ENST00000427277,;WNK2,upstream_gene_variant,,ENST00000411624,; T ENST00000297954 Transcript synonymous_variant 1095/7138 1095/6894 365/2297 A gcG/gcT rs550073972,COSM3908977,COSM3908978,COSM3908979 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 4/30 PROSITE_profiles:PS50011,hmmpanther:PTHR13902:SF10,hmmpanther:PTHR13902,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs550073972 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 93234827 93234827 G T 1 0 0 0 0 0 0 0 1 17934 1074 38 1 1 WNK2 9 93234827 Silent SNP G C3N-01030_T 729239 93234827 45159890 384 21165 PTPDC1 0 . GRCh38 9 94101629 94101629 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.2077C>G p.Leu693Val p.L693V ENST00000620992 7/9 182 149 33 167 167 0 strelka-varscan-mutect PTPDC1,missense_variant,p.Leu639Val,ENST00000375360,NM_177995.2,NM_001253830.1;PTPDC1,missense_variant,p.Leu693Val,ENST00000620992,NM_001253829.1;PTPDC1,missense_variant,p.Leu691Val,ENST00000288976,NM_152422.4;PTPDC1,non_coding_transcript_exon_variant,,ENST00000467049,; G ENST00000620992 Transcript missense_variant 2179/4437 2077/2427 693/808 L/V Cta/Gta 1 1 PTPDC1 HGNC HGNC:30184 protein_coding YES CCDS75860.1 ENSP00000477817 A0A087WTF0 UPI0000E0BDFA NM_001253829.1 deleterious(0) 7/9 hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF72 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 94101629 94101629 C G 1 0 0 0 0 1 0 0 0 12930 680 24 4 4 PTPDC1 9 94101629 Missense_Mutation SNP C C3N-01030_T 866802 94101629 44293088 385 21166 TDRD7 0 . GRCh38 9 97464846 97464847 + Frame_Shift_Ins INS - - T novel C3N-01030_T C3N-01030_N - - c.1448dupT p.Lys485GlnfsTer13 p.K485Qfs*13 ENST00000355295 8/17 253 191 62 277 277 0 sindel-varindel-pindel TDRD7,frameshift_variant,p.Lys485GlnfsTer13,ENST00000355295,NM_001302884.1,NM_014290.2; T ENST00000355295 Transcript frameshift_variant 1742-1743/3834 1447-1448/3297 483/1098 V/VX gtg/gTtg 1 1 TDRD7 HGNC HGNC:30831 protein_coding YES CCDS6725.1 ENSP00000347444 Q8NHU6 UPI00002114B5 NM_001302884.1,NM_014290.2 8/17 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF14,Pfam_domain:PF00567 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 70 97464846 97464846 - T 1 0 1 1 0 0 0 0 0 16145 1391 48 0 0 TDRD7 9 97464846 Frame_Shift_Ins INS - C3N-01030_T 3363217 97464846 40929871 386 21167 OR13C4 0 . GRCh38 9 104526340 104526340 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.870G>T p.Met290Ile p.M290I ENST00000277216 1/1 105 78 27 110 110 0 strelka-varscan-mutect OR13C4,missense_variant,p.Met290Ile,ENST00000277216,NM_001001919.1;RP11-317C20.9,intron_variant,,ENST00000635678,; A ENST00000277216 Transcript missense_variant 870/957 870/957 290/318 M/I atG/atT 1 -1 OR13C4 HGNC HGNC:14722 protein_coding YES CCDS35088.1 ENSP00000277216 Q8NGS5 A0A126GVC9 UPI0000041B46 NM_001001919.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF14,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 104526340 104526340 C A 1 0 0 0 0 1 0 0 0 11012 478 17 2 2 OR13C4 9 104526340 Missense_Mutation SNP C C3N-01030_T 7061494 104526340 33868377 387 21168 AKNA 0 . GRCh38 9 114341561 114341561 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.4039C>T p.Pro1347Ser p.P1347S ENST00000307564 21/22 221 178 43 182 182 0 strelka-varscan-mutect AKNA,missense_variant,p.Pro1347Ser,ENST00000307564,NM_030767.4;AKNA,missense_variant,p.Pro1347Ser,ENST00000374088,NM_001317950.1,NM_001317952.1;AKNA,missense_variant,p.Pro1266Ser,ENST00000374075,;AKNA,missense_variant,p.Pro807Ser,ENST00000223791,;AKNA,missense_variant,p.Pro292Ser,ENST00000374079,;AKNA,non_coding_transcript_exon_variant,,ENST00000492875,; A ENST00000307564 Transcript missense_variant 4201/7380 4039/4320 1347/1439 P/S Ccc/Tcc 1 -1 AKNA HGNC HGNC:24108 protein_coding YES CCDS6805.1 ENSP00000303769 Q7Z591 UPI000021168C NM_030767.4 deleterious(0) 21/22 hmmpanther:PTHR21510:SF15,hmmpanther:PTHR21510 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 114341561 114341561 G A 1 0 0 0 0 1 0 0 0 547 1174 41 3 3 AKNA 9 114341561 Missense_Mutation SNP G C3N-01030_T 9815221 114341561 24053156 388 21169 BRINP1 0 . GRCh38 9 119313224 119313224 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.132C>G p.Asp44Glu p.D44E ENST00000265922 2/8 282 216 66 287 287 0 strelka-varscan-mutect BRINP1,missense_variant,p.Asp44Glu,ENST00000265922,NM_014618.2;BRINP1,missense_variant,p.Asp44Glu,ENST00000373964,; C ENST00000265922 Transcript missense_variant 594/3202 132/2286 44/761 D/E gaC/gaG 1 -1 BRINP1 HGNC HGNC:2687 protein_coding YES CCDS6822.1 ENSP00000265922 O60477 UPI000013D6A7 NM_014618.2 tolerated(0.1) 2/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF7 MODERATE 1 SNV 1 1 PASS rs1366967570 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 119313224 119313224 G C 1 0 0 0 0 1 0 0 0 1685 1368 48 4 4 BRINP1 9 119313224 Missense_Mutation SNP G C3N-01030_T 4971663 119313224 19081493 389 21170 OR1N2 0 . GRCh38 9 122553858 122553858 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.689T>A p.Leu230Gln p.L230Q ENST00000373688 1/1 246 186 60 208 208 0 strelka-varscan-mutect OR1N2,missense_variant,p.Leu230Gln,ENST00000373688,NM_001004457.1;OR1N2,missense_variant,p.Leu212Gln,ENST00000616791,; A ENST00000373688 Transcript missense_variant 747/1103 689/993 230/330 L/Q cTg/cAg 1 1 OR1N2 HGNC HGNC:15111 protein_coding YES CCDS35123.1 ENSP00000362792 Q8NGR9 UPI000004618C NM_001004457.1 tolerated(0.08) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF156,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 122553858 122553858 T A 1 0 0 0 0 1 0 0 0 11048 1580 55 4 4 OR1N2 9 122553858 Missense_Mutation SNP T C3N-01030_T 3240634 122553858 15840859 390 21171 GAPVD1 0 . GRCh38 9 125360691 125360691 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.4289A>T p.Asp1430Val p.D1430V ENST00000394105 26/27 217 170 47 196 196 0 strelka-varscan-mutect GAPVD1,missense_variant,p.Asp1376Val,ENST00000470056,;GAPVD1,missense_variant,p.Asp1421Val,ENST00000394104,;GAPVD1,missense_variant,p.Asp1403Val,ENST00000297933,NM_001282680.1;GAPVD1,missense_variant,p.Asp1421Val,ENST00000495955,NM_001282679.1;GAPVD1,missense_variant,p.Asp1430Val,ENST00000394105,NM_015635.3;GAPVD1,missense_variant,p.Asp1355Val,ENST00000394083,;GAPVD1,missense_variant,p.Asp1382Val,ENST00000312123,NM_001282681.1;GAPVD1,non_coding_transcript_exon_variant,,ENST00000474637,;GAPVD1,downstream_gene_variant,,ENST00000467707,; T ENST00000394105 Transcript missense_variant 4449/5207 4289/4464 1430/1487 D/V gAc/gTc 1 1 GAPVD1 HGNC HGNC:23375 protein_coding YES CCDS35138.1 ENSP00000377665 Q14C86 A0A024R8A2 UPI00001D76F1 NM_015635.3 deleterious(0) 26/27 PROSITE_profiles:PS51205,hmmpanther:PTHR23101:SF68,hmmpanther:PTHR23101,Pfam_domain:PF02204,SMART_domains:SM00167,Superfamily_domains:0044157 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 125360691 125360691 A T 1 0 0 0 0 1 0 0 0 6107 275 10 4 4 GAPVD1 9 125360691 Missense_Mutation SNP A C3N-01030_T 2806833 125360691 13034026 391 21172 TTC16 0 . GRCh38 9 127724797 127724797 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1159G>T p.Asp387Tyr p.D387Y ENST00000373289 9/14 260 212 48 169 169 0 strelka-varscan-mutect TTC16,missense_variant,p.Asp387Tyr,ENST00000373289,NM_144965.1;PTRH1,5_prime_UTR_variant,,ENST00000419060,;PTRH1,non_coding_transcript_exon_variant,,ENST00000429848,;TTC16,non_coding_transcript_exon_variant,,ENST00000488285,;TTC16,intron_variant,,ENST00000489226,; T ENST00000373289 Transcript missense_variant 1239/2897 1159/2622 387/873 D/Y Gac/Tac 1 1 TTC16 HGNC HGNC:26536 protein_coding YES CCDS6875.1 ENSP00000362386 Q8NEE8 UPI000006FE14 NM_144965.1 deleterious(0) 9/14 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR23083:SF438,hmmpanther:PTHR23083,Gene3D:1.25.40.10,Pfam_domain:PF00515,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 127724797 127724797 G T 1 0 0 0 0 1 0 0 0 17192 1174 41 2 2 TTC16 9 127724797 Missense_Mutation SNP G C3N-01030_T 2364106 127724797 10669920 392 21173 HMCN2 0 . GRCh38 9 130285288 130285288 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.458T>A p.Leu153Gln p.L153Q ENST00000624552 3/98 173 133 40 127 127 0 strelka-varscan-mutect HMCN2,missense_variant,p.Leu153Gln,ENST00000624552,NM_001291815.1; A ENST00000624552 Transcript missense_variant 458/15610 458/15180 153/5059 L/Q cTg/cAg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0.01) 3/98 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,Low_complexity_(Seg):seg,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 130285288 130285288 T A 1 0 0 0 0 1 0 0 0 7112 1580 55 4 4 HMCN2 9 130285288 Missense_Mutation SNP T C3N-01030_T 2560491 130285288 8109429 393 21174 FIBCD1 0 . GRCh38 9 130905259 130905259 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1101C>A p.= p.T367T ENST00000372338 6/7 130 96 34 101 101 0 strelka-varscan-mutect FIBCD1,synonymous_variant,p.=,ENST00000372338,NM_032843.4;FIBCD1,synonymous_variant,p.=,ENST00000448616,NM_001145106.1;FIBCD1,synonymous_variant,p.=,ENST00000372337,;FIBCD1,intron_variant,,ENST00000444139,; T ENST00000372338 Transcript synonymous_variant 1344/3253 1101/1386 367/461 T acC/acA 1 -1 FIBCD1 HGNC HGNC:25922 protein_coding YES CCDS6937.1 ENSP00000361413 Q8N539 UPI0000049DF9 NM_032843.4 6/7 PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF239,Gene3D:3.90.215.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496 LOW 1 SNV 1 1 PASS rs1386838057 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 130905259 130905259 G T 1 0 0 0 0 0 0 0 1 5749 1103 39 1 1 FIBCD1 9 130905259 Silent SNP G C3N-01030_T 619971 130905259 7489458 394 21175 TTF1 0 . GRCh38 9 132402479 132402479 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.343A>G p.Thr115Ala p.T115A ENST00000334270 2/11 170 124 46 200 200 0 strelka-varscan-mutect TTF1,missense_variant,p.Thr115Ala,ENST00000334270,NM_007344.3;TTF1,intron_variant,,ENST00000612514,NM_001205296.1; C ENST00000334270 Transcript missense_variant 383/3052 343/2718 115/905 T/A Aca/Gca 1 -1 TTF1 HGNC HGNC:12397 protein_coding YES CCDS6948.1 ENSP00000333920 Q15361 A0A024R8C1 UPI00001B55A7 NM_007344.3 tolerated(0.14) 2/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 132402479 132402479 T C 1 0 0 0 0 1 0 0 0 17228 1696 59 5 5 TTF1 9 132402479 Missense_Mutation SNP T C3N-01030_T 1497220 132402479 5992238 395 21176 VAV2 0 . GRCh38 9 133791781 133791781 + Splice_Site SNP A A C novel C3N-01030_T C3N-01030_N A A c.1188+2T>G p.X396_splice ENST00000371850 172 132 40 151 151 0 strelka-varscan-mutect VAV2,splice_donor_variant,,ENST00000371851,;VAV2,splice_donor_variant,,ENST00000371850,NM_001134398.1;VAV2,splice_donor_variant,,ENST00000406606,NM_003371.3; C ENST00000371850 Transcript splice_donor_variant -/4837 1188/2637 396/878 1 -1 VAV2 HGNC HGNC:12658 protein_coding YES CCDS48053.1 ENSP00000360916 P52735 UPI000013E06E NM_001134398.1 13/29 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 70 133791781 133791781 A C 1 0 0 0 0 0 0 1 0 17677 173 6 5 5 VAV2 9 133791781 Splice_Site SNP A C3N-01030_T 1389302 133791781 4602936 396 21177 PPP1R26 0 . GRCh38 9 135487950 135487950 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.3441delG p.Lys1148ArgfsTer6 p.K1148Rfs*6 ENST00000356818 4/4 56 41 15 40 40 0 sindel-varindel-pindel PPP1R26,frameshift_variant,p.Lys1148ArgfsTer6,ENST00000356818,NM_014811.3;PPP1R26,frameshift_variant,p.Lys1148ArgfsTer6,ENST00000401470,;PPP1R26,frameshift_variant,p.Lys1148ArgfsTer6,ENST00000605286,;PPP1R26,frameshift_variant,p.Lys1148ArgfsTer6,ENST00000604351,;PPP1R26,frameshift_variant,p.Lys1148ArgfsTer6,ENST00000605660,;PPP1R26,intron_variant,,ENST00000602993,; - ENST00000356818 Transcript frameshift_variant 3989/4932 3440/3630 1147/1209 R/X aGg/ag 1 1 PPP1R26 HGNC HGNC:29089 protein_coding YES CCDS6988.1 ENSP00000349274 Q5T8A7 UPI000013DB17 NM_014811.3 4/4 hmmpanther:PTHR15724 HIGH 1 deletion 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 135487950 135487950 G - 1 0 1 0 1 0 0 0 0 12484 1000 35 0 0 PPP1R26 9 135487950 Frame_Shift_Del DEL G C3N-01030_T 1696169 135487950 2906767 397 21178 PFKP 0 . GRCh38 10 3113501 3113501 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1354G>T p.Gly452Cys p.G452C ENST00000381125 13/22 144 113 31 126 126 0 strelka-varscan-mutect PFKP,missense_variant,p.Gly444Cys,ENST00000381075,NM_001242339.1;PFKP,missense_variant,p.Gly452Cys,ENST00000381125,NM_001323069.1,NM_001323067.1,NM_002627.4;PFKP,missense_variant,p.Gly236Cys,ENST00000415005,;PFKP,missense_variant,p.Gly16Cys,ENST00000413079,;PFKP,downstream_gene_variant,,ENST00000468050,; T ENST00000381125 Transcript missense_variant 1430/2654 1354/2355 452/784 G/C Ggc/Tgc 1 1 PFKP HGNC HGNC:8878 protein_coding YES CCDS7059.1 ENSP00000370517 Q01813 UPI00000012D2 NM_001323069.1,NM_001323067.1,NM_002627.4 deleterious(0) 13/22 Gene3D:3.40.50.450,HAMAP:MF_03184,Pfam_domain:PF00365,PIRSF_domain:PIRSF000533,hmmpanther:PTHR13697,hmmpanther:PTHR13697:SF5,Superfamily_domains:SSF53784,TIGRFAM_domain:TIGR02478 MODERATE 1 SNV 1 1 PASS rs1446950087 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 3113501 3113501 G T 1 0 0 0 0 1 0 0 0 11856 1116 39 1 1 PFKP 10 3113501 Missense_Mutation SNP G C3N-01030_T 3113501 130683921 398 21179 SFMBT2 0 . GRCh38 10 7200437 7200437 + Nonsense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1535T>A p.Leu512Ter p.L512* ENST00000397167 14/21 59 48 11 77 77 0 strelka-varscan-mutect SFMBT2,stop_gained,p.Leu512Ter,ENST00000397167,NM_001029880.2;SFMBT2,stop_gained,p.Leu512Ter,ENST00000361972,NM_001018039.1; T ENST00000397167 Transcript stop_gained 1728/8024 1535/2685 512/894 L/* tTa/tAa 1 -1 SFMBT2 HGNC HGNC:20256 protein_coding YES CCDS31138.1 ENSP00000380353 Q5VUG0 UPI00001C1EDF NM_001029880.2 14/21 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF62,Superfamily_domains:SSF63748 HIGH 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 7200437 7200437 A T 1 0 0 0 0 0 1 0 0 14436 372 13 4 4 SFMBT2 10 7200437 Nonsense_Mutation SNP A C3N-01030_T 4086936 7200437 126596985 399 21180 TAF3 0 . GRCh38 10 7964948 7964948 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1438G>T p.Gly480Ter p.G480* ENST00000344293 3/7 334 263 71 294 291 3 strelka-varscan-mutect TAF3,stop_gained,p.Gly480Ter,ENST00000344293,NM_031923.3; T ENST00000344293 Transcript stop_gained 1644/4872 1438/2790 480/929 G/* Gga/Tga 1 1 TAF3 HGNC HGNC:17303 protein_coding YES CCDS41487.1 ENSP00000340271 Q5VWG9 UPI00004588FA NM_031923.3 3/7 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 7964948 7964948 G T 1 0 0 0 0 0 1 0 0 15921 1233 43 2 2 TAF3 10 7964948 Nonsense_Mutation SNP G C3N-01030_T 764511 7964948 125832474 400 21181 ITGA8 0 . GRCh38 10 15613660 15613660 + Missense_Mutation SNP C C A rs186867501 C3N-01030_T C3N-01030_N C C c.1553G>T p.Cys518Phe p.C518F ENST00000378076 15/30 88 64 24 88 88 0 strelka-varscan-mutect ITGA8,missense_variant,p.Cys518Phe,ENST00000378076,NM_003638.2,NM_001291494.1;ITGA8,non_coding_transcript_exon_variant,,ENST00000468882,; A ENST00000378076 Transcript missense_variant,splice_region_variant 1907/6755 1553/3192 518/1063 C/F tGc/tTc rs186867501 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 deleterious(0.01) 15/30 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs186867501 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 15613660 15613660 C A 1 0 0 0 0 1 0 0 0 7789 608 21 2 2 ITGA8 10 15613660 Missense_Mutation SNP C C3N-01030_T 7648712 15613660 118183762 401 21182 CUBN 0 . GRCh38 10 16840363 16840363 + Frame_Shift_Del DEL C C - rs374885106 C3N-01030_T C3N-01030_N C C c.9999delG p.Gln3334ArgfsTer35 p.Q3334Rfs*35 ENST00000377833 62/67 216 156 60 241 241 0 sindel-varindel-pindel CUBN,frameshift_variant,p.Gln3334ArgfsTer35,ENST00000377833,NM_001081.3; - ENST00000377833 Transcript frameshift_variant 10065/11949 9999/10872 3333/3623 T/X acG/ac rs374885106 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 62/67 PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 16840363 16840363 C - 1 0 1 0 1 0 0 0 0 3861 755 27 0 0 CUBN 10 16840363 Frame_Shift_Del DEL C C3N-01030_T 1226703 16840363 116957059 402 21183 MRC1 0 . GRCh38 10 17861444 17861444 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.1576delG p.Ala526GlnfsTer14 p.A526Qfs*14 ENST00000569591 10/30 224 179 45 332 332 0 sindel-varindel-pindel MRC1,frameshift_variant,p.Ala526GlnfsTer14,ENST00000569591,NM_002438.3;RP11-457D2.3,downstream_gene_variant,,ENST00000442231,; - ENST00000569591 Transcript frameshift_variant 1698/5198 1576/4371 526/1456 A/X Gca/ca 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 10/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 17861444 17861444 G - 1 0 1 0 1 0 0 0 0 9722 1319 46 0 0 MRC1 10 17861444 Frame_Shift_Del DEL G C3N-01030_T 1021081 17861444 115935978 403 21184 MYO3A 0 . GRCh38 10 26176843 26176843 + Nonsense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.4436C>A p.Ser1479Ter p.S1479* ENST00000265944 31/35 265 204 61 309 309 0 strelka-varscan-mutect MYO3A,stop_gained,p.Ser1479Ter,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; A ENST00000265944 Transcript stop_gained,splice_region_variant 4602/5581 4436/4851 1479/1616 S/* tCa/tAa COSM5334824 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 31/35 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 26176843 26176843 C A 1 0 0 0 0 0 1 0 0 10077 840 29 2 2 MYO3A 10 26176843 Nonsense_Mutation SNP C C3N-01030_T 8315399 26176843 107620579 404 21185 ANKRD26 0 . GRCh38 10 27060348 27060348 + Missense_Mutation SNP C C A rs376035947 C3N-01030_T C3N-01030_N C C c.1561G>T p.Ala521Ser p.A521S ENST00000376087 15/34 175 137 38 261 261 0 strelka-varscan-mutect ANKRD26,missense_variant,p.Ala537Ser,ENST00000436985,;ANKRD26,missense_variant,p.Ala521Ser,ENST00000376087,NM_014915.2,NM_001256053.1; A ENST00000376087 Transcript missense_variant 1727/6591 1561/5133 521/1710 A/S Gca/Tca rs376035947 1 -1 ANKRD26 HGNC HGNC:29186 protein_coding YES CCDS41499.1 ENSP00000365255 Q9UPS8 UPI000006FC41 NM_014915.2,NM_001256053.1 tolerated(1) 15/34 hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF24 MODERATE 1 SNV 5 1 PASS rs376035947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 27060348 27060348 C A 1 0 0 0 0 1 0 0 0 757 811 28 2 2 ANKRD26 10 27060348 Missense_Mutation SNP C C3N-01030_T 883505 27060348 106737074 405 21186 MASTL 0 . GRCh38 10 27159631 27159631 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.337C>G p.Leu113Val p.L113V ENST00000375940 3/12 114 86 28 193 193 0 strelka-varscan-mutect MASTL,missense_variant,p.Leu113Val,ENST00000375946,NM_032844.3;MASTL,missense_variant,p.Leu113Val,ENST00000375940,NM_001172303.1;MASTL,missense_variant,p.Leu113Val,ENST00000342386,NM_001172304.1;YME1L1,upstream_gene_variant,,ENST00000477432,; G ENST00000375940 Transcript missense_variant 394/3080 337/2640 113/879 L/V Ctt/Gtt 1 1 MASTL HGNC HGNC:19042 protein_coding YES CCDS53502.1 ENSP00000365107 Q96GX5 UPI000004060D NM_001172303.1 deleterious(0) 3/12 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF1,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999977 1 1 1 0 G 3 3 70 27159631 27159631 C G 1 0 0 0 0 1 0 0 0 9254 913 32 4 4 MASTL 10 27159631 Missense_Mutation SNP C C3N-01030_T 99283 27159631 106637791 406 21187 CCDC7 0 . GRCh38 10 32544281 32544281 + Missense_Mutation SNP G G C rs746776900 C3N-01030_T C3N-01030_N G G c.1114G>C p.Glu372Gln p.E372Q ENST00000362006 14/18 111 95 16 158 158 0 strelka-varscan-mutect CCDC7,missense_variant,p.Glu372Gln,ENST00000362006,NM_145023.5,NM_001026383.2;CCDC7,missense_variant,p.Glu372Gln,ENST00000277657,; C ENST00000362006 Transcript missense_variant 1621/2093 1114/1461 372/486 E/Q Gaa/Caa rs746776900 1 1 CCDC7 HGNC HGNC:26533 protein_coding YES CCDS7173.1 ENSP00000355078 Q96M83 UPI00000745EB NM_145023.5,NM_001026383.2 deleterious(0.05) 14/18 hmmpanther:PTHR22035:SF4,hmmpanther:PTHR22035 MODERATE 1 SNV 1 1 PASS rs746776900 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 32544281 32544281 G C 1 0 0 0 0 1 0 0 0 2542 943 33 4 4 CCDC7 10 32544281 Missense_Mutation SNP G C3N-01030_T 5384650 32544281 101253141 407 21188 RET 0 . GRCh38 10 43118476 43118476 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2388G>T p.Gln796His p.Q796H ENST00000355710 13/20 327 253 74 313 313 0 strelka-varscan-mutect RET,missense_variant,p.Gln796His,ENST00000355710,NM_020975.4;RET,missense_variant,p.Gln796His,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000615310,;RET,downstream_gene_variant,,ENST00000498820,; T ENST00000355710 Transcript missense_variant 2620/5659 2388/3345 796/1114 Q/H caG/caT 1 1 RET HGNC HGNC:9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 A0A024R7T2 UPI00001336E1 NM_020975.4 deleterious(0.04) 13/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000631,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF345,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs1328507414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 43118476 43118476 G T 1 0 0 0 0 1 0 0 0 13406 1014 35 2 2 RET 10 43118476 Missense_Mutation SNP G C3N-01030_T 10574195 43118476 90678946 408 21189 CXCL12 0 . GRCh38 10 44380815 44380815 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.127A>T p.Asn43Tyr p.N43Y ENST00000395794 2/4 237 179 58 217 217 0 strelka-varscan-mutect CXCL12,missense_variant,p.Asn43Tyr,ENST00000374429,NM_000609.6;CXCL12,missense_variant,p.Asn43Tyr,ENST00000343575,NM_199168.3;CXCL12,missense_variant,p.Asn43Tyr,ENST00000395794,NM_001178134.1;CXCL12,missense_variant,p.Asn43Tyr,ENST00000374426,NM_001033886.2;CXCL12,intron_variant,,ENST00000395793,NM_001277990.1;CXCL12,intron_variant,,ENST00000395795,;CXCL12,non_coding_transcript_exon_variant,,ENST00000496375,;CXCL12,non_coding_transcript_exon_variant,,ENST00000488591,; A ENST00000395794 Transcript missense_variant 171/1052 127/423 43/140 N/Y Aac/Tac 1 -1 CXCL12 HGNC HGNC:10672 protein_coding YES CCDS53527.1 ENSP00000379140 P48061 UPI0000684849 NM_001178134.1 tolerated(0.29) 2/4 Gene3D:2.40.50.40,Pfam_domain:PF00048,Prints_domain:PR00436,hmmpanther:PTHR18837,hmmpanther:PTHR18837:SF3,SMART_domains:SM00199,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 44380815 44380815 T A 1 0 0 0 0 1 0 0 0 3890 1812 63 4 4 CXCL12 10 44380815 Missense_Mutation SNP T C3N-01030_T 1262339 44380815 89416607 409 21190 GDF10 0 . GRCh38 10 47310307 47310307 + Frame_Shift_Del DEL C C - rs371903896 C3N-01030_T C3N-01030_N C C c.831delC p.Ala278GlnfsTer54 p.A278Qfs*54 ENST00000580279 2/3 137 103 34 155 155 0 sindel-varindel-pindel GDF10,frameshift_variant,p.Ala278GlnfsTer54,ENST00000580279,NM_004962.3; - ENST00000580279 Transcript frameshift_variant 1097/2458 831/1437 277/478 R/X cgC/cg rs371903896 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 2/3 PIRSF_domain:PIRSF037403,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF145 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 47310307 47310307 C - 1 0 1 0 1 0 0 0 0 6184 755 27 0 0 GDF10 10 47310307 Frame_Shift_Del DEL C C3N-01030_T 2929492 47310307 86487115 410 21191 FRMPD2 0 . GRCh38 10 48236515 48236515 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.960C>T p.= p.A320A ENST00000374201 9/29 222 174 48 195 194 1 strelka-varscan-mutect FRMPD2,synonymous_variant,p.=,ENST00000374201,NM_001018071.3;FRMPD2,synonymous_variant,p.=,ENST00000305531,NM_001318191.1;FRMPD2,synonymous_variant,p.=,ENST00000636244,;FRMPD2,3_prime_UTR_variant,,ENST00000637395,;FRMPD2,non_coding_transcript_exon_variant,,ENST00000486151,; A ENST00000374201 Transcript synonymous_variant 1263/4997 960/3930 320/1309 A gcC/gcT 1 -1 FRMPD2 HGNC HGNC:28572 protein_coding YES CCDS31195.1 ENSP00000363317 Q68DX3 UPI0000D60F5F NM_001018071.3 9/29 hmmpanther:PTHR19964:SF42,hmmpanther:PTHR19964 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 48236515 48236515 G A 1 0 0 0 0 0 0 0 1 5928 1219 43 3 3 FRMPD2 10 48236515 Silent SNP G C3N-01030_T 926208 48236515 85560907 411 21192 C10orf71 0 . GRCh38 10 49325411 49325411 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2866G>T p.Gly956Trp p.G956W ENST00000374144 3/3 103 71 32 105 104 1 strelka-varscan-mutect C10orf71,missense_variant,p.Gly956Trp,ENST00000374144,NM_001135196.1; T ENST00000374144 Transcript missense_variant 3154/5230 2866/4308 956/1435 G/W Ggg/Tgg 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0.05) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 49325411 49325411 G T 1 0 0 0 0 1 0 0 0 1769 1232 43 2 2 C10orf71 10 49325411 Missense_Mutation SNP G C3N-01030_T 1088896 49325411 84472011 412 21193 PCDH15 0 . GRCh38 10 53808847 53808847 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.5218G>T p.Glu1740Ter p.E1740* ENST00000613657 37/37 362 289 73 366 365 1 strelka-varscan-mutect PCDH15,stop_gained,p.Glu1740Ter,ENST00000613657,NM_001142769.1;PCDH15,stop_gained,p.Glu1733Ter,ENST00000395445,;PCDH15,stop_gained,p.Glu1739Ter,ENST00000612394,;PCDH15,stop_gained,p.Glu931Ter,ENST00000395446,;PCDH15,stop_gained,p.Glu669Ter,ENST00000395440,;PCDH15,stop_gained,p.Glu600Ter,ENST00000395442,;PCDH15,3_prime_UTR_variant,,ENST00000617271,NM_001142770.1;PCDH15,3_prime_UTR_variant,,ENST00000395438,;PCDH15,3_prime_UTR_variant,,ENST00000409834,;PCDH15,3_prime_UTR_variant,,ENST00000615043,;PCDH15,intron_variant,,ENST00000614895,;PCDH15,intron_variant,,ENST00000373965,NM_001142772.1;PCDH15,intron_variant,,ENST00000414778,;PCDH15,intron_variant,,ENST00000616114,;PCDH15,intron_variant,,ENST00000621708,NM_001142771.1;PCDH15,intron_variant,,ENST00000495484,;PCDH15,intron_variant,,ENST00000618301,;PCDH15,3_prime_UTR_variant,,ENST00000414367,;PCDH15,intron_variant,,ENST00000476074,; A ENST00000613657 Transcript stop_gained 5613/6329 5218/5373 1740/1790 E/* Gag/Tag 1 -1 PCDH15 HGNC HGNC:14674 protein_coding CCDS73138.1 ENSP00000482794 A0A087WZN9 UPI0001884905 NM_001142769.1 37/37 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Low_complexity_(Seg):seg HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 53808847 53808847 C A 1 0 0 0 0 0 1 0 0 11598 835 29 2 2 PCDH15 10 53808847 Nonsense_Mutation SNP C C3N-01030_T 4483436 53808847 79988575 413 21194 BICC1 0 . GRCh38 10 58620901 58620901 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.237G>T p.Lys79Asn p.K79N ENST00000373886 2/21 104 76 28 126 126 0 strelka-varscan-mutect BICC1,missense_variant,p.Lys79Asn,ENST00000373886,NM_001080512.2;BICC1,splice_region_variant,,ENST00000476684,; T ENST00000373886 Transcript missense_variant,splice_region_variant 241/5475 237/2925 79/974 K/N aaG/aaT 1 1 BICC1 HGNC HGNC:19351 protein_coding YES CCDS31206.1 ENSP00000362993 Q9H694 UPI000059D156 NM_001080512.2 tolerated(0.11) 2/21 Gene3D:3.30.1370.10,hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF38,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 2 1 PASS . . 0 204 2 4 0 0 0 0 -20 0.9999107 1 1 1 0 T 3 4 70 58620901 58620901 G T 1 0 0 0 0 1 0 0 0 1576 1014 35 2 2 BICC1 10 58620901 Missense_Mutation SNP G C3N-01030_T 4812054 58620901 75176521 414 21195 TMEM26 0 . GRCh38 10 61410347 61410347 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.1082C>A p.Ser361Tyr p.S361Y ENST00000399298 6/6 110 83 27 101 101 0 strelka-varscan-mutect TMEM26,missense_variant,p.Ser361Tyr,ENST00000399298,NM_178505.6;TMEM26,downstream_gene_variant,,ENST00000277749,;TMEM26,non_coding_transcript_exon_variant,,ENST00000507507,;TMEM26,missense_variant,p.Ser361Tyr,ENST00000503886,;TMEM26,downstream_gene_variant,,ENST00000488505,; T ENST00000399298 Transcript missense_variant 1451/5151 1082/1107 361/368 S/Y tCc/tAc COSM684772 1 -1 TMEM26 HGNC HGNC:28550 protein_coding YES CCDS41530.1 ENSP00000382237 Q6ZUK4 UPI00001C0B3F NM_178505.6 deleterious_low_confidence(0.02) 6/6 hmmpanther:PTHR22168,hmmpanther:PTHR22168:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 61410347 61410347 G T 1 0 0 0 0 1 0 0 0 16620 1174 41 2 2 TMEM26 10 61410347 Missense_Mutation SNP G C3N-01030_T 2789446 61410347 72387075 415 21196 KCNMA1 0 . GRCh38 10 77108507 77108508 + Frame_Shift_Ins INS - - C novel C3N-01030_T C3N-01030_N - - c.1196dupG p.Ser400LeufsTer3 p.S400Lfs*3 ENST00000286628 9/28 309 236 73 329 329 0 sindel-varindel-pindel KCNMA1,frameshift_variant,p.Ser261LeufsTer3,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000286627,NM_002247.3;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000286628,NM_001161352.1;KCNMA1,frameshift_variant,p.Ser232LeufsTer3,ENST00000354353,;KCNMA1,frameshift_variant,p.Ser232LeufsTer3,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000372443,;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000372440,NM_001014797.2;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000404771,;KCNMA1,frameshift_variant,p.Ser374LeufsTer3,ENST00000457953,;KCNMA1,frameshift_variant,p.Ser400LeufsTer3,ENST00000626620,NM_001161353.1;KCNMA1,frameshift_variant,p.Ser335LeufsTer3,ENST00000372437,;KCNMA1,frameshift_variant,p.Ser374LeufsTer3,ENST00000372421,;KCNMA1,frameshift_variant,p.Ser337LeufsTer3,ENST00000372408,;KCNMA1,frameshift_variant,p.Ser351LeufsTer3,ENST00000372403,;KCNMA1,frameshift_variant,p.Ser232LeufsTer3,ENST00000404857,NM_001271518.1;KCNMA1,frameshift_variant,p.Ser79LeufsTer3,ENST00000434208,;KCNMA1,downstream_gene_variant,,ENST00000637862,; C ENST00000286628 Transcript frameshift_variant 1196-1197/6100 1196-1197/3711 399/1236 G/GX ggc/ggGc 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 9/28 hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 70 77108507 77108507 - C 1 0 1 1 0 0 0 0 0 7990 958 34 0 0 KCNMA1 10 77108507 Frame_Shift_Ins INS - C3N-01030_T 15698160 77108507 56688915 416 21197 NUTM2B 0 . GRCh38 10 79706179 79706179 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.520G>T p.Gly174Cys p.G174C ENST00000429828 2/7 241 211 30 192 192 0 varscan-mutect NUTM2B,missense_variant,p.Gly107Cys,ENST00000372321,;NUTM2B,missense_variant,p.Gly174Cys,ENST00000429828,NM_001278495.1;NUTM2B,upstream_gene_variant,,ENST00000342531,;NUTM2B-AS1,intron_variant,,ENST00000601369,;NUTM2B-AS1,intron_variant,,ENST00000600376,;NUTM2B-AS1,intron_variant,,ENST00000596088,; T ENST00000429828 Transcript missense_variant 903/3292 520/2637 174/878 G/C Ggc/Tgc COSM5316975 1 1 NUTM2B HGNC HGNC:23445 protein_coding YES CCDS60574.1 ENSP00000394623 A6NNL0 UPI0000199D26 NM_001278495.1 deleterious(0.02) 2/7 Pfam_domain:PF12881,hmmpanther:PTHR22879 1 MODERATE 1 SNV 5 1 1 PASS rs1342127227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 79706179 79706179 G T 1 0 0 0 0 1 0 0 0 10848 1116 39 1 1 NUTM2B 10 79706179 Missense_Mutation SNP G C3N-01030_T 2597672 79706179 54091243 417 21198 GRID1 0 . GRCh38 10 85647232 85647232 + Nonsense_Mutation SNP G G T rs374077562 C3N-01030_T C3N-01030_N G G c.2163C>A p.Cys721Ter p.C721* ENST00000327946 13/16 129 94 35 106 106 0 strelka-varscan-mutect GRID1,stop_gained,p.Cys721Ter,ENST00000327946,NM_017551.2;RP11-93H12.4,non_coding_transcript_exon_variant,,ENST00000474115,;RN7SKP238,downstream_gene_variant,,ENST00000516483,;GRID1,stop_gained,p.Cys721Ter,ENST00000464741,; T ENST00000327946 Transcript stop_gained 2249/5834 2163/3030 721/1009 C/* tgC/tgA rs374077562,COSM1506024,COSM4016359 1 -1 GRID1 HGNC HGNC:4575 protein_coding YES CCDS31236.1 ENSP00000330148 Q9ULK0 UPI00001D8051 NM_017551.2 13/16 Pfam_domain:PF00060,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF108,SMART_domains:SM00079,Superfamily_domains:SSF53850 0,1,1 HIGH 1 SNV 2 0,1,1 1 PASS rs374077562 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 85647232 85647232 G T 1 0 0 0 0 0 1 0 0 6651 1079 38 1 1 GRID1 10 85647232 Nonsense_Mutation SNP G C3N-01030_T 5941053 85647232 48150190 418 21199 MMRN2 0 . GRCh38 10 86942625 86942625 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.2159G>T p.Gly720Val p.G720V ENST00000372027 6/7 120 91 29 124 124 0 strelka-varscan-mutect MMRN2,missense_variant,p.Gly720Val,ENST00000372027,NM_024756.2;MMRN2,downstream_gene_variant,,ENST00000610081,;MMRN2,downstream_gene_variant,,ENST00000609457,;MMRN2,downstream_gene_variant,,ENST00000474994,;MMRN2,downstream_gene_variant,,ENST00000488950,;MMRN2,downstream_gene_variant,,ENST00000608090,;MMRN2,downstream_gene_variant,,ENST00000608753,; A ENST00000372027 Transcript missense_variant 2481/4375 2159/2850 720/949 G/V gGg/gTg COSM1349427 1 -1 MMRN2 HGNC HGNC:19888 protein_coding YES CCDS7379.1 ENSP00000361097 Q9H8L6 UPI000013F046 NM_024756.2 tolerated(0.37) 6/7 Low_complexity_(Seg):seg,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF6 1 MODERATE 1 SNV 1 1 1 PASS rs765670198 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 86942625 86942625 C A 1 0 0 0 0 1 0 0 0 9634 623 22 2 2 MMRN2 10 86942625 Missense_Mutation SNP C C3N-01030_T 1295393 86942625 46854797 419 21200 IFIT2 0 . GRCh38 10 89307299 89307299 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1343A>T p.Gln448Leu p.Q448L ENST00000638108 5/5 106 79 27 89 89 0 strelka-varscan-mutect IFIT2,missense_variant,p.Gln448Leu,ENST00000638108,;IFIT2,missense_variant,p.Gln448Leu,ENST00000371826,NM_001547.4;IFIT2,missense_variant,p.Gln448Leu,ENST00000611722,;LIPA,intron_variant,,ENST00000371837,;LIPA,intron_variant,,ENST00000282673,;LIPA,intron_variant,,ENST00000487618,;LIPA,intron_variant,,ENST00000463623,; T ENST00000638108 Transcript missense_variant 2102/3703 1343/1419 448/472 Q/L cAa/cTa 1 1 IFIT2 HGNC HGNC:5409 protein_coding YES CCDS41548.1 ENSP00000490935 UPI000012D3E4 tolerated(0.08) 5/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10271:SF4,hmmpanther:PTHR10271,Gene3D:1.25.40.10 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 89307299 89307299 A T 1 0 0 0 0 1 0 0 0 7423 130 5 4 4 IFIT2 10 89307299 Missense_Mutation SNP A C3N-01030_T 2364674 89307299 44490123 420 21201 BTAF1 0 . GRCh38 10 92026746 92026746 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.5230G>T p.Gly1744Trp p.G1744W ENST00000265990 36/38 66 53 13 69 69 0 strelka-varscan-mutect BTAF1,missense_variant,p.Gly1744Trp,ENST00000265990,NM_003972.2;BTAF1,missense_variant,p.Gly1744Trp,ENST00000544642,; T ENST00000265990 Transcript missense_variant 5538/7250 5230/5550 1744/1849 G/W Ggg/Tgg COSM1349802 1 1 BTAF1 HGNC HGNC:17307 protein_coding YES CCDS7419.1 ENSP00000265990 O14981 Q2M1V9 UPI0000136782 NM_003972.2 deleterious(0) 36/38 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,SMART_domains:SM00490,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999964 1 1 1 0 T 3 4 70 92026746 92026746 G T 1 0 0 0 0 1 0 0 0 1711 1362 47 2 2 BTAF1 10 92026746 Missense_Mutation SNP G C3N-01030_T 2719447 92026746 41770676 421 21202 MARCH5 0 . GRCh38 10 92349704 92349704 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.587A>T p.Glu196Val p.E196V ENST00000358935 5/6 151 117 34 144 144 0 strelka-varscan-mutect MARCH5,missense_variant,p.Glu196Val,ENST00000358935,NM_017824.4;MARCH5,non_coding_transcript_exon_variant,,ENST00000467521,;MARCH5,non_coding_transcript_exon_variant,,ENST00000492319,;MARCH5,downstream_gene_variant,,ENST00000462465,; T ENST00000358935 Transcript missense_variant 919/3926 587/837 196/278 E/V gAg/gTg 1 1 MARCH5 HGNC HGNC:26025 protein_coding YES CCDS7420.1 ENSP00000351813 Q9NX47 UPI000006D0BC NM_017824.4 tolerated(0.21) 5/6 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF70 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 92349704 92349704 A T 1 0 0 0 0 1 0 0 0 9229 304 11 4 4 MARCH5 10 92349704 Missense_Mutation SNP A C3N-01030_T 322958 92349704 41447718 422 21203 CYP2C18 0 . GRCh38 10 94688165 94688165 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.372G>T p.= p.R124R ENST00000285979 3/9 191 147 44 188 188 0 strelka-varscan-mutect CYP2C18,synonymous_variant,p.=,ENST00000285979,NM_000772.2;CYP2C18,synonymous_variant,p.=,ENST00000339022,NM_001128925.1;RP11-400G3.5,synonymous_variant,p.=,ENST00000464755,; T ENST00000285979 Transcript synonymous_variant 571/2418 372/1473 124/490 R cgG/cgT 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 3/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs1252596055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 94688165 94688165 G T 1 0 0 0 0 0 0 0 1 3968 1190 42 2 2 CYP2C18 10 94688165 Silent SNP G C3N-01030_T 2338461 94688165 39109257 423 21204 SORBS1 0 . GRCh38 10 95339274 95339274 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2724G>T p.Arg908Ser p.R908S ENST00000371247 29/33 97 72 25 82 82 0 strelka-varscan-mutect SORBS1,missense_variant,p.Arg908Ser,ENST00000371247,;SORBS1,missense_variant,p.Arg862Ser,ENST00000371227,NM_001290294.1;SORBS1,missense_variant,p.Arg930Ser,ENST00000371246,;SORBS1,missense_variant,p.Arg690Ser,ENST00000371249,NM_015385.3;SORBS1,missense_variant,p.Arg655Ser,ENST00000306402,NM_024991.2,NM_001290295.1;SORBS1,missense_variant,p.Arg1168Ser,ENST00000607232,;SORBS1,missense_variant,p.Arg908Ser,ENST00000361941,NM_001034954.1;SORBS1,missense_variant,p.Arg930Ser,ENST00000277982,NM_001034955.1;SORBS1,missense_variant,p.Arg878Ser,ENST00000354106,NM_001290296.1,NM_001290298.1;SORBS1,missense_variant,p.Arg759Ser,ENST00000371245,NM_001034956.1;SORBS1,missense_variant,p.Arg685Ser,ENST00000371239,NM_001290297.1;SORBS1,missense_variant,p.Arg558Ser,ENST00000371241,NM_006434.2,NM_001034957.1;SORBS1,missense_variant,p.Arg381Ser,ENST00000634504,;SORBS1,downstream_gene_variant,,ENST00000371228,;SORBS1,downstream_gene_variant,,ENST00000474353,; A ENST00000371247 Transcript missense_variant 2914/7354 2724/3879 908/1292 R/S agG/agT 1 -1 SORBS1 HGNC HGNC:14565 protein_coding YES CCDS31255.1 ENSP00000360293 Q9BX66 UPI000013D6B7 deleterious(0.04) 29/33 PROSITE_profiles:PS50002,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF202,Pfam_domain:PF00018,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 95339274 95339274 C A 1 0 0 0 0 1 0 0 0 15249 854 30 2 2 SORBS1 10 95339274 Missense_Mutation SNP C C3N-01030_T 651109 95339274 38458148 424 21205 TLL2 0 . GRCh38 10 96368135 96368135 + Silent SNP G G T rs768503540 C3N-01030_T C3N-01030_N G G c.3001C>A p.= p.R1001R ENST00000357947 21/21 181 146 35 158 158 0 strelka-varscan-mutect TLL2,synonymous_variant,p.=,ENST00000357947,NM_012465.3;TLL2,downstream_gene_variant,,ENST00000506028,; T ENST00000357947 Transcript synonymous_variant 3227/6756 3001/3048 1001/1015 R Cga/Aga rs768503540 1 -1 TLL2 HGNC HGNC:11844 protein_coding YES CCDS7449.1 ENSP00000350630 Q9Y6L7 UPI0000073AEE NM_012465.3 21/21 PROSITE_profiles:PS01180,hmmpanther:PTHR10127:SF638,hmmpanther:PTHR10127,Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS rs768503540 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 96368135 96368135 G T 1 0 0 0 0 0 0 0 1 16392 1124 39 1 1 TLL2 10 96368135 Silent SNP G C3N-01030_T 1028861 96368135 37429287 425 21206 CNNM1 0 . GRCh38 10 99387975 99387975 + Silent SNP G G T rs373509693 C3N-01030_T C3N-01030_N G G c.2496G>T p.= p.T832T ENST00000356713 8/11 59 47 12 49 49 0 strelka-varscan-mutect CNNM1,synonymous_variant,p.=,ENST00000356713,NM_020348.2; T ENST00000356713 Transcript synonymous_variant 2785/5959 2496/2856 832/951 T acG/acT rs373509693 1 1 CNNM1 HGNC HGNC:102 protein_coding YES CCDS7478.2 ENSP00000349147 Q9NRU3 UPI0000E19A44 NM_020348.2 8/11 LOW 1 SNV 1 1 PASS rs373509693 . 0 201 9 0 0 0 0 0 -20 0.9999966 1 1 1 0 T 2 4 70 99387975 99387975 G T 1 0 0 0 0 0 0 0 1 3392 1074 38 1 1 CNNM1 10 99387975 Silent SNP G C3N-01030_T 3019840 99387975 34409447 426 21207 DNMBP 0 . GRCh38 10 99969197 99969197 + Silent SNP G G C novel C3N-01030_T C3N-01030_N G G c.186C>G p.= p.P62P ENST00000324109 3/17 126 98 28 134 134 0 strelka-varscan-mutect DNMBP,synonymous_variant,p.=,ENST00000324109,NM_015221.2; C ENST00000324109 Transcript synonymous_variant 278/6400 186/4734 62/1577 P ccC/ccG 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 3/17 hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834,Gene3D:2.30.30.40,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 99969197 99969197 G C 1 0 0 0 0 0 0 0 1 4487 1335 47 4 4 DNMBP 10 99969197 Silent SNP G C3N-01030_T 581222 99969197 33828225 427 21208 CNNM2 0 . GRCh38 10 102918791 102918791 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.311G>T p.Arg104Leu p.R104L ENST00000369878 1/8 156 118 38 131 131 0 strelka-varscan-mutect CNNM2,missense_variant,p.Arg104Leu,ENST00000369878,NM_017649.4;CNNM2,missense_variant,p.Arg104Leu,ENST00000433628,NM_199076.2;CNNM2,missense_variant,p.Arg104Leu,ENST00000369875,NM_199077.2;RP11-724N1.1,downstream_gene_variant,,ENST00000610034,; T ENST00000369878 Transcript missense_variant 499/15857 311/2628 104/875 R/L cGg/cTg 1 1 CNNM2 HGNC HGNC:103 protein_coding YES CCDS44474.1 ENSP00000358894 Q9H8M5 UPI0000231CA6 NM_017649.4 deleterious(0) 1/8 hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF22 MODERATE 1 SNV 1 1 PASS rs976703670 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 102918791 102918791 G T 1 0 0 0 0 1 0 0 0 3393 1116 39 1 1 CNNM2 10 102918791 Missense_Mutation SNP G C3N-01030_T 2949594 102918791 30878631 428 21209 TCF7L2 0 . GRCh38 10 112951597 112951597 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.371C>T p.Thr124Ile p.T124I ENST00000627217 3/14 177 154 23 93 93 0 strelka-mutect TCF7L2,missense_variant,p.Thr18Ile,ENST00000542695,;TCF7L2,missense_variant,p.Thr124Ile,ENST00000355995,;TCF7L2,missense_variant,p.Thr124Ile,ENST00000543371,;TCF7L2,missense_variant,p.Thr124Ile,ENST00000538897,NM_001198529.1,NM_001146284.1,NM_001198531.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000536810,NM_001146285.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000369397,NM_030756.4;TCF7L2,missense_variant,p.Thr124Ile,ENST00000534894,NM_001198530.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000627217,NM_001146274.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000545257,NM_001198525.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000355717,NM_001146286.1,NM_001146283.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000629706,NM_001198526.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000352065,NM_001198528.1;TCF7L2,missense_variant,p.Thr124Ile,ENST00000369395,NM_001198527.1;TCF7L2,missense_variant,p.Thr71Ile,ENST00000346198,;RP11-57H14.2,intron_variant,,ENST00000369391,; T ENST00000627217 Transcript missense_variant 721/3680 371/1809 124/602 T/I aCc/aTc 1 1 TCF7L2 HGNC HGNC:11641 protein_coding YES CCDS53577.1 ENSP00000486891 Q9NQB0 UPI000002B4A6 NM_001146274.1 tolerated(0.14) 3/14 hmmpanther:PTHR10373,hmmpanther:PTHR10373:SF32,Pfam_domain:PF08347 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 112951597 112951597 C T 1 0 0 0 0 1 0 0 0 16105 507 18 3 3 TCF7L2 10 112951597 Missense_Mutation SNP C C3N-01030_T 10032806 112951597 20845825 429 21210 PNLIPRP1 0 . GRCh38 10 116605448 116605448 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1235C>A p.Thr412Lys p.T412K ENST00000528052 12/13 74 64 10 81 81 0 strelka-varscan-mutect PNLIPRP1,missense_variant,p.Thr412Lys,ENST00000528052,NM_001303135.1;PNLIPRP1,missense_variant,p.Thr412Lys,ENST00000358834,NM_006229.3;PNLIPRP1,missense_variant,p.Thr412Lys,ENST00000534537,;PNLIPRP1,3_prime_UTR_variant,,ENST00000482833,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,downstream_gene_variant,,ENST00000534513,; A ENST00000528052 Transcript missense_variant 1306/1533 1235/1404 412/467 T/K aCa/aAa 1 1 PNLIPRP1 HGNC HGNC:9156 protein_coding YES CCDS7595.1 ENSP00000433933 P54315 UPI000012E6AA NM_001303135.1 tolerated(1) 12/13 Gene3D:2.60.60.20,Pfam_domain:PF01477,PIRSF_domain:PIRSF000865,Prints_domain:PR00821,PROSITE_profiles:PS50095,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF108,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 116605448 116605448 C A 1 0 0 0 0 1 0 0 0 12258 478 17 2 2 PNLIPRP1 10 116605448 Missense_Mutation SNP C C3N-01030_T 3653851 116605448 17191974 430 21211 TACC2 0 . GRCh38 10 122084421 122084421 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1921G>C p.Ala641Pro p.A641P ENST00000369005 4/23 249 179 70 217 217 0 strelka-varscan-mutect TACC2,missense_variant,p.Ala641Pro,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Ala641Pro,ENST00000334433,;TACC2,missense_variant,p.Ala641Pro,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Ala641Pro,ENST00000453444,;TACC2,missense_variant,p.Ala641Pro,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; C ENST00000369005 Transcript missense_variant 2261/9673 1921/8847 641/2948 A/P Gct/Cct 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 tolerated(1) 4/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS rs1311374362 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 122084421 122084421 G C 1 0 0 0 0 1 0 0 0 15898 1319 46 4 4 TACC2 10 122084421 Missense_Mutation SNP G C3N-01030_T 5478973 122084421 11713001 431 21212 DPYSL4 0 . GRCh38 10 132194846 132194846 + Missense_Mutation SNP G G T rs762781240 C3N-01030_T C3N-01030_N G G c.315G>T p.Leu105Phe p.L105F ENST00000338492 4/14 92 72 20 78 78 0 strelka-varscan-mutect DPYSL4,missense_variant,p.Leu105Phe,ENST00000338492,NM_006426.2;DPYSL4,missense_variant,p.Leu28Phe,ENST00000368627,;DPYSL4,splice_region_variant,,ENST00000493882,;DPYSL4,downstream_gene_variant,,ENST00000493927,; T ENST00000338492 Transcript missense_variant,splice_region_variant 479/2729 315/1719 105/572 L/F ttG/ttT rs762781240 1 1 DPYSL4 HGNC HGNC:3016 protein_coding YES CCDS7665.1 ENSP00000339850 O14531 UPI000013DC70 NM_006426.2 deleterious(0.03) 4/14 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11647,hmmpanther:PTHR11647:SF55,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02033 MODERATE 1 SNV 1 1 PASS rs762781240 . 0 202 8 0 0 0 0 0 -20 0.9999991 1 1 1 0 T 3 4 70 132194846 132194846 G T 1 0 0 0 0 1 0 0 0 4564 1362 47 2 2 DPYSL4 10 132194846 Missense_Mutation SNP G C3N-01030_T 10110425 132194846 1602576 432 21213 LRRC27 0 . GRCh38 10 132365487 132365489 + In_Frame_Del DEL AAG AAG - novel C3N-01030_T C3N-01030_N AAG AAG c.1357_1359delAGA p.Arg453del p.R453del ENST00000368614 10/11 316 287 29 340 340 0 sindel-varindel-pindel LRRC27,inframe_deletion,p.Arg453del,ENST00000368614,NM_030626.2;LRRC27,inframe_deletion,p.Arg453del,ENST00000368613,NM_001143757.1;LRRC27,inframe_deletion,p.Arg391del,ENST00000368612,;LRRC27,non_coding_transcript_exon_variant,,ENST00000462656,;LRRC27,non_coding_transcript_exon_variant,,ENST00000472556,;LRRC27,non_coding_transcript_exon_variant,,ENST00000487000,;LRRC27,non_coding_transcript_exon_variant,,ENST00000476889,;LRRC27,downstream_gene_variant,,ENST00000472387,;LRRC27,non_coding_transcript_exon_variant,,ENST00000475747,; - ENST00000368614 Transcript inframe_deletion 1458-1460/6374 1353-1355/1593 451-452/530 QR/Q caAAGa/caa 1 1 LRRC27 HGNC HGNC:29346 protein_coding YES CCDS31316.1 ENSP00000357603 Q9C0I9 A0A140VJN2 UPI0000141386 NM_030626.2 10/11 MODERATE 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 132365487 132365487 AAG - 1 0 1 0 1 0 0 0 0 8876 11 1 0 0 LRRC27 10 132365487 In_Frame_Del DEL AAG C3N-01030_T 170641 132365487 1431935 433 21214 MUC5B 0 . GRCh38 11 1255136 1255136 + Missense_Mutation SNP G G T rs201710759 C3N-01030_T C3N-01030_N G G c.15760G>T p.Asp5254Tyr p.D5254Y ENST00000529681 36/49 211 164 47 119 118 1 strelka-varscan-mutect MUC5B,missense_variant,p.Asp5254Tyr,ENST00000529681,NM_002458.2;MUC5B,upstream_gene_variant,,ENST00000526859,;MIR6744,upstream_gene_variant,,ENST00000619480,;MUC5B,upstream_gene_variant,,ENST00000527802,; T ENST00000529681 Transcript missense_variant 15818/17911 15760/17289 5254/5762 D/Y Gac/Tac rs201710759 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 deleterious(0.03) 36/49 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF269 MODERATE 1 SNV 5 1 PASS rs201710759 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 1255136 1255136 G T 1 0 0 0 0 1 0 0 0 9979 1058 37 1 1 MUC5B 11 1255136 Missense_Mutation SNP G C3N-01030_T 1255136 133831486 434 21215 OR52A5 0 . GRCh38 11 5132160 5132160 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.483C>T p.= p.S161S ENST00000307388 1/1 170 141 29 183 183 0 strelka-varscan-mutect OR52A5,synonymous_variant,p.=,ENST00000307388,NM_001005160.2; A ENST00000307388 Transcript synonymous_variant 483/951 483/951 161/316 S tcC/tcT 1 -1 OR52A5 HGNC HGNC:19580 protein_coding YES CCDS31373.1 ENSP00000303469 Q9H2C5 A0A126GWD2 UPI0000046AEF NM_001005160.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF48,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs1453837989 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 5132160 5132160 G A 1 0 0 0 0 0 0 0 1 11183 987 35 3 3 OR52A5 11 5132160 Silent SNP G C3N-01030_T 3877024 5132160 129954462 435 21216 TRIM22 0 . GRCh38 11 5709630 5709630 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.1479G>A p.= p.V493V ENST00000379965 8/8 77 64 13 82 82 0 strelka-varscan-mutect TRIM22,synonymous_variant,p.=,ENST00000379965,NM_001199573.1,NM_006074.4;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM22,intron_variant,,ENST00000444844,;TRIM22,intron_variant,,ENST00000429063,;TRIM5,intron_variant,,ENST00000412903,;TRIM22,intron_variant,,ENST00000450670,;TRIM22,downstream_gene_variant,,ENST00000454828,;TRIM22,downstream_gene_variant,,ENST00000480395,;TRIM22,downstream_gene_variant,,ENST00000414897,;TRIM22,downstream_gene_variant,,ENST00000493494,; A ENST00000379965 Transcript synonymous_variant 1756/2989 1479/1497 493/498 V gtG/gtA 1 1 TRIM22 HGNC HGNC:16379 protein_coding YES CCDS41612.1 ENSP00000369299 Q8IYM9 UPI0000074222 NM_001199573.1,NM_006074.4 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF416,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 5709630 5709630 G A 1 0 0 0 0 0 0 0 1 16985 1364 48 3 3 TRIM22 11 5709630 Silent SNP G C3N-01030_T 577470 5709630 129376992 436 21217 OR52E4 0 . GRCh38 11 5884698 5884698 + Missense_Mutation SNP A A G C3N-01030_T C3N-01030_N A A c.406A>G p.Met136Val p.M136V ENST00000316987 1/1 265 233 32 264 264 0 strelka-varscan-mutect OR52E4,missense_variant,p.Met136Val,ENST00000316987,NM_001005165.1;TRIM5,intron_variant,,ENST00000412903,; G ENST00000316987 Transcript missense_variant 428/1030 406/939 136/312 M/V Atg/Gtg COSM1508974 1 1 OR52E4 HGNC HGNC:15213 protein_coding YES CCDS31401.1 ENSP00000321426 Q8NGH9 UPI0000041BE2 NM_001005165.1 tolerated(0.2) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF13,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 5884698 5884698 A G 1 0 0 0 0 1 0 0 0 11188 217 8 5 5 OR52E4 11 5884698 Missense_Mutation SNP A C3N-01030_T 175068 5884698 129201924 437 21218 OR56A5 0 . GRCh38 11 5967836 5967836 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.659C>T p.Ser220Phe p.S220F ENST00000532411 1/1 254 176 78 225 225 0 strelka-varscan-mutect OR56A5,missense_variant,p.Ser220Phe,ENST00000532411,NM_001146033.1;OR56A5,missense_variant,p.Ser152Phe,ENST00000340110,; A ENST00000532411 Transcript missense_variant 659/942 659/942 220/313 S/F tCt/tTt 1 -1 OR56A5 HGNC HGNC:14792 protein_coding YES CCDS73248.1 ENSP00000481594 P0C7T3 A0A126GWP3 UPI00006C10F9 NM_001146033.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF60,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1296334592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 5967836 5967836 G A 1 0 0 0 0 1 0 0 0 11208 942 33 3 3 OR56A5 11 5967836 Missense_Mutation SNP G C3N-01030_T 83138 5967836 129118786 438 21219 DCHS1 0 . GRCh38 11 6622164 6622164 + Missense_Mutation SNP G G T rs748691401 C3N-01030_T C3N-01030_N G G c.9512C>A p.Pro3171His p.P3171H ENST00000299441 21/21 169 150 19 134 134 0 strelka-varscan-mutect DCHS1,missense_variant,p.Pro3171His,ENST00000299441,NM_003737.3;TPP1,upstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,upstream_gene_variant,,ENST00000533371,;TPP1,upstream_gene_variant,,ENST00000528657,;TPP1,upstream_gene_variant,,ENST00000436873,;RP11-732A19.5,non_coding_transcript_exon_variant,,ENST00000526456,;RP11-732A19.9,downstream_gene_variant,,ENST00000545572,;TPP1,upstream_gene_variant,,ENST00000534644,;TPP1,upstream_gene_variant,,ENST00000528807,;TPP1,upstream_gene_variant,,ENST00000524903,;TPP1,upstream_gene_variant,,ENST00000524788,;TPP1,upstream_gene_variant,,ENST00000530040,;TPP1,upstream_gene_variant,,ENST00000428886,;TPP1,upstream_gene_variant,,ENST00000531754,;TPP1,upstream_gene_variant,,ENST00000528571,;TPP1,upstream_gene_variant,,ENST00000528917,; T ENST00000299441 Transcript missense_variant 9924/10765 9512/9897 3171/3298 P/H cCt/cAt rs748691401 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0) 21/21 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335 MODERATE 1 SNV 1 1 PASS rs748691401 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 6622164 6622164 G T 1 0 0 0 0 1 0 0 0 4090 1000 35 2 2 DCHS1 11 6622164 Missense_Mutation SNP G C3N-01030_T 654328 6622164 128464458 439 21220 OR10A2 0 . GRCh38 11 6869872 6869872 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.118C>A p.Pro40Thr p.P40T ENST00000307322 1/1 334 244 90 324 323 1 strelka-varscan-mutect OR10A2,missense_variant,p.Pro40Thr,ENST00000307322,NM_001004460.1;RP11-413N10.3,intron_variant,,ENST00000637205,; A ENST00000307322 Transcript missense_variant 180/1053 118/912 40/303 P/T Ccc/Acc 1 1 OR10A2 HGNC HGNC:8161 protein_coding YES CCDS31415.1 ENSP00000303862 Q9H208 UPI000015F21C NM_001004460.1 tolerated(0.08) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 6869872 6869872 C A 1 0 0 0 0 1 0 0 0 10966 623 22 2 2 OR10A2 11 6869872 Missense_Mutation SNP C C3N-01030_T 247708 6869872 128216750 440 21221 NLRP14 0 . GRCh38 11 7042513 7042513 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.487G>T p.Glu163Ter p.E163* ENST00000299481 4/12 218 173 45 269 268 1 strelka-varscan-mutect NLRP14,stop_gained,p.Glu163Ter,ENST00000299481,NM_176822.3; T ENST00000299481 Transcript stop_gained 833/3628 487/3282 163/1093 E/* Gaa/Taa 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 4/12 hmmpanther:PTHR24106:SF154,hmmpanther:PTHR24106,Superfamily_domains:SSF52540 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 7042513 7042513 G T 1 0 0 0 0 0 1 0 0 10513 1175 41 2 2 NLRP14 11 7042513 Nonsense_Mutation SNP G C3N-01030_T 172641 7042513 128044109 441 21222 OR5P2 0 . GRCh38 11 7796035 7796035 + Missense_Mutation SNP C C A rs868368864 C3N-01030_T C3N-01030_N C C c.908G>T p.Arg303Ile p.R303I ENST00000329434 1/1 164 130 34 151 151 0 strelka-varscan-mutect OR5P2,missense_variant,p.Arg303Ile,ENST00000329434,NM_153444.1;RP11-35J10.5,intron_variant,,ENST00000527565,;RP11-494M8.4,intron_variant,,ENST00000529488,; A ENST00000329434 Transcript missense_variant 939/1069 908/969 303/322 R/I aGa/aTa rs868368864,COSM1703548 1 -1 OR5P2 HGNC HGNC:14783 protein_coding YES CCDS7782.1 ENSP00000331823 Q8WZ92 A0A126GVJ7 UPI00000015AC NM_153444.1 deleterious(0.02) 1/1 Pfam_domain:PF13853,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF179,Superfamily_domains:SSF81321 0,1 MODERATE SNV 0,1 1 PASS rs868368864 . 2 194 6 8 0 0 0 0 -20 0.9809941 1 1 1 0 A 3 1 70 7796035 7796035 C A 1 0 0 0 0 1 0 0 0 11247 913 32 2 2 OR5P2 11 7796035 Missense_Mutation SNP C C3N-01030_T 753522 7796035 127290587 442 21223 NLRP10 0 . GRCh38 11 7959651 7959651 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.1961A>G p.Tyr654Cys p.Y654C ENST00000328600 2/2 46 31 15 58 58 0 strelka-varscan-mutect NLRP10,missense_variant,p.Tyr654Cys,ENST00000328600,NM_176821.3;NLRP10,downstream_gene_variant,,ENST00000526590,; C ENST00000328600 Transcript missense_variant 2123/2350 1961/1968 654/655 Y/C tAc/tGc 1 -1 NLRP10 HGNC HGNC:21464 protein_coding YES CCDS7784.1 ENSP00000327763 Q86W26 UPI0000167F6C NM_176821.3 2/2 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 7959651 7959651 T C 1 0 0 0 0 1 0 0 0 10509 1638 57 5 5 NLRP10 11 7959651 Missense_Mutation SNP T C3N-01030_T 163616 7959651 127126971 443 21224 TMEM41B 0 . GRCh38 11 9283495 9283495 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.805C>G p.Leu269Val p.L269V ENST00000528080 7/7 211 184 27 192 192 0 strelka-varscan-mutect TMEM41B,missense_variant,p.Leu269Val,ENST00000528080,NM_015012.3;TMEM41B,missense_variant,p.Leu269Val,ENST00000611268,;TMEM41B,downstream_gene_variant,,ENST00000527813,;Metazoa_SRP,upstream_gene_variant,,ENST00000613468,;TMEM41B,missense_variant,p.Leu269Val,ENST00000299596,;TMEM41B,3_prime_UTR_variant,,ENST00000524543,;TMEM41B,non_coding_transcript_exon_variant,,ENST00000533867,; C ENST00000528080 Transcript missense_variant 1144/3968 805/876 269/291 L/V Ctg/Gtg 1 -1 TMEM41B HGNC HGNC:28948 protein_coding YES CCDS31424.1 ENSP00000433126 Q5BJD5 UPI00001C1EF6 NM_015012.3 deleterious(0.05) 7/7 hmmpanther:PTHR12677,hmmpanther:PTHR12677:SF15,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1251987984 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 9283495 9283495 G C 1 0 0 0 0 1 0 0 0 16642 933 33 4 4 TMEM41B 11 9283495 Missense_Mutation SNP G C3N-01030_T 1323844 9283495 125803127 444 21225 MRVI1 0 . GRCh38 11 10626581 10626581 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.753C>A p.Asn251Lys p.N251K ENST00000423302 9/21 71 48 23 38 38 0 strelka-varscan-mutect MRVI1,missense_variant,p.Asn251Lys,ENST00000423302,NM_130385.3;MRVI1,missense_variant,p.Asn243Lys,ENST00000531107,NM_001098579.2;MRVI1,missense_variant,p.Asn160Lys,ENST00000527509,NM_001100163.2;MRVI1,splice_region_variant,,ENST00000547195,NM_001206881.1;MRVI1,splice_region_variant,,ENST00000424001,;MRVI1,splice_region_variant,,ENST00000558540,NM_001100167.2;MRVI1,splice_region_variant,,ENST00000534266,;MRVI1,intron_variant,,ENST00000541483,NM_001206880.1;MRVI1,downstream_gene_variant,,ENST00000532037,;MRVI1,splice_region_variant,,ENST00000529448,;MRVI1,intron_variant,,ENST00000526414,;MRVI1,intron_variant,,ENST00000533631,; T ENST00000423302 Transcript missense_variant,splice_region_variant 903/6126 753/2739 251/912 N/K aaC/aaA 1 -1 MRVI1 HGNC HGNC:7237 protein_coding YES CCDS55746.1 ENSP00000412130 Q9Y6F6 UPI0001F78343 NM_130385.3 deleterious(0.04) 9/21 hmmpanther:PTHR15352,hmmpanther:PTHR15352:SF2 MODERATE 1 SNV 2 1 PASS rs1436996576 . 0 199 9 2 0 0 0 0 -20 0.9998938 1 1 1 0 T 3 4 70 10626581 10626581 G T 1 0 0 0 0 1 0 0 0 9830 1159 40 1 1 MRVI1 11 10626581 Missense_Mutation SNP G C3N-01030_T 1343086 10626581 124460041 445 21226 RASSF10 0 . GRCh38 11 13010635 13010635 + Missense_Mutation SNP A A C novel C3N-01030_T C3N-01030_N A A c.1059A>C p.Glu353Asp p.E353D ENST00000529419 1/1 185 131 54 111 110 1 strelka-varscan-mutect RASSF10,missense_variant,p.Glu353Asp,ENST00000529419,NM_001080521.2;CTC-497E21.3,upstream_gene_variant,,ENST00000533002,; C ENST00000529419 Transcript missense_variant 1059/2530 1059/1524 353/507 E/D gaA/gaC 1 1 RASSF10 HGNC HGNC:33984 protein_coding YES ENSP00000485526 A6NK89 UPI0001722D5E NM_001080521.2 deleterious(0.01) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF13 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 13010635 13010635 A C 1 0 0 0 0 1 0 0 0 13246 40 2 5 5 RASSF10 11 13010635 Missense_Mutation SNP A C3N-01030_T 2384054 13010635 122075987 446 21227 RASSF10 0 . GRCh38 11 13010969 13010969 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1393G>A p.Asp465Asn p.D465N ENST00000529419 1/1 221 193 28 140 140 0 strelka-varscan-mutect RASSF10,missense_variant,p.Asp465Asn,ENST00000529419,NM_001080521.2;CTC-497E21.3,upstream_gene_variant,,ENST00000533002,; A ENST00000529419 Transcript missense_variant 1393/2530 1393/1524 465/507 D/N Gac/Aac 1 1 RASSF10 HGNC HGNC:33984 protein_coding YES ENSP00000485526 A6NK89 UPI0001722D5E NM_001080521.2 tolerated(0.44) 1/1 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF13 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 13010969 13010969 G A 1 0 0 0 0 1 0 0 0 13246 1058 37 1 1 RASSF10 11 13010969 Missense_Mutation SNP G C3N-01030_T 334 13010969 122075653 447 21228 SPON1 0 . GRCh38 11 14259625 14259625 + Missense_Mutation SNP C C G C3N-01030_T C3N-01030_N C C c.1755C>G p.Ile585Met p.I585M ENST00000576479 13/16 190 144 46 150 150 0 strelka-varscan-mutect SPON1,missense_variant,p.Ile585Met,ENST00000576479,NM_006108.3;RP11-21L19.1,downstream_gene_variant,,ENST00000534587,;SPON1,upstream_gene_variant,,ENST00000591785,; G ENST00000576479 Transcript missense_variant 1971/4837 1755/2424 585/807 I/M atC/atG COSM5577770 1 1 SPON1 HGNC HGNC:11252 protein_coding YES CCDS73262.1 ENSP00000460236 Q9HCB6 UPI000044404A NM_006108.3 tolerated(0.12) 13/16 PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF18,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 14259625 14259625 C G 1 0 0 0 0 1 0 0 0 15435 816 29 4 4 SPON1 11 14259625 Missense_Mutation SNP C C3N-01030_T 1248656 14259625 120826997 448 21229 PLEKHA7 0 . GRCh38 11 16816816 16816816 + Missense_Mutation SNP C C A rs746658901 C3N-01030_T C3N-01030_N C C c.1850G>T p.Arg617Leu p.R617L ENST00000355661 11/23 136 112 24 94 93 1 strelka-varscan-mutect PLEKHA7,missense_variant,p.Arg617Leu,ENST00000355661,NM_175058.4;PLEKHA7,missense_variant,p.Arg617Leu,ENST00000531066,;PLEKHA7,missense_variant,p.Arg248Leu,ENST00000530489,;PLEKHA7,missense_variant,p.Arg516Leu,ENST00000637162,;PLEKHA7,intron_variant,,ENST00000532079,;PLEKHA7,upstream_gene_variant,,ENST00000636113,;PLEKHA7,upstream_gene_variant,,ENST00000525581,;PLEKHA7,non_coding_transcript_exon_variant,,ENST00000525781,;PLEKHA7,upstream_gene_variant,,ENST00000525049,; A ENST00000355661 Transcript missense_variant 1861/4980 1850/3366 617/1121 R/L cGg/cTg rs746658901 1 -1 PLEKHA7 HGNC HGNC:27049 protein_coding YES CCDS31434.1 ENSP00000347883 Q6IQ23 UPI0000456498 NM_175058.4 tolerated(0.14) 11/23 hmmpanther:PTHR12752:SF4,hmmpanther:PTHR12752 MODERATE 1 SNV 1 1 PASS rs746658901 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 16816816 16816816 C A 1 0 0 0 0 1 0 0 0 12154 652 23 1 1 PLEKHA7 11 16816816 Missense_Mutation SNP C C3N-01030_T 2557191 16816816 118269806 449 21230 OTOG 0 . GRCh38 11 17576597 17576597 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2564C>A p.Pro855His p.P855H ENST00000399391 20/55 188 134 54 153 153 0 strelka-varscan-mutect OTOG,missense_variant,p.Pro843His,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Pro855His,ENST00000399391,NM_001277269.1;OTOG,upstream_gene_variant,,ENST00000342528,; A ENST00000399391 Transcript missense_variant 2564/8778 2564/8778 855/2925 P/H cCc/cAc 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 20/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Gene3D:2.10.25.10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 17576597 17576597 C A 1 0 0 0 0 1 0 0 0 11370 623 22 2 2 OTOG 11 17576597 Missense_Mutation SNP C C3N-01030_T 759781 17576597 117510025 450 21231 OTOG 0 . GRCh38 11 17635705 17635708 + Frame_Shift_Del DEL CAGT CAGT - novel C3N-01030_T C3N-01030_N CAGT CAGT c.7825_7828delCAGT p.Gln2609ValfsTer74 p.Q2609Vfs*74 ENST00000399391 46/55 164 121 43 153 153 0 sindel-varindel-pindel OTOG,frameshift_variant,p.Gln2597ValfsTer74,ENST00000399397,NM_001292063.1;OTOG,frameshift_variant,p.Gln2609ValfsTer74,ENST00000399391,NM_001277269.1;OTOG,frameshift_variant,p.Gln1473ValfsTer?,ENST00000342528,; - ENST00000399391 Transcript frameshift_variant 7825-7828/8778 7825-7828/8778 2609-2610/2925 QC/X CAGTgt/gt 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 46/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 17635705 17635705 CAGT - 1 0 1 0 1 0 0 0 0 11370 595 21 0 0 OTOG 11 17635705 Frame_Shift_Del DEL CAGT C3N-01030_T 59108 17635705 117450917 451 21232 PTPN5 0 . GRCh38 11 18744083 18744083 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.214C>A p.Pro72Thr p.P72T ENST00000358540 4/15 151 118 33 107 107 0 strelka-varscan-mutect PTPN5,missense_variant,p.Pro72Thr,ENST00000396170,NM_001039970.1,NM_001278236.1;PTPN5,missense_variant,p.Pro72Thr,ENST00000358540,NM_032781.3,NM_006906.1;PTPN5,missense_variant,p.Pro48Thr,ENST00000396168,NM_001278238.1,NM_001278239.1;PTPN5,upstream_gene_variant,,ENST00000477854,;RP11-1081L13.4,downstream_gene_variant,,ENST00000527285,;PTPN5,non_coding_transcript_exon_variant,,ENST00000496201,; T ENST00000358540 Transcript missense_variant 645/3135 214/1698 72/565 P/T Cca/Aca 1 -1 PTPN5 HGNC HGNC:9657 protein_coding YES CCDS7845.1 ENSP00000351342 P54829 UPI00001AE663 NM_032781.3,NM_006906.1 tolerated_low_confidence(0.27) 4/15 Low_complexity_(Seg):seg,hmmpanther:PTHR19134:SF40,hmmpanther:PTHR19134,PIRSF_domain:PIRSF001997 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 18744083 18744083 G T 1 0 0 0 0 1 0 0 0 12945 1203 42 2 2 PTPN5 11 18744083 Missense_Mutation SNP G C3N-01030_T 1108378 18744083 116342539 452 21233 NELL1 0 . GRCh38 11 20928385 20928385 + Silent SNP C C A rs746083104 C3N-01030_T C3N-01030_N C C c.987C>A p.= p.A329A ENST00000298925 10/21 406 321 85 380 380 0 strelka-varscan-mutect NELL1,synonymous_variant,p.=,ENST00000298925,NM_001288713.1;NELL1,synonymous_variant,p.=,ENST00000325319,NM_001288714.1;NELL1,synonymous_variant,p.=,ENST00000357134,NM_006157.4;NELL1,synonymous_variant,p.=,ENST00000532434,NM_201551.2;NELL1,non_coding_transcript_exon_variant,,ENST00000528495,; A ENST00000298925 Transcript synonymous_variant 1140/3329 987/2517 329/838 A gcC/gcA rs746083104 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 10/21 Gene3D:2.10.70.10,Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 LOW 1 SNV 2 1 PASS rs746083104 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 20928385 20928385 C A 1 0 0 0 0 0 0 0 1 10364 639 23 1 1 NELL1 11 20928385 Silent SNP C C3N-01030_T 2184302 20928385 114158237 453 21234 NELL1 0 . GRCh38 11 21560358 21560358 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2040C>A p.Asp680Glu p.D680E ENST00000298925 18/21 75 60 15 89 89 0 strelka-varscan-mutect NELL1,missense_variant,p.Asp680Glu,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Asp595Glu,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Asp652Glu,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Asp605Glu,ENST00000532434,NM_201551.2;NELL1,intron_variant,,ENST00000529218,; A ENST00000298925 Transcript missense_variant 2193/3329 2040/2517 680/838 D/E gaC/gaA 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 tolerated(0.08) 18/21 Gene3D:2.10.70.10,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00214 MODERATE 1 SNV 2 1 PASS rs1033687418 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 21560358 21560358 C A 1 0 0 0 0 1 0 0 0 10364 477 17 2 2 NELL1 11 21560358 Missense_Mutation SNP C C3N-01030_T 631973 21560358 113526264 454 21235 SLC17A6 0 . GRCh38 11 22377513 22377513 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.1522C>A p.Pro508Thr p.P508T ENST00000263160 12/12 223 175 48 216 214 2 strelka-varscan-mutect SLC17A6,missense_variant,p.Pro508Thr,ENST00000263160,NM_020346.2; A ENST00000263160 Transcript missense_variant 1959/3949 1522/1749 508/582 P/T Ccg/Acg COSM4795408 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 deleterious(0.01) 12/12 hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201 1 MODERATE 1 SNV 1 1 1 PASS rs1409446098 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 22377513 22377513 C A 1 0 0 0 0 1 0 0 0 14686 623 22 2 2 SLC17A6 11 22377513 Missense_Mutation SNP C C3N-01030_T 817155 22377513 112709109 455 21236 SLC5A12 0 . GRCh38 11 26698441 26698441 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.916C>A p.Pro306Thr p.P306T ENST00000396005 7/15 177 134 43 134 134 0 strelka-varscan-mutect SLC5A12,missense_variant,p.Pro306Thr,ENST00000396005,NM_178498.3;SLC5A12,missense_variant,p.Pro306Thr,ENST00000280467,;SLC5A12,missense_variant,p.Pro118Thr,ENST00000533617,;SLC5A12,missense_variant,p.Pro118Thr,ENST00000527405,; T ENST00000396005 Transcript missense_variant 1226/6250 916/1857 306/618 P/T Cct/Act 1 -1 SLC5A12 HGNC HGNC:28750 protein_coding YES CCDS7860.2 ENSP00000379326 Q1EHB4 UPI000003ED2C NM_178498.3 deleterious(0) 7/15 PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF152,Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 26698441 26698441 G T 1 0 0 0 0 1 0 0 0 14947 1232 43 2 2 SLC5A12 11 26698441 Missense_Mutation SNP G C3N-01030_T 4320928 26698441 108388181 456 21237 DCDC1 0 . GRCh38 11 30931822 30931822 + Missense_Mutation SNP T T G novel C3N-01030_T C3N-01030_N T T c.167A>C p.Asn56Thr p.N56T ENST00000406071 3/20 177 135 42 180 180 0 strelka-varscan-mutect DCDC1,missense_variant,p.Asn949Thr,ENST00000597505,;DCDC1,missense_variant,p.Asn56Thr,ENST00000406071,NM_020869.3;DCDC1,non_coding_transcript_exon_variant,,ENST00000437348,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,; G ENST00000406071 Transcript missense_variant 483/4758 167/2673 56/890 N/T aAc/aCc 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 tolerated(0.32) 3/20 PROSITE_profiles:PS50309,hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 30931822 30931822 T G 1 0 0 0 0 1 0 0 0 4086 1725 60 5 5 DCDC1 11 30931822 Missense_Mutation SNP T C3N-01030_T 4233381 30931822 104154800 457 21238 PAX6 0 . GRCh38 11 31794659 31794659 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.695C>T p.Thr232Ile p.T232I ENST00000419022 9/14 350 290 60 322 322 0 strelka-varscan-mutect PAX6,missense_variant,p.Thr232Ile,ENST00000419022,NM_001310158.1,NM_001310161.1,NM_001258462.1;PAX6,missense_variant,p.Thr232Ile,ENST00000606377,NM_001310161.1,NM_001258463.1;PAX6,missense_variant,p.Thr232Ile,ENST00000379129,;PAX6,missense_variant,p.Thr232Ile,ENST00000379107,;PAX6,missense_variant,p.Thr218Ile,ENST00000379132,NM_001127612.1;PAX6,missense_variant,p.Thr218Ile,ENST00000379123,NM_001258464.1,NM_000280.4;PAX6,missense_variant,p.Thr218Ile,ENST00000379109,;PAX6,missense_variant,p.Thr232Ile,ENST00000379115,NM_001604.5;PAX6,missense_variant,p.Thr218Ile,ENST00000241001,;PAX6,missense_variant,p.Thr218Ile,ENST00000379111,NM_001258465.1;PAX6,downstream_gene_variant,,ENST00000455099,;PAX6,non_coding_transcript_exon_variant,,ENST00000471303,;PAX6,non_coding_transcript_exon_variant,,ENST00000531910,;PAX6,non_coding_transcript_exon_variant,,ENST00000530373,;PAX6,non_coding_transcript_exon_variant,,ENST00000533333,;PAX6,non_coding_transcript_exon_variant,,ENST00000470027,;PAX6,non_coding_transcript_exon_variant,,ENST00000494377,;PAX6,non_coding_transcript_exon_variant,,ENST00000464174,;PAX6,upstream_gene_variant,,ENST00000474783,;PAX6,upstream_gene_variant,,ENST00000532916,; A ENST00000419022 Transcript missense_variant 1164/6922 695/1311 232/436 T/I aCc/aTc 1 -1 PAX6 HGNC HGNC:8620 protein_coding YES CCDS31452.1 ENSP00000404100 P26367 F1T0F8 UPI000002B0A0 NM_001310158.1,NM_001310161.1,NM_001258462.1 deleterious(0) 9/14 Gene3D:1.10.10.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF294,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 31794659 31794659 G A 1 0 0 0 0 1 0 0 0 11568 1261 44 3 3 PAX6 11 31794659 Missense_Mutation SNP G C3N-01030_T 862837 31794659 103291963 458 21239 FBXO3 0 . GRCh38 11 33747309 33747309 + Missense_Mutation SNP T T A rs777801349 C3N-01030_T C3N-01030_N T T c.1060A>T p.Ile354Phe p.I354F ENST00000265651 10/11 209 172 37 210 210 0 strelka-varscan-mutect FBXO3,missense_variant,p.Ile349Phe,ENST00000530401,;FBXO3,missense_variant,p.Ile241Phe,ENST00000526785,;FBXO3,missense_variant,p.Ile354Phe,ENST00000534136,;FBXO3,missense_variant,p.Ile354Phe,ENST00000265651,NM_012175.3;FBXO3,missense_variant,p.Ile354Phe,ENST00000448981,NM_033406.2;FBXO3,missense_variant,p.Ile41Phe,ENST00000531080,;FBXO3,missense_variant,p.Ile41Phe,ENST00000532057,;FBXO3,non_coding_transcript_exon_variant,,ENST00000527772,;FBXO3,3_prime_UTR_variant,,ENST00000532927,;FBXO3,non_coding_transcript_exon_variant,,ENST00000530013,; A ENST00000265651 Transcript missense_variant 1079/2397 1060/1416 354/471 I/F Atc/Ttc rs777801349 1 -1 FBXO3 HGNC HGNC:13582 protein_coding YES CCDS7887.1 ENSP00000265651 Q9UK99 UPI000000DB30 NM_012175.3 deleterious(0) 10/11 PROSITE_profiles:PS51087,hmmpanther:PTHR14289,hmmpanther:PTHR14289:SF16,Gene3D:1xvsA00,Pfam_domain:PF04379,Superfamily_domains:SSF110069 MODERATE 1 SNV 1 1 PASS rs777801349 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 33747309 33747309 T A 1 0 0 0 0 1 0 0 0 5602 1493 52 4 4 FBXO3 11 33747309 Missense_Mutation SNP T C3N-01030_T 1952650 33747309 101339313 459 21240 LMO2 0 . GRCh38 11 33859441 33859441 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.599T>A p.Val200Glu p.V200E ENST00000257818 6/6 334 253 81 224 223 1 strelka-varscan-mutect LMO2,missense_variant,p.Val200Glu,ENST00000257818,NM_005574.3;LMO2,missense_variant,p.Val131Glu,ENST00000395833,NM_001142315.1,NM_001142316.1;LMO2,3_prime_UTR_variant,,ENST00000411482,;LMO2,non_coding_transcript_exon_variant,,ENST00000464025,; T ENST00000257818 Transcript missense_variant 1429/2294 599/684 200/227 V/E gTa/gAa 1 -1 LMO2 HGNC HGNC:6642 protein_coding YES CCDS7888.2 ENSP00000257818 P25791 UPI00001F9F84 NM_005574.3 deleterious(0) 6/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF109,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 33859441 33859441 A T 1 0 0 0 0 1 0 0 0 8778 391 14 4 4 LMO2 11 33859441 Missense_Mutation SNP A C3N-01030_T 112132 33859441 101227181 460 21241 CD44 0 . GRCh38 11 35189947 35189947 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.549C>T p.= p.S183S ENST00000428726 5/18 434 319 115 362 362 0 strelka-varscan-mutect CD44,synonymous_variant,p.=,ENST00000263398,NM_001001391.1;CD44,synonymous_variant,p.=,ENST00000428726,NM_000610.3;CD44,synonymous_variant,p.=,ENST00000415148,NM_001001389.1;CD44,synonymous_variant,p.=,ENST00000433892,NM_001001390.1;CD44,synonymous_variant,p.=,ENST00000442151,NM_001202557.1;CD44,synonymous_variant,p.=,ENST00000434472,NM_001202555.1;CD44,synonymous_variant,p.=,ENST00000352818,NM_001202556.1;CD44,synonymous_variant,p.=,ENST00000279452,;CD44,synonymous_variant,p.=,ENST00000531110,;CD44,synonymous_variant,p.=,ENST00000525211,;CD44,synonymous_variant,p.=,ENST00000525685,;CD44,synonymous_variant,p.=,ENST00000526000,;CD44,synonymous_variant,p.=,ENST00000278385,;CD44,synonymous_variant,p.=,ENST00000528455,;CD44,synonymous_variant,p.=,ENST00000531873,;CD44,synonymous_variant,p.=,ENST00000533222,;CD44,synonymous_variant,p.=,ENST00000525688,;CD44,synonymous_variant,p.=,ENST00000527889,;CD44,intron_variant,,ENST00000526669,;CD44,intron_variant,,ENST00000278386,NM_001001392.1;CD44,upstream_gene_variant,,ENST00000524922,;CD44,non_coding_transcript_exon_variant,,ENST00000525209,;CD44,intron_variant,,ENST00000528086,;CD44,3_prime_UTR_variant,,ENST00000425428,;CD44,non_coding_transcript_exon_variant,,ENST00000531118,;CD44,non_coding_transcript_exon_variant,,ENST00000534296,;CD44,non_coding_transcript_exon_variant,,ENST00000525241,; T ENST00000428726 Transcript synonymous_variant 672/3046 549/2229 183/742 S tcC/tcT 1 1 CD44 HGNC HGNC:1681 protein_coding YES CCDS7897.1 ENSP00000398632 P16070 UPI000013D3FE NM_000610.3 5/18 hmmpanther:PTHR10225,hmmpanther:PTHR10225:SF6,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 35189947 35189947 C T 1 0 0 0 0 0 0 0 1 2721 581 21 3 3 CD44 11 35189947 Silent SNP C C3N-01030_T 1330506 35189947 99896675 461 21242 LRRC4C 0 . GRCh38 11 40116219 40116219 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.74C>A p.Pro25His p.P25H ENST00000278198 2/2 120 92 28 113 113 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Pro25His,ENST00000278198,;LRRC4C,missense_variant,p.Pro25His,ENST00000527150,;LRRC4C,missense_variant,p.Pro25His,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Pro25His,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Pro25His,ENST00000619527,;LRRC4C,missense_variant,p.Pro25His,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript missense_variant 2038/4054 74/1923 25/640 P/H cCc/cAc COSM3447230 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 tolerated_low_confidence(0.15) 2/2 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8 1 MODERATE 1 SNV 1 1 1 PASS rs1450656731 . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 40116219 40116219 G T 1 0 0 0 0 1 0 0 0 8903 1232 43 2 2 LRRC4C 11 40116219 Missense_Mutation SNP G C3N-01030_T 4926272 40116219 94970403 462 21243 RAPSN 0 . GRCh38 11 47438805 47438805 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1093C>G p.Leu365Val p.L365V ENST00000298854 7/8 97 64 33 67 67 0 strelka-varscan-mutect RAPSN,missense_variant,p.Leu365Val,ENST00000298854,NM_005055.4;RAPSN,missense_variant,p.Leu312Val,ENST00000524487,;RAPSN,missense_variant,p.Leu306Val,ENST00000352508,NM_032645.4;RAPSN,missense_variant,p.Leu306Val,ENST00000529341,;RAPSN,intron_variant,,ENST00000528356,; C ENST00000298854 Transcript missense_variant 1307/1671 1093/1239 365/412 L/V Ctg/Gtg 1 -1 RAPSN HGNC HGNC:9863 protein_coding YES CCDS7936.1 ENSP00000298854 Q13702 A0A0S2Z4F8 UPI0000071D46 NM_005055.4 tolerated(0.94) 7/8 PROSITE_profiles:PS50089,hmmpanther:PTHR10098,Gene3D:3.30.40.10,Pfam_domain:PF13639,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 47438805 47438805 G C 1 0 0 0 0 1 0 0 0 13210 991 35 4 4 RAPSN 11 47438805 Missense_Mutation SNP G C3N-01030_T 7322586 47438805 87647817 463 21244 FOLH1 0 . GRCh38 11 49146929 49146929 + Missense_Mutation SNP G G A rs200462865 C3N-01030_T C3N-01030_N G G c.2080C>T p.Pro694Ser p.P694S ENST00000256999 19/19 70 57 13 67 67 0 strelka-varscan-mutect FOLH1,missense_variant,p.Pro679Ser,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Pro694Ser,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Pro663Ser,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Pro386Ser,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Pro648Ser,ENST00000533034,NM_001193472.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,; A ENST00000256999 Transcript missense_variant 2341/2635 2080/2253 694/750 P/S Cca/Tca rs200462865 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 19/19 Gene3D:3kasA03,Pfam_domain:PF04253,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF47672 MODERATE 1 SNV 1 1 PASS rs200462865 . 0 202 8 0 0 0 0 0 -20 0.9999988 1 1 1 0 A 3 1 70 49146929 49146929 G A 1 0 0 0 0 1 0 0 0 5840 1174 41 3 3 FOLH1 11 49146929 Missense_Mutation SNP G C3N-01030_T 1708124 49146929 85939693 464 21245 FOLH1 0 . GRCh38 11 49154339 49154339 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1777C>A p.Leu593Ile p.L593I ENST00000256999 16/19 173 134 39 211 211 0 strelka-varscan-mutect FOLH1,missense_variant,p.Leu578Ile,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Leu593Ile,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Leu593Ile,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Leu285Ile,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Leu578Ile,ENST00000533034,NM_001193472.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,;FOLH1,non_coding_transcript_exon_variant,,ENST00000532018,; T ENST00000256999 Transcript missense_variant 2038/2635 1777/2253 593/750 L/I Ctc/Atc 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 tolerated(0.58) 16/19 Gene3D:3.40.630.10,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36 MODERATE 1 SNV 1 1 PASS rs1175189208 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 49154339 49154339 G T 1 0 0 0 0 1 0 0 0 5840 971 34 2 2 FOLH1 11 49154339 Missense_Mutation SNP G C3N-01030_T 7410 49154339 85932283 465 21246 OR8H1 0 . GRCh38 11 56290726 56290726 + Missense_Mutation SNP G G A rs746476605 C3N-01030_T C3N-01030_N G G c.337C>T p.Leu113Phe p.L113F ENST00000313022 1/1 124 111 13 168 168 0 strelka-varscan-mutect OR8H1,missense_variant,p.Leu113Phe,ENST00000313022,NM_001005199.1;OR8H1,missense_variant,p.Leu109Phe,ENST00000610894,; A ENST00000313022 Transcript missense_variant 365/1038 337/936 113/311 L/F Ctt/Ttt rs746476605,COSM3791579 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 0,1 1 PASS rs746476605 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 56290726 56290726 G A 1 0 0 0 0 1 0 0 0 11305 942 33 3 3 OR8H1 11 56290726 Missense_Mutation SNP G C3N-01030_T 7136387 56290726 78795896 466 21247 OR5M9 0 . GRCh38 11 56462697 56462697 + Silent SNP C C A rs373884757 C3N-01030_T C3N-01030_N C C c.705G>T p.= p.A235A ENST00000279791 1/1 120 101 19 132 132 0 strelka-varscan-mutect OR5M9,synonymous_variant,p.=,ENST00000279791,NM_001004743.1; A ENST00000279791 Transcript synonymous_variant 705/933 705/933 235/310 A gcG/gcT rs373884757 1 -1 OR5M9 HGNC HGNC:15294 protein_coding YES CCDS31531.1 ENSP00000279791 Q8NGP3 A0A126GVK6 UPI0000061E81 NM_001004743.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF13,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs373884757 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 56462697 56462697 C A 1 0 0 0 0 0 0 0 1 11246 523 19 1 1 OR5M9 11 56462697 Silent SNP C C3N-01030_T 171971 56462697 78623925 467 21248 SERPING1 0 . GRCh38 11 57614460 57614460 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.1382C>T p.Ala461Val p.A461V ENST00000278407 8/8 208 148 60 158 158 0 strelka-varscan-mutect SERPING1,missense_variant,p.Ala504Val,ENST00000403558,;SERPING1,missense_variant,p.Ala461Val,ENST00000278407,NM_000062.2,NM_001032295.1;SERPING1,missense_variant,p.Ala409Val,ENST00000378324,;SERPING1,missense_variant,p.Ala466Val,ENST00000378323,;SERPING1,missense_variant,p.Ala424Val,ENST00000340687,;SERPING1,3_prime_UTR_variant,,ENST00000619430,;SERPING1,3_prime_UTR_variant,,ENST00000531133,;SERPING1,3_prime_UTR_variant,,ENST00000528996,;SERPING1,3_prime_UTR_variant,,ENST00000531797,;SERPING1,non_coding_transcript_exon_variant,,ENST00000530113,; T ENST00000278407 Transcript missense_variant 1609/2002 1382/1503 461/500 A/V gCc/gTc CM973246 1 1 SERPING1 HGNC HGNC:1228 protein_coding YES CCDS7962.1 ENSP00000278407 P05155 E9KL26 UPI000000123F NM_000062.2,NM_001032295.1 tolerated(0.14) 8/8 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF159,Low_complexity_(Seg):seg,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 57614460 57614460 C T 1 0 0 0 0 1 0 0 0 14392 739 26 3 3 SERPING1 11 57614460 Missense_Mutation SNP C C3N-01030_T 1151763 57614460 77472162 468 21249 OR9Q2 0 . GRCh38 11 58190543 58190543 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.53C>A p.Thr18Asn p.T18N ENST00000311591 1/1 96 72 24 115 115 0 strelka-varscan-mutect OR9Q2,missense_variant,p.Thr18Asn,ENST00000311591,NM_001005283.2; A ENST00000311591 Transcript missense_variant 110/1085 53/945 18/314 T/N aCt/aAt 1 1 OR9Q2 HGNC HGNC:15328 protein_coding YES CCDS31544.1 ENSP00000308714 Q8NGE9 A0A126GW85 UPI0000061ECB NM_001005283.2 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF155,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1216792493 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 58190543 58190543 C A 1 0 0 0 0 1 0 0 0 11322 565 20 2 2 OR9Q2 11 58190543 Missense_Mutation SNP C C3N-01030_T 576083 58190543 76896079 469 21250 OR5B17 0 . GRCh38 11 58358824 58358824 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.246G>T p.= p.G82G ENST00000357377 1/1 173 154 19 204 204 0 strelka-varscan-mutect OR5B17,synonymous_variant,p.=,ENST00000357377,NM_001005489.1;AP000435.3,upstream_gene_variant,,ENST00000528539,; A ENST00000357377 Transcript synonymous_variant 246/946 246/945 82/314 G ggG/ggT 1 -1 OR5B17 HGNC HGNC:15267 protein_coding YES CCDS31548.1 ENSP00000349945 Q8NGF7 A0A126GVL8 UPI0000041DFA NM_001005489.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF185,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 58358824 58358824 C A 1 0 0 0 0 0 0 0 1 11220 494 18 2 2 OR5B17 11 58358824 Silent SNP C C3N-01030_T 168281 58358824 76727798 470 21251 AHNAK 0 . GRCh38 11 62524663 62524663 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.9754G>T p.Ala3252Ser p.A3252S ENST00000378024 5/5 265 203 62 315 315 0 strelka-varscan-mutect AHNAK,missense_variant,p.Ala3252Ser,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; A ENST00000378024 Transcript missense_variant 10029/18787 9754/17673 3252/5890 A/S Gct/Tct 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 tolerated(0.43) 5/5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 62524663 62524663 C A 1 0 0 0 0 1 0 0 0 491 710 25 2 2 AHNAK 11 62524663 Missense_Mutation SNP C C3N-01030_T 4165839 62524663 72561959 471 21252 AHNAK 0 . GRCh38 11 62526241 62526241 + Frame_Shift_Del DEL C C - rs749354718 C3N-01030_T C3N-01030_N C C c.8176delG p.Asp2726MetfsTer39 p.D2726Mfs*39 ENST00000378024 5/5 218 165 53 267 267 0 sindel-varindel-pindel AHNAK,frameshift_variant,p.Asp2726MetfsTer39,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; - ENST00000378024 Transcript frameshift_variant 8451/18787 8176/17673 2726/5890 D/X Gat/at rs749354718 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 62526241 62526241 C - 1 0 1 0 1 0 0 0 0 491 855 30 0 0 AHNAK 11 62526241 Frame_Shift_Del DEL C C3N-01030_T 1578 62526241 72560381 472 21253 SLC22A6 0 . GRCh38 11 62981299 62981299 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.882C>A p.= p.I294I ENST00000377871 5/10 269 227 42 226 226 0 strelka-varscan-mutect SLC22A6,synonymous_variant,p.=,ENST00000377871,NM_004790.4;SLC22A6,synonymous_variant,p.=,ENST00000360421,NM_153276.2;SLC22A6,synonymous_variant,p.=,ENST00000421062,NM_153278.2;SLC22A6,synonymous_variant,p.=,ENST00000458333,NM_153277.2;SLC22A6,non_coding_transcript_exon_variant,,ENST00000537349,;SLC22A6,3_prime_UTR_variant,,ENST00000540654,; T ENST00000377871 Transcript synonymous_variant 1149/2151 882/1692 294/563 I atC/atA 1 -1 SLC22A6 HGNC HGNC:10970 protein_coding YES CCDS31591.1 ENSP00000367102 Q4U2R8 UPI00000747EC NM_004790.4 5/10 PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF231,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 62981299 62981299 G T 1 0 0 0 0 0 0 0 1 14724 1280 45 2 2 SLC22A6 11 62981299 Silent SNP G C3N-01030_T 455058 62981299 72105323 473 21254 MEN1 0 . GRCh38 11 64807672 64807672 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.678G>T p.= p.L226L ENST00000337652 4/10 318 250 68 269 267 2 strelka-varscan-mutect MEN1,synonymous_variant,p.=,ENST00000337652,NM_130803.2;MEN1,synonymous_variant,p.=,ENST00000394374,NM_000244.3,NM_130801.2,NM_130800.2,NM_130802.2;MEN1,synonymous_variant,p.=,ENST00000377326,;MEN1,synonymous_variant,p.=,ENST00000315422,;MEN1,synonymous_variant,p.=,ENST00000394376,NM_130804.2;MEN1,synonymous_variant,p.=,ENST00000377316,;MEN1,synonymous_variant,p.=,ENST00000312049,NM_130799.2;MEN1,synonymous_variant,p.=,ENST00000377321,;MEN1,synonymous_variant,p.=,ENST00000377313,;MEN1,synonymous_variant,p.=,ENST00000440873,;MEN1,synonymous_variant,p.=,ENST00000450708,;MEN1,synonymous_variant,p.=,ENST00000413626,;MAP4K2,upstream_gene_variant,,ENST00000294066,NM_004579.3;MAP4K2,upstream_gene_variant,,ENST00000377350,NM_001307990.1;MAP4K2,upstream_gene_variant,,ENST00000439069,;MEN1,downstream_gene_variant,,ENST00000429702,;MEN1,downstream_gene_variant,,ENST00000424912,;MAP4K2,upstream_gene_variant,,ENST00000468062,;MAP4K2,upstream_gene_variant,,ENST00000482314,;MEN1,upstream_gene_variant,,ENST00000487019,;MAP4K2,upstream_gene_variant,,ENST00000435926,;MAP4K2,upstream_gene_variant,,ENST00000433890,;MEN1,upstream_gene_variant,,ENST00000478548,;MAP4K2,upstream_gene_variant,,ENST00000444560,; A ENST00000337652 Transcript synonymous_variant 1182/3162 678/1848 226/615 L ctG/ctT 1 -1 MEN1 HGNC HGNC:7010 protein_coding YES CCDS8083.1 ENSP00000337088 O00255 UPI0000246DC0 NM_130803.2 4/10 Pfam_domain:PF05053,hmmpanther:PTHR12693,hmmpanther:PTHR12693:SF3 LOW SNV 5 1 PASS rs1466764986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 64807672 64807672 C A 1 0 0 0 0 0 0 0 1 9417 465 17 2 2 MEN1 11 64807672 Silent SNP C C3N-01030_T 1826373 64807672 70278950 474 21255 ZNHIT2 0 . GRCh38 11 65117646 65117646 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.8C>T p.Pro3Leu p.P3L ENST00000310597 1/1 24 20 4 20 20 0 strelka-mutect ZNHIT2,missense_variant,p.Pro3Leu,ENST00000310597,NM_014205.3;ZNHIT2,missense_variant,p.Pro3Leu,ENST00000528598,;MRPL49,upstream_gene_variant,,ENST00000279242,NM_004927.3;TM7SF2,downstream_gene_variant,,ENST00000279263,NM_003273.3;TM7SF2,downstream_gene_variant,,ENST00000345348,NM_001277233.1;FAU,downstream_gene_variant,,ENST00000529259,;TM7SF2,downstream_gene_variant,,ENST00000525385,;TM7SF2,downstream_gene_variant,,ENST00000531321,;TM7SF2,downstream_gene_variant,,ENST00000534371,;FAU,downstream_gene_variant,,ENST00000529639,NM_001997.4;TM7SF2,downstream_gene_variant,,ENST00000526809,;TM7SF2,downstream_gene_variant,,ENST00000529414,;TM7SF2,downstream_gene_variant,,ENST00000524986,;FAU,downstream_gene_variant,,ENST00000531743,;TM7SF2,downstream_gene_variant,,ENST00000528802,;MRPL49,upstream_gene_variant,,ENST00000533943,;TM7SF2,downstream_gene_variant,,ENST00000526085,;TM7SF2,downstream_gene_variant,,ENST00000527968,;FAU,downstream_gene_variant,,ENST00000527548,;FAU,downstream_gene_variant,,ENST00000434372,;MRPL49,upstream_gene_variant,,ENST00000534078,;FAU,downstream_gene_variant,,ENST00000526555,;MRPL49,upstream_gene_variant,,ENST00000526171,;MRPL49,upstream_gene_variant,,ENST00000531705,;FAU,downstream_gene_variant,,ENST00000279259,;TM7SF2,downstream_gene_variant,,ENST00000530750,;FAU,downstream_gene_variant,,ENST00000525297,;AP003068.12,downstream_gene_variant,,ENST00000527789,;MRPL49,upstream_gene_variant,,ENST00000524482,;RP11-399J13.2,upstream_gene_variant,,ENST00000623192,;MRPL49,upstream_gene_variant,,ENST00000528529,;TM7SF2,downstream_gene_variant,,ENST00000531029,;TM7SF2,downstream_gene_variant,,ENST00000533646,;TM7SF2,downstream_gene_variant,,ENST00000530650,;MRPL49,upstream_gene_variant,,ENST00000526319,;TM7SF2,downstream_gene_variant,,ENST00000529601,;TM7SF2,downstream_gene_variant,,ENST00000533766,;FAU,downstream_gene_variant,,ENST00000531357,;TM7SF2,downstream_gene_variant,,ENST00000529292,;TM7SF2,downstream_gene_variant,,ENST00000526048,;TM7SF2,downstream_gene_variant,,ENST00000527851,;TM7SF2,downstream_gene_variant,,ENST00000524690,;TM7SF2,downstream_gene_variant,,ENST00000529233,;TM7SF2,downstream_gene_variant,,ENST00000530892,;SYVN1,downstream_gene_variant,,ENST00000530451,;TM7SF2,downstream_gene_variant,,ENST00000528026,;TM7SF2,downstream_gene_variant,,ENST00000532328,;TM7SF2,downstream_gene_variant,,ENST00000534667,; A ENST00000310597 Transcript missense_variant 63/1306 8/1212 3/403 P/L cCg/cTg 1 -1 ZNHIT2 HGNC HGNC:1177 protein_coding YES CCDS8094.1 ENSP00000308548 Q9UHR6 UPI0000049CD6 NM_014205.3 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR15555,hmmpanther:PTHR15555:SF0 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 65117646 65117646 G A 1 0 0 0 0 1 0 0 0 18800 1116 39 1 1 ZNHIT2 11 65117646 Missense_Mutation SNP G C3N-01030_T 309974 65117646 69968976 475 21256 CATSPER1 0 . GRCh38 11 66021533 66021533 + Silent SNP G G T rs756955557 C3N-01030_T C3N-01030_N G G c.1654C>A p.= p.R552R ENST00000312106 4/12 246 185 61 233 233 0 strelka-varscan-mutect CATSPER1,synonymous_variant,p.=,ENST00000312106,NM_053054.3;CATSPER1,upstream_gene_variant,,ENST00000529244,; T ENST00000312106 Transcript synonymous_variant 1792/2619 1654/2343 552/780 R Cgg/Agg rs756955557 1 -1 CATSPER1 HGNC HGNC:17116 protein_coding YES CCDS8127.1 ENSP00000309052 Q8NEC5 UPI000045651C NM_053054.3 4/12 Low_complexity_(Seg):seg,hmmpanther:PTHR10037:SF216,hmmpanther:PTHR10037,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS rs756955557 . 0 207 0 0 3 0 0 0 -20 0.9867087 1 1 1 0 T 2 4 70 66021533 66021533 G T 1 0 0 0 0 0 0 0 1 2387 1086 38 1 1 CATSPER1 11 66021533 Silent SNP G C3N-01030_T 903887 66021533 69065089 476 21257 TMEM151A 0 . GRCh38 11 66294437 66294437 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.191T>A p.Leu64Gln p.L64Q ENST00000327259 2/2 164 130 34 154 154 0 strelka-varscan-mutect TMEM151A,missense_variant,p.Leu64Gln,ENST00000327259,NM_153266.3; A ENST00000327259 Transcript missense_variant 335/2562 191/1407 64/468 L/Q cTg/cAg 1 1 TMEM151A HGNC HGNC:28497 protein_coding YES CCDS8133.1 ENSP00000326244 Q8N4L1 UPI0000070F9B NM_153266.3 deleterious(0) 2/2 Pfam_domain:PF14857,hmmpanther:PTHR31893,hmmpanther:PTHR31893:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 66294437 66294437 T A 1 0 0 0 0 1 0 0 0 16512 1580 55 4 4 TMEM151A 11 66294437 Missense_Mutation SNP T C3N-01030_T 272904 66294437 68792185 477 21258 KDM2A 0 . GRCh38 11 67215441 67215441 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.588G>T p.= p.V196V ENST00000529006 7/21 89 69 20 96 96 0 strelka-varscan-mutect KDM2A,synonymous_variant,p.=,ENST00000529006,NM_012308.2;KDM2A,synonymous_variant,p.=,ENST00000398645,;KDM2A,synonymous_variant,p.=,ENST00000308783,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000528380,;KDM2A,upstream_gene_variant,,ENST00000531696,;KDM2A,upstream_gene_variant,,ENST00000525379,; T ENST00000529006 Transcript synonymous_variant 1034/6967 588/3489 196/1162 V gtG/gtT 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 7/21 Gene3D:1vrbA01,PROSITE_profiles:PS51184,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,SMART_domains:SM00558,Superfamily_domains:SSF51197 LOW 1 SNV 1 1 PASS rs1376342927 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 67215441 67215441 G T 1 0 0 0 0 0 0 0 1 8042 1333 46 2 2 KDM2A 11 67215441 Silent SNP G C3N-01030_T 921004 67215441 67871181 478 21259 SSH3 0 . GRCh38 11 67311687 67311687 + Nonsense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1780C>T p.Gln594Ter p.Q594* ENST00000308127 14/14 373 324 49 280 279 1 strelka-varscan-mutect SSH3,stop_gained,p.Gln448Ter,ENST00000376757,;SSH3,stop_gained,p.Gln594Ter,ENST00000308127,NM_017857.3;SSH3,stop_gained,p.Gln329Ter,ENST00000308298,;SSH3,downstream_gene_variant,,ENST00000532181,;SSH3,downstream_gene_variant,,ENST00000527821,;SSH3,intron_variant,,ENST00000525913,;SSH3,downstream_gene_variant,,ENST00000529224,;SSH3,downstream_gene_variant,,ENST00000531495,;SSH3,3_prime_UTR_variant,,ENST00000532881,;SSH3,downstream_gene_variant,,ENST00000532600,; T ENST00000308127 Transcript stop_gained 1958/2871 1780/1980 594/659 Q/* Cag/Tag 1 1 SSH3 HGNC HGNC:30581 protein_coding YES CCDS8157.1 ENSP00000312081 Q8TE77 A0A024R5J4 UPI0000038D01 NM_017857.3 14/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 67311687 67311687 C T 1 0 0 0 0 0 1 0 0 15562 827 29 3 3 SSH3 11 67311687 Nonsense_Mutation SNP C C3N-01030_T 96246 67311687 67774935 479 21260 PITPNM1 0 . GRCh38 11 67500221 67500221 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.841G>T p.Ala281Ser p.A281S ENST00000356404 6/24 116 83 33 78 78 0 strelka-varscan-mutect PITPNM1,missense_variant,p.Ala281Ser,ENST00000356404,NM_004910.2;PITPNM1,missense_variant,p.Ala281Ser,ENST00000436757,NM_001130848.1;PITPNM1,missense_variant,p.Ala281Ser,ENST00000534749,;PITPNM1,downstream_gene_variant,,ENST00000528559,;PITPNM1,downstream_gene_variant,,ENST00000533391,;PITPNM1,downstream_gene_variant,,ENST00000524901,;PITPNM1,downstream_gene_variant,,ENST00000532703,;PITPNM1,downstream_gene_variant,,ENST00000527527,;PITPNM1,downstream_gene_variant,,ENST00000527103,;PITPNM1,non_coding_transcript_exon_variant,,ENST00000530381,;PITPNM1,upstream_gene_variant,,ENST00000527370,;PITPNM1,downstream_gene_variant,,ENST00000529203,;PITPNM1,upstream_gene_variant,,ENST00000526602,;PITPNM1,upstream_gene_variant,,ENST00000525568,;PITPNM1,upstream_gene_variant,,ENST00000525521,; A ENST00000356404 Transcript missense_variant 1067/4225 841/3735 281/1244 A/S Gcg/Tcg 1 -1 PITPNM1 HGNC HGNC:9003 protein_coding YES CCDS31620.1 ENSP00000348772 O00562 A0A024R5I7 UPI00001FAD31 NM_004910.2 tolerated(0.63) 6/24 hmmpanther:PTHR10658:SF40,hmmpanther:PTHR10658 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 67500221 67500221 C A 1 0 0 0 0 1 0 0 0 12046 710 25 2 2 PITPNM1 11 67500221 Missense_Mutation SNP C C3N-01030_T 188534 67500221 67586401 480 21261 ANO1 0 . GRCh38 11 70104079 70104079 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.621C>T p.= p.P207P ENST00000355303 4/26 183 146 37 156 155 1 strelka-varscan-mutect ANO1,synonymous_variant,p.=,ENST00000355303,NM_018043.5;ANO1,synonymous_variant,p.=,ENST00000530676,;ANO1,synonymous_variant,p.=,ENST00000316296,;ANO1,synonymous_variant,p.=,ENST00000530480,;ANO1,synonymous_variant,p.=,ENST00000531604,;ANO1,upstream_gene_variant,,ENST00000531349,;ANO1,upstream_gene_variant,,ENST00000529913,; T ENST00000355303 Transcript synonymous_variant 926/4790 621/2961 207/986 P ccC/ccT 1 1 ANO1 HGNC HGNC:21625 protein_coding YES CCDS44663.1 ENSP00000347454 Q5XXA6 UPI000013CE03 NM_018043.5 4/26 Pfam_domain:PF16178,hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF13 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 70104079 70104079 C T 1 0 0 0 0 0 0 0 1 802 581 21 3 3 ANO1 11 70104079 Silent SNP C C3N-01030_T 2603858 70104079 64982543 481 21262 CTTN 0 . GRCh38 11 70433155 70433155 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1210G>T p.Glu404Ter p.E404* ENST00000376561 15/19 193 151 42 142 142 0 strelka-varscan-mutect CTTN,stop_gained,p.Glu441Ter,ENST00000301843,NM_005231.3;CTTN,stop_gained,p.Glu404Ter,ENST00000346329,NM_138565.2;CTTN,stop_gained,p.Glu404Ter,ENST00000376561,NM_001184740.1;CTTN,stop_gained,p.Glu98Ter,ENST00000529736,;CTTN,non_coding_transcript_exon_variant,,ENST00000393747,;CTTN,stop_gained,p.Glu75Ter,ENST00000533931,;CTTN,downstream_gene_variant,,ENST00000527962,;CTTN,downstream_gene_variant,,ENST00000498223,; T ENST00000376561 Transcript stop_gained 1381/2247 1210/1905 404/634 E/* Gag/Tag 1 1 CTTN HGNC HGNC:3338 protein_coding YES CCDS53676.1 ENSP00000365745 Q14247 UPI000006E3C2 NM_001184740.1 15/19 hmmpanther:PTHR10829:SF15,hmmpanther:PTHR10829 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 70433155 70433155 G T 1 0 0 0 0 0 1 0 0 3853 1175 41 2 2 CTTN 11 70433155 Nonsense_Mutation SNP G C3N-01030_T 329076 70433155 64653467 482 21263 PAK1 0 . GRCh38 11 77336283 77336283 + Splice_Site SNP C C A novel C3N-01030_T C3N-01030_N C C c.1217-1G>T p.X406_splice ENST00000278568 55 45 10 56 56 0 strelka-varscan-mutect PAK1,splice_acceptor_variant,,ENST00000356341,NM_002576.4;PAK1,splice_acceptor_variant,,ENST00000530617,;PAK1,splice_acceptor_variant,,ENST00000278568,NM_001128620.1;PAK1,splice_acceptor_variant,,ENST00000528203,;PAK1,splice_acceptor_variant,,ENST00000533285,;PAK1,splice_acceptor_variant,,ENST00000525542,;PAK1,splice_acceptor_variant,,ENST00000527457,;PAK1,splice_acceptor_variant,,ENST00000532991,;PAK1,splice_acceptor_variant,,ENST00000527535,;PAK1,splice_acceptor_variant,,ENST00000532711,; A ENST00000278568 Transcript splice_acceptor_variant -/2543 1217/1662 406/553 1 -1 PAK1 HGNC HGNC:8590 protein_coding YES CCDS44687.1 ENSP00000278568 Q13153 UPI000013DB7F NM_001128620.1 12/15 HIGH 1 SNV 2 1 PASS . . 0 161 42 6 0 0 0 0 -18.17014 0.6086205 0 1 1 0 A 5 1 70 77336283 77336283 C A 1 0 0 0 0 0 0 1 0 11479 811 28 2 2 PAK1 11 77336283 Splice_Site SNP C C3N-01030_T 6903128 77336283 57750339 483 21264 DDIAS 0 . GRCh38 11 82928802 82928802 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.139A>G p.Thr47Ala p.T47A ENST00000533655 4/6 143 112 31 204 204 0 strelka-varscan-mutect DDIAS,missense_variant,p.Thr47Ala,ENST00000533655,NM_145018.3;DDIAS,missense_variant,p.Thr47Ala,ENST00000329143,;DDIAS,missense_variant,p.Thr47Ala,ENST00000525361,;DDIAS,missense_variant,p.Thr47Ala,ENST00000525388,;DDIAS,missense_variant,p.Thr47Ala,ENST00000532277,;DDIAS,missense_variant,p.Thr108Ala,ENST00000532764,;DDIAS,missense_variant,p.Thr47Ala,ENST00000524921,;DDIAS,missense_variant,p.Thr47Ala,ENST00000528262,;DDIAS,missense_variant,p.Thr47Ala,ENST00000532589,;DDIAS,intron_variant,,ENST00000528759,;PRCP,intron_variant,,ENST00000534396,;DDIAS,non_coding_transcript_exon_variant,,ENST00000533750,;DDIAS,non_coding_transcript_exon_variant,,ENST00000528189,; G ENST00000533655 Transcript missense_variant 351/3533 139/2997 47/998 T/A Act/Gct 1 1 DDIAS HGNC HGNC:26351 protein_coding YES CCDS8263.1 ENSP00000435421 Q8IXT1 UPI00001AF966 NM_145018.3 tolerated(0.08) 4/6 hmmpanther:PTHR35537,hmmpanther:PTHR35537:SF1,Pfam_domain:PF08646,Gene3D:2.40.50.140,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 82928802 82928802 A G 1 0 0 0 0 1 0 0 0 4133 391 14 5 5 DDIAS 11 82928802 Missense_Mutation SNP A C3N-01030_T 5592519 82928802 52157820 484 21265 TRIM64B 0 . GRCh38 11 89870698 89870698 + Missense_Mutation SNP C C A rs564890926 C3N-01030_T C3N-01030_N C C c.1273G>T p.Gly425Cys p.G425C ENST00000329862 6/6 238 204 34 288 288 0 varscan-mutect TRIM64B,missense_variant,p.Gly425Cys,ENST00000329862,NM_001164397.1; A ENST00000329862 Transcript missense_variant 1273/2689 1273/1350 425/449 G/C Ggt/Tgt rs564890926,COSM5660772 1 -1 TRIM64B HGNC HGNC:37147 protein_coding YES CCDS53693.1 ENSP00000332969 A6NI03 UPI0001662600 NM_001164397.1 deleterious(0) 6/6 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF354,SMART_domains:SM00449,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs564890926 . 3 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 89870698 89870698 C A 1 0 0 0 0 1 0 0 0 17032 681 24 2 2 TRIM64B 11 89870698 Missense_Mutation SNP C C3N-01030_T 6941896 89870698 45215924 485 21266 FAT3 0 . GRCh38 11 92866924 92866924 + Nonsense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.11392C>T p.Gln3798Ter p.Q3798* ENST00000525166 21/27 190 139 51 121 121 0 strelka-varscan-mutect FAT3,stop_gained,p.Gln3948Ter,ENST00000409404,NM_001008781.2;FAT3,stop_gained,p.Gln3798Ter,ENST00000525166,;FAT3,stop_gained,p.Gln283Ter,ENST00000533797,; T ENST00000525166 Transcript stop_gained 11414/18699 11392/13320 3798/4439 Q/* Cag/Tag 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 21/27 PROSITE_profiles:PS50025,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.120.200,Pfam_domain:PF02210,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 92866924 92866924 C T 1 0 0 0 0 0 1 0 0 5551 595 21 3 3 FAT3 11 92866924 Nonsense_Mutation SNP C C3N-01030_T 2996226 92866924 42219698 486 21267 CEP295 0 . GRCh38 11 93696920 93696920 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2008G>T p.Glu670Ter p.E670* ENST00000325212 15/30 221 163 58 271 270 1 strelka-varscan-mutect CEP295,stop_gained,p.Glu670Ter,ENST00000325212,NM_033395.1;CEP295,stop_gained,p.Glu231Ter,ENST00000531877,;CEP295,intron_variant,,ENST00000531700,;CEP295,upstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000531622,; T ENST00000325212 Transcript stop_gained 2170/8057 2008/7806 670/2601 E/* Gaa/Taa 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 15/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 93696920 93696920 G T 1 0 0 0 0 0 1 0 0 2970 943 33 2 2 CEP295 11 93696920 Nonsense_Mutation SNP G C3N-01030_T 829996 93696920 41389702 487 21268 HEPHL1 0 . GRCh38 11 94075365 94075365 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1696C>A p.Leu566Ile p.L566I ENST00000315765 9/20 146 109 37 120 120 0 strelka-varscan-mutect HEPHL1,missense_variant,p.Leu566Ile,ENST00000315765,NM_001098672.1; A ENST00000315765 Transcript missense_variant 1704/5345 1696/3480 566/1159 L/I Ctc/Atc 1 1 HEPHL1 HGNC HGNC:30477 protein_coding YES CCDS44710.1 ENSP00000313699 Q6MZM0 UPI0000237563 NM_001098672.1 deleterious(0.01) 9/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF655,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 94075365 94075365 C A 1 0 0 0 0 1 0 0 0 6939 681 24 2 2 HEPHL1 11 94075365 Missense_Mutation SNP C C3N-01030_T 378445 94075365 41011257 488 21269 PGR 0 . GRCh38 11 101128828 101128828 + Silent SNP C C A rs770422665 C3N-01030_T C3N-01030_N C C c.243G>T p.= p.S81S ENST00000325455 1/8 319 248 71 276 274 2 strelka-varscan-mutect PGR,synonymous_variant,p.=,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,synonymous_variant,p.=,ENST00000619228,;PGR,synonymous_variant,p.=,ENST00000617858,;PGR,synonymous_variant,p.=,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,NM_001271162.1;PGR,upstream_gene_variant,,ENST00000632634,;RP11-788M5.4,upstream_gene_variant,,ENST00000632820,;PGR,synonymous_variant,p.=,ENST00000534780,;PGR,synonymous_variant,p.=,ENST00000528960,;PGR,synonymous_variant,p.=,ENST00000526300,; A ENST00000325455 Transcript synonymous_variant 1697/13748 243/2802 81/933 S tcG/tcT rs770422665,COSM4860390,COSM685858 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 1/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Pfam_domain:PF02161 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs770422665 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 101128828 101128828 C A 1 0 0 0 0 0 0 0 1 11894 639 23 1 1 PGR 11 101128828 Silent SNP C C3N-01030_T 7053463 101128828 33957794 489 21270 GRIA4 0 . GRCh38 11 105612389 105612389 + Frame_Shift_Del DEL G G - C3N-01030_T C3N-01030_N G G c.202delG p.Val68TrpfsTer12 p.V68Wfs*12 ENST00000282499 3/17 180 141 39 190 190 0 sindel-varindel-pindel GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000393127,NM_001077243.2;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000282499,NM_000829.3;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000530497,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000393125,NM_001077244.1;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000525187,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000428631,NM_001112812.1;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000527669,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000531011,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000531986,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000525921,;GRIA4,frameshift_variant,p.Val68TrpfsTer12,ENST00000527177,;GRIA4,non_coding_transcript_exon_variant,,ENST00000525032,; - ENST00000282499 Transcript frameshift_variant 648/5508 202/2709 68/902 V/X Gtg/tg COSM330781,COSM330782 1 1 GRIA4 HGNC HGNC:4574 protein_coding YES CCDS8333.1 ENSP00000282499 P48058 UPI000013DCE6 NM_000829.3 3/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF100,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 1,1 HIGH 1 deletion 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 105612389 105612389 G - 1 0 1 0 1 0 0 0 0 6650 1377 48 0 0 GRIA4 11 105612389 Frame_Shift_Del DEL G C3N-01030_T 4483561 105612389 29474233 490 21271 CUL5 0 . GRCh38 11 108097659 108097659 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.1929C>T p.= p.L643L ENST00000393094 17/19 87 65 22 135 135 0 strelka-varscan-mutect CUL5,synonymous_variant,p.=,ENST00000393094,NM_003478.3;CUL5,synonymous_variant,p.=,ENST00000531427,; T ENST00000393094 Transcript synonymous_variant 2545/6351 1929/2343 643/780 L ctC/ctT 1 1 CUL5 HGNC HGNC:2556 protein_coding YES CCDS31668.1 ENSP00000376808 Q93034 UPI00001380B0 NM_003478.3 17/19 Gene3D:1.10.10.10,Pfam_domain:PF00888,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF76,Superfamily_domains:SSF75632 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 108097659 108097659 C T 1 0 0 0 0 0 0 0 1 3869 813 29 3 3 CUL5 11 108097659 Silent SNP C C3N-01030_T 2485270 108097659 26988963 491 21272 C11orf53 0 . GRCh38 11 111285779 111285779 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.436C>A p.Gln146Lys p.Q146K ENST00000637637 4/4 101 78 23 112 112 0 strelka-varscan-mutect C11orf53,missense_variant,p.Gln196Lys,ENST00000280325,;C11orf53,missense_variant,p.Gln146Lys,ENST00000637637,NM_198498.2;C11orf53,downstream_gene_variant,,ENST00000635886,; A ENST00000637637 Transcript missense_variant 583/1049 436/711 146/236 Q/K Cag/Aag 1 1 C11orf53 HGNC HGNC:30527 protein_coding YES CCDS31674.1 ENSP00000489630 UPI0000074367 NM_198498.2 tolerated(0.61) 4/4 hmmpanther:PTHR28376 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 111285779 111285779 C A 1 0 0 0 0 1 0 0 0 1786 595 21 2 2 C11orf53 11 111285779 Missense_Mutation SNP C C3N-01030_T 3188120 111285779 23800843 492 21273 CEP164 0 . GRCh38 11 117397286 117397286 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.3474G>A p.= p.L1158L ENST00000278935 27/33 115 85 30 107 107 0 strelka-varscan-mutect CEP164,synonymous_variant,p.=,ENST00000278935,NM_001271933.1,NM_014956.4;CEP164,non_coding_transcript_exon_variant,,ENST00000533706,;CEP164,non_coding_transcript_exon_variant,,ENST00000533223,;CEP164,non_coding_transcript_exon_variant,,ENST00000533675,; A ENST00000278935 Transcript synonymous_variant 3621/5630 3474/4383 1158/1460 L ctG/ctA 1 1 CEP164 HGNC HGNC:29182 protein_coding YES CCDS31683.1 ENSP00000278935 Q9UPV0 UPI00001FA422 NM_001271933.1,NM_014956.4 27/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF27 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 117397286 117397286 G A 1 0 0 0 0 0 0 0 1 2963 1335 47 3 3 CEP164 11 117397286 Silent SNP G C3N-01030_T 6111507 117397286 17689336 493 21274 CRTAM 0 . GRCh38 11 122868029 122868030 + Frame_Shift_Del DEL AC AC - novel C3N-01030_T C3N-01030_N AC AC c.987_988delAC p.Leu330ArgfsTer9 p.L330Rfs*9 ENST00000227348 9/10 91 67 24 165 165 0 sindel-pindel CRTAM,frameshift_variant,p.Leu330ArgfsTer9,ENST00000227348,NM_019604.3;CRTAM,frameshift_variant,p.Leu131ArgfsTer9,ENST00000533709,NM_001304782.1;CRTAM,non_coding_transcript_exon_variant,,ENST00000533416,; - ENST00000227348 Transcript frameshift_variant 1028-1029/2469 981-982/1182 327-328/393 EH/EX gaACac/gaac 1 1 CRTAM HGNC HGNC:24313 protein_coding YES CCDS8437.1 ENSP00000227348 O95727 UPI000013C8B4 NM_019604.3 9/10 hmmpanther:PTHR23277:SF48,hmmpanther:PTHR23277 HIGH 1 deletion 1 6 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 122868029 122868029 AC - 1 0 1 0 1 0 0 0 0 3699 40 2 0 0 CRTAM 11 122868029 Frame_Shift_Del DEL AC C3N-01030_T 5470743 122868029 12218593 494 21275 GRAMD1B 0 . GRCh38 11 123603462 123603462 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.679C>A p.Gln227Lys p.Q227K ENST00000456860 9/21 220 168 52 204 203 1 strelka-varscan-mutect GRAMD1B,missense_variant,p.Gln220Lys,ENST00000529750,NM_020716.2;GRAMD1B,missense_variant,p.Gln180Lys,ENST00000529432,NM_001286564.1;GRAMD1B,missense_variant,p.Gln180Lys,ENST00000638157,;GRAMD1B,missense_variant,p.Gln363Lys,ENST00000635736,;GRAMD1B,missense_variant,p.Gln227Lys,ENST00000456860,NM_001286563.1;GRAMD1B,missense_variant,p.Gln249Lys,ENST00000638086,;GRAMD1B,missense_variant,p.Gln220Lys,ENST00000322282,;GRAMD1B,missense_variant,p.Gln216Lys,ENST00000534764,;GRAMD1B,upstream_gene_variant,,ENST00000450171,;GRAMD1B,downstream_gene_variant,,ENST00000633646,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;SF3A3P2,upstream_gene_variant,,ENST00000528675,; A ENST00000456860 Transcript missense_variant 1192/2805 679/2238 227/745 Q/K Cag/Aag 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 deleterious(0.03) 9/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 123603462 123603462 C A 1 0 0 0 0 1 0 0 0 6627 595 21 2 2 GRAMD1B 11 123603462 Missense_Mutation SNP C C3N-01030_T 735433 123603462 11483160 495 21276 OR6X1 0 . GRCh38 11 123754227 123754227 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.292C>A p.Gln98Lys p.Q98K ENST00000327930 1/1 235 177 58 205 205 0 strelka-varscan-mutect OR6X1,missense_variant,p.Gln98Lys,ENST00000327930,NM_001005188.1; T ENST00000327930 Transcript missense_variant 319/1058 292/939 98/312 Q/K Cag/Aag 1 -1 OR6X1 HGNC HGNC:14737 protein_coding YES CCDS31695.1 ENSP00000333724 Q8NH79 A0A126GVM0 UPI000004B1D5 NM_001005188.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF30,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 123754227 123754227 G T 1 0 0 0 0 1 0 0 0 11282 1328 46 2 2 OR6X1 11 123754227 Missense_Mutation SNP G C3N-01030_T 150765 123754227 11332395 496 21277 OR8D4 0 . GRCh38 11 123906845 123906845 + Silent SNP T T C novel C3N-01030_T C3N-01030_N T T c.414T>C p.= p.P138P ENST00000321355 1/1 135 95 40 182 182 0 strelka-varscan-mutect OR8D4,synonymous_variant,p.=,ENST00000321355,NM_001005197.1; C ENST00000321355 Transcript synonymous_variant 700/1331 414/945 138/314 P ccT/ccC 1 1 OR8D4 HGNC HGNC:14840 protein_coding YES CCDS31698.1 ENSP00000325381 Q8NGM9 UPI0000040A83 NM_001005197.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF21,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS rs1448047921 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 123906845 123906845 T C 1 0 0 0 0 0 0 0 1 11302 1509 53 5 5 OR8D4 11 123906845 Silent SNP T C3N-01030_T 152618 123906845 11179777 497 21278 OR4D5 0 . GRCh38 11 123940056 123940056 + Missense_Mutation SNP C C A rs201503357 C3N-01030_T C3N-01030_N C C c.440C>A p.Ala147Asp p.A147D ENST00000307033 1/1 120 93 27 101 100 1 strelka-varscan-mutect OR4D5,missense_variant,p.Ala147Asp,ENST00000307033,NM_001001965.1;OR6T1,downstream_gene_variant,,ENST00000321252,NM_001005187.1; A ENST00000307033 Transcript missense_variant 514/1095 440/957 147/318 A/D gCc/gAc rs201503357 1 1 OR4D5 HGNC HGNC:14852 protein_coding YES CCDS31699.1 ENSP00000305970 Q8NGN0 A0A126GVD9 UPI000003F227 NM_001001965.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF73,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs201503357 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 123940056 123940056 C A 1 0 0 0 0 1 0 0 0 11134 739 26 2 2 OR4D5 11 123940056 Missense_Mutation SNP C C3N-01030_T 33211 123940056 11146566 498 21279 HEPACAM 0 . GRCh38 11 124923385 124923385 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.758T>A p.Leu253His p.L253H ENST00000298251 4/7 397 312 85 396 396 0 strelka-varscan-mutect HEPACAM,missense_variant,p.Leu253His,ENST00000298251,NM_152722.4;HEPN1,downstream_gene_variant,,ENST00000408930,NM_001037558.2;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; T ENST00000298251 Transcript missense_variant 1164/3602 758/1251 253/416 L/H cTt/cAt 1 -1 HEPACAM HGNC HGNC:26361 protein_coding YES CCDS8456.1 ENSP00000298251 Q14CZ8 UPI000013E4B5 NM_152722.4 deleterious(0) 4/7 hmmpanther:PTHR12080,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 124923385 124923385 A T 1 0 0 0 0 1 0 0 0 6936 72 3 4 4 HEPACAM 11 124923385 Missense_Mutation SNP A C3N-01030_T 983329 124923385 10163237 499 21280 PRDM10 0 . GRCh38 11 129918660 129918660 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.2105A>T p.Lys702Met p.K702M ENST00000358825 15/22 184 129 55 118 118 0 strelka-varscan-mutect PRDM10,missense_variant,p.Lys702Met,ENST00000358825,NM_020228.2;PRDM10,missense_variant,p.Lys698Met,ENST00000360871,NM_199437.1;PRDM10,missense_variant,p.Lys672Met,ENST00000528746,;PRDM10,missense_variant,p.Lys616Met,ENST00000423662,NM_199438.1;PRDM10,missense_variant,p.Lys612Met,ENST00000304538,NM_199439.1;PRDM10,missense_variant,p.Lys616Met,ENST00000526082,;PRDM10,missense_variant,p.Lys415Met,ENST00000533431,; A ENST00000358825 Transcript missense_variant 2337/6322 2105/3483 702/1160 K/M aAg/aTg 1 -1 PRDM10 HGNC HGNC:13995 protein_coding YES CCDS44771.1 ENSP00000351686 Q9NQV6 UPI00002371B3 NM_020228.2 deleterious(0.01) 15/22 hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF30 MODERATE 1 SNV 1 1 PASS rs1449976107 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 129918660 129918660 T A 1 0 0 0 0 1 0 0 0 12582 1609 56 4 4 PRDM10 11 129918660 Missense_Mutation SNP T C3N-01030_T 4995275 129918660 5167962 500 21281 APLP2 0 . GRCh38 11 130121669 130121669 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.572G>T p.Gly191Val p.G191V ENST00000263574 5/18 143 98 45 158 158 0 strelka-varscan-mutect APLP2,missense_variant,p.Gly191Val,ENST00000263574,NM_001642.2;APLP2,missense_variant,p.Gly201Val,ENST00000278756,NM_001243299.1;APLP2,missense_variant,p.Gly191Val,ENST00000338167,NM_001142276.1;APLP2,missense_variant,p.Gly191Val,ENST00000528499,NM_001142277.1;APLP2,intron_variant,,ENST00000345598,NM_001142278.1;APLP2,downstream_gene_variant,,ENST00000533713,;APLP2,non_coding_transcript_exon_variant,,ENST00000534001,;APLP2,non_coding_transcript_exon_variant,,ENST00000527702,;APLP2,non_coding_transcript_exon_variant,,ENST00000534761,;APLP2,intron_variant,,ENST00000526330,;APLP2,intron_variant,,ENST00000529701,;APLP2,downstream_gene_variant,,ENST00000529235,;APLP2,downstream_gene_variant,,ENST00000529483,;APLP2,3_prime_UTR_variant,,ENST00000533616,;APLP2,3_prime_UTR_variant,,ENST00000534582,;APLP2,downstream_gene_variant,,ENST00000533618,; T ENST00000263574 Transcript missense_variant 644/3727 572/2292 191/763 G/V gGg/gTg 1 1 APLP2 HGNC HGNC:598 protein_coding YES CCDS8486.1 ENSP00000263574 Q06481 UPI0000125CAE NM_001642.2 deleterious(0) 5/18 Superfamily_domains:0042059,Gene3D:2fmaA00,Pfam_domain:PF12924,hmmpanther:PTHR23103,hmmpanther:PTHR23103:SF14,SMART_domains:SM00006 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 130121669 130121669 G T 1 0 0 0 0 1 0 0 0 901 1232 43 2 2 APLP2 11 130121669 Missense_Mutation SNP G C3N-01030_T 203009 130121669 4964953 501 21282 OPCML 0 . GRCh38 11 132943087 132943087 + Silent SNP C C G novel C3N-01030_T C3N-01030_N C C c.6G>C p.= p.G2G ENST00000331898 1/7 95 78 17 68 68 0 strelka-varscan-mutect OPCML,synonymous_variant,p.=,ENST00000331898,NM_001319106.1,NM_001319105.1,NM_002545.3;OPCML,synonymous_variant,p.=,ENST00000541867,;OPCML,synonymous_variant,p.=,ENST00000612177,;OPCML,intron_variant,,ENST00000524381,NM_001012393.1;OPCML,intron_variant,,ENST00000374778,;OPCML,intron_variant,,ENST00000529038,;OPCML,upstream_gene_variant,,ENST00000525412,; G ENST00000331898 Transcript synonymous_variant 585/6833 6/1038 2/345 G ggG/ggC 1 -1 OPCML HGNC HGNC:8143 protein_coding YES CCDS8492.1 ENSP00000330862 Q14982 A8K0Y0 UPI0000055AE0 NM_001319106.1,NM_001319105.1,NM_002545.3 1/7 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs1270111167 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 132943087 132943087 C G 1 0 0 0 0 0 0 0 1 10951 637 22 4 4 OPCML 11 132943087 Silent SNP C C3N-01030_T 2821418 132943087 2143535 502 21283 NCAPD3 0 . GRCh38 11 134194113 134194113 + Missense_Mutation SNP C C A rs73603039 C3N-01030_T C3N-01030_N C C c.1727G>T p.Gly576Val p.G576V ENST00000534548 15/35 134 107 27 110 110 0 strelka-varscan-mutect NCAPD3,missense_variant,p.Gly576Val,ENST00000534548,NM_015261.2;NCAPD3,missense_variant,p.Gly576Val,ENST00000534532,;NCAPD3,missense_variant,p.Gly576Val,ENST00000525964,; A ENST00000534548 Transcript missense_variant 1792/5061 1727/4497 576/1498 G/V gGc/gTc rs73603039 1 -1 NCAPD3 HGNC HGNC:28952 protein_coding YES CCDS31723.1 ENSP00000433681 P42695 UPI00001C1EFE NM_015261.2 tolerated(0.52) 15/35 hmmpanther:PTHR14222:SF1,hmmpanther:PTHR14222,Gene3D:1.25.10.10,PIRSF_domain:PIRSF036508,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs73603039 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 134194113 134194113 C A 1 0 0 0 0 1 0 0 0 10222 739 26 2 2 NCAPD3 11 134194113 Missense_Mutation SNP C C3N-01030_T 1251026 134194113 892509 503 21284 VWF 0 . GRCh38 12 5991899 5991899 + Missense_Mutation SNP C C A rs748791680 C3N-01030_T C3N-01030_N C C c.6718G>T p.Asp2240Tyr p.D2240Y ENST00000261405 38/52 309 187 122 326 325 1 strelka-varscan-mutect VWF,missense_variant,p.Asp2240Tyr,ENST00000261405,NM_000552.3;VWF,downstream_gene_variant,,ENST00000538635,; A ENST00000261405 Transcript missense_variant 6973/8838 6718/8442 2240/2813 D/Y Gat/Tat rs748791680 1 -1 VWF HGNC HGNC:12726 protein_coding YES CCDS8539.1 ENSP00000261405 P04275 UPI00001AE7EE NM_000552.3 deleterious(0.01) 38/52 hmmpanther:PTHR11339:SF259,hmmpanther:PTHR11339,Pfam_domain:PF01826,Gene3D:2.10.25.10,PIRSF_domain:PIRSF002495,Superfamily_domains:SSF57567 MODERATE 1 SNV 1 1 PASS rs748791680 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 5991899 5991899 C A 1 0 0 0 0 1 0 0 0 17806 913 32 2 2 VWF 12 5991899 Missense_Mutation SNP C C3N-01030_T 5991899 127283410 504 21285 USP5 0 . GRCh38 12 6858610 6858610 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1051C>G p.Gln351Glu p.Q351E ENST00000229268 8/20 50 43 7 35 35 0 strelka-varscan-mutect USP5,missense_variant,p.Gln351Glu,ENST00000229268,NM_001098536.1;USP5,missense_variant,p.Gln351Glu,ENST00000389231,NM_003481.2;USP5,intron_variant,,ENST00000542087,;USP5,upstream_gene_variant,,ENST00000541969,;USP5,non_coding_transcript_exon_variant,,ENST00000537267,;USP5,non_coding_transcript_exon_variant,,ENST00000535080,;USP5,upstream_gene_variant,,ENST00000542371,; G ENST00000229268 Transcript missense_variant 1103/3181 1051/2577 351/858 Q/E Cag/Gag 1 1 USP5 HGNC HGNC:12628 protein_coding YES CCDS41743.1 ENSP00000229268 P45974 A0A140VJZ1 UPI00001379E1 NM_001098536.1 tolerated(0.43) 8/20 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF449,hmmpanther:PTHR24006,PIRSF_domain:PIRSF016308,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -17.23307 1 1 1 1 0 G 3 3 70 6858610 6858610 C G 1 0 0 0 0 1 0 0 0 17624 595 21 4 4 USP5 12 6858610 Missense_Mutation SNP C C3N-01030_T 866711 6858610 126416699 505 21286 TAS2R20 0 . GRCh38 12 10997207 10997207 + Silent SNP G G T rs766164891 C3N-01030_T C3N-01030_N G G c.669C>A p.= p.I223I ENST00000538986 1/1 180 150 30 201 200 1 strelka-varscan-mutect TAS2R20,synonymous_variant,p.=,ENST00000538986,NM_176889.2;PRR4,intron_variant,,ENST00000535024,;PRH1,intron_variant,,ENST00000539853,;TAS2R14,intron_variant,,ENST00000381852,;PRH1,intron_variant,,ENST00000536086,;PRR4,intron_variant,,ENST00000534923,;PRH1,intron_variant,,ENST00000541977,;PRH1-PRR4,intron_variant,,ENST00000536668,; T ENST00000538986 Transcript synonymous_variant 669/1381 669/930 223/309 I atC/atA rs766164891 1 -1 TAS2R20 HGNC HGNC:19109 protein_coding YES CCDS8639.1 ENSP00000441624 P59543 UPI000000D822 NM_176889.2 1/1 hmmpanther:PTHR11394:SF35,hmmpanther:PTHR11394,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS rs766164891 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 10997207 10997207 G T 1 0 0 0 0 0 0 0 1 15970 1164 41 2 2 TAS2R20 12 10997207 Silent SNP G C3N-01030_T 4138597 10997207 122278102 506 21287 TAS2R43 0 . GRCh38 12 11091412 11091412 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.818C>T p.Ser273Leu p.S273L ENST00000531678 1/1 201 124 77 149 149 0 strelka-varscan-mutect TAS2R43,missense_variant,p.Ser273Leu,ENST00000531678,NM_176884.2;PRR4,intron_variant,,ENST00000535024,;TAS2R14,intron_variant,,ENST00000381852,;PRR4,intron_variant,,ENST00000546265,;PRH1,intron_variant,,ENST00000541977,;PRH1-PRR4,intron_variant,,ENST00000536668,; A ENST00000531678 Transcript missense_variant 902/1027 818/930 273/309 S/L tCa/tTa 1 -1 TAS2R43 HGNC HGNC:18875 protein_coding YES CCDS53749.1 ENSP00000431719 P59537 UPI000000D81F NM_176884.2 tolerated(0.13) 1/1 hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF77,Gene3D:1.20.1070.10,Pfam_domain:PF05296,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 14 194 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 11091412 11091412 G A 1 0 0 0 0 1 0 0 0 15980 1294 45 3 3 TAS2R43 12 11091412 Missense_Mutation SNP G C3N-01030_T 94205 11091412 122183897 507 21288 LRP6 0 . GRCh38 12 12162200 12162200 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.2272G>T p.Ala758Ser p.A758S ENST00000261349 10/23 174 89 85 174 174 0 varscan-mutect LRP6,missense_variant,p.Ala758Ser,ENST00000261349,NM_002336.2;LRP6,missense_variant,p.Ala758Ser,ENST00000543091,;LRP6,missense_variant,p.Ala623Ser,ENST00000538239,;BCL2L14,intron_variant,,ENST00000298566,; A ENST00000261349 Transcript missense_variant 2349/10020 2272/4842 758/1613 A/S Gcc/Tcc 1 -1 LRP6 HGNC HGNC:6698 protein_coding YES CCDS8647.1 ENSP00000261349 O75581 UPI00001FB66C NM_002336.2 tolerated(0.46) 10/23 PROSITE_profiles:PS51120,hmmpanther:PTHR10529:SF109,hmmpanther:PTHR10529,PIRSF_domain:PIRSF036314,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 12162200 12162200 C A 1 0 0 0 0 1 0 0 0 8857 710 25 2 2 LRP6 12 12162200 Missense_Mutation SNP C C3N-01030_T 1070788 12162200 121113109 508 21289 ATF7IP 0 . GRCh38 12 14424339 14424339 + Nonsense_Mutation SNP G G T rs767883210 C3N-01030_T C3N-01030_N G G c.448G>T p.Gly150Ter p.G150* ENST00000544627 2/15 202 96 106 195 195 0 strelka-varscan-mutect ATF7IP,stop_gained,p.Gly142Ter,ENST00000261168,NM_018179.4;ATF7IP,stop_gained,p.Gly142Ter,ENST00000536444,NM_001286514.1;ATF7IP,stop_gained,p.Gly142Ter,ENST00000543189,NM_001286515.1;ATF7IP,stop_gained,p.Gly150Ter,ENST00000544627,NM_181352.1;ATF7IP,stop_gained,p.Gly142Ter,ENST00000540793,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000396279,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000539057,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000541056,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000545769,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000542967,;ATF7IP,stop_gained,p.Gly142Ter,ENST00000534828,;ATF7IP,intron_variant,,ENST00000545723,;ATF7IP,intron_variant,,ENST00000538511,;ATF7IP,downstream_gene_variant,,ENST00000542508,;ATF7IP,downstream_gene_variant,,ENST00000542514,;ATF7IP,downstream_gene_variant,,ENST00000542991,;ATF7IP,downstream_gene_variant,,ENST00000535132,;ATF7IP,downstream_gene_variant,,ENST00000536279,;ATF7IP,downstream_gene_variant,,ENST00000428217,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000541654,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000539659,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000537653,; T ENST00000544627 Transcript stop_gained 768/4847 448/3837 150/1278 G/* Gga/Tga rs767883210,COSM344127 1 1 ATF7IP HGNC HGNC:20092 protein_coding YES CCDS66326.1 ENSP00000440440 Q6VMQ6 UPI0001EE42CD NM_181352.1 2/15 Low_complexity_(Seg):seg,hmmpanther:PTHR23210,hmmpanther:PTHR23210:SF22 0,1 HIGH 1 SNV 1 0,1 1 PASS rs767883210 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 14424339 14424339 G T 1 0 0 0 0 0 1 0 0 1236 1117 39 1 1 ATF7IP 12 14424339 Nonsense_Mutation SNP G C3N-01030_T 2262139 14424339 118850970 509 21290 SLCO1A2 0 . GRCh38 12 21295597 21295597 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.1271G>T p.Gly424Val p.G424V ENST00000307378 11/16 53 27 26 122 122 0 varscan-mutect SLCO1A2,missense_variant,p.Gly424Val,ENST00000307378,NM_021094.3,NM_134431.3;SLCO1A2,missense_variant,p.Gly292Val,ENST00000458504,;SLCO1A2,splice_region_variant,,ENST00000463718,;SLCO1A2,splice_region_variant,,ENST00000544290,;SLCO1A2,splice_region_variant,,ENST00000544020,;SLCO1A2,non_coding_transcript_exon_variant,,ENST00000480394,; A ENST00000307378 Transcript missense_variant,splice_region_variant 1992/7682 1271/2013 424/670 G/V gGa/gTa COSM3725427,COSM3725428 1 -1 SLCO1A2 HGNC HGNC:10956 protein_coding YES CCDS8686.1 ENSP00000305974 P46721 A0A024RAT5 UPI0000037575 NM_021094.3,NM_134431.3 deleterious(0) 11/16 Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF16,TIGRFAM_domain:TIGR00805 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 1 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 21295597 21295597 C A 1 0 0 0 0 1 0 0 0 15008 637 22 2 2 SLCO1A2 12 21295597 Missense_Mutation SNP C C3N-01030_T 6871258 21295597 111979712 510 21291 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-01030_T C3N-01030_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 250 126 124 282 282 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-01030_T 3949754 25245351 108029958 511 21292 ADAMTS20 0 . GRCh38 12 43427434 43427434 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.3981G>T p.Arg1327Ser p.R1327S ENST00000389420 27/39 108 90 18 117 116 1 strelka-varscan-mutect ADAMTS20,missense_variant,p.Arg1327Ser,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Arg1327Ser,ENST00000395541,;ADAMTS20,missense_variant,p.Arg1327Ser,ENST00000553158,;ADAMTS20,missense_variant,p.Arg457Ser,ENST00000549670,; A ENST00000389420 Transcript missense_variant 3981/6076 3981/5733 1327/1910 R/S agG/agT 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0) 27/39 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 43427434 43427434 C A 1 0 0 0 0 1 0 0 0 310 622 22 2 2 ADAMTS20 12 43427434 Missense_Mutation SNP C C3N-01030_T 18182083 43427434 89847875 512 21293 NELL2 0 . GRCh38 12 44520142 44520142 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.2413T>A p.Cys805Ser p.C805S ENST00000437801 20/21 96 64 32 141 141 0 strelka-varscan-mutect NELL2,missense_variant,p.Cys755Ser,ENST00000429094,NM_001145108.1;NELL2,missense_variant,p.Cys805Ser,ENST00000437801,NM_001145107.1;NELL2,missense_variant,p.Cys754Ser,ENST00000395487,NM_001145109.1;NELL2,missense_variant,p.Cys755Ser,ENST00000452445,NM_006159.2;NELL2,missense_variant,p.Cys707Ser,ENST00000551601,;NELL2,missense_variant,p.Cys754Ser,ENST00000549027,;NELL2,missense_variant,p.Cys778Ser,ENST00000333837,NM_001145110.1;NELL2,downstream_gene_variant,,ENST00000550139,;NELL2,downstream_gene_variant,,ENST00000547636,; T ENST00000437801 Transcript missense_variant 2785/3279 2413/2601 805/866 C/S Tgt/Agt 1 -1 NELL2 HGNC HGNC:7751 protein_coding YES CCDS44863.1 ENSP00000416341 Q99435 UPI000191537D NM_001145107.1 deleterious(0) 20/21 PROSITE_profiles:PS50184,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF0,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 44520142 44520142 A T 1 0 0 0 0 1 0 0 0 10365 188 7 4 4 NELL2 12 44520142 Missense_Mutation SNP A C3N-01030_T 1092708 44520142 88755167 513 21294 DDN 0 . GRCh38 12 48997874 48997874 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1002A>T p.Gln334His p.Q334H ENST00000421952 2/2 162 126 36 169 169 0 strelka-varscan-mutect DDN,missense_variant,p.Gln334His,ENST00000421952,NM_015086.1;PRKAG1,downstream_gene_variant,,ENST00000548065,NM_002733.4;PRKAG1,downstream_gene_variant,,ENST00000316299,NM_001206709.1;PRKAG1,downstream_gene_variant,,ENST00000547306,;PRKAG1,downstream_gene_variant,,ENST00000552212,NM_001206710.1;PRKAG1,downstream_gene_variant,,ENST00000551770,;PRKAG1,downstream_gene_variant,,ENST00000548362,;RP11-386G11.5,upstream_gene_variant,,ENST00000547866,;RP11-386G11.5,upstream_gene_variant,,ENST00000552933,;RP11-386G11.5,upstream_gene_variant,,ENST00000552284,;RP11-386G11.5,upstream_gene_variant,,ENST00000547395,;RP11-386G11.3,downstream_gene_variant,,ENST00000549516,;PRKAG1,downstream_gene_variant,,ENST00000546531,; A ENST00000421952 Transcript missense_variant 1024/3749 1002/2136 334/711 Q/H caA/caT 1 -1 DDN HGNC HGNC:24458 protein_coding YES CCDS31791.2 ENSP00000390590 O94850 UPI000019821C NM_015086.1 tolerated_low_confidence(0.06) 2/2 Pfam_domain:PF15498,hmmpanther:PTHR16757 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 48997874 48997874 T A 1 0 0 0 0 1 0 0 0 4137 1606 56 4 4 DDN 12 48997874 Missense_Mutation SNP T C3N-01030_T 4477732 48997874 84277435 514 21295 C1QL4 0 . GRCh38 12 49336244 49336244 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.234A>T p.Arg78Ser p.R78S ENST00000334221 1/2 35 28 7 36 36 0 strelka-varscan-mutect C1QL4,missense_variant,p.Arg78Ser,ENST00000334221,NM_001008223.1;TROAP,downstream_gene_variant,,ENST00000551245,;TROAP,downstream_gene_variant,,ENST00000257909,NM_005480.3;TROAP,downstream_gene_variant,,ENST00000547923,; A ENST00000334221 Transcript missense_variant 945/2071 234/717 78/238 R/S agA/agT 1 -1 C1QL4 HGNC HGNC:31416 protein_coding YES CCDS31793.1 ENSP00000335285 Q86Z23 UPI00000033B3 NM_001008223.1 tolerated(0.38) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -18.14705 1 1 1 1 0 A 3 1 70 49336244 49336244 T A 1 0 0 0 0 1 0 0 0 1939 1548 54 4 4 C1QL4 12 49336244 Missense_Mutation SNP T C3N-01030_T 338370 49336244 83939065 515 21296 SLC4A8 0 . GRCh38 12 51505890 51505890 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.3229A>G p.Lys1077Glu p.K1077E ENST00000453097 24/25 96 89 7 111 111 0 strelka-varscan-mutect SLC4A8,missense_variant,p.Lys1077Glu,ENST00000453097,NM_001039960.2;SLC4A8,missense_variant,p.Lys1024Glu,ENST00000358657,NM_001258401.2;SLC4A8,non_coding_transcript_exon_variant,,ENST00000546875,; G ENST00000453097 Transcript missense_variant 3446/11824 3229/3282 1077/1093 K/E Aaa/Gaa 1 1 SLC4A8 HGNC HGNC:11034 protein_coding YES CCDS44890.1 ENSP00000405812 Q2Y0W8 UPI00005E6FB4 NM_001039960.2 deleterious(0) 24/25 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF37 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 51505890 51505890 A G 1 0 0 0 0 1 0 0 0 14936 247 9 5 5 SLC4A8 12 51505890 Missense_Mutation SNP A C3N-01030_T 2169646 51505890 81769419 516 21297 SCN8A 0 . GRCh38 12 51790499 51790499 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.4521C>A p.= p.P1507P ENST00000354534 25/27 224 128 96 169 168 1 strelka-varscan-mutect SCN8A,synonymous_variant,p.=,ENST00000354534,NM_014191.3;SCN8A,synonymous_variant,p.=,ENST00000545061,NM_001177984.2;SCN8A,synonymous_variant,p.=,ENST00000599343,;SCN8A,synonymous_variant,p.=,ENST00000627620,;SCN8A,synonymous_variant,p.=,ENST00000355133,;SCN8A,downstream_gene_variant,,ENST00000548086,;SCN8A,downstream_gene_variant,,ENST00000637540,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,3_prime_UTR_variant,,ENST00000636945,; A ENST00000354534 Transcript synonymous_variant 4699/11556 4521/5943 1507/1980 P ccC/ccA 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 25/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 51790499 51790499 C A 1 0 0 0 0 0 0 0 1 14193 695 24 2 2 SCN8A 12 51790499 Silent SNP C C3N-01030_T 284609 51790499 81484810 517 21298 KRT85 0 . GRCh38 12 52362920 52362920 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.1011G>A p.= p.E337E ENST00000257901 6/9 1024 472 552 497 497 0 strelka-varscan-mutect KRT85,synonymous_variant,p.=,ENST00000257901,NM_002283.3;KRT85,synonymous_variant,p.=,ENST00000544265,NM_001300810.1;KRT85,non_coding_transcript_exon_variant,,ENST00000552537,; T ENST00000257901 Transcript synonymous_variant 1087/2447 1011/1524 337/507 E gaG/gaA 1 -1 KRT85 HGNC HGNC:6462 protein_coding YES CCDS8824.1 ENSP00000257901 P78386 UPI000006EB3B NM_002283.3 6/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01276,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF113,SMART_domains:SM01391 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 52362920 52362920 C T 1 0 0 0 0 0 0 0 1 8381 680 24 3 3 KRT85 12 52362920 Silent SNP C C3N-01030_T 572421 52362920 80912389 518 21299 KRT2 0 . GRCh38 12 52651917 52651917 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.226G>T p.Val76Leu p.V76L ENST00000309680 1/9 287 240 47 121 121 0 strelka-varscan-mutect KRT2,missense_variant,p.Val76Leu,ENST00000309680,NM_000423.2;KRT2,upstream_gene_variant,,ENST00000547106,; A ENST00000309680 Transcript missense_variant 248/2403 226/1920 76/639 V/L Gtg/Ttg 1 -1 KRT2 HGNC HGNC:6439 protein_coding YES CCDS8835.1 ENSP00000310861 P35908 UPI0000367804 NM_000423.2 tolerated(0.15) 1/9 hmmpanther:PTHR23239:SF134,hmmpanther:PTHR23239,Pfam_domain:PF16208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 52651917 52651917 C A 1 0 0 0 0 1 0 0 0 8339 478 17 2 2 KRT2 12 52651917 Missense_Mutation SNP C C3N-01030_T 288997 52651917 80623392 519 21300 KRT77 0 . GRCh38 12 52696378 52696378 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.811C>A p.Leu271Met p.L271M ENST00000341809 3/9 122 92 30 151 151 0 strelka-varscan-mutect KRT77,missense_variant,p.Leu271Met,ENST00000341809,NM_175078.2;RP11-641A6.3,splice_acceptor_variant,,ENST00000547533,;KRT77,3_prime_UTR_variant,,ENST00000553168,;KRT77,upstream_gene_variant,,ENST00000550823,; T ENST00000341809 Transcript missense_variant 840/3305 811/1737 271/578 L/M Ctg/Atg 1 -1 KRT77 HGNC HGNC:20411 protein_coding YES CCDS8837.1 ENSP00000342710 Q7Z794 UPI00001D797A NM_175078.2 deleterious(0.01) 3/9 hmmpanther:PTHR23239:SF87,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391,Prints_domain:PR01276 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 52696378 52696378 G T 1 0 0 0 0 1 0 0 0 8372 991 35 2 2 KRT77 12 52696378 Missense_Mutation SNP G C3N-01030_T 44461 52696378 80578931 520 21301 HOXC12 0 . GRCh38 12 53955233 53955233 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.304G>T p.Gly102Cys p.G102C ENST00000243103 1/2 78 60 18 90 90 0 strelka-varscan-mutect HOXC12,missense_variant,p.Gly102Cys,ENST00000243103,NM_173860.1; T ENST00000243103 Transcript missense_variant 400/3335 304/849 102/282 G/C Ggt/Tgt 1 1 HOXC12 HGNC HGNC:5124 protein_coding YES CCDS8866.1 ENSP00000243103 P31275 UPI000012CF7E NM_173860.1 deleterious(0.01) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF164,hmmpanther:PTHR24326 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 53955233 53955233 G T 1 0 0 0 0 1 0 0 0 7205 1232 43 2 2 HOXC12 12 53955233 Missense_Mutation SNP G C3N-01030_T 1258855 53955233 79320076 521 21302 PDE1B 0 . GRCh38 12 54549979 54549979 + Missense_Mutation SNP G G T rs761218249 C3N-01030_T C3N-01030_N G G c.107G>T p.Arg36Leu p.R36L ENST00000243052 2/16 89 66 23 71 71 0 strelka-varscan-mutect PDE1B,missense_variant,p.Arg36Leu,ENST00000243052,NM_000924.3;NCKAP1L,downstream_gene_variant,,ENST00000293373,NM_005337.4;PDE1B,upstream_gene_variant,,ENST00000538346,NM_001288768.1,NM_001288769.1;PDE1B,missense_variant,p.Arg36Leu,ENST00000550285,;PDE1B,missense_variant,p.Arg36Leu,ENST00000611899,;PDE1B,non_coding_transcript_exon_variant,,ENST00000548855,; T ENST00000243052 Transcript missense_variant 543/3444 107/1611 36/536 R/L cGg/cTg rs761218249,COSM5461158 1 1 PDE1B HGNC HGNC:8775 protein_coding YES CCDS8882.1 ENSP00000243052 Q01064 A0A024RB59 UPI0000001607 NM_000924.3 tolerated(0.13) 2/16 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF128 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761218249 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 54549979 54549979 G T 1 0 0 0 0 1 0 0 0 11722 1116 39 1 1 PDE1B 12 54549979 Missense_Mutation SNP G C3N-01030_T 594746 54549979 78725330 522 21303 OR6C3 0 . GRCh38 12 55332129 55332129 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.429G>T p.= p.L143L ENST00000379667 1/1 129 94 35 167 167 0 strelka-mutect OR6C3,synonymous_variant,p.=,ENST00000379667,NM_054104.1; T ENST00000379667 Transcript synonymous_variant 429/936 429/936 143/311 L ctG/ctT 1 1 OR6C3 HGNC HGNC:15437 protein_coding YES CCDS31819.1 ENSP00000368989 Q9NZP0 A0A126GW44 UPI000016150E NM_054104.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF39,hmmpanther:PTHR26454,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 55332129 55332129 G T 1 0 0 0 0 0 0 0 1 11260 1364 48 2 2 OR6C3 12 55332129 Silent SNP G C3N-01030_T 782150 55332129 77943180 523 21304 LGR5 0 . GRCh38 12 71524425 71524425 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.304C>A p.Leu102Met p.L102M ENST00000266674 3/18 135 102 33 196 196 0 strelka-varscan-mutect LGR5,missense_variant,p.Leu102Met,ENST00000266674,NM_003667.3;LGR5,missense_variant,p.Leu102Met,ENST00000540815,NM_001277226.1;LGR5,missense_variant,p.Leu102Met,ENST00000536515,NM_001277227.1;LGR5,non_coding_transcript_exon_variant,,ENST00000550851,; A ENST00000266674 Transcript missense_variant 615/4611 304/2724 102/907 L/M Ctg/Atg 1 1 LGR5 HGNC HGNC:4504 protein_coding YES CCDS9000.1 ENSP00000266674 O75473 A0A0A8K8C7 UPI000004B65C NM_003667.3 deleterious(0) 3/18 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF259,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 71524425 71524425 C A 1 0 0 0 0 1 0 0 0 8667 912 32 2 2 LGR5 12 71524425 Missense_Mutation SNP C C3N-01030_T 16192296 71524425 61750884 524 21305 TRHDE 0 . GRCh38 12 72652347 72652347 + Missense_Mutation SNP G G T rs746911625 C3N-01030_T C3N-01030_N G G c.2566G>T p.Val856Leu p.V856L ENST00000261180 16/19 67 60 7 110 110 0 strelka-varscan-mutect TRHDE,missense_variant,p.Val856Leu,ENST00000261180,NM_013381.2; T ENST00000261180 Transcript missense_variant 2662/10733 2566/3075 856/1024 V/L Gta/Tta rs746911625,COSM943364 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0) 16/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746911625 . 0 201 4 5 0 0 0 0 -12.00704 0.9955747 1 1 1 0 T 3 4 70 72652347 72652347 G T 1 0 0 0 0 1 0 0 0 16968 1145 40 1 1 TRHDE 12 72652347 Missense_Mutation SNP G C3N-01030_T 1127922 72652347 60622962 525 21306 GLIPR1L2 0 . GRCh38 12 75430714 75430714 + Splice_Site SNP G G T novel C3N-01030_T C3N-01030_N G G c.671-1G>T p.X224_splice ENST00000550916 127 94 33 176 175 1 strelka-varscan-mutect GLIPR1L2,splice_acceptor_variant,,ENST00000550916,NM_001270396.1;GLIPR1L2,splice_acceptor_variant,,ENST00000378692,; T ENST00000550916 Transcript splice_acceptor_variant -/2609 671/1035 224/344 1 1 GLIPR1L2 HGNC HGNC:28592 protein_coding YES CCDS58258.1 ENSP00000448248 Q4G1C9 UPI00001408B2 NM_001270396.1 4/5 HIGH 1 SNV 1 1 PASS rs1255012358 . 0 204 0 3 3 0 0 0 -19.99992 0.9540007 1 1 1 0 T 5 4 70 75430714 75430714 G T 1 0 0 0 0 0 0 1 0 6321 1014 35 2 2 GLIPR1L2 12 75430714 Splice_Site SNP G C3N-01030_T 2778367 75430714 57844595 526 21307 ZDHHC17 0 . GRCh38 12 76828470 76828470 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1121G>T p.Trp374Leu p.W374L ENST00000426126 10/17 135 115 20 201 201 0 strelka-varscan-mutect ZDHHC17,missense_variant,p.Trp374Leu,ENST00000426126,NM_015336.2;ZDHHC17,downstream_gene_variant,,ENST00000550876,;ZDHHC17,downstream_gene_variant,,ENST00000546778,;ZDHHC17,downstream_gene_variant,,ENST00000552453,; T ENST00000426126 Transcript missense_variant 1770/5259 1121/1899 374/632 W/L tGg/tTg 1 1 ZDHHC17 HGNC HGNC:18412 protein_coding YES CCDS44946.1 ENSP00000403397 Q8IUH5 UPI0000051F55 NM_015336.2 deleterious(0) 10/17 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24161:SF18,hmmpanther:PTHR24161 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 76828470 76828470 G T 1 0 0 0 0 1 0 0 0 18183 1357 47 2 2 ZDHHC17 12 76828470 Missense_Mutation SNP G C3N-01030_T 1397756 76828470 56446839 527 21308 NAV3 0 . GRCh38 12 78137235 78137235 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.4500C>G p.Asn1500Lys p.N1500K ENST00000397909 19/40 105 89 16 116 116 0 strelka-mutect NAV3,missense_variant,p.Asn1500Lys,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Asn1500Lys,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Asn395Lys,ENST00000552895,;NAV3,missense_variant,p.Asn129Lys,ENST00000550788,; G ENST00000397909 Transcript missense_variant 4673/9821 4500/7158 1500/2385 N/K aaC/aaG 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 19/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999939 1 1 1 0 G 3 3 70 78137235 78137235 C G 1 0 0 0 0 1 0 0 0 10194 477 17 4 4 NAV3 12 78137235 Missense_Mutation SNP C C3N-01030_T 1308765 78137235 55138074 528 21309 OTOGL 0 . GRCh38 12 80358692 80358692 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.6116C>G p.Pro2039Arg p.P2039R ENST00000458043 50/58 113 98 15 193 193 0 strelka-varscan-mutect OTOGL,missense_variant,p.Pro2039Arg,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Pro2027Arg,ENST00000547103,;OTOGL,missense_variant,p.Pro482Arg,ENST00000298820,;OTOGL,missense_variant,p.Pro56Arg,ENST00000550182,;OTOGL,missense_variant,p.Pro91Arg,ENST00000551340,;OTOGL,non_coding_transcript_exon_variant,,ENST00000546620,; G ENST00000458043 Transcript missense_variant 6122/8083 6116/7035 2039/2344 P/R cCt/cGt 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0.02) 50/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225 MODERATE 1 SNV 5 1 PASS rs1253264001 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 80358692 80358692 C G 1 0 0 0 0 1 0 0 0 11371 681 24 4 4 OTOGL 12 80358692 Missense_Mutation SNP C C3N-01030_T 2221457 80358692 52916617 529 21310 LIN7A 0 . GRCh38 12 80889361 80889361 + Nonsense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.91A>T p.Arg31Ter p.R31* ENST00000552864 2/6 104 88 16 175 175 0 strelka-varscan-mutect LIN7A,stop_gained,p.Arg31Ter,ENST00000552864,NM_001324423.1,NM_004664.2;LIN7A,stop_gained,p.Arg25Ter,ENST00000549417,;LIN7A,upstream_gene_variant,,ENST00000552093,;LIN7A,stop_gained,p.Arg31Ter,ENST00000261203,; A ENST00000552864 Transcript stop_gained 294/6112 91/702 31/233 R/* Aga/Tga 1 -1 LIN7A HGNC HGNC:17787 protein_coding YES CCDS9021.1 ENSP00000447488 O14910 UPI0000073ECD NM_001324423.1,NM_004664.2 2/6 Pfam_domain:PF02828,PROSITE_profiles:PS51022,hmmpanther:PTHR14063,hmmpanther:PTHR14063:SF4,SMART_domains:SM00569,Superfamily_domains:SSF101288 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 80889361 80889361 T A 1 0 0 0 0 0 1 0 0 8718 1617 56 4 4 LIN7A 12 80889361 Nonsense_Mutation SNP T C3N-01030_T 530669 80889361 52385948 530 21311 MGAT4C 0 . GRCh38 12 85979605 85979605 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1121C>T p.Ser374Leu p.S374L ENST00000611864 4/4 162 142 20 227 227 0 strelka-varscan-mutect MGAT4C,missense_variant,p.Ser374Leu,ENST00000611864,;MGAT4C,missense_variant,p.Ser374Leu,ENST00000620241,;MGAT4C,missense_variant,p.Ser374Leu,ENST00000621808,NM_013244.3;MGAT4C,missense_variant,p.Ser374Leu,ENST00000548651,;MGAT4C,missense_variant,p.Ser374Leu,ENST00000552808,;MGAT4C,missense_variant,p.Ser374Leu,ENST00000547225,;MGAT4C,downstream_gene_variant,,ENST00000552435,; A ENST00000611864 Transcript missense_variant 1177/25116 1121/1437 374/478 S/L tCa/tTa 1 -1 MGAT4C HGNC HGNC:30871 protein_coding YES CCDS9030.1 ENSP00000481096 Q9UBM8 UPI00001B002C tolerated(0.23) 4/4 hmmpanther:PTHR12062,hmmpanther:PTHR12062:SF14 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 85979605 85979605 G A 1 0 0 0 0 1 0 0 0 9507 1294 45 3 3 MGAT4C 12 85979605 Missense_Mutation SNP G C3N-01030_T 5090244 85979605 47295704 531 21312 EPYC 0 . GRCh38 12 90972981 90972981 + Splice_Site SNP C C G novel C3N-01030_T C3N-01030_N C C c.341-1G>C p.X114_splice ENST00000261172 85 70 15 88 88 0 strelka-varscan-mutect EPYC,splice_acceptor_variant,,ENST00000261172,NM_004950.4;EPYC,splice_acceptor_variant,,ENST00000551767,;EPYC,splice_acceptor_variant,,ENST00000550203,; G ENST00000261172 Transcript splice_acceptor_variant -/1539 341/969 114/322 1 -1 EPYC HGNC HGNC:3053 protein_coding YES CCDS31870.1 ENSP00000261172 Q99645 A0A024RBC3 UPI000013D136 NM_004950.4 3/6 HIGH 1 SNV 1 1 PASS rs1291861382 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 70 90972981 90972981 C G 1 0 0 0 0 0 0 1 0 5049 927 32 4 4 EPYC 12 90972981 Splice_Site SNP C C3N-01030_T 4993376 90972981 42302328 532 21313 DCN 0 . GRCh38 12 91158408 91158408 + Missense_Mutation SNP C C A rs776646201 C3N-01030_T C3N-01030_N C C c.426G>T p.Lys142Asn p.K142N ENST00000052754 4/8 183 165 18 245 245 0 strelka-varscan-mutect DCN,missense_variant,p.Lys142Asn,ENST00000052754,NM_001920.3;DCN,missense_variant,p.Lys142Asn,ENST00000393155,NM_133503.2;DCN,missense_variant,p.Lys142Asn,ENST00000552962,;DCN,missense_variant,p.Lys142Asn,ENST00000547937,;DCN,missense_variant,p.Lys142Asn,ENST00000552145,;DCN,missense_variant,p.Lys142Asn,ENST00000550563,;DCN,intron_variant,,ENST00000425043,NM_133505.2;DCN,intron_variant,,ENST00000547568,;DCN,intron_variant,,ENST00000420120,NM_133504.2;DCN,intron_variant,,ENST00000546391,;DCN,intron_variant,,ENST00000441303,NM_133506.2;DCN,intron_variant,,ENST00000456569,NM_133507.2;DCN,downstream_gene_variant,,ENST00000549513,; A ENST00000052754 Transcript missense_variant 928/7156 426/1080 142/359 K/N aaG/aaT rs776646201,COSM4437551,COSM5376200 1 -1 DCN HGNC HGNC:2705 protein_coding YES CCDS9039.1 ENSP00000052754 P07585 Q6FH10 UPI000013187E NM_001920.3 tolerated(0.09) 4/8 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF5,PIRSF_domain:PIRSF002490,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs776646201 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 91158408 91158408 C A 1 0 0 0 0 1 0 0 0 4099 680 24 2 2 DCN 12 91158408 Missense_Mutation SNP C C3N-01030_T 185427 91158408 42116901 533 21314 UHRF1BP1L 0 . GRCh38 12 100142609 100142609 + Silent SNP G G A C3N-01030_T C3N-01030_N G G c.27C>T p.= p.I9I ENST00000279907 1/21 256 224 32 221 221 0 strelka-varscan-mutect UHRF1BP1L,synonymous_variant,p.=,ENST00000279907,NM_015054.1;UHRF1BP1L,synonymous_variant,p.=,ENST00000356828,NM_001006947.1;RP11-175P13.2,upstream_gene_variant,,ENST00000550886,;UHRF1BP1L,synonymous_variant,p.=,ENST00000547428,; A ENST00000279907 Transcript synonymous_variant 240/5168 27/4395 9/1464 I atC/atT COSM4406755,COSM4406756 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 1/21 Pfam_domain:PF12624,hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 100142609 100142609 G A 1 0 0 0 0 0 0 0 1 17493 932 33 3 3 UHRF1BP1L 12 100142609 Silent SNP G C3N-01030_T 8984201 100142609 33132700 534 21315 ANO4 0 . GRCh38 12 100939445 100939445 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.291G>T p.= p.G97G ENST00000392977 4/28 73 68 5 81 80 1 strelka-mutect ANO4,synonymous_variant,p.=,ENST00000392979,NM_178826.3;ANO4,synonymous_variant,p.=,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,synonymous_variant,p.=,ENST00000549155,; T ENST00000392977 Transcript synonymous_variant 501/3509 291/2868 97/955 G ggG/ggT 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 4/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28 LOW 1 SNV 2 1 PASS . . 0 199 10 0 0 0 0 0 -11.07977 0.9999112 1 1 1 0 T 2 4 70 100939445 100939445 G T 1 0 0 0 0 0 0 0 1 806 1219 43 2 2 ANO4 12 100939445 Silent SNP G C3N-01030_T 796836 100939445 32335864 535 21316 PAH 0 . GRCh38 12 102843669 102843669 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1176T>A p.Phe392Leu p.F392L ENST00000553106 11/13 417 364 53 370 370 0 strelka-varscan-mutect PAH,missense_variant,p.Phe392Leu,ENST00000553106,NM_000277.1;PAH,missense_variant,p.Phe387Leu,ENST00000307000,;PAH,missense_variant,p.Phe94Leu,ENST00000635477,;PAH,non_coding_transcript_exon_variant,,ENST00000551114,;PAH,non_coding_transcript_exon_variant,,ENST00000549247,;PAH,non_coding_transcript_exon_variant,,ENST00000635528,; T ENST00000553106 Transcript missense_variant 1649/4122 1176/1359 392/452 F/L ttT/ttA 1 -1 PAH HGNC HGNC:8582 protein_coding YES CCDS9092.1 ENSP00000448059 P00439 A0A024RBG4 UPI00001318A0 NM_000277.1 deleterious(0.05) 11/13 PROSITE_profiles:PS51410,hmmpanther:PTHR11473,Gene3D:1.10.800.10,Pfam_domain:PF00351,PIRSF_domain:PIRSF000336,TIGRFAM_domain:TIGR01268,Superfamily_domains:SSF56534,Prints_domain:PR00372 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 102843669 102843669 A T 1 0 0 0 0 1 0 0 0 11474 359 13 4 4 PAH 12 102843669 Missense_Mutation SNP A C3N-01030_T 1904224 102843669 30431640 536 21317 STAB2 0 . GRCh38 12 103673955 103673955 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2420G>T p.Gly807Val p.G807V ENST00000388887 23/69 97 86 11 110 110 0 strelka-varscan-mutect STAB2,missense_variant,p.Gly807Val,ENST00000388887,NM_017564.9;RP11-341G23.3,upstream_gene_variant,,ENST00000550175,; T ENST00000388887 Transcript missense_variant 2624/8251 2420/7656 807/2551 G/V gGg/gTg 1 1 STAB2 HGNC HGNC:18629 protein_coding YES CCDS31888.1 ENSP00000373539 Q8WWQ8 UPI00001ADDF4 NM_017564.9 deleterious(0) 23/69 hmmpanther:PTHR24038:SF0,hmmpanther:PTHR24038,Gene3D:2gy5A03,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99953 1 1 1 1 0 T 3 4 70 103673955 103673955 G T 1 0 0 0 0 1 0 0 0 15616 1232 43 2 2 STAB2 12 103673955 Missense_Mutation SNP G C3N-01030_T 830286 103673955 29601354 537 21318 RIC8B 0 . GRCh38 12 106860320 106860320 + Silent SNP G G T rs778697988 C3N-01030_T C3N-01030_N G G c.1359G>T p.= p.A453A ENST00000392839 8/9 97 89 8 81 81 0 strelka-varscan-mutect RIC8B,synonymous_variant,p.=,ENST00000392837,;RIC8B,synonymous_variant,p.=,ENST00000355478,;RIC8B,synonymous_variant,p.=,ENST00000392839,NM_018157.2;RIC8B,5_prime_UTR_variant,,ENST00000549643,;RIC8B,downstream_gene_variant,,ENST00000548914,;RIC8B,synonymous_variant,p.=,ENST00000470960,;RIC8B,synonymous_variant,p.=,ENST00000462949,;RIC8B,non_coding_transcript_exon_variant,,ENST00000470628,; T ENST00000392839 Transcript synonymous_variant 1465/2440 1359/1563 453/520 A gcG/gcT rs778697988 1 1 RIC8B HGNC HGNC:25555 protein_coding YES CCDS9109.2 ENSP00000376583 Q9NVN3 UPI00001FB46B NM_018157.2 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR12425,hmmpanther:PTHR12425:SF2,Pfam_domain:PF10165,Prints_domain:PR01802 LOW 1 SNV 1 1 PASS rs778697988 . 0 206 3 0 0 0 0 0 -16.68277 1 1 1 1 0 T 2 4 70 106860320 106860320 G T 1 0 0 0 0 0 0 0 1 13530 1103 39 1 1 RIC8B 12 106860320 Silent SNP G C3N-01030_T 3186365 106860320 26414989 538 21319 DDX54 0 . GRCh38 12 113175051 113175051 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.859G>T p.Glu287Ter p.E287* ENST00000314045 8/20 176 130 46 139 139 0 strelka-varscan-mutect DDX54,stop_gained,p.Glu287Ter,ENST00000314045,NM_001111322.1;DDX54,stop_gained,p.Glu287Ter,ENST00000306014,NM_024072.3;DDX54,stop_gained,p.Glu204Ter,ENST00000552375,;Y_RNA,downstream_gene_variant,,ENST00000364338,;DDX54,3_prime_UTR_variant,,ENST00000551344,;DDX54,downstream_gene_variant,,ENST00000546869,; A ENST00000314045 Transcript stop_gained 887/4380 859/2649 287/882 E/* Gaa/Taa 1 -1 DDX54 HGNC HGNC:20084 protein_coding YES CCDS44984.1 ENSP00000323858 Q8TDD1 UPI000006F3A5 NM_001111322.1 8/20 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF292,hmmpanther:PTHR24031,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 113175051 113175051 C A 1 0 0 0 0 0 1 0 0 4175 864 30 2 2 DDX54 12 113175051 Nonsense_Mutation SNP C C3N-01030_T 6314731 113175051 20100258 539 21320 NOS1 0 . GRCh38 12 117278029 117278029 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1594A>T p.Asn532Tyr p.N532Y ENST00000618760 9/30 73 65 8 100 100 0 strelka-varscan-mutect NOS1,missense_variant,p.Asn532Tyr,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Asn532Tyr,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Asn532Tyr,ENST00000338101,;NOS1,missense_variant,p.Asn531Tyr,ENST00000344089,; A ENST00000618760 Transcript missense_variant 2305/12283 1594/4407 532/1468 N/Y Aac/Tac 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 deleterious(0) 9/30 Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -17.82414 1 1 1 1 0 A 3 1 70 117278029 117278029 T A 1 0 0 0 0 1 0 0 0 10586 1812 63 4 4 NOS1 12 117278029 Missense_Mutation SNP T C3N-01030_T 4102978 117278029 15997280 540 21321 HNF1A 0 . GRCh38 12 120999544 120999544 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1706C>G p.Ala569Gly p.A569G ENST00000544413 9/10 239 203 36 186 186 0 strelka-varscan-mutect HNF1A,missense_variant,p.Ala562Gly,ENST00000257555,NM_000545.5;HNF1A,missense_variant,p.Ala593Gly,ENST00000541395,;HNF1A,missense_variant,p.Ala383Gly,ENST00000543427,;HNF1A,missense_variant,p.Ala158Gly,ENST00000615446,;HNF1A,missense_variant,p.Ala569Gly,ENST00000544413,NM_001306179.1;HNF1A,3_prime_UTR_variant,,ENST00000617366,;C12orf43,downstream_gene_variant,,ENST00000288757,NM_022895.2,NM_001286192.1;C12orf43,downstream_gene_variant,,ENST00000445832,NM_001286198.1;HNF1A,downstream_gene_variant,,ENST00000400024,;C12orf43,downstream_gene_variant,,ENST00000537817,NM_001286191.1;C12orf43,downstream_gene_variant,,ENST00000539736,NM_001286195.1,NM_001286196.1;C12orf43,downstream_gene_variant,,ENST00000535367,;C12orf43,downstream_gene_variant,,ENST00000538296,NM_001286197.1;HNF1A,downstream_gene_variant,,ENST00000538626,;HNF1A,downstream_gene_variant,,ENST00000535955,;HNF1A,3_prime_UTR_variant,,ENST00000540108,;HNF1A,3_prime_UTR_variant,,ENST00000560968,;HNF1A,downstream_gene_variant,,ENST00000402929,;C12orf43,downstream_gene_variant,,ENST00000502891,;HNF1A,downstream_gene_variant,,ENST00000538646,;HNF1A,downstream_gene_variant,,ENST00000541924,;C12orf43,downstream_gene_variant,,ENST00000546272,;HNF1A,downstream_gene_variant,,ENST00000543255,;HNF1A,downstream_gene_variant,,ENST00000544574,; G ENST00000544413 Transcript missense_variant 1726/2014 1706/1917 569/638 A/G gCc/gGc 1 1 HNF1A HGNC HGNC:11621 protein_coding YES CCDS76611.1 ENSP00000438804 F5H0K0 UPI000204ABCC NM_001306179.1 tolerated_low_confidence(0.09) 9/10 Pfam_domain:PF04813,hmmpanther:PTHR11568,hmmpanther:PTHR11568:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 120999544 120999544 C G 1 0 0 0 0 1 0 0 0 7142 739 26 4 4 HNF1A 12 120999544 Missense_Mutation SNP C C3N-01030_T 3721515 120999544 12275765 541 21322 MLXIP 0 . GRCh38 12 122130873 122130873 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.940C>T p.Pro314Ser p.P314S ENST00000319080 7/17 126 85 41 161 161 0 strelka-varscan-mutect MLXIP,missense_variant,p.Pro314Ser,ENST00000319080,NM_014938.5;MLXIP,missense_variant,p.Pro65Ser,ENST00000535430,;MLXIP,upstream_gene_variant,,ENST00000538698,;MLXIP,upstream_gene_variant,,ENST00000366272,;MLXIP,upstream_gene_variant,,ENST00000377037,;MLXIP,upstream_gene_variant,,ENST00000542417,;MLXIP,upstream_gene_variant,,ENST00000535996,;MLXIP,non_coding_transcript_exon_variant,,ENST00000539861,;MLXIP,non_coding_transcript_exon_variant,,ENST00000538061,;MLXIP,upstream_gene_variant,,ENST00000541750,;MLXIP,downstream_gene_variant,,ENST00000535876,; T ENST00000319080 Transcript missense_variant 1072/8427 940/2760 314/919 P/S Ccg/Tcg 1 1 MLXIP HGNC HGNC:17055 protein_coding YES CCDS73540.1 ENSP00000312834 Q9HAP2 UPI0000D6226F NM_014938.5 deleterious(0) 7/17 hmmpanther:PTHR15741,hmmpanther:PTHR15741:SF23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 122130873 122130873 C T 1 0 0 0 0 1 0 0 0 9599 739 26 3 3 MLXIP 12 122130873 Missense_Mutation SNP C C3N-01030_T 1131329 122130873 11144436 542 21323 HCAR2 0 . GRCh38 12 122703071 122703071 + Silent SNP C C T rs200828023 C3N-01030_T C3N-01030_N C C c.213G>A p.= p.V71V ENST00000328880 1/1 324 248 76 376 376 0 strelka-varscan-mutect HCAR2,synonymous_variant,p.=,ENST00000328880,NM_177551.3;RP11-324E6.6,intron_variant,,ENST00000543611,; T ENST00000328880 Transcript synonymous_variant 273/2051 213/1092 71/363 V gtG/gtA rs200828023,COSM3870975 1 -1 HCAR2 HGNC HGNC:24827 protein_coding YES CCDS9235.1 ENSP00000375066 Q8TDS4 UPI000003BCD5 NM_177551.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW SNV 0,1 1 PASS rs200828023 . 0 205 0 0 5 0 0 0 -20 0.8436622 1 1 1 0 T 2 4 70 122703071 122703071 C T 1 0 0 0 0 0 0 0 1 6876 581 21 3 3 HCAR2 12 122703071 Silent SNP C C3N-01030_T 572198 122703071 10572238 543 21324 ATP6V0A2 0 . GRCh38 12 123748588 123748588 + Nonsense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1738A>T p.Lys580Ter p.K580* ENST00000330342 15/20 323 224 99 408 408 0 strelka-varscan-mutect ATP6V0A2,stop_gained,p.Lys580Ter,ENST00000330342,NM_012463.3;ATP6V0A2,downstream_gene_variant,,ENST00000504192,;ATP6V0A2,upstream_gene_variant,,ENST00000534943,;ATP6V0A2,downstream_gene_variant,,ENST00000536426,;ATP6V0A2,downstream_gene_variant,,ENST00000545059,; T ENST00000330342 Transcript stop_gained 1986/6542 1738/2571 580/856 K/* Aag/Tag 1 1 ATP6V0A2 HGNC HGNC:18481 protein_coding YES CCDS9254.1 ENSP00000332247 Q9Y487 UPI00001AFC09 NM_012463.3 15/20 hmmpanther:PTHR11629:SF22,hmmpanther:PTHR11629,Pfam_domain:PF01496,PIRSF_domain:PIRSF001293 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 123748588 123748588 A T 1 0 0 0 0 0 1 0 0 1322 247 9 4 4 ATP6V0A2 12 123748588 Nonsense_Mutation SNP A C3N-01030_T 1045517 123748588 9526721 544 21325 TMEM132B 0 . GRCh38 12 125653789 125653789 + Silent SNP C C A rs751675215 C3N-01030_T C3N-01030_N C C c.2316C>A p.= p.T772T ENST00000299308 9/9 215 159 56 246 246 0 strelka-varscan-mutect TMEM132B,synonymous_variant,p.=,ENST00000299308,NM_052907.3;TMEM132B,synonymous_variant,p.=,ENST00000613307,NM_001286219.1;TMEM132B,non_coding_transcript_exon_variant,,ENST00000535886,; A ENST00000299308 Transcript synonymous_variant 2324/10906 2316/3237 772/1078 T acC/acA rs751675215 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 9/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388 LOW 1 SNV 5 1 PASS rs751675215 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 125653789 125653789 C A 1 0 0 0 0 0 0 0 1 16490 581 21 2 2 TMEM132B 12 125653789 Silent SNP C C3N-01030_T 1905201 125653789 7621520 545 21326 FZD10 0 . GRCh38 12 130164480 130164480 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.1538T>C p.Val513Ala p.V513A ENST00000229030 1/1 125 117 8 88 88 0 strelka-varscan-mutect FZD10,missense_variant,p.Val513Ala,ENST00000229030,NM_007197.3;FZD10,3_prime_UTR_variant,,ENST00000539839,;FZD10-AS1,upstream_gene_variant,,ENST00000505807,;FZD10-AS1,upstream_gene_variant,,ENST00000509760,;FZD10-AS1,upstream_gene_variant,,ENST00000537095,;FZD10-AS1,upstream_gene_variant,,ENST00000542000,; C ENST00000229030 Transcript missense_variant 2022/3281 1538/1746 513/581 V/A gTg/gCg 1 1 FZD10 HGNC HGNC:4039 protein_coding YES CCDS9267.1 ENSP00000229030 Q9ULW2 UPI000004EC92 NM_007197.3 tolerated(0.09) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF86,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330,Prints_domain:PR00489 MODERATE SNV 1 PASS . . 0 208 0 2 0 0 0 0 -11.64768 0.9999996 1 1 1 0 C 3 2 70 130164480 130164480 T C 1 0 0 0 0 1 0 0 0 6000 1696 59 5 5 FZD10 12 130164480 Missense_Mutation SNP T C3N-01030_T 4510691 130164480 3110829 546 21327 PIWIL1 0 . GRCh38 12 130354925 130354925 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1209G>A p.Met403Ile p.M403I ENST00000245255 11/21 119 103 16 158 158 0 strelka-varscan-mutect PIWIL1,missense_variant,p.Met403Ile,ENST00000245255,NM_004764.4,NM_001190971.1;RP11-200K12.3,upstream_gene_variant,,ENST00000624997,; A ENST00000245255 Transcript missense_variant 1481/3897 1209/2586 403/861 M/I atG/atA 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 deleterious(0) 11/21 Pfam_domain:PF02170,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF46,SMART_domains:SM00949,Superfamily_domains:SSF101690 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 130354925 130354925 G A 1 0 0 0 0 1 0 0 0 12053 1290 45 3 3 PIWIL1 12 130354925 Missense_Mutation SNP G C3N-01030_T 190445 130354925 2920384 547 21328 GOLGA3 0 . GRCh38 12 132780816 132780816 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.3564G>A p.= p.V1188V ENST00000204726 18/24 190 156 34 181 181 0 strelka-varscan-mutect GOLGA3,synonymous_variant,p.=,ENST00000204726,NM_005895.3;GOLGA3,synonymous_variant,p.=,ENST00000450791,;GOLGA3,synonymous_variant,p.=,ENST00000456883,;AC127070.1,downstream_gene_variant,,ENST00000545875,NM_001172557.1;GOLGA3,downstream_gene_variant,,ENST00000537452,;GOLGA3,upstream_gene_variant,,ENST00000541013,; T ENST00000204726 Transcript synonymous_variant 4123/9252 3564/4497 1188/1498 V gtG/gtA 1 -1 GOLGA3 HGNC HGNC:4426 protein_coding YES CCDS9281.1 ENSP00000204726 Q08378 UPI0000190979 NM_005895.3 18/24 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18902,hmmpanther:PTHR18902:SF26 LOW SNV 5 1 PASS rs1393264657 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 132780816 132780816 C T 1 0 0 0 0 0 0 0 1 6432 813 29 3 3 GOLGA3 12 132780816 Silent SNP C C3N-01030_T 2425891 132780816 494493 548 21329 RXFP2 0 . GRCh38 13 31765058 31765058 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.341G>T p.Cys114Phe p.C114F ENST00000298386 4/18 173 121 52 266 266 0 strelka-varscan-mutect RXFP2,missense_variant,p.Cys114Phe,ENST00000298386,NM_130806.3;RXFP2,missense_variant,p.Cys114Phe,ENST00000380314,NM_001166058.1; T ENST00000298386 Transcript missense_variant 412/3319 341/2265 114/754 C/F tGc/tTc 1 1 RXFP2 HGNC HGNC:17318 protein_coding YES CCDS9342.1 ENSP00000298386 Q8WXD0 UPI0000049589 NM_130806.3 tolerated(0.2) 4/18 hmmpanther:PTHR24365:SF226,hmmpanther:PTHR24365,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 31765058 31765058 G T 1 0 0 0 0 1 0 0 0 14021 1319 46 2 2 RXFP2 13 31765058 Missense_Mutation SNP G C3N-01030_T 31765058 82599270 549 21330 ZAR1L 0 . GRCh38 13 32311348 32311348 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.578C>A p.Pro193Gln p.P193Q ENST00000533490 3/6 155 109 46 124 123 1 strelka-varscan-mutect ZAR1L,missense_variant,p.Pro193Gln,ENST00000533490,;ZAR1L,missense_variant,p.Pro193Gln,ENST00000345108,NM_001136571.1;BRCA2,upstream_gene_variant,,ENST00000380152,;BRCA2,upstream_gene_variant,,ENST00000544455,NM_000059.3;BRCA2,upstream_gene_variant,,ENST00000530893,; T ENST00000533490 Transcript missense_variant 997/1564 578/966 193/321 P/Q cCg/cAg 1 -1 ZAR1L HGNC HGNC:37116 protein_coding YES CCDS45023.1 ENSP00000437289 A6NP61 UPI00006C1387 tolerated(0.2) 3/6 hmmpanther:PTHR31054:SF5,hmmpanther:PTHR31054 MODERATE 1 SNV 5 1 PASS rs1030646054 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 32311348 32311348 G T 1 0 0 0 0 1 0 0 0 18077 1116 39 1 1 ZAR1L 13 32311348 Missense_Mutation SNP G C3N-01030_T 546290 32311348 82052980 550 21331 ZAR1L 0 . GRCh38 13 32311408 32311408 + Nonsense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.518C>G p.Ser173Ter p.S173* ENST00000533490 3/6 223 192 31 210 210 0 strelka-varscan-mutect ZAR1L,stop_gained,p.Ser173Ter,ENST00000533490,;ZAR1L,stop_gained,p.Ser173Ter,ENST00000345108,NM_001136571.1;BRCA2,upstream_gene_variant,,ENST00000380152,;BRCA2,upstream_gene_variant,,ENST00000544455,NM_000059.3;BRCA2,upstream_gene_variant,,ENST00000530893,; C ENST00000533490 Transcript stop_gained 937/1564 518/966 173/321 S/* tCa/tGa 1 -1 ZAR1L HGNC HGNC:37116 protein_coding YES CCDS45023.1 ENSP00000437289 A6NP61 UPI00006C1387 3/6 hmmpanther:PTHR31054:SF5,hmmpanther:PTHR31054 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 70 32311408 32311408 G C 1 0 0 0 0 0 1 0 0 18077 1294 45 4 4 ZAR1L 13 32311408 Nonsense_Mutation SNP G C3N-01030_T 60 32311408 82052920 551 21332 ENOX1 0 . GRCh38 13 43359991 43359991 + Missense_Mutation SNP G G A C3N-01030_T C3N-01030_N G G c.449C>T p.Pro150Leu p.P150L ENST00000261488 7/17 209 160 49 293 293 0 strelka-varscan-mutect ENOX1,missense_variant,p.Pro150Leu,ENST00000261488,NM_001242863.1,NM_017993.3,NM_001127615.1;ENOX1,non_coding_transcript_exon_variant,,ENST00000482207,; A ENST00000261488 Transcript missense_variant 1027/2982 449/1932 150/643 P/L cCa/cTa COSM385847,COSM385848 1 -1 ENOX1 HGNC HGNC:25474 protein_coding YES CCDS9389.1 ENSP00000261488 Q8TC92 A0A024RDT8 UPI0000071D6F NM_001242863.1,NM_017993.3,NM_001127615.1 deleterious(0) 7/17 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR16001,hmmpanther:PTHR16001:SF6,SMART_domains:SM00360,Superfamily_domains:SSF54928 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 43359991 43359991 G A 1 0 0 0 0 1 0 0 0 4971 1348 47 3 3 ENOX1 13 43359991 Missense_Mutation SNP G C3N-01030_T 11048583 43359991 71004337 552 21333 LCP1 0 . GRCh38 13 46158570 46158570 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.310G>A p.Gly104Ser p.G104S ENST00000398576 7/19 182 155 27 222 222 0 strelka-varscan-mutect LCP1,missense_variant,p.Gly104Ser,ENST00000398576,;LCP1,missense_variant,p.Gly104Ser,ENST00000323076,NM_002298.4;LCP1,missense_variant,p.Gly104Ser,ENST00000416500,;LCP1,downstream_gene_variant,,ENST00000442275,;LCP1,downstream_gene_variant,,ENST00000460190,; T ENST00000398576 Transcript missense_variant 699/3944 310/1884 104/627 G/S Ggt/Agt 1 -1 LCP1 HGNC HGNC:6528 protein_coding YES CCDS9403.1 ENSP00000381581 P13796 A0A024RDT4 UPI0000070B5C tolerated(0.11) 7/19 hmmpanther:PTHR19961,hmmpanther:PTHR19961:SF35 MODERATE 1 SNV 5 1 PASS rs1278205681 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 46158570 46158570 C T 1 0 0 0 0 1 0 0 0 8597 652 23 1 1 LCP1 13 46158570 Missense_Mutation SNP C C3N-01030_T 2798579 46158570 68205758 553 21334 KIAA0226L 0 . GRCh38 13 46356456 46356456 + Missense_Mutation SNP C C A rs779437381 C3N-01030_T C3N-01030_N C C c.1306G>T p.Gly436Cys p.G436C ENST00000429979 10/15 133 120 13 146 146 0 strelka-varscan-mutect KIAA0226L,missense_variant,p.Gly436Cys,ENST00000429979,NM_025113.3;KIAA0226L,missense_variant,p.Gly436Cys,ENST00000389908,NM_001286761.1;KIAA0226L,missense_variant,p.Gly279Cys,ENST00000378781,NM_001286765.1;KIAA0226L,missense_variant,p.Gly221Cys,ENST00000378797,NM_001286766.1;KIAA0226L,missense_variant,p.Gly279Cys,ENST00000409879,;KIAA0226L,missense_variant,p.Gly436Cys,ENST00000378787,NM_001286762.1;KIAA0226L,missense_variant,p.Gly369Cys,ENST00000378784,NM_001286763.1;KIAA0226L,missense_variant,p.Gly301Cys,ENST00000631139,NM_001286764.1;KIAA0226L,3_prime_UTR_variant,,ENST00000441284,; A ENST00000429979 Transcript missense_variant 1911/3979 1306/1989 436/662 G/C Ggc/Tgc rs779437381 1 -1 KIAA0226L HGNC HGNC:20420 protein_coding YES CCDS31970.2 ENSP00000396935 Q9H714 UPI00001FCD59 NM_025113.3 deleterious(0) 10/15 hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF14 MODERATE 1 SNV 5 1 PASS rs779437381 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 46356456 46356456 C A 1 0 0 0 0 1 0 0 0 8078 652 23 1 1 KIAA0226L 13 46356456 Missense_Mutation SNP C C3N-01030_T 197886 46356456 68007872 554 21335 ATP7B 0 . GRCh38 13 51974491 51974491 + Frame_Shift_Del DEL A A - novel C3N-01030_T C3N-01030_N A A c.729delT p.Phe243LeufsTer19 p.F243Lfs*19 ENST00000242839 2/21 288 216 72 364 364 0 sindel-varindel-pindel ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000242839,NM_000053.3;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000448424,;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000400366,NM_001243182.1;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000344297,NM_001005918.2;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000634844,;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000418097,;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000400370,;ATP7B,non_coding_transcript_exon_variant,,ENST00000482841,;ATP7B,intron_variant,,ENST00000635406,;ATP7B,upstream_gene_variant,,ENST00000483772,;ATP7B,frameshift_variant,p.Phe243LeufsTer19,ENST00000634308,;ATP7B,upstream_gene_variant,,ENST00000634620,; - ENST00000242839 Transcript frameshift_variant 886/6638 729/4398 243/1465 F/X ttT/tt 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 2/21 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 51974491 51974491 A - 1 0 1 0 1 0 0 0 0 1344 359 13 0 0 ATP7B 13 51974491 Frame_Shift_Del DEL A C3N-01030_T 5618035 51974491 62389837 555 21336 LECT1 0 . GRCh38 13 52703712 52703712 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.888C>A p.= p.I296I ENST00000377962 7/7 173 146 27 167 167 0 strelka-varscan-mutect LECT1,synonymous_variant,p.=,ENST00000448904,NM_001011705.1;LECT1,synonymous_variant,p.=,ENST00000377962,NM_007015.2;SUGT1,downstream_gene_variant,,ENST00000310528,NM_006704.3; T ENST00000377962 Transcript synonymous_variant 967/1410 888/1005 296/334 I atC/atA 1 -1 LECT1 HGNC HGNC:17005 protein_coding YES CCDS9437.1 ENSP00000367198 O75829 UPI000003F666 NM_007015.2 7/7 hmmpanther:PTHR14064:SF6,hmmpanther:PTHR14064 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -14.26646 0.9971074 1 1 1 0 T 2 4 70 52703712 52703712 G T 1 0 0 0 0 0 0 0 1 8620 932 33 2 2 LECT1 13 52703712 Silent SNP G C3N-01030_T 729221 52703712 61660616 556 21337 PCDH8 0 . GRCh38 13 52846753 52846753 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1684T>A p.Tyr562Asn p.Y562N ENST00000377942 1/3 111 79 32 118 118 0 strelka-varscan-mutect PCDH8,missense_variant,p.Tyr562Asn,ENST00000377942,NM_002590.3;PCDH8,missense_variant,p.Tyr562Asn,ENST00000338862,NM_032949.2;PCDH8,upstream_gene_variant,,ENST00000613548,; T ENST00000377942 Transcript missense_variant 1888/5088 1684/3213 562/1070 Y/N Tac/Aac 1 -1 PCDH8 HGNC HGNC:8660 protein_coding YES CCDS9438.1 ENSP00000367177 O95206 UPI0000072D47 NM_002590.3 deleterious(0.01) 1/3 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF46,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 52846753 52846753 A T 1 0 0 0 0 1 0 0 0 11604 420 15 4 4 PCDH8 13 52846753 Missense_Mutation SNP A C3N-01030_T 143041 52846753 61517575 557 21338 SLITRK1 0 . GRCh38 13 83880890 83880890 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.618G>C p.Glu206Asp p.E206D ENST00000377084 1/1 347 304 43 402 402 0 strelka-varscan-mutect SLITRK1,missense_variant,p.Glu206Asp,ENST00000377084,NM_052910.2,NM_001281503.1; G ENST00000377084 Transcript missense_variant 1504/5189 618/2091 206/696 E/D gaG/gaC 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 deleterious(0) 1/1 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 PASS rs1216228073 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 83880890 83880890 C G 1 0 0 0 0 1 0 0 0 15033 912 32 4 4 SLITRK1 13 83880890 Missense_Mutation SNP C C3N-01030_T 31034137 83880890 30483438 558 21339 TM9SF2 0 . GRCh38 13 99541621 99541621 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.971G>T p.Arg324Leu p.R324L ENST00000376387 9/17 110 90 20 192 192 0 strelka-varscan-mutect TM9SF2,missense_variant,p.Arg324Leu,ENST00000376387,NM_004800.2;TM9SF2,non_coding_transcript_exon_variant,,ENST00000466555,;TM9SF2,downstream_gene_variant,,ENST00000463709,; T ENST00000376387 Transcript missense_variant 1161/3430 971/1992 324/663 R/L cGg/cTg 1 1 TM9SF2 HGNC HGNC:11865 protein_coding YES CCDS9493.1 ENSP00000365567 Q99805 A0A024QYR8 UPI000013684D NM_004800.2 deleterious(0) 9/17 hmmpanther:PTHR10766,hmmpanther:PTHR10766:SF36,Pfam_domain:PF02990 MODERATE 1 SNV 1 1 PASS rs1393669448 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 99541621 99541621 G T 1 0 0 0 0 1 0 0 0 16422 1116 39 1 1 TM9SF2 13 99541621 Missense_Mutation SNP G C3N-01030_T 15660731 99541621 14822707 559 21340 NALCN 0 . GRCh38 13 101067986 101067986 + Nonsense_Mutation SNP G G A C3N-01030_T C3N-01030_N G G c.4378C>T p.Gln1460Ter p.Q1460* ENST00000251127 39/44 106 90 16 212 211 1 strelka-varscan-mutect NALCN,stop_gained,p.Gln1460Ter,ENST00000251127,NM_052867.2; A ENST00000251127 Transcript stop_gained 4460/6818 4378/5217 1460/1738 Q/* Cag/Tag COSM469139 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 39/44 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214 1 HIGH 1 SNV 1 1 1 PASS rs1335710703 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 101067986 101067986 G A 1 0 0 0 0 0 1 0 0 10155 1357 47 3 3 NALCN 13 101067986 Nonsense_Mutation SNP G C3N-01030_T 1526365 101067986 13296342 560 21341 CCDC168 0 . GRCh38 13 102741220 102741220 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.9477G>T p.Leu3159Phe p.L3159F ENST00000322527 4/4 95 85 10 159 159 0 strelka-varscan-mutect CCDC168,missense_variant,p.Leu3159Phe,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; A ENST00000322527 Transcript missense_variant 9615/21466 9477/21246 3159/7081 L/F ttG/ttT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.02) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 207 0 3 0 0 0 0 -15.7529 0.9999869 1 1 1 0 A 3 1 70 102741220 102741220 C A 1 0 0 0 0 1 0 0 0 2484 593 21 2 2 CCDC168 13 102741220 Missense_Mutation SNP C C3N-01030_T 1673234 102741220 11623108 561 21342 COL4A2 0 . GRCh38 13 110450379 110450379 + Missense_Mutation SNP G G A rs779091629 C3N-01030_T C3N-01030_N G G c.1264G>A p.Gly422Arg p.G422R ENST00000360467 20/48 189 160 29 174 174 0 strelka-varscan-mutect COL4A2,missense_variant,p.Gly422Arg,ENST00000360467,NM_001846.2; A ENST00000360467 Transcript missense_variant 1570/6281 1264/5139 422/1712 G/R Ggg/Agg rs779091629,COSM4673813 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 tolerated(0.07) 20/48 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs779091629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 110450379 110450379 G A 1 0 0 0 0 1 0 0 0 3479 1116 39 1 1 COL4A2 13 110450379 Missense_Mutation SNP G C3N-01030_T 7709159 110450379 3913949 562 21343 GRK1 0 . GRCh38 13 113735344 113735344 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1673G>A p.Gly558Glu p.G558E ENST00000335678 7/7 18 15 3 31 31 0 strelka-mutect GRK1,missense_variant,p.Gly558Glu,ENST00000335678,;GRK1,downstream_gene_variant,,ENST00000545304,;GRK1,non_coding_transcript_exon_variant,,ENST00000606140,; A ENST00000335678 Transcript missense_variant 1905/4296 1673/1692 558/563 G/E gGg/gAg 1 1 GRK1 HGNC HGNC:10013 protein_coding YES ENSP00000334876 Q15835 UPI0000133B08 deleterious(0) 7/7 hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.04008 1 1 1 1 0 A 3 1 70 113735344 113735344 G A 1 0 0 0 0 1 0 0 0 6671 1232 43 3 3 GRK1 13 113735344 Missense_Mutation SNP G C3N-01030_T 3284965 113735344 628984 563 21344 RASA3 0 . GRCh38 13 114011213 114011213 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1548C>A p.= p.S516S ENST00000334062 16/24 202 171 31 232 232 0 strelka-varscan-mutect RASA3,synonymous_variant,p.=,ENST00000334062,NM_001320822.1,NM_007368.2; T ENST00000334062 Transcript synonymous_variant 1670/4191 1548/2505 516/834 S tcC/tcA 1 -1 RASA3 HGNC HGNC:20331 protein_coding YES CCDS32016.1 ENSP00000335029 Q14644 UPI000000DBC1 NM_001320822.1,NM_007368.2 16/24 Gene3D:1.10.506.10,Pfam_domain:PF00616,PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF53,SMART_domains:SM00323,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 114011213 114011213 G T 1 0 0 0 0 0 0 0 1 13221 1335 47 2 2 RASA3 13 114011213 Silent SNP G C3N-01030_T 275869 114011213 353115 564 21345 OR11H6 0 . GRCh38 14 20224092 20224092 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.383C>A p.Thr128Lys p.T128K ENST00000315519 1/1 194 137 57 211 211 0 strelka-varscan-mutect OR11H6,missense_variant,p.Thr128Lys,ENST00000315519,NM_001004480.1; A ENST00000315519 Transcript missense_variant 461/1174 383/993 128/330 T/K aCa/aAa 1 1 OR11H6 HGNC HGNC:15349 protein_coding YES CCDS32033.1 ENSP00000319071 Q8NGC7 A0A126GVP4 UPI000004B1F1 NM_001004480.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF90,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1184166572 . 0 206 0 3 0 0 0 0 -20 0.9999983 1 1 1 0 A 3 1 70 20224092 20224092 C A 1 0 0 0 0 1 0 0 0 11006 478 17 2 2 OR11H6 14 20224092 Missense_Mutation SNP C C3N-01030_T 20224092 86819626 565 21346 CCNB1IP1 0 . GRCh38 14 20313489 20313489 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.610G>C p.Gly204Arg p.G204R ENST00000437553 7/8 54 43 11 63 63 0 strelka-varscan-mutect CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000437553,NM_182852.3;CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000398169,;CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000398160,;CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000398163,;CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000358932,NM_021178.4;CCNB1IP1,missense_variant,p.Gly204Arg,ENST00000353689,NM_182849.2;CCNB1IP1,downstream_gene_variant,,ENST00000557665,;CCNB1IP1,downstream_gene_variant,,ENST00000556563,;CCNB1IP1,downstream_gene_variant,,ENST00000553291,;CCNB1IP1,downstream_gene_variant,,ENST00000553516,;CCNB1IP1,3_prime_UTR_variant,,ENST00000556854,;CCNB1IP1,3_prime_UTR_variant,,ENST00000554184,;CCNB1IP1,downstream_gene_variant,,ENST00000554047,; G ENST00000437553 Transcript missense_variant 1280/1686 610/834 204/277 G/R Ggt/Cgt 1 -1 CCNB1IP1 HGNC HGNC:19437 protein_coding YES CCDS9547.1 ENSP00000409896 Q9NPC3 UPI000000CBC0 NM_182852.3 tolerated_low_confidence(0.08) 7/8 hmmpanther:PTHR14305 MODERATE 1 SNV 5 1 PASS rs1207876894 . 0 198 12 0 0 0 0 0 -20 0.999955 1 1 1 0 G 3 3 70 20313489 20313489 C G 1 0 0 0 0 1 0 0 0 2611 594 21 4 4 CCNB1IP1 14 20313489 Missense_Mutation SNP C C3N-01030_T 89397 20313489 86730229 566 21347 PRMT5 0 . GRCh38 14 22928571 22928571 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.155G>T p.Arg52Met p.R52M ENST00000324366 2/17 284 229 55 197 197 0 strelka-varscan-mutect PRMT5,missense_variant,p.Arg52Met,ENST00000324366,NM_006109.4;PRMT5,missense_variant,p.Arg35Met,ENST00000397441,NM_001039619.2;PRMT5,missense_variant,p.Arg35Met,ENST00000216350,NM_001282954.1,NM_001282953.1;PRMT5,missense_variant,p.Arg35Met,ENST00000397440,NM_001282956.1;PRMT5,missense_variant,p.Arg52Met,ENST00000553897,NM_001282955.1;PRMT5,missense_variant,p.Arg52Met,ENST00000553550,;PRMT5,missense_variant,p.Arg10Met,ENST00000554910,;PRMT5,missense_variant,p.Arg52Met,ENST00000421938,;PRMT5,missense_variant,p.Arg52Met,ENST00000554867,;PRMT5,intron_variant,,ENST00000556616,;PRMT5,intron_variant,,ENST00000627278,;PRMT5,upstream_gene_variant,,ENST00000555530,;PRMT5,upstream_gene_variant,,ENST00000555454,;PRMT5,upstream_gene_variant,,ENST00000556043,;PRMT5,upstream_gene_variant,,ENST00000553502,;PRMT5-AS1,downstream_gene_variant,,ENST00000599580,;PRMT5-AS1,downstream_gene_variant,,ENST00000587245,;PRMT5-AS1,downstream_gene_variant,,ENST00000590290,;PRMT5-AS1,downstream_gene_variant,,ENST00000595662,;RP11-298I3.1,upstream_gene_variant,,ENST00000548322,;RP11-298I3.1,upstream_gene_variant,,ENST00000548819,;PRMT5,non_coding_transcript_exon_variant,,ENST00000553641,;PRMT5,non_coding_transcript_exon_variant,,ENST00000556426,;PRMT5,non_coding_transcript_exon_variant,,ENST00000554716,;PRMT5,non_coding_transcript_exon_variant,,ENST00000556032,;PRMT5,non_coding_transcript_exon_variant,,ENST00000557015,;PRMT5,intron_variant,,ENST00000553915,;PRMT5,intron_variant,,ENST00000557415,;PRMT5,intron_variant,,ENST00000553787,;PRMT5,upstream_gene_variant,,ENST00000553417,; A ENST00000324366 Transcript missense_variant 379/2531 155/1914 52/637 R/M aGg/aTg 1 -1 PRMT5 HGNC HGNC:10894 protein_coding YES CCDS9579.1 ENSP00000319169 O14744 UPI000006F09F NM_006109.4 deleterious(0.01) 2/17 hmmpanther:PTHR10738,PIRSF_domain:PIRSF015894 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 22928571 22928571 C A 1 0 0 0 0 1 0 0 0 12670 681 24 2 2 PRMT5 14 22928571 Missense_Mutation SNP C C3N-01030_T 2615082 22928571 84115147 567 21348 NYNRIN 0 . GRCh38 14 24417183 24417183 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.5434G>T p.Ala1812Ser p.A1812S ENST00000382554 9/9 171 134 37 144 143 1 strelka-varscan-mutect NYNRIN,missense_variant,p.Ala1812Ser,ENST00000382554,NM_025081.2;NYNRIN,downstream_gene_variant,,ENST00000554505,; T ENST00000382554 Transcript missense_variant 5752/7857 5434/5697 1812/1898 A/S Gcc/Tcc 1 1 NYNRIN HGNC HGNC:20165 protein_coding YES CCDS45090.1 ENSP00000371994 Q9P2P1 UPI0000251E63 NM_025081.2 deleterious_low_confidence(0.04) 9/9 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 24417183 24417183 G T 1 0 0 0 0 1 0 0 0 10874 1203 42 2 2 NYNRIN 14 24417183 Missense_Mutation SNP G C3N-01030_T 1488612 24417183 82626535 568 21349 CTSG 0 . GRCh38 14 24575299 24575299 + Missense_Mutation SNP C C G rs749550003 C3N-01030_T C3N-01030_N C C c.169G>C p.Asp57His p.D57H ENST00000216336 2/5 215 169 46 143 143 0 strelka-varscan-mutect CTSG,missense_variant,p.Asp57His,ENST00000216336,NM_001911.2;CTSG,non_coding_transcript_exon_variant,,ENST00000552252,; G ENST00000216336 Transcript missense_variant 206/886 169/768 57/255 D/H Gac/Cac rs749550003,COSM4050338 1 -1 CTSG HGNC HGNC:2532 protein_coding YES CCDS9631.1 ENSP00000216336 P08311 UPI00001270AC NM_001911.2 deleterious(0) 2/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF13,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs749550003 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 24575299 24575299 C G 1 0 0 0 0 1 0 0 0 3844 913 32 4 4 CTSG 14 24575299 Missense_Mutation SNP C C3N-01030_T 158116 24575299 82468419 569 21350 NOVA1 0 . GRCh38 14 26448818 26448818 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.665C>A p.Thr222Asn p.T222N ENST00000539517 5/5 244 181 63 273 273 0 strelka-varscan-mutect NOVA1,missense_variant,p.Thr222Asn,ENST00000539517,NM_002515.2;NOVA1,missense_variant,p.Thr198Asn,ENST00000465357,NM_006489.2;NOVA1,missense_variant,p.Thr181Asn,ENST00000449198,;NOVA1,missense_variant,p.Thr76Asn,ENST00000347476,;NOVA1,downstream_gene_variant,,ENST00000549571,;NOVA1,downstream_gene_variant,,ENST00000549146,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,3_prime_UTR_variant,,ENST00000546546,; T ENST00000539517 Transcript missense_variant 983/3912 665/1524 222/507 T/N aCt/aAt 1 -1 NOVA1 HGNC HGNC:7886 protein_coding YES CCDS32061.1 ENSP00000438875 P51513 UPI000013D74E NM_002515.2 deleterious(0.05) 5/5 PROSITE_profiles:PS50084,hmmpanther:PTHR10288:SF150,hmmpanther:PTHR10288,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 26448818 26448818 G T 1 0 0 0 0 1 0 0 0 10600 1029 36 2 2 NOVA1 14 26448818 Missense_Mutation SNP G C3N-01030_T 1873519 26448818 80594900 570 21351 COCH 0 . GRCh38 14 30886289 30886289 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1454C>A p.Pro485His p.P485H ENST00000396618 11/12 144 113 31 138 138 0 strelka-varscan-mutect COCH,missense_variant,p.Pro373His,ENST00000460581,;COCH,missense_variant,p.Pro485His,ENST00000396618,NM_004086.2;COCH,missense_variant,p.Pro485His,ENST00000216361,NM_001135058.1;COCH,missense_variant,p.Pro369His,ENST00000468826,;COCH,missense_variant,p.Pro485His,ENST00000475087,;COCH,downstream_gene_variant,,ENST00000555881,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000555108,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000556786,;RP11-829H16.3,non_coding_transcript_exon_variant,,ENST00000468444,;RP11-829H16.3,upstream_gene_variant,,ENST00000555421,;COCH,downstream_gene_variant,,ENST00000557065,;COCH,downstream_gene_variant,,ENST00000553772,; A ENST00000396618 Transcript missense_variant 1510/2536 1454/1653 485/550 P/H cCt/cAt 1 1 COCH HGNC HGNC:2180 protein_coding YES CCDS9640.1 ENSP00000379862 O43405 UPI0000048EBB NM_004086.2 deleterious(0) 11/12 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF83,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 30886289 30886289 C A 1 0 0 0 0 1 0 0 0 3444 681 24 2 2 COCH 14 30886289 Missense_Mutation SNP C C3N-01030_T 4437471 30886289 76157429 571 21352 KIAA0586 0 . GRCh38 14 58498919 58498919 + Missense_Mutation SNP G G T rs764294275 C3N-01030_T C3N-01030_N G G c.4286G>T p.Cys1429Phe p.C1429F ENST00000354386 29/34 109 85 24 144 144 0 strelka-varscan-mutect KIAA0586,missense_variant,p.Cys1361Phe,ENST00000619416,NM_001244190.1;KIAA0586,missense_variant,p.Cys1332Phe,ENST00000556134,;KIAA0586,missense_variant,p.Cys1291Phe,ENST00000619722,NM_001244191.1;KIAA0586,missense_variant,p.Cys1332Phe,ENST00000423743,NM_001244192.1;KIAA0586,missense_variant,p.Cys1429Phe,ENST00000354386,NM_001244189.1;KIAA0586,missense_variant,p.Cys1300Phe,ENST00000261244,NM_014749.3;KIAA0586,missense_variant,p.Cys58Phe,ENST00000555397,;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571,; T ENST00000354386 Transcript missense_variant 4530/5226 4286/4935 1429/1644 C/F tGt/tTt rs764294275 1 1 KIAA0586 HGNC HGNC:19960 protein_coding YES CCDS58320.1 ENSP00000346359 Q9BVV6 UPI0001AE6998 NM_001244189.1 tolerated(0.06) 29/34 hmmpanther:PTHR15721:SF2,hmmpanther:PTHR15721 MODERATE 1 SNV 2 1 PASS rs764294275 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 58498919 58498919 G T 1 0 0 0 0 1 0 0 0 8089 1377 48 2 2 KIAA0586 14 58498919 Missense_Mutation SNP G C3N-01030_T 27612630 58498919 48544799 572 21353 CCDC175 0 . GRCh38 14 59568246 59568246 + Missense_Mutation SNP C C A rs17834244 C3N-01030_T C3N-01030_N C C c.490G>T p.Gly164Trp p.G164W ENST00000537690 4/20 102 86 16 105 105 0 strelka-varscan-mutect CCDC175,missense_variant,p.Gly164Trp,ENST00000537690,NM_001164399.1;CCDC175,missense_variant,p.Gly164Trp,ENST00000281581,;CCDC175,upstream_gene_variant,,ENST00000556996,;CCDC175,upstream_gene_variant,,ENST00000556936,; A ENST00000537690 Transcript missense_variant,splice_region_variant 546/2616 490/2382 164/793 G/W Ggg/Tgg rs17834244 1 -1 CCDC175 HGNC HGNC:19847 protein_coding YES CCDS53898.1 ENSP00000453940 P0C221 UPI000059D254 NM_001164399.1 deleterious(0) 4/20 hmmpanther:PTHR35347 MODERATE 1 SNV 5 1 PASS rs17834244 . 0 204 2 0 0 0 0 4 -2.527255 0 0 1 0 0 A 3 1 70 59568246 59568246 C A 1 0 0 0 0 1 0 0 0 2492 637 22 2 2 CCDC175 14 59568246 Missense_Mutation SNP C C3N-01030_T 1069327 59568246 47475472 573 21354 PPM1A 0 . GRCh38 14 60283463 60283463 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.979G>T p.Val327Leu p.V327L ENST00000325642 2/6 110 84 26 169 168 1 strelka-mutect PPM1A,missense_variant,p.Val254Leu,ENST00000395076,NM_021003.4;PPM1A,missense_variant,p.Val254Leu,ENST00000325658,NM_177951.2;PPM1A,missense_variant,p.Val327Leu,ENST00000325642,NM_177952.2;PPM1A,downstream_gene_variant,,ENST00000525399,;PPM1A,downstream_gene_variant,,ENST00000531937,;PPM1A,downstream_gene_variant,,ENST00000528241,;PPM1A,3_prime_UTR_variant,,ENST00000531143,;PPM1A,intron_variant,,ENST00000532036,; T ENST00000325642 Transcript missense_variant 1075/1713 979/1368 327/455 V/L Gta/Tta 1 1 PPM1A HGNC HGNC:9275 protein_coding YES CCDS45120.1 ENSP00000327255 P35813 UPI0000E01530 NM_177952.2 deleterious(0.03) 2/6 PROSITE_profiles:PS51746,hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF262,Pfam_domain:PF00481,Gene3D:3.60.40.10,SMART_domains:SM00332,Superfamily_domains:SSF81606 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 60283463 60283463 G T 1 0 0 0 0 1 0 0 0 12445 1377 48 2 2 PPM1A 14 60283463 Missense_Mutation SNP G C3N-01030_T 715217 60283463 46760255 574 21355 PLEKHG3 0 . GRCh38 14 64741397 64741397 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1880G>A p.Ser627Asn p.S627N ENST00000247226 16/17 182 151 31 157 157 0 strelka-varscan-mutect PLEKHG3,missense_variant,p.Ser627Asn,ENST00000247226,NM_001308147.1;PLEKHG3,missense_variant,p.Ser571Asn,ENST00000394691,NM_015549.1;PLEKHG3,missense_variant,p.Ser160Asn,ENST00000471182,;PLEKHG3,missense_variant,p.Ser132Asn,ENST00000484731,;PLEKHG3,missense_variant,p.Ser571Asn,ENST00000634379,;SPTB,downstream_gene_variant,,ENST00000556626,;SPTB,downstream_gene_variant,,ENST00000389722,NM_001024858.2;PLEKHG3,upstream_gene_variant,,ENST00000492928,;PLEKHG3,non_coding_transcript_exon_variant,,ENST00000490180,; A ENST00000247226 Transcript missense_variant 2027/10351 1880/3660 627/1219 S/N aGt/aAt 1 1 PLEKHG3 HGNC HGNC:20364 protein_coding YES CCDS76690.1 ENSP00000247226 A1L390 UPI0000ECF248 NM_001308147.1 tolerated(0.48) 16/17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 64741397 64741397 G A 1 0 0 0 0 1 0 0 0 12163 1029 36 3 3 PLEKHG3 14 64741397 Missense_Mutation SNP G C3N-01030_T 4457934 64741397 42302321 575 21356 FNTB 0 . GRCh38 14 65040869 65040869 + Missense_Mutation SNP G G A rs771996889 C3N-01030_T C3N-01030_N G G c.772G>A p.Ala258Thr p.A258T ENST00000246166 8/12 161 151 10 159 159 0 strelka-varscan-mutect FNTB,missense_variant,p.Ala258Thr,ENST00000246166,NM_001202558.1,NM_002028.3;CHURC1-FNTB,missense_variant,p.Ala292Thr,ENST00000549987,NM_001202559.1;MAX,intron_variant,,ENST00000341653,NM_197957.3;MIR4706,upstream_gene_variant,,ENST00000582134,;FNTB,downstream_gene_variant,,ENST00000556709,;CHURC1-FNTB,3_prime_UTR_variant,,ENST00000552941,;FNTB,non_coding_transcript_exon_variant,,ENST00000554334,; A ENST00000246166 Transcript missense_variant 1006/2834 772/1314 258/437 A/T Gcg/Acg rs771996889,COSM4051904 1 1 FNTB HGNC HGNC:3785 protein_coding YES CCDS9769.1 ENSP00000246166 P49356 UPI0000111EF4 NM_001202558.1,NM_002028.3 tolerated(0.12) 8/12 hmmpanther:PTHR11774:SF6,hmmpanther:PTHR11774,Gene3D:1.50.10.20,Pfam_domain:PF00432,Superfamily_domains:SSF48239 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771996889 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 65040869 65040869 G A 1 0 0 0 0 1 0 0 0 5836 1087 38 1 1 FNTB 14 65040869 Missense_Mutation SNP G C3N-01030_T 299472 65040869 42002849 576 21357 SMOC1 0 . GRCh38 14 70023220 70023220 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1064C>A p.Pro355His p.P355H ENST00000361956 11/12 283 248 35 246 246 0 strelka-varscan-mutect SMOC1,missense_variant,p.Pro355His,ENST00000381280,NM_022137.5;SMOC1,missense_variant,p.Pro355His,ENST00000361956,NM_001034852.2; A ENST00000361956 Transcript missense_variant 1327/2040 1064/1308 355/435 P/H cCc/cAc 1 1 SMOC1 HGNC HGNC:20318 protein_coding YES CCDS32110.1 ENSP00000355110 Q9H4F8 UPI0000071CCF NM_001034852.2 deleterious(0) 11/12 hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF13,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 70023220 70023220 C A 1 0 0 0 0 1 0 0 0 15122 623 22 2 2 SMOC1 14 70023220 Missense_Mutation SNP C C3N-01030_T 4982351 70023220 37020498 577 21358 LTBP2 0 . GRCh38 14 74552988 74552988 + Missense_Mutation SNP G G T rs368186583 C3N-01030_T C3N-01030_N G G c.1096C>A p.Arg366Ser p.R366S ENST00000261978 5/36 339 261 78 341 340 1 strelka-varscan-mutect LTBP2,missense_variant,p.Arg366Ser,ENST00000261978,NM_000428.2;LTBP2,missense_variant,p.Arg366Ser,ENST00000556690,;CTD-2207P18.1,intron_variant,,ENST00000554552,;LTBP2,intron_variant,,ENST00000557425,;LTBP2,missense_variant,p.Arg366Ser,ENST00000553939,; T ENST00000261978 Transcript missense_variant 1483/8567 1096/5466 366/1821 R/S Cgt/Agt rs368186583 1 -1 LTBP2 HGNC HGNC:6715 protein_coding YES CCDS9831.1 ENSP00000261978 Q14767 UPI000013D239 NM_000428.2 tolerated(0.66) 5/36 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF49 MODERATE 1 SNV 1 1 PASS rs368186583 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 74552988 74552988 G T 1 0 0 0 0 1 0 0 0 8980 1116 39 1 1 LTBP2 14 74552988 Missense_Mutation SNP G C3N-01030_T 4529768 74552988 32490730 578 21359 TSHR 0 . GRCh38 14 81143562 81143562 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.1504G>C p.Val502Leu p.V502L ENST00000541158 11/11 336 288 48 295 295 0 strelka-varscan-mutect TSHR,missense_variant,p.Val502Leu,ENST00000541158,;TSHR,missense_variant,p.Val502Leu,ENST00000298171,NM_000369.2;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,non_coding_transcript_exon_variant,,ENST00000636454,;TSHR,missense_variant,p.Val137Leu,ENST00000637447,; C ENST00000541158 Transcript missense_variant 1826/4566 1504/2295 502/764 V/L Gtc/Ctc 1 1 TSHR HGNC HGNC:12373 protein_coding YES CCDS9872.1 ENSP00000441235 A0A0A0MTJ0 UPI000013E4A2 deleterious(0) 11/11 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00373,PROSITE_profiles:PS50262,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 81143562 81143562 G C 1 0 0 0 0 1 0 0 0 17127 1377 48 4 4 TSHR 14 81143562 Missense_Mutation SNP G C3N-01030_T 6590574 81143562 25900156 579 21360 TSHR 0 . GRCh38 14 81143882 81143882 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.1824C>A p.= p.V608V ENST00000541158 11/11 339 247 92 359 358 1 strelka-varscan-mutect TSHR,synonymous_variant,p.=,ENST00000541158,;TSHR,synonymous_variant,p.=,ENST00000298171,NM_000369.2;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,downstream_gene_variant,,ENST00000636454,;TSHR,synonymous_variant,p.=,ENST00000637447,; A ENST00000541158 Transcript synonymous_variant 2146/4566 1824/2295 608/764 V gtC/gtA 1 1 TSHR HGNC HGNC:12373 protein_coding YES CCDS9872.1 ENSP00000441235 A0A0A0MTJ0 UPI000013E4A2 11/11 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0,Superfamily_domains:SSF81321 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 81143882 81143882 C A 1 0 0 0 0 0 0 0 1 17127 842 30 2 2 TSHR 14 81143882 Silent SNP C C3N-01030_T 320 81143882 25899836 580 21361 STON2 0 . GRCh38 14 81371144 81371144 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.415delG p.Asp139ThrfsTer8 p.D139Tfs*8 ENST00000555447 5/8 183 124 59 207 207 0 sindel-varindel-pindel STON2,frameshift_variant,p.Asp139ThrfsTer8,ENST00000555447,NM_001256430.1;STON2,frameshift_variant,p.Asp139ThrfsTer8,ENST00000267540,NM_033104.3;STON2,frameshift_variant,p.Asp139ThrfsTer8,ENST00000614646,; - ENST00000555447 Transcript frameshift_variant 828/4302 415/2763 139/920 D/X Gac/ac 1 -1 STON2 HGNC HGNC:30652 protein_coding YES CCDS58332.1 ENSP00000450857 Q8WXE9 UPI00001FD96B NM_001256430.1 5/8 PIRSF_domain:PIRSF037099,Pfam_domain:PF12016 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 81371144 81371144 C - 1 0 1 0 1 0 0 0 0 15696 826 29 0 0 STON2 14 81371144 Frame_Shift_Del DEL C C3N-01030_T 227262 81371144 25672574 581 21362 SERPINA11 0 . GRCh38 14 94442725 94442725 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1150C>A p.Leu384Met p.L384M ENST00000334708 5/5 119 104 15 94 94 0 strelka-varscan-mutect SERPINA11,missense_variant,p.Leu384Met,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; T ENST00000334708 Transcript missense_variant 1215/1476 1150/1269 384/422 L/M Ctg/Atg 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 tolerated(0.12) 5/5 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 94442725 94442725 G T 1 0 0 0 0 1 0 0 0 14364 933 33 2 2 SERPINA11 14 94442725 Missense_Mutation SNP G C3N-01030_T 13071581 94442725 12600993 582 21363 MAGEL2 0 . GRCh38 15 23644986 23644986 + Silent SNP C C T C3N-01030_T C3N-01030_N C C c.2757G>A p.= p.L919L ENST00000532292 1/1 87 69 18 127 127 0 strelka-varscan-mutect MAGEL2,synonymous_variant,p.=,ENST00000532292,NM_019066.4; T ENST00000532292 Transcript synonymous_variant 2856/4298 2757/3750 919/1249 L ctG/ctA COSM1147461 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 1/1 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF66 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 23644986 23644986 C T 1 0 0 0 0 0 0 0 1 9107 813 29 3 3 MAGEL2 15 23644986 Silent SNP C C3N-01030_T 23644986 78346203 583 21364 NPAP1 0 . GRCh38 15 24677045 24677045 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1178G>T p.Ser393Ile p.S393I ENST00000329468 1/1 157 111 46 290 290 0 strelka-varscan-mutect NPAP1,missense_variant,p.Ser393Ile,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript missense_variant 1178/7526 1178/3471 393/1156 S/I aGc/aTc 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 deleterious(0.02) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 24677045 24677045 G T 1 0 0 0 0 1 0 0 0 10609 971 34 2 2 NPAP1 15 24677045 Missense_Mutation SNP G C3N-01030_T 1032059 24677045 77314144 584 21365 OCA2 0 . GRCh38 15 27957679 27957679 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.1693A>T p.Ser565Cys p.S565C ENST00000354638 16/24 389 252 137 331 331 0 strelka-varscan-mutect OCA2,missense_variant,p.Ser565Cys,ENST00000354638,NM_000275.2;OCA2,missense_variant,p.Ser541Cys,ENST00000353809,NM_001300984.1; A ENST00000354638 Transcript missense_variant 1849/3186 1693/2517 565/838 S/C Agc/Tgc 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 deleterious(0) 16/24 hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283,Pfam_domain:PF03600 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 27957679 27957679 T A 1 0 0 0 0 1 0 0 0 10892 1580 55 4 4 OCA2 15 27957679 Missense_Mutation SNP T C3N-01030_T 3280634 27957679 74033510 585 21366 FAN1 0 . GRCh38 15 30905273 30905273 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.610C>A p.Gln204Lys p.Q204K ENST00000362065 2/15 102 88 14 147 147 0 strelka-varscan-mutect FAN1,missense_variant,p.Gln204Lys,ENST00000362065,NM_014967.4;FAN1,missense_variant,p.Gln204Lys,ENST00000561594,NM_001146095.1;FAN1,missense_variant,p.Gln204Lys,ENST00000561607,NM_001146094.1,NM_001146096.1;FAN1,missense_variant,p.Gln204Lys,ENST00000565466,;FAN1,intron_variant,,ENST00000562892,;FAN1,missense_variant,p.Gln204Lys,ENST00000565280,;RP11-540B6.3,downstream_gene_variant,,ENST00000565492,; A ENST00000362065 Transcript missense_variant 901/4891 610/3054 204/1017 Q/K Caa/Aaa 1 1 FAN1 HGNC HGNC:29170 protein_coding YES CCDS32186.1 ENSP00000354497 Q9Y2M0 UPI000006D713 NM_014967.4 tolerated(0.57) 2/15 hmmpanther:PTHR15749:SF4,hmmpanther:PTHR15749 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 30905273 30905273 C A 1 0 0 0 0 1 0 0 0 5520 827 29 2 2 FAN1 15 30905273 Missense_Mutation SNP C C3N-01030_T 2947594 30905273 71085916 586 21367 RYR3 0 . GRCh38 15 33613277 33613277 + Missense_Mutation SNP C C G rs759252909 C3N-01030_T C3N-01030_N C C c.2259C>G p.Ile753Met p.I753M ENST00000634891 19/104 155 109 46 169 169 0 strelka-mutect RYR3,missense_variant,p.Ile753Met,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Ile753Met,ENST00000622037,;RYR3,missense_variant,p.Ile753Met,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Ile753Met,ENST00000389232,;RYR3,missense_variant,p.Ile753Met,ENST00000634418,; G ENST00000634891 Transcript missense_variant 2360/15591 2259/14613 753/4870 I/M atC/atG rs759252909,COSM4478675 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 tolerated(0.15) 19/104 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,SMART_domains:SM00449,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759252909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 33613277 33613277 C G 1 0 0 0 0 1 0 0 0 14030 903 32 4 4 RYR3 15 33613277 Missense_Mutation SNP C C3N-01030_T 2708004 33613277 68377912 587 21368 PLCB2 0 . GRCh38 15 40299153 40299153 + Nonsense_Mutation SNP C C A rs752312361 C3N-01030_T C3N-01030_N C C c.658G>T p.Glu220Ter p.E220* ENST00000260402 8/32 81 57 24 112 112 0 strelka-varscan-mutect PLCB2,stop_gained,p.Glu220Ter,ENST00000260402,NM_004573.2;PLCB2,stop_gained,p.Glu220Ter,ENST00000557821,NM_001284297.1;PLCB2,stop_gained,p.Glu220Ter,ENST00000456256,NM_001284298.1;PLCB2,downstream_gene_variant,,ENST00000543785,NM_001284299.1;PLCB2-AS1,upstream_gene_variant,,ENST00000559520,;PLCB2,non_coding_transcript_exon_variant,,ENST00000558588,;PLCB2,non_coding_transcript_exon_variant,,ENST00000560093,;PLCB2,downstream_gene_variant,,ENST00000559634,;PLCB2,upstream_gene_variant,,ENST00000558409,; A ENST00000260402 Transcript stop_gained 908/4616 658/3558 220/1185 E/* Gaa/Taa rs752312361,COSM1678359,COSM1678360 1 -1 PLCB2 HGNC HGNC:9055 protein_coding YES CCDS42020.1 ENSP00000260402 Q00722 UPI0000D79B75 NM_004573.2 8/32 hmmpanther:PTHR10336:SF10,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000956,Gene3D:1.10.238.10,Pfam_domain:PF09279,Superfamily_domains:SSF47473 0,1,1 HIGH 1 SNV 2 0,1,1 1 PASS rs752312361 . 0 206 2 2 0 0 0 0 -20 0.9999995 1 1 1 0 A 4 1 70 40299153 40299153 C A 1 0 0 0 0 0 1 0 0 12122 922 32 2 2 PLCB2 15 40299153 Nonsense_Mutation SNP C C3N-01030_T 6685876 40299153 61692036 588 21369 DNAJC17 0 . GRCh38 15 40775057 40775057 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.574G>T p.Asp192Tyr p.D192Y ENST00000220496 8/11 149 96 53 162 162 0 strelka-varscan-mutect DNAJC17,missense_variant,p.Asp192Tyr,ENST00000220496,NM_018163.2;C15orf62,downstream_gene_variant,,ENST00000344320,NM_001130448.2;DNAJC17,downstream_gene_variant,,ENST00000627802,;DNAJC17,upstream_gene_variant,,ENST00000558727,;DNAJC17,downstream_gene_variant,,ENST00000561044,;DNAJC17,3_prime_UTR_variant,,ENST00000559238,;DNAJC17,3_prime_UTR_variant,,ENST00000560645,;DNAJC17,3_prime_UTR_variant,,ENST00000561018,;DNAJC17,3_prime_UTR_variant,,ENST00000559310,;DNAJC17,3_prime_UTR_variant,,ENST00000560065,;DNAJC17,non_coding_transcript_exon_variant,,ENST00000561110,;DNAJC17,downstream_gene_variant,,ENST00000560301,;DNAJC17,downstream_gene_variant,,ENST00000558769,; A ENST00000220496 Transcript missense_variant 605/3731 574/915 192/304 D/Y Gac/Tac 1 -1 DNAJC17 HGNC HGNC:25556 protein_coding YES CCDS10065.1 ENSP00000220496 Q9NVM6 UPI00000375AE NM_018163.2 deleterious(0) 8/11 Gene3D:3.30.70.330,Pfam_domain:PF00076,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 40775057 40775057 C A 1 0 0 0 0 1 0 0 0 4450 913 32 2 2 DNAJC17 15 40775057 Missense_Mutation SNP C C3N-01030_T 475904 40775057 61216132 589 21370 ATP8B4 0 . GRCh38 15 49931210 49931210 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1551C>A p.= p.T517T ENST00000284509 16/28 157 115 42 194 194 0 strelka-varscan-mutect ATP8B4,synonymous_variant,p.=,ENST00000284509,NM_024837.3;ATP8B4,synonymous_variant,p.=,ENST00000559829,;ATP8B4,synonymous_variant,p.=,ENST00000557955,;ATP8B4,synonymous_variant,p.=,ENST00000558458,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,; T ENST00000284509 Transcript synonymous_variant 1693/5676 1551/3579 517/1192 T acC/acA 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 16/28 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF80,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Pfam_domain:PF13246,Superfamily_domains:SSF81660 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 49931210 49931210 G T 1 0 0 0 0 0 0 0 1 1350 1335 47 2 2 ATP8B4 15 49931210 Silent SNP G C3N-01030_T 9156153 49931210 52059979 590 21371 DMXL2 0 . GRCh38 15 51499189 51499189 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.4035A>T p.= p.P1345P ENST00000543779 18/43 78 55 23 149 149 0 strelka-varscan-mutect DMXL2,synonymous_variant,p.=,ENST00000251076,NM_015263.3;DMXL2,synonymous_variant,p.=,ENST00000543779,NM_001174116.1;DMXL2,intron_variant,,ENST00000449909,NM_001174117.1;RP11-707P17.1,downstream_gene_variant,,ENST00000561007,; A ENST00000543779 Transcript synonymous_variant 4125/10400 4035/9114 1345/3037 P ccA/ccT 1 -1 DMXL2 HGNC HGNC:2938 protein_coding YES CCDS53946.1 ENSP00000441858 Q8TDJ6 UPI00001FE4C2 NM_001174116.1 18/43 Pfam_domain:PF12234,hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF11 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 51499189 51499189 T A 1 0 0 0 0 0 0 0 1 4404 1683 59 4 4 DMXL2 15 51499189 Silent SNP T C3N-01030_T 1567979 51499189 50492000 591 21372 MYO5C 0 . GRCh38 15 52271846 52271846 + Splice_Site SNP T T A C3N-01030_T C3N-01030_N T T c.751-2A>T p.X251_splice ENST00000261839 30 19 11 44 44 0 strelka-varscan-mutect MYO5C,splice_acceptor_variant,,ENST00000261839,NM_018728.3;MYO5C,downstream_gene_variant,,ENST00000558479,;MYO5C,intron_variant,,ENST00000541028,;MYO5C,splice_acceptor_variant,,ENST00000558902,;MYO5C,splice_acceptor_variant,,ENST00000559459,;MYO5C,intron_variant,,ENST00000560809,; A ENST00000261839 Transcript splice_acceptor_variant -/6971 751/5229 251/1742 COSM4779875 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 6/40 1 HIGH 1 SNV 1 1 1 PASS rs1185303699 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 70 52271846 52271846 T A 1 0 0 0 0 0 0 1 0 10081 1594 55 4 4 MYO5C 15 52271846 Splice_Site SNP T C3N-01030_T 772657 52271846 49719343 592 21373 CCDC33 0 . GRCh38 15 74244027 74244027 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.64A>T p.Thr22Ser p.T22S ENST00000398814 2/19 55 43 12 76 76 0 strelka-varscan-mutect CCDC33,missense_variant,p.Thr22Ser,ENST00000398814,NM_025055.4;CCDC33,missense_variant,p.Thr240Ser,ENST00000635913,; T ENST00000398814 Transcript missense_variant 495/2787 64/2268 22/755 T/S Acg/Tcg 1 1 CCDC33 HGNC HGNC:26552 protein_coding YES CCDS42058.1 ENSP00000381795 Q8N5R6 UPI0000E671FE NM_025055.4 tolerated(0.21) 2/19 hmmpanther:PTHR21623,hmmpanther:PTHR21623:SF3 MODERATE 1 SNV 2 1 PASS rs1424443692 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 74244027 74244027 A T 1 0 0 0 0 1 0 0 0 2516 159 6 4 4 CCDC33 15 74244027 Missense_Mutation SNP A C3N-01030_T 21972181 74244027 27747162 593 21374 SEMA7A 0 . GRCh38 15 74411921 74411921 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.1386G>T p.= p.A462A ENST00000261918 11/14 170 126 44 162 160 2 strelka-varscan-mutect SEMA7A,synonymous_variant,p.=,ENST00000261918,NM_003612.3;SEMA7A,synonymous_variant,p.=,ENST00000542748,NM_001146030.1;SEMA7A,synonymous_variant,p.=,ENST00000543145,NM_001146029.1;SEMA7A,downstream_gene_variant,,ENST00000567345,;MIR6881,upstream_gene_variant,,ENST00000616450,;SEMA7A,upstream_gene_variant,,ENST00000569617,; A ENST00000261918 Transcript synonymous_variant 1935/3885 1386/2001 462/666 A gcG/gcT 1 -1 SEMA7A HGNC HGNC:10741 protein_coding YES CCDS10262.1 ENSP00000261918 O75326 UPI00000312F0 NM_003612.3 11/14 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF80,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 LOW 1 SNV 1 1 PASS rs1412913730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 74411921 74411921 C A 1 0 0 0 0 0 0 0 1 14319 639 23 1 1 SEMA7A 15 74411921 Silent SNP C C3N-01030_T 167894 74411921 27579268 594 21375 MAN2C1 0 . GRCh38 15 75356804 75356804 + Silent SNP G G C rs752020927 C3N-01030_T C3N-01030_N G G c.2697C>G p.= p.L899L ENST00000565683 22/26 124 104 20 147 147 0 strelka-varscan-mutect MAN2C1,synonymous_variant,p.=,ENST00000565683,NM_001256494.1;MAN2C1,synonymous_variant,p.=,ENST00000267978,NM_006715.3;MAN2C1,synonymous_variant,p.=,ENST00000569482,NM_001256495.1;MAN2C1,synonymous_variant,p.=,ENST00000563622,NM_001256496.1;MAN2C1,synonymous_variant,p.=,ENST00000618257,;NEIL1,3_prime_UTR_variant,,ENST00000355059,NM_024608.3;NEIL1,downstream_gene_variant,,ENST00000564784,;NEIL1,downstream_gene_variant,,ENST00000569035,NM_001256552.1;NEIL1,downstream_gene_variant,,ENST00000565051,;NEIL1,downstream_gene_variant,,ENST00000567657,;NEIL1,downstream_gene_variant,,ENST00000567005,;MAN2C1,upstream_gene_variant,,ENST00000384904,;NEIL1,downstream_gene_variant,,ENST00000567959,;MAN2C1,downstream_gene_variant,,ENST00000566253,;MAN2C1,upstream_gene_variant,,ENST00000631426,;MAN2C1,upstream_gene_variant,,ENST00000563660,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000567163,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000566099,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000561693,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000564929,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000566569,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000564570,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000562067,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563528,;MAN2C1,downstream_gene_variant,,ENST00000564785,;NEIL1,downstream_gene_variant,,ENST00000561643,;MAN2C1,downstream_gene_variant,,ENST00000563441,;MAN2C1,downstream_gene_variant,,ENST00000566634,;NEIL1,downstream_gene_variant,,ENST00000567393,;NEIL1,downstream_gene_variant,,ENST00000565121,;MAN2C1,downstream_gene_variant,,ENST00000421803,;MAN2C1,downstream_gene_variant,,ENST00000570257,;MAN2C1,downstream_gene_variant,,ENST00000569176,;MAN2C1,downstream_gene_variant,,ENST00000563013,;MAN2C1,downstream_gene_variant,,ENST00000563794,;MAN2C1,downstream_gene_variant,,ENST00000566013,;NEIL1,downstream_gene_variant,,ENST00000568519,;MAN2C1,downstream_gene_variant,,ENST00000563368,;MAN2C1,downstream_gene_variant,,ENST00000562228,;NEIL1,downstream_gene_variant,,ENST00000567547,;MAN2C1,downstream_gene_variant,,ENST00000563596,;NEIL1,downstream_gene_variant,,ENST00000564738,;MAN2C1,downstream_gene_variant,,ENST00000563058,;MAN2C1,downstream_gene_variant,,ENST00000562461,;MAN2C1,downstream_gene_variant,,ENST00000568944,;MAN2C1,downstream_gene_variant,,ENST00000565953,;NEIL1,downstream_gene_variant,,ENST00000569758,;MAN2C1,downstream_gene_variant,,ENST00000567360,; C ENST00000565683 Transcript synonymous_variant 2709/3300 2697/3174 899/1057 L ctC/ctG rs752020927 1 -1 MAN2C1 HGNC HGNC:6827 protein_coding YES CCDS58391.1 ENSP00000457788 Q9NTJ4 UPI0000229CBC NM_001256494.1 22/26 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF15,Pfam_domain:PF07748,Superfamily_domains:SSF74650 LOW 1 SNV 1 1 PASS rs752020927 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 75356804 75356804 G C 1 0 0 0 0 0 0 0 1 9139 1277 45 4 4 MAN2C1 15 75356804 Silent SNP G C3N-01030_T 944883 75356804 26634385 595 21376 ISL2 0 . GRCh38 15 76338486 76338486 + Silent SNP T T C novel C3N-01030_T C3N-01030_N T T c.483T>C p.= p.L161L ENST00000290759 3/6 44 39 5 72 71 1 strelka-mutect ISL2,synonymous_variant,p.=,ENST00000290759,NM_145805.2;RP11-685G9.2,downstream_gene_variant,,ENST00000559539,;ISL2,non_coding_transcript_exon_variant,,ENST00000558437,;ISL2,intron_variant,,ENST00000558656,; C ENST00000290759 Transcript synonymous_variant 643/1881 483/1080 161/359 L ctT/ctC 1 1 ISL2 HGNC HGNC:18524 protein_coding YES CCDS10290.1 ENSP00000290759 Q96A47 UPI000012D8FC NM_145805.2 3/6 hmmpanther:PTHR24204:SF2,hmmpanther:PTHR24204 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.94872 1 1 1 1 0 C 2 2 70 76338486 76338486 T C 1 0 0 0 0 0 0 0 1 7764 1770 62 5 5 ISL2 15 76338486 Silent SNP T C3N-01030_T 981682 76338486 25652703 596 21377 FSD2 0 . GRCh38 15 82759426 82759426 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.2172C>A p.= p.P724P ENST00000334574 13/13 166 113 53 278 277 1 strelka-varscan-mutect FSD2,synonymous_variant,p.=,ENST00000334574,NM_001007122.3;FSD2,synonymous_variant,p.=,ENST00000541889,NM_001281806.1,NM_001281805.1;SCARNA15,downstream_gene_variant,,ENST00000516881,;SNHG21,downstream_gene_variant,,ENST00000561107,;SNHG21,downstream_gene_variant,,ENST00000558174,;SNHG21,downstream_gene_variant,,ENST00000559366,;SNHG21,downstream_gene_variant,,ENST00000544685,;SNHG21,downstream_gene_variant,,ENST00000558687,;SCARNA15,downstream_gene_variant,,ENST00000607520,; T ENST00000334574 Transcript synonymous_variant 2354/6418 2172/2250 724/749 P ccC/ccA 1 -1 FSD2 HGNC HGNC:18024 protein_coding YES CCDS45332.1 ENSP00000335651 A1L4K1 UPI0000161097 NM_001007122.3 13/13 PROSITE_profiles:PS50188,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF6,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1289166488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 82759426 82759426 G T 1 0 0 0 0 0 0 0 1 5945 987 35 2 2 FSD2 15 82759426 Silent SNP G C3N-01030_T 6420940 82759426 19231763 597 21378 WHAMM 0 . GRCh38 15 82826413 82826413 + Nonsense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1462C>T p.Gln488Ter p.Q488* ENST00000286760 7/10 114 71 43 138 138 0 strelka-varscan-mutect WHAMM,stop_gained,p.Gln488Ter,ENST00000286760,NM_001080435.2;WHAMM,non_coding_transcript_exon_variant,,ENST00000560964,; T ENST00000286760 Transcript stop_gained 1561/5101 1462/2430 488/809 Q/* Cag/Tag 1 1 WHAMM HGNC HGNC:30493 protein_coding YES CCDS45333.1 ENSP00000286760 Q8TF30 UPI00001C1F94 NM_001080435.2 7/10 hmmpanther:PTHR23330,hmmpanther:PTHR23330:SF6 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 82826413 82826413 C T 1 0 0 0 0 0 1 0 0 17918 840 29 3 3 WHAMM 15 82826413 Nonsense_Mutation SNP C C3N-01030_T 66987 82826413 19164776 598 21379 NTRK3 0 . GRCh38 15 87933079 87933079 + Missense_Mutation SNP C C A rs760692815 C3N-01030_T C3N-01030_N C C c.1822G>T p.Gly608Cys p.G608C ENST00000360948 16/20 214 166 48 313 313 0 strelka-varscan-mutect NTRK3,missense_variant,p.Gly608Cys,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Gly600Cys,ENST00000558676,;NTRK3,missense_variant,p.Gly608Cys,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Gly600Cys,ENST00000357724,;NTRK3,missense_variant,p.Gly600Cys,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Gly608Cys,ENST00000626019,;NTRK3,missense_variant,p.Gly608Cys,ENST00000629765,;NTRK3,missense_variant,p.Gly600Cys,ENST00000557856,;NTRK3,missense_variant,p.Gly510Cys,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Gly5Cys,ENST00000558576,;NTRK3,non_coding_transcript_exon_variant,,ENST00000559680,; A ENST00000360948 Transcript missense_variant 2128/3004 1822/2520 608/839 G/C Ggc/Tgc rs760692815,COSM1517967,COSM1517968,COSM4708559,COSM88799 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0.01) 16/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs760692815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 87933079 87933079 C A 1 0 0 0 0 1 0 0 0 10774 652 23 1 1 NTRK3 15 87933079 Missense_Mutation SNP C C3N-01030_T 5106666 87933079 14058110 599 21380 ACAN 0 . GRCh38 15 88871389 88871389 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.6954G>T p.Glu2318Asp p.E2318D ENST00000439576 14/18 145 102 43 176 174 2 strelka-varscan-mutect ACAN,missense_variant,p.Glu2318Asp,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Glu2261Asp,ENST00000617301,;ACAN,missense_variant,p.Glu2280Asp,ENST00000559004,;ACAN,missense_variant,p.Glu2318Asp,ENST00000561243,;ACAN,missense_variant,p.Glu2280Asp,ENST00000352105,NM_001135.3;ACAN,missense_variant,p.Glu193Asp,ENST00000560601,;ACAN,upstream_gene_variant,,ENST00000558704,;ACAN,upstream_gene_variant,,ENST00000558604,; T ENST00000439576 Transcript missense_variant 7328/8840 6954/7593 2318/2530 E/D gaG/gaT 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 tolerated(0.18) 14/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804,Gene3D:3.10.100.10,Superfamily_domains:SSF56436 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 88871389 88871389 G T 1 0 0 0 0 1 0 0 0 160 991 35 2 2 ACAN 15 88871389 Missense_Mutation SNP G C3N-01030_T 938310 88871389 13119800 600 21381 CLCN7 0 . GRCh38 16 1451660 1451660 + Silent SNP C C A rs751240482 C3N-01030_T C3N-01030_N C C c.1410G>T p.= p.P470P ENST00000382745 16/25 251 232 19 213 213 0 strelka-varscan-mutect CLCN7,synonymous_variant,p.=,ENST00000382745,NM_001287.5;CLCN7,synonymous_variant,p.=,ENST00000448525,NM_001114331.2;CLCN7,synonymous_variant,p.=,ENST00000262318,;LA16c-390E6.4,upstream_gene_variant,,ENST00000563610,;CLCN7,non_coding_transcript_exon_variant,,ENST00000563642,;CLCN7,upstream_gene_variant,,ENST00000565092,;CLCN7,downstream_gene_variant,,ENST00000563822,;CLCN7,upstream_gene_variant,,ENST00000567836,;CLCN7,upstream_gene_variant,,ENST00000567789,; A ENST00000382745 Transcript synonymous_variant 2016/4720 1410/2418 470/805 P ccG/ccT rs751240482 1 -1 CLCN7 HGNC HGNC:2025 protein_coding YES CCDS32361.1 ENSP00000372193 P51798 UPI000004904C NM_001287.5 16/25 Gene3D:1otsB00,Pfam_domain:PF00654,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF92,Superfamily_domains:SSF81340 LOW 1 SNV 1 1 PASS rs751240482 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 1451660 1451660 C A 1 0 0 0 0 0 0 0 1 3232 639 23 1 1 CLCN7 16 1451660 Silent SNP C C3N-01030_T 1451660 88886685 601 21382 HS3ST6 0 . GRCh38 16 1911904 1911904 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.715T>C p.Phe239Leu p.F239L ENST00000454677 2/2 51 44 7 61 61 0 strelka-varscan-mutect HS3ST6,missense_variant,p.Phe239Leu,ENST00000454677,NM_001009606.3; G ENST00000454677 Transcript missense_variant 832/1273 715/1029 239/342 F/L Ttc/Ctc 1 -1 HS3ST6 HGNC HGNC:14178 protein_coding YES ENSP00000416741 Q96QI5 J3KR40 UPI00004E18B8 NM_001009606.3 deleterious(0) 2/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF41,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -16.86031 1 1 1 1 0 G 3 3 70 1911904 1911904 A G 1 0 0 0 0 1 0 0 0 7263 72 3 5 5 HS3ST6 16 1911904 Missense_Mutation SNP A C3N-01030_T 460244 1911904 88426441 602 21383 HCFC1R1 0 . GRCh38 16 3023254 3023254 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.260C>T p.Ser87Phe p.S87F ENST00000248089 3/4 31 20 11 21 21 0 strelka-varscan-mutect HCFC1R1,missense_variant,p.Ser87Phe,ENST00000248089,NM_001002018.2,NM_017885.3;HCFC1R1,missense_variant,p.Ser87Phe,ENST00000574980,NM_001288665.1;HCFC1R1,missense_variant,p.Ser85Phe,ENST00000354679,NM_001288667.1;HCFC1R1,missense_variant,p.Ser68Phe,ENST00000574151,NM_001288666.1,NM_001002017.2;HCFC1R1,missense_variant,p.Ser47Phe,ENST00000572355,NM_001308070.1;HCFC1R1,missense_variant,p.Ser87Phe,ENST00000573842,;BICDL2,downstream_gene_variant,,ENST00000573514,;BICDL2,downstream_gene_variant,,ENST00000572449,;BICDL2,downstream_gene_variant,,ENST00000389347,NM_001103175.1;CLDN6,upstream_gene_variant,,ENST00000396925,;THOC6,upstream_gene_variant,,ENST00000326266,NM_024339.3;THOC6,upstream_gene_variant,,ENST00000575576,;THOC6,upstream_gene_variant,,ENST00000574549,;THOC6,upstream_gene_variant,,ENST00000253952,NM_001142350.1;TNFRSF12A,downstream_gene_variant,,ENST00000575124,;TNFRSF12A,downstream_gene_variant,,ENST00000326577,NM_016639.2;TNFRSF12A,downstream_gene_variant,,ENST00000341627,;TNFRSF12A,downstream_gene_variant,,ENST00000573001,;TNFRSF12A,downstream_gene_variant,,ENST00000575836,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000575214,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000576921,;HCFC1R1,non_coding_transcript_exon_variant,,ENST00000573095,;BICDL2,downstream_gene_variant,,ENST00000572240,;TNFRSF12A,downstream_gene_variant,,ENST00000571351,;THOC6,upstream_gene_variant,,ENST00000574957,;THOC6,upstream_gene_variant,,ENST00000573704,;THOC6,upstream_gene_variant,,ENST00000571057,;THOC6,upstream_gene_variant,,ENST00000576143,;THOC6,upstream_gene_variant,,ENST00000574498,;THOC6,upstream_gene_variant,,ENST00000571046,;TNFRSF12A,downstream_gene_variant,,ENST00000574699,; A ENST00000248089 Transcript missense_variant 565/965 260/417 87/138 S/F tCc/tTc 1 -1 HCFC1R1 HGNC HGNC:21198 protein_coding YES CCDS10490.1 ENSP00000248089 Q9NWW0 UPI000000D826 NM_001002018.2,NM_017885.3 deleterious_low_confidence(0) 3/4 hmmpanther:PTHR16246,Pfam_domain:PF15226 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 3023254 3023254 G A 1 0 0 0 0 1 0 0 0 6880 1174 41 3 3 HCFC1R1 16 3023254 Missense_Mutation SNP G C3N-01030_T 1111350 3023254 87315091 603 21384 C16orf96 0 . GRCh38 16 4576296 4576296 + Missense_Mutation SNP G G A rs770766977 C3N-01030_T C3N-01030_N G G c.1816G>A p.Ala606Thr p.A606T ENST00000444310 5/16 176 159 17 198 198 0 strelka-varscan-mutect C16orf96,missense_variant,p.Ala606Thr,ENST00000444310,NM_001145011.1; A ENST00000444310 Transcript missense_variant 1816/3823 1816/3426 606/1141 A/T Gcc/Acc rs770766977,COSM970737 1 1 C16orf96 HGNC HGNC:40031 protein_coding YES CCDS53986.1 ENSP00000415027 A6NNT2 UPI0001929538 NM_001145011.1 tolerated(1) 5/16 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs770766977 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 4576296 4576296 G A 1 0 0 0 0 1 0 0 0 1875 1087 38 1 1 C16orf96 16 4576296 Missense_Mutation SNP G C3N-01030_T 1553042 4576296 85762049 604 21385 PDILT 0 . GRCh38 16 20376124 20376124 + Missense_Mutation SNP C C G rs143949312 C3N-01030_T C3N-01030_N C C c.487G>C p.Glu163Gln p.E163Q ENST00000302451 4/12 182 139 43 198 198 0 strelka-varscan-mutect PDILT,missense_variant,p.Glu163Gln,ENST00000302451,NM_174924.1; G ENST00000302451 Transcript missense_variant 736/2153 487/1755 163/584 E/Q Gag/Cag rs143949312,COSM5582083 1 -1 PDILT HGNC HGNC:27338 protein_coding YES CCDS10584.1 ENSP00000305465 Q8N807 UPI000000DAC6 NM_174924.1 tolerated(0.79) 4/12 hmmpanther:PTHR18929:SF58,hmmpanther:PTHR18929,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs143949312 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 20376124 20376124 C G 1 0 0 0 0 1 0 0 0 11762 893 31 4 4 PDILT 16 20376124 Missense_Mutation SNP C C3N-01030_T 15799828 20376124 69962221 605 21386 PDILT 0 . GRCh38 16 20399119 20399119 + Missense_Mutation SNP C C A rs772997693 C3N-01030_T C3N-01030_N C C c.182G>T p.Arg61Leu p.R61L ENST00000302451 2/12 187 157 30 162 161 1 strelka-varscan-mutect PDILT,missense_variant,p.Arg61Leu,ENST00000302451,NM_174924.1;PDILT,missense_variant,p.Arg61Leu,ENST00000575561,; A ENST00000302451 Transcript missense_variant 431/2153 182/1755 61/584 R/L cGc/cTc rs772997693,COSM968046 1 -1 PDILT HGNC HGNC:27338 protein_coding YES CCDS10584.1 ENSP00000305465 Q8N807 UPI000000DAC6 NM_174924.1 deleterious(0.01) 2/12 hmmpanther:PTHR18929:SF58,hmmpanther:PTHR18929,Pfam_domain:PF00085,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772997693 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 20399119 20399119 C A 1 0 0 0 0 1 0 0 0 11762 768 27 1 1 PDILT 16 20399119 Missense_Mutation SNP C C3N-01030_T 22995 20399119 69939226 606 21387 DNAH3 0 . GRCh38 16 21067387 21067387 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.3414C>A p.Asp1138Glu p.D1138E ENST00000261383 24/62 181 138 43 198 197 1 strelka-varscan-mutect DNAH3,missense_variant,p.Asp1138Glu,ENST00000261383,NM_017539.2;DNAH3,upstream_gene_variant,,ENST00000572640,; T ENST00000261383 Transcript missense_variant 3414/12394 3414/12351 1138/4116 D/E gaC/gaA 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 tolerated(0.93) 24/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF08393 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 21067387 21067387 G T 1 0 0 0 0 1 0 0 0 4418 1252 44 2 2 DNAH3 16 21067387 Missense_Mutation SNP G C3N-01030_T 668268 21067387 69270958 607 21388 UBFD1 0 . GRCh38 16 23557990 23557990 + Silent SNP G G T rs771559898 C3N-01030_T C3N-01030_N G G c.66G>T p.= p.V22V ENST00000395878 2/7 32 24 8 35 35 0 strelka-varscan-mutect UBFD1,synonymous_variant,p.=,ENST00000395878,NM_019116.2;UBFD1,synonymous_variant,p.=,ENST00000567212,;UBFD1,synonymous_variant,p.=,ENST00000567264,;EARS2,upstream_gene_variant,,ENST00000449606,NM_001083614.1;EARS2,upstream_gene_variant,,ENST00000563459,;EARS2,upstream_gene_variant,,ENST00000564501,;EARS2,upstream_gene_variant,,ENST00000563232,NM_001308211.1;UBFD1,non_coding_transcript_exon_variant,,ENST00000571064,;UBFD1,upstream_gene_variant,,ENST00000563366,;EARS2,upstream_gene_variant,,ENST00000564461,;EARS2,upstream_gene_variant,,ENST00000561859,;UBFD1,non_coding_transcript_exon_variant,,ENST00000566669,;UBFD1,upstream_gene_variant,,ENST00000569919,;UBFD1,upstream_gene_variant,,ENST00000565634,;EARS2,upstream_gene_variant,,ENST00000564668,;EARS2,upstream_gene_variant,,ENST00000564997,;EARS2,upstream_gene_variant,,ENST00000562799,;EARS2,upstream_gene_variant,,ENST00000563499,;EARS2,upstream_gene_variant,,ENST00000562581,; T ENST00000395878 Transcript synonymous_variant 447/5110 66/930 22/309 V gtG/gtT rs771559898 1 1 UBFD1 HGNC HGNC:30565 protein_coding YES CCDS10613.2 ENSP00000379217 O14562 UPI00001FF0A3 NM_019116.2 2/7 hmmpanther:PTHR16470,Low_complexity_(Seg):seg LOW SNV 2 1 PASS rs771559898 . 4 203 3 0 0 0 0 0 -19.97719 1 1 1 1 0 T 2 4 70 23557990 23557990 G T 1 0 0 0 0 0 0 0 1 17408 1335 47 2 2 UBFD1 16 23557990 Silent SNP G C3N-01030_T 2490603 23557990 66780355 608 21389 ARHGAP17 0 . GRCh38 16 24931143 24931143 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.2156delC p.Pro719LeufsTer7 p.P719Lfs*7 ENST00000289968 19/20 43 34 9 61 61 0 sindel-varindel-pindel ARHGAP17,frameshift_variant,p.Pro719LeufsTer7,ENST00000289968,NM_001006634.2;ARHGAP17,frameshift_variant,p.Pro641LeufsTer7,ENST00000303665,NM_018054.5;ARHGAP17,frameshift_variant,p.Pro87LeufsTer7,ENST00000573765,;ARHGAP17,frameshift_variant,p.Pro7LeufsTer7,ENST00000571843,;ARHGAP17,upstream_gene_variant,,ENST00000571406,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000572314,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000570320,;ARHGAP17,non_coding_transcript_exon_variant,,ENST00000575283,; - ENST00000289968 Transcript frameshift_variant 2226/3461 2156/2646 719/881 P/X cCt/ct 1 -1 ARHGAP17 HGNC HGNC:18239 protein_coding YES CCDS32409.1 ENSP00000289968 Q68EM7 UPI00000433FD NM_001006634.2 19/20 hmmpanther:PTHR14130,hmmpanther:PTHR14130:SF3,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 197 12 0 0 0 0 0 -19.99407 0.9999556 1 1 1 0 - 7 5 70 24931143 24931143 G - 1 0 1 0 1 0 0 0 0 991 1000 35 0 0 ARHGAP17 16 24931143 Frame_Shift_Del DEL G C3N-01030_T 1373153 24931143 65407202 609 21390 C16orf82 0 . GRCh38 16 27067268 27067268 + Nonsense_Mutation SNP C C A rs751190448 C3N-01030_T C3N-01030_N C C c.462C>A p.Tyr154Ter p.Y154* ENST00000505035 1/1 238 202 36 213 213 0 strelka-varscan-mutect C16orf82,stop_gained,p.Tyr154Ter,ENST00000505035,;C16orf82,stop_gained,p.Tyr91Ter,ENST00000418886,NM_001145545.1;RP11-673P17.2,intron_variant,,ENST00000565783,; A ENST00000505035 Transcript stop_gained 562/2459 462/654 154/217 Y/* taC/taA rs751190448 1 1 C16orf82 HGNC HGNC:30755 protein_coding YES ENSP00000489874 Q7Z2V1 UPI00001B3F63 1/1 Pfam_domain:PF15765,hmmpanther:PTHR40139,hmmpanther:PTHR40139:SF1 HIGH SNV 1 PASS rs751190448 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 27067268 27067268 C A 1 0 0 0 0 0 1 0 0 1867 547 19 1 1 C16orf82 16 27067268 Nonsense_Mutation SNP C C3N-01030_T 2136125 27067268 63271077 610 21391 FAM57B 0 . GRCh38 16 30026685 30026685 + Missense_Mutation SNP C C A rs779223633 C3N-01030_T C3N-01030_N C C c.368G>T p.Arg123Leu p.R123L ENST00000380495 3/5 263 229 34 210 210 0 strelka-varscan-mutect FAM57B,missense_variant,p.Arg123Leu,ENST00000380495,NM_031478.4;FAM57B,missense_variant,p.Arg73Leu,ENST00000564806,;FAM57B,missense_variant,p.Arg73Leu,ENST00000279389,NM_001318504.1;FAM57B,missense_variant,p.Arg123Leu,ENST00000561666,;C16orf92,intron_variant,,ENST00000569198,;C16orf92,intron_variant,,ENST00000567847,;C16orf92,downstream_gene_variant,,ENST00000300575,NM_001109659.1,NM_001109660.1;DOC2A,upstream_gene_variant,,ENST00000567824,;DOC2A,upstream_gene_variant,,ENST00000572637,;DOC2A,upstream_gene_variant,,ENST00000570194,;DOC2A,upstream_gene_variant,,ENST00000564075,;FAM57B,3_prime_UTR_variant,,ENST00000569508,;C16orf92,downstream_gene_variant,,ENST00000561910,; A ENST00000380495 Transcript missense_variant 1100/2313 368/825 123/274 R/L cGt/cTt rs779223633,COSM557640 1 -1 FAM57B HGNC HGNC:25295 protein_coding YES CCDS10667.2 ENSP00000369863 Q71RH2 F1T0F5 UPI000022EE26 NM_031478.4 tolerated(0.16) 3/5 Pfam_domain:PF03798,PROSITE_profiles:PS50922,SMART_domains:SM00724 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779223633 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 30026685 30026685 C A 1 0 0 0 0 1 0 0 0 5459 536 19 1 1 FAM57B 16 30026685 Missense_Mutation SNP C C3N-01030_T 2959417 30026685 60311660 611 21392 ITGAX 0 . GRCh38 16 31360039 31360039 + Nonsense_Mutation SNP C C A rs751181508 C3N-01030_T C3N-01030_N C C c.681C>A p.Tyr227Ter p.Y227* ENST00000562522 7/31 180 158 22 138 138 0 strelka-varscan-mutect ITGAX,stop_gained,p.Tyr227Ter,ENST00000268296,NM_000887.4;ITGAX,stop_gained,p.Tyr227Ter,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;ITGAX,downstream_gene_variant,,ENST00000567409,;ITGAX,downstream_gene_variant,,ENST00000564308,;RP11-120K18.3,downstream_gene_variant,,ENST00000561830,; A ENST00000562522 Transcript stop_gained 714/3990 681/3510 227/1169 Y/* taC/taA rs751181508 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 7/31 Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 HIGH 1 SNV 1 1 PASS rs751181508 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 31360039 31360039 C A 1 0 0 0 0 0 1 0 0 7796 489 17 2 2 ITGAX 16 31360039 Nonsense_Mutation SNP C C3N-01030_T 1333354 31360039 58978306 612 21393 ITGAX 0 . GRCh38 16 31380005 31380005 + Silent SNP A A T novel C3N-01030_T C3N-01030_N A A c.3000A>T p.= p.S1000S ENST00000562522 26/31 220 203 17 215 215 0 strelka-mutect ITGAX,synonymous_variant,p.=,ENST00000268296,NM_000887.4;ITGAX,synonymous_variant,p.=,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,; T ENST00000562522 Transcript synonymous_variant 3033/3990 3000/3510 1000/1169 S tcA/tcT 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 26/31 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69179 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 31380005 31380005 A T 1 0 0 0 0 0 0 0 1 7796 175 7 4 4 ITGAX 16 31380005 Silent SNP A C3N-01030_T 19966 31380005 58958340 613 21394 ITGAX 0 . GRCh38 16 31380948 31380948 + Missense_Mutation SNP G G T rs770053055 C3N-01030_T C3N-01030_N G G c.3328G>T p.Val1110Leu p.V1110L ENST00000562522 29/31 207 176 31 175 175 0 strelka-varscan-mutect ITGAX,missense_variant,p.Val1110Leu,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Val1110Leu,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,; T ENST00000562522 Transcript missense_variant 3361/3990 3328/3510 1110/1169 V/L Gta/Tta rs770053055 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.1) 29/31 Gene3D:2k1aA00,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs770053055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 31380948 31380948 G T 1 0 0 0 0 1 0 0 0 7796 1145 40 1 1 ITGAX 16 31380948 Missense_Mutation SNP G C3N-01030_T 943 31380948 58957397 614 21395 TP53TG3D 0 . GRCh38 16 32253620 32253620 + Silent SNP T T A novel C3N-01030_T C3N-01030_N T T c.267T>A p.= p.A89A ENST00000398664 1/2 124 108 16 126 126 0 varscan-mutect TP53TG3D,synonymous_variant,p.=,ENST00000398664,NM_001243722.2;TP53TG3D,intron_variant,,ENST00000569631,;RP11-56L13.7,intron_variant,,ENST00000562604,;TP53TG3D,upstream_gene_variant,,ENST00000564810,;TP53TG3D,synonymous_variant,p.=,ENST00000380148,;TP53TG3D,intron_variant,,ENST00000563025,;TP53TG3D,upstream_gene_variant,,ENST00000568044,;TP53TG3D,upstream_gene_variant,,ENST00000567978,; A ENST00000398664 Transcript synonymous_variant 902/2029 267/375 89/124 A gcT/gcA 1 1 TP53TG3D HGNC HGNC:44657 protein_coding YES CCDS58456.1 ENSP00000455596 Q9ULZ0 UPI000006D8DD NM_001243722.2 1/2 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 32253620 32253620 T A 1 0 0 0 0 0 0 0 1 16869 1567 55 4 4 TP53TG3D 16 32253620 Silent SNP T C3N-01030_T 872672 32253620 58084725 615 21396 CDH11 0 . GRCh38 16 64948710 64948710 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.1972T>C p.Phe658Leu p.F658L ENST00000394156 13/14 108 77 31 165 165 0 strelka-varscan-mutect CDH11,missense_variant,p.Phe658Leu,ENST00000394156,NM_001308392.1;CDH11,intron_variant,,ENST00000268603,NM_001797.2;CDH11,intron_variant,,ENST00000566827,; G ENST00000394156 Transcript missense_variant 2426/6874 1972/2082 658/693 F/L Ttt/Ctt 1 -1 CDH11 HGNC HGNC:1750 protein_coding ENSP00000377711 P55287 UPI000016039D NM_001308392.1 13/14 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 64948710 64948710 A G 1 0 0 0 0 1 0 0 0 2800 101 4 5 5 CDH11 16 64948710 Missense_Mutation SNP A C3N-01030_T 32695090 64948710 25389635 616 21397 FA2H 0 . GRCh38 16 74719044 74719045 + Frame_Shift_Ins INS - - G novel C3N-01030_T C3N-01030_N - - c.729dupC p.Ser244GlnfsTer69 p.S244Qfs*69 ENST00000219368 5/7 199 119 80 231 231 0 sindel-varindel-pindel FA2H,frameshift_variant,p.Ser244GlnfsTer69,ENST00000219368,NM_024306.4;FA2H,frameshift_variant,p.Ser178GlnfsTer?,ENST00000569949,;FA2H,3_prime_UTR_variant,,ENST00000567683,;FA2H,upstream_gene_variant,,ENST00000562145,; G ENST00000219368 Transcript frameshift_variant 799-800/2424 729-730/1119 243-244/372 -/X -/C 1 -1 FA2H HGNC HGNC:21197 protein_coding YES CCDS10911.1 ENSP00000219368 Q7L5A8 UPI000013C77C NM_024306.4 5/7 hmmpanther:PTHR12863,PIRSF_domain:PIRSF005149,Pfam_domain:PF04116 HIGH 1 insertion 1 1 PASS . . 0 207 0 0 3 0 0 0 -20 0.9941562 1 1 1 0 G 7 5 70 74719044 74719044 - G 1 0 1 1 0 0 0 0 0 5221 1580 55 0 0 FA2H 16 74719044 Frame_Shift_Ins INS - C3N-01030_T 9770334 74719044 15619301 617 21398 CNTNAP4 0 . GRCh38 16 76452546 76452546 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1110G>T p.Met370Ile p.M370I ENST00000611870 8/24 176 133 43 301 300 1 strelka-varscan-mutect CNTNAP4,missense_variant,p.Met370Ile,ENST00000307431,;CNTNAP4,missense_variant,p.Met370Ile,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Met322Ile,ENST00000377504,;CNTNAP4,missense_variant,p.Met373Ile,ENST00000476707,;CNTNAP4,missense_variant,p.Met322Ile,ENST00000622250,;CNTNAP4,missense_variant,p.Met297Ile,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; T ENST00000611870 Transcript missense_variant 1495/4867 1110/3927 370/1308 M/I atG/atT 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 tolerated(0.05) 8/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 76452546 76452546 G T 1 0 0 0 0 1 0 0 0 3431 1319 46 2 2 CNTNAP4 16 76452546 Missense_Mutation SNP G C3N-01030_T 1733502 76452546 13885799 618 21399 MON1B 0 . GRCh38 16 77191564 77191564 + Nonsense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.79G>T p.Glu27Ter p.E27* ENST00000248248 2/6 80 59 21 93 93 0 strelka-varscan-mutect MON1B,stop_gained,p.Glu27Ter,ENST00000248248,NM_014940.3;MON1B,stop_gained,p.Glu27Ter,ENST00000439557,NM_001286639.1;MON1B,stop_gained,p.Glu27Ter,ENST00000567291,;MON1B,stop_gained,p.Glu27Ter,ENST00000563612,;MON1B,stop_gained,p.Glu27Ter,ENST00000569610,;MON1B,stop_gained,p.Glu27Ter,ENST00000563279,;MON1B,intron_variant,,ENST00000545553,NM_001286640.1;MON1B,stop_gained,p.Glu27Ter,ENST00000564006,;MON1B,non_coding_transcript_exon_variant,,ENST00000566963,;MON1B,upstream_gene_variant,,ENST00000566455,; T ENST00000248248 Transcript stop_gained 429/6091 79/1644 27/547 E/* Gaa/Taa 1 1 MON1B HGNC HGNC:25020 protein_coding YES CCDS10925.1 ENSP00000248248 Q7L1V2 UPI0000072AD7 NM_014940.3 2/6 hmmpanther:PTHR13027:SF13,hmmpanther:PTHR13027 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 77191564 77191564 G T 1 0 0 0 0 0 1 0 0 9663 1175 41 2 2 MON1B 16 77191564 Nonsense_Mutation SNP G C3N-01030_T 739018 77191564 13146781 619 21400 MBTPS1 0 . GRCh38 16 84095658 84095658 + Missense_Mutation SNP G G C rs138035660 C3N-01030_T C3N-01030_N G G c.569C>G p.Pro190Arg p.P190R ENST00000343411 4/23 218 149 69 187 187 0 strelka-varscan-mutect MBTPS1,missense_variant,p.Pro190Arg,ENST00000343411,NM_003791.3;MBTPS1,intron_variant,,ENST00000570012,;MBTPS1,upstream_gene_variant,,ENST00000569770,;MBTPS1,upstream_gene_variant,,ENST00000565863,;MBTPS1,upstream_gene_variant,,ENST00000563231,; C ENST00000343411 Transcript missense_variant 1065/4338 569/3159 190/1052 P/R cCg/cGg rs138035660 1 -1 MBTPS1 HGNC HGNC:15456 protein_coding YES CCDS10941.1 ENSP00000344223 Q14703 UPI0000033348 NM_003791.3 tolerated(0.23) 4/23 hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF363 MODERATE 1 SNV 1 1 PASS rs138035660 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 84095658 84095658 G C 1 0 0 0 0 1 0 0 0 9294 1116 39 4 4 MBTPS1 16 84095658 Missense_Mutation SNP G C3N-01030_T 6904094 84095658 6242687 620 21401 FOXC2 0 . GRCh38 16 86567832 86567832 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.497G>T p.Arg166Leu p.R166L ENST00000320354 1/1 134 94 40 168 167 1 strelka-varscan-mutect FOXC2,missense_variant,p.Arg166Leu,ENST00000320354,NM_005251.2;FOXC2-AS1,upstream_gene_variant,,ENST00000563280,; T ENST00000320354 Transcript missense_variant 582/2478 497/1506 166/501 R/L cGg/cTg 1 1 FOXC2 HGNC HGNC:3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 UPI000012ADC6 NM_005251.2 deleterious(0) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF189,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 86567832 86567832 G T 1 0 0 0 0 1 0 0 0 5855 1116 39 1 1 FOXC2 16 86567832 Missense_Mutation SNP G C3N-01030_T 2472174 86567832 3770513 621 21402 ZNF469 0 . GRCh38 16 88436416 88436416 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.8862T>A p.Asp2954Glu p.D2954E ENST00000437464 2/2 221 162 59 226 226 0 strelka-varscan-mutect ZNF469,missense_variant,p.Asp2982Glu,ENST00000565624,;ZNF469,missense_variant,p.Asp2954Glu,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 8862/13203 8862/11778 2954/3925 D/E gaT/gaA 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.77) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 88436416 88436416 T A 1 0 0 0 0 1 0 0 0 18500 1432 50 4 4 ZNF469 16 88436416 Missense_Mutation SNP T C3N-01030_T 1868584 88436416 1901929 622 21403 CPNE7 0 . GRCh38 16 89589942 89589942 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.1332C>A p.= p.P444P ENST00000268720 13/17 194 139 55 171 171 0 strelka-varscan-mutect CPNE7,synonymous_variant,p.=,ENST00000268720,NM_014427.4;CPNE7,synonymous_variant,p.=,ENST00000319518,NM_153636.2;CPNE7,synonymous_variant,p.=,ENST00000529800,;CPNE7,upstream_gene_variant,,ENST00000566398,;CPNE7,synonymous_variant,p.=,ENST00000568977,;CPNE7,downstream_gene_variant,,ENST00000532500,; A ENST00000268720 Transcript synonymous_variant 1462/2657 1332/1902 444/633 P ccC/ccA 1 1 CPNE7 HGNC HGNC:2320 protein_coding YES CCDS10980.1 ENSP00000268720 Q9UBL6 UPI0000127C17 NM_014427.4 13/17 Pfam_domain:PF07002,PROSITE_profiles:PS50234,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF6,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 89589942 89589942 C A 1 0 0 0 0 0 0 0 1 3612 581 21 2 2 CPNE7 16 89589942 Silent SNP C C3N-01030_T 1153526 89589942 748403 623 21404 GLOD4 0 . GRCh38 17 775813 775813 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.368A>T p.Tyr123Phe p.Y123F ENST00000301329 4/9 154 87 67 180 180 0 strelka-varscan-mutect GLOD4,missense_variant,p.Tyr327Phe,ENST00000536578,;GLOD4,missense_variant,p.Tyr123Phe,ENST00000301329,NM_016080.3;GLOD4,missense_variant,p.Tyr138Phe,ENST00000301328,;GLOD4,missense_variant,p.Tyr123Phe,ENST00000576419,;GLOD4,upstream_gene_variant,,ENST00000573137,;GLOD4,downstream_gene_variant,,ENST00000625892,;GLOD4,downstream_gene_variant,,ENST00000628529,;AC087392.1,upstream_gene_variant,,ENST00000631259,;GLOD4,3_prime_UTR_variant,,ENST00000574554,;GLOD4,3_prime_UTR_variant,,ENST00000575851,;GLOD4,3_prime_UTR_variant,,ENST00000575790,;GLOD4,3_prime_UTR_variant,,ENST00000574581,;GLOD4,3_prime_UTR_variant,,ENST00000572220,;GLOD4,non_coding_transcript_exon_variant,,ENST00000576239,;GLOD4,non_coding_transcript_exon_variant,,ENST00000571073,;GLOD4,upstream_gene_variant,,ENST00000575528,;GLOD4,downstream_gene_variant,,ENST00000576670,;GLOD4,downstream_gene_variant,,ENST00000574354,;GLOD4,downstream_gene_variant,,ENST00000576750,; A ENST00000301329 Transcript missense_variant 454/2059 368/897 123/298 Y/F tAt/tTt 1 -1 GLOD4 HGNC HGNC:14111 protein_coding YES CCDS32520.1 ENSP00000301329 Q9HC38 UPI000003CA3C NM_016080.3 deleterious(0.01) 4/9 Superfamily_domains:SSF54593 MODERATE 1 SNV 1 1 PASS rs1319836718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 775813 775813 T A 1 0 0 0 0 1 0 0 0 6329 1406 49 4 4 GLOD4 17 775813 Missense_Mutation SNP T C3N-01030_T 775813 82481628 624 21405 ANKFY1 0 . GRCh38 17 4217056 4217056 + Nonsense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.511A>T p.Arg171Ter p.R171* ENST00000570535 4/25 158 93 65 176 176 0 strelka-varscan-mutect ANKFY1,stop_gained,p.Arg129Ter,ENST00000341657,;ANKFY1,stop_gained,p.Arg171Ter,ENST00000570535,NM_001257999.1;ANKFY1,stop_gained,p.Arg129Ter,ENST00000574367,NM_016376.3;ANKFY1,3_prime_UTR_variant,,ENST00000572412,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000570934,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000575955,; A ENST00000570535 Transcript stop_gained 628/6458 511/3636 171/1211 R/* Aga/Tga 1 -1 ANKFY1 HGNC HGNC:20763 protein_coding YES CCDS58502.1 ENSP00000459943 Q9P2R3 UPI00003FECB0 NM_001257999.1 4/25 PROSITE_profiles:PS50097,hmmpanther:PTHR24189,hmmpanther:PTHR24189:SF34,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 HIGH 1 SNV 1 1 PASS rs1451926252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 4217056 4217056 T A 1 0 0 0 0 0 1 0 0 728 1588 55 4 4 ANKFY1 17 4217056 Nonsense_Mutation SNP T C3N-01030_T 3441243 4217056 79040385 625 21406 MINK1 0 . GRCh38 17 4893060 4893060 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2393G>T p.Arg798Leu p.R798L ENST00000355280 20/32 147 89 58 124 122 2 strelka-varscan-mutect MINK1,missense_variant,p.Arg798Leu,ENST00000355280,NM_153827.4,NM_015716.4;MINK1,missense_variant,p.Arg761Leu,ENST00000347992,NM_170663.4;MINK1,missense_variant,p.Arg778Leu,ENST00000453408,NM_001024937.3;CHRNE,downstream_gene_variant,,ENST00000293780,NM_000080.3;MINK1,upstream_gene_variant,,ENST00000576037,;MINK1,3_prime_UTR_variant,,ENST00000574453,NM_001321236.1;MINK1,3_prime_UTR_variant,,ENST00000571207,;MINK1,non_coding_transcript_exon_variant,,ENST00000572330,;MINK1,non_coding_transcript_exon_variant,,ENST00000572629,;MINK1,upstream_gene_variant,,ENST00000574871,;CHRNE,downstream_gene_variant,,ENST00000572438,;MINK1,upstream_gene_variant,,ENST00000575511,;MINK1,upstream_gene_variant,,ENST00000572304,;MINK1,upstream_gene_variant,,ENST00000571526,; T ENST00000355280 Transcript missense_variant 2589/4961 2393/3999 798/1332 R/L cGg/cTg 1 1 MINK1 HGNC HGNC:17565 protein_coding YES CCDS45588.1 ENSP00000347427 Q8N4C8 UPI00001678BB NM_153827.4,NM_015716.4 deleterious(0) 20/32 MODERATE 1 SNV 1 1 PASS rs1238194870 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 4893060 4893060 G T 1 0 0 0 0 1 0 0 0 9551 1116 39 1 1 MINK1 17 4893060 Missense_Mutation SNP G C3N-01030_T 676004 4893060 78364381 626 21407 PITPNM3 0 . GRCh38 17 6474562 6474562 + Silent SNP C C A rs146033772 C3N-01030_T C3N-01030_N C C c.1128G>T p.= p.A376A ENST00000262483 10/20 185 104 81 202 201 1 strelka-varscan-mutect PITPNM3,synonymous_variant,p.=,ENST00000262483,NM_031220.3;PITPNM3,synonymous_variant,p.=,ENST00000421306,NM_001165966.1;PITPNM3,upstream_gene_variant,,ENST00000576664,;PITPNM3,non_coding_transcript_exon_variant,,ENST00000572795,; A ENST00000262483 Transcript synonymous_variant 1216/7086 1128/2925 376/974 A gcG/gcT rs146033772 1 -1 PITPNM3 HGNC HGNC:21043 protein_coding YES CCDS11076.1 ENSP00000262483 Q9BZ71 UPI000022A281 NM_031220.3 10/20 hmmpanther:PTHR10658 LOW 1 SNV 1 1 PASS rs146033772 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 6474562 6474562 C A 1 0 0 0 0 0 0 0 1 12048 639 23 1 1 PITPNM3 17 6474562 Silent SNP C C3N-01030_T 1581502 6474562 76782879 627 21408 TP53 0 . GRCh38 17 7675232 7675232 + Missense_Mutation SNP G G A rs730881999 C3N-01030_T C3N-01030_N G G c.380C>T p.Ser127Phe p.S127F ENST00000269305 5/11 253 161 92 225 225 0 strelka-varscan-mutect TP53,missense_variant,p.Ser127Phe,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Ser127Phe,ENST00000420246,;TP53,missense_variant,p.Ser88Phe,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Ser88Phe,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Ser127Phe,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Ser88Phe,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Ser127Phe,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Ser88Phe,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Ser127Phe,ENST00000445888,;TP53,missense_variant,p.Ser88Phe,ENST00000619485,;TP53,missense_variant,p.Ser127Phe,ENST00000359597,;TP53,missense_variant,p.Ser116Phe,ENST00000615910,;TP53,missense_variant,p.Ser127Phe,ENST00000413465,;TP53,missense_variant,p.Ser127Phe,ENST00000508793,;TP53,missense_variant,p.Ser127Phe,ENST00000503591,;TP53,missense_variant,p.Ser34Phe,ENST00000514944,;TP53,5_prime_UTR_variant,,ENST00000510385,NM_001126116.1;TP53,5_prime_UTR_variant,,ENST00000618944,NM_001276698.1;TP53,5_prime_UTR_variant,,ENST00000504290,NM_001126117.1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001276699.1;TP53,5_prime_UTR_variant,,ENST00000504937,NM_001126115.1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001276697.1;TP53,5_prime_UTR_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000604348,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Ser88Phe,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 570/2579 380/1182 127/393 S/F tCc/tTc rs730881999,TP53_g.12368del,TP53_g.12368C>T,TP53_g.12368C>A,TP53_g.12368C>G,COSM1637542,COSM1649368,COSM216412,COSM216413,COSM216414,COSM3378368,COSM3403294,COSM3403295,COSM3403296,COSM3403297,COSM3403298,COSM43970,COSM44226,COSM45483,COSM46131,COSM5301945,COSM562618,COSM562619,COSM562620 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance,likely_pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs730881999 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 7675232 7675232 G A 1 0 0 0 0 1 0 0 0 16859 1188 41 3 3 TP53 17 7675232 Missense_Mutation SNP G C3N-01030_T 1200670 7675232 75582209 628 21409 ALOX15B 0 . GRCh38 17 8039594 8039594 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.356A>T p.Gln119Leu p.Q119L ENST00000380183 2/14 59 40 19 50 50 0 strelka-varscan-mutect ALOX15B,missense_variant,p.Gln119Leu,ENST00000380183,NM_001141.2;ALOX15B,missense_variant,p.Gln119Leu,ENST00000380173,NM_001039130.1;ALOX15B,missense_variant,p.Gln119Leu,ENST00000572022,;ALOX15B,missense_variant,p.Gln119Leu,ENST00000573359,NM_001039131.1;ALOX15B,non_coding_transcript_exon_variant,,ENST00000571240,; T ENST00000380183 Transcript missense_variant 495/2739 356/2031 119/676 Q/L cAg/cTg 1 1 ALOX15B HGNC HGNC:434 protein_coding YES CCDS11128.1 ENSP00000369530 O15296 UPI0000140991 NM_001141.2 deleterious(0.04) 2/14 PROSITE_profiles:PS50095,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF58,SMART_domains:SM00308,Superfamily_domains:SSF48484 MODERATE 1 SNV 1 1 PASS rs1372970034 . 0 194 15 0 0 0 0 0 -20 0.9998888 1 1 1 0 T 3 4 70 8039594 8039594 A T 1 0 0 0 0 1 0 0 0 639 188 7 4 4 ALOX15B 17 8039594 Missense_Mutation SNP A C3N-01030_T 364362 8039594 75217847 629 21410 MYH1 0 . GRCh38 17 10501464 10501464 + Silent SNP T T C novel C3N-01030_T C3N-01030_N T T c.3384A>G p.= p.A1128A ENST00000226207 27/40 288 172 116 278 278 0 strelka-varscan-mutect MYH1,synonymous_variant,p.=,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; C ENST00000226207 Transcript synonymous_variant 3479/6024 3384/5820 1128/1939 A gcA/gcG 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,Low_complexity_(Seg):seg,Superfamily_domains:SSF90257 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 10501464 10501464 T C 1 0 0 0 0 0 0 0 1 10029 1567 55 5 5 MYH1 17 10501464 Silent SNP T C3N-01030_T 2461870 10501464 72755977 630 21411 MYOCD 0 . GRCh38 17 12752791 12752791 + Silent SNP G G C C3N-01030_T C3N-01030_N G G c.1503G>C p.= p.L501L ENST00000425538 10/14 158 97 61 138 138 0 strelka-varscan-mutect MYOCD,synonymous_variant,p.=,ENST00000425538,NM_001146312.2;MYOCD,synonymous_variant,p.=,ENST00000443061,;MYOCD,synonymous_variant,p.=,ENST00000343344,NM_153604.3;MYOCD,non_coding_transcript_exon_variant,,ENST00000395988,; C ENST00000425538 Transcript synonymous_variant 1703/8466 1503/2961 501/986 L ctG/ctC COSM4853912,COSM4853913,COSM4853914 1 1 MYOCD HGNC HGNC:16067 protein_coding YES CCDS54091.1 ENSP00000401678 Q8IZQ8 UPI000022A2E2 NM_001146312.2 10/14 hmmpanther:PTHR22793:SF11,hmmpanther:PTHR22793 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 70 12752791 12752791 G C 1 0 0 0 0 0 0 0 1 10088 1277 45 4 4 MYOCD 17 12752791 Silent SNP G C3N-01030_T 2251327 12752791 70504650 631 21412 ZNF287 0 . GRCh38 17 16552529 16552530 + Frame_Shift_Ins INS - - AT novel C3N-01030_T C3N-01030_N - - c.1611_1612dupAT p.Cys538TyrfsTer228 p.C538Yfs*228 ENST00000395824 6/6 84 54 30 185 185 0 sindel-varindel-pindel ZNF287,frameshift_variant,p.Cys538TyrfsTer228,ENST00000395824,;ZNF287,frameshift_variant,p.Cys538TyrfsTer228,ENST00000395825,NM_020653.2;ZNF287,downstream_gene_variant,,ENST00000498796,; AT ENST00000395824 Transcript frameshift_variant 2230-2231/3373 1612-1613/2286 538/761 C/YX tgc/tATgc 1 -1 ZNF287 HGNC HGNC:13502 protein_coding YES CCDS11179.2 ENSP00000379168 Q9HBT7 UPI0000200A57 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24402:SF236,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 AT 7 5 70 16552529 16552529 - AT 1 0 1 1 0 0 0 0 0 18401 710 25 0 0 ZNF287 17 16552529 Frame_Shift_Ins INS - C3N-01030_T 3799738 16552529 66704912 632 21413 ZNF624 0 . GRCh38 17 16624340 16624340 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.546G>C p.Gln182His p.Q182H ENST00000311331 6/6 107 61 46 162 162 0 strelka-varscan-mutect ZNF624,missense_variant,p.Gln182His,ENST00000311331,NM_020787.3;ZNF624,non_coding_transcript_exon_variant,,ENST00000579528,; G ENST00000311331 Transcript missense_variant 638/4241 546/2598 182/865 Q/H caG/caC 1 -1 ZNF624 HGNC HGNC:29254 protein_coding YES CCDS11180.1 ENSP00000310472 Q9P2J8 UPI0000456A22 NM_020787.3 tolerated(0.11) 6/6 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 16624340 16624340 C G 1 0 0 0 0 1 0 0 0 18623 680 24 4 4 ZNF624 17 16624340 Missense_Mutation SNP C C3N-01030_T 71811 16624340 66633101 633 21414 MYO19 0 . GRCh38 17 36506557 36506557 + Frame_Shift_Del DEL G G - novel C3N-01030_T C3N-01030_N G G c.1696delC p.Leu566CysfsTer27 p.L566Cfs*27 ENST00000614623 18/26 59 25 34 56 56 0 sindel-varindel-pindel MYO19,frameshift_variant,p.Leu566CysfsTer27,ENST00000614623,NM_001163735.1;MYO19,intron_variant,,ENST00000610930,NM_025109.5;MYO19,frameshift_variant,p.Leu566CysfsTer27,ENST00000610992,;MYO19,non_coding_transcript_exon_variant,,ENST00000611622,;MYO19,non_coding_transcript_exon_variant,,ENST00000611794,;MYO19,non_coding_transcript_exon_variant,,ENST00000611125,;MYO19,non_coding_transcript_exon_variant,,ENST00000614416,;MYO19,intron_variant,,ENST00000621550,;MYO19,upstream_gene_variant,,ENST00000617189,;MYO19,upstream_gene_variant,,ENST00000620943,;MYO19,downstream_gene_variant,,ENST00000611063,;MYO19,downstream_gene_variant,,ENST00000612097,;MYO19,upstream_gene_variant,,ENST00000610576,;MYO19,downstream_gene_variant,,ENST00000615902,;MYO19,downstream_gene_variant,,ENST00000620413,; - ENST00000614623 Transcript frameshift_variant 2219/4054 1696/2913 566/970 L/X Ctg/tg 1 -1 MYO19 HGNC HGNC:26234 protein_coding YES CCDS54112.1 ENSP00000479518 Q96H55 UPI000173AA19 NM_001163735.1 18/26 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF289,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 deletion 2 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999937 1 1 1 0 - 7 5 70 36506557 36506557 G - 1 0 1 0 1 0 0 0 0 10068 991 35 0 0 MYO19 17 36506557 Frame_Shift_Del DEL G C3N-01030_T 19882217 36506557 46750884 634 21415 KRT39 0 . GRCh38 17 40963780 40963780 + Nonsense_Mutation SNP G G T rs761258011 C3N-01030_T C3N-01030_N G G c.555C>A p.Tyr185Ter p.Y185* ENST00000355612 3/7 37 17 20 31 31 0 strelka-varscan-mutect KRT39,stop_gained,p.Tyr185Ter,ENST00000355612,NM_213656.3;AC004231.2,intron_variant,,ENST00000418393,;KRT39,3_prime_UTR_variant,,ENST00000578078,;KRT39,upstream_gene_variant,,ENST00000578029,; T ENST00000355612 Transcript stop_gained 591/1696 555/1476 185/491 Y/* taC/taA rs761258011 1 -1 KRT39 HGNC HGNC:32971 protein_coding YES CCDS11382.1 ENSP00000347823 Q6A163 UPI0000237913 NM_213656.3 3/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF106,Pfam_domain:PF00038,SMART_domains:SM01391,Prints_domain:PR01248 HIGH 1 SNV 1 1 PASS rs761258011 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 40963780 40963780 G T 1 0 0 0 0 0 1 0 0 8358 1159 40 1 1 KRT39 17 40963780 Nonsense_Mutation SNP G C3N-01030_T 4457223 40963780 42293661 635 21416 KRTAP2-4 0 . GRCh38 17 41065667 41065667 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.179G>T p.Arg60Leu p.R60L ENST00000394015 1/1 60 28 32 57 57 0 strelka-varscan-mutect KRTAP2-4,missense_variant,p.Arg60Leu,ENST00000394015,NM_033184.3; A ENST00000394015 Transcript missense_variant 213/764 179/387 60/128 R/L cGc/cTc 1 -1 KRTAP2-4 HGNC HGNC:18891 protein_coding YES CCDS32648.1 ENSP00000377583 Q9BYR9 UPI000006EB3A NM_033184.3 deleterious(0.01) 1/1 hmmpanther:PTHR23262:SF6,hmmpanther:PTHR23262,Pfam_domain:PF01500 MODERATE 1 SNV 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999966 1 1 1 0 A 3 1 70 41065667 41065667 C A 1 0 0 0 0 1 0 0 0 8422 768 27 1 1 KRTAP2-4 17 41065667 Missense_Mutation SNP C C3N-01030_T 101887 41065667 42191774 636 21417 KRT16 0 . GRCh38 17 41610195 41610195 + Missense_Mutation SNP C C A rs772428048 C3N-01030_T C3N-01030_N C C c.1322G>T p.Arg441Leu p.R441L ENST00000301653 7/8 453 191 262 345 345 0 strelka-varscan-mutect KRT16,missense_variant,p.Arg441Leu,ENST00000301653,NM_005557.3;KRT16,downstream_gene_variant,,ENST00000593067,;KRT16,downstream_gene_variant,,ENST00000590990,;KRT16,downstream_gene_variant,,ENST00000588319,; A ENST00000301653 Transcript missense_variant 1387/1644 1322/1422 441/473 R/L cGc/cTc rs772428048 1 -1 KRT16 HGNC HGNC:6423 protein_coding YES CCDS11401.1 ENSP00000301653 P08779 UPI0000001C7B NM_005557.3 tolerated(0.23) 7/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105 MODERATE 1 SNV 1 1 PASS rs772428048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 41610195 41610195 C A 1 0 0 0 0 1 0 0 0 8335 782 27 1 1 KRT16 17 41610195 Missense_Mutation SNP C C3N-01030_T 544528 41610195 41647246 637 21418 KRT16 0 . GRCh38 17 41610405 41610405 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1206C>A p.= p.I402I ENST00000301653 6/8 465 201 264 390 390 0 strelka-varscan-mutect KRT16,synonymous_variant,p.=,ENST00000301653,NM_005557.3;KRT16,downstream_gene_variant,,ENST00000593067,;KRT16,downstream_gene_variant,,ENST00000590990,;KRT16,downstream_gene_variant,,ENST00000588319,; T ENST00000301653 Transcript synonymous_variant 1271/1644 1206/1422 402/473 I atC/atA 1 -1 KRT16 HGNC HGNC:6423 protein_coding YES CCDS11401.1 ENSP00000301653 P08779 UPI0000001C7B NM_005557.3 6/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF105,Gene3D:1.20.5.170,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS rs1379574978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 41610405 41610405 G T 1 0 0 0 0 0 0 0 1 8335 932 33 2 2 KRT16 17 41610405 Silent SNP G C3N-01030_T 210 41610405 41647036 638 21419 OR4D1 0 . GRCh38 17 58155951 58155951 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.798C>T p.= p.L266L ENST00000268912 1/1 254 118 136 214 214 0 strelka-varscan-mutect OR4D1,synonymous_variant,p.=,ENST00000268912,NM_012374.1;MSX2P1,upstream_gene_variant,,ENST00000584100,; T ENST00000268912 Transcript synonymous_variant 819/1024 798/933 266/310 L ctC/ctT 1 1 OR4D1 HGNC HGNC:8293 protein_coding YES CCDS42365.1 ENSP00000365451 Q15615 UPI0000041E8C NM_012374.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF310,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 58155951 58155951 C T 1 0 0 0 0 0 0 0 1 11130 813 29 3 3 OR4D1 17 58155951 Silent SNP C C3N-01030_T 16545546 58155951 25101490 639 21420 BCAS3 0 . GRCh38 17 60889709 60889709 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.676C>T p.Pro226Ser p.P226S ENST00000390652 10/25 186 83 103 221 221 0 strelka-varscan-mutect BCAS3,missense_variant,p.Pro226Ser,ENST00000589222,NM_001320470.1;BCAS3,missense_variant,p.Pro226Ser,ENST00000588462,;BCAS3,missense_variant,p.Pro226Ser,ENST00000390652,NM_001099432.1;BCAS3,missense_variant,p.Pro226Ser,ENST00000408905,;BCAS3,missense_variant,p.Pro226Ser,ENST00000407086,NM_017679.3;BCAS3,5_prime_UTR_variant,,ENST00000588874,;BCAS3,5_prime_UTR_variant,,ENST00000585744,;BCAS3,5_prime_UTR_variant,,ENST00000586484,;BCAS3,5_prime_UTR_variant,,ENST00000590128,;BCAS3,5_prime_UTR_variant,,ENST00000586705,;BCAS3,upstream_gene_variant,,ENST00000586041,;BCAS3,3_prime_UTR_variant,,ENST00000592848,; T ENST00000390652 Transcript missense_variant 707/3531 676/2787 226/928 P/S Cca/Tca 1 1 BCAS3 HGNC HGNC:14347 protein_coding YES CCDS45749.1 ENSP00000375067 Q9H6U6 UPI00001AE949 NM_001099432.1 tolerated(0.11) 10/25 hmmpanther:PTHR13268,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 60889709 60889709 C T 1 0 0 0 0 1 0 0 0 1499 855 30 3 3 BCAS3 17 60889709 Missense_Mutation SNP C C3N-01030_T 2733758 60889709 22367732 640 21421 MARCH10 0 . GRCh38 17 62744430 62744430 + Nonsense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.595A>T p.Arg199Ter p.R199* ENST00000583600 6/12 230 96 134 153 153 0 strelka-varscan-mutect MARCH10,stop_gained,p.Arg160Ter,ENST00000544856,NM_001288780.1;MARCH10,stop_gained,p.Arg199Ter,ENST00000583600,NM_001288779.1;MARCH10,stop_gained,p.Arg161Ter,ENST00000311269,NM_152598.3;MARCH10,stop_gained,p.Arg161Ter,ENST00000456609,NM_001100875.2;MARCH10,stop_gained,p.Arg29Ter,ENST00000580520,; A ENST00000583600 Transcript stop_gained 880/3214 595/2541 199/846 R/* Aga/Tga 1 -1 MARCH10 HGNC HGNC:26655 protein_coding YES CCDS74123.1 ENSP00000463080 J3KTN9 UPI0000EE65AE NM_001288779.1 6/12 hmmpanther:PTHR14471,hmmpanther:PTHR14471:SF5 HIGH 1 SNV 1 1 PASS rs1256509236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 62744430 62744430 T A 1 0 0 0 0 0 1 0 0 9224 1588 55 4 4 MARCH10 17 62744430 Nonsense_Mutation SNP T C3N-01030_T 1854721 62744430 20513011 641 21422 RGS9 0 . GRCh38 17 65225268 65225268 + Missense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.1674G>T p.Glu558Asp p.E558D ENST00000262406 18/19 276 115 161 175 174 1 strelka-varscan-mutect RGS9,missense_variant,p.Glu555Asp,ENST00000449996,NM_001081955.2;RGS9,missense_variant,p.Glu558Asp,ENST00000262406,NM_003835.3;RGS9,missense_variant,p.Glu558Asp,ENST00000635833,;RGS9,missense_variant,p.Glu555Asp,ENST00000443584,NM_001165933.1;RGS9,3_prime_UTR_variant,,ENST00000584234,;RGS9,non_coding_transcript_exon_variant,,ENST00000577595,; T ENST00000262406 Transcript missense_variant 1741/2375 1674/2025 558/674 E/D gaG/gaT COSM3795972 1 1 RGS9 HGNC HGNC:10004 protein_coding YES CCDS42373.1 ENSP00000262406 O75916 UPI000013382A NM_003835.3 tolerated_low_confidence(0.15) 18/19 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF170 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 65225268 65225268 G T 1 0 0 0 0 1 0 0 0 13484 991 35 2 2 RGS9 17 65225268 Missense_Mutation SNP G C3N-01030_T 2480838 65225268 18032173 642 21423 SLC16A5 0 . GRCh38 17 75100414 75100414 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.751G>T p.Gly251Cys p.G251C ENST00000450736 4/6 272 106 166 206 206 0 strelka-varscan-mutect SLC16A5,missense_variant,p.Gly251Cys,ENST00000450736,;SLC16A5,missense_variant,p.Gly251Cys,ENST00000580123,NM_001271765.1;SLC16A5,missense_variant,p.Gly251Cys,ENST00000329783,NM_004695.3;SLC16A5,missense_variant,p.Gly291Cys,ENST00000538213,;SLC16A5,missense_variant,p.Gly251Cys,ENST00000578376,;SLC16A5,downstream_gene_variant,,ENST00000584118,;SLC16A5,downstream_gene_variant,,ENST00000584207,;SLC16A5,downstream_gene_variant,,ENST00000585293,;SLC16A5,downstream_gene_variant,,ENST00000582048,; T ENST00000450736 Transcript missense_variant 1166/2051 751/1518 251/505 G/C Ggc/Tgc 1 1 SLC16A5 HGNC HGNC:10926 protein_coding YES CCDS11713.1 ENSP00000390564 O15375 UPI0000000DC7 deleterious(0) 4/6 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF21,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00892,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 75100414 75100414 G T 1 0 0 0 0 1 0 0 0 14677 1232 43 2 2 SLC16A5 17 75100414 Missense_Mutation SNP G C3N-01030_T 9875146 75100414 8157027 643 21424 RPTOR 0 . GRCh38 17 80892761 80892761 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.2134C>T p.Pro712Ser p.P712S ENST00000306801 19/34 203 86 117 184 184 0 strelka-varscan-mutect RPTOR,missense_variant,p.Pro712Ser,ENST00000306801,NM_020761.2;RPTOR,missense_variant,p.Pro554Ser,ENST00000544334,NM_001163034.1;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,; T ENST00000306801 Transcript missense_variant 2496/6408 2134/4008 712/1335 P/S Ccg/Tcg 1 1 RPTOR HGNC HGNC:30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 UPI000007000F NM_020761.2 tolerated(0.32) 19/34 hmmpanther:PTHR12848 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 80892761 80892761 C T 1 0 0 0 0 1 0 0 0 13920 623 22 3 3 RPTOR 17 80892761 Missense_Mutation SNP C C3N-01030_T 5792347 80892761 2364680 644 21425 HGS 0 . GRCh38 17 81694836 81694836 + Missense_Mutation SNP G G A C3N-01030_T C3N-01030_N G G c.958G>A p.Glu320Lys p.E320K ENST00000329138 12/22 489 408 81 332 332 0 strelka-varscan-mutect HGS,missense_variant,p.Glu320Lys,ENST00000329138,NM_004712.4;HGS,missense_variant,p.Glu40Lys,ENST00000571237,;HGS,downstream_gene_variant,,ENST00000572392,;MIR6786,downstream_gene_variant,,ENST00000616843,;RP13-1032I1.11,downstream_gene_variant,,ENST00000620344,;HGS,non_coding_transcript_exon_variant,,ENST00000575058,;HGS,upstream_gene_variant,,ENST00000571647,;HGS,downstream_gene_variant,,ENST00000573080,;HGS,downstream_gene_variant,,ENST00000576498,;HGS,downstream_gene_variant,,ENST00000576393,;HGS,upstream_gene_variant,,ENST00000570355,;HGS,downstream_gene_variant,,ENST00000576087,;HGS,upstream_gene_variant,,ENST00000573949,;HGS,upstream_gene_variant,,ENST00000571885,; A ENST00000329138 Transcript missense_variant 1093/2970 958/2334 320/777 E/K Gag/Aag COSM437794 1 1 HGS HGNC HGNC:4897 protein_coding YES CCDS11784.1 ENSP00000331201 O14964 A0A0S2Z4R4 UPI000004493D NM_004712.4 tolerated(0.09) 12/22 PIRSF_domain:PIRSF036956,hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF83 1 MODERATE 1 SNV 1 1 1 PASS rs1483430322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 81694836 81694836 G A 1 0 0 0 0 1 0 0 0 6972 1291 45 3 3 HGS 17 81694836 Missense_Mutation SNP G C3N-01030_T 802075 81694836 1562605 645 21426 B3GNTL1 0 . GRCh38 17 83051761 83051761 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.36G>C p.Glu12Asp p.E12D ENST00000320865 1/13 131 67 64 106 106 0 strelka-varscan-mutect B3GNTL1,missense_variant,p.Glu12Asp,ENST00000320865,NM_001009905.1;B3GNTL1,upstream_gene_variant,,ENST00000576599,;B3GNTL1,upstream_gene_variant,,ENST00000571954,;B3GNTL1,upstream_gene_variant,,ENST00000573629,;B3GNTL1,upstream_gene_variant,,ENST00000570947,;B3GNTL1,missense_variant,p.Glu12Asp,ENST00000571218,; G ENST00000320865 Transcript missense_variant 50/1383 36/1086 12/361 E/D gaG/gaC 1 -1 B3GNTL1 HGNC HGNC:21727 protein_coding YES CCDS32778.1 ENSP00000319979 Q67FW5 A0A024R8X6 UPI00003B5C5A NM_001009905.1 tolerated_low_confidence(0.5) 1/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 83051761 83051761 C G 1 0 0 0 0 1 0 0 0 1421 912 32 4 4 B3GNTL1 17 83051761 Missense_Mutation SNP C C3N-01030_T 1356925 83051761 205680 646 21427 CLUL1 0 . GRCh38 18 645079 645079 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1535A>T p.Lys512Met p.K512M ENST00000540035 10/11 82 65 17 66 66 0 strelka-varscan-mutect CLUL1,missense_variant,p.Lys485Met,ENST00000581619,;CLUL1,missense_variant,p.Lys512Met,ENST00000540035,NM_001289036.1;CLUL1,missense_variant,p.Lys512Met,ENST00000620089,;CLUL1,missense_variant,p.Lys460Met,ENST00000400606,NM_014410.4;CLUL1,missense_variant,p.Lys460Met,ENST00000338387,NM_001318522.1,NM_199167.1;CLUL1,missense_variant,p.Lys460Met,ENST00000579494,;CLUL1,intron_variant,,ENST00000585155,;TYMSOS,intron_variant,,ENST00000585033,;TYMSOS,downstream_gene_variant,,ENST00000323813,; T ENST00000540035 Transcript missense_variant 1744/2199 1535/1557 512/518 K/M aAg/aTg 1 1 CLUL1 HGNC HGNC:2096 protein_coding YES CCDS74187.1 ENSP00000441726 F5GWQ8 UPI000206520E NM_001289036.1 deleterious(0) 10/11 hmmpanther:PTHR10970:SF2,hmmpanther:PTHR10970,Pfam_domain:PF01093,SMART_domains:SM00035 MODERATE SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 645079 645079 A T 1 0 0 0 0 1 0 0 0 3343 72 3 4 4 CLUL1 18 645079 Missense_Mutation SNP A C3N-01030_T 645079 79728206 647 21428 ENOSF1 0 . GRCh38 18 683260 683260 + Missense_Mutation SNP C C A rs376976768 C3N-01030_T C3N-01030_N C C c.925G>T p.Ala309Ser p.A309S ENST00000340116 11/15 121 88 33 117 117 0 strelka-varscan-mutect ENOSF1,missense_variant,p.Ala206Ser,ENST00000383578,NM_001318759.1,NM_001126123.3;ENOSF1,missense_variant,p.Ala288Ser,ENST00000251101,NM_017512.5;ENOSF1,missense_variant,p.Ala309Ser,ENST00000340116,NM_202758.3;ENOSF1,missense_variant,p.Ala212Ser,ENST00000580982,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000583973,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000581928,;ENOSF1,3_prime_UTR_variant,,ENST00000581475,NM_001318760.1;ENOSF1,3_prime_UTR_variant,,ENST00000585128,;ENOSF1,3_prime_UTR_variant,,ENST00000584453,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000584259,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000578651,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000582745,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000578647,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000584706,;ENOSF1,downstream_gene_variant,,ENST00000585004,;ENOSF1,downstream_gene_variant,,ENST00000577334,; A ENST00000340116 Transcript missense_variant 963/1658 925/1353 309/450 A/S Gcc/Tcc rs376976768,COSM3145564,COSM3145565 1 -1 ENOSF1 HGNC HGNC:30365 protein_coding YES CCDS11823.1 ENSP00000345974 Q7L5Y1 UPI0000252153 NM_202758.3 deleterious(0.02) 11/15 Gene3D:3.20.20.120,Pfam_domain:PF13378,hmmpanther:PTHR13794,hmmpanther:PTHR13794:SF58,SMART_domains:SM00922,Superfamily_domains:SSF51604 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs376976768 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 683260 683260 C A 1 0 0 0 0 1 0 0 0 4970 768 27 1 1 ENOSF1 18 683260 Missense_Mutation SNP C C3N-01030_T 38181 683260 79690025 648 21429 ENOSF1 0 . GRCh38 18 712406 712406 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.101C>G p.Ala34Gly p.A34G ENST00000340116 1/15 163 122 41 86 86 0 strelka-varscan-mutect ENOSF1,missense_variant,p.Ala34Gly,ENST00000340116,NM_202758.3;ENOSF1,intron_variant,,ENST00000383578,NM_001318759.1,NM_001126123.3;ENOSF1,intron_variant,,ENST00000251101,NM_017512.5;ENOSF1,intron_variant,,ENST00000580982,;ENOSF1,intron_variant,,ENST00000583771,;RP11-806L2.6,downstream_gene_variant,,ENST00000580007,;ENOSF1,non_coding_transcript_exon_variant,,ENST00000581332,;ENOSF1,intron_variant,,ENST00000580605,;ENOSF1,intron_variant,,ENST00000581475,NM_001318760.1;ENOSF1,intron_variant,,ENST00000585004,;ENOSF1,intron_variant,,ENST00000585128,;ENOSF1,intron_variant,,ENST00000584453,;ENOSF1,intron_variant,,ENST00000578651,; C ENST00000340116 Transcript missense_variant 139/1658 101/1353 34/450 A/G gCg/gGg 1 -1 ENOSF1 HGNC HGNC:30365 protein_coding YES CCDS11823.1 ENSP00000345974 Q7L5Y1 UPI0000252153 NM_202758.3 tolerated_low_confidence(0.15) 1/15 hmmpanther:PTHR13794,hmmpanther:PTHR13794:SF58 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 712406 712406 G C 1 0 0 0 0 1 0 0 0 4970 1087 38 4 4 ENOSF1 18 712406 Missense_Mutation SNP G C3N-01030_T 29146 712406 79660879 649 21430 SMCHD1 0 . GRCh38 18 2752487 2752487 + Splice_Site SNP G G T novel C3N-01030_T C3N-01030_N G G c.4282-1G>T p.X1428_splice ENST00000320876 198 158 40 284 280 4 strelka-varscan-mutect SMCHD1,splice_acceptor_variant,,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,splice_acceptor_variant,,ENST00000577880,;SMCHD1,splice_acceptor_variant,,ENST00000584897,;SMCHD1,splice_acceptor_variant,,ENST00000583441,; T ENST00000320876 Transcript splice_acceptor_variant -/8821 4282/6018 1428/2005 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 33/47 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 70 2752487 2752487 G T 1 0 0 0 0 0 0 1 0 15081 1014 35 2 2 SMCHD1 18 2752487 Splice_Site SNP G C3N-01030_T 2040081 2752487 77620798 650 21431 EPB41L3 0 . GRCh38 18 5397190 5397190 + Silent SNP C C T C3N-01030_T C3N-01030_N C C c.2709G>A p.= p.E903E ENST00000341928 18/23 288 262 26 225 225 0 strelka-varscan-mutect EPB41L3,synonymous_variant,p.=,ENST00000341928,NM_012307.3;EPB41L3,synonymous_variant,p.=,ENST00000342933,;EPB41L3,synonymous_variant,p.=,ENST00000400111,;EPB41L3,synonymous_variant,p.=,ENST00000544123,NM_001281533.1;EPB41L3,synonymous_variant,p.=,ENST00000540638,NM_001281534.1;EPB41L3,synonymous_variant,p.=,ENST00000545076,NM_001281535.1;EPB41L3,synonymous_variant,p.=,ENST00000578524,;EPB41L3,synonymous_variant,p.=,ENST00000581292,;EPB41L3,upstream_gene_variant,,ENST00000579951,;EPB41L3,downstream_gene_variant,,ENST00000579271,;EPB41L3,downstream_gene_variant,,ENST00000581387,;EPB41L3,downstream_gene_variant,,ENST00000580647,;EPB41L3,downstream_gene_variant,,ENST00000580316,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000542652,;EPB41L3,downstream_gene_variant,,ENST00000582729,;EPB41L3,3_prime_UTR_variant,,ENST00000637651,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578618,;EPB41L3,downstream_gene_variant,,ENST00000584055,;EPB41L3,downstream_gene_variant,,ENST00000578196,; T ENST00000341928 Transcript synonymous_variant 3050/4706 2709/3264 903/1087 E gaG/gaA COSM4869269,COSM4869270,COSM989060 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 18/23 Low_complexity_(Seg):seg 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 5397190 5397190 C T 1 0 0 0 0 0 0 0 1 5001 680 24 3 3 EPB41L3 18 5397190 Silent SNP C C3N-01030_T 2644703 5397190 74976095 651 21432 LAMA1 0 . GRCh38 18 7117660 7117660 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.61G>T p.Gly21Cys p.G21C ENST00000389658 1/63 391 303 88 261 261 0 strelka-varscan-mutect LAMA1,missense_variant,p.Gly21Cys,ENST00000389658,NM_005559.3;LAMA1,splice_region_variant,,ENST00000579014,; A ENST00000389658 Transcript missense_variant,splice_region_variant 155/9657 61/9228 21/3075 G/C Ggc/Tgc 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0.01) 1/63 PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00136 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 7117660 7117660 C A 1 0 0 0 0 1 0 0 0 8509 695 24 2 2 LAMA1 18 7117660 Missense_Mutation SNP C C3N-01030_T 1720470 7117660 73255625 652 21433 ANKRD30B 0 . GRCh38 18 14796416 14796416 + Splice_Site SNP G G C novel C3N-01030_T C3N-01030_N G G c.1927+1G>C p.X643_splice ENST00000358984 76 62 14 108 108 0 strelka-varscan-mutect ANKRD30B,splice_donor_variant,,ENST00000358984,NM_001145029.1;ANKRD30B,intron_variant,,ENST00000579292,;ANKRD30B,splice_donor_variant,,ENST00000580206,; C ENST00000358984 Transcript splice_donor_variant -/4359 1927/4179 643/1392 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 18/35 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 70 14796416 14796416 G C 1 0 0 0 0 0 0 1 0 762 1275 44 4 4 ANKRD30B 18 14796416 Splice_Site SNP G C3N-01030_T 7678756 14796416 65576869 653 21434 DSG1 0 . GRCh38 18 31355021 31355021 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.2825A>T p.Glu942Val p.E942V ENST00000257192 15/15 249 174 75 266 266 0 strelka-varscan-mutect DSG1,missense_variant,p.Glu942Val,ENST00000257192,NM_001942.3;DSG1,missense_variant,p.Glu301Val,ENST00000462981,;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578477,;DSG1-AS1,intron_variant,,ENST00000581452,;DSG1-AS1,upstream_gene_variant,,ENST00000578119,; T ENST00000257192 Transcript missense_variant 3037/5045 2825/3150 942/1049 E/V gAg/gTg 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 deleterious(0) 15/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 31355021 31355021 A T 1 0 0 0 0 1 0 0 0 4597 304 11 4 4 DSG1 18 31355021 Missense_Mutation SNP A C3N-01030_T 16558605 31355021 49018264 654 21435 RIT2 0 . GRCh38 18 42923632 42923632 + Missense_Mutation SNP G G C rs762070204 C3N-01030_T C3N-01030_N G G c.366C>G p.His122Gln p.H122Q ENST00000326695 4/5 127 101 26 187 186 1 strelka-mutect RIT2,missense_variant,p.His122Gln,ENST00000589109,NM_001272077.1;RIT2,missense_variant,p.His122Gln,ENST00000326695,NM_002930.3;RIT2,missense_variant,p.Thr143Arg,ENST00000590910,;RIT2,non_coding_transcript_exon_variant,,ENST00000594852,; C ENST00000326695 Transcript missense_variant 538/1092 366/654 122/217 H/Q caC/caG rs762070204 1 -1 RIT2 HGNC HGNC:10017 protein_coding YES CCDS11921.1 ENSP00000321805 Q99578 UPI0000073E97 NM_002930.3 tolerated(0.14) 4/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF203,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 1 1 PASS rs762070204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 42923632 42923632 G C 1 0 0 0 0 1 0 0 0 13562 1377 48 4 4 RIT2 18 42923632 Missense_Mutation SNP G C3N-01030_T 11568611 42923632 37449653 655 21436 TCEB3B 0 . GRCh38 18 47034311 47034311 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.954C>A p.= p.P318P ENST00000332567 1/1 66 43 23 91 91 0 strelka-varscan-mutect TCEB3B,synonymous_variant,p.=,ENST00000332567,NM_016427.2;KATNAL2,intron_variant,,ENST00000245121,NM_031303.2;TCEB3B,intron_variant,,ENST00000620522,;KATNAL2,intron_variant,,ENST00000356157,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,intron_variant,,ENST00000585469,;TCEB3C,upstream_gene_variant,,ENST00000330682,NM_145653.3; T ENST00000332567 Transcript synonymous_variant 1311/3050 954/2262 318/753 P ccC/ccA 1 -1 TCEB3B HGNC HGNC:30771 protein_coding YES CCDS11932.1 ENSP00000331302 Q8IYF1 UPI0000140A82 NM_016427.2 1/1 hmmpanther:PTHR15141:SF7,hmmpanther:PTHR15141 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 47034311 47034311 G T 1 0 0 0 0 0 0 0 1 16089 1335 47 2 2 TCEB3B 18 47034311 Silent SNP G C3N-01030_T 4110679 47034311 33338974 656 21437 SERPINB5 0 . GRCh38 18 63489459 63489459 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.419C>A p.Thr140Lys p.T140K ENST00000382771 4/7 52 33 19 91 91 0 strelka-mutect SERPINB5,missense_variant,p.Thr140Lys,ENST00000382771,NM_002639.4;SERPINB5,missense_variant,p.Thr140Lys,ENST00000489441,;SERPINB5,downstream_gene_variant,,ENST00000424602,;RP11-635N19.3,downstream_gene_variant,,ENST00000602456,;SERPINB5,upstream_gene_variant,,ENST00000464346,;SERPINB5,upstream_gene_variant,,ENST00000465652,;SERPINB5,non_coding_transcript_exon_variant,,ENST00000588986,; A ENST00000382771 Transcript missense_variant 711/2783 419/1128 140/375 T/K aCa/aAa 1 1 SERPINB5 HGNC HGNC:8949 protein_coding YES CCDS32839.1 ENSP00000372221 P36952 A0A024R2B6 UPI0000201E51 NM_002639.4 deleterious(0) 4/7 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF55,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 63489459 63489459 C A 1 0 0 0 0 1 0 0 0 14380 492 17 2 2 SERPINB5 18 63489459 Missense_Mutation SNP C C3N-01030_T 16455148 63489459 16883826 657 21438 DOK6 0 . GRCh38 18 69401304 69401304 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.60G>T p.Lys20Asn p.K20N ENST00000382713 1/8 48 33 15 47 47 0 strelka-varscan-mutect DOK6,missense_variant,p.Lys20Asn,ENST00000382713,NM_152721.5;RP11-17E3.1,upstream_gene_variant,,ENST00000619582,; T ENST00000382713 Transcript missense_variant 250/8890 60/996 20/331 K/N aaG/aaT 1 1 DOK6 HGNC HGNC:28301 protein_coding YES CCDS32841.1 ENSP00000372160 Q6PKX4 UPI000035EC7C NM_152721.5 tolerated(0.26) 1/8 Gene3D:2.30.29.30,hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF43,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 69401304 69401304 G T 1 0 0 0 0 1 0 0 0 4516 962 34 2 2 DOK6 18 69401304 Missense_Mutation SNP G C3N-01030_T 5911845 69401304 10971981 658 21439 ZNF516 0 . GRCh38 18 76441402 76441402 + Silent SNP C C A rs753884582 C3N-01030_T C3N-01030_N C C c.1653G>T p.= p.A551A ENST00000443185 3/7 130 92 38 128 128 0 strelka-varscan-mutect ZNF516,synonymous_variant,p.=,ENST00000443185,NM_014643.3;ZNF516,downstream_gene_variant,,ENST00000532857,; A ENST00000443185 Transcript synonymous_variant 1971/8118 1653/3492 551/1163 A gcG/gcT rs753884582 1 -1 ZNF516 HGNC HGNC:28990 protein_coding YES CCDS74234.1 ENSP00000394757 Q92618 UPI00001394A1 NM_014643.3 3/7 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3 LOW 1 SNV 1 1 PASS rs753884582 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 76441402 76441402 C A 1 0 0 0 0 0 0 0 1 18532 639 23 1 1 ZNF516 18 76441402 Silent SNP C C3N-01030_T 7040098 76441402 3931883 659 21440 SF3A2 0 . GRCh38 19 2243452 2243452 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.34G>T p.Gly12Trp p.G12W ENST00000221494 2/9 51 39 12 51 51 0 strelka-varscan-mutect SF3A2,missense_variant,p.Gly12Trp,ENST00000221494,NM_007165.4;SF3A2,missense_variant,p.Gly12Trp,ENST00000586396,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592314,;SF3A2,non_coding_transcript_exon_variant,,ENST00000589118,;SF3A2,non_coding_transcript_exon_variant,,ENST00000592839,;SF3A2,non_coding_transcript_exon_variant,,ENST00000590034,;SF3A2,upstream_gene_variant,,ENST00000587637,; T ENST00000221494 Transcript missense_variant 469/1963 34/1395 12/464 G/W Ggg/Tgg 1 1 SF3A2 HGNC HGNC:10766 protein_coding YES CCDS12084.1 ENSP00000221494 Q15428 UPI0000135468 NM_007165.4 deleterious_low_confidence(0) 2/9 hmmpanther:PTHR23205,hmmpanther:PTHR23205:SF0 MODERATE 1 SNV 1 1 PASS rs1285527225 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 2243452 2243452 G T 1 0 0 0 0 1 0 0 0 14426 1116 39 1 1 SF3A2 19 2243452 Missense_Mutation SNP G C3N-01030_T 2243452 56374164 660 21441 NFIC 0 . GRCh38 19 3366644 3366644 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.8C>T p.Ser3Leu p.S3L ENST00000443272 1/11 53 38 15 44 44 0 strelka-varscan-mutect NFIC,missense_variant,p.Ser3Leu,ENST00000443272,NM_001245002.1;NFIC,missense_variant,p.Ser3Leu,ENST00000341919,NM_005597.3;NFIC,missense_variant,p.Ser3Leu,ENST00000590282,NM_001245004.1;NFIC,intron_variant,,ENST00000589123,NM_205843.2;NFIC,intron_variant,,ENST00000395111,NM_001245005.1;NFIC,intron_variant,,ENST00000586919,;AC005514.2,upstream_gene_variant,,ENST00000623521,; T ENST00000443272 Transcript missense_variant 59/1716 8/1527 3/508 S/L tCg/tTg 1 1 NFIC HGNC HGNC:7786 protein_coding YES CCDS59330.1 ENSP00000396843 P08651 UPI000012FFC8 NM_001245002.1 tolerated(0.05) 1/11 PROSITE_profiles:PS51080,hmmpanther:PTHR11492 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 3366644 3366644 C T 1 0 0 0 0 1 0 0 0 10409 893 31 1 1 NFIC 19 3366644 Missense_Mutation SNP C C3N-01030_T 1123192 3366644 55250972 661 21442 CREB3L3 0 . GRCh38 19 4157275 4157275 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.437C>A p.Ala146Asp p.A146D ENST00000078445 3/10 220 152 68 189 189 0 strelka-varscan-mutect CREB3L3,missense_variant,p.Ala146Asp,ENST00000078445,NM_032607.2;CREB3L3,missense_variant,p.Ala145Asp,ENST00000595923,NM_001271995.1;CREB3L3,missense_variant,p.Ala146Asp,ENST00000602257,NM_001271996.1;CREB3L3,missense_variant,p.Ala146Asp,ENST00000602147,NM_001271997.1; A ENST00000078445 Transcript missense_variant 584/2618 437/1386 146/461 A/D gCc/gAc 1 1 CREB3L3 HGNC HGNC:18855 protein_coding YES CCDS12121.1 ENSP00000078445 Q68CJ9 UPI000006FCF0 NM_032607.2 deleterious(0.05) 3/10 hmmpanther:PTHR22952,hmmpanther:PTHR22952:SF98 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 4157275 4157275 C A 1 0 0 0 0 1 0 0 0 3658 739 26 2 2 CREB3L3 19 4157275 Missense_Mutation SNP C C3N-01030_T 790631 4157275 54460341 662 21443 PTPRS 0 . GRCh38 19 5231534 5231534 + Missense_Mutation SNP G G A rs758460182 C3N-01030_T C3N-01030_N G G c.1931C>T p.Pro644Leu p.P644L ENST00000587303 13/37 286 248 38 183 183 0 strelka-varscan-mutect PTPRS,missense_variant,p.Pro644Leu,ENST00000587303,NM_002850.3;PTPRS,missense_variant,p.Pro631Leu,ENST00000588012,NM_130854.2;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000592099,NM_130853.2;PTPRS,intron_variant,,ENST00000353284,NM_130855.2;PTPRS,intron_variant,,ENST00000588552,; A ENST00000587303 Transcript missense_variant 2031/6353 1931/5847 644/1948 P/L cCg/cTg rs758460182,COSM5364972,COSM5364973 1 -1 PTPRS HGNC HGNC:9681 protein_coding YES CCDS45930.1 ENSP00000467537 Q13332 UPI000059D63E NM_002850.3 tolerated(0.28) 13/37 PROSITE_profiles:PS50853,hmmpanther:PTHR19134:SF204,hmmpanther:PTHR19134,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs758460182 . 0 196 0 7 7 0 0 0 -15.68549 0.1521513 1 1 0 0 A 3 1 70 5231534 5231534 G A 1 0 0 0 0 1 0 0 0 12966 1116 39 1 1 PTPRS 19 5231534 Missense_Mutation SNP G C3N-01030_T 1074259 5231534 53386082 663 21444 SAFB 0 . GRCh38 19 5667107 5667107 + Missense_Mutation SNP G G T rs201604799 C3N-01030_T C3N-01030_N G G c.2396G>T p.Gly799Val p.G799V ENST00000588852 18/21 219 160 59 156 156 0 strelka-varscan-mutect SAFB,missense_variant,p.Gly799Val,ENST00000292123,NM_001320572.1,NM_002967.3;SAFB,missense_variant,p.Gly798Val,ENST00000592224,NM_001201339.1;SAFB,missense_variant,p.Gly799Val,ENST00000588852,NM_001201338.1;SAFB,missense_variant,p.Gly730Val,ENST00000454510,NM_001201340.1;SAFB,downstream_gene_variant,,ENST00000589006,;SAFB,3_prime_UTR_variant,,ENST00000589863,NM_001320571.1;SAFB,non_coding_transcript_exon_variant,,ENST00000591991,;SAFB,non_coding_transcript_exon_variant,,ENST00000592555,;SAFB,downstream_gene_variant,,ENST00000586281,; T ENST00000588852 Transcript missense_variant 2449/2842 2396/2754 799/917 G/V gGg/gTg rs201604799 1 1 SAFB HGNC HGNC:10520 protein_coding YES CCDS59339.1 ENSP00000467423 Q15424 UPI0000E5BE82 NM_001201338.1 deleterious(0.02) 18/21 hmmpanther:PTHR15683:SF6,hmmpanther:PTHR15683 MODERATE 1 SNV 1 1 PASS rs201604799 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 5667107 5667107 G T 1 0 0 0 0 1 0 0 0 14065 1232 43 2 2 SAFB 19 5667107 Missense_Mutation SNP G C3N-01030_T 435573 5667107 52950509 664 21445 GTF2F1 0 . GRCh38 19 6380682 6380682 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1240G>T p.Val414Leu p.V414L ENST00000394456 12/13 189 132 57 114 114 0 strelka-varscan-mutect GTF2F1,missense_variant,p.Val414Leu,ENST00000394456,NM_002096.2;GTF2F1,missense_variant,p.Val330Leu,ENST00000593678,;PSPN,upstream_gene_variant,,ENST00000597721,;GTF2F1,downstream_gene_variant,,ENST00000595047,;PSPN,upstream_gene_variant,,ENST00000245810,NM_004158.2;GTF2F1,non_coding_transcript_exon_variant,,ENST00000594213,;GTF2F1,non_coding_transcript_exon_variant,,ENST00000594965,; A ENST00000394456 Transcript missense_variant 1705/2731 1240/1554 414/517 V/L Gtg/Ttg 1 -1 GTF2F1 HGNC HGNC:4652 protein_coding YES CCDS12165.1 ENSP00000377969 P35269 UPI000007323F NM_002096.2 tolerated(0.19) 12/13 hmmpanther:PTHR13011,Pfam_domain:PF05793 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 6380682 6380682 C A 1 0 0 0 0 1 0 0 0 6740 507 18 2 2 GTF2F1 19 6380682 Missense_Mutation SNP C C3N-01030_T 713575 6380682 52236934 665 21446 ADGRE1 0 . GRCh38 19 6901957 6901957 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.597C>A p.Cys199Ter p.C199* ENST00000312053 6/21 203 146 57 190 189 1 strelka-varscan-mutect ADGRE1,stop_gained,p.Cys199Ter,ENST00000312053,NM_001974.4;ADGRE1,stop_gained,p.Cys147Ter,ENST00000381404,NM_001256252.1;ADGRE1,stop_gained,p.Cys199Ter,ENST00000250572,NM_001256253.1;ADGRE1,stop_gained,p.Cys165Ter,ENST00000595026,;ADGRE1,intron_variant,,ENST00000381407,NM_001256254.1;ADGRE1,intron_variant,,ENST00000450315,NM_001256255.1;ADGRE1,downstream_gene_variant,,ENST00000601198,;ADGRE1,downstream_gene_variant,,ENST00000596944,;CTC-312O10.2,downstream_gene_variant,,ENST00000595362,; A ENST00000312053 Transcript stop_gained 634/3128 597/2661 199/886 C/* tgC/tgA 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 6/21 PROSITE_profiles:PS50026,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303,PROSITE_patterns:PS00010,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 6901957 6901957 C A 1 0 0 0 0 0 1 0 0 359 718 25 2 2 ADGRE1 19 6901957 Nonsense_Mutation SNP C C3N-01030_T 521275 6901957 51715659 666 21447 CD209 0 . GRCh38 19 7747321 7747321 + Missense_Mutation SNP A A G C3N-01030_T C3N-01030_N A A c.91T>C p.Tyr31His p.Y31H ENST00000315599 2/7 193 148 45 164 164 0 strelka-varscan-mutect CD209,missense_variant,p.Tyr31His,ENST00000315599,NM_021155.3;CD209,missense_variant,p.Tyr31His,ENST00000593660,;CD209,missense_variant,p.Tyr31His,ENST00000601951,;CD209,missense_variant,p.Tyr31His,ENST00000394173,NM_001144899.1;CD209,missense_variant,p.Tyr31His,ENST00000354397,NM_001144897.1;CD209,missense_variant,p.Tyr31His,ENST00000315591,NM_001144896.1;CD209,missense_variant,p.Tyr31His,ENST00000601256,;CD209,missense_variant,p.Tyr31His,ENST00000602261,NM_001144895.1;CD209,missense_variant,p.Tyr31His,ENST00000394161,;CD209,intron_variant,,ENST00000204801,NM_001144894.1;CD209,intron_variant,,ENST00000593821,NM_001144893.1;RPL21P129,upstream_gene_variant,,ENST00000491732,; G ENST00000315599 Transcript missense_variant 114/4283 91/1215 31/404 Y/H Tac/Cac COSM1200268,COSM1200269 1 -1 CD209 HGNC HGNC:1641 protein_coding YES CCDS12186.1 ENSP00000315477 Q9NNX6 UPI000003422C NM_021155.3 tolerated(0.49) 2/7 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1447855974 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 7747321 7747321 A G 1 0 0 0 0 1 0 0 0 2687 449 16 5 5 CD209 19 7747321 Missense_Mutation SNP A C3N-01030_T 845364 7747321 50870295 667 21448 PRAM1 0 . GRCh38 19 8499011 8499011 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.797C>G p.Ser266Cys p.S266C ENST00000423345 2/10 278 157 121 201 201 0 strelka-varscan-mutect PRAM1,missense_variant,p.Ser266Cys,ENST00000423345,NM_032152.4;PRAM1,downstream_gene_variant,,ENST00000600262,; C ENST00000423345 Transcript missense_variant 1318/2667 797/2013 266/670 S/C tCc/tGc 1 -1 PRAM1 HGNC HGNC:30091 protein_coding YES CCDS45954.2 ENSP00000408342 Q96QH2 UPI00001AE786 NM_032152.4 tolerated(0.18) 2/10 hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 8499011 8499011 G C 1 0 0 0 0 1 0 0 0 12552 1174 41 4 4 PRAM1 19 8499011 Missense_Mutation SNP G C3N-01030_T 751690 8499011 50118605 668 21449 MUC16 0 . GRCh38 19 8936710 8936710 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.34245C>A p.= p.T11415T ENST00000397910 5/84 259 218 41 262 262 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 34449/43816 34245/43524 11415/14507 T acC/acA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 8936710 8936710 G T 1 0 0 0 0 0 0 0 1 9972 1335 47 2 2 MUC16 19 8936710 Silent SNP G C3N-01030_T 437699 8936710 49680906 669 21450 MUC16 0 . GRCh38 19 8938146 8938146 + Silent SNP G G A rs746420551 C3N-01030_T C3N-01030_N G G c.32809C>T p.= p.L10937L ENST00000397910 5/84 237 219 18 203 203 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript synonymous_variant 33013/43816 32809/43524 10937/14507 L Ctg/Ttg rs746420551,COSM363816,COSM363817,COSM3933268,COSM3933269 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 Low_complexity_(Seg):seg 0,1,1,1,1 LOW 1 SNV 5 0,1,1,1,1 1 PASS rs746420551 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 8938146 8938146 G A 1 0 0 0 0 0 0 0 1 9972 933 33 3 3 MUC16 19 8938146 Silent SNP G C3N-01030_T 1436 8938146 49679470 670 21451 OR7E24 0 . GRCh38 19 9252017 9252017 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.974G>A p.Arg325Lys p.R325K ENST00000456448 1/1 159 138 21 152 152 0 strelka-varscan-mutect OR7E24,missense_variant,p.Arg325Lys,ENST00000456448,NM_001079935.1; A ENST00000456448 Transcript missense_variant 1088/1550 974/1020 325/339 R/K aGa/aAa 1 1 OR7E24 HGNC HGNC:8396 protein_coding YES CCDS45955.1 ENSP00000387523 Q6IFN5 UPI00003B2886 NM_001079935.1 tolerated(0.2) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF173,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 9252017 9252017 G A 1 0 0 0 0 1 0 0 0 11291 942 33 3 3 OR7E24 19 9252017 Missense_Mutation SNP G C3N-01030_T 313871 9252017 49365599 671 21452 ZNF561 0 . GRCh38 19 9610200 9610200 + Nonstop_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1461G>T p.Ter487TyrextTer7 p.*487Yext*7 ENST00000302851 6/6 35 23 12 47 47 0 strelka-varscan-mutect ZNF561,stop_lost,p.Ter487TyrextTer7,ENST00000302851,NM_152289.2;ZNF561,stop_lost,p.Ter418TyrextTer7,ENST00000424629,;ZNF561,3_prime_UTR_variant,,ENST00000326044,;ZNF561,downstream_gene_variant,,ENST00000444611,;ZNF561,downstream_gene_variant,,ENST00000495503,;ZNF561,downstream_gene_variant,,ENST00000465974,;ZNF561,intron_variant,,ENST00000444802,;ZNF561,downstream_gene_variant,,ENST00000443819,;ZNF561,downstream_gene_variant,,ENST00000457965,;ZNF561,downstream_gene_variant,,ENST00000483768,;ZNF561,downstream_gene_variant,,ENST00000494276,; A ENST00000302851 Transcript stop_lost 1825/4693 1461/1461 487/486 */Y taG/taT 1 -1 ZNF561 HGNC HGNC:28684 protein_coding YES CCDS12216.2 ENSP00000303915 Q8N587 UPI000037525C NM_152289.2 6/6 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 9610200 9610200 C A 1 0 0 0 0 0 0 0 0 18566 808 28 2 2 ZNF561 19 9610200 Nonstop_Mutation SNP C C3N-01030_T 358183 9610200 49007416 672 21453 RDH8 0 . GRCh38 19 10018827 10018827 + Missense_Mutation SNP G G T rs768005242 C3N-01030_T C3N-01030_N G G c.419G>T p.Arg140Leu p.R140L ENST00000591589 3/6 117 75 42 93 93 0 strelka-varscan-mutect RDH8,missense_variant,p.Arg140Leu,ENST00000591589,NM_015725.2;RDH8,upstream_gene_variant,,ENST00000587782,;RDH8,intron_variant,,ENST00000589570,; T ENST00000591589 Transcript missense_variant 608/1715 419/996 140/331 R/L cGt/cTt rs768005242 1 1 RDH8 HGNC HGNC:14423 protein_coding YES CCDS12223.2 ENSP00000466058 K7ELF7 UPI000059D661 NM_015725.2 deleterious(0) 3/6 hmmpanther:PTHR24322:SF323,hmmpanther:PTHR24322,Pfam_domain:PF00106,PIRSF_domain:PIRSF000095,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS rs768005242 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 10018827 10018827 G T 1 0 0 0 0 1 0 0 0 13365 1145 40 1 1 RDH8 19 10018827 Missense_Mutation SNP G C3N-01030_T 408627 10018827 48598789 673 21454 DNMT1 0 . GRCh38 19 10166619 10166619 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.870G>A p.= p.E290E ENST00000359526 11/41 620 504 116 431 431 0 strelka-varscan-mutect DNMT1,synonymous_variant,p.=,ENST00000340748,NM_001318730.1,NM_001379.2;DNMT1,synonymous_variant,p.=,ENST00000359526,NM_001130823.1;DNMT1,5_prime_UTR_variant,,ENST00000540357,;DNMT1,3_prime_UTR_variant,,ENST00000592705,NM_001318731.1;DNMT1,non_coding_transcript_exon_variant,,ENST00000589349,;DNMT1,non_coding_transcript_exon_variant,,ENST00000591764,;DNMT1,downstream_gene_variant,,ENST00000586988,;DNMT1,upstream_gene_variant,,ENST00000585920,; T ENST00000359526 Transcript synonymous_variant 1050/5206 870/4899 290/1632 E gaG/gaA 1 -1 DNMT1 HGNC HGNC:2976 protein_coding YES CCDS45958.1 ENSP00000352516 P26358 UPI000002A823 NM_001130823.1 11/41 Low_complexity_(Seg):seg,hmmpanther:PTHR10629:SF11,hmmpanther:PTHR10629,PIRSF_domain:PIRSF037404 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 10166619 10166619 C T 1 0 0 0 0 0 0 0 1 4488 680 24 3 3 DNMT1 19 10166619 Silent SNP C C3N-01030_T 147792 10166619 48450997 674 21455 ADGRL1 0 . GRCh38 19 14157146 14157146 + Splice_Site SNP C C G novel C3N-01030_T C3N-01030_N C C c.2761-1G>C p.X921_splice ENST00000340736 267 236 31 197 197 0 strelka-varscan-mutect ADGRL1,splice_acceptor_variant,,ENST00000340736,NM_001008701.2;ADGRL1,splice_acceptor_variant,,ENST00000361434,NM_014921.4;ADGRL1,upstream_gene_variant,,ENST00000592164,;ADGRL1,upstream_gene_variant,,ENST00000593005,;ADGRL1,downstream_gene_variant,,ENST00000589616,;CTB-55O6.12,intron_variant,,ENST00000588387,;CTB-55O6.12,intron_variant,,ENST00000592086,;CTB-55O6.12,downstream_gene_variant,,ENST00000588658,;ADGRL1,downstream_gene_variant,,ENST00000588677,; G ENST00000340736 Transcript splice_acceptor_variant -/7853 2761/4425 921/1474 1 -1 ADGRL1 HGNC HGNC:20973 protein_coding YES CCDS32928.1 ENSP00000340688 O94910 UPI000005046A NM_001008701.2 15/23 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 70 14157146 14157146 C G 1 0 0 0 0 0 0 1 0 375 927 32 4 4 ADGRL1 19 14157146 Splice_Site SNP C C3N-01030_T 3990527 14157146 44460470 675 21456 OR7C2 0 . GRCh38 19 14942407 14942407 + Missense_Mutation SNP G G T rs774724699 C3N-01030_T C3N-01030_N G G c.919G>T p.Ala307Ser p.A307S ENST00000248072 1/1 96 75 21 78 78 0 strelka-varscan-mutect OR7C2,missense_variant,p.Ala307Ser,ENST00000248072,NM_012377.1; T ENST00000248072 Transcript missense_variant 919/960 919/960 307/319 A/S Gca/Tca rs774724699 1 1 OR7C2 HGNC HGNC:8374 protein_coding YES CCDS12320.1 ENSP00000248072 O60412 UPI0000041E80 NM_012377.1 tolerated_low_confidence(0.15) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF307,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs774724699 . 0 202 8 0 0 0 0 0 -20 0.9999991 1 1 1 0 T 3 4 70 14942407 14942407 G T 1 0 0 0 0 1 0 0 0 11288 1203 42 2 2 OR7C2 19 14942407 Missense_Mutation SNP G C3N-01030_T 785261 14942407 43675209 676 21457 CASP14 0 . GRCh38 19 15056062 15056062 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.702C>A p.= p.T234T ENST00000427043 7/7 235 172 63 226 223 3 strelka-varscan-mutect CASP14,synonymous_variant,p.=,ENST00000427043,NM_012114.2;CASP14,non_coding_transcript_exon_variant,,ENST00000598738,; A ENST00000427043 Transcript synonymous_variant 1010/3241 702/729 234/242 T acC/acA 1 1 CASP14 HGNC HGNC:1502 protein_coding YES CCDS12323.1 ENSP00000393417 P31944 B2CIS9 UPI0000044176 NM_012114.2 7/7 PROSITE_profiles:PS50207,hmmpanther:PTHR10454:SF131,hmmpanther:PTHR10454,Gene3D:3.40.50.1460,Pfam_domain:PF00656,SMART_domains:SM00115,Superfamily_domains:SSF52129,Prints_domain:PR00376 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 15056062 15056062 C A 1 0 0 0 0 0 0 0 1 2370 610 22 2 2 CASP14 19 15056062 Silent SNP C C3N-01030_T 113655 15056062 43561554 677 21458 TMEM38A 0 . GRCh38 19 16688271 16688271 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.800G>T p.Ser267Ile p.S267I ENST00000187762 6/6 83 70 13 59 59 0 strelka-varscan-mutect TMEM38A,missense_variant,p.Ser267Ile,ENST00000187762,NM_024074.1;TMEM38A,intron_variant,,ENST00000599479,; T ENST00000187762 Transcript missense_variant 891/2649 800/900 267/299 S/I aGc/aTc 1 1 TMEM38A HGNC HGNC:28462 protein_coding YES CCDS12349.1 ENSP00000187762 Q9H6F2 UPI000006E0B9 NM_024074.1 tolerated(0.1) 6/6 hmmpanther:PTHR12454,hmmpanther:PTHR12454:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 16688271 16688271 G T 1 0 0 0 0 1 0 0 0 16636 971 34 2 2 TMEM38A 19 16688271 Missense_Mutation SNP G C3N-01030_T 1632209 16688271 41929345 678 21459 UNC13A 0 . GRCh38 19 17658160 17658160 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.669C>A p.= p.V223V ENST00000519716 9/44 484 332 152 345 345 0 strelka-varscan-mutect UNC13A,synonymous_variant,p.=,ENST00000519716,NM_001080421.2;UNC13A,synonymous_variant,p.=,ENST00000551649,;UNC13A,synonymous_variant,p.=,ENST00000552293,;UNC13A,synonymous_variant,p.=,ENST00000550896,; T ENST00000519716 Transcript synonymous_variant 669/9838 669/5112 223/1703 V gtC/gtA 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 9/44 hmmpanther:PTHR10480 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 17658160 17658160 G T 1 0 0 0 0 0 0 0 1 17508 1161 41 2 2 UNC13A 19 17658160 Silent SNP G C3N-01030_T 969889 17658160 40959456 679 21460 JUND 0 . GRCh38 19 18280447 18280447 + Silent SNP C C G novel C3N-01030_T C3N-01030_N C C c.1038G>C p.= p.A346A ENST00000252818 1/1 455 298 157 281 281 0 strelka-varscan-mutect JUND,synonymous_variant,p.=,ENST00000252818,NM_001286968.1,NM_005354.5;JUND,intron_variant,,ENST00000600972,;MIR3188,upstream_gene_variant,,ENST00000583494,;RPL39P38,downstream_gene_variant,,ENST00000467018,; G ENST00000252818 Transcript synonymous_variant 1176/1863 1038/1044 346/347 A gcG/gcC 1 -1 JUND HGNC HGNC:6206 protein_coding YES CCDS32959.1 ENSP00000252818 P17535 UPI00001AE750 NM_001286968.1,NM_005354.5 1/1 hmmpanther:PTHR11462,hmmpanther:PTHR11462:SF7 LOW 1 SNV 1 PASS rs1468576035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 18280447 18280447 C G 1 0 0 0 0 0 0 0 1 7881 523 19 4 4 JUND 19 18280447 Silent SNP C C3N-01030_T 622287 18280447 40337169 680 21461 ZNF100 0 . GRCh38 19 21727817 21727817 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.495A>T p.Leu165Phe p.L165F ENST00000358296 5/5 92 65 27 117 117 0 strelka-varscan-mutect ZNF100,missense_variant,p.Leu165Phe,ENST00000358296,NM_173531.3;ZNF100,missense_variant,p.Leu101Phe,ENST00000305570,;ZNF100,missense_variant,p.Leu164Phe,ENST00000608416,;ZNF100,downstream_gene_variant,,ENST00000594401,; A ENST00000358296 Transcript missense_variant 694/5745 495/1629 165/542 L/F ttA/ttT 1 -1 ZNF100 HGNC HGNC:12880 protein_coding YES CCDS42538.1 ENSP00000351042 Q8IYN0 UPI00001614AC NM_173531.3 tolerated(0.08) 5/5 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF131 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 21727817 21727817 T A 1 0 0 0 0 1 0 0 0 18292 1751 61 4 4 ZNF100 19 21727817 Missense_Mutation SNP T C3N-01030_T 3447370 21727817 36889799 681 21462 ZNF99 0 . GRCh38 19 22758945 22758945 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.964T>A p.Phe322Ile p.F322I ENST00000596209 4/4 220 152 68 304 303 1 strelka-varscan-mutect ZNF99,missense_variant,p.Phe322Ile,ENST00000596209,NM_001080409.2;ZNF99,missense_variant,p.Phe231Ile,ENST00000397104,; T ENST00000596209 Transcript missense_variant 1055/7817 964/2595 322/864 F/I Ttt/Att 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 deleterious(0.02) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 22758945 22758945 A T 1 0 0 0 0 1 0 0 0 18797 14 1 4 4 ZNF99 19 22758945 Missense_Mutation SNP A C3N-01030_T 1031128 22758945 35858671 682 21463 ZNF99 0 . GRCh38 19 22759541 22759541 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.368delG p.Gly123ValfsTer29 p.G123Vfs*29 ENST00000596209 4/4 96 62 34 156 156 0 sindel-varindel-pindel ZNF99,frameshift_variant,p.Gly123ValfsTer29,ENST00000596209,NM_001080409.2;ZNF99,frameshift_variant,p.Gly144ValfsTer29,ENST00000397104,; - ENST00000596209 Transcript frameshift_variant 459/7817 368/2595 123/864 G/X gGt/gt 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 4/4 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 22759541 22759541 C - 1 0 1 0 1 0 0 0 0 18797 507 18 0 0 ZNF99 19 22759541 Frame_Shift_Del DEL C C3N-01030_T 596 22759541 35858075 683 21464 ZNF536 0 . GRCh38 19 30445608 30445608 + Silent SNP G G T rs746307749 C3N-01030_T C3N-01030_N G G c.2046G>T p.= p.S682S ENST00000355537 2/5 176 146 30 133 133 0 strelka-varscan-mutect ZNF536,synonymous_variant,p.=,ENST00000355537,NM_014717.1;ZNF536,synonymous_variant,p.=,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript synonymous_variant 2193/4945 2046/3903 682/1300 S tcG/tcT rs746307749 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 2/5 Pfam_domain:PF16606,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 LOW 1 SNV 1 1 PASS rs746307749 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 30445608 30445608 G T 1 0 0 0 0 0 0 0 1 18547 1103 39 1 1 ZNF536 19 30445608 Silent SNP G C3N-01030_T 7686067 30445608 28172008 684 21465 PRODH2 0 . GRCh38 19 35803027 35803027 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.1281C>A p.= p.P427P ENST00000301175 9/11 72 60 12 45 45 0 strelka-varscan-mutect PRODH2,synonymous_variant,p.=,ENST00000301175,NM_021232.1;PRODH2,synonymous_variant,p.=,ENST00000589835,;PRODH2,synonymous_variant,p.=,ENST00000588266,;PRODH2,non_coding_transcript_exon_variant,,ENST00000587695,;PRODH2,upstream_gene_variant,,ENST00000587808,; T ENST00000301175 Transcript synonymous_variant 1299/1677 1281/1611 427/536 P ccC/ccA 1 -1 PRODH2 HGNC HGNC:17325 protein_coding YES CCDS12478.1 ENSP00000301175 Q9UF12 UPI000006EE59 NM_021232.1 9/11 hmmpanther:PTHR13914,hmmpanther:PTHR13914:SF5,Pfam_domain:PF01619,Gene3D:3.20.20.220,Superfamily_domains:SSF51730 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 35803027 35803027 G T 1 0 0 0 0 0 0 0 1 12682 1335 47 2 2 PRODH2 19 35803027 Silent SNP G C3N-01030_T 5357419 35803027 22814589 685 21466 ZNF569 0 . GRCh38 19 37413691 37413691 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.967G>T p.Glu323Ter p.E323* ENST00000316950 6/6 81 59 22 118 118 0 strelka-varscan-mutect ZNF569,stop_gained,p.Glu323Ter,ENST00000316950,NM_152484.2;ZNF569,stop_gained,p.Glu323Ter,ENST00000392149,;ZNF569,stop_gained,p.Glu164Ter,ENST00000392150,;ZNF569,downstream_gene_variant,,ENST00000448051,;ZNF569,downstream_gene_variant,,ENST00000592490,; A ENST00000316950 Transcript stop_gained 1525/4061 967/2061 323/686 E/* Gag/Tag 1 -1 ZNF569 HGNC HGNC:24737 protein_coding YES CCDS12503.1 ENSP00000325018 Q5MCW4 A0A024R0G4 UPI0000202203 NM_152484.2 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF68,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 37413691 37413691 C A 1 0 0 0 0 0 1 0 0 18574 864 30 2 2 ZNF569 19 37413691 Nonsense_Mutation SNP C C3N-01030_T 1610664 37413691 21203925 686 21467 ZNF573 0 . GRCh38 19 37771643 37771643 + Silent SNP C C T novel C3N-01030_T C3N-01030_N C C c.123G>A p.= p.E41E ENST00000536220 3/5 151 101 50 133 133 0 strelka-varscan-mutect ZNF573,synonymous_variant,p.=,ENST00000536220,NM_001172691.1,NM_001172690.1;ZNF573,synonymous_variant,p.=,ENST00000590414,;ZNF573,synonymous_variant,p.=,ENST00000588218,;ZNF573,synonymous_variant,p.=,ENST00000378445,;ZNF573,5_prime_UTR_variant,,ENST00000392138,;ZNF573,intron_variant,,ENST00000357309,NM_001172692.1,NM_001172689.1;ZNF573,intron_variant,,ENST00000585724,;ZNF573,non_coding_transcript_exon_variant,,ENST00000494605,;ZNF573,synonymous_variant,p.=,ENST00000589632,;ZNF573,synonymous_variant,p.=,ENST00000586155,;ZNF573,synonymous_variant,p.=,ENST00000489148,;ZNF573,synonymous_variant,p.=,ENST00000591516,; T ENST00000536220 Transcript synonymous_variant 192/2257 123/1998 41/665 E gaG/gaA 1 -1 ZNF573 HGNC HGNC:26420 protein_coding YES CCDS59381.1 ENSP00000440464 Q86YE8 UPI000059D70C NM_001172691.1,NM_001172690.1 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF159,SMART_domains:SM00349 LOW 1 SNV 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 37771643 37771643 C T 1 0 0 0 0 0 0 0 1 18579 564 20 3 3 ZNF573 19 37771643 Silent SNP C C3N-01030_T 357952 37771643 20845973 687 21468 RYR1 0 . GRCh38 19 38466359 38466359 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.3139G>T p.Gly1047Cys p.G1047C ENST00000359596 24/106 253 208 45 135 134 1 strelka-varscan-mutect RYR1,missense_variant,p.Gly1047Cys,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Gly1047Cys,ENST00000359596,NM_000540.2;RYR1,non_coding_transcript_exon_variant,,ENST00000594111,; T ENST00000359596 Transcript missense_variant 3139/15117 3139/15117 1047/5038 G/C Ggc/Tgc 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.03) 24/106 PROSITE_profiles:PS50188,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF02026 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 38466359 38466359 G T 1 0 0 0 0 1 0 0 0 14028 1232 43 2 2 RYR1 19 38466359 Missense_Mutation SNP G C3N-01030_T 694716 38466359 20151257 688 21469 LIPE 0 . GRCh38 19 42407383 42407383 + Nonsense_Mutation SNP G G T rs867573767 C3N-01030_T C3N-01030_N G G c.1928C>A p.Ser643Ter p.S643* ENST00000244289 6/10 201 148 53 128 128 0 strelka-varscan-mutect LIPE,stop_gained,p.Ser643Ter,ENST00000244289,NM_005357.3;LIPE,downstream_gene_variant,,ENST00000599783,;LIPE,upstream_gene_variant,,ENST00000597620,;LIPE,upstream_gene_variant,,ENST00000599918,;LIPE,downstream_gene_variant,,ENST00000597001,;LIPE,downstream_gene_variant,,ENST00000599211,;LIPE,downstream_gene_variant,,ENST00000601189,;LIPE-AS1,intron_variant,,ENST00000594624,;LIPE-AS1,intron_variant,,ENST00000597203,;LIPE-AS1,intron_variant,,ENST00000593491,;LIPE-AS1,intron_variant,,ENST00000599276,;LIPE,downstream_gene_variant,,ENST00000602000,;LIPE,upstream_gene_variant,,ENST00000600224,; T ENST00000244289 Transcript stop_gained 2205/3813 1928/3231 643/1076 S/* tCg/tAg rs867573767 1 -1 LIPE HGNC HGNC:6621 protein_coding YES CCDS12607.1 ENSP00000244289 Q05469 UPI000013CB66 NM_005357.3 6/10 hmmpanther:PTHR23025,hmmpanther:PTHR23025:SF3,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 HIGH 1 SNV 1 1 PASS rs867573767 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 42407383 42407383 G T 1 0 0 0 0 0 1 0 0 8742 1059 37 1 1 LIPE 19 42407383 Nonsense_Mutation SNP G C3N-01030_T 3941024 42407383 16210233 689 21470 PSG1 0 . GRCh38 19 42868266 42868266 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1078C>A p.Pro360Thr p.P360T ENST00000312439 5/6 281 251 30 237 237 0 strelka-varscan-mutect PSG1,missense_variant,p.Pro360Thr,ENST00000244296,NM_006905.2;PSG1,missense_variant,p.Pro360Thr,ENST00000436291,NM_001184825.1;PSG1,missense_variant,p.Pro360Thr,ENST00000595356,NM_001184826.1;PSG1,missense_variant,p.Pro360Thr,ENST00000312439,NM_001297773.1;PSG1,missense_variant,p.Pro267Thr,ENST00000403380,;PSG1,missense_variant,p.Pro267Thr,ENST00000595124,;PSG1,missense_variant,p.Pro188Thr,ENST00000597058,;PSG1,downstream_gene_variant,,ENST00000595930,;PSG1,non_coding_transcript_exon_variant,,ENST00000602039,; T ENST00000312439 Transcript missense_variant 1164/1882 1078/1287 360/428 P/T Cca/Aca 1 -1 PSG1 HGNC HGNC:9514 protein_coding YES CCDS74380.1 ENSP00000308970 P11464 UPI000006DB43 NM_001297773.1 tolerated(0.56) 5/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 42868266 42868266 G T 1 0 0 0 0 1 0 0 0 12804 1232 43 2 2 PSG1 19 42868266 Missense_Mutation SNP G C3N-01030_T 460883 42868266 15749350 690 21471 PSG11 0 . GRCh38 19 43015319 43015319 + Missense_Mutation SNP C C A C3N-01030_T C3N-01030_N C C c.761G>T p.Gly254Val p.G254V ENST00000320078 4/6 151 120 31 121 121 0 varscan-mutect PSG11,missense_variant,p.Gly254Val,ENST00000320078,NM_002785.2;PSG11,missense_variant,p.Gly132Val,ENST00000403486,NM_203287.1,NM_001113410.1;PSG11,missense_variant,p.Gly254Val,ENST00000598133,;PSG11,missense_variant,p.Gly132Val,ENST00000306322,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG11,downstream_gene_variant,,ENST00000595312,;PSG11,upstream_gene_variant,,ENST00000599976,;PSG11,non_coding_transcript_exon_variant,,ENST00000595138,;PSG11,non_coding_transcript_exon_variant,,ENST00000594655,;PSG11,intron_variant,,ENST00000593983,;PSG11,upstream_gene_variant,,ENST00000593994,;PSG11,downstream_gene_variant,,ENST00000597093,;PSG11,downstream_gene_variant,,ENST00000488205,; A ENST00000320078 Transcript missense_variant 901/1575 761/1008 254/335 G/V gGa/gTa COSM3535108 1 -1 PSG11 HGNC HGNC:9516 protein_coding YES CCDS12614.2 ENSP00000319140 Q9UQ72 UPI000004EE8C NM_002785.2 deleterious(0.02) 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF615,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 43015319 43015319 C A 1 0 0 0 0 1 0 0 0 12805 855 30 2 2 PSG11 19 43015319 Missense_Mutation SNP C C3N-01030_T 147053 43015319 15602297 691 21472 PSG9 0 . GRCh38 19 43269419 43269419 + Missense_Mutation SNP G G C rs768183364 C3N-01030_T C3N-01030_N G G c.13C>G p.Pro5Ala p.P5A ENST00000270077 1/6 246 153 93 171 171 0 strelka-varscan-mutect PSG9,missense_variant,p.Pro5Ala,ENST00000244293,;PSG9,missense_variant,p.Pro5Ala,ENST00000621109,;PSG9,missense_variant,p.Pro5Ala,ENST00000596730,;PSG9,missense_variant,p.Pro5Ala,ENST00000418820,;PSG9,missense_variant,p.Pro5Ala,ENST00000270077,NM_002784.4;PSG9,missense_variant,p.Pro5Ala,ENST00000593948,NM_001301708.1;PSG9,missense_variant,p.Pro5Ala,ENST00000443718,NM_001301707.1;PSG9,missense_variant,p.Pro5Ala,ENST00000291752,NM_001301709.1; C ENST00000270077 Transcript missense_variant 110/1705 13/1281 5/426 P/A Cca/Gca rs768183364 1 -1 PSG9 HGNC HGNC:9526 protein_coding YES CCDS12618.1 ENSP00000270077 Q00887 UPI00001327A5 NM_002784.4 deleterious(0.01) 1/6 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs768183364 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 43269419 43269419 G C 1 0 0 0 0 1 0 0 0 12813 1232 43 4 4 PSG9 19 43269419 Missense_Mutation SNP G C3N-01030_T 254100 43269419 15348197 692 21473 SRRM5 0 . GRCh38 19 43613892 43613892 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.1771A>G p.Arg591Gly p.R591G ENST00000607544 3/3 469 312 157 354 354 0 strelka-varscan-mutect SRRM5,missense_variant,p.Arg591Gly,ENST00000607544,;SRRM5,missense_variant,p.Arg591Gly,ENST00000417606,NM_001145641.1;ZNF428,intron_variant,,ENST00000300811,NM_182498.3;ZNF428,intron_variant,,ENST00000598676,;ZNF428,downstream_gene_variant,,ENST00000595304,; G ENST00000607544 Transcript missense_variant 2093/2698 1771/2148 591/715 R/G Aga/Gga 1 1 SRRM5 HGNC HGNC:37248 protein_coding YES CCDS46095.1 ENSP00000476253 B3KS81 UPI000059D73E tolerated(0.07) 3/3 hmmpanther:PTHR39414,hmmpanther:PTHR39414:SF1,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 43613892 43613892 A G 1 0 0 0 0 1 0 0 0 15533 296 11 5 5 SRRM5 19 43613892 Missense_Mutation SNP A C3N-01030_T 344473 43613892 15003724 693 21474 ZNF226 0 . GRCh38 19 44176491 44176491 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.1229A>T p.Gln410Leu p.Q410L ENST00000590089 7/7 190 125 65 200 200 0 strelka-varscan-mutect ZNF226,missense_variant,p.Gln410Leu,ENST00000590089,NM_016444.2;ZNF226,missense_variant,p.Gln410Leu,ENST00000454662,NM_001319090.1,NM_001319089.1,NM_001319088.1,NM_001032372.1;ZNF226,missense_variant,p.Gln410Leu,ENST00000337433,NM_001032373.1;ZNF226,3_prime_UTR_variant,,ENST00000588883,;ZNF226,downstream_gene_variant,,ENST00000300823,NM_015919.3;ZNF226,downstream_gene_variant,,ENST00000413984,NM_001032374.1;ZNF226,downstream_gene_variant,,ENST00000589160,;ZNF226,downstream_gene_variant,,ENST00000588795,;ZNF226,downstream_gene_variant,,ENST00000590524,;ZNF226,downstream_gene_variant,,ENST00000585678,;ZNF226,downstream_gene_variant,,ENST00000586914,;ZNF226,downstream_gene_variant,,ENST00000588127,;ZNF226,downstream_gene_variant,,ENST00000586203,;ZNF226,downstream_gene_variant,,ENST00000590578,;ZNF226,downstream_gene_variant,,ENST00000590467,;ZNF226,downstream_gene_variant,,ENST00000586286,;ZNF226,downstream_gene_variant,,ENST00000585560,;ZNF226,downstream_gene_variant,,ENST00000588742,NM_001146220.2;ZNF226,downstream_gene_variant,,ENST00000590759,; T ENST00000590089 Transcript missense_variant 1596/2788 1229/2412 410/803 Q/L cAa/cTa 1 1 ZNF226 HGNC HGNC:13019 protein_coding YES CCDS46102.1 ENSP00000465121 Q9NYT6 A0A024R0P4 UPI000013C32A NM_016444.2 deleterious(0.03) 7/7 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF177,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1444059711 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 44176491 44176491 A T 1 0 0 0 0 1 0 0 0 18357 130 5 4 4 ZNF226 19 44176491 Missense_Mutation SNP A C3N-01030_T 562599 44176491 14441125 694 21475 SAE1 0 . GRCh38 19 47143558 47143558 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.163C>G p.Leu55Val p.L55V ENST00000270225 2/9 240 215 25 178 178 0 strelka-varscan-mutect SAE1,missense_variant,p.Leu55Val,ENST00000413379,NM_001145713.1;SAE1,missense_variant,p.Leu55Val,ENST00000270225,NM_005500.2;SAE1,missense_variant,p.Leu55Val,ENST00000392776,NM_001145714.1;SAE1,missense_variant,p.Leu55Val,ENST00000598840,;SAE1,missense_variant,p.Leu23Val,ENST00000600706,;SAE1,5_prime_UTR_variant,,ENST00000594144,;SAE1,5_prime_UTR_variant,,ENST00000594526,;SAE1,5_prime_UTR_variant,,ENST00000597808,;SAE1,intron_variant,,ENST00000600753,;SAE1,missense_variant,p.Leu55Val,ENST00000414294,;SAE1,3_prime_UTR_variant,,ENST00000596995,; G ENST00000270225 Transcript missense_variant 231/2049 163/1041 55/346 L/V Ctc/Gtc 1 1 SAE1 HGNC HGNC:30660 protein_coding YES CCDS12696.1 ENSP00000270225 Q9UBE0 A0A024R0R4 UPI0000037725 NM_005500.2 tolerated(0.24) 2/9 Gene3D:3.40.50.720,Pfam_domain:PF00899,Prints_domain:PR01849,hmmpanther:PTHR10953,Superfamily_domains:SSF69572 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 47143558 47143558 C G 1 0 0 0 0 1 0 0 0 14064 913 32 4 4 SAE1 19 47143558 Missense_Mutation SNP C C3N-01030_T 2967067 47143558 11474058 695 21476 GLTSCR1 0 . GRCh38 19 47680184 47680184 + Silent SNP G G T rs768646880 C3N-01030_T C3N-01030_N G G c.1014G>T p.= p.P338P ENST00000396720 6/15 107 84 23 74 74 0 strelka-varscan-mutect GLTSCR1,synonymous_variant,p.=,ENST00000396720,NM_015711.3;GLTSCR1,synonymous_variant,p.=,ENST00000614245,;GLTSCR1,downstream_gene_variant,,ENST00000594866,;CTD-2571L23.8,intron_variant,,ENST00000599924,; T ENST00000396720 Transcript synonymous_variant 1208/5739 1014/4683 338/1560 P ccG/ccT rs768646880 1 1 GLTSCR1 HGNC HGNC:4332 protein_coding YES CCDS46134.1 ENSP00000379946 Q9NZM4 UPI00016278EE NM_015711.3 6/15 hmmpanther:PTHR15572:SF1,hmmpanther:PTHR15572 LOW 1 SNV 5 1 PASS rs768646880 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 70 47680184 47680184 G T 1 0 0 0 0 0 0 0 1 6350 1103 39 1 1 GLTSCR1 19 47680184 Silent SNP G C3N-01030_T 536626 47680184 10937432 696 21477 ZNF114 0 . GRCh38 19 48286469 48286469 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.845G>T p.Gly282Val p.G282V ENST00000595607 6/6 186 123 63 171 171 0 strelka-varscan-mutect ZNF114,missense_variant,p.Gly282Val,ENST00000595607,NM_153608.2;ZNF114,missense_variant,p.Gly282Val,ENST00000315849,;ZNF114,missense_variant,p.Gly248Val,ENST00000597695,NM_001301062.1;ZNF114,missense_variant,p.Gly282Val,ENST00000600687,;ZNF114,downstream_gene_variant,,ENST00000595408,;ZNF114,downstream_gene_variant,,ENST00000594024,;ZNF114,downstream_gene_variant,,ENST00000601320,;ZNF114,downstream_gene_variant,,ENST00000598898,; T ENST00000595607 Transcript missense_variant 1339/2478 845/1254 282/417 G/V gGg/gTg 1 1 ZNF114 HGNC HGNC:12894 protein_coding YES CCDS12713.1 ENSP00000469998 Q8NC26 UPI000007282E NM_153608.2 tolerated(0.15) 6/6 MODERATE 1 SNV 1 1 PASS rs1390137296 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 48286469 48286469 G T 1 0 0 0 0 1 0 0 0 18297 1232 43 2 2 ZNF114 19 48286469 Missense_Mutation SNP G C3N-01030_T 606285 48286469 10331147 697 21478 RUVBL2 0 . GRCh38 19 49009847 49009847 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.534G>A p.Met178Ile p.M178I ENST00000595090 7/15 267 253 14 182 182 0 strelka-varscan-mutect RUVBL2,missense_variant,p.Met178Ile,ENST00000595090,NM_001321191.1,NM_006666.1;RUVBL2,missense_variant,p.Met133Ile,ENST00000601968,;RUVBL2,missense_variant,p.Met133Ile,ENST00000627972,;RUVBL2,downstream_gene_variant,,ENST00000596837,;MIR6798,upstream_gene_variant,,ENST00000612887,;RUVBL2,missense_variant,p.Met178Ile,ENST00000221413,;RUVBL2,3_prime_UTR_variant,,ENST00000596247,;RUVBL2,3_prime_UTR_variant,,ENST00000593570,;RUVBL2,non_coding_transcript_exon_variant,,ENST00000594338,;RUVBL2,non_coding_transcript_exon_variant,,ENST00000594017,; A ENST00000595090 Transcript missense_variant 998/2009 534/1392 178/463 M/I atG/atA 1 1 RUVBL2 HGNC HGNC:10475 protein_coding YES CCDS42588.1 ENSP00000473172 Q9Y230 UPI0000044738 NM_001321191.1,NM_006666.1 tolerated(0.66) 7/15 Gene3D:3.40.50.300,Pfam_domain:PF06068,hmmpanther:PTHR11093,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 49009847 49009847 G A 1 0 0 0 0 1 0 0 0 14014 1290 45 3 3 RUVBL2 19 49009847 Missense_Mutation SNP G C3N-01030_T 723378 49009847 9607769 698 21479 CCDC155 0 . GRCh38 19 49408991 49408991 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1018C>A p.Leu340Met p.L340M ENST00000447857 13/20 221 185 36 153 152 1 strelka-varscan-mutect CCDC155,missense_variant,p.Leu340Met,ENST00000447857,NM_144688.4;CCDC155,missense_variant,p.Leu304Met,ENST00000600570,;CCDC155,non_coding_transcript_exon_variant,,ENST00000593362,;CCDC155,non_coding_transcript_exon_variant,,ENST00000596130,;CCDC155,non_coding_transcript_exon_variant,,ENST00000596419,; A ENST00000447857 Transcript missense_variant 1223/2378 1018/1689 340/562 L/M Ctg/Atg 1 1 CCDC155 HGNC HGNC:26520 protein_coding YES CCDS46140.1 ENSP00000404220 Q8N6L0 UPI000006F690 NM_144688.4 deleterious(0) 13/20 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14662,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF341 MODERATE 1 SNV 1 1 PASS rs1248113221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 49408991 49408991 C A 1 0 0 0 0 1 0 0 0 2476 680 24 2 2 CCDC155 19 49408991 Missense_Mutation SNP C C3N-01030_T 399144 49408991 9208625 699 21480 PRR12 0 . GRCh38 19 49595844 49595844 + Silent SNP G G A C3N-01030_T C3N-01030_N G G c.1509G>A p.= p.Q503Q ENST00000418929 4/14 206 179 27 152 152 0 strelka-varscan-mutect PRR12,synonymous_variant,p.=,ENST00000418929,NM_020719.1;PRR12,intron_variant,,ENST00000615927,;PRRG2,downstream_gene_variant,,ENST00000246794,NM_000951.2;PRRG2,downstream_gene_variant,,ENST00000543867,;PRRG2,downstream_gene_variant,,ENST00000597121,NM_001316335.1; A ENST00000418929 Transcript synonymous_variant 1521/6955 1509/6111 503/2036 Q caG/caA COSM5563784 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1 1 LOW SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 49595844 49595844 G A 1 0 0 0 0 0 0 0 1 12719 991 35 3 3 PRR12 19 49595844 Silent SNP G C3N-01030_T 186853 49595844 9021772 700 21481 SHANK1 0 . GRCh38 19 50667015 50667015 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.4945G>T p.Gly1649Cys p.G1649C ENST00000293441 22/23 46 34 12 53 52 1 strelka-varscan-mutect SHANK1,missense_variant,p.Gly1649Cys,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Gly1657Cys,ENST00000391814,;SHANK1,missense_variant,p.Gly1640Cys,ENST00000359082,;SHANK1,missense_variant,p.Gly1036Cys,ENST00000391813,;SHANK1,upstream_gene_variant,,ENST00000483981,;SHANK1,upstream_gene_variant,,ENST00000468654,; A ENST00000293441 Transcript missense_variant 4964/6643 4945/6486 1649/2161 G/C Ggc/Tgc 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 tolerated(0.12) 22/23 Low_complexity_(Seg):seg,hmmpanther:PTHR24135:SF3,hmmpanther:PTHR24135 MODERATE 1 SNV 1 1 PASS rs1348003450 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 50667015 50667015 C A 1 0 0 0 0 1 0 0 0 14523 681 24 2 2 SHANK1 19 50667015 Missense_Mutation SNP C C3N-01030_T 1071171 50667015 7950601 701 21482 SHANK1 0 . GRCh38 19 50716914 50716914 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.6C>T p.= p.T2T ENST00000293441 1/23 17 14 3 20 20 0 strelka-mutect SHANK1,synonymous_variant,p.=,ENST00000293441,NM_016148.2;SHANK1,synonymous_variant,p.=,ENST00000391814,;SHANK1,synonymous_variant,p.=,ENST00000359082,;SHANK1,upstream_gene_variant,,ENST00000483128,; A ENST00000293441 Transcript synonymous_variant 25/6643 6/6486 2/2161 T acC/acT 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 1/23 LOW 1 SNV 1 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 50716914 50716914 G A 1 0 0 0 0 0 0 0 1 14523 1219 43 3 3 SHANK1 19 50716914 Silent SNP G C3N-01030_T 49899 50716914 7900702 702 21483 KLK13 0 . GRCh38 19 51058659 51058659 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.524C>T p.Thr175Ile p.T175I ENST00000595793 4/5 179 137 42 188 188 0 strelka-varscan-mutect KLK13,missense_variant,p.Thr175Ile,ENST00000595793,NM_015596.1;KLK13,missense_variant,p.Thr102Ile,ENST00000595547,;KLK13,missense_variant,p.Thr23Ile,ENST00000335422,;KLK13,downstream_gene_variant,,ENST00000596955,;KLK13,3_prime_UTR_variant,,ENST00000441527,;KLK13,3_prime_UTR_variant,,ENST00000601975,;KLK13,3_prime_UTR_variant,,ENST00000602090,;KLK13,3_prime_UTR_variant,,ENST00000376799,;KLK13,3_prime_UTR_variant,,ENST00000156476,; A ENST00000595793 Transcript missense_variant 567/927 524/834 175/277 T/I aCt/aTt 1 -1 KLK13 HGNC HGNC:6361 protein_coding YES CCDS12822.1 ENSP00000470555 Q9UKR3 UPI000004CA07 NM_015596.1 deleterious(0.04) 4/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF3,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 51058659 51058659 G A 1 0 0 0 0 1 0 0 0 8270 1029 36 3 3 KLK13 19 51058659 Missense_Mutation SNP G C3N-01030_T 341745 51058659 7558957 703 21484 CD33 0 . GRCh38 19 51225928 51225928 + Missense_Mutation SNP G G T rs776690717 C3N-01030_T C3N-01030_N G G c.544G>T p.Ala182Ser p.A182S ENST00000262262 3/7 371 278 93 230 228 2 strelka-varscan-mutect CD33,missense_variant,p.Ala55Ser,ENST00000436584,;CD33,missense_variant,p.Ala182Ser,ENST00000262262,NM_001772.3;CD33,missense_variant,p.Ala182Ser,ENST00000391796,NM_001177608.1;CD33,missense_variant,p.Ala55Ser,ENST00000421133,NM_001082618.1;CD33,non_coding_transcript_exon_variant,,ENST00000601785,;CD33,upstream_gene_variant,,ENST00000598473,; T ENST00000262262 Transcript missense_variant 565/1444 544/1095 182/364 A/S Gct/Tct rs776690717 1 1 CD33 HGNC HGNC:1659 protein_coding YES CCDS33084.1 ENSP00000262262 P20138 Q546G0 UPI000013D285 NM_001772.3 tolerated(0.06) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF52,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF00047,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs776690717 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 51225928 51225928 G T 1 0 0 0 0 1 0 0 0 2709 971 34 2 2 CD33 19 51225928 Missense_Mutation SNP G C3N-01030_T 167269 51225928 7391688 704 21485 SIGLEC8 0 . GRCh38 19 51452589 51452589 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1290G>T p.Lys430Asn p.K430N ENST00000321424 7/7 42 29 13 21 21 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Lys430Asn,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Lys321Asn,ENST00000430817,;SIGLEC8,missense_variant,p.Lys337Asn,ENST00000340550,;SIGLEC8,downstream_gene_variant,,ENST00000597352,; A ENST00000321424 Transcript missense_variant 1357/2949 1290/1500 430/499 K/N aaG/aaT 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 tolerated(0.47) 7/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 51452589 51452589 C A 1 0 0 0 0 1 0 0 0 14578 796 28 2 2 SIGLEC8 19 51452589 Missense_Mutation SNP C C3N-01030_T 226661 51452589 7165027 705 21486 HAS1 0 . GRCh38 19 51717071 51717071 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.825C>A p.= p.S275S ENST00000222115 3/5 445 341 104 307 305 2 strelka-varscan-mutect HAS1,synonymous_variant,p.=,ENST00000540069,NM_001297436.1;HAS1,synonymous_variant,p.=,ENST00000222115,NM_001523.3;HAS1,synonymous_variant,p.=,ENST00000601714,;HAS1,synonymous_variant,p.=,ENST00000594621,;HAS1,synonymous_variant,p.=,ENST00000601667,;SPACA6,downstream_gene_variant,,ENST00000573896,; T ENST00000222115 Transcript synonymous_variant 860/2087 825/1737 275/578 S tcC/tcA 1 -1 HAS1 HGNC HGNC:4818 protein_coding YES CCDS12838.1 ENSP00000222115 Q92839 UPI000006D531 NM_001523.3 3/5 hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF4,Gene3D:3.90.550.10,Pfam_domain:PF13641,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS rs1232444326 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 51717071 51717071 G T 1 0 0 0 0 0 0 0 1 6847 987 35 2 2 HAS1 19 51717071 Silent SNP G C3N-01030_T 264482 51717071 6900545 706 21487 ZNF534 0 . GRCh38 19 52437852 52437852 + Missense_Mutation SNP G G T rs752468310 C3N-01030_T C3N-01030_N G G c.431G>T p.Gly144Val p.G144V ENST00000332323 4/4 99 74 25 132 131 1 strelka-varscan-mutect ZNF534,missense_variant,p.Gly144Val,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Gly131Val,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; T ENST00000332323 Transcript missense_variant 492/2086 431/2025 144/674 G/V gGa/gTa rs752468310 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 tolerated(0.14) 4/4 hmmpanther:PTHR24377:SF187,hmmpanther:PTHR24377 MODERATE 1 SNV 1 1 PASS rs752468310 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 52437852 52437852 G T 1 0 0 0 0 1 0 0 0 18546 1174 41 2 2 ZNF534 19 52437852 Missense_Mutation SNP G C3N-01030_T 720781 52437852 6179764 707 21488 VN1R4 0 . GRCh38 19 53267173 53267173 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.493G>A p.Gly165Arg p.G165R ENST00000311170 1/1 112 104 8 105 105 0 varscan-mutect VN1R4,missense_variant,p.Gly165Arg,ENST00000311170,NM_173857.2;CTD-2245F17.9,downstream_gene_variant,,ENST00000599803,; T ENST00000311170 Transcript missense_variant 551/1048 493/906 165/301 G/R Gga/Aga 1 -1 VN1R4 HGNC HGNC:19871 protein_coding YES CCDS33099.1 ENSP00000310856 Q7Z5H5 UPI000004B23A NM_173857.2 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF03402,PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF80,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs1457191324 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 53267173 53267173 C T 1 0 0 0 0 1 0 0 0 17728 632 22 3 3 VN1R4 19 53267173 Missense_Mutation SNP C C3N-01030_T 829321 53267173 5350443 708 21489 OSCAR 0 . GRCh38 19 54096987 54096987 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.260C>A p.Ala87Glu p.A87E ENST00000611261 5/6 379 319 60 263 263 0 strelka-varscan-mutect OSCAR,missense_variant,p.Ala87Glu,ENST00000611261,NM_206818.2;OSCAR,missense_variant,p.Ala83Glu,ENST00000284648,NM_001282349.1;OSCAR,missense_variant,p.Ala72Glu,ENST00000616215,NM_001282350.1;OSCAR,missense_variant,p.Ala87Glu,ENST00000359649,;OSCAR,missense_variant,p.Ala72Glu,ENST00000391761,;OSCAR,missense_variant,p.Ala87Glu,ENST00000617140,NM_130771.4;OSCAR,missense_variant,p.Ala83Glu,ENST00000358375,NM_133169.4;OSCAR,missense_variant,p.Ala72Glu,ENST00000351806,NM_133168.4;OSCAR,missense_variant,p.Ala88Glu,ENST00000616447,;OSCAR,missense_variant,p.Ala87Glu,ENST00000356532,;OSCAR,synonymous_variant,p.=,ENST00000391760,; T ENST00000611261 Transcript missense_variant 452/2061 260/861 87/286 A/E gCa/gAa 1 -1 OSCAR HGNC HGNC:29960 protein_coding YES CCDS12876.1 ENSP00000479089 A0A087WV17 UPI00034F23BB NM_206818.2 deleterious(0.01) 5/6 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 54096987 54096987 G T 1 0 0 0 0 1 0 0 0 11351 1333 46 2 2 OSCAR 19 54096987 Missense_Mutation SNP G C3N-01030_T 829814 54096987 4520629 709 21490 LILRA6 0 . GRCh38 19 54240348 54240348 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1184G>T p.Arg395Met p.R395M ENST00000396365 6/8 501 433 68 366 366 0 varscan-mutect LILRA6,missense_variant,p.Arg395Met,ENST00000396365,NM_024318.3;LILRA6,missense_variant,p.Arg395Met,ENST00000245621,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000270464,; A ENST00000396365 Transcript missense_variant 1224/1890 1184/1446 395/481 R/M aGg/aTg 1 -1 LILRA6 HGNC HGNC:15495 protein_coding YES CCDS42610.1 ENSP00000379651 Q6PI73 U5XH19 UPI000292EF7A NM_024318.3 deleterious(0) 6/8 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF116,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1360077826 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 54240348 54240348 C A 1 0 0 0 0 1 0 0 0 8697 681 24 2 2 LILRA6 19 54240348 Missense_Mutation SNP C C3N-01030_T 143361 54240348 4377268 710 21491 LILRB5 0 . GRCh38 19 54254038 54254038 + Missense_Mutation SNP G G C rs531344109 C3N-01030_T C3N-01030_N G G c.1337C>G p.Thr446Arg p.T446R ENST00000449561 8/13 158 105 53 112 112 0 strelka-varscan-mutect LILRB5,missense_variant,p.Thr445Arg,ENST00000316219,NM_006840.4;LILRB5,missense_variant,p.Thr446Arg,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,missense_variant,p.Thr346Arg,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000621581,;LILRB5,non_coding_transcript_exon_variant,,ENST00000615654,; C ENST00000449561 Transcript missense_variant 1408/2137 1337/1776 446/591 T/R aCg/aGg rs531344109 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 tolerated(0.42) 8/13 MODERATE 1 SNV 1 1 PASS rs531344109 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 54254038 54254038 G C 1 0 0 0 0 1 0 0 0 8702 1145 40 4 4 LILRB5 19 54254038 Missense_Mutation SNP G C3N-01030_T 13690 54254038 4363578 711 21492 LILRB1 0 . GRCh38 19 54631635 54631635 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.206G>C p.Trp69Ser p.W69S ENST00000324602 4/15 515 452 63 452 452 0 strelka-varscan-mutect LILRB1,missense_variant,p.Trp69Ser,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Trp69Ser,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Trp69Ser,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Trp69Ser,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Trp105Ser,ENST00000427581,;LILRB1,missense_variant,p.Trp69Ser,ENST00000396315,;LILRB1,missense_variant,p.Trp69Ser,ENST00000396317,NM_001278398.2;AC009892.10,downstream_gene_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000480257,;LILRB1,upstream_gene_variant,,ENST00000462628,;LILRB1,upstream_gene_variant,,ENST00000473412,;LILRB1,missense_variant,p.Trp69Ser,ENST00000421584,;LILRB1,upstream_gene_variant,,ENST00000480375,;LILRB1,upstream_gene_variant,,ENST00000487425,; C ENST00000324602 Transcript missense_variant 371/2774 206/1959 69/652 W/S tGg/tCg COSM1722178 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 deleterious(0.01) 4/15 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 54631635 54631635 G C 1 0 0 0 0 1 0 0 0 8698 1357 47 4 4 LILRB1 19 54631635 Missense_Mutation SNP G C3N-01030_T 377597 54631635 3985981 712 21493 LILRB1 0 . GRCh38 19 54636864 54636864 + Missense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.1945C>G p.Leu649Val p.L649V ENST00000324602 15/15 154 135 19 112 112 0 strelka-varscan-mutect LILRB1,missense_variant,p.Leu647Val,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Leu648Val,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Leu648Val,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Leu649Val,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Leu698Val,ENST00000427581,;LILRB1,missense_variant,p.Leu649Val,ENST00000396315,;LILRB1,missense_variant,p.Leu631Val,ENST00000396317,NM_001278398.2;AC009892.10,intron_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,3_prime_UTR_variant,,ENST00000421584,;LILRB1,downstream_gene_variant,,ENST00000480375,;LILRB1,downstream_gene_variant,,ENST00000487425,; G ENST00000324602 Transcript missense_variant 2110/2774 1945/1959 649/652 L/V Ctg/Gtg 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 deleterious(0.02) 15/15 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 54636864 54636864 C G 1 0 0 0 0 1 0 0 0 8698 912 32 4 4 LILRB1 19 54636864 Missense_Mutation SNP C C3N-01030_T 5229 54636864 3980752 713 21494 KIR3DL3 0 . GRCh38 19 54735320 54735320 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.1017C>A p.= p.L339L ENST00000291860 6/8 195 141 54 172 172 0 strelka-varscan-mutect KIR3DL3,synonymous_variant,p.=,ENST00000291860,NM_153443.4;KIR2DL3,upstream_gene_variant,,ENST00000342376,NM_015868.2;CTB-61M7.1,intron_variant,,ENST00000400864,; A ENST00000291860 Transcript synonymous_variant 1035/1691 1017/1233 339/410 L ctC/ctA 1 1 KIR3DL3 HGNC HGNC:16312 protein_coding YES CCDS12903.1 ENSP00000291860 A0A0B4J1R5 UPI00005056C3 NM_153443.4 6/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11738:SF91,hmmpanther:PTHR11738 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 54735320 54735320 C A 1 0 0 0 0 0 0 0 1 8186 900 32 2 2 KIR3DL3 19 54735320 Silent SNP C C3N-01030_T 98456 54735320 3882296 714 21495 FCAR 0 . GRCh38 19 54889816 54889816 + Missense_Mutation SNP T T A novel C3N-01030_T C3N-01030_N T T c.817T>A p.Cys273Ser p.C273S ENST00000355524 5/5 199 161 38 150 150 0 strelka-varscan-mutect FCAR,missense_variant,p.Cys273Ser,ENST00000355524,NM_002000.3;FCAR,missense_variant,p.Cys251Ser,ENST00000391725,NM_133269.3;FCAR,missense_variant,p.Cys261Ser,ENST00000359272,NM_133272.3;FCAR,missense_variant,p.Cys239Ser,ENST00000391724,NM_133278.3;FCAR,missense_variant,p.Cys165Ser,ENST00000391726,NM_133273.3;FCAR,missense_variant,p.Cys177Ser,ENST00000345937,NM_133271.3;FCAR,missense_variant,p.Cys164Ser,ENST00000353758,NM_133277.3;FCAR,3_prime_UTR_variant,,ENST00000391723,NM_133274.3;FCAR,downstream_gene_variant,,ENST00000469767,;CTB-61M7.2,upstream_gene_variant,,ENST00000594721,;FCAR,non_coding_transcript_exon_variant,,ENST00000482092,;FCAR,non_coding_transcript_exon_variant,,ENST00000471750,;FCAR,non_coding_transcript_exon_variant,,ENST00000472634,;FCAR,downstream_gene_variant,,ENST00000488066,; A ENST00000355524 Transcript missense_variant 827/1483 817/864 273/287 C/S Tgt/Agt 1 1 FCAR HGNC HGNC:3608 protein_coding YES CCDS12907.1 ENSP00000347714 P24071 UPI000011B429 NM_002000.3 tolerated(0.28) 5/5 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF4 MODERATE 1 SNV 1 1 PASS rs1261713596 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 54889816 54889816 T A 1 0 0 0 0 1 0 0 0 5636 1696 59 4 4 FCAR 19 54889816 Missense_Mutation SNP T C3N-01030_T 154496 54889816 3727800 715 21496 PPP6R1 0 . GRCh38 19 55230815 55230815 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.2529G>T p.= p.G843G ENST00000412770 22/24 133 109 24 119 119 0 strelka-varscan-mutect PPP6R1,synonymous_variant,p.=,ENST00000412770,NM_014931.3;PPP6R1,synonymous_variant,p.=,ENST00000587283,;TMEM86B,upstream_gene_variant,,ENST00000327042,NM_173804.4;MIR6804,downstream_gene_variant,,ENST00000614724,;PPP6R1,non_coding_transcript_exon_variant,,ENST00000587457,;CTD-2587H24.14,upstream_gene_variant,,ENST00000586923,;TMEM86B,upstream_gene_variant,,ENST00000585416,;TMEM86B,upstream_gene_variant,,ENST00000589190,; A ENST00000412770 Transcript synonymous_variant 3096/3961 2529/2646 843/881 G ggG/ggT 1 -1 PPP6R1 HGNC HGNC:29195 protein_coding YES CCDS46186.1 ENSP00000414202 Q9UPN7 UPI0000202C6D NM_014931.3 22/24 hmmpanther:PTHR12634:SF13,hmmpanther:PTHR12634 LOW 1 SNV 1 1 PASS rs1164245427 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 55230815 55230815 C A 1 0 0 0 0 0 0 0 1 12534 610 22 2 2 PPP6R1 19 55230815 Silent SNP C C3N-01030_T 340999 55230815 3386801 716 21497 ZNF579 0 . GRCh38 19 55578770 55578770 + Silent SNP C C G novel C3N-01030_T C3N-01030_N C C c.870G>C p.= p.L290L ENST00000325421 2/2 79 50 29 81 81 0 strelka-varscan-mutect ZNF579,synonymous_variant,p.=,ENST00000325421,NM_152600.2;ZNF579,downstream_gene_variant,,ENST00000592239,; G ENST00000325421 Transcript synonymous_variant 899/2899 870/1689 290/562 L ctG/ctC 1 -1 ZNF579 HGNC HGNC:26646 protein_coding YES CCDS12927.1 ENSP00000320188 Q8NAF0 UPI0000141657 NM_152600.2 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24383,hmmpanther:PTHR24383:SF13,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 70 55578770 55578770 C G 1 0 0 0 0 0 0 0 1 18585 581 21 4 4 ZNF579 19 55578770 Silent SNP C C3N-01030_T 347955 55578770 3038846 717 21498 NLRP9 0 . GRCh38 19 55732056 55732056 + Missense_Mutation SNP G G T rs375858611 C3N-01030_T C3N-01030_N G G c.1775C>A p.Thr592Lys p.T592K ENST00000332836 2/9 74 53 21 69 69 0 strelka-varscan-mutect NLRP9,missense_variant,p.Thr592Lys,ENST00000332836,NM_176820.3;NLRP9,missense_variant,p.Thr592Lys,ENST00000590200,; T ENST00000332836 Transcript missense_variant 1803/3484 1775/2976 592/991 T/K aCg/aAg rs375858611 1 -1 NLRP9 HGNC HGNC:22941 protein_coding YES CCDS12934.1 ENSP00000331857 Q7RTR0 UPI00001B6B39 NM_176820.3 tolerated(1) 2/9 hmmpanther:PTHR24106:SF72,hmmpanther:PTHR24106,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS rs375858611 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 70 55732056 55732056 G T 1 0 0 0 0 1 0 0 0 10522 1145 40 1 1 NLRP9 19 55732056 Missense_Mutation SNP G C3N-01030_T 153286 55732056 2885560 718 21499 RFPL4A 0 . GRCh38 19 55761804 55761804 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.4G>T p.Ala2Ser p.A2S ENST00000434937 2/3 171 122 49 194 194 0 strelka-varscan-mutect RFPL4A,missense_variant,p.Ala2Ser,ENST00000434937,NM_001145014.1; T ENST00000434937 Transcript missense_variant 175/1035 4/864 2/287 A/S Gct/Tct 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 deleterious(0.03) 2/3 hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228 MODERATE 1 SNV 5 1 PASS rs1187737950 . 6 203 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 55761804 55761804 G T 1 0 0 0 0 1 0 0 0 13428 1203 42 2 2 RFPL4A 19 55761804 Missense_Mutation SNP G C3N-01030_T 29748 55761804 2855812 719 21500 PEG3 0 . GRCh38 19 56824592 56824592 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.64G>T p.Glu22Ter p.E22* ENST00000326441 4/10 99 74 25 95 95 0 strelka-varscan-mutect PEG3,stop_gained,p.Glu22Ter,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,stop_gained,p.Glu22Ter,ENST00000599534,;PEG3,stop_gained,p.Glu22Ter,ENST00000599577,;PEG3,stop_gained,p.Glu22Ter,ENST00000594389,;PEG3,5_prime_UTR_variant,,ENST00000600833,;PEG3,intron_variant,,ENST00000598410,NM_001146187.1;PEG3,intron_variant,,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;ZIM2,upstream_gene_variant,,ENST00000593931,;PEG3,intron_variant,,ENST00000594706,;PEG3,intron_variant,,ENST00000596261,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript stop_gained 428/8723 64/4767 22/1588 E/* Gag/Tag 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 4/10 hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF78 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 56824592 56824592 C A 1 0 0 0 0 0 1 0 0 11808 835 29 2 2 PEG3 19 56824592 Nonsense_Mutation SNP C C3N-01030_T 1062788 56824592 1793024 720 21501 SIGLEC1 0 . GRCh38 20 3698002 3698002 + Missense_Mutation SNP C C A rs749370161 C3N-01030_T C3N-01030_N C C c.1918G>T p.Asp640Tyr p.D640Y ENST00000344754 8/21 118 86 32 101 101 0 strelka-varscan-mutect SIGLEC1,missense_variant,p.Asp640Tyr,ENST00000344754,NM_023068.3;SIGLEC1,upstream_gene_variant,,ENST00000419548,; A ENST00000344754 Transcript missense_variant 1918/6720 1918/5130 640/1709 D/Y Gac/Tac rs749370161 1 -1 SIGLEC1 HGNC HGNC:11127 protein_coding YES CCDS13060.1 ENSP00000341141 Q9BZZ2 UPI0000049BA6 NM_023068.3 deleterious(0.01) 8/21 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs749370161 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 3698002 3698002 C A 1 0 0 0 0 1 0 0 0 14569 855 30 2 2 SIGLEC1 20 3698002 Missense_Mutation SNP C C3N-01030_T 3698002 60746165 721 21502 HSPA12B 0 . GRCh38 20 3751598 3751598 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1493C>A p.Ala498Glu p.A498E ENST00000254963 13/13 40 27 13 40 40 0 strelka-varscan-mutect HSPA12B,missense_variant,p.Ala498Glu,ENST00000254963,NM_052970.4,NM_001197327.1;HSPA12B,missense_variant,p.Ala412Glu,ENST00000399701,NM_001318322.1;C20orf27,downstream_gene_variant,,ENST00000379772,NM_001258429.1;C20orf27,downstream_gene_variant,,ENST00000399672,NM_001258430.1;C20orf27,downstream_gene_variant,,ENST00000217195,NM_001039140.2;C20orf27,downstream_gene_variant,,ENST00000399683,; A ENST00000254963 Transcript missense_variant 1638/3151 1493/2061 498/686 A/E gCg/gAg 1 1 HSPA12B HGNC HGNC:16193 protein_coding YES CCDS13061.1 ENSP00000254963 Q96MM6 UPI00001285E5 NM_052970.4,NM_001197327.1 tolerated(0.28) 13/13 Gene3D:3.30.420.40,hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF39,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 3751598 3751598 C A 1 0 0 0 0 1 0 0 0 7301 768 27 1 1 HSPA12B 20 3751598 Missense_Mutation SNP C C3N-01030_T 53596 3751598 60692569 722 21503 C20orf196 0 . GRCh38 20 5863147 5863147 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.302G>C p.Arg101Thr p.R101T ENST00000303142 3/3 231 212 19 231 231 0 strelka-varscan-mutect C20orf196,missense_variant,p.Arg101Thr,ENST00000303142,NM_001303477.1,NM_152504.3;C20orf196,missense_variant,p.Arg148Thr,ENST00000442185,;C20orf196,missense_variant,p.Arg101Thr,ENST00000445603,; C ENST00000303142 Transcript missense_variant 389/1154 302/618 101/205 R/T aGa/aCa 1 1 C20orf196 HGNC HGNC:26318 protein_coding YES CCDS13091.1 ENSP00000305875 Q8IYI0 UPI0000074251 NM_001303477.1,NM_152504.3 tolerated(0.4) 3/3 Pfam_domain:PF15021,hmmpanther:PTHR36863,hmmpanther:PTHR36863:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 5863147 5863147 G C 1 0 0 0 0 1 0 0 0 2006 942 33 4 4 C20orf196 20 5863147 Missense_Mutation SNP G C3N-01030_T 2111549 5863147 58581020 723 21504 SEL1L2 0 . GRCh38 20 13850236 13850236 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1563G>T p.Met521Ile p.M521I ENST00000378072 17/18 238 217 21 217 217 0 strelka-varscan-mutect SEL1L2,missense_variant,p.Met634Ile,ENST00000284951,;SEL1L2,missense_variant,p.Met521Ile,ENST00000378072,NM_001271539.1;SEL1L2,non_coding_transcript_exon_variant,,ENST00000486903,;SEL1L2,non_coding_transcript_exon_variant,,ENST00000482196,;SEL1L2,non_coding_transcript_exon_variant,,ENST00000492548,;SEL1L2,3_prime_UTR_variant,,ENST00000423870,;SEL1L2,3_prime_UTR_variant,,ENST00000475649,; A ENST00000378072 Transcript missense_variant 1645/1892 1563/1728 521/575 M/I atG/atT 1 -1 SEL1L2 HGNC HGNC:15897 protein_coding YES CCDS59443.1 ENSP00000367312 Q5TEA6 UPI000003BCBF NM_001271539.1 tolerated_low_confidence(0.06) 17/18 hmmpanther:PTHR11102:SF53,hmmpanther:PTHR11102 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 13850236 13850236 C A 1 0 0 0 0 1 0 0 0 14288 826 29 2 2 SEL1L2 20 13850236 Missense_Mutation SNP C C3N-01030_T 7987089 13850236 50593931 724 21505 FLRT3 0 . GRCh38 20 14326965 14326965 + Missense_Mutation SNP C C A rs750841856 C3N-01030_T C3N-01030_N C C c.542G>T p.Arg181Leu p.R181L ENST00000378053 2/2 149 119 30 144 144 0 strelka-varscan-mutect FLRT3,missense_variant,p.Arg181Leu,ENST00000378053,NM_013281.3;FLRT3,missense_variant,p.Arg181Leu,ENST00000341420,NM_198391.2;MACROD2,intron_variant,,ENST00000217246,NM_080676.5;MACROD2,intron_variant,,ENST00000477147,;MACROD2,intron_variant,,ENST00000494602,;MACROD2,intron_variant,,ENST00000490428,;FLRT3,downstream_gene_variant,,ENST00000462077,; A ENST00000378053 Transcript missense_variant 799/4776 542/1950 181/649 R/L cGc/cTc rs750841856 1 -1 FLRT3 HGNC HGNC:3762 protein_coding YES CCDS13121.1 ENSP00000367292 Q9NZU0 UPI0000001BE7 NM_013281.3 deleterious(0) 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF4,Pfam_domain:PF13855,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs750841856 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 14326965 14326965 C A 1 0 0 0 0 1 0 0 0 5796 768 27 1 1 FLRT3 20 14326965 Missense_Mutation SNP C C3N-01030_T 476729 14326965 50117202 725 21506 RALGAPA2 0 . GRCh38 20 20605366 20605366 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1847C>T p.Ser616Phe p.S616F ENST00000202677 15/40 203 151 52 153 153 0 strelka-varscan-mutect RALGAPA2,missense_variant,p.Ser433Phe,ENST00000430436,;RALGAPA2,missense_variant,p.Ser616Phe,ENST00000202677,NM_020343.3;RALGAPA2,non_coding_transcript_exon_variant,,ENST00000495793,; A ENST00000202677 Transcript missense_variant 1855/6152 1847/5622 616/1873 S/F tCt/tTt 1 -1 RALGAPA2 HGNC HGNC:16207 protein_coding YES CCDS46584.1 ENSP00000202677 Q2PPJ7 UPI000040F987 NM_020343.3 deleterious(0) 15/40 hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 20605366 20605366 G A 1 0 0 0 0 1 0 0 0 13173 942 33 3 3 RALGAPA2 20 20605366 Missense_Mutation SNP G C3N-01030_T 6278401 20605366 43838801 726 21507 CST9L 0 . GRCh38 20 23568309 23568309 + Missense_Mutation SNP G G C rs758015425 C3N-01030_T C3N-01030_N G G c.142C>G p.Pro48Ala p.P48A ENST00000376979 1/3 348 281 67 316 316 0 strelka-varscan-mutect CST9L,missense_variant,p.Pro48Ala,ENST00000376979,NM_080610.2; C ENST00000376979 Transcript missense_variant 441/959 142/444 48/147 P/A Cct/Gct rs758015425 1 -1 CST9L HGNC HGNC:16233 protein_coding YES CCDS13157.1 ENSP00000366178 Q9H4G1 A0A140VJH1 UPI0000038A07 NM_080610.2 tolerated(0.27) 1/3 hmmpanther:PTHR11413:SF22,hmmpanther:PTHR11413,Gene3D:3.10.450.10,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS rs758015425 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 23568309 23568309 G C 1 0 0 0 0 1 0 0 0 3780 1232 43 4 4 CST9L 20 23568309 Missense_Mutation SNP G C3N-01030_T 2962943 23568309 40875858 727 21508 CST2 0 . GRCh38 20 23824048 23824048 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.398T>A p.Leu133Gln p.L133Q ENST00000304725 3/3 202 147 55 218 218 0 strelka-varscan-mutect CST2,missense_variant,p.Leu133Gln,ENST00000304725,NM_001322.2; T ENST00000304725 Transcript missense_variant 469/748 398/426 133/141 L/Q cTg/cAg 1 -1 CST2 HGNC HGNC:2474 protein_coding YES CCDS13161.1 ENSP00000307540 P09228 UPI0000128D74 NM_001322.2 deleterious(0) 3/3 hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF48,Gene3D:3.10.450.10,SMART_domains:SM00043,Superfamily_domains:SSF54403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 23824048 23824048 A T 1 0 0 0 0 1 0 0 0 3772 188 7 4 4 CST2 20 23824048 Missense_Mutation SNP A C3N-01030_T 255739 23824048 40620119 728 21509 DUSP15 0 . GRCh38 20 31861641 31861641 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.470G>T p.Ser157Ile p.S157I ENST00000339738 7/7 166 125 41 130 130 0 strelka-varscan-mutect DUSP15,missense_variant,p.Ser54Ile,ENST00000486996,;DUSP15,missense_variant,p.Ser157Ile,ENST00000339738,NM_080611.3;DUSP15,missense_variant,p.Ser54Ile,ENST00000398084,NM_177991.1;DUSP15,missense_variant,p.Ser54Ile,ENST00000398083,NM_001012644.1;DUSP15,missense_variant,p.Ser154Ile,ENST00000375966,NM_001320478.1;DUSP15,intron_variant,,ENST00000278979,NM_001320479.1;DUSP15,downstream_gene_variant,,ENST00000428829,;DUSP15,downstream_gene_variant,,ENST00000493115,;DUSP15,downstream_gene_variant,,ENST00000459848,; A ENST00000339738 Transcript missense_variant 880/1454 470/708 157/235 S/I aGc/aTc 1 -1 DUSP15 HGNC HGNC:16236 protein_coding YES CCDS13193.1 ENSP00000341658 Q9H1R2 UPI0000129966 NM_080611.3 tolerated(0.05) 7/7 hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF30,Gene3D:3.90.190.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 31861641 31861641 C A 1 0 0 0 0 1 0 0 0 4637 797 28 2 2 DUSP15 20 31861641 Missense_Mutation SNP C C3N-01030_T 8037593 31861641 32582526 729 21510 ROMO1 0 . GRCh38 20 35700781 35700781 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.138C>A p.= p.I46I ENST00000374072 3/3 197 175 22 158 158 0 strelka-varscan-mutect ROMO1,synonymous_variant,p.=,ENST00000374072,;ROMO1,intron_variant,,ENST00000374078,NM_080748.2;ROMO1,intron_variant,,ENST00000336695,;ROMO1,intron_variant,,ENST00000374077,;ROMO1,intron_variant,,ENST00000397416,;NFS1,upstream_gene_variant,,ENST00000374092,NM_021100.4;RBM39,downstream_gene_variant,,ENST00000361162,NM_001323424.1,NM_004902.3;NFS1,upstream_gene_variant,,ENST00000374085,;RBM39,downstream_gene_variant,,ENST00000253363,NM_184234.2;RBM39,downstream_gene_variant,,ENST00000528062,NM_001242600.1,NM_001242599.1;NFS1,upstream_gene_variant,,ENST00000397425,;NFS1,upstream_gene_variant,,ENST00000541387,NM_001198989.1;RBM39,downstream_gene_variant,,ENST00000448303,;NFS1,upstream_gene_variant,,ENST00000306750,;NFS1,upstream_gene_variant,,ENST00000419569,;NFS1,upstream_gene_variant,,ENST00000421540,;RBM39,downstream_gene_variant,,ENST00000470563,;RBM39,downstream_gene_variant,,ENST00000463004,;RBM39,downstream_gene_variant,,ENST00000403542,;RBM39,downstream_gene_variant,,ENST00000338163,;RBM39,downstream_gene_variant,,ENST00000461283,;RBM39,downstream_gene_variant,,ENST00000492779,;RBM39,downstream_gene_variant,,ENST00000429968,;RBM39,downstream_gene_variant,,ENST00000444878,;NFS1,upstream_gene_variant,,ENST00000440385,;RBM39,downstream_gene_variant,,ENST00000482563,;RBM39,downstream_gene_variant,,ENST00000465158,;RBM39,downstream_gene_variant,,ENST00000495293,;RBM39,downstream_gene_variant,,ENST00000476806,;NFS1,upstream_gene_variant,,ENST00000456462,;NFS1,upstream_gene_variant,,ENST00000413203,;RBM39,downstream_gene_variant,,ENST00000496183,;RBM39,downstream_gene_variant,,ENST00000490354,; A ENST00000374072 Transcript synonymous_variant 153/350 138/180 46/59 I atC/atA 1 1 ROMO1 HGNC HGNC:16185 protein_coding ENSP00000363185 P60602 UPI000046FF49 3/3 Low_complexity_(Seg):seg,SMART_domains:SM01378 LOW SNV 5 1 PASS rs996890574 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 35700781 35700781 C A 1 0 0 0 0 0 0 0 1 13699 903 32 2 2 ROMO1 20 35700781 Silent SNP C C3N-01030_T 3839140 35700781 28743386 730 21511 PTPRT 0 . GRCh38 20 42315967 42315967 + Missense_Mutation SNP C C A rs766880457 C3N-01030_T C3N-01030_N C C c.1895G>T p.Arg632Leu p.R632L ENST00000373198 12/32 164 121 43 151 151 0 strelka-varscan-mutect PTPRT,missense_variant,p.Arg632Leu,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Arg632Leu,ENST00000373193,;PTPRT,missense_variant,p.Arg632Leu,ENST00000373201,;PTPRT,missense_variant,p.Arg632Leu,ENST00000373190,;PTPRT,missense_variant,p.Arg632Leu,ENST00000373184,;PTPRT,missense_variant,p.Arg632Leu,ENST00000356100,;PTPRT,missense_variant,p.Arg632Leu,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Arg250Leu,ENST00000612229,;PTPRT,missense_variant,p.Arg248Leu,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 2131/12746 1895/4383 632/1460 R/L cGa/cTa rs766880457 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0.02) 12/32 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208 MODERATE 1 SNV 2 1 PASS rs766880457 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 42315967 42315967 C A 1 0 0 0 0 1 0 0 0 12967 884 31 1 1 PTPRT 20 42315967 Missense_Mutation SNP C C3N-01030_T 6615186 42315967 22128200 731 21512 SGK2 0 . GRCh38 20 43576228 43576228 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.878C>A p.Pro293His p.P293H ENST00000341458 10/12 79 55 24 71 71 0 strelka-varscan-mutect SGK2,missense_variant,p.Pro293His,ENST00000341458,NM_016276.3;SGK2,missense_variant,p.Pro233His,ENST00000373100,;SGK2,missense_variant,p.Pro233His,ENST00000423407,NM_001199264.1;SGK2,missense_variant,p.Pro233His,ENST00000373092,NM_170693.2;SGK2,missense_variant,p.Pro259His,ENST00000426287,;SGK2,downstream_gene_variant,,ENST00000412111,;SGK2,missense_variant,p.Pro233His,ENST00000496343,;SGK2,missense_variant,p.Pro233His,ENST00000373077,; A ENST00000341458 Transcript missense_variant 1431/2498 878/1284 293/427 P/H cCc/cAc 1 1 SGK2 HGNC HGNC:13900 protein_coding YES CCDS13320.1 ENSP00000340608 Q9HBY8 UPI0000033528 NM_016276.3 deleterious(0) 10/12 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF197,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 70 43576228 43576228 C A 1 0 0 0 0 1 0 0 0 14468 637 22 2 2 SGK2 20 43576228 Missense_Mutation SNP C C3N-01030_T 1260261 43576228 20867939 732 21513 SEMG1 0 . GRCh38 20 45207592 45207592 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.295C>T p.His99Tyr p.H99Y ENST00000372781 2/3 120 90 30 132 132 0 strelka-varscan-mutect SEMG1,missense_variant,p.His99Tyr,ENST00000372781,NM_003007.3; T ENST00000372781 Transcript missense_variant 352/1662 295/1389 99/462 H/Y Cat/Tat 1 1 SEMG1 HGNC HGNC:10742 protein_coding YES CCDS13345.1 ENSP00000361867 P04279 UPI0000135844 NM_003007.3 tolerated(0.38) 2/3 hmmpanther:PTHR10547:SF4,hmmpanther:PTHR10547,Pfam_domain:PF05474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 45207592 45207592 C T 1 0 0 0 0 1 0 0 0 14320 478 17 3 3 SEMG1 20 45207592 Missense_Mutation SNP C C3N-01030_T 1631364 45207592 19236575 733 21514 WFDC2 0 . GRCh38 20 45480016 45480016 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.298G>T p.Asp100Tyr p.D100Y ENST00000372676 3/4 282 213 69 213 213 0 strelka-varscan-mutect WFDC2,missense_variant,p.Asp49Tyr,ENST00000342873,;WFDC2,missense_variant,p.Asp100Tyr,ENST00000372676,NM_006103.3;WFDC2,missense_variant,p.Asp52Tyr,ENST00000339946,;WFDC2,downstream_gene_variant,,ENST00000217425,;WFDC2,non_coding_transcript_exon_variant,,ENST00000488143,;WFDC2,non_coding_transcript_exon_variant,,ENST00000462062,;WFDC2,3_prime_UTR_variant,,ENST00000447118,; T ENST00000372676 Transcript missense_variant 374/614 298/375 100/124 D/Y Gac/Tac 1 1 WFDC2 HGNC HGNC:15939 protein_coding YES CCDS35501.1 ENSP00000361761 Q14508 UPI000000D8F6 NM_006103.3 deleterious(0.01) 3/4 PROSITE_profiles:PS51390,hmmpanther:PTHR19441,Gene3D:4.10.75.10,Pfam_domain:PF00095,SMART_domains:SM00217,Superfamily_domains:SSF57256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 45480016 45480016 G T 1 0 0 0 0 1 0 0 0 17909 1174 41 2 2 WFDC2 20 45480016 Missense_Mutation SNP G C3N-01030_T 272424 45480016 18964151 734 21515 SLC13A3 0 . GRCh38 20 46651377 46651377 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.45delG p.Arg16GlyfsTer46 p.R16Gfs*46 ENST00000279027 1/13 127 91 36 86 86 0 sindel-varindel-pindel SLC13A3,frameshift_variant,p.Arg16GlyfsTer46,ENST00000279027,NM_022829.5;SLC13A3,frameshift_variant,p.Arg16GlyfsTer46,ENST00000413164,NM_001193339.1;SLC13A3,intron_variant,,ENST00000290317,NM_001193342.1,NM_001011554.2;SLC13A3,intron_variant,,ENST00000472148,NM_001193340.1;SLC13A3,intron_variant,,ENST00000468915,;SLC13A3,intron_variant,,ENST00000417157,;SLC13A3,intron_variant,,ENST00000372121,; - ENST00000279027 Transcript frameshift_variant 64/4017 45/1809 15/602 R/X cgG/cg 1 -1 SLC13A3 HGNC HGNC:14430 protein_coding YES CCDS13400.1 ENSP00000279027 Q8WWT9 UPI000013542F NM_022829.5 1/13 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF62,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-TM,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999886 1 1 1 0 - 7 5 70 46651377 46651377 C - 1 0 1 0 1 0 0 0 0 14658 726 26 0 0 SLC13A3 20 46651377 Frame_Shift_Del DEL C C3N-01030_T 1171361 46651377 17792790 735 21516 TPTE 0 . GRCh38 21 10602062 10602062 + Missense_Mutation SNP T T C novel C3N-01030_T C3N-01030_N T T c.1361T>C p.Leu454Pro p.L454P ENST00000618007 22/24 293 273 20 415 415 0 varscan-mutect TPTE,missense_variant,p.Leu436Pro,ENST00000622113,NM_199259.3;TPTE,missense_variant,p.Leu454Pro,ENST00000618007,NM_199261.3;TPTE,missense_variant,p.Leu416Pro,ENST00000427445,NM_199260.3;TPTE,missense_variant,p.Leu316Pro,ENST00000612746,NM_001290224.1;AL078471.5,non_coding_transcript_exon_variant,,ENST00000612267,; C ENST00000618007 Transcript missense_variant 1691/2150 1361/1656 454/551 L/P cTt/cCt 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 deleterious(0.02) 22/24 PROSITE_profiles:PS51182,hmmpanther:PTHR12305:SF56,hmmpanther:PTHR12305,Pfam_domain:PF10409,Gene3D:1d5rA02,SMART_domains:SM01326,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 10602062 10602062 T C 1 0 0 0 0 1 0 0 0 16911 1623 56 5 5 TPTE 21 10602062 Missense_Mutation SNP T C3N-01030_T 10602062 36107921 736 21517 LIPI 0 . GRCh38 21 14144660 14144660 + Nonsense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.1321C>T p.Gln441Ter p.Q441* ENST00000344577 9/10 107 80 27 150 150 0 strelka-varscan-mutect LIPI,stop_gained,p.Gln441Ter,ENST00000344577,NM_198996.3;LIPI,stop_gained,p.Gln411Ter,ENST00000536861,NM_001303000.1,NM_001302998.1;LIPI,stop_gained,p.Gln381Ter,ENST00000614229,NM_001302999.1;AP001347.6,downstream_gene_variant,,ENST00000428809,;AP001347.6,downstream_gene_variant,,ENST00000432621,;ERLEC1P1,downstream_gene_variant,,ENST00000433806,; A ENST00000344577 Transcript stop_gained 1347/1652 1321/1446 441/481 Q/* Cag/Tag 1 -1 LIPI HGNC HGNC:18821 protein_coding YES CCDS13564.1 ENSP00000343331 Q6XZB0 UPI000462096D NM_198996.3 9/10 hmmpanther:PTHR11610:SF103,hmmpanther:PTHR11610,PIRSF_domain:PIRSF000865 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 14144660 14144660 G A 1 0 0 0 0 0 1 0 0 8746 1357 47 3 3 LIPI 21 14144660 Nonsense_Mutation SNP G C3N-01030_T 3542598 14144660 32565323 737 21518 KRTAP13-2 0 . GRCh38 21 30372179 30372179 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.35C>A p.Ser12Tyr p.S12Y ENST00000399889 1/1 88 71 17 78 78 0 strelka-varscan-mutect KRTAP13-2,missense_variant,p.Ser12Tyr,ENST00000399889,NM_181621.3;MIR4327,downstream_gene_variant,,ENST00000581194,; T ENST00000399889 Transcript missense_variant 79/867 35/528 12/175 S/Y tCc/tAc 1 -1 KRTAP13-2 HGNC HGNC:18923 protein_coding YES CCDS13589.1 ENSP00000382777 Q52LG2 UPI000003B46A NM_181621.3 deleterious(0) 1/1 hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF17,Pfam_domain:PF05287 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 30372179 30372179 G T 1 0 0 0 0 1 0 0 0 8406 1174 41 2 2 KRTAP13-2 21 30372179 Missense_Mutation SNP G C3N-01030_T 16227519 30372179 16337804 738 21519 TIAM1 0 . GRCh38 21 31251884 31251884 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.1269G>T p.= p.S423S ENST00000286827 6/29 262 222 40 154 154 0 strelka-varscan-mutect TIAM1,synonymous_variant,p.=,ENST00000286827,NM_003253.2;TIAM1,synonymous_variant,p.=,ENST00000541036,;TIAM1,non_coding_transcript_exon_variant,,ENST00000469412,; A ENST00000286827 Transcript synonymous_variant 1741/7200 1269/4776 423/1591 S tcG/tcT 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 6/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88 LOW 1 SNV 1 1 PASS rs1436455799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 31251884 31251884 C A 1 0 0 0 0 0 0 0 1 16324 639 23 1 1 TIAM1 21 31251884 Silent SNP C C3N-01030_T 879705 31251884 15458099 739 21520 URB1 0 . GRCh38 21 32321859 32321859 + Missense_Mutation SNP C C G rs866144203 C3N-01030_T C3N-01030_N C C c.5426G>C p.Gly1809Ala p.G1809A ENST00000382751 34/39 264 173 91 162 162 0 strelka-varscan-mutect URB1,missense_variant,p.Gly1809Ala,ENST00000382751,NM_014825.2; G ENST00000382751 Transcript missense_variant 5542/10832 5426/6816 1809/2271 G/A gGc/gCc rs866144203 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 tolerated(0.18) 34/39 hmmpanther:PTHR13500,Pfam_domain:PF16201,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs866144203 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 32321859 32321859 C G 1 0 0 0 0 1 0 0 0 17554 739 26 4 4 URB1 21 32321859 Missense_Mutation SNP C C3N-01030_T 1069975 32321859 14388124 740 21521 OLIG1 0 . GRCh38 21 33070862 33070862 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.616G>C p.Gly206Arg p.G206R ENST00000382348 1/1 50 45 5 28 28 0 strelka-mutect OLIG1,missense_variant,p.Gly206Arg,ENST00000382348,NM_138983.2;OLIG1,upstream_gene_variant,,ENST00000426947,;AP000282.2,intron_variant,,ENST00000454622,;OLIG1,upstream_gene_variant,,ENST00000498799,; C ENST00000382348 Transcript missense_variant 719/2277 616/816 206/271 G/R Ggc/Cgc 1 1 OLIG1 HGNC HGNC:16983 protein_coding YES CCDS42920.2 ENSP00000371785 Q8TAK6 UPI0000130C80 NM_138983.2 deleterious(0.01) 1/1 hmmpanther:PTHR19290,hmmpanther:PTHR19290:SF7,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 206 4 0 0 0 0 0 -12.48141 1 1 1 1 0 C 3 2 70 33070862 33070862 G C 1 0 0 0 0 1 0 0 0 10935 1116 39 4 4 OLIG1 21 33070862 Missense_Mutation SNP G C3N-01030_T 749003 33070862 13639121 741 21522 DSCAM 0 . GRCh38 21 40187244 40187244 + Missense_Mutation SNP G G A novel C3N-01030_T C3N-01030_N G G c.2666C>T p.Pro889Leu p.P889L ENST00000400454 14/33 148 112 36 139 139 0 strelka-varscan-mutect DSCAM,missense_variant,p.Pro889Leu,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Pro724Leu,ENST00000617870,;DSCAM,missense_variant,p.Pro641Leu,ENST00000404019,; A ENST00000400454 Transcript missense_variant 3144/8552 2666/6039 889/2012 P/L cCc/cTc 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 deleterious(0.01) 14/33 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 40187244 40187244 G A 1 0 0 0 0 1 0 0 0 4589 1232 43 3 3 DSCAM 21 40187244 Missense_Mutation SNP G C3N-01030_T 7116382 40187244 6522739 742 21523 KRTAP10-7 0 . GRCh38 21 44600797 44600797 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.176C>A p.Pro59Gln p.P59Q ENST00000609664 1/1 406 312 94 299 297 2 strelka-varscan-mutect KRTAP10-7,missense_variant,p.Pro59Gln,ENST00000609664,NM_198689.2;KRTAP10-7,missense_variant,p.Pro54Gln,ENST00000616689,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,; A ENST00000609664 Transcript missense_variant 201/1578 176/1113 59/370 P/Q cCa/cAa 1 1 KRTAP10-7 HGNC HGNC:22970 protein_coding YES CCDS74803.1 ENSP00000476821 P60409 UPI000021C43E NM_198689.2 deleterious(0) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 44600797 44600797 C A 1 0 0 0 0 1 0 0 0 8397 594 21 2 2 KRTAP10-7 21 44600797 Missense_Mutation SNP C C3N-01030_T 4413553 44600797 2109186 743 21524 COL6A2 0 . GRCh38 21 46132375 46132375 + Silent SNP G G A rs369756029 C3N-01030_T C3N-01030_N G G c.2883G>A p.= p.A961A ENST00000300527 28/28 226 206 20 161 161 0 strelka-varscan-mutect COL6A2,synonymous_variant,p.=,ENST00000300527,NM_001849.3;COL6A2,downstream_gene_variant,,ENST00000310645,NM_058175.2;COL6A2,downstream_gene_variant,,ENST00000409416,;COL6A2,downstream_gene_variant,,ENST00000397763,NM_058174.2;FTCD,downstream_gene_variant,,ENST00000397748,NM_001320412.1;FTCD,downstream_gene_variant,,ENST00000291670,NM_006657.2;FTCD,downstream_gene_variant,,ENST00000397746,NM_206965.1;FTCD,downstream_gene_variant,,ENST00000397743,;FTCD,downstream_gene_variant,,ENST00000446405,;FTCD,downstream_gene_variant,,ENST00000498355,;FTCD,downstream_gene_variant,,ENST00000460011,;FTCD,downstream_gene_variant,,ENST00000494498,;FTCD,downstream_gene_variant,,ENST00000483568,; A ENST00000300527 Transcript synonymous_variant 2987/3461 2883/3060 961/1019 A gcG/gcA rs369756029 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 28/28 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS rs369756029 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 46132375 46132375 G A 1 0 0 0 0 0 0 0 1 3489 1074 38 1 1 COL6A2 21 46132375 Silent SNP G C3N-01030_T 1531578 46132375 577608 744 21525 MICAL3 0 . GRCh38 22 17818935 17818935 + Silent SNP C C A rs372011453 C3N-01030_T C3N-01030_N C C c.3726G>T p.= p.P1242P ENST00000441493 26/32 22 17 5 33 33 0 strelka-mutect MICAL3,synonymous_variant,p.=,ENST00000441493,NM_015241.2;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,; A ENST00000441493 Transcript synonymous_variant 4079/9445 3726/6009 1242/2002 P ccG/ccT rs372011453 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 26/32 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF239 LOW 1 SNV 5 1 PASS rs372011453 . 0 198 12 0 0 0 0 0 -14.24527 0.9999636 1 1 1 0 A 2 1 70 17818935 17818935 C A 1 0 0 0 0 0 0 0 1 9528 755 27 1 1 MICAL3 22 17818935 Silent SNP C C3N-01030_T 17818935 32999533 745 21526 SLC7A4 0 . GRCh38 22 21030178 21030178 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1156G>T p.Asp386Tyr p.D386Y ENST00000382932 3/5 304 233 71 220 220 0 strelka-varscan-mutect SLC7A4,missense_variant,p.Asp386Tyr,ENST00000382932,NM_004173.2;SLC7A4,missense_variant,p.Asp386Tyr,ENST00000403586,;P2RX6,downstream_gene_variant,,ENST00000413302,NM_005446.3;P2RX6,downstream_gene_variant,,ENST00000401443,NM_001159554.1;SLC7A4,downstream_gene_variant,,ENST00000426145,;MIR649,downstream_gene_variant,,ENST00000384843,;AC002472.11,upstream_gene_variant,,ENST00000450652,;P2RX6,downstream_gene_variant,,ENST00000442475,;P2RX6,downstream_gene_variant,,ENST00000432930,;P2RX6,downstream_gene_variant,,ENST00000422210,;P2RX6,downstream_gene_variant,,ENST00000487342,; A ENST00000382932 Transcript missense_variant 1224/2313 1156/1908 386/635 D/Y Gac/Tac 1 -1 SLC7A4 HGNC HGNC:11062 protein_coding YES CCDS33608.1 ENSP00000372390 O43246 UPI0000169EC7 NM_004173.2 deleterious(0) 3/5 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF410,Pfam_domain:PF13520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 21030178 21030178 C A 1 0 0 0 0 1 0 0 0 14982 855 30 2 2 SLC7A4 22 21030178 Missense_Mutation SNP C C3N-01030_T 3211243 21030178 29788290 746 21527 VPREB3 0 . GRCh38 22 23753013 23753013 + Missense_Mutation SNP G G A rs779221030 C3N-01030_T C3N-01030_N G G c.235C>T p.Arg79Trp p.R79W ENST00000248948 2/2 433 304 129 315 314 1 strelka-varscan-mutect VPREB3,missense_variant,p.Arg79Trp,ENST00000248948,NM_013378.2;VPREB3,missense_variant,p.Arg63Trp,ENST00000398465,;ZNF70,upstream_gene_variant,,ENST00000341976,NM_021916.3; A ENST00000248948 Transcript missense_variant 340/610 235/372 79/123 R/W Cgg/Tgg rs779221030,COSM1270240 1 -1 VPREB3 HGNC HGNC:12710 protein_coding YES CCDS13813.1 ENSP00000248948 Q9UKI3 UPI0000049DEB NM_013378.2 deleterious(0) 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR23267:SF133,hmmpanther:PTHR23267,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779221030 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 23753013 23753013 G A 1 0 0 0 0 1 0 0 0 17734 1115 39 1 1 VPREB3 22 23753013 Missense_Mutation SNP G C3N-01030_T 2722835 23753013 27065455 747 21528 CABIN1 0 . GRCh38 22 24166795 24166795 + Missense_Mutation SNP G G C novel C3N-01030_T C3N-01030_N G G c.5164G>C p.Gly1722Arg p.G1722R ENST00000398319 32/37 210 141 69 218 218 0 strelka-varscan-mutect CABIN1,missense_variant,p.Gly1722Arg,ENST00000398319,NM_001199281.1;CABIN1,missense_variant,p.Gly1722Arg,ENST00000263119,NM_012295.3;CABIN1,missense_variant,p.Gly1672Arg,ENST00000617531,NM_001201429.1;CABIN1,missense_variant,p.Gly1643Arg,ENST00000405822,;CABIN1,missense_variant,p.Gly147Arg,ENST00000337989,;CABIN1,upstream_gene_variant,,ENST00000485008,;CABIN1,downstream_gene_variant,,ENST00000495121,; C ENST00000398319 Transcript missense_variant 5549/7480 5164/6663 1722/2220 G/R Gga/Cga 1 1 CABIN1 HGNC HGNC:24187 protein_coding YES CCDS13823.1 ENSP00000381364 Q9Y6J0 A0A024R1E5 UPI0000126D6C NM_001199281.1 tolerated_low_confidence(0.06) 32/37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 24166795 24166795 G C 1 0 0 0 0 1 0 0 0 2214 1001 35 4 4 CABIN1 22 24166795 Missense_Mutation SNP G C3N-01030_T 413782 24166795 26651673 748 21529 ADORA2A 0 . GRCh38 22 24433487 24433487 + Missense_Mutation SNP G G T rs763237836 C3N-01030_T C3N-01030_N G G c.83G>T p.Cys28Phe p.C28F ENST00000610595 3/4 171 146 25 161 160 1 strelka-varscan-mutect ADORA2A,missense_variant,p.Cys28Phe,ENST00000610595,NM_001278497.1;ADORA2A,missense_variant,p.Cys28Phe,ENST00000618076,NM_001278498.1;ADORA2A,missense_variant,p.Cys28Phe,ENST00000337539,NM_000675.5,NM_001278499.1;ADORA2A,missense_variant,p.Cys28Phe,ENST00000611543,NM_001278500.1;ADORA2A,missense_variant,p.Cys28Phe,ENST00000444262,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000486108,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000472248,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000496258,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000436735,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000424232,;ADORA2A,missense_variant,p.Cys28Phe,ENST00000439591,;ADORA2A,downstream_gene_variant,,ENST00000464977,;ADORA2A-AS1,intron_variant,,ENST00000326341,;ADORA2A-AS1,downstream_gene_variant,,ENST00000427813,;ADORA2A,intron_variant,,ENST00000496497,;ADORA2A,downstream_gene_variant,,ENST00000486351,;ADORA2A,downstream_gene_variant,,ENST00000467385,;SPECC1L-ADORA2A,3_prime_UTR_variant,,ENST00000358654,; T ENST00000610595 Transcript missense_variant 713/2736 83/1239 28/412 C/F tGc/tTc rs763237836 1 1 ADORA2A HGNC HGNC:263 protein_coding YES CCDS13826.1 ENSP00000480012 X5DNB4 UPI00000503E2 NM_001278497.1 deleterious(0) 3/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00553,PROSITE_profiles:PS50262,hmmpanther:PTHR24246,hmmpanther:PTHR24246:SF28,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs763237836 . 0 206 0 4 0 0 0 0 -20 0.9999141 1 1 1 0 T 3 4 70 24433487 24433487 G T 1 0 0 0 0 1 0 0 0 402 1319 46 2 2 ADORA2A 22 24433487 Missense_Mutation SNP G C3N-01030_T 266692 24433487 26384981 749 21530 OSBP2 0 . GRCh38 22 30741173 30741173 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.657A>T p.Glu219Asp p.E219D ENST00000332585 2/14 91 69 22 95 95 0 strelka-varscan-mutect OSBP2,missense_variant,p.Glu219Asp,ENST00000332585,NM_030758.3;OSBP2,missense_variant,p.Glu46Asp,ENST00000407373,;OSBP2,missense_variant,p.Glu219Asp,ENST00000446658,NM_001282739.1;OSBP2,missense_variant,p.Glu54Asp,ENST00000438716,NM_001282738.1;OSBP2,5_prime_UTR_variant,,ENST00000403222,; T ENST00000332585 Transcript missense_variant 761/4340 657/2751 219/916 E/D gaA/gaT 1 1 OSBP2 HGNC HGNC:8504 protein_coding YES CCDS43002.1 ENSP00000332576 Q969R2 UPI0000161E15 NM_030758.3 tolerated(0.06) 2/14 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF51,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 30741173 30741173 A T 1 0 0 0 0 1 0 0 0 11340 11 1 4 4 OSBP2 22 30741173 Missense_Mutation SNP A C3N-01030_T 6307686 30741173 20077295 750 21531 OSBP2 0 . GRCh38 22 30887604 30887604 + Missense_Mutation SNP A A G novel C3N-01030_T C3N-01030_N A A c.1286A>G p.Lys429Arg p.K429R ENST00000332585 4/14 86 66 20 73 73 0 strelka-varscan-mutect OSBP2,missense_variant,p.Lys429Arg,ENST00000332585,NM_030758.3;OSBP2,missense_variant,p.Lys150Arg,ENST00000403222,;OSBP2,missense_variant,p.Lys256Arg,ENST00000407373,;OSBP2,missense_variant,p.Lys171Arg,ENST00000437268,NM_001282741.1;OSBP2,missense_variant,p.Lys101Arg,ENST00000431368,;OSBP2,missense_variant,p.Lys429Arg,ENST00000446658,NM_001282739.1;OSBP2,missense_variant,p.Lys60Arg,ENST00000452656,;OSBP2,missense_variant,p.Lys264Arg,ENST00000438716,NM_001282738.1;OSBP2,missense_variant,p.Lys63Arg,ENST00000401475,NM_001282740.1;OSBP2,missense_variant,p.Lys101Arg,ENST00000453621,;OSBP2,missense_variant,p.Lys63Arg,ENST00000424224,;OSBP2,missense_variant,p.Lys101Arg,ENST00000454145,;OSBP2,5_prime_UTR_variant,,ENST00000535268,NM_001282742.1;OSBP2,downstream_gene_variant,,ENST00000445781,;OSBP2,upstream_gene_variant,,ENST00000496575,; G ENST00000332585 Transcript missense_variant 1390/4340 1286/2751 429/916 K/R aAg/aGg 1 1 OSBP2 HGNC HGNC:8504 protein_coding YES CCDS43002.1 ENSP00000332576 Q969R2 UPI0000161E15 NM_030758.3 tolerated(0.2) 4/14 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF51 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 30887604 30887604 A G 1 0 0 0 0 1 0 0 0 11340 72 3 5 5 OSBP2 22 30887604 Missense_Mutation SNP A C3N-01030_T 146431 30887604 19930864 751 21532 SYN3 0 . GRCh38 22 32596704 32596704 + Frame_Shift_Del DEL C C - novel C3N-01030_T C3N-01030_N C C c.744delG p.Lys248AsnfsTer59 p.K248Nfs*59 ENST00000358763 7/14 106 71 35 145 145 0 sindel-varindel SYN3,frameshift_variant,p.Lys248AsnfsTer59,ENST00000358763,NM_001135774.1,NM_003490.3,NM_133633.2; - ENST00000358763 Transcript frameshift_variant 987/3126 744/1743 248/580 K/X aaG/aa 1 -1 SYN3 HGNC HGNC:11496 protein_coding YES CCDS13908.1 ENSP00000351614 O14994 A0A024R1I8 UPI00001365D3 NM_001135774.1,NM_003490.3,NM_133633.2 7/14 hmmpanther:PTHR10841,Pfam_domain:PF02750,Gene3D:3.30.1490.20,Superfamily_domains:SSF56059 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 32596704 32596704 C - 1 0 1 0 1 0 0 0 0 15832 796 28 0 0 SYN3 22 32596704 Frame_Shift_Del DEL C C3N-01030_T 1709100 32596704 18221764 752 21533 CACNA1I 0 . GRCh38 22 39679418 39679418 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.5367G>T p.Leu1789Phe p.L1789F ENST00000402142 32/37 54 33 21 58 58 0 varscan-mutect CACNA1I,missense_variant,p.Leu1789Phe,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Leu1754Phe,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Leu1789Phe,ENST00000401624,;CACNA1I,missense_variant,p.Leu1754Phe,ENST00000407673,; T ENST00000402142 Transcript missense_variant 5367/10004 5367/6672 1789/2223 L/F ttG/ttT 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 tolerated(0.12) 32/37 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 39679418 39679418 G T 1 0 0 0 0 1 0 0 0 2234 1368 48 2 2 CACNA1I 22 39679418 Missense_Mutation SNP G C3N-01030_T 7082714 39679418 11139050 753 21534 MXRA5 0 . GRCh38 X 3321723 3321723 + Nonsense_Mutation SNP G G T C3N-01030_T C3N-01030_N G G c.3962C>A p.Ser1321Ter p.S1321* ENST00000217939 5/7 64 29 35 63 63 0 strelka-varscan-mutect MXRA5,stop_gained,p.Ser1321Ter,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript stop_gained 4117/9793 3962/8487 1321/2828 S/* tCa/tAa COSM4981446,COSM4981447 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 5/7 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF680 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 70 3321723 3321723 G T 1 0 0 0 0 0 1 0 0 10002 1294 45 2 2 MXRA5 23 3321723 Nonsense_Mutation SNP G C3N-01030_T 3321723 152719172 754 21535 VCX 0 . GRCh38 X 7843263 7843263 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.60G>A p.= p.R20R ENST00000381059 2/3 135 91 44 79 79 0 strelka-varscan-mutect VCX,synonymous_variant,p.=,ENST00000381059,NM_013452.2;VCX,synonymous_variant,p.=,ENST00000620630,;VCX,synonymous_variant,p.=,ENST00000341408,; A ENST00000381059 Transcript synonymous_variant 279/967 60/621 20/206 R agG/agA 1 1 VCX HGNC HGNC:12667 protein_coding YES CCDS14128.1 ENSP00000370447 Q9H320 UPI0000138291 NM_013452.2 2/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 7843263 7843263 G A 1 0 0 0 0 0 0 0 1 17688 1165 41 3 3 VCX 23 7843263 Silent SNP G C3N-01030_T 4521540 7843263 148197632 755 21536 SHROOM2 0 . GRCh38 X 9895140 9895140 + Missense_Mutation SNP C C T C3N-01030_T C3N-01030_N C C c.1232C>T p.Ser411Phe p.S411F ENST00000380913 4/10 94 46 48 92 92 0 strelka-varscan-mutect SHROOM2,missense_variant,p.Ser411Phe,ENST00000380913,NM_001649.2;SHROOM2,upstream_gene_variant,,ENST00000493668,; T ENST00000380913 Transcript missense_variant 1322/7447 1232/4851 411/1616 S/F tCt/tTt COSM1126539 1 1 SHROOM2 HGNC HGNC:630 protein_coding YES CCDS14135.1 ENSP00000370299 Q13796 UPI0000125D05 NM_001649.2 deleterious(0) 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR15012:SF8,hmmpanther:PTHR15012 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 9895140 9895140 C T 1 0 0 0 0 1 0 0 0 14557 913 32 3 3 SHROOM2 23 9895140 Missense_Mutation SNP C C3N-01030_T 2051877 9895140 146145755 756 21537 PHEX 0 . GRCh38 X 22096980 22096980 + Missense_Mutation SNP C C G rs768862054 C3N-01030_T C3N-01030_N C C c.875C>G p.Thr292Ser p.T292S ENST00000379374 8/22 129 81 48 184 184 0 strelka-varscan-mutect PHEX,missense_variant,p.Thr292Ser,ENST00000379374,NM_001282754.1,NM_000444.5;PHEX,non_coding_transcript_exon_variant,,ENST00000475778,; G ENST00000379374 Transcript missense_variant 1440/6172 875/2250 292/749 T/S aCc/aGc rs768862054,COSM756523 1 1 PHEX HGNC HGNC:8918 protein_coding YES CCDS14204.1 ENSP00000368682 P78562 UPI0000033C42 NM_001282754.1,NM_000444.5 tolerated(0.74) 8/22 Pfam_domain:PF05649,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF149,Superfamily_domains:SSF55486 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768862054 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 70 22096980 22096980 C G 1 0 0 0 0 1 0 0 0 11908 507 18 4 4 PHEX 23 22096980 Missense_Mutation SNP C C3N-01030_T 12201840 22096980 133943915 757 21538 PPP4R3CP 0 . GRCh38 X 27461589 27461589 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1708G>T p.Glu570Ter p.E570* ENST00000412172 1/1 77 43 34 119 118 1 strelka-varscan-mutect PPP4R3CP,stop_gained,p.Glu570Ter,ENST00000412172,; A ENST00000412172 Transcript stop_gained 1753/3131 1708/2499 570/832 E/* Gaa/Taa 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF48371 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 27461589 27461589 C A 1 0 0 0 0 0 1 0 0 12529 835 29 2 2 PPP4R3CP 23 27461589 Nonsense_Mutation SNP C C3N-01030_T 5364609 27461589 128579306 758 21539 MAGEB4 0 . GRCh38 X 30242581 30242581 + Missense_Mutation SNP A A T novel C3N-01030_T C3N-01030_N A A c.446A>T p.Glu149Val p.E149V ENST00000378982 1/1 91 45 46 77 77 0 strelka-varscan-mutect MAGEB4,missense_variant,p.Glu149Val,ENST00000378982,NM_002367.3;MAGEB1,upstream_gene_variant,,ENST00000378981,NM_002363.4;MAGEB1,upstream_gene_variant,,ENST00000397550,NM_177415.2;MAGEB1,upstream_gene_variant,,ENST00000397548,NM_177404.2; T ENST00000378982 Transcript missense_variant 530/2142 446/1041 149/346 E/V gAg/gTg 1 1 MAGEB4 HGNC HGNC:6811 protein_coding YES CCDS14221.1 ENSP00000368266 O15481 UPI000012F055 NM_002367.3 deleterious(0.04) 1/1 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF75,SMART_domains:SM01373 MODERATE SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 30242581 30242581 A T 1 0 0 0 0 1 0 0 0 9094 304 11 4 4 MAGEB4 23 30242581 Missense_Mutation SNP A C3N-01030_T 2780992 30242581 125798314 759 21540 FAM47A 0 . GRCh38 X 34131134 34131134 + Missense_Mutation SNP G G T rs759260358 C3N-01030_T C3N-01030_N G G c.1145C>A p.Thr382Asn p.T382N ENST00000346193 1/1 43 21 22 42 42 0 strelka-varscan-mutect FAM47A,missense_variant,p.Thr382Asn,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.Thr382Asn,ENST00000613251,; T ENST00000346193 Transcript missense_variant 1178/2556 1145/2376 382/791 T/N aCt/aAt rs759260358 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 tolerated(0.16) 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS rs759260358 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 34131134 34131134 G T 1 0 0 0 0 1 0 0 0 5447 1029 36 2 2 FAM47A 23 34131134 Missense_Mutation SNP G C3N-01030_T 3888553 34131134 121909761 760 21541 CFAP47 0 . GRCh38 X 35967731 35967731 + Missense_Mutation SNP C C A rs145448150 C3N-01030_T C3N-01030_N C C c.1713C>A p.His571Gln p.H571Q ENST00000297866 10/16 158 86 72 166 166 0 strelka-varscan-mutect CFAP47,missense_variant,p.His571Gln,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.His571Gln,ENST00000297866,NM_152632.3;CFAP47,missense_variant,p.His571Gln,ENST00000493930,; A ENST00000297866 Transcript missense_variant 1779/3608 1713/2931 571/976 H/Q caC/caA rs145448150,COSM1734359,COSM1734360 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 deleterious(0) 10/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs145448150 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 35967731 35967731 C A 1 0 0 0 0 1 0 0 0 3022 477 17 2 2 CFAP47 23 35967731 Missense_Mutation SNP C C3N-01030_T 1836597 35967731 120073164 761 21542 DUSP21 0 . GRCh38 X 44844480 44844480 + Silent SNP G G T novel C3N-01030_T C3N-01030_N G G c.348G>T p.= p.L116L ENST00000339042 1/1 75 33 42 65 64 1 strelka-varscan-mutect DUSP21,synonymous_variant,p.=,ENST00000339042,NM_022076.3; T ENST00000339042 Transcript synonymous_variant 477/885 348/573 116/190 L ctG/ctT 1 1 DUSP21 HGNC HGNC:20476 protein_coding YES CCDS14264.1 ENSP00000343244 Q9H596 UPI00000342DF NM_022076.3 1/1 Gene3D:3.90.190.10,Pfam_domain:PF00782,PROSITE_profiles:PS50054,PROSITE_profiles:PS50056,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF386,SMART_domains:SM00195,Superfamily_domains:SSF52799 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 70 44844480 44844480 G T 1 0 0 0 0 0 0 0 1 4642 1364 48 2 2 DUSP21 23 44844480 Silent SNP G C3N-01030_T 8876749 44844480 111196415 762 21543 RBM10 0 . GRCh38 X 47180505 47180505 + Missense_Mutation SNP A A T C3N-01030_T C3N-01030_N A A c.1442A>T p.Gln481Leu p.Q481L ENST00000329236 12/24 155 86 69 110 110 0 strelka-varscan-mutect RBM10,missense_variant,p.Gln416Leu,ENST00000377604,NM_005676.4,NM_001204467.1;RBM10,missense_variant,p.Gln481Leu,ENST00000329236,NM_001204468.1;RBM10,missense_variant,p.Gln339Leu,ENST00000345781,NM_001204466.1;RBM10,missense_variant,p.Gln338Leu,ENST00000628161,NM_152856.2;RBM10,splice_region_variant,,ENST00000478410,;RBM10,intron_variant,,ENST00000496012,; T ENST00000329236 Transcript missense_variant,splice_region_variant 1442/3201 1442/2988 481/995 Q/L cAg/cTg COSM1558303 1 1 RBM10 HGNC HGNC:9896 protein_coding YES CCDS75969.1 ENSP00000328848 A0A0A0MR66 UPI0000211F0E NM_001204468.1 deleterious(0) 12/24 hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF4,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 47180505 47180505 A T 1 0 0 0 0 1 0 0 0 13277 202 7 4 4 RBM10 23 47180505 Missense_Mutation SNP A C3N-01030_T 2336025 47180505 108860390 763 21544 WNK3 0 . GRCh38 X 54255792 54255792 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2198C>A p.Ala733Asp p.A733D ENST00000354646 12/24 96 56 40 111 111 0 strelka-varscan-mutect WNK3,missense_variant,p.Ala733Asp,ENST00000354646,NM_020922.4;WNK3,missense_variant,p.Ala733Asp,ENST00000375169,NM_001002838.3;WNK3,missense_variant,p.Ala733Asp,ENST00000375159,;WNK3,missense_variant,p.Ala733Asp,ENST00000620763,; T ENST00000354646 Transcript missense_variant 2637/11341 2198/5403 733/1800 A/D gCt/gAt 1 -1 WNK3 HGNC HGNC:14543 protein_coding YES CCDS14357.1 ENSP00000346667 Q9BYP7 UPI00001AF003 NM_020922.4 deleterious(0) 12/24 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF47 MODERATE 1 SNV 1 1 PASS rs1447824802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 54255792 54255792 G T 1 0 0 0 0 1 0 0 0 17935 971 34 2 2 WNK3 23 54255792 Missense_Mutation SNP G C3N-01030_T 7075287 54255792 101785103 764 21545 ITIH6 0 . GRCh38 X 54751292 54751292 + Silent SNP G G A novel C3N-01030_T C3N-01030_N G G c.3441C>T p.= p.V1147V ENST00000218436 12/13 133 73 60 91 90 1 strelka-varscan-mutect ITIH6,synonymous_variant,p.=,ENST00000218436,NM_198510.2; A ENST00000218436 Transcript synonymous_variant 3471/4968 3441/3942 1147/1313 V gtC/gtT 1 -1 ITIH6 HGNC HGNC:28907 protein_coding YES CCDS14361.1 ENSP00000218436 Q6UXX5 UPI00000540C8 NM_198510.2 12/13 Pfam_domain:PF06668,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 54751292 54751292 G A 1 0 0 0 0 0 0 0 1 7814 1277 45 3 3 ITIH6 23 54751292 Silent SNP G C3N-01030_T 495500 54751292 101289603 765 21546 AMER1 0 . GRCh38 X 64192143 64192143 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1144G>T p.Glu382Ter p.E382* ENST00000330258 2/2 76 36 40 101 101 0 strelka-varscan-mutect AMER1,stop_gained,p.Glu382Ter,ENST00000330258,NM_152424.3;AMER1,stop_gained,p.Glu382Ter,ENST00000374869,; A ENST00000330258 Transcript stop_gained 1417/8443 1144/3408 382/1135 E/* Gaa/Taa 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 2/2 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22237:SF0,hmmpanther:PTHR22237,Pfam_domain:PF09422 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 64192143 64192143 C A 1 0 0 0 0 0 1 0 0 667 864 30 2 2 AMER1 23 64192143 Nonsense_Mutation SNP C C3N-01030_T 9440851 64192143 91848752 766 21547 IL2RG 0 . GRCh38 X 71109245 71109245 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.740G>A p.Gly247Glu p.G247E ENST00000374202 5/8 111 44 67 103 103 0 strelka-varscan-mutect IL2RG,missense_variant,p.Gly247Glu,ENST00000374202,NM_000206.2;IL2RG,missense_variant,p.Gly203Glu,ENST00000464642,;IL2RG,missense_variant,p.Gly57Glu,ENST00000456850,;IL2RG,missense_variant,p.Gly52Glu,ENST00000482750,;IL2RG,synonymous_variant,p.=,ENST00000374188,;IL2RG,downstream_gene_variant,,ENST00000487883,;CXorf65,upstream_gene_variant,,ENST00000374251,NM_001025265.2;IL2RG,downstream_gene_variant,,ENST00000473378,;IL2RG,non_coding_transcript_exon_variant,,ENST00000276110,;IL2RG,non_coding_transcript_exon_variant,,ENST00000512747,;CXorf65,upstream_gene_variant,,ENST00000438526,;CXorf65,upstream_gene_variant,,ENST00000483257,;CXorf65,upstream_gene_variant,,ENST00000466160,; T ENST00000374202 Transcript missense_variant 832/1534 740/1110 247/369 G/E gGg/gAg 1 -1 IL2RG HGNC HGNC:6010 protein_coding YES CCDS14406.1 ENSP00000363318 P31785 UPI0000000DEA NM_000206.2 deleterious(0) 5/8 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF97,Gene3D:2.60.40.10 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 71109245 71109245 C T 1 0 0 0 0 1 0 0 0 7587 623 22 3 3 IL2RG 23 71109245 Missense_Mutation SNP C C3N-01030_T 6917102 71109245 84931650 767 21548 ITGB1BP2 0 . GRCh38 X 71302526 71302526 + Nonsense_Mutation SNP C C G novel C3N-01030_T C3N-01030_N C C c.287C>G p.Ser96Ter p.S96* ENST00000373829 4/11 51 27 24 48 48 0 strelka-varscan-mutect ITGB1BP2,stop_gained,p.Ser78Ter,ENST00000538820,;ITGB1BP2,stop_gained,p.Ser96Ter,ENST00000373829,NM_012278.2;NONO,downstream_gene_variant,,ENST00000535149,NM_001145410.1;NONO,downstream_gene_variant,,ENST00000276079,NM_007363.4;NONO,downstream_gene_variant,,ENST00000373841,NM_001145409.1;NONO,downstream_gene_variant,,ENST00000373856,NM_001145408.1;NONO,downstream_gene_variant,,ENST00000418921,;ITGB1BP2,intron_variant,,ENST00000483897,;NONO,downstream_gene_variant,,ENST00000490044,;NONO,downstream_gene_variant,,ENST00000473525,;ITGB1BP2,upstream_gene_variant,,ENST00000465388,;NONO,downstream_gene_variant,,ENST00000471419,;NONO,downstream_gene_variant,,ENST00000474431,;ITGB1BP2,upstream_gene_variant,,ENST00000475413,;NONO,downstream_gene_variant,,ENST00000472185,; G ENST00000373829 Transcript stop_gained 360/1296 287/1044 96/347 S/* tCa/tGa 1 1 ITGB1BP2 HGNC HGNC:6154 protein_coding YES CCDS14411.1 ENSP00000362935 Q9UKP3 UPI000000103C NM_012278.2 4/11 hmmpanther:PTHR12621:SF8,hmmpanther:PTHR12621 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 70 71302526 71302526 C G 1 0 0 0 0 0 1 0 0 7799 838 29 4 4 ITGB1BP2 23 71302526 Nonsense_Mutation SNP C C3N-01030_T 193281 71302526 84738369 768 21549 MAGEE1 0 . GRCh38 X 76428238 76428238 + Missense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.308C>A p.Ser103Tyr p.S103Y ENST00000361470 1/1 130 72 58 107 107 0 strelka-varscan-mutect MAGEE1,missense_variant,p.Ser103Tyr,ENST00000361470,NM_020932.2; A ENST00000361470 Transcript missense_variant 515/3630 308/2874 103/957 S/Y tCc/tAc 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 70 76428238 76428238 C A 1 0 0 0 0 1 0 0 0 9103 855 30 2 2 MAGEE1 23 76428238 Missense_Mutation SNP C C3N-01030_T 5125712 76428238 79612657 769 21550 PABPC5 0 . GRCh38 X 91435755 91435755 + Missense_Mutation SNP G G C C3N-01030_T C3N-01030_N G G c.178G>C p.Gly60Arg p.G60R ENST00000312600 2/2 106 58 48 81 81 0 strelka-varscan-mutect PABPC5,missense_variant,p.Gly60Arg,ENST00000312600,NM_080832.2;PABPC5,intron_variant,,ENST00000373105,;PABPC5-AS1,upstream_gene_variant,,ENST00000456187,; C ENST00000312600 Transcript missense_variant 392/3221 178/1149 60/382 G/R Ggc/Cgc COSM5681167 1 1 PABPC5 HGNC HGNC:13629 protein_coding YES CCDS14460.1 ENSP00000308012 Q96DU9 UPI0000087790 NM_080832.2 deleterious(0) 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF407,SMART_domains:SM00360,Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01628 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 70 91435755 91435755 G C 1 0 0 0 0 1 0 0 0 11445 1232 43 4 4 PABPC5 23 91435755 Missense_Mutation SNP G C3N-01030_T 15007517 91435755 64605140 770 21551 PCDH11X 0 . GRCh38 X 91877606 91877606 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.1366G>T p.Val456Leu p.V456L ENST00000373094 2/7 122 65 57 140 140 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Val456Leu,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Val456Leu,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Val456Leu,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Val456Leu,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Val456Leu,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Val456Leu,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Val456Leu,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 2211/9179 1366/4044 456/1347 V/L Gtg/Ttg 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 tolerated(0.21) 2/7 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 91877606 91877606 G T 1 0 0 0 0 1 0 0 0 11595 1029 36 2 2 PCDH11X 23 91877606 Missense_Mutation SNP G C3N-01030_T 441851 91877606 64163289 771 21552 SLC25A53 0 . GRCh38 X 104104454 104104454 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.804G>T p.= p.L268L ENST00000594199 2/2 154 72 82 169 167 2 strelka-varscan-mutect SLC25A53,synonymous_variant,p.=,ENST00000594199,NM_001012755.4; A ENST00000594199 Transcript synonymous_variant 985/6225 804/924 268/307 L ctG/ctT 1 -1 SLC25A53 HGNC HGNC:31894 protein_coding YES CCDS35363.1 ENSP00000468980 Q5H9E4 UPI0000140AFF NM_001012755.4 2/2 Superfamily_domains:0048588,Gene3D:1okcA00,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF235 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 104104454 104104454 C A 1 0 0 0 0 0 0 0 1 14782 813 29 2 2 SLC25A53 23 104104454 Silent SNP C C3N-01030_T 12226848 104104454 51936441 772 21553 IRS4 0 . GRCh38 X 108733889 108733889 + Missense_Mutation SNP G G T novel C3N-01030_T C3N-01030_N G G c.2456C>A p.Pro819His p.P819H ENST00000372129 1/1 201 86 115 148 148 0 strelka-varscan-mutect IRS4,missense_variant,p.Pro819His,ENST00000372129,NM_003604.2;RP6-24A23.6,upstream_gene_variant,,ENST00000563887,;RP6-24A23.3,upstream_gene_variant,,ENST00000436013,;RP6-24A23.3,upstream_gene_variant,,ENST00000608811,; T ENST00000372129 Transcript missense_variant 2521/3928 2456/3774 819/1257 P/H cCt/cAt 1 -1 IRS4 HGNC HGNC:6128 protein_coding YES CCDS14544.1 ENSP00000361202 O14654 UPI0000073FE7 NM_003604.2 deleterious(0.05) 1/1 hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF2 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 108733889 108733889 G T 1 0 0 0 0 1 0 0 0 7750 1000 35 2 2 IRS4 23 108733889 Missense_Mutation SNP G C3N-01030_T 4629435 108733889 47307006 773 21554 IRS4 0 . GRCh38 X 108734721 108734721 + Missense_Mutation SNP C C T novel C3N-01030_T C3N-01030_N C C c.1624G>A p.Gly542Arg p.G542R ENST00000372129 1/1 164 72 92 114 114 0 strelka-varscan-mutect IRS4,missense_variant,p.Gly542Arg,ENST00000372129,NM_003604.2;RP6-24A23.6,upstream_gene_variant,,ENST00000563887,;RP6-24A23.3,upstream_gene_variant,,ENST00000436013,;RP6-24A23.3,upstream_gene_variant,,ENST00000608811,; T ENST00000372129 Transcript missense_variant 1689/3928 1624/3774 542/1257 G/R Gga/Aga 1 -1 IRS4 HGNC HGNC:6128 protein_coding YES CCDS14544.1 ENSP00000361202 O14654 UPI0000073FE7 NM_003604.2 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR10614,hmmpanther:PTHR10614:SF2,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 70 108734721 108734721 C T 1 0 0 0 0 1 0 0 0 7750 690 24 3 3 IRS4 23 108734721 Missense_Mutation SNP C C3N-01030_T 832 108734721 47306174 774 21555 RBMXL3 0 . GRCh38 X 115192147 115192147 + Silent SNP C C A novel C3N-01030_T C3N-01030_N C C c.2706C>A p.= p.G902G ENST00000424776 1/1 163 76 87 110 110 0 strelka-varscan-mutect RBMXL3,synonymous_variant,p.=,ENST00000424776,NM_001145346.1;LRCH2,intron_variant,,ENST00000317135,NM_020871.3;LRCH2,intron_variant,,ENST00000538422,NM_001243963.1; A ENST00000424776 Transcript synonymous_variant 2721/3442 2706/3204 902/1067 G ggC/ggA 1 1 RBMXL3 HGNC HGNC:26859 protein_coding YES CCDS55478.1 ENSP00000417451 Q8N7X1 UPI0001932819 NM_001145346.1 1/1 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 70 115192147 115192147 C A 1 0 0 0 0 0 0 0 1 13321 726 26 2 2 RBMXL3 23 115192147 Silent SNP C C3N-01030_T 6457426 115192147 40848748 775 21556 MAGEC3 0 . GRCh38 X 141895369 141895369 + Nonsense_Mutation SNP C C A novel C3N-01030_T C3N-01030_N C C c.1010C>A p.Ser337Ter p.S337* ENST00000298296 5/8 126 61 65 95 95 0 strelka-varscan-mutect MAGEC3,stop_gained,p.Ser337Ter,ENST00000298296,NM_138702.1;MAGEC3,5_prime_UTR_variant,,ENST00000544766,NM_177456.2;MAGEC3,intron_variant,,ENST00000443323,;MAGEC3,upstream_gene_variant,,ENST00000409007,;MAGEC3,non_coding_transcript_exon_variant,,ENST00000483584,; A ENST00000298296 Transcript stop_gained 1010/1932 1010/1932 337/643 S/* tCa/tAa 1 1 MAGEC3 HGNC HGNC:23798 protein_coding YES CCDS14676.1 ENSP00000298296 Q8TD91 UPI000006E09B NM_138702.1 5/8 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF86,SMART_domains:SM01373 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 70 141895369 141895369 C A 1 0 0 0 0 0 1 0 0 9100 838 29 2 2 MAGEC3 23 141895369 Nonsense_Mutation SNP C C3N-01030_T 26703222 141895369 14145526 776 21557 MAGEA12 0 . GRCh38 X 152736838 152736839 + Frame_Shift_Del DEL GT GT - novel C3N-01030_T C3N-01030_N GT GT c.681_682delGT p.Leu228GlyfsTer4 p.L228Gfs*4 ENST00000393900 3/3 198 85 113 184 184 0 sindel-varindel-pindel MAGEA12,frameshift_variant,p.Leu228GlyfsTer4,ENST00000393900,NM_001166386.3;MAGEA12,frameshift_variant,p.Leu228GlyfsTer4,ENST00000393869,NM_001166387.3;MAGEA12,frameshift_variant,p.Leu228GlyfsTer4,ENST00000357916,NM_005367.6;CSAG1,upstream_gene_variant,,ENST00000370291,;CSAG1,upstream_gene_variant,,ENST00000370287,NM_153478.2;CSAG1,upstream_gene_variant,,ENST00000452779,NM_001102576.2;CSAG4,intron_variant,,ENST00000361201,;CSAG1,upstream_gene_variant,,ENST00000361211,;CSAG4,upstream_gene_variant,,ENST00000583763,; - ENST00000393900 Transcript frameshift_variant 1031-1032/1853 677-678/945 226/314 S/X aGT/a 1 1 MAGEA12 HGNC HGNC:6799 protein_coding YES CCDS76048.1 ENSP00000377478 P43365 Q6FHH8 UPI0000000C51 NM_001166386.3 3/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF74,Pfam_domain:PF01454,SMART_domains:SM01373 HIGH 1 deletion 1 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 70 152736838 152736838 GT - 1 0 1 0 1 0 0 0 0 9082 1029 36 0 0 MAGEA12 23 152736838 Frame_Shift_Del DEL GT C3N-01030_T 10841469 152736838 3304057 777 21558 VPS13D 0 . GRCh38 1 12304532 12304532 + Silent SNP G G T rs756013448 C3N-01071_T C3N-01071_N G G c.6243G>T p.= p.T2081T ENST00000620676 26/70 270 233 37 310 310 0 strelka-varscan-mutect VPS13D,synonymous_variant,p.=,ENST00000620676,NM_015378.3;VPS13D,synonymous_variant,p.=,ENST00000613099,NM_018156.3;VPS13D,synonymous_variant,p.=,ENST00000011700,;VPS13D,non_coding_transcript_exon_variant,,ENST00000460333,; T ENST00000620676 Transcript synonymous_variant 6373/16320 6243/13167 2081/4388 T acG/acT rs756013448 1 1 VPS13D HGNC HGNC:23595 protein_coding YES CCDS30588.1 ENSP00000478104 Q5THJ4 UPI0000451CA9 NM_015378.3 26/70 hmmpanther:PTHR16166:SF104,hmmpanther:PTHR16166 LOW 1 SNV 1 1 PASS rs756013448 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 12304532 12304532 G T 1 0 0 0 0 0 0 0 1 17739 1103 39 1 1 VPS13D 1 12304532 Silent SNP G C3N-01071_T 12304532 236651890 1 21559 FBXO42 0 . GRCh38 1 16315227 16315227 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.192G>T p.= p.P64P ENST00000375592 2/10 199 178 21 182 182 0 strelka-varscan-mutect FBXO42,synonymous_variant,p.=,ENST00000375592,NM_018994.2;FBXO42,non_coding_transcript_exon_variant,,ENST00000478089,; A ENST00000375592 Transcript synonymous_variant 409/6202 192/2154 64/717 P ccG/ccT 1 -1 FBXO42 HGNC HGNC:29249 protein_coding YES CCDS30613.1 ENSP00000364742 Q6P3S6 A0A024QZB0 UPI0000161A51 NM_018994.2 2/10 Gene3D:1.20.1280.50,Pfam_domain:PF12937,PROSITE_profiles:PS50181,SMART_domains:SM00256,Superfamily_domains:SSF81383 LOW 1 SNV 1 1 PASS rs909076125 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 16315227 16315227 C A 1 0 0 0 0 0 0 0 1 5614 523 19 1 1 FBXO42 1 16315227 Silent SNP C C3N-01071_T 4010695 16315227 232641195 2 21560 SYF2 0 . GRCh38 1 25223422 25223422 + Missense_Mutation SNP T T A rs754264978 C3N-01071_T C3N-01071_N T T c.576A>T p.Lys192Asn p.K192N ENST00000236273 7/7 98 88 10 102 102 0 strelka-varscan-mutect SYF2,missense_variant,p.Lys192Asn,ENST00000236273,NM_015484.4;SYF2,missense_variant,p.Lys150Asn,ENST00000354361,NM_207170.3; A ENST00000236273 Transcript missense_variant 602/1345 576/732 192/243 K/N aaA/aaT rs754264978 1 -1 SYF2 HGNC HGNC:19824 protein_coding YES CCDS259.1 ENSP00000236273 O95926 UPI0000073D39 NM_015484.4 deleterious(0) 7/7 hmmpanther:PTHR13264:SF5,hmmpanther:PTHR13264,Pfam_domain:PF08231 MODERATE 1 SNV 1 1 PASS rs754264978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 25223422 25223422 T A 1 0 0 0 0 1 0 0 0 15827 1722 60 4 4 SYF2 1 25223422 Missense_Mutation SNP T C3N-01071_T 8908195 25223422 223733000 3 21561 ZBTB8B 0 . GRCh38 1 32470989 32470989 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.365T>C p.Leu122Pro p.L122P ENST00000609129 2/4 603 557 46 456 456 0 strelka-varscan-mutect ZBTB8B,missense_variant,p.Leu122Pro,ENST00000609129,NM_001145720.1;RP1-27O5.3,missense_variant,p.Leu122Pro,ENST00000480336,; C ENST00000609129 Transcript missense_variant 443/12834 365/1488 122/495 L/P cTc/cCc 1 1 ZBTB8B HGNC HGNC:37057 protein_coding YES CCDS44104.1 ENSP00000476499 Q8NAP8 UPI000195170E NM_001145720.1 deleterious(0) 2/4 hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF26,SMART_domains:SM00225 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 32470989 32470989 T C 1 0 0 0 0 1 0 0 0 18127 1551 54 5 5 ZBTB8B 1 32470989 Missense_Mutation SNP T C3N-01071_T 7247567 32470989 216485433 4 21562 C1orf94 0 . GRCh38 1 34197445 34197445 + Nonsense_Mutation SNP G G T rs564666730 C3N-01071_T C3N-01071_N G G c.541G>T p.Gly181Ter p.G181* ENST00000488417 2/7 177 166 11 159 159 0 strelka-varscan-mutect C1orf94,stop_gained,p.Gly181Ter,ENST00000488417,NM_001134734.1;C1orf94,5_prime_UTR_variant,,ENST00000373374,NM_032884.4; T ENST00000488417 Transcript stop_gained 661/2287 541/1797 181/598 G/* Gga/Tga rs564666730 1 1 C1orf94 HGNC HGNC:28250 protein_coding YES CCDS44108.1 ENSP00000435634 Q6P1W5 UPI0000D4BFB0 NM_001134734.1 2/7 hmmpanther:PTHR35674,hmmpanther:PTHR35674:SF1 HIGH 1 SNV 1 1 PASS rs564666730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 71 34197445 34197445 G T 1 0 0 0 0 0 1 0 0 2000 1117 39 1 1 C1orf94 1 34197445 Nonsense_Mutation SNP G C3N-01071_T 1726456 34197445 214758977 5 21563 TIE1 0 . GRCh38 1 43312128 43312128 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.1627C>T p.Pro543Ser p.P543S ENST00000372476 11/23 25 20 5 11 11 0 strelka-mutect TIE1,missense_variant,p.Pro543Ser,ENST00000372476,NM_005424.4,NM_001253357.1;TIE1,downstream_gene_variant,,ENST00000538015,;TIE1,non_coding_transcript_exon_variant,,ENST00000488437,;TIE1,upstream_gene_variant,,ENST00000473014,;TIE1,upstream_gene_variant,,ENST00000461061,;TIE1,upstream_gene_variant,,ENST00000471187,;TIE1,downstream_gene_variant,,ENST00000480269,; T ENST00000372476 Transcript missense_variant 1706/3882 1627/3417 543/1138 P/S Cct/Tct 1 1 TIE1 HGNC HGNC:11809 protein_coding YES CCDS482.1 ENSP00000361554 P35590 UPI0000032E59 NM_005424.4,NM_001253357.1 tolerated(0.34) 11/23 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF341,hmmpanther:PTHR24416,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 43312128 43312128 C T 1 0 0 0 0 1 0 0 0 16329 869 30 3 3 TIE1 1 43312128 Missense_Mutation SNP C C3N-01071_T 9114683 43312128 205644294 6 21564 ZCCHC11 0 . GRCh38 1 52525598 52525598 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.683G>T p.Ser228Ile p.S228I ENST00000257177 2/30 178 160 18 137 137 0 strelka-varscan-mutect ZCCHC11,missense_variant,p.Ser228Ile,ENST00000371544,NM_015269.2;ZCCHC11,missense_variant,p.Ser228Ile,ENST00000257177,NM_001009881.2;ZCCHC11,missense_variant,p.Ser228Ile,ENST00000528642,;ZCCHC11,missense_variant,p.Ser228Ile,ENST00000355809,;ZCCHC11,intron_variant,,ENST00000484723,;ZCCHC11,downstream_gene_variant,,ENST00000470626,;ZCCHC11,downstream_gene_variant,,ENST00000524582,;ZCCHC11,non_coding_transcript_exon_variant,,ENST00000371541,;ZCCHC11,missense_variant,p.Ser228Ile,ENST00000473856,; A ENST00000257177 Transcript missense_variant 828/5743 683/4938 228/1645 S/I aGt/aTt 1 -1 ZCCHC11 HGNC HGNC:28981 protein_coding YES CCDS30715.1 ENSP00000257177 A0A0C4DFM7 UPI00001D7D0C NM_001009881.2 deleterious_low_confidence(0.03) 2/30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 52525598 52525598 C A 1 0 0 0 0 1 0 0 0 18155 565 20 2 2 ZCCHC11 1 52525598 Missense_Mutation SNP C C3N-01071_T 9213470 52525598 196430824 7 21565 FUBP1 0 . GRCh38 1 77949219 77949219 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.1862A>T p.Gln621Leu p.Q621L ENST00000370768 19/20 278 246 32 240 240 0 strelka-varscan-mutect FUBP1,missense_variant,p.Gln621Leu,ENST00000370767,;FUBP1,missense_variant,p.Gln621Leu,ENST00000370768,NM_003902.4,NM_001303433.1;FUBP1,non_coding_transcript_exon_variant,,ENST00000492405,;FUBP1,non_coding_transcript_exon_variant,,ENST00000488814,;FUBP1,non_coding_transcript_exon_variant,,ENST00000492724,;FUBP1,non_coding_transcript_exon_variant,,ENST00000487684,;FUBP1,upstream_gene_variant,,ENST00000489495,;FUBP1,upstream_gene_variant,,ENST00000474632,;FUBP1,upstream_gene_variant,,ENST00000483894,;FUBP1,upstream_gene_variant,,ENST00000480673,;FUBP1,missense_variant,p.Gln620Leu,ENST00000294623,; A ENST00000370768 Transcript missense_variant 1944/2378 1862/1935 621/644 Q/L cAa/cTa 1 -1 FUBP1 HGNC HGNC:4004 protein_coding YES CCDS683.1 ENSP00000359804 Q96AE4 UPI0000070218 NM_003902.4,NM_001303433.1 deleterious(0) 19/20 Low_complexity_(Seg):seg,Pfam_domain:PF09005 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 77949219 77949219 T A 1 0 0 0 0 1 0 0 0 5963 1812 63 4 4 FUBP1 1 77949219 Missense_Mutation SNP T C3N-01071_T 25423621 77949219 171007203 8 21566 IGSF3 0 . GRCh38 1 116608269 116608269 + Nonsense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.895G>T p.Glu299Ter p.E299* ENST00000369483 5/12 126 108 18 112 112 0 varscan-mutect IGSF3,stop_gained,p.Glu299Ter,ENST00000369483,NM_001542.3;IGSF3,stop_gained,p.Glu299Ter,ENST00000369486,NM_001007237.2;IGSF3,stop_gained,p.Glu299Ter,ENST00000318837,; A ENST00000369483 Transcript stop_gained 1663/7326 895/3645 299/1214 E/* Gag/Tag 1 -1 IGSF3 HGNC HGNC:5950 protein_coding YES CCDS30814.1 ENSP00000358495 O75054 UPI0000140437 NM_001542.3 5/12 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF21,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 4 1 71 116608269 116608269 C A 1 0 0 0 0 0 1 0 0 7509 864 30 2 2 IGSF3 1 116608269 Nonsense_Mutation SNP C C3N-01071_T 38659050 116608269 132348153 9 21567 NOTCH2 0 . GRCh38 1 119925564 119925564 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.4252C>T p.Pro1418Ser p.P1418S ENST00000256646 25/34 459 434 25 372 372 0 strelka-varscan-mutect NOTCH2,missense_variant,p.Pro1418Ser,ENST00000256646,NM_024408.3;NOTCH2,upstream_gene_variant,,ENST00000493703,; A ENST00000256646 Transcript missense_variant 4472/11389 4252/7416 1418/2471 P/S Ccc/Tcc 1 -1 NOTCH2 HGNC HGNC:7882 protein_coding YES CCDS908.1 ENSP00000256646 Q04721 UPI000013CF1D NM_024408.3 tolerated(0.07) 25/34 PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF66,SMART_domains:SM00004 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 119925564 119925564 G A 1 0 0 0 0 1 0 0 0 10593 1232 43 3 3 NOTCH2 1 119925564 Missense_Mutation SNP G C3N-01071_T 3317295 119925564 129030858 10 21568 SF3B4 0 . GRCh38 1 149926456 149926456 + Missense_Mutation SNP T T G novel C3N-01071_T C3N-01071_N T T c.626A>C p.Gln209Pro p.Q209P ENST00000271628 3/6 290 203 87 201 201 0 strelka-varscan-mutect SF3B4,missense_variant,p.Gln209Pro,ENST00000271628,NM_005850.4;SF3B4,missense_variant,p.Gln166Pro,ENST00000457312,;MTMR11,downstream_gene_variant,,ENST00000439741,NM_001145862.1;MTMR11,downstream_gene_variant,,ENST00000369140,NM_181873.3;MTMR11,downstream_gene_variant,,ENST00000492824,;MTMR11,downstream_gene_variant,,ENST00000482025,;MTMR11,downstream_gene_variant,,ENST00000466496,;MTMR11,downstream_gene_variant,,ENST00000490310,;MTMR11,downstream_gene_variant,,ENST00000495054,;MTMR11,downstream_gene_variant,,ENST00000493562,;MTMR11,downstream_gene_variant,,ENST00000482343,; G ENST00000271628 Transcript missense_variant 1211/2085 626/1275 209/424 Q/P cAg/cCg 1 -1 SF3B4 HGNC HGNC:10771 protein_coding YES CCDS72900.1 ENSP00000271628 Q15427 UPI0000135472 NM_005850.4 deleterious(0.02) 3/6 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 149926456 149926456 T G 1 0 0 0 0 1 0 0 0 14431 1580 55 5 5 SF3B4 1 149926456 Missense_Mutation SNP T C3N-01071_T 30000892 149926456 99029966 11 21569 RPRD2 0 . GRCh38 1 150472996 150472996 + Missense_Mutation SNP G G A rs770483785 C3N-01071_T C3N-01071_N G G c.4048G>A p.Gly1350Arg p.G1350R ENST00000369068 11/11 235 153 82 163 163 0 strelka-varscan-mutect RPRD2,missense_variant,p.Gly1324Arg,ENST00000401000,NM_001297674.1,NM_001297673.1;RPRD2,missense_variant,p.Gly1350Arg,ENST00000369068,NM_015203.4;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,; A ENST00000369068 Transcript missense_variant 4052/4612 4048/4386 1350/1461 G/R Ggg/Agg rs770483785,COSM2182118,COSM2182119 1 1 RPRD2 HGNC HGNC:29039 protein_coding YES CCDS44216.1 ENSP00000358064 Q5VT52 UPI00001D7CA8 NM_015203.4 tolerated_low_confidence(0.51) 11/11 hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF0 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770483785 . 0 203 0 6 0 0 0 0 -20 0.9996528 1 1 1 0 A 3 1 71 150472996 150472996 G A 1 0 0 0 0 1 0 0 0 13871 1116 39 1 1 RPRD2 1 150472996 Missense_Mutation SNP G C3N-01071_T 546540 150472996 98483426 12 21570 MCL1 0 . GRCh38 1 150579054 150579054 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.477A>G p.= p.S159S ENST00000369026 1/3 428 320 108 344 344 0 strelka-varscan-mutect MCL1,synonymous_variant,p.=,ENST00000369026,NM_021960.4;MCL1,synonymous_variant,p.=,ENST00000307940,NM_182763.2;MCL1,intron_variant,,ENST00000620947,NM_001197320.1;ADAMTSL4-AS1,upstream_gene_variant,,ENST00000617352,;MCL1,upstream_gene_variant,,ENST00000464132,; C ENST00000369026 Transcript synonymous_variant 537/3932 477/1053 159/350 S tcA/tcG 1 -1 MCL1 HGNC HGNC:6943 protein_coding YES CCDS957.1 ENSP00000358022 Q07820 UPI000006D775 NM_021960.4 1/3 hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF46,Superfamily_domains:SSF56854 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 150579054 150579054 T C 1 0 0 0 0 0 0 0 1 9316 1683 59 5 5 MCL1 1 150579054 Silent SNP T C3N-01071_T 106058 150579054 98377368 13 21571 ATP1A4 0 . GRCh38 1 160181997 160181997 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.2935G>T p.Gly979Cys p.G979C ENST00000368081 20/22 327 306 21 184 184 0 strelka-varscan ATP1A4,missense_variant,p.Gly979Cys,ENST00000368081,NM_144699.3;ATP1A4,missense_variant,p.Gly115Cys,ENST00000470705,NM_001001734.1;ATP1A4,non_coding_transcript_exon_variant,,ENST00000418334,;ATP1A4,non_coding_transcript_exon_variant,,ENST00000466526,;ATP1A4,3_prime_UTR_variant,,ENST00000477338,;ATP1A4,non_coding_transcript_exon_variant,,ENST00000469023,; T ENST00000368081 Transcript missense_variant 3406/3839 2935/3090 979/1029 G/C Ggc/Tgc 1 1 ATP1A4 HGNC HGNC:14073 protein_coding YES CCDS1197.1 ENSP00000357060 Q13733 UPI0000124FC5 NM_144699.3 deleterious(0) 20/22 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,Prints_domain:PR00121,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF309,TIGRFAM_domain:TIGR01106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 160181997 160181997 G T 1 0 0 0 0 1 0 0 0 1283 1000 35 2 2 ATP1A4 1 160181997 Missense_Mutation SNP G C3N-01071_T 9602943 160181997 88774425 14 21572 LRRC52 0 . GRCh38 1 165563526 165563526 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.644T>C p.Val215Ala p.V215A ENST00000294818 2/2 140 95 45 110 110 0 strelka-varscan LRRC52,missense_variant,p.Val215Ala,ENST00000294818,NM_001005214.3;RP11-280O1.2,intron_variant,,ENST00000438275,;RP11-280O1.2,intron_variant,,ENST00000421273,;RP11-280O1.2,intron_variant,,ENST00000416424,; C ENST00000294818 Transcript missense_variant 934/1369 644/942 215/313 V/A gTg/gCg 1 1 LRRC52 HGNC HGNC:32156 protein_coding YES CCDS30930.1 ENSP00000294818 Q8N7C0 UPI000013E1BE NM_001005214.3 tolerated(0.52) 2/2 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF37,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 165563526 165563526 T C 1 0 0 0 0 1 0 0 0 8904 1696 59 5 5 LRRC52 1 165563526 Missense_Mutation SNP T C3N-01071_T 5381529 165563526 83392896 15 21573 F5 0 . GRCh38 1 169556859 169556859 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.739G>T p.Val247Phe p.V247F ENST00000367797 6/25 540 502 38 413 412 1 strelka-varscan-mutect F5,missense_variant,p.Val247Phe,ENST00000367796,;F5,missense_variant,p.Val247Phe,ENST00000367797,NM_000130.4; A ENST00000367797 Transcript missense_variant 941/7024 739/6675 247/2224 V/F Gtt/Ttt 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 tolerated(0.06) 6/25 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,Gene3D:2.60.40.420,PIRSF_domain:PIRSF000354,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 169556859 169556859 C A 1 0 0 0 0 1 0 0 0 5216 565 20 2 2 F5 1 169556859 Missense_Mutation SNP C C3N-01071_T 3993333 169556859 79399563 16 21574 DNM3 0 . GRCh38 1 172044447 172044447 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.1191T>C p.= p.G397G ENST00000627582 9/21 187 174 13 132 132 0 strelka-varscan-mutect DNM3,synonymous_variant,p.=,ENST00000627582,NM_015569.4;DNM3,synonymous_variant,p.=,ENST00000367731,NM_001136127.2;DNM3,synonymous_variant,p.=,ENST00000520906,;DNM3,synonymous_variant,p.=,ENST00000355305,;DNM3,synonymous_variant,p.=,ENST00000367733,NM_001278252.1;DNM3,synonymous_variant,p.=,ENST00000523513,; C ENST00000627582 Transcript synonymous_variant 1348/7625 1191/2592 397/863 G ggT/ggC 1 1 DNM3 HGNC HGNC:29125 protein_coding YES CCDS53431.1 ENSP00000486701 Q9UQ16 UPI0000251D91 NM_015569.4 9/21 Pfam_domain:PF01031,hmmpanther:PTHR11566,hmmpanther:PTHR11566:SF54 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 172044447 172044447 T C 1 0 0 0 0 0 0 0 1 4486 1652 57 5 5 DNM3 1 172044447 Silent SNP T C3N-01071_T 2487588 172044447 76911975 17 21575 SUCO 0 . GRCh38 1 172532592 172532592 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.120T>C p.= p.S40S ENST00000367723 1/23 427 316 111 444 444 0 strelka-varscan-mutect SUCO,synonymous_variant,p.=,ENST00000367723,NM_016227.3;SUCO,synonymous_variant,p.=,ENST00000608151,;SUCO,upstream_gene_variant,,ENST00000263688,NM_014283.4;SUCO,upstream_gene_variant,,ENST00000616058,NM_001282751.1;SUCO,upstream_gene_variant,,ENST00000610051,NM_001282750.1;SUCO,upstream_gene_variant,,ENST00000608566,; C ENST00000367723 Transcript synonymous_variant 244/5916 120/4218 40/1405 S tcT/tcC 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 1/23 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 172532592 172532592 T C 1 0 0 0 0 0 0 0 1 15751 1509 53 5 5 SUCO 1 172532592 Silent SNP T C3N-01071_T 488145 172532592 76423830 18 21576 CEP350 0 . GRCh38 1 180094027 180094027 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.7922A>G p.Gln2641Arg p.Q2641R ENST00000367607 34/38 217 188 29 183 183 0 strelka-varscan-mutect CEP350,missense_variant,p.Gln2641Arg,ENST00000367607,NM_014810.4;CEP350,missense_variant,p.Gln816Arg,ENST00000429851,;CEP350,missense_variant,p.Gln105Arg,ENST00000417046,;CEP350,non_coding_transcript_exon_variant,,ENST00000490141,;CEP350,upstream_gene_variant,,ENST00000496440,;CEP350,downstream_gene_variant,,ENST00000484356,; G ENST00000367607 Transcript missense_variant 8340/13491 7922/9354 2641/3117 Q/R cAg/cGg 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 tolerated(0.42) 34/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 180094027 180094027 A G 1 0 0 0 0 1 0 0 0 2972 188 7 5 5 CEP350 1 180094027 Missense_Mutation SNP A C3N-01071_T 7561435 180094027 68862395 19 21577 HMCN1 0 . GRCh38 1 186007241 186007241 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.4589C>T p.Ala1530Val p.A1530V ENST00000271588 30/107 265 241 24 237 237 0 strelka-varscan-mutect HMCN1,missense_variant,p.Ala1530Val,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript missense_variant 4818/18208 4589/16908 1530/5635 A/V gCa/gTa 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.16) 30/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 186007241 186007241 C T 1 0 0 0 0 1 0 0 0 7111 710 25 3 3 HMCN1 1 186007241 Missense_Mutation SNP C C3N-01071_T 5913214 186007241 62949181 20 21578 NEK7 0 . GRCh38 1 198279032 198279032 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.560G>A p.Ser187Asn p.S187N ENST00000367385 7/10 174 150 24 217 217 0 strelka-varscan-mutect NEK7,missense_variant,p.Ser187Asn,ENST00000367385,NM_133494.2;NEK7,missense_variant,p.Ser187Asn,ENST00000538004,;NEK7,non_coding_transcript_exon_variant,,ENST00000493790,; A ENST00000367385 Transcript missense_variant 902/4149 560/909 187/302 S/N aGc/aAc 1 1 NEK7 HGNC HGNC:13386 protein_coding YES CCDS1394.1 ENSP00000356355 Q8TDX7 A0A024R964 UPI0000073180 NM_133494.2 deleterious(0.04) 7/10 PROSITE_profiles:PS50011,hmmpanther:PTHR24362,Gene3D:1.10.510.10,PIRSF_domain:PIRSF000654,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999921 1 1 1 0 A 3 1 71 198279032 198279032 G A 1 0 0 0 0 1 0 0 0 10357 971 34 3 3 NEK7 1 198279032 Missense_Mutation SNP G C3N-01071_T 12271791 198279032 50677390 21 21579 PKP1 0 . GRCh38 1 201324466 201324466 + Silent SNP A A G novel C3N-01071_T C3N-01071_N A A c.1782A>G p.= p.E594E ENST00000263946 11/15 517 485 32 520 520 0 strelka-varscan-mutect PKP1,synonymous_variant,p.=,ENST00000263946,NM_000299.3;PKP1,synonymous_variant,p.=,ENST00000367324,NM_001005337.2;PKP1,synonymous_variant,p.=,ENST00000352845,;PKP1,downstream_gene_variant,,ENST00000475988,;PKP1,upstream_gene_variant,,ENST00000477817,; G ENST00000263946 Transcript synonymous_variant 2033/5447 1782/2244 594/747 E gaA/gaG 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 11/15 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 201324466 201324466 A G 1 0 0 0 0 0 0 0 1 12080 11 1 5 5 PKP1 1 201324466 Silent SNP A C3N-01071_T 3045434 201324466 47631956 22 21580 USH2A 0 . GRCh38 1 216070138 216070138 + Silent SNP A A C novel C3N-01071_T C3N-01071_N A A c.6012T>G p.= p.S2004S ENST00000307340 30/72 369 324 45 324 324 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;RP11-22M7.2,upstream_gene_variant,,ENST00000446411,;RP11-22M7.2,upstream_gene_variant,,ENST00000430890,;RP11-22M7.2,upstream_gene_variant,,ENST00000445619,; C ENST00000307340 Transcript synonymous_variant 6399/18883 6012/15609 2004/5202 S tcT/tcG 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 30/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 216070138 216070138 A C 1 0 0 0 0 0 0 0 1 17570 175 7 5 5 USH2A 1 216070138 Silent SNP A C3N-01071_T 14745672 216070138 32886284 23 21581 USH2A 0 . GRCh38 1 216175260 216175260 + Missense_Mutation SNP T T C C3N-01071_T C3N-01071_N T T c.4619A>G p.Asp1540Gly p.D1540G ENST00000307340 21/72 318 275 43 325 325 0 strelka-varscan USH2A,missense_variant,p.Asp1540Gly,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Asp1540Gly,ENST00000366942,NM_007123.5; C ENST00000307340 Transcript missense_variant 5006/18883 4619/15609 1540/5202 D/G gAc/gGc COSM5008491,COSM5008492,COSM5008493 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.15) 21/72 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,PROSITE_profiles:PS50853,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 216175260 216175260 T C 1 0 0 0 0 1 0 0 0 17570 1667 58 5 5 USH2A 1 216175260 Missense_Mutation SNP T C3N-01071_T 105122 216175260 32781162 24 21582 SLC35F3 0 . GRCh38 1 233905570 233905570 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.95C>A p.Ser32Tyr p.S32Y ENST00000366618 2/8 176 167 9 184 184 0 strelka-varscan SLC35F3,missense_variant,p.Ser32Tyr,ENST00000366618,NM_173508.3; A ENST00000366618 Transcript missense_variant 240/2891 95/1473 32/490 S/Y tCc/tAc 1 1 SLC35F3 HGNC HGNC:23616 protein_coding YES CCDS1600.1 ENSP00000355577 Q8IY50 UPI000006DD13 NM_173508.3 deleterious_low_confidence(0) 2/8 hmmpanther:PTHR19346,hmmpanther:PTHR19346:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 233905570 233905570 C A 1 0 0 0 0 1 0 0 0 14861 855 30 2 2 SLC35F3 1 233905570 Missense_Mutation SNP C C3N-01071_T 17730310 233905570 15050852 25 21583 RYR2 0 . GRCh38 1 237610989 237610989 + Splice_Site SNP G G C novel C3N-01071_T C3N-01071_N G G c.4910+1G>C p.X1637_splice ENST00000366574 139 126 13 102 102 0 strelka-varscan RYR2,splice_donor_variant,,ENST00000366574,NM_001035.2;RYR2,splice_donor_variant,,ENST00000360064,; C ENST00000366574 Transcript splice_donor_variant -/16562 4910/14904 1637/4967 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 36/104 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 71 237610989 237610989 G C 1 0 0 0 0 0 0 1 0 14029 1275 44 4 4 RYR2 1 237610989 Splice_Site SNP G C3N-01071_T 3705419 237610989 11345433 26 21584 OR2M4 0 . GRCh38 1 248239488 248239488 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.560T>A p.Leu187Gln p.L187Q ENST00000306687 1/1 182 160 22 208 208 0 strelka-varscan OR2M4,missense_variant,p.Leu187Gln,ENST00000306687,NM_017504.1; A ENST00000306687 Transcript missense_variant 560/936 560/936 187/311 L/Q cTa/cAa 1 1 OR2M4 HGNC HGNC:8270 protein_coding YES CCDS31108.1 ENSP00000306688 Q96R27 A0A126GV73 UPI000004B233 NM_017504.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF91,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 248239488 248239488 T A 1 0 0 0 0 1 0 0 0 11090 1522 53 4 4 OR2M4 1 248239488 Missense_Mutation SNP T C3N-01071_T 10628499 248239488 716934 27 21585 NBAS 0 . GRCh38 2 15232470 15232470 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.6188A>T p.Lys2063Met p.K2063M ENST00000281513 47/52 284 250 34 299 299 0 strelka-varscan-mutect NBAS,missense_variant,p.Lys2063Met,ENST00000281513,NM_015909.3;NBAS,missense_variant,p.Lys1111Met,ENST00000442506,;NBAS,missense_variant,p.Lys155Met,ENST00000417461,; A ENST00000281513 Transcript missense_variant 6214/7281 6188/7116 2063/2371 K/M aAg/aTg 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 deleterious(0.01) 47/52 hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 15232470 15232470 T A 1 0 0 0 0 1 0 0 0 10197 1609 56 4 4 NBAS 2 15232470 Missense_Mutation SNP T C3N-01071_T 15232470 226961059 28 21586 TDRD15 0 . GRCh38 2 21140837 21140837 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.3370T>C p.= p.L1124L ENST00000405799 4/4 104 93 11 90 90 0 strelka-varscan-mutect TDRD15,synonymous_variant,p.=,ENST00000405799,;TDRD15,synonymous_variant,p.=,ENST00000622654,; C ENST00000405799 Transcript synonymous_variant 3700/6135 3370/5805 1124/1934 L Ttg/Ctg 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 21140837 21140837 T C 1 0 0 0 0 0 0 0 1 16141 1490 52 5 5 TDRD15 2 21140837 Silent SNP T C3N-01071_T 5908367 21140837 221052692 29 21587 SLC30A3 0 . GRCh38 2 27262847 27262847 + Silent SNP G G A rs150529372 C3N-01071_T C3N-01071_N G G c.60C>T p.= p.D20D ENST00000233535 1/8 94 85 9 106 106 0 strelka-varscan-mutect SLC30A3,synonymous_variant,p.=,ENST00000233535,NM_003459.4;SLC30A3,synonymous_variant,p.=,ENST00000445870,;SLC30A3,intron_variant,,ENST00000426924,;SLC30A3,intron_variant,,ENST00000432351,;SLC30A3,intron_variant,,ENST00000424577,;SLC30A3,intron_variant,,ENST00000426569,;SLC30A3,upstream_gene_variant,,ENST00000450118,;SLC30A3,upstream_gene_variant,,ENST00000497341,;SLC30A3,upstream_gene_variant,,ENST00000486309,; A ENST00000233535 Transcript synonymous_variant 413/2260 60/1167 20/388 D gaC/gaT rs150529372 1 -1 SLC30A3 HGNC HGNC:11014 protein_coding YES CCDS1743.1 ENSP00000233535 Q99726 UPI000006D0B4 NM_003459.4 1/8 hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF30 LOW 1 SNV 1 1 PASS rs150529372 . 0 202 6 2 0 0 0 0 -14.34614 0.9998009 1 1 1 0 A 2 1 71 27262847 27262847 G A 1 0 0 0 0 0 0 0 1 14826 1252 44 3 3 SLC30A3 2 27262847 Silent SNP G C3N-01071_T 6122010 27262847 214930682 30 21588 BIRC6 0 . GRCh38 2 32439642 32439642 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.3766G>A p.Gly1256Ser p.G1256S ENST00000421745 16/74 191 177 14 191 191 0 strelka-varscan BIRC6,missense_variant,p.Gly1256Ser,ENST00000421745,NM_016252.3;BIRC6,missense_variant,p.Gly142Ser,ENST00000444173,;BIRC6,missense_variant,p.Gly83Ser,ENST00000431454,;BIRC6,upstream_gene_variant,,ENST00000483194,; A ENST00000421745 Transcript missense_variant 3900/15703 3766/14574 1256/4857 G/S Ggt/Agt 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 tolerated(0.48) 16/74 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 32439642 32439642 G A 1 0 0 0 0 1 0 0 0 1589 1232 43 3 3 BIRC6 2 32439642 Missense_Mutation SNP G C3N-01071_T 5176795 32439642 209753887 31 21589 SIX3 0 . GRCh38 2 44944661 44944661 + Silent SNP G G T novel C3N-01071_T C3N-01071_N G G c.900G>T p.= p.A300A ENST00000260653 2/2 331 304 27 235 235 0 strelka-varscan SIX3,synonymous_variant,p.=,ENST00000260653,NM_005413.3;SIX3-AS1,upstream_gene_variant,,ENST00000419364,;SIX3-AS1,upstream_gene_variant,,ENST00000456467,;Six3os1_7,downstream_gene_variant,,ENST00000621512,; T ENST00000260653 Transcript synonymous_variant 1107/2523 900/999 300/332 A gcG/gcT 1 1 SIX3 HGNC HGNC:10889 protein_coding YES CCDS1821.1 ENSP00000260653 O95343 UPI00001359C4 NM_005413.3 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR10390:SF31,hmmpanther:PTHR10390 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 44944661 44944661 G T 1 0 0 0 0 0 0 0 1 14611 1103 39 1 1 SIX3 2 44944661 Silent SNP G C3N-01071_T 12505019 44944661 197248868 32 21590 CLHC1 0 . GRCh38 2 55206337 55206337 + Silent SNP T T A novel C3N-01071_T C3N-01071_N T T c.939A>T p.= p.A313A ENST00000401408 9/13 258 240 18 251 251 0 strelka-varscan CLHC1,synonymous_variant,p.=,ENST00000401408,NM_152385.2;CLHC1,synonymous_variant,p.=,ENST00000407122,;CLHC1,synonymous_variant,p.=,ENST00000406076,NM_001135598.1;CLHC1,non_coding_transcript_exon_variant,,ENST00000487320,;CLHC1,non_coding_transcript_exon_variant,,ENST00000466020,;CLHC1,intron_variant,,ENST00000494539,;CLHC1,3_prime_UTR_variant,,ENST00000411884,;CLHC1,intron_variant,,ENST00000428621,; A ENST00000401408 Transcript synonymous_variant 1285/2248 939/1761 313/586 A gcA/gcT 1 -1 CLHC1 HGNC HGNC:26453 protein_coding YES CCDS33201.1 ENSP00000384869 Q8NHS4 UPI00004DEC65 NM_152385.2 9/13 Gene3D:1bpoA02,Pfam_domain:PF13838,PIRSF_domain:PIRSF037469,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF11,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 55206337 55206337 T A 1 0 0 0 0 0 0 0 1 3293 1567 55 4 4 CLHC1 2 55206337 Silent SNP T C3N-01071_T 10261676 55206337 186987192 33 21591 CNRIP1 0 . GRCh38 2 68319230 68319230 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.171G>T p.= p.L57L ENST00000263655 1/3 69 60 9 63 63 0 strelka-varscan CNRIP1,synonymous_variant,p.=,ENST00000263655,NM_015463.2;CNRIP1,synonymous_variant,p.=,ENST00000409862,;CNRIP1,synonymous_variant,p.=,ENST00000409559,NM_001111101.1;CNRIP1,non_coding_transcript_exon_variant,,ENST00000481714,; A ENST00000263655 Transcript synonymous_variant 777/1953 171/495 57/164 L ctG/ctT 1 -1 CNRIP1 HGNC HGNC:24546 protein_coding YES CCDS1886.1 ENSP00000263655 Q96F85 UPI0000070FBE NM_015463.2 1/3 Pfam_domain:PF15043,hmmpanther:PTHR31952 LOW 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.64741 0.9999994 1 1 1 0 A 2 1 71 68319230 68319230 C A 1 0 0 0 0 0 0 0 1 3415 697 25 2 2 CNRIP1 2 68319230 Silent SNP C C3N-01071_T 13112893 68319230 173874299 34 21592 SLC4A5 0 . GRCh38 2 74233471 74233471 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.2526G>A p.= p.V842V ENST00000346834 20/29 181 168 13 157 157 0 strelka-varscan SLC4A5,synonymous_variant,p.=,ENST00000394019,NM_133478.2;SLC4A5,synonymous_variant,p.=,ENST00000346834,NM_021196.3;SLC4A5,synonymous_variant,p.=,ENST00000423644,;SLC4A5,synonymous_variant,p.=,ENST00000377634,;SLC4A5,synonymous_variant,p.=,ENST00000358683,;SLC4A5,synonymous_variant,p.=,ENST00000377632,;SLC4A5,synonymous_variant,p.=,ENST00000425249,;SLC4A5,non_coding_transcript_exon_variant,,ENST00000483195,;RP11-287D1.3,3_prime_UTR_variant,,ENST00000451608,; T ENST00000346834 Transcript synonymous_variant 2762/6233 2526/3414 842/1137 V gtG/gtA 1 -1 SLC4A5 HGNC HGNC:18168 protein_coding YES CCDS1936.1 ENSP00000251768 Q9BY07 UPI000013C97B NM_021196.3 20/29 Pfam_domain:PF00955,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF20,TIGRFAM_domain:TIGR00834,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 74233471 74233471 C T 1 0 0 0 0 0 0 0 1 14934 813 29 3 3 SLC4A5 2 74233471 Silent SNP C C3N-01071_T 5914241 74233471 167960058 35 21593 ST3GAL5 0 . GRCh38 2 85863361 85863361 + Splice_Site SNP C C G novel C3N-01071_T C3N-01071_N C C c.206+1G>C p.X69_splice ENST00000377332 341 294 47 318 318 0 strelka-varscan ST3GAL5,splice_donor_variant,,ENST00000377332,NM_003896.3;ST3GAL5,splice_donor_variant,,ENST00000393805,;ST3GAL5,splice_donor_variant,,ENST00000393808,NM_001042437.1;ST3GAL5,splice_donor_variant,,ENST00000455892,;ST3GAL5,splice_donor_variant,,ENST00000484728,;ST3GAL5,splice_donor_variant,,ENST00000461892,;ST3GAL5,splice_donor_variant,,ENST00000461199,;ST3GAL5,splice_donor_variant,,ENST00000473122,;ST3GAL5,downstream_gene_variant,,ENST00000490946,;ST3GAL5,splice_donor_variant,,ENST00000306262,;ST3GAL5,splice_donor_variant,,ENST00000433665,; G ENST00000377332 Transcript splice_donor_variant -/2366 206/1257 69/418 1 -1 ST3GAL5 HGNC HGNC:10872 protein_coding YES CCDS1986.2 ENSP00000366549 Q9UNP4 UPI000015F319 NM_003896.3 2/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 71 85863361 85863361 C G 1 0 0 0 0 0 0 1 0 15596 579 20 4 4 ST3GAL5 2 85863361 Splice_Site SNP C C3N-01071_T 11629890 85863361 156330168 36 21594 CNNM4 0 . GRCh38 2 96797610 96797610 + Silent SNP G G C rs764568597 C3N-01071_T C3N-01071_N G G c.1644G>C p.= p.P548P ENST00000377075 3/7 701 661 40 528 528 0 strelka-varscan CNNM4,synonymous_variant,p.=,ENST00000377075,NM_020184.3;MIR3127,upstream_gene_variant,,ENST00000583925,;CNNM4,non_coding_transcript_exon_variant,,ENST00000496186,;CNNM4,non_coding_transcript_exon_variant,,ENST00000493384,;CNNM4,non_coding_transcript_exon_variant,,ENST00000482716,; C ENST00000377075 Transcript synonymous_variant 1742/4800 1644/2328 548/775 P ccG/ccC rs764568597,COSM2825800,COSM4316866 1 1 CNNM4 HGNC HGNC:105 protein_coding YES CCDS2024.2 ENSP00000366275 Q6P4Q7 UPI0000207C95 NM_020184.3 3/7 hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF26 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 96797610 96797610 G C 1 0 0 0 0 0 0 0 1 3395 1074 38 4 4 CNNM4 2 96797610 Silent SNP G C3N-01071_T 10934249 96797610 145395919 37 21595 MRPS9 0 . GRCh38 2 105049342 105049342 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.307G>A p.Asp103Asn p.D103N ENST00000258455 2/11 120 108 12 198 198 0 strelka-varscan MRPS9,missense_variant,p.Asp103Asn,ENST00000258455,NM_182640.2; A ENST00000258455 Transcript missense_variant 417/1500 307/1191 103/396 D/N Gat/Aat 1 1 MRPS9 HGNC HGNC:14501 protein_coding YES CCDS2065.1 ENSP00000258455 P82933 UPI00000467F9 NM_182640.2 deleterious(0.03) 2/11 hmmpanther:PTHR21569,hmmpanther:PTHR21569:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 105049342 105049342 G A 1 0 0 0 0 1 0 0 0 9826 942 33 3 3 MRPS9 2 105049342 Missense_Mutation SNP G C3N-01071_T 8251732 105049342 137144187 38 21596 GPR45 0 . GRCh38 2 105242859 105242859 + Frame_Shift_Del DEL C C - rs755001691 C3N-01071_T C3N-01071_N C C c.1002delC p.Cys335AlafsTer2 p.C335Afs*2 ENST00000258456 1/1 333 313 20 293 293 0 sindel-varindel-pindel GPR45,frameshift_variant,p.Cys335AlafsTer2,ENST00000258456,NM_007227.3; - ENST00000258456 Transcript frameshift_variant 1117/1307 1001/1119 334/372 A/X gCc/gc rs755001691 1 1 GPR45 HGNC HGNC:4503 protein_coding YES CCDS2066.1 ENSP00000258456 Q9Y5Y3 B5B0C1 UPI000013CFD3 NM_007227.3 1/1 hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF4,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 71 105242859 105242859 C - 1 0 1 0 1 0 0 0 0 6581 739 26 0 0 GPR45 2 105242859 Frame_Shift_Del DEL C C3N-01071_T 193517 105242859 136950670 39 21597 TGFBRAP1 0 . GRCh38 2 105269541 105269541 + Nonsense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.2137C>T p.Gln713Ter p.Q713* ENST00000393359 11/12 129 115 14 146 146 0 strelka-varscan TGFBRAP1,stop_gained,p.Gln713Ter,ENST00000393359,NM_001142621.2,NM_004257.5;TGFBRAP1,stop_gained,p.Gln713Ter,ENST00000595531,;TGFBRAP1,stop_gained,p.Gln713Ter,ENST00000258449,; A ENST00000393359 Transcript stop_gained 2564/5979 2137/2583 713/860 Q/* Cag/Tag 1 -1 TGFBRAP1 HGNC HGNC:16836 protein_coding YES CCDS2067.1 ENSP00000377027 Q8WUH2 UPI0000072CA9 NM_001142621.2,NM_004257.5 11/12 PROSITE_profiles:PS50236,hmmpanther:PTHR12894:SF17,hmmpanther:PTHR12894 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 71 105269541 105269541 G A 1 0 0 0 0 0 1 0 0 16257 1357 47 3 3 TGFBRAP1 2 105269541 Nonsense_Mutation SNP G C3N-01071_T 26682 105269541 136923988 40 21598 GLI2 0 . GRCh38 2 120988392 120988392 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.2478C>G p.Ile826Met p.I826M ENST00000452319 14/14 82 75 7 67 67 0 strelka-varscan-mutect GLI2,missense_variant,p.Ile826Met,ENST00000452319,;GLI2,missense_variant,p.Ile826Met,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,3_prime_UTR_variant,,ENST00000437950,; G ENST00000452319 Transcript missense_variant 2538/6799 2478/4761 826/1586 I/M atC/atG 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 deleterious(0) 14/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 MODERATE 1 SNV 5 1 PASS rs1449592421 . 0 204 6 0 0 0 0 0 -14.97705 0.9999998 1 1 1 0 G 3 3 71 120988392 120988392 C G 1 0 0 0 0 1 0 0 0 6316 903 32 4 4 GLI2 2 120988392 Missense_Mutation SNP C C3N-01071_T 15718851 120988392 121205137 41 21599 CNTNAP5 0 . GRCh38 2 124647864 124647864 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1980C>A p.Ser660Arg p.S660R ENST00000431078 13/24 191 180 11 172 172 0 strelka-mutect CNTNAP5,missense_variant,p.Ser660Arg,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 2344/5284 1980/3921 660/1306 S/R agC/agA 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0.02) 13/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 124647864 124647864 C A 1 0 0 0 0 1 0 0 0 3432 709 25 2 2 CNTNAP5 2 124647864 Missense_Mutation SNP C C3N-01071_T 3659472 124647864 117545665 42 21600 LRP1B 0 . GRCh38 2 140238223 140238223 + Missense_Mutation SNP T T C rs749162634 C3N-01071_T C3N-01071_N T T c.13489A>G p.Met4497Val p.M4497V ENST00000389484 89/91 186 170 16 153 153 0 strelka-varscan-mutect LRP1B,missense_variant,p.Met4497Val,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Met729Val,ENST00000437977,;LRP1B,missense_variant,p.Met267Val,ENST00000442974,;uc_338,upstream_gene_variant,,ENST00000622722,; C ENST00000389484 Transcript missense_variant 14461/16535 13489/13800 4497/4599 M/V Atg/Gtg rs749162634 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0.02) 89/91 MODERATE 1 SNV 1 1 PASS rs749162634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 140238223 140238223 T C 1 0 0 0 0 1 0 0 0 8850 1464 51 5 5 LRP1B 2 140238223 Missense_Mutation SNP T C3N-01071_T 15590359 140238223 101955306 43 21601 LRP1B 0 . GRCh38 2 140350890 140350890 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.11799T>A p.Asp3933Glu p.D3933E ENST00000389484 77/91 192 179 13 215 215 0 strelka-varscan-mutect LRP1B,missense_variant,p.Asp3933Glu,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Asp165Glu,ENST00000437977,; T ENST00000389484 Transcript missense_variant 12771/16535 11799/13800 3933/4599 D/E gaT/gaA 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.4) 77/91 PROSITE_profiles:PS51120,Gene3D:2.120.10.30,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 140350890 140350890 A T 1 0 0 0 0 1 0 0 0 8850 446 16 4 4 LRP1B 2 140350890 Missense_Mutation SNP A C3N-01071_T 112667 140350890 101842639 44 21602 LRP1B 0 . GRCh38 2 140923002 140923002 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.3282G>T p.Leu1094Phe p.L1094F ENST00000389484 21/91 181 166 15 129 128 1 strelka-varscan-mutect LRP1B,missense_variant,p.Leu1094Phe,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Leu239Phe,ENST00000434794,; A ENST00000389484 Transcript missense_variant 4254/16535 3282/13800 1094/4599 L/F ttG/ttT 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 tolerated(0.3) 21/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF105,hmmpanther:PTHR10529,SMART_domains:SM00192 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 140923002 140923002 C A 1 0 0 0 0 1 0 0 0 8850 477 17 2 2 LRP1B 2 140923002 Missense_Mutation SNP C C3N-01071_T 572112 140923002 101270527 45 21603 NR4A2 0 . GRCh38 2 156329630 156329630 + Missense_Mutation SNP G G T rs539532822 C3N-01071_T C3N-01071_N G G c.557C>A p.Pro186Gln p.P186Q ENST00000339562 3/8 92 83 9 84 84 0 strelka-varscan-mutect NR4A2,missense_variant,p.Pro186Gln,ENST00000339562,NM_006186.3;NR4A2,missense_variant,p.Pro186Gln,ENST00000409572,;NR4A2,missense_variant,p.Pro123Gln,ENST00000426264,;NR4A2,missense_variant,p.Pro186Gln,ENST00000409108,;NR4A2,missense_variant,p.Pro123Gln,ENST00000429376,;NR4A2,missense_variant,p.Pro186Gln,ENST00000424077,;NR4A2,intron_variant,,ENST00000406048,;NR4A2,downstream_gene_variant,,ENST00000421709,;NR4A2,missense_variant,p.Pro123Gln,ENST00000417972,;NR4A2,missense_variant,p.Pro123Gln,ENST00000417764,; T ENST00000339562 Transcript missense_variant 920/3472 557/1797 186/598 P/Q cCg/cAg rs539532822 1 -1 NR4A2 HGNC HGNC:7981 protein_coding YES CCDS2201.1 ENSP00000344479 P43354 F1D8N6 UPI0000036A18 NM_006186.3 tolerated(0.1) 3/8 hmmpanther:PTHR24085,hmmpanther:PTHR24085:SF0,Prints_domain:PR01287 MODERATE 1 SNV 1 1 PASS rs539532822 . 0 202 7 0 0 0 0 0 -18.58546 0.9999989 1 1 1 0 T 3 4 71 156329630 156329630 G T 1 0 0 0 0 1 0 0 0 10689 1116 39 1 1 NR4A2 2 156329630 Missense_Mutation SNP G C3N-01071_T 15406628 156329630 85863899 46 21604 MFSD6 0 . GRCh38 2 190436288 190436288 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.259C>T p.Pro87Ser p.P87S ENST00000392328 3/8 329 311 18 234 234 0 strelka-varscan-mutect MFSD6,missense_variant,p.Pro87Ser,ENST00000392328,NM_017694.3;MFSD6,missense_variant,p.Pro87Ser,ENST00000281416,;MFSD6,missense_variant,p.Pro87Ser,ENST00000445546,;MFSD6,missense_variant,p.Pro87Ser,ENST00000432036,;MFSD6,upstream_gene_variant,,ENST00000434582,;MFSD6,downstream_gene_variant,,ENST00000417958,; T ENST00000392328 Transcript missense_variant 583/4797 259/2376 87/791 P/S Ccc/Tcc 1 1 MFSD6 HGNC HGNC:24711 protein_coding YES CCDS2306.1 ENSP00000376141 Q6ZSS7 UPI000022BD91 NM_017694.3 deleterious(0) 3/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR16172,hmmpanther:PTHR16172:SF2,Pfam_domain:PF12832,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 190436288 190436288 C T 1 0 0 0 0 1 0 0 0 9493 855 30 3 3 MFSD6 2 190436288 Missense_Mutation SNP C C3N-01071_T 34106658 190436288 51757241 47 21605 FZD7 0 . GRCh38 2 202035573 202035573 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.926T>C p.Leu309Pro p.L309P ENST00000286201 1/1 195 176 19 159 159 0 strelka-varscan-mutect FZD7,missense_variant,p.Leu309Pro,ENST00000286201,NM_003507.1;RP11-107N15.1,upstream_gene_variant,,ENST00000608741,; C ENST00000286201 Transcript missense_variant 987/3859 926/1725 309/574 L/P cTa/cCa 1 1 FZD7 HGNC HGNC:4045 protein_coding YES CCDS2351.1 ENSP00000286201 O75084 UPI0000051051 NM_003507.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF31,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 202035573 202035573 T C 1 0 0 0 0 1 0 0 0 6006 1522 53 5 5 FZD7 2 202035573 Missense_Mutation SNP T C3N-01071_T 11599285 202035573 40157956 48 21606 CXCR2 0 . GRCh38 2 218135425 218135425 + Silent SNP G G A C3N-01071_T C3N-01071_N G G c.624G>A p.= p.R208R ENST00000318507 3/3 232 210 22 191 191 0 strelka-varscan-mutect CXCR2,synonymous_variant,p.=,ENST00000318507,NM_001168298.1,NM_001557.3;CXCR2,downstream_gene_variant,,ENST00000453237,;CXCR2,downstream_gene_variant,,ENST00000428565,;CXCR2,downstream_gene_variant,,ENST00000454148,;CXCR2,downstream_gene_variant,,ENST00000415392,;CXCR2,downstream_gene_variant,,ENST00000449014,;CXCR2,downstream_gene_variant,,ENST00000418878,; A ENST00000318507 Transcript synonymous_variant 1051/2879 624/1083 208/360 R cgG/cgA COSM3577633 1 1 CXCR2 HGNC HGNC:6027 protein_coding YES CCDS2408.1 ENSP00000319635 P25025 Q53PC4 UPI000004358A NM_001168298.1,NM_001557.3 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00427,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF632,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 218135425 218135425 G A 1 0 0 0 0 0 0 0 1 3902 1161 41 3 3 CXCR2 2 218135425 Silent SNP G C3N-01071_T 16099852 218135425 24058104 49 21607 SPEG 0 . GRCh38 2 219484654 219484654 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.7191C>T p.= p.L2397L ENST00000312358 30/41 156 144 12 203 203 0 strelka-varscan-mutect SPEG,synonymous_variant,p.=,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript synonymous_variant 7323/10782 7191/9804 2397/3267 L ctC/ctT 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 219484654 219484654 C T 1 0 0 0 0 0 0 0 1 15387 813 29 3 3 SPEG 2 219484654 Silent SNP C C3N-01071_T 1349229 219484654 22708875 50 21608 USP40 0 . GRCh38 2 233496824 233496824 + Silent SNP T T A novel C3N-01071_T C3N-01071_N T T c.2757A>T p.= p.T919T ENST00000450966 23/31 173 155 18 105 105 0 strelka-varscan-mutect USP40,synonymous_variant,p.=,ENST00000251722,;USP40,synonymous_variant,p.=,ENST00000450966,NM_018218.2;USP40,synonymous_variant,p.=,ENST00000427112,;USP40,synonymous_variant,p.=,ENST00000409945,;USP40,synonymous_variant,p.=,ENST00000430158,;USP40,non_coding_transcript_exon_variant,,ENST00000483216,;USP40,upstream_gene_variant,,ENST00000450940,; A ENST00000450966 Transcript synonymous_variant 2757/5616 2757/3744 919/1247 T acA/acT 1 -1 USP40 HGNC HGNC:20069 protein_coding YES CCDS46547.1 ENSP00000415434 Q9NVE5 UPI0000232F06 NM_018218.2 23/31 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 233496824 233496824 T A 1 0 0 0 0 0 0 0 1 17614 1683 59 4 4 USP40 2 233496824 Silent SNP T C3N-01071_T 14012170 233496824 8696705 51 21609 COL6A3 0 . GRCh38 2 237394840 237394840 + Silent SNP T T C C3N-01071_T C3N-01071_N T T c.456A>G p.= p.G152G ENST00000295550 3/44 95 86 9 109 109 0 strelka-varscan-mutect COL6A3,synonymous_variant,p.=,ENST00000295550,NM_004369.3;COL6A3,synonymous_variant,p.=,ENST00000433762,;COL6A3,intron_variant,,ENST00000353578,NM_057167.3;COL6A3,intron_variant,,ENST00000409809,;COL6A3,intron_variant,,ENST00000472056,NM_057166.4;COL6A3,intron_variant,,ENST00000347401,;COL6A3,intron_variant,,ENST00000392004,NM_057165.4;COL6A3,intron_variant,,ENST00000392003,NM_057164.4; C ENST00000295550 Transcript synonymous_variant 909/10749 456/9534 152/3177 G ggA/ggG COSM1018374 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 3/44 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF74,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 1 LOW 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.96119 1 1 1 1 0 C 2 2 71 237394840 237394840 T C 1 0 0 0 0 0 0 0 1 3490 1654 58 5 5 COL6A3 2 237394840 Silent SNP T C3N-01071_T 3898016 237394840 4798689 52 21610 CROCC2 0 . GRCh38 2 240949695 240949695 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.2645G>T p.Arg882Met p.R882M ENST00000443866 17/32 110 104 6 75 75 0 strelka-mutect CROCC2,missense_variant,p.Arg882Met,ENST00000443866,;AC104809.4,downstream_gene_variant,,ENST00000418218,;CROCC2,non_coding_transcript_exon_variant,,ENST00000480779,; T ENST00000443866 Transcript missense_variant 2829/5382 2645/4968 882/1655 R/M aGg/aTg 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A deleterious(0) 17/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -12.22865 1 1 1 1 0 T 3 4 71 240949695 240949695 G T 1 0 0 0 0 1 0 0 0 3695 1000 35 2 2 CROCC2 2 240949695 Missense_Mutation SNP G C3N-01071_T 3554855 240949695 1243834 53 21611 SNED1 0 . GRCh38 2 241052398 241052398 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.2013C>A p.= p.T671T ENST00000310397 15/32 50 44 6 40 40 0 strelka-varscan-mutect SNED1,synonymous_variant,p.=,ENST00000310397,NM_001080437.1;SNED1,synonymous_variant,p.=,ENST00000405547,;SNED1,synonymous_variant,p.=,ENST00000401884,;SNED1,downstream_gene_variant,,ENST00000401644,;SNED1,downstream_gene_variant,,ENST00000431690,;AC005237.4,intron_variant,,ENST00000458377,;SNED1,non_coding_transcript_exon_variant,,ENST00000469006,;SNED1,downstream_gene_variant,,ENST00000483962,; A ENST00000310397 Transcript synonymous_variant 2013/8174 2013/4242 671/1413 T acC/acA 1 1 SNED1 HGNC HGNC:24696 protein_coding YES CCDS46562.1 ENSP00000308893 Q8TER0 UPI0000DD7AB0 NM_001080437.1 15/32 PROSITE_profiles:PS50026,hmmpanther:PTHR24033,Gene3D:2gy5A03,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 LOW SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -14.57636 1 1 1 1 0 A 2 1 71 241052398 241052398 C A 1 0 0 0 0 0 0 0 1 15166 668 24 2 2 SNED1 2 241052398 Silent SNP C C3N-01071_T 102703 241052398 1141131 54 21612 GAL3ST2 0 . GRCh38 2 241803884 241803884 + Silent SNP G G T novel C3N-01071_T C3N-01071_N G G c.915G>T p.= p.G305G ENST00000192314 4/4 61 56 5 58 58 0 strelka-varscan-mutect GAL3ST2,synonymous_variant,p.=,ENST00000192314,NM_022134.2;NEU4,upstream_gene_variant,,ENST00000407683,NM_001167601.2,NM_001167600.2;AC114730.3,downstream_gene_variant,,ENST00000413820,;AC114730.5,upstream_gene_variant,,ENST00000437438,; T ENST00000192314 Transcript synonymous_variant 1046/1370 915/1197 305/398 G ggG/ggT 1 1 GAL3ST2 HGNC HGNC:24869 protein_coding YES CCDS33427.1 ENSP00000192314 Q9H3Q3 UPI000049DF44 NM_022134.2 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF55,Pfam_domain:PF06990 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.8554 1 1 1 1 0 T 2 4 71 241803884 241803884 G T 1 0 0 0 0 0 0 0 1 6066 1219 43 2 2 GAL3ST2 2 241803884 Silent SNP G C3N-01071_T 751486 241803884 389645 55 21613 TATDN2 0 . GRCh38 3 10249484 10249484 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.284G>C p.Gly95Ala p.G95A ENST00000287652 2/8 111 100 11 118 118 0 strelka-varscan-mutect TATDN2,missense_variant,p.Gly95Ala,ENST00000287652,NM_014760.3;TATDN2,missense_variant,p.Gly95Ala,ENST00000448281,;RP11-438J1.1,missense_variant,p.Gly38Ala,ENST00000450534,;RP11-438J1.1,missense_variant,p.Gly38Ala,ENST00000437082,; C ENST00000287652 Transcript missense_variant 1335/5342 284/2286 95/761 G/A gGg/gCg 1 1 TATDN2 HGNC HGNC:28988 protein_coding YES CCDS33698.1 ENSP00000287652 Q93075 A0A024R2F3 UPI000013DEC1 NM_014760.3 tolerated(0.36) 2/8 MODERATE 1 SNV 1 1 PASS rs1328201926 . 0 203 7 0 0 0 0 0 -19.99421 0.999999 1 1 1 0 C 3 2 71 10249484 10249484 G C 1 0 0 0 0 1 0 0 0 15991 1232 43 4 4 TATDN2 3 10249484 Missense_Mutation SNP G C3N-01071_T 10249484 188046075 56 21614 DCLK3 0 . GRCh38 3 36737682 36737682 + Silent SNP C C T rs753013409 C3N-01071_T C3N-01071_N C C c.978G>A p.= p.K326K ENST00000416516 2/5 82 65 17 106 106 0 strelka-varscan-mutect DCLK3,synonymous_variant,p.=,ENST00000636136,;DCLK3,synonymous_variant,p.=,ENST00000416516,NM_033403.1; T ENST00000416516 Transcript synonymous_variant 1469/5344 978/1947 326/648 K aaG/aaA rs753013409 1 -1 DCLK3 HGNC HGNC:19005 protein_coding YES CCDS43064.1 ENSP00000394484 Q9C098 UPI0000E2657D NM_033403.1 2/5 LOW 1 SNV 5 1 PASS rs753013409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 36737682 36737682 C T 1 0 0 0 0 0 0 0 1 4095 912 32 3 3 DCLK3 3 36737682 Silent SNP C C3N-01071_T 26488198 36737682 161557877 57 21615 MLH1 0 . GRCh38 3 37049014 37049014 + Silent SNP G G A C3N-01071_T C3N-01071_N G G c.2100G>A p.= p.Q700Q ENST00000231790 18/19 460 431 29 442 442 0 strelka-varscan-mutect MLH1,synonymous_variant,p.=,ENST00000231790,NM_000249.3;MLH1,synonymous_variant,p.=,ENST00000458205,NM_001258274.1;MLH1,synonymous_variant,p.=,ENST00000536378,NM_001258273.1;MLH1,synonymous_variant,p.=,ENST00000435176,NM_001167617.1;MLH1,synonymous_variant,p.=,ENST00000539477,NM_001167619.1;MLH1,synonymous_variant,p.=,ENST00000455445,NM_001167618.1;MLH1,intron_variant,,ENST00000456676,NM_001258271.1;MLH1,intron_variant,,ENST00000413740,;MLH1,intron_variant,,ENST00000450420,;LRRFIP2,downstream_gene_variant,,ENST00000336686,NM_006309.3;LRRFIP2,downstream_gene_variant,,ENST00000354379,NM_017724.2;LRRFIP2,downstream_gene_variant,,ENST00000421276,NM_001134369.2;LRRFIP2,downstream_gene_variant,,ENST00000440230,;LRRFIP2,downstream_gene_variant,,ENST00000396428,NM_001282691.1;MLH1,downstream_gene_variant,,ENST00000616768,;LRRFIP2,downstream_gene_variant,,ENST00000496479,;LRRFIP2,downstream_gene_variant,,ENST00000460646,; A ENST00000231790 Transcript synonymous_variant 2316/2752 2100/2271 700/756 Q caG/caA COSM1043975 1 1 MLH1 HGNC HGNC:7127 protein_coding YES CCDS2663.1 ENSP00000231790 P40692 UPI0000000C7E NM_000249.3 18/19 Pfam_domain:PF16413,hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF40 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 37049014 37049014 G A 1 0 0 0 0 0 0 0 1 9584 985 34 3 3 MLH1 3 37049014 Silent SNP G C3N-01071_T 311332 37049014 161246545 58 21616 RPL29 0 . GRCh38 3 51994024 51994024 + Missense_Mutation SNP C C T C3N-01071_T C3N-01071_N C C c.205G>A p.Ala69Thr p.A69T ENST00000466397 4/4 119 111 8 98 98 0 varscan-mutect RPL29,missense_variant,p.Ala69Thr,ENST00000466397,;RPL29,missense_variant,p.Ala69Thr,ENST00000294189,NM_000992.2;RPL29,missense_variant,p.Ala69Thr,ENST00000495383,;RPL29,missense_variant,p.Ala69Thr,ENST00000479017,;RPL29,missense_variant,p.Ala69Thr,ENST00000475248,;RPL29,missense_variant,p.Ala69Thr,ENST00000492277,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637978,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000463937,;ACY1,downstream_gene_variant,,ENST00000636358,NM_001198895.1,NM_000666.2;ACY1,downstream_gene_variant,,ENST00000404366,;ACY1,downstream_gene_variant,,ENST00000476351,NM_001198898.1;ACY1,downstream_gene_variant,,ENST00000476854,NM_001198897.1;ACY1,downstream_gene_variant,,ENST00000494103,NM_001198896.1;ACY1,downstream_gene_variant,,ENST00000635797,;RPL29,downstream_gene_variant,,ENST00000481629,;ACY1,downstream_gene_variant,,ENST00000637149,;RPL29,3_prime_UTR_variant,,ENST00000480306,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637778,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637130,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000635937,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636490,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636826,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637025,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637730,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637563,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636718,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000635946,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637696,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636089,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000635951,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636646,;ACY1,downstream_gene_variant,,ENST00000638136,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000463721,NM_001316331.1;ABHD14A-ACY1,downstream_gene_variant,,ENST00000636942,;ACY1,downstream_gene_variant,,ENST00000635941,;ABHD14A-ACY1,downstream_gene_variant,,ENST00000637512,;ACY1,downstream_gene_variant,,ENST00000636880,;ACY1,downstream_gene_variant,,ENST00000491318,;ACY1,downstream_gene_variant,,ENST00000490244,;ACY1,downstream_gene_variant,,ENST00000637199,;ACY1,downstream_gene_variant,,ENST00000637034,;ACY1,downstream_gene_variant,,ENST00000637746,;RPL29,downstream_gene_variant,,ENST00000486565,;ACY1,downstream_gene_variant,,ENST00000638077,; T ENST00000466397 Transcript missense_variant 346/742 205/480 69/159 A/T Gcc/Acc COSM1046807 1 -1 RPL29 HGNC HGNC:10331 protein_coding YES CCDS2845.1 ENSP00000418868 P47914 UPI0000167B81 tolerated(0.07) 4/4 hmmpanther:PTHR12884 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 51994024 51994024 C T 1 0 0 0 0 1 0 0 0 13830 710 25 3 3 RPL29 3 51994024 Missense_Mutation SNP C C3N-01071_T 14945010 51994024 146301535 59 21617 OR5K4 0 . GRCh38 3 98354562 98354562 + Missense_Mutation SNP G G A C3N-01071_T C3N-01071_N G G c.709G>A p.Ala237Thr p.A237T ENST00000354924 1/1 185 149 36 160 160 0 strelka-varscan-mutect OR5K4,missense_variant,p.Ala237Thr,ENST00000354924,NM_001005517.1;RP11-325B23.2,intron_variant,,ENST00000508616,; A ENST00000354924 Transcript missense_variant 709/966 709/966 237/321 A/T Gca/Aca COSM5441373 1 1 OR5K4 HGNC HGNC:31291 protein_coding YES CCDS33802.1 ENSP00000347003 A6NMS3 UPI000044D411 NM_001005517.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF198,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS rs966876742 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 98354562 98354562 G A 1 0 0 0 0 1 0 0 0 11239 971 34 3 3 OR5K4 3 98354562 Missense_Mutation SNP G C3N-01071_T 46360538 98354562 99940997 60 21618 OR5K2 0 . GRCh38 3 98497811 98497811 + Missense_Mutation SNP G G T rs529759510 C3N-01071_T C3N-01071_N G G c.131G>T p.Ser44Ile p.S44I ENST00000427338 1/1 315 281 34 219 219 0 varscan-mutect OR5K2,missense_variant,p.Ser44Ile,ENST00000427338,NM_001004737.1;CLDND1,downstream_gene_variant,,ENST00000507874,;CLDND1,downstream_gene_variant,,ENST00000502288,; T ENST00000427338 Transcript missense_variant 208/1060 131/951 44/316 S/I aGt/aTt rs529759510 1 1 OR5K2 HGNC HGNC:14774 protein_coding YES CCDS33804.1 ENSP00000393889 Q8NHB8 A0A126GVB4 UPI000004B1DF NM_001004737.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF311,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs529759510 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 98497811 98497811 G T 1 0 0 0 0 1 0 0 0 11237 1029 36 2 2 OR5K2 3 98497811 Missense_Mutation SNP G C3N-01071_T 143249 98497811 99797748 61 21619 GPR15 0 . GRCh38 3 98532648 98532648 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.615T>A p.Phe205Leu p.F205L ENST00000284311 1/1 198 178 20 199 199 0 strelka-varscan-mutect GPR15,missense_variant,p.Phe205Leu,ENST00000284311,NM_005290.2;CPOX,intron_variant,,ENST00000512905,; A ENST00000284311 Transcript missense_variant 750/1252 615/1083 205/360 F/L ttT/ttA 1 1 GPR15 HGNC HGNC:4469 protein_coding YES CCDS2931.1 ENSP00000284311 P49685 B6V9G9 UPI0000000EAC NM_005290.2 tolerated(0.2) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1479230848 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 98532648 98532648 T A 1 0 0 0 0 1 0 0 0 6541 1809 63 4 4 GPR15 3 98532648 Missense_Mutation SNP T C3N-01071_T 34837 98532648 99762911 62 21620 DCBLD2 0 . GRCh38 3 98800598 98800598 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.1839G>T p.= p.V613V ENST00000326840 15/16 146 129 17 106 106 0 strelka-varscan-mutect DCBLD2,synonymous_variant,p.=,ENST00000326840,NM_080927.3;DCBLD2,synonymous_variant,p.=,ENST00000326857,;ST3GAL6,downstream_gene_variant,,ENST00000394162,NM_001323352.1,NM_001323365.1,NM_006100.3;ST3GAL6,downstream_gene_variant,,ENST00000613264,NM_001271145.1;ST3GAL6,downstream_gene_variant,,ENST00000265261,NM_001271147.1,NM_001271142.1;RNU6-26P,downstream_gene_variant,,ENST00000383985,;ST3GAL6,intron_variant,,ENST00000491912,;ST3GAL6,upstream_gene_variant,,ENST00000495502,;DCBLD2,non_coding_transcript_exon_variant,,ENST00000496736,;ST3GAL6,downstream_gene_variant,,ENST00000486249,;DCBLD2,downstream_gene_variant,,ENST00000494614,; A ENST00000326840 Transcript synonymous_variant 2202/6122 1839/2328 613/775 V gtG/gtT 1 -1 DCBLD2 HGNC HGNC:24627 protein_coding YES CCDS46878.1 ENSP00000321573 Q96PD2 UPI0000072ABB NM_080927.3 15/16 hmmpanther:PTHR10127 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 98800598 98800598 C A 1 0 0 0 0 0 0 0 1 4083 697 25 2 2 DCBLD2 3 98800598 Silent SNP C C3N-01071_T 267950 98800598 99494961 63 21621 ABI3BP 0 . GRCh38 3 100837145 100837145 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.2131G>A p.Glu711Lys p.E711K ENST00000471714 27/67 180 167 13 212 212 0 strelka-varscan-mutect ABI3BP,missense_variant,p.Glu711Lys,ENST00000471714,;ABI3BP,missense_variant,p.Glu711Lys,ENST00000495063,;ABI3BP,missense_variant,p.Glu118Lys,ENST00000495591,;ABI3BP,missense_variant,p.Glu77Lys,ENST00000533795,;ABI3BP,missense_variant,p.Glu81Lys,ENST00000534256,;ABI3BP,intron_variant,,ENST00000284322,NM_015429.3;ABI3BP,intron_variant,,ENST00000528490,;ABI3BP,intron_variant,,ENST00000466947,;ABI3BP,intron_variant,,ENST00000534413,;ABI3BP,intron_variant,,ENST00000528305,;ABI3BP,upstream_gene_variant,,ENST00000471901,;ABI3BP,downstream_gene_variant,,ENST00000533855,;ABI3BP,upstream_gene_variant,,ENST00000478235,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487249,;ABI3BP,intron_variant,,ENST00000470336,; T ENST00000471714 Transcript missense_variant 2241/6783 2131/5334 711/1777 E/K Gaa/Aaa 1 -1 ABI3BP HGNC HGNC:17265 protein_coding ENSP00000420524 D3YTG3 UPI00004225FE tolerated(0.07) 27/67 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF10 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 100837145 100837145 C T 1 0 0 0 0 1 0 0 0 101 835 29 3 3 ABI3BP 3 100837145 Missense_Mutation SNP C C3N-01071_T 2036547 100837145 97458414 64 21622 CEP97 0 . GRCh38 3 101758292 101758292 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.1686C>T p.= p.A562A ENST00000341893 9/11 356 332 24 263 263 0 strelka-varscan-mutect CEP97,synonymous_variant,p.=,ENST00000341893,NM_024548.3;CEP97,synonymous_variant,p.=,ENST00000494050,NM_001303401.1;CEP97,downstream_gene_variant,,ENST00000462076,;CEP97,3_prime_UTR_variant,,ENST00000467655,;CEP97,non_coding_transcript_exon_variant,,ENST00000489172,; T ENST00000341893 Transcript synonymous_variant 2438/8361 1686/2598 562/865 A gcC/gcT 1 1 CEP97 HGNC HGNC:26244 protein_coding YES CCDS2944.1 ENSP00000342510 Q8IW35 UPI0000074569 NM_024548.3 9/11 PROSITE_profiles:PS50096 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -6.020847 0.9860121 1 1 1 0 T 2 4 71 101758292 101758292 C T 1 0 0 0 0 0 0 0 1 2989 581 21 3 3 CEP97 3 101758292 Silent SNP C C3N-01071_T 921147 101758292 96537267 65 21623 TMPRSS7 0 . GRCh38 3 112057052 112057052 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.853C>G p.Leu285Val p.L285V ENST00000617607 7/15 144 133 11 114 114 0 strelka-mutect TMPRSS7,missense_variant,p.Leu411Val,ENST00000452346,;TMPRSS7,missense_variant,p.Leu285Val,ENST00000617607,;TMPRSS7,missense_variant,p.Leu285Val,ENST00000419127,NM_001042575.2;TMPRSS7,3_prime_UTR_variant,,ENST00000435737,; G ENST00000617607 Transcript missense_variant 891/2377 853/2154 285/717 L/V Ctg/Gtg 1 1 TMPRSS7 HGNC HGNC:30846 protein_coding YES CCDS43129.2 ENSP00000478830 Q7RTY8 UPI000192A2F1 tolerated(0.5) 7/15 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.96052 1 1 1 1 0 G 3 3 71 112057052 112057052 C G 1 0 0 0 0 1 0 0 0 16728 564 20 4 4 TMPRSS7 3 112057052 Missense_Mutation SNP C C3N-01071_T 10298760 112057052 86238507 66 21624 MSL2 0 . GRCh38 3 136151421 136151421 + Missense_Mutation SNP C C G rs867479221 C3N-01071_T C3N-01071_N C C c.1460G>C p.Arg487Pro p.R487P ENST00000309993 2/2 711 648 63 470 470 0 strelka-varscan MSL2,missense_variant,p.Arg487Pro,ENST00000309993,NM_018133.3;MSL2,missense_variant,p.Arg413Pro,ENST00000434835,NM_001145417.1;PPP2R3A,downstream_gene_variant,,ENST00000264977,NM_002718.4;MSL2,downstream_gene_variant,,ENST00000481989,;MSL2,downstream_gene_variant,,ENST00000491050,;MSL2,downstream_gene_variant,,ENST00000473093,;TDGF1P6,upstream_gene_variant,,ENST00000463873,; G ENST00000309993 Transcript missense_variant 2193/4692 1460/1734 487/577 R/P cGc/cCc rs867479221,COSM5566224 1 -1 MSL2 HGNC HGNC:25544 protein_coding YES CCDS33861.1 ENSP00000311827 Q9HCI7 UPI000020A2D7 NM_018133.3 deleterious(0.01) 2/2 Pfam_domain:PF16682,hmmpanther:PTHR16048,hmmpanther:PTHR16048:SF3,SMART_domains:SM01114 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 136151421 136151421 C G 1 0 0 0 0 1 0 0 0 9861 768 27 4 4 MSL2 3 136151421 Missense_Mutation SNP C C3N-01071_T 24094369 136151421 62144138 67 21625 A4GNT 0 . GRCh38 3 138131138 138131138 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.119A>T p.Gln40Leu p.Q40L ENST00000236709 2/3 186 167 19 146 146 0 strelka-varscan A4GNT,missense_variant,p.Gln40Leu,ENST00000236709,NM_016161.2; A ENST00000236709 Transcript missense_variant 321/1771 119/1023 40/340 Q/L cAg/cTg 1 -1 A4GNT HGNC HGNC:17968 protein_coding YES CCDS3097.1 ENSP00000236709 Q9UNA3 UPI000003FF93 NM_016161.2 tolerated(0.68) 2/3 hmmpanther:PTHR12042:SF16,hmmpanther:PTHR12042,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 138131138 138131138 T A 1 0 0 0 0 1 0 0 0 7 1580 55 4 4 A4GNT 3 138131138 Missense_Mutation SNP T C3N-01071_T 1979717 138131138 60164421 68 21626 SPSB4 0 . GRCh38 3 141066243 141066243 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.139G>T p.Gly47Trp p.G47W ENST00000310546 2/3 126 105 21 85 85 0 strelka-varscan SPSB4,missense_variant,p.Gly47Trp,ENST00000310546,NM_080862.2;SPSB4,upstream_gene_variant,,ENST00000508126,; T ENST00000310546 Transcript missense_variant 883/2908 139/822 47/273 G/W Ggg/Tgg 1 1 SPSB4 HGNC HGNC:30630 protein_coding YES CCDS3115.1 ENSP00000311609 Q96A44 UPI00000734A4 NM_080862.2 deleterious(0.01) 2/3 PROSITE_profiles:PS50188,hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF3,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 141066243 141066243 G T 1 0 0 0 0 1 0 0 0 15471 1232 43 2 2 SPSB4 3 141066243 Missense_Mutation SNP G C3N-01071_T 2935105 141066243 57229316 69 21627 SI 0 . GRCh38 3 165055226 165055226 + Missense_Mutation SNP G G T C3N-01071_T C3N-01071_N G G c.1480C>A p.His494Asn p.H494N ENST00000264382 13/48 294 220 74 250 250 0 strelka-varscan SI,missense_variant,p.His494Asn,ENST00000264382,NM_001041.3; T ENST00000264382 Transcript missense_variant 1543/6011 1480/5484 494/1827 H/N Cat/Aat COSM729348 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0.04) 13/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF01055,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 165055226 165055226 G T 1 0 0 0 0 1 0 0 0 14561 1348 47 2 2 SI 3 165055226 Missense_Mutation SNP G C3N-01071_T 23988983 165055226 33240333 70 21628 BCHE 0 . GRCh38 3 165829857 165829857 + Missense_Mutation SNP C C T rs115129687 C3N-01071_T C3N-01071_N C C c.1177G>A p.Gly393Arg p.G393R ENST00000264381 2/4 132 102 30 91 91 0 strelka-varscan BCHE,missense_variant,p.Gly393Arg,ENST00000264381,NM_000055.2;BCHE,intron_variant,,ENST00000488954,;BCHE,intron_variant,,ENST00000479451,;BCHE,missense_variant,p.Gly393Arg,ENST00000482958,;BCHE,missense_variant,p.Gly393Arg,ENST00000497011,; T ENST00000264381 Transcript missense_variant 1344/2454 1177/1809 393/602 G/R Gga/Aga rs115129687,CM921036,CM990286,COSM309446,COSM5527306 1 -1 BCHE HGNC HGNC:983 protein_coding YES CCDS3198.1 ENSP00000264381 P06276 UPI0000127866 NM_000055.2 deleterious(0.05) 2/4 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF215,Superfamily_domains:SSF53474 0,0,0,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 165829857 165829857 C T 1 0 0 0 0 1 0 0 0 1505 603 21 3 3 BCHE 3 165829857 Missense_Mutation SNP C C3N-01071_T 774631 165829857 32465702 71 21629 ZBBX 0 . GRCh38 3 167368506 167368506 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.137T>A p.Leu46Gln p.L46Q ENST00000455345 4/21 344 292 52 304 304 0 strelka-varscan ZBBX,missense_variant,p.Leu46Gln,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Leu46Gln,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Leu46Gln,ENST00000307529,;ZBBX,missense_variant,p.Leu17Gln,ENST00000392767,;ZBBX,missense_variant,p.Leu17Gln,ENST00000392764,NM_001199202.1;ZBBX,missense_variant,p.Leu17Gln,ENST00000485651,;ZBBX,missense_variant,p.Leu46Gln,ENST00000474464,;ZBBX,intron_variant,,ENST00000469220,;ZBBX,non_coding_transcript_exon_variant,,ENST00000473888,; T ENST00000455345 Transcript missense_variant 421/3185 137/2520 46/839 L/Q cTg/cAg 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 deleterious(0.02) 4/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 167368506 167368506 A T 1 0 0 0 0 1 0 0 0 18078 188 7 4 4 ZBBX 3 167368506 Missense_Mutation SNP A C3N-01071_T 1538649 167368506 30927053 72 21630 PLD1 0 . GRCh38 3 171792577 171792577 + Silent SNP T T G novel C3N-01071_T C3N-01071_N T T c.232A>C p.= p.R78R ENST00000331659 2/2 197 161 36 177 177 0 strelka-varscan PLD1,synonymous_variant,p.=,ENST00000331659,;PLD1,intron_variant,,ENST00000356327,NM_001130081.2;PLD1,intron_variant,,ENST00000351298,NM_002662.4;PLD1,intron_variant,,ENST00000497307,;PLD1,intron_variant,,ENST00000460926,;PLD1,intron_variant,,ENST00000498278,;PLD1,intron_variant,,ENST00000440204,; G ENST00000331659 Transcript synonymous_variant 2119/2906 232/459 78/152 R Agg/Cgg 1 -1 PLD1 HGNC HGNC:9067 protein_coding ENSP00000328422 Q8WYW5 UPI000007269B 2/2 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 171792577 171792577 T G 1 0 0 0 0 0 0 0 1 12139 1579 55 5 5 PLD1 3 171792577 Silent SNP T C3N-01071_T 4424071 171792577 26502982 73 21631 PCGF3 0 . GRCh38 4 733691 733691 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.11G>A p.Arg4Lys p.R4K ENST00000362003 4/11 104 88 16 130 130 0 strelka-varscan-mutect PCGF3,missense_variant,p.Arg4Lys,ENST00000362003,NM_006315.4;PCGF3,missense_variant,p.Arg4Lys,ENST00000470161,;PCGF3,missense_variant,p.Arg4Lys,ENST00000400151,;PCGF3,missense_variant,p.Arg4Lys,ENST00000433814,;PCGF3,missense_variant,p.Arg4Lys,ENST00000419774,;PCGF3,missense_variant,p.Arg4Lys,ENST00000427463,;PCGF3,non_coding_transcript_exon_variant,,ENST00000482726,;PCGF3,missense_variant,p.Arg4Lys,ENST00000440452,;PCGF3,missense_variant,p.Arg4Lys,ENST00000430644,;PCGF3,non_coding_transcript_exon_variant,,ENST00000484141,;PCGF3,downstream_gene_variant,,ENST00000475288,; A ENST00000362003 Transcript missense_variant 406/5685 11/729 4/242 R/K aGg/aAg 1 1 PCGF3 HGNC HGNC:10066 protein_coding YES CCDS3339.2 ENSP00000354724 Q3KNV8 UPI00001A9628 NM_006315.4 deleterious(0.03) 4/11 Gene3D:3.30.40.10,hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF37 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 733691 733691 G A 1 0 0 0 0 1 0 0 0 11664 1000 35 3 3 PCGF3 4 733691 Missense_Mutation SNP G C3N-01071_T 733691 189480864 74 21632 PCGF3 0 . GRCh38 4 764988 764988 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.605A>T p.Asp202Val p.D202V ENST00000362003 10/11 162 153 9 179 179 0 strelka-varscan-mutect PCGF3,missense_variant,p.Asp202Val,ENST00000362003,NM_006315.4;PCGF3,missense_variant,p.Asp202Val,ENST00000470161,;PCGF3,upstream_gene_variant,,ENST00000620529,;AC139887.4,non_coding_transcript_exon_variant,,ENST00000454037,;RP11-440L14.1,intron_variant,,ENST00000503571,;RP11-440L14.1,downstream_gene_variant,,ENST00000507446,;PCGF3,downstream_gene_variant,,ENST00000488032,;PCGF3,3_prime_UTR_variant,,ENST00000440452,;PCGF3,3_prime_UTR_variant,,ENST00000430644,; T ENST00000362003 Transcript missense_variant 1000/5685 605/729 202/242 D/V gAc/gTc 1 1 PCGF3 HGNC HGNC:10066 protein_coding YES CCDS3339.2 ENSP00000354724 Q3KNV8 UPI00001A9628 NM_006315.4 deleterious(0.04) 10/11 Pfam_domain:PF16207,hmmpanther:PTHR10825,hmmpanther:PTHR10825:SF37 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 764988 764988 A T 1 0 0 0 0 1 0 0 0 11664 289 10 4 4 PCGF3 4 764988 Missense_Mutation SNP A C3N-01071_T 31297 764988 189449567 75 21633 FGFRL1 0 . GRCh38 4 1022377 1022377 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.254A>T p.Lys85Met p.K85M ENST00000398484 4/8 196 172 24 176 176 0 strelka-varscan-mutect FGFRL1,missense_variant,p.Lys85Met,ENST00000398484,;FGFRL1,missense_variant,p.Lys85Met,ENST00000264748,NM_001004358.1,NM_021923.3;FGFRL1,missense_variant,p.Lys85Met,ENST00000510644,NM_001004356.2;FGFRL1,missense_variant,p.Lys85Met,ENST00000504138,;FGFRL1,missense_variant,p.Lys85Met,ENST00000507339,;FGFRL1,downstream_gene_variant,,ENST00000512174,; T ENST00000398484 Transcript missense_variant 834/3639 254/1515 85/504 K/M aAg/aTg 1 1 FGFRL1 HGNC HGNC:3693 protein_coding YES CCDS3344.1 ENSP00000381498 Q8N441 UPI000003ED0B deleterious(0) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR19890,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 1022377 1022377 A T 1 0 0 0 0 1 0 0 0 5733 72 3 4 4 FGFRL1 4 1022377 Missense_Mutation SNP A C3N-01071_T 257389 1022377 189192178 76 21634 MAEA 0 . GRCh38 4 1339164 1339164 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.1186A>C p.Met396Leu p.M396L ENST00000303400 9/9 269 246 23 210 210 0 strelka-varscan-mutect MAEA,missense_variant,p.Met396Leu,ENST00000303400,NM_001297430.1,NM_001017405.2;MAEA,missense_variant,p.Met355Leu,ENST00000264750,NM_005882.4;MAEA,missense_variant,p.Met328Leu,ENST00000514708,NM_001297431.1;MAEA,missense_variant,p.Met395Leu,ENST00000510794,NM_001297432.1;MAEA,missense_variant,p.Met348Leu,ENST00000505839,NM_001297433.1;MAEA,missense_variant,p.Met434Leu,ENST00000505177,;MAEA,downstream_gene_variant,,ENST00000503653,;MAEA,non_coding_transcript_exon_variant,,ENST00000512289,;MAEA,3_prime_UTR_variant,,ENST00000509531,;MAEA,non_coding_transcript_exon_variant,,ENST00000506530,;MAEA,non_coding_transcript_exon_variant,,ENST00000515766,;MAEA,non_coding_transcript_exon_variant,,ENST00000503162,; C ENST00000303400 Transcript missense_variant 1249/2222 1186/1191 396/396 M/L Atg/Ctg 1 1 MAEA HGNC HGNC:13731 protein_coding YES CCDS33936.1 ENSP00000302830 Q7L5Y9 UPI00000343F4 NM_001297430.1,NM_001017405.2 tolerated(0.06) 9/9 hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 1339164 1339164 A C 1 0 0 0 0 1 0 0 0 9069 217 8 5 5 MAEA 4 1339164 Missense_Mutation SNP A C3N-01071_T 316787 1339164 188875391 77 21635 STX18 0 . GRCh38 4 4471707 4471707 + Splice_Site SNP C C G novel C3N-01071_T C3N-01071_N C C c.169-1G>C p.X57_splice ENST00000306200 73 66 7 52 52 0 strelka-varscan-mutect STX18,splice_acceptor_variant,,ENST00000306200,NM_016930.2;STX18,splice_acceptor_variant,,ENST00000505286,;STX18,splice_acceptor_variant,,ENST00000507908,;STX18-IT1,downstream_gene_variant,,ENST00000515487,;STX18,splice_acceptor_variant,,ENST00000512780,; G ENST00000306200 Transcript splice_acceptor_variant -/2138 169/1008 57/335 1 -1 STX18 HGNC HGNC:15942 protein_coding YES CCDS3377.1 ENSP00000305810 Q9P2W9 UPI0000049FDD NM_016930.2 1/10 HIGH 1 SNV 1 1 PASS . . 0 196 12 2 0 0 0 0 -12.10215 0.996317 1 1 1 0 G 5 3 71 4471707 4471707 C G 1 0 0 0 0 0 0 1 0 15725 927 32 4 4 STX18 4 4471707 Splice_Site SNP C C3N-01071_T 3132543 4471707 185742848 78 21636 AFAP1 0 . GRCh38 4 7843339 7843339 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.346G>T p.Asp116Tyr p.D116Y ENST00000420658 5/18 178 151 27 198 198 0 strelka-varscan-mutect AFAP1,missense_variant,p.Asp116Tyr,ENST00000420658,NM_001134647.1;AFAP1,missense_variant,p.Asp116Tyr,ENST00000358461,NM_198595.2;AFAP1,missense_variant,p.Asp116Tyr,ENST00000360265,;AFAP1,missense_variant,p.Asp116Tyr,ENST00000382543,;AFAP1,non_coding_transcript_exon_variant,,ENST00000513856,;AFAP1,non_coding_transcript_exon_variant,,ENST00000612691,; A ENST00000420658 Transcript missense_variant 619/7768 346/2445 116/814 D/Y Gat/Tat 1 -1 AFAP1 HGNC HGNC:24017 protein_coding YES CCDS47010.1 ENSP00000410689 Q8N556 UPI000048041E NM_001134647.1 deleterious(0) 5/18 hmmpanther:PTHR14338,hmmpanther:PTHR14338:SF8,Low_complexity_(Seg):seg,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS rs1025152013 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 7843339 7843339 C A 1 0 0 0 0 1 0 0 0 430 884 31 1 1 AFAP1 4 7843339 Missense_Mutation SNP C C3N-01071_T 3371632 7843339 182371216 79 21637 CLNK 0 . GRCh38 4 10528096 10528096 + Splice_Site SNP T T A rs373636256 C3N-01071_T C3N-01071_N T T c.631-2A>T p.X211_splice ENST00000226951 37 28 9 21 21 0 strelka-varscan-mutect CLNK,splice_acceptor_variant,,ENST00000226951,NM_052964.2;CLNK,splice_acceptor_variant,,ENST00000442825,;CLNK,downstream_gene_variant,,ENST00000507719,; A ENST00000226951 Transcript splice_acceptor_variant -/5599 631/1287 211/428 rs373636256 1 -1 CLNK HGNC HGNC:17438 protein_coding YES CCDS47024.1 ENSP00000226951 Q7Z7G1 UPI000004A23A NM_052964.2 12/18 HIGH 1 SNV 1 1 PASS rs373636256 . 1 204 5 0 0 0 0 0 -19.99952 1 1 1 1 0 A 5 1 71 10528096 10528096 T A 1 0 0 0 0 0 0 1 0 3317 1594 55 4 4 CLNK 4 10528096 Splice_Site SNP T C3N-01071_T 2684757 10528096 179686459 80 21638 BOD1L1 0 . GRCh38 4 13570028 13570028 + Missense_Mutation SNP T T C C3N-01071_T C3N-01071_N T T c.9139A>G p.Lys3047Glu p.K3047E ENST00000040738 26/26 76 71 5 103 103 0 strelka-varscan-mutect BOD1L1,missense_variant,p.Lys3047Glu,ENST00000040738,NM_148894.2;BOD1L1,missense_variant,p.Lys203Glu,ENST00000507943,;BOD1L1,non_coding_transcript_exon_variant,,ENST00000505343,; C ENST00000040738 Transcript missense_variant 9275/10565 9139/9156 3047/3051 K/E Aaa/Gaa COSM291960 1 -1 BOD1L1 HGNC HGNC:31792 protein_coding YES CCDS3411.2 ENSP00000040738 Q8NFC6 UPI000066D9E3 NM_148894.2 deleterious(0) 26/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31532,hmmpanther:PTHR31532:SF3 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 13570028 13570028 T C 1 0 0 0 0 1 0 0 0 1639 1792 62 5 5 BOD1L1 4 13570028 Missense_Mutation SNP T C3N-01071_T 3041932 13570028 176644527 81 21639 TECRL 0 . GRCh38 4 64409209 64409209 + Missense_Mutation SNP G G C C3N-01071_T C3N-01071_N G G c.143C>G p.Pro48Arg p.P48R ENST00000381210 1/12 302 256 46 394 394 0 strelka-varscan-mutect TECRL,missense_variant,p.Pro48Arg,ENST00000381210,NM_001010874.4;TECRL,missense_variant,p.Pro48Arg,ENST00000507440,;TECRL,missense_variant,p.Pro48Arg,ENST00000509536,;TECRL,non_coding_transcript_exon_variant,,ENST00000511356,; C ENST00000381210 Transcript missense_variant 254/3573 143/1092 48/363 P/R cCa/cGa COSM1642506 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 tolerated(0.19) 1/12 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 64409209 64409209 G C 1 0 0 0 0 1 0 0 0 16157 1348 47 4 4 TECRL 4 64409209 Missense_Mutation SNP G C3N-01071_T 50839181 64409209 125805346 82 21640 CNOT6L 0 . GRCh38 4 77774580 77774580 + Silent SNP G G C novel C3N-01071_T C3N-01071_N G G c.264C>G p.= p.S88S ENST00000504123 3/12 137 117 20 131 131 0 strelka-varscan-mutect CNOT6L,synonymous_variant,p.=,ENST00000504123,NM_144571.2,NM_001286790.1;CNOT6L,synonymous_variant,p.=,ENST00000515506,;CNOT6L,synonymous_variant,p.=,ENST00000512485,;CNOT6L,synonymous_variant,p.=,ENST00000515441,;CNOT6L,non_coding_transcript_exon_variant,,ENST00000506166,;CNOT6L,3_prime_UTR_variant,,ENST00000504804,; C ENST00000504123 Transcript synonymous_variant 395/8843 264/1668 88/555 S tcC/tcG 1 -1 CNOT6L HGNC HGNC:18042 protein_coding YES CCDS68731.1 ENSP00000424896 Q96LI5 UPI0000E445DF NM_144571.2,NM_001286790.1 3/12 PROSITE_profiles:PS51450,hmmpanther:PTHR12121:SF35,hmmpanther:PTHR12121,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 2 1 PASS rs1320945727 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 77774580 77774580 G C 1 0 0 0 0 0 0 0 1 3403 1335 47 4 4 CNOT6L 4 77774580 Silent SNP G C3N-01071_T 13365371 77774580 112439975 83 21641 ATOH1 0 . GRCh38 4 93829863 93829863 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.937C>A p.Pro313Thr p.P313T ENST00000306011 1/1 148 135 13 200 199 1 strelka-varscan-mutect ATOH1,missense_variant,p.Pro313Thr,ENST00000306011,NM_005172.1; A ENST00000306011 Transcript missense_variant 1111/2212 937/1065 313/354 P/T Cct/Act 1 1 ATOH1 HGNC HGNC:797 protein_coding YES CCDS3638.1 ENSP00000302216 Q92858 UPI0000126231 NM_005172.1 deleterious(0) 1/1 hmmpanther:PTHR19290:SF82,hmmpanther:PTHR19290 MODERATE 1 SNV 1 PASS rs1472903204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 93829863 93829863 C A 1 0 0 0 0 1 0 0 0 1264 855 30 2 2 ATOH1 4 93829863 Missense_Mutation SNP C C3N-01071_T 16055283 93829863 96384692 84 21642 UNC5C 0 . GRCh38 4 95182970 95182970 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.2378T>C p.Leu793Pro p.L793P ENST00000453304 14/16 147 130 17 150 150 0 strelka-varscan-mutect UNC5C,missense_variant,p.Leu793Pro,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Leu752Pro,ENST00000610318,;UNC5C,downstream_gene_variant,,ENST00000513796,; G ENST00000453304 Transcript missense_variant 2727/9875 2378/2796 793/931 L/P cTg/cCg 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 deleterious(0) 14/16 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 95182970 95182970 A G 1 0 0 0 0 1 0 0 0 17517 188 7 5 5 UNC5C 4 95182970 Missense_Mutation SNP A C3N-01071_T 1353107 95182970 95031585 85 21643 ADH5 0 . GRCh38 4 99076499 99076499 + Silent SNP T T A novel C3N-01071_T C3N-01071_N T T c.618A>T p.= p.A206A ENST00000296412 6/9 177 123 54 179 179 0 strelka-varscan-mutect ADH5,synonymous_variant,p.=,ENST00000296412,NM_000671.4;ADH5,synonymous_variant,p.=,ENST00000503130,;ADH5,3_prime_UTR_variant,,ENST00000626055,;ADH5,non_coding_transcript_exon_variant,,ENST00000512991,;ADH5,downstream_gene_variant,,ENST00000508146,;ADH5,downstream_gene_variant,,ENST00000512604,;ADH5,3_prime_UTR_variant,,ENST00000512659,;ADH5,3_prime_UTR_variant,,ENST00000502590,;ADH5,non_coding_transcript_exon_variant,,ENST00000508511,;ADH5,non_coding_transcript_exon_variant,,ENST00000512621,;ADH5,downstream_gene_variant,,ENST00000505652,; A ENST00000296412 Transcript synonymous_variant 669/2615 618/1125 206/374 A gcA/gcT 1 -1 ADH5 HGNC HGNC:253 protein_coding YES CCDS47111.1 ENSP00000296412 P11766 Q6IRT1 UPI0000000DE6 NM_000671.4 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF606,TIGRFAM_domain:TIGR02818,Gene3D:3.40.50.720,Pfam_domain:PF00107,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 99076499 99076499 T A 1 0 0 0 0 0 0 0 1 384 1567 55 4 4 ADH5 4 99076499 Silent SNP T C3N-01071_T 3893529 99076499 91138056 86 21644 C4orf17 0 . GRCh38 4 99529897 99529897 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.485C>A p.Thr162Asn p.T162N ENST00000326581 5/9 185 154 31 198 198 0 strelka-varscan-mutect C4orf17,missense_variant,p.Thr162Asn,ENST00000514652,;C4orf17,missense_variant,p.Thr162Asn,ENST00000326581,NM_032149.2;C4orf17,non_coding_transcript_exon_variant,,ENST00000503257,;C4orf17,missense_variant,p.Thr162Asn,ENST00000477187,; A ENST00000326581 Transcript missense_variant 847/1636 485/1080 162/359 T/N aCc/aAc 1 1 C4orf17 HGNC HGNC:25274 protein_coding YES CCDS3649.1 ENSP00000322582 Q53FE4 UPI0000141987 NM_032149.2 tolerated(0.17) 5/9 Pfam_domain:PF15256,hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 99529897 99529897 C A 1 0 0 0 0 1 0 0 0 2078 507 18 2 2 C4orf17 4 99529897 Missense_Mutation SNP C C3N-01071_T 453398 99529897 90684658 87 21645 TACR3 0 . GRCh38 4 103591494 103591494 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.1078A>T p.Asn360Tyr p.N360Y ENST00000304883 4/5 283 235 48 282 282 0 strelka-varscan-mutect TACR3,missense_variant,p.Asn360Tyr,ENST00000304883,NM_001059.2;RP11-297P16.3,intron_variant,,ENST00000502936,;RP11-297P16.3,intron_variant,,ENST00000512401,; A ENST00000304883 Transcript missense_variant 1219/5190 1078/1398 360/465 N/Y Aat/Tat 1 -1 TACR3 HGNC HGNC:11528 protein_coding YES CCDS3664.1 ENSP00000303325 P29371 UPI0000050413 NM_001059.2 deleterious(0) 4/5 Gene3D:1.20.1070.10,Prints_domain:PR00237,Prints_domain:PR00244,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF46,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 103591494 103591494 T A 1 0 0 0 0 1 0 0 0 15903 1783 62 4 4 TACR3 4 103591494 Missense_Mutation SNP T C3N-01071_T 4061597 103591494 86623061 88 21646 MYOZ2 0 . GRCh38 4 119158088 119158088 + Missense_Mutation SNP C C A rs748809573 C3N-01071_T C3N-01071_N C C c.313C>A p.Pro105Thr p.P105T ENST00000307128 4/6 426 378 48 420 419 1 strelka-varscan-mutect MYOZ2,missense_variant,p.Pro105Thr,ENST00000307128,NM_016599.4; A ENST00000307128 Transcript missense_variant 526/2597 313/795 105/264 P/T Ccc/Acc rs748809573 1 1 MYOZ2 HGNC HGNC:1330 protein_coding YES CCDS3711.1 ENSP00000306997 Q9NPC6 UPI000004665D NM_016599.4 deleterious(0.03) 4/6 Pfam_domain:PF05556,hmmpanther:PTHR15941,hmmpanther:PTHR15941:SF9,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs748809573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 119158088 119158088 C A 1 0 0 0 0 1 0 0 0 10097 623 22 2 2 MYOZ2 4 119158088 Missense_Mutation SNP C C3N-01071_T 15566594 119158088 71056467 89 21647 ADAD1 0 . GRCh38 4 122380241 122380241 + Missense_Mutation SNP G G C rs201000111 C3N-01071_T C3N-01071_N G G c.172G>C p.Gly58Arg p.G58R ENST00000296513 3/13 86 70 16 92 92 0 strelka-varscan-mutect ADAD1,missense_variant,p.Gly58Arg,ENST00000296513,NM_139243.3;ADAD1,missense_variant,p.Gly40Arg,ENST00000388725,NM_001159295.1;ADAD1,missense_variant,p.Gly58Arg,ENST00000388724,NM_001159285.1;ADAD1,missense_variant,p.Gly58Arg,ENST00000439307,;ADAD1,missense_variant,p.Gly58Arg,ENST00000446706,;ADAD1,upstream_gene_variant,,ENST00000492454,;ADAD1,downstream_gene_variant,,ENST00000464160,; C ENST00000296513 Transcript missense_variant,splice_region_variant 357/1961 172/1731 58/576 G/R Ggt/Cgt rs201000111 1 1 ADAD1 HGNC HGNC:30713 protein_coding YES CCDS34058.1 ENSP00000296513 Q96M93 UPI000006DF76 NM_139243.3 deleterious(0.03) 3/13 MODERATE 1 SNV 2 1 PASS rs201000111 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 122380241 122380241 G C 1 0 0 0 0 1 0 0 0 275 1246 43 4 4 ADAD1 4 122380241 Missense_Mutation SNP G C3N-01071_T 3222153 122380241 67834314 90 21648 JADE1 0 . GRCh38 4 128871371 128871371 + Nonsense_Mutation SNP C C A C3N-01071_T C3N-01071_N C C c.1638C>A p.Cys546Ter p.C546* ENST00000226319 11/11 75 70 5 79 79 0 strelka-varscan-mutect JADE1,stop_gained,p.Cys546Ter,ENST00000226319,NM_199320.3;JADE1,stop_gained,p.Cys546Ter,ENST00000611140,NM_001287443.1;JADE1,stop_gained,p.Cys546Ter,ENST00000610919,NM_001287442.1;JADE1,stop_gained,p.Cys534Ter,ENST00000452328,NM_001287437.1;JADE1,stop_gained,p.Cys546Ter,ENST00000512960,NM_001287439.1,NM_001287440.1;SCLT1,intron_variant,,ENST00000503565,; A ENST00000226319 Transcript stop_gained 1919/5772 1638/2529 546/842 C/* tgC/tgA COSM5638262 1 1 JADE1 HGNC HGNC:30027 protein_coding YES CCDS34062.1 ENSP00000226319 Q6IE81 UPI000020B45B NM_199320.3 11/11 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF79,Low_complexity_(Seg):seg 1 HIGH 1 SNV 5 1 1 PASS . . 0 199 10 0 0 0 0 0 -11.00858 0.999906 1 1 1 0 A 4 1 71 128871371 128871371 C A 1 0 0 0 0 0 1 0 0 7844 805 28 2 2 JADE1 4 128871371 Nonsense_Mutation SNP C C3N-01071_T 6491130 128871371 61343184 91 21649 PCDH10 0 . GRCh38 4 133151091 133151091 + Missense_Mutation SNP C C A rs768053081 C3N-01071_T C3N-01071_N C C c.951C>A p.Asp317Glu p.D317E ENST00000264360 1/5 179 151 28 221 221 0 strelka-varscan-mutect PCDH10,missense_variant,p.Asp317Glu,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Asp317Glu,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; A ENST00000264360 Transcript missense_variant 1777/8489 951/3123 317/1040 D/E gaC/gaA rs768053081 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 deleterious(0) 1/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs768053081 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 133151091 133151091 C A 1 0 0 0 0 1 0 0 0 11594 564 20 2 2 PCDH10 4 133151091 Missense_Mutation SNP C C3N-01071_T 4279720 133151091 57063464 92 21650 SLC7A11 0 . GRCh38 4 138241797 138241797 + Silent SNP T T A novel C3N-01071_T C3N-01071_N T T c.273A>T p.= p.L91L ENST00000280612 1/12 107 97 10 131 131 0 strelka-varscan-mutect SLC7A11,synonymous_variant,p.=,ENST00000280612,NM_014331.3; A ENST00000280612 Transcript synonymous_variant 553/9645 273/1506 91/501 L ctA/ctT 1 -1 SLC7A11 HGNC HGNC:11059 protein_coding YES CCDS3742.1 ENSP00000280612 Q9UPY5 UPI0000138FD5 NM_014331.3 1/12 Pfam_domain:PF13520,PIRSF_domain:PIRSF006060,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF323,TIGRFAM_domain:TIGR00911,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.88586 1 1 1 1 0 A 2 1 71 138241797 138241797 T A 1 0 0 0 0 0 0 0 1 14977 1420 49 4 4 SLC7A11 4 138241797 Silent SNP T C3N-01071_T 5090706 138241797 51972758 93 21651 SMARCA5 0 . GRCh38 4 143538849 143538849 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.1681G>A p.Ala561Thr p.A561T ENST00000283131 13/24 148 137 11 159 159 0 strelka-varscan-mutect SMARCA5,missense_variant,p.Ala561Thr,ENST00000283131,NM_003601.3;SMARCA5,upstream_gene_variant,,ENST00000515531,; A ENST00000283131 Transcript missense_variant 2143/7923 1681/3159 561/1052 A/T Gct/Act 1 1 SMARCA5 HGNC HGNC:11101 protein_coding YES CCDS3761.1 ENSP00000283131 O60264 UPI000006E693 NM_003601.3 deleterious(0) 13/24 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF691,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 143538849 143538849 G A 1 0 0 0 0 1 0 0 0 15064 1319 46 3 3 SMARCA5 4 143538849 Missense_Mutation SNP G C3N-01071_T 5297052 143538849 46675706 94 21652 FREM3 0 . GRCh38 4 143698556 143698556 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.2120C>A p.Pro707Gln p.P707Q ENST00000329798 1/8 404 344 60 456 456 0 strelka-varscan-mutect FREM3,missense_variant,p.Pro707Gln,ENST00000329798,NM_001168235.1;RP13-578N3.3,upstream_gene_variant,,ENST00000499587,; T ENST00000329798 Transcript missense_variant 2120/6729 2120/6420 707/2139 P/Q cCa/cAa 1 -1 FREM3 HGNC HGNC:25172 protein_coding YES CCDS54808.1 ENSP00000332886 P0C091 UPI0000D615C2 NM_001168235.1 deleterious(0.01) 1/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF31 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 143698556 143698556 G T 1 0 0 0 0 1 0 0 0 5913 1348 47 2 2 FREM3 4 143698556 Missense_Mutation SNP G C3N-01071_T 159707 143698556 46515999 95 21653 SH3D19 0 . GRCh38 4 151143908 151143908 + Splice_Site SNP A A T novel C3N-01071_T C3N-01071_N A A c.1452+2T>A p.X484_splice ENST00000304527 82 66 16 96 96 0 strelka-varscan-mutect SH3D19,splice_donor_variant,,ENST00000409598,NM_001128923.1;SH3D19,splice_donor_variant,,ENST00000304527,NM_001009555.3;SH3D19,splice_donor_variant,,ENST00000604030,;SH3D19,splice_donor_variant,,ENST00000514152,NM_001243349.1;SH3D19,splice_donor_variant,,ENST00000409252,;SH3D19,splice_donor_variant,,ENST00000427414,NM_001128924.1;RP11-372K14.2,downstream_gene_variant,,ENST00000603472,;SH3D19,splice_donor_variant,,ENST00000478503,;SH3D19,splice_donor_variant,,ENST00000508492,; T ENST00000304527 Transcript splice_donor_variant -/5273 1452/2373 484/790 1 -1 SH3D19 HGNC HGNC:30418 protein_coding YES CCDS34077.2 ENSP00000302913 Q5HYK7 UPI0000251D9A NM_001009555.3 13/20 HIGH 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 71 151143908 151143908 A T 1 0 0 0 0 0 0 1 0 14507 405 14 4 4 SH3D19 4 151143908 Splice_Site SNP A C3N-01071_T 7445352 151143908 39070647 96 21654 NAF1 0 . GRCh38 4 163166686 163166686 + Silent SNP C C G novel C3N-01071_T C3N-01071_N C C c.42G>C p.= p.L14L ENST00000274054 1/8 215 198 17 272 272 0 strelka-varscan-mutect NAF1,synonymous_variant,p.=,ENST00000274054,NM_138386.2;NAF1,synonymous_variant,p.=,ENST00000422287,NM_001128931.1;NAF1,non_coding_transcript_exon_variant,,ENST00000509232,;NAF1,non_coding_transcript_exon_variant,,ENST00000502973,; G ENST00000274054 Transcript synonymous_variant 236/1907 42/1485 14/494 L ctG/ctC 1 -1 NAF1 HGNC HGNC:25126 protein_coding YES CCDS3803.1 ENSP00000274054 Q96HR8 UPI000013D9EB NM_138386.2 1/8 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 163166686 163166686 C G 1 0 0 0 0 0 0 0 1 10147 813 29 4 4 NAF1 4 163166686 Silent SNP C C3N-01071_T 12022778 163166686 27047869 97 21655 DDX60L 0 . GRCh38 4 168430511 168430511 + Missense_Mutation SNP C C A C3N-01071_T C3N-01071_N C C c.1644G>T p.Glu548Asp p.E548D ENST00000260184 13/38 99 87 12 114 114 0 strelka-mutect DDX60L,missense_variant,p.Glu548Asp,ENST00000511577,;DDX60L,missense_variant,p.Glu548Asp,ENST00000260184,NM_001012967.2;DDX60L,missense_variant,p.Glu548Asp,ENST00000505890,NM_001291510.1;DDX60L,missense_variant,p.Glu276Asp,ENST00000505863,; A ENST00000260184 Transcript missense_variant 1865/6754 1644/5121 548/1706 E/D gaG/gaT COSM3601925,COSM4898967 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 tolerated(0.19) 13/38 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 168430511 168430511 C A 1 0 0 0 0 1 0 0 0 4182 680 24 2 2 DDX60L 4 168430511 Missense_Mutation SNP C C3N-01071_T 5263825 168430511 21784044 98 21656 WDR17 0 . GRCh38 4 176173337 176173337 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.3432T>C p.= p.R1144R ENST00000280190 27/31 155 134 21 170 170 0 strelka-varscan-mutect WDR17,synonymous_variant,p.=,ENST00000443118,;WDR17,synonymous_variant,p.=,ENST00000280190,NM_170710.4;WDR17,synonymous_variant,p.=,ENST00000508596,NM_181265.3;WDR17,synonymous_variant,p.=,ENST00000507824,;WDR17,non_coding_transcript_exon_variant,,ENST00000508773,; C ENST00000280190 Transcript synonymous_variant 3588/4705 3432/3969 1144/1322 R cgT/cgC 1 1 WDR17 HGNC HGNC:16661 protein_coding YES CCDS3825.1 ENSP00000280190 Q8IZU2 UPI000019C575 NM_170710.4 27/31 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 176173337 176173337 T C 1 0 0 0 0 0 0 0 1 17837 1625 57 5 5 WDR17 4 176173337 Silent SNP T C3N-01071_T 7742826 176173337 14041218 99 21657 FBXL7 0 . GRCh38 5 15936806 15936806 + Missense_Mutation SNP G G C C3N-01071_T C3N-01071_N G G c.1096G>C p.Val366Leu p.V366L ENST00000504595 4/4 276 206 70 199 199 0 strelka-varscan-mutect FBXL7,missense_variant,p.Val366Leu,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Val324Leu,ENST00000329673,;FBXL7,missense_variant,p.Val319Leu,ENST00000510662,NM_001278317.1;MIR887,downstream_gene_variant,,ENST00000401258,; C ENST00000504595 Transcript missense_variant 1577/4562 1096/1476 366/491 V/L Gtg/Ctg COSM3613407,COSM5293715 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.13) 4/4 Gene3D:3.80.10.10,Pfam_domain:PF13516,hmmpanther:PTHR24006,SMART_domains:SM00367,Superfamily_domains:SSF52047 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1384577870 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 15936806 15936806 G C 1 0 0 0 0 1 0 0 0 5587 1145 40 4 4 FBXL7 5 15936806 Missense_Mutation SNP G C3N-01071_T 15936806 165601453 100 21658 CDH9 0 . GRCh38 5 26885640 26885640 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.1856T>A p.Ile619Asn p.I619N ENST00000231021 11/12 211 155 56 210 210 0 strelka-varscan-mutect CDH9,missense_variant,p.Ile619Asn,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505020,; T ENST00000231021 Transcript missense_variant 2029/3079 1856/2370 619/789 I/N aTt/aAt 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0) 11/12 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 26885640 26885640 A T 1 0 0 0 0 1 0 0 0 2820 101 4 4 4 CDH9 5 26885640 Missense_Mutation SNP A C3N-01071_T 10948834 26885640 154652619 101 21659 IQGAP2 0 . GRCh38 5 76600930 76600930 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.1190C>G p.Pro397Arg p.P397R ENST00000274364 11/36 266 218 48 283 283 0 strelka-varscan IQGAP2,missense_variant,p.Pro397Arg,ENST00000274364,NM_006633.3;IQGAP2,missense_variant,p.Pro347Arg,ENST00000379730,NM_001285460.1;IQGAP2,missense_variant,p.Pro347Arg,ENST00000505766,;IQGAP2,missense_variant,p.Pro370Arg,ENST00000514350,;IQGAP2,downstream_gene_variant,,ENST00000504815,; G ENST00000274364 Transcript missense_variant 1487/5844 1190/4728 397/1575 P/R cCc/cGc 1 1 IQGAP2 HGNC HGNC:6111 protein_coding YES CCDS34188.1 ENSP00000274364 Q13576 UPI000020CB2C NM_006633.3 deleterious(0) 11/36 hmmpanther:PTHR14149:SF12,hmmpanther:PTHR14149 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 76600930 76600930 C G 1 0 0 0 0 1 0 0 0 7721 623 22 4 4 IQGAP2 5 76600930 Missense_Mutation SNP C C3N-01071_T 49715290 76600930 104937329 102 21660 CMYA5 0 . GRCh38 5 79733576 79733576 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.4811G>T p.Gly1604Val p.G1604V ENST00000446378 2/13 179 155 24 155 154 1 strelka-varscan CMYA5,missense_variant,p.Gly1604Val,ENST00000446378,NM_153610.4;CMYA5,upstream_gene_variant,,ENST00000506603,; T ENST00000446378 Transcript missense_variant 4842/12847 4811/12210 1604/4069 G/V gGa/gTa 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 deleterious(0.01) 2/13 hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 79733576 79733576 G T 1 0 0 0 0 1 0 0 0 3368 1174 41 2 2 CMYA5 5 79733576 Missense_Mutation SNP G C3N-01071_T 3132646 79733576 101804683 103 21661 ATG10 0 . GRCh38 5 82253324 82253325 + Frame_Shift_Del DEL TA TA - novel C3N-01071_T C3N-01071_N TA TA c.565_566delAT p.Ile189HisfsTer27 p.I189Hfs*27 ENST00000282185 7/8 162 142 20 217 217 0 sindel-varindel-pindel ATG10,frameshift_variant,p.Ile189HisfsTer27,ENST00000282185,NM_031482.4;ATG10,frameshift_variant,p.Ile189HisfsTer27,ENST00000458350,NM_001131028.1;ATG10,downstream_gene_variant,,ENST00000513634,;ATG10,intron_variant,,ENST00000514253,;ATG10,intron_variant,,ENST00000508814,;ATG10,3_prime_UTR_variant,,ENST00000504770,; - ENST00000282185 Transcript frameshift_variant 856-857/3033 562-563/663 188/220 Y/X TAt/t 1 1 ATG10 HGNC HGNC:20315 protein_coding YES CCDS4057.1 ENSP00000282185 Q9H0Y0 UPI0000037BF4 NM_031482.4 7/8 hmmpanther:PTHR14957 HIGH 1 deletion 1 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 71 82253324 82253324 TA - 1 0 1 0 1 0 0 0 0 1238 1522 53 0 0 ATG10 5 82253324 Frame_Shift_Del DEL TA C3N-01071_T 2519748 82253324 99284935 104 21662 PCDHB6 0 . GRCh38 5 141151726 141151726 + Missense_Mutation SNP C C A C3N-01071_T C3N-01071_N C C c.1469C>A p.Pro490Gln p.P490Q ENST00000231136 1/1 943 758 185 813 812 1 strelka-varscan-mutect PCDHB6,missense_variant,p.Pro490Gln,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Pro354Gln,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; A ENST00000231136 Transcript missense_variant 1705/3266 1469/2385 490/794 P/Q cCg/cAg COSM5309697 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 deleterious(0.01) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 PASS rs1274457917 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 141151726 141151726 C A 1 0 0 0 0 1 0 0 0 11633 652 23 1 1 PCDHB6 5 141151726 Missense_Mutation SNP C C3N-01071_T 58898402 141151726 40386533 105 21663 DCTN4 0 . GRCh38 5 150711186 150711186 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.1367A>T p.Gln456Leu p.Q456L ENST00000446090 14/14 301 217 84 222 222 0 strelka-varscan-mutect DCTN4,missense_variant,p.Gln449Leu,ENST00000447998,NM_016221.3;DCTN4,missense_variant,p.Gln392Leu,ENST00000424236,NM_001135644.1;DCTN4,missense_variant,p.Gln456Leu,ENST00000446090,NM_001135643.1;DCTN4,3_prime_UTR_variant,,ENST00000627368,; A ENST00000446090 Transcript missense_variant 1409/1737 1367/1404 456/467 Q/L cAg/cTg 1 -1 DCTN4 HGNC HGNC:15518 protein_coding YES CCDS47310.1 ENSP00000414906 Q9UJW0 UPI0000EE3766 NM_001135643.1 deleterious(0.01) 14/14 hmmpanther:PTHR13034 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 150711186 150711186 T A 1 0 0 0 0 1 0 0 0 4112 1580 55 4 4 DCTN4 5 150711186 Missense_Mutation SNP T C3N-01071_T 9559460 150711186 30827073 106 21664 SLC36A1 0 . GRCh38 5 151479424 151479424 + Missense_Mutation SNP G G C rs555693703 C3N-01071_T C3N-01071_N G G c.1094G>C p.Arg365Pro p.R365P ENST00000243389 10/11 222 174 48 261 261 0 strelka-varscan-mutect SLC36A1,missense_variant,p.Arg365Pro,ENST00000243389,NM_078483.2;SLC36A1,missense_variant,p.Arg365Pro,ENST00000520701,;SLC36A1,missense_variant,p.Arg365Pro,ENST00000521925,;SLC36A1,missense_variant,p.Arg365Pro,ENST00000616007,;SLC36A1,missense_variant,p.Arg124Pro,ENST00000517628,;RNA5SP197,upstream_gene_variant,,ENST00000363357,;SLC36A1,3_prime_UTR_variant,,ENST00000522185,; C ENST00000243389 Transcript missense_variant 1317/5781 1094/1431 365/476 R/P cGa/cCa rs555693703,COSM1542658 1 1 SLC36A1 HGNC HGNC:18761 protein_coding YES CCDS4316.1 ENSP00000243389 Q7Z2H8 UPI00001A9D3C NM_078483.2 deleterious(0) 10/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF188 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs555693703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 151479424 151479424 G C 1 0 0 0 0 1 0 0 0 14871 1058 37 4 4 SLC36A1 5 151479424 Missense_Mutation SNP G C3N-01071_T 768238 151479424 30058835 107 21665 GEMIN5 0 . GRCh38 5 154921388 154921388 + Missense_Mutation SNP C C A rs772849763 C3N-01071_T C3N-01071_N C C c.1417G>T p.Val473Leu p.V473L ENST00000285873 10/28 90 72 18 165 165 0 strelka-varscan-mutect GEMIN5,missense_variant,p.Val473Leu,ENST00000285873,NM_001252156.1,NM_015465.4; A ENST00000285873 Transcript missense_variant 1493/5397 1417/4527 473/1508 V/L Gta/Tta rs772849763 1 -1 GEMIN5 HGNC HGNC:20043 protein_coding YES CCDS4330.1 ENSP00000285873 Q8TEQ6 UPI000020D072 NM_001252156.1,NM_015465.4 deleterious(0.02) 10/28 Gene3D:2.130.10.10,Pfam_domain:PF12894,PROSITE_profiles:PS50294,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS rs772849763 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 154921388 154921388 C A 1 0 0 0 0 1 0 0 0 6205 478 17 2 2 GEMIN5 5 154921388 Missense_Mutation SNP C C3N-01071_T 3441964 154921388 26616871 108 21666 HAVCR1 0 . GRCh38 5 157052470 157052470 + Silent SNP C C A rs759408704 C3N-01071_T C3N-01071_N C C c.564G>T p.= p.T188T ENST00000625904 3/7 598 497 101 502 502 0 strelka-varscan-mutect HAVCR1,synonymous_variant,p.=,ENST00000339252,NM_001099414.1,NM_012206.2;HAVCR1,synonymous_variant,p.=,ENST00000625904,;HAVCR1,synonymous_variant,p.=,ENST00000522693,NM_001308156.1;HAVCR1,synonymous_variant,p.=,ENST00000523175,NM_001173393.1;HAVCR1,synonymous_variant,p.=,ENST00000518745,;HAVCR1,upstream_gene_variant,,ENST00000517644,; A ENST00000625904 Transcript synonymous_variant 1097/1807 564/1206 188/401 T acG/acT rs759408704,COSM3919457,COSM3919458 1 -1 HAVCR1 HGNC HGNC:17866 protein_coding YES CCDS78076.1 ENSP00000487363 E9PFX0 UPI000020C020 3/7 hmmpanther:PTHR15498,hmmpanther:PTHR15498:SF8,Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs759408704 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 157052470 157052470 C A 1 0 0 0 0 0 0 0 1 6859 871 31 1 1 HAVCR1 5 157052470 Silent SNP C C3N-01071_T 2131082 157052470 24485789 109 21667 FAM71B 0 . GRCh38 5 157162533 157162533 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.1732C>A p.Gln578Lys p.Q578K ENST00000302938 2/2 290 233 57 293 293 0 strelka-varscan-mutect FAM71B,missense_variant,p.Gln578Lys,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; T ENST00000302938 Transcript missense_variant 1828/2515 1732/1818 578/605 Q/K Cag/Aag 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 tolerated(0.34) 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 157162533 157162533 G T 1 0 0 0 0 1 0 0 0 5472 1357 47 2 2 FAM71B 5 157162533 Missense_Mutation SNP G C3N-01071_T 110063 157162533 24375726 110 21668 ADAM19 0 . GRCh38 5 157519970 157519970 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.469G>T p.Gly157Cys p.G157C ENST00000257527 6/23 170 148 22 176 176 0 strelka-varscan-mutect ADAM19,missense_variant,p.Gly157Cys,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Gly157Cys,ENST00000517905,;ADAM19,missense_variant,p.Gly157Cys,ENST00000517951,; A ENST00000257527 Transcript missense_variant 548/6481 469/2757 157/918 G/C Ggc/Tgc 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 deleterious(0.02) 6/23 hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905,Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 157519970 157519970 C A 1 0 0 0 0 1 0 0 0 284 623 22 2 2 ADAM19 5 157519970 Missense_Mutation SNP C C3N-01071_T 357437 157519970 24018289 111 21669 FAM196B 0 . GRCh38 5 169882838 169882838 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1061G>T p.Cys354Phe p.C354F ENST00000377365 2/4 93 87 6 122 122 0 strelka-varscan FAM196B,missense_variant,p.Cys354Phe,ENST00000377365,NM_001129891.1;DOCK2,intron_variant,,ENST00000256935,NM_004946.2;DOCK2,intron_variant,,ENST00000520908,;DOCK2,intron_variant,,ENST00000519628,;DOCK2,intron_variant,,ENST00000523351,;FAM196B,downstream_gene_variant,,ENST00000523970,;DOCK2,intron_variant,,ENST00000524185,; A ENST00000377365 Transcript missense_variant 2443/2999 1061/1608 354/535 C/F tGt/tTt 1 -1 FAM196B HGNC HGNC:37271 protein_coding YES CCDS47336.1 ENSP00000366582 A6NMK8 UPI0000480500 NM_001129891.1 deleterious(0) 2/4 Pfam_domain:PF15265,hmmpanther:PTHR28682,hmmpanther:PTHR28682:SF2 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 169882838 169882838 C A 1 0 0 0 0 1 0 0 0 5374 478 17 2 2 FAM196B 5 169882838 Missense_Mutation SNP C C3N-01071_T 12362868 169882838 11655421 112 21670 UIMC1 0 . GRCh38 5 176943458 176943458 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1474G>T p.Val492Leu p.V492L ENST00000377227 10/15 126 114 12 155 155 0 strelka-varscan UIMC1,missense_variant,p.Val492Leu,ENST00000377227,NM_016290.4;UIMC1,missense_variant,p.Val492Leu,ENST00000511320,NM_001199297.1,NM_001199298.1;UIMC1,missense_variant,p.Val326Leu,ENST00000506128,;UIMC1,missense_variant,p.Val122Leu,ENST00000510698,;UIMC1,non_coding_transcript_exon_variant,,ENST00000503273,;UIMC1,3_prime_UTR_variant,,ENST00000512031,; A ENST00000377227 Transcript missense_variant 1607/2570 1474/2160 492/719 V/L Gta/Tta 1 -1 UIMC1 HGNC HGNC:30298 protein_coding YES CCDS4408.1 ENSP00000366434 Q96RL1 A0A024R7R0 UPI00001A9954 NM_016290.4 tolerated(0.15) 10/15 hmmpanther:PTHR15932,hmmpanther:PTHR15932:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 176943458 176943458 C A 1 0 0 0 0 1 0 0 0 17495 565 20 2 2 UIMC1 5 176943458 Missense_Mutation SNP C C3N-01071_T 7060620 176943458 4594801 113 21671 FOXF2 0 . GRCh38 6 1390177 1390177 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.230G>A p.Gly77Asp p.G77D ENST00000259806 1/2 135 106 29 143 143 0 strelka-varscan-mutect FOXF2,missense_variant,p.Gly77Asp,ENST00000259806,NM_001452.1;MIR6720,downstream_gene_variant,,ENST00000611664,; A ENST00000259806 Transcript missense_variant 344/2187 230/1335 77/444 G/D gGc/gAc 1 1 FOXF2 HGNC HGNC:3810 protein_coding YES CCDS4472.1 ENSP00000259806 Q12947 UPI000012ADD6 NM_001452.1 tolerated_low_confidence(0.13) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF224 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999917 1 1 1 0 A 3 1 71 1390177 1390177 G A 1 0 0 0 0 1 0 0 0 5868 1203 42 3 3 FOXF2 6 1390177 Missense_Mutation SNP G C3N-01071_T 1390177 169415802 114 21672 SLC35B3 0 . GRCh38 6 8413701 8413701 + Splice_Site SNP T T A novel C3N-01071_T C3N-01071_N T T c.1056-2A>T p.X352_splice ENST00000379660 83 76 7 93 93 0 strelka-varscan-mutect SLC35B3,splice_acceptor_variant,,ENST00000379660,NM_015948.4,NM_001142541.2; A ENST00000379660 Transcript splice_acceptor_variant -/2137 1056/1206 352/401 1 -1 SLC35B3 HGNC HGNC:21601 protein_coding YES CCDS4508.1 ENSP00000368981 Q9H1N7 A0A024R008 UPI0000071D1B NM_015948.4,NM_001142541.2 10/10 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -14.80903 0.9999936 1 1 1 0 A 5 1 71 8413701 8413701 T A 1 0 0 0 0 0 0 1 0 14847 1536 53 4 4 SLC35B3 6 8413701 Splice_Site SNP T C3N-01071_T 7023524 8413701 162392278 115 21673 TMEM14B 0 . GRCh38 6 10755165 10755165 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.226G>T p.Gly76Cys p.G76C ENST00000467317 5/6 176 159 17 158 158 0 varscan-mutect TMEM14B,missense_variant,p.Gly76Cys,ENST00000467317,NM_001286488.1;TMEM14B,missense_variant,p.Gly42Cys,ENST00000481240,NM_001286489.1;TMEM14B,missense_variant,p.Gly76Cys,ENST00000475942,;TMEM14B,missense_variant,p.Gly76Cys,ENST00000379542,NM_030969.4;TMEM14B,missense_variant,p.Gly65Cys,ENST00000612333,NM_001286484.1;TMEM14B,missense_variant,p.Gly42Cys,ENST00000379530,NM_001127711.2;TMEM14B,missense_variant,p.Trp16Leu,ENST00000473276,;TMEM14B,missense_variant,p.Gly42Cys,ENST00000461342,;RNA5SP203,upstream_gene_variant,,ENST00000410451,;TMEM14B,non_coding_transcript_exon_variant,,ENST00000491103,;TMEM14B,non_coding_transcript_exon_variant,,ENST00000486421,;TMEM14B,non_coding_transcript_exon_variant,,ENST00000480194,;TMEM14B,missense_variant,p.Gly31Cys,ENST00000467229,;TMEM14B,intron_variant,,ENST00000463448,;RP11-637O19.3,intron_variant,,ENST00000480294,;TMEM14B,intron_variant,,ENST00000473166,;TMEM14B,intron_variant,,ENST00000460341,;TMEM14B,intron_variant,,ENST00000473807,;TMEM14B,intron_variant,,ENST00000463100,;TMEM14B,intron_variant,,ENST00000478732,; T ENST00000467317 Transcript missense_variant 321/1224 226/456 76/151 G/C Ggt/Tgt 1 1 TMEM14B HGNC HGNC:21384 protein_coding YES CCDS75396.1 ENSP00000420658 C9JCY4 UPI0001B79353 NM_001286488.1 deleterious(0) 5/6 hmmpanther:PTHR12668,hmmpanther:PTHR12668:SF4,Pfam_domain:PF03647,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs1353311216 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 10755165 10755165 G T 1 0 0 0 0 1 0 0 0 16507 1357 47 2 2 TMEM14B 6 10755165 Missense_Mutation SNP G C3N-01071_T 2341464 10755165 160050814 116 21674 NRSN1 0 . GRCh38 6 24145944 24145944 + Nonstop_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.586T>C p.Ter196ArgextTer16 p.*196Rext*16 ENST00000378478 4/4 68 63 5 81 81 0 varscan-mutect NRSN1,stop_lost,p.Ter196ArgextTer16,ENST00000378478,NM_080723.4;NRSN1,stop_lost,p.Ter196ArgextTer16,ENST00000378491,;NRSN1,downstream_gene_variant,,ENST00000378475,;NRSN1,downstream_gene_variant,,ENST00000378477,;NRSN1,intron_variant,,ENST00000468195,; C ENST00000378478 Transcript stop_lost 823/2408 586/588 196/195 */R Tga/Cga 1 1 NRSN1 HGNC HGNC:17881 protein_coding YES CCDS4549.1 ENSP00000367739 Q8IZ57 UPI000003E7D6 NM_080723.4 4/4 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -11.42183 0.999998 1 1 1 0 C 4 2 71 24145944 24145944 T C 1 0 0 0 0 0 0 0 0 10721 1593 55 5 5 NRSN1 6 24145944 Nonstop_Mutation SNP T C3N-01071_T 13390779 24145944 146660035 117 21675 DPCR1 0 . GRCh38 6 30951441 30951441 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.2977A>G p.Asn993Asp p.N993D ENST00000462446 2/3 338 269 69 317 317 0 strelka-varscan DPCR1,missense_variant,p.Asn1060Asp,ENST00000636043,;DPCR1,missense_variant,p.Asn993Asp,ENST00000462446,NM_080870.3;DPCR1,intron_variant,,ENST00000304311,;SFTA2,intron_variant,,ENST00000634371,;HCG21,intron_variant,,ENST00000419481,; G ENST00000462446 Transcript missense_variant 3005/5314 2977/4182 993/1393 N/D Aac/Gac 1 1 DPCR1 HGNC HGNC:21666 protein_coding YES CCDS4692.2 ENSP00000417182 E9PEI6 UPI0000596C17 NM_080870.3 deleterious(0.04) 2/3 hmmpanther:PTHR22094,hmmpanther:PTHR22094:SF0,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 30951441 30951441 A G 1 0 0 0 0 1 0 0 0 4526 246 9 5 5 DPCR1 6 30951441 Missense_Mutation SNP A C3N-01071_T 6805497 30951441 139854538 118 21676 SLC44A4 0 . GRCh38 6 31870862 31870862 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.887C>A p.Thr296Asn p.T296N ENST00000229729 10/21 582 469 113 462 462 0 strelka-varscan SLC44A4,missense_variant,p.Thr220Asn,ENST00000544672,NM_001178045.1;SLC44A4,missense_variant,p.Thr296Asn,ENST00000229729,NM_025257.2;SLC44A4,missense_variant,p.Thr254Asn,ENST00000375562,NM_001178044.1;SLC44A4,intron_variant,,ENST00000414427,;SLC44A4,downstream_gene_variant,,ENST00000465707,;SLC44A4,downstream_gene_variant,,ENST00000462671,;SLC44A4,non_coding_transcript_exon_variant,,ENST00000479777,;SLC44A4,non_coding_transcript_exon_variant,,ENST00000475563,; T ENST00000229729 Transcript missense_variant 908/2589 887/2133 296/710 T/N aCc/aAc 1 -1 SLC44A4 HGNC HGNC:13941 protein_coding YES CCDS4724.2 ENSP00000229729 Q53GD3 A0A140VJH4 UPI00004702CE NM_025257.2 tolerated(0.07) 10/21 hmmpanther:PTHR12385,hmmpanther:PTHR12385:SF37 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 31870862 31870862 G T 1 0 0 0 0 1 0 0 0 14915 1261 44 2 2 SLC44A4 6 31870862 Missense_Mutation SNP G C3N-01071_T 919421 31870862 138935117 119 21677 GLYATL3 0 . GRCh38 6 49521671 49521671 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.340T>A p.Ser114Thr p.S114T ENST00000371197 5/6 98 85 13 84 84 0 strelka-varscan GLYATL3,missense_variant,p.Ser114Thr,ENST00000371197,NM_001010904.1;GLYATL3,missense_variant,p.Ser114Thr,ENST00000545705,; A ENST00000371197 Transcript missense_variant 453/1113 340/867 114/288 S/T Tcc/Acc 1 1 GLYATL3 HGNC HGNC:21349 protein_coding YES CCDS47440.1 ENSP00000360240 Q5SZD4 UPI000023780B NM_001010904.1 tolerated(0.14) 5/6 Pfam_domain:PF06021,hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF6,Superfamily_domains:SSF55729 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 49521671 49521671 T A 1 0 0 0 0 1 0 0 0 6360 1783 62 4 4 GLYATL3 6 49521671 Missense_Mutation SNP T C3N-01071_T 17650809 49521671 121284308 120 21678 GFRAL 0 . GRCh38 6 55351482 55351482 + Missense_Mutation SNP G G T C3N-01071_T C3N-01071_N G G c.600G>T p.Gln200His p.Q200H ENST00000340465 5/9 240 227 13 234 234 0 strelka-varscan GFRAL,missense_variant,p.Gln200His,ENST00000340465,NM_207410.2; T ENST00000340465 Transcript missense_variant 686/1911 600/1185 200/394 Q/H caG/caT COSM742465 1 1 GFRAL HGNC HGNC:32789 protein_coding YES CCDS4957.1 ENSP00000343636 Q6UXV0 UPI000023780D NM_207410.2 deleterious(0) 5/9 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF1,Pfam_domain:PF02351,SMART_domains:SM00907,Superfamily_domains:0042655 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 55351482 55351482 G T 1 0 0 0 0 1 0 0 0 6225 1020 36 2 2 GFRAL 6 55351482 Missense_Mutation SNP G C3N-01071_T 5829811 55351482 115454497 121 21679 PHF3 0 . GRCh38 6 63706090 63706090 + Silent SNP A A T novel C3N-01071_T C3N-01071_N A A c.3429A>T p.= p.V1143V ENST00000262043 12/16 166 142 24 130 130 0 strelka-varscan PHF3,synonymous_variant,p.=,ENST00000262043,NM_001290259.1;PHF3,synonymous_variant,p.=,ENST00000393387,NM_015153.3;PHF3,synonymous_variant,p.=,ENST00000506783,;PHF3,synonymous_variant,p.=,ENST00000515594,;PHF3,upstream_gene_variant,,ENST00000505138,;PHF3,non_coding_transcript_exon_variant,,ENST00000503248,;PHF3,3_prime_UTR_variant,,ENST00000509876,; T ENST00000262043 Transcript synonymous_variant 3769/8233 3429/6120 1143/2039 V gtA/gtT 1 1 PHF3 HGNC HGNC:8921 protein_coding YES CCDS4966.1 ENSP00000262043 Q92576 UPI000007154D NM_001290259.1 12/16 Low_complexity_(Seg):seg,hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF10 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 63706090 63706090 A T 1 0 0 0 0 0 0 0 1 11923 407 15 4 4 PHF3 6 63706090 Silent SNP A C3N-01071_T 8354608 63706090 107099889 122 21680 ASCC3 0 . GRCh38 6 100516258 100516258 + Silent SNP C C A C3N-01071_T C3N-01071_N C C c.5997G>T p.= p.L1999L ENST00000369162 39/42 406 375 31 432 431 1 strelka-varscan ASCC3,synonymous_variant,p.=,ENST00000369162,NM_006828.3; A ENST00000369162 Transcript synonymous_variant 6342/8146 5997/6609 1999/2202 L ctG/ctT COSM3947837 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 39/42 hmmpanther:PTHR24075,hmmpanther:PTHR24075:SF0,Pfam_domain:PF02889,PIRSF_domain:PIRSF039073,SMART_domains:SM00973,Superfamily_domains:SSF158702 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 100516258 100516258 C A 1 0 0 0 0 0 0 0 1 1175 813 29 2 2 ASCC3 6 100516258 Silent SNP C C3N-01071_T 36810168 100516258 70289721 123 21681 CDC40 0 . GRCh38 6 110209082 110209082 + Splice_Site SNP A A T novel C3N-01071_T C3N-01071_N A A c.491-2A>T p.X164_splice ENST00000368932 125 116 9 108 107 1 strelka-varscan-mutect CDC40,splice_acceptor_variant,,ENST00000368932,;CDC40,splice_acceptor_variant,,ENST00000307731,NM_015891.2;CDC40,splice_acceptor_variant,,ENST00000368930,;CDC40,splice_acceptor_variant,,ENST00000453107,;CDC40,splice_acceptor_variant,,ENST00000606893,;CDC40,splice_acceptor_variant,,ENST00000431461,; T ENST00000368932 Transcript splice_acceptor_variant -/3933 491/1740 164/579 1 1 CDC40 HGNC HGNC:17350 protein_coding YES CCDS5081.1 ENSP00000357928 O60508 UPI0000132145 5/15 HIGH 1 SNV 5 1 PASS . . 0 199 11 0 0 0 0 0 -17.04136 0.9998256 1 1 1 0 T 5 4 71 110209082 110209082 A T 1 0 0 0 0 0 0 1 0 2773 434 15 4 4 CDC40 6 110209082 Splice_Site SNP A C3N-01071_T 9692824 110209082 60596897 124 21682 LAMA4 0 . GRCh38 6 112144924 112144924 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.2363T>C p.Leu788Pro p.L788P ENST00000230538 19/39 471 409 62 398 398 0 strelka-varscan-mutect LAMA4,missense_variant,p.Leu788Pro,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Leu781Pro,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Leu781Pro,ENST00000389463,;LAMA4,missense_variant,p.Leu781Pro,ENST00000424408,;LAMA4,3_prime_UTR_variant,,ENST00000523765,; G ENST00000230538 Transcript missense_variant 2761/6547 2363/5472 788/1823 L/P cTg/cCg 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0) 19/39 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,Pfam_domain:PF06009 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 112144924 112144924 A G 1 0 0 0 0 1 0 0 0 8512 188 7 5 5 LAMA4 6 112144924 Missense_Mutation SNP A C3N-01071_T 1935842 112144924 58661055 125 21683 RFX6 0 . GRCh38 6 116894019 116894019 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.599G>A p.Ser200Asn p.S200N ENST00000332958 5/19 323 276 47 369 369 0 strelka-varscan-mutect RFX6,missense_variant,p.Ser200Asn,ENST00000332958,NM_173560.3;RFX6,non_coding_transcript_exon_variant,,ENST00000471966,;RFX6,non_coding_transcript_exon_variant,,ENST00000487683,; A ENST00000332958 Transcript missense_variant 615/3460 599/2787 200/928 S/N aGc/aAc 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 tolerated(0.05) 5/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 116894019 116894019 G A 1 0 0 0 0 1 0 0 0 13441 971 34 3 3 RFX6 6 116894019 Missense_Mutation SNP G C3N-01071_T 4749095 116894019 53911960 126 21684 ROS1 0 . GRCh38 6 117394226 117394226 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1100G>T p.Gly367Val p.G367V ENST00000368508 10/43 112 104 8 153 153 0 strelka-mutect ROS1,missense_variant,p.Gly367Val,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Gly376Val,ENST00000368507,;RP1-179P9.3,intron_variant,,ENST00000467125,; A ENST00000368508 Transcript missense_variant 1299/7435 1100/7044 367/2347 G/V gGa/gTa 1 -1 ROS1 HGNC HGNC:10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 tolerated(0.11) 10/43 Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.07309 0.9999997 1 1 1 0 A 3 1 71 117394226 117394226 C A 1 0 0 0 0 1 0 0 0 13708 855 30 2 2 ROS1 6 117394226 Missense_Mutation SNP C C3N-01071_T 500207 117394226 53411753 127 21685 TRDN 0 . GRCh38 6 123218625 123218625 + Silent SNP T T G novel C3N-01071_T C3N-01071_N T T c.2166A>C p.= p.P722P ENST00000334268 41/41 120 102 18 142 142 0 strelka-varscan-mutect TRDN,synonymous_variant,p.=,ENST00000334268,NM_006073.3; G ENST00000334268 Transcript synonymous_variant 2484/4770 2166/2190 722/729 P ccA/ccC 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 41/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 123218625 123218625 T G 1 0 0 0 0 0 0 0 1 16957 1567 55 5 5 TRDN 6 123218625 Silent SNP T C3N-01071_T 5824399 123218625 47587354 128 21686 VNN3 0 . GRCh38 6 132734656 132734656 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.37T>A p.Phe13Ile p.F13I ENST00000367927 1/7 165 148 17 127 127 0 strelka-mutect VNN3,missense_variant,p.Phe13Ile,ENST00000425515,;VNN3,missense_variant,p.Phe13Ile,ENST00000367927,NM_001291703.1,NM_001291702.1;VNN3,missense_variant,p.Phe13Ile,ENST00000509351,;VNN3,missense_variant,p.Phe13Ile,ENST00000392393,;VNN3,missense_variant,p.Phe13Ile,ENST00000519686,;VNN3,missense_variant,p.Phe13Ile,ENST00000414302,;VNN3,missense_variant,p.Phe13Ile,ENST00000275223,;VNN3,missense_variant,p.Phe13Ile,ENST00000427187,;VNN3,missense_variant,p.Phe13Ile,ENST00000417437,;VNN3,missense_variant,p.Phe13Ile,ENST00000423615,;VNN3,missense_variant,p.Phe13Ile,ENST00000450865,;VNN3,upstream_gene_variant,,ENST00000544102,;VNN3,upstream_gene_variant,,ENST00000580813,;VNN3,non_coding_transcript_exon_variant,,ENST00000448644,; T ENST00000367927 Transcript missense_variant 110/1717 37/825 13/274 F/I Ttt/Att 1 -1 VNN3 HGNC HGNC:16431 protein_coding YES ENSP00000438024 Q9NY84 UPI0000072390 NM_001291703.1,NM_001291702.1 deleterious(0.04) 1/7 hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF4,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 132734656 132734656 A T 1 0 0 0 0 1 0 0 0 17731 14 1 4 4 VNN3 6 132734656 Missense_Mutation SNP A C3N-01071_T 9516031 132734656 38071323 129 21687 GRM1 0 . GRCh38 6 146399509 146399509 + Missense_Mutation SNP A A G C3N-01071_T C3N-01071_N A A c.2470A>G p.Thr824Ala p.T824A ENST00000361719 8/9 618 574 44 503 503 0 strelka-varscan-mutect GRM1,missense_variant,p.Thr824Ala,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,missense_variant,p.Thr824Ala,ENST00000361719,;GRM1,missense_variant,p.Thr824Ala,ENST00000282753,NM_001278064.1;GRM1,missense_variant,p.Thr824Ala,ENST00000355289,NM_001278067.1;GRM1,missense_variant,p.Thr824Ala,ENST00000507907,; G ENST00000361719 Transcript missense_variant 2837/6754 2470/3585 824/1194 T/A Aca/Gca COSM3017890,COSM3017891 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD deleterious(0.03) 8/9 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Pfam_domain:PF00003,Prints_domain:PR00593 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 146399509 146399509 A G 1 0 0 0 0 1 0 0 0 6678 43 2 5 5 GRM1 6 146399509 Missense_Mutation SNP A C3N-01071_T 13664853 146399509 24406470 130 21688 ARID1B 0 . GRCh38 6 157148908 157148908 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.2836G>T p.Ala946Ser p.A946S ENST00000346085 9/20 196 177 19 206 206 0 strelka-varscan-mutect ARID1B,missense_variant,p.Ala946Ser,ENST00000346085,NM_020732.3;ARID1B,missense_variant,p.Ala933Ser,ENST00000636930,;ARID1B,missense_variant,p.Ala933Ser,ENST00000350026,NM_017519.2;ARID1B,missense_variant,p.Ala402Ser,ENST00000414678,;ARID1B,missense_variant,p.Ala183Ser,ENST00000637904,;ARID1B,missense_variant,p.Ala123Ser,ENST00000635849,;ARID1B,missense_variant,p.Ala96Ser,ENST00000637015,;ARID1B,missense_variant,p.Ala183Ser,ENST00000637810,;ARID1B,missense_variant,p.Ala1Ser,ENST00000635957,;ARID1B,missense_variant,p.Ala354Ser,ENST00000319584,;ARID1B,upstream_gene_variant,,ENST00000400790,;ARID1B,missense_variant,p.Ala31Ser,ENST00000637568,;ARID1B,non_coding_transcript_exon_variant,,ENST00000452544,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636426,; T ENST00000346085 Transcript missense_variant 3392/10194 2836/6750 946/2249 A/S Gcc/Tcc 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 tolerated_low_confidence(0.07) 9/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999837 1 1 1 0 T 3 4 71 157148908 157148908 G T 1 0 0 0 0 1 0 0 0 1050 971 34 2 2 ARID1B 6 157148908 Missense_Mutation SNP G C3N-01071_T 10749399 157148908 13657071 131 21689 FNDC1 0 . GRCh38 6 159234367 159234367 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.3855C>T p.= p.A1285A ENST00000297267 11/23 380 350 30 456 456 0 strelka-varscan-mutect FNDC1,synonymous_variant,p.=,ENST00000297267,NM_032532.2;FNDC1,synonymous_variant,p.=,ENST00000329629,; T ENST00000297267 Transcript synonymous_variant 4055/6552 3855/5685 1285/1894 A gcC/gcT 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 11/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 159234367 159234367 C T 1 0 0 0 0 0 0 0 1 5824 610 22 3 3 FNDC1 6 159234367 Silent SNP C C3N-01071_T 2085459 159234367 11571612 132 21690 RPS6KA2 0 . GRCh38 6 166412824 166412824 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.2164G>C p.Val722Leu p.V722L ENST00000503859 22/22 203 191 12 180 180 0 strelka-varscan-mutect RPS6KA2,missense_variant,p.Val739Leu,ENST00000510118,NM_001318936.1;RPS6KA2,missense_variant,p.Val714Leu,ENST00000265678,NM_001318938.1,NM_001318937.1,NM_021135.4;RPS6KA2,missense_variant,p.Val722Leu,ENST00000503859,NM_001006932.1;RPS6KA2,missense_variant,p.Val625Leu,ENST00000481261,;RPS6KA2,missense_variant,p.Val625Leu,ENST00000405189,;RPS6KA2,non_coding_transcript_exon_variant,,ENST00000509742,; G ENST00000503859 Transcript missense_variant 2545/4137 2164/2226 722/741 V/L Gtg/Ctg 1 -1 RPS6KA2 HGNC HGNC:10431 protein_coding YES CCDS34570.1 ENSP00000427015 Q15349 UPI000020D48C NM_001006932.1 deleterious(0) 22/22 PIRSF_domain:PIRSF000606,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs890556346 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 166412824 166412824 C G 1 0 0 0 0 1 0 0 0 13906 536 19 4 4 RPS6KA2 6 166412824 Missense_Mutation SNP C C3N-01071_T 7178457 166412824 4393155 133 21691 TCP10 0 . GRCh38 6 167373199 167373199 + Silent SNP G G T rs375831091 C3N-01071_T C3N-01071_N G G c.951C>A p.= p.A317A ENST00000397829 8/8 205 187 18 206 205 1 varscan-mutect TCP10,synonymous_variant,p.=,ENST00000617120,;TCP10,synonymous_variant,p.=,ENST00000397829,NM_004610.3;TCP10,intron_variant,,ENST00000366827,;TCP10,downstream_gene_variant,,ENST00000460930,;TCP10,non_coding_transcript_exon_variant,,ENST00000514083,;TCP10,intron_variant,,ENST00000508373,;TCP10,downstream_gene_variant,,ENST00000463894,;TCP10,downstream_gene_variant,,ENST00000491085,; T ENST00000397829 Transcript synonymous_variant 1119/2141 951/981 317/326 A gcC/gcA rs375831091 1 -1 TCP10 HGNC HGNC:11656 protein_coding YES CCDS43527.1 ENSP00000380929 D1MPS5 UPI0000D820CE NM_004610.3 8/8 LOW 1 SNV 1 1 PASS rs375831091 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 167373199 167373199 G T 1 0 0 0 0 0 0 0 1 16117 1103 39 1 1 TCP10 6 167373199 Silent SNP G C3N-01071_T 960375 167373199 3432780 134 21692 MLLT4 0 . GRCh38 6 167948298 167948298 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.3507G>C p.Gln1169His p.Q1169H ENST00000366806 28/33 105 97 8 81 81 0 strelka-varscan-mutect MLLT4,missense_variant,p.Gln1209His,ENST00000400822,;MLLT4,missense_variant,p.Gln1193His,ENST00000392112,NM_001207008.1;MLLT4,missense_variant,p.Gln1210His,ENST00000392108,NM_001040000.2;MLLT4,missense_variant,p.Gln1169His,ENST00000366806,NM_001291964.1;MLLT4,missense_variant,p.Gln1217His,ENST00000351017,;MLLT4,missense_variant,p.Gln1210His,ENST00000447894,;MLLT4,missense_variant,p.Gln1210His,ENST00000344191,;MLLT4,upstream_gene_variant,,ENST00000507704,;MLLT4,upstream_gene_variant,,ENST00000476946,;MLLT4,downstream_gene_variant,,ENST00000507679,;MLLT4,non_coding_transcript_exon_variant,,ENST00000511637,;MLLT4,non_coding_transcript_exon_variant,,ENST00000366809,;MLLT4,non_coding_transcript_exon_variant,,ENST00000509296,; C ENST00000366806 Transcript missense_variant 3826/5962 3507/5346 1169/1781 Q/H caG/caC 1 1 MLLT4 HGNC HGNC:7137 protein_coding YES CCDS78199.1 ENSP00000355771 A8MQ02 UPI00045D52FC NM_001291964.1 deleterious_low_confidence(0) 28/33 hmmpanther:PTHR10398 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.24161 1 1 1 1 0 C 3 2 71 167948298 167948298 G C 1 0 0 0 0 1 0 0 0 9592 956 33 4 4 MLLT4 6 167948298 Missense_Mutation SNP G C3N-01071_T 575099 167948298 2857681 135 21693 TCTE3 0 . GRCh38 6 169744124 169744124 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.271C>T p.Pro91Ser p.P91S ENST00000366774 2/4 292 269 23 256 255 1 strelka-mutect TCTE3,missense_variant,p.Pro91Ser,ENST00000366774,NM_174910.1; A ENST00000366774 Transcript missense_variant 372/769 271/597 91/198 P/S Cca/Tca 1 -1 TCTE3 HGNC HGNC:11695 protein_coding YES CCDS5310.1 ENSP00000355736 Q8IZS6 UPI0000061E54 NM_174910.1 tolerated(0.12) 2/4 hmmpanther:PTHR21255:SF27,hmmpanther:PTHR21255 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 169744124 169744124 G A 1 0 0 0 0 1 0 0 0 16126 1203 42 3 3 TCTE3 6 169744124 Missense_Mutation SNP G C3N-01071_T 1795826 169744124 1061855 136 21694 SNX10 0 . GRCh38 7 26371848 26371848 + Silent SNP A A C rs182313404 C3N-01071_T C3N-01071_N A A c.339A>C p.= p.S113S ENST00000446848 6/7 246 228 18 228 228 0 strelka-varscan-mutect SNX10,synonymous_variant,p.=,ENST00000446848,NM_001199835.1;SNX10,synonymous_variant,p.=,ENST00000338523,NM_013322.2;SNX10,synonymous_variant,p.=,ENST00000396376,NM_001199837.1,NM_001318199.1;SNX10,synonymous_variant,p.=,ENST00000619420,;SNX10,synonymous_variant,p.=,ENST00000409838,NM_001199838.1;SNX10,synonymous_variant,p.=,ENST00000416246,;SNX10,synonymous_variant,p.=,ENST00000409367,;AC004540.4,downstream_gene_variant,,ENST00000451368,;AC004540.4,downstream_gene_variant,,ENST00000451264,;SNX10,non_coding_transcript_exon_variant,,ENST00000462993,; C ENST00000446848 Transcript synonymous_variant 601/2613 339/606 113/201 S tcA/tcC rs182313404 1 1 SNX10 HGNC HGNC:14974 protein_coding YES CCDS5399.1 ENSP00000395474 Q9Y5X0 A0A024RA70 UPI000003E7DF NM_001199835.1 6/7 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,hmmpanther:PTHR10555,hmmpanther:PTHR10555:SF128,Low_complexity_(Seg):seg,SMART_domains:SM00312,Superfamily_domains:SSF64268 LOW 1 SNV 1 1 PASS rs182313404 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 26371848 26371848 A C 1 0 0 0 0 0 0 0 1 15202 175 7 5 5 SNX10 7 26371848 Silent SNP A C3N-01071_T 26371848 132974125 137 21695 GCK 0 . GRCh38 7 44152399 44152399 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.238C>A p.Leu80Met p.L80M ENST00000345378 3/10 677 535 142 581 581 0 strelka-varscan-mutect GCK,missense_variant,p.Leu79Met,ENST00000403799,NM_000162.3;GCK,missense_variant,p.Leu78Met,ENST00000395796,NM_033508.1;GCK,missense_variant,p.Leu80Met,ENST00000345378,NM_033507.1;GCK,missense_variant,p.Leu78Met,ENST00000616242,;GCK,missense_variant,p.Leu79Met,ENST00000437084,;GCK,downstream_gene_variant,,ENST00000476008,; T ENST00000345378 Transcript missense_variant 400/2421 238/1401 80/466 L/M Ctg/Atg 1 -1 GCK HGNC HGNC:4195 protein_coding YES CCDS5480.1 ENSP00000223366 P35557 UPI000002AB76 NM_033507.1 deleterious(0) 3/10 Gene3D:3.30.420.40,Pfam_domain:PF00349,Prints_domain:PR00475,PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF3,Superfamily_domains:SSF53067 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 44152399 44152399 G T 1 0 0 0 0 1 0 0 0 6163 991 35 2 2 GCK 7 44152399 Missense_Mutation SNP G C3N-01071_T 17780551 44152399 115193574 138 21696 C7orf72 0 . GRCh38 7 50096440 50096440 + Missense_Mutation SNP T T G novel C3N-01071_T C3N-01071_N T T c.355T>G p.Leu119Val p.L119V ENST00000297001 1/9 92 74 18 74 74 0 strelka-varscan-mutect C7orf72,missense_variant,p.Leu119Val,ENST00000297001,NM_001161834.2;ZPBP,intron_variant,,ENST00000450231,;ZPBP,upstream_gene_variant,,ENST00000046087,NM_007009.2;ZPBP,upstream_gene_variant,,ENST00000419417,NM_001159878.1;ZPBP,upstream_gene_variant,,ENST00000413331,; G ENST00000297001 Transcript missense_variant 405/2028 355/1317 119/438 L/V Tta/Gta 1 1 C7orf72 HGNC HGNC:22564 protein_coding YES CCDS47585.1 ENSP00000297001 A4D263 UPI00001D7424 NM_001161834.2 deleterious(0.04) 1/9 hmmpanther:PTHR34759 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 50096440 50096440 T G 1 0 0 0 0 1 0 0 0 2147 1838 64 5 5 C7orf72 7 50096440 Missense_Mutation SNP T C3N-01071_T 5944041 50096440 109249533 139 21697 COBL 0 . GRCh38 7 51029181 51029181 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.2086C>T p.His696Tyr p.H696Y ENST00000395542 11/14 203 185 18 234 234 0 strelka-varscan-mutect COBL,missense_variant,p.His696Tyr,ENST00000395542,NM_001287436.1;COBL,missense_variant,p.His639Tyr,ENST00000265136,NM_015198.3;COBL,missense_variant,p.His524Tyr,ENST00000431948,;COBL,missense_variant,p.His531Tyr,ENST00000445054,;COBL,incomplete_terminal_codon_variant,p.=,ENST00000452534,;COBL,non_coding_transcript_exon_variant,,ENST00000462395,; A ENST00000395542 Transcript missense_variant 2271/5339 2086/3816 696/1271 H/Y Cac/Tac 1 -1 COBL HGNC HGNC:22199 protein_coding YES CCDS75602.1 ENSP00000378912 O75128 UPI0001F992C3 NM_001287436.1 tolerated(1) 11/14 hmmpanther:PTHR21557,hmmpanther:PTHR21557:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 51029181 51029181 G A 1 0 0 0 0 1 0 0 0 3442 1290 45 3 3 COBL 7 51029181 Missense_Mutation SNP G C3N-01071_T 932741 51029181 108316792 140 21698 POM121L12 0 . GRCh38 7 53036199 53036199 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.528G>T p.Glu176Asp p.E176D ENST00000408890 1/1 197 168 29 206 206 0 strelka-varscan-mutect POM121L12,missense_variant,p.Glu176Asp,ENST00000408890,NM_182595.3; T ENST00000408890 Transcript missense_variant 558/1283 528/891 176/296 E/D gaG/gaT 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.06) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 53036199 53036199 G T 1 0 0 0 0 1 0 0 0 12352 933 33 2 2 POM121L12 7 53036199 Missense_Mutation SNP G C3N-01071_T 2007018 53036199 106309774 141 21699 ZNF736 0 . GRCh38 7 64348707 64348707 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.844G>A p.Glu282Lys p.E282K ENST00000423484 4/4 118 110 8 129 129 0 varscan-mutect ZNF736,missense_variant,p.Glu282Lys,ENST00000423484,NM_001170905.2;ZNF736,missense_variant,p.Glu282Lys,ENST00000355095,; A ENST00000423484 Transcript missense_variant 966/7119 844/1284 282/427 E/K Gag/Aag 1 1 ZNF736 HGNC HGNC:32467 protein_coding YES CCDS55114.1 ENSP00000400852 B4DX44 UPI0001662442 NM_001170905.2 tolerated(0.08) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF98,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -11.87056 0.9999996 1 1 1 0 A 3 1 71 64348707 64348707 G A 1 0 0 0 0 1 0 0 0 18707 943 33 3 3 ZNF736 7 64348707 Missense_Mutation SNP G C3N-01071_T 11312508 64348707 94997266 142 21700 CLDN4 0 . GRCh38 7 73831241 73831241 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.40G>T p.Ala14Ser p.A14S ENST00000435050 2/2 50 46 4 36 36 0 strelka-mutect CLDN4,missense_variant,p.Ala14Ser,ENST00000435050,;CLDN4,missense_variant,p.Ala14Ser,ENST00000431918,;CLDN4,missense_variant,p.Ala14Ser,ENST00000340958,NM_001305.4;WBSCR27,downstream_gene_variant,,ENST00000297873,NM_152559.2;CLDN4,downstream_gene_variant,,ENST00000466411,;CLDN4,downstream_gene_variant,,ENST00000476494,;WBSCR27,downstream_gene_variant,,ENST00000458679,; T ENST00000435050 Transcript missense_variant 2720/4163 40/630 14/209 A/S Gcc/Tcc 1 1 CLDN4 HGNC HGNC:2046 protein_coding YES CCDS5560.1 ENSP00000409544 O14493 Q75L80 UPI0000044941 tolerated(0.89) 2/2 Pfam_domain:PF00822,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF112,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS rs1175384945 . 0 203 7 0 0 0 0 0 -10.12287 0.9999983 1 1 1 0 T 3 4 71 73831241 73831241 G T 1 0 0 0 0 1 0 0 0 3253 1203 42 2 2 CLDN4 7 73831241 Missense_Mutation SNP G C3N-01071_T 9482534 73831241 85514732 143 21701 PCLO 0 . GRCh38 7 82965844 82965844 + Missense_Mutation SNP T T C C3N-01071_T C3N-01071_N T T c.3944A>G p.Lys1315Arg p.K1315R ENST00000333891 4/25 141 123 18 163 163 0 strelka-varscan-mutect PCLO,missense_variant,p.Lys1315Arg,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Lys1315Arg,ENST00000423517,NM_014510.2;PCLO,downstream_gene_variant,,ENST00000461143,; C ENST00000333891 Transcript missense_variant 4282/20329 3944/15429 1315/5142 K/R aAa/aGa COSM485630,COSM485631,COSM485632 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.32) 4/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 82965844 82965844 T C 1 0 0 0 0 1 0 0 0 11671 1841 64 5 5 PCLO 7 82965844 Missense_Mutation SNP T C3N-01071_T 9134603 82965844 76380129 144 21702 CALCR 0 . GRCh38 7 93438128 93438128 + Splice_Site SNP T T A novel C3N-01071_T C3N-01071_N T T c.966-2A>T p.X322_splice ENST00000359558 248 213 35 244 244 0 strelka-varscan-mutect CALCR,splice_acceptor_variant,,ENST00000359558,NM_001164737.1;CALCR,splice_acceptor_variant,,ENST00000421592,;CALCR,splice_acceptor_variant,,ENST00000394441,NM_001164738.1;CALCR,splice_acceptor_variant,,ENST00000426151,NM_001742.3;CALCR,splice_acceptor_variant,,ENST00000360249,;CALCR,splice_acceptor_variant,,ENST00000423724,;CALCR,splice_acceptor_variant,,ENST00000415529,; A ENST00000359558 Transcript splice_acceptor_variant -/3696 966/1527 322/508 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 12/15 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -16.04033 0.9965167 1 1 1 0 A 5 1 71 93438128 93438128 T A 1 0 0 0 0 0 0 1 0 2269 1594 55 4 4 CALCR 7 93438128 Splice_Site SNP T C3N-01071_T 10472284 93438128 65907845 145 21703 TAF6 0 . GRCh38 7 100114089 100114089 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.232G>C p.Asp78His p.D78H ENST00000437822 2/15 175 141 34 166 166 0 strelka-varscan-mutect TAF6,missense_variant,p.Asp41His,ENST00000344095,NM_005641.3;TAF6,missense_variant,p.Asp98His,ENST00000472509,;TAF6,missense_variant,p.Asp41His,ENST00000453269,NM_139315.2;TAF6,missense_variant,p.Asp78His,ENST00000437822,NM_001190415.1;TAF6,missense_variant,p.Asp41His,ENST00000452041,;TAF6,missense_variant,p.Asp41His,ENST00000493322,;TAF6,missense_variant,p.Asp41His,ENST00000440225,;TAF6,missense_variant,p.Asp41His,ENST00000523306,;TAF6,missense_variant,p.Asp41His,ENST00000451699,;TAF6,missense_variant,p.Asp41His,ENST00000449571,;TAF6,missense_variant,p.Asp41His,ENST00000452438,;TAF6,missense_variant,p.Asp41His,ENST00000520135,;TAF6,missense_variant,p.Asp41His,ENST00000417349,;AP4M1,downstream_gene_variant,,ENST00000421755,;AP4M1,downstream_gene_variant,,ENST00000450807,;TAF6,downstream_gene_variant,,ENST00000460673,;TAF6,downstream_gene_variant,,ENST00000431404,;RP11-506M12.1,downstream_gene_variant,,ENST00000494221,;TAF6,downstream_gene_variant,,ENST00000497233,;TAF6,missense_variant,p.Asp41His,ENST00000421980,;TAF6,non_coding_transcript_exon_variant,,ENST00000487288,;TAF6,upstream_gene_variant,,ENST00000487115,; G ENST00000437822 Transcript missense_variant 327/2318 232/2145 78/714 D/H Gat/Cat 1 -1 TAF6 HGNC HGNC:11540 protein_coding YES CCDS55135.1 ENSP00000399982 P49848 UPI00017A7AA3 NM_001190415.1 deleterious(0.02) 2/15 Gene3D:1.10.20.10,Pfam_domain:PF02969,hmmpanther:PTHR10221,hmmpanther:PTHR10221:SF12,SMART_domains:SM00803,Superfamily_domains:SSF47113 MODERATE 1 SNV 2 1 PASS rs1455482147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 100114089 100114089 C G 1 0 0 0 0 1 0 0 0 15926 855 30 4 4 TAF6 7 100114089 Missense_Mutation SNP C C3N-01071_T 6675961 100114089 59231884 146 21704 NAT16 0 . GRCh38 7 101172225 101172225 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.964C>A p.Pro322Thr p.P322T ENST00000300303 4/4 159 131 28 258 258 0 strelka-varscan-mutect NAT16,missense_variant,p.Pro322Thr,ENST00000300303,NM_198571.2;NAT16,missense_variant,p.Pro322Thr,ENST00000455377,;NAT16,downstream_gene_variant,,ENST00000443096,;NAT16,downstream_gene_variant,,ENST00000444446,; T ENST00000300303 Transcript missense_variant 1203/2935 964/1110 322/369 P/T Ccg/Acg 1 -1 NAT16 HGNC HGNC:22030 protein_coding YES CCDS5713.1 ENSP00000300303 Q8N8M0 UPI000013E649 NM_198571.2 tolerated(0.19) 4/4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 101172225 101172225 G T 1 0 0 0 0 1 0 0 0 10185 1232 43 2 2 NAT16 7 101172225 Missense_Mutation SNP G C3N-01071_T 1058136 101172225 58173748 147 21705 CDHR3 0 . GRCh38 7 106004668 106004668 + Missense_Mutation SNP T T G novel C3N-01071_T C3N-01071_N T T c.1033T>G p.Cys345Gly p.C345G ENST00000317716 8/19 209 187 22 459 457 2 strelka-varscan-mutect CDHR3,missense_variant,p.Cys345Gly,ENST00000317716,NM_152750.4;CDHR3,missense_variant,p.Cys257Gly,ENST00000478080,NM_001301161.1;CDHR3,missense_variant,p.Cys103Gly,ENST00000466045,;CDHR3,non_coding_transcript_exon_variant,,ENST00000470188,;CDHR3,non_coding_transcript_exon_variant,,ENST00000461766,;CDHR3,3_prime_UTR_variant,,ENST00000496633,;CDHR3,non_coding_transcript_exon_variant,,ENST00000471910,;CDHR3,non_coding_transcript_exon_variant,,ENST00000466351,;CDHR3,downstream_gene_variant,,ENST00000488386,; G ENST00000317716 Transcript missense_variant 1113/3813 1033/2658 345/885 C/G Tgc/Ggc 1 1 CDHR3 HGNC HGNC:26308 protein_coding YES CCDS47684.1 ENSP00000325954 Q6ZTQ4 UPI00001C0C6E NM_152750.4 deleterious(0) 8/19 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF336,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 106004668 106004668 T G 1 0 0 0 0 1 0 0 0 2823 1464 51 5 5 CDHR3 7 106004668 Missense_Mutation SNP T C3N-01071_T 4832443 106004668 53341305 148 21706 ZNF277 0 . GRCh38 7 112318216 112318216 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.500A>T p.Asn167Ile p.N167I ENST00000361822 5/12 274 254 20 221 221 0 strelka-varscan-mutect ZNF277,missense_variant,p.Asn167Ile,ENST00000361822,NM_021994.2;ZNF277,missense_variant,p.Asn167Ile,ENST00000450657,;ZNF277,intron_variant,,ENST00000425229,;ZNF277,3_prime_UTR_variant,,ENST00000361946,;ZNF277,3_prime_UTR_variant,,ENST00000457808,; T ENST00000361822 Transcript missense_variant 629/1849 500/1353 167/450 N/I aAt/aTt 1 1 ZNF277 HGNC HGNC:13070 protein_coding YES CCDS5755.2 ENSP00000354501 Q9NRM2 UPI00000437E2 NM_021994.2 tolerated(0.14) 5/12 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13267,hmmpanther:PTHR13267:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 112318216 112318216 A T 1 0 0 0 0 1 0 0 0 18388 101 4 4 4 ZNF277 7 112318216 Missense_Mutation SNP A C3N-01071_T 6313548 112318216 47027757 149 21707 PPP1R3A 0 . GRCh38 7 113878348 113878348 + Frame_Shift_Del DEL G G - C3N-01071_T C3N-01071_N G G c.2744delC p.Pro915LeufsTer20 p.P915Lfs*20 ENST00000284601 4/4 258 244 14 209 209 0 varindel-pindel PPP1R3A,frameshift_variant,p.Pro915LeufsTer20,ENST00000284601,NM_002711.3;PPP1R3A,downstream_gene_variant,,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; - ENST00000284601 Transcript frameshift_variant 2813/4384 2744/3369 915/1122 P/X cCt/ct COSM3922500,COSM3922501 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 4/4 hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF2 1,1 HIGH 1 deletion 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 71 113878348 113878348 G - 1 0 1 0 1 0 0 0 0 12492 1000 35 0 0 PPP1R3A 7 113878348 Frame_Shift_Del DEL G C3N-01071_T 1560132 113878348 45467625 150 21708 RNF133 0 . GRCh38 7 122698693 122698693 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.226G>T p.Val76Leu p.V76L ENST00000340112 1/1 129 102 27 110 110 0 strelka-varscan-mutect RNF133,missense_variant,p.Val76Leu,ENST00000340112,NM_139175.1;CADPS2,intron_variant,,ENST00000615869,;CADPS2,intron_variant,,ENST00000313070,NM_001167940.1;CADPS2,intron_variant,,ENST00000334010,;CADPS2,intron_variant,,ENST00000412584,NM_001009571.3;CADPS2,intron_variant,,ENST00000449022,NM_017954.10;RNF148,downstream_gene_variant,,ENST00000434824,NM_198085.1;RNF148,downstream_gene_variant,,ENST00000447240,; A ENST00000340112 Transcript missense_variant 464/1445 226/1131 76/376 V/L Gtg/Ttg 1 -1 RNF133 HGNC HGNC:21154 protein_coding YES CCDS5784.1 ENSP00000344489 Q8WVZ7 UPI0000070D9A NM_139175.1 tolerated(0.16) 1/1 hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF38 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 122698693 122698693 C A 1 0 0 0 0 1 0 0 0 13617 565 20 2 2 RNF133 7 122698693 Missense_Mutation SNP C C3N-01071_T 8820345 122698693 36647280 151 21709 ZNF786 0 . GRCh38 7 149071533 149071533 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1239G>T p.Gln413His p.Q413H ENST00000491431 4/4 265 246 19 180 180 0 strelka-varscan-mutect ZNF786,missense_variant,p.Gln327His,ENST00000316286,;ZNF786,missense_variant,p.Gln413His,ENST00000491431,NM_152411.3; A ENST00000491431 Transcript missense_variant 1304/2874 1239/2349 413/782 Q/H caG/caT 1 -1 ZNF786 HGNC HGNC:21806 protein_coding YES CCDS47738.1 ENSP00000417470 Q8N393 UPI000013FD40 NM_152411.3 tolerated(0.1) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF228,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 149071533 149071533 C A 1 0 0 0 0 1 0 0 0 18742 680 24 2 2 ZNF786 7 149071533 Missense_Mutation SNP C C3N-01071_T 26372840 149071533 10274440 152 21710 ACTR3C 0 . GRCh38 7 150293325 150293325 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.140A>T p.His47Leu p.H47L ENST00000252071 3/8 224 187 37 196 196 0 strelka-varscan-mutect ACTR3C,missense_variant,p.His47Leu,ENST00000252071,NM_001164458.1,NM_001164459.1;ACTR3C,missense_variant,p.His146Leu,ENST00000477871,;ACTR3C,missense_variant,p.His47Leu,ENST00000539352,;ACTR3C,missense_variant,p.His47Leu,ENST00000477367,;ACTR3C,intron_variant,,ENST00000478393,; A ENST00000252071 Transcript missense_variant 330/1218 140/633 47/210 H/L cAt/cTt 1 -1 ACTR3C HGNC HGNC:37282 protein_coding YES CCDS47744.1 ENSP00000252071 Q9C0K3 UPI000007168D NM_001164458.1,NM_001164459.1 deleterious(0.01) 3/8 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF170,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 150293325 150293325 T A 1 0 0 0 0 1 0 0 0 257 1464 51 4 4 ACTR3C 7 150293325 Missense_Mutation SNP T C3N-01071_T 1221792 150293325 9052648 153 21711 REPIN1 0 . GRCh38 7 150372598 150372598 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.1528C>T p.His510Tyr p.H510Y ENST00000489432 3/3 127 112 15 124 124 0 strelka-varscan-mutect REPIN1,missense_variant,p.His453Tyr,ENST00000397281,NM_013400.3;REPIN1,missense_variant,p.His453Tyr,ENST00000444957,NM_001099696.2;REPIN1,missense_variant,p.His453Tyr,ENST00000425389,NM_014374.3;REPIN1,missense_variant,p.His510Tyr,ENST00000489432,NM_001099695.1;REPIN1,3_prime_UTR_variant,,ENST00000479668,;ZNF775,intron_variant,,ENST00000478789,;REPIN1,downstream_gene_variant,,ENST00000488943,;REPIN1,downstream_gene_variant,,ENST00000475514,;REPIN1,downstream_gene_variant,,ENST00000482680,;REPIN1,downstream_gene_variant,,ENST00000466559,;REPIN1,downstream_gene_variant,,ENST00000519397,;REPIN1,downstream_gene_variant,,ENST00000518514,;RP4-584D14.5,upstream_gene_variant,,ENST00000488310,;REPIN1,downstream_gene_variant,,ENST00000518462,;REPIN1,downstream_gene_variant,,ENST00000473391,;REPIN1,downstream_gene_variant,,ENST00000469309,;REPIN1,downstream_gene_variant,,ENST00000467980,;REPIN1,downstream_gene_variant,,ENST00000486714,;REPIN1,downstream_gene_variant,,ENST00000495535,;REPIN1,downstream_gene_variant,,ENST00000522266,;REPIN1,downstream_gene_variant,,ENST00000487455,; T ENST00000489432 Transcript missense_variant 1711/2058 1528/1875 510/624 H/Y Cac/Tac 1 1 REPIN1 HGNC HGNC:17922 protein_coding YES CCDS47745.1 ENSP00000417291 Q9BWE0 UPI0001596898 NM_001099695.1 deleterious(0) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24406,hmmpanther:PTHR24406:SF1,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs1198696228 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 150372598 150372598 C T 1 0 0 0 0 1 0 0 0 13397 594 21 3 3 REPIN1 7 150372598 Missense_Mutation SNP C C3N-01071_T 79273 150372598 8973375 154 21712 CSMD1 0 . GRCh38 8 3359271 3359271 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.3188G>T p.Gly1063Val p.G1063V ENST00000520002 22/71 211 180 31 237 237 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly924Val,ENST00000537824,;CSMD1,missense_variant,p.Gly543Val,ENST00000335551,;CSMD1,missense_variant,p.Gly1063Val,ENST00000520002,;CSMD1,missense_variant,p.Gly1063Val,ENST00000602557,;CSMD1,missense_variant,p.Gly1062Val,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly1063Val,ENST00000400186,;CSMD1,missense_variant,p.Gly1063Val,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; A ENST00000520002 Transcript missense_variant 3744/11740 3188/10698 1063/3565 G/V gGt/gTt 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.01) 22/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 3359271 3359271 C A 1 0 0 0 0 1 0 0 0 3745 507 18 2 2 CSMD1 8 3359271 Missense_Mutation SNP C C3N-01071_T 3359271 141779365 155 21713 PRSS55 0 . GRCh38 8 10538517 10538517 + Silent SNP T T G novel C3N-01071_T C3N-01071_N T T c.783T>G p.= p.G261G ENST00000328655 5/5 117 110 7 129 129 0 strelka-varscan-mutect PRSS55,synonymous_variant,p.=,ENST00000328655,NM_198464.3;PRSS51,intron_variant,,ENST00000637190,;PRSS55,intron_variant,,ENST00000522210,NM_001197020.1;PRSS55,intron_variant,,ENST00000518641,;PRSS51,intron_variant,,ENST00000523024,; G ENST00000328655 Transcript synonymous_variant 823/1124 783/1059 261/352 G ggT/ggG 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 5/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF191,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -10.29131 0.9999548 1 1 1 0 G 2 3 71 10538517 10538517 T G 1 0 0 0 0 0 0 0 1 12783 1683 59 5 5 PRSS55 8 10538517 Silent SNP T C3N-01071_T 7179246 10538517 134600119 156 21714 NUGGC 0 . GRCh38 8 28060486 28060486 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.1037G>A p.Cys346Tyr p.C346Y ENST00000413272 8/19 166 150 16 185 185 0 strelka-varscan-mutect NUGGC,missense_variant,p.Cys346Tyr,ENST00000413272,NM_001010906.1; T ENST00000413272 Transcript missense_variant 1180/3887 1037/2391 346/796 C/Y tGt/tAt 1 -1 NUGGC HGNC HGNC:33550 protein_coding YES CCDS47833.1 ENSP00000408697 Q68CJ6 UPI0000237454 NM_001010906.1 deleterious(0.02) 8/19 hmmpanther:PTHR19331,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS rs1190067544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 28060486 28060486 C T 1 0 0 0 0 1 0 0 0 10814 478 17 3 3 NUGGC 8 28060486 Missense_Mutation SNP C C3N-01071_T 17521969 28060486 117078150 157 21715 TEX15 0 . GRCh38 8 30845491 30845491 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.3527C>T p.Ser1176Phe p.S1176F ENST00000256246 1/4 176 161 15 107 107 0 strelka-varscan-mutect TEX15,missense_variant,p.Ser1176Phe,ENST00000256246,NM_031271.3;TEX15,downstream_gene_variant,,ENST00000523186,; A ENST00000256246 Transcript missense_variant 3602/10187 3527/8370 1176/2789 S/F tCc/tTc 1 -1 TEX15 HGNC HGNC:11738 protein_coding YES CCDS6080.1 ENSP00000256246 Q9BXT5 UPI000013CEF9 NM_031271.3 deleterious(0.02) 1/4 hmmpanther:PTHR22380,hmmpanther:PTHR22380:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 30845491 30845491 G A 1 0 0 0 0 1 0 0 0 16201 1174 41 3 3 TEX15 8 30845491 Missense_Mutation SNP G C3N-01071_T 2785005 30845491 114293145 158 21716 NRG1 0 . GRCh38 8 32764215 32764215 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.1751A>G p.Asp584Gly p.D584G ENST00000287842 13/13 256 228 28 294 294 0 strelka-varscan-mutect NRG1,missense_variant,p.Asp576Gly,ENST00000356819,NM_013957.3;NRG1,missense_variant,p.Asp652Gly,ENST00000523534,;NRG1,missense_variant,p.Asp584Gly,ENST00000287842,NM_013956.3;NRG1,missense_variant,p.Asp579Gly,ENST00000405005,NM_013964.3;NRG1,missense_variant,p.Asp529Gly,ENST00000519301,NM_001160001.1;NRG1,3_prime_UTR_variant,,ENST00000539990,NM_001159996.1;NRG1,downstream_gene_variant,,ENST00000523079,NM_001160008.1,NM_001160004.1;NRG1,downstream_gene_variant,,ENST00000521670,NM_013960.3;NRG1,downstream_gene_variant,,ENST00000518104,NM_001159995.1,NM_001159999.1; G ENST00000287842 Transcript missense_variant 1843/2035 1751/1938 584/645 D/G gAt/gGt 1 1 NRG1 HGNC HGNC:7997 protein_coding YES CCDS6083.1 ENSP00000287842 Q02297 UPI000013DED7 NM_013956.3 deleterious(0) 13/13 Low_complexity_(Seg):seg,hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF7,Pfam_domain:PF02158 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 32764215 32764215 A G 1 0 0 0 0 1 0 0 0 10705 333 12 5 5 NRG1 8 32764215 Missense_Mutation SNP A C3N-01071_T 1918724 32764215 112374421 159 21717 ADAM2 0 . GRCh38 8 39821651 39821651 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.279C>A p.His93Gln p.H93Q ENST00000265708 5/21 186 174 12 132 132 0 strelka-varscan-mutect ADAM2,missense_variant,p.His93Gln,ENST00000265708,NM_001464.4;ADAM2,missense_variant,p.His93Gln,ENST00000347580,NM_001278113.1;ADAM2,missense_variant,p.His93Gln,ENST00000622267,;ADAM2,missense_variant,p.His93Gln,ENST00000379853,;ADAM2,missense_variant,p.His93Gln,ENST00000521880,NM_001278114.1;ADAM2,non_coding_transcript_exon_variant,,ENST00000523181,; T ENST00000265708 Transcript missense_variant 383/2672 279/2208 93/735 H/Q caC/caA 1 -1 ADAM2 HGNC HGNC:198 protein_coding YES CCDS34884.1 ENSP00000265708 Q99965 UPI00001254C2 NM_001464.4 deleterious(0.01) 5/21 hmmpanther:PTHR11905:SF108,hmmpanther:PTHR11905,Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 39821651 39821651 G T 1 0 0 0 0 1 0 0 0 285 1020 36 2 2 ADAM2 8 39821651 Missense_Mutation SNP G C3N-01071_T 7057436 39821651 105316985 160 21718 SLCO5A1 0 . GRCh38 8 69761860 69761860 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.923T>C p.Met308Thr p.M308T ENST00000260126 3/10 162 149 13 178 178 0 strelka-varscan-mutect SLCO5A1,missense_variant,p.Met308Thr,ENST00000260126,NM_030958.2;SLCO5A1,missense_variant,p.Met308Thr,ENST00000524945,NM_001146008.1;SLCO5A1,missense_variant,p.Met308Thr,ENST00000530307,NM_001146009.1;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000528658,;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000532388,;SLCO5A1,intron_variant,,ENST00000526750,; G ENST00000260126 Transcript missense_variant 1630/9076 923/2547 308/848 M/T aTg/aCg 1 -1 SLCO5A1 HGNC HGNC:19046 protein_coding YES CCDS6205.1 ENSP00000260126 Q9H2Y9 UPI0000140F53 NM_030958.2 tolerated(0.13) 3/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF91,Pfam_domain:PF03137,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs1450064645 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 69761860 69761860 A G 1 0 0 0 0 1 0 0 0 15018 217 8 5 5 SLCO5A1 8 69761860 Missense_Mutation SNP A C3N-01071_T 29940209 69761860 75376776 161 21719 ZFHX4 0 . GRCh38 8 76854424 76854424 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.7503C>A p.= p.A2501A ENST00000521891 10/11 303 285 18 259 259 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript synonymous_variant 7951/14019 7503/10851 2501/3616 A gcC/gcA 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 PROSITE_patterns:PS00028,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 76854424 76854424 C A 1 0 0 0 0 0 0 0 1 18213 668 24 2 2 ZFHX4 8 76854424 Silent SNP C C3N-01071_T 7092564 76854424 68284212 162 21720 ZFHX4 0 . GRCh38 8 76854947 76854947 + Silent SNP C C A C3N-01071_T C3N-01071_N C C c.8026C>A p.= p.R2676R ENST00000521891 10/11 184 155 29 155 155 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript synonymous_variant 8474/14019 8026/10851 2676/3616 R Cgg/Agg COSM1101789,COSM4742569 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 PROSITE_profiles:PS50157,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355 1,1 LOW 1 SNV 5 1,1 1 PASS rs1260222919 . 0 207 0 3 0 0 0 0 -20 0.9999943 1 1 1 0 A 2 1 71 76854947 76854947 C A 1 0 0 0 0 0 0 0 1 18213 527 19 1 1 ZFHX4 8 76854947 Silent SNP C C3N-01071_T 523 76854947 68283689 163 21721 ZFHX4 0 . GRCh38 8 76864133 76864133 + Missense_Mutation SNP G G T C3N-01071_T C3N-01071_N G G c.10419G>T p.Glu3473Asp p.E3473D ENST00000521891 11/11 272 242 30 275 275 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Glu3473Asp,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Glu3447Asp,ENST00000518282,; T ENST00000521891 Transcript missense_variant 10867/14019 10419/10851 3473/3616 E/D gaG/gaT COSM751677 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0.05) 11/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00451 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 76864133 76864133 G T 1 0 0 0 0 1 0 0 0 18213 933 33 2 2 ZFHX4 8 76864133 Missense_Mutation SNP G C3N-01071_T 9186 76864133 68274503 164 21722 TMEM64 0 . GRCh38 8 90645616 90645616 + Missense_Mutation SNP C C A rs535015087 C3N-01071_T C3N-01071_N C C c.290G>T p.Gly97Val p.G97V ENST00000458549 1/3 208 169 39 147 147 0 strelka-varscan-mutect TMEM64,missense_variant,p.Gly97Val,ENST00000458549,NM_001008495.3;TMEM64,missense_variant,p.Gly97Val,ENST00000418210,NM_001146273.1;TMEM64,intron_variant,,ENST00000519519,;TMEM64,intron_variant,,ENST00000521852,;TMEM64,upstream_gene_variant,,ENST00000422900,;RP11-68L18.1,upstream_gene_variant,,ENST00000501194,;RP11-68L18.1,upstream_gene_variant,,ENST00000519233,;RP11-68L18.1,upstream_gene_variant,,ENST00000522132,; A ENST00000458549 Transcript missense_variant 468/4997 290/1143 97/380 G/V gGc/gTc rs535015087 1 -1 TMEM64 HGNC HGNC:25441 protein_coding YES CCDS34920.2 ENSP00000414786 Q6YI46 UPI0000DBEF28 NM_001008495.3 deleterious_low_confidence(0.01) 1/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs535015087 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 90645616 90645616 C A 1 0 0 0 0 1 0 0 0 16669 739 26 2 2 TMEM64 8 90645616 Missense_Mutation SNP C C3N-01071_T 13781483 90645616 54493020 165 21723 DCSTAMP 0 . GRCh38 8 104354964 104354964 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.1117C>G p.Leu373Val p.L373V ENST00000297581 3/4 332 234 98 233 233 0 strelka-varscan-mutect DCSTAMP,missense_variant,p.Leu373Val,ENST00000297581,NM_030788.3;DCSTAMP,intron_variant,,ENST00000622554,NM_001257317.1;DCSTAMP,intron_variant,,ENST00000517991,;DPYS,intron_variant,,ENST00000521601,;DCSTAMP,intron_variant,,ENST00000518051,;DCSTAMP,upstream_gene_variant,,ENST00000520080,; G ENST00000297581 Transcript missense_variant 1166/1953 1117/1413 373/470 L/V Cta/Gta 1 1 DCSTAMP HGNC HGNC:18549 protein_coding YES CCDS6301.1 ENSP00000297581 Q9H295 UPI000003BCB5 NM_030788.3 tolerated(0.13) 3/4 Pfam_domain:PF07782,hmmpanther:PTHR21041,hmmpanther:PTHR21041:SF2 MODERATE 1 SNV 1 1 PASS rs970571597 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 104354964 104354964 C G 1 0 0 0 0 1 0 0 0 4106 912 32 4 4 DCSTAMP 8 104354964 Missense_Mutation SNP C C3N-01071_T 13709348 104354964 40783672 166 21724 ABRA 0 . GRCh38 8 106761126 106761126 + Missense_Mutation SNP G G T rs747204189 C3N-01071_T C3N-01071_N G G c.1057C>A p.Arg353Ser p.R353S ENST00000311955 2/2 345 286 59 250 250 0 strelka-varscan-mutect ABRA,missense_variant,p.Arg353Ser,ENST00000311955,NM_139166.4; T ENST00000311955 Transcript missense_variant 1112/2755 1057/1146 353/381 R/S Cgt/Agt rs747204189 1 -1 ABRA HGNC HGNC:30655 protein_coding YES CCDS6305.1 ENSP00000311436 Q8N0Z2 UPI000006F0DE NM_139166.4 deleterious(0) 2/2 hmmpanther:PTHR22739,hmmpanther:PTHR22739:SF7,Pfam_domain:PF14705,SMART_domains:SM01283 MODERATE 1 SNV 1 1 PASS rs747204189 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 106761126 106761126 G T 1 0 0 0 0 1 0 0 0 109 1087 38 1 1 ABRA 8 106761126 Missense_Mutation SNP G C3N-01071_T 2406162 106761126 38377510 167 21725 PKHD1L1 0 . GRCh38 8 109412399 109412399 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.2220G>A p.= p.L740L ENST00000378402 20/78 131 116 15 86 86 0 strelka-varscan-mutect PKHD1L1,synonymous_variant,p.=,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript synonymous_variant 2324/13076 2220/12732 740/4243 L ttG/ttA 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 20/78 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 109412399 109412399 G A 1 0 0 0 0 0 0 0 1 12068 1368 48 3 3 PKHD1L1 8 109412399 Silent SNP G C3N-01071_T 2651273 109412399 35726237 168 21726 PKHD1L1 0 . GRCh38 8 109429386 109429386 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.3047C>T p.Thr1016Ile p.T1016I ENST00000378402 26/78 234 210 24 307 307 0 strelka-mutect PKHD1L1,missense_variant,p.Thr1016Ile,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript missense_variant 3151/13076 3047/12732 1016/4243 T/I aCa/aTa 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 tolerated(0.07) 26/78 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 109429386 109429386 C T 1 0 0 0 0 1 0 0 0 12068 478 17 3 3 PKHD1L1 8 109429386 Missense_Mutation SNP C C3N-01071_T 16987 109429386 35709250 169 21727 PKHD1L1 0 . GRCh38 8 109449377 109449377 + Missense_Mutation SNP C C A rs780741007 C3N-01071_T C3N-01071_N C C c.6065C>A p.Thr2022Asn p.T2022N ENST00000378402 40/78 233 205 28 149 149 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Thr2022Asn,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 6169/13076 6065/12732 2022/4243 T/N aCc/aAc rs780741007 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0.04) 40/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,Low_complexity_(Seg):seg,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs780741007 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 109449377 109449377 C A 1 0 0 0 0 1 0 0 0 12068 507 18 2 2 PKHD1L1 8 109449377 Missense_Mutation SNP C C3N-01071_T 19991 109449377 35689259 170 21728 CSMD3 0 . GRCh38 8 112314023 112314023 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.7579T>A p.Ser2527Thr p.S2527T ENST00000297405 49/71 418 335 83 301 301 0 strelka-varscan-mutect CSMD3,missense_variant,p.Ser2527Thr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ser2487Thr,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ser2423Thr,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ser1797Thr,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000492692,; T ENST00000297405 Transcript missense_variant 7824/13212 7579/11124 2527/3707 S/T Tcc/Acc 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.29) 49/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 112314023 112314023 A T 1 0 0 0 0 1 0 0 0 3747 246 9 4 4 CSMD3 8 112314023 Missense_Mutation SNP A C3N-01071_T 2864646 112314023 32824613 171 21729 CSMD3 0 . GRCh38 8 112689910 112689910 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.2113C>G p.Gln705Glu p.Q705E ENST00000297405 14/71 226 180 46 200 200 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gln705Glu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gln665Glu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gln601Glu,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gln45Glu,ENST00000339701,; C ENST00000297405 Transcript missense_variant 2358/13212 2113/11124 705/3707 Q/E Caa/Gaa 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.02) 14/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 112689910 112689910 G C 1 0 0 0 0 1 0 0 0 3747 1299 45 4 4 CSMD3 8 112689910 Missense_Mutation SNP G C3N-01071_T 375887 112689910 32448726 172 21730 TRPS1 0 . GRCh38 8 115619647 115619647 + Missense_Mutation SNP C C T C3N-01071_T C3N-01071_N C C c.451G>A p.Asp151Asn p.D151N ENST00000395715 3/7 237 222 15 174 174 0 strelka-varscan-mutect TRPS1,missense_variant,p.Asp151Asn,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Asp138Asn,ENST00000220888,;TRPS1,missense_variant,p.Asp142Asn,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Asp92Asn,ENST00000519076,;TRPS1,missense_variant,p.Asp138Asn,ENST00000519674,;TRPS1,missense_variant,p.Asp142Asn,ENST00000517323,;TRPS1,downstream_gene_variant,,ENST00000519815,;TRPS1,downstream_gene_variant,,ENST00000395713,;TRPS1,downstream_gene_variant,,ENST00000422939,;TRPS1,downstream_gene_variant,,ENST00000451156,; T ENST00000395715 Transcript missense_variant 1029/9990 451/3885 151/1294 D/N Gat/Aat COSM748535,COSM748536 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 deleterious_low_confidence(0.01) 3/7 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 115619647 115619647 C T 1 0 0 0 0 1 0 0 0 17099 913 32 3 3 TRPS1 8 115619647 Missense_Mutation SNP C C3N-01071_T 2929737 115619647 29518989 173 21731 WDYHV1 0 . GRCh38 8 123430011 123430011 + Missense_Mutation SNP C C G rs200183331 C3N-01071_T C3N-01071_N C C c.212C>G p.Pro71Arg p.P71R ENST00000287387 3/6 211 193 18 195 195 0 strelka-varscan-mutect WDYHV1,missense_variant,p.Pro11Arg,ENST00000523984,NM_001283024.1,NM_001283027.1;WDYHV1,missense_variant,p.Pro71Arg,ENST00000287387,NM_018024.2;WDYHV1,missense_variant,p.Pro71Arg,ENST00000523356,;WDYHV1,missense_variant,p.Pro71Arg,ENST00000522194,;WDYHV1,5_prime_UTR_variant,,ENST00000518125,;WDYHV1,non_coding_transcript_exon_variant,,ENST00000517609,;WDYHV1,non_coding_transcript_exon_variant,,ENST00000523551,;WDYHV1,non_coding_transcript_exon_variant,,ENST00000524254,;WDYHV1,3_prime_UTR_variant,,ENST00000519199,; G ENST00000287387 Transcript missense_variant 337/1349 212/618 71/205 P/R cCt/cGt rs200183331 1 1 WDYHV1 HGNC HGNC:25490 protein_coding YES CCDS6344.1 ENSP00000287387 Q96HA8 UPI0000073310 NM_018024.2 tolerated(0.64) 3/6 Gene3D:3c9qA00,Pfam_domain:PF09764,hmmpanther:PTHR13035,hmmpanther:PTHR13035:SF0 MODERATE 1 SNV 1 1 PASS rs200183331 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 123430011 123430011 C G 1 0 0 0 0 1 0 0 0 17900 681 24 4 4 WDYHV1 8 123430011 Missense_Mutation SNP C C3N-01071_T 7810364 123430011 21708625 174 21732 KCNQ3 0 . GRCh38 8 132184262 132184262 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.583A>T p.Arg195Trp p.R195W ENST00000388996 3/15 650 500 150 534 534 0 strelka-varscan-mutect KCNQ3,missense_variant,p.Arg195Trp,ENST00000388996,NM_004519.3;KCNQ3,missense_variant,p.Arg74Trp,ENST00000621976,;KCNQ3,missense_variant,p.Arg195Trp,ENST00000519445,;KCNQ3,missense_variant,p.Arg75Trp,ENST00000521134,NM_001204824.1;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,; A ENST00000388996 Transcript missense_variant 1004/11441 583/2619 195/872 R/W Agg/Tgg 1 -1 KCNQ3 HGNC HGNC:6297 protein_coding YES CCDS34943.1 ENSP00000373648 O43525 UPI00001279F0 NM_004519.3 deleterious(0) 3/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR01459,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF5,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 132184262 132184262 T A 1 0 0 0 0 1 0 0 0 8000 1579 55 4 4 KCNQ3 8 132184262 Missense_Mutation SNP T C3N-01071_T 8754251 132184262 12954374 175 21733 TMEM71 0 . GRCh38 8 132757241 132757241 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.94T>C p.Phe32Leu p.F32L ENST00000356838 3/10 242 228 14 223 223 0 strelka-varscan-mutect TMEM71,missense_variant,p.Phe32Leu,ENST00000356838,NM_144649.2;TMEM71,missense_variant,p.Phe32Leu,ENST00000523829,;TMEM71,missense_variant,p.Phe32Leu,ENST00000377901,NM_001145153.1;TMEM71,missense_variant,p.Phe32Leu,ENST00000519187,;TMEM71,missense_variant,p.Phe32Leu,ENST00000519304,;TMEM71,5_prime_UTR_variant,,ENST00000522334,;TMEM71,intron_variant,,ENST00000519016,;TMEM71,non_coding_transcript_exon_variant,,ENST00000517538,;TMEM71,downstream_gene_variant,,ENST00000522594,; G ENST00000356838 Transcript missense_variant 237/1993 94/831 32/276 F/L Ttc/Ctc 1 -1 TMEM71 HGNC HGNC:26572 protein_coding YES CCDS6366.1 ENSP00000349296 Q6P5X7 UPI000013E44E NM_144649.2 tolerated(0.11) 3/10 Pfam_domain:PF15121,hmmpanther:PTHR35255,hmmpanther:PTHR35255:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 132757241 132757241 A G 1 0 0 0 0 1 0 0 0 16675 14 1 5 5 TMEM71 8 132757241 Missense_Mutation SNP A C3N-01071_T 572979 132757241 12381395 176 21734 COL22A1 0 . GRCh38 8 138589387 138589387 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.4747C>T p.Pro1583Ser p.P1583S ENST00000303045 65/65 100 75 25 126 126 0 strelka-varscan-mutect COL22A1,missense_variant,p.Pro1583Ser,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Pro1276Ser,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; A ENST00000303045 Transcript missense_variant 5194/6346 4747/4881 1583/1626 P/S Cct/Tct 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.13) 65/65 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 138589387 138589387 G A 1 0 0 0 0 1 0 0 0 3469 1232 43 3 3 COL22A1 8 138589387 Missense_Mutation SNP G C3N-01071_T 5832146 138589387 6549249 177 21735 WASH1 0 . GRCh38 9 24937 24937 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.63G>A p.= p.Q21Q ENST00000442898 2/11 226 214 12 211 210 1 varscan-mutect WASH1,synonymous_variant,p.=,ENST00000442898,NM_182905.4;MIR1302-9,upstream_gene_variant,,ENST00000422679,; T ENST00000442898 Transcript synonymous_variant 206/1827 63/1398 21/465 Q caG/caA 1 -1 WASH1 HGNC HGNC:24361 protein_coding YES CCDS78375.1 ENSP00000485627 A8K0Z3 UPI0000251DC1 NM_182905.4 2/11 Pfam_domain:PF11945,hmmpanther:PTHR23331,hmmpanther:PTHR23331:SF1 LOW 1 SNV 2 1 PASS . . 57 149 4 0 0 0 0 0 -19.75675 0.9999998 1 1 1 0 T 2 4 71 24937 24937 C T 1 0 0 0 0 0 0 0 1 17815 796 28 3 3 WASH1 9 24937 Silent SNP C C3N-01071_T 24937 138369780 178 21736 LINGO2 0 . GRCh38 9 27950345 27950345 + Silent SNP G G T C3N-01071_T C3N-01071_N G G c.327C>A p.= p.S109S ENST00000379992 6/6 137 128 9 219 219 0 strelka-varscan-mutect LINGO2,synonymous_variant,p.=,ENST00000379992,NM_152570.2,NM_001258282.1;LINGO2,synonymous_variant,p.=,ENST00000308675,;LINGO2,synonymous_variant,p.=,ENST00000613945,; T ENST00000379992 Transcript synonymous_variant 777/3044 327/1821 109/606 S tcC/tcA COSM1489923,COSM1489924 1 -1 LINGO2 HGNC HGNC:21207 protein_coding YES CCDS6524.1 ENSP00000369328 Q7L985 UPI000004C7CD NM_152570.2,NM_001258282.1 6/6 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF38,Low_complexity_(Seg):seg,SMART_domains:SM00369,Superfamily_domains:SSF52058 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -12.70753 0.9999996 1 1 1 0 T 2 4 71 27950345 27950345 G T 1 0 0 0 0 0 0 0 1 8736 1219 43 2 2 LINGO2 9 27950345 Silent SNP G C3N-01071_T 27925408 27950345 110444372 179 21737 GOLM1 0 . GRCh38 9 86033315 86033315 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1096G>T p.Ala366Ser p.A366S ENST00000388712 9/10 234 214 20 232 231 1 strelka-varscan-mutect GOLM1,missense_variant,p.Ala366Ser,ENST00000388712,NM_016548.3;GOLM1,missense_variant,p.Ala366Ser,ENST00000388711,NM_177937.2;GOLM1,downstream_gene_variant,,ENST00000257504,;GOLM1,downstream_gene_variant,,ENST00000464314,; A ENST00000388712 Transcript missense_variant 1265/3046 1096/1206 366/401 A/S Gca/Tca 1 -1 GOLM1 HGNC HGNC:15451 protein_coding YES CCDS35054.1 ENSP00000373364 Q8NBJ4 B3KNK9 UPI000003B10E NM_016548.3 deleterious(0) 9/10 hmmpanther:PTHR15896,hmmpanther:PTHR15896:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 86033315 86033315 C A 1 0 0 0 0 1 0 0 0 6461 797 28 2 2 GOLM1 9 86033315 Missense_Mutation SNP C C3N-01071_T 58082970 86033315 52361402 180 21738 SHC3 0 . GRCh38 9 89046978 89046978 + Nonsense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.979G>T p.Glu327Ter p.E327* ENST00000375835 8/12 81 59 22 84 84 0 strelka-varscan-mutect SHC3,stop_gained,p.Glu327Ter,ENST00000375835,NM_016848.5;SHC3,upstream_gene_variant,,ENST00000375831,; A ENST00000375835 Transcript stop_gained 1286/9768 979/1785 327/594 E/* Gag/Tag 1 -1 SHC3 HGNC HGNC:18181 protein_coding YES CCDS6681.1 ENSP00000364995 Q92529 UPI0000073E1F NM_016848.5 8/12 hmmpanther:PTHR10337:SF4,hmmpanther:PTHR10337 HIGH 1 SNV 1 1 PASS . . 0 202 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 71 89046978 89046978 C A 1 0 0 0 0 0 1 0 0 14531 835 29 2 2 SHC3 9 89046978 Nonsense_Mutation SNP C C3N-01071_T 3013663 89046978 49347739 181 21739 SEMA4D 0 . GRCh38 9 89389018 89389018 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.804G>T p.Gln268His p.Q268H ENST00000450295 10/16 153 137 16 183 183 0 strelka-mutect SEMA4D,missense_variant,p.Gln268His,ENST00000450295,;SEMA4D,missense_variant,p.Gln268His,ENST00000438547,NM_006378.3;SEMA4D,missense_variant,p.Gln268His,ENST00000356444,;SEMA4D,missense_variant,p.Gln268His,ENST00000422704,;SEMA4D,missense_variant,p.Gln268His,ENST00000420987,NM_001142287.1;SEMA4D,missense_variant,p.Gln268His,ENST00000339861,;SEMA4D,missense_variant,p.Gln268His,ENST00000455551,;SEMA4D,downstream_gene_variant,,ENST00000420681,;SEMA4D,missense_variant,p.Gln268His,ENST00000429836,;SEMA4D,missense_variant,p.Gln268His,ENST00000537934,;SEMA4D,upstream_gene_variant,,ENST00000544513,;SEMA4D,upstream_gene_variant,,ENST00000474258,; A ENST00000450295 Transcript missense_variant 1581/5684 804/2589 268/862 Q/H caG/caT 1 -1 SEMA4D HGNC HGNC:10732 protein_coding YES CCDS6685.1 ENSP00000416523 Q92854 UPI0000135A6C deleterious(0) 10/16 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF18,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 89389018 89389018 C A 1 0 0 0 0 1 0 0 0 14310 912 32 2 2 SEMA4D 9 89389018 Missense_Mutation SNP C C3N-01071_T 342040 89389018 49005699 182 21740 GADD45G 0 . GRCh38 9 89605992 89605992 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.393G>A p.= p.K131K ENST00000252506 4/4 250 230 20 196 196 0 strelka-varscan-mutect GADD45G,synonymous_variant,p.=,ENST00000252506,NM_006705.3;GADD45G,synonymous_variant,p.=,ENST00000375769,;GADD45G,non_coding_transcript_exon_variant,,ENST00000494726,; A ENST00000252506 Transcript synonymous_variant 502/1065 393/480 131/159 K aaG/aaA 1 1 GADD45G HGNC HGNC:4097 protein_coding YES CCDS6686.1 ENSP00000252506 O95257 UPI000012AEF1 NM_006705.3 4/4 hmmpanther:PTHR10411,hmmpanther:PTHR10411:SF4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 89605992 89605992 G A 1 0 0 0 0 0 0 0 1 6054 991 35 3 3 GADD45G 9 89605992 Silent SNP G C3N-01071_T 216974 89605992 48788725 183 21741 ZBTB26 0 . GRCh38 9 122919651 122919651 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.284T>G p.Phe95Cys p.F95C ENST00000373656 2/2 181 156 25 179 179 0 strelka-varscan-mutect ZBTB26,missense_variant,p.Phe95Cys,ENST00000373656,NM_001304363.1,NM_020924.3;ZBTB26,missense_variant,p.Phe95Cys,ENST00000373654,NM_001304364.1; C ENST00000373656 Transcript missense_variant 358/4443 284/1326 95/441 F/C tTc/tGc 1 -1 ZBTB26 HGNC HGNC:23383 protein_coding YES CCDS6847.1 ENSP00000362760 Q9HCK0 UPI0000126991 NM_001304363.1,NM_020924.3 deleterious(0) 2/2 PROSITE_profiles:PS50097,hmmpanther:PTHR19303:SF259,hmmpanther:PTHR19303,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 122919651 122919651 A C 1 0 0 0 0 1 0 0 0 18102 246 9 5 5 ZBTB26 9 122919651 Missense_Mutation SNP A C3N-01071_T 33313659 122919651 15475066 184 21742 CRB2 0 . GRCh38 9 123362927 123362927 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.157T>A p.Cys53Ser p.C53S ENST00000373631 2/13 141 124 17 83 82 1 strelka-varscan-mutect CRB2,missense_variant,p.Cys53Ser,ENST00000373631,NM_173689.6;CRB2,missense_variant,p.Cys53Ser,ENST00000359999,; A ENST00000373631 Transcript missense_variant 158/5550 157/3858 53/1285 C/S Tgc/Agc 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 deleterious(0) 2/13 hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999735 1 1 1 0 A 3 1 71 123362927 123362927 T A 1 0 0 0 0 1 0 0 0 3649 1696 59 4 4 CRB2 9 123362927 Missense_Mutation SNP T C3N-01071_T 443276 123362927 15031790 185 21743 LMX1B 0 . GRCh38 9 126690857 126690857 + Missense_Mutation SNP C C A rs772070765 C3N-01071_T C3N-01071_N C C c.348C>A p.Ser116Arg p.S116R ENST00000355497 3/8 292 249 43 238 238 0 strelka-varscan-mutect LMX1B,missense_variant,p.Ser116Arg,ENST00000355497,NM_001174146.1;LMX1B,missense_variant,p.Ser116Arg,ENST00000373474,NM_001174147.1;LMX1B,missense_variant,p.Ser93Arg,ENST00000561065,;LMX1B,missense_variant,p.Ser116Arg,ENST00000526117,NM_002316.3; A ENST00000355497 Transcript missense_variant 355/5809 348/1221 116/406 S/R agC/agA rs772070765 1 1 LMX1B HGNC HGNC:6654 protein_coding YES CCDS55343.1 ENSP00000347684 O60663 UPI0001CE94D0 NM_001174146.1 deleterious(0.05) 3/8 Gene3D:2.10.110.10,Pfam_domain:PF00412,PROSITE_patterns:PS00478,PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF96,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS rs772070765 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 71 126690857 126690857 C A 1 0 0 0 0 1 0 0 0 8789 767 27 1 1 LMX1B 9 126690857 Missense_Mutation SNP C C3N-01071_T 3327930 126690857 11703860 186 21744 C9orf69 0 . GRCh38 9 136116878 136116878 + Missense_Mutation SNP C C A rs756312560 C3N-01071_T C3N-01071_N C C c.23G>T p.Arg8Leu p.R8L ENST00000418388 2/2 174 155 19 160 160 0 strelka-varscan-mutect C9orf69,missense_variant,p.Arg8Leu,ENST00000418388,NM_152833.2;C9orf69,missense_variant,p.Arg8Leu,ENST00000561457,NM_001256526.1;C9orf69,missense_variant,p.Arg8Leu,ENST00000447934,;C9orf69,missense_variant,p.Arg8Leu,ENST00000448040,;C9orf69,missense_variant,p.Arg8Leu,ENST00000557985,; A ENST00000418388 Transcript missense_variant 526/2823 23/420 8/139 R/L cGg/cTg rs756312560 1 -1 C9orf69 HGNC HGNC:31009 protein_coding YES CCDS59155.1 ENSP00000453019 H0YL14 UPI0000210F31 NM_152833.2 tolerated(0.23) 2/2 hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF59 MODERATE 1 SNV 1 1 PASS rs756312560 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 136116878 136116878 C A 1 0 0 0 0 1 0 0 0 2189 652 23 1 1 C9orf69 9 136116878 Missense_Mutation SNP C C3N-01071_T 9426021 136116878 2277839 187 21745 OLAH 0 . GRCh38 10 15064488 15064488 + Missense_Mutation SNP G G T rs77356311 C3N-01071_T C3N-01071_N G G c.547G>T p.Ala183Ser p.A183S ENST00000378217 6/9 93 87 6 113 113 0 strelka-varscan-mutect OLAH,missense_variant,p.Ala183Ser,ENST00000378217,NM_018324.2;OLAH,missense_variant,p.Ala130Ser,ENST00000378228,NM_001039702.2;OLAH,missense_variant,p.Ala130Ser,ENST00000429028,;OLAH,missense_variant,p.Ala130Ser,ENST00000428897,;OLAH,downstream_gene_variant,,ENST00000378225,;OLAH,non_coding_transcript_exon_variant,,ENST00000493912,;OLAH,upstream_gene_variant,,ENST00000485251,; T ENST00000378217 Transcript missense_variant 734/1767 547/957 183/318 A/S Gca/Tca rs77356311 1 1 OLAH HGNC HGNC:25625 protein_coding YES CCDS7106.1 ENSP00000367462 Q9NV23 UPI000007139E NM_018324.2 tolerated(0.08) 6/9 Gene3D:3.40.50.1820,Pfam_domain:PF00975,hmmpanther:PTHR11487,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS rs77356311 . 0 208 2 0 0 0 0 0 -13.04412 1 1 1 1 0 T 3 4 71 15064488 15064488 G T 1 0 0 0 0 1 0 0 0 10926 1319 46 2 2 OLAH 10 15064488 Missense_Mutation SNP G C3N-01071_T 15064488 118732934 188 21746 NRP1 0 . GRCh38 10 33256376 33256376 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.754G>T p.Ala252Ser p.A252S ENST00000265371 6/18 321 287 34 273 273 0 strelka-mutect NRP1,missense_variant,p.Ala252Ser,ENST00000265371,;NRP1,missense_variant,p.Ala252Ser,ENST00000374867,NM_003873.5,NM_001244973.1,NM_001244972.1;NRP1,missense_variant,p.Ala252Ser,ENST00000395995,;NRP1,missense_variant,p.Ala71Ser,ENST00000374875,;NRP1,missense_variant,p.Ala252Ser,ENST00000432372,;NRP1,missense_variant,p.Ala252Ser,ENST00000374823,;NRP1,missense_variant,p.Ala252Ser,ENST00000374816,;NRP1,missense_variant,p.Ala252Ser,ENST00000374822,NM_001024628.2;NRP1,missense_variant,p.Ala252Ser,ENST00000374821,NM_001024629.2;NRP1,missense_variant,p.Ala53Ser,ENST00000455749,; A ENST00000265371 Transcript missense_variant 1280/5882 754/2772 252/923 A/S Gcg/Tcg 1 -1 NRP1 HGNC HGNC:8004 protein_coding YES CCDS7177.1 ENSP00000265371 O14786 UPI000013D60A deleterious(0) 6/18 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF036960,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF654,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS rs1300083541 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 33256376 33256376 C A 1 0 0 0 0 1 0 0 0 10718 768 27 1 1 NRP1 10 33256376 Missense_Mutation SNP C C3N-01071_T 18191888 33256376 100541046 189 21747 CTNNA3 0 . GRCh38 10 66379228 66379228 + Silent SNP C C A rs577330671 C3N-01071_T C3N-01071_N C C c.1656G>T p.= p.T552T ENST00000433211 12/18 444 390 54 506 506 0 strelka-varscan-mutect CTNNA3,synonymous_variant,p.=,ENST00000433211,NM_001127384.2,NM_013266.3; A ENST00000433211 Transcript synonymous_variant 1831/10675 1656/2688 552/895 T acG/acT rs577330671,COSM343878,COSM343879 1 -1 CTNNA3 HGNC HGNC:2511 protein_coding YES CCDS7269.1 ENSP00000389714 Q9UI47 UPI000004A0E6 NM_001127384.2,NM_013266.3 12/18 hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF21,Gene3D:1.20.120.230,Pfam_domain:PF01044,Superfamily_domains:SSF47220 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs577330671 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 66379228 66379228 C A 1 0 0 0 0 0 0 0 1 3823 639 23 1 1 CTNNA3 10 66379228 Silent SNP C C3N-01071_T 33122852 66379228 67418194 190 21748 DLG5 0 . GRCh38 10 77829421 77829421 + Missense_Mutation SNP G G A C3N-01071_T C3N-01071_N G G c.2119C>T p.Arg707Trp p.R707W ENST00000372391 12/32 214 201 13 220 220 0 strelka-varscan-mutect DLG5,missense_variant,p.Arg707Trp,ENST00000372391,NM_004747.3;DLG5,missense_variant,p.Arg8Trp,ENST00000424842,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;DLG5,upstream_gene_variant,,ENST00000466198,; A ENST00000372391 Transcript missense_variant 2125/7415 2119/5760 707/1919 R/W Cgg/Tgg COSM3686882 1 -1 DLG5 HGNC HGNC:2904 protein_coding YES CCDS7353.2 ENSP00000361467 Q8TDM6 UPI0000470041 NM_004747.3 deleterious(0) 12/32 PROSITE_profiles:PS50106,PROSITE_profiles:PS50106,hmmpanther:PTHR13865:SF31,hmmpanther:PTHR13865,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 1 MODERATE 1 SNV 1 1 1 PASS rs1488016884 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 77829421 77829421 G A 1 0 0 0 0 1 0 0 0 4365 1086 38 1 1 DLG5 10 77829421 Missense_Mutation SNP G C3N-01071_T 11450193 77829421 55968001 191 21749 CPN1 0 . GRCh38 10 100076042 100076042 + Missense_Mutation SNP G G T C3N-01071_T C3N-01071_N G G c.289C>A p.Leu97Met p.L97M ENST00000370418 2/9 463 436 27 384 384 0 strelka-varscan-mutect CPN1,missense_variant,p.Leu97Met,ENST00000370418,NM_001308.2; T ENST00000370418 Transcript missense_variant 541/1863 289/1377 97/458 L/M Ctg/Atg COSM913872 1 -1 CPN1 HGNC HGNC:2312 protein_coding YES CCDS7486.1 ENSP00000359446 P15169 UPI00000012AC NM_001308.2 deleterious(0) 2/9 hmmpanther:PTHR11532:SF7,hmmpanther:PTHR11532,PROSITE_patterns:PS00132,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 100076042 100076042 G T 1 0 0 0 0 1 0 0 0 3604 962 34 2 2 CPN1 10 100076042 Missense_Mutation SNP G C3N-01071_T 22246621 100076042 33721380 192 21750 SORCS3 0 . GRCh38 10 105214479 105214479 + Missense_Mutation SNP C C A C3N-01071_T C3N-01071_N C C c.2413C>A p.Leu805Ile p.L805I ENST00000369701 18/27 159 147 12 267 267 0 strelka-varscan-mutect SORCS3,missense_variant,p.Leu805Ile,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Leu805Ile,ENST00000369699,;SORCS3,downstream_gene_variant,,ENST00000393176,; A ENST00000369701 Transcript missense_variant 2640/5757 2413/3669 805/1222 L/I Cta/Ata COSM1504103,COSM3748492 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0.03) 18/27 Pfam_domain:PF15901,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,SMART_domains:SM00602,Superfamily_domains:SSF49299 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 105214479 105214479 C A 1 0 0 0 0 1 0 0 0 15254 796 28 2 2 SORCS3 10 105214479 Missense_Mutation SNP C C3N-01071_T 5138437 105214479 28582943 193 21751 PDCD4 0 . GRCh38 10 110889563 110889563 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.808G>A p.Gly270Arg p.G270R ENST00000280154 7/12 198 173 25 248 248 0 strelka-varscan-mutect PDCD4,missense_variant,p.Gly259Arg,ENST00000393104,NM_145341.3;PDCD4,missense_variant,p.Gly270Arg,ENST00000280154,NM_014456.4,NM_001199492.1;PDCD4,downstream_gene_variant,,ENST00000444997,;PDCD4,non_coding_transcript_exon_variant,,ENST00000481353,;PDCD4,non_coding_transcript_exon_variant,,ENST00000489049,;PDCD4,non_coding_transcript_exon_variant,,ENST00000483595,;PDCD4,intron_variant,,ENST00000462577,;PDCD4,upstream_gene_variant,,ENST00000498367,;PDCD4,downstream_gene_variant,,ENST00000492932,;PDCD4,downstream_gene_variant,,ENST00000483670,;PDCD4,downstream_gene_variant,,ENST00000467574,; A ENST00000280154 Transcript missense_variant 1082/3602 808/1410 270/469 G/R Gga/Aga 1 1 PDCD4 HGNC HGNC:8763 protein_coding YES CCDS7567.1 ENSP00000280154 Q53EL6 UPI000013FD3F NM_014456.4,NM_001199492.1 deleterious(0.02) 7/12 PROSITE_profiles:PS51366,hmmpanther:PTHR12626:SF3,hmmpanther:PTHR12626,Gene3D:1.25.40.180,Pfam_domain:PF02847,SMART_domains:SM00544,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 110889563 110889563 G A 1 0 0 0 0 1 0 0 0 11709 1349 47 3 3 PDCD4 10 110889563 Missense_Mutation SNP G C3N-01071_T 5675084 110889563 22907859 194 21752 CCDC186 0 . GRCh38 10 114131271 114131271 + Silent SNP G G C novel C3N-01071_T C3N-01071_N G G c.1977C>G p.= p.L659L ENST00000369287 12/16 94 86 8 158 158 0 strelka-mutect CCDC186,synonymous_variant,p.=,ENST00000369287,NM_001321829.1,NM_018017.2;CCDC186,synonymous_variant,p.=,ENST00000428953,;CCDC186,non_coding_transcript_exon_variant,,ENST00000497592,;CCDC186,non_coding_transcript_exon_variant,,ENST00000490661,; C ENST00000369287 Transcript synonymous_variant 2244/7245 1977/2697 659/898 L ctC/ctG 1 -1 CCDC186 HGNC HGNC:24349 protein_coding YES CCDS7587.1 ENSP00000358293 Q7Z3E2 UPI00001D3EF5 NM_001321829.1,NM_018017.2 12/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18911 LOW 1 SNV 1 1 PASS rs1481071537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 114131271 114131271 G C 1 0 0 0 0 0 0 0 1 2502 1045 37 4 4 CCDC186 10 114131271 Silent SNP G C3N-01071_T 3241708 114131271 19666151 195 21753 TACC2 0 . GRCh38 10 122083271 122083271 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.771G>A p.= p.Q257Q ENST00000369005 4/23 175 165 10 172 172 0 strelka-varscan-mutect TACC2,synonymous_variant,p.=,ENST00000369005,NM_206862.3;TACC2,synonymous_variant,p.=,ENST00000334433,;TACC2,synonymous_variant,p.=,ENST00000515273,NM_001291877.1;TACC2,synonymous_variant,p.=,ENST00000453444,;TACC2,synonymous_variant,p.=,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,;TACC2,downstream_gene_variant,,ENST00000498721,; A ENST00000369005 Transcript synonymous_variant 1111/9673 771/8847 257/2948 Q caG/caA 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 4/23 hmmpanther:PTHR13924:SF11,hmmpanther:PTHR13924 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 122083271 122083271 G A 1 0 0 0 0 0 0 0 1 15898 962 34 3 3 TACC2 10 122083271 Silent SNP G C3N-01071_T 7952000 122083271 11714151 196 21754 DMBT1 0 . GRCh38 10 122629891 122629891 + Missense_Mutation SNP C C T rs774605711 C3N-01071_T C3N-01071_N C C c.5333C>T p.Ser1778Phe p.S1778F ENST00000368909 44/53 191 174 17 223 222 1 strelka-varscan-mutect DMBT1,missense_variant,p.Ser1778Phe,ENST00000338354,NM_001320644.1;DMBT1,missense_variant,p.Ser1778Phe,ENST00000368909,NM_001320644.1,NM_007329.2;DMBT1,missense_variant,p.Ser1778Phe,ENST00000619379,NM_001320644.1;DMBT1,missense_variant,p.Ser1768Phe,ENST00000344338,;DMBT1,missense_variant,p.Ser1768Phe,ENST00000368955,NM_017579.2;DMBT1,missense_variant,p.Ser1150Phe,ENST00000330163,;DMBT1,missense_variant,p.Ser1150Phe,ENST00000368956,NM_004406.2;DMBT1,missense_variant,p.Ser498Phe,ENST00000359586,; T ENST00000368909 Transcript missense_variant 5439/7686 5333/7242 1778/2413 S/F tCc/tTc rs774605711 1 1 DMBT1 HGNC HGNC:2926 protein_coding YES CCDS44490.1 ENSP00000357905 Q9UGM3 UPI000047021C NM_001320644.1,NM_007329.2 deleterious(0.03) 44/53 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS rs774605711 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 122629891 122629891 C T 1 0 0 0 0 1 0 0 0 4384 855 30 3 3 DMBT1 10 122629891 Missense_Mutation SNP C C3N-01071_T 546620 122629891 11167531 197 21755 IFITM1 0 . GRCh38 11 314269 314269 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.99G>A p.= p.V33V ENST00000408968 1/2 313 282 31 318 318 0 strelka-varscan-mutect IFITM1,synonymous_variant,p.=,ENST00000408968,NM_003641.3;IFITM1,synonymous_variant,p.=,ENST00000328221,;IFITM1,synonymous_variant,p.=,ENST00000528780,;IFITM2,intron_variant,,ENST00000399815,;IFITM2,downstream_gene_variant,,ENST00000616316,;IFITM2,downstream_gene_variant,,ENST00000399817,NM_006435.2;IFITM2,downstream_gene_variant,,ENST00000602569,;RP11-326C3.11,upstream_gene_variant,,ENST00000602429,;RP11-326C3.11,upstream_gene_variant,,ENST00000602756,;RP11-326C3.7,upstream_gene_variant,,ENST00000526612,;RP11-326C3.11,upstream_gene_variant,,ENST00000508004,;IFITM1,upstream_gene_variant,,ENST00000525554,;IFITM2,downstream_gene_variant,,ENST00000527146,; A ENST00000408968 Transcript synonymous_variant 417/855 99/378 33/125 V gtG/gtA 1 1 IFITM1 HGNC HGNC:5412 protein_coding YES CCDS41584.1 ENSP00000386187 P13164 UPI0000228B1B NM_003641.3 1/2 hmmpanther:PTHR13999,hmmpanther:PTHR13999:SF6 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -10.58074 0.9932552 1 1 1 0 A 2 1 71 314269 314269 G A 1 0 0 0 0 0 0 0 1 7426 1306 46 3 3 IFITM1 11 314269 Silent SNP G C3N-01071_T 314269 134772353 198 21756 MRPL23 0 . GRCh38 11 1956365 1956365 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.407A>T p.Gln136Leu p.Q136L ENST00000397298 5/5 142 131 11 156 156 0 varscan-mutect MRPL23,missense_variant,p.Gln136Leu,ENST00000397298,NM_021134.3;MRPL23,missense_variant,p.Gln136Leu,ENST00000381519,;MRPL23,intron_variant,,ENST00000381514,;MRPL23,intron_variant,,ENST00000397297,;MRPL23,intron_variant,,ENST00000397294,;MRPL23,non_coding_transcript_exon_variant,,ENST00000462288,;MRPL23,downstream_gene_variant,,ENST00000484918,;MRPL23,3_prime_UTR_variant,,ENST00000429295,;MRPL23,downstream_gene_variant,,ENST00000466346,; T ENST00000397298 Transcript missense_variant 492/736 407/462 136/153 Q/L cAg/cTg 1 1 MRPL23 HGNC HGNC:10322 protein_coding YES CCDS31336.1 ENSP00000380466 Q16540 A0A024RCB2 UPI000006EBEF NM_021134.3 tolerated(0.45) 5/5 hmmpanther:PTHR12059:SF5,hmmpanther:PTHR12059 MODERATE 1 SNV 1 1 PASS . . 8 199 2 0 0 0 0 0 -19.96651 1 1 1 1 0 T 3 4 71 1956365 1956365 A T 1 0 0 0 0 1 0 0 0 9764 188 7 4 4 MRPL23 11 1956365 Missense_Mutation SNP A C3N-01071_T 1642096 1956365 133130257 199 21757 76 2 MRPL23 0 . GRCh38 11 1956367 1956367 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.409A>T p.Arg137Trp p.R137W ENST00000397298 5/5 136 125 11 154 153 1 varscan-mutect MRPL23,missense_variant,p.Arg137Trp,ENST00000397298,NM_021134.3;MRPL23,missense_variant,p.Arg137Trp,ENST00000381519,;MRPL23,intron_variant,,ENST00000381514,;MRPL23,intron_variant,,ENST00000397297,;MRPL23,intron_variant,,ENST00000397294,;MRPL23,non_coding_transcript_exon_variant,,ENST00000462288,;MRPL23,downstream_gene_variant,,ENST00000484918,;MRPL23,3_prime_UTR_variant,,ENST00000429295,;MRPL23,downstream_gene_variant,,ENST00000466346,; T ENST00000397298 Transcript missense_variant 494/736 409/462 137/153 R/W Agg/Tgg 1 1 MRPL23 HGNC HGNC:10322 protein_coding YES CCDS31336.1 ENSP00000380466 Q16540 A0A024RCB2 UPI000006EBEF NM_021134.3 deleterious(0.04) 5/5 hmmpanther:PTHR12059:SF5,hmmpanther:PTHR12059 MODERATE 1 SNV 1 1 PASS . . 8 200 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 1956367 1956367 A T 1 0 0 0 0 1 0 0 0 9764 295 11 4 4 MRPL23 11 1956367 Missense_Mutation SNP A C3N-01071_T 2 1956367 133130255 200 21758 76 2 RRM1 0 . GRCh38 11 4122167 4122167 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.1065G>T p.Glu355Asp p.E355D ENST00000300738 11/19 180 152 28 216 216 0 strelka-varscan-mutect RRM1,missense_variant,p.Glu355Asp,ENST00000300738,NM_001033.3;RRM1,missense_variant,p.Glu133Asp,ENST00000534285,;RRM1,non_coding_transcript_exon_variant,,ENST00000528470,;RRM1,non_coding_transcript_exon_variant,,ENST00000526304,;RRM1,3_prime_UTR_variant,,ENST00000532170,;RRM1,3_prime_UTR_variant,,ENST00000533349,NM_001318064.1;RRM1,3_prime_UTR_variant,,ENST00000533495,NM_001318065.1;RRM1,3_prime_UTR_variant,,ENST00000528442,;RRM1,non_coding_transcript_exon_variant,,ENST00000531591,;RRM1,non_coding_transcript_exon_variant,,ENST00000529109,; T ENST00000300738 Transcript missense_variant 1269/3076 1065/2379 355/792 E/D gaG/gaT 1 1 RRM1 HGNC HGNC:10451 protein_coding YES CCDS7750.1 ENSP00000300738 P23921 UPI0000000C7C NM_001033.3 deleterious_low_confidence(0.03) 11/19 hmmpanther:PTHR11573,Pfam_domain:PF02867,TIGRFAM_domain:TIGR02506,Superfamily_domains:SSF51998 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 4122167 4122167 G T 1 0 0 0 0 1 0 0 0 13935 1020 36 2 2 RRM1 11 4122167 Missense_Mutation SNP G C3N-01071_T 2165800 4122167 130964455 201 21759 UBQLNL 0 . GRCh38 11 5516046 5516046 + Missense_Mutation SNP G G T rs764471232 C3N-01071_T C3N-01071_N G G c.396C>A p.Ser132Arg p.S132R ENST00000380184 1/1 132 109 23 134 134 0 strelka-varscan-mutect UBQLNL,missense_variant,p.Ser132Arg,ENST00000380184,NM_145053.4;HBG2,intron_variant,,ENST00000380259,;OLFM5P,downstream_gene_variant,,ENST00000411807,; T ENST00000380184 Transcript missense_variant 660/2313 396/1428 132/475 S/R agC/agA rs764471232 1 -1 UBQLNL HGNC HGNC:28294 protein_coding YES CCDS31385.1 ENSP00000369531 Q8IYU4 UPI000066D8EC NM_145053.4 deleterious(0.01) 1/1 hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF9 MODERATE SNV 1 PASS rs764471232 . 0 207 0 3 0 0 0 0 -20 0.9999953 1 1 1 0 T 3 4 71 5516046 5516046 G T 1 0 0 0 0 1 0 0 0 17424 1310 46 2 2 UBQLNL 11 5516046 Missense_Mutation SNP G C3N-01071_T 1393879 5516046 129570576 202 21760 DNHD1 0 . GRCh38 11 6511417 6511417 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.1380C>T p.= p.S460S ENST00000254579 7/43 109 91 18 99 99 0 strelka-varscan-mutect DNHD1,synonymous_variant,p.=,ENST00000254579,NM_144666.2;DNHD1,synonymous_variant,p.=,ENST00000527990,;DNHD1,synonymous_variant,p.=,ENST00000354685,NM_173589.3;DNHD1,non_coding_transcript_exon_variant,,ENST00000472080,; T ENST00000254579 Transcript synonymous_variant 1944/14862 1380/14262 460/4753 S tcC/tcT 1 1 DNHD1 HGNC HGNC:26532 protein_coding YES CCDS44532.1 ENSP00000254579 Q96M86 UPI0001929529 NM_144666.2 7/43 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF244 LOW 1 SNV 5 1 PASS rs1272973050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 6511417 6511417 C T 1 0 0 0 0 0 0 0 1 4481 581 21 3 3 DNHD1 11 6511417 Silent SNP C C3N-01071_T 995371 6511417 128575205 203 21761 OTOG 0 . GRCh38 11 17561112 17561112 + Nonsense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.1509G>A p.Trp503Ter p.W503* ENST00000399391 13/55 237 197 40 258 258 0 strelka-varscan-mutect OTOG,stop_gained,p.Trp491Ter,ENST00000399397,NM_001292063.1;OTOG,stop_gained,p.Trp503Ter,ENST00000399391,NM_001277269.1;OTOG,non_coding_transcript_exon_variant,,ENST00000498332,;OTOG,downstream_gene_variant,,ENST00000485669,; A ENST00000399391 Transcript stop_gained 1509/8778 1509/8778 503/2925 W/* tgG/tgA 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 13/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,SMART_domains:SM00215,SMART_domains:SM00216,Superfamily_domains:SSF57603 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 71 17561112 17561112 G A 1 0 0 0 0 0 1 0 0 11370 1241 43 3 3 OTOG 11 17561112 Nonsense_Mutation SNP G C3N-01071_T 11049695 17561112 117525510 204 21762 NAV2 0 . GRCh38 11 20068207 20068207 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.5074G>C p.Glu1692Gln p.E1692Q ENST00000396087 23/41 326 289 37 253 253 0 strelka-varscan-mutect NAV2,missense_variant,p.Glu1692Gln,ENST00000527559,;NAV2,missense_variant,p.Glu1636Gln,ENST00000540292,;NAV2,missense_variant,p.Glu1636Gln,ENST00000396085,NM_182964.5;NAV2,missense_variant,p.Glu1636Gln,ENST00000349880,NM_145117.4;NAV2,missense_variant,p.Glu1572Gln,ENST00000360655,NM_001111018.1;NAV2,missense_variant,p.Glu1692Gln,ENST00000396087,NM_001244963.1;NAV2,missense_variant,p.Glu700Gln,ENST00000533917,NM_001111019.2;NAV2,missense_variant,p.Glu685Gln,ENST00000525322,; C ENST00000396087 Transcript missense_variant,splice_region_variant 5173/7882 5074/7467 1692/2488 E/Q Gag/Cag 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 tolerated(0.13) 23/41 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 20068207 20068207 G C 1 0 0 0 0 1 0 0 0 10193 956 33 4 4 NAV2 11 20068207 Missense_Mutation SNP G C3N-01071_T 2507095 20068207 115018415 205 21763 NELL1 0 . GRCh38 11 21229439 21229439 + Missense_Mutation SNP G G C rs768262280 C3N-01071_T C3N-01071_N G G c.1618G>C p.Gly540Arg p.G540R ENST00000298925 15/21 210 181 29 173 173 0 strelka-varscan-mutect NELL1,missense_variant,p.Gly540Arg,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Gly455Arg,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Gly512Arg,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Gly512Arg,ENST00000532434,NM_201551.2;NELL1,downstream_gene_variant,,ENST00000530672,; C ENST00000298925 Transcript missense_variant 1771/3329 1618/2517 540/838 G/R Ggg/Cgg rs768262280,COSM182980,COSM4641449 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 deleterious(0.01) 15/21 Gene3D:2.10.25.10,Pfam_domain:PF12947,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs768262280 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 21229439 21229439 G C 1 0 0 0 0 1 0 0 0 10364 1116 39 4 4 NELL1 11 21229439 Missense_Mutation SNP G C3N-01071_T 1161232 21229439 113857183 206 21764 SLC17A6 0 . GRCh38 11 22341529 22341529 + Missense_Mutation SNP G G A rs367738817 C3N-01071_T C3N-01071_N G G c.88G>A p.Val30Met p.V30M ENST00000263160 2/12 132 125 7 147 147 0 strelka-varscan-mutect SLC17A6,missense_variant,p.Val30Met,ENST00000263160,NM_020346.2;CTD-2140G10.2,upstream_gene_variant,,ENST00000528009,;CTD-2140G10.2,upstream_gene_variant,,ENST00000531304,;CTD-2140G10.2,upstream_gene_variant,,ENST00000530569,;SLC17A6,upstream_gene_variant,,ENST00000534115,; A ENST00000263160 Transcript missense_variant,splice_region_variant 525/3949 88/1749 30/582 V/M Gtg/Atg rs367738817,COSM4574279 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 tolerated(0.24) 2/12 hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367738817 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 22341529 22341529 G A 1 0 0 0 0 1 0 0 0 14686 1275 44 3 3 SLC17A6 11 22341529 Missense_Mutation SNP G C3N-01071_T 1112090 22341529 112745093 207 21765 ARFGAP2 0 . GRCh38 11 47171503 47171503 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.864G>A p.= p.E288E ENST00000524782 10/16 192 164 28 156 156 0 strelka-varscan-mutect ARFGAP2,synonymous_variant,p.=,ENST00000524782,NM_032389.4;ARFGAP2,synonymous_variant,p.=,ENST00000426335,NM_001242832.1;ARFGAP2,synonymous_variant,p.=,ENST00000627920,;ARFGAP2,synonymous_variant,p.=,ENST00000525398,;ARFGAP2,synonymous_variant,p.=,ENST00000527927,;ARFGAP2,synonymous_variant,p.=,ENST00000527776,;ARFGAP2,intron_variant,,ENST00000526342,;ARFGAP2,downstream_gene_variant,,ENST00000525314,;ARFGAP2,downstream_gene_variant,,ENST00000528444,;ARFGAP2,downstream_gene_variant,,ENST00000530596,;ARFGAP2,downstream_gene_variant,,ENST00000629231,;RP11-390K5.6,upstream_gene_variant,,ENST00000524412,;ARFGAP2,non_coding_transcript_exon_variant,,ENST00000395449,;ARFGAP2,downstream_gene_variant,,ENST00000531750,;ARFGAP2,downstream_gene_variant,,ENST00000533939,;ARFGAP2,downstream_gene_variant,,ENST00000529599,;ARFGAP2,3_prime_UTR_variant,,ENST00000533243,;ARFGAP2,3_prime_UTR_variant,,ENST00000532478,;ARFGAP2,3_prime_UTR_variant,,ENST00000529455,;ARFGAP2,3_prime_UTR_variant,,ENST00000532438,;ARFGAP2,downstream_gene_variant,,ENST00000526185,;ARFGAP2,downstream_gene_variant,,ENST00000524727,;ARFGAP2,downstream_gene_variant,,ENST00000527097,;ARFGAP2,downstream_gene_variant,,ENST00000528041,;ARFGAP2,downstream_gene_variant,,ENST00000526948,;ARFGAP2,downstream_gene_variant,,ENST00000529439,;ARFGAP2,downstream_gene_variant,,ENST00000528708,;ARFGAP2,downstream_gene_variant,,ENST00000524586,;ARFGAP2,downstream_gene_variant,,ENST00000528072,;ARFGAP2,upstream_gene_variant,,ENST00000525635,;ARFGAP2,downstream_gene_variant,,ENST00000530794,; T ENST00000524782 Transcript synonymous_variant 1093/2976 864/1566 288/521 E gaG/gaA 1 -1 ARFGAP2 HGNC HGNC:13504 protein_coding YES CCDS7926.1 ENSP00000434442 Q8N6H7 UPI000006F4C6 NM_032389.4 10/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF194 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 47171503 47171503 C T 1 0 0 0 0 0 0 0 1 973 680 24 3 3 ARFGAP2 11 47171503 Silent SNP C C3N-01071_T 24829974 47171503 87915119 208 21766 NRXN2 0 . GRCh38 11 64660894 64660894 + Missense_Mutation SNP C C G C3N-01071_T C3N-01071_N C C c.2044G>C p.Val682Leu p.V682L ENST00000265459 10/23 115 82 33 94 94 0 strelka-varscan-mutect NRXN2,missense_variant,p.Val682Leu,ENST00000265459,NM_015080.3;NRXN2,missense_variant,p.Val651Leu,ENST00000377559,NM_138732.2;NRXN2,missense_variant,p.Val675Leu,ENST00000409571,;NRXN2,missense_variant,p.Val682Leu,ENST00000377551,;AP001092.4,downstream_gene_variant,,ENST00000433606,;NRXN2,non_coding_transcript_exon_variant,,ENST00000496291,;NRXN2,upstream_gene_variant,,ENST00000486057,; G ENST00000265459 Transcript missense_variant 2506/6621 2044/5139 682/1712 V/L Gtt/Ctt COSM544470 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 tolerated(0.06) 10/23 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF593,Superfamily_domains:SSF49899 1 MODERATE SNV 5 1 1 PASS rs1056113277 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 64660894 64660894 C G 1 0 0 0 0 1 0 0 0 10725 536 19 4 4 NRXN2 11 64660894 Missense_Mutation SNP C C3N-01071_T 17489391 64660894 70425728 209 21767 KCNK7 0 . GRCh38 11 65593132 65593132 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.797G>A p.Gly266Glu p.G266E ENST00000340313 3/3 370 309 61 398 398 0 strelka-varscan-mutect KCNK7,missense_variant,p.Gly266Glu,ENST00000340313,NM_033347.1;KCNK7,missense_variant,p.Gly31Glu,ENST00000530380,;KCNK7,3_prime_UTR_variant,,ENST00000394216,NM_005714.1;KCNK7,3_prime_UTR_variant,,ENST00000394217,NM_033348.1,NM_033455.1;KCNK7,3_prime_UTR_variant,,ENST00000342202,;KCNK7,3_prime_UTR_variant,,ENST00000525254,;EHBP1L1,downstream_gene_variant,,ENST00000309295,NM_001099409.1;MAP3K11,downstream_gene_variant,,ENST00000309100,NM_002419.3;MAP3K11,downstream_gene_variant,,ENST00000530153,;MAP3K11,downstream_gene_variant,,ENST00000532507,;EHBP1L1,downstream_gene_variant,,ENST00000529596,;EHBP1L1,downstream_gene_variant,,ENST00000529099,;EHBP1L1,downstream_gene_variant,,ENST00000529056,;MAP3K11,downstream_gene_variant,,ENST00000524848,;EHBP1L1,downstream_gene_variant,,ENST00000533364,;EHBP1L1,downstream_gene_variant,,ENST00000527214,; T ENST00000340313 Transcript missense_variant 1021/1298 797/924 266/307 G/E gGg/gAg 1 -1 KCNK7 HGNC HGNC:6282 protein_coding YES CCDS31608.1 ENSP00000344820 Q9Y2U2 UPI0000127A52 NM_033347.1 tolerated(0.43) 3/3 hmmpanther:PTHR11003:SF31,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061,Prints_domain:PR01586 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 65593132 65593132 C T 1 0 0 0 0 1 0 0 0 7988 623 22 3 3 KCNK7 11 65593132 Missense_Mutation SNP C C3N-01071_T 932238 65593132 69493490 210 21768 ARHGEF17 0 . GRCh38 11 73362156 73362156 + Silent SNP G G A rs369670623 C3N-01071_T C3N-01071_N G G c.4611G>A p.= p.P1537P ENST00000263674 13/21 317 248 69 325 325 0 strelka-varscan-mutect ARHGEF17,synonymous_variant,p.=,ENST00000263674,NM_014786.3;ARHGEF17,upstream_gene_variant,,ENST00000543530,;ARHGEF17,upstream_gene_variant,,ENST00000536481,; A ENST00000263674 Transcript synonymous_variant 4961/7853 4611/6192 1537/2063 P ccG/ccA rs369670623 1 1 ARHGEF17 HGNC HGNC:21726 protein_coding YES CCDS8221.1 ENSP00000263674 Q96PE2 UPI000004980B NM_014786.3 13/21 hmmpanther:PTHR12877:SF15,hmmpanther:PTHR12877 LOW 1 SNV 1 1 PASS rs369670623 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 73362156 73362156 G A 1 0 0 0 0 0 0 0 1 1030 1103 39 1 1 ARHGEF17 11 73362156 Silent SNP G C3N-01071_T 7769024 73362156 61724466 211 21769 TRIM49 0 . GRCh38 11 89798267 89798267 + Silent SNP G G T C3N-01071_T C3N-01071_N G G c.1222C>A p.= p.R408R ENST00000329758 8/8 165 143 22 150 150 0 varscan-mutect TRIM49,synonymous_variant,p.=,ENST00000329758,NM_020358.2;TRIM49,synonymous_variant,p.=,ENST00000532501,; T ENST00000329758 Transcript synonymous_variant 1551/2163 1222/1359 408/452 R Cga/Aga COSM215500 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 8/8 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00449,Superfamily_domains:SSF49899 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 71 89798267 89798267 G T 1 0 0 0 0 0 0 0 1 17014 1124 39 1 1 TRIM49 11 89798267 Silent SNP G C3N-01071_T 16436111 89798267 45288355 212 21770 CEP295 0 . GRCh38 11 93727330 93727330 + Nonsense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.6854C>G p.Ser2285Ter p.S2285* ENST00000325212 24/30 184 150 34 172 172 0 strelka-varscan-mutect CEP295,stop_gained,p.Ser2285Ter,ENST00000325212,NM_033395.1;CEP295,stop_gained,p.Ser465Ter,ENST00000531700,;CEP295,stop_gained,p.Ser297Ter,ENST00000531404,;CEP295,downstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000529185,;SNORA25,downstream_gene_variant,,ENST00000384384,;SNORA1,downstream_gene_variant,,ENST00000384107,;SNORA32,downstream_gene_variant,,ENST00000384072,;SNORD6,downstream_gene_variant,,ENST00000365444,;RP11-178H8.7,non_coding_transcript_exon_variant,,ENST00000624493,;TAF1D,downstream_gene_variant,,ENST00000546088,;TAF1D,downstream_gene_variant,,ENST00000530089,;TAF1D,downstream_gene_variant,,ENST00000530769,;TAF1D,downstream_gene_variant,,ENST00000323981,;TAF1D,downstream_gene_variant,,ENST00000526015,;TAF1D,downstream_gene_variant,,ENST00000525928,;TAF1D,downstream_gene_variant,,ENST00000527169,;TAF1D,downstream_gene_variant,,ENST00000529900,;TAF1D,downstream_gene_variant,,ENST00000529435,;TAF1D,downstream_gene_variant,,ENST00000534079,;TAF1D,downstream_gene_variant,,ENST00000393259,;TAF1D,downstream_gene_variant,,ENST00000540232,; G ENST00000325212 Transcript stop_gained 7016/8057 6854/7806 2285/2601 S/* tCa/tGa 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 24/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25 HIGH 1 SNV 2 1 PASS . . 0 139 0 13 57 0 0 0 -17.94387 0 0 1 0 0 G 4 3 71 93727330 93727330 C G 1 0 0 0 0 0 1 0 0 2970 838 29 4 4 CEP295 11 93727330 Nonsense_Mutation SNP C C3N-01071_T 3929063 93727330 41359292 213 21771 C11orf70 0 . GRCh38 11 102066521 102066521 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.305C>G p.Pro102Arg p.P102R ENST00000434758 4/7 203 166 37 169 169 0 strelka-varscan-mutect C11orf70,missense_variant,p.Pro102Arg,ENST00000434758,NM_032930.2;C11orf70,missense_variant,p.Pro102Arg,ENST00000526781,;C11orf70,intron_variant,,ENST00000534360,NM_001195005.1;C11orf70,upstream_gene_variant,,ENST00000529204,;C11orf70,non_coding_transcript_exon_variant,,ENST00000530659,; G ENST00000434758 Transcript missense_variant 333/2193 305/804 102/267 P/R cCt/cGt 1 1 C11orf70 HGNC HGNC:28188 protein_coding YES CCDS8313.2 ENSP00000414390 Q9BRQ4 UPI00001FA24F NM_032930.2 deleterious(0.04) 4/7 Pfam_domain:PF14926,hmmpanther:PTHR31078,hmmpanther:PTHR31078:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 102066521 102066521 C G 1 0 0 0 0 1 0 0 0 1793 681 24 4 4 C11orf70 11 102066521 Missense_Mutation SNP C C3N-01071_T 8339191 102066521 33020101 214 21772 DSCAML1 0 . GRCh38 11 117432359 117432359 + Silent SNP T T A novel C3N-01071_T C3N-01071_N T T c.5352A>T p.= p.P1784P ENST00000321322 30/33 133 123 10 147 146 1 strelka-varscan-mutect DSCAML1,synonymous_variant,p.=,ENST00000321322,NM_020693.3;DSCAML1,synonymous_variant,p.=,ENST00000527706,; A ENST00000321322 Transcript synonymous_variant 5354/6899 5352/6342 1784/2113 P ccA/ccT 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 30/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 117432359 117432359 T A 1 0 0 0 0 0 0 0 1 4590 1567 55 4 4 DSCAML1 11 117432359 Silent SNP T C3N-01071_T 15365838 117432359 17654263 215 21773 TECTA 0 . GRCh38 11 121118517 121118517 + Missense_Mutation SNP C C A rs35282525 C3N-01071_T C3N-01071_N C C c.1002C>A p.Asp334Glu p.D334E ENST00000392793 7/24 437 415 22 410 410 0 strelka-varscan-mutect TECTA,missense_variant,p.Asp334Glu,ENST00000392793,;TECTA,missense_variant,p.Asp334Glu,ENST00000264037,NM_005422.2; A ENST00000392793 Transcript missense_variant 1273/7426 1002/6468 334/2155 D/E gaC/gaA rs35282525 1 1 TECTA HGNC HGNC:11720 protein_coding YES CCDS8434.1 ENSP00000376543 O75443 UPI000045659D deleterious(0) 7/24 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF235,hmmpanther:PTHR11339,Pfam_domain:PF00094,SMART_domains:SM00216,SMART_domains:SM00215 MODERATE 1 SNV 5 1 PASS rs35282525 . 0 208 0 0 2 0 0 0 -4.137748 0.9754988 1 1 1 0 A 3 1 71 121118517 121118517 C A 1 0 0 0 0 1 0 0 0 16158 535 19 1 1 TECTA 11 121118517 Missense_Mutation SNP C C3N-01071_T 3686158 121118517 13968105 216 21774 APLP2 0 . GRCh38 11 130110592 130110592 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.334A>G p.Ile112Val p.I112V ENST00000263574 3/18 210 174 36 258 258 0 strelka-varscan-mutect APLP2,missense_variant,p.Ile112Val,ENST00000263574,NM_001642.2;APLP2,missense_variant,p.Ile122Val,ENST00000278756,NM_001243299.1;APLP2,missense_variant,p.Ile112Val,ENST00000338167,NM_001142276.1;APLP2,missense_variant,p.Ile112Val,ENST00000528499,NM_001142277.1;APLP2,missense_variant,p.Ile112Val,ENST00000345598,NM_001142278.1;APLP2,missense_variant,p.Ile137Val,ENST00000533195,;APLP2,missense_variant,p.Ile97Val,ENST00000533713,;U4,downstream_gene_variant,,ENST00000618561,;APLP2,splice_region_variant,,ENST00000526330,;APLP2,non_coding_transcript_exon_variant,,ENST00000532456,;APLP2,non_coding_transcript_exon_variant,,ENST00000534001,;APLP2,non_coding_transcript_exon_variant,,ENST00000527702,;APLP2,non_coding_transcript_exon_variant,,ENST00000529235,;APLP2,non_coding_transcript_exon_variant,,ENST00000529483,;APLP2,intron_variant,,ENST00000529701,;APLP2,intron_variant,,ENST00000534761,;APLP2,non_coding_transcript_exon_variant,,ENST00000533618,;APLP2,intron_variant,,ENST00000533616,;APLP2,intron_variant,,ENST00000534582,;APLP2,downstream_gene_variant,,ENST00000533532,;APLP2,downstream_gene_variant,,ENST00000461918,;APLP2,downstream_gene_variant,,ENST00000530132,;APLP2,downstream_gene_variant,,ENST00000525215,; G ENST00000263574 Transcript missense_variant 406/3727 334/2292 112/763 I/V Att/Gtt 1 1 APLP2 HGNC HGNC:598 protein_coding YES CCDS8486.1 ENSP00000263574 Q06481 UPI0000125CAE NM_001642.2 tolerated(0.07) 3/18 Superfamily_domains:0041119,Gene3D:1mwpA00,Pfam_domain:PF02177,hmmpanther:PTHR23103,hmmpanther:PTHR23103:SF14,SMART_domains:SM00006 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 130110592 130110592 A G 1 0 0 0 0 1 0 0 0 901 449 16 5 5 APLP2 11 130110592 Missense_Mutation SNP A C3N-01071_T 8992075 130110592 4976030 217 21775 CACNA1C 0 . GRCh38 12 2677198 2677198 + Nonsense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.5077C>T p.Gln1693Ter p.Q1693* ENST00000347598 42/49 213 172 41 126 126 0 strelka-varscan-mutect CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399655,NM_000719.6;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399634,NM_001167625.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000406454,;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399617,NM_001167624.2;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399603,NM_001167623.1;CACNA1C,stop_gained,p.Gln1670Ter,ENST00000335762,;CACNA1C,stop_gained,p.Gln1693Ter,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,stop_gained,p.Gln1686Ter,ENST00000344100,NM_001129829.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000327702,NM_001129830.2;CACNA1C,stop_gained,p.Gln1673Ter,ENST00000399638,NM_001129831.1;CACNA1C,stop_gained,p.Gln1665Ter,ENST00000399606,NM_001129832.1;CACNA1C,stop_gained,p.Gln1664Ter,ENST00000399621,NM_001129834.1;CACNA1C,stop_gained,p.Gln1664Ter,ENST00000399637,NM_001129835.1;CACNA1C,stop_gained,p.Gln1664Ter,ENST00000402845,NM_001129833.1;CACNA1C,stop_gained,p.Gln1662Ter,ENST00000399629,NM_001129836.1;CACNA1C,stop_gained,p.Gln1653Ter,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,stop_gained,p.Gln1653Ter,ENST00000399595,NM_001129837.1;CACNA1C,stop_gained,p.Gln1651Ter,ENST00000399649,NM_001129839.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399601,NM_001129843.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399641,NM_001129840.1;CACNA1C,stop_gained,p.Gln1645Ter,ENST00000399644,NM_001129841.1;CACNA1C,stop_gained,p.Gln336Ter,ENST00000616390,;CACNA1C-AS1,non_coding_transcript_exon_variant,,ENST00000501371,;CACNA1C-AS2,upstream_gene_variant,,ENST00000545526,;CACNA1C,non_coding_transcript_exon_variant,,ENST00000465934,; T ENST00000347598 Transcript stop_gained 5077/6655 5077/6561 1693/2186 Q/* Cag/Tag 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 42/49 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 71 2677198 2677198 C T 1 0 0 0 0 0 1 0 0 2228 595 21 3 3 CACNA1C 12 2677198 Nonsense_Mutation SNP C C3N-01071_T 2677198 130598111 218 21776 CD163 0 . GRCh38 12 7496869 7496869 + Missense_Mutation SNP T T A rs776894691 C3N-01071_T C3N-01071_N T T c.1043A>T p.His348Leu p.H348L ENST00000359156 5/17 268 249 19 425 425 0 strelka-varscan-mutect CD163,missense_variant,p.His348Leu,ENST00000359156,NM_004244.5;CD163,missense_variant,p.His348Leu,ENST00000396620,;CD163,missense_variant,p.His348Leu,ENST00000432237,NM_203416.3;CD163,missense_variant,p.His336Leu,ENST00000541972,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,; A ENST00000359156 Transcript missense_variant 1246/4268 1043/3471 348/1156 H/L cAt/cTt rs776894691 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 tolerated(0.25) 5/17 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF324,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS rs776894691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 7496869 7496869 T A 1 0 0 0 0 1 0 0 0 2670 1464 51 4 4 CD163 12 7496869 Missense_Mutation SNP T C3N-01071_T 4819671 7496869 125778440 219 21777 TAS2R10 0 . GRCh38 12 10825828 10825828 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.442G>A p.Ala148Thr p.A148T ENST00000240619 1/1 132 109 23 70 70 0 strelka-varscan-mutect TAS2R10,missense_variant,p.Ala148Thr,ENST00000240619,NM_023921.1;PRH1,intron_variant,,ENST00000538332,; T ENST00000240619 Transcript missense_variant 531/1042 442/924 148/307 A/T Gcg/Acg 1 -1 TAS2R10 HGNC HGNC:14918 protein_coding YES CCDS8634.1 ENSP00000240619 Q9NYW0 UPI0000038B12 NM_023921.1 tolerated(0.49) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF05296,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF63,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 10825828 10825828 C T 1 0 0 0 0 1 0 0 0 15965 710 25 3 3 TAS2R10 12 10825828 Missense_Mutation SNP C C3N-01071_T 3328959 10825828 122449481 220 21778 PRB2 0 . GRCh38 12 11393672 11393672 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.406C>A p.Pro136Thr p.P136T ENST00000389362 3/4 46 39 7 41 41 0 strelka-varscan-mutect PRB2,missense_variant,p.Pro136Thr,ENST00000389362,NM_006248.3;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,; T ENST00000389362 Transcript missense_variant 442/1429 406/1251 136/416 P/T Cca/Aca 1 -1 PRB2 HGNC HGNC:9338 protein_coding YES CCDS41757.2 ENSP00000374013 P02812 UPI0000EE5993 NM_006248.3 tolerated(0.38) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23203,hmmpanther:PTHR23203:SF2,SMART_domains:SM01412 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -17.53719 1 1 1 1 0 T 3 4 71 11393672 11393672 G T 1 0 0 0 0 1 0 0 0 12574 1174 41 2 2 PRB2 12 11393672 Missense_Mutation SNP G C3N-01071_T 567844 11393672 121881637 221 21779 CDKN1B 0 . GRCh38 12 12721091 12721091 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.502A>C p.Lys168Gln p.K168Q ENST00000396340 2/2 80 73 7 65 65 0 strelka-varscan-mutect CDKN1B,missense_variant,p.Lys168Gln,ENST00000396340,;CDKN1B,3_prime_UTR_variant,,ENST00000228872,NM_004064.4;CDKN1B,3_prime_UTR_variant,,ENST00000442489,;APOLD1,upstream_gene_variant,,ENST00000326765,NM_001130415.1;RP11-180M15.7,downstream_gene_variant,,ENST00000614874,;RP11-180M15.4,downstream_gene_variant,,ENST00000542291,;CDKN1B,non_coding_transcript_exon_variant,,ENST00000477087,;APOLD1,upstream_gene_variant,,ENST00000534843,;APOLD1,upstream_gene_variant,,ENST00000540583,;APOLD1,upstream_gene_variant,,ENST00000588943,; C ENST00000396340 Transcript missense_variant 520/897 502/618 168/205 K/Q Aag/Cag 1 1 CDKN1B HGNC HGNC:1785 protein_coding ENSP00000379629 E7ES52 UPI000155D50D tolerated_low_confidence(0.11) 2/2 MODERATE SNV 3 1 PASS . . 0 206 4 0 0 0 0 0 -15.24096 1 1 1 1 0 C 3 2 71 12721091 12721091 A C 1 0 0 0 0 1 0 0 0 2863 247 9 5 5 CDKN1B 12 12721091 Missense_Mutation SNP A C3N-01071_T 1327419 12721091 120554218 222 21780 GRIN2B 0 . GRCh38 12 13753514 13753514 + Silent SNP C C T rs201732785 C3N-01071_T C3N-01071_N C C c.813G>A p.= p.A271A ENST00000609686 3/13 322 297 25 263 263 0 strelka-varscan-mutect GRIN2B,synonymous_variant,p.=,ENST00000609686,NM_000834.3; T ENST00000609686 Transcript synonymous_variant 1267/30355 813/4455 271/1484 A gcG/gcA rs201732785 1 -1 GRIN2B HGNC HGNC:4586 protein_coding YES CCDS8662.1 ENSP00000477455 Q13224 UPI000013026C NM_000834.3 3/13 Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF192,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS rs201732785 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 13753514 13753514 C T 1 0 0 0 0 0 0 0 1 6662 639 23 1 1 GRIN2B 12 13753514 Silent SNP C C3N-01071_T 1032423 13753514 119521795 223 21781 SLCO1C1 0 . GRCh38 12 20699661 20699661 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.85T>A p.Tyr29Asn p.Y29N ENST00000545604 3/16 217 197 20 229 229 0 strelka-varscan-mutect SLCO1C1,missense_variant,p.Tyr29Asn,ENST00000266509,NM_017435.4;SLCO1C1,missense_variant,p.Tyr29Asn,ENST00000545604,NM_001145946.1;SLCO1C1,missense_variant,p.Tyr29Asn,ENST00000540354,NM_001145945.1;SLCO1C1,intron_variant,,ENST00000545102,NM_001145944.1;SLCO1C1,downstream_gene_variant,,ENST00000535609,;SLCO1C1,downstream_gene_variant,,ENST00000534996,;SLCO1C1,downstream_gene_variant,,ENST00000539443,;SLCO1C1,missense_variant,p.Tyr29Asn,ENST00000539415,;SLCO1C1,non_coding_transcript_exon_variant,,ENST00000497911,; A ENST00000545604 Transcript missense_variant 315/2557 85/2193 29/730 Y/N Tat/Aat 1 1 SLCO1C1 HGNC HGNC:13819 protein_coding YES CCDS53757.1 ENSP00000444149 Q9NYB5 UPI00004C3E1B NM_001145946.1 tolerated(0.31) 3/16 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF99,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 20699661 20699661 T A 1 0 0 0 0 1 0 0 0 15012 1406 49 4 4 SLCO1C1 12 20699661 Missense_Mutation SNP T C3N-01071_T 6946147 20699661 112575648 224 21782 TMTC1 0 . GRCh38 12 29520683 29520683 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1823G>T p.Gly608Val p.G608V ENST00000539277 12/18 202 169 33 206 206 0 strelka-varscan-mutect TMTC1,missense_variant,p.Gly500Val,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Gly670Val,ENST00000551659,;TMTC1,missense_variant,p.Gly632Val,ENST00000552618,;TMTC1,missense_variant,p.Gly608Val,ENST00000539277,NM_001193451.1;RP11-310I24.1,intron_variant,,ENST00000549070,;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,upstream_gene_variant,,ENST00000552925,; A ENST00000539277 Transcript missense_variant 1882/2758 1823/2649 608/882 G/V gGa/gTa 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 tolerated(0.06) 12/18 Gene3D:1.25.40.10,Pfam_domain:PF13432,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00028,SMART_domains:SM00386,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 29520683 29520683 C A 1 0 0 0 0 1 0 0 0 16734 855 30 2 2 TMTC1 12 29520683 Missense_Mutation SNP C C3N-01071_T 8821022 29520683 103754626 225 21783 FGD4 0 . GRCh38 12 32582356 32582356 + Silent SNP A A G novel C3N-01071_T C3N-01071_N A A c.825A>G p.= p.P275P ENST00000525053 4/17 155 145 10 142 142 0 strelka-varscan-mutect FGD4,synonymous_variant,p.=,ENST00000427716,NM_139241.3,NM_001304483.1;FGD4,synonymous_variant,p.=,ENST00000546442,NM_001304484.1;FGD4,synonymous_variant,p.=,ENST00000534526,;FGD4,synonymous_variant,p.=,ENST00000525053,NM_001304480.1;FGD4,synonymous_variant,p.=,ENST00000531134,NM_001304481.1;FGD4,synonymous_variant,p.=,ENST00000472289,;FGD4,downstream_gene_variant,,ENST00000473513,;FGD4,downstream_gene_variant,,ENST00000550091,;FGD4,synonymous_variant,p.=,ENST00000493087,;FGD4,synonymous_variant,p.=,ENST00000395740,;FGD4,non_coding_transcript_exon_variant,,ENST00000494275,;FGD4,intron_variant,,ENST00000551984,;FGD4,upstream_gene_variant,,ENST00000494977,; G ENST00000525053 Transcript synonymous_variant 909/2925 825/2637 275/878 P ccA/ccG 1 1 FGD4 HGNC HGNC:19125 protein_coding YES CCDS76545.1 ENSP00000433666 E9PJX4 UPI0001F78470 NM_001304480.1 4/17 hmmpanther:PTHR12673:SF98,hmmpanther:PTHR12673 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 32582356 32582356 A G 1 0 0 0 0 0 0 0 1 5699 175 7 5 5 FGD4 12 32582356 Silent SNP A C3N-01071_T 3061673 32582356 100692953 226 21784 C12orf40 0 . GRCh38 12 39721251 39721251 + Silent SNP A A G rs867253891 C3N-01071_T C3N-01071_N A A c.1959A>G p.= p.*653* ENST00000324616 13/13 98 87 11 153 153 0 strelka-varscan-mutect C12orf40,stop_retained_variant,p.=,ENST00000324616,NM_001031748.2;C12orf40,intron_variant,,ENST00000468200,; G ENST00000324616 Transcript stop_retained_variant 2113/2776 1959/1959 653/652 * taA/taG rs867253891 1 1 C12orf40 HGNC HGNC:26846 protein_coding YES CCDS41770.1 ENSP00000317671 Q86WS4 UPI000069A925 NM_001031748.2 13/13 LOW 1 SNV 1 1 PASS rs867253891 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 39721251 39721251 A G 1 0 0 0 0 0 0 0 1 1809 108 4 5 5 C12orf40 12 39721251 Silent SNP A C3N-01071_T 7138895 39721251 93554058 227 21785 WNT1 0 . GRCh38 12 48981150 48981150 + Splice_Site SNP A A C novel C3N-01071_T C3N-01071_N A A c.625-2A>C p.X209_splice ENST00000293549 174 147 27 146 146 0 strelka-varscan-mutect WNT1,splice_acceptor_variant,,ENST00000613114,;WNT1,splice_acceptor_variant,,ENST00000293549,NM_005430.3; C ENST00000293549 Transcript splice_acceptor_variant -/1185 625/1113 209/370 1 1 WNT1 HGNC HGNC:12774 protein_coding YES CCDS8776.1 ENSP00000293549 P04628 UPI0000051043 NM_005430.3 3/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 71 48981150 48981150 A C 1 0 0 0 0 0 0 1 0 17937 202 7 5 5 WNT1 12 48981150 Splice_Site SNP A C3N-01071_T 9259899 48981150 84294159 228 21786 GRASP 0 . GRCh38 12 52007186 52007186 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.167A>G p.Tyr56Cys p.Y56C ENST00000293662 1/8 93 85 8 111 111 0 strelka-mutect GRASP,missense_variant,p.Tyr56Cys,ENST00000293662,NM_181711.3;GRASP,upstream_gene_variant,,ENST00000552049,NM_001271856.1;GRASP,upstream_gene_variant,,ENST00000546756,;GRASP,upstream_gene_variant,,ENST00000552963,;GRASP,upstream_gene_variant,,ENST00000547749,;GRASP,upstream_gene_variant,,ENST00000550809,; G ENST00000293662 Transcript missense_variant 247/1933 167/1188 56/395 Y/C tAc/tGc 1 1 GRASP HGNC HGNC:18707 protein_coding YES CCDS8817.1 ENSP00000293662 Q7Z6J2 UPI00001A9479 NM_181711.3 deleterious(0.02) 1/8 hmmpanther:PTHR15963,hmmpanther:PTHR15963:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 52007186 52007186 A G 1 0 0 0 0 1 0 0 0 6634 391 14 5 5 GRASP 12 52007186 Missense_Mutation SNP A C3N-01071_T 3026036 52007186 81268123 229 21787 ATP5G2 0 . GRCh38 12 53669158 53669158 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.472G>A p.Gly158Ser p.G158S ENST00000394349 4/5 60 46 14 68 68 0 strelka-varscan-mutect ATP5G2,missense_variant,p.Gly101Ser,ENST00000552242,;ATP5G2,missense_variant,p.Gly117Ser,ENST00000338662,NM_001002031.2;ATP5G2,missense_variant,p.Gly158Ser,ENST00000394349,NM_005176.5;ATP5G2,missense_variant,p.Gly101Ser,ENST00000549164,;ATP5G2,missense_variant,p.Gly101Ser,ENST00000602871,;ATP5G2,5_prime_UTR_variant,,ENST00000549748,;ATP5G2,non_coding_transcript_exon_variant,,ENST00000550241,;ATP5G2,non_coding_transcript_exon_variant,,ENST00000495596,;ATP5G2,downstream_gene_variant,,ENST00000552120,; T ENST00000394349 Transcript missense_variant 605/878 472/597 158/198 G/S Ggt/Agt 1 -1 ATP5G2 HGNC HGNC:842 protein_coding YES CCDS8863.2 ENSP00000377878 Q06055 UPI000015A460 NM_005176.5 deleterious(0.03) 4/5 Superfamily_domains:0035882,Gene3D:1.20.20.10,HAMAP:MF_01396,Pfam_domain:PF00137,Prints_domain:PR00124,hmmpanther:PTHR10031,hmmpanther:PTHR10031:SF12,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 201 7 2 0 0 0 0 -20 0.999934 1 1 1 0 T 3 4 71 53669158 53669158 C T 1 0 0 0 0 1 0 0 0 1307 594 21 3 3 ATP5G2 12 53669158 Missense_Mutation SNP C C3N-01071_T 1661972 53669158 79606151 230 21788 HELB 0 . GRCh38 12 66315245 66315245 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.1862A>T p.Asp621Val p.D621V ENST00000247815 6/13 58 49 9 54 54 0 strelka-varscan-mutect HELB,missense_variant,p.Asp621Val,ENST00000247815,NM_033647.3;HELB,missense_variant,p.Asp621Val,ENST00000545134,;HELB,missense_variant,p.Asp621Val,ENST00000542394,;HELB,missense_variant,p.Thr562Ser,ENST00000440906,; T ENST00000247815 Transcript missense_variant 1921/12866 1862/3264 621/1087 D/V gAc/gTc 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 deleterious(0) 6/13 Gene3D:3.40.50.300,Pfam_domain:PF13604,Superfamily_domains:SSF52540,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 1 199 9 0 0 0 0 0 -19.90048 0.9999935 1 1 1 0 T 3 4 71 66315245 66315245 A T 1 0 0 0 0 1 0 0 0 6927 289 10 4 4 HELB 12 66315245 Missense_Mutation SNP A C3N-01071_T 12646087 66315245 66960064 231 21789 CFAP54 0 . GRCh38 12 96651654 96651654 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.4939A>G p.Thr1647Ala p.T1647A ENST00000524981 36/68 305 277 28 269 269 0 strelka-varscan-mutect CFAP54,missense_variant,p.Thr1647Ala,ENST00000524981,NM_001306084.1;CFAP54,missense_variant,p.Thr553Ala,ENST00000637336,;CFAP54,downstream_gene_variant,,ENST00000550977,;CFAP54,non_coding_transcript_exon_variant,,ENST00000342887,; G ENST00000524981 Transcript missense_variant 4962/9766 4939/9291 1647/3096 T/A Act/Gct 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 tolerated(0.05) 36/68 hmmpanther:PTHR33487,hmmpanther:PTHR33487:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 96651654 96651654 A G 1 0 0 0 0 1 0 0 0 3025 391 14 5 5 CFAP54 12 96651654 Missense_Mutation SNP A C3N-01071_T 30336409 96651654 36623655 232 21790 TBX3 0 . GRCh38 12 114674753 114674753 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.1182G>A p.= p.K394K ENST00000257566 7/8 425 376 49 357 357 0 strelka-varscan-mutect TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,downstream_gene_variant,,ENST00000548503,; T ENST00000257566 Transcript synonymous_variant 1572/4208 1182/2232 394/743 K aaG/aaA 1 -1 TBX3 HGNC HGNC:11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 A0A024RBL6 UPI0000136AA0 NM_016569.3 7/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,Pfam_domain:PF12598 LOW 1 SNV 1 1 PASS rs1242201658 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 114674753 114674753 C T 1 0 0 0 0 0 0 0 1 16064 912 32 3 3 TBX3 12 114674753 Silent SNP C C3N-01071_T 18023099 114674753 18600556 233 21791 FBXO21 0 . GRCh38 12 117158079 117158079 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.1332C>T p.= p.F444F ENST00000330622 10/12 141 127 14 166 166 0 strelka-mutect FBXO21,synonymous_variant,p.=,ENST00000330622,NM_033624.2;FBXO21,synonymous_variant,p.=,ENST00000548840,;FBXO21,intron_variant,,ENST00000622495,NM_015002.2;FBXO21,intron_variant,,ENST00000427718,;FBXO21,intron_variant,,ENST00000550180,;FBXO21,upstream_gene_variant,,ENST00000547806,; A ENST00000330622 Transcript synonymous_variant 1332/2906 1332/1887 444/628 F ttC/ttT 1 -1 FBXO21 HGNC HGNC:13592 protein_coding YES CCDS9184.1 ENSP00000328187 O94952 A0A024RBR2 UPI000013CF6D NM_033624.2 10/12 hmmpanther:PTHR31350,hmmpanther:PTHR31350:SF7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 117158079 117158079 G A 1 0 0 0 0 0 0 0 1 5596 956 33 3 3 FBXO21 12 117158079 Silent SNP G C3N-01071_T 2483326 117158079 16117230 234 21792 TMEM132D 0 . GRCh38 12 129209528 129209528 + Missense_Mutation SNP C C A rs756867549 C3N-01071_T C3N-01071_N C C c.1435G>T p.Val479Leu p.V479L ENST00000422113 5/9 172 145 27 120 120 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Val479Leu,ENST00000422113,NM_133448.2;RP11-669N7.3,intron_variant,,ENST00000542578,; A ENST00000422113 Transcript missense_variant 1762/5776 1435/3300 479/1099 V/L Gtg/Ttg rs756867549,COSM203566 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 deleterious(0) 5/9 Pfam_domain:PF16070,hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs756867549 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 129209528 129209528 C A 1 0 0 0 0 1 0 0 0 16492 536 19 1 1 TMEM132D 12 129209528 Missense_Mutation SNP C C3N-01071_T 12051449 129209528 4065781 235 21793 ZNF605 0 . GRCh38 12 132933066 132933066 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.105G>T p.Met35Ile p.M35I ENST00000392321 3/5 91 86 5 77 77 0 strelka-mutect ZNF605,missense_variant,p.Met35Ile,ENST00000360187,NM_183238.3;ZNF605,missense_variant,p.Met35Ile,ENST00000392321,NM_001164715.1;CHFR,intron_variant,,ENST00000536932,;ZNF605,non_coding_transcript_exon_variant,,ENST00000331711,;ZNF605,non_coding_transcript_exon_variant,,ENST00000412621,; A ENST00000392321 Transcript missense_variant 331/6156 105/2019 35/672 M/I atG/atT 1 -1 ZNF605 HGNC HGNC:28068 protein_coding YES CCDS53850.1 ENSP00000376135 Q86T29 UPI000058F1FC NM_001164715.1 deleterious(0.03) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF120,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -10.65599 0.9999962 1 1 1 0 A 3 1 71 132933066 132933066 C A 1 0 0 0 0 1 0 0 0 18606 478 17 2 2 ZNF605 12 132933066 Missense_Mutation SNP C C3N-01071_T 3723538 132933066 342243 236 21794 ELF1 0 . GRCh38 13 40943005 40943005 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.753G>A p.= p.G251G ENST00000239882 7/9 117 93 24 69 69 0 strelka-varscan-mutect ELF1,synonymous_variant,p.=,ENST00000239882,NM_172373.3;ELF1,synonymous_variant,p.=,ENST00000635415,;ELF1,synonymous_variant,p.=,ENST00000625359,NM_001145353.1;ELF1,5_prime_UTR_variant,,ENST00000442101,;ELF1,3_prime_UTR_variant,,ENST00000498824,; T ENST00000239882 Transcript synonymous_variant 1068/3566 753/1860 251/619 G ggG/ggA 1 -1 ELF1 HGNC HGNC:3316 protein_coding YES CCDS9374.1 ENSP00000239882 P32519 A0A024RDU6 UPI000007071F NM_172373.3 7/9 Gene3D:1.10.10.10,Pfam_domain:PF00178,Prints_domain:PR00454,PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF156,SMART_domains:SM00413,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS . . 0 197 9 4 0 0 0 0 -20 0.9976189 1 1 1 0 T 2 4 71 40943005 40943005 C T 1 0 0 0 0 0 0 0 1 4886 842 30 3 3 ELF1 13 40943005 Silent SNP C C3N-01071_T 40943005 73421323 237 21795 RNASEH2B 0 . GRCh38 13 50927437 50927437 + Missense_Mutation SNP A A C rs377417708 C3N-01071_T C3N-01071_N A A c.95A>C p.Lys32Thr p.K32T ENST00000336617 2/11 302 258 44 319 319 0 strelka-varscan-mutect RNASEH2B,missense_variant,p.Lys32Thr,ENST00000422660,NM_001142279.2;RNASEH2B,missense_variant,p.Lys32Thr,ENST00000336617,NM_024570.3;RNASEH2B,missense_variant,p.Lys2Thr,ENST00000611510,;RNASEH2B,missense_variant,p.Lys2Thr,ENST00000636524,;RNASEH2B,missense_variant,p.Lys2Thr,ENST00000637648,;RNASEH2B,upstream_gene_variant,,ENST00000495244,;RNASEH2B,upstream_gene_variant,,ENST00000459681,; C ENST00000336617 Transcript missense_variant 494/1629 95/939 32/312 K/T aAa/aCa rs377417708 1 1 RNASEH2B HGNC HGNC:25671 protein_coding YES CCDS9425.1 ENSP00000337623 Q5TBB1 UPI000013CFE7 NM_024570.3 deleterious(0.03) 2/11 hmmpanther:PTHR13383:SF11,hmmpanther:PTHR13383,Pfam_domain:PF09468 MODERATE 1 SNV 1 1 PASS rs377417708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 50927437 50927437 A C 1 0 0 0 0 1 0 0 0 13592 14 1 5 5 RNASEH2B 13 50927437 Missense_Mutation SNP A C3N-01071_T 9984432 50927437 63436891 238 21796 PCDH9 0 . GRCh38 13 67226801 67226801 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.1640A>T p.Asn547Ile p.N547I ENST00000377865 2/5 228 207 21 239 239 0 strelka-varscan-mutect PCDH9,missense_variant,p.Asn547Ile,ENST00000377861,;PCDH9,missense_variant,p.Asn547Ile,ENST00000544246,NM_020403.4;PCDH9,missense_variant,p.Asn547Ile,ENST00000377865,NM_203487.2;PCDH9,missense_variant,p.Asn547Ile,ENST00000456367,; A ENST00000377865 Transcript missense_variant 1814/5709 1640/3714 547/1237 N/I aAt/aTt 1 -1 PCDH9 HGNC HGNC:8661 protein_coding YES CCDS9444.1 ENSP00000367096 Q9HC56 X5D7N0 UPI00001FCE90 NM_203487.2 deleterious(0.01) 2/5 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 67226801 67226801 T A 1 0 0 0 0 1 0 0 0 11605 1493 52 4 4 PCDH9 13 67226801 Missense_Mutation SNP T C3N-01071_T 16299364 67226801 47137527 239 21797 MYCBP2 0 . GRCh38 13 77205568 77205568 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.3506A>T p.Asp1169Val p.D1169V ENST00000544440 25/83 237 222 15 168 168 0 strelka-varscan-mutect MYCBP2,missense_variant,p.Asp1169Val,ENST00000357337,NM_015057.4;MYCBP2,missense_variant,p.Asp1169Val,ENST00000544440,; A ENST00000544440 Transcript missense_variant 3524/14664 3506/13923 1169/4640 D/V gAc/gTc 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 deleterious(0) 25/83 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 77205568 77205568 T A 1 0 0 0 0 1 0 0 0 10018 1667 58 4 4 MYCBP2 13 77205568 Missense_Mutation SNP T C3N-01071_T 9978767 77205568 37158760 240 21798 SLITRK1 0 . GRCh38 13 83881313 83881313 + Silent SNP C C G rs368351965 C3N-01071_T C3N-01071_N C C c.195G>C p.= p.L65L ENST00000377084 1/1 568 401 167 371 371 0 strelka-varscan-mutect SLITRK1,synonymous_variant,p.=,ENST00000377084,NM_052910.2,NM_001281503.1; G ENST00000377084 Transcript synonymous_variant 1081/5189 195/2091 65/696 L ctG/ctC rs368351965,COSM4844947 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF33,Superfamily_domains:SSF52058 0,1 LOW 1 SNV 0,1 1 PASS rs368351965 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 83881313 83881313 C G 1 0 0 0 0 0 0 0 1 15033 697 25 4 4 SLITRK1 13 83881313 Silent SNP C C3N-01071_T 6675745 83881313 30483015 241 21799 SLITRK6 0 . GRCh38 13 85795667 85795667 + Missense_Mutation SNP C C G rs772627817 C3N-01071_T C3N-01071_N C C c.842G>C p.Gly281Ala p.G281A ENST00000400286 2/2 265 238 27 203 203 0 strelka-varscan-mutect SLITRK6,missense_variant,p.Gly281Ala,ENST00000400286,NM_032229.2; G ENST00000400286 Transcript missense_variant 1441/4318 842/2526 281/841 G/A gGa/gCa rs772627817 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 tolerated(0.32) 2/2 MODERATE 1 SNV 1 1 PASS rs772627817 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 71 85795667 85795667 C G 1 0 0 0 0 1 0 0 0 15038 855 30 4 4 SLITRK6 13 85795667 Missense_Mutation SNP C C3N-01071_T 1914354 85795667 28568661 242 21800 RNASE2 0 . GRCh38 14 20955870 20955870 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.99C>A p.= p.T33T ENST00000304625 2/2 225 182 43 251 251 0 strelka-varscan-mutect RNASE2,synonymous_variant,p.=,ENST00000304625,NM_002934.2; A ENST00000304625 Transcript synonymous_variant 189/755 99/486 33/161 T acC/acA 1 1 RNASE2 HGNC HGNC:10045 protein_coding YES CCDS9561.1 ENSP00000303276 P10153 W0UV60 UPI000004D2F8 NM_002934.2 2/2 Gene3D:3.10.130.10,PD000535,hmmpanther:PTHR11437,hmmpanther:PTHR11437:SF3,SMART_domains:SM00092,Superfamily_domains:SSF54076 LOW 1 SNV 1 1 PASS rs1297226667 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 20955870 20955870 C A 1 0 0 0 0 0 0 0 1 13583 668 24 2 2 RNASE2 14 20955870 Silent SNP C C3N-01071_T 20955870 86087848 243 21801 DACT1 0 . GRCh38 14 58638305 58638305 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.103G>A p.Gly35Ser p.G35S ENST00000335867 1/4 41 37 4 54 54 0 strelka-mutect DACT1,missense_variant,p.Gly35Ser,ENST00000395153,NM_001079520.1;DACT1,missense_variant,p.Gly35Ser,ENST00000335867,NM_016651.5;DACT1,intron_variant,,ENST00000556859,;DACT1,intron_variant,,ENST00000421793,;DACT1,upstream_gene_variant,,ENST00000541264,;DACT1,intron_variant,,ENST00000555845,; A ENST00000335867 Transcript missense_variant 127/2571 103/2511 35/836 G/S Ggc/Agc 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 deleterious(0.05) 1/4 hmmpanther:PTHR15919:SF12,hmmpanther:PTHR15919 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -10.92873 1 1 1 1 0 A 3 1 71 58638305 58638305 G A 1 0 0 0 0 1 0 0 0 4023 1232 43 3 3 DACT1 14 58638305 Missense_Mutation SNP G C3N-01071_T 37682435 58638305 48405413 244 21802 KCNH5 0 . GRCh38 14 62981241 62981241 + Silent SNP G G T C3N-01071_T C3N-01071_N G G c.573C>A p.= p.I191I ENST00000322893 6/11 211 200 11 267 266 1 strelka-varscan-mutect KCNH5,synonymous_variant,p.=,ENST00000322893,NM_139318.4;KCNH5,synonymous_variant,p.=,ENST00000420622,NM_172375.2;KCNH5,synonymous_variant,p.=,ENST00000394968,;KCNH5,non_coding_transcript_exon_variant,,ENST00000394964,; T ENST00000322893 Transcript synonymous_variant 842/11290 573/2967 191/988 I atC/atA COSM5596905,COSM5596906 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 6/11 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Prints_domain:PR01464 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -13.43822 0.9999993 1 1 1 0 T 2 4 71 62981241 62981241 G T 1 0 0 0 0 0 0 0 1 7951 1164 41 2 2 KCNH5 14 62981241 Silent SNP G C3N-01071_T 4342936 62981241 44062477 245 21803 GPHN 0 . GRCh38 14 66922767 66922767 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.558G>C p.Leu186Phe p.L186F ENST00000478722 7/23 238 225 13 237 237 0 strelka-mutect GPHN,missense_variant,p.Leu186Phe,ENST00000478722,NM_020806.4;GPHN,missense_variant,p.Leu186Phe,ENST00000315266,NM_001024218.1;GPHN,missense_variant,p.Leu199Phe,ENST00000543237,;GPHN,missense_variant,p.Leu168Phe,ENST00000459628,;GPHN,missense_variant,p.Leu119Phe,ENST00000555456,;GPHN,non_coding_transcript_exon_variant,,ENST00000544752,;GPHN,downstream_gene_variant,,ENST00000556633,; C ENST00000478722 Transcript missense_variant 1679/4297 558/2310 186/769 L/F ttG/ttC 1 1 GPHN HGNC HGNC:15465 protein_coding YES CCDS9777.1 ENSP00000417901 Q9NQX3 UPI0000072592 NM_020806.4 deleterious(0.04) 7/23 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 66922767 66922767 G C 1 0 0 0 0 1 0 0 0 6512 1310 46 4 4 GPHN 14 66922767 Missense_Mutation SNP G C3N-01071_T 3941526 66922767 40120951 246 21804 ACOT2 0 . GRCh38 14 73569607 73569607 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.367G>T p.Asp123Tyr p.D123Y ENST00000238651 1/3 249 235 14 226 226 0 varscan-mutect ACOT2,missense_variant,p.Asp123Tyr,ENST00000238651,NM_006821.5;ACOT2,missense_variant,p.Asp61Tyr,ENST00000622407,;ACOT2,missense_variant,p.Asp103Tyr,ENST00000613168,;ACOT2,upstream_gene_variant,,ENST00000557857,;ACOT2,intron_variant,,ENST00000538782,;NT5CP1,downstream_gene_variant,,ENST00000554092,; T ENST00000238651 Transcript missense_variant 549/1774 367/1452 123/483 D/Y Gac/Tac 1 1 ACOT2 HGNC HGNC:18431 protein_coding YES CCDS9816.1 ENSP00000238651 P49753 UPI000013CA4E NM_006821.5 deleterious(0) 1/3 hmmpanther:PTHR10824,hmmpanther:PTHR10824:SF16,PIRSF_domain:PIRSF016521,Pfam_domain:PF04775 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 73569607 73569607 G T 1 0 0 0 0 1 0 0 0 194 1174 41 2 2 ACOT2 14 73569607 Missense_Mutation SNP G C3N-01071_T 6646840 73569607 33474111 247 21805 ESRRB 0 . GRCh38 14 76498377 76498377 + Silent SNP G G T novel C3N-01071_T C3N-01071_N G G c.1221G>T p.= p.V407V ENST00000509242 7/9 556 521 35 469 469 0 strelka-varscan-mutect ESRRB,synonymous_variant,p.=,ENST00000509242,;ESRRB,synonymous_variant,p.=,ENST00000380887,NM_004452.3;ESRRB,synonymous_variant,p.=,ENST00000512784,;ESRRB,synonymous_variant,p.=,ENST00000556177,;RP11-187O7.3,intron_variant,,ENST00000554926,;ESRRB,synonymous_variant,p.=,ENST00000505752,;ESRRB,upstream_gene_variant,,ENST00000611036,; T ENST00000509242 Transcript synonymous_variant 1429/2849 1221/1527 407/508 V gtG/gtT 1 1 ESRRB HGNC HGNC:3473 protein_coding YES CCDS9850.2 ENSP00000422488 O95718 UPI000003157B 7/9 Gene3D:1.10.565.10,Pfam_domain:PF00104,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939,Prints_domain:PR00398,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF23,Superfamily_domains:SSF48508 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 76498377 76498377 G T 1 0 0 0 0 0 0 0 1 5123 1306 46 2 2 ESRRB 14 76498377 Silent SNP G C3N-01071_T 2928770 76498377 30545341 248 21806 TNFAIP2 0 . GRCh38 14 103135348 103135348 + Silent SNP A A T novel C3N-01071_T C3N-01071_N A A c.1953A>T p.= p.I651I ENST00000560869 12/12 55 46 9 77 77 0 strelka-varscan-mutect TNFAIP2,synonymous_variant,p.=,ENST00000560869,;TNFAIP2,synonymous_variant,p.=,ENST00000333007,NM_006291.2;TNFAIP2,synonymous_variant,p.=,ENST00000559255,;TNFAIP2,synonymous_variant,p.=,ENST00000560670,;NDUFB4P11,upstream_gene_variant,,ENST00000600530,;TNFAIP2,upstream_gene_variant,,ENST00000561217,;TNFAIP2,3_prime_UTR_variant,,ENST00000559406,;TNFAIP2,3_prime_UTR_variant,,ENST00000560562,;TNFAIP2,downstream_gene_variant,,ENST00000560428,;TNFAIP2,downstream_gene_variant,,ENST00000561156,;NDUFB4P11,upstream_gene_variant,,ENST00000560510,; T ENST00000560869 Transcript synonymous_variant 2592/4683 1953/1965 651/654 I atA/atT 1 1 TNFAIP2 HGNC HGNC:11895 protein_coding YES CCDS9979.1 ENSP00000452634 Q03169 UPI0000164A41 12/12 hmmpanther:PTHR21292:SF4,hmmpanther:PTHR21292 LOW 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -19.95957 0.9999999 1 1 1 0 T 2 4 71 103135348 103135348 A T 1 0 0 0 0 0 0 0 1 16747 352 13 4 4 TNFAIP2 14 103135348 Silent SNP A C3N-01071_T 26636971 103135348 3908370 249 21807 AHNAK2 0 . GRCh38 14 104944665 104944665 + Missense_Mutation SNP C C T rs371361988 C3N-01071_T C3N-01071_N C C c.10786G>A p.Asp3596Asn p.D3596N ENST00000333244 7/7 439 378 61 348 348 0 strelka-varscan-mutect AHNAK2,missense_variant,p.Asp3596Asn,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; T ENST00000333244 Transcript missense_variant 10906/18254 10786/17388 3596/5795 D/N Gat/Aat rs371361988 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.06) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS rs371361988 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 104944665 104944665 C T 1 0 0 0 0 1 0 0 0 492 884 31 1 1 AHNAK2 14 104944665 Missense_Mutation SNP C C3N-01071_T 1809317 104944665 2099053 250 21808 FAM189A1 0 . GRCh38 15 29570544 29570544 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.180C>T p.= p.A60A ENST00000261275 1/11 102 84 18 111 111 0 strelka-varscan-mutect FAM189A1,synonymous_variant,p.=,ENST00000261275,NM_015307.1;FAM189A1,upstream_gene_variant,,ENST00000560050,; A ENST00000261275 Transcript synonymous_variant 180/4705 180/1620 60/539 A gcC/gcT 1 -1 FAM189A1 HGNC HGNC:29075 protein_coding YES CCDS45198.1 ENSP00000261275 O60320 UPI0001641C10 NM_015307.1 1/11 Pfam_domain:PF04103,hmmpanther:PTHR17615,hmmpanther:PTHR17615:SF6 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 29570544 29570544 G A 1 0 0 0 0 0 0 0 1 5367 1219 43 3 3 FAM189A1 15 29570544 Silent SNP G C3N-01071_T 29570544 72420645 251 21809 SPRED1 0 . GRCh38 15 38351483 38351483 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.1154G>C p.Gly385Ala p.G385A ENST00000299084 7/7 335 289 46 341 341 0 strelka-varscan-mutect SPRED1,missense_variant,p.Gly385Ala,ENST00000299084,NM_152594.2; C ENST00000299084 Transcript missense_variant 2014/7780 1154/1335 385/444 G/A gGa/gCa 1 1 SPRED1 HGNC HGNC:20249 protein_coding YES CCDS32193.1 ENSP00000299084 Q7Z699 UPI0000072FBD NM_152594.2 deleterious(0) 7/7 PROSITE_profiles:PS51227,hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF18,Pfam_domain:PF05210 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 38351483 38351483 G C 1 0 0 0 0 1 0 0 0 15446 1174 41 4 4 SPRED1 15 38351483 Missense_Mutation SNP G C3N-01071_T 8780939 38351483 63639706 252 21810 PLA2G4F 0 . GRCh38 15 42147649 42147649 + Silent SNP C C G novel C3N-01071_T C3N-01071_N C C c.1173G>C p.= p.L391L ENST00000397272 12/20 203 180 23 185 185 0 strelka-varscan-mutect PLA2G4F,synonymous_variant,p.=,ENST00000397272,NM_213600.3;PLA2G4F,3_prime_UTR_variant,,ENST00000569985,;PLA2G4F,3_prime_UTR_variant,,ENST00000290497,;PLA2G4F,non_coding_transcript_exon_variant,,ENST00000561893,;PLA2G4F,upstream_gene_variant,,ENST00000562320,;PLA2G4F,downstream_gene_variant,,ENST00000561627,; G ENST00000397272 Transcript synonymous_variant 1260/5587 1173/2550 391/849 L ctG/ctC 1 -1 PLA2G4F HGNC HGNC:27396 protein_coding YES CCDS32204.1 ENSP00000380442 Q68DD2 UPI0000160965 NM_213600.3 12/20 Gene3D:3.40.1090.10,Pfam_domain:PF01735,PROSITE_profiles:PS51210,hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF22,SMART_domains:SM00022,Superfamily_domains:SSF52151 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 42147649 42147649 C G 1 0 0 0 0 0 0 0 1 12102 813 29 4 4 PLA2G4F 15 42147649 Silent SNP C C3N-01071_T 3796166 42147649 59843540 253 21811 FBN1 0 . GRCh38 15 48465589 48465589 + Missense_Mutation SNP C C G rs749438833 C3N-01071_T C3N-01071_N C C c.4921G>C p.Glu1641Gln p.E1641Q ENST00000316623 40/66 339 316 23 325 325 0 strelka-mutect FBN1,missense_variant,p.Glu1641Gln,ENST00000316623,NM_000138.4;FBN1,missense_variant,p.Glu77Gln,ENST00000559133,;FBN1,3_prime_UTR_variant,,ENST00000537463,; G ENST00000316623 Transcript missense_variant 5377/11756 4921/8616 1641/2871 E/Q Gaa/Caa rs749438833 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 tolerated(0.08) 40/66 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs749438833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 48465589 48465589 C G 1 0 0 0 0 1 0 0 0 5565 835 29 4 4 FBN1 15 48465589 Missense_Mutation SNP C C3N-01071_T 6317940 48465589 53525600 254 21812 ITGA11 0 . GRCh38 15 68357233 68357233 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.667A>G p.Lys223Glu p.K223E ENST00000315757 7/30 202 183 19 230 230 0 strelka-varscan-mutect ITGA11,missense_variant,p.Lys223Glu,ENST00000423218,;ITGA11,missense_variant,p.Lys223Glu,ENST00000315757,NM_001004439.1;ITGA11,non_coding_transcript_exon_variant,,ENST00000562826,;ITGA11,non_coding_transcript_exon_variant,,ENST00000568677,;ITGA11,non_coding_transcript_exon_variant,,ENST00000565868,; C ENST00000315757 Transcript missense_variant 763/3955 667/3567 223/1188 K/E Aaa/Gaa 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 tolerated(1) 7/30 PROSITE_profiles:PS50234,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 68357233 68357233 T C 1 0 0 0 0 1 0 0 0 7781 1850 64 5 5 ITGA11 15 68357233 Missense_Mutation SNP T C3N-01071_T 19891644 68357233 33633956 255 21813 ADPGK 0 . GRCh38 15 72752816 72752816 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.1016A>T p.His339Leu p.H339L ENST00000311669 7/7 165 154 11 160 160 0 strelka-varscan-mutect ADPGK,missense_variant,p.His339Leu,ENST00000311669,NM_031284.4;ADPGK,missense_variant,p.His65Leu,ENST00000456471,;ADPGK,3_prime_UTR_variant,,ENST00000563907,;ADPGK,downstream_gene_variant,,ENST00000565814,;ADPGK,downstream_gene_variant,,ENST00000567733,;ADPGK,3_prime_UTR_variant,,ENST00000567941,;ADPGK,3_prime_UTR_variant,,ENST00000569534,;ADPGK,3_prime_UTR_variant,,ENST00000569693,;ADPGK,3_prime_UTR_variant,,ENST00000569517,;ADPGK,non_coding_transcript_exon_variant,,ENST00000562621,; A ENST00000311669 Transcript missense_variant 1110/2557 1016/1491 339/496 H/L cAc/cTc 1 -1 ADPGK HGNC HGNC:25250 protein_coding YES CCDS42057.1 ENSP00000312250 Q9BRR6 UPI0000039E98 NM_031284.4 deleterious(0) 7/7 Gene3D:3.40.1190.20,Pfam_domain:PF04587,PROSITE_profiles:PS51255,hmmpanther:PTHR21208,hmmpanther:PTHR21208:SF0,Superfamily_domains:SSF53613 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -14.6968 0.9999996 1 1 1 0 A 3 1 71 72752816 72752816 T A 1 0 0 0 0 1 0 0 0 405 1696 59 4 4 ADPGK 15 72752816 Missense_Mutation SNP T C3N-01071_T 4395583 72752816 29238373 256 21814 CEMIP 0 . GRCh38 15 80933337 80933337 + Missense_Mutation SNP C C A rs773913269 C3N-01071_T C3N-01071_N C C c.2886C>A p.Asp962Glu p.D962E ENST00000394685 23/30 480 432 48 419 419 0 strelka-varscan-mutect CEMIP,missense_variant,p.Asp962Glu,ENST00000394685,NM_001293298.1;CEMIP,missense_variant,p.Asp962Glu,ENST00000356249,NM_001293304.1;CEMIP,missense_variant,p.Asp962Glu,ENST00000220244,NM_018689.2;CEMIP,missense_variant,p.Asp962Glu,ENST00000611615,;CEMIP,upstream_gene_variant,,ENST00000560027,;RP11-351M8.2,intron_variant,,ENST00000560873,;CEMIP,upstream_gene_variant,,ENST00000495041,; A ENST00000394685 Transcript missense_variant 3305/7357 2886/4086 962/1361 D/E gaC/gaA rs773913269,COSM4974047 1 1 CEMIP HGNC HGNC:29213 protein_coding YES CCDS10315.1 ENSP00000378177 Q8WUJ3 UPI00001D7799 NM_001293298.1 deleterious(0) 23/30 hmmpanther:PTHR15535,hmmpanther:PTHR15535:SF15,Superfamily_domains:SSF51126 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs773913269 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 80933337 80933337 C A 1 0 0 0 0 1 0 0 0 2931 535 19 1 1 CEMIP 15 80933337 Missense_Mutation SNP C C3N-01071_T 8180521 80933337 21057852 257 21815 BTBD1 0 . GRCh38 15 83030141 83030141 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.1050A>G p.= p.R350R ENST00000261721 5/8 245 232 13 292 292 0 strelka-varscan-mutect BTBD1,synonymous_variant,p.=,ENST00000261721,NM_025238.3;BTBD1,synonymous_variant,p.=,ENST00000379403,NM_001011885.1;RP11-382A20.5,intron_variant,,ENST00000566841,;RP11-382A20.6,intron_variant,,ENST00000568441,;RP11-382A20.7,intron_variant,,ENST00000570202,;BTBD1,non_coding_transcript_exon_variant,,ENST00000560015,;BTBD1,3_prime_UTR_variant,,ENST00000559652,;BTBD1,non_coding_transcript_exon_variant,,ENST00000558344,; C ENST00000261721 Transcript synonymous_variant 1253/3297 1050/1449 350/482 R cgA/cgG 1 -1 BTBD1 HGNC HGNC:1120 protein_coding YES CCDS10322.1 ENSP00000261721 Q9H0C5 A0A024R224 UPI00000012BE NM_025238.3 5/8 hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF15,Pfam_domain:PF08005 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 83030141 83030141 T C 1 0 0 0 0 0 0 0 1 1712 1797 62 5 5 BTBD1 15 83030141 Silent SNP T C3N-01071_T 2096804 83030141 18961048 258 21816 SEC11A 0 . GRCh38 15 84680776 84680776 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.368G>T p.Arg123Leu p.R123L ENST00000558134 4/5 108 101 7 120 120 0 strelka-varscan-mutect SEC11A,missense_variant,p.Arg123Leu,ENST00000268220,NM_014300.3;SEC11A,missense_variant,p.Arg73Leu,ENST00000559729,NM_001271921.1;SEC11A,missense_variant,p.Arg97Leu,ENST00000455959,NM_001271918.1;SEC11A,missense_variant,p.Arg123Leu,ENST00000560266,NM_001271920.1;SEC11A,missense_variant,p.Arg123Leu,ENST00000558134,NM_001271922.1;SEC11A,missense_variant,p.Arg97Leu,ENST00000558196,;SEC11A,intron_variant,,ENST00000558217,NM_001271919.1;SEC11A,missense_variant,p.Arg123Leu,ENST00000560409,; A ENST00000558134 Transcript missense_variant 382/971 368/558 123/185 R/L cGa/cTa 1 -1 SEC11A HGNC HGNC:17718 protein_coding YES CCDS61743.1 ENSP00000452697 P67812 UPI00022F86B3 NM_001271922.1 tolerated(0.14) 4/5 hmmpanther:PTHR10806,hmmpanther:PTHR10806:SF9,PROSITE_patterns:PS00761,TIGRFAM_domain:TIGR02228,Gene3D:2.10.109.10,Superfamily_domains:SSF51306 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 84680776 84680776 C A 1 0 0 0 0 1 0 0 0 14254 884 31 1 1 SEC11A 15 84680776 Missense_Mutation SNP C C3N-01071_T 1650635 84680776 17310413 259 21817 OR4F6 0 . GRCh38 15 101806201 101806201 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.482C>A p.Ala161Asp p.A161D ENST00000328882 1/1 136 123 13 164 164 0 strelka-varscan-mutect OR4F6,missense_variant,p.Ala161Asp,ENST00000328882,NM_001005326.1;OR4F15,intron_variant,,ENST00000536946,; A ENST00000328882 Transcript missense_variant 503/988 482/939 161/312 A/D gCt/gAt 1 1 OR4F6 HGNC HGNC:15372 protein_coding YES CCDS32341.1 ENSP00000327525 Q8NGB9 A0A126GV96 UPI0000041BF4 NM_001005326.1 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF441,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 101806201 101806201 C A 1 0 0 0 0 1 0 0 0 11143 797 28 2 2 OR4F6 15 101806201 Missense_Mutation SNP C C3N-01071_T 17125425 101806201 184988 260 21818 CCDC154 0 . GRCh38 16 1438889 1438889 + Nonsense_Mutation SNP C C A rs867487247 C3N-01071_T C3N-01071_N C C c.832G>T p.Glu278Ter p.E278* ENST00000389176 8/17 131 116 15 104 104 0 strelka-varscan-mutect CCDC154,stop_gained,p.Glu133Ter,ENST00000409671,;CCDC154,stop_gained,p.Glu278Ter,ENST00000389176,NM_001143980.1;LA16c-312E8.4,non_coding_transcript_exon_variant,,ENST00000624543,;CCDC154,upstream_gene_variant,,ENST00000483702,;CCDC154,upstream_gene_variant,,ENST00000463299,; A ENST00000389176 Transcript stop_gained 999/2212 832/2025 278/674 E/* Gag/Tag rs867487247 1 -1 CCDC154 HGNC HGNC:34454 protein_coding YES ENSP00000373828 A6NI56 UPI000178DF39 NM_001143980.1 8/17 hmmpanther:PTHR35153,Pfam_domain:PF15450 HIGH 1 SNV 5 1 PASS rs867487247 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 71 1438889 1438889 C A 1 0 0 0 0 0 1 0 0 2475 893 31 1 1 CCDC154 16 1438889 Nonsense_Mutation SNP C C3N-01071_T 1438889 88899456 261 21819 CASKIN1 0 . GRCh38 16 2180227 2180227 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.3141G>T p.= p.V1047V ENST00000343516 18/20 205 194 11 191 191 0 strelka-varscan-mutect CASKIN1,synonymous_variant,p.=,ENST00000343516,NM_020764.3;TRAF7,downstream_gene_variant,,ENST00000326181,NM_032271.2;CASKIN1,downstream_gene_variant,,ENST00000564289,; A ENST00000343516 Transcript synonymous_variant 3234/5759 3141/4296 1047/1431 V gtG/gtT 1 -1 CASKIN1 HGNC HGNC:20879 protein_coding YES CCDS42103.1 ENSP00000345436 Q8WXD9 UPI0000073A3B NM_020764.3 18/20 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 2180227 2180227 C A 1 0 0 0 0 0 0 0 1 2366 813 29 2 2 CASKIN1 16 2180227 Silent SNP C C3N-01071_T 741338 2180227 88158118 262 21820 C16orf59 0 . GRCh38 16 2462233 2462233 + Silent SNP G G A C3N-01071_T C3N-01071_N G G c.744G>A p.= p.Q248Q ENST00000361837 6/10 212 195 17 210 210 0 strelka-varscan-mutect C16orf59,synonymous_variant,p.=,ENST00000569496,;C16orf59,synonymous_variant,p.=,ENST00000563531,;C16orf59,synonymous_variant,p.=,ENST00000483320,;C16orf59,synonymous_variant,p.=,ENST00000361837,NM_025108.2;C16orf59,synonymous_variant,p.=,ENST00000567489,;C16orf59,synonymous_variant,p.=,ENST00000568753,;CCNF,downstream_gene_variant,,ENST00000397066,NM_001761.2;RP11-715J22.4,upstream_gene_variant,,ENST00000566085,;RP11-715J22.4,upstream_gene_variant,,ENST00000565827,;MIR6768,upstream_gene_variant,,ENST00000610734,;RP11-715J22.2,downstream_gene_variant,,ENST00000563775,;C16orf59,missense_variant,p.Arg143Lys,ENST00000565716,;C16orf59,non_coding_transcript_exon_variant,,ENST00000569994,;C16orf59,non_coding_transcript_exon_variant,,ENST00000566580,;CCNF,downstream_gene_variant,,ENST00000293968,NM_001323538.1;C16orf59,downstream_gene_variant,,ENST00000569664,;C16orf59,downstream_gene_variant,,ENST00000562253,;C16orf59,downstream_gene_variant,,ENST00000569665,;C16orf59,downstream_gene_variant,,ENST00000565537,; A ENST00000361837 Transcript synonymous_variant 809/1662 744/1302 248/433 Q caG/caA COSM3508058 1 1 C16orf59 HGNC HGNC:25849 protein_coding YES CCDS10468.2 ENSP00000355022 Q7L2K0 UPI000059D2F3 NM_025108.2 6/10 Pfam_domain:PF15764,hmmpanther:PTHR14870 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 2462233 2462233 G A 1 0 0 0 0 0 0 0 1 1860 933 33 3 3 C16orf59 16 2462233 Silent SNP G C3N-01071_T 282006 2462233 87876112 263 21821 XYLT1 0 . GRCh38 16 17470746 17470746 + Silent SNP C C A rs779580489 C3N-01071_T C3N-01071_N C C c.51G>T p.= p.A17A ENST00000261381 1/12 75 56 19 65 65 0 strelka-varscan-mutect XYLT1,synonymous_variant,p.=,ENST00000261381,NM_022166.3; A ENST00000261381 Transcript synonymous_variant 136/9891 51/2880 17/959 A gcG/gcT rs779580489 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 1/12 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs779580489 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 17470746 17470746 C A 1 0 0 0 0 0 0 0 1 18022 755 27 1 1 XYLT1 16 17470746 Silent SNP C C3N-01071_T 15008513 17470746 72867599 264 21822 VWA3A 0 . GRCh38 16 22126227 22126227 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.1582C>G p.His528Asp p.H528D ENST00000389398 17/34 183 164 19 253 253 0 strelka-varscan-mutect VWA3A,missense_variant,p.His528Asp,ENST00000389398,NM_173615.4;VWA3A,missense_variant,p.His549Asp,ENST00000568328,;VWA3A,missense_variant,p.His138Asp,ENST00000299840,;VWA3A,non_coding_transcript_exon_variant,,ENST00000566668,; G ENST00000389398 Transcript missense_variant 1678/4600 1582/3555 528/1184 H/D Cat/Gat 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 deleterious(0) 17/34 hmmpanther:PTHR10338:SF95,hmmpanther:PTHR10338,Pfam_domain:PF13768,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 22126227 22126227 C G 1 0 0 0 0 1 0 0 0 17794 826 29 4 4 VWA3A 16 22126227 Missense_Mutation SNP C C3N-01071_T 4655481 22126227 68212118 265 21823 PRKCB 0 . GRCh38 16 24214813 24214813 + Silent SNP C C T novel C3N-01071_T C3N-01071_N C C c.2019C>T p.= p.S673S ENST00000303531 17/17 110 103 7 77 77 0 strelka-varscan-mutect PRKCB,synonymous_variant,p.=,ENST00000303531,NM_002738.6;PRKCB,intron_variant,,ENST00000321728,NM_212535.2; T ENST00000303531 Transcript synonymous_variant 2171/7969 2019/2022 673/673 S agC/agT 1 1 PRKCB HGNC HGNC:9395 protein_coding YES CCDS10619.1 ENSP00000305355 P05771 UPI000002ACF9 NM_002738.6 17/17 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 24214813 24214813 C T 1 0 0 0 0 0 0 0 1 12641 796 28 3 3 PRKCB 16 24214813 Silent SNP C C3N-01071_T 2088586 24214813 66123532 266 21824 CLN3 0 . GRCh38 16 28477611 28477611 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1222G>T p.Ala408Ser p.A408S ENST00000569430 17/17 541 479 62 448 446 2 strelka-varscan-mutect CLN3,missense_variant,p.Ala408Ser,ENST00000569430,;CLN3,missense_variant,p.Ala408Ser,ENST00000636147,NM_001042432.1;CLN3,missense_variant,p.Ala408Ser,ENST00000359984,NM_000086.2;CLN3,missense_variant,p.Ala384Ser,ENST00000360019,NM_001286104.1;CLN3,missense_variant,p.Ala354Ser,ENST00000357857,NM_001286110.1;CLN3,missense_variant,p.Ala384Ser,ENST00000333496,;CLN3,missense_variant,p.Ala311Ser,ENST00000631023,;CLN3,missense_variant,p.Ala309Ser,ENST00000357806,;CLN3,missense_variant,p.Ala354Ser,ENST00000567963,NM_001286109.1;CLN3,missense_variant,p.Ala255Ser,ENST00000395653,;CLN3,missense_variant,p.Ala391Ser,ENST00000565316,;CLN3,missense_variant,p.Ala306Ser,ENST00000636228,;CLN3,missense_variant,p.Ala360Ser,ENST00000355477,;CLN3,missense_variant,p.Ala308Ser,ENST00000637551,NM_001286105.1;CLN3,intron_variant,,ENST00000637100,;RP11-435I10.4,intron_variant,,ENST00000637378,;CLN3,downstream_gene_variant,,ENST00000635973,;CLN3,downstream_gene_variant,,ENST00000568497,;CLN3,downstream_gene_variant,,ENST00000565778,;CLN3,downstream_gene_variant,,ENST00000565047,;RP11-435I10.4,missense_variant,p.Ala408Ser,ENST00000635887,;RP11-435I10.4,missense_variant,p.Ala408Ser,ENST00000636766,;RP11-435I10.4,missense_variant,p.Ala330Ser,ENST00000568224,;RP11-435I10.4,missense_variant,p.Ala129Ser,ENST00000638036,;CLN3,missense_variant,p.Ala188Ser,ENST00000564091,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000636503,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000637376,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000636866,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000636017,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000637299,;CLN3,3_prime_UTR_variant,,ENST00000637107,;CLN3,3_prime_UTR_variant,,ENST00000637184,;CLN3,3_prime_UTR_variant,,ENST00000637871,;CLN3,3_prime_UTR_variant,,ENST00000637578,;CLN3,3_prime_UTR_variant,,ENST00000636172,;CLN3,3_prime_UTR_variant,,ENST00000635861,;CLN3,3_prime_UTR_variant,,ENST00000637699,;CLN3,3_prime_UTR_variant,,ENST00000565140,;CLN3,3_prime_UTR_variant,,ENST00000628023,;CLN3,3_prime_UTR_variant,,ENST00000568422,;CLN3,3_prime_UTR_variant,,ENST00000569030,;CLN3,3_prime_UTR_variant,,ENST00000566057,;RP11-435I10.4,3_prime_UTR_variant,,ENST00000637745,;CLN3,non_coding_transcript_exon_variant,,ENST00000563874,;CLN3,non_coding_transcript_exon_variant,,ENST00000636977,;RP11-435I10.4,non_coding_transcript_exon_variant,,ENST00000636078,;CLN3,non_coding_transcript_exon_variant,,ENST00000636853,;CLN3,non_coding_transcript_exon_variant,,ENST00000636839,;CLN3,non_coding_transcript_exon_variant,,ENST00000568076,;CLN3,non_coding_transcript_exon_variant,,ENST00000561689,;CLN3,non_coding_transcript_exon_variant,,ENST00000635958,;CLN3,non_coding_transcript_exon_variant,,ENST00000637050,;CLN3,non_coding_transcript_exon_variant,,ENST00000636907,;CLN3,non_coding_transcript_exon_variant,,ENST00000568452,;CLN3,non_coding_transcript_exon_variant,,ENST00000636351,;CLN3,non_coding_transcript_exon_variant,,ENST00000565354,;CLN3,downstream_gene_variant,,ENST00000566083,;CLN3,downstream_gene_variant,,ENST00000566824,;CLN3,downstream_gene_variant,,ENST00000564574,;CLN3,downstream_gene_variant,,ENST00000568472,;CLN3,downstream_gene_variant,,ENST00000636685,; A ENST00000569430 Transcript missense_variant 3550/3867 1222/1317 408/438 A/S Gca/Tca 1 -1 CLN3 HGNC HGNC:2074 protein_coding YES CCDS10632.1 ENSP00000454229 Q13286 A0A024QZB8 UPI00000000ED tolerated(0.39) 17/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR10981:SF0,hmmpanther:PTHR10981,Pfam_domain:PF02487,PIRSF_domain:PIRSF015974,Superfamily_domains:SSF103473,Prints_domain:PR01315 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 28477611 28477611 C A 1 0 0 0 0 1 0 0 0 3313 710 25 2 2 CLN3 16 28477611 Missense_Mutation SNP C C3N-01071_T 4262798 28477611 61860734 267 21825 ASPHD1 0 . GRCh38 16 29901350 29901350 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.379G>T p.Gly127Trp p.G127W ENST00000308748 1/3 71 63 8 57 57 0 strelka-mutect ASPHD1,missense_variant,p.Gly127Trp,ENST00000308748,NM_181718.3;ASPHD1,intron_variant,,ENST00000483405,;ASPHD1,intron_variant,,ENST00000563177,;SEZ6L2,upstream_gene_variant,,ENST00000308713,NM_201575.3,NM_001114099.2;SEZ6L2,upstream_gene_variant,,ENST00000617533,NM_001243332.1;SEZ6L2,upstream_gene_variant,,ENST00000537485,NM_001243333.1;SEZ6L2,upstream_gene_variant,,ENST00000350527,NM_012410.3;SEZ6L2,upstream_gene_variant,,ENST00000346932,NM_001114100.2;KCTD13,downstream_gene_variant,,ENST00000568000,NM_178863.4;SEZ6L2,upstream_gene_variant,,ENST00000568380,;SEZ6L2,upstream_gene_variant,,ENST00000562159,;ASPHD1,missense_variant,p.Gly127Trp,ENST00000566693,;ASPHD1,missense_variant,p.Gly127Trp,ENST00000414952,;KCTD13,downstream_gene_variant,,ENST00000566842,;KCTD13,downstream_gene_variant,,ENST00000308768,; T ENST00000308748 Transcript missense_variant 631/1584 379/1173 127/390 G/W Ggg/Tgg 1 1 ASPHD1 HGNC HGNC:27380 protein_coding YES CCDS10660.1 ENSP00000311447 Q5U4P2 UPI0000197DF0 NM_181718.3 deleterious(0.02) 1/3 hmmpanther:PTHR12366,hmmpanther:PTHR12366:SF27,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 197 12 0 0 0 0 0 -17.33673 0.9998506 1 1 1 0 T 3 4 71 29901350 29901350 G T 1 0 0 0 0 1 0 0 0 1201 1116 39 1 1 ASPHD1 16 29901350 Missense_Mutation SNP G C3N-01071_T 1423739 29901350 60436995 268 21826 SETD1A 0 . GRCh38 16 30965396 30965396 + Missense_Mutation SNP G G A C3N-01071_T C3N-01071_N G G c.1654G>A p.Ala552Thr p.A552T ENST00000262519 7/19 109 99 10 92 92 0 strelka-varscan-mutect SETD1A,missense_variant,p.Ala552Thr,ENST00000262519,NM_014712.2;SETD1A,downstream_gene_variant,,ENST00000452917,; A ENST00000262519 Transcript missense_variant 2340/6903 1654/5124 552/1707 A/T Gca/Aca COSM3707008 1 1 SETD1A HGNC HGNC:29010 protein_coding YES CCDS32435.1 ENSP00000262519 O15047 UPI00001C1FA9 NM_014712.2 tolerated_low_confidence(0.06) 7/19 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF295 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.71511 1 1 1 1 0 A 3 1 71 30965396 30965396 G A 1 0 0 0 0 1 0 0 0 14407 1203 42 3 3 SETD1A 16 30965396 Missense_Mutation SNP G C3N-01071_T 1064046 30965396 59372949 269 21827 ZNF267 0 . GRCh38 16 31915470 31915470 + Silent SNP A A G novel C3N-01071_T C3N-01071_N A A c.1221A>G p.= p.P407P ENST00000300870 4/4 156 138 18 137 137 0 strelka-varscan-mutect ZNF267,synonymous_variant,p.=,ENST00000300870,NM_003414.5;ZNF267,downstream_gene_variant,,ENST00000394846,;ZNF267,downstream_gene_variant,,ENST00000562971,;ZNF267,non_coding_transcript_exon_variant,,ENST00000575471,;ZNF267,downstream_gene_variant,,ENST00000566541,;ZNF267,downstream_gene_variant,,ENST00000561814,; G ENST00000300870 Transcript synonymous_variant 1430/3317 1221/2232 407/743 P ccA/ccG 1 1 ZNF267 HGNC HGNC:13060 protein_coding YES CCDS32440.1 ENSP00000300870 Q14586 UPI000045696F NM_003414.5 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF184,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 204 3 2 0 0 0 0 -20 0.9999886 1 1 1 0 G 2 3 71 31915470 31915470 A G 1 0 0 0 0 0 0 0 1 18382 204 8 5 5 ZNF267 16 31915470 Silent SNP A C3N-01071_T 950074 31915470 58422875 270 21828 CYLD 0 . GRCh38 16 50779841 50779841 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.1315T>C p.Ser439Pro p.S439P ENST00000427738 8/18 237 202 35 207 207 0 strelka-varscan-mutect CYLD,missense_variant,p.Ser439Pro,ENST00000427738,;CYLD,missense_variant,p.Ser439Pro,ENST00000311559,NM_015247.2;CYLD,missense_variant,p.Ser436Pro,ENST00000398568,NM_001042412.1;CYLD,missense_variant,p.Ser436Pro,ENST00000569418,NM_001042355.1;CYLD,missense_variant,p.Ser436Pro,ENST00000564326,;CYLD,missense_variant,p.Ser436Pro,ENST00000566206,;CYLD,intron_variant,,ENST00000568704,;RP11-327F22.4,downstream_gene_variant,,ENST00000564510,;RP11-327F22.4,downstream_gene_variant,,ENST00000575917,;CYLD,non_coding_transcript_exon_variant,,ENST00000569891,;CYLD,non_coding_transcript_exon_variant,,ENST00000563629,;CYLD,downstream_gene_variant,,ENST00000563976,; C ENST00000427738 Transcript missense_variant 1520/8503 1315/2871 439/956 S/P Tct/Cct 1 1 CYLD HGNC HGNC:2584 protein_coding YES CCDS45482.1 ENSP00000392025 Q9NQC7 UPI0000073A15 deleterious(0.02) 8/18 Pfam_domain:PF16607 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 50779841 50779841 T C 1 0 0 0 0 1 0 0 0 3946 1783 62 5 5 CYLD 16 50779841 Missense_Mutation SNP T C3N-01071_T 18864371 50779841 39558504 271 21829 CPNE2 0 . GRCh38 16 57115475 57115475 + Splice_Site SNP G G T novel C3N-01071_T C3N-01071_N G G c.361-1G>T p.X121_splice ENST00000290776 109 97 12 100 100 0 strelka-varscan-mutect CPNE2,splice_acceptor_variant,,ENST00000290776,NM_152727.5;CPNE2,splice_acceptor_variant,,ENST00000535318,;CPNE2,splice_acceptor_variant,,ENST00000565874,;CPNE2,splice_acceptor_variant,,ENST00000567487,;CPNE2,upstream_gene_variant,,ENST00000565766,;CPNE2,downstream_gene_variant,,ENST00000566259,; T ENST00000290776 Transcript splice_acceptor_variant -/2645 361/1647 121/548 1 1 CPNE2 HGNC HGNC:2315 protein_coding YES CCDS10774.1 ENSP00000290776 Q96FN4 UPI000017DA4F NM_152727.5 3/15 HIGH 1 SNV 1 1 PASS rs1283632939 . 0 205 4 0 0 0 0 0 -19.99998 1 1 1 1 0 T 5 4 71 57115475 57115475 G T 1 0 0 0 0 0 0 1 0 3607 956 33 2 2 CPNE2 16 57115475 Splice_Site SNP G C3N-01071_T 6335634 57115475 33222870 272 21830 MMP15 0 . GRCh38 16 58045363 58045363 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.1927A>T p.Thr643Ser p.T643S ENST00000219271 10/10 185 173 12 231 231 0 strelka-varscan-mutect MMP15,missense_variant,p.Thr643Ser,ENST00000219271,NM_002428.2;MMP15,downstream_gene_variant,,ENST00000570065,; T ENST00000219271 Transcript missense_variant 2712/4250 1927/2010 643/669 T/S Acc/Tcc 1 1 MMP15 HGNC HGNC:7161 protein_coding YES CCDS10792.1 ENSP00000219271 P51511 A0A024R6U8 UPI000003DC75 NM_002428.2 deleterious(0.04) 10/10 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,Pfam_domain:PF11857 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 58045363 58045363 A T 1 0 0 0 0 1 0 0 0 9617 159 6 4 4 MMP15 16 58045363 Missense_Mutation SNP A C3N-01071_T 929888 58045363 32292982 273 21831 CNOT1 0 . GRCh38 16 58525287 58525287 + Missense_Mutation SNP C C G C3N-01071_T C3N-01071_N C C c.6676G>C p.Ala2226Pro p.A2226P ENST00000317147 46/49 429 399 30 409 409 0 strelka-varscan-mutect CNOT1,missense_variant,p.Ala2226Pro,ENST00000317147,NM_016284.4;CNOT1,missense_variant,p.Ala2221Pro,ENST00000569240,NM_001265612.1;SETD6,downstream_gene_variant,,ENST00000394266,;RP11-481J2.4,downstream_gene_variant,,ENST00000622896,;CNOT1,3_prime_UTR_variant,,ENST00000567188,;CNOT1,non_coding_transcript_exon_variant,,ENST00000563130,;CNOT1,non_coding_transcript_exon_variant,,ENST00000569924,;CNOT1,downstream_gene_variant,,ENST00000570139,; G ENST00000317147 Transcript missense_variant 7009/8471 6676/7131 2226/2376 A/P Gcc/Ccc COSM2992808 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 deleterious(0) 46/49 hmmpanther:PTHR13162,Pfam_domain:PF04054 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 58525287 58525287 C G 1 0 0 0 0 1 0 0 0 3396 739 26 4 4 CNOT1 16 58525287 Missense_Mutation SNP C C3N-01071_T 479924 58525287 31813058 274 21832 AARS 0 . GRCh38 16 70253934 70253934 + Silent SNP G G A rs769571173 C3N-01071_T C3N-01071_N G G c.2505C>T p.= p.A835A ENST00000261772 18/21 811 770 41 678 678 0 strelka-varscan-mutect AARS,synonymous_variant,p.=,ENST00000261772,NM_001605.2;EXOSC6,upstream_gene_variant,,ENST00000435634,NM_058219.2;AARS,downstream_gene_variant,,ENST00000565361,;AARS,downstream_gene_variant,,ENST00000564359,;AARS,non_coding_transcript_exon_variant,,ENST00000569825,; A ENST00000261772 Transcript synonymous_variant 2649/3477 2505/2907 835/968 A gcC/gcT rs769571173,COSM4644011 1 -1 AARS HGNC HGNC:20 protein_coding YES CCDS32474.1 ENSP00000261772 P49588 UPI0000169F0B NM_001605.2 18/21 HAMAP:MF_00036_B,hmmpanther:PTHR11777:SF9,hmmpanther:PTHR11777,TIGRFAM_domain:TIGR00344 0,1 LOW 1 SNV 1 0,1 1 PASS rs769571173 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 70253934 70253934 G A 1 0 0 0 0 0 0 0 1 23 1103 39 1 1 AARS 16 70253934 Silent SNP G C3N-01071_T 11728647 70253934 20084411 275 21833 PLCG2 0 . GRCh38 16 81938800 81938800 + Splice_Site SNP G G A novel C3N-01071_T C3N-01071_N G G c.3199-1G>A p.X1067_splice ENST00000564138 123 115 8 121 121 0 strelka-varscan-mutect PLCG2,splice_acceptor_variant,,ENST00000564138,NM_002661.4;PLCG2,splice_acceptor_variant,,ENST00000359376,;PLCG2,splice_acceptor_variant,,ENST00000563834,;PLCG2,splice_acceptor_variant,,ENST00000567373,;PLCG2,non_coding_transcript_exon_variant,,ENST00000567356,;PLCG2,downstream_gene_variant,,ENST00000563269,; A ENST00000564138 Transcript splice_acceptor_variant -/8707 3199/3798 1067/1265 1 1 PLCG2 HGNC HGNC:9066 protein_coding YES CCDS42204.1 ENSP00000482457 P16885 UPI00001411F7 NM_002661.4 28/32 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 71 81938800 81938800 G A 1 0 0 0 0 0 0 1 0 12130 1014 35 3 3 PLCG2 16 81938800 Splice_Site SNP G C3N-01071_T 11684866 81938800 8399545 276 21834 NECAB2 0 . GRCh38 16 83978544 83978544 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.327C>A p.Asp109Glu p.D109E ENST00000305202 3/13 133 121 12 162 162 0 strelka-mutect NECAB2,missense_variant,p.Thr35Lys,ENST00000565691,;NECAB2,missense_variant,p.Asp109Glu,ENST00000305202,NM_019065.2;NECAB2,upstream_gene_variant,,ENST00000566836,; A ENST00000305202 Transcript missense_variant 344/1608 327/1161 109/386 D/E gaC/gaA 1 1 NECAB2 HGNC HGNC:23746 protein_coding YES CCDS10940.1 ENSP00000307449 Q7Z6G3 UPI00001A9944 NM_019065.2 deleterious(0.02) 3/13 PROSITE_profiles:PS50222,hmmpanther:PTHR12178:SF2,hmmpanther:PTHR12178,PROSITE_patterns:PS00018,Gene3D:1.10.238.10,Pfam_domain:PF13833,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs35610958 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 83978544 83978544 C A 1 0 0 0 0 1 0 0 0 10329 478 17 2 2 NECAB2 16 83978544 Missense_Mutation SNP C C3N-01071_T 2039744 83978544 6359801 277 21835 HIC1 0 . GRCh38 17 2057550 2057550 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.917C>T p.Pro306Leu p.P306L ENST00000322941 2/2 338 273 65 418 418 0 strelka-varscan-mutect HIC1,missense_variant,p.Pro287Leu,ENST00000619757,;HIC1,missense_variant,p.Pro287Leu,ENST00000399849,NM_006497.3;HIC1,missense_variant,p.Pro306Leu,ENST00000322941,NM_001098202.1;SMG6,downstream_gene_variant,,ENST00000263073,NM_017575.4;SMG6,downstream_gene_variant,,ENST00000354901,NM_001256827.1;SMG6,downstream_gene_variant,,ENST00000536871,NM_001256828.1;HIC1,downstream_gene_variant,,ENST00000574370,;HIC1,downstream_gene_variant,,ENST00000571875,;HIC1,downstream_gene_variant,,ENST00000576444,;HIC1,downstream_gene_variant,,ENST00000571990,;SMG6,downstream_gene_variant,,ENST00000573166,;SMG6,downstream_gene_variant,,ENST00000570756,;SMG6,downstream_gene_variant,,ENST00000576218,;SMG6,downstream_gene_variant,,ENST00000573827,;SMG6,downstream_gene_variant,,ENST00000573153,;SMG6,downstream_gene_variant,,ENST00000574501,; T ENST00000322941 Transcript missense_variant 917/3053 917/2202 306/733 P/L cCa/cTa 1 1 HIC1 HGNC HGNC:4909 protein_coding YES CCDS42229.1 ENSP00000314080 Q14526 UPI0000140F7F NM_001098202.1 tolerated(0.06) 2/2 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 2057550 2057550 C T 1 0 0 0 0 1 0 0 0 6985 594 21 3 3 HIC1 17 2057550 Missense_Mutation SNP C C3N-01071_T 2057550 81199891 278 21836 OR1G1 0 . GRCh38 17 3127171 3127171 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.381C>T p.= p.C127C ENST00000328890 1/1 199 172 27 181 181 0 strelka-varscan-mutect OR1G1,synonymous_variant,p.=,ENST00000328890,NM_003555.1; A ENST00000328890 Transcript synonymous_variant 411/998 381/942 127/313 C tgC/tgT 1 -1 OR1G1 HGNC HGNC:8204 protein_coding YES CCDS11020.1 ENSP00000331545 P47890 A0A126GW57 UPI0000041B68 NM_003555.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF247,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 3127171 3127171 G A 1 0 0 0 0 0 0 0 1 11035 1195 42 3 3 OR1G1 17 3127171 Silent SNP G C3N-01071_T 1069621 3127171 80130270 279 21837 CYB5D2 0 . GRCh38 17 4150010 4150010 + Nonsense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.370G>T p.Glu124Ter p.E124* ENST00000301391 2/4 206 189 17 330 330 0 strelka-varscan-mutect CYB5D2,stop_gained,p.Glu124Ter,ENST00000301391,NM_144611.3;CYB5D2,stop_gained,p.Glu12Ter,ENST00000575251,NM_001254755.1;CYB5D2,stop_gained,p.Glu12Ter,ENST00000577075,NM_001254756.1;CYB5D2,stop_gained,p.Glu12Ter,ENST00000573984,;CYB5D2,non_coding_transcript_exon_variant,,ENST00000575411,; T ENST00000301391 Transcript stop_gained 870/1910 370/795 124/264 E/* Gag/Tag 1 1 CYB5D2 HGNC HGNC:28471 protein_coding YES CCDS11044.1 ENSP00000301391 Q8WUJ1 UPI000006E3B0 NM_144611.3 2/4 Gene3D:3.10.120.10,Pfam_domain:PF00173,hmmpanther:PTHR10281,hmmpanther:PTHR10281:SF4,SMART_domains:SM01117,Superfamily_domains:SSF55856 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 71 4150010 4150010 G T 1 0 0 0 0 0 1 0 0 3929 1291 45 2 2 CYB5D2 17 4150010 Nonsense_Mutation SNP G C3N-01071_T 1022839 4150010 79107431 280 21838 TP53 0 . GRCh38 17 7673781 7673781 + Missense_Mutation SNP C C T rs121912660 C3N-01071_T C3N-01071_N C C c.839G>A p.Arg280Lys p.R280K ENST00000269305 8/11 774 658 116 692 692 0 strelka-varscan-mutect TP53,missense_variant,p.Arg280Lys,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg280Lys,ENST00000420246,;TP53,missense_variant,p.Arg241Lys,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg241Lys,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg280Lys,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg241Lys,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg280Lys,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg241Lys,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg280Lys,ENST00000445888,;TP53,missense_variant,p.Arg241Lys,ENST00000619485,;TP53,missense_variant,p.Arg148Lys,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg121Lys,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg148Lys,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg121Lys,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg148Lys,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg121Lys,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg280Lys,ENST00000359597,;TP53,missense_variant,p.Arg269Lys,ENST00000615910,;TP53,missense_variant,p.Arg148Lys,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg241Lys,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 1029/2579 839/1182 280/393 R/K aGa/aAa rs121912660,CM993218,TP53_g.13819G>C,TP53_g.13819G>T,TP53_g.13819G>A,COSM10724,COSM10728,COSM11287,COSM129830,COSM1646813,COSM1649340,COSM1659144,COSM254987,COSM3522694,COSM3723939,COSM3733332,COSM562340 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.04) 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance,pathogenic 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912660 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 7673781 7673781 C T 1 0 0 0 0 1 0 0 0 16859 913 32 3 3 TP53 17 7673781 Missense_Mutation SNP C C3N-01071_T 3523771 7673781 75583660 281 21839 GAS7 0 . GRCh38 17 9943137 9943137 + Nonsense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.715G>T p.Glu239Ter p.E239* ENST00000432992 7/14 96 84 12 98 98 0 strelka-varscan-mutect GAS7,stop_gained,p.Glu179Ter,ENST00000323816,;GAS7,stop_gained,p.Glu175Ter,ENST00000437099,NM_001130831.1;GAS7,stop_gained,p.Glu239Ter,ENST00000432992,NM_201433.1;GAS7,stop_gained,p.Glu179Ter,ENST00000585266,NM_201432.1;GAS7,stop_gained,p.Glu99Ter,ENST00000580865,NM_003644.2;GAS7,stop_gained,p.Glu175Ter,ENST00000542249,;GAS7,stop_gained,p.Glu175Ter,ENST00000579158,;GAS7,stop_gained,p.Glu175Ter,ENST00000584146,;GAS7,intron_variant,,ENST00000396115,;GAS7,intron_variant,,ENST00000583882,;GAS7,downstream_gene_variant,,ENST00000578599,;GAS7,downstream_gene_variant,,ENST00000584389,;GAS7,non_coding_transcript_exon_variant,,ENST00000580811,;GAS7,non_coding_transcript_exon_variant,,ENST00000581871,;GAS7,non_coding_transcript_exon_variant,,ENST00000579140,;GAS7,downstream_gene_variant,,ENST00000578655,; A ENST00000432992 Transcript stop_gained 876/4970 715/1431 239/476 E/* Gaa/Taa 1 -1 GAS7 HGNC HGNC:4169 protein_coding YES CCDS11152.1 ENSP00000407552 O60861 UPI00001B4B17 NM_201433.1 7/14 Pfam_domain:PF00611,PROSITE_profiles:PS51741,hmmpanther:PTHR23065,SMART_domains:SM00055,Superfamily_domains:SSF103657 HIGH 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -19.18048 0.9999908 1 1 1 0 A 4 1 71 9943137 9943137 C A 1 0 0 0 0 0 1 0 0 6120 922 32 2 2 GAS7 17 9943137 Nonsense_Mutation SNP C C3N-01071_T 2269356 9943137 73314304 282 21840 MYH4 0 . GRCh38 17 10447989 10447989 + Silent SNP C C G novel C3N-01071_T C3N-01071_N C C c.4794G>C p.= p.V1598V ENST00000255381 34/40 251 206 45 265 265 0 strelka-varscan-mutect MYH4,synonymous_variant,p.=,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; G ENST00000255381 Transcript synonymous_variant 4905/6016 4794/5820 1598/1939 V gtG/gtC 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 34/40 Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF271 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 10447989 10447989 C G 1 0 0 0 0 0 0 0 1 10037 581 21 4 4 MYH4 17 10447989 Silent SNP C C3N-01071_T 504852 10447989 72809452 283 21841 MYH1 0 . GRCh38 17 10494436 10494436 + Missense_Mutation SNP C C A rs770764395 C3N-01071_T C3N-01071_N C C c.5585G>T p.Arg1862Leu p.R1862L ENST00000226207 39/40 141 123 18 179 178 1 strelka-varscan-mutect MYH1,missense_variant,p.Arg1862Leu,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 5680/6024 5585/5820 1862/1939 R/L cGc/cTc rs770764395,COSM1630049 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 39/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,Superfamily_domains:SSF57997 0,1 MODERATE SNV 5 0,1 1 PASS rs770764395 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 10494436 10494436 C A 1 0 0 0 0 1 0 0 0 10029 768 27 1 1 MYH1 17 10494436 Missense_Mutation SNP C C3N-01071_T 46447 10494436 72763005 284 21842 DNAH9 0 . GRCh38 17 11768548 11768548 + Silent SNP C C T rs201337796 C3N-01071_T C3N-01071_N C C c.7266C>T p.= p.I2422I ENST00000262442 37/69 214 202 12 220 220 0 strelka-varscan-mutect DNAH9,synonymous_variant,p.=,ENST00000262442,NM_001372.3;DNAH9,synonymous_variant,p.=,ENST00000454412,; T ENST00000262442 Transcript synonymous_variant 7334/13750 7266/13461 2422/4486 I atC/atT rs201337796,COSM3387707,COSM3514133 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 37/69 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs201337796 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 11768548 11768548 C T 1 0 0 0 0 0 0 0 1 4423 874 31 1 1 DNAH9 17 11768548 Silent SNP C C3N-01071_T 1274112 11768548 71488893 285 21843 VTN 0 . GRCh38 17 28369707 28369707 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.329C>T p.Pro110Leu p.P110L ENST00000226218 3/8 323 274 49 367 367 0 strelka-varscan-mutect VTN,missense_variant,p.Pro110Leu,ENST00000226218,NM_000638.3;VTN,missense_variant,p.Pro110Leu,ENST00000542029,;SARM1,upstream_gene_variant,,ENST00000585482,NM_015077.3;CTB-96E2.2,upstream_gene_variant,,ENST00000555059,;SEBOX,upstream_gene_variant,,ENST00000536498,NM_001080837.3;CTB-96E2.10,upstream_gene_variant,,ENST00000613598,;SARM1,intron_variant,,ENST00000379061,;CTB-96E2.3,intron_variant,,ENST00000591482,;CTB-96E2.6,downstream_gene_variant,,ENST00000623773,;VTN,upstream_gene_variant,,ENST00000539746,; A ENST00000226218 Transcript missense_variant 948/2149 329/1437 110/478 P/L cCt/cTt 1 -1 VTN HGNC HGNC:12724 protein_coding YES CCDS11229.1 ENSP00000226218 P04004 D9ZGG2 UPI0000138E65 NM_000638.3 tolerated(0.13) 3/8 hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 28369707 28369707 G A 1 0 0 0 0 1 0 0 0 17791 1000 35 3 3 VTN 17 28369707 Missense_Mutation SNP G C3N-01071_T 16601159 28369707 54887734 286 21844 NF1 0 . GRCh38 17 31338139 31338139 + Missense_Mutation SNP G G C C3N-01071_T C3N-01071_N G G c.6819G>C p.Lys2273Asn p.K2273N ENST00000358273 45/58 387 363 24 360 360 0 strelka-varscan-mutect NF1,missense_variant,p.Lys2273Asn,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Lys2252Asn,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Lys1918Asn,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,missense_variant,p.Lys68Asn,ENST00000471572,;NF1,splice_region_variant,,ENST00000579081,;NF1,splice_region_variant,,ENST00000584328,;NF1,intron_variant,,ENST00000581790,;NF1,downstream_gene_variant,,ENST00000479536,;NF1,upstream_gene_variant,,ENST00000582892,; C ENST00000358273 Transcript missense_variant,splice_region_variant 7202/12425 6819/8520 2273/2839 K/N aaG/aaC COSM5609525,COSM5609526,COSM5609527 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0.02) 45/58 Gene3D:1.25.10.10,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,Superfamily_domains:SSF48371 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1060500373 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 31338139 31338139 G C 1 0 0 0 0 1 0 0 0 10393 1014 35 4 4 NF1 17 31338139 Missense_Mutation SNP G C3N-01071_T 2968432 31338139 51919302 287 21845 C17orf78 0 . GRCh38 17 37388749 37388749 + Missense_Mutation SNP T T A novel C3N-01071_T C3N-01071_N T T c.588T>A p.Ser196Arg p.S196R ENST00000615133 5/7 310 251 59 317 317 0 strelka-varscan-mutect C17orf78,missense_variant,p.Ser196Arg,ENST00000615133,NM_173625.3;ACACA,intron_variant,,ENST00000616317,NM_198834.2;C17orf78,intron_variant,,ENST00000611038,NM_001321399.1;ACACA,intron_variant,,ENST00000616352,;RP11-378E13.3,downstream_gene_variant,,ENST00000617427,;ACACA,intron_variant,,ENST00000618351,;ACACA,intron_variant,,ENST00000615229,;ACACA,intron_variant,,ENST00000617548,; A ENST00000615133 Transcript missense_variant 638/1862 588/828 196/275 S/R agT/agA 1 1 C17orf78 HGNC HGNC:26831 protein_coding YES CCDS45655.1 ENSP00000478886 Q8N4C9 UPI0000140B91 NM_173625.3 tolerated(0.13) 5/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR36870,hmmpanther:PTHR36870:SF1,Pfam_domain:PF15829 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 37388749 37388749 T A 1 0 0 0 0 1 0 0 0 1890 1693 59 4 4 C17orf78 17 37388749 Missense_Mutation SNP T C3N-01071_T 6050610 37388749 45868692 288 21846 LRRC3C 0 . GRCh38 17 39944218 39944218 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.312C>A p.= p.V104V ENST00000377924 2/2 122 111 11 116 116 0 strelka-varscan-mutect LRRC3C,synonymous_variant,p.=,ENST00000377924,NM_001195545.1;RP11-387H17.4,downstream_gene_variant,,ENST00000582263,; A ENST00000377924 Transcript synonymous_variant 362/891 312/828 104/275 V gtC/gtA 1 1 LRRC3C HGNC HGNC:40034 protein_coding YES CCDS54121.1 ENSP00000367157 A6NJW4 UPI0000198ACC NM_001195545.1 2/2 PROSITE_profiles:PS51450,hmmpanther:PTHR24369,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 3 1 PASS rs1178778848 . 0 206 2 2 0 0 0 0 -16.27134 0.9999944 1 1 1 0 A 2 1 71 39944218 39944218 C A 1 0 0 0 0 0 0 0 1 8892 842 30 2 2 LRRC3C 17 39944218 Silent SNP C C3N-01071_T 2555469 39944218 43313223 289 21847 HOXB2 0 . GRCh38 17 48543452 48543452 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.687G>T p.= p.A229A ENST00000330070 2/2 147 136 11 136 136 0 strelka-varscan-mutect HOXB2,synonymous_variant,p.=,ENST00000330070,NM_002145.3;HOXB-AS1,upstream_gene_variant,,ENST00000435312,;HOXB-AS1,upstream_gene_variant,,ENST00000504972,;HOXB-AS1,upstream_gene_variant,,ENST00000502764,;HOXB-AS1,upstream_gene_variant,,ENST00000508688,;HOXB2,non_coding_transcript_exon_variant,,ENST00000571287,;HOXB2,upstream_gene_variant,,ENST00000504772,; A ENST00000330070 Transcript synonymous_variant 765/1562 687/1071 229/356 A gcG/gcT 1 -1 HOXB2 HGNC HGNC:5113 protein_coding YES CCDS11527.1 ENSP00000331741 P14652 UPI000012CF4C NM_002145.3 2/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF179,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 48543452 48543452 C A 1 0 0 0 0 0 0 0 1 7195 639 23 1 1 HOXB2 17 48543452 Silent SNP C C3N-01071_T 8599234 48543452 34713989 290 21848 MYCBPAP 0 . GRCh38 17 50517442 50517442 + Silent SNP G G T novel C3N-01071_T C3N-01071_N G G c.483G>T p.= p.L161L ENST00000323776 3/19 507 360 147 535 535 0 strelka-varscan-mutect MYCBPAP,synonymous_variant,p.=,ENST00000323776,NM_032133.4;MYCBPAP,synonymous_variant,p.=,ENST00000436259,;MYCBPAP,synonymous_variant,p.=,ENST00000452039,;MYCBPAP,downstream_gene_variant,,ENST00000576179,;MYCBPAP,upstream_gene_variant,,ENST00000468821,;MYCBPAP,synonymous_variant,p.=,ENST00000437498,;MYCBPAP,3_prime_UTR_variant,,ENST00000458692,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,;MYCBPAP,upstream_gene_variant,,ENST00000459754,; T ENST00000323776 Transcript synonymous_variant 645/3186 483/2955 161/984 L ctG/ctT 1 1 MYCBPAP HGNC HGNC:19677 protein_coding YES CCDS32680.2 ENSP00000323184 Q8TBZ2 A0A140VK87 UPI0000E5A00B NM_032133.4 3/19 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 50517442 50517442 G T 1 0 0 0 0 0 0 0 1 10019 1335 47 2 2 MYCBPAP 17 50517442 Silent SNP G C3N-01071_T 1973990 50517442 32739999 291 21849 KIF2B 0 . GRCh38 17 53823769 53823769 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.736G>T p.Val246Leu p.V246L ENST00000268919 1/1 257 206 51 373 373 0 strelka-varscan-mutect KIF2B,missense_variant,p.Val246Leu,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 869/2313 736/2022 246/673 V/L Gtg/Ttg 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 deleterious(0.03) 1/1 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 53823769 53823769 G T 1 0 0 0 0 1 0 0 0 8163 1261 44 2 2 KIF2B 17 53823769 Missense_Mutation SNP G C3N-01071_T 3306327 53823769 29433672 292 21850 COIL 0 . GRCh38 17 56949420 56949420 + Silent SNP T T C novel C3N-01071_T C3N-01071_N T T c.1455A>G p.= p.T485T ENST00000240316 4/7 102 94 8 115 115 0 strelka-varscan-mutect COIL,synonymous_variant,p.=,ENST00000240316,NM_004645.2;COIL,downstream_gene_variant,,ENST00000573008,;RP5-1107A17.2,upstream_gene_variant,,ENST00000570407,; C ENST00000240316 Transcript synonymous_variant 1490/2650 1455/1731 485/576 T acA/acG 1 -1 COIL HGNC HGNC:2184 protein_coding YES CCDS11592.1 ENSP00000240316 P38432 UPI0000131068 NM_004645.2 4/7 hmmpanther:PTHR15197:SF0,hmmpanther:PTHR15197 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 56949420 56949420 T C 1 0 0 0 0 0 0 0 1 3453 1451 51 5 5 COIL 17 56949420 Silent SNP T C3N-01071_T 3125651 56949420 26308021 293 21851 EPX 0 . GRCh38 17 58192891 58192891 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.45C>A p.= p.V15V ENST00000225371 1/13 663 618 45 527 527 0 strelka-varscan-mutect EPX,synonymous_variant,p.=,ENST00000225371,NM_000502.4; A ENST00000225371 Transcript synonymous_variant 155/2708 45/2148 15/715 V gtC/gtA 1 1 EPX HGNC HGNC:3423 protein_coding YES CCDS11602.1 ENSP00000225371 P11678 UPI0000131629 NM_000502.4 1/13 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11475:SF63,hmmpanther:PTHR11475 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 58192891 58192891 C A 1 0 0 0 0 0 0 0 1 5048 842 30 2 2 EPX 17 58192891 Silent SNP C C3N-01071_T 1243471 58192891 25064550 294 21852 TSPOAP1 0 . GRCh38 17 58311993 58311993 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.2828C>G p.Ala943Gly p.A943G ENST00000343736 17/32 111 103 8 96 96 0 strelka-varscan-mutect TSPOAP1,missense_variant,p.Ala883Gly,ENST00000268893,NM_024418.2;TSPOAP1,missense_variant,p.Ala943Gly,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1,upstream_gene_variant,,ENST00000582679,;TSPOAP1,upstream_gene_variant,,ENST00000580669,;TSPOAP1,upstream_gene_variant,,ENST00000578486,;TSPOAP1,upstream_gene_variant,,ENST00000585149,; C ENST00000343736 Transcript missense_variant 2992/5947 2828/5574 943/1857 A/G gCc/gGc 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 deleterious(0.01) 17/32 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -16.02044 1 1 1 1 0 C 3 2 71 58311993 58311993 G C 1 0 0 0 0 1 0 0 0 17163 1203 42 4 4 TSPOAP1 17 58311993 Missense_Mutation SNP G C3N-01071_T 119102 58311993 24945448 295 21853 USP32 0 . GRCh38 17 60214660 60214660 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.1982T>C p.Ile661Thr p.I661T ENST00000300896 17/34 168 140 28 148 148 0 strelka-varscan-mutect USP32,missense_variant,p.Ile661Thr,ENST00000300896,NM_032582.3;USP32,missense_variant,p.Ile331Thr,ENST00000592339,;USP32,missense_variant,p.Ile658Thr,ENST00000590133,;USP32,missense_variant,p.Ile206Thr,ENST00000591768,;USP32,downstream_gene_variant,,ENST00000587651,;USP32,downstream_gene_variant,,ENST00000589552,; G ENST00000300896 Transcript missense_variant 2177/5171 1982/4815 661/1604 I/T aTt/aCt 1 -1 USP32 HGNC HGNC:19143 protein_coding YES CCDS32697.1 ENSP00000300896 Q8NFA0 UPI0000047AF8 NM_032582.3 deleterious(0) 17/34 Pfam_domain:PF14836 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 60214660 60214660 A G 1 0 0 0 0 1 0 0 0 17605 101 4 5 5 USP32 17 60214660 Missense_Mutation SNP A C3N-01071_T 1902667 60214660 23042781 296 21854 USP32 0 . GRCh38 17 60219766 60219766 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.1771G>C p.Asp591His p.D591H ENST00000300896 16/34 193 183 10 181 181 0 varscan-mutect USP32,missense_variant,p.Asp591His,ENST00000300896,NM_032582.3;USP32,missense_variant,p.Asp261His,ENST00000592339,;USP32,missense_variant,p.Asp588His,ENST00000590133,;USP32,missense_variant,p.Asp122His,ENST00000591768,;USP32,3_prime_UTR_variant,,ENST00000589552,;USP32,non_coding_transcript_exon_variant,,ENST00000587651,; G ENST00000300896 Transcript missense_variant 1966/5171 1771/4815 591/1604 D/H Gac/Cac 1 -1 USP32 HGNC HGNC:19143 protein_coding YES CCDS32697.1 ENSP00000300896 Q8NFA0 UPI0000047AF8 NM_032582.3 tolerated(0.08) 16/34 Gene3D:3jyuB01 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 60219766 60219766 C G 1 0 0 0 0 1 0 0 0 17605 913 32 4 4 USP32 17 60219766 Missense_Mutation SNP C C3N-01071_T 5106 60219766 23037675 297 21855 TBX2 0 . GRCh38 17 61401770 61401770 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.482A>T p.Asp161Val p.D161V ENST00000240328 2/7 346 322 24 357 357 0 strelka-varscan-mutect TBX2,missense_variant,p.Asp161Val,ENST00000240328,NM_005994.3;TBX2-AS1,intron_variant,,ENST00000592009,;TBX2-AS1,upstream_gene_variant,,ENST00000590421,;TBX2-AS1,upstream_gene_variant,,ENST00000591313,;TBX2-AS1,upstream_gene_variant,,ENST00000589814,;RP11-332H18.5,upstream_gene_variant,,ENST00000585765,;TBX2,3_prime_UTR_variant,,ENST00000419047,;TBX2,non_coding_transcript_exon_variant,,ENST00000477081,; T ENST00000240328 Transcript missense_variant 763/3339 482/2139 161/712 D/V gAc/gTc 1 1 TBX2 HGNC HGNC:11597 protein_coding YES CCDS11627.2 ENSP00000240328 Q13207 A0A024QZ86 UPI000020116F NM_005994.3 deleterious(0) 2/7 PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF82,Pfam_domain:PF00907,Gene3D:1h6fA00,SMART_domains:SM00425,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 61401770 61401770 A T 1 0 0 0 0 1 0 0 0 16060 275 10 4 4 TBX2 17 61401770 Missense_Mutation SNP A C3N-01071_T 1182004 61401770 21855671 298 21856 OTOP3 0 . GRCh38 17 74941791 74941791 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.472G>A p.Gly158Arg p.G158R ENST00000328801 2/7 104 70 34 69 69 0 strelka-varscan-mutect OTOP3,missense_variant,p.Gly158Arg,ENST00000328801,NM_001272005.1,NM_178233.2;OTOP3,3_prime_UTR_variant,,ENST00000580749,; A ENST00000328801 Transcript missense_variant 472/2363 472/1791 158/596 G/R Ggg/Agg 1 1 OTOP3 HGNC HGNC:19658 protein_coding YES CCDS11709.1 ENSP00000328090 Q7RTS5 UPI000019097F NM_001272005.1,NM_178233.2 deleterious(0) 2/7 hmmpanther:PTHR21522:SF36,hmmpanther:PTHR21522 MODERATE 1 SNV 2 1 PASS rs1449985684 . 0 200 10 0 0 0 0 0 -20 0.9999963 1 1 1 0 A 3 1 71 74941791 74941791 G A 1 0 0 0 0 1 0 0 0 11375 1232 43 3 3 OTOP3 17 74941791 Missense_Mutation SNP G C3N-01071_T 13540021 74941791 8315650 299 21857 THOC1 0 . GRCh38 18 214670 214670 + Missense_Mutation SNP C C G novel C3N-01071_T C3N-01071_N C C c.1930G>C p.Asp644His p.D644H ENST00000261600 21/21 290 275 15 262 262 0 strelka-varscan-mutect THOC1,missense_variant,p.Asp644His,ENST00000261600,NM_005131.2;THOC1,missense_variant,p.Asp644His,ENST00000616322,;THOC1,3_prime_UTR_variant,,ENST00000631280,;USP14,downstream_gene_variant,,ENST00000261601,NM_005151.3;USP14,downstream_gene_variant,,ENST00000383589,;USP14,downstream_gene_variant,,ENST00000582707,NM_001037334.1;USP14,downstream_gene_variant,,ENST00000400266,;THOC1,downstream_gene_variant,,ENST00000579891,;THOC1,3_prime_UTR_variant,,ENST00000580038,;THOC1,non_coding_transcript_exon_variant,,ENST00000583228,;THOC1,non_coding_transcript_exon_variant,,ENST00000578529,;THOC1,non_coding_transcript_exon_variant,,ENST00000579232,;THOC1,non_coding_transcript_exon_variant,,ENST00000584470,;THOC1,non_coding_transcript_exon_variant,,ENST00000577429,;USP14,downstream_gene_variant,,ENST00000578942,;USP14,downstream_gene_variant,,ENST00000578786,;THOC1,downstream_gene_variant,,ENST00000585307,; G ENST00000261600 Transcript missense_variant 1938/2087 1930/1974 644/657 D/H Gac/Cac 1 -1 THOC1 HGNC HGNC:19070 protein_coding YES CCDS45820.1 ENSP00000261600 Q96FV9 UPI0000071782 NM_005131.2 deleterious(0.01) 21/21 Gene3D:1.10.533.10,Pfam_domain:PF00531,PROSITE_profiles:PS50017,hmmpanther:PTHR13265,hmmpanther:PTHR13265:SF2,SMART_domains:SM00005,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 214670 214670 C G 1 0 0 0 0 1 0 0 0 16299 826 29 4 4 THOC1 18 214670 Missense_Mutation SNP C C3N-01071_T 214670 80158615 300 21858 LAMA1 0 . GRCh38 18 7014009 7014009 + Missense_Mutation SNP C C A rs141907708 C3N-01071_T C3N-01071_N C C c.3169G>T p.Asp1057Tyr p.D1057Y ENST00000389658 23/63 642 585 57 440 439 1 strelka-varscan-mutect LAMA1,missense_variant,p.Asp1057Tyr,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript missense_variant 3263/9657 3169/9228 1057/3075 D/Y Gat/Tat rs141907708,COSM4073155 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 deleterious(0) 23/63 Gene3D:2.10.25.10,Pfam_domain:PF00053,Prints_domain:PR00011,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs141907708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 7014009 7014009 C A 1 0 0 0 0 1 0 0 0 8509 884 31 1 1 LAMA1 18 7014009 Missense_Mutation SNP C C3N-01071_T 6799339 7014009 73359276 301 21859 VAPA 0 . GRCh38 18 9931858 9931858 + Missense_Mutation SNP C C G C3N-01071_T C3N-01071_N C C c.128C>G p.Ser43Trp p.S43W ENST00000340541 2/7 206 195 11 185 185 0 varscan-mutect VAPA,missense_variant,p.Ser43Trp,ENST00000400000,NM_194434.2;VAPA,missense_variant,p.Ser43Trp,ENST00000340541,NM_003574.5;VAPA,non_coding_transcript_exon_variant,,ENST00000584796,;VAPA,3_prime_UTR_variant,,ENST00000585042,;VAPA,non_coding_transcript_exon_variant,,ENST00000577901,;VAPA,non_coding_transcript_exon_variant,,ENST00000583879,;VAPA,upstream_gene_variant,,ENST00000583475,; G ENST00000340541 Transcript missense_variant 323/1227 128/885 43/294 S/W tCg/tGg COSM1389985 1 1 VAPA HGNC HGNC:12648 protein_coding YES CCDS11847.2 ENSP00000345656 Q9P0L0 UPI000059D45E NM_003574.5 deleterious(0.02) 2/7 PROSITE_profiles:PS50202,hmmpanther:PTHR10809,hmmpanther:PTHR10809:SF40,Pfam_domain:PF00635,PIRSF_domain:PIRSF019693,Gene3D:2.60.40.360,Superfamily_domains:SSF49354 1 MODERATE 1 SNV 5 1 1 PASS rs955956154 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 9931858 9931858 C G 1 0 0 0 0 1 0 0 0 17666 893 31 4 4 VAPA 18 9931858 Missense_Mutation SNP C C3N-01071_T 2917849 9931858 70441427 302 21860 MAPK4 0 . GRCh38 18 50664452 50664452 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.494A>G p.Lys165Arg p.K165R ENST00000400384 2/6 79 70 9 70 70 0 strelka-varscan-mutect MAPK4,missense_variant,p.Lys165Arg,ENST00000400384,NM_002747.3;MAPK4,missense_variant,p.Lys165Arg,ENST00000592595,NM_001292040.1;MAPK4,missense_variant,p.Lys165Arg,ENST00000588540,;MAPK4,intron_variant,,ENST00000540640,NM_001292039.1;MAPK4,non_coding_transcript_exon_variant,,ENST00000587823,;MAPK4,downstream_gene_variant,,ENST00000586735,; G ENST00000400384 Transcript missense_variant 1530/4770 494/1764 165/587 K/R aAg/aGg 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 deleterious(0.03) 2/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF25,hmmpanther:PTHR24055,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR01771 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.49389 1 1 1 1 0 G 3 3 71 50664452 50664452 A G 1 0 0 0 0 1 0 0 0 9204 72 3 5 5 MAPK4 18 50664452 Missense_Mutation SNP A C3N-01071_T 40732594 50664452 29708833 303 21861 MAPK4 0 . GRCh38 18 50715217 50715217 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.685T>C p.Phe229Leu p.F229L ENST00000400384 3/6 102 86 16 114 114 0 strelka-varscan-mutect MAPK4,missense_variant,p.Phe229Leu,ENST00000400384,NM_002747.3;MAPK4,missense_variant,p.Phe229Leu,ENST00000592595,NM_001292040.1;MAPK4,missense_variant,p.Phe18Leu,ENST00000540640,NM_001292039.1; C ENST00000400384 Transcript missense_variant 1721/4770 685/1764 229/587 F/L Ttt/Ctt 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 deleterious(0) 3/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF25,hmmpanther:PTHR24055,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112,Prints_domain:PR01771 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 50715217 50715217 T C 1 0 0 0 0 1 0 0 0 9204 1609 56 5 5 MAPK4 18 50715217 Missense_Mutation SNP T C3N-01071_T 50765 50715217 29658068 304 21862 RAX 0 . GRCh38 18 59272508 59272508 + Silent SNP G G C novel C3N-01071_T C3N-01071_N G G c.396C>G p.= p.P132P ENST00000334889 2/3 503 466 37 392 392 0 strelka-varscan-mutect RAX,synonymous_variant,p.=,ENST00000334889,NM_013435.2;RAX,intron_variant,,ENST00000256852,;CPLX4,downstream_gene_variant,,ENST00000587244,;RAX,downstream_gene_variant,,ENST00000555288,;RAX,non_coding_transcript_exon_variant,,ENST00000591550,; C ENST00000334889 Transcript synonymous_variant 583/3197 396/1041 132/346 P ccC/ccG 1 -1 RAX HGNC HGNC:18662 protein_coding YES CCDS11972.1 ENSP00000334813 Q9Y2V3 UPI000013CF2F NM_013435.2 2/3 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF302,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 59272508 59272508 G C 1 0 0 0 0 0 0 0 1 13257 1335 47 4 4 RAX 18 59272508 Silent SNP G C3N-01071_T 8557291 59272508 21100777 305 21863 C3 0 . GRCh38 19 6718268 6718268 + Missense_Mutation SNP T T G novel C3N-01071_T C3N-01071_N T T c.412A>C p.Ile138Leu p.I138L ENST00000245907 3/41 766 694 72 690 689 1 strelka-varscan-mutect C3,missense_variant,p.Ile138Leu,ENST00000245907,NM_000064.3;C3,missense_variant,p.Ile97Leu,ENST00000600744,;CTD-3128G10.7,upstream_gene_variant,,ENST00000614781,;C3,upstream_gene_variant,,ENST00000597442,;C3,upstream_gene_variant,,ENST00000594270,;C3,non_coding_transcript_exon_variant,,ENST00000594936,;C3,upstream_gene_variant,,ENST00000595577,; G ENST00000245907 Transcript missense_variant 505/5263 412/4992 138/1663 I/L Atc/Ctc 1 -1 C3 HGNC HGNC:1318 protein_coding YES CCDS32883.1 ENSP00000245907 P01024 V9HWA9 UPI000013EC9B NM_000064.3 tolerated(0.13) 3/41 hmmpanther:PTHR11412:SF90,hmmpanther:PTHR11412,Pfam_domain:PF01835 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 6718268 6718268 T G 1 0 0 0 0 1 0 0 0 2057 1464 51 5 5 C3 19 6718268 Missense_Mutation SNP T C3N-01071_T 6718268 51899348 306 21864 SMARCA4 0 . GRCh38 19 11059810 11059810 + Nonsense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.4693G>T p.Glu1565Ter p.E1565* ENST00000429416 34/36 486 418 68 465 464 1 strelka-varscan-mutect SMARCA4,stop_gained,p.Glu1565Ter,ENST00000429416,NM_001128844.1;SMARCA4,stop_gained,p.Glu1599Ter,ENST00000413806,;SMARCA4,stop_gained,p.Glu1597Ter,ENST00000450717,NM_001128849.1;SMARCA4,stop_gained,p.Glu1565Ter,ENST00000344626,NM_003072.3;SMARCA4,stop_gained,p.Glu1532Ter,ENST00000590574,NM_001128847.1;SMARCA4,stop_gained,p.Glu1534Ter,ENST00000589677,NM_001128846.1;SMARCA4,stop_gained,p.Glu1535Ter,ENST00000541122,NM_001128845.1;SMARCA4,stop_gained,p.Glu1531Ter,ENST00000444061,NM_001128848.1;SMARCA4,stop_gained,p.Glu39Ter,ENST00000586985,;SMARCA4,upstream_gene_variant,,ENST00000586921,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,; T ENST00000429416 Transcript stop_gained 4974/5691 4693/4944 1565/1647 E/* Gag/Tag 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 34/36 SMART_domains:SM00297,Superfamily_domains:SSF47370 HIGH 1 SNV 2 1 PASS rs1375203306 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 71 11059810 11059810 G T 1 0 0 0 0 0 1 0 0 15063 1059 37 1 1 SMARCA4 19 11059810 Nonsense_Mutation SNP G C3N-01071_T 4341542 11059810 47557806 307 21865 NWD1 0 . GRCh38 19 16808107 16808107 + Missense_Mutation SNP C C T rs147984852 C3N-01071_T C3N-01071_N C C c.4258C>T p.Arg1420Cys p.R1420C ENST00000524140 18/19 203 170 33 196 196 0 strelka-varscan-mutect NWD1,missense_variant,p.Arg1420Cys,ENST00000524140,NM_001007525.3;NWD1,missense_variant,p.Arg1420Cys,ENST00000379808,;NWD1,missense_variant,p.Arg1420Cys,ENST00000552788,NM_001290355.1;NWD1,missense_variant,p.Arg1378Cys,ENST00000549814,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; T ENST00000524140 Transcript missense_variant 4676/7641 4258/4299 1420/1432 R/C Cgc/Tgc rs147984852,COSM4075219,COSM4075220 1 1 NWD1 HGNC HGNC:27619 protein_coding YES CCDS32945.2 ENSP00000428579 Q149M9 UPI0000D6173E NM_001007525.3 tolerated(1) 18/19 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,Superfamily_domains:SSF50978 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs147984852 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 16808107 16808107 C T 1 0 0 0 0 1 0 0 0 10854 536 19 1 1 NWD1 19 16808107 Missense_Mutation SNP C C3N-01071_T 5748297 16808107 41809509 308 21866 NR2F6 0 . GRCh38 19 17235751 17235751 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.688G>A p.Asp230Asn p.D230N ENST00000291442 3/4 174 161 13 151 151 0 strelka-varscan-mutect NR2F6,missense_variant,p.Asp230Asn,ENST00000291442,NM_005234.3;NR2F6,missense_variant,p.Asp110Asn,ENST00000596878,;AC010646.3,downstream_gene_variant,,ENST00000594059,; T ENST00000291442 Transcript missense_variant 1408/2404 688/1215 230/404 D/N Gac/Aac 1 -1 NR2F6 HGNC HGNC:7977 protein_coding YES CCDS12352.1 ENSP00000291442 P10588 F1D8R3 UPI0000129B28 NM_005234.3 deleterious(0) 3/4 Gene3D:1.10.565.10,Pfam_domain:PF00104,Prints_domain:PR00398,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF44,SMART_domains:SM00430,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -17.30622 0.9999997 1 1 1 0 T 3 4 71 17235751 17235751 C T 1 0 0 0 0 1 0 0 0 10685 884 31 1 1 NR2F6 19 17235751 Missense_Mutation SNP C C3N-01071_T 427644 17235751 41381865 309 21867 ZNF493 0 . GRCh38 19 21424173 21424173 + Frame_Shift_Del DEL G G - novel C3N-01071_T C3N-01071_N G G c.1514delG p.Ser505IlefsTer5 p.S505Ifs*5 ENST00000392288 4/4 197 164 33 218 218 0 sindel-varindel-pindel ZNF493,frameshift_variant,p.Ser505IlefsTer5,ENST00000392288,NM_001076678.2;ZNF493,frameshift_variant,p.Ser377IlefsTer5,ENST00000355504,NM_175910.6;ZNF493,downstream_gene_variant,,ENST00000596302,;CTD-2561J22.3,intron_variant,,ENST00000600810,;ZNF493,downstream_gene_variant,,ENST00000598152,; - ENST00000392288 Transcript frameshift_variant 1623/5023 1514/2325 505/774 S/X aGt/at 1 1 ZNF493 HGNC HGNC:23708 protein_coding YES CCDS42536.1 ENSP00000376110 Q6ZR52 UPI000022ABBF NM_001076678.2 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF247,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 PASS . . 0 176 0 3 31 0 0 0 -16.40047 0 0 1 0 0 - 7 5 71 21424173 21424173 G - 1 0 1 0 1 0 0 0 0 18517 1029 36 0 0 ZNF493 19 21424173 Frame_Shift_Del DEL G C3N-01071_T 4188422 21424173 37193443 310 21868 FFAR3 0 . GRCh38 19 35359767 35359767 + Silent SNP A A C novel C3N-01071_T C3N-01071_N A A c.877A>C p.= p.R293R ENST00000327809 2/2 500 440 60 513 513 0 varscan-mutect FFAR3,synonymous_variant,p.=,ENST00000327809,NM_005304.3;FFAR3,synonymous_variant,p.=,ENST00000594310,; C ENST00000327809 Transcript synonymous_variant 1078/1796 877/1041 293/346 R Agg/Cgg 1 1 FFAR3 HGNC HGNC:4499 protein_coding YES CCDS12459.1 ENSP00000328230 O14843 A0A0K0PUW7 UPI0000001C3F NM_005304.3 2/2 hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 71 35359767 35359767 A C 1 0 0 0 0 0 0 0 1 5692 295 11 5 5 FFAR3 19 35359767 Silent SNP A C3N-01071_T 13935594 35359767 23257849 311 21869 GPR42 0 . GRCh38 19 35372236 35372236 + Silent SNP A A C novel C3N-01071_T C3N-01071_N A A c.877A>C p.= p.R293R ENST00000597214 1/1 71 64 7 68 68 0 varscan-mutect GPR42,synonymous_variant,p.=,ENST00000454971,;GPR42,synonymous_variant,p.=,ENST00000597214,; C ENST00000597214 Transcript synonymous_variant 947/1182 877/1041 293/346 R Agg/Cgg 1 1 GPR42 HGNC HGNC:4500 protein_coding YES ENSP00000473212 O15529 A0A0K0PUY3 UPI0000040740 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 8 194 6 2 0 0 0 0 -12.20015 0.9997445 1 1 1 0 C 2 2 71 35372236 35372236 A C 1 0 0 0 0 0 0 0 1 6580 295 11 5 5 GPR42 19 35372236 Silent SNP A C3N-01071_T 12469 35372236 23245380 312 21870 ZNF420 0 . GRCh38 19 37128282 37128282 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.1291G>T p.Gly431Cys p.G431C ENST00000337995 5/5 234 217 17 203 203 0 strelka-varscan-mutect ZNF420,missense_variant,p.Gly431Cys,ENST00000337995,NM_144689.3;ZNF420,missense_variant,p.Gly431Cys,ENST00000304239,;ZNF420,missense_variant,p.Gly40Cys,ENST00000585862,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,downstream_gene_variant,,ENST00000589245,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000590332,;CTC-454I21.4,downstream_gene_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,upstream_gene_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,; T ENST00000337995 Transcript missense_variant 1506/3535 1291/2067 431/688 G/C Ggc/Tgc 1 1 ZNF420 HGNC HGNC:20649 protein_coding YES CCDS12498.1 ENSP00000338770 Q8TAQ5 UPI000007049F NM_144689.3 tolerated(0.19) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF290,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 37128282 37128282 G T 1 0 0 0 0 1 0 0 0 18469 1348 47 2 2 ZNF420 19 37128282 Missense_Mutation SNP G C3N-01071_T 1756046 37128282 21489334 313 21871 ZNF585B 0 . GRCh38 19 37186533 37186534 + Frame_Shift_Ins INS - - AGACCTTCCC novel C3N-01071_T C3N-01071_N - - c.994_1003dupGGGAAGGTCT p.Phe335TrpfsTer7 p.F335Wfs*7 ENST00000532828 5/5 254 210 44 236 236 0 sindel-varindel ZNF585B,frameshift_variant,p.Phe335TrpfsTer7,ENST00000532828,NM_152279.3;ZNF585B,frameshift_variant,p.Phe280TrpfsTer7,ENST00000531805,;ZNF585B,3_prime_UTR_variant,,ENST00000527838,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585B,downstream_gene_variant,,ENST00000591492,;ZNF585B,downstream_gene_variant,,ENST00000586320,;CTC-454I21.3,intron_variant,,ENST00000585860,;CTC-454I21.3,intron_variant,,ENST00000590245,;ZNF585B,downstream_gene_variant,,ENST00000392156,;ZNF585B,downstream_gene_variant,,ENST00000591273,;ZNF585B,downstream_gene_variant,,ENST00000526705,; AGACCTTCCC ENST00000532828 Transcript frameshift_variant 1255-1256/6210 1003-1004/2310 335/769 F/WEGLX ttc/tGGGAAGGTCTtc 1 -1 ZNF585B HGNC HGNC:30948 protein_coding YES CCDS12500.1 ENSP00000433773 Q52M93 UPI00001AF01B NM_152279.3 5/5 PROSITE_profiles:PS50157,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 HIGH 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 AGACCTTCCC 7 5 71 37186533 37186533 - AGACCTTCCC 1 0 1 1 0 0 0 0 0 18592 246 9 0 0 ZNF585B 19 37186533 Frame_Shift_Ins INS - C3N-01071_T 58251 37186533 21431083 314 21872 LRFN1 0 . GRCh38 19 39314067 39314067 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1270G>T p.Ala424Ser p.A424S ENST00000248668 1/2 278 226 52 225 224 1 strelka-varscan-mutect LRFN1,missense_variant,p.Ala424Ser,ENST00000248668,NM_020862.1;CTC-246B18.8,downstream_gene_variant,,ENST00000601911,; A ENST00000248668 Transcript missense_variant 1270/3381 1270/2316 424/771 A/S Gct/Tct 1 -1 LRFN1 HGNC HGNC:29290 protein_coding YES CCDS46071.1 ENSP00000248668 Q9P244 UPI00001A5C55 NM_020862.1 tolerated(0.75) 1/2 PROSITE_profiles:PS50853,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF34,SMART_domains:SM00060 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 39314067 39314067 C A 1 0 0 0 0 1 0 0 0 8831 739 26 2 2 LRFN1 19 39314067 Missense_Mutation SNP C C3N-01071_T 2127534 39314067 19303549 315 21873 CYP2A6 0 . GRCh38 19 40845347 40845347 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.1108T>G p.Leu370Val p.L370V ENST00000301141 7/9 448 361 87 377 377 0 strelka-varscan-mutect CYP2A6,missense_variant,p.Leu370Val,ENST00000301141,NM_000762.5;CTC-490E21.11,downstream_gene_variant,,ENST00000623128,;CYP2A6,non_coding_transcript_exon_variant,,ENST00000596719,;CTC-490E21.12,intron_variant,,ENST00000601627,;CYP2A6,downstream_gene_variant,,ENST00000600495,;CYP2A6,upstream_gene_variant,,ENST00000599960,; C ENST00000301141 Transcript missense_variant 1129/1764 1108/1485 370/494 L/V Ttg/Gtg 1 -1 CYP2A6 HGNC HGNC:2610 protein_coding YES CCDS12568.1 ENSP00000301141 P11509 UPI0000157752 NM_000762.5 tolerated(0.94) 7/9 hmmpanther:PTHR24300:SF186,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 40845347 40845347 A C 1 0 0 0 0 1 0 0 0 3965 11 1 5 5 CYP2A6 19 40845347 Missense_Mutation SNP A C3N-01071_T 1531280 40845347 17772269 316 21874 CD79A 0 . GRCh38 19 41879539 41879539 + Silent SNP G G T rs782014534 C3N-01071_T C3N-01071_N G G c.384G>T p.= p.P128P ENST00000221972 3/5 120 112 8 89 89 0 strelka-varscan-mutect CD79A,missense_variant,p.Arg210Leu,ENST00000597454,;CD79A,synonymous_variant,p.=,ENST00000221972,NM_001783.3;CD79A,synonymous_variant,p.=,ENST00000444740,NM_021601.3;ARHGEF1,upstream_gene_variant,,ENST00000599846,;ARHGEF1,upstream_gene_variant,,ENST00000354532,NM_004706.3;ARHGEF1,upstream_gene_variant,,ENST00000337665,NM_199002.1;ARHGEF1,upstream_gene_variant,,ENST00000347545,NM_198977.1;ARHGEF1,upstream_gene_variant,,ENST00000378152,;ARHGEF1,upstream_gene_variant,,ENST00000596957,;ARHGEF1,upstream_gene_variant,,ENST00000600274,;ARHGEF1,upstream_gene_variant,,ENST00000600387,; T ENST00000221972 Transcript synonymous_variant 569/1258 384/681 128/226 P ccG/ccT rs782014534,COSM5074765 1 1 CD79A HGNC HGNC:1698 protein_coding YES CCDS12589.1 ENSP00000221972 P11912 UPI000011398E NM_001783.3 3/5 Gene3D:2.60.40.10,hmmpanther:PTHR14334,hmmpanther:PTHR14334:SF1,Superfamily_domains:SSF48726 0,1 LOW 1 SNV 1 0,1 1 PASS rs782014534 . 0 197 11 2 0 0 0 0 -11.80532 0.9948746 1 1 1 0 T 2 4 71 41879539 41879539 G T 1 0 0 0 0 0 0 0 1 2740 1101 38 1 1 CD79A 19 41879539 Silent SNP G C3N-01071_T 1034192 41879539 16738077 317 21875 ARHGAP35 0 . GRCh38 19 46922175 46922175 + Missense_Mutation SNP G G T rs759708637 C3N-01071_T C3N-01071_N G G c.3500G>T p.Arg1167Leu p.R1167L ENST00000404338 1/6 171 134 37 183 183 0 strelka-varscan-mutect ARHGAP35,missense_variant,p.Arg1167Leu,ENST00000404338,NM_004491.4;ARHGAP35,missense_variant,p.Arg1167Leu,ENST00000614079,;ARHGAP35,intron_variant,,ENST00000615647,; T ENST00000404338 Transcript missense_variant 3500/8889 3500/4500 1167/1499 R/L cGg/cTg rs759708637 1 1 ARHGAP35 HGNC HGNC:4591 protein_coding YES CCDS46127.1 ENSP00000385720 Q9NRY4 UPI0000163F71 NM_004491.4 deleterious(0.01) 1/6 MODERATE 1 SNV 1 1 PASS rs759708637 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 46922175 46922175 G T 1 0 0 0 0 1 0 0 0 1008 1116 39 1 1 ARHGAP35 19 46922175 Missense_Mutation SNP G C3N-01071_T 5042636 46922175 11695441 318 21876 GLTSCR1 0 . GRCh38 19 47694439 47694439 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.2608G>C p.Glu870Gln p.E870Q ENST00000396720 8/15 128 98 30 133 133 0 strelka-varscan-mutect GLTSCR1,missense_variant,p.Glu870Gln,ENST00000396720,NM_015711.3;GLTSCR1,missense_variant,p.Glu818Gln,ENST00000614245,;CTD-2571L23.8,intron_variant,,ENST00000599924,; C ENST00000396720 Transcript missense_variant 2802/5739 2608/4683 870/1560 E/Q Gag/Cag 1 1 GLTSCR1 HGNC HGNC:4332 protein_coding YES CCDS46134.1 ENSP00000379946 Q9NZM4 UPI00016278EE NM_015711.3 tolerated(0.7) 8/15 Low_complexity_(Seg):seg,hmmpanther:PTHR15572:SF1,hmmpanther:PTHR15572 MODERATE 1 SNV 5 1 PASS . . 0 204 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 47694439 47694439 G C 1 0 0 0 0 1 0 0 0 6350 1291 45 4 4 GLTSCR1 19 47694439 Missense_Mutation SNP G C3N-01071_T 772264 47694439 10923177 319 21877 ZNF845 0 . GRCh38 19 53352834 53352834 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.2159A>C p.Lys720Thr p.K720T ENST00000458035 4/4 269 249 20 248 248 0 strelka-varscan-mutect ZNF845,missense_variant,p.Lys720Thr,ENST00000458035,NM_138374.1;ZNF845,missense_variant,p.Lys720Thr,ENST00000595091,;ZNF525,intron_variant,,ENST00000635711,;ZNF845,downstream_gene_variant,,ENST00000601857,; C ENST00000458035 Transcript missense_variant 2276/4311 2159/2913 720/970 K/T aAg/aCg 1 1 ZNF845 HGNC HGNC:25112 protein_coding YES CCDS46170.1 ENSP00000388311 Q96IR2 UPI0001662BAC NM_138374.1 deleterious(0.02) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF162,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 53352834 53352834 A C 1 0 0 0 0 1 0 0 0 18779 72 3 5 5 ZNF845 19 53352834 Missense_Mutation SNP A C3N-01071_T 5658395 53352834 5264782 320 21878 RFPL4A 0 . GRCh38 19 55762886 55762886 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.575G>T p.Arg192Ile p.R192I ENST00000434937 3/3 1107 981 126 1071 1071 0 varscan-mutect RFPL4A,missense_variant,p.Arg192Ile,ENST00000434937,NM_001145014.1; T ENST00000434937 Transcript missense_variant 746/1035 575/864 192/287 R/I aGa/aTa 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 deleterious(0) 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 55762886 55762886 G T 1 0 0 0 0 1 0 0 0 13428 942 33 2 2 RFPL4A 19 55762886 Missense_Mutation SNP G C3N-01071_T 2410052 55762886 2854730 321 21879 SNPH 0 . GRCh38 20 1304883 1304883 + Missense_Mutation SNP C C A C3N-01071_T C3N-01071_N C C c.314C>A p.Thr105Lys p.T105K ENST00000381873 6/6 112 98 14 103 103 0 strelka-varscan-mutect SNPH,missense_variant,p.Thr149Lys,ENST00000381867,NM_001318234.1;SNPH,missense_variant,p.Thr149Lys,ENST00000614659,;SNPH,missense_variant,p.Thr105Lys,ENST00000381873,NM_014723.2; A ENST00000381873 Transcript missense_variant 550/4995 314/1485 105/494 T/K aCa/aAa COSM4728692,COSM4728693 1 1 SNPH HGNC HGNC:15931 protein_coding YES CCDS13012.1 ENSP00000371297 O15079 UPI000007424E NM_014723.2 deleterious(0.03) 6/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16208:SF1,hmmpanther:PTHR16208,Pfam_domain:PF15290 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 1304883 1304883 C A 1 0 0 0 0 1 0 0 0 15170 492 17 2 2 SNPH 20 1304883 Missense_Mutation SNP C C3N-01071_T 1304883 63139284 322 21880 SNPH 0 . GRCh38 20 1304944 1304944 + Missense_Mutation SNP G G T rs145538484 C3N-01071_T C3N-01071_N G G c.375G>T p.Glu125Asp p.E125D ENST00000381873 6/6 284 255 29 252 252 0 strelka-varscan-mutect SNPH,missense_variant,p.Glu169Asp,ENST00000381867,NM_001318234.1;SNPH,missense_variant,p.Glu169Asp,ENST00000614659,;SNPH,missense_variant,p.Glu125Asp,ENST00000381873,NM_014723.2;SDCBP2,downstream_gene_variant,,ENST00000381812,; T ENST00000381873 Transcript missense_variant 611/4995 375/1485 125/494 E/D gaG/gaT rs145538484 1 1 SNPH HGNC HGNC:15931 protein_coding YES CCDS13012.1 ENSP00000371297 O15079 UPI000007424E NM_014723.2 deleterious(0) 6/6 hmmpanther:PTHR16208:SF1,hmmpanther:PTHR16208,Pfam_domain:PF15290 MODERATE 1 SNV 1 1 PASS rs145538484 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 1304944 1304944 G T 1 0 0 0 0 1 0 0 0 15170 1020 36 2 2 SNPH 20 1304944 Missense_Mutation SNP G C3N-01071_T 61 1304944 63139223 323 21881 CDC25B 0 . GRCh38 20 3802933 3802933 + Missense_Mutation SNP C C G rs371343744 C3N-01071_T C3N-01071_N C C c.1218C>G p.Asp406Glu p.D406E ENST00000245960 12/16 294 268 26 239 239 0 strelka-varscan-mutect CDC25B,missense_variant,p.Asp406Glu,ENST00000245960,NM_001287519.1,NM_001287520.1,NM_021873.3;CDC25B,missense_variant,p.Asp392Glu,ENST00000439880,NM_004358.4;CDC25B,missense_variant,p.Asp342Glu,ENST00000344256,NM_001287516.1,NM_001287517.1;CDC25B,missense_variant,p.Asp315Glu,ENST00000379598,NM_001287518.1;CDC25B,missense_variant,p.Asp365Glu,ENST00000340833,NM_001287522.1,NM_021872.3;CDC25B,non_coding_transcript_exon_variant,,ENST00000467519,;CDC25B,non_coding_transcript_exon_variant,,ENST00000480816,;CDC25B,non_coding_transcript_exon_variant,,ENST00000468979,;CDC25B,non_coding_transcript_exon_variant,,ENST00000495915,; G ENST00000245960 Transcript missense_variant 1915/3597 1218/1743 406/580 D/E gaC/gaG rs371343744 1 1 CDC25B HGNC HGNC:1726 protein_coding YES CCDS13067.1 ENSP00000245960 P30305 UPI000012F474 NM_001287519.1,NM_001287520.1,NM_021873.3 tolerated(0.47) 12/16 Gene3D:3.40.250.10,Prints_domain:PR00716,hmmpanther:PTHR10828,hmmpanther:PTHR10828:SF48,Superfamily_domains:SSF52821 MODERATE 1 SNV 1 1 PASS rs371343744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 3802933 3802933 C G 1 0 0 0 0 1 0 0 0 2766 535 19 4 4 CDC25B 20 3802933 Missense_Mutation SNP C C3N-01071_T 2497989 3802933 60641234 324 21882 PCSK2 0 . GRCh38 20 17453904 17453904 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.1048A>T p.Thr350Ser p.T350S ENST00000262545 9/12 507 453 54 377 377 0 strelka-varscan-mutect PCSK2,missense_variant,p.Thr350Ser,ENST00000262545,NM_002594.4;PCSK2,missense_variant,p.Thr331Ser,ENST00000377899,NM_001201528.1;PCSK2,missense_variant,p.Thr315Ser,ENST00000536609,NM_001201529.2; T ENST00000262545 Transcript missense_variant 1363/4740 1048/1917 350/638 T/S Acc/Tcc 1 1 PCSK2 HGNC HGNC:8744 protein_coding YES CCDS13125.1 ENSP00000262545 P16519 UPI0000000C6E NM_002594.4 deleterious(0.01) 9/12 Gene3D:3.40.50.200,Pfam_domain:PF00082,hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF11,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 17453904 17453904 A T 1 0 0 0 0 1 0 0 0 11689 159 6 4 4 PCSK2 20 17453904 Missense_Mutation SNP A C3N-01071_T 13650971 17453904 46990263 325 21883 RALGAPA2 0 . GRCh38 20 20472827 20472827 + Splice_Site SNP A A G novel C3N-01071_T C3N-01071_N A A c.5495+2T>C p.X1832_splice ENST00000202677 134 118 16 123 123 0 strelka-varscan-mutect RALGAPA2,splice_donor_variant,,ENST00000430436,;RALGAPA2,splice_donor_variant,,ENST00000202677,NM_020343.3;RALGAPA2,splice_donor_variant,,ENST00000620717,;RALGAPA2,missense_variant,p.Tyr244His,ENST00000427175,; G ENST00000202677 Transcript splice_donor_variant -/6152 5495/5622 1832/1873 1 -1 RALGAPA2 HGNC HGNC:16207 protein_coding YES CCDS46584.1 ENSP00000202677 Q2PPJ7 UPI000040F987 NM_020343.3 37/39 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 71 20472827 20472827 A G 1 0 0 0 0 0 0 1 0 13173 405 14 5 5 RALGAPA2 20 20472827 Splice_Site SNP A C3N-01071_T 3018923 20472827 43971340 326 21884 GSS 0 . GRCh38 20 34929460 34929460 + Silent SNP G G A novel C3N-01071_T C3N-01071_N G G c.1242C>T p.= p.G414G ENST00000216951 12/13 406 382 24 324 324 0 strelka-varscan-mutect GSS,synonymous_variant,p.=,ENST00000216951,NM_001322494.1,NM_000178.2;GSS,synonymous_variant,p.=,ENST00000451957,;ACSS2,downstream_gene_variant,,ENST00000360596,NM_001242393.1,NM_018677.3;ACSS2,downstream_gene_variant,,ENST00000253382,NM_001076552.2;ACSS2,downstream_gene_variant,,ENST00000476922,;ACSS2,downstream_gene_variant,,ENST00000481284,;ACSS2,downstream_gene_variant,,ENST00000477932,;ACSS2,downstream_gene_variant,,ENST00000494727,;ACSS2,downstream_gene_variant,,ENST00000491533,;ACSS2,downstream_gene_variant,,ENST00000480978,; A ENST00000216951 Transcript synonymous_variant 1341/1922 1242/1425 414/474 G ggC/ggT 1 -1 GSS HGNC HGNC:4624 protein_coding YES CCDS13245.1 ENSP00000216951 P48637 V9HWJ1 UPI0000111B5F NM_001322494.1,NM_000178.2 12/13 Pfam_domain:PF03917,PIRSF_domain:PIRSF001558,hmmpanther:PTHR11130,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01986 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 34929460 34929460 G A 1 0 0 0 0 0 0 0 1 6713 1306 46 3 3 GSS 20 34929460 Silent SNP G C3N-01071_T 14456633 34929460 29514707 327 21885 GSS 0 . GRCh38 20 34942976 34942976 + Silent SNP A A G novel C3N-01071_T C3N-01071_N A A c.306T>C p.= p.R102R ENST00000216951 4/13 675 610 65 618 618 0 strelka-varscan-mutect GSS,synonymous_variant,p.=,ENST00000216951,NM_001322494.1,NM_000178.2;GSS,intron_variant,,ENST00000451957,; G ENST00000216951 Transcript synonymous_variant 405/1922 306/1425 102/474 R cgT/cgC 1 -1 GSS HGNC HGNC:4624 protein_coding YES CCDS13245.1 ENSP00000216951 P48637 V9HWJ1 UPI0000111B5F NM_001322494.1,NM_000178.2 4/13 Gene3D:1.10.1080.10,Pfam_domain:PF03917,PIRSF_domain:PIRSF001558,hmmpanther:PTHR11130,Superfamily_domains:SSF56059,TIGRFAM_domain:TIGR01986 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 71 34942976 34942976 A G 1 0 0 0 0 0 0 0 1 6713 262 10 5 5 GSS 20 34942976 Silent SNP A C3N-01071_T 13516 34942976 29501191 328 21886 MYH7B 0 . GRCh38 20 34999866 34999866 + Silent SNP C C A rs780992553 C3N-01071_T C3N-01071_N C C c.4867C>A p.= p.R1623R ENST00000262873 36/43 301 285 16 228 228 0 strelka-varscan-mutect MYH7B,synonymous_variant,p.=,ENST00000262873,NM_020884.4;MYH7B,synonymous_variant,p.=,ENST00000618182,;TRPC4AP,downstream_gene_variant,,ENST00000252015,NM_015638.2;TRPC4AP,downstream_gene_variant,,ENST00000451813,NM_199368.1;MYH7B,upstream_gene_variant,,ENST00000435272,;MYH7B,upstream_gene_variant,,ENST00000456649,;MYH7B,upstream_gene_variant,,ENST00000446156,;MYH7B,upstream_gene_variant,,ENST00000433934,;MYH7B,upstream_gene_variant,,ENST00000453028,; A ENST00000262873 Transcript synonymous_variant 4959/6293 4867/5952 1623/1983 R Cgg/Agg rs780992553 1 1 MYH7B HGNC HGNC:15906 protein_coding YES CCDS42869.1 ENSP00000262873 A7E2Y1 UPI000046D367 NM_020884.4 36/43 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF358 LOW 1 SNV 1 1 PASS rs780992553 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 34999866 34999866 C A 1 0 0 0 0 0 0 0 1 10040 643 23 1 1 MYH7B 20 34999866 Silent SNP C C3N-01071_T 56890 34999866 29444301 329 21887 RALGAPB 0 . GRCh38 20 38517530 38517530 + Missense_Mutation SNP G G A rs766802567 C3N-01071_T C3N-01071_N G G c.1076G>A p.Ser359Asn p.S359N ENST00000262879 8/30 78 70 8 79 79 0 strelka-varscan-mutect RALGAPB,missense_variant,p.Ser359Asn,ENST00000262879,NM_001282917.1,NM_020336.3;RALGAPB,missense_variant,p.Ser359Asn,ENST00000397042,NM_001282918.1;RALGAPB,missense_variant,p.Ser359Asn,ENST00000397040,;RALGAPB,missense_variant,p.Ser187Asn,ENST00000438490,;MIR548O2,downstream_gene_variant,,ENST00000616090,;RALGAPB,non_coding_transcript_exon_variant,,ENST00000461423,; A ENST00000262879 Transcript missense_variant 1360/8663 1076/4485 359/1494 S/N aGt/aAt rs766802567 1 1 RALGAPB HGNC HGNC:29221 protein_coding YES CCDS13305.1 ENSP00000262879 Q86X10 UPI000000DBFD NM_001282917.1,NM_020336.3 tolerated(0.05) 8/30 hmmpanther:PTHR21344 MODERATE 1 SNV 1 1 PASS rs766802567 . 0 207 3 0 0 0 0 0 -17.55742 1 1 1 1 0 A 3 1 71 38517530 38517530 G A 1 0 0 0 0 1 0 0 0 13174 1029 36 3 3 RALGAPB 20 38517530 Missense_Mutation SNP G C3N-01071_T 3517664 38517530 25926637 330 21888 FAM65C 0 . GRCh38 20 50596231 50596231 + Missense_Mutation SNP A A T novel C3N-01071_T C3N-01071_N A A c.1811T>A p.Leu604Gln p.L604Q ENST00000327979 15/22 291 258 33 247 247 0 strelka-varscan-mutect FAM65C,missense_variant,p.Leu604Gln,ENST00000327979,NM_001290268.1;FAM65C,missense_variant,p.Leu604Gln,ENST00000045083,NM_080829.3;FAM65C,non_coding_transcript_exon_variant,,ENST00000488529,;FAM65C,upstream_gene_variant,,ENST00000482129,;FAM65C,downstream_gene_variant,,ENST00000462493,; T ENST00000327979 Transcript missense_variant 2223/4377 1811/2841 604/946 L/Q cTg/cAg 1 -1 FAM65C HGNC HGNC:16168 protein_coding YES CCDS13431.2 ENSP00000332663 Q96MK2 UPI0000DA5AF4 NM_001290268.1 tolerated(0.14) 15/22 hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF15,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 50596231 50596231 A T 1 0 0 0 0 1 0 0 0 5467 188 7 4 4 FAM65C 20 50596231 Missense_Mutation SNP A C3N-01071_T 12078701 50596231 13847936 331 21889 ZFP64 0 . GRCh38 20 52084942 52084942 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.1553G>T p.Cys518Phe p.C518F ENST00000361387 9/9 149 133 16 121 121 0 strelka-varscan-mutect ZFP64,missense_variant,p.Cys518Phe,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.Cys299Phe,ENST00000371523,NM_001319146.1;ZFP64,intron_variant,,ENST00000371518,;ZFP64,downstream_gene_variant,,ENST00000395989,;ZFP64,downstream_gene_variant,,ENST00000456175,;ZFP64,downstream_gene_variant,,ENST00000477786,;ZFP64,downstream_gene_variant,,ENST00000467811,; A ENST00000361387 Transcript missense_variant 1614/2545 1553/1938 518/645 C/F tGt/tTt 1 -1 ZFP64 HGNC HGNC:15940 protein_coding CCDS13439.1 ENSP00000355179 Q9NTW7 UPI000013C56C NM_199427.2 deleterious(0.02) 9/9 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF34,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 52084942 52084942 C A 1 0 0 0 0 1 0 0 0 18228 478 17 2 2 ZFP64 20 52084942 Missense_Mutation SNP C C3N-01071_T 1488711 52084942 12359225 332 21890 NCAM2 0 . GRCh38 21 21432120 21432120 + Missense_Mutation SNP G G C novel C3N-01071_T C3N-01071_N G G c.1493G>C p.Ser498Thr p.S498T ENST00000400546 12/18 129 120 9 89 89 0 strelka-varscan-mutect NCAM2,missense_variant,p.Ser498Thr,ENST00000400546,NM_004540.3;NCAM2,missense_variant,p.Ser480Thr,ENST00000284894,; C ENST00000400546 Transcript missense_variant 1742/8135 1493/2514 498/837 S/T aGt/aCt 1 1 NCAM2 HGNC HGNC:7657 protein_coding YES CCDS42910.1 ENSP00000383392 O15394 UPI00001A3703 NM_004540.3 tolerated(0.07) 12/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF35,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 71 21432120 21432120 G C 1 0 0 0 0 1 0 0 0 10219 1029 36 4 4 NCAM2 21 21432120 Missense_Mutation SNP G C3N-01071_T 21432120 25277863 333 21891 LCA5L 0 . GRCh38 21 39410034 39410034 + Silent SNP A A T novel C3N-01071_T C3N-01071_N A A c.1227T>A p.= p.I409I ENST00000358268 9/10 174 138 36 270 270 0 strelka-varscan-mutect LCA5L,synonymous_variant,p.=,ENST00000358268,;LCA5L,synonymous_variant,p.=,ENST00000288350,NM_152505.3;LCA5L,synonymous_variant,p.=,ENST00000380671,;WRB,downstream_gene_variant,,ENST00000415847,;WRB,upstream_gene_variant,,ENST00000478273,;LCA5L,non_coding_transcript_exon_variant,,ENST00000495240,;LCA5L,downstream_gene_variant,,ENST00000484878,;WRB,intron_variant,,ENST00000623703,; T ENST00000358268 Transcript synonymous_variant 1756/2564 1227/2013 409/670 I atT/atA 1 -1 LCA5L HGNC HGNC:1255 protein_coding YES CCDS13665.1 ENSP00000351008 O95447 UPI00000015EE 9/10 hmmpanther:PTHR16650,hmmpanther:PTHR16650:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 39410034 39410034 A T 1 0 0 0 0 0 0 0 1 8562 242 9 4 4 LCA5L 21 39410034 Silent SNP A C3N-01071_T 17977914 39410034 7299949 334 21892 TSPEAR 0 . GRCh38 21 44529925 44529925 + Silent SNP C C G rs781960229 C3N-01071_T C3N-01071_N C C c.663G>C p.= p.P221P ENST00000323084 5/12 106 98 8 85 85 0 strelka-varscan-mutect TSPEAR,synonymous_variant,p.=,ENST00000614657,NM_001272037.1;TSPEAR,synonymous_variant,p.=,ENST00000323084,NM_144991.2;TSPEAR,synonymous_variant,p.=,ENST00000397916,;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR-AS2,downstream_gene_variant,,ENST00000465978,; G ENST00000323084 Transcript synonymous_variant 729/3967 663/2010 221/669 P ccG/ccC rs781960229,COSM3551424 1 -1 TSPEAR HGNC HGNC:1268 protein_coding YES CCDS13712.1 ENSP00000321987 Q8WU66 UPI0000137746 NM_144991.2 5/12 hmmpanther:PTHR15261,SMART_domains:SM00210,Superfamily_domains:SSF49899 0,1 LOW 1 SNV 1 0,1 1 PASS rs781960229 . 0 205 5 0 0 0 0 0 -16.10696 1 1 1 1 0 G 2 3 71 44529925 44529925 C G 1 0 0 0 0 0 0 0 1 17160 639 23 4 4 TSPEAR 21 44529925 Silent SNP C C3N-01071_T 5119891 44529925 2180058 335 21893 RNF185 0 . GRCh38 22 31204522 31204522 + Missense_Mutation SNP A A G novel C3N-01071_T C3N-01071_N A A c.515A>G p.Gln172Arg p.Q172R ENST00000326132 7/7 191 162 29 158 158 0 varscan-mutect RNF185,missense_variant,p.Gln172Arg,ENST00000326132,NM_152267.3;RNF185,missense_variant,p.Gln116Arg,ENST00000266252,NM_001135825.1;RNF185,3_prime_UTR_variant,,ENST00000426256,;RNF185-AS1,downstream_gene_variant,,ENST00000526089,;RNF185,missense_variant,p.Gln172Arg,ENST00000518626,;RNF185,non_coding_transcript_exon_variant,,ENST00000471384,;RNF185,non_coding_transcript_exon_variant,,ENST00000494514,; G ENST00000326132 Transcript missense_variant 674/3171 515/579 172/192 Q/R cAg/cGg 1 1 RNF185 HGNC HGNC:26783 protein_coding YES CCDS13890.1 ENSP00000320508 Q96GF1 A0A024R1F5 UPI0000036022 NM_152267.3 tolerated(0.14) 7/7 hmmpanther:PTHR12313,hmmpanther:PTHR12313:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 31204522 31204522 A G 1 0 0 0 0 1 0 0 0 13645 188 7 5 5 RNF185 22 31204522 Missense_Mutation SNP A C3N-01071_T 31204522 19613946 336 21894 PIK3IP1 0 . GRCh38 22 31289588 31289588 + Missense_Mutation SNP C C T novel C3N-01071_T C3N-01071_N C C c.419G>A p.Arg140Gln p.R140Q ENST00000215912 4/6 77 73 4 44 44 0 strelka-mutect PIK3IP1,missense_variant,p.Arg140Gln,ENST00000215912,NM_052880.4;PIK3IP1,missense_variant,p.Arg140Gln,ENST00000441972,NM_001135911.1;PIK3IP1,missense_variant,p.Arg140Gln,ENST00000402249,;PIK3IP1,downstream_gene_variant,,ENST00000443175,;PIK3IP1-AS1,upstream_gene_variant,,ENST00000440456,;PIK3IP1,non_coding_transcript_exon_variant,,ENST00000480654,;PIK3IP1,non_coding_transcript_exon_variant,,ENST00000493034,; T ENST00000215912 Transcript missense_variant 603/2467 419/792 140/263 R/Q cGg/cAg 1 -1 PIK3IP1 HGNC HGNC:24942 protein_coding YES CCDS13893.1 ENSP00000215912 Q96FE7 A0A024R1M3 UPI000003F53C NM_052880.4 tolerated(0.44) 4/6 hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF211 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -9.024116 0.9998473 1 1 1 0 T 3 4 71 31289588 31289588 C T 1 0 0 0 0 1 0 0 0 12012 652 23 1 1 PIK3IP1 22 31289588 Missense_Mutation SNP C C3N-01071_T 85066 31289588 19528880 337 21895 SLC5A4 0 . GRCh38 22 32218548 32218548 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.1946C>T p.Ala649Val p.A649V ENST00000266086 15/15 211 182 29 270 269 1 strelka-varscan-mutect SLC5A4,missense_variant,p.Ala649Val,ENST00000266086,NM_014227.2;RP1-90G24.10,intron_variant,,ENST00000434942,; A ENST00000266086 Transcript missense_variant 1958/2030 1946/1980 649/659 A/V gCt/gTt 1 -1 SLC5A4 HGNC HGNC:11039 protein_coding YES CCDS13903.1 ENSP00000266086 Q9NY91 UPI00001359F4 NM_014227.2 tolerated(0.07) 15/15 Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1464023137 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 32218548 32218548 G A 1 0 0 0 0 1 0 0 0 14950 971 34 3 3 SLC5A4 22 32218548 Missense_Mutation SNP G C3N-01071_T 928960 32218548 18599920 338 21896 MAPK12 0 . GRCh38 22 50256126 50256126 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.578C>A p.Ala193Asp p.A193D ENST00000215659 7/12 114 97 17 109 109 0 strelka-varscan-mutect MAPK12,missense_variant,p.Ala193Asp,ENST00000215659,NM_002969.4;MAPK12,missense_variant,p.Ala183Asp,ENST00000622558,NM_001303252.1;MAPK12,missense_variant,p.Ala103Asp,ENST00000395780,;HDAC10,upstream_gene_variant,,ENST00000216271,NM_032019.5;HDAC10,upstream_gene_variant,,ENST00000626012,;HDAC10,upstream_gene_variant,,ENST00000448072,;MAPK12,downstream_gene_variant,,ENST00000395778,;MAPK12,non_coding_transcript_exon_variant,,ENST00000497036,;HDAC10,upstream_gene_variant,,ENST00000498366,;HDAC10,upstream_gene_variant,,ENST00000483222,;HDAC10,upstream_gene_variant,,ENST00000470965,;HDAC10,upstream_gene_variant,,ENST00000489424,;HDAC10,upstream_gene_variant,,ENST00000497483,;MAPK12,downstream_gene_variant,,ENST00000492218,;MAPK12,non_coding_transcript_exon_variant,,ENST00000496942,;MAPK12,non_coding_transcript_exon_variant,,ENST00000482969,;MAPK12,non_coding_transcript_exon_variant,,ENST00000497738,;MAPK12,non_coding_transcript_exon_variant,,ENST00000467891,;MAPK12,non_coding_transcript_exon_variant,,ENST00000488504,;HDAC10,upstream_gene_variant,,ENST00000415993,; T ENST00000215659 Transcript missense_variant 894/1918 578/1104 193/367 A/D gCt/gAt 1 -1 MAPK12 HGNC HGNC:6874 protein_coding YES CCDS14089.1 ENSP00000215659 P53778 UPI000012F180 NM_002969.4 deleterious(0) 7/12 PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF146,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.99996 1 1 1 0 T 3 4 71 50256126 50256126 G T 1 0 0 0 0 1 0 0 0 9198 971 34 2 2 MAPK12 22 50256126 Missense_Mutation SNP G C3N-01071_T 18037578 50256126 562342 339 21897 NLGN4X 0 . GRCh38 X 5893066 5893066 + Missense_Mutation SNP C C A novel C3N-01071_T C3N-01071_N C C c.2202G>T p.Met734Ile p.M734I ENST00000381095 6/6 247 177 70 209 209 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Met734Ile,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Met734Ile,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Met734Ile,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Met734Ile,ENST00000381092,;NLGN4X,missense_variant,p.Met735Ile,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,; A ENST00000381095 Transcript missense_variant 2830/5870 2202/2451 734/816 M/I atG/atT 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 tolerated_low_confidence(0.16) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 5893066 5893066 C A 1 0 0 0 0 1 0 0 0 10501 826 29 2 2 NLGN4X 23 5893066 Missense_Mutation SNP C C3N-01071_T 5893066 150147829 340 21898 GLRA2 0 . GRCh38 X 14604372 14604372 + Missense_Mutation SNP G G T novel C3N-01071_T C3N-01071_N G G c.552G>T p.Gln184His p.Q184H ENST00000218075 5/9 160 144 16 90 90 0 strelka-varscan-mutect GLRA2,missense_variant,p.Gln184His,ENST00000218075,NM_001118885.1,NM_002063.3;GLRA2,missense_variant,p.Gln95His,ENST00000443437,NM_001171942.1;GLRA2,missense_variant,p.Gln184His,ENST00000355020,NM_001118886.1;GLRA2,missense_variant,p.Gln168His,ENST00000415367,; T ENST00000218075 Transcript missense_variant 1082/3216 552/1359 184/452 Q/H caG/caT 1 1 GLRA2 HGNC HGNC:4327 protein_coding YES CCDS14160.1 ENSP00000218075 P23416 UPI000012BA64 NM_001118885.1,NM_002063.3 deleterious(0) 5/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF28,PROSITE_patterns:PS00236,Gene3D:2.70.170.10,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 14604372 14604372 G T 1 0 0 0 0 1 0 0 0 6334 933 33 2 2 GLRA2 23 14604372 Missense_Mutation SNP G C3N-01071_T 8711306 14604372 141436523 341 21899 BMX 0 . GRCh38 X 15508393 15508393 + Nonsense_Mutation SNP A A T rs748739673 C3N-01071_T C3N-01071_N A A c.40A>T p.Arg14Ter p.R14* ENST00000357607 2/19 60 43 17 56 56 0 strelka-varscan-mutect BMX,stop_gained,p.Arg14Ter,ENST00000357607,;BMX,stop_gained,p.Arg14Ter,ENST00000348343,NM_001320866.1,NM_203281.2;BMX,stop_gained,p.Arg14Ter,ENST00000342014,NM_001721.6;BMX,non_coding_transcript_exon_variant,,ENST00000463891,; T ENST00000357607 Transcript stop_gained 228/2598 40/2028 14/675 R/* Aga/Tga rs748739673 1 1 BMX HGNC HGNC:1079 protein_coding YES CCDS14168.1 ENSP00000350224 P51813 UPI0000000DFF 2/19 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF91,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 SNV 2 1 PASS rs748739673 . 3 205 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 71 15508393 15508393 A T 1 0 0 0 0 0 1 0 0 1629 64 3 4 4 BMX 23 15508393 Nonsense_Mutation SNP A C3N-01071_T 904021 15508393 140532502 342 21900 MAGEB16 0 . GRCh38 X 35802520 35802520 + Silent SNP G G T novel C3N-01071_T C3N-01071_N G G c.324G>T p.= p.V108V ENST00000399989 2/2 65 54 11 43 43 0 strelka-varscan-mutect MAGEB16,synonymous_variant,p.=,ENST00000399989,NM_001099921.1;MAGEB16,synonymous_variant,p.=,ENST00000399987,;MAGEB16,synonymous_variant,p.=,ENST00000399992,;MAGEB16,synonymous_variant,p.=,ENST00000399988,;MAGEB16,synonymous_variant,p.=,ENST00000399985,; T ENST00000399989 Transcript synonymous_variant 603/1818 324/975 108/324 V gtG/gtT 1 1 MAGEB16 HGNC HGNC:21188 protein_coding YES CCDS43927.1 ENSP00000382871 A2A368 UPI00006C1BC1 NM_001099921.1 2/2 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF24 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 71 35802520 35802520 G T 1 0 0 0 0 0 0 0 1 9089 1306 46 2 2 MAGEB16 23 35802520 Silent SNP G C3N-01071_T 20294127 35802520 120238375 343 21901 FAM47C 0 . GRCh38 X 37010846 37010846 + Silent SNP C C A novel C3N-01071_T C3N-01071_N C C c.2436C>A p.= p.L812L ENST00000358047 1/1 219 159 60 175 175 0 strelka-varscan-mutect FAM47C,synonymous_variant,p.=,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript synonymous_variant 2450/3270 2436/3108 812/1035 L ctC/ctA 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 1/1 Pfam_domain:PF14642 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 71 37010846 37010846 C A 1 0 0 0 0 0 0 0 1 5449 900 32 2 2 FAM47C 23 37010846 Silent SNP C C3N-01071_T 1208326 37010846 119030049 344 21902 RBM10 0 . GRCh38 X 47181385 47181386 + Frame_Shift_Ins INS - - T novel C3N-01071_T C3N-01071_N - - c.1614_1615insT p.Asp539Ter p.D539* ENST00000329236 13/24 86 74 12 60 60 0 sindel-varindel-pindel RBM10,frameshift_variant,p.Asp474Ter,ENST00000377604,NM_005676.4,NM_001204467.1;RBM10,frameshift_variant,p.Asp539Ter,ENST00000329236,NM_001204468.1;RBM10,frameshift_variant,p.Asp397Ter,ENST00000345781,NM_001204466.1;RBM10,frameshift_variant,p.Asp396Ter,ENST00000628161,NM_152856.2;RBM10,non_coding_transcript_exon_variant,,ENST00000478410,;RBM10,non_coding_transcript_exon_variant,,ENST00000496012,; T ENST00000329236 Transcript frameshift_variant 1614-1615/3201 1614-1615/2988 538-539/995 -/X -/T 1 1 RBM10 HGNC HGNC:9896 protein_coding YES CCDS75969.1 ENSP00000328848 A0A0A0MR66 UPI0000211F0E NM_001204468.1 13/24 Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 203 5 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 71 47181385 47181385 - T 1 0 1 1 0 0 0 0 0 13277 1219 43 0 0 RBM10 23 47181385 Frame_Shift_Ins INS - C3N-01071_T 10170539 47181385 108859510 345 21903 ARR3 0 . GRCh38 X 70276435 70276435 + Missense_Mutation SNP G G A novel C3N-01071_T C3N-01071_N G G c.348G>A p.Met116Ile p.M116I ENST00000307959 7/17 130 121 9 121 121 0 strelka-varscan-mutect ARR3,missense_variant,p.Met116Ile,ENST00000620997,;ARR3,missense_variant,p.Met116Ile,ENST00000374495,;ARR3,missense_variant,p.Met116Ile,ENST00000307959,NM_004312.2;ARR3,missense_variant,p.Met65Ile,ENST00000480877,; A ENST00000307959 Transcript missense_variant,splice_region_variant 399/1292 348/1167 116/388 M/I atG/atA 1 1 ARR3 HGNC HGNC:710 protein_coding YES CCDS14399.1 ENSP00000311538 P36575 UPI0000457850 NM_004312.2 tolerated(1) 7/17 Gene3D:1g4mA01,Pfam_domain:PF00339,hmmpanther:PTHR11792,hmmpanther:PTHR11792:SF19,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 70276435 70276435 G A 1 0 0 0 0 1 0 0 0 1122 1362 47 3 3 ARR3 23 70276435 Missense_Mutation SNP G C3N-01071_T 23095050 70276435 85764460 346 21904 ZMYM3 0 . GRCh38 X 71252964 71252964 + Missense_Mutation SNP C C A rs150071449 C3N-01071_T C3N-01071_N C C c.292G>T p.Gly98Cys p.G98C ENST00000314425 2/25 64 55 9 79 79 0 strelka-varscan-mutect ZMYM3,missense_variant,p.Gly98Cys,ENST00000373998,NM_001171162.1;ZMYM3,missense_variant,p.Gly98Cys,ENST00000373988,;ZMYM3,missense_variant,p.Gly98Cys,ENST00000314425,NM_201599.2,NM_005096.3;ZMYM3,missense_variant,p.Gly98Cys,ENST00000373984,;ZMYM3,missense_variant,p.Gly98Cys,ENST00000373982,;ZMYM3,missense_variant,p.Gly98Cys,ENST00000373981,NM_001171163.1;ZMYM3,missense_variant,p.Gly98Cys,ENST00000373978,;ZMYM3,non_coding_transcript_exon_variant,,ENST00000489332,; A ENST00000314425 Transcript missense_variant 423/5536 292/4113 98/1370 G/C Ggt/Tgt rs150071449 1 -1 ZMYM3 HGNC HGNC:13054 protein_coding YES CCDS14409.1 ENSP00000322845 Q14202 UPI000013C339 NM_201599.2,NM_005096.3 deleterious_low_confidence(0.02) 2/25 MODERATE 1 SNV 1 1 PASS rs150071449 . 0 206 2 2 0 0 0 0 -16.06223 0.9999978 1 1 1 0 A 3 1 71 71252964 71252964 C A 1 0 0 0 0 1 0 0 0 18281 652 23 1 1 ZMYM3 23 71252964 Missense_Mutation SNP C C3N-01071_T 976529 71252964 84787931 347 21905 ATP7A 0 . GRCh38 X 78011652 78011652 + Missense_Mutation SNP T T G novel C3N-01071_T C3N-01071_N T T c.2150T>G p.Phe717Cys p.F717C ENST00000341514 9/23 190 149 41 195 195 0 strelka-varscan-mutect ATP7A,missense_variant,p.Phe717Cys,ENST00000341514,NM_000052.6;ATP7A,missense_variant,p.Phe717Cys,ENST00000343533,NM_001282224.1; G ENST00000341514 Transcript missense_variant 2305/8483 2150/4503 717/1500 F/C tTt/tGt 1 1 ATP7A HGNC HGNC:869 protein_coding YES CCDS35339.1 ENSP00000345728 Q04656 UPI000044D414 NM_000052.6 deleterious(0) 9/23 Prints_domain:PR00942,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 71 78011652 78011652 T G 1 0 0 0 0 1 0 0 0 1343 1841 64 5 5 ATP7A 23 78011652 Missense_Mutation SNP T C3N-01071_T 6758688 78011652 78029243 348 21906 DRP2 0 . GRCh38 X 101247153 101247153 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.1241A>C p.Lys414Thr p.K414T ENST00000395209 12/24 110 101 9 100 100 0 strelka-varscan-mutect DRP2,missense_variant,p.Lys414Thr,ENST00000395209,NM_001939.2;DRP2,missense_variant,p.Lys414Thr,ENST00000402866,;DRP2,missense_variant,p.Lys414Thr,ENST00000538510,;DRP2,missense_variant,p.Lys336Thr,ENST00000541709,NM_001171184.1;DRP2,3_prime_UTR_variant,,ENST00000372916,; C ENST00000395209 Transcript missense_variant 1768/7277 1241/2874 414/957 K/T aAa/aCa 1 1 DRP2 HGNC HGNC:3032 protein_coding YES CCDS14480.2 ENSP00000378635 Q13474 A0A024RCH3 UPI000013D388 NM_001939.2 deleterious(0) 12/24 hmmpanther:PTHR11915,Pfam_domain:PF09068,PIRSF_domain:PIRSF038205,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -13.65748 0.9999931 1 1 1 0 C 3 2 71 101247153 101247153 A C 1 0 0 0 0 1 0 0 0 4585 14 1 5 5 DRP2 23 101247153 Missense_Mutation SNP A C3N-01071_T 23235501 101247153 54793742 349 21907 ARMCX4 0 . GRCh38 X 101488603 101488603 + Missense_Mutation SNP A A C novel C3N-01071_T C3N-01071_N A A c.14A>C p.Gln5Pro p.Q5P ENST00000423738 2/2 112 103 9 76 76 0 strelka-varscan-mutect ARMCX4,missense_variant,p.Gln5Pro,ENST00000423738,NM_001256155.2;ARMCX4,missense_variant,p.Gln109Pro,ENST00000433011,;ARMCX4,missense_variant,p.Gln109Pro,ENST00000452188,;ARMCX4,missense_variant,p.Gln97Pro,ENST00000354842,;ARMCX4,missense_variant,p.Gln97Pro,ENST00000455331,;ARMCX4,intron_variant,,ENST00000442270,;ARMCX4,intron_variant,,ENST00000445416,; C ENST00000423738 Transcript missense_variant 216/7424 14/6873 5/2290 Q/P cAg/cCg 1 1 ARMCX4 HGNC HGNC:28615 protein_coding YES CCDS59170.1 ENSP00000404304 F8W8Y7 UPI000442CF06 NM_001256155.2 deleterious(0.03) 2/2 hmmpanther:PTHR15712,hmmpanther:PTHR15712:SF21 MODERATE 1 SNV 5 1 PASS . . 0 206 0 3 0 0 0 0 -13.4029 0.9999758 1 1 1 0 C 3 2 71 101488603 101488603 A C 1 0 0 0 0 1 0 0 0 1102 188 7 5 5 ARMCX4 23 101488603 Missense_Mutation SNP A C3N-01071_T 241450 101488603 54552292 350 21908 RBMXL3 0 . GRCh38 X 115190033 115190033 + Missense_Mutation SNP C C A rs374672415 C3N-01071_T C3N-01071_N C C c.592C>A p.Arg198Ser p.R198S ENST00000424776 1/1 51 31 20 39 39 0 strelka-varscan-mutect RBMXL3,missense_variant,p.Arg198Ser,ENST00000424776,NM_001145346.1;LRCH2,intron_variant,,ENST00000317135,NM_020871.3;LRCH2,intron_variant,,ENST00000538422,NM_001243963.1; A ENST00000424776 Transcript missense_variant 607/3442 592/3204 198/1067 R/S Cgc/Agc rs374672415,COSM5480175 1 1 RBMXL3 HGNC HGNC:26859 protein_coding YES CCDS55478.1 ENSP00000417451 Q8N7X1 UPI0001932819 NM_001145346.1 tolerated_low_confidence(0.09) 1/1 0,1 MODERATE SNV 0,1 1 PASS rs374672415 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 71 115190033 115190033 C A 1 0 0 0 0 1 0 0 0 13321 768 27 1 1 RBMXL3 23 115190033 Missense_Mutation SNP C C3N-01071_T 13701430 115190033 40850862 351 21909 CT47B1 0 . GRCh38 X 120875064 120875064 + Missense_Mutation SNP G G T rs756067552 C3N-01071_T C3N-01071_N G G c.607C>A p.Pro203Thr p.P203T ENST00000371311 1/3 546 404 142 443 443 0 strelka-varscan-mutect CT47B1,missense_variant,p.Pro203Thr,ENST00000371311,NM_001145718.1;RP1-321E8.5,downstream_gene_variant,,ENST00000613352,;RP1-321E8.4,upstream_gene_variant,,ENST00000604718,; T ENST00000371311 Transcript missense_variant 866/1328 607/900 203/299 P/T Cca/Aca rs756067552 1 -1 CT47B1 HGNC HGNC:33293 protein_coding YES CCDS48161.1 ENSP00000360360 P0C2W7 UPI000036776D NM_001145718.1 deleterious(0.05) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32157:SF4,hmmpanther:PTHR32157,Pfam_domain:PF15623 MODERATE SNV 5 1 PASS rs756067552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 71 120875064 120875064 G T 1 0 0 0 0 1 0 0 0 3791 1232 43 2 2 CT47B1 23 120875064 Missense_Mutation SNP G C3N-01071_T 5685031 120875064 35165831 352 21910 IKBKG 0 . GRCh38 X 154560484 154560484 + Missense_Mutation SNP T T C novel C3N-01071_T C3N-01071_N T T c.800T>C p.Val267Ala p.V267A ENST00000618670 5/10 38 33 5 34 34 0 varscan-mutect IKBKG,missense_variant,p.Val199Ala,ENST00000594239,NM_001321397.1,NM_001099857.2;IKBKG,missense_variant,p.Val199Ala,ENST00000611071,NM_003639.4;IKBKG,missense_variant,p.Val267Ala,ENST00000618670,NM_001099856.3;IKBKG,missense_variant,p.Val198Ala,ENST00000617207,;IKBKG,missense_variant,p.Val199Ala,ENST00000619941,;IKBKG,missense_variant,p.Val198Ala,ENST00000615874,;IKBKG,missense_variant,p.Val199Ala,ENST00000440286,;IKBKG,missense_variant,p.Val187Ala,ENST00000413620,;IKBKG,missense_variant,p.Val65Ala,ENST00000615186,;IKBKG,intron_variant,,ENST00000611176,NM_001145255.2;IKBKG,downstream_gene_variant,,ENST00000422680,;IKBKG,downstream_gene_variant,,ENST00000445622,;IKBKG,downstream_gene_variant,,ENST00000492469,;IKBKG,intron_variant,,ENST00000617838,;IKBKG,3_prime_UTR_variant,,ENST00000612051,NM_001321396.1; C ENST00000618670 Transcript missense_variant 820/2069 800/1464 267/487 V/A gTg/gCg 1 1 IKBKG HGNC HGNC:5961 protein_coding YES CCDS48196.1 ENSP00000483825 Q9Y6K9 UPI00001A36E3 NM_001099856.3 tolerated(0.08) 5/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31553,hmmpanther:PTHR31553:SF3 MODERATE 1 SNV 1 1 PASS . . 4 203 3 0 0 0 0 0 -13.34382 1 1 1 1 0 C 3 2 71 154560484 154560484 T C 1 0 0 0 0 1 0 0 0 7521 1696 59 5 5 IKBKG 23 154560484 Missense_Mutation SNP T C3N-01071_T 33685420 154560484 1480411 353 21911 PRDM16 0 . GRCh38 1 3411686 3411686 + Missense_Mutation SNP A A T novel C3N-01072_T C3N-01072_N A A c.1489A>T p.Ser497Cys p.S497C ENST00000270722 9/17 97 74 23 109 109 0 strelka-varscan-mutect PRDM16,missense_variant,p.Ser497Cys,ENST00000270722,NM_022114.3;PRDM16,missense_variant,p.Ser497Cys,ENST00000378391,NM_199454.2;PRDM16,missense_variant,p.Ser498Cys,ENST00000511072,;PRDM16,missense_variant,p.Ser498Cys,ENST00000514189,;PRDM16,missense_variant,p.Ser306Cys,ENST00000509860,;PRDM16,non_coding_transcript_exon_variant,,ENST00000512462,; T ENST00000270722 Transcript missense_variant 1538/8690 1489/3831 497/1276 S/C Agc/Tgc 1 1 PRDM16 HGNC HGNC:14000 protein_coding YES CCDS41236.2 ENSP00000270722 Q9HAZ2 UPI0000458A29 NM_022114.3 deleterious(0.02) 9/17 hmmpanther:PTHR24393,hmmpanther:PTHR24393:SF5 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 3411686 3411686 A T 1 0 0 0 0 1 0 0 0 12588 304 11 4 4 PRDM16 1 3411686 Missense_Mutation SNP A C3N-01072_T 3411686 245544736 1 21912 SRSF4 0 . GRCh38 1 29148481 29148481 + Missense_Mutation SNP A A T rs762382718 C3N-01072_T C3N-01072_N A A c.1414T>A p.Ser472Thr p.S472T ENST00000373795 6/6 90 71 19 122 122 0 strelka-varscan-mutect SRSF4,missense_variant,p.Ser472Thr,ENST00000373795,NM_005626.4;SRSF4,downstream_gene_variant,,ENST00000466448,;RP11-242O24.3,upstream_gene_variant,,ENST00000413004,;SRSF4,non_coding_transcript_exon_variant,,ENST00000634348,; T ENST00000373795 Transcript missense_variant 1649/2387 1414/1485 472/494 S/T Tcc/Acc rs762382718 1 -1 SRSF4 HGNC HGNC:10786 protein_coding YES CCDS333.1 ENSP00000362900 Q08170 UPI00001358BF NM_005626.4 deleterious_low_confidence(0) 6/6 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs762382718 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 29148481 29148481 A T 1 0 0 0 0 1 0 0 0 15541 275 10 4 4 SRSF4 1 29148481 Missense_Mutation SNP A C3N-01072_T 25736795 29148481 219807941 2 21913 PGM1 0 . GRCh38 1 63648606 63648606 + Missense_Mutation SNP A A T rs567337429 C3N-01072_T C3N-01072_N A A c.1288A>T p.Ile430Phe p.I430F ENST00000371083 8/11 496 385 111 494 494 0 strelka-varscan-mutect PGM1,missense_variant,p.Ile430Phe,ENST00000371083,NM_001172818.1;PGM1,missense_variant,p.Ile412Phe,ENST00000371084,NM_002633.2;PGM1,missense_variant,p.Ile215Phe,ENST00000540265,NM_001172819.1;PGM1,upstream_gene_variant,,ENST00000483707,; T ENST00000371083 Transcript missense_variant 1656/2657 1288/1743 430/580 I/F Att/Ttt rs567337429 1 1 PGM1 HGNC HGNC:8905 protein_coding YES CCDS53323.1 ENSP00000360124 P36871 UPI000016A812 NM_001172818.1 deleterious(0) 8/11 hmmpanther:PTHR22573,hmmpanther:PTHR22573:SF37,Pfam_domain:PF02880,Gene3D:3.40.120.10,Superfamily_domains:SSF53738 MODERATE 1 SNV 2 1 PASS rs567337429 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 63648606 63648606 A T 1 0 0 0 0 1 0 0 0 11886 217 8 4 4 PGM1 1 63648606 Missense_Mutation SNP A C3N-01072_T 34500125 63648606 185307816 3 21914 TTLL7 0 . GRCh38 1 83933680 83933680 + Silent SNP G G A C3N-01072_T C3N-01072_N G G c.975C>T p.= p.S325S ENST00000260505 9/21 192 149 43 150 150 0 strelka-varscan-mutect TTLL7,synonymous_variant,p.=,ENST00000260505,NM_024686.4;TTLL7,synonymous_variant,p.=,ENST00000610996,;TTLL7,non_coding_transcript_exon_variant,,ENST00000477524,;TTLL7,non_coding_transcript_exon_variant,,ENST00000472688,;TTLL7,non_coding_transcript_exon_variant,,ENST00000488014,;TTLL7,intron_variant,,ENST00000482783,;TTLL7,synonymous_variant,p.=,ENST00000480174,;TTLL7,synonymous_variant,p.=,ENST00000474957,;TTLL7,synonymous_variant,p.=,ENST00000485638,; A ENST00000260505 Transcript synonymous_variant 1353/7976 975/2664 325/887 S agC/agT COSM5418420 1 -1 TTLL7 HGNC HGNC:26242 protein_coding YES CCDS690.2 ENSP00000260505 Q6ZT98 UPI000020391D NM_024686.4 9/21 Pfam_domain:PF03133,PROSITE_profiles:PS51221,hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF102,Superfamily_domains:SSF56059 1 LOW 1 SNV 2 1 1 PASS rs963199827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 72 83933680 83933680 G A 1 0 0 0 0 0 0 0 1 17243 1078 38 1 1 TTLL7 1 83933680 Silent SNP G C3N-01072_T 20285074 83933680 165022742 4 21915 PRPF38B 0 . GRCh38 1 108696309 108696309 + Missense_Mutation SNP G G T novel C3N-01072_T C3N-01072_N G G c.530G>T p.Trp177Leu p.W177L ENST00000370025 4/6 187 148 39 205 204 1 strelka-varscan-mutect PRPF38B,missense_variant,p.Trp66Leu,ENST00000370021,;PRPF38B,missense_variant,p.Trp177Leu,ENST00000370025,NM_018061.2;PRPF38B,missense_variant,p.Trp177Leu,ENST00000370022,;PRPF38B,non_coding_transcript_exon_variant,,ENST00000467302,;PRPF38B,upstream_gene_variant,,ENST00000485810,; T ENST00000370025 Transcript missense_variant 799/3693 530/1641 177/546 W/L tGg/tTg 1 1 PRPF38B HGNC HGNC:25512 protein_coding YES CCDS788.1 ENSP00000359042 Q5VTL8 UPI000013CF13 NM_018061.2 deleterious(0) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR23142,Pfam_domain:PF03371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 108696309 108696309 G T 1 0 0 0 0 1 0 0 0 12704 1357 47 2 2 PRPF38B 1 108696309 Missense_Mutation SNP G C3N-01072_T 24762629 108696309 140260113 5 21916 RUSC1 0 . GRCh38 1 155326926 155326926 + Silent SNP C C T novel C3N-01072_T C3N-01072_N C C c.2208C>T p.= p.A736A ENST00000368352 8/10 291 224 67 304 304 0 strelka-varscan-mutect RUSC1,synonymous_variant,p.=,ENST00000368352,NM_001105203.1;RUSC1,synonymous_variant,p.=,ENST00000368354,NM_001105204.1;RUSC1,synonymous_variant,p.=,ENST00000368347,NM_001105205.1;RUSC1,synonymous_variant,p.=,ENST00000292254,NM_001278230.1;RUSC1,synonymous_variant,p.=,ENST00000368349,NM_001278229.1,NM_014328.4,NM_001278227.1,NM_001278228.1;RUSC1,synonymous_variant,p.=,ENST00000490373,;RUSC1,synonymous_variant,p.=,ENST00000497930,;RUSC1,synonymous_variant,p.=,ENST00000479924,;RUSC1,synonymous_variant,p.=,ENST00000485924,;RUSC1,5_prime_UTR_variant,,ENST00000471876,;RUSC1,downstream_gene_variant,,ENST00000489860,;RUSC1-AS1,upstream_gene_variant,,ENST00000450199,;RUSC1-AS1,upstream_gene_variant,,ENST00000443642,;RUSC1,non_coding_transcript_exon_variant,,ENST00000462780,;RUSC1,downstream_gene_variant,,ENST00000492536,;RUSC1,downstream_gene_variant,,ENST00000467820,;RUSC1,downstream_gene_variant,,ENST00000473331,;RUSC1,downstream_gene_variant,,ENST00000468764,; T ENST00000368352 Transcript synonymous_variant 2359/3403 2208/2709 736/902 A gcC/gcT 1 1 RUSC1 HGNC HGNC:17153 protein_coding YES CCDS41410.1 ENSP00000357336 Q9BVN2 UPI000046FDA5 NM_001105203.1 8/10 hmmpanther:PTHR15591 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 72 155326926 155326926 C T 1 0 0 0 0 0 0 0 1 14011 668 24 3 3 RUSC1 1 155326926 Silent SNP C C3N-01072_T 46630617 155326926 93629496 6 21917 KCNJ10 0 . GRCh38 1 160041541 160041541 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.992A>G p.Asp331Gly p.D331G ENST00000368089 2/2 483 388 95 489 489 0 strelka-varscan-mutect KCNJ10,missense_variant,p.Asp331Gly,ENST00000368089,NM_002241.4;KCNJ10,intron_variant,,ENST00000637644,;KCNJ10,intron_variant,,ENST00000636689,;KCNJ10,intron_variant,,ENST00000509700,; C ENST00000368089 Transcript missense_variant 1219/5293 992/1140 331/379 D/G gAc/gGc 1 -1 KCNJ10 HGNC HGNC:6256 protein_coding YES CCDS1193.1 ENSP00000357068 P78508 UPI000012D8A6 NM_002241.4 tolerated(0.14) 2/2 hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF21,PIRSF_domain:PIRSF005465,Gene3D:2.60.40.1400,Pfam_domain:PF01007,Superfamily_domains:SSF81296,Prints_domain:PR01320,Prints_domain:PR01322 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 160041541 160041541 T C 1 0 0 0 0 1 0 0 0 7960 1667 58 5 5 KCNJ10 1 160041541 Missense_Mutation SNP T C3N-01072_T 4714615 160041541 88914881 7 21918 VANGL2 0 . GRCh38 1 160419327 160419327 + Missense_Mutation SNP C C A novel C3N-01072_T C3N-01072_N C C c.518C>A p.Ala173Asp p.A173D ENST00000368061 4/8 574 476 98 544 542 2 strelka-varscan-mutect VANGL2,missense_variant,p.Ala173Asp,ENST00000368061,NM_020335.2;VANGL2,upstream_gene_variant,,ENST00000483408,; A ENST00000368061 Transcript missense_variant 992/5340 518/1566 173/521 A/D gCc/gAc 1 1 VANGL2 HGNC HGNC:15511 protein_coding YES CCDS30915.1 ENSP00000357040 Q9ULK5 UPI00001C1D79 NM_020335.2 deleterious(0) 4/8 hmmpanther:PTHR20886,PIRSF_domain:PIRSF007991,Pfam_domain:PF06638 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 160419327 160419327 C A 1 0 0 0 0 1 0 0 0 17665 739 26 2 2 VANGL2 1 160419327 Missense_Mutation SNP C C3N-01072_T 377786 160419327 88537095 8 21919 CACNA1E 0 . GRCh38 1 181733016 181733016 + Missense_Mutation SNP G G A novel C3N-01072_T C3N-01072_N G G c.2930G>A p.Arg977Lys p.R977K ENST00000367573 20/48 70 53 17 70 70 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Arg958Lys,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Arg977Lys,ENST00000621551,;CACNA1E,missense_variant,p.Arg977Lys,ENST00000367567,;CACNA1E,missense_variant,p.Arg958Lys,ENST00000358338,;CACNA1E,missense_variant,p.Arg977Lys,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Arg977Lys,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Arg976Lys,ENST00000357570,;CACNA1E,missense_variant,p.Arg958Lys,ENST00000360108,; A ENST00000367573 Transcript missense_variant 2930/7067 2930/6942 977/2313 R/K aGa/aAa 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 tolerated(0.4) 20/48 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 181733016 181733016 G A 1 0 0 0 0 1 0 0 0 2230 942 33 3 3 CACNA1E 1 181733016 Missense_Mutation SNP G C3N-01072_T 21313689 181733016 67223406 9 21920 APOB 0 . GRCh38 2 21011202 21011202 + Missense_Mutation SNP G G A novel C3N-01072_T C3N-01072_N G G c.5666C>T p.Ser1889Leu p.S1889L ENST00000233242 26/29 277 232 45 285 285 0 strelka-varscan-mutect APOB,missense_variant,p.Ser1889Leu,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript missense_variant 5794/14121 5666/13692 1889/4563 S/L tCa/tTa 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0.03) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 21011202 21011202 G A 1 0 0 0 0 1 0 0 0 907 1294 45 3 3 APOB 2 21011202 Missense_Mutation SNP G C3N-01072_T 21011202 221182327 10 21921 BIRC6 0 . GRCh38 2 32476299 32476300 + Frame_Shift_Ins INS - - A novel C3N-01072_T C3N-01072_N - - c.6810dupA p.Leu2271ThrfsTer17 p.L2271Tfs*17 ENST00000421745 34/74 247 211 36 206 205 1 sindel-varindel-pindel BIRC6,frameshift_variant,p.Leu2271ThrfsTer17,ENST00000421745,NM_016252.3;BIRC6,downstream_gene_variant,,ENST00000462504,; A ENST00000421745 Transcript frameshift_variant 6941-6942/15703 6807-6808/14574 2269-2270/4857 -/X -/A 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 34/74 hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF123 HIGH 1 insertion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 72 32476299 32476299 - A 1 0 1 1 0 0 0 0 0 1589 1413 49 0 0 BIRC6 2 32476299 Frame_Shift_Ins INS - C3N-01072_T 11465097 32476299 209717230 11 21922 TSPYL6 0 . GRCh38 2 54255612 54255612 + Silent SNP T T A novel C3N-01072_T C3N-01072_N T T c.540A>T p.= p.I180I ENST00000317802 1/1 276 224 52 326 326 0 strelka-varscan-mutect TSPYL6,synonymous_variant,p.=,ENST00000317802,NM_001003937.2;ACYP2,intron_variant,,ENST00000394666,NM_138448.3;ACYP2,intron_variant,,ENST00000607452,;ACYP2,intron_variant,,ENST00000303536,;ACYP2,intron_variant,,ENST00000606865,;ACYP2,intron_variant,,ENST00000494922,; A ENST00000317802 Transcript synonymous_variant 661/3089 540/1233 180/410 I atA/atT 1 -1 TSPYL6 HGNC HGNC:14521 protein_coding YES CCDS42682.1 ENSP00000417919 Q8N831 A0A140VJY4 UPI000006CF77 NM_001003937.2 1/1 hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF29,Superfamily_domains:SSF143113 LOW SNV 1 PASS rs1458759042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 72 54255612 54255612 T A 1 0 0 0 0 0 0 0 1 17170 1512 53 4 4 TSPYL6 2 54255612 Silent SNP T C3N-01072_T 21779313 54255612 187937917 12 21923 HTRA2 0 . GRCh38 2 74530813 74530814 + Frame_Shift_Ins INS - - A novel C3N-01072_T C3N-01072_N - - c.704dupA p.Thr236AspfsTer2 p.T236Dfs*2 ENST00000258080 2/8 524 429 95 565 564 1 sindel-varindel-pindel HTRA2,frameshift_variant,p.Thr236AspfsTer2,ENST00000258080,NM_013247.4;HTRA2,frameshift_variant,p.Thr223AspfsTer2,ENST00000437202,;HTRA2,frameshift_variant,p.Thr236AspfsTer2,ENST00000352222,NM_145074.2;LOXL3,downstream_gene_variant,,ENST00000264094,NM_032603.3;LOXL3,downstream_gene_variant,,ENST00000409549,;DQX1,upstream_gene_variant,,ENST00000404568,NM_133637.2;DQX1,upstream_gene_variant,,ENST00000393951,;LOXL3,downstream_gene_variant,,ENST00000409249,;LOXL3,downstream_gene_variant,,ENST00000393937,NM_001289164.1;LOXL3,downstream_gene_variant,,ENST00000409986,;AUP1,upstream_gene_variant,,ENST00000377526,NM_181575.4;DQX1,upstream_gene_variant,,ENST00000451518,;LOXL3,downstream_gene_variant,,ENST00000420535,;HTRA2,non_coding_transcript_exon_variant,,ENST00000467961,;HTRA2,non_coding_transcript_exon_variant,,ENST00000462909,;HTRA2,non_coding_transcript_exon_variant,,ENST00000484881,;LOXL3,downstream_gene_variant,,ENST00000481835,;DQX1,upstream_gene_variant,,ENST00000498552,;HTRA2,non_coding_transcript_exon_variant,,ENST00000484352,;HTRA2,non_coding_transcript_exon_variant,,ENST00000482331,;HTRA2,non_coding_transcript_exon_variant,,ENST00000465521,;HTRA2,non_coding_transcript_exon_variant,,ENST00000482205,;LOXL3,downstream_gene_variant,,ENST00000470907,;DQX1,upstream_gene_variant,,ENST00000473508,;AUP1,upstream_gene_variant,,ENST00000466894,;AUP1,upstream_gene_variant,,ENST00000463900,;AUP1,upstream_gene_variant,,ENST00000425118,;AUP1,upstream_gene_variant,,ENST00000486234,;AUP1,upstream_gene_variant,,ENST00000464887,;AUP1,upstream_gene_variant,,ENST00000472800,;AUP1,upstream_gene_variant,,ENST00000462297,; A ENST00000258080 Transcript frameshift_variant 1333-1334/2370 703-704/1377 235/458 Q/QX cag/cAag 1 1 HTRA2 HGNC HGNC:14348 protein_coding YES CCDS1951.1 ENSP00000258080 O43464 UPI000012CB84 NM_013247.4 2/8 hmmpanther:PTHR22939,hmmpanther:PTHR22939:SF69,Pfam_domain:PF13365,Gene3D:2.40.10.10,Superfamily_domains:SSF50494 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 72 74530813 74530813 - A 1 0 1 1 0 0 0 0 0 7350 827 29 0 0 HTRA2 2 74530813 Frame_Shift_Ins INS - C3N-01072_T 20275201 74530813 167662716 13 21924 ST3GAL5 0 . GRCh38 2 85863477 85863477 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.91A>C p.Ser31Arg p.S31R ENST00000377332 2/7 370 300 70 316 315 1 strelka-varscan-mutect ST3GAL5,missense_variant,p.Ser31Arg,ENST00000377332,NM_003896.3;ST3GAL5,missense_variant,p.Ser3Arg,ENST00000393805,;ST3GAL5,missense_variant,p.Ser8Arg,ENST00000393808,NM_001042437.1;ST3GAL5,missense_variant,p.Ser3Arg,ENST00000455892,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000484728,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000461892,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000461199,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000473122,;ST3GAL5,non_coding_transcript_exon_variant,,ENST00000490946,;ST3GAL5,missense_variant,p.Ser31Arg,ENST00000306262,;ST3GAL5,3_prime_UTR_variant,,ENST00000433665,; G ENST00000377332 Transcript missense_variant 200/2366 91/1257 31/418 S/R Agt/Cgt 1 -1 ST3GAL5 HGNC HGNC:10872 protein_coding YES CCDS1986.2 ENSP00000366549 Q9UNP4 UPI000015F319 NM_003896.3 tolerated_low_confidence(0.07) 2/7 hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF60 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 85863477 85863477 T G 1 0 0 0 0 1 0 0 0 15596 1609 56 5 5 ST3GAL5 2 85863477 Missense_Mutation SNP T C3N-01072_T 11332664 85863477 156330052 14 21925 DARS 0 . GRCh38 2 135979362 135979362 + Silent SNP T T G novel C3N-01072_T C3N-01072_N T T c.129A>C p.= p.R43R ENST00000264161 3/16 194 150 44 207 206 1 strelka-varscan-mutect DARS,synonymous_variant,p.=,ENST00000264161,NM_001293312.1,NM_001349.3;DARS,synonymous_variant,p.=,ENST00000456565,;DARS,synonymous_variant,p.=,ENST00000441323,;DARS,synonymous_variant,p.=,ENST00000449218,;DARS,non_coding_transcript_exon_variant,,ENST00000463008,;DARS,synonymous_variant,p.=,ENST00000435076,;DARS,non_coding_transcript_exon_variant,,ENST00000474184,; G ENST00000264161 Transcript synonymous_variant 345/2361 129/1506 43/501 R cgA/cgC 1 -1 DARS HGNC HGNC:2678 protein_coding YES CCDS2180.1 ENSP00000264161 P14868 A0A140VJW5 UPI000013639B NM_001293312.1,NM_001349.3 3/16 Gene3D:2.40.50.140,hmmpanther:PTHR22594,hmmpanther:PTHR22594:SF33,Superfamily_domains:SSF50249 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 72 135979362 135979362 T G 1 0 0 0 0 0 0 0 1 4041 1565 54 5 5 DARS 2 135979362 Silent SNP T C3N-01072_T 50115885 135979362 106214167 15 21926 CTNNB1 0 . GRCh38 3 41224646 41224646 + Missense_Mutation SNP C C T rs121913409 C3N-01072_T C3N-01072_N C C c.134C>T p.Ser45Phe p.S45F ENST00000349496 3/15 494 383 111 526 526 0 strelka-varscan-mutect CTNNB1,missense_variant,p.Ser45Phe,ENST00000349496,NM_001904.3;CTNNB1,missense_variant,p.Ser45Phe,ENST00000396185,NM_001098209.1;CTNNB1,missense_variant,p.Ser45Phe,ENST00000396183,NM_001098210.1;CTNNB1,missense_variant,p.Ser38Phe,ENST00000453024,;CTNNB1,missense_variant,p.Ser45Phe,ENST00000405570,;CTNNB1,missense_variant,p.Ser45Phe,ENST00000450969,;CTNNB1,missense_variant,p.Ser45Phe,ENST00000431914,;CTNNB1,missense_variant,p.Ser45Phe,ENST00000441708,;CTNNB1,missense_variant,p.Ser38Phe,ENST00000426215,;CTNNB1,downstream_gene_variant,,ENST00000433400,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000488914,; T ENST00000349496 Transcript missense_variant 414/3737 134/2346 45/781 S/F tCt/tTt rs121913409,COSM5667,COSM5689,COSM5692,COSM6100 1 1 CTNNB1 HGNC HGNC:2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 A0A024R2Q3 UPI000012862F NM_001904.3 deleterious(0) 3/15 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53 pathogenic 0,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs121913409 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 41224646 41224646 C T 1 0 0 0 0 1 0 0 0 3825 913 32 3 3 CTNNB1 3 41224646 Missense_Mutation SNP C C3N-01072_T 41224646 157070913 16 21927 PXK 0 . GRCh38 3 58391188 58391188 + Missense_Mutation SNP A A C novel C3N-01072_T C3N-01072_N A A c.508A>C p.Asn170His p.N170H ENST00000356151 6/18 185 148 37 220 220 0 strelka-varscan-mutect PXK,missense_variant,p.Asn170His,ENST00000383716,NM_001289098.1;PXK,missense_variant,p.Asn137His,ENST00000463280,NM_001289101.1,NM_001289100.1;PXK,missense_variant,p.Asn153His,ENST00000479241,NM_001289095.1;PXK,missense_variant,p.Asn170His,ENST00000356151,NM_001289099.1,NM_001289096.1,NM_017771.4;PXK,missense_variant,p.Asn170His,ENST00000484288,;PXK,missense_variant,p.Asn170His,ENST00000302779,;PXK,missense_variant,p.Asn153His,ENST00000383715,;PXK,upstream_gene_variant,,ENST00000479134,;PXK,3_prime_UTR_variant,,ENST00000468776,;PXK,intron_variant,,ENST00000477308,; C ENST00000356151 Transcript missense_variant 617/2037 508/1737 170/578 N/H Aat/Cat 1 1 PXK HGNC HGNC:23326 protein_coding YES CCDS2889.1 ENSP00000348472 Q7Z7A4 UPI000004A035 NM_001289099.1,NM_001289096.1,NM_017771.4 tolerated(0.11) 6/18 PROSITE_profiles:PS50011,hmmpanther:PTHR22999 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 58391188 58391188 A C 1 0 0 0 0 1 0 0 0 13003 14 1 5 5 PXK 3 58391188 Missense_Mutation SNP A C3N-01072_T 17166542 58391188 139904371 17 21928 COPG1 0 . GRCh38 3 129272834 129272834 + Missense_Mutation SNP A A C novel C3N-01072_T C3N-01072_N A A c.2186A>C p.Lys729Thr p.K729T ENST00000314797 21/24 149 132 17 126 126 0 strelka-varscan-mutect COPG1,missense_variant,p.Lys729Thr,ENST00000314797,NM_016128.3;COPG1,missense_variant,p.Lys43Thr,ENST00000509889,;MIR6826,downstream_gene_variant,,ENST00000617808,;COPG1,missense_variant,p.Lys50Thr,ENST00000514478,;COPG1,non_coding_transcript_exon_variant,,ENST00000515725,;COPG1,upstream_gene_variant,,ENST00000512034,; C ENST00000314797 Transcript missense_variant 2290/3078 2186/2625 729/874 K/T aAg/aCg 1 1 COPG1 HGNC HGNC:2236 protein_coding YES CCDS33851.1 ENSP00000325002 Q9Y678 UPI000000095F NM_016128.3 deleterious(0.04) 21/24 Gene3D:1r4xA01,Pfam_domain:PF08752,PIRSF_domain:PIRSF037093,hmmpanther:PTHR10261,hmmpanther:PTHR10261:SF3,Superfamily_domains:SSF49348 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 129272834 129272834 A C 1 0 0 0 0 1 0 0 0 3523 72 3 5 5 COPG1 3 129272834 Missense_Mutation SNP A C3N-01072_T 70881646 129272834 69022725 18 21929 GK5 0 . GRCh38 3 142172447 142172447 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.1153A>C p.Asn385His p.N385H ENST00000392993 13/16 212 191 21 175 175 0 strelka-varscan-mutect GK5,missense_variant,p.Asn385His,ENST00000392993,NM_001039547.2;GK5,missense_variant,p.Asn39His,ENST00000486459,;GK5,3_prime_UTR_variant,,ENST00000480757,;GK5,3_prime_UTR_variant,,ENST00000492097,;GK5,3_prime_UTR_variant,,ENST00000463349,;GK5,non_coding_transcript_exon_variant,,ENST00000460515,; G ENST00000392993 Transcript missense_variant 1305/9837 1153/1590 385/529 N/H Aat/Cat 1 -1 GK5 HGNC HGNC:28635 protein_coding YES CCDS33871.1 ENSP00000418001 Q6ZS86 UPI000069B0CB NM_001039547.2 deleterious(0.04) 13/16 Gene3D:3.30.420.40,Pfam_domain:PF02782,PIRSF_domain:PIRSF000538,hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF68,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 142172447 142172447 T G 1 0 0 0 0 1 0 0 0 6300 1841 64 5 5 GK5 3 142172447 Missense_Mutation SNP T C3N-01072_T 12899613 142172447 56123112 19 21930 IGSF10 0 . GRCh38 3 151438436 151438457 + Frame_Shift_Del DEL TGGTCAATTTTGGCAGGTTTCA TGGTCAATTTTGGCAGGTTTCA - novel C3N-01072_T C3N-01072_N TGGTCAATTTTGGCAGGTTTCA TGGTCAATTTTGGCAGGTTTCA c.6104_6125delTGAAACCTGCCAAAATTGACCA p.Leu2035ProfsTer17 p.L2035Pfs*17 ENST00000282466 6/6 495 428 67 375 375 0 sindel-varindel-pindel IGSF10,frameshift_variant,p.Leu2035ProfsTer17,ENST00000282466,NM_178822.4;IGSF10,intron_variant,,ENST00000489791,;MED12L,downstream_gene_variant,,ENST00000474524,NM_053002.5;MED12L,downstream_gene_variant,,ENST00000273432,;IGSF10,non_coding_transcript_exon_variant,,ENST00000495443,;IGSF10,non_coding_transcript_exon_variant,,ENST00000493841,;IGSF10,upstream_gene_variant,,ENST00000497472,; - ENST00000282466 Transcript frameshift_variant 6104-6125/11067 6104-6125/7872 2035-2042/2623 LKPAKIDH/X cTGAAACCTGCCAAAATTGACCAc/cc 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 6/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 72 151438436 151438436 TGGTCAATTTTGGCAGGTTTCA - 1 0 1 0 1 0 0 0 0 7504 1696 59 0 0 IGSF10 3 151438436 Frame_Shift_Del DEL TGGTCAATTTTGGCAGGTTTCA C3N-01072_T 9265989 151438436 46857123 20 21931 WDR49 0 . GRCh38 3 167566851 167566851 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.1553A>C p.Asn518Thr p.N518T ENST00000479765 9/10 131 102 29 113 113 0 strelka-varscan-mutect WDR49,missense_variant,p.Asn518Thr,ENST00000479765,;WDR49,intron_variant,,ENST00000308378,NM_178824.3;WDR49,intron_variant,,ENST00000472600,;WDR49,intron_variant,,ENST00000466760,;WDR49,non_coding_transcript_exon_variant,,ENST00000476376,;WDR49,intron_variant,,ENST00000460448,; G ENST00000479765 Transcript missense_variant 1777/2108 1553/1557 518/518 N/T aAt/aCt 1 -1 WDR49 HGNC HGNC:26587 protein_coding ENSP00000419749 E9PDB0 UPI000013ED1E 9/10 Coiled-coils_(Ncoils):Coil MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 167566851 167566851 T G 1 0 0 0 0 1 0 0 0 17862 1493 52 5 5 WDR49 3 167566851 Missense_Mutation SNP T C3N-01072_T 16128415 167566851 30728708 21 21932 VWA5B2 0 . GRCh38 3 184233231 184233231 + Missense_Mutation SNP G G C novel C3N-01072_T C3N-01072_N G G c.364G>C p.Gly122Arg p.G122R ENST00000426955 3/19 200 164 36 186 186 0 strelka-varscan-mutect VWA5B2,missense_variant,p.Gly122Arg,ENST00000426955,NM_138345.1;VWA5B2,upstream_gene_variant,,ENST00000273794,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000497229,;VWA5B2,upstream_gene_variant,,ENST00000461141,;VWA5B2,upstream_gene_variant,,ENST00000474580,; C ENST00000426955 Transcript missense_variant 464/4120 364/3729 122/1242 G/R Ggc/Cgc 1 1 VWA5B2 HGNC HGNC:25144 protein_coding YES CCDS54686.1 ENSP00000398688 Q8N398 UPI0000412DE9 NM_138345.1 deleterious(0) 3/19 PROSITE_profiles:PS51468,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF107 MODERATE 1 SNV 1 1 PASS rs1041312243 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 184233231 184233231 G C 1 0 0 0 0 1 0 0 0 17798 1000 35 4 4 VWA5B2 3 184233231 Missense_Mutation SNP G C3N-01072_T 16666380 184233231 14062328 22 21933 CPE 0 . GRCh38 4 165467792 165467792 + Silent SNP A A G novel C3N-01072_T C3N-01072_N A A c.609A>G p.= p.K203K ENST00000402744 3/9 232 180 52 181 181 0 strelka-varscan-mutect CPE,synonymous_variant,p.=,ENST00000402744,NM_001873.2;CPE,synonymous_variant,p.=,ENST00000431967,;CPE,synonymous_variant,p.=,ENST00000513982,;CPE,synonymous_variant,p.=,ENST00000511992,; G ENST00000402744 Transcript synonymous_variant 889/2421 609/1431 203/476 K aaA/aaG 1 1 CPE HGNC HGNC:2303 protein_coding YES CCDS3810.1 ENSP00000386104 P16870 UPI000000163E NM_001873.2 3/9 hmmpanther:PTHR11532,Pfam_domain:PF00246,Gene3D:3.40.630.10,SMART_domains:SM00631,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS rs750690232 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 72 165467792 165467792 A G 1 0 0 0 0 0 0 0 1 3593 69 3 5 5 CPE 4 165467792 Silent SNP A C3N-01072_T 165467792 24746763 23 21934 RASGRF2 0 . GRCh38 5 81080138 81080138 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.905T>G p.Leu302Arg p.L302R ENST00000265080 6/27 185 152 33 146 145 1 strelka-varscan-mutect RASGRF2,missense_variant,p.Leu302Arg,ENST00000265080,NM_006909.2;RASGRF2,non_coding_transcript_exon_variant,,ENST00000502677,;RASGRF2,missense_variant,p.Leu302Arg,ENST00000503795,; G ENST00000265080 Transcript missense_variant 972/8167 905/3714 302/1237 L/R cTt/cGt 1 1 RASGRF2 HGNC HGNC:9876 protein_coding YES CCDS4052.1 ENSP00000265080 O14827 UPI0000047ABF NM_006909.2 deleterious(0) 6/27 PROSITE_profiles:PS50010,hmmpanther:PTHR23113:SF187,hmmpanther:PTHR23113,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 81080138 81080138 T G 1 0 0 0 0 1 0 0 0 13234 1609 56 5 5 RASGRF2 5 81080138 Missense_Mutation SNP T C3N-01072_T 81080138 100458121 24 21935 DNAJC18 0 . GRCh38 5 139420091 139420091 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.914A>C p.Asp305Ala p.D305A ENST00000302060 7/8 102 77 25 94 94 0 varscan-mutect DNAJC18,missense_variant,p.Asp305Ala,ENST00000302060,NM_152686.3;DNAJC18,missense_variant,p.Asp138Ala,ENST00000508445,;DNAJC18,missense_variant,p.Asp97Ala,ENST00000514052,;DNAJC18,downstream_gene_variant,,ENST00000507405,;DNAJC18,non_coding_transcript_exon_variant,,ENST00000510770,;DNAJC18,downstream_gene_variant,,ENST00000505568,;DNAJC18,downstream_gene_variant,,ENST00000506870,; G ENST00000302060 Transcript missense_variant 995/5103 914/1077 305/358 D/A gAt/gCt 1 -1 DNAJC18 HGNC HGNC:28429 protein_coding YES CCDS4214.1 ENSP00000302843 Q9H819 UPI00000375B2 NM_152686.3 tolerated(0.72) 7/8 Pfam_domain:PF09320 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 139420091 139420091 T G 1 0 0 0 0 1 0 0 0 4451 1435 50 5 5 DNAJC18 5 139420091 Missense_Mutation SNP T C3N-01072_T 58339953 139420091 42118168 25 21936 TENM2 0 . GRCh38 5 168199926 168199926 + Missense_Mutation SNP A A C novel C3N-01072_T C3N-01072_N A A c.3225A>C p.Arg1075Ser p.R1075S ENST00000518659 17/29 315 250 65 258 258 0 strelka-varscan-mutect TENM2,missense_variant,p.Arg954Ser,ENST00000519204,;TENM2,missense_variant,p.Arg1075Ser,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Arg843Ser,ENST00000520394,; C ENST00000518659 Transcript missense_variant 3264/8550 3225/8325 1075/2774 R/S agA/agC 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 17/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 168199926 168199926 A C 1 0 0 0 0 1 0 0 0 16172 243 9 5 5 TENM2 5 168199926 Missense_Mutation SNP A C3N-01072_T 28779835 168199926 13338333 26 21937 CPLX2 0 . GRCh38 5 175879028 175879028 + Missense_Mutation SNP A A C novel C3N-01072_T C3N-01072_N A A c.152A>C p.Lys51Thr p.K51T ENST00000359546 4/5 174 139 35 164 164 0 strelka-varscan-mutect CPLX2,missense_variant,p.Lys51Thr,ENST00000359546,NM_006650.3;CPLX2,missense_variant,p.Lys51Thr,ENST00000514150,;CPLX2,missense_variant,p.Lys51Thr,ENST00000393745,NM_001008220.1;CPLX2,missense_variant,p.Lys51Thr,ENST00000515094,;CPLX2,missense_variant,p.Lys51Thr,ENST00000509837,;CPLX2,missense_variant,p.Lys51Thr,ENST00000502265,;CPLX2,missense_variant,p.Lys51Thr,ENST00000512824,;CPLX2,downstream_gene_variant,,ENST00000515025,;CPLX2,downstream_gene_variant,,ENST00000515502,; C ENST00000359546 Transcript missense_variant 795/5023 152/405 51/134 K/T aAg/aCg 1 1 CPLX2 HGNC HGNC:2310 protein_coding YES CCDS4396.1 ENSP00000352544 Q6PUV4 UPI0000027525 NM_006650.3 deleterious(0) 4/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16705,hmmpanther:PTHR16705:SF9,Gene3D:1kilE00,Pfam_domain:PF05835,Superfamily_domains:SSF58038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 175879028 175879028 A C 1 0 0 0 0 1 0 0 0 3600 72 3 5 5 CPLX2 5 175879028 Missense_Mutation SNP A C3N-01072_T 7679102 175879028 5659231 27 21938 HLA-C 0 . GRCh38 6 31270478 31270478 + Silent SNP T T C novel C3N-01072_T C3N-01072_N T T c.627A>G p.= p.P209P ENST00000376228 4/8 126 107 19 130 130 0 strelka-varscan HLA-C,synonymous_variant,p.=,ENST00000383329,;HLA-C,synonymous_variant,p.=,ENST00000376228,NM_002117.5;HLA-C,synonymous_variant,p.=,ENST00000415537,;HLA-C,3_prime_UTR_variant,,ENST00000376237,;HLA-C,non_coding_transcript_exon_variant,,ENST00000487245,;HLA-C,non_coding_transcript_exon_variant,,ENST00000495835,;HLA-C,upstream_gene_variant,,ENST00000470363,;HLA-C,downstream_gene_variant,,ENST00000484378,;HLA-C,upstream_gene_variant,,ENST00000466892,; C ENST00000376228 Transcript synonymous_variant 642/1536 627/1101 209/366 P ccA/ccG 1 -1 HLA-C HGNC HGNC:4933 protein_coding YES CCDS34393.1 ENSP00000365402 P10321 Q6R739 UPI000008AEBB NM_002117.5 4/8 PROSITE_profiles:PS50835,hmmpanther:PTHR16675:SF185,hmmpanther:PTHR16675,Gene3D:3.30.500.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 72 31270478 31270478 T C 1 0 0 0 0 0 0 0 1 7086 1799 63 5 5 HLA-C 6 31270478 Silent SNP T C3N-01072_T 31270478 139535501 28 21939 DGKB 0 . GRCh38 7 14338551 14338551 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.2089G>A p.Val697Ile p.V697I ENST00000403951 23/26 95 79 16 100 100 0 strelka-varscan-mutect DGKB,missense_variant,p.Val697Ile,ENST00000403951,;DGKB,missense_variant,p.Val697Ile,ENST00000399322,NM_004080.2;DGKB,missense_variant,p.Val696Ile,ENST00000402815,;DGKB,missense_variant,p.Val689Ile,ENST00000407950,;DGKB,missense_variant,p.Val697Ile,ENST00000406247,NM_145695.2;DGKB,non_coding_transcript_exon_variant,,ENST00000403963,; T ENST00000403951 Transcript missense_variant 2509/6917 2089/2415 697/804 V/I Gtc/Atc 1 -1 DGKB HGNC HGNC:2850 protein_coding YES CCDS47547.1 ENSP00000385780 Q9Y6T7 UPI0000033B9B tolerated(0.87) 23/26 Pfam_domain:PF00609,SMART_domains:SM00045 MODERATE 1 SNV 5 1 PASS rs1424437545 . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 72 14338551 14338551 C T 1 0 0 0 0 1 0 0 0 4272 536 19 1 1 DGKB 7 14338551 Missense_Mutation SNP C C3N-01072_T 14338551 145007422 29 21940 MYO1G 0 . GRCh38 7 44969706 44969706 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.1502A>G p.Gln501Arg p.Q501R ENST00000258787 11/22 150 123 27 154 154 0 strelka-varscan-mutect MYO1G,missense_variant,p.Gln501Arg,ENST00000258787,NM_033054.2;MYO1G,splice_region_variant,,ENST00000488554,;MYO1G,splice_region_variant,,ENST00000463516,;MYO1G,splice_region_variant,,ENST00000483585,;MYO1G,splice_region_variant,,ENST00000495831,;MYO1G,splice_region_variant,,ENST00000464434,;MYO1G,non_coding_transcript_exon_variant,,ENST00000480503,; C ENST00000258787 Transcript missense_variant,splice_region_variant 1639/3267 1502/3057 501/1018 Q/R cAg/cGg 1 -1 MYO1G HGNC HGNC:13880 protein_coding YES CCDS34629.1 ENSP00000258787 B0I1T2 UPI00001D747C NM_033054.2 tolerated(0.21) 11/22 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF381,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 44969706 44969706 T C 1 0 0 0 0 1 0 0 0 10075 1594 55 5 5 MYO1G 7 44969706 Missense_Mutation SNP T C3N-01072_T 30631155 44969706 114376267 30 21941 ABCA13 0 . GRCh38 7 48506367 48506367 + Silent SNP G G C novel C3N-01072_T C3N-01072_N G G c.13323G>C p.= p.G4441G ENST00000435803 49/62 275 235 40 293 293 0 strelka-varscan-mutect ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000544596,;ABCA13,synonymous_variant,p.=,ENST00000411975,;ABCA13,upstream_gene_variant,,ENST00000435451,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,synonymous_variant,p.=,ENST00000453246,; C ENST00000435803 Transcript synonymous_variant 13347/17184 13323/15177 4441/5058 G ggG/ggC 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 49/62 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Pfam_domain:PF12698 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 72 48506367 48506367 G C 1 0 0 0 0 0 0 0 1 35 1219 43 4 4 ABCA13 7 48506367 Silent SNP G C3N-01072_T 3536661 48506367 110839606 31 21942 GTF2IRD1 0 . GRCh38 7 74601073 74601073 + Missense_Mutation SNP A A G novel C3N-01072_T C3N-01072_N A A c.2755A>G p.Arg919Gly p.R919G ENST00000455841 26/27 230 180 50 233 233 0 strelka-varscan-mutect GTF2IRD1,missense_variant,p.Arg887Gly,ENST00000476977,;GTF2IRD1,missense_variant,p.Arg902Gly,ENST00000265755,NM_016328.2;GTF2IRD1,missense_variant,p.Arg919Gly,ENST00000455841,NM_001199207.1;GTF2IRD1,missense_variant,p.Arg887Gly,ENST00000424337,NM_005685.3;GTF2IRD1,missense_variant,p.Arg265Gly,ENST00000470715,;GTF2IRD1,non_coding_transcript_exon_variant,,ENST00000486086,; G ENST00000455841 Transcript missense_variant 2968/3315 2755/2931 919/976 R/G Aga/Gga 1 1 GTF2IRD1 HGNC HGNC:4661 protein_coding YES CCDS56492.1 ENSP00000397566 Q9UHL9 UPI00003BF92B NM_001199207.1 deleterious(0.05) 26/27 PIRSF_domain:PIRSF016441 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 74601073 74601073 A G 1 0 0 0 0 1 0 0 0 6749 296 11 5 5 GTF2IRD1 7 74601073 Missense_Mutation SNP A C3N-01072_T 26094706 74601073 84744900 32 21943 CYP3A43 0 . GRCh38 7 99828162 99828162 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.47C>T p.Ala16Val p.A16V ENST00000222382 1/13 77 63 14 101 101 0 strelka-varscan-mutect CYP3A43,missense_variant,p.Ala16Val,ENST00000354829,NM_057095.2;CYP3A43,missense_variant,p.Ala16Val,ENST00000222382,NM_022820.4;CYP3A43,missense_variant,p.Ala16Val,ENST00000342499,;CYP3A43,missense_variant,p.Ala16Val,ENST00000312017,NM_057096.3;CYP3A43,missense_variant,p.Ala16Val,ENST00000417625,NM_001278921.1;CYP3A43,missense_variant,p.Ala16Val,ENST00000415413,;CYP3A43,missense_variant,p.Ala16Val,ENST00000631161,;CYP3A43,synonymous_variant,p.=,ENST00000444905,;CYP3A43,non_coding_transcript_exon_variant,,ENST00000477658,;CYP3A43,non_coding_transcript_exon_variant,,ENST00000491648,;CYP3A43,non_coding_transcript_exon_variant,,ENST00000495115,;CYP3A43,non_coding_transcript_exon_variant,,ENST00000463915,;CYP3A43,missense_variant,p.Ala16Val,ENST00000434806,;CYP3A43,missense_variant,p.Ala16Val,ENST00000433277,;CYP3A43,missense_variant,p.Ala16Val,ENST00000436834,;CYP3A43,non_coding_transcript_exon_variant,,ENST00000481362,; T ENST00000222382 Transcript missense_variant 47/1515 47/1515 16/504 A/V gCt/gTt 1 1 CYP3A43 HGNC HGNC:17450 protein_coding YES CCDS5675.1 ENSP00000222382 Q9HB55 UPI000002A50E NM_022820.4 tolerated(0.51) 1/13 Prints_domain:PR01689,hmmpanther:PTHR24302,hmmpanther:PTHR24302:SF6,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999986 1 1 1 0 T 3 4 72 99828162 99828162 C T 1 0 0 0 0 1 0 0 0 3982 797 28 3 3 CYP3A43 7 99828162 Missense_Mutation SNP C C3N-01072_T 25227089 99828162 59517811 33 21944 OR2AE1 0 . GRCh38 7 99876605 99876605 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.429G>A p.Met143Ile p.M143I ENST00000316368 1/1 346 271 75 299 299 0 strelka-varscan-mutect OR2AE1,missense_variant,p.Met143Ile,ENST00000316368,NM_001005276.1;TRIM4,downstream_gene_variant,,ENST00000447480,;CYP3A52P,downstream_gene_variant,,ENST00000563326,; T ENST00000316368 Transcript missense_variant 453/1071 429/972 143/323 M/I atG/atA 1 -1 OR2AE1 HGNC HGNC:15087 protein_coding YES CCDS34696.1 ENSP00000313936 Q8NHA4 UPI000004B1E7 NM_001005276.1 tolerated(0.11) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF196,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1486112581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 99876605 99876605 C T 1 0 0 0 0 1 0 0 0 11060 826 29 3 3 OR2AE1 7 99876605 Missense_Mutation SNP C C3N-01072_T 48443 99876605 59469368 34 21945 ZNF786 0 . GRCh38 7 149071939 149071939 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.833G>A p.Arg278Gln p.R278Q ENST00000491431 4/4 105 80 25 99 99 0 strelka-varscan-mutect ZNF786,missense_variant,p.Arg192Gln,ENST00000316286,;ZNF786,missense_variant,p.Arg278Gln,ENST00000491431,NM_152411.3; T ENST00000491431 Transcript missense_variant 898/2874 833/2349 278/782 R/Q cGa/cAa 1 -1 ZNF786 HGNC HGNC:21806 protein_coding YES CCDS47738.1 ENSP00000417470 Q8N393 UPI000013FD40 NM_152411.3 tolerated(0.54) 4/4 Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1445416724 . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 72 149071939 149071939 C T 1 0 0 0 0 1 0 0 0 18742 884 31 1 1 ZNF786 7 149071939 Missense_Mutation SNP C C3N-01072_T 49195334 149071939 10274034 35 21946 PARP10 0 . GRCh38 8 143983376 143983376 + Missense_Mutation SNP G G A rs782458070 C3N-01072_T C3N-01072_N G G c.2213C>T p.Thr738Met p.T738M ENST00000313028 8/11 203 174 29 216 216 0 strelka-varscan-mutect PARP10,missense_variant,p.Thr738Met,ENST00000313028,NM_032789.3;PARP10,missense_variant,p.Thr729Met,ENST00000524918,;PARP10,missense_variant,p.Thr750Met,ENST00000525773,NM_001317895.1;PARP10,downstream_gene_variant,,ENST00000313059,;PARP10,downstream_gene_variant,,ENST00000525879,;PARP10,downstream_gene_variant,,ENST00000528136,;PARP10,downstream_gene_variant,,ENST00000529842,;PARP10,downstream_gene_variant,,ENST00000528625,;PARP10,downstream_gene_variant,,ENST00000528914,;PARP10,downstream_gene_variant,,ENST00000530478,;PARP10,downstream_gene_variant,,ENST00000531537,;PARP10,downstream_gene_variant,,ENST00000525486,;PARP10,downstream_gene_variant,,ENST00000529311,;PARP10,downstream_gene_variant,,ENST00000531707,;PARP10,downstream_gene_variant,,ENST00000532311,;PARP10,downstream_gene_variant,,ENST00000533665,;PARP10,downstream_gene_variant,,ENST00000534737,;PARP10,downstream_gene_variant,,ENST00000532660,;PARP10,missense_variant,p.Thr738Met,ENST00000527262,;PARP10,non_coding_transcript_exon_variant,,ENST00000526007,;PARP10,downstream_gene_variant,,ENST00000528963,;PARP10,downstream_gene_variant,,ENST00000526985,;PARP10,downstream_gene_variant,,ENST00000528580,; A ENST00000313028 Transcript missense_variant 2308/3497 2213/3078 738/1025 T/M aCg/aTg rs782458070 1 -1 PARP10 HGNC HGNC:25895 protein_coding YES CCDS34960.1 ENSP00000325618 Q53GL7 UPI0000251FAB NM_032789.3 deleterious(0.01) 8/11 hmmpanther:PTHR14453:SF53,hmmpanther:PTHR14453 MODERATE 1 SNV 1 1 PASS rs782458070 . 0 206 0 3 0 0 0 0 -20 0.9999927 1 1 1 0 A 3 1 72 143983376 143983376 G A 1 0 0 0 0 1 0 0 0 11535 1145 40 1 1 PARP10 8 143983376 Missense_Mutation SNP G C3N-01072_T 143983376 1155260 36 21947 RANBP6 0 . GRCh38 9 6013011 6013011 + Frame_Shift_Del DEL A A - novel C3N-01072_T C3N-01072_N A A c.2597delT p.Leu866TyrfsTer10 p.L866Yfs*10 ENST00000259569 1/1 160 117 43 179 179 0 sindel-varindel-pindel RANBP6,frameshift_variant,p.Leu866TyrfsTer10,ENST00000259569,NM_012416.3;RANBP6,downstream_gene_variant,,ENST00000485372,NM_001243203.1;RANBP6,downstream_gene_variant,,ENST00000623170,; - ENST00000259569 Transcript frameshift_variant 2608/4576 2597/3318 866/1105 L/X tTa/ta 1 -1 RANBP6 HGNC HGNC:9851 protein_coding YES CCDS6467.1 ENSP00000259569 O60518 UPI000013D061 NM_012416.3 1/1 Gene3D:1.25.10.10,hmmpanther:PTHR10527,hmmpanther:PTHR10527:SF16,Superfamily_domains:SSF48371 HIGH 1 deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 72 6013011 6013011 A - 1 0 1 0 1 0 0 0 0 13190 372 13 0 0 RANBP6 9 6013011 Frame_Shift_Del DEL A C3N-01072_T 6013011 132381706 37 21948 GADD45G 0 . GRCh38 9 89605128 89605128 + Missense_Mutation SNP C C G novel C3N-01072_T C3N-01072_N C C c.7C>G p.Leu3Val p.L3V ENST00000252506 1/4 265 201 64 307 307 0 strelka-varscan-mutect GADD45G,missense_variant,p.Leu3Val,ENST00000252506,NM_006705.3;GADD45G,5_prime_UTR_variant,,ENST00000375769,;GADD45G,non_coding_transcript_exon_variant,,ENST00000494726,; G ENST00000252506 Transcript missense_variant 116/1065 7/480 3/159 L/V Ctg/Gtg 1 1 GADD45G HGNC HGNC:4097 protein_coding YES CCDS6686.1 ENSP00000252506 O95257 UPI000012AEF1 NM_006705.3 deleterious(0.03) 1/4 hmmpanther:PTHR10411,hmmpanther:PTHR10411:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 89605128 89605128 C G 1 0 0 0 0 1 0 0 0 6054 912 32 4 4 GADD45G 9 89605128 Missense_Mutation SNP C C3N-01072_T 83592117 89605128 48789589 38 21949 SLIT1 0 . GRCh38 10 97043505 97043505 + Missense_Mutation SNP C C T rs756326446 C3N-01072_T C3N-01072_N C C c.1862G>A p.Arg621Gln p.R621Q ENST00000266058 19/37 176 146 30 217 217 0 strelka-varscan-mutect SLIT1,missense_variant,p.Arg621Gln,ENST00000266058,NM_003061.2;SLIT1,missense_variant,p.Arg621Gln,ENST00000371070,;SLIT1,missense_variant,p.Arg614Gln,ENST00000314867,; T ENST00000266058 Transcript missense_variant 2108/7925 1862/4605 621/1534 R/Q cGg/cAg rs756326446,COSM386304 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 deleterious(0.01) 19/37 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs756326446 . 0 207 0 3 0 0 0 0 -20 0.9999951 1 1 1 0 T 3 4 72 97043505 97043505 C T 1 0 0 0 0 1 0 0 0 15030 652 23 1 1 SLIT1 10 97043505 Missense_Mutation SNP C C3N-01072_T 97043505 36753917 39 21950 C10orf62 0 . GRCh38 10 97589940 97589952 + Frame_Shift_Del DEL GAGTGTCCATCAG GAGTGTCCATCAG - novel C3N-01072_T C3N-01072_N GAGTGTCCATCAG GAGTGTCCATCAG c.43_55delGAGTGTCCATCAG p.Glu15ThrfsTer57 p.E15Tfs*57 ENST00000370640 1/1 150 116 34 192 192 0 sindel-varindel-pindel C10orf62,frameshift_variant,p.Glu15ThrfsTer57,ENST00000370640,NM_001009997.2;HOGA1,intron_variant,,ENST00000370646,NM_138413.3;HOGA1,intron_variant,,ENST00000370647,NM_001134670.1;RP11-548K23.11,intron_variant,,ENST00000370649,;HOGA1,intron_variant,,ENST00000465608,; - ENST00000370640 Transcript frameshift_variant 214-226/1208 43-55/672 15-19/223 ECPSD/X GAGTGTCCATCAGac/ac 1 1 C10orf62 HGNC HGNC:23294 protein_coding YES CCDS31261.1 ENSP00000359674 Q5T681 UPI000046FEE3 NM_001009997.2 1/1 hmmpanther:PTHR23008:SF0,hmmpanther:PTHR23008 HIGH deletion 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 72 97589940 97589940 GAGTGTCCATCAG - 1 0 1 0 1 0 0 0 0 1767 1291 45 0 0 C10orf62 10 97589940 Frame_Shift_Del DEL GAGTGTCCATCAG C3N-01072_T 546435 97589940 36207482 40 21951 UBQLN3 0 . GRCh38 11 5508982 5508982 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.577G>A p.Asp193Asn p.D193N ENST00000311659 2/2 182 150 32 181 181 0 strelka-varscan-mutect UBQLN3,missense_variant,p.Asp193Asn,ENST00000311659,NM_017481.2;UBQLN3,missense_variant,p.Asp193Asn,ENST00000445998,;HBG2,intron_variant,,ENST00000380259,;HBE1,upstream_gene_variant,,ENST00000380237,;HBG2,upstream_gene_variant,,ENST00000380252,;HBE1,upstream_gene_variant,,ENST00000396895,;AC104389.28,upstream_gene_variant,,ENST00000415970,;AC104389.28,upstream_gene_variant,,ENST00000418729,;AC104389.28,upstream_gene_variant,,ENST00000420465,;AC104389.28,upstream_gene_variant,,ENST00000420726,; T ENST00000311659 Transcript missense_variant 725/2407 577/1968 193/655 D/N Gac/Aac 1 -1 UBQLN3 HGNC HGNC:12510 protein_coding YES CCDS7758.1 ENSP00000347997 Q9H347 A0A140VJZ3 UPI000006E3A0 NM_017481.2 tolerated(0.5) 2/2 hmmpanther:PTHR10677:SF4,hmmpanther:PTHR10677 MODERATE 1 SNV 1 1 PASS rs756933169 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 5508982 5508982 C T 1 0 0 0 0 1 0 0 0 17422 826 29 3 3 UBQLN3 11 5508982 Missense_Mutation SNP C C3N-01072_T 5508982 129577640 41 21952 FERMT3 0 . GRCh38 11 64210838 64210838 + Missense_Mutation SNP C C G novel C3N-01072_T C3N-01072_N C C c.388C>G p.Leu130Val p.L130V ENST00000279227 3/15 305 243 62 325 325 0 strelka-varscan-mutect FERMT3,missense_variant,p.Leu130Val,ENST00000279227,NM_178443.2;FERMT3,missense_variant,p.Leu130Val,ENST00000345728,NM_031471.5;FERMT3,missense_variant,p.Leu130Val,ENST00000544997,;FERMT3,5_prime_UTR_variant,,ENST00000541252,;FERMT3,upstream_gene_variant,,ENST00000541326,;FERMT3,upstream_gene_variant,,ENST00000546255,; G ENST00000279227 Transcript missense_variant 483/2489 388/2004 130/667 L/V Ctc/Gtc 1 1 FERMT3 HGNC HGNC:23151 protein_coding YES CCDS8060.1 ENSP00000279227 Q86UX7 UPI000019270B NM_178443.2 tolerated(0.28) 3/15 hmmpanther:PTHR16160,hmmpanther:PTHR16160:SF1,SMART_domains:SM00295 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 64210838 64210838 C G 1 0 0 0 0 1 0 0 0 5682 681 24 4 4 FERMT3 11 64210838 Missense_Mutation SNP C C3N-01072_T 58701856 64210838 70875784 42 21953 KCNE3 0 . GRCh38 11 74457556 74457556 + Missense_Mutation SNP G G A novel C3N-01072_T C3N-01072_N G G c.8C>T p.Thr3Ile p.T3I ENST00000310128 3/3 220 176 44 257 257 0 strelka-varscan-mutect KCNE3,missense_variant,p.Thr3Ile,ENST00000310128,NM_005472.4;KCNE3,missense_variant,p.Thr3Ile,ENST00000525550,;KCNE3,missense_variant,p.Thr3Ile,ENST00000531854,;KCNE3,missense_variant,p.Thr3Ile,ENST00000532569,;KCNE3,missense_variant,p.Thr3Ile,ENST00000529425,;KCNE3,missense_variant,p.Thr3Ile,ENST00000526855,;RP11-702H23.4,intron_variant,,ENST00000533008,;RP11-702H23.6,downstream_gene_variant,,ENST00000530510,; A ENST00000310128 Transcript missense_variant 428/3143 8/312 3/103 T/I aCt/aTt 1 -1 KCNE3 HGNC HGNC:6243 protein_coding YES CCDS8232.1 ENSP00000310557 Q9Y6H6 Q6IAE6 UPI000012F15C NM_005472.4 tolerated_low_confidence(0.15) 3/3 hmmpanther:PTHR15282:SF6,hmmpanther:PTHR15282,Prints_domain:PR01606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 74457556 74457556 G A 1 0 0 0 0 1 0 0 0 7940 1029 36 3 3 KCNE3 11 74457556 Missense_Mutation SNP G C3N-01072_T 10246718 74457556 60629066 43 21954 PANX1 0 . GRCh38 11 94179720 94179725 + In_Frame_Del DEL ATCATT ATCATT - novel C3N-01072_T C3N-01072_N ATCATT ATCATT c.666_671delCATTAT p.Ile223_Ile224del p.I223_I224del ENST00000227638 4/5 176 137 39 190 190 0 sindel-varindel-pindel PANX1,inframe_deletion,p.Ile223_Ile224del,ENST00000227638,NM_015368.3;PANX1,inframe_deletion,p.Ile223_Ile224del,ENST00000436171,; - ENST00000227638 Transcript inframe_deletion 1049-1054/2769 664-669/1281 222-223/426 II/- ATCATT/- 1 1 PANX1 HGNC HGNC:8599 protein_coding YES CCDS8296.1 ENSP00000227638 Q96RD7 A0A024R397 UPI000004C63F NM_015368.3 4/5 Pfam_domain:PF00876,PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF5,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 72 94179720 94179720 ATCATT - 1 0 1 0 1 0 0 0 0 11501 217 8 0 0 PANX1 11 94179720 In_Frame_Del DEL ATCATT C3N-01072_T 19722164 94179720 40906902 44 21955 CWF19L2 0 . GRCh38 11 107441620 107441620 + Missense_Mutation SNP C C G novel C3N-01072_T C3N-01072_N C C c.453G>C p.Arg151Ser p.R151S ENST00000282251 5/18 95 79 16 78 78 0 strelka-varscan-mutect CWF19L2,missense_variant,p.Arg151Ser,ENST00000282251,NM_152434.2;CWF19L2,missense_variant,p.Arg32Ser,ENST00000431778,;CWF19L2,missense_variant,p.Arg32Ser,ENST00000532251,; G ENST00000282251 Transcript missense_variant,splice_region_variant 481/3278 453/2685 151/894 R/S agG/agC 1 -1 CWF19L2 HGNC HGNC:26508 protein_coding YES CCDS8336.2 ENSP00000282251 Q2TBE0 UPI00005A81B4 NM_152434.2 deleterious(0) 5/18 hmmpanther:PTHR12072,hmmpanther:PTHR12072:SF5 MODERATE 1 SNV 1 1 PASS rs777663682 . 0 192 18 0 0 0 0 0 -20 0.9987259 1 1 1 0 G 3 3 72 107441620 107441620 C G 1 0 0 0 0 1 0 0 0 3882 637 22 4 4 CWF19L2 11 107441620 Missense_Mutation SNP C C3N-01072_T 13261900 107441620 27645002 45 21956 PLCZ1 0 . GRCh38 12 18712900 18712900 + Frame_Shift_Del DEL A A - novel C3N-01072_T C3N-01072_N A A c.656delT p.Leu219ProfsTer20 p.L219Pfs*20 ENST00000266505 6/15 329 261 68 310 310 0 sindel-varindel-pindel PLCZ1,frameshift_variant,p.Leu219ProfsTer20,ENST00000266505,NM_033123.3;PLCZ1,frameshift_variant,p.Leu4ProfsTer22,ENST00000540421,;PLCZ1,5_prime_UTR_variant,,ENST00000538330,;PLCZ1,intron_variant,,ENST00000539875,;PLCZ1,intron_variant,,ENST00000543242,;PLCZ1,intron_variant,,ENST00000539072,;RP11-361I14.2,upstream_gene_variant,,ENST00000536931,;PLCZ1,non_coding_transcript_exon_variant,,ENST00000542762,;PLCZ1,non_coding_transcript_exon_variant,,ENST00000545129,;PLCZ1,frameshift_variant,p.Leu91ProfsTer20,ENST00000540270,;PLCZ1,3_prime_UTR_variant,,ENST00000318197,;PLCZ1,3_prime_UTR_variant,,ENST00000539207,;PLCZ1,downstream_gene_variant,,ENST00000535429,; - ENST00000266505 Transcript frameshift_variant 920/2148 656/1827 219/608 L/X cTc/cc 1 -1 PLCZ1 HGNC HGNC:19218 protein_coding YES CCDS8680.1 ENSP00000266505 Q86YW0 A0A140VJR9 UPI000000D7E3 NM_033123.3 6/15 PROSITE_profiles:PS50007,hmmpanther:PTHR10336:SF29,hmmpanther:PTHR10336,Gene3D:3.20.20.190,Pfam_domain:PF00388,SMART_domains:SM00148,Superfamily_domains:SSF51695 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 72 18712900 18712900 A - 1 0 1 0 1 0 0 0 0 12138 304 11 0 0 PLCZ1 12 18712900 Frame_Shift_Del DEL A C3N-01072_T 18712900 114562409 46 21957 LRRK2 0 . GRCh38 12 40257253 40257253 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.1294T>C p.Phe432Leu p.F432L ENST00000298910 12/51 191 160 31 198 198 0 strelka-mutect LRRK2,missense_variant,p.Phe432Leu,ENST00000298910,NM_198578.3;LRRK2,missense_variant,p.Phe432Leu,ENST00000343742,;LRRK2,intron_variant,,ENST00000416796,; C ENST00000298910 Transcript missense_variant 1352/9158 1294/7584 432/2527 F/L Ttc/Ctc 1 1 LRRK2 HGNC HGNC:18618 protein_coding YES CCDS31774.1 ENSP00000298910 Q5S007 UPI00006C128E NM_198578.3 tolerated(0.59) 12/51 Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 40257253 40257253 T C 1 0 0 0 0 1 0 0 0 8939 1855 64 5 5 LRRK2 12 40257253 Missense_Mutation SNP T C3N-01072_T 21544353 40257253 93018056 47 21958 LRP1 0 . GRCh38 12 57173796 57173796 + Silent SNP A A G novel C3N-01072_T C3N-01072_N A A c.3363A>G p.= p.K1121K ENST00000243077 22/89 278 221 57 284 284 0 strelka-varscan-mutect LRP1,synonymous_variant,p.=,ENST00000243077,NM_002332.2;LRP1,downstream_gene_variant,,ENST00000553446,; G ENST00000243077 Transcript synonymous_variant 3829/14897 3363/13635 1121/4544 K aaA/aaG 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 22/89 Gene3D:1n7dA02,Pfam_domain:PF00057,Prints_domain:PR00261,PROSITE_patterns:PS01209,PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF100,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 72 57173796 57173796 A G 1 0 0 0 0 0 0 0 1 8846 69 3 5 5 LRP1 12 57173796 Silent SNP A C3N-01072_T 16916543 57173796 76101513 48 21959 TSFM 0 . GRCh38 12 57796504 57796504 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.962T>C p.Val321Ala p.V321A ENST00000323833 7/7 29 18 11 32 32 0 strelka-varscan-mutect TSFM,missense_variant,p.Val300Ala,ENST00000454289,NM_005726.5;TSFM,missense_variant,p.Val321Ala,ENST00000323833,NM_001172696.1;TSFM,3_prime_UTR_variant,,ENST00000540550,NM_001172695.1;TSFM,intron_variant,,ENST00000550559,;TSFM,intron_variant,,ENST00000548851,;TSFM,intron_variant,,ENST00000543727,NM_001172697.1;AVIL,downstream_gene_variant,,ENST00000257861,NM_006576.3;TSFM,downstream_gene_variant,,ENST00000457189,;TSFM,downstream_gene_variant,,ENST00000434359,;TSFM,downstream_gene_variant,,ENST00000497617,;AVIL,downstream_gene_variant,,ENST00000549851,;AVIL,downstream_gene_variant,,ENST00000546952,;AVIL,downstream_gene_variant,,ENST00000551248,; C ENST00000323833 Transcript missense_variant 988/1218 962/1041 321/346 V/A gTg/gCg 1 1 TSFM HGNC HGNC:12367 protein_coding YES CCDS53809.1 ENSP00000313877 P43897 UPI000002A8C3 NM_001172696.1 deleterious(0.01) 7/7 Gene3D:3.30.479.20,HAMAP:MF_00050,hmmpanther:PTHR11741,Superfamily_domains:SSF54713 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 57796504 57796504 T C 1 0 0 0 0 1 0 0 0 17121 1696 59 5 5 TSFM 12 57796504 Missense_Mutation SNP T C3N-01072_T 622708 57796504 75478805 49 21960 FRS2 0 . GRCh38 12 69574240 69574240 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.812T>G p.Leu271Arg p.L271R ENST00000550389 7/7 362 287 75 321 321 0 strelka-varscan-mutect FRS2,missense_variant,p.Leu271Arg,ENST00000550389,NM_001278357.1;FRS2,missense_variant,p.Leu271Arg,ENST00000397997,;FRS2,missense_variant,p.Leu271Arg,ENST00000549921,NM_001278354.1,NM_001278356.1,NM_001278355.1,NM_001278351.1,NM_006654.4,NM_001042555.2,NM_001278353.1;FRS2,downstream_gene_variant,,ENST00000550937,;FRS2,downstream_gene_variant,,ENST00000551325,;FRS2,downstream_gene_variant,,ENST00000547219,;FRS2,downstream_gene_variant,,ENST00000548154,;FRS2,downstream_gene_variant,,ENST00000549092,;FRS2,downstream_gene_variant,,ENST00000547414,; G ENST00000550389 Transcript missense_variant 1058/6600 812/1527 271/508 L/R cTt/cGt 1 1 FRS2 HGNC HGNC:16971 protein_coding YES CCDS41809.1 ENSP00000447241 Q8WU20 L7RTG7 UPI000003F143 NM_001278357.1 tolerated(0.41) 7/7 hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF40 MODERATE 1 SNV 1 1 PASS rs943493754 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 69574240 69574240 T G 1 0 0 0 0 1 0 0 0 5933 1609 56 5 5 FRS2 12 69574240 Missense_Mutation SNP T C3N-01072_T 11777736 69574240 63701069 50 21961 TMTC2 0 . GRCh38 12 83050948 83050948 + Missense_Mutation SNP A A G novel C3N-01072_T C3N-01072_N A A c.2197A>G p.Met733Val p.M733V ENST00000321196 10/12 185 148 37 176 176 0 strelka-varscan-mutect TMTC2,missense_variant,p.Met727Val,ENST00000549919,;TMTC2,missense_variant,p.Met733Val,ENST00000321196,NM_152588.1;TMTC2,3_prime_UTR_variant,,ENST00000546590,NM_001320321.1; G ENST00000321196 Transcript missense_variant 2904/5681 2197/2511 733/836 M/V Atg/Gtg 1 1 TMTC2 HGNC HGNC:25440 protein_coding YES CCDS9025.1 ENSP00000322300 Q8N394 UPI0000073F0F NM_152588.1 tolerated(0.11) 10/12 Low_complexity_(Seg):seg,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF390,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs1217850064 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 83050948 83050948 A G 1 0 0 0 0 1 0 0 0 16735 333 12 5 5 TMTC2 12 83050948 Missense_Mutation SNP A C3N-01072_T 13476708 83050948 50224361 51 21962 ACACB 0 . GRCh38 12 109172283 109172283 + Nonsense_Mutation SNP G G A novel C3N-01072_T C3N-01072_N G G c.1044G>A p.Trp348Ter p.W348* ENST00000338432 6/53 118 102 16 130 130 0 strelka-varscan-mutect ACACB,stop_gained,p.Trp348Ter,ENST00000338432,;ACACB,stop_gained,p.Trp348Ter,ENST00000377848,NM_001093.3;ACACB,stop_gained,p.Trp146Ter,ENST00000544726,;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,upstream_gene_variant,,ENST00000543080,; A ENST00000338432 Transcript stop_gained 1163/9360 1044/7377 348/2458 W/* tgG/tgA 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB 6/53 PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF00289,Gene3D:3.40.50.20,Superfamily_domains:SSF52440 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 72 109172283 109172283 G A 1 0 0 0 0 0 1 0 0 150 1241 43 3 3 ACACB 12 109172283 Nonsense_Mutation SNP G C3N-01072_T 26121335 109172283 24103026 52 21963 C12orf49 0 . GRCh38 12 116720319 116720319 + Missense_Mutation SNP A A T novel C3N-01072_T C3N-01072_N A A c.397T>A p.Ser133Thr p.S133T ENST00000261318 3/5 143 123 20 96 96 0 strelka-varscan-mutect C12orf49,missense_variant,p.Ser133Thr,ENST00000261318,NM_024738.2;C12orf49,intron_variant,,ENST00000547606,;C12orf49,upstream_gene_variant,,ENST00000548356,;C12orf49,3_prime_UTR_variant,,ENST00000547630,; T ENST00000261318 Transcript missense_variant 558/8404 397/618 133/205 S/T Tcc/Acc 1 -1 C12orf49 HGNC HGNC:26128 protein_coding YES CCDS9179.1 ENSP00000261318 Q9H741 A0A024RBQ8 UPI000004A078 NM_024738.2 deleterious(0) 3/5 Pfam_domain:PF10218,hmmpanther:PTHR13481 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 116720319 116720319 A T 1 0 0 0 0 1 0 0 0 1813 304 11 4 4 C12orf49 12 116720319 Missense_Mutation SNP A C3N-01072_T 7548036 116720319 16554990 53 21964 DCLK1 0 . GRCh38 13 35774657 35774657 + Silent SNP G G A C3N-01072_T C3N-01072_N G G c.2175C>T p.= p.D725D ENST00000255448 18/18 205 173 32 177 177 0 strelka-varscan-mutect DCLK1,missense_variant,p.Arg701Cys,ENST00000360631,;DCLK1,missense_variant,p.Arg394Cys,ENST00000379893,NM_001195416.1;DCLK1,synonymous_variant,p.=,ENST00000615680,NM_001195415.1;DCLK1,synonymous_variant,p.=,ENST00000255448,NM_004734.4; A ENST00000255448 Transcript synonymous_variant 2387/5703 2175/2190 725/729 D gaC/gaT COSM1249804,COSM1249805,COSM1249806 1 -1 DCLK1 HGNC HGNC:2700 protein_coding YES CCDS9354.1 ENSP00000255448 O15075 UPI000002A7C2 NM_004734.4 18/18 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 72 35774657 35774657 G A 1 0 0 0 0 0 0 0 1 4093 1145 40 1 1 DCLK1 13 35774657 Silent SNP G C3N-01072_T 35774657 78589671 54 21965 CTSG 0 . GRCh38 14 24573781 24573781 + Missense_Mutation SNP G G T rs763445044 C3N-01072_T C3N-01072_N G G c.624C>A p.Asn208Lys p.N208K ENST00000216336 5/5 137 114 23 142 142 0 strelka-varscan-mutect CTSG,missense_variant,p.Asn208Lys,ENST00000216336,NM_001911.2;CTSG,non_coding_transcript_exon_variant,,ENST00000552252,; T ENST00000216336 Transcript missense_variant 661/886 624/768 208/255 N/K aaC/aaA rs763445044 1 -1 CTSG HGNC HGNC:2532 protein_coding YES CCDS9631.1 ENSP00000216336 P08311 UPI00001270AC NM_001911.2 tolerated(0.58) 5/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF13,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs763445044 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 24573781 24573781 G T 1 0 0 0 0 1 0 0 0 3844 1368 48 2 2 CTSG 14 24573781 Missense_Mutation SNP G C3N-01072_T 24573781 82469937 55 21966 GALNT16 0 . GRCh38 14 69333104 69333104 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.798T>G p.His266Gln p.H266Q ENST00000337827 8/16 216 163 53 276 276 0 strelka-varscan-mutect GALNT16,missense_variant,p.His266Gln,ENST00000337827,NM_001168368.1,NM_020692.2;GALNT16,missense_variant,p.His266Gln,ENST00000448469,;GALNT16,missense_variant,p.His266Gln,ENST00000553669,;GALNT16,non_coding_transcript_exon_variant,,ENST00000556677,;GALNT16,missense_variant,p.His266Gln,ENST00000553471,; G ENST00000337827 Transcript missense_variant 1125/5708 798/1677 266/558 H/Q caT/caG 1 1 GALNT16 HGNC HGNC:23233 protein_coding YES CCDS32107.1 ENSP00000336729 Q8N428 Q68VJ8 UPI000004D296 NM_001168368.1,NM_020692.2 tolerated(0.14) 8/16 hmmpanther:PTHR11675:SF3,hmmpanther:PTHR11675,Pfam_domain:PF00535,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 69333104 69333104 T G 1 0 0 0 0 1 0 0 0 6082 1490 52 5 5 GALNT16 14 69333104 Missense_Mutation SNP T C3N-01072_T 44759323 69333104 37710614 56 21967 AQR 0 . GRCh38 15 34915096 34915096 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.1426G>A p.Glu476Lys p.E476K ENST00000156471 16/35 150 128 22 166 166 0 strelka-varscan-mutect AQR,missense_variant,p.Glu476Lys,ENST00000156471,NM_014691.2;AQR,missense_variant,p.Glu476Lys,ENST00000543879,; T ENST00000156471 Transcript missense_variant 1652/9694 1426/4458 476/1485 E/K Gaa/Aaa 1 -1 AQR HGNC HGNC:29513 protein_coding YES CCDS42013.1 ENSP00000156471 O60306 A0A024R9L1 UPI00001C1F85 NM_014691.2 deleterious(0) 16/35 hmmpanther:PTHR10887:SF5,hmmpanther:PTHR10887,Pfam_domain:PF16399,PIRSF_domain:PIRSF038901 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 34915096 34915096 C T 1 0 0 0 0 1 0 0 0 957 922 32 3 3 AQR 15 34915096 Missense_Mutation SNP C C3N-01072_T 34915096 67076093 57 21968 MGA 0 . GRCh38 15 41754568 41754568 + Splice_Site SNP G G T C3N-01072_T C3N-01072_N G G c.7139+1G>T p.X2380_splice ENST00000219905 71 54 17 66 66 0 strelka-varscan-mutect MGA,splice_donor_variant,,ENST00000566586,;MGA,splice_donor_variant,,ENST00000219905,NM_001164273.1;MGA,splice_donor_variant,,ENST00000570161,;MGA,splice_donor_variant,,ENST00000545763,NM_001080541.2;MGA,splice_donor_variant,,ENST00000564190,;MGA,downstream_gene_variant,,ENST00000566288,; T ENST00000219905 Transcript splice_donor_variant -/12042 7139/9198 2380/3065 COSM961530 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 18/23 1 HIGH 1 SNV 5 1 1 PASS . . 0 196 14 0 0 0 0 0 -20 0.9998886 1 1 1 0 T 5 4 72 41754568 41754568 G T 1 0 0 0 0 0 0 1 0 9498 1159 40 1 1 MGA 15 41754568 Splice_Site SNP G C3N-01072_T 6839472 41754568 60236621 58 21969 PLA2G4F 0 . GRCh38 15 42142680 42142680 + Missense_Mutation SNP C C A rs375597223 C3N-01072_T C3N-01072_N C C c.2177G>T p.Arg726Leu p.R726L ENST00000397272 19/20 413 350 63 405 405 0 strelka-varscan-mutect PLA2G4F,missense_variant,p.Arg726Leu,ENST00000397272,NM_213600.3;PLA2G4F,synonymous_variant,p.=,ENST00000562320,;PLA2G4F,3_prime_UTR_variant,,ENST00000569985,;PLA2G4F,3_prime_UTR_variant,,ENST00000290497,;PLA2G4F,downstream_gene_variant,,ENST00000561893,; A ENST00000397272 Transcript missense_variant 2264/5587 2177/2550 726/849 R/L cGa/cTa rs375597223 1 -1 PLA2G4F HGNC HGNC:27396 protein_coding YES CCDS32204.1 ENSP00000380442 Q68DD2 UPI0000160965 NM_213600.3 deleterious(0.03) 19/20 Gene3D:3.40.1090.10,PROSITE_profiles:PS51210,hmmpanther:PTHR10728,hmmpanther:PTHR10728:SF22,SMART_domains:SM00022,Superfamily_domains:SSF52151 MODERATE 1 SNV 1 1 PASS rs375597223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 42142680 42142680 C A 1 0 0 0 0 1 0 0 0 12102 884 31 1 1 PLA2G4F 15 42142680 Missense_Mutation SNP C C3N-01072_T 388112 42142680 59848509 59 21970 ZNF668 0 . GRCh38 16 31062041 31062041 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.956G>A p.Arg319His p.R319H ENST00000539836 4/4 305 248 57 219 219 0 strelka-varscan-mutect ZNF668,missense_variant,p.Arg296His,ENST00000538906,NM_001172668.1;ZNF668,missense_variant,p.Arg296His,ENST00000300849,NM_024706.4;ZNF668,missense_variant,p.Arg296His,ENST00000394983,;ZNF668,missense_variant,p.Arg319His,ENST00000539836,NM_001172669.1;ZNF668,missense_variant,p.Arg296His,ENST00000535577,NM_001172670.1;ZNF668,missense_variant,p.Arg319His,ENST00000426488,;ZNF668,downstream_gene_variant,,ENST00000442862,;ZNF668,downstream_gene_variant,,ENST00000414399,;ZNF668,downstream_gene_variant,,ENST00000417935,;RP11-196G11.6,non_coding_transcript_exon_variant,,ENST00000622229,;RP11-196G11.6,non_coding_transcript_exon_variant,,ENST00000417110,;AC135050.5,upstream_gene_variant,,ENST00000568708,;ZNF668,downstream_gene_variant,,ENST00000564456,; T ENST00000539836 Transcript missense_variant 1279/2469 956/1929 319/642 R/H cGt/cAt 1 -1 ZNF668 HGNC HGNC:25821 protein_coding YES CCDS54003.1 ENSP00000442573 Q96K58 UPI0001C53D29 NM_001172669.1 deleterious(0.03) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF353,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13894,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 31062041 31062041 C T 1 0 0 0 0 1 0 0 0 18649 536 19 1 1 ZNF668 16 31062041 Missense_Mutation SNP C C3N-01072_T 31062041 59276304 60 21971 ATPAF2 0 . GRCh38 17 18028279 18028279 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.277G>A p.Glu93Lys p.E93K ENST00000474627 3/8 277 201 76 367 367 0 strelka-varscan-mutect ATPAF2,missense_variant,p.Glu93Lys,ENST00000474627,NM_145691.3;ATPAF2,missense_variant,p.Glu93Lys,ENST00000444058,;ATPAF2,intron_variant,,ENST00000585101,;ATPAF2,upstream_gene_variant,,ENST00000581698,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000577586,;RP11-384M20.1,upstream_gene_variant,,ENST00000624345,;ATPAF2,upstream_gene_variant,,ENST00000469327,;ATPAF2,non_coding_transcript_exon_variant,,ENST00000497871,;ATPAF2,intron_variant,,ENST00000462733,;ATPAF2,intron_variant,,ENST00000584205,;ATPAF2,upstream_gene_variant,,ENST00000496852,;ATPAF2,upstream_gene_variant,,ENST00000488753,; T ENST00000474627 Transcript missense_variant 432/1564 277/870 93/289 E/K Gag/Aag 1 -1 ATPAF2 HGNC HGNC:18802 protein_coding YES CCDS32585.1 ENSP00000417190 Q8N5M1 UPI00000720DC NM_145691.3 deleterious(0) 3/8 hmmpanther:PTHR21013,Gene3D:2r6iA01,Pfam_domain:PF07542,Superfamily_domains:SSF160909 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 18028279 18028279 C T 1 0 0 0 0 1 0 0 0 1354 835 29 3 3 ATPAF2 17 18028279 Missense_Mutation SNP C C3N-01072_T 18028279 65229162 61 21972 SOST 0 . GRCh38 17 43755570 43755570 + Silent SNP G G A novel C3N-01072_T C3N-01072_N G G c.414C>T p.= p.R138R ENST00000301691 2/2 200 151 49 238 238 0 strelka-varscan-mutect SOST,synonymous_variant,p.=,ENST00000301691,NM_025237.2; A ENST00000301691 Transcript synonymous_variant 461/2300 414/642 138/213 R cgC/cgT 1 -1 SOST HGNC HGNC:13771 protein_coding YES CCDS11468.1 ENSP00000301691 Q9BQB4 UPI0000035BBE NM_025237.2 2/2 Pfam_domain:PF05463,hmmpanther:PTHR14903,hmmpanther:PTHR14903:SF4,SMART_domains:SM00041 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 72 43755570 43755570 G A 1 0 0 0 0 0 0 0 1 15260 958 34 3 3 SOST 17 43755570 Silent SNP G C3N-01072_T 25727291 43755570 39501871 62 21973 OR4D2 0 . GRCh38 17 58170444 58170444 + Silent SNP T T C novel C3N-01072_T C3N-01072_N T T c.789T>C p.= p.T263T ENST00000545221 1/1 645 521 124 667 666 1 strelka-varscan-mutect OR4D2,synonymous_variant,p.=,ENST00000545221,NM_001004707.3; C ENST00000545221 Transcript synonymous_variant 789/924 789/924 263/307 T acT/acC 1 1 OR4D2 HGNC HGNC:8294 protein_coding YES CCDS32688.1 ENSP00000441354 P58180 A0A126GWK0 UPI0000000DB3 NM_001004707.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF348,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 72 58170444 58170444 T C 1 0 0 0 0 0 0 0 1 11133 1538 54 5 5 OR4D2 17 58170444 Silent SNP T C3N-01072_T 14414874 58170444 25086997 63 21974 RGS9 0 . GRCh38 17 65160878 65160878 + Missense_Mutation SNP A A C C3N-01072_T C3N-01072_N A A c.392A>C p.Lys131Thr p.K131T ENST00000262406 6/19 407 313 94 434 434 0 strelka-varscan-mutect RGS9,missense_variant,p.Lys131Thr,ENST00000449996,NM_001081955.2;RGS9,missense_variant,p.Lys131Thr,ENST00000262406,NM_003835.3;RGS9,missense_variant,p.Lys131Thr,ENST00000635833,;RGS9,missense_variant,p.Lys131Thr,ENST00000443584,NM_001165933.1;RGS9,non_coding_transcript_exon_variant,,ENST00000577186,;RGS9,missense_variant,p.Lys131Thr,ENST00000584234,;RGS9,non_coding_transcript_exon_variant,,ENST00000581175,;RGS9,downstream_gene_variant,,ENST00000583473,; C ENST00000262406 Transcript missense_variant 459/2375 392/2025 131/674 K/T aAa/aCa COSM1680011 1 1 RGS9 HGNC HGNC:10004 protein_coding YES CCDS42373.1 ENSP00000262406 O75916 UPI000013382A NM_003835.3 deleterious(0) 6/19 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF170 1 MODERATE 1 SNV 1 1 1 PASS rs1399438731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 65160878 65160878 A C 1 0 0 0 0 1 0 0 0 13484 14 1 5 5 RGS9 17 65160878 Missense_Mutation SNP A C3N-01072_T 6990434 65160878 18096563 64 21975 PTPRM 0 . GRCh38 18 8244108 8244108 + Missense_Mutation SNP T T A novel C3N-01072_T C3N-01072_N T T c.2351T>A p.Met784Lys p.M784K ENST00000580170 15/33 193 129 64 184 184 0 strelka-varscan-mutect PTPRM,missense_variant,p.Met784Lys,ENST00000332175,NM_002845.3;PTPRM,missense_variant,p.Met784Lys,ENST00000580170,NM_001105244.1;PTPRM,missense_variant,p.Met722Lys,ENST00000400053,;PTPRM,missense_variant,p.Met137Lys,ENST00000577468,;PTPRM,5_prime_UTR_variant,,ENST00000400060,;PTPRM,non_coding_transcript_exon_variant,,ENST00000578093,;PTPRM,upstream_gene_variant,,ENST00000580838,;PTPRM,non_coding_transcript_exon_variant,,ENST00000577827,; A ENST00000580170 Transcript missense_variant 3388/5941 2351/4398 784/1465 M/K aTg/aAg 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 tolerated(0.69) 15/33 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 8244108 8244108 T A 1 0 0 0 0 1 0 0 0 12960 1464 51 4 4 PTPRM 18 8244108 Missense_Mutation SNP T C3N-01072_T 8244108 72129177 65 21976 SERPINB2 0 . GRCh38 18 63902910 63902910 + Nonsense_Mutation SNP G G T C3N-01072_T C3N-01072_N G G c.853G>T p.Glu285Ter p.E285* ENST00000457692 9/9 103 81 22 86 86 0 varscan-mutect SERPINB2,stop_gained,p.Glu285Ter,ENST00000457692,NM_001143818.1;SERPINB2,stop_gained,p.Glu285Ter,ENST00000299502,NM_002575.2;SERPINB10,stop_gained,p.Glu162Ter,ENST00000397996,;SERPINB10,stop_gained,p.Glu162Ter,ENST00000418725,;SERPINB2,downstream_gene_variant,,ENST00000482254,; T ENST00000457692 Transcript stop_gained 1186/2155 853/1248 285/415 E/* Gaa/Taa COSM24389 1 1 SERPINB2 HGNC HGNC:8584 protein_coding YES CCDS11989.1 ENSP00000401645 P05120 UPI000002BB06 NM_001143818.1 9/9 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF61,SMART_domains:SM00093,Superfamily_domains:SSF56574 1 HIGH 1 SNV 5 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 72 63902910 63902910 G T 1 0 0 0 0 0 1 0 0 14377 1291 45 2 2 SERPINB2 18 63902910 Nonsense_Mutation SNP G C3N-01072_T 55658802 63902910 16470375 66 21977 MUC16 0 . GRCh38 19 8945536 8945536 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.31234A>G p.Ser10412Gly p.S10412G ENST00000397910 3/84 102 75 27 103 103 0 strelka-varscan-mutect MUC16,missense_variant,p.Ser10412Gly,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 31438/43816 31234/43524 10412/14507 S/G Agt/Ggt 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 72 8945536 8945536 T C 1 0 0 0 0 1 0 0 0 9972 1609 56 5 5 MUC16 19 8945536 Missense_Mutation SNP T C3N-01072_T 8945536 49672080 67 21978 CYP4F2 0 . GRCh38 19 15897492 15897492 + Silent SNP G G A rs752779520 C3N-01072_T C3N-01072_N G G c.120C>T p.= p.A40A ENST00000221700 2/13 198 141 57 240 240 0 strelka-varscan-mutect CYP4F2,synonymous_variant,p.=,ENST00000221700,NM_001082.4;CYP4F2,synonymous_variant,p.=,ENST00000011989,;CYP4F2,synonymous_variant,p.=,ENST00000586927,;CYP4F2,synonymous_variant,p.=,ENST00000587671,;CYP4F2,non_coding_transcript_exon_variant,,ENST00000608168,;CYP4F2,intron_variant,,ENST00000392846,;AC005336.5,downstream_gene_variant,,ENST00000593183,; A ENST00000221700 Transcript synonymous_variant 216/2407 120/1563 40/520 A gcC/gcT rs752779520 1 -1 CYP4F2 HGNC HGNC:2645 protein_coding YES CCDS12336.1 ENSP00000221700 P78329 UPI0000052BE6 NM_001082.4 2/13 hmmpanther:PTHR24291:SF45,hmmpanther:PTHR24291 LOW 1 SNV 1 1 PASS rs752779520 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 72 15897492 15897492 G A 1 0 0 0 0 0 0 0 1 3991 987 35 3 3 CYP4F2 19 15897492 Silent SNP G C3N-01072_T 6951956 15897492 42720124 68 21979 USHBP1 0 . GRCh38 19 17259674 17259674 + Missense_Mutation SNP T T C novel C3N-01072_T C3N-01072_N T T c.827A>G p.Gln276Arg p.Q276R ENST00000252597 6/13 129 83 46 117 117 0 strelka-varscan-mutect USHBP1,missense_variant,p.Gln276Arg,ENST00000252597,NM_031941.3;USHBP1,missense_variant,p.Gln212Arg,ENST00000431146,NM_001297703.1;USHBP1,downstream_gene_variant,,ENST00000594190,;USHBP1,downstream_gene_variant,,ENST00000598309,;AC010646.3,upstream_gene_variant,,ENST00000594059,;USHBP1,downstream_gene_variant,,ENST00000598570,;USHBP1,downstream_gene_variant,,ENST00000595993,;USHBP1,missense_variant,p.Gln276Arg,ENST00000324554,;USHBP1,3_prime_UTR_variant,,ENST00000597928,;USHBP1,downstream_gene_variant,,ENST00000600286,;USHBP1,downstream_gene_variant,,ENST00000596436,; C ENST00000252597 Transcript missense_variant 1001/3335 827/2112 276/703 Q/R cAg/cGg 1 -1 USHBP1 HGNC HGNC:24058 protein_coding YES CCDS12353.1 ENSP00000252597 Q8N6Y0 A0A024R7H3 UPI000006F7A8 NM_031941.3 deleterious(0.04) 6/13 hmmpanther:PTHR23347:SF5,hmmpanther:PTHR23347 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999988 1 1 1 0 C 3 2 72 17259674 17259674 T C 1 0 0 0 0 1 0 0 0 17571 1580 55 5 5 USHBP1 19 17259674 Missense_Mutation SNP T C3N-01072_T 1362182 17259674 41357942 69 21980 GPI 0 . GRCh38 19 34366826 34366826 + Missense_Mutation SNP A A G rs370578920 C3N-01072_T C3N-01072_N A A c.374A>G p.Asn125Ser p.N125S ENST00000415930 4/18 229 150 79 268 268 0 strelka-varscan-mutect GPI,missense_variant,p.Asn125Ser,ENST00000415930,NM_001184722.1;GPI,missense_variant,p.Asn86Ser,ENST00000356487,NM_000175.3,NM_001289790.1;GPI,missense_variant,p.Asn101Ser,ENST00000588991,NM_001289789.1;GPI,missense_variant,p.Asn86Ser,ENST00000586425,;GPI,missense_variant,p.Asn125Ser,ENST00000587384,;GPI,missense_variant,p.Asn125Ser,ENST00000592277,;GPI,missense_variant,p.Asn86Ser,ENST00000589640,;GPI,missense_variant,p.Asn86Ser,ENST00000589399,;GPI,missense_variant,p.Asn86Ser,ENST00000591204,;GPI,missense_variant,p.Asn86Ser,ENST00000590375,;GPI,downstream_gene_variant,,ENST00000587521,;GPI,3_prime_UTR_variant,,ENST00000592144,;GPI,non_coding_transcript_exon_variant,,ENST00000589504,; G ENST00000415930 Transcript missense_variant 544/4000 374/1710 125/569 N/S aAt/aGt rs370578920,COSM288550 1 1 GPI HGNC HGNC:4458 protein_coding YES CCDS54246.1 ENSP00000405573 P06744 UPI00017A6DE4 NM_001184722.1 tolerated_low_confidence(1) 4/18 Gene3D:3.40.50.10490,HAMAP:MF_00473,Pfam_domain:PF00342,PROSITE_profiles:PS51463,hmmpanther:PTHR11469,hmmpanther:PTHR11469:SF4,Superfamily_domains:SSF53697 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs370578920 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 34366826 34366826 A G 1 0 0 0 0 1 0 0 0 6513 101 4 5 5 GPI 19 34366826 Missense_Mutation SNP A C3N-01072_T 17107152 34366826 24250790 70 21981 RYR1 0 . GRCh38 19 38543848 38543848 + Missense_Mutation SNP C C A rs536629932 C3N-01072_T C3N-01072_N C C c.11985C>A p.Phe3995Leu p.F3995L ENST00000359596 87/106 576 324 252 638 638 0 strelka-varscan-mutect RYR1,missense_variant,p.Phe3990Leu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Phe3995Leu,ENST00000359596,NM_000540.2;RYR1,3_prime_UTR_variant,,ENST00000594335,;RYR1,3_prime_UTR_variant,,ENST00000593322,; A ENST00000359596 Transcript missense_variant 11985/15117 11985/15117 3995/5038 F/L ttC/ttA rs536629932,COSM1645559 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.01) 87/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs536629932 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 72 38543848 38543848 C A 1 0 0 0 0 1 0 0 0 14028 883 31 1 1 RYR1 19 38543848 Missense_Mutation SNP C C3N-01072_T 4177022 38543848 20073768 71 21982 CYTH2 0 . GRCh38 19 48473328 48473328 + Silent SNP T T C novel C3N-01072_T C3N-01072_N T T c.384T>C p.= p.A128A ENST00000452733 5/12 311 207 104 327 327 0 strelka-varscan-mutect CYTH2,synonymous_variant,p.=,ENST00000452733,NM_004228.6;CYTH2,synonymous_variant,p.=,ENST00000427476,NM_017457.5;CYTH2,synonymous_variant,p.=,ENST00000325139,;CYTH2,synonymous_variant,p.=,ENST00000595765,;CYTH2,upstream_gene_variant,,ENST00000620214,;CTC-273B12.7,downstream_gene_variant,,ENST00000595676,;CTC-273B12.5,upstream_gene_variant,,ENST00000600650,;CTC-273B12.5,upstream_gene_variant,,ENST00000593476,;CTC-273B12.5,upstream_gene_variant,,ENST00000596497,;CYTH2,synonymous_variant,p.=,ENST00000391881,;CYTH2,non_coding_transcript_exon_variant,,ENST00000493260,;CYTH2,non_coding_transcript_exon_variant,,ENST00000467412,;CYTH2,non_coding_transcript_exon_variant,,ENST00000460595,;CYTH2,non_coding_transcript_exon_variant,,ENST00000474209,;CYTH2,downstream_gene_variant,,ENST00000474049,;CYTH2,downstream_gene_variant,,ENST00000462117,; C ENST00000452733 Transcript synonymous_variant 860/4780 384/1200 128/399 A gcT/gcC 1 1 CYTH2 HGNC HGNC:9502 protein_coding YES CCDS12722.1 ENSP00000408236 Q99418 UPI000000009E NM_004228.6 5/12 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,Gene3D:1.10.220.20,Pfam_domain:PF01369,SMART_domains:SM00222,Superfamily_domains:SSF48425 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 72 48473328 48473328 T C 1 0 0 0 0 0 0 0 1 4009 1596 56 5 5 CYTH2 19 48473328 Silent SNP T C3N-01072_T 9929480 48473328 10144288 72 21983 SNX5 0 . GRCh38 20 17954000 17954000 + Missense_Mutation SNP C C T novel C3N-01072_T C3N-01072_N C C c.385G>A p.Glu129Lys p.E129K ENST00000377768 5/14 165 133 32 175 175 0 strelka-varscan-mutect SNX5,missense_variant,p.Glu129Lys,ENST00000377768,NM_152227.2,NM_001282454.1;SNX5,missense_variant,p.Glu129Lys,ENST00000377759,NM_014426.3;SNX5,missense_variant,p.Glu92Lys,ENST00000431277,;SNX5,missense_variant,p.Glu94Lys,ENST00000419004,;SNX5,upstream_gene_variant,,ENST00000463050,;SNX5,non_coding_transcript_exon_variant,,ENST00000483485,;SNX5,non_coding_transcript_exon_variant,,ENST00000490175,;SNX5,non_coding_transcript_exon_variant,,ENST00000476648,;SNX5,non_coding_transcript_exon_variant,,ENST00000475716,;SNX5,non_coding_transcript_exon_variant,,ENST00000474883,;SNX5,non_coding_transcript_exon_variant,,ENST00000494401,;SNX5,downstream_gene_variant,,ENST00000469704,;OVOL2,downstream_gene_variant,,ENST00000486776,; T ENST00000377768 Transcript missense_variant 698/2288 385/1215 129/404 E/K Gaa/Aaa 1 -1 SNX5 HGNC HGNC:14969 protein_coding YES CCDS13130.1 ENSP00000366998 Q9Y5X3 UPI0000135B43 NM_152227.2,NM_001282454.1 deleterious(0) 5/14 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PIRSF_domain:PIRSF036924,PROSITE_profiles:PS50195,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 17954000 17954000 C T 1 0 0 0 0 1 0 0 0 15226 869 30 3 3 SNX5 20 17954000 Missense_Mutation SNP C C3N-01072_T 17954000 46490167 73 21984 ZNF335 0 . GRCh38 20 45960509 45960509 + Missense_Mutation SNP T T G novel C3N-01072_T C3N-01072_N T T c.1799A>C p.Lys600Thr p.K600T ENST00000322927 13/28 376 295 81 389 389 0 strelka-varscan-mutect ZNF335,missense_variant,p.Lys600Thr,ENST00000322927,NM_022095.3;ZNF335,downstream_gene_variant,,ENST00000475002,; G ENST00000322927 Transcript missense_variant 1900/4430 1799/4029 600/1342 K/T aAg/aCg 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 tolerated(0.07) 13/28 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF36,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 72 45960509 45960509 T G 1 0 0 0 0 1 0 0 0 18424 1609 56 5 5 ZNF335 20 45960509 Missense_Mutation SNP T C3N-01072_T 28006509 45960509 18483658 74 21985 KRTAP10-2 0 . GRCh38 21 44550889 44550889 + Silent SNP A A G rs76021731 C3N-01072_T C3N-01072_N A A c.570T>C p.= p.P190P ENST00000391621 1/1 134 122 12 245 241 4 varscan-mutect KRTAP10-2,synonymous_variant,p.=,ENST00000391621,NM_198693.3;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,;KRTAP10-2,intron_variant,,ENST00000498210,; G ENST00000391621 Transcript synonymous_variant 617/1149 570/768 190/255 P ccT/ccC rs76021731 1 -1 KRTAP10-2 HGNC HGNC:22967 protein_coding YES CCDS42955.1 ENSP00000375479 P60368 UPI000021C438 NM_198693.3 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF8,Low_complexity_(Seg):seg LOW SNV 1 PASS rs76021731 . 0 113 0 0 0 0 0 97 -3.77856 0 0 1 0 0 G 2 3 72 44550889 44550889 A G 1 0 0 0 0 0 0 0 1 8392 175 7 5 5 KRTAP10-2 21 44550889 Silent SNP A C3N-01072_T 44550889 2159094 75 21986 SYN3 0 . GRCh38 22 32518051 32518051 + Silent SNP C C T rs771047148 C3N-01072_T C3N-01072_N C C c.1602G>A p.= p.P534P ENST00000358763 13/14 35 30 5 24 24 0 strelka-mutect SYN3,synonymous_variant,p.=,ENST00000358763,NM_001135774.1,NM_003490.3,NM_133633.2;SYN3,synonymous_variant,p.=,ENST00000332840,;SYN3,non_coding_transcript_exon_variant,,ENST00000467095,;SYN3,downstream_gene_variant,,ENST00000459990,;SYN3,downstream_gene_variant,,ENST00000468922,;SYN3,non_coding_transcript_exon_variant,,ENST00000483062,;SYN3,non_coding_transcript_exon_variant,,ENST00000461446,; T ENST00000358763 Transcript synonymous_variant 1845/3126 1602/1743 534/580 P ccG/ccA rs771047148,COSM3694038 1 -1 SYN3 HGNC HGNC:11496 protein_coding YES CCDS13908.1 ENSP00000351614 O14994 A0A024R1I8 UPI00001365D3 NM_001135774.1,NM_003490.3,NM_133633.2 13/14 hmmpanther:PTHR10841 0,1 LOW 1 SNV 5 0,1 1 PASS rs771047148 . 6 199 5 0 0 0 0 0 -13.34488 1 1 1 1 0 T 2 4 72 32518051 32518051 C T 1 0 0 0 0 0 0 0 1 15832 755 27 1 1 SYN3 22 32518051 Silent SNP C C3N-01072_T 32518051 18300417 76 21987 KDM6A 0 . GRCh38 X 44974664 44974664 + Splice_Site SNP A A G novel C3N-01072_T C3N-01072_N A A c.335-2A>G p.X112_splice ENST00000377967 124 81 43 127 127 0 strelka-varscan-mutect KDM6A,splice_acceptor_variant,,ENST00000611820,NM_001291415.1;KDM6A,splice_acceptor_variant,,ENST00000382899,NM_001291416.1;KDM6A,splice_acceptor_variant,,ENST00000543216,;KDM6A,splice_acceptor_variant,,ENST00000536777,NM_001291417.1,NM_001291418.1;KDM6A,splice_acceptor_variant,,ENST00000377967,NM_021140.3;KDM6A,splice_acceptor_variant,,ENST00000621147,;KDM6A,splice_acceptor_variant,,ENST00000475233,; G ENST00000377967 Transcript splice_acceptor_variant -/5438 335/4206 112/1401 1 1 KDM6A HGNC HGNC:12637 protein_coding YES CCDS14265.1 ENSP00000367203 O15550 UPI000013DA92 NM_021140.3 3/28 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 72 44974664 44974664 A G 1 0 0 0 0 0 0 1 0 8055 202 7 5 5 KDM6A 23 44974664 Splice_Site SNP A C3N-01072_T 44974664 111066231 77 21988 NRK 0 . GRCh38 X 105945962 105945962 + Missense_Mutation SNP C C T rs754007962 C3N-01072_T C3N-01072_N C C c.4150C>T p.Pro1384Ser p.P1384S ENST00000243300 25/29 136 87 49 144 144 0 strelka-varscan-mutect NRK,missense_variant,p.Pro1384Ser,ENST00000243300,NM_198465.3;NRK,upstream_gene_variant,,ENST00000540278,; T ENST00000243300 Transcript missense_variant 4453/8062 4150/4749 1384/1582 P/S Cca/Tca rs754007962,COSM3556282 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0.03) 25/29 PROSITE_profiles:PS50219,Pfam_domain:PF00780,SMART_domains:SM00036 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754007962 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 72 105945962 105945962 C T 1 0 0 0 0 1 0 0 0 10713 855 30 3 3 NRK 23 105945962 Missense_Mutation SNP C C3N-01072_T 60971298 105945962 50094933 78 21989 GNB1 0 . GRCh38 1 1815847 1815847 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.112G>T p.Asp38Tyr p.D38Y ENST00000610897 4/11 212 200 12 193 193 0 strelka-varscan-mutect GNB1,missense_variant,p.Asp38Tyr,ENST00000610897,NM_001282539.1;GNB1,missense_variant,p.Asp38Tyr,ENST00000378609,NM_002074.4;GNB1,missense_variant,p.Asp38Tyr,ENST00000434686,;GNB1,missense_variant,p.Asp25Tyr,ENST00000439272,;GNB1,missense_variant,p.Asp38Tyr,ENST00000437146,;GNB1,intron_variant,,ENST00000615252,NM_001282538.1;GNB1,non_coding_transcript_exon_variant,,ENST00000471354,; A ENST00000610897 Transcript missense_variant 456/3145 112/1023 38/340 D/Y Gac/Tac 1 -1 GNB1 HGNC HGNC:4396 protein_coding YES CCDS34.1 ENSP00000481878 P62873 A0A024R056 UPI00000230B3 NM_001282539.1 deleterious(0) 4/11 PIRSF_domain:PIRSF002394,hmmpanther:PTHR19850,hmmpanther:PTHR19850:SF32,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 1815847 1815847 C A 1 0 0 0 0 1 0 0 0 6395 884 31 1 1 GNB1 1 1815847 Missense_Mutation SNP C C3N-01074_T 1815847 247140575 1 21990 AJAP1 0 . GRCh38 1 4712042 4712042 + Frame_Shift_Del DEL C C - novel C3N-01074_T C3N-01074_N C C c.175delC p.Arg59GlyfsTer94 p.R59Gfs*94 ENST00000378191 2/6 113 75 38 129 129 0 sindel-varindel AJAP1,frameshift_variant,p.Arg59GlyfsTer94,ENST00000378191,NM_018836.3;AJAP1,frameshift_variant,p.Arg59GlyfsTer94,ENST00000378190,NM_001042478.1;AJAP1,non_coding_transcript_exon_variant,,ENST00000466761,; - ENST00000378191 Transcript frameshift_variant 553/11666 172/1236 58/411 P/X Ccc/cc 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR32422 HIGH 1 deletion 1 3 1 PASS . . 0 202 3 5 0 0 0 0 -20 0.9996407 1 1 1 0 - 7 5 73 4712042 4712042 C - 1 0 1 0 1 0 0 0 0 516 739 26 0 0 AJAP1 1 4712042 Frame_Shift_Del DEL C C3N-01074_T 2896195 4712042 244244380 2 21991 CHD5 0 . GRCh38 1 6154699 6154699 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.706C>A p.Pro236Thr p.P236T ENST00000262450 5/42 68 38 30 64 64 0 strelka-varscan-mutect CHD5,missense_variant,p.Pro236Thr,ENST00000262450,NM_015557.2;CHD5,missense_variant,p.Pro236Thr,ENST00000496404,; T ENST00000262450 Transcript missense_variant 806/9646 706/5865 236/1954 P/T Cct/Act 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 deleterious_low_confidence(0.04) 5/42 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 6154699 6154699 G T 1 0 0 0 0 1 0 0 0 3087 1203 42 2 2 CHD5 1 6154699 Missense_Mutation SNP G C3N-01074_T 1442657 6154699 242801723 3 21992 PER3 0 . GRCh38 1 7785552 7785552 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.240C>T p.= p.L80L ENST00000613533 3/22 174 129 45 168 168 0 strelka-varscan-mutect PER3,synonymous_variant,p.=,ENST00000613533,NM_001289862.1;PER3,synonymous_variant,p.=,ENST00000377532,;PER3,synonymous_variant,p.=,ENST00000614998,NM_001289861.1,NM_001289863.1,NM_001289864.1;PER3,synonymous_variant,p.=,ENST00000361923,NM_016831.2;PER3,synonymous_variant,p.=,ENST00000377541,;VAMP3,downstream_gene_variant,,ENST00000054666,NM_004781.3;PER3,non_coding_transcript_exon_variant,,ENST00000473653,;PER3,upstream_gene_variant,,ENST00000602883,; T ENST00000613533 Transcript synonymous_variant 504/6318 240/3633 80/1210 L ctC/ctT 1 1 PER3 HGNC HGNC:8847 protein_coding YES CCDS72695.1 ENSP00000482093 P56645 UPI00003664CA NM_001289862.1 3/22 hmmpanther:PTHR11269,hmmpanther:PTHR11269:SF13 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 7785552 7785552 C T 1 0 0 0 0 0 0 0 1 11819 813 29 3 3 PER3 1 7785552 Silent SNP C C3N-01074_T 1630853 7785552 241170870 4 21993 SLC25A33 0 . GRCh38 1 9580123 9580123 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.652C>A p.Pro218Thr p.P218T ENST00000302692 6/7 152 143 9 239 239 0 varscan-mutect SLC25A33,missense_variant,p.Pro218Thr,ENST00000302692,NM_032315.2;RP13-15M17.1,downstream_gene_variant,,ENST00000435277,; A ENST00000302692 Transcript missense_variant 862/3854 652/966 218/321 P/T Cca/Aca 1 1 SLC25A33 HGNC HGNC:29681 protein_coding YES CCDS103.1 ENSP00000306328 Q9BSK2 UPI000004D33B NM_032315.2 tolerated(0.37) 6/7 Superfamily_domains:0048588,Gene3D:1okcA00,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF263 MODERATE 1 SNV 1 1 PASS rs947584270 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 9580123 9580123 C A 1 0 0 0 0 1 0 0 0 14762 855 30 2 2 SLC25A33 1 9580123 Missense_Mutation SNP C C3N-01074_T 1794571 9580123 239376299 5 21994 C1orf127 0 . GRCh38 1 10948604 10948604 + Missense_Mutation SNP C C A rs765001510 C3N-01074_T C3N-01074_N C C c.1531G>T p.Val511Leu p.V511L ENST00000377004 12/13 142 88 54 131 131 0 strelka-varscan-mutect C1orf127,missense_variant,p.Val511Leu,ENST00000377004,NM_001170754.1;C1orf127,missense_variant,p.Val463Leu,ENST00000520253,;C1orf127,missense_variant,p.Val346Leu,ENST00000418570,;C1orf127,upstream_gene_variant,,ENST00000468348,;C1orf127,non_coding_transcript_exon_variant,,ENST00000476357,; A ENST00000377004 Transcript missense_variant 1531/2761 1531/2472 511/823 V/L Gtg/Ttg rs765001510 1 -1 C1orf127 HGNC HGNC:26730 protein_coding YES CCDS53267.1 ENSP00000366203 G8JLG8 UPI0001C0B385 NM_001170754.1 tolerated(1) 12/13 hmmpanther:PTHR38653 MODERATE 1 SNV 5 1 PASS rs765001510 . 0 206 2 2 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 73 10948604 10948604 C A 1 0 0 0 0 1 0 0 0 1964 536 19 1 1 C1orf127 1 10948604 Missense_Mutation SNP C C3N-01074_T 1368481 10948604 238007818 6 21995 SH2D5 0 . GRCh38 1 20724222 20724222 + Silent SNP G G T rs766444839 C3N-01074_T C3N-01074_N G G c.660C>A p.= p.A220A ENST00000444387 7/10 165 88 77 140 138 2 strelka-varscan SH2D5,synonymous_variant,p.=,ENST00000375031,NM_001103160.1;SH2D5,synonymous_variant,p.=,ENST00000444387,NM_001103161.1;SH2D5,downstream_gene_variant,,ENST00000517430,;SH2D5,downstream_gene_variant,,ENST00000447746,;SH2D5,downstream_gene_variant,,ENST00000519434,;SH2D5,downstream_gene_variant,,ENST00000518294,;SH2D5,non_coding_transcript_exon_variant,,ENST00000460804,; T ENST00000444387 Transcript synonymous_variant 1058/1934 660/1272 220/423 A gcC/gcA rs766444839 1 -1 SH2D5 HGNC HGNC:28819 protein_coding YES CCDS44080.1 ENSP00000406026 Q6ZV89 UPI0000EE70C3 NM_001103161.1 7/10 LOW 1 SNV 2 1 PASS . . 0 202 3 5 0 0 0 0 -20 0.9998002 1 1 1 0 T 2 4 73 20724222 20724222 G T 1 0 0 0 0 0 0 0 1 14495 1219 43 2 2 SH2D5 1 20724222 Silent SNP G C3N-01074_T 9775618 20724222 228232200 7 21996 EPHA8 0 . GRCh38 1 22601627 22601627 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2904G>T p.Gln968His p.Q968H ENST00000166244 17/17 344 323 21 402 402 0 strelka-mutect EPHA8,missense_variant,p.Gln968His,ENST00000166244,NM_020526.3; T ENST00000166244 Transcript missense_variant,splice_region_variant 2976/4943 2904/3018 968/1005 Q/H caG/caT 1 1 EPHA8 HGNC HGNC:3391 protein_coding YES CCDS225.1 ENSP00000166244 P29322 UPI000012A07B NM_020526.3 deleterious(0.02) 17/17 PROSITE_profiles:PS50105,hmmpanther:PTHR24416:SF339,hmmpanther:PTHR24416,Pfam_domain:PF00536,Gene3D:1.10.150.50,PIRSF_domain:PIRSF000666,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 2 1 PASS rs1422425621 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 22601627 22601627 G T 1 0 0 0 0 1 0 0 0 5020 1246 43 2 2 EPHA8 1 22601627 Missense_Mutation SNP G C3N-01074_T 1877405 22601627 226354795 8 21997 DLGAP3 0 . GRCh38 1 34867109 34867109 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2660C>A p.Thr887Asn p.T887N ENST00000373347 11/12 462 246 216 444 442 2 strelka-varscan-mutect DLGAP3,missense_variant,p.Thr887Asn,ENST00000373347,NM_001080418.2;DLGAP3,missense_variant,p.Thr887Asn,ENST00000235180,; T ENST00000373347 Transcript missense_variant 2929/3856 2660/2940 887/979 T/N aCc/aAc 1 -1 DLGAP3 HGNC HGNC:30368 protein_coding YES CCDS30670.1 ENSP00000362444 O95886 UPI00003D4D81 NM_001080418.2 deleterious(0.02) 11/12 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF4,Pfam_domain:PF03359 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 34867109 34867109 G T 1 0 0 0 0 1 0 0 0 4368 1261 44 2 2 DLGAP3 1 34867109 Missense_Mutation SNP G C3N-01074_T 12265482 34867109 214089313 9 21998 GJA9 0 . GRCh38 1 38875433 38875433 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.666A>T p.= p.S222S ENST00000360786 1/1 224 106 118 345 344 1 strelka-varscan-mutect GJA9,synonymous_variant,p.=,ENST00000360786,;GJA9,synonymous_variant,p.=,ENST00000357771,NM_030772.4;RP5-864K19.6,intron_variant,,ENST00000621281,;MYCBP,upstream_gene_variant,,ENST00000397572,NM_012333.4;MYCBP,upstream_gene_variant,,ENST00000494695,;RP5-864K19.4,intron_variant,,ENST00000433671,;RP5-864K19.4,intron_variant,,ENST00000456813,;RP5-864K19.4,intron_variant,,ENST00000443161,;RP5-864K19.6,intron_variant,,ENST00000489575,;RP5-864K19.7,upstream_gene_variant,,ENST00000622355,;MYCBP,upstream_gene_variant,,ENST00000495043,;MYCBP,upstream_gene_variant,,ENST00000465771,;RP5-864K19.6,synonymous_variant,p.=,ENST00000454994,;RP5-864K19.6,non_coding_transcript_exon_variant,,ENST00000489803,; A ENST00000360786 Transcript synonymous_variant 919/1901 666/1548 222/515 S tcA/tcT 1 -1 GJA9 HGNC HGNC:19155 protein_coding YES CCDS432.1 ENSP00000354020 P57773 UPI000006E09A 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR11984:SF60,hmmpanther:PTHR11984,Gene3D:2zw3A00,Pfam_domain:PF00029,SMART_domains:SM01089,Prints_domain:PR00206 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 38875433 38875433 T A 1 0 0 0 0 0 0 0 1 6285 1683 59 4 4 GJA9 1 38875433 Silent SNP T C3N-01074_T 4008324 38875433 210080989 10 21999 KCNQ4 0 . GRCh38 1 40784276 40784276 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.183G>A p.= p.P61P ENST00000347132 1/14 205 107 98 217 217 0 strelka-varscan-mutect KCNQ4,synonymous_variant,p.=,ENST00000347132,NM_004700.3;KCNQ4,synonymous_variant,p.=,ENST00000509682,NM_172163.2; A ENST00000347132 Transcript synonymous_variant 265/4099 183/2088 61/695 P ccG/ccA 1 1 KCNQ4 HGNC HGNC:6298 protein_coding YES CCDS456.1 ENSP00000262916 P56696 UPI000013D35B NM_004700.3 1/14 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs921904898 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 40784276 40784276 G A 1 0 0 0 0 0 0 0 1 8001 1103 39 1 1 KCNQ4 1 40784276 Silent SNP G C3N-01074_T 1908843 40784276 208172146 11 22000 SLC1A7 0 . GRCh38 1 53114955 53114955 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.234C>T p.= p.A78A ENST00000620347 3/11 238 134 104 194 194 0 strelka-varscan-mutect SLC1A7,synonymous_variant,p.=,ENST00000620288,;SLC1A7,synonymous_variant,p.=,ENST00000620347,NM_001287595.1;SLC1A7,synonymous_variant,p.=,ENST00000371494,NM_006671.5;SLC1A7,synonymous_variant,p.=,ENST00000371491,NM_001287596.1;SLC1A7,intron_variant,,ENST00000611397,NM_001287597.1;RP11-334A14.8,non_coding_transcript_exon_variant,,ENST00000439621,; A ENST00000620347 Transcript synonymous_variant 417/2873 234/1860 78/619 A gcC/gcT 1 -1 SLC1A7 HGNC HGNC:10945 protein_coding YES CCDS72797.1 ENSP00000478639 A0A087WUF9 UPI000387D8A4 NM_001287595.1 3/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF22,Gene3D:2nwlC00,Pfam_domain:PF00375,Superfamily_domains:0053221,Prints_domain:PR00173 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 53114955 53114955 G A 1 0 0 0 0 0 0 0 1 14703 987 35 3 3 SLC1A7 1 53114955 Silent SNP G C3N-01074_T 12330679 53114955 195841467 12 22001 ZRANB2 0 . GRCh38 1 71065080 71065080 + Missense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.987G>C p.Lys329Asn p.K329N ENST00000370920 10/10 136 73 63 157 157 0 strelka-varscan-mutect ZRANB2,missense_variant,p.Lys329Asn,ENST00000370920,NM_203350.2;ZRANB2,3_prime_UTR_variant,,ENST00000254821,NM_005455.4;ZRANB2,downstream_gene_variant,,ENST00000611683,;MIR186,downstream_gene_variant,,ENST00000384988,;ZRANB2-AS1,intron_variant,,ENST00000426999,;ZRANB2-AS1,intron_variant,,ENST00000450461,;ZRANB2,non_coding_transcript_exon_variant,,ENST00000477096,;ZRANB2,non_coding_transcript_exon_variant,,ENST00000487510,;ZRANB2,non_coding_transcript_exon_variant,,ENST00000479947,;ZRANB2,downstream_gene_variant,,ENST00000473260,; G ENST00000370920 Transcript missense_variant 1289/3078 987/993 329/330 K/N aaG/aaC COSM1344207 1 -1 ZRANB2 HGNC HGNC:13058 protein_coding YES CCDS659.1 ENSP00000359958 O95218 UPI000013CE63 NM_203350.2 deleterious_low_confidence(0) 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR12999,PIRSF_domain:PIRSF037956 1 MODERATE 1 SNV 1 1 1 PASS rs998372565 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 71065080 71065080 C G 1 0 0 0 0 1 0 0 0 18816 912 32 4 4 ZRANB2 1 71065080 Missense_Mutation SNP C C3N-01074_T 17950125 71065080 177891342 13 22002 LRRC53 0 . GRCh38 1 74471933 74471933 + Silent SNP A A T novel C3N-01074_T C3N-01074_N A A c.1689T>A p.= p.P563P ENST00000294635 5/5 16 13 3 29 29 0 strelka-mutect LRRC53,synonymous_variant,p.=,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2;RP4-650F12.2,downstream_gene_variant,,ENST00000442876,;RP4-650F12.2,downstream_gene_variant,,ENST00000411417,; T ENST00000294635 Transcript synonymous_variant 1804/3859 1689/3744 563/1247 P ccT/ccA 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE 5/5 LOW SNV 5 1 PASS . . 23 187 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 74471933 74471933 A T 1 0 0 0 0 0 0 0 1 8905 407 15 4 4 LRRC53 1 74471933 Silent SNP A C3N-01074_T 3406853 74471933 174484489 14 22003 MSH4 0 . GRCh38 1 75879005 75879005 + Silent SNP A A G novel C3N-01074_T C3N-01074_N A A c.1554A>G p.= p.Q518Q ENST00000263187 12/20 164 152 12 198 198 0 strelka-varscan MSH4,synonymous_variant,p.=,ENST00000263187,NM_002440.3; G ENST00000263187 Transcript synonymous_variant 1658/3266 1554/2811 518/936 Q caA/caG 1 1 MSH4 HGNC HGNC:7327 protein_coding YES CCDS670.1 ENSP00000263187 O15457 UPI000006D934 NM_002440.3 12/20 Gene3D:1.10.1420.10,Pfam_domain:PF05190,Pfam_domain:PF05192,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF21,SMART_domains:SM00533,Superfamily_domains:SSF48334 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 75879005 75879005 A G 1 0 0 0 0 0 0 0 1 9855 40 2 5 5 MSH4 1 75879005 Silent SNP A C3N-01074_T 1407072 75879005 173077417 15 22004 AK5 0 . GRCh38 1 77340396 77340396 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.719T>A p.Val240Glu p.V240E ENST00000354567 6/14 121 110 11 154 154 0 strelka-varscan-mutect AK5,missense_variant,p.Val214Glu,ENST00000344720,NM_012093.3;AK5,missense_variant,p.Val240Glu,ENST00000354567,NM_174858.2;AK5,non_coding_transcript_exon_variant,,ENST00000524494,;AK5,upstream_gene_variant,,ENST00000465146,; A ENST00000354567 Transcript missense_variant 982/3251 719/1689 240/562 V/E gTg/gAg 1 1 AK5 HGNC HGNC:365 protein_coding YES CCDS675.1 ENSP00000346577 Q9Y6K8 UPI0000167E20 NM_174858.2 deleterious(0) 6/14 HAMAP:MF_00235,hmmpanther:PTHR23359:SF79,hmmpanther:PTHR23359,Pfam_domain:PF00406,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 77340396 77340396 T A 1 0 0 0 0 1 0 0 0 522 1696 59 4 4 AK5 1 77340396 Missense_Mutation SNP T C3N-01074_T 1461391 77340396 171616026 16 22005 PTGFR 0 . GRCh38 1 78536555 78536555 + Nonsense_Mutation SNP T T A rs773200902 C3N-01074_T C3N-01074_N T T c.948T>A p.Tyr316Ter p.Y316* ENST00000370757 3/3 420 396 24 414 414 0 strelka-varscan-mutect PTGFR,stop_gained,p.Tyr316Ter,ENST00000370757,NM_000959.3;PTGFR,stop_gained,p.Tyr316Ter,ENST00000370758,;PTGFR,3_prime_UTR_variant,,ENST00000370756,NM_001039585.1;PTGFR,3_prime_UTR_variant,,ENST00000497923,; A ENST00000370757 Transcript stop_gained 1185/4379 948/1080 316/359 Y/* taT/taA rs773200902 1 1 PTGFR HGNC HGNC:9600 protein_coding YES CCDS686.1 ENSP00000359793 P43088 UPI0000001C40 NM_000959.3 3/3 Gene3D:1.20.1070.10,Prints_domain:PR00855,hmmpanther:PTHR11866,hmmpanther:PTHR11866:SF4,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS rs773200902 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 78536555 78536555 T A 1 0 0 0 0 0 1 0 0 12905 1413 49 4 4 PTGFR 1 78536555 Nonsense_Mutation SNP T C3N-01074_T 1196159 78536555 170419867 17 22006 CTBS 0 . GRCh38 1 84563399 84563399 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.815C>T p.Ala272Val p.A272V ENST00000370630 6/7 92 77 15 128 128 0 strelka-varscan-mutect CTBS,missense_variant,p.Ala272Val,ENST00000370630,NM_004388.2;CTBS,non_coding_transcript_exon_variant,,ENST00000477677,;SPATA1,intron_variant,,ENST00000460286,;CTBS,3_prime_UTR_variant,,ENST00000465118,;CTBS,3_prime_UTR_variant,,ENST00000370625,; A ENST00000370630 Transcript missense_variant 864/6600 815/1158 272/385 A/V gCa/gTa 1 -1 CTBS HGNC HGNC:2496 protein_coding YES CCDS698.1 ENSP00000359664 Q01459 UPI00001293CB NM_004388.2 tolerated(0.14) 6/7 hmmpanther:PTHR11177:SF150,hmmpanther:PTHR11177,Gene3D:3.20.20.80,Pfam_domain:PF00704,SMART_domains:SM00636 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 84563399 84563399 G A 1 0 0 0 0 1 0 0 0 3805 1319 46 3 3 CTBS 1 84563399 Missense_Mutation SNP G C3N-01074_T 6026844 84563399 164393023 18 22007 OLFM3 0 . GRCh38 1 101804611 101804611 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1064G>T p.Gly355Val p.G355V ENST00000338858 6/6 175 164 11 255 254 1 strelka-varscan-mutect OLFM3,missense_variant,p.Gly335Val,ENST00000370103,NM_058170.3;OLFM3,missense_variant,p.Gly355Val,ENST00000338858,NM_001288821.1;OLFM3,3_prime_UTR_variant,,ENST00000536598,;OLFM3,non_coding_transcript_exon_variant,,ENST00000462354,;OLFM3,non_coding_transcript_exon_variant,,ENST00000465523,; A ENST00000338858 Transcript missense_variant 1064/2189 1064/1437 355/478 G/V gGg/gTg 1 -1 OLFM3 HGNC HGNC:17990 protein_coding YES CCDS72832.1 ENSP00000345192 Q96PB7 Q6IMJ0 UPI000004C626 NM_001288821.1 deleterious(0) 6/6 Pfam_domain:PF02191,PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF36,SMART_domains:SM00284 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 101804611 101804611 C A 1 0 0 0 0 1 0 0 0 10929 623 22 2 2 OLFM3 1 101804611 Missense_Mutation SNP C C3N-01074_T 17241212 101804611 147151811 19 22008 GPR89B 0 . GRCh38 1 147928574 147928574 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.38C>T p.Ser13Phe p.S13F ENST00000314163 1/14 324 267 57 262 262 0 strelka-varscan-mutect GPR89B,missense_variant,p.Ser13Phe,ENST00000314163,NM_016334.3;GPR89B,missense_variant,p.Ser13Phe,ENST00000468618,;GPR89B,missense_variant,p.Ser13Phe,ENST00000488165,;GPR89B,non_coding_transcript_exon_variant,,ENST00000478307,; T ENST00000314163 Transcript missense_variant 182/1934 38/1368 13/455 S/F tCc/tTc 1 1 GPR89B HGNC HGNC:13840 protein_coding YES CCDS930.1 ENSP00000358233 P0CG08 X5D7G6 UPI00000389CC NM_016334.3 deleterious(0) 1/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR15948 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 147928574 147928574 C T 1 0 0 0 0 1 0 0 0 6600 869 30 3 3 GPR89B 1 147928574 Missense_Mutation SNP C C3N-01074_T 46123963 147928574 101027848 20 22009 CGN 0 . GRCh38 1 151532435 151532435 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2605C>A p.Leu869Met p.L869M ENST00000271636 14/21 77 54 23 82 82 0 strelka-mutect CGN,missense_variant,p.Leu869Met,ENST00000271636,NM_020770.2;SNORA44,upstream_gene_variant,,ENST00000517031,;CGN,upstream_gene_variant,,ENST00000473377,;CGN,upstream_gene_variant,,ENST00000467998,;CGN,downstream_gene_variant,,ENST00000464886,; A ENST00000271636 Transcript missense_variant 2738/5091 2605/3612 869/1203 L/M Ctg/Atg 1 1 CGN HGNC HGNC:17429 protein_coding YES CCDS999.1 ENSP00000271636 Q9P2M7 UPI0000161C1E NM_020770.2 tolerated(0.09) 14/21 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF474,Pfam_domain:PF01576 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 73 151532435 151532435 C A 1 0 0 0 0 1 0 0 0 3061 680 24 2 2 CGN 1 151532435 Missense_Mutation SNP C C3N-01074_T 3603861 151532435 97423987 21 22010 FLG 0 . GRCh38 1 152309536 152309536 + Missense_Mutation SNP G G T rs753760290 C3N-01074_T C3N-01074_N G G c.5350C>A p.Pro1784Thr p.P1784T ENST00000368799 3/3 585 525 60 564 564 0 strelka-varscan-mutect FLG,missense_variant,p.Pro1784Thr,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 5386/12747 5350/12186 1784/4061 P/T Ccc/Acc rs753760290 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.91) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS rs753760290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 152309536 152309536 G T 1 0 0 0 0 1 0 0 0 5784 1203 42 2 2 FLG 1 152309536 Missense_Mutation SNP G C3N-01074_T 777101 152309536 96646886 22 22011 FLG 0 . GRCh38 1 152310752 152310752 + Silent SNP A A T C3N-01074_T C3N-01074_N A A c.4134T>A p.= p.A1378A ENST00000368799 3/3 698 613 85 688 688 0 strelka-varscan-mutect FLG,synonymous_variant,p.=,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript synonymous_variant 4170/12747 4134/12186 1378/4061 A gcT/gcA COSM5433556 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 Pfam_domain:PF03516 1 LOW 1 SNV 1 1 1 PASS rs1175659353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 152310752 152310752 A T 1 0 0 0 0 0 0 0 1 5784 59 3 4 4 FLG 1 152310752 Silent SNP A C3N-01074_T 1216 152310752 96645670 23 22012 FLG2 0 . GRCh38 1 152355666 152355666 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2120G>T p.Gly707Val p.G707V ENST00000388718 3/3 635 527 108 650 648 2 strelka-varscan-mutect FLG2,missense_variant,p.Gly707Val,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; A ENST00000388718 Transcript missense_variant 2193/9124 2120/7176 707/2391 G/V gGt/gTt 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious_low_confidence(0) 3/3 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 152355666 152355666 C A 1 0 0 0 0 1 0 0 0 5785 507 18 2 2 FLG2 1 152355666 Missense_Mutation SNP C C3N-01074_T 44914 152355666 96600756 24 22013 KPRP 0 . GRCh38 1 152760463 152760463 + Missense_Mutation SNP C C A rs770961240 C3N-01074_T C3N-01074_N C C c.875C>A p.Pro292His p.P292H ENST00000606109 1/1 195 138 57 187 187 0 strelka-varscan-mutect KPRP,missense_variant,p.Pro292His,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript missense_variant 903/2492 875/1740 292/579 P/H cCt/cAt rs770961240 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 tolerated(0.55) 1/1 hmmpanther:PTHR12241:SF98,hmmpanther:PTHR12241 MODERATE 1 SNV 1 PASS rs770961240 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 152760463 152760463 C A 1 0 0 0 0 1 0 0 0 8316 681 24 2 2 KPRP 1 152760463 Missense_Mutation SNP C C3N-01074_T 404797 152760463 96195959 25 22014 LELP1 0 . GRCh38 1 153204925 153204925 + Missense_Mutation SNP C C A rs748074067 C3N-01074_T C3N-01074_N C C c.218C>A p.Pro73His p.P73H ENST00000368747 2/2 385 269 116 334 334 0 strelka-varscan-mutect LELP1,missense_variant,p.Pro73His,ENST00000368747,NM_001010857.2; A ENST00000368747 Transcript missense_variant 328/523 218/297 73/98 P/H cCc/cAc rs748074067,COSM3474375 1 1 LELP1 HGNC HGNC:32046 protein_coding YES CCDS30869.1 ENSP00000357736 Q5T871 UPI000015D3CE NM_001010857.2 deleterious_low_confidence(0.01) 2/2 Pfam_domain:PF15042,Prints_domain:PR00021,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF11,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748074067 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 153204925 153204925 C A 1 0 0 0 0 1 0 0 0 8626 623 22 2 2 LELP1 1 153204925 Missense_Mutation SNP C C3N-01074_T 444462 153204925 95751497 26 22015 DENND4B 0 . GRCh38 1 153933857 153933857 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2956G>T p.Gly986Trp p.G986W ENST00000361217 20/28 429 292 137 316 316 0 strelka-varscan-mutect DENND4B,missense_variant,p.Gly986Trp,ENST00000361217,NM_014856.2;DENND4B,missense_variant,p.Gly997Trp,ENST00000368646,;DENND4B,upstream_gene_variant,,ENST00000474386,;DENND4B,upstream_gene_variant,,ENST00000480340,;DENND4B,upstream_gene_variant,,ENST00000492898,;DENND4B,upstream_gene_variant,,ENST00000462423,;DENND4B,upstream_gene_variant,,ENST00000531748,;DENND4B,downstream_gene_variant,,ENST00000477746,; A ENST00000361217 Transcript missense_variant 3375/5706 2956/4491 986/1496 G/W Ggg/Tgg 1 -1 DENND4B HGNC HGNC:29044 protein_coding YES CCDS44228.1 ENSP00000354597 O75064 UPI000047EA3E NM_014856.2 deleterious(0.04) 20/28 hmmpanther:PTHR12296:SF18,hmmpanther:PTHR12296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 153933857 153933857 C A 1 0 0 0 0 1 0 0 0 4238 623 22 2 2 DENND4B 1 153933857 Missense_Mutation SNP C C3N-01074_T 728932 153933857 95022565 27 22016 RIT1 0 . GRCh38 1 155900511 155900511 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.588A>T p.= p.V196V ENST00000368322 6/6 581 486 95 421 421 0 strelka-varscan-mutect RIT1,synonymous_variant,p.=,ENST00000368323,NM_006912.5;RIT1,synonymous_variant,p.=,ENST00000539040,NM_001256820.1;RIT1,synonymous_variant,p.=,ENST00000368322,NM_001256821.1;RIT1,downstream_gene_variant,,ENST00000609492,;RIT1,3_prime_UTR_variant,,ENST00000461050,; A ENST00000368322 Transcript synonymous_variant 618/855 588/711 196/236 V gtA/gtT 1 -1 RIT1 HGNC HGNC:10023 protein_coding YES CCDS58037.1 ENSP00000357305 Q92963 UPI0000458860 NM_001256821.1 6/6 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF208,Pfam_domain:PF00071,Gene3D:3.40.50.300,SMART_domains:SM00175,SMART_domains:SM00176,SMART_domains:SM00173,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 155900511 155900511 T A 1 0 0 0 0 0 0 0 1 13561 1625 57 4 4 RIT1 1 155900511 Silent SNP T C3N-01074_T 1966654 155900511 93055911 28 22017 INSRR 0 . GRCh38 1 156851986 156851986 + Frame_Shift_Del DEL G G - novel C3N-01074_T C3N-01074_N G G c.843delC p.Ser282AlafsTer49 p.S282Afs*49 ENST00000368195 3/22 109 90 19 130 130 0 sindel-varindel-pindel INSRR,frameshift_variant,p.Ser282AlafsTer49,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; - ENST00000368195 Transcript frameshift_variant 1240/5101 843/3894 281/1297 A/X gcC/gc 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 3/22 hmmpanther:PTHR24416:SF338,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620,Gene3D:2.10.220.10,Pfam_domain:PF00757,Superfamily_domains:SSF57184 HIGH 1 deletion 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 156851986 156851986 G - 1 0 1 0 1 0 0 0 0 7676 1335 47 0 0 INSRR 1 156851986 Frame_Shift_Del DEL G C3N-01074_T 951475 156851986 92104436 29 22018 FCRL5 0 . GRCh38 1 157527852 157527852 + Silent SNP G G T C3N-01074_T C3N-01074_N G G c.1725C>A p.= p.A575A ENST00000361835 9/17 87 62 25 111 111 0 strelka-varscan-mutect FCRL5,synonymous_variant,p.=,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,synonymous_variant,p.=,ENST00000368190,;FCRL5,downstream_gene_variant,,ENST00000368189,;FCRL5,non_coding_transcript_exon_variant,,ENST00000497286,; T ENST00000361835 Transcript synonymous_variant 1883/5390 1725/2934 575/977 A gcC/gcA COSM3863044,COSM3863045 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 9/17 PROSITE_profiles:PS50835,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 2 4 73 157527852 157527852 G T 1 0 0 0 0 0 0 0 1 5660 1219 43 2 2 FCRL5 1 157527852 Silent SNP G C3N-01074_T 675866 157527852 91428570 30 22019 SPTA1 0 . GRCh38 1 158681528 158681528 + Missense_Mutation SNP T T C novel C3N-01074_T C3N-01074_N T T c.530A>G p.Lys177Arg p.K177R ENST00000368147 4/52 514 456 58 507 507 0 strelka-varscan-mutect SPTA1,missense_variant,p.Lys177Arg,ENST00000368147,NM_003126.2;SPTA1,intron_variant,,ENST00000467387,; C ENST00000368147 Transcript missense_variant,splice_region_variant 711/7999 530/7260 177/2419 K/R aAg/aGg 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.06) 4/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 158681528 158681528 T C 1 0 0 0 0 1 0 0 0 15472 1623 56 5 5 SPTA1 1 158681528 Missense_Mutation SNP T C3N-01074_T 1153676 158681528 90274894 31 22020 CADM3 0 . GRCh38 1 159197048 159197048 + Missense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.1042C>G p.Leu348Val p.L348V ENST00000368124 8/10 138 113 25 139 139 0 strelka-varscan-mutect CADM3,missense_variant,p.Leu314Val,ENST00000368125,NM_001127173.1;CADM3,missense_variant,p.Leu348Val,ENST00000368124,NM_021189.3;CADM3,downstream_gene_variant,,ENST00000416746,;CADM3-AS1,non_coding_transcript_exon_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; G ENST00000368124 Transcript missense_variant 1199/2546 1042/1299 348/432 L/V Ctc/Gtc COSM3476428 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 deleterious(0.03) 8/10 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 159197048 159197048 C G 1 0 0 0 0 1 0 0 0 2258 681 24 4 4 CADM3 1 159197048 Missense_Mutation SNP C C3N-01074_T 515520 159197048 89759374 32 22021 DEDD 0 . GRCh38 1 161122323 161122323 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.781C>T p.Arg261Cys p.R261C ENST00000368006 6/6 343 232 111 314 314 0 strelka-varscan-mutect DEDD,missense_variant,p.Arg261Cys,ENST00000368006,NM_032998.2;DEDD,missense_variant,p.Arg261Cys,ENST00000545495,NM_001039711.1;DEDD,missense_variant,p.Arg261Cys,ENST00000458050,NM_001039712.1;DEDD,missense_variant,p.Arg261Cys,ENST00000490843,;DEDD,missense_variant,p.Arg291Cys,ENST00000368005,;DEDD,missense_variant,p.Arg261Cys,ENST00000464113,;NIT1,intron_variant,,ENST00000368008,NM_001185092.1;NIT1,downstream_gene_variant,,ENST00000368007,NM_001185093.1;NIT1,downstream_gene_variant,,ENST00000392190,NM_001185094.1;NIT1,downstream_gene_variant,,ENST00000368009,NM_005600.2;PFDN2,upstream_gene_variant,,ENST00000368010,NM_012394.3;DEDD,non_coding_transcript_exon_variant,,ENST00000489249,;DEDD,non_coding_transcript_exon_variant,,ENST00000486041,;DEDD,non_coding_transcript_exon_variant,,ENST00000473679,;NIT1,non_coding_transcript_exon_variant,,ENST00000479728,;DEDD,intron_variant,,ENST00000472996,;NIT1,downstream_gene_variant,,ENST00000496861,;NIT1,downstream_gene_variant,,ENST00000491497,;NIT1,downstream_gene_variant,,ENST00000485594,;DEDD,downstream_gene_variant,,ENST00000463227,;DEDD,downstream_gene_variant,,ENST00000496632,;NIT1,downstream_gene_variant,,ENST00000492411,;NIT1,downstream_gene_variant,,ENST00000496768,;NIT1,downstream_gene_variant,,ENST00000461376,;NIT1,downstream_gene_variant,,ENST00000479266,;NIT1,downstream_gene_variant,,ENST00000486962,;NIT1,downstream_gene_variant,,ENST00000477684,;PFDN2,upstream_gene_variant,,ENST00000468311,;NIT1,downstream_gene_variant,,ENST00000478277,;NIT1,downstream_gene_variant,,ENST00000473918,; A ENST00000368006 Transcript missense_variant 996/2345 781/957 261/318 R/C Cgt/Tgt 1 -1 DEDD HGNC HGNC:2755 protein_coding YES CCDS1219.1 ENSP00000356985 O75618 UPI0000031CE9 NM_032998.2 tolerated(0.08) 6/6 hmmpanther:PTHR15205,hmmpanther:PTHR15205:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 161122323 161122323 G A 1 0 0 0 0 1 0 0 0 4187 1087 38 1 1 DEDD 1 161122323 Missense_Mutation SNP G C3N-01074_T 1925275 161122323 87834099 33 22022 HSPA6 0 . GRCh38 1 161526294 161526294 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1636G>T p.Ala546Ser p.A546S ENST00000309758 1/1 295 201 94 257 256 1 strelka-varscan-mutect HSPA6,missense_variant,p.Ala546Ser,ENST00000309758,NM_002155.4;RP11-25K21.6,intron_variant,,ENST00000537821,;FCGR2A,downstream_gene_variant,,ENST00000491841,;FCGR2A,downstream_gene_variant,,ENST00000467525,; T ENST00000309758 Transcript missense_variant 1755/2371 1636/1932 546/643 A/S Gcc/Tcc 1 1 HSPA6 HGNC HGNC:5239 protein_coding YES CCDS1231.1 ENSP00000310219 P17066 UPI0000074238 NM_002155.4 tolerated_low_confidence(1) 1/1 hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF168,Gene3D:1.20.1270.10,Pfam_domain:PF00012,Superfamily_domains:SSF100934 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 161526294 161526294 G T 1 0 0 0 0 1 0 0 0 7311 1203 42 2 2 HSPA6 1 161526294 Missense_Mutation SNP G C3N-01074_T 403971 161526294 87430128 34 22023 SH2D1B 0 . GRCh38 1 162411893 162411893 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.124C>A p.Leu42Ile p.L42I ENST00000367929 1/4 200 135 65 174 174 0 strelka-varscan-mutect SH2D1B,missense_variant,p.Leu42Ile,ENST00000367929,NM_053282.4;SH2D1B,non_coding_transcript_exon_variant,,ENST00000493550,; T ENST00000367929 Transcript missense_variant 234/2523 124/399 42/132 L/I Ctc/Atc 1 -1 SH2D1B HGNC HGNC:30416 protein_coding YES CCDS30928.1 ENSP00000356906 O14796 UPI00000015D1 NM_053282.4 deleterious(0) 1/4 Gene3D:3.30.505.10,Pfam_domain:PF00017,Prints_domain:PR00401,PROSITE_profiles:PS50001,hmmpanther:PTHR11200,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 162411893 162411893 G T 1 0 0 0 0 1 0 0 0 14489 1000 35 2 2 SH2D1B 1 162411893 Missense_Mutation SNP G C3N-01074_T 885599 162411893 86544529 35 22024 FAM78B 0 . GRCh38 1 166070517 166070517 + Silent SNP C C A rs143651089 C3N-01074_T C3N-01074_N C C c.510G>T p.= p.T170T ENST00000338353 3/3 122 97 25 142 142 0 strelka-varscan-mutect FAM78B,synonymous_variant,p.=,ENST00000338353,;FAM78B,synonymous_variant,p.=,ENST00000354422,NM_001017961.3;FAM78B,synonymous_variant,p.=,ENST00000435676,;FAM78B,synonymous_variant,p.=,ENST00000456900,;FAM78B,synonymous_variant,p.=,ENST00000441649,; A ENST00000338353 Transcript synonymous_variant 1100/1597 510/786 170/261 T acG/acT rs143651089,TMP_ESP_1_166039754_166039754,COSM108432 1 -1 FAM78B HGNC HGNC:13495 protein_coding YES CCDS30931.1 ENSP00000339681 Q5VT40 UPI00001612B4 3/3 hmmpanther:PTHR31655,hmmpanther:PTHR31655:SF0 1,0,1 LOW 1 SNV 1 0,0,1 1 PASS rs143651089 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 166070517 166070517 C A 1 0 0 0 0 0 0 0 1 5488 871 31 1 1 FAM78B 1 166070517 Silent SNP C C3N-01074_T 3658624 166070517 82885905 36 22025 MAEL 0 . GRCh38 1 166989419 166989419 + Missense_Mutation SNP C C T C3N-01074_T C3N-01074_N C C c.67C>T p.Arg23Trp p.R23W ENST00000367872 1/12 247 210 37 205 205 0 strelka-varscan-mutect MAEL,missense_variant,p.Arg23Trp,ENST00000367872,NM_032858.2;MAEL,missense_variant,p.Arg23Trp,ENST00000367870,NM_001286377.1;MAEL,missense_variant,p.Arg23Trp,ENST00000447624,;MAEL,5_prime_UTR_variant,,ENST00000622874,NM_001286378.1;MAEL,upstream_gene_variant,,ENST00000491055,; T ENST00000367872 Transcript missense_variant 311/1908 67/1305 23/434 R/W Cgg/Tgg COSM5189278 1 1 MAEL HGNC HGNC:25929 protein_coding YES CCDS1257.1 ENSP00000356846 Q96JY0 A0A140VJP0 UPI0000042202 NM_032858.2 deleterious(0) 1/12 Gene3D:1.10.30.10,Pfam_domain:PF09011,hmmpanther:PTHR21358,hmmpanther:PTHR21358:SF4,Superfamily_domains:SSF47095 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 166989419 166989419 C T 1 0 0 0 0 1 0 0 0 9070 527 19 1 1 MAEL 1 166989419 Missense_Mutation SNP C C3N-01074_T 918902 166989419 81967003 37 22026 METTL18 0 . GRCh38 1 169793673 169793674 + Frame_Shift_Del DEL GT GT - novel C3N-01074_T C3N-01074_N GT GT c.22_23delAC p.Thr8TyrfsTer8 p.T8Yfs*8 ENST00000310392 2/2 82 67 15 108 108 0 sindel-varindel-pindel METTL18,frameshift_variant,p.Thr8TyrfsTer8,ENST00000310392,NM_001320199.1,NM_033418.2;METTL18,frameshift_variant,p.Thr8TyrfsTer8,ENST00000303469,NM_001320201.1;METTL18,frameshift_variant,p.Thr8TyrfsTer8,ENST00000454472,;C1orf112,upstream_gene_variant,,ENST00000286031,NM_018186.2;C1orf112,upstream_gene_variant,,ENST00000359326,;C1orf112,upstream_gene_variant,,ENST00000413811,;C1orf112,upstream_gene_variant,,ENST00000472795,NM_001320051.1;C1orf112,upstream_gene_variant,,ENST00000496973,;C1orf112,intron_variant,,ENST00000498289,;C1orf112,upstream_gene_variant,,ENST00000459772,;C1orf112,upstream_gene_variant,,ENST00000466580,;C1orf112,upstream_gene_variant,,ENST00000481744,; - ENST00000310392 Transcript frameshift_variant 376-377/1521 22-23/1119 8/372 T/X ACt/t 1 -1 METTL18 HGNC HGNC:28793 protein_coding YES CCDS1284.1 ENSP00000307975 O95568 A0A024R8Y7 UPI000006EC5C NM_001320199.1,NM_033418.2 2/2 HIGH 1 deletion 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 169793673 169793673 GT - 1 0 1 0 1 0 0 0 0 9444 1029 36 0 0 METTL18 1 169793673 Frame_Shift_Del DEL GT C3N-01074_T 2804254 169793673 79162749 38 22027 BRINP2 0 . GRCh38 1 177230084 177230084 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.208G>T p.Glu70Ter p.E70* ENST00000361539 2/8 175 140 35 137 137 0 strelka-varscan-mutect BRINP2,stop_gained,p.Glu70Ter,ENST00000361539,NM_021165.3; T ENST00000361539 Transcript stop_gained 520/3558 208/2352 70/783 E/* Gag/Tag 1 1 BRINP2 HGNC HGNC:13746 protein_coding YES CCDS1320.1 ENSP00000354481 Q9C0B6 UPI000006DF55 NM_021165.3 2/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF8 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 177230084 177230084 G T 1 0 0 0 0 0 1 0 0 1686 1175 41 2 2 BRINP2 1 177230084 Nonsense_Mutation SNP G C3N-01074_T 7436411 177230084 71726338 39 22028 CFHR4 0 . GRCh38 1 196906869 196906869 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.445G>T p.Asp149Tyr p.D149Y ENST00000367416 4/10 132 87 45 177 177 0 strelka-varscan-mutect CFHR4,missense_variant,p.Asp149Tyr,ENST00000367416,NM_001201551.1,NM_001201550.2;CFHR4,intron_variant,,ENST00000608469,;CFHR4,intron_variant,,ENST00000251424,NM_006684.4;CFHR4,intron_variant,,ENST00000367418,;RP4-608O15.3,intron_variant,,ENST00000367421,; T ENST00000367416 Transcript missense_variant 582/2178 445/1734 149/577 D/Y Gat/Tat 1 1 CFHR4 HGNC HGNC:16979 protein_coding YES CCDS55671.1 ENSP00000356386 Q92496 UPI0001F6C576 NM_001201551.1,NM_001201550.2 deleterious(0) 4/10 Gene3D:2.10.70.10,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF366,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 196906869 196906869 G T 1 0 0 0 0 1 0 0 0 3045 1290 45 2 2 CFHR4 1 196906869 Missense_Mutation SNP G C3N-01074_T 19676785 196906869 52049553 40 22029 CRB1 0 . GRCh38 1 197347411 197347411 + Nonsense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.920C>A p.Ser307Ter p.S307* ENST00000367400 4/12 449 381 68 392 392 0 strelka-varscan-mutect CRB1,stop_gained,p.Ser238Ter,ENST00000535699,NM_001257965.1;CRB1,stop_gained,p.Ser307Ter,ENST00000367400,NM_201253.2;CRB1,stop_gained,p.Ser307Ter,ENST00000538660,NM_001257966.1;CRB1,intron_variant,,ENST00000367399,NM_001193640.1;CRB1,stop_gained,p.Ser307Ter,ENST00000484075,;CRB1,non_coding_transcript_exon_variant,,ENST00000475659,; A ENST00000367400 Transcript stop_gained 1055/4932 920/4221 307/1406 S/* tCa/tAa 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 4/12 Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_profiles:PS50026,hmmpanther:PTHR24049,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 HIGH 1 SNV 1 1 PASS rs1386566957 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 197347411 197347411 C A 1 0 0 0 0 0 1 0 0 3648 838 29 2 2 CRB1 1 197347411 Nonsense_Mutation SNP C C3N-01074_T 440542 197347411 51609011 41 22030 ZNF281 0 . GRCh38 1 200407098 200407098 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2608G>T p.Gly870Trp p.G870W ENST00000294740 2/2 238 201 37 234 234 0 strelka-varscan-mutect ZNF281,missense_variant,p.Gly870Trp,ENST00000294740,NM_012482.4,NM_001281293.1;ZNF281,missense_variant,p.Gly870Trp,ENST00000367353,;ZNF281,missense_variant,p.Gly834Trp,ENST00000367352,NM_001281294.1;RP11-469A15.2,intron_variant,,ENST00000637430,;RP11-469A15.2,upstream_gene_variant,,ENST00000634596,;RP11-469A15.2,upstream_gene_variant,,ENST00000635220,; A ENST00000294740 Transcript missense_variant 2733/4891 2608/2688 870/895 G/W Ggg/Tgg 1 -1 ZNF281 HGNC HGNC:13075 protein_coding YES CCDS1402.1 ENSP00000294740 Q9Y2X9 UPI000013C345 NM_012482.4,NM_001281293.1 deleterious(0) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 200407098 200407098 C A 1 0 0 0 0 1 0 0 0 18394 681 24 2 2 ZNF281 1 200407098 Missense_Mutation SNP C C3N-01074_T 3059687 200407098 48549324 42 22031 C1orf106 0 . GRCh38 1 200911972 200911972 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.1479G>T p.= p.R493R ENST00000413687 9/10 144 110 34 142 141 1 strelka-varscan-mutect C1orf106,synonymous_variant,p.=,ENST00000367342,NM_018265.3;C1orf106,synonymous_variant,p.=,ENST00000413687,NM_001142569.2;C1orf106,non_coding_transcript_exon_variant,,ENST00000465162,;C1orf106,downstream_gene_variant,,ENST00000526172,;C1orf106,downstream_gene_variant,,ENST00000531649,; T ENST00000413687 Transcript synonymous_variant 1840/2197 1479/1737 493/578 R cgG/cgT 1 1 C1orf106 HGNC HGNC:25599 protein_coding YES CCDS44292.1 ENSP00000392105 Q3KP66 UPI0000204714 NM_001142569.2 9/10 hmmpanther:PTHR16093,hmmpanther:PTHR16093:SF4 LOW 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 200911972 200911972 G T 1 0 0 0 0 0 0 0 1 1956 1219 43 2 2 C1orf106 1 200911972 Silent SNP G C3N-01074_T 504874 200911972 48044450 43 22032 REN 0 . GRCh38 1 204162097 204162097 + Silent SNP C C T rs367565954 C3N-01074_T C3N-01074_N C C c.165G>A p.= p.R55R ENST00000272190 2/10 548 459 89 387 386 1 strelka-varscan-mutect REN,synonymous_variant,p.=,ENST00000638118,;REN,synonymous_variant,p.=,ENST00000272190,NM_000537.3; T ENST00000272190 Transcript synonymous_variant 194/1447 165/1221 55/406 R agG/agA rs367565954 1 -1 REN HGNC HGNC:9958 protein_coding YES CCDS30981.1 ENSP00000272190 P00797 UPI000000091F NM_000537.3 2/10 hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF77,Superfamily_domains:SSF50630 LOW 1 SNV 1 1 PASS rs367565954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 204162097 204162097 C T 1 0 0 0 0 0 0 0 1 13394 738 26 3 3 REN 1 204162097 Silent SNP C C3N-01074_T 3250125 204162097 44794325 44 22033 SLC41A1 0 . GRCh38 1 205794927 205794927 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.1299G>T p.= p.G433G ENST00000367137 10/11 464 368 96 377 377 0 strelka-varscan-mutect SLC41A1,synonymous_variant,p.=,ENST00000367137,NM_173854.5;SLC41A1,non_coding_transcript_exon_variant,,ENST00000468057,;SLC41A1,non_coding_transcript_exon_variant,,ENST00000484228,; A ENST00000367137 Transcript synonymous_variant 2314/4997 1299/1542 433/513 G ggG/ggT 1 -1 SLC41A1 HGNC HGNC:19429 protein_coding YES CCDS30988.1 ENSP00000356105 Q8IVJ1 B2RMP2 UPI000013E1E6 NM_173854.5 10/11 Superfamily_domains:0054748,Gene3D:2zy9B03,Pfam_domain:PF01769,hmmpanther:PTHR16228,hmmpanther:PTHR16228:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 205794927 205794927 C A 1 0 0 0 0 0 0 0 1 14907 726 26 2 2 SLC41A1 1 205794927 Silent SNP C C3N-01074_T 1632830 205794927 43161495 45 22034 SRGAP2 0 . GRCh38 1 206454154 206454154 + Nonstop_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.2368T>A p.Ter790ArgextTer21 p.*790Rext*21 ENST00000605610 20/20 236 219 17 217 217 0 strelka-varscan-mutect SRGAP2,stop_lost,p.Ter790ArgextTer21,ENST00000605610,NM_001300952.1;SRGAP2,intron_variant,,ENST00000573034,NM_015326.4;SRGAP2,intron_variant,,ENST00000624873,NM_001170637.3;SRGAP2,intron_variant,,ENST00000605476,;SRGAP2,intron_variant,,ENST00000604925,;SRGAP2,intron_variant,,ENST00000604010,;SRGAP2,non_coding_transcript_exon_variant,,ENST00000604247,; A ENST00000605610 Transcript stop_lost 2666/3212 2368/2370 790/789 */R Tga/Aga 1 1 SRGAP2 HGNC HGNC:19751 protein_coding CCDS76261.1 ENSP00000473954 A0A075B7B5 UPI0003335127 NM_001300952.1 20/20 HIGH SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 206454154 206454154 T A 1 0 0 0 0 0 0 0 0 15505 1593 55 4 4 SRGAP2 1 206454154 Nonstop_Mutation SNP T C3N-01074_T 659227 206454154 42502268 46 22035 SLC30A10 0 . GRCh38 1 219918466 219918466 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.747C>A p.= p.A249A ENST00000366926 3/4 103 80 23 101 101 0 strelka-varscan SLC30A10,synonymous_variant,p.=,ENST00000366926,NM_018713.2;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484079,;SLC30A10,non_coding_transcript_exon_variant,,ENST00000484239,;SLC30A10,3_prime_UTR_variant,,ENST00000356609,; T ENST00000366926 Transcript synonymous_variant 909/1915 747/1458 249/485 A gcC/gcA 1 -1 SLC30A10 HGNC HGNC:25355 protein_coding YES CCDS31026.1 ENSP00000355893 Q6XR72 UPI000040E993 NM_018713.2 3/4 Superfamily_domains:0054606,Gene3D:3h90A01,Pfam_domain:PF01545,hmmpanther:PTHR11562,hmmpanther:PTHR11562:SF14,TIGRFAM_domain:TIGR01297,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 219918466 219918466 G T 1 0 0 0 0 0 0 0 1 14824 1219 43 2 2 SLC30A10 1 219918466 Silent SNP G C3N-01074_T 13464312 219918466 29037956 47 22036 TP53BP2 0 . GRCh38 1 223821319 223821319 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.76G>A p.Val26Ile p.V26I ENST00000343537 2/18 441 310 131 440 440 0 strelka-varscan TP53BP2,missense_variant,p.Val26Ile,ENST00000343537,NM_001031685.2;TP53BP2,5_prime_UTR_variant,,ENST00000391878,NM_005426.2;TP53BP2,non_coding_transcript_exon_variant,,ENST00000473135,;TP53BP2,non_coding_transcript_exon_variant,,ENST00000472180,;TP53BP2,upstream_gene_variant,,ENST00000496282,;TP53BP2,intron_variant,,ENST00000465119,; T ENST00000343537 Transcript missense_variant 368/4651 76/3405 26/1134 V/I Gtt/Att 1 -1 TP53BP2 HGNC HGNC:12000 protein_coding YES CCDS44319.1 ENSP00000341957 Q13625 UPI0000D4B5F2 NM_001031685.2 deleterious(0) 2/18 hmmpanther:PTHR24131:SF8,hmmpanther:PTHR24131,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 223821319 223821319 C T 1 0 0 0 0 1 0 0 0 16862 565 20 3 3 TP53BP2 1 223821319 Missense_Mutation SNP C C3N-01074_T 3902853 223821319 25135103 48 22037 TAF5L 0 . GRCh38 1 229595001 229595001 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1066G>T p.Gly356Trp p.G356W ENST00000258281 5/5 198 165 33 202 202 0 strelka-varscan TAF5L,missense_variant,p.Gly356Trp,ENST00000258281,NM_014409.3;TAF5L,missense_variant,p.Gly356Trp,ENST00000366676,;TAF5L,downstream_gene_variant,,ENST00000366675,NM_001025247.1; A ENST00000258281 Transcript missense_variant 1232/3112 1066/1770 356/589 G/W Ggg/Tgg 1 -1 TAF5L HGNC HGNC:17304 protein_coding YES CCDS1581.1 ENSP00000258281 O75529 UPI0000073E93 NM_014409.3 tolerated(0.18) 5/5 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19879,hmmpanther:PTHR19879:SF6,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 229595001 229595001 C A 1 0 0 0 0 1 0 0 0 15925 681 24 2 2 TAF5L 1 229595001 Missense_Mutation SNP C C3N-01074_T 5773682 229595001 19361421 49 22038 ACTN2 0 . GRCh38 1 236737122 236737122 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.784G>T p.Ala262Ser p.A262S ENST00000542672 9/21 401 335 66 305 305 0 strelka-varscan ACTN2,missense_variant,p.Ala54Ser,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Ala262Ser,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Ala262Ser,ENST00000366578,NM_001103.3;ACTN2,splice_region_variant,,ENST00000492634,;ACTN2,non_coding_transcript_exon_variant,,ENST00000494762,; T ENST00000542672 Transcript missense_variant,splice_region_variant 1004/4906 784/2685 262/894 A/S Gcc/Tcc 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.08) 9/21 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 236737122 236737122 G T 1 0 0 0 0 1 0 0 0 249 1217 42 2 2 ACTN2 1 236737122 Missense_Mutation SNP G C3N-01074_T 7142121 236737122 12219300 50 22039 KIF26B 0 . GRCh38 1 245609509 245609510 + Frame_Shift_Ins INS - - C novel C3N-01074_T C3N-01074_N - - c.1899dupC p.Ile634HisfsTer39 p.I634Hfs*39 ENST00000407071 8/15 36 27 9 49 49 0 sindel-varindel KIF26B,frameshift_variant,p.Ile253HisfsTer39,ENST00000366518,;KIF26B,frameshift_variant,p.Ile634HisfsTer39,ENST00000407071,NM_018012.3; C ENST00000407071 Transcript frameshift_variant 2335-2336/7287 1895-1896/6327 632/2108 D/DX gac/gaCc 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 8/15 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF407,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 HIGH 1 insertion 1 4 1 PASS . . 0 206 4 0 0 0 0 0 -19.99972 1 1 1 1 0 C 7 5 73 245609509 245609509 - C 1 0 1 1 0 0 0 0 0 8160 275 10 0 0 KIF26B 1 245609509 Frame_Shift_Ins INS - C3N-01074_T 8872387 245609509 3346913 51 22040 OR11L1 0 . GRCh38 1 247841555 247841555 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.342C>A p.= p.L114L ENST00000355784 1/1 306 261 45 372 372 0 strelka-varscan OR11L1,synonymous_variant,p.=,ENST00000355784,NM_001001959.1; T ENST00000355784 Transcript synonymous_variant 342/969 342/969 114/322 L ctC/ctA 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 247841555 247841555 G T 1 0 0 0 0 0 0 0 1 11007 1161 41 2 2 OR11L1 1 247841555 Silent SNP G C3N-01074_T 2232046 247841555 1114867 52 22041 PGBD2 0 . GRCh38 1 248916624 248916624 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.40A>T p.Ile14Phe p.I14F ENST00000329291 3/3 298 214 84 229 229 0 strelka-varscan PGBD2,missense_variant,p.Ile14Phe,ENST00000329291,NM_170725.2;PGBD2,intron_variant,,ENST00000355360,NM_001017434.1;RNU6-1205P,upstream_gene_variant,,ENST00000363625,;PGBD2,intron_variant,,ENST00000462488,; T ENST00000329291 Transcript missense_variant 187/2136 40/1779 14/592 I/F Atc/Ttc 1 1 PGBD2 HGNC HGNC:19399 protein_coding YES CCDS31128.1 ENSP00000331643 Q6P3X8 UPI000016196D NM_170725.2 tolerated_low_confidence(0.76) 3/3 hmmpanther:PTHR28576,hmmpanther:PTHR28576:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 248916624 248916624 A T 1 0 0 0 0 1 0 0 0 11871 449 16 4 4 PGBD2 1 248916624 Missense_Mutation SNP A C3N-01074_T 1075069 248916624 39798 53 22042 TPO 0 . GRCh38 2 1433540 1433540 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.282G>C p.Met94Ile p.M94I ENST00000345913 4/17 401 350 51 454 454 0 strelka-varscan-mutect TPO,missense_variant,p.Met23Ile,ENST00000422464,;TPO,missense_variant,p.Met94Ile,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Met94Ile,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Met94Ile,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Met94Ile,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Met94Ile,ENST00000382198,NM_175722.3;TPO,missense_variant,p.Met94Ile,ENST00000539820,;TPO,missense_variant,p.Met94Ile,ENST00000382269,;TPO,missense_variant,p.Met94Ile,ENST00000423320,;TPO,intron_variant,,ENST00000497517,; C ENST00000345913 Transcript missense_variant 373/3145 282/2802 94/933 M/I atG/atC 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 deleterious(0.02) 4/17 hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 1433540 1433540 G C 1 0 0 0 0 1 0 0 0 16891 1348 47 4 4 TPO 2 1433540 Missense_Mutation SNP G C3N-01074_T 1433540 240759989 54 22043 TDRD15 0 . GRCh38 2 21140303 21140303 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2836C>A p.Pro946Thr p.P946T ENST00000405799 4/4 202 180 22 251 251 0 strelka-varscan TDRD15,missense_variant,p.Pro946Thr,ENST00000405799,;TDRD15,missense_variant,p.Pro946Thr,ENST00000622654,; A ENST00000405799 Transcript missense_variant 3166/6135 2836/5805 946/1934 P/T Cca/Aca 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 tolerated(0.15) 4/4 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 MODERATE 1 SNV 2 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 21140303 21140303 C A 1 0 0 0 0 1 0 0 0 16141 623 22 2 2 TDRD15 2 21140303 Missense_Mutation SNP C C3N-01074_T 19706763 21140303 221053226 55 22044 GAREM2 0 . GRCh38 2 26187536 26187536 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1904G>T p.Gly635Val p.G635V ENST00000401533 6/6 47 30 17 57 56 1 strelka-varscan GAREM2,missense_variant,p.Gly635Val,ENST00000401533,NM_001168241.1;GAREM2,intron_variant,,ENST00000407684,NM_001191033.1;HADHA,downstream_gene_variant,,ENST00000380649,NM_000182.4;HADHA,downstream_gene_variant,,ENST00000492433,;GAREM2,downstream_gene_variant,,ENST00000496070,; T ENST00000401533 Transcript missense_variant 2034/4161 1904/2625 635/874 G/V gGg/gTg 1 1 GAREM2 HGNC HGNC:27172 protein_coding YES CCDS54336.1 ENSP00000384593 Q75VX8 UPI0000237273 NM_001168241.1 deleterious(0.02) 6/6 hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 182 26 2 0 0 0 0 -20 0.9901227 0 1 1 0 T 3 4 73 26187536 26187536 G T 1 0 0 0 0 1 0 0 0 6110 1232 43 2 2 GAREM2 2 26187536 Missense_Mutation SNP G C3N-01074_T 5047233 26187536 216005993 56 22045 SLC5A6 0 . GRCh38 2 27201035 27201035 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.1727C>T p.Ser576Phe p.S576F ENST00000310574 16/17 83 70 13 86 86 0 strelka-varscan SLC5A6,missense_variant,p.Ser576Phe,ENST00000310574,NM_021095.2;SLC5A6,missense_variant,p.Ser576Phe,ENST00000408041,;SLC5A6,downstream_gene_variant,,ENST00000412471,;SLC5A6,downstream_gene_variant,,ENST00000461319,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000488743,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000461757,;SLC5A6,downstream_gene_variant,,ENST00000445802,;SLC5A6,downstream_gene_variant,,ENST00000476319,;SLC5A6,downstream_gene_variant,,ENST00000492069,;SLC5A6,downstream_gene_variant,,ENST00000464538,;SLC5A6,downstream_gene_variant,,ENST00000481751,; A ENST00000310574 Transcript missense_variant 2201/3231 1727/1908 576/635 S/F tCc/tTc 1 -1 SLC5A6 HGNC HGNC:11041 protein_coding YES CCDS1740.1 ENSP00000310208 Q9Y289 UPI000006DE33 NM_021095.2 tolerated(0.43) 16/17 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF140,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 27201035 27201035 G A 1 0 0 0 0 1 0 0 0 14952 1174 41 3 3 SLC5A6 2 27201035 Missense_Mutation SNP G C3N-01074_T 1013499 27201035 214992494 57 22046 MPV17 0 . GRCh38 2 27322485 27322485 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.33G>T p.= p.L11L ENST00000380044 2/8 496 320 176 375 373 2 strelka-varscan MPV17,synonymous_variant,p.=,ENST00000380044,NM_002437.4;MPV17,synonymous_variant,p.=,ENST00000233545,;MPV17,synonymous_variant,p.=,ENST00000402310,;MPV17,synonymous_variant,p.=,ENST00000405983,;MPV17,synonymous_variant,p.=,ENST00000402722,;MPV17,synonymous_variant,p.=,ENST00000399052,;MPV17,synonymous_variant,p.=,ENST00000403262,;MPV17,synonymous_variant,p.=,ENST00000405076,;MPV17,5_prime_UTR_variant,,ENST00000428910,;MPV17,intron_variant,,ENST00000357186,;GTF3C2,downstream_gene_variant,,ENST00000359541,NM_001318909.1;GTF3C2,downstream_gene_variant,,ENST00000264720,NM_001521.3,NM_001035521.2;GTF3C2,downstream_gene_variant,,ENST00000454704,;GTF3C2,downstream_gene_variant,,ENST00000457098,;GTF3C2,downstream_gene_variant,,ENST00000431028,;MPV17,synonymous_variant,p.=,ENST00000426513,;MPV17,synonymous_variant,p.=,ENST00000415514,;MPV17,non_coding_transcript_exon_variant,,ENST00000617583,;MPV17,non_coding_transcript_exon_variant,,ENST00000621183,;MPV17,non_coding_transcript_exon_variant,,ENST00000622003,;MPV17,non_coding_transcript_exon_variant,,ENST00000621470,;MPV17,non_coding_transcript_exon_variant,,ENST00000494436,;MPV17,non_coding_transcript_exon_variant,,ENST00000486898,;GTF3C2,downstream_gene_variant,,ENST00000495298,;GTF3C2,downstream_gene_variant,,ENST00000415683,; A ENST00000380044 Transcript synonymous_variant 89/1005 33/531 11/176 L ctG/ctT 1 -1 MPV17 HGNC HGNC:7224 protein_coding YES CCDS1748.1 ENSP00000369383 P39210 A0A0S2Z3Z9 UPI000012F4BD NM_002437.4 2/8 hmmpanther:PTHR11266 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 27322485 27322485 C A 1 0 0 0 0 0 0 0 1 9711 581 21 2 2 MPV17 2 27322485 Silent SNP C C3N-01074_T 121450 27322485 214871044 58 22047 PLB1 0 . GRCh38 2 28516852 28516852 + Missense_Mutation SNP G G T rs751867991 C3N-01074_T C3N-01074_N G G c.100G>T p.Gly34Trp p.G34W ENST00000327757 2/58 234 177 57 184 184 0 strelka-varscan PLB1,missense_variant,p.Gly34Trp,ENST00000422425,NM_001170585.1;PLB1,missense_variant,p.Gly34Trp,ENST00000327757,NM_153021.4;PLB1,missense_variant,p.Gly33Trp,ENST00000404858,;PLB1,5_prime_UTR_variant,,ENST00000416713,; T ENST00000327757 Transcript missense_variant 144/5107 100/4377 34/1458 G/W Ggg/Tgg rs751867991 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 deleterious(0.04) 2/58 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 28516852 28516852 G T 1 0 0 0 0 1 0 0 0 12118 1000 35 2 2 PLB1 2 28516852 Missense_Mutation SNP G C3N-01074_T 1194367 28516852 213676677 59 22048 GALNT14 0 . GRCh38 2 30932125 30932125 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.1016T>A p.Val339Asp p.V339D ENST00000324589 11/16 77 55 22 46 46 0 strelka-varscan GALNT14,missense_variant,p.Val334Asp,ENST00000349752,NM_024572.3;GALNT14,missense_variant,p.Val314Asp,ENST00000406653,NM_001253827.1;GALNT14,missense_variant,p.Val339Asp,ENST00000324589,NM_001253826.1;GALNT14,missense_variant,p.Val301Asp,ENST00000430167,;GALNT14,non_coding_transcript_exon_variant,,ENST00000486564,;GALNT14,non_coding_transcript_exon_variant,,ENST00000464038,;GALNT14,downstream_gene_variant,,ENST00000481023,;GALNT14,3_prime_UTR_variant,,ENST00000455477,; T ENST00000324589 Transcript missense_variant 1077/2169 1016/1674 339/557 V/D gTc/gAc 1 -1 GALNT14 HGNC HGNC:22946 protein_coding YES CCDS58706.1 ENSP00000314500 Q96FL9 UPI0000073A6F NM_001253826.1 deleterious(0) 11/16 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF8,Superfamily_domains:SSF53448 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 73 30932125 30932125 A T 1 0 0 0 0 1 0 0 0 6080 275 10 4 4 GALNT14 2 30932125 Missense_Mutation SNP A C3N-01074_T 2415273 30932125 211261404 60 22049 NLRC4 0 . GRCh38 2 32249916 32249916 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.1948T>A p.Ser650Thr p.S650T ENST00000404025 5/10 304 243 61 335 335 0 strelka-varscan NLRC4,missense_variant,p.Ser650Thr,ENST00000404025,;NLRC4,missense_variant,p.Ser650Thr,ENST00000360906,NM_001199139.1,NM_021209.4;NLRC4,missense_variant,p.Ser650Thr,ENST00000402280,NM_001199138.1;NLRC4,intron_variant,,ENST00000342905,NM_001302504.1; T ENST00000404025 Transcript missense_variant 2437/3581 1948/3075 650/1024 S/T Tct/Act 1 -1 NLRC4 HGNC HGNC:16412 protein_coding YES CCDS33174.1 ENSP00000385090 Q9NPP4 UPI0000126FAD deleterious(0.01) 5/10 hmmpanther:PTHR10044:SF104,hmmpanther:PTHR10044,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 32249916 32249916 A T 1 0 0 0 0 1 0 0 0 10506 333 12 4 4 NLRC4 2 32249916 Missense_Mutation SNP A C3N-01074_T 1317791 32249916 209943613 61 22050 VIT 0 . GRCh38 2 36767194 36767194 + Silent SNP C C T rs764843769 C3N-01074_T C3N-01074_N C C c.588C>T p.= p.T196T ENST00000379242 7/16 202 123 79 157 157 0 strelka-varscan VIT,synonymous_variant,p.=,ENST00000379242,NM_053276.3;VIT,synonymous_variant,p.=,ENST00000389975,NM_001177969.1;VIT,synonymous_variant,p.=,ENST00000379241,NM_001177971.1;VIT,synonymous_variant,p.=,ENST00000404084,;VIT,synonymous_variant,p.=,ENST00000401530,NM_001177970.1;VIT,5_prime_UTR_variant,,ENST00000497382,; T ENST00000379242 Transcript synonymous_variant 890/2810 588/2082 196/693 T acC/acT rs764843769 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 7/16 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 36767194 36767194 C T 1 0 0 0 0 0 0 0 1 17718 610 22 3 3 VIT 2 36767194 Silent SNP C C3N-01074_T 4517278 36767194 205426335 62 22051 EPCAM 0 . GRCh38 2 47374002 47374002 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.379A>T p.Thr127Ser p.T127S ENST00000263735 3/9 419 333 86 382 381 1 strelka-varscan EPCAM,missense_variant,p.Thr127Ser,ENST00000263735,NM_002354.2;EPCAM,missense_variant,p.Thr155Ser,ENST00000405271,;EPCAM,downstream_gene_variant,,ENST00000419334,;MIR559,upstream_gene_variant,,ENST00000385188,;EPCAM,missense_variant,p.Thr155Ser,ENST00000456133,;EPCAM,non_coding_transcript_exon_variant,,ENST00000490733,;EPCAM,non_coding_transcript_exon_variant,,ENST00000474691,; T ENST00000263735 Transcript missense_variant 737/1724 379/945 127/314 T/S Aca/Tca 1 1 EPCAM HGNC HGNC:11529 protein_coding YES CCDS1833.1 ENSP00000263735 P16422 UPI000013D450 NM_002354.2 deleterious(0.02) 3/9 PROSITE_profiles:PS51162,hmmpanther:PTHR14168:SF2,hmmpanther:PTHR14168,Pfam_domain:PF00086,Gene3D:4.10.800.10,SMART_domains:SM00211,Superfamily_domains:SSF57610 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 47374002 47374002 A T 1 0 0 0 0 1 0 0 0 5008 43 2 4 4 EPCAM 2 47374002 Missense_Mutation SNP A C3N-01074_T 10606808 47374002 194819527 63 22052 CCDC85A 0 . GRCh38 2 56372404 56372404 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1378G>T p.Gly460Trp p.G460W ENST00000407595 4/6 144 95 49 138 138 0 strelka-varscan CCDC85A,missense_variant,p.Gly460Trp,ENST00000407595,NM_001080433.1;RP11-482H16.1,intron_variant,,ENST00000607540,; T ENST00000407595 Transcript missense_variant 1880/3982 1378/1662 460/553 G/W Ggg/Tgg 1 1 CCDC85A HGNC HGNC:29400 protein_coding YES CCDS46290.1 ENSP00000384040 Q96PX6 UPI00001C1DC1 NM_001080433.1 tolerated_low_confidence(0.06) 4/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 56372404 56372404 G T 1 0 0 0 0 1 0 0 0 2557 1232 43 2 2 CCDC85A 2 56372404 Missense_Mutation SNP G C3N-01074_T 8998402 56372404 185821125 64 22053 ADD2 0 . GRCh38 2 70690924 70690924 + Silent SNP C C A rs782694329 C3N-01074_T C3N-01074_N C C c.711G>T p.= p.S237S ENST00000264436 8/16 114 76 38 88 88 0 strelka-varscan ADD2,synonymous_variant,p.=,ENST00000264436,NM_001617.3;ADD2,synonymous_variant,p.=,ENST00000413157,NM_017482.3;ADD2,synonymous_variant,p.=,ENST00000407644,NM_001185054.1;ADD2,synonymous_variant,p.=,ENST00000355733,NM_017488.3;ADD2,synonymous_variant,p.=,ENST00000430656,NM_001185055.1;ADD2,synonymous_variant,p.=,ENST00000456320,;ADD2,intron_variant,,ENST00000522886,;ADD2,downstream_gene_variant,,ENST00000415348,;AC007395.3,intron_variant,,ENST00000457851,;ADD2,synonymous_variant,p.=,ENST00000403045,; A ENST00000264436 Transcript synonymous_variant 1156/9267 711/2181 237/726 S tcG/tcT rs782694329 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 8/16 hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6,Pfam_domain:PF00596,Gene3D:3.40.225.10,SMART_domains:SM01007,Superfamily_domains:SSF53639 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 70690924 70690924 C A 1 0 0 0 0 0 0 0 1 349 666 23 1 1 ADD2 2 70690924 Silent SNP C C3N-01074_T 14318520 70690924 171502605 65 22054 KCMF1 0 . GRCh38 2 85046240 85046240 + Missense_Mutation SNP A A G novel C3N-01074_T C3N-01074_N A A c.563A>G p.Tyr188Cys p.Y188C ENST00000409785 5/7 238 199 39 209 209 0 strelka-varscan KCMF1,missense_variant,p.Tyr188Cys,ENST00000409785,NM_020122.4;KCMF1,missense_variant,p.Tyr137Cys,ENST00000453448,; G ENST00000409785 Transcript missense_variant 922/7568 563/1146 188/381 Y/C tAt/tGt 1 1 KCMF1 HGNC HGNC:20589 protein_coding YES CCDS46350.1 ENSP00000386738 Q9P0J7 UPI000003615C NM_020122.4 tolerated(0.13) 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR12268 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 85046240 85046240 A G 1 0 0 0 0 1 0 0 0 7916 449 16 5 5 KCMF1 2 85046240 Missense_Mutation SNP A C3N-01074_T 14355316 85046240 157147289 66 22055 MRPS9 0 . GRCh38 2 105080000 105080000 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.427G>C p.Asp143His p.D143H ENST00000258455 5/11 257 184 73 285 285 0 strelka-varscan MRPS9,missense_variant,p.Asp143His,ENST00000258455,NM_182640.2; C ENST00000258455 Transcript missense_variant 537/1500 427/1191 143/396 D/H Gat/Cat 1 1 MRPS9 HGNC HGNC:14501 protein_coding YES CCDS2065.1 ENSP00000258455 P82933 UPI00000467F9 NM_182640.2 deleterious(0) 5/11 hmmpanther:PTHR21569,hmmpanther:PTHR21569:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 105080000 105080000 G C 1 0 0 0 0 1 0 0 0 9826 942 33 4 4 MRPS9 2 105080000 Missense_Mutation SNP G C3N-01074_T 20033760 105080000 137113529 67 22056 IL36G 0 . GRCh38 2 112980139 112980139 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.291G>A p.= p.L97L ENST00000259205 4/5 205 179 26 198 198 0 strelka-varscan-mutect IL36G,synonymous_variant,p.=,ENST00000259205,NM_019618.3;IL36G,synonymous_variant,p.=,ENST00000376489,NM_001278568.1;IL36G,downstream_gene_variant,,ENST00000447128,;HMGN2P23,downstream_gene_variant,,ENST00000456759,; A ENST00000259205 Transcript synonymous_variant 360/1195 291/510 97/169 L ttG/ttA 1 1 IL36G HGNC HGNC:15741 protein_coding YES CCDS2108.1 ENSP00000259205 Q9NZH8 UPI0000038BF0 NM_019618.3 4/5 hmmpanther:PTHR10078:SF27,hmmpanther:PTHR10078,Gene3D:2.80.10.50,Pfam_domain:PF00340,SMART_domains:SM00125,Superfamily_domains:SSF50353,Prints_domain:PR01360 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 112980139 112980139 G A 1 0 0 0 0 0 0 0 1 7596 1310 46 3 3 IL36G 2 112980139 Silent SNP G C3N-01074_T 7900139 112980139 129213390 68 22057 LIMS2 0 . GRCh38 2 127654424 127654424 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.431G>C p.Arg144Thr p.R144T ENST00000324938 4/10 221 133 88 183 183 0 strelka-varscan-mutect LIMS2,missense_variant,p.Arg115Thr,ENST00000409455,;LIMS2,missense_variant,p.Arg115Thr,ENST00000410011,NM_001161404.1;LIMS2,missense_variant,p.Arg115Thr,ENST00000409808,;LIMS2,missense_variant,p.Arg144Thr,ENST00000324938,NM_017980.4;LIMS2,missense_variant,p.Arg120Thr,ENST00000355119,NM_001161403.1;LIMS2,missense_variant,p.Arg142Thr,ENST00000545738,NM_001136037.2;GPR17,downstream_gene_variant,,ENST00000544369,NM_001161415.1;GPR17,downstream_gene_variant,,ENST00000272644,NM_005291.2;GPR17,downstream_gene_variant,,ENST00000393018,;LIMS2,upstream_gene_variant,,ENST00000409254,;GPR17,downstream_gene_variant,,ENST00000423019,;GPR17,downstream_gene_variant,,ENST00000486700,;GPR17,downstream_gene_variant,,ENST00000496086,;LIMS2,splice_region_variant,,ENST00000469300,;LIMS2,splice_region_variant,,ENST00000466410,;LIMS2,splice_region_variant,,ENST00000476932,;LIMS2,upstream_gene_variant,,ENST00000413578,; G ENST00000324938 Transcript missense_variant,splice_region_variant 589/2111 431/1098 144/365 R/T aGg/aCg 1 -1 LIMS2 HGNC HGNC:16084 protein_coding YES CCDS2147.1 ENSP00000326888 Q7Z4I7 UPI00001B5BF3 NM_017980.4 deleterious(0) 4/10 PROSITE_profiles:PS50023,hmmpanther:PTHR24210:SF10,hmmpanther:PTHR24210,Gene3D:2.10.110.10,Pfam_domain:PF00412,PIRSF_domain:PIRSF038003,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 127654424 127654424 C G 1 0 0 0 0 1 0 0 0 8712 695 24 4 4 LIMS2 2 127654424 Missense_Mutation SNP C C3N-01074_T 14674285 127654424 114539105 69 22058 CCDC74B 0 . GRCh38 2 130142338 130142338 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.339G>C p.Leu113Phe p.L113F ENST00000310463 3/8 155 95 60 167 167 0 strelka-varscan-mutect CCDC74B,missense_variant,p.Leu113Phe,ENST00000310463,NM_207310.2;CCDC74B,missense_variant,p.Leu113Phe,ENST00000392984,;CCDC74B,missense_variant,p.Leu155Phe,ENST00000457413,;CCDC74B,intron_variant,,ENST00000409943,NM_001258307.1;CCDC74B,intron_variant,,ENST00000409128,;CCDC74B,downstream_gene_variant,,ENST00000409234,;CCDC74B,downstream_gene_variant,,ENST00000441670,;MED15P9,downstream_gene_variant,,ENST00000427638,;CCDC74B,missense_variant,p.Trp104Ser,ENST00000423263,;CCDC74B,3_prime_UTR_variant,,ENST00000434929,;CCDC74B,non_coding_transcript_exon_variant,,ENST00000496704,;CCDC74B,upstream_gene_variant,,ENST00000498526,;MED15P9,downstream_gene_variant,,ENST00000424716,; G ENST00000310463 Transcript missense_variant 477/1549 339/1143 113/380 L/F ttG/ttC 1 -1 CCDC74B HGNC HGNC:25267 protein_coding YES CCDS2155.1 ENSP00000308873 Q96LY2 UPI000006D822 NM_207310.2 tolerated(0.71) 3/8 hmmpanther:PTHR14882,hmmpanther:PTHR14882:SF5 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 130142338 130142338 C G 1 0 0 0 0 1 0 0 0 2548 593 21 4 4 CCDC74B 2 130142338 Missense_Mutation SNP C C3N-01074_T 2487914 130142338 112051191 70 22059 AMER3 0 . GRCh38 2 130763888 130763888 + Silent SNP C C A rs781541050 C3N-01074_T C3N-01074_N C C c.1816C>A p.= p.R606R ENST00000423981 2/2 195 123 72 224 224 0 strelka-varscan-mutect AMER3,synonymous_variant,p.=,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,synonymous_variant,p.=,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; A ENST00000423981 Transcript synonymous_variant 1926/6172 1816/2586 606/861 R Cga/Aga rs781541050 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2 LOW 1 SNV 4 1 PASS rs781541050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 130763888 130763888 C A 1 0 0 0 0 0 0 0 1 669 528 19 1 1 AMER3 2 130763888 Silent SNP C C3N-01074_T 621550 130763888 111429641 71 22060 LRP1B 0 . GRCh38 2 140444627 140444627 + Silent SNP A A T rs536761851 C3N-01074_T C3N-01074_N A A c.10110T>A p.= p.A3370A ENST00000389484 64/91 312 274 38 324 324 0 strelka-varscan-mutect LRP1B,synonymous_variant,p.=,ENST00000389484,NM_018557.2; T ENST00000389484 Transcript synonymous_variant 11082/16535 10110/13800 3370/4599 A gcT/gcA rs536761851 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 64/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,PROSITE_patterns:PS01209,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS rs536761851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 140444627 140444627 A T 1 0 0 0 0 0 0 0 1 8850 291 11 4 4 LRP1B 2 140444627 Silent SNP A C3N-01074_T 9680739 140444627 101748902 72 22061 PLA2R1 0 . GRCh38 2 159979851 159979851 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2247G>T p.Trp749Cys p.W749C ENST00000283243 14/30 269 178 91 245 245 0 strelka-varscan-mutect PLA2R1,missense_variant,p.Trp749Cys,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.Trp749Cys,ENST00000392771,NM_001007267.2; A ENST00000283243 Transcript missense_variant 2454/14371 2247/4392 749/1463 W/C tgG/tgT 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 deleterious(0) 14/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 159979851 159979851 C A 1 0 0 0 0 1 0 0 0 12106 624 22 2 2 PLA2R1 2 159979851 Missense_Mutation SNP C C3N-01074_T 19535224 159979851 82213678 73 22062 XIRP2 0 . GRCh38 2 167244692 167244692 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.3300C>A p.= p.T1100T ENST00000409195 9/11 237 162 75 286 286 0 strelka-varscan-mutect XIRP2,synonymous_variant,p.=,ENST00000409195,NM_152381.5;XIRP2,synonymous_variant,p.=,ENST00000409273,NM_001199144.1;XIRP2,synonymous_variant,p.=,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript synonymous_variant 3389/12675 3300/10650 1100/3549 T acC/acA 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 9/11 Pfam_domain:PF08043,PROSITE_profiles:PS51389,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 167244692 167244692 C A 1 0 0 0 0 0 0 0 1 17989 610 22 2 2 XIRP2 2 167244692 Silent SNP C C3N-01074_T 7264841 167244692 74948837 74 22063 AC013461.1 0 . GRCh38 2 173221170 173221170 + Silent SNP A A G rs150222131 C3N-01074_T C3N-01074_N A A c.1008A>G p.= p.A336A ENST00000338983 12/12 36 22 14 61 61 0 strelka-varscan-mutect AC013461.1,synonymous_variant,p.=,ENST00000338983,NM_133646.2;AC013461.1,synonymous_variant,p.=,ENST00000539448,;AC013461.1,intron_variant,,ENST00000375213,NM_016653.2;AC013461.1,intron_variant,,ENST00000409176,;MLK7-AS1,intron_variant,,ENST00000423106,;MLK7-AS1,intron_variant,,ENST00000422703,; G ENST00000338983 Transcript synonymous_variant 1203/7179 1008/1368 336/455 A gcA/gcG rs150222131 1 1 AC013461.1 Clone_based_vega_gene protein_coding CCDS2251.1 ENSP00000340257 D4Q8H0 UPI00000709DD NM_133646.2 12/12 LOW SNV 1 1 PASS rs150222131 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 173221170 173221170 A G 1 0 0 0 0 0 0 0 1 124 117 5 5 5 AC013461.1 2 173221170 Silent SNP A C3N-01074_T 5976478 173221170 68972359 75 22064 SP9 0 . GRCh38 2 174337020 174337020 + Missense_Mutation SNP A A C novel C3N-01074_T C3N-01074_N A A c.935A>C p.Asn312Thr p.N312T ENST00000394967 2/2 119 90 29 177 177 0 strelka-varscan-mutect SP9,missense_variant,p.Asn312Thr,ENST00000394967,NM_001145250.1;RP11-572N21.1,non_coding_transcript_exon_variant,,ENST00000624790,; C ENST00000394967 Transcript missense_variant 1082/2554 935/1455 312/484 N/T aAc/aCc 1 1 SP9 HGNC HGNC:30690 protein_coding YES CCDS46453.1 ENSP00000378418 P0CG40 UPI0000EE2E67 NM_001145250.1 deleterious(0) 2/2 hmmpanther:PTHR23235 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 174337020 174337020 A C 1 0 0 0 0 1 0 0 0 15297 43 2 5 5 SP9 2 174337020 Missense_Mutation SNP A C3N-01074_T 1115850 174337020 67856509 76 22065 HOXD10 0 . GRCh38 2 176116971 176116971 + Nonsense_Mutation SNP T T A C3N-01074_T C3N-01074_N T T c.138T>A p.Tyr46Ter p.Y46* ENST00000249501 1/2 219 188 31 263 262 1 strelka-varscan-mutect HOXD10,stop_gained,p.Tyr46Ter,ENST00000249501,NM_002148.3;HOXD-AS2,downstream_gene_variant,,ENST00000440016,;HOXD10,intron_variant,,ENST00000490088,;HOXD10,intron_variant,,ENST00000549469,; A ENST00000249501 Transcript stop_gained 393/1989 138/1023 46/340 Y/* taT/taA COSM1669427 1 1 HOXD10 HGNC HGNC:5133 protein_coding YES CCDS2266.1 ENSP00000249501 P28358 UPI000013CC87 NM_002148.3 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF49 1 HIGH 1 SNV 1 1 1 PASS rs1171005235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 176116971 176116971 T A 1 0 0 0 0 0 1 0 0 7213 1471 51 4 4 HOXD10 2 176116971 Nonsense_Mutation SNP T C3N-01074_T 1779951 176116971 66076558 77 22066 DNAH7 0 . GRCh38 2 195886238 195886238 + Missense_Mutation SNP C C A rs753498231 C3N-01074_T C3N-01074_N C C c.5441G>T p.Arg1814Leu p.R1814L ENST00000312428 34/65 190 156 34 194 193 1 strelka-varscan-mutect DNAH7,missense_variant,p.Arg1814Leu,ENST00000312428,NM_018897.2; A ENST00000312428 Transcript missense_variant 5542/12394 5441/12075 1814/4024 R/L cGg/cTg rs753498231,COSM5025818 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 tolerated(0.64) 34/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753498231 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 195886238 195886238 C A 1 0 0 0 0 1 0 0 0 4421 652 23 1 1 DNAH7 2 195886238 Missense_Mutation SNP C C3N-01074_T 19769267 195886238 46307291 78 22067 ZDBF2 0 . GRCh38 2 206310120 206310120 + Missense_Mutation SNP G G C rs750716878 C3N-01074_T C3N-01074_N G G c.5592G>C p.Glu1864Asp p.E1864D ENST00000374423 5/5 203 171 32 278 278 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Glu1864Asp,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Glu1862Asp,ENST00000611847,NM_001285549.1; C ENST00000374423 Transcript missense_variant 5978/10286 5592/7065 1864/2354 E/D gaG/gaC rs750716878 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 deleterious(0.05) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS rs750716878 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 206310120 206310120 G C 1 0 0 0 0 1 0 0 0 18174 933 33 4 4 ZDBF2 2 206310120 Missense_Mutation SNP G C3N-01074_T 10423882 206310120 35883409 79 22068 DYTN 0 . GRCh38 2 206705791 206705791 + Silent SNP G G T rs200713304 C3N-01074_T C3N-01074_N G G c.379C>A p.= p.R127R ENST00000452335 4/12 309 263 46 217 217 0 strelka-varscan-mutect DYTN,synonymous_variant,p.=,ENST00000452335,NM_001093730.1;Y_RNA,upstream_gene_variant,,ENST00000384589,;DYTN,non_coding_transcript_exon_variant,,ENST00000477734,; T ENST00000452335 Transcript synonymous_variant 496/2051 379/1737 127/578 R Cga/Aga rs200713304 1 -1 DYTN HGNC HGNC:23279 protein_coding YES CCDS46502.1 ENSP00000396593 A2CJ06 UPI0000EE0AB9 NM_001093730.1 4/12 hmmpanther:PTHR11915:SF282,hmmpanther:PTHR11915,Gene3D:1.10.238.10,Pfam_domain:PF09069,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS rs200713304 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 206705791 206705791 G T 1 0 0 0 0 0 0 0 1 4684 1130 39 1 1 DYTN 2 206705791 Silent SNP G C3N-01074_T 395671 206705791 35487738 80 22069 SPEG 0 . GRCh38 2 219435150 219435150 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.173G>A p.Ser58Asn p.S58N ENST00000312358 1/41 208 172 36 206 206 0 strelka-varscan-mutect SPEG,missense_variant,p.Ser58Asn,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000498378,; A ENST00000312358 Transcript missense_variant 305/10782 173/9804 58/3267 S/N aGc/aAc 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.1) 1/41 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 219435150 219435150 G A 1 0 0 0 0 1 0 0 0 15387 971 34 3 3 SPEG 2 219435150 Missense_Mutation SNP G C3N-01074_T 12729359 219435150 22758379 81 22070 NMUR1 0 . GRCh38 2 231528529 231528529 + Silent SNP C C A rs780891109 C3N-01074_T C3N-01074_N C C c.492G>T p.= p.V164V ENST00000305141 2/3 181 111 70 186 186 0 strelka-varscan-mutect NMUR1,synonymous_variant,p.=,ENST00000305141,NM_006056.4; A ENST00000305141 Transcript synonymous_variant 626/3298 492/1281 164/426 V gtG/gtT rs780891109 1 -1 NMUR1 HGNC HGNC:4518 protein_coding YES CCDS2486.1 ENSP00000305877 Q9HB89 UPI0000071CAE NM_006056.4 2/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF109,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs780891109 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 231528529 231528529 C A 1 0 0 0 0 0 0 0 1 10547 697 25 2 2 NMUR1 2 231528529 Silent SNP C C3N-01074_T 12093379 231528529 10665000 82 22071 MROH2A 0 . GRCh38 2 233829072 233829072 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.4488C>A p.Asn1496Lys p.N1496K ENST00000610772 37/42 51 35 16 76 76 0 strelka-varscan-mutect MROH2A,missense_variant,p.Asn1482Lys,ENST00000389758,;MROH2A,missense_variant,p.Asn1496Lys,ENST00000610772,NM_001287395.1;MROH2A,splice_region_variant,,ENST00000487979,;HJURP,downstream_gene_variant,,ENST00000433484,; A ENST00000610772 Transcript missense_variant,splice_region_variant 4581/5324 4488/5067 1496/1688 N/K aaC/aaA 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 deleterious(0.02) 37/42 Gene3D:1.25.10.10,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 233829072 233829072 C A 1 0 0 0 0 1 0 0 0 9744 550 19 1 1 MROH2A 2 233829072 Missense_Mutation SNP C C3N-01074_T 2300543 233829072 8364457 83 22072 KIF1A 0 . GRCh38 2 240758444 240758444 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2498C>A p.Ser833Tyr p.S833Y ENST00000498729 26/49 119 95 24 114 114 0 strelka-varscan-mutect KIF1A,missense_variant,p.Ser833Tyr,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Ser824Tyr,ENST00000320389,NM_004321.6;KIF1A,missense_variant,p.Ser833Tyr,ENST00000404283,; T ENST00000498729 Transcript missense_variant 2745/9223 2498/5376 833/1791 S/Y tCc/tAc 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 deleterious(0) 26/49 Pfam_domain:PF12423,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF361 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 240758444 240758444 G T 1 0 0 0 0 1 0 0 0 8147 1174 41 2 2 KIF1A 2 240758444 Missense_Mutation SNP G C3N-01074_T 6929372 240758444 1435085 84 22073 PASK 0 . GRCh38 2 241124027 241124027 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2826G>T p.Arg942Ser p.R942S ENST00000358649 11/18 361 294 67 342 342 0 strelka-varscan-mutect PASK,missense_variant,p.Arg942Ser,ENST00000403638,NM_001252124.1;PASK,missense_variant,p.Arg942Ser,ENST00000405260,;PASK,missense_variant,p.Arg942Ser,ENST00000544142,NM_001252120.1;PASK,missense_variant,p.Arg942Ser,ENST00000234040,NM_015148.3,NM_001252122.1;PASK,missense_variant,p.Arg942Ser,ENST00000358649,NM_001252119.1;PASK,downstream_gene_variant,,ENST00000459710,;PASK,non_coding_transcript_exon_variant,,ENST00000493544,; A ENST00000358649 Transcript missense_variant 2890/4326 2826/3993 942/1330 R/S agG/agT 1 -1 PASK HGNC HGNC:17270 protein_coding YES CCDS58759.1 ENSP00000351475 Q96RG2 UPI0000456F4C NM_001252119.1 deleterious(0.02) 11/18 hmmpanther:PTHR22971,hmmpanther:PTHR22971:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 241124027 241124027 C A 1 0 0 0 0 1 0 0 0 11553 854 30 2 2 PASK 2 241124027 Missense_Mutation SNP C C3N-01074_T 365583 241124027 1069502 85 22074 ITPR1 0 . GRCh38 3 4645665 4645665 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.792G>T p.= p.L264L ENST00000302640 10/61 170 106 64 189 187 2 strelka-varscan-mutect ITPR1,synonymous_variant,p.=,ENST00000354582,;ITPR1,synonymous_variant,p.=,ENST00000302640,NM_001168272.1;ITPR1,synonymous_variant,p.=,ENST00000357086,NM_001099952.2;ITPR1,synonymous_variant,p.=,ENST00000456211,NM_002222.5;ITPR1,synonymous_variant,p.=,ENST00000443694,;ITPR1,synonymous_variant,p.=,ENST00000544951,;ITPR1,non_coding_transcript_exon_variant,,ENST00000477577,;ITPR1,non_coding_transcript_exon_variant,,ENST00000467056,; T ENST00000302640 Transcript synonymous_variant 1142/10197 792/8232 264/2743 L ctG/ctT 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 10/61 PROSITE_profiles:PS50919,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52,Pfam_domain:PF02815,Gene3D:2.80.10.50,SMART_domains:SM00472,Superfamily_domains:SSF82109 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 4645665 4645665 G T 1 0 0 0 0 0 0 0 1 7826 1277 45 2 2 ITPR1 3 4645665 Silent SNP G C3N-01074_T 4645665 193649894 86 22075 SETD5 0 . GRCh38 3 9434860 9434860 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.366G>T p.= p.R122R ENST00000402198 6/23 137 79 58 108 108 0 strelka-varscan-mutect SETD5,synonymous_variant,p.=,ENST00000402198,NM_001080517.2;SETD5,synonymous_variant,p.=,ENST00000406341,;SETD5,synonymous_variant,p.=,ENST00000407969,;SETD5,synonymous_variant,p.=,ENST00000302463,NM_001292043.1;SETD5,synonymous_variant,p.=,ENST00000450326,;SETD5,synonymous_variant,p.=,ENST00000442373,;SETD5,non_coding_transcript_exon_variant,,ENST00000490791,;SETD5,downstream_gene_variant,,ENST00000478475,;SETD5,downstream_gene_variant,,ENST00000466172,;SETD5,3_prime_UTR_variant,,ENST00000443339,;SETD5,3_prime_UTR_variant,,ENST00000431285,;SETD5,non_coding_transcript_exon_variant,,ENST00000493918,;SETD5,downstream_gene_variant,,ENST00000415650,; T ENST00000402198 Transcript synonymous_variant 801/6827 366/4329 122/1442 R cgG/cgT 1 1 SETD5 HGNC HGNC:25566 protein_coding YES CCDS46741.1 ENSP00000385852 Q9C0A6 UPI0000411FEE NM_001080517.2 6/23 LOW 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 73 9434860 9434860 G T 1 0 0 0 0 0 0 0 1 14412 1190 42 2 2 SETD5 3 9434860 Silent SNP G C3N-01074_T 4789195 9434860 188860699 87 22076 FGD5 0 . GRCh38 3 14820554 14820554 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.1483G>C p.Glu495Gln p.E495Q ENST00000285046 1/20 81 45 36 116 116 0 strelka-varscan-mutect FGD5,missense_variant,p.Glu254Gln,ENST00000543601,NM_001320276.1;FGD5,missense_variant,p.Glu495Gln,ENST00000285046,NM_152536.3;FGD5,upstream_gene_variant,,ENST00000457774,; C ENST00000285046 Transcript missense_variant 1593/5720 1483/4389 495/1462 E/Q Gaa/Caa 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 deleterious(0) 1/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF13 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 14820554 14820554 G C 1 0 0 0 0 1 0 0 0 5700 943 33 4 4 FGD5 3 14820554 Missense_Mutation SNP G C3N-01074_T 5385694 14820554 183475005 88 22077 TRANK1 0 . GRCh38 3 36846380 36846380 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.4927C>A p.Leu1643Met p.L1643M ENST00000429976 16/23 149 81 68 177 177 0 strelka-varscan-mutect TRANK1,missense_variant,p.Leu1643Met,ENST00000429976,NM_014831.2;TRANK1,non_coding_transcript_exon_variant,,ENST00000463984,; T ENST00000429976 Transcript missense_variant 5175/10481 4927/8778 1643/2925 L/M Ctg/Atg 1 -1 TRANK1 HGNC HGNC:29011 protein_coding YES CCDS46789.2 ENSP00000416168 O15050 UPI00017BE82B NM_014831.2 deleterious(0) 16/23 hmmpanther:PTHR21529,hmmpanther:PTHR21529:SF4,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 36846380 36846380 G T 1 0 0 0 0 1 0 0 0 16937 962 34 2 2 TRANK1 3 36846380 Missense_Mutation SNP G C3N-01074_T 22025826 36846380 161449179 89 22078 STAB1 0 . GRCh38 3 52512839 52512839 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.3039C>A p.= p.I1013I ENST00000321725 29/69 131 61 70 146 146 0 strelka-varscan-mutect STAB1,synonymous_variant,p.=,ENST00000321725,NM_015136.2;STAB1,upstream_gene_variant,,ENST00000461325,;STAB1,downstream_gene_variant,,ENST00000481607,;STAB1,downstream_gene_variant,,ENST00000484850,; A ENST00000321725 Transcript synonymous_variant 3115/7928 3039/7713 1013/2570 I atC/atA 1 1 STAB1 HGNC HGNC:18628 protein_coding YES CCDS33768.1 ENSP00000312946 Q9NY15 UPI0000140C12 NM_015136.2 29/69 Gene3D:2.30.180.10,Pfam_domain:PF02469,PROSITE_profiles:PS50213,hmmpanther:PTHR24038,hmmpanther:PTHR24038:SF2,Superfamily_domains:SSF82153 LOW 1 SNV 1 1 PASS rs1370451793 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 52512839 52512839 C A 1 0 0 0 0 0 0 0 1 15615 816 29 2 2 STAB1 3 52512839 Silent SNP C C3N-01074_T 15666459 52512839 145782720 90 22079 IL17RD 0 . GRCh38 3 57101317 57101317 + Silent SNP T T C novel C3N-01074_T C3N-01074_N T T c.1026A>G p.= p.T342T ENST00000296318 11/13 167 108 59 228 228 0 strelka-varscan-mutect IL17RD,synonymous_variant,p.=,ENST00000296318,NM_001318864.1,NM_017563.3;IL17RD,synonymous_variant,p.=,ENST00000320057,;IL17RD,synonymous_variant,p.=,ENST00000463523,;IL17RD,downstream_gene_variant,,ENST00000467210,;IL17RD,non_coding_transcript_exon_variant,,ENST00000469841,; C ENST00000296318 Transcript synonymous_variant 1115/8720 1026/2220 342/739 T acA/acG 1 -1 IL17RD HGNC HGNC:17616 protein_coding YES CCDS2880.2 ENSP00000296318 Q8NFM7 UPI0000047CC3 NM_001318864.1,NM_017563.3 11/13 hmmpanther:PTHR15583:SF14,hmmpanther:PTHR15583 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 57101317 57101317 T C 1 0 0 0 0 0 0 0 1 7550 1451 51 5 5 IL17RD 3 57101317 Silent SNP T C3N-01074_T 4588478 57101317 141194242 91 22080 LRIG1 0 . GRCh38 3 66380667 66380667 + Missense_Mutation SNP G G C rs751112607 C3N-01074_T C3N-01074_N G G c.2965C>G p.Pro989Ala p.P989A ENST00000273261 18/19 318 185 133 384 383 1 strelka-varscan-mutect LRIG1,missense_variant,p.Pro966Ala,ENST00000383703,;LRIG1,missense_variant,p.Pro989Ala,ENST00000273261,NM_015541.2;SLC25A26,downstream_gene_variant,,ENST00000354883,NM_173471.3;SLC25A26,downstream_gene_variant,,ENST00000413054,;SLC25A26,downstream_gene_variant,,ENST00000336733,NM_001164796.1;LRIG1,non_coding_transcript_exon_variant,,ENST00000496559,;LRIG1,non_coding_transcript_exon_variant,,ENST00000495037,;SLC25A26,3_prime_UTR_variant,,ENST00000464350,;SLC25A26,downstream_gene_variant,,ENST00000483224,; C ENST00000273261 Transcript missense_variant 3490/5273 2965/3282 989/1093 P/A Ccc/Gcc rs751112607 1 -1 LRIG1 HGNC HGNC:17360 protein_coding YES CCDS33783.1 ENSP00000273261 Q96JA1 UPI000004C5BE NM_015541.2 tolerated(1) 18/19 MODERATE 1 SNV 1 1 PASS rs751112607 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 66380667 66380667 G C 1 0 0 0 0 1 0 0 0 8839 1232 43 4 4 LRIG1 3 66380667 Missense_Mutation SNP G C3N-01074_T 9279350 66380667 131914892 92 22081 BOC 0 . GRCh38 3 113284350 113284350 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.2672T>A p.Leu891Gln p.L891Q ENST00000273395 17/20 155 82 73 188 187 1 strelka-varscan-mutect BOC,missense_variant,p.Leu890Gln,ENST00000495514,NM_033254.3;BOC,missense_variant,p.Leu890Gln,ENST00000355385,;BOC,missense_variant,p.Leu891Gln,ENST00000273395,NM_001301861.1;BOC,upstream_gene_variant,,ENST00000473008,;BOC,non_coding_transcript_exon_variant,,ENST00000466059,;BOC,non_coding_transcript_exon_variant,,ENST00000479182,;CFAP44,downstream_gene_variant,,ENST00000489244,;BOC,downstream_gene_variant,,ENST00000463971,;BOC,upstream_gene_variant,,ENST00000488486,; A ENST00000273395 Transcript missense_variant 3011/4276 2672/3348 891/1115 L/Q cTg/cAg 1 1 BOC HGNC HGNC:17173 protein_coding YES CCDS77788.1 ENSP00000273395 Q9BWV1 UPI0000D61B53 NM_001301861.1 deleterious(0.01) 17/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF11 MODERATE 1 SNV 1 1 PASS rs1379277969 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 113284350 113284350 T A 1 0 0 0 0 1 0 0 0 1637 1580 55 4 4 BOC 3 113284350 Missense_Mutation SNP T C3N-01074_T 46903683 113284350 85011209 93 22082 SI 0 . GRCh38 3 165032558 165032558 + Missense_Mutation SNP G G T rs752079960 C3N-01074_T C3N-01074_N G G c.2700C>A p.Asn900Lys p.N900K ENST00000264382 24/48 162 95 67 188 188 0 strelka-varscan SI,missense_variant,p.Asn900Lys,ENST00000264382,NM_001041.3; T ENST00000264382 Transcript missense_variant 2763/6011 2700/5484 900/1827 N/K aaC/aaA rs752079960 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.91) 24/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 165032558 165032558 G T 1 0 0 0 0 1 0 0 0 14561 1136 40 1 1 SI 3 165032558 Missense_Mutation SNP G C3N-01074_T 51748208 165032558 33263001 94 22083 FGF12 0 . GRCh38 3 192144038 192144038 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.703G>T p.Gly235Cys p.G235C ENST00000454309 5/5 241 143 98 294 293 1 strelka-varscan FGF12,missense_variant,p.Gly173Cys,ENST00000445105,NM_004113.5;FGF12,missense_variant,p.Gly235Cys,ENST00000454309,NM_021032.4;FGF12,missense_variant,p.Gly173Cys,ENST00000450716,;FGF12,missense_variant,p.Gly136Cys,ENST00000430714,;FGF12,downstream_gene_variant,,ENST00000448795,;FGF12,non_coding_transcript_exon_variant,,ENST00000440901,; A ENST00000454309 Transcript missense_variant 1529/3058 703/732 235/243 G/C Ggc/Tgc 1 -1 FGF12 HGNC HGNC:3668 protein_coding YES CCDS3301.1 ENSP00000413496 P61328 UPI0000003FDD NM_021032.4 deleterious(0) 5/5 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 192144038 192144038 C A 1 0 0 0 0 1 0 0 0 5705 681 24 2 2 FGF12 3 192144038 Missense_Mutation SNP C C3N-01074_T 27111480 192144038 6151521 95 22084 CPN2 0 . GRCh38 3 194341456 194341456 + Missense_Mutation SNP C C A rs183919676 C3N-01074_T C3N-01074_N C C c.1247G>T p.Arg416Leu p.R416L ENST00000323830 2/2 238 138 100 274 273 1 strelka-varscan CPN2,missense_variant,p.Arg416Leu,ENST00000323830,NM_001291988.1,NM_001080513.3;CPN2,missense_variant,p.Arg416Leu,ENST00000429275,; A ENST00000323830 Transcript missense_variant 1337/3028 1247/1638 416/545 R/L cGg/cTg rs183919676 1 -1 CPN2 HGNC HGNC:2313 protein_coding YES CCDS33920.1 ENSP00000319464 P22792 UPI0001AE76B7 NM_001291988.1,NM_001080513.3 tolerated(0.5) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF278,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 194341456 194341456 C A 1 0 0 0 0 1 0 0 0 3605 652 23 1 1 CPN2 3 194341456 Missense_Mutation SNP C C3N-01074_T 2197418 194341456 3954103 96 22085 NSG1 0 . GRCh38 4 4391511 4391511 + Missense_Mutation SNP C C A rs761111231 C3N-01074_T C3N-01074_N C C c.166C>A p.Arg56Ser p.R56S ENST00000421177 7/9 183 92 91 101 101 0 strelka-varscan-mutect NSG1,missense_variant,p.Arg56Ser,ENST00000421177,;NSG1,missense_variant,p.Arg56Ser,ENST00000513555,;NSG1,missense_variant,p.Arg56Ser,ENST00000397958,NM_001287763.1;NSG1,missense_variant,p.Arg56Ser,ENST00000433139,NM_001287764.1,NM_001040101.1;NSG1,missense_variant,p.Arg56Ser,ENST00000621129,NM_014392.4;NSG1,missense_variant,p.Arg56Ser,ENST00000505246,;NSG1,missense_variant,p.Arg56Ser,ENST00000506380,;NSG1,intron_variant,,ENST00000504171,;NSG1,missense_variant,p.Arg56Ser,ENST00000513829,; A ENST00000421177 Transcript missense_variant 2157/4172 166/558 56/185 R/S Cgc/Agc rs761111231 1 1 NSG1 EntrezGene protein_coding YES CCDS3376.1 ENSP00000388823 P42857 B2R5R8 UPI0000130549 tolerated(0.57) 7/9 Pfam_domain:PF06387,PIRSF_domain:PIRSF002383,hmmpanther:PTHR28546 MODERATE 1 SNV 5 1 PASS rs761111231 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 4391511 4391511 C A 1 0 0 0 0 1 0 0 0 10732 652 23 1 1 NSG1 4 4391511 Missense_Mutation SNP C C3N-01074_T 4391511 185823044 97 22086 NWD2 0 . GRCh38 4 37445353 37445353 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.3365C>A p.Thr1122Asn p.T1122N ENST00000309447 7/7 494 273 221 411 411 0 strelka-varscan-mutect NWD2,missense_variant,p.Thr1122Asn,ENST00000309447,NM_001144990.1; A ENST00000309447 Transcript missense_variant 4213/8325 3365/5229 1122/1742 T/N aCc/aAc 1 1 NWD2 HGNC HGNC:29229 protein_coding YES CCDS47040.1 ENSP00000309501 Q9ULI1 UPI00006C0875 NM_001144990.1 deleterious(0.01) 7/7 hmmpanther:PTHR19857,hmmpanther:PTHR19857:SF18,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 37445353 37445353 C A 1 0 0 0 0 1 0 0 0 10855 507 18 2 2 NWD2 4 37445353 Missense_Mutation SNP C C3N-01074_T 33053842 37445353 152769202 98 22087 LNX1 0 . GRCh38 4 53496099 53496099 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1274A>T p.Glu425Val p.E425V ENST00000263925 6/11 249 157 92 254 254 0 strelka-varscan-mutect LNX1,missense_variant,p.Glu329Val,ENST00000306888,NM_032622.2;LNX1,missense_variant,p.Glu425Val,ENST00000263925,NM_001126328.2;RP11-231C18.3,intron_variant,,ENST00000507166,;LNX1-AS1,upstream_gene_variant,,ENST00000510785,;LNX1-AS1,upstream_gene_variant,,ENST00000502373,;LNX1,downstream_gene_variant,,ENST00000511398,; A ENST00000263925 Transcript missense_variant 1589/2953 1274/2187 425/728 E/V gAg/gTg 1 -1 LNX1 HGNC HGNC:6657 protein_coding YES CCDS47057.1 ENSP00000263925 Q8TBB1 UPI000012E7A6 NM_001126328.2 tolerated(0.28) 6/11 PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF14,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 53496099 53496099 T A 1 0 0 0 0 1 0 0 0 8792 1551 54 4 4 LNX1 4 53496099 Missense_Mutation SNP T C3N-01074_T 16050746 53496099 136718456 99 22088 KIAA1211 0 . GRCh38 4 56307669 56307669 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.255G>T p.Gln85His p.Q85H ENST00000504228 3/9 210 151 59 215 214 1 strelka-varscan-mutect KIAA1211,missense_variant,p.Gln85His,ENST00000504228,;KIAA1211,missense_variant,p.Gln78His,ENST00000541073,;KIAA1211,missense_variant,p.Gln85His,ENST00000264229,NM_020722.1;KIAA1211,missense_variant,p.Gln85His,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000505410,;KIAA1211,downstream_gene_variant,,ENST00000503618,; T ENST00000504228 Transcript missense_variant 360/4628 255/3702 85/1233 Q/H caG/caT 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 deleterious(0) 3/9 Pfam_domain:PF15262 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 56307669 56307669 G T 1 0 0 0 0 1 0 0 0 8107 991 35 2 2 KIAA1211 4 56307669 Missense_Mutation SNP G C3N-01074_T 2811570 56307669 133906886 100 22089 TECRL 0 . GRCh38 4 64314733 64314733 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.466C>A p.Leu156Ile p.L156I ENST00000381210 5/12 299 234 65 321 320 1 strelka-varscan-mutect TECRL,missense_variant,p.Leu156Ile,ENST00000381210,NM_001010874.4;TECRL,missense_variant,p.Leu156Ile,ENST00000507440,;TECRL,non_coding_transcript_exon_variant,,ENST00000513125,;TECRL,non_coding_transcript_exon_variant,,ENST00000511356,; T ENST00000381210 Transcript missense_variant 577/3573 466/1092 156/363 L/I Cta/Ata 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 tolerated(0.26) 5/12 hmmpanther:PTHR10556,hmmpanther:PTHR10556:SF27,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 64314733 64314733 G T 1 0 0 0 0 1 0 0 0 16157 962 34 2 2 TECRL 4 64314733 Missense_Mutation SNP G C3N-01074_T 8007064 64314733 125899822 101 22090 GNRHR 0 . GRCh38 4 67754061 67754061 + Missense_Mutation SNP A A T C3N-01074_T C3N-01074_N A A c.275T>A p.Leu92Gln p.L92Q ENST00000226413 1/3 477 375 102 518 518 0 strelka-varscan-mutect GNRHR,missense_variant,p.Leu92Gln,ENST00000226413,NM_000406.2;GNRHR,missense_variant,p.Leu92Gln,ENST00000420975,NM_001012763.1;UBA6-AS1,intron_variant,,ENST00000500538,;UBA6-AS1,intron_variant,,ENST00000502758,; T ENST00000226413 Transcript missense_variant 300/2164 275/987 92/328 L/Q cTg/cAg CM119294 1 -1 GNRHR HGNC HGNC:4421 protein_coding YES CCDS3517.1 ENSP00000226413 P30968 UPI000004EEC8 NM_000406.2 deleterious(0) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF22,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 67754061 67754061 A T 1 0 0 0 0 1 0 0 0 6428 188 7 4 4 GNRHR 4 67754061 Missense_Mutation SNP A C3N-01074_T 3439328 67754061 122460494 102 22091 MUC7 0 . GRCh38 4 70481587 70481587 + Silent SNP A A T novel C3N-01074_T C3N-01074_N A A c.843A>T p.= p.T281T ENST00000413702 4/4 528 418 110 528 527 1 strelka-varscan-mutect MUC7,synonymous_variant,p.=,ENST00000413702,NM_001145006.1;MUC7,synonymous_variant,p.=,ENST00000456088,NM_001145007.1;MUC7,synonymous_variant,p.=,ENST00000304887,NM_152291.2;MUC7,downstream_gene_variant,,ENST00000505411,;MUC7,downstream_gene_variant,,ENST00000514512,;MUC7,downstream_gene_variant,,ENST00000504482,; T ENST00000413702 Transcript synonymous_variant 1131/2540 843/1134 281/377 T acA/acT 1 1 MUC7 HGNC HGNC:7518 protein_coding YES CCDS3541.1 ENSP00000407422 Q8TAX7 UPI000013E9DD NM_001145006.1 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR41683:SF1,hmmpanther:PTHR41683 LOW 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 70481587 70481587 A T 1 0 0 0 0 0 0 0 1 9981 175 7 4 4 MUC7 4 70481587 Silent SNP A C3N-01074_T 2727526 70481587 119732968 103 22092 PPEF2 0 . GRCh38 4 75876401 75876401 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.1206G>A p.= p.R402R ENST00000286719 11/17 187 139 48 179 178 1 strelka-varscan-mutect PPEF2,synonymous_variant,p.=,ENST00000286719,NM_006239.2;PPEF2,synonymous_variant,p.=,ENST00000621010,;PPEF2,3_prime_UTR_variant,,ENST00000511880,; T ENST00000286719 Transcript synonymous_variant 1563/3414 1206/2262 402/753 R cgG/cgA 1 -1 PPEF2 HGNC HGNC:9244 protein_coding YES CCDS34013.1 ENSP00000286719 O14830 UPI0000163923 NM_006239.2 11/17 PIRSF_domain:PIRSF000912,SMART_domains:SM00156 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 75876401 75876401 C T 1 0 0 0 0 0 0 0 1 12417 726 26 3 3 PPEF2 4 75876401 Silent SNP C C3N-01074_T 5394814 75876401 114338154 104 22093 SDAD1 0 . GRCh38 4 75990758 75990758 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.84C>T p.= p.I28I ENST00000356260 1/22 396 311 85 478 478 0 strelka-varscan-mutect SDAD1,synonymous_variant,p.=,ENST00000356260,NM_001288984.1,NM_018115.3;SDAD1,synonymous_variant,p.=,ENST00000395711,NM_001288983.1;AC112719.1,upstream_gene_variant,,ENST00000629900,;RP11-630D6.5,intron_variant,,ENST00000501239,;SDAD1,non_coding_transcript_exon_variant,,ENST00000504975,;SDAD1,synonymous_variant,p.=,ENST00000395710,;SDAD1,synonymous_variant,p.=,ENST00000503411,;SDAD1,5_prime_UTR_variant,,ENST00000514710,; A ENST00000356260 Transcript synonymous_variant 203/3017 84/2064 28/687 I atC/atT 1 -1 SDAD1 HGNC HGNC:25537 protein_coding YES CCDS3573.2 ENSP00000348596 Q9NVU7 UPI000020B02A NM_001288984.1,NM_018115.3 1/22 hmmpanther:PTHR12730:SF0,hmmpanther:PTHR12730 LOW 1 SNV 1 1 PASS rs1314455737 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 75990758 75990758 G A 1 0 0 0 0 0 0 0 1 14222 1048 37 1 1 SDAD1 4 75990758 Silent SNP G C3N-01074_T 114357 75990758 114223797 105 22094 HPSE 0 . GRCh38 4 83322335 83322335 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.257G>T p.Gly86Val p.G86V ENST00000405413 3/13 152 116 36 177 177 0 strelka-varscan-mutect HPSE,missense_variant,p.Gly86Val,ENST00000405413,NM_006665.5;HPSE,missense_variant,p.Gly86Val,ENST00000311412,NM_001098540.2;HPSE,missense_variant,p.Gly86Val,ENST00000512196,NM_001166498.2;HPSE,missense_variant,p.Gly86Val,ENST00000513463,NM_001199830.1;HPSE,missense_variant,p.Gly86Val,ENST00000509906,;HPSE,missense_variant,p.Gly86Val,ENST00000507150,;HPSE,missense_variant,p.Gly86Val,ENST00000508891,; A ENST00000405413 Transcript missense_variant 394/4652 257/1632 86/543 G/V gGc/gTc 1 -1 HPSE HGNC HGNC:5164 protein_coding YES CCDS3602.1 ENSP00000384262 Q9Y251 UPI000013F168 NM_006665.5 deleterious(0) 3/13 hmmpanther:PTHR14363,hmmpanther:PTHR14363:SF10,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS rs1184183162 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 83322335 83322335 C A 1 0 0 0 0 1 0 0 0 7239 739 26 2 2 HPSE 4 83322335 Missense_Mutation SNP C C3N-01074_T 7331577 83322335 106892220 106 22095 RP11-766F14.2 0 . GRCh38 4 99653207 99653207 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1442C>A p.Pro481Gln p.P481Q ENST00000511828 1/2 91 71 20 131 130 1 strelka-varscan-mutect RP11-766F14.2,missense_variant,p.Pro481Gln,ENST00000511828,; T ENST00000511828 Transcript missense_variant 1442/10086 1442/5382 481/1793 P/Q cCa/cAa 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE tolerated_low_confidence(0.1) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1372708334 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 99653207 99653207 G T 1 0 0 0 0 1 0 0 0 13762 1348 47 2 2 RP11-766F14.2 4 99653207 Missense_Mutation SNP G C3N-01074_T 16330872 99653207 90561348 107 22096 TACR3 0 . GRCh38 4 103719584 103719584 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.92G>T p.Gly31Val p.G31V ENST00000304883 1/5 72 59 13 114 113 1 strelka-varscan-mutect TACR3,missense_variant,p.Gly31Val,ENST00000304883,NM_001059.2; A ENST00000304883 Transcript missense_variant 233/5190 92/1398 31/465 G/V gGg/gTg 1 -1 TACR3 HGNC HGNC:11528 protein_coding YES CCDS3664.1 ENSP00000303325 P29371 UPI0000050413 NM_001059.2 deleterious_low_confidence(0.01) 1/5 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 73 103719584 103719584 C A 1 0 0 0 0 1 0 0 0 15903 623 22 2 2 TACR3 4 103719584 Missense_Mutation SNP C C3N-01074_T 4066377 103719584 86494971 108 22097 PITX2 0 . GRCh38 4 110618479 110618479 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.621G>T p.Met207Ile p.M207I ENST00000306732 3/3 155 116 39 185 185 0 strelka-varscan-mutect PITX2,stop_gained,p.Glu132Ter,ENST00000394595,;PITX2,missense_variant,p.Met200Ile,ENST00000354925,NM_001204397.1;PITX2,missense_variant,p.Met200Ile,ENST00000613094,NM_153426.2;PITX2,missense_variant,p.Met154Ile,ENST00000616641,NM_001204399.1,NM_153427.2;PITX2,missense_variant,p.Met207Ile,ENST00000306732,NM_000325.5;PITX2,missense_variant,p.Met154Ile,ENST00000355080,;PITX2,missense_variant,p.Met200Ile,ENST00000394598,;PITX2,missense_variant,p.Met200Ile,ENST00000614423,NM_001204398.1;PITX2,missense_variant,p.Met200Ile,ENST00000511837,;PITX2,downstream_gene_variant,,ENST00000557119,;PITX2,downstream_gene_variant,,ENST00000511990,;PANCR,upstream_gene_variant,,ENST00000503456,;PANCR,upstream_gene_variant,,ENST00000513690,;PITX2,non_coding_transcript_exon_variant,,ENST00000556049,;PITX2,non_coding_transcript_exon_variant,,ENST00000607868,; A ENST00000306732 Transcript missense_variant 1264/2320 621/975 207/324 M/I atG/atT COSM398245,COSM398246 1 -1 PITX2 HGNC HGNC:9005 protein_coding YES CCDS3694.1 ENSP00000304169 Q99697 UPI000002B122 NM_000325.5 deleterious(0.03) 3/3 PIRSF_domain:PIRSF000563,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF254 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 110618479 110618479 C A 1 0 0 0 0 1 0 0 0 12051 835 29 2 2 PITX2 4 110618479 Missense_Mutation SNP C C3N-01074_T 6898895 110618479 79596076 109 22098 ABCE1 0 . GRCh38 4 145109142 145109142 + Missense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.298C>G p.Pro100Ala p.P100A ENST00000296577 5/18 249 209 40 328 328 0 strelka-varscan-mutect ABCE1,missense_variant,p.Pro100Ala,ENST00000296577,NM_001040876.1,NM_002940.2;ABCE1,missense_variant,p.Pro100Ala,ENST00000502586,;ABCE1,intron_variant,,ENST00000502803,;ABCE1,intron_variant,,ENST00000506506,;OTUD4,downstream_gene_variant,,ENST00000455611,;ABCE1,missense_variant,p.Pro100Ala,ENST00000507193,;ABCE1,missense_variant,p.Pro33Ala,ENST00000504292,; G ENST00000296577 Transcript missense_variant 813/3921 298/1800 100/599 P/A Cct/Gct COSM3917220 1 1 ABCE1 HGNC HGNC:69 protein_coding YES CCDS34071.1 ENSP00000296577 P61221 UPI0000001226 NM_001040876.1,NM_002940.2 deleterious(0) 5/18 PROSITE_profiles:PS50893,hmmpanther:PTHR19248,Superfamily_domains:SSF54862 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 145109142 145109142 C G 1 0 0 0 0 1 0 0 0 68 623 22 4 4 ABCE1 4 145109142 Missense_Mutation SNP C C3N-01074_T 34490663 145109142 45105413 110 22099 PRMT9 0 . GRCh38 4 147654189 147654189 + Nonsense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1708G>T p.Gly570Ter p.G570* ENST00000322396 9/12 258 207 51 396 396 0 strelka-varscan-mutect PRMT9,stop_gained,p.Gly570Ter,ENST00000322396,NM_001304458.1,NM_138364.3;TMEM184C,intron_variant,,ENST00000508208,;PRMT9,3_prime_UTR_variant,,ENST00000514886,;PRMT9,non_coding_transcript_exon_variant,,ENST00000510269,; A ENST00000322396 Transcript stop_gained 1951/3528 1708/2538 570/845 G/* Gga/Tga 1 -1 PRMT9 HGNC HGNC:25099 protein_coding YES CCDS3771.1 ENSP00000314396 Q6P2P2 UPI000004971D NM_001304458.1,NM_138364.3 9/12 PROSITE_profiles:PS51678 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 147654189 147654189 C A 1 0 0 0 0 0 1 0 0 12674 603 21 2 2 PRMT9 4 147654189 Nonsense_Mutation SNP C C3N-01074_T 2545047 147654189 42560366 111 22100 DCHS2 0 . GRCh38 4 154237040 154237040 + Nonsense_Mutation SNP C C A rs773711092 C3N-01074_T C3N-01074_N C C c.6247G>T p.Gly2083Ter p.G2083* ENST00000623607 25/25 267 211 56 391 391 0 strelka-varscan-mutect DCHS2,stop_gained,p.Gly2083Ter,ENST00000357232,;DCHS2,stop_gained,p.Gly2083Ter,ENST00000623607,NM_017639.3;RP11-9N12.2,non_coding_transcript_exon_variant,,ENST00000625026,;RP11-290O12.2,intron_variant,,ENST00000624941,;RP11-290O12.2,intron_variant,,ENST00000623325,; A ENST00000623607 Transcript stop_gained 6247/8912 6247/8751 2083/2916 G/* Gga/Tga rs773711092 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 25/25 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 SNV 1 1 PASS rs773711092 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 154237040 154237040 C A 1 0 0 0 0 0 1 0 0 4091 690 24 2 2 DCHS2 4 154237040 Nonsense_Mutation SNP C C3N-01074_T 6582851 154237040 35977515 112 22101 GRIA2 0 . GRCh38 4 157303580 157303580 + Silent SNP T T C novel C3N-01074_T C3N-01074_N T T c.258T>C p.= p.Y86Y ENST00000296526 3/16 208 155 53 258 258 0 strelka-varscan-mutect GRIA2,synonymous_variant,p.=,ENST00000296526,NM_000826.3;GRIA2,synonymous_variant,p.=,ENST00000393815,NM_001083620.1;GRIA2,synonymous_variant,p.=,ENST00000264426,NM_001083619.1;GRIA2,synonymous_variant,p.=,ENST00000507898,;GRIA2,synonymous_variant,p.=,ENST00000505888,;GRIA2,synonymous_variant,p.=,ENST00000509417,;GRIA2,synonymous_variant,p.=,ENST00000506284,;GRIA2,5_prime_UTR_variant,,ENST00000503437,;GRIA2,non_coding_transcript_exon_variant,,ENST00000504801,;GRIA2,synonymous_variant,p.=,ENST00000323661,;GRIA2,non_coding_transcript_exon_variant,,ENST00000471736,; C ENST00000296526 Transcript synonymous_variant 583/5621 258/2652 86/883 Y taT/taC 1 1 GRIA2 HGNC HGNC:4572 protein_coding YES CCDS3797.1 ENSP00000296526 P42262 UPI000002AA8D NM_000826.3 3/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF206,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 157303580 157303580 T C 1 0 0 0 0 0 0 0 1 6648 1471 51 5 5 GRIA2 4 157303580 Silent SNP T C3N-01074_T 3066540 157303580 32910975 113 22102 GPM6A 0 . GRCh38 4 175673745 175673745 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.322G>T p.Gly108Trp p.G108W ENST00000280187 4/8 174 142 32 151 151 0 strelka-varscan-mutect GPM6A,missense_variant,p.Gly108Trp,ENST00000280187,NM_005277.4;GPM6A,missense_variant,p.Gly108Trp,ENST00000393658,NM_201591.2;GPM6A,missense_variant,p.Gly97Trp,ENST00000506894,NM_201592.2;GPM6A,missense_variant,p.Gly101Trp,ENST00000515090,NM_001261448.1;GPM6A,missense_variant,p.Gly100Trp,ENST00000503397,;GPM6A,missense_variant,p.Gly108Trp,ENST00000513365,;GPM6A,missense_variant,p.Gly45Trp,ENST00000505561,;GPM6A,missense_variant,p.Gly45Trp,ENST00000502754,;GPM6A,missense_variant,p.Gly45Trp,ENST00000512610,;GPM6A,missense_variant,p.Gly45Trp,ENST00000513667,;GPM6A,missense_variant,p.Gly45Trp,ENST00000507520,;GPM6A,missense_variant,p.Gly45Trp,ENST00000512509,;GPM6A,missense_variant,p.Gly45Trp,ENST00000505375,;GPM6A,missense_variant,p.Gly45Trp,ENST00000509865,;GPM6A,downstream_gene_variant,,ENST00000512897,;GPM6A,downstream_gene_variant,,ENST00000507540,; A ENST00000280187 Transcript missense_variant 368/2854 322/837 108/278 G/W Ggg/Tgg COSM3602148 1 -1 GPM6A HGNC HGNC:4460 protein_coding YES CCDS3824.1 ENSP00000280187 P51674 UPI000012EAE1 NM_005277.4 deleterious(0.01) 4/8 hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF4,Pfam_domain:PF01275,Prints_domain:PR00214 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 175673745 175673745 C A 1 0 0 0 0 1 0 0 0 6517 594 21 2 2 GPM6A 4 175673745 Missense_Mutation SNP C C3N-01074_T 18370165 175673745 14540810 114 22103 PLEKHG4B 0 . GRCh38 5 174045 174045 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.3281C>A p.Ala1094Glu p.A1094E ENST00000283426 16/18 277 232 45 199 198 1 strelka-varscan-mutect PLEKHG4B,missense_variant,p.Ala1450Glu,ENST00000637938,;PLEKHG4B,missense_variant,p.Ala1094Glu,ENST00000283426,NM_052909.3;PLEKHG4B,non_coding_transcript_exon_variant,,ENST00000504041,; A ENST00000283426 Transcript missense_variant 3331/11515 3281/3816 1094/1271 A/E gCa/gAa 1 1 PLEKHG4B HGNC HGNC:29399 protein_coding YES CCDS34124.1 ENSP00000283426 Q96PX9 UPI0000D615EE NM_052909.3 deleterious(0) 16/18 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF119,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 174045 174045 C A 1 0 0 0 0 1 0 0 0 12165 710 25 2 2 PLEKHG4B 5 174045 Missense_Mutation SNP C C3N-01074_T 174045 181364214 115 22104 SDHA 0 . GRCh38 5 251428 251428 + Missense_Mutation SNP G G T rs752360961 C3N-01074_T C3N-01074_N G G c.1754G>T p.Arg585Leu p.R585L ENST00000264932 13/15 471 304 167 404 404 0 strelka-varscan-mutect SDHA,missense_variant,p.Arg585Leu,ENST00000264932,NM_004168.3;SDHA,missense_variant,p.Arg537Leu,ENST00000510361,NM_001294332.1;SDHA,missense_variant,p.Arg440Leu,ENST00000617470,;SDHA,missense_variant,p.Arg31Leu,ENST00000509564,;SDHA,intron_variant,,ENST00000504309,;SDHA,intron_variant,,ENST00000515815,;SDHA,non_coding_transcript_exon_variant,,ENST00000507522,;SDHA,intron_variant,,ENST00000509082,;SDHA,non_coding_transcript_exon_variant,,ENST00000511810,;SDHA,non_coding_transcript_exon_variant,,ENST00000503674,;SDHA,non_coding_transcript_exon_variant,,ENST00000505555,;SDHA,non_coding_transcript_exon_variant,,ENST00000514027,;SDHA,non_coding_transcript_exon_variant,,ENST00000515752,;SDHA,downstream_gene_variant,,ENST00000507266,; T ENST00000264932 Transcript missense_variant 1869/2390 1754/1995 585/664 R/L cGg/cTg rs752360961,COSM1067147 1 1 SDHA HGNC HGNC:10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 A0A024QZ30 UPI0000000C2C NM_004168.3 deleterious_low_confidence(0) 13/15 Gene3D:1.20.58.100,Pfam_domain:PF02910,PIRSF_domain:PIRSF000171,hmmpanther:PTHR11632,hmmpanther:PTHR11632:SF51,Superfamily_domains:SSF46977,TIGRFAM_domain:TIGR01812,TIGRFAM_domain:TIGR01816 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs752360961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 251428 251428 G T 1 0 0 0 0 1 0 0 0 14235 1116 39 1 1 SDHA 5 251428 Missense_Mutation SNP G C3N-01074_T 77383 251428 181286831 116 22105 ICE1 0 . GRCh38 5 5461175 5461175 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.1841A>T p.Asp614Val p.D614V ENST00000296564 13/19 140 81 59 224 223 1 strelka-varscan-mutect ICE1,missense_variant,p.Asp614Val,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 2063/7927 1841/6801 614/2266 D/V gAc/gTc 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 tolerated(0.22) 13/19 Low_complexity_(Seg):seg,hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 5461175 5461175 A T 1 0 0 0 0 1 0 0 0 7384 275 10 4 4 ICE1 5 5461175 Missense_Mutation SNP A C3N-01074_T 5209747 5461175 176077084 117 22106 SEMA5A 0 . GRCh38 5 9122788 9122788 + Missense_Mutation SNP G G T rs371178121 C3N-01074_T C3N-01074_N G G c.1649C>A p.Thr550Lys p.T550K ENST00000382496 14/23 87 40 47 93 93 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Thr550Lys,ENST00000382496,NM_003966.2; T ENST00000382496 Transcript missense_variant 2315/11762 1649/3225 550/1074 T/K aCg/aAg rs371178121,COSM1439143 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 tolerated(0.55) 14/23 PROSITE_profiles:PS50092,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs371178121 . 0 198 12 0 0 0 0 0 -20 0.9999929 1 1 1 0 T 3 4 73 9122788 9122788 G T 1 0 0 0 0 1 0 0 0 14313 1145 40 1 1 SEMA5A 5 9122788 Missense_Mutation SNP G C3N-01074_T 3661613 9122788 172415471 118 22107 CTNND2 0 . GRCh38 5 11732253 11732253 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.57C>A p.Asp19Glu p.D19E ENST00000304623 2/22 190 122 68 182 182 0 strelka-varscan-mutect CTNND2,missense_variant,p.Asp19Glu,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Asp5Glu,ENST00000508761,;CTNND2,missense_variant,p.Asp5Glu,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000511278,;CTNND2,non_coding_transcript_exon_variant,,ENST00000509868,;CTNND2,missense_variant,p.Asp19Glu,ENST00000513588,;CTNND2,missense_variant,p.Asp19Glu,ENST00000504499,; T ENST00000304623 Transcript missense_variant 247/5481 57/3678 19/1225 D/E gaC/gaA 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(1) 2/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 11732253 11732253 G T 1 0 0 0 0 1 0 0 0 3829 1252 44 2 2 CTNND2 5 11732253 Missense_Mutation SNP G C3N-01074_T 2609465 11732253 169806006 119 22108 FBXL7 0 . GRCh38 5 15936877 15936877 + Silent SNP C C A rs774533739 C3N-01074_T C3N-01074_N C C c.1167C>A p.= p.I389I ENST00000504595 4/4 204 187 17 259 258 1 strelka-varscan-mutect FBXL7,synonymous_variant,p.=,ENST00000504595,NM_012304.4;FBXL7,synonymous_variant,p.=,ENST00000329673,;FBXL7,synonymous_variant,p.=,ENST00000510662,NM_001278317.1;MIR887,downstream_gene_variant,,ENST00000401258,; A ENST00000504595 Transcript synonymous_variant 1648/4562 1167/1476 389/491 I atC/atA rs774533739 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 4/4 Gene3D:3.80.10.10,Pfam_domain:PF13516,hmmpanther:PTHR24006,SMART_domains:SM00367,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS rs774533739 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 15936877 15936877 C A 1 0 0 0 0 0 0 0 1 5587 816 29 2 2 FBXL7 5 15936877 Silent SNP C C3N-01074_T 4204624 15936877 165601382 120 22109 SPEF2 0 . GRCh38 5 35709123 35709123 + Splice_Site SNP T T C novel C3N-01074_T C3N-01074_N T T c.2839+2T>C p.X947_splice ENST00000356031 300 258 42 299 299 0 strelka-varscan SPEF2,splice_donor_variant,,ENST00000637569,;SPEF2,splice_donor_variant,,ENST00000440995,;SPEF2,splice_donor_variant,,ENST00000356031,NM_024867.3;SPEF2,synonymous_variant,p.=,ENST00000509059,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,downstream_gene_variant,,ENST00000504054,;SPEF2,non_coding_transcript_exon_variant,,ENST00000503074,;SPEF2,downstream_gene_variant,,ENST00000508817,; C ENST00000356031 Transcript splice_donor_variant -/5681 2839/5469 947/1822 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 19/36 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 73 35709123 35709123 T C 1 0 0 0 0 0 0 1 0 15386 1710 59 5 5 SPEF2 5 35709123 Splice_Site SNP T C3N-01074_T 19772246 35709123 145829136 121 22110 IL7R 0 . GRCh38 5 35867385 35867385 + Missense_Mutation SNP C C A rs772953676 C3N-01074_T C3N-01074_N C C c.301C>A p.Leu101Met p.L101M ENST00000303115 3/8 266 169 97 323 323 0 strelka-varscan IL7R,missense_variant,p.Leu101Met,ENST00000303115,NM_002185.3;IL7R,missense_variant,p.Leu101Met,ENST00000506850,;IL7R,missense_variant,p.Leu101Met,ENST00000511982,;IL7R,non_coding_transcript_exon_variant,,ENST00000511031,;IL7R,missense_variant,p.Leu101Met,ENST00000514217,; A ENST00000303115 Transcript missense_variant 430/4626 301/1380 101/459 L/M Ctg/Atg rs772953676 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 tolerated(0.07) 3/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 35867385 35867385 C A 1 0 0 0 0 1 0 0 0 7609 564 20 2 2 IL7R 5 35867385 Missense_Mutation SNP C C3N-01074_T 158262 35867385 145670874 122 22111 IL7R 0 . GRCh38 5 35876097 35876097 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.991C>A p.Gln331Lys p.Q331K ENST00000303115 8/8 483 412 71 476 476 0 strelka-varscan IL7R,missense_variant,p.Gln331Lys,ENST00000303115,NM_002185.3;IL7R,3_prime_UTR_variant,,ENST00000505093,;IL7R,downstream_gene_variant,,ENST00000506850,;IL7R,3_prime_UTR_variant,,ENST00000514217,;IL7R,non_coding_transcript_exon_variant,,ENST00000505875,;IL7R,downstream_gene_variant,,ENST00000509668,; A ENST00000303115 Transcript missense_variant 1120/4626 991/1380 331/459 Q/K Caa/Aaa 1 1 IL7R HGNC HGNC:6024 protein_coding YES CCDS3911.1 ENSP00000306157 P16871 UPI000013E861 NM_002185.3 tolerated(0.16) 8/8 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 35876097 35876097 C A 1 0 0 0 0 1 0 0 0 7609 711 25 2 2 IL7R 5 35876097 Missense_Mutation SNP C C3N-01074_T 8712 35876097 145662162 123 22112 LMBRD2 0 . GRCh38 5 36122935 36122935 + Missense_Mutation SNP C C A rs374425943 C3N-01074_T C3N-01074_N C C c.849G>T p.Met283Ile p.M283I ENST00000296603 8/18 200 164 36 259 258 1 strelka-varscan LMBRD2,missense_variant,p.Met283Ile,ENST00000296603,NM_001007527.1; A ENST00000296603 Transcript missense_variant 1312/8185 849/2088 283/695 M/I atG/atT rs374425943 1 -1 LMBRD2 HGNC HGNC:25287 protein_coding YES CCDS34145.1 ENSP00000296603 Q68DH5 UPI00001602FC NM_001007527.1 tolerated(0.19) 8/18 Pfam_domain:PF04791,hmmpanther:PTHR21355,hmmpanther:PTHR21355:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 36122935 36122935 C A 1 0 0 0 0 1 0 0 0 8767 594 21 2 2 LMBRD2 5 36122935 Missense_Mutation SNP C C3N-01074_T 246838 36122935 145415324 124 22113 FYB 0 . GRCh38 5 39201901 39201901 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1090G>T p.Gly364Cys p.G364C ENST00000512982 2/19 256 166 90 250 249 1 strelka-varscan FYB,missense_variant,p.Gly354Cys,ENST00000351578,NM_199335.3;FYB,missense_variant,p.Gly354Cys,ENST00000505428,NM_001465.4;FYB,missense_variant,p.Gly364Cys,ENST00000512982,NM_001243093.1;FYB,missense_variant,p.Gly354Cys,ENST00000515010,;FYB,downstream_gene_variant,,ENST00000506557,;FYB,downstream_gene_variant,,ENST00000510188,;FYB,downstream_gene_variant,,ENST00000504542,;FYB,downstream_gene_variant,,ENST00000509072,;FYB,downstream_gene_variant,,ENST00000512138,; A ENST00000512982 Transcript missense_variant 1176/2747 1090/2520 364/839 G/C Ggt/Tgt 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 deleterious(0) 2/19 hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF13,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 39201901 39201901 C A 1 0 0 0 0 1 0 0 0 5995 623 22 2 2 FYB 5 39201901 Missense_Mutation SNP C C3N-01074_T 3078966 39201901 142336358 125 22114 C7 0 . GRCh38 5 40959542 40959542 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1583C>A p.Pro528His p.P528H ENST00000313164 12/18 134 90 44 110 110 0 strelka-varscan C7,missense_variant,p.Pro528His,ENST00000313164,NM_000587.2;C7,upstream_gene_variant,,ENST00000486779,; A ENST00000313164 Transcript missense_variant 1942/4257 1583/2532 528/843 P/H cCc/cAc 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0) 12/18 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 40959542 40959542 C A 1 0 0 0 0 1 0 0 0 2134 623 22 2 2 C7 5 40959542 Missense_Mutation SNP C C3N-01074_T 1757641 40959542 140578717 126 22115 HSPB3 0 . GRCh38 5 54455880 54455880 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.91G>T p.Asp31Tyr p.D31Y ENST00000302005 1/1 426 355 71 427 427 0 strelka-varscan HSPB3,missense_variant,p.Asp31Tyr,ENST00000302005,NM_006308.2; T ENST00000302005 Transcript missense_variant 280/784 91/453 31/150 D/Y Gat/Tat 1 1 HSPB3 HGNC HGNC:5248 protein_coding YES CCDS3961.1 ENSP00000303394 Q12988 Q6ICS9 UPI000012CCD3 NM_006308.2 deleterious(0.05) 1/1 hmmpanther:PTHR11527,hmmpanther:PTHR11527:SF29 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 54455880 54455880 G T 1 0 0 0 0 1 0 0 0 7317 1174 41 2 2 HSPB3 5 54455880 Missense_Mutation SNP G C3N-01074_T 13496338 54455880 127082379 127 22116 ADGRV1 0 . GRCh38 5 90789700 90789700 + Splice_Site SNP A A T novel C3N-01074_T C3N-01074_N A A c.13894-2A>T p.X4632_splice ENST00000405460 92 76 16 119 119 0 strelka-varscan ADGRV1,splice_acceptor_variant,,ENST00000405460,NM_032119.3;ADGRV1,splice_acceptor_variant,,ENST00000425867,;ADGRV1,upstream_gene_variant,,ENST00000507314,; T ENST00000405460 Transcript splice_acceptor_variant -/19338 13894/18921 4632/6306 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 68/89 HIGH 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999389 1 1 1 0 T 5 4 73 90789700 90789700 A T 1 0 0 0 0 0 0 1 0 379 434 15 4 4 ADGRV1 5 90789700 Splice_Site SNP A C3N-01074_T 36333820 90789700 90748559 128 22117 NUDT12 0 . GRCh38 5 103560152 103560152 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.97A>T p.Ser33Cys p.S33C ENST00000230792 2/7 371 297 74 412 412 0 strelka-varscan-mutect NUDT12,missense_variant,p.Ser33Cys,ENST00000230792,NM_031438.3;NUDT12,missense_variant,p.Ser33Cys,ENST00000507423,NM_001300741.1;NUDT12,upstream_gene_variant,,ENST00000515407,;NUDT12,non_coding_transcript_exon_variant,,ENST00000508889,; A ENST00000230792 Transcript missense_variant 194/3492 97/1389 33/462 S/C Agt/Tgt 1 -1 NUDT12 HGNC HGNC:18826 protein_coding YES CCDS4096.1 ENSP00000230792 Q9BQG2 UPI0000073C53 NM_031438.3 deleterious(0.01) 2/7 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs1438400455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 103560152 103560152 T A 1 0 0 0 0 1 0 0 0 10792 1580 55 4 4 NUDT12 5 103560152 Missense_Mutation SNP T C3N-01074_T 12770452 103560152 77978107 129 22118 MCC 0 . GRCh38 5 113385094 113385094 + Frame_Shift_Del DEL G G - C3N-01074_T C3N-01074_N G G c.289delC p.Arg97AlafsTer13 p.R97Afs*13 ENST00000408903 2/19 329 275 54 381 381 0 sindel-varindel-pindel MCC,frameshift_variant,p.Arg97AlafsTer13,ENST00000408903,NM_001085377.1;CTD-2201G3.1,intron_variant,,ENST00000416046,; - ENST00000408903 Transcript frameshift_variant 705/3476 289/3060 97/1019 R/X Cgc/gc COSM1671809 1 -1 MCC HGNC HGNC:6935 protein_coding YES CCDS43351.1 ENSP00000386227 P23508 UPI00015E06EA NM_001085377.1 2/19 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR23347,hmmpanther:PTHR23347:SF4,SMART_domains:SM00054,Superfamily_domains:SSF47473 1 HIGH 1 deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 113385094 113385094 G - 1 0 1 0 1 0 0 0 0 9303 1116 39 0 0 MCC 5 113385094 Frame_Shift_Del DEL G C3N-01074_T 9824942 113385094 68153165 130 22119 SNCAIP 0 . GRCh38 5 122451288 122451288 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.2582T>A p.Leu861Gln p.L861Q ENST00000261367 12/14 344 284 60 438 438 0 strelka-varscan-mutect SNCAIP,missense_variant,p.Leu861Gln,ENST00000261367,NM_001308100.1;SNCAIP,missense_variant,p.Leu814Gln,ENST00000261368,NM_005460.2;SNCAIP,missense_variant,p.Leu754Gln,ENST00000509154,;SNCAIP,missense_variant,p.Leu448Gln,ENST00000379538,NM_001242935.1;SNCAIP,3_prime_UTR_variant,,ENST00000542191,;SNCAIP,3_prime_UTR_variant,,ENST00000504884,;SNCAIP,3_prime_UTR_variant,,ENST00000414317,;MGC32805,intron_variant,,ENST00000510972,;MGC32805,intron_variant,,ENST00000509993,;MGC32805,intron_variant,,ENST00000506053,;MGC32805,intron_variant,,ENST00000503529,;MGC32805,intron_variant,,ENST00000505546,;SNCAIP,3_prime_UTR_variant,,ENST00000395469,;SNCAIP,3_prime_UTR_variant,,ENST00000512385,;SNCAIP,3_prime_UTR_variant,,ENST00000508017,;SNCAIP,3_prime_UTR_variant,,ENST00000510658,;SNCAIP,3_prime_UTR_variant,,ENST00000509023,;SNCAIP,3_prime_UTR_variant,,ENST00000395466,;SNCAIP,3_prime_UTR_variant,,ENST00000512146,;SNCAIP,3_prime_UTR_variant,,ENST00000515215,;SNCAIP,non_coding_transcript_exon_variant,,ENST00000513719,; A ENST00000261367 Transcript missense_variant 4010/4986 2582/3051 861/1016 L/Q cTg/cAg 1 1 SNCAIP HGNC HGNC:11139 protein_coding YES CCDS78054.1 ENSP00000261367 Q9Y6H5 UPI000023272B NM_001308100.1 deleterious(0) 12/14 hmmpanther:PTHR22882 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 122451288 122451288 T A 1 0 0 0 0 1 0 0 0 15162 1580 55 4 4 SNCAIP 5 122451288 Missense_Mutation SNP T C3N-01074_T 9066194 122451288 59086971 131 22120 PCDHB7 0 . GRCh38 5 141174091 141174091 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1256T>A p.Ile419Asn p.I419N ENST00000231137 1/1 350 281 69 409 409 0 strelka-varscan PCDHB7,missense_variant,p.Ile419Asn,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000624802,;AC005754.7,upstream_gene_variant,,ENST00000625128,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; A ENST00000231137 Transcript missense_variant 1473/3765 1256/2382 419/793 I/N aTc/aAc 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 141174091 141174091 T A 1 0 0 0 0 1 0 0 0 11634 1435 50 4 4 PCDHB7 5 141174091 Missense_Mutation SNP T C3N-01074_T 18722803 141174091 40364168 132 22121 PCDHB10 0 . GRCh38 5 141193004 141193004 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.452C>A p.Ala151Glu p.A151E ENST00000239446 1/1 320 272 48 468 467 1 strelka-varscan PCDHB10,missense_variant,p.Ala151Glu,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,intron_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; A ENST00000239446 Transcript missense_variant 652/3290 452/2403 151/800 A/E gCa/gAa COSM4762082 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 tolerated_low_confidence(0.12) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 141193004 141193004 C A 1 0 0 0 0 1 0 0 0 11622 710 25 2 2 PCDHB10 5 141193004 Missense_Mutation SNP C C3N-01074_T 18913 141193004 40345255 133 22122 PCDHB10 0 . GRCh38 5 141193992 141193992 + Silent SNP G G T rs17844567 C3N-01074_T C3N-01074_N G G c.1440G>T p.= p.S480S ENST00000239446 1/1 127 103 24 221 220 1 strelka-varscan PCDHB10,synonymous_variant,p.=,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,intron_variant,,ENST00000625144,; T ENST00000239446 Transcript synonymous_variant 1640/3290 1440/2403 480/800 S tcG/tcT rs17844567,COSM1243494 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 LOW SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 141193992 141193992 G T 1 0 0 0 0 0 0 0 1 11622 1103 39 1 1 PCDHB10 5 141193992 Silent SNP G C3N-01074_T 988 141193992 40344267 134 22123 PCDHGA2 0 . GRCh38 5 141340870 141340870 + Frame_Shift_Del DEL G G - novel C3N-01074_T C3N-01074_N G G c.1900delG p.Asp634ThrfsTer99 p.D634Tfs*99 ENST00000394576 1/4 297 238 59 475 475 0 sindel-varindel-pindel PCDHGA2,frameshift_variant,p.Asp634ThrfsTer99,ENST00000394576,NM_018915.3;PCDHGA2,frameshift_variant,p.Asp634ThrfsTer99,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; - ENST00000394576 Transcript frameshift_variant 1899/4605 1899/2799 633/932 L/X ctG/ct 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 141340870 141340870 G - 1 0 1 0 1 0 0 0 0 11641 1335 47 0 0 PCDHGA2 5 141340870 Frame_Shift_Del DEL G C3N-01074_T 146878 141340870 40197389 135 22124 PCDHGA4 0 . GRCh38 5 141357157 141357157 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.2050C>T p.Pro684Ser p.P684S ENST00000571252 1/4 136 106 30 212 211 1 strelka-varscan PCDHGA4,missense_variant,p.Pro684Ser,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Pro684Ser,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 2133/4778 2050/2889 684/962 P/S Cct/Tct 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 141357157 141357157 C T 1 0 0 0 0 1 0 0 0 11643 623 22 3 3 PCDHGA4 5 141357157 Missense_Mutation SNP C C3N-01074_T 16287 141357157 40181102 136 22125 STK32A 0 . GRCh38 5 147323976 147323976 + Silent SNP A A G novel C3N-01074_T C3N-01074_N A A c.339A>G p.= p.Q113Q ENST00000398523 5/14 192 164 28 264 264 0 strelka-varscan STK32A,synonymous_variant,p.=,ENST00000397936,NM_001112724.1;STK32A,synonymous_variant,p.=,ENST00000398523,NM_001287740.1;STK32A,synonymous_variant,p.=,ENST00000626951,NM_145001.3;STK32A,non_coding_transcript_exon_variant,,ENST00000306304,; G ENST00000398523 Transcript synonymous_variant 510/1637 339/1224 113/407 Q caA/caG 1 1 STK32A HGNC HGNC:28317 protein_coding YES CCDS75351.1 ENSP00000381535 B7Z9H7 UPI0000044971 NM_001287740.1 5/14 PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF143,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 147323976 147323976 A G 1 0 0 0 0 0 0 0 1 15674 40 2 5 5 STK32A 5 147323976 Silent SNP A C3N-01074_T 5966819 147323976 34214283 137 22126 SH3TC2 0 . GRCh38 5 149027796 149027796 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1936C>A p.Leu646Ile p.L646I ENST00000515425 11/17 270 208 62 368 367 1 strelka-varscan SH3TC2,missense_variant,p.Leu646Ile,ENST00000515425,NM_024577.3;SH3TC2,missense_variant,p.Leu639Ile,ENST00000512049,;SH3TC2,downstream_gene_variant,,ENST00000513340,;SH3TC2,downstream_gene_variant,,ENST00000503071,;SH3TC2,missense_variant,p.Leu646Ile,ENST00000504690,;SH3TC2,3_prime_UTR_variant,,ENST00000323829,;SH3TC2,3_prime_UTR_variant,,ENST00000504517,;SH3TC2,3_prime_UTR_variant,,ENST00000513604,;SH3TC2,3_prime_UTR_variant,,ENST00000511307,;SH3TC2,3_prime_UTR_variant,,ENST00000510779,; T ENST00000515425 Transcript missense_variant 2038/4059 1936/3867 646/1288 L/I Cta/Ata 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 deleterious(0) 11/17 Gene3D:1.25.40.10,hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF2,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 149027796 149027796 G T 1 0 0 0 0 1 0 0 0 14521 991 35 2 2 SH3TC2 5 149027796 Missense_Mutation SNP G C3N-01074_T 1703820 149027796 32510463 138 22127 SLC26A2 0 . GRCh38 5 149980443 149980443 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.850G>T p.Gly284Cys p.G284C ENST00000286298 3/3 332 265 67 466 465 1 strelka-varscan SLC26A2,missense_variant,p.Gly284Cys,ENST00000286298,NM_000112.3;SLC26A2,intron_variant,,ENST00000503336,;SLC26A2,downstream_gene_variant,,ENST00000433184,; T ENST00000286298 Transcript missense_variant 1118/8080 850/2220 284/739 G/C Ggc/Tgc 1 1 SLC26A2 HGNC HGNC:10994 protein_coding YES CCDS4300.1 ENSP00000286298 P50443 UPI000013DE3D NM_000112.3 deleterious(0.01) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF16,Pfam_domain:PF00916,TIGRFAM_domain:TIGR00815 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 149980443 149980443 G T 1 0 0 0 0 1 0 0 0 14787 1232 43 2 2 SLC26A2 5 149980443 Missense_Mutation SNP G C3N-01074_T 952647 149980443 31557816 139 22128 NDST1 0 . GRCh38 5 150553255 150553255 + Missense_Mutation SNP G G A rs773934403 C3N-01074_T C3N-01074_N G G c.2572G>A p.Glu858Lys p.E858K ENST00000261797 15/15 447 356 91 482 481 1 strelka-varscan NDST1,missense_variant,p.Glu858Lys,ENST00000261797,NM_001543.4;NDST1,missense_variant,p.Glu801Lys,ENST00000523767,NM_001301063.1;NDST1,non_coding_transcript_exon_variant,,ENST00000521752,;NDST1,downstream_gene_variant,,ENST00000624156,; A ENST00000261797 Transcript missense_variant 3074/8030 2572/2649 858/882 E/K Gag/Aag rs773934403 1 1 NDST1 HGNC HGNC:7680 protein_coding YES CCDS34277.1 ENSP00000261797 P52848 UPI000012CDA5 NM_001543.4 tolerated(0.13) 15/15 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF30,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 150553255 150553255 G A 1 0 0 0 0 1 0 0 0 10276 1059 37 1 1 NDST1 5 150553255 Missense_Mutation SNP G C3N-01074_T 572812 150553255 30985004 140 22129 SGCD 0 . GRCh38 5 156759364 156759364 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.847C>A p.Gln283Lys p.Q283K ENST00000337851 9/9 75 58 17 113 113 0 strelka-varscan SGCD,missense_variant,p.Gln282Lys,ENST00000435422,NM_001128209.1;SGCD,missense_variant,p.Gln283Lys,ENST00000337851,NM_000337.5;SGCD,downstream_gene_variant,,ENST00000517913,NM_172244.2; A ENST00000337851 Transcript missense_variant 1366/1606 847/873 283/290 Q/K Cag/Aag 1 1 SGCD HGNC HGNC:10807 protein_coding YES CCDS47325.1 ENSP00000338343 Q92629 UPI00001678CF NM_000337.5 deleterious(0.04) 9/9 hmmpanther:PTHR12939:SF6,hmmpanther:PTHR12939 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 156759364 156759364 C A 1 0 0 0 0 1 0 0 0 14461 827 29 2 2 SGCD 5 156759364 Missense_Mutation SNP C C3N-01074_T 6206109 156759364 24778895 141 22130 FAM71B 0 . GRCh38 5 157165748 157165748 + Missense_Mutation SNP G G T rs767513722 C3N-01074_T C3N-01074_N G G c.421C>A p.Arg141Ser p.R141S ENST00000302938 1/2 183 141 42 267 267 0 strelka-varscan FAM71B,missense_variant,p.Arg141Ser,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,; T ENST00000302938 Transcript missense_variant 517/2515 421/1818 141/605 R/S Cgc/Agc rs767513722,COSM4683176 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 deleterious(0) 1/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2,Pfam_domain:PF12480 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999643 1 1 1 0 T 3 4 73 157165748 157165748 G T 1 0 0 0 0 1 0 0 0 5472 1087 38 1 1 FAM71B 5 157165748 Missense_Mutation SNP G C3N-01074_T 406384 157165748 24372511 142 22131 ATP10B 0 . GRCh38 5 160603965 160603965 + Missense_Mutation SNP C C A rs8180469 C3N-01074_T C3N-01074_N C C c.3237G>T p.Gln1079His p.Q1079H ENST00000327245 20/26 131 104 27 194 193 1 strelka-varscan ATP10B,missense_variant,p.Gln1079His,ENST00000327245,NM_025153.2;ATP10B,upstream_gene_variant,,ENST00000523758,;ATP10B,non_coding_transcript_exon_variant,,ENST00000517815,; A ENST00000327245 Transcript missense_variant,splice_region_variant 4084/7566 3237/4386 1079/1461 Q/H caG/caT rs8180469,COSM5334325 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0) 20/26 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF79,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF56784 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 160603965 160603965 C A 1 0 0 0 0 1 0 0 0 1269 695 24 2 2 ATP10B 5 160603965 Missense_Mutation SNP C C3N-01074_T 3438217 160603965 20934294 143 22132 WWC1 0 . GRCh38 5 168414401 168414401 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.995G>A p.Gly332Glu p.G332E ENST00000521089 9/23 254 193 61 308 308 0 strelka-varscan WWC1,missense_variant,p.Gly332Glu,ENST00000265293,NM_015238.2;WWC1,missense_variant,p.Gly294Glu,ENST00000393895,;WWC1,missense_variant,p.Gly332Glu,ENST00000521089,NM_001161662.1,NM_001161661.1;WWC1,missense_variant,p.Gly109Glu,ENST00000524228,;WWC1,non_coding_transcript_exon_variant,,ENST00000624315,;WWC1,non_coding_transcript_exon_variant,,ENST00000517425,;WWC1,non_coding_transcript_exon_variant,,ENST00000517646,;WWC1,non_coding_transcript_exon_variant,,ENST00000518334,;WWC1,downstream_gene_variant,,ENST00000519659,; A ENST00000521089 Transcript missense_variant 998/3562 995/3360 332/1119 G/E gGg/gAg 1 1 WWC1 HGNC HGNC:29435 protein_coding YES CCDS54945.1 ENSP00000427772 Q8IX03 UPI00017A7149 NM_001161662.1,NM_001161661.1 deleterious(0) 9/23 hmmpanther:PTHR14791,hmmpanther:PTHR14791:SF22 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 168414401 168414401 G A 1 0 0 0 0 1 0 0 0 17969 1232 43 3 3 WWC1 5 168414401 Missense_Mutation SNP G C3N-01074_T 7810436 168414401 13123858 144 22133 SLIT3 0 . GRCh38 5 169300511 169300511 + Splice_Site SNP A A T novel C3N-01074_T C3N-01074_N A A c.197+2T>A p.X66_splice ENST00000332966 57 41 16 78 78 0 strelka-varscan SLIT3,splice_donor_variant,,ENST00000519560,NM_003062.3;SLIT3,splice_donor_variant,,ENST00000332966,NM_001271946.1;SLIT3,splice_donor_variant,,ENST00000521130,;SLIT3,splice_donor_variant,,ENST00000518140,; T ENST00000332966 Transcript splice_donor_variant -/4895 197/4593 66/1530 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 1/35 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 73 169300511 169300511 A T 1 0 0 0 0 0 0 1 0 15032 173 6 4 4 SLIT3 5 169300511 Splice_Site SNP A C3N-01074_T 886110 169300511 12237748 145 22134 DOCK2 0 . GRCh38 5 169637334 169637334 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.8C>A p.Pro3His p.P3H ENST00000256935 1/52 36 25 11 52 52 0 strelka-varscan DOCK2,missense_variant,p.Pro3His,ENST00000256935,NM_004946.2;DOCK2,non_coding_transcript_exon_variant,,ENST00000522138,;DOCK2,missense_variant,p.Pro3His,ENST00000524185,; A ENST00000256935 Transcript missense_variant 88/6097 8/5493 3/1830 P/H cCc/cAc 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 tolerated(0.13) 1/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Gene3D:2.30.30.40 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 169637334 169637334 C A 1 0 0 0 0 1 0 0 0 4502 623 22 2 2 DOCK2 5 169637334 Missense_Mutation SNP C C3N-01074_T 336823 169637334 11900925 146 22135 FAF2 0 . GRCh38 5 176498973 176498973 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.899C>G p.Ser300Cys p.S300C ENST00000261942 9/11 182 146 36 159 159 0 strelka-varscan FAF2,missense_variant,p.Ser300Cys,ENST00000261942,NM_014613.2;FAF2,non_coding_transcript_exon_variant,,ENST00000504983,;FAF2,downstream_gene_variant,,ENST00000513627,; G ENST00000261942 Transcript missense_variant 952/4515 899/1338 300/445 S/C tCt/tGt 1 1 FAF2 HGNC HGNC:24666 protein_coding YES CCDS34296.1 ENSP00000261942 Q96CS3 UPI000007478A NM_014613.2 deleterious(0.02) 9/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23322,hmmpanther:PTHR23322:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 176498973 176498973 C G 1 0 0 0 0 1 0 0 0 5242 913 32 4 4 FAF2 5 176498973 Missense_Mutation SNP C C3N-01074_T 6861639 176498973 5039286 147 22136 DSP 0 . GRCh38 6 7585800 7585800 + Silent SNP G G C novel C3N-01074_T C3N-01074_N G G c.8538G>C p.= p.R2846R ENST00000379802 24/24 197 148 49 194 193 1 strelka-varscan-mutect DSP,synonymous_variant,p.=,ENST00000379802,NM_004415.2;DSP,synonymous_variant,p.=,ENST00000418664,NM_001008844.1;SNRNP48,upstream_gene_variant,,ENST00000342415,NM_152551.3;SNRNP48,upstream_gene_variant,,ENST00000634363,; C ENST00000379802 Transcript synonymous_variant 8879/9796 8538/8616 2846/2871 R cgG/cgC 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 24/24 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 7585800 7585800 G C 1 0 0 0 0 0 0 0 1 4602 1161 41 4 4 DSP 6 7585800 Silent SNP G C3N-01074_T 7585800 163220179 148 22137 ZBED9 0 . GRCh38 6 28586451 28586451 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.267G>T p.Glu89Asp p.E89D ENST00000452236 1/4 441 383 58 436 434 2 strelka-varscan ZBED9,missense_variant,p.Glu89Asp,ENST00000452236,NM_052923.1;RP5-1186N24.3,upstream_gene_variant,,ENST00000499525,;ZBED9,non_coding_transcript_exon_variant,,ENST00000526291,;ZBED9,intron_variant,,ENST00000530247,;ZBED9,downstream_gene_variant,,ENST00000524745,; A ENST00000452236 Transcript missense_variant 885/4877 267/3978 89/1325 E/D gaG/gaT 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50804,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 28586451 28586451 C A 1 0 0 0 0 1 0 0 0 18086 796 28 2 2 ZBED9 6 28586451 Missense_Mutation SNP C C3N-01074_T 21000651 28586451 142219528 149 22138 ZFP57 0 . GRCh38 6 29672911 29672911 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.1200C>A p.= p.S400S ENST00000488757 4/4 934 678 256 760 760 0 strelka-varscan ZFP57,synonymous_variant,p.=,ENST00000376883,;ZFP57,synonymous_variant,p.=,ENST00000488757,NM_001109809.2;ZFP57,synonymous_variant,p.=,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.3;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.3;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.5;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.4;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.3;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.3;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.2;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.2;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.1;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,; T ENST00000488757 Transcript synonymous_variant 1351/1870 1200/1611 400/536 S tcC/tcA 1 -1 ZFP57 HGNC HGNC:18791 protein_coding YES CCDS43436.2 ENSP00000418259 Q9NU63 UPI0001951170 NM_001109809.2 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF179,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 29672911 29672911 G T 1 0 0 0 0 0 0 0 1 18226 1335 47 2 2 ZFP57 6 29672911 Silent SNP G C3N-01074_T 1086460 29672911 141133068 150 22139 DXO 0 . GRCh38 6 31971566 31971566 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.110C>A p.Ser37Tyr p.S37Y ENST00000375349 2/7 445 328 117 320 319 1 strelka-varscan DXO,missense_variant,p.Ser37Tyr,ENST00000375349,;DXO,missense_variant,p.Ser37Tyr,ENST00000337523,NM_005510.3;DXO,missense_variant,p.Ser37Tyr,ENST00000375356,;STK19,intron_variant,,ENST00000460018,;SKIV2L,downstream_gene_variant,,ENST00000375394,NM_006929.4;STK19,upstream_gene_variant,,ENST00000375331,NM_004197.1;STK19,upstream_gene_variant,,ENST00000375333,NM_032454.1;SKIV2L,downstream_gene_variant,,ENST00000491994,;DXO,upstream_gene_variant,,ENST00000495340,;DXO,non_coding_transcript_exon_variant,,ENST00000474587,;DXO,non_coding_transcript_exon_variant,,ENST00000487914,;DXO,intron_variant,,ENST00000478221,;SKIV2L,downstream_gene_variant,,ENST00000471818,;SKIV2L,downstream_gene_variant,,ENST00000461915,;STK19,upstream_gene_variant,,ENST00000463823,;STK19,upstream_gene_variant,,ENST00000466336,;SKIV2L,downstream_gene_variant,,ENST00000470453,;DXO,missense_variant,p.Ser37Tyr,ENST00000480240,;DXO,non_coding_transcript_exon_variant,,ENST00000477826,;DXO,non_coding_transcript_exon_variant,,ENST00000473976,;DXO,non_coding_transcript_exon_variant,,ENST00000485557,;DXO,non_coding_transcript_exon_variant,,ENST00000498357,;DXO,non_coding_transcript_exon_variant,,ENST00000492946,;DXO,non_coding_transcript_exon_variant,,ENST00000491327,;DXO,non_coding_transcript_exon_variant,,ENST00000460058,;STK19,intron_variant,,ENST00000466132,;SKIV2L,downstream_gene_variant,,ENST00000465703,;SKIV2L,downstream_gene_variant,,ENST00000474839,;STK19,upstream_gene_variant,,ENST00000473983,;STK19,upstream_gene_variant,,ENST00000492583,;STK19,upstream_gene_variant,,ENST00000479644,;SKIV2L,downstream_gene_variant,,ENST00000483553,;STK19,upstream_gene_variant,,ENST00000491861,;STK19,upstream_gene_variant,,ENST00000519179,;STK19,upstream_gene_variant,,ENST00000483801,;STK19,upstream_gene_variant,,ENST00000469907,;SKIV2L,downstream_gene_variant,,ENST00000484835,;SKIV2L,downstream_gene_variant,,ENST00000494058,;STK19,upstream_gene_variant,,ENST00000478486,;SKIV2L,downstream_gene_variant,,ENST00000485349,;STK19,upstream_gene_variant,,ENST00000484540,;STK19,upstream_gene_variant,,ENST00000471028,; T ENST00000375349 Transcript missense_variant 522/1667 110/1191 37/396 S/Y tCt/tAt 1 -1 DXO HGNC HGNC:2992 protein_coding YES CCDS4732.1 ENSP00000364498 O77932 A0A024RCW8 UPI00000710F6 deleterious(0.01) 2/7 hmmpanther:PTHR12395,hmmpanther:PTHR12395:SF9 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 31971566 31971566 G T 1 0 0 0 0 1 0 0 0 4660 942 33 2 2 DXO 6 31971566 Missense_Mutation SNP G C3N-01074_T 2298655 31971566 138834413 151 22140 PRRT1 0 . GRCh38 6 32150480 32150480 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.446C>T p.Pro149Leu p.P149L ENST00000211413 2/4 84 72 12 65 65 0 strelka-varscan PRRT1,missense_variant,p.Pro149Leu,ENST00000211413,NM_030651.3;PRRT1,missense_variant,p.Pro68Leu,ENST00000375150,;PPT2,upstream_gene_variant,,ENST00000395523,;PPT2,upstream_gene_variant,,ENST00000324816,NM_001204103.1,NM_005155.6;PPT2,upstream_gene_variant,,ENST00000375137,;PPT2,upstream_gene_variant,,ENST00000361568,NM_138717.2;PPT2,upstream_gene_variant,,ENST00000375143,;PPT2,upstream_gene_variant,,ENST00000414204,;PPT2,upstream_gene_variant,,ENST00000424499,;PRRT1,downstream_gene_variant,,ENST00000428778,;PRRT1,intron_variant,,ENST00000472641,;PRRT1,upstream_gene_variant,,ENST00000467780,;PPT2-EGFL8,upstream_gene_variant,,ENST00000453656,;PPT2,upstream_gene_variant,,ENST00000493548,;PRRT1,downstream_gene_variant,,ENST00000486917,;PPT2,upstream_gene_variant,,ENST00000478521,;PRRT1,downstream_gene_variant,,ENST00000485392,;PRRT1,downstream_gene_variant,,ENST00000498575,;PRRT1,downstream_gene_variant,,ENST00000497552,;PRRT1,downstream_gene_variant,,ENST00000475826,;PRRT1,downstream_gene_variant,,ENST00000494332,;PPT2,upstream_gene_variant,,ENST00000465047,;PRRT1,non_coding_transcript_exon_variant,,ENST00000495191,;PPT2-EGFL8,upstream_gene_variant,,ENST00000422437,;PPT2-EGFL8,upstream_gene_variant,,ENST00000428388,;PPT2-EGFL8,upstream_gene_variant,,ENST00000583227,;PPT2-EGFL8,upstream_gene_variant,,ENST00000585246,;PPT2,upstream_gene_variant,,ENST00000436118,; A ENST00000211413 Transcript missense_variant 571/1909 446/921 149/306 P/L cCc/cTc 1 -1 PRRT1 HGNC HGNC:13943 protein_coding YES CCDS4739.1 ENSP00000211413 Q99946 UPI000012FFED NM_030651.3 deleterious_low_confidence(0.02) 2/4 hmmpanther:PTHR14948,hmmpanther:PTHR14948:SF21 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 32150480 32150480 G A 1 0 0 0 0 1 0 0 0 12755 1232 43 3 3 PRRT1 6 32150480 Missense_Mutation SNP G C3N-01074_T 178914 32150480 138655499 152 22141 PI16 0 . GRCh38 6 36963612 36963612 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.1270G>A p.Gly424Ser p.G424S ENST00000373674 5/7 106 82 24 117 117 0 strelka-varscan PI16,missense_variant,p.Gly424Ser,ENST00000373674,NM_153370.2;PI16,missense_variant,p.Gly424Ser,ENST00000611814,NM_001199159.1;MTCH1,downstream_gene_variant,,ENST00000373627,NM_001271641.1;MTCH1,downstream_gene_variant,,ENST00000373616,NM_014341.2;PI16,intron_variant,,ENST00000491324,; A ENST00000373674 Transcript missense_variant,splice_region_variant 1598/2190 1270/1392 424/463 G/S Ggt/Agt 1 1 PI16 HGNC HGNC:21245 protein_coding YES CCDS34440.1 ENSP00000362778 Q6UXB8 UPI000004C657 NM_153370.2 deleterious(0.02) 5/7 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 A 3 1 73 36963612 36963612 G A 1 0 0 0 0 1 0 0 0 11958 1014 35 3 3 PI16 6 36963612 Missense_Mutation SNP G C3N-01074_T 4813132 36963612 133842367 153 22142 LRFN2 0 . GRCh38 6 40392425 40392425 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.1888G>T p.Gly630Trp p.G630W ENST00000338305 3/3 161 111 50 162 162 0 strelka-varscan LRFN2,missense_variant,p.Gly630Trp,ENST00000338305,NM_020737.2; A ENST00000338305 Transcript missense_variant 2431/3270 1888/2370 630/789 G/W Ggg/Tgg COSM3697857 1 -1 LRFN2 HGNC HGNC:21226 protein_coding YES CCDS34443.1 ENSP00000345985 Q9ULH4 UPI00001C1E47 NM_020737.2 deleterious(0.02) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF25 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 40392425 40392425 C A 1 0 0 0 0 1 0 0 0 8832 594 21 2 2 LRFN2 6 40392425 Missense_Mutation SNP C C3N-01074_T 3428813 40392425 130413554 154 22143 EYS 0 . GRCh38 6 64590858 64590858 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.5009C>A p.Pro1670His p.P1670H ENST00000370621 26/44 208 152 56 276 275 1 strelka-varscan-mutect EYS,missense_variant,p.Pro1670His,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Pro1670His,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; T ENST00000370621 Transcript missense_variant 5536/10485 5009/9498 1670/3165 P/H cCt/cAt 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious_low_confidence(0) 26/44 MODERATE 1 SNV 1 1 PASS rs1477933157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 64590858 64590858 G T 1 0 0 0 0 1 0 0 0 5200 1000 35 2 2 EYS 6 64590858 Missense_Mutation SNP G C3N-01074_T 24198433 64590858 106215121 155 22144 EYS 0 . GRCh38 6 64591333 64591333 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.4534G>T p.Ala1512Ser p.A1512S ENST00000370621 26/44 503 386 117 501 500 1 strelka-varscan-mutect EYS,missense_variant,p.Ala1512Ser,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Ala1512Ser,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; A ENST00000370621 Transcript missense_variant 5061/10485 4534/9498 1512/3165 A/S Gct/Tct 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated_low_confidence(0.16) 26/44 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 64591333 64591333 C A 1 0 0 0 0 1 0 0 0 5200 797 28 2 2 EYS 6 64591333 Missense_Mutation SNP C C3N-01074_T 475 64591333 106214646 156 22145 SENP6 0 . GRCh38 6 75697501 75697501 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2272G>T p.Val758Leu p.V758L ENST00000447266 18/24 152 129 23 192 192 0 strelka-varscan-mutect SENP6,missense_variant,p.Val758Leu,ENST00000447266,NM_015571.3;SENP6,missense_variant,p.Val751Leu,ENST00000370010,NM_001100409.2;SENP6,missense_variant,p.Val374Leu,ENST00000503501,;SENP6,non_coding_transcript_exon_variant,,ENST00000474906,; T ENST00000447266 Transcript missense_variant 2750/6501 2272/3339 758/1112 V/L Gta/Tta 1 1 SENP6 HGNC HGNC:20944 protein_coding YES CCDS47454.1 ENSP00000402527 Q9GZR1 UPI0000141B65 NM_015571.3 deleterious(0) 18/24 Gene3D:1euvA02,Pfam_domain:PF02902,PROSITE_profiles:PS50600,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF350,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 75697501 75697501 G T 1 0 0 0 0 1 0 0 0 14326 1377 48 2 2 SENP6 6 75697501 Missense_Mutation SNP G C3N-01074_T 11106168 75697501 95108478 157 22146 TTK 0 . GRCh38 6 80039773 80039773 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2208G>T p.Gln736His p.Q736H ENST00000369798 19/22 215 145 70 248 247 1 strelka-varscan-mutect TTK,missense_variant,p.Gln735His,ENST00000509894,;TTK,missense_variant,p.Gln735His,ENST00000230510,NM_001166691.1;TTK,missense_variant,p.Gln736His,ENST00000369798,NM_003318.4;TTK,non_coding_transcript_exon_variant,,ENST00000504590,; T ENST00000369798 Transcript missense_variant 2319/3010 2208/2574 736/857 Q/H caG/caT 1 1 TTK HGNC HGNC:12401 protein_coding YES CCDS4993.1 ENSP00000358813 P33981 UPI0000073C7B NM_003318.4 tolerated(1) 19/22 PROSITE_profiles:PS50011,hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF21,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 80039773 80039773 G T 1 0 0 0 0 1 0 0 0 17232 933 33 2 2 TTK 6 80039773 Missense_Mutation SNP G C3N-01074_T 4342272 80039773 90766206 158 22147 TBX18 0 . GRCh38 6 84763941 84763941 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.241G>T p.Ala81Ser p.A81S ENST00000369663 1/8 173 117 56 174 174 0 strelka-varscan-mutect TBX18,missense_variant,p.Ala81Ser,ENST00000369663,NM_001080508.2;TBX18,upstream_gene_variant,,ENST00000606784,;TBX18,upstream_gene_variant,,ENST00000606325,;TBX18,upstream_gene_variant,,ENST00000606621,;TBX18,upstream_gene_variant,,ENST00000606521,; A ENST00000369663 Transcript missense_variant 579/6245 241/1824 81/607 A/S Gcg/Tcg COSM5622482 1 -1 TBX18 HGNC HGNC:11595 protein_coding YES CCDS34495.1 ENSP00000358677 O95935 UPI00001A3A8A NM_001080508.2 tolerated(0.8) 1/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF20 1 MODERATE 1 SNV 1 1 1 PASS rs1045759239 . 0 208 0 0 0 2 0 0 -6.304817 0.8031158 1 1 1 0 A 3 1 73 84763941 84763941 C A 1 0 0 0 0 1 0 0 0 16058 739 26 2 2 TBX18 6 84763941 Missense_Mutation SNP C C3N-01074_T 4724168 84763941 86042038 159 22148 ASCC3 0 . GRCh38 6 100601932 100601932 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.5181A>T p.Leu1727Phe p.L1727F ENST00000369162 34/42 319 271 48 303 303 0 strelka-varscan-mutect ASCC3,missense_variant,p.Leu1727Phe,ENST00000369162,NM_006828.3; A ENST00000369162 Transcript missense_variant 5526/8146 5181/6609 1727/2202 L/F ttA/ttT 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 deleterious(0.02) 34/42 PROSITE_profiles:PS51194,PIRSF_domain:PIRSF039073,Superfamily_domains:SSF46785 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 100601932 100601932 T A 1 0 0 0 0 1 0 0 0 1175 1420 49 4 4 ASCC3 6 100601932 Missense_Mutation SNP T C3N-01074_T 15837991 100601932 70204047 160 22149 LAMA4 0 . GRCh38 6 112216464 112216464 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.201C>A p.Cys67Ter p.C67* ENST00000230538 3/39 507 433 74 520 518 2 strelka-varscan-mutect LAMA4,stop_gained,p.Cys67Ter,ENST00000230538,NM_001105206.2;LAMA4,stop_gained,p.Cys67Ter,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,stop_gained,p.Cys67Ter,ENST00000389463,;LAMA4,stop_gained,p.Cys67Ter,ENST00000424408,;LAMA4,stop_gained,p.Cys67Ter,ENST00000521398,;LAMA4,stop_gained,p.Cys67Ter,ENST00000431543,;LAMA4,stop_gained,p.Cys67Ter,ENST00000519932,;LAMA4,stop_gained,p.Cys67Ter,ENST00000243219,;LAMA4,stop_gained,p.Cys67Ter,ENST00000521690,;RP1-142L7.9,downstream_gene_variant,,ENST00000603682,;LAMA4,non_coding_transcript_exon_variant,,ENST00000524032,;LAMA4,upstream_gene_variant,,ENST00000423735,; T ENST00000230538 Transcript stop_gained 599/6547 201/5472 67/1823 C/* tgC/tgA 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 3/39 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 112216464 112216464 G T 1 0 0 0 0 0 1 0 0 8512 1333 46 2 2 LAMA4 6 112216464 Nonsense_Mutation SNP G C3N-01074_T 11614532 112216464 58589515 161 22150 VGLL2 0 . GRCh38 6 117270984 117270984 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.833C>A p.Ala278Asp p.A278D ENST00000326274 3/4 21 15 6 27 27 0 strelka-varscan-mutect VGLL2,missense_variant,p.Ala278Asp,ENST00000326274,NM_182645.3;VGLL2,intron_variant,,ENST00000352536,NM_153453.1; A ENST00000326274 Transcript missense_variant 1023/2212 833/954 278/317 A/D gCc/gAc 1 1 VGLL2 HGNC HGNC:20232 protein_coding YES CCDS5115.1 ENSP00000320957 Q8N8G2 UPI000006FF57 NM_182645.3 tolerated(0.09) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15950,hmmpanther:PTHR15950:SF17 MODERATE 1 SNV 1 1 PASS rs1319613362 . 74 136 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 117270984 117270984 C A 1 0 0 0 0 1 0 0 0 17705 739 26 2 2 VGLL2 6 117270984 Missense_Mutation SNP C C3N-01074_T 5054520 117270984 53534995 162 22151 NUS1 0 . GRCh38 6 117675971 117675971 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.301A>T p.Met101Leu p.M101L ENST00000368494 1/5 234 196 38 314 313 1 strelka-varscan-mutect NUS1,missense_variant,p.Met101Leu,ENST00000368494,NM_138459.3; T ENST00000368494 Transcript missense_variant 470/4676 301/882 101/293 M/L Atg/Ttg 1 1 NUS1 HGNC HGNC:21042 protein_coding YES CCDS5118.1 ENSP00000357480 Q96E22 UPI000006FECA NM_138459.3 tolerated(0.56) 1/5 Gene3D:1uehA00,hmmpanther:PTHR21528,hmmpanther:PTHR21528:SF0,Superfamily_domains:SSF64005 MODERATE 1 SNV 1 1 PASS rs988797644 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 117675971 117675971 A T 1 0 0 0 0 1 0 0 0 10843 449 16 4 4 NUS1 6 117675971 Missense_Mutation SNP A C3N-01074_T 404987 117675971 53130008 163 22152 TRDN 0 . GRCh38 6 123438117 123438117 + Missense_Mutation SNP C C T C3N-01074_T C3N-01074_N C C c.997G>A p.Glu333Lys p.E333K ENST00000334268 12/41 182 116 66 177 175 2 strelka-varscan-mutect TRDN,missense_variant,p.Glu333Lys,ENST00000334268,NM_006073.3;RP11-532N4.2,intron_variant,,ENST00000587106,;RP11-532N4.2,upstream_gene_variant,,ENST00000625262,;RP11-532N4.2,upstream_gene_variant,,ENST00000629087,;RP11-532N4.2,upstream_gene_variant,,ENST00000418467,;RP11-532N4.2,upstream_gene_variant,,ENST00000589182,;RP11-532N4.2,upstream_gene_variant,,ENST00000628939,;RP11-532N4.2,upstream_gene_variant,,ENST00000587049,;RP11-532N4.2,upstream_gene_variant,,ENST00000610906,;RP11-532N4.2,upstream_gene_variant,,ENST00000618357,;RP11-532N4.2,upstream_gene_variant,,ENST00000434768,;RP11-532N4.2,upstream_gene_variant,,ENST00000625415,;RP11-532N4.2,upstream_gene_variant,,ENST00000619147,;RP11-532N4.2,upstream_gene_variant,,ENST00000615864,;RP11-532N4.2,upstream_gene_variant,,ENST00000427828,; T ENST00000334268 Transcript missense_variant 1315/4770 997/2190 333/729 E/K Gaa/Aaa COSM1072861 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 tolerated_low_confidence(0.1) 12/41 Low_complexity_(Seg):seg,hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 123438117 123438117 C T 1 0 0 0 0 1 0 0 0 16957 927 32 3 3 TRDN 6 123438117 Missense_Mutation SNP C C3N-01074_T 5762146 123438117 47367862 164 22153 ARFGEF3 0 . GRCh38 6 138334778 138334778 + Missense_Mutation SNP A A C novel C3N-01074_T C3N-01074_N A A c.5932A>C p.Ser1978Arg p.S1978R ENST00000251691 33/34 109 96 13 158 158 0 strelka-varscan-mutect ARFGEF3,missense_variant,p.Ser1978Arg,ENST00000251691,NM_020340.4; C ENST00000251691 Transcript missense_variant 6098/14877 5932/6534 1978/2177 S/R Agc/Cgc 1 1 ARFGEF3 HGNC HGNC:21213 protein_coding YES CCDS5189.2 ENSP00000251691 Q5TH69 UPI000150AF4A NM_020340.4 tolerated(0.41) 33/34 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 138334778 138334778 A C 1 0 0 0 0 1 0 0 0 977 304 11 5 5 ARFGEF3 6 138334778 Missense_Mutation SNP A C3N-01074_T 14896661 138334778 32471201 165 22154 NMBR 0 . GRCh38 6 142075745 142075745 + Missense_Mutation SNP G G C rs768869842 C3N-01074_T C3N-01074_N G G c.1076C>G p.Ala359Gly p.A359G ENST00000258042 3/3 316 259 57 297 297 0 strelka-varscan-mutect NMBR,missense_variant,p.Ala359Gly,ENST00000258042,NM_002511.2;NMBR,splice_region_variant,,ENST00000480652,; C ENST00000258042 Transcript missense_variant 1217/1354 1076/1173 359/390 A/G gCg/gGg rs768869842 1 -1 NMBR HGNC HGNC:7843 protein_coding YES CCDS5196.1 ENSP00000258042 P28336 UPI000013CFAB NM_002511.2 tolerated(0.13) 3/3 hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF53,Prints_domain:PR00639 MODERATE 1 SNV 1 1 PASS rs768869842 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 142075745 142075745 G C 1 0 0 0 0 1 0 0 0 10525 1087 38 4 4 NMBR 6 142075745 Missense_Mutation SNP G C3N-01074_T 3740967 142075745 28730234 166 22155 PEX3 0 . GRCh38 6 143468159 143468161 + In_Frame_Del DEL ATA ATA - novel C3N-01074_T C3N-01074_N ATA ATA c.329_331delTAA p.Ile110del p.I110del ENST00000367591 4/12 281 236 45 324 324 0 sindel-varindel-pindel PEX3,inframe_deletion,p.Ile110del,ENST00000367591,NM_003630.2;PEX3,inframe_deletion,p.Ile66del,ENST00000367592,; - ENST00000367591 Transcript inframe_deletion 388-390/1969 325-327/1122 109/373 I/- ATA/- 1 1 PEX3 HGNC HGNC:8858 protein_coding YES CCDS5199.1 ENSP00000356563 P56589 UPI00001316E1 NM_003630.2 4/12 hmmpanther:PTHR28080,hmmpanther:PTHR28080:SF1,Pfam_domain:PF04882 MODERATE 1 deletion 1 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 143468159 143468159 ATA - 1 0 1 0 1 0 0 0 0 11837 333 12 0 0 PEX3 6 143468159 In_Frame_Del DEL ATA C3N-01074_T 1392414 143468159 27337820 167 22156 SYNE1 0 . GRCh38 6 152505226 152505226 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.753G>T p.= p.G251G ENST00000367255 9/146 387 333 54 339 339 0 strelka-varscan-mutect SYNE1,synonymous_variant,p.=,ENST00000367255,NM_182961.3;SYNE1,synonymous_variant,p.=,ENST00000423061,NM_033071.3;SYNE1,synonymous_variant,p.=,ENST00000341594,;SYNE1,synonymous_variant,p.=,ENST00000367248,;SYNE1,synonymous_variant,p.=,ENST00000367253,;SYNE1,synonymous_variant,p.=,ENST00000413186,;SYNE1,synonymous_variant,p.=,ENST00000537750,;SYNE1,synonymous_variant,p.=,ENST00000466159,;SYNE1,synonymous_variant,p.=,ENST00000610489,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; A ENST00000367255 Transcript synonymous_variant 1355/27748 753/26394 251/8797 G ggG/ggT 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 9/146 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS rs1259174577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 152505226 152505226 C A 1 0 0 0 0 0 0 0 1 15837 842 30 2 2 SYNE1 6 152505226 Silent SNP C C3N-01074_T 9037067 152505226 18300753 168 22157 ELFN1 0 . GRCh38 7 1746115 1746115 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1519G>T p.Glu507Ter p.E507* ENST00000424383 3/3 130 87 43 144 144 0 strelka-varscan-mutect ELFN1,stop_gained,p.Glu507Ter,ENST00000424383,;ELFN1,stop_gained,p.Glu507Ter,ENST00000561626,NM_001128636.2;ELFN1-AS1,upstream_gene_variant,,ENST00000453348,;ELFN1-AS1,upstream_gene_variant,,ENST00000415399,; T ENST00000424383 Transcript stop_gained 2006/3845 1519/2487 507/828 E/* Gag/Tag 1 1 ELFN1 HGNC HGNC:33154 protein_coding YES CCDS59046.1 ENSP00000456548 P0C7U0 UPI0000251E11 3/3 hmmpanther:PTHR24367:SF34,hmmpanther:PTHR24367 HIGH SNV 5 1 PASS rs1205018884 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 1746115 1746115 G T 1 0 0 0 0 0 1 0 0 4891 1175 41 2 2 ELFN1 7 1746115 Nonsense_Mutation SNP G C3N-01074_T 1746115 157599858 169 22158 SDK1 0 . GRCh38 7 4220267 4220267 + Nonsense_Mutation SNP G G T rs200608621 C3N-01074_T C3N-01074_N G G c.5698G>T p.Glu1900Ter p.E1900* ENST00000404826 39/45 108 76 32 95 95 0 strelka-varscan-mutect SDK1,stop_gained,p.Glu1900Ter,ENST00000404826,NM_152744.3;SDK1,stop_gained,p.Glu1900Ter,ENST00000615806,;SDK1,stop_gained,p.Glu1880Ter,ENST00000389531,;SDK1,non_coding_transcript_exon_variant,,ENST00000476701,; T ENST00000404826 Transcript stop_gained 5837/10397 5698/6642 1900/2213 E/* Gag/Tag rs200608621,COSM4776107 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 39/45 hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 0,1 HIGH 1 SNV 5 0,1 1 PASS rs200608621 . 0 201 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 4 4 73 4220267 4220267 G T 1 0 0 0 0 0 1 0 0 14243 1072 37 1 1 SDK1 7 4220267 Nonsense_Mutation SNP G C3N-01074_T 2474152 4220267 155125706 170 22159 PAPOLB 0 . GRCh38 7 4860325 4860325 + Frame_Shift_Del DEL G G - novel C3N-01074_T C3N-01074_N G G c.1486delC p.Gln496SerfsTer21 p.Q496Sfs*21 ENST00000404991 1/1 371 327 44 413 413 0 sindel-varindel-pindel PAPOLB,frameshift_variant,p.Gln496SerfsTer21,ENST00000404991,NM_020144.4;RADIL,intron_variant,,ENST00000399583,NM_018059.4;RADIL,intron_variant,,ENST00000445392,; - ENST00000404991 Transcript frameshift_variant 1670/4262 1486/1914 496/637 Q/X Cag/ag 1 -1 PAPOLB HGNC HGNC:15970 protein_coding YES CCDS78202.1 ENSP00000384700 Q9NRJ5 A4D1Z6 UPI00005CE292 NM_020144.4 1/1 PIRSF_domain:PIRSF018425,hmmpanther:PTHR10682,hmmpanther:PTHR10682:SF19,Superfamily_domains:SSF55003 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 4860325 4860325 G - 1 0 1 0 1 0 0 0 0 11510 1357 47 0 0 PAPOLB 7 4860325 Frame_Shift_Del DEL G C3N-01074_T 640058 4860325 154485648 171 22160 TNRC18 0 . GRCh38 7 5388916 5388916 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.908G>T p.Gly303Val p.G303V ENST00000430969 5/30 228 156 72 151 150 1 strelka-varscan-mutect TNRC18,missense_variant,p.Gly303Val,ENST00000399537,;TNRC18,missense_variant,p.Gly303Val,ENST00000430969,NM_001080495.2;TNRC18,downstream_gene_variant,,ENST00000399434,;TNRC18,upstream_gene_variant,,ENST00000413081,;TNRC18,downstream_gene_variant,,ENST00000434361,; A ENST00000430969 Transcript missense_variant 1257/10562 908/8907 303/2968 G/V gGg/gTg 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 tolerated(0.33) 5/30 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1006921088 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 5388916 5388916 C A 1 0 0 0 0 1 0 0 0 16812 623 22 2 2 TNRC18 7 5388916 Missense_Mutation SNP C C3N-01074_T 528591 5388916 153957057 172 22161 PKD1L1 0 . GRCh38 7 47835029 47835029 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.6065G>A p.Gly2022Glu p.G2022E ENST00000289672 39/57 133 97 36 119 119 0 strelka-varscan-mutect PKD1L1,missense_variant,p.Gly2022Glu,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; T ENST00000289672 Transcript missense_variant 6116/9092 6065/8550 2022/2849 G/E gGg/gAg 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.46) 39/57 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF145 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 47835029 47835029 C T 1 0 0 0 0 1 0 0 0 12060 623 22 3 3 PKD1L1 7 47835029 Missense_Mutation SNP C C3N-01074_T 42446113 47835029 111510944 173 22162 CLIP2 0 . GRCh38 7 74338709 74338709 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.383G>A p.Arg128His p.R128H ENST00000223398 3/17 343 282 61 351 351 0 strelka-varscan-mutect CLIP2,missense_variant,p.Arg128His,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Arg128His,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Arg128His,ENST00000395060,; A ENST00000223398 Transcript missense_variant 710/5563 383/3141 128/1046 R/H cGc/cAc 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 deleterious(0) 3/17 Gene3D:2.30.30.190,Pfam_domain:PF01302,PROSITE_patterns:PS00845,PROSITE_profiles:PS50245,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10,SMART_domains:SM01052,Superfamily_domains:SSF74924 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 74338709 74338709 G A 1 0 0 0 0 1 0 0 0 3302 1087 38 1 1 CLIP2 7 74338709 Missense_Mutation SNP G C3N-01074_T 26503680 74338709 85007264 174 22163 MAGI2 0 . GRCh38 7 78521627 78521627 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.557C>A p.Pro186Gln p.P186Q ENST00000354212 4/22 250 191 59 274 273 1 strelka-varscan-mutect MAGI2,missense_variant,p.Pro186Gln,ENST00000354212,NM_012301.3;MAGI2,missense_variant,p.Pro186Gln,ENST00000419488,NM_001301128.1;MAGI2,missense_variant,p.Pro23Gln,ENST00000629359,;MAGI2,missense_variant,p.Pro48Gln,ENST00000628980,;MAGI2,missense_variant,p.Pro48Gln,ENST00000535697,;MAGI2,missense_variant,p.Pro186Gln,ENST00000637441,;MAGI2,missense_variant,p.Pro186Gln,ENST00000522391,;MAGI2,missense_variant,p.Pro23Gln,ENST00000626691,;MAGI2,missense_variant,p.Pro23Gln,ENST00000628781,;MAGI2,missense_variant,p.Pro18Gln,ENST00000636717,;MAGI2,5_prime_UTR_variant,,ENST00000630991,;MAGI2,non_coding_transcript_exon_variant,,ENST00000635863,;MAGI2,non_coding_transcript_exon_variant,,ENST00000637728,;MAGI2,non_coding_transcript_exon_variant,,ENST00000517762,;MAGI2,upstream_gene_variant,,ENST00000637824,;MAGI2,missense_variant,p.Pro23Gln,ENST00000637486,; T ENST00000354212 Transcript missense_variant 811/6880 557/4368 186/1455 P/Q cCa/cAa 1 -1 MAGI2 HGNC HGNC:18957 protein_coding YES CCDS5594.1 ENSP00000346151 Q86UL8 UPI00001615D2 NM_012301.3 deleterious(0) 4/22 Low_complexity_(Seg):seg,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF27,Pfam_domain:PF00625,Gene3D:3.30.63.10,SMART_domains:SM00072,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 78521627 78521627 G T 1 0 0 0 0 1 0 0 0 9109 1348 47 2 2 MAGI2 7 78521627 Missense_Mutation SNP G C3N-01074_T 4182918 78521627 80824346 175 22164 CACNA2D1 0 . GRCh38 7 81959745 81959745 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.3051A>T p.= p.R1017R ENST00000356860 37/39 391 331 60 412 412 0 strelka-varscan-mutect CACNA2D1,synonymous_variant,p.=,ENST00000356860,NM_000722.3;CACNA2D1,synonymous_variant,p.=,ENST00000356253,;CACNA2D1,downstream_gene_variant,,ENST00000469297,; A ENST00000356860 Transcript synonymous_variant 3390/7563 3051/3276 1017/1091 R cgA/cgT 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 37/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 81959745 81959745 T A 1 0 0 0 0 0 0 0 1 2236 1654 58 4 4 CACNA2D1 7 81959745 Silent SNP T C3N-01074_T 3438118 81959745 77386228 176 22165 PCLO 0 . GRCh38 7 82953129 82953129 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.7824A>T p.= p.S2608S ENST00000333891 5/25 209 152 57 263 263 0 strelka-varscan-mutect PCLO,synonymous_variant,p.=,ENST00000333891,NM_033026.5;PCLO,synonymous_variant,p.=,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript synonymous_variant 8162/20329 7824/15429 2608/5142 S tcA/tcT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 82953129 82953129 T A 1 0 0 0 0 0 0 0 1 11671 1683 59 4 4 PCLO 7 82953129 Silent SNP T C3N-01074_T 993384 82953129 76392844 177 22166 PEX1 0 . GRCh38 7 92499745 92499745 + Missense_Mutation SNP C C A rs770527236 C3N-01074_T C3N-01074_N C C c.2677G>T p.Val893Leu p.V893L ENST00000248633 16/24 496 407 89 433 433 0 strelka-varscan-mutect PEX1,missense_variant,p.Val893Leu,ENST00000248633,NM_000466.2;PEX1,missense_variant,p.Val836Leu,ENST00000428214,NM_001282677.1;PEX1,missense_variant,p.Val571Leu,ENST00000438045,NM_001282678.1;PEX1,non_coding_transcript_exon_variant,,ENST00000496420,;PEX1,non_coding_transcript_exon_variant,,ENST00000484913,;PEX1,downstream_gene_variant,,ENST00000496092,; A ENST00000248633 Transcript missense_variant 2773/4385 2677/3852 893/1283 V/L Gta/Tta rs770527236 1 -1 PEX1 HGNC HGNC:8850 protein_coding YES CCDS5627.1 ENSP00000248633 O43933 UPI0000001C39 NM_000466.2 deleterious(0.02) 16/24 hmmpanther:PTHR23077:SF12,hmmpanther:PTHR23077,Pfam_domain:PF00004,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs770527236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 92499745 92499745 C A 1 0 0 0 0 1 0 0 0 11825 507 18 2 2 PEX1 7 92499745 Missense_Mutation SNP C C3N-01074_T 9546616 92499745 66846228 178 22167 LMTK2 0 . GRCh38 7 98204056 98204056 + Silent SNP G G T rs371508931 C3N-01074_T C3N-01074_N G G c.4353G>T p.= p.P1451P ENST00000297293 13/14 607 408 199 478 478 0 strelka-varscan-mutect LMTK2,synonymous_variant,p.=,ENST00000297293,NM_014916.3; T ENST00000297293 Transcript synonymous_variant 4646/8946 4353/4512 1451/1503 P ccG/ccT rs371508931,COSM4971609 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 13/14 0,1 LOW 1 SNV 1 0,1 1 PASS rs371508931 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 98204056 98204056 G T 1 0 0 0 0 0 0 0 1 8786 1074 38 1 1 LMTK2 7 98204056 Silent SNP G C3N-01074_T 5704311 98204056 61141917 179 22168 PVRIG 0 . GRCh38 7 100221082 100221082 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.812C>A p.Pro271His p.P271H ENST00000317271 6/6 195 125 70 176 175 1 strelka-varscan-mutect PVRIG,missense_variant,p.Pro271His,ENST00000317271,NM_024070.3;GATS,intron_variant,,ENST00000436886,NM_178831.6;GATS,intron_variant,,ENST00000454084,;GATS,intron_variant,,ENST00000440058,;GATS,intron_variant,,ENST00000437485,;GATS,downstream_gene_variant,,ENST00000538588,;PVRIG,downstream_gene_variant,,ENST00000471803,;STAG3,3_prime_UTR_variant,,ENST00000451963,;GATS,intron_variant,,ENST00000328453,;GATS,intron_variant,,ENST00000543273,;GATS,intron_variant,,ENST00000414739,;GATS,intron_variant,,ENST00000435519,; A ENST00000317271 Transcript missense_variant 1175/1583 812/981 271/326 P/H cCt/cAt 1 1 PVRIG HGNC HGNC:32190 protein_coding YES CCDS5690.1 ENSP00000316675 Q6DKI7 UPI000013FFF0 NM_024070.3 tolerated(0.17) 6/6 hmmpanther:PTHR39220,hmmpanther:PTHR39220:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 100221082 100221082 C A 1 0 0 0 0 1 0 0 0 12996 681 24 2 2 PVRIG 7 100221082 Missense_Mutation SNP C C3N-01074_T 2017026 100221082 59124891 180 22169 TFR2 0 . GRCh38 7 100629263 100629263 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.1380G>C p.Met460Ile p.M460I ENST00000462107 11/19 682 563 119 529 529 0 strelka-varscan-mutect TFR2,missense_variant,p.Met460Ile,ENST00000462107,;TFR2,missense_variant,p.Met460Ile,ENST00000223051,NM_003227.3,NM_001206855.1;TFR2,3_prime_UTR_variant,,ENST00000431692,;TFR2,3_prime_UTR_variant,,ENST00000490084,;TFR2,non_coding_transcript_exon_variant,,ENST00000465294,;TFR2,non_coding_transcript_exon_variant,,ENST00000476304,;TFR2,intron_variant,,ENST00000462090,;TFR2,intron_variant,,ENST00000473374,;TFR2,intron_variant,,ENST00000473963,;TFR2,upstream_gene_variant,,ENST00000461176,;TFR2,downstream_gene_variant,,ENST00000473571,;TFR2,downstream_gene_variant,,ENST00000475011,; G ENST00000462107 Transcript missense_variant 1668/3131 1380/2406 460/801 M/I atG/atC 1 -1 TFR2 HGNC HGNC:11762 protein_coding YES CCDS34707.1 ENSP00000420525 Q9UP52 UPI0000136C99 tolerated(0.09) 11/19 hmmpanther:PTHR10404:SF33,hmmpanther:PTHR10404,Pfam_domain:PF04389,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 100629263 100629263 C G 1 0 0 0 0 1 0 0 0 16244 594 21 4 4 TFR2 7 100629263 Missense_Mutation SNP C C3N-01074_T 408181 100629263 58716710 181 22170 MUC12 0 . GRCh38 7 100991162 100991162 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.599C>G p.Pro200Arg p.P200R ENST00000536621 2/12 285 245 40 358 358 0 strelka-varscan-mutect MUC12,missense_variant,p.Pro343Arg,ENST00000379442,;MUC12,missense_variant,p.Pro200Arg,ENST00000536621,NM_001164462.1; G ENST00000536621 Transcript missense_variant 599/16321 599/16008 200/5335 P/R cCc/cGc 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 deleterious(0) 2/12 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1414045561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 100991162 100991162 C G 1 0 0 0 0 1 0 0 0 9969 623 22 4 4 MUC12 7 100991162 Missense_Mutation SNP C C3N-01074_T 361899 100991162 58354811 182 22171 MUC12 0 . GRCh38 7 100991700 100991700 + Silent SNP T T G novel C3N-01074_T C3N-01074_N T T c.1137T>G p.= p.T379T ENST00000536621 2/12 565 528 37 655 654 1 varscan-mutect MUC12,synonymous_variant,p.=,ENST00000379442,;MUC12,synonymous_variant,p.=,ENST00000536621,NM_001164462.1; G ENST00000536621 Transcript synonymous_variant 1137/16321 1137/16008 379/5335 T acT/acG 1 1 MUC12 HGNC HGNC:7510 protein_coding YES CCDS55139.1 ENSP00000441929 Q9UKN1 UPI0001B25898 NM_001164462.1 2/12 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 100991700 100991700 T G 1 0 0 0 0 0 0 0 1 9969 1596 56 5 5 MUC12 7 100991700 Silent SNP T C3N-01074_T 538 100991700 58354273 183 22172 VGF 0 . GRCh38 7 101162801 101162801 + Missense_Mutation SNP G G T rs767612486 C3N-01074_T C3N-01074_N G G c.1126C>A p.Arg376Ser p.R376S ENST00000611537 4/4 214 142 72 190 190 0 strelka-varscan-mutect VGF,missense_variant,p.Arg376Ser,ENST00000611537,;VGF,3_prime_UTR_variant,,ENST00000249330,NM_003378.3;VGF,3_prime_UTR_variant,,ENST00000445482,;AP1S1,downstream_gene_variant,,ENST00000337619,NM_001283.3;AP1S1,downstream_gene_variant,,ENST00000429457,;MIR4653,downstream_gene_variant,,ENST00000585107,;AP1S1,downstream_gene_variant,,ENST00000443943,; T ENST00000611537 Transcript missense_variant 1331/1622 1126/1134 376/377 R/S Cgc/Agc rs767612486 1 -1 VGF HGNC HGNC:12684 protein_coding ENSP00000480817 Q05BJ3 UPI0000E57486 4/4 MODERATE SNV 5 1 PASS rs767612486 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 101162801 101162801 G T 1 0 0 0 0 1 0 0 0 17703 1116 39 1 1 VGF 7 101162801 Missense_Mutation SNP G C3N-01074_T 171101 101162801 58183172 184 22173 SPDYE6 0 . GRCh38 7 102348359 102348359 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.1074G>T p.= p.L358L ENST00000563237 6/8 309 253 56 395 394 1 strelka-varscan-mutect SPDYE6,synonymous_variant,p.=,ENST00000563237,NM_001146210.2; A ENST00000563237 Transcript synonymous_variant 1495/1691 1074/1209 358/402 L ctG/ctT 1 -1 SPDYE6 HGNC HGNC:35465 protein_coding YES CCDS78265.1 ENSP00000485230 A0A096LNU6 UPI0001A5C537 NM_001146210.2 6/8 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF12,Pfam_domain:PF11357 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 102348359 102348359 C A 1 0 0 0 0 0 0 0 1 15382 465 17 2 2 SPDYE6 7 102348359 Silent SNP C C3N-01074_T 1185558 102348359 56997614 185 22174 SPDYE2 0 . GRCh38 7 102554553 102554553 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.355C>A p.His119Asn p.H119N ENST00000507918 3/9 648 579 69 603 603 0 varscan-mutect SPDYE2,missense_variant,p.His119Asn,ENST00000507918,NM_001031618.3;SPDYE2,missense_variant,p.His119Asn,ENST00000432940,;POLR2J3,intron_variant,,ENST00000513506,;RP11-514P8.7,intron_variant,,ENST00000514917,;SPDYE2,upstream_gene_variant,,ENST00000341656,;POLR2J3,intron_variant,,ENST00000503564,;POLR2J3,intron_variant,,ENST00000506060,;POLR2J3,intron_variant,,ENST00000511773,;POLR2J3,intron_variant,,ENST00000502415,;POLR2J3,intron_variant,,ENST00000504677,;POLR2J3,intron_variant,,ENST00000489144,;POLR2J3,intron_variant,,ENST00000464525,;POLR2J3,intron_variant,,ENST00000379340,;POLR2J3,intron_variant,,ENST00000486319,;POLR2J3,intron_variant,,ENST00000508848,;POLR2J3,intron_variant,,ENST00000507355,; A ENST00000507918 Transcript missense_variant 829/1742 355/1209 119/402 H/N Cac/Aac 1 1 SPDYE2 HGNC HGNC:33841 protein_coding YES CCDS34716.2 ENSP00000421686 Q495Y8 I6XC90 UPI0001AE70B7 NM_001031618.3 deleterious(0) 3/9 hmmpanther:PTHR31156,hmmpanther:PTHR31156:SF12 MODERATE 1 SNV 2 1 PASS rs1185662626 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 102554553 102554553 C A 1 0 0 0 0 1 0 0 0 15378 594 21 2 2 SPDYE2 7 102554553 Missense_Mutation SNP C C3N-01074_T 206194 102554553 56791420 186 22175 CPED1 0 . GRCh38 7 121128487 121128487 + Splice_Site SNP G G C novel C3N-01074_T C3N-01074_N G G c.1407+1G>C p.X469_splice ENST00000310396 158 116 42 145 145 0 strelka-varscan-mutect CPED1,splice_donor_variant,,ENST00000310396,NM_024913.4;CPED1,splice_donor_variant,,ENST00000450913,NM_001105533.1;CPED1,splice_donor_variant,,ENST00000428526,;CPED1,splice_donor_variant,,ENST00000423795,;CPED1,splice_donor_variant,,ENST00000443817,; C ENST00000310396 Transcript splice_donor_variant -/5340 1407/3081 469/1026 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 11/22 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 73 121128487 121128487 G C 1 0 0 0 0 0 0 1 0 3598 1275 44 4 4 CPED1 7 121128487 Splice_Site SNP G C3N-01074_T 18573934 121128487 38217486 187 22176 SPAM1 0 . GRCh38 7 123953636 123953636 + Silent SNP G G A C3N-01074_T C3N-01074_N G G c.66G>A p.= p.Q22Q ENST00000340011 3/7 165 131 34 176 176 0 strelka-varscan-mutect SPAM1,synonymous_variant,p.=,ENST00000340011,NM_003117.4;SPAM1,synonymous_variant,p.=,ENST00000439500,NM_001174046.1,NM_001174045.1;SPAM1,synonymous_variant,p.=,ENST00000460182,NM_001174044.1,NM_153189.2;SPAM1,synonymous_variant,p.=,ENST00000223028,;SPAM1,synonymous_variant,p.=,ENST00000402183,;SPAM1,synonymous_variant,p.=,ENST00000413927,; A ENST00000340011 Transcript synonymous_variant 423/2349 66/1536 22/511 Q caG/caA COSM744749,COSM744750 1 1 SPAM1 HGNC HGNC:11217 protein_coding YES CCDS5790.1 ENSP00000345849 P38567 UPI0000072166 NM_003117.4 3/7 hmmpanther:PTHR11769,hmmpanther:PTHR11769:SF20,PIRSF_domain:PIRSF500773,PIRSF_domain:PIRSF038193,Prints_domain:PR00848 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 123953636 123953636 G A 1 0 0 0 0 0 0 0 1 15317 933 33 3 3 SPAM1 7 123953636 Silent SNP G C3N-01074_T 2825149 123953636 35392337 188 22177 GRM8 0 . GRCh38 7 126533392 126533392 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1990G>T p.Ala664Ser p.A664S ENST00000339582 9/11 237 148 89 314 313 1 strelka-varscan-mutect GRM8,missense_variant,p.Ala664Ser,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Ala664Ser,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Ala172Ser,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Ala664Ser,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; A ENST00000339582 Transcript missense_variant 2799/4057 1990/2727 664/908 A/S Gca/Tca 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.91) 9/11 Pfam_domain:PF00003,Prints_domain:PR00248,Prints_domain:PR00593,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 126533392 126533392 C A 1 0 0 0 0 1 0 0 0 6685 710 25 2 2 GRM8 7 126533392 Missense_Mutation SNP C C3N-01074_T 2579756 126533392 32812581 189 22178 PRRT4 0 . GRCh38 7 128351164 128351164 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2392G>T p.Gly798Cys p.G798C ENST00000446477 6/6 191 141 50 188 188 0 strelka-varscan-mutect PRRT4,missense_variant,p.Gly798Cys,ENST00000446477,NM_001174164.1;PRRT4,missense_variant,p.Gly798Cys,ENST00000535159,;PRRT4,missense_variant,p.Gln327His,ENST00000480290,;PRRT4,3_prime_UTR_variant,,ENST00000489835,NM_001114726.2;PRRT4,downstream_gene_variant,,ENST00000489517,; A ENST00000446477 Transcript missense_variant 2706/3544 2392/2700 798/899 G/C Ggc/Tgc 1 -1 PRRT4 HGNC HGNC:37280 protein_coding YES CCDS55160.1 ENSP00000415026 C9JH25 UPI0000DD7E1D NM_001174164.1 tolerated(0.06) 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR35578,hmmpanther:PTHR35578:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 128351164 128351164 C A 1 0 0 0 0 1 0 0 0 12758 681 24 2 2 PRRT4 7 128351164 Missense_Mutation SNP C C3N-01074_T 1817772 128351164 30994809 190 22179 SMO 0 . GRCh38 7 129205369 129205369 + Missense_Mutation SNP C C T rs142599757 C3N-01074_T C3N-01074_N C C c.704C>T p.Ala235Val p.A235V ENST00000249373 3/12 359 277 82 325 325 0 strelka-varscan-mutect SMO,missense_variant,p.Ala235Val,ENST00000249373,NM_005631.4;RP11-286H14.8,downstream_gene_variant,,ENST00000466717,;SMO,upstream_gene_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000495998,; T ENST00000249373 Transcript missense_variant 984/3738 704/2364 235/787 A/V gCg/gTg rs142599757,COSM1226876 1 1 SMO HGNC HGNC:11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 UPI0000050447 NM_005631.4 deleterious(0.04) 3/12 PROSITE_profiles:PS50261,hmmpanther:PTHR11309:SF35,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330,Prints_domain:PR00489,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs142599757 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 129205369 129205369 C T 1 0 0 0 0 1 0 0 0 15121 768 27 1 1 SMO 7 129205369 Missense_Mutation SNP C C3N-01074_T 854205 129205369 30140604 191 22180 C7orf34 0 . GRCh38 7 142939575 142939575 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.29G>T p.Trp10Leu p.W10L ENST00000409607 1/2 68 52 16 66 66 0 strelka-varscan-mutect C7orf34,missense_variant,p.Trp10Leu,ENST00000409607,NM_178829.4;C7orf34,intron_variant,,ENST00000458732,;KEL,downstream_gene_variant,,ENST00000355265,NM_000420.2;KEL,downstream_gene_variant,,ENST00000470850,;KEL,downstream_gene_variant,,ENST00000465697,;KEL,downstream_gene_variant,,ENST00000478969,; T ENST00000409607 Transcript missense_variant 70/766 29/444 10/147 W/L tGg/tTg 1 1 C7orf34 HGNC HGNC:21750 protein_coding YES CCDS5876.2 ENSP00000386450 Q96L11 UPI00005A76EA NM_178829.4 tolerated_low_confidence(0.39) 1/2 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 142939575 142939575 G T 1 0 0 0 0 1 0 0 0 2139 1357 47 2 2 C7orf34 7 142939575 Missense_Mutation SNP G C3N-01074_T 13734206 142939575 16406398 192 22181 CTAGE4 0 . GRCh38 7 144185820 144185820 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.2317C>T p.Pro773Ser p.P773S ENST00000486333 1/1 56 47 9 76 76 0 varscan-mutect CTAGE4,missense_variant,p.Pro773Ser,ENST00000486333,NM_198495.2;ARHGEF35,downstream_gene_variant,,ENST00000378115,NM_001003702.2; T ENST00000486333 Transcript missense_variant 2355/2588 2317/2334 773/777 P/S Ccc/Tcc 1 1 CTAGE4 HGNC HGNC:24772 protein_coding YES CCDS55176.1 ENSP00000419539 Q8IX94 UPI00001C1E89 NM_198495.2 deleterious(0.03) 1/1 hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF39 MODERATE SNV 1 PASS . . 5 202 3 0 0 0 0 0 -19.97506 1 1 1 1 0 T 3 4 73 144185820 144185820 C T 1 0 0 0 0 1 0 0 0 3798 623 22 3 3 CTAGE4 7 144185820 Missense_Mutation SNP C C3N-01074_T 1246245 144185820 15160153 193 22182 CNTNAP2 0 . GRCh38 7 148229676 148229676 + Missense_Mutation SNP G G T rs796052391 C3N-01074_T C3N-01074_N G G c.3278G>T p.Gly1093Val p.G1093V ENST00000361727 20/24 529 457 72 451 450 1 strelka-varscan-mutect CNTNAP2,missense_variant,p.Gly1093Val,ENST00000361727,NM_014141.5;CNTNAP2,missense_variant,p.Gly152Val,ENST00000628930,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637020,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000627772,; T ENST00000361727 Transcript missense_variant 3796/9896 3278/3996 1093/1331 G/V gGc/gTc rs796052391 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(0.26) 20/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs796052391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 148229676 148229676 G T 1 0 0 0 0 1 0 0 0 3428 1203 42 2 2 CNTNAP2 7 148229676 Missense_Mutation SNP G C3N-01074_T 4043856 148229676 11116297 194 22183 GIMAP5 0 . GRCh38 7 150742881 150742881 + Missense_Mutation SNP A A C novel C3N-01074_T C3N-01074_N A A c.742A>C p.Lys248Gln p.K248Q ENST00000358647 3/3 315 257 58 299 299 0 strelka-varscan-mutect GIMAP5,missense_variant,p.Lys248Gln,ENST00000358647,NM_018384.4;GIMAP1-GIMAP5,missense_variant,p.Lys452Gln,ENST00000611999,NM_001199577.1;GIMAP5,missense_variant,p.Lys248Gln,ENST00000498181,;GIMAP5,non_coding_transcript_exon_variant,,ENST00000479556,;GIMAP5,intron_variant,,ENST00000466347,;GIMAP5,downstream_gene_variant,,ENST00000493304,;GIMAP5,non_coding_transcript_exon_variant,,ENST00000476324,;GIMAP5,downstream_gene_variant,,ENST00000469272,;GIMAP3P,downstream_gene_variant,,ENST00000495150,; C ENST00000358647 Transcript missense_variant 1109/2291 742/924 248/307 K/Q Aaa/Caa 1 1 GIMAP5 HGNC HGNC:18005 protein_coding YES CCDS5907.1 ENSP00000351473 Q96F15 UPI000004EC77 NM_018384.4 tolerated(0.28) 3/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10903:SF69,hmmpanther:PTHR10903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 150742881 150742881 A C 1 0 0 0 0 1 0 0 0 6262 131 5 5 5 GIMAP5 7 150742881 Missense_Mutation SNP A C3N-01074_T 2513205 150742881 8603092 195 22184 DPP6 0 . GRCh38 7 154807067 154807067 + Missense_Mutation SNP G G T rs755543207 C3N-01074_T C3N-01074_N G G c.1621G>T p.Ala541Ser p.A541S ENST00000377770 16/26 149 116 33 161 159 2 strelka-varscan-mutect DPP6,missense_variant,p.Ala477Ser,ENST00000404039,NM_001039350.2;DPP6,missense_variant,p.Ala479Ser,ENST00000332007,NM_001936.4;DPP6,missense_variant,p.Ala541Ser,ENST00000377770,NM_130797.3;DPP6,missense_variant,p.Ala434Ser,ENST00000427557,NM_001290252.1;DPP6,non_coding_transcript_exon_variant,,ENST00000493268,; T ENST00000377770 Transcript missense_variant 1762/3710 1621/2598 541/865 A/S Gct/Tct rs755543207,COSM4410027,COSM4410028,COSM4410029 1 1 DPP6 HGNC HGNC:3010 protein_coding YES CCDS75683.1 ENSP00000367001 P42658 UPI00001AE746 NM_130797.3 tolerated(0.07) 16/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF20,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs755543207 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 154807067 154807067 G T 1 0 0 0 0 1 0 0 0 4545 1087 38 1 1 DPP6 7 154807067 Missense_Mutation SNP G C3N-01074_T 4064186 154807067 4538906 196 22185 CSMD1 0 . GRCh38 8 2966634 2966634 + Silent SNP T T C C3N-01074_T C3N-01074_N T T c.9039A>G p.= p.S3013S ENST00000520002 59/71 312 276 36 242 242 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,; C ENST00000520002 Transcript synonymous_variant 9595/11740 9039/10698 3013/3565 S tcA/tcG COSM4674940,COSM4674941 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 59/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 LOW 1 SNV 5 1,1 1 PASS rs1326037234 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 2966634 2966634 T C 1 0 0 0 0 0 0 0 1 3745 1567 55 5 5 CSMD1 8 2966634 Silent SNP T C3N-01074_T 2966634 142172002 197 22186 CSMD1 0 . GRCh38 8 2978765 2978765 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.8416G>T p.Ala2806Ser p.A2806S ENST00000520002 56/71 166 126 40 183 183 0 strelka-varscan-mutect CSMD1,missense_variant,p.Ala2667Ser,ENST00000537824,;CSMD1,missense_variant,p.Ala2223Ser,ENST00000335551,;CSMD1,missense_variant,p.Ala2806Ser,ENST00000520002,;CSMD1,missense_variant,p.Ala2806Ser,ENST00000602557,;CSMD1,missense_variant,p.Ala2805Ser,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Ala2748Ser,ENST00000400186,;CSMD1,missense_variant,p.Ala2748Ser,ENST00000602723,; A ENST00000520002 Transcript missense_variant 8972/11740 8416/10698 2806/3565 A/S Gcc/Tcc 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(1) 56/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 2978765 2978765 C A 1 0 0 0 0 1 0 0 0 3745 710 25 2 2 CSMD1 8 2978765 Missense_Mutation SNP C C3N-01074_T 12131 2978765 142159871 198 22187 FAM167A 0 . GRCh38 8 11444179 11444179 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.233G>T p.Gly78Val p.G78V ENST00000284486 2/3 179 109 70 165 163 2 strelka-varscan-mutect FAM167A,missense_variant,p.Gly78Val,ENST00000284486,NM_053279.2;FAM167A,missense_variant,p.Gly78Val,ENST00000534308,;FAM167A,missense_variant,p.Gly78Val,ENST00000528897,;FAM167A,missense_variant,p.Gly78Val,ENST00000531804,;FAM167A,intron_variant,,ENST00000527445,;FAM167A,upstream_gene_variant,,ENST00000531564,;FAM167A,downstream_gene_variant,,ENST00000528111,; A ENST00000284486 Transcript missense_variant 772/4094 233/645 78/214 G/V gGg/gTg 1 -1 FAM167A HGNC HGNC:15549 protein_coding YES CCDS5981.1 ENSP00000284486 Q96KS9 UPI0000127668 NM_053279.2 tolerated(0.15) 2/3 hmmpanther:PTHR32289,hmmpanther:PTHR32289:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 11444179 11444179 C A 1 0 0 0 0 1 0 0 0 5329 623 22 2 2 FAM167A 8 11444179 Missense_Mutation SNP C C3N-01074_T 8465414 11444179 133694457 199 22188 USP17L2 0 . GRCh38 8 12137437 12137437 + Missense_Mutation SNP C C T rs760152249 C3N-01074_T C3N-01074_N C C c.1324G>A p.Glu442Lys p.E442K ENST00000333796 1/1 453 173 280 374 374 0 strelka-varscan USP17L2,missense_variant,p.Glu442Lys,ENST00000333796,NM_201402.2;USP17L7,upstream_gene_variant,,ENST00000530447,NM_001256869.1;FAM66D,intron_variant,,ENST00000434078,; T ENST00000333796 Transcript missense_variant 1641/1910 1324/1593 442/530 E/K Gag/Aag rs760152249 1 -1 USP17L2 HGNC HGNC:34434 protein_coding YES CCDS43713.1 ENSP00000333329 Q6R6M4 UPI0000198137 NM_201402.2 deleterious(0.03) 1/1 MODERATE SNV 1 PASS . . 28 178 0 0 2 0 0 0 -20 0.9993442 1 1 1 0 T 3 4 73 12137437 12137437 C T 1 0 0 0 0 1 0 0 0 17586 922 32 3 3 USP17L2 8 12137437 Missense_Mutation SNP C C3N-01074_T 693258 12137437 133001199 200 22189 ADAM7 0 . GRCh38 8 24482216 24482216 + Silent SNP A A G novel C3N-01074_T C3N-01074_N A A c.780A>G p.= p.L260L ENST00000175238 9/22 256 208 48 258 258 0 strelka-varscan-mutect ADAM7,synonymous_variant,p.=,ENST00000175238,NM_003817.3;ADAM7,synonymous_variant,p.=,ENST00000380789,;ADAM7,synonymous_variant,p.=,ENST00000520720,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,; G ENST00000175238 Transcript synonymous_variant 863/3367 780/2265 260/754 L ctA/ctG 1 1 ADAM7 HGNC HGNC:214 protein_coding YES CCDS6045.1 ENSP00000175238 Q9H2U9 UPI000013C5CC NM_003817.3 9/22 PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF21,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 24482216 24482216 A G 1 0 0 0 0 0 0 0 1 295 436 16 5 5 ADAM7 8 24482216 Silent SNP A C3N-01074_T 12344779 24482216 120656420 201 22190 ADAM7 0 . GRCh38 8 24526768 24526768 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1538G>T p.Gly513Val p.G513V ENST00000520720 15/15 152 130 22 169 169 0 strelka-varscan-mutect ADAM7,missense_variant,p.Gly513Val,ENST00000520720,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523578,; T ENST00000520720 Transcript missense_variant 1668/1870 1538/1551 513/516 G/V gGa/gTa 1 1 ADAM7 HGNC HGNC:214 protein_coding ENSP00000430400 E5RK87 UPI0001E8EF41 tolerated_low_confidence(0.05) 15/15 MODERATE 1 SNV 1 1 PASS rs1368474638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 24526768 24526768 G T 1 0 0 0 0 1 0 0 0 295 1174 41 2 2 ADAM7 8 24526768 Missense_Mutation SNP G C3N-01074_T 44552 24526768 120611868 202 22191 DOCK5 0 . GRCh38 8 25363047 25363047 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.2950G>C p.Asp984His p.D984H ENST00000276440 29/52 188 145 43 206 206 0 strelka-varscan-mutect DOCK5,missense_variant,p.Asp984His,ENST00000276440,NM_024940.6;DOCK5,missense_variant,p.Asp756His,ENST00000444569,;DOCK5,splice_region_variant,,ENST00000467709,;DOCK5,splice_region_variant,,ENST00000481728,; C ENST00000276440 Transcript missense_variant,splice_region_variant 2994/10075 2950/5613 984/1870 D/H Gac/Cac 1 1 DOCK5 HGNC HGNC:23476 protein_coding YES CCDS6047.1 ENSP00000276440 Q9H7D0 UPI000022D4F3 NM_024940.6 deleterious(0) 29/52 hmmpanther:PTHR23317:SF68,hmmpanther:PTHR23317 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 25363047 25363047 G C 1 0 0 0 0 1 0 0 0 4505 1188 41 4 4 DOCK5 8 25363047 Missense_Mutation SNP G C3N-01074_T 836279 25363047 119775589 203 22192 TM2D2 0 . GRCh38 8 38996280 38996280 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.160G>T p.Gly54Cys p.G54C ENST00000456397 1/4 260 216 44 194 194 0 strelka-varscan-mutect TM2D2,missense_variant,p.Gly54Cys,ENST00000456397,NM_078473.2;TM2D2,5_prime_UTR_variant,,ENST00000397070,NM_031940.3;TM2D2,intron_variant,,ENST00000456845,NM_001024380.1,NM_001024381.1;TM2D2,intron_variant,,ENST00000522142,;TM2D2,intron_variant,,ENST00000517872,;TM2D2,intron_variant,,ENST00000520152,;ADAM9,upstream_gene_variant,,ENST00000487273,NM_003816.2;ADAM9,upstream_gene_variant,,ENST00000481513,;ADAM9,upstream_gene_variant,,ENST00000466936,;TM2D2,intron_variant,,ENST00000522434,;TM2D2,upstream_gene_variant,,ENST00000521060,;TM2D2,non_coding_transcript_exon_variant,,ENST00000519186,;ADAM9,upstream_gene_variant,,ENST00000379917,;ADAM9,upstream_gene_variant,,ENST00000481873,;ADAM9,upstream_gene_variant,,ENST00000468065,;TM2D2,upstream_gene_variant,,ENST00000524331,; A ENST00000456397 Transcript missense_variant 254/3263 160/645 54/214 G/C Ggc/Tgc 1 -1 TM2D2 HGNC HGNC:24127 protein_coding YES CCDS6111.1 ENSP00000416050 Q9BX73 UPI000006FCA0 NM_078473.2 deleterious_low_confidence(0.05) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR21016,hmmpanther:PTHR21016:SF4 MODERATE 1 SNV 1 1 PASS rs1455742111 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 38996280 38996280 C A 1 0 0 0 0 1 0 0 0 16409 623 22 2 2 TM2D2 8 38996280 Missense_Mutation SNP C C3N-01074_T 13633233 38996280 106142356 204 22193 ADAM32 0 . GRCh38 8 39270912 39270912 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2199C>A p.Ser733Arg p.S733R ENST00000379907 20/25 241 192 49 287 287 0 strelka-varscan-mutect ADAM32,missense_variant,p.Ser733Arg,ENST00000379907,NM_145004.5;ADAM32,missense_variant,p.Ser634Arg,ENST00000437682,NM_001313994.1;ADAM32,intron_variant,,ENST00000519315,;ADAM32,splice_region_variant,,ENST00000524303,;ADAM32,splice_region_variant,,ENST00000517416,;ADAM32,intron_variant,,ENST00000520691,; A ENST00000379907 Transcript missense_variant,splice_region_variant 2326/2601 2199/2364 733/787 S/R agC/agA 1 1 ADAM32 HGNC HGNC:15479 protein_coding YES CCDS47846.1 ENSP00000369238 Q8TC27 UPI000013F62F NM_145004.5 tolerated(0.13) 20/25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 39270912 39270912 C A 1 0 0 0 0 1 0 0 0 293 753 26 2 2 ADAM32 8 39270912 Missense_Mutation SNP C C3N-01074_T 274632 39270912 105867724 205 22194 SNTG1 0 . GRCh38 8 50449666 50449666 + Splice_Site SNP A A C novel C3N-01074_T C3N-01074_N A A c.220-2A>C p.X74_splice ENST00000522124 114 101 13 93 93 0 strelka-varscan-mutect SNTG1,splice_acceptor_variant,,ENST00000522124,NM_018967.3;SNTG1,splice_acceptor_variant,,ENST00000518864,NM_001287813.1;SNTG1,splice_acceptor_variant,,ENST00000517473,NM_001287814.1;SNTG1,splice_acceptor_variant,,ENST00000523085,;SNTG1,splice_acceptor_variant,,ENST00000520825,; C ENST00000522124 Transcript splice_acceptor_variant -/3504 220/1554 74/517 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 5/18 HIGH 1 SNV 1 1 PASS . . 0 201 7 2 0 0 0 0 -19.65329 0.9997362 1 1 1 0 C 5 2 73 50449666 50449666 A C 1 0 0 0 0 0 0 1 0 15194 202 7 5 5 SNTG1 8 50449666 Splice_Site SNP A C3N-01074_T 11178754 50449666 94688970 206 22195 NCOA2 0 . GRCh38 8 70123910 70123910 + Missense_Mutation SNP C C A rs771376592 C3N-01074_T C3N-01074_N C C c.4267G>T p.Gly1423Trp p.G1423W ENST00000452400 21/23 180 134 46 127 126 1 strelka-varscan-mutect NCOA2,missense_variant,p.Gly1423Trp,ENST00000452400,NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2;NCOA2,missense_variant,p.Gly549Trp,ENST00000518363,;NCOA2,3_prime_UTR_variant,,ENST00000518287,;NCOA2,downstream_gene_variant,,ENST00000521239,; A ENST00000452400 Transcript missense_variant 4449/8447 4267/4395 1423/1464 G/W Ggg/Tgg rs771376592 1 -1 NCOA2 HGNC HGNC:7669 protein_coding YES CCDS47872.1 ENSP00000399968 Q15596 UPI000012FE42 NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2 deleterious(0) 21/23 hmmpanther:PTHR10684:SF2,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 MODERATE 1 SNV 1 1 PASS rs771376592 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 70123910 70123910 C A 1 0 0 0 0 1 0 0 0 10248 681 24 2 2 NCOA2 8 70123910 Missense_Mutation SNP C C3N-01074_T 19674244 70123910 75014726 207 22196 ZFHX4 0 . GRCh38 8 76855335 76855335 + Nonsense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.8414C>A p.Ser2805Ter p.S2805* ENST00000521891 10/11 309 234 75 229 228 1 strelka-varscan-mutect ZFHX4,stop_gained,p.Ser2805Ter,ENST00000521891,NM_024721.4;ZFHX4,stop_gained,p.Ser2779Ter,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript stop_gained 8862/14019 8414/10851 2805/3616 S/* tCg/tAg COSM1101803,COSM4397386 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 76855335 76855335 C A 1 0 0 0 0 0 1 0 0 18213 893 31 1 1 ZFHX4 8 76855335 Nonsense_Mutation SNP C C3N-01074_T 6731425 76855335 68283301 208 22197 DPY19L4 0 . GRCh38 8 94766668 94766668 + Silent SNP T T C novel C3N-01074_T C3N-01074_N T T c.1158T>C p.= p.F386F ENST00000414645 11/19 287 204 83 201 201 0 strelka-varscan-mutect DPY19L4,synonymous_variant,p.=,ENST00000414645,NM_181787.2;DPY19L4,synonymous_variant,p.=,ENST00000523020,; C ENST00000414645 Transcript synonymous_variant 1257/6197 1158/2172 386/723 F ttT/ttC 1 1 DPY19L4 HGNC HGNC:27829 protein_coding YES CCDS34924.1 ENSP00000389630 Q7Z388 A0A024R9F2 UPI00001A9D7A NM_181787.2 11/19 hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 94766668 94766668 T C 1 0 0 0 0 0 0 0 1 4558 1809 63 5 5 DPY19L4 8 94766668 Silent SNP T C3N-01074_T 17911333 94766668 50371968 209 22198 RIMS2 0 . GRCh38 8 103931323 103931323 + Missense_Mutation SNP G G C C3N-01074_T C3N-01074_N G G c.2305G>C p.Asp769His p.D769H ENST00000504942 12/24 430 318 112 319 319 0 strelka-varscan-mutect RIMS2,missense_variant,p.Asp561His,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Asp547His,ENST00000436393,;RIMS2,missense_variant,p.Asp769His,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Asp711His,ENST00000626043,;RIMS2,missense_variant,p.Asp561His,ENST00000408894,;RIMS2,missense_variant,p.Asp608His,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Asp757His,ENST00000632716,;RIMS2,missense_variant,p.Asp163His,ENST00000507677,;RIMS2,missense_variant,p.Asp561His,ENST00000515551,; C ENST00000504942 Transcript missense_variant 2444/4228 2305/4050 769/1349 D/H Gat/Cat COSM3643558,COSM3643559,COSM3643560,COSM3643561,COSM3643562 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 12/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 1,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 103931323 103931323 G C 1 0 0 0 0 1 0 0 0 13543 942 33 4 4 RIMS2 8 103931323 Missense_Mutation SNP G C3N-01074_T 9164655 103931323 41207313 210 22199 C8orf76 0 . GRCh38 8 123231433 123231433 + Missense_Mutation SNP C C A rs756347830 C3N-01074_T C3N-01074_N C C c.682G>T p.Val228Leu p.V228L ENST00000276704 4/6 1831 1354 477 410 409 1 strelka-varscan-mutect C8orf76,missense_variant,p.Val228Leu,ENST00000276704,NM_032847.2;ZHX1-C8orf76,missense_variant,p.Val196Leu,ENST00000357082,NM_001204180.1;ZHX1-C8orf76,downstream_gene_variant,,ENST00000622816,;C8orf76,non_coding_transcript_exon_variant,,ENST00000521310,;C8orf76,non_coding_transcript_exon_variant,,ENST00000517760,;C8orf76,intron_variant,,ENST00000519791,;C8orf76,non_coding_transcript_exon_variant,,ENST00000518996,; A ENST00000276704 Transcript missense_variant 734/1341 682/1143 228/380 V/L Gtg/Ttg rs756347830 1 -1 C8orf76 HGNC HGNC:25924 protein_coding YES CCDS6341.1 ENSP00000276704 Q96K31 UPI000006E851 NM_032847.2 tolerated(0.37) 4/6 hmmpanther:PTHR31919,hmmpanther:PTHR31919:SF1 MODERATE 1 SNV 1 1 PASS rs756347830 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 123231433 123231433 C A 1 0 0 0 0 1 0 0 0 2164 478 17 2 2 C8orf76 8 123231433 Missense_Mutation SNP C C3N-01074_T 19300110 123231433 21907203 211 22200 TG 0 . GRCh38 8 132941351 132941351 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.5042G>T p.Gly1681Val p.G1681V ENST00000220616 26/48 672 452 220 495 495 0 strelka-varscan-mutect TG,missense_variant,p.Gly1681Val,ENST00000220616,NM_003235.4;TG,intron_variant,,ENST00000519178,;TG,splice_region_variant,,ENST00000523756,; T ENST00000220616 Transcript missense_variant,splice_region_variant 5082/8450 5042/8307 1681/2768 G/V gGc/gTc COSM5335573 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 deleterious(0.01) 26/48 PIRSF_domain:PIRSF001831 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 132941351 132941351 G T 1 0 0 0 0 1 0 0 0 16246 1217 42 2 2 TG 8 132941351 Missense_Mutation SNP G C3N-01074_T 9709918 132941351 12197285 212 22201 KHDRBS3 0 . GRCh38 8 135542759 135542759 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.313G>A p.Asp105Asn p.D105N ENST00000355849 3/9 244 187 57 185 185 0 strelka-varscan-mutect KHDRBS3,missense_variant,p.Asp105Asn,ENST00000355849,NM_006558.2;KHDRBS3,missense_variant,p.Asp77Asn,ENST00000524199,;KHDRBS3,missense_variant,p.Asp78Asn,ENST00000517394,;KHDRBS3,missense_variant,p.Asp20Asn,ENST00000524282,;KHDRBS3,intron_variant,,ENST00000520981,;KHDRBS3,missense_variant,p.Asp30Asn,ENST00000517859,;KHDRBS3,non_coding_transcript_exon_variant,,ENST00000519600,; A ENST00000355849 Transcript missense_variant 723/1977 313/1041 105/346 D/N Gac/Aac 1 1 KHDRBS3 HGNC HGNC:18117 protein_coding YES CCDS6374.1 ENSP00000348108 O75525 UPI0000073E6F NM_006558.2 deleterious(0) 3/9 hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF29,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 135542759 135542759 G A 1 0 0 0 0 1 0 0 0 8069 942 33 3 3 KHDRBS3 8 135542759 Missense_Mutation SNP G C3N-01074_T 2601408 135542759 9595877 213 22202 CCDC166 0 . GRCh38 8 143707199 143707199 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.815T>A p.Leu272Gln p.L272Q ENST00000542437 2/2 48 37 11 61 61 0 strelka-varscan-mutect CCDC166,missense_variant,p.Leu272Gln,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; T ENST00000542437 Transcript missense_variant 815/1320 815/1320 272/439 L/Q cTg/cAg 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 deleterious(0) 2/2 hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 1 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 143707199 143707199 A T 1 0 0 0 0 1 0 0 0 2482 188 7 4 4 CCDC166 8 143707199 Missense_Mutation SNP A C3N-01074_T 8164440 143707199 1431437 214 22203 TTC39B 0 . GRCh38 9 15172040 15172040 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2028G>T p.Trp676Cys p.W676C ENST00000512701 20/20 179 127 52 202 202 0 strelka-varscan-mutect TTC39B,missense_variant,p.Trp676Cys,ENST00000512701,NM_152574.2,NM_001168339.1;TTC39B,missense_variant,p.Trp663Cys,ENST00000380850,NM_001168340.1;TTC39B,missense_variant,p.Trp607Cys,ENST00000297615,NM_001168341.1;TTC39B,missense_variant,p.Trp511Cys,ENST00000507285,;TTC39B,missense_variant,p.Trp511Cys,ENST00000507993,NM_001168342.1;TTC39B,non_coding_transcript_exon_variant,,ENST00000380853,; A ENST00000512701 Transcript missense_variant 2065/10483 2028/2049 676/682 W/C tgG/tgT 1 -1 TTC39B HGNC HGNC:23704 protein_coding YES CCDS6477.2 ENSP00000422496 Q5VTQ0 UPI0001BE810F NM_152574.2,NM_001168339.1 tolerated(0.05) 20/20 hmmpanther:PTHR31859,hmmpanther:PTHR31859:SF4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 15172040 15172040 C A 1 0 0 0 0 1 0 0 0 17217 856 30 2 2 TTC39B 9 15172040 Missense_Mutation SNP C C3N-01074_T 15172040 123222677 215 22204 SLC24A2 0 . GRCh38 9 19516383 19516383 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1756C>A p.Leu586Met p.L586M ENST00000341998 10/10 152 111 41 240 240 0 strelka-varscan-mutect SLC24A2,missense_variant,p.Leu586Met,ENST00000341998,NM_020344.3;SLC24A2,missense_variant,p.Leu569Met,ENST00000286344,NM_001193288.2; T ENST00000341998 Transcript missense_variant 1818/10749 1756/1986 586/661 L/M Ctg/Atg 1 -1 SLC24A2 HGNC HGNC:10976 protein_coding YES CCDS6493.1 ENSP00000344801 Q9UI40 UPI000004FA46 NM_020344.3 tolerated(0.07) 10/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF41,Pfam_domain:PF01699,TIGRFAM_domain:TIGR00367 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 19516383 19516383 G T 1 0 0 0 0 1 0 0 0 14732 991 35 2 2 SLC24A2 9 19516383 Missense_Mutation SNP G C3N-01074_T 4344343 19516383 118878334 216 22205 SPATA31A6 0 . GRCh38 9 42186953 42186953 + Missense_Mutation SNP G G T rs778011715 C3N-01074_T C3N-01074_N G G c.1251G>T p.Trp417Cys p.W417C ENST00000332857 4/4 571 479 92 625 625 0 strelka-varscan-mutect SPATA31A6,missense_variant,p.Trp417Cys,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; T ENST00000332857 Transcript missense_variant 1280/4209 1251/4032 417/1343 W/C tgG/tgT rs778011715 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 deleterious(0) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859,Pfam_domain:PF14650 MODERATE 1 SNV 5 1 PASS rs778011715 . 10 200 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 42186953 42186953 G T 1 0 0 0 0 1 0 0 0 15345 1241 43 2 2 SPATA31A6 9 42186953 Missense_Mutation SNP G C3N-01074_T 22670570 42186953 96207764 217 22206 FOXD4L5 0 . GRCh38 9 65283971 65283971 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.407C>A p.Ala136Asp p.A136D ENST00000377420 1/1 203 187 16 240 240 0 varscan-mutect FOXD4L5,missense_variant,p.Ala136Asp,ENST00000377420,NM_001126334.1;RP11-15J10.1,downstream_gene_variant,,ENST00000445695,; T ENST00000377420 Transcript missense_variant 1239/3109 407/1251 136/416 A/D gCc/gAc 1 -1 FOXD4L5 HGNC HGNC:18522 protein_coding YES CCDS47977.1 ENSP00000366637 Q5VV16 UPI0000458A33 NM_001126334.1 tolerated(0.44) 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 65283971 65283971 G T 1 0 0 0 0 1 0 0 0 5863 1203 42 2 2 FOXD4L5 9 65283971 Missense_Mutation SNP G C3N-01074_T 23097018 65283971 73110746 218 22207 FOXD4L4 0 . GRCh38 9 65737552 65737552 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.407C>A p.Ala136Asp p.A136D ENST00000377413 1/1 296 281 15 484 483 1 varscan-mutect FOXD4L4,missense_variant,p.Ala136Asp,ENST00000377413,NM_199244.3;CBWD5,downstream_gene_variant,,ENST00000377392,NM_001286835.1;CBWD5,downstream_gene_variant,,ENST00000382405,;CBWD5,downstream_gene_variant,,ENST00000430059,;CBWD5,downstream_gene_variant,,ENST00000429800,;CBWD5,downstream_gene_variant,,ENST00000377395,NM_001024916.3;CBWD5,downstream_gene_variant,,ENST00000489273,;CBWD5,downstream_gene_variant,,ENST00000476797,;CBWD5,downstream_gene_variant,,ENST00000468066,;CBWD5,downstream_gene_variant,,ENST00000486191,;CBWD5,downstream_gene_variant,,ENST00000485088,;CBWD5,downstream_gene_variant,,ENST00000461932,;CBWD5,downstream_gene_variant,,ENST00000480229,;CBWD5,downstream_gene_variant,,ENST00000377389,;CBWD5,downstream_gene_variant,,ENST00000486221,;CBWD5,downstream_gene_variant,,ENST00000497250,;CBWD5,downstream_gene_variant,,ENST00000463075,;CBWD5,downstream_gene_variant,,ENST00000491485,;CBWD5,downstream_gene_variant,,ENST00000480819,; A ENST00000377413 Transcript missense_variant 998/2230 407/1251 136/416 A/D gCc/gAc 1 1 FOXD4L4 HGNC HGNC:23762 protein_coding YES CCDS75845.1 ENSP00000366630 Q8WXT5 UPI0000246F14 NM_199244.3 tolerated(0.49) 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF149,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 65737552 65737552 C A 1 0 0 0 0 1 0 0 0 5862 739 26 2 2 FOXD4L4 9 65737552 Missense_Mutation SNP C C3N-01074_T 453581 65737552 72657165 219 22208 TMOD1 0 . GRCh38 9 97546231 97546231 + Missense_Mutation SNP A A G novel C3N-01074_T C3N-01074_N A A c.167A>G p.Lys56Arg p.K56R ENST00000259365 3/10 210 170 40 198 198 0 strelka-varscan-mutect TMOD1,missense_variant,p.Lys56Arg,ENST00000259365,NM_003275.3;TMOD1,missense_variant,p.Lys56Arg,ENST00000395211,NM_001166116.1; G ENST00000259365 Transcript missense_variant 380/3343 167/1080 56/359 K/R aAg/aGg 1 1 TMOD1 HGNC HGNC:11871 protein_coding YES CCDS6726.1 ENSP00000259365 P28289 UPI000013707E NM_003275.3 deleterious(0.04) 3/10 hmmpanther:PTHR10901:SF8,hmmpanther:PTHR10901,Pfam_domain:PF03250 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 97546231 97546231 A G 1 0 0 0 0 1 0 0 0 16709 72 3 5 5 TMOD1 9 97546231 Missense_Mutation SNP A C3N-01074_T 31808679 97546231 40848486 220 22209 GABBR2 0 . GRCh38 9 98394210 98394210 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.1343C>T p.Thr448Ile p.T448I ENST00000259455 9/19 220 176 44 232 232 0 strelka-varscan-mutect GABBR2,missense_variant,p.Thr448Ile,ENST00000259455,NM_005458.7;GABBR2,non_coding_transcript_exon_variant,,ENST00000637410,; A ENST00000259455 Transcript missense_variant 1803/5788 1343/2826 448/941 T/I aCa/aTa 1 -1 GABBR2 HGNC HGNC:4507 protein_coding YES CCDS6736.1 ENSP00000259455 O75899 H9NIL8 UPI0000035832 NM_005458.7 tolerated(0.2) 9/19 Prints_domain:PR01178,hmmpanther:PTHR10519,hmmpanther:PTHR10519:SF40,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 98394210 98394210 G A 1 0 0 0 0 1 0 0 0 6027 1377 48 3 3 GABBR2 9 98394210 Missense_Mutation SNP G C3N-01074_T 847979 98394210 40000507 221 22210 COL27A1 0 . GRCh38 9 114183058 114183059 + Frame_Shift_Ins INS - - T novel C3N-01074_T C3N-01074_N - - c.1999_2000insT p.Gly667ValfsTer26 p.G667Vfs*26 ENST00000356083 5/61 201 172 29 208 208 0 sindel-varindel-pindel COL27A1,frameshift_variant,p.Gly667ValfsTer26,ENST00000356083,NM_032888.3;COL27A1,frameshift_variant,p.Gly614ValfsTer8,ENST00000451716,;COL27A1,frameshift_variant,p.Gly317ValfsTer8,ENST00000494090,; T ENST00000356083 Transcript frameshift_variant 2390-2391/7790 1999-2000/5583 667/1860 G/VX ggc/gTgc 1 1 COL27A1 HGNC HGNC:22986 protein_coding YES CCDS6802.1 ENSP00000348385 Q8IZC6 UPI0000062271 NM_032888.3 5/61 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF549,Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999928 1 1 1 0 T 7 5 73 114183058 114183058 - T 1 0 1 1 0 0 0 0 0 3474 1116 39 0 0 COL27A1 9 114183058 Frame_Shift_Ins INS - C3N-01074_T 15788848 114183058 24211659 222 22211 WHRN 0 . GRCh38 9 114406490 114406490 + Missense_Mutation SNP C C A rs111373159 C3N-01074_T C3N-01074_N C C c.2101G>T p.Gly701Cys p.G701C ENST00000362057 9/12 190 138 52 252 252 0 strelka-varscan-mutect WHRN,missense_variant,p.Gly701Cys,ENST00000362057,NM_015404.3,NM_001173425.1;WHRN,missense_variant,p.Gly350Cys,ENST00000374059,;WHRN,missense_variant,p.Gly318Cys,ENST00000265134,NM_001083885.2; A ENST00000362057 Transcript missense_variant 2270/3566 2101/2724 701/907 G/C Ggc/Tgc rs111373159 1 -1 WHRN HGNC HGNC:16361 protein_coding YES CCDS6806.1 ENSP00000354623 A0A0C4DFT9 UPI00003519A7 NM_015404.3,NM_001173425.1 tolerated(0.09) 9/12 hmmpanther:PTHR23116:SF37,hmmpanther:PTHR23116 MODERATE 1 SNV 1 1 PASS rs111373159 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 114406490 114406490 C A 1 0 0 0 0 1 0 0 0 17919 623 22 2 2 WHRN 9 114406490 Missense_Mutation SNP C C3N-01074_T 223432 114406490 23988227 223 22212 OR1L4 0 . GRCh38 9 122724361 122724361 + Silent SNP G G C novel C3N-01074_T C3N-01074_N G G c.372G>C p.= p.L124L ENST00000259466 1/1 219 164 55 328 328 0 strelka-varscan-mutect OR1L4,synonymous_variant,p.=,ENST00000259466,NM_001005235.1; C ENST00000259466 Transcript synonymous_variant 372/936 372/936 124/311 L ctG/ctC 1 1 OR1L4 HGNC HGNC:8216 protein_coding YES CCDS35129.1 ENSP00000259466 Q8NGR5 UPI0000061E7A NM_001005235.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF342,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 122724361 122724361 G C 1 0 0 0 0 0 0 0 1 11043 1335 47 4 4 OR1L4 9 122724361 Silent SNP G C3N-01074_T 8317871 122724361 15670356 224 22213 ODF2 0 . GRCh38 9 128484043 128484043 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.1093A>T p.Met365Leu p.M365L ENST00000434106 11/21 361 290 71 386 386 0 strelka-varscan-mutect ODF2,missense_variant,p.Met360Leu,ENST00000351030,NM_001242352.1;ODF2,missense_variant,p.Met365Leu,ENST00000434106,NM_153433.1;ODF2,missense_variant,p.Met341Leu,ENST00000393527,NM_002540.4,NM_153435.1;ODF2,missense_variant,p.Met365Leu,ENST00000604420,NM_001242353.1;ODF2,missense_variant,p.Met360Leu,ENST00000372807,;ODF2,missense_variant,p.Met341Leu,ENST00000444119,;ODF2,missense_variant,p.Met346Leu,ENST00000372791,NM_153437.2;ODF2,missense_variant,p.Met409Leu,ENST00000372814,NM_153432.1,NM_153439.1;ODF2,missense_variant,p.Met346Leu,ENST00000546203,NM_153440.1;ODF2,missense_variant,p.Met365Leu,ENST00000393533,NM_153436.1;ODF2,missense_variant,p.Met284Leu,ENST00000448249,NM_001242354.1;ODF2,missense_variant,p.Met308Leu,ENST00000421776,; T ENST00000434106 Transcript missense_variant 1456/3890 1093/2490 365/829 M/L Atg/Ttg 1 1 ODF2 HGNC HGNC:8114 protein_coding YES CCDS56588.1 ENSP00000403453 Q5BJF6 UPI0000211922 NM_153433.1 tolerated(0.08) 11/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23162,hmmpanther:PTHR23162:SF8 MODERATE 1 SNV 1 1 PASS rs910853145 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 128484043 128484043 A T 1 0 0 0 0 1 0 0 0 10905 217 8 4 4 ODF2 9 128484043 Missense_Mutation SNP A C3N-01074_T 5759682 128484043 9910674 225 22214 HMCN2 0 . GRCh38 9 130404913 130404914 + Frame_Shift_Ins INS - - A novel C3N-01074_T C3N-01074_N - - c.12135dupA p.Gly4046ArgfsTer15 p.G4046Rfs*15 ENST00000624552 81/98 56 51 5 97 97 0 varindel-pindel HMCN2,frameshift_variant,p.Gly4046ArgfsTer15,ENST00000624552,NM_001291815.1;RN7SL665P,downstream_gene_variant,,ENST00000578793,;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,non_coding_transcript_exon_variant,,ENST00000480829,; A ENST00000624552 Transcript frameshift_variant 12133-12134/15610 12133-12134/15180 4045/5059 E/EX gaa/gAaa 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 81/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 insertion 5 2 1 PASS . . 0 194 12 2 0 0 0 2 -3.752376 0 0 1 0 0 A 7 5 73 130404913 130404913 - A 1 0 1 1 0 0 0 0 0 7112 1059 37 0 0 HMCN2 9 130404913 Frame_Shift_Ins INS - C3N-01074_T 1920870 130404913 7989804 226 22215 ABL1 0 . GRCh38 9 130872146 130872146 + Frame_Shift_Del DEL G G - novel C3N-01074_T C3N-01074_N G G c.898delG p.Glu300LysfsTer4 p.E300Kfs*4 ENST00000372348 5/11 136 101 35 119 119 0 sindel-varindel-pindel ABL1,frameshift_variant,p.Glu281LysfsTer4,ENST00000318560,NM_005157.5;ABL1,frameshift_variant,p.Glu300LysfsTer4,ENST00000372348,NM_007313.2; - ENST00000372348 Transcript frameshift_variant 1271/3824 897/3450 299/1149 V/X gtG/gt 1 1 ABL1 HGNC HGNC:76 protein_coding YES CCDS35165.1 ENSP00000361423 P00519 UPI000013E4DE NM_007313.2 5/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF88,Gene3D:3.30.200.20,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 130872146 130872146 G - 1 0 1 0 1 0 0 0 0 102 1335 47 0 0 ABL1 9 130872146 Frame_Shift_Del DEL G C3N-01074_T 467233 130872146 7522571 227 22216 LAMC3 0 . GRCh38 9 131009364 131009364 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.150C>T p.= p.A50A ENST00000361069 1/28 214 161 53 231 231 0 strelka-varscan-mutect LAMC3,synonymous_variant,p.=,ENST00000361069,NM_006059.3;LAMC3,non_coding_transcript_exon_variant,,ENST00000480883,; T ENST00000361069 Transcript synonymous_variant 283/6133 150/4728 50/1575 A gcC/gcT 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 1/28 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF240,SMART_domains:SM00136 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 131009364 131009364 C T 1 0 0 0 0 0 0 0 1 8520 668 24 3 3 LAMC3 9 131009364 Silent SNP C C3N-01074_T 137218 131009364 7385353 228 22217 PRRC2B 0 . GRCh38 9 131485018 131485018 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.5636G>T p.Gly1879Val p.G1879V ENST00000357304 24/31 182 132 50 178 178 0 strelka-varscan-mutect PRRC2B,missense_variant,p.Gly1879Val,ENST00000357304,NM_013318.3;PRRC2B,missense_variant,p.Gly1185Val,ENST00000405995,;PRRC2B,upstream_gene_variant,,ENST00000320547,;PRRC2B,downstream_gene_variant,,ENST00000451855,;PRRC2B,upstream_gene_variant,,ENST00000458550,;SNORD62A,upstream_gene_variant,,ENST00000428514,; T ENST00000357304 Transcript missense_variant 5691/11042 5636/6690 1879/2229 G/V gGc/gTc 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 tolerated(0.13) 24/31 hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 131485018 131485018 G T 1 0 0 0 0 1 0 0 0 12749 1203 42 2 2 PRRC2B 9 131485018 Missense_Mutation SNP G C3N-01074_T 475654 131485018 6909699 229 22218 KCNT1 0 . GRCh38 9 135765648 135765648 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.1225C>G p.Pro409Ala p.P409A ENST00000371757 13/31 81 61 20 89 89 0 strelka-varscan-mutect KCNT1,missense_variant,p.Pro364Ala,ENST00000628528,NM_001272003.1;KCNT1,missense_variant,p.Pro376Ala,ENST00000263604,;KCNT1,missense_variant,p.Pro409Ala,ENST00000371757,NM_020822.2;KCNT1,missense_variant,p.Pro390Ala,ENST00000631073,;KCNT1,missense_variant,p.Pro409Ala,ENST00000487664,;KCNT1,missense_variant,p.Pro370Ala,ENST00000486577,;KCNT1,missense_variant,p.Pro390Ala,ENST00000490355,;KCNT1,missense_variant,p.Pro390Ala,ENST00000488444,;KCNT1,missense_variant,p.Pro390Ala,ENST00000491806,;KCNT1,missense_variant,p.Pro356Ala,ENST00000630792,;KCNT1,upstream_gene_variant,,ENST00000636003,;KCNT1,upstream_gene_variant,,ENST00000637082,;KCNT1,upstream_gene_variant,,ENST00000636995,;KCNT1,upstream_gene_variant,,ENST00000637668,;KCNT1,upstream_gene_variant,,ENST00000637798,;KCNT1,3_prime_UTR_variant,,ENST00000460750,;KCNT1,non_coding_transcript_exon_variant,,ENST00000490363,; G ENST00000371757 Transcript missense_variant 1292/4717 1225/3708 409/1235 P/A Ccc/Gcc 1 1 KCNT1 HGNC HGNC:18865 protein_coding YES CCDS35175.2 ENSP00000360822 Q5JUK3 UPI000192C42B NM_020822.2 deleterious(0.04) 13/31 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF14 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 135765648 135765648 C G 1 0 0 0 0 1 0 0 0 8007 623 22 4 4 KCNT1 9 135765648 Missense_Mutation SNP C C3N-01074_T 4280630 135765648 2629069 230 22219 SDCCAG3 0 . GRCh38 9 136407347 136407347 + Nonsense_Mutation SNP G G T rs373282483 C3N-01074_T C3N-01074_N G G c.617C>A p.Ser206Ter p.S206* ENST00000357365 5/10 199 149 50 169 169 0 strelka-varscan-mutect SDCCAG3,stop_gained,p.Ser183Ter,ENST00000298537,NM_006643.3;SDCCAG3,stop_gained,p.Ser206Ter,ENST00000357365,NM_001039707.1;SDCCAG3,stop_gained,p.Ser133Ter,ENST00000371725,NM_001039708.1;SDCCAG3,stop_gained,p.Ser156Ter,ENST00000371723,;PMPCA,upstream_gene_variant,,ENST00000371717,NM_015160.2;PMPCA,upstream_gene_variant,,ENST00000399219,NM_001282946.1,NM_001282944.1;SDCCAG3,upstream_gene_variant,,ENST00000417512,;SDCCAG3,downstream_gene_variant,,ENST00000446833,;SDCCAG3,non_coding_transcript_exon_variant,,ENST00000468963,;SDCCAG3,upstream_gene_variant,,ENST00000461693,;PMPCA,upstream_gene_variant,,ENST00000610649,;SDCCAG3,upstream_gene_variant,,ENST00000486441,;SDCCAG3,upstream_gene_variant,,ENST00000466579,;SDCCAG3,upstream_gene_variant,,ENST00000481114,;PMPCA,upstream_gene_variant,,ENST00000612553,;PMPCA,upstream_gene_variant,,ENST00000622209,;PMPCA,upstream_gene_variant,,ENST00000371720,;PMPCA,upstream_gene_variant,,ENST00000620412,;PMPCA,upstream_gene_variant,,ENST00000620895,;PMPCA,upstream_gene_variant,,ENST00000614402,;PMPCA,upstream_gene_variant,,ENST00000619192,; T ENST00000357365 Transcript stop_gained 747/2304 617/1308 206/435 S/* tCg/tAg rs373282483,COSM213471 1 -1 SDCCAG3 HGNC HGNC:10667 protein_coding YES CCDS43904.1 ENSP00000349929 Q96C92 UPI00006C511A NM_001039707.1 5/10 hmmpanther:PTHR31259 0,1 HIGH SNV 5 0,1 1 PASS rs373282483 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 136407347 136407347 G T 1 0 0 0 0 0 1 0 0 14229 1059 37 1 1 SDCCAG3 9 136407347 Nonsense_Mutation SNP G C3N-01074_T 641699 136407347 1987370 231 22220 NOTCH1 0 . GRCh38 9 136504825 136504825 + Silent SNP G G A rs772314400 C3N-01074_T C3N-01074_N G G c.4866C>T p.= p.R1622R ENST00000277541 26/34 298 242 56 282 282 0 strelka-varscan-mutect NOTCH1,synonymous_variant,p.=,ENST00000277541,NM_017617.3;NOTCH1,non_coding_transcript_exon_variant,,ENST00000494783,; A ENST00000277541 Transcript synonymous_variant 4942/9371 4866/7668 1622/2555 R cgC/cgT rs772314400,COSM308620 1 -1 NOTCH1 HGNC HGNC:7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 UPI0000210F68 NM_017617.3 26/34 PIRSF_domain:PIRSF002279,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF69,SMART_domains:SM01338 0,1 LOW 1 SNV 1 0,1 1 PASS rs772314400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 136504825 136504825 G A 1 0 0 0 0 0 0 0 1 10592 1074 38 1 1 NOTCH1 9 136504825 Silent SNP G C3N-01074_T 97478 136504825 1889892 232 22221 NOTCH1 0 . GRCh38 9 136516092 136516092 + Missense_Mutation SNP A A T rs770672556 C3N-01074_T C3N-01074_N A A c.1558T>A p.Phe520Ile p.F520I ENST00000277541 10/34 283 232 51 263 263 0 strelka-mutect NOTCH1,missense_variant,p.Phe520Ile,ENST00000277541,NM_017617.3;MIR4673,downstream_gene_variant,,ENST00000584777,; T ENST00000277541 Transcript missense_variant,splice_region_variant 1634/9371 1558/7668 520/2555 F/I Ttc/Atc rs770672556 1 -1 NOTCH1 HGNC HGNC:7881 protein_coding YES CCDS43905.1 ENSP00000277541 P46531 UPI0000210F68 NM_017617.3 deleterious(0) 10/34 Gene3D:2.10.25.10,Pfam_domain:PF00008,PIRSF_domain:PIRSF002279,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF69,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs770672556 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 136516092 136516092 A T 1 0 0 0 0 1 0 0 0 10592 86 3 4 4 NOTCH1 9 136516092 Missense_Mutation SNP A C3N-01074_T 11267 136516092 1878625 233 22222 NELFB 0 . GRCh38 9 137272616 137272616 + Splice_Site SNP G G T novel C3N-01074_T C3N-01074_N G G c.1596+1G>T p.X532_splice ENST00000634710 120 94 26 129 129 0 strelka-varscan-mutect NELFB,splice_donor_variant,,ENST00000343053,;NELFB,splice_donor_variant,,ENST00000634710,NM_015456.3; T ENST00000634710 Transcript splice_donor_variant -/2565 1596/1743 532/580 1 1 NELFB HGNC HGNC:24324 protein_coding YES CCDS7040.1 ENSP00000489248 Q8WX92 UPI0000070699 NM_015456.3 12/12 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 73 137272616 137272616 G T 1 0 0 0 0 0 0 1 0 10361 1275 44 2 2 NELFB 9 137272616 Splice_Site SNP G C3N-01074_T 756524 137272616 1122101 234 22223 CACNA1B 0 . GRCh38 9 138114410 138114410 + Missense_Mutation SNP G G T rs763934366 C3N-01074_T C3N-01074_N G G c.5569G>T p.Ala1857Ser p.A1857S ENST00000371372 41/47 260 219 41 264 264 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Ala1857Ser,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Ala1855Ser,ENST00000371363,;CACNA1B,missense_variant,p.Ala1858Ser,ENST00000371355,;CACNA1B,missense_variant,p.Ala1856Ser,ENST00000371357,;CACNA1B,missense_variant,p.Ala1857Ser,ENST00000277549,;CACNA1B,missense_variant,p.Ala1857Ser,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 5714/9790 5569/7020 1857/2339 A/S Gct/Tct rs763934366 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 tolerated(0.06) 41/47 Pfam_domain:PF08763,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,SMART_domains:SM01062 MODERATE 1 SNV 5 1 PASS rs763934366 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 73 138114410 138114410 G T 1 0 0 0 0 1 0 0 0 2227 971 34 2 2 CACNA1B 9 138114410 Missense_Mutation SNP G C3N-01074_T 841794 138114410 280307 235 22224 CACNA1B 0 . GRCh38 9 138117979 138117979 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.5811C>T p.= p.V1937V ENST00000371372 43/47 66 50 16 82 82 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript synonymous_variant 5956/9790 5811/7020 1937/2339 V gtC/gtT 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 43/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 138117979 138117979 C T 1 0 0 0 0 0 0 0 1 2227 900 32 3 3 CACNA1B 9 138117979 Silent SNP C C3N-01074_T 3569 138117979 276738 236 22225 FAM171A1 0 . GRCh38 10 15283877 15283877 + Splice_Site SNP C C G novel C3N-01074_T C3N-01074_N C C c.325+1G>C p.X109_splice ENST00000378116 176 146 30 198 198 0 strelka-varscan-mutect FAM171A1,splice_donor_variant,,ENST00000378116,NM_001010924.1;FAM171A1,splice_donor_variant,,ENST00000455654,; G ENST00000378116 Transcript splice_donor_variant -/3952 325/2673 109/890 1 -1 FAM171A1 HGNC HGNC:23522 protein_coding YES CCDS31154.1 ENSP00000367356 Q5VUB5 UPI00001414CA NM_001010924.1 2/7 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 73 15283877 15283877 C G 1 0 0 0 0 0 0 1 0 5337 521 18 4 4 FAM171A1 10 15283877 Splice_Site SNP C C3N-01074_T 15283877 118513545 237 22226 CACNB2 0 . GRCh38 10 18514259 18514259 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.694T>A p.Leu232Ile p.L232I ENST00000324631 7/14 602 419 183 564 564 0 strelka-varscan-mutect CACNB2,missense_variant,p.Leu177Ile,ENST00000396576,NM_000724.3;CACNB2,missense_variant,p.Leu204Ile,ENST00000282343,NM_201571.3,NM_001167945.1;CACNB2,missense_variant,p.Leu184Ile,ENST00000377315,NM_201570.2;CACNB2,missense_variant,p.Leu232Ile,ENST00000324631,NM_201596.2,NM_201593.2;CACNB2,missense_variant,p.Leu178Ile,ENST00000377329,NM_201590.2;CACNB2,intron_variant,,ENST00000617363,;CACNB2,intron_variant,,ENST00000612134,;CACNB2,intron_variant,,ENST00000615785,;CACNB2,intron_variant,,ENST00000377319,;CACNB2,intron_variant,,ENST00000352115,NM_201597.2;CACNB2,intron_variant,,ENST00000377331,NM_201572.3;CACNB2,intron_variant,,ENST00000377328,;CACNB2,intron_variant,,ENST00000612743,;RP11-499P20.2,intron_variant,,ENST00000425669,; A ENST00000324631 Transcript missense_variant 754/3446 694/1983 232/660 L/I Tta/Ata 1 1 CACNB2 HGNC HGNC:1402 protein_coding YES CCDS7125.1 ENSP00000320025 Q08289 UPI00001AEA80 NM_201596.2,NM_201593.2 tolerated(0.11) 7/14 hmmpanther:PTHR11824:SF9,hmmpanther:PTHR11824,Prints_domain:PR01628 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 18514259 18514259 T A 1 0 0 0 0 1 0 0 0 2241 1606 56 4 4 CACNB2 10 18514259 Missense_Mutation SNP T C3N-01074_T 3230382 18514259 115283163 238 22227 PTCHD3 0 . GRCh38 10 27399032 27399032 + Silent SNP G G T rs754250965 C3N-01074_T C3N-01074_N G G c.1566C>A p.= p.T522T ENST00000438700 4/4 193 117 76 213 212 1 strelka-varscan-mutect PTCHD3,synonymous_variant,p.=,ENST00000438700,NM_001034842.3;PTCHD3,intron_variant,,ENST00000622555,; T ENST00000438700 Transcript synonymous_variant 1684/2529 1566/2304 522/767 T acC/acA rs754250965 1 -1 PTCHD3 HGNC HGNC:24776 protein_coding YES CCDS31173.1 ENSP00000417658 Q3KNS1 UPI000004E892 NM_001034842.3 4/4 Gene3D:2j8sB01,Pfam_domain:PF02460,PROSITE_profiles:PS50156,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF60,Superfamily_domains:SSF82866,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs754250965 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 27399032 27399032 G T 1 0 0 0 0 0 0 0 1 12886 1219 43 2 2 PTCHD3 10 27399032 Silent SNP G C3N-01074_T 8884773 27399032 106398390 239 22228 ZEB1 0 . GRCh38 10 31527072 31527072 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.3186G>T p.= p.G1062G ENST00000361642 9/9 424 267 157 425 425 0 strelka-varscan-mutect ZEB1,synonymous_variant,p.=,ENST00000446923,NM_001323656.1,NM_001323664.1,NM_001323657.1,NM_001323650.1,NM_001128128.2,NM_001174094.1;ZEB1,synonymous_variant,p.=,ENST00000361642,NM_001174096.1;ZEB1,synonymous_variant,p.=,ENST00000320985,NM_030751.5;ZEB1,synonymous_variant,p.=,ENST00000560721,NM_001174093.1;ZEB1,synonymous_variant,p.=,ENST00000542815,NM_001174095.1;ZEB1,downstream_gene_variant,,ENST00000559858,;ZEB1,3_prime_UTR_variant,,ENST00000437844,NM_001323663.1,NM_001323661.1,NM_001323644.1,NM_001323649.1,NM_001323659.1,NM_001323652.1,NM_001323673.1,NM_001323662.1,NM_001323676.1,NM_001323653.1,NM_001323655.1,NM_001323645.1,NM_001323647.1,NM_001323660.1,NM_001323671.1,NM_001323638.1,NM_001323665.1,NM_001323643.1,NM_001323677.1,NM_001323641.1,NM_001323642.1,NM_001323658.1,NM_001323651.1,NM_001323672.1,NM_001323654.1;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,downstream_gene_variant,,ENST00000558655,; T ENST00000361642 Transcript synonymous_variant 3249/5990 3186/3378 1062/1125 G ggG/ggT 1 1 ZEB1 HGNC HGNC:11642 protein_coding YES CCDS53505.1 ENSP00000354487 P37275 UPI000068F51D NM_001174096.1 9/9 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF17,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 31527072 31527072 G T 1 0 0 0 0 0 0 0 1 18199 1219 43 2 2 ZEB1 10 31527072 Silent SNP G C3N-01074_T 4128040 31527072 102270350 240 22229 ZNF25 0 . GRCh38 10 37971707 37971707 + Splice_Site SNP C C A novel C3N-01074_T C3N-01074_N C C c.15+1G>T p.X5_splice ENST00000302609 294 237 57 210 210 0 strelka-varscan-mutect ZNF25,splice_donor_variant,,ENST00000302609,NM_145011.2;ZNF25,splice_donor_variant,,ENST00000374633,;ZNF25,splice_donor_variant,,ENST00000467975,; A ENST00000302609 Transcript splice_donor_variant -/4139 15/1371 5/456 1 -1 ZNF25 HGNC HGNC:13043 protein_coding YES CCDS7195.1 ENSP00000302222 P17030 UPI0000071FFD NM_145011.2 2/5 HIGH 1 SNV 1 1 PASS rs1286519553 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 73 37971707 37971707 C A 1 0 0 0 0 0 0 1 0 18370 521 18 2 2 ZNF25 10 37971707 Splice_Site SNP C C3N-01074_T 6444635 37971707 95825715 241 22230 ZNF487 0 . GRCh38 10 43481475 43481475 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.180A>T p.Gln60His p.Q60H ENST00000437590 4/4 302 241 61 266 266 0 strelka-varscan-mutect ZNF487,missense_variant,p.Gln60His,ENST00000437590,;ZNF487,missense_variant,p.Gln122His,ENST00000315429,;ZNF487,missense_variant,p.Gln28His,ENST00000456416,; T ENST00000437590 Transcript missense_variant 407/2111 180/627 60/208 Q/H caA/caT 1 1 ZNF487 HGNC HGNC:23488 protein_coding YES ENSP00000392335 B1APH4 UPI00019151EB deleterious(0.04) 4/4 hmmpanther:PTHR24381:SF30,hmmpanther:PTHR24381 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 43481475 43481475 A T 1 0 0 0 0 1 0 0 0 18512 69 3 4 4 ZNF487 10 43481475 Missense_Mutation SNP A C3N-01074_T 5509768 43481475 90315947 242 22231 WDFY4 0 . GRCh38 10 48811603 48811603 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.5109C>A p.= p.V1703V ENST00000325239 29/61 270 222 48 222 221 1 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1;WDFY4,synonymous_variant,p.=,ENST00000374161,; A ENST00000325239 Transcript synonymous_variant 5109/9555 5109/9555 1703/3184 V gtC/gtA 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 29/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 48811603 48811603 C A 1 0 0 0 0 0 0 0 1 17831 900 32 2 2 WDFY4 10 48811603 Silent SNP C C3N-01074_T 5330128 48811603 84985819 243 22232 OGDHL 0 . GRCh38 10 49747063 49747063 + Missense_Mutation SNP T T A rs373158682 C3N-01074_T C3N-01074_N T T c.1133A>T p.Glu378Val p.E378V ENST00000374103 9/23 157 116 41 138 138 0 strelka-varscan-mutect OGDHL,missense_variant,p.Glu378Val,ENST00000374103,NM_018245.2;OGDHL,missense_variant,p.Glu321Val,ENST00000419399,NM_001143996.1;OGDHL,missense_variant,p.Glu169Val,ENST00000432695,NM_001143997.1;OGDHL,upstream_gene_variant,,ENST00000496884,; A ENST00000374103 Transcript missense_variant 1219/3704 1133/3033 378/1010 E/V gAg/gTg rs373158682 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 tolerated(0.16) 9/23 Gene3D:3.40.50.970,Pfam_domain:PF00676,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS rs373158682 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 49747063 49747063 T A 1 0 0 0 0 1 0 0 0 10914 1551 54 4 4 OGDHL 10 49747063 Missense_Mutation SNP T C3N-01074_T 935460 49747063 84050359 244 22233 PALD1 0 . GRCh38 10 70538959 70538959 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1520G>T p.Arg507Leu p.R507L ENST00000263563 13/20 426 319 107 314 314 0 strelka-varscan-mutect PALD1,missense_variant,p.Arg507Leu,ENST00000263563,NM_014431.2; T ENST00000263563 Transcript missense_variant 1788/4555 1520/2571 507/856 R/L cGg/cTg 1 1 PALD1 HGNC HGNC:23530 protein_coding YES CCDS31215.1 ENSP00000263563 Q9ULE6 A0A024QZM5 UPI00001C1EDC NM_014431.2 deleterious(0) 13/20 hmmpanther:PTHR23339,hmmpanther:PTHR23339:SF54,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 70538959 70538959 G T 1 0 0 0 0 1 0 0 0 11486 1116 39 1 1 PALD1 10 70538959 Missense_Mutation SNP G C3N-01074_T 20791896 70538959 63258463 245 22234 PLAU 0 . GRCh38 10 73913079 73913079 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.349G>T p.Gly117Trp p.G117W ENST00000372764 5/11 164 111 53 118 118 0 strelka-varscan-mutect PLAU,missense_variant,p.Gly100Trp,ENST00000446342,NM_001145031.1;PLAU,missense_variant,p.Gly117Trp,ENST00000372764,NM_001319191.1,NM_002658.3;C10orf55,splice_region_variant,,ENST00000412307,NM_001001791.2;PLAU,downstream_gene_variant,,ENST00000481390,;C10orf55,splice_region_variant,,ENST00000409178,;PLAU,non_coding_transcript_exon_variant,,ENST00000494287,;PLAU,downstream_gene_variant,,ENST00000496926,; T ENST00000372764 Transcript missense_variant 442/2321 349/1296 117/431 G/W Ggg/Tgg 1 1 PLAU HGNC HGNC:9052 protein_coding YES CCDS7339.1 ENSP00000361850 P00749 UPI000013CB02 NM_001319191.1,NM_002658.3 deleterious(0) 5/11 PROSITE_profiles:PS50070,hmmpanther:PTHR24264:SF18,hmmpanther:PTHR24264,Pfam_domain:PF00051,Gene3D:2.40.20.10,SMART_domains:SM00130,Superfamily_domains:SSF57440,Prints_domain:PR00018 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 73913079 73913079 G T 1 0 0 0 0 1 0 0 0 12116 1246 43 2 2 PLAU 10 73913079 Missense_Mutation SNP G C3N-01074_T 3374120 73913079 59884343 246 22235 LRIT1 0 . GRCh38 10 84234192 84234192 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.776G>T p.Gly259Val p.G259V ENST00000372105 3/4 184 138 46 112 112 0 strelka-varscan-mutect LRIT1,missense_variant,p.Gly259Val,ENST00000372105,NM_015613.2; A ENST00000372105 Transcript missense_variant 798/2228 776/1872 259/623 G/V gGa/gTa COSM685177 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 tolerated(0.06) 3/4 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 84234192 84234192 C A 1 0 0 0 0 1 0 0 0 8842 855 30 2 2 LRIT1 10 84234192 Missense_Mutation SNP C C3N-01074_T 10321113 84234192 49563230 247 22236 LIPF 0 . GRCh38 10 88667287 88667287 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.20G>T p.Ser7Ile p.S7I ENST00000394375 3/11 186 136 50 158 157 1 strelka-varscan-mutect LIPF,missense_variant,p.Ser7Ile,ENST00000394375,NM_001198829.1;LIPF,missense_variant,p.Ser7Ile,ENST00000355843,NM_001198830.1;LIPF,splice_region_variant,,ENST00000238983,NM_004190.3;LIPF,splice_region_variant,,ENST00000608620,NM_001198828.1;LIPF,splice_region_variant,,ENST00000609378,; T ENST00000394375 Transcript missense_variant,splice_region_variant 133/1470 20/1227 7/408 S/I aGc/aTc 1 1 LIPF HGNC HGNC:6622 protein_coding YES CCDS55718.1 ENSP00000377900 P07098 UPI0001E92A2A NM_001198829.1 tolerated(0.2) 3/11 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF15,PIRSF_domain:PIRSF000862 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 88667287 88667287 G T 1 0 0 0 0 1 0 0 0 8743 1217 42 2 2 LIPF 10 88667287 Missense_Mutation SNP G C3N-01074_T 4433095 88667287 45130135 248 22237 PPP1R3C 0 . GRCh38 10 91630071 91630071 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.810G>T p.Met270Ile p.M270I ENST00000238994 2/2 368 255 113 380 380 0 strelka-varscan-mutect PPP1R3C,missense_variant,p.Met270Ile,ENST00000238994,NM_005398.5; A ENST00000238994 Transcript missense_variant 895/2524 810/954 270/317 M/I atG/atT 1 -1 PPP1R3C HGNC HGNC:9293 protein_coding YES CCDS7416.1 ENSP00000238994 Q9UQK1 UPI000006EFF1 NM_005398.5 tolerated(0.2) 2/2 PIRSF_domain:PIRSF038207,PIRSF_domain:PIRSF500813,hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 91630071 91630071 C A 1 0 0 0 0 1 0 0 0 12494 594 21 2 2 PPP1R3C 10 91630071 Missense_Mutation SNP C C3N-01074_T 2962784 91630071 42167351 249 22238 ACSM6 0 . GRCh38 10 95207366 95207366 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.562G>C p.Val188Leu p.V188L ENST00000341686 4/11 629 449 180 473 472 1 strelka-varscan-mutect ACSM6,missense_variant,p.Val188Leu,ENST00000341686,NM_207321.2;ACSM6,missense_variant,p.Val188Leu,ENST00000394005,;ACSM6,3_prime_UTR_variant,,ENST00000327739,;ACSM6,3_prime_UTR_variant,,ENST00000404473,; C ENST00000341686 Transcript missense_variant 687/1712 562/1443 188/480 V/L Gtg/Ctg 1 1 ACSM6 HGNC HGNC:31665 protein_coding YES CCDS7440.2 ENSP00000340296 Q6P461 UPI00017BCE82 NM_207321.2 deleterious(0.03) 4/11 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF143,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS rs1270718616 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 95207366 95207366 G C 1 0 0 0 0 1 0 0 0 230 1261 44 4 4 ACSM6 10 95207366 Missense_Mutation SNP G C3N-01074_T 3577295 95207366 38590056 250 22239 SLIT1 0 . GRCh38 10 97056409 97056409 + Nonsense_Mutation SNP G G A C3N-01074_T C3N-01074_N G G c.1213C>T p.Gln405Ter p.Q405* ENST00000266058 13/37 249 181 68 201 201 0 strelka-varscan-mutect SLIT1,stop_gained,p.Gln405Ter,ENST00000266058,NM_003061.2;SLIT1,stop_gained,p.Gln405Ter,ENST00000371070,;SLIT1,stop_gained,p.Gln398Ter,ENST00000314867,;SLIT1,downstream_gene_variant,,ENST00000371041,; A ENST00000266058 Transcript stop_gained 1459/7925 1213/4605 405/1534 Q/* Cag/Tag COSM4645014,COSM4645015 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 13/37 Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 97056409 97056409 G A 1 0 0 0 0 0 1 0 0 15030 1328 46 3 3 SLIT1 10 97056409 Nonsense_Mutation SNP G C3N-01074_T 1849043 97056409 36741013 251 22240 SLIT1 0 . GRCh38 10 97057231 97057231 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.1136G>A p.Gly379Asp p.G379D ENST00000266058 12/37 218 175 43 215 215 0 strelka-varscan-mutect SLIT1,missense_variant,p.Gly379Asp,ENST00000266058,NM_003061.2;SLIT1,missense_variant,p.Gly379Asp,ENST00000371070,;SLIT1,missense_variant,p.Gly372Asp,ENST00000314867,;SLIT1,downstream_gene_variant,,ENST00000371041,; T ENST00000266058 Transcript missense_variant 1382/7925 1136/4605 379/1534 G/D gGc/gAc 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 deleterious(0.05) 12/37 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF39,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 97057231 97057231 C T 1 0 0 0 0 1 0 0 0 15030 739 26 3 3 SLIT1 10 97057231 Missense_Mutation SNP C C3N-01074_T 822 97057231 36740191 252 22241 INA 0 . GRCh38 10 103277662 103277662 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.451C>T p.Arg151Cys p.R151C ENST00000369849 1/3 64 43 21 73 73 0 strelka-varscan-mutect INA,missense_variant,p.Arg151Cys,ENST00000369849,NM_032727.3; T ENST00000369849 Transcript missense_variant 500/3231 451/1500 151/499 R/C Cgc/Tgc 1 1 INA HGNC HGNC:6057 protein_coding YES CCDS7545.1 ENSP00000358865 Q16352 UPI000012573C NM_032727.3 deleterious(0) 1/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239:SF132,hmmpanther:PTHR23239,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 103277662 103277662 C T 1 0 0 0 0 1 0 0 0 7632 768 27 1 1 INA 10 103277662 Missense_Mutation SNP C C3N-01074_T 6220431 103277662 30519760 253 22242 PNLIPRP1 0 . GRCh38 10 116598163 116598163 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.811G>T p.Ala271Ser p.A271S ENST00000528052 8/13 125 93 32 144 144 0 strelka-varscan-mutect PNLIPRP1,missense_variant,p.Ala271Ser,ENST00000528052,NM_001303135.1;PNLIPRP1,missense_variant,p.Ala271Ser,ENST00000358834,NM_006229.3;PNLIPRP1,missense_variant,p.Ala271Ser,ENST00000534537,;PNLIPRP1,downstream_gene_variant,,ENST00000531984,;PNLIPRP1,downstream_gene_variant,,ENST00000530319,;PNLIPRP1,downstream_gene_variant,,ENST00000527980,;PNLIPRP1,downstream_gene_variant,,ENST00000471549,;PNLIPRP1,downstream_gene_variant,,ENST00000480870,;PNLIPRP1,downstream_gene_variant,,ENST00000525157,;PNLIPRP1,downstream_gene_variant,,ENST00000510125,;PNLIPRP1,missense_variant,p.Ala161Ser,ENST00000482833,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000534513,;PNLIPRP1,downstream_gene_variant,,ENST00000482159,;PNLIPRP1,downstream_gene_variant,,ENST00000497792,;PNLIPRP1,downstream_gene_variant,,ENST00000484402,;PNLIPRP1,downstream_gene_variant,,ENST00000529584,; T ENST00000528052 Transcript missense_variant 882/1533 811/1404 271/467 A/S Gcg/Tcg 1 1 PNLIPRP1 HGNC HGNC:9156 protein_coding YES CCDS7595.1 ENSP00000433933 P54315 UPI000012E6AA NM_001303135.1 tolerated(0.24) 8/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF108,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 116598163 116598163 G T 1 0 0 0 0 1 0 0 0 12258 1217 42 2 2 PNLIPRP1 10 116598163 Missense_Mutation SNP G C3N-01074_T 13320501 116598163 17199259 254 22243 HSPA12A 0 . GRCh38 10 116674890 116674890 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.1919G>T p.Arg640Met p.R640M ENST00000369209 12/12 439 306 133 359 358 1 strelka-varscan-mutect HSPA12A,missense_variant,p.Arg657Met,ENST00000635765,;HSPA12A,missense_variant,p.Arg640Met,ENST00000369209,NM_025015.2;C10orf82,upstream_gene_variant,,ENST00000369210,NM_144661.2;C10orf82,upstream_gene_variant,,ENST00000588184,;RP11-498B4.5,downstream_gene_variant,,ENST00000433600,;C10orf82,upstream_gene_variant,,ENST00000588224,;C10orf82,upstream_gene_variant,,ENST00000467153,; A ENST00000369209 Transcript missense_variant 2024/5722 1919/2028 640/675 R/M aGg/aTg COSM5588008 1 -1 HSPA12A HGNC HGNC:19022 protein_coding YES CCDS41569.1 ENSP00000358211 O43301 UPI00001B3DE3 NM_025015.2 deleterious(0) 12/12 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF46 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 116674890 116674890 C A 1 0 0 0 0 1 0 0 0 7300 681 24 2 2 HSPA12A 10 116674890 Missense_Mutation SNP C C3N-01074_T 76727 116674890 17122532 255 22244 TACC2 0 . GRCh38 10 122086324 122086325 + Frame_Shift_Del DEL CA CA - novel C3N-01074_T C3N-01074_N CA CA c.3825_3826delAC p.Leu1276CysfsTer37 p.L1276Cfs*37 ENST00000369005 4/23 224 187 37 238 238 0 sindel-varindel-pindel TACC2,frameshift_variant,p.Leu1276CysfsTer37,ENST00000369005,NM_206862.3;TACC2,frameshift_variant,p.Leu1276CysfsTer37,ENST00000334433,;TACC2,frameshift_variant,p.Leu1276CysfsTer37,ENST00000515273,NM_001291877.1;TACC2,frameshift_variant,p.Leu1276CysfsTer37,ENST00000453444,;TACC2,frameshift_variant,p.Leu1276CysfsTer37,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,; - ENST00000369005 Transcript frameshift_variant 4164-4165/9673 3824-3825/8847 1275/2948 P/X cCA/c 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 4/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 122086324 122086324 CA - 1 0 1 0 1 0 0 0 0 15898 594 21 0 0 TACC2 10 122086324 Frame_Shift_Del DEL CA C3N-01074_T 5411434 122086324 11711098 256 22245 ADAM12 0 . GRCh38 10 126049408 126049408 + Silent SNP G G T rs780909978 C3N-01074_T C3N-01074_N G G c.1771C>A p.= p.R591R ENST00000368679 16/23 395 288 107 290 290 0 strelka-varscan-mutect ADAM12,synonymous_variant,p.=,ENST00000368679,NM_003474.5,NM_001288973.1;ADAM12,synonymous_variant,p.=,ENST00000368676,NM_021641.4,NM_001288974.1,NM_001288975.1;ADAM12,downstream_gene_variant,,ENST00000467145,; T ENST00000368679 Transcript synonymous_variant 2081/7938 1771/2730 591/909 R Cgg/Agg rs780909978 1 -1 ADAM12 HGNC HGNC:190 protein_coding YES CCDS7653.1 ENSP00000357668 O43184 UPI000036672C NM_003474.5,NM_001288973.1 16/23 Pfam_domain:PF08516,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF112,SMART_domains:SM00608 LOW 1 SNV 1 1 PASS rs780909978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 126049408 126049408 G T 1 0 0 0 0 0 0 0 1 280 1115 39 1 1 ADAM12 10 126049408 Silent SNP G C3N-01074_T 3963084 126049408 7748014 257 22246 CFAP46 0 . GRCh38 10 132808587 132808587 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.7982C>A p.Ala2661Asp p.A2661D ENST00000368586 58/58 302 202 100 182 182 0 strelka-varscan-mutect CFAP46,missense_variant,p.Ala2661Asp,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript missense_variant 8083/8278 7982/8148 2661/2715 A/D gCc/gAc 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 tolerated_low_confidence(0.06) 58/58 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 132808587 132808587 G T 1 0 0 0 0 1 0 0 0 3021 1203 42 2 2 CFAP46 10 132808587 Missense_Mutation SNP G C3N-01074_T 6759179 132808587 988835 258 22247 MUC5AC 0 . GRCh38 11 1186746 1186746 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.8601C>T p.= p.S2867S ENST00000621226 31/49 287 245 42 277 277 0 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript synonymous_variant 8648/17448 8601/16965 2867/5654 S agC/agT 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 31/49 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 1186746 1186746 C T 1 0 0 0 0 0 0 0 1 9978 709 25 3 3 MUC5AC 11 1186746 Silent SNP C C3N-01074_T 1186746 133899876 259 22248 BRSK2 0 . GRCh38 11 1445385 1445385 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.1042G>A p.Val348Met p.V348M ENST00000382179 10/20 320 225 95 259 259 0 strelka-varscan-mutect BRSK2,missense_variant,p.Val302Met,ENST00000308219,NM_003957.3;BRSK2,missense_variant,p.Val302Met,ENST00000528841,NM_001256627.1;BRSK2,missense_variant,p.Val348Met,ENST00000382179,NM_001256630.1;BRSK2,missense_variant,p.Val242Met,ENST00000528710,NM_001282218.1;BRSK2,missense_variant,p.Val302Met,ENST00000531197,NM_001256629.1;BRSK2,missense_variant,p.Val302Met,ENST00000526678,;BRSK2,downstream_gene_variant,,ENST00000528596,;BRSK2,downstream_gene_variant,,ENST00000524702,;BRSK2,missense_variant,p.Val302Met,ENST00000529433,;BRSK2,3_prime_UTR_variant,,ENST00000529951,;BRSK2,non_coding_transcript_exon_variant,,ENST00000531078,; A ENST00000382179 Transcript missense_variant 1295/3576 1042/2301 348/766 V/M Gtg/Atg 1 1 BRSK2 HGNC HGNC:11405 protein_coding YES CCDS58108.1 ENSP00000371614 Q8IWQ3 UPI000035E827 NM_001256630.1 deleterious(0) 10/20 hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF84 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 1445385 1445385 G A 1 0 0 0 0 1 0 0 0 1698 1145 40 1 1 BRSK2 11 1445385 Missense_Mutation SNP G C3N-01074_T 258639 1445385 133641237 260 22249 HBD 0 . GRCh38 11 5234167 5234168 + Frame_Shift_Ins INS - - A novel C3N-01074_T C3N-01074_N - - c.138dupT p.Gly47TrpfsTer7 p.G47Wfs*7 ENST00000380299 2/3 426 365 61 532 532 0 sindel-varindel-pindel HBD,frameshift_variant,p.Gly47TrpfsTer7,ENST00000380299,NM_000519.3;HBD,frameshift_variant,p.Gly47TrpfsTer7,ENST00000429817,;HBD,frameshift_variant,p.Gly47TrpfsTer7,ENST00000292901,;HBD,intron_variant,,ENST00000417377,;HBB,upstream_gene_variant,,ENST00000380315,; A ENST00000380299 Transcript frameshift_variant 353-354/785 138-139/444 46-47/147 -/X -/T 1 -1 HBD HGNC HGNC:4829 protein_coding YES CCDS31376.1 ENSP00000369654 P02042 A0N071 UPI0000161DC2 NM_000519.3 2/3 PROSITE_profiles:PS01033,hmmpanther:PTHR11442:SF50,hmmpanther:PTHR11442,Pfam_domain:PF00042,Gene3D:1.10.490.10,Superfamily_domains:SSF46458 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 73 5234167 5234167 - A 1 0 1 1 0 0 0 0 0 6865 594 21 0 0 HBD 11 5234167 Frame_Shift_Ins INS - C3N-01074_T 3788782 5234167 129852455 261 22250 UBQLNL 0 . GRCh38 11 5515398 5515398 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.1044C>T p.= p.T348T ENST00000380184 1/1 264 181 83 296 296 0 strelka-varscan-mutect UBQLNL,synonymous_variant,p.=,ENST00000380184,NM_145053.4;HBG2,intron_variant,,ENST00000380259,;OLFM5P,downstream_gene_variant,,ENST00000411807,; A ENST00000380184 Transcript synonymous_variant 1308/2313 1044/1428 348/475 T acC/acT 1 -1 UBQLNL HGNC HGNC:28294 protein_coding YES CCDS31385.1 ENSP00000369531 Q8IYU4 UPI000066D8EC NM_145053.4 1/1 hmmpanther:PTHR10677,hmmpanther:PTHR10677:SF9 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 5515398 5515398 G A 1 0 0 0 0 0 0 0 1 17424 1219 43 3 3 UBQLNL 11 5515398 Silent SNP G C3N-01074_T 281231 5515398 129571224 262 22251 OR52N1 0 . GRCh38 11 5788473 5788473 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.344G>T p.Gly115Val p.G115V ENST00000317078 1/1 351 245 106 426 426 0 strelka-varscan-mutect OR52N1,missense_variant,p.Gly115Val,ENST00000317078,NM_001001913.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000317078 Transcript missense_variant 344/963 344/963 115/320 G/V gGg/gTg 1 -1 OR52N1 HGNC HGNC:14853 protein_coding YES CCDS31398.1 ENSP00000322823 Q8NH53 UPI0000041BDD NM_001001913.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF145,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1467260512 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 5788473 5788473 C A 1 0 0 0 0 1 0 0 0 11200 623 22 2 2 OR52N1 11 5788473 Missense_Mutation SNP C C3N-01074_T 273075 5788473 129298149 263 22252 C11orf42 0 . GRCh38 11 6210547 6210547 + Missense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.770C>G p.Ala257Gly p.A257G ENST00000316375 2/3 202 164 38 239 239 0 strelka-varscan-mutect C11orf42,missense_variant,p.Ala257Gly,ENST00000316375,NM_173525.2;FAM160A2,downstream_gene_variant,,ENST00000265978,NM_032127.3;FAM160A2,downstream_gene_variant,,ENST00000449352,NM_001098794.1;FAM160A2,downstream_gene_variant,,ENST00000529360,; G ENST00000316375 Transcript missense_variant 820/1142 770/1002 257/333 A/G gCc/gGc COSM5003445 1 1 C11orf42 HGNC HGNC:28541 protein_coding YES CCDS7759.1 ENSP00000321021 Q8N5U0 UPI000013FD81 NM_173525.2 tolerated_low_confidence(0.25) 2/3 Pfam_domain:PF15668,hmmpanther:PTHR36872,hmmpanther:PTHR36872:SF1,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 6210547 6210547 C G 1 0 0 0 0 1 0 0 0 1782 739 26 4 4 C11orf42 11 6210547 Missense_Mutation SNP C C3N-01074_T 422074 6210547 128876075 264 22253 OR10A3 0 . GRCh38 11 7938626 7938626 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.895A>T p.Arg299Trp p.R299W ENST00000360759 1/1 158 112 46 189 188 1 strelka-varscan-mutect OR10A3,missense_variant,p.Arg299Trp,ENST00000360759,NM_001003745.1; A ENST00000360759 Transcript missense_variant 969/1061 895/945 299/314 R/W Agg/Tgg 1 -1 OR10A3 HGNC HGNC:8162 protein_coding YES CCDS31421.1 ENSP00000353988 P58181 A0A126GVZ2 UPI00000015AD NM_001003745.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF30,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1218621958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 7938626 7938626 T A 1 0 0 0 0 1 0 0 0 10967 1550 54 4 4 OR10A3 11 7938626 Missense_Mutation SNP T C3N-01074_T 1728079 7938626 127147996 265 22254 C11orf16 0 . GRCh38 11 8926994 8926994 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.505C>G p.Gln169Glu p.Q169E ENST00000326053 4/7 333 271 62 279 279 0 strelka-varscan-mutect C11orf16,missense_variant,p.Gln169Glu,ENST00000326053,NM_020643.2;C11orf16,missense_variant,p.Gln169Glu,ENST00000525780,;C11orf16,downstream_gene_variant,,ENST00000528998,;C11orf16,downstream_gene_variant,,ENST00000526227,;C11orf16,downstream_gene_variant,,ENST00000527607,;C11orf16,downstream_gene_variant,,ENST00000528830,; C ENST00000326053 Transcript missense_variant 612/1908 505/1404 169/467 Q/E Cag/Gag 1 -1 C11orf16 HGNC HGNC:1169 protein_coding YES CCDS7794.1 ENSP00000318999 Q9NQ32 UPI0000456489 NM_020643.2 deleterious(0) 4/7 hmmpanther:PTHR14343,hmmpanther:PTHR14343:SF3,Pfam_domain:PF15057 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 8926994 8926994 G C 1 0 0 0 0 1 0 0 0 1777 1328 46 4 4 C11orf16 11 8926994 Missense_Mutation SNP G C3N-01074_T 988368 8926994 126159628 266 22255 ALX4 0 . GRCh38 11 44267571 44267571 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.829C>A p.Gln277Lys p.Q277K ENST00000329255 3/4 296 256 40 294 293 1 strelka-varscan-mutect ALX4,missense_variant,p.Gln277Lys,ENST00000329255,NM_021926.3; T ENST00000329255 Transcript missense_variant 933/5750 829/1236 277/411 Q/K Cag/Aag 1 -1 ALX4 HGNC HGNC:450 protein_coding YES CCDS31468.1 ENSP00000332744 Q9H161 UPI000016A402 NM_021926.3 tolerated(0.26) 3/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF322 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -17.15396 0.996225 1 1 1 0 T 3 4 73 44267571 44267571 G T 1 0 0 0 0 1 0 0 0 656 1328 46 2 2 ALX4 11 44267571 Missense_Mutation SNP G C3N-01074_T 35340577 44267571 90819051 267 22256 OR4P4 0 . GRCh38 11 55638446 55638446 + Missense_Mutation SNP T T C novel C3N-01074_T C3N-01074_N T T c.89T>C p.Leu30Ser p.L30S ENST00000314612 1/1 99 47 52 84 84 0 strelka-varscan-mutect OR4P4,missense_variant,p.Leu30Ser,ENST00000314612,NM_001004124.2; C ENST00000314612 Transcript missense_variant 89/939 89/939 30/312 L/S tTg/tCg 1 1 OR4P4 HGNC HGNC:15180 protein_coding YES CCDS31504.1 ENSP00000324831 Q8NGL7 UPI0000061E8A NM_001004124.2 tolerated(0.23) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF386,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 23 186 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 55638446 55638446 T C 1 0 0 0 0 1 0 0 0 11156 1821 63 5 5 OR4P4 11 55638446 Missense_Mutation SNP T C3N-01074_T 11370875 55638446 79448176 268 22257 OR5D16 0 . GRCh38 11 55839565 55839565 + Missense_Mutation SNP A A T rs750491150 C3N-01074_T C3N-01074_N A A c.814A>T p.Thr272Ser p.T272S ENST00000378396 1/1 319 220 99 334 334 0 strelka-varscan-mutect OR5D16,missense_variant,p.Thr272Ser,ENST00000378396,NM_001005496.1; T ENST00000378396 Transcript missense_variant 814/987 814/987 272/328 T/S Aca/Tca rs750491150 1 1 OR5D16 HGNC HGNC:15283 protein_coding YES CCDS31512.1 ENSP00000367649 Q8NGK9 UPI0000046198 NM_001005496.1 tolerated(0.24) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs750491150 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 55839565 55839565 A T 1 0 0 0 0 1 0 0 0 11226 159 6 4 4 OR5D16 11 55839565 Missense_Mutation SNP A C3N-01074_T 201119 55839565 79247057 269 22258 OR5M11 0 . GRCh38 11 56543179 56543179 + Missense_Mutation SNP G G A rs781692218 C3N-01074_T C3N-01074_N G G c.79C>T p.Leu27Phe p.L27F ENST00000528616 1/1 254 211 43 216 216 0 strelka-varscan-mutect OR5M11,missense_variant,p.Leu27Phe,ENST00000528616,NM_001005245.1; A ENST00000528616 Transcript missense_variant 79/918 79/918 27/305 L/F Ctt/Ttt rs781692218,COSM5318905 1 -1 OR5M11 HGNC HGNC:15291 protein_coding YES CCDS53629.1 ENSP00000432417 Q96RB7 A0A126GVL9 UPI00000405CF NM_001005245.1 tolerated(0.24) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF97,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs781692218 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 56543179 56543179 G A 1 0 0 0 0 1 0 0 0 11243 971 34 3 3 OR5M11 11 56543179 Missense_Mutation SNP G C3N-01074_T 703614 56543179 78543443 270 22259 OR9Q2 0 . GRCh38 11 58191251 58191251 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.761C>A p.Thr254Asn p.T254N ENST00000311591 1/1 169 98 71 253 249 4 strelka-varscan-mutect OR9Q2,missense_variant,p.Thr254Asn,ENST00000311591,NM_001005283.2; A ENST00000311591 Transcript missense_variant 818/1085 761/945 254/314 T/N aCc/aAc 1 1 OR9Q2 HGNC HGNC:15328 protein_coding YES CCDS31544.1 ENSP00000308714 Q8NGE9 A0A126GW85 UPI0000061ECB NM_001005283.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF155,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 58191251 58191251 C A 1 0 0 0 0 1 0 0 0 11322 507 18 2 2 OR9Q2 11 58191251 Missense_Mutation SNP C C3N-01074_T 1648072 58191251 76895371 271 22260 OR5B17 0 . GRCh38 11 58358938 58358938 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.132C>A p.= p.I44I ENST00000357377 1/1 263 223 40 297 296 1 strelka-varscan-mutect OR5B17,synonymous_variant,p.=,ENST00000357377,NM_001005489.1;AP000435.3,upstream_gene_variant,,ENST00000528539,; T ENST00000357377 Transcript synonymous_variant 132/946 132/945 44/314 I atC/atA 1 -1 OR5B17 HGNC HGNC:15267 protein_coding YES CCDS31548.1 ENSP00000349945 Q8NGF7 A0A126GVL8 UPI0000041DFA NM_001005489.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF185,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 58358938 58358938 G T 1 0 0 0 0 0 0 0 1 11220 1280 45 2 2 OR5B17 11 58358938 Silent SNP G C3N-01074_T 167687 58358938 76727684 272 22261 MS4A14 0 . GRCh38 11 60400426 60400426 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.290C>A p.Thr97Lys p.T97K ENST00000531783 3/6 113 99 14 106 106 0 strelka-varscan-mutect MS4A14,missense_variant,p.Thr97Lys,ENST00000300187,NM_032597.4;MS4A14,missense_variant,p.Thr97Lys,ENST00000531783,NM_001261828.1;MS4A14,missense_variant,p.Thr56Lys,ENST00000534688,;MS4A14,intron_variant,,ENST00000395001,NM_001261827.1;MS4A14,intron_variant,,ENST00000395005,NM_001079692.2;MS4A14,intron_variant,,ENST00000531787,;MS4A14,intron_variant,,ENST00000526375,;MS4A7,downstream_gene_variant,,ENST00000358246,NM_206940.1,NM_206938.1;MS4A14,missense_variant,p.Thr97Lys,ENST00000525397,;MS4A14,3_prime_UTR_variant,,ENST00000531949,;MS4A14,intron_variant,,ENST00000530662,;MS4A14,intron_variant,,ENST00000527841,;MS4A6E,downstream_gene_variant,,ENST00000532756,; A ENST00000531783 Transcript missense_variant 381/2910 290/2139 97/712 T/K aCa/aAa 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 deleterious(0) 3/6 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF10 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999994 1 1 1 0 A 3 1 73 60400426 60400426 C A 1 0 0 0 0 1 0 0 0 9835 478 17 2 2 MS4A14 11 60400426 Missense_Mutation SNP C C3N-01074_T 2041488 60400426 74686196 273 22262 AHNAK 0 . GRCh38 11 62530294 62530294 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.4123G>A p.Gly1375Ser p.G1375S ENST00000378024 5/5 456 311 145 471 470 1 strelka-varscan-mutect AHNAK,missense_variant,p.Gly1375Ser,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000528508,; T ENST00000378024 Transcript missense_variant 4398/18787 4123/17673 1375/5890 G/S Ggc/Agc 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 tolerated(0.08) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 62530294 62530294 C T 1 0 0 0 0 1 0 0 0 491 594 21 3 3 AHNAK 11 62530294 Missense_Mutation SNP C C3N-01074_T 2129868 62530294 72556328 274 22263 GAL3ST3 0 . GRCh38 11 66042874 66042874 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.929C>A p.Ala310Glu p.A310E ENST00000312006 3/3 67 34 33 60 60 0 strelka-varscan-mutect GAL3ST3,missense_variant,p.Ala310Glu,ENST00000312006,NM_033036.2;GAL3ST3,missense_variant,p.Ala310Glu,ENST00000527878,;GAL3ST3,downstream_gene_variant,,ENST00000527048,; T ENST00000312006 Transcript missense_variant 1211/2133 929/1296 310/431 A/E gCg/gAg 1 -1 GAL3ST3 HGNC HGNC:24144 protein_coding YES CCDS8128.1 ENSP00000308591 Q96A11 UPI0000071842 NM_033036.2 tolerated(0.98) 3/3 hmmpanther:PTHR14647:SF1,hmmpanther:PTHR14647,Pfam_domain:PF06990 MODERATE 1 SNV 1 1 PASS . . 1 204 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 66042874 66042874 G T 1 0 0 0 0 1 0 0 0 6067 1087 38 1 1 GAL3ST3 11 66042874 Missense_Mutation SNP G C3N-01074_T 3512580 66042874 69043748 275 22264 GPR152 0 . GRCh38 11 67452632 67452632 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.93G>T p.Trp31Cys p.W31C ENST00000312457 1/1 82 61 21 110 110 0 strelka-varscan-mutect GPR152,missense_variant,p.Trp31Cys,ENST00000312457,NM_206997.1;CABP4,5_prime_UTR_variant,,ENST00000438189,NM_001300896.1,NM_001300895.1;CABP4,upstream_gene_variant,,ENST00000325656,NM_145200.3;CABP4,non_coding_transcript_exon_variant,,ENST00000542025,;CABP4,non_coding_transcript_exon_variant,,ENST00000538060,;CABP4,upstream_gene_variant,,ENST00000542233,;CABP4,non_coding_transcript_exon_variant,,ENST00000545040,;CABP4,upstream_gene_variant,,ENST00000545777,; A ENST00000312457 Transcript missense_variant 98/1429 93/1413 31/470 W/C tgG/tgT 1 -1 GPR152 HGNC HGNC:23622 protein_coding YES CCDS8165.1 ENSP00000310255 Q8TDT2 A0A0I9RJ67 UPI000003B364 NM_206997.1 deleterious(0) 1/1 hmmpanther:PTHR11334:SF1,hmmpanther:PTHR11334,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999862 1 1 1 0 A 3 1 73 67452632 67452632 C A 1 0 0 0 0 1 0 0 0 6544 624 22 2 2 GPR152 11 67452632 Missense_Mutation SNP C C3N-01074_T 1409758 67452632 67633990 276 22265 TENM4 0 . GRCh38 11 78771057 78771057 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2474G>T p.Trp825Leu p.W825L ENST00000278550 18/34 340 225 115 275 274 1 strelka-varscan-mutect TENM4,missense_variant,p.Trp825Leu,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Trp130Leu,ENST00000533525,; A ENST00000278550 Transcript missense_variant 2937/14000 2474/8310 825/2769 W/L tGg/tTg 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 deleterious(0) 18/34 PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9,SMART_domains:SM00181 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 78771057 78771057 C A 1 0 0 0 0 1 0 0 0 16174 595 21 2 2 TENM4 11 78771057 Missense_Mutation SNP C C3N-01074_T 11318425 78771057 56315565 277 22266 FAT3 0 . GRCh38 11 92844497 92844497 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.10680C>T p.= p.S3560S ENST00000525166 18/27 263 215 48 276 276 0 strelka-varscan-mutect FAT3,synonymous_variant,p.=,ENST00000409404,NM_001008781.2;FAT3,synonymous_variant,p.=,ENST00000525166,;FAT3,synonymous_variant,p.=,ENST00000533797,; T ENST00000525166 Transcript synonymous_variant 10702/18699 10680/13320 3560/4439 S agC/agT 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 18/27 hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 92844497 92844497 C T 1 0 0 0 0 0 0 0 1 5551 767 27 1 1 FAT3 11 92844497 Silent SNP C C3N-01074_T 14073440 92844497 42242125 278 22267 PIWIL4 0 . GRCh38 11 94595401 94595401 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.1243G>T p.Ala415Ser p.A415S ENST00000299001 10/20 97 58 39 76 76 0 strelka-varscan-mutect PIWIL4,missense_variant,p.Ala415Ser,ENST00000299001,NM_152431.2;RP11-867G2.8,intron_variant,,ENST00000536540,;RP11-867G2.8,intron_variant,,ENST00000537874,;PIWIL4,missense_variant,p.Ala388Ser,ENST00000446230,;PIWIL4,missense_variant,p.Ala346Ser,ENST00000543336,; T ENST00000299001 Transcript missense_variant 1454/3199 1243/2559 415/852 A/S Gcc/Tcc COSM5023072 1 1 PIWIL4 HGNC HGNC:18444 protein_coding YES CCDS31656.1 ENSP00000299001 Q7Z3Z4 A0A140VKG8 UPI000006D0EC NM_152431.2 tolerated(0.58) 10/20 hmmpanther:PTHR22891:SF43,hmmpanther:PTHR22891,Superfamily_domains:SSF101690 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 6 4 0 0 0 0 -20 0.9997393 1 1 1 0 T 3 4 73 94595401 94595401 G T 1 0 0 0 0 1 0 0 0 12056 1203 42 2 2 PIWIL4 11 94595401 Missense_Mutation SNP G C3N-01074_T 1750904 94595401 40491221 279 22268 TRPC6 0 . GRCh38 11 101504759 101504759 + Silent SNP T T G rs141153400 C3N-01074_T C3N-01074_N T T c.210A>C p.= p.T70T ENST00000344327 2/13 56 37 19 72 72 0 strelka-varscan-mutect TRPC6,synonymous_variant,p.=,ENST00000344327,NM_004621.5;TRPC6,synonymous_variant,p.=,ENST00000532133,;TRPC6,synonymous_variant,p.=,ENST00000360497,;TRPC6,synonymous_variant,p.=,ENST00000348423,;TRPC6,non_coding_transcript_exon_variant,,ENST00000526713,;TRPC6,upstream_gene_variant,,ENST00000527240,; G ENST00000344327 Transcript synonymous_variant 635/4612 210/2796 70/931 T acA/acC rs141153400 1 -1 TRPC6 HGNC HGNC:12338 protein_coding YES CCDS8311.1 ENSP00000340913 Q9Y210 UPI00001374BA NM_004621.5 2/13 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF7 LOW 1 SNV 1 1 PASS rs141153400 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 101504759 101504759 T G 1 0 0 0 0 0 0 0 1 17089 1567 55 5 5 TRPC6 11 101504759 Silent SNP T C3N-01074_T 6909358 101504759 33581863 280 22269 UBE4A 0 . GRCh38 11 118369536 118369536 + Splice_Site SNP G G T novel C3N-01074_T C3N-01074_N G G c.408+1G>T p.X136_splice ENST00000431736 213 139 74 166 166 0 strelka-varscan-mutect UBE4A,splice_donor_variant,,ENST00000252108,NM_001204077.1;UBE4A,splice_donor_variant,,ENST00000431736,NM_004788.3; T ENST00000431736 Transcript splice_donor_variant -/6061 408/3222 136/1073 1 1 UBE4A HGNC HGNC:12499 protein_coding YES CCDS8396.1 ENSP00000387362 Q14139 UPI000013CD3F NM_004788.3 4/19 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 73 118369536 118369536 G T 1 0 0 0 0 0 0 1 0 17406 1275 44 2 2 UBE4A 11 118369536 Splice_Site SNP G C3N-01074_T 16864777 118369536 16717086 281 22270 PHLDB1 0 . GRCh38 11 118644084 118644084 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.3031A>T p.Thr1011Ser p.T1011S ENST00000361417 16/24 251 211 40 194 194 0 strelka-varscan-mutect PHLDB1,missense_variant,p.Thr1011Ser,ENST00000361417,NM_015157.3;PHLDB1,missense_variant,p.Thr1011Ser,ENST00000600882,NM_001144758.2;PHLDB1,missense_variant,p.Thr964Ser,ENST00000356063,NM_001144759.2;PHLDB1,missense_variant,p.Thr286Ser,ENST00000534140,;PHLDB1,intron_variant,,ENST00000601898,;PHLDB1,downstream_gene_variant,,ENST00000613413,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000614369,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000527898,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000524713,;PHLDB1,intron_variant,,ENST00000528875,;PHLDB1,upstream_gene_variant,,ENST00000529005,;PHLDB1,downstream_gene_variant,,ENST00000527500,;PHLDB1,missense_variant,p.Thr964Ser,ENST00000530994,;PHLDB1,missense_variant,p.Thr964Ser,ENST00000528594,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000532517,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000392852,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000531987,;PHLDB1,non_coding_transcript_exon_variant,,ENST00000526826,;PHLDB1,downstream_gene_variant,,ENST00000612681,;PHLDB1,upstream_gene_variant,,ENST00000526537,;PHLDB1,upstream_gene_variant,,ENST00000525226,;PHLDB1,downstream_gene_variant,,ENST00000526699,; T ENST00000361417 Transcript missense_variant 3442/5753 3031/4134 1011/1377 T/S Acc/Tcc 1 1 PHLDB1 HGNC HGNC:23697 protein_coding YES CCDS8401.1 ENSP00000354498 Q86UU1 A0A024R3H6 UPI0000192101 NM_015157.3 tolerated(0.61) 16/24 hmmpanther:PTHR12156:SF23,hmmpanther:PTHR12156 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 73 118644084 118644084 A T 1 0 0 0 0 1 0 0 0 11939 159 6 4 4 PHLDB1 11 118644084 Missense_Mutation SNP A C3N-01074_T 274548 118644084 16442538 282 22271 TMEM225 0 . GRCh38 11 123885365 123885365 + Missense_Mutation SNP C C A rs760483112 C3N-01074_T C3N-01074_N C C c.61G>T p.Val21Leu p.V21L ENST00000375026 1/4 220 190 30 238 238 0 strelka-varscan-mutect TMEM225,missense_variant,p.Val21Leu,ENST00000375026,NM_001013743.2;TMEM225,intron_variant,,ENST00000528595,; A ENST00000375026 Transcript missense_variant 278/1107 61/678 21/225 V/L Gta/Tta rs760483112 1 -1 TMEM225 HGNC HGNC:32390 protein_coding YES CCDS31697.1 ENSP00000364166 Q6GV28 UPI000443236D NM_001013743.2 tolerated(1) 1/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR36477 MODERATE 1 SNV 1 1 PASS rs760483112 . 0 206 0 4 0 0 0 0 -20 0.9999015 1 1 1 0 A 3 1 73 123885365 123885365 C A 1 0 0 0 0 1 0 0 0 16588 536 19 1 1 TMEM225 11 123885365 Missense_Mutation SNP C C3N-01074_T 5241281 123885365 11201257 283 22272 OR10G4 0 . GRCh38 11 124016288 124016288 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.714G>T p.Gln238His p.Q238H ENST00000320891 1/1 155 133 22 238 238 0 strelka-varscan-mutect OR10G4,missense_variant,p.Gln238His,ENST00000320891,NM_001004462.1; T ENST00000320891 Transcript missense_variant 714/936 714/936 238/311 Q/H caG/caT 1 1 OR10G4 HGNC HGNC:14809 protein_coding YES CCDS31702.1 ENSP00000325076 Q8NGN3 A0A126GWS5 UPI0000041BAD NM_001004462.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF6,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 124016288 124016288 G T 1 0 0 0 0 1 0 0 0 10977 933 33 2 2 OR10G4 11 124016288 Missense_Mutation SNP G C3N-01074_T 130923 124016288 11070334 284 22273 OR8D1 0 . GRCh38 11 124310084 124310084 + Missense_Mutation SNP A A G rs199953194 C3N-01074_T C3N-01074_N A A c.683T>C p.Ile228Thr p.I228T ENST00000357821 1/1 164 106 58 199 199 0 strelka-varscan-mutect OR8D1,missense_variant,p.Ile228Thr,ENST00000357821,NM_001002917.1; G ENST00000357821 Transcript missense_variant 754/1026 683/927 228/308 I/T aTc/aCc rs199953194 1 -1 OR8D1 HGNC HGNC:8481 protein_coding YES CCDS31706.1 ENSP00000350474 Q8WZ84 A0A126GVG6 UPI0000041D9D NM_001002917.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF66,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs199953194 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 124310084 124310084 A G 1 0 0 0 0 1 0 0 0 11301 333 12 5 5 OR8D1 11 124310084 Missense_Mutation SNP A C3N-01074_T 293796 124310084 10776538 285 22274 PANX3 0 . GRCh38 11 124611627 124611627 + Missense_Mutation SNP G G T rs147954369 C3N-01074_T C3N-01074_N G G c.71G>T p.Arg24Leu p.R24L ENST00000284288 1/4 242 203 39 198 198 0 strelka-varscan-mutect PANX3,missense_variant,p.Arg24Leu,ENST00000284288,NM_052959.2; T ENST00000284288 Transcript missense_variant 138/1667 71/1179 24/392 R/L cGc/cTc rs147954369,COSM3666159 1 1 PANX3 HGNC HGNC:20573 protein_coding YES CCDS8447.1 ENSP00000284288 Q96QZ0 UPI0000131264 NM_052959.2 deleterious(0.02) 1/4 hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs147954369 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 124611627 124611627 G T 1 0 0 0 0 1 0 0 0 11503 1087 38 1 1 PANX3 11 124611627 Missense_Mutation SNP G C3N-01074_T 301543 124611627 10474995 286 22275 KIRREL3 0 . GRCh38 11 126521454 126521454 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.294G>T p.Gln98His p.Q98H ENST00000525144 4/17 141 118 23 110 110 0 strelka-varscan-mutect KIRREL3,missense_variant,p.Gln98His,ENST00000525144,NM_032531.3;KIRREL3,missense_variant,p.Gln98His,ENST00000529097,NM_001301097.1;KIRREL3,missense_variant,p.Gln98His,ENST00000525704,NM_001161707.1; A ENST00000525144 Transcript missense_variant 544/3808 294/2337 98/778 Q/H caG/caT 1 -1 KIRREL3 HGNC HGNC:23204 protein_coding YES CCDS53723.1 ENSP00000435466 Q8IZU9 UPI00000740A0 NM_032531.3 deleterious(0) 4/17 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF49,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1367795436 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 126521454 126521454 C A 1 0 0 0 0 1 0 0 0 8190 564 20 2 2 KIRREL3 11 126521454 Missense_Mutation SNP C C3N-01074_T 1909827 126521454 8565168 287 22276 ST14 0 . GRCh38 11 130194696 130194696 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1072G>T p.Gly358Cys p.G358C ENST00000278742 9/19 668 569 99 484 483 1 strelka-varscan-mutect ST14,missense_variant,p.Gly358Cys,ENST00000278742,NM_021978.3;ST14,non_coding_transcript_exon_variant,,ENST00000530532,;ST14,non_coding_transcript_exon_variant,,ENST00000524718,;ST14,non_coding_transcript_exon_variant,,ENST00000530376,; T ENST00000278742 Transcript missense_variant 1490/3539 1072/2568 358/855 G/C Ggc/Tgc 1 1 ST14 HGNC HGNC:11344 protein_coding YES CCDS8487.1 ENSP00000278742 Q9Y5Y6 UPI00000012E9 NM_021978.3 deleterious(0) 9/19 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF036370,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 130194696 130194696 G T 1 0 0 0 0 1 0 0 0 15589 1000 35 2 2 ST14 11 130194696 Missense_Mutation SNP G C3N-01074_T 3673242 130194696 4891926 288 22277 ADAMTS8 0 . GRCh38 11 130408570 130408570 + Missense_Mutation SNP C C T rs776551880 C3N-01074_T C3N-01074_N C C c.1993G>A p.Gly665Ser p.G665S ENST00000257359 8/9 329 228 101 269 269 0 strelka-varscan-mutect ADAMTS8,missense_variant,p.Gly665Ser,ENST00000257359,NM_007037.4;RP11-121M22.1,downstream_gene_variant,,ENST00000616197,;ADAMTS8,non_coding_transcript_exon_variant,,ENST00000531752,; T ENST00000257359 Transcript missense_variant 2700/4010 1993/2670 665/889 G/S Ggc/Agc rs776551880,COSM4019362,COSM4019363,COSM4019364 1 -1 ADAMTS8 HGNC HGNC:224 protein_coding YES CCDS41732.1 ENSP00000257359 Q9UP79 UPI000013CF5D NM_007037.4 deleterious(0) 8/9 hmmpanther:PTHR13723:SF41,hmmpanther:PTHR13723,Prints_domain:PR01857 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs776551880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 130408570 130408570 C T 1 0 0 0 0 1 0 0 0 316 652 23 1 1 ADAMTS8 11 130408570 Missense_Mutation SNP C C3N-01074_T 213874 130408570 4678052 289 22278 KDM5A 0 . GRCh38 12 318362 318362 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2641G>T p.Gly881Cys p.G881C ENST00000399788 19/28 482 202 280 287 287 0 strelka-varscan-mutect KDM5A,missense_variant,p.Gly881Cys,ENST00000399788,NM_001042603.2;KDM5A,missense_variant,p.Gly500Cys,ENST00000544760,;KDM5A,downstream_gene_variant,,ENST00000541335,; A ENST00000399788 Transcript missense_variant 3004/10763 2641/5073 881/1690 G/C Ggc/Tgc 1 -1 KDM5A HGNC HGNC:9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.2 deleterious(0) 19/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17,Pfam_domain:PF08429 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 318362 318362 C A 1 0 0 0 0 1 0 0 0 8051 623 22 2 2 KDM5A 12 318362 Missense_Mutation SNP C C3N-01074_T 318362 132956947 290 22279 KCNA5 0 . GRCh38 12 5044738 5044738 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.591G>T p.= p.A197A ENST00000252321 1/1 761 622 139 415 414 1 strelka-varscan-mutect KCNA5,synonymous_variant,p.=,ENST00000252321,NM_002234.3; T ENST00000252321 Transcript synonymous_variant 750/2800 591/1842 197/613 A gcG/gcT 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 1/1 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,SMART_domains:SM00225,Superfamily_domains:SSF54695 LOW 1 SNV 1 PASS rs1443012925 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 5044738 5044738 G T 1 0 0 0 0 0 0 0 1 7922 1103 39 1 1 KCNA5 12 5044738 Silent SNP G C3N-01074_T 4726376 5044738 128230571 291 22280 ACSM4 0 . GRCh38 12 7324552 7324552 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1490T>A p.Val497Asp p.V497D ENST00000399422 11/13 803 365 438 436 436 0 strelka-varscan-mutect ACSM4,missense_variant,p.Val497Asp,ENST00000399422,NM_001080454.1; A ENST00000399422 Transcript missense_variant 1538/2142 1490/1743 497/580 V/D gTt/gAt 1 1 ACSM4 HGNC HGNC:32016 protein_coding YES CCDS44825.1 ENSP00000382349 P0C7M7 UPI0000DD812A NM_001080454.1 deleterious(0) 11/13 Low_complexity_(Seg):seg,hmmpanther:PTHR24095:SF127,hmmpanther:PTHR24095,Gene3D:3.30.300.30,Pfam_domain:PF13193,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 7324552 7324552 T A 1 0 0 0 0 1 0 0 0 228 1725 60 4 4 ACSM4 12 7324552 Missense_Mutation SNP T C3N-01074_T 2279814 7324552 125950757 292 22281 MFAP5 0 . GRCh38 12 8660895 8660895 + Nonsense_Mutation SNP C C T rs724159961 C3N-01074_T C3N-01074_N C C c.62G>A p.Trp21Ter p.W21* ENST00000359478 3/10 295 159 136 179 179 0 strelka-varscan-mutect MFAP5,stop_gained,p.Trp21Ter,ENST00000359478,NM_003480.3;MFAP5,stop_gained,p.Trp21Ter,ENST00000433590,NM_001297711.1;MFAP5,stop_gained,p.Trp21Ter,ENST00000396549,NM_001297709.1;MFAP5,stop_gained,p.Trp11Ter,ENST00000535411,;MFAP5,stop_gained,p.Trp21Ter,ENST00000544889,;MFAP5,stop_gained,p.Trp21Ter,ENST00000535336,NM_001297712.1;MFAP5,stop_gained,p.Trp21Ter,ENST00000540087,;MFAP5,intron_variant,,ENST00000543369,NM_001297710.1;RP11-20D14.3,upstream_gene_variant,,ENST00000544922,;RP11-20D14.3,upstream_gene_variant,,ENST00000539089,;MFAP5,non_coding_transcript_exon_variant,,ENST00000538107,;MFAP5,upstream_gene_variant,,ENST00000538694,;MFAP5,stop_gained,p.Trp21Ter,ENST00000544211,;MFAP5,stop_gained,p.Trp21Ter,ENST00000537009,;MFAP5,non_coding_transcript_exon_variant,,ENST00000537128,;MFAP5,non_coding_transcript_exon_variant,,ENST00000534833,; T ENST00000359478 Transcript stop_gained 250/2845 62/522 21/173 W/* tGg/tAg rs724159961 1 -1 MFAP5 HGNC HGNC:29673 protein_coding YES CCDS8595.1 ENSP00000352455 Q13361 UPI000012F034 NM_003480.3 3/10 Pfam_domain:PF05507,hmmpanther:PTHR16485,hmmpanther:PTHR16485:SF6,Cleavage_site_(Signalp):SignalP-noTM pathogenic HIGH 1 SNV 1 1 1 PASS rs724159961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 8660895 8660895 C T 1 0 0 0 0 0 1 0 0 9471 608 21 3 3 MFAP5 12 8660895 Nonsense_Mutation SNP C C3N-01074_T 1336343 8660895 124614414 293 22282 PZP 0 . GRCh38 12 9160393 9160393 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.2970C>A p.= p.I990I ENST00000261336 24/36 406 188 218 217 217 0 strelka-varscan-mutect PZP,synonymous_variant,p.=,ENST00000261336,NM_002864.2;PZP,downstream_gene_variant,,ENST00000539983,;PZP,downstream_gene_variant,,ENST00000546197,;PZP,downstream_gene_variant,,ENST00000543108,;PZP,downstream_gene_variant,,ENST00000540995,;PZP,3_prime_UTR_variant,,ENST00000535230,;TPT1P12,upstream_gene_variant,,ENST00000448968,; T ENST00000261336 Transcript synonymous_variant 2999/4610 2970/4449 990/1482 I atC/atA 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 24/36 Gene3D:1.50.10.20,Pfam_domain:PF10569,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92,Superfamily_domains:SSF48239 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 9160393 9160393 G T 1 0 0 0 0 0 0 0 1 13025 932 33 2 2 PZP 12 9160393 Silent SNP G C3N-01074_T 499498 9160393 124114916 294 22283 CLEC9A 0 . GRCh38 12 10061176 10061176 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.222A>T p.Gln74His p.Q74H ENST00000355819 6/9 692 630 62 373 373 0 strelka-varscan-mutect CLEC9A,missense_variant,p.Gln74His,ENST00000355819,NM_207345.3;CLEC9A,non_coding_transcript_exon_variant,,ENST00000538482,; T ENST00000355819 Transcript missense_variant 835/1734 222/726 74/241 Q/H caA/caT 1 1 CLEC9A HGNC HGNC:26705 protein_coding YES CCDS8611.1 ENSP00000348074 Q6UXN8 UPI00001D696C NM_207345.3 tolerated(0.13) 6/9 hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF171 MODERATE 1 SNV 1 1 PASS rs1158095754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 10061176 10061176 A T 1 0 0 0 0 1 0 0 0 3290 40 2 4 4 CLEC9A 12 10061176 Missense_Mutation SNP A C3N-01074_T 900783 10061176 123214133 295 22284 EPS8 0 . GRCh38 12 15670901 15670901 + Silent SNP C C A rs779513717 C3N-01074_T C3N-01074_N C C c.159G>T p.= p.R53R ENST00000281172 4/21 499 399 100 244 242 2 strelka-varscan-mutect EPS8,synonymous_variant,p.=,ENST00000281172,NM_004447.5;EPS8,synonymous_variant,p.=,ENST00000543523,;EPS8,synonymous_variant,p.=,ENST00000543612,;EPS8,synonymous_variant,p.=,ENST00000544064,;EPS8,synonymous_variant,p.=,ENST00000536793,;EPS8,synonymous_variant,p.=,ENST00000535752,;EPS8,synonymous_variant,p.=,ENST00000546311,;EPS8,synonymous_variant,p.=,ENST00000543363,;RNU6-251P,downstream_gene_variant,,ENST00000363235,;EPS8,stop_gained,p.Gly28Ter,ENST00000536956,;EPS8,synonymous_variant,p.=,ENST00000543468,;EPS8,upstream_gene_variant,,ENST00000508018,;EPS8,upstream_gene_variant,,ENST00000546261,; A ENST00000281172 Transcript synonymous_variant 596/4061 159/2469 53/822 R cgG/cgT rs779513717 1 -1 EPS8 HGNC HGNC:3420 protein_coding YES CCDS31753.1 ENSP00000281172 Q12929 UPI000012A0BC NM_004447.5 4/21 hmmpanther:PTHR12287:SF21,hmmpanther:PTHR12287 LOW 1 SNV 1 1 PASS rs779513717 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 15670901 15670901 C A 1 0 0 0 0 0 0 0 1 5042 610 22 2 2 EPS8 12 15670901 Silent SNP C C3N-01074_T 5609725 15670901 117604408 296 22285 SLCO1B1 0 . GRCh38 12 21205988 21205988 + Silent SNP C C A rs74064211 C3N-01074_T C3N-01074_N C C c.1452C>A p.= p.P484P ENST00000256958 11/15 570 253 317 379 379 0 strelka-varscan-mutect SLCO1B1,synonymous_variant,p.=,ENST00000256958,NM_006446.4; A ENST00000256958 Transcript synonymous_variant 1548/2229 1452/2076 484/691 P ccC/ccA rs74064211 1 1 SLCO1B1 HGNC HGNC:10959 protein_coding YES CCDS8685.1 ENSP00000256958 Q9Y6L6 A0A024RAU7 UPI0000043BED NM_006446.4 11/15 Gene3D:3.30.60.30,Pfam_domain:PF03137,Pfam_domain:PF07648,PROSITE_profiles:PS50850,PROSITE_profiles:PS51465,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Superfamily_domains:SSF100895,TIGRFAM_domain:TIGR00805 LOW 1 SNV 1 1 PASS rs74064211 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 21205988 21205988 C A 1 0 0 0 0 0 0 0 1 15009 668 24 2 2 SLCO1B1 12 21205988 Silent SNP C C3N-01074_T 5535087 21205988 112069321 297 22286 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-01074_T C3N-01074_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 974 353 621 440 439 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-01074_T 4039363 25245351 108029958 298 22287 OVCH1 0 . GRCh38 12 29455334 29455334 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2352G>T p.Trp784Cys p.W784C ENST00000318184 20/28 702 639 63 202 202 0 strelka-varscan-mutect OVCH1,missense_variant,p.Trp784Cys,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;OVCH1-AS1,intron_variant,,ENST00000550906,; A ENST00000318184 Transcript missense_variant 2352/3405 2352/3405 784/1134 W/C tgG/tgT 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 deleterious(0.01) 20/28 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 2 1 PASS rs894730241 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 73 29455334 29455334 C A 1 0 0 0 0 1 0 0 0 11393 624 22 2 2 OVCH1 12 29455334 Missense_Mutation SNP C C3N-01074_T 4209983 29455334 103819975 299 22288 OVOS2 0 . GRCh38 12 31139215 31139215 + Frame_Shift_Del DEL G G - rs538258593 C3N-01074_T C3N-01074_N G G c.1820delC p.Pro607ArgfsTer35 p.P607Rfs*35 ENST00000632817 14/34 150 41 109 75 75 0 sindel-varindel OVOS2,frameshift_variant,p.Pro607ArgfsTer35,ENST00000398963,;OVOS2,frameshift_variant,p.Pro607ArgfsTer35,ENST00000632817,; - ENST00000632817 Transcript frameshift_variant 1820/4299 1820/4299 607/1432 P/X cCg/cg rs538258593 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 14/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 HIGH 1 deletion 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999997 1 1 1 0 - 7 5 73 31139215 31139215 G - 1 0 1 0 1 0 0 0 0 11399 1116 39 0 0 OVOS2 12 31139215 Frame_Shift_Del DEL G C3N-01074_T 1683881 31139215 102136094 300 22289 ABCD2 0 . GRCh38 12 39586199 39586199 + Missense_Mutation SNP C C A rs151149571 C3N-01074_T C3N-01074_N C C c.1745G>T p.Arg582Leu p.R582L ENST00000308666 7/10 258 222 36 261 261 0 strelka-varscan-mutect ABCD2,missense_variant,p.Arg582Leu,ENST00000308666,NM_005164.3; A ENST00000308666 Transcript missense_variant 1881/6238 1745/2223 582/740 R/L cGt/cTt rs151149571,COSM468309 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 tolerated(0.28) 7/10 PROSITE_profiles:PS50893,hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs151149571 . 0 206 0 3 0 0 0 0 -20 0.9999923 1 1 1 0 A 3 1 73 39586199 39586199 C A 1 0 0 0 0 1 0 0 0 65 536 19 1 1 ABCD2 12 39586199 Missense_Mutation SNP C C3N-01074_T 8446984 39586199 93689110 301 22290 YAF2 0 . GRCh38 12 42160748 42160748 + Silent SNP T T G novel C3N-01074_T C3N-01074_N T T c.456A>C p.= p.T152T ENST00000327791 5/5 518 351 167 361 361 0 strelka-varscan-mutect YAF2,synonymous_variant,p.=,ENST00000327791,NM_001190979.1;YAF2,synonymous_variant,p.=,ENST00000534854,NM_005748.4;YAF2,synonymous_variant,p.=,ENST00000380790,NM_001190977.1;YAF2,downstream_gene_variant,,ENST00000548917,;YAF2,non_coding_transcript_exon_variant,,ENST00000547622,;YAF2,downstream_gene_variant,,ENST00000547724,;YAF2,3_prime_UTR_variant,,ENST00000552109,;YAF2,3_prime_UTR_variant,,ENST00000547351,;YAF2,non_coding_transcript_exon_variant,,ENST00000550315,;YAF2,downstream_gene_variant,,ENST00000551268,;YAF2,downstream_gene_variant,,ENST00000546726,;YAF2,downstream_gene_variant,,ENST00000547254,;YAF2,downstream_gene_variant,,ENST00000552928,;YAF2,downstream_gene_variant,,ENST00000551528,;YAF2,downstream_gene_variant,,ENST00000546972,;YAF2,downstream_gene_variant,,ENST00000548661,; G ENST00000327791 Transcript synonymous_variant 512/4156 456/615 152/204 T acA/acC 1 -1 YAF2 HGNC HGNC:17363 protein_coding YES CCDS53779.1 ENSP00000328004 Q8IY57 UPI00000742C8 NM_001190979.1 5/5 hmmpanther:PTHR12920 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 42160748 42160748 T G 1 0 0 0 0 0 0 0 1 18025 1567 55 5 5 YAF2 12 42160748 Silent SNP T C3N-01074_T 2574549 42160748 91114561 302 22291 COL2A1 0 . GRCh38 12 47977113 47977113 + Silent SNP G G T rs374036874 C3N-01074_T C3N-01074_N G G c.3316C>A p.= p.R1106R ENST00000380518 47/54 525 346 179 500 500 0 strelka-varscan-mutect COL2A1,synonymous_variant,p.=,ENST00000380518,NM_001844.4;COL2A1,synonymous_variant,p.=,ENST00000337299,NM_033150.2;COL2A1,non_coding_transcript_exon_variant,,ENST00000493991,;COL2A1,non_coding_transcript_exon_variant,,ENST00000546974,;COL2A1,downstream_gene_variant,,ENST00000483376,; T ENST00000380518 Transcript synonymous_variant 3481/5071 3316/4464 1106/1487 R Cgg/Agg rs374036874 1 -1 COL2A1 HGNC HGNC:2200 protein_coding YES CCDS41778.1 ENSP00000369889 P02458 UPI0000D79713 NM_001844.4 47/54 hmmpanther:PTHR24023:SF548,hmmpanther:PTHR24023 LOW 1 SNV 1 1 PASS rs374036874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 47977113 47977113 G T 1 0 0 0 0 0 0 0 1 3476 1115 39 1 1 COL2A1 12 47977113 Silent SNP G C3N-01074_T 5816365 47977113 85298196 303 22292 NCKAP5L 0 . GRCh38 12 49795796 49795796 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.2064C>T p.= p.A688A ENST00000335999 8/13 218 172 46 184 184 0 strelka-varscan-mutect NCKAP5L,synonymous_variant,p.=,ENST00000335999,NM_001037806.3;NCKAP5L,synonymous_variant,p.=,ENST00000433948,; A ENST00000335999 Transcript synonymous_variant 2266/4900 2064/4005 688/1334 A gcC/gcT 1 -1 NCKAP5L HGNC HGNC:29321 protein_coding YES CCDS41781.2 ENSP00000337998 Q9HCH0 UPI00006C1298 NM_001037806.3 8/13 hmmpanther:PTHR21740 LOW 1 SNV 5 1 PASS rs1370955489 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 49795796 49795796 G A 1 0 0 0 0 0 0 0 1 10242 1335 47 3 3 NCKAP5L 12 49795796 Silent SNP G C3N-01074_T 1818683 49795796 83479513 304 22293 FAM186A 0 . GRCh38 12 50355080 50355080 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.1752C>G p.Ser584Arg p.S584R ENST00000327337 4/8 383 331 52 374 374 0 strelka-varscan-mutect FAM186A,missense_variant,p.Ser584Arg,ENST00000543111,;FAM186A,missense_variant,p.Ser584Arg,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; C ENST00000327337 Transcript missense_variant 1752/7127 1752/7056 584/2351 S/R agC/agG 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 tolerated(0.25) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 50355080 50355080 G C 1 0 0 0 0 1 0 0 0 5361 1194 42 4 4 FAM186A 12 50355080 Missense_Mutation SNP G C3N-01074_T 559284 50355080 82920229 305 22294 ANKRD33 0 . GRCh38 12 51890803 51890803 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.857G>T p.Arg286Leu p.R286L ENST00000301190 5/5 193 157 36 207 207 0 strelka-varscan-mutect ANKRD33,missense_variant,p.Arg286Leu,ENST00000301190,NM_182608.3;ANKRD33,missense_variant,p.Arg161Leu,ENST00000340970,NM_001130015.1;ANKRD33,non_coding_transcript_exon_variant,,ENST00000547119,;ANKRD33,downstream_gene_variant,,ENST00000549316,;ANKRD33,3_prime_UTR_variant,,ENST00000549751,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548526,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548383,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000550652,; T ENST00000301190 Transcript missense_variant 1084/1935 857/1359 286/452 R/L cGg/cTg 1 1 ANKRD33 HGNC HGNC:13788 protein_coding YES CCDS8815.1 ENSP00000301190 Q7Z3H0 UPI00003668C0 NM_182608.3 tolerated(0.3) 5/5 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF29 MODERATE 1 SNV 2 1 PASS rs1195613220 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 51890803 51890803 G T 1 0 0 0 0 1 0 0 0 765 1116 39 1 1 ANKRD33 12 51890803 Missense_Mutation SNP G C3N-01074_T 1535723 51890803 81384506 306 22295 KRT71 0 . GRCh38 12 52546402 52546402 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.1209G>C p.Gln403His p.Q403H ENST00000267119 7/9 347 227 120 306 306 0 strelka-varscan-mutect KRT71,missense_variant,p.Gln403His,ENST00000267119,NM_033448.2; G ENST00000267119 Transcript missense_variant 1279/2265 1209/1572 403/523 Q/H caG/caC 1 -1 KRT71 HGNC HGNC:28927 protein_coding YES CCDS8831.1 ENSP00000267119 Q3SY84 UPI0000052B57 NM_033448.2 deleterious(0.02) 7/9 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF116,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs757049898 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 52546402 52546402 C G 1 0 0 0 0 1 0 0 0 8366 680 24 4 4 KRT71 12 52546402 Missense_Mutation SNP C C3N-01074_T 655599 52546402 80728907 307 22296 TESPA1 0 . GRCh38 12 54962566 54962566 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1332G>T p.Gln444His p.Q444H ENST00000449076 9/11 353 304 49 418 418 0 strelka-varscan-mutect TESPA1,missense_variant,p.Gln306His,ENST00000524622,NM_001261844.1,NM_014796.2;TESPA1,missense_variant,p.Gln444His,ENST00000449076,NM_001136030.2;TESPA1,missense_variant,p.Gln306His,ENST00000532804,;TESPA1,missense_variant,p.Gln444His,ENST00000316577,NM_001098815.2;TESPA1,missense_variant,p.Gln306His,ENST00000531122,;TESPA1,missense_variant,p.Gln44His,ENST00000528240,;TESPA1,intron_variant,,ENST00000532757,;TESPA1,downstream_gene_variant,,ENST00000526532,;TESPA1,downstream_gene_variant,,ENST00000533446,;TESPA1,downstream_gene_variant,,ENST00000524959,;TESPA1,3_prime_UTR_variant,,ENST00000524923,;TESPA1,downstream_gene_variant,,ENST00000525978,; A ENST00000449076 Transcript missense_variant 1465/2010 1332/1566 444/521 Q/H caG/caT 1 -1 TESPA1 HGNC HGNC:29109 protein_coding YES CCDS44913.1 ENSP00000400892 A2RU30 A0A024RB73 UPI00001FC438 NM_001136030.2 tolerated_low_confidence(0.07) 9/11 hmmpanther:PTHR17469 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 54962566 54962566 C A 1 0 0 0 0 1 0 0 0 16189 912 32 2 2 TESPA1 12 54962566 Missense_Mutation SNP C C3N-01074_T 2416164 54962566 78312743 308 22297 OR6C75 0 . GRCh38 12 55365952 55365952 + Missense_Mutation SNP C C G rs570110426 C3N-01074_T C3N-01074_N C C c.842C>G p.Pro281Arg p.P281R ENST00000343399 1/1 219 136 83 212 212 0 strelka-varscan-mutect OR6C75,missense_variant,p.Pro281Arg,ENST00000343399,NM_001005497.1; G ENST00000343399 Transcript missense_variant 842/939 842/939 281/312 P/R cCt/cGt rs570110426 1 1 OR6C75 HGNC HGNC:31304 protein_coding YES CCDS31820.1 ENSP00000368987 A6NL08 A0A126GW92 UPI000023786C NM_001005497.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs570110426 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 55365952 55365952 C G 1 0 0 0 0 1 0 0 0 11267 681 24 4 4 OR6C75 12 55365952 Missense_Mutation SNP C C3N-01074_T 403386 55365952 77909357 309 22298 RBMS2 0 . GRCh38 12 56571804 56571804 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.491C>G p.Thr164Ser p.T164S ENST00000262031 5/14 50 45 5 44 44 0 varscan-mutect RBMS2,missense_variant,p.Thr164Ser,ENST00000262031,NM_002898.3;RBMS2,missense_variant,p.Thr164Ser,ENST00000552247,;RBMS2,missense_variant,p.Thr39Ser,ENST00000550726,;RBMS2,intron_variant,,ENST00000542360,;RBMS2,non_coding_transcript_exon_variant,,ENST00000552228,;RBMS2,downstream_gene_variant,,ENST00000549945,;RBMS2,3_prime_UTR_variant,,ENST00000552916,;RBMS2,downstream_gene_variant,,ENST00000551369,; G ENST00000262031 Transcript missense_variant 586/8382 491/1224 164/407 T/S aCc/aGc 1 1 RBMS2 HGNC HGNC:9909 protein_coding YES CCDS8923.1 ENSP00000262031 Q15434 UPI000006EEB0 NM_002898.3 deleterious(0.04) 5/14 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF429,hmmpanther:PTHR24012,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 56571804 56571804 C G 1 0 0 0 0 1 0 0 0 13315 507 18 4 4 RBMS2 12 56571804 Missense_Mutation SNP C C3N-01074_T 1205852 56571804 76703505 310 22299 NAV3 0 . GRCh38 12 78118171 78118171 + Missense_Mutation SNP C C A rs766000550 C3N-01074_T C3N-01074_N C C c.2914C>A p.Pro972Thr p.P972T ENST00000397909 14/40 375 322 53 292 292 0 strelka-varscan-mutect NAV3,missense_variant,p.Pro972Thr,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Pro972Thr,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Pro44Thr,ENST00000552895,;NAV3,upstream_gene_variant,,ENST00000550788,; A ENST00000397909 Transcript missense_variant 3087/9821 2914/7158 972/2385 P/T Ccc/Acc rs766000550 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 tolerated(0.13) 14/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS rs766000550 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 78118171 78118171 C A 1 0 0 0 0 1 0 0 0 10194 623 22 2 2 NAV3 12 78118171 Missense_Mutation SNP C C3N-01074_T 21546367 78118171 55157138 311 22300 CEP290 0 . GRCh38 12 88080391 88080391 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.5017C>A p.Gln1673Lys p.Q1673K ENST00000552810 38/54 121 77 44 154 154 0 strelka-varscan-mutect CEP290,missense_variant,p.Gln1673Lys,ENST00000552810,NM_025114.3;CEP290,missense_variant,p.Gln1675Lys,ENST00000309041,;CEP290,missense_variant,p.Gln733Lys,ENST00000547691,; T ENST00000552810 Transcript missense_variant 5361/7948 5017/7440 1673/2479 Q/K Caa/Aaa 1 -1 CEP290 HGNC HGNC:29021 protein_coding YES CCDS55858.1 ENSP00000448012 O15078 UPI0000D60D15 NM_025114.3 tolerated(0.11) 38/54 hmmpanther:PTHR18879:SF20,hmmpanther:PTHR18879,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 88080391 88080391 G T 1 0 0 0 0 1 0 0 0 2969 1304 45 2 2 CEP290 12 88080391 Missense_Mutation SNP G C3N-01074_T 9962220 88080391 45194918 312 22301 CCER1 0 . GRCh38 12 90954712 90954712 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.31C>A p.Pro11Thr p.P11T ENST00000358859 1/1 142 109 33 104 103 1 strelka-varscan-mutect CCER1,missense_variant,p.Pro11Thr,ENST00000358859,NM_152638.3;CCER1,intron_variant,,ENST00000548187,;CCER1,upstream_gene_variant,,ENST00000549707,; T ENST00000358859 Transcript missense_variant 465/2962 31/1221 11/406 P/T Cct/Act 1 -1 CCER1 HGNC HGNC:28373 protein_coding YES CCDS9036.1 ENSP00000351727 Q8TC90 UPI000006EE70 NM_152638.3 deleterious(0) 1/1 hmmpanther:PTHR37337:SF1,hmmpanther:PTHR37337,Pfam_domain:PF15482 MODERATE 1 SNV 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 90954712 90954712 G T 1 0 0 0 0 1 0 0 0 2574 1232 43 2 2 CCER1 12 90954712 Missense_Mutation SNP G C3N-01074_T 2874321 90954712 42320597 313 22302 HCFC2 0 . GRCh38 12 104087984 104087984 + Splice_Site SNP A A T novel C3N-01074_T C3N-01074_N A A c.1232-2A>T p.X411_splice ENST00000229330 253 183 70 187 187 0 strelka-varscan-mutect HCFC2,splice_acceptor_variant,,ENST00000229330,NM_013320.2;HCFC2,upstream_gene_variant,,ENST00000550335,;HCFC2,intron_variant,,ENST00000544223,; T ENST00000229330 Transcript splice_acceptor_variant -/5734 1232/2379 411/792 1 1 HCFC2 HGNC HGNC:24972 protein_coding YES CCDS9097.1 ENSP00000229330 Q9Y5Z7 UPI000006CF31 NM_013320.2 8/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 73 104087984 104087984 A T 1 0 0 0 0 0 0 1 0 6881 202 7 4 4 HCFC2 12 104087984 Splice_Site SNP A C3N-01074_T 13133272 104087984 29187325 314 22303 CUX2 0 . GRCh38 12 111348207 111348207 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.4343G>T p.Ser1448Ile p.S1448I ENST00000261726 22/22 387 277 110 272 271 1 strelka-varscan-mutect CUX2,missense_variant,p.Ser1448Ile,ENST00000261726,NM_015267.3; T ENST00000261726 Transcript missense_variant 4497/6844 4343/4461 1448/1486 S/I aGt/aTt 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 deleterious_low_confidence(0) 22/22 hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 111348207 111348207 G T 1 0 0 0 0 1 0 0 0 3875 1029 36 2 2 CUX2 12 111348207 Missense_Mutation SNP G C3N-01074_T 7260223 111348207 21927102 315 22304 OAS1 0 . GRCh38 12 112919632 112919632 + Missense_Mutation SNP A A T rs754565362 C3N-01074_T C3N-01074_N A A c.1184A>T p.Gln395Leu p.Q395L ENST00000445409 6/6 220 153 67 182 182 0 strelka-varscan-mutect OAS1,missense_variant,p.Gln395Leu,ENST00000445409,NM_001032409.1;OAS1,3_prime_UTR_variant,,ENST00000202917,NM_016816.2;OAS1,intron_variant,,ENST00000551241,;OAS1,intron_variant,,ENST00000552526,;OAS1,downstream_gene_variant,,ENST00000452357,NM_002534.2;OAS1,downstream_gene_variant,,ENST00000550689,;OAS1,downstream_gene_variant,,ENST00000553152,;OAS1,downstream_gene_variant,,ENST00000550883,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS1,intron_variant,,ENST00000540589,;OAS1,downstream_gene_variant,,ENST00000549820,; T ENST00000445409 Transcript missense_variant 1441/1684 1184/1245 395/414 Q/L cAg/cTg rs754565362 1 1 OAS1 HGNC HGNC:8086 protein_coding YES CCDS31905.1 ENSP00000388001 P00973 UPI00005B2E03 NM_001032409.1 deleterious_low_confidence(0) 6/6 MODERATE 1 SNV 1 1 PASS rs754565362 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 112919632 112919632 A T 1 0 0 0 0 1 0 0 0 10878 188 7 4 4 OAS1 12 112919632 Missense_Mutation SNP A C3N-01074_T 1571425 112919632 20355677 316 22305 ORAI1 0 . GRCh38 12 121627037 121627037 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.101C>G p.Ser34Cys p.S34C ENST00000617316 1/2 537 462 75 360 360 0 strelka-varscan-mutect ORAI1,missense_variant,p.Ser34Cys,ENST00000617316,NM_032790.3;ORAI1,missense_variant,p.Ser34Cys,ENST00000611718,; G ENST00000617316 Transcript missense_variant 488/2138 101/717 34/238 S/C tCc/tGc 1 1 ORAI1 HGNC HGNC:25896 protein_coding YES ENSP00000482568 A0A0B4J2E8 UPI0000036A44 NM_032790.3 deleterious(0) 1/2 Pfam_domain:PF07856,hmmpanther:PTHR31501,hmmpanther:PTHR31501:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 121627037 121627037 C G 1 0 0 0 0 1 0 0 0 11323 855 30 4 4 ORAI1 12 121627037 Missense_Mutation SNP C C3N-01074_T 8707405 121627037 11648272 317 22306 ZCCHC8 0 . GRCh38 12 122481564 122481564 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.976G>T p.Ala326Ser p.A326S ENST00000633063 10/14 380 275 105 243 242 1 strelka-varscan-mutect ZCCHC8,missense_variant,p.Ala88Ser,ENST00000543897,;ZCCHC8,missense_variant,p.Ala326Ser,ENST00000633063,NM_017612.4;ZCCHC8,missense_variant,p.Ala88Ser,ENST00000536306,;ZCCHC8,missense_variant,p.Ala88Ser,ENST00000544054,;ZCCHC8,missense_variant,p.Ala88Ser,ENST00000536663,;ZCCHC8,downstream_gene_variant,,ENST00000540586,;ZCCHC8,non_coding_transcript_exon_variant,,ENST00000546149,;ZCCHC8,upstream_gene_variant,,ENST00000538116,;ZCCHC8,upstream_gene_variant,,ENST00000542892,;ZCCHC8,downstream_gene_variant,,ENST00000538493,; A ENST00000633063 Transcript missense_variant 1209/2955 976/2124 326/707 A/S Gct/Tct 1 -1 ZCCHC8 HGNC HGNC:25265 protein_coding YES ENSP00000488055 Q6NZY4 UPI00001E0582 NM_017612.4 deleterious(0) 10/14 Pfam_domain:PF04046,hmmpanther:PTHR13316,hmmpanther:PTHR13316:SF0,SMART_domains:SM00581 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 122481564 122481564 C A 1 0 0 0 0 1 0 0 0 18169 739 26 2 2 ZCCHC8 12 122481564 Missense_Mutation SNP C C3N-01074_T 854527 122481564 10793745 318 22307 HIP1R 0 . GRCh38 12 122857141 122857141 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1741G>T p.Glu581Ter p.E581* ENST00000253083 18/32 666 474 192 447 446 1 strelka-varscan-mutect HIP1R,stop_gained,p.Glu581Ter,ENST00000253083,NM_003959.2;HIP1R,upstream_gene_variant,,ENST00000535012,;HIP1R,upstream_gene_variant,,ENST00000537322,;HIP1R,non_coding_transcript_exon_variant,,ENST00000535831,;HIP1R,non_coding_transcript_exon_variant,,ENST00000452196,;HIP1R,upstream_gene_variant,,ENST00000536617,;HIP1R,downstream_gene_variant,,ENST00000536847,;HIP1R,upstream_gene_variant,,ENST00000538236,;HIP1R,upstream_gene_variant,,ENST00000541712,;HIP1R,downstream_gene_variant,,ENST00000536772,; T ENST00000253083 Transcript stop_gained 1866/4539 1741/3207 581/1068 E/* Gag/Tag 1 1 HIP1R HGNC HGNC:18415 protein_coding YES CCDS31922.1 ENSP00000253083 O75146 UPI000012C72C NM_003959.2 18/32 hmmpanther:PTHR10407,hmmpanther:PTHR10407:SF10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 122857141 122857141 G T 1 0 0 0 0 0 1 0 0 7003 943 33 2 2 HIP1R 12 122857141 Nonsense_Mutation SNP G C3N-01074_T 375577 122857141 10418168 319 22308 TMEM132C 0 . GRCh38 12 128693921 128693921 + Missense_Mutation SNP C C A rs771980544 C3N-01074_T C3N-01074_N C C c.1542C>A p.Ser514Arg p.S514R ENST00000435159 6/9 554 407 147 421 421 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Ser514Arg,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript missense_variant 1542/4947 1542/3327 514/1108 S/R agC/agA rs771980544 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0.01) 6/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 MODERATE 1 SNV 5 1 PASS rs771980544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 128693921 128693921 C A 1 0 0 0 0 1 0 0 0 16491 767 27 1 1 TMEM132C 12 128693921 Missense_Mutation SNP C C3N-01074_T 5836780 128693921 4581388 320 22309 TMEM132C 0 . GRCh38 12 128705973 128705973 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.3005C>A p.Pro1002Gln p.P1002Q ENST00000435159 9/9 267 182 85 232 232 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Pro1002Gln,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript missense_variant 3005/4947 3005/3327 1002/1108 P/Q cCg/cAg 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 tolerated(0.58) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 MODERATE 1 SNV 5 1 PASS rs1026852551 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 128705973 128705973 C A 1 0 0 0 0 1 0 0 0 16491 652 23 1 1 TMEM132C 12 128705973 Missense_Mutation SNP C C3N-01074_T 12052 128705973 4569336 321 22310 COL4A1 0 . GRCh38 13 110206674 110206674 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.849A>T p.= p.P283P ENST00000375820 15/52 413 211 202 482 482 0 strelka-varscan-mutect COL4A1,synonymous_variant,p.=,ENST00000375820,NM_001845.5;COL4A1,synonymous_variant,p.=,ENST00000543140,NM_001303110.1;COL4A1,synonymous_variant,p.=,ENST00000615732,; A ENST00000375820 Transcript synonymous_variant 971/6532 849/5010 283/1669 P ccA/ccT 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 15/52 Pfam_domain:PF01391,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 110206674 110206674 T A 1 0 0 0 0 0 0 0 1 3478 1567 55 4 4 COL4A1 13 110206674 Silent SNP T C3N-01074_T 110206674 4157654 322 22311 POTEG 0 . GRCh38 14 19433881 19433881 + Silent SNP G G T rs776577612 C3N-01074_T C3N-01074_N G G c.409C>A p.= p.R137R ENST00000547848 1/11 506 439 67 763 763 0 varscan-mutect POTEG,synonymous_variant,p.=,ENST00000547848,NM_001005356.2;POTEG,synonymous_variant,p.=,ENST00000547722,;POTEG,synonymous_variant,p.=,ENST00000622767,; T ENST00000547848 Transcript synonymous_variant 461/2204 409/1527 137/508 R Cga/Aga rs776577612 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 1/11 hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS rs776577612 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 19433881 19433881 G T 1 0 0 0 0 0 0 0 1 12380 1066 37 1 1 POTEG 14 19433881 Silent SNP G C3N-01074_T 19433881 87609837 323 22312 OR4Q3 0 . GRCh38 14 19747805 19747805 + Silent SNP C C A C3N-01074_T C3N-01074_N C C c.378C>A p.= p.A126A ENST00000331723 1/1 289 215 74 517 517 0 strelka-varscan-mutect OR4Q3,synonymous_variant,p.=,ENST00000331723,NM_172194.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000331723 Transcript synonymous_variant 378/942 378/942 126/313 A gcC/gcA COSM5691854 1 1 OR4Q3 HGNC HGNC:15426 protein_coding YES CCDS32020.1 ENSP00000330049 Q8NH05 A0A126GW32 UPI0000061EF0 NM_172194.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF208,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 19747805 19747805 C A 1 0 0 0 0 0 0 0 1 11157 581 21 2 2 OR4Q3 14 19747805 Silent SNP C C3N-01074_T 313924 19747805 87295913 324 22313 OR4K2 0 . GRCh38 14 19876720 19876720 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.453G>T p.Met151Ile p.M151I ENST00000298642 1/1 320 228 92 552 550 2 strelka-varscan-mutect OR4K2,missense_variant,p.Met151Ile,ENST00000298642,NM_001005501.1; T ENST00000298642 Transcript missense_variant 489/1078 453/945 151/314 M/I atG/atT 1 1 OR4K2 HGNC HGNC:14728 protein_coding YES CCDS32023.1 ENSP00000298642 Q8NGD2 A0A126GVP5 UPI0000041B4D NM_001005501.1 tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF260,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 19876720 19876720 G T 1 0 0 0 0 1 0 0 0 11149 1348 47 2 2 OR4K2 14 19876720 Missense_Mutation SNP G C3N-01074_T 128915 19876720 87166998 325 22314 MYH6 0 . GRCh38 14 23405680 23405680 + Nonsense_Mutation SNP C C A rs140596256 C3N-01074_T C3N-01074_N C C c.292G>T p.Glu98Ter p.E98* ENST00000405093 4/39 322 190 132 382 381 1 strelka-varscan-mutect MYH6,stop_gained,p.Glu98Ter,ENST00000405093,NM_002471.3;MYH6,stop_gained,p.Glu98Ter,ENST00000356287,;MYH6,non_coding_transcript_exon_variant,,ENST00000557461,; A ENST00000405093 Transcript stop_gained 363/5941 292/5820 98/1939 E/* Gag/Tag rs140596256,COSM3885896 1 -1 MYH6 HGNC HGNC:7576 protein_coding YES CCDS9600.1 ENSP00000386041 P13533 UPI0000160969 NM_002471.3 4/39 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,SMART_domains:SM00242,Superfamily_domains:SSF52540 uncertain_significance 0,1 HIGH 1 SNV 5 1,1 1 PASS rs140596256 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 23405680 23405680 C A 1 0 0 0 0 0 1 0 0 10038 893 31 1 1 MYH6 14 23405680 Nonsense_Mutation SNP C C3N-01074_T 3528960 23405680 83638038 326 22315 FOXG1 0 . GRCh38 14 28767933 28767933 + Nonsense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.654C>G p.Tyr218Ter p.Y218* ENST00000313071 1/1 1212 1129 83 507 507 0 strelka-varscan-mutect FOXG1,stop_gained,p.Tyr218Ter,ENST00000313071,NM_005249.4;LINC01551,upstream_gene_variant,,ENST00000399387,;LINC01551,upstream_gene_variant,,ENST00000552957,;LINC01551,upstream_gene_variant,,ENST00000548213,;FOXG1-AS1,upstream_gene_variant,,ENST00000551395,;FOXG1-AS1,upstream_gene_variant,,ENST00000546560,;FOXG1-AS1,upstream_gene_variant,,ENST00000549487,;FOXG1,downstream_gene_variant,,ENST00000637817,;FOXG1,downstream_gene_variant,,ENST00000636893,;FOXG1,downstream_gene_variant,,ENST00000636353,;FOXG1,downstream_gene_variant,,ENST00000637220,;FOXG1,downstream_gene_variant,,ENST00000636346,;FOXG1,downstream_gene_variant,,ENST00000636604,;FOXG1,downstream_gene_variant,,ENST00000637351,; G ENST00000313071 Transcript stop_gained 2546/4890 654/1470 218/489 Y/* taC/taG COSM5172962 1 1 FOXG1 HGNC HGNC:3811 protein_coding YES CCDS9636.1 ENSP00000339004 P55316 UPI00001AE46C NM_005249.4 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF165,SMART_domains:SM00339,Superfamily_domains:SSF46785 1 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 73 28767933 28767933 C G 1 0 0 0 0 0 1 0 0 5869 518 18 4 4 FOXG1 14 28767933 Nonsense_Mutation SNP C C3N-01074_T 5362253 28767933 78275785 327 22316 PRKD1 0 . GRCh38 14 29597759 29597759 + Splice_Site SNP C C A novel C3N-01074_T C3N-01074_N C C c.2167-1G>T p.X723_splice ENST00000331968 189 157 32 110 110 0 strelka-varscan-mutect PRKD1,splice_acceptor_variant,,ENST00000331968,NM_002742.2;PRKD1,splice_acceptor_variant,,ENST00000616995,;PRKD1,splice_acceptor_variant,,ENST00000415220,;PRKD1,upstream_gene_variant,,ENST00000490795,; A ENST00000331968 Transcript splice_acceptor_variant -/3726 2167/2739 723/912 1 -1 PRKD1 HGNC HGNC:9407 protein_coding YES CCDS9637.1 ENSP00000333568 Q15139 UPI0000456761 NM_002742.2 15/17 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999985 1 1 1 0 A 5 1 73 29597759 29597759 C A 1 0 0 0 0 0 0 1 0 12651 695 24 2 2 PRKD1 14 29597759 Splice_Site SNP C C3N-01074_T 829826 29597759 77445959 328 22317 AKAP6 0 . GRCh38 14 32678418 32678418 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2838G>T p.Glu946Asp p.E946D ENST00000280979 8/14 602 244 358 271 270 1 strelka-varscan-mutect AKAP6,missense_variant,p.Glu946Asp,ENST00000280979,NM_004274.4;AKAP6,missense_variant,p.Glu946Asp,ENST00000557354,;AKAP6,missense_variant,p.Glu946Asp,ENST00000557272,;AKAP6,non_coding_transcript_exon_variant,,ENST00000555207,;AKAP6,non_coding_transcript_exon_variant,,ENST00000555950,; T ENST00000280979 Transcript missense_variant 3008/15006 2838/6960 946/2319 E/D gaG/gaT 1 1 AKAP6 HGNC HGNC:376 protein_coding YES CCDS9644.1 ENSP00000280979 Q13023 UPI000013DC48 NM_004274.4 tolerated(0.09) 8/14 hmmpanther:PTHR14514,hmmpanther:PTHR14514:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 32678418 32678418 G T 1 0 0 0 0 1 0 0 0 539 1020 36 2 2 AKAP6 14 32678418 Missense_Mutation SNP G C3N-01074_T 3080659 32678418 74365300 329 22318 SEC23A 0 . GRCh38 14 39063329 39063329 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1393A>T p.Asn465Tyr p.N465Y ENST00000307712 12/20 534 322 212 341 341 0 strelka-varscan-mutect SEC23A,missense_variant,p.Asn263Tyr,ENST00000537403,;SEC23A,missense_variant,p.Asn465Tyr,ENST00000307712,NM_006364.2;SEC23A,missense_variant,p.Asn436Tyr,ENST00000545328,;SEC23A,downstream_gene_variant,,ENST00000553925,; A ENST00000307712 Transcript missense_variant 1911/4135 1393/2298 465/765 N/Y Aat/Tat 1 -1 SEC23A HGNC HGNC:10701 protein_coding YES CCDS9668.1 ENSP00000306881 Q15436 UPI000013EC46 NM_006364.2 deleterious(0) 12/20 Gene3D:2nutA01,Pfam_domain:PF08033,hmmpanther:PTHR11141,hmmpanther:PTHR11141:SF7,Superfamily_domains:SSF81995 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 39063329 39063329 T A 1 0 0 0 0 1 0 0 0 14268 1826 63 4 4 SEC23A 14 39063329 Missense_Mutation SNP T C3N-01074_T 6384911 39063329 67980389 330 22319 FSCB 0 . GRCh38 14 44505315 44505315 + Missense_Mutation SNP T T A C3N-01074_T C3N-01074_N T T c.1673A>T p.Glu558Val p.E558V ENST00000340446 1/1 403 342 61 275 275 0 strelka-varscan-mutect FSCB,missense_variant,p.Glu558Val,ENST00000340446,NM_032135.3;RP11-163M18.1,upstream_gene_variant,,ENST00000557465,;RP11-163M18.1,upstream_gene_variant,,ENST00000556228,;RP11-163M18.1,upstream_gene_variant,,ENST00000555433,; A ENST00000340446 Transcript missense_variant 1965/2938 1673/2478 558/825 E/V gAa/gTa COSM4245936 1 -1 FSCB HGNC HGNC:20494 protein_coding YES CCDS9679.1 ENSP00000344579 Q5H9T9 UPI00001FD466 NM_032135.3 tolerated(0.12) 1/1 hmmpanther:PTHR36135,Low_complexity_(Seg):seg 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 44505315 44505315 T A 1 0 0 0 0 1 0 0 0 5939 1783 62 4 4 FSCB 14 44505315 Missense_Mutation SNP T C3N-01074_T 5441986 44505315 62538403 331 22320 FRMD6 0 . GRCh38 14 51725837 51725837 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.1551G>C p.Lys517Asn p.K517N ENST00000344768 13/14 823 732 91 311 311 0 strelka-varscan-mutect FRMD6,missense_variant,p.Lys509Asn,ENST00000395718,NM_152330.3;FRMD6,missense_variant,p.Lys509Asn,ENST00000356218,NM_001042481.2;FRMD6,missense_variant,p.Lys440Asn,ENST00000554167,;FRMD6,missense_variant,p.Lys517Asn,ENST00000344768,NM_001267046.1;FRMD6,missense_variant,p.Lys159Asn,ENST00000553556,NM_001267047.1;FRMD6,downstream_gene_variant,,ENST00000555703,;RNU6-301P,downstream_gene_variant,,ENST00000384277,;FRMD6,non_coding_transcript_exon_variant,,ENST00000557522,; C ENST00000344768 Transcript missense_variant 1747/2972 1551/1869 517/622 K/N aaG/aaC 1 1 FRMD6 HGNC HGNC:19839 protein_coding YES CCDS58318.1 ENSP00000343899 Q96NE9 UPI00000473F6 NM_001267046.1 deleterious(0) 13/14 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF9 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 51725837 51725837 G C 1 0 0 0 0 1 0 0 0 5924 962 34 4 4 FRMD6 14 51725837 Missense_Mutation SNP G C3N-01074_T 7220522 51725837 55317881 332 22321 IFT43 0 . GRCh38 14 76058757 76058757 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.331C>T p.His111Tyr p.H111Y ENST00000556742 4/4 211 112 99 280 279 1 strelka-varscan-mutect IFT43,missense_variant,p.His111Tyr,ENST00000556742,NM_001255995.1;IFT43,intron_variant,,ENST00000314067,NM_001102564.1;IFT43,intron_variant,,ENST00000238628,NM_052873.2;IFT43,intron_variant,,ENST00000553438,;IFT43,intron_variant,,ENST00000555305,;IFT43,intron_variant,,ENST00000554026,;IFT43,intron_variant,,ENST00000542766,;IFT43,intron_variant,,ENST00000554233,;IFT43,intron_variant,,ENST00000554423,;IFT43,intron_variant,,ENST00000555370,; T ENST00000556742 Transcript missense_variant 334/848 331/342 111/113 H/Y Cac/Tac 1 1 IFT43 HGNC HGNC:29669 protein_coding CCDS58330.1 ENSP00000451096 Q96FT9 UPI00001FD8DE NM_001255995.1 deleterious_low_confidence(0) 4/4 MODERATE SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 76058757 76058757 C T 1 0 0 0 0 1 0 0 0 7465 594 21 3 3 IFT43 14 76058757 Missense_Mutation SNP C C3N-01074_T 24332920 76058757 30984961 333 22322 MARK3 0 . GRCh38 14 103458764 103458764 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.521C>T p.Ser174Phe p.S174F ENST00000416682 7/17 148 99 49 201 201 0 strelka-varscan-mutect MARK3,missense_variant,p.Ser174Phe,ENST00000416682,;MARK3,missense_variant,p.Ser174Phe,ENST00000335102,;MARK3,intron_variant,,ENST00000429436,NM_001128918.2;MARK3,intron_variant,,ENST00000303622,NM_002376.6;MARK3,intron_variant,,ENST00000216288,NM_001128920.2;MARK3,intron_variant,,ENST00000440884,NM_001128921.2;MARK3,intron_variant,,ENST00000553942,NM_001128919.2;MARK3,intron_variant,,ENST00000560417,;MARK3,non_coding_transcript_exon_variant,,ENST00000559268,;MARK3,intron_variant,,ENST00000561071,;MARK3,intron_variant,,ENST00000561164,;MARK3,intron_variant,,ENST00000558698,;MARK3,downstream_gene_variant,,ENST00000560731,;MARK3,intron_variant,,ENST00000558223,; T ENST00000416682 Transcript missense_variant 1098/2969 521/2259 174/752 S/F tCc/tTc 1 1 MARK3 HGNC HGNC:6897 protein_coding ENSP00000408092 A0A0A0MSZ1 UPI000002AE4D tolerated_low_confidence(0.71) 7/17 PROSITE_profiles:PS50011,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 103458764 103458764 C T 1 0 0 0 0 1 0 0 0 9239 855 30 3 3 MARK3 14 103458764 Missense_Mutation SNP C C3N-01074_T 27400007 103458764 3584954 334 22323 UBE3A 0 . GRCh38 15 25360405 25360405 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.1740G>A p.= p.E580E ENST00000397954 8/14 415 307 108 475 475 0 strelka-varscan-mutect UBE3A,synonymous_variant,p.=,ENST00000635914,;UBE3A,synonymous_variant,p.=,ENST00000638155,;UBE3A,synonymous_variant,p.=,ENST00000438097,;UBE3A,synonymous_variant,p.=,ENST00000638011,;UBE3A,synonymous_variant,p.=,ENST00000614096,NM_130839.2;UBE3A,synonymous_variant,p.=,ENST00000637886,;UBE3A,synonymous_variant,p.=,ENST00000630424,;UBE3A,synonymous_variant,p.=,ENST00000232165,NM_130838.1;UBE3A,synonymous_variant,p.=,ENST00000625778,;UBE3A,synonymous_variant,p.=,ENST00000566215,;UBE3A,synonymous_variant,p.=,ENST00000428984,;UBE3A,synonymous_variant,p.=,ENST00000397954,NM_000462.3;UBE3A,upstream_gene_variant,,ENST00000604860,;UBE3A,upstream_gene_variant,,ENST00000626176,;SNHG14,intron_variant,,ENST00000453082,;SNHG14,intron_variant,,ENST00000554726,;UBE3A,upstream_gene_variant,,ENST00000631247,; T ENST00000397954 Transcript synonymous_variant 1985/2873 1740/2628 580/875 E gaG/gaA 1 -1 UBE3A HGNC HGNC:12496 protein_coding YES CCDS45192.1 ENSP00000381045 Q05086 UPI0000161F3B NM_000462.3 8/14 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,PIRSF_domain:PIRSF037201,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 25360405 25360405 C T 1 0 0 0 0 0 0 0 1 17402 680 24 3 3 UBE3A 15 25360405 Silent SNP C C3N-01074_T 25360405 76630784 335 22324 GABRB3 0 . GRCh38 15 26583354 26583354 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.522C>A p.Asn174Lys p.N174K ENST00000311550 5/9 609 510 99 580 579 1 strelka-varscan-mutect GABRB3,missense_variant,p.Asn230Lys,ENST00000541819,;GABRB3,missense_variant,p.Asn89Lys,ENST00000622697,NM_001278631.1;GABRB3,missense_variant,p.Asn174Lys,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Asn89Lys,ENST00000628124,NM_001191320.1;GABRB3,missense_variant,p.Asn89Lys,ENST00000636466,;GABRB3,missense_variant,p.Asn174Lys,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Asn141Lys,ENST00000638099,;GABRB3,missense_variant,p.Asn103Lys,ENST00000400188,NM_001191321.2;GABRB3,missense_variant,p.Asn89Lys,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,non_coding_transcript_exon_variant,,ENST00000636512,;GABRB3,missense_variant,p.Asn69Lys,ENST00000635994,;GABRB3,missense_variant,p.Leu101Met,ENST00000554556,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;GABRB3,upstream_gene_variant,,ENST00000557765,; T ENST00000311550 Transcript missense_variant 634/5781 522/1422 174/473 N/K aaC/aaA 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 deleterious(0.01) 5/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,PROSITE_patterns:PS00236,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 26583354 26583354 G T 1 0 0 0 0 1 0 0 0 6039 1020 36 2 2 GABRB3 15 26583354 Missense_Mutation SNP G C3N-01074_T 1222949 26583354 75407835 336 22325 GABRG3 0 . GRCh38 15 27527469 27527469 + Missense_Mutation SNP C C G C3N-01074_T C3N-01074_N C C c.902C>G p.Thr301Ser p.T301S ENST00000615808 8/10 119 97 22 142 142 0 strelka-varscan-mutect GABRG3,missense_variant,p.Thr301Ser,ENST00000615808,NM_033223.4;GABRG3,missense_variant,p.Thr122Ser,ENST00000333743,;GABRG3,missense_variant,p.Thr243Ser,ENST00000554696,;GABRG3,missense_variant,p.Thr64Ser,ENST00000451330,;RP11-100M12.3,intron_variant,,ENST00000556642,; G ENST00000615808 Transcript missense_variant 1156/10768 902/1404 301/467 T/S aCc/aGc COSM960062 1 1 GABRG3 HGNC HGNC:4088 protein_coding YES CCDS45195.1 ENSP00000479113 Q99928 UPI000012AFCB NM_033223.4 tolerated(0.12) 8/10 Gene3D:1.20.58.390,Pfam_domain:PF02932,Prints_domain:PR00253,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF195,Low_complexity_(Seg):seg,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 27527469 27527469 C G 1 0 0 0 0 1 0 0 0 6044 507 18 4 4 GABRG3 15 27527469 Missense_Mutation SNP C C3N-01074_T 944115 27527469 74463720 337 22326 APBA2 0 . GRCh38 15 29054455 29054455 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.571G>T p.Glu191Ter p.E191* ENST00000558402 5/16 734 628 106 724 720 4 strelka-varscan-mutect APBA2,stop_gained,p.Glu191Ter,ENST00000558402,;APBA2,stop_gained,p.Glu191Ter,ENST00000558259,NM_005503.3;APBA2,stop_gained,p.Glu191Ter,ENST00000411764,NM_001130414.1;APBA2,stop_gained,p.Glu191Ter,ENST00000558330,;APBA2,stop_gained,p.Glu191Ter,ENST00000561069,;APBA2,stop_gained,p.Glu191Ter,ENST00000558358,;APBA2,downstream_gene_variant,,ENST00000560283,;APBA2,downstream_gene_variant,,ENST00000559709,;APBA2,downstream_gene_variant,,ENST00000558206,;APBA2,downstream_gene_variant,,ENST00000558804,;APBA2,non_coding_transcript_exon_variant,,ENST00000559814,; T ENST00000558402 Transcript stop_gained 1170/4031 571/2250 191/749 E/* Gag/Tag 1 1 APBA2 HGNC HGNC:579 protein_coding YES CCDS10022.1 ENSP00000453293 Q99767 UPI0000046798 5/16 hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF12 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 29054455 29054455 G T 1 0 0 0 0 0 1 0 0 877 943 33 2 2 APBA2 15 29054455 Nonsense_Mutation SNP G C3N-01074_T 1526986 29054455 72936734 338 22327 OTUD7A 0 . GRCh38 15 31483629 31483629 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2446G>T p.Ala816Ser p.A816S ENST00000307050 11/11 32 20 12 32 32 0 strelka-varscan-mutect OTUD7A,missense_variant,p.Ala816Ser,ENST00000307050,NM_130901.1; A ENST00000307050 Transcript missense_variant 2539/10770 2446/2781 816/926 A/S Gcc/Tcc 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 tolerated_low_confidence(0.5) 11/11 hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367 MODERATE 1 SNV 1 1 PASS rs1408480931 . 9 199 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 31483629 31483629 C A 1 0 0 0 0 1 0 0 0 11387 768 27 1 1 OTUD7A 15 31483629 Missense_Mutation SNP C C3N-01074_T 2429174 31483629 70507560 339 22328 GOLGA8O 0 . GRCh38 15 32446528 32446528 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.1314G>A p.= p.E438E ENST00000509311 15/19 465 425 40 459 459 0 varscan-mutect GOLGA8O,synonymous_variant,p.=,ENST00000509311,NM_001277308.1;GOLGA8O,downstream_gene_variant,,ENST00000562377,;RN7SL539P,downstream_gene_variant,,ENST00000610974,; T ENST00000509311 Transcript synonymous_variant 1412/1997 1314/1899 438/632 E gaG/gaA 1 -1 GOLGA8O HGNC HGNC:44406 protein_coding YES CCDS59252.1 ENSP00000423159 A6NCC3 UPI0000DD8295 NM_001277308.1 15/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881,Pfam_domain:PF15070 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 32446528 32446528 C T 1 0 0 0 0 0 0 0 1 6455 680 24 3 3 GOLGA8O 15 32446528 Silent SNP C C3N-01074_T 962899 32446528 69544661 340 22329 GOLGA8A 0 . GRCh38 15 34386697 34386697 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.213C>T p.= p.C71C ENST00000359187 3/16 245 232 13 255 255 0 varscan-mutect GOLGA8A,synonymous_variant,p.=,ENST00000432566,;GOLGA8A,synonymous_variant,p.=,ENST00000359187,NM_181077.3;MIR1233-1,upstream_gene_variant,,ENST00000408722,;GOLGA8A,non_coding_transcript_exon_variant,,ENST00000473125,; A ENST00000359187 Transcript synonymous_variant 278/1877 213/1812 71/603 C tgC/tgT 1 -1 GOLGA8A HGNC HGNC:31972 protein_coding YES CCDS10038.1 ENSP00000352111 A7E2F4 UPI000019C425 NM_181077.3 3/16 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 34386697 34386697 G A 1 0 0 0 0 0 0 0 1 6447 1195 42 3 3 GOLGA8A 15 34386697 Silent SNP G C3N-01074_T 1940169 34386697 67604492 341 22330 ACTC1 0 . GRCh38 15 34793514 34793514 + Missense_Mutation SNP C C T C3N-01074_T C3N-01074_N C C c.185G>A p.Ser62Asn p.S62N ENST00000290378 3/7 248 210 38 308 307 1 strelka-varscan-mutect ACTC1,missense_variant,p.Ser62Asn,ENST00000290378,NM_005159.4;RP11-814P5.1,intron_variant,,ENST00000503496,;RP11-814P5.1,downstream_gene_variant,,ENST00000558707,;ACTC1,upstream_gene_variant,,ENST00000557860,;ACTC1,upstream_gene_variant,,ENST00000560563,; T ENST00000290378 Transcript missense_variant 841/4106 185/1134 62/377 S/N aGc/aAc COSM960891 1 -1 ACTC1 HGNC HGNC:143 protein_coding YES CCDS10041.1 ENSP00000290378 P68032 UPI0000003F15 NM_005159.4 deleterious_low_confidence(0.04) 3/7 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,PROSITE_patterns:PS00406,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF238,SMART_domains:SM00268,Superfamily_domains:SSF53067 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 34793514 34793514 C T 1 0 0 0 0 1 0 0 0 238 797 28 3 3 ACTC1 15 34793514 Missense_Mutation SNP C C3N-01074_T 406817 34793514 67197675 342 22331 THBS1 0 . GRCh38 15 39587390 39587390 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1164G>T p.Trp388Cys p.W388C ENST00000260356 8/22 125 87 38 105 105 0 strelka-varscan-mutect THBS1,missense_variant,p.Trp388Cys,ENST00000260356,NM_003246.2;THBS1,downstream_gene_variant,,ENST00000397591,;CTD-2033D15.2,downstream_gene_variant,,ENST00000478845,;CTD-2033D15.3,downstream_gene_variant,,ENST00000616754,;THBS1,upstream_gene_variant,,ENST00000560894,;THBS1,upstream_gene_variant,,ENST00000497720,;THBS1,upstream_gene_variant,,ENST00000466755,;THBS1,upstream_gene_variant,,ENST00000490247,; T ENST00000260356 Transcript missense_variant 1329/7775 1164/3513 388/1170 W/C tgG/tgT 1 1 THBS1 HGNC HGNC:11785 protein_coding YES CCDS32194.1 ENSP00000260356 P07996 UPI00001FE219 NM_003246.2 deleterious(0) 8/22 PROSITE_profiles:PS50092,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF78,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 39587390 39587390 G T 1 0 0 0 0 1 0 0 0 16286 1183 41 2 2 THBS1 15 39587390 Missense_Mutation SNP G C3N-01074_T 4793876 39587390 62403799 343 22332 ATP8B4 0 . GRCh38 15 49931269 49931269 + Frame_Shift_Del DEL C C - rs770589258 C3N-01074_T C3N-01074_N C C c.1492delG p.Ala498LeufsTer2 p.A498Lfs*2 ENST00000284509 16/28 194 147 47 194 194 0 sindel-varindel-pindel ATP8B4,frameshift_variant,p.Ala498LeufsTer2,ENST00000284509,NM_024837.3;ATP8B4,frameshift_variant,p.Ala498LeufsTer2,ENST00000559829,;ATP8B4,frameshift_variant,p.Ala498LeufsTer2,ENST00000557955,;ATP8B4,3_prime_UTR_variant,,ENST00000559726,;ATP8B4,intron_variant,,ENST00000558906,;ATP8B4,upstream_gene_variant,,ENST00000558458,; - ENST00000284509 Transcript frameshift_variant 1634/5676 1492/3579 498/1192 A/X Gct/ct rs770589258 1 -1 ATP8B4 HGNC HGNC:13536 protein_coding YES CCDS32238.1 ENSP00000284509 Q8TF62 UPI0000055904 NM_024837.3 16/28 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF80,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01652,Pfam_domain:PF13246,Superfamily_domains:SSF81660 HIGH 1 deletion 5 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999975 1 1 1 0 - 7 5 73 49931269 49931269 C - 1 0 1 0 1 0 0 0 0 1350 739 26 0 0 ATP8B4 15 49931269 Frame_Shift_Del DEL C C3N-01074_T 10343879 49931269 52059920 344 22333 GLDN 0 . GRCh38 15 51383815 51383815 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.464A>T p.His155Leu p.H155L ENST00000335449 4/10 215 178 37 240 240 0 strelka-varscan-mutect GLDN,missense_variant,p.His155Leu,ENST00000335449,NM_181789.2;GLDN,missense_variant,p.His31Leu,ENST00000396399,;GLDN,missense_variant,p.His118Leu,ENST00000560215,;GLDN,missense_variant,p.His31Leu,ENST00000612989,;GLDN,missense_variant,p.His41Leu,ENST00000558426,;GLDN,non_coding_transcript_exon_variant,,ENST00000464150,;GLDN,non_coding_transcript_exon_variant,,ENST00000560690,;GLDN,non_coding_transcript_exon_variant,,ENST00000558286,;GLDN,non_coding_transcript_exon_variant,,ENST00000559317,;GLDN,non_coding_transcript_exon_variant,,ENST00000561194,; T ENST00000335449 Transcript missense_variant 520/4971 464/1656 155/551 H/L cAc/cTc 1 1 GLDN HGNC HGNC:29514 protein_coding YES CCDS10140.2 ENSP00000335196 Q6ZMI3 UPI000015FAA3 NM_181789.2 tolerated(0.21) 4/10 Pfam_domain:PF01391,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1161077771 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 51383815 51383815 A T 1 0 0 0 0 1 0 0 0 6312 159 6 4 4 GLDN 15 51383815 Missense_Mutation SNP A C3N-01074_T 1452546 51383815 50607374 345 22334 ZNF609 0 . GRCh38 15 64499787 64499787 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.368G>T p.Gly123Val p.G123V ENST00000326648 1/9 269 212 57 296 295 1 strelka-varscan-mutect ZNF609,missense_variant,p.Gly123Val,ENST00000326648,NM_015042.1;ZNF609,missense_variant,p.Gly123Val,ENST00000416172,;ZNF609,upstream_gene_variant,,ENST00000558680,; T ENST00000326648 Transcript missense_variant 496/8746 368/4236 123/1411 G/V gGg/gTg 1 1 ZNF609 HGNC HGNC:29003 protein_coding YES CCDS32270.1 ENSP00000316527 O15014 UPI00001D7783 NM_015042.1 deleterious(0) 1/9 hmmpanther:PTHR21564:SF3,hmmpanther:PTHR21564 MODERATE 1 SNV 5 1 PASS rs1181707944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 64499787 64499787 G T 1 0 0 0 0 1 0 0 0 18610 1232 43 2 2 ZNF609 15 64499787 Missense_Mutation SNP G C3N-01074_T 13115972 64499787 37491402 346 22335 IGDCC3 0 . GRCh38 15 65331206 65331206 + Nonsense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1405G>T p.Glu469Ter p.E469* ENST00000327987 9/14 150 119 31 144 144 0 varscan-mutect IGDCC3,stop_gained,p.Glu469Ter,ENST00000327987,NM_004884.3;IGDCC3,stop_gained,p.Glu332Ter,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559058,;IGDCC3,non_coding_transcript_exon_variant,,ENST00000559231,; A ENST00000327987 Transcript stop_gained 1657/4479 1405/2445 469/814 E/* Gag/Tag 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 9/14 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 65331206 65331206 C A 1 0 0 0 0 0 1 0 0 7474 864 30 2 2 IGDCC3 15 65331206 Nonsense_Mutation SNP C C3N-01074_T 831419 65331206 36659983 347 22336 SLC24A1 0 . GRCh38 15 65650851 65650851 + Nonsense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.2702G>A p.Trp901Ter p.W901* ENST00000261892 7/10 339 233 106 353 353 0 strelka-varscan-mutect SLC24A1,stop_gained,p.Trp901Ter,ENST00000261892,NM_004727.2;SLC24A1,stop_gained,p.Trp901Ter,ENST00000339868,;SLC24A1,stop_gained,p.Trp883Ter,ENST00000537259,NM_001301033.1;SLC24A1,stop_gained,p.Trp901Ter,ENST00000399033,NM_001301031.1;SLC24A1,stop_gained,p.Trp883Ter,ENST00000546330,NM_001301032.1;SLC24A1,stop_gained,p.Trp787Ter,ENST00000544319,;SLC24A1,upstream_gene_variant,,ENST00000505666,;RP11-16E23.5,downstream_gene_variant,,ENST00000613686,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000449142,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000434116,;SLC24A1,downstream_gene_variant,,ENST00000539516,; A ENST00000261892 Transcript stop_gained 2989/5768 2702/3300 901/1099 W/* tGg/tAg 1 1 SLC24A1 HGNC HGNC:10975 protein_coding YES CCDS45284.1 ENSP00000261892 O60721 UPI000013020C NM_004727.2 7/10 hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF36,TIGRFAM_domain:TIGR00367 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 65650851 65650851 G A 1 0 0 0 0 0 1 0 0 14731 1357 47 3 3 SLC24A1 15 65650851 Nonsense_Mutation SNP G C3N-01074_T 319645 65650851 36340338 348 22337 ITGA11 0 . GRCh38 15 68358548 68358548 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.510T>A p.Asp170Glu p.D170E ENST00000315757 6/30 183 129 54 165 165 0 strelka-varscan-mutect ITGA11,missense_variant,p.Asp170Glu,ENST00000423218,;ITGA11,missense_variant,p.Asp170Glu,ENST00000315757,NM_001004439.1;ITGA11,non_coding_transcript_exon_variant,,ENST00000562826,;ITGA11,non_coding_transcript_exon_variant,,ENST00000568677,;ITGA11,non_coding_transcript_exon_variant,,ENST00000565868,; T ENST00000315757 Transcript missense_variant 606/3955 510/3567 170/1188 D/E gaT/gaA 1 -1 ITGA11 HGNC HGNC:6136 protein_coding YES CCDS45291.1 ENSP00000327290 Q9UKX5 UPI00001FE74D NM_001004439.1 deleterious(0) 6/30 PROSITE_profiles:PS50234,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300,Prints_domain:PR00453 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 68358548 68358548 A T 1 0 0 0 0 1 0 0 0 7781 214 8 4 4 ITGA11 15 68358548 Missense_Mutation SNP A C3N-01074_T 2707697 68358548 33632641 349 22338 C15orf59 0 . GRCh38 15 73750992 73750992 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.139G>T p.Ala47Ser p.A47S ENST00000569673 2/3 184 161 23 166 166 0 strelka-varscan-mutect C15orf59,missense_variant,p.Ala47Ser,ENST00000569673,;C15orf59,missense_variant,p.Ala47Ser,ENST00000379822,NM_001039614.2;C15orf59,missense_variant,p.Ala19Ser,ENST00000559817,;C15orf59-AS1,upstream_gene_variant,,ENST00000615095,; A ENST00000569673 Transcript missense_variant 1344/6573 139/882 47/293 A/S Gcc/Tcc 1 -1 C15orf59 HGNC HGNC:33753 protein_coding YES CCDS32289.1 ENSP00000457205 Q2T9L4 UPI00001D778D deleterious(0.03) 2/3 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF3 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 73750992 73750992 C A 1 0 0 0 0 1 0 0 0 1850 739 26 2 2 C15orf59 15 73750992 Missense_Mutation SNP C C3N-01074_T 5392444 73750992 28240197 350 22339 LINGO1 0 . GRCh38 15 77615776 77615776 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.131C>A p.Pro44His p.P44H ENST00000355300 2/2 53 47 6 61 61 0 strelka-mutect LINGO1,missense_variant,p.Pro44His,ENST00000355300,NM_032808.6;LINGO1,missense_variant,p.Pro38His,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,missense_variant,p.Pro49His,ENST00000557798,;LINGO1,missense_variant,p.Pro38His,ENST00000561686,;LINGO1,missense_variant,p.Pro38His,ENST00000566711,;LINGO1,missense_variant,p.Pro38His,ENST00000567726,;LINGO1,missense_variant,p.Pro38His,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000564472,; T ENST00000355300 Transcript missense_variant 306/3055 131/1863 44/620 P/H cCc/cAc 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 deleterious(0.01) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,SMART_domains:SM00013 MODERATE 1 SNV 1 1 PASS rs1164446608 . 0 200 10 0 0 0 0 0 -14.09186 0.9999699 1 1 1 0 T 3 4 73 77615776 77615776 G T 1 0 0 0 0 1 0 0 0 8735 1232 43 2 2 LINGO1 15 77615776 Missense_Mutation SNP G C3N-01074_T 3864784 77615776 24375413 351 22340 77 2 LINGO1 0 . GRCh38 15 77615778 77615778 + Silent SNP C C A rs748472533 C3N-01074_T C3N-01074_N C C c.129G>T p.= p.P43P ENST00000355300 2/2 51 36 15 61 61 0 strelka-varscan-mutect LINGO1,synonymous_variant,p.=,ENST00000355300,NM_032808.6;LINGO1,synonymous_variant,p.=,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,synonymous_variant,p.=,ENST00000557798,;LINGO1,synonymous_variant,p.=,ENST00000561686,;LINGO1,synonymous_variant,p.=,ENST00000566711,;LINGO1,synonymous_variant,p.=,ENST00000567726,;LINGO1,synonymous_variant,p.=,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000564472,; A ENST00000355300 Transcript synonymous_variant 304/3055 129/1863 43/620 P ccG/ccT rs748472533 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,SMART_domains:SM00013 LOW 1 SNV 1 1 PASS rs748472533 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 77615778 77615778 C A 1 0 0 0 0 0 0 0 1 8735 755 27 1 1 LINGO1 15 77615778 Silent SNP C C3N-01074_T 2 77615778 24375411 352 22341 77 2 GOLGA6L9 0 . GRCh38 15 82434414 82434414 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.814G>T p.Glu272Ter p.E272* ENST00000618348 6/9 542 481 61 595 594 1 varscan-mutect GOLGA6L9,stop_gained,p.Glu272Ter,ENST00000618348,NM_198181.3;RP11-152F13.8,downstream_gene_variant,,ENST00000613086,;GOLGA6L9,non_coding_transcript_exon_variant,,ENST00000618706,;GOLGA6L9,downstream_gene_variant,,ENST00000558668,; T ENST00000618348 Transcript stop_gained 874/1710 814/1299 272/432 E/* Gag/Tag 1 1 GOLGA6L9 HGNC HGNC:37229 protein_coding YES CCDS45326.1 ENSP00000481078 A6NEM1 UPI000442D01A NM_198181.3 6/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF12,Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 82434414 82434414 G T 1 0 0 0 0 0 1 0 0 6444 1175 41 2 2 GOLGA6L9 15 82434414 Nonsense_Mutation SNP G C3N-01074_T 4818636 82434414 19556775 353 22342 SLC28A1 0 . GRCh38 15 84895108 84895108 + Missense_Mutation SNP T T C novel C3N-01074_T C3N-01074_N T T c.446T>C p.Leu149Pro p.L149P ENST00000394573 6/19 271 177 94 257 257 0 strelka-varscan-mutect SLC28A1,missense_variant,p.Leu149Pro,ENST00000394573,NM_004213.4;SLC28A1,missense_variant,p.Leu149Pro,ENST00000286749,NM_001287762.1;SLC28A1,missense_variant,p.Leu149Pro,ENST00000538177,NM_001287761.1;SLC28A1,missense_variant,p.Leu149Pro,ENST00000338602,NM_201651.2; C ENST00000394573 Transcript missense_variant 669/2769 446/1950 149/649 L/P cTg/cCg 1 1 SLC28A1 HGNC HGNC:11001 protein_coding YES CCDS10334.1 ENSP00000378074 O00337 UPI000013DE67 NM_004213.4 tolerated(0.2) 6/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR10590:SF16,hmmpanther:PTHR10590 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 84895108 84895108 T C 1 0 0 0 0 1 0 0 0 14801 1580 55 5 5 SLC28A1 15 84895108 Missense_Mutation SNP T C3N-01074_T 2460694 84895108 17096081 354 22343 NTRK3 0 . GRCh38 15 87933016 87933016 + Missense_Mutation SNP G G A C3N-01074_T C3N-01074_N G G c.1885C>T p.Leu629Phe p.L629F ENST00000360948 16/20 501 362 139 443 442 1 strelka-varscan-mutect NTRK3,missense_variant,p.Leu629Phe,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Leu621Phe,ENST00000558676,;NTRK3,missense_variant,p.Leu629Phe,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Leu621Phe,ENST00000357724,;NTRK3,missense_variant,p.Leu621Phe,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Leu629Phe,ENST00000626019,;NTRK3,missense_variant,p.Leu629Phe,ENST00000629765,;NTRK3,missense_variant,p.Leu621Phe,ENST00000557856,;NTRK3,missense_variant,p.Leu531Phe,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Leu26Phe,ENST00000558576,;NTRK3,non_coding_transcript_exon_variant,,ENST00000559680,; A ENST00000360948 Transcript missense_variant 2191/3004 1885/2520 629/839 L/F Ctc/Ttc COSM5028023,COSM5028024 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0) 16/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 87933016 87933016 G A 1 0 0 0 0 1 0 0 0 10774 1014 35 3 3 NTRK3 15 87933016 Missense_Mutation SNP G C3N-01074_T 3037908 87933016 14058173 355 22344 NR2F2 0 . GRCh38 15 96332169 96332169 + Nonsense_Mutation SNP C C T C3N-01074_T C3N-01074_N C C c.64C>T p.Gln22Ter p.Q22* ENST00000394166 1/3 130 122 8 87 87 0 strelka-varscan-mutect NR2F2,stop_gained,p.Gln22Ter,ENST00000394166,NM_021005.3;NR2F2,intron_variant,,ENST00000421109,NM_001145155.1;NR2F2,upstream_gene_variant,,ENST00000394171,NM_001145156.1;NR2F2,upstream_gene_variant,,ENST00000453270,NM_001145157.1;NR2F2,upstream_gene_variant,,ENST00000559679,;NR2F2,upstream_gene_variant,,ENST00000410719,;NR2F2-AS1,upstream_gene_variant,,ENST00000502125,;NR2F2-AS1,upstream_gene_variant,,ENST00000561344,;NR2F2-AS1,upstream_gene_variant,,ENST00000560170,;NR2F2-AS1,upstream_gene_variant,,ENST00000560010,; T ENST00000394166 Transcript stop_gained 1453/5275 64/1245 22/414 Q/* Cag/Tag COSM4985866 1 1 NR2F2 HGNC HGNC:7976 protein_coding YES CCDS10375.1 ENSP00000377721 P24468 F1D8R0 UPI000000052E NM_021005.3 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF45 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -15.69519 1 1 1 1 0 T 4 4 73 96332169 96332169 C T 1 0 0 0 0 0 1 0 0 10684 595 21 3 3 NR2F2 15 96332169 Nonsense_Mutation SNP C C3N-01074_T 8399153 96332169 5659020 356 22345 RHOT2 0 . GRCh38 16 672509 672509 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.1347G>A p.= p.Q449Q ENST00000315082 16/19 147 118 29 166 166 0 strelka-varscan-mutect RHOT2,synonymous_variant,p.=,ENST00000315082,NM_138769.2;WDR90,downstream_gene_variant,,ENST00000549091,;WDR90,downstream_gene_variant,,ENST00000293879,NM_145294.4;WDR90,downstream_gene_variant,,ENST00000547944,;RHBDL1,upstream_gene_variant,,ENST00000219551,NM_001318733.1;RHBDL1,upstream_gene_variant,,ENST00000352681,NM_001278720.1;WDR90,downstream_gene_variant,,ENST00000315764,;RHBDL1,upstream_gene_variant,,ENST00000561556,NM_001278721.1;RHOT2,downstream_gene_variant,,ENST00000563134,;RHOT2,downstream_gene_variant,,ENST00000561929,;WDR90,downstream_gene_variant,,ENST00000551100,;RHOT2,upstream_gene_variant,,ENST00000569197,;WDR90,downstream_gene_variant,,ENST00000546896,;RHOT2,downstream_gene_variant,,ENST00000569943,;RHOT2,non_coding_transcript_exon_variant,,ENST00000602564,;RHOT2,non_coding_transcript_exon_variant,,ENST00000568636,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569675,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569358,;RHOT2,non_coding_transcript_exon_variant,,ENST00000565004,;RHOT2,non_coding_transcript_exon_variant,,ENST00000561711,;WDR90,downstream_gene_variant,,ENST00000547407,;WDR90,downstream_gene_variant,,ENST00000552728,;WDR90,downstream_gene_variant,,ENST00000549024,;WDR90,downstream_gene_variant,,ENST00000553080,;RHBDL1,upstream_gene_variant,,ENST00000450775,;RHOT2,downstream_gene_variant,,ENST00000568950,;RHOT2,downstream_gene_variant,,ENST00000567017,;RHOT2,downstream_gene_variant,,ENST00000562333,;RHOT2,downstream_gene_variant,,ENST00000561983,;RHOT2,downstream_gene_variant,,ENST00000563637,;RHOT2,downstream_gene_variant,,ENST00000563776,;RHOT2,downstream_gene_variant,,ENST00000566965,;RHOT2,upstream_gene_variant,,ENST00000564659,;RHOT2,downstream_gene_variant,,ENST00000570280,;RHOT2,downstream_gene_variant,,ENST00000566214,;RHOT2,downstream_gene_variant,,ENST00000570092,;RHOT2,downstream_gene_variant,,ENST00000562708,;RHOT2,downstream_gene_variant,,ENST00000562598,;RHOT2,downstream_gene_variant,,ENST00000569706,;RHOT2,downstream_gene_variant,,ENST00000567589,;RHOT2,upstream_gene_variant,,ENST00000562957,; A ENST00000315082 Transcript synonymous_variant 1461/2539 1347/1857 449/618 Q caG/caA 1 1 RHOT2 HGNC HGNC:21169 protein_coding YES CCDS10417.1 ENSP00000321971 Q8IXI1 UPI000007310B NM_138769.2 16/19 Gene3D:3.40.50.300,PIRSF_domain:PIRSF037488,PROSITE_profiles:PS51423,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 672509 672509 G A 1 0 0 0 0 0 0 0 1 13517 962 34 3 3 RHOT2 16 672509 Silent SNP G C3N-01074_T 672509 89665836 357 22346 HAGHL 0 . GRCh38 16 729415 729415 + Missense_Mutation SNP G G C rs577972426 C3N-01074_T C3N-01074_N G G c.808G>C p.Ala270Pro p.A270P ENST00000389703 8/8 217 175 42 194 194 0 strelka-varscan-mutect HAGHL,missense_variant,p.Ala270Pro,ENST00000389703,NM_001290137.1,NM_001290139.1,NM_032304.3;HAGHL,3_prime_UTR_variant,,ENST00000549114,;HAGHL,3_prime_UTR_variant,,ENST00000341413,;HAGHL,3_prime_UTR_variant,,ENST00000564537,;NARFL,downstream_gene_variant,,ENST00000540986,NM_001304799.1;NARFL,downstream_gene_variant,,ENST00000568545,;NARFL,downstream_gene_variant,,ENST00000251588,NM_022493.2;CCDC78,upstream_gene_variant,,ENST00000293889,NM_001031737.2;CCDC78,upstream_gene_variant,,ENST00000345165,;HAGHL,downstream_gene_variant,,ENST00000561546,;NARFL,downstream_gene_variant,,ENST00000562421,;HAGHL,downstream_gene_variant,,ENST00000568141,;HAGHL,downstream_gene_variant,,ENST00000567414,;HAGHL,downstream_gene_variant,,ENST00000564545,;HAGHL,downstream_gene_variant,,ENST00000562141,;CCDC78,upstream_gene_variant,,ENST00000423653,;NARFL,downstream_gene_variant,,ENST00000567403,;HAGHL,downstream_gene_variant,,ENST00000563792,;HAGHL,downstream_gene_variant,,ENST00000562187,;HAGHL,intron_variant,,ENST00000563156,;HAGHL,upstream_gene_variant,,ENST00000569604,;NARFL,downstream_gene_variant,,ENST00000562862,;NARFL,downstream_gene_variant,,ENST00000569759,;HAGHL,non_coding_transcript_exon_variant,,ENST00000567696,;HAGHL,non_coding_transcript_exon_variant,,ENST00000389701,;CCDC78,upstream_gene_variant,,ENST00000482878,;CCDC78,upstream_gene_variant,,ENST00000481804,;CCDC78,upstream_gene_variant,,ENST00000478979,;NARFL,downstream_gene_variant,,ENST00000563051,;NARFL,downstream_gene_variant,,ENST00000566650,;NARFL,downstream_gene_variant,,ENST00000565425,;CCDC78,upstream_gene_variant,,ENST00000466708,;CCDC78,upstream_gene_variant,,ENST00000463539,;CCDC78,upstream_gene_variant,,ENST00000485091,;NARFL,downstream_gene_variant,,ENST00000565341,;NARFL,downstream_gene_variant,,ENST00000564285,;CCDC78,upstream_gene_variant,,ENST00000538176,;CCDC78,upstream_gene_variant,,ENST00000439619,;NARFL,downstream_gene_variant,,ENST00000562752,;CCDC78,upstream_gene_variant,,ENST00000482152,;CCDC78,upstream_gene_variant,,ENST00000460023,;CCDC78,upstream_gene_variant,,ENST00000471861,;HAGHL,downstream_gene_variant,,ENST00000561750,;HAGHL,downstream_gene_variant,,ENST00000569143,;CCDC78,upstream_gene_variant,,ENST00000544996,;CCDC78,upstream_gene_variant,,ENST00000474647,;HAGHL,downstream_gene_variant,,ENST00000569385,;HAGHL,downstream_gene_variant,,ENST00000561561,; C ENST00000389703 Transcript missense_variant 1047/1347 808/849 270/282 A/P Gcg/Ccg rs577972426 1 1 HAGHL HGNC HGNC:14177 protein_coding YES CCDS32354.1 ENSP00000374353 Q6PII5 UPI00000498AB NM_001290137.1,NM_001290139.1,NM_032304.3 deleterious_low_confidence(0) 8/8 hmmpanther:PTHR11935:SF77,hmmpanther:PTHR11935 MODERATE 1 SNV 1 1 PASS rs577972426 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 729415 729415 G C 1 0 0 0 0 1 0 0 0 6832 1319 46 4 4 HAGHL 16 729415 Missense_Mutation SNP G C3N-01074_T 56906 729415 89608930 358 22347 RBFOX1 0 . GRCh38 16 7597410 7597410 + Missense_Mutation SNP A A C novel C3N-01074_T C3N-01074_N A A c.730A>C p.Thr244Pro p.T244P ENST00000422070 9/16 223 168 55 247 247 0 strelka-varscan-mutect RBFOX1,missense_variant,p.Thr201Pro,ENST00000550418,NM_018723.3;RBFOX1,missense_variant,p.Thr206Pro,ENST00000340209,;RBFOX1,missense_variant,p.Thr206Pro,ENST00000620507,;RBFOX1,missense_variant,p.Thr244Pro,ENST00000547372,;RBFOX1,missense_variant,p.Thr221Pro,ENST00000355637,NM_145893.2;RBFOX1,missense_variant,p.Thr221Pro,ENST00000311745,NM_145891.2;RBFOX1,missense_variant,p.Thr201Pro,ENST00000553186,NM_001142333.1;RBFOX1,missense_variant,p.Thr200Pro,ENST00000547605,;RBFOX1,missense_variant,p.Thr244Pro,ENST00000422070,NM_001308117.1;RBFOX1,missense_variant,p.Thr158Pro,ENST00000535565,;RBFOX1,missense_variant,p.Thr221Pro,ENST00000436368,NM_145892.2;RBFOX1,missense_variant,p.Thr201Pro,ENST00000547338,NM_001142334.1;RBFOX1,missense_variant,p.Thr218Pro,ENST00000552089,;RBFOX1,missense_variant,p.Thr201Pro,ENST00000551752,;RBFOX1,downstream_gene_variant,,ENST00000570626,;RBFOX1,non_coding_transcript_exon_variant,,ENST00000564850,; C ENST00000422070 Transcript missense_variant 926/1684 730/1278 244/425 T/P Acc/Ccc 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 tolerated_low_confidence(0.21) 9/16 hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 7597410 7597410 A C 1 0 0 0 0 1 0 0 0 13271 275 10 5 5 RBFOX1 16 7597410 Missense_Mutation SNP A C3N-01074_T 6867995 7597410 82740935 359 22348 USP7 0 . GRCh38 16 8923357 8923357 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.241C>A p.Leu81Met p.L81M ENST00000344836 3/31 386 334 52 300 299 1 strelka-varscan-mutect USP7,missense_variant,p.Leu81Met,ENST00000344836,NM_001321858.1,NM_003470.2;USP7,missense_variant,p.Leu65Met,ENST00000381886,NM_001286458.1,NM_001286457.1;USP7,missense_variant,p.Leu67Met,ENST00000566273,;USP7,missense_variant,p.Leu23Met,ENST00000569230,;USP7,missense_variant,p.Leu23Met,ENST00000566004,;USP7,missense_variant,p.Leu23Met,ENST00000564117,;USP7,5_prime_UTR_variant,,ENST00000563085,;USP7,non_coding_transcript_exon_variant,,ENST00000566224,;USP7,missense_variant,p.Leu81Met,ENST00000563961,;USP7,missense_variant,p.Leu23Met,ENST00000542333,;USP7,3_prime_UTR_variant,,ENST00000565455,; T ENST00000344836 Transcript missense_variant 440/5412 241/3309 81/1102 L/M Ctg/Atg COSM4792276 1 -1 USP7 HGNC HGNC:12630 protein_coding YES CCDS32385.1 ENSP00000343535 Q93009 UPI000013F0BE NM_001321858.1,NM_003470.2 tolerated(0.17) 3/31 PROSITE_profiles:PS50144,Pfam_domain:PF00917,SMART_domains:SM00061,Superfamily_domains:SSF49599 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 8923357 8923357 G T 1 0 0 0 0 1 0 0 0 17631 1020 36 2 2 USP7 16 8923357 Missense_Mutation SNP G C3N-01074_T 1325947 8923357 81414988 360 22349 NOMO1 0 . GRCh38 16 14863143 14863143 + Nonsense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1351G>T p.Gly451Ter p.G451* ENST00000287667 12/31 136 113 23 159 158 1 strelka-varscan-mutect NOMO1,stop_gained,p.Gly451Ter,ENST00000287667,NM_014287.3;NOMO1,stop_gained,p.Gly451Ter,ENST00000620755,;NOMO1,stop_gained,p.Gly284Ter,ENST00000610363,;NOMO1,downstream_gene_variant,,ENST00000566883,;RP11-719K4.7,upstream_gene_variant,,ENST00000603741,; T ENST00000287667 Transcript stop_gained 1522/4355 1351/3669 451/1222 G/* Gga/Tga 1 1 NOMO1 HGNC HGNC:30060 protein_coding YES CCDS10556.1 ENSP00000287667 Q15155 UPI000013D37E NM_014287.3 12/31 Gene3D:2.60.40.10,hmmpanther:PTHR23303 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 14863143 14863143 G T 1 0 0 0 0 0 1 0 0 10575 1349 47 2 2 NOMO1 16 14863143 Nonsense_Mutation SNP G C3N-01074_T 5939786 14863143 75475202 361 22350 HS3ST2 0 . GRCh38 16 22814825 22814825 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.215C>G p.Pro72Arg p.P72R ENST00000261374 1/2 367 299 68 363 363 0 strelka-varscan-mutect HS3ST2,missense_variant,p.Pro72Arg,ENST00000261374,NM_006043.1;CTC-591M7.1,upstream_gene_variant,,ENST00000636354,;CTC-591M7.1,upstream_gene_variant,,ENST00000636266,;HS3ST2,missense_variant,p.Pro72Arg,ENST00000473392,; G ENST00000261374 Transcript missense_variant 649/2314 215/1104 72/367 P/R cCc/cGc 1 1 HS3ST2 HGNC HGNC:5195 protein_coding YES CCDS10606.1 ENSP00000261374 Q9Y278 UPI000004C63A NM_006043.1 tolerated(0.61) 1/2 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 22814825 22814825 C G 1 0 0 0 0 1 0 0 0 7258 623 22 4 4 HS3ST2 16 22814825 Missense_Mutation SNP C C3N-01074_T 7951682 22814825 67523520 362 22351 EARS2 0 . GRCh38 16 23544561 23544561 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.438G>T p.= p.R146R ENST00000563232 3/8 202 154 48 117 117 0 strelka-varscan-mutect EARS2,synonymous_variant,p.=,ENST00000449606,NM_001083614.1;EARS2,synonymous_variant,p.=,ENST00000563459,;EARS2,synonymous_variant,p.=,ENST00000564501,;EARS2,synonymous_variant,p.=,ENST00000563232,NM_001308211.1;EARS2,splice_region_variant,,ENST00000564987,;EARS2,non_coding_transcript_exon_variant,,ENST00000564461,;EARS2,non_coding_transcript_exon_variant,,ENST00000566017,;EARS2,non_coding_transcript_exon_variant,,ENST00000561859,;EARS2,3_prime_UTR_variant,,ENST00000564668,;EARS2,3_prime_UTR_variant,,ENST00000562581,;EARS2,downstream_gene_variant,,ENST00000564997,; A ENST00000563232 Transcript synonymous_variant 439/1709 438/1605 146/534 R cgG/cgT 1 -1 EARS2 HGNC HGNC:29419 protein_coding YES CCDS76844.1 ENSP00000456218 Q5JPH6 UPI000019839B NM_001308211.1 3/8 HAMAP:MF_00022_B,hmmpanther:PTHR11451:SF26,hmmpanther:PTHR11451,Pfam_domain:PF00749,Gene3D:3.90.800.10,TIGRFAM_domain:TIGR00464,Superfamily_domains:SSF52374 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 23544561 23544561 C A 1 0 0 0 0 0 0 0 1 4702 726 26 2 2 EARS2 16 23544561 Silent SNP C C3N-01074_T 729736 23544561 66793784 363 22352 SPNS1 0 . GRCh38 16 28982041 28982041 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.950G>T p.Cys317Phe p.C317F ENST00000311008 7/12 177 130 47 167 166 1 strelka-varscan-mutect SPNS1,missense_variant,p.Cys317Phe,ENST00000311008,NM_001142448.1,NM_032038.2;SPNS1,missense_variant,p.Cys244Phe,ENST00000323081,NM_001142450.1;SPNS1,missense_variant,p.Cys362Phe,ENST00000565975,;SPNS1,missense_variant,p.Cys311Phe,ENST00000566059,;SPNS1,intron_variant,,ENST00000334536,NM_001142451.1;SPNS1,intron_variant,,ENST00000352260,NM_001142449.1;SPNS1,intron_variant,,ENST00000564476,;SPNS1,intron_variant,,ENST00000568829,;LAT,upstream_gene_variant,,ENST00000395456,NM_001014987.1;LAT,upstream_gene_variant,,ENST00000360872,NM_014387.3;LAT,upstream_gene_variant,,ENST00000395461,NM_001014989.1;LAT,upstream_gene_variant,,ENST00000454369,NM_001014988.1;LAT,upstream_gene_variant,,ENST00000564277,;SPNS1,downstream_gene_variant,,ENST00000567771,;LAT,upstream_gene_variant,,ENST00000566177,;SPNS1,downstream_gene_variant,,ENST00000568388,;LAT,upstream_gene_variant,,ENST00000570232,;LAT,upstream_gene_variant,,ENST00000630764,;RP11-264B17.4,upstream_gene_variant,,ENST00000567209,;SPNS1,intron_variant,,ENST00000561868,;RP11-264B17.3,upstream_gene_variant,,ENST00000354453,;LAT,upstream_gene_variant,,ENST00000563964,;RP11-264B17.3,non_coding_transcript_exon_variant,,ENST00000569969,;SPNS1,downstream_gene_variant,,ENST00000568900,;LAT,upstream_gene_variant,,ENST00000566270,;LAT,upstream_gene_variant,,ENST00000562701,;LAT,upstream_gene_variant,,ENST00000568899,;LAT,upstream_gene_variant,,ENST00000562472,;LAT,upstream_gene_variant,,ENST00000568440,; T ENST00000311008 Transcript missense_variant 1327/2208 950/1587 317/528 C/F tGc/tTc 1 1 SPNS1 HGNC HGNC:30621 protein_coding YES CCDS10646.1 ENSP00000309945 Q9H2V7 UPI000004DB99 NM_001142448.1,NM_032038.2 deleterious(0) 7/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF13,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 28982041 28982041 G T 1 0 0 0 0 1 0 0 0 15427 1319 46 2 2 SPNS1 16 28982041 Missense_Mutation SNP G C3N-01074_T 5437480 28982041 61356304 364 22353 ZNF720 0 . GRCh38 16 31753982 31753982 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.233C>A p.Thr78Lys p.T78K ENST00000398696 2/2 263 190 73 284 284 0 strelka-varscan-mutect ZNF720,missense_variant,p.Thr78Lys,ENST00000398696,;ZNF720,intron_variant,,ENST00000316491,NM_001130913.1;ZNF720,intron_variant,,ENST00000539915,;ZNF720,intron_variant,,ENST00000534369,;ZNF720,intron_variant,,ENST00000529515,;ZNF720,downstream_gene_variant,,ENST00000530881,;ZNF720,intron_variant,,ENST00000531864,;ZNF720,intron_variant,,ENST00000533488,;ZNF720,intron_variant,,ENST00000544044,;ZNF720,intron_variant,,ENST00000542684,;ZNF720,3_prime_UTR_variant,,ENST00000529943,;ZNF720,intron_variant,,ENST00000534277,;ZNF720,intron_variant,,ENST00000398707,; A ENST00000398696 Transcript missense_variant 393/1339 233/537 78/178 T/K aCa/aAa 1 1 ZNF720 HGNC HGNC:26987 protein_coding ENSP00000443758 Q7Z2F6 UPI00001C1064 tolerated(0.93) 2/2 MODERATE SNV 4 1 PASS rs1366613643 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 31753982 31753982 C A 1 0 0 0 0 1 0 0 0 18697 478 17 2 2 ZNF720 16 31753982 Missense_Mutation SNP C C3N-01074_T 2771941 31753982 58584363 365 22354 PRSS54 0 . GRCh38 16 58284683 58284683 + Silent SNP G G T rs142166944 C3N-01074_T C3N-01074_N G G c.561C>A p.= p.I187I ENST00000219301 6/7 290 197 93 252 251 1 strelka-varscan-mutect PRSS54,synonymous_variant,p.=,ENST00000219301,NM_001305173.1,NM_001080492.1;PRSS54,synonymous_variant,p.=,ENST00000567164,;PRSS54,synonymous_variant,p.=,ENST00000543437,NM_001305174.1;PRSS54,synonymous_variant,p.=,ENST00000569079,;CCDC113,downstream_gene_variant,,ENST00000219299,NM_014157.3;CCDC113,downstream_gene_variant,,ENST00000443128,NM_001142302.1;PRSS54,downstream_gene_variant,,ENST00000569727,;PRSS54,non_coding_transcript_exon_variant,,ENST00000563336,; T ENST00000219301 Transcript synonymous_variant 956/1810 561/1188 187/395 I atC/atA rs142166944,COSM971972,COSM971973 1 -1 PRSS54 HGNC HGNC:26336 protein_coding YES CCDS32463.1 ENSP00000219301 Q6PEW0 A0A140VKC3 UPI0000199F24 NM_001305173.1,NM_001080492.1 6/7 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF208,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1,1 LOW SNV 5 0,1,1 1 PASS rs142166944 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 58284683 58284683 G T 1 0 0 0 0 0 0 0 1 12782 932 33 2 2 PRSS54 16 58284683 Silent SNP G C3N-01074_T 26530701 58284683 32053662 366 22355 CARMIL2 0 . GRCh38 16 67647875 67647875 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.988A>T p.Thr330Ser p.T330S ENST00000334583 13/38 95 84 11 114 114 0 strelka-varscan-mutect CARMIL2,missense_variant,p.Thr330Ser,ENST00000334583,NM_001013838.1;CARMIL2,missense_variant,p.Thr330Ser,ENST00000545661,NM_001317026.1;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602321,;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602742,;CARMIL2,downstream_gene_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602931,;CARMIL2,downstream_gene_variant,,ENST00000602467,; T ENST00000334583 Transcript missense_variant 1316/4687 988/4308 330/1435 T/S Acc/Tcc 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 tolerated(0.5) 13/38 hmmpanther:PTHR24112:SF32,hmmpanther:PTHR24112,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.99916 0.9999992 1 1 1 0 T 3 4 73 67647875 67647875 A T 1 0 0 0 0 1 0 0 0 2352 159 6 4 4 CARMIL2 16 67647875 Missense_Mutation SNP A C3N-01074_T 9363192 67647875 22690470 367 22356 NQO1 0 . GRCh38 16 69711076 69711076 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.725A>T p.Glu242Val p.E242V ENST00000320623 6/6 342 300 42 313 313 0 strelka-varscan-mutect NQO1,missense_variant,p.Glu242Val,ENST00000320623,NM_000903.2;NQO1,missense_variant,p.Glu208Val,ENST00000379047,NM_001025433.1;NQO1,missense_variant,p.Glu204Val,ENST00000379046,NM_001025434.1;NQO1,missense_variant,p.Glu170Val,ENST00000439109,NM_001286137.1;NQO1,missense_variant,p.Glu221Val,ENST00000564043,;NQO1,missense_variant,p.Glu204Val,ENST00000561500,;CTD-2033A16.1,downstream_gene_variant,,ENST00000562696,; A ENST00000320623 Transcript missense_variant 1237/2912 725/825 242/274 E/V gAg/gTg 1 -1 NQO1 HGNC HGNC:2874 protein_coding YES CCDS10883.1 ENSP00000319788 P15559 UPI0000000C86 NM_000903.2 deleterious(0) 6/6 Superfamily_domains:SSF52218 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 69711076 69711076 T A 1 0 0 0 0 1 0 0 0 10667 1565 54 4 4 NQO1 16 69711076 Missense_Mutation SNP T C3N-01074_T 2063201 69711076 20627269 368 22357 PKD1L3 0 . GRCh38 16 71949969 71949969 + Frame_Shift_Del DEL G G - novel C3N-01074_T C3N-01074_N G G c.3432delC p.Ile1145SerfsTer9 p.I1145Sfs*9 ENST00000620267 21/30 293 204 89 266 266 0 sindel-varindel-pindel PKD1L3,frameshift_variant,p.Ile1145SerfsTer9,ENST00000620267,NM_181536.1; - ENST00000620267 Transcript frameshift_variant 3432/5199 3432/5199 1144/1732 P/X ccC/cc 1 -1 PKD1L3 HGNC HGNC:21716 protein_coding YES CCDS73912.1 ENSP00000480090 Q7Z443 UPI00001A36E5 NM_181536.1 21/30 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF136 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 71949969 71949969 G - 1 0 1 0 1 0 0 0 0 12061 1335 47 0 0 PKD1L3 16 71949969 Frame_Shift_Del DEL G C3N-01074_T 2238893 71949969 18388376 369 22358 PMFBP1 0 . GRCh38 16 72126027 72126027 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2194G>T p.Asp732Tyr p.D732Y ENST00000237353 15/21 323 274 49 311 311 0 strelka-varscan-mutect PMFBP1,missense_variant,p.Asp737Tyr,ENST00000537465,;PMFBP1,missense_variant,p.Asp732Tyr,ENST00000237353,NM_031293.2;PMFBP1,missense_variant,p.Asp587Tyr,ENST00000355636,NM_001160213.1;PMFBP1,upstream_gene_variant,,ENST00000537792,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,;PMFBP1,3_prime_UTR_variant,,ENST00000537392,; A ENST00000237353 Transcript missense_variant 2456/3527 2194/3024 732/1007 D/Y Gat/Tat 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 deleterious(0) 15/21 hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 72126027 72126027 C A 1 0 0 0 0 1 0 0 0 12241 826 29 2 2 PMFBP1 16 72126027 Missense_Mutation SNP C C3N-01074_T 176058 72126027 18212318 370 22359 NUDT7 0 . GRCh38 16 77741735 77741735 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.502C>T p.His168Tyr p.H168Y ENST00000268533 4/4 291 238 53 338 338 0 strelka-varscan-mutect NUDT7,missense_variant,p.His168Tyr,ENST00000268533,NM_001105663.2;NUDT7,missense_variant,p.His153Tyr,ENST00000613075,NM_001243660.1;NUDT7,missense_variant,p.His115Tyr,ENST00000437314,NM_001243661.1;NUDT7,3_prime_UTR_variant,,ENST00000564085,NM_001243657.1;NUDT7,3_prime_UTR_variant,,ENST00000563839,;RP11-264M12.2,non_coding_transcript_exon_variant,,ENST00000563690,;NUDT7,non_coding_transcript_exon_variant,,ENST00000564031,; T ENST00000268533 Transcript missense_variant 571/1096 502/717 168/238 H/Y Cac/Tac 1 1 NUDT7 HGNC HGNC:8054 protein_coding YES CCDS42195.1 ENSP00000268533 P0C024 UPI000003EFFE NM_001105663.2 tolerated(1) 4/4 Gene3D:3.90.79.10,PROSITE_profiles:PS51462,hmmpanther:PTHR12992,Superfamily_domains:SSF55811 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 77741735 77741735 C T 1 0 0 0 0 1 0 0 0 10808 826 29 3 3 NUDT7 16 77741735 Missense_Mutation SNP C C3N-01074_T 5615708 77741735 12596610 371 22360 KCNG4 0 . GRCh38 16 84222565 84222565 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1212C>A p.Ser404Arg p.S404R ENST00000308251 3/3 183 109 74 308 308 0 strelka-varscan-mutect KCNG4,missense_variant,p.Ser404Arg,ENST00000308251,NM_172347.2; T ENST00000308251 Transcript missense_variant 1281/5179 1212/1560 404/519 S/R agC/agA 1 -1 KCNG4 HGNC HGNC:19697 protein_coding YES CCDS10945.1 ENSP00000312129 Q8TDN1 Q547S7 UPI00000557D8 NM_172347.2 deleterious(0) 3/3 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF167,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 84222565 84222565 G T 1 0 0 0 0 1 0 0 0 7946 1310 46 2 2 KCNG4 16 84222565 Missense_Mutation SNP G C3N-01074_T 6480830 84222565 6115780 372 22361 ZNF469 0 . GRCh38 16 88429784 88429784 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2314G>T p.Gly772Trp p.G772W ENST00000437464 1/2 130 104 26 176 175 1 strelka-varscan-mutect ZNF469,missense_variant,p.Gly772Trp,ENST00000565624,;ZNF469,missense_variant,p.Gly772Trp,ENST00000437464,NM_001127464.2; T ENST00000437464 Transcript missense_variant 2314/13203 2314/11778 772/3925 G/W Ggg/Tgg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 deleterious(0.01) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 88429784 88429784 G T 1 0 0 0 0 1 0 0 0 18500 1348 47 2 2 ZNF469 16 88429784 Missense_Mutation SNP G C3N-01074_T 4207219 88429784 1908561 373 22362 GSG2 0 . GRCh38 17 3723955 3723955 + Missense_Mutation SNP G G T rs772739493 C3N-01074_T C3N-01074_N G G c.20G>T p.Gly7Val p.G7V ENST00000325418 1/1 48 22 26 86 86 0 strelka-varscan-mutect GSG2,missense_variant,p.Gly7Val,ENST00000325418,NM_031965.2;ITGAE,intron_variant,,ENST00000263087,NM_002208.4;ITGAE,downstream_gene_variant,,ENST00000574026,;CTD-3195I5.3,downstream_gene_variant,,ENST00000571741,;ITGAE,downstream_gene_variant,,ENST00000571185,;ITGAE,upstream_gene_variant,,ENST00000570360,;ITGAE,upstream_gene_variant,,ENST00000572179,;ITGAE,intron_variant,,ENST00000570415,;ITGAE,upstream_gene_variant,,ENST00000572433,; T ENST00000325418 Transcript missense_variant 53/2797 20/2397 7/798 G/V gGa/gTa rs772739493 1 1 GSG2 HGNC HGNC:19682 protein_coding YES CCDS11036.1 ENSP00000325290 Q8TF76 UPI0000141654 NM_031965.2 tolerated_low_confidence(0.11) 1/1 MODERATE SNV 1 PASS rs772739493 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 3723955 3723955 G T 1 0 0 0 0 1 0 0 0 6706 1174 41 2 2 GSG2 17 3723955 Missense_Mutation SNP G C3N-01074_T 3723955 79533486 374 22363 MYBBP1A 0 . GRCh38 17 4555294 4555295 + Frame_Shift_Del DEL AC AC - novel C3N-01074_T C3N-01074_N AC AC c.30_31delGT p.Met10IlefsTer36 p.M10Ifs*36 ENST00000381556 1/27 215 190 25 233 233 0 sindel-varindel-pindel MYBBP1A,frameshift_variant,p.Met10IlefsTer36,ENST00000254718,NM_014520.3;MYBBP1A,frameshift_variant,p.Met10IlefsTer36,ENST00000381556,NM_001105538.1;MYBBP1A,upstream_gene_variant,,ENST00000573116,;GGT6,downstream_gene_variant,,ENST00000301395,NM_001288704.1,NM_153338.3;GGT6,downstream_gene_variant,,ENST00000574154,NM_001122890.2;GGT6,downstream_gene_variant,,ENST00000381550,NM_001288702.1;GGT6,downstream_gene_variant,,ENST00000573591,;GGT6,downstream_gene_variant,,ENST00000574584,NM_001288703.1;MYBBP1A,non_coding_transcript_exon_variant,,ENST00000570986,;GGT6,downstream_gene_variant,,ENST00000575573,; - ENST00000381556 Transcript frameshift_variant 92-93/4104 30-31/3999 10-11/1332 MS/IX atGTcg/atcg 1 -1 MYBBP1A HGNC HGNC:7546 protein_coding YES CCDS42238.1 ENSP00000370968 Q9BQG0 UPI0000551C8B NM_001105538.1 1/27 hmmpanther:PTHR13213,hmmpanther:PTHR13213:SF2 HIGH deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 4555294 4555294 AC - 1 0 1 0 1 0 0 0 0 10008 275 10 0 0 MYBBP1A 17 4555294 Frame_Shift_Del DEL AC C3N-01074_T 831339 4555294 78702147 375 22364 TP53 0 . GRCh38 17 7674893 7674893 + Missense_Mutation SNP C C G rs587778720 C3N-01074_T C3N-01074_N C C c.638G>C p.Arg213Pro p.R213P ENST00000269305 6/11 438 242 196 477 477 0 strelka-varscan-mutect TP53,missense_variant,p.Arg213Pro,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg213Pro,ENST00000420246,;TP53,missense_variant,p.Arg174Pro,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg174Pro,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg213Pro,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg174Pro,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg213Pro,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg174Pro,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg213Pro,ENST00000445888,;TP53,missense_variant,p.Arg174Pro,ENST00000619485,;TP53,missense_variant,p.Arg81Pro,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg54Pro,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg81Pro,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg54Pro,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg81Pro,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg54Pro,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg213Pro,ENST00000359597,;TP53,missense_variant,p.Arg202Pro,ENST00000615910,;TP53,missense_variant,p.Arg213Pro,ENST00000413465,;TP53,missense_variant,p.Arg81Pro,ENST00000509690,;TP53,missense_variant,p.Arg120Pro,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Arg174Pro,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 828/2579 638/1182 213/393 R/P cGa/cCa rs587778720,CM004906,CM022474,TP53_g.12707G>C,TP53_g.12707G>T,TP53_g.12707G>A,COSM10735,COSM11860,COSM131466,COSM131467,COSM131468,COSM131469,COSM1726594,COSM1741334,COSM241997,COSM241998,COSM241999,COSM242000,COSM3378349,COSM3403265,COSM3717650,COSM3717651,COSM3717652,COSM3717653,COSM3717654,COSM3717655,COSM43650 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 not_provided,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs587778720 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 7674893 7674893 C G 1 0 0 0 0 1 0 0 0 16859 884 31 4 4 TP53 17 7674893 Missense_Mutation SNP C C3N-01074_T 3119599 7674893 75582548 376 22365 DNAH2 0 . GRCh38 17 7770914 7770914 + Missense_Mutation SNP G G A rs140070507 C3N-01074_T C3N-01074_N G G c.4343G>A p.Arg1448His p.R1448H ENST00000572933 27/86 126 61 65 175 175 0 strelka-varscan-mutect DNAH2,missense_variant,p.Arg1448His,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Arg1448His,ENST00000389173,;DNAH2,3_prime_UTR_variant,,ENST00000574518,; A ENST00000572933 Transcript missense_variant 5803/14955 4343/13284 1448/4427 R/H cGt/cAt rs140070507,COSM3989382 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious(0.02) 27/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183,Pfam_domain:PF08393 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs140070507 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 7770914 7770914 G A 1 0 0 0 0 1 0 0 0 4417 1145 40 1 1 DNAH2 17 7770914 Missense_Mutation SNP G C3N-01074_T 96021 7770914 75486527 377 22366 CFAP52 0 . GRCh38 17 9585944 9585944 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.242C>A p.Ser81Tyr p.S81Y ENST00000352665 2/14 172 92 80 229 229 0 strelka-varscan-mutect CFAP52,missense_variant,p.Ser81Tyr,ENST00000352665,NM_145054.4;CFAP52,missense_variant,p.Ser81Tyr,ENST00000576499,;CFAP52,intron_variant,,ENST00000396219,NM_001080556.1;CFAP52,3_prime_UTR_variant,,ENST00000576630,;CFAP52,non_coding_transcript_exon_variant,,ENST00000576320,;CFAP52,intron_variant,,ENST00000575247,;CFAP52,intron_variant,,ENST00000572333,;CFAP52,intron_variant,,ENST00000574937,;RPL19P18,downstream_gene_variant,,ENST00000466869,; A ENST00000352665 Transcript missense_variant 311/2193 242/1863 81/620 S/Y tCc/tAc 1 1 CFAP52 HGNC HGNC:16053 protein_coding YES CCDS11149.2 ENSP00000339449 Q8N1V2 UPI00001AECC1 NM_145054.4 deleterious(0) 2/14 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF14,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 9585944 9585944 C A 1 0 0 0 0 1 0 0 0 3023 855 30 2 2 CFAP52 17 9585944 Missense_Mutation SNP C C3N-01074_T 1815030 9585944 73671497 378 22367 MYH13 0 . GRCh38 17 10359961 10359961 + Missense_Mutation SNP T T G novel C3N-01074_T C3N-01074_N T T c.644A>C p.Gln215Pro p.Q215P ENST00000418404 6/41 165 90 75 230 230 0 strelka-varscan-mutect MYH13,missense_variant,p.Gln215Pro,ENST00000418404,;MYH13,missense_variant,p.Gln215Pro,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Gln215Pro,ENST00000621918,; G ENST00000418404 Transcript missense_variant,splice_region_variant 808/6296 644/5817 215/1938 Q/P cAg/cCg 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA tolerated(0.08) 6/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs951790879 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 10359961 10359961 T G 1 0 0 0 0 1 0 0 0 10032 1594 55 5 5 MYH13 17 10359961 Missense_Mutation SNP T C3N-01074_T 774017 10359961 72897480 379 22368 MYOCD 0 . GRCh38 17 12744311 12744311 + Missense_Mutation SNP G G A novel C3N-01074_T C3N-01074_N G G c.846G>A p.Met282Ile p.M282I ENST00000425538 8/14 397 240 157 404 403 1 strelka-varscan-mutect MYOCD,missense_variant,p.Met282Ile,ENST00000425538,NM_001146312.2;MYOCD,missense_variant,p.Met282Ile,ENST00000343344,NM_153604.3;MYOCD,upstream_gene_variant,,ENST00000443061,;MYOCD,non_coding_transcript_exon_variant,,ENST00000395988,; A ENST00000425538 Transcript missense_variant 1046/8466 846/2961 282/986 M/I atG/atA 1 1 MYOCD HGNC HGNC:16067 protein_coding YES CCDS54091.1 ENSP00000401678 Q8IZQ8 UPI000022A2E2 NM_001146312.2 deleterious(0) 8/14 hmmpanther:PTHR22793:SF11,hmmpanther:PTHR22793 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 12744311 12744311 G A 1 0 0 0 0 1 0 0 0 10088 1348 47 3 3 MYOCD 17 12744311 Missense_Mutation SNP G C3N-01074_T 2384350 12744311 70513130 380 22369 MAPK7 0 . GRCh38 17 19382201 19382201 + Missense_Mutation SNP G G C novel C3N-01074_T C3N-01074_N G G c.1898G>C p.Cys633Ser p.C633S ENST00000308406 5/7 226 181 45 272 272 0 strelka-varscan-mutect MAPK7,missense_variant,p.Cys633Ser,ENST00000308406,NM_139033.2;MAPK7,missense_variant,p.Cys633Ser,ENST00000395604,NM_002749.3;MAPK7,missense_variant,p.Cys633Ser,ENST00000395602,NM_139034.2;MAPK7,missense_variant,p.Cys494Ser,ENST00000299612,NM_139032.2;MFAP4,downstream_gene_variant,,ENST00000395592,NM_001198695.1;MFAP4,downstream_gene_variant,,ENST00000497081,;MFAP4,downstream_gene_variant,,ENST00000299610,NM_002404.2;B9D1,upstream_gene_variant,,ENST00000477478,;B9D1,upstream_gene_variant,,ENST00000575403,NM_001243475.1;MAPK7,downstream_gene_variant,,ENST00000443215,;MAPK7,downstream_gene_variant,,ENST00000482850,;MAPK7,downstream_gene_variant,,ENST00000579284,;MAPK7,downstream_gene_variant,,ENST00000603493,;B9D1,upstream_gene_variant,,ENST00000487415,;MAPK7,intron_variant,,ENST00000571657,;MFAP4,downstream_gene_variant,,ENST00000574313,;MAPK7,downstream_gene_variant,,ENST00000572968,;MAPK7,downstream_gene_variant,,ENST00000573417,;B9D1,upstream_gene_variant,,ENST00000468679,;MAPK7,non_coding_transcript_exon_variant,,ENST00000570306,;MAPK7,non_coding_transcript_exon_variant,,ENST00000490660,;MFAP4,downstream_gene_variant,,ENST00000571210,;B9D1,upstream_gene_variant,,ENST00000476298,;MAPK7,downstream_gene_variant,,ENST00000572716,;MAPK7,downstream_gene_variant,,ENST00000581260,;MAPK7,downstream_gene_variant,,ENST00000573466,;MAPK7,downstream_gene_variant,,ENST00000486905,;MAPK7,downstream_gene_variant,,ENST00000572853,; C ENST00000308406 Transcript missense_variant 2284/3149 1898/2451 633/816 C/S tGc/tCc 1 1 MAPK7 HGNC HGNC:6880 protein_coding YES CCDS11206.1 ENSP00000311005 Q13164 A0A024QZ20 UPI000006FED0 NM_139033.2 tolerated(0.64) 5/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 19382201 19382201 G C 1 0 0 0 0 1 0 0 0 9206 1319 46 4 4 MAPK7 17 19382201 Missense_Mutation SNP G C3N-01074_T 6637890 19382201 63875240 381 22370 NF1 0 . GRCh38 17 31235771 31235771 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.3869A>T p.Lys1290Met p.K1290M ENST00000358273 28/58 502 349 153 516 516 0 strelka-varscan-mutect NF1,missense_variant,p.Lys1290Met,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Lys1290Met,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Lys956Met,ENST00000456735,;NF1,missense_variant,p.Lys1324Met,ENST00000579081,;NF1,missense_variant,p.Lys116Met,ENST00000466819,;NF1,missense_variant,p.Lys116Met,ENST00000479614,;NF1,splice_region_variant,,ENST00000495910,;NF1,splice_region_variant,,ENST00000493220,; T ENST00000358273 Transcript missense_variant,splice_region_variant 4252/12425 3869/8520 1290/2839 K/M aAg/aTg 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0) 28/58 Gene3D:1.10.494.10,PROSITE_profiles:PS50018,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,SMART_domains:SM00323,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 31235771 31235771 A T 1 0 0 0 0 1 0 0 0 10393 86 3 4 4 NF1 17 31235771 Missense_Mutation SNP A C3N-01074_T 11853570 31235771 52021670 382 22371 TMEM132E 0 . GRCh38 17 34638153 34638153 + Missense_Mutation SNP C C A rs368990611 C3N-01074_T C3N-01074_N C C c.2876C>A p.Pro959Gln p.P959Q ENST00000321639 10/10 168 141 27 147 147 0 strelka-varscan-mutect TMEM132E,missense_variant,p.Pro1049Gln,ENST00000631683,NM_001304438.1;TMEM132E,missense_variant,p.Pro959Gln,ENST00000321639,;TMEM132E,downstream_gene_variant,,ENST00000577271,; A ENST00000321639 Transcript missense_variant 3204/4369 2876/2955 959/984 P/Q cCg/cAg rs368990611 1 1 TMEM132E HGNC HGNC:26991 protein_coding YES ENSP00000316532 Q6IEE7 UPI000035960F tolerated(1) 10/10 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF7 MODERATE 1 SNV 5 1 PASS rs368990611 . 0 207 0 3 0 0 0 0 -20 0.9999945 1 1 1 0 A 3 1 73 34638153 34638153 C A 1 0 0 0 0 1 0 0 0 16493 652 23 1 1 TMEM132E 17 34638153 Missense_Mutation SNP C C3N-01074_T 3402382 34638153 48619288 383 22372 MRM1 0 . GRCh38 17 36607714 36607714 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.681C>T p.= p.C227C ENST00000614766 3/5 251 178 73 191 191 0 strelka-varscan-mutect MRM1,synonymous_variant,p.=,ENST00000614766,NM_024864.4;MRM1,synonymous_variant,p.=,ENST00000612760,; T ENST00000614766 Transcript synonymous_variant 920/1857 681/1062 227/353 C tgC/tgT 1 1 MRM1 HGNC HGNC:26202 protein_coding YES CCDS32631.1 ENSP00000481559 Q6IN84 UPI000004B637 NM_024864.4 3/5 hmmpanther:PTHR12029,hmmpanther:PTHR12029:SF58,Pfam_domain:PF00588,Gene3D:3.40.1280.10,TIGRFAM_domain:TIGR00186,Superfamily_domains:SSF75217 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 36607714 36607714 C T 1 0 0 0 0 0 0 0 1 9739 747 26 3 3 MRM1 17 36607714 Silent SNP C C3N-01074_T 1969561 36607714 46649727 384 22373 PGAP3 0 . GRCh38 17 39673256 39673256 + Splice_Site SNP C C A novel C3N-01074_T C3N-01074_N C C c.695-1G>T p.X232_splice ENST00000300658 173 102 71 160 160 0 strelka-varscan-mutect PGAP3,splice_acceptor_variant,,ENST00000300658,NM_033419.4;PGAP3,splice_acceptor_variant,,ENST00000378011,NM_001291726.1;PGAP3,splice_acceptor_variant,,ENST00000619169,;PGAP3,splice_acceptor_variant,,ENST00000429199,NM_001291728.1;PGAP3,intron_variant,,ENST00000579146,NM_001291733.1;PNMT,downstream_gene_variant,,ENST00000269582,NM_002686.4;PNMT,downstream_gene_variant,,ENST00000394246,;PNMT,downstream_gene_variant,,ENST00000581428,;PGAP3,splice_acceptor_variant,,ENST00000309862,;PGAP3,splice_acceptor_variant,,ENST00000577337,;PGAP3,downstream_gene_variant,,ENST00000584620,;PGAP3,downstream_gene_variant,,ENST00000580898,;PGAP3,downstream_gene_variant,,ENST00000582276,; A ENST00000300658 Transcript splice_acceptor_variant -/2737 695/963 232/320 1 -1 PGAP3 HGNC HGNC:23719 protein_coding YES CCDS32641.1 ENSP00000300658 Q96FM1 UPI0000039EAA NM_033419.4 6/7 HIGH 1 SNV 1 1 PASS rs1426093227 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 73 39673256 39673256 C A 1 0 0 0 0 0 0 1 0 11869 695 24 2 2 PGAP3 17 39673256 Splice_Site SNP C C3N-01074_T 3065542 39673256 43584185 385 22374 KRTAP2-1 0 . GRCh38 17 41047019 41047019 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.249G>T p.= p.S83S ENST00000391419 1/1 68 58 10 100 100 0 strelka-varscan-mutect KRTAP2-1,synonymous_variant,p.=,ENST00000391419,NM_001123387.1;KRTAP2-1,synonymous_variant,p.=,ENST00000542137,; A ENST00000391419 Transcript synonymous_variant 298/776 249/387 83/128 S tcG/tcT 1 -1 KRTAP2-1 HGNC HGNC:16775 protein_coding YES CCDS42325.1 ENSP00000375238 Q9BYU5 UPI00001606E4 NM_001123387.1 1/1 hmmpanther:PTHR23262:SF6,hmmpanther:PTHR23262 LOW 1 SNV 1 PASS rs1414077631 . 0 199 10 0 0 0 0 0 -19.99644 0.9999815 1 1 1 0 A 2 1 73 41047019 41047019 C A 1 0 0 0 0 0 0 0 1 8420 523 19 1 1 KRTAP2-1 17 41047019 Silent SNP C C3N-01074_T 1373763 41047019 42210422 386 22375 KRT34 0 . GRCh38 17 41382045 41382045 + Missense_Mutation SNP C C T rs781546162 C3N-01074_T C3N-01074_N C C c.328G>A p.Ala110Thr p.A110T ENST00000394001 1/7 590 390 200 597 596 1 strelka-varscan-mutect KRT34,missense_variant,p.Ala110Thr,ENST00000394001,NM_021013.3; T ENST00000394001 Transcript missense_variant 359/1751 328/1311 110/436 A/T Gcc/Acc rs781546162,COSM4923265 1 -1 KRT34 HGNC HGNC:6452 protein_coding YES CCDS11390.1 ENSP00000377570 O76011 UPI000013CD0C NM_021013.3 deleterious(0.01) 1/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF165,SMART_domains:SM01391,Superfamily_domains:SSF64593 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781546162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 41382045 41382045 C T 1 0 0 0 0 1 0 0 0 8353 739 26 3 3 KRT34 17 41382045 Missense_Mutation SNP C C3N-01074_T 335026 41382045 41875396 387 22376 KRT38 0 . GRCh38 17 41440879 41440879 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.43A>T p.Thr15Ser p.T15S ENST00000246646 1/7 37 25 12 60 60 0 strelka-varscan-mutect KRT38,missense_variant,p.Thr15Ser,ENST00000246646,NM_006771.3; A ENST00000246646 Transcript missense_variant 43/2337 43/1371 15/456 T/S Acc/Tcc 1 -1 KRT38 HGNC HGNC:6456 protein_coding YES CCDS11392.1 ENSP00000246646 O76015 UPI000013CBF9 NM_006771.3 tolerated(1) 1/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF166 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 41440879 41440879 T A 1 0 0 0 0 1 0 0 0 8357 1696 59 4 4 KRT38 17 41440879 Missense_Mutation SNP T C3N-01074_T 58834 41440879 41816562 388 22377 KRT36 0 . GRCh38 17 41488302 41488302 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.640G>A p.Glu214Lys p.E214K ENST00000328119 3/7 226 149 77 203 203 0 strelka-varscan-mutect KRT36,missense_variant,p.Glu164Lys,ENST00000393986,;KRT36,missense_variant,p.Glu214Lys,ENST00000328119,NM_003771.4; T ENST00000328119 Transcript missense_variant 640/1644 640/1404 214/467 E/K Gag/Aag 1 -1 KRT36 HGNC HGNC:6454 protein_coding YES CCDS11395.1 ENSP00000329165 O76013 UPI000012DAFA NM_003771.4 deleterious(0) 3/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,Prints_domain:PR01248,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF193,SMART_domains:SM01391,Superfamily_domains:SSF46579 MODERATE 1 SNV 2 1 PASS rs1404257939 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 41488302 41488302 C T 1 0 0 0 0 1 0 0 0 8355 864 30 3 3 KRT36 17 41488302 Missense_Mutation SNP C C3N-01074_T 47423 41488302 41769139 389 22378 CRHR1 0 . GRCh38 17 45834704 45834704 + Silent SNP C C A rs551094849 C3N-01074_T C3N-01074_N C C c.663C>A p.= p.S221S ENST00000634540 15/15 246 159 87 200 200 0 strelka-varscan-mutect CRHR1,synonymous_variant,p.=,ENST00000634540,NM_001256299.2,NM_001303018.1;CRHR1,synonymous_variant,p.=,ENST00000293493,;CRHR1,synonymous_variant,p.=,ENST00000314537,NM_004382.4;CRHR1,synonymous_variant,p.=,ENST00000339069,NM_001303016.1,NM_001303020.1;CRHR1,synonymous_variant,p.=,ENST00000398285,NM_001145146.1;CRHR1,synonymous_variant,p.=,ENST00000577353,NM_001145148.1;CRHR1,synonymous_variant,p.=,ENST00000352855,NM_001145147.1;CRHR1,3_prime_UTR_variant,,ENST00000619154,;CRHR1,downstream_gene_variant,,ENST00000580876,;MAPT-AS1,intron_variant,,ENST00000634876,;CRHR1,3_prime_UTR_variant,,ENST00000347197,;CRHR1,3_prime_UTR_variant,,ENST00000535778,;CRHR1,3_prime_UTR_variant,,ENST00000583888,;CRHR1,downstream_gene_variant,,ENST00000582766,;CRHR1,downstream_gene_variant,,ENST00000581479,;CRHR1,downstream_gene_variant,,ENST00000580955,; A ENST00000634540 Transcript synonymous_variant 1573/2695 663/723 221/240 S tcC/tcA rs551094849 1 1 CRHR1 EntrezGene HGNC:2357 protein_coding YES ENSP00000488912 A0A024R9X9 UPI0000D4A34F NM_001256299.2,NM_001303018.1 15/15 Prints_domain:PR01279,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF175 LOW SNV 2 1 PASS rs551094849 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 45834704 45834704 C A 1 0 0 0 0 0 0 0 1 3672 581 21 2 2 CRHR1 17 45834704 Silent SNP C C3N-01074_T 4346402 45834704 37422737 390 22379 SPPL2C 0 . GRCh38 17 45845663 45845663 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.757C>A p.Pro253Thr p.P253T ENST00000329196 1/1 255 197 58 246 245 1 strelka-varscan-mutect SPPL2C,missense_variant,p.Pro253Thr,ENST00000329196,NM_175882.2;MAPT-AS1,intron_variant,,ENST00000634876,;MAPT-AS1,intron_variant,,ENST00000579599,;MAPT-AS1,intron_variant,,ENST00000579244,;MAPT-AS1,upstream_gene_variant,,ENST00000581125,; A ENST00000329196 Transcript missense_variant 829/2238 757/2055 253/684 P/T Ccg/Acg 1 1 SPPL2C HGNC HGNC:28902 protein_coding YES CCDS32673.1 ENSP00000332488 Q8IUH8 UPI0000EE80B4 NM_175882.2 deleterious(0.01) 1/1 Pfam_domain:PF04258,hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF38,SMART_domains:SM00730,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 45845663 45845663 C A 1 0 0 0 0 1 0 0 0 15443 739 26 2 2 SPPL2C 17 45845663 Missense_Mutation SNP C C3N-01074_T 10959 45845663 37411778 391 22380 ACSF2 0 . GRCh38 17 50460735 50460735 + Missense_Mutation SNP G G T rs757956148 C3N-01074_T C3N-01074_N G G c.262G>T p.Gly88Trp p.G88W ENST00000427954 3/17 328 226 102 207 204 3 strelka-varscan-mutect ACSF2,missense_variant,p.Gly88Trp,ENST00000427954,NM_001288968.1;ACSF2,missense_variant,p.Gly63Trp,ENST00000300441,NM_025149.5;ACSF2,missense_variant,p.Gly63Trp,ENST00000502667,NM_001288969.1;ACSF2,missense_variant,p.Gly63Trp,ENST00000504392,NM_001288972.1,NM_001288970.1,NM_001288971.1;ACSF2,missense_variant,p.Gly63Trp,ENST00000506582,;CHAD,downstream_gene_variant,,ENST00000508540,NM_001267.2;CHAD,downstream_gene_variant,,ENST00000258969,;CHAD,downstream_gene_variant,,ENST00000506187,;ACSF2,upstream_gene_variant,,ENST00000509806,;ACSF2,3_prime_UTR_variant,,ENST00000503408,;ACSF2,non_coding_transcript_exon_variant,,ENST00000504945,;ACSF2,non_coding_transcript_exon_variant,,ENST00000570356,;ACSF2,intron_variant,,ENST00000510410,;ACSF2,upstream_gene_variant,,ENST00000506052,;ACSF2,upstream_gene_variant,,ENST00000508245,;ACSF2,upstream_gene_variant,,ENST00000507769,;ACSF2,upstream_gene_variant,,ENST00000513101,;ACSF2,upstream_gene_variant,,ENST00000510262,; T ENST00000427954 Transcript missense_variant 305/2251 262/1923 88/640 G/W Ggg/Tgg rs757956148 1 1 ACSF2 HGNC HGNC:26101 protein_coding YES CCDS74103.1 ENSP00000401831 Q96CM8 UPI00017A6F63 NM_001288968.1 deleterious(0) 3/17 hmmpanther:PTHR24095 MODERATE SNV 2 1 PASS rs757956148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 50460735 50460735 G T 1 0 0 0 0 1 0 0 0 217 1232 43 2 2 ACSF2 17 50460735 Missense_Mutation SNP G C3N-01074_T 4615072 50460735 32796706 392 22381 KIF2B 0 . GRCh38 17 53824962 53824962 + Silent SNP C C G novel C3N-01074_T C3N-01074_N C C c.1929C>G p.= p.S643S ENST00000268919 1/1 275 233 42 292 292 0 strelka-varscan-mutect KIF2B,synonymous_variant,p.=,ENST00000268919,NM_032559.4; G ENST00000268919 Transcript synonymous_variant 2062/2313 1929/2022 643/673 S tcC/tcG 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 53824962 53824962 C G 1 0 0 0 0 0 0 0 1 8163 581 21 4 4 KIF2B 17 53824962 Silent SNP C C3N-01074_T 3364227 53824962 29432479 393 22382 OR4D2 0 . GRCh38 17 58170031 58170031 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.376A>T p.Ile126Phe p.I126F ENST00000545221 1/1 709 459 250 651 650 1 strelka-varscan-mutect OR4D2,missense_variant,p.Ile126Phe,ENST00000545221,NM_001004707.3; T ENST00000545221 Transcript missense_variant 376/924 376/924 126/307 I/F Atc/Ttc 1 1 OR4D2 HGNC HGNC:8294 protein_coding YES CCDS32688.1 ENSP00000441354 P58180 A0A126GWK0 UPI0000000DB3 NM_001004707.3 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF348,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 58170031 58170031 A T 1 0 0 0 0 1 0 0 0 11133 217 8 4 4 OR4D2 17 58170031 Missense_Mutation SNP A C3N-01074_T 4345069 58170031 25087410 394 22383 TEX14 0 . GRCh38 17 58622909 58622909 + Missense_Mutation SNP C C A rs145427452 C3N-01074_T C3N-01074_N C C c.355G>T p.Asp119Tyr p.D119Y ENST00000240361 4/33 121 83 38 94 94 0 strelka-varscan-mutect TEX14,missense_variant,p.Asp119Tyr,ENST00000389934,NM_198393.3;TEX14,missense_variant,p.Asp119Tyr,ENST00000240361,NM_001201457.1;TEX14,missense_variant,p.Asp119Tyr,ENST00000349033,NM_031272.4;TEX14,3_prime_UTR_variant,,ENST00000582740,; A ENST00000240361 Transcript missense_variant 441/4911 355/4494 119/1497 D/Y Gat/Tat rs145427452 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 deleterious(0) 4/33 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR23060,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs145427452 . 0 201 9 0 0 0 0 0 -20 0.9999986 1 1 1 0 A 3 1 73 58622909 58622909 C A 1 0 0 0 0 1 0 0 0 16200 884 31 1 1 TEX14 17 58622909 Missense_Mutation SNP C C3N-01074_T 452878 58622909 24634532 395 22384 PSMD12 0 . GRCh38 17 67344739 67344739 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.950G>C p.Trp317Ser p.W317S ENST00000356126 9/11 126 117 9 118 118 0 varscan-mutect PSMD12,missense_variant,p.Trp317Ser,ENST00000356126,NM_002816.3;PSMD12,missense_variant,p.Trp297Ser,ENST00000357146,NM_174871.2;PSMD12,3_prime_UTR_variant,,ENST00000584008,;PSMD12,downstream_gene_variant,,ENST00000584289,;PSMD12,upstream_gene_variant,,ENST00000577724,; G ENST00000356126 Transcript missense_variant 1058/4406 950/1371 317/456 W/S tGg/tCg 1 -1 PSMD12 HGNC HGNC:9557 protein_coding YES CCDS11669.1 ENSP00000348442 O00232 A0A0S2Z489 UPI0000132792 NM_002816.3 deleterious(0) 9/11 Pfam_domain:PF01399,hmmpanther:PTHR10855,hmmpanther:PTHR10855:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -17.56927 1 1 1 1 0 G 3 3 73 67344739 67344739 C G 1 0 0 0 0 1 0 0 0 12846 595 21 4 4 PSMD12 17 67344739 Missense_Mutation SNP C C3N-01074_T 8721830 67344739 15912702 396 22385 BTBD17 0 . GRCh38 17 74360194 74360194 + Missense_Mutation SNP G G C C3N-01074_T C3N-01074_N G G c.137C>G p.Ser46Cys p.S46C ENST00000375366 2/3 144 109 35 145 145 0 strelka-varscan-mutect BTBD17,missense_variant,p.Ser46Cys,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000389916,NM_153209.3; C ENST00000375366 Transcript missense_variant 264/1805 137/1437 46/478 S/C tCc/tGc COSM5578141 1 -1 BTBD17 HGNC HGNC:33758 protein_coding YES CCDS32719.1 ENSP00000364515 A6NE02 UPI00001D7961 NM_001080466.1 deleterious(0) 2/3 hmmpanther:PTHR24410:SF12,hmmpanther:PTHR24410,Gene3D:3.30.710.10,Superfamily_domains:SSF54695 1 MODERATE 1 SNV 2 1 1 PASS rs1421201540 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 73 74360194 74360194 G C 1 0 0 0 0 1 0 0 0 1716 1174 41 4 4 BTBD17 17 74360194 Missense_Mutation SNP G C3N-01074_T 7015455 74360194 8897247 397 22386 CDR2L 0 . GRCh38 17 75003844 75003844 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.1168C>T p.Arg390Cys p.R390C ENST00000337231 5/5 132 108 24 133 133 0 varscan-mutect CDR2L,missense_variant,p.Arg390Cys,ENST00000337231,NM_014603.2; T ENST00000337231 Transcript missense_variant 1580/3536 1168/1398 390/465 R/C Cgc/Tgc 1 1 CDR2L HGNC HGNC:29999 protein_coding YES CCDS11710.2 ENSP00000336587 Q86X02 A0A024R8R6 UPI00005AE46D NM_014603.2 deleterious(0) 5/5 hmmpanther:PTHR19232:SF10,hmmpanther:PTHR19232 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 73 75003844 75003844 C T 1 0 0 0 0 1 0 0 0 2878 768 27 1 1 CDR2L 17 75003844 Missense_Mutation SNP C C3N-01074_T 643650 75003844 8253597 398 22387 BAHCC1 0 . GRCh38 17 81443235 81443235 + Missense_Mutation SNP A A G novel C3N-01074_T C3N-01074_N A A c.1886A>G p.Glu629Gly p.E629G ENST00000584436 5/29 256 206 50 258 258 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Glu629Gly,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Glu629Gly,ENST00000307745,;BAHCC1,upstream_gene_variant,,ENST00000585224,; G ENST00000584436 Transcript missense_variant 2253/10801 1886/7920 629/2639 E/G gAg/gGg 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0.02) 5/29 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF22 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 81443235 81443235 A G 1 0 0 0 0 1 0 0 0 1451 304 11 5 5 BAHCC1 17 81443235 Missense_Mutation SNP A C3N-01074_T 6439391 81443235 1814206 399 22388 ACTG1 0 . GRCh38 17 81510936 81510936 + Frame_Shift_Del DEL C C - novel C3N-01074_T C3N-01074_N C C c.975delG p.Met325IlefsTer65 p.M325Ifs*65 ENST00000575842 4/5 453 410 43 499 499 0 sindel-varindel-pindel ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000575842,;ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000573283,NM_001199954.1;ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000575087,;ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000331925,NM_001614.3;ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000615544,;ACTG1,downstream_gene_variant,,ENST00000575994,;ACTG1,downstream_gene_variant,,ENST00000571721,;ACTG1,downstream_gene_variant,,ENST00000571691,;ACTG1,downstream_gene_variant,,ENST00000575659,;ACTG1,downstream_gene_variant,,ENST00000570382,;RP13-766D20.2,upstream_gene_variant,,ENST00000430912,;ACTG1,frameshift_variant,p.Met325IlefsTer65,ENST00000576544,;ACTG1,3_prime_UTR_variant,,ENST00000572105,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576917,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576209,;ACTG1,non_coding_transcript_exon_variant,,ENST00000574671,;ACTG1,downstream_gene_variant,,ENST00000576214,;RP13-766D20.1,upstream_gene_variant,,ENST00000448147,; - ENST00000575842 Transcript frameshift_variant 1402/2256 975/1128 325/375 M/X atG/at 1 -1 ACTG1 HGNC HGNC:144 protein_coding YES CCDS11782.1 ENSP00000458162 P63261 UPI0000000C38 4/5 hmmpanther:PTHR11937:SF244,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 81510936 81510936 C - 1 0 1 0 1 0 0 0 0 239 826 29 0 0 ACTG1 17 81510936 Frame_Shift_Del DEL C C3N-01074_T 67701 81510936 1746505 400 22389 SMCHD1 0 . GRCh38 18 2707561 2707561 + Splice_Site SNP A A C novel C3N-01074_T C3N-01074_N A A c.2064-2A>C p.X688_splice ENST00000320876 151 100 51 154 153 1 strelka-varscan-mutect SMCHD1,splice_acceptor_variant,,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,splice_acceptor_variant,,ENST00000577880,;SMCHD1,splice_acceptor_variant,,ENST00000584897,;SMCHD1,non_coding_transcript_exon_variant,,ENST00000581711,;SMCHD1,downstream_gene_variant,,ENST00000577300,; C ENST00000320876 Transcript splice_acceptor_variant -/8821 2064/6018 688/2005 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 15/47 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 73 2707561 2707561 A C 1 0 0 0 0 0 0 1 0 15081 202 7 5 5 SMCHD1 18 2707561 Splice_Site SNP A C3N-01074_T 2707561 77665724 401 22390 PPP4R1 0 . GRCh38 18 9550051 9550051 + Splice_Site SNP C C A C3N-01074_T C3N-01074_N C C c.2547+1G>T p.X849_splice ENST00000400556 241 166 75 239 238 1 strelka-varscan-mutect PPP4R1,splice_donor_variant,,ENST00000400556,NM_001042388.2;PPP4R1,splice_donor_variant,,ENST00000400555,NM_005134.3;PPP4R1,splice_donor_variant,,ENST00000579609,;PPP4R1,downstream_gene_variant,,ENST00000584754,;PPP4R1,splice_donor_variant,,ENST00000582594,;PPP4R1,splice_donor_variant,,ENST00000285124,;PPP4R1,splice_donor_variant,,ENST00000578329,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000578010,; A ENST00000400556 Transcript splice_donor_variant -/3925 2547/2853 849/950 COSM564310 1 -1 PPP4R1 HGNC HGNC:9320 protein_coding YES CCDS42412.1 ENSP00000383402 Q8TF05 UPI000006D6DE NM_001042388.2 18/19 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 73 9550051 9550051 C A 1 0 0 0 0 0 0 1 0 12525 521 18 2 2 PPP4R1 18 9550051 Splice_Site SNP C C3N-01074_T 6842490 9550051 70823234 402 22391 ROCK1 0 . GRCh38 18 21045342 21045342 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.540A>T p.= p.A180A ENST00000399799 5/33 186 135 51 181 181 0 strelka-varscan-mutect ROCK1,synonymous_variant,p.=,ENST00000399799,NM_005406.2;ROCK1,synonymous_variant,p.=,ENST00000635540,;ROCK1,non_coding_transcript_exon_variant,,ENST00000582445,; A ENST00000399799 Transcript synonymous_variant 1481/9484 540/4065 180/1354 A gcA/gcT 1 -1 ROCK1 HGNC HGNC:10251 protein_coding YES CCDS11870.2 ENSP00000382697 Q13464 UPI000006F0A4 NM_005406.2 5/33 PROSITE_profiles:PS50011,hmmpanther:PTHR22988:SF33,hmmpanther:PTHR22988,PIRSF_domain:PIRSF037568,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 21045342 21045342 T A 1 0 0 0 0 0 0 0 1 13695 1567 55 4 4 ROCK1 18 21045342 Silent SNP T C3N-01074_T 11495291 21045342 59327943 403 22392 GREB1L 0 . GRCh38 18 21401270 21401270 + Missense_Mutation SNP A A T C3N-01074_T C3N-01074_N A A c.653A>T p.Tyr218Phe p.Y218F ENST00000580732 6/33 402 305 97 252 251 1 strelka-varscan-mutect GREB1L,missense_variant,p.Tyr218Phe,ENST00000580732,;GREB1L,missense_variant,p.Tyr218Phe,ENST00000424526,NM_001142966.1;GREB1L,missense_variant,p.Tyr218Phe,ENST00000269218,;GREB1L,missense_variant,p.Tyr16Phe,ENST00000579454,;RP11-296E23.1,intron_variant,,ENST00000584611,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578368,;GREB1L,non_coding_transcript_exon_variant,,ENST00000584446,; T ENST00000580732 Transcript missense_variant 1034/8749 653/5772 218/1923 Y/F tAc/tTc COSM2884839,COSM2884840 1 1 GREB1L HGNC HGNC:31042 protein_coding YES CCDS45836.1 ENSP00000464162 Q9C091 UPI0001642876 deleterious(0.02) 6/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF12 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 21401270 21401270 A T 1 0 0 0 0 1 0 0 0 6640 391 14 4 4 GREB1L 18 21401270 Missense_Mutation SNP A C3N-01074_T 355928 21401270 58972015 404 22393 CTAGE1 0 . GRCh38 18 22415876 22415876 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.1936G>T p.Asp646Tyr p.D646Y ENST00000391403 1/1 772 553 219 741 739 2 strelka-varscan-mutect CTAGE1,missense_variant,p.Asp646Tyr,ENST00000391403,NM_172241.2;CTAGE1,upstream_gene_variant,,ENST00000525417,;RP11-863N1.4,downstream_gene_variant,,ENST00000603437,; A ENST00000391403 Transcript missense_variant 2040/4313 1936/2238 646/745 D/Y Gat/Tat 1 -1 CTAGE1 HGNC HGNC:24346 protein_coding YES CCDS45837.1 ENSP00000375220 Q96RT6 UPI00000721F4 NM_172241.2 deleterious(0) 1/1 hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 22415876 22415876 C A 1 0 0 0 0 1 0 0 0 3796 826 29 2 2 CTAGE1 18 22415876 Missense_Mutation SNP C C3N-01074_T 1014606 22415876 57957409 405 22394 DSG4 0 . GRCh38 18 31411115 31411115 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.2079T>A p.Phe693Leu p.F693L ENST00000359747 14/15 107 72 35 125 125 0 strelka-varscan-mutect DSG4,missense_variant,p.Phe693Leu,ENST00000359747,NM_001134453.1;DSG4,intron_variant,,ENST00000308128,NM_177986.3;DSG1-AS1,intron_variant,,ENST00000581856,;DSG1-AS1,intron_variant,,ENST00000578477,; A ENST00000359747 Transcript missense_variant 2108/4526 2079/3180 693/1059 F/L ttT/ttA 1 1 DSG4 HGNC HGNC:21307 protein_coding YES CCDS45845.1 ENSP00000352785 Q86SJ6 UPI000035DB4E NM_001134453.1 deleterious(0.05) 14/15 hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 31411115 31411115 T A 1 0 0 0 0 1 0 0 0 4600 1768 61 4 4 DSG4 18 31411115 Missense_Mutation SNP T C3N-01074_T 8995239 31411115 48962170 406 22395 MOCOS 0 . GRCh38 18 36199738 36199738 + Missense_Mutation SNP G G T rs367827518 C3N-01074_T C3N-01074_N G G c.355G>T p.Gly119Trp p.G119W ENST00000261326 4/15 332 228 104 275 274 1 strelka-varscan-mutect MOCOS,missense_variant,p.Gly119Trp,ENST00000261326,NM_017947.2; T ENST00000261326 Transcript missense_variant 376/6160 355/2667 119/888 G/W Ggg/Tgg rs367827518 1 1 MOCOS HGNC HGNC:18234 protein_coding YES CCDS11919.1 ENSP00000261326 Q96EN8 UPI000013D165 NM_017947.2 deleterious(0) 4/15 Gene3D:3.40.640.10,HAMAP:MF_03050,Pfam_domain:PF00266,hmmpanther:PTHR14237,hmmpanther:PTHR14237:SF19,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs367827518 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 36199738 36199738 G T 1 0 0 0 0 1 0 0 0 9652 1116 39 1 1 MOCOS 18 36199738 Missense_Mutation SNP G C3N-01074_T 4788623 36199738 44173547 407 22396 EPG5 0 . GRCh38 18 45852555 45852555 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.7652G>T p.Gly2551Val p.G2551V ENST00000282041 44/44 396 300 96 309 307 2 strelka-varscan-mutect EPG5,missense_variant,p.Gly2551Val,ENST00000282041,NM_020964.2;EPG5,missense_variant,p.Gly477Val,ENST00000590854,;EPG5,downstream_gene_variant,,ENST00000587262,; A ENST00000282041 Transcript missense_variant 7687/12633 7652/7740 2551/2579 G/V gGc/gTc 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 deleterious(0.04) 44/44 hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 45852555 45852555 C A 1 0 0 0 0 1 0 0 0 5010 739 26 2 2 EPG5 18 45852555 Missense_Mutation SNP C C3N-01074_T 9652817 45852555 34520730 408 22397 C18orf25 0 . GRCh38 18 46216142 46216142 + Missense_Mutation SNP G G T rs866720576 C3N-01074_T C3N-01074_N G G c.262G>T p.Asp88Tyr p.D88Y ENST00000615052 2/5 505 362 143 440 440 0 strelka-varscan-mutect C18orf25,missense_variant,p.Asp88Tyr,ENST00000615052,NM_145055.3;C18orf25,missense_variant,p.Asp88Tyr,ENST00000619301,NM_001008239.2;C18orf25,missense_variant,p.Asp88Tyr,ENST00000615553,;C18orf25,missense_variant,p.Asp88Tyr,ENST00000587591,;C18orf25,intron_variant,,ENST00000588730,;C18orf25,non_coding_transcript_exon_variant,,ENST00000619230,; T ENST00000615052 Transcript missense_variant 636/5462 262/1215 88/404 D/Y Gac/Tac rs866720576 1 1 C18orf25 HGNC HGNC:28172 protein_coding YES CCDS42430.1 ENSP00000481626 Q5BIX2 UPI0000071DC1 NM_145055.3 deleterious(0) 2/5 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF56,Pfam_domain:PF15303 MODERATE 1 SNV 5 1 PASS rs866720576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 46216142 46216142 G T 1 0 0 0 0 1 0 0 0 1898 1290 45 2 2 C18orf25 18 46216142 Missense_Mutation SNP G C3N-01074_T 363587 46216142 34157143 409 22398 LOXHD1 0 . GRCh38 18 46577796 46577796 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1881A>T p.Lys627Asn p.K627N ENST00000536736 14/40 398 295 103 274 274 0 strelka-varscan-mutect LOXHD1,missense_variant,p.Lys627Asn,ENST00000536736,NM_144612.6;LOXHD1,missense_variant,p.Lys627Asn,ENST00000441551,;LOXHD1,non_coding_transcript_exon_variant,,ENST00000335730,; A ENST00000536736 Transcript missense_variant 1881/6848 1881/6636 627/2211 K/N aaA/aaT 1 -1 LOXHD1 HGNC HGNC:26521 protein_coding ENSP00000444586 F5GZB4 UPI0001A595CE NM_144612.6 tolerated(0.11) 14/40 Gene3D:2.60.60.20,Pfam_domain:PF01477,PROSITE_profiles:PS50095,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF137,SMART_domains:SM00308,Superfamily_domains:SSF49723 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 46577796 46577796 T A 1 0 0 0 0 1 0 0 0 8801 1606 56 4 4 LOXHD1 18 46577796 Missense_Mutation SNP T C3N-01074_T 361654 46577796 33795489 410 22399 CCDC68 0 . GRCh38 18 54928825 54928825 + Missense_Mutation SNP T T G novel C3N-01074_T C3N-01074_N T T c.658A>C p.Lys220Gln p.K220Q ENST00000591504 8/12 286 206 80 257 257 0 strelka-varscan-mutect CCDC68,missense_variant,p.Lys220Gln,ENST00000591504,NM_025214.2;CCDC68,missense_variant,p.Lys220Gln,ENST00000432185,;CCDC68,missense_variant,p.Lys220Gln,ENST00000337363,NM_001143829.1;CCDC68,missense_variant,p.Lys88Gln,ENST00000592040,;CCDC68,downstream_gene_variant,,ENST00000592294,; G ENST00000591504 Transcript missense_variant 933/4132 658/1008 220/335 K/Q Aaa/Caa 1 -1 CCDC68 HGNC HGNC:24350 protein_coding YES CCDS11959.1 ENSP00000466690 Q9H2F9 A0A024R2B9 UPI00000435F1 NM_025214.2 tolerated(0.37) 8/12 hmmpanther:PTHR23171,hmmpanther:PTHR23171:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 54928825 54928825 T G 1 0 0 0 0 1 0 0 0 2540 1821 63 5 5 CCDC68 18 54928825 Missense_Mutation SNP T C3N-01074_T 8351029 54928825 25444460 411 22400 ALPK2 0 . GRCh38 18 58537458 58537458 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.2729A>T p.Asn910Ile p.N910I ENST00000361673 5/13 98 82 16 107 107 0 strelka-varscan-mutect ALPK2,missense_variant,p.Asn910Ile,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,upstream_gene_variant,,ENST00000589204,; A ENST00000361673 Transcript missense_variant 2943/7303 2729/6513 910/2170 N/I aAt/aTt 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 deleterious(0.04) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 58537458 58537458 T A 1 0 0 0 0 1 0 0 0 645 1493 52 4 4 ALPK2 18 58537458 Missense_Mutation SNP T C3N-01074_T 3608633 58537458 21835827 412 22401 ZCCHC2 0 . GRCh38 18 62524162 62524162 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.738G>T p.= p.R246R ENST00000269499 1/14 309 212 97 305 304 1 strelka-varscan-mutect ZCCHC2,synonymous_variant,p.=,ENST00000269499,NM_017742.5;ZCCHC2,synonymous_variant,p.=,ENST00000588676,;ZCCHC2,upstream_gene_variant,,ENST00000621048,;RP11-120K19.4,downstream_gene_variant,,ENST00000612025,;ZCCHC2,upstream_gene_variant,,ENST00000591632,;ZCCHC2,synonymous_variant,p.=,ENST00000585873,; T ENST00000269499 Transcript synonymous_variant 1156/5959 738/3537 246/1178 R cgG/cgT 1 1 ZCCHC2 HGNC HGNC:22916 protein_coding YES CCDS45880.1 ENSP00000269499 Q9C0B9 UPI00016D385A NM_017742.5 1/14 hmmpanther:PTHR16195,hmmpanther:PTHR16195:SF14 LOW 1 SNV 5 1 PASS rs1330761628 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 62524162 62524162 G T 1 0 0 0 0 0 0 0 1 18162 1219 43 2 2 ZCCHC2 18 62524162 Silent SNP G C3N-01074_T 3986704 62524162 17849123 413 22402 CCDC102B 0 . GRCh38 18 68837105 68837105 + Frame_Shift_Del DEL C C - novel C3N-01074_T C3N-01074_N C C c.342delC p.Asn114LysfsTer12 p.N114Kfs*12 ENST00000360242 2/8 478 359 119 507 507 0 sindel-varindel-pindel CCDC102B,frameshift_variant,p.Asn114LysfsTer12,ENST00000360242,NM_001093729.1,NM_024781.2;CCDC102B,frameshift_variant,p.Asn114LysfsTer12,ENST00000584156,;CCDC102B,frameshift_variant,p.Asn114LysfsTer12,ENST00000584775,;CCDC102B,frameshift_variant,p.Asn114LysfsTer?,ENST00000582371,;CCDC102B,frameshift_variant,p.Asn114LysfsTer12,ENST00000581520,;CCDC102B,upstream_gene_variant,,ENST00000358653,;CCDC102B,downstream_gene_variant,,ENST00000578970,;CCDC102B,non_coding_transcript_exon_variant,,ENST00000577772,; - ENST00000360242 Transcript frameshift_variant 459/2711 342/1542 114/513 N/X aaC/aa 1 1 CCDC102B HGNC HGNC:26295 protein_coding YES CCDS11996.2 ENSP00000353377 Q68D86 UPI0000201E87 NM_001093729.1,NM_024781.2 2/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF479,hmmpanther:PTHR13140 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 68837105 68837105 C - 1 0 1 0 1 0 0 0 0 2435 477 17 0 0 CCDC102B 18 68837105 Frame_Shift_Del DEL C C3N-01074_T 6312943 68837105 11536180 414 22403 ZNF407 0 . GRCh38 18 74634708 74634708 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.3689G>T p.Cys1230Phe p.C1230F ENST00000299687 1/8 316 214 102 285 285 0 strelka-varscan-mutect ZNF407,missense_variant,p.Cys1230Phe,ENST00000299687,NM_017757.2;ZNF407,missense_variant,p.Cys1230Phe,ENST00000577538,NM_001146189.1;ZNF407,missense_variant,p.Cys1230Phe,ENST00000582337,;ZNF407,missense_variant,p.Cys1230Phe,ENST00000309902,NM_001146190.1; T ENST00000299687 Transcript missense_variant 3689/7948 3689/6747 1230/2248 C/F tGt/tTt 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 tolerated(0.2) 1/8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 74634708 74634708 G T 1 0 0 0 0 1 0 0 0 18459 1377 48 2 2 ZNF407 18 74634708 Missense_Mutation SNP G C3N-01074_T 5797603 74634708 5738577 415 22404 SMIM21 0 . GRCh38 18 75410882 75410882 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.288C>A p.Asn96Lys p.N96K ENST00000579022 3/3 399 345 54 362 362 0 strelka-varscan-mutect SMIM21,missense_variant,p.Asn96Lys,ENST00000579022,NM_001037331.3;SMIM21,missense_variant,p.His53Asn,ENST00000382638,;RP11-321M21.3,intron_variant,,ENST00000578340,;RP11-321M21.3,intron_variant,,ENST00000579386,; T ENST00000579022 Transcript missense_variant 428/1834 288/306 96/101 N/K aaC/aaA 1 -1 SMIM21 HGNC HGNC:27598 protein_coding YES CCDS32845.1 ENSP00000462106 Q3B7S5 UPI00001B64CE NM_001037331.3 deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 75410882 75410882 G T 1 0 0 0 0 1 0 0 0 15108 1368 48 2 2 SMIM21 18 75410882 Missense_Mutation SNP G C3N-01074_T 776174 75410882 4962403 416 22405 SALL3 0 . GRCh38 18 78993017 78993017 + Silent SNP G G T novel C3N-01074_T C3N-01074_N G G c.1026G>T p.= p.T342T ENST00000537592 2/3 82 54 28 82 82 0 strelka-varscan-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000536229,;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,intron_variant,,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript synonymous_variant 1026/6555 1026/3903 342/1300 T acG/acT 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 LOW 1 SNV 5 1 PASS rs1267389959 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 78993017 78993017 G T 1 0 0 0 0 0 0 0 1 14071 1074 38 1 1 SALL3 18 78993017 Silent SNP G C3N-01074_T 3582135 78993017 1380268 417 22406 ADNP2 0 . GRCh38 18 80136704 80136704 + Nonsense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.1291C>T p.Gln431Ter p.Q431* ENST00000262198 4/4 113 79 34 144 143 1 strelka-varscan-mutect ADNP2,stop_gained,p.Gln431Ter,ENST00000262198,NM_014913.3;ADNP2,intron_variant,,ENST00000561195,;ADNP2,downstream_gene_variant,,ENST00000560752,;ADNP2,downstream_gene_variant,,ENST00000559951,;ADNP2,downstream_gene_variant,,ENST00000560561,; T ENST00000262198 Transcript stop_gained 1746/5393 1291/3396 431/1131 Q/* Cag/Tag 1 1 ADNP2 HGNC HGNC:23803 protein_coding YES CCDS32853.1 ENSP00000262198 Q6IQ32 A0A024R377 UPI0000071DEA NM_014913.3 4/4 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 4 4 73 80136704 80136704 C T 1 0 0 0 0 0 1 0 0 399 711 25 3 3 ADNP2 18 80136704 Nonsense_Mutation SNP C C3N-01074_T 1143687 80136704 236581 418 22407 PLPPR3 0 . GRCh38 19 812824 812824 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1987C>A p.Pro663Thr p.P663T ENST00000359894 7/7 17 8 9 17 17 0 strelka-varscan-mutect PLPPR3,missense_variant,p.Pro663Thr,ENST00000359894,NM_024888.2;PLPPR3,missense_variant,p.Pro635Thr,ENST00000520876,NM_001270366.1;PTBP1,downstream_gene_variant,,ENST00000635647,;PTBP1,downstream_gene_variant,,ENST00000356948,NM_002819.4;PTBP1,downstream_gene_variant,,ENST00000394601,NM_031990.3;PTBP1,downstream_gene_variant,,ENST00000349038,NM_031991.3;PTBP1,downstream_gene_variant,,ENST00000350092,;PTBP1,downstream_gene_variant,,ENST00000627714,;PLPPR3,downstream_gene_variant,,ENST00000519502,;PTBP1,downstream_gene_variant,,ENST00000585956,;PLPPR3,downstream_gene_variant,,ENST00000517665,;PTBP1,downstream_gene_variant,,ENST00000587191,;PTBP1,downstream_gene_variant,,ENST00000585535,;MIR3187,upstream_gene_variant,,ENST00000583431,;PTBP1,downstream_gene_variant,,ENST00000586944,;PTBP1,downstream_gene_variant,,ENST00000585856,;PTBP1,downstream_gene_variant,,ENST00000621737,;PTBP1,downstream_gene_variant,,ENST00000585932,; T ENST00000359894 Transcript missense_variant 2051/2387 1987/2241 663/746 P/T Ccg/Acg 1 -1 PLPPR3 HGNC HGNC:23497 protein_coding YES CCDS12043.1 ENSP00000352962 Q6T4P5 UPI00000730B6 NM_024888.2 tolerated(0.12) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1478660281 . 55 153 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 812824 812824 G T 1 0 0 0 0 1 0 0 0 12211 1232 43 2 2 PLPPR3 19 812824 Missense_Mutation SNP G C3N-01074_T 812824 57804792 419 22408 STK11 0 . GRCh38 19 1221229 1221229 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.751G>T p.Gly251Cys p.G251C ENST00000326873 6/10 138 81 57 157 157 0 strelka-varscan-mutect STK11,missense_variant,p.Gly251Cys,ENST00000586243,;STK11,missense_variant,p.Gly251Cys,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript missense_variant 1201/2611 751/1302 251/433 G/C Ggt/Tgt CM981868,COSM5305090,COSM5337089,COSM5337090,COSM564708 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 deleterious(0) 6/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 1221229 1221229 G T 1 0 0 0 0 1 0 0 0 15664 1232 43 2 2 STK11 19 1221229 Missense_Mutation SNP G C3N-01074_T 408405 1221229 57396387 420 22409 MEX3D 0 . GRCh38 19 1556642 1556642 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.877G>A p.Gly293Ser p.G293S ENST00000402693 2/2 212 129 83 274 274 0 strelka-varscan-mutect MEX3D,missense_variant,p.Gly293Ser,ENST00000402693,NM_203304.3,NM_001174118.1;MEX3D,missense_variant,p.Gly117Ser,ENST00000605173,; T ENST00000402693 Transcript missense_variant 877/2850 877/1956 293/651 G/S Ggc/Agc 1 -1 MEX3D HGNC HGNC:16734 protein_coding YES CCDS32865.2 ENSP00000384398 Q86XN8 UPI000059D61B NM_203304.3,NM_001174118.1 deleterious(0) 2/2 PROSITE_profiles:PS50084,hmmpanther:PTHR23285,hmmpanther:PTHR23285:SF3,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 1556642 1556642 C T 1 0 0 0 0 1 0 0 0 9465 623 22 3 3 MEX3D 19 1556642 Missense_Mutation SNP C C3N-01074_T 335413 1556642 57060974 421 22410 SAFB2 0 . GRCh38 19 5587257 5587257 + Missense_Mutation SNP T T G rs746356562 C3N-01074_T C3N-01074_N T T c.2848A>C p.Thr950Pro p.T950P ENST00000252542 21/21 126 118 8 117 116 1 varscan-mutect SAFB2,missense_variant,p.Thr950Pro,ENST00000252542,NM_014649.2;SAFB2,non_coding_transcript_exon_variant,,ENST00000587802,;SAFB2,downstream_gene_variant,,ENST00000589925,;SAFB2,downstream_gene_variant,,ENST00000590000,; G ENST00000252542 Transcript missense_variant 3113/3371 2848/2862 950/953 T/P Acc/Ccc rs746356562 1 -1 SAFB2 HGNC HGNC:21605 protein_coding YES CCDS32879.1 ENSP00000252542 Q14151 UPI0000071DB7 NM_014649.2 deleterious(0) 21/21 hmmpanther:PTHR15683,hmmpanther:PTHR15683:SF4 MODERATE 1 SNV 1 1 PASS rs746356562 . 0 170 23 13 4 0 0 0 -3.55268 0.03325763 0 1 0 0 G 3 3 73 5587257 5587257 T G 1 0 0 0 0 1 0 0 0 14066 1696 59 5 5 SAFB2 19 5587257 Missense_Mutation SNP T C3N-01074_T 4030615 5587257 53030359 422 22411 INSR 0 . GRCh38 19 7172424 7172424 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.1134A>T p.= p.A378A ENST00000302850 5/22 445 252 193 554 553 1 strelka-varscan-mutect INSR,synonymous_variant,p.=,ENST00000341500,NM_001079817.1;INSR,synonymous_variant,p.=,ENST00000302850,NM_000208.2;INSR,upstream_gene_variant,,ENST00000600492,;INSR,non_coding_transcript_exon_variant,,ENST00000598216,; A ENST00000302850 Transcript synonymous_variant 1277/4721 1134/4149 378/1382 A gcA/gcT 1 -1 INSR HGNC HGNC:6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 UPI000020324D NM_000208.2 5/22 Gene3D:3.80.20.20,Pfam_domain:PF01030,PIRSF_domain:PIRSF000620,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF325,Low_complexity_(Seg):seg,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs1455977199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 7172424 7172424 T A 1 0 0 0 0 0 0 0 1 7675 1567 55 4 4 INSR 19 7172424 Silent SNP T C3N-01074_T 1585167 7172424 51445192 423 22412 MUC16 0 . GRCh38 19 8953510 8953510 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.23260C>A p.Leu7754Met p.L7754M ENST00000397910 3/84 330 184 146 345 345 0 strelka-varscan-mutect MUC16,missense_variant,p.Leu7754Met,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 23464/43816 23260/43524 7754/14507 L/M Ctg/Atg 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 8953510 8953510 G T 1 0 0 0 0 1 0 0 0 9972 1020 36 2 2 MUC16 19 8953510 Missense_Mutation SNP G C3N-01074_T 1781086 8953510 49664106 424 22413 OR7G2 0 . GRCh38 19 9103168 9103168 + Missense_Mutation SNP C C T rs201831795 C3N-01074_T C3N-01074_N C C c.139G>A p.Val47Ile p.V47I ENST00000305456 1/1 351 212 139 447 447 0 strelka-varscan-mutect OR7G2,missense_variant,p.Val47Ile,ENST00000305456,NM_001005193.1; T ENST00000305456 Transcript missense_variant 139/1038 139/1038 47/345 V/I Gtc/Atc rs201831795 1 -1 OR7G2 HGNC HGNC:8466 protein_coding YES CCDS32897.1 ENSP00000303822 Q8NG99 UPI00000472B7 NM_001005193.1 tolerated(0.17) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF326,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs201831795 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 9103168 9103168 C T 1 0 0 0 0 1 0 0 0 11293 536 19 1 1 OR7G2 19 9103168 Missense_Mutation SNP C C3N-01074_T 149658 9103168 49514448 425 22414 SMARCA4 0 . GRCh38 19 11023548 11023548 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.2890A>T p.Ile964Phe p.I964F ENST00000429416 21/36 378 295 83 380 379 1 strelka-varscan-mutect SMARCA4,missense_variant,p.Ile964Phe,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Ile1028Phe,ENST00000413806,;SMARCA4,missense_variant,p.Ile964Phe,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.Ile964Phe,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Ile964Phe,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.Ile964Phe,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.Ile964Phe,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.Ile964Phe,ENST00000444061,NM_001128848.1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000586122,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000587988,; T ENST00000429416 Transcript missense_variant 3171/5691 2890/4944 964/1647 I/F Atc/Ttc 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 deleterious(0.01) 21/36 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Pfam_domain:PF00176,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 11023548 11023548 A T 1 0 0 0 0 1 0 0 0 15063 217 8 4 4 SMARCA4 19 11023548 Missense_Mutation SNP A C3N-01074_T 1920380 11023548 47594068 426 22415 ZNF490 0 . GRCh38 19 12581492 12581492 + Nonsense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.583A>T p.Lys195Ter p.K195* ENST00000311437 5/5 245 155 90 385 384 1 strelka-varscan-mutect ZNF490,stop_gained,p.Lys195Ter,ENST00000311437,NM_020714.2;ZNF490,downstream_gene_variant,,ENST00000440366,;ZNF490,downstream_gene_variant,,ENST00000465656,;ZNF490,3_prime_UTR_variant,,ENST00000414906,;CTD-2192J16.20,upstream_gene_variant,,ENST00000593682,; A ENST00000311437 Transcript stop_gained 706/4237 583/1590 195/529 K/* Aaa/Taa 1 -1 ZNF490 HGNC HGNC:23705 protein_coding YES CCDS12272.1 ENSP00000311521 Q9ULM2 UPI0000001C6F NM_020714.2 5/5 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF16,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 12581492 12581492 T A 1 0 0 0 0 0 1 0 0 18514 1763 61 4 4 ZNF490 19 12581492 Nonsense_Mutation SNP T C3N-01074_T 1557944 12581492 46036124 427 22416 ZNF486 0 . GRCh38 19 20197880 20197880 + Frame_Shift_Del DEL T T - novel C3N-01074_T C3N-01074_N T T c.1170delT p.Ala391GlnfsTer31 p.A391Qfs*31 ENST00000335117 4/4 226 118 108 362 362 0 sindel-varindel ZNF486,frameshift_variant,p.Ala391GlnfsTer31,ENST00000335117,NM_052852.3;CTC-260E6.6,intron_variant,,ENST00000585498,;CTC-260E6.6,intron_variant,,ENST00000593655,;CTC-260E6.6,intron_variant,,ENST00000586657,; - ENST00000335117 Transcript frameshift_variant 1227/3837 1170/1392 390/463 S/X tcT/tc 1 1 ZNF486 HGNC HGNC:20807 protein_coding YES CCDS46029.1 ENSP00000335042 Q96H40 UPI00002376E8 NM_052852.3 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF95,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 73 20197880 20197880 T - 1 0 1 0 1 0 0 0 0 18511 1567 55 0 0 ZNF486 19 20197880 Frame_Shift_Del DEL T C3N-01074_T 7616388 20197880 38419736 428 22417 ZNF208 0 . GRCh38 19 21987266 21987266 + Missense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.176G>T p.Gly59Val p.G59V ENST00000397126 3/4 109 73 36 154 154 0 strelka-varscan-mutect ZNF208,missense_variant,p.Gly59Val,ENST00000397126,NM_007153.3;ZNF208,missense_variant,p.Gly59Val,ENST00000609966,;ZNF208,missense_variant,p.Gly59Val,ENST00000601773,;ZNF208,missense_variant,p.Gly27Val,ENST00000597040,;ZNF208,missense_variant,p.Gly59Val,ENST00000599916,;ZNF208,missense_variant,p.Gly58Val,ENST00000599723,;ZNF208,downstream_gene_variant,,ENST00000601993,; A ENST00000397126 Transcript missense_variant 325/3992 176/3843 59/1280 G/V gGa/gTa COSM710750,COSM710751,COSM710752 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 deleterious(0.02) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF103,SMART_domains:SM00349,Superfamily_domains:0044637 1,1,1 MODERATE 1 SNV 3 1,1,1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 21987266 21987266 C A 1 0 0 0 0 1 0 0 0 18343 855 30 2 2 ZNF208 19 21987266 Missense_Mutation SNP C C3N-01074_T 1789386 21987266 36630350 429 22418 ZNF492 0 . GRCh38 19 22664181 22664181 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.512G>T p.Cys171Phe p.C171F ENST00000456783 4/4 115 85 30 191 191 0 strelka-varscan-mutect ZNF492,missense_variant,p.Cys171Phe,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; T ENST00000456783 Transcript missense_variant 756/4245 512/1596 171/531 C/F tGt/tTt 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.03) 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 22664181 22664181 G T 1 0 0 0 0 1 0 0 0 18516 1377 48 2 2 ZNF492 19 22664181 Missense_Mutation SNP G C3N-01074_T 676915 22664181 35953435 430 22419 ZNF728 0 . GRCh38 19 22976019 22976019 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1318A>T p.Thr440Ser p.T440S ENST00000594710 4/4 172 106 66 326 326 0 strelka-varscan-mutect ZNF728,missense_variant,p.Thr440Ser,ENST00000594710,NM_001267716.1;ZNF728,downstream_gene_variant,,ENST00000599851,; A ENST00000594710 Transcript missense_variant 1464/2015 1318/1869 440/622 T/S Act/Tct 1 -1 ZNF728 HGNC HGNC:32463 protein_coding YES CCDS59370.1 ENSP00000471593 P0DKX0 UPI0002656E4B NM_001267716.1 tolerated(0.19) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF239,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 22976019 22976019 T A 1 0 0 0 0 1 0 0 0 18702 1638 57 4 4 ZNF728 19 22976019 Missense_Mutation SNP T C3N-01074_T 311838 22976019 35641597 431 22420 ZNF536 0 . GRCh38 19 30547981 30547981 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.2362G>T p.Gly788Cys p.G788C ENST00000355537 4/5 81 56 25 89 89 0 strelka-varscan-mutect ZNF536,missense_variant,p.Gly788Cys,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Gly788Cys,ENST00000585628,;ZNF536,upstream_gene_variant,,ENST00000592773,; T ENST00000355537 Transcript missense_variant 2509/4945 2362/3903 788/1300 G/C Ggc/Tgc 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 deleterious(0) 4/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1251303551 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 30547981 30547981 G T 1 0 0 0 0 1 0 0 0 18547 1116 39 1 1 ZNF536 19 30547981 Missense_Mutation SNP G C3N-01074_T 7571962 30547981 28069635 432 22421 ZNF536 0 . GRCh38 19 30549038 30549038 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.3419A>T p.His1140Leu p.H1140L ENST00000355537 4/5 399 300 99 358 355 3 strelka-varscan-mutect ZNF536,missense_variant,p.His1140Leu,ENST00000355537,NM_014717.1;ZNF536,downstream_gene_variant,,ENST00000585628,;ZNF536,upstream_gene_variant,,ENST00000592773,;CTD-2001J20.1,upstream_gene_variant,,ENST00000623331,; T ENST00000355537 Transcript missense_variant 3566/4945 3419/3903 1140/1300 H/L cAc/cTc 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated_low_confidence(0.33) 4/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 30549038 30549038 A T 1 0 0 0 0 1 0 0 0 18547 159 6 4 4 ZNF536 19 30549038 Missense_Mutation SNP A C3N-01074_T 1057 30549038 28068578 433 22422 HPN 0 . GRCh38 19 35060475 35060475 + Missense_Mutation SNP G G T rs868306911 C3N-01074_T C3N-01074_N G G c.583G>T p.Gly195Trp p.G195W ENST00000262626 8/13 278 202 76 249 249 0 strelka-varscan-mutect HPN,missense_variant,p.Gly195Trp,ENST00000262626,NM_182983.2;HPN,missense_variant,p.Gly195Trp,ENST00000392226,NM_002151.2;HPN,intron_variant,,ENST00000597419,;HPN,downstream_gene_variant,,ENST00000600390,;HPN-AS1,intron_variant,,ENST00000392227,;HPN,downstream_gene_variant,,ENST00000600675,;HPN,non_coding_transcript_exon_variant,,ENST00000593305,;HPN,non_coding_transcript_exon_variant,,ENST00000599363,;HPN,non_coding_transcript_exon_variant,,ENST00000541345,;HPN,downstream_gene_variant,,ENST00000596662,; T ENST00000262626 Transcript missense_variant 1408/2363 583/1254 195/417 G/W Ggg/Tgg rs868306911,COSM4691065 1 1 HPN HGNC HGNC:5155 protein_coding YES CCDS32993.1 ENSP00000262626 P05981 A0A140VJK9 UPI000003FE67 NM_182983.2 deleterious(0.02) 8/13 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF130,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs868306911 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 35060475 35060475 G T 1 0 0 0 0 1 0 0 0 7231 1116 39 1 1 HPN 19 35060475 Missense_Mutation SNP G C3N-01074_T 4511437 35060475 23557141 434 22423 ZNF585B 0 . GRCh38 19 37189701 37189701 + Silent SNP T T C novel C3N-01074_T C3N-01074_N T T c.252A>G p.= p.P84P ENST00000532828 4/5 476 429 47 363 363 0 strelka-varscan-mutect ZNF585B,synonymous_variant,p.=,ENST00000532828,NM_152279.3;ZNF585B,synonymous_variant,p.=,ENST00000531805,;ZNF585B,synonymous_variant,p.=,ENST00000527838,;ZNF585B,synonymous_variant,p.=,ENST00000591492,;ZNF585B,synonymous_variant,p.=,ENST00000586320,;CTC-454I21.3,intron_variant,,ENST00000588873,;CTC-454I21.3,synonymous_variant,p.=,ENST00000585860,;CTC-454I21.3,intron_variant,,ENST00000590245,;ZNF585B,downstream_gene_variant,,ENST00000392156,;ZNF585B,downstream_gene_variant,,ENST00000591273,;ZNF585B,downstream_gene_variant,,ENST00000526705,; C ENST00000532828 Transcript synonymous_variant 504/6210 252/2310 84/769 P ccA/ccG 1 -1 ZNF585B HGNC HGNC:30948 protein_coding YES CCDS12500.1 ENSP00000433773 Q52M93 UPI00001AF01B NM_152279.3 4/5 PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF105,hmmpanther:PTHR24377,SMART_domains:SM00349 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 37189701 37189701 T C 1 0 0 0 0 0 0 0 1 18592 1451 51 5 5 ZNF585B 19 37189701 Silent SNP T C3N-01074_T 2129226 37189701 21427915 435 22424 ECH1 0 . GRCh38 19 38817487 38817487 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.438C>T p.= p.I146I ENST00000221418 4/10 267 192 75 177 177 0 strelka-varscan-mutect ECH1,synonymous_variant,p.=,ENST00000221418,NM_001398.2;AC104534.3,synonymous_variant,p.=,ENST00000594769,;ECH1,synonymous_variant,p.=,ENST00000601778,;ECH1,synonymous_variant,p.=,ENST00000595470,;AC104534.3,synonymous_variant,p.=,ENST00000602021,;LGALS4,upstream_gene_variant,,ENST00000307751,NM_006149.3;LGALS4,upstream_gene_variant,,ENST00000594209,;AC104534.2,upstream_gene_variant,,ENST00000594558,;LGALS4,upstream_gene_variant,,ENST00000597803,;ECH1,3_prime_UTR_variant,,ENST00000594164,;ECH1,non_coding_transcript_exon_variant,,ENST00000600178,;ECH1,non_coding_transcript_exon_variant,,ENST00000598707,;ECH1,non_coding_transcript_exon_variant,,ENST00000601060,;ECH1,non_coding_transcript_exon_variant,,ENST00000598316,;LGALS4,upstream_gene_variant,,ENST00000595278,;LGALS4,upstream_gene_variant,,ENST00000597153,;ECH1,upstream_gene_variant,,ENST00000594391,;ECH1,upstream_gene_variant,,ENST00000601333,; A ENST00000221418 Transcript synonymous_variant 671/1411 438/987 146/328 I atC/atT 1 -1 ECH1 HGNC HGNC:3149 protein_coding YES CCDS33014.1 ENSP00000221418 Q13011 UPI0000071141 NM_001398.2 4/10 Gene3D:3.90.226.10,Pfam_domain:PF00378,hmmpanther:PTHR11941,hmmpanther:PTHR11941:SF43,Superfamily_domains:SSF52096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 38817487 38817487 G A 1 0 0 0 0 0 0 0 1 4718 1280 45 3 3 ECH1 19 38817487 Silent SNP G C3N-01074_T 1627786 38817487 19800129 436 22425 SUPT5H 0 . GRCh38 19 39470119 39470119 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.1375G>T p.Asp459Tyr p.D459Y ENST00000599117 18/31 199 179 20 132 132 0 strelka-varscan-mutect SUPT5H,missense_variant,p.Asp459Tyr,ENST00000599117,NM_001319990.1;SUPT5H,missense_variant,p.Asp455Tyr,ENST00000359191,NM_001319991.1;SUPT5H,missense_variant,p.Asp459Tyr,ENST00000598725,NM_001319990.1,NM_003169.3;SUPT5H,missense_variant,p.Asp459Tyr,ENST00000432763,NM_001111020.2,NM_001130824.1;SUPT5H,missense_variant,p.Asp455Tyr,ENST00000402194,NM_001130825.1;SUPT5H,downstream_gene_variant,,ENST00000593727,;SUPT5H,splice_region_variant,,ENST00000599335,;SUPT5H,non_coding_transcript_exon_variant,,ENST00000598117,;SUPT5H,downstream_gene_variant,,ENST00000598520,;SUPT5H,upstream_gene_variant,,ENST00000596208,; T ENST00000599117 Transcript missense_variant,splice_region_variant 1742/3902 1375/3264 459/1087 D/Y Gac/Tac 1 1 SUPT5H HGNC HGNC:11469 protein_coding YES CCDS12536.1 ENSP00000470252 O00267 UPI000006D81A NM_001319990.1 deleterious(0) 18/31 hmmpanther:PTHR11125,PIRSF_domain:PIRSF036945 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 39470119 39470119 G T 1 0 0 0 0 1 0 0 0 15786 1188 41 2 2 SUPT5H 19 39470119 Missense_Mutation SNP G C3N-01074_T 652632 39470119 19147497 437 22426 CYP2A13 0 . GRCh38 19 41088545 41088545 + Missense_Mutation SNP G G A rs8192784 C3N-01074_T C3N-01074_N G G c.74G>A p.Arg25Gln p.R25Q ENST00000330436 1/9 256 221 35 216 216 0 strelka-varscan-mutect CYP2A13,missense_variant,p.Arg25Gln,ENST00000330436,NM_000766.4; A ENST00000330436 Transcript missense_variant 74/1739 74/1485 25/494 R/Q cGg/cAg rs8192784 1 1 CYP2A13 HGNC HGNC:2608 protein_coding YES CCDS12571.1 ENSP00000332679 Q16696 UPI000013E07A NM_000766.4 tolerated(0.2) 1/9 hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF186,Gene3D:1.10.630.10 24212786 MODERATE 1 SNV 1 1 PASS rs8192784 . 0 188 0 2 0 0 0 20 -3.321597 0 0 1 0 0 A 3 1 73 41088545 41088545 G A 1 0 0 0 0 1 0 0 0 3964 1116 39 1 1 CYP2A13 19 41088545 Missense_Mutation SNP G C3N-01074_T 1618426 41088545 17529071 438 22427 PSG3 0 . GRCh38 19 42738814 42738814 + Silent SNP G G T rs149473391 C3N-01074_T C3N-01074_N G G c.340C>A p.= p.R114R ENST00000327495 2/7 419 304 115 362 362 0 strelka-varscan-mutect PSG3,synonymous_variant,p.=,ENST00000327495,NM_021016.3;PSG3,synonymous_variant,p.=,ENST00000595140,;PSG3,synonymous_variant,p.=,ENST00000614582,;PSG3,non_coding_transcript_exon_variant,,ENST00000490592,;PSG3,synonymous_variant,p.=,ENST00000594378,;PSG3,non_coding_transcript_exon_variant,,ENST00000597009,; T ENST00000327495 Transcript synonymous_variant 525/1961 340/1287 114/428 R Cgg/Agg rs149473391,COSM381157,COSM5265929 1 -1 PSG3 HGNC HGNC:9520 protein_coding YES CCDS12611.1 ENSP00000332215 Q16557 UPI0000073DC1 NM_021016.3 2/7 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs149473391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 42738814 42738814 G T 1 0 0 0 0 0 0 0 1 12807 1115 39 1 1 PSG3 19 42738814 Silent SNP G C3N-01074_T 1650269 42738814 15878802 439 22428 PSG9 0 . GRCh38 19 43259130 43259130 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.715C>A p.Leu239Met p.L239M ENST00000270077 4/6 158 118 40 206 206 0 strelka-varscan-mutect PSG9,missense_variant,p.Leu239Met,ENST00000621109,;PSG9,missense_variant,p.Leu146Met,ENST00000418820,;PSG9,missense_variant,p.Leu239Met,ENST00000270077,NM_002784.4;PSG9,missense_variant,p.Leu146Met,ENST00000443718,NM_001301707.1;PSG9,intron_variant,,ENST00000244293,;PSG9,intron_variant,,ENST00000596730,;PSG9,intron_variant,,ENST00000593948,NM_001301708.1;PSG9,intron_variant,,ENST00000291752,NM_001301709.1;PSG9,non_coding_transcript_exon_variant,,ENST00000595404,; T ENST00000270077 Transcript missense_variant 812/1705 715/1281 239/426 L/M Ctg/Atg 1 -1 PSG9 HGNC HGNC:9526 protein_coding YES CCDS12618.1 ENSP00000270077 Q00887 UPI00001327A5 NM_002784.4 tolerated(0.25) 4/6 hmmpanther:PTHR10489 MODERATE 1 SNV 1 1 PASS . . 14 194 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 43259130 43259130 G T 1 0 0 0 0 1 0 0 0 12813 985 34 2 2 PSG9 19 43259130 Missense_Mutation SNP G C3N-01074_T 520316 43259130 15358486 440 22429 ZNF234 0 . GRCh38 19 44156467 44156467 + Missense_Mutation SNP G G A C3N-01074_T C3N-01074_N G G c.451G>A p.Asp151Asn p.D151N ENST00000426739 6/6 166 109 57 198 198 0 strelka-varscan-mutect ZNF234,missense_variant,p.Asp151Asn,ENST00000426739,NM_006630.2;ZNF234,missense_variant,p.Asp151Asn,ENST00000592437,NM_001144824.1; A ENST00000426739 Transcript missense_variant 709/4551 451/2103 151/700 D/N Gat/Aat COSM4918008 1 1 ZNF234 HGNC HGNC:13027 protein_coding YES CCDS46101.1 ENSP00000400878 Q14588 A0A024R0N3 UPI0000070C95 NM_006630.2 tolerated(1) 6/6 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 73 44156467 44156467 G A 1 0 0 0 0 1 0 0 0 18364 1290 45 3 3 ZNF234 19 44156467 Missense_Mutation SNP G C3N-01074_T 897337 44156467 14461149 441 22430 ZNF235 0 . GRCh38 19 44288971 44288971 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.464A>T p.Asp155Val p.D155V ENST00000291182 5/5 147 111 36 183 183 0 strelka-varscan-mutect ZNF235,missense_variant,p.Asp155Val,ENST00000291182,NM_004234.4;ZNF235,missense_variant,p.Asp77Val,ENST00000616224,;ZNF235,missense_variant,p.Asp240Val,ENST00000591609,;ZNF235,intron_variant,,ENST00000589799,;ZNF235,intron_variant,,ENST00000589248,;ZNF235,non_coding_transcript_exon_variant,,ENST00000587921,;ZNF235,intron_variant,,ENST00000592844,;CTC-512J12.7,upstream_gene_variant,,ENST00000605717,; A ENST00000291182 Transcript missense_variant 567/3188 464/2217 155/738 D/V gAc/gTc 1 -1 ZNF235 HGNC HGNC:12866 protein_coding YES CCDS33048.1 ENSP00000291182 Q14590 UPI00002025C2 NM_004234.4 deleterious(0.02) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 44288971 44288971 T A 1 0 0 0 0 1 0 0 0 18365 1667 58 4 4 ZNF235 19 44288971 Missense_Mutation SNP T C3N-01074_T 132504 44288971 14328645 442 22431 PNMAL2 0 . GRCh38 19 46494862 46494862 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.604C>A p.Leu202Met p.L202M ENST00000599531 1/1 322 224 98 295 293 2 strelka-varscan-mutect PNMAL2,missense_variant,p.Leu202Met,ENST00000599531,NM_020709.2;PPP5D1,intron_variant,,ENST00000602017,NM_001205281.1;CTB-158D10.3,non_coding_transcript_exon_variant,,ENST00000377652,;PNMAL2,intron_variant,,ENST00000594749,;PPP5D1,upstream_gene_variant,,ENST00000595691,; T ENST00000599531 Transcript missense_variant 1637/5308 604/1908 202/635 L/M Ctg/Atg 1 -1 PNMAL2 HGNC HGNC:29206 protein_coding YES CCDS59400.1 ENSP00000473036 Q9ULN7 UPI0000237925 NM_020709.2 deleterious(0) 1/1 hmmpanther:PTHR23095:SF25,hmmpanther:PTHR23095 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 46494862 46494862 G T 1 0 0 0 0 1 0 0 0 12266 991 35 2 2 PNMAL2 19 46494862 Missense_Mutation SNP G C3N-01074_T 2205891 46494862 12122754 443 22432 CA11 0 . GRCh38 19 48639816 48639816 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.539G>T p.Gly180Val p.G180V ENST00000084798 5/9 279 205 74 231 231 0 strelka-varscan-mutect CA11,missense_variant,p.Gly180Val,ENST00000084798,NM_001217.3;DBP,upstream_gene_variant,,ENST00000222122,NM_001352.4;DBP,upstream_gene_variant,,ENST00000601104,;CA11,upstream_gene_variant,,ENST00000596080,;SEC1P,intron_variant,,ENST00000430145,;SEC1P,intron_variant,,ENST00000474419,;SEC1P,intron_variant,,ENST00000483163,;DBP,upstream_gene_variant,,ENST00000594723,;CA11,upstream_gene_variant,,ENST00000599267,;CA11,upstream_gene_variant,,ENST00000594088,; A ENST00000084798 Transcript missense_variant 1219/1844 539/987 180/328 G/V gGc/gTc 1 -1 CA11 HGNC HGNC:1370 protein_coding YES CCDS12729.1 ENSP00000084798 O75493 UPI000004C652 NM_001217.3 deleterious(0) 5/9 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF93,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057,Superfamily_domains:SSF51069 MODERATE 1 SNV 1 1 PASS rs1280737421 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 48639816 48639816 C A 1 0 0 0 0 1 0 0 0 2198 739 26 2 2 CA11 19 48639816 Missense_Mutation SNP C C3N-01074_T 2144954 48639816 9977800 444 22433 NTN5 0 . GRCh38 19 48663520 48663520 + Missense_Mutation SNP T T A rs570039276 C3N-01074_T C3N-01074_N T T c.1048A>T p.Asn350Tyr p.N350Y ENST00000270235 6/7 202 148 54 211 211 0 strelka-varscan-mutect NTN5,missense_variant,p.Asn350Tyr,ENST00000270235,NM_145807.2;NTN5,missense_variant,p.Asn31Tyr,ENST00000596844,;SEC1P,intron_variant,,ENST00000430145,;SEC1P,intron_variant,,ENST00000474419,;SEC1P,intron_variant,,ENST00000483163,;NTN5,non_coding_transcript_exon_variant,,ENST00000600468,; A ENST00000270235 Transcript missense_variant 1144/1836 1048/1470 350/489 N/Y Aat/Tat rs570039276 1 -1 NTN5 HGNC HGNC:25208 protein_coding YES CCDS33068.1 ENSP00000270235 Q8WTR8 UPI000007032D NM_145807.2 deleterious(0.01) 6/7 PROSITE_profiles:PS50189,hmmpanther:PTHR10574,Gene3D:2.40.50.120,Superfamily_domains:SSF50242 MODERATE 1 SNV 1 1 PASS rs570039276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 48663520 48663520 T A 1 0 0 0 0 1 0 0 0 10768 1812 63 4 4 NTN5 19 48663520 Missense_Mutation SNP T C3N-01074_T 23704 48663520 9954096 445 22434 KLK5 0 . GRCh38 19 50943698 50943698 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.815C>A p.Pro272Gln p.P272Q ENST00000336334 6/6 195 133 62 154 154 0 strelka-varscan-mutect KLK5,missense_variant,p.Pro272Gln,ENST00000336334,NM_012427.4;KLK5,missense_variant,p.Pro272Gln,ENST00000391809,NM_001077491.1;KLK5,missense_variant,p.Pro272Gln,ENST00000593428,NM_001077492.1;KLK5,non_coding_transcript_exon_variant,,ENST00000595585,; T ENST00000336334 Transcript missense_variant 1168/1563 815/882 272/293 P/Q cCg/cAg 1 -1 KLK5 HGNC HGNC:6366 protein_coding YES CCDS12810.1 ENSP00000337733 Q9Y337 A0A024R4G4 UPI000003751F NM_012427.4 deleterious(0) 6/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF270,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 50943698 50943698 G T 1 0 0 0 0 1 0 0 0 8276 1116 39 1 1 KLK5 19 50943698 Missense_Mutation SNP G C3N-01074_T 2280178 50943698 7673918 446 22435 SIGLECL1 0 . GRCh38 19 51265537 51265537 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.192C>A p.= p.P64P ENST00000316401 3/6 264 213 51 211 210 1 strelka-varscan-mutect SIGLECL1,synonymous_variant,p.=,ENST00000316401,NM_173635.1;SIGLECL1,synonymous_variant,p.=,ENST00000614422,;SIGLECL1,synonymous_variant,p.=,ENST00000601727,;SIGLECL1,synonymous_variant,p.=,ENST00000597610,;SIGLECL1,intron_variant,,ENST00000597824,NM_001308437.1;SIGLECL1,downstream_gene_variant,,ENST00000596117,;CTD-3187F8.2,intron_variant,,ENST00000597569,;SIGLECL1,intron_variant,,ENST00000593968,;SIGLECL1,downstream_gene_variant,,ENST00000599553,; A ENST00000316401 Transcript synonymous_variant 573/1708 192/594 64/197 P ccC/ccA 1 1 SIGLECL1 HGNC HGNC:26856 protein_coding YES CCDS12827.1 ENSP00000321249 Q8N7X8 UPI000006D35D NM_173635.1 3/6 Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF2,Superfamily_domains:SSF48726 LOW 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 51265537 51265537 C A 1 0 0 0 0 0 0 0 1 14580 668 24 2 2 SIGLECL1 19 51265537 Silent SNP C C3N-01074_T 321839 51265537 7352079 447 22436 SIGLEC8 0 . GRCh38 19 51458089 51458089 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.299G>T p.Gly100Val p.G100V ENST00000321424 1/7 761 536 225 604 604 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Gly100Val,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Gly100Val,ENST00000430817,;SIGLEC8,missense_variant,p.Gly100Val,ENST00000340550,;SIGLEC8,upstream_gene_variant,,ENST00000597352,; A ENST00000321424 Transcript missense_variant 366/2949 299/1500 100/499 G/V gGg/gTg 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 deleterious(0) 1/7 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 51458089 51458089 C A 1 0 0 0 0 1 0 0 0 14578 623 22 2 2 SIGLEC8 19 51458089 Missense_Mutation SNP C C3N-01074_T 192552 51458089 7159527 448 22437 SIGLEC12 0 . GRCh38 19 51491645 51491645 + Missense_Mutation SNP T T A novel C3N-01074_T C3N-01074_N T T c.1784A>T p.Lys595Met p.K595M ENST00000291707 8/8 307 217 90 238 238 0 strelka-varscan-mutect SIGLEC12,missense_variant,p.Lys595Met,ENST00000291707,NM_053003.3;SIGLEC12,missense_variant,p.Lys477Met,ENST00000598614,NM_033329.2;CEACAM18,downstream_gene_variant,,ENST00000396477,NM_001278392.1;SIGLEC12,3_prime_UTR_variant,,ENST00000596742,; A ENST00000291707 Transcript missense_variant 1840/2121 1784/1788 595/595 K/M aAg/aTg 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 deleterious(0) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 51491645 51491645 T A 1 0 0 0 0 1 0 0 0 14572 1623 56 4 4 SIGLEC12 19 51491645 Missense_Mutation SNP T C3N-01074_T 33556 51491645 7125971 449 22438 HAS1 0 . GRCh38 19 51713846 51713846 + Missense_Mutation SNP C C T novel C3N-01074_T C3N-01074_N C C c.1318G>A p.Gly440Ser p.G440S ENST00000222115 5/5 320 233 87 290 289 1 strelka-varscan-mutect HAS1,missense_variant,p.Gly439Ser,ENST00000540069,NM_001297436.1;HAS1,missense_variant,p.Gly440Ser,ENST00000222115,NM_001523.3;HAS1,missense_variant,p.Gly447Ser,ENST00000601714,;HAS1,downstream_gene_variant,,ENST00000594621,;HAS1,downstream_gene_variant,,ENST00000601667,;SPACA6,downstream_gene_variant,,ENST00000573896,; T ENST00000222115 Transcript missense_variant 1353/2087 1318/1737 440/578 G/S Ggc/Agc 1 -1 HAS1 HGNC HGNC:4818 protein_coding YES CCDS12838.1 ENSP00000222115 Q92839 UPI000006D531 NM_001523.3 tolerated(0.42) 5/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 51713846 51713846 C T 1 0 0 0 0 1 0 0 0 6847 623 22 3 3 HAS1 19 51713846 Missense_Mutation SNP C C3N-01074_T 222201 51713846 6903770 450 22439 FPR1 0 . GRCh38 19 51746060 51746060 + Missense_Mutation SNP A A T novel C3N-01074_T C3N-01074_N A A c.935T>A p.Leu312Gln p.L312Q ENST00000595042 3/3 457 340 117 367 367 0 strelka-varscan-mutect FPR1,missense_variant,p.Leu312Gln,ENST00000595042,NM_001193306.1;FPR1,missense_variant,p.Leu312Gln,ENST00000304748,NM_002029.3;FPR1,downstream_gene_variant,,ENST00000600815,;FPR1,downstream_gene_variant,,ENST00000594900,; T ENST00000595042 Transcript missense_variant 1077/1965 935/1053 312/350 L/Q cTg/cAg 1 -1 FPR1 HGNC HGNC:3826 protein_coding YES CCDS12839.1 ENSP00000471493 P21462 UPI0000050484 NM_001193306.1 deleterious(0) 3/3 hmmpanther:PTHR24225:SF15,hmmpanther:PTHR24225,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00526 MODERATE 1 SNV 2 1 PASS rs1314613984 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 51746060 51746060 A T 1 0 0 0 0 1 0 0 0 5904 188 7 4 4 FPR1 19 51746060 Missense_Mutation SNP A C3N-01074_T 32214 51746060 6871556 451 22440 FPR2 0 . GRCh38 19 51769067 51769067 + Missense_Mutation SNP C C T rs763580618 C3N-01074_T C3N-01074_N C C c.409C>T p.Arg137Cys p.R137C ENST00000598776 2/2 355 255 100 350 350 0 strelka-varscan-mutect FPR2,missense_variant,p.Arg137Cys,ENST00000598776,NM_001462.3;FPR2,missense_variant,p.Arg137Cys,ENST00000340023,NM_001005738.1;FPR2,missense_variant,p.Arg137Cys,ENST00000598953,;FPR2,incomplete_terminal_codon_variant,p.=,ENST00000599326,;FPR1,intron_variant,,ENST00000594900,;FPR2,downstream_gene_variant,,ENST00000600258,;FPR2,downstream_gene_variant,,ENST00000600722,; T ENST00000598776 Transcript missense_variant 1181/2621 409/1056 137/351 R/C Cgc/Tgc rs763580618,COSM4080708 1 1 FPR2 HGNC HGNC:3827 protein_coding YES CCDS12840.1 ENSP00000468897 P25090 A0A024R4P3 UPI00000012D0 NM_001462.3 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00526,PROSITE_profiles:PS50262,hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF16,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763580618 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 51769067 51769067 C T 1 0 0 0 0 1 0 0 0 5905 652 23 1 1 FPR2 19 51769067 Missense_Mutation SNP C C3N-01074_T 23007 51769067 6848549 452 22441 LILRA1 0 . GRCh38 19 54596409 54596409 + Silent SNP G G C novel C3N-01074_T C3N-01074_N G G c.1179G>C p.= p.G393G ENST00000251372 7/10 710 486 224 575 575 0 strelka-varscan-mutect LILRA1,synonymous_variant,p.=,ENST00000251372,NM_006863.3;LILRA1,synonymous_variant,p.=,ENST00000618665,;LILRA1,intron_variant,,ENST00000453777,NM_001278318.1;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,non_coding_transcript_exon_variant,,ENST00000495417,;LILRA1,non_coding_transcript_exon_variant,,ENST00000477255,; C ENST00000251372 Transcript synonymous_variant 1361/1910 1179/1470 393/489 G ggG/ggC 1 1 LILRA1 HGNC HGNC:6602 protein_coding YES CCDS12901.1 ENSP00000251372 O75019 UPI0000034C00 NM_006863.3 7/10 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 54596409 54596409 G C 1 0 0 0 0 0 0 0 1 8693 1161 41 4 4 LILRA1 19 54596409 Silent SNP G C3N-01074_T 2827342 54596409 4021207 453 22442 NLRP7 0 . GRCh38 19 54941681 54941681 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.31C>A p.Gln11Lys p.Q11K ENST00000588756 4/13 120 109 11 149 148 1 strelka-varscan-mutect NLRP7,missense_variant,p.Gln11Lys,ENST00000588756,;NLRP7,missense_variant,p.Gln11Lys,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Gln11Lys,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Gln11Lys,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Gln11Lys,ENST00000590030,;NLRP7,missense_variant,p.Gln11Lys,ENST00000590659,;NLRP7,missense_variant,p.Gln11Lys,ENST00000587103,;NLRP7,missense_variant,p.Gln11Lys,ENST00000587844,;NLRP7,missense_variant,p.Gln11Lys,ENST00000586379,; T ENST00000588756 Transcript missense_variant 518/3826 31/3114 11/1037 Q/K Cag/Aag COSM4910748,COSM4910749,COSM4910750 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 tolerated(0.46) 4/13 Low_complexity_(Seg):seg,PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF14,hmmpanther:PTHR24106,Pfam_domain:PF02758,Gene3D:1.10.533.10,SMART_domains:SM01289,Superfamily_domains:SSF47986 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 202 6 2 0 0 0 0 -16.35847 0.9997827 1 1 1 0 T 3 4 73 54941681 54941681 G T 1 0 0 0 0 1 0 0 0 10520 1328 46 2 2 NLRP7 19 54941681 Missense_Mutation SNP G C3N-01074_T 345272 54941681 3675935 454 22443 NLRP2 0 . GRCh38 19 54982177 54982177 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.479G>T p.Cys160Phe p.C160F ENST00000543010 6/13 428 321 107 333 332 1 strelka-varscan-mutect NLRP2,missense_variant,p.Cys160Phe,ENST00000543010,NM_001174081.1;NLRP2,missense_variant,p.Cys160Phe,ENST00000448584,NM_017852.3;NLRP2,missense_variant,p.Cys138Phe,ENST00000537859,NM_001174082.1;NLRP2,missense_variant,p.Cys157Phe,ENST00000263437,;NLRP2,missense_variant,p.Cys138Phe,ENST00000339757,;NLRP2,missense_variant,p.Cys136Phe,ENST00000391721,;NLRP2,missense_variant,p.Cys137Phe,ENST00000427260,NM_001174083.1;NLRP2,missense_variant,p.Cys91Phe,ENST00000585500,;NLRP2,missense_variant,p.Cys92Phe,ENST00000397169,;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000588107,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; T ENST00000543010 Transcript missense_variant 622/3576 479/3189 160/1062 C/F tGc/tTc 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 tolerated(0.39) 6/13 hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 54982177 54982177 G T 1 0 0 0 0 1 0 0 0 10514 1319 46 2 2 NLRP2 19 54982177 Missense_Mutation SNP G C3N-01074_T 40496 54982177 3635439 455 22444 ZNF835 0 . GRCh38 19 56664336 56664336 + Frame_Shift_Del DEL G G - C3N-01074_T C3N-01074_N G G c.863delC p.Ala288GlyfsTer6 p.A288Gfs*6 ENST00000537055 2/2 353 274 79 375 375 0 sindel-varindel-pindel ZNF835,frameshift_variant,p.Ala288GlyfsTer6,ENST00000537055,NM_001005850.2;ZNF835,downstream_gene_variant,,ENST00000601659,; - ENST00000537055 Transcript frameshift_variant 1095/3450 863/1614 288/537 A/X gCg/gg COSM2971119 1 -1 ZNF835 HGNC HGNC:34332 protein_coding YES CCDS56105.1 ENSP00000444747 Q9Y2P0 UPI0000EE7244 NM_001005850.2 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF368,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 HIGH 1 deletion 2 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.998503 1 1 1 0 - 7 5 73 56664336 56664336 G - 1 0 1 0 1 0 0 0 0 18771 1087 38 0 0 ZNF835 19 56664336 Frame_Shift_Del DEL G C3N-01074_T 1682159 56664336 1953280 456 22445 ANGPT4 0 . GRCh38 20 890340 890340 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.338G>T p.Arg113Met p.R113M ENST00000381922 2/9 147 122 25 121 121 0 strelka-varscan-mutect ANGPT4,missense_variant,p.Arg113Met,ENST00000381922,NM_015985.2; A ENST00000381922 Transcript missense_variant 441/4676 338/1512 113/503 R/M aGg/aTg 1 -1 ANGPT4 HGNC HGNC:487 protein_coding YES CCDS13009.1 ENSP00000371347 Q9Y264 UPI0000062232 NM_015985.2 deleterious(0) 2/9 hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 890340 890340 C A 1 0 0 0 0 1 0 0 0 710 681 24 2 2 ANGPT4 20 890340 Missense_Mutation SNP C C3N-01074_T 890340 63553827 457 22446 TMC2 0 . GRCh38 20 2613247 2613247 + Silent SNP G G C novel C3N-01074_T C3N-01074_N G G c.1797G>C p.= p.L599L ENST00000358864 14/20 214 177 37 230 230 0 strelka-varscan-mutect TMC2,synonymous_variant,p.=,ENST00000358864,NM_080751.2;TMC2,non_coding_transcript_exon_variant,,ENST00000496948,; C ENST00000358864 Transcript synonymous_variant 1812/3169 1797/2721 599/906 L ctG/ctC 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 14/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17,Pfam_domain:PF07810 LOW 1 SNV 1 1 PASS rs1054308075 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 73 2613247 2613247 G C 1 0 0 0 0 0 0 0 1 16431 1306 46 4 4 TMC2 20 2613247 Silent SNP G C3N-01074_T 1722907 2613247 61830920 458 22447 LAMP5 0 . GRCh38 20 9529659 9529659 + Missense_Mutation SNP G G A C3N-01074_T C3N-01074_N G G c.682G>A p.Asp228Asn p.D228N ENST00000246070 6/6 104 61 43 116 116 0 strelka-varscan-mutect LAMP5,missense_variant,p.Asp228Asn,ENST00000246070,NM_012261.3;LAMP5,missense_variant,p.Asp184Asn,ENST00000427562,NM_001199897.1; A ENST00000246070 Transcript missense_variant 1174/2039 682/843 228/280 D/N Gat/Aat COSM5327010 1 1 LAMP5 HGNC HGNC:16097 protein_coding YES CCDS13106.1 ENSP00000246070 Q9UJQ1 UPI0000128675 NM_012261.3 deleterious(0.01) 6/6 hmmpanther:PTHR11506,Pfam_domain:PF01299 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 9529659 9529659 G A 1 0 0 0 0 1 0 0 0 8524 1174 41 3 3 LAMP5 20 9529659 Missense_Mutation SNP G C3N-01074_T 6916412 9529659 54914508 459 22448 NINL 0 . GRCh38 20 25476138 25476138 + Silent SNP C C T novel C3N-01074_T C3N-01074_N C C c.3153G>A p.= p.L1051L ENST00000278886 17/24 360 306 54 316 315 1 strelka-varscan-mutect NINL,synonymous_variant,p.=,ENST00000278886,NM_025176.4;NINL,intron_variant,,ENST00000422516,NM_001318226.1;NINL,intron_variant,,ENST00000336104,; T ENST00000278886 Transcript synonymous_variant 3227/4969 3153/4149 1051/1382 L ctG/ctA 1 -1 NINL HGNC HGNC:29163 protein_coding YES CCDS33452.1 ENSP00000278886 Q9Y2I6 UPI0000206B64 NM_025176.4 17/24 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18905:SF12,hmmpanther:PTHR18905 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 73 25476138 25476138 C T 1 0 0 0 0 0 0 0 1 10455 581 21 3 3 NINL 20 25476138 Silent SNP C C3N-01074_T 15946479 25476138 38968029 460 22449 TTI1 0 . GRCh38 20 38013076 38013076 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.741G>T p.Met247Ile p.M247I ENST00000373448 3/9 269 242 27 298 298 0 strelka-varscan-mutect TTI1,missense_variant,p.Met247Ile,ENST00000373448,NM_014657.2;TTI1,missense_variant,p.Met247Ile,ENST00000373447,NM_001303457.1;TTI1,missense_variant,p.Met247Ile,ENST00000449821,;TTI1,intron_variant,,ENST00000487362,; A ENST00000373448 Transcript missense_variant 980/3958 741/3270 247/1089 M/I atG/atT 1 -1 TTI1 HGNC HGNC:29029 protein_coding YES CCDS13300.1 ENSP00000362547 O43156 UPI000012DB27 NM_014657.2 deleterious(0.01) 3/9 hmmpanther:PTHR18460,Gene3D:1.25.10.10,PIRSF_domain:PIRSF005250 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 38013076 38013076 C A 1 0 0 0 0 1 0 0 0 17230 594 21 2 2 TTI1 20 38013076 Missense_Mutation SNP C C3N-01074_T 12536938 38013076 26431091 461 22450 MYBL2 0 . GRCh38 20 43699891 43699891 + Silent SNP A A G rs762020366 C3N-01074_T C3N-01074_N A A c.798A>G p.= p.T266T ENST00000217026 7/14 501 345 156 422 422 0 strelka-varscan-mutect MYBL2,synonymous_variant,p.=,ENST00000396863,NM_001278610.1;MYBL2,synonymous_variant,p.=,ENST00000217026,NM_002466.3; G ENST00000217026 Transcript synonymous_variant 925/2639 798/2103 266/700 T acA/acG rs762020366 1 1 MYBL2 HGNC HGNC:7548 protein_coding YES CCDS13322.1 ENSP00000217026 P10244 UPI000012FAE1 NM_002466.3 7/14 hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF461 LOW 1 SNV 1 1 PASS rs762020366 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 73 43699891 43699891 A G 1 0 0 0 0 0 0 0 1 10010 146 6 5 5 MYBL2 20 43699891 Silent SNP A C3N-01074_T 5686815 43699891 20744276 462 22451 OSER1 0 . GRCh38 20 44197530 44197530 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.401G>T p.Ser134Ile p.S134I ENST00000372970 6/6 473 403 70 486 486 0 strelka-varscan-mutect OSER1,missense_variant,p.Ser134Ile,ENST00000372970,;OSER1,missense_variant,p.Ser134Ile,ENST00000255174,NM_016470.7; A ENST00000372970 Transcript missense_variant 582/1616 401/879 134/292 S/I aGc/aTc 1 -1 OSER1 HGNC HGNC:16105 protein_coding YES CCDS13327.1 ENSP00000362061 Q9NX31 UPI000004A0E4 tolerated(0.19) 6/6 Pfam_domain:PF05604,hmmpanther:PTHR31383,hmmpanther:PTHR31383:SF2 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 44197530 44197530 C A 1 0 0 0 0 1 0 0 0 11353 797 28 2 2 OSER1 20 44197530 Missense_Mutation SNP C C3N-01074_T 497639 44197530 20246637 463 22452 PREX1 0 . GRCh38 20 48642490 48642490 + Splice_Site SNP C C T novel C3N-01074_T C3N-01074_N C C c.3602-1G>A p.X1201_splice ENST00000371941 59 47 12 71 71 0 strelka-mutect PREX1,splice_acceptor_variant,,ENST00000371941,NM_020820.3;PREX1,non_coding_transcript_exon_variant,,ENST00000496915,;PREX1,splice_acceptor_variant,,ENST00000482556,; T ENST00000371941 Transcript splice_acceptor_variant -/6636 3602/4980 1201/1659 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 27/39 HIGH 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 73 48642490 48642490 C T 1 0 0 0 0 0 0 1 0 12610 695 24 3 3 PREX1 20 48642490 Splice_Site SNP C C3N-01074_T 4444960 48642490 15801677 464 22453 SALL4 0 . GRCh38 20 51791357 51791357 + Nonsense_Mutation SNP C C A C3N-01074_T C3N-01074_N C C c.1126G>T p.Glu376Ter p.E376* ENST00000217086 2/4 439 354 85 510 510 0 strelka-varscan-mutect SALL4,stop_gained,p.Glu376Ter,ENST00000217086,NM_020436.3;SALL4,stop_gained,p.Glu376Ter,ENST00000395997,;SALL4,intron_variant,,ENST00000371539,;SALL4,downstream_gene_variant,,ENST00000483130,;SALL4,downstream_gene_variant,,ENST00000481363,; A ENST00000217086 Transcript stop_gained 1238/5208 1126/3162 376/1053 E/* Gag/Tag COSM1240123 1 -1 SALL4 HGNC HGNC:15924 protein_coding YES CCDS13438.1 ENSP00000217086 Q9UJQ4 UPI0000135527 NM_020436.3 2/4 hmmpanther:PTHR23233:SF19,hmmpanther:PTHR23233 1 HIGH 1 SNV 1 1 1 PASS rs1428338003 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 73 51791357 51791357 C A 1 0 0 0 0 0 1 0 0 14072 893 31 1 1 SALL4 20 51791357 Nonsense_Mutation SNP C C3N-01074_T 3148867 51791357 12652810 465 22454 CASS4 0 . GRCh38 20 56450616 56450616 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.579G>T p.Gln193His p.Q193H ENST00000360314 5/7 236 154 82 265 264 1 strelka-varscan-mutect CASS4,missense_variant,p.Gln193His,ENST00000434344,NM_001164115.1;CASS4,missense_variant,p.Gln193His,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; T ENST00000360314 Transcript missense_variant 804/2619 579/2361 193/786 Q/H caG/caT 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 deleterious(0) 5/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 56450616 56450616 G T 1 0 0 0 0 1 0 0 0 2382 1020 36 2 2 CASS4 20 56450616 Missense_Mutation SNP G C3N-01074_T 4659259 56450616 7993551 466 22455 SYCP2 0 . GRCh38 20 59881021 59881021 + Missense_Mutation SNP A A T rs535578209 C3N-01074_T C3N-01074_N A A c.2717T>A p.Val906Glu p.V906E ENST00000357552 30/45 133 99 34 194 194 0 strelka-varscan-mutect SYCP2,missense_variant,p.Val906Glu,ENST00000357552,;SYCP2,missense_variant,p.Val906Glu,ENST00000371001,NM_014258.2;SYCP2,missense_variant,p.Val906Glu,ENST00000446834,;SYCP2,splice_region_variant,,ENST00000474749,; T ENST00000357552 Transcript missense_variant,splice_region_variant 2943/5567 2717/4593 906/1530 V/E gTa/gAa rs535578209 1 -1 SYCP2 HGNC HGNC:11490 protein_coding YES CCDS13482.1 ENSP00000350162 Q9BX26 UPI0000135683 tolerated(0.1) 30/45 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12 MODERATE 1 SNV 1 1 PASS rs535578209 . 1 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 59881021 59881021 A T 1 0 0 0 0 1 0 0 0 15822 405 14 4 4 SYCP2 20 59881021 Missense_Mutation SNP A C3N-01074_T 3430405 59881021 4563146 467 22456 COL20A1 0 . GRCh38 20 63321098 63321098 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.3239C>A p.Pro1080Gln p.P1080Q ENST00000358894 26/36 204 124 80 145 145 0 strelka-varscan-mutect COL20A1,missense_variant,p.Pro1087Gln,ENST00000422202,;COL20A1,missense_variant,p.Pro1080Gln,ENST00000358894,NM_020882.2;COL20A1,missense_variant,p.Pro183Gln,ENST00000415763,;COL20A1,missense_variant,p.Pro88Gln,ENST00000455906,;COL20A1,splice_region_variant,,ENST00000479501,;COL20A1,upstream_gene_variant,,ENST00000471582,; A ENST00000358894 Transcript missense_variant,splice_region_variant 3339/4172 3239/3855 1080/1284 P/Q cCa/cAa 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 deleterious(0) 26/36 Pfam_domain:PF01391,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF131,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 63321098 63321098 C A 1 0 0 0 0 1 0 0 0 3467 608 21 2 2 COL20A1 20 63321098 Missense_Mutation SNP C C3N-01074_T 3440077 63321098 1123069 468 22457 TPTE 0 . GRCh38 21 10596040 10596041 + Frame_Shift_Ins INS - - A novel C3N-01074_T C3N-01074_N - - c.1231dupA p.Arg411LysfsTer20 p.R411Kfs*20 ENST00000618007 20/24 454 398 56 553 553 0 sindel-varindel-pindel TPTE,frameshift_variant,p.Arg393LysfsTer20,ENST00000622113,NM_199259.3;TPTE,frameshift_variant,p.Arg411LysfsTer20,ENST00000618007,NM_199261.3;TPTE,frameshift_variant,p.Arg373LysfsTer20,ENST00000427445,NM_199260.3;TPTE,frameshift_variant,p.Arg273LysfsTer20,ENST00000612746,NM_001290224.1;AL078471.5,intron_variant,,ENST00000612267,; A ENST00000618007 Transcript frameshift_variant 1559-1560/2150 1229-1230/1656 410/551 P/PX cca/ccAa 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 20/24 hmmpanther:PTHR12305:SF56,hmmpanther:PTHR12305,Pfam_domain:PF10409,SMART_domains:SM01326,Superfamily_domains:SSF49562 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 73 10596040 10596040 - A 1 0 1 1 0 0 0 0 0 16911 594 21 0 0 TPTE 21 10596040 Frame_Shift_Ins INS - C3N-01074_T 10596040 36113943 469 22458 MRPL39 0 . GRCh38 21 25592944 25592944 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.789G>T p.= p.V263V ENST00000307301 8/11 102 57 45 186 186 0 strelka-varscan-mutect MRPL39,synonymous_variant,p.=,ENST00000307301,NM_080794.3;MRPL39,synonymous_variant,p.=,ENST00000352957,NM_017446.3;MRPL39,synonymous_variant,p.=,ENST00000419219,; A ENST00000307301 Transcript synonymous_variant 831/1199 789/1062 263/353 V gtG/gtT 1 -1 MRPL39 HGNC HGNC:14027 protein_coding YES CCDS33522.1 ENSP00000305682 Q9NYK5 UPI00001AEAC0 NM_080794.3 8/11 Gene3D:1tkeA03,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF34,Superfamily_domains:SSF55186 LOW 1 SNV 5 1 PASS rs1457476495 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 25592944 25592944 C A 1 0 0 0 0 0 0 0 1 9777 813 29 2 2 MRPL39 21 25592944 Silent SNP C C3N-01074_T 14996904 25592944 21117039 470 22459 SYNJ1 0 . GRCh38 21 32684120 32684120 + Splice_Site SNP C C A novel C3N-01074_T C3N-01074_N C C c.1236-1G>T p.X412_splice ENST00000433931 252 181 71 225 225 0 strelka-varscan-mutect SYNJ1,splice_acceptor_variant,,ENST00000382499,NM_203446.2;SYNJ1,splice_acceptor_variant,,ENST00000357345,NM_001160302.1;SYNJ1,splice_acceptor_variant,,ENST00000382491,;SYNJ1,splice_acceptor_variant,,ENST00000630077,NM_001160306.1;SYNJ1,splice_acceptor_variant,,ENST00000433931,NM_003895.3;SYNJ1,splice_acceptor_variant,,ENST00000429236,; A ENST00000433931 Transcript splice_acceptor_variant -/4852 1236/4839 412/1612 1 -1 SYNJ1 HGNC HGNC:11503 protein_coding YES CCDS33539.2 ENSP00000409667 J3KQV8 UPI0001A47572 NM_003895.3 9/31 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 73 32684120 32684120 C A 1 0 0 0 0 0 0 1 0 15846 927 32 2 2 SYNJ1 21 32684120 Splice_Site SNP C C3N-01074_T 7091176 32684120 14025863 471 22460 LSS 0 . GRCh38 21 46209617 46209617 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.1203G>T p.= p.G401G ENST00000397728 13/22 172 124 48 127 127 0 strelka-varscan-mutect LSS,synonymous_variant,p.=,ENST00000397728,NM_002340.5;LSS,synonymous_variant,p.=,ENST00000457828,NM_001145437.1;LSS,synonymous_variant,p.=,ENST00000356396,NM_001001438.2;LSS,synonymous_variant,p.=,ENST00000522411,NM_001145436.1; A ENST00000397728 Transcript synonymous_variant 1282/4936 1203/2199 401/732 G ggG/ggT 1 -1 LSS HGNC HGNC:6708 protein_coding YES CCDS13733.1 ENSP00000380837 P48449 UPI000012A14D NM_002340.5 13/22 Gene3D:1.50.10.20,Pfam_domain:PF13243,hmmpanther:PTHR11764,hmmpanther:PTHR11764:SF20,Superfamily_domains:SSF48239,TIGRFAM_domain:TIGR01787 LOW 1 SNV 1 1 PASS rs1426778237 . 0 205 0 5 0 0 0 0 -20 0.9998601 1 1 1 0 A 2 1 73 46209617 46209617 C A 1 0 0 0 0 0 0 0 1 8972 726 26 2 2 LSS 21 46209617 Silent SNP C C3N-01074_T 13525497 46209617 500366 472 22461 MICAL3 0 . GRCh38 22 17818490 17818490 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.4171C>A p.Leu1391Met p.L1391M ENST00000441493 26/32 174 146 28 209 209 0 strelka-varscan-mutect MICAL3,missense_variant,p.Leu1391Met,ENST00000441493,NM_015241.2;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,; T ENST00000441493 Transcript missense_variant 4524/9445 4171/6009 1391/2002 L/M Ctg/Atg 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 tolerated_low_confidence(0.07) 26/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF239 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 17818490 17818490 G T 1 0 0 0 0 1 0 0 0 9528 991 35 2 2 MICAL3 22 17818490 Missense_Mutation SNP G C3N-01074_T 17818490 32999978 473 22462 TPST2 0 . GRCh38 22 26541613 26541613 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.18G>T p.= p.R6R ENST00000338754 3/7 180 135 45 191 191 0 strelka-varscan-mutect TPST2,synonymous_variant,p.=,ENST00000338754,NM_003595.3;TPST2,synonymous_variant,p.=,ENST00000403880,;TPST2,synonymous_variant,p.=,ENST00000398110,NM_001008566.1;TPST2,synonymous_variant,p.=,ENST00000442495,;TPST2,synonymous_variant,p.=,ENST00000454778,;TPST2,synonymous_variant,p.=,ENST00000440953,;TPST2,synonymous_variant,p.=,ENST00000450022,;TPST2,synonymous_variant,p.=,ENST00000453117,;TPST2,upstream_gene_variant,,ENST00000445720,; A ENST00000338754 Transcript synonymous_variant 289/5697 18/1134 6/377 R cgG/cgT 1 -1 TPST2 HGNC HGNC:12021 protein_coding YES CCDS13839.1 ENSP00000339813 O60704 A0A024R1G9 UPI0000000C23 NM_003595.3 3/7 hmmpanther:PTHR12788,hmmpanther:PTHR12788:SF5,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 26541613 26541613 C A 1 0 0 0 0 0 0 0 1 16909 842 30 2 2 TPST2 22 26541613 Silent SNP C C3N-01074_T 8723123 26541613 24276855 474 22463 CRYBB1 0 . GRCh38 22 26616140 26616140 + Missense_Mutation SNP C C G novel C3N-01074_T C3N-01074_N C C c.180G>C p.Arg60Ser p.R60S ENST00000215939 2/6 385 312 73 377 377 0 strelka-varscan-mutect CRYBB1,missense_variant,p.Arg60Ser,ENST00000215939,NM_001887.3; G ENST00000215939 Transcript missense_variant,splice_region_variant 311/1102 180/759 60/252 R/S agG/agC 1 -1 CRYBB1 HGNC HGNC:2397 protein_coding YES CCDS13840.1 ENSP00000215939 P53674 UPI000000165D NM_001887.3 deleterious(0.01) 2/6 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF12,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 26616140 26616140 C G 1 0 0 0 0 1 0 0 0 3712 637 22 4 4 CRYBB1 22 26616140 Missense_Mutation SNP C C3N-01074_T 74527 26616140 24202328 475 22464 BPIFC 0 . GRCh38 22 32435809 32435809 + Silent SNP G G A novel C3N-01074_T C3N-01074_N G G c.819C>T p.= p.R273R ENST00000397452 9/16 274 234 40 285 285 0 strelka-varscan-mutect BPIFC,synonymous_variant,p.=,ENST00000397452,;BPIFC,synonymous_variant,p.=,ENST00000300399,NM_174932.2;BPIFC,synonymous_variant,p.=,ENST00000534972,; A ENST00000397452 Transcript synonymous_variant 930/2091 819/1524 273/507 R cgC/cgT 1 -1 BPIFC HGNC HGNC:16503 protein_coding YES CCDS13906.1 ENSP00000380594 Q8NFQ6 UPI0000071B53 9/16 hmmpanther:PTHR10504:SF17,hmmpanther:PTHR10504,Pfam_domain:PF02886,PIRSF_domain:PIRSF002417,Gene3D:1ewfA02,SMART_domains:SM00329,Superfamily_domains:SSF55394 LOW 1 SNV 5 1 PASS rs1363259632 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 32435809 32435809 G A 1 0 0 0 0 0 0 0 1 1662 1306 46 3 3 BPIFC 22 32435809 Silent SNP G C3N-01074_T 5819669 32435809 18382659 476 22465 FAM227A 0 . GRCh38 22 38599818 38599818 + Missense_Mutation SNP T T G novel C3N-01074_T C3N-01074_N T T c.1310A>C p.Gln437Pro p.Q437P ENST00000355830 14/19 169 142 27 184 184 0 strelka-varscan-mutect FAM227A,missense_variant,p.Gln442Pro,ENST00000535113,NM_001291030.1,NM_001013647.1;FAM227A,missense_variant,p.Gln437Pro,ENST00000355830,;FAM227A,non_coding_transcript_exon_variant,,ENST00000540952,;FAM227A,non_coding_transcript_exon_variant,,ENST00000544346,;FAM227A,non_coding_transcript_exon_variant,,ENST00000541689,; G ENST00000355830 Transcript missense_variant 1606/2417 1310/1941 437/646 Q/P cAg/cCg 1 -1 FAM227A HGNC HGNC:44197 protein_coding YES ENSP00000348086 A0A0A0MRD0 UPI000165DBC2 tolerated(0.42) 14/19 hmmpanther:PTHR33560,hmmpanther:PTHR33560:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 38599818 38599818 T G 1 0 0 0 0 1 0 0 0 5418 1580 55 5 5 FAM227A 22 38599818 Missense_Mutation SNP T C3N-01074_T 6164009 38599818 12218650 477 22466 MAGEB5 0 . GRCh38 X 26217994 26217994 + Silent SNP C C A novel C3N-01074_T C3N-01074_N C C c.693C>A p.= p.A231A ENST00000602297 2/2 149 83 66 188 188 0 strelka-varscan-mutect MAGEB5,synonymous_variant,p.=,ENST00000602297,NM_001271752.1; A ENST00000602297 Transcript synonymous_variant 940/1216 693/828 231/275 A gcC/gcA 1 1 MAGEB5 HGNC HGNC:23795 protein_coding YES CCDS65233.1 ENSP00000473493 Q9BZ81 UPI0000237754 NM_001271752.1 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF35 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 26217994 26217994 C A 1 0 0 0 0 0 0 0 1 9095 668 24 2 2 MAGEB5 23 26217994 Silent SNP C C3N-01074_T 26217994 129822901 478 22467 MED14 0 . GRCh38 X 40654458 40654458 + Silent SNP T T A novel C3N-01074_T C3N-01074_N T T c.4197A>T p.= p.A1399A ENST00000324817 30/31 198 104 94 195 195 0 strelka-varscan-mutect MED14,synonymous_variant,p.=,ENST00000324817,NM_004229.3;MED14,synonymous_variant,p.=,ENST00000433003,;MED14,synonymous_variant,p.=,ENST00000416199,;MED14,downstream_gene_variant,,ENST00000472736,; A ENST00000324817 Transcript synonymous_variant 4316/7984 4197/4365 1399/1454 A gcA/gcT 1 -1 MED14 HGNC HGNC:2370 protein_coding YES CCDS14254.1 ENSP00000323720 O60244 UPI00001414B1 NM_004229.3 30/31 hmmpanther:PTHR12809 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 73 40654458 40654458 T A 1 0 0 0 0 0 0 0 1 9371 1567 55 4 4 MED14 23 40654458 Silent SNP T C3N-01074_T 14436464 40654458 115386437 479 22468 TSPYL2 0 . GRCh38 X 53083189 53083189 + Missense_Mutation SNP A A G novel C3N-01074_T C3N-01074_N A A c.691A>G p.Ile231Val p.I231V ENST00000375442 1/7 255 180 75 264 264 0 strelka-varscan-mutect TSPYL2,missense_variant,p.Ile231Val,ENST00000375442,NM_022117.3;TSPYL2,intron_variant,,ENST00000579390,;GPR173,downstream_gene_variant,,ENST00000332582,NM_018969.5;TSPYL2,missense_variant,p.Ile67Val,ENST00000578306,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000556808,;TSPYL2,non_coding_transcript_exon_variant,,ENST00000553557,;TSPYL2,upstream_gene_variant,,ENST00000463525,; G ENST00000375442 Transcript missense_variant 823/2815 691/2082 231/693 I/V Atc/Gtc 1 1 TSPYL2 HGNC HGNC:24358 protein_coding YES CCDS14350.1 ENSP00000364591 Q9H2G4 UPI000004B6D6 NM_022117.3 tolerated(0.08) 1/7 hmmpanther:PTHR11875,hmmpanther:PTHR11875:SF72,Superfamily_domains:SSF143113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 73 53083189 53083189 A G 1 0 0 0 0 1 0 0 0 17167 217 8 5 5 TSPYL2 23 53083189 Missense_Mutation SNP A C3N-01074_T 12428731 53083189 102957706 480 22469 TRO 0 . GRCh38 X 54929435 54929435 + Missense_Mutation SNP G G T C3N-01074_T C3N-01074_N G G c.2711G>T p.Ser904Ile p.S904I ENST00000173898 12/13 90 59 31 145 145 0 strelka-varscan-mutect TRO,missense_variant,p.Ser904Ile,ENST00000173898,NM_001039705.2;TRO,missense_variant,p.Ser435Ile,ENST00000420798,NM_001271183.1;TRO,missense_variant,p.Ser507Ile,ENST00000375041,NM_001271184.1;TRO,intron_variant,,ENST00000319167,NM_016157.3;TRO,intron_variant,,ENST00000375022,NM_177556.2;TRO,intron_variant,,ENST00000622017,;TRO,intron_variant,,ENST00000399736,NM_177557.2;PFKFB1,downstream_gene_variant,,ENST00000375006,NM_001271804.1,NM_002625.3;PFKFB1,downstream_gene_variant,,ENST00000545676,NM_001271805.1;PFKFB1,downstream_gene_variant,,ENST00000614686,;PFKFB1,downstream_gene_variant,,ENST00000374992,;TRO,downstream_gene_variant,,ENST00000431115,;SNORA11,downstream_gene_variant,,ENST00000408823,;TRO,intron_variant,,ENST00000475183,;TRO,downstream_gene_variant,,ENST00000484031,;TRO,downstream_gene_variant,,ENST00000492142,;TRO,non_coding_transcript_exon_variant,,ENST00000492706,;TRO,intron_variant,,ENST00000445561,;TRO,downstream_gene_variant,,ENST00000469211,; T ENST00000173898 Transcript missense_variant 2823/4647 2711/4296 904/1431 S/I aGc/aTc COSM4772339 1 1 TRO HGNC HGNC:12326 protein_coding YES CCDS43959.1 ENSP00000173898 Q12816 UPI000021208F NM_001039705.2 deleterious(0) 12/13 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 54929435 54929435 G T 1 0 0 0 0 1 0 0 0 17079 971 34 2 2 TRO 23 54929435 Missense_Mutation SNP G C3N-01074_T 1846246 54929435 101111460 481 22470 FAM46D 0 . GRCh38 X 80443119 80443119 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.580C>A p.Leu194Ile p.L194I ENST00000538312 5/5 141 104 37 156 156 0 strelka-varscan-mutect FAM46D,missense_variant,p.Leu194Ile,ENST00000538312,NM_001170574.1;FAM46D,missense_variant,p.Leu194Ile,ENST00000308293,NM_152630.4; A ENST00000538312 Transcript missense_variant 914/3106 580/1170 194/389 L/I Cta/Ata 1 1 FAM46D HGNC HGNC:28399 protein_coding YES CCDS14446.1 ENSP00000443410 Q8NEK8 UPI0000073CF3 NM_001170574.1 tolerated(0.32) 5/5 hmmpanther:PTHR12974:SF30,hmmpanther:PTHR12974,Pfam_domain:PF07984,SMART_domains:SM01153 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 80443119 80443119 C A 1 0 0 0 0 1 0 0 0 5446 796 28 2 2 FAM46D 23 80443119 Missense_Mutation SNP C C3N-01074_T 25513684 80443119 75597776 482 22471 PCDH11X 0 . GRCh38 X 91878657 91878657 + Missense_Mutation SNP C C A novel C3N-01074_T C3N-01074_N C C c.2417C>A p.Pro806Gln p.P806Q ENST00000373094 2/7 223 106 117 217 217 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Pro806Gln,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Pro806Gln,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Pro806Gln,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Pro806Gln,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Pro806Gln,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Pro806Gln,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Pro806Gln,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; A ENST00000373094 Transcript missense_variant 3262/9179 2417/4044 806/1347 P/Q cCa/cAa 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 tolerated(0.32) 2/7 Pfam_domain:PF08374,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 73 91878657 91878657 C A 1 0 0 0 0 1 0 0 0 11595 594 21 2 2 PCDH11X 23 91878657 Missense_Mutation SNP C C3N-01074_T 11435538 91878657 64162238 483 22472 INTS6L 0 . GRCh38 X 135577355 135577355 + Nonsense_Mutation SNP G G T rs138551817 C3N-01074_T C3N-01074_N G G c.1936G>T p.Gly646Ter p.G646* ENST00000370752 14/17 259 215 44 195 195 0 strelka-varscan-mutect INTS6L,stop_gained,p.Gly646Ter,ENST00000370752,NM_182540.4;INTS6L,intron_variant,,ENST00000481908,;INTS6L,upstream_gene_variant,,ENST00000481429,;INTS6L,upstream_gene_variant,,ENST00000494957,;INTS6L,intron_variant,,ENST00000493637,; T ENST00000370752 Transcript stop_gained 2270/3793 1936/2586 646/861 G/* Gga/Tga rs138551817 1 1 INTS6L HGNC HGNC:27334 protein_coding YES CCDS35401.1 ENSP00000359788 Q5JSJ4 UPI00004A3AAF NM_182540.4 14/17 hmmpanther:PTHR12957,hmmpanther:PTHR12957:SF22 HIGH 1 SNV 1 1 PASS rs138551817 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 73 135577355 135577355 G T 1 0 0 0 0 0 1 0 0 7685 1117 39 1 1 INTS6L 23 135577355 Nonsense_Mutation SNP G C3N-01074_T 43698698 135577355 20463540 484 22473 GPR50 0 . GRCh38 X 151180235 151180235 + Missense_Mutation SNP G G T novel C3N-01074_T C3N-01074_N G G c.652G>T p.Ala218Ser p.A218S ENST00000218316 2/2 141 51 90 116 116 0 strelka-varscan-mutect GPR50,missense_variant,p.Ala218Ser,ENST00000218316,NM_004224.3;AF003625.3,upstream_gene_variant,,ENST00000602313,;GPR50-AS1,upstream_gene_variant,,ENST00000454196,; T ENST00000218316 Transcript missense_variant 721/1951 652/1854 218/617 A/S Gcc/Tcc 1 1 GPR50 HGNC HGNC:4506 protein_coding YES CCDS44012.1 ENSP00000218316 Q13585 UPI000013C755 NM_004224.3 tolerated(0.18) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF51,hmmpanther:PTHR24242,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01151 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 73 151180235 151180235 G T 1 0 0 0 0 1 0 0 0 6582 1203 42 2 2 GPR50 23 151180235 Missense_Mutation SNP G C3N-01074_T 15602880 151180235 4860660 485 22474 AGRN 0 . GRCh38 1 1046904 1046904 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.3335G>T p.Cys1112Phe p.C1112F ENST00000379370 19/36 225 179 46 177 177 0 strelka-varscan-mutect AGRN,missense_variant,p.Cys974Phe,ENST00000620552,NM_001305275.1;AGRN,missense_variant,p.Cys1112Phe,ENST00000379370,NM_198576.3;AGRN,upstream_gene_variant,,ENST00000419249,;AGRN,upstream_gene_variant,,ENST00000492947,;AGRN,downstream_gene_variant,,ENST00000479707,;AGRN,upstream_gene_variant,,ENST00000466223,;AGRN,upstream_gene_variant,,ENST00000478677,; T ENST00000379370 Transcript missense_variant 3385/7323 3335/6138 1112/2045 C/F tGc/tTc 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 deleterious(0) 19/36 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 1046904 1046904 G T 1 0 0 0 0 1 0 0 0 476 1319 46 2 2 AGRN 1 1046904 Missense_Mutation SNP G C3N-01405_T 1046904 247909518 1 22475 TNFRSF9 0 . GRCh38 1 7937697 7937697 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.406T>C p.Trp136Arg p.W136R ENST00000615230 6/9 150 128 22 147 147 0 strelka-varscan-mutect TNFRSF9,missense_variant,p.Trp136Arg,ENST00000615230,NM_001561.5;TNFRSF9,missense_variant,p.Trp136Arg,ENST00000377507,;TNFRSF9,upstream_gene_variant,,ENST00000474475,;TNFRSF9,missense_variant,p.Trp58Arg,ENST00000492571,;RP5-892F13.2,upstream_gene_variant,,ENST00000603760,; G ENST00000615230 Transcript missense_variant 667/5970 406/768 136/255 W/R Tgg/Cgg 1 -1 TNFRSF9 HGNC HGNC:11924 protein_coding YES CCDS92.1 ENSP00000478699 Q07011 UPI00001370F1 NM_001561.5 deleterious(0) 6/9 hmmpanther:PTHR23097,hmmpanther:PTHR23097:SF136,Gene3D:2.10.50.10,SMART_domains:SM00208,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 7937697 7937697 A G 1 0 0 0 0 1 0 0 0 16774 188 7 5 5 TNFRSF9 1 7937697 Missense_Mutation SNP A C3N-01405_T 6890793 7937697 241018725 2 22476 CASZ1 0 . GRCh38 1 10654053 10654053 + Silent SNP G G A rs763713117 C3N-01405_T C3N-01405_N G G c.2004C>T p.= p.F668F ENST00000377022 11/21 316 275 41 249 249 0 strelka-varscan-mutect CASZ1,synonymous_variant,p.=,ENST00000377022,NM_001079843.2;CASZ1,synonymous_variant,p.=,ENST00000344008,NM_017766.4;RP4-734G22.3,non_coding_transcript_exon_variant,,ENST00000606802,;CASZ1,non_coding_transcript_exon_variant,,ENST00000496432,;CASZ1,downstream_gene_variant,,ENST00000492173,;CASZ1,upstream_gene_variant,,ENST00000490176,; A ENST00000377022 Transcript synonymous_variant 2322/7936 2004/5280 668/1759 F ttC/ttT rs763713117 1 -1 CASZ1 HGNC HGNC:26002 protein_coding YES CCDS41246.1 ENSP00000366221 Q86V15 UPI0000EBB7D6 NM_001079843.2 11/21 PROSITE_profiles:PS50157,hmmpanther:PTHR12451,hmmpanther:PTHR12451:SF0,SMART_domains:SM00355 LOW 1 SNV 1 1 PASS rs763713117 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 10654053 10654053 G A 1 0 0 0 0 0 0 0 1 2384 1165 41 3 3 CASZ1 1 10654053 Silent SNP G C3N-01405_T 2716356 10654053 238302369 3 22477 TAS1R2 0 . GRCh38 1 18841753 18841753 + Missense_Mutation SNP C C A rs148798381 C3N-01405_T C3N-01405_N C C c.1567G>T p.Gly523Cys p.G523C ENST00000375371 5/6 94 77 17 82 82 0 strelka-varscan-mutect TAS1R2,missense_variant,p.Gly523Cys,ENST00000375371,NM_152232.2; A ENST00000375371 Transcript missense_variant 1589/2542 1567/2520 523/839 G/C Ggc/Tgc rs148798381 1 -1 TAS1R2 HGNC HGNC:14905 protein_coding YES CCDS187.1 ENSP00000364520 Q8TE23 UPI0000456168 NM_152232.2 deleterious(0) 5/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF441,PROSITE_patterns:PS00980,Pfam_domain:PF07562 MODERATE 1 SNV 2 1 PASS rs148798381 . 0 199 10 0 0 0 0 0 -20 0.9999878 1 1 1 0 A 3 1 74 18841753 18841753 C A 1 0 0 0 0 1 0 0 0 15962 652 23 1 1 TAS1R2 1 18841753 Missense_Mutation SNP C C3N-01405_T 8187700 18841753 230114669 4 22478 HNRNPR 0 . GRCh38 1 23310999 23310999 + Missense_Mutation SNP C C G rs748400587 C3N-01405_T C3N-01405_N C C c.1366G>C p.Gly456Arg p.G456R ENST00000374616 11/11 224 202 22 186 186 0 strelka-varscan-mutect HNRNPR,missense_variant,p.Gly355Arg,ENST00000478691,NM_001102399.2,NM_001297621.1,NM_001102397.2;HNRNPR,missense_variant,p.Gly453Arg,ENST00000374612,NM_005826.4;HNRNPR,missense_variant,p.Gly456Arg,ENST00000374616,NM_001102398.2;HNRNPR,missense_variant,p.Gly453Arg,ENST00000302271,;HNRNPR,missense_variant,p.Gly314Arg,ENST00000606561,NM_001297622.1;HNRNPR,missense_variant,p.Gly415Arg,ENST00000427764,NM_001297620.1;HNRNPR,non_coding_transcript_exon_variant,,ENST00000476660,;HNRNPR,downstream_gene_variant,,ENST00000463552,;HNRNPR,downstream_gene_variant,,ENST00000470941,;HNRNPR,upstream_gene_variant,,ENST00000464516,; G ENST00000374616 Transcript missense_variant 1475/2691 1366/1911 456/636 G/R Ggg/Cgg rs748400587,COSM425655,COSM425656 1 -1 HNRNPR HGNC HGNC:5047 protein_coding YES CCDS44085.1 ENSP00000363745 O43390 UPI000006F30B NM_001102398.2 tolerated(0.43) 11/11 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF482,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR01648 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748400587 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 23310999 23310999 C G 1 0 0 0 0 1 0 0 0 7167 594 21 4 4 HNRNPR 1 23310999 Missense_Mutation SNP C C3N-01405_T 4469246 23310999 225645423 5 22479 SLC9A1 0 . GRCh38 1 27102099 27102099 + Missense_Mutation SNP G G A C3N-01405_T C3N-01405_N G G c.1852C>T p.Arg618Cys p.R618C ENST00000263980 9/12 278 248 30 245 245 0 strelka-varscan-mutect SLC9A1,missense_variant,p.Arg618Cys,ENST00000263980,NM_003047.4;SLC9A1,downstream_gene_variant,,ENST00000374086,;SLC9A1,upstream_gene_variant,,ENST00000490329,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000374089,;SLC9A1,non_coding_transcript_exon_variant,,ENST00000447808,; A ENST00000263980 Transcript missense_variant 2428/4516 1852/2448 618/815 R/C Cgc/Tgc COSM907817 1 -1 SLC9A1 HGNC HGNC:11071 protein_coding YES CCDS295.1 ENSP00000263980 P19634 UPI000012FD1B NM_003047.4 deleterious(0) 9/12 Pfam_domain:PF16644,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF59,TIGRFAM_domain:TIGR00840 1 MODERATE 1 SNV 1 1 1 PASS rs1189050207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 27102099 27102099 G A 1 0 0 0 0 1 0 0 0 14993 1087 38 1 1 SLC9A1 1 27102099 Missense_Mutation SNP G C3N-01405_T 3791100 27102099 221854323 6 22480 ADGRB2 0 . GRCh38 1 31741886 31741886 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1499G>T p.Arg500Leu p.R500L ENST00000373655 9/33 78 60 18 49 49 0 strelka-varscan-mutect ADGRB2,missense_variant,p.Arg500Leu,ENST00000373658,;ADGRB2,missense_variant,p.Arg500Leu,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Arg433Leu,ENST00000398542,;ADGRB2,missense_variant,p.Arg500Leu,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Arg448Leu,ENST00000398556,;ADGRB2,missense_variant,p.Arg433Leu,ENST00000398547,;ADGRB2,missense_variant,p.Arg488Leu,ENST00000398538,;ADGRB2,missense_variant,p.Arg438Leu,ENST00000420125,;ADGRB2,missense_variant,p.Arg479Leu,ENST00000533175,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000530134,;ADGRB2,downstream_gene_variant,,ENST00000468430,;ADGRB2,upstream_gene_variant,,ENST00000466109,; A ENST00000373655 Transcript missense_variant 1841/5400 1499/4755 500/1584 R/L cGc/cTc 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 deleterious(0.01) 9/33 PROSITE_profiles:PS50092,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF41,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS rs1222903561 . 0 194 13 3 0 0 0 0 -20 0.9974358 1 1 1 0 A 3 1 74 31741886 31741886 C A 1 0 0 0 0 1 0 0 0 356 768 27 1 1 ADGRB2 1 31741886 Missense_Mutation SNP C C3N-01405_T 4639787 31741886 217214536 7 22481 GJB4 0 . GRCh38 1 34761791 34761791 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.537G>T p.= p.R179R ENST00000339480 2/2 282 241 41 230 230 0 strelka-varscan-mutect GJB4,synonymous_variant,p.=,ENST00000339480,NM_153212.2;GJB5,downstream_gene_variant,,ENST00000338513,NM_005268.3;RP1-34M23.5,non_coding_transcript_exon_variant,,ENST00000542839,;SMIM12,intron_variant,,ENST00000426886,; T ENST00000339480 Transcript synonymous_variant 907/2840 537/801 179/266 R cgG/cgT 1 1 GJB4 HGNC HGNC:4286 protein_coding YES CCDS383.1 ENSP00000345868 Q9NTQ9 UPI0000051E4B NM_153212.2 2/2 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,PROSITE_patterns:PS00408,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF30,SMART_domains:SM01089 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 34761791 34761791 G T 1 0 0 0 0 0 0 0 1 6287 1190 42 2 2 GJB4 1 34761791 Silent SNP G C3N-01405_T 3019905 34761791 214194631 8 22482 INPP5B 0 . GRCh38 1 37931565 37931565 + Nonsense_Mutation SNP C C A C3N-01405_T C3N-01405_N C C c.880G>T p.Glu294Ter p.E294* ENST00000373021 6/6 429 374 55 344 344 0 strelka-varscan-mutect INPP5B,stop_gained,p.Glu294Ter,ENST00000373021,;INPP5B,intron_variant,,ENST00000373023,;INPP5B,intron_variant,,ENST00000458109,;INPP5B,intron_variant,,ENST00000373027,NM_001297434.1;INPP5B,intron_variant,,ENST00000373026,;INPP5B,intron_variant,,ENST00000373024,NM_005540.2; A ENST00000373021 Transcript stop_gained 906/3934 880/960 294/319 E/* Gaa/Taa COSM4853980 1 -1 INPP5B HGNC HGNC:6077 protein_coding ENSP00000362112 B1ARF3 UPI0000197DB9 6/6 1 HIGH SNV 1 1 1 PASS rs1205432572 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 37931565 37931565 C A 1 0 0 0 0 0 1 0 0 7658 893 31 1 1 INPP5B 1 37931565 Nonsense_Mutation SNP C C3N-01405_T 3169774 37931565 211024857 9 22483 TRIT1 0 . GRCh38 1 39844623 39844623 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.1024C>T p.Pro342Ser p.P342S ENST00000316891 9/11 208 188 20 156 156 0 strelka-varscan-mutect TRIT1,missense_variant,p.Pro342Ser,ENST00000316891,NM_017646.4;TRIT1,missense_variant,p.Pro316Ser,ENST00000372818,NM_001312691.1;TRIT1,missense_variant,p.Pro38Ser,ENST00000537440,;TRIT1,missense_variant,p.Pro260Ser,ENST00000441669,NM_001312692.1;TRIT1,5_prime_UTR_variant,,ENST00000541099,;TRIT1,non_coding_transcript_exon_variant,,ENST00000491865,;TRIT1,non_coding_transcript_exon_variant,,ENST00000465417,;TRIT1,3_prime_UTR_variant,,ENST00000495175,;TRIT1,3_prime_UTR_variant,,ENST00000492612,;TRIT1,intron_variant,,ENST00000462797,;TRIT1,downstream_gene_variant,,ENST00000489945,;TRIT1,downstream_gene_variant,,ENST00000486825,;TRIT1,downstream_gene_variant,,ENST00000469476,;TRIT1,downstream_gene_variant,,ENST00000467774,; A ENST00000316891 Transcript missense_variant 1039/2112 1024/1404 342/467 P/S Ccc/Tcc 1 -1 TRIT1 HGNC HGNC:20286 protein_coding YES CCDS30681.1 ENSP00000321810 Q9H3H1 UPI000006E2FB NM_017646.4 deleterious(0) 9/11 HAMAP:MF_00185,PIRSF_domain:PIRSF039110,hmmpanther:PTHR11088,hmmpanther:PTHR11088:SF25 MODERATE 1 SNV 1 1 PASS rs1022582532 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 39844623 39844623 G A 1 0 0 0 0 1 0 0 0 17058 1232 43 3 3 TRIT1 1 39844623 Missense_Mutation SNP G C3N-01405_T 1913058 39844623 209111799 10 22484 MFSD2A 0 . GRCh38 1 39968681 39968681 + Missense_Mutation SNP T T G novel C3N-01405_T C3N-01405_N T T c.1504T>G p.Phe502Val p.F502V ENST00000372809 13/14 267 244 23 236 236 0 strelka-varscan-mutect MFSD2A,missense_variant,p.Phe502Val,ENST00000372809,NM_001136493.2;MFSD2A,missense_variant,p.Phe489Val,ENST00000372811,NM_032793.4,NM_001287809.1;MFSD2A,missense_variant,p.Phe333Val,ENST00000420632,NM_001287808.1;MFSD2A,downstream_gene_variant,,ENST00000434861,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000480630,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000483824,;MFSD2A,non_coding_transcript_exon_variant,,ENST00000491515,;MFSD2A,downstream_gene_variant,,ENST00000469745,;MFSD2A,downstream_gene_variant,,ENST00000481612,;MFSD2A,downstream_gene_variant,,ENST00000459917,; G ENST00000372809 Transcript missense_variant 1647/2173 1504/1632 502/543 F/V Ttc/Gtc 1 1 MFSD2A HGNC HGNC:25897 protein_coding YES CCDS44118.1 ENSP00000361895 Q8NA29 UPI0000072562 NM_001136493.2 deleterious(0.05) 13/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR11328:SF29,hmmpanther:PTHR11328,Pfam_domain:PF13347,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 39968681 39968681 T G 1 0 0 0 0 1 0 0 0 9487 1609 56 5 5 MFSD2A 1 39968681 Missense_Mutation SNP T C3N-01405_T 124058 39968681 208987741 11 22485 NFYC 0 . GRCh38 1 40747568 40747568 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.140G>A p.Arg47His p.R47H ENST00000425457 3/11 205 185 20 198 198 0 strelka-varscan-mutect NFYC,missense_variant,p.Arg47His,ENST00000372652,NM_001308115.1;NFYC,missense_variant,p.Arg47His,ENST00000308733,NM_001308114.1;NFYC,missense_variant,p.Arg47His,ENST00000447388,NM_014223.4;NFYC,missense_variant,p.Arg47His,ENST00000456393,NM_001142587.1;NFYC,missense_variant,p.Arg47His,ENST00000372653,NM_001142590.1;NFYC,missense_variant,p.Arg47His,ENST00000440226,;NFYC,missense_variant,p.Arg47His,ENST00000425457,NM_001142588.1;NFYC,missense_variant,p.Arg47His,ENST00000372654,;NFYC,missense_variant,p.Arg47His,ENST00000427410,NM_001142589.1;NFYC,missense_variant,p.Arg47His,ENST00000372651,;NFYC,missense_variant,p.Arg47His,ENST00000372669,;NFYC,missense_variant,p.Arg47His,ENST00000453631,;NFYC,missense_variant,p.Arg47His,ENST00000534399,;NFYC,missense_variant,p.Arg47His,ENST00000416859,;NFYC,missense_variant,p.Arg47His,ENST00000531464,;NFYC,missense_variant,p.Arg47His,ENST00000525290,;NFYC,intron_variant,,ENST00000530965,;NFYC,non_coding_transcript_exon_variant,,ENST00000467203,;NFYC,intron_variant,,ENST00000424419,; A ENST00000425457 Transcript missense_variant 300/1536 140/1065 47/354 R/H cGt/cAt 1 1 NFYC HGNC HGNC:7806 protein_coding YES CCDS44120.1 ENSP00000396620 Q13952 UPI0000D4DA2D NM_001142588.1 deleterious(0.01) 3/11 Gene3D:1.10.20.10,Pfam_domain:PF00808,hmmpanther:PTHR10252,hmmpanther:PTHR10252:SF8,Superfamily_domains:SSF47113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 40747568 40747568 G A 1 0 0 0 0 1 0 0 0 10427 1145 40 1 1 NFYC 1 40747568 Missense_Mutation SNP G C3N-01405_T 778887 40747568 208208854 12 22486 NFYC 0 . GRCh38 1 40762929 40762929 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.603G>T p.= p.V201V ENST00000425457 7/11 78 67 11 79 79 0 strelka-varscan-mutect NFYC,synonymous_variant,p.=,ENST00000372652,NM_001308115.1;NFYC,synonymous_variant,p.=,ENST00000308733,NM_001308114.1;NFYC,synonymous_variant,p.=,ENST00000447388,NM_014223.4;NFYC,synonymous_variant,p.=,ENST00000456393,NM_001142587.1;NFYC,synonymous_variant,p.=,ENST00000440226,;NFYC,synonymous_variant,p.=,ENST00000425457,NM_001142588.1;NFYC,synonymous_variant,p.=,ENST00000372654,;NFYC,synonymous_variant,p.=,ENST00000427410,NM_001142589.1;NFYC,synonymous_variant,p.=,ENST00000372651,;NFYC,synonymous_variant,p.=,ENST00000372669,;NFYC,synonymous_variant,p.=,ENST00000414185,;NFYC,synonymous_variant,p.=,ENST00000416859,;NFYC,intron_variant,,ENST00000372653,NM_001142590.1;NFYC,downstream_gene_variant,,ENST00000525290,;NFYC,upstream_gene_variant,,ENST00000483091,;NFYC,non_coding_transcript_exon_variant,,ENST00000424419,;NFYC,non_coding_transcript_exon_variant,,ENST00000525349,;NFYC,downstream_gene_variant,,ENST00000467203,; T ENST00000425457 Transcript synonymous_variant 763/1536 603/1065 201/354 V gtG/gtT 1 1 NFYC HGNC HGNC:7806 protein_coding YES CCDS44120.1 ENSP00000396620 Q13952 UPI0000D4DA2D NM_001142588.1 7/11 hmmpanther:PTHR10252,hmmpanther:PTHR10252:SF8,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs941749774 . 0 207 2 0 0 0 0 0 -19.99998 1 1 1 1 0 T 2 4 74 40762929 40762929 G T 1 0 0 0 0 0 0 0 1 10427 1306 46 2 2 NFYC 1 40762929 Silent SNP G C3N-01405_T 15361 40762929 208193493 13 22487 MAST2 0 . GRCh38 1 46031160 46031160 + Silent SNP A A G novel C3N-01405_T C3N-01405_N A A c.2862A>G p.= p.P954P ENST00000361297 23/29 54 44 10 35 35 0 strelka-varscan-mutect MAST2,synonymous_variant,p.=,ENST00000361297,NM_001324320.1,NM_001319245.1,NM_015112.2;MAST2,synonymous_variant,p.=,ENST00000372009,;MAST2,downstream_gene_variant,,ENST00000372008,;MAST2,downstream_gene_variant,,ENST00000477968,;MAST2,upstream_gene_variant,,ENST00000492813,; G ENST00000361297 Transcript synonymous_variant 3145/5738 2862/5397 954/1798 P ccA/ccG 1 1 MAST2 HGNC HGNC:19035 protein_coding YES CCDS41326.1 ENSP00000354671 Q6P0Q8 UPI0000458AEB NM_001324320.1,NM_001319245.1,NM_015112.2 23/29 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99993 1 1 1 1 0 G 2 3 74 46031160 46031160 A G 1 0 0 0 0 0 0 0 1 9251 146 6 5 5 MAST2 1 46031160 Silent SNP A C3N-01405_T 5268231 46031160 202925262 14 22488 DMBX1 0 . GRCh38 1 46511195 46511195 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.594C>A p.= p.P198P ENST00000360032 3/4 179 145 34 122 122 0 strelka-varscan-mutect DMBX1,synonymous_variant,p.=,ENST00000371956,NM_147192.2;DMBX1,synonymous_variant,p.=,ENST00000360032,NM_172225.1; A ENST00000360032 Transcript synonymous_variant 608/2880 594/1134 198/377 P ccC/ccA 1 1 DMBX1 HGNC HGNC:19026 protein_coding YES CCDS536.1 ENSP00000353132 Q8NFW5 UPI0000070B63 NM_172225.1 3/4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 46511195 46511195 C A 1 0 0 0 0 0 0 0 1 4385 581 21 2 2 DMBX1 1 46511195 Silent SNP C C3N-01405_T 480035 46511195 202445227 15 22489 FOXD2 0 . GRCh38 1 47438600 47438600 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.465G>C p.Glu155Asp p.E155D ENST00000334793 1/1 468 351 117 338 338 0 strelka-varscan-mutect FOXD2,missense_variant,p.Glu155Asp,ENST00000334793,NM_004474.3;FOXD2-AS1,upstream_gene_variant,,ENST00000445551,; C ENST00000334793 Transcript missense_variant 2584/4675 465/1488 155/495 E/D gaG/gaC 1 1 FOXD2 HGNC HGNC:3803 protein_coding YES CCDS30708.1 ENSP00000335493 O60548 UPI000014153E NM_004474.3 tolerated(0.3) 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF168,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 47438600 47438600 G C 1 0 0 0 0 1 0 0 0 5857 1020 36 4 4 FOXD2 1 47438600 Missense_Mutation SNP G C3N-01405_T 927405 47438600 201517822 16 22490 LRRC53 0 . GRCh38 1 74480345 74480345 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.712C>A p.His238Asn p.H238N ENST00000294635 3/5 205 175 30 177 176 1 strelka-varscan-mutect LRRC53,missense_variant,p.His238Asn,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2; T ENST00000294635 Transcript missense_variant 827/3859 712/3744 238/1247 H/N Cac/Aac 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE tolerated(0.06) 3/5 Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 74480345 74480345 G T 1 0 0 0 0 1 0 0 0 8905 1290 45 2 2 LRRC53 1 74480345 Missense_Mutation SNP G C3N-01405_T 27041745 74480345 174476077 17 22491 RABGGTB 0 . GRCh38 1 75791549 75791549 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.557G>T p.Gly186Val p.G186V ENST00000319942 6/9 196 168 28 144 144 0 strelka-varscan-mutect RABGGTB,missense_variant,p.Gly186Val,ENST00000319942,NM_004582.3;RABGGTB,downstream_gene_variant,,ENST00000370826,;SNORD45A,downstream_gene_variant,,ENST00000384512,;SNORD45C,downstream_gene_variant,,ENST00000383893,;SNORD45B,downstream_gene_variant,,ENST00000364617,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000496055,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000471759,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000461653,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000491266,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000470201,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000485459,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000473406,;RABGGTB,non_coding_transcript_exon_variant,,ENST00000467748,;RABGGTB,downstream_gene_variant,,ENST00000497648,;RABGGTB,upstream_gene_variant,,ENST00000459697,;RABGGTB,downstream_gene_variant,,ENST00000489450,;RABGGTB,downstream_gene_variant,,ENST00000462042,;ACADM,downstream_gene_variant,,ENST00000528016,; T ENST00000319942 Transcript missense_variant 628/1496 557/996 186/331 G/V gGt/gTt 1 1 RABGGTB HGNC HGNC:9796 protein_coding YES CCDS669.1 ENSP00000317473 P53611 Q6IB63 UPI0000131891 NM_004582.3 deleterious(0) 6/9 Gene3D:1.50.10.20,Pfam_domain:PF00432,hmmpanther:PTHR11774,hmmpanther:PTHR11774:SF11,Superfamily_domains:SSF48239 MODERATE 1 SNV 1 1 PASS rs1175443975 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 75791549 75791549 G T 1 0 0 0 0 1 0 0 0 13127 1261 44 2 2 RABGGTB 1 75791549 Missense_Mutation SNP G C3N-01405_T 1311204 75791549 173164873 18 22492 COL11A1 0 . GRCh38 1 103004618 103004618 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1889A>T p.Asp630Val p.D630V ENST00000370096 19/67 265 213 52 278 278 0 strelka-varscan-mutect COL11A1,missense_variant,p.Asp642Val,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Asp630Val,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Asp591Val,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Asp514Val,ENST00000512756,NM_080630.3;COL11A1,downstream_gene_variant,,ENST00000427239,;COL11A1,non_coding_transcript_exon_variant,,ENST00000461720,;COL11A1,upstream_gene_variant,,ENST00000475980,;COL11A1,missense_variant,p.Asp403Val,ENST00000635193,; A ENST00000370096 Transcript missense_variant 2202/7286 1889/5421 630/1806 D/V gAt/gTt 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.02) 19/67 Pfam_domain:PF01391,Pfam_domain:PF01391,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 103004618 103004618 T A 1 0 0 0 0 1 0 0 0 3455 1435 50 4 4 COL11A1 1 103004618 Missense_Mutation SNP T C3N-01405_T 27213069 103004618 145951804 19 22493 AMY2B 0 . GRCh38 1 103579453 103579453 + Missense_Mutation SNP T T G novel C3N-01405_T C3N-01405_N T T c.1489T>G p.Ser497Ala p.S497A ENST00000361355 12/12 281 241 40 304 304 0 strelka-varscan-mutect AMY2B,missense_variant,p.Ser497Ala,ENST00000361355,NM_020978.4;AMY2B,missense_variant,p.Ser497Ala,ENST00000610648,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,non_coding_transcript_exon_variant,,ENST00000481821,;AMY2B,downstream_gene_variant,,ENST00000462971,;AMY2B,3_prime_UTR_variant,,ENST00000477657,; G ENST00000361355 Transcript missense_variant 2105/2181 1489/1536 497/511 S/A Tct/Gct 1 1 AMY2B HGNC HGNC:478 protein_coding YES CCDS782.1 ENSP00000354610 P19961 UPI0000000CB1 NM_020978.4 tolerated(0.37) 12/12 hmmpanther:PTHR10357:SF105,hmmpanther:PTHR10357,Pfam_domain:PF02806,Gene3D:2.60.40.1180,SMART_domains:SM00632,Superfamily_domains:SSF51011 MODERATE 1 SNV 1 1 PASS rs1160741045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 103579453 103579453 T G 1 0 0 0 0 1 0 0 0 692 1551 54 5 5 AMY2B 1 103579453 Missense_Mutation SNP T C3N-01405_T 574835 103579453 145376969 20 22494 SPAG17 0 . GRCh38 1 117996406 117996406 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.5017A>T p.Thr1673Ser p.T1673S ENST00000336338 34/49 100 81 19 97 97 0 strelka-mutect SPAG17,missense_variant,p.Thr1673Ser,ENST00000336338,NM_206996.2;SPAG17,missense_variant,p.Thr153Ser,ENST00000437255,; A ENST00000336338 Transcript missense_variant 5083/6924 5017/6672 1673/2223 T/S Act/Tct 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 deleterious(0.04) 34/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 117996406 117996406 T A 1 0 0 0 0 1 0 0 0 15310 1638 57 4 4 SPAG17 1 117996406 Missense_Mutation SNP T C3N-01405_T 14416953 117996406 130960016 21 22495 SF3B4 0 . GRCh38 1 149924014 149924014 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.914G>C p.Gly305Ala p.G305A ENST00000271628 5/6 360 174 186 166 166 0 strelka-varscan-mutect SF3B4,missense_variant,p.Gly305Ala,ENST00000271628,NM_005850.4;MTMR11,downstream_gene_variant,,ENST00000439741,NM_001145862.1;MTMR11,downstream_gene_variant,,ENST00000369140,NM_181873.3;SF3B4,downstream_gene_variant,,ENST00000457312,;MTMR11,downstream_gene_variant,,ENST00000492824,;MTMR11,downstream_gene_variant,,ENST00000482025,;MTMR11,downstream_gene_variant,,ENST00000466496,;MTMR11,downstream_gene_variant,,ENST00000482343,; G ENST00000271628 Transcript missense_variant,splice_region_variant 1499/2085 914/1275 305/424 G/A gGg/gCg 1 -1 SF3B4 HGNC HGNC:10771 protein_coding YES CCDS72900.1 ENSP00000271628 Q15427 UPI0000135472 NM_005850.4 tolerated(0.31) 5/6 Low_complexity_(Seg):seg,Prints_domain:PR01217 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 149924014 149924014 C G 1 0 0 0 0 1 0 0 0 14431 637 22 4 4 SF3B4 1 149924014 Missense_Mutation SNP C C3N-01405_T 31927608 149924014 99032408 22 22496 SPRR3 0 . GRCh38 1 153003489 153003489 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.469G>C p.Val157Leu p.V157L ENST00000331860 3/3 238 218 20 124 124 0 strelka-varscan-mutect SPRR3,missense_variant,p.Val157Leu,ENST00000331860,NM_005416.2;SPRR3,missense_variant,p.Val157Leu,ENST00000295367,NM_001097589.1;SPRR3,missense_variant,p.Val157Leu,ENST00000443178,;SPRR3,downstream_gene_variant,,ENST00000495845,; C ENST00000331860 Transcript missense_variant 619/985 469/510 157/169 V/L Gtc/Ctc 1 1 SPRR3 HGNC HGNC:11268 protein_coding YES CCDS1033.1 ENSP00000330391 Q9UBC9 UPI0000127F1F NM_005416.2 deleterious(0.04) 3/3 Pfam_domain:PF02389,Prints_domain:PR00021 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 153003489 153003489 G C 1 0 0 0 0 1 0 0 0 15458 1261 44 4 4 SPRR3 1 153003489 Missense_Mutation SNP G C3N-01405_T 3079475 153003489 95952933 23 22497 NUP210L 0 . GRCh38 1 154001947 154001947 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.4969G>C p.Glu1657Gln p.E1657Q ENST00000368559 36/40 297 269 28 173 173 0 strelka-varscan-mutect NUP210L,missense_variant,p.Glu1657Gln,ENST00000368559,NM_207308.2;NUP210L,intron_variant,,ENST00000271854,NM_001159484.1;NUP210L,intron_variant,,ENST00000368553,; G ENST00000368559 Transcript missense_variant 5041/5889 4969/5667 1657/1888 E/Q Gag/Cag 1 -1 NUP210L HGNC HGNC:29915 protein_coding YES CCDS41399.1 ENSP00000357547 Q5VU65 UPI000023724F NM_207308.2 tolerated(0.15) 36/40 hmmpanther:PTHR23019,hmmpanther:PTHR23019:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 154001947 154001947 C G 1 0 0 0 0 1 0 0 0 10826 922 32 4 4 NUP210L 1 154001947 Missense_Mutation SNP C C3N-01405_T 998458 154001947 94954475 24 22498 IQGAP3 0 . GRCh38 1 156533011 156533011 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.4072G>A p.Asp1358Asn p.D1358N ENST00000361170 32/38 400 379 21 225 225 0 strelka-varscan-mutect IQGAP3,missense_variant,p.Asp1358Asn,ENST00000361170,NM_178229.4;IQGAP3,downstream_gene_variant,,ENST00000498755,;IQGAP3,downstream_gene_variant,,ENST00000476565,;IQGAP3,missense_variant,p.Asp1315Asn,ENST00000491900,; T ENST00000361170 Transcript missense_variant 4083/5988 4072/4896 1358/1631 D/N Gat/Aat 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 tolerated(0.07) 32/38 hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149 MODERATE 1 SNV 1 1 PASS rs1442287727 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 156533011 156533011 C T 1 0 0 0 0 1 0 0 0 7722 826 29 3 3 IQGAP3 1 156533011 Missense_Mutation SNP C C3N-01405_T 2531064 156533011 92423411 25 22499 INSRR 0 . GRCh38 1 156843188 156843188 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.2942T>A p.Ile981Lys p.I981K ENST00000368195 17/22 431 390 41 243 243 0 strelka-varscan-mutect INSRR,missense_variant,p.Ile981Lys,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; T ENST00000368195 Transcript missense_variant 3339/5101 2942/3894 981/1297 I/K aTa/aAa 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 deleterious(0) 17/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF338,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000620,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 156843188 156843188 A T 1 0 0 0 0 1 0 0 0 7676 449 16 4 4 INSRR 1 156843188 Missense_Mutation SNP A C3N-01405_T 310177 156843188 92113234 26 22500 PEAR1 0 . GRCh38 1 156906790 156906790 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.554C>A p.Pro185His p.P185H ENST00000338302 7/24 652 352 300 355 355 0 strelka-varscan-mutect PEAR1,missense_variant,p.Pro185His,ENST00000338302,;PEAR1,missense_variant,p.Pro185His,ENST00000292357,NM_001080471.1;PEAR1,downstream_gene_variant,,ENST00000455314,;PEAR1,non_coding_transcript_exon_variant,,ENST00000469390,;PEAR1,downstream_gene_variant,,ENST00000444016,;PEAR1,upstream_gene_variant,,ENST00000482505,; A ENST00000338302 Transcript missense_variant 779/4970 554/3114 185/1037 P/H cCt/cAt 1 1 PEAR1 HGNC HGNC:33631 protein_coding YES CCDS30892.1 ENSP00000344465 Q5VY43 UPI000045889A tolerated(0.09) 7/24 hmmpanther:PTHR24052,hmmpanther:PTHR24052:SF12,Gene3D:2gy5A03,SMART_domains:SM00180,PD936484 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 156906790 156906790 C A 1 0 0 0 0 1 0 0 0 11801 681 24 2 2 PEAR1 1 156906790 Missense_Mutation SNP C C3N-01405_T 63602 156906790 92049632 27 22501 SPTA1 0 . GRCh38 1 158623128 158623128 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.5975A>G p.Lys1992Arg p.K1992R ENST00000368147 43/52 810 760 50 424 424 0 strelka-varscan-mutect SPTA1,missense_variant,p.Lys1992Arg,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000484520,; C ENST00000368147 Transcript missense_variant 6156/7999 5975/7260 1992/2419 K/R aAg/aGg 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.02) 43/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 158623128 158623128 T C 1 0 0 0 0 1 0 0 0 15472 1609 56 5 5 SPTA1 1 158623128 Missense_Mutation SNP T C3N-01405_T 1716338 158623128 90333294 28 22502 SPTA1 0 . GRCh38 1 158656642 158656642 + Missense_Mutation SNP C C A rs759064678 C3N-01405_T C3N-01405_N C C c.2820G>T p.Lys940Asn p.K940N ENST00000368147 20/52 490 272 218 345 345 0 strelka-varscan-mutect SPTA1,missense_variant,p.Lys940Asn,ENST00000368147,NM_003126.2; A ENST00000368147 Transcript missense_variant 3001/7999 2820/7260 940/2419 K/N aaG/aaT rs759064678,COSM1335232,COSM897820 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 20/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs759064678 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 158656642 158656642 C A 1 0 0 0 0 1 0 0 0 15472 796 28 2 2 SPTA1 1 158656642 Missense_Mutation SNP C C3N-01405_T 33514 158656642 90299780 29 22503 SPTA1 0 . GRCh38 1 158662792 158662792 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.2374C>A p.Leu792Ile p.L792I ENST00000368147 17/52 570 307 263 390 390 0 strelka-varscan-mutect SPTA1,missense_variant,p.Leu792Ile,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 2555/7999 2374/7260 792/2419 L/I Ctt/Att 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.46) 17/52 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Gene3D:1.20.58.60,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 158662792 158662792 G T 1 0 0 0 0 1 0 0 0 15472 1000 35 2 2 SPTA1 1 158662792 Missense_Mutation SNP G C3N-01405_T 6150 158662792 90293630 30 22504 IGSF8 0 . GRCh38 1 160094100 160094100 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.514C>A p.Pro172Thr p.P172T ENST00000368086 3/7 410 334 76 190 190 0 strelka-varscan-mutect IGSF8,missense_variant,p.Pro172Thr,ENST00000368086,NM_001320247.1;IGSF8,missense_variant,p.Pro172Thr,ENST00000314485,NM_052868.4;IGSF8,missense_variant,p.Pro172Thr,ENST00000614243,NM_001206665.2;IGSF8,missense_variant,p.Pro172Thr,ENST00000448417,;KCNJ9,downstream_gene_variant,,ENST00000368088,NM_004983.2;IGSF8,non_coding_transcript_exon_variant,,ENST00000460351,; T ENST00000368086 Transcript missense_variant 731/2366 514/1842 172/613 P/T Cca/Aca 1 -1 IGSF8 HGNC HGNC:17813 protein_coding YES CCDS1195.1 ENSP00000357065 Q969P0 UPI0000073CBA NM_001320247.1 tolerated(1) 3/7 hmmpanther:PTHR12207:SF22,hmmpanther:PTHR12207,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 160094100 160094100 G T 1 0 0 0 0 1 0 0 0 7512 1232 43 2 2 IGSF8 1 160094100 Missense_Mutation SNP G C3N-01405_T 1431308 160094100 88862322 31 22505 SUCO 0 . GRCh38 1 172532759 172532759 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.287C>G p.Pro96Arg p.P96R ENST00000367723 1/23 186 168 18 97 97 0 strelka-varscan-mutect SUCO,missense_variant,p.Pro96Arg,ENST00000367723,NM_016227.3;SUCO,missense_variant,p.Pro96Arg,ENST00000608151,;SUCO,upstream_gene_variant,,ENST00000263688,NM_014283.4;SUCO,upstream_gene_variant,,ENST00000616058,NM_001282751.1;SUCO,upstream_gene_variant,,ENST00000610051,NM_001282750.1;SUCO,upstream_gene_variant,,ENST00000608566,; G ENST00000367723 Transcript missense_variant 411/5916 287/4218 96/1405 P/R cCa/cGa 1 1 SUCO HGNC HGNC:1240 protein_coding YES CCDS65726.1 ENSP00000356696 Q9UBS9 A0A024R929 UPI0000EE3C11 NM_016227.3 tolerated_low_confidence(0.4) 1/23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 172532759 172532759 C G 1 0 0 0 0 1 0 0 0 15751 594 21 4 4 SUCO 1 172532759 Missense_Mutation SNP C C3N-01405_T 12438659 172532759 76423663 32 22506 TNN 0 . GRCh38 1 175135867 175135867 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.3353G>T p.Gly1118Val p.G1118V ENST00000239462 16/19 230 200 30 223 223 0 strelka-varscan-mutect TNN,missense_variant,p.Gly1118Val,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Gly941Val,ENST00000621086,;TNN,missense_variant,p.Gly941Val,ENST00000622870,; T ENST00000239462 Transcript missense_variant 3466/5008 3353/3900 1118/1299 G/V gGg/gTg 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 deleterious(0) 16/19 PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 175135867 175135867 G T 1 0 0 0 0 1 0 0 0 16796 1232 43 2 2 TNN 1 175135867 Missense_Mutation SNP G C3N-01405_T 2603108 175135867 73820555 33 22507 TNR 0 . GRCh38 1 175324376 175324376 + Missense_Mutation SNP C C A rs565736776 C3N-01405_T C3N-01405_N C C c.3937G>T p.Gly1313Trp p.G1313W ENST00000367674 22/23 191 171 20 152 152 0 strelka-varscan-mutect TNR,missense_variant,p.Gly1313Trp,ENST00000367674,;TNR,missense_variant,p.Gly1313Trp,ENST00000263525,NM_003285.2;RP3-518E13.2,intron_variant,,ENST00000569593,; A ENST00000367674 Transcript missense_variant 4646/12949 3937/4077 1313/1358 G/W Ggg/Tgg rs565736776 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0) 22/23 Gene3D:4.10.530.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE SNV 5 1 PASS rs565736776 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 175324376 175324376 C A 1 0 0 0 0 1 0 0 0 16811 652 23 1 1 TNR 1 175324376 Missense_Mutation SNP C C3N-01405_T 188509 175324376 73632046 34 22508 PAPPA2 0 . GRCh38 1 176765817 176765817 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.4303C>A p.Gln1435Lys p.Q1435K ENST00000367662 15/23 144 108 36 131 131 0 strelka-varscan-mutect PAPPA2,missense_variant,p.Gln1435Lys,ENST00000367662,NM_020318.2; A ENST00000367662 Transcript missense_variant 5467/9691 4303/5376 1435/1791 Q/K Cag/Aag 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated(1) 15/23 hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325,SMART_domains:SM00032 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 176765817 176765817 C A 1 0 0 0 0 1 0 0 0 11513 711 25 2 2 PAPPA2 1 176765817 Missense_Mutation SNP C C3N-01405_T 1441441 176765817 72190605 35 22509 ASTN1 0 . GRCh38 1 176894748 176894748 + Silent SNP T T A novel C3N-01405_T C3N-01405_N T T c.2754A>T p.= p.S918S ENST00000361833 17/23 321 289 32 271 271 0 strelka-varscan-mutect ASTN1,synonymous_variant,p.=,ENST00000361833,NM_004319.2;ASTN1,synonymous_variant,p.=,ENST00000367657,NM_001286164.1;ASTN1,synonymous_variant,p.=,ENST00000424564,NM_207108.2; A ENST00000361833 Transcript synonymous_variant 2768/7116 2754/3885 918/1294 S tcA/tcT 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 17/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592,SMART_domains:SM00457 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 176894748 176894748 T A 1 0 0 0 0 0 0 0 1 1211 1567 55 4 4 ASTN1 1 176894748 Silent SNP T C3N-01405_T 128931 176894748 72061674 36 22510 SEC16B 0 . GRCh38 1 177932770 177932770 + Missense_Mutation SNP G G T rs762261014 C3N-01405_T C3N-01405_N G G c.2860C>A p.Leu954Met p.L954M ENST00000308284 23/26 189 164 25 153 152 1 strelka-varscan-mutect SEC16B,missense_variant,p.Leu954Met,ENST00000308284,NM_033127.2;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000354921,;SEC16B,non_coding_transcript_exon_variant,,ENST00000495165,;SEC16B,intron_variant,,ENST00000327037,;SEC16B,upstream_gene_variant,,ENST00000441371,;SEC16B,3_prime_UTR_variant,,ENST00000528461,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000466953,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,; T ENST00000308284 Transcript missense_variant 2950/3985 2860/3183 954/1060 L/M Ctg/Atg rs762261014 1 -1 SEC16B HGNC HGNC:30301 protein_coding YES CCDS44281.1 ENSP00000308339 Q96JE7 UPI0000203C4D NM_033127.2 tolerated(0.2) 23/26 Low_complexity_(Seg):seg,hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF11 MODERATE 1 SNV 1 1 PASS rs762261014 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 177932770 177932770 G T 1 0 0 0 0 1 0 0 0 14264 991 35 2 2 SEC16B 1 177932770 Missense_Mutation SNP G C3N-01405_T 1038022 177932770 71023652 37 22511 TDRD5 0 . GRCh38 1 179662104 179662104 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.2323G>C p.Asp775His p.D775H ENST00000444136 15/18 52 42 10 60 60 0 strelka-varscan-mutect TDRD5,missense_variant,p.Asp775His,ENST00000444136,NM_001199085.1,NM_001199089.1;TDRD5,missense_variant,p.Asp721His,ENST00000367614,NM_001199091.1;TDRD5,missense_variant,p.Asp721His,ENST00000294848,NM_173533.3;TDRD5,missense_variant,p.Asp231His,ENST00000417329,; C ENST00000444136 Transcript missense_variant,splice_region_variant 2841/3946 2323/3108 775/1035 D/H Gat/Cat 1 1 TDRD5 HGNC HGNC:20614 protein_coding YES CCDS55663.1 ENSP00000406052 Q8NAT2 UPI000022AC96 NM_001199085.1,NM_001199089.1 deleterious(0.01) 15/18 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF19 MODERATE 1 SNV 1 1 PASS rs1295276272 . 0 197 13 0 0 0 0 0 -19.9998 0.9999045 1 1 1 0 C 3 2 74 179662104 179662104 G C 1 0 0 0 0 1 0 0 0 16143 1188 41 4 4 TDRD5 1 179662104 Missense_Mutation SNP G C3N-01405_T 1729334 179662104 69294318 38 22512 COLGALT2 0 . GRCh38 1 183964059 183964059 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.5T>A p.Phe2Tyr p.F2Y ENST00000367520 1/7 63 48 15 44 44 0 strelka-varscan-mutect COLGALT2,missense_variant,p.Phe2Tyr,ENST00000367520,;COLGALT2,intron_variant,,ENST00000361927,NM_001303420.1,NM_015101.3,NM_001303421.1; T ENST00000367520 Transcript missense_variant 442/2325 5/1092 2/363 F/Y tTt/tAt 1 -1 COLGALT2 HGNC HGNC:16790 protein_coding ENSP00000356490 Q5SXQ3 UPI00004701F5 1/7 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 183964059 183964059 A T 1 0 0 0 0 1 0 0 0 3504 14 1 4 4 COLGALT2 1 183964059 Missense_Mutation SNP A C3N-01405_T 4301955 183964059 64992363 39 22513 PRG4 0 . GRCh38 1 186307101 186307101 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1382C>A p.Pro461His p.P461H ENST00000445192 7/13 493 374 119 416 415 1 strelka-varscan-mutect PRG4,missense_variant,p.Pro461His,ENST00000445192,NM_005807.4;PRG4,missense_variant,p.Pro420His,ENST00000367483,NM_001127708.2;PRG4,missense_variant,p.Pro418His,ENST00000635041,NM_001303232.1;PRG4,missense_variant,p.Pro368His,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,missense_variant,p.Pro327His,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; A ENST00000445192 Transcript missense_variant 1427/5044 1382/4215 461/1404 P/H cCc/cAc 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 deleterious(0) 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 186307101 186307101 C A 1 0 0 0 0 1 0 0 0 12615 623 22 2 2 PRG4 1 186307101 Missense_Mutation SNP C C3N-01405_T 2343042 186307101 62649321 40 22514 BRINP3 0 . GRCh38 1 190098238 190098238 + Missense_Mutation SNP C C T rs539178233 C3N-01405_T C3N-01405_N C C c.2081G>A p.Gly694Glu p.G694E ENST00000367462 8/8 173 156 17 144 144 0 strelka-varscan-mutect BRINP3,missense_variant,p.Gly694Glu,ENST00000367462,NM_199051.1; T ENST00000367462 Transcript missense_variant 2566/3142 2081/2301 694/766 G/E gGa/gAa rs539178233,COSM3480447 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 deleterious(0.03) 8/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs539178233 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 190098238 190098238 C T 1 0 0 0 0 1 0 0 0 1687 855 30 3 3 BRINP3 1 190098238 Missense_Mutation SNP C C3N-01405_T 3791137 190098238 58858184 41 22515 F13B 0 . GRCh38 1 197050787 197050787 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1648G>C p.Glu550Gln p.E550Q ENST00000367412 10/12 191 163 28 194 194 0 strelka-varscan-mutect F13B,missense_variant,p.Glu550Gln,ENST00000367412,NM_001994.2;F13B,non_coding_transcript_exon_variant,,ENST00000490002,; G ENST00000367412 Transcript missense_variant 1692/2217 1648/1986 550/661 E/Q Gaa/Caa 1 -1 F13B HGNC HGNC:3534 protein_coding YES CCDS1388.1 ENSP00000356382 P05160 UPI000013D8E0 NM_001994.2 tolerated(0.59) 10/12 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF314,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 197050787 197050787 C G 1 0 0 0 0 1 0 0 0 5209 922 32 4 4 F13B 1 197050787 Missense_Mutation SNP C C3N-01405_T 6952549 197050787 51905635 42 22516 NAV1 0 . GRCh38 1 201649347 201649347 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.679G>T p.Ala227Ser p.A227S ENST00000367296 1/30 146 130 16 98 98 0 strelka-varscan-mutect NAV1,missense_variant,p.Ala227Ser,ENST00000367296,NM_020443.4;NAV1,missense_variant,p.Ala240Ser,ENST00000367302,; T ENST00000367296 Transcript missense_variant 1099/13091 679/5634 227/1877 A/S Gcc/Tcc 1 1 NAV1 HGNC HGNC:15989 protein_coding YES CCDS1414.2 ENSP00000356265 Q8NEY1 UPI00004562D4 NM_020443.4 tolerated(0.64) 1/30 hmmpanther:PTHR12784,hmmpanther:PTHR12784:SF3 MODERATE 1 SNV 5 1 PASS rs1350152222 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 201649347 201649347 G T 1 0 0 0 0 1 0 0 0 10192 1087 38 1 1 NAV1 1 201649347 Missense_Mutation SNP G C3N-01405_T 4598560 201649347 47307075 43 22517 ATP2B4 0 . GRCh38 1 203722567 203722567 + Missense_Mutation SNP G G T rs748753019 C3N-01405_T C3N-01405_N G G c.2902G>T p.Val968Leu p.V968L ENST00000357681 18/21 469 408 61 357 356 1 strelka-varscan-mutect ATP2B4,missense_variant,p.Val968Leu,ENST00000357681,NM_001684.4;ATP2B4,missense_variant,p.Val968Leu,ENST00000367218,NM_001001396.2;ATP2B4,missense_variant,p.Val968Leu,ENST00000341360,;ATP2B4,upstream_gene_variant,,ENST00000356729,;ATP2B4,upstream_gene_variant,,ENST00000458092,;ATP2B4,upstream_gene_variant,,ENST00000466407,;ATP2B4,upstream_gene_variant,,ENST00000484746,; T ENST00000357681 Transcript missense_variant 4025/8968 2902/3618 968/1205 V/L Gtg/Ttg rs748753019 1 1 ATP2B4 HGNC HGNC:817 protein_coding YES CCDS1440.1 ENSP00000350310 P23634 A0A024R968 UPI000002A464 NM_001684.4 deleterious(0.01) 18/21 Transmembrane_helices:TMhelix,hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00689,Gene3D:1.20.1110.10,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS rs748753019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 203722567 203722567 G T 1 0 0 0 0 1 0 0 0 1295 1145 40 1 1 ATP2B4 1 203722567 Missense_Mutation SNP G C3N-01405_T 2073220 203722567 45233855 44 22518 NFASC 0 . GRCh38 1 204981982 204981982 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.2432C>G p.Pro811Arg p.P811R ENST00000339876 21/30 50 39 11 49 49 0 strelka-varscan-mutect NFASC,missense_variant,p.Pro811Arg,ENST00000339876,NM_001005388.2;NFASC,missense_variant,p.Pro811Arg,ENST00000401399,;NFASC,missense_variant,p.Pro807Arg,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Pro807Arg,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Pro790Arg,ENST00000404076,;NFASC,missense_variant,p.Pro807Arg,ENST00000404907,;NFASC,missense_variant,p.Pro798Arg,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Pro781Arg,ENST00000367173,;NFASC,missense_variant,p.Pro807Arg,ENST00000513543,;NFASC,missense_variant,p.Pro43Arg,ENST00000425360,;NFASC,downstream_gene_variant,,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,non_coding_transcript_exon_variant,,ENST00000471392,;NFASC,non_coding_transcript_exon_variant,,ENST00000468328,;NFASC,upstream_gene_variant,,ENST00000495396,;NFASC,3_prime_UTR_variant,,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000512826,; G ENST00000339876 Transcript missense_variant 2760/10333 2432/3723 811/1240 P/R cCt/cGt 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 deleterious(0) 21/30 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Pfam_domain:PF00041,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 204981982 204981982 C G 1 0 0 0 0 1 0 0 0 10396 681 24 4 4 NFASC 1 204981982 Missense_Mutation SNP C C3N-01405_T 1259415 204981982 43974440 45 22519 USH2A 0 . GRCh38 1 215888840 215888840 + Nonsense_Mutation SNP G G T rs766915522 C3N-01405_T C3N-01405_N G G c.7809C>A p.Cys2603Ter p.C2603* ENST00000307340 41/72 413 323 90 318 318 0 strelka-varscan USH2A,stop_gained,p.Cys2603Ter,ENST00000307340,NM_206933.2;RP5-1111A8.3,intron_variant,,ENST00000414995,; T ENST00000307340 Transcript stop_gained 8196/18883 7809/15609 2603/5202 C/* tgC/tgA rs766915522 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 41/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 215888840 215888840 G T 1 0 0 0 0 0 1 0 0 17570 1311 46 2 2 USH2A 1 215888840 Nonsense_Mutation SNP G C3N-01405_T 10906858 215888840 33067582 46 22520 GPATCH2 0 . GRCh38 1 217514822 217514822 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.1166A>G p.Asp389Gly p.D389G ENST00000366935 6/10 161 128 33 118 118 0 strelka-varscan GPATCH2,missense_variant,p.Asp389Gly,ENST00000366935,NM_018040.3;GPATCH2,splice_region_variant,,ENST00000470014,;GPATCH2,splice_region_variant,,ENST00000485274,; C ENST00000366935 Transcript missense_variant,splice_region_variant 1277/5851 1166/1587 389/528 D/G gAc/gGc 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 deleterious(0) 6/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 217514822 217514822 T C 1 0 0 0 0 1 0 0 0 6491 1565 54 5 5 GPATCH2 1 217514822 Missense_Mutation SNP T C3N-01405_T 1625982 217514822 31441600 47 22521 SPATA17 0 . GRCh38 1 217774460 217774460 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.646G>A p.Asp216Asn p.D216N ENST00000366933 7/11 292 249 43 241 241 0 strelka-varscan SPATA17,missense_variant,p.Asp216Asn,ENST00000366933,NM_138796.3;SPATA17,non_coding_transcript_exon_variant,,ENST00000492747,;SPATA17,downstream_gene_variant,,ENST00000470448,; A ENST00000366933 Transcript missense_variant 701/5818 646/1086 216/361 D/N Gat/Aat 1 1 SPATA17 HGNC HGNC:25184 protein_coding YES CCDS1519.1 ENSP00000355900 Q96L03 UPI00000717C2 NM_138796.3 tolerated(0.42) 7/11 hmmpanther:PTHR22706 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 217774460 217774460 G A 1 0 0 0 0 1 0 0 0 15332 1290 45 3 3 SPATA17 1 217774460 Missense_Mutation SNP G C3N-01405_T 259638 217774460 31181962 48 22522 WNT9A 0 . GRCh38 1 227925512 227925512 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.103G>T p.Gly35Cys p.G35C ENST00000272164 2/4 58 39 19 44 44 0 strelka-varscan WNT9A,missense_variant,p.Gly35Cys,ENST00000272164,NM_003395.2; A ENST00000272164 Transcript missense_variant 114/3971 103/1098 35/365 G/C Ggc/Tgc 1 -1 WNT9A HGNC HGNC:12778 protein_coding YES CCDS31045.1 ENSP00000272164 O14904 D9ZGG3 UPI000005104B NM_003395.2 deleterious(0) 2/4 hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF75 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 227925512 227925512 C A 1 0 0 0 0 1 0 0 0 17954 623 22 2 2 WNT9A 1 227925512 Missense_Mutation SNP C C3N-01405_T 10151052 227925512 21030910 49 22523 OBSCN 0 . GRCh38 1 228212238 228212238 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.455A>G p.Glu152Gly p.E152G ENST00000570156 2/116 333 308 25 245 245 0 strelka-varscan OBSCN,missense_variant,p.Glu152Gly,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Glu152Gly,ENST00000366707,;OBSCN,missense_variant,p.Glu152Gly,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Glu152Gly,ENST00000636875,;OBSCN,missense_variant,p.Glu152Gly,ENST00000284548,NM_052843.3;C1orf145,intron_variant,,ENST00000295012,;OBSCN,upstream_gene_variant,,ENST00000493977,;C1orf145,intron_variant,,ENST00000337335,;C1orf145,intron_variant,,ENST00000472613,; G ENST00000570156 Transcript missense_variant 529/26925 455/26772 152/8923 E/G gAg/gGg 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.08) 2/116 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF708,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 228212238 228212238 A G 1 0 0 0 0 1 0 0 0 10889 304 11 5 5 OBSCN 1 228212238 Missense_Mutation SNP A C3N-01405_T 286726 228212238 20744184 50 22524 OBSCN 0 . GRCh38 1 228264358 228264358 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.5380G>T p.Asp1794Tyr p.D1794Y ENST00000570156 18/116 122 99 23 121 121 0 strelka-varscan OBSCN,missense_variant,p.Asp1794Tyr,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Asp1794Tyr,ENST00000366707,;OBSCN,missense_variant,p.Asp1610Tyr,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Asp1610Tyr,ENST00000636875,;OBSCN,missense_variant,p.Asp1610Tyr,ENST00000284548,NM_052843.3; T ENST00000570156 Transcript missense_variant 5454/26925 5380/26772 1794/8923 D/Y Gat/Tat 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 deleterious(0) 18/116 Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 228264358 228264358 G T 1 0 0 0 0 1 0 0 0 10889 1174 41 2 2 OBSCN 1 228264358 Missense_Mutation SNP G C3N-01405_T 52120 228264358 20692064 51 22525 DISC1 0 . GRCh38 1 231694292 231694292 + Silent SNP A A T rs542010946 C3N-01405_T C3N-01405_N A A c.534A>T p.= p.P178P ENST00000366633 2/10 500 440 60 378 378 0 strelka-varscan-mutect DISC1,synonymous_variant,p.=,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,synonymous_variant,p.=,ENST00000622252,;DISC1,synonymous_variant,p.=,ENST00000366637,NM_001012957.1;DISC1,synonymous_variant,p.=,ENST00000620189,NM_001164540.1;DISC1,synonymous_variant,p.=,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,synonymous_variant,p.=,ENST00000366633,NM_001164539.1;DISC1,synonymous_variant,p.=,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,synonymous_variant,p.=,ENST00000317586,NM_001012958.1;DISC1,synonymous_variant,p.=,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,synonymous_variant,p.=,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,synonymous_variant,p.=,ENST00000537876,;DISC1,synonymous_variant,p.=,ENST00000366636,NM_001012959.1;DISC1,intron_variant,,ENST00000602873,NM_001164556.1;DISC1,downstream_gene_variant,,ENST00000602600,;DISC1,synonymous_variant,p.=,ENST00000535944,;DISC1,synonymous_variant,p.=,ENST00000295051,;DISC1,synonymous_variant,p.=,ENST00000602822,;DISC1,synonymous_variant,p.=,ENST00000602713,;DISC1,synonymous_variant,p.=,ENST00000602700,;DISC1,synonymous_variant,p.=,ENST00000366632,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,non_coding_transcript_exon_variant,,ENST00000468399,; T ENST00000366633 Transcript synonymous_variant 587/2676 534/2268 178/755 P ccA/ccT rs542010946 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 2/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 LOW 1 SNV 1 1 PASS rs542010946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 231694292 231694292 A T 1 0 0 0 0 0 0 0 1 4344 204 8 4 4 DISC1 1 231694292 Silent SNP A C3N-01405_T 3429934 231694292 17262130 52 22526 DISC1 0 . GRCh38 1 231694369 231694369 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.611G>A p.Ser204Asn p.S204N ENST00000366633 2/10 576 500 76 521 521 0 strelka-varscan-mutect DISC1,missense_variant,p.Ser204Asn,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,missense_variant,p.Ser204Asn,ENST00000622252,;DISC1,missense_variant,p.Ser204Asn,ENST00000366637,NM_001012957.1;DISC1,missense_variant,p.Ser204Asn,ENST00000620189,NM_001164540.1;DISC1,missense_variant,p.Ser204Asn,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,missense_variant,p.Ser204Asn,ENST00000366633,NM_001164539.1;DISC1,missense_variant,p.Ser204Asn,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,missense_variant,p.Ser204Asn,ENST00000317586,NM_001012958.1;DISC1,missense_variant,p.Ser204Asn,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,missense_variant,p.Ser204Asn,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,missense_variant,p.Ser204Asn,ENST00000537876,;DISC1,missense_variant,p.Ser204Asn,ENST00000366636,NM_001012959.1;DISC1,intron_variant,,ENST00000602873,NM_001164556.1;DISC1,downstream_gene_variant,,ENST00000602600,;DISC1,missense_variant,p.Ser204Asn,ENST00000535944,;DISC1,missense_variant,p.Ser204Asn,ENST00000295051,;DISC1,missense_variant,p.Ser204Asn,ENST00000602822,;DISC1,missense_variant,p.Ser204Asn,ENST00000602713,;DISC1,missense_variant,p.Ser204Asn,ENST00000602700,;DISC1,missense_variant,p.Ser204Asn,ENST00000366632,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602962,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602567,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602634,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602956,;TSNAX-DISC1,3_prime_UTR_variant,,ENST00000602885,;DISC1,3_prime_UTR_variant,,ENST00000422590,;DISC1,non_coding_transcript_exon_variant,,ENST00000468399,; A ENST00000366633 Transcript missense_variant 664/2676 611/2268 204/755 S/N aGt/aAt 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 deleterious(0.02) 2/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 231694369 231694369 G A 1 0 0 0 0 1 0 0 0 4344 1029 36 3 3 DISC1 1 231694369 Missense_Mutation SNP G C3N-01405_T 77 231694369 17262053 53 22527 NID1 0 . GRCh38 1 236048947 236048947 + Nonsense_Mutation SNP T T A rs146770492 C3N-01405_T C3N-01405_N T T c.268A>T p.Lys90Ter p.K90* ENST00000264187 2/20 332 268 64 275 275 0 strelka-varscan-mutect NID1,stop_gained,p.Lys90Ter,ENST00000264187,NM_002508.2;NID1,stop_gained,p.Lys90Ter,ENST00000366595,; A ENST00000264187 Transcript stop_gained 351/5864 268/3744 90/1247 K/* Aaa/Taa rs146770492 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 2/20 HIGH 1 SNV 1 1 PASS rs146770492 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 236048947 236048947 T A 1 0 0 0 0 0 1 0 0 10447 1821 63 4 4 NID1 1 236048947 Nonsense_Mutation SNP T C3N-01405_T 4354578 236048947 12907475 54 22528 ACTN2 0 . GRCh38 1 236761144 236761144 + Missense_Mutation SNP G G A rs200854335 C3N-01405_T C3N-01405_N G G c.2497G>A p.Ala833Thr p.A833T ENST00000542672 20/21 469 441 28 363 363 0 strelka-varscan-mutect ACTN2,missense_variant,p.Ala625Thr,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Ala833Thr,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Ala833Thr,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; A ENST00000542672 Transcript missense_variant 2717/4906 2497/2685 833/894 A/T Gcc/Acc rs200854335,COSM1340383,COSM5154476,COSM5269719,COSM533501 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.11) 20/21 Gene3D:1.10.238.10,Pfam_domain:PF08726,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM01184,Superfamily_domains:SSF47473 uncertain_significance 0,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS rs200854335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 236761144 236761144 G A 1 0 0 0 0 1 0 0 0 249 1087 38 1 1 ACTN2 1 236761144 Missense_Mutation SNP G C3N-01405_T 712197 236761144 12195278 55 22529 GREM2 0 . GRCh38 1 240493440 240493440 + Silent SNP C C A C3N-01405_T C3N-01405_N C C c.36G>T p.= p.V12V ENST00000318160 2/2 54 37 17 43 43 0 strelka-varscan-mutect GREM2,synonymous_variant,p.=,ENST00000318160,NM_022469.3; A ENST00000318160 Transcript synonymous_variant 303/4170 36/507 12/168 V gtG/gtT COSM3804551 1 -1 GREM2 HGNC HGNC:17655 protein_coding YES CCDS31070.1 ENSP00000318650 Q9H772 A0A024R3Y1 UPI000006F961 NM_022469.3 2/2 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR15283:SF2,hmmpanther:PTHR15283,PIRSF_domain:PIRSF037254 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 240493440 240493440 C A 1 0 0 0 0 0 0 0 1 6642 581 21 2 2 GREM2 1 240493440 Silent SNP C C3N-01405_T 3732296 240493440 8462982 56 22530 OR14I1 0 . GRCh38 1 248681583 248681583 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.722C>A p.Pro241His p.P241H ENST00000342623 1/1 125 111 14 134 134 0 strelka-varscan-mutect OR14I1,missense_variant,p.Pro241His,ENST00000342623,NM_001004734.1; T ENST00000342623 Transcript missense_variant 722/936 722/936 241/311 P/H cCc/cAc 1 -1 OR14I1 HGNC HGNC:19575 protein_coding YES CCDS31125.1 ENSP00000339726 A6ND48 UPI0000199BC9 NM_001004734.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF316,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1272040059 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 248681583 248681583 G T 1 0 0 0 0 1 0 0 0 11024 1232 43 2 2 OR14I1 1 248681583 Missense_Mutation SNP G C3N-01405_T 8188143 248681583 274839 57 22531 TPO 0 . GRCh38 2 1456174 1456174 + Missense_Mutation SNP C C G rs756113203 C3N-01405_T C3N-01405_N C C c.711C>G p.Ile237Met p.I237M ENST00000345913 7/17 554 449 105 416 416 0 strelka-varscan-mutect TPO,missense_variant,p.Ile166Met,ENST00000422464,;TPO,missense_variant,p.Ile237Met,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Ile237Met,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Ile237Met,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Ile237Met,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Ile237Met,ENST00000382198,NM_175722.3;TPO,downstream_gene_variant,,ENST00000423320,;TPO,intron_variant,,ENST00000497517,; G ENST00000345913 Transcript missense_variant 802/3145 711/2802 237/933 I/M atC/atG rs756113203 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 deleterious(0.03) 7/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS rs756113203 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 1456174 1456174 C G 1 0 0 0 0 1 0 0 0 16891 874 31 4 4 TPO 2 1456174 Missense_Mutation SNP C C3N-01405_T 1456174 240737355 58 22532 TPO 0 . GRCh38 2 1484686 1484686 + Missense_Mutation SNP G G A rs761068957 C3N-01405_T C3N-01405_N G G c.1429G>A p.Ala477Thr p.A477T ENST00000345913 9/17 502 410 92 437 437 0 strelka-varscan-mutect TPO,missense_variant,p.Ala406Thr,ENST00000422464,;TPO,missense_variant,p.Ala477Thr,ENST00000345913,NM_000547.5;TPO,missense_variant,p.Ala477Thr,ENST00000329066,NM_001206744.1;TPO,missense_variant,p.Ala477Thr,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,missense_variant,p.Ala477Thr,ENST00000346956,NM_175721.3;TPO,missense_variant,p.Ala304Thr,ENST00000382198,NM_175722.3;TPO,missense_variant,p.Ala9Thr,ENST00000446278,;TPO,missense_variant,p.Ala8Thr,ENST00000469607,;TPO,non_coding_transcript_exon_variant,,ENST00000497517,;TPO,non_coding_transcript_exon_variant,,ENST00000462973,; A ENST00000345913 Transcript missense_variant 1520/3145 1429/2802 477/933 A/T Gcc/Acc rs761068957,COSM4987513,COSM4987514 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 tolerated(0.08) 9/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs761068957 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 1484686 1484686 G A 1 0 0 0 0 1 0 0 0 16891 1087 38 1 1 TPO 2 1484686 Missense_Mutation SNP G C3N-01405_T 28512 1484686 240708843 59 22533 APOB 0 . GRCh38 2 21007671 21007671 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.9197G>T p.Gly3066Val p.G3066V ENST00000233242 26/29 287 220 67 219 218 1 strelka-varscan-mutect APOB,missense_variant,p.Gly3066Val,ENST00000233242,NM_000384.2; A ENST00000233242 Transcript missense_variant 9325/14121 9197/13692 3066/4563 G/V gGg/gTg 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 deleterious(0) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 21007671 21007671 C A 1 0 0 0 0 1 0 0 0 907 623 22 2 2 APOB 2 21007671 Missense_Mutation SNP C C3N-01405_T 19522985 21007671 221185858 60 22534 ADCY3 0 . GRCh38 2 24834850 24834850 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1749G>T p.Glu583Asp p.E583D ENST00000260600 9/21 223 189 34 156 156 0 strelka-varscan-mutect ADCY3,missense_variant,p.Glu583Asp,ENST00000260600,NM_004036.3;ADCY3,missense_variant,p.Glu583Asp,ENST00000405392,NM_001320613.1;ADCY3,missense_variant,p.Glu276Asp,ENST00000606682,;ADCY3,downstream_gene_variant,,ENST00000435135,;ADCY3,downstream_gene_variant,,ENST00000427849,;ADCY3,upstream_gene_variant,,ENST00000455323,;ADCY3,upstream_gene_variant,,ENST00000450524,;ADCY3,downstream_gene_variant,,ENST00000454027,; A ENST00000260600 Transcript missense_variant 2601/5050 1749/3435 583/1144 E/D gaG/gaT 1 -1 ADCY3 HGNC HGNC:234 protein_coding YES CCDS1715.1 ENSP00000260600 O60266 UPI000013D0ED NM_004036.3 tolerated(0.1) 9/21 Low_complexity_(Seg):seg,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF291,PIRSF_domain:PIRSF039050 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 24834850 24834850 C A 1 0 0 0 0 1 0 0 0 339 796 28 2 2 ADCY3 2 24834850 Missense_Mutation SNP C C3N-01405_T 3827179 24834850 217358679 61 22535 C2orf71 0 . GRCh38 2 29070654 29070654 + Missense_Mutation SNP G G T rs757774860 C3N-01405_T C3N-01405_N G G c.3608C>A p.Pro1203Gln p.P1203Q ENST00000331664 1/2 457 343 114 298 298 0 strelka-varscan C2orf71,missense_variant,p.Pro1203Gln,ENST00000331664,NM_001029883.2; T ENST00000331664 Transcript missense_variant 3608/7044 3608/3867 1203/1288 P/Q cCg/cAg rs757774860,COSM3380137 1 -1 C2orf71 HGNC HGNC:34383 protein_coding YES CCDS42669.1 ENSP00000332809 A6NGG8 UPI0000251DD8 NM_001029883.2 tolerated(0.26) 1/2 Pfam_domain:PF15449,hmmpanther:PTHR22017 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 29070654 29070654 G T 1 0 0 0 0 1 0 0 0 2045 1116 39 1 1 C2orf71 2 29070654 Missense_Mutation SNP G C3N-01405_T 4235804 29070654 213122875 62 22536 ALK 0 . GRCh38 2 29193742 29193742 + Missense_Mutation SNP A A T rs763814257 C3N-01405_T C3N-01405_N A A c.4345T>A p.Ser1449Thr p.S1449T ENST00000389048 29/29 83 64 19 55 55 0 strelka-varscan ALK,missense_variant,p.Ser1449Thr,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Ser1072Thr,ENST00000618119,;ALK,missense_variant,p.Ser409Thr,ENST00000431873,;CLIP4,downstream_gene_variant,,ENST00000401617,; T ENST00000389048 Transcript missense_variant 5252/6220 4345/4863 1449/1620 S/T Tct/Act rs763814257 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 tolerated(0.39) 29/29 Low_complexity_(Seg):seg,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF276 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 29193742 29193742 A T 1 0 0 0 0 1 0 0 0 625 304 11 4 4 ALK 2 29193742 Missense_Mutation SNP A C3N-01405_T 123088 29193742 212999787 63 22537 EHD3 0 . GRCh38 2 31260663 31260663 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.656A>T p.Asn219Ile p.N219I ENST00000322054 4/6 180 150 30 111 111 0 strelka-varscan EHD3,missense_variant,p.Asn219Ile,ENST00000322054,NM_014600.2; T ENST00000322054 Transcript missense_variant 941/4636 656/1608 219/535 N/I aAc/aTc 1 1 EHD3 HGNC HGNC:3244 protein_coding YES CCDS1774.1 ENSP00000327116 Q9NZN3 UPI0000140D07 NM_014600.2 deleterious(0) 4/6 Gene3D:3.40.50.300,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00350,PROSITE_profiles:PS51718,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF67,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 31260663 31260663 A T 1 0 0 0 0 1 0 0 0 4815 43 2 4 4 EHD3 2 31260663 Missense_Mutation SNP A C3N-01405_T 2066921 31260663 210932866 64 22538 SRD5A2 0 . GRCh38 2 31531441 31531441 + Silent SNP T T A novel C3N-01405_T C3N-01405_N T T c.477A>T p.= p.I159I ENST00000622030 3/5 261 207 54 218 218 0 strelka-varscan SRD5A2,synonymous_variant,p.=,ENST00000622030,NM_000348.3;AL133247.2,intron_variant,,ENST00000435713,; A ENST00000622030 Transcript synonymous_variant 644/4648 477/765 159/254 I atA/atT 1 -1 SRD5A2 HGNC HGNC:11285 protein_coding YES CCDS74503.1 ENSP00000477587 P31213 UPI000017954A NM_000348.3 3/5 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50244,hmmpanther:PTHR10556,PIRSF_domain:PIRSF015596,Pfam_domain:PF02544 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 31531441 31531441 T A 1 0 0 0 0 0 0 0 1 15496 1744 61 4 4 SRD5A2 2 31531441 Silent SNP T C3N-01405_T 270778 31531441 210662088 65 22539 VIT 0 . GRCh38 2 36775044 36775044 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.779C>A p.Pro260His p.P260H ENST00000379242 9/16 224 171 53 135 135 0 strelka-varscan VIT,missense_variant,p.Pro260His,ENST00000379242,NM_053276.3;VIT,missense_variant,p.Pro260His,ENST00000389975,NM_001177969.1;VIT,missense_variant,p.Pro260His,ENST00000401530,NM_001177970.1;VIT,missense_variant,p.Pro27His,ENST00000464309,;VIT,5_prime_UTR_variant,,ENST00000497382,;VIT,intron_variant,,ENST00000379241,NM_001177971.1;VIT,intron_variant,,ENST00000404084,; A ENST00000379242 Transcript missense_variant 1081/2810 779/2082 260/693 P/H cCt/cAt 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 deleterious(0) 9/16 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 36775044 36775044 C A 1 0 0 0 0 1 0 0 0 17718 681 24 2 2 VIT 2 36775044 Missense_Mutation SNP C C3N-01405_T 5243603 36775044 205418485 66 22540 DYNC2LI1 0 . GRCh38 2 43800850 43800850 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.667A>G p.Lys223Glu p.K223E ENST00000605786 9/13 163 109 54 137 137 0 strelka-varscan DYNC2LI1,missense_variant,p.Lys222Glu,ENST00000260605,NM_016008.3;DYNC2LI1,missense_variant,p.Lys223Glu,ENST00000605786,NM_001193464.1;DYNC2LI1,missense_variant,p.Lys206Glu,ENST00000378587,;DYNC2LI1,non_coding_transcript_exon_variant,,ENST00000489222,;DYNC2LI1,downstream_gene_variant,,ENST00000462426,;DYNC2LI1,downstream_gene_variant,,ENST00000479242,;DYNC2LI1,upstream_gene_variant,,ENST00000482738,; G ENST00000605786 Transcript missense_variant 724/1346 667/1059 223/352 K/E Aaa/Gaa 1 1 DYNC2LI1 HGNC HGNC:24595 protein_coding YES CCDS62903.1 ENSP00000474032 Q8TCX1 UPI00000704B1 NM_001193464.1 deleterious(0.04) 9/13 Gene3D:3.40.50.300,hmmpanther:PTHR13236 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 43800850 43800850 A G 1 0 0 0 0 1 0 0 0 4671 363 13 5 5 DYNC2LI1 2 43800850 Missense_Mutation SNP A C3N-01405_T 7025806 43800850 198392679 67 22541 LRPPRC 0 . GRCh38 2 43976146 43976146 + Missense_Mutation SNP G G T rs540075575 C3N-01405_T C3N-01405_N G G c.734C>A p.Ala245Asp p.A245D ENST00000260665 6/38 205 155 50 179 179 0 strelka-varscan LRPPRC,missense_variant,p.Ala245Asp,ENST00000260665,NM_133259.3;LRPPRC,missense_variant,p.Ala245Asp,ENST00000409946,;LRPPRC,missense_variant,p.Ala245Asp,ENST00000409659,;LRPPRC,missense_variant,p.Ala219Asp,ENST00000447246,; T ENST00000260665 Transcript missense_variant 792/6335 734/4185 245/1394 A/D gCt/gAt rs540075575 1 -1 LRPPRC HGNC HGNC:15714 protein_coding YES CCDS33189.1 ENSP00000260665 P42704 E5KNY5 UPI000019B4D2 NM_133259.3 deleterious(0) 6/38 PROSITE_profiles:PS51375,hmmpanther:PTHR24015,hmmpanther:PTHR24015:SF187,TIGRFAM_domain:TIGR00756,Pfam_domain:PF17177 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 43976146 43976146 G T 1 0 0 0 0 1 0 0 0 8860 985 34 2 2 LRPPRC 2 43976146 Missense_Mutation SNP G C3N-01405_T 175296 43976146 198217383 68 22542 NRXN1 0 . GRCh38 2 50053295 50053295 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.4224C>A p.= p.P1408P ENST00000404971 22/24 240 195 45 175 175 0 strelka-varscan NRXN1,synonymous_variant,p.=,ENST00000406316,NM_004801.4;NRXN1,synonymous_variant,p.=,ENST00000625672,;NRXN1,synonymous_variant,p.=,ENST00000404971,NM_001135659.1;NRXN1,synonymous_variant,p.=,ENST00000401669,;NRXN1,synonymous_variant,p.=,ENST00000405472,;NRXN1,synonymous_variant,p.=,ENST00000630543,;NRXN1,synonymous_variant,p.=,ENST00000342183,NM_138735.2;NRXN1,synonymous_variant,p.=,ENST00000401710,;NRXN1,synonymous_variant,p.=,ENST00000628364,;NRXN1,synonymous_variant,p.=,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,3_prime_UTR_variant,,ENST00000637906,; T ENST00000404971 Transcript synonymous_variant 5564/7578 4224/4644 1408/1547 P ccC/ccA 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 22/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 50053295 50053295 G T 1 0 0 0 0 0 0 0 1 10724 1219 43 2 2 NRXN1 2 50053295 Silent SNP G C3N-01405_T 6077149 50053295 192140234 69 22543 NRXN1 0 . GRCh38 2 50053493 50053493 + Nonsense_Mutation SNP G G T rs774439924 C3N-01405_T C3N-01405_N G G c.4026C>A p.Tyr1342Ter p.Y1342* ENST00000404971 22/24 439 341 98 298 298 0 strelka-varscan NRXN1,stop_gained,p.Tyr1272Ter,ENST00000406316,NM_004801.4;NRXN1,stop_gained,p.Tyr1294Ter,ENST00000625672,;NRXN1,stop_gained,p.Tyr1342Ter,ENST00000404971,NM_001135659.1;NRXN1,stop_gained,p.Tyr1302Ter,ENST00000401669,;NRXN1,stop_gained,p.Tyr1290Ter,ENST00000405472,;NRXN1,stop_gained,p.Tyr1294Ter,ENST00000630543,;NRXN1,stop_gained,p.Tyr237Ter,ENST00000342183,NM_138735.2;NRXN1,stop_gained,p.Tyr267Ter,ENST00000401710,;NRXN1,stop_gained,p.Tyr267Ter,ENST00000628364,;NRXN1,5_prime_UTR_variant,,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,3_prime_UTR_variant,,ENST00000637906,; T ENST00000404971 Transcript stop_gained 5366/7578 4026/4644 1342/1547 Y/* taC/taA rs774439924 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 22/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 50053493 50053493 G T 1 0 0 0 0 0 1 0 0 10724 1372 48 2 2 NRXN1 2 50053493 Nonsense_Mutation SNP G C3N-01405_T 198 50053493 192140036 70 22544 AFTPH 0 . GRCh38 2 64552384 64552384 + Missense_Mutation SNP A A T rs138916712 C3N-01405_T C3N-01405_N A A c.910A>T p.Ile304Leu p.I304L ENST00000238855 2/10 187 136 51 129 129 0 strelka-varscan AFTPH,missense_variant,p.Ile304Leu,ENST00000238855,NM_203437.3;AFTPH,missense_variant,p.Ile304Leu,ENST00000238856,NM_001002243.2,NM_017657.4;AFTPH,missense_variant,p.Ile304Leu,ENST00000409933,;AFTPH,upstream_gene_variant,,ENST00000409183,;AC008074.1,downstream_gene_variant,,ENST00000623932,;AFTPH,non_coding_transcript_exon_variant,,ENST00000498706,;AFTPH,upstream_gene_variant,,ENST00000487769,; T ENST00000238855 Transcript missense_variant 1250/4113 910/2811 304/936 I/L Ata/Tta rs138916712 1 1 AFTPH HGNC HGNC:25951 protein_coding YES CCDS46303.1 ENSP00000238855 Q6ULP2 UPI00003E1F8E NM_203437.3 tolerated_low_confidence(1) 2/10 hmmpanther:PTHR16156:SF9,hmmpanther:PTHR16156 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 64552384 64552384 A T 1 0 0 0 0 1 0 0 0 441 217 8 4 4 AFTPH 2 64552384 Missense_Mutation SNP A C3N-01405_T 14498891 64552384 177641145 71 22545 MEIS1 0 . GRCh38 2 66569095 66569095 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1160G>T p.Trp387Leu p.W387L ENST00000272369 12/13 241 197 44 132 132 0 strelka-varscan MEIS1,missense_variant,p.Trp387Leu,ENST00000272369,NM_002398.2;MEIS1,missense_variant,p.Trp322Leu,ENST00000495021,;MEIS1,3_prime_UTR_variant,,ENST00000488550,;MEIS1,intron_variant,,ENST00000398506,;MEIS1,downstream_gene_variant,,ENST00000560281,;AC007392.3,upstream_gene_variant,,ENST00000433396,;MEIS1,non_coding_transcript_exon_variant,,ENST00000409517,;MEIS1,intron_variant,,ENST00000542964,;MEIS1,downstream_gene_variant,,ENST00000475239,;MEIS1,downstream_gene_variant,,ENST00000606455,;MEIS1,downstream_gene_variant,,ENST00000450027,; T ENST00000272369 Transcript missense_variant 1617/4291 1160/1173 387/390 W/L tGg/tTg 1 1 MEIS1 HGNC HGNC:7000 protein_coding YES CCDS46309.1 ENSP00000272369 O00470 UPI000000DA5A NM_002398.2 deleterious_low_confidence(0) 12/13 hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF126 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 66569095 66569095 G T 1 0 0 0 0 1 0 0 0 9411 1357 47 2 2 MEIS1 2 66569095 Missense_Mutation SNP G C3N-01405_T 2016711 66569095 175624434 72 22546 RAB11FIP5 0 . GRCh38 2 73089189 73089189 + Silent SNP T T G novel C3N-01405_T C3N-01405_N T T c.558A>C p.= p.P186P ENST00000258098 2/5 593 490 103 399 399 0 strelka-varscan RAB11FIP5,synonymous_variant,p.=,ENST00000486777,;RAB11FIP5,synonymous_variant,p.=,ENST00000258098,NM_015470.2;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000475951,;RAB11FIP5,upstream_gene_variant,,ENST00000482554,;RAB11FIP5,upstream_gene_variant,,ENST00000479196,; G ENST00000258098 Transcript synonymous_variant 799/4342 558/1962 186/653 P ccA/ccC 1 -1 RAB11FIP5 HGNC HGNC:24845 protein_coding YES CCDS1923.1 ENSP00000258098 Q9BXF6 UPI000007079C NM_015470.2 2/5 hmmpanther:PTHR15746:SF14,hmmpanther:PTHR15746 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 73089189 73089189 T G 1 0 0 0 0 0 0 0 1 13055 1799 63 5 5 RAB11FIP5 2 73089189 Silent SNP T C3N-01405_T 6520094 73089189 169104340 73 22547 REG1A 0 . GRCh38 2 79120925 79120925 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.64G>T p.Gly22Cys p.G22C ENST00000233735 2/6 72 65 7 56 56 0 strelka-varscan REG1A,missense_variant,p.Gly22Cys,ENST00000233735,NM_002909.4;REG1A,splice_region_variant,,ENST00000488524,;REG1A,splice_region_variant,,ENST00000485184,;REG1A,splice_region_variant,,ENST00000461579,; T ENST00000233735 Transcript missense_variant,splice_region_variant 167/808 64/501 22/166 G/C Ggc/Tgc COSM5646780 1 1 REG1A HGNC HGNC:9951 protein_coding YES CCDS1964.1 ENSP00000233735 P05451 UPI000012E72D NM_002909.4 deleterious(0) 2/6 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF55 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -15.61677 1 1 1 1 0 T 3 4 74 79120925 79120925 G T 1 0 0 0 0 1 0 0 0 13380 1014 35 2 2 REG1A 2 79120925 Missense_Mutation SNP G C3N-01405_T 6031736 79120925 163072604 74 22548 DNAH6 0 . GRCh38 2 84707000 84707000 + Silent SNP A A G novel C3N-01405_T C3N-01405_N A A c.8832A>G p.= p.V2944V ENST00000389394 53/77 150 113 37 157 157 0 strelka-varscan DNAH6,synonymous_variant,p.=,ENST00000389394,NM_001370.1;DNAH6,synonymous_variant,p.=,ENST00000237449,; G ENST00000389394 Transcript synonymous_variant 8969/12795 8832/12477 2944/4158 V gtA/gtG 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 53/77 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF12777 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 84707000 84707000 A G 1 0 0 0 0 0 0 0 1 4420 349 13 5 5 DNAH6 2 84707000 Silent SNP A C3N-01405_T 5586075 84707000 157486529 75 22549 SNRNP200 0 . GRCh38 2 96297424 96297424 + Missense_Mutation SNP C C A rs754637490 C3N-01405_T C3N-01405_N C C c.1316G>T p.Arg439Leu p.R439L ENST00000323853 11/45 465 380 85 327 327 0 strelka-varscan SNRNP200,missense_variant,p.Arg439Leu,ENST00000323853,NM_014014.4; A ENST00000323853 Transcript missense_variant 1394/7165 1316/6411 439/2136 R/L cGt/cTt rs754637490 1 -1 SNRNP200 HGNC HGNC:30859 protein_coding YES CCDS2020.1 ENSP00000317123 O75643 UPI0000207C53 NM_014014.4 tolerated(0.63) 11/45 PIRSF_domain:PIRSF039073,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 96297424 96297424 C A 1 0 0 0 0 1 0 0 0 15172 536 19 1 1 SNRNP200 2 96297424 Missense_Mutation SNP C C3N-01405_T 11590424 96297424 145896105 76 22550 RNF149 0 . GRCh38 2 101308278 101308278 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.311G>T p.Arg104Leu p.R104L ENST00000295317 1/7 225 199 26 160 160 0 strelka-varscan RNF149,missense_variant,p.Arg104Leu,ENST00000295317,NM_173647.3;MIR5696,upstream_gene_variant,,ENST00000578474,;RNF149,missense_variant,p.Arg104Leu,ENST00000424632,; A ENST00000295317 Transcript missense_variant 419/2458 311/1203 104/400 R/L cGa/cTa 1 -1 RNF149 HGNC HGNC:23137 protein_coding YES CCDS2051.1 ENSP00000295317 Q8NC42 UPI0000366F4A NM_173647.3 tolerated(0.4) 1/7 Gene3D:3.50.30.30,hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF39,Superfamily_domains:SSF52025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 101308278 101308278 C A 1 0 0 0 0 1 0 0 0 13628 884 31 1 1 RNF149 2 101308278 Missense_Mutation SNP C C3N-01405_T 5010854 101308278 140885251 77 22551 IL18R1 0 . GRCh38 2 102386925 102386925 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.874C>A p.Leu292Ile p.L292I ENST00000409599 9/12 331 280 51 245 243 2 strelka-varscan IL18R1,missense_variant,p.Leu292Ile,ENST00000409599,;IL18R1,missense_variant,p.Leu292Ile,ENST00000233957,NM_003855.3,NM_001282399.1;IL18R1,missense_variant,p.Leu292Ile,ENST00000410040,; A ENST00000409599 Transcript missense_variant 1230/3854 874/1626 292/541 L/I Cta/Ata 1 1 IL18R1 HGNC HGNC:5988 protein_coding YES CCDS2060.1 ENSP00000387211 Q13478 UPI000012D871 tolerated(0.06) 9/12 PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF6,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 102386925 102386925 C A 1 0 0 0 0 1 0 0 0 7555 912 32 2 2 IL18R1 2 102386925 Missense_Mutation SNP C C3N-01405_T 1078647 102386925 139806604 78 22552 ST6GAL2 0 . GRCh38 2 106843733 106843733 + Missense_Mutation SNP C C T rs751305558 C3N-01405_T C3N-01405_N C C c.245G>A p.Arg82His p.R82H ENST00000409382 2/6 98 81 17 72 72 0 strelka-varscan ST6GAL2,missense_variant,p.Arg82His,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Arg82His,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Arg82His,ENST00000409087,NM_001142352.1;ST6GAL2,downstream_gene_variant,,ENST00000419159,;AC016994.2,downstream_gene_variant,,ENST00000425419,; T ENST00000409382 Transcript missense_variant 856/7275 245/1590 82/529 R/H cGc/cAc rs751305558 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 2/6 hmmpanther:PTHR13713:SF61,hmmpanther:PTHR13713 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 74 106843733 106843733 C T 1 0 0 0 0 1 0 0 0 15600 768 27 1 1 ST6GAL2 2 106843733 Missense_Mutation SNP C C3N-01405_T 4456808 106843733 135349796 79 22553 LRP1B 0 . GRCh38 2 140867687 140867687 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.4482A>T p.Lys1494Asn p.K1494N ENST00000389484 27/91 176 166 10 157 157 0 strelka-varscan LRP1B,missense_variant,p.Lys1494Asn,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Lys639Asn,ENST00000434794,; A ENST00000389484 Transcript missense_variant 5454/16535 4482/13800 1494/4599 K/N aaA/aaT 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 27/91 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF105,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.98222 0.9999995 1 1 1 0 A 3 1 74 140867687 140867687 T A 1 0 0 0 0 1 0 0 0 8850 1606 56 4 4 LRP1B 2 140867687 Missense_Mutation SNP T C3N-01405_T 34023954 140867687 101325842 80 22554 KCNJ3 0 . GRCh38 2 154855134 154855134 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1327G>C p.Val443Leu p.V443L ENST00000295101 3/3 178 162 16 162 162 0 strelka-varscan KCNJ3,missense_variant,p.Val443Leu,ENST00000295101,NM_002239.3;KCNJ3,3_prime_UTR_variant,,ENST00000544049,NM_001260508.1;KCNJ3,downstream_gene_variant,,ENST00000493505,; C ENST00000295101 Transcript missense_variant 1804/5021 1327/1506 443/501 V/L Gtt/Ctt 1 1 KCNJ3 HGNC HGNC:6264 protein_coding YES CCDS2200.1 ENSP00000295101 P48549 UPI000012D899 NM_002239.3 tolerated_low_confidence(0.2) 3/3 Prints_domain:PR01327 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 154855134 154855134 G C 1 0 0 0 0 1 0 0 0 7969 1029 36 4 4 KCNJ3 2 154855134 Missense_Mutation SNP G C3N-01405_T 13987447 154855134 87338395 81 22555 CCDC148 0 . GRCh38 2 158220617 158220617 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1348C>A p.Gln450Lys p.Q450K ENST00000283233 11/14 167 129 38 213 213 0 strelka-varscan CCDC148,missense_variant,p.Gln450Lys,ENST00000283233,NM_138803.3,NM_001301684.1;CCDC148,missense_variant,p.Gln459Lys,ENST00000409187,;CCDC148-AS1,intron_variant,,ENST00000412781,;CCDC148,3_prime_UTR_variant,,ENST00000454257,;CCDC148,3_prime_UTR_variant,,ENST00000448656,; T ENST00000283233 Transcript missense_variant 1662/3122 1348/1776 450/591 Q/K Cag/Aag 1 -1 CCDC148 HGNC HGNC:25191 protein_coding YES CCDS33304.1 ENSP00000283233 Q8NFR7 UPI0000208F63 NM_138803.3,NM_001301684.1 deleterious(0) 11/14 hmmpanther:PTHR21549,hmmpanther:PTHR21549:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 158220617 158220617 G T 1 0 0 0 0 1 0 0 0 2468 1386 48 2 2 CCDC148 2 158220617 Missense_Mutation SNP G C3N-01405_T 3365483 158220617 83972912 82 22556 PLA2R1 0 . GRCh38 2 159984005 159984005 + Silent SNP A A G novel C3N-01405_T C3N-01405_N A A c.2106T>C p.= p.F702F ENST00000283243 13/30 107 80 27 135 135 0 strelka-varscan PLA2R1,synonymous_variant,p.=,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,synonymous_variant,p.=,ENST00000392771,NM_001007267.2; G ENST00000283243 Transcript synonymous_variant 2313/14371 2106/4392 702/1463 F ttT/ttC 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 13/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 159984005 159984005 A G 1 0 0 0 0 0 0 0 1 12106 127 5 5 5 PLA2R1 2 159984005 Silent SNP A C3N-01405_T 1763388 159984005 82209524 83 22557 SCN7A 0 . GRCh38 2 166429244 166429244 + Missense_Mutation SNP T T A C3N-01405_T C3N-01405_N T T c.2623A>T p.Ser875Cys p.S875C ENST00000409855 16/25 171 126 45 173 173 0 strelka-varscan SCN7A,missense_variant,p.Ser875Cys,ENST00000619410,;SCN7A,missense_variant,p.Ser875Cys,ENST00000621965,;SCN7A,missense_variant,p.Ser875Cys,ENST00000409855,NM_002976.3;SCN7A,downstream_gene_variant,,ENST00000419992,;SCN7A,3_prime_UTR_variant,,ENST00000424326,; A ENST00000409855 Transcript missense_variant 2750/7183 2623/5049 875/1682 S/C Agt/Tgt COSM3313741,COSM3313742 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0.01) 16/25 Low_complexity_(Seg):seg,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF06512 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 166429244 166429244 T A 1 0 0 0 0 1 0 0 0 14192 1580 55 4 4 SCN7A 2 166429244 Missense_Mutation SNP T C3N-01405_T 6445239 166429244 75764285 84 22558 SCN7A 0 . GRCh38 2 166465882 166465882 + Missense_Mutation SNP C C A rs560243693 C3N-01405_T C3N-01405_N C C c.770G>T p.Gly257Val p.G257V ENST00000409855 7/25 325 259 66 275 275 0 strelka-varscan SCN7A,missense_variant,p.Gly257Val,ENST00000619410,;SCN7A,missense_variant,p.Gly257Val,ENST00000621965,;SCN7A,missense_variant,p.Gly257Val,ENST00000409855,NM_002976.3;SCN7A,missense_variant,p.Gly257Val,ENST00000419992,;SCN7A,missense_variant,p.Gly257Val,ENST00000441411,;SCN7A,missense_variant,p.Gly257Val,ENST00000424326,;SCN7A,upstream_gene_variant,,ENST00000497562,; A ENST00000409855 Transcript missense_variant 897/7183 770/5049 257/1682 G/V gGg/gTg rs560243693 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0) 7/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 166465882 166465882 C A 1 0 0 0 0 1 0 0 0 14192 623 22 2 2 SCN7A 2 166465882 Missense_Mutation SNP C C3N-01405_T 36638 166465882 75727647 85 22559 G6PC2 0 . GRCh38 2 168907954 168907954 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.943C>G p.His315Asp p.H315D ENST00000375363 5/5 456 358 98 375 375 0 strelka-varscan G6PC2,missense_variant,p.His315Asp,ENST00000375363,NM_021176.2;SPC25,intron_variant,,ENST00000451987,;G6PC2,downstream_gene_variant,,ENST00000429379,NM_001081686.1;G6PC2,downstream_gene_variant,,ENST00000421979,;G6PC2,non_coding_transcript_exon_variant,,ENST00000461586,;SPC25,intron_variant,,ENST00000472216,;G6PC2,3_prime_UTR_variant,,ENST00000282075,; G ENST00000375363 Transcript missense_variant 1035/1214 943/1068 315/355 H/D Cac/Gac 1 1 G6PC2 HGNC HGNC:28906 protein_coding YES CCDS2230.1 ENSP00000364512 Q9NQR9 UPI0000048D51 NM_021176.2 tolerated(0.46) 5/5 PIRSF_domain:PIRSF000905,hmmpanther:PTHR12591,hmmpanther:PTHR12591:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 168907954 168907954 C G 1 0 0 0 0 1 0 0 0 6015 826 29 4 4 G6PC2 2 168907954 Missense_Mutation SNP C C3N-01405_T 2442072 168907954 73285575 86 22560 LRP2 0 . GRCh38 2 169280391 169280391 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1300C>A p.His434Asn p.H434N ENST00000263816 11/79 247 227 20 209 209 0 strelka-varscan LRP2,missense_variant,p.His434Asn,ENST00000263816,NM_004525.2;LRP2,missense_variant,p.His434Asn,ENST00000443831,; T ENST00000263816 Transcript missense_variant 1586/15808 1300/13968 434/4655 H/N Cac/Aac 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 tolerated(0.47) 11/79 Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 169280391 169280391 G T 1 0 0 0 0 1 0 0 0 8851 1290 45 2 2 LRP2 2 169280391 Missense_Mutation SNP G C3N-01405_T 372437 169280391 72913138 87 22561 UBR3 0 . GRCh38 2 169895194 169895194 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1119G>T p.Met373Ile p.M373I ENST00000418381 7/39 60 51 9 96 96 0 strelka-varscan UBR3,missense_variant,p.Met373Ile,ENST00000272793,;UBR3,missense_variant,p.Met373Ile,ENST00000418381,NM_172070.3; T ENST00000418381 Transcript missense_variant 1119/7951 1119/5667 373/1888 M/I atG/atT 1 1 UBR3 HGNC HGNC:30467 protein_coding YES CCDS2238.2 ENSP00000396068 Q6ZT12 UPI00015FA088 NM_172070.3 tolerated(0.23) 7/39 hmmpanther:PTHR21497 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -19.90449 0.9999999 1 1 1 0 T 3 4 74 169895194 169895194 G T 1 0 0 0 0 1 0 0 0 17427 1348 47 2 2 UBR3 2 169895194 Missense_Mutation SNP G C3N-01405_T 614803 169895194 72298335 88 22562 SP3 0 . GRCh38 2 173955575 173955575 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.937G>T p.Gly313Cys p.G313C ENST00000310015 4/7 290 229 61 293 292 1 strelka-varscan SP3,missense_variant,p.Gly313Cys,ENST00000310015,NM_003111.4,NM_001172712.1;SP3,missense_variant,p.Gly245Cys,ENST00000418194,NM_001017371.4;SP3,missense_variant,p.Gly270Cys,ENST00000416195,;SP3,downstream_gene_variant,,ENST00000483084,;SP3,downstream_gene_variant,,ENST00000462904,;SP3,downstream_gene_variant,,ENST00000490182,; A ENST00000310015 Transcript missense_variant 1468/6359 937/2346 313/781 G/C Ggt/Tgt 1 -1 SP3 HGNC HGNC:11208 protein_coding YES CCDS2254.1 ENSP00000310301 Q02447 UPI000019B3E0 NM_003111.4,NM_001172712.1 deleterious(0.01) 4/7 hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 173955575 173955575 C A 1 0 0 0 0 1 0 0 0 15291 594 21 2 2 SP3 2 173955575 Missense_Mutation SNP C C3N-01405_T 4060381 173955575 68237954 89 22563 HOXD9 0 . GRCh38 2 176123286 176123286 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.518C>A p.Ala173Asp p.A173D ENST00000249499 1/2 74 55 19 57 57 0 strelka-varscan HOXD9,missense_variant,p.Ala173Asp,ENST00000249499,NM_014213.3;HOXD10,downstream_gene_variant,,ENST00000249501,NM_002148.3;HOXD-AS2,intron_variant,,ENST00000440016,;HOXD10,downstream_gene_variant,,ENST00000490088,;HOXD10,downstream_gene_variant,,ENST00000549469,; A ENST00000249499 Transcript missense_variant 567/1870 518/1059 173/352 A/D gCc/gAc 1 1 HOXD9 HGNC HGNC:5140 protein_coding YES CCDS2267.2 ENSP00000249499 P28356 UPI000004A10E NM_014213.3 tolerated(0.64) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF113,Pfam_domain:PF04617 MODERATE 1 SNV 1 1 PASS . . 0 194 15 0 0 0 0 0 -20 0.9998308 1 1 1 0 A 3 1 74 176123286 176123286 C A 1 0 0 0 0 1 0 0 0 7220 739 26 2 2 HOXD9 2 176123286 Missense_Mutation SNP C C3N-01405_T 2167711 176123286 66070243 90 22564 DNAJC10 0 . GRCh38 2 182743677 182743677 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.1271A>T p.Lys424Ile p.K424I ENST00000264065 14/24 192 180 12 218 218 0 strelka-varscan DNAJC10,missense_variant,p.Lys424Ile,ENST00000264065,NM_018981.2;DNAJC10,missense_variant,p.Lys378Ile,ENST00000616986,NM_001271581.1;DNAJC10,intron_variant,,ENST00000613960,;DNAJC10,downstream_gene_variant,,ENST00000537515,;DNAJC10,3_prime_UTR_variant,,ENST00000418559,;DNAJC10,non_coding_transcript_exon_variant,,ENST00000491074,;DNAJC10,downstream_gene_variant,,ENST00000444005,; T ENST00000264065 Transcript missense_variant 1686/20129 1271/2382 424/793 K/I aAa/aTa 1 1 DNAJC10 HGNC HGNC:24637 protein_coding YES CCDS33345.1 ENSP00000264065 Q8IXB1 UPI000007376C NM_018981.2 deleterious(0) 14/24 hmmpanther:PTHR24078:SF235,hmmpanther:PTHR24078,Gene3D:3.40.30.10,PIRSF_domain:PIRSF037293,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 182743677 182743677 A T 1 0 0 0 0 1 0 0 0 4443 14 1 4 4 DNAJC10 2 182743677 Missense_Mutation SNP A C3N-01405_T 6620391 182743677 59449852 91 22565 ZNF804A 0 . GRCh38 2 184935946 184935946 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.550G>T p.Ala184Ser p.A184S ENST00000302277 4/4 164 119 45 142 142 0 strelka-varscan ZNF804A,missense_variant,p.Ala184Ser,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Ala99Ser,ENST00000613975,; T ENST00000302277 Transcript missense_variant 1144/4690 550/3630 184/1209 A/S Gct/Tct 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.84) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 184935946 184935946 G T 1 0 0 0 0 1 0 0 0 18755 1319 46 2 2 ZNF804A 2 184935946 Missense_Mutation SNP G C3N-01405_T 2192269 184935946 57257583 92 22566 DNAH7 0 . GRCh38 2 195897746 195897746 + Missense_Mutation SNP T T A rs769316672 C3N-01405_T C3N-01405_N T T c.4568A>T p.Asn1523Ile p.N1523I ENST00000312428 29/65 60 40 20 75 74 1 strelka-varscan DNAH7,missense_variant,p.Asn1523Ile,ENST00000312428,NM_018897.2;DNAH7,non_coding_transcript_exon_variant,,ENST00000475293,; A ENST00000312428 Transcript missense_variant 4669/12394 4568/12075 1523/4024 N/I aAt/aTt rs769316672 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0) 29/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 195897746 195897746 T A 1 0 0 0 0 1 0 0 0 4421 1493 52 4 4 DNAH7 2 195897746 Missense_Mutation SNP T C3N-01405_T 10961800 195897746 46295783 93 22567 MARCH4 0 . GRCh38 2 216259317 216259317 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.1228G>A p.Val410Met p.V410M ENST00000273067 4/4 13 7 6 16 16 0 strelka-varscan MARCH4,missense_variant,p.Val410Met,ENST00000273067,NM_020814.2;AC012513.6,upstream_gene_variant,,ENST00000417481,; T ENST00000273067 Transcript missense_variant 2995/4447 1228/1233 410/410 V/M Gtg/Atg 1 -1 MARCH4 HGNC HGNC:29269 protein_coding YES CCDS33376.1 ENSP00000273067 Q9P2E8 UPI00001C1DB9 NM_020814.2 deleterious(0) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.37175 1 1 1 1 0 T 3 4 74 216259317 216259317 C T 1 0 0 0 0 1 0 0 0 9228 565 20 3 3 MARCH4 2 216259317 Missense_Mutation SNP C C3N-01405_T 20361571 216259317 25934212 94 22568 PTPRN 0 . GRCh38 2 219294992 219294992 + Silent SNP G G T C3N-01405_T C3N-01405_N G G c.2658C>A p.= p.P886P ENST00000295718 19/23 113 78 35 105 105 0 strelka-varscan PTPRN,synonymous_variant,p.=,ENST00000295718,NM_002846.3;PTPRN,synonymous_variant,p.=,ENST00000409251,NM_001199763.1;PTPRN,synonymous_variant,p.=,ENST00000423636,NM_001199764.1;PTPRN,synonymous_variant,p.=,ENST00000443981,;MIR153-1,upstream_gene_variant,,ENST00000384914,;AC114803.3,upstream_gene_variant,,ENST00000417355,;PTPRN,non_coding_transcript_exon_variant,,ENST00000497977,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,upstream_gene_variant,,ENST00000460801,;PTPRN,downstream_gene_variant,,ENST00000489650,;PTPRN,downstream_gene_variant,,ENST00000486480,; T ENST00000295718 Transcript synonymous_variant 2899/3784 2658/2940 886/979 P ccC/ccA COSM719895 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 19/23 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 219294992 219294992 G T 1 0 0 0 0 0 0 0 1 12961 1219 43 2 2 PTPRN 2 219294992 Silent SNP G C3N-01405_T 3035675 219294992 22898537 95 22569 SPEG 0 . GRCh38 2 219484101 219484101 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.6638A>T p.Asp2213Val p.D2213V ENST00000312358 30/41 270 208 62 234 234 0 strelka-varscan SPEG,missense_variant,p.Asp2213Val,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript missense_variant 6770/10782 6638/9804 2213/3267 D/V gAc/gTc 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0.01) 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 219484101 219484101 A T 1 0 0 0 0 1 0 0 0 15387 275 10 4 4 SPEG 2 219484101 Missense_Mutation SNP A C3N-01405_T 189109 219484101 22709428 96 22570 NYAP2 0 . GRCh38 2 225409048 225409048 + Silent SNP C C G novel C3N-01405_T C3N-01405_N C C c.168C>G p.= p.A56A ENST00000636099 3/7 209 158 51 223 223 0 strelka-varscan NYAP2,synonymous_variant,p.=,ENST00000636099,;NYAP2,synonymous_variant,p.=,ENST00000272907,NM_020864.1; G ENST00000636099 Transcript synonymous_variant 1214/5461 168/1962 56/653 A gcC/gcG 1 1 NYAP2 HGNC HGNC:29291 protein_coding YES CCDS46529.1 ENSP00000490942 UPI00001C1DB6 3/7 hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF1,Pfam_domain:PF15439 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 225409048 225409048 C G 1 0 0 0 0 0 0 0 1 10873 668 24 4 4 NYAP2 2 225409048 Silent SNP C C3N-01405_T 5924947 225409048 16784481 97 22571 SNED1 0 . GRCh38 2 241053295 241053295 + Missense_Mutation SNP C C G rs376197439 C3N-01405_T C3N-01405_N C C c.2226C>G p.His742Gln p.H742Q ENST00000310397 16/32 38 31 7 44 44 0 strelka-varscan-mutect SNED1,missense_variant,p.His742Gln,ENST00000310397,NM_001080437.1;SNED1,missense_variant,p.His742Gln,ENST00000405547,;SNED1,missense_variant,p.His742Gln,ENST00000401884,;SNED1,downstream_gene_variant,,ENST00000401644,;SNED1,downstream_gene_variant,,ENST00000431690,;AC005237.4,intron_variant,,ENST00000458377,;SNED1,non_coding_transcript_exon_variant,,ENST00000469006,;SNED1,downstream_gene_variant,,ENST00000483962,; G ENST00000310397 Transcript missense_variant 2226/8174 2226/4242 742/1413 H/Q caC/caG rs376197439,COSM2910037,COSM4311757 1 1 SNED1 HGNC HGNC:24696 protein_coding YES CCDS46562.1 ENSP00000308893 Q8TER0 UPI0000DD7AB0 NM_001080437.1 tolerated(1) 16/32 PROSITE_profiles:PS50923,hmmpanther:PTHR24033,Gene3D:2gy5A03,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs376197439 . 0 201 9 0 0 0 0 0 -17.58921 0.9999958 1 1 1 0 G 3 3 74 241053295 241053295 C G 1 0 0 0 0 1 0 0 0 15166 535 19 4 4 SNED1 2 241053295 Missense_Mutation SNP C C3N-01405_T 15644247 241053295 1140234 98 22572 CHL1 0 . GRCh38 3 365997 365997 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1633T>A p.Leu545Met p.L545M ENST00000256509 15/28 210 188 22 159 158 1 strelka-mutect CHL1,missense_variant,p.Leu545Met,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Leu545Met,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Leu529Met,ENST00000397491,NM_001253387.1;CHL1-AS1,intron_variant,,ENST00000417612,;CHL1-AS1,intron_variant,,ENST00000608098,;CHL1,downstream_gene_variant,,ENST00000471332,;CHL1,3_prime_UTR_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant 2275/8023 1633/3675 545/1224 L/M Ttg/Atg 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 deleterious(0.01) 15/28 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 365997 365997 T A 1 0 0 0 0 1 0 0 0 3108 1490 52 4 4 CHL1 3 365997 Missense_Mutation SNP T C3N-01405_T 365997 197929562 99 22573 TOP2B 0 . GRCh38 3 25598354 25598354 + Nonsense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.4819G>T p.Glu1607Ter p.E1607* ENST00000435706 36/36 128 120 8 118 118 0 strelka-varscan-mutect TOP2B,stop_gained,p.Glu1607Ter,ENST00000435706,NM_001068.3;TOP2B,stop_gained,p.Glu1612Ter,ENST00000264331,;RARB,downstream_gene_variant,,ENST00000330688,NM_001290266.1,NM_001290277.1,NM_000965.4;RARB,downstream_gene_variant,,ENST00000437042,NM_001290276.1,NM_016152.3;RARB,downstream_gene_variant,,ENST00000458646,NM_001290217.1;RARB,downstream_gene_variant,,ENST00000383772,NM_001290216.1;RARB,downstream_gene_variant,,ENST00000462272,;RARB,downstream_gene_variant,,ENST00000479097,;RARB,downstream_gene_variant,,ENST00000480001,;TOP2B,3_prime_UTR_variant,,ENST00000413971,; A ENST00000435706 Transcript stop_gained 5021/5389 4819/4866 1607/1621 E/* Gag/Tag 1 -1 TOP2B HGNC HGNC:11990 protein_coding YES CCDS46776.1 ENSP00000396704 Q02880 UPI000002B59A NM_001068.3 36/36 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 25598354 25598354 C A 1 0 0 0 0 0 1 0 0 16842 922 32 2 2 TOP2B 3 25598354 Nonsense_Mutation SNP C C3N-01405_T 25232357 25598354 172697205 100 22574 CCDC13 0 . GRCh38 3 42752660 42752660 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.428A>G p.Lys143Arg p.K143R ENST00000310232 4/16 256 209 47 232 232 0 strelka-varscan-mutect CCDC13,missense_variant,p.Lys143Arg,ENST00000310232,NM_144719.3;CCDC13,non_coding_transcript_exon_variant,,ENST00000435327,;CCDC13,non_coding_transcript_exon_variant,,ENST00000492806,;CCDC13,non_coding_transcript_exon_variant,,ENST00000479576,;RP4-613B23.5,downstream_gene_variant,,ENST00000431549,; C ENST00000310232 Transcript missense_variant 512/2943 428/2148 143/715 K/R aAg/aGg 1 -1 CCDC13 HGNC HGNC:26358 protein_coding YES CCDS2705.1 ENSP00000309836 Q8IYE1 UPI00001AEF4E NM_144719.3 tolerated(0.37) 4/16 hmmpanther:PTHR31935,hmmpanther:PTHR31935:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 42752660 42752660 T C 1 0 0 0 0 1 0 0 0 2457 1609 56 5 5 CCDC13 3 42752660 Missense_Mutation SNP T C3N-01405_T 17154306 42752660 155542899 101 22575 LMOD3 0 . GRCh38 3 69120007 69120007 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.348C>A p.= p.A116A ENST00000420581 2/3 127 94 33 129 129 0 strelka-varscan-mutect LMOD3,synonymous_variant,p.=,ENST00000420581,;LMOD3,synonymous_variant,p.=,ENST00000475434,;LMOD3,synonymous_variant,p.=,ENST00000489031,NM_001304418.1,NM_198271.4; T ENST00000420581 Transcript synonymous_variant 528/4086 348/1683 116/560 A gcC/gcA 1 -1 LMOD3 HGNC HGNC:6649 protein_coding YES CCDS46862.1 ENSP00000414670 Q0VAK6 UPI00001612AC 2/3 hmmpanther:PTHR10901:SF3,hmmpanther:PTHR10901,Pfam_domain:PF03250 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 69120007 69120007 G T 1 0 0 0 0 0 0 0 1 8785 1219 43 2 2 LMOD3 3 69120007 Silent SNP G C3N-01405_T 26367347 69120007 129175552 102 22576 FRG2C 0 . GRCh38 3 75665643 75665643 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.451A>T p.Arg151Trp p.R151W ENST00000308062 4/4 394 316 78 305 305 0 strelka-varscan-mutect FRG2C,missense_variant,p.Arg151Trp,ENST00000308062,NM_001124759.1;FRG2C,missense_variant,p.Arg150Trp,ENST00000464571,;DUX4L26,upstream_gene_variant,,ENST00000489078,; T ENST00000308062 Transcript missense_variant 501/2078 451/849 151/282 R/W Agg/Tgg 1 1 FRG2C HGNC HGNC:33626 protein_coding YES CCDS43108.1 ENSP00000312299 A6NGY1 UPI0000160BC9 NM_001124759.1 deleterious(0.01) 4/4 Pfam_domain:PF15315,Prints_domain:PR02074,hmmpanther:PTHR31883,hmmpanther:PTHR31883:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 75665643 75665643 A T 1 0 0 0 0 1 0 0 0 5917 179 7 4 4 FRG2C 3 75665643 Missense_Mutation SNP A C3N-01405_T 6545636 75665643 122629916 103 22577 ROBO1 0 . GRCh38 3 78639777 78639777 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.3004A>T p.Ser1002Cys p.S1002C ENST00000464233 22/31 133 106 27 104 103 1 strelka-varscan-mutect ROBO1,missense_variant,p.Ser882Cys,ENST00000436010,;ROBO1,missense_variant,p.Ser957Cys,ENST00000618833,;ROBO1,missense_variant,p.Ser876Cys,ENST00000618846,;ROBO1,missense_variant,p.Ser1002Cys,ENST00000464233,NM_002941.3;ROBO1,missense_variant,p.Ser957Cys,ENST00000495273,NM_133631.3;ROBO1,missense_variant,p.Ser957Cys,ENST00000467549,NM_001145845.1;ROBO1,non_coding_transcript_exon_variant,,ENST00000498428,; A ENST00000464233 Transcript missense_variant 3118/6742 3004/4956 1002/1651 S/C Agc/Tgc 1 -1 ROBO1 HGNC HGNC:10249 protein_coding YES CCDS54611.1 ENSP00000420321 Q9Y6N7 UPI00000713D9 NM_002941.3 deleterious(0.01) 22/31 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF107 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 78639777 78639777 T A 1 0 0 0 0 1 0 0 0 13691 1580 55 4 4 ROBO1 3 78639777 Missense_Mutation SNP T C3N-01405_T 2974134 78639777 119655782 104 22578 OR5AC2 0 . GRCh38 3 98087369 98087369 + Missense_Mutation SNP G G T rs145997815 C3N-01405_T C3N-01405_N G G c.197G>T p.Gly66Val p.G66V ENST00000358642 1/1 163 127 36 106 106 0 strelka-varscan-mutect OR5AC2,missense_variant,p.Gly66Val,ENST00000358642,NM_054106.1; T ENST00000358642 Transcript missense_variant 197/930 197/930 66/309 G/V gGt/gTt rs145997815 1 1 OR5AC2 HGNC HGNC:15431 protein_coding YES CCDS33796.1 ENSP00000351466 Q9NZP5 UPI0000441EFD NM_054106.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF96,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs145997815 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 98087369 98087369 G T 1 0 0 0 0 1 0 0 0 11213 1261 44 2 2 OR5AC2 3 98087369 Missense_Mutation SNP G C3N-01405_T 19447592 98087369 100208190 105 22579 SIDT1 0 . GRCh38 3 113616118 113616118 + Missense_Mutation SNP G G T rs376051655 C3N-01405_T C3N-01405_N G G c.2000G>T p.Arg667Leu p.R667L ENST00000393830 21/26 345 282 63 282 282 0 strelka-varscan-mutect SIDT1,missense_variant,p.Arg662Leu,ENST00000264852,NM_001322294.1,NM_001322299.1,NM_017699.2;SIDT1,missense_variant,p.Arg667Leu,ENST00000393830,NM_001308350.1;SIDT1,non_coding_transcript_exon_variant,,ENST00000463226,;SIDT1,non_coding_transcript_exon_variant,,ENST00000481891,; T ENST00000393830 Transcript missense_variant 2039/2572 2000/2499 667/832 R/L cGg/cTg rs376051655 1 1 SIDT1 HGNC HGNC:25967 protein_coding YES CCDS77790.1 ENSP00000377416 Q9NXL6 UPI0000DA58D9 NM_001308350.1 deleterious(0.02) 21/26 Pfam_domain:PF13965,hmmpanther:PTHR12185,hmmpanther:PTHR12185:SF15 MODERATE 1 SNV 1 1 PASS rs376051655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 113616118 113616118 G T 1 0 0 0 0 1 0 0 0 14566 1116 39 1 1 SIDT1 3 113616118 Missense_Mutation SNP G C3N-01405_T 15528749 113616118 84679441 106 22580 ALDH1L1 0 . GRCh38 3 126110109 126110109 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.2212G>T p.Val738Leu p.V738L ENST00000273450 20/23 109 99 10 75 75 0 strelka-varscan-mutect ALDH1L1,missense_variant,p.Val728Leu,ENST00000393434,NM_012190.3;ALDH1L1,missense_variant,p.Val738Leu,ENST00000273450,NM_001270364.1;ALDH1L1,missense_variant,p.Val728Leu,ENST00000472186,;ALDH1L1,missense_variant,p.Val627Leu,ENST00000452905,NM_001270365.1;ALDH1L1,splice_region_variant,,ENST00000455064,;ALDH1L1,splice_region_variant,,ENST00000393431,;ALDH1L1-AS1,downstream_gene_variant,,ENST00000512384,;ALDH1L1,splice_region_variant,,ENST00000467370,;ALDH1L1,non_coding_transcript_exon_variant,,ENST00000462808,; A ENST00000273450 Transcript missense_variant,splice_region_variant 2430/3179 2212/2739 738/912 V/L Gta/Tta 1 -1 ALDH1L1 HGNC HGNC:3978 protein_coding YES CCDS58851.1 ENSP00000273450 O75891 UPI0000425C57 NM_001270364.1 tolerated(0.07) 20/23 Gene3D:3.40.309.10,Pfam_domain:PF00171,PIRSF_domain:PIRSF036489,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF120,Low_complexity_(Seg):seg,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.75905 1 1 1 1 0 A 3 1 74 126110109 126110109 C A 1 0 0 0 0 1 0 0 0 594 521 18 2 2 ALDH1L1 3 126110109 Missense_Mutation SNP C C3N-01405_T 12493991 126110109 72185450 107 22581 COL6A5 0 . GRCh38 3 130422756 130422756 + Nonsense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.5074G>T p.Gly1692Ter p.G1692* ENST00000265379 28/43 167 140 27 147 147 0 strelka-varscan-mutect COL6A5,stop_gained,p.Gly1692Ter,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,stop_gained,p.Gly1692Ter,ENST00000312481,; T ENST00000265379 Transcript stop_gained 5568/9214 5074/7836 1692/2611 G/* Gga/Tga 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 28/43 Low_complexity_(Seg):seg,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 130422756 130422756 G T 1 0 0 0 0 0 1 0 0 3491 1349 47 2 2 COL6A5 3 130422756 Nonsense_Mutation SNP G C3N-01405_T 4312647 130422756 67872803 108 22582 CHST2 0 . GRCh38 3 143121553 143121553 + Missense_Mutation SNP C C T C3N-01405_T C3N-01405_N C C c.737C>T p.Thr246Met p.T246M ENST00000309575 2/2 95 78 17 56 56 0 strelka-varscan-mutect CHST2,missense_variant,p.Thr246Met,ENST00000309575,NM_004267.4;RP11-80H8.4,upstream_gene_variant,,ENST00000483262,; T ENST00000309575 Transcript missense_variant 2121/4582 737/1593 246/530 T/M aCg/aTg COSM4672339 1 1 CHST2 HGNC HGNC:1970 protein_coding YES CCDS3129.1 ENSP00000307911 Q9Y4C5 V9HVX9 UPI0000073CBC NM_004267.4 deleterious(0.01) 2/2 Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1352238913 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 143121553 143121553 C T 1 0 0 0 0 1 0 0 0 3164 536 19 1 1 CHST2 3 143121553 Missense_Mutation SNP C C3N-01405_T 12698797 143121553 55174006 109 22583 MED12L 0 . GRCh38 3 151430344 151430344 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.6349G>T p.Ala2117Ser p.A2117S ENST00000474524 42/43 164 137 27 127 127 0 strelka-varscan-mutect MED12L,missense_variant,p.Ala2117Ser,ENST00000474524,NM_053002.5;MED12L,missense_variant,p.Ala1781Ser,ENST00000273432,;IGSF10,intron_variant,,ENST00000489791,;IGSF10,downstream_gene_variant,,ENST00000282466,NM_178822.4;MED12L,downstream_gene_variant,,ENST00000488092,;IGSF10,downstream_gene_variant,,ENST00000497472,; T ENST00000474524 Transcript missense_variant 6387/10744 6349/6438 2117/2145 A/S Gcc/Tcc 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 deleterious_low_confidence(0) 42/43 Low_complexity_(Seg):seg,hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999948 1 1 1 0 T 3 4 74 151430344 151430344 G T 1 0 0 0 0 1 0 0 0 9368 1203 42 2 2 MED12L 3 151430344 Missense_Mutation SNP G C3N-01405_T 8308791 151430344 46865215 110 22584 RSRC1 0 . GRCh38 3 158354886 158354886 + Silent SNP A A G C3N-01405_T C3N-01405_N A A c.561A>G p.= p.L187L ENST00000611884 6/10 96 72 24 66 66 0 strelka-varscan-mutect RSRC1,synonymous_variant,p.=,ENST00000464171,;RSRC1,synonymous_variant,p.=,ENST00000611884,NM_001271838.1;RSRC1,synonymous_variant,p.=,ENST00000295930,NM_016625.3;RSRC1,synonymous_variant,p.=,ENST00000312179,NM_001271834.1;RSRC1,synonymous_variant,p.=,ENST00000480820,;RSRC1,synonymous_variant,p.=,ENST00000475278,;RSRC1,synonymous_variant,p.=,ENST00000482822,;RSRC1,synonymous_variant,p.=,ENST00000476899,;RSRC1,synonymous_variant,p.=,ENST00000471994,;RSRC1,non_coding_transcript_exon_variant,,ENST00000471911,;RSRC1,3_prime_UTR_variant,,ENST00000480119,;RSRC1,3_prime_UTR_variant,,ENST00000477788,; G ENST00000611884 Transcript synonymous_variant 735/1738 561/1005 187/334 L ctA/ctG COSM1536876 1 1 RSRC1 HGNC HGNC:24152 protein_coding YES CCDS3181.1 ENSP00000481697 Q96IZ7 UPI000006EB23 NM_001271838.1 6/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR31968,hmmpanther:PTHR31968:SF3 1 LOW 1 SNV 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 158354886 158354886 A G 1 0 0 0 0 0 0 0 1 13972 378 14 5 5 RSRC1 3 158354886 Silent SNP A C3N-01405_T 6924542 158354886 39940673 111 22585 SI 0 . GRCh38 3 164992362 164992362 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.4877A>T p.Lys1626Met p.K1626M ENST00000264382 42/48 287 223 64 232 232 0 strelka-varscan-mutect SI,missense_variant,p.Lys1626Met,ENST00000264382,NM_001041.3; A ENST00000264382 Transcript missense_variant 4940/6011 4877/5484 1626/1827 K/M aAg/aTg 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0.01) 42/48 Pfam_domain:PF01055,Superfamily_domains:SSF51011 MODERATE 1 SNV 1 1 PASS rs1305513594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 164992362 164992362 T A 1 0 0 0 0 1 0 0 0 14561 1609 56 4 4 SI 3 164992362 Missense_Mutation SNP T C3N-01405_T 6637476 164992362 33303197 112 22586 BCHE 0 . GRCh38 3 165829680 165829680 + Silent SNP G G T rs530517316 C3N-01405_T C3N-01405_N G G c.1354C>A p.= p.R452R ENST00000264381 2/4 295 237 58 235 235 0 strelka-varscan-mutect BCHE,synonymous_variant,p.=,ENST00000264381,NM_000055.2;BCHE,intron_variant,,ENST00000488954,;BCHE,intron_variant,,ENST00000479451,;BCHE,synonymous_variant,p.=,ENST00000482958,;BCHE,synonymous_variant,p.=,ENST00000497011,; T ENST00000264381 Transcript synonymous_variant 1521/2454 1354/1809 452/602 R Cga/Aga rs530517316,CM034211,COSM1040847 1 -1 BCHE HGNC HGNC:983 protein_coding YES CCDS3198.1 ENSP00000264381 P06276 UPI0000127866 NM_000055.2 2/4 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF215,Superfamily_domains:SSF53474 0,0,1 LOW 1 SNV 1 0,1,1 1 PASS rs530517316 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 165829680 165829680 G T 1 0 0 0 0 0 0 0 1 1505 1124 39 1 1 BCHE 3 165829680 Silent SNP G C3N-01405_T 837318 165829680 32465879 113 22587 YEATS2 0 . GRCh38 3 183803989 183803989 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.3585G>T p.Trp1195Cys p.W1195C ENST00000305135 27/31 189 178 11 128 127 1 varscan-mutect YEATS2,missense_variant,p.Trp1195Cys,ENST00000305135,NM_018023.4;YEATS2-AS1,downstream_gene_variant,,ENST00000425008,;YEATS2-AS1,downstream_gene_variant,,ENST00000609195,;YEATS2-AS1,downstream_gene_variant,,ENST00000625709,;YEATS2-AS1,downstream_gene_variant,,ENST00000609871,;YEATS2,non_coding_transcript_exon_variant,,ENST00000472593,;YEATS2,upstream_gene_variant,,ENST00000468850,;YEATS2,downstream_gene_variant,,ENST00000497765,;YEATS2,upstream_gene_variant,,ENST00000481343,; T ENST00000305135 Transcript missense_variant,splice_region_variant 3780/6506 3585/4269 1195/1422 W/C tgG/tgT 1 1 YEATS2 HGNC HGNC:25489 protein_coding YES CCDS43175.1 ENSP00000306983 Q9ULM3 UPI00001BB2B9 NM_018023.4 deleterious(0) 27/31 MODERATE 1 SNV 1 1 PASS . . 0 160 0 30 20 0 0 0 -2.914726 0 0 1 0 0 T 3 4 74 183803989 183803989 G T 1 0 0 0 0 1 0 0 0 18034 1217 42 2 2 YEATS2 3 183803989 Missense_Mutation SNP G C3N-01405_T 17974309 183803989 14491570 114 22588 DGKG 0 . GRCh38 3 186298078 186298078 + Missense_Mutation SNP T T G novel C3N-01405_T C3N-01405_N T T c.296A>C p.Glu99Ala p.E99A ENST00000265022 4/25 110 87 23 79 79 0 strelka-varscan-mutect DGKG,missense_variant,p.Glu99Ala,ENST00000265022,NM_001346.2;DGKG,missense_variant,p.Glu99Ala,ENST00000344484,NM_001080744.1;DGKG,missense_variant,p.Glu99Ala,ENST00000382164,NM_001080745.1;DGKG,non_coding_transcript_exon_variant,,ENST00000480809,; G ENST00000265022 Transcript missense_variant 836/5805 296/2376 99/791 E/A gAg/gCg 1 -1 DGKG HGNC HGNC:2853 protein_coding YES CCDS3274.1 ENSP00000265022 P49619 UPI000013D5AB NM_001346.2 tolerated(0.3) 4/25 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF36,Pfam_domain:PF14513 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 186298078 186298078 T G 1 0 0 0 0 1 0 0 0 4275 1551 54 5 5 DGKG 3 186298078 Missense_Mutation SNP T C3N-01405_T 2494089 186298078 11997481 115 22589 MB21D2 0 . GRCh38 3 192798893 192798893 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.969G>T p.= p.R323R ENST00000392452 2/2 133 92 41 77 77 0 strelka-varscan-mutect MB21D2,synonymous_variant,p.=,ENST00000392452,NM_178496.3; A ENST00000392452 Transcript synonymous_variant 1290/3368 969/1476 323/491 R cgG/cgT 1 -1 MB21D2 HGNC HGNC:30438 protein_coding YES CCDS3302.2 ENSP00000376246 Q8IYB1 UPI000013FAFE NM_178496.3 2/2 hmmpanther:PTHR10656,hmmpanther:PTHR10656:SF47,Pfam_domain:PF03281,SMART_domains:SM01265 LOW 1 SNV 1 1 PASS rs1227976692 . 0 205 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 192798893 192798893 C A 1 0 0 0 0 0 0 0 1 9270 726 26 2 2 MB21D2 3 192798893 Silent SNP C C3N-01405_T 6500815 192798893 5496666 116 22590 MELTF 0 . GRCh38 3 197021465 197021465 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.651G>T p.= p.L217L ENST00000296350 6/16 264 201 63 187 187 0 strelka-varscan-mutect MELTF,synonymous_variant,p.=,ENST00000296350,NM_005929.5;MELTF,synonymous_variant,p.=,ENST00000296351,NM_033316.3;MELTF,downstream_gene_variant,,ENST00000439320,;MELTF,non_coding_transcript_exon_variant,,ENST00000489445,;MELTF,downstream_gene_variant,,ENST00000473501,;MELTF,downstream_gene_variant,,ENST00000491399,; A ENST00000296350 Transcript synonymous_variant 765/3963 651/2217 217/738 L ctG/ctT 1 -1 MELTF HGNC HGNC:7037 protein_coding YES CCDS3325.1 ENSP00000296350 P08582 UPI000013E329 NM_005929.5 6/16 Gene3D:3.40.190.10,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,Prints_domain:PR00422,PROSITE_patterns:PS00206,PROSITE_profiles:PS51408,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF21,SMART_domains:SM00094,Superfamily_domains:SSF53850 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 197021465 197021465 C A 1 0 0 0 0 0 0 0 1 9415 581 21 2 2 MELTF 3 197021465 Silent SNP C C3N-01405_T 4222572 197021465 1274094 117 22591 PDE6B 0 . GRCh38 4 625650 625650 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.24C>A p.= p.A8A ENST00000496514 1/22 260 227 33 181 181 0 strelka-varscan-mutect PDE6B,synonymous_variant,p.=,ENST00000255622,NM_001145291.1;PDE6B,synonymous_variant,p.=,ENST00000496514,NM_000283.3; A ENST00000496514 Transcript synonymous_variant 45/3232 24/2565 8/854 A gcC/gcA 1 1 PDE6B HGNC HGNC:8786 protein_coding YES CCDS33932.1 ENSP00000420295 P35913 UPI0000DBEE72 NM_000283.3 1/22 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF73 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 74 625650 625650 C A 1 0 0 0 0 0 0 0 1 11734 610 22 2 2 PDE6B 4 625650 Silent SNP C C3N-01405_T 625650 189588905 118 22592 LETM1 0 . GRCh38 4 1834847 1834847 + Nonsense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.874A>T p.Lys292Ter p.K292* ENST00000302787 5/14 150 132 18 108 107 1 strelka-varscan-mutect LETM1,stop_gained,p.Lys292Ter,ENST00000302787,NM_012318.2;LETM1,non_coding_transcript_exon_variant,,ENST00000505551,;LETM1,non_coding_transcript_exon_variant,,ENST00000466175,;LETM1,non_coding_transcript_exon_variant,,ENST00000512669,;LETM1,upstream_gene_variant,,ENST00000511977,; A ENST00000302787 Transcript stop_gained,splice_region_variant 1171/5462 874/2220 292/739 K/* Aag/Tag 1 -1 LETM1 HGNC HGNC:6556 protein_coding YES CCDS3355.1 ENSP00000305653 O95202 UPI0000073989 NM_012318.2 5/14 PROSITE_profiles:PS51758,hmmpanther:PTHR14009:SF8,hmmpanther:PTHR14009,Pfam_domain:PF07766 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 1834847 1834847 T A 1 0 0 0 0 0 1 0 0 8639 1797 62 4 4 LETM1 4 1834847 Nonsense_Mutation SNP T C3N-01405_T 1209197 1834847 188379708 119 22593 RGS12 0 . GRCh38 4 3430603 3430603 + Silent SNP C C G novel C3N-01405_T C3N-01405_N C C c.3762C>G p.= p.A1254A ENST00000344733 17/18 104 94 10 75 75 0 strelka-varscan-mutect RGS12,synonymous_variant,p.=,ENST00000382788,NM_002926.3;RGS12,synonymous_variant,p.=,ENST00000344733,NM_198229.2;RGS12,synonymous_variant,p.=,ENST00000336727,;RGS12,synonymous_variant,p.=,ENST00000338806,NM_198227.1;RGS12,intron_variant,,ENST00000509772,;RGS12,downstream_gene_variant,,ENST00000508158,;RGS12,downstream_gene_variant,,ENST00000515521,;RGS12,downstream_gene_variant,,ENST00000507246,;RGS12,non_coding_transcript_exon_variant,,ENST00000504194,;RGS12,downstream_gene_variant,,ENST00000513991,;RGS12,downstream_gene_variant,,ENST00000507041,; G ENST00000344733 Transcript synonymous_variant 4666/5469 3762/4344 1254/1447 A gcC/gcG 1 1 RGS12 HGNC HGNC:9994 protein_coding YES CCDS3366.1 ENSP00000339381 O14924 UPI0000133830 NM_198229.2 17/18 Pfam_domain:PF16612 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.81129 1 1 1 1 0 G 2 3 74 3430603 3430603 C G 1 0 0 0 0 0 0 0 1 13466 668 24 4 4 RGS12 4 3430603 Silent SNP C C3N-01405_T 1595756 3430603 186783952 120 22594 C4orf50 0 . GRCh38 4 5980246 5980246 + Silent SNP G G C novel C3N-01405_T C3N-01405_N G G c.3792C>G p.= p.L1264L ENST00000531445 7/12 144 126 18 90 90 0 strelka-varscan-mutect C4orf50,synonymous_variant,p.=,ENST00000531445,;C4orf50,synonymous_variant,p.=,ENST00000324058,; C ENST00000531445 Transcript synonymous_variant 3868/6860 3792/4527 1264/1508 L ctC/ctG 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 7/12 hmmpanther:PTHR36866,Pfam_domain:PF15030 LOW 1 SNV 1 1 PASS rs1410848481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 5980246 5980246 G C 1 0 0 0 0 0 0 0 1 2089 1277 45 4 4 C4orf50 4 5980246 Silent SNP G C3N-01405_T 2549643 5980246 184234309 121 22595 CPZ 0 . GRCh38 4 8606736 8606736 + Splice_Site SNP G G T C3N-01405_T C3N-01405_N G G c.907-1G>T p.X303_splice ENST00000360986 144 105 39 103 103 0 strelka-varscan-mutect CPZ,splice_acceptor_variant,,ENST00000382480,NM_001014448.2;CPZ,splice_acceptor_variant,,ENST00000360986,NM_001014447.2;CPZ,splice_acceptor_variant,,ENST00000315782,NM_003652.3;GPR78,splice_acceptor_variant,,ENST00000514302,;GPR78,splice_acceptor_variant,,ENST00000513120,;CPZ,splice_acceptor_variant,,ENST00000515606,; T ENST00000360986 Transcript splice_acceptor_variant -/2267 907/1959 303/652 COSM5351129 1 1 CPZ HGNC HGNC:2333 protein_coding YES CCDS33953.1 ENSP00000354255 Q66K79 UPI000020BCC5 NM_001014447.2 5/10 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 74 8606736 8606736 G T 1 0 0 0 0 0 0 1 0 3637 1014 35 2 2 CPZ 4 8606736 Splice_Site SNP G C3N-01405_T 2626490 8606736 181607819 122 22596 FAM184B 0 . GRCh38 4 17639291 17639291 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.2625C>T p.= p.A875A ENST00000265018 14/18 254 173 81 190 190 0 strelka-varscan-mutect FAM184B,synonymous_variant,p.=,ENST00000265018,NM_015688.1; A ENST00000265018 Transcript synonymous_variant 2838/6622 2625/3183 875/1060 A gcC/gcT 1 -1 FAM184B HGNC HGNC:29235 protein_coding YES CCDS47033.1 ENSP00000265018 Q9ULE4 UPI000020BD7C NM_015688.1 14/18 Low_complexity_(Seg):seg,hmmpanther:PTHR18870:SF8,hmmpanther:PTHR18870,Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 17639291 17639291 G A 1 0 0 0 0 0 0 0 1 5359 1219 43 3 3 FAM184B 4 17639291 Silent SNP G C3N-01405_T 9032555 17639291 172575264 123 22597 SLIT2 0 . GRCh38 4 20618901 20618901 + Silent SNP G G T rs763687239 C3N-01405_T C3N-01405_N G G c.4482G>T p.= p.P1494P ENST00000504154 37/37 247 226 21 172 172 0 strelka-varscan-mutect SLIT2,synonymous_variant,p.=,ENST00000504154,NM_004787.2;SLIT2,synonymous_variant,p.=,ENST00000622093,;SLIT2,synonymous_variant,p.=,ENST00000503823,NM_001289136.1;SLIT2,synonymous_variant,p.=,ENST00000273739,;SLIT2,synonymous_variant,p.=,ENST00000503837,NM_001289135.1;SLIT2,intron_variant,,ENST00000512993,;SLIT2,non_coding_transcript_exon_variant,,ENST00000508541,; T ENST00000504154 Transcript synonymous_variant 4734/6390 4482/4590 1494/1529 P ccG/ccT rs763687239,COSM1054495,COSM5278158 1 1 SLIT2 HGNC HGNC:11086 protein_coding YES CCDS3426.1 ENSP00000422591 O94813 UPI00000747E4 NM_004787.2 37/37 PROSITE_profiles:PS01225,PROSITE_patterns:PS01185,SMART_domains:SM00041 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs763687239 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 20618901 20618901 G T 1 0 0 0 0 0 0 0 1 15031 1074 38 1 1 SLIT2 4 20618901 Silent SNP G C3N-01405_T 2979610 20618901 169595654 124 22598 LIMCH1 0 . GRCh38 4 41646630 41646630 + Nonsense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.1402A>T p.Arg468Ter p.R468* ENST00000313860 12/27 366 258 108 260 260 0 strelka-varscan-mutect LIMCH1,stop_gained,p.Arg468Ter,ENST00000313860,NM_014988.3;LIMCH1,stop_gained,p.Arg314Ter,ENST00000396595,NM_001112719.2;LIMCH1,stop_gained,p.Arg302Ter,ENST00000381753,NM_001112720.2;LIMCH1,stop_gained,p.Arg853Ter,ENST00000503057,;LIMCH1,stop_gained,p.Arg297Ter,ENST00000513024,NM_001289124.1;LIMCH1,stop_gained,p.Arg456Ter,ENST00000512820,NM_001289122.1;LIMCH1,stop_gained,p.Arg468Ter,ENST00000512946,NM_001112717.2;LIMCH1,stop_gained,p.Arg468Ter,ENST00000508501,NM_001112718.2;LIMCH1,stop_gained,p.Arg468Ter,ENST00000512632,;LIMCH1,stop_gained,p.Arg309Ter,ENST00000514096,;LIMCH1,stop_gained,p.Arg302Ter,ENST00000509277,;LIMCH1,stop_gained,p.Arg309Ter,ENST00000511496,;LIMCH1,stop_gained,p.Arg303Ter,ENST00000508466,; T ENST00000313860 Transcript stop_gained 1456/6165 1402/3252 468/1083 R/* Aga/Tga 1 1 LIMCH1 HGNC HGNC:29191 protein_coding YES CCDS33977.1 ENSP00000316891 Q9UPQ0 UPI0000D61554 NM_014988.3 12/27 hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 41646630 41646630 A T 1 0 0 0 0 0 1 0 0 8705 64 3 4 4 LIMCH1 4 41646630 Nonsense_Mutation SNP A C3N-01405_T 21027729 41646630 148567925 125 22599 GRXCR1 0 . GRCh38 4 42963133 42963133 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.626G>T p.Gly209Val p.G209V ENST00000399770 2/4 298 275 23 195 194 1 strelka-varscan-mutect GRXCR1,missense_variant,p.Gly209Val,ENST00000399770,NM_001080476.2; T ENST00000399770 Transcript missense_variant,splice_region_variant 626/991 626/873 209/290 G/V gGg/gTg 1 1 GRXCR1 HGNC HGNC:31673 protein_coding YES CCDS43225.1 ENSP00000382670 A8MXD5 UPI00004191A5 NM_001080476.2 deleterious(0) 2/4 PROSITE_profiles:PS51354,hmmpanther:PTHR10168:SF65,hmmpanther:PTHR10168,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 42963133 42963133 G T 1 0 0 0 0 1 0 0 0 6694 1246 43 2 2 GRXCR1 4 42963133 Missense_Mutation SNP G C3N-01405_T 1316503 42963133 147251422 126 22600 ATP10D 0 . GRCh38 4 47591316 47591316 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.4216G>C p.Asp1406His p.D1406H ENST00000273859 23/23 188 158 30 116 116 0 strelka-varscan-mutect ATP10D,missense_variant,p.Asp1406His,ENST00000273859,NM_020453.3;CORIN,downstream_gene_variant,,ENST00000273857,NM_006587.3;CORIN,downstream_gene_variant,,ENST00000610355,NM_001278585.1;CORIN,downstream_gene_variant,,ENST00000508498,;CORIN,downstream_gene_variant,,ENST00000502252,;CORIN,downstream_gene_variant,,ENST00000505909,;ATP10D,downstream_gene_variant,,ENST00000505476,;ATP10D,downstream_gene_variant,,ENST00000505277,;ATP10D,3_prime_UTR_variant,,ENST00000503288,; C ENST00000273859 Transcript missense_variant 4485/6655 4216/4281 1406/1426 D/H Gat/Cat 1 1 ATP10D HGNC HGNC:13549 protein_coding YES CCDS3476.1 ENSP00000273859 Q9P241 UPI00001AE9B7 NM_020453.3 deleterious_low_confidence(0) 23/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 47591316 47591316 G C 1 0 0 0 0 1 0 0 0 1270 942 33 4 4 ATP10D 4 47591316 Missense_Mutation SNP G C3N-01405_T 4628183 47591316 142623239 127 22601 KDR 0 . GRCh38 4 55096254 55096254 + Frame_Shift_Del DEL A A - novel C3N-01405_T C3N-01405_N A A c.2703delT p.Leu902Ter p.L902* ENST00000263923 19/30 382 313 69 213 213 0 sindel-varindel KDR,frameshift_variant,p.Leu902Ter,ENST00000263923,NM_002253.2;RP11-530I17.1,downstream_gene_variant,,ENST00000511222,;KDR,non_coding_transcript_exon_variant,,ENST00000509309,; - ENST00000263923 Transcript frameshift_variant 2999/5831 2703/4071 901/1356 L/X ctT/ct 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 19/30 Gene3D:3.30.200.20,Pfam_domain:PF07714,PROSITE_patterns:PS00240,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00219,Superfamily_domains:SSF56112 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 55096254 55096254 A - 1 0 1 0 1 0 0 0 0 8059 233 9 0 0 KDR 4 55096254 Frame_Shift_Del DEL A C3N-01405_T 7504938 55096254 135118301 128 22602 EPHA5 0 . GRCh38 4 65490536 65490536 + Missense_Mutation SNP G G T rs746506231 C3N-01405_T C3N-01405_N G G c.1243C>A p.Leu415Ile p.L415I ENST00000622150 5/18 489 330 159 355 355 0 strelka-varscan EPHA5,missense_variant,p.Leu415Ile,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Leu415Ile,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Leu415Ile,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Leu415Ile,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Leu415Ile,ENST00000354839,NM_182472.3;EPHA5,intron_variant,,ENST00000432638,; T ENST00000622150 Transcript missense_variant 1996/8421 1243/3117 415/1038 L/I Ctt/Att rs746506231 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.41) 5/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 65490536 65490536 G T 1 0 0 0 0 1 0 0 0 5017 1000 35 2 2 EPHA5 4 65490536 Missense_Mutation SNP G C3N-01405_T 10394282 65490536 124724019 129 22603 FRAS1 0 . GRCh38 4 78477910 78477910 + Silent SNP C C T novel C3N-01405_T C3N-01405_N C C c.7947C>T p.= p.L2649L ENST00000512123 55/74 255 173 82 213 213 0 strelka-varscan FRAS1,synonymous_variant,p.=,ENST00000512123,NM_025074.6; T ENST00000512123 Transcript synonymous_variant 8387/15624 7947/12039 2649/4012 L ctC/ctT 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 55/74 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29,SMART_domains:SM00237,Superfamily_domains:SSF141072 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 78477910 78477910 C T 1 0 0 0 0 0 0 0 1 5908 813 29 3 3 FRAS1 4 78477910 Silent SNP C C3N-01405_T 12987374 78477910 111736645 130 22604 MAPK10 0 . GRCh38 4 86067879 86067879 + Silent SNP T T A rs752807441 C3N-01405_T C3N-01405_N T T c.879A>T p.= p.T293T ENST00000359221 10/14 155 112 43 128 127 1 strelka-varscan MAPK10,synonymous_variant,p.=,ENST00000395161,;MAPK10,synonymous_variant,p.=,ENST00000395169,NM_138980.2;MAPK10,synonymous_variant,p.=,ENST00000395166,;MAPK10,synonymous_variant,p.=,ENST00000359221,NM_138982.2;MAPK10,synonymous_variant,p.=,ENST00000449047,;MAPK10,synonymous_variant,p.=,ENST00000361569,NM_002753.3;MAPK10,synonymous_variant,p.=,ENST00000395160,NM_138981.2;MAPK10,synonymous_variant,p.=,ENST00000395157,;MAPK10,synonymous_variant,p.=,ENST00000515400,;MAPK10,non_coding_transcript_exon_variant,,ENST00000489368,;MAPK10,3_prime_UTR_variant,,ENST00000310816,;MAPK10,non_coding_transcript_exon_variant,,ENST00000508262,; A ENST00000359221 Transcript synonymous_variant 1406/2672 879/1395 293/464 T acA/acT rs752807441 1 -1 MAPK10 HGNC HGNC:6872 protein_coding YES CCDS34026.1 ENSP00000352157 P53779 UPI0000049042 NM_138982.2 10/14 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF162,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 86067879 86067879 T A 1 0 0 0 0 0 0 0 1 9196 1567 55 4 4 MAPK10 4 86067879 Silent SNP T C3N-01405_T 7589969 86067879 104146676 131 22605 GALNTL6 0 . GRCh38 4 172813652 172813652 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.852C>A p.Asp284Glu p.D284E ENST00000506823 7/13 85 68 17 74 74 0 strelka-varscan GALNTL6,missense_variant,p.Asp284Glu,ENST00000506823,NM_001034845.2;GALNTL6,missense_variant,p.Asp267Glu,ENST00000508122,;GALNTL6,missense_variant,p.Asp100Glu,ENST00000616459,; A ENST00000506823 Transcript missense_variant 1509/3922 852/1806 284/601 D/E gaC/gaA 1 1 GALNTL6 HGNC HGNC:33844 protein_coding YES CCDS34104.1 ENSP00000423313 Q49A17 E5D8G0 UPI000058EB5C NM_001034845.2 deleterious(0) 7/13 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF40,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 172813652 172813652 C A 1 0 0 0 0 1 0 0 0 6093 564 20 2 2 GALNTL6 4 172813652 Missense_Mutation SNP C C3N-01405_T 86745773 172813652 17400903 132 22606 78 2 GALNTL6 0 . GRCh38 4 172813656 172813656 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.856G>A p.Glu286Lys p.E286K ENST00000506823 7/13 81 67 14 65 65 0 strelka-varscan GALNTL6,missense_variant,p.Glu286Lys,ENST00000506823,NM_001034845.2;GALNTL6,missense_variant,p.Glu269Lys,ENST00000508122,;GALNTL6,missense_variant,p.Glu102Lys,ENST00000616459,; A ENST00000506823 Transcript missense_variant 1513/3922 856/1806 286/601 E/K Gaa/Aaa 1 1 GALNTL6 HGNC HGNC:33844 protein_coding YES CCDS34104.1 ENSP00000423313 Q49A17 E5D8G0 UPI000058EB5C NM_001034845.2 tolerated(0.18) 7/13 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF40,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 203 4 3 0 0 0 0 -19.99993 0.9998827 1 1 1 0 A 3 1 74 172813656 172813656 G A 1 0 0 0 0 1 0 0 0 6093 1175 41 3 3 GALNTL6 4 172813656 Missense_Mutation SNP G C3N-01405_T 4 172813656 17400899 133 22607 78 2 SLC9A3 0 . GRCh38 5 479935 479935 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1548C>A p.Ser516Arg p.S516R ENST00000264938 10/17 221 205 16 98 98 0 strelka-varscan-mutect SLC9A3,missense_variant,p.Ser516Arg,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.Ser507Arg,ENST00000514375,NM_001284351.1;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000607286,;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000606288,;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000607005,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606319,;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000534918,;CTD-2228K2.7,non_coding_transcript_exon_variant,,ENST00000606107,;SLC9A3,non_coding_transcript_exon_variant,,ENST00000507407,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606074,; T ENST00000264938 Transcript missense_variant 1558/2584 1548/2505 516/834 S/R agC/agA 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 tolerated(0.1) 10/17 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 479935 479935 G T 1 0 0 0 0 1 0 0 0 14995 1310 46 2 2 SLC9A3 5 479935 Missense_Mutation SNP G C3N-01405_T 479935 181058324 134 22608 CTNND2 0 . GRCh38 5 11022859 11022859 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.2909T>A p.Val970Glu p.V970E ENST00000304623 17/22 663 617 46 348 347 1 strelka-varscan-mutect CTNND2,missense_variant,p.Val970Glu,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Val879Glu,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Val633Glu,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Val65Glu,ENST00000458100,;RNU6-429P,upstream_gene_variant,,ENST00000384582,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,upstream_gene_variant,,ENST00000506324,;CTNND2,missense_variant,p.Val749Glu,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 3099/5481 2909/3678 970/1225 V/E gTg/gAg 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0) 17/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 11022859 11022859 A T 1 0 0 0 0 1 0 0 0 3829 159 6 4 4 CTNND2 5 11022859 Missense_Mutation SNP A C3N-01405_T 10542924 11022859 170515400 135 22609 CTNND2 0 . GRCh38 5 11346376 11346376 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.1624C>A p.Pro542Thr p.P542T ENST00000304623 9/22 28 14 14 23 23 0 strelka-varscan-mutect CTNND2,missense_variant,p.Pro542Thr,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Pro451Thr,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Pro205Thr,ENST00000503622,NM_001288716.1;CTNND2,downstream_gene_variant,,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,downstream_gene_variant,,ENST00000504354,;CTNND2,downstream_gene_variant,,ENST00000506735,;CTNND2,missense_variant,p.Pro296Thr,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 1814/5481 1624/3678 542/1225 P/T Ccc/Acc COSM1695385 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0) 9/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 1 MODERATE 1 SNV 1 1 1 PASS . . 1 204 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 11346376 11346376 G T 1 0 0 0 0 1 0 0 0 3829 1188 41 2 2 CTNND2 5 11346376 Missense_Mutation SNP G C3N-01405_T 323517 11346376 170191883 136 22610 CDH18 0 . GRCh38 5 19483483 19483483 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1700C>G p.Pro567Arg p.P567R ENST00000507958 14/15 268 134 134 169 169 0 strelka-varscan-mutect CDH18,missense_variant,p.Pro567Arg,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Pro567Arg,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Pro567Arg,ENST00000274170,;CDH18,intron_variant,,ENST00000506372,NM_001291957.1;CDH18,intron_variant,,ENST00000502796,NM_001167667.1;CDH18,intron_variant,,ENST00000515257,;CDH18,upstream_gene_variant,,ENST00000510297,; C ENST00000507958 Transcript missense_variant 2691/3542 1700/2373 567/790 P/R cCc/cGc 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 14/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999994 1 1 1 0 C 3 2 74 19483483 19483483 G C 1 0 0 0 0 1 0 0 0 2806 1232 43 4 4 CDH18 5 19483483 Missense_Mutation SNP G C3N-01405_T 8137107 19483483 162054776 137 22611 CDH12 0 . GRCh38 5 21842195 21842195 + Silent SNP G G T rs76592602 C3N-01405_T C3N-01405_N G G c.780C>A p.= p.T260T ENST00000382254 8/15 181 105 76 91 91 0 strelka-varscan-mutect CDH12,synonymous_variant,p.=,ENST00000382254,NM_004061.3;CDH12,synonymous_variant,p.=,ENST00000504376,;CDH12,synonymous_variant,p.=,ENST00000522262,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript synonymous_variant 1867/4164 780/2385 260/794 T acC/acA rs76592602 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 8/15 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs76592602 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 21842195 21842195 G T 1 0 0 0 0 0 0 0 1 2801 1103 39 1 1 CDH12 5 21842195 Silent SNP G C3N-01405_T 2358712 21842195 159696064 138 22612 PRDM9 0 . GRCh38 5 23509473 23509473 + Frame_Shift_Del DEL A A - novel C3N-01405_T C3N-01405_N A A c.75delA p.Asp26MetfsTer29 p.D26Mfs*29 ENST00000296682 3/11 376 196 180 256 256 0 sindel-varindel-pindel PRDM9,frameshift_variant,p.Asp26MetfsTer29,ENST00000296682,NM_020227.2;PRDM9,frameshift_variant,p.Asp26MetfsTer29,ENST00000502755,;PRDM9,intron_variant,,ENST00000635252,; - ENST00000296682 Transcript frameshift_variant 255/3691 73/2685 25/894 K/X Aaa/aa 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 3/11 PROSITE_profiles:PS50806 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 23509473 23509473 A - 1 0 1 0 1 0 0 0 0 12595 144 5 0 0 PRDM9 5 23509473 Frame_Shift_Del DEL A C3N-01405_T 1667278 23509473 158028786 139 22613 EGFLAM 0 . GRCh38 5 38409068 38409068 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1313T>A p.Met438Lys p.M438K ENST00000354891 10/23 247 140 107 138 138 0 strelka-varscan-mutect EGFLAM,missense_variant,p.Met438Lys,ENST00000322350,NM_152403.3;EGFLAM,missense_variant,p.Met438Lys,ENST00000354891,NM_001205301.1;EGFLAM,missense_variant,p.Met204Lys,ENST00000336740,NM_182798.2;EGFLAM,intron_variant,,ENST00000397202,; A ENST00000354891 Transcript missense_variant 1659/3963 1313/3054 438/1017 M/K aTg/aAg 1 1 EGFLAM HGNC HGNC:26810 protein_coding YES CCDS56363.1 ENSP00000346964 Q63HQ2 UPI000022C806 NM_001205301.1 deleterious(0) 10/23 PROSITE_profiles:PS50025,hmmpanther:PTHR10574:SF202,hmmpanther:PTHR10574,Gene3D:2.60.120.200,Pfam_domain:PF00054,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1391961685 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 38409068 38409068 T A 1 0 0 0 0 1 0 0 0 4802 1464 51 4 4 EGFLAM 5 38409068 Missense_Mutation SNP T C3N-01405_T 14899595 38409068 143129191 140 22614 C6 0 . GRCh38 5 41160252 41160252 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.1574C>T p.Pro525Leu p.P525L ENST00000263413 11/18 543 304 239 298 298 0 strelka-varscan-mutect C6,missense_variant,p.Pro525Leu,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Pro525Leu,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000475349,;C6,downstream_gene_variant,,ENST00000473450,;C6,non_coding_transcript_exon_variant,,ENST00000511470,; A ENST00000263413 Transcript missense_variant 1839/3661 1574/2805 525/934 P/L cCa/cTa 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 deleterious(0.01) 11/18 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Prints_domain:PR00764 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 41160252 41160252 G A 1 0 0 0 0 1 0 0 0 2111 1348 47 3 3 C6 5 41160252 Missense_Mutation SNP G C3N-01405_T 2751184 41160252 140378007 141 22615 C6 0 . GRCh38 5 41199779 41199779 + Missense_Mutation SNP C C G rs757730138 C3N-01405_T C3N-01405_N C C c.434G>C p.Arg145Pro p.R145P ENST00000263413 4/18 492 287 205 280 280 0 strelka-varscan-mutect C6,missense_variant,p.Arg145Pro,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Arg145Pro,ENST00000337836,NM_000065.3;C6,downstream_gene_variant,,ENST00000417809,;C6,downstream_gene_variant,,ENST00000433294,; G ENST00000263413 Transcript missense_variant 699/3661 434/2805 145/934 R/P cGc/cCc rs757730138,COSM738765 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 deleterious(0.04) 4/18 PROSITE_profiles:PS50068,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424,Prints_domain:PR00764 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757730138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 41199779 41199779 C G 1 0 0 0 0 1 0 0 0 2111 768 27 4 4 C6 5 41199779 Missense_Mutation SNP C C3N-01405_T 39527 41199779 140338480 142 22616 C6 0 . GRCh38 5 41203221 41203221 + Missense_Mutation SNP G G A rs150931891 C3N-01405_T C3N-01405_N G G c.10C>T p.Arg4Cys p.R4C ENST00000263413 2/18 446 409 37 255 255 0 strelka-varscan-mutect C6,missense_variant,p.Arg4Cys,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Arg4Cys,ENST00000337836,NM_000065.3;C6,missense_variant,p.Arg4Cys,ENST00000417809,;C6,missense_variant,p.Arg4Cys,ENST00000433294,; A ENST00000263413 Transcript missense_variant 275/3661 10/2805 4/934 R/C Cgc/Tgc rs150931891,COSM3855304 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 tolerated(0.12) 2/18 Cleavage_site_(Signalp):SignalP-noTM 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs150931891 . 0 208 0 0 0 0 0 2 -13.16892 0 0 1 0 0 A 3 1 74 41203221 41203221 G A 1 0 0 0 0 1 0 0 0 2111 1145 40 1 1 C6 5 41203221 Missense_Mutation SNP G C3N-01405_T 3442 41203221 140335038 143 22617 FAM169A 0 . GRCh38 5 74781765 74781765 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1708G>C p.Asp570His p.D570H ENST00000389156 13/13 144 127 17 125 125 0 strelka-varscan-mutect FAM169A,missense_variant,p.Asp570His,ENST00000389156,NM_015566.2;FAM169A,missense_variant,p.Asp510His,ENST00000510496,;NSA2,downstream_gene_variant,,ENST00000610426,NM_014886.4;NSA2,downstream_gene_variant,,ENST00000296802,NM_001271665.1;NSA2,downstream_gene_variant,,ENST00000515524,;RNU6-1330P,downstream_gene_variant,,ENST00000362775,;FAM169A,3_prime_UTR_variant,,ENST00000514215,;FAM169A,3_prime_UTR_variant,,ENST00000510609,; G ENST00000389156 Transcript missense_variant 1799/5990 1708/2013 570/670 D/H Gac/Cac 1 -1 FAM169A HGNC HGNC:29138 protein_coding YES CCDS43330.1 ENSP00000373808 Q9Y6X4 UPI000013E38E NM_015566.2 deleterious(0) 13/13 hmmpanther:PTHR22442:SF3,hmmpanther:PTHR22442 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 74781765 74781765 C G 1 0 0 0 0 1 0 0 0 5333 913 32 4 4 FAM169A 5 74781765 Missense_Mutation SNP C C3N-01405_T 33578544 74781765 106756494 144 22618 ANKRD31 0 . GRCh38 5 75104498 75104498 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.4890G>T p.= p.G1630G ENST00000274361 21/25 170 119 51 199 199 0 strelka-varscan-mutect ANKRD31,synonymous_variant,p.=,ENST00000506364,;ANKRD31,synonymous_variant,p.=,ENST00000274361,NM_001164443.1;ANKRD31,non_coding_transcript_exon_variant,,ENST00000504022,; A ENST00000274361 Transcript synonymous_variant 5082/6036 4890/5622 1630/1873 G ggG/ggT 1 -1 ANKRD31 HGNC HGNC:26853 protein_coding YES CCDS47233.1 ENSP00000274361 Q8N7Z5 UPI00001D7FAE NM_001164443.1 21/25 hmmpanther:PTHR24176,hmmpanther:PTHR24176:SF14 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 75104498 75104498 C A 1 0 0 0 0 0 0 0 1 764 610 22 2 2 ANKRD31 5 75104498 Silent SNP C C3N-01405_T 322733 75104498 106433761 145 22619 CMYA5 0 . GRCh38 5 79791027 79791027 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.11747G>T p.Ser3916Ile p.S3916I ENST00000446378 11/13 125 92 33 173 173 0 strelka-varscan-mutect CMYA5,missense_variant,p.Ser3916Ile,ENST00000446378,NM_153610.4;CTC-431G16.2,intron_variant,,ENST00000421252,;CMYA5,non_coding_transcript_exon_variant,,ENST00000506603,; T ENST00000446378 Transcript missense_variant 11778/12847 11747/12210 3916/4069 S/I aGt/aTt 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 deleterious(0) 11/13 PROSITE_profiles:PS50188,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7,Superfamily_domains:SSF49899 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 79791027 79791027 G T 1 0 0 0 0 1 0 0 0 3368 1029 36 2 2 CMYA5 5 79791027 Missense_Mutation SNP G C3N-01405_T 4686529 79791027 101747232 146 22620 RASGRF2 0 . GRCh38 5 81212512 81212512 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.3303C>A p.Asn1101Lys p.N1101K ENST00000265080 23/27 140 105 35 113 113 0 strelka-varscan-mutect RASGRF2,missense_variant,p.Asn1101Lys,ENST00000265080,NM_006909.2;CKMT2-AS1,intron_variant,,ENST00000511495,;CKMT2-AS1,intron_variant,,ENST00000503483,;RASGRF2,missense_variant,p.Asn1101Lys,ENST00000503795,; A ENST00000265080 Transcript missense_variant 3370/8167 3303/3714 1101/1237 N/K aaC/aaA 1 1 RASGRF2 HGNC HGNC:9876 protein_coding YES CCDS4052.1 ENSP00000265080 O14827 UPI0000047ABF NM_006909.2 deleterious(0.04) 23/27 PROSITE_profiles:PS50009,hmmpanther:PTHR23113:SF187,hmmpanther:PTHR23113,Pfam_domain:PF00617,Gene3D:2ii0A02,SMART_domains:SM00147,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 81212512 81212512 C A 1 0 0 0 0 1 0 0 0 13234 477 17 2 2 RASGRF2 5 81212512 Missense_Mutation SNP C C3N-01405_T 1421485 81212512 100325747 147 22621 FBN2 0 . GRCh38 5 128336025 128336025 + Silent SNP A A G novel C3N-01405_T C3N-01405_N A A c.3687T>C p.= p.P1229P ENST00000508053 34/71 417 310 107 367 367 0 strelka-varscan-mutect FBN2,synonymous_variant,p.=,ENST00000508053,;FBN2,synonymous_variant,p.=,ENST00000262464,NM_001999.3;FBN2,synonymous_variant,p.=,ENST00000619499,;FBN2,synonymous_variant,p.=,ENST00000508989,;FBN2,synonymous_variant,p.=,ENST00000507835,; G ENST00000508053 Transcript synonymous_variant 4662/11132 3687/8739 1229/2912 P ccT/ccC 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 34/71 Gene3D:2.10.25.10,PD968187,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184,Superfamily_domains:SSF57196 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 128336025 128336025 A G 1 0 0 0 0 0 0 0 1 5566 175 7 5 5 FBN2 5 128336025 Silent SNP A C3N-01405_T 47123513 128336025 53202234 148 22622 SMAD5 0 . GRCh38 5 136177387 136177387 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1305G>T p.Trp435Cys p.W435C ENST00000545279 8/8 264 184 80 288 288 0 strelka-varscan-mutect SMAD5,missense_variant,p.Trp435Cys,ENST00000545279,NM_005903.6,NM_001001419.2;SMAD5,missense_variant,p.Trp435Cys,ENST00000545620,NM_001001420.2;SMAD5,downstream_gene_variant,,ENST00000507637,;SMAD5,downstream_gene_variant,,ENST00000514777,;SMAD5,intron_variant,,ENST00000513418,; T ENST00000545279 Transcript missense_variant 1667/7012 1305/1398 435/465 W/C tgG/tgT 1 1 SMAD5 HGNC HGNC:6771 protein_coding YES CCDS75308.1 ENSP00000441954 Q99717 Q68DB7 UPI0000135A7E NM_005903.6,NM_001001419.2 deleterious(0) 8/8 PROSITE_profiles:PS51076,hmmpanther:PTHR13703:SF36,hmmpanther:PTHR13703,Gene3D:2.60.200.10,Pfam_domain:PF03166,SMART_domains:SM00524,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 136177387 136177387 G T 1 0 0 0 0 1 0 0 0 15054 1183 41 2 2 SMAD5 5 136177387 Missense_Mutation SNP G C3N-01405_T 7841362 136177387 45360872 149 22623 KLHL3 0 . GRCh38 5 137634036 137634036 + Splice_Site SNP C C A novel C3N-01405_T C3N-01405_N C C c.1450+1G>T p.X484_splice ENST00000309755 256 189 67 248 248 0 strelka-varscan-mutect KLHL3,splice_donor_variant,,ENST00000508657,NM_001257194.1;KLHL3,splice_donor_variant,,ENST00000309755,NM_017415.2;KLHL3,splice_donor_variant,,ENST00000506491,NM_001257195.1;KLHL3,downstream_gene_variant,,ENST00000505853,;KLHL3,splice_donor_variant,,ENST00000506873,;KLHL3,downstream_gene_variant,,ENST00000502381,;KLHL3,intron_variant,,ENST00000504208,;KLHL3,upstream_gene_variant,,ENST00000447439,; A ENST00000309755 Transcript splice_donor_variant -/6806 1450/1764 484/587 1 -1 KLHL3 HGNC HGNC:6354 protein_coding YES CCDS4192.1 ENSP00000312397 Q9UH77 UPI000012DE05 NM_017415.2 12/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 74 137634036 137634036 C A 1 0 0 0 0 0 0 1 0 8248 521 18 2 2 KLHL3 5 137634036 Splice_Site SNP C C3N-01405_T 1456649 137634036 43904223 150 22624 PCDHB5 0 . GRCh38 5 141135795 141135795 + Silent SNP C C T novel C3N-01405_T C3N-01405_N C C c.361C>T p.= p.L121L ENST00000231134 1/1 136 97 39 122 122 0 strelka-varscan-mutect PCDHB5,synonymous_variant,p.=,ENST00000231134,NM_015669.4;PCDHB5,intron_variant,,ENST00000623915,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;CH17-140K24.2,downstream_gene_variant,,ENST00000624192,; T ENST00000231134 Transcript synonymous_variant 578/3408 361/2388 121/795 L Ctg/Ttg 1 1 PCDHB5 HGNC HGNC:8690 protein_coding YES CCDS4247.1 ENSP00000231134 Q9Y5E4 UPI0000169DEA NM_015669.4 1/1 PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 141135795 141135795 C T 1 0 0 0 0 0 0 0 1 11632 912 32 3 3 PCDHB5 5 141135795 Silent SNP C C3N-01405_T 3501759 141135795 40402464 151 22625 PCDHB13 0 . GRCh38 5 141215443 141215443 + Silent SNP G G C novel C3N-01405_T C3N-01405_N G G c.1320G>C p.= p.L440L ENST00000341948 1/1 352 263 89 338 337 1 strelka-varscan-mutect PCDHB13,synonymous_variant,p.=,ENST00000341948,NM_018933.3;PCDHB12,downstream_gene_variant,,ENST00000239450,NM_018932.3;PCDHB12,downstream_gene_variant,,ENST00000622978,;PCDHB12,downstream_gene_variant,,ENST00000624949,;CH17-140K24.2,intron_variant,,ENST00000624192,; C ENST00000341948 Transcript synonymous_variant 1525/5061 1320/2397 440/798 L ctG/ctC 1 1 PCDHB13 HGNC HGNC:8684 protein_coding YES CCDS4255.1 ENSP00000345491 Q9Y5F0 UPI0000047816 NM_018933.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF129,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 141215443 141215443 G C 1 0 0 0 0 0 0 0 1 11625 1277 45 4 4 PCDHB13 5 141215443 Silent SNP G C3N-01405_T 79648 141215443 40322816 152 22626 PCDHGB4 0 . GRCh38 5 141389433 141389433 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1549G>T p.Ala517Ser p.A517S ENST00000519479 1/4 427 379 48 383 383 0 strelka-varscan-mutect PCDHGB4,missense_variant,p.Ala517Ser,ENST00000615384,NM_032098.1;PCDHGB4,missense_variant,p.Ala517Ser,ENST00000519479,NM_003736.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000519479 Transcript missense_variant 1549/4578 1549/2772 517/923 A/S Gcc/Tcc 1 1 PCDHGB4 HGNC HGNC:8711 protein_coding YES CCDS54928.1 ENSP00000428288 Q9UN71 UPI000006F773 NM_003736.2 tolerated(1) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF117,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 141389433 141389433 G T 1 0 0 0 0 1 0 0 0 11652 1087 38 1 1 PCDHGB4 5 141389433 Missense_Mutation SNP G C3N-01405_T 173990 141389433 40148826 153 22627 ADAM19 0 . GRCh38 5 157488335 157488335 + Missense_Mutation SNP C C G C3N-01405_T C3N-01405_N C C c.2480G>C p.Arg827Thr p.R827T ENST00000257527 21/23 186 138 48 170 170 0 strelka-varscan-mutect ADAM19,missense_variant,p.Arg827Thr,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Arg827Thr,ENST00000517905,;ADAM19,missense_variant,p.Arg398Thr,ENST00000517374,;ADAM19,3_prime_UTR_variant,,ENST00000517951,; G ENST00000257527 Transcript missense_variant 2559/6481 2480/2757 827/918 R/T aGg/aCg COSM3613282,COSM3613283,COSM3613284,COSM4906070 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 tolerated(0.33) 21/23 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 157488335 157488335 C G 1 0 0 0 0 1 0 0 0 284 681 24 4 4 ADAM19 5 157488335 Missense_Mutation SNP C C3N-01405_T 16098902 157488335 24049924 154 22628 EBF1 0 . GRCh38 5 159099434 159099434 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.45G>T p.Met15Ile p.M15I ENST00000313708 1/16 134 100 34 178 177 1 strelka-varscan-mutect EBF1,missense_variant,p.Met15Ile,ENST00000313708,NM_001324107.1,NM_024007.3,NM_001290360.1;EBF1,missense_variant,p.Met15Ile,ENST00000380654,NM_182708.1;EBF1,missense_variant,p.Met15Ile,ENST00000517373,;RP11-175K6.1,upstream_gene_variant,,ENST00000499583,;RP11-175K6.1,upstream_gene_variant,,ENST00000517335,;RP11-175K6.1,upstream_gene_variant,,ENST00000523301,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,upstream_gene_variant,,ENST00000523315,;EBF1,upstream_gene_variant,,ENST00000519739,;EBF1,upstream_gene_variant,,ENST00000522192,; A ENST00000313708 Transcript missense_variant 328/5250 45/1776 15/591 M/I atG/atT 1 -1 EBF1 HGNC HGNC:3126 protein_coding YES CCDS4343.1 ENSP00000322898 Q9UH73 UPI000000D95E NM_001324107.1,NM_024007.3,NM_001290360.1 deleterious_low_confidence(0.04) 1/16 hmmpanther:PTHR10747 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 159099434 159099434 C A 1 0 0 0 0 1 0 0 0 4704 826 29 2 2 EBF1 5 159099434 Missense_Mutation SNP C C3N-01405_T 1611099 159099434 22438825 155 22629 KCNMB1 0 . GRCh38 5 170383693 170383693 + Missense_Mutation SNP C C A C3N-01405_T C3N-01405_N C C c.292G>T p.Asp98Tyr p.D98Y ENST00000274629 3/4 397 313 84 366 365 1 strelka-varscan-mutect KCNMB1,missense_variant,p.Asp98Tyr,ENST00000274629,NM_004137.3;KCNMB1,missense_variant,p.Asp98Tyr,ENST00000521859,;KCNIP1,intron_variant,,ENST00000377360,NM_001034838.2;KCNIP1,intron_variant,,ENST00000518527,;KCNIP1,intron_variant,,ENST00000517344,; A ENST00000274629 Transcript missense_variant 735/5052 292/576 98/191 D/Y Gac/Tac COSM1696729 1 -1 KCNMB1 HGNC HGNC:6285 protein_coding YES CCDS4373.1 ENSP00000274629 Q16558 UPI0000000DBA NM_004137.3 deleterious(0) 3/4 hmmpanther:PTHR10258:SF1,hmmpanther:PTHR10258,Pfam_domain:PF03185,Prints_domain:PR01450 1 MODERATE 1 SNV 1 1 1 PASS rs1211658154 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 170383693 170383693 C A 1 0 0 0 0 1 0 0 0 7991 855 30 2 2 KCNMB1 5 170383693 Missense_Mutation SNP C C3N-01405_T 11284259 170383693 11154566 156 22630 GMPR 0 . GRCh38 6 16250296 16250296 + Missense_Mutation SNP A A C novel C3N-01405_T C3N-01405_N A A c.220A>C p.Thr74Pro p.T74P ENST00000259727 3/9 233 218 15 191 191 0 strelka-varscan-mutect GMPR,missense_variant,p.Thr74Pro,ENST00000259727,NM_006877.3; C ENST00000259727 Transcript missense_variant 334/1515 220/1038 74/345 T/P Aca/Cca 1 1 GMPR HGNC HGNC:4376 protein_coding YES CCDS4537.1 ENSP00000259727 P36959 UPI000012B8B2 NM_006877.3 deleterious(0.01) 3/9 Gene3D:3.20.20.70,HAMAP:MF_00596,Pfam_domain:PF00478,PIRSF_domain:PIRSF000235,hmmpanther:PTHR11911,hmmpanther:PTHR11911:SF61,SMART_domains:SM01240,Superfamily_domains:SSF51412,TIGRFAM_domain:TIGR01305 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 16250296 16250296 A C 1 0 0 0 0 1 0 0 0 6376 391 14 5 5 GMPR 6 16250296 Missense_Mutation SNP A C3N-01405_T 16250296 154555683 157 22631 NUP153 0 . GRCh38 6 17637613 17637613 + Silent SNP T T A novel C3N-01405_T C3N-01405_N T T c.2097A>T p.= p.L699L ENST00000537253 17/23 283 194 89 224 224 0 strelka-varscan-mutect NUP153,synonymous_variant,p.=,ENST00000537253,NM_001278209.1;NUP153,synonymous_variant,p.=,ENST00000613258,NM_001278210.1;NUP153,synonymous_variant,p.=,ENST00000262077,NM_005124.3; A ENST00000537253 Transcript synonymous_variant 2544/6030 2097/4521 699/1506 L ctA/ctT 1 -1 NUP153 HGNC HGNC:8062 protein_coding YES CCDS64359.1 ENSP00000444029 P49790 UPI0001AE7240 NM_001278209.1 17/23 PROSITE_profiles:PS50199,hmmpanther:PTHR23193:SF26,hmmpanther:PTHR23193,PROSITE_patterns:PS01358,Pfam_domain:PF00641,SMART_domains:SM00547,Superfamily_domains:SSF90209 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 17637613 17637613 T A 1 0 0 0 0 0 0 0 1 10820 1625 57 4 4 NUP153 6 17637613 Silent SNP T C3N-01405_T 1387317 17637613 153168366 158 22632 SLC17A4 0 . GRCh38 6 25769069 25769069 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.176T>C p.Ile59Thr p.I59T ENST00000377905 3/12 478 431 47 343 343 0 strelka-varscan SLC17A4,missense_variant,p.Ile5Thr,ENST00000439485,NM_001286121.1;SLC17A4,missense_variant,p.Ile59Thr,ENST00000377905,NM_005495.2;SLC17A4,missense_variant,p.Ile5Thr,ENST00000397076,; C ENST00000377905 Transcript missense_variant 295/3616 176/1494 59/497 I/T aTt/aCt 1 1 SLC17A4 HGNC HGNC:10932 protein_coding YES CCDS4564.1 ENSP00000367137 Q9Y2C5 A0A024R013 UPI0000073585 NM_005495.2 deleterious(0) 3/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF284,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 25769069 25769069 T C 1 0 0 0 0 1 0 0 0 14684 1493 52 5 5 SLC17A4 6 25769069 Missense_Mutation SNP T C3N-01405_T 8131456 25769069 145036910 159 22633 HIST1H2AH 0 . GRCh38 6 27147492 27147492 + Missense_Mutation SNP G G A C3N-01405_T C3N-01405_N G G c.364G>A p.Glu122Lys p.E122K ENST00000377459 1/1 183 165 18 137 137 0 strelka-varscan HIST1H2AH,missense_variant,p.Glu122Lys,ENST00000377459,NM_080596.2;HIST1H2BK,upstream_gene_variant,,ENST00000356950,NM_080593.2;MIR3143,upstream_gene_variant,,ENST00000584253,; A ENST00000377459 Transcript missense_variant 364/387 364/387 122/128 E/K Gag/Aag COSM4835669 1 1 HIST1H2AH HGNC HGNC:13671 protein_coding YES CCDS4622.1 ENSP00000366679 Q96KK5 A3KPC7 UPI0000073C8A NM_080596.2 tolerated_low_confidence(0.21) 1/1 hmmpanther:PTHR23430,Gene3D:1.10.20.10,Pfam_domain:PF16211,SMART_domains:SM00414 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 27147492 27147492 G A 1 0 0 0 0 1 0 0 0 7022 1291 45 3 3 HIST1H2AH 6 27147492 Missense_Mutation SNP G C3N-01405_T 1378423 27147492 143658487 160 22634 VARS2 0 . GRCh38 6 30922192 30922192 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.1973G>T p.Arg658Leu p.R658L ENST00000541562 20/30 162 146 16 121 120 1 strelka-varscan VARS2,missense_variant,p.Arg628Leu,ENST00000321897,NM_020442.5;VARS2,missense_variant,p.Arg626Leu,ENST00000542001,;VARS2,missense_variant,p.Arg658Leu,ENST00000541562,NM_001167734.1;VARS2,missense_variant,p.Arg488Leu,ENST00000625423,NM_001167733.2;VARS2,downstream_gene_variant,,ENST00000428017,;VARS2,non_coding_transcript_exon_variant,,ENST00000476162,;VARS2,downstream_gene_variant,,ENST00000467717,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;VARS2,non_coding_transcript_exon_variant,,ENST00000469358,;VARS2,upstream_gene_variant,,ENST00000473916,;VARS2,downstream_gene_variant,,ENST00000490699,;VARS2,upstream_gene_variant,,ENST00000477052,; T ENST00000541562 Transcript missense_variant 2054/3566 1973/3282 658/1093 R/L cGc/cTc COSM185214 1 1 VARS2 HGNC HGNC:21642 protein_coding YES CCDS54980.1 ENSP00000441000 Q5ST30 UPI0001BDAB0F NM_001167734.1 deleterious(0) 20/30 hmmpanther:PTHR11946,hmmpanther:PTHR11946:SF71,Gene3D:3.40.50.620,Pfam_domain:PF00133,TIGRFAM_domain:TIGR00422,Superfamily_domains:SSF52374,Prints_domain:PR00986 1 MODERATE 1 SNV 2 1 1 PASS . . 0 199 0 9 0 0 0 0 -19.99245 0.9602728 1 1 1 0 T 3 4 74 30922192 30922192 G T 1 0 0 0 0 1 0 0 0 17669 1087 38 1 1 VARS2 6 30922192 Missense_Mutation SNP G C3N-01405_T 3774700 30922192 139883787 161 22635 TCF19 0 . GRCh38 6 31161894 31161894 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.686G>T p.Arg229Leu p.R229L ENST00000376257 3/4 187 173 14 141 141 0 strelka-varscan TCF19,missense_variant,p.Arg229Leu,ENST00000376257,NM_007109.2;TCF19,missense_variant,p.Arg229Leu,ENST00000376255,NM_001077511.1;TCF19,missense_variant,p.Arg149Leu,ENST00000542218,;CCHCR1,upstream_gene_variant,,ENST00000396268,NM_001105564.1;CCHCR1,upstream_gene_variant,,ENST00000376266,NM_019052.3;CCHCR1,upstream_gene_variant,,ENST00000451521,NM_001105563.1;CCHCR1,upstream_gene_variant,,ENST00000396263,;POU5F1,downstream_gene_variant,,ENST00000513407,NM_001285986.1;POU5F1,downstream_gene_variant,,ENST00000471529,;POU5F1,downstream_gene_variant,,ENST00000620031,NM_001173531.2,NM_001285987.1,NM_203289.5;POU5F1,downstream_gene_variant,,ENST00000259915,NM_002701.5;POU5F1,downstream_gene_variant,,ENST00000606567,;POU5F1,downstream_gene_variant,,ENST00000512818,;POU5F1,downstream_gene_variant,,ENST00000441888,;CCHCR1,upstream_gene_variant,,ENST00000506831,;CCHCR1,upstream_gene_variant,,ENST00000426967,;CCHCR1,upstream_gene_variant,,ENST00000448162,;CCHCR1,upstream_gene_variant,,ENST00000455279,;CCHCR1,upstream_gene_variant,,ENST00000448141,;CCHCR1,upstream_gene_variant,,ENST00000502557,;CCHCR1,upstream_gene_variant,,ENST00000507829,;CCHCR1,upstream_gene_variant,,ENST00000507751,;CCHCR1,upstream_gene_variant,,ENST00000503420,;CCHCR1,upstream_gene_variant,,ENST00000508683,;CCHCR1,upstream_gene_variant,,ENST00000503934,;CCHCR1,upstream_gene_variant,,ENST00000507226,;CCHCR1,upstream_gene_variant,,ENST00000513222,;CCHCR1,upstream_gene_variant,,ENST00000507892,;CCHCR1,upstream_gene_variant,,ENST00000428174,;TCF19,non_coding_transcript_exon_variant,,ENST00000496421,;CCHCR1,upstream_gene_variant,,ENST00000480060,;CCHCR1,upstream_gene_variant,,ENST00000509552,;POU5F1,downstream_gene_variant,,ENST00000461401,;CCHCR1,upstream_gene_variant,,ENST00000475684,;CCHCR1,upstream_gene_variant,,ENST00000488920,;CCHCR1,upstream_gene_variant,,ENST00000508852,;CCHCR1,upstream_gene_variant,,ENST00000507459,;CCHCR1,upstream_gene_variant,,ENST00000512418,;CCHCR1,upstream_gene_variant,,ENST00000505392,; T ENST00000376257 Transcript missense_variant 1440/3290 686/1038 229/345 R/L cGa/cTa 1 1 TCF19 HGNC HGNC:11629 protein_coding YES CCDS43446.1 ENSP00000365433 Q9Y242 UPI0000071646 NM_007109.2 tolerated(0.14) 3/4 hmmpanther:PTHR15464,hmmpanther:PTHR15464:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.31979 0.9999997 1 1 1 0 T 3 4 74 31161894 31161894 G T 1 0 0 0 0 1 0 0 0 16096 1058 37 1 1 TCF19 6 31161894 Missense_Mutation SNP G C3N-01405_T 239702 31161894 139644085 162 22636 BTNL2 0 . GRCh38 6 32396154 32396154 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.963G>C p.Glu321Asp p.E321D ENST00000454136 5/7 335 242 93 256 256 0 strelka-varscan BTNL2,missense_variant,p.Glu321Asp,ENST00000454136,NM_001304561.1;BTNL2,missense_variant,p.Glu321Asp,ENST00000374993,;BTNL2,missense_variant,p.Glu44Asp,ENST00000544175,;HCG23,downstream_gene_variant,,ENST00000426643,;BTNL2,3_prime_UTR_variant,,ENST00000465865,; G ENST00000454136 Transcript missense_variant 968/1460 963/1449 321/482 E/D gaG/gaC 1 -1 BTNL2 HGNC HGNC:1142 protein_coding YES CCDS78126.1 ENSP00000390613 F8WBA1 UPI0001B79374 NM_001304561.1 deleterious(0.04) 5/7 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF15,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 32396154 32396154 C G 1 0 0 0 0 1 0 0 0 1741 680 24 4 4 BTNL2 6 32396154 Missense_Mutation SNP C C3N-01405_T 1234260 32396154 138409825 163 22637 CLPSL2 0 . GRCh38 6 35777472 35777472 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.98G>T p.Arg33Met p.R33M ENST00000360454 2/4 122 83 39 78 78 0 strelka-varscan CLPSL2,missense_variant,p.Arg33Met,ENST00000360454,NM_001286550.1;CLPSL2,missense_variant,p.Arg33Met,ENST00000403376,NM_207409.3;CLPSL1,upstream_gene_variant,,ENST00000373861,NM_001010886.3;CLPSL2,non_coding_transcript_exon_variant,,ENST00000481904,;CLPSL2,intron_variant,,ENST00000467122,; T ENST00000360454 Transcript missense_variant 102/488 98/462 33/153 R/M aGg/aTg 1 1 CLPSL2 HGNC HGNC:21250 protein_coding YES CCDS69095.1 ENSP00000353639 Q6UWE3 UPI000045742B NM_001286550.1 deleterious_low_confidence(0) 2/4 hmmpanther:PTHR10041,hmmpanther:PTHR10041:SF3,Gene3D:2.10.80.10,Pfam_domain:PF15083 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 74 35777472 35777472 G T 1 0 0 0 0 1 0 0 0 3325 1000 35 2 2 CLPSL2 6 35777472 Missense_Mutation SNP G C3N-01405_T 3381318 35777472 135028507 164 22638 GLTSCR1L 0 . GRCh38 6 42865013 42865013 + Missense_Mutation SNP G G T rs769380369 C3N-01405_T C3N-01405_N G G c.2807G>T p.Gly936Val p.G936V ENST00000314073 13/13 291 246 45 218 218 0 strelka-varscan GLTSCR1L,missense_variant,p.Gly936Val,ENST00000314073,NM_001318819.1;GLTSCR1L,missense_variant,p.Gly936Val,ENST00000394168,NM_015349.1;GLTSCR1L,missense_variant,p.Gly936Val,ENST00000614467,; T ENST00000314073 Transcript missense_variant 2983/6530 2807/3240 936/1079 G/V gGc/gTc rs769380369 1 1 GLTSCR1L HGNC HGNC:21111 protein_coding YES CCDS34451.1 ENSP00000313933 Q6AI39 UPI0000161939 NM_001318819.1 tolerated_low_confidence(0.23) 13/13 hmmpanther:PTHR15572 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 42865013 42865013 G T 1 0 0 0 0 1 0 0 0 6351 1203 42 2 2 GLTSCR1L 6 42865013 Missense_Mutation SNP G C3N-01405_T 7087541 42865013 127940966 165 22639 TTBK1 0 . GRCh38 6 43284251 43284251 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.3511C>G p.Gln1171Glu p.Q1171E ENST00000259750 14/15 104 78 26 62 62 0 strelka-varscan TTBK1,missense_variant,p.Gln1171Glu,ENST00000259750,NM_032538.1; G ENST00000259750 Transcript missense_variant 3594/6932 3511/3966 1171/1321 Q/E Cag/Gag 1 1 TTBK1 HGNC HGNC:19140 protein_coding YES CCDS34455.1 ENSP00000259750 Q5TCY1 UPI000041512B NM_032538.1 tolerated_low_confidence(0.39) 14/15 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 43284251 43284251 C G 1 0 0 0 0 1 0 0 0 17186 595 21 4 4 TTBK1 6 43284251 Missense_Mutation SNP C C3N-01405_T 419238 43284251 127521728 166 22640 PGK2 0 . GRCh38 6 49786322 49786322 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.866G>T p.Gly289Val p.G289V ENST00000304801 1/1 253 218 35 218 217 1 strelka-varscan PGK2,missense_variant,p.Gly289Val,ENST00000304801,NM_138733.4; A ENST00000304801 Transcript missense_variant 986/1657 866/1254 289/417 G/V gGg/gTg 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 deleterious(0) 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 49786322 49786322 C A 1 0 0 0 0 1 0 0 0 11880 623 22 2 2 PGK2 6 49786322 Missense_Mutation SNP C C3N-01405_T 6502071 49786322 121019657 167 22641 EYS 0 . GRCh38 6 65405329 65405329 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.901C>T p.= p.L301L ENST00000370621 6/44 183 155 28 189 189 0 strelka-varscan EYS,synonymous_variant,p.=,ENST00000503581,NM_001142800.1;EYS,synonymous_variant,p.=,ENST00000370621,NM_001292009.1;EYS,synonymous_variant,p.=,ENST00000393380,NM_001142801.1;EYS,synonymous_variant,p.=,ENST00000342421,NM_198283.1; A ENST00000370621 Transcript synonymous_variant 1428/10485 901/9498 301/3165 L Ctg/Ttg 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 6/44 hmmpanther:PTHR24033 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 65405329 65405329 G A 1 0 0 0 0 0 0 0 1 5200 933 33 3 3 EYS 6 65405329 Silent SNP G C3N-01405_T 15619007 65405329 105400650 168 22642 RRAGD 0 . GRCh38 6 89372480 89372480 + Silent SNP C C G novel C3N-01405_T C3N-01405_N C C c.1008G>C p.= p.L336L ENST00000369415 6/7 106 90 16 121 121 0 strelka-varscan RRAGD,synonymous_variant,p.=,ENST00000369415,NM_021244.4;RRAGD,synonymous_variant,p.=,ENST00000359203,; G ENST00000369415 Transcript synonymous_variant 1285/4900 1008/1203 336/400 L ctG/ctC 1 -1 RRAGD HGNC HGNC:19903 protein_coding YES CCDS5022.1 ENSP00000358423 Q9NQL2 UPI000006E549 NM_021244.4 6/7 hmmpanther:PTHR11259,hmmpanther:PTHR11259:SF5 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999938 1 1 1 0 G 2 3 74 89372480 89372480 C G 1 0 0 0 0 0 0 0 1 13929 581 21 4 4 RRAGD 6 89372480 Silent SNP C C3N-01405_T 23967151 89372480 81433499 169 22643 GPR63 0 . GRCh38 6 96799012 96799012 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.720G>T p.Gln240His p.Q240H ENST00000229955 2/2 168 111 57 186 185 1 strelka-varscan GPR63,missense_variant,p.Gln240His,ENST00000229955,NM_030784.3,NM_001143957.2;RP3-417O22.3,downstream_gene_variant,,ENST00000442184,; A ENST00000229955 Transcript missense_variant 1066/5952 720/1260 240/419 Q/H caG/caT 1 -1 GPR63 HGNC HGNC:13302 protein_coding YES CCDS5036.1 ENSP00000229955 Q9BZJ6 A8K1C4 UPI0000037594 NM_030784.3,NM_001143957.2 tolerated(0.23) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF1,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 96799012 96799012 C A 1 0 0 0 0 1 0 0 0 6588 680 24 2 2 GPR63 6 96799012 Missense_Mutation SNP C C3N-01405_T 7426532 96799012 74006967 170 22644 KLHL32 0 . GRCh38 6 97085342 97085342 + Splice_Site SNP G G C novel C3N-01405_T C3N-01405_N G G c.627+1G>C p.X209_splice ENST00000369261 98 78 20 103 103 0 strelka-varscan KLHL32,splice_donor_variant,,ENST00000536676,NM_001286250.1;KLHL32,splice_donor_variant,,ENST00000369261,NM_001323260.1,NM_052904.3;KLHL32,splice_donor_variant,,ENST00000539200,NM_001286251.1;KLHL32,splice_donor_variant,,ENST00000620278,NM_001286254.1;KLHL32,splice_donor_variant,,ENST00000447886,;KLHL32,intron_variant,,ENST00000544166,;KLHL32,intron_variant,,ENST00000369254,; C ENST00000369261 Transcript splice_donor_variant -/3698 627/1863 209/620 1 1 KLHL32 HGNC HGNC:21221 protein_coding YES CCDS5038.1 ENSP00000358265 Q96NJ5 UPI000020DFAB NM_001323260.1,NM_052904.3 6/10 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 74 97085342 97085342 G C 1 0 0 0 0 0 0 1 0 8251 1275 44 4 4 KLHL32 6 97085342 Splice_Site SNP G C3N-01405_T 286330 97085342 73720637 171 22645 ENPP1 0 . GRCh38 6 131852196 131852196 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.578A>T p.Glu193Val p.E193V ENST00000360971 5/25 249 177 72 251 251 0 strelka-varscan-mutect ENPP1,missense_variant,p.Glu193Val,ENST00000360971,NM_006208.2;ENPP1,missense_variant,p.Glu193Val,ENST00000513998,;ENPP1,downstream_gene_variant,,ENST00000486853,; T ENST00000360971 Transcript missense_variant 598/7442 578/2778 193/925 E/V gAa/gTa 1 1 ENPP1 HGNC HGNC:3356 protein_coding YES CCDS5150.2 ENSP00000354238 P22413 UPI00001303F0 NM_006208.2 deleterious(0.01) 5/25 hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF77 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 131852196 131852196 A T 1 0 0 0 0 1 0 0 0 4974 246 9 4 4 ENPP1 6 131852196 Missense_Mutation SNP A C3N-01405_T 34766854 131852196 38953783 172 22646 CYP2W1 0 . GRCh38 7 985270 985270 + Missense_Mutation SNP C C A rs769483359 C3N-01405_T C3N-01405_N C C c.592C>A p.Leu198Met p.L198M ENST00000308919 4/9 211 137 74 154 153 1 strelka-varscan-mutect CYP2W1,missense_variant,p.Leu142Met,ENST00000340150,;CYP2W1,missense_variant,p.Leu198Met,ENST00000308919,NM_017781.2;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000462453,;CYP2W1,upstream_gene_variant,,ENST00000468456,; A ENST00000308919 Transcript missense_variant 605/2304 592/1473 198/490 L/M Ctg/Atg rs769483359 1 1 CYP2W1 HGNC HGNC:20243 protein_coding YES CCDS5319.2 ENSP00000310149 Q8TAV3 UPI000013C59A NM_017781.2 deleterious(0) 4/9 hmmpanther:PTHR24300:SF183,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs769483359 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 985270 985270 C A 1 0 0 0 0 1 0 0 0 3979 680 24 2 2 CYP2W1 7 985270 Missense_Mutation SNP C C3N-01405_T 985270 158360703 173 22647 VWDE 0 . GRCh38 7 12370850 12370850 + Silent SNP A A T novel C3N-01405_T C3N-01405_N A A c.1602T>A p.= p.S534S ENST00000275358 11/29 146 91 55 115 115 0 strelka-varscan-mutect VWDE,synonymous_variant,p.=,ENST00000275358,NM_001135924.1;VWDE,5_prime_UTR_variant,,ENST00000614403,;VWDE,missense_variant,p.Trp347Arg,ENST00000521169,;VWDE,synonymous_variant,p.=,ENST00000452576,; T ENST00000275358 Transcript synonymous_variant 1791/5260 1602/4773 534/1590 S tcT/tcA 1 -1 VWDE HGNC HGNC:21897 protein_coding YES CCDS47544.1 ENSP00000275358 Q8N2E2 UPI00006C0B98 NM_001135924.1 11/29 PROSITE_profiles:PS51233,Pfam_domain:PF00094,SMART_domains:SM00216 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 12370850 12370850 A T 1 0 0 0 0 0 0 0 1 17805 175 7 4 4 VWDE 7 12370850 Silent SNP A C3N-01405_T 11385580 12370850 146975123 174 22648 POU6F2 0 . GRCh38 7 39433272 39433272 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1222C>G p.Pro408Ala p.P408A ENST00000403058 8/11 146 88 58 96 96 0 strelka-varscan POU6F2,missense_variant,p.Pro408Ala,ENST00000518318,NM_001166018.1;POU6F2,missense_variant,p.Pro353Ala,ENST00000559001,;POU6F2,missense_variant,p.Pro408Ala,ENST00000403058,NM_007252.3;POU6F2,missense_variant,p.Pro353Ala,ENST00000524147,;POU6F2,missense_variant,p.Pro400Ala,ENST00000520104,;POU6F2,missense_variant,p.Pro107Ala,ENST00000416452,; G ENST00000403058 Transcript missense_variant 1376/2335 1222/2076 408/691 P/A Ccc/Gcc 1 1 POU6F2 HGNC HGNC:21694 protein_coding YES CCDS34620.2 ENSP00000384004 P78424 UPI0000480E81 NM_007252.3 tolerated(0.06) 8/11 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF68 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 39433272 39433272 C G 1 0 0 0 0 1 0 0 0 12401 739 26 4 4 POU6F2 7 39433272 Missense_Mutation SNP C C3N-01405_T 27062422 39433272 119912701 175 22649 GCK 0 . GRCh38 7 44145709 44145709 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1044G>C p.Gln348His p.Q348H ENST00000345378 9/10 309 259 50 198 198 0 strelka-varscan-mutect GCK,missense_variant,p.Gln347His,ENST00000403799,NM_000162.3;GCK,missense_variant,p.Gln346His,ENST00000395796,NM_033508.1;GCK,missense_variant,p.Gln348His,ENST00000345378,NM_033507.1;GCK,missense_variant,p.Gln346His,ENST00000616242,;GCK,missense_variant,p.Gln330His,ENST00000437084,;GCK,missense_variant,p.Gln31His,ENST00000336642,;MYL7,upstream_gene_variant,,ENST00000458240,;MYL7,upstream_gene_variant,,ENST00000457314,;MYL7,upstream_gene_variant,,ENST00000223364,NM_021223.2;MYL7,upstream_gene_variant,,ENST00000447951,;MYL7,upstream_gene_variant,,ENST00000431007,;GCK,non_coding_transcript_exon_variant,,ENST00000473353,;MYL7,upstream_gene_variant,,ENST00000434895,;GCK,non_coding_transcript_exon_variant,,ENST00000459642,;MYL7,upstream_gene_variant,,ENST00000457910,;MYL7,upstream_gene_variant,,ENST00000431289,; G ENST00000345378 Transcript missense_variant 1206/2421 1044/1401 348/466 Q/H caG/caC 1 -1 GCK HGNC HGNC:4195 protein_coding YES CCDS5480.1 ENSP00000223366 P35557 UPI000002AB76 NM_033507.1 deleterious(0.02) 9/10 Gene3D:3.40.367.20,Pfam_domain:PF03727,PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF3,Superfamily_domains:SSF53067 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 44145709 44145709 C G 1 0 0 0 0 1 0 0 0 6163 912 32 4 4 GCK 7 44145709 Missense_Mutation SNP C C3N-01405_T 4712437 44145709 115200264 176 22650 MAGI2 0 . GRCh38 7 78256506 78256506 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1484C>G p.Ser495Cys p.S495C ENST00000354212 10/22 404 359 45 272 272 0 strelka-varscan MAGI2,missense_variant,p.Ser495Cys,ENST00000354212,NM_012301.3;MAGI2,missense_variant,p.Ser495Cys,ENST00000419488,NM_001301128.1;MAGI2,missense_variant,p.Ser332Cys,ENST00000629359,;MAGI2,missense_variant,p.Ser357Cys,ENST00000628980,;MAGI2,missense_variant,p.Ser357Cys,ENST00000535697,;MAGI2,missense_variant,p.Ser495Cys,ENST00000637441,;MAGI2,missense_variant,p.Ser185Cys,ENST00000636039,;MAGI2,missense_variant,p.Ser495Cys,ENST00000522391,;MAGI2,missense_variant,p.Ser332Cys,ENST00000626691,;MAGI2,missense_variant,p.Ser104Cys,ENST00000519748,;MAGI2,missense_variant,p.Ser104Cys,ENST00000637282,;MAGI2,missense_variant,p.Ser272Cys,ENST00000630991,;MAGI2,missense_variant,p.Ser185Cys,ENST00000636178,;MAGI2,missense_variant,p.Ser332Cys,ENST00000628781,;MAGI2,missense_variant,p.Ser327Cys,ENST00000636717,;MAGI2,downstream_gene_variant,,ENST00000636593,;MAGI2,downstream_gene_variant,,ENST00000636936,;MAGI2,missense_variant,p.Ser332Cys,ENST00000637486,;MAGI2,non_coding_transcript_exon_variant,,ENST00000520379,; C ENST00000354212 Transcript missense_variant 1738/6880 1484/4368 495/1455 S/C tCt/tGt 1 -1 MAGI2 HGNC HGNC:18957 protein_coding YES CCDS5594.1 ENSP00000346151 Q86UL8 UPI00001615D2 NM_012301.3 deleterious(0.03) 10/22 PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF27,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 78256506 78256506 G C 1 0 0 0 0 1 0 0 0 9109 942 33 4 4 MAGI2 7 78256506 Missense_Mutation SNP G C3N-01405_T 34110797 78256506 81089467 177 22651 HGF 0 . GRCh38 7 81752145 81752145 + Silent SNP G G T C3N-01405_T C3N-01405_N G G c.600C>A p.= p.V200V ENST00000222390 5/18 252 197 55 245 245 0 strelka-varscan HGF,synonymous_variant,p.=,ENST00000222390,NM_000601.4;HGF,synonymous_variant,p.=,ENST00000457544,NM_001010932.1;HGF,synonymous_variant,p.=,ENST00000423064,NM_001010934.1;HGF,synonymous_variant,p.=,ENST00000444829,NM_001010931.1;HGF,synonymous_variant,p.=,ENST00000453411,NM_001010933.1;HGF,downstream_gene_variant,,ENST00000354224,;HGF,downstream_gene_variant,,ENST00000453018,;HGF,non_coding_transcript_exon_variant,,ENST00000465234,; T ENST00000222390 Transcript synonymous_variant 827/5989 600/2187 200/728 V gtC/gtA COSM3882619 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 5/18 PROSITE_profiles:PS50070,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 81752145 81752145 G T 1 0 0 0 0 0 0 0 1 6969 929 33 2 2 HGF 7 81752145 Silent SNP G C3N-01405_T 3495639 81752145 77593828 178 22652 PCLO 0 . GRCh38 7 82954431 82954431 + Silent SNP T T A novel C3N-01405_T C3N-01405_N T T c.6522A>T p.= p.T2174T ENST00000333891 5/25 233 198 35 203 203 0 strelka-varscan PCLO,synonymous_variant,p.=,ENST00000333891,NM_033026.5;PCLO,synonymous_variant,p.=,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript synonymous_variant 6860/20329 6522/15429 2174/5142 T acA/acT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 5/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 82954431 82954431 T A 1 0 0 0 0 0 0 0 1 11671 1451 51 4 4 PCLO 7 82954431 Silent SNP T C3N-01405_T 1202286 82954431 76391542 179 22653 PCLO 0 . GRCh38 7 82966481 82966481 + Nonsense_Mutation SNP C C A rs780629154 C3N-01405_T C3N-01405_N C C c.3307G>T p.Glu1103Ter p.E1103* ENST00000333891 4/25 60 51 9 51 51 0 strelka-varscan PCLO,stop_gained,p.Glu1103Ter,ENST00000333891,NM_033026.5;PCLO,stop_gained,p.Glu1103Ter,ENST00000423517,NM_014510.2;PCLO,non_coding_transcript_exon_variant,,ENST00000461143,; A ENST00000333891 Transcript stop_gained 3645/20329 3307/15429 1103/5142 E/* Gaa/Taa rs780629154 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 4/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113,Gene3D:3.30.40.10,Pfam_domain:PF05715,Superfamily_domains:SSF57903 HIGH 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -19.91902 1 1 1 1 0 A 4 1 74 82966481 82966481 C A 1 0 0 0 0 0 1 0 0 11671 922 32 2 2 PCLO 7 82966481 Nonsense_Mutation SNP C C3N-01405_T 12050 82966481 76379492 180 22654 GRM3 0 . GRCh38 7 86839344 86839344 + Silent SNP G G T rs375932723 C3N-01405_T C3N-01405_N G G c.1830G>T p.= p.S610S ENST00000361669 4/6 300 268 32 264 263 1 strelka-varscan GRM3,synonymous_variant,p.=,ENST00000361669,NM_000840.2;GRM3,intron_variant,,ENST00000439827,; T ENST00000361669 Transcript synonymous_variant 2929/4268 1830/2640 610/879 S tcG/tcT rs375932723 1 1 GRM3 HGNC HGNC:4595 protein_coding YES CCDS5600.1 ENSP00000355316 Q14832 A4D1D0 UPI0000153EFC NM_000840.2 4/6 PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF107,Pfam_domain:PF00003,Prints_domain:PR00248 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 86839344 86839344 G T 1 0 0 0 0 0 0 0 1 6680 1103 39 1 1 GRM3 7 86839344 Silent SNP G C3N-01405_T 3872863 86839344 72506629 181 22655 ERVW-1 0 . GRCh38 7 92469028 92469028 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.1354T>A p.Leu452Ile p.L452I ENST00000493463 1/1 233 200 33 200 199 1 strelka-varscan ERVW-1,missense_variant,p.Leu452Ile,ENST00000493463,NM_014590.3;ERVW-1,missense_variant,p.Leu452Ile,ENST00000603053,NM_001130925.1;AC007566.10,intron_variant,,ENST00000427458,;ERVW-1,intron_variant,,ENST00000604270,;ERVW-1,intron_variant,,ENST00000603704,; T ENST00000493463 Transcript missense_variant 2278/2925 1354/1617 452/538 L/I Tta/Ata 1 -1 ERVW-1 HGNC HGNC:13525 protein_coding YES CCDS5626.1 ENSP00000419945 Q9UQF0 D0EYG5 UPI00000389BB NM_014590.3 deleterious(0.02) 1/1 Pfam_domain:PF00429,hmmpanther:PTHR10424,hmmpanther:PTHR10424:SF48,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 92469028 92469028 A T 1 0 0 0 0 1 0 0 0 5108 69 3 4 4 ERVW-1 7 92469028 Missense_Mutation SNP A C3N-01405_T 5629684 92469028 66876945 182 22656 TRRAP 0 . GRCh38 7 99011396 99011396 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.11156G>A p.Gly3719Glu p.G3719E ENST00000359863 71/72 265 241 24 150 150 0 strelka-varscan TRRAP,missense_variant,p.Gly3719Glu,ENST00000359863,NM_001244580.1;TRRAP,missense_variant,p.Gly3708Glu,ENST00000628380,;TRRAP,missense_variant,p.Gly3690Glu,ENST00000355540,NM_003496.3;TRRAP,missense_variant,p.Gly3708Glu,ENST00000446306,;TRRAP,missense_variant,p.Gly3448Glu,ENST00000456197,;AC004893.11,upstream_gene_variant,,ENST00000360902,; A ENST00000359863 Transcript missense_variant 11365/12677 11156/11580 3719/3859 G/E gGa/gAa 1 1 TRRAP HGNC HGNC:12347 protein_coding YES CCDS59066.1 ENSP00000352925 Q9Y4A5 UPI00004575B4 NM_001244580.1 tolerated(0.12) 71/72 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_profiles:PS50290,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF1,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 99011396 99011396 G A 1 0 0 0 0 1 0 0 0 17107 1174 41 3 3 TRRAP 7 99011396 Missense_Mutation SNP G C3N-01405_T 6542368 99011396 60334577 183 22657 MUC17 0 . GRCh38 7 101041412 101041412 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.9996C>A p.= p.T3332T ENST00000306151 3/13 170 148 22 173 173 0 strelka-varscan MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; A ENST00000306151 Transcript synonymous_variant 10060/14247 9996/13482 3332/4493 T acC/acA 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 101041412 101041412 C A 1 0 0 0 0 0 0 0 1 9973 668 24 2 2 MUC17 7 101041412 Silent SNP C C3N-01405_T 2030016 101041412 58304561 184 22658 RELN 0 . GRCh38 7 103492004 103492004 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.9392C>G p.Thr3131Ser p.T3131S ENST00000428762 58/65 317 280 37 342 342 0 strelka-varscan RELN,missense_variant,p.Thr3131Ser,ENST00000424685,;RELN,missense_variant,p.Thr3131Ser,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Thr3131Ser,ENST00000343529,NM_173054.2;CTB-107G13.1,intron_variant,,ENST00000422488,; C ENST00000428762 Transcript missense_variant 9552/11571 9392/10383 3131/3460 T/S aCt/aGt 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.87) 58/65 hmmpanther:PTHR11841 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 103492004 103492004 G C 1 0 0 0 0 1 0 0 0 13390 1029 36 4 4 RELN 7 103492004 Missense_Mutation SNP G C3N-01405_T 2450592 103492004 55853969 185 22659 PUS7 0 . GRCh38 7 105470824 105470824 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1262G>T p.Cys421Phe p.C421F ENST00000356362 11/16 64 43 21 45 45 0 strelka-varscan PUS7,missense_variant,p.Cys421Phe,ENST00000356362,NM_001318163.1,NM_001318164.1,NM_019042.3;PUS7,missense_variant,p.Cys421Phe,ENST00000469408,;PUS7,missense_variant,p.Cys421Phe,ENST00000481939,;PUS7,non_coding_transcript_exon_variant,,ENST00000478208,; A ENST00000356362 Transcript missense_variant 1477/3480 1262/1986 421/661 C/F tGc/tTc 1 -1 PUS7 HGNC HGNC:26033 protein_coding YES CCDS34725.1 ENSP00000348722 Q96PZ0 UPI00001D483E NM_001318163.1,NM_001318164.1,NM_019042.3 deleterious(0.05) 11/16 Pfam_domain:PF01142,PROSITE_profiles:PS50984,hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF1,TIGRFAM_domain:TIGR00094 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 105470824 105470824 C A 1 0 0 0 0 1 0 0 0 12991 710 25 2 2 PUS7 7 105470824 Missense_Mutation SNP C C3N-01405_T 1978820 105470824 53875149 186 22660 CPED1 0 . GRCh38 7 121130217 121130217 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.1500C>A p.= p.T500T ENST00000310396 12/23 258 226 32 224 224 0 strelka-varscan CPED1,synonymous_variant,p.=,ENST00000310396,NM_024913.4;CPED1,synonymous_variant,p.=,ENST00000450913,NM_001105533.1;CPED1,synonymous_variant,p.=,ENST00000428526,;CPED1,synonymous_variant,p.=,ENST00000423795,;CPED1,synonymous_variant,p.=,ENST00000443817,; A ENST00000310396 Transcript synonymous_variant 1967/5340 1500/3081 500/1026 T acC/acA 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 12/23 hmmpanther:PTHR14776 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 121130217 121130217 C A 1 0 0 0 0 0 0 0 1 3598 610 22 2 2 CPED1 7 121130217 Silent SNP C C3N-01405_T 15659393 121130217 38215756 187 22661 CPED1 0 . GRCh38 7 121141987 121141987 + Missense_Mutation SNP C C A rs750206720 C3N-01405_T C3N-01405_N C C c.1901C>A p.Pro634His p.P634H ENST00000310396 16/23 89 78 11 62 62 0 strelka-varscan CPED1,missense_variant,p.Pro634His,ENST00000310396,NM_024913.4;CPED1,missense_variant,p.Pro634His,ENST00000450913,NM_001105533.1;CPED1,missense_variant,p.Pro414His,ENST00000423795,; A ENST00000310396 Transcript missense_variant 2368/5340 1901/3081 634/1026 P/H cCt/cAt rs750206720 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 deleterious(0) 16/23 Pfam_domain:PF12733,hmmpanther:PTHR14776 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99974 1 1 1 1 0 A 3 1 74 121141987 121141987 C A 1 0 0 0 0 1 0 0 0 3598 681 24 2 2 CPED1 7 121141987 Missense_Mutation SNP C C3N-01405_T 11770 121141987 38203986 188 22662 GRM8 0 . GRCh38 7 126902615 126902615 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1083A>T p.Glu361Asp p.E361D ENST00000339582 6/11 135 113 22 117 117 0 strelka-varscan GRM8,missense_variant,p.Glu361Asp,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Glu361Asp,ENST00000358373,NM_001127323.1;GRM8,downstream_gene_variant,,ENST00000457830,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,non_coding_transcript_exon_variant,,ENST00000448250,;GRM8,missense_variant,p.Glu361Asp,ENST00000472701,;GRM8,missense_variant,p.Glu361Asp,ENST00000341617,; A ENST00000339582 Transcript missense_variant 1892/4057 1083/2727 361/908 E/D gaA/gaT 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.09) 6/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 126902615 126902615 T A 1 0 0 0 0 1 0 0 0 6685 1490 52 4 4 GRM8 7 126902615 Missense_Mutation SNP T C3N-01405_T 5760628 126902615 32443358 189 22663 PAX4 0 . GRCh38 7 127613807 127613807 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.487C>A p.His163Asn p.H163N ENST00000341640 4/9 248 206 42 190 190 0 strelka-varscan PAX4,missense_variant,p.His163Asn,ENST00000341640,NM_006193.2;PAX4,missense_variant,p.His161Asn,ENST00000463946,;PAX4,missense_variant,p.His161Asn,ENST00000611453,;PAX4,missense_variant,p.His163Asn,ENST00000378740,;PAX4,missense_variant,p.His171Asn,ENST00000338516,;PAX4,missense_variant,p.His161Asn,ENST00000483494,;PAX4,non_coding_transcript_exon_variant,,ENST00000477423,; T ENST00000341640 Transcript missense_variant 693/2010 487/1032 163/343 H/N Cac/Aac 1 -1 PAX4 HGNC HGNC:8618 protein_coding YES CCDS5797.1 ENSP00000339906 O43316 UPI000013C824 NM_006193.2 tolerated(0.05) 4/9 PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF14,hmmpanther:PTHR24329,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 127613807 127613807 G T 1 0 0 0 0 1 0 0 0 11566 1348 47 2 2 PAX4 7 127613807 Missense_Mutation SNP G C3N-01405_T 711192 127613807 31732166 190 22664 KLHDC10 0 . GRCh38 7 130125868 130125868 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.868C>T p.His290Tyr p.H290Y ENST00000335420 7/10 221 174 47 213 213 0 strelka-varscan KLHDC10,missense_variant,p.His290Tyr,ENST00000335420,NM_014997.3;KLHDC10,downstream_gene_variant,,ENST00000468226,; T ENST00000335420 Transcript missense_variant 1002/6437 868/1329 290/442 H/Y Cat/Tat 1 1 KLHDC10 HGNC HGNC:22194 protein_coding YES CCDS5815.1 ENSP00000334140 Q6PID8 UPI0000160705 NM_014997.3 tolerated(0.13) 7/10 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF306,SMART_domains:SM00612,Superfamily_domains:SSF101898 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 130125868 130125868 C T 1 0 0 0 0 1 0 0 0 8220 608 21 3 3 KLHDC10 7 130125868 Missense_Mutation SNP C C3N-01405_T 2512061 130125868 29220105 191 22665 COPG2 0 . GRCh38 7 130610978 130610978 + Missense_Mutation SNP G G A rs782715453 C3N-01405_T C3N-01405_N G G c.712C>T p.Arg238Cys p.R238C ENST00000425248 9/24 192 146 46 178 178 0 strelka-varscan COPG2,missense_variant,p.Arg238Cys,ENST00000425248,NM_012133.5;COPG2,missense_variant,p.Arg238Cys,ENST00000330992,NM_001290033.1; A ENST00000425248 Transcript missense_variant 792/3134 712/2616 238/871 R/C Cgc/Tgc rs782715453 1 -1 COPG2 HGNC HGNC:2237 protein_coding YES CCDS75662.1 ENSP00000402346 Q9UBF2 A0A140VK12 UPI0000000960 NM_012133.5 deleterious(0) 9/24 hmmpanther:PTHR10261:SF4,hmmpanther:PTHR10261,Pfam_domain:PF01602,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037093,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 130610978 130610978 G A 1 0 0 0 0 1 0 0 0 3524 1058 37 1 1 COPG2 7 130610978 Missense_Mutation SNP G C3N-01405_T 485110 130610978 28734995 192 22666 NUP205 0 . GRCh38 7 135587870 135587871 + Frame_Shift_Del DEL AA AA - novel C3N-01405_T C3N-01405_N AA AA c.1354_1355delAA p.Lys452GlufsTer47 p.K452Efs*47 ENST00000285968 10/43 87 70 17 74 74 0 sindel-varindel-pindel NUP205,frameshift_variant,p.Lys452GlufsTer47,ENST00000285968,NM_015135.2; - ENST00000285968 Transcript frameshift_variant 1377-1378/6266 1351-1352/6039 451/2012 K/X AAa/a 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 10/43 Pfam_domain:PF11894,hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 HIGH 1 deletion 1 3 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999963 1 1 1 0 - 7 5 74 135587870 135587870 AA - 1 0 1 0 1 0 0 0 0 10824 363 13 0 0 NUP205 7 135587870 Frame_Shift_Del DEL AA C3N-01405_T 4976892 135587870 23758103 193 22667 MGAM 0 . GRCh38 7 142056051 142056051 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.3535G>T p.Asp1179Tyr p.D1179Y ENST00000549489 29/48 294 264 30 255 255 0 strelka-varscan MGAM,missense_variant,p.Asp1179Tyr,ENST00000475668,;MGAM,missense_variant,p.Asp1179Tyr,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Asp1179Tyr,ENST00000620571,; T ENST00000549489 Transcript missense_variant 3630/6525 3535/5574 1179/1857 D/Y Gac/Tac 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 29/48 Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 142056051 142056051 G T 1 0 0 0 0 1 0 0 0 9499 1174 41 2 2 MGAM 7 142056051 Missense_Mutation SNP G C3N-01405_T 6468181 142056051 17289922 194 22668 MGAM2 0 . GRCh38 7 142140832 142140832 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1117G>T p.Asp373Tyr p.D373Y ENST00000477922 11/48 166 136 30 173 173 0 strelka-varscan MGAM2,missense_variant,p.Asp373Tyr,ENST00000477922,NM_001293626.1;MGAM2,missense_variant,p.Asp373Tyr,ENST00000550469,; T ENST00000477922 Transcript missense_variant 1171/7867 1117/7548 373/2515 D/Y Gat/Tat 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 11/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51445 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 142140832 142140832 G T 1 0 0 0 0 1 0 0 0 9500 1174 41 2 2 MGAM2 7 142140832 Missense_Mutation SNP G C3N-01405_T 84781 142140832 17205141 195 22669 NOBOX 0 . GRCh38 7 144398553 144398553 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1503G>T p.Glu501Asp p.E501D ENST00000467773 9/10 114 101 13 76 76 0 strelka-varscan NOBOX,missense_variant,p.Glu501Asp,ENST00000467773,NM_001080413.3;NOBOX,missense_variant,p.Glu469Asp,ENST00000483238,; A ENST00000467773 Transcript missense_variant 1503/2076 1503/2076 501/691 E/D gaG/gaT 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 deleterious(0.04) 9/10 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 144398553 144398553 C A 1 0 0 0 0 1 0 0 0 10554 680 24 2 2 NOBOX 7 144398553 Missense_Mutation SNP C C3N-01405_T 2257721 144398553 14947420 196 22670 SSPO 0 . GRCh38 7 149827805 149827805 + Silent SNP G G T rs780559328 C3N-01405_T C3N-01405_N G G c.14811G>T p.= p.P4937P ENST00000378016 102/107 65 51 14 44 44 0 strelka-varscan SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000492965,;SSPO,non_coding_transcript_exon_variant,,ENST00000488835,;SSPO,non_coding_transcript_exon_variant,,ENST00000461331,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,; T ENST00000378016 Transcript synonymous_variant 14811/15589 14811/15453 4937/5150 P ccG/ccT rs780559328 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 102/107 Gene3D:2.10.25.10,Superfamily_domains:SSF57567 LOW 1 SNV 5 1 PASS . . 0 189 21 0 0 0 0 0 -20 0.9978199 1 1 1 0 T 2 4 74 149827805 149827805 G T 1 0 0 0 0 0 0 0 1 15566 1103 39 1 1 SSPO 7 149827805 Silent SNP G C3N-01405_T 5429252 149827805 9518168 197 22671 ATG9B 0 . GRCh38 7 151017116 151017116 + Missense_Mutation SNP G G T rs534489154 C3N-01405_T C3N-01405_N G G c.2209C>A p.Gln737Lys p.Q737K ENST00000605952 9/17 167 151 16 161 161 0 strelka-varscan ATG9B,missense_variant,p.Gln737Lys,ENST00000469530,NM_173681.5;NOS3,downstream_gene_variant,,ENST00000297494,NM_000603.4;NOS3,downstream_gene_variant,,ENST00000461406,;ATG9B,non_coding_transcript_exon_variant,,ENST00000617967,;ATG9B,non_coding_transcript_exon_variant,,ENST00000611177,;ATG9B,downstream_gene_variant,,ENST00000473409,;NOS3,downstream_gene_variant,,ENST00000477227,;NOS3,downstream_gene_variant,,ENST00000468293,;ATG9B,upstream_gene_variant,,ENST00000476282,;ATG9B,downstream_gene_variant,,ENST00000466157,;ATG9B,upstream_gene_variant,,ENST00000498521,;ATG9B,missense_variant,p.Gln737Lys,ENST00000605952,;ATG9B,upstream_gene_variant,,ENST00000404733,;ATG9B,downstream_gene_variant,,ENST00000473134,;ATG9B,upstream_gene_variant,,ENST00000471797,;NOS3,downstream_gene_variant,,ENST00000475454,; T ENST00000605952 Transcript missense_variant,NMD_transcript_variant 2285/4572 2209/2775 737/924 Q/K Caa/Aaa rs534489154 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 tolerated(0.21) 9/17 hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038 MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 151017116 151017116 G T 1 0 0 0 0 1 0 0 0 1255 1386 48 2 2 ATG9B 7 151017116 Missense_Mutation SNP G C3N-01405_T 1189311 151017116 8328857 198 22672 MSR1 0 . GRCh38 8 16177977 16177977 + Missense_Mutation SNP C C A rs747530059 C3N-01405_T C3N-01405_N C C c.12G>T p.Trp4Cys p.W4C ENST00000262101 2/10 271 207 64 293 293 0 strelka-varscan-mutect MSR1,missense_variant,p.Trp4Cys,ENST00000350896,NM_138716.2;MSR1,missense_variant,p.Trp4Cys,ENST00000381998,NM_002445.3;MSR1,missense_variant,p.Trp4Cys,ENST00000262101,NM_138715.2;MSR1,missense_variant,p.Trp22Cys,ENST00000445506,;MSR1,missense_variant,p.Trp4Cys,ENST00000355282,;MSR1,missense_variant,p.Trp15Cys,ENST00000518026,;MSR1,missense_variant,p.Trp4Cys,ENST00000518960,;MSR1,missense_variant,p.Trp4Cys,ENST00000519060,; A ENST00000262101 Transcript missense_variant 134/2132 12/1356 4/451 W/C tgG/tgT rs747530059 1 -1 MSR1 HGNC HGNC:7376 protein_coding YES CCDS5995.1 ENSP00000262101 P21757 UPI000012F686 NM_138715.2 deleterious(0.04) 2/10 MODERATE 1 SNV 1 1 PASS rs747530059 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 16177977 16177977 C A 1 0 0 0 0 1 0 0 0 9869 624 22 2 2 MSR1 8 16177977 Missense_Mutation SNP C C3N-01405_T 16177977 128960659 199 22673 GFRA2 0 . GRCh38 8 21705089 21705089 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.941C>A p.Pro314His p.P314H ENST00000524240 6/9 160 109 51 130 129 1 strelka-varscan-mutect GFRA2,missense_variant,p.Pro314His,ENST00000524240,NM_001495.4;GFRA2,missense_variant,p.Pro314His,ENST00000517328,;GFRA2,missense_variant,p.Pro181His,ENST00000518077,NM_001165039.1;GFRA2,missense_variant,p.Pro209His,ENST00000517892,NM_001165038.1;GFRA2,3_prime_UTR_variant,,ENST00000306793,; T ENST00000524240 Transcript missense_variant 1592/4921 941/1395 314/464 P/H cCc/cAc 1 -1 GFRA2 HGNC HGNC:4244 protein_coding YES CCDS47816.1 ENSP00000428518 O00451 UPI000000D9B1 NM_001495.4 tolerated(0.57) 6/9 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF4,PIRSF_domain:PIRSF038071,Pfam_domain:PF02351,SMART_domains:SM00907,Superfamily_domains:0042655 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 21705089 21705089 G T 1 0 0 0 0 1 0 0 0 6222 1232 43 2 2 GFRA2 8 21705089 Missense_Mutation SNP G C3N-01405_T 5527112 21705089 123433547 200 22674 TEX15 0 . GRCh38 8 30846178 30846178 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.2840T>A p.Leu947Gln p.L947Q ENST00000256246 1/4 125 92 33 139 139 0 strelka-varscan-mutect TEX15,missense_variant,p.Leu947Gln,ENST00000256246,NM_031271.3;TEX15,downstream_gene_variant,,ENST00000523186,; T ENST00000256246 Transcript missense_variant 2915/10187 2840/8370 947/2789 L/Q cTa/cAa 1 -1 TEX15 HGNC HGNC:11738 protein_coding YES CCDS6080.1 ENSP00000256246 Q9BXT5 UPI000013CEF9 NM_031271.3 deleterious(0.01) 1/4 hmmpanther:PTHR22380,hmmpanther:PTHR22380:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 30846178 30846178 A T 1 0 0 0 0 1 0 0 0 16201 420 15 4 4 TEX15 8 30846178 Missense_Mutation SNP A C3N-01405_T 9141089 30846178 114292458 201 22675 TACC1 0 . GRCh38 8 38787644 38787644 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.62C>A p.Ala21Glu p.A21E ENST00000317827 1/13 115 102 13 97 97 0 strelka-varscan-mutect TACC1,missense_variant,p.Ala21Glu,ENST00000317827,NM_006283.2;TACC1,missense_variant,p.Ala21Glu,ENST00000276520,NM_001122824.1;TACC1,missense_variant,p.Ala21Glu,ENST00000524354,;TACC1,intron_variant,,ENST00000519416,;TACC1,intron_variant,,ENST00000520615,NM_001146216.2;TACC1,intron_variant,,ENST00000518415,;TACC1,intron_variant,,ENST00000520340,;TACC1,intron_variant,,ENST00000522904,;TACC1,intron_variant,,ENST00000521642,;TACC1,intron_variant,,ENST00000521050,;TACC1,upstream_gene_variant,,ENST00000520973,;TACC1,upstream_gene_variant,,ENST00000521935,;TACC1,upstream_gene_variant,,ENST00000521528,;TACC1,intron_variant,,ENST00000522752,;TACC1,intron_variant,,ENST00000523239,;TACC1,intron_variant,,ENST00000522544,;TACC1,upstream_gene_variant,,ENST00000523834,;TACC1,upstream_gene_variant,,ENST00000521154,; A ENST00000317827 Transcript missense_variant 441/7802 62/2418 21/805 A/E gCg/gAg 1 1 TACC1 HGNC HGNC:11522 protein_coding YES CCDS6109.1 ENSP00000321703 O75410 UPI000013DACE NM_006283.2 deleterious(0) 1/13 hmmpanther:PTHR13924 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.51167 0.9999881 1 1 1 0 A 3 1 74 38787644 38787644 C A 1 0 0 0 0 1 0 0 0 15897 768 27 1 1 TACC1 8 38787644 Missense_Mutation SNP C C3N-01405_T 7941466 38787644 106350992 202 22676 HGSNAT 0 . GRCh38 8 43199568 43199568 + Nonstop_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1907G>C p.Ter636SerextTer12 p.*636Sext*12 ENST00000379644 18/18 31 23 8 30 30 0 strelka-varscan-mutect HGSNAT,stop_lost,p.Ter636SerextTer12,ENST00000379644,NM_152419.2;HGSNAT,stop_lost,p.Ter353SerextTer12,ENST00000521576,;HGSNAT,downstream_gene_variant,,ENST00000524016,;HGSNAT,non_coding_transcript_exon_variant,,ENST00000519705,;HGSNAT,downstream_gene_variant,,ENST00000523989,; C ENST00000379644 Transcript stop_lost 1949/5236 1907/1908 636/635 */S tGa/tCa 1 1 HGSNAT HGNC HGNC:26527 protein_coding YES CCDS47852.1 ENSP00000368965 Q68CP4 UPI000057A06E NM_152419.2 18/18 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.98878 1 1 1 1 0 C 4 2 74 43199568 43199568 G C 1 0 0 0 0 0 0 0 0 6973 1285 45 4 4 HGSNAT 8 43199568 Nonstop_Mutation SNP G C3N-01405_T 4411924 43199568 101939068 203 22677 ARFGEF1 0 . GRCh38 8 67216650 67216650 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.4626G>T p.Trp1542Cys p.W1542C ENST00000262215 33/39 161 139 22 87 87 0 strelka-varscan-mutect ARFGEF1,missense_variant,p.Trp1542Cys,ENST00000262215,NM_006421.4;ARFGEF1,missense_variant,p.Trp1021Cys,ENST00000520381,;ARFGEF1,missense_variant,p.Trp503Cys,ENST00000518230,; A ENST00000262215 Transcript missense_variant 5016/7225 4626/5550 1542/1849 W/C tgG/tgT 1 -1 ARFGEF1 HGNC HGNC:15772 protein_coding YES CCDS6199.1 ENSP00000262215 Q9Y6D6 A0A024R7X0 UPI000013D275 NM_006421.4 deleterious(0) 33/39 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF137 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 67216650 67216650 C A 1 0 0 0 0 1 0 0 0 975 740 26 2 2 ARFGEF1 8 67216650 Missense_Mutation SNP C C3N-01405_T 24017082 67216650 77921986 204 22678 SULF1 0 . GRCh38 8 69603247 69603247 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1117G>T p.Gly373Trp p.G373W ENST00000260128 11/23 296 184 112 194 193 1 strelka-varscan-mutect SULF1,missense_variant,p.Gly373Trp,ENST00000260128,NM_015170.2;SULF1,missense_variant,p.Gly373Trp,ENST00000458141,NM_001128204.1;SULF1,missense_variant,p.Gly373Trp,ENST00000402687,NM_001128205.1;SULF1,missense_variant,p.Gly373Trp,ENST00000419716,NM_001128206.1;SULF1,missense_variant,p.Gly157Trp,ENST00000616868,;SULF1,non_coding_transcript_exon_variant,,ENST00000521946,; T ENST00000260128 Transcript missense_variant 1834/5710 1117/2616 373/871 G/W Ggg/Tgg 1 1 SULF1 HGNC HGNC:20391 protein_coding YES CCDS6204.1 ENSP00000260128 Q8IWU6 A0A024R809 UPI000003FD82 NM_015170.2 deleterious(0) 11/23 hmmpanther:PTHR10342:SF210,hmmpanther:PTHR10342,PIRSF_domain:PIRSF036665,Gene3D:3.40.720.10,Pfam_domain:PF00884,Superfamily_domains:SSF53649 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 69603247 69603247 G T 1 0 0 0 0 1 0 0 0 15758 1348 47 2 2 SULF1 8 69603247 Missense_Mutation SNP G C3N-01405_T 2386597 69603247 75535389 205 22679 SLCO5A1 0 . GRCh38 8 69831974 69831974 + Missense_Mutation SNP C C G C3N-01405_T C3N-01405_N C C c.700G>C p.Asp234His p.D234H ENST00000260126 2/10 118 99 19 73 73 0 strelka-varscan-mutect SLCO5A1,missense_variant,p.Asp234His,ENST00000260126,NM_030958.2;SLCO5A1,missense_variant,p.Asp234His,ENST00000524945,NM_001146008.1;SLCO5A1,missense_variant,p.Asp234His,ENST00000530307,NM_001146009.1;RP11-159H10.3,upstream_gene_variant,,ENST00000528800,;RP11-159H10.3,upstream_gene_variant,,ENST00000501104,;RP11-159H10.3,upstream_gene_variant,,ENST00000533300,;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000528658,;SLCO5A1,downstream_gene_variant,,ENST00000531422,;SLCO5A1,downstream_gene_variant,,ENST00000524703,;SLCO5A1,missense_variant,p.Asp234His,ENST00000526750,;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000532388,; G ENST00000260126 Transcript missense_variant 1407/9076 700/2547 234/848 D/H Gac/Cac COSM1101382 1 -1 SLCO5A1 HGNC HGNC:19046 protein_coding YES CCDS6205.1 ENSP00000260126 Q9H2Y9 UPI0000140F53 NM_030958.2 deleterious(0.01) 2/10 PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF91,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805 1 MODERATE 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 G 3 3 74 69831974 69831974 C G 1 0 0 0 0 1 0 0 0 15018 884 31 4 4 SLCO5A1 8 69831974 Missense_Mutation SNP C C3N-01405_T 228727 69831974 75306662 206 22680 PRDM14 0 . GRCh38 8 70058683 70058683 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1343G>T p.Arg448Leu p.R448L ENST00000276594 6/8 360 305 55 227 227 0 strelka-varscan-mutect PRDM14,missense_variant,p.Arg448Leu,ENST00000276594,NM_024504.3; A ENST00000276594 Transcript missense_variant 1545/2344 1343/1716 448/571 R/L cGg/cTg 1 -1 PRDM14 HGNC HGNC:14001 protein_coding YES CCDS6206.1 ENSP00000276594 Q9GZV8 UPI0000132186 NM_024504.3 deleterious(0) 6/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1211840014 . 0 208 0 0 2 0 0 0 -19.99999 0.9969915 1 1 1 0 A 3 1 74 70058683 70058683 C A 1 0 0 0 0 1 0 0 0 12586 652 23 1 1 PRDM14 8 70058683 Missense_Mutation SNP C C3N-01405_T 226709 70058683 75079953 207 22681 KCNB2 0 . GRCh38 8 72568017 72568017 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.283G>A p.Ala95Thr p.A95T ENST00000523207 2/3 325 291 34 178 178 0 strelka-varscan-mutect KCNB2,missense_variant,p.Ala95Thr,ENST00000523207,NM_004770.2; A ENST00000523207 Transcript missense_variant 871/3582 283/2736 95/911 A/T Gcc/Acc 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 tolerated(0.09) 2/3 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF134,Gene3D:3.30.710.10,Pfam_domain:PF02214,SMART_domains:SM00225,Superfamily_domains:SSF54695,Prints_domain:PR01491,Prints_domain:PR00169 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 72568017 72568017 G A 1 0 0 0 0 1 0 0 0 7929 971 34 3 3 KCNB2 8 72568017 Missense_Mutation SNP G C3N-01405_T 2509334 72568017 72570619 208 22682 KIAA1429 0 . GRCh38 8 94511258 94511258 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.3317C>G p.Pro1106Arg p.P1106R ENST00000297591 13/24 405 264 141 273 273 0 strelka-varscan-mutect KIAA1429,missense_variant,p.Pro1106Arg,ENST00000297591,NM_015496.4;KIAA1429,missense_variant,p.Pro1106Arg,ENST00000421249,NM_183009.2;KIAA1429,non_coding_transcript_exon_variant,,ENST00000523405,;KIAA1429,missense_variant,p.Pro459Arg,ENST00000522263,;KIAA1429,non_coding_transcript_exon_variant,,ENST00000521080,; C ENST00000297591 Transcript missense_variant 3393/6528 3317/5439 1106/1812 P/R cCt/cGt 1 -1 KIAA1429 HGNC HGNC:24500 protein_coding YES CCDS34923.1 ENSP00000297591 Q69YN4 UPI00001BBB23 NM_015496.4 deleterious(0) 13/24 hmmpanther:PTHR23185 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 94511258 94511258 G C 1 0 0 0 0 1 0 0 0 8114 1000 35 4 4 KIAA1429 8 94511258 Missense_Mutation SNP G C3N-01405_T 21943241 94511258 50627378 209 22683 RIMS2 0 . GRCh38 8 103885896 103885896 + Missense_Mutation SNP C C T C3N-01405_T C3N-01405_N C C c.1297C>T p.Pro433Ser p.P433S ENST00000504942 4/24 255 234 21 137 137 0 strelka-varscan-mutect RIMS2,missense_variant,p.Pro241Ser,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Pro211Ser,ENST00000436393,;RIMS2,missense_variant,p.Pro433Ser,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Pro375Ser,ENST00000626043,;RIMS2,missense_variant,p.Pro241Ser,ENST00000408894,;RIMS2,missense_variant,p.Pro241Ser,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Pro437Ser,ENST00000632716,;RIMS2,missense_variant,p.Pro241Ser,ENST00000515551,; T ENST00000504942 Transcript missense_variant 1436/4228 1297/4050 433/1349 P/S Cct/Tct COSM3951086,COSM3951087,COSM3951088,COSM3951089,COSM3951090 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 tolerated_low_confidence(0.1) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 1,1,1,1,1 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS rs1020266564 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 103885896 103885896 C T 1 0 0 0 0 1 0 0 0 13543 855 30 3 3 RIMS2 8 103885896 Missense_Mutation SNP C C3N-01405_T 9374638 103885896 41252740 210 22684 CSMD3 0 . GRCh38 8 112311078 112311078 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.7785C>A p.= p.A2595A ENST00000297405 50/71 369 301 68 247 247 0 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,;CSMD3,non_coding_transcript_exon_variant,,ENST00000492692,; T ENST00000297405 Transcript synonymous_variant 8030/13212 7785/11124 2595/3707 A gcC/gcA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 50/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 112311078 112311078 G T 1 0 0 0 0 0 0 0 1 3747 987 35 2 2 CSMD3 8 112311078 Silent SNP G C3N-01405_T 8425182 112311078 32827558 211 22685 CSMD3 0 . GRCh38 8 112685522 112685522 + Missense_Mutation SNP C C A C3N-01405_T C3N-01405_N C C c.2366G>T p.Gly789Val p.G789V ENST00000297405 15/71 327 287 40 208 208 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gly789Val,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly749Val,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly685Val,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gly129Val,ENST00000339701,; A ENST00000297405 Transcript missense_variant 2611/13212 2366/11124 789/3707 G/V gGa/gTa COSM1732891,COSM1732892 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 15/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 112685522 112685522 C A 1 0 0 0 0 1 0 0 0 3747 855 30 2 2 CSMD3 8 112685522 Missense_Mutation SNP C C3N-01405_T 374444 112685522 32453114 212 22686 CSMD3 0 . GRCh38 8 112829729 112829729 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.1816G>A p.Gly606Ser p.G606S ENST00000297405 12/71 599 492 107 313 313 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gly606Ser,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gly566Ser,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gly502Ser,ENST00000455883,NM_052900.2; T ENST00000297405 Transcript missense_variant 2061/13212 1816/11124 606/3707 G/S Ggc/Agc 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.03) 12/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 112829729 112829729 C T 1 0 0 0 0 1 0 0 0 3747 594 21 3 3 CSMD3 8 112829729 Missense_Mutation SNP C C3N-01405_T 144207 112829729 32308907 213 22687 HAS2 0 . GRCh38 8 121629327 121629327 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.14G>A p.Arg5Lys p.R5K ENST00000303924 2/4 132 114 18 77 77 0 strelka-varscan-mutect HAS2,missense_variant,p.Arg5Lys,ENST00000303924,NM_005328.2; T ENST00000303924 Transcript missense_variant 552/4190 14/1659 5/552 R/K aGg/aAg 1 -1 HAS2 HGNC HGNC:4819 protein_coding YES CCDS6335.1 ENSP00000306991 Q92819 UPI000012C0A9 NM_005328.2 tolerated(0.82) 2/4 hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF7 MODERATE 1 SNV 1 1 PASS rs1452705240 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 121629327 121629327 C T 1 0 0 0 0 1 0 0 0 6848 681 24 3 3 HAS2 8 121629327 Missense_Mutation SNP C C3N-01405_T 8799598 121629327 23509309 214 22688 ADCY8 0 . GRCh38 8 130821369 130821369 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.2727C>T p.= p.L909L ENST00000286355 13/18 284 244 40 192 192 0 strelka-varscan-mutect ADCY8,synonymous_variant,p.=,ENST00000286355,NM_001115.2;ADCY8,synonymous_variant,p.=,ENST00000377928,; A ENST00000286355 Transcript synonymous_variant 4820/5938 2727/3756 909/1251 L ctC/ctT 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 13/18 Low_complexity_(Seg):seg,hmmpanther:PTHR11920:SF320,hmmpanther:PTHR11920,PIRSF_domain:PIRSF039050 LOW 1 SNV 1 1 PASS rs1429233594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 130821369 130821369 G A 1 0 0 0 0 0 0 0 1 344 1161 41 3 3 ADCY8 8 130821369 Silent SNP G C3N-01405_T 9192042 130821369 14317267 215 22689 TG 0 . GRCh38 8 132871375 132871375 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.302A>T p.Gln101Leu p.Q101L ENST00000220616 4/48 672 398 274 422 422 0 strelka-varscan-mutect TG,missense_variant,p.Gln101Leu,ENST00000220616,NM_003235.4;TG,3_prime_UTR_variant,,ENST00000523901,; T ENST00000220616 Transcript missense_variant 342/8450 302/8307 101/2768 Q/L cAg/cTg 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 deleterious(0.02) 4/48 PROSITE_profiles:PS51162,hmmpanther:PTHR14093:SF16,hmmpanther:PTHR14093,Pfam_domain:PF00086,PIRSF_domain:PIRSF001831,Superfamily_domains:SSF57610 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 132871375 132871375 A T 1 0 0 0 0 1 0 0 0 16246 188 7 4 4 TG 8 132871375 Missense_Mutation SNP A C3N-01405_T 2050006 132871375 12267261 216 22690 TG 0 . GRCh38 8 132882957 132882957 + Nonsense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1033G>T p.Glu345Ter p.E345* ENST00000220616 8/48 219 168 51 139 139 0 strelka-varscan-mutect TG,stop_gained,p.Glu345Ter,ENST00000220616,NM_003235.4;TG,non_coding_transcript_exon_variant,,ENST00000520769,;TG,downstream_gene_variant,,ENST00000523901,; T ENST00000220616 Transcript stop_gained 1073/8450 1033/8307 345/2768 E/* Gaa/Taa 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 8/48 PROSITE_profiles:PS51162,hmmpanther:PTHR14093:SF16,hmmpanther:PTHR14093,Pfam_domain:PF00086,PIRSF_domain:PIRSF001831,Gene3D:4.10.800.10,SMART_domains:SM00211,Superfamily_domains:SSF57610 HIGH 1 SNV 1 1 PASS rs1049761427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 132882957 132882957 G T 1 0 0 0 0 0 1 0 0 16246 1175 41 2 2 TG 8 132882957 Nonsense_Mutation SNP G C3N-01405_T 11582 132882957 12255679 217 22691 FAM135B 0 . GRCh38 8 138265741 138265741 + Missense_Mutation SNP C C A rs768257554 C3N-01405_T C3N-01405_N C C c.259G>T p.Val87Leu p.V87L ENST00000395297 4/20 273 229 44 155 155 0 strelka-varscan-mutect FAM135B,missense_variant,p.Val87Leu,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Val87Leu,ENST00000160713,;FAM135B,downstream_gene_variant,,ENST00000517849,;FAM135B,missense_variant,p.Val87Leu,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; A ENST00000395297 Transcript missense_variant 430/6962 259/4221 87/1406 V/L Gtg/Ttg rs768257554 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.09) 4/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS rs768257554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 138265741 138265741 C A 1 0 0 0 0 1 0 0 0 5299 478 17 2 2 FAM135B 8 138265741 Missense_Mutation SNP C C3N-01405_T 5382784 138265741 6872895 218 22692 COL22A1 0 . GRCh38 8 138613915 138613915 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.3930C>T p.= p.D1310D ENST00000303045 56/65 360 315 45 170 170 0 strelka-varscan-mutect COL22A1,synonymous_variant,p.=,ENST00000303045,NM_152888.2;COL22A1,synonymous_variant,p.=,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,;COL22A1,non_coding_transcript_exon_variant,,ENST00000487854,; A ENST00000303045 Transcript synonymous_variant 4377/6346 3930/4881 1310/1626 D gaC/gaT 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 56/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 138613915 138613915 G A 1 0 0 0 0 0 0 0 1 3469 1391 48 3 3 COL22A1 8 138613915 Silent SNP G C3N-01405_T 348174 138613915 6524721 219 22693 ADGRB1 0 . GRCh38 8 142479378 142479378 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.1617G>T p.= p.G539G ENST00000517894 8/31 39 35 4 22 22 0 strelka-mutect ADGRB1,synonymous_variant,p.=,ENST00000517894,;ADGRB1,synonymous_variant,p.=,ENST00000323289,NM_001702.2;ADGRB1,synonymous_variant,p.=,ENST00000521208,;ADGRB1,non_coding_transcript_exon_variant,,ENST00000518820,; T ENST00000517894 Transcript synonymous_variant 2511/6241 1617/4755 539/1584 G ggG/ggT 1 1 ADGRB1 HGNC HGNC:943 protein_coding YES CCDS64985.1 ENSP00000430945 O14514 UPI00002109E8 8/31 PROSITE_profiles:PS50092,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF39,Gene3D:2.20.100.10,Pfam_domain:PF00090,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -10.9146 1 1 1 1 0 T 2 4 74 142479378 142479378 G T 1 0 0 0 0 0 0 0 1 355 1219 43 2 2 ADGRB1 8 142479378 Silent SNP G C3N-01405_T 3865463 142479378 2659258 220 22694 MROH6 0 . GRCh38 8 143571679 143571679 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.590T>C p.Leu197Pro p.L197P ENST00000398882 3/14 398 340 58 207 207 0 strelka-varscan-mutect MROH6,missense_variant,p.Leu197Pro,ENST00000398882,NM_001100878.1;MROH6,missense_variant,p.Leu197Pro,ENST00000529971,;NAPRT,downstream_gene_variant,,ENST00000449291,NM_145201.5;MROH6,upstream_gene_variant,,ENST00000533679,;NAPRT,downstream_gene_variant,,ENST00000435154,;MROH6,upstream_gene_variant,,ENST00000524906,;MROH6,upstream_gene_variant,,ENST00000534459,;NAPRT,downstream_gene_variant,,ENST00000426292,NM_001286829.1;MROH6,upstream_gene_variant,,ENST00000532862,;RP11-661A12.9,upstream_gene_variant,,ENST00000531730,;MROH6,upstream_gene_variant,,ENST00000532704,;MROH6,upstream_gene_variant,,ENST00000533582,;MROH6,upstream_gene_variant,,ENST00000533210,;NAPRT,downstream_gene_variant,,ENST00000340490,;NAPRT,downstream_gene_variant,,ENST00000464332,;NAPRT,downstream_gene_variant,,ENST00000480946,;NAPRT,downstream_gene_variant,,ENST00000525583,;NAPRT,downstream_gene_variant,,ENST00000488096,;NAPRT,downstream_gene_variant,,ENST00000532645,;MROH6,upstream_gene_variant,,ENST00000533120,;NAPRT,downstream_gene_variant,,ENST00000460623,;MROH6,upstream_gene_variant,,ENST00000533083,;NAPRT,downstream_gene_variant,,ENST00000529179,;NAPRT,downstream_gene_variant,,ENST00000498076,; G ENST00000398882 Transcript missense_variant 847/3469 590/2160 197/719 L/P cTg/cCg 1 -1 MROH6 HGNC HGNC:27814 protein_coding YES CCDS47928.1 ENSP00000381857 A6NGR9 UPI0000DD7EFB NM_001100878.1 deleterious(0.03) 3/14 hmmpanther:PTHR23120:SF7,hmmpanther:PTHR23120 MODERATE SNV 5 1 PASS rs1278043713 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 143571679 143571679 A G 1 0 0 0 0 1 0 0 0 9746 188 7 5 5 MROH6 8 143571679 Missense_Mutation SNP A C3N-01405_T 1092301 143571679 1566957 221 22695 GLDC 0 . GRCh38 9 6553371 6553371 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.2454C>G p.Ile818Met p.I818M ENST00000321612 20/25 291 239 52 164 164 0 strelka-varscan-mutect GLDC,missense_variant,p.Ile818Met,ENST00000321612,NM_000170.2;GLDC,downstream_gene_variant,,ENST00000460457,;GLDC,downstream_gene_variant,,ENST00000467946,; C ENST00000321612 Transcript missense_variant 2605/3767 2454/3063 818/1020 I/M atC/atG 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0.02) 20/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 6553371 6553371 G C 1 0 0 0 0 1 0 0 0 6311 1304 45 4 4 GLDC 9 6553371 Missense_Mutation SNP G C3N-01405_T 6553371 131841346 222 22696 GLDC 0 . GRCh38 9 6604626 6604626 + Missense_Mutation SNP C C A rs563039693 C3N-01405_T C3N-01405_N C C c.1020G>T p.Leu340Phe p.L340F ENST00000321612 7/25 250 212 38 208 208 0 strelka-varscan-mutect GLDC,missense_variant,p.Leu340Phe,ENST00000321612,NM_000170.2;GLDC,intron_variant,,ENST00000463305,; A ENST00000321612 Transcript missense_variant 1171/3767 1020/3063 340/1020 L/F ttG/ttT rs563039693 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 tolerated(0.49) 7/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Gene3D:3.40.640.10,Pfam_domain:PF02347,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs563039693 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 6604626 6604626 C A 1 0 0 0 0 1 0 0 0 6311 593 21 2 2 GLDC 9 6604626 Missense_Mutation SNP C C3N-01405_T 51255 6604626 131790091 223 22697 PTPRD 0 . GRCh38 9 8733779 8733779 + Splice_Site SNP C C T novel C3N-01405_T C3N-01405_N C C c.64+1G>A p.X22_splice ENST00000381196 186 161 25 204 204 0 strelka-varscan-mutect PTPRD,splice_donor_variant,,ENST00000381196,NM_002839.3;PTPRD,splice_donor_variant,,ENST00000356435,;PTPRD,splice_donor_variant,,ENST00000355233,NM_130392.3;PTPRD,splice_donor_variant,,ENST00000397617,;PTPRD,splice_donor_variant,,ENST00000397611,NM_001040712.2;PTPRD,splice_donor_variant,,ENST00000537002,NM_130393.3;PTPRD,splice_donor_variant,,ENST00000540109,;PTPRD,splice_donor_variant,,ENST00000486161,NM_130391.3;PTPRD,splice_donor_variant,,ENST00000397606,NM_001171025.1;PTPRD,splice_donor_variant,,ENST00000463477,;PTPRD,splice_donor_variant,,ENST00000481079,; T ENST00000381196 Transcript splice_donor_variant -/9911 64/5739 22/1912 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 9/42 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 74 8733779 8733779 C T 1 0 0 0 0 0 0 1 0 12953 579 20 3 3 PTPRD 9 8733779 Splice_Site SNP C C3N-01405_T 2129153 8733779 129660938 224 22698 BNC2 0 . GRCh38 9 16436711 16436711 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1483C>A p.Pro495Thr p.P495T ENST00000380672 6/7 457 350 107 417 417 0 strelka-varscan-mutect BNC2,missense_variant,p.Pro495Thr,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Pro321Thr,ENST00000545497,;BNC2,missense_variant,p.Pro452Thr,ENST00000418777,;BNC2,missense_variant,p.Pro428Thr,ENST00000380667,;BNC2,upstream_gene_variant,,ENST00000411752,;BNC2,downstream_gene_variant,,ENST00000380666,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,missense_variant,p.Pro495Thr,ENST00000484726,; T ENST00000380672 Transcript missense_variant 1541/12844 1483/3300 495/1099 P/T Cct/Act 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 deleterious(0) 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021,SMART_domains:SM00355 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 16436711 16436711 G T 1 0 0 0 0 1 0 0 0 1631 1174 41 2 2 BNC2 9 16436711 Missense_Mutation SNP G C3N-01405_T 7702932 16436711 121958006 225 22699 FRMPD1 0 . GRCh38 9 37746709 37746709 + Silent SNP G G T C3N-01405_T C3N-01405_N G G c.4677G>T p.= p.T1559T ENST00000539465 16/16 222 167 55 178 176 2 strelka-varscan-mutect FRMPD1,synonymous_variant,p.=,ENST00000539465,;FRMPD1,synonymous_variant,p.=,ENST00000377765,NM_014907.2;RP11-613M10.9,intron_variant,,ENST00000540557,; T ENST00000539465 Transcript synonymous_variant 5270/5465 4677/4737 1559/1578 T acG/acT COSM2775846 1 1 FRMPD1 HGNC HGNC:29159 protein_coding YES CCDS6612.1 ENSP00000444411 Q5SYB0 UPI000013D2CC 16/16 1 LOW 1 SNV 1 1 1 PASS rs903349045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 37746709 37746709 G T 1 0 0 0 0 0 0 0 1 5927 1103 39 1 1 FRMPD1 9 37746709 Silent SNP G C3N-01405_T 21309998 37746709 100648008 226 22700 GDA 0 . GRCh38 9 72202636 72202636 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.278G>T p.Ser93Ile p.S93I ENST00000238018 3/16 158 141 17 163 162 1 strelka-varscan-mutect GDA,missense_variant,p.Ser19Ile,ENST00000545168,NM_001242507.2,NM_001242506.2;GDA,missense_variant,p.Ser93Ile,ENST00000358399,NM_004293.4;GDA,missense_variant,p.Ser93Ile,ENST00000238018,NM_001242505.2;GDA,missense_variant,p.Ser51Ile,ENST00000376986,;GDA,non_coding_transcript_exon_variant,,ENST00000477618,;GDA,missense_variant,p.Ser93Ile,ENST00000475764,; T ENST00000238018 Transcript missense_variant 487/2074 278/1416 93/471 S/I aGt/aTt 1 1 GDA HGNC HGNC:4212 protein_coding YES CCDS56576.1 ENSP00000238018 Q9Y2T3 UPI000015828B NM_001242505.2 tolerated(0.07) 3/16 Gene3D:3.20.20.140,Pfam_domain:PF01979,hmmpanther:PTHR11271,hmmpanther:PTHR11271:SF6,Superfamily_domains:SSF51556,TIGRFAM_domain:TIGR02967 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 72202636 72202636 G T 1 0 0 0 0 1 0 0 0 6178 1029 36 2 2 GDA 9 72202636 Missense_Mutation SNP G C3N-01405_T 34455927 72202636 66192081 227 22701 CEP78 0 . GRCh38 9 78248339 78248339 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.941G>T p.Arg314Met p.R314M ENST00000376597 7/16 175 130 45 202 202 0 strelka-varscan-mutect CEP78,missense_variant,p.Arg314Met,ENST00000424347,;CEP78,missense_variant,p.Arg314Met,ENST00000415759,NM_032171.1;CEP78,missense_variant,p.Arg314Met,ENST00000376597,NM_001098802.1;CEP78,missense_variant,p.Arg314Met,ENST00000277082,;CEP78,missense_variant,p.Arg314Met,ENST00000376598,;CEP78,intron_variant,,ENST00000476652,;CEP78,upstream_gene_variant,,ENST00000487108,;CEP78,non_coding_transcript_exon_variant,,ENST00000536374,; T ENST00000376597 Transcript missense_variant 1085/2618 941/2169 314/722 R/M aGg/aTg 1 1 CEP78 HGNC HGNC:25740 protein_coding YES CCDS47984.1 ENSP00000365782 Q5JTW2 UPI000153BFA4 NM_001098802.1 deleterious(0.03) 7/16 hmmpanther:PTHR24110,hmmpanther:PTHR24110:SF3,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 78248339 78248339 G T 1 0 0 0 0 1 0 0 0 2983 1000 35 2 2 CEP78 9 78248339 Missense_Mutation SNP G C3N-01405_T 6045703 78248339 60146378 228 22702 WNK2 0 . GRCh38 9 93229843 93229843 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.829C>A p.Leu277Met p.L277M ENST00000297954 2/30 145 127 18 89 88 1 strelka-varscan-mutect WNK2,missense_variant,p.Leu273Met,ENST00000432730,;WNK2,missense_variant,p.Leu277Met,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Leu277Met,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Leu277Met,ENST00000448039,;WNK2,5_prime_UTR_variant,,ENST00000427277,; A ENST00000297954 Transcript missense_variant 829/7138 829/6894 277/2297 L/M Ctg/Atg 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0) 2/30 PROSITE_profiles:PS50011,hmmpanther:PTHR13902:SF10,hmmpanther:PTHR13902,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1363811526 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 93229843 93229843 C A 1 0 0 0 0 1 0 0 0 17934 796 28 2 2 WNK2 9 93229843 Missense_Mutation SNP C C3N-01405_T 14981504 93229843 45164874 229 22703 SLC35D2 0 . GRCh38 9 96351142 96351142 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.449G>T p.Ser150Ile p.S150I ENST00000253270 6/12 223 180 43 222 222 0 strelka-varscan-mutect SLC35D2,missense_variant,p.Ser150Ile,ENST00000253270,NM_007001.2;SLC35D2,missense_variant,p.Ser150Ile,ENST00000375259,NM_001286990.1;SLC35D2,missense_variant,p.Ser150Ile,ENST00000375257,;SLC35D2,non_coding_transcript_exon_variant,,ENST00000482643,; A ENST00000253270 Transcript missense_variant 512/1613 449/1014 150/337 S/I aGt/aTt 1 -1 SLC35D2 HGNC HGNC:20799 protein_coding YES CCDS6717.1 ENSP00000253270 Q76EJ3 A0A024R9N5 UPI000003778E NM_007001.2 deleterious(0.01) 6/12 Pfam_domain:PF03151,hmmpanther:PTHR11132,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 96351142 96351142 C A 1 0 0 0 0 1 0 0 0 14852 565 20 2 2 SLC35D2 9 96351142 Missense_Mutation SNP C C3N-01405_T 3121299 96351142 42043575 230 22704 NUTM2G 0 . GRCh38 9 96932213 96932213 + Missense_Mutation SNP G G T rs200771234,rs780462082 C3N-01405_T C3N-01405_N G G c.508G>T p.Val170Leu p.V170L ENST00000372322 2/7 588 553 35 430 430 0 varscan-mutect NUTM2G,missense_variant,p.Val170Leu,ENST00000354649,NM_001045477.2;NUTM2G,missense_variant,p.Val170Leu,ENST00000372322,NM_001170741.1;MFSD14C,intron_variant,,ENST00000637409,;MFSD14C,intron_variant,,ENST00000506067,;MFSD14C,intron_variant,,ENST00000637076,;MFSD14C,downstream_gene_variant,,ENST00000637099,; T ENST00000372322 Transcript missense_variant 529/2516 508/2226 170/741 V/L Gtg/Ttg rs200771234,rs780462082,COSM2733876,COSM2733877 1 1 NUTM2G HGNC HGNC:23449 protein_coding YES CCDS55329.1 ENSP00000361397 Q5VZR2 UPI000175026B NM_001170741.1 deleterious(0.05) 2/7 Pfam_domain:PF12881,hmmpanther:PTHR22879,hmmpanther:PTHR22879:SF12 0,0,1,1 MODERATE 1 SNV 5 0,0,1,1 1 PASS rs200771234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 96932213 96932213 G T 1 0 0 0 0 1 0 0 0 10852 1145 40 1 1 NUTM2G 9 96932213 Missense_Mutation SNP G C3N-01405_T 581071 96932213 41462504 231 22705 GRIN3A 0 . GRCh38 9 101737308 101737308 + Silent SNP C C T novel C3N-01405_T C3N-01405_N C C c.672G>A p.= p.V224V ENST00000361820 1/9 265 244 21 209 209 0 strelka-varscan-mutect GRIN3A,synonymous_variant,p.=,ENST00000361820,NM_133445.2; T ENST00000361820 Transcript synonymous_variant 1273/7770 672/3348 224/1115 V gtG/gtA 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 1/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 101737308 101737308 C T 1 0 0 0 0 0 0 0 1 6665 697 25 3 3 GRIN3A 9 101737308 Silent SNP C C3N-01405_T 4805095 101737308 36657409 232 22706 ZNF462 0 . GRCh38 9 106925245 106925245 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1333C>G p.Pro445Ala p.P445A ENST00000277225 3/13 229 197 32 143 143 0 strelka-varscan-mutect ZNF462,missense_variant,p.Pro445Ala,ENST00000277225,NM_021224.4;ZNF462,intron_variant,,ENST00000472574,;ZNF462,upstream_gene_variant,,ENST00000374686,;ZNF462,upstream_gene_variant,,ENST00000441147,;ZNF462,upstream_gene_variant,,ENST00000497489,;ZNF462,upstream_gene_variant,,ENST00000480607,; G ENST00000277225 Transcript missense_variant 1622/10414 1333/7521 445/2506 P/A Cct/Gct 1 1 ZNF462 HGNC HGNC:21684 protein_coding YES CCDS35096.1 ENSP00000277225 Q96JM2 UPI0000470106 NM_021224.4 tolerated_low_confidence(0.94) 3/13 SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 106925245 106925245 C G 1 0 0 0 0 1 0 0 0 18497 855 30 4 4 ZNF462 9 106925245 Missense_Mutation SNP C C3N-01405_T 5187937 106925245 31469472 233 22707 C5 0 . GRCh38 9 121021544 121021544 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.1267A>G p.Asn423Asp p.N423D ENST00000223642 11/41 233 189 44 272 271 1 strelka-varscan-mutect C5,missense_variant,p.Asn423Asp,ENST00000223642,NM_001317163.1,NM_001735.2;C5,downstream_gene_variant,,ENST00000460578,; C ENST00000223642 Transcript missense_variant 1297/5465 1267/5031 423/1676 N/D Aat/Gat 1 -1 C5 HGNC HGNC:1331 protein_coding YES CCDS6826.1 ENSP00000223642 P01031 UPI000013C838 NM_001317163.1,NM_001735.2 deleterious(0.03) 11/41 hmmpanther:PTHR11412:SF83,hmmpanther:PTHR11412 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 121021544 121021544 T C 1 0 0 0 0 1 0 0 0 2091 1754 61 5 5 C5 9 121021544 Missense_Mutation SNP T C3N-01405_T 14096299 121021544 17373173 234 22708 SETX 0 . GRCh38 9 132329332 132329332 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.2266G>C p.Glu756Gln p.E756Q ENST00000224140 10/26 173 154 19 130 130 0 strelka-varscan-mutect SETX,missense_variant,p.Glu756Gln,ENST00000224140,NM_015046.5; G ENST00000224140 Transcript missense_variant 2449/11100 2266/8034 756/2677 E/Q Gaa/Caa 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 tolerated(0.16) 10/26 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 132329332 132329332 C G 1 0 0 0 0 1 0 0 0 14420 864 30 4 4 SETX 9 132329332 Missense_Mutation SNP C C3N-01405_T 11307788 132329332 6065385 235 22709 FAM171A1 0 . GRCh38 10 15284052 15284052 + Missense_Mutation SNP C C T rs373169282 C3N-01405_T C3N-01405_N C C c.151G>A p.Asp51Asn p.D51N ENST00000378116 2/8 450 376 74 260 259 1 strelka-varscan-mutect FAM171A1,missense_variant,p.Asp51Asn,ENST00000378116,NM_001010924.1;FAM171A1,missense_variant,p.Asp51Asn,ENST00000455654,; T ENST00000378116 Transcript missense_variant 158/3952 151/2673 51/890 D/N Gat/Aat rs373169282 1 -1 FAM171A1 HGNC HGNC:23522 protein_coding YES CCDS31154.1 ENSP00000367356 Q5VUB5 UPI00001414CA NM_001010924.1 tolerated(0.38) 2/8 hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF1,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS rs373169282 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 15284052 15284052 C T 1 0 0 0 0 1 0 0 0 5337 913 32 3 3 FAM171A1 10 15284052 Missense_Mutation SNP C C3N-01405_T 15284052 118513370 236 22710 SLC39A12 0 . GRCh38 10 18000692 18000692 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1626C>G p.Ile542Met p.I542M ENST00000377369 11/13 223 172 51 146 146 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Ile542Met,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Ile541Met,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Ile505Met,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Ile408Met,ENST00000539911,NM_001282734.1;SLC39A12-AS1,downstream_gene_variant,,ENST00000439319,;SLC39A12-AS1,downstream_gene_variant,,ENST00000445287,; G ENST00000377369 Transcript missense_variant 1899/2808 1626/2076 542/691 I/M atC/atG 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 deleterious(0.02) 11/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 18000692 18000692 C G 1 0 0 0 0 1 0 0 0 14893 816 29 4 4 SLC39A12 10 18000692 Missense_Mutation SNP C C3N-01405_T 2716640 18000692 115796730 237 22711 GPR158 0 . GRCh38 10 25596739 25596739 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.2095A>G p.Ser699Gly p.S699G ENST00000376351 10/11 203 161 42 128 128 0 strelka-varscan-mutect GPR158,missense_variant,p.Ser699Gly,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; G ENST00000376351 Transcript missense_variant 2454/6959 2095/3648 699/1215 S/G Agt/Ggt 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0) 10/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 25596739 25596739 A G 1 0 0 0 0 1 0 0 0 6549 188 7 5 5 GPR158 10 25596739 Missense_Mutation SNP A C3N-01405_T 7596047 25596739 108200683 238 22712 GPR158 0 . GRCh38 10 25598209 25598209 + Frame_Shift_Del DEL A A - C3N-01405_T C3N-01405_N A A c.2586delA p.Glu863LysfsTer44 p.E863Kfs*44 ENST00000376351 11/11 322 229 93 253 252 1 sindel-varindel-pindel GPR158,frameshift_variant,p.Glu863LysfsTer44,ENST00000376351,NM_020752.2;GPR158,non_coding_transcript_exon_variant,,ENST00000490549,; - ENST00000376351 Transcript frameshift_variant 2942/6959 2583/3648 861/1215 L/X ctA/ct COSM4946459 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 11/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 1 HIGH 1 deletion 1 3 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 25598209 25598209 A - 1 0 1 0 1 0 0 0 0 6549 349 13 0 0 GPR158 10 25598209 Frame_Shift_Del DEL A C3N-01405_T 1470 25598209 108199213 239 22713 PCDH15 0 . GRCh38 10 53806596 53806596 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.5029C>A p.Pro1677Thr p.P1677T ENST00000614895 35/35 186 163 23 134 134 0 strelka-varscan-mutect PCDH15,missense_variant,p.Pro1677Thr,ENST00000614895,;PCDH15,missense_variant,p.Pro1673Thr,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Pro1672Thr,ENST00000414778,;PCDH15,missense_variant,p.Pro1671Thr,ENST00000616114,;PCDH15,missense_variant,p.Pro1678Thr,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Pro412Thr,ENST00000495484,;PCDH15,missense_variant,p.Pro456Thr,ENST00000618301,;PCDH15,downstream_gene_variant,,ENST00000617271,NM_001142770.1;PCDH15,downstream_gene_variant,,ENST00000613657,NM_001142769.1;PCDH15,downstream_gene_variant,,ENST00000395445,;PCDH15,downstream_gene_variant,,ENST00000395438,;PCDH15,downstream_gene_variant,,ENST00000612394,;PCDH15,downstream_gene_variant,,ENST00000409834,;PCDH15,downstream_gene_variant,,ENST00000395446,;PCDH15,downstream_gene_variant,,ENST00000395440,;PCDH15,downstream_gene_variant,,ENST00000395442,;PCDH15,downstream_gene_variant,,ENST00000615043,;PCDH15,downstream_gene_variant,,ENST00000414367,;PCDH15,downstream_gene_variant,,ENST00000476074,; T ENST00000614895 Transcript missense_variant 5424/9249 5029/5046 1677/1681 P/T Cca/Aca 1 -1 PCDH15 HGNC HGNC:14674 protein_coding ENSP00000478512 A0A087WUA8 UPI0004E4CB60 deleterious_low_confidence(0) 35/35 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 53806596 53806596 G T 1 0 0 0 0 1 0 0 0 11598 1261 44 2 2 PCDH15 10 53806596 Missense_Mutation SNP G C3N-01405_T 28208387 53806596 79990826 240 22714 IPMK 0 . GRCh38 10 58199273 58199273 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.595G>A p.Gly199Arg p.G199R ENST00000373935 5/6 172 162 10 128 128 0 strelka-varscan-mutect IPMK,missense_variant,p.Gly199Arg,ENST00000373935,NM_152230.4; T ENST00000373935 Transcript missense_variant 918/6133 595/1251 199/416 G/R Gga/Aga 1 -1 IPMK HGNC HGNC:20739 protein_coding YES CCDS7250.1 ENSP00000363046 Q8NFU5 UPI000006FB8E NM_152230.4 deleterious(0.02) 5/6 hmmpanther:PTHR12400:SF51,hmmpanther:PTHR12400,Pfam_domain:PF03770,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS rs1350051529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 58199273 58199273 C T 1 0 0 0 0 1 0 0 0 7695 661 23 1 1 IPMK 10 58199273 Missense_Mutation SNP C C3N-01405_T 4392677 58199273 75598149 241 22715 CCDC6 0 . GRCh38 10 59906230 59906230 + Silent SNP C C G novel C3N-01405_T C3N-01405_N C C c.195G>C p.= p.S65S ENST00000263102 1/9 447 414 33 286 286 0 strelka-varscan-mutect CCDC6,synonymous_variant,p.=,ENST00000263102,NM_005436.4; G ENST00000263102 Transcript synonymous_variant 427/5811 195/1425 65/474 S tcG/tcC 1 -1 CCDC6 HGNC HGNC:18782 protein_coding YES CCDS7257.1 ENSP00000263102 Q16204 UPI000035B25A NM_005436.4 1/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15276,hmmpanther:PTHR15276:SF0,Pfam_domain:PF09755 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 59906230 59906230 C G 1 0 0 0 0 0 0 0 1 2532 755 27 4 4 CCDC6 10 59906230 Silent SNP C C3N-01405_T 1706957 59906230 73891192 242 22716 TMEM26 0 . GRCh38 10 61410416 61410416 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1013C>A p.Ser338Tyr p.S338Y ENST00000399298 6/6 376 262 114 234 233 1 strelka-varscan-mutect TMEM26,missense_variant,p.Ser338Tyr,ENST00000399298,NM_178505.6;TMEM26,downstream_gene_variant,,ENST00000277749,;TMEM26,non_coding_transcript_exon_variant,,ENST00000507507,;TMEM26,missense_variant,p.Ser338Tyr,ENST00000503886,;TMEM26,downstream_gene_variant,,ENST00000488505,; T ENST00000399298 Transcript missense_variant 1382/5151 1013/1107 338/368 S/Y tCt/tAt 1 -1 TMEM26 HGNC HGNC:28550 protein_coding YES CCDS41530.1 ENSP00000382237 Q6ZUK4 UPI00001C0B3F NM_178505.6 deleterious(0.04) 6/6 hmmpanther:PTHR22168,hmmpanther:PTHR22168:SF3 MODERATE 1 SNV 1 1 PASS rs1266792461 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 61410416 61410416 G T 1 0 0 0 0 1 0 0 0 16620 942 33 2 2 TMEM26 10 61410416 Missense_Mutation SNP G C3N-01405_T 1504186 61410416 72387006 243 22717 MYPN 0 . GRCh38 10 68158598 68158598 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.1430A>G p.Asp477Gly p.D477G ENST00000358913 7/20 365 290 75 282 282 0 strelka-varscan-mutect MYPN,missense_variant,p.Asp183Gly,ENST00000613327,NM_001256268.1;MYPN,missense_variant,p.Asp477Gly,ENST00000358913,NM_032578.3;MYPN,missense_variant,p.Asp477Gly,ENST00000540630,NM_001256267.1;MYPN,missense_variant,p.Asp202Gly,ENST00000354393,;MYPN,missense_variant,p.Asp477Gly,ENST00000373675,;RN7SKP202,downstream_gene_variant,,ENST00000410439,; G ENST00000358913 Transcript missense_variant 1918/6013 1430/3963 477/1320 D/G gAt/gGt 1 1 MYPN HGNC HGNC:23246 protein_coding YES CCDS7275.1 ENSP00000351790 Q86TC9 UPI00002288CF NM_032578.3 deleterious(0.01) 7/20 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF617,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 68158598 68158598 A G 1 0 0 0 0 1 0 0 0 10099 333 12 5 5 MYPN 10 68158598 Missense_Mutation SNP A C3N-01405_T 6748182 68158598 65638824 244 22718 CDH23 0 . GRCh38 10 71793340 71793340 + Missense_Mutation SNP G G C rs111033473 C3N-01405_T C3N-01405_N G G c.6427G>C p.Glu2143Gln p.E2143Q ENST00000224721 48/70 531 361 170 345 345 0 strelka-varscan-mutect CDH23,missense_variant,p.Glu2143Gln,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Glu2138Gln,ENST00000622827,;CDH23,upstream_gene_variant,,ENST00000398788,NM_001171933.1;CDH23,upstream_gene_variant,,ENST00000619887,NM_001171934.1;MIR7152,downstream_gene_variant,,ENST00000619512,;CDH23,upstream_gene_variant,,ENST00000475158,; C ENST00000224721 Transcript missense_variant 6817/11139 6427/10080 2143/3359 E/Q Gag/Cag rs111033473 1 1 CDH23 HGNC HGNC:13733 protein_coding ENSP00000224721 A0A0A0MQS6 UPI0002B831D5 NM_022124.5 tolerated(0.57) 48/70 PROSITE_profiles:PS50268,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 likely_pathogenic MODERATE SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 71793340 71793340 G C 1 0 0 0 0 1 0 0 0 2811 1175 41 4 4 CDH23 10 71793340 Missense_Mutation SNP G C3N-01405_T 3634742 71793340 62004082 245 22719 SEC24C 0 . GRCh38 10 73769720 73769720 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.2669C>A p.Ser890Tyr p.S890Y ENST00000339365 20/24 245 204 41 146 146 0 strelka-varscan-mutect SEC24C,missense_variant,p.Ser890Tyr,ENST00000339365,NM_004922.3;SEC24C,missense_variant,p.Ser890Tyr,ENST00000345254,NM_198597.2;FUT11,upstream_gene_variant,,ENST00000394790,NM_001284194.1;FUT11,upstream_gene_variant,,ENST00000372841,NM_173540.2;RP11-574K11.32,non_coding_transcript_exon_variant,,ENST00000623453,;SEC24C,non_coding_transcript_exon_variant,,ENST00000496827,;FUT11,upstream_gene_variant,,ENST00000465695,;FUT11,upstream_gene_variant,,ENST00000489264,;SEC24C,missense_variant,p.Ser890Tyr,ENST00000465076,;SEC24C,3_prime_UTR_variant,,ENST00000635550,; A ENST00000339365 Transcript missense_variant 2831/4513 2669/3285 890/1094 S/Y tCc/tAc 1 1 SEC24C HGNC HGNC:10705 protein_coding YES CCDS7332.1 ENSP00000343405 P53992 A0A024QZM6 UPI000013F621 NM_004922.3 deleterious(0) 20/24 Pfam_domain:PF04815,hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF5,Superfamily_domains:SSF81811 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 73769720 73769720 C A 1 0 0 0 0 1 0 0 0 14273 855 30 2 2 SEC24C 10 73769720 Missense_Mutation SNP C C3N-01405_T 1976380 73769720 60027702 246 22720 MYOF 0 . GRCh38 10 93329731 93329731 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.4915A>T p.Ile1639Phe p.I1639F ENST00000359263 44/54 327 306 21 287 287 0 strelka-varscan-mutect MYOF,missense_variant,p.Ile1639Phe,ENST00000359263,NM_013451.3;MYOF,missense_variant,p.Ile1626Phe,ENST00000358334,NM_133337.2;MYOF,non_coding_transcript_exon_variant,,ENST00000485212,;MYOF,missense_variant,p.Ile1033Phe,ENST00000463743,; A ENST00000359263 Transcript missense_variant 4915/6719 4915/6186 1639/2061 I/F Att/Ttt 1 -1 MYOF HGNC HGNC:3656 protein_coding YES CCDS41551.1 ENSP00000352208 Q9NZM1 UPI000012FBA1 NM_013451.3 deleterious(0) 44/54 Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF40,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 93329731 93329731 T A 1 0 0 0 0 1 0 0 0 10090 1406 49 4 4 MYOF 10 93329731 Missense_Mutation SNP T C3N-01405_T 19560011 93329731 40467691 247 22721 GLRX3 0 . GRCh38 10 130175028 130175028 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.896G>T p.Trp299Leu p.W299L ENST00000368644 10/12 178 141 37 239 239 0 strelka-varscan-mutect GLRX3,missense_variant,p.Trp299Leu,ENST00000368644,NM_001199868.1;GLRX3,missense_variant,p.Trp299Leu,ENST00000331244,NM_006541.4;GLRX3,upstream_gene_variant,,ENST00000496195,;GLRX3,missense_variant,p.Trp299Leu,ENST00000481034,; T ENST00000368644 Transcript missense_variant 918/3827 896/1008 299/335 W/L tGg/tTg 1 1 GLRX3 HGNC HGNC:15987 protein_coding YES CCDS7661.1 ENSP00000357633 O76003 A0A140VJK1 UPI000006E4EA NM_001199868.1 deleterious(0) 10/12 PROSITE_profiles:PS51354,hmmpanther:PTHR10293,hmmpanther:PTHR10293:SF40,TIGRFAM_domain:TIGR00365,Pfam_domain:PF00462,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 130175028 130175028 G T 1 0 0 0 0 1 0 0 0 6340 1357 47 2 2 GLRX3 10 130175028 Missense_Mutation SNP G C3N-01405_T 36845297 130175028 3622394 248 22722 ADGRA1 0 . GRCh38 10 133127242 133127242 + Silent SNP C C T C3N-01405_T C3N-01405_N C C c.411C>T p.= p.L137L ENST00000392607 6/7 69 51 18 58 58 0 strelka-varscan-mutect ADGRA1,synonymous_variant,p.=,ENST00000607359,;ADGRA1,synonymous_variant,p.=,ENST00000392607,NM_001083909.2;ADGRA1,synonymous_variant,p.=,ENST00000392606,NM_001291085.1; T ENST00000392607 Transcript synonymous_variant 847/4283 411/1683 137/560 L ctC/ctT COSM916440 1 1 ADGRA1 HGNC HGNC:13838 protein_coding YES CCDS41580.1 ENSP00000376384 Q86SQ6 UPI00003D41AD NM_001083909.2 6/7 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF261,Pfam_domain:PF00002 1 LOW 1 SNV 5 1 1 PASS rs1309435104 . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 T 2 4 74 133127242 133127242 C T 1 0 0 0 0 0 0 0 1 352 871 31 1 1 ADGRA1 10 133127242 Silent SNP C C3N-01405_T 2952214 133127242 670180 249 22723 ANO9 0 . GRCh38 11 421013 421013 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.1422C>T p.= p.L474L ENST00000332826 17/23 47 43 4 53 53 0 strelka-mutect ANO9,synonymous_variant,p.=,ENST00000332826,NM_001012302.2;SIGIRR,upstream_gene_variant,,ENST00000332725,NM_021805.2,NM_001135053.1;SIGIRR,upstream_gene_variant,,ENST00000397632,;ANO9,non_coding_transcript_exon_variant,,ENST00000532094,;ANO9,non_coding_transcript_exon_variant,,ENST00000526142,;ANO9,non_coding_transcript_exon_variant,,ENST00000528927,;ANO9,non_coding_transcript_exon_variant,,ENST00000534161,;ANO9,non_coding_transcript_exon_variant,,ENST00000525804,;SIGIRR,upstream_gene_variant,,ENST00000527295,;ANO9,upstream_gene_variant,,ENST00000524802,; A ENST00000332826 Transcript synonymous_variant 1507/2542 1422/2349 474/782 L ctC/ctT 1 -1 ANO9 HGNC HGNC:20679 protein_coding YES CCDS31326.1 ENSP00000332788 A1A5B4 UPI0001505B10 NM_001012302.2 17/23 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF37,Pfam_domain:PF04547 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -10.62708 1 1 1 1 0 A 2 1 74 421013 421013 G A 1 0 0 0 0 0 0 0 1 811 929 33 3 3 ANO9 11 421013 Silent SNP G C3N-01405_T 421013 134665609 250 22724 HRAS 0 . GRCh38 11 532690 532690 + Missense_Mutation SNP G G T rs765180494 C3N-01405_T C3N-01405_N G G c.516C>A p.Asn172Lys p.N172K ENST00000451590 5/5 382 336 46 293 293 0 strelka-varscan-mutect HRAS,missense_variant,p.Asn172Lys,ENST00000451590,NM_005343.2,NM_001130442.1;HRAS,missense_variant,p.Asn172Lys,ENST00000397596,;HRAS,missense_variant,p.Asn172Lys,ENST00000311189,;HRAS,3_prime_UTR_variant,,ENST00000417302,NM_176795.3;HRAS,3_prime_UTR_variant,,ENST00000397594,;LRRC56,upstream_gene_variant,,ENST00000270115,NM_198075.3;RP13-46H24.1,downstream_gene_variant,,ENST00000526431,;HRAS,non_coding_transcript_exon_variant,,ENST00000462734,;HRAS,non_coding_transcript_exon_variant,,ENST00000479482,;HRAS,intron_variant,,ENST00000478324,;HRAS,downstream_gene_variant,,ENST00000468682,;HRAS,downstream_gene_variant,,ENST00000482021,;HRAS,3_prime_UTR_variant,,ENST00000493230,NM_001318054.1; T ENST00000451590 Transcript missense_variant 704/1151 516/570 172/189 N/K aaC/aaA rs765180494 1 -1 HRAS HGNC HGNC:5173 protein_coding YES CCDS7698.1 ENSP00000407586 P01112 X5D945 UPI0000001251 NM_005343.2,NM_001130442.1 tolerated(0.22) 5/5 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF184 MODERATE SNV 2 1 PASS rs765180494 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 532690 532690 G T 1 0 0 0 0 1 0 0 0 7243 1252 44 2 2 HRAS 11 532690 Missense_Mutation SNP G C3N-01405_T 111677 532690 134553932 251 22725 BRSK2 0 . GRCh38 11 1443362 1443362 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.730G>A p.Asp244Asn p.D244N ENST00000382179 7/20 120 86 34 115 115 0 strelka-varscan-mutect BRSK2,missense_variant,p.Asp198Asn,ENST00000308219,NM_003957.3;BRSK2,missense_variant,p.Asp198Asn,ENST00000528841,NM_001256627.1;BRSK2,missense_variant,p.Asp244Asn,ENST00000382179,NM_001256630.1;BRSK2,missense_variant,p.Asp138Asn,ENST00000528710,NM_001282218.1;BRSK2,missense_variant,p.Asp198Asn,ENST00000531197,NM_001256629.1;BRSK2,missense_variant,p.Asp198Asn,ENST00000526678,;BRSK2,downstream_gene_variant,,ENST00000528596,;BRSK2,downstream_gene_variant,,ENST00000524702,;BRSK2,missense_variant,p.Asp198Asn,ENST00000529433,;BRSK2,missense_variant,p.Asp104Asn,ENST00000529951,;BRSK2,non_coding_transcript_exon_variant,,ENST00000531078,; A ENST00000382179 Transcript missense_variant 983/3576 730/2301 244/766 D/N Gac/Aac 1 1 BRSK2 HGNC HGNC:11405 protein_coding YES CCDS58108.1 ENSP00000371614 Q8IWQ3 UPI000035E827 NM_001256630.1 deleterious(0) 7/20 PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF84,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 1443362 1443362 G A 1 0 0 0 0 1 0 0 0 1698 1174 41 3 3 BRSK2 11 1443362 Missense_Mutation SNP G C3N-01405_T 910672 1443362 133643260 252 22726 OR51B4 0 . GRCh38 11 5301169 5301169 + Missense_Mutation SNP T T A rs772754106 C3N-01405_T C3N-01405_N T T c.778A>T p.Arg260Trp p.R260W ENST00000380224 1/1 182 141 41 169 169 0 strelka-varscan-mutect OR51B4,missense_variant,p.Arg260Trp,ENST00000380224,NM_033179.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,downstream_gene_variant,,ENST00000420465,; A ENST00000380224 Transcript missense_variant 828/983 778/933 260/310 R/W Agg/Tgg rs772754106 1 -1 OR51B4 HGNC HGNC:14708 protein_coding YES CCDS7757.1 ENSP00000369573 Q9Y5P0 UPI0000041B31 NM_033179.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF154,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs772754106 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 5301169 5301169 T A 1 0 0 0 0 1 0 0 0 11164 1579 55 4 4 OR51B4 11 5301169 Missense_Mutation SNP T C3N-01405_T 3857807 5301169 129785453 253 22727 TRIM34 0 . GRCh38 11 5634763 5634763 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.1714G>A p.Glu572Lys p.E572K ENST00000354852 10/14 154 112 42 189 189 0 strelka-varscan-mutect TRIM6-TRIM34,missense_variant,p.Glu572Lys,ENST00000354852,NM_001003819.3;TRIM34,missense_variant,p.Glu218Lys,ENST00000514226,NM_001003827.1;TRIM34,missense_variant,p.Glu218Lys,ENST00000429814,NM_021616.5;HBG2,intron_variant,,ENST00000380259,;TRIM34,upstream_gene_variant,,ENST00000495668,;TRIM34,non_coding_transcript_exon_variant,,ENST00000491385,; A ENST00000354852 Transcript missense_variant 1887/3391 1714/2529 572/842 E/K Gag/Aag 1 1 TRIM6-TRIM34 HGNC HGNC:33440 protein_coding YES CCDS31388.1 ENSP00000346916 B2RNG4 UPI000041A254 NM_001003819.3 tolerated(0.27) 10/14 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103:SF51,hmmpanther:PTHR24103 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 5634763 5634763 G A 1 0 0 0 0 1 0 0 0 16997 943 33 3 3 TRIM34 11 5634763 Missense_Mutation SNP G C3N-01405_T 333594 5634763 129451859 254 22728 OR10A2 0 . GRCh38 11 6870085 6870085 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.331G>C p.Val111Leu p.V111L ENST00000307322 1/1 273 199 74 259 259 0 strelka-varscan-mutect OR10A2,missense_variant,p.Val111Leu,ENST00000307322,NM_001004460.1;RP11-413N10.3,intron_variant,,ENST00000637205,; C ENST00000307322 Transcript missense_variant 393/1053 331/912 111/303 V/L Gtg/Ctg 1 1 OR10A2 HGNC HGNC:8161 protein_coding YES CCDS31415.1 ENSP00000303862 Q9H208 UPI000015F21C NM_001004460.1 deleterious(0.04) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF148,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 6870085 6870085 G C 1 0 0 0 0 1 0 0 0 10966 1377 48 4 4 OR10A2 11 6870085 Missense_Mutation SNP G C3N-01405_T 1235322 6870085 128216537 255 22729 SAAL1 0 . GRCh38 11 18092245 18092245 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.413G>T p.Gly138Val p.G138V ENST00000524803 4/12 135 92 43 150 149 1 strelka-varscan-mutect SAAL1,missense_variant,p.Gly138Val,ENST00000524803,NM_138421.2;SAAL1,missense_variant,p.Gly138Val,ENST00000300013,;SAAL1,missense_variant,p.Gly138Val,ENST00000529318,;SAAL1,missense_variant,p.Gly27Val,ENST00000531751,;SAAL1,missense_variant,p.Gly138Val,ENST00000530180,;SAAL1,intron_variant,,ENST00000532452,;SAAL1,upstream_gene_variant,,ENST00000530436,;SAAL1,splice_region_variant,,ENST00000533851,;SAAL1,downstream_gene_variant,,ENST00000530736,;SAAL1,missense_variant,p.Gly138Val,ENST00000531581,;SAAL1,upstream_gene_variant,,ENST00000528002,; A ENST00000524803 Transcript missense_variant,splice_region_variant 463/1582 413/1425 138/474 G/V gGg/gTg 1 -1 SAAL1 HGNC HGNC:25158 protein_coding YES CCDS31439.1 ENSP00000432487 Q96ER3 G1UCX3 UPI00001F9E3B NM_138421.2 tolerated(0.34) 4/12 Gene3D:1.25.10.10,hmmpanther:PTHR23424,hmmpanther:PTHR23424:SF4,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999986 1 1 1 0 A 3 1 74 18092245 18092245 C A 1 0 0 0 0 1 0 0 0 14060 637 22 2 2 SAAL1 11 18092245 Missense_Mutation SNP C C3N-01405_T 11222160 18092245 116994377 256 22730 NAV2 0 . GRCh38 11 20054091 20054091 + Missense_Mutation SNP C C T rs751924820 C3N-01405_T C3N-01405_N C C c.4562C>T p.Thr1521Ile p.T1521I ENST00000396087 19/41 220 161 59 238 238 0 strelka-varscan-mutect NAV2,missense_variant,p.Thr1521Ile,ENST00000527559,;NAV2,missense_variant,p.Thr1498Ile,ENST00000540292,;NAV2,missense_variant,p.Thr1498Ile,ENST00000396085,NM_182964.5;NAV2,missense_variant,p.Thr1498Ile,ENST00000349880,NM_145117.4;NAV2,missense_variant,p.Thr1434Ile,ENST00000360655,NM_001111018.1;NAV2,missense_variant,p.Thr1521Ile,ENST00000396087,NM_001244963.1;NAV2,missense_variant,p.Thr562Ile,ENST00000533917,NM_001111019.2;NAV2,missense_variant,p.Thr547Ile,ENST00000525322,;NAV2-AS2,upstream_gene_variant,,ENST00000533767,; T ENST00000396087 Transcript missense_variant 4661/7882 4562/7467 1521/2488 T/I aCc/aTc rs751924820 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 deleterious(0) 19/41 hmmpanther:PTHR12784:SF6,hmmpanther:PTHR12784 MODERATE SNV 5 1 PASS rs751924820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 20054091 20054091 C T 1 0 0 0 0 1 0 0 0 10193 507 18 3 3 NAV2 11 20054091 Missense_Mutation SNP C C3N-01405_T 1961846 20054091 115032531 257 22731 CCDC73 0 . GRCh38 11 32614594 32614594 + Missense_Mutation SNP G G A rs562518207 C3N-01405_T C3N-01405_N G G c.1724C>T p.Ser575Leu p.S575L ENST00000335185 16/18 109 75 34 155 155 0 strelka-varscan-mutect CCDC73,missense_variant,p.Ser575Leu,ENST00000335185,NM_001008391.3;CCDC73,intron_variant,,ENST00000528333,;CCDC73,downstream_gene_variant,,ENST00000534415,; A ENST00000335185 Transcript missense_variant 1768/3849 1724/3240 575/1079 S/L tCa/tTa rs562518207 1 -1 CCDC73 HGNC HGNC:23261 protein_coding YES CCDS41630.1 ENSP00000335325 Q6ZRK6 UPI000066725E NM_001008391.3 tolerated(0.16) 16/18 Pfam_domain:PF15818,hmmpanther:PTHR28660,hmmpanther:PTHR28660:SF1 MODERATE 1 SNV 2 1 PASS rs562518207 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 32614594 32614594 G A 1 0 0 0 0 1 0 0 0 2546 1294 45 3 3 CCDC73 11 32614594 Missense_Mutation SNP G C3N-01405_T 12560503 32614594 102472028 258 22732 TRIM44 0 . GRCh38 11 35663169 35663169 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.58G>A p.Glu20Lys p.E20K ENST00000299413 1/5 23 14 9 14 14 0 strelka-varscan-mutect TRIM44,missense_variant,p.Glu20Lys,ENST00000299413,NM_017583.5;RP1-276E15.1,downstream_gene_variant,,ENST00000525573,; A ENST00000299413 Transcript missense_variant 365/12964 58/1035 20/344 E/K Gag/Aag 1 1 TRIM44 HGNC HGNC:19016 protein_coding YES CCDS31461.1 ENSP00000299413 Q96DX7 UPI00000725C5 NM_017583.5 tolerated(0.15) 1/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF365 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 35663169 35663169 G A 1 0 0 0 0 1 0 0 0 17009 1059 37 1 1 TRIM44 11 35663169 Missense_Mutation SNP G C3N-01405_T 3048575 35663169 99423453 259 22733 OR4C15 0 . GRCh38 11 55554413 55554413 + Missense_Mutation SNP C C A rs757414964 C3N-01405_T C3N-01405_N C C c.107C>A p.Pro36His p.P36H ENST00000314644 1/1 188 154 34 261 260 1 strelka-varscan-mutect OR4C15,missense_variant,p.Pro36His,ENST00000314644,NM_001001920.1; A ENST00000314644 Transcript missense_variant 107/1113 107/1113 36/370 P/H cCt/cAt rs757414964,COSM145722 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 tolerated_low_confidence(0.23) 1/1 0,1 MODERATE 1 SNV 0,1 1 PASS rs757414964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 55554413 55554413 C A 1 0 0 0 0 1 0 0 0 11125 681 24 2 2 OR4C15 11 55554413 Missense_Mutation SNP C C3N-01405_T 19891244 55554413 79532209 260 22734 OR5D14 0 . GRCh38 11 55795696 55795696 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.141G>T p.Met47Ile p.M47I ENST00000335605 1/1 101 77 24 127 127 0 strelka-varscan-mutect OR5D14,missense_variant,p.Met47Ile,ENST00000335605,NM_001004735.1; T ENST00000335605 Transcript missense_variant 141/945 141/945 47/314 M/I atG/atT COSM4194741 1 1 OR5D14 HGNC HGNC:15281 protein_coding YES CCDS31508.1 ENSP00000334456 Q8NGL3 UPI000004B1F6 NM_001004735.1 tolerated(0.14) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF67,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 55795696 55795696 G T 1 0 0 0 0 1 0 0 0 11225 1290 45 2 2 OR5D14 11 55795696 Missense_Mutation SNP G C3N-01405_T 241283 55795696 79290926 261 22735 OR5W2 0 . GRCh38 11 55913981 55913981 + Missense_Mutation SNP G G T rs781229540 C3N-01405_T C3N-01405_N G G c.602C>A p.Thr201Asn p.T201N ENST00000344514 1/1 115 84 31 103 103 0 strelka-mutect OR5W2,missense_variant,p.Thr201Asn,ENST00000344514,NM_001001960.1; T ENST00000344514 Transcript missense_variant 602/933 602/933 201/310 T/N aCc/aAc rs781229540 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs781229540 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 55913981 55913981 G T 1 0 0 0 0 1 0 0 0 11253 1261 44 2 2 OR5W2 11 55913981 Missense_Mutation SNP G C3N-01405_T 118285 55913981 79172641 262 22736 OR5M11 0 . GRCh38 11 56543231 56543231 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.27C>A p.= p.I9I ENST00000528616 1/1 75 55 20 79 79 0 strelka-varscan-mutect OR5M11,synonymous_variant,p.=,ENST00000528616,NM_001005245.1; T ENST00000528616 Transcript synonymous_variant 27/918 27/918 9/305 I atC/atA 1 -1 OR5M11 HGNC HGNC:15291 protein_coding YES CCDS53629.1 ENSP00000432417 Q96RB7 A0A126GVL9 UPI00000405CF NM_001005245.1 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF97,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 56543231 56543231 G T 1 0 0 0 0 0 0 0 1 11243 1280 45 2 2 OR5M11 11 56543231 Silent SNP G C3N-01405_T 629250 56543231 78543391 263 22737 OR5AP2 0 . GRCh38 11 56642035 56642035 + Silent SNP G G A rs374654172 C3N-01405_T C3N-01405_N G G c.405C>T p.= p.P135P ENST00000302981 1/1 178 127 51 157 156 1 strelka-varscan-mutect OR5AP2,synonymous_variant,p.=,ENST00000544374,;OR5AP2,synonymous_variant,p.=,ENST00000302981,NM_001002925.1; A ENST00000302981 Transcript synonymous_variant 405/951 405/951 135/316 P ccC/ccT rs374654172,COSM5296543 1 -1 OR5AP2 HGNC HGNC:15258 protein_coding YES CCDS31534.1 ENSP00000303111 Q8NGF4 UPI0000061EE6 NM_001002925.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF151,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 LOW 1 SNV 0,1 1 PASS rs374654172 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 56642035 56642035 G A 1 0 0 0 0 0 0 0 1 11216 1219 43 3 3 OR5AP2 11 56642035 Silent SNP G C3N-01405_T 98804 56642035 78444587 264 22738 GLYAT 0 . GRCh38 11 58715347 58715347 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.158T>A p.Phe53Tyr p.F53Y ENST00000611865 2/5 149 109 40 167 167 0 strelka-varscan-mutect GLYAT,missense_variant,p.Phe53Tyr,ENST00000611865,;GLYAT,missense_variant,p.Phe53Tyr,ENST00000344743,NM_201648.2;GLYAT,missense_variant,p.Phe53Tyr,ENST00000278400,NM_005838.3;GLYAT,missense_variant,p.Phe53Tyr,ENST00000529732,;GLYAT,upstream_gene_variant,,ENST00000586098,; T ENST00000611865 Transcript missense_variant 158/1899 158/891 53/296 F/Y tTt/tAt 1 -1 GLYAT HGNC HGNC:13734 protein_coding YES CCDS7970.1 ENSP00000484592 Q6IB77 UPI00003667C7 tolerated(0.58) 2/5 hmmpanther:PTHR15298:SF9,hmmpanther:PTHR15298,Pfam_domain:PF06021,Superfamily_domains:SSF55729 MODERATE 1 SNV 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 58715347 58715347 A T 1 0 0 0 0 1 0 0 0 6356 14 1 4 4 GLYAT 11 58715347 Missense_Mutation SNP A C3N-01405_T 2073312 58715347 76371275 265 22739 OR5A1 0 . GRCh38 11 59443519 59443519 + Silent SNP C C T novel C3N-01405_T C3N-01405_N C C c.351C>T p.= p.L117L ENST00000302030 1/1 157 143 14 105 105 0 strelka-varscan-mutect OR5A1,synonymous_variant,p.=,ENST00000302030,NM_001004728.1; T ENST00000302030 Transcript synonymous_variant 376/1051 351/948 117/315 L ctC/ctT 1 1 OR5A1 HGNC HGNC:8319 protein_coding YES CCDS31561.1 ENSP00000303096 Q8NGJ0 UPI0000041C97 NM_001004728.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF354,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 59443519 59443519 C T 1 0 0 0 0 0 0 0 1 11211 842 30 3 3 OR5A1 11 59443519 Silent SNP C C3N-01405_T 728172 59443519 75643103 266 22740 FLRT1 0 . GRCh38 11 64117356 64117356 + Frame_Shift_Del DEL C C - rs550169038 C3N-01405_T C3N-01405_N C C c.1090delC p.Arg364GlyfsTer80 p.R364Gfs*80 ENST00000246841 2/2 77 63 14 85 85 0 sindel-varindel-pindel FLRT1,frameshift_variant,p.Arg364GlyfsTer80,ENST00000246841,NM_013280.4;MACROD1,intron_variant,,ENST00000255681,NM_014067.3;RP11-21A7A.3,downstream_gene_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000545464,; - ENST00000246841 Transcript frameshift_variant 2132/3949 1089/2025 363/674 V/X gtC/gt rs550169038 1 1 FLRT1 HGNC HGNC:3760 protein_coding YES CCDS8057.1 ENSP00000246841 Q9NZU1 UPI0000039F94 NM_013280.4 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF30,SMART_domains:SM00082,Superfamily_domains:SSF52058 HIGH 1 deletion 1 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 - 7 5 74 64117356 64117356 C - 1 0 1 0 1 0 0 0 0 5794 842 30 0 0 FLRT1 11 64117356 Frame_Shift_Del DEL C C3N-01405_T 4673837 64117356 70969266 267 22741 CDC42BPG 0 . GRCh38 11 64829618 64829618 + Missense_Mutation SNP C C A rs374392572 C3N-01405_T C3N-01405_N C C c.3820G>T p.Gly1274Trp p.G1274W ENST00000342711 30/37 423 321 102 311 311 0 strelka-varscan-mutect CDC42BPG,missense_variant,p.Gly1274Trp,ENST00000342711,NM_017525.2;CDC42BPG,downstream_gene_variant,,ENST00000491280,;CDC42BPG,downstream_gene_variant,,ENST00000468512,;CDC42BPG,downstream_gene_variant,,ENST00000480767,; A ENST00000342711 Transcript missense_variant 3820/5742 3820/4656 1274/1551 G/W Ggg/Tgg rs374392572 1 -1 CDC42BPG HGNC HGNC:29829 protein_coding YES CCDS31601.1 ENSP00000345133 Q6DT37 UPI000047C9E2 NM_017525.2 tolerated(0.18) 30/37 Low_complexity_(Seg):seg,PROSITE_profiles:PS50219,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS rs374392572 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 64829618 64829618 C A 1 0 0 0 0 1 0 0 0 2777 652 23 1 1 CDC42BPG 11 64829618 Missense_Mutation SNP C C3N-01405_T 712262 64829618 70257004 268 22742 EED 0 . GRCh38 11 86245330 86245330 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.101C>G p.Ser34Cys p.S34C ENST00000351625 1/13 262 201 61 187 187 0 strelka-varscan-mutect EED,missense_variant,p.Ser34Cys,ENST00000263360,NM_003797.3;EED,missense_variant,p.Ser34Cys,ENST00000327320,NM_152991.2;EED,missense_variant,p.Ser34Cys,ENST00000528180,;EED,missense_variant,p.Ser34Cys,ENST00000351625,NM_001308007.1;EED,missense_variant,p.Ser33Cys,ENST00000534595,;EED,non_coding_transcript_exon_variant,,ENST00000525244,; G ENST00000351625 Transcript missense_variant 108/1696 101/1401 34/466 S/C tCt/tGt 1 1 EED HGNC HGNC:3188 protein_coding YES CCDS76463.1 ENSP00000338186 O75530 UPI00003534F9 NM_001308007.1 deleterious(0) 1/13 hmmpanther:PTHR10253 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 86245330 86245330 C G 1 0 0 0 0 1 0 0 0 4751 913 32 4 4 EED 11 86245330 Missense_Mutation SNP C C3N-01405_T 21415712 86245330 48841292 269 22743 CNTN5 0 . GRCh38 11 100193648 100193648 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1869T>A p.Phe623Leu p.F623L ENST00000524871 15/25 239 183 56 269 269 0 strelka-varscan-mutect CNTN5,missense_variant,p.Phe623Leu,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Phe607Leu,ENST00000279463,;CNTN5,missense_variant,p.Phe545Leu,ENST00000619298,;CNTN5,missense_variant,p.Phe623Leu,ENST00000527185,NM_001243271.1;CNTN5,missense_variant,p.Phe623Leu,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Phe549Leu,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000524560,;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; A ENST00000524871 Transcript missense_variant 2159/6258 1869/3303 623/1100 F/L ttT/ttA 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 deleterious(0.04) 15/25 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 100193648 100193648 T A 1 0 0 0 0 1 0 0 0 3425 1809 63 4 4 CNTN5 11 100193648 Missense_Mutation SNP T C3N-01405_T 13948318 100193648 34892974 270 22744 GUCY1A2 0 . GRCh38 11 107017907 107017907 + Missense_Mutation SNP G G T rs772392728 C3N-01405_T C3N-01405_N G G c.149C>A p.Pro50Gln p.P50Q ENST00000282249 1/9 50 38 12 47 47 0 strelka-varscan-mutect GUCY1A2,missense_variant,p.Pro50Gln,ENST00000526355,NM_000855.2;GUCY1A2,missense_variant,p.Pro50Gln,ENST00000282249,NM_001256424.1;GUCY1A2,missense_variant,p.Pro50Gln,ENST00000347596,; T ENST00000282249 Transcript missense_variant 539/3047 149/2292 50/763 P/Q cCg/cAg rs772392728 1 -1 GUCY1A2 HGNC HGNC:4684 protein_coding YES CCDS58170.1 ENSP00000282249 P33402 UPI000002A79C NM_001256424.1 tolerated_low_confidence(0.23) 1/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs772392728 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 107017907 107017907 G T 1 0 0 0 0 1 0 0 0 6775 1116 39 1 1 GUCY1A2 11 107017907 Missense_Mutation SNP G C3N-01405_T 6824259 107017907 28068715 271 22745 NCAM1 0 . GRCh38 11 113260246 113260246 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.2132T>A p.Val711Glu p.V711E ENST00000619839 18/21 244 216 28 189 189 0 strelka-varscan-mutect NCAM1,missense_variant,p.Val711Glu,ENST00000615285,;NCAM1,missense_variant,p.Val685Glu,ENST00000615112,;NCAM1,missense_variant,p.Val675Glu,ENST00000618266,;NCAM1,missense_variant,p.Val685Glu,ENST00000316851,NM_181351.4;NCAM1,missense_variant,p.Val710Glu,ENST00000621518,;NCAM1,missense_variant,p.Val675Glu,ENST00000621128,NM_001242608.1;NCAM1,missense_variant,p.Val711Glu,ENST00000619839,NM_001242607.1;NCAM1,missense_variant,p.Val675Glu,ENST00000531044,NM_000615.6;NCAM1,missense_variant,p.Val710Glu,ENST00000621850,NM_001076682.3;NCAM1,missense_variant,p.Val674Glu,ENST00000401611,;NCAM1,missense_variant,p.Val23Glu,ENST00000528158,;NCAM1,missense_variant,p.Val184Glu,ENST00000533073,;NCAM1,missense_variant,p.Val254Glu,ENST00000526322,;NCAM1,missense_variant,p.Val199Glu,ENST00000528590,;NCAM1,missense_variant,p.Val93Glu,ENST00000620046,;NCAM1,missense_variant,p.Val52Glu,ENST00000524916,;NCAM1,downstream_gene_variant,,ENST00000530543,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,3_prime_UTR_variant,,ENST00000531817,;NCAM1,non_coding_transcript_exon_variant,,ENST00000525691,;NCAM1,non_coding_transcript_exon_variant,,ENST00000530090,;NCAM1,non_coding_transcript_exon_variant,,ENST00000534516,;NCAM1,non_coding_transcript_exon_variant,,ENST00000525355,; A ENST00000619839 Transcript missense_variant 2470/2993 2132/2655 711/884 V/E gTg/gAg 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 deleterious(0) 18/21 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 113260246 113260246 T A 1 0 0 0 0 1 0 0 0 10218 1696 59 4 4 NCAM1 11 113260246 Missense_Mutation SNP T C3N-01405_T 6242339 113260246 21826376 272 22746 H2AFX 0 . GRCh38 11 119095298 119095298 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.97C>T p.Arg33Trp p.R33W ENST00000530167 1/1 129 117 12 87 87 0 strelka-varscan-mutect H2AFX,missense_variant,p.Arg33Trp,ENST00000530167,NM_002105.2;DPAGT1,downstream_gene_variant,,ENST00000409993,;DPAGT1,downstream_gene_variant,,ENST00000354202,NM_001382.3;HMBS,downstream_gene_variant,,ENST00000537841,;HMBS,downstream_gene_variant,,ENST00000442944,;HMBS,downstream_gene_variant,,ENST00000278715,NM_000190.3;HMBS,downstream_gene_variant,,ENST00000542729,NM_001258209.1;HMBS,downstream_gene_variant,,ENST00000392841,NM_001024382.1;HMBS,downstream_gene_variant,,ENST00000544387,NM_001258208.1;HMBS,downstream_gene_variant,,ENST00000543090,;HMBS,downstream_gene_variant,,ENST00000539986,;HMBS,downstream_gene_variant,,ENST00000535253,;HMBS,downstream_gene_variant,,ENST00000546302,;DPAGT1,downstream_gene_variant,,ENST00000636404,;HMBS,downstream_gene_variant,,ENST00000534956,;H2AFX,missense_variant,p.Arg33Trp,ENST00000375167,;DPAGT1,downstream_gene_variant,,ENST00000481084,;DPAGT1,downstream_gene_variant,,ENST00000461999,;HMBS,downstream_gene_variant,,ENST00000546226,;DPAGT1,downstream_gene_variant,,ENST00000392834,;HMBS,downstream_gene_variant,,ENST00000543543,;DPAGT1,downstream_gene_variant,,ENST00000414373,;HMBS,downstream_gene_variant,,ENST00000542044,;HMBS,downstream_gene_variant,,ENST00000544182,;HMBS,downstream_gene_variant,,ENST00000545621,;DPAGT1,downstream_gene_variant,,ENST00000533687,;DPAGT1,downstream_gene_variant,,ENST00000525456,;DPAGT1,downstream_gene_variant,,ENST00000442480,;HMBS,downstream_gene_variant,,ENST00000542822,;HMBS,downstream_gene_variant,,ENST00000542345,;HMBS,downstream_gene_variant,,ENST00000539045,;HMBS,downstream_gene_variant,,ENST00000535793,;DPAGT1,downstream_gene_variant,,ENST00000530052,;HMBS,downstream_gene_variant,,ENST00000544360,;DPAGT1,downstream_gene_variant,,ENST00000524658,; A ENST00000530167 Transcript missense_variant 170/1614 97/432 33/143 R/W Cgg/Tgg 1 -1 H2AFX HGNC HGNC:4739 protein_coding YES CCDS8410.1 ENSP00000434024 P16104 UPI0000048D69 NM_002105.2 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR23430,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620 MODERATE SNV 1 PASS rs1364679785 . 0 207 3 0 0 0 0 0 -19.99985 1 1 1 1 0 A 3 1 74 119095298 119095298 G A 1 0 0 0 0 1 0 0 0 6809 1115 39 1 1 H2AFX 11 119095298 Missense_Mutation SNP G C3N-01405_T 5835052 119095298 15991324 273 22747 BSX 0 . GRCh38 11 122981577 122981577 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.95C>A p.Pro32Gln p.P32Q ENST00000343035 1/3 166 133 33 139 139 0 strelka-varscan-mutect BSX,missense_variant,p.Pro32Gln,ENST00000343035,NM_001098169.1; T ENST00000343035 Transcript missense_variant 144/830 95/702 32/233 P/Q cCg/cAg 1 -1 BSX HGNC HGNC:20450 protein_coding YES CCDS41728.1 ENSP00000344285 Q3C1V8 UPI000036683F NM_001098169.1 deleterious(0.05) 1/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF35 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 122981577 122981577 G T 1 0 0 0 0 1 0 0 0 1710 1116 39 1 1 BSX 11 122981577 Missense_Mutation SNP G C3N-01405_T 3886279 122981577 12105045 274 22748 OR10G8 0 . GRCh38 11 124029763 124029763 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.141C>A p.= p.I47I ENST00000431524 1/1 363 287 76 295 295 0 strelka-varscan-mutect OR10G8,synonymous_variant,p.=,ENST00000431524,NM_001004464.1; A ENST00000431524 Transcript synonymous_variant 174/1045 141/936 47/311 I atC/atA 1 1 OR10G8 HGNC HGNC:14845 protein_coding YES CCDS31704.1 ENSP00000389072 Q8NGN5 A0A126GVX3 UPI0000040A8F NM_001004464.1 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF146,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 124029763 124029763 C A 1 0 0 0 0 0 0 0 1 10980 816 29 2 2 OR10G8 11 124029763 Silent SNP C C3N-01405_T 1048186 124029763 11056859 275 22749 ESAM 0 . GRCh38 11 124754274 124754274 + Missense_Mutation SNP C C A rs764306357 C3N-01405_T C3N-01405_N C C c.797G>T p.Gly266Val p.G266V ENST00000278927 6/7 194 171 23 149 149 0 strelka-varscan-mutect ESAM,missense_variant,p.Gly266Val,ENST00000278927,NM_138961.2;ESAM,missense_variant,p.Gly139Val,ENST00000435477,;ESAM,missense_variant,p.Gly87Val,ENST00000444566,;VSIG2,upstream_gene_variant,,ENST00000403470,;VSIG2,upstream_gene_variant,,ENST00000326621,NM_014312.3;RP11-677M14.3,upstream_gene_variant,,ENST00000504932,;ESAM,3_prime_UTR_variant,,ENST00000417453,;ESAM,non_coding_transcript_exon_variant,,ENST00000464067,;ESAM,non_coding_transcript_exon_variant,,ENST00000485116,; A ENST00000278927 Transcript missense_variant 927/1826 797/1173 266/390 G/V gGg/gTg rs764306357 1 -1 ESAM HGNC HGNC:17474 protein_coding YES CCDS8453.1 ENSP00000278927 Q96AP7 UPI000003721A NM_138961.2 tolerated(0.65) 6/7 hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF126,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs764306357 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 124754274 124754274 C A 1 0 0 0 0 1 0 0 0 5109 623 22 2 2 ESAM 11 124754274 Missense_Mutation SNP C C3N-01405_T 724511 124754274 10332348 276 22750 ROBO4 0 . GRCh38 11 124895191 124895191 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.1039C>T p.Pro347Ser p.P347S ENST00000306534 7/18 139 125 14 137 137 0 strelka-mutect ROBO4,missense_variant,p.Pro347Ser,ENST00000306534,NM_019055.5;ROBO4,missense_variant,p.Pro202Ser,ENST00000533054,NM_001301088.1;RP11-664I21.6,downstream_gene_variant,,ENST00000524433,;ROBO4,downstream_gene_variant,,ENST00000526899,;ROBO4,downstream_gene_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000529941,;ROBO4,upstream_gene_variant,,ENST00000534407,;ROBO4,upstream_gene_variant,,ENST00000532216,;ROBO4,upstream_gene_variant,,ENST00000525182,;ROBO4,downstream_gene_variant,,ENST00000533337,;ROBO4,downstream_gene_variant,,ENST00000532300,; A ENST00000306534 Transcript missense_variant,splice_region_variant 1525/4710 1039/3024 347/1007 P/S Ccc/Tcc 1 -1 ROBO4 HGNC HGNC:17985 protein_coding YES CCDS8455.1 ENSP00000304945 Q8WZ75 UPI000004A023 NM_019055.5 deleterious(0) 7/18 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.81655 0.9999999 1 1 1 0 A 3 1 74 124895191 124895191 G A 1 0 0 0 0 1 0 0 0 13694 1217 42 3 3 ROBO4 11 124895191 Missense_Mutation SNP G C3N-01405_T 140917 124895191 10191431 277 22751 EI24 0 . GRCh38 11 125579048 125579048 + Nonsense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.541C>T p.Gln181Ter p.Q181* ENST00000278903 7/11 210 154 56 175 175 0 strelka-varscan-mutect EI24,stop_gained,p.Gln181Ter,ENST00000278903,NM_004879.4;EI24,stop_gained,p.Gln8Ter,ENST00000618552,;EI24,stop_gained,p.Gln181Ter,ENST00000620753,;EI24,stop_gained,p.Gln181Ter,ENST00000527235,;EI24,stop_gained,p.Gln167Ter,ENST00000534546,NM_001290135.1;EI24,stop_gained,p.Gln8Ter,ENST00000615917,;EI24,stop_gained,p.Gln181Ter,ENST00000527842,;EI24,downstream_gene_variant,,ENST00000524723,;EI24,downstream_gene_variant,,ENST00000527131,;EI24,downstream_gene_variant,,ENST00000527520,;RNU6-1156P,downstream_gene_variant,,ENST00000410365,;STT3A-AS1,intron_variant,,ENST00000530526,;EI24,3_prime_UTR_variant,,ENST00000531636,;EI24,downstream_gene_variant,,ENST00000529765,;EI24,upstream_gene_variant,,ENST00000530540,; T ENST00000278903 Transcript stop_gained 969/2455 541/1023 181/340 Q/* Cag/Tag 1 1 EI24 HGNC HGNC:13276 protein_coding YES CCDS73410.1 ENSP00000278903 O14681 A0A024R3I8 UPI000006CFDB NM_004879.4 7/11 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR21389:SF0,hmmpanther:PTHR21389,Pfam_domain:PF07264 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 125579048 125579048 C T 1 0 0 0 0 0 1 0 0 4821 711 25 3 3 EI24 11 125579048 Nonsense_Mutation SNP C C3N-01405_T 683857 125579048 9507574 278 22752 GLB1L2 0 . GRCh38 11 134370316 134370316 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1132G>T p.Asp378Tyr p.D378Y ENST00000535456 12/19 279 246 33 146 145 1 strelka-varscan-mutect GLB1L2,missense_variant,p.Asp378Tyr,ENST00000535456,NM_138342.3;GLB1L2,missense_variant,p.Asp378Tyr,ENST00000339772,;GLB1L2,non_coding_transcript_exon_variant,,ENST00000529077,;GLB1L2,downstream_gene_variant,,ENST00000533324,; T ENST00000535456 Transcript missense_variant 1320/3365 1132/1911 378/636 D/Y Gac/Tac 1 1 GLB1L2 HGNC HGNC:25129 protein_coding YES CCDS31724.1 ENSP00000444628 Q8IW92 A0A024R3N9 UPI0000074534 NM_138342.3 deleterious(0.02) 12/19 Low_complexity_(Seg):seg,hmmpanther:PTHR23421:SF53,hmmpanther:PTHR23421,PIRSF_domain:PIRSF006336 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 134370316 134370316 G T 1 0 0 0 0 1 0 0 0 6307 1290 45 2 2 GLB1L2 11 134370316 Missense_Mutation SNP G C3N-01405_T 8791268 134370316 716306 279 22753 WNK1 0 . GRCh38 12 890462 890462 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.6214A>T p.Met2072Leu p.M2072L ENST00000340908 22/28 335 285 50 391 391 0 strelka-varscan-mutect WNK1,missense_variant,p.Met2233Leu,ENST00000530271,;WNK1,missense_variant,p.Met2080Leu,ENST00000537687,NM_001184985.1;WNK1,missense_variant,p.Met2072Leu,ENST00000340908,NM_213655.4;WNK1,missense_variant,p.Met1820Leu,ENST00000315939,NM_018979.3;WNK1,missense_variant,p.Met1573Leu,ENST00000535572,NM_014823.2; T ENST00000340908 Transcript missense_variant 6857/11208 6214/7905 2072/2634 M/L Atg/Ttg 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 tolerated_low_confidence(0.14) 22/28 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46 MODERATE 1 SNV 5 1 PASS rs1007706533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 890462 890462 A T 1 0 0 0 0 1 0 0 0 17933 217 8 4 4 WNK1 12 890462 Missense_Mutation SNP A C3N-01405_T 890462 132384847 280 22754 NTF3 0 . GRCh38 12 5494884 5494884 + Missense_Mutation SNP G G A rs777521890 C3N-01405_T C3N-01405_N G G c.709G>A p.Val237Ile p.V237I ENST00000423158 2/2 180 154 26 156 156 0 strelka-varscan-mutect NTF3,missense_variant,p.Val237Ile,ENST00000423158,NM_001102654.1;NTF3,missense_variant,p.Val224Ile,ENST00000331010,NM_002527.4;NTF3,intron_variant,,ENST00000535299,;NTF3,downstream_gene_variant,,ENST00000543548,; A ENST00000423158 Transcript missense_variant 921/1336 709/813 237/270 V/I Gtc/Atc rs777521890 1 1 NTF3 HGNC HGNC:8023 protein_coding YES CCDS44806.1 ENSP00000397297 P20783 UPI0000D4F126 NM_001102654.1 deleterious(0) 2/2 Gene3D:2.10.90.10,PD002052,Pfam_domain:PF00243,PIRSF_domain:PIRSF001789,Prints_domain:PR00268,PROSITE_profiles:PS50270,hmmpanther:PTHR11589,hmmpanther:PTHR11589:SF4,SMART_domains:SM00140,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS rs777521890 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 5494884 5494884 G A 1 0 0 0 0 1 0 0 0 10760 1145 40 1 1 NTF3 12 5494884 Missense_Mutation SNP G C3N-01405_T 4604422 5494884 127780425 281 22755 GDF3 0 . GRCh38 12 7689977 7689977 + Silent SNP G G C novel C3N-01405_T C3N-01405_N G G c.996C>G p.= p.T332T ENST00000329913 2/2 270 212 58 222 222 0 strelka-varscan-mutect GDF3,synonymous_variant,p.=,ENST00000329913,NM_020634.1; C ENST00000329913 Transcript synonymous_variant 1044/1239 996/1095 332/364 T acC/acG 1 -1 GDF3 HGNC HGNC:4218 protein_coding YES CCDS8581.1 ENSP00000331745 Q9NR23 UPI0000049E0E NM_020634.1 2/2 PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF38,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 7689977 7689977 G C 1 0 0 0 0 0 0 0 1 6187 1335 47 4 4 GDF3 12 7689977 Silent SNP G C3N-01405_T 2195093 7689977 125585332 282 22756 KLRB1 0 . GRCh38 12 9598542 9598542 + Missense_Mutation SNP G G T rs768631912 C3N-01405_T C3N-01405_N G G c.371C>A p.Thr124Asn p.T124N ENST00000229402 4/6 121 110 11 95 95 0 strelka-varscan-mutect KLRB1,missense_variant,p.Thr124Asn,ENST00000229402,NM_002258.2; T ENST00000229402 Transcript missense_variant 418/1448 371/678 124/225 T/N aCc/aAc rs768631912 1 -1 KLRB1 HGNC HGNC:6373 protein_coding YES CCDS8601.1 ENSP00000229402 Q12918 UPI000006E273 NM_002258.2 tolerated(0.14) 4/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22800:SF181,hmmpanther:PTHR22800,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs768631912 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 9598542 9598542 G T 1 0 0 0 0 1 0 0 0 8283 1261 44 2 2 KLRB1 12 9598542 Missense_Mutation SNP G C3N-01405_T 1908565 9598542 123676767 283 22757 TAS2R9 0 . GRCh38 12 10809623 10809623 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.453T>A p.Asp151Glu p.D151E ENST00000240691 1/1 173 157 16 187 187 0 strelka-varscan-mutect TAS2R9,missense_variant,p.Asp151Glu,ENST00000240691,NM_023917.2;TAS2R8,upstream_gene_variant,,ENST00000240615,NM_023918.1; T ENST00000240691 Transcript missense_variant 546/1032 453/939 151/312 D/E gaT/gaA 1 -1 TAS2R9 HGNC HGNC:14917 protein_coding YES CCDS8633.1 ENSP00000240691 Q9NYW1 UPI0000038B11 NM_023917.2 tolerated(0.18) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF29,Gene3D:1.20.1070.10,Pfam_domain:PF05296,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 10809623 10809623 A T 1 0 0 0 0 1 0 0 0 15987 446 16 4 4 TAS2R9 12 10809623 Missense_Mutation SNP A C3N-01405_T 1211081 10809623 122465686 284 22758 CAPZA3 0 . GRCh38 12 18738409 18738409 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.141A>T p.Gln47His p.Q47H ENST00000317658 1/1 219 194 25 194 194 0 strelka-varscan-mutect CAPZA3,missense_variant,p.Gln47His,ENST00000317658,NM_033328.2;PLCZ1,upstream_gene_variant,,ENST00000266505,NM_033123.3;PLCZ1,upstream_gene_variant,,ENST00000539875,;PLCZ1,upstream_gene_variant,,ENST00000543242,;PLCZ1,upstream_gene_variant,,ENST00000541966,;PLCZ1,upstream_gene_variant,,ENST00000539072,;RP11-361I14.2,downstream_gene_variant,,ENST00000536931,;PLCZ1,upstream_gene_variant,,ENST00000545129,;PLCZ1,upstream_gene_variant,,ENST00000541109,;PLCZ1,upstream_gene_variant,,ENST00000318197,;PLCZ1,upstream_gene_variant,,ENST00000539207,;PLCZ1,upstream_gene_variant,,ENST00000544849,;PLCZ1,upstream_gene_variant,,ENST00000535429,; T ENST00000317658 Transcript missense_variant 309/1087 141/900 47/299 Q/H caA/caT 1 1 CAPZA3 HGNC HGNC:24205 protein_coding YES CCDS8681.1 ENSP00000326238 Q96KX2 A0A140VKF6 UPI00001270FE NM_033328.2 deleterious(0.02) 1/1 hmmpanther:PTHR10653,hmmpanther:PTHR10653:SF6,Pfam_domain:PF01267,Superfamily_domains:SSF90096 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 18738409 18738409 A T 1 0 0 0 0 1 0 0 0 2337 69 3 4 4 CAPZA3 12 18738409 Missense_Mutation SNP A C3N-01405_T 7928786 18738409 114536900 285 22759 SLCO1C1 0 . GRCh38 12 20722047 20722047 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1019G>C p.Arg340Thr p.R340T ENST00000545604 9/16 78 73 5 78 78 0 strelka-varscan-mutect SLCO1C1,missense_variant,p.Arg340Thr,ENST00000266509,NM_017435.4;SLCO1C1,missense_variant,p.Arg222Thr,ENST00000545102,NM_001145944.1;SLCO1C1,missense_variant,p.Arg340Thr,ENST00000545604,NM_001145946.1;SLCO1C1,missense_variant,p.Arg291Thr,ENST00000540354,NM_001145945.1;SLCO1C1,splice_region_variant,,ENST00000539415,; C ENST00000545604 Transcript missense_variant,splice_region_variant 1249/2557 1019/2193 340/730 R/T aGa/aCa 1 1 SLCO1C1 HGNC HGNC:13819 protein_coding YES CCDS53757.1 ENSP00000444149 Q9NYB5 UPI00004C3E1B NM_001145946.1 tolerated(0.16) 9/16 hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF99,Pfam_domain:PF03137,TIGRFAM_domain:TIGR00805,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -11.12725 0.9999996 1 1 1 0 C 3 2 74 20722047 20722047 G C 1 0 0 0 0 1 0 0 0 15012 956 33 4 4 SLCO1C1 12 20722047 Missense_Mutation SNP G C3N-01405_T 1983638 20722047 112553262 286 22760 ADAMTS20 0 . GRCh38 12 43468603 43468603 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.1220A>T p.His407Leu p.H407L ENST00000389420 8/39 246 174 72 219 219 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.His407Leu,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.His407Leu,ENST00000395541,;ADAMTS20,missense_variant,p.His407Leu,ENST00000553158,; A ENST00000389420 Transcript missense_variant 1220/6076 1220/5733 407/1910 H/L cAc/cTc 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0) 8/39 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 43468603 43468603 T A 1 0 0 0 0 1 0 0 0 310 1710 59 4 4 ADAMTS20 12 43468603 Missense_Mutation SNP T C3N-01405_T 22746556 43468603 89806706 287 22761 TROAP 0 . GRCh38 12 49329977 49329977 + Missense_Mutation SNP G G C rs780443691 C3N-01405_T C3N-01405_N G G c.1285G>C p.Glu429Gln p.E429Q ENST00000257909 12/15 154 107 47 101 101 0 strelka-varscan-mutect TROAP,missense_variant,p.Glu429Gln,ENST00000551245,;TROAP,missense_variant,p.Glu429Gln,ENST00000257909,NM_005480.3;TROAP,missense_variant,p.Glu137Gln,ENST00000547923,;C1QL4,downstream_gene_variant,,ENST00000334221,NM_001008223.1;TROAP,downstream_gene_variant,,ENST00000547807,;TROAP,downstream_gene_variant,,ENST00000550346,;TROAP,downstream_gene_variant,,ENST00000551567,;TROAP,downstream_gene_variant,,ENST00000551192,;TROAP,downstream_gene_variant,,ENST00000546735,;TROAP,downstream_gene_variant,,ENST00000546776,;TROAP,downstream_gene_variant,,ENST00000549891,;TROAP,downstream_gene_variant,,ENST00000548817,; C ENST00000257909 Transcript missense_variant 1361/2527 1285/2337 429/778 E/Q Gag/Cag rs780443691,COSM324004 1 1 TROAP HGNC HGNC:12327 protein_coding YES CCDS8784.1 ENSP00000257909 Q12815 UPI000007108A NM_005480.3 tolerated(0.05) 12/15 hmmpanther:PTHR15289,hmmpanther:PTHR15289:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780443691 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 49329977 49329977 G C 1 0 0 0 0 1 0 0 0 17080 1175 41 4 4 TROAP 12 49329977 Missense_Mutation SNP G C3N-01405_T 5861374 49329977 83945332 288 22762 FAM186A 0 . GRCh38 12 50353204 50353204 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.3628C>G p.Gln1210Glu p.Q1210E ENST00000327337 4/8 309 291 18 230 230 0 varscan-mutect FAM186A,missense_variant,p.Gln1210Glu,ENST00000543111,;FAM186A,missense_variant,p.Gln1210Glu,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; C ENST00000327337 Transcript missense_variant 3628/7127 3628/7056 1210/2351 Q/E Cag/Gag 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 tolerated(0.34) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 50353204 50353204 G C 1 0 0 0 0 1 0 0 0 5361 1299 45 4 4 FAM186A 12 50353204 Missense_Mutation SNP G C3N-01405_T 1023227 50353204 82922105 289 22763 HOXC9 0 . GRCh38 12 54000281 54000281 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.93C>A p.= p.T31T ENST00000303450 1/2 465 325 140 323 323 0 strelka-varscan-mutect HOXC9,synonymous_variant,p.=,ENST00000303450,NM_006897.1;HOXC9,synonymous_variant,p.=,ENST00000508190,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,intron_variant,,ENST00000504315,;HOXC6,intron_variant,,ENST00000509328,;HOXC-AS1,upstream_gene_variant,,ENST00000505700,;HOXC-AS2,upstream_gene_variant,,ENST00000513533,;HOXC-AS1,upstream_gene_variant,,ENST00000512427,;HOXC9,intron_variant,,ENST00000504557,;HOXC-AS2,upstream_gene_variant,,ENST00000604081,; A ENST00000303450 Transcript synonymous_variant 163/1516 93/783 31/260 T acC/acA 1 1 HOXC9 HGNC HGNC:5130 protein_coding YES CCDS8869.1 ENSP00000302836 P31274 A0A024RAZ6 UPI000012CF79 NM_006897.1 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF145,Pfam_domain:PF04617,PIRSF_domain:PIRSF037109 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 54000281 54000281 C A 1 0 0 0 0 0 0 0 1 7211 639 23 1 1 HOXC9 12 54000281 Silent SNP C C3N-01405_T 3647077 54000281 79275028 290 22764 HOXC9 0 . GRCh38 12 54002470 54002470 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.579G>T p.Arg193Ser p.R193S ENST00000303450 2/2 168 140 28 133 133 0 strelka-varscan-mutect HOXC9,missense_variant,p.Arg193Ser,ENST00000303450,NM_006897.1;HOXC9,missense_variant,p.Arg193Ser,ENST00000508190,;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,intron_variant,,ENST00000504315,;HOXC6,intron_variant,,ENST00000509328,;HOXC-AS1,upstream_gene_variant,,ENST00000505700,;HOXC-AS1,upstream_gene_variant,,ENST00000512427,;HOXC9,non_coding_transcript_exon_variant,,ENST00000504557,; T ENST00000303450 Transcript missense_variant 649/1516 579/783 193/260 R/S agG/agT 1 1 HOXC9 HGNC HGNC:5130 protein_coding YES CCDS8869.1 ENSP00000302836 P31274 A0A024RAZ6 UPI000012CF79 NM_006897.1 deleterious(0) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF145,Gene3D:1.10.10.60,Pfam_domain:PF00046,PIRSF_domain:PIRSF037109,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 54002470 54002470 G T 1 0 0 0 0 1 0 0 0 7211 1165 41 2 2 HOXC9 12 54002470 Missense_Mutation SNP G C3N-01405_T 2189 54002470 79272839 291 22765 TESPA1 0 . GRCh38 12 54963003 54963003 + Silent SNP G G T rs753442863 C3N-01405_T C3N-01405_N G G c.895C>A p.= p.R299R ENST00000449076 9/11 193 174 19 143 143 0 strelka-varscan-mutect TESPA1,synonymous_variant,p.=,ENST00000524622,NM_001261844.1,NM_014796.2;TESPA1,synonymous_variant,p.=,ENST00000449076,NM_001136030.2;TESPA1,synonymous_variant,p.=,ENST00000532804,;TESPA1,synonymous_variant,p.=,ENST00000316577,NM_001098815.2;TESPA1,synonymous_variant,p.=,ENST00000531122,;TESPA1,intron_variant,,ENST00000532757,;TESPA1,downstream_gene_variant,,ENST00000524668,;TESPA1,downstream_gene_variant,,ENST00000526532,;TESPA1,upstream_gene_variant,,ENST00000528240,;TESPA1,downstream_gene_variant,,ENST00000533446,;TESPA1,downstream_gene_variant,,ENST00000524959,;TESPA1,3_prime_UTR_variant,,ENST00000524923,;TESPA1,downstream_gene_variant,,ENST00000525978,; T ENST00000449076 Transcript synonymous_variant 1028/2010 895/1566 299/521 R Cgg/Agg rs753442863,COSM5130233,COSM5130234 1 -1 TESPA1 HGNC HGNC:29109 protein_coding YES CCDS44913.1 ENSP00000400892 A2RU30 A0A024RB73 UPI00001FC438 NM_001136030.2 9/11 Low_complexity_(Seg):seg,hmmpanther:PTHR17469 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs753442863 . 0 206 0 4 0 0 0 0 -20 0.9998117 1 1 1 0 T 2 4 74 54963003 54963003 G T 1 0 0 0 0 0 0 0 1 16189 1115 39 1 1 TESPA1 12 54963003 Silent SNP G C3N-01405_T 960533 54963003 78312306 292 22766 DPY19L2 0 . GRCh38 12 63580693 63580693 + Silent SNP A A C rs755975116 C3N-01405_T C3N-01405_N A A c.1869T>G p.= p.L623L ENST00000324472 19/22 93 81 12 80 80 0 varscan-mutect DPY19L2,synonymous_variant,p.=,ENST00000324472,NM_173812.4;DPY19L2,non_coding_transcript_exon_variant,,ENST00000413230,;DPY19L2,intron_variant,,ENST00000439061,; C ENST00000324472 Transcript synonymous_variant 2053/4060 1869/2277 623/758 L ctT/ctG rs755975116 1 -1 DPY19L2 HGNC HGNC:19414 protein_coding YES CCDS31851.1 ENSP00000315988 Q6NUT2 UPI000006EC0C NM_173812.4 19/22 Pfam_domain:PF10034,hmmpanther:PTHR31488,hmmpanther:PTHR31488:SF6 LOW 1 SNV 1 1 PASS rs755975116 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 63580693 63580693 A C 1 0 0 0 0 0 0 0 1 4556 1 1 5 5 DPY19L2 12 63580693 Silent SNP A C3N-01405_T 8617690 63580693 69694616 293 22767 HELB 0 . GRCh38 12 66309955 66309955 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1027G>T p.Val343Leu p.V343L ENST00000247815 4/13 226 141 85 168 168 0 strelka-varscan-mutect HELB,missense_variant,p.Val343Leu,ENST00000247815,NM_033647.3;HELB,missense_variant,p.Val343Leu,ENST00000545134,;HELB,missense_variant,p.Val343Leu,ENST00000542394,;HELB,missense_variant,p.Val343Leu,ENST00000440906,; T ENST00000247815 Transcript missense_variant 1086/12866 1027/3264 343/1087 V/L Gtg/Ttg 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 deleterious(0.01) 4/13 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF135,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1450391472 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 66309955 66309955 G T 1 0 0 0 0 1 0 0 0 6927 1377 48 2 2 HELB 12 66309955 Missense_Mutation SNP G C3N-01405_T 2729262 66309955 66965354 294 22768 NAV3 0 . GRCh38 12 78177625 78177625 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.5303C>T p.Pro1768Leu p.P1768L ENST00000397909 28/40 194 136 58 179 179 0 strelka-varscan-mutect NAV3,missense_variant,p.Pro1768Leu,ENST00000397909,NM_001024383.1;NAV3,intron_variant,,ENST00000536525,NM_014903.5;NAV3,intron_variant,,ENST00000552895,;NAV3,intron_variant,,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000552300,;NAV3,upstream_gene_variant,,ENST00000548948,; T ENST00000397909 Transcript missense_variant 5476/9821 5303/7158 1768/2385 P/L cCc/cTc 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 tolerated(0.3) 28/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS rs1377149299 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 78177625 78177625 C T 1 0 0 0 0 1 0 0 0 10194 637 22 3 3 NAV3 12 78177625 Missense_Mutation SNP C C3N-01405_T 11867670 78177625 55097684 295 22769 PTPRQ 0 . GRCh38 12 80506155 80506155 + Nonsense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.2404G>T p.Gly802Ter p.G802* ENST00000614701 15/45 112 67 45 129 128 1 strelka-varscan-mutect PTPRQ,stop_gained,p.Gly802Ter,ENST00000614701,NM_001145026.1;PTPRQ,stop_gained,p.Gly844Ter,ENST00000616559,; T ENST00000614701 Transcript stop_gained 2582/8289 2404/6900 802/2299 G/* Gga/Tga 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 15/45 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF414,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 80506155 80506155 G T 1 0 0 0 0 0 1 0 0 12964 1349 47 2 2 PTPRQ 12 80506155 Nonsense_Mutation SNP G C3N-01405_T 2328530 80506155 52769154 296 22770 EPYC 0 . GRCh38 12 90971874 90971874 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.628C>A p.Pro210Thr p.P210T ENST00000261172 5/7 239 153 86 214 214 0 strelka-varscan-mutect EPYC,missense_variant,p.Pro210Thr,ENST00000261172,NM_004950.4;EPYC,missense_variant,p.Pro210Thr,ENST00000551767,;EPYC,downstream_gene_variant,,ENST00000550203,; T ENST00000261172 Transcript missense_variant 721/1539 628/969 210/322 P/T Cca/Aca 1 -1 EPYC HGNC HGNC:3053 protein_coding YES CCDS31870.1 ENSP00000261172 Q99645 A0A024RBC3 UPI000013D136 NM_004950.4 deleterious(0) 5/7 PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF123,hmmpanther:PTHR24373,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 90971874 90971874 G T 1 0 0 0 0 1 0 0 0 5049 1203 42 2 2 EPYC 12 90971874 Missense_Mutation SNP G C3N-01405_T 10465719 90971874 42303435 297 22771 SOCS2 0 . GRCh38 12 93574886 93574886 + Nonsense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.304G>T p.Gly102Ter p.G102* ENST00000622746 3/3 315 217 98 231 231 0 strelka-varscan-mutect SOCS2,stop_gained,p.Gly102Ter,ENST00000622746,NM_001270469.1,NM_001270470.1;SOCS2,stop_gained,p.Gly102Ter,ENST00000340600,NM_003877.4,NM_001270471.1;SOCS2,stop_gained,p.Gly102Ter,ENST00000549122,;SOCS2,stop_gained,p.Gly102Ter,ENST00000549206,NM_001270467.1;SOCS2,stop_gained,p.Gly102Ter,ENST00000551556,;SOCS2,stop_gained,p.Gly102Ter,ENST00000536696,NM_001270468.1;SOCS2,stop_gained,p.Gly102Ter,ENST00000549887,;SOCS2,stop_gained,p.Gly102Ter,ENST00000548091,;SOCS2,3_prime_UTR_variant,,ENST00000548537,;SOCS2,upstream_gene_variant,,ENST00000551883,;SOCS2,upstream_gene_variant,,ENST00000549510,;SOCS2,downstream_gene_variant,,ENST00000547229,;SOCS2-AS1,upstream_gene_variant,,ENST00000499137,;SOCS2-AS1,upstream_gene_variant,,ENST00000500986,;SOCS2-AS1,upstream_gene_variant,,ENST00000551626,; T ENST00000622746 Transcript stop_gained 1023/2881 304/597 102/198 G/* Gga/Tga COSM4045433 1 1 SOCS2 HGNC HGNC:19382 protein_coding YES CCDS9047.1 ENSP00000481249 O14508 A0A024RBD2 UPI0000135B63 NM_001270469.1,NM_001270470.1 3/3 Gene3D:3.30.505.10,Pfam_domain:PF00017,PROSITE_profiles:PS50001,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF75,SMART_domains:SM00252,Superfamily_domains:SSF55550 1 HIGH SNV 3 1 1 PASS rs1225826658 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 93574886 93574886 G T 1 0 0 0 0 0 1 0 0 15235 1117 39 1 1 SOCS2 12 93574886 Nonsense_Mutation SNP G C3N-01405_T 2603012 93574886 39700423 298 22772 UHRF1BP1L 0 . GRCh38 12 100058976 100058976 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.2301G>T p.Lys767Asn p.K767N ENST00000279907 14/21 362 270 92 273 273 0 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Lys767Asn,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Lys417Asn,ENST00000545232,; A ENST00000279907 Transcript missense_variant 2514/5168 2301/4395 767/1464 K/N aaG/aaT 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 deleterious(0.01) 14/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 100058976 100058976 C A 1 0 0 0 0 1 0 0 0 17493 796 28 2 2 UHRF1BP1L 12 100058976 Missense_Mutation SNP C C3N-01405_T 6484090 100058976 33216333 299 22773 PARPBP 0 . GRCh38 12 102178665 102178665 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.1079T>C p.Leu360Ser p.L360S ENST00000327680 8/11 127 117 10 116 116 0 strelka-varscan-mutect PARPBP,missense_variant,p.Leu360Ser,ENST00000327680,NM_001319994.1,NM_017915.3;PARPBP,missense_variant,p.Leu437Ser,ENST00000541394,;PARPBP,missense_variant,p.Leu279Ser,ENST00000392911,;PARPBP,intron_variant,,ENST00000417507,;PARPBP,intron_variant,,ENST00000412715,;PARPBP,intron_variant,,ENST00000543784,;PARPBP,intron_variant,,ENST00000535811,;PARPBP,3_prime_UTR_variant,,ENST00000457614,; C ENST00000327680 Transcript missense_variant 1124/3014 1079/1740 360/579 L/S tTg/tCg 1 1 PARPBP HGNC HGNC:26074 protein_coding YES CCDS9090.2 ENSP00000332915 Q9NWS1 UPI000004A06B NM_001319994.1,NM_017915.3 deleterious(0.01) 8/11 hmmpanther:PTHR32121 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 102178665 102178665 T C 1 0 0 0 0 1 0 0 0 11547 1821 63 5 5 PARPBP 12 102178665 Missense_Mutation SNP T C3N-01405_T 2119689 102178665 31096644 300 22774 PWP1 0 . GRCh38 12 107688701 107688701 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.218G>A p.Arg73Lys p.R73K ENST00000412830 3/15 292 232 60 242 242 0 strelka-varscan-mutect PWP1,missense_variant,p.Arg73Lys,ENST00000412830,NM_001317962.1,NM_007062.1;PWP1,missense_variant,p.Arg11Lys,ENST00000541166,;PWP1,missense_variant,p.Arg11Lys,ENST00000547995,;PWP1,missense_variant,p.Arg73Lys,ENST00000552760,;PWP1,upstream_gene_variant,,ENST00000547120,; A ENST00000412830 Transcript missense_variant 386/2621 218/1506 73/501 R/K aGa/aAa 1 1 PWP1 HGNC HGNC:17015 protein_coding YES CCDS9114.1 ENSP00000387365 Q13610 A0A024RBH5 UPI0000132B9C NM_001317962.1,NM_007062.1 tolerated(0.81) 3/15 hmmpanther:PTHR14091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 107688701 107688701 G A 1 0 0 0 0 1 0 0 0 12997 942 33 3 3 PWP1 12 107688701 Missense_Mutation SNP G C3N-01405_T 5510036 107688701 25586608 301 22775 NOS1 0 . GRCh38 12 117259077 117259077 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.2421C>A p.= p.V807V ENST00000618760 15/30 173 159 14 111 109 2 strelka-varscan NOS1,synonymous_variant,p.=,ENST00000618760,NM_001204218.1;NOS1,synonymous_variant,p.=,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,synonymous_variant,p.=,ENST00000338101,;NOS1,synonymous_variant,p.=,ENST00000344089,; T ENST00000618760 Transcript synonymous_variant 3132/12283 2421/4407 807/1468 V gtC/gtA 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 15/30 Low_complexity_(Seg):seg,PROSITE_profiles:PS50902,hmmpanther:PTHR19384:SF63,hmmpanther:PTHR19384,Gene3D:3.40.50.360,Pfam_domain:PF00258,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF52218 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 117259077 117259077 G T 1 0 0 0 0 0 0 0 1 10586 1161 41 2 2 NOS1 12 117259077 Silent SNP G C3N-01405_T 9570376 117259077 16016232 302 22776 ACADS 0 . GRCh38 12 120738532 120738532 + Splice_Site SNP G G T C3N-01405_T C3N-01405_N G G c.796-1G>T p.X266_splice ENST00000242592 360 253 107 241 241 0 strelka-varscan-mutect ACADS,splice_acceptor_variant,,ENST00000242592,NM_000017.3;ACADS,splice_acceptor_variant,,ENST00000411593,NM_001302554.1;RP11-173P15.7,downstream_gene_variant,,ENST00000542620,;ACADS,downstream_gene_variant,,ENST00000539690,; T ENST00000242592 Transcript splice_acceptor_variant -/1950 796/1239 266/412 COSM3968028 1 1 ACADS HGNC HGNC:90 protein_coding YES CCDS9207.1 ENSP00000242592 P16219 E5KSD5 UPI000004A863 NM_000017.3 6/9 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 74 120738532 120738532 G T 1 0 0 0 0 0 0 1 0 157 985 34 2 2 ACADS 12 120738532 Splice_Site SNP G C3N-01405_T 3479455 120738532 12536777 303 22777 IL31 0 . GRCh38 12 122174165 122174165 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.8C>T p.Ser3Phe p.S3F ENST00000377035 1/3 295 274 21 203 203 0 strelka-varscan-mutect IL31,missense_variant,p.Ser3Phe,ENST00000377035,NM_001014336.1;LRRC43,intron_variant,,ENST00000537729,; A ENST00000377035 Transcript missense_variant 35/904 8/495 3/164 S/F tCt/tTt 1 -1 IL31 HGNC HGNC:19372 protein_coding YES CCDS31919.1 ENSP00000366234 Q6EBC2 UPI00003BF6FE NM_001014336.1 deleterious(0.01) 1/3 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR38652:SF1,hmmpanther:PTHR38652 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 122174165 122174165 G A 1 0 0 0 0 1 0 0 0 7589 942 33 3 3 IL31 12 122174165 Missense_Mutation SNP G C3N-01405_T 1435633 122174165 11101144 304 22778 DNAH10 0 . GRCh38 12 123864718 123864718 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.6678C>A p.= p.A2226A ENST00000638045 39/78 183 123 60 126 126 0 strelka-varscan-mutect DNAH10,synonymous_variant,p.=,ENST00000409039,;DNAH10,synonymous_variant,p.=,ENST00000638045,NM_207437.3;DNAH10,3_prime_UTR_variant,,ENST00000497783,; A ENST00000638045 Transcript synonymous_variant 6703/13678 6678/13416 2226/4471 A gcC/gcA 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 39/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF07728,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 123864718 123864718 C A 1 0 0 0 0 0 0 0 1 4411 610 22 2 2 DNAH10 12 123864718 Silent SNP C C3N-01405_T 1690553 123864718 9410591 305 22779 ULK1 0 . GRCh38 12 131916573 131916573 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.2054C>G p.Pro685Arg p.P685R ENST00000321867 20/28 92 83 9 67 67 0 strelka-varscan-mutect ULK1,missense_variant,p.Pro685Arg,ENST00000321867,NM_003565.2;ULK1,non_coding_transcript_exon_variant,,ENST00000541761,;ULK1,upstream_gene_variant,,ENST00000540568,;ULK1,upstream_gene_variant,,ENST00000544718,;ULK1,upstream_gene_variant,,ENST00000540647,; G ENST00000321867 Transcript missense_variant 2405/5310 2054/3153 685/1050 P/R cCc/cGc 1 1 ULK1 HGNC HGNC:12558 protein_coding YES CCDS9274.1 ENSP00000324560 O75385 UPI00001FB0D9 NM_003565.2 tolerated(0.54) 20/28 PIRSF_domain:PIRSF000580,hmmpanther:PTHR24348,hmmpanther:PTHR24348:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.08962 1 1 1 1 0 G 3 3 74 131916573 131916573 C G 1 0 0 0 0 1 0 0 0 17499 623 22 4 4 ULK1 12 131916573 Missense_Mutation SNP C C3N-01405_T 8051855 131916573 1358736 306 22780 SACS 0 . GRCh38 13 23333597 23333597 + Missense_Mutation SNP C C G C3N-01405_T C3N-01405_N C C c.10279G>C p.Gly3427Arg p.G3427R ENST00000382292 9/9 337 263 74 274 274 0 strelka-varscan-mutect SACS,missense_variant,p.Gly3427Arg,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Gly2677Arg,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; G ENST00000382292 Transcript missense_variant 10553/15324 10279/13740 3427/4579 G/R Gga/Cga COSM1365877,COSM1365878 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 tolerated(0.33) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 23333597 23333597 C G 1 0 0 0 0 1 0 0 0 14063 603 21 4 4 SACS 13 23333597 Missense_Mutation SNP C C3N-01405_T 23333597 91030731 307 22781 FLT1 0 . GRCh38 13 28322942 28322942 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.2801C>T p.Ala934Val p.A934V ENST00000282397 21/30 302 234 68 251 251 0 strelka-varscan-mutect FLT1,missense_variant,p.Ala934Val,ENST00000282397,NM_002019.4;FLT1,missense_variant,p.Ala29Val,ENST00000615611,;FLT1,5_prime_UTR_variant,,ENST00000540678,;FLT1,upstream_gene_variant,,ENST00000543394,; A ENST00000282397 Transcript missense_variant 3053/7092 2801/4017 934/1338 A/V gCa/gTa 1 -1 FLT1 HGNC HGNC:3763 protein_coding YES CCDS9330.1 ENSP00000282397 P17948 L7RSL3 UPI000013DCDD NM_002019.4 tolerated(0.12) 21/30 Pfam_domain:PF07714,PROSITE_profiles:PS50011,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 28322942 28322942 G A 1 0 0 0 0 1 0 0 0 5797 1333 46 3 3 FLT1 13 28322942 Missense_Mutation SNP G C3N-01405_T 4989345 28322942 86041386 308 22782 BRCA2 0 . GRCh38 13 32337625 32337625 + Missense_Mutation SNP G G T rs80358574 C3N-01405_T C3N-01405_N G G c.3270G>T p.Met1090Ile p.M1090I ENST00000380152 11/27 44 34 10 47 47 0 strelka-varscan-mutect BRCA2,missense_variant,p.Met1090Ile,ENST00000380152,;BRCA2,missense_variant,p.Met1090Ile,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,;BRCA2,downstream_gene_variant,,ENST00000530893,; T ENST00000380152 Transcript missense_variant 3503/11986 3270/10257 1090/3418 M/I atG/atT rs80358574 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC tolerated(0.41) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 uncertain_significance,not_provided MODERATE 1 SNV 5 1 1 PASS rs80358574 . 0 204 6 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 74 32337625 32337625 G T 1 0 0 0 0 1 0 0 0 1669 1377 48 2 2 BRCA2 13 32337625 Missense_Mutation SNP G C3N-01405_T 4014683 32337625 82026703 309 22783 FREM2 0 . GRCh38 13 38690161 38690161 + Missense_Mutation SNP A A C novel C3N-01405_T C3N-01405_N A A c.2817A>C p.Glu939Asp p.E939D ENST00000280481 1/24 289 207 82 237 237 0 strelka-varscan-mutect FREM2,missense_variant,p.Glu939Asp,ENST00000280481,NM_207361.5; C ENST00000280481 Transcript missense_variant 3033/16070 2817/9510 939/3169 E/D gaA/gaC 1 1 FREM2 HGNC HGNC:25396 protein_coding YES CCDS31960.1 ENSP00000280481 Q5SZK8 UPI000443805C NM_207361.5 deleterious(0.03) 1/24 hmmpanther:PTHR11878:SF32,hmmpanther:PTHR11878 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 38690161 38690161 A C 1 0 0 0 0 1 0 0 0 5912 69 3 5 5 FREM2 13 38690161 Missense_Mutation SNP A C3N-01405_T 6352536 38690161 75674167 310 22784 INTS6 0 . GRCh38 13 51452027 51452027 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.140G>T p.Gly47Val p.G47V ENST00000311234 2/18 241 192 49 245 245 0 strelka-varscan-mutect INTS6,missense_variant,p.Gly47Val,ENST00000442263,NM_001039938.1;INTS6,missense_variant,p.Gly34Val,ENST00000398119,NM_001039937.1;INTS6,missense_variant,p.Gly47Val,ENST00000311234,NM_012141.2;INTS6,missense_variant,p.Gly34Val,ENST00000483288,;INTS6,missense_variant,p.Gly34Val,ENST00000485178,;INTS6,upstream_gene_variant,,ENST00000491189,;INTS6,upstream_gene_variant,,ENST00000488009,;INTS6-AS1,upstream_gene_variant,,ENST00000601034,;INTS6-AS1,upstream_gene_variant,,ENST00000594604,;INTS6-AS1,upstream_gene_variant,,ENST00000598905,;INTS6-AS1,upstream_gene_variant,,ENST00000594959,;INTS6-AS1,upstream_gene_variant,,ENST00000601572,;INTS6-AS1,upstream_gene_variant,,ENST00000596050,;INTS6-AS1,upstream_gene_variant,,ENST00000598864,;INTS6-AS1,upstream_gene_variant,,ENST00000599315,;INTS6-AS1,upstream_gene_variant,,ENST00000595435,;INTS6-AS1,upstream_gene_variant,,ENST00000597745,;INTS6-AS1,upstream_gene_variant,,ENST00000602089,;INTS6-AS1,upstream_gene_variant,,ENST00000593672,;INTS6-AS1,upstream_gene_variant,,ENST00000594358,;INTS6-AS1,upstream_gene_variant,,ENST00000596180,;INTS6-AS1,upstream_gene_variant,,ENST00000593429,;INTS6-AS1,upstream_gene_variant,,ENST00000593709,;INTS6-AS1,upstream_gene_variant,,ENST00000601318,;INTS6-AS1,upstream_gene_variant,,ENST00000593928,;INTS6-AS1,upstream_gene_variant,,ENST00000600477,;INTS6-AS1,upstream_gene_variant,,ENST00000596303,;INTS6-AS1,upstream_gene_variant,,ENST00000626895,;INTS6-AS1,upstream_gene_variant,,ENST00000594488,;INTS6-AS1,upstream_gene_variant,,ENST00000629988,;INTS6-AS1,upstream_gene_variant,,ENST00000434512,;INTS6-AS1,upstream_gene_variant,,ENST00000595997,;INTS6-AS1,upstream_gene_variant,,ENST00000610618,;INTS6-AS1,upstream_gene_variant,,ENST00000595424,;INTS6,non_coding_transcript_exon_variant,,ENST00000491723,;INTS6,non_coding_transcript_exon_variant,,ENST00000461515,;INTS6,non_coding_transcript_exon_variant,,ENST00000486195,;RPS4XP16,upstream_gene_variant,,ENST00000595905,;RPS4XP16,upstream_gene_variant,,ENST00000596904,;INTS6,upstream_gene_variant,,ENST00000491997,;INTS6,missense_variant,p.Gly47Val,ENST00000469430,; A ENST00000311234 Transcript missense_variant 613/3662 140/2664 47/887 G/V gGa/gTa 1 -1 INTS6 HGNC HGNC:14879 protein_coding YES CCDS9428.1 ENSP00000310260 Q9UL03 A0A024RDU0 UPI0000030C84 NM_012141.2 deleterious(0.02) 2/18 PROSITE_profiles:PS50234,hmmpanther:PTHR12957:SF23,hmmpanther:PTHR12957,Pfam_domain:PF13519,Gene3D:3.40.50.410,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 51452027 51452027 C A 1 0 0 0 0 1 0 0 0 7684 855 30 2 2 INTS6 13 51452027 Missense_Mutation SNP C C3N-01405_T 12761866 51452027 62912301 311 22785 ATP7B 0 . GRCh38 13 51937493 51937493 + Missense_Mutation SNP C C A rs199821556 C3N-01405_T C3N-01405_N C C c.3886G>T p.Asp1296Tyr p.D1296Y ENST00000242839 18/21 491 367 124 384 384 0 strelka-varscan-mutect ATP7B,missense_variant,p.Asp1296Tyr,ENST00000242839,NM_000053.3;ATP7B,missense_variant,p.Asp1218Tyr,ENST00000448424,;ATP7B,missense_variant,p.Asp1185Tyr,ENST00000400366,NM_001243182.1;ATP7B,missense_variant,p.Asp1089Tyr,ENST00000344297,NM_001005918.2;ATP7B,missense_variant,p.Asp1248Tyr,ENST00000634844,;ATP7B,missense_variant,p.Asp1231Tyr,ENST00000418097,;ATP7B,missense_variant,p.Asp866Tyr,ENST00000400370,;ATP7B,upstream_gene_variant,,ENST00000634519,;ATP7B,3_prime_UTR_variant,,ENST00000634308,;ATP7B,3_prime_UTR_variant,,ENST00000634296,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634810,;ATP7B,non_coding_transcript_exon_variant,,ENST00000634620,; A ENST00000242839 Transcript missense_variant 4043/6638 3886/4398 1296/1465 D/Y Gac/Tac rs199821556,CM023025 1 -1 ATP7B HGNC HGNC:870 protein_coding YES CCDS41892.1 ENSP00000242839 P35670 A0A024RDX3 UPI00001FCE15 NM_000053.3 deleterious(0) 18/21 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,TIGRFAM_domain:TIGR01494,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01525,Superfamily_domains:SSF56784,Prints_domain:PR00119 uncertain_significance MODERATE 1 SNV 1 1,1 1 PASS rs199821556 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 51937493 51937493 C A 1 0 0 0 0 1 0 0 0 1344 884 31 1 1 ATP7B 13 51937493 Missense_Mutation SNP C C3N-01405_T 485466 51937493 62426835 312 22786 CCDC168 0 . GRCh38 13 102733240 102733240 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.17457G>T p.Trp5819Cys p.W5819C ENST00000322527 4/4 167 147 20 146 146 0 strelka-varscan-mutect CCDC168,missense_variant,p.Trp5819Cys,ENST00000322527,NM_001146197.1; A ENST00000322527 Transcript missense_variant 17595/21466 17457/21246 5819/7081 W/C tgG/tgT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.18) 4/4 hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 102733240 102733240 C A 1 0 0 0 0 1 0 0 0 2484 856 30 2 2 CCDC168 13 102733240 Missense_Mutation SNP C C3N-01405_T 50795747 102733240 11631088 313 22787 CCDC168 0 . GRCh38 13 102741635 102741635 + Missense_Mutation SNP A A C novel C3N-01405_T C3N-01405_N A A c.9062T>G p.Leu3021Trp p.L3021W ENST00000322527 4/4 212 166 46 239 239 0 strelka-varscan-mutect CCDC168,missense_variant,p.Leu3021Trp,ENST00000322527,NM_001146197.1;LINC00283,upstream_gene_variant,,ENST00000430111,; C ENST00000322527 Transcript missense_variant 9200/21466 9062/21246 3021/7081 L/W tTg/tGg 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.03) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 102741635 102741635 A C 1 0 0 0 0 1 0 0 0 2484 131 5 5 5 CCDC168 13 102741635 Missense_Mutation SNP A C3N-01405_T 8395 102741635 11622693 314 22788 COL4A2 0 . GRCh38 13 110450380 110450380 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1265G>T p.Gly422Val p.G422V ENST00000360467 20/48 257 220 37 187 187 0 strelka-varscan-mutect COL4A2,missense_variant,p.Gly422Val,ENST00000360467,NM_001846.2; T ENST00000360467 Transcript missense_variant 1571/6281 1265/5139 422/1712 G/V gGg/gTg 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 tolerated(0.09) 20/48 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1338436328 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 110450380 110450380 G T 1 0 0 0 0 1 0 0 0 3479 1232 43 2 2 COL4A2 13 110450380 Missense_Mutation SNP G C3N-01405_T 7708745 110450380 3913948 315 22789 OR11H12 0 . GRCh38 14 18602032 18602032 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.916A>T p.Ser306Cys p.S306C ENST00000550708 1/1 127 84 43 81 81 0 strelka-varscan-mutect OR11H12,missense_variant,p.Ser306Cys,ENST00000550708,NM_001013354.1; T ENST00000550708 Transcript missense_variant 988/1085 916/981 306/326 S/C Agc/Tgc 1 1 OR11H12 HGNC HGNC:30738 protein_coding YES CCDS32017.1 ENSP00000449002 B2RN74 UPI00004EAFF2 NM_001013354.1 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF201,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 23 187 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 18602032 18602032 A T 1 0 0 0 0 1 0 0 0 11003 420 15 4 4 OR11H12 14 18602032 Missense_Mutation SNP A C3N-01405_T 18602032 88441686 316 22790 TTC6 0 . GRCh38 14 37622280 37622280 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.77G>T p.Arg26Leu p.R26L ENST00000556845 3/3 215 198 17 167 167 0 strelka-varscan-mutect TTC6,missense_variant,p.Arg26Leu,ENST00000556845,;TTC6,synonymous_variant,p.=,ENST00000553443,;TTC6,synonymous_variant,p.=,ENST00000533625,; T ENST00000556845 Transcript missense_variant 473/511 77/115 26/38 R/L cGt/cTt 1 1 TTC6 HGNC HGNC:19739 protein_coding ENSP00000450572 G3V2C3 UPI00021CF1B3 3/3 Low_complexity_(Seg):seg MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 37622280 37622280 G T 1 0 0 0 0 1 0 0 0 17221 1132 40 1 1 TTC6 14 37622280 Missense_Mutation SNP G C3N-01405_T 19020248 37622280 69421438 317 22791 SOCS4 0 . GRCh38 14 55043254 55043254 + Silent SNP T T C novel C3N-01405_T C3N-01405_N T T c.213T>C p.= p.C71C ENST00000395472 2/2 233 192 41 175 175 0 strelka-varscan-mutect SOCS4,synonymous_variant,p.=,ENST00000395472,NM_080867.2;SOCS4,synonymous_variant,p.=,ENST00000339298,;SOCS4,synonymous_variant,p.=,ENST00000555846,NM_199421.1; C ENST00000395472 Transcript synonymous_variant 545/6779 213/1323 71/440 C tgT/tgC 1 1 SOCS4 HGNC HGNC:19392 protein_coding YES CCDS9722.1 ENSP00000378855 Q8WXH5 Q5H9R6 UPI000000CC33 NM_080867.2 2/2 Pfam_domain:PF12610 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 55043254 55043254 T C 1 0 0 0 0 0 0 0 1 15237 1731 60 5 5 SOCS4 14 55043254 Silent SNP T C3N-01405_T 17420974 55043254 52000464 318 22792 RTN1 0 . GRCh38 14 59607377 59607377 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.1881G>T p.= p.L627L ENST00000267484 4/9 447 347 100 347 346 1 strelka-varscan-mutect RTN1,synonymous_variant,p.=,ENST00000267484,NM_021136.2;RTN1,synonymous_variant,p.=,ENST00000611068,;RTN1,synonymous_variant,p.=,ENST00000342503,NM_206852.2;RTN1,synonymous_variant,p.=,ENST00000395090,;RTN1,non_coding_transcript_exon_variant,,ENST00000557422,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,;RTN1,non_coding_transcript_exon_variant,,ENST00000474911,;RTN1,upstream_gene_variant,,ENST00000481205,;RTN1,upstream_gene_variant,,ENST00000490111,; A ENST00000267484 Transcript synonymous_variant 2217/3435 1881/2331 627/776 L ctG/ctT 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 4/9 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50845,hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994,Pfam_domain:PF02453 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 59607377 59607377 C A 1 0 0 0 0 0 0 0 1 13985 581 21 2 2 RTN1 14 59607377 Silent SNP C C3N-01405_T 4564123 59607377 47436341 319 22793 ZFYVE26 0 . GRCh38 14 67762241 67762241 + Missense_Mutation SNP C C G C3N-01405_T C3N-01405_N C C c.6331G>C p.Glu2111Gln p.E2111Q ENST00000347230 34/42 411 355 56 282 282 0 strelka-varscan-mutect ZFYVE26,missense_variant,p.Glu2111Gln,ENST00000347230,NM_015346.3;ZFYVE26,missense_variant,p.Glu2111Gln,ENST00000555452,;ZFYVE26,upstream_gene_variant,,ENST00000557306,;ZFYVE26,3_prime_UTR_variant,,ENST00000554557,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000554523,;ZFYVE26,non_coding_transcript_exon_variant,,ENST00000394455,; G ENST00000347230 Transcript missense_variant 6470/9675 6331/7620 2111/2539 E/Q Gag/Cag COSM698889 1 -1 ZFYVE26 HGNC HGNC:20761 protein_coding YES CCDS9788.1 ENSP00000251119 Q68DK2 UPI00001FD735 NM_015346.3 tolerated(1) 34/42 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 67762241 67762241 C G 1 0 0 0 0 1 0 0 0 18245 835 29 4 4 ZFYVE26 14 67762241 Missense_Mutation SNP C C3N-01405_T 8154864 67762241 39281477 320 22794 ZNF410 0 . GRCh38 14 73898141 73898141 + Silent SNP C C G novel C3N-01405_T C3N-01405_N C C c.510C>G p.= p.L170L ENST00000442160 6/14 243 179 64 209 209 0 strelka-varscan-mutect ZNF410,synonymous_variant,p.=,ENST00000555044,NM_021188.2,NM_001242928.1;ZNF410,synonymous_variant,p.=,ENST00000324593,NM_001242926.1;ZNF410,synonymous_variant,p.=,ENST00000334521,;ZNF410,synonymous_variant,p.=,ENST00000442160,NM_001242924.1;ZNF410,synonymous_variant,p.=,ENST00000540593,NM_001242927.1;ZNF410,synonymous_variant,p.=,ENST00000615736,;ZNF410,synonymous_variant,p.=,ENST00000556797,;ZNF410,synonymous_variant,p.=,ENST00000557363,;ZNF410,downstream_gene_variant,,ENST00000556160,;ZNF410,downstream_gene_variant,,ENST00000556659,;ZNF410,downstream_gene_variant,,ENST00000557495,;ZNF410,downstream_gene_variant,,ENST00000555730,;ZNF410,downstream_gene_variant,,ENST00000554797,;RP5-1021I20.5,intron_variant,,ENST00000554009,;ZNF410,non_coding_transcript_exon_variant,,ENST00000412490,;ZNF410,non_coding_transcript_exon_variant,,ENST00000541357,;ZNF410,non_coding_transcript_exon_variant,,ENST00000555602,;ZNF410,synonymous_variant,p.=,ENST00000398139,;RP5-1021I20.4,3_prime_UTR_variant,,ENST00000556551,;ZNF410,3_prime_UTR_variant,,ENST00000556396,;ZNF410,3_prime_UTR_variant,,ENST00000554582,; G ENST00000442160 Transcript synonymous_variant 704/2076 510/1551 170/516 L ctC/ctG 1 1 ZNF410 HGNC HGNC:20144 protein_coding YES CCDS55929.1 ENSP00000407130 Q86VK4 UPI00017A6BE1 NM_001242924.1 6/14 LOW 1 SNV 1 1 PASS rs1490364649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 73898141 73898141 C G 1 0 0 0 0 0 0 0 1 18462 900 32 4 4 ZNF410 14 73898141 Silent SNP C C3N-01405_T 6135900 73898141 33145577 321 22795 SERPINA9 0 . GRCh38 14 94469631 94469631 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.264C>G p.Phe88Leu p.F88L ENST00000337425 2/5 168 117 51 135 135 0 strelka-varscan-mutect SERPINA9,missense_variant,p.Phe88Leu,ENST00000337425,NM_001284275.1,NM_175739.3;SERPINA9,missense_variant,p.Phe88Leu,ENST00000298845,NM_001042518.1;SERPINA9,missense_variant,p.Phe70Leu,ENST00000380365,;SERPINA9,missense_variant,p.Phe52Leu,ENST00000546329,;SERPINA9,5_prime_UTR_variant,,ENST00000448305,;SERPINA9,intron_variant,,ENST00000424550,NM_001284276.1;RP11-349I1.2,downstream_gene_variant,,ENST00000536735,;SERPINA9,downstream_gene_variant,,ENST00000539349,;SERPINA9,missense_variant,p.Leu116Val,ENST00000538527,; C ENST00000337425 Transcript missense_variant 339/1755 264/1308 88/435 F/L ttC/ttG 1 -1 SERPINA9 HGNC HGNC:15995 protein_coding YES CCDS41982.1 ENSP00000337133 Q86WD7 UPI000024706E NM_001284275.1,NM_175739.3 deleterious(0.03) 2/5 hmmpanther:PTHR11461:SF40,hmmpanther:PTHR11461,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 94469631 94469631 G C 1 0 0 0 0 1 0 0 0 14371 933 33 4 4 SERPINA9 14 94469631 Missense_Mutation SNP G C3N-01405_T 20571490 94469631 12574087 322 22796 BCL11B 0 . GRCh38 14 99175566 99175566 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.1270G>A p.Ala424Thr p.A424T ENST00000357195 4/4 97 86 11 98 98 0 strelka-varscan-mutect BCL11B,missense_variant,p.Ala353Thr,ENST00000345514,NM_001282238.1,NM_022898.2;BCL11B,missense_variant,p.Ala424Thr,ENST00000357195,NM_001282237.1,NM_138576.3;BCL11B,missense_variant,p.Ala230Thr,ENST00000443726,; T ENST00000357195 Transcript missense_variant 1280/7559 1270/2685 424/894 A/T Gcc/Acc 1 -1 BCL11B HGNC HGNC:13222 protein_coding YES CCDS9950.1 ENSP00000349723 Q9C0K0 L8B7P7 UPI000006E083 NM_001282237.1,NM_138576.3 tolerated(0.6) 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF45,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1163567345 . 0 205 4 0 0 0 0 0 -19.99938 1 1 1 1 0 T 3 4 74 99175566 99175566 C T 1 0 0 0 0 1 0 0 0 1511 797 28 3 3 BCL11B 14 99175566 Missense_Mutation SNP C C3N-01405_T 4705935 99175566 7868152 323 22797 BCL11B 0 . GRCh38 14 99176040 99176040 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.796C>A p.Pro266Thr p.P266T ENST00000357195 4/4 110 94 16 68 67 1 strelka-varscan-mutect BCL11B,missense_variant,p.Pro195Thr,ENST00000345514,NM_001282238.1,NM_022898.2;BCL11B,missense_variant,p.Pro266Thr,ENST00000357195,NM_001282237.1,NM_138576.3;BCL11B,missense_variant,p.Pro72Thr,ENST00000443726,; T ENST00000357195 Transcript missense_variant 806/7559 796/2685 266/894 P/T Ccg/Acg 1 -1 BCL11B HGNC HGNC:13222 protein_coding YES CCDS9950.1 ENSP00000349723 Q9C0K0 L8B7P7 UPI000006E083 NM_001282237.1,NM_138576.3 deleterious(0.02) 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF45 MODERATE 1 SNV 1 1 PASS rs1290896821 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 99176040 99176040 G T 1 0 0 0 0 1 0 0 0 1511 1232 43 2 2 BCL11B 14 99176040 Missense_Mutation SNP G C3N-01405_T 474 99176040 7867678 324 22798 TDRD9 0 . GRCh38 14 103998677 103998677 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1432C>A p.Gln478Lys p.Q478K ENST00000409874 13/36 171 153 18 196 196 0 strelka-varscan-mutect TDRD9,missense_variant,p.Gln478Lys,ENST00000409874,NM_153046.2;TDRD9,missense_variant,p.Gln193Lys,ENST00000339063,;TDRD9,missense_variant,p.Gln205Lys,ENST00000557332,; A ENST00000409874 Transcript missense_variant 1480/4782 1432/4149 478/1382 Q/K Cag/Aag 1 1 TDRD9 HGNC HGNC:20122 protein_coding YES CCDS9987.2 ENSP00000387303 Q8NDG6 UPI0001642306 NM_153046.2 deleterious(0.02) 13/36 PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF113,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 103998677 103998677 C A 1 0 0 0 0 1 0 0 0 16146 827 29 2 2 TDRD9 14 103998677 Missense_Mutation SNP C C3N-01405_T 4822637 103998677 3045041 325 22799 TMEM121 0 . GRCh38 14 105529140 105529140 + Silent SNP C C G C3N-01405_T C3N-01405_N C C c.306C>G p.= p.R102R ENST00000392519 2/2 237 181 56 185 185 0 strelka-varscan-mutect TMEM121,synonymous_variant,p.=,ENST00000392519,NM_025268.2;TMEM121,synonymous_variant,p.=,ENST00000431372,;TMEM121,downstream_gene_variant,,ENST00000552019,; G ENST00000392519 Transcript synonymous_variant 470/1532 306/960 102/319 R cgC/cgG COSM1267997 1 1 TMEM121 HGNC HGNC:20511 protein_coding YES CCDS10006.1 ENSP00000376304 Q9BTD3 UPI0000073639 NM_025268.2 2/2 Pfam_domain:PF14997,hmmpanther:PTHR31046,hmmpanther:PTHR31046:SF0 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 105529140 105529140 C G 1 0 0 0 0 0 0 0 1 16479 755 27 4 4 TMEM121 14 105529140 Silent SNP C C3N-01405_T 1530463 105529140 1514578 326 22800 NPAP1 0 . GRCh38 15 24677795 24677795 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1928C>A p.Ala643Asp p.A643D ENST00000329468 1/1 278 215 63 204 203 1 strelka-varscan-mutect NPAP1,missense_variant,p.Ala643Asp,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript missense_variant 1928/7526 1928/3471 643/1156 A/D gCc/gAc 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.49) 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 MODERATE 1 SNV 1 PASS rs1190298963 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 24677795 24677795 C A 1 0 0 0 0 1 0 0 0 10609 739 26 2 2 NPAP1 15 24677795 Missense_Mutation SNP C C3N-01405_T 24677795 77313394 327 22801 RYR3 0 . GRCh38 15 33586086 33586086 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.1758C>A p.= p.S586S ENST00000634891 16/104 160 121 39 152 152 0 strelka-varscan-mutect RYR3,synonymous_variant,p.=,ENST00000634891,NM_001036.4;RYR3,synonymous_variant,p.=,ENST00000622037,;RYR3,synonymous_variant,p.=,ENST00000415757,NM_001243996.2;RYR3,synonymous_variant,p.=,ENST00000389232,;RYR3,synonymous_variant,p.=,ENST00000634418,; A ENST00000634891 Transcript synonymous_variant 1859/15591 1758/14613 586/4870 S tcC/tcA 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 16/104 Pfam_domain:PF01365,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs1453797967 . 0 208 0 0 2 0 0 0 -20 0.9987174 1 1 1 0 A 2 1 74 33586086 33586086 C A 1 0 0 0 0 0 0 0 1 14030 610 22 2 2 RYR3 15 33586086 Silent SNP C C3N-01405_T 8908291 33586086 68405103 328 22802 MAPKBP1 0 . GRCh38 15 41817664 41817664 + Silent SNP G G T rs749115120 C3N-01405_T C3N-01405_N G G c.1851G>T p.= p.T617T ENST00000456763 17/32 239 188 51 257 257 0 strelka-varscan-mutect MAPKBP1,synonymous_variant,p.=,ENST00000457542,NM_014994.2;MAPKBP1,synonymous_variant,p.=,ENST00000456763,NM_001128608.1;MAPKBP1,synonymous_variant,p.=,ENST00000514566,NM_001265611.1;MAPKBP1,3_prime_UTR_variant,,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,downstream_gene_variant,,ENST00000502292,;MAPKBP1,downstream_gene_variant,,ENST00000515164,;MAPKBP1,upstream_gene_variant,,ENST00000508050,;MAPKBP1,upstream_gene_variant,,ENST00000512433,;MAPKBP1,upstream_gene_variant,,ENST00000502695,;MAPKBP1,upstream_gene_variant,,ENST00000506301,;MAPKBP1,downstream_gene_variant,,ENST00000503526,; T ENST00000456763 Transcript synonymous_variant 2047/7158 1851/4545 617/1514 T acG/acT rs749115120 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 17/32 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF432,hmmpanther:PTHR22847,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs749115120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 41817664 41817664 G T 1 0 0 0 0 0 0 0 1 9216 1045 37 1 1 MAPKBP1 15 41817664 Silent SNP G C3N-01405_T 8231578 41817664 60173525 329 22803 MAPKBP1 0 . GRCh38 15 41825207 41825207 + Splice_Site SNP A A T novel C3N-01405_T C3N-01405_N A A c.4318-2A>T p.X1440_splice ENST00000456763 34 25 9 34 34 0 strelka-varscan-mutect MAPKBP1,splice_acceptor_variant,,ENST00000457542,NM_014994.2;MAPKBP1,splice_acceptor_variant,,ENST00000456763,NM_001128608.1;MAPKBP1,splice_acceptor_variant,,ENST00000514566,NM_001265611.1;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000382448,NM_005090.3;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000342159,NM_001198588.1;JMJD7,upstream_gene_variant,,ENST00000397299,NM_001114632.1;JMJD7,upstream_gene_variant,,ENST00000408047,;JMJD7,upstream_gene_variant,,ENST00000431823,;RP11-23P13.4,non_coding_transcript_exon_variant,,ENST00000510176,;RP11-23P13.4,downstream_gene_variant,,ENST00000512295,;JMJD7,upstream_gene_variant,,ENST00000405106,;MAPKBP1,splice_acceptor_variant,,ENST00000505061,;MAPKBP1,splice_acceptor_variant,,ENST00000512970,;MAPKBP1,splice_acceptor_variant,,ENST00000505373,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000491746,;JMJD7-PLA2G4B,upstream_gene_variant,,ENST00000490848,;MAPKBP1,downstream_gene_variant,,ENST00000508050,;MAPKBP1,downstream_gene_variant,,ENST00000512433,;MAPKBP1,downstream_gene_variant,,ENST00000502695,;MAPKBP1,downstream_gene_variant,,ENST00000506301,; T ENST00000456763 Transcript splice_acceptor_variant -/7158 4318/4545 1440/1514 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 31/31 HIGH 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.9997 0.9999994 1 1 1 0 T 5 4 74 41825207 41825207 A T 1 0 0 0 0 0 0 1 0 9216 202 7 4 4 MAPKBP1 15 41825207 Splice_Site SNP A C3N-01405_T 7543 41825207 60165982 330 22804 CAPN3 0 . GRCh38 15 42394264 42394264 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.1038C>G p.Phe346Leu p.F346L ENST00000397163 8/24 364 305 59 313 313 0 strelka-varscan-mutect CAPN3,missense_variant,p.Phe346Leu,ENST00000397163,NM_000070.2;CAPN3,missense_variant,p.Phe298Leu,ENST00000318023,;CAPN3,missense_variant,p.Phe298Leu,ENST00000349748,NM_173087.1;CAPN3,missense_variant,p.Phe346Leu,ENST00000357568,NM_024344.1;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000495723,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000466369,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000549793,;RP11-164J13.1,non_coding_transcript_exon_variant,,ENST00000483208,;CAPN3,non_coding_transcript_exon_variant,,ENST00000638141,; G ENST00000397163 Transcript missense_variant 1257/3228 1038/2466 346/821 F/L ttC/ttG 1 1 CAPN3 HGNC HGNC:1480 protein_coding YES CCDS45245.1 ENSP00000380349 P20807 UPI000000103F NM_000070.2 tolerated(0.17) 8/24 PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF320,Pfam_domain:PF00648,Gene3D:3.90.70.10,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs1469128441 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 42394264 42394264 C G 1 0 0 0 0 1 0 0 0 2322 825 29 4 4 CAPN3 15 42394264 Missense_Mutation SNP C C3N-01405_T 569057 42394264 59596925 331 22805 TGM7 0 . GRCh38 15 43279216 43279216 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1740G>T p.Lys580Asn p.K580N ENST00000452443 11/13 169 138 31 165 165 0 strelka-varscan-mutect TGM7,missense_variant,p.Lys580Asn,ENST00000452443,NM_052955.2;TGM7,upstream_gene_variant,,ENST00000562372,; A ENST00000452443 Transcript missense_variant 1745/2313 1740/2133 580/710 K/N aaG/aaT 1 -1 TGM7 HGNC HGNC:30790 protein_coding YES CCDS32213.1 ENSP00000389466 Q96PF1 UPI0000049F68 NM_052955.2 deleterious(0.05) 11/13 hmmpanther:PTHR11590:SF41,hmmpanther:PTHR11590,PIRSF_domain:PIRSF000459,Gene3D:2.60.40.10,Superfamily_domains:SSF49309 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 43279216 43279216 C A 1 0 0 0 0 1 0 0 0 16268 796 28 2 2 TGM7 15 43279216 Missense_Mutation SNP C C3N-01405_T 884952 43279216 58711973 332 22806 IL16 0 . GRCh38 15 81282722 81282722 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1165C>A p.Pro389Thr p.P389T ENST00000302987 8/18 174 133 41 139 139 0 strelka-varscan-mutect IL16,missense_variant,p.Pro389Thr,ENST00000394660,NM_001172128.1;IL16,missense_variant,p.Pro389Thr,ENST00000302987,NM_172217.3;IL16,missense_variant,p.Pro389Thr,ENST00000559383,;IL16,missense_variant,p.Pro389Thr,ENST00000360547,;IL16,missense_variant,p.Pro106Thr,ENST00000560115,;IL16,missense_variant,p.Pro389Thr,ENST00000560241,; A ENST00000302987 Transcript missense_variant 1165/3999 1165/3999 389/1332 P/T Cca/Aca 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 deleterious(0) 8/18 PROSITE_profiles:PS50106,hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 81282722 81282722 C A 1 0 0 0 0 1 0 0 0 7541 507 18 2 2 IL16 15 81282722 Missense_Mutation SNP C C3N-01405_T 38003506 81282722 20708467 333 22807 ADAMTSL3 0 . GRCh38 15 83820019 83820019 + Nonsense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.572T>A p.Leu191Ter p.L191* ENST00000286744 6/30 201 155 46 181 181 0 strelka-varscan-mutect ADAMTSL3,stop_gained,p.Leu191Ter,ENST00000286744,NM_207517.2;ADAMTSL3,stop_gained,p.Leu191Ter,ENST00000567476,NM_001301110.1;RNU6-1339P,downstream_gene_variant,,ENST00000363574,;ADAMTSL3,downstream_gene_variant,,ENST00000565653,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000561483,;ADAMTSL3,non_coding_transcript_exon_variant,,ENST00000569510,; A ENST00000286744 Transcript stop_gained 796/7336 572/5076 191/1691 L/* tTg/tAg 1 1 ADAMTSL3 HGNC HGNC:14633 protein_coding YES CCDS10326.1 ENSP00000286744 P82987 UPI00001615A5 NM_207517.2 6/30 Prints_domain:PR01857,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF169 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 83820019 83820019 T A 1 0 0 0 0 0 1 0 0 320 1821 63 4 4 ADAMTSL3 15 83820019 Nonsense_Mutation SNP T C3N-01405_T 2537297 83820019 18171170 334 22808 ST8SIA2 0 . GRCh38 15 92444868 92444868 + Nonsense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.781A>T p.Lys261Ter p.K261* ENST00000268164 5/6 225 164 61 165 165 0 strelka-varscan-mutect ST8SIA2,stop_gained,p.Lys261Ter,ENST00000268164,NM_006011.3;ST8SIA2,stop_gained,p.Lys240Ter,ENST00000539113,;ST8SIA2,stop_gained,p.Lys218Ter,ENST00000555434,;ST8SIA2,non_coding_transcript_exon_variant,,ENST00000556382,; T ENST00000268164 Transcript stop_gained 1018/5708 781/1128 261/375 K/* Aag/Tag 1 1 ST8SIA2 HGNC HGNC:10870 protein_coding YES CCDS10372.1 ENSP00000268164 Q92186 B2R9U8 UPI0000135970 NM_006011.3 5/6 hmmpanther:PTHR11987,hmmpanther:PTHR11987:SF30,PIRSF_domain:PIRSF005557,Pfam_domain:PF00777 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 92444868 92444868 A T 1 0 0 0 0 0 1 0 0 15610 247 9 4 4 ST8SIA2 15 92444868 Nonsense_Mutation SNP A C3N-01405_T 8624849 92444868 9546321 335 22809 FAM169B 0 . GRCh38 15 98480745 98480745 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.39C>A p.Phe13Leu p.F13L ENST00000332908 2/5 104 80 24 120 120 0 strelka-varscan-mutect FAM169B,missense_variant,p.Phe13Leu,ENST00000332908,NM_182562.2;FAM169B,non_coding_transcript_exon_variant,,ENST00000558256,;FAM169B,non_coding_transcript_exon_variant,,ENST00000636796,; T ENST00000332908 Transcript missense_variant 39/579 39/579 13/192 F/L ttC/ttA COSM1659815 1 -1 FAM169B HGNC HGNC:26835 protein_coding YES CCDS45360.1 ENSP00000332615 Q8N8A8 A0A0A0MR76 UPI0000199E5A NM_182562.2 deleterious(0) 2/5 hmmpanther:PTHR22442 1 MODERATE 1 SNV 2 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 98480745 98480745 G T 1 0 0 0 0 1 0 0 0 5334 1281 45 2 2 FAM169B 15 98480745 Missense_Mutation SNP G C3N-01405_T 6035877 98480745 3510444 336 22810 BAIAP3 0 . GRCh38 16 1346670 1346670 + Missense_Mutation SNP G G T rs542503250 C3N-01405_T C3N-01405_N G G c.2733G>T p.Lys911Asn p.K911N ENST00000324385 27/34 206 163 43 177 177 0 strelka-varscan-mutect BAIAP3,missense_variant,p.Lys893Asn,ENST00000628027,;BAIAP3,missense_variant,p.Lys911Asn,ENST00000324385,NM_003933.4;BAIAP3,missense_variant,p.Lys893Asn,ENST00000397488,NM_001286464.1;BAIAP3,missense_variant,p.Lys876Asn,ENST00000426824,NM_001199097.1;BAIAP3,missense_variant,p.Lys840Asn,ENST00000421665,NM_001199096.1;BAIAP3,missense_variant,p.Lys848Asn,ENST00000568887,NM_001199099.1;BAIAP3,missense_variant,p.Lys853Asn,ENST00000562208,NM_001199098.1;BAIAP3,missense_variant,p.Lys133Asn,ENST00000561793,;BAIAP3,intron_variant,,ENST00000566162,;TSR3,downstream_gene_variant,,ENST00000007390,NM_001001410.2;BAIAP3,non_coding_transcript_exon_variant,,ENST00000564213,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000567203,;BAIAP3,downstream_gene_variant,,ENST00000567825,;BAIAP3,upstream_gene_variant,,ENST00000566389,;BAIAP3,downstream_gene_variant,,ENST00000568198,;TSR3,downstream_gene_variant,,ENST00000566296,;BAIAP3,downstream_gene_variant,,ENST00000561602,; T ENST00000324385 Transcript missense_variant 2891/4678 2733/3564 911/1187 K/N aaG/aaT rs542503250 1 1 BAIAP3 HGNC HGNC:948 protein_coding YES CCDS10434.1 ENSP00000324510 O94812 UPI0000071E58 NM_003933.4 deleterious(0.01) 27/34 PROSITE_profiles:PS51259,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF65 MODERATE 1 SNV 1 1 PASS rs542503250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 1346670 1346670 G T 1 0 0 0 0 1 0 0 0 1456 991 35 2 2 BAIAP3 16 1346670 Missense_Mutation SNP G C3N-01405_T 1346670 88991675 337 22811 PKD1 0 . GRCh38 16 2110740 2110740 + Missense_Mutation SNP G G A rs563980883 C3N-01405_T C3N-01405_N G G c.4427C>T p.Ser1476Phe p.S1476F ENST00000262304 15/46 291 259 32 266 266 0 varscan-mutect PKD1,missense_variant,p.Ser1476Phe,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Ser1476Phe,ENST00000423118,NM_000296.3;PKD1,intron_variant,,ENST00000488185,;PKD1,intron_variant,,ENST00000483024,;PKD1,upstream_gene_variant,,ENST00000612014,;RP11-304L19.4,upstream_gene_variant,,ENST00000568795,;PKD1,intron_variant,,ENST00000468674,;PKD1,upstream_gene_variant,,ENST00000561991,;PKD1,upstream_gene_variant,,ENST00000473780,;PKD1,upstream_gene_variant,,ENST00000483558,;PKD1,upstream_gene_variant,,ENST00000564865,;PKD1,intron_variant,,ENST00000483731,;PKD1,intron_variant,,ENST00000415938,;PKD1,intron_variant,,ENST00000568591,;PKD1,intron_variant,,ENST00000565639,;PKD1,intron_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000487932,;PKD1,upstream_gene_variant,,ENST00000486339,;PKD1,upstream_gene_variant,,ENST00000496574,;PKD1,downstream_gene_variant,,ENST00000469241,;PKD1,upstream_gene_variant,,ENST00000564890,; A ENST00000262304 Transcript missense_variant 4636/14138 4427/12912 1476/4303 S/F tCc/tTc rs563980883 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 deleterious(0) 15/46 Gene3D:2.60.40.670,Pfam_domain:PF00801,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143,SMART_domains:SM00089,TIGRFAM_domain:TIGR00864 MODERATE 1 SNV 1 1 PASS rs563980883 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 2110740 2110740 G A 1 0 0 0 0 1 0 0 0 12059 1174 41 3 3 PKD1 16 2110740 Missense_Mutation SNP G C3N-01405_T 764070 2110740 88227605 338 22812 ZNF423 0 . GRCh38 16 49638133 49638133 + Missense_Mutation SNP C C G C3N-01405_T C3N-01405_N C C c.1019G>C p.Cys340Ser p.C340S ENST00000561648 5/9 445 332 113 441 441 0 strelka-varscan-mutect ZNF423,missense_variant,p.Cys340Ser,ENST00000561648,;ZNF423,missense_variant,p.Cys280Ser,ENST00000563137,;ZNF423,missense_variant,p.Cys340Ser,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Cys280Ser,ENST00000562871,;ZNF423,missense_variant,p.Cys223Ser,ENST00000535559,;ZNF423,missense_variant,p.Cys280Ser,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Cys223Ser,ENST00000567169,; G ENST00000561648 Transcript missense_variant 1320/7907 1019/3855 340/1284 C/S tGc/tCc COSM971186,COSM971187 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC tolerated(0.81) 5/9 PROSITE_patterns:PS00028,SMART_domains:SM00355 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 49638133 49638133 C G 1 0 0 0 0 1 0 0 0 18470 710 25 4 4 ZNF423 16 49638133 Missense_Mutation SNP C C3N-01405_T 47527393 49638133 40700212 339 22813 CETP 0 . GRCh38 16 56969638 56969638 + Silent SNP C C T C3N-01405_T C3N-01405_N C C c.396C>T p.= p.F132F ENST00000200676 4/16 609 537 72 543 543 0 strelka-varscan-mutect CETP,synonymous_variant,p.=,ENST00000200676,NM_000078.2;CETP,synonymous_variant,p.=,ENST00000566128,;CETP,synonymous_variant,p.=,ENST00000379780,NM_001286085.1;CETP,non_coding_transcript_exon_variant,,ENST00000569082,; T ENST00000200676 Transcript synonymous_variant 526/1791 396/1482 132/493 F ttC/ttT COSM5583382 1 1 CETP HGNC HGNC:1869 protein_coding YES CCDS10772.1 ENSP00000200676 P11597 A0A0S2Z3F6 UPI000013C62C NM_000078.2 4/16 hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF12,Gene3D:1ewfA01,Pfam_domain:PF01273,PIRSF_domain:PIRSF037185,SMART_domains:SM00328,Superfamily_domains:SSF55394 1 LOW 1 SNV 1 1 1 PASS rs879848326 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 56969638 56969638 C T 1 0 0 0 0 0 0 0 1 3009 883 31 1 1 CETP 16 56969638 Silent SNP C C3N-01405_T 7331505 56969638 33368707 340 22814 RP11-457D20.2 0 . GRCh38 16 60358750 60358750 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.731G>T p.Gly244Val p.G244V ENST00000614215 1/1 203 160 43 194 194 0 strelka-varscan-mutect RP11-457D20.2,missense_variant,p.Gly244Val,ENST00000614215,NM_001282301.1;RP11-354I13.2,upstream_gene_variant,,ENST00000565506,;RP11-354I13.2,upstream_gene_variant,,ENST00000565133,;RP11-457D20.1,downstream_gene_variant,,ENST00000563482,; A ENST00000614215 Transcript missense_variant 731/1026 731/1026 244/341 G/V gGc/gTc 1 -1 RP11-457D20.2 Clone_based_vega_gene protein_coding YES ENSP00000482925 A8MU76 UPI00017616FE NM_001282301.1 tolerated(0.26) 1/1 Pfam_domain:PF15229,hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF76 MODERATE SNV 1 PASS rs1338865527 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 60358750 60358750 C A 1 0 0 0 0 1 0 0 0 13744 739 26 2 2 RP11-457D20.2 16 60358750 Missense_Mutation SNP C C3N-01405_T 3389112 60358750 29979595 341 22815 LCAT 0 . GRCh38 16 67942530 67942530 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.581C>T p.Ala194Val p.A194V ENST00000264005 5/6 322 289 33 289 288 1 strelka-varscan-mutect LCAT,missense_variant,p.Ala194Val,ENST00000264005,NM_000229.1;LCAT,missense_variant,p.Ala122Val,ENST00000570980,;LCAT,missense_variant,p.Ala17Val,ENST00000576450,;LCAT,intron_variant,,ENST00000570369,;SLC12A4,downstream_gene_variant,,ENST00000316341,NM_001145961.1,NM_005072.4;SLC12A4,downstream_gene_variant,,ENST00000422611,NM_001145962.1;SLC12A4,downstream_gene_variant,,ENST00000576616,;SLC12A4,downstream_gene_variant,,ENST00000541864,NM_001145964.1;SLC12A4,downstream_gene_variant,,ENST00000572037,;SLC12A4,downstream_gene_variant,,ENST00000537830,NM_001145963.1;LCAT,upstream_gene_variant,,ENST00000570396,;LCAT,missense_variant,p.Ala75Val,ENST00000573538,;LCAT,3_prime_UTR_variant,,ENST00000575467,;LCAT,non_coding_transcript_exon_variant,,ENST00000575277,;LCAT,non_coding_transcript_exon_variant,,ENST00000573846,;SLC12A4,downstream_gene_variant,,ENST00000570802,;SLC12A4,downstream_gene_variant,,ENST00000573023,;SLC12A4,downstream_gene_variant,,ENST00000575857,;SLC12A4,downstream_gene_variant,,ENST00000570616,; A ENST00000264005 Transcript missense_variant 611/1507 581/1323 194/440 A/V gCc/gTc 1 -1 LCAT HGNC HGNC:6522 protein_coding YES CCDS10854.1 ENSP00000264005 P04180 A0A140VK24 UPI0000000DE7 NM_000229.1 tolerated(0.25) 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF02450,hmmpanther:PTHR11440,hmmpanther:PTHR11440:SF18,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 67942530 67942530 G A 1 0 0 0 0 1 0 0 0 8563 1203 42 3 3 LCAT 16 67942530 Missense_Mutation SNP G C3N-01405_T 7583780 67942530 22395815 342 22816 DHRS7C 0 . GRCh38 17 9772777 9772777 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.720C>T p.= p.S240S ENST00000330255 5/6 128 111 17 114 114 0 strelka-varscan-mutect DHRS7C,synonymous_variant,p.=,ENST00000330255,NM_001220493.1;DHRS7C,synonymous_variant,p.=,ENST00000571134,NM_001105571.2;DHRS7C,intron_variant,,ENST00000571771,;RP11-477N12.6,intron_variant,,ENST00000634974,; A ENST00000330255 Transcript synonymous_variant 733/1006 720/939 240/312 S tcC/tcT 1 -1 DHRS7C HGNC HGNC:32423 protein_coding YES CCDS56020.1 ENSP00000327975 A6NNS2 UPI000178DECB NM_001220493.1 5/6 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 9772777 9772777 G A 1 0 0 0 0 0 0 0 1 4301 1335 47 3 3 DHRS7C 17 9772777 Silent SNP G C3N-01405_T 9772777 73484664 343 22817 FAM83G 0 . GRCh38 17 18988397 18988397 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.540G>T p.Met180Ile p.M180I ENST00000388995 3/6 116 86 30 79 79 0 strelka-varscan-mutect FAM83G,missense_variant,p.Met180Ile,ENST00000388995,NM_001039999.2;FAM83G,missense_variant,p.Met180Ile,ENST00000345041,;SLC5A10,intron_variant,,ENST00000317977,NM_001282417.1;SLC5A10,intron_variant,,ENST00000395647,NM_152351.4;SLC5A10,intron_variant,,ENST00000395645,NM_001042450.2;SLC5A10,intron_variant,,ENST00000417251,NM_001270649.1;SLC5A10,intron_variant,,ENST00000395643,NM_001270648.1;FAM83G,non_coding_transcript_exon_variant,,ENST00000399096,;RP11-28B23.1,upstream_gene_variant,,ENST00000573133,; A ENST00000388995 Transcript missense_variant 764/5266 540/2472 180/823 M/I atG/atT 1 -1 FAM83G HGNC HGNC:32554 protein_coding YES CCDS42276.1 ENSP00000373647 A6ND36 UPI0000E03260 NM_001039999.2 deleterious(0) 3/6 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF5,Pfam_domain:PF07894,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 18988397 18988397 C A 1 0 0 0 0 1 0 0 0 5497 594 21 2 2 FAM83G 17 18988397 Missense_Mutation SNP C C3N-01405_T 9215620 18988397 64269044 344 22818 SLC47A2 0 . GRCh38 17 19679992 19679992 + Silent SNP A A T rs772470758 C3N-01405_T C3N-01405_N A A c.1548T>A p.= p.T516T ENST00000325411 16/17 121 102 19 121 121 0 strelka-varscan-mutect SLC47A2,synonymous_variant,p.=,ENST00000350657,NM_001256663.1;SLC47A2,synonymous_variant,p.=,ENST00000325411,NM_001099646.1,NM_152908.3;ALDH3A2,downstream_gene_variant,,ENST00000176643,;ALDH3A2,downstream_gene_variant,,ENST00000339618,NM_001031806.1;ALDH3A2,downstream_gene_variant,,ENST00000631291,;ALDH3A2,downstream_gene_variant,,ENST00000395575,;ALDH3A2,downstream_gene_variant,,ENST00000579855,NM_000382.2;ALDH3A2,downstream_gene_variant,,ENST00000581518,;ALDH3A2,downstream_gene_variant,,ENST00000630662,;ALDH3A2,downstream_gene_variant,,ENST00000571163,;ALDH3A2,downstream_gene_variant,,ENST00000575384,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000463318,;ALDH3A2,downstream_gene_variant,,ENST00000574597,;SLC47A2,3_prime_UTR_variant,,ENST00000574239,;SLC47A2,non_coding_transcript_exon_variant,,ENST00000467609,;ALDH3A2,downstream_gene_variant,,ENST00000472059,;ALDH3A2,downstream_gene_variant,,ENST00000573505,;ALDH3A2,downstream_gene_variant,,ENST00000582991,;ALDH3A2,downstream_gene_variant,,ENST00000476965,;ALDH3A2,downstream_gene_variant,,ENST00000573565,;ALDH3A2,downstream_gene_variant,,ENST00000573947,; T ENST00000325411 Transcript synonymous_variant 1599/2258 1548/1809 516/602 T acT/acA rs772470758 1 -1 SLC47A2 HGNC HGNC:26439 protein_coding YES CCDS11211.1 ENSP00000326671 Q86VL8 UPI0000190813 NM_001099646.1,NM_152908.3 16/17 hmmpanther:PTHR11206,hmmpanther:PTHR11206:SF81 LOW 1 SNV 1 1 PASS rs772470758 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 19679992 19679992 A T 1 0 0 0 0 0 0 0 1 14925 175 7 4 4 SLC47A2 17 19679992 Silent SNP A C3N-01405_T 691595 19679992 63577449 345 22819 NF1 0 . GRCh38 17 31214524 31214524 + Missense_Mutation SNP A A G rs137854557 C3N-01405_T C3N-01405_N A A c.1466A>G p.Tyr489Cys p.Y489C ENST00000358273 13/58 162 133 29 192 192 0 strelka-varscan-mutect NF1,missense_variant,p.Tyr489Cys,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Tyr489Cys,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Tyr155Cys,ENST00000456735,;NF1,missense_variant,p.Tyr489Cys,ENST00000431387,NM_001128147.2;NF1,missense_variant,p.Tyr523Cys,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,; G ENST00000358273 Transcript missense_variant 1849/12425 1466/8520 489/2839 Y/C tAt/tGt rs137854557,CS992455,COSM1290665,COSM329089 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 tolerated(0.08) 13/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 pathogenic 0,0,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs137854557 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 31214524 31214524 A G 1 0 0 0 0 1 0 0 0 10393 449 16 5 5 NF1 17 31214524 Missense_Mutation SNP A C3N-01405_T 11534532 31214524 52042917 346 22820 GGNBP2 0 . GRCh38 17 36586171 36586171 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.1614A>T p.Lys538Asn p.K538N ENST00000613102 12/14 146 120 26 104 104 0 strelka-varscan-mutect GGNBP2,missense_variant,p.Lys538Asn,ENST00000613102,NM_024835.4;GGNBP2,missense_variant,p.Lys13Asn,ENST00000615952,;GGNBP2,non_coding_transcript_exon_variant,,ENST00000612563,;GGNBP2,downstream_gene_variant,,ENST00000617860,;GGNBP2,downstream_gene_variant,,ENST00000618837,;GGNBP2,downstream_gene_variant,,ENST00000619573,;GGNBP2,upstream_gene_variant,,ENST00000620927,; T ENST00000613102 Transcript missense_variant 1930/2847 1614/2094 538/697 K/N aaA/aaT 1 1 GGNBP2 HGNC HGNC:19357 protein_coding YES CCDS11314.1 ENSP00000478220 Q9H3C7 UPI00000728CB NM_024835.4 tolerated_low_confidence(0.35) 12/14 Low_complexity_(Seg):seg,hmmpanther:PTHR13601 MODERATE 1 SNV 1 1 PASS rs1294064517 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 36586171 36586171 A T 1 0 0 0 0 1 0 0 0 6235 11 1 4 4 GGNBP2 17 36586171 Missense_Mutation SNP A C3N-01405_T 5371647 36586171 46671270 347 22821 HAP1 0 . GRCh38 17 41724986 41724986 + Silent SNP C C T novel C3N-01405_T C3N-01405_N C C c.1575G>A p.= p.G525G ENST00000347901 11/11 168 142 26 107 107 0 strelka-varscan-mutect HAP1,synonymous_variant,p.=,ENST00000393939,NM_001079871.1;HAP1,synonymous_variant,p.=,ENST00000310778,;HAP1,synonymous_variant,p.=,ENST00000347901,NM_177977.2;HAP1,synonymous_variant,p.=,ENST00000341193,NM_001079870.1;HAP1,synonymous_variant,p.=,ENST00000458656,;HAP1,intron_variant,,ENST00000442364,;HAP1,intron_variant,,ENST00000455021,; T ENST00000347901 Transcript synonymous_variant 1585/3931 1575/1860 525/619 G ggG/ggA 1 -1 HAP1 HGNC HGNC:4812 protein_coding YES CCDS11406.1 ENSP00000334002 P54257 UPI000024700D NM_177977.2 11/11 hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF14 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 41724986 41724986 C T 1 0 0 0 0 0 0 0 1 6839 610 22 3 3 HAP1 17 41724986 Silent SNP C C3N-01405_T 5138815 41724986 41532455 348 22822 PLCD3 0 . GRCh38 17 45121064 45121064 + Missense_Mutation SNP C C A rs774017109 C3N-01405_T C3N-01405_N C C c.392G>T p.Gly131Val p.G131V ENST00000619929 3/15 150 124 26 112 112 0 strelka-varscan-mutect PLCD3,missense_variant,p.Gly131Val,ENST00000619929,NM_133373.4;PLCD3,missense_variant,p.Gly108Val,ENST00000590644,;PLCD3,missense_variant,p.Gly67Val,ENST00000538093,;PLCD3,upstream_gene_variant,,ENST00000611986,;PLCD3,downstream_gene_variant,,ENST00000544446,;PLCD3,upstream_gene_variant,,ENST00000538988,;PLCD3,upstream_gene_variant,,ENST00000546350,;PLCD3,upstream_gene_variant,,ENST00000542173,; A ENST00000619929 Transcript missense_variant 480/6107 392/2370 131/789 G/V gGt/gTt rs774017109 1 -1 PLCD3 HGNC HGNC:9061 protein_coding YES CCDS74077.1 ENSP00000479636 Q8N3E9 UPI0000070705 NM_133373.4 tolerated(0.14) 3/15 Gene3D:2.30.29.30,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF33,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs774017109 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 45121064 45121064 C A 1 0 0 0 0 1 0 0 0 12126 507 18 2 2 PLCD3 17 45121064 Missense_Mutation SNP C C3N-01405_T 3396078 45121064 38136377 349 22823 SPPL2C 0 . GRCh38 17 45846107 45846107 + Nonsense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1201G>T p.Glu401Ter p.E401* ENST00000329196 1/1 304 246 58 196 196 0 strelka-varscan-mutect SPPL2C,stop_gained,p.Glu401Ter,ENST00000329196,NM_175882.2;MAPT-AS1,intron_variant,,ENST00000634876,;MAPT-AS1,intron_variant,,ENST00000579599,;MAPT-AS1,intron_variant,,ENST00000579244,;MAPT-AS1,upstream_gene_variant,,ENST00000581125,; T ENST00000329196 Transcript stop_gained 1273/2238 1201/2055 401/684 E/* Gag/Tag 1 1 SPPL2C HGNC HGNC:28902 protein_coding YES CCDS32673.1 ENSP00000332488 Q8IUH8 UPI0000EE80B4 NM_175882.2 1/1 Pfam_domain:PF04258,hmmpanther:PTHR12174,hmmpanther:PTHR12174:SF38,SMART_domains:SM00730 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 45846107 45846107 G T 1 0 0 0 0 0 1 0 0 15443 1291 45 2 2 SPPL2C 17 45846107 Nonsense_Mutation SNP G C3N-01405_T 725043 45846107 37411334 350 22824 SPOP 0 . GRCh38 17 49621998 49621998 + Missense_Mutation SNP C C T C3N-01405_T C3N-01405_N C C c.148G>A p.Glu50Lys p.E50K ENST00000393328 4/11 275 194 81 236 236 0 strelka-varscan-mutect SPOP,missense_variant,p.Glu50Lys,ENST00000393328,NM_003563.3,NM_001007226.1;SPOP,missense_variant,p.Glu50Lys,ENST00000347630,NM_001007227.1,NM_001007229.1,NM_001007230.1;SPOP,missense_variant,p.Glu50Lys,ENST00000503676,;SPOP,missense_variant,p.Glu50Lys,ENST00000504102,NM_001007228.1;SPOP,missense_variant,p.Glu50Lys,ENST00000509079,;SPOP,missense_variant,p.Glu50Lys,ENST00000505581,;SPOP,missense_variant,p.Glu50Lys,ENST00000507970,;SPOP,missense_variant,p.Glu50Lys,ENST00000514121,;SPOP,missense_variant,p.Glu50Lys,ENST00000510476,;SPOP,missense_variant,p.Glu50Lys,ENST00000515508,;SPOP,downstream_gene_variant,,ENST00000451526,;SPOP,downstream_gene_variant,,ENST00000508805,;SPOP,non_coding_transcript_exon_variant,,ENST00000513080,;SPOP,downstream_gene_variant,,ENST00000502385,;SPOP,3_prime_UTR_variant,,ENST00000506399,;SPOP,3_prime_UTR_variant,,ENST00000504212,;SPOP,upstream_gene_variant,,ENST00000509869,;SPOP,downstream_gene_variant,,ENST00000509765,; T ENST00000393328 Transcript missense_variant 514/2985 148/1125 50/374 E/K Gaa/Aaa COSM980818 1 -1 SPOP HGNC HGNC:11254 protein_coding YES CCDS11551.1 ENSP00000377001 O43791 UPI0000003F5C NM_003563.3,NM_001007226.1 tolerated(0.06) 4/11 Gene3D:2.60.210.10,PROSITE_profiles:PS50144,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF97,SMART_domains:SM00061,Superfamily_domains:SSF49599 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 49621998 49621998 C T 1 0 0 0 0 1 0 0 0 15437 835 29 3 3 SPOP 17 49621998 Missense_Mutation SNP C C3N-01405_T 3775891 49621998 33635443 351 22825 CACNA1G 0 . GRCh38 17 50575687 50575687 + Frame_Shift_Del DEL C C - novel C3N-01405_T C3N-01405_N C C c.1287delC p.Gly430AlafsTer134 p.G430Afs*134 ENST00000359106 8/38 501 391 110 377 377 0 sindel-varindel-pindel CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000354983,NM_198396.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000352832,NM_198387.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000359106,NM_018896.4;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000360761,NM_198382.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000442258,NM_198388.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000429973,NM_198386.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000507336,NM_198377.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000358244,NM_198376.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000507510,NM_198385.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000515765,NM_198380.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000515411,NM_001256324.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000502264,NM_198383.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000510115,NM_198379.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000514079,NM_001256325.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000513689,NM_001256326.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000515165,NM_198384.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000507609,NM_001256327.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000512389,NM_198378.2;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000514181,NM_001256328.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000510366,NM_001256331.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000514717,NM_001256332.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000505165,NM_001256333.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000507896,NM_001256334.1;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000416767,;CACNA1G,downstream_gene_variant,,ENST00000570567,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000506406,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000504076,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000511765,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000503436,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000511768,;CACNA1G,frameshift_variant,p.Gly430AlafsTer134,ENST00000503607,; - ENST00000359106 Transcript frameshift_variant 1285/7648 1285/7134 429/2377 P/X Ccc/cc 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 8/38 Prints_domain:PR01629,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 50575687 50575687 C - 1 0 1 0 1 0 0 0 0 2232 739 26 0 0 CACNA1G 17 50575687 Frame_Shift_Del DEL C C3N-01405_T 953689 50575687 32681754 352 22826 CACNA1G 0 . GRCh38 17 50626407 50626407 + Nonsense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.6790G>T p.Glu2264Ter p.E2264* ENST00000359106 38/38 110 95 15 67 67 0 strelka-mutect CACNA1G,stop_gained,p.Glu2230Ter,ENST00000354983,NM_198396.2;CACNA1G,stop_gained,p.Glu2137Ter,ENST00000352832,NM_198387.2;CACNA1G,stop_gained,p.Glu2264Ter,ENST00000359106,NM_018896.4;CACNA1G,stop_gained,p.Glu2148Ter,ENST00000360761,NM_198382.2;CACNA1G,stop_gained,p.Glu2130Ter,ENST00000442258,NM_198388.2;CACNA1G,stop_gained,p.Glu2153Ter,ENST00000429973,NM_198386.2;CACNA1G,stop_gained,p.Glu2253Ter,ENST00000507336,NM_198377.2;CACNA1G,stop_gained,p.Glu2058Ter,ENST00000358244,NM_198376.2;CACNA1G,stop_gained,p.Glu2219Ter,ENST00000507510,NM_198385.2;CACNA1G,stop_gained,p.Glu2208Ter,ENST00000515765,NM_198380.2;CACNA1G,stop_gained,p.Glu2201Ter,ENST00000515411,NM_001256324.1;CACNA1G,stop_gained,p.Glu2193Ter,ENST00000502264,NM_198383.2;CACNA1G,stop_gained,p.Glu2185Ter,ENST00000510115,NM_198379.2;CACNA1G,stop_gained,p.Glu2178Ter,ENST00000514079,NM_001256325.1;CACNA1G,stop_gained,p.Glu2174Ter,ENST00000513689,NM_001256326.1;CACNA1G,stop_gained,p.Glu2171Ter,ENST00000515165,NM_198384.2;CACNA1G,stop_gained,p.Glu2164Ter,ENST00000507609,NM_001256327.1;CACNA1G,stop_gained,p.Glu2160Ter,ENST00000512389,NM_198378.2;CACNA1G,stop_gained,p.Glu2146Ter,ENST00000514181,NM_001256328.1;CACNA1G,stop_gained,p.Glu2137Ter,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,stop_gained,p.Glu2126Ter,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,stop_gained,p.Glu2119Ter,ENST00000510366,NM_001256331.1;CACNA1G,stop_gained,p.Glu2114Ter,ENST00000514717,NM_001256332.1;CACNA1G,stop_gained,p.Glu2092Ter,ENST00000505165,NM_001256333.1;CACNA1G,stop_gained,p.Glu2081Ter,ENST00000507896,NM_001256334.1;CTB-22K21.2,downstream_gene_variant,,ENST00000502435,;CACNA1G,3_prime_UTR_variant,,ENST00000506406,;CACNA1G,3_prime_UTR_variant,,ENST00000504076,;CACNA1G,3_prime_UTR_variant,,ENST00000511765,;CACNA1G,3_prime_UTR_variant,,ENST00000503436,;CACNA1G,3_prime_UTR_variant,,ENST00000511768,;CACNA1G,3_prime_UTR_variant,,ENST00000503607,; T ENST00000359106 Transcript stop_gained 6790/7648 6790/7134 2264/2377 E/* Gag/Tag 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 38/38 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 50626407 50626407 G T 1 0 0 0 0 0 1 0 0 2232 1291 45 2 2 CACNA1G 17 50626407 Nonsense_Mutation SNP G C3N-01405_T 50720 50626407 32631034 353 22827 TSPOAP1 0 . GRCh38 17 58310111 58310111 + Silent SNP C C A C3N-01405_T C3N-01405_N C C c.3747G>T p.= p.V1249V ENST00000343736 21/32 176 131 45 118 118 0 strelka-varscan-mutect TSPOAP1,synonymous_variant,p.=,ENST00000268893,NM_024418.2;TSPOAP1,synonymous_variant,p.=,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1,synonymous_variant,p.=,ENST00000582679,;TSPOAP1,upstream_gene_variant,,ENST00000581675,;TSPOAP1,upstream_gene_variant,,ENST00000580669,;TSPOAP1,upstream_gene_variant,,ENST00000581692,;TSPOAP1,upstream_gene_variant,,ENST00000578511,;TSPOAP1,upstream_gene_variant,,ENST00000577871,;TSPOAP1,upstream_gene_variant,,ENST00000578486,;TSPOAP1,downstream_gene_variant,,ENST00000585149,; A ENST00000343736 Transcript synonymous_variant 3911/5947 3747/5574 1249/1857 V gtG/gtT COSM4545277,COSM4545278 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 21/32 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 58310111 58310111 C A 1 0 0 0 0 0 0 0 1 17163 581 21 2 2 TSPOAP1 17 58310111 Silent SNP C C3N-01405_T 7683704 58310111 24947330 354 22828 TEX14 0 . GRCh38 17 58586038 58586038 + Missense_Mutation SNP T T A rs750735439 C3N-01405_T C3N-01405_N T T c.2851A>T p.Thr951Ser p.T951S ENST00000240361 18/33 179 143 36 113 113 0 strelka-varscan-mutect TEX14,missense_variant,p.Thr945Ser,ENST00000389934,NM_198393.3;TEX14,missense_variant,p.Thr951Ser,ENST00000240361,NM_001201457.1;TEX14,missense_variant,p.Thr945Ser,ENST00000349033,NM_031272.4;TEX14,3_prime_UTR_variant,,ENST00000582740,; A ENST00000240361 Transcript missense_variant 2937/4911 2851/4494 951/1497 T/S Aca/Tca rs750735439 1 -1 TEX14 HGNC HGNC:11737 protein_coding YES CCDS56042.1 ENSP00000240361 Q8IWB6 UPI0000DAC9CA NM_001201457.1 tolerated(0.67) 18/33 hmmpanther:PTHR23060 MODERATE 1 SNV 1 1 PASS rs750735439 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 58586038 58586038 T A 1 0 0 0 0 1 0 0 0 16200 1696 59 4 4 TEX14 17 58586038 Missense_Mutation SNP T C3N-01405_T 275927 58586038 24671403 355 22829 NOL11 0 . GRCh38 17 67719722 67719722 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.190A>T p.Ile64Phe p.I64F ENST00000253247 2/18 222 195 27 176 176 0 strelka-mutect NOL11,missense_variant,p.Ile64Phe,ENST00000253247,NM_015462.4,NM_001303272.1;NOL11,missense_variant,p.Ile83Phe,ENST00000581106,;NOL11,upstream_gene_variant,,ENST00000580833,;NOL11,non_coding_transcript_exon_variant,,ENST00000581966,;NOL11,missense_variant,p.Ile64Phe,ENST00000581375,;NOL11,non_coding_transcript_exon_variant,,ENST00000584942,;NOL11,upstream_gene_variant,,ENST00000580914,; T ENST00000253247 Transcript missense_variant 305/2947 190/2160 64/719 I/F Att/Ttt 1 1 NOL11 HGNC HGNC:24557 protein_coding YES CCDS11671.1 ENSP00000253247 Q9H8H0 UPI0000072B83 NM_015462.4,NM_001303272.1 tolerated(0.06) 2/18 hmmpanther:PTHR15633,hmmpanther:PTHR15633:SF2,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 67719722 67719722 A T 1 0 0 0 0 1 0 0 0 10564 101 4 4 4 NOL11 17 67719722 Missense_Mutation SNP A C3N-01405_T 9133684 67719722 15537719 356 22830 USH1G 0 . GRCh38 17 74919597 74919597 + Silent SNP G G T rs766986350 C3N-01405_T C3N-01405_N G G c.1239C>A p.= p.I413I ENST00000614341 2/3 492 405 87 304 304 0 strelka-varscan-mutect USH1G,synonymous_variant,p.=,ENST00000614341,NM_001282489.2,NM_173477.4;OTOP2,upstream_gene_variant,,ENST00000331427,NM_178160.2;USH1G,3_prime_UTR_variant,,ENST00000579243,;OTOP2,upstream_gene_variant,,ENST00000584711,; T ENST00000614341 Transcript synonymous_variant 1422/3558 1239/1386 413/461 I atC/atA rs766986350 1 -1 USH1G HGNC HGNC:16356 protein_coding YES CCDS32725.1 ENSP00000480279 Q495M9 UPI00001BC010 NM_001282489.2,NM_173477.4 2/3 hmmpanther:PTHR24161:SF24,hmmpanther:PTHR24161,Gene3D:1.10.150.50,Pfam_domain:PF00536,SMART_domains:SM00454,Superfamily_domains:SSF47769 LOW 1 SNV 1 1 PASS rs766986350 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 74919597 74919597 G T 1 0 0 0 0 0 0 0 1 17569 1048 37 1 1 USH1G 17 74919597 Silent SNP G C3N-01405_T 7199875 74919597 8337844 357 22831 MYADML2 0 . GRCh38 17 81941146 81941146 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.596C>A p.Ala199Asp p.A199D ENST00000409745 3/3 265 199 66 161 161 0 strelka-varscan-mutect MYADML2,missense_variant,p.Ala199Asp,ENST00000409745,NM_001145113.2;PYCR1,intron_variant,,ENST00000582198,;PYCR1,upstream_gene_variant,,ENST00000619204,NM_001282280.1;PYCR1,upstream_gene_variant,,ENST00000337943,NM_153824.2;PYCR1,upstream_gene_variant,,ENST00000329875,NM_006907.3;PYCR1,upstream_gene_variant,,ENST00000403172,NM_001282279.1;PYCR1,upstream_gene_variant,,ENST00000629768,;PYCR1,upstream_gene_variant,,ENST00000402252,NM_001282281.1;PYCR1,upstream_gene_variant,,ENST00000577756,;PYCR1,upstream_gene_variant,,ENST00000584848,;PYCR1,upstream_gene_variant,,ENST00000405481,;PYCR1,upstream_gene_variant,,ENST00000585215,;PYCR1,upstream_gene_variant,,ENST00000579366,;PYCR1,upstream_gene_variant,,ENST00000585244,;PYCR1,upstream_gene_variant,,ENST00000579698,;PYCR1,upstream_gene_variant,,ENST00000581271,;PYCR1,upstream_gene_variant,,ENST00000577624,;PYCR1,upstream_gene_variant,,ENST00000583564,;AC137723.5,upstream_gene_variant,,ENST00000415556,; T ENST00000409745 Transcript missense_variant 951/2452 596/924 199/307 A/D gCc/gAc 1 -1 MYADML2 HGNC HGNC:34548 protein_coding YES CCDS45815.1 ENSP00000386702 A6NDP7 UPI0000EE5F22 NM_001145113.2 deleterious(0) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51225,hmmpanther:PTHR17068:SF5,hmmpanther:PTHR17068,Pfam_domain:PF01284 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 81941146 81941146 G T 1 0 0 0 0 1 0 0 0 10006 1203 42 2 2 MYADML2 17 81941146 Missense_Mutation SNP G C3N-01405_T 7021549 81941146 1316295 358 22832 TMEM200C 0 . GRCh38 18 5891985 5891985 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.79C>G p.Arg27Gly p.R27G ENST00000581347 3/3 227 171 56 238 238 0 strelka-varscan-mutect TMEM200C,missense_variant,p.Arg27Gly,ENST00000581347,;TMEM200C,missense_variant,p.Arg27Gly,ENST00000383490,NM_001080209.1;RP11-945C19.4,intron_variant,,ENST00000577694,;RP11-945C19.4,downstream_gene_variant,,ENST00000582939,;RP11-945C19.4,downstream_gene_variant,,ENST00000580845,; C ENST00000581347 Transcript missense_variant 725/10638 79/1866 27/621 R/G Cgc/Ggc 1 -1 TMEM200C HGNC HGNC:37208 protein_coding YES CCDS45825.1 ENSP00000463375 A6NKL6 UPI000020198E deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR31815,hmmpanther:PTHR31815:SF2,Pfam_domain:PF10177 MODERATE SNV 5 1 PASS rs1287027998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 5891985 5891985 G C 1 0 0 0 0 1 0 0 0 16564 1087 38 4 4 TMEM200C 18 5891985 Missense_Mutation SNP G C3N-01405_T 5891985 74481300 359 22833 TMEM241 0 . GRCh38 18 23352274 23352274 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.687C>G p.Phe229Leu p.F229L ENST00000383233 13/15 137 120 17 116 116 0 strelka-varscan-mutect TMEM241,missense_variant,p.Phe229Leu,ENST00000383233,NM_032933.4;TMEM241,missense_variant,p.Phe190Leu,ENST00000578520,;TMEM241,3_prime_UTR_variant,,ENST00000542162,;TMEM241,3_prime_UTR_variant,,ENST00000473688,;TMEM241,3_prime_UTR_variant,,ENST00000477053,;TMEM241,3_prime_UTR_variant,,ENST00000581444,;TMEM241,3_prime_UTR_variant,,ENST00000460322,;TMEM241,non_coding_transcript_exon_variant,,ENST00000583048,;TMEM241,downstream_gene_variant,,ENST00000497608,;TMEM241,downstream_gene_variant,,ENST00000482411,;TMEM241,downstream_gene_variant,,ENST00000577531,; C ENST00000383233 Transcript missense_variant 740/2934 687/891 229/296 F/L ttC/ttG 1 -1 TMEM241 HGNC HGNC:31723 protein_coding YES CCDS11876.2 ENSP00000372720 Q24JQ0 UPI000022A6E0 NM_032933.4 deleterious(0.01) 13/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF111 MODERATE 1 SNV 1 1 PASS . . 0 201 0 8 0 0 0 0 -19.99999 0.9865139 1 1 1 0 C 3 2 74 23352274 23352274 G C 1 0 0 0 0 1 0 0 0 16601 933 33 4 4 TMEM241 18 23352274 Missense_Mutation SNP G C3N-01405_T 17460289 23352274 57021011 360 22834 LAMA3 0 . GRCh38 18 23847576 23847576 + Frame_Shift_Del DEL C C - novel C3N-01405_T C3N-01405_N C C c.4047delC p.Met1350TrpfsTer81 p.M1350Wfs*81 ENST00000313654 32/75 478 427 51 402 402 0 sindel-varindel-pindel LAMA3,frameshift_variant,p.Met1350TrpfsTer81,ENST00000313654,NM_198129.2;LAMA3,frameshift_variant,p.Met1350TrpfsTer81,ENST00000399516,NM_001127717.2; - ENST00000313654 Transcript frameshift_variant 4285/10661 4044/10002 1348/3333 H/X caC/ca 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 32/75 Gene3D:2.10.25.10,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF285,SMART_domains:SM00180 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 23847576 23847576 C - 1 0 1 0 1 0 0 0 0 8511 506 18 0 0 LAMA3 18 23847576 Frame_Shift_Del DEL C C3N-01405_T 495302 23847576 56525709 361 22835 ZNF521 0 . GRCh38 18 25225314 25225314 + Silent SNP G G T novel C3N-01405_T C3N-01405_N G G c.2604C>A p.= p.S868S ENST00000361524 4/8 403 352 51 294 294 0 strelka-varscan-mutect ZNF521,synonymous_variant,p.=,ENST00000361524,NM_015461.2;ZNF521,synonymous_variant,p.=,ENST00000584787,NM_001308225.1;ZNF521,synonymous_variant,p.=,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,synonymous_variant,p.=,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; T ENST00000361524 Transcript synonymous_variant 2753/4871 2604/3936 868/1311 S tcC/tcA 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 4/8 hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 25225314 25225314 G T 1 0 0 0 0 0 0 0 1 18537 1219 43 2 2 ZNF521 18 25225314 Silent SNP G C3N-01405_T 1377738 25225314 55147971 362 22836 ASXL3 0 . GRCh38 18 33738690 33738690 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.1286C>A p.Pro429Gln p.P429Q ENST00000269197 11/12 164 138 26 137 137 0 strelka-varscan-mutect ASXL3,missense_variant,p.Pro429Gln,ENST00000269197,NM_030632.1;ASXL3,3_prime_UTR_variant,,ENST00000592288,; A ENST00000269197 Transcript missense_variant 1341/11399 1286/6747 429/2248 P/Q cCa/cAa 1 1 ASXL3 HGNC HGNC:29357 protein_coding YES CCDS45847.1 ENSP00000269197 Q9C0F0 UPI000156D0F3 NM_030632.1 deleterious_low_confidence(0) 11/12 hmmpanther:PTHR13578,hmmpanther:PTHR13578:SF18 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 33738690 33738690 C A 1 0 0 0 0 1 0 0 0 1216 594 21 2 2 ASXL3 18 33738690 Missense_Mutation SNP C C3N-01405_T 8513376 33738690 46634595 363 22837 ELP2 0 . GRCh38 18 36171063 36171076 + Frame_Shift_Del DEL GGATTGGAGTGTGG GGATTGGAGTGTGG - novel C3N-01405_T C3N-01405_N GGATTGGAGTGTGG GGATTGGAGTGTGG c.2422_2435delGGATTGGAGTGTGG p.Gly808LysfsTer11 p.G808Kfs*11 ENST00000442325 22/23 405 359 46 434 434 0 sindel-varindel-pindel ELP2,frameshift_variant,p.Gly743LysfsTer11,ENST00000358232,NM_018255.2;ELP2,frameshift_variant,p.Gly808LysfsTer11,ENST00000442325,NM_001242875.1;ELP2,frameshift_variant,p.Gly738LysfsTer11,ENST00000350494,NM_001242876.1;ELP2,frameshift_variant,p.Gly717LysfsTer11,ENST00000351393,NM_001242877.1;ELP2,frameshift_variant,p.Gly673LysfsTer11,ENST00000423854,NM_001242879.1;ELP2,frameshift_variant,p.Gly673LysfsTer11,ENST00000542824,NM_001242878.1;ELP2,non_coding_transcript_exon_variant,,ENST00000545302,;ELP2,3_prime_UTR_variant,,ENST00000539560,;ELP2,3_prime_UTR_variant,,ENST00000540766,;ELP2,non_coding_transcript_exon_variant,,ENST00000541748,;ELP2,non_coding_transcript_exon_variant,,ENST00000536830,;ELP2,non_coding_transcript_exon_variant,,ENST00000544274,; - ENST00000442325 Transcript frameshift_variant 2458-2471/2722 2422-2435/2676 808-812/891 GLECG/X GGATTGGAGTGTGGa/a 1 1 ELP2 HGNC HGNC:18248 protein_coding YES CCDS56065.1 ENSP00000414851 Q6IA86 UPI0000E03DE9 NM_001242875.1 22/23 hmmpanther:PTHR22847:SF471,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 36171063 36171063 GGATTGGAGTGTGG - 1 0 1 0 1 0 0 0 0 4914 1001 35 0 0 ELP2 18 36171063 Frame_Shift_Del DEL GGATTGGAGTGTGG C3N-01405_T 2432373 36171063 44202222 364 22838 SYT4 0 . GRCh38 18 43271765 43271765 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.917T>C p.Val306Ala p.V306A ENST00000255224 3/4 200 174 26 207 207 0 strelka-varscan-mutect SYT4,missense_variant,p.Val306Ala,ENST00000255224,NM_020783.3;SYT4,missense_variant,p.Val288Ala,ENST00000590752,;SYT4,missense_variant,p.Val36Ala,ENST00000596867,;SYT4,missense_variant,p.Val133Ala,ENST00000593720,;SYT4,non_coding_transcript_exon_variant,,ENST00000585604,;SYT4,non_coding_transcript_exon_variant,,ENST00000589479,;SYT4,intron_variant,,ENST00000586678,;SYT4,downstream_gene_variant,,ENST00000591820,; G ENST00000255224 Transcript missense_variant 1286/4110 917/1278 306/425 V/A gTg/gCg 1 -1 SYT4 HGNC HGNC:11512 protein_coding YES CCDS11922.1 ENSP00000255224 Q9H2B2 UPI000013669E NM_020783.3 deleterious(0.02) 3/4 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF114,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 43271765 43271765 A G 1 0 0 0 0 1 0 0 0 15870 159 6 5 5 SYT4 18 43271765 Missense_Mutation SNP A C3N-01405_T 7100702 43271765 37101520 365 22839 TCF4 0 . GRCh38 18 55279580 55279580 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.932G>C p.Ser311Thr p.S311T ENST00000398339 10/21 410 364 46 380 380 0 strelka-varscan-mutect TCF4,missense_variant,p.Ser185Thr,ENST00000636400,;TCF4,missense_variant,p.Ser209Thr,ENST00000356073,NM_003199.2;TCF4,missense_variant,p.Ser125Thr,ENST00000616053,;TCF4,missense_variant,p.Ser209Thr,ENST00000635822,;TCF4,missense_variant,p.Ser209Thr,ENST00000638154,;TCF4,missense_variant,p.Ser79Thr,ENST00000636822,;TCF4,missense_variant,p.Ser209Thr,ENST00000629387,;TCF4,missense_variant,p.Ser209Thr,ENST00000564999,;TCF4,missense_variant,p.Ser209Thr,ENST00000354452,NM_001083962.1;TCF4,missense_variant,p.Ser49Thr,ENST00000570287,NM_001243235.1;TCF4,missense_variant,p.Ser185Thr,ENST00000537578,NM_001243227.1;TCF4,missense_variant,p.Ser215Thr,ENST00000564403,NM_001243228.1;TCF4,missense_variant,p.Ser184Thr,ENST00000568740,;TCF4,missense_variant,p.Ser185Thr,ENST00000540999,NM_001306207.1;TCF4,missense_variant,p.Ser311Thr,ENST00000398339,NM_001243226.2;TCF4,missense_variant,p.Ser167Thr,ENST00000543082,NM_001243231.1;TCF4,missense_variant,p.Ser185Thr,ENST00000568673,;TCF4,missense_variant,p.Ser49Thr,ENST00000457482,NM_001243234.1;TCF4,missense_variant,p.Ser125Thr,ENST00000565018,;TCF4,missense_variant,p.Ser138Thr,ENST00000544241,NM_001243232.1;TCF4,missense_variant,p.Ser79Thr,ENST00000561992,NM_001243233.1;TCF4,missense_variant,p.Ser149Thr,ENST00000566279,;TCF4,missense_variant,p.Ser207Thr,ENST00000566286,NM_001243230.1;TCF4,missense_variant,p.Ser79Thr,ENST00000537856,;TCF4,missense_variant,p.Ser149Thr,ENST00000567880,;TCF4,missense_variant,p.Ser138Thr,ENST00000564228,NM_001306208.1;TCF4,missense_variant,p.Ser79Thr,ENST00000570177,;TCF4,missense_variant,p.Ser49Thr,ENST00000561831,NM_001243236.1;TCF4,missense_variant,p.Ser49Thr,ENST00000630720,;TCF4,missense_variant,p.Ser79Thr,ENST00000628078,;TCF4,missense_variant,p.Ser79Thr,ENST00000562030,;TCF4,missense_variant,p.Ser196Thr,ENST00000566514,;TCF4,missense_variant,p.Ser185Thr,ENST00000627685,;TCF4,missense_variant,p.Ser213Thr,ENST00000568169,;TCF4,missense_variant,p.Ser209Thr,ENST00000626595,;TCF4,missense_variant,p.Ser79Thr,ENST00000630712,;TCF4,missense_variant,p.Ser79Thr,ENST00000628636,;TCF4,missense_variant,p.Ser79Thr,ENST00000629343,;TCF4,missense_variant,p.Ser185Thr,ENST00000565908,;TCF4,missense_variant,p.Ser79Thr,ENST00000625849,;TCF4,missense_variant,p.Ser132Thr,ENST00000630319,;TCF4,missense_variant,p.Ser139Thr,ENST00000630828,;TCF4,missense_variant,p.Ser79Thr,ENST00000566777,;TCF4,missense_variant,p.Ser79Thr,ENST00000630268,;TCF4,missense_variant,p.Ser79Thr,ENST00000625925,;TCF4,missense_variant,p.Ser79Thr,ENST00000562607,;TCF4,missense_variant,p.Ser79Thr,ENST00000568186,;TCF4,missense_variant,p.Ser79Thr,ENST00000569012,;TCF4,missense_variant,p.Ser79Thr,ENST00000562638,;TCF4,5_prime_UTR_variant,,ENST00000637169,;TCF4,5_prime_UTR_variant,,ENST00000626584,;TCF4,upstream_gene_variant,,ENST00000570146,;TCF4,downstream_gene_variant,,ENST00000626425,;TCF4,non_coding_transcript_exon_variant,,ENST00000637239,;TCF4,non_coding_transcript_exon_variant,,ENST00000637250,;TCF4,non_coding_transcript_exon_variant,,ENST00000635990,;TCF4,non_coding_transcript_exon_variant,,ENST00000563760,;TCF4,non_coding_transcript_exon_variant,,ENST00000565580,;TCF4,non_coding_transcript_exon_variant,,ENST00000631043,;TCF4,non_coding_transcript_exon_variant,,ENST00000637068,;TCF4,intron_variant,,ENST00000627136,;TCF4,missense_variant,p.Ala76Pro,ENST00000637923,;TCF4,missense_variant,p.Ser49Thr,ENST00000628689,;TCF4,3_prime_UTR_variant,,ENST00000636751,;TCF4,3_prime_UTR_variant,,ENST00000637115,;TCF4,non_coding_transcript_exon_variant,,ENST00000563686,;TCF4,non_coding_transcript_exon_variant,,ENST00000562680,; G ENST00000398339 Transcript missense_variant 1062/2551 932/2322 311/773 S/T aGc/aCc 1 -1 TCF4 HGNC HGNC:11634 protein_coding YES CCDS58631.1 ENSP00000381382 E9PH57 UPI0000EE5B9B NM_001243226.2 tolerated(0.15) 10/21 hmmpanther:PTHR11793:SF10,hmmpanther:PTHR11793 MODERATE 1 SNV 1 1 PASS rs1450223406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 55279580 55279580 C G 1 0 0 0 0 1 0 0 0 16102 797 28 4 4 TCF4 18 55279580 Missense_Mutation SNP C C3N-01405_T 12007815 55279580 25093705 366 22840 MALT1 0 . GRCh38 18 58741883 58741883 + Missense_Mutation SNP T T C novel C3N-01405_T C3N-01405_N T T c.1622T>C p.Leu541Pro p.L541P ENST00000348428 14/17 44 39 5 33 33 0 strelka-mutect MALT1,missense_variant,p.Leu541Pro,ENST00000348428,NM_006785.3;MALT1,missense_variant,p.Leu530Pro,ENST00000345724,NM_173844.2;RP11-126O1.4,intron_variant,,ENST00000588835,;MALT1,non_coding_transcript_exon_variant,,ENST00000589873,;MALT1,non_coding_transcript_exon_variant,,ENST00000587438,; C ENST00000348428 Transcript missense_variant 1880/9368 1622/2475 541/824 L/P cTt/cCt 1 1 MALT1 HGNC HGNC:6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 UPI000004D05E NM_006785.3 tolerated(0.09) 14/17 Pfam_domain:PF00656,hmmpanther:PTHR22576,hmmpanther:PTHR22576:SF29,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 58741883 58741883 T C 1 0 0 0 0 1 0 0 0 9123 1609 56 5 5 MALT1 18 58741883 Missense_Mutation SNP T C3N-01405_T 3462303 58741883 21631402 367 22841 ZNF532 0 . GRCh38 18 58953550 58953550 + Silent SNP G G C C3N-01405_T C3N-01405_N G G c.2901G>C p.= p.G967G ENST00000336078 8/11 116 100 16 116 116 0 varscan-mutect ZNF532,synonymous_variant,p.=,ENST00000336078,NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4;ZNF532,synonymous_variant,p.=,ENST00000589288,;ZNF532,synonymous_variant,p.=,ENST00000591083,;ZNF532,synonymous_variant,p.=,ENST00000591808,;ZNF532,synonymous_variant,p.=,ENST00000591230,;ZNF532,intron_variant,,ENST00000586997,;ZNF532,non_coding_transcript_exon_variant,,ENST00000592249,;ZNF532,synonymous_variant,p.=,ENST00000585662,; C ENST00000336078 Transcript synonymous_variant 3677/6696 2901/3906 967/1301 G ggG/ggC COSM1289153 1 1 ZNF532 HGNC HGNC:30940 protein_coding YES CCDS11969.1 ENSP00000338217 Q9HCE3 A0A024R283 UPI000013D30C NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4 8/11 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF204 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 74 58953550 58953550 G C 1 0 0 0 0 0 0 0 1 18545 1190 42 4 4 ZNF532 18 58953550 Silent SNP G C3N-01405_T 211667 58953550 21419735 368 22842 HCN2 0 . GRCh38 19 616296 616296 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.2492C>A p.Ala831Asp p.A831D ENST00000251287 8/8 54 47 7 67 67 0 strelka-varscan-mutect HCN2,missense_variant,p.Ala831Asp,ENST00000251287,NM_001194.3;POLRMT,downstream_gene_variant,,ENST00000588649,NM_005035.3;POLRMT,downstream_gene_variant,,ENST00000590336,;POLRMT,downstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000589961,;POLRMT,downstream_gene_variant,,ENST00000592633,; A ENST00000251287 Transcript missense_variant 2545/3408 2492/2670 831/889 A/D gCc/gAc 1 1 HCN2 HGNC HGNC:4846 protein_coding YES CCDS12035.1 ENSP00000251287 Q9UL51 UPI000013CCF6 NM_001194.3 deleterious_low_confidence(0.04) 8/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF372 MODERATE 1 SNV 1 1 PASS rs1381620056 . 0 195 6 8 0 0 0 0 -12.57115 0.9584356 1 1 1 0 A 3 1 74 616296 616296 C A 1 0 0 0 0 1 0 0 0 6884 739 26 2 2 HCN2 19 616296 Missense_Mutation SNP C C3N-01405_T 616296 58001320 369 22843 SAFB 0 . GRCh38 19 5668185 5668185 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.2648G>T p.Gly883Val p.G883V ENST00000588852 21/21 140 111 29 111 111 0 strelka-varscan-mutect SAFB,missense_variant,p.Gly881Val,ENST00000292123,NM_001320572.1,NM_002967.3;SAFB,missense_variant,p.Gly882Val,ENST00000592224,NM_001201339.1;SAFB,missense_variant,p.Gly883Val,ENST00000588852,NM_001201338.1;SAFB,missense_variant,p.Gly814Val,ENST00000454510,NM_001201340.1;SAFB,downstream_gene_variant,,ENST00000589006,;SAFB,3_prime_UTR_variant,,ENST00000589863,NM_001320571.1;SAFB,non_coding_transcript_exon_variant,,ENST00000591991,;SAFB,non_coding_transcript_exon_variant,,ENST00000592555,;SAFB,downstream_gene_variant,,ENST00000586281,; T ENST00000588852 Transcript missense_variant 2701/2842 2648/2754 883/917 G/V gGg/gTg 1 1 SAFB HGNC HGNC:10520 protein_coding YES CCDS59339.1 ENSP00000467423 Q15424 UPI0000E5BE82 NM_001201338.1 deleterious(0) 21/21 hmmpanther:PTHR15683:SF6,hmmpanther:PTHR15683 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 5668185 5668185 G T 1 0 0 0 0 1 0 0 0 14065 1232 43 2 2 SAFB 19 5668185 Missense_Mutation SNP G C3N-01405_T 5051889 5668185 52949431 370 22844 ADGRE1 0 . GRCh38 19 6896523 6896523 + Missense_Mutation SNP C C A C3N-01405_T C3N-01405_N C C c.220C>A p.Pro74Thr p.P74T ENST00000312053 3/21 99 69 30 87 87 0 strelka-varscan-mutect ADGRE1,missense_variant,p.Pro74Thr,ENST00000312053,NM_001974.4;ADGRE1,missense_variant,p.Pro74Thr,ENST00000381404,NM_001256252.1;ADGRE1,missense_variant,p.Pro74Thr,ENST00000250572,NM_001256253.1;ADGRE1,missense_variant,p.Pro74Thr,ENST00000381407,NM_001256254.1;ADGRE1,missense_variant,p.Pro74Thr,ENST00000450315,NM_001256255.1;ADGRE1,missense_variant,p.Pro40Thr,ENST00000595026,;CTC-312O10.3,non_coding_transcript_exon_variant,,ENST00000624996,;ADGRE1,non_coding_transcript_exon_variant,,ENST00000601198,;ADGRE1,non_coding_transcript_exon_variant,,ENST00000596944,;CTC-312O10.2,upstream_gene_variant,,ENST00000595362,; A ENST00000312053 Transcript missense_variant 257/3128 220/2661 74/886 P/T Cca/Aca COSM713972 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 tolerated(0.11) 3/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 6896523 6896523 C A 1 0 0 0 0 1 0 0 0 359 855 30 2 2 ADGRE1 19 6896523 Missense_Mutation SNP C C3N-01405_T 1228338 6896523 51721093 371 22845 INSR 0 . GRCh38 19 7117253 7117253 + Nonsense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.3952G>T p.Glu1318Ter p.E1318* ENST00000302850 22/22 308 244 64 269 269 0 strelka-varscan-mutect INSR,stop_gained,p.Glu1306Ter,ENST00000341500,NM_001079817.1;INSR,stop_gained,p.Glu1318Ter,ENST00000302850,NM_000208.2;INSR,downstream_gene_variant,,ENST00000601099,; A ENST00000302850 Transcript stop_gained 4095/4721 3952/4149 1318/1382 E/* Gag/Tag 1 -1 INSR HGNC HGNC:6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 UPI000020324D NM_000208.2 22/22 PIRSF_domain:PIRSF000620,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF325,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 7117253 7117253 C A 1 0 0 0 0 0 1 0 0 7675 864 30 2 2 INSR 19 7117253 Nonsense_Mutation SNP C C3N-01405_T 220730 7117253 51500363 372 22846 EVI5L 0 . GRCh38 19 7847921 7847921 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.327G>T p.Lys109Asn p.K109N ENST00000538904 2/19 70 59 11 50 50 0 strelka-varscan-mutect EVI5L,missense_variant,p.Lys109Asn,ENST00000270530,NM_145245.4;EVI5L,missense_variant,p.Lys109Asn,ENST00000538904,NM_001159944.2;EVI5L,upstream_gene_variant,,ENST00000599036,;EVI5L,upstream_gene_variant,,ENST00000601984,;EVI5L,upstream_gene_variant,,ENST00000597440,; T ENST00000538904 Transcript missense_variant,splice_region_variant 327/2418 327/2418 109/805 K/N aaG/aaT 1 1 EVI5L HGNC HGNC:30464 protein_coding YES CCDS54209.1 ENSP00000445905 Q96CN4 UPI00019145BF NM_001159944.2 deleterious(0) 2/19 Low_complexity_(Seg):seg,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF254,Gene3D:2qq8A02,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS rs1226460301 . 0 205 4 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 74 7847921 7847921 G T 1 0 0 0 0 1 0 0 0 5157 1014 35 2 2 EVI5L 19 7847921 Missense_Mutation SNP G C3N-01405_T 730668 7847921 50769695 373 22847 MUC16 0 . GRCh38 19 8922971 8922971 + Missense_Mutation SNP C C G novel C3N-01405_T C3N-01405_N C C c.36290G>C p.Arg12097Thr p.R12097T ENST00000397910 9/84 136 96 40 180 180 0 strelka-varscan-mutect MUC16,missense_variant,p.Arg12097Thr,ENST00000397910,NM_024690.2; G ENST00000397910 Transcript missense_variant 36494/43816 36290/43524 12097/14507 R/T aGg/aCg 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 9/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,SMART_domains:SM00200,Superfamily_domains:0047452 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 8922971 8922971 C G 1 0 0 0 0 1 0 0 0 9972 681 24 4 4 MUC16 19 8922971 Missense_Mutation SNP C C3N-01405_T 1075050 8922971 49694645 374 22848 MUC16 0 . GRCh38 19 8949971 8949971 + Missense_Mutation SNP C C A rs747191511 C3N-01405_T C3N-01405_N C C c.26799G>T p.Gln8933His p.Q8933H ENST00000397910 3/84 185 145 40 200 200 0 strelka-varscan-mutect MUC16,missense_variant,p.Gln8933His,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 27003/43816 26799/43524 8933/14507 Q/H caG/caT rs747191511 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS rs747191511 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 8949971 8949971 C A 1 0 0 0 0 1 0 0 0 9972 796 28 2 2 MUC16 19 8949971 Missense_Mutation SNP C C3N-01405_T 27000 8949971 49667645 375 22849 MUC16 0 . GRCh38 19 8972433 8972433 + Silent SNP A A T novel C3N-01405_T C3N-01405_N A A c.8706T>A p.= p.T2902T ENST00000397910 1/84 130 98 32 134 133 1 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 8910/43816 8706/43524 2902/14507 T acT/acA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 8972433 8972433 A T 1 0 0 0 0 0 0 0 1 9972 407 15 4 4 MUC16 19 8972433 Silent SNP A C3N-01405_T 22462 8972433 49645183 376 22850 ANGPTL6 0 . GRCh38 19 10096085 10096085 + Missense_Mutation SNP A A T rs771917209 C3N-01405_T C3N-01405_N A A c.479T>A p.Leu160Gln p.L160Q ENST00000253109 2/6 76 61 15 53 53 0 strelka-varscan-mutect ANGPTL6,missense_variant,p.Leu160Gln,ENST00000253109,NM_031917.2;ANGPTL6,missense_variant,p.Leu160Gln,ENST00000592641,NM_001321411.1;ANGPTL6,missense_variant,p.Leu160Gln,ENST00000589181,;C19orf66,downstream_gene_variant,,ENST00000397881,;C19orf66,downstream_gene_variant,,ENST00000253110,NM_018381.2;C19orf66,downstream_gene_variant,,ENST00000591813,NM_001308277.1;C19orf66,downstream_gene_variant,,ENST00000593131,;ANGPTL6,non_coding_transcript_exon_variant,,ENST00000586910,;C19orf66,downstream_gene_variant,,ENST00000585919,;C19orf66,downstream_gene_variant,,ENST00000586730,;C19orf66,downstream_gene_variant,,ENST00000587710,; T ENST00000253109 Transcript missense_variant 718/1900 479/1413 160/470 L/Q cTg/cAg rs771917209 1 -1 ANGPTL6 HGNC HGNC:23140 protein_coding YES CCDS12224.1 ENSP00000253109 Q8NI99 A0A024R7A9 UPI000004BA54 NM_031917.2 deleterious(0) 2/6 hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF209 MODERATE 1 SNV 1 1 PASS rs771917209 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 10096085 10096085 A T 1 0 0 0 0 1 0 0 0 716 188 7 4 4 ANGPTL6 19 10096085 Missense_Mutation SNP A C3N-01405_T 1123652 10096085 48521531 377 22851 KEAP1 0 . GRCh38 19 10499890 10499903 + Frame_Shift_Del DEL GCCATGCTGGGAGG GCCATGCTGGGAGG - novel C3N-01405_T C3N-01405_N GCCATGCTGGGAGG GCCATGCTGGGAGG c.131_144delCCTCCCAGCATGGC p.Pro44GlnfsTer30 p.P44Qfs*30 ENST00000171111 2/6 77 67 10 65 65 0 sindel-pindel KEAP1,frameshift_variant,p.Pro44GlnfsTer30,ENST00000171111,NM_203500.1;KEAP1,frameshift_variant,p.Pro44GlnfsTer30,ENST00000393623,NM_012289.3;KEAP1,frameshift_variant,p.Pro44GlnfsTer30,ENST00000591419,;KEAP1,frameshift_variant,p.Pro44GlnfsTer30,ENST00000592055,;KEAP1,frameshift_variant,p.Pro44GlnfsTer30,ENST00000591039,;KEAP1,upstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000585845,; - ENST00000171111 Transcript frameshift_variant 679-692/2955 131-144/1875 44-48/624 PSQHG/X cCCTCCCAGCATGGC/c 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 2/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037 HIGH 1 deletion 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99102 0.9999999 1 1 1 0 - 7 5 74 10499890 10499890 GCCATGCTGGGAGG - 1 0 1 0 1 0 0 0 0 8061 1306 46 0 0 KEAP1 19 10499890 Frame_Shift_Del DEL GCCATGCTGGGAGG C3N-01405_T 403805 10499890 48117726 378 22852 CACNA1A 0 . GRCh38 19 13255182 13255182 + Nonsense_Mutation SNP G G T rs370203027 C3N-01405_T C3N-01405_N G G c.4668C>A p.Tyr1556Ter p.Y1556* ENST00000360228 29/47 99 70 29 87 87 0 strelka-varscan-mutect CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000638009,NM_001127221.1;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000635895,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000637769,;CACNA1A,stop_gained,p.Tyr1556Ter,ENST00000360228,NM_001127222.1;CACNA1A,stop_gained,p.Tyr1560Ter,ENST00000614285,;CACNA1A,stop_gained,p.Tyr1510Ter,ENST00000637736,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000636389,;CACNA1A,stop_gained,p.Tyr1560Ter,ENST00000638029,NM_023035.2;CACNA1A,stop_gained,p.Tyr1560Ter,ENST00000637432,NM_000068.3;CACNA1A,stop_gained,p.Tyr1558Ter,ENST00000573710,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000635727,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000636012,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000637276,;CACNA1A,stop_gained,p.Tyr1558Ter,ENST00000637927,;CACNA1A,stop_gained,p.Tyr1557Ter,ENST00000636549,NM_001174080.1;CACNA1A,stop_gained,p.Tyr43Ter,ENST00000587525,;CACNA1A,stop_gained,p.Tyr22Ter,ENST00000637819,;CACNA1A,intron_variant,,ENST00000637297,;CACNA1A,upstream_gene_variant,,ENST00000585802,;CACNA1A,upstream_gene_variant,,ENST00000636473,;CACNA1A,upstream_gene_variant,,ENST00000574822,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637004,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636816,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635742,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635917,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637692,;CACNA1A,downstream_gene_variant,,ENST00000590205,;CACNA1A,downstream_gene_variant,,ENST00000637168,;CACNA1A,downstream_gene_variant,,ENST00000636984,;CACNA1A,upstream_gene_variant,,ENST00000573891,;CACNA1A,upstream_gene_variant,,ENST00000636058,; T ENST00000360228 Transcript stop_gained 4903/8627 4668/7521 1556/2506 Y/* taC/taA rs370203027,COSM3529028,COSM3529029,COSM3529030,COSM3529031 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 29/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Gene3D:1.20.120.350 0,1,1,1,1 HIGH 1 SNV 1 0,1,1,1,1 1 PASS rs370203027 . 0 203 5 2 0 0 0 0 -20 0.9999893 1 1 1 0 T 4 4 74 13255182 13255182 G T 1 0 0 0 0 0 1 0 0 2226 1256 44 2 2 CACNA1A 19 13255182 Nonsense_Mutation SNP G C3N-01405_T 2755292 13255182 45362434 379 22853 COMP 0 . GRCh38 19 18790922 18790922 + Silent SNP G G A novel C3N-01405_T C3N-01405_N G G c.93C>T p.= p.G31G ENST00000222271 2/19 317 272 45 220 220 0 strelka-varscan-mutect COMP,synonymous_variant,p.=,ENST00000222271,NM_000095.2;COMP,synonymous_variant,p.=,ENST00000425807,;COMP,5_prime_UTR_variant,,ENST00000542601,;COMP,upstream_gene_variant,,ENST00000612179,; A ENST00000222271 Transcript synonymous_variant 138/2461 93/2274 31/757 G ggC/ggT 1 -1 COMP HGNC HGNC:2227 protein_coding YES CCDS12385.1 ENSP00000222271 P49747 UPI000013C7F6 NM_000095.2 2/19 Gene3D:1.20.5.10,Pfam_domain:PF11598,Superfamily_domains:0053531 LOW 1 SNV 1 1 PASS rs1172549461 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 18790922 18790922 G A 1 0 0 0 0 0 0 0 1 3516 1190 42 3 3 COMP 19 18790922 Silent SNP G C3N-01405_T 5535740 18790922 39826694 380 22854 HKR1 0 . GRCh38 19 37363007 37363007 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.1212G>C p.Lys404Asn p.K404N ENST00000324411 6/6 178 132 46 185 185 0 strelka-varscan-mutect HKR1,missense_variant,p.Lys131Asn,ENST00000591471,;HKR1,missense_variant,p.Lys404Asn,ENST00000324411,NM_181786.2;HKR1,missense_variant,p.Lys131Asn,ENST00000544914,;HKR1,missense_variant,p.Lys385Asn,ENST00000392153,;HKR1,missense_variant,p.Lys343Asn,ENST00000541583,;HKR1,missense_variant,p.Lys386Asn,ENST00000589392,;HKR1,intron_variant,,ENST00000591134,;HKR1,downstream_gene_variant,,ENST00000591259,;HKR1,downstream_gene_variant,,ENST00000590582,;HKR1,downstream_gene_variant,,ENST00000592768,;HKR1,downstream_gene_variant,,ENST00000585623,;HKR1,downstream_gene_variant,,ENST00000592168,;HKR1,downstream_gene_variant,,ENST00000591391,;HKR1,downstream_gene_variant,,ENST00000591417,;HKR1,downstream_gene_variant,,ENST00000586897,;HKR1,non_coding_transcript_exon_variant,,ENST00000588820,;HKR1,downstream_gene_variant,,ENST00000590570,; C ENST00000324411 Transcript missense_variant 1481/2929 1212/1980 404/659 K/N aaG/aaC 1 1 HKR1 HGNC HGNC:4928 protein_coding YES CCDS12502.1 ENSP00000315505 P10072 UPI00001AE470 NM_181786.2 deleterious(0) 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF129,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 37363007 37363007 G C 1 0 0 0 0 1 0 0 0 7083 933 33 4 4 HKR1 19 37363007 Missense_Mutation SNP G C3N-01405_T 18572085 37363007 21254609 381 22855 AXL 0 . GRCh38 19 41257528 41257528 + Silent SNP A A G novel C3N-01405_T C3N-01405_N A A c.2232A>G p.= p.T744T ENST00000301178 19/20 224 173 51 181 181 0 strelka-varscan-mutect AXL,synonymous_variant,p.=,ENST00000301178,NM_021913.4;AXL,synonymous_variant,p.=,ENST00000359092,NM_001699.5;AXL,synonymous_variant,p.=,ENST00000593513,NM_001278599.1;HNRNPUL1,upstream_gene_variant,,ENST00000352456,;HNRNPUL1,upstream_gene_variant,,ENST00000595018,NM_144732.3; G ENST00000301178 Transcript synonymous_variant 2422/4737 2232/2685 744/894 T acA/acG 1 1 AXL HGNC HGNC:905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 UPI000014319B NM_021913.4 19/20 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF323,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 74 41257528 41257528 A G 1 0 0 0 0 0 0 0 1 1395 117 5 5 5 AXL 19 41257528 Silent SNP A C3N-01405_T 3894521 41257528 17360088 382 22856 TGFB1 0 . GRCh38 19 41348354 41348354 + Frame_Shift_Del DEL C C - novel C3N-01405_T C3N-01405_N C C c.457delG p.Ala153GlnfsTer6 p.A153Qfs*6 ENST00000221930 2/7 316 225 91 327 327 0 sindel-varindel-pindel TGFB1,frameshift_variant,p.Ala153GlnfsTer6,ENST00000221930,NM_000660.5;TMEM91,upstream_gene_variant,,ENST00000539627,;CTC-435M10.3,upstream_gene_variant,,ENST00000604424,;TGFB1,upstream_gene_variant,,ENST00000600196,;TGFB1,upstream_gene_variant,,ENST00000597453,; - ENST00000221930 Transcript frameshift_variant 1324/2769 457/1173 153/390 A/X Gca/ca 1 -1 TGFB1 HGNC HGNC:11766 protein_coding YES CCDS33031.1 ENSP00000221930 P01137 UPI000013C7E1 NM_000660.5 2/7 Low_complexity_(Seg):seg,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF125,PIRSF_domain:PIRSF001787,Pfam_domain:PF00688,Prints_domain:PR01424 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 41348354 41348354 C - 1 0 1 0 1 0 0 0 0 16249 739 26 0 0 TGFB1 19 41348354 Frame_Shift_Del DEL C C3N-01405_T 90826 41348354 17269262 383 22857 GPR32 0 . GRCh38 19 50771482 50771482 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.882G>A p.Met294Ile p.M294I ENST00000270590 1/1 150 132 18 160 160 0 strelka-varscan-mutect GPR32,missense_variant,p.Met294Ile,ENST00000270590,NM_001506.2;CTD-2568A17.1,downstream_gene_variant,,ENST00000563228,; A ENST00000270590 Transcript missense_variant 1019/1269 882/1071 294/356 M/I atG/atA 1 1 GPR32 HGNC HGNC:4487 protein_coding YES CCDS12801.1 ENSP00000270590 O75388 H9NIL6 UPI000005045C NM_001506.2 tolerated(0.16) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF27,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 50771482 50771482 G A 1 0 0 0 0 1 0 0 0 6572 1319 46 3 3 GPR32 19 50771482 Missense_Mutation SNP G C3N-01405_T 9423128 50771482 7846134 384 22858 PPP6R1 0 . GRCh38 19 55230835 55230835 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.2509C>G p.Pro837Ala p.P837A ENST00000412770 22/24 157 140 17 135 135 0 strelka-varscan-mutect PPP6R1,missense_variant,p.Pro837Ala,ENST00000412770,NM_014931.3;PPP6R1,missense_variant,p.Pro837Ala,ENST00000587283,;TMEM86B,upstream_gene_variant,,ENST00000327042,NM_173804.4;MIR6804,downstream_gene_variant,,ENST00000614724,;PPP6R1,non_coding_transcript_exon_variant,,ENST00000587457,;CTD-2587H24.14,upstream_gene_variant,,ENST00000586923,;TMEM86B,upstream_gene_variant,,ENST00000585416,;TMEM86B,upstream_gene_variant,,ENST00000589190,; C ENST00000412770 Transcript missense_variant 3076/3961 2509/2646 837/881 P/A Ccc/Gcc 1 -1 PPP6R1 HGNC HGNC:29195 protein_coding YES CCDS46186.1 ENSP00000414202 Q9UPN7 UPI0000202C6D NM_014931.3 tolerated_low_confidence(0.26) 22/24 hmmpanther:PTHR12634:SF13,hmmpanther:PTHR12634 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 55230835 55230835 G C 1 0 0 0 0 1 0 0 0 12534 1203 42 4 4 PPP6R1 19 55230835 Missense_Mutation SNP G C3N-01405_T 4459353 55230835 3386781 385 22859 IL11 0 . GRCh38 19 55366103 55366103 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.504G>T p.Trp168Cys p.W168C ENST00000264563 5/5 172 127 45 125 124 1 strelka-varscan-mutect IL11,missense_variant,p.Trp168Cys,ENST00000264563,NM_000641.3;IL11,missense_variant,p.Trp168Cys,ENST00000585513,;IL11,missense_variant,p.Trp89Cys,ENST00000590625,NM_001267718.1;FAM71E2,upstream_gene_variant,,ENST00000424985,NM_001145402.1;IL11,downstream_gene_variant,,ENST00000587093,;FAM71E2,upstream_gene_variant,,ENST00000585734,; A ENST00000264563 Transcript missense_variant 567/2281 504/600 168/199 W/C tgG/tgT 1 -1 IL11 HGNC HGNC:5966 protein_coding YES CCDS12923.1 ENSP00000264563 P20809 A8K3F7 UPI000000D8E5 NM_000641.3 deleterious(0) 5/5 Pfam_domain:PF07400,hmmpanther:PTHR16922,hmmpanther:PTHR16922:SF0,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 55366103 55366103 C A 1 0 0 0 0 1 0 0 0 7530 624 22 2 2 IL11 19 55366103 Missense_Mutation SNP C C3N-01405_T 135268 55366103 3251513 386 22860 ZSCAN5A 0 . GRCh38 19 56222031 56222031 + Silent SNP C C A rs765875730 C3N-01405_T C3N-01405_N C C c.1035G>T p.= p.P345P ENST00000391713 5/5 257 182 75 207 207 0 strelka-varscan-mutect ZSCAN5A,synonymous_variant,p.=,ENST00000391713,NM_024303.1;ZSCAN5A,synonymous_variant,p.=,ENST00000587340,NM_001322072.1;ZSCAN5A,synonymous_variant,p.=,ENST00000592355,;ZSCAN5A,synonymous_variant,p.=,ENST00000587492,;ZSCAN5A,downstream_gene_variant,,ENST00000592679,;ZSCAN5A,downstream_gene_variant,,ENST00000593106,;ZSCAN5A,downstream_gene_variant,,ENST00000592509,;ZSCAN5A,downstream_gene_variant,,ENST00000588442,;ZSCAN5A,downstream_gene_variant,,ENST00000588955,;ZSCAN5A,downstream_gene_variant,,ENST00000592101,;CTD-2086L14.1,upstream_gene_variant,,ENST00000474329,; A ENST00000391713 Transcript synonymous_variant 1201/3562 1035/1491 345/496 P ccG/ccT rs765875730 1 -1 ZSCAN5A HGNC HGNC:23710 protein_coding YES CCDS12941.1 ENSP00000375593 Q9BUG6 A0A024R4S6 UPI0000072024 NM_024303.1 5/5 hmmpanther:PTHR10032:SF164,hmmpanther:PTHR10032 LOW 1 SNV 1 1 PASS rs765875730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 56222031 56222031 C A 1 0 0 0 0 0 0 0 1 18837 639 23 1 1 ZSCAN5A 19 56222031 Silent SNP C C3N-01405_T 855928 56222031 2395585 387 22861 ZIK1 0 . GRCh38 19 57588646 57588646 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.180T>A p.Phe60Leu p.F60L ENST00000597850 3/4 31 18 13 28 28 0 strelka-varscan-mutect ZIK1,missense_variant,p.Phe60Leu,ENST00000597850,NM_001010879.2;ZIK1,missense_variant,p.Phe47Leu,ENST00000536878,NM_001321145.1;ZIK1,missense_variant,p.Phe5Leu,ENST00000599456,;ZIK1,missense_variant,p.Phe41Leu,ENST00000600053,;ZIK1,missense_variant,p.Phe33Leu,ENST00000598689,;ZIK1,intron_variant,,ENST00000307468,;ZIK1,downstream_gene_variant,,ENST00000597219,;ZIK1,downstream_gene_variant,,ENST00000598726,; A ENST00000597850 Transcript missense_variant 395/4181 180/1464 60/487 F/L ttT/ttA 1 1 ZIK1 HGNC HGNC:33104 protein_coding YES CCDS33135.1 ENSP00000472867 Q3SY52 UPI00001609B2 NM_001010879.2 tolerated(0.37) 3/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF219,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 57588646 57588646 T A 1 0 0 0 0 1 0 0 0 18261 1809 63 4 4 ZIK1 19 57588646 Missense_Mutation SNP T C3N-01405_T 1366615 57588646 1028970 388 22862 SNRPB 0 . GRCh38 20 2463814 2463814 + Missense_Mutation SNP A A G novel C3N-01405_T C3N-01405_N A A c.353T>C p.Val118Ala p.V118A ENST00000438552 4/7 149 118 31 109 109 0 strelka-varscan-mutect SNRPB,missense_variant,p.Val118Ala,ENST00000381342,NM_003091.3;SNRPB,missense_variant,p.Val118Ala,ENST00000438552,NM_198216.1;SNRPB,3_prime_UTR_variant,,ENST00000474384,;RP4-734P14.4,downstream_gene_variant,,ENST00000461548,; G ENST00000438552 Transcript missense_variant 516/1008 353/723 118/240 V/A gTt/gCt 1 -1 SNRPB HGNC HGNC:11153 protein_coding YES CCDS13026.1 ENSP00000412566 P14678 UPI00001351FF NM_198216.1 tolerated(0.35) 4/7 hmmpanther:PTHR10701:SF3,hmmpanther:PTHR10701,PIRSF_domain:PIRSF037187,Superfamily_domains:SSF50182 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 74 2463814 2463814 A G 1 0 0 0 0 1 0 0 0 15181 43 2 5 5 SNRPB 20 2463814 Missense_Mutation SNP A C3N-01405_T 2463814 61980353 389 22863 XRN2 0 . GRCh38 20 21365484 21365484 + Silent SNP A A T novel C3N-01405_T C3N-01405_N A A c.2319A>T p.= p.G773G ENST00000377191 25/30 164 131 33 149 149 0 strelka-varscan-mutect XRN2,synonymous_variant,p.=,ENST00000377191,NM_001317960.1,NM_012255.3; T ENST00000377191 Transcript synonymous_variant 2414/3437 2319/2853 773/950 G ggA/ggT 1 1 XRN2 HGNC HGNC:12836 protein_coding YES CCDS13144.1 ENSP00000366396 Q9H0D6 UPI0000037D02 NM_001317960.1,NM_012255.3 25/30 PIRSF_domain:PIRSF037239,hmmpanther:PTHR12341,hmmpanther:PTHR12341:SF35 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 21365484 21365484 A T 1 0 0 0 0 0 0 0 1 18018 318 11 4 4 XRN2 20 21365484 Silent SNP A C3N-01405_T 18901670 21365484 43078683 390 22864 NKX2-4 0 . GRCh38 20 21396257 21396257 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.719A>T p.His240Leu p.H240L ENST00000351817 2/2 511 451 60 393 393 0 strelka-varscan-mutect NKX2-4,missense_variant,p.His240Leu,ENST00000351817,NM_033176.1;RP11-227D2.3,upstream_gene_variant,,ENST00000419666,;RP11-227D2.3,upstream_gene_variant,,ENST00000552439,; A ENST00000351817 Transcript missense_variant 1348/2238 719/1065 240/354 H/L cAc/cTc 1 -1 NKX2-4 HGNC HGNC:7837 protein_coding YES CCDS42855.1 ENSP00000345147 Q9H2Z4 UPI00001AE6EC NM_033176.1 deleterious(0) 2/2 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50071,hmmpanther:PTHR24340,hmmpanther:PTHR24340:SF40,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00024 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 21396257 21396257 T A 1 0 0 0 0 1 0 0 0 10488 1696 59 4 4 NKX2-4 20 21396257 Missense_Mutation SNP T C3N-01405_T 30773 21396257 43047910 391 22865 SUN5 0 . GRCh38 20 32995649 32995649 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.504G>T p.Lys168Asn p.K168N ENST00000356173 8/13 222 206 16 190 190 0 strelka-varscan-mutect SUN5,missense_variant,p.Lys168Asn,ENST00000356173,NM_080675.3;SUN5,missense_variant,p.Lys143Asn,ENST00000375523,;SUN5,downstream_gene_variant,,ENST00000420875,;SUN5,downstream_gene_variant,,ENST00000375519,; A ENST00000356173 Transcript missense_variant 597/1254 504/1140 168/379 K/N aaG/aaT 1 -1 SUN5 HGNC HGNC:16252 protein_coding YES CCDS13209.1 ENSP00000348496 Q8TC36 UPI0000135D7C NM_080675.3 deleterious(0.03) 8/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12911,hmmpanther:PTHR12911:SF19 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.73038 0.9999997 1 1 1 0 A 3 1 74 32995649 32995649 C A 1 0 0 0 0 1 0 0 0 15780 796 28 2 2 SUN5 20 32995649 Missense_Mutation SNP C C3N-01405_T 11599392 32995649 31448518 392 22866 CHD6 0 . GRCh38 20 41564027 41564027 + Nonsense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.122C>G p.Ser41Ter p.S41* ENST00000373222 2/7 129 103 26 119 119 0 strelka-varscan-mutect CHD6,stop_gained,p.Ser41Ter,ENST00000373222,;CHD6,intron_variant,,ENST00000373233,NM_032221.4;CHD6,intron_variant,,ENST00000440647,;CHD6,intron_variant,,ENST00000482596,; C ENST00000373222 Transcript stop_gained 161/2477 122/1122 41/373 S/* tCa/tGa 1 -1 CHD6 HGNC HGNC:19057 protein_coding ENSP00000362319 Q8TD26 UPI0000470956 2/7 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 74 41564027 41564027 G C 1 0 0 0 0 0 1 0 0 3088 1294 45 4 4 CHD6 20 41564027 Nonsense_Mutation SNP G C3N-01405_T 8568378 41564027 22880140 393 22867 PTPRT 0 . GRCh38 20 42106867 42106867 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.3366G>T p.Met1122Ile p.M1122I ENST00000373198 25/32 199 183 16 153 153 0 strelka-varscan-mutect PTPRT,missense_variant,p.Met1122Ile,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Met1125Ile,ENST00000373193,;PTPRT,missense_variant,p.Met1093Ile,ENST00000373201,;PTPRT,missense_variant,p.Met1102Ile,ENST00000373190,;PTPRT,missense_variant,p.Met1113Ile,ENST00000373184,;PTPRT,missense_variant,p.Met1112Ile,ENST00000356100,;PTPRT,missense_variant,p.Met1103Ile,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Met721Ile,ENST00000612229,;PTPRT,missense_variant,p.Met738Ile,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 3602/12746 3366/4383 1122/1460 M/I atG/atT 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 25/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 42106867 42106867 C A 1 0 0 0 0 1 0 0 0 12967 594 21 2 2 PTPRT 20 42106867 Missense_Mutation SNP C C3N-01405_T 542840 42106867 22337300 394 22868 SRSF6 0 . GRCh38 20 43460054 43460054 + Nonsense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.403G>T p.Glu135Ter p.E135* ENST00000244020 4/6 268 212 56 234 234 0 strelka-varscan-mutect SRSF6,stop_gained,p.Glu135Ter,ENST00000244020,NM_006275.5;SRSF6,3_prime_UTR_variant,,ENST00000483871,; T ENST00000244020 Transcript stop_gained 509/4325 403/1035 135/344 E/* Gaa/Taa COSM5039658 1 1 SRSF6 HGNC HGNC:10788 protein_coding YES CCDS13318.1 ENSP00000244020 Q13247 UPI00001358C1 NM_006275.5 4/6 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF487,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 43460054 43460054 G T 1 0 0 0 0 0 1 0 0 15543 1291 45 2 2 SRSF6 20 43460054 Nonsense_Mutation SNP G C3N-01405_T 1353187 43460054 20984113 395 22869 OSER1 0 . GRCh38 20 44197195 44197195 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.736C>G p.Leu246Val p.L246V ENST00000372970 6/6 207 167 40 137 137 0 strelka-varscan-mutect OSER1,missense_variant,p.Leu246Val,ENST00000372970,;OSER1,missense_variant,p.Leu246Val,ENST00000255174,NM_016470.7; C ENST00000372970 Transcript missense_variant 917/1616 736/879 246/292 L/V Ctg/Gtg 1 -1 OSER1 HGNC HGNC:16105 protein_coding YES CCDS13327.1 ENSP00000362061 Q9NX31 UPI000004A0E4 tolerated(0.32) 6/6 hmmpanther:PTHR31383,hmmpanther:PTHR31383:SF2 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 44197195 44197195 G C 1 0 0 0 0 1 0 0 0 11353 933 33 4 4 OSER1 20 44197195 Missense_Mutation SNP G C3N-01405_T 737141 44197195 20246972 396 22870 RBPJL 0 . GRCh38 20 45316768 45316768 + Missense_Mutation SNP A A T novel C3N-01405_T C3N-01405_N A A c.1363A>T p.Ile455Phe p.I455F ENST00000343694 12/12 251 208 43 189 189 0 strelka-varscan-mutect RBPJL,missense_variant,p.Ile455Phe,ENST00000343694,NM_014276.3;RBPJL,missense_variant,p.Asn458Ile,ENST00000372741,NM_001281448.1;RBPJL,missense_variant,p.Ile454Phe,ENST00000372743,NM_001281449.1;RBPJL,missense_variant,p.Asn171Ile,ENST00000464504,;RBPJL,non_coding_transcript_exon_variant,,ENST00000622729,; T ENST00000343694 Transcript missense_variant 1435/2489 1363/1554 455/517 I/F Atc/Ttc 1 1 RBPJL HGNC HGNC:13761 protein_coding YES CCDS13349.1 ENSP00000341243 Q9UBG7 UPI0000047297 NM_014276.3 deleterious(0) 12/12 Gene3D:2.60.40.10,hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,Superfamily_domains:SSF81296 MODERATE 1 SNV 2 1 PASS rs1056529995 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 45316768 45316768 A T 1 0 0 0 0 1 0 0 0 13330 101 4 4 4 RBPJL 20 45316768 Missense_Mutation SNP A C3N-01405_T 1119573 45316768 19127399 397 22871 PREX1 0 . GRCh38 20 48676244 48676244 + Silent SNP G G T rs6019366 C3N-01405_T C3N-01405_N G G c.1614C>A p.= p.T538T ENST00000371941 14/40 316 265 51 235 235 0 strelka-varscan-mutect PREX1,synonymous_variant,p.=,ENST00000371941,NM_020820.3; T ENST00000371941 Transcript synonymous_variant 1637/6636 1614/4980 538/1659 T acC/acA rs6019366 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 14/40 PROSITE_profiles:PS50186,hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829,Gene3D:1.10.10.10,Pfam_domain:PF00610,SMART_domains:SM00049,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS rs6019366 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 74 48676244 48676244 G T 1 0 0 0 0 0 0 0 1 12610 987 35 2 2 PREX1 20 48676244 Silent SNP G C3N-01405_T 3359476 48676244 15767923 398 22872 PHACTR3 0 . GRCh38 20 59773278 59773278 + Splice_Site SNP G G T novel C3N-01405_T C3N-01405_N G G c.752-1G>T p.X251_splice ENST00000371015 105 98 7 64 64 0 strelka-varscan-mutect PHACTR3,splice_acceptor_variant,,ENST00000371015,NM_080672.4;PHACTR3,splice_acceptor_variant,,ENST00000395636,NM_183244.1;PHACTR3,splice_acceptor_variant,,ENST00000541461,NM_001281507.1;PHACTR3,splice_acceptor_variant,,ENST00000359926,NM_001199505.1;PHACTR3,splice_acceptor_variant,,ENST00000355648,NM_001199506.1;PHACTR3,splice_acceptor_variant,,ENST00000361300,NM_183246.1; T ENST00000371015 Transcript splice_acceptor_variant -/2728 752/1680 251/559 1 1 PHACTR3 HGNC HGNC:15833 protein_coding YES CCDS13480.1 ENSP00000360054 Q96KR7 UPI000006D452 NM_080672.4 5/12 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.10249 0.9999996 1 1 1 0 T 5 4 74 59773278 59773278 G T 1 0 0 0 0 0 0 1 0 11900 1014 35 2 2 PHACTR3 20 59773278 Splice_Site SNP G C3N-01405_T 11097034 59773278 4670889 399 22873 KCNQ2 0 . GRCh38 20 63414977 63414977 + Nonsense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.1451G>A p.Trp484Ter p.W484* ENST00000359125 13/17 371 313 58 235 235 0 strelka-varscan-mutect KCNQ2,stop_gained,p.Trp466Ter,ENST00000626839,NM_172106.1;KCNQ2,stop_gained,p.Trp484Ter,ENST00000359125,NM_172107.2;KCNQ2,stop_gained,p.Trp456Ter,ENST00000370224,;KCNQ2,stop_gained,p.Trp283Ter,ENST00000637193,;KCNQ2,stop_gained,p.Trp444Ter,ENST00000625514,;KCNQ2,stop_gained,p.Trp456Ter,ENST00000629241,;KCNQ2,stop_gained,p.Trp456Ter,ENST00000360480,NM_004518.4;KCNQ2,stop_gained,p.Trp454Ter,ENST00000344462,NM_172108.3;KCNQ2,stop_gained,p.Trp340Ter,ENST00000357249,;KCNQ2,stop_gained,p.Trp456Ter,ENST00000629676,;KCNQ2,stop_gained,p.Trp171Ter,ENST00000627221,;KCNQ2,stop_gained,p.Trp20Ter,ENST00000629318,;KCNQ2,upstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000635867,;KCNQ2,upstream_gene_variant,,ENST00000636499,;KCNQ2,downstream_gene_variant,,ENST00000637584,; T ENST00000359125 Transcript stop_gained 1578/3253 1451/2619 484/872 W/* tGg/tAg 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 13/17 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF6,Pfam_domain:PF03520 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 74 63414977 63414977 C T 1 0 0 0 0 0 1 0 0 7999 595 21 3 3 KCNQ2 20 63414977 Nonsense_Mutation SNP C C3N-01405_T 3641699 63414977 1029190 400 22874 TPTE 0 . GRCh38 21 10578535 10578535 + Silent SNP C C A rs759764021 C3N-01405_T C3N-01405_N C C c.957C>A p.= p.T319T ENST00000618007 17/24 385 345 40 405 405 0 varscan-mutect TPTE,synonymous_variant,p.=,ENST00000622113,NM_199259.3;TPTE,synonymous_variant,p.=,ENST00000618007,NM_199261.3;TPTE,synonymous_variant,p.=,ENST00000427445,NM_199260.3;TPTE,synonymous_variant,p.=,ENST00000612746,NM_001290224.1;AL078471.5,non_coding_transcript_exon_variant,,ENST00000612267,;CYCSP41,downstream_gene_variant,,ENST00000616920,; A ENST00000618007 Transcript synonymous_variant 1287/2150 957/1656 319/551 T acC/acA rs759764021 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 17/24 PROSITE_profiles:PS51181,hmmpanther:PTHR12305:SF56,hmmpanther:PTHR12305,Pfam_domain:PF00782,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS rs759764021 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 10578535 10578535 C A 1 0 0 0 0 0 0 0 1 16911 581 21 2 2 TPTE 21 10578535 Silent SNP C C3N-01405_T 10578535 36131448 401 22875 SON 0 . GRCh38 21 33553993 33553993 + Missense_Mutation SNP G G C novel C3N-01405_T C3N-01405_N G G c.4762G>C p.Asp1588His p.D1588H ENST00000356577 3/12 274 214 60 209 209 0 strelka-varscan-mutect SON,missense_variant,p.Asp1588His,ENST00000356577,NM_138927.2;SON,missense_variant,p.Asp1588His,ENST00000381679,NM_001291411.1;SON,missense_variant,p.Asp1588His,ENST00000300278,NM_032195.2;SON,missense_variant,p.Asp583His,ENST00000436227,;SON,intron_variant,,ENST00000381692,NM_001291412.1;SON,upstream_gene_variant,,ENST00000421541,;SON,downstream_gene_variant,,ENST00000290239,;SON,missense_variant,p.Asp1588His,ENST00000455528,; C ENST00000356577 Transcript missense_variant 5237/8813 4762/7281 1588/2426 D/H Gat/Cat 1 1 SON HGNC HGNC:11183 protein_coding YES CCDS13629.1 ENSP00000348984 P18583 UPI0000140BFD NM_138927.2 deleterious_low_confidence(0) 3/12 hmmpanther:PTHR23106,hmmpanther:PTHR23106:SF13 MODERATE 1 SNV 1 1 PASS rs1326366375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 33553993 33553993 G C 1 0 0 0 0 1 0 0 0 15248 1290 45 4 4 SON 21 33553993 Missense_Mutation SNP G C3N-01405_T 22975458 33553993 13155990 402 22876 KRTAP10-9 0 . GRCh38 21 44627991 44627991 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.820C>A p.Pro274Thr p.P274T ENST00000397911 1/1 211 153 58 135 135 0 strelka-varscan-mutect KRTAP10-9,missense_variant,p.Pro274Thr,ENST00000397911,NM_198690.2;KRTAP10-9,missense_variant,p.Pro174Thr,ENST00000616529,;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;KRTAP10-9,intron_variant,,ENST00000484861,; A ENST00000397911 Transcript missense_variant 869/1171 820/879 274/292 P/T Cct/Act 1 1 KRTAP10-9 HGNC HGNC:22971 protein_coding YES CCDS42961.1 ENSP00000381009 P60411 UPI000036709D NM_198690.2 deleterious(0.01) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 44627991 44627991 C A 1 0 0 0 0 1 0 0 0 8399 623 22 2 2 KRTAP10-9 21 44627991 Missense_Mutation SNP C C3N-01405_T 11073998 44627991 2081992 403 22877 SLC7A4 0 . GRCh38 22 21031518 21031519 + Frame_Shift_Ins INS - - G novel C3N-01405_T C3N-01405_N - - c.294dupC p.Thr99HisfsTer56 p.T99Hfs*56 ENST00000382932 2/5 65 53 12 76 75 1 sindel-varindel SLC7A4,frameshift_variant,p.Thr99HisfsTer56,ENST00000382932,NM_004173.2;SLC7A4,frameshift_variant,p.Thr99HisfsTer56,ENST00000403586,;P2RX6,downstream_gene_variant,,ENST00000413302,NM_005446.3;P2RX6,downstream_gene_variant,,ENST00000401443,NM_001159554.1;SLC7A4,downstream_gene_variant,,ENST00000426145,;MIR649,downstream_gene_variant,,ENST00000384843,;AC002472.11,intron_variant,,ENST00000450652,;P2RX6P,downstream_gene_variant,,ENST00000439119,;P2RX6,downstream_gene_variant,,ENST00000442475,;P2RX6,downstream_gene_variant,,ENST00000432930,;P2RX6,downstream_gene_variant,,ENST00000422210,;P2RX6,downstream_gene_variant,,ENST00000487342,; G ENST00000382932 Transcript frameshift_variant 362-363/2313 294-295/1908 98-99/635 -/X -/C 1 -1 SLC7A4 HGNC HGNC:11062 protein_coding YES CCDS33608.1 ENSP00000372390 O43246 UPI0000169EC7 NM_004173.2 2/5 hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF410,Pfam_domain:PF13520 HIGH 1 insertion 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 74 21031518 21031518 - G 1 0 1 1 0 0 0 0 0 14982 1696 59 0 0 SLC7A4 22 21031518 Frame_Shift_Ins INS - C3N-01405_T 21031518 29786950 404 22878 MTMR3 0 . GRCh38 22 30020207 30020207 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.2548G>T p.Val850Leu p.V850L ENST00000401950 17/20 393 299 94 360 360 0 strelka-varscan-mutect MTMR3,missense_variant,p.Val850Leu,ENST00000333027,NM_153050.2;MTMR3,missense_variant,p.Val850Leu,ENST00000401950,NM_021090.3;MTMR3,missense_variant,p.Val714Leu,ENST00000323630,;MTMR3,missense_variant,p.Val850Leu,ENST00000351488,NM_153051.2;MTMR3,missense_variant,p.Val850Leu,ENST00000406629,;RP3-394A18.1,non_coding_transcript_exon_variant,,ENST00000624945,;HORMAD2-AS1,intron_variant,,ENST00000429350,;HORMAD2-AS1,intron_variant,,ENST00000453743,;MTMR3,upstream_gene_variant,,ENST00000491251,;MTMR3,downstream_gene_variant,,ENST00000492087,; T ENST00000401950 Transcript missense_variant 2890/6018 2548/3597 850/1198 V/L Gtg/Ttg 1 1 MTMR3 HGNC HGNC:7451 protein_coding YES CCDS13870.1 ENSP00000384651 Q13615 UPI0000073EF2 NM_021090.3 tolerated_low_confidence(0.28) 17/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 30020207 30020207 G T 1 0 0 0 0 1 0 0 0 9932 1029 36 2 2 MTMR3 22 30020207 Missense_Mutation SNP G C3N-01405_T 8988689 30020207 20798261 405 22879 KLHDC7B 0 . GRCh38 22 50549462 50549462 + Silent SNP G G T C3N-01405_T C3N-01405_N G G c.1296G>T p.= p.A432A ENST00000395676 1/1 132 96 36 112 111 1 strelka-varscan-mutect KLHDC7B,synonymous_variant,p.=,ENST00000395676,NM_138433.3;SYCE3,downstream_gene_variant,,ENST00000406915,NM_001123225.1;SYCE3,downstream_gene_variant,,ENST00000402753,;CTA-384D8.31,downstream_gene_variant,,ENST00000434237,; T ENST00000395676 Transcript synonymous_variant 1430/2991 1296/1785 432/594 A gcG/gcT COSM1130397 1 1 KLHDC7B HGNC HGNC:25145 protein_coding YES CCDS14097.2 ENSP00000379034 Q96G42 UPI00005A75D4 NM_138433.3 1/1 hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF206,Pfam_domain:PF01344,Gene3D:1zgkA00,SMART_domains:SM00612,Superfamily_domains:0052715 1 LOW SNV 1 1 PASS . . 0 204 0 5 0 0 0 0 -20 0.9998488 1 1 1 0 T 2 4 74 50549462 50549462 G T 1 0 0 0 0 0 0 0 1 8225 1074 38 1 1 KLHDC7B 22 50549462 Silent SNP G C3N-01405_T 20529255 50549462 269006 406 22880 ARSA 0 . GRCh38 22 50626847 50626847 + Missense_Mutation SNP T T A novel C3N-01405_T C3N-01405_N T T c.671A>T p.Tyr224Phe p.Y224F ENST00000216124 3/8 130 93 37 75 75 0 strelka-varscan-mutect ARSA,missense_variant,p.Tyr224Phe,ENST00000216124,NM_000487.5;ARSA,missense_variant,p.Tyr224Phe,ENST00000395621,NM_001085425.2;ARSA,missense_variant,p.Tyr224Phe,ENST00000356098,NM_001085426.2;ARSA,missense_variant,p.Tyr224Phe,ENST00000395619,NM_001085427.2;ARSA,missense_variant,p.Tyr138Phe,ENST00000453344,NM_001085428.2;ARSA,upstream_gene_variant,,ENST00000610191,;ARSA,non_coding_transcript_exon_variant,,ENST00000551731,;ARSA,upstream_gene_variant,,ENST00000608497,; A ENST00000216124 Transcript missense_variant 1064/2050 671/1530 224/509 Y/F tAc/tTc 1 -1 ARSA HGNC HGNC:713 protein_coding YES CCDS14100.2 ENSP00000216124 A0A0C4DFZ2 UPI000013C6C4 NM_000487.5 deleterious(0.01) 3/8 Gene3D:3.40.720.10,Pfam_domain:PF00884,hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF229,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS rs1189586905 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 50626847 50626847 T A 1 0 0 0 0 1 0 0 0 1130 1638 57 4 4 ARSA 22 50626847 Missense_Mutation SNP T C3N-01405_T 77385 50626847 191621 407 22881 SHOX 0 . GRCh38 X 644450 644450 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.693C>A p.His231Gln p.H231Q ENST00000381578 6/6 291 237 54 261 261 0 strelka-varscan-mutect SHOX,missense_variant,p.His231Gln,ENST00000381578,NM_000451.3;SHOX,missense_variant,p.His231Gln,ENST00000554971,;SHOX,intron_variant,,ENST00000334060,NM_006883.2;SHOX,intron_variant,,ENST00000381575,; A ENST00000381578 Transcript missense_variant 1384/3757 693/879 231/292 H/Q caC/caA 1 1 SHOX HGNC HGNC:10853 protein_coding YES CCDS14107.1 ENSP00000370990 O15266 A0A024R385 UPI0000053471 NM_000451.3 tolerated(0.14) 6/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 644450 644450 C A 1 0 0 0 0 1 0 0 0 14551 506 18 2 2 SHOX 23 644450 Missense_Mutation SNP C C3N-01405_T 644450 155396445 408 22882 ARSF 0 . GRCh38 X 3084452 3084452 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.616G>T p.Gly206Trp p.G206W ENST00000381127 6/11 162 120 42 146 146 0 strelka-varscan-mutect ARSF,missense_variant,p.Gly206Trp,ENST00000381127,NM_001201538.1,NM_001201539.1;ARSF,missense_variant,p.Gly206Trp,ENST00000359361,NM_004042.4; T ENST00000381127 Transcript missense_variant 837/2164 616/1773 206/590 G/W Ggg/Tgg COSM5596300 1 1 ARSF HGNC HGNC:721 protein_coding YES CCDS14123.1 ENSP00000370519 P54793 UPI00001A9629 NM_001201538.1,NM_001201539.1 tolerated(0.18) 6/11 hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF220,Pfam_domain:PF00884,Superfamily_domains:SSF53649 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 3084452 3084452 G T 1 0 0 0 0 1 0 0 0 1134 1348 47 2 2 ARSF 23 3084452 Missense_Mutation SNP G C3N-01405_T 2440002 3084452 152956443 409 22883 BCOR 0 . GRCh38 X 40062370 40062370 + Missense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.4197G>T p.Lys1399Asn p.K1399N ENST00000378444 10/15 232 174 58 195 195 0 strelka-varscan-mutect BCOR,missense_variant,p.Lys1365Asn,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Lys1399Asn,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Lys1347Asn,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Lys1365Asn,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Lys242Asn,ENST00000378463,;BCOR,missense_variant,p.Lys72Asn,ENST00000442018,;BCOR,missense_variant,p.Lys94Asn,ENST00000427012,;BCOR,missense_variant,p.Lys269Asn,ENST00000413905,;BCOR,downstream_gene_variant,,ENST00000406200,; A ENST00000378444 Transcript missense_variant 4426/6358 4197/5268 1399/1755 K/N aaG/aaT 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 deleterious(0.02) 10/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117,Pfam_domain:PF15808 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 40062370 40062370 C A 1 0 0 0 0 1 0 0 0 1533 796 28 2 2 BCOR 23 40062370 Missense_Mutation SNP C C3N-01405_T 36977918 40062370 115978525 410 22884 KDM5C 0 . GRCh38 X 53192776 53192776 + Missense_Mutation SNP C C A rs782299839 C3N-01405_T C3N-01405_N C C c.4108G>T p.Gly1370Trp p.G1370W ENST00000452825 24/24 22 13 9 13 13 0 strelka-varscan-mutect KDM5C,missense_variant,p.Gly1370Trp,ENST00000452825,NM_001146702.1;KDM5C,3_prime_UTR_variant,,ENST00000375401,NM_004187.3;KDM5C,3_prime_UTR_variant,,ENST00000404049,NM_001282622.1;KDM5C,downstream_gene_variant,,ENST00000375379,;KDM5C,downstream_gene_variant,,ENST00000375383,;MIR6895,downstream_gene_variant,,ENST00000613497,;KDM5C,downstream_gene_variant,,ENST00000477109,; A ENST00000452825 Transcript missense_variant 4641/6096 4108/4140 1370/1379 G/W Ggg/Tgg rs782299839 1 -1 KDM5C HGNC HGNC:11114 protein_coding CCDS55417.1 ENSP00000445176 P41229 UPI000199A537 NM_001146702.1 deleterious_low_confidence(0.02) 24/24 MODERATE SNV 5 1 PASS rs782299839 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 53192776 53192776 C A 1 0 0 0 0 1 0 0 0 8053 623 22 2 2 KDM5C 23 53192776 Missense_Mutation SNP C C3N-01405_T 13130406 53192776 102848119 411 22885 NONO 0 . GRCh38 X 71294421 71294421 + Frame_Shift_Del DEL G G - rs776947124 C3N-01405_T C3N-01405_N G G c.544delG p.Asp182MetfsTer34 p.D182Mfs*34 ENST00000276079 5/12 145 112 33 163 163 0 sindel-pindel NONO,frameshift_variant,p.Asp93MetfsTer34,ENST00000535149,NM_001145410.1;NONO,frameshift_variant,p.Asp182MetfsTer34,ENST00000276079,NM_007363.4;NONO,frameshift_variant,p.Asp182MetfsTer34,ENST00000373841,NM_001145409.1;NONO,frameshift_variant,p.Asp182MetfsTer34,ENST00000373856,NM_001145408.1;NONO,frameshift_variant,p.Asp182MetfsTer?,ENST00000454976,;NONO,frameshift_variant,p.Asp44MetfsTer34,ENST00000418921,;NONO,intron_variant,,ENST00000413858,;NONO,downstream_gene_variant,,ENST00000420903,;NONO,downstream_gene_variant,,ENST00000450092,;NONO,non_coding_transcript_exon_variant,,ENST00000490044,;NONO,non_coding_transcript_exon_variant,,ENST00000471419,;NONO,intron_variant,,ENST00000474431,;NONO,intron_variant,,ENST00000472185,;NONO,upstream_gene_variant,,ENST00000473525,;NONO,downstream_gene_variant,,ENST00000486613,; - ENST00000276079 Transcript frameshift_variant 748/2713 543/1416 181/471 V/X gtG/gt rs776947124 1 1 NONO HGNC HGNC:7871 protein_coding YES CCDS14410.1 ENSP00000276079 Q15233 A0A0S2Z4Z9 UPI000002EFDD NM_007363.4 5/12 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR23189,hmmpanther:PTHR23189:SF15,SMART_domains:SM00360,Superfamily_domains:SSF54928 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 74 71294421 71294421 G - 1 0 1 0 1 0 0 0 0 10578 1335 47 0 0 NONO 23 71294421 Frame_Shift_Del DEL G C3N-01405_T 18101645 71294421 84746474 412 22886 GPR174 0 . GRCh38 X 79171716 79171716 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.709G>A p.Gly237Arg p.G237R ENST00000276077 1/1 119 88 31 107 107 0 strelka-varscan-mutect GPR174,missense_variant,p.Gly237Arg,ENST00000276077,NM_032553.1; A ENST00000276077 Transcript missense_variant 745/1258 709/1002 237/333 G/R Ggg/Agg 1 1 GPR174 HGNC HGNC:30245 protein_coding YES CCDS14443.1 ENSP00000276077 Q9BXC1 UPI0000050477 NM_032553.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF4,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1467607894 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 79171716 79171716 G A 1 0 0 0 0 1 0 0 0 6556 1000 35 3 3 GPR174 23 79171716 Missense_Mutation SNP G C3N-01405_T 7877295 79171716 76869179 413 22887 GPR174 0 . GRCh38 X 79171909 79171909 + Missense_Mutation SNP G G T C3N-01405_T C3N-01405_N G G c.902G>T p.Arg301Ile p.R301I ENST00000276077 1/1 65 50 15 51 50 1 strelka-varscan-mutect GPR174,missense_variant,p.Arg301Ile,ENST00000276077,NM_032553.1; T ENST00000276077 Transcript missense_variant 938/1258 902/1002 301/333 R/I aGa/aTa COSM488659 1 1 GPR174 HGNC HGNC:30245 protein_coding YES CCDS14443.1 ENSP00000276077 Q9BXC1 UPI0000050477 NM_032553.1 tolerated(0.08) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF4,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 79171909 79171909 G T 1 0 0 0 0 1 0 0 0 6556 942 33 2 2 GPR174 23 79171909 Missense_Mutation SNP G C3N-01405_T 193 79171909 76868986 414 22888 POF1B 0 . GRCh38 X 85303457 85303457 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1598C>A p.Ser533Tyr p.S533Y ENST00000373145 15/16 85 58 27 101 100 1 strelka-varscan-mutect POF1B,missense_variant,p.Ser533Tyr,ENST00000262753,NM_024921.3;POF1B,missense_variant,p.Ser533Tyr,ENST00000373145,NM_001307940.1; T ENST00000373145 Transcript missense_variant 1718/1972 1598/1788 533/595 S/Y tCc/tAc 1 -1 POF1B HGNC HGNC:13711 protein_coding YES CCDS78497.1 ENSP00000362238 Q8WVV4 UPI00001AE9F1 NM_001307940.1 deleterious_low_confidence(0) 15/16 hmmpanther:PTHR22546 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 85303457 85303457 G T 1 0 0 0 0 1 0 0 0 12291 1174 41 2 2 POF1B 23 85303457 Missense_Mutation SNP G C3N-01405_T 6131548 85303457 70737438 415 22889 PCDH11X 0 . GRCh38 X 91877114 91877114 + Missense_Mutation SNP G G T rs6618811 C3N-01405_T C3N-01405_N G G c.874G>T p.Val292Phe p.V292F ENST00000373094 2/7 59 45 14 40 40 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Val292Phe,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Val292Phe,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Val292Phe,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Val292Phe,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Val292Phe,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Val292Phe,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Val292Phe,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; T ENST00000373094 Transcript missense_variant 1719/9179 874/4044 292/1347 V/F Gtc/Ttc rs6618811 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0) 2/7 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs6618811 . 0 204 4 2 0 0 0 0 -20 0.9999932 1 1 1 0 T 3 4 74 91877114 91877114 G T 1 0 0 0 0 1 0 0 0 11595 1029 36 2 2 PCDH11X 23 91877114 Missense_Mutation SNP G C3N-01405_T 6573657 91877114 64163781 416 22890 TMEM35A 0 . GRCh38 X 101094605 101094605 + Silent SNP C C A rs748303170 C3N-01405_T C3N-01405_N C C c.153C>A p.= p.L51L ENST00000372930 2/2 46 38 8 48 48 0 strelka-varscan-mutect TMEM35A,synonymous_variant,p.=,ENST00000372930,NM_021637.2;CENPI,upstream_gene_variant,,ENST00000403304,;CENPI,upstream_gene_variant,,ENST00000435570,;TRMT2B-AS1,upstream_gene_variant,,ENST00000443801,;TMEM35A,non_coding_transcript_exon_variant,,ENST00000478351,; A ENST00000372930 Transcript synonymous_variant 436/2195 153/504 51/167 L ctC/ctA rs748303170 1 1 TMEM35A HGNC HGNC:25864 protein_coding YES CCDS14478.1 ENSP00000362021 Q53FP2 UPI0000035FFB NM_021637.2 2/2 Pfam_domain:PF13564,hmmpanther:PTHR13163,hmmpanther:PTHR13163:SF0 LOW 1 SNV 1 1 PASS rs748303170 . 0 208 2 0 0 0 0 0 -19.64702 1 1 1 1 0 A 2 1 74 101094605 101094605 C A 1 0 0 0 0 0 0 0 1 16633 842 30 2 2 TMEM35A 23 101094605 Silent SNP C C3N-01405_T 9217491 101094605 54946290 417 22891 ESX1 0 . GRCh38 X 104250738 104250738 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.711G>T p.= p.L237L ENST00000372588 4/4 139 104 35 127 127 0 strelka-varscan-mutect ESX1,synonymous_variant,p.=,ENST00000372588,NM_153448.3; A ENST00000372588 Transcript synonymous_variant 795/1495 711/1221 237/406 L ctG/ctT 1 -1 ESX1 HGNC HGNC:14865 protein_coding YES CCDS14516.1 ENSP00000361669 Q8N693 UPI0000073D09 NM_153448.3 4/4 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 104250738 104250738 C A 1 0 0 0 0 0 0 0 1 5125 581 21 2 2 ESX1 23 104250738 Silent SNP C C3N-01405_T 3156133 104250738 51790157 418 22892 PAK3 0 . GRCh38 X 111194311 111194311 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1111G>T p.Gly371Cys p.G371C ENST00000360648 12/16 178 138 40 189 189 0 strelka-varscan-mutect PAK3,missense_variant,p.Gly335Cys,ENST00000372007,NM_001324327.1,NM_001324326.1,NM_001324331.1,NM_001324333.1,NM_001324332.1,NM_001324334.1,NM_001324328.1,NM_001324330.1,NM_001324325.1,NM_002578.3;PAK3,missense_variant,p.Gly356Cys,ENST00000519681,;PAK3,missense_variant,p.Gly350Cys,ENST00000372010,;PAK3,missense_variant,p.Gly335Cys,ENST00000446737,NM_001128166.1;PAK3,missense_variant,p.Gly335Cys,ENST00000425146,NM_001128167.1;PAK3,missense_variant,p.Gly371Cys,ENST00000360648,NM_001128168.1;PAK3,missense_variant,p.Gly356Cys,ENST00000417227,NM_001128172.1;PAK3,missense_variant,p.Gly350Cys,ENST00000262836,NM_001128173.1;PAK3,missense_variant,p.Gly334Cys,ENST00000620137,;PAK3,missense_variant,p.Gly371Cys,ENST00000518291,; T ENST00000360648 Transcript missense_variant 1138/2241 1111/1743 371/580 G/C Ggt/Tgt 1 1 PAK3 HGNC HGNC:8592 protein_coding YES CCDS48151.1 ENSP00000353864 O75914 UPI0000D61DBC NM_001128168.1 deleterious(0.02) 12/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF250,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 111194311 111194311 G T 1 0 0 0 0 1 0 0 0 11482 1232 43 2 2 PAK3 23 111194311 Missense_Mutation SNP G C3N-01405_T 6943573 111194311 44846584 419 22893 RBMXL3 0 . GRCh38 X 115190145 115190145 + Nonsense_Mutation SNP C C A novel C3N-01405_T C3N-01405_N C C c.704C>A p.Ser235Ter p.S235* ENST00000424776 1/1 39 27 12 36 36 0 strelka-varscan-mutect RBMXL3,stop_gained,p.Ser235Ter,ENST00000424776,NM_001145346.1;LRCH2,intron_variant,,ENST00000317135,NM_020871.3;LRCH2,intron_variant,,ENST00000538422,NM_001243963.1; A ENST00000424776 Transcript stop_gained 719/3442 704/3204 235/1067 S/* tCa/tAa 1 1 RBMXL3 HGNC HGNC:26859 protein_coding YES CCDS55478.1 ENSP00000417451 Q8N7X1 UPI0001932819 NM_001145346.1 1/1 HIGH SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 74 115190145 115190145 C A 1 0 0 0 0 0 1 0 0 13321 838 29 2 2 RBMXL3 23 115190145 Nonsense_Mutation SNP C C3N-01405_T 3995834 115190145 40850750 420 22894 IL13RA1 0 . GRCh38 X 118741055 118741055 + Missense_Mutation SNP G G A novel C3N-01405_T C3N-01405_N G G c.127G>A p.Glu43Lys p.E43K ENST00000371666 2/11 123 94 29 129 129 0 strelka-varscan-mutect IL13RA1,missense_variant,p.Glu43Lys,ENST00000371666,NM_001560.2;IL13RA1,missense_variant,p.Glu43Lys,ENST00000371642,;SNORA35,downstream_gene_variant,,ENST00000458908,; A ENST00000371666 Transcript missense_variant 194/4036 127/1284 43/427 E/K Gaa/Aaa 1 1 IL13RA1 HGNC HGNC:5974 protein_coding YES CCDS14573.1 ENSP00000360730 P78552 UPI0000000CA3 NM_001560.2 tolerated(0.21) 2/11 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF89 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 74 118741055 118741055 G A 1 0 0 0 0 1 0 0 0 7537 1291 45 3 3 IL13RA1 23 118741055 Missense_Mutation SNP G C3N-01405_T 3550910 118741055 37299840 421 22895 GLUD2 0 . GRCh38 X 121048773 121048773 + Missense_Mutation SNP G G T novel C3N-01405_T C3N-01405_N G G c.1089G>T p.Lys363Asn p.K363N ENST00000328078 1/1 216 152 64 218 218 0 strelka-varscan-mutect GLUD2,missense_variant,p.Lys363Asn,ENST00000328078,NM_012084.3; T ENST00000328078 Transcript missense_variant 1186/2493 1089/1677 363/558 K/N aaG/aaT 1 1 GLUD2 HGNC HGNC:4336 protein_coding YES CCDS14603.1 ENSP00000327589 P49448 A0A140VK14 UPI0000129301 NM_012084.3 tolerated(1) 1/1 Gene3D:3.40.50.720,Pfam_domain:PF00208,hmmpanther:PTHR11606,hmmpanther:PTHR11606:SF15,SMART_domains:SM00839,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 121048773 121048773 G T 1 0 0 0 0 1 0 0 0 6354 991 35 2 2 GLUD2 23 121048773 Missense_Mutation SNP G C3N-01405_T 2307718 121048773 34992122 422 22896 GPR119 0 . GRCh38 X 130385266 130385266 + Missense_Mutation SNP A A C novel C3N-01405_T C3N-01405_N A A c.182T>G p.Leu61Arg p.L61R ENST00000276218 1/1 86 60 26 77 77 0 strelka-varscan-mutect GPR119,missense_variant,p.Leu61Arg,ENST00000276218,NM_178471.2; C ENST00000276218 Transcript missense_variant 182/1008 182/1008 61/335 L/R cTa/cGa 1 -1 GPR119 HGNC HGNC:19060 protein_coding YES CCDS14625.1 ENSP00000276218 Q8TDV5 UPI000003AFD2 NM_178471.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF7,hmmpanther:PTHR22750,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 74 130385266 130385266 A C 1 0 0 0 0 1 0 0 0 6527 420 15 5 5 GPR119 23 130385266 Missense_Mutation SNP A C3N-01405_T 9336493 130385266 25655629 423 22897 CT45A10 0 . GRCh38 X 135883144 135883144 + Silent SNP C C A C3N-01405_T C3N-01405_N C C c.282G>T p.= p.V94V ENST00000611668 3/5 209 157 52 215 215 0 strelka-varscan-mutect CT45A10,synonymous_variant,p.=,ENST00000611668,NM_001291527.1,NM_001291528.1;CT45A10,synonymous_variant,p.=,ENST00000617981,NM_001291529.1,NM_001291530.1; A ENST00000611668 Transcript synonymous_variant 527/1010 282/570 94/189 V gtG/gtT COSM3231111 1 -1 CT45A10 HGNC HGNC:51263 protein_coding YES CCDS76035.1 ENSP00000484601 P0DMU9 UPI00002125B4 NM_001291527.1,NM_001291528.1 3/5 hmmpanther:PTHR12957,hmmpanther:PTHR12957:SF8 1 LOW 1 SNV 1 1 1 PASS . . 15 195 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 135883144 135883144 C A 1 0 0 0 0 0 0 0 1 3789 581 21 2 2 CT45A10 23 135883144 Silent SNP C C3N-01405_T 5497878 135883144 20157751 424 22898 MCF2 0 . GRCh38 X 139604977 139604977 + Missense_Mutation SNP C C T novel C3N-01405_T C3N-01405_N C C c.1793G>A p.Arg598Lys p.R598K ENST00000519895 18/29 37 23 14 40 40 0 strelka-mutect MCF2,missense_variant,p.Arg582Lys,ENST00000520602,;MCF2,missense_variant,p.Arg582Lys,ENST00000414978,NM_001099855.1;MCF2,missense_variant,p.Arg522Lys,ENST00000370576,NM_005369.4;MCF2,missense_variant,p.Arg483Lys,ENST00000536274,NM_001171877.1;MCF2,missense_variant,p.Arg598Lys,ENST00000519895,NM_001171876.1;MCF2,missense_variant,p.Arg538Lys,ENST00000338585,NM_001171879.1;MCF2,missense_variant,p.Arg522Lys,ENST00000370573,NM_001171878.1;MCF2,missense_variant,p.Arg26Lys,ENST00000437564,;MCF2,missense_variant,p.Arg125Lys,ENST00000446225,;MCF2,downstream_gene_variant,,ENST00000483690,; T ENST00000519895 Transcript missense_variant 1959/3346 1793/3006 598/1001 R/K aGa/aAa 1 -1 MCF2 HGNC HGNC:6940 protein_coding YES CCDS55517.1 ENSP00000430276 P10911 UPI0001C33995 NM_001171876.1 tolerated(0.59) 18/29 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF138,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 2 1 PASS . . 1 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 74 139604977 139604977 C T 1 0 0 0 0 1 0 0 0 9309 913 32 3 3 MCF2 23 139604977 Missense_Mutation SNP C C3N-01405_T 3721833 139604977 16435918 425 22899 ATP2B3 0 . GRCh38 X 153562164 153562164 + Silent SNP C C A novel C3N-01405_T C3N-01405_N C C c.3081C>A p.= p.P1027P ENST00000263519 18/20 115 86 29 105 105 0 strelka-varscan-mutect ATP2B3,synonymous_variant,p.=,ENST00000370186,;ATP2B3,synonymous_variant,p.=,ENST00000263519,NM_001001344.2;ATP2B3,synonymous_variant,p.=,ENST00000349466,;ATP2B3,synonymous_variant,p.=,ENST00000359149,NM_021949.3;ATP2B3,synonymous_variant,p.=,ENST00000393842,;ATP2B3,downstream_gene_variant,,ENST00000460549,; A ENST00000263519 Transcript synonymous_variant 3207/6420 3081/3663 1027/1220 P ccC/ccA 1 1 ATP2B3 HGNC HGNC:816 protein_coding YES CCDS35440.1 ENSP00000263519 Q16720 UPI00001AE881 NM_001001344.2 18/20 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF284,Gene3D:1.20.1110.10,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00689,Superfamily_domains:0049473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 74 153562164 153562164 C A 1 0 0 0 0 0 0 0 1 1294 668 24 2 2 ATP2B3 23 153562164 Silent SNP C C3N-01405_T 13957187 153562164 2478731 426 22900 PRAMEF1 0 . GRCh38 1 12794462 12794462 + Missense_Mutation SNP T T G novel C3N-01410_T C3N-01410_N T T c.835T>G p.Phe279Val p.F279V ENST00000332296 3/4 317 281 36 390 390 0 strelka-varscan-mutect PRAMEF1,missense_variant,p.Phe279Val,ENST00000332296,NM_001291380.1,NM_023013.4;PRAMEF1,upstream_gene_variant,,ENST00000400814,; G ENST00000332296 Transcript missense_variant 938/2160 835/1425 279/474 F/V Ttc/Gtc 1 1 PRAMEF1 HGNC HGNC:28840 protein_coding YES CCDS148.1 ENSP00000332134 O95521 UPI0004620BB8 NM_001291380.1,NM_023013.4 deleterious(0.01) 3/4 Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF2,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 12794462 12794462 T G 1 0 0 0 0 1 0 0 0 12554 1609 56 5 5 PRAMEF1 1 12794462 Missense_Mutation SNP T C3N-01410_T 12794462 236161960 1 22901 FHAD1 0 . GRCh38 1 15381423 15381423 + Nonsense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.3928G>T p.Gly1310Ter p.G1310* ENST00000358897 29/31 222 142 80 229 229 0 strelka-varscan-mutect FHAD1,stop_gained,p.Gly1310Ter,ENST00000358897,NM_052929.1;FHAD1,stop_gained,p.Gly1310Ter,ENST00000375998,;FHAD1,stop_gained,p.Gly629Ter,ENST00000444385,;FHAD1,stop_gained,p.Gly545Ter,ENST00000314668,;FHAD1,stop_gained,p.Gly581Ter,ENST00000529606,;FHAD1,non_coding_transcript_exon_variant,,ENST00000471347,;FHAD1,non_coding_transcript_exon_variant,,ENST00000477846,;FHAD1,non_coding_transcript_exon_variant,,ENST00000495195,;FHAD1,upstream_gene_variant,,ENST00000472086,;FHAD1,stop_gained,p.Gly327Ter,ENST00000481324,; T ENST00000358897 Transcript stop_gained 4066/5090 3928/4239 1310/1412 G/* Gga/Tga 1 1 FHAD1 HGNC HGNC:29408 protein_coding YES ENSP00000351770 B1AJZ9 UPI0001761703 NM_052929.1 29/31 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18853,hmmpanther:PTHR18853:SF7 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 15381423 15381423 G T 1 0 0 0 0 0 1 0 0 5740 1001 35 2 2 FHAD1 1 15381423 Nonsense_Mutation SNP G C3N-01410_T 2586961 15381423 233574999 2 22902 SPEN 0 . GRCh38 1 15929284 15929284 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.3044T>A p.Leu1015His p.L1015H ENST00000375759 11/15 180 150 30 208 208 0 strelka-varscan-mutect SPEN,missense_variant,p.Leu1015His,ENST00000375759,NM_015001.2; A ENST00000375759 Transcript missense_variant 3248/12232 3044/10995 1015/3664 L/H cTt/cAt 1 1 SPEN HGNC HGNC:17575 protein_coding YES CCDS164.1 ENSP00000364912 Q96T58 UPI000006FF0C NM_015001.2 tolerated(0.19) 11/15 hmmpanther:PTHR23189:SF48,hmmpanther:PTHR23189 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 15929284 15929284 T A 1 0 0 0 0 1 0 0 0 15389 1609 56 4 4 SPEN 1 15929284 Missense_Mutation SNP T C3N-01410_T 547861 15929284 233027138 3 22903 SNRNP40 0 . GRCh38 1 31293267 31293267 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.223C>T p.His75Tyr p.H75Y ENST00000263694 2/10 206 127 79 223 222 1 strelka-varscan-mutect SNRNP40,missense_variant,p.His75Tyr,ENST00000263694,NM_004814.2;ZCCHC17,upstream_gene_variant,,ENST00000373714,NM_001282568.1;ZCCHC17,upstream_gene_variant,,ENST00000546109,NM_001282569.1;ZCCHC17,upstream_gene_variant,,ENST00000615916,NM_001282566.1;ZCCHC17,upstream_gene_variant,,ENST00000344147,NM_016505.3;ZCCHC17,upstream_gene_variant,,ENST00000616393,NM_001282571.1;ZCCHC17,upstream_gene_variant,,ENST00000618216,NM_001282572.1,NM_001282574.1;ZCCHC17,upstream_gene_variant,,ENST00000616859,NM_001282573.1;ZCCHC17,upstream_gene_variant,,ENST00000627541,NM_001282570.1,NM_001282567.1;SNRNP40,non_coding_transcript_exon_variant,,ENST00000463988,;ZCCHC17,upstream_gene_variant,,ENST00000479629,;SNRNP40,upstream_gene_variant,,ENST00000474025,; A ENST00000263694 Transcript missense_variant 242/1597 223/1074 75/357 H/Y Cac/Tac 1 -1 SNRNP40 HGNC HGNC:30857 protein_coding YES CCDS340.1 ENSP00000263694 Q96DI7 A0MNP2 UPI000006FD38 NM_004814.2 tolerated(0.1) 2/10 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF501,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 31293267 31293267 G A 1 0 0 0 0 1 0 0 0 15176 1348 47 3 3 SNRNP40 1 31293267 Missense_Mutation SNP G C3N-01410_T 15363983 31293267 217663155 4 22904 SFPQ 0 . GRCh38 1 35190883 35190883 + Missense_Mutation SNP T T C C3N-01410_T C3N-01410_N T T c.1130A>G p.Asn377Ser p.N377S ENST00000357214 3/10 320 261 59 348 348 0 strelka-varscan-mutect SFPQ,missense_variant,p.Asn377Ser,ENST00000357214,NM_005066.2;SFPQ,upstream_gene_variant,,ENST00000470472,;SFPQ,upstream_gene_variant,,ENST00000460428,; C ENST00000357214 Transcript missense_variant 1229/3747 1130/2124 377/707 N/S aAt/aGt COSM5443485 1 -1 SFPQ HGNC HGNC:10774 protein_coding YES CCDS388.1 ENSP00000349748 P23246 UPI00001358B9 NM_005066.2 deleterious(0.01) 3/10 PROSITE_profiles:PS50102,hmmpanther:PTHR23189:SF42,hmmpanther:PTHR23189,Gene3D:3.30.70.330,Pfam_domain:PF00076,SMART_domains:SM00360,Superfamily_domains:SSF54928 1 MODERATE 1 SNV 1 1 1 PASS rs1324288871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 35190883 35190883 T C 1 0 0 0 0 1 0 0 0 14438 1493 52 5 5 SFPQ 1 35190883 Missense_Mutation SNP T C3N-01410_T 3897616 35190883 213765539 5 22905 FOXD2 0 . GRCh38 1 47438583 47438583 + Silent SNP T T C C3N-01410_T C3N-01410_N T T c.448T>C p.= p.L150L ENST00000334793 1/1 422 304 118 345 345 0 strelka-varscan-mutect FOXD2,synonymous_variant,p.=,ENST00000334793,NM_004474.3;FOXD2-AS1,upstream_gene_variant,,ENST00000445551,; C ENST00000334793 Transcript synonymous_variant 2567/4675 448/1488 150/495 L Ttg/Ctg COSM681859 1 1 FOXD2 HGNC HGNC:3803 protein_coding YES CCDS30708.1 ENSP00000335493 O60548 UPI000014153E NM_004474.3 1/1 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF168,SMART_domains:SM00339,Superfamily_domains:SSF46785 1 LOW 1 SNV 1 1 PASS rs930070272 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 47438583 47438583 T C 1 0 0 0 0 0 0 0 1 5857 1722 60 5 5 FOXD2 1 47438583 Silent SNP T C3N-01410_T 12247700 47438583 201517839 6 22906 COL11A1 0 . GRCh38 1 102962652 102962652 + Splice_Site SNP C C A novel C3N-01410_T C3N-01410_N C C c.3024+1G>T p.X1008_splice ENST00000370096 228 152 76 340 340 0 strelka-varscan-mutect COL11A1,splice_donor_variant,,ENST00000358392,NM_080629.2;COL11A1,splice_donor_variant,,ENST00000370096,NM_001854.3;COL11A1,splice_donor_variant,,ENST00000353414,NM_001190709.1;COL11A1,splice_donor_variant,,ENST00000512756,NM_080630.3;COL11A1,splice_donor_variant,,ENST00000635193,;COL11A1,splice_donor_variant,,ENST00000465209,; A ENST00000370096 Transcript splice_donor_variant -/7286 3024/5421 1008/1806 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 39/66 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 75 102962652 102962652 C A 1 0 0 0 0 0 0 1 0 3455 521 18 2 2 COL11A1 1 102962652 Splice_Site SNP C C3N-01410_T 55524069 102962652 145993770 7 22907 MAN1A2 0 . GRCh38 1 117502961 117502961 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.1784A>G p.Glu595Gly p.E595G ENST00000356554 12/13 210 147 63 128 128 0 strelka-varscan-mutect MAN1A2,missense_variant,p.Glu595Gly,ENST00000356554,NM_006699.3;MAN1A2,missense_variant,p.Glu328Gly,ENST00000449370,;MAN1A2,missense_variant,p.Glu162Gly,ENST00000421535,;MAN1A2,missense_variant,p.Glu34Gly,ENST00000422329,; G ENST00000356554 Transcript missense_variant 2519/8576 1784/1926 595/641 E/G gAa/gGa 1 1 MAN1A2 HGNC HGNC:6822 protein_coding YES CCDS895.1 ENSP00000348959 O60476 UPI0000052B45 NM_006699.3 deleterious(0) 12/13 Gene3D:1.50.10.50,Pfam_domain:PF01532,Prints_domain:PR00747,hmmpanther:PTHR11742,hmmpanther:PTHR11742:SF40,Superfamily_domains:SSF48225 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 117502961 117502961 A G 1 0 0 0 0 1 0 0 0 9132 246 9 5 5 MAN1A2 1 117502961 Missense_Mutation SNP A C3N-01410_T 14540309 117502961 131453461 8 22908 LIX1L 0 . GRCh38 1 145936427 145936427 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.897G>T p.Glu299Asp p.E299D ENST00000604000 6/6 575 371 204 457 457 0 strelka-varscan-mutect LIX1L,missense_variant,p.Glu299Asp,ENST00000604000,NM_153713.2;CH17-270A2.2,intron_variant,,ENST00000625258,;RP11-315I20.1,non_coding_transcript_exon_variant,,ENST00000601726,;RP11-315I20.1,intron_variant,,ENST00000598354,;RP11-315I20.1,intron_variant,,ENST00000630257,;RP11-315I20.1,intron_variant,,ENST00000598103,;RP11-315I20.1,intron_variant,,ENST00000599626,;RP11-315I20.1,intron_variant,,ENST00000599469,;RP11-315I20.1,intron_variant,,ENST00000597144,;RP11-315I20.1,intron_variant,,ENST00000595518,;RP11-315I20.1,intron_variant,,ENST00000595494,;RP11-315I20.1,intron_variant,,ENST00000600340,;RP11-315I20.1,intron_variant,,ENST00000412239,;RP11-315I20.1,intron_variant,,ENST00000599147,;RP11-315I20.1,intron_variant,,ENST00000437797,;RP11-315I20.1,intron_variant,,ENST00000448561,;RP11-315I20.1,intron_variant,,ENST00000421764,;RP11-315I20.1,upstream_gene_variant,,ENST00000366105,;RP11-315I20.1,upstream_gene_variant,,ENST00000437207,;CH17-270A2.2,intron_variant,,ENST00000630636,; A ENST00000604000 Transcript missense_variant 971/3975 897/1014 299/337 E/D gaG/gaT 1 -1 LIX1L HGNC HGNC:28715 protein_coding YES CCDS72873.1 ENSP00000474487 Q8IVB5 UPI0000074663 NM_153713.2 tolerated(0.08) 6/6 hmmpanther:PTHR31139,Pfam_domain:PF14954 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 145936427 145936427 C A 1 0 0 0 0 1 0 0 0 8755 796 28 2 2 LIX1L 1 145936427 Missense_Mutation SNP C C3N-01410_T 28433466 145936427 103019995 9 22909 KPRP 0 . GRCh38 1 152760746 152760746 + Silent SNP G G T novel C3N-01410_T C3N-01410_N G G c.1158G>T p.= p.R386R ENST00000606109 1/1 307 270 37 199 199 0 strelka-varscan-mutect KPRP,synonymous_variant,p.=,ENST00000606109,NM_001025231.1; T ENST00000606109 Transcript synonymous_variant 1186/2492 1158/1740 386/579 R cgG/cgT 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 1/1 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 152760746 152760746 G T 1 0 0 0 0 0 0 0 1 8316 1190 42 2 2 KPRP 1 152760746 Silent SNP G C3N-01410_T 6824319 152760746 96195676 10 22910 KCNN3 0 . GRCh38 1 154869293 154869293 + Silent SNP C C G C3N-01410_T C3N-01410_N C C c.672G>C p.= p.R224R ENST00000618040 1/9 225 178 47 126 126 0 strelka-varscan-mutect KCNN3,synonymous_variant,p.=,ENST00000618040,NM_001204087.1;KCNN3,synonymous_variant,p.=,ENST00000271915,NM_002249.5;KCNN3,upstream_gene_variant,,ENST00000358505,; G ENST00000618040 Transcript synonymous_variant 986/13057 672/2241 224/746 R cgG/cgC COSM1491778 1 -1 KCNN3 HGNC HGNC:6292 protein_coding YES CCDS72928.1 ENSP00000481848 A0A087WYJ0 UPI0001F936D2 NM_001204087.1 1/9 hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF40 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 75 154869293 154869293 C G 1 0 0 0 0 0 0 0 1 7996 610 22 4 4 KCNN3 1 154869293 Silent SNP C C3N-01410_T 2108547 154869293 94087129 11 22911 FCRL2 0 . GRCh38 1 157769919 157769919 + Missense_Mutation SNP G G A rs756244463 C3N-01410_T C3N-01410_N G G c.542C>T p.Thr181Met p.T181M ENST00000361516 4/12 131 105 26 123 122 1 strelka-varscan-mutect FCRL2,missense_variant,p.Thr181Met,ENST00000361516,NM_030764.3;FCRL2,intron_variant,,ENST00000368181,;FCRL2,upstream_gene_variant,,ENST00000469986,;FCRL2,non_coding_transcript_exon_variant,,ENST00000368178,;FCRL2,non_coding_transcript_exon_variant,,ENST00000462774,; A ENST00000361516 Transcript missense_variant 591/2579 542/1527 181/508 T/M aCg/aTg rs756244463,COSM2149629 1 -1 FCRL2 HGNC HGNC:14875 protein_coding YES CCDS1168.1 ENSP00000355157 Q96LA5 UPI000006E1F3 NM_030764.3 deleterious(0.04) 4/12 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF61,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs756244463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 157769919 157769919 G A 1 0 0 0 0 1 0 0 0 5658 1145 40 1 1 FCRL2 1 157769919 Missense_Mutation SNP G C3N-01410_T 2900626 157769919 91186503 12 22912 CD1B 0 . GRCh38 1 158329980 158329980 + Missense_Mutation SNP T T G novel C3N-01410_T C3N-01410_N T T c.479A>C p.Gln160Pro p.Q160P ENST00000368168 3/6 364 300 64 357 357 0 strelka-varscan-mutect CD1B,missense_variant,p.Gln160Pro,ENST00000368168,NM_001764.2;CD1B,missense_variant,p.Gln128Pro,ENST00000451207,; G ENST00000368168 Transcript missense_variant 587/1395 479/1002 160/333 Q/P cAg/cCg 1 -1 CD1B HGNC HGNC:1635 protein_coding YES CCDS1176.1 ENSP00000357150 P29016 UPI0000127333 NM_001764.2 deleterious(0.01) 3/6 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF130,Pfam_domain:PF16497,Gene3D:3.30.500.10,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 158329980 158329980 T G 1 0 0 0 0 1 0 0 0 2678 1580 55 5 5 CD1B 1 158329980 Missense_Mutation SNP T C3N-01410_T 560061 158329980 90626442 13 22913 OR10K2 0 . GRCh38 1 158420430 158420430 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.437C>A p.Ala146Asp p.A146D ENST00000314902 1/1 454 398 56 423 423 0 strelka-varscan-mutect OR10K2,missense_variant,p.Ala146Asp,ENST00000314902,NM_001004476.1; T ENST00000314902 Transcript missense_variant 437/939 437/939 146/312 A/D gCt/gAt 1 -1 OR10K2 HGNC HGNC:14826 protein_coding YES CCDS30896.1 ENSP00000324251 Q6IF99 A0A126GV65 UPI0000041BC2 NM_001004476.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF400,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1031316708 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 158420430 158420430 G T 1 0 0 0 0 1 0 0 0 10991 971 34 2 2 OR10K2 1 158420430 Missense_Mutation SNP G C3N-01410_T 90450 158420430 90535992 14 22914 CADM3 0 . GRCh38 1 159200907 159200907 + Silent SNP G G A C3N-01410_T C3N-01410_N G G c.1284G>A p.= p.K428K ENST00000368124 10/10 60 41 19 47 47 0 strelka-varscan-mutect CADM3,synonymous_variant,p.=,ENST00000368125,NM_001127173.1;CADM3,synonymous_variant,p.=,ENST00000368124,NM_021189.3;ACKR1,upstream_gene_variant,,ENST00000537147,;ACKR1,upstream_gene_variant,,ENST00000368122,NM_002036.3;ACKR1,upstream_gene_variant,,ENST00000368121,NM_001122951.2;CADM3,downstream_gene_variant,,ENST00000416746,;ACKR1,upstream_gene_variant,,ENST00000435307,;CADM3-AS1,non_coding_transcript_exon_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; A ENST00000368124 Transcript synonymous_variant 1441/2546 1284/1299 428/432 K aaG/aaA COSM3476435 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 10/10 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 159200907 159200907 G A 1 0 0 0 0 0 0 0 1 2258 991 35 3 3 CADM3 1 159200907 Silent SNP G C3N-01410_T 780477 159200907 89755515 15 22915 VANGL2 0 . GRCh38 1 160419443 160419443 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.634T>A p.Tyr212Asn p.Y212N ENST00000368061 4/8 336 277 59 318 318 0 strelka-varscan-mutect VANGL2,missense_variant,p.Tyr212Asn,ENST00000368061,NM_020335.2;VANGL2,upstream_gene_variant,,ENST00000483408,; A ENST00000368061 Transcript missense_variant 1108/5340 634/1566 212/521 Y/N Tac/Aac 1 1 VANGL2 HGNC HGNC:15511 protein_coding YES CCDS30915.1 ENSP00000357040 Q9ULK5 UPI00001C1D79 NM_020335.2 deleterious(0) 4/8 hmmpanther:PTHR20886,PIRSF_domain:PIRSF007991,Pfam_domain:PF06638 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 160419443 160419443 T A 1 0 0 0 0 1 0 0 0 17665 1522 53 4 4 VANGL2 1 160419443 Missense_Mutation SNP T C3N-01410_T 1218536 160419443 88536979 16 22916 PLEKHA6 0 . GRCh38 1 204249211 204249211 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.1647G>T p.= p.R549R ENST00000272203 11/23 153 128 25 140 140 0 strelka-varscan PLEKHA6,synonymous_variant,p.=,ENST00000272203,NM_014935.4;PLEKHA6,synonymous_variant,p.=,ENST00000637508,;PLEKHA6,synonymous_variant,p.=,ENST00000414478,; A ENST00000272203 Transcript synonymous_variant 1964/7401 1647/3147 549/1048 R cgG/cgT 1 -1 PLEKHA6 HGNC HGNC:17053 protein_coding YES CCDS1444.1 ENSP00000272203 Q9Y2H5 UPI000013D935 NM_014935.4 11/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12752,hmmpanther:PTHR12752:SF5 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 75 204249211 204249211 C A 1 0 0 0 0 0 0 0 1 12153 726 26 2 2 PLEKHA6 1 204249211 Silent SNP C C3N-01410_T 43829768 204249211 44707211 17 22917 LRRN2 0 . GRCh38 1 204618713 204618713 + Missense_Mutation SNP C C T rs138573874 C3N-01410_T C3N-01410_N C C c.1280G>A p.Arg427Gln p.R427Q ENST00000367175 1/1 61 44 17 53 53 0 strelka-varscan LRRN2,missense_variant,p.Arg427Gln,ENST00000367175,;LRRN2,missense_variant,p.Arg427Gln,ENST00000367177,NM_201630.1;LRRN2,missense_variant,p.Arg427Gln,ENST00000367176,NM_006338.2;RP11-430C7.4,downstream_gene_variant,,ENST00000453895,;LRRN2,downstream_gene_variant,,ENST00000496057,; T ENST00000367175 Transcript missense_variant 3493/5036 1280/2142 427/713 R/Q cGa/cAa rs138573874,COSM2214523 1 -1 LRRN2 HGNC HGNC:16914 protein_coding YES CCDS1448.1 ENSP00000356143 O75325 A0A024R993 UPI000013E8AC tolerated(0.2) 1/1 PROSITE_profiles:PS50835,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF162,Superfamily_domains:SSF48726 0,1 MODERATE SNV 0,1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 204618713 204618713 C T 1 0 0 0 0 1 0 0 0 8941 884 31 1 1 LRRN2 1 204618713 Missense_Mutation SNP C C3N-01410_T 369502 204618713 44337709 18 22918 GUK1 0 . GRCh38 1 228140319 228140319 + Missense_Mutation SNP T T C novel C3N-01410_T C3N-01410_N T T c.17T>C p.Leu6Pro p.L6P ENST00000366728 1/7 209 180 29 178 178 0 strelka-varscan GUK1,missense_variant,p.Leu6Pro,ENST00000391865,NM_001159390.1;GUK1,missense_variant,p.Leu6Pro,ENST00000366723,;GUK1,missense_variant,p.Leu6Pro,ENST00000366728,NM_001242840.1;GUK1,missense_variant,p.Leu6Pro,ENST00000453943,;GUK1,5_prime_UTR_variant,,ENST00000312726,NM_000858.5;GUK1,5_prime_UTR_variant,,ENST00000366726,;GUK1,5_prime_UTR_variant,,ENST00000435153,;GUK1,5_prime_UTR_variant,,ENST00000366722,;GUK1,intron_variant,,ENST00000366730,NM_001242839.1;GUK1,upstream_gene_variant,,ENST00000366718,NM_001159391.1;GUK1,upstream_gene_variant,,ENST00000412265,;GUK1,upstream_gene_variant,,ENST00000366721,;GUK1,non_coding_transcript_exon_variant,,ENST00000492871,;GUK1,non_coding_transcript_exon_variant,,ENST00000485083,;GUK1,non_coding_transcript_exon_variant,,ENST00000498092,;GUK1,non_coding_transcript_exon_variant,,ENST00000469973,;GUK1,non_coding_transcript_exon_variant,,ENST00000485838,;GUK1,non_coding_transcript_exon_variant,,ENST00000493209,;GUK1,non_coding_transcript_exon_variant,,ENST00000493138,;GUK1,non_coding_transcript_exon_variant,,ENST00000462807,;GUK1,upstream_gene_variant,,ENST00000470040,;GUK1,upstream_gene_variant,,ENST00000491613,;GUK1,upstream_gene_variant,,ENST00000460224,;GUK1,upstream_gene_variant,,ENST00000485733,;GUK1,upstream_gene_variant,,ENST00000472939,;GUK1,upstream_gene_variant,,ENST00000484953,; C ENST00000366728 Transcript missense_variant 30/842 17/726 6/241 L/P cTg/cCg 1 1 GUK1 HGNC HGNC:4693 protein_coding YES CCDS55689.1 ENSP00000355689 Q16774 UPI000046FFA0 NM_001242840.1 deleterious_low_confidence(0) 1/7 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 228140319 228140319 T C 1 0 0 0 0 1 0 0 0 6782 1594 55 5 5 GUK1 1 228140319 Missense_Mutation SNP T C3N-01410_T 23521606 228140319 20816103 19 22919 RYR2 0 . GRCh38 1 237610861 237610861 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.4783C>A p.Leu1595Met p.L1595M ENST00000366574 36/105 269 236 33 264 264 0 strelka-varscan RYR2,missense_variant,p.Leu1595Met,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu1579Met,ENST00000360064,; A ENST00000366574 Transcript missense_variant 5100/16562 4783/14904 1595/4967 L/M Ctg/Atg 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.21) 36/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 237610861 237610861 C A 1 0 0 0 0 1 0 0 0 14029 680 24 2 2 RYR2 1 237610861 Missense_Mutation SNP C C3N-01410_T 9470542 237610861 11345561 20 22920 RGS7 0 . GRCh38 1 240930752 240930752 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.350C>A p.Pro117Gln p.P117Q ENST00000366565 6/18 270 175 95 308 307 1 strelka-varscan RGS7,missense_variant,p.Pro117Gln,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Pro117Gln,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Pro117Gln,ENST00000366563,NM_001282775.1;RGS7,intron_variant,,ENST00000348120,NM_001282773.1; T ENST00000366565 Transcript missense_variant 732/2494 350/1464 117/487 P/Q cCa/cAa 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 deleterious(0) 6/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 240930752 240930752 G T 1 0 0 0 0 1 0 0 0 13481 1348 47 2 2 RGS7 1 240930752 Missense_Mutation SNP G C3N-01410_T 3319891 240930752 8025670 21 22921 WDR64 0 . GRCh38 1 241775122 241775122 + Silent SNP T T C novel C3N-01410_T C3N-01410_N T T c.2418T>C p.= p.D806D ENST00000366552 20/27 147 96 51 186 186 0 strelka-varscan WDR64,synonymous_variant,p.=,ENST00000366552,NM_144625.4;WDR64,synonymous_variant,p.=,ENST00000425826,;WDR64,intron_variant,,ENST00000437684,;WDR64,intron_variant,,ENST00000414635,;WDR64,synonymous_variant,p.=,ENST00000472717,;WDR64,non_coding_transcript_exon_variant,,ENST00000478331,; C ENST00000366552 Transcript synonymous_variant 2625/4371 2418/3246 806/1081 D gaT/gaC 1 1 WDR64 HGNC HGNC:26570 protein_coding YES ENSP00000355510 B1ANS9 UPI0000519142 NM_144625.4 20/27 Gene3D:2.130.10.10,hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF124,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 241775122 241775122 T C 1 0 0 0 0 0 0 0 1 17874 1403 49 5 5 WDR64 1 241775122 Silent SNP T C3N-01410_T 844370 241775122 7181300 22 22922 ZNF669 0 . GRCh38 1 247100949 247100949 + Nonsense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.820G>T p.Gly274Ter p.G274* ENST00000343381 4/4 126 98 28 141 141 0 strelka-varscan ZNF669,stop_gained,p.Gly274Ter,ENST00000343381,NM_024804.2;ZNF669,stop_gained,p.Gly188Ter,ENST00000448299,NM_001142572.1;ZNF669,3_prime_UTR_variant,,ENST00000366501,;ZNF669,downstream_gene_variant,,ENST00000476158,;ZNF669,downstream_gene_variant,,ENST00000366500,; A ENST00000343381 Transcript stop_gained 993/1951 820/1395 274/464 G/* Gga/Tga 1 -1 ZNF669 HGNC HGNC:25736 protein_coding YES CCDS31088.1 ENSP00000342818 Q96BR6 A0A024R5S3 UPI000013E1E0 NM_024804.2 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF127,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 247100949 247100949 C A 1 0 0 0 0 0 1 0 0 18650 690 24 2 2 ZNF669 1 247100949 Nonsense_Mutation SNP C C3N-01410_T 5325827 247100949 1855473 23 22923 OR2T10 0 . GRCh38 1 248593351 248593351 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.418G>T p.Val140Leu p.V140L ENST00000330500 1/1 331 285 46 381 380 1 strelka-varscan OR2T10,missense_variant,p.Val140Leu,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; A ENST00000330500 Transcript missense_variant 418/939 418/939 140/312 V/L Gta/Tta 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 tolerated(0.32) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 248593351 248593351 C A 1 0 0 0 0 1 0 0 0 11095 507 18 2 2 OR2T10 1 248593351 Missense_Mutation SNP C C3N-01410_T 1492402 248593351 363071 24 22924 GREB1 0 . GRCh38 2 11634195 11634195 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.5056C>A p.Pro1686Thr p.P1686T ENST00000381486 29/33 354 274 80 379 379 0 strelka-varscan-mutect GREB1,missense_variant,p.Pro1686Thr,ENST00000381486,NM_014668.3;GREB1,missense_variant,p.Pro1686Thr,ENST00000234142,;GREB1,missense_variant,p.Pro684Thr,ENST00000396123,; A ENST00000381486 Transcript missense_variant 5356/8484 5056/5850 1686/1949 P/T Ccc/Acc 1 1 GREB1 HGNC HGNC:24885 protein_coding YES CCDS42655.1 ENSP00000370896 Q4ZG55 UPI0000163937 NM_014668.3 deleterious(0.02) 29/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF13 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 11634195 11634195 C A 1 0 0 0 0 1 0 0 0 6639 623 22 2 2 GREB1 2 11634195 Missense_Mutation SNP C C3N-01410_T 11634195 230559334 25 22925 TRIB2 0 . GRCh38 2 12718552 12718552 + Missense_Mutation SNP A A C novel C3N-01410_T C3N-01410_N A A c.245A>C p.His82Pro p.H82P ENST00000155926 1/3 148 115 33 135 135 0 strelka-varscan-mutect TRIB2,missense_variant,p.His82Pro,ENST00000155926,NM_021643.3;TRIB2,missense_variant,p.His82Pro,ENST00000405331,;TRIB2,intron_variant,,ENST00000381465,;RP11-333O1.1,downstream_gene_variant,,ENST00000569860,;TRIB2,downstream_gene_variant,,ENST00000483034,; C ENST00000155926 Transcript missense_variant 1664/4391 245/1032 82/343 H/P cAc/cCc 1 1 TRIB2 HGNC HGNC:30809 protein_coding YES CCDS1683.1 ENSP00000155926 Q92519 UPI0000051C55 NM_021643.3 tolerated(0.35) 1/3 Gene3D:3.30.200.20,PROSITE_profiles:PS50011,hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF15,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 12718552 12718552 A C 1 0 0 0 0 1 0 0 0 16972 159 6 5 5 TRIB2 2 12718552 Missense_Mutation SNP A C3N-01410_T 1084357 12718552 229474977 26 22926 APOB 0 . GRCh38 2 21006451 21006451 + Missense_Mutation SNP C C T rs150790543 C3N-01410_T C3N-01410_N C C c.10417G>A p.Ala3473Thr p.A3473T ENST00000233242 26/29 301 227 74 251 251 0 strelka-varscan APOB,missense_variant,p.Ala3473Thr,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 10545/14121 10417/13692 3473/4563 A/T Gct/Act rs150790543,COSM1245204 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(0.19) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 21006451 21006451 C T 1 0 0 0 0 1 0 0 0 907 768 27 1 1 APOB 2 21006451 Missense_Mutation SNP C C3N-01410_T 8287899 21006451 221187078 27 22927 CGREF1 0 . GRCh38 2 27102405 27102405 + Missense_Mutation SNP G G C rs768771588 C3N-01410_T C3N-01410_N G G c.172C>G p.Leu58Val p.L58V ENST00000402394 4/6 294 259 35 273 272 1 strelka-varscan CGREF1,missense_variant,p.Leu58Val,ENST00000402394,NM_006569.5;CGREF1,missense_variant,p.Leu58Val,ENST00000312734,;CGREF1,missense_variant,p.Leu58Val,ENST00000402550,NM_001166240.1;CGREF1,missense_variant,p.Leu180Val,ENST00000404694,;CGREF1,missense_variant,p.Leu58Val,ENST00000405600,NM_001166239.1;CGREF1,missense_variant,p.Leu58Val,ENST00000260595,;KHK,downstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,downstream_gene_variant,,ENST00000260598,NM_006488.2;KHK,downstream_gene_variant,,ENST00000429697,;KHK,downstream_gene_variant,,ENST00000490823,;CGREF1,non_coding_transcript_exon_variant,,ENST00000467539,;CGREF1,intron_variant,,ENST00000440612,;KHK,downstream_gene_variant,,ENST00000464371,;KHK,downstream_gene_variant,,ENST00000469936,; C ENST00000402394 Transcript missense_variant 441/1906 172/957 58/318 L/V Cta/Gta rs768771588 1 -1 CGREF1 HGNC HGNC:16962 protein_coding YES CCDS33162.2 ENSP00000385452 Q99674 UPI000013D0EB NM_006569.5 tolerated(0.06) 4/6 hmmpanther:PTHR23104,hmmpanther:PTHR23104:SF11 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 27102405 27102405 G C 1 0 0 0 0 1 0 0 0 3063 1020 36 4 4 CGREF1 2 27102405 Missense_Mutation SNP G C3N-01410_T 6095954 27102405 215091124 28 22928 C2orf16 0 . GRCh38 2 27578872 27578873 + Frame_Shift_Ins INS - - A novel C3N-01410_T C3N-01410_N - - c.2306dupA p.Asn769LysfsTer10 p.N769Kfs*10 ENST00000408964 1/1 283 253 30 273 273 0 sindel-varindel-pindel C2orf16,frameshift_variant,p.Asn769LysfsTer10,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; A ENST00000408964 Transcript frameshift_variant 2351-2352/6199 2300-2301/5955 767/1984 I/IX ata/atAa 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 1/1 hmmpanther:PTHR33888 HIGH insertion 6 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 75 27578872 27578872 - A 1 0 1 1 0 0 0 0 0 2032 1406 49 0 0 C2orf16 2 27578872 Frame_Shift_Ins INS - C3N-01410_T 476467 27578872 214614657 29 22929 CAPN14 0 . GRCh38 2 31194408 31194408 + Splice_Site SNP C C T novel C3N-01410_T C3N-01410_N C C c.950+1G>A p.X317_splice ENST00000403897 261 187 74 265 265 0 strelka-varscan CAPN14,splice_donor_variant,,ENST00000403897,NM_001145122.1;CAPN14,splice_donor_variant,,ENST00000398824,NM_001321270.1; T ENST00000403897 Transcript splice_donor_variant -/2197 950/2055 317/684 1 -1 CAPN14 HGNC HGNC:16664 protein_coding YES CCDS46254.1 ENSP00000385247 A8MX76 UPI000173A463 NM_001145122.1 9/21 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 75 31194408 31194408 C T 1 0 0 0 0 0 0 1 0 2319 521 18 3 3 CAPN14 2 31194408 Splice_Site SNP C C3N-01410_T 3615536 31194408 210999121 30 22930 IMMT 0 . GRCh38 2 86144466 86144466 + Nonsense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.2079T>A p.Tyr693Ter p.Y693* ENST00000410111 15/15 487 332 155 390 390 0 strelka-varscan-mutect IMMT,stop_gained,p.Tyr693Ter,ENST00000410111,NM_006839.2;IMMT,stop_gained,p.Tyr682Ter,ENST00000449247,NM_001100170.1;IMMT,stop_gained,p.Tyr692Ter,ENST00000442664,NM_001100169.1;IMMT,stop_gained,p.Tyr594Ter,ENST00000254636,;IMMT,stop_gained,p.Tyr646Ter,ENST00000409051,;IMMT,stop_gained,p.Tyr548Ter,ENST00000419070,;IMMT,stop_gained,p.Tyr307Ter,ENST00000620815,;PTCD3,downstream_gene_variant,,ENST00000254630,NM_017952.5; T ENST00000410111 Transcript stop_gained 2467/3001 2079/2277 693/758 Y/* taT/taA 1 -1 IMMT HGNC HGNC:6047 protein_coding YES CCDS46355.1 ENSP00000387262 Q16891 UPI0000073828 NM_006839.2 15/15 hmmpanther:PTHR15415:SF7,hmmpanther:PTHR15415,Pfam_domain:PF09731 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 86144466 86144466 A T 1 0 0 0 0 0 1 0 0 7621 224 8 4 4 IMMT 2 86144466 Nonsense_Mutation SNP A C3N-01410_T 54950058 86144466 156049063 31 22931 ANAPC1 0 . GRCh38 2 111778681 111778681 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.5379G>T p.Met1793Ile p.M1793I ENST00000341068 45/48 86 73 13 85 85 0 strelka-varscan-mutect ANAPC1,missense_variant,p.Met1793Ile,ENST00000341068,NM_022662.3;ANAPC1,missense_variant,p.Met1328Ile,ENST00000427997,;ANAPC1,non_coding_transcript_exon_variant,,ENST00000462785,; A ENST00000341068 Transcript missense_variant 6152/8262 5379/5835 1793/1944 M/I atG/atT 1 -1 ANAPC1 HGNC HGNC:19988 protein_coding YES CCDS2093.1 ENSP00000339109 Q9H1A4 UPI000006EC6E NM_022662.3 tolerated(1) 45/48 hmmpanther:PTHR12827 MODERATE 1 SNV 1 1 PASS rs1422897069 . 0 202 8 0 0 0 0 0 -20 0.9999981 1 1 1 0 A 3 1 75 111778681 111778681 C A 1 0 0 0 0 1 0 0 0 695 594 21 2 2 ANAPC1 2 111778681 Missense_Mutation SNP C C3N-01410_T 25634215 111778681 130414848 32 22932 CNTNAP5 0 . GRCh38 2 124446766 124446766 + Silent SNP G G T rs370435489 C3N-01410_T C3N-01410_N G G c.747G>T p.= p.A249A ENST00000431078 6/24 67 55 12 76 76 0 strelka-varscan-mutect CNTNAP5,synonymous_variant,p.=,ENST00000431078,NM_130773.3; T ENST00000431078 Transcript synonymous_variant 1111/5284 747/3921 249/1306 A gcG/gcT rs370435489 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 6/24 PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs370435489 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 124446766 124446766 G T 1 0 0 0 0 0 0 0 1 3432 1074 38 1 1 CNTNAP5 2 124446766 Silent SNP G C3N-01410_T 12668085 124446766 117746763 33 22933 PROC 0 . GRCh38 2 127423380 127423380 + Silent SNP G G A C3N-01410_T C3N-01410_N G G c.507G>A p.= p.G169G ENST00000234071 6/9 77 66 11 86 86 0 strelka-varscan-mutect PROC,synonymous_variant,p.=,ENST00000234071,NM_000312.3;PROC,synonymous_variant,p.=,ENST00000409048,;PROC,synonymous_variant,p.=,ENST00000402125,;PROC,synonymous_variant,p.=,ENST00000442644,;PROC,downstream_gene_variant,,ENST00000427769,;PROC,downstream_gene_variant,,ENST00000429925,;MIR4783,downstream_gene_variant,,ENST00000580343,;PROC,non_coding_transcript_exon_variant,,ENST00000464089,;PROC,downstream_gene_variant,,ENST00000431364,;PROC,downstream_gene_variant,,ENST00000474030,;PROC,downstream_gene_variant,,ENST00000419985,; A ENST00000234071 Transcript synonymous_variant 594/1773 507/1386 169/461 G ggG/ggA COSM5523583,COSM5523584 1 1 PROC HGNC HGNC:9451 protein_coding YES CCDS2145.1 ENSP00000234071 P04070 UPI0000001646 NM_000312.3 6/9 hmmpanther:PTHR24278,hmmpanther:PTHR24278:SF0,PROSITE_patterns:PS01186,PIRSF_domain:PIRSF001143,Pfam_domain:PF14670,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF50494 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 203 6 0 0 0 0 0 -19.99995 0.9999999 1 1 1 0 A 2 1 75 127423380 127423380 G A 1 0 0 0 0 0 0 0 1 12679 1219 43 3 3 PROC 2 127423380 Silent SNP G C3N-01410_T 2976614 127423380 114770149 34 22934 MYO7B 0 . GRCh38 2 127625466 127625466 + Frame_Shift_Del DEL C C - novel C3N-01410_T C3N-01410_N C C c.4072delC p.His1358ThrfsTer70 p.H1358Tfs*70 ENST00000428314 30/47 99 79 20 118 118 0 sindel-varindel-pindel MYO7B,frameshift_variant,p.His1358ThrfsTer70,ENST00000428314,NM_001080527.1;MYO7B,frameshift_variant,p.His1358ThrfsTer70,ENST00000409816,;MYO7B,frameshift_variant,p.His211ThrfsTer70,ENST00000409090,;MYO7B,downstream_gene_variant,,ENST00000437387,;RP11-286H15.1,downstream_gene_variant,,ENST00000609697,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,; - ENST00000428314 Transcript frameshift_variant 4121/6715 4068/6351 1356/2116 I/X atC/at 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 30/47 Gene3D:1.20.80.10,PROSITE_profiles:PS50057,SMART_domains:SM00295,Superfamily_domains:SSF47031 HIGH 1 deletion 5 4 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 75 127625466 127625466 C - 1 0 1 0 1 0 0 0 0 10084 845 30 0 0 MYO7B 2 127625466 Frame_Shift_Del DEL C C3N-01410_T 202086 127625466 114568063 35 22935 LRP1B 0 . GRCh38 2 140274460 140274460 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.13106G>T p.Cys4369Phe p.C4369F ENST00000389484 85/91 228 193 35 346 346 0 strelka-mutect LRP1B,missense_variant,p.Cys4369Phe,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Cys601Phe,ENST00000437977,;LRP1B,missense_variant,p.Cys101Phe,ENST00000442974,; A ENST00000389484 Transcript missense_variant 14078/16535 13106/13800 4369/4599 C/F tGc/tTc 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 85/91 SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 140274460 140274460 C A 1 0 0 0 0 1 0 0 0 8850 710 25 2 2 LRP1B 2 140274460 Missense_Mutation SNP C C3N-01410_T 12648994 140274460 101919069 36 22936 GTDC1 0 . GRCh38 2 144208613 144208613 + Nonsense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.169G>T p.Glu57Ter p.E57* ENST00000392869 3/11 125 106 19 98 98 0 strelka-varscan-mutect GTDC1,stop_gained,p.Glu57Ter,ENST00000392869,;GTDC1,stop_gained,p.Glu57Ter,ENST00000409214,NM_001006636.3;GTDC1,stop_gained,p.Glu57Ter,ENST00000542155,NM_001164629.3;GTDC1,stop_gained,p.Glu57Ter,ENST00000344850,;GTDC1,stop_gained,p.Glu57Ter,ENST00000392867,NM_024659.4;GTDC1,stop_gained,p.Glu57Ter,ENST00000241391,NM_001284233.1;GTDC1,stop_gained,p.Glu57Ter,ENST00000409298,;GTDC1,stop_gained,p.Glu57Ter,ENST00000437114,;GTDC1,stop_gained,p.Glu57Ter,ENST00000417450,;GTDC1,intron_variant,,ENST00000463875,NM_001284234.1;GTDC1,downstream_gene_variant,,ENST00000467352,;GTDC1,stop_gained,p.Glu57Ter,ENST00000415569,;GTDC1,stop_gained,p.Glu57Ter,ENST00000392871,;GTDC1,stop_gained,p.Glu57Ter,ENST00000429978,;GTDC1,non_coding_transcript_exon_variant,,ENST00000491448,;GTDC1,non_coding_transcript_exon_variant,,ENST00000484303,; A ENST00000392869 Transcript stop_gained 322/10514 169/1377 57/458 E/* Gag/Tag 1 -1 GTDC1 HGNC HGNC:20887 protein_coding YES CCDS33300.1 ENSP00000376608 Q4AE62 UPI000022BC3B 3/11 hmmpanther:PTHR13615,hmmpanther:PTHR13615:SF3,Pfam_domain:PF12038 HIGH 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 144208613 144208613 C A 1 0 0 0 0 0 1 0 0 6733 835 29 2 2 GTDC1 2 144208613 Nonsense_Mutation SNP C C3N-01410_T 3934153 144208613 97984916 37 22937 NEB 0 . GRCh38 2 151640501 151640501 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.8539G>T p.Val2847Leu p.V2847L ENST00000618972 61/183 354 274 80 457 457 0 strelka-varscan-mutect NEB,missense_variant,p.Val2847Leu,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Val2847Leu,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Val2847Leu,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Val2847Leu,ENST00000603639,;NEB,missense_variant,p.Val2847Leu,ENST00000604864,;NEB,missense_variant,p.Val2847Leu,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Val2847Leu,ENST00000172853,; A ENST00000618972 Transcript missense_variant 8742/26307 8539/25683 2847/8560 V/L Gtg/Ttg 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.44) 61/183 PROSITE_profiles:PS51216,hmmpanther:PTHR11039,hmmpanther:PTHR11039:SF37,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 151640501 151640501 C A 1 0 0 0 0 1 0 0 0 10326 565 20 2 2 NEB 2 151640501 Missense_Mutation SNP C C3N-01410_T 7431888 151640501 90553028 38 22938 TTN 0 . GRCh38 2 178720180 178720180 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.23462T>A p.Phe7821Tyr p.F7821Y ENST00000589042 81/363 202 172 30 171 171 0 strelka-varscan-mutect TTN,missense_variant,p.Phe7821Tyr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Phe7504Tyr,ENST00000591111,;TTN,missense_variant,p.Phe7504Tyr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Phe6577Tyr,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,upstream_gene_variant,,ENST00000590024,; T ENST00000589042 Transcript missense_variant 23687/109224 23462/107976 7821/35991 F/Y tTc/tAc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 81/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 178720180 178720180 A T 1 0 0 0 0 1 0 0 0 17245 246 9 4 4 TTN 2 178720180 Missense_Mutation SNP A C3N-01410_T 27079679 178720180 63473349 39 22939 TTN 0 . GRCh38 2 178775882 178775882 + Silent SNP C C T rs573823772 C3N-01410_T C3N-01410_N C C c.5982G>A p.= p.S1994S ENST00000589042 28/363 265 221 44 243 243 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN,synonymous_variant,p.=,ENST00000360870,NM_133379.4;TTN-AS1,intron_variant,,ENST00000629094,;TTN-AS1,upstream_gene_variant,,ENST00000582038,;TTN-AS1,downstream_gene_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000584485,;TTN-AS1,downstream_gene_variant,,ENST00000610005,; T ENST00000589042 Transcript synonymous_variant 6207/109224 5982/107976 1994/35991 S tcG/tcA rs573823772,COSM3379936,COSM3379937,COSM3379938,COSM3379939,COSM3379941 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 28/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 0,1,1,1,1,1 LOW 1 SNV 5 0,1,1,1,1,1 1 PASS rs573823772 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 178775882 178775882 C T 1 0 0 0 0 0 0 0 1 17245 639 23 1 1 TTN 2 178775882 Silent SNP C C3N-01410_T 55702 178775882 63417647 40 22940 CRYGC 0 . GRCh38 2 208128398 208128398 + Silent SNP G G T novel C3N-01410_T C3N-01410_N G G c.330C>A p.= p.P110P ENST00000282141 3/3 262 175 87 281 280 1 strelka-varscan-mutect CRYGC,synonymous_variant,p.=,ENST00000282141,NM_020989.3;CRYGD,upstream_gene_variant,,ENST00000264376,NM_006891.3; T ENST00000282141 Transcript synonymous_variant 368/629 330/525 110/174 P ccC/ccA 1 -1 CRYGC HGNC HGNC:2410 protein_coding YES CCDS2379.1 ENSP00000282141 P07315 A0A0X8GLL6 UPI000013DCBD NM_020989.3 3/3 PROSITE_profiles:PS50915,hmmpanther:PTHR11818:SF32,hmmpanther:PTHR11818,Pfam_domain:PF00030,Gene3D:2.60.20.10,SMART_domains:SM00247,Superfamily_domains:SSF49695 LOW 1 SNV 1 1 PASS rs864309689 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 208128398 208128398 G T 1 0 0 0 0 0 0 0 1 3718 1335 47 2 2 CRYGC 2 208128398 Silent SNP G C3N-01410_T 29352516 208128398 34065131 41 22941 ABCA12 0 . GRCh38 2 214978450 214978450 + Missense_Mutation SNP G G T rs142794443 C3N-01410_T C3N-01410_N G G c.4994C>A p.Thr1665Asn p.T1665N ENST00000272895 33/53 309 266 43 330 328 2 strelka-varscan-mutect ABCA12,missense_variant,p.Thr1665Asn,ENST00000272895,NM_173076.2;ABCA12,missense_variant,p.Thr1347Asn,ENST00000389661,NM_015657.3; T ENST00000272895 Transcript missense_variant 5214/9100 4994/7788 1665/2595 T/N aCc/aAc rs142794443 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 deleterious(0.01) 33/53 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF29 MODERATE 1 SNV 1 1 PASS rs142794443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 214978450 214978450 G T 1 0 0 0 0 1 0 0 0 34 1261 44 2 2 ABCA12 2 214978450 Missense_Mutation SNP G C3N-01410_T 6850052 214978450 27215079 42 22942 ESPNL 0 . GRCh38 2 238130924 238130924 + Missense_Mutation SNP G G T rs772056400 C3N-01410_T C3N-01410_N G G c.2210G>T p.Arg737Leu p.R737L ENST00000343063 9/9 147 120 27 91 91 0 strelka-varscan-mutect ESPNL,missense_variant,p.Arg737Leu,ENST00000343063,NM_194312.2;ESPNL,missense_variant,p.Arg693Leu,ENST00000409169,;ESPNL,missense_variant,p.Arg369Leu,ENST00000409506,NM_001308370.1;ESPNL,5_prime_UTR_variant,,ENST00000612395,;ESPNL,downstream_gene_variant,,ENST00000423032,;ESPNL,non_coding_transcript_exon_variant,,ENST00000477241,; T ENST00000343063 Transcript missense_variant 2473/4836 2210/3018 737/1005 R/L cGc/cTc rs772056400 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 deleterious(0) 9/9 hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153 MODERATE 1 SNV 2 1 PASS rs772056400 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 238130924 238130924 G T 1 0 0 0 0 1 0 0 0 5117 1087 38 1 1 ESPNL 2 238130924 Missense_Mutation SNP G C3N-01410_T 23152474 238130924 4062605 43 22943 CHL1 0 . GRCh38 3 399085 399085 + Missense_Mutation SNP C C A rs763802045 C3N-01410_T C3N-01410_N C C c.3322C>A p.Leu1108Ile p.L1108I ENST00000256509 26/28 177 111 66 259 259 0 strelka-varscan-mutect CHL1,missense_variant,p.Leu1108Ile,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Leu1055Ile,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Leu1092Ile,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Leu242Ile,ENST00000445697,;CHL1,3_prime_UTR_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant 3964/8023 3322/3675 1108/1224 L/I Ctt/Att rs763802045 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 deleterious(0.03) 26/28 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs763802045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 399085 399085 C A 1 0 0 0 0 1 0 0 0 3108 913 32 2 2 CHL1 3 399085 Missense_Mutation SNP C C3N-01410_T 399085 197896474 44 22944 ARPP21 0 . GRCh38 3 35729507 35729507 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1328C>A p.Pro443His p.P443H ENST00000417925 13/19 194 118 76 159 159 0 strelka-varscan-mutect ARPP21,missense_variant,p.Pro477His,ENST00000187397,NM_016300.4;ARPP21,missense_variant,p.Pro423His,ENST00000444190,NM_001267617.1;ARPP21,missense_variant,p.Pro443His,ENST00000417925,NM_001267619.1;ARPP21,missense_variant,p.Pro250His,ENST00000425289,;ARPP21,non_coding_transcript_exon_variant,,ENST00000476327,;ARPP21,missense_variant,p.Pro135His,ENST00000457165,;ARPP21,3_prime_UTR_variant,,ENST00000427590,;ARPP21,downstream_gene_variant,,ENST00000481854,; A ENST00000417925 Transcript missense_variant 1542/3086 1328/2442 443/813 P/H cCt/cAt 1 1 ARPP21 HGNC HGNC:16968 protein_coding YES CCDS58823.1 ENSP00000412326 Q9UBL0 UPI0000209B3D NM_001267619.1 deleterious(0) 13/19 hmmpanther:PTHR15672,hmmpanther:PTHR15672:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 35729507 35729507 C A 1 0 0 0 0 1 0 0 0 1121 681 24 2 2 ARPP21 3 35729507 Missense_Mutation SNP C C3N-01410_T 35330422 35729507 162566052 45 22945 SCN10A 0 . GRCh38 3 38713994 38713994 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.3768G>T p.= p.R1256R ENST00000449082 21/27 192 136 56 238 238 0 strelka-varscan-mutect SCN10A,synonymous_variant,p.=,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; A ENST00000449082 Transcript synonymous_variant 3768/6418 3768/5871 1256/1956 R cgG/cgT 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 21/27 Low_complexity_(Seg):seg,hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037,Gene3D:1.20.120.350,Pfam_domain:PF00520,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 38713994 38713994 C A 1 0 0 0 0 0 0 0 1 14181 726 26 2 2 SCN10A 3 38713994 Silent SNP C C3N-01410_T 2984487 38713994 159581565 46 22946 SCN10A 0 . GRCh38 3 38752450 38752450 + Silent SNP C C A C3N-01410_T C3N-01410_N C C c.1524G>T p.= p.R508R ENST00000449082 11/27 65 39 26 96 96 0 strelka-varscan-mutect SCN10A,synonymous_variant,p.=,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; A ENST00000449082 Transcript synonymous_variant 1524/6418 1524/5871 508/1956 R cgG/cgT COSM5399283 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 11/27 hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037 1 LOW 1 SNV 1 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 38752450 38752450 C A 1 0 0 0 0 0 0 0 1 14181 494 18 2 2 SCN10A 3 38752450 Silent SNP C C3N-01410_T 38456 38752450 159543109 47 22947 DOCK3 0 . GRCh38 3 51270884 51270884 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.2425G>A p.Ala809Thr p.A809T ENST00000266037 24/53 190 122 68 215 214 1 strelka-varscan DOCK3,missense_variant,p.Ala809Thr,ENST00000266037,NM_004947.4; A ENST00000266037 Transcript missense_variant 2448/8755 2425/6093 809/2030 A/T Gca/Aca 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 tolerated(0.1) 24/53 hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 51270884 51270884 G A 1 0 0 0 0 1 0 0 0 4503 1203 42 3 3 DOCK3 3 51270884 Missense_Mutation SNP G C3N-01410_T 12518434 51270884 147024675 48 22948 GXYLT2 0 . GRCh38 3 72888471 72888471 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.238G>T p.Gly80Cys p.G80C ENST00000389617 1/7 27 19 8 37 37 0 strelka-varscan GXYLT2,missense_variant,p.Gly80Cys,ENST00000389617,NM_001080393.1;LAPTM4BP2,downstream_gene_variant,,ENST00000604542,; T ENST00000389617 Transcript missense_variant 399/3260 238/1332 80/443 G/C Ggc/Tgc 1 1 GXYLT2 HGNC HGNC:33383 protein_coding YES CCDS46870.1 ENSP00000374268 A0PJZ3 UPI00001D7E8F NM_001080393.1 deleterious(0) 1/7 Low_complexity_(Seg):seg,hmmpanther:PTHR12270,hmmpanther:PTHR12270:SF15 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 72888471 72888471 G T 1 0 0 0 0 1 0 0 0 6787 1232 43 2 2 GXYLT2 3 72888471 Missense_Mutation SNP G C3N-01410_T 21617587 72888471 125407088 49 22949 PDZRN3 0 . GRCh38 3 73391096 73391096 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1275G>T p.Met425Ile p.M425I ENST00000263666 6/10 132 111 21 166 166 0 strelka-varscan PDZRN3,missense_variant,p.Met425Ile,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Met82Ile,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Met142Ile,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Met82Ile,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Met22Ile,ENST00000494559,;PDZRN3,missense_variant,p.Met123Ile,ENST00000492909,NM_001303139.1;PDZRN3,non_coding_transcript_exon_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000498048,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000477434,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000484487,;PDZRN3,upstream_gene_variant,,ENST00000478209,; A ENST00000263666 Transcript missense_variant 1390/4248 1275/3201 425/1066 M/I atG/atT 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 tolerated(0.21) 6/10 PROSITE_profiles:PS50106,hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Pfam_domain:PF00595,Gene3D:2.30.42.10,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999944 1 1 1 0 A 3 1 75 73391096 73391096 C A 1 0 0 0 0 1 0 0 0 11797 826 29 2 2 PDZRN3 3 73391096 Missense_Mutation SNP C C3N-01410_T 502625 73391096 124904463 50 22950 CBLB 0 . GRCh38 3 105702275 105702275 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1778G>T p.Trp593Leu p.W593L ENST00000264122 12/19 398 225 173 357 356 1 strelka-varscan CBLB,missense_variant,p.Trp593Leu,ENST00000264122,NM_001321786.1,NM_001321788.1,NM_170662.3;CBLB,missense_variant,p.Trp593Leu,ENST00000403724,;CBLB,missense_variant,p.Trp593Leu,ENST00000405772,;CBLB,upstream_gene_variant,,ENST00000394030,; A ENST00000264122 Transcript missense_variant 2100/6780 1778/2949 593/982 W/L tGg/tTg 1 -1 CBLB HGNC HGNC:1542 protein_coding YES CCDS2948.1 ENSP00000264122 Q13191 UPI00001AE89F NM_001321786.1,NM_001321788.1,NM_170662.3 tolerated_low_confidence(0.1) 12/19 hmmpanther:PTHR23007:SF3,hmmpanther:PTHR23007 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 105702275 105702275 C A 1 0 0 0 0 1 0 0 0 2402 595 21 2 2 CBLB 3 105702275 Missense_Mutation SNP C C3N-01410_T 32311179 105702275 92593284 51 22951 PLA1A 0 . GRCh38 3 119628779 119628779 + Missense_Mutation SNP G G T rs374852182 C3N-01410_T C3N-01410_N G G c.1200G>T p.Lys400Asn p.K400N ENST00000273371 10/11 262 142 120 268 268 0 strelka-varscan PLA1A,missense_variant,p.Lys400Asn,ENST00000273371,NM_015900.3;PLA1A,missense_variant,p.Lys384Asn,ENST00000494440,NM_001293225.1;PLA1A,missense_variant,p.Lys384Asn,ENST00000495992,NM_001206960.1;PLA1A,missense_variant,p.Lys227Asn,ENST00000488919,NM_001206961.1; T ENST00000273371 Transcript missense_variant 1272/1786 1200/1371 400/456 K/N aaG/aaT rs374852182 1 1 PLA1A HGNC HGNC:17661 protein_coding YES CCDS2991.1 ENSP00000273371 Q53H76 UPI0000073F97 NM_015900.3 deleterious(0) 10/11 hmmpanther:PTHR11610:SF111,hmmpanther:PTHR11610,PIRSF_domain:PIRSF000865 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 119628779 119628779 G T 1 0 0 0 0 1 0 0 0 12084 1020 36 2 2 PLA1A 3 119628779 Missense_Mutation SNP G C3N-01410_T 13926504 119628779 78666780 52 22952 ERICH6 0 . GRCh38 3 150659903 150659903 + Missense_Mutation SNP C C T C3N-01410_T C3N-01410_N C C c.1981G>A p.Glu661Lys p.E661K ENST00000295910 14/14 85 48 37 91 91 0 strelka-varscan ERICH6,missense_variant,p.Glu661Lys,ENST00000295910,NM_152394.4;ERICH6,missense_variant,p.Glu515Lys,ENST00000491361,NM_001308234.1;ERICH6,non_coding_transcript_exon_variant,,ENST00000491716,; T ENST00000295910 Transcript missense_variant 2034/2052 1981/1992 661/663 E/K Gaa/Aaa COSM4533440 1 -1 ERICH6 HGNC HGNC:28602 protein_coding YES CCDS3151.2 ENSP00000295910 Q7L0X2 UPI000023281A NM_152394.4 tolerated(0.09) 14/14 hmmpanther:PTHR23093 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 150659903 150659903 C T 1 0 0 0 0 1 0 0 0 5086 835 29 3 3 ERICH6 3 150659903 Missense_Mutation SNP C C3N-01410_T 31031124 150659903 47635656 53 22953 ZBBX 0 . GRCh38 3 167333921 167333921 + Missense_Mutation SNP G G C rs868172448 C3N-01410_T C3N-01410_N G G c.593C>G p.Pro198Arg p.P198R ENST00000455345 9/21 130 79 51 117 117 0 strelka-varscan ZBBX,missense_variant,p.Pro198Arg,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Pro198Arg,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Pro198Arg,ENST00000307529,;ZBBX,missense_variant,p.Pro169Arg,ENST00000392767,;ZBBX,missense_variant,p.Pro169Arg,ENST00000392764,NM_001199202.1;ZBBX,intron_variant,,ENST00000469220,; C ENST00000455345 Transcript missense_variant 877/3185 593/2520 198/839 P/R cCa/cGa rs868172448 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 deleterious(0) 9/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 167333921 167333921 G C 1 0 0 0 0 1 0 0 0 18078 1348 47 4 4 ZBBX 3 167333921 Missense_Mutation SNP G C3N-01410_T 16674018 167333921 30961638 54 22954 CCDC39 0 . GRCh38 3 180651534 180651534 + Splice_Site SNP C C A novel C3N-01410_T C3N-01410_N C C c.1035-1G>T p.X345_splice ENST00000442201 124 64 60 174 174 0 strelka-varscan CCDC39,splice_acceptor_variant,,ENST00000442201,NM_181426.1;CCDC39,splice_acceptor_variant,,ENST00000476379,; A ENST00000442201 Transcript splice_acceptor_variant -/3279 1035/2826 345/941 1 -1 CCDC39 HGNC HGNC:25244 protein_coding YES CCDS46964.1 ENSP00000405708 Q9UFE4 UPI00015D7298 NM_181426.1 8/19 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 75 180651534 180651534 C A 1 0 0 0 0 0 0 1 0 2520 695 24 2 2 CCDC39 3 180651534 Splice_Site SNP C C3N-01410_T 13317613 180651534 17644025 55 22955 TNK2 0 . GRCh38 3 195870135 195870135 + Frame_Shift_Del DEL G G - rs757643410 C3N-01410_T C3N-01410_N G G c.1711delC p.Gln571SerfsTer3 p.Q571Sfs*3 ENST00000381916 11/15 23 10 13 13 13 0 sindel-varindel TNK2,frameshift_variant,p.Gln508SerfsTer3,ENST00000333602,NM_005781.4;TNK2,frameshift_variant,p.Gln540SerfsTer3,ENST00000428187,NM_001308046.1;TNK2,frameshift_variant,p.Gln571SerfsTer3,ENST00000381916,NM_001010938.1;TNK2,frameshift_variant,p.Gln60SerfsTer3,ENST00000416152,;TNK2,frameshift_variant,p.Gln118SerfsTer3,ENST00000424563,;TNK2,frameshift_variant,p.Gln153SerfsTer3,ENST00000411741,;TNK2,non_coding_transcript_exon_variant,,ENST00000478623,;TNK2,non_coding_transcript_exon_variant,,ENST00000495247,;TNK2,downstream_gene_variant,,ENST00000486523,;TNK2,3_prime_UTR_variant,,ENST00000439230,;TNK2,non_coding_transcript_exon_variant,,ENST00000481865,;TNK2,non_coding_transcript_exon_variant,,ENST00000464041,;TNK2,non_coding_transcript_exon_variant,,ENST00000489628,;TNK2,non_coding_transcript_exon_variant,,ENST00000478715,;TNK2,upstream_gene_variant,,ENST00000420716,;TNK2,downstream_gene_variant,,ENST00000468680,; - ENST00000381916 Transcript frameshift_variant 1856/4223 1711/3261 571/1086 Q/X Cag/ag rs757643410,COSM1421943,COSM1421944,COSM1421945 1 -1 TNK2 HGNC HGNC:19297 protein_coding YES CCDS33927.1 ENSP00000371341 Q07912 UPI00004C9B08 NM_001010938.1 11/15 Pfam_domain:PF09027 0,1,1,1 HIGH 1 deletion 2 0,1,1,1 1 PASS . . 3 185 22 0 0 0 0 0 -20 0.9994192 0 1 1 0 - 7 5 75 195870135 195870135 G - 1 0 1 0 1 0 0 0 0 16791 1357 47 0 0 TNK2 3 195870135 Frame_Shift_Del DEL G C3N-01410_T 15218601 195870135 2425424 56 22956 PROM1 0 . GRCh38 4 16006673 16006673 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.1319T>A p.Val440Asp p.V440D ENST00000510224 13/28 158 129 29 202 202 0 strelka-varscan-mutect PROM1,missense_variant,p.Val431Asp,ENST00000505450,NM_001145848.1;PROM1,missense_variant,p.Val431Asp,ENST00000508167,NM_001145847.1;PROM1,missense_variant,p.Val440Asp,ENST00000510224,;PROM1,missense_variant,p.Val440Asp,ENST00000447510,NM_006017.2;PROM1,missense_variant,p.Val440Asp,ENST00000540805,NM_001145849.1,NM_001145851.1;PROM1,missense_variant,p.Val440Asp,ENST00000539194,NM_001145850.1,NM_001145852.1;PROM1,3_prime_UTR_variant,,ENST00000511153,; T ENST00000510224 Transcript missense_variant 1568/4006 1319/2598 440/865 V/D gTc/gAc 1 -1 PROM1 HGNC HGNC:9454 protein_coding YES CCDS47029.1 ENSP00000426809 O43490 UPI000004ECD6 deleterious(0) 13/28 Transmembrane_helices:TMhelix,hmmpanther:PTHR22730,hmmpanther:PTHR22730:SF3,Pfam_domain:PF05478 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 16006673 16006673 A T 1 0 0 0 0 1 0 0 0 12687 275 10 4 4 PROM1 4 16006673 Missense_Mutation SNP A C3N-01410_T 16006673 174207882 57 22957 CORIN 0 . GRCh38 4 47680236 47680236 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1037C>A p.Thr346Lys p.T346K ENST00000273857 8/22 169 145 24 147 147 0 strelka-varscan-mutect CORIN,missense_variant,p.Thr346Lys,ENST00000273857,NM_006587.3;CORIN,missense_variant,p.Thr207Lys,ENST00000508498,;CORIN,missense_variant,p.Thr279Lys,ENST00000502252,;CORIN,intron_variant,,ENST00000610355,NM_001278585.1;CORIN,intron_variant,,ENST00000505909,;CORIN,intron_variant,,ENST00000504584,NM_001278586.1;CORIN,non_coding_transcript_exon_variant,,ENST00000502726,;CORIN,intron_variant,,ENST00000503821,; T ENST00000273857 Transcript missense_variant 1037/4852 1037/3129 346/1042 T/K aCa/aAa 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 tolerated(1) 8/22 Gene3D:4.10.400.10,Pfam_domain:PF00057,PIRSF_domain:PIRSF036376,PROSITE_profiles:PS50068,hmmpanther:PTHR24270,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 47680236 47680236 G T 1 0 0 0 0 1 0 0 0 3546 1377 48 2 2 CORIN 4 47680236 Missense_Mutation SNP G C3N-01410_T 31673563 47680236 142534319 58 22958 FRYL 0 . GRCh38 4 48595902 48595902 + Silent SNP A A C novel C3N-01410_T C3N-01410_N A A c.1134T>G p.= p.T378T ENST00000358350 14/64 137 123 14 130 129 1 strelka-varscan-mutect FRYL,synonymous_variant,p.=,ENST00000358350,NM_015030.1;FRYL,synonymous_variant,p.=,ENST00000503238,;FRYL,synonymous_variant,p.=,ENST00000507711,;FRYL,synonymous_variant,p.=,ENST00000506685,; C ENST00000358350 Transcript synonymous_variant 1739/11706 1134/9042 378/3013 T acT/acG 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 14/64 Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 48595902 48595902 A C 1 0 0 0 0 0 0 0 1 5936 318 11 5 5 FRYL 4 48595902 Silent SNP A C3N-01410_T 915666 48595902 141618653 59 22959 PDGFRA 0 . GRCh38 4 54267420 54267420 + Silent SNP G G A novel C3N-01410_T C3N-01410_N G G c.891G>A p.= p.R297R ENST00000257290 6/23 384 313 71 369 369 0 strelka-varscan-mutect PDGFRA,synonymous_variant,p.=,ENST00000257290,NM_006206.4;RP11-231C18.3,intron_variant,,ENST00000507166,;PDGFRA,downstream_gene_variant,,ENST00000508170,;PDGFRA,downstream_gene_variant,,ENST00000504461,;PDGFRA,downstream_gene_variant,,ENST00000503856,;PDGFRA,downstream_gene_variant,,ENST00000512522,;PDGFRA,synonymous_variant,p.=,ENST00000509490,;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092,; A ENST00000257290 Transcript synonymous_variant 1222/6576 891/3270 297/1089 R agG/agA 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 6/23 PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000615,Pfam_domain:PF07679,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 54267420 54267420 G A 1 0 0 0 0 0 0 0 1 11749 1223 43 3 3 PDGFRA 4 54267420 Silent SNP G C3N-01410_T 5671518 54267420 135947135 60 22960 ADGRL3 0 . GRCh38 4 62070127 62070127 + Missense_Mutation SNP C C T C3N-01410_T C3N-01410_N C C c.3629C>T p.Ala1210Val p.A1210V ENST00000514591 25/25 96 80 16 94 94 0 strelka-varscan-mutect ADGRL3,missense_variant,p.Ala1210Val,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.Ala1321Val,ENST00000506720,;ADGRL3,missense_variant,p.Ala1312Val,ENST00000506746,;ADGRL3,missense_variant,p.Ala1269Val,ENST00000507625,;ADGRL3,missense_variant,p.Ala1253Val,ENST00000508946,;ADGRL3,missense_variant,p.Ala1244Val,ENST00000514996,;ADGRL3,missense_variant,p.Ala659Val,ENST00000502815,;ADGRL3,synonymous_variant,p.=,ENST00000512091,NM_001322246.1;ADGRL3,synonymous_variant,p.=,ENST00000509896,;ADGRL3,synonymous_variant,p.=,ENST00000511324,;ADGRL3,synonymous_variant,p.=,ENST00000508693,;ADGRL3,synonymous_variant,p.=,ENST00000507164,;ADGRL3,synonymous_variant,p.=,ENST00000506700,;ADGRL3,synonymous_variant,p.=,ENST00000504896,;ADGRL3,synonymous_variant,p.=,ENST00000514157,;ADGRL3-AS1,downstream_gene_variant,,ENST00000506704,;ADGRL3-AS1,downstream_gene_variant,,ENST00000504135,;ADGRL3-AS1,downstream_gene_variant,,ENST00000509461,; T ENST00000514591 Transcript missense_variant 3958/6297 3629/4410 1210/1469 A/V gCc/gTc COSM3303208,COSM3303209,COSM3303210 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 tolerated(0.09) 25/25 hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF02354 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 75 62070127 62070127 C T 1 0 0 0 0 1 0 0 0 377 748 26 3 3 ADGRL3 4 62070127 Missense_Mutation SNP C C3N-01410_T 7802707 62070127 128144428 61 22961 SLC4A4 0 . GRCh38 4 71339446 71339446 + Silent SNP G G C rs772559707 C3N-01410_T C3N-01410_N G G c.330G>C p.= p.T110T ENST00000425175 4/25 279 196 83 251 251 0 strelka-varscan-mutect SLC4A4,synonymous_variant,p.=,ENST00000340595,NM_003759.3;SLC4A4,synonymous_variant,p.=,ENST00000425175,NM_001134742.1;SLC4A4,synonymous_variant,p.=,ENST00000264485,NM_001098484.2;SLC4A4,synonymous_variant,p.=,ENST00000351898,;SLC4A4,synonymous_variant,p.=,ENST00000512686,;SLC4A4,non_coding_transcript_exon_variant,,ENST00000514331,; C ENST00000425175 Transcript synonymous_variant 447/7596 330/3285 110/1094 T acG/acC rs772559707 1 1 SLC4A4 HGNC HGNC:11030 protein_coding YES CCDS47071.1 ENSP00000393557 Q9Y6R1 A5JJ20 UPI000152897D NM_001134742.1 4/25 Gene3D:1hynR00,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF10,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 5 1 PASS rs772559707 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 71339446 71339446 G C 1 0 0 0 0 0 0 0 1 14933 1103 39 4 4 SLC4A4 4 71339446 Silent SNP G C3N-01410_T 9269319 71339446 118875109 62 22962 PKD2 0 . GRCh38 4 88008163 88008163 + Missense_Mutation SNP T T G novel C3N-01410_T C3N-01410_N T T c.430T>G p.Tyr144Asp p.Y144D ENST00000237596 1/15 157 140 17 133 133 0 strelka-varscan-mutect PKD2,missense_variant,p.Tyr144Asp,ENST00000237596,NM_000297.3;PKD2,upstream_gene_variant,,ENST00000506727,; G ENST00000237596 Transcript missense_variant 496/5056 430/2907 144/968 Y/D Tac/Gac 1 1 PKD2 HGNC HGNC:9009 protein_coding YES CCDS3627.1 ENSP00000237596 Q13563 UPI000013CA1D NM_000297.3 tolerated(0.12) 1/15 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF114 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 88008163 88008163 T G 1 0 0 0 0 1 0 0 0 12062 1522 53 5 5 PKD2 4 88008163 Missense_Mutation SNP T C3N-01410_T 16668717 88008163 102206392 63 22963 FAT4 0 . GRCh38 4 125448975 125448975 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.7959G>T p.Glu2653Asp p.E2653D ENST00000394329 9/17 173 155 18 207 207 0 strelka-varscan-mutect FAT4,missense_variant,p.Glu2653Asp,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Glu951Asp,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; T ENST00000394329 Transcript missense_variant 7972/16123 7959/14946 2653/4981 E/D gaG/gaT 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.61) 9/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 125448975 125448975 G T 1 0 0 0 0 1 0 0 0 5552 933 33 2 2 FAT4 4 125448975 Missense_Mutation SNP G C3N-01410_T 37440812 125448975 64765580 64 22964 SMAD1 0 . GRCh38 4 145553799 145553799 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.1013A>G p.Tyr338Cys p.Y338C ENST00000515385 6/7 104 85 19 114 114 0 strelka-varscan-mutect SMAD1,missense_variant,p.Tyr338Cys,ENST00000515385,;SMAD1,missense_variant,p.Tyr338Cys,ENST00000302085,NM_005900.2;SMAD1,missense_variant,p.Tyr338Cys,ENST00000394092,NM_001003688.1;SMAD1,non_coding_transcript_exon_variant,,ENST00000510948,;SMAD1,non_coding_transcript_exon_variant,,ENST00000511125,;SMAD1,non_coding_transcript_exon_variant,,ENST00000511255,; G ENST00000515385 Transcript missense_variant 1555/2085 1013/1398 338/465 Y/C tAt/tGt 1 1 SMAD1 HGNC HGNC:6767 protein_coding YES CCDS3765.1 ENSP00000426568 Q15797 UPI0000135A76 deleterious(0.01) 6/7 Gene3D:2.60.200.10,Pfam_domain:PF03166,PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF23,SMART_domains:SM00524,Superfamily_domains:SSF49879 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 145553799 145553799 A G 1 0 0 0 0 1 0 0 0 15050 449 16 5 5 SMAD1 4 145553799 Missense_Mutation SNP A C3N-01410_T 20104824 145553799 44660756 65 22965 GLRA3 0 . GRCh38 4 174644032 174644032 + Silent SNP G G A novel C3N-01410_T C3N-01410_N G G c.1149C>T p.= p.F383F ENST00000274093 10/10 117 99 18 86 86 0 strelka-varscan-mutect GLRA3,synonymous_variant,p.=,ENST00000274093,NM_006529.3;GLRA3,synonymous_variant,p.=,ENST00000340217,NM_001042543.2; A ENST00000274093 Transcript synonymous_variant 1652/8770 1149/1395 383/464 F ttC/ttT 1 -1 GLRA3 HGNC HGNC:4328 protein_coding YES CCDS3822.1 ENSP00000274093 O75311 UPI0000001C50 NM_006529.3 10/10 hmmpanther:PTHR18945:SF455,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 174644032 174644032 G A 1 0 0 0 0 0 0 0 1 6335 1281 45 3 3 GLRA3 4 174644032 Silent SNP G C3N-01410_T 29090233 174644032 15570523 66 22966 TENM3 0 . GRCh38 4 182681888 182681888 + Nonsense_Mutation SNP G G T rs754999907 C3N-01410_T C3N-01410_N G G c.1909G>T p.Gly637Ter p.G637* ENST00000511685 11/28 171 133 38 223 222 1 strelka-varscan-mutect TENM3,stop_gained,p.Gly637Ter,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,;TENM3,non_coding_transcript_exon_variant,,ENST00000507737,; T ENST00000511685 Transcript stop_gained 2032/10896 1909/8100 637/2699 G/* Gga/Tga rs754999907,COSM3780248 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 11/28 Gene3D:2.10.25.10,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10,SMART_domains:SM00181 0,1 HIGH 1 SNV 5 0,1 1 PASS rs754999907 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 182681888 182681888 G T 1 0 0 0 0 0 1 0 0 16173 1233 43 2 2 TENM3 4 182681888 Nonsense_Mutation SNP G C3N-01410_T 8037856 182681888 7532667 67 22967 SLC12A7 0 . GRCh38 5 1111938 1111938 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.54G>T p.= p.G18G ENST00000264930 1/24 43 37 6 24 24 0 strelka-mutect SLC12A7,synonymous_variant,p.=,ENST00000264930,NM_006598.2; A ENST00000264930 Transcript synonymous_variant 98/5280 54/3252 18/1083 G ggG/ggT 1 -1 SLC12A7 HGNC HGNC:10915 protein_coding YES CCDS34129.1 ENSP00000264930 Q9Y666 UPI0000141815 NM_006598.2 1/24 LOW 1 SNV 1 1 PASS rs965334624 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 1111938 1111938 C A 1 0 0 0 0 0 0 0 1 14653 610 22 2 2 SLC12A7 5 1111938 Silent SNP C C3N-01410_T 1111938 180426321 68 22968 SEMA5A 0 . GRCh38 5 9066490 9066490 + Missense_Mutation SNP C C T novel C3N-01410_T C3N-01410_N C C c.2230G>A p.Glu744Lys p.E744K ENST00000382496 17/23 453 329 124 418 418 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Glu744Lys,ENST00000382496,NM_003966.2; T ENST00000382496 Transcript missense_variant 2896/11762 2230/3225 744/1074 E/K Gaa/Aaa 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 tolerated(0.4) 17/23 hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 9066490 9066490 C T 1 0 0 0 0 1 0 0 0 14313 864 30 3 3 SEMA5A 5 9066490 Missense_Mutation SNP C C3N-01410_T 7954552 9066490 172471769 69 22969 MARCH6 0 . GRCh38 5 10390432 10390432 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.508G>C p.Gly170Arg p.G170R ENST00000274140 6/26 243 177 66 241 241 0 strelka-varscan-mutect MARCH6,missense_variant,p.Gly170Arg,ENST00000274140,NM_005885.3;MARCH6,missense_variant,p.Gly122Arg,ENST00000449913,NM_001270660.1;MARCH6,missense_variant,p.Gly65Arg,ENST00000503788,NM_001270661.1;MARCH6,non_coding_transcript_exon_variant,,ENST00000507863,;MARCH6,non_coding_transcript_exon_variant,,ENST00000510872,;MARCH6,3_prime_UTR_variant,,ENST00000502795,;MARCH6,non_coding_transcript_exon_variant,,ENST00000511802,;MARCH6,non_coding_transcript_exon_variant,,ENST00000506131,; C ENST00000274140 Transcript missense_variant 640/9569 508/2733 170/910 G/R Ggg/Cgg 1 1 MARCH6 HGNC HGNC:30550 protein_coding YES CCDS34135.1 ENSP00000274140 O60337 UPI00001B94D6 NM_005885.3 deleterious(0) 6/26 hmmpanther:PTHR13145 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 10390432 10390432 G C 1 0 0 0 0 1 0 0 0 9230 1348 47 4 4 MARCH6 5 10390432 Missense_Mutation SNP G C3N-01410_T 1323942 10390432 171147827 70 22970 CDH18 0 . GRCh38 5 19473315 19473315 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.2284C>G p.Gln762Glu p.Q762E ENST00000507958 15/15 374 276 98 274 274 0 strelka-varscan CDH18,missense_variant,p.Gln762Glu,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Gln762Glu,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Gln762Glu,ENST00000274170,;CDH18,downstream_gene_variant,,ENST00000506372,NM_001291957.1;CDH18,downstream_gene_variant,,ENST00000502796,NM_001167667.1;CDH18,downstream_gene_variant,,ENST00000515257,;CDH18,non_coding_transcript_exon_variant,,ENST00000510297,; C ENST00000507958 Transcript missense_variant 3275/3542 2284/2373 762/790 Q/E Cag/Gag 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 tolerated(0.19) 15/15 hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Pfam_domain:PF01049,Gene3D:4.10.900.10 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 19473315 19473315 G C 1 0 0 0 0 1 0 0 0 2806 1357 47 4 4 CDH18 5 19473315 Missense_Mutation SNP G C3N-01410_T 9082883 19473315 162064944 71 22971 MROH2B 0 . GRCh38 5 41009982 41009982 + Missense_Mutation SNP G G T C3N-01410_T C3N-01410_N G G c.3233C>A p.Ala1078Asp p.A1078D ENST00000399564 31/42 226 169 57 204 204 0 strelka-varscan-mutect MROH2B,missense_variant,p.Ala1078Asp,ENST00000399564,NM_173489.4;MROH2B,missense_variant,p.Ala633Asp,ENST00000506092,;MROH2B,non_coding_transcript_exon_variant,,ENST00000515297,;MROH2B,non_coding_transcript_exon_variant,,ENST00000503890,; T ENST00000399564 Transcript missense_variant 3684/5239 3233/4758 1078/1585 A/D gCc/gAc COSM592491 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 deleterious(0) 31/42 hmmpanther:PTHR23120:SF22,hmmpanther:PTHR23120,Gene3D:1.25.10.10 1 MODERATE 1 SNV 1 1 1 PASS rs1343869368 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 41009982 41009982 G T 1 0 0 0 0 1 0 0 0 9745 1203 42 2 2 MROH2B 5 41009982 Missense_Mutation SNP G C3N-01410_T 21536667 41009982 140528277 72 22972 AP3B1 0 . GRCh38 5 78227532 78227532 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.376G>T p.Asp126Tyr p.D126Y ENST00000255194 5/27 277 240 37 291 290 1 strelka-varscan AP3B1,missense_variant,p.Asp126Tyr,ENST00000255194,NM_003664.4;AP3B1,missense_variant,p.Asp77Tyr,ENST00000519295,NM_001271769.1; A ENST00000255194 Transcript missense_variant,splice_region_variant 552/5838 376/3285 126/1094 D/Y Gac/Tac 1 -1 AP3B1 HGNC HGNC:566 protein_coding YES CCDS4041.1 ENSP00000255194 O00203 A0A0S2Z5J4 UPI00001AE77D NM_003664.4 deleterious(0) 5/27 Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF037096,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 78227532 78227532 C A 1 0 0 0 0 1 0 0 0 860 869 30 2 2 AP3B1 5 78227532 Missense_Mutation SNP C C3N-01410_T 37217550 78227532 103310727 73 22973 CMYA5 0 . GRCh38 5 79737137 79737137 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.8372C>A p.Ser2791Tyr p.S2791Y ENST00000446378 2/13 217 180 37 156 156 0 strelka-varscan CMYA5,missense_variant,p.Ser2791Tyr,ENST00000446378,NM_153610.4;CMYA5,upstream_gene_variant,,ENST00000506603,; A ENST00000446378 Transcript missense_variant 8403/12847 8372/12210 2791/4069 S/Y tCc/tAc 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 deleterious(0) 2/13 hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 79737137 79737137 C A 1 0 0 0 0 1 0 0 0 3368 855 30 2 2 CMYA5 5 79737137 Missense_Mutation SNP C C3N-01410_T 1509605 79737137 101801122 74 22974 EDIL3 0 . GRCh38 5 84064698 84064698 + Splice_Site SNP A A C novel C3N-01410_T C3N-01410_N A A c.952+2T>G p.X318_splice ENST00000296591 84 69 15 81 81 0 strelka-varscan EDIL3,splice_donor_variant,,ENST00000296591,NM_005711.4;EDIL3,splice_donor_variant,,ENST00000380138,NM_001278642.1;EDIL3,splice_donor_variant,,ENST00000510271,; C ENST00000296591 Transcript splice_donor_variant -/4727 952/1443 318/480 1 -1 EDIL3 HGNC HGNC:3173 protein_coding YES CCDS4062.1 ENSP00000296591 O43854 UPI000004D126 NM_005711.4 8/10 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 75 84064698 84064698 A C 1 0 0 0 0 0 0 1 0 4743 405 14 5 5 EDIL3 5 84064698 Splice_Site SNP A C3N-01410_T 4327561 84064698 97473561 75 22975 CAST 0 . GRCh38 5 96766104 96766104 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.1966A>G p.Ile656Val p.I656V ENST00000395812 25/30 171 146 25 149 149 0 strelka-varscan-mutect CAST,missense_variant,p.Ile656Val,ENST00000395812,NM_001042440.3;CAST,missense_variant,p.Ile614Val,ENST00000395813,;CAST,missense_variant,p.Ile592Val,ENST00000309190,NM_173060.3,NM_001284212.1;CAST,missense_variant,p.Ile366Val,ENST00000437034,;CAST,missense_variant,p.Ile336Val,ENST00000325674,;CAST,missense_variant,p.Ile599Val,ENST00000511049,;CAST,missense_variant,p.Ile601Val,ENST00000338252,NM_001190442.1;CAST,missense_variant,p.Ile697Val,ENST00000508830,;CAST,missense_variant,p.Ile614Val,ENST00000341926,;CAST,missense_variant,p.Ile600Val,ENST00000511782,;CAST,missense_variant,p.Ile660Val,ENST00000508608,;CAST,missense_variant,p.Ile542Val,ENST00000504465,NM_001284213.1;CAST,missense_variant,p.Ile675Val,ENST00000510756,;CAST,missense_variant,p.Ile579Val,ENST00000509903,;CAST,missense_variant,p.Ile614Val,ENST00000510156,;CAST,missense_variant,p.Ile371Val,ENST00000510500,;CAST,missense_variant,p.Ile329Val,ENST00000508579,;CAST,missense_variant,p.Ile337Val,ENST00000515663,;ERAP1,intron_variant,,ENST00000296754,NM_016442.3;CAST,non_coding_transcript_exon_variant,,ENST00000348386,;CAST,missense_variant,p.Ile356Val,ENST00000484552,;CAST,missense_variant,p.Ile109Val,ENST00000510098,;CAST,upstream_gene_variant,,ENST00000509529,; G ENST00000395812 Transcript missense_variant 2152/4506 1966/2253 656/750 I/V Atc/Gtc 1 1 CAST HGNC HGNC:1515 protein_coding YES CCDS54882.1 ENSP00000379157 P20810 UPI0000DA4C59 NM_001042440.3 deleterious(0.01) 25/30 hmmpanther:PTHR10077,hmmpanther:PTHR10077:SF0,Pfam_domain:PF00748 MODERATE 1 SNV 1 1 PASS rs1265097638 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 96766104 96766104 A G 1 0 0 0 0 1 0 0 0 2383 449 16 5 5 CAST 5 96766104 Missense_Mutation SNP A C3N-01410_T 12701406 96766104 84772155 76 22976 DDX46 0 . GRCh38 5 134767047 134767047 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.337A>G p.Lys113Glu p.K113E ENST00000452510 3/23 105 85 20 110 110 0 strelka-varscan DDX46,missense_variant,p.Lys113Glu,ENST00000452510,NM_001300860.1;DDX46,missense_variant,p.Lys113Glu,ENST00000354283,NM_014829.3;DDX46,intron_variant,,ENST00000628477,;DDX46,intron_variant,,ENST00000507392,; G ENST00000452510 Transcript missense_variant 495/5689 337/3099 113/1032 K/E Aaa/Gaa 1 1 DDX46 HGNC HGNC:18681 protein_coding YES CCDS75306.1 ENSP00000416534 A0A0C4DG89 UPI000006F4C9 NM_001300860.1 tolerated(0.37) 3/23 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 134767047 134767047 A G 1 0 0 0 0 1 0 0 0 4167 247 9 5 5 DDX46 5 134767047 Missense_Mutation SNP A C3N-01410_T 38000943 134767047 46771212 77 22977 PCDHA13 0 . GRCh38 5 140883708 140883708 + Missense_Mutation SNP G G T rs782444555 C3N-01410_T C3N-01410_N G G c.1440G>T p.Gln480His p.Q480H ENST00000289272 1/4 619 531 88 544 544 0 strelka-varscan PCDHA13,missense_variant,p.Gln480His,ENST00000289272,NM_018904.2;PCDHA13,missense_variant,p.Gln480His,ENST00000409494,;PCDHA13,missense_variant,p.Gln480His,ENST00000617769,NM_031865.1;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;AC005609.17,upstream_gene_variant,,ENST00000625195,; T ENST00000289272 Transcript missense_variant 1440/5260 1440/2853 480/950 Q/H caG/caT rs782444555 1 1 PCDHA13 HGNC HGNC:8667 protein_coding YES CCDS4240.1 ENSP00000289272 Q9Y5I0 UPI00001273D6 NM_018904.2 tolerated_low_confidence(0.13) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 140883708 140883708 G T 1 0 0 0 0 1 0 0 0 11610 991 35 2 2 PCDHA13 5 140883708 Missense_Mutation SNP G C3N-01410_T 6116661 140883708 40654551 78 22978 PCDHB8 0 . GRCh38 5 141180007 141180007 + Missense_Mutation SNP C C A rs781988348 C3N-01410_T C3N-01410_N C C c.1973C>A p.Thr658Lys p.T658K ENST00000239444 1/1 468 347 121 418 418 0 strelka-varscan PCDHB8,missense_variant,p.Thr658Lys,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; A ENST00000239444 Transcript missense_variant 2218/2740 1973/2406 658/801 T/K aCg/aAg rs781988348,COSM314002 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 141180007 141180007 C A 1 0 0 0 0 1 0 0 0 11635 536 19 1 1 PCDHB8 5 141180007 Missense_Mutation SNP C C3N-01410_T 296299 141180007 40358252 79 22979 PCDHB12 0 . GRCh38 5 141211132 141211132 + Missense_Mutation SNP C C G novel C3N-01410_T C3N-01410_N C C c.2225C>G p.Thr742Ser p.T742S ENST00000239450 1/1 208 156 52 242 242 0 strelka-varscan PCDHB12,missense_variant,p.Thr742Ser,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Thr405Ser,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; G ENST00000239450 Transcript missense_variant 2414/3853 2225/2388 742/795 T/S aCc/aGc 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 deleterious_low_confidence(0.04) 1/1 hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Pfam_domain:PF16492 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 141211132 141211132 C G 1 0 0 0 0 1 0 0 0 11624 507 18 4 4 PCDHB12 5 141211132 Missense_Mutation SNP C C3N-01410_T 31125 141211132 40327127 80 22980 SLC36A2 0 . GRCh38 5 151343583 151343583 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.271C>A p.Leu91Met p.L91M ENST00000335244 3/10 213 174 39 183 183 0 strelka-varscan SLC36A2,missense_variant,p.Leu91Met,ENST00000335244,NM_181776.2;SLC36A2,missense_variant,p.Leu91Met,ENST00000521967,;SLC36A2,missense_variant,p.Leu91Met,ENST00000518617,;SLC36A2,missense_variant,p.Leu91Met,ENST00000518280,;SLC36A2,non_coding_transcript_exon_variant,,ENST00000522829,; T ENST00000335244 Transcript missense_variant 401/3421 271/1452 91/483 L/M Ctg/Atg 1 -1 SLC36A2 HGNC HGNC:18762 protein_coding YES CCDS4315.1 ENSP00000334223 Q495M3 UPI000020D008 NM_181776.2 deleterious(0.01) 3/10 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF185,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 151343583 151343583 G T 1 0 0 0 0 1 0 0 0 14872 933 33 2 2 SLC36A2 5 151343583 Missense_Mutation SNP G C3N-01410_T 10132451 151343583 30194676 81 22981 FAM71B 0 . GRCh38 5 157162457 157162457 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.1808A>T p.Lys603Ile p.K603I ENST00000302938 2/2 97 80 17 89 89 0 strelka-varscan-mutect FAM71B,missense_variant,p.Lys603Ile,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; A ENST00000302938 Transcript missense_variant 1904/2515 1808/1818 603/605 K/I aAa/aTa 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 deleterious(0) 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 157162457 157162457 T A 1 0 0 0 0 1 0 0 0 5472 1841 64 4 4 FAM71B 5 157162457 Missense_Mutation SNP T C3N-01410_T 5818874 157162457 24375802 82 22982 ATP10B 0 . GRCh38 5 160670627 160670627 + Missense_Mutation SNP G G T rs185209751 C3N-01410_T C3N-01410_N G G c.511C>A p.Arg171Ser p.R171S ENST00000327245 7/26 204 176 28 207 207 0 strelka-varscan-mutect ATP10B,missense_variant,p.Arg171Ser,ENST00000327245,NM_025153.2;ATP10B,non_coding_transcript_exon_variant,,ENST00000326831,;ATP10B,non_coding_transcript_exon_variant,,ENST00000517802,;ATP10B,non_coding_transcript_exon_variant,,ENST00000521033,; T ENST00000327245 Transcript missense_variant 1358/7566 511/4386 171/1461 R/S Cgc/Agc rs185209751 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 tolerated(0.08) 7/26 hmmpanther:PTHR24092:SF79,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01652,Pfam_domain:PF00122,Gene3D:2.70.150.10,Superfamily_domains:0049471 MODERATE 1 SNV 1 1 PASS rs185209751 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 75 160670627 160670627 G T 1 0 0 0 0 1 0 0 0 1269 1087 38 1 1 ATP10B 5 160670627 Missense_Mutation SNP G C3N-01410_T 3508170 160670627 20867632 83 22983 WWC1 0 . GRCh38 5 168464869 168464869 + Silent SNP G G T novel C3N-01410_T C3N-01410_N G G c.3075G>T p.= p.L1025L ENST00000521089 21/23 304 224 80 300 300 0 strelka-varscan-mutect WWC1,synonymous_variant,p.=,ENST00000265293,NM_015238.2;WWC1,synonymous_variant,p.=,ENST00000393895,;WWC1,synonymous_variant,p.=,ENST00000521089,NM_001161662.1,NM_001161661.1;WWC1,synonymous_variant,p.=,ENST00000524228,;WWC1,synonymous_variant,p.=,ENST00000524038,;WWC1,non_coding_transcript_exon_variant,,ENST00000522140,;WWC1,upstream_gene_variant,,ENST00000521391,;WWC1,upstream_gene_variant,,ENST00000518204,; T ENST00000521089 Transcript synonymous_variant 3078/3562 3075/3360 1025/1119 L ctG/ctT 1 1 WWC1 HGNC HGNC:29435 protein_coding YES CCDS54945.1 ENSP00000427772 Q8IX03 UPI00017A7149 NM_001161662.1,NM_001161661.1 21/23 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14791,hmmpanther:PTHR14791:SF22 LOW 1 SNV 2 1 PASS rs1309751024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 168464869 168464869 G T 1 0 0 0 0 0 0 0 1 17969 1335 47 2 2 WWC1 5 168464869 Silent SNP G C3N-01410_T 7794242 168464869 13073390 84 22984 DOCK2 0 . GRCh38 5 169699453 169699453 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1127G>T p.Gly376Val p.G376V ENST00000256935 12/52 80 58 22 73 73 0 strelka-varscan-mutect DOCK2,missense_variant,p.Gly376Val,ENST00000256935,NM_004946.2;DOCK2,upstream_gene_variant,,ENST00000520908,;DOCK2,upstream_gene_variant,,ENST00000540750,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523684,;DOCK2,non_coding_transcript_exon_variant,,ENST00000519734,;DOCK2,missense_variant,p.Gly376Val,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000519223,; T ENST00000256935 Transcript missense_variant 1207/6097 1127/5493 376/1830 G/V gGg/gTg 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0.01) 12/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF16172 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 169699453 169699453 G T 1 0 0 0 0 1 0 0 0 4502 1246 43 2 2 DOCK2 5 169699453 Missense_Mutation SNP G C3N-01410_T 1234584 169699453 11838806 85 22985 FGFR4 0 . GRCh38 5 177092425 177092425 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.832C>A p.Gln278Lys p.Q278K ENST00000292408 7/18 86 53 33 83 82 1 strelka-varscan-mutect FGFR4,missense_variant,p.Gln278Lys,ENST00000292408,NM_213647.2,NM_002011.4;FGFR4,missense_variant,p.Gln278Lys,ENST00000393648,NM_001291980.1;FGFR4,missense_variant,p.Gln278Lys,ENST00000502906,;FGFR4,missense_variant,p.Gln278Lys,ENST00000393637,NM_022963.3;FGFR4,upstream_gene_variant,,ENST00000511076,;FGFR4,downstream_gene_variant,,ENST00000503708,;FGFR4,downstream_gene_variant,,ENST00000510911,;FGFR4,downstream_gene_variant,,ENST00000513166,;FGFR4,downstream_gene_variant,,ENST00000514472,;FGFR4,downstream_gene_variant,,ENST00000507708,;FGFR4,non_coding_transcript_exon_variant,,ENST00000509511,;FGFR4,non_coding_transcript_exon_variant,,ENST00000508139,;FGFR4,downstream_gene_variant,,ENST00000430285,;FGFR4,downstream_gene_variant,,ENST00000426612,;FGFR4,upstream_gene_variant,,ENST00000483872,;FGFR4,upstream_gene_variant,,ENST00000513423,; A ENST00000292408 Transcript missense_variant 1077/3122 832/2409 278/802 Q/K Cag/Aag 1 1 FGFR4 HGNC HGNC:3691 protein_coding YES CCDS4410.1 ENSP00000292408 P22455 UPI000012A72D NM_213647.2,NM_002011.4 deleterious(0.02) 7/18 Gene3D:2.60.40.10,Pfam_domain:PF13927,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF343,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 75 177092425 177092425 C A 1 0 0 0 0 1 0 0 0 5732 595 21 2 2 FGFR4 5 177092425 Missense_Mutation SNP C C3N-01410_T 7392972 177092425 4445834 86 22986 NSD1 0 . GRCh38 5 177257135 177257135 + Missense_Mutation SNP T T G novel C3N-01410_T C3N-01410_N T T c.4950T>G p.Asn1650Lys p.N1650K ENST00000439151 13/23 325 282 43 313 313 0 strelka-varscan-mutect NSD1,missense_variant,p.Asn1650Lys,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Asn1381Lys,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Asn1381Lys,ENST00000347982,; G ENST00000439151 Transcript missense_variant 4995/12892 4950/8091 1650/2696 N/K aaT/aaG 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 tolerated(0.08) 13/23 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,SMART_domains:SM00249 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 177257135 177257135 T G 1 0 0 0 0 1 0 0 0 10728 1461 51 5 5 NSD1 5 177257135 Missense_Mutation SNP T C3N-01410_T 164710 177257135 4281124 87 22987 NSD1 0 . GRCh38 5 177280604 177280604 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.5662G>T p.Asp1888Tyr p.D1888Y ENST00000439151 18/23 422 346 76 342 342 0 strelka-varscan-mutect NSD1,missense_variant,p.Asp1888Tyr,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Asp1619Tyr,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Asp1619Tyr,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000503056,; T ENST00000439151 Transcript missense_variant 5707/12892 5662/8091 1888/2696 D/Y Gac/Tac 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 deleterious(0.01) 18/23 Gene3D:2.170.270.10,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF312,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 177280604 177280604 G T 1 0 0 0 0 1 0 0 0 10728 942 33 2 2 NSD1 5 177280604 Missense_Mutation SNP G C3N-01410_T 23469 177280604 4257655 88 22988 DSP 0 . GRCh38 6 7562655 7562655 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.601G>A p.Glu201Lys p.E201K ENST00000379802 5/24 585 386 199 549 549 0 strelka-varscan-mutect DSP,missense_variant,p.Glu201Lys,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Glu201Lys,ENST00000418664,NM_001008844.1;DSP,non_coding_transcript_exon_variant,,ENST00000506617,; A ENST00000379802 Transcript missense_variant 942/9796 601/8616 201/2871 E/K Gag/Aag 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 tolerated(0.16) 5/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 7562655 7562655 G A 1 0 0 0 0 1 0 0 0 4602 1188 41 3 3 DSP 6 7562655 Missense_Mutation SNP G C3N-01410_T 7562655 163243324 89 22989 TRIM10 0 . GRCh38 6 30160749 30160749 + Missense_Mutation SNP C C G rs758582202 C3N-01410_T C3N-01410_N C C c.110G>C p.Arg37Pro p.R37P ENST00000449742 1/7 276 194 82 285 285 0 strelka-varscan-mutect TRIM10,missense_variant,p.Arg37Pro,ENST00000449742,NM_006778.3;TRIM10,missense_variant,p.Arg37Pro,ENST00000376704,NM_052828.2;TRIM15,upstream_gene_variant,,ENST00000619857,;TRIM15,upstream_gene_variant,,ENST00000376694,NM_033229.2;TRIM15,upstream_gene_variant,,ENST00000376688,; G ENST00000449742 Transcript missense_variant 186/3546 110/1446 37/481 R/P cGg/cCg rs758582202 1 -1 TRIM10 HGNC HGNC:10072 protein_coding YES CCDS34375.1 ENSP00000397073 Q9UDY6 UPI000000D736 NM_006778.3 deleterious(0) 1/7 Gene3D:3.30.40.10,Pfam_domain:PF15227,PROSITE_patterns:PS00518,PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF329,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs758582202 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 30160749 30160749 C G 1 0 0 0 0 1 0 0 0 16975 652 23 4 4 TRIM10 6 30160749 Missense_Mutation SNP C C3N-01410_T 22598094 30160749 140645230 90 22990 TCP11 0 . GRCh38 6 35118459 35118459 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1361G>T p.Gly454Val p.G454V ENST00000311875 10/10 236 147 89 190 190 0 strelka-varscan-mutect TCP11,missense_variant,p.Gly454Val,ENST00000311875,NM_001093728.2;TCP11,missense_variant,p.Gly378Val,ENST00000611141,NM_001261821.1,NM_001261820.1;TCP11,missense_variant,p.Gly379Val,ENST00000244645,NM_018679.5;TCP11,missense_variant,p.Gly379Val,ENST00000373979,;TCP11,missense_variant,p.Gly449Val,ENST00000444780,NM_001261817.1;TCP11,missense_variant,p.Gly403Val,ENST00000412155,NM_001261819.1;TCP11,missense_variant,p.Gly408Val,ENST00000373974,NM_001261818.1;TCP11,missense_variant,p.Gly441Val,ENST00000512012,;TCP11,missense_variant,p.Gly378Val,ENST00000418521,;TCP11,intron_variant,,ENST00000502480,;TCP11,downstream_gene_variant,,ENST00000486638,;TCP11,downstream_gene_variant,,ENST00000507706,;TCP11,downstream_gene_variant,,ENST00000492680,;TCP11,downstream_gene_variant,,ENST00000505400,;TCP11,3_prime_UTR_variant,,ENST00000504758,;TCP11,3_prime_UTR_variant,,ENST00000505911,;TCP11,3_prime_UTR_variant,,ENST00000455706,;TCP11,downstream_gene_variant,,ENST00000427376,;TCP11,downstream_gene_variant,,ENST00000469514,;TCP11,downstream_gene_variant,,ENST00000479418,;TCP11,downstream_gene_variant,,ENST00000509988,;TCP11,downstream_gene_variant,,ENST00000505335,; A ENST00000311875 Transcript missense_variant 1779/2166 1361/1551 454/516 G/V gGt/gTt 1 -1 TCP11 HGNC HGNC:11658 protein_coding YES CCDS47413.1 ENSP00000308708 Q8WWU5 A0A140VK95 UPI0000EE4D7F NM_001093728.2 deleterious(0) 10/10 Pfam_domain:PF05794,hmmpanther:PTHR12832,hmmpanther:PTHR12832:SF14 MODERATE 1 SNV 2 1 PASS rs1353727033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 35118459 35118459 C A 1 0 0 0 0 1 0 0 0 16120 507 18 2 2 TCP11 6 35118459 Missense_Mutation SNP C C3N-01410_T 4957710 35118459 135687520 91 22991 PEX6 0 . GRCh38 6 42965742 42965742 + Nonsense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.2410G>T p.Glu804Ter p.E804* ENST00000304611 13/17 343 238 105 292 291 1 strelka-varscan-mutect PEX6,stop_gained,p.Glu804Ter,ENST00000304611,NM_000287.3;PEX6,missense_variant,p.Met721Ile,ENST00000244546,;GNMT,downstream_gene_variant,,ENST00000372808,NM_018960.4; A ENST00000304611 Transcript stop_gained 2480/3478 2410/2943 804/980 E/* Gaa/Taa 1 -1 PEX6 HGNC HGNC:8859 protein_coding YES CCDS4877.1 ENSP00000303511 Q13608 A0A024RD09 UPI00001316EC NM_000287.3 13/17 Gene3D:3.40.50.300,Pfam_domain:PF00004,hmmpanther:PTHR23077,hmmpanther:PTHR23077:SF9,SMART_domains:SM00382,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 42965742 42965742 C A 1 0 0 0 0 0 1 0 0 11840 835 29 2 2 PEX6 6 42965742 Nonsense_Mutation SNP C C3N-01410_T 7847283 42965742 127840237 92 22992 IL17A 0 . GRCh38 6 52189140 52189140 + Missense_Mutation SNP G G A rs745674559 C3N-01410_T C3N-01410_N G G c.316G>A p.Val106Met p.V106M ENST00000340057 3/3 297 260 37 246 244 2 strelka-mutect IL17A,missense_variant,p.Val106Met,ENST00000340057,NM_002190.2; A ENST00000340057 Transcript missense_variant 361/1859 316/468 106/155 V/M Gtg/Atg rs745674559,COSM5139528 1 1 IL17A HGNC HGNC:5981 protein_coding YES CCDS4937.1 ENSP00000344192 Q16552 UPI0000047D95 NM_002190.2 tolerated(0.23) 3/3 hmmpanther:PTHR21295:SF2,hmmpanther:PTHR21295,Pfam_domain:PF06083,Gene3D:2.10.90.10,Superfamily_domains:SSF57501 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs745674559 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 52189140 52189140 G A 1 0 0 0 0 1 0 0 0 7542 1145 40 1 1 IL17A 6 52189140 Missense_Mutation SNP G C3N-01410_T 9223398 52189140 118616839 93 22993 EYS 0 . GRCh38 6 64591297 64591297 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.4570A>T p.Ser1524Cys p.S1524C ENST00000370621 26/44 379 266 113 313 313 0 strelka-varscan-mutect EYS,missense_variant,p.Ser1524Cys,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Ser1524Cys,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; A ENST00000370621 Transcript missense_variant 5097/10485 4570/9498 1524/3165 S/C Agt/Tgt 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0) 26/44 MODERATE 1 SNV 1 1 PASS rs1424789262 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 64591297 64591297 T A 1 0 0 0 0 1 0 0 0 5200 1580 55 4 4 EYS 6 64591297 Missense_Mutation SNP T C3N-01410_T 12402157 64591297 106214682 94 22994 EYS 0 . GRCh38 6 64591510 64591510 + Missense_Mutation SNP C C T novel C3N-01410_T C3N-01410_N C C c.4357G>A p.Ala1453Thr p.A1453T ENST00000370621 26/44 446 383 63 371 369 2 strelka-varscan-mutect EYS,missense_variant,p.Ala1453Thr,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Ala1453Thr,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; T ENST00000370621 Transcript missense_variant 4884/10485 4357/9498 1453/3165 A/T Gcc/Acc 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.13) 26/44 MODERATE 1 SNV 1 1 PASS rs761238771 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 64591510 64591510 C T 1 0 0 0 0 1 0 0 0 5200 710 25 3 3 EYS 6 64591510 Missense_Mutation SNP C C3N-01410_T 213 64591510 106214469 95 22995 RWDD2A 0 . GRCh38 6 83195896 83195896 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.503A>T p.Gln168Leu p.Q168L ENST00000369724 3/3 170 105 65 164 164 0 strelka-varscan-mutect RWDD2A,missense_variant,p.Gln168Leu,ENST00000369724,NM_001322335.1,NM_033411.3;PGM3,upstream_gene_variant,,ENST00000513973,NM_015599.2;PGM3,upstream_gene_variant,,ENST00000616566,NM_001199918.1;PGM3,upstream_gene_variant,,ENST00000283977,;PGM3,upstream_gene_variant,,ENST00000512866,NM_001199919.1;PGM3,upstream_gene_variant,,ENST00000506587,NM_001199917.1;PGM3,upstream_gene_variant,,ENST00000510258,;PGM3,upstream_gene_variant,,ENST00000508748,;PGM3,upstream_gene_variant,,ENST00000503094,;PGM3,upstream_gene_variant,,ENST00000507554,;PGM3,upstream_gene_variant,,ENST00000515333,;PGM3,upstream_gene_variant,,ENST00000505470,; T ENST00000369724 Transcript missense_variant 708/3744 503/879 168/292 Q/L cAg/cTg 1 1 RWDD2A HGNC HGNC:21385 protein_coding YES CCDS4998.1 ENSP00000358739 Q9UIY3 UPI0000139BF2 NM_001322335.1,NM_033411.3 deleterious(0.01) 3/3 hmmpanther:PTHR15955:SF2,hmmpanther:PTHR15955,PIRSF_domain:PIRSF038021,Pfam_domain:PF06544 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 83195896 83195896 A T 1 0 0 0 0 1 0 0 0 14016 188 7 4 4 RWDD2A 6 83195896 Missense_Mutation SNP A C3N-01410_T 18604386 83195896 87610083 96 22996 TBX18 0 . GRCh38 6 84744267 84744267 + Missense_Mutation SNP C C G rs372777291 C3N-01410_T C3N-01410_N C C c.998G>C p.Arg333Pro p.R333P ENST00000369663 6/8 175 115 60 242 242 0 strelka-varscan-mutect TBX18,missense_variant,p.Arg333Pro,ENST00000369663,NM_001080508.2;TBX18,missense_variant,p.Arg175Pro,ENST00000606784,;TBX18,missense_variant,p.Arg175Pro,ENST00000606325,;TBX18,non_coding_transcript_exon_variant,,ENST00000606521,;TBX18,upstream_gene_variant,,ENST00000607343,; G ENST00000369663 Transcript missense_variant 1336/6245 998/1824 333/607 R/P cGc/cCc rs372777291,COSM1082160 1 -1 TBX18 HGNC HGNC:11595 protein_coding YES CCDS34495.1 ENSP00000358677 O95935 UPI00001A3A8A NM_001080508.2 deleterious(0.01) 6/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF20,Gene3D:1h6fA00,SMART_domains:SM00425,Superfamily_domains:SSF49417 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372777291 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 84744267 84744267 C G 1 0 0 0 0 1 0 0 0 16058 768 27 4 4 TBX18 6 84744267 Missense_Mutation SNP C C3N-01410_T 1548371 84744267 86061712 97 22997 SYNE1 0 . GRCh38 6 152442129 152442129 + Missense_Mutation SNP C C A rs752836961 C3N-01410_T C3N-01410_N C C c.3954G>T p.Glu1318Asp p.E1318D ENST00000367255 31/146 255 199 56 295 295 0 strelka-varscan-mutect SYNE1,missense_variant,p.Glu1318Asp,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Glu1325Asp,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Glu1367Asp,ENST00000341594,;SYNE1,missense_variant,p.Glu1308Asp,ENST00000367248,;SYNE1,missense_variant,p.Glu1318Asp,ENST00000367253,;SYNE1,missense_variant,p.Glu1318Asp,ENST00000413186,;SYNE1,non_coding_transcript_exon_variant,,ENST00000461872,; A ENST00000367255 Transcript missense_variant 4556/27748 3954/26394 1318/8797 E/D gaG/gaT rs752836961 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 31/146 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267 MODERATE 1 SNV 1 1 PASS rs752836961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 152442129 152442129 C A 1 0 0 0 0 1 0 0 0 15837 912 32 2 2 SYNE1 6 152442129 Missense_Mutation SNP C C3N-01410_T 67697862 152442129 18363850 98 22998 HDAC9 0 . GRCh38 7 18585455 18585455 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.197C>A p.Ala66Glu p.A66E ENST00000441542 2/25 395 337 58 324 324 0 strelka-varscan-mutect HDAC9,missense_variant,p.Ala66Glu,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Ala66Glu,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,missense_variant,p.Ala66Glu,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Ala94Glu,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,missense_variant,p.Ala66Glu,ENST00000401921,;HDAC9,missense_variant,p.Ala66Glu,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Ala66Glu,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Ala108Glu,ENST00000417496,NM_001204144.1;HDAC9,missense_variant,p.Ala66Glu,ENST00000428307,NM_001204145.1;HDAC9,missense_variant,p.Ala35Glu,ENST00000456174,NM_001204148.1;HDAC9,missense_variant,p.Ala35Glu,ENST00000524023,NM_001204147.1;HDAC9,missense_variant,p.Ala66Glu,ENST00000413380,;HDAC9,missense_variant,p.Ala35Glu,ENST00000441986,;HDAC9,missense_variant,p.Ala66Glu,ENST00000413509,;HDAC9,missense_variant,p.Ala35Glu,ENST00000430454,;HDAC9,downstream_gene_variant,,ENST00000433709,;HDAC9,non_coding_transcript_exon_variant,,ENST00000476135,;HDAC9,3_prime_UTR_variant,,ENST00000446646,;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,non_coding_transcript_exon_variant,,ENST00000461159,; A ENST00000441542 Transcript missense_variant 197/3210 197/3210 66/1069 A/E gCa/gAa 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0.01) 2/25 Pfam_domain:PF12203,PIRSF_domain:PIRSF037911,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 18585455 18585455 C A 1 0 0 0 0 1 0 0 0 6901 710 25 2 2 HDAC9 7 18585455 Missense_Mutation SNP C C3N-01410_T 18585455 140760518 99 22999 POM121L12 0 . GRCh38 7 53036497 53036497 + Missense_Mutation SNP G G A rs765574512 C3N-01410_T C3N-01410_N G G c.826G>A p.Gly276Ser p.G276S ENST00000408890 1/1 129 103 26 126 126 0 strelka-varscan-mutect POM121L12,missense_variant,p.Gly276Ser,ENST00000408890,NM_182595.3; A ENST00000408890 Transcript missense_variant 856/1283 826/891 276/296 G/S Ggc/Agc rs765574512 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 deleterious_low_confidence(0.02) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS rs765574512 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 53036497 53036497 G A 1 0 0 0 0 1 0 0 0 12352 1116 39 1 1 POM121L12 7 53036497 Missense_Mutation SNP G C3N-01410_T 34451042 53036497 106309476 100 23000 SEPT14 0 . GRCh38 7 55807207 55807207 + Missense_Mutation SNP C C T novel C3N-01410_T C3N-01410_N C C c.869G>A p.Cys290Tyr p.C290Y ENST00000388975 8/10 143 125 18 165 163 2 strelka-varscan-mutect SEPT14,missense_variant,p.Cys290Tyr,ENST00000388975,NM_207366.2;RP11-419M24.1,downstream_gene_variant,,ENST00000443044,; T ENST00000388975 Transcript missense_variant 986/3785 869/1299 290/432 C/Y tGt/tAt 1 -1 SEPT14 HGNC HGNC:33280 protein_coding YES CCDS5519.2 ENSP00000373627 Q6ZU15 UPI0000E0AB69 NM_207366.2 tolerated(0.06) 8/10 PROSITE_profiles:PS51719,hmmpanther:PTHR18884:SF51,hmmpanther:PTHR18884,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 55807207 55807207 C T 1 0 0 0 0 1 0 0 0 14339 478 17 3 3 SEPT14 7 55807207 Missense_Mutation SNP C C3N-01410_T 2770710 55807207 103538766 101 23001 WBSCR28 0 . GRCh38 7 73865763 73865763 + Nonsense_Mutation SNP G G T C3N-01410_T C3N-01410_N G G c.688G>T p.Glu230Ter p.E230* ENST00000320531 3/3 303 260 43 282 282 0 strelka-varscan-mutect WBSCR28,stop_gained,p.Glu230Ter,ENST00000320531,NM_182504.3;WBSCR28,3_prime_UTR_variant,,ENST00000426490,; T ENST00000320531 Transcript stop_gained 724/854 688/798 230/265 E/* Gag/Tag COSM3640406 1 1 WBSCR28 HGNC HGNC:23018 protein_coding YES CCDS43597.1 ENSP00000316775 Q6UE05 UPI00001408E5 NM_182504.3 3/3 hmmpanther:PTHR37369,Pfam_domain:PF15164 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 73865763 73865763 G T 1 0 0 0 0 0 1 0 0 17826 1175 41 2 2 WBSCR28 7 73865763 Nonsense_Mutation SNP G C3N-01410_T 18058556 73865763 85480210 102 23002 PCLO 0 . GRCh38 7 82822547 82822547 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.14739G>T p.= p.G4913G ENST00000333891 20/25 475 326 149 428 426 2 strelka-varscan-mutect PCLO,synonymous_variant,p.=,ENST00000333891,NM_033026.5;PCLO,synonymous_variant,p.=,ENST00000423517,NM_014510.2;PCLO,synonymous_variant,p.=,ENST00000618073,;PCLO,non_coding_transcript_exon_variant,,ENST00000426442,;PCLO,non_coding_transcript_exon_variant,,ENST00000432078,; A ENST00000333891 Transcript synonymous_variant 15077/20329 14739/15429 4913/5142 G ggG/ggT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 20/25 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 82822547 82822547 C A 1 0 0 0 0 0 0 0 1 11671 610 22 2 2 PCLO 7 82822547 Silent SNP C C3N-01410_T 8956784 82822547 76523426 103 23003 FZD1 0 . GRCh38 7 91266575 91266575 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1695G>T p.Trp565Cys p.W565C ENST00000287934 1/1 194 160 34 176 176 0 strelka-varscan-mutect FZD1,missense_variant,p.Trp565Cys,ENST00000287934,NM_003505.1; T ENST00000287934 Transcript missense_variant 2212/6963 1695/1944 565/647 W/C tgG/tgT 1 1 FZD1 HGNC HGNC:4038 protein_coding YES CCDS5620.1 ENSP00000287934 Q9UP38 UPI000005104D NM_003505.1 deleterious(0) 1/1 PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF81,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 91266575 91266575 G T 1 0 0 0 0 1 0 0 0 5999 1241 43 2 2 FZD1 7 91266575 Missense_Mutation SNP G C3N-01410_T 8444028 91266575 68079398 104 23004 ZAN 0 . GRCh38 7 100750867 100750867 + Missense_Mutation SNP G G A C3N-01410_T C3N-01410_N G G c.1492G>A p.Val498Ile p.V498I ENST00000613979 12/48 49 40 9 34 34 0 strelka-varscan-mutect ZAN,missense_variant,p.Val498Ile,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Val498Ile,ENST00000618565,;ZAN,missense_variant,p.Val498Ile,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Val498Ile,ENST00000546292,;ZAN,missense_variant,p.Val498Ile,ENST00000542585,;ZAN,missense_variant,p.Val498Ile,ENST00000538115,;ZAN,missense_variant,p.Val498Ile,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; A ENST00000613979 Transcript missense_variant 1657/8669 1492/8439 498/2812 V/I Gtc/Atc COSM5165912 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 tolerated(1) 12/48 Pfam_domain:PF00629,PROSITE_profiles:PS50060,SMART_domains:SM00137,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS rs1301080537 . 0 202 7 0 0 0 0 0 -19.98589 0.9999997 1 1 1 0 A 3 1 75 100750867 100750867 G A 1 0 0 0 0 1 0 0 0 18074 1145 40 1 1 ZAN 7 100750867 Missense_Mutation SNP G C3N-01410_T 9484292 100750867 58595106 105 23005 CDHR3 0 . GRCh38 7 106017928 106017928 + Silent SNP G G T novel C3N-01410_T C3N-01410_N G G c.1509G>T p.= p.G503G ENST00000317716 12/19 258 176 82 253 253 0 strelka-varscan-mutect CDHR3,synonymous_variant,p.=,ENST00000317716,NM_152750.4;CDHR3,synonymous_variant,p.=,ENST00000478080,NM_001301161.1;CDHR3,intron_variant,,ENST00000466045,;CDHR3,intron_variant,,ENST00000468477,;CDHR3,intron_variant,,ENST00000470188,;CDHR3,downstream_gene_variant,,ENST00000496633,; T ENST00000317716 Transcript synonymous_variant 1589/3813 1509/2658 503/885 G ggG/ggT 1 1 CDHR3 HGNC HGNC:26308 protein_coding YES CCDS47684.1 ENSP00000325954 Q6ZTQ4 UPI00001C0C6E NM_152750.4 12/19 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF336,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs1359852987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 106017928 106017928 G T 1 0 0 0 0 0 0 0 1 2823 1219 43 2 2 CDHR3 7 106017928 Silent SNP G C3N-01410_T 5267061 106017928 53328045 106 23006 NRCAM 0 . GRCh38 7 108191270 108191270 + Silent SNP A A T novel C3N-01410_T C3N-01410_N A A c.1917T>A p.= p.T639T ENST00000379028 19/33 177 126 51 211 211 0 strelka-varscan-mutect NRCAM,synonymous_variant,p.=,ENST00000379028,;NRCAM,synonymous_variant,p.=,ENST00000413765,NM_001193582.1;NRCAM,synonymous_variant,p.=,ENST00000379024,NM_001193583.1,NM_001193584.1;NRCAM,synonymous_variant,p.=,ENST00000425651,NM_001037132.2;NRCAM,synonymous_variant,p.=,ENST00000379022,;NRCAM,intron_variant,,ENST00000351718,NM_005010.4;NRCAM,intron_variant,,ENST00000613830,; T ENST00000379028 Transcript synonymous_variant 2403/6685 1917/3915 639/1304 T acT/acA 1 -1 NRCAM HGNC HGNC:7994 protein_coding YES CCDS47686.1 ENSP00000368314 Q92823 UPI00005E2661 19/33 Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF42,Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 108191270 108191270 A T 1 0 0 0 0 0 0 0 1 10700 291 11 4 4 NRCAM 7 108191270 Silent SNP A C3N-01410_T 2173342 108191270 51154703 107 23007 CFTR 0 . GRCh38 7 117594988 117594988 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.2549T>A p.Leu850His p.L850H ENST00000003084 15/27 326 269 57 362 362 0 strelka-varscan-mutect CFTR,missense_variant,p.Leu850His,ENST00000003084,NM_000492.3;CFTR,missense_variant,p.Leu820His,ENST00000426809,; A ENST00000003084 Transcript missense_variant 2681/6132 2549/4443 850/1480 L/H cTt/cAt 1 1 CFTR HGNC HGNC:1884 protein_coding YES CCDS5773.1 ENSP00000003084 P13569 A0A024R730 UPI000013C4D4 NM_000492.3 deleterious(0) 15/27 Prints_domain:PR01851,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF19,Superfamily_domains:SSF90123,TIGRFAM_domain:TIGR01271 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 117594988 117594988 T A 1 0 0 0 0 1 0 0 0 3052 1609 56 4 4 CFTR 7 117594988 Missense_Mutation SNP T C3N-01410_T 9403718 117594988 41750985 108 23008 POT1 0 . GRCh38 7 124853123 124853123 + Nonsense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.718A>T p.Arg240Ter p.R240* ENST00000357628 10/19 102 65 37 103 103 0 strelka-varscan-mutect POT1,stop_gained,p.Arg240Ter,ENST00000357628,NM_015450.2;POT1,stop_gained,p.Arg109Ter,ENST00000393329,NM_001042594.1;POT1,stop_gained,p.Arg38Ter,ENST00000610141,;POT1,stop_gained,p.Arg240Ter,ENST00000609106,;POT1,stop_gained,p.Arg240Ter,ENST00000608057,;POT1,stop_gained,p.Arg240Ter,ENST00000607932,;POT1,non_coding_transcript_exon_variant,,ENST00000608126,; A ENST00000357628 Transcript stop_gained 1317/4080 718/1905 240/634 R/* Aga/Tga 1 -1 POT1 HGNC HGNC:17284 protein_coding YES CCDS5793.1 ENSP00000350249 Q9NUX5 A0A024R739 UPI0000073E3F NM_015450.2 10/19 Gene3D:1xjvA02,Pfam_domain:PF16686,hmmpanther:PTHR14513,hmmpanther:PTHR14513:SF2,Superfamily_domains:SSF50249 HIGH 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 124853123 124853123 T A 1 0 0 0 0 0 1 0 0 12374 1530 53 4 4 POT1 7 124853123 Nonsense_Mutation SNP T C3N-01410_T 7258135 124853123 34492850 109 23009 MGAM2 0 . GRCh38 7 142187813 142187813 + Missense_Mutation SNP A A C novel C3N-01410_T C3N-01410_N A A c.4186A>C p.Asn1396His p.N1396H ENST00000477922 36/48 130 116 14 116 116 0 strelka-varscan-mutect MGAM2,missense_variant,p.Asn1396His,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; C ENST00000477922 Transcript missense_variant 4240/7867 4186/7548 1396/2515 N/H Aat/Cat 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.01) 36/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 142187813 142187813 A C 1 0 0 0 0 1 0 0 0 9500 14 1 5 5 MGAM2 7 142187813 Missense_Mutation SNP A C3N-01410_T 17334690 142187813 17158160 110 23010 TNKS 0 . GRCh38 8 9751777 9751777 + Nonsense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.3001G>T p.Glu1001Ter p.E1001* ENST00000310430 19/27 403 197 206 280 280 0 strelka-varscan-mutect TNKS,stop_gained,p.Glu1001Ter,ENST00000310430,NM_003747.2;TNKS,stop_gained,p.Glu764Ter,ENST00000518281,;TNKS,downstream_gene_variant,,ENST00000519191,;TNKS,downstream_gene_variant,,ENST00000518635,; T ENST00000310430 Transcript stop_gained 3027/9620 3001/3984 1001/1327 E/* Gag/Tag 1 1 TNKS HGNC HGNC:11941 protein_coding YES CCDS5974.1 ENSP00000311579 O95271 UPI000013F00D NM_003747.2 19/27 hmmpanther:PTHR24180,hmmpanther:PTHR24180:SF3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 9751777 9751777 G T 1 0 0 0 0 0 1 0 0 16792 943 33 2 2 TNKS 8 9751777 Nonsense_Mutation SNP G C3N-01410_T 9751777 135386859 111 23011 DEFB135 0 . GRCh38 8 11984512 11984512 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.156A>T p.Glu52Asp p.E52D ENST00000382208 2/2 89 81 8 53 53 0 strelka-varscan-mutect DEFB135,missense_variant,p.Glu52Asp,ENST00000382208,NM_001033017.2; T ENST00000382208 Transcript missense_variant 156/234 156/234 52/77 E/D gaA/gaT 1 1 DEFB135 HGNC HGNC:32400 protein_coding YES CCDS43710.1 ENSP00000371643 Q30KP9 UPI0000591BA1 NM_001033017.2 deleterious(0) 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF21,Pfam_domain:PF13841,PD866254 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -12.97314 0.9999944 1 1 1 0 T 3 4 75 11984512 11984512 A T 1 0 0 0 0 1 0 0 0 4223 40 2 4 4 DEFB135 8 11984512 Missense_Mutation SNP A C3N-01410_T 2232735 11984512 133154124 112 23012 REEP4 0 . GRCh38 8 22139051 22139051 + Missense_Mutation SNP G G T rs756827594 C3N-01410_T C3N-01410_N G G c.428C>A p.Ala143Glu p.A143E ENST00000306306 6/8 54 44 10 35 35 0 strelka-varscan-mutect REEP4,missense_variant,p.Ala143Glu,ENST00000306306,NM_025232.2;REEP4,missense_variant,p.Ala143Glu,ENST00000523293,;REEP4,intron_variant,,ENST00000334530,NM_001316965.1;REEP4,downstream_gene_variant,,ENST00000521744,;REEP4,non_coding_transcript_exon_variant,,ENST00000519074,;REEP4,non_coding_transcript_exon_variant,,ENST00000518664,;REEP4,downstream_gene_variant,,ENST00000519875,; T ENST00000306306 Transcript missense_variant 897/1710 428/774 143/257 A/E gCg/gAg rs756827594 1 -1 REEP4 HGNC HGNC:26176 protein_coding YES CCDS6024.1 ENSP00000303482 Q9H6H4 UPI000006E42E NM_025232.2 deleterious(0) 6/8 hmmpanther:PTHR12300,hmmpanther:PTHR12300:SF36 MODERATE 1 SNV 1 1 PASS rs756827594 . 0 202 8 0 0 0 0 0 -19.99981 0.9999988 1 1 1 0 T 3 4 75 22139051 22139051 G T 1 0 0 0 0 1 0 0 0 13377 1087 38 1 1 REEP4 8 22139051 Missense_Mutation SNP G C3N-01410_T 10154539 22139051 122999585 113 23013 SFTPC 0 . GRCh38 8 22163774 22163774 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.440G>A p.Ser147Asn p.S147N ENST00000437090 5/5 410 366 44 302 302 0 strelka-varscan-mutect SFTPC,missense_variant,p.Ser147Asn,ENST00000437090,;SFTPC,3_prime_UTR_variant,,ENST00000522109,;SFTPC,intron_variant,,ENST00000521315,NM_001172357.1;SFTPC,intron_variant,,ENST00000318561,NM_001317778.1,NM_001317780.1,NM_003018.3,NM_001172410.1;SFTPC,intron_variant,,ENST00000524255,;SFTPC,intron_variant,,ENST00000520605,;SFTPC,intron_variant,,ENST00000523296,;BMP1,upstream_gene_variant,,ENST00000306385,NM_006129.4;BMP1,upstream_gene_variant,,ENST00000354870,;BMP1,upstream_gene_variant,,ENST00000306349,NM_001199.3;BMP1,upstream_gene_variant,,ENST00000397814,;SFTPC,downstream_gene_variant,,ENST00000522880,;SFTPC,downstream_gene_variant,,ENST00000524318,;SFTPC,downstream_gene_variant,,ENST00000524350,;BMP1,upstream_gene_variant,,ENST00000520970,;BMP1,upstream_gene_variant,,ENST00000520626,;BMP1,upstream_gene_variant,,ENST00000520982,;BMP1,upstream_gene_variant,,ENST00000471755,;BMP1,upstream_gene_variant,,ENST00000518913,;BMP1,upstream_gene_variant,,ENST00000483364,;BMP1,upstream_gene_variant,,ENST00000521385,;BMP1,upstream_gene_variant,,ENST00000518656,;SFTPC,downstream_gene_variant,,ENST00000518615,;SFTPC,downstream_gene_variant,,ENST00000522630,; A ENST00000437090 Transcript missense_variant 471/773 440/486 147/161 S/N aGc/aAc 1 1 SFTPC HGNC HGNC:10802 protein_coding ENSP00000407931 C9JYF6 UPI000020FCC2 tolerated_low_confidence(0.2) 5/5 PROSITE_profiles:PS50869,hmmpanther:PTHR10800,SMART_domains:SM00019,SMART_domains:SM01039 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 22163774 22163774 G A 1 0 0 0 0 1 0 0 0 14452 985 34 3 3 SFTPC 8 22163774 Missense_Mutation SNP G C3N-01410_T 24723 22163774 122974862 114 23014 FUT10 0 . GRCh38 8 33461401 33461401 + Missense_Mutation SNP C C T novel C3N-01410_T C3N-01410_N C C c.52G>A p.Ala18Thr p.A18T ENST00000327671 2/5 101 84 17 56 56 0 strelka-varscan-mutect FUT10,missense_variant,p.Ala18Thr,ENST00000327671,NM_032664.3;FUT10,intron_variant,,ENST00000518672,;FUT10,intron_variant,,ENST00000524021,;FUT10,non_coding_transcript_exon_variant,,ENST00000520503,;FUT10,non_coding_transcript_exon_variant,,ENST00000416169,;FUT10,non_coding_transcript_exon_variant,,ENST00000520767,; T ENST00000327671 Transcript missense_variant 684/3825 52/1440 18/479 A/T Gcc/Acc 1 -1 FUT10 HGNC HGNC:19234 protein_coding YES CCDS6088.1 ENSP00000332757 Q6P4F1 UPI00001C0364 NM_032664.3 tolerated(0.13) 2/5 PIRSF_domain:PIRSF037332,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -20 0.9999685 1 1 1 0 T 3 4 75 33461401 33461401 C T 1 0 0 0 0 1 0 0 0 5974 797 28 3 3 FUT10 8 33461401 Missense_Mutation SNP C C3N-01410_T 11297627 33461401 111677235 115 23015 RGS20 0 . GRCh38 8 53879274 53879274 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.182A>G p.Gln61Arg p.Q61R ENST00000297313 2/6 541 500 41 243 243 0 strelka-varscan-mutect RGS20,missense_variant,p.Gln61Arg,ENST00000297313,NM_170587.3;RGS20,intron_variant,,ENST00000344277,NM_001286673.1;RGS20,upstream_gene_variant,,ENST00000276500,NM_003702.4;RGS20,upstream_gene_variant,,ENST00000522225,;RP11-1070A24.2,upstream_gene_variant,,ENST00000606037,;RGS20,upstream_gene_variant,,ENST00000523414,;RGS20,upstream_gene_variant,,ENST00000523064,;RGS20,upstream_gene_variant,,ENST00000518286,;RGS20,intron_variant,,ENST00000517659,NM_001286675.1;RGS20,intron_variant,,ENST00000523280,NM_001286674.1; G ENST00000297313 Transcript missense_variant 274/2104 182/1167 61/388 Q/R cAg/cGg 1 1 RGS20 HGNC HGNC:14600 protein_coding YES CCDS6155.1 ENSP00000297313 O76081 UPI000013383C NM_170587.3 tolerated_low_confidence(0.26) 2/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 53879274 53879274 A G 1 0 0 0 0 1 0 0 0 13474 188 7 5 5 RGS20 8 53879274 Missense_Mutation SNP A C3N-01410_T 20417873 53879274 91259362 116 23016 ZFHX4 0 . GRCh38 8 76851514 76851514 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.4593G>T p.Met1531Ile p.M1531I ENST00000521891 10/11 455 419 36 216 215 1 strelka-varscan-mutect ZFHX4,missense_variant,p.Met1531Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Met1505Ile,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; T ENST00000521891 Transcript missense_variant 5041/14019 4593/10851 1531/3616 M/I atG/atT 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 76851514 76851514 G T 1 0 0 0 0 1 0 0 0 18213 1348 47 2 2 ZFHX4 8 76851514 Missense_Mutation SNP G C3N-01410_T 22972240 76851514 68287122 117 23017 CNBD1 0 . GRCh38 8 86866549 86866549 + Missense_Mutation SNP C C G novel C3N-01410_T C3N-01410_N C C c.54C>G p.Asn18Lys p.N18K ENST00000518476 1/11 235 206 29 243 243 0 strelka-varscan-mutect CNBD1,missense_variant,p.Asn18Lys,ENST00000518476,NM_173538.2;CNBD1,non_coding_transcript_exon_variant,,ENST00000517748,; G ENST00000518476 Transcript missense_variant 105/1594 54/1311 18/436 N/K aaC/aaG 1 1 CNBD1 HGNC HGNC:26663 protein_coding YES CCDS55259.1 ENSP00000430073 Q8NA66 UPI000006EA68 NM_173538.2 tolerated(0.15) 1/11 hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF142 MODERATE 1 SNV 1 1 PASS rs1369119298 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 86866549 86866549 C G 1 0 0 0 0 1 0 0 0 3369 477 17 4 4 CNBD1 8 86866549 Missense_Mutation SNP C C3N-01410_T 10015035 86866549 58272087 118 23018 SLC30A8 0 . GRCh38 8 117157748 117157748 + Missense_Mutation SNP T T A rs578012694 C3N-01410_T C3N-01410_N T T c.476T>A p.Val159Glu p.V159E ENST00000456015 4/8 192 140 52 211 211 0 strelka-varscan-mutect SLC30A8,missense_variant,p.Val110Glu,ENST00000427715,NM_001172815.1,NM_001172813.1;SLC30A8,missense_variant,p.Val110Glu,ENST00000519688,NM_001172814.1;SLC30A8,missense_variant,p.Val159Glu,ENST00000456015,NM_173851.2;SLC30A8,missense_variant,p.Val110Glu,ENST00000521243,NM_001172811.1;SLC30A8,downstream_gene_variant,,ENST00000518521,;SLC30A8,downstream_gene_variant,,ENST00000524274,; A ENST00000456015 Transcript missense_variant 476/2520 476/1110 159/369 V/E gTg/gAg rs578012694 1 1 SLC30A8 HGNC HGNC:20303 protein_coding YES CCDS6322.1 ENSP00000415011 Q8IWU4 UPI00001B00D6 NM_173851.2 deleterious(0) 4/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11562:SF37,hmmpanther:PTHR11562,Gene3D:3h90A01,Pfam_domain:PF01545,TIGRFAM_domain:TIGR01297,Superfamily_domains:0054606 MODERATE 1 SNV 1 1 PASS rs578012694 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 117157748 117157748 T A 1 0 0 0 0 1 0 0 0 14831 1696 59 4 4 SLC30A8 8 117157748 Missense_Mutation SNP T C3N-01410_T 30291199 117157748 27980888 119 23019 EPPK1 0 . GRCh38 8 143868402 143868402 + Missense_Mutation SNP C C A rs201170631 C3N-01410_T C3N-01410_N C C c.4852G>T p.Val1618Leu p.V1618L ENST00000615648 2/2 197 144 53 130 130 0 strelka-varscan-mutect EPPK1,missense_variant,p.Val1618Leu,ENST00000615648,NM_031308.3;EPPK1,missense_variant,p.Val1593Leu,ENST00000568225,; A ENST00000615648 Transcript missense_variant 4924/16002 4852/15267 1618/5088 V/L Gtg/Ttg rs201170631 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 tolerated(0.12) 2/2 Gene3D:3.90.1290.10,Pfam_domain:PF00681,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF252,SMART_domains:SM00250,Superfamily_domains:SSF75399 MODERATE 1 SNV 5 1 PASS rs201170631 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 143868402 143868402 C A 1 0 0 0 0 1 0 0 0 5038 536 19 1 1 EPPK1 8 143868402 Missense_Mutation SNP C C3N-01410_T 26710654 143868402 1270234 120 23020 EPPK1 0 . GRCh38 8 143868510 143868510 + Nonsense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.4744C>T p.Gln1582Ter p.Q1582* ENST00000615648 2/2 171 128 43 89 89 0 strelka-varscan-mutect EPPK1,stop_gained,p.Gln1582Ter,ENST00000615648,NM_031308.3;EPPK1,stop_gained,p.Gln1557Ter,ENST00000568225,; A ENST00000615648 Transcript stop_gained 4816/16002 4744/15267 1582/5088 Q/* Cag/Tag 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 2/2 Gene3D:3.90.1290.10,Pfam_domain:PF00681,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF252,SMART_domains:SM00250,Superfamily_domains:SSF75399 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 143868510 143868510 G A 1 0 0 0 0 0 1 0 0 5038 1357 47 3 3 EPPK1 8 143868510 Nonsense_Mutation SNP G C3N-01410_T 108 143868510 1270126 121 23021 PAX5 0 . GRCh38 9 36882006 36882006 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1010C>A p.Pro337His p.P337H ENST00000358127 8/10 213 159 54 180 180 0 strelka-varscan-mutect PAX5,missense_variant,p.Pro337His,ENST00000358127,NM_016734.2;PAX5,missense_variant,p.Pro337His,ENST00000377853,NM_001280548.1;PAX5,missense_variant,p.Pro294His,ENST00000414447,NM_001280554.1;PAX5,missense_variant,p.Pro229His,ENST00000522003,NM_001280556.1;PAX5,missense_variant,p.Pro294His,ENST00000520281,NM_001280553.1;PAX5,missense_variant,p.Pro164His,ENST00000524340,;PAX5,intron_variant,,ENST00000377852,NM_001280547.1;PAX5,intron_variant,,ENST00000523241,NM_001280549.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000446742,NM_001280555.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000522932,;PAX5,splice_region_variant,,ENST00000377840,;PAX5,splice_region_variant,,ENST00000523493,; T ENST00000358127 Transcript missense_variant,splice_region_variant 1164/8615 1010/1176 337/391 P/H cCt/cAt 1 -1 PAX5 HGNC HGNC:8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 UPI000013136C NM_016734.2 deleterious(0.01) 8/10 Pfam_domain:PF12403 MODERATE 1 SNV 1 1 PASS rs1443254567 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 36882006 36882006 G T 1 0 0 0 0 1 0 0 0 11567 1014 35 2 2 PAX5 9 36882006 Missense_Mutation SNP G C3N-01410_T 36882006 101512711 122 23022 ABCA1 0 . GRCh38 9 104791970 104791970 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.5786T>C p.Val1929Ala p.V1929A ENST00000374736 43/50 362 298 64 433 433 0 strelka-varscan-mutect ABCA1,missense_variant,p.Val1929Ala,ENST00000374736,NM_005502.3; G ENST00000374736 Transcript missense_variant 6181/10494 5786/6786 1929/2261 V/A gTt/gCt 1 -1 ABCA1 HGNC HGNC:29 protein_coding YES CCDS6762.1 ENSP00000363868 O95477 UPI000013E441 NM_005502.3 deleterious(0) 43/50 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF34,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 104791970 104791970 A G 1 0 0 0 0 1 0 0 0 32 43 2 5 5 ABCA1 9 104791970 Missense_Mutation SNP A C3N-01410_T 67909964 104791970 33602747 123 23023 PAPPA 0 . GRCh38 9 116396557 116396557 + Silent SNP C C A rs750316557 C3N-01410_T C3N-01410_N C C c.4825C>A p.= p.R1609R ENST00000328252 22/22 126 87 39 139 138 1 strelka-varscan-mutect PAPPA,synonymous_variant,p.=,ENST00000328252,NM_002581.3;PAPPA-AS1,downstream_gene_variant,,ENST00000445861,;PAPPA,non_coding_transcript_exon_variant,,ENST00000483254,; A ENST00000328252 Transcript synonymous_variant 5194/10959 4825/4884 1609/1627 R Cgg/Agg rs750316557 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 22/22 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 LOW 1 SNV 1 1 PASS rs750316557 . 0 207 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 A 2 1 75 116396557 116396557 C A 1 0 0 0 0 0 0 0 1 11512 875 31 1 1 PAPPA 9 116396557 Silent SNP C C3N-01410_T 11604587 116396557 21998160 124 23024 PRRC2B 0 . GRCh38 9 131447792 131447792 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1108G>T p.Asp370Tyr p.D370Y ENST00000357304 8/31 46 35 11 58 58 0 strelka-mutect PRRC2B,missense_variant,p.Asp370Tyr,ENST00000357304,NM_013318.3;PRRC2B,missense_variant,p.Asp370Tyr,ENST00000405995,;PRRC2B,non_coding_transcript_exon_variant,,ENST00000489593,; T ENST00000357304 Transcript missense_variant 1163/11042 1108/6690 370/2229 D/Y Gat/Tat 1 1 PRRC2B HGNC HGNC:28121 protein_coding YES CCDS48044.1 ENSP00000349856 Q5JSZ5 UPI00002374A3 NM_013318.3 deleterious(0) 8/31 Low_complexity_(Seg):seg,hmmpanther:PTHR14038:SF4,hmmpanther:PTHR14038 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 131447792 131447792 G T 1 0 0 0 0 1 0 0 0 12749 1290 45 2 2 PRRC2B 9 131447792 Missense_Mutation SNP G C3N-01410_T 15051235 131447792 6946925 125 23025 PAEP 0 . GRCh38 9 135561854 135561854 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.53C>A p.Ala18Asp p.A18D ENST00000479141 1/7 89 60 29 102 102 0 strelka-varscan-mutect PAEP,missense_variant,p.Ala18Asp,ENST00000479141,NM_002571.2;PAEP,missense_variant,p.Ala18Asp,ENST00000371766,;PAEP,missense_variant,p.Ala4Asp,ENST00000433563,;PAEP,missense_variant,p.Ala18Asp,ENST00000277508,NM_001018049.1;PAEP,missense_variant,p.Ala18Asp,ENST00000611414,;PAEP,upstream_gene_variant,,ENST00000454923,;PAEP,upstream_gene_variant,,ENST00000457014,;PAEP,upstream_gene_variant,,ENST00000418284,;PAEP,missense_variant,p.Ala18Asp,ENST00000371768,; A ENST00000479141 Transcript missense_variant 97/990 53/543 18/180 A/D gCc/gAc 1 1 PAEP HGNC HGNC:8573 protein_coding YES CCDS35173.1 ENSP00000417898 P09466 A0A024R8D8 UPI0000038E3A NM_002571.2 tolerated(0.1) 1/7 hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF72,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 135561854 135561854 C A 1 0 0 0 0 1 0 0 0 11460 739 26 2 2 PAEP 9 135561854 Missense_Mutation SNP C C3N-01410_T 4114062 135561854 2832863 126 23026 DIP2C 0 . GRCh38 10 440904 440904 + Missense_Mutation SNP C C T rs748869768 C3N-01410_T C3N-01410_N C C c.361G>A p.Val121Met p.V121M ENST00000280886 4/37 104 72 32 153 153 0 strelka-varscan-mutect DIP2C,missense_variant,p.Val121Met,ENST00000280886,NM_014974.2;DIP2C,missense_variant,p.Val102Met,ENST00000381496,;DIP2C,missense_variant,p.Val177Met,ENST00000634311,;RP11-490E15.2,intron_variant,,ENST00000425723,; T ENST00000280886 Transcript missense_variant 451/7888 361/4671 121/1556 V/M Gtg/Atg rs748869768,COSM5687240,COSM5687241,COSM5687242 1 -1 DIP2C HGNC HGNC:29150 protein_coding YES CCDS7054.1 ENSP00000280886 Q9Y2E4 UPI00001833B9 NM_014974.2 deleterious(0.03) 4/37 hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF25 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs748869768 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 440904 440904 C T 1 0 0 0 0 1 0 0 0 4334 536 19 1 1 DIP2C 10 440904 Missense_Mutation SNP C C3N-01410_T 440904 133356518 127 23027 FAM107B 0 . GRCh38 10 14667652 14667652 + Nonsense_Mutation SNP C C A C3N-01410_T C3N-01410_N C C c.451G>T p.Glu151Ter p.E151* ENST00000181796 2/5 151 119 32 195 194 1 strelka-varscan-mutect FAM107B,stop_gained,p.Glu151Ter,ENST00000181796,NM_031453.3;RNA5SP302,upstream_gene_variant,,ENST00000364896,;FAM107B,stop_gained,p.Glu151Ter,ENST00000487335,; A ENST00000181796 Transcript stop_gained 685/3785 451/921 151/306 E/* Gag/Tag COSM32625 1 -1 FAM107B HGNC HGNC:23726 protein_coding YES CCDS7102.1 ENSP00000181796 Q9H098 UPI00001C0E1E NM_031453.3 2/5 hmmpanther:PTHR16768:SF1,hmmpanther:PTHR16768 1 HIGH 1 SNV 2 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 14667652 14667652 C A 1 0 0 0 0 0 1 0 0 5258 864 30 2 2 FAM107B 10 14667652 Nonsense_Mutation SNP C C3N-01410_T 14226748 14667652 119129770 128 23028 DCLRE1C 0 . GRCh38 10 14936585 14936585 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.315G>T p.Glu105Asp p.E105D ENST00000378278 5/14 179 136 43 273 273 0 strelka-varscan-mutect DCLRE1C,missense_variant,p.Glu105Asp,ENST00000378289,;DCLRE1C,missense_variant,p.Glu105Asp,ENST00000378278,NM_001033855.2;DCLRE1C,5_prime_UTR_variant,,ENST00000378255,NM_001289079.1;DCLRE1C,5_prime_UTR_variant,,ENST00000396817,NM_001033858.2;DCLRE1C,5_prime_UTR_variant,,ENST00000378254,NM_001289077.1;DCLRE1C,5_prime_UTR_variant,,ENST00000378258,NM_001033857.2;DCLRE1C,5_prime_UTR_variant,,ENST00000418843,;DCLRE1C,5_prime_UTR_variant,,ENST00000378241,;DCLRE1C,intron_variant,,ENST00000378246,NM_022487.3;DCLRE1C,intron_variant,,ENST00000378249,NM_001289078.1;DCLRE1C,intron_variant,,ENST00000357717,NM_001289076.1;DCLRE1C,intron_variant,,ENST00000456122,; A ENST00000378278 Transcript missense_variant 353/2354 315/2079 105/692 E/D gaG/gaT 1 -1 DCLRE1C HGNC HGNC:17642 protein_coding YES CCDS31149.1 ENSP00000367527 Q96SD1 UPI000013EEDC NM_001033855.2 tolerated(0.81) 5/14 hmmpanther:PTHR23240,hmmpanther:PTHR23240:SF8,Pfam_domain:PF12706,Gene3D:3.60.15.10,Superfamily_domains:SSF56281 MODERATE 1 SNV 1 1 PASS rs1477434785 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 14936585 14936585 C A 1 0 0 0 0 1 0 0 0 4098 912 32 2 2 DCLRE1C 10 14936585 Missense_Mutation SNP C C3N-01410_T 268933 14936585 118860837 129 23029 MLLT10 0 . GRCh38 10 21726268 21726268 + Missense_Mutation SNP C C G novel C3N-01410_T C3N-01410_N C C c.1903C>G p.Leu635Val p.L635V ENST00000307729 15/23 150 122 28 212 212 0 strelka-varscan-mutect MLLT10,missense_variant,p.Leu651Val,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Leu635Val,ENST00000307729,;MLLT10,missense_variant,p.Leu635Val,ENST00000631589,;MLLT10,missense_variant,p.Leu635Val,ENST00000377059,NM_001195626.1;MLLT10,missense_variant,p.Leu294Val,ENST00000438473,; G ENST00000307729 Transcript missense_variant 2081/5032 1903/3207 635/1068 L/V Ctc/Gtc 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 deleterious(0.01) 15/23 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93 MODERATE 1 SNV 1 1 PASS rs1220079829 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 21726268 21726268 C G 1 0 0 0 0 1 0 0 0 9589 913 32 4 4 MLLT10 10 21726268 Missense_Mutation SNP C C3N-01410_T 6789683 21726268 112071154 130 23030 PIP4K2A 0 . GRCh38 10 22607954 22607954 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.312G>T p.Arg104Ser p.R104S ENST00000376573 3/10 113 104 9 169 169 0 strelka-varscan-mutect PIP4K2A,missense_variant,p.Arg104Ser,ENST00000376573,NM_005028.4;PIP4K2A,missense_variant,p.Arg45Ser,ENST00000545335,;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000422321,;PIP4K2A,non_coding_transcript_exon_variant,,ENST00000432610,; A ENST00000376573 Transcript missense_variant 541/3802 312/1221 104/406 R/S agG/agT 1 -1 PIP4K2A HGNC HGNC:8997 protein_coding YES CCDS7141.1 ENSP00000365757 P48426 UPI0000001052 NM_005028.4 deleterious(0) 3/10 Gene3D:2gk9B01,PROSITE_profiles:PS51455,hmmpanther:PTHR23086,hmmpanther:PTHR23086:SF21,SMART_domains:SM00330,Superfamily_domains:SSF56104 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 22607954 22607954 C A 1 0 0 0 0 1 0 0 0 12031 506 18 2 2 PIP4K2A 10 22607954 Missense_Mutation SNP C C3N-01410_T 881686 22607954 111189468 131 23031 LYZL2 0 . GRCh38 10 30612853 30612853 + Missense_Mutation SNP T T C novel C3N-01410_T C3N-01410_N T T c.484A>G p.Ile162Val p.I162V ENST00000375318 4/5 171 142 29 132 132 0 strelka-varscan-mutect LYZL2,missense_variant,p.Ile162Val,ENST00000375318,NM_183058.2; C ENST00000375318 Transcript missense_variant 541/818 484/585 162/194 I/V Att/Gtt 1 -1 LYZL2 HGNC HGNC:29613 protein_coding YES CCDS7167.2 ENSP00000364467 Q7Z4W2 A0A080YUZ9 UPI0000160E06 NM_183058.2 tolerated(0.52) 4/5 PROSITE_profiles:PS51348,hmmpanther:PTHR11407:SF35,hmmpanther:PTHR11407,Gene3D:1.10.530.10,Pfam_domain:PF00062,SMART_domains:SM00263,Superfamily_domains:SSF53955,Prints_domain:PR00135 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 30612853 30612853 T C 1 0 0 0 0 1 0 0 0 9045 1493 52 5 5 LYZL2 10 30612853 Missense_Mutation SNP T C3N-01410_T 8004899 30612853 103184569 132 23032 ANKRD30A 0 . GRCh38 10 37141923 37141923 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.858G>T p.Leu286Phe p.L286F ENST00000361713 7/36 262 222 40 296 296 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Leu286Phe,ENST00000374660,;ANKRD30A,missense_variant,p.Leu342Phe,ENST00000611781,;ANKRD30A,missense_variant,p.Leu286Phe,ENST00000602533,;ANKRD30A,missense_variant,p.Leu286Phe,ENST00000361713,NM_052997.2; T ENST00000361713 Transcript missense_variant 957/4405 858/4026 286/1341 L/F ttG/ttT 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.13) 7/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 37141923 37141923 G T 1 0 0 0 0 1 0 0 0 761 1339 47 2 2 ANKRD30A 10 37141923 Missense_Mutation SNP G C3N-01410_T 6529070 37141923 96655499 133 23033 PCDH15 0 . GRCh38 10 54020330 54020330 + Silent SNP T T A novel C3N-01410_T C3N-01410_N T T c.2628A>T p.= p.T876T ENST00000373957 21/35 427 353 74 428 427 1 strelka-varscan-mutect PCDH15,synonymous_variant,p.=,ENST00000614895,;PCDH15,synonymous_variant,p.=,ENST00000373965,NM_001142772.1;PCDH15,synonymous_variant,p.=,ENST00000414778,;PCDH15,synonymous_variant,p.=,ENST00000617051,;PCDH15,synonymous_variant,p.=,ENST00000373957,NM_001142763.1;PCDH15,synonymous_variant,p.=,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,synonymous_variant,p.=,ENST00000395430,NM_001142766.1;PCDH15,synonymous_variant,p.=,ENST00000395433,NM_001142773.1;PCDH15,synonymous_variant,p.=,ENST00000395432,NM_001142767.1;PCDH15,synonymous_variant,p.=,ENST00000320301,NM_033056.3;PCDH15,synonymous_variant,p.=,ENST00000622048,;PCDH15,synonymous_variant,p.=,ENST00000437009,NM_001142765.1;PCDH15,synonymous_variant,p.=,ENST00000617271,NM_001142770.1;PCDH15,synonymous_variant,p.=,ENST00000613657,NM_001142769.1;PCDH15,synonymous_variant,p.=,ENST00000395445,;PCDH15,synonymous_variant,p.=,ENST00000616114,;PCDH15,synonymous_variant,p.=,ENST00000395438,;PCDH15,synonymous_variant,p.=,ENST00000612394,;PCDH15,synonymous_variant,p.=,ENST00000621708,NM_001142771.1;PCDH15,synonymous_variant,p.=,ENST00000409834,;PCDH15,synonymous_variant,p.=,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript synonymous_variant 3023/7032 2628/5889 876/1962 T acA/acT 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 21/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 54020330 54020330 T A 1 0 0 0 0 0 0 0 1 11598 1567 55 4 4 PCDH15 10 54020330 Silent SNP T C3N-01410_T 16878407 54020330 79777092 134 23034 PCDH15 0 . GRCh38 10 54236920 54236920 + Missense_Mutation SNP G G T C3N-01410_T C3N-01410_N G G c.903C>A p.Asn301Lys p.N301K ENST00000373957 10/35 372 282 90 388 385 3 strelka-varscan-mutect PCDH15,missense_variant,p.Asn301Lys,ENST00000614895,;PCDH15,missense_variant,p.Asn296Lys,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000414778,;PCDH15,missense_variant,p.Asn301Lys,ENST00000617051,;PCDH15,missense_variant,p.Asn301Lys,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Asn274Lys,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Asn259Lys,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Asn296Lys,ENST00000622048,;PCDH15,missense_variant,p.Asn296Lys,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Asn301Lys,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000395445,;PCDH15,missense_variant,p.Asn296Lys,ENST00000616114,;PCDH15,missense_variant,p.Asn296Lys,ENST00000395438,;PCDH15,missense_variant,p.Asn301Lys,ENST00000612394,;PCDH15,missense_variant,p.Asn301Lys,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Asn296Lys,ENST00000373955,;PCDH15,missense_variant,p.Asn296Lys,ENST00000395446,;PCDH15,missense_variant,p.Asn296Lys,ENST00000395440,;PCDH15,missense_variant,p.Asn296Lys,ENST00000395442,;PCDH15,intron_variant,,ENST00000409834,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Asn296Lys,ENST00000448885,;PCDH15,missense_variant,p.Asn296Lys,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; T ENST00000373957 Transcript missense_variant 1298/7032 903/5889 301/1962 N/K aaC/aaA COSM1180220,COSM1180221,COSM1180222,COSM1180223 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 deleterious(0.04) 10/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS rs1280363858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 54236920 54236920 G T 1 0 0 0 0 1 0 0 0 11598 1252 44 2 2 PCDH15 10 54236920 Missense_Mutation SNP G C3N-01410_T 216590 54236920 79560502 135 23035 LRRTM3 0 . GRCh38 10 66928183 66928183 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1267G>T p.Gly423Cys p.G423C ENST00000361320 2/3 279 185 94 209 206 3 strelka-varscan-mutect LRRTM3,missense_variant,p.Gly423Cys,ENST00000361320,NM_178011.4;CTNNA3,intron_variant,,ENST00000433211,NM_001127384.2,NM_013266.3;CTNNA3,intron_variant,,ENST00000494580,; T ENST00000361320 Transcript missense_variant 1845/4358 1267/1746 423/581 G/C Ggc/Tgc 1 1 LRRTM3 HGNC HGNC:19410 protein_coding YES CCDS7270.1 ENSP00000355187 Q86VH5 UPI0000088C0F NM_178011.4 deleterious(0) 2/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF54 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 66928183 66928183 G T 1 0 0 0 0 1 0 0 0 8947 1232 43 2 2 LRRTM3 10 66928183 Missense_Mutation SNP G C3N-01410_T 12691263 66928183 66869239 136 23036 OIT3 0 . GRCh38 10 72913354 72913354 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.837G>C p.Arg279Ser p.R279S ENST00000334011 6/9 76 64 12 43 43 0 strelka-varscan-mutect OIT3,missense_variant,p.Arg279Ser,ENST00000334011,NM_152635.2;OIT3,missense_variant,p.Arg279Ser,ENST00000622652,;NPM1P24,downstream_gene_variant,,ENST00000428039,; C ENST00000334011 Transcript missense_variant 1055/2365 837/1638 279/545 R/S agG/agC 1 1 OIT3 HGNC HGNC:29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.2 deleterious(0.05) 6/9 PROSITE_profiles:PS51034,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF326,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 72913354 72913354 G C 1 0 0 0 0 1 0 0 0 10924 1223 43 4 4 OIT3 10 72913354 Missense_Mutation SNP G C3N-01410_T 5985171 72913354 60884068 137 23037 C10orf99 0 . GRCh38 10 84184726 84184726 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.206C>A p.Pro69His p.P69H ENST00000372126 3/3 258 212 46 211 211 0 strelka-varscan-mutect C10orf99,missense_variant,p.Pro69His,ENST00000372126,NM_207373.2;C10orf99,intron_variant,,ENST00000472542,; A ENST00000372126 Transcript missense_variant 320/888 206/246 69/81 P/H cCc/cAc 1 1 C10orf99 HGNC HGNC:31428 protein_coding YES CCDS7371.1 ENSP00000361199 Q6UWK7 UPI0000046D02 NM_207373.2 tolerated(0.6) 3/3 Pfam_domain:PF15854 MODERATE 1 SNV 1 1 PASS rs1384994724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 84184726 84184726 C A 1 0 0 0 0 1 0 0 0 1775 623 22 2 2 C10orf99 10 84184726 Missense_Mutation SNP C C3N-01410_T 11271372 84184726 49612696 138 23038 CDHR1 0 . GRCh38 10 84214269 84214269 + Missense_Mutation SNP G G T rs767546090 C3N-01410_T C3N-01410_N G G c.2228G>T p.Arg743Leu p.R743L ENST00000623527 17/17 608 409 199 587 587 0 strelka-varscan-mutect CDHR1,missense_variant,p.Arg743Leu,ENST00000623527,NM_033100.3;CDHR1,missense_variant,p.Arg482Leu,ENST00000372117,;CDHR1,intron_variant,,ENST00000332904,NM_001171971.2;CDHR1,intron_variant,,ENST00000623399,;CDHR1,non_coding_transcript_exon_variant,,ENST00000459673,;CDHR1,downstream_gene_variant,,ENST00000622973,; T ENST00000623527 Transcript missense_variant 2354/6781 2228/2580 743/859 R/L cGg/cTg rs767546090 1 1 CDHR1 HGNC HGNC:14550 protein_coding YES CCDS7372.1 ENSP00000485478 Q96JP9 F1T0L2 UPI0000161C2F NM_033100.3 deleterious_low_confidence(0) 17/17 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF340 MODERATE 1 SNV 1 1 PASS rs767546090 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 84214269 84214269 G T 1 0 0 0 0 1 0 0 0 2821 1116 39 1 1 CDHR1 10 84214269 Missense_Mutation SNP G C3N-01410_T 29543 84214269 49583153 139 23039 HTR7 0 . GRCh38 10 90749444 90749444 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.690G>T p.= p.V230V ENST00000336152 2/4 208 149 59 186 186 0 strelka-varscan-mutect HTR7,synonymous_variant,p.=,ENST00000336152,NM_019859.3;HTR7,synonymous_variant,p.=,ENST00000371719,NM_019860.3;HTR7,synonymous_variant,p.=,ENST00000277874,NM_000872.4; A ENST00000336152 Transcript synonymous_variant 717/3126 690/1440 230/479 V gtG/gtT 1 -1 HTR7 HGNC HGNC:5302 protein_coding YES CCDS7408.1 ENSP00000337949 P34969 UPI0000049B68 NM_019859.3 2/4 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF116,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 90749444 90749444 C A 1 0 0 0 0 0 0 0 1 7348 465 17 2 2 HTR7 10 90749444 Silent SNP C C3N-01410_T 6535175 90749444 43047978 140 23040 CPN1 0 . GRCh38 10 100081568 100081568 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.58C>A p.Pro20Thr p.P20T ENST00000370418 1/9 527 461 66 483 481 2 strelka-varscan-mutect CPN1,missense_variant,p.Pro20Thr,ENST00000370418,NM_001308.2; T ENST00000370418 Transcript missense_variant 310/1863 58/1377 20/458 P/T Ccg/Acg 1 -1 CPN1 HGNC HGNC:2312 protein_coding YES CCDS7486.1 ENSP00000359446 P15169 UPI00000012AC NM_001308.2 tolerated(0.1) 1/9 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11532:SF7,hmmpanther:PTHR11532,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 100081568 100081568 G T 1 0 0 0 0 1 0 0 0 3604 1232 43 2 2 CPN1 10 100081568 Missense_Mutation SNP G C3N-01410_T 9332124 100081568 33715854 141 23041 PKD2L1 0 . GRCh38 10 100293362 100293362 + Silent SNP G G A rs777226908 C3N-01410_T C3N-01410_N G G c.1677C>T p.= p.I559I ENST00000318222 10/16 159 95 64 187 187 0 strelka-varscan-mutect PKD2L1,synonymous_variant,p.=,ENST00000318222,NM_001253837.1,NM_016112.2;PKD2L1,intron_variant,,ENST00000465680,;PKD2L1,3_prime_UTR_variant,,ENST00000528248,; A ENST00000318222 Transcript synonymous_variant 2060/3043 1677/2418 559/805 I atC/atT rs777226908 1 -1 PKD2L1 HGNC HGNC:9011 protein_coding YES CCDS7492.1 ENSP00000325296 Q9P0L9 UPI0000130FED NM_001253837.1,NM_016112.2 10/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF105,Pfam_domain:PF08016,Superfamily_domains:SSF81324,Prints_domain:PR01433 LOW 1 SNV 1 1 PASS rs777226908 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 100293362 100293362 G A 1 0 0 0 0 0 0 0 1 12063 1280 45 3 3 PKD2L1 10 100293362 Silent SNP G C3N-01410_T 211794 100293362 33504060 142 23042 RBM20 0 . GRCh38 10 110821795 110821795 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.3176C>A p.Pro1059Gln p.P1059Q ENST00000369519 11/14 324 219 105 145 145 0 strelka-varscan-mutect RBM20,missense_variant,p.Pro1059Gln,ENST00000369519,NM_001134363.2;RBM20,upstream_gene_variant,,ENST00000471172,; A ENST00000369519 Transcript missense_variant 3234/7233 3176/3684 1059/1227 P/Q cCa/cAa 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 tolerated(0.1) 11/14 MODERATE 1 SNV 1 1 PASS rs1478811231 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 110821795 110821795 C A 1 0 0 0 0 1 0 0 0 13287 594 21 2 2 RBM20 10 110821795 Missense_Mutation SNP C C3N-01410_T 10528433 110821795 22975627 143 23043 AFAP1L2 0 . GRCh38 10 114310361 114310361 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.875G>T p.Cys292Phe p.C292F ENST00000304129 8/19 99 81 18 101 101 0 strelka-mutect AFAP1L2,missense_variant,p.Cys292Phe,ENST00000369271,NM_032550.3;AFAP1L2,missense_variant,p.Cys292Phe,ENST00000304129,NM_001287824.1,NM_001001936.2;AFAP1L2,missense_variant,p.Cys310Phe,ENST00000419268,; A ENST00000304129 Transcript missense_variant 905/3705 875/2457 292/818 C/F tGc/tTc 1 -1 AFAP1L2 HGNC HGNC:25901 protein_coding YES CCDS31286.1 ENSP00000303042 Q8N4X5 UPI0000071FAF NM_001287824.1,NM_001001936.2 deleterious(0.04) 8/19 hmmpanther:PTHR14338:SF4,hmmpanther:PTHR14338 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 114310361 114310361 C A 1 0 0 0 0 1 0 0 0 432 710 25 2 2 AFAP1L2 10 114310361 Missense_Mutation SNP C C3N-01410_T 3488566 114310361 19487061 144 23044 ATRNL1 0 . GRCh38 10 115301879 115301879 + Missense_Mutation SNP C C A rs202112185 C3N-01410_T C3N-01410_N C C c.2654C>A p.Pro885Gln p.P885Q ENST00000355044 17/29 99 64 35 120 120 0 varscan-mutect ATRNL1,missense_variant,p.Pro885Gln,ENST00000355044,NM_207303.4;ATRNL1,missense_variant,p.Pro15Gln,ENST00000526373,;ATRNL1,upstream_gene_variant,,ENST00000534530,; A ENST00000355044 Transcript missense_variant 2780/8479 2654/4140 885/1379 P/Q cCg/cAg rs202112185 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 tolerated(1) 17/29 hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574 MODERATE 1 SNV 1 1 PASS rs202112185 . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 75 115301879 115301879 C A 1 0 0 0 0 1 0 0 0 1360 652 23 1 1 ATRNL1 10 115301879 Missense_Mutation SNP C C3N-01410_T 991518 115301879 18495543 145 23045 NSMCE4A 0 . GRCh38 10 121965369 121965369 + Nonsense_Mutation SNP C C A rs143064887 C3N-01410_T C3N-01410_N C C c.670G>T p.Gly224Ter p.G224* ENST00000369023 5/11 169 115 54 171 171 0 strelka-varscan-mutect NSMCE4A,stop_gained,p.Gly224Ter,ENST00000369023,NM_001167865.1,NM_017615.2;NSMCE4A,stop_gained,p.Gly224Ter,ENST00000369017,;RP11-500G22.5,upstream_gene_variant,,ENST00000620490,;NSMCE4A,non_coding_transcript_exon_variant,,ENST00000489266,;NSMCE4A,non_coding_transcript_exon_variant,,ENST00000468209,;NSMCE4A,non_coding_transcript_exon_variant,,ENST00000464321,;NSMCE4A,downstream_gene_variant,,ENST00000472431,;NSMCE4A,downstream_gene_variant,,ENST00000465189,;NSMCE4A,downstream_gene_variant,,ENST00000481320,;NSMCE4A,upstream_gene_variant,,ENST00000483541,; A ENST00000369023 Transcript stop_gained 722/1394 670/1158 224/385 G/* Gga/Tga rs143064887,COSM4573419 1 -1 NSMCE4A HGNC HGNC:25935 protein_coding YES CCDS7624.1 ENSP00000358019 Q9NXX6 UPI000013D40C NM_001167865.1,NM_017615.2 5/11 hmmpanther:PTHR16140,hmmpanther:PTHR16140:SF2 0,1 HIGH 1 SNV 1 0,1 1 PASS rs143064887 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 121965369 121965369 C A 1 0 0 0 0 0 1 0 0 10738 661 23 1 1 NSMCE4A 10 121965369 Nonsense_Mutation SNP C C3N-01410_T 6663490 121965369 11832053 146 23046 TCERG1L 0 . GRCh38 10 131260386 131260386 + Silent SNP G G C rs149055623 C3N-01410_T C3N-01410_N G G c.729C>G p.= p.A243A ENST00000368642 4/12 51 37 14 45 45 0 strelka-varscan-mutect TCERG1L,synonymous_variant,p.=,ENST00000368642,NM_174937.3;TCERG1L,upstream_gene_variant,,ENST00000483040,; C ENST00000368642 Transcript synonymous_variant 815/2618 729/1761 243/586 A gcC/gcG rs149055623,COSM3665587,COSM4781383 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 4/12 hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5,Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs149055623 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 131260386 131260386 G C 1 0 0 0 0 0 0 0 1 16093 1103 39 4 4 TCERG1L 10 131260386 Silent SNP G C3N-01410_T 9295017 131260386 2537036 147 23047 MUC5B 0 . GRCh38 11 1245652 1245652 + Silent SNP T T C novel C3N-01410_T C3N-01410_N T T c.8772T>C p.= p.G2924G ENST00000529681 31/49 108 83 25 80 80 0 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; C ENST00000529681 Transcript synonymous_variant 8830/17911 8772/17289 2924/5762 G ggT/ggC 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 31/49 Pfam_domain:PF13330 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 1245652 1245652 T C 1 0 0 0 0 0 0 0 1 9979 1683 59 5 5 MUC5B 11 1245652 Silent SNP T C3N-01410_T 1245652 133840970 148 23048 MUC5B 0 . GRCh38 11 1249759 1249759 + Silent SNP T T C novel C3N-01410_T C3N-01410_N T T c.12879T>C p.= p.S4293S ENST00000529681 31/49 229 185 44 254 254 0 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,; C ENST00000529681 Transcript synonymous_variant 12937/17911 12879/17289 4293/5762 S agT/agC 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 31/49 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 1249759 1249759 T C 1 0 0 0 0 0 0 0 1 9979 1722 60 5 5 MUC5B 11 1249759 Silent SNP T C3N-01410_T 4107 1249759 133836863 149 23049 TRPM5 0 . GRCh38 11 2412915 2412915 + Missense_Mutation SNP C C T rs754942616 C3N-01410_T C3N-01410_N C C c.2194G>A p.Val732Met p.V732M ENST00000155858 15/24 261 208 53 298 298 0 strelka-varscan-mutect TRPM5,missense_variant,p.Val732Met,ENST00000155858,NM_014555.3;TRPM5,missense_variant,p.Val726Met,ENST00000533881,;TRPM5,missense_variant,p.Val732Met,ENST00000533060,;TRPM5,missense_variant,p.Val732Met,ENST00000528453,; T ENST00000155858 Transcript missense_variant 2203/3929 2194/3498 732/1165 V/M Gtg/Atg rs754942616,COSM428852 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 deleterious(0) 15/24 Transmembrane_helices:TMhelix,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754942616 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 2412915 2412915 C T 1 0 0 0 0 1 0 0 0 17095 536 19 1 1 TRPM5 11 2412915 Missense_Mutation SNP C C3N-01410_T 1163156 2412915 132673707 150 23050 RRM1 0 . GRCh38 11 4106046 4106046 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.109G>T p.Ala37Ser p.A37S ENST00000300738 3/19 225 179 46 245 245 0 strelka-varscan-mutect RRM1,missense_variant,p.Ala37Ser,ENST00000300738,NM_001033.3;RRM1,splice_region_variant,,ENST00000526865,;RRM1,splice_region_variant,,ENST00000532710,;RRM1,missense_variant,p.Arg65Ser,ENST00000532170,;RRM1,splice_region_variant,,ENST00000526350,;RRM1,splice_region_variant,,ENST00000530368,;RRM1,intron_variant,,ENST00000533349,NM_001318064.1; T ENST00000300738 Transcript missense_variant,splice_region_variant 313/3076 109/2379 37/792 A/S Gct/Tct 1 1 RRM1 HGNC HGNC:10451 protein_coding YES CCDS7750.1 ENSP00000300738 P23921 UPI0000000C7C NM_001033.3 tolerated_low_confidence(0.1) 3/19 PROSITE_profiles:PS51161,hmmpanther:PTHR11573,Pfam_domain:PF03477,Superfamily_domains:SSF48168 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 4106046 4106046 G T 1 0 0 0 0 1 0 0 0 13935 1217 42 2 2 RRM1 11 4106046 Missense_Mutation SNP G C3N-01410_T 1693131 4106046 130980576 151 23051 OR51A7 0 . GRCh38 11 4908169 4908169 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.800A>G p.Lys267Arg p.K267R ENST00000359350 1/1 310 260 50 325 325 0 strelka-varscan-mutect OR51A7,missense_variant,p.Lys267Arg,ENST00000359350,NM_001004749.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; G ENST00000359350 Transcript missense_variant 800/939 800/939 267/312 K/R aAa/aGa 1 1 OR51A7 HGNC HGNC:15188 protein_coding YES CCDS31364.1 ENSP00000352305 Q8NH64 UPI0000041C23 NM_001004749.1 tolerated(0.25) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF120,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 4908169 4908169 A G 1 0 0 0 0 1 0 0 0 11163 14 1 5 5 OR51A7 11 4908169 Missense_Mutation SNP A C3N-01410_T 802123 4908169 130178453 152 23052 OR52E8 0 . GRCh38 11 5857407 5857407 + Missense_Mutation SNP G G C C3N-01410_T C3N-01410_N G G c.296C>G p.Ser99Cys p.S99C ENST00000537935 1/1 192 160 32 198 198 0 strelka-varscan-mutect OR52E8,missense_variant,p.Ser99Cys,ENST00000537935,NM_001005168.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; C ENST00000537935 Transcript missense_variant 328/1061 296/954 99/317 S/C tCt/tGt COSM3450174 1 -1 OR52E8 HGNC HGNC:15217 protein_coding YES CCDS31400.1 ENSP00000444054 Q6IFG1 A0A126GVH0 UPI000004B211 NM_001005168.1 tolerated(0.1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF170,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 5857407 5857407 G C 1 0 0 0 0 1 0 0 0 11191 942 33 4 4 OR52E8 11 5857407 Missense_Mutation SNP G C3N-01410_T 949238 5857407 129229215 153 23053 OR56A4 0 . GRCh38 11 6002749 6002749 + Missense_Mutation SNP G G A C3N-01410_T C3N-01410_N G G c.400C>T p.Pro134Ser p.P134S ENST00000330728 1/1 127 104 23 141 140 1 strelka-varscan-mutect OR56A4,missense_variant,p.Pro134Ser,ENST00000330728,NM_001005179.2; A ENST00000330728 Transcript missense_variant 446/1209 400/1098 134/365 P/S Ccc/Tcc COSM1298261 1 -1 OR56A4 HGNC HGNC:14791 protein_coding YES CCDS31404.1 ENSP00000328215 Q8NGH8 UPI000041A756 NM_001005179.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF81,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 6002749 6002749 G A 1 0 0 0 0 1 0 0 0 11207 1232 43 3 3 OR56A4 11 6002749 Missense_Mutation SNP G C3N-01410_T 145342 6002749 129083873 154 23054 ILK 0 . GRCh38 11 6609379 6609379 + Missense_Mutation SNP G G C C3N-01410_T C3N-01410_N G G c.699G>C p.Arg233Ser p.R233S ENST00000396751 7/12 493 403 90 518 518 0 strelka-varscan-mutect ILK,missense_variant,p.Arg233Ser,ENST00000396751,NM_001014795.2;ILK,missense_variant,p.Arg233Ser,ENST00000299421,NM_001014794.2,NM_004517.3;ILK,missense_variant,p.Arg264Ser,ENST00000537806,;ILK,missense_variant,p.Arg233Ser,ENST00000420936,;ILK,missense_variant,p.Arg99Ser,ENST00000532063,NM_001278442.1;ILK,missense_variant,p.Arg172Ser,ENST00000528995,NM_001278441.1;ILK,intron_variant,,ENST00000526318,;TPP1,downstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,downstream_gene_variant,,ENST00000533371,;TAF10,downstream_gene_variant,,ENST00000299424,NM_006284.3;TAF10,downstream_gene_variant,,ENST00000527248,;ILK,downstream_gene_variant,,ENST00000627400,;RP11-732A19.2,intron_variant,,ENST00000527398,;RP11-732A19.8,upstream_gene_variant,,ENST00000527191,;ILK,non_coding_transcript_exon_variant,,ENST00000534706,;ILK,downstream_gene_variant,,ENST00000534565,;ILK,downstream_gene_variant,,ENST00000524735,;TAF10,downstream_gene_variant,,ENST00000531760,;ILK,3_prime_UTR_variant,,ENST00000526711,;ILK,3_prime_UTR_variant,,ENST00000527121,;TAF10,non_coding_transcript_exon_variant,,ENST00000616342,;ILK,non_coding_transcript_exon_variant,,ENST00000530016,;ILK,non_coding_transcript_exon_variant,,ENST00000528784,;ILK,downstream_gene_variant,,ENST00000526114,;TAF10,downstream_gene_variant,,ENST00000532344,; C ENST00000396751 Transcript missense_variant 1155/2074 699/1359 233/452 R/S agG/agC COSM5373329 1 1 ILK HGNC HGNC:6040 protein_coding YES CCDS7768.1 ENSP00000379975 Q13418 V9HWF0 UPI0000000DC2 NM_001014795.2 deleterious(0.04) 7/12 Gene3D:3.30.200.20,Pfam_domain:PF07714,PIRSF_domain:PIRSF000654,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF30,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 6609379 6609379 G C 1 0 0 0 0 1 0 0 0 7616 1223 43 4 4 ILK 11 6609379 Missense_Mutation SNP G C3N-01410_T 606630 6609379 128477243 155 23055 DCHS1 0 . GRCh38 11 6625638 6625638 + Missense_Mutation SNP C C A rs768078918 C3N-01410_T C3N-01410_N C C c.6821G>T p.Arg2274Leu p.R2274L ENST00000299441 18/21 161 135 26 171 171 0 strelka-varscan-mutect DCHS1,missense_variant,p.Arg2274Leu,ENST00000299441,NM_003737.3;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.6,upstream_gene_variant,,ENST00000526633,; A ENST00000299441 Transcript missense_variant 7233/10765 6821/9897 2274/3298 R/L cGc/cTc rs768078918,COSM4676444 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0.03) 18/21 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768078918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 6625638 6625638 C A 1 0 0 0 0 1 0 0 0 4090 768 27 1 1 DCHS1 11 6625638 Missense_Mutation SNP C C3N-01410_T 16259 6625638 128460984 156 23056 ZBED5 0 . GRCh38 11 10853782 10853782 + Silent SNP T T C novel C3N-01410_T C3N-01410_N T T c.1164A>G p.= p.L388L ENST00000432999 3/3 167 135 32 146 146 0 strelka-varscan-mutect ZBED5,synonymous_variant,p.=,ENST00000432999,NM_021211.3,NM_001143667.1;ZBED5,synonymous_variant,p.=,ENST00000413761,;ZBED5,downstream_gene_variant,,ENST00000526020,;ZBED5,downstream_gene_variant,,ENST00000534690,;ZBED5,downstream_gene_variant,,ENST00000526852,;ZBED5,downstream_gene_variant,,ENST00000528289,;ZBED5-AS1,upstream_gene_variant,,ENST00000501079,;ZBED5-AS1,upstream_gene_variant,,ENST00000529014,;ZBED5,intron_variant,,ENST00000525350,;ZBED5,intron_variant,,ENST00000533925,;ZBED5,downstream_gene_variant,,ENST00000530570,; C ENST00000432999 Transcript synonymous_variant 1663/2741 1164/2082 388/693 L ctA/ctG 1 -1 ZBED5 HGNC HGNC:30803 protein_coding YES ENSP00000398106 Q49AG3 UPI000013CCBF NM_021211.3,NM_001143667.1 3/3 hmmpanther:PTHR11697:SF118,hmmpanther:PTHR11697,Superfamily_domains:SSF53098 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 10853782 10853782 T C 1 0 0 0 0 0 0 0 1 18082 1741 61 5 5 ZBED5 11 10853782 Silent SNP T C3N-01410_T 4228144 10853782 124232840 157 23057 TEAD1 0 . GRCh38 11 12883110 12883110 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.684G>T p.Gln228His p.Q228H ENST00000527636 9/13 368 299 69 420 419 1 strelka-varscan-mutect TEAD1,missense_variant,p.Gln132His,ENST00000526600,;TEAD1,missense_variant,p.Gln217His,ENST00000334310,;TEAD1,missense_variant,p.Gln228His,ENST00000527575,;TEAD1,missense_variant,p.Gln228His,ENST00000527636,NM_021961.5; T ENST00000527636 Transcript missense_variant 1135/2544 684/1281 228/426 Q/H caG/caT 1 1 TEAD1 HGNC HGNC:11714 protein_coding YES CCDS7810.2 ENSP00000435233 H0YE88 UPI000013D412 NM_021961.5 deleterious(0.03) 9/13 hmmpanther:PTHR11834,PIRSF_domain:PIRSF002603 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 12883110 12883110 G T 1 0 0 0 0 1 0 0 0 16149 962 34 2 2 TEAD1 11 12883110 Missense_Mutation SNP G C3N-01410_T 2029328 12883110 122203512 158 23058 SPON1 0 . GRCh38 11 14075353 14075353 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.488T>A p.Ile163Asn p.I163N ENST00000576479 4/16 191 154 37 217 217 0 strelka-varscan-mutect SPON1,missense_variant,p.Ile163Asn,ENST00000576479,NM_006108.3; A ENST00000576479 Transcript missense_variant 704/4837 488/2424 163/807 I/N aTc/aAc 1 1 SPON1 HGNC HGNC:11252 protein_coding YES CCDS73262.1 ENSP00000460236 Q9HCB6 UPI000044404A NM_006108.3 deleterious(0) 4/16 PROSITE_profiles:PS51019,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF18,Pfam_domain:PF02014 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 14075353 14075353 T A 1 0 0 0 0 1 0 0 0 15435 1435 50 4 4 SPON1 11 14075353 Missense_Mutation SNP T C3N-01410_T 1192243 14075353 121011269 159 23059 SLC6A5 0 . GRCh38 11 20652381 20652381 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.2163G>T p.Met721Ile p.M721I ENST00000525748 15/16 358 299 59 381 379 2 strelka-varscan-mutect SLC6A5,missense_variant,p.Met721Ile,ENST00000525748,NM_004211.3;SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; T ENST00000525748 Transcript missense_variant 2436/7084 2163/2394 721/797 M/I atG/atT 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 tolerated(0.08) 15/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 20652381 20652381 G T 1 0 0 0 0 1 0 0 0 14970 1319 46 2 2 SLC6A5 11 20652381 Missense_Mutation SNP G C3N-01410_T 6577028 20652381 114434241 160 23060 OR4A16 0 . GRCh38 11 55343792 55343792 + Missense_Mutation SNP G G T rs570625324 C3N-01410_T C3N-01410_N G G c.592G>T p.Val198Phe p.V198F ENST00000314721 1/1 377 311 66 310 310 0 strelka-varscan-mutect OR4A16,missense_variant,p.Val198Phe,ENST00000314721,NM_001005274.1; T ENST00000314721 Transcript missense_variant 592/987 592/987 198/328 V/F Gtt/Ttt rs570625324,COSM2157031 1 1 OR4A16 HGNC HGNC:15153 protein_coding YES CCDS31499.1 ENSP00000325128 Q8NH70 A0A126GW87 UPI0000061EB2 NM_001005274.1 deleterious_low_confidence(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF355,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs570625324 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 55343792 55343792 G T 1 0 0 0 0 1 0 0 0 11118 1261 44 2 2 OR4A16 11 55343792 Missense_Mutation SNP G C3N-01410_T 34691411 55343792 79742830 161 23061 OR5D18 0 . GRCh38 11 55820445 55820445 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.816C>A p.= p.V272V ENST00000333976 1/1 213 182 31 192 192 0 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; A ENST00000333976 Transcript synonymous_variant 816/942 816/942 272/313 V gtC/gtA 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 55820445 55820445 C A 1 0 0 0 0 0 0 0 1 11227 813 29 2 2 OR5D18 11 55820445 Silent SNP C C3N-01410_T 476653 55820445 79266177 162 23062 OR10AG1 0 . GRCh38 11 55967733 55967733 + Missense_Mutation SNP C C A rs867582684 C3N-01410_T C3N-01410_N C C c.731G>T p.Gly244Val p.G244V ENST00000312345 1/1 186 117 69 192 192 0 strelka-varscan-mutect OR10AG1,missense_variant,p.Gly244Val,ENST00000312345,NM_001005491.1; A ENST00000312345 Transcript missense_variant 731/906 731/906 244/301 G/V gGa/gTa rs867582684 1 -1 OR10AG1 HGNC HGNC:19607 protein_coding YES CCDS31514.1 ENSP00000311477 Q8NH19 A0A126GVM8 UPI000004B22B NM_001005491.1 deleterious(0.04) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF159,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs867582684 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 55967733 55967733 C A 1 0 0 0 0 1 0 0 0 10972 855 30 2 2 OR10AG1 11 55967733 Missense_Mutation SNP C C3N-01410_T 147288 55967733 79118889 163 23063 OR4D9 0 . GRCh38 11 59515776 59515776 + Silent SNP G G C rs145790540 C3N-01410_T C3N-01410_N G G c.864G>C p.= p.T288T ENST00000329328 1/1 140 102 38 171 171 0 strelka-varscan-mutect OR4D9,synonymous_variant,p.=,ENST00000329328,NM_001004711.1; C ENST00000329328 Transcript synonymous_variant 864/945 864/945 288/314 T acG/acC rs145790540 1 1 OR4D9 HGNC HGNC:15178 protein_coding YES CCDS31564.1 ENSP00000328563 Q8NGE8 A0A126GVP8 UPI0000061EE8 NM_001004711.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF272,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs145790540 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 75 59515776 59515776 G C 1 0 0 0 0 0 0 0 1 11136 1074 38 4 4 OR4D9 11 59515776 Silent SNP G C3N-01410_T 3548043 59515776 75570846 164 23064 CTSC 0 . GRCh38 11 88312507 88312507 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.366G>T p.Met122Ile p.M122I ENST00000227266 3/7 177 60 117 145 145 0 strelka-varscan-mutect CTSC,missense_variant,p.Met122Ile,ENST00000227266,NM_001814.4;CTSC,missense_variant,p.Met79Ile,ENST00000527018,;CTSC,non_coding_transcript_exon_variant,,ENST00000533865,; A ENST00000227266 Transcript missense_variant 481/1921 366/1392 122/463 M/I atG/atT 1 -1 CTSC HGNC HGNC:2528 protein_coding YES CCDS8282.1 ENSP00000227266 P53634 UPI000006D22D NM_001814.4 tolerated(0.09) 3/7 Pfam_domain:PF08773,Gene3D:2djfA00,Superfamily_domains:SSF75001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 88312507 88312507 C A 1 0 0 0 0 1 0 0 0 3840 826 29 2 2 CTSC 11 88312507 Missense_Mutation SNP C C3N-01410_T 28796731 88312507 46774115 165 23065 CUL5 0 . GRCh38 11 108072390 108072390 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.933G>C p.Leu311Phe p.L311F ENST00000393094 9/19 125 98 27 138 138 0 strelka-varscan-mutect CUL5,missense_variant,p.Leu311Phe,ENST00000393094,NM_003478.3;CUL5,upstream_gene_variant,,ENST00000531843,;CUL5,missense_variant,p.Leu311Phe,ENST00000531427,; C ENST00000393094 Transcript missense_variant 1549/6351 933/2343 311/780 L/F ttG/ttC 1 1 CUL5 HGNC HGNC:2556 protein_coding YES CCDS31668.1 ENSP00000376808 Q93034 UPI00001380B0 NM_003478.3 deleterious(0.01) 9/19 Gene3D:1.20.1310.10,Pfam_domain:PF00888,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF76,Superfamily_domains:SSF74788 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 108072390 108072390 G C 1 0 0 0 0 1 0 0 0 3869 1281 45 4 4 CUL5 11 108072390 Missense_Mutation SNP G C3N-01410_T 19759883 108072390 27014232 166 23066 ATM 0 . GRCh38 11 108257499 108257499 + Nonsense_Mutation SNP G G T rs587779819 C3N-01410_T C3N-01410_N G G c.2269G>T p.Gly757Ter p.G757* ENST00000278616 15/63 209 105 104 245 245 0 strelka-varscan-mutect ATM,stop_gained,p.Gly757Ter,ENST00000278616,NM_000051.3;ATM,stop_gained,p.Gly757Ter,ENST00000452508,;ATM,stop_gained,p.Gly757Ter,ENST00000527805,;ATM,downstream_gene_variant,,ENST00000525012,;ATM,downstream_gene_variant,,ENST00000533526,; T ENST00000278616 Transcript stop_gained 2654/13147 2269/9171 757/3056 G/* Gga/Tga rs587779819 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 15/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF72 uncertain_significance HIGH 1 SNV 5 1 1 PASS rs587779819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 75 108257499 108257499 G T 1 0 0 0 0 0 1 0 0 1261 1001 35 2 2 ATM 11 108257499 Nonsense_Mutation SNP G C3N-01410_T 185109 108257499 26829123 167 23067 NCAM1 0 . GRCh38 11 113232723 113232723 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.1509C>A p.= p.T503T ENST00000619839 13/21 155 65 90 141 141 0 strelka-varscan-mutect NCAM1,synonymous_variant,p.=,ENST00000615285,;NCAM1,synonymous_variant,p.=,ENST00000615112,;NCAM1,synonymous_variant,p.=,ENST00000618266,;NCAM1,synonymous_variant,p.=,ENST00000316851,NM_181351.4;NCAM1,synonymous_variant,p.=,ENST00000621518,;NCAM1,synonymous_variant,p.=,ENST00000621128,NM_001242608.1;NCAM1,synonymous_variant,p.=,ENST00000619839,NM_001242607.1;NCAM1,synonymous_variant,p.=,ENST00000531044,NM_000615.6;NCAM1,synonymous_variant,p.=,ENST00000621850,NM_001076682.3;NCAM1,synonymous_variant,p.=,ENST00000401611,;NCAM1,synonymous_variant,p.=,ENST00000526322,;NCAM1,synonymous_variant,p.=,ENST00000530543,;NCAM1,intron_variant,,ENST00000620046,;NCAM1,upstream_gene_variant,,ENST00000533073,;NCAM1,upstream_gene_variant,,ENST00000528590,;NCAM1,downstream_gene_variant,,ENST00000613217,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,non_coding_transcript_exon_variant,,ENST00000534046,;NCAM1,upstream_gene_variant,,ENST00000531817,;NCAM1,upstream_gene_variant,,ENST00000525355,; A ENST00000619839 Transcript synonymous_variant 1847/2993 1509/2655 503/884 T acC/acA 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 13/21 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 113232723 113232723 C A 1 0 0 0 0 0 0 0 1 10218 637 22 2 2 NCAM1 11 113232723 Silent SNP C C3N-01410_T 4975224 113232723 21853899 168 23068 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-01410_T C3N-01410_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 355 220 135 303 303 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-01410_T 25245351 108029958 169 23069 SSPN 0 . GRCh38 12 26195788 26195788 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.116G>T p.Cys39Phe p.C39F ENST00000242729 1/3 96 65 31 87 87 0 strelka-varscan-mutect SSPN,missense_variant,p.Cys39Phe,ENST00000242729,NM_005086.4;SSPN,missense_variant,p.Cys39Phe,ENST00000535504,;SSPN,intron_variant,,ENST00000422622,NM_001135823.1;SSPN,intron_variant,,ENST00000540266,;SSPN,intron_variant,,ENST00000538142,;SSPN,intron_variant,,ENST00000544231,;SSPN,intron_variant,,ENST00000534829,; T ENST00000242729 Transcript missense_variant 293/2788 116/732 39/243 C/F tGc/tTc 1 1 SSPN HGNC HGNC:11322 protein_coding YES CCDS8707.1 ENSP00000242729 Q14714 UPI0000135FF0 NM_005086.4 tolerated(0.53) 1/3 hmmpanther:PTHR15260 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 26195788 26195788 G T 1 0 0 0 0 1 0 0 0 15565 1319 46 2 2 SSPN 12 26195788 Missense_Mutation SNP G C3N-01410_T 950437 26195788 107079521 170 23070 PKP2 0 . GRCh38 12 32869030 32869030 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1067C>A p.Ala356Glu p.A356E ENST00000070846 4/14 317 279 38 329 329 0 strelka-varscan-mutect PKP2,missense_variant,p.Ala356Glu,ENST00000340811,NM_001005242.2;PKP2,missense_variant,p.Ala356Glu,ENST00000070846,NM_004572.3; T ENST00000070846 Transcript missense_variant 1092/4241 1067/2646 356/881 A/E gCa/gAa 1 -1 PKP2 HGNC HGNC:9024 protein_coding YES CCDS8731.1 ENSP00000070846 Q99959 UPI000013C576 NM_004572.3 deleterious(0.03) 4/14 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF25,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 32869030 32869030 G T 1 0 0 0 0 1 0 0 0 12081 1319 46 2 2 PKP2 12 32869030 Missense_Mutation SNP G C3N-01410_T 6673242 32869030 100406279 171 23071 ADAMTS20 0 . GRCh38 12 43376094 43376094 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.5275C>A p.Gln1759Lys p.Q1759K ENST00000389420 35/39 178 144 34 140 140 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Gln1759Lys,ENST00000389420,NM_025003.3; T ENST00000389420 Transcript missense_variant 5275/6076 5275/5733 1759/1910 Q/K Caa/Aaa 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 tolerated(1) 35/39 PROSITE_profiles:PS51046,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF08685 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 43376094 43376094 G T 1 0 0 0 0 1 0 0 0 310 1357 47 2 2 ADAMTS20 12 43376094 Missense_Mutation SNP G C3N-01410_T 10507064 43376094 89899215 172 23072 KRT18 0 . GRCh38 12 52951810 52951810 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.902G>C p.Arg301Pro p.R301P ENST00000388835 5/7 549 472 77 451 451 0 strelka-varscan-mutect KRT18,missense_variant,p.Arg301Pro,ENST00000550600,;KRT18,missense_variant,p.Arg301Pro,ENST00000388835,NM_000224.2;KRT18,missense_variant,p.Arg301Pro,ENST00000388837,NM_199187.1;KRT8,upstream_gene_variant,,ENST00000619952,;KRT8,upstream_gene_variant,,ENST00000552551,;KRT8,upstream_gene_variant,,ENST00000546897,NM_001256293.1;KRT8,upstream_gene_variant,,ENST00000546826,;KRT8,upstream_gene_variant,,ENST00000548998,;KRT8,upstream_gene_variant,,ENST00000549198,;KRT8,upstream_gene_variant,,ENST00000551318,;KRT18,non_coding_transcript_exon_variant,,ENST00000549078,;KRT18,non_coding_transcript_exon_variant,,ENST00000548496,;KRT18,non_coding_transcript_exon_variant,,ENST00000546656,;KRT18,downstream_gene_variant,,ENST00000548015,;KRT8,upstream_gene_variant,,ENST00000546921,; C ENST00000388835 Transcript missense_variant 1112/1562 902/1293 301/430 R/P cGt/cCt 1 1 KRT18 HGNC HGNC:6430 protein_coding YES CCDS31809.1 ENSP00000373487 P05783 A0A024RAY2 UPI000004284B NM_000224.2 deleterious(0.03) 5/7 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF35,Pfam_domain:PF00038,SMART_domains:SM01391,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS rs1169724462 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 52951810 52951810 G C 1 0 0 0 0 1 0 0 0 8337 1145 40 4 4 KRT18 12 52951810 Missense_Mutation SNP G C3N-01410_T 9575716 52951810 80323499 173 23073 TNS2 0 . GRCh38 12 53054304 53054304 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.415T>A p.Trp139Arg p.W139R ENST00000314276 7/29 285 210 75 223 223 0 strelka-varscan-mutect TNS2,missense_variant,p.Trp129Arg,ENST00000314250,NM_170754.2;TNS2,missense_variant,p.Trp139Arg,ENST00000314276,NM_015319.2;TNS2,missense_variant,p.Trp5Arg,ENST00000379902,NM_198316.1;TNS2,missense_variant,p.Trp129Arg,ENST00000552570,;TNS2,missense_variant,p.Trp129Arg,ENST00000549700,;TNS2,missense_variant,p.Trp129Arg,ENST00000546602,;TNS2,upstream_gene_variant,,ENST00000602335,;MIR6757,upstream_gene_variant,,ENST00000612099,;RP11-983P16.4,intron_variant,,ENST00000546793,;RP11-983P16.4,intron_variant,,ENST00000550601,;RP11-983P16.4,intron_variant,,ENST00000551890,;TNS2,non_coding_transcript_exon_variant,,ENST00000549311,;TNS2,non_coding_transcript_exon_variant,,ENST00000549498,;TNS2,non_coding_transcript_exon_variant,,ENST00000551693,;TNS2,upstream_gene_variant,,ENST00000547223,;TNS2,downstream_gene_variant,,ENST00000552403,;TNS2,downstream_gene_variant,,ENST00000551302,;TNS2,upstream_gene_variant,,ENST00000546759,;TNS2,upstream_gene_variant,,ENST00000549789,; A ENST00000314276 Transcript missense_variant 610/4944 415/4260 139/1419 W/R Tgg/Agg 1 1 TNS2 HGNC HGNC:19737 protein_coding YES CCDS8842.1 ENSP00000319756 Q63HR2 UPI000013F790 NM_015319.2 tolerated(0.05) 7/29 PROSITE_profiles:PS51181,hmmpanther:PTHR12305:SF58,hmmpanther:PTHR12305,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 53054304 53054304 T A 1 0 0 0 0 1 0 0 0 16817 1580 55 4 4 TNS2 12 53054304 Missense_Mutation SNP T C3N-01410_T 102494 53054304 80221005 174 23074 TIMELESS 0 . GRCh38 12 56429047 56429047 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1140G>T p.Trp380Cys p.W380C ENST00000553532 11/29 351 239 112 393 393 0 strelka-varscan-mutect TIMELESS,missense_variant,p.Trp380Cys,ENST00000553532,NM_003920.3;TIMELESS,missense_variant,p.Trp379Cys,ENST00000229201,;TIMELESS,upstream_gene_variant,,ENST00000557589,; A ENST00000553532 Transcript missense_variant 1291/5121 1140/3627 380/1208 W/C tgG/tgT 1 -1 TIMELESS HGNC HGNC:11813 protein_coding YES CCDS8918.1 ENSP00000450607 Q9UNS1 UPI000013C8EA NM_003920.3 deleterious(0) 11/29 hmmpanther:PTHR22940,hmmpanther:PTHR22940:SF4 MODERATE 1 SNV 1 1 PASS rs1336041942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 56429047 56429047 C A 1 0 0 0 0 1 0 0 0 16342 624 22 2 2 TIMELESS 12 56429047 Missense_Mutation SNP C C3N-01410_T 3374743 56429047 76846262 175 23075 NAV3 0 . GRCh38 12 78177168 78177168 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.5152G>T p.Gly1718Trp p.G1718W ENST00000397909 27/40 300 256 44 314 314 0 strelka-varscan-mutect NAV3,missense_variant,p.Gly1718Trp,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Gly1718Trp,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Gly613Trp,ENST00000552895,;NAV3,missense_variant,p.Gly340Trp,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000552300,;NAV3,upstream_gene_variant,,ENST00000548948,; T ENST00000397909 Transcript missense_variant 5325/9821 5152/7158 1718/2385 G/W Ggg/Tgg 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 27/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 78177168 78177168 G T 1 0 0 0 0 1 0 0 0 10194 1348 47 2 2 NAV3 12 78177168 Missense_Mutation SNP G C3N-01410_T 21748121 78177168 55098141 176 23076 LUM 0 . GRCh38 12 91108422 91108422 + Silent SNP G G A rs144214151 C3N-01410_T C3N-01410_N G G c.558C>T p.= p.L186L ENST00000266718 2/3 252 231 21 162 162 0 strelka-varscan-mutect LUM,synonymous_variant,p.=,ENST00000266718,NM_002345.3;LUM,non_coding_transcript_exon_variant,,ENST00000546642,;LUM,intron_variant,,ENST00000548071,; A ENST00000266718 Transcript synonymous_variant 1013/3008 558/1017 186/338 L ctC/ctT rs144214151,COSM944377 1 -1 LUM HGNC HGNC:6724 protein_coding YES CCDS9038.1 ENSP00000266718 P51884 UPI0000001C4D NM_002345.3 2/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF119,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00365,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058,Prints_domain:PR00019 0,1 LOW 1 SNV 1 0,1 1 PASS rs144214151 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 91108422 91108422 G A 1 0 0 0 0 0 0 0 1 8992 1045 37 1 1 LUM 12 91108422 Silent SNP G C3N-01410_T 12931254 91108422 42166887 177 23077 PLXNC1 0 . GRCh38 12 94301014 94301014 + Missense_Mutation SNP C C T novel C3N-01410_T C3N-01410_N C C c.4343C>T p.Ala1448Val p.A1448V ENST00000258526 28/31 190 154 36 129 129 0 strelka-varscan-mutect PLXNC1,missense_variant,p.Ala1448Val,ENST00000258526,NM_005761.2;PLXNC1,missense_variant,p.Ala495Val,ENST00000547057,;PLXNC1,missense_variant,p.Ala187Val,ENST00000545312,;PLXNC1,3_prime_UTR_variant,,ENST00000549217,; T ENST00000258526 Transcript missense_variant 4592/7346 4343/4707 1448/1568 A/V gCa/gTa 1 1 PLXNC1 HGNC HGNC:9106 protein_coding YES CCDS9049.1 ENSP00000258526 O60486 UPI0000038AF4 NM_005761.2 deleterious(0) 28/31 hmmpanther:PTHR22625:SF4,hmmpanther:PTHR22625,Pfam_domain:PF08337,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 94301014 94301014 C T 1 0 0 0 0 1 0 0 0 12232 710 25 3 3 PLXNC1 12 94301014 Missense_Mutation SNP C C3N-01410_T 3192592 94301014 38974295 178 23078 TMCC3 0 . GRCh38 12 94582085 94582085 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.532C>T p.Pro178Ser p.P178S ENST00000261226 2/4 224 194 30 187 187 0 strelka-varscan-mutect TMCC3,missense_variant,p.Pro178Ser,ENST00000261226,NM_020698.3;TMCC3,missense_variant,p.Pro147Ser,ENST00000551457,NM_001301036.1;TMCC3,downstream_gene_variant,,ENST00000548918,; A ENST00000261226 Transcript missense_variant 664/5877 532/1434 178/477 P/S Ccc/Tcc 1 -1 TMCC3 HGNC HGNC:29199 protein_coding YES CCDS31877.1 ENSP00000261226 Q9ULS5 UPI00001FB2DD NM_020698.3 tolerated(0.62) 2/4 Pfam_domain:PF10267,hmmpanther:PTHR17613,hmmpanther:PTHR17613:SF8 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 94582085 94582085 G A 1 0 0 0 0 1 0 0 0 16440 1232 43 3 3 TMCC3 12 94582085 Missense_Mutation SNP G C3N-01410_T 281071 94582085 38693224 179 23079 ANKS1B 0 . GRCh38 12 99246473 99246473 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.2148G>T p.= p.L716L ENST00000547776 13/26 184 152 32 128 128 0 strelka-varscan-mutect ANKS1B,synonymous_variant,p.=,ENST00000547776,NM_152788.4;ANKS1B,synonymous_variant,p.=,ENST00000547010,;ANKS1B,downstream_gene_variant,,ENST00000549866,;ANKS1B,upstream_gene_variant,,ENST00000550778,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000550833,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000546631,;ANKS1B,downstream_gene_variant,,ENST00000550157,; A ENST00000547776 Transcript synonymous_variant 2148/3885 2148/3747 716/1248 L ctG/ctT 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 13/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 LOW 1 SNV 1 1 PASS rs1458384655 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 99246473 99246473 C A 1 0 0 0 0 0 0 0 1 795 581 21 2 2 ANKS1B 12 99246473 Silent SNP C C3N-01410_T 4664388 99246473 34028836 180 23080 SVOP 0 . GRCh38 12 108938864 108938864 + Missense_Mutation SNP G G T rs374889554 C3N-01410_T C3N-01410_N G G c.860C>A p.Ala287Asp p.A287D ENST00000610966 9/16 275 214 61 274 274 0 strelka-varscan-mutect SVOP,missense_variant,p.Ala287Asp,ENST00000610966,NM_018711.4;SVOP,non_coding_transcript_exon_variant,,ENST00000551211,;SVOP,downstream_gene_variant,,ENST00000550436,; T ENST00000610966 Transcript missense_variant 1232/6813 860/1647 287/548 A/D gCt/gAt rs374889554 1 -1 SVOP HGNC HGNC:25417 protein_coding YES CCDS73520.1 ENSP00000479104 Q8N4V2 UPI000006E50F NM_018711.4 deleterious(0.04) 9/16 PROSITE_profiles:PS50850,hmmpanther:PTHR24064:SF280,hmmpanther:PTHR24064,Pfam_domain:PF00083,TIGRFAM_domain:TIGR00898,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS rs374889554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 108938864 108938864 G T 1 0 0 0 0 1 0 0 0 15808 971 34 2 2 SVOP 12 108938864 Missense_Mutation SNP G C3N-01410_T 9692391 108938864 24336445 181 23081 UBE3B 0 . GRCh38 12 109521157 109521157 + Missense_Mutation SNP G G C rs145812083 C3N-01410_T C3N-01410_N G G c.2086G>C p.Glu696Gln p.E696Q ENST00000342494 20/28 121 85 36 93 93 0 strelka-varscan-mutect UBE3B,missense_variant,p.Glu696Gln,ENST00000342494,NM_130466.3;UBE3B,missense_variant,p.Glu696Gln,ENST00000434735,NM_183415.2;UBE3B,missense_variant,p.Glu696Gln,ENST00000539599,;UBE3B,3_prime_UTR_variant,,ENST00000449510,;UBE3B,non_coding_transcript_exon_variant,,ENST00000538070,;UBE3B,non_coding_transcript_exon_variant,,ENST00000539584,; C ENST00000342494 Transcript missense_variant 2681/5722 2086/3207 696/1068 E/Q Gag/Cag rs145812083 1 1 UBE3B HGNC HGNC:13478 protein_coding YES CCDS9129.1 ENSP00000340596 Q7Z3V4 A0A024RBI2 UPI000013DC3B NM_130466.3 tolerated(0.42) 20/28 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF352,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS rs145812083 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 109521157 109521157 G C 1 0 0 0 0 1 0 0 0 17403 1059 37 4 4 UBE3B 12 109521157 Missense_Mutation SNP G C3N-01410_T 582293 109521157 23754152 182 23082 ATXN2 0 . GRCh38 12 111552319 111552319 + Missense_Mutation SNP C C A rs776233562 C3N-01410_T C3N-01410_N C C c.1012G>T p.Val338Leu p.V338L ENST00000377617 5/25 169 119 50 125 124 1 strelka-varscan-mutect ATXN2,missense_variant,p.Val338Leu,ENST00000377617,NM_002973.3;ATXN2,missense_variant,p.Val338Leu,ENST00000550104,;ATXN2,missense_variant,p.Val49Leu,ENST00000616825,;ATXN2,missense_variant,p.Val178Leu,ENST00000608853,;ATXN2,missense_variant,p.Val73Leu,ENST00000389153,;ATXN2,missense_variant,p.Val73Leu,ENST00000542287,;ATXN2,missense_variant,p.Val49Leu,ENST00000535949,;ATXN2,missense_variant,p.Val81Leu,ENST00000548492,;ATXN2,intron_variant,,ENST00000549455,;ATXN2,missense_variant,p.Val259Leu,ENST00000483311,;ATXN2,non_coding_transcript_exon_variant,,ENST00000392645,;ATXN2,non_coding_transcript_exon_variant,,ENST00000471866,; A ENST00000377617 Transcript missense_variant 1174/4702 1012/3942 338/1313 V/L Gta/Tta rs776233562 1 -1 ATXN2 HGNC HGNC:10555 protein_coding YES CCDS31902.1 ENSP00000366843 Q99700 UPI0000DBEEFC NM_002973.3 tolerated(0.08) 5/25 hmmpanther:PTHR12854:SF11,hmmpanther:PTHR12854,Pfam_domain:PF14438 MODERATE 1 SNV 1 1 PASS rs776233562 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 111552319 111552319 C A 1 0 0 0 0 1 0 0 0 1365 507 18 2 2 ATXN2 12 111552319 Missense_Mutation SNP C C3N-01410_T 2031162 111552319 21722990 183 23083 KNTC1 0 . GRCh38 12 122573181 122573181 + Missense_Mutation SNP G G T rs759849356 C3N-01410_T C3N-01410_N G G c.2179G>T p.Val727Leu p.V727L ENST00000333479 26/64 290 241 49 241 240 1 strelka-varscan-mutect KNTC1,missense_variant,p.Val727Leu,ENST00000333479,NM_014708.4;KNTC1,missense_variant,p.Val690Leu,ENST00000450485,; T ENST00000333479 Transcript missense_variant 2356/6975 2179/6630 727/2209 V/L Gtg/Ttg rs759849356,COSM4654688 1 1 KNTC1 HGNC HGNC:17255 protein_coding YES CCDS45002.1 ENSP00000328236 P50748 UPI0000047FD6 NM_014708.4 deleterious(0.01) 26/64 hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759849356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 122573181 122573181 G T 1 0 0 0 0 1 0 0 0 8308 1029 36 2 2 KNTC1 12 122573181 Missense_Mutation SNP G C3N-01410_T 11020862 122573181 10702128 184 23084 RNF6 0 . GRCh38 13 26215186 26215186 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.696G>T p.Leu232Phe p.L232F ENST00000381588 5/5 227 97 130 182 181 1 strelka-varscan-mutect RNF6,missense_variant,p.Leu232Phe,ENST00000381588,NM_005977.3;RNF6,missense_variant,p.Leu232Phe,ENST00000381570,NM_183044.2;RNF6,missense_variant,p.Leu232Phe,ENST00000346166,NM_183043.2;RNF6,non_coding_transcript_exon_variant,,ENST00000498039,;RNF6,intron_variant,,ENST00000468480,;RNF6,downstream_gene_variant,,ENST00000476347,; A ENST00000381588 Transcript missense_variant 1288/3706 696/2058 232/685 L/F ttG/ttT 1 -1 RNF6 HGNC HGNC:10069 protein_coding YES CCDS9316.1 ENSP00000371000 Q9Y252 A0A024RDP2 UPI0000000A0A NM_005977.3 tolerated(0.15) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 26215186 26215186 C A 1 0 0 0 0 1 0 0 0 13678 593 21 2 2 RNF6 13 26215186 Missense_Mutation SNP C C3N-01410_T 26215186 88149142 185 23085 BRCA2 0 . GRCh38 13 32356465 32356465 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.7473G>T p.Gln2491His p.Q2491H ENST00000380152 15/27 304 152 152 287 287 0 strelka-varscan-mutect BRCA2,missense_variant,p.Gln2491His,ENST00000380152,;BRCA2,missense_variant,p.Gln2491His,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,; T ENST00000380152 Transcript missense_variant 7706/11986 7473/10257 2491/3418 Q/H caG/caT 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC deleterious(0) 15/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397,Pfam_domain:PF09169,Superfamily_domains:SSF81872 MODERATE 1 SNV 5 1 PASS rs80359653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 32356465 32356465 G T 1 0 0 0 0 1 0 0 0 1669 991 35 2 2 BRCA2 13 32356465 Missense_Mutation SNP G C3N-01410_T 6141279 32356465 82007863 186 23086 NEK5 0 . GRCh38 13 52065565 52065565 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.1969T>A p.Trp657Arg p.W657R ENST00000355568 22/22 199 107 92 167 167 0 strelka-varscan-mutect NEK5,missense_variant,p.Trp657Arg,ENST00000355568,NM_199289.2;NEK5,missense_variant,p.Trp657Arg,ENST00000617045,;NEK5,upstream_gene_variant,,ENST00000529080,;NEK5,3_prime_UTR_variant,,ENST00000465811,; T ENST00000355568 Transcript missense_variant 2109/2918 1969/2127 657/708 W/R Tgg/Agg 1 -1 NEK5 HGNC HGNC:7748 protein_coding YES CCDS31979.1 ENSP00000347767 Q6P3R8 UPI0000227E77 NM_199289.2 deleterious(0.01) 22/22 hmmpanther:PTHR24362,hmmpanther:PTHR24362:SF292 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 52065565 52065565 A T 1 0 0 0 0 1 0 0 0 10355 159 6 4 4 NEK5 13 52065565 Missense_Mutation SNP A C3N-01410_T 19709100 52065565 62298763 187 23087 CCDC168 0 . GRCh38 13 102735607 102735607 + Silent SNP T T A novel C3N-01410_T C3N-01410_N T T c.15090A>T p.= p.T5030T ENST00000322527 4/4 216 149 67 238 238 0 strelka-varscan-mutect CCDC168,synonymous_variant,p.=,ENST00000322527,NM_001146197.1; A ENST00000322527 Transcript synonymous_variant 15228/21466 15090/21246 5030/7081 T acA/acT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 4/4 Pfam_domain:PF15804,hmmpanther:PTHR35542,hmmpanther:PTHR35542:SF1 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 102735607 102735607 T A 1 0 0 0 0 0 0 0 1 2484 1567 55 4 4 CCDC168 13 102735607 Silent SNP T C3N-01410_T 50670042 102735607 11628721 188 23088 KLHL33 0 . GRCh38 14 20430260 20430260 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.416C>G p.Ala139Gly p.A139G ENST00000344581 2/4 320 252 68 349 349 0 strelka-varscan-mutect KLHL33,missense_variant,p.Ala403Gly,ENST00000637228,;KLHL33,missense_variant,p.Ala403Gly,ENST00000636854,;KLHL33,missense_variant,p.Ala139Gly,ENST00000344581,NM_001109997.2; C ENST00000344581 Transcript missense_variant 639/1863 416/1602 139/533 A/G gCt/gGt 1 -1 KLHL33 HGNC HGNC:31952 protein_coding YES CCDS53882.1 ENSP00000341549 A6NCF5 UPI00016630E8 NM_001109997.2 tolerated(0.11) 2/4 hmmpanther:PTHR24412:SF195,hmmpanther:PTHR24412,Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,SMART_domains:SM00875 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 20430260 20430260 G C 1 0 0 0 0 1 0 0 0 8252 971 34 4 4 KLHL33 14 20430260 Missense_Mutation SNP G C3N-01410_T 20430260 86613458 189 23089 TRIM9 0 . GRCh38 14 50982948 50982948 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.1840T>A p.Leu614Met p.L614M ENST00000338969 10/12 140 64 76 69 69 0 strelka-varscan-mutect TRIM9,missense_variant,p.Leu614Met,ENST00000338969,;TRIM9,intron_variant,,ENST00000298355,NM_015163.5;TRIM9,non_coding_transcript_exon_variant,,ENST00000557456,;TRIM9,non_coding_transcript_exon_variant,,ENST00000555933,;TRIM9,upstream_gene_variant,,ENST00000555170,; T ENST00000338969 Transcript missense_variant 2230/3312 1840/2409 614/802 L/M Ttg/Atg 1 -1 TRIM9 HGNC HGNC:16288 protein_coding ENSP00000342970 Q9C026 UPI00001B57AD tolerated_low_confidence(0.14) 10/12 PROSITE_profiles:PS50188 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 50982948 50982948 A T 1 0 0 0 0 1 0 0 0 17046 40 2 4 4 TRIM9 14 50982948 Missense_Mutation SNP A C3N-01410_T 30552688 50982948 56060770 190 23090 ADAM21 0 . GRCh38 14 70458054 70458054 + Silent SNP G G A novel C3N-01410_T C3N-01410_N G G c.555G>A p.= p.L185L ENST00000603540 2/2 218 114 104 162 162 0 strelka-varscan-mutect ADAM21,synonymous_variant,p.=,ENST00000603540,NM_003813.3;RP11-486O13.4,intron_variant,,ENST00000556646,; A ENST00000603540 Transcript synonymous_variant 813/2658 555/2169 185/722 L ttG/ttA 1 1 ADAM21 HGNC HGNC:200 protein_coding YES CCDS9804.1 ENSP00000474385 Q9UKJ8 UPI000013D756 NM_003813.3 2/2 hmmpanther:PTHR11905:SF116,hmmpanther:PTHR11905 LOW 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 70458054 70458054 G A 1 0 0 0 0 0 0 0 1 287 1339 47 3 3 ADAM21 14 70458054 Silent SNP G C3N-01410_T 19475106 70458054 36585664 191 23091 SERPINA4 0 . GRCh38 14 94564008 94564008 + Missense_Mutation SNP G G C novel C3N-01410_T C3N-01410_N G G c.526G>C p.Val176Leu p.V176L ENST00000557004 2/5 698 627 71 526 526 0 strelka-varscan-mutect SERPINA4,missense_variant,p.Val176Leu,ENST00000557004,NM_006215.3;SERPINA4,missense_variant,p.Val176Leu,ENST00000555095,NM_001289032.1;SERPINA4,missense_variant,p.Val176Leu,ENST00000298841,NM_001289033.1;SERPINA5,intron_variant,,ENST00000553780,;SERPINA5,intron_variant,,ENST00000554220,; C ENST00000557004 Transcript missense_variant 947/2012 526/1284 176/427 V/L Gtg/Ctg 1 1 SERPINA4 HGNC HGNC:8948 protein_coding YES CCDS9927.1 ENSP00000450838 P29622 A0A024R6I9 UPI000000CBEF NM_006215.3 tolerated(0.32) 2/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF194,Gene3D:3.30.497.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 94564008 94564008 G C 1 0 0 0 0 1 0 0 0 14367 1377 48 4 4 SERPINA4 14 94564008 Missense_Mutation SNP G C3N-01410_T 24105954 94564008 12479710 192 23092 NPAP1 0 . GRCh38 15 24677149 24677149 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1282G>T p.Asp428Tyr p.D428Y ENST00000329468 1/1 158 124 34 140 140 0 strelka-varscan-mutect NPAP1,missense_variant,p.Asp428Tyr,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript missense_variant 1282/7526 1282/3471 428/1156 D/Y Gac/Tac 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 tolerated(0.3) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF15 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 24677149 24677149 G T 1 0 0 0 0 1 0 0 0 10609 1290 45 2 2 NPAP1 15 24677149 Missense_Mutation SNP G C3N-01410_T 24677149 77314040 193 23093 GABRA5 0 . GRCh38 15 26869256 26869256 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.8A>G p.Asn3Ser p.N3S ENST00000335625 3/11 110 87 23 114 114 0 strelka-varscan-mutect GABRA5,missense_variant,p.Asn3Ser,ENST00000335625,NM_000810.3;GABRA5,missense_variant,p.Asn3Ser,ENST00000400081,NM_001165037.1;GABRA5,missense_variant,p.Asn3Ser,ENST00000355395,;GABRA5,missense_variant,p.Asn3Ser,ENST00000554596,;GABRA5,missense_variant,p.Asn3Ser,ENST00000554038,;GABRA5,missense_variant,p.Asn3Ser,ENST00000554599,;GABRA5,missense_variant,p.Asn3Ser,ENST00000555060,;GABRB3,intron_variant,,ENST00000541819,;GABRA5,intron_variant,,ENST00000555182,;GABRA5,non_coding_transcript_exon_variant,,ENST00000557449,;GABRA5,non_coding_transcript_exon_variant,,ENST00000557484,; G ENST00000335625 Transcript missense_variant 896/3251 8/1389 3/462 N/S aAt/aGt 1 1 GABRA5 HGNC HGNC:4079 protein_coding YES CCDS45194.1 ENSP00000335592 P31644 UPI000002D731 NM_000810.3 tolerated_low_confidence(0.45) 3/11 Prints_domain:PR01618,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF23,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 26869256 26869256 A G 1 0 0 0 0 1 0 0 0 6035 101 4 5 5 GABRA5 15 26869256 Missense_Mutation SNP A C3N-01410_T 2192107 26869256 75121933 194 23094 FAM63B 0 . GRCh38 15 58851902 58851903 + Frame_Shift_Ins INS - - CAATA novel C3N-01410_T C3N-01410_N - - c.1676_1680dupAATAC p.Tyr561AsnfsTer98 p.Y561Nfs*98 ENST00000559228 8/9 105 87 18 122 122 0 sindel-pindel FAM63B,frameshift_variant,p.Tyr561AsnfsTer98,ENST00000559228,NM_001040450.1;FAM63B,frameshift_variant,p.Tyr561AsnfsTer97,ENST00000450403,NM_001040453.1;RP11-30K9.5,downstream_gene_variant,,ENST00000558042,;FAM63B,3_prime_UTR_variant,,ENST00000316848,;FAM63B,3_prime_UTR_variant,,ENST00000560289,; CAATA ENST00000559228 Transcript frameshift_variant 1756-1757/9238 1674-1675/1866 558-559/621 -/QX -/CAATA 1 1 FAM63B HGNC HGNC:26954 protein_coding YES CCDS42046.1 ENSP00000452885 Q8NBR6 UPI0000D74C47 NM_001040450.1 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR18063,hmmpanther:PTHR18063:SF8 HIGH 1 insertion 2 6 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 CAATA 7 5 75 58851902 58851902 - CAATA 1 0 1 1 0 0 0 0 0 5463 1538 54 0 0 FAM63B 15 58851902 Frame_Shift_Ins INS - C3N-01410_T 31982646 58851902 43139287 195 23095 MYO9A 0 . GRCh38 15 71938918 71938918 + Missense_Mutation SNP C C A rs770800325 C3N-01410_T C3N-01410_N C C c.2312G>T p.Arg771Leu p.R771L ENST00000356056 16/42 159 128 31 203 203 0 strelka-varscan-mutect MYO9A,missense_variant,p.Arg771Leu,ENST00000356056,NM_006901.3;MYO9A,missense_variant,p.Arg771Leu,ENST00000564571,;MYO9A,missense_variant,p.Arg771Leu,ENST00000444904,;MYO9A,missense_variant,p.Arg391Leu,ENST00000566885,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563542,;MYO9A,non_coding_transcript_exon_variant,,ENST00000566744,;MYO9A,non_coding_transcript_exon_variant,,ENST00000563648,;MYO9A,non_coding_transcript_exon_variant,,ENST00000567095,;MYO9A,non_coding_transcript_exon_variant,,ENST00000565528,; A ENST00000356056 Transcript missense_variant 2785/12411 2312/7647 771/2548 R/L cGg/cTg rs770800325 1 -1 MYO9A HGNC HGNC:7608 protein_coding YES CCDS10239.1 ENSP00000348349 B2RTY4 UPI000013D213 NM_006901.3 deleterious(0.01) 16/42 PROSITE_profiles:PS51456,SMART_domains:SM00242 MODERATE 1 SNV 1 1 PASS rs770800325 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 71938918 71938918 C A 1 0 0 0 0 1 0 0 0 10085 652 23 1 1 MYO9A 15 71938918 Missense_Mutation SNP C C3N-01410_T 13087016 71938918 30052271 196 23096 NPTN 0 . GRCh38 15 73561925 73561925 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1182G>T p.Gln394His p.Q394H ENST00000345330 8/9 95 78 17 112 112 0 strelka-varscan-mutect NPTN,missense_variant,p.Gln278His,ENST00000351217,NM_017455.3;NPTN,missense_variant,p.Gln394His,ENST00000345330,NM_012428.3;NPTN,missense_variant,p.Gln390His,ENST00000563691,NM_001161363.1;NPTN,missense_variant,p.Gln274His,ENST00000562924,NM_001161364.1;NPTN,3_prime_UTR_variant,,ENST00000565325,;REC114,downstream_gene_variant,,ENST00000331090,NM_001042367.1;REC114,downstream_gene_variant,,ENST00000560581,;NPTN,non_coding_transcript_exon_variant,,ENST00000561898,; A ENST00000345330 Transcript missense_variant 1380/2444 1182/1197 394/398 Q/H caG/caT 1 -1 NPTN HGNC HGNC:17867 protein_coding YES CCDS10249.1 ENSP00000290401 Q9Y639 UPI0000072D5C NM_012428.3 deleterious(0.03) 8/9 hmmpanther:PTHR10075:SF5,hmmpanther:PTHR10075 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 73561925 73561925 C A 1 0 0 0 0 1 0 0 0 10657 912 32 2 2 NPTN 15 73561925 Missense_Mutation SNP C C3N-01410_T 1623007 73561925 28429264 197 23097 LINGO1 0 . GRCh38 15 77614895 77614895 + Missense_Mutation SNP G G A rs763246298 C3N-01410_T C3N-01410_N G G c.1012C>T p.Arg338Cys p.R338C ENST00000355300 2/2 295 236 59 261 261 0 strelka-varscan-mutect LINGO1,missense_variant,p.Arg338Cys,ENST00000355300,NM_032808.6;LINGO1,missense_variant,p.Arg332Cys,ENST00000561030,NM_001301199.1,NM_001301194.1,NM_001301191.1,NM_001301197.1,NM_001301200.1,NM_001301187.1,NM_001301189.1,NM_001301186.1,NM_001301195.1,NM_001301198.1,NM_001301192.1;LINGO1,downstream_gene_variant,,ENST00000557798,;LINGO1,downstream_gene_variant,,ENST00000561686,;LINGO1,downstream_gene_variant,,ENST00000566711,;LINGO1,downstream_gene_variant,,ENST00000567726,;LINGO1,downstream_gene_variant,,ENST00000570216,;LINGO1,downstream_gene_variant,,ENST00000562933,;LINGO1,downstream_gene_variant,,ENST00000563316,;LINGO1,downstream_gene_variant,,ENST00000559893,;LINGO1,downstream_gene_variant,,ENST00000564472,; A ENST00000355300 Transcript missense_variant 1187/3055 1012/1863 338/620 R/C Cgc/Tgc rs763246298,COSM965260 1 -1 LINGO1 HGNC HGNC:21205 protein_coding YES CCDS45313.1 ENSP00000347451 Q96FE5 UPI00000377A0 NM_032808.6 deleterious(0) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF31,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763246298 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 77614895 77614895 G A 1 0 0 0 0 1 0 0 0 8735 1087 38 1 1 LINGO1 15 77614895 Missense_Mutation SNP G C3N-01410_T 4052970 77614895 24376294 198 23098 CHSY1 0 . GRCh38 15 101178492 101178492 + Silent SNP G G A novel C3N-01410_T C3N-01410_N G G c.1305C>T p.= p.G435G ENST00000254190 3/3 259 182 77 156 156 0 strelka-varscan-mutect CHSY1,synonymous_variant,p.=,ENST00000254190,NM_014918.4;CHSY1,non_coding_transcript_exon_variant,,ENST00000543813,;CHSY1,downstream_gene_variant,,ENST00000561414,;CHSY1,downstream_gene_variant,,ENST00000560766,; A ENST00000254190 Transcript synonymous_variant 1781/4550 1305/2409 435/802 G ggC/ggT 1 -1 CHSY1 HGNC HGNC:17198 protein_coding YES CCDS10390.1 ENSP00000254190 Q86X52 UPI000000DB6C NM_014918.4 3/3 hmmpanther:PTHR12369:SF16,hmmpanther:PTHR12369,Pfam_domain:PF05679 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 101178492 101178492 G A 1 0 0 0 0 0 0 0 1 3172 958 34 3 3 CHSY1 15 101178492 Silent SNP G C3N-01410_T 23563597 101178492 812697 199 23099 RAB11FIP3 0 . GRCh38 16 520497 520497 + Silent SNP C C T rs201637223 C3N-01410_T C3N-01410_N C C c.2055C>T p.= p.N685N ENST00000262305 13/14 187 132 55 194 194 0 strelka-varscan-mutect RAB11FIP3,synonymous_variant,p.=,ENST00000262305,NM_014700.3;RAB11FIP3,synonymous_variant,p.=,ENST00000434585,;RAB11FIP3,synonymous_variant,p.=,ENST00000450428,NM_001142272.1;LINC00235,downstream_gene_variant,,ENST00000622160,;RAB11FIP3,downstream_gene_variant,,ENST00000487899,;RAB11FIP3,downstream_gene_variant,,ENST00000461009,;RAB11FIP3,downstream_gene_variant,,ENST00000464263,; T ENST00000262305 Transcript synonymous_variant 2443/4831 2055/2271 685/756 N aaC/aaT rs201637223,COSM3691060,COSM3691061 1 1 RAB11FIP3 HGNC HGNC:17224 protein_coding YES CCDS32351.1 ENSP00000262305 O75154 UPI0000129C9C NM_014700.3 13/14 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15726,hmmpanther:PTHR15726:SF6 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs201637223 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 520497 520497 C T 1 0 0 0 0 0 0 0 1 13053 535 19 1 1 RAB11FIP3 16 520497 Silent SNP C C3N-01410_T 520497 89817848 200 23100 WDR90 0 . GRCh38 16 662831 662831 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.4298G>T p.Gly1433Val p.G1433V ENST00000293879 34/41 140 95 45 139 139 0 strelka-varscan-mutect WDR90,missense_variant,p.Gly1435Val,ENST00000549091,;WDR90,missense_variant,p.Gly1433Val,ENST00000293879,NM_145294.4;WDR90,upstream_gene_variant,,ENST00000547944,;WDR90,upstream_gene_variant,,ENST00000315764,;WDR90,upstream_gene_variant,,ENST00000551100,;WDR90,downstream_gene_variant,,ENST00000550739,;WDR90,upstream_gene_variant,,ENST00000546896,;WDR90,non_coding_transcript_exon_variant,,ENST00000548603,;WDR90,upstream_gene_variant,,ENST00000547543,;WDR90,downstream_gene_variant,,ENST00000548844,;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,;WDR90,non_coding_transcript_exon_variant,,ENST00000546516,;WDR90,non_coding_transcript_exon_variant,,ENST00000552683,;WDR90,non_coding_transcript_exon_variant,,ENST00000549024,;WDR90,intron_variant,,ENST00000552728,;WDR90,downstream_gene_variant,,ENST00000552943,;WDR90,upstream_gene_variant,,ENST00000553080,;WDR90,downstream_gene_variant,,ENST00000546923,;WDR90,upstream_gene_variant,,ENST00000548448,;WDR90,downstream_gene_variant,,ENST00000550902,; T ENST00000293879 Transcript missense_variant 4298/5488 4298/5247 1433/1748 G/V gGc/gTc 1 1 WDR90 HGNC HGNC:26960 protein_coding YES CCDS42092.1 ENSP00000293879 Q96KV7 UPI0000D67C48 NM_145294.4 deleterious(0) 34/41 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720:SF24,hmmpanther:PTHR13720,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 662831 662831 G T 1 0 0 0 0 1 0 0 0 17893 1203 42 2 2 WDR90 16 662831 Missense_Mutation SNP G C3N-01410_T 142334 662831 89675514 201 23101 ZSCAN10 0 . GRCh38 16 3090374 3090374 + Missense_Mutation SNP C C A rs537870698 C3N-01410_T C3N-01410_N C C c.649G>T p.Val217Leu p.V217L ENST00000538082 5/5 195 139 56 143 143 0 strelka-varscan-mutect ZSCAN10,missense_variant,p.Val354Leu,ENST00000576985,NM_032805.2;ZSCAN10,missense_variant,p.Val299Leu,ENST00000252463,;ZSCAN10,missense_variant,p.Val217Leu,ENST00000538082,NM_001282416.1;ZSCAN10,5_prime_UTR_variant,,ENST00000575108,NM_001282415.1;ZSCAN10,5_prime_UTR_variant,,ENST00000572431,;ZSCAN10,downstream_gene_variant,,ENST00000576483,;ZSCAN10,downstream_gene_variant,,ENST00000572548,;RP11-473M20.9,upstream_gene_variant,,ENST00000571404,;RP11-473M20.9,upstream_gene_variant,,ENST00000574387,;RNU1-22P,downstream_gene_variant,,ENST00000363334,;ZSCAN10,non_coding_transcript_exon_variant,,ENST00000571903,;ZSCAN10,downstream_gene_variant,,ENST00000577059,; A ENST00000538082 Transcript missense_variant 965/2350 649/1932 217/643 V/L Gtg/Ttg rs537870698 1 -1 ZSCAN10 HGNC HGNC:12997 protein_coding YES CCDS61814.1 ENSP00000440047 Q96SZ4 UPI0001639829 NM_001282416.1 tolerated(0.34) 5/5 PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF369,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 4 1 PASS rs537870698 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 3090374 3090374 C A 1 0 0 0 0 1 0 0 0 18821 507 18 2 2 ZSCAN10 16 3090374 Missense_Mutation SNP C C3N-01410_T 2427543 3090374 87247971 202 23102 ACSM2B 0 . GRCh38 16 20548457 20548457 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.911C>A p.Pro304Gln p.P304Q ENST00000329697 7/14 250 198 52 264 264 0 strelka-varscan-mutect ACSM2B,missense_variant,p.Pro304Gln,ENST00000329697,NM_001105069.1;ACSM2B,missense_variant,p.Pro304Gln,ENST00000414188,;ACSM2B,missense_variant,p.Pro304Gln,ENST00000565232,;ACSM2B,missense_variant,p.Pro304Gln,ENST00000567001,NM_182617.3;ACSM2B,missense_variant,p.Pro225Gln,ENST00000565322,;ACSM2B,missense_variant,p.Pro73Gln,ENST00000567288,;ACSM2B,downstream_gene_variant,,ENST00000569163,;ACSM2B,upstream_gene_variant,,ENST00000568098,;ACSM2B,3_prime_UTR_variant,,ENST00000569327,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000566998,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,;ACSM2B,upstream_gene_variant,,ENST00000569131,; T ENST00000329697 Transcript missense_variant 1080/2935 911/1734 304/577 P/Q cCa/cAa 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 deleterious(0.01) 7/14 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF188,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 20548457 20548457 G T 1 0 0 0 0 1 0 0 0 226 1348 47 2 2 ACSM2B 16 20548457 Missense_Mutation SNP G C3N-01410_T 17458083 20548457 69789888 203 23103 ZNF629 0 . GRCh38 16 30782066 30782066 + Silent SNP G G A novel C3N-01410_T C3N-01410_N G G c.2262C>T p.= p.V754V ENST00000262525 3/3 25 14 11 36 36 0 strelka-mutect ZNF629,synonymous_variant,p.=,ENST00000262525,NM_001080417.1; A ENST00000262525 Transcript synonymous_variant 2470/6087 2262/2610 754/869 V gtC/gtT 1 -1 ZNF629 HGNC HGNC:29008 protein_coding YES CCDS45463.1 ENSP00000262525 Q9UEG4 UPI00001C1FA5 NM_001080417.1 3/3 Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 30782066 30782066 G A 1 0 0 0 0 0 0 0 1 18628 1161 41 3 3 ZNF629 16 30782066 Silent SNP G C3N-01410_T 10233609 30782066 59556279 204 23104 CES2 0 . GRCh38 16 66938114 66938114 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.346A>T p.Asn116Tyr p.N116Y ENST00000317091 2/12 292 155 137 247 247 0 strelka-varscan-mutect CES2,missense_variant,p.Asn116Tyr,ENST00000317091,NM_003869.5;CES2,missense_variant,p.Asn116Tyr,ENST00000417689,NM_198061.2;CES2,intron_variant,,ENST00000561697,;CES2,downstream_gene_variant,,ENST00000566182,;CES2,upstream_gene_variant,,ENST00000564420,;FAM96B,upstream_gene_variant,,ENST00000567511,;FAM96B,upstream_gene_variant,,ENST00000422424,NM_016062.3;FAM96B,upstream_gene_variant,,ENST00000568572,;RP11-361L15.4,upstream_gene_variant,,ENST00000566869,;CES2,3_prime_UTR_variant,,ENST00000568470,;CES2,3_prime_UTR_variant,,ENST00000570032,;CES2,non_coding_transcript_exon_variant,,ENST00000566359,;CES2,upstream_gene_variant,,ENST00000568347,;FAM96B,upstream_gene_variant,,ENST00000563490,;FAM96B,upstream_gene_variant,,ENST00000562362,;FAM96B,upstream_gene_variant,,ENST00000569299,;CES2,upstream_gene_variant,,ENST00000561843,;CES2,upstream_gene_variant,,ENST00000567128,;CES2,upstream_gene_variant,,ENST00000563988,; T ENST00000317091 Transcript missense_variant 1330/3927 346/1872 116/623 N/Y Aat/Tat 1 1 CES2 HGNC HGNC:1864 protein_coding YES CCDS10825.1 ENSP00000317842 A0A024R6X1 UPI0000074733 NM_003869.5 deleterious(0) 2/12 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF149,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 66938114 66938114 A T 1 0 0 0 0 1 0 0 0 3002 130 5 4 4 CES2 16 66938114 Missense_Mutation SNP A C3N-01410_T 36156048 66938114 23400231 205 23105 MTSS1L 0 . GRCh38 16 70674463 70674463 + Missense_Mutation SNP T T C rs748292625 C3N-01410_T C3N-01410_N T T c.896A>G p.Tyr299Cys p.Y299C ENST00000338779 11/15 290 199 91 322 321 1 strelka-varscan-mutect MTSS1L,missense_variant,p.Tyr299Cys,ENST00000338779,NM_138383.2;MTSS1L,missense_variant,p.Tyr298Cys,ENST00000616026,;MTSS1L,intron_variant,,ENST00000562883,;MTSS1L,downstream_gene_variant,,ENST00000576338,; C ENST00000338779 Transcript missense_variant 1171/4992 896/2244 299/747 Y/C tAc/tGc rs748292625,COSM3273347 1 -1 MTSS1L HGNC HGNC:25094 protein_coding YES CCDS32476.1 ENSP00000341171 Q765P7 UPI00001D627C NM_138383.2 tolerated(0.14) 11/15 hmmpanther:PTHR15708 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748292625 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 75 70674463 70674463 T C 1 0 0 0 0 1 0 0 0 9960 1638 57 5 5 MTSS1L 16 70674463 Missense_Mutation SNP T C3N-01410_T 3736349 70674463 19663882 206 23106 DPEP1 0 . GRCh38 16 89637866 89637866 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.960G>T p.Lys320Asn p.K320N ENST00000393092 10/11 191 119 72 156 156 0 strelka-varscan-mutect DPEP1,missense_variant,p.Lys320Asn,ENST00000393092,NM_004413.3;DPEP1,missense_variant,p.Lys320Asn,ENST00000421184,NM_001128141.2;DPEP1,missense_variant,p.Lys320Asn,ENST00000261615,;DPEP1,downstream_gene_variant,,ENST00000570029,;DPEP1,downstream_gene_variant,,ENST00000568281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000564281,;DPEP1,non_coding_transcript_exon_variant,,ENST00000564645,;DPEP1,downstream_gene_variant,,ENST00000565249,;DPEP1,downstream_gene_variant,,ENST00000561484,; T ENST00000393092 Transcript missense_variant 1251/1734 960/1236 320/411 K/N aaG/aaT 1 1 DPEP1 HGNC HGNC:3002 protein_coding YES CCDS10982.1 ENSP00000376807 P16444 A0A140VJI3 UPI000006DF95 NM_004413.3 deleterious(0.01) 10/11 PROSITE_profiles:PS51365,hmmpanther:PTHR10443,hmmpanther:PTHR10443:SF17,Gene3D:3.20.20.140,Pfam_domain:PF01244,Superfamily_domains:SSF51556 MODERATE 1 SNV 1 1 PASS rs1424925632 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 89637866 89637866 G T 1 0 0 0 0 1 0 0 0 4527 1020 36 2 2 DPEP1 16 89637866 Missense_Mutation SNP G C3N-01410_T 18963403 89637866 700479 207 23107 ANKFY1 0 . GRCh38 17 4197376 4197376 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1226G>T p.Gly409Val p.G409V ENST00000570535 8/25 249 185 64 165 163 2 strelka-varscan-mutect ANKFY1,missense_variant,p.Gly367Val,ENST00000341657,;ANKFY1,missense_variant,p.Gly409Val,ENST00000570535,NM_001257999.1;ANKFY1,missense_variant,p.Gly367Val,ENST00000574367,NM_016376.3;ANKFY1,3_prime_UTR_variant,,ENST00000572412,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000570934,;ANKFY1,non_coding_transcript_exon_variant,,ENST00000573250,; A ENST00000570535 Transcript missense_variant 1343/6458 1226/3636 409/1211 G/V gGg/gTg 1 -1 ANKFY1 HGNC HGNC:20763 protein_coding YES CCDS58502.1 ENSP00000459943 Q9P2R3 UPI00003FECB0 NM_001257999.1 deleterious(0) 8/25 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24189,hmmpanther:PTHR24189:SF34,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 4197376 4197376 C A 1 0 0 0 0 1 0 0 0 728 637 22 2 2 ANKFY1 17 4197376 Missense_Mutation SNP C C3N-01410_T 4197376 79060065 208 23108 ZNF594 0 . GRCh38 17 5182551 5182551 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1706G>T p.Trp569Leu p.W569L ENST00000399604 1/1 426 303 123 379 379 0 strelka-varscan-mutect ZNF594,missense_variant,p.Trp569Leu,ENST00000399604,;ZNF594,missense_variant,p.Trp569Leu,ENST00000575779,NM_032530.1;ZNF594,downstream_gene_variant,,ENST00000576772,; A ENST00000399604 Transcript missense_variant 1847/4862 1706/2424 569/807 W/L tGg/tTg 1 -1 ZNF594 HGNC HGNC:29392 protein_coding YES CCDS42241.1 ENSP00000382513 Q96JF6 UPI00001C1FDF tolerated(0.07) 1/1 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF155,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS rs1471951438 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 5182551 5182551 C A 1 0 0 0 0 1 0 0 0 18599 595 21 2 2 ZNF594 17 5182551 Missense_Mutation SNP C C3N-01410_T 985175 5182551 78074890 209 23109 DHRS7C 0 . GRCh38 17 9771556 9771556 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.871C>A p.Pro291Thr p.P291T ENST00000330255 6/6 32 23 9 29 29 0 strelka-varscan-mutect DHRS7C,missense_variant,p.Pro291Thr,ENST00000330255,NM_001220493.1;DHRS7C,missense_variant,p.Pro290Thr,ENST00000571134,NM_001105571.2;DHRS7C,missense_variant,p.Pro111Thr,ENST00000571771,;RP11-477N12.6,intron_variant,,ENST00000634974,; T ENST00000330255 Transcript missense_variant 884/1006 871/939 291/312 P/T Ccg/Acg 1 -1 DHRS7C HGNC HGNC:32423 protein_coding YES CCDS56020.1 ENSP00000327975 A6NNS2 UPI000178DECB NM_001220493.1 deleterious(0) 6/6 MODERATE 1 SNV 1 1 PASS rs957007375 . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 3 4 75 9771556 9771556 G T 1 0 0 0 0 1 0 0 0 4301 1232 43 2 2 DHRS7C 17 9771556 Missense_Mutation SNP G C3N-01410_T 4589005 9771556 73485885 210 23110 TLCD1 0 . GRCh38 17 28724650 28724651 + Frame_Shift_Ins INS - - C novel C3N-01410_T C3N-01410_N - - c.603dupG p.Thr202AspfsTer28 p.T202Dfs*28 ENST00000292090 4/4 287 235 52 346 346 0 sindel-varindel-pindel TLCD1,frameshift_variant,p.Thr202AspfsTer28,ENST00000292090,NM_138463.3;TLCD1,frameshift_variant,p.Thr155AspfsTer28,ENST00000394933,NM_001160407.1;TLCD1,frameshift_variant,p.Thr131AspfsTer?,ENST00000580518,;TLCD1,frameshift_variant,p.Pro40ThrfsTer47,ENST00000581236,;NEK8,upstream_gene_variant,,ENST00000268766,NM_178170.2;RPL23A,downstream_gene_variant,,ENST00000422514,NM_000984.5;RPL23A,downstream_gene_variant,,ENST00000394938,;NEK8,upstream_gene_variant,,ENST00000579060,;NEK8,upstream_gene_variant,,ENST00000579671,;RPL23A,downstream_gene_variant,,ENST00000472628,;RPL23A,downstream_gene_variant,,ENST00000496182,;RPL23A,downstream_gene_variant,,ENST00000578181,;RPL23A,downstream_gene_variant,,ENST00000355731,;RPL23A,downstream_gene_variant,,ENST00000394935,;SNORD4B,downstream_gene_variant,,ENST00000459083,;SNORD4A,downstream_gene_variant,,ENST00000459174,;SNORD42B,downstream_gene_variant,,ENST00000458893,;SNORD42A,downstream_gene_variant,,ENST00000459584,;AC010761.8,upstream_gene_variant,,ENST00000582718,;AC010761.14,upstream_gene_variant,,ENST00000587898,;NEK8,upstream_gene_variant,,ENST00000593261,;NEK8,upstream_gene_variant,,ENST00000543014,;NEK8,upstream_gene_variant,,ENST00000584342,;RPL23A,downstream_gene_variant,,ENST00000582736,;NEK8,upstream_gene_variant,,ENST00000581000,;RPL23A,downstream_gene_variant,,ENST00000580755,; C ENST00000292090 Transcript frameshift_variant 714-715/1017 603-604/744 201-202/247 -/X -/G 1 -1 TLCD1 HGNC HGNC:25177 protein_coding YES CCDS11242.1 ENSP00000292090 Q96CP7 UPI000006DF3D NM_138463.3 4/4 PROSITE_profiles:PS50922,hmmpanther:PTHR13439,hmmpanther:PTHR13439:SF5,Pfam_domain:PF03798,SMART_domains:SM00724 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 75 28724650 28724650 - C 1 0 1 1 0 0 0 0 0 16380 1667 58 0 0 TLCD1 17 28724650 Frame_Shift_Ins INS - C3N-01410_T 18953094 28724650 54532791 211 23111 TAOK1 0 . GRCh38 17 29467211 29467211 + Missense_Mutation SNP A A T novel C3N-01410_T C3N-01410_N A A c.199A>T p.Thr67Ser p.T67S ENST00000261716 3/20 88 49 39 123 121 2 strelka-varscan-mutect TAOK1,missense_variant,p.Thr67Ser,ENST00000261716,NM_020791.2;TAOK1,missense_variant,p.Thr67Ser,ENST00000536202,NM_025142.1;TAOK1,missense_variant,p.Thr67Ser,ENST00000583121,; T ENST00000261716 Transcript missense_variant 718/12407 199/3006 67/1001 T/S Act/Tct 1 1 TAOK1 HGNC HGNC:29259 protein_coding YES CCDS32601.1 ENSP00000261716 Q7L7X3 A0A024QZ70 UPI000004A033 NM_020791.2 tolerated(0.38) 3/20 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF369,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 29467211 29467211 A T 1 0 0 0 0 1 0 0 0 15946 405 14 4 4 TAOK1 17 29467211 Missense_Mutation SNP A C3N-01410_T 742561 29467211 53790230 212 23112 PSME3 0 . GRCh38 17 42841530 42841530 + Silent SNP C C A rs202070240 C3N-01410_T C3N-01410_N C C c.756C>A p.= p.I252I ENST00000293362 11/11 112 98 14 117 116 1 strelka-varscan-mutect PSME3,synonymous_variant,p.=,ENST00000541124,;PSME3,synonymous_variant,p.=,ENST00000622892,;PSME3,synonymous_variant,p.=,ENST00000293362,NM_176863.2;PSME3,synonymous_variant,p.=,ENST00000545225,;PSME3,synonymous_variant,p.=,ENST00000441946,NM_001267045.1;PSME3,synonymous_variant,p.=,ENST00000590720,NM_005789.3;PSME3,synonymous_variant,p.=,ENST00000592169,;AOC2,upstream_gene_variant,,ENST00000253799,NM_009590.2;AOC2,upstream_gene_variant,,ENST00000452774,NM_001158.3;PSME3,downstream_gene_variant,,ENST00000585805,;PSME3,downstream_gene_variant,,ENST00000591152,;PSME3,downstream_gene_variant,,ENST00000589469,;PSME3,downstream_gene_variant,,ENST00000586114,;PSME3,3_prime_UTR_variant,,ENST00000543428,;PSME3,downstream_gene_variant,,ENST00000586312,;PSME3,downstream_gene_variant,,ENST00000593111,;PSME3,downstream_gene_variant,,ENST00000591722,; A ENST00000293362 Transcript synonymous_variant 917/3144 756/804 252/267 I atC/atA rs202070240,COSM3189638 1 1 PSME3 HGNC HGNC:9570 protein_coding YES CCDS11442.1 ENSP00000293362 P61289 UPI000002B1BA NM_176863.2 11/11 Gene3D:1.20.120.180,Pfam_domain:PF02252,hmmpanther:PTHR10660,hmmpanther:PTHR10660:SF4,Superfamily_domains:SSF47216 0,1 LOW 1 SNV 1 0,1 1 PASS rs202070240 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 42841530 42841530 C A 1 0 0 0 0 0 0 0 1 12859 874 31 1 1 PSME3 17 42841530 Silent SNP C C3N-01410_T 13374319 42841530 40415911 213 23113 DBF4B 0 . GRCh38 17 44750863 44750863 + Silent SNP G G T C3N-01410_T C3N-01410_N G G c.1458G>T p.= p.A486A ENST00000315005 14/14 423 365 58 361 361 0 strelka-varscan-mutect DBF4B,synonymous_variant,p.=,ENST00000315005,NM_145663.2;DBF4B,intron_variant,,ENST00000393547,NM_025104.3;DBF4B,downstream_gene_variant,,ENST00000526924,;DBF4B,downstream_gene_variant,,ENST00000527862,; T ENST00000315005 Transcript synonymous_variant 1596/2997 1458/1848 486/615 A gcG/gcT COSM5123012 1 1 DBF4B HGNC HGNC:17883 protein_coding YES CCDS11485.1 ENSP00000323663 Q8NFT6 UPI00000473C7 NM_145663.2 14/14 hmmpanther:PTHR15375:SF24,hmmpanther:PTHR15375 1 LOW 1 SNV 1 1 1 PASS rs1156354839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 44750863 44750863 G T 1 0 0 0 0 0 0 0 1 4049 1103 39 1 1 DBF4B 17 44750863 Silent SNP G C3N-01410_T 1909333 44750863 38506578 214 23114 BAHCC1 0 . GRCh38 17 81461425 81461425 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.6855G>T p.Lys2285Asn p.K2285N ENST00000584436 27/29 53 36 17 32 32 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Lys2285Asn,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Lys2254Asn,ENST00000307745,;RP11-1055B8.8,intron_variant,,ENST00000572590,;BAHCC1,downstream_gene_variant,,ENST00000578541,;BAHCC1,downstream_gene_variant,,ENST00000584330,;BAHCC1,upstream_gene_variant,,ENST00000582709,; T ENST00000584436 Transcript missense_variant 7222/10801 6855/7920 2285/2639 K/N aaG/aaT 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0) 27/29 hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 MODERATE SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 81461425 81461425 G T 1 0 0 0 0 1 0 0 0 1451 991 35 2 2 BAHCC1 17 81461425 Missense_Mutation SNP G C3N-01410_T 36710562 81461425 1796016 215 23115 PIEZO2 0 . GRCh38 18 10800436 10800436 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.1279C>A p.His427Asn p.H427N ENST00000503781 11/52 131 102 29 144 144 0 strelka-varscan-mutect PIEZO2,missense_variant,p.His376Asn,ENST00000383408,;PIEZO2,missense_variant,p.His427Asn,ENST00000302079,;PIEZO2,missense_variant,p.His427Asn,ENST00000580640,;PIEZO2,missense_variant,p.His427Asn,ENST00000503781,NM_022068.3;PIEZO2,missense_variant,p.His137Asn,ENST00000579112,;PIEZO2,missense_variant,p.His427Asn,ENST00000582913,; T ENST00000503781 Transcript missense_variant 1279/8259 1279/8259 427/2752 H/N Cac/Aac 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 tolerated(0.17) 11/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 10800436 10800436 G T 1 0 0 0 0 1 0 0 0 11975 1348 47 2 2 PIEZO2 18 10800436 Missense_Mutation SNP G C3N-01410_T 10800436 69572849 216 23116 GREB1L 0 . GRCh38 18 21496664 21496664 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.3357C>A p.= p.P1119P ENST00000580732 21/33 200 160 40 211 211 0 strelka-varscan-mutect GREB1L,synonymous_variant,p.=,ENST00000580732,;GREB1L,synonymous_variant,p.=,ENST00000424526,NM_001142966.1;GREB1L,synonymous_variant,p.=,ENST00000269218,;GREB1L,non_coding_transcript_exon_variant,,ENST00000578955,; A ENST00000580732 Transcript synonymous_variant 3738/8749 3357/5772 1119/1923 P ccC/ccA 1 1 GREB1L HGNC HGNC:31042 protein_coding YES CCDS45836.1 ENSP00000464162 Q9C091 UPI0001642876 21/33 Pfam_domain:PF15782,hmmpanther:PTHR15720,hmmpanther:PTHR15720:SF12 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 21496664 21496664 C A 1 0 0 0 0 0 0 0 1 6640 610 22 2 2 GREB1L 18 21496664 Silent SNP C C3N-01410_T 10696228 21496664 58876621 217 23117 DSC1 0 . GRCh38 18 31134613 31134613 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.1835A>T p.Asp612Val p.D612V ENST00000257198 12/16 137 107 30 132 132 0 strelka-mutect DSC1,missense_variant,p.Asp612Val,ENST00000257197,NM_004948.3;DSC1,missense_variant,p.Asp612Val,ENST00000257198,NM_024421.2;DSCAS,intron_variant,,ENST00000581836,;RP11-408H20.3,downstream_gene_variant,,ENST00000582307,; A ENST00000257198 Transcript missense_variant 2097/4225 1835/2685 612/894 D/V gAt/gTt 1 -1 DSC1 HGNC HGNC:3035 protein_coding YES CCDS11894.1 ENSP00000257198 Q08554 UPI000006DF10 NM_024421.2 deleterious(0.03) 12/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF8,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS rs1340530110 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 31134613 31134613 T A 1 0 0 0 0 1 0 0 0 4586 1435 50 4 4 DSC1 18 31134613 Missense_Mutation SNP T C3N-01410_T 9637949 31134613 49238672 218 23118 POLI 0 . GRCh38 18 54282978 54282978 + Missense_Mutation SNP A A T rs765990947 C3N-01410_T C3N-01410_N A A c.938A>T p.Glu313Val p.E313V ENST00000579534 6/10 132 105 27 135 135 0 strelka-varscan-mutect POLI,missense_variant,p.Glu313Val,ENST00000579534,NM_007195.2;POLI,missense_variant,p.Glu210Val,ENST00000579434,;POLI,missense_variant,p.Glu251Val,ENST00000217800,;POLI,missense_variant,p.Glu234Val,ENST00000406285,;POLI,missense_variant,p.Glu25Val,ENST00000579823,;POLI,downstream_gene_variant,,ENST00000583136,;POLI,downstream_gene_variant,,ENST00000577612,;POLI,downstream_gene_variant,,ENST00000580880,;POLI,upstream_gene_variant,,ENST00000582366,;POLI,downstream_gene_variant,,ENST00000580905,;POLI,missense_variant,p.Glu40Val,ENST00000585023,;POLI,missense_variant,p.Glu42Val,ENST00000581950,;POLI,downstream_gene_variant,,ENST00000577971,;POLI,upstream_gene_variant,,ENST00000577361,;POLI,upstream_gene_variant,,ENST00000583576,; T ENST00000579534 Transcript missense_variant 1081/6133 938/2223 313/740 E/V gAg/gTg rs765990947 1 1 POLI HGNC HGNC:9182 protein_coding YES CCDS11954.2 ENSP00000462664 Q9UNA4 UPI00004DDD95 NM_007195.2 tolerated(0.19) 6/10 Gene3D:1.10.150.20,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF10,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS rs765990947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 54282978 54282978 A T 1 0 0 0 0 1 0 0 0 12313 304 11 4 4 POLI 18 54282978 Missense_Mutation SNP A C3N-01410_T 23148365 54282978 26090307 219 23119 FECH 0 . GRCh38 18 57586608 57586608 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.13G>T p.Gly5Cys p.G5C ENST00000382873 1/11 254 208 46 287 287 0 strelka-varscan-mutect FECH,missense_variant,p.Gly5Cys,ENST00000262093,NM_000140.3;FECH,missense_variant,p.Gly5Cys,ENST00000382873,NM_001012515.2;FECH,missense_variant,p.Gly5Cys,ENST00000592699,;FECH,missense_variant,p.Gly5Cys,ENST00000585747,;FECH,5_prime_UTR_variant,,ENST00000591215,;RP11-706P11.2,downstream_gene_variant,,ENST00000611316,;FECH,non_coding_transcript_exon_variant,,ENST00000585699,;FECH,missense_variant,p.Gly5Cys,ENST00000585494,;FECH,non_coding_transcript_exon_variant,,ENST00000585878,;FECH,non_coding_transcript_exon_variant,,ENST00000592111,; A ENST00000382873 Transcript missense_variant 47/2526 13/1290 5/429 G/C Ggc/Tgc 1 -1 FECH HGNC HGNC:3647 protein_coding YES CCDS32836.1 ENSP00000372326 P22830 UPI00004E55EB NM_001012515.2 deleterious_low_confidence(0) 1/11 hmmpanther:PTHR11108,hmmpanther:PTHR11108:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1310448576 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 57586608 57586608 C A 1 0 0 0 0 1 0 0 0 5671 652 23 1 1 FECH 18 57586608 Missense_Mutation SNP C C3N-01410_T 3303630 57586608 22786677 220 23120 STK11 0 . GRCh38 19 1218501 1218501 + Splice_Site SNP A A G C3N-01410_T C3N-01410_N A A c.374+1A>G p.X125_splice ENST00000326873 195 139 56 215 215 0 strelka-varscan-mutect STK11,splice_donor_variant,,ENST00000586243,;STK11,splice_donor_variant,,ENST00000326873,NM_000455.4;STK11,splice_donor_variant,,ENST00000585748,;STK11,intron_variant,,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,splice_donor_variant,,ENST00000589152,;STK11,splice_donor_variant,,ENST00000586358,;STK11,splice_donor_variant,,ENST00000593219,;STK11,upstream_gene_variant,,ENST00000591133,; G ENST00000326873 Transcript splice_donor_variant -/2611 374/1302 125/433 CS021376 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 2/9 HIGH 1 SNV 1 1 1 PASS rs1131690951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 75 1218501 1218501 A G 1 0 0 0 0 0 0 1 0 15664 463 16 5 5 STK11 19 1218501 Splice_Site SNP A C3N-01410_T 1218501 57399115 221 23121 PDE4A 0 . GRCh38 19 10454864 10454864 + Silent SNP G G T rs749421091 C3N-01410_T C3N-01410_N G G c.819G>T p.= p.L273L ENST00000380702 7/15 172 108 64 254 254 0 strelka-varscan-mutect PDE4A,synonymous_variant,p.=,ENST00000380702,NM_001111307.1;PDE4A,synonymous_variant,p.=,ENST00000592685,NM_001243121.1;PDE4A,synonymous_variant,p.=,ENST00000293683,NM_001111308.1;PDE4A,synonymous_variant,p.=,ENST00000344979,NM_006202.2;PDE4A,synonymous_variant,p.=,ENST00000440014,NM_001111309.1;PDE4A,synonymous_variant,p.=,ENST00000591971,;PDE4A,synonymous_variant,p.=,ENST00000589073,;PDE4A,non_coding_transcript_exon_variant,,ENST00000586275,;PDE4A,upstream_gene_variant,,ENST00000590407,; T ENST00000380702 Transcript synonymous_variant 929/4781 819/2661 273/886 L ctG/ctT rs749421091 1 1 PDE4A HGNC HGNC:8780 protein_coding YES CCDS45961.1 ENSP00000370078 P27815 UPI0000047003 NM_001111307.1 7/15 hmmpanther:PTHR11347:SF74,hmmpanther:PTHR11347 LOW 1 SNV 1 1 PASS rs749421091 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 75 10454864 10454864 G T 1 0 0 0 0 0 0 0 1 11727 1364 48 2 2 PDE4A 19 10454864 Silent SNP G C3N-01410_T 9236363 10454864 48162752 222 23122 PODNL1 0 . GRCh38 19 13936040 13936040 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.345G>T p.= p.L115L ENST00000339560 4/8 96 58 38 122 122 0 strelka-varscan-mutect PODNL1,synonymous_variant,p.=,ENST00000538517,NM_001146255.1;PODNL1,synonymous_variant,p.=,ENST00000339560,NM_024825.3;PODNL1,synonymous_variant,p.=,ENST00000538371,NM_001146254.1;PODNL1,intron_variant,,ENST00000254320,;PODNL1,intron_variant,,ENST00000586075,;PODNL1,intron_variant,,ENST00000585607,;PODNL1,upstream_gene_variant,,ENST00000587954,;PODNL1,upstream_gene_variant,,ENST00000588872,;PODNL1,downstream_gene_variant,,ENST00000587458,;PODNL1,upstream_gene_variant,,ENST00000588764,;PODNL1,upstream_gene_variant,,ENST00000591353,;PODNL1,intron_variant,,ENST00000587288,; A ENST00000339560 Transcript synonymous_variant 619/2165 345/1539 115/512 L ctG/ctT 1 -1 PODNL1 HGNC HGNC:26275 protein_coding YES CCDS12300.1 ENSP00000345175 Q6PEZ8 UPI0000366D47 NM_024825.3 4/8 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF59,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS rs1406827267 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 13936040 13936040 C A 1 0 0 0 0 0 0 0 1 12288 724 25 2 2 PODNL1 19 13936040 Silent SNP C C3N-01410_T 3481176 13936040 44681576 223 23123 CYP4F12 0 . GRCh38 19 15683666 15683666 + Missense_Mutation SNP G G T rs781561176 C3N-01410_T C3N-01410_N G G c.821G>T p.Arg274Leu p.R274L ENST00000550308 7/13 74 48 26 120 120 0 strelka-varscan-mutect CYP4F12,missense_variant,p.Arg274Leu,ENST00000550308,NM_023944.3;CYP4F12,missense_variant,p.Arg274Leu,ENST00000324632,;CYP4F12,downstream_gene_variant,,ENST00000551607,;CYP4F12,3_prime_UTR_variant,,ENST00000517734,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000546608,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000550627,;CYP4F12,non_coding_transcript_exon_variant,,ENST00000518629,;CYP4F12,downstream_gene_variant,,ENST00000430608,;CYP4F12,downstream_gene_variant,,ENST00000451750,;CYP4F12,downstream_gene_variant,,ENST00000546792,;CYP4F12,downstream_gene_variant,,ENST00000548237,;CYP4F12,downstream_gene_variant,,ENST00000548501,;CYP4F12,downstream_gene_variant,,ENST00000547332,;CYP4F12,downstream_gene_variant,,ENST00000547471,;CYP4F12,downstream_gene_variant,,ENST00000549622,;CYP4F12,downstream_gene_variant,,ENST00000548435,; T ENST00000550308 Transcript missense_variant 1201/2044 821/1575 274/524 R/L cGg/cTg rs781561176,COSM4879367 1 1 CYP4F12 HGNC HGNC:18857 protein_coding YES CCDS42517.1 ENSP00000448998 A0A0A0MR49 UPI00020B9EFD NM_023944.3 deleterious(0) 7/13 hmmpanther:PTHR24291:SF27,hmmpanther:PTHR24291,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781561176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 15683666 15683666 G T 1 0 0 0 0 1 0 0 0 3990 1116 39 1 1 CYP4F12 19 15683666 Missense_Mutation SNP G C3N-01410_T 1747626 15683666 42933950 224 23124 ZNF257 0 . GRCh38 19 22088396 22088396 + Missense_Mutation SNP C C T C3N-01410_T C3N-01410_N C C c.646C>T p.Leu216Phe p.L216F ENST00000594947 4/4 124 99 25 117 117 0 strelka-varscan-mutect ZNF257,missense_variant,p.Leu216Phe,ENST00000594947,NM_033468.2;ZNF257,3_prime_UTR_variant,,ENST00000600162,;ZNF257,downstream_gene_variant,,ENST00000597927,;ZNF257,3_prime_UTR_variant,,ENST00000435820,NM_001316996.1; T ENST00000594947 Transcript missense_variant 790/3874 646/1692 216/563 L/F Ctt/Ttt COSM4503699 1 1 ZNF257 HGNC HGNC:13498 protein_coding YES CCDS46030.1 ENSP00000470209 Q9Y2Q1 UPI0000E045CA NM_033468.2 tolerated(0.16) 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 4 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 22088396 22088396 C T 1 0 0 0 0 1 0 0 0 18376 913 32 3 3 ZNF257 19 22088396 Missense_Mutation SNP C C3N-01410_T 6404730 22088396 36529220 225 23125 ZNF254 0 . GRCh38 19 24126399 24126399 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.399G>T p.Lys133Asn p.K133N ENST00000357002 4/4 74 40 34 85 85 0 strelka-varscan-mutect ZNF254,missense_variant,p.Lys92Asn,ENST00000613065,NM_001278677.1,NM_001278661.1,NM_001278662.1;ZNF254,missense_variant,p.Lys60Asn,ENST00000611359,NM_001278664.1;ZNF254,missense_variant,p.Lys133Asn,ENST00000357002,NM_203282.3;ZNF254,missense_variant,p.Lys48Asn,ENST00000616028,NM_001278663.1,NM_001278678.1;ZNF254,3_prime_UTR_variant,,ENST00000594886,;ZNF254,downstream_gene_variant,,ENST00000595187,; T ENST00000357002 Transcript missense_variant 514/3967 399/1980 133/659 K/N aaG/aaT 1 1 ZNF254 HGNC HGNC:13047 protein_coding YES CCDS32983.1 ENSP00000349494 O75437 UPI0000366DB6 NM_203282.3 tolerated(0.09) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 24126399 24126399 G T 1 0 0 0 0 1 0 0 0 18374 991 35 2 2 ZNF254 19 24126399 Missense_Mutation SNP G C3N-01410_T 2038003 24126399 34491217 226 23126 PSG5 0 . GRCh38 19 43186357 43186357 + Missense_Mutation SNP C C A C3N-01410_T C3N-01410_N C C c.49G>T p.Gly17Trp p.G17W ENST00000366175 1/6 188 159 29 226 226 0 strelka-varscan-mutect PSG5,missense_variant,p.Gly17Trp,ENST00000404580,;PSG5,missense_variant,p.Gly17Trp,ENST00000599812,;PSG5,missense_variant,p.Gly17Trp,ENST00000366175,;PSG5,missense_variant,p.Gly17Trp,ENST00000342951,NM_001130014.1,NM_002781.3;PSG5,missense_variant,p.Gly17Trp,ENST00000407356,;PSG5,missense_variant,p.Gly17Trp,ENST00000407568,;PSG5,non_coding_transcript_exon_variant,,ENST00000401992,;PSG5,upstream_gene_variant,,ENST00000489220,;PSG5,non_coding_transcript_exon_variant,,ENST00000600817,; A ENST00000366175 Transcript missense_variant 180/1766 49/1008 17/335 G/W Ggg/Tgg COSM3535173 1 -1 PSG5 HGNC HGNC:9522 protein_coding YES CCDS12617.1 ENSP00000382334 Q15238 A0A024R0S1 UPI000013C7B9 deleterious(0) 1/6 Cleavage_site_(Signalp):SignalP-noTM 1 MODERATE 1 SNV 5 1 1 PASS rs951631742 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 43186357 43186357 C A 1 0 0 0 0 1 0 0 0 12809 623 22 2 2 PSG5 19 43186357 Missense_Mutation SNP C C3N-01410_T 19059958 43186357 15431259 227 23127 EML2 0 . GRCh38 19 45634470 45634470 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.784T>C p.Tyr262His p.Y262H ENST00000587152 7/22 155 132 23 180 179 1 strelka-varscan-mutect EML2,missense_variant,p.Tyr208His,ENST00000536630,NM_001193269.1;EML2,missense_variant,p.Tyr262His,ENST00000587152,NM_001193268.1;EML2,missense_variant,p.Tyr61His,ENST00000589876,;EML2,missense_variant,p.Tyr61His,ENST00000245925,NM_012155.2;EML2,missense_variant,p.Tyr39His,ENST00000586770,;EML2,missense_variant,p.Tyr39His,ENST00000593255,;EML2,missense_variant,p.Tyr39His,ENST00000590018,;EML2,missense_variant,p.Tyr39His,ENST00000591721,;EML2,missense_variant,p.Tyr39His,ENST00000590043,;EML2,upstream_gene_variant,,ENST00000588496,;EML2,upstream_gene_variant,,ENST00000588272,;EML2,downstream_gene_variant,,ENST00000362196,;EML2,upstream_gene_variant,,ENST00000586902,;EML2,upstream_gene_variant,,ENST00000590580,;EML2,missense_variant,p.Tyr219His,ENST00000399594,;EML2,missense_variant,p.Tyr61His,ENST00000588308,;EML2,splice_region_variant,,ENST00000588000,;EML2,splice_region_variant,,ENST00000588610,;EML2,splice_region_variant,,ENST00000588889,;EML2,non_coding_transcript_exon_variant,,ENST00000587804,;EML2,intron_variant,,ENST00000586195,;EML2,upstream_gene_variant,,ENST00000592853,; G ENST00000587152 Transcript missense_variant,splice_region_variant 969/2763 784/2553 262/850 Y/H Tat/Cat 1 -1 EML2 HGNC HGNC:18035 protein_coding YES CCDS59399.1 ENSP00000468312 O95834 UPI0001DD21BF NM_001193268.1 deleterious(0.01) 7/22 Pfam_domain:PF03451,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF32,Superfamily_domains:SSF50998 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 45634470 45634470 A G 1 0 0 0 0 1 0 0 0 4940 434 15 5 5 EML2 19 45634470 Missense_Mutation SNP A C3N-01410_T 2448113 45634470 12983146 228 23128 AP2A1 0 . GRCh38 19 49795630 49795630 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.706A>G p.Ile236Val p.I236V ENST00000359032 7/24 105 48 57 108 108 0 strelka-varscan-mutect AP2A1,missense_variant,p.Ile236Val,ENST00000354293,NM_130787.2;AP2A1,missense_variant,p.Ile236Val,ENST00000359032,NM_014203.2;MIR6799,downstream_gene_variant,,ENST00000620297,;AP2A1,splice_region_variant,,ENST00000600199,;AP2A1,splice_region_variant,,ENST00000597774,; G ENST00000359032 Transcript missense_variant,splice_region_variant 706/3286 706/2934 236/977 I/V Atc/Gtc 1 1 AP2A1 HGNC HGNC:561 protein_coding YES CCDS46148.1 ENSP00000351926 O95782 UPI0000167B50 NM_014203.2 tolerated(0.1) 7/24 hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF19,Gene3D:1.25.10.10,PIRSF_domain:PIRSF037091,Pfam_domain:PF01602,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 49795630 49795630 A G 1 0 0 0 0 1 0 0 0 855 347 12 5 5 AP2A1 19 49795630 Missense_Mutation SNP A C3N-01410_T 4161160 49795630 8821986 229 23129 CTU1 0 . GRCh38 19 51104252 51104252 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.318G>T p.= p.A106A ENST00000421832 2/3 233 131 102 205 205 0 strelka-varscan-mutect CTU1,synonymous_variant,p.=,ENST00000421832,NM_145232.3; A ENST00000421832 Transcript synonymous_variant 363/2087 318/1047 106/348 A gcG/gcT 1 -1 CTU1 HGNC HGNC:29590 protein_coding YES CCDS12824.1 ENSP00000390011 Q7Z7A3 UPI000013D897 NM_145232.3 2/3 Low_complexity_(Seg):seg,HAMAP:MF_03053,hmmpanther:PTHR11807,hmmpanther:PTHR11807:SF12,PIRSF_domain:PIRSF004976,Pfam_domain:PF01171,Gene3D:3.40.50.620,Superfamily_domains:SSF52402 LOW 1 SNV 2 1 PASS rs1377150979 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 51104252 51104252 C A 1 0 0 0 0 0 0 0 1 3856 639 23 1 1 CTU1 19 51104252 Silent SNP C C3N-01410_T 1308622 51104252 7513364 230 23130 ZNF578 0 . GRCh38 19 52511137 52511137 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.756C>A p.= p.I252I ENST00000421239 6/6 206 104 102 183 183 0 strelka-varscan-mutect ZNF578,synonymous_variant,p.=,ENST00000421239,NM_001099694.1;ZNF578,synonymous_variant,p.=,ENST00000601120,;CTD-3099C6.5,downstream_gene_variant,,ENST00000599143,; A ENST00000421239 Transcript synonymous_variant 1000/2017 756/1773 252/590 I atC/atA 1 1 ZNF578 HGNC HGNC:26449 protein_coding YES CCDS54310.1 ENSP00000459216 Q96N58 UPI000048A457 NM_001099694.1 6/6 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 52511137 52511137 C A 1 0 0 0 0 0 0 0 1 18584 845 30 2 2 ZNF578 19 52511137 Silent SNP C C3N-01410_T 1406885 52511137 6106479 231 23131 ZNF160 0 . GRCh38 19 53068754 53068754 + Missense_Mutation SNP T T G novel C3N-01410_T C3N-01410_N T T c.1780A>C p.Lys594Gln p.K594Q ENST00000429604 7/7 171 85 86 174 174 0 strelka-varscan-mutect ZNF160,missense_variant,p.Lys558Gln,ENST00000601421,;ZNF160,missense_variant,p.Lys594Gln,ENST00000429604,NM_001322132.1,NM_001322129.1,NM_001322138.1,NM_001322134.1,NM_001322131.1,NM_001322133.1,NM_198893.2,NM_001102603.1;ZNF160,missense_variant,p.Lys594Gln,ENST00000599056,NM_001322138.1;ZNF160,missense_variant,p.Lys594Gln,ENST00000418871,NM_001322135.1,NM_001322128.1,NM_001322138.1,NM_001322136.1,NM_033288.3;ZNF160,downstream_gene_variant,,ENST00000599247,;ZNF160,downstream_gene_variant,,ENST00000355147,NM_001322126.1;ZNF160,downstream_gene_variant,,ENST00000601982,; G ENST00000429604 Transcript missense_variant 2196/4336 1780/2457 594/818 K/Q Aag/Cag 1 -1 ZNF160 HGNC HGNC:12948 protein_coding YES CCDS12859.1 ENSP00000406201 Q9HCG1 A0A024R4Q2 UPI0000202B37 NM_001322132.1,NM_001322129.1,NM_001322138.1,NM_001322134.1,NM_001322131.1,NM_001322133.1,NM_198893.2,NM_001102603.1 deleterious(0.05) 7/7 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF132,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 53068754 53068754 T G 1 0 0 0 0 1 0 0 0 18320 1821 63 5 5 ZNF160 19 53068754 Missense_Mutation SNP T C3N-01410_T 557617 53068754 5548862 232 23132 ZNF329 0 . GRCh38 19 58128772 58128772 + Nonsense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.732C>A p.Tyr244Ter p.Y244* ENST00000597186 5/5 60 39 21 57 57 0 strelka-varscan-mutect ZNF329,stop_gained,p.Tyr244Ter,ENST00000597186,;ZNF329,stop_gained,p.Tyr244Ter,ENST00000598312,NM_024620.3;ZNF329,stop_gained,p.Tyr244Ter,ENST00000358067,;ZNF329,downstream_gene_variant,,ENST00000601887,;ZNF329,stop_gained,p.Tyr244Ter,ENST00000500161,; T ENST00000597186 Transcript stop_gained 1410/3930 732/1626 244/541 Y/* taC/taA 1 -1 ZNF329 HGNC HGNC:14209 protein_coding YES CCDS12972.1 ENSP00000470323 Q86UD4 A0A024R4Q4 UPI0000246E79 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF118,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 75 58128772 58128772 G T 1 0 0 0 0 0 1 0 0 18419 1372 48 2 2 ZNF329 19 58128772 Nonsense_Mutation SNP G C3N-01410_T 5060018 58128772 488844 233 23133 SLC27A5 0 . GRCh38 19 58509869 58509869 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.1035G>T p.= p.G345G ENST00000263093 3/10 101 49 52 104 104 0 strelka-varscan-mutect SLC27A5,synonymous_variant,p.=,ENST00000263093,NM_012254.2;SLC27A5,synonymous_variant,p.=,ENST00000601355,NM_001321196.1;ZBTB45,downstream_gene_variant,,ENST00000594051,NM_001316979.1;ZBTB45,downstream_gene_variant,,ENST00000354590,NM_032792.2;ZBTB45,downstream_gene_variant,,ENST00000600990,;SLC27A5,non_coding_transcript_exon_variant,,ENST00000593745,;SLC27A5,non_coding_transcript_exon_variant,,ENST00000594683,; A ENST00000263093 Transcript synonymous_variant 1145/2361 1035/2073 345/690 G ggG/ggT 1 -1 SLC27A5 HGNC HGNC:10999 protein_coding YES CCDS12983.1 ENSP00000263093 Q9Y2P5 UPI0000072ECE NM_012254.2 3/10 Gene3D:3.40.50.980,Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF99,Superfamily_domains:SSF56801 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 58509869 58509869 C A 1 0 0 0 0 0 0 0 1 14799 842 30 2 2 SLC27A5 19 58509869 Silent SNP C C3N-01410_T 381097 58509869 107747 234 23134 TMC2 0 . GRCh38 20 2641349 2641349 + Nonstop_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.2719T>A p.Ter907ArgextTer44 p.*907Rext*44 ENST00000358864 20/20 132 107 25 89 89 0 strelka-varscan-mutect TMC2,stop_lost,p.Ter907ArgextTer44,ENST00000358864,NM_080751.2; A ENST00000358864 Transcript stop_lost 2734/3169 2719/2721 907/906 */R Tga/Aga 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 20/20 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 2641349 2641349 T A 1 0 0 0 0 0 0 0 0 16431 1593 55 4 4 TMC2 20 2641349 Nonstop_Mutation SNP T C3N-01410_T 2641349 61802818 235 23135 FAM83C 0 . GRCh38 20 35292111 35292111 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.194C>A p.Ser65Tyr p.S65Y ENST00000374408 1/4 384 324 60 377 377 0 strelka-varscan-mutect FAM83C,missense_variant,p.Ser65Tyr,ENST00000374408,NM_178468.5; T ENST00000374408 Transcript missense_variant 291/3145 194/2244 65/747 S/Y tCc/tAc 1 -1 FAM83C HGNC HGNC:16121 protein_coding YES CCDS13251.1 ENSP00000363529 Q9BQN1 UPI0000072DC0 NM_178468.5 deleterious(0) 1/4 Pfam_domain:PF07894,hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 35292111 35292111 G T 1 0 0 0 0 1 0 0 0 5493 1174 41 2 2 FAM83C 20 35292111 Missense_Mutation SNP G C3N-01410_T 32650762 35292111 29152056 236 23136 CPNE1 0 . GRCh38 20 35632007 35632007 + Missense_Mutation SNP C C A rs773196207 C3N-01410_T C3N-01410_N C C c.490G>T p.Asp164Tyr p.D164Y ENST00000317677 6/16 199 140 59 199 199 0 strelka-varscan-mutect CPNE1,missense_variant,p.Asp159Tyr,ENST00000352393,NM_152928.2;CPNE1,missense_variant,p.Asp164Tyr,ENST00000317677,NM_003915.5;CPNE1,missense_variant,p.Asp159Tyr,ENST00000397443,NM_001198863.1,NM_152925.2,NM_152927.2,NM_152926.2;CPNE1,missense_variant,p.Asp159Tyr,ENST00000437340,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000397442,;CPNE1,missense_variant,p.Asp135Tyr,ENST00000430570,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000414664,;CPNE1,missense_variant,p.Asp135Tyr,ENST00000412056,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000434795,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000420363,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000439806,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000440240,;CPNE1,missense_variant,p.Asp135Tyr,ENST00000416778,;CPNE1,missense_variant,p.Asp135Tyr,ENST00000458038,;CPNE1,downstream_gene_variant,,ENST00000437100,;CPNE1,upstream_gene_variant,,ENST00000415920,;CPNE1,downstream_gene_variant,,ENST00000414711,;CPNE1,downstream_gene_variant,,ENST00000435747,;CPNE1,upstream_gene_variant,,ENST00000498814,;CPNE1,upstream_gene_variant,,ENST00000498056,;CPNE1,missense_variant,p.Asp159Tyr,ENST00000401607,;CPNE1,3_prime_UTR_variant,,ENST00000439669,;CPNE1,non_coding_transcript_exon_variant,,ENST00000483359,;CPNE1,non_coding_transcript_exon_variant,,ENST00000483495,;CPNE1,non_coding_transcript_exon_variant,,ENST00000486021,;RP1-309K20.6,downstream_gene_variant,,ENST00000541176,;CPNE1,upstream_gene_variant,,ENST00000473373,;RP1-309K20.6,downstream_gene_variant,,ENST00000454607,;RP1-309K20.6,downstream_gene_variant,,ENST00000441563,; A ENST00000317677 Transcript missense_variant 625/1961 490/1629 164/542 D/Y Gat/Tat rs773196207 1 -1 CPNE1 HGNC HGNC:2314 protein_coding YES CCDS46595.1 ENSP00000317257 B0QZ18 UPI0000D4B36B NM_003915.5 deleterious(0.01) 6/16 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF2,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs773196207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 35632007 35632007 C A 1 0 0 0 0 1 0 0 0 3606 913 32 2 2 CPNE1 20 35632007 Missense_Mutation SNP C C3N-01410_T 339896 35632007 28812160 237 23137 CTCFL 0 . GRCh38 20 57498666 57498666 + Nonsense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1876G>T p.Glu626Ter p.E626* ENST00000423479 11/12 159 107 52 153 153 0 strelka-varscan-mutect CTCFL,stop_gained,p.Glu626Ter,ENST00000608263,NM_001269041.1;CTCFL,stop_gained,p.Glu576Ter,ENST00000429804,NM_001269046.1;CTCFL,stop_gained,p.Glu626Ter,ENST00000609232,NM_080618.3;CTCFL,stop_gained,p.Glu626Ter,ENST00000243914,;CTCFL,stop_gained,p.Glu626Ter,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,stop_gained,p.Glu626Ter,ENST00000423479,NM_001269043.1;CTCFL,downstream_gene_variant,,ENST00000608440,NM_001269044.1;CTCFL,downstream_gene_variant,,ENST00000433949,NM_001269049.1;CTCFL,downstream_gene_variant,,ENST00000502686,NM_001269054.1;CTCFL,downstream_gene_variant,,ENST00000426658,;CTCFL,downstream_gene_variant,,ENST00000422109,; A ENST00000423479 Transcript stop_gained 1967/2478 1876/2103 626/700 E/* Gaa/Taa 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 11/12 hmmpanther:PTHR24375:SF96,hmmpanther:PTHR24375 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 57498666 57498666 C A 1 0 0 0 0 0 1 0 0 3808 922 32 2 2 CTCFL 20 57498666 Nonsense_Mutation SNP C C3N-01410_T 21866659 57498666 6945501 238 23138 TUBB1 0 . GRCh38 20 59024141 59024141 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.714C>A p.= p.T238T ENST00000217133 4/4 356 255 101 334 333 1 strelka-varscan-mutect TUBB1,synonymous_variant,p.=,ENST00000217133,NM_030773.3;ATP5E,downstream_gene_variant,,ENST00000243997,NM_006886.3;ATP5E,downstream_gene_variant,,ENST00000395659,;ATP5E,downstream_gene_variant,,ENST00000395663,; A ENST00000217133 Transcript synonymous_variant 983/3496 714/1356 238/451 T acC/acA 1 1 TUBB1 HGNC HGNC:16257 protein_coding YES CCDS13475.1 ENSP00000217133 Q9H4B7 UPI0000071B14 NM_030773.3 4/4 Gene3D:3.40.50.1440,Prints_domain:PR01163,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF112,SMART_domains:SM00864,Superfamily_domains:SSF52490 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 59024141 59024141 C A 1 0 0 0 0 0 0 0 1 17264 668 24 2 2 TUBB1 20 59024141 Silent SNP C C3N-01410_T 1525475 59024141 5420026 239 23139 UBASH3A 0 . GRCh38 21 42426701 42426701 + Missense_Mutation SNP T T A novel C3N-01410_T C3N-01410_N T T c.1051T>A p.Tyr351Asn p.Y351N ENST00000319294 8/15 127 77 50 136 136 0 strelka-varscan-mutect UBASH3A,missense_variant,p.Tyr351Asn,ENST00000319294,NM_018961.3;UBASH3A,missense_variant,p.Tyr313Asn,ENST00000291535,NM_001001895.2;UBASH3A,missense_variant,p.Tyr313Asn,ENST00000398367,NM_001243467.1;UBASH3A,missense_variant,p.Tyr313Asn,ENST00000473381,;UBASH3A,missense_variant,p.Tyr313Asn,ENST00000635325,; A ENST00000319294 Transcript missense_variant 1082/2504 1051/1986 351/661 Y/N Tac/Aac 1 1 UBASH3A HGNC HGNC:12462 protein_coding YES CCDS13687.1 ENSP00000317327 P57075 UPI0000137941 NM_018961.3 deleterious(0.01) 8/15 hmmpanther:PTHR16469:SF7,hmmpanther:PTHR16469 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 42426701 42426701 T A 1 0 0 0 0 1 0 0 0 17361 1652 57 4 4 UBASH3A 21 42426701 Missense_Mutation SNP T C3N-01410_T 42426701 4283282 240 23140 KRTAP10-2 0 . GRCh38 21 44550779 44550779 + Missense_Mutation SNP G G T novel C3N-01410_T C3N-01410_N G G c.680C>A p.Pro227His p.P227H ENST00000391621 1/1 291 192 99 419 419 0 strelka-varscan-mutect KRTAP10-2,missense_variant,p.Pro227His,ENST00000391621,NM_198693.3;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,;KRTAP10-2,intron_variant,,ENST00000498210,; T ENST00000391621 Transcript missense_variant 727/1149 680/768 227/255 P/H cCc/cAc 1 -1 KRTAP10-2 HGNC HGNC:22967 protein_coding YES CCDS42955.1 ENSP00000375479 P60368 UPI000021C438 NM_198693.3 deleterious(0) 1/1 Pfam_domain:PF13885,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF8,Low_complexity_(Seg):seg MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 44550779 44550779 G T 1 0 0 0 0 1 0 0 0 8392 1232 43 2 2 KRTAP10-2 21 44550779 Missense_Mutation SNP G C3N-01410_T 2124078 44550779 2159204 241 23141 IFT27 0 . GRCh38 22 36766138 36766138 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.234G>T p.Leu78Phe p.L78F ENST00000433985 4/7 195 110 85 240 240 0 strelka-varscan-mutect IFT27,missense_variant,p.Leu77Phe,ENST00000340630,NM_006860.4;IFT27,missense_variant,p.Leu78Phe,ENST00000433985,NM_001177701.2;IFT27,missense_variant,p.Leu117Phe,ENST00000417951,;IFT27,missense_variant,p.Leu37Phe,ENST00000440696,;IFT27,missense_variant,p.Leu77Phe,ENST00000430701,;IFT27,missense_variant,p.Leu53Phe,ENST00000415653,;IFT27,splice_region_variant,,ENST00000471809,;IFT27,splice_region_variant,,ENST00000495555,;IFT27,downstream_gene_variant,,ENST00000465023,; A ENST00000433985 Transcript missense_variant,splice_region_variant 660/1095 234/561 78/186 L/F ttG/ttT 1 -1 IFT27 HGNC HGNC:18626 protein_coding YES CCDS54523.1 ENSP00000393541 Q9BW83 UPI000013314C NM_001177701.2 tolerated(0.54) 4/7 PROSITE_profiles:PS51419,hmmpanther:PTHR24073:SF547,hmmpanther:PTHR24073,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00174,SMART_domains:SM00173,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 36766138 36766138 C A 1 0 0 0 0 1 0 0 0 7464 608 21 2 2 IFT27 22 36766138 Missense_Mutation SNP C C3N-01410_T 36766138 14052330 242 23142 AKAP17A 0 . GRCh38 X 1601369 1601369 + Silent SNP G G T novel C3N-01410_T C3N-01410_N G G c.1863G>T p.= p.R621R ENST00000313871 5/5 66 53 13 55 55 0 strelka-varscan-mutect AKAP17A,synonymous_variant,p.=,ENST00000313871,NM_005088.2;AKAP17A,downstream_gene_variant,,ENST00000381261,;AKAP17A,3_prime_UTR_variant,,ENST00000474361,; T ENST00000313871 Transcript synonymous_variant 2059/3204 1863/2088 621/695 R cgG/cgT 1 1 AKAP17A HGNC HGNC:18783 protein_coding YES CCDS14116.1 ENSP00000324827 Q02040 UPI00001AF072 NM_005088.2 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR12484,hmmpanther:PTHR12484:SF2 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 75 1601369 1601369 G T 1 0 0 0 0 0 0 0 1 534 1190 42 2 2 AKAP17A 23 1601369 Silent SNP G C3N-01410_T 1601369 154439526 243 23143 DHRSX 0 . GRCh38 X 2266940 2266940 + Silent SNP C C A rs771423972 C3N-01410_T C3N-01410_N C C c.396G>T p.= p.V132V ENST00000334651 5/7 198 170 28 196 196 0 strelka-varscan-mutect DHRSX,synonymous_variant,p.=,ENST00000334651,NM_145177.2;DHRSX,synonymous_variant,p.=,ENST00000444280,;DHRSX,synonymous_variant,p.=,ENST00000412516,;DHRSX,upstream_gene_variant,,ENST00000464935,;DHRSX,3_prime_UTR_variant,,ENST00000441131,; A ENST00000334651 Transcript synonymous_variant 449/2571 396/993 132/330 V gtG/gtT rs771423972 1 -1 DHRSX HGNC HGNC:18399 protein_coding YES CCDS35195.1 ENSP00000334113 Q8N5I4 UPI0000D61D1C NM_145177.2 5/7 hmmpanther:PTHR24319,hmmpanther:PTHR24319:SF33,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735,Prints_domain:PR00081 LOW 1 SNV 1 1 PASS rs771423972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 2266940 2266940 C A 1 0 0 0 0 0 0 0 1 4303 813 29 2 2 DHRSX 23 2266940 Silent SNP C C3N-01410_T 665571 2266940 153773955 244 23144 MAGEB6P1 0 . GRCh38 X 26161761 26161761 + Nonsense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1161C>A p.Tyr387Ter p.Y387* ENST00000416929 1/1 129 62 67 98 98 0 strelka-varscan-mutect MAGEB6P1,stop_gained,p.Tyr387Ter,ENST00000416929,; A ENST00000416929 Transcript stop_gained 1161/1224 1161/1224 387/407 Y/* taC/taA 1 1 MAGEB6P1 HGNC HGNC:28824 protein_coding YES ENSP00000488257 A0A0J9YX57 UPI0000237759 1/1 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736 HIGH 1 SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 75 26161761 26161761 C A 1 0 0 0 0 0 1 0 0 9097 518 18 2 2 MAGEB6P1 23 26161761 Nonsense_Mutation SNP C C3N-01410_T 23894821 26161761 129879134 245 23145 FGD1 0 . GRCh38 X 54468858 54468858 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.1120G>T p.Val374Leu p.V374L ENST00000375135 5/18 222 110 112 165 165 0 strelka-varscan-mutect FGD1,missense_variant,p.Val374Leu,ENST00000375135,NM_004463.2; A ENST00000375135 Transcript missense_variant 1854/4275 1120/2886 374/961 V/L Gtg/Ttg 1 -1 FGD1 HGNC HGNC:3663 protein_coding YES CCDS14359.1 ENSP00000364277 P98174 A0A024R9Y5 UPI000012A705 NM_004463.2 tolerated(1) 5/18 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF79,Gene3D:1.20.900.10,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS rs1397655152 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 54468858 54468858 C A 1 0 0 0 0 1 0 0 0 5696 507 18 2 2 FGD1 23 54468858 Missense_Mutation SNP C C3N-01410_T 28307097 54468858 101572037 246 23146 AMER1 0 . GRCh38 X 64191797 64191797 + Missense_Mutation SNP C C G C3N-01410_T C3N-01410_N C C c.1490G>C p.Arg497Pro p.R497P ENST00000330258 2/2 101 37 64 58 58 0 strelka-varscan-mutect AMER1,missense_variant,p.Arg497Pro,ENST00000330258,NM_152424.3;AMER1,missense_variant,p.Arg497Pro,ENST00000374869,; G ENST00000330258 Transcript missense_variant 1763/8443 1490/3408 497/1135 R/P cGa/cCa COSM3390741,COSM3390742 1 -1 AMER1 HGNC HGNC:26837 protein_coding YES CCDS14377.2 ENSP00000329117 Q5JTC6 UPI0000EDA0FC NM_152424.3 deleterious(0) 2/2 hmmpanther:PTHR22237:SF0,hmmpanther:PTHR22237,Pfam_domain:PF09422 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1259792397 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 64191797 64191797 C G 1 0 0 0 0 1 0 0 0 667 884 31 4 4 AMER1 23 64191797 Missense_Mutation SNP C C3N-01410_T 9722939 64191797 91849098 247 23147 NRK 0 . GRCh38 X 105946324 105946324 + Missense_Mutation SNP A A G novel C3N-01410_T C3N-01410_N A A c.4213A>G p.Thr1405Ala p.T1405A ENST00000243300 26/29 52 38 14 36 36 0 strelka-varscan-mutect NRK,missense_variant,p.Thr1405Ala,ENST00000243300,NM_198465.3;NRK,upstream_gene_variant,,ENST00000540278,; G ENST00000243300 Transcript missense_variant 4516/8062 4213/4749 1405/1582 T/A Aca/Gca 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0.03) 26/29 PROSITE_profiles:PS50219,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS rs1378907401 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 75 105946324 105946324 A G 1 0 0 0 0 1 0 0 0 10713 43 2 5 5 NRK 23 105946324 Missense_Mutation SNP A C3N-01410_T 41754527 105946324 50094571 248 23148 ZBTB33 0 . GRCh38 X 120255049 120255049 + Missense_Mutation SNP C C T C3N-01410_T C3N-01410_N C C c.1634C>T p.Thr545Ile p.T545I ENST00000326624 2/2 194 76 118 167 167 0 strelka-varscan-mutect ZBTB33,missense_variant,p.Thr545Ile,ENST00000326624,NM_006777.3;ZBTB33,missense_variant,p.Thr545Ile,ENST00000557385,NM_001184742.1;TMEM255A,downstream_gene_variant,,ENST00000371369,NM_001104544.1;TMEM255A,downstream_gene_variant,,ENST00000309720,NM_017938.3;TMEM255A,downstream_gene_variant,,ENST00000440464,NM_001104545.1;TMEM255A,downstream_gene_variant,,ENST00000371352,; T ENST00000326624 Transcript missense_variant 1862/5211 1634/2019 545/672 T/I aCa/aTa COSM4850664 1 1 ZBTB33 HGNC HGNC:16682 protein_coding YES CCDS14596.1 ENSP00000314153 Q86T24 UPI0000072F87 NM_006777.3 deleterious(0) 2/2 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF301,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 120255049 120255049 C T 1 0 0 0 0 1 0 0 0 18105 478 17 3 3 ZBTB33 23 120255049 Missense_Mutation SNP C C3N-01410_T 14308725 120255049 35785846 249 23149 GPR101 0 . GRCh38 X 137030268 137030268 + Silent SNP C C A novel C3N-01410_T C3N-01410_N C C c.1407G>T p.= p.L469L ENST00000298110 1/1 85 70 15 61 61 0 strelka-varscan-mutect GPR101,synonymous_variant,p.=,ENST00000298110,NM_054021.1; A ENST00000298110 Transcript synonymous_variant 1407/1527 1407/1527 469/508 L ctG/ctT 1 -1 GPR101 HGNC HGNC:14963 protein_coding YES CCDS14662.1 ENSP00000298110 Q96P66 UPI000003BCCD NM_054021.1 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF2,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 75 137030268 137030268 C A 1 0 0 0 0 0 0 0 1 6524 813 29 2 2 GPR101 23 137030268 Silent SNP C C3N-01410_T 16775219 137030268 19010627 250 23150 ZIC3 0 . GRCh38 X 137567270 137567270 + Missense_Mutation SNP C C A novel C3N-01410_T C3N-01410_N C C c.579C>A p.Phe193Leu p.F193L ENST00000287538 1/3 169 119 50 118 118 0 strelka-varscan-mutect ZIC3,missense_variant,p.Phe193Leu,ENST00000287538,NM_003413.3;ZIC3,missense_variant,p.Phe193Leu,ENST00000370606,;RP1-137H15.2,upstream_gene_variant,,ENST00000442841,;RP1-137H15.2,upstream_gene_variant,,ENST00000456631,;ZIC3,upstream_gene_variant,,ENST00000478471,; A ENST00000287538 Transcript missense_variant 1129/3469 579/1404 193/467 F/L ttC/ttA 1 1 ZIC3 HGNC HGNC:12874 protein_coding YES CCDS14663.1 ENSP00000287538 O60481 UPI000013C3DD NM_003413.3 tolerated(0.12) 1/3 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF25 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 137567270 137567270 C A 1 0 0 0 0 1 0 0 0 18259 883 31 1 1 ZIC3 23 137567270 Missense_Mutation SNP C C3N-01410_T 537002 137567270 18473625 251 23151 AFF2 0 . GRCh38 X 148966853 148966853 + Missense_Mutation SNP A A T C3N-01410_T C3N-01410_N A A c.2977A>T p.Thr993Ser p.T993S ENST00000370460 14/21 173 82 91 148 148 0 strelka-varscan-mutect AFF2,missense_variant,p.Thr993Ser,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Thr634Ser,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Thr958Ser,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Thr958Ser,ENST00000370457,NM_001169124.1,NM_001169125.1; T ENST00000370460 Transcript missense_variant 3456/13746 2977/3936 993/1311 T/S Act/Tct COSM1466238,COSM1466239,COSM1466240 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 tolerated(0.53) 14/21 Low_complexity_(Seg):seg,Pfam_domain:PF05110 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 75 148966853 148966853 A T 1 0 0 0 0 1 0 0 0 434 159 6 4 4 AFF2 23 148966853 Missense_Mutation SNP A C3N-01410_T 11399583 148966853 7074042 252 23152 PLXNB3 0 . GRCh38 X 153772928 153772928 + Missense_Mutation SNP G G A novel C3N-01410_T C3N-01410_N G G c.2887G>A p.Ala963Thr p.A963T ENST00000538966 18/37 25 9 16 37 37 0 strelka-varscan-mutect PLXNB3,missense_variant,p.Ala963Thr,ENST00000538966,NM_001163257.1;PLXNB3,missense_variant,p.Ala940Thr,ENST00000361971,NM_005393.2;SRPK3,upstream_gene_variant,,ENST00000489426,;PLXNB3,upstream_gene_variant,,ENST00000411613,;PLXNB3,upstream_gene_variant,,ENST00000448847,;PLXNB3,upstream_gene_variant,,ENST00000455214,;PLXNB3,upstream_gene_variant,,ENST00000485980,;PLXNB3,upstream_gene_variant,,ENST00000482654,; A ENST00000538966 Transcript missense_variant 3158/6377 2887/5799 963/1932 A/T Gca/Aca 1 1 PLXNB3 HGNC HGNC:9105 protein_coding YES CCDS55536.1 ENSP00000442736 Q9ULL4 UPI0001AFF680 NM_001163257.1 deleterious(0) 18/37 Gene3D:2.60.40.10,Pfam_domain:PF01833,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF33,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 5 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 153772928 153772928 G A 1 0 0 0 0 1 0 0 0 12231 1203 42 3 3 PLXNB3 23 153772928 Missense_Mutation SNP G C3N-01410_T 4806075 153772928 2267967 253 23153 SRPK3 0 . GRCh38 X 153784016 153784016 + Missense_Mutation SNP C C A rs782203334 C3N-01410_T C3N-01410_N C C c.950C>A p.Ser317Tyr p.S317Y ENST00000370101 10/15 63 27 36 37 37 0 strelka-varscan-mutect SRPK3,missense_variant,p.Ser384Tyr,ENST00000489426,;SRPK3,missense_variant,p.Ser317Tyr,ENST00000370101,NM_014370.3;SRPK3,missense_variant,p.Ser316Tyr,ENST00000393786,NM_001170761.1;SRPK3,missense_variant,p.Ser316Tyr,ENST00000370108,;SRPK3,missense_variant,p.Ser316Tyr,ENST00000370104,NM_001170760.1;SRPK3,missense_variant,p.Ser274Tyr,ENST00000370100,;PLXNB3,downstream_gene_variant,,ENST00000538966,NM_001163257.1;PLXNB3,downstream_gene_variant,,ENST00000361971,NM_005393.2;IDH3G,downstream_gene_variant,,ENST00000370092,NM_174869.2;IDH3G,downstream_gene_variant,,ENST00000370093,;IDH3G,downstream_gene_variant,,ENST00000427365,;IDH3G,downstream_gene_variant,,ENST00000217901,NM_004135.3;IDH3G,downstream_gene_variant,,ENST00000619865,;IDH3G,downstream_gene_variant,,ENST00000444450,;IDH3G,downstream_gene_variant,,ENST00000454076,;SRPK3,downstream_gene_variant,,ENST00000430541,;IDH3G,downstream_gene_variant,,ENST00000444338,;SRPK3,upstream_gene_variant,,ENST00000458681,;IDH3G,downstream_gene_variant,,ENST00000497043,;IDH3G,downstream_gene_variant,,ENST00000461215,;IDH3G,downstream_gene_variant,,ENST00000495356,;PLXNB3,downstream_gene_variant,,ENST00000472415,;PLXNB3,downstream_gene_variant,,ENST00000469190,; A ENST00000370101 Transcript missense_variant 996/1958 950/1704 317/567 S/Y tCt/tAt rs782203334 1 1 SRPK3 HGNC HGNC:11402 protein_coding YES CCDS35441.1 ENSP00000359119 Q9UPE1 UPI000050571A NM_014370.3 tolerated(0.06) 10/15 Low_complexity_(Seg):seg,PROSITE_profiles:PS50011,SMART_domains:SM00220 MODERATE 1 SNV 1 1 PASS rs782203334 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 75 153784016 153784016 C A 1 0 0 0 0 1 0 0 0 15522 913 32 2 2 SRPK3 23 153784016 Missense_Mutation SNP C C3N-01410_T 11088 153784016 2256879 254 23154 ENO1 0 . GRCh38 1 8866460 8866460 + Silent SNP C C T novel C3N-01413_T C3N-01413_N C C c.486G>A p.= p.K162K ENST00000234590 7/12 260 247 13 259 259 0 strelka-varscan-mutect ENO1,synonymous_variant,p.=,ENST00000234590,NM_001428.3;ENO1,synonymous_variant,p.=,ENST00000497492,;MIR6728,downstream_gene_variant,,ENST00000618792,;ENO1,non_coding_transcript_exon_variant,,ENST00000464920,;ENO1,downstream_gene_variant,,ENST00000492343,;ENO1,downstream_gene_variant,,ENST00000486051,; T ENST00000234590 Transcript synonymous_variant 606/1783 486/1305 162/434 K aaG/aaA 1 -1 ENO1 HGNC HGNC:3350 protein_coding YES CCDS97.1 ENSP00000234590 P06733 A0A024R4F1 UPI000013C9AF NM_001428.3 7/12 HAMAP:MF_00318,hmmpanther:PTHR11902,TIGRFAM_domain:TIGR01060,Pfam_domain:PF00113,Gene3D:3.20.20.120,PIRSF_domain:PIRSF001400,SMART_domains:SM01192,Superfamily_domains:SSF51604 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 8866460 8866460 C T 1 0 0 0 0 0 0 0 1 4965 796 28 3 3 ENO1 1 8866460 Silent SNP C C3N-01413_T 8866460 240089962 1 23155 ZNF362 0 . GRCh38 1 33295290 33295290 + Silent SNP G G C rs867453488 C3N-01413_T C3N-01413_N G G c.1131G>C p.= p.G377G ENST00000539719 8/9 164 140 24 129 129 0 strelka-varscan-mutect ZNF362,synonymous_variant,p.=,ENST00000539719,NM_152493.2;ZNF362,synonymous_variant,p.=,ENST00000373428,; C ENST00000539719 Transcript synonymous_variant 1301/3106 1131/1263 377/420 G ggG/ggC rs867453488 1 1 ZNF362 HGNC HGNC:18079 protein_coding YES CCDS377.1 ENSP00000446335 Q5T0B9 UPI000013E046 NM_152493.2 8/9 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS rs867453488 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 76 33295290 33295290 G C 1 0 0 0 0 0 0 0 1 18440 1190 42 4 4 ZNF362 1 33295290 Silent SNP G C3N-01413_T 24428830 33295290 215661132 2 23156 MAST2 0 . GRCh38 1 46025689 46025689 + Missense_Mutation SNP C C T novel C3N-01413_T C3N-01413_N C C c.1793C>T p.Ala598Val p.A598V ENST00000361297 16/29 169 150 19 146 146 0 strelka-varscan-mutect MAST2,missense_variant,p.Ala598Val,ENST00000361297,NM_001324320.1,NM_001319245.1,NM_015112.2;MAST2,missense_variant,p.Ala236Val,ENST00000372009,;MAST2,missense_variant,p.Ala483Val,ENST00000372008,;MAST2,upstream_gene_variant,,ENST00000477968,;MAST2,downstream_gene_variant,,ENST00000467367,;MAST2,downstream_gene_variant,,ENST00000498668,; T ENST00000361297 Transcript missense_variant 2076/5738 1793/5397 598/1798 A/V gCc/gTc 1 1 MAST2 HGNC HGNC:19035 protein_coding YES CCDS41326.1 ENSP00000354671 Q6P0Q8 UPI0000458AEB NM_001324320.1,NM_001319245.1,NM_015112.2 deleterious_low_confidence(0) 16/29 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF136,hmmpanther:PTHR24356,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9998556 1 1 1 0 T 3 4 76 46025689 46025689 C T 1 0 0 0 0 1 0 0 0 9251 739 26 3 3 MAST2 1 46025689 Missense_Mutation SNP C C3N-01413_T 12730399 46025689 202930733 3 23157 ZYG11B 0 . GRCh38 1 52779899 52779899 + Missense_Mutation SNP G G A rs753924795 C3N-01413_T C3N-01413_N G G c.998G>A p.Arg333His p.R333H ENST00000294353 4/14 273 256 17 297 297 0 strelka-varscan-mutect ZYG11B,missense_variant,p.Arg333His,ENST00000294353,NM_024646.2;ZYG11B,missense_variant,p.Arg333His,ENST00000545132,; A ENST00000294353 Transcript missense_variant 1143/8093 998/2235 333/744 R/H cGt/cAt rs753924795,COSM2193055 1 1 ZYG11B HGNC HGNC:25820 protein_coding YES CCDS30717.1 ENSP00000294353 Q9C0D3 UPI00001C1D70 NM_024646.2 deleterious(0.01) 4/14 hmmpanther:PTHR12904:SF21,hmmpanther:PTHR12904 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753924795 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 52779899 52779899 G A 1 0 0 0 0 1 0 0 0 18857 1145 40 1 1 ZYG11B 1 52779899 Missense_Mutation SNP G C3N-01413_T 6754210 52779899 196176523 4 23158 ASB17 0 . GRCh38 1 75922258 75922258 + Missense_Mutation SNP T T A novel C3N-01413_T C3N-01413_N T T c.503A>T p.Gln168Leu p.Q168L ENST00000284142 2/3 258 244 14 282 282 0 strelka-varscan-mutect ASB17,missense_variant,p.Gln168Leu,ENST00000284142,NM_080868.2; A ENST00000284142 Transcript missense_variant 643/1107 503/888 168/295 Q/L cAa/cTa 1 -1 ASB17 HGNC HGNC:19769 protein_coding YES CCDS671.1 ENSP00000284142 Q8WXJ9 UPI0000073CD7 NM_080868.2 tolerated(0.08) 2/3 Gene3D:1.25.40.20,hmmpanther:PTHR20966,hmmpanther:PTHR20966:SF2,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 75922258 75922258 T A 1 0 0 0 0 1 0 0 0 1163 1812 63 4 4 ASB17 1 75922258 Missense_Mutation SNP T C3N-01413_T 23142359 75922258 173034164 5 23159 FCER1A 0 . GRCh38 1 159304157 159304157 + Silent SNP A A G novel C3N-01413_T C3N-01413_N A A c.306A>G p.= p.E102E ENST00000368115 4/6 148 97 51 129 129 0 strelka-varscan-mutect FCER1A,synonymous_variant,p.=,ENST00000368115,NM_002001.3;FCER1A,synonymous_variant,p.=,ENST00000368114,; G ENST00000368115 Transcript synonymous_variant 405/1165 306/774 102/257 E gaA/gaG 1 1 FCER1A HGNC HGNC:3609 protein_coding YES CCDS1184.1 ENSP00000357097 P12319 UPI000002CFDB NM_002001.3 4/6 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF12,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 76 159304157 159304157 A G 1 0 0 0 0 0 0 0 1 5637 40 2 5 5 FCER1A 1 159304157 Silent SNP A C3N-01413_T 83381899 159304157 89652265 6 23160 FCRLB 0 . GRCh38 1 161727549 161727549 + Silent SNP C C T novel C3N-01413_T C3N-01413_N C C c.1168C>T p.= p.L390L ENST00000367948 8/8 294 211 83 184 184 0 strelka-varscan-mutect FCRLB,synonymous_variant,p.=,ENST00000367948,NM_001320241.1,NM_001002901.3;FCRLB,3_prime_UTR_variant,,ENST00000336830,NM_001288831.1;FCRLB,3_prime_UTR_variant,,ENST00000367944,NM_001288832.1;FCRLB,3_prime_UTR_variant,,ENST00000367946,NM_001288829.1;FCRLB,3_prime_UTR_variant,,ENST00000367945,NM_001288830.1;FCRLB,non_coding_transcript_exon_variant,,ENST00000495397,; T ENST00000367948 Transcript synonymous_variant 1383/1977 1168/1281 390/426 L Ctg/Ttg 1 1 FCRLB HGNC HGNC:26431 protein_coding YES CCDS30927.1 ENSP00000356925 Q6BAA4 UPI00003FF782 NM_001320241.1,NM_001002901.3 8/8 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 161727549 161727549 C T 1 0 0 0 0 0 0 0 1 5663 680 24 3 3 FCRLB 1 161727549 Silent SNP C C3N-01413_T 2423392 161727549 87228873 7 23161 MTIF2 0 . GRCh38 2 55236650 55236650 + Nonstop_Mutation SNP A A G novel C3N-01413_T C3N-01413_N A A c.2182T>C p.Ter728GlnextTer? p.*728Qext*? ENST00000263629 16/16 70 63 7 74 74 0 strelka-varscan MTIF2,stop_lost,p.Ter728GlnextTer?,ENST00000263629,NM_001321001.1,NM_001005369.1,NM_002453.2;MTIF2,stop_lost,p.Ter728GlnextTer?,ENST00000403721,NM_001321002.1;MTIF2,stop_lost,p.Ter728GlnextTer?,ENST00000394600,;CLHC1,upstream_gene_variant,,ENST00000401408,NM_152385.2;CLHC1,upstream_gene_variant,,ENST00000407122,;CLHC1,upstream_gene_variant,,ENST00000406076,NM_001135598.1;RPS27A,downstream_gene_variant,,ENST00000272317,NM_002954.5;MTIF2,downstream_gene_variant,,ENST00000418823,;RPS27A,downstream_gene_variant,,ENST00000404735,NM_001177413.1;RPS27A,downstream_gene_variant,,ENST00000402285,NM_001135592.2;CLHC1,upstream_gene_variant,,ENST00000451916,;RPS27A,downstream_gene_variant,,ENST00000449323,;CLHC1,upstream_gene_variant,,ENST00000494539,;CLHC1,upstream_gene_variant,,ENST00000487320,;CLHC1,upstream_gene_variant,,ENST00000463300,;CLHC1,upstream_gene_variant,,ENST00000464243,;CLHC1,upstream_gene_variant,,ENST00000466020,;CLHC1,upstream_gene_variant,,ENST00000428621,;RPS27A,downstream_gene_variant,,ENST00000495843,;RPS27A,downstream_gene_variant,,ENST00000468810,;RPS27A,downstream_gene_variant,,ENST00000463185,;RPS27A,downstream_gene_variant,,ENST00000478196,;RPS27A,downstream_gene_variant,,ENST00000471772,;RPS27A,downstream_gene_variant,,ENST00000494756,; G ENST00000263629 Transcript stop_lost 2498/2528 2182/2184 728/727 */Q Taa/Caa 1 -1 MTIF2 HGNC HGNC:7441 protein_coding YES CCDS1853.1 ENSP00000263629 P46199 UPI000013D42F NM_001321001.1,NM_001005369.1,NM_002453.2 16/16 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.71755 1 1 1 1 0 G 4 3 76 55236650 55236650 A G 1 0 0 0 0 0 0 0 0 9923 375 13 5 5 MTIF2 2 55236650 Nonstop_Mutation SNP A C3N-01413_T 55236650 186956879 8 23162 KANSL3 0 . GRCh38 2 96631375 96631375 + Missense_Mutation SNP A A G novel C3N-01413_T C3N-01413_N A A c.323T>C p.Ile108Thr p.I108T ENST00000431828 3/21 272 247 25 260 260 0 strelka-varscan KANSL3,missense_variant,p.Ile108Thr,ENST00000431828,NM_001115016.2;KANSL3,intron_variant,,ENST00000448075,;KANSL3,non_coding_transcript_exon_variant,,ENST00000487070,;KANSL3,non_coding_transcript_exon_variant,,ENST00000475820,;KANSL3,missense_variant,p.Ile108Thr,ENST00000420155,;KANSL3,missense_variant,p.Ile37Thr,ENST00000447759,;KANSL3,missense_variant,p.Ile108Thr,ENST00000597150,;KANSL3,missense_variant,p.Ile108Thr,ENST00000444759,;KANSL3,missense_variant,p.Ile108Thr,ENST00000451819,;KANSL3,missense_variant,p.Ile21Thr,ENST00000418735,;KANSL3,3_prime_UTR_variant,,ENST00000354204,;KANSL3,3_prime_UTR_variant,,ENST00000425656,;KANSL3,3_prime_UTR_variant,,ENST00000452268,;KANSL3,intron_variant,,ENST00000416138,; G ENST00000431828 Transcript missense_variant 400/5153 323/2637 108/878 I/T aTc/aCc 1 -1 KANSL3 HGNC HGNC:25473 protein_coding YES CCDS46361.1 ENSP00000396749 Q9P2N6 UPI0000207C82 NM_001115016.2 tolerated(0.38) 3/21 hmmpanther:PTHR13136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 76 96631375 96631375 A G 1 0 0 0 0 1 0 0 0 7892 333 12 5 5 KANSL3 2 96631375 Missense_Mutation SNP A C3N-01413_T 41394725 96631375 145562154 9 23163 MARCH7 0 . GRCh38 2 159762956 159762956 + Missense_Mutation SNP T T C novel C3N-01413_T C3N-01413_N T T c.1970T>C p.Met657Thr p.M657T ENST00000259050 8/10 187 170 17 205 205 0 strelka-varscan MARCH7,missense_variant,p.Met657Thr,ENST00000259050,NM_022826.3;MARCH7,missense_variant,p.Met601Thr,ENST00000539065,NM_001282806.1;MARCH7,missense_variant,p.Met657Thr,ENST00000409175,NM_001282805.1;MARCH7,missense_variant,p.Met619Thr,ENST00000409591,NM_001282807.1;MARCH7,missense_variant,p.Met90Thr,ENST00000420397,;MARCH7,non_coding_transcript_exon_variant,,ENST00000478396,; C ENST00000259050 Transcript missense_variant 2092/5922 1970/2115 657/704 M/T aTg/aCg 1 1 MARCH7 HGNC HGNC:17393 protein_coding YES CCDS2210.1 ENSP00000259050 Q9H992 UPI00000733EE NM_022826.3 deleterious(0) 8/10 hmmpanther:PTHR14471:SF1,hmmpanther:PTHR14471 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 159762956 159762956 T C 1 0 0 0 0 1 0 0 0 9231 1464 51 5 5 MARCH7 2 159762956 Missense_Mutation SNP T C3N-01413_T 63131581 159762956 82430573 10 23164 CHRNG 0 . GRCh38 2 232542497 232542497 + Missense_Mutation SNP T T A novel C3N-01413_T C3N-01413_N T T c.581T>A p.Phe194Tyr p.F194Y ENST00000389494 6/12 389 360 29 347 346 1 strelka-varscan-mutect CHRNG,missense_variant,p.Phe194Tyr,ENST00000389494,NM_005199.4;CHRNG,missense_variant,p.Phe142Tyr,ENST00000389492,;CHRNG,downstream_gene_variant,,ENST00000485094,; A ENST00000389494 Transcript missense_variant 602/2262 581/1554 194/517 F/Y tTc/tAc 1 1 CHRNG HGNC HGNC:1967 protein_coding YES CCDS33400.1 ENSP00000374145 P07510 UPI000022BE9E NM_005199.4 tolerated(1) 6/12 hmmpanther:PTHR18945:SF60,hmmpanther:PTHR18945,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 MODERATE 1 SNV 5 1 PASS rs1403722602 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 232542497 232542497 T A 1 0 0 0 0 1 0 0 0 3156 1783 62 4 4 CHRNG 2 232542497 Missense_Mutation SNP T C3N-01413_T 72779541 232542497 9651032 11 23165 ITIH1 0 . GRCh38 3 52784434 52784434 + Missense_Mutation SNP C C T novel C3N-01413_T C3N-01413_N C C c.1364C>T p.Ala455Val p.A455V ENST00000273283 11/22 181 156 25 139 138 1 strelka-varscan-mutect ITIH1,missense_variant,p.Ala455Val,ENST00000273283,NM_002215.3,NM_001166434.2;ITIH1,missense_variant,p.Ala167Val,ENST00000537050,NM_001166435.2,NM_001166436.2;ITIH1,missense_variant,p.Ala8Val,ENST00000428133,;ITIH1,upstream_gene_variant,,ENST00000405128,;ITIH1,non_coding_transcript_exon_variant,,ENST00000628722,;ITIH1,downstream_gene_variant,,ENST00000487686,;ITIH1,downstream_gene_variant,,ENST00000478667,;ITIH1,downstream_gene_variant,,ENST00000480409,;ITIH1,upstream_gene_variant,,ENST00000482836,;ITIH1,downstream_gene_variant,,ENST00000494603,;ITIH1,upstream_gene_variant,,ENST00000484844,; T ENST00000273283 Transcript missense_variant 1388/2911 1364/2736 455/911 A/V gCc/gTc 1 1 ITIH1 HGNC HGNC:6166 protein_coding YES CCDS2864.1 ENSP00000273283 P19827 UPI000012DA1C NM_002215.3,NM_001166434.2 deleterious(0.03) 11/22 PROSITE_profiles:PS50234,hmmpanther:PTHR10338:SF106,hmmpanther:PTHR10338,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 76 52784434 52784434 C T 1 0 0 0 0 1 0 0 0 7809 739 26 3 3 ITIH1 3 52784434 Missense_Mutation SNP C C3N-01413_T 52784434 145511125 12 23166 SLMAP 0 . GRCh38 3 57860792 57860792 + Missense_Mutation SNP G G C novel C3N-01413_T C3N-01413_N G G c.781G>C p.Val261Leu p.V261L ENST00000428312 8/22 204 175 29 236 236 0 strelka-varscan-mutect SLMAP,missense_variant,p.Val261Leu,ENST00000383718,;SLMAP,missense_variant,p.Val261Leu,ENST00000295951,;SLMAP,missense_variant,p.Val261Leu,ENST00000295952,NM_007159.3;SLMAP,missense_variant,p.Val261Leu,ENST00000428312,NM_001304420.1;SLMAP,missense_variant,p.Val261Leu,ENST00000449503,NM_001304421.1;SLMAP,upstream_gene_variant,,ENST00000416658,;SLMAP,upstream_gene_variant,,ENST00000465203,;SLMAP,upstream_gene_variant,,ENST00000475055,;SLMAP,non_coding_transcript_exon_variant,,ENST00000467901,; C ENST00000428312 Transcript missense_variant 875/4132 781/2487 261/828 V/L Gtt/Ctt 1 1 SLMAP HGNC HGNC:16643 protein_coding YES CCDS77757.1 ENSP00000398661 Q14BN4 UPI00005796CD NM_001304420.1 tolerated(0.15) 8/22 hmmpanther:PTHR15715,hmmpanther:PTHR15715:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 57860792 57860792 G C 1 0 0 0 0 1 0 0 0 15040 1261 44 4 4 SLMAP 3 57860792 Missense_Mutation SNP G C3N-01413_T 5076358 57860792 140434767 13 23167 DCBLD2 0 . GRCh38 3 98901239 98901239 + Missense_Mutation SNP G G A rs190637453 C3N-01413_T C3N-01413_N G G c.88C>T p.Leu30Phe p.L30F ENST00000326840 1/16 171 150 21 143 143 0 strelka-varscan-mutect DCBLD2,missense_variant,p.Leu30Phe,ENST00000326840,NM_080927.3;DCBLD2,missense_variant,p.Leu30Phe,ENST00000326857,;DCBLD2,upstream_gene_variant,,ENST00000449482,;CTD-2021J15.1,upstream_gene_variant,,ENST00000474798,;DCBLD2,upstream_gene_variant,,ENST00000469648,; A ENST00000326840 Transcript missense_variant 451/6122 88/2328 30/775 L/F Ctc/Ttc rs190637453 1 -1 DCBLD2 HGNC HGNC:24627 protein_coding YES CCDS46878.1 ENSP00000321573 Q96PD2 UPI0000072ABB NM_080927.3 deleterious_low_confidence(0) 1/16 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs190637453 . 0 207 0 0 0 0 0 2 -4.326107 0 0 1 0 0 A 3 1 76 98901239 98901239 G A 1 0 0 0 0 1 0 0 0 4083 971 34 3 3 DCBLD2 3 98901239 Missense_Mutation SNP G C3N-01413_T 41040447 98901239 99394320 14 23168 ATR 0 . GRCh38 3 142556086 142556086 + Missense_Mutation SNP A A C novel C3N-01413_T C3N-01413_N A A c.2132T>G p.Leu711Arg p.L711R ENST00000350721 10/47 185 171 14 186 185 1 strelka-varscan-mutect ATR,missense_variant,p.Leu711Arg,ENST00000350721,NM_001184.3;ATR,downstream_gene_variant,,ENST00000515149,;ATR,non_coding_transcript_exon_variant,,ENST00000515863,;ATR,downstream_gene_variant,,ENST00000507148,; C ENST00000350721 Transcript missense_variant 2254/8249 2132/7935 711/2644 L/R cTt/cGt 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 deleterious(0.01) 10/47 Gene3D:1.25.10.10,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF69,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 142556086 142556086 A C 1 0 0 0 0 1 0 0 0 1356 72 3 5 5 ATR 3 142556086 Missense_Mutation SNP A C3N-01413_T 43654847 142556086 55739473 15 23169 SHOX2 0 . GRCh38 3 158105829 158105829 + Nonsense_Mutation SNP C C A novel C3N-01413_T C3N-01413_N C C c.196G>T p.Gly66Ter p.G66* ENST00000389589 1/6 131 124 7 103 103 0 varscan-mutect SHOX2,stop_gained,p.Gly66Ter,ENST00000441443,NM_006884.3;SHOX2,stop_gained,p.Gly66Ter,ENST00000389589,NM_003030.4;SHOX2,stop_gained,p.Gly66Ter,ENST00000483851,NM_001163678.1;RSRC1,upstream_gene_variant,,ENST00000464171,;RSRC1,upstream_gene_variant,,ENST00000611884,NM_001271838.1;RSRC1,upstream_gene_variant,,ENST00000295930,NM_016625.3;SHOX2,upstream_gene_variant,,ENST00000425436,;RSRC1,upstream_gene_variant,,ENST00000312179,NM_001271834.1;RSRC1,upstream_gene_variant,,ENST00000480820,;RSRC1,upstream_gene_variant,,ENST00000475278,;RSRC1,upstream_gene_variant,,ENST00000476899,;RSRC1,upstream_gene_variant,,ENST00000471994,;RSRC1,upstream_gene_variant,,ENST00000494002,;SHOX2,upstream_gene_variant,,ENST00000554685,;RSRC1,upstream_gene_variant,,ENST00000471911,;RSRC1,upstream_gene_variant,,ENST00000468344,;SHOX2,upstream_gene_variant,,ENST00000490689,;RSRC1,upstream_gene_variant,,ENST00000480119,; A ENST00000389589 Transcript stop_gained 332/2072 196/1068 66/355 G/* Gga/Tga 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 1/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 76 158105829 158105829 C A 1 0 0 0 0 0 1 0 0 14552 690 24 2 2 SHOX2 3 158105829 Nonsense_Mutation SNP C C3N-01413_T 15549743 158105829 40189730 16 23170 SLC34A2 0 . GRCh38 4 25667891 25667891 + Frame_Shift_Del DEL C C - rs552759498 C3N-01413_T C3N-01413_N C C c.535delC p.Arg179GlyfsTer66 p.R179Gfs*66 ENST00000382051 6/13 369 338 31 386 386 0 sindel-varindel-pindel SLC34A2,frameshift_variant,p.Arg179GlyfsTer66,ENST00000382051,NM_006424.2;SLC34A2,frameshift_variant,p.Arg178GlyfsTer66,ENST00000503434,NM_001177999.1;SLC34A2,frameshift_variant,p.Arg178GlyfsTer66,ENST00000504570,NM_001177998.1;SLC34A2,downstream_gene_variant,,ENST00000507530,;SLC34A2,downstream_gene_variant,,ENST00000513204,;SLC34A2,non_coding_transcript_exon_variant,,ENST00000510033,; - ENST00000382051 Transcript frameshift_variant 585/4122 535/2073 179/690 R/X Cgg/gg rs552759498,COSM1226285 1 1 SLC34A2 HGNC HGNC:11020 protein_coding YES CCDS3435.1 ENSP00000371483 O95436 UPI000013DF24 NM_006424.2 6/13 hmmpanther:PTHR10010,hmmpanther:PTHR10010:SF23,Pfam_domain:PF02690,TIGRFAM_domain:TIGR01013 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 76 25667891 25667891 C - 1 0 1 0 1 0 0 0 0 14838 875 31 0 0 SLC34A2 4 25667891 Frame_Shift_Del DEL C C3N-01413_T 25667891 164546664 17 23171 CWH43 0 . GRCh38 4 49017282 49017282 + Missense_Mutation SNP G G T rs765646676 C3N-01413_T C3N-01413_N G G c.1220G>T p.Gly407Val p.G407V ENST00000226432 9/16 174 159 15 180 179 1 strelka-varscan-mutect CWH43,missense_variant,p.Gly407Val,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Gly380Val,ENST00000513409,NM_001286791.1;CWH43,3_prime_UTR_variant,,ENST00000514053,;CWH43,non_coding_transcript_exon_variant,,ENST00000506221,;TPI1P4,upstream_gene_variant,,ENST00000513630,; T ENST00000226432 Transcript missense_variant 1403/2472 1220/2100 407/699 G/V gGa/gTa rs765646676 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.01) 9/16 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS rs765646676 . 0 206 0 4 0 0 0 0 -19.70902 0.999754 1 1 1 0 T 3 4 76 49017282 49017282 G T 1 0 0 0 0 1 0 0 0 3883 1174 41 2 2 CWH43 4 49017282 Missense_Mutation SNP G C3N-01413_T 23349391 49017282 141197273 18 23172 NPY1R 0 . GRCh38 4 163326127 163326127 + Missense_Mutation SNP A A C novel C3N-01413_T C3N-01413_N A A c.428T>G p.Ile143Ser p.I143S ENST00000296533 2/3 326 298 28 377 377 0 strelka-varscan-mutect NPY1R,missense_variant,p.Ile143Ser,ENST00000296533,NM_000909.5;NPY1R,5_prime_UTR_variant,,ENST00000512819,;NPY1R,intron_variant,,ENST00000509586,;NPY1R,intron_variant,,ENST00000504391,;NPY1R,downstream_gene_variant,,ENST00000515701,;NPY1R,downstream_gene_variant,,ENST00000511901,;NPY1R,downstream_gene_variant,,ENST00000504790,; C ENST00000296533 Transcript missense_variant 960/3029 428/1155 143/384 I/S aTc/aGc 1 -1 NPY1R HGNC HGNC:7956 protein_coding YES CCDS34089.1 ENSP00000354652 P25929 UPI000002D509 NM_000909.5 deleterious(0) 2/3 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF222,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 163326127 163326127 A C 1 0 0 0 0 1 0 0 0 10663 333 12 5 5 NPY1R 4 163326127 Missense_Mutation SNP A C3N-01413_T 114308845 163326127 26888428 19 23173 SLC1A3 0 . GRCh38 5 36683939 36683939 + Silent SNP G G T novel C3N-01413_T C3N-01413_N G G c.1365G>T p.= p.L455L ENST00000265113 9/10 465 438 27 350 350 0 strelka-varscan-mutect SLC1A3,synonymous_variant,p.=,ENST00000265113,NM_004172.4;SLC1A3,synonymous_variant,p.=,ENST00000613445,NM_001289939.1;SLC1A3,synonymous_variant,p.=,ENST00000612708,NM_001289940.1;SLC1A3,intron_variant,,ENST00000381918,NM_001166695.2;CTD-2353F22.1,intron_variant,,ENST00000510740,;SLC1A3,non_coding_transcript_exon_variant,,ENST00000506178,; T ENST00000265113 Transcript synonymous_variant 1841/4170 1365/1629 455/542 L ctG/ctT 1 1 SLC1A3 HGNC HGNC:10941 protein_coding YES CCDS3919.1 ENSP00000265113 P43003 A0A024R050 UPI0000129B0F NM_004172.4 9/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF24,Gene3D:2nwlC00,Pfam_domain:PF00375,Superfamily_domains:0053221,Prints_domain:PR00173 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 36683939 36683939 G T 1 0 0 0 0 0 0 0 1 14699 1277 45 2 2 SLC1A3 5 36683939 Silent SNP G C3N-01413_T 36683939 144854320 20 23174 TNFRSF21 0 . GRCh38 6 47286549 47286549 + Nonsense_Mutation SNP G G T rs566872069 C3N-01413_T C3N-01413_N G G c.143C>A p.Ser48Ter p.S48* ENST00000296861 2/6 101 85 16 87 87 0 strelka-varscan-mutect TNFRSF21,stop_gained,p.Ser48Ter,ENST00000296861,NM_014452.4; T ENST00000296861 Transcript stop_gained 537/3595 143/1968 48/655 S/* tCg/tAg rs566872069 1 -1 TNFRSF21 HGNC HGNC:13469 protein_coding YES CCDS4921.1 ENSP00000296861 O75509 A0A024RD71 UPI000004680F NM_014452.4 2/6 hmmpanther:PTHR23097:SF127,hmmpanther:PTHR23097 HIGH 1 SNV 1 1 PASS rs566872069 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 76 47286549 47286549 G T 1 0 0 0 0 0 1 0 0 16769 1059 37 1 1 TNFRSF21 6 47286549 Nonsense_Mutation SNP G C3N-01413_T 47286549 123519430 21 23175 DST 0 . GRCh38 6 56592199 56592199 + Nonsense_Mutation SNP G G A novel C3N-01413_T C3N-01413_N G G c.6115C>T p.Gln2039Ter p.Q2039* ENST00000312431 41/95 489 450 39 396 396 0 strelka-varscan DST,stop_gained,p.Gln4085Ter,ENST00000361203,;DST,stop_gained,p.Gln1999Ter,ENST00000421834,NM_183380.3;DST,stop_gained,p.Gln2039Ter,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,stop_gained,p.Gln1999Ter,ENST00000370788,;DST,stop_gained,p.Gln1673Ter,ENST00000244364,NM_015548.4;DST,stop_gained,p.Gln333Ter,ENST00000518398,; A ENST00000312431 Transcript stop_gained 6241/17756 6115/16614 2039/5537 Q/* Caa/Taa 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 41/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 76 56592199 56592199 G A 1 0 0 0 0 0 1 0 0 4604 1328 46 3 3 DST 6 56592199 Nonsense_Mutation SNP G C3N-01413_T 9305650 56592199 114213780 22 23176 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-01413_T C3N-01413_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 472 344 128 498 498 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 76 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-01413_T 55174772 104171201 23 23177 NOBOX 0 . GRCh38 7 144401231 144401231 + Missense_Mutation SNP G G A rs750862438 C3N-01413_T C3N-01413_N G G c.659C>T p.Pro220Leu p.P220L ENST00000467773 4/10 237 225 12 191 191 0 strelka-mutect NOBOX,missense_variant,p.Pro220Leu,ENST00000467773,NM_001080413.3;NOBOX,missense_variant,p.Pro220Leu,ENST00000483238,; A ENST00000467773 Transcript missense_variant 659/2076 659/2076 220/691 P/L cCg/cTg rs750862438,COSM5062274,COSM5062275 1 -1 NOBOX HGNC HGNC:22448 protein_coding YES ENSP00000419457 O60393 UPI00019B220B NM_001080413.3 deleterious(0.03) 4/10 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs750862438 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 144401231 144401231 G A 1 0 0 0 0 1 0 0 0 10554 1116 39 1 1 NOBOX 7 144401231 Missense_Mutation SNP G C3N-01413_T 89226459 144401231 14944742 24 23178 SMARCA2 0 . GRCh38 9 2047332 2047332 + Silent SNP C C T novel C3N-01413_T C3N-01413_N C C c.894C>T p.= p.P298P ENST00000382203 5/34 52 46 6 18 18 0 strelka-mutect SMARCA2,synonymous_variant,p.=,ENST00000382203,NM_001289396.1;SMARCA2,synonymous_variant,p.=,ENST00000357248,NM_139045.3;SMARCA2,synonymous_variant,p.=,ENST00000349721,NM_003070.4;SMARCA2,synonymous_variant,p.=,ENST00000382194,;SMARCA2,synonymous_variant,p.=,ENST00000450198,NM_001289397.1;SMARCA2,synonymous_variant,p.=,ENST00000635226,;SMARCA2,downstream_gene_variant,,ENST00000637806,;SMARCA2,downstream_gene_variant,,ENST00000636559,;SMARCA2,downstream_gene_variant,,ENST00000637103,;SMARCA2,downstream_gene_variant,,ENST00000636903,;RP11-264I13.2,upstream_gene_variant,,ENST00000426860,;SMARCA2,synonymous_variant,p.=,ENST00000634760,; T ENST00000382203 Transcript synonymous_variant 1103/5867 894/4773 298/1590 P ccC/ccT 1 1 SMARCA2 HGNC HGNC:11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 UPI00001AE8EB NM_001289396.1 5/34 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -14.30668 0.9999992 1 1 1 0 T 2 4 76 2047332 2047332 C T 1 0 0 0 0 0 0 0 1 15062 639 23 1 1 SMARCA2 9 2047332 Silent SNP C C3N-01413_T 2047332 136347385 25 23179 KIF24 0 . GRCh38 9 34306372 34306372 + Silent SNP G G A novel C3N-01413_T C3N-01413_N G G c.693C>T p.= p.R231R ENST00000402558 2/12 143 129 14 153 152 1 strelka-varscan-mutect KIF24,synonymous_variant,p.=,ENST00000402558,NM_194313.2;KIF24,synonymous_variant,p.=,ENST00000379174,; A ENST00000402558 Transcript synonymous_variant 718/6131 693/4107 231/1368 R cgC/cgT 1 -1 KIF24 HGNC HGNC:19916 protein_coding YES CCDS6551.2 ENSP00000384433 Q5T7B8 UPI00004F9D23 NM_194313.2 2/12 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF410,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 76 34306372 34306372 G A 1 0 0 0 0 0 0 0 1 8157 1190 42 3 3 KIF24 9 34306372 Silent SNP G C3N-01413_T 32259040 34306372 104088345 26 23180 CYP2C8 0 . GRCh38 10 95038923 95038923 + Missense_Mutation SNP C C T novel C3N-01413_T C3N-01413_N C C c.1265G>A p.Ser422Asn p.S422N ENST00000371270 8/9 299 262 37 319 319 0 strelka-mutect CYP2C8,missense_variant,p.Ser352Asn,ENST00000539050,NM_001198855.1;CYP2C8,missense_variant,p.Ser352Asn,ENST00000623108,NM_001198853.1;CYP2C8,missense_variant,p.Ser422Asn,ENST00000371270,NM_000770.3;CYP2C8,missense_variant,p.Ser320Asn,ENST00000535898,NM_001198854.1;CYP2C8,downstream_gene_variant,,ENST00000628935,;CYP2C8,3_prime_UTR_variant,,ENST00000490994,;CYP2C8,3_prime_UTR_variant,,ENST00000527420,;CYP2C8,3_prime_UTR_variant,,ENST00000525991,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000527953,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000526814,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000533320,;CYP2C8,non_coding_transcript_exon_variant,,ENST00000531714,;CYP2C8,downstream_gene_variant,,ENST00000479946,; T ENST00000371270 Transcript missense_variant 1360/1923 1265/1473 422/490 S/N aGt/aAt 1 -1 CYP2C8 HGNC HGNC:2622 protein_coding YES CCDS7438.1 ENSP00000360317 P10632 UPI0000128256 NM_000770.3 tolerated(0.14) 8/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF187,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 76 95038923 95038923 C T 1 0 0 0 0 1 0 0 0 3970 565 20 3 3 CYP2C8 10 95038923 Missense_Mutation SNP C C3N-01413_T 95038923 38758499 27 23181 CCDC186 0 . GRCh38 10 114157577 114157577 + Nonsense_Mutation SNP G G A novel C3N-01413_T C3N-01413_N G G c.736C>T p.Gln246Ter p.Q246* ENST00000369287 3/16 183 173 10 227 227 0 strelka-mutect CCDC186,stop_gained,p.Gln246Ter,ENST00000369287,NM_001321829.1,NM_018017.2;CCDC186,downstream_gene_variant,,ENST00000369285,NM_153249.1;CCDC186,downstream_gene_variant,,ENST00000369286,; A ENST00000369287 Transcript stop_gained 1003/7245 736/2697 246/898 Q/* Cag/Tag 1 -1 CCDC186 HGNC HGNC:24349 protein_coding YES CCDS7587.1 ENSP00000358293 Q7Z3E2 UPI00001D3EF5 NM_001321829.1,NM_018017.2 3/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18911 HIGH 1 SNV 1 1 PASS rs1467549823 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 76 114157577 114157577 G A 1 0 0 0 0 0 1 0 0 2502 1328 46 3 3 CCDC186 10 114157577 Nonsense_Mutation SNP G C3N-01413_T 19118654 114157577 19639845 28 23182 TACC2 0 . GRCh38 10 122143587 122143588 + Frame_Shift_Ins INS - - G novel C3N-01413_T C3N-01413_N - - c.5716dupG p.Ala1906GlyfsTer22 p.A1906Gfs*22 ENST00000369005 7/23 131 105 26 123 123 0 sindel-varindel-pindel TACC2,frameshift_variant,p.Ala1906GlyfsTer22,ENST00000369005,NM_206862.3;TACC2,frameshift_variant,p.Ala1906GlyfsTer22,ENST00000334433,;TACC2,intron_variant,,ENST00000515273,NM_001291877.1;TACC2,intron_variant,,ENST00000453444,;TACC2,intron_variant,,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,intron_variant,,ENST00000369000,;TACC2,intron_variant,,ENST00000369001,NM_001291879.1;TACC2,non_coding_transcript_exon_variant,,ENST00000493951,;TACC2,intron_variant,,ENST00000492237,; G ENST00000369005 Transcript frameshift_variant 6055-6056/9673 5715-5716/8847 1905-1906/2948 -/X -/G 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 7/23 Low_complexity_(Seg):seg,hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 HIGH 1 insertion 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 76 122143587 122143587 - G 1 0 1 1 0 0 0 0 0 15898 1567 55 0 0 TACC2 10 122143587 Frame_Shift_Ins INS - C3N-01413_T 7986010 122143587 11653835 29 23183 UCP2 0 . GRCh38 11 73978074 73978074 + Missense_Mutation SNP G G C rs562888818 C3N-01413_T C3N-01413_N G G c.149C>G p.Pro50Arg p.P50R ENST00000310473 4/8 273 256 17 253 252 1 strelka-varscan-mutect UCP2,missense_variant,p.Pro50Arg,ENST00000310473,NM_003355.2;UCP2,missense_variant,p.Pro50Arg,ENST00000536983,;UCP2,missense_variant,p.Pro23Arg,ENST00000544615,;UCP2,downstream_gene_variant,,ENST00000539764,;UCP2,upstream_gene_variant,,ENST00000545212,;UCP2,downstream_gene_variant,,ENST00000542615,;UCP2,downstream_gene_variant,,ENST00000541027,;UCP2,downstream_gene_variant,,ENST00000539330,;UCP2,downstream_gene_variant,,ENST00000543714,;UCP2,upstream_gene_variant,,ENST00000545562,; C ENST00000310473 Transcript missense_variant 992/2113 149/930 50/309 P/R cCa/cGa rs562888818 1 -1 UCP2 HGNC HGNC:12518 protein_coding YES CCDS8228.1 ENSP00000312029 P55851 A0A024R5N5 UPI000003627C NM_003355.2 tolerated(0.1) 4/8 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,Prints_domain:PR00784,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF167 MODERATE 1 SNV 1 1 PASS rs562888818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 73978074 73978074 G C 1 0 0 0 0 1 0 0 0 17455 1348 47 4 4 UCP2 11 73978074 Missense_Mutation SNP G C3N-01413_T 73978074 61108548 30 23184 PANX3 0 . GRCh38 11 124611647 124611647 + Missense_Mutation SNP G G A C3N-01413_T C3N-01413_N G G c.91G>A p.Glu31Lys p.E31K ENST00000284288 1/4 214 200 14 164 164 0 strelka-varscan-mutect PANX3,missense_variant,p.Glu31Lys,ENST00000284288,NM_052959.2; A ENST00000284288 Transcript missense_variant 158/1667 91/1179 31/392 E/K Gaa/Aaa COSM3444840 1 1 PANX3 HGNC HGNC:20573 protein_coding YES CCDS8447.1 ENSP00000284288 Q96QZ0 UPI0000131264 NM_052959.2 deleterious(0) 1/4 PROSITE_profiles:PS51013,hmmpanther:PTHR15759,hmmpanther:PTHR15759:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 124611647 124611647 G A 1 0 0 0 0 1 0 0 0 11503 1175 41 3 3 PANX3 11 124611647 Missense_Mutation SNP G C3N-01413_T 50633573 124611647 10474975 31 23185 TMEM132D 0 . GRCh38 12 129699891 129699891 + Missense_Mutation SNP G G A novel C3N-01413_T C3N-01413_N G G c.887C>T p.Pro296Leu p.P296L ENST00000422113 2/9 273 252 21 277 277 0 strelka-varscan-mutect TMEM132D,missense_variant,p.Pro296Leu,ENST00000422113,NM_133448.2;RP11-174M13.2,upstream_gene_variant,,ENST00000544036,; A ENST00000422113 Transcript missense_variant 1214/5776 887/3300 296/1099 P/L cCa/cTa 1 -1 TMEM132D HGNC HGNC:29411 protein_coding YES CCDS9266.1 ENSP00000408581 Q14C87 UPI000023759C NM_133448.2 tolerated(0.2) 2/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 129699891 129699891 G A 1 0 0 0 0 1 0 0 0 16492 1348 47 3 3 TMEM132D 12 129699891 Missense_Mutation SNP G C3N-01413_T 129699891 3575418 32 23186 MGA 0 . GRCh38 15 41762210 41762210 + Missense_Mutation SNP A A C novel C3N-01413_T C3N-01413_N A A c.7592A>C p.Lys2531Thr p.K2531T ENST00000219905 22/24 326 282 44 341 341 0 strelka-varscan-mutect MGA,missense_variant,p.Lys2322Thr,ENST00000566586,;MGA,missense_variant,p.Lys2531Thr,ENST00000219905,NM_001164273.1;MGA,missense_variant,p.Lys2531Thr,ENST00000570161,;MGA,missense_variant,p.Lys2322Thr,ENST00000545763,NM_001080541.2;MGA,downstream_gene_variant,,ENST00000564190,;MGA,non_coding_transcript_exon_variant,,ENST00000568255,; C ENST00000219905 Transcript missense_variant 7773/12042 7592/9198 2531/3065 K/T aAg/aCg 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 deleterious(0) 22/24 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 76 41762210 41762210 A C 1 0 0 0 0 1 0 0 0 9498 72 3 5 5 MGA 15 41762210 Missense_Mutation SNP A C3N-01413_T 41762210 60228979 33 23187 MYO5C 0 . GRCh38 15 52224946 52224946 + Missense_Mutation SNP T T A novel C3N-01413_T C3N-01413_N T T c.3401A>T p.Asp1134Val p.D1134V ENST00000261839 28/41 270 253 17 342 341 1 strelka-varscan-mutect MYO5C,missense_variant,p.Asp1134Val,ENST00000261839,NM_018728.3;MYO5C,3_prime_UTR_variant,,ENST00000560809,;MYO5C,downstream_gene_variant,,ENST00000558902,; A ENST00000261839 Transcript missense_variant 3563/6971 3401/5229 1134/1742 D/V gAt/gTt 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 tolerated(0.08) 28/41 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 52224946 52224946 T A 1 0 0 0 0 1 0 0 0 10081 1435 50 4 4 MYO5C 15 52224946 Missense_Mutation SNP T C3N-01413_T 10462736 52224946 49766243 34 23188 IGDCC4 0 . GRCh38 15 65386002 65386002 + Silent SNP G G A novel C3N-01413_T C3N-01413_N G G c.3009C>T p.= p.S1003S ENST00000352385 18/20 78 71 7 97 97 0 strelka-varscan-mutect IGDCC4,synonymous_variant,p.=,ENST00000352385,NM_020962.2;IGDCC4,upstream_gene_variant,,ENST00000558048,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000560319,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000561309,; A ENST00000352385 Transcript synonymous_variant 3219/6508 3009/3753 1003/1250 S tcC/tcT 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 18/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -15.15502 0.9999998 1 1 1 0 A 2 1 76 65386002 65386002 G A 1 0 0 0 0 0 0 0 1 7475 1335 47 3 3 IGDCC4 15 65386002 Silent SNP G C3N-01413_T 13161056 65386002 36605187 35 23189 GPR139 0 . GRCh38 16 20031900 20031900 + Silent SNP C C T rs758294318 C3N-01413_T C3N-01413_N C C c.897G>A p.= p.T299T ENST00000570682 2/2 405 376 29 354 354 0 strelka-varscan-mutect GPR139,synonymous_variant,p.=,ENST00000570682,NM_001002911.2;GPR139,3_prime_UTR_variant,,ENST00000326571,; T ENST00000570682 Transcript synonymous_variant 1198/1613 897/1062 299/353 T acG/acA rs758294318,COSM471421,COSM5251403 1 -1 GPR139 HGNC HGNC:19995 protein_coding YES CCDS32398.1 ENSP00000458791 Q6DWJ6 A0A142CHG1 UPI000004C566 NM_001002911.2 2/2 hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF49,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs758294318 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 20031900 20031900 C T 1 0 0 0 0 0 0 0 1 6534 755 27 1 1 GPR139 16 20031900 Silent SNP C C3N-01413_T 20031900 70306445 36 23190 RP11-566K11.2 0 . GRCh38 16 89919426 89919426 + Silent SNP C C T rs373707533 C3N-01413_T C3N-01413_N C C c.168C>T p.= p.N56N ENST00000555147 1/1 294 276 18 246 246 0 strelka-varscan-mutect MC1R,synonymous_variant,p.=,ENST00000555427,;MC1R,synonymous_variant,p.=,ENST00000555147,NM_002386.3;RP11-566K11.2,synonymous_variant,p.=,ENST00000556922,;TUBB3,upstream_gene_variant,,ENST00000554444,NM_001197181.1;TUBB3,upstream_gene_variant,,ENST00000315491,NM_006086.3;TUBB3,upstream_gene_variant,,ENST00000554336,;TUBB3,upstream_gene_variant,,ENST00000555810,;TUBB3,upstream_gene_variant,,ENST00000553967,;TUBB3,upstream_gene_variant,,ENST00000555576,;TUBB3,upstream_gene_variant,,ENST00000625617,;TUBB3,upstream_gene_variant,,ENST00000556565,;RP11-566K11.4,downstream_gene_variant,,ENST00000554623,;TUBB3,upstream_gene_variant,,ENST00000554116,;MC1R,downstream_gene_variant,,ENST00000539976,;TUBB3,upstream_gene_variant,,ENST00000555609,;TUBB3,upstream_gene_variant,,ENST00000556536,;TUBB3,upstream_gene_variant,,ENST00000557262,;TUBB3,upstream_gene_variant,,ENST00000557490,;TUBB3,upstream_gene_variant,,ENST00000554927,;RP11-566K11.7,downstream_gene_variant,,ENST00000570217,;TUBB3,upstream_gene_variant,,ENST00000553656,; T ENST00000555147 Transcript synonymous_variant 1548/3099 168/954 56/317 N aaC/aaT rs373707533,COSM2923832 1 1 MC1R HGNC HGNC:6929 protein_coding YES CCDS56011.1 ENSP00000451605 Q01726 Q1JUL4 UPI00000622C3 NM_002386.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF2,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 LOW SNV 0,1 1 PASS rs373707533 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 89919426 89919426 C T 1 0 0 0 0 0 0 0 1 13753 535 19 1 1 RP11-566K11.2 16 89919426 Silent SNP C C3N-01413_T 69887526 89919426 418919 37 23191 TP53 0 . GRCh38 17 7674963 7674963 + Missense_Mutation SNP G G T C3N-01413_T C3N-01413_N G G c.568C>A p.Pro190Thr p.P190T ENST00000269305 6/11 450 397 53 454 452 2 strelka-varscan-mutect TP53,missense_variant,p.Pro190Thr,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Pro190Thr,ENST00000420246,;TP53,missense_variant,p.Pro151Thr,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Pro151Thr,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Pro190Thr,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Pro151Thr,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Pro190Thr,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Pro151Thr,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Pro190Thr,ENST00000445888,;TP53,missense_variant,p.Pro151Thr,ENST00000619485,;TP53,missense_variant,p.Pro58Thr,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Pro31Thr,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Pro58Thr,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Pro31Thr,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Pro58Thr,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Pro31Thr,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Pro190Thr,ENST00000359597,;TP53,missense_variant,p.Pro179Thr,ENST00000615910,;TP53,missense_variant,p.Pro190Thr,ENST00000413465,;TP53,missense_variant,p.Pro58Thr,ENST00000509690,;TP53,missense_variant,p.Pro97Thr,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Pro151Thr,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 758/2579 568/1182 190/393 P/T Cct/Act TP53_g.12637C>A,TP53_g.12637C>T,TP53_g.12637del,TP53_g.12637C>G,COSM1736075,COSM1736076,COSM1736077,COSM1736078,COSM1736079,COSM44426,COSM44438,COSM44682,COSM44936,COSM5610913 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.02) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1,1,1 1 PASS rs876660254 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 76 7674963 7674963 G T 1 0 0 0 0 1 0 0 0 16859 1232 43 2 2 TP53 17 7674963 Missense_Mutation SNP G C3N-01413_T 7674963 75582478 38 23192 SHMT1 0 . GRCh38 17 18353776 18353776 + Silent SNP A A T novel C3N-01413_T C3N-01413_N A A c.138T>A p.= p.V46V ENST00000316694 3/12 475 409 66 441 441 0 strelka-varscan-mutect SHMT1,synonymous_variant,p.=,ENST00000316694,NM_004169.4;SHMT1,synonymous_variant,p.=,ENST00000354098,NM_148918.2;SHMT1,synonymous_variant,p.=,ENST00000582653,;SHMT1,5_prime_UTR_variant,,ENST00000352886,NM_001281786.1;SHMT1,downstream_gene_variant,,ENST00000583780,;SHMT1,synonymous_variant,p.=,ENST00000580002,;SHMT1,non_coding_transcript_exon_variant,,ENST00000579558,;SHMT1,non_coding_transcript_exon_variant,,ENST00000395682,; T ENST00000316694 Transcript synonymous_variant 273/2464 138/1452 46/483 V gtT/gtA 1 -1 SHMT1 HGNC HGNC:10850 protein_coding YES CCDS11196.1 ENSP00000318868 P34896 UPI0000001C71 NM_004169.4 3/12 HAMAP:MF_00051,hmmpanther:PTHR11680:SF14,hmmpanther:PTHR11680,Pfam_domain:PF00464,PIRSF_domain:PIRSF000412,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 76 18353776 18353776 A T 1 0 0 0 0 0 0 0 1 14548 117 5 4 4 SHMT1 17 18353776 Silent SNP A C3N-01413_T 10678813 18353776 64903665 39 23193 KRTAP4-4 0 . GRCh38 17 41160367 41160367 + Missense_Mutation SNP G G T novel C3N-01413_T C3N-01413_N G G c.325C>A p.Gln109Lys p.Q109K ENST00000390661 1/1 538 479 59 434 430 4 strelka-varscan-mutect KRTAP4-4,missense_variant,p.Gln109Lys,ENST00000390661,NM_032524.1; T ENST00000390661 Transcript missense_variant 365/1081 325/501 109/166 Q/K Cag/Aag 1 -1 KRTAP4-4 HGNC HGNC:16928 protein_coding YES CCDS11383.1 ENSP00000375076 Q9BYR3 UPI000006DEC1 NM_032524.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF57,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 76 41160367 41160367 G T 1 0 0 0 0 1 0 0 0 8447 1357 47 2 2 KRTAP4-4 17 41160367 Missense_Mutation SNP G C3N-01413_T 22806591 41160367 42097074 40 23194 RBBP8 0 . GRCh38 18 22949639 22949639 + Silent SNP A A G novel C3N-01413_T C3N-01413_N A A c.174A>G p.= p.E58E ENST00000399722 4/19 279 243 36 312 312 0 strelka-varscan-mutect RBBP8,synonymous_variant,p.=,ENST00000399722,NM_203291.1;RBBP8,synonymous_variant,p.=,ENST00000327155,NM_002894.2;RBBP8,synonymous_variant,p.=,ENST00000399725,NM_203292.1;RBBP8,synonymous_variant,p.=,ENST00000360790,;RBBP8,synonymous_variant,p.=,ENST00000399721,;RBBP8,synonymous_variant,p.=,ENST00000582354,;RBBP8,synonymous_variant,p.=,ENST00000581819,;RBBP8,synonymous_variant,p.=,ENST00000579124,;RBBP8,non_coding_transcript_exon_variant,,ENST00000580892,; G ENST00000399722 Transcript synonymous_variant 525/3293 174/2694 58/897 E gaA/gaG 1 1 RBBP8 HGNC HGNC:9891 protein_coding YES CCDS11875.1 ENSP00000382628 Q99708 A0A024RC34 UPI000013D1A9 NM_203291.1 4/19 hmmpanther:PTHR15107:SF4,hmmpanther:PTHR15107,Pfam_domain:PF10482 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 76 22949639 22949639 A G 1 0 0 0 0 0 0 0 1 13266 98 4 5 5 RBBP8 18 22949639 Silent SNP A C3N-01413_T 22949639 57423646 41 23195 MAPK4 0 . GRCh38 18 50715204 50715204 + Silent SNP G G A rs550266883 C3N-01413_T C3N-01413_N G G c.672G>A p.= p.T224T ENST00000400384 3/6 138 124 14 154 154 0 strelka-varscan-mutect MAPK4,synonymous_variant,p.=,ENST00000400384,NM_002747.3;MAPK4,synonymous_variant,p.=,ENST00000592595,NM_001292040.1;MAPK4,synonymous_variant,p.=,ENST00000540640,NM_001292039.1; A ENST00000400384 Transcript synonymous_variant 1708/4770 672/1764 224/587 T acG/acA rs550266883,COSM1257316 1 1 MAPK4 HGNC HGNC:6878 protein_coding YES CCDS42437.1 ENSP00000383234 P31152 UPI0000201D20 NM_002747.3 3/6 PROSITE_profiles:PS50011,hmmpanther:PTHR24055:SF25,hmmpanther:PTHR24055,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 LOW 1 SNV 1 0,1 1 PASS rs550266883 . 0 204 2 4 0 0 0 0 -19.71192 0.9994193 1 1 1 0 A 2 1 76 50715204 50715204 G A 1 0 0 0 0 0 0 0 1 9204 1103 39 1 1 MAPK4 18 50715204 Silent SNP G C3N-01413_T 27765565 50715204 29658081 42 23196 ZNF8 0 . GRCh38 19 58295055 58295055 + Missense_Mutation SNP A A T novel C3N-01413_T C3N-01413_N A A c.1247A>T p.Gln416Leu p.Q416L ENST00000621650 4/4 255 217 38 250 250 0 strelka-varscan-mutect ZNF8,missense_variant,p.Gln416Leu,ENST00000621650,NM_021089.2;AC010642.1,3_prime_UTR_variant,,ENST00000591325,;CTD-3138B18.4,3_prime_UTR_variant,,ENST00000637233,; T ENST00000621650 Transcript missense_variant 1378/9128 1247/1728 416/575 Q/L cAg/cTg 1 1 ZNF8 HGNC HGNC:13154 protein_coding YES CCDS12974.1 ENSP00000477716 P17098 UPI0000185FEA NM_021089.2 tolerated(0.05) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF186,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 76 58295055 58295055 A T 1 0 0 0 0 1 0 0 0 18752 188 7 4 4 ZNF8 19 58295055 Missense_Mutation SNP A C3N-01413_T 58295055 322561 43 23197 POFUT1 0 . GRCh38 20 32234636 32234636 + Missense_Mutation SNP C C T novel C3N-01413_T C3N-01413_N C C c.1142C>T p.Pro381Leu p.P381L ENST00000375749 7/7 74 67 7 59 59 0 strelka-varscan-mutect POFUT1,missense_variant,p.Pro381Leu,ENST00000375749,NM_015352.1;POFUT1,upstream_gene_variant,,ENST00000408740,;POFUT1,downstream_gene_variant,,ENST00000486717,;POFUT1,downstream_gene_variant,,ENST00000465791,;POFUT1,upstream_gene_variant,,ENST00000434904,; T ENST00000375749 Transcript missense_variant 1204/5235 1142/1167 381/388 P/L cCc/cTc 1 1 POFUT1 HGNC HGNC:14988 protein_coding YES CCDS13198.1 ENSP00000364902 Q9H488 UPI0000130C42 NM_015352.1 deleterious(0.05) 7/7 hmmpanther:PTHR21420,hmmpanther:PTHR21420:SF3 MODERATE 1 SNV 1 1 PASS rs1442284952 . 0 202 8 0 0 0 0 0 -15.21785 0.999995 1 1 1 0 T 3 4 76 32234636 32234636 C T 1 0 0 0 0 1 0 0 0 12292 623 22 3 3 POFUT1 20 32234636 Missense_Mutation SNP C C3N-01413_T 32234636 32209531 44 23198 DSCAM 0 . GRCh38 21 40013213 40013213 + Missense_Mutation SNP C C T rs750989668 C3N-01413_T C3N-01413_N C C c.5860G>A p.Ala1954Thr p.A1954T ENST00000400454 33/33 132 96 36 119 119 0 strelka-varscan-mutect DSCAM,missense_variant,p.Ala1954Thr,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Ala1789Thr,ENST00000617870,;DSCAM,missense_variant,p.Ala1688Thr,ENST00000404019,; T ENST00000400454 Transcript missense_variant 6338/8552 5860/6039 1954/2012 A/T Gcc/Acc rs750989668 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 tolerated_low_confidence(0.4) 33/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16 MODERATE 1 SNV 1 1 PASS rs750989668 . 0 204 4 2 0 0 0 0 -20 0.9999948 1 1 1 0 T 3 4 76 40013213 40013213 C T 1 0 0 0 0 1 0 0 0 4589 768 27 1 1 DSCAM 21 40013213 Missense_Mutation SNP C C3N-01413_T 40013213 6696770 45 23199 ATP6AP1 0 . GRCh38 X 154435284 154435284 + Missense_Mutation SNP G G A novel C3N-01413_T C3N-01413_N G G c.982G>A p.Ala328Thr p.A328T ENST00000369762 9/10 301 263 38 198 198 0 strelka-varscan-mutect ATP6AP1,missense_variant,p.Ala139Thr,ENST00000619046,;ATP6AP1,missense_variant,p.Ala328Thr,ENST00000369762,NM_001183.5;ATP6AP1,missense_variant,p.Ala242Thr,ENST00000422890,;GDI1,upstream_gene_variant,,ENST00000447750,NM_001493.2;GDI1,upstream_gene_variant,,ENST00000630693,;ATP6AP1,downstream_gene_variant,,ENST00000449556,;GDI1,upstream_gene_variant,,ENST00000475976,;GDI1,upstream_gene_variant,,ENST00000485143,;ATP6AP1,downstream_gene_variant,,ENST00000484908,;GDI1,upstream_gene_variant,,ENST00000471972,;ATP6AP1,3_prime_UTR_variant,,ENST00000455205,;ATP6AP1,3_prime_UTR_variant,,ENST00000429585,;ATP6AP1,non_coding_transcript_exon_variant,,ENST00000491569,;GDI1,upstream_gene_variant,,ENST00000491154,;GDI1,upstream_gene_variant,,ENST00000481304,;GDI1,upstream_gene_variant,,ENST00000489589,;GDI1,upstream_gene_variant,,ENST00000434049,;ATP6AP1,downstream_gene_variant,,ENST00000439372,;ATP6AP1,downstream_gene_variant,,ENST00000446552,;GDI1,upstream_gene_variant,,ENST00000445564,;GDI1,upstream_gene_variant,,ENST00000415109,; A ENST00000369762 Transcript missense_variant 1043/2099 982/1413 328/470 A/T Gcc/Acc 1 1 ATP6AP1 HGNC HGNC:868 protein_coding YES CCDS35451.1 ENSP00000358777 Q15904 UPI000013811E NM_001183.5 tolerated(0.62) 9/10 Pfam_domain:PF05827,hmmpanther:PTHR12471,hmmpanther:PTHR12471:SF2 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 76 154435284 154435284 G A 1 0 0 0 0 1 0 0 0 1318 1203 42 3 3 ATP6AP1 23 154435284 Missense_Mutation SNP G C3N-01413_T 154435284 1605611 46 23200 GABRD 0 . GRCh38 1 2029162 2029162 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.743G>A p.Gly248Asp p.G248D ENST00000378585 7/9 173 137 36 300 300 0 strelka-varscan-mutect GABRD,missense_variant,p.Gly248Asp,ENST00000378585,NM_000815.4; A ENST00000378585 Transcript missense_variant 843/1928 743/1359 248/452 G/D gGc/gAc 1 1 GABRD HGNC HGNC:4084 protein_coding YES CCDS36.1 ENSP00000367848 O14764 UPI0000070D0A NM_000815.4 deleterious(0.01) 7/9 Prints_domain:PR00252,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF34,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 2029162 2029162 G A 1 0 0 0 0 1 0 0 0 6040 1203 42 3 3 GABRD 1 2029162 Missense_Mutation SNP G C3N-01414_T 2029162 246927260 1 23201 SKI 0 . GRCh38 1 2303023 2303023 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.1015A>G p.Thr339Ala p.T339A ENST00000378536 2/7 352 313 39 553 553 0 strelka-varscan-mutect SKI,missense_variant,p.Thr339Ala,ENST00000378536,NM_003036.3;SKI,non_coding_transcript_exon_variant,,ENST00000478223,;SKI,non_coding_transcript_exon_variant,,ENST00000508416,;SKI,upstream_gene_variant,,ENST00000507179,; G ENST00000378536 Transcript missense_variant 1087/5613 1015/2187 339/728 T/A Acc/Gcc 1 1 SKI HGNC HGNC:10896 protein_coding YES CCDS39.1 ENSP00000367797 P12755 UPI00001359DE NM_003036.3 tolerated(0.8) 2/7 hmmpanther:PTHR10005:SF15,hmmpanther:PTHR10005 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 2303023 2303023 A G 1 0 0 0 0 1 0 0 0 14619 159 6 5 5 SKI 1 2303023 Missense_Mutation SNP A C3N-01414_T 273861 2303023 246653399 2 23202 TAS1R1 0 . GRCh38 1 6575048 6575048 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.916T>C p.Ser306Pro p.S306P ENST00000333172 3/6 44 32 12 61 61 0 strelka-varscan-mutect TAS1R1,missense_variant,p.Ser306Pro,ENST00000333172,NM_138697.3;TAS1R1,missense_variant,p.Ser232Pro,ENST00000411823,;TAS1R1,intron_variant,,ENST00000351136,NM_177540.2;TAS1R1,intron_variant,,ENST00000415267,;ZBTB48,upstream_gene_variant,,ENST00000377674,NM_005341.3,NM_001278647.1,NM_001278648.1;ZBTB48,upstream_gene_variant,,ENST00000319084,;ZBTB48,upstream_gene_variant,,ENST00000435905,; C ENST00000333172 Transcript missense_variant 1109/2892 916/2526 306/841 S/P Tcc/Ccc 1 1 TAS1R1 HGNC HGNC:14448 protein_coding YES CCDS81.1 ENSP00000331867 Q7RTX1 UPI000004737B NM_138697.3 deleterious(0.01) 3/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF3,Pfam_domain:PF01094,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 6575048 6575048 T C 1 0 0 0 0 1 0 0 0 15961 1551 54 5 5 TAS1R1 1 6575048 Missense_Mutation SNP T C3N-01414_T 4272025 6575048 242381374 3 23203 PRAMEF7 0 . GRCh38 1 12920408 12920408 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1420T>A p.Cys474Ser p.C474S ENST00000616979 4/4 160 144 16 257 257 0 varscan-mutect PRAMEF7,missense_variant,p.Cys474Ser,ENST00000616979,NM_001012277.4;PRAMEF7,missense_variant,p.Cys474Ser,ENST00000330881,;RNU6-1072P,upstream_gene_variant,,ENST00000384703,; A ENST00000616979 Transcript missense_variant 1518/1592 1420/1425 474/474 C/S Tgt/Agt 1 1 PRAMEF7 HGNC HGNC:28415 protein_coding YES CCDS30593.1 ENSP00000484237 Q5VXH5 UPI000058F1DF NM_001012277.4 deleterious(0) 4/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 12920408 12920408 T A 1 0 0 0 0 1 0 0 0 12569 1580 55 4 4 PRAMEF7 1 12920408 Missense_Mutation SNP T C3N-01414_T 6345360 12920408 236036014 4 23204 CLCNKA 0 . GRCh38 1 16027310 16027310 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.656G>T p.Gly219Val p.G219V ENST00000331433 8/20 262 225 37 392 391 1 strelka-varscan-mutect CLCNKA,missense_variant,p.Gly219Val,ENST00000375692,NM_001042704.1;CLCNKA,missense_variant,p.Gly219Val,ENST00000331433,NM_004070.3;CLCNKA,missense_variant,p.Gly176Val,ENST00000439316,NM_001257139.1;CLCNKA,splice_region_variant,,ENST00000464764,;CLCNKA,splice_region_variant,,ENST00000491433,;CLCNKA,downstream_gene_variant,,ENST00000495784,; T ENST00000331433 Transcript missense_variant,splice_region_variant 675/2475 656/2064 219/687 G/V gGc/gTc 1 1 CLCNKA HGNC HGNC:2026 protein_coding YES CCDS167.1 ENSP00000332771 P51800 UPI0000127993 NM_004070.3 deleterious(0.01) 8/20 Gene3D:1otsB00,Pfam_domain:PF00654,Prints_domain:PR00762,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF95,Superfamily_domains:SSF81340,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1286133127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 16027310 16027310 G T 1 0 0 0 0 1 0 0 0 3233 1217 42 2 2 CLCNKA 1 16027310 Missense_Mutation SNP G C3N-01414_T 3106902 16027310 232929112 5 23205 C1QC 0 . GRCh38 1 22647232 22647232 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.187C>A p.Pro63Thr p.P63T ENST00000374639 3/3 222 169 53 338 338 0 strelka-varscan-mutect C1QC,missense_variant,p.Pro63Thr,ENST00000374639,NM_001114101.1;C1QC,missense_variant,p.Pro63Thr,ENST00000374640,NM_172369.3;C1QC,missense_variant,p.Pro63Thr,ENST00000374637,; A ENST00000374639 Transcript missense_variant 305/1183 187/738 63/245 P/T Cca/Aca 1 1 C1QC HGNC HGNC:1245 protein_coding YES CCDS227.1 ENSP00000363770 P02747 A0A024RAA7 UPI0000126BF3 NM_001114101.1 deleterious(0.03) 3/3 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF558,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 22647232 22647232 C A 1 0 0 0 0 1 0 0 0 1935 637 22 2 2 C1QC 1 22647232 Missense_Mutation SNP C C3N-01414_T 6619922 22647232 226309190 6 23206 SPOCD1 0 . GRCh38 1 31792308 31792308 + Missense_Mutation SNP C C A rs751875735 C3N-01414_T C3N-01414_N C C c.2869G>T p.Gly957Trp p.G957W ENST00000360482 15/16 302 265 37 465 465 0 strelka-varscan-mutect SPOCD1,missense_variant,p.Gly957Trp,ENST00000360482,NM_144569.5;SPOCD1,missense_variant,p.Gly957Trp,ENST00000533231,NM_001281987.1;SPOCD1,missense_variant,p.Gly450Trp,ENST00000257100,NM_001281988.1;SPOCD1,missense_variant,p.Gly393Trp,ENST00000452755,;SPOCD1,downstream_gene_variant,,ENST00000528579,;RP11-84A19.3,downstream_gene_variant,,ENST00000527035,;SPOCD1,intron_variant,,ENST00000473361,;SPOCD1,downstream_gene_variant,,ENST00000485944,;SPOCD1,downstream_gene_variant,,ENST00000468720,;SPOCD1,downstream_gene_variant,,ENST00000460061,;SPOCD1,downstream_gene_variant,,ENST00000531039,;SPOCD1,downstream_gene_variant,,ENST00000532604,; A ENST00000360482 Transcript missense_variant 2999/3960 2869/3651 957/1216 G/W Ggg/Tgg rs751875735 1 -1 SPOCD1 HGNC HGNC:26338 protein_coding YES CCDS347.1 ENSP00000353670 Q6ZMY3 UPI000035E7DD NM_144569.5 deleterious(0) 15/16 hmmpanther:PTHR11477:SF18,hmmpanther:PTHR11477,Pfam_domain:PF07744 MODERATE 1 SNV 2 1 PASS rs751875735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 31792308 31792308 C A 1 0 0 0 0 1 0 0 0 15431 652 23 1 1 SPOCD1 1 31792308 Missense_Mutation SNP C C3N-01414_T 9145076 31792308 217164114 7 23207 AGO3 0 . GRCh38 1 36055106 36055106 + Missense_Mutation SNP T T G novel C3N-01414_T C3N-01414_N T T c.2435T>G p.Phe812Cys p.F812C ENST00000373191 18/19 264 242 22 436 434 2 strelka-varscan-mutect AGO3,missense_variant,p.Phe812Cys,ENST00000373191,NM_024852.3;AGO3,missense_variant,p.Phe578Cys,ENST00000246314,NM_177422.2;AGO3,3_prime_UTR_variant,,ENST00000634486,;AGO3,non_coding_transcript_exon_variant,,ENST00000471099,; G ENST00000373191 Transcript missense_variant 2784/19687 2435/2583 812/860 F/C tTt/tGt 1 1 AGO3 HGNC HGNC:18421 protein_coding YES CCDS399.1 ENSP00000362287 Q9H9G7 UPI0000141361 NM_024852.3 deleterious(0) 18/19 HAMAP:MF_03032,PROSITE_profiles:PS50822,hmmpanther:PTHR22891:SF3,hmmpanther:PTHR22891,Pfam_domain:PF02171,Gene3D:3.30.420.10,SMART_domains:SM00950,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 36055106 36055106 T G 1 0 0 0 0 1 0 0 0 466 1841 64 5 5 AGO3 1 36055106 Missense_Mutation SNP T C3N-01414_T 4262798 36055106 212901316 8 23208 ERI3 0 . GRCh38 1 44319642 44319642 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.592C>T p.Pro198Ser p.P198S ENST00000372257 4/9 146 129 17 239 238 1 strelka-varscan-mutect ERI3,missense_variant,p.Pro198Ser,ENST00000372257,NM_001301698.1,NM_024066.2;ERI3,missense_variant,p.Pro83Ser,ENST00000372259,;ERI3,missense_variant,p.Pro37Ser,ENST00000456170,;ERI3,missense_variant,p.Pro196Ser,ENST00000457571,;ERI3,missense_variant,p.Pro80Ser,ENST00000452396,;ERI3,non_coding_transcript_exon_variant,,ENST00000495828,; A ENST00000372257 Transcript missense_variant 774/1684 592/1014 198/337 P/S Cca/Tca 1 -1 ERI3 HGNC HGNC:17276 protein_coding YES CCDS30696.1 ENSP00000361331 O43414 UPI00001C1D9B NM_001301698.1,NM_024066.2 tolerated(0.22) 4/9 Gene3D:3.30.420.10,Pfam_domain:PF00929,hmmpanther:PTHR23044,SMART_domains:SM00479,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99999 0.9999999 1 1 1 0 A 3 1 77 44319642 44319642 G A 1 0 0 0 0 1 0 0 0 5080 1232 43 3 3 ERI3 1 44319642 Missense_Mutation SNP G C3N-01414_T 8264536 44319642 204636780 9 23209 USP24 0 . GRCh38 1 55166567 55166567 + Splice_Site DEL C C - novel C3N-01414_T C3N-01414_N C C c.861+1delG p.X287_splice ENST00000294383 150 112 38 332 331 1 sindel-varindel-pindel USP24,splice_donor_variant,,ENST00000294383,NM_015306.2; - ENST00000294383 Transcript splice_donor_variant -/10549 861/7863 287/2620 1 -1 USP24 HGNC HGNC:12623 protein_coding YES CCDS44154.2 ENSP00000294383 Q9UPU5 UPI000059CFDE NM_015306.2 6/67 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 8 5 77 55166567 55166567 C - 1 0 1 0 1 0 0 1 0 17596 521 18 0 0 USP24 1 55166567 Splice_Site DEL C C3N-01414_T 10846925 55166567 193789855 10 23210 LRRC7 0 . GRCh38 1 70036558 70036558 + Missense_Mutation SNP G G T rs140092259 C3N-01414_T C3N-01414_N G G c.2108G>T p.Arg703Leu p.R703L ENST00000035383 18/25 180 151 29 333 331 2 strelka-varscan-mutect LRRC7,missense_variant,p.Arg708Leu,ENST00000310961,;LRRC7,missense_variant,p.Arg703Leu,ENST00000035383,NM_020794.2;LRRC7,intron_variant,,ENST00000415775,; T ENST00000035383 Transcript missense_variant 2138/5000 2108/4614 703/1537 R/L cGg/cTg rs140092259,COSM464911,COSM71495 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated_low_confidence(0.14) 18/25 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs140092259 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 70036558 70036558 G T 1 0 0 0 0 1 0 0 0 8916 1116 39 1 1 LRRC7 1 70036558 Missense_Mutation SNP G C3N-01414_T 14869991 70036558 178919864 11 23211 ASB17 0 . GRCh38 1 75922293 75922293 + Missense_Mutation SNP C C G C3N-01414_T C3N-01414_N C C c.468G>C p.Gln156His p.Q156H ENST00000284142 2/3 115 97 18 273 273 0 strelka-varscan-mutect ASB17,missense_variant,p.Gln156His,ENST00000284142,NM_080868.2; G ENST00000284142 Transcript missense_variant 608/1107 468/888 156/295 Q/H caG/caC COSM426695 1 -1 ASB17 HGNC HGNC:19769 protein_coding YES CCDS671.1 ENSP00000284142 Q8WXJ9 UPI0000073CD7 NM_080868.2 deleterious(0.01) 2/3 Gene3D:1.25.40.20,hmmpanther:PTHR20966,hmmpanther:PTHR20966:SF2,Superfamily_domains:SSF48403 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 77 75922293 75922293 C G 1 0 0 0 0 1 0 0 0 1163 912 32 4 4 ASB17 1 75922293 Missense_Mutation SNP C C3N-01414_T 5885735 75922293 173034129 12 23212 PKN2 0 . GRCh38 1 88771460 88771460 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.662A>T p.Glu221Val p.E221V ENST00000370521 5/22 132 98 34 294 294 0 strelka-varscan-mutect PKN2,missense_variant,p.Glu221Val,ENST00000370521,NM_006256.2;PKN2,missense_variant,p.Glu221Val,ENST00000370513,;PKN2,missense_variant,p.Glu221Val,ENST00000316005,;PKN2,missense_variant,p.Glu3Val,ENST00000436111,; T ENST00000370521 Transcript missense_variant 1021/6121 662/2955 221/984 E/V gAa/gTa 1 1 PKN2 HGNC HGNC:9406 protein_coding YES CCDS714.1 ENSP00000359552 Q16513 UPI000004D291 NM_006256.2 deleterious(0) 5/22 Pfam_domain:PF02185,Gene3D:1.10.287.160,SMART_domains:SM00742,Superfamily_domains:SSF46585 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 88771460 88771460 A T 1 0 0 0 0 1 0 0 0 12076 246 9 4 4 PKN2 1 88771460 Missense_Mutation SNP A C3N-01414_T 12849167 88771460 160184962 13 23213 GFI1 0 . GRCh38 1 92476173 92476173 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1125G>T p.Lys375Asn p.K375N ENST00000370332 7/7 334 286 48 528 525 3 strelka-varscan-mutect GFI1,missense_variant,p.Lys375Asn,ENST00000370332,NM_001127215.1;GFI1,missense_variant,p.Lys375Asn,ENST00000294702,NM_005263.3;GFI1,missense_variant,p.Lys375Asn,ENST00000427103,NM_001127216.1; A ENST00000370332 Transcript missense_variant 1444/2855 1125/1269 375/422 K/N aaG/aaT 1 -1 GFI1 HGNC HGNC:4237 protein_coding YES CCDS30773.1 ENSP00000359357 Q99684 UPI000006D7FD NM_001127215.1 deleterious(0.02) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR19303:SF239,hmmpanther:PTHR19303,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 92476173 92476173 C A 1 0 0 0 0 1 0 0 0 6213 680 24 2 2 GFI1 1 92476173 Missense_Mutation SNP C C3N-01414_T 3704713 92476173 156480249 14 23214 ABCA4 0 . GRCh38 1 94019668 94019668 + Nonsense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.5110G>T p.Glu1704Ter p.E1704* ENST00000370225 36/50 267 235 32 477 477 0 strelka-mutect ABCA4,stop_gained,p.Glu1704Ter,ENST00000370225,NM_000350.2;ABCA4,stop_gained,p.Glu496Ter,ENST00000536513,;ABCA4,non_coding_transcript_exon_variant,,ENST00000460514,;ABCA4,non_coding_transcript_exon_variant,,ENST00000470771,; A ENST00000370225 Transcript stop_gained 5197/7309 5110/6822 1704/2273 E/* Gag/Tag CD109660 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 36/50 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF97,Pfam_domain:PF12698,TIGRFAM_domain:TIGR01257 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 94019668 94019668 C A 1 0 0 0 0 0 1 0 0 38 864 30 2 2 ABCA4 1 94019668 Nonsense_Mutation SNP C C3N-01414_T 1543495 94019668 154936754 15 23215 DPYD 0 . GRCh38 1 97193249 97193249 + Splice_Site SNP C C T novel C3N-01414_T C3N-01414_N C C c.2443-1G>A p.X815_splice ENST00000370192 329 294 35 486 486 0 strelka-varscan-mutect DPYD,splice_acceptor_variant,,ENST00000370192,NM_000110.3;DPYD-AS1,intron_variant,,ENST00000422980,; T ENST00000370192 Transcript splice_acceptor_variant -/4412 2443/3078 815/1025 1 -1 DPYD HGNC HGNC:3012 protein_coding YES CCDS30777.1 ENSP00000359211 Q12882 UPI00000727C7 NM_000110.3 19/22 HIGH 1 SNV 1 1 PASS rs1319681736 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 77 97193249 97193249 C T 1 0 0 0 0 0 0 1 0 4560 695 24 3 3 DPYD 1 97193249 Splice_Site SNP C C3N-01414_T 3173581 97193249 151763173 16 23216 PLPPR4 0 . GRCh38 1 99305838 99305838 + Missense_Mutation SNP G G T rs761930735 C3N-01414_T C3N-01414_N G G c.1120G>T p.Gly374Cys p.G374C ENST00000370185 7/7 277 209 68 474 474 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Gly374Cys,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Gly316Cys,ENST00000457765,NM_001166252.1;PLPPR4,missense_variant,p.Gly216Cys,ENST00000370184,; T ENST00000370185 Transcript missense_variant 1617/5369 1120/2292 374/763 G/C Ggc/Tgc rs761930735 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0) 7/7 hmmpanther:PTHR10165:SF13,hmmpanther:PTHR10165 MODERATE 1 SNV 1 1 PASS rs761930735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 99305838 99305838 G T 1 0 0 0 0 1 0 0 0 12212 1000 35 2 2 PLPPR4 1 99305838 Missense_Mutation SNP G C3N-01414_T 2112589 99305838 149650584 17 23217 COL11A1 0 . GRCh38 1 102940339 102940339 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.3372A>T p.Glu1124Asp p.E1124D ENST00000370096 43/67 267 232 35 454 453 1 strelka-varscan-mutect COL11A1,missense_variant,p.Glu1136Asp,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Glu1124Asp,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Glu1085Asp,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Glu1008Asp,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; A ENST00000370096 Transcript missense_variant 3685/7286 3372/5421 1124/1806 E/D gaA/gaT 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 tolerated(0.08) 43/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 102940339 102940339 T A 1 0 0 0 0 1 0 0 0 3455 1606 56 4 4 COL11A1 1 102940339 Missense_Mutation SNP T C3N-01414_T 3634501 102940339 146016083 18 23218 SPAG17 0 . GRCh38 1 117996641 117996641 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.4879C>A p.Leu1627Ile p.L1627I ENST00000336338 33/49 140 105 35 317 317 0 strelka-varscan-mutect SPAG17,missense_variant,p.Leu1627Ile,ENST00000336338,NM_206996.2;SPAG17,missense_variant,p.Leu107Ile,ENST00000437255,; T ENST00000336338 Transcript missense_variant 4945/6924 4879/6672 1627/2223 L/I Ctt/Att 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 tolerated(0.28) 33/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS rs1467293897 . 0 203 5 2 0 0 0 0 -20 0.9999855 1 1 1 0 T 3 4 77 117996641 117996641 G T 1 0 0 0 0 1 0 0 0 15310 1000 35 2 2 SPAG17 1 117996641 Missense_Mutation SNP G C3N-01414_T 15056302 117996641 130959781 19 23219 POLR3GL 0 . GRCh38 1 145974897 145974897 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.32G>T p.Gly11Val p.G11V ENST00000369314 2/8 99 89 10 73 73 0 strelka-varscan-mutect POLR3GL,missense_variant,p.Gly11Val,ENST00000369314,NM_032305.1;POLR3GL,missense_variant,p.Gly11Val,ENST00000369313,;CH17-270A2.2,intron_variant,,ENST00000625258,;CH17-270A2.2,intron_variant,,ENST00000630636,;POLR3GL,non_coding_transcript_exon_variant,,ENST00000622508,;POLR3GL,non_coding_transcript_exon_variant,,ENST00000471706,; T ENST00000369314 Transcript missense_variant 139/1165 32/657 11/218 G/V gGc/gTc 1 1 POLR3GL HGNC HGNC:28466 protein_coding YES CCDS72875.1 ENSP00000358320 Q9BT43 UPI000006F290 NM_032305.1 deleterious(0) 2/8 Pfam_domain:PF11705,hmmpanther:PTHR15367,hmmpanther:PTHR15367:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.88247 1 1 1 1 0 T 3 4 77 145974897 145974897 G T 1 0 0 0 0 1 0 0 0 12346 1203 42 2 2 POLR3GL 1 145974897 Missense_Mutation SNP G C3N-01414_T 27978256 145974897 102981525 20 23220 PDE4DIP 0 . GRCh38 1 148981366 148981367 + Frame_Shift_Del DEL AA AA - novel C3N-01414_T C3N-01414_N AA AA c.2785_2786delAA p.Asn929GlnfsTer16 p.N929Qfs*16 ENST00000369356 21/44 349 308 41 442 442 0 sindel-varindel-pindel PDE4DIP,frameshift_variant,p.Asn1092GlnfsTer49,ENST00000529945,;PDE4DIP,frameshift_variant,p.Asn1066GlnfsTer16,ENST00000585156,;PDE4DIP,frameshift_variant,p.Asn929GlnfsTer16,ENST00000369356,NM_001198834.3;PDE4DIP,frameshift_variant,p.Asn1066GlnfsTer16,ENST00000524974,;PDE4DIP,frameshift_variant,p.Asn929GlnfsTer16,ENST00000369354,NM_014644.5;PDE4DIP,frameshift_variant,p.Asn995GlnfsTer16,ENST00000618462,NM_001198832.2;PDE4DIP,frameshift_variant,p.Asn1092GlnfsTer16,ENST00000313431,NM_001002811.2;PDE4DIP,frameshift_variant,p.Asn929GlnfsTer16,ENST00000369351,;PDE4DIP,frameshift_variant,p.Asn929GlnfsTer16,ENST00000369349,NM_001002812.2;PDE4DIP,frameshift_variant,p.Asn716GlnfsTer49,ENST00000479408,;PDE4DIP,frameshift_variant,p.Asn52GlnfsTer16,ENST00000491426,;PDE4DIP,intron_variant,,ENST00000467859,;PDE4DIP,intron_variant,,ENST00000530062,; - ENST00000369356 Transcript frameshift_variant 3075-3076/8307 2784-2785/7089 928-929/2362 LN/LX ttAAac/ttac 1 1 PDE4DIP HGNC HGNC:15580 protein_coding YES CCDS72892.1 ENSP00000358363 A0A0A0MRM1 UPI000292EFC6 NM_001198834.3 21/44 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 148981366 148981366 AA - 1 0 1 0 1 0 0 0 0 11731 359 13 0 0 PDE4DIP 1 148981366 Frame_Shift_Del DEL AA C3N-01414_T 3006469 148981366 99975056 21 23221 NBPF9 0 . GRCh38 1 149055689 149055689 + Silent SNP C C G novel C3N-01414_T C3N-01414_N C C c.3303G>C p.= p.L1101L ENST00000615421 29/29 481 399 82 499 499 0 strelka-varscan-mutect NBPF9,synonymous_variant,p.=,ENST00000615421,;NBPF9,synonymous_variant,p.=,ENST00000621645,;NBPF9,synonymous_variant,p.=,ENST00000584027,NM_001277444.1;NBPF9,synonymous_variant,p.=,ENST00000613969,NM_001037501.2;NBPF9,synonymous_variant,p.=,ENST00000613595,NM_001037675.3;NBPF9,synonymous_variant,p.=,ENST00000621074,;NBPF9,synonymous_variant,p.=,ENST00000610300,;NBPF9,3_prime_UTR_variant,,ENST00000483630,;RP4-791M13.3,downstream_gene_variant,,ENST00000466343,;NBPF9,downstream_gene_variant,,ENST00000611593,; G ENST00000615421 Transcript synonymous_variant 4173/5835 3303/3336 1101/1111 L ctG/ctC 1 -1 NBPF9 HGNC HGNC:31991 protein_coding YES CCDS72896.1 ENSP00000477979 A0A075B761 UPI000292EE30 29/29 PROSITE_profiles:PS51316,hmmpanther:PTHR14199:SF20,hmmpanther:PTHR14199 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 149055689 149055689 C G 1 0 0 0 0 0 0 0 1 10215 581 21 4 4 NBPF9 1 149055689 Silent SNP C C3N-01414_T 74323 149055689 99900733 22 23222 CGN 0 . GRCh38 1 151529971 151529971 + Silent SNP G G C novel C3N-01414_T C3N-01414_N G G c.2169G>C p.= p.T723T ENST00000271636 12/21 197 165 32 168 168 0 strelka-varscan-mutect CGN,synonymous_variant,p.=,ENST00000271636,NM_020770.2;SNORA44,upstream_gene_variant,,ENST00000517031,;CGN,upstream_gene_variant,,ENST00000473377,;CGN,downstream_gene_variant,,ENST00000464886,; C ENST00000271636 Transcript synonymous_variant 2302/5091 2169/3612 723/1203 T acG/acC 1 1 CGN HGNC HGNC:17429 protein_coding YES CCDS999.1 ENSP00000271636 Q9P2M7 UPI0000161C1E NM_020770.2 12/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF474 LOW 1 SNV 1 1 PASS rs908870060 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 151529971 151529971 G C 1 0 0 0 0 0 0 0 1 3061 1045 37 4 4 CGN 1 151529971 Silent SNP G C3N-01414_T 2474282 151529971 97426451 23 23223 C2CD4D 0 . GRCh38 1 151838039 151838039 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.951C>T p.= p.R317R ENST00000454109 2/2 266 178 88 278 278 0 strelka-varscan-mutect C2CD4D,synonymous_variant,p.=,ENST00000454109,NM_001136003.1;AL450992.2,upstream_gene_variant,,ENST00000434182,;Y_RNA,downstream_gene_variant,,ENST00000364264,; A ENST00000454109 Transcript synonymous_variant 1537/1757 951/1062 317/353 R cgC/cgT 1 -1 C2CD4D HGNC HGNC:37210 protein_coding YES CCDS44224.1 ENSP00000389554 B7Z1M9 UPI0001747AE2 NM_001136003.1 2/2 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF179,SMART_domains:SM00239,Superfamily_domains:SSF49562 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 151838039 151838039 G A 1 0 0 0 0 0 0 0 1 2029 1306 46 3 3 C2CD4D 1 151838039 Silent SNP G C3N-01414_T 308068 151838039 97118383 24 23224 HRNR 0 . GRCh38 1 152214268 152214268 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.7361C>A p.Ser2454Tyr p.S2454Y ENST00000368801 3/3 943 807 136 864 864 0 strelka-varscan-mutect HRNR,missense_variant,p.Ser2454Tyr,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368801 Transcript missense_variant 7437/9623 7361/8553 2454/2850 S/Y tCc/tAc 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 deleterious(0.04) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 152214268 152214268 G T 1 0 0 0 0 1 0 0 0 7254 1174 41 2 2 HRNR 1 152214268 Missense_Mutation SNP G C3N-01414_T 376229 152214268 96742154 25 23225 HRNR 0 . GRCh38 1 152220387 152220387 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.1242C>A p.= p.G414G ENST00000368801 3/3 489 409 80 498 498 0 strelka-varscan-mutect HRNR,synonymous_variant,p.=,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368801 Transcript synonymous_variant 1318/9623 1242/8553 414/2850 G ggC/ggA 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 152220387 152220387 G T 1 0 0 0 0 0 0 0 1 7254 1190 42 2 2 HRNR 1 152220387 Silent SNP G C3N-01414_T 6119 152220387 96736035 26 23226 ARHGEF11 0 . GRCh38 1 156940302 156940302 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.3638G>T p.Gly1213Val p.G1213V ENST00000368194 36/41 113 79 34 115 114 1 strelka-varscan-mutect ARHGEF11,missense_variant,p.Gly1213Val,ENST00000368194,NM_198236.2;ARHGEF11,missense_variant,p.Gly1173Val,ENST00000361409,NM_014784.3;MIR765,upstream_gene_variant,,ENST00000390226,;ARHGEF11,non_coding_transcript_exon_variant,,ENST00000487682,;ARHGEF11,upstream_gene_variant,,ENST00000492592,; A ENST00000368194 Transcript missense_variant 4678/6889 3638/4689 1213/1562 G/V gGa/gTa 1 -1 ARHGEF11 HGNC HGNC:14580 protein_coding YES CCDS1163.1 ENSP00000357177 O15085 UPI00001D62A7 NM_198236.2 tolerated_low_confidence(0.08) 36/41 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 156940302 156940302 C A 1 0 0 0 0 1 0 0 0 1026 855 30 2 2 ARHGEF11 1 156940302 Missense_Mutation SNP C C3N-01414_T 4719915 156940302 92016120 27 23227 SPTA1 0 . GRCh38 1 158620461 158620461 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.6126G>T p.Glu2042Asp p.E2042D ENST00000368147 44/52 291 254 37 318 318 0 strelka-varscan-mutect SPTA1,missense_variant,p.Glu2042Asp,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000484520,;SPTA1,downstream_gene_variant,,ENST00000461624,;SPTA1,upstream_gene_variant,,ENST00000492934,;SPTA1,upstream_gene_variant,,ENST00000498708,; A ENST00000368147 Transcript missense_variant 6307/7999 6126/7260 2042/2419 E/D gaG/gaT COSM3476187,COSM897787 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.05) 44/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Gene3D:1.20.58.60,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 158620461 158620461 C A 1 0 0 0 0 1 0 0 0 15472 695 24 2 2 SPTA1 1 158620461 Missense_Mutation SNP C C3N-01414_T 1680159 158620461 90335961 28 23228 PYHIN1 0 . GRCh38 1 158973755 158973755 + Missense_Mutation SNP G G T rs780923953 C3N-01414_T C3N-01414_N G G c.1468G>T p.Ala490Ser p.A490S ENST00000368140 8/9 253 222 31 257 257 0 strelka-varscan-mutect PYHIN1,missense_variant,p.Ala490Ser,ENST00000368140,NM_152501.4;PYHIN1,missense_variant,p.Ala481Ser,ENST00000368138,NM_198928.4;PYHIN1,intron_variant,,ENST00000392254,NM_198929.4;PYHIN1,intron_variant,,ENST00000392252,NM_198930.3; T ENST00000368140 Transcript missense_variant 1713/2083 1468/1479 490/492 A/S Gca/Tca rs780923953,COSM241327,COSM5613794 1 1 PYHIN1 HGNC HGNC:28894 protein_coding YES CCDS1178.1 ENSP00000357122 Q6K0P9 UPI0000225618 NM_152501.4 8/9 hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF14 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs780923953 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 158973755 158973755 G T 1 0 0 0 0 1 0 0 0 13019 971 34 2 2 PYHIN1 1 158973755 Missense_Mutation SNP G C3N-01414_T 353294 158973755 89982667 29 23229 NHLH1 0 . GRCh38 1 160370890 160370890 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.159T>A p.= p.P53P ENST00000302101 2/2 402 310 92 478 476 2 strelka-varscan-mutect NHLH1,synonymous_variant,p.=,ENST00000302101,NM_005598.3; A ENST00000302101 Transcript synonymous_variant 605/2563 159/402 53/133 P ccT/ccA 1 1 NHLH1 HGNC HGNC:7817 protein_coding YES CCDS1204.1 ENSP00000302189 Q02575 Q5T203 UPI000012C5FE NM_005598.3 2/2 hmmpanther:PTHR13864,hmmpanther:PTHR13864:SF20,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1268200522 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 160370890 160370890 T A 1 0 0 0 0 0 0 0 1 10436 1567 55 4 4 NHLH1 1 160370890 Silent SNP T C3N-01414_T 1397135 160370890 88585532 30 23230 FCRLA 0 . GRCh38 1 161713233 161713233 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.1002G>T p.= p.G334G ENST00000367959 6/6 474 440 34 510 509 1 strelka-varscan-mutect FCRLA,synonymous_variant,p.=,ENST00000367959,NM_001184866.1;FCRLA,synonymous_variant,p.=,ENST00000236938,NM_032738.3;FCRLA,synonymous_variant,p.=,ENST00000546024,NM_001184867.1;FCRLA,synonymous_variant,p.=,ENST00000367953,;FCRLA,synonymous_variant,p.=,ENST00000540521,NM_001184870.1;FCRLA,synonymous_variant,p.=,ENST00000367949,NM_001184873.1;FCRLA,synonymous_variant,p.=,ENST00000367957,NM_001184872.1;FCRLA,synonymous_variant,p.=,ENST00000350710,NM_001184871.1;FCRLA,synonymous_variant,p.=,ENST00000309691,;FCRLA,synonymous_variant,p.=,ENST00000349527,;FCRLA,synonymous_variant,p.=,ENST00000367950,;FCRLA,synonymous_variant,p.=,ENST00000294796,;FCRLA,non_coding_transcript_exon_variant,,ENST00000470841,;FCRLA,downstream_gene_variant,,ENST00000465403,; T ENST00000367959 Transcript synonymous_variant 1244/2362 1002/1149 334/382 G ggG/ggT 1 1 FCRLA HGNC HGNC:18504 protein_coding YES CCDS53415.1 ENSP00000356936 Q7L513 UPI0001D3957E NM_001184866.1 6/6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 161713233 161713233 G T 1 0 0 0 0 0 0 0 1 5662 1161 41 2 2 FCRLA 1 161713233 Silent SNP G C3N-01414_T 1342343 161713233 87243189 31 23231 METTL11B 0 . GRCh38 1 170166697 170166697 + Nonsense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.526G>T p.Glu176Ter p.E176* ENST00000439373 3/4 324 270 54 363 362 1 strelka-mutect METTL11B,stop_gained,p.Glu176Ter,ENST00000439373,NM_001136107.1;METTL11B,non_coding_transcript_exon_variant,,ENST00000367764,; T ENST00000439373 Transcript stop_gained 633/992 526/852 176/283 E/* Gaa/Taa COSM4551349 1 1 METTL11B HGNC HGNC:31932 protein_coding YES CCDS44275.1 ENSP00000408058 Q5VVY1 UPI0000418EF1 NM_001136107.1 3/4 hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 170166697 170166697 G T 1 0 0 0 0 0 1 0 0 9437 1175 41 2 2 METTL11B 1 170166697 Nonsense_Mutation SNP G C3N-01414_T 8453464 170166697 78789725 32 23232 PRRC2C 0 . GRCh38 1 171584417 171584417 + Splice_Site SNP A A T novel C3N-01414_T C3N-01414_N A A c.7636-2A>T p.X2546_splice ENST00000338920 150 87 63 149 149 0 strelka-varscan-mutect PRRC2C,splice_acceptor_variant,,ENST00000367742,;PRRC2C,splice_acceptor_variant,,ENST00000338920,NM_015172.3;PRRC2C,splice_acceptor_variant,,ENST00000426496,;PRRC2C,splice_acceptor_variant,,ENST00000495585,;PRRC2C,upstream_gene_variant,,ENST00000498596,;PRRC2C,upstream_gene_variant,,ENST00000492811,; T ENST00000338920 Transcript splice_acceptor_variant -/10355 7636/8454 2546/2817 1 1 PRRC2C HGNC HGNC:24903 protein_coding YES CCDS1296.2 ENSP00000343629 Q9Y520 UPI0000E265EC NM_015172.3 29/33 HIGH 1 SNV 5 1 PASS . . 0 199 9 2 0 0 0 0 -20 0.9999341 1 1 1 0 T 5 4 77 171584417 171584417 A T 1 0 0 0 0 0 0 1 0 12750 434 15 4 4 PRRC2C 1 171584417 Splice_Site SNP A C3N-01414_T 1417720 171584417 77372005 33 23233 ASTN1 0 . GRCh38 1 177029675 177029675 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1079C>A p.Thr360Asn p.T360N ENST00000361833 5/23 204 188 16 220 220 0 strelka-varscan-mutect ASTN1,missense_variant,p.Thr360Asn,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Thr360Asn,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Thr360Asn,ENST00000424564,NM_207108.2;MIR488,upstream_gene_variant,,ENST00000365739,;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,;ASTN1,non_coding_transcript_exon_variant,,ENST00000473640,; T ENST00000361833 Transcript missense_variant 1093/7116 1079/3885 360/1294 T/N aCc/aAc 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious_low_confidence(0) 5/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 177029675 177029675 G T 1 0 0 0 0 1 0 0 0 1211 1261 44 2 2 ASTN1 1 177029675 Missense_Mutation SNP G C3N-01414_T 5445258 177029675 71926747 34 23234 SEC16B 0 . GRCh38 1 177958867 177958867 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.1107C>T p.= p.L369L ENST00000308284 9/26 150 138 12 220 220 0 strelka-varscan-mutect SEC16B,synonymous_variant,p.=,ENST00000308284,NM_033127.2;SEC16B,synonymous_variant,p.=,ENST00000464631,;SEC16B,synonymous_variant,p.=,ENST00000527976,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000354921,;SEC16B,3_prime_UTR_variant,,ENST00000528461,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000466953,;RP4-798P15.3,non_coding_transcript_exon_variant,,ENST00000464428,;SEC16B,upstream_gene_variant,,ENST00000526773,; A ENST00000308284 Transcript synonymous_variant 1197/3985 1107/3183 369/1060 L ctC/ctT 1 -1 SEC16B HGNC HGNC:30301 protein_coding YES CCDS44281.1 ENSP00000308339 Q96JE7 UPI0000203C4D NM_033127.2 9/26 Low_complexity_(Seg):seg,hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF11,Pfam_domain:PF12932 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 177958867 177958867 G A 1 0 0 0 0 0 0 0 1 14264 929 33 3 3 SEC16B 1 177958867 Silent SNP G C3N-01414_T 929192 177958867 70997555 35 23235 CACNA1E 0 . GRCh38 1 181785733 181785733 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.5700G>T p.Gln1900His p.Q1900H ENST00000367573 43/48 349 292 57 386 386 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Gln1881His,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Gln1900His,ENST00000621551,;CACNA1E,missense_variant,p.Gln1900His,ENST00000367567,;CACNA1E,missense_variant,p.Gln1881His,ENST00000358338,;CACNA1E,missense_variant,p.Gln1900His,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Gln1900His,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Gln1899His,ENST00000357570,;CACNA1E,missense_variant,p.Gln1881His,ENST00000360108,; T ENST00000367573 Transcript missense_variant 5700/7067 5700/6942 1900/2313 Q/H caG/caT 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 tolerated(0.11) 43/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 181785733 181785733 G T 1 0 0 0 0 1 0 0 0 2230 962 34 2 2 CACNA1E 1 181785733 Missense_Mutation SNP G C3N-01414_T 3826866 181785733 67170689 36 23236 CFH 0 . GRCh38 1 196685210 196685210 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.937G>T p.Gly313Cys p.G313C ENST00000367429 7/22 452 377 75 465 463 2 strelka-varscan-mutect CFH,missense_variant,p.Gly313Cys,ENST00000367429,NM_000186.3;CFH,missense_variant,p.Gly313Cys,ENST00000630130,NM_001014975.2;CFH,missense_variant,p.Gly249Cys,ENST00000359637,;CFH,non_coding_transcript_exon_variant,,ENST00000466229,; T ENST00000367429 Transcript missense_variant 1177/4127 937/3696 313/1231 G/C Ggc/Tgc 1 1 CFH HGNC HGNC:4883 protein_coding YES CCDS1385.1 ENSP00000356399 P08603 A0A024R962 UPI000013C4D1 NM_000186.3 deleterious(0) 7/22 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 196685210 196685210 G T 1 0 0 0 0 1 0 0 0 3041 1348 47 2 2 CFH 1 196685210 Missense_Mutation SNP G C3N-01414_T 14899477 196685210 52271212 37 23237 CRB1 0 . GRCh38 1 197421515 197421515 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1687A>T p.Ser563Cys p.S563C ENST00000367400 6/12 555 456 99 658 658 0 strelka-varscan-mutect CRB1,missense_variant,p.Ser494Cys,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Ser563Cys,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Ser451Cys,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Ser563Cys,ENST00000538660,NM_001257966.1;CRB1,5_prime_UTR_variant,,ENST00000367397,;CRB1,downstream_gene_variant,,ENST00000476483,;CRB1,upstream_gene_variant,,ENST00000480086,;CRB1,missense_variant,p.Ser563Cys,ENST00000484075,; T ENST00000367400 Transcript missense_variant 1822/4932 1687/4221 563/1406 S/C Agc/Tgc 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0) 6/12 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24049,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1193275021 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 197421515 197421515 A T 1 0 0 0 0 1 0 0 0 3648 188 7 4 4 CRB1 1 197421515 Missense_Mutation SNP A C3N-01414_T 736305 197421515 51534907 38 23238 CRB1 0 . GRCh38 1 197435432 197435432 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.3569A>T p.Asn1190Ile p.N1190I ENST00000367400 9/12 78 46 32 86 86 0 strelka-varscan-mutect CRB1,missense_variant,p.Asn571Ile,ENST00000367397,;CRB1,missense_variant,p.Asn1166Ile,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Asn1190Ile,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Asn1078Ile,ENST00000367399,NM_001193640.1;CRB1,intron_variant,,ENST00000538660,NM_001257966.1;RP11-75C23.1,downstream_gene_variant,,ENST00000422250,;CRB1,missense_variant,p.Asn1190Ile,ENST00000484075,; T ENST00000367400 Transcript missense_variant 3704/4932 3569/4221 1190/1406 N/I aAc/aTc 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0) 9/12 Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24049,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 197435432 197435432 A T 1 0 0 0 0 1 0 0 0 3648 43 2 4 4 CRB1 1 197435432 Missense_Mutation SNP A C3N-01414_T 13917 197435432 51520990 39 23239 ATP2B4 0 . GRCh38 1 203711059 203711059 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1982A>T p.Glu661Val p.E661V ENST00000357681 12/21 386 311 75 389 389 0 strelka-varscan-mutect ATP2B4,missense_variant,p.Glu661Val,ENST00000357681,NM_001684.4;ATP2B4,missense_variant,p.Glu661Val,ENST00000367218,NM_001001396.2;ATP2B4,missense_variant,p.Glu661Val,ENST00000341360,; T ENST00000357681 Transcript missense_variant 3105/8968 1982/3618 661/1205 E/V gAa/gTa 1 1 ATP2B4 HGNC HGNC:817 protein_coding YES CCDS1440.1 ENSP00000350310 P23634 A0A024R968 UPI000002A464 NM_001684.4 deleterious(0) 12/21 hmmpanther:PTHR24093:SF276,hmmpanther:PTHR24093,TIGRFAM_domain:TIGR01517,Pfam_domain:PF00702,Gene3D:1.20.1110.10,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 203711059 203711059 A T 1 0 0 0 0 1 0 0 0 1295 246 9 4 4 ATP2B4 1 203711059 Missense_Mutation SNP A C3N-01414_T 6275627 203711059 45245363 40 23240 REN 0 . GRCh38 1 204161305 204161305 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.360C>A p.= p.L120L ENST00000272190 3/10 52 44 8 58 58 0 strelka-mutect REN,synonymous_variant,p.=,ENST00000638118,;REN,synonymous_variant,p.=,ENST00000272190,NM_000537.3; T ENST00000272190 Transcript synonymous_variant 389/1447 360/1221 120/406 L ctC/ctA 1 -1 REN HGNC HGNC:9958 protein_coding YES CCDS30981.1 ENSP00000272190 P00797 UPI000000091F NM_000537.3 3/10 Gene3D:2.40.70.10,Pfam_domain:PF00026,PROSITE_profiles:PS51767,hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF77,Superfamily_domains:SSF50630 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 204161305 204161305 G T 1 0 0 0 0 0 0 0 1 13394 929 33 2 2 REN 1 204161305 Silent SNP G C3N-01414_T 450246 204161305 44795117 41 23241 ESRRG 0 . GRCh38 1 216677377 216677377 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.186C>A p.Ser62Arg p.S62R ENST00000366937 3/8 274 238 36 345 345 0 strelka-varscan-mutect ESRRG,missense_variant,p.Ser34Arg,ENST00000391890,NM_001243515.1,NM_001243519.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000360012,NM_001243514.1;ESRRG,missense_variant,p.Ser62Arg,ENST00000366937,NM_001243518.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000361525,NM_206594.2;ESRRG,missense_variant,p.Ser34Arg,ENST00000366940,NM_001134285.2,NM_001243511.2;ESRRG,missense_variant,p.Ser34Arg,ENST00000493603,NM_001243510.2;ESRRG,missense_variant,p.Ser34Arg,ENST00000366938,NM_001243513.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000361395,;ESRRG,missense_variant,p.Ser57Arg,ENST00000408911,NM_001438.3;ESRRG,missense_variant,p.Ser34Arg,ENST00000359162,NM_206595.2,NM_001243506.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000616180,;ESRRG,missense_variant,p.Ser34Arg,ENST00000463665,NM_001243507.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000487276,NM_001243512.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000493748,NM_001243509.1;ESRRG,missense_variant,p.Ser34Arg,ENST00000475275,;ESRRG,missense_variant,p.Ser34Arg,ENST00000481543,;ESRRG,missense_variant,p.Ser34Arg,ENST00000469486,;ESRRG,missense_variant,p.Ser34Arg,ENST00000459955,;ESRRG,intron_variant,,ENST00000586199,; T ENST00000366937 Transcript missense_variant 453/5365 186/1413 62/470 S/R agC/agA 1 -1 ESRRG HGNC HGNC:3474 protein_coding YES CCDS58061.1 ENSP00000355904 P62508 UPI0000D4BFAB NM_001243518.1 deleterious(0) 3/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF21,PIRSF_domain:PIRSF500939,PIRSF_domain:PIRSF002527 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 216677377 216677377 G T 1 0 0 0 0 1 0 0 0 5124 1194 42 2 2 ESRRG 1 216677377 Missense_Mutation SNP G C3N-01414_T 12516072 216677377 32279045 42 23242 CCDC185 0 . GRCh38 1 223395319 223395319 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1844G>T p.Arg615Leu p.R615L ENST00000366875 1/1 36 31 5 45 45 0 strelka-varscan-mutect CCDC185,missense_variant,p.Arg615Leu,ENST00000366875,NM_152610.2; T ENST00000366875 Transcript missense_variant 1903/2054 1844/1872 615/623 R/L cGt/cTt 1 1 CCDC185 HGNC HGNC:26654 protein_coding YES CCDS1537.1 ENSP00000355840 Q8N715 UPI000006F948 NM_152610.2 tolerated(0.47) 1/1 hmmpanther:PTHR33663,hmmpanther:PTHR33663:SF3,Pfam_domain:PF15558 MODERATE 1 SNV 1 PASS rs1359211119 . 4 204 2 0 0 0 0 0 -13.66635 1 1 1 1 0 T 3 4 77 223395319 223395319 G T 1 0 0 0 0 1 0 0 0 2501 1145 40 1 1 CCDC185 1 223395319 Missense_Mutation SNP G C3N-01414_T 6717942 223395319 25561103 43 23243 PRSS38 0 . GRCh38 1 227817412 227817412 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.515C>A p.Ala172Glu p.A172E ENST00000366757 3/5 359 332 27 329 329 0 strelka-varscan-mutect PRSS38,missense_variant,p.Ala172Glu,ENST00000366757,NM_183062.2; A ENST00000366757 Transcript missense_variant 539/1267 515/981 172/326 A/E gCa/gAa COSM3804149 1 1 PRSS38 HGNC HGNC:29625 protein_coding YES CCDS1563.1 ENSP00000355719 A1L453 UPI00001BBB34 NM_183062.2 deleterious(0) 3/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24250,hmmpanther:PTHR24250:SF30,SMART_domains:SM00020,Superfamily_domains:SSF50494 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 227817412 227817412 C A 1 0 0 0 0 1 0 0 0 12774 710 25 2 2 PRSS38 1 227817412 Missense_Mutation SNP C C3N-01414_T 4422093 227817412 21139010 44 23244 OBSCN 0 . GRCh38 1 228213676 228213676 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1224G>T p.Glu408Asp p.E408D ENST00000570156 3/116 192 162 30 196 195 1 strelka-varscan-mutect OBSCN,missense_variant,p.Glu408Asp,ENST00000570156,NM_001271223.2;OBSCN,missense_variant,p.Glu408Asp,ENST00000366707,;OBSCN,missense_variant,p.Glu408Asp,ENST00000422127,NM_001098623.2;OBSCN,missense_variant,p.Glu408Asp,ENST00000636875,;OBSCN,missense_variant,p.Glu408Asp,ENST00000284548,NM_052843.3;C1orf145,upstream_gene_variant,,ENST00000295012,;OBSCN,upstream_gene_variant,,ENST00000493977,;C1orf145,upstream_gene_variant,,ENST00000337335,;C1orf145,upstream_gene_variant,,ENST00000472613,; T ENST00000570156 Transcript missense_variant 1298/26925 1224/26772 408/8923 E/D gaG/gaT 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 tolerated(0.59) 3/116 PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409 MODERATE SNV 5 1 PASS rs1331337644 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 228213676 228213676 G T 1 0 0 0 0 1 0 0 0 10889 991 35 2 2 OBSCN 1 228213676 Missense_Mutation SNP G C3N-01414_T 396264 228213676 20742746 45 23245 DISC1 0 . GRCh38 1 231693826 231693826 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.68G>C p.Gly23Ala p.G23A ENST00000366633 2/10 561 482 79 562 562 0 strelka-varscan-mutect DISC1,missense_variant,p.Gly23Ala,ENST00000439617,NM_001164537.1,NM_018662.2;DISC1,missense_variant,p.Gly23Ala,ENST00000622252,;DISC1,missense_variant,p.Gly23Ala,ENST00000366637,NM_001012957.1;DISC1,missense_variant,p.Gly23Ala,ENST00000620189,NM_001164540.1;DISC1,missense_variant,p.Gly23Ala,ENST00000602281,NM_001164542.1,NM_001164544.1;DISC1,missense_variant,p.Gly23Ala,ENST00000366633,NM_001164539.1;DISC1,missense_variant,p.Gly23Ala,ENST00000539444,NM_001164545.1,NM_001164548.1;DISC1,missense_variant,p.Gly23Ala,ENST00000317586,NM_001012958.1;DISC1,missense_variant,p.Gly23Ala,ENST00000535983,NM_001164541.1,NM_001164538.1;DISC1,missense_variant,p.Gly23Ala,ENST00000628350,NM_001164546.1,NM_001164549.1,NM_001164547.1;DISC1,missense_variant,p.Gly23Ala,ENST00000537876,;DISC1,missense_variant,p.Gly23Ala,ENST00000366636,NM_001012959.1;DISC1,intron_variant,,ENST00000602873,NM_001164556.1;DISC1,splice_region_variant,,ENST00000602600,;TSNAX-DISC1,missense_variant,p.Ala166Pro,ENST00000602956,;DISC1,missense_variant,p.Gly23Ala,ENST00000535944,;DISC1,missense_variant,p.Gly23Ala,ENST00000295051,;DISC1,missense_variant,p.Gly23Ala,ENST00000602822,;DISC1,missense_variant,p.Gly23Ala,ENST00000602713,;DISC1,missense_variant,p.Gly23Ala,ENST00000602700,;DISC1,missense_variant,p.Gly23Ala,ENST00000366632,;TSNAX-DISC1,splice_region_variant,,ENST00000602962,;TSNAX-DISC1,splice_region_variant,,ENST00000602567,;TSNAX-DISC1,splice_region_variant,,ENST00000602634,;TSNAX-DISC1,splice_region_variant,,ENST00000602885,;DISC1,splice_region_variant,,ENST00000422590,;DISC1,splice_region_variant,,ENST00000468399,; C ENST00000366633 Transcript missense_variant,splice_region_variant 121/2676 68/2268 23/755 G/A gGc/gCc 1 1 DISC1 HGNC HGNC:2888 protein_coding YES CCDS53482.1 ENSP00000355593 Q9NRI5 UPI0001A61692 NM_001164539.1 deleterious(0.01) 2/10 hmmpanther:PTHR14332,hmmpanther:PTHR14332:SF4 MODERATE 1 SNV 1 1 PASS rs1312907239 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 231693826 231693826 G C 1 0 0 0 0 1 0 0 0 4344 1217 42 4 4 DISC1 1 231693826 Missense_Mutation SNP G C3N-01414_T 3480150 231693826 17262596 46 23246 SLC35F3 0 . GRCh38 1 234316668 234316668 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.895C>A p.His299Asn p.H299N ENST00000366618 5/8 140 120 20 120 120 0 strelka-varscan-mutect SLC35F3,missense_variant,p.His299Asn,ENST00000366618,NM_173508.3;SLC35F3,missense_variant,p.His230Asn,ENST00000366617,NM_001300845.1; A ENST00000366618 Transcript missense_variant 1040/2891 895/1473 299/490 H/N Cac/Aac 1 1 SLC35F3 HGNC HGNC:23616 protein_coding YES CCDS1600.1 ENSP00000355577 Q8IY50 UPI000006DD13 NM_173508.3 tolerated(0.54) 5/8 hmmpanther:PTHR19346,hmmpanther:PTHR19346:SF3 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 234316668 234316668 C A 1 0 0 0 0 1 0 0 0 14861 594 21 2 2 SLC35F3 1 234316668 Missense_Mutation SNP C C3N-01414_T 2622842 234316668 14639754 47 23247 RYR2 0 . GRCh38 1 237784431 237784431 + Missense_Mutation SNP C C T C3N-01414_T C3N-01414_N C C c.12719C>T p.Thr4240Met p.T4240M ENST00000366574 90/105 690 626 64 688 688 0 strelka-varscan-mutect RYR2,missense_variant,p.Thr4240Met,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Thr4224Met,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript missense_variant 13036/16562 12719/14904 4240/4967 T/M aCg/aTg COSM5053275,COSM5053276 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.08) 90/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 237784431 237784431 C T 1 0 0 0 0 1 0 0 0 14029 536 19 1 1 RYR2 1 237784431 Missense_Mutation SNP C C3N-01414_T 3467763 237784431 11171991 48 23248 CHRM3 0 . GRCh38 1 239908616 239908616 + Missense_Mutation SNP C C A rs748889549 C3N-01414_T C3N-01414_N C C c.1165C>A p.Leu389Met p.L389M ENST00000255380 5/5 131 106 25 130 130 0 strelka-varscan-mutect CHRM3,missense_variant,p.Leu389Met,ENST00000255380,NM_000740.2;CHRM3,missense_variant,p.Leu389Met,ENST00000615928,;CHRM3,downstream_gene_variant,,ENST00000448020,; A ENST00000255380 Transcript missense_variant 1944/8780 1165/1773 389/590 L/M Ctg/Atg rs748889549 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 tolerated(0.19) 5/5 Pfam_domain:PF00001,PROSITE_profiles:PS50262,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS rs748889549 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 239908616 239908616 C A 1 0 0 0 0 1 0 0 0 3138 680 24 2 2 CHRM3 1 239908616 Missense_Mutation SNP C C3N-01414_T 2124185 239908616 9047806 49 23249 FMN2 0 . GRCh38 1 240092204 240092204 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.95T>A p.Val32Glu p.V32E ENST00000319653 1/18 114 80 34 122 122 0 strelka-varscan-mutect FMN2,missense_variant,p.Val32Glu,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,intron_variant,,ENST00000447095,; A ENST00000319653 Transcript missense_variant 325/6434 95/5169 32/1722 V/E gTg/gAg 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 tolerated_low_confidence(0.08) 1/18 MODERATE 1 SNV 5 1 PASS . . 0 178 29 3 0 0 0 0 -20 0.9675028 0 1 1 0 A 3 1 77 240092204 240092204 T A 1 0 0 0 0 1 0 0 0 5806 1696 59 4 4 FMN2 1 240092204 Missense_Mutation SNP T C3N-01414_T 183588 240092204 8864218 50 23250 PLD5 0 . GRCh38 1 242100746 242100746 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.1276A>G p.Thr426Ala p.T426A ENST00000536534 9/10 263 237 26 280 280 0 strelka-varscan-mutect PLD5,missense_variant,p.Thr426Ala,ENST00000536534,;PLD5,missense_variant,p.Thr426Ala,ENST00000442594,NM_001320272.1,NM_152666.2;PLD5,missense_variant,p.Thr364Ala,ENST00000427495,NM_001195812.1,NM_001195811.1;PLD5,3_prime_UTR_variant,,ENST00000314833,;PLD5,3_prime_UTR_variant,,ENST00000366545,; C ENST00000536534 Transcript missense_variant 1518/8721 1276/1611 426/536 T/A Aca/Gca 1 -1 PLD5 HGNC HGNC:26879 protein_coding YES CCDS1621.2 ENSP00000440896 Q8N7P1 UPI000040E1A4 tolerated(0.67) 9/10 hmmpanther:PTHR10185:SF9,hmmpanther:PTHR10185,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 242100746 242100746 T C 1 0 0 0 0 1 0 0 0 12143 1638 57 5 5 PLD5 1 242100746 Missense_Mutation SNP T C3N-01414_T 2008542 242100746 6855676 51 23251 HNRNPU 0 . GRCh38 1 244856727 244856727 + Splice_Site SNP C C T novel C3N-01414_T C3N-01414_N C C c.1743+1G>A p.X581_splice ENST00000283179 140 125 15 141 141 0 strelka-varscan-mutect HNRNPU,splice_donor_variant,,ENST00000444376,NM_004501.3;HNRNPU,splice_donor_variant,,ENST00000283179,NM_031844.2;HNRNPU,downstream_gene_variant,,ENST00000440865,;HNRNPU,splice_donor_variant,,ENST00000366525,;HNRNPU,splice_donor_variant,,ENST00000483966,;HNRNPU,splice_donor_variant,,ENST00000468690,;HNRNPU,downstream_gene_variant,,ENST00000465881,;HNRNPU,upstream_gene_variant,,ENST00000475997,;HNRNPU,upstream_gene_variant,,ENST00000489705,; T ENST00000283179 Transcript splice_donor_variant -/3704 1743/2478 581/825 1 -1 HNRNPU HGNC HGNC:5048 protein_coding YES CCDS41479.1 ENSP00000283179 Q00839 UPI000040E1C8 NM_031844.2 9/13 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 77 244856727 244856727 C T 1 0 0 0 0 0 0 1 0 7168 521 18 3 3 HNRNPU 1 244856727 Splice_Site SNP C C3N-01414_T 2755981 244856727 4099695 52 23252 KIF26B 0 . GRCh38 1 245684285 245684285 + Missense_Mutation SNP C C A rs373588212 C3N-01414_T C3N-01414_N C C c.2311C>A p.Arg771Ser p.R771S ENST00000407071 11/15 174 100 74 199 199 0 strelka-varscan-mutect KIF26B,missense_variant,p.Arg390Ser,ENST00000366518,;KIF26B,missense_variant,p.Arg771Ser,ENST00000407071,NM_018012.3;KIF26B,non_coding_transcript_exon_variant,,ENST00000483253,; A ENST00000407071 Transcript missense_variant 2751/7287 2311/6327 771/2108 R/S Cgt/Agt rs373588212,COSM4165118,COSM4165119 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 deleterious(0) 11/15 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF407,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs373588212 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 245684285 245684285 C A 1 0 0 0 0 1 0 0 0 8160 652 23 1 1 KIF26B 1 245684285 Missense_Mutation SNP C C3N-01414_T 827558 245684285 3272137 53 23253 GCSAML 0 . GRCh38 1 247574148 247574148 + Missense_Mutation SNP C C A rs768929122 C3N-01414_T C3N-01414_N C C c.174C>A p.Asn58Lys p.N58K ENST00000536561 7/7 205 186 19 243 242 1 strelka-varscan-mutect GCSAML,missense_variant,p.Asn38Lys,ENST00000366491,NM_001281834.1;GCSAML,missense_variant,p.Asn58Lys,ENST00000536561,NM_001281853.1;GCSAML,missense_variant,p.Asn38Lys,ENST00000366489,NM_001281835.1;GCSAML,missense_variant,p.Asn26Lys,ENST00000623578,NM_001281837.1;GCSAML,missense_variant,p.Asn58Lys,ENST00000366488,NM_145278.4;GCSAML,missense_variant,p.Asn26Lys,ENST00000463359,;GCSAML,missense_variant,p.Asn26Lys,ENST00000527084,NM_001281836.1;GCSAML,missense_variant,p.Asn26Lys,ENST00000527541,NM_001281838.1;GCSAML,missense_variant,p.Asn26Lys,ENST00000529512,;GCSAML,missense_variant,p.Asn58Lys,ENST00000526896,;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000536561 Transcript missense_variant 521/4063 174/408 58/135 N/K aaC/aaA rs768929122,COSM3771687 1 1 GCSAML HGNC HGNC:29583 protein_coding YES CCDS1635.1 ENSP00000446460 Q5JQS6 UPI000004EBD8 NM_001281853.1 tolerated(0.13) 7/7 Pfam_domain:PF15666,hmmpanther:PTHR35351,hmmpanther:PTHR35351:SF1,Low_complexity_(Seg):seg 0,1 MODERATE SNV 4 0,1 1 PASS rs768929122 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 247574148 247574148 C A 1 0 0 0 0 1 0 0 0 6176 550 19 1 1 GCSAML 1 247574148 Missense_Mutation SNP C C3N-01414_T 1889863 247574148 1382274 54 23254 OR2G2 0 . GRCh38 1 247589109 247589109 + Silent SNP G G A rs756487359 C3N-01414_T C3N-01414_N G G c.750G>A p.= p.V250V ENST00000320065 1/1 265 238 27 302 302 0 strelka-varscan-mutect OR2G2,synonymous_variant,p.=,ENST00000320065,NM_001001915.1;RP11-978I15.10,intron_variant,,ENST00000435333,;RP11-978I15.10,intron_variant,,ENST00000446347,; A ENST00000320065 Transcript synonymous_variant 750/954 750/954 250/317 V gtG/gtA rs756487359,COSM680682 1 1 OR2G2 HGNC HGNC:15007 protein_coding YES CCDS31092.1 ENSP00000326349 Q8NGZ5 UPI0000061EB9 NM_001001915.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF132,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW SNV 0,1 1 PASS rs756487359 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 247589109 247589109 G A 1 0 0 0 0 0 0 0 1 11076 1335 47 3 3 OR2G2 1 247589109 Silent SNP G C3N-01414_T 14961 247589109 1367313 55 23255 OR2T12 0 . GRCh38 1 248294885 248294885 + Missense_Mutation SNP G G A rs200352170 C3N-01414_T C3N-01414_N G G c.694C>T p.Arg232Cys p.R232C ENST00000317996 1/1 432 390 42 508 508 0 varscan-mutect OR2T12,missense_variant,p.Arg232Cys,ENST00000317996,NM_001004692.1; A ENST00000317996 Transcript missense_variant 694/963 694/963 232/320 R/C Cgc/Tgc rs200352170,COSM3400604 1 -1 OR2T12 HGNC HGNC:19592 protein_coding YES CCDS31110.1 ENSP00000324583 Q8NG77 UPI000004B235 NM_001004692.1 tolerated(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs200352170 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 248294885 248294885 G A 1 0 0 0 0 1 0 0 0 11096 1116 39 1 1 OR2T12 1 248294885 Missense_Mutation SNP G C3N-01414_T 705776 248294885 661537 56 23256 OR2T10 0 . GRCh38 1 248593464 248593464 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.305A>T p.Tyr102Phe p.Y102F ENST00000330500 1/1 114 69 45 158 158 0 strelka-varscan-mutect OR2T10,missense_variant,p.Tyr102Phe,ENST00000330500,NM_001004693.1;Y_RNA,downstream_gene_variant,,ENST00000364732,; A ENST00000330500 Transcript missense_variant 305/939 305/939 102/312 Y/F tAc/tTc 1 -1 OR2T10 HGNC HGNC:19573 protein_coding YES CCDS31121.1 ENSP00000329210 Q8NGZ9 A0A126GV79 UPI000004F23B NM_001004693.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF101,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 4 204 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 248593464 248593464 T A 1 0 0 0 0 1 0 0 0 11095 1638 57 4 4 OR2T10 1 248593464 Missense_Mutation SNP T C3N-01414_T 298579 248593464 362958 57 23257 OR14I1 0 . GRCh38 1 248681943 248681943 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.362A>T p.Tyr121Phe p.Y121F ENST00000342623 1/1 295 193 102 329 329 0 strelka-varscan-mutect OR14I1,missense_variant,p.Tyr121Phe,ENST00000342623,NM_001004734.1; A ENST00000342623 Transcript missense_variant 362/936 362/936 121/311 Y/F tAt/tTt 1 -1 OR14I1 HGNC HGNC:19575 protein_coding YES CCDS31125.1 ENSP00000339726 A6ND48 UPI0000199BC9 NM_001004734.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF316,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1470562860 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 248681943 248681943 T A 1 0 0 0 0 1 0 0 0 11024 1406 49 4 4 OR14I1 1 248681943 Missense_Mutation SNP T C3N-01414_T 88479 248681943 274479 58 23258 SNTG2 0 . GRCh38 2 1237998 1237998 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.830G>T p.Arg277Met p.R277M ENST00000308624 10/17 148 118 30 166 165 1 strelka-varscan-mutect SNTG2,missense_variant,p.Arg277Met,ENST00000308624,NM_018968.3;SNTG2,missense_variant,p.Arg150Met,ENST00000407292,;SNTG2,intron_variant,,ENST00000494178,; T ENST00000308624 Transcript missense_variant 959/1888 830/1620 277/539 R/M aGg/aTg 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 tolerated(0.07) 10/17 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 1237998 1237998 G T 1 0 0 0 0 1 0 0 0 15195 1000 35 2 2 SNTG2 2 1237998 Missense_Mutation SNP G C3N-01414_T 1237998 240955531 59 23259 SNTG2 0 . GRCh38 2 1367422 1367422 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1568C>G p.Pro523Arg p.P523R ENST00000308624 17/17 238 200 38 273 273 0 strelka-varscan-mutect SNTG2,missense_variant,p.Pro523Arg,ENST00000308624,NM_018968.3;SNTG2,missense_variant,p.Pro396Arg,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000471239,;SNTG2,non_coding_transcript_exon_variant,,ENST00000472606,; G ENST00000308624 Transcript missense_variant 1697/1888 1568/1620 523/539 P/R cCc/cGc 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 deleterious(0) 17/17 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 1367422 1367422 C G 1 0 0 0 0 1 0 0 0 15195 623 22 4 4 SNTG2 2 1367422 Missense_Mutation SNP C C3N-01414_T 129424 1367422 240826107 60 23260 PXDN 0 . GRCh38 2 1638918 1638918 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.4134T>A p.Asp1378Glu p.D1378E ENST00000252804 21/23 226 156 70 306 305 1 strelka-varscan-mutect PXDN,missense_variant,p.Asp1378Glu,ENST00000252804,NM_012293.2;PXDN,downstream_gene_variant,,ENST00000477093,;PXDN,non_coding_transcript_exon_variant,,ENST00000478155,;PXDN,intron_variant,,ENST00000453308,;PXDN,upstream_gene_variant,,ENST00000493654,; T ENST00000252804 Transcript missense_variant 4185/6808 4134/4440 1378/1479 D/E gaT/gaA 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 tolerated(1) 21/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 1638918 1638918 A T 1 0 0 0 0 1 0 0 0 13001 214 8 4 4 PXDN 2 1638918 Missense_Mutation SNP A C3N-01414_T 271496 1638918 240554611 61 23261 NT5C1B 0 . GRCh38 2 18584741 18584741 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.676C>G p.Gln226Glu p.Q226E ENST00000359846 5/10 154 125 29 185 185 0 strelka-varscan-mutect NT5C1B,missense_variant,p.Gln166Glu,ENST00000304081,NM_033253.3;NT5C1B,missense_variant,p.Gln226Glu,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Gln226Glu,ENST00000532967,NM_001199104.1;NT5C1B-RDH14,missense_variant,p.Gln168Glu,ENST00000444297,NM_001199103.1;NT5C1B,upstream_gene_variant,,ENST00000418427,;NT5C1B,downstream_gene_variant,,ENST00000416783,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,synonymous_variant,p.=,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,; C ENST00000359846 Transcript missense_variant 754/2475 676/1833 226/610 Q/E Cag/Gag 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 tolerated_low_confidence(1) 5/10 hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 18584741 18584741 G C 1 0 0 0 0 1 0 0 0 10749 1357 47 4 4 NT5C1B 2 18584741 Missense_Mutation SNP G C3N-01414_T 16945823 18584741 223608788 62 23262 APOB 0 . GRCh38 2 21004326 21004326 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.12030C>A p.= p.G4010G ENST00000233242 28/29 371 303 68 395 394 1 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; T ENST00000233242 Transcript synonymous_variant 12158/14121 12030/13692 4010/4563 G ggC/ggA 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 28/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 21004326 21004326 G T 1 0 0 0 0 0 0 0 1 907 1306 46 2 2 APOB 2 21004326 Silent SNP G C3N-01414_T 2419585 21004326 221189203 63 23263 APOB 0 . GRCh38 2 21009363 21009363 + Nonsense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.7505C>A p.Ser2502Ter p.S2502* ENST00000233242 26/29 423 279 144 483 483 0 strelka-varscan-mutect APOB,stop_gained,p.Ser2502Ter,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript stop_gained 7633/14121 7505/13692 2502/4563 S/* tCa/tAa CM075985 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 HIGH 1 SNV 1 1 1 PASS rs1282766946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 21009363 21009363 G T 1 0 0 0 0 0 1 0 0 907 1294 45 2 2 APOB 2 21009363 Nonsense_Mutation SNP G C3N-01414_T 5037 21009363 221184166 64 23264 SLC8A1 0 . GRCh38 2 40428560 40428560 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.1721A>G p.Tyr574Cys p.Y574C ENST00000403092 2/11 202 178 24 191 191 0 strelka-varscan-mutect SLC8A1,missense_variant,p.Tyr574Cys,ENST00000406785,;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000403092,;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000405269,;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Tyr574Cys,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,missense_variant,p.Tyr571Cys,ENST00000407929,; C ENST00000403092 Transcript missense_variant 1755/3178 1721/2922 574/973 Y/C tAt/tGt 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 deleterious(0) 2/11 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,SMART_domains:SM00237,Superfamily_domains:SSF141072,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 77 40428560 40428560 T C 1 0 0 0 0 1 0 0 0 14989 1406 49 5 5 SLC8A1 2 40428560 Missense_Mutation SNP T C3N-01414_T 19419197 40428560 201764969 65 23265 NRXN1 0 . GRCh38 2 51028021 51028021 + Missense_Mutation SNP G G C C3N-01414_T C3N-01414_N G G c.253C>G p.Arg85Gly p.R85G ENST00000404971 2/24 106 85 21 110 110 0 strelka-varscan-mutect NRXN1,missense_variant,p.Arg85Gly,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Arg85Gly,ENST00000625672,;NRXN1,missense_variant,p.Arg85Gly,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Arg85Gly,ENST00000401669,;NRXN1,missense_variant,p.Arg85Gly,ENST00000405472,;NRXN1,missense_variant,p.Arg85Gly,ENST00000405581,;NRXN1,missense_variant,p.Arg85Gly,ENST00000630543,;NRXN1,missense_variant,p.Arg85Gly,ENST00000637511,;NRXN1,missense_variant,p.Arg85Gly,ENST00000628515,;NRXN1,missense_variant,p.Arg85Gly,ENST00000626899,;NRXN1,upstream_gene_variant,,ENST00000636066,;NRXN1,upstream_gene_variant,,ENST00000627198,;NRXN1,upstream_gene_variant,,ENST00000496792,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000635126,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,upstream_gene_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; C ENST00000404971 Transcript missense_variant 1593/7578 253/4644 85/1547 R/G Cgc/Ggc COSM1021560,COSM1021561,COSM1592153,COSM4314236 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.02) 2/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 51028021 51028021 G C 1 0 0 0 0 1 0 0 0 10724 1087 38 4 4 NRXN1 2 51028021 Missense_Mutation SNP G C3N-01414_T 10599461 51028021 191165508 66 23266 TSPYL6 0 . GRCh38 2 54254934 54254934 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.1218G>A p.= p.G406G ENST00000317802 1/1 96 85 11 130 129 1 strelka-varscan-mutect TSPYL6,synonymous_variant,p.=,ENST00000317802,NM_001003937.2;ACYP2,intron_variant,,ENST00000394666,NM_138448.3;ACYP2,intron_variant,,ENST00000607452,;ACYP2,intron_variant,,ENST00000303536,;ACYP2,intron_variant,,ENST00000606865,;ACYP2,intron_variant,,ENST00000494922,; T ENST00000317802 Transcript synonymous_variant 1339/3089 1218/1233 406/410 G ggG/ggA 1 -1 TSPYL6 HGNC HGNC:14521 protein_coding YES CCDS42682.1 ENSP00000417919 Q8N831 A0A140VJY4 UPI000006CF77 NM_001003937.2 1/1 LOW SNV 1 PASS . . 0 206 4 0 0 0 0 0 -19.99946 1 1 1 1 0 T 2 4 77 54254934 54254934 C T 1 0 0 0 0 0 0 0 1 17170 494 18 3 3 TSPYL6 2 54254934 Silent SNP C C3N-01414_T 3226913 54254934 187938595 67 23267 USP34 0 . GRCh38 2 61331288 61331289 + Frame_Shift_Del DEL TG TG - novel C3N-01414_T C3N-01414_N TG TG c.2917_2918delCA p.Gln973LysfsTer8 p.Q973Kfs*8 ENST00000398571 20/80 210 172 38 306 306 0 sindel-varindel-pindel USP34,frameshift_variant,p.Gln973LysfsTer8,ENST00000398571,NM_014709.3; - ENST00000398571 Transcript frameshift_variant 2994-2995/11357 2917-2918/10641 973/3546 Q/X CAa/a 1 -1 USP34 HGNC HGNC:20066 protein_coding YES CCDS42686.1 ENSP00000381577 Q70CQ2 UPI0000410E09 NM_014709.3 20/80 HIGH 1 deletion 2 1 PASS . . 0 200 0 5 5 0 0 0 -19.88519 0.5293312 1 1 1 0 - 7 5 77 61331288 61331288 TG - 1 0 1 0 1 0 0 0 0 17607 1812 63 0 0 USP34 2 61331288 Frame_Shift_Del DEL TG C3N-01414_T 7076354 61331288 180862241 68 23268 ASPRV1 0 . GRCh38 2 69961355 69961355 + Missense_Mutation SNP C C T rs554895120 C3N-01414_T C3N-01414_N C C c.334G>A p.Val112Ile p.V112I ENST00000320256 1/1 223 202 21 230 230 0 strelka-varscan-mutect ASPRV1,missense_variant,p.Val112Ile,ENST00000320256,NM_152792.2;PCBP1-AS1,downstream_gene_variant,,ENST00000435880,;PCBP1-AS1,downstream_gene_variant,,ENST00000630214,;PCBP1-AS1,downstream_gene_variant,,ENST00000419542,;PCBP1-AS1,downstream_gene_variant,,ENST00000627327,;PCBP1-AS1,downstream_gene_variant,,ENST00000629533,;PCBP1-AS1,downstream_gene_variant,,ENST00000627918,;PCBP1-AS1,downstream_gene_variant,,ENST00000627181,;PCBP1-AS1,downstream_gene_variant,,ENST00000628305,;PCBP1-AS1,downstream_gene_variant,,ENST00000626515,;PCBP1-AS1,downstream_gene_variant,,ENST00000625625,;PCBP1-AS1,downstream_gene_variant,,ENST00000628308,;PCBP1-AS1,downstream_gene_variant,,ENST00000626898,;PCBP1-AS1,downstream_gene_variant,,ENST00000629605,;PCBP1-AS1,downstream_gene_variant,,ENST00000630746,;PCBP1-AS1,downstream_gene_variant,,ENST00000630975,;PCBP1-AS1,downstream_gene_variant,,ENST00000630522,;PCBP1-AS1,downstream_gene_variant,,ENST00000625447,;PCBP1-AS1,downstream_gene_variant,,ENST00000627398,;PCBP1-AS1,downstream_gene_variant,,ENST00000628659,;PCBP1-AS1,downstream_gene_variant,,ENST00000627050,;PCBP1-AS1,downstream_gene_variant,,ENST00000626343,;PCBP1-AS1,downstream_gene_variant,,ENST00000628920,;PCBP1-AS1,downstream_gene_variant,,ENST00000628883,;PCBP1-AS1,downstream_gene_variant,,ENST00000630759,;PCBP1-AS1,downstream_gene_variant,,ENST00000629603,;PCBP1-AS1,downstream_gene_variant,,ENST00000629339,;PCBP1-AS1,downstream_gene_variant,,ENST00000628837,;PCBP1-AS1,downstream_gene_variant,,ENST00000613944,;PCBP1-AS1,downstream_gene_variant,,ENST00000631110,;PCBP1-AS1,downstream_gene_variant,,ENST00000625215,;PCBP1-AS1,downstream_gene_variant,,ENST00000631107,;PCBP1-AS1,downstream_gene_variant,,ENST00000625783,;PCBP1-AS1,downstream_gene_variant,,ENST00000628551,;PCBP1-AS1,downstream_gene_variant,,ENST00000626609,;PCBP1-AS1,downstream_gene_variant,,ENST00000629909,;PCBP1-AS1,downstream_gene_variant,,ENST00000596259,;PCBP1-AS1,downstream_gene_variant,,ENST00000626370,;PCBP1-AS1,downstream_gene_variant,,ENST00000628374,;PCBP1-AS1,downstream_gene_variant,,ENST00000625888,;PCBP1-AS1,downstream_gene_variant,,ENST00000626495,;PCBP1-AS1,downstream_gene_variant,,ENST00000629084,;PCBP1-AS1,downstream_gene_variant,,ENST00000628667,;PCBP1-AS1,downstream_gene_variant,,ENST00000625864,;PCBP1-AS1,downstream_gene_variant,,ENST00000626842,;PCBP1-AS1,downstream_gene_variant,,ENST00000627189,;PCBP1-AS1,downstream_gene_variant,,ENST00000629184,;PCBP1-AS1,downstream_gene_variant,,ENST00000629415,;PCBP1-AS1,downstream_gene_variant,,ENST00000629836,;PCBP1-AS1,downstream_gene_variant,,ENST00000626735,;PCBP1-AS1,downstream_gene_variant,,ENST00000626632,;PCBP1-AS1,downstream_gene_variant,,ENST00000628322,;PCBP1-AS1,downstream_gene_variant,,ENST00000627325,;PCBP1-AS1,downstream_gene_variant,,ENST00000629506,;PCBP1-AS1,downstream_gene_variant,,ENST00000625490,;PCBP1-AS1,downstream_gene_variant,,ENST00000627630,;PCBP1-AS1,downstream_gene_variant,,ENST00000625439,;PCBP1-AS1,downstream_gene_variant,,ENST00000630457,;PCBP1-AS1,downstream_gene_variant,,ENST00000628201,;PCBP1-AS1,downstream_gene_variant,,ENST00000625838,;PCBP1-AS1,downstream_gene_variant,,ENST00000413436,;PCBP1-AS1,downstream_gene_variant,,ENST00000630985,;PCBP1-AS1,downstream_gene_variant,,ENST00000630280,;PCBP1-AS1,downstream_gene_variant,,ENST00000626683,;PCBP1-AS1,downstream_gene_variant,,ENST00000625691,;PCBP1-AS1,downstream_gene_variant,,ENST00000628147,;PCBP1-AS1,downstream_gene_variant,,ENST00000418564,;PCBP1-AS1,downstream_gene_variant,,ENST00000457076,;PCBP1-AS1,downstream_gene_variant,,ENST00000415222,;PCBP1-AS1,downstream_gene_variant,,ENST00000626834,; T ENST00000320256 Transcript missense_variant 911/2177 334/1032 112/343 V/I Gtc/Atc rs554895120,COSM4630792 1 -1 ASPRV1 HGNC HGNC:26321 protein_coding YES CCDS1897.1 ENSP00000315383 Q53RT3 UPI0000140820 NM_152792.2 tolerated(0.2) 1/1 hmmpanther:PTHR37006 0,1 MODERATE 1 SNV 0,1 1 PASS rs554895120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 69961355 69961355 C T 1 0 0 0 0 1 0 0 0 1205 536 19 1 1 ASPRV1 2 69961355 Missense_Mutation SNP C C3N-01414_T 8630067 69961355 172232174 69 23269 RMND5A 0 . GRCh38 2 86765184 86765184 + Missense_Mutation SNP C C T rs143570524 C3N-01414_T C3N-01414_N C C c.679C>T p.His227Tyr p.H227Y ENST00000283632 5/9 94 72 22 120 120 0 strelka-varscan-mutect RMND5A,missense_variant,p.His227Tyr,ENST00000283632,NM_022780.3;RMND5A,upstream_gene_variant,,ENST00000472843,; T ENST00000283632 Transcript missense_variant 1174/6301 679/1176 227/391 H/Y Cat/Tat rs143570524,COSM108567 1 1 RMND5A HGNC HGNC:25850 protein_coding YES CCDS1991.1 ENSP00000283632 Q9H871 UPI000000DC2B NM_022780.3 tolerated(0.17) 5/9 hmmpanther:PTHR12170,hmmpanther:PTHR12170:SF5,Pfam_domain:PF10607,SMART_domains:SM00757 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs143570524 . 0 178 29 3 0 0 0 0 -20 0.9518064 0 1 1 0 T 3 4 77 86765184 86765184 C T 1 0 0 0 0 1 0 0 0 13576 826 29 3 3 RMND5A 2 86765184 Missense_Mutation SNP C C3N-01414_T 16803829 86765184 155428345 70 23270 SMYD1 0 . GRCh38 2 88096614 88096614 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.718G>C p.Gly240Arg p.G240R ENST00000419482 6/10 110 100 10 144 144 0 strelka-varscan SMYD1,missense_variant,p.Gly240Arg,ENST00000419482,NM_198274.3;SMYD1,missense_variant,p.Gly227Arg,ENST00000444564,;SMYD1,intron_variant,,ENST00000438570,; C ENST00000419482 Transcript missense_variant 803/4433 718/1473 240/490 G/R Ggc/Cgc 1 1 SMYD1 HGNC HGNC:20986 protein_coding YES CCDS33240.1 ENSP00000393453 Q8NB12 A0A0A6YYB2 UPI000006EB68 NM_198274.3 tolerated(0.69) 6/10 PROSITE_profiles:PS50280,hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF184,Pfam_domain:PF00856,Gene3D:2.170.270.10,SMART_domains:SM00317,Superfamily_domains:SSF82199 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.69292 1 1 1 1 0 C 3 2 77 88096614 88096614 G C 1 0 0 0 0 1 0 0 0 15142 1000 35 4 4 SMYD1 2 88096614 Missense_Mutation SNP G C3N-01414_T 1331430 88096614 154096915 71 23271 SEMA4C 0 . GRCh38 2 96861305 96861305 + Missense_Mutation SNP C C A rs752586989 C3N-01414_T C3N-01414_N C C c.1823G>T p.Arg608Leu p.R608L ENST00000305476 15/15 219 173 46 210 210 0 strelka-varscan-mutect SEMA4C,missense_variant,p.Arg608Leu,ENST00000305476,NM_017789.4;ANKRD39,upstream_gene_variant,,ENST00000393537,NM_016466.5;SEMA4C,downstream_gene_variant,,ENST00000449330,;SEMA4C,downstream_gene_variant,,ENST00000442264,;ANKRD23,upstream_gene_variant,,ENST00000462692,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000482925,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000467747,;SEMA4C,non_coding_transcript_exon_variant,,ENST00000474420,;ANKRD39,upstream_gene_variant,,ENST00000443120,; A ENST00000305476 Transcript missense_variant 1956/3545 1823/2502 608/833 R/L cGg/cTg rs752586989 1 -1 SEMA4C HGNC HGNC:10731 protein_coding YES CCDS2029.1 ENSP00000306844 Q9C0C4 UPI00001A7981 NM_017789.4 tolerated(0.1) 15/15 PROSITE_profiles:PS50835,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF16,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs752586989 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 96861305 96861305 C A 1 0 0 0 0 1 0 0 0 14309 652 23 1 1 SEMA4C 2 96861305 Missense_Mutation SNP C C3N-01414_T 8764691 96861305 145332224 72 23272 ZC3H6 0 . GRCh38 2 112331263 112331263 + Missense_Mutation SNP C C T rs769924975 C3N-01414_T C3N-01414_N C C c.2345C>T p.Ala782Val p.A782V ENST00000409871 12/12 254 227 27 310 310 0 strelka-varscan-mutect ZC3H6,missense_variant,p.Ala782Val,ENST00000409871,NM_198581.2;ZC3H6,missense_variant,p.Ala782Val,ENST00000343936,;ZC3H6,upstream_gene_variant,,ENST00000502881,; T ENST00000409871 Transcript missense_variant 2746/11542 2345/3570 782/1189 A/V gCg/gTg rs769924975,COSM1005516 1 1 ZC3H6 HGNC HGNC:24762 protein_coding YES CCDS46393.1 ENSP00000386764 P61129 UPI00004215E8 NM_198581.2 tolerated(0.35) 12/12 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF22 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs769924975 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 77 112331263 112331263 C T 1 0 0 0 0 1 0 0 0 18146 768 27 1 1 ZC3H6 2 112331263 Missense_Mutation SNP C C3N-01414_T 15469958 112331263 129862266 73 23273 MYO7B 0 . GRCh38 2 127631266 127631266 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.4920C>A p.His1640Gln p.H1640Q ENST00000428314 36/47 163 94 69 149 148 1 strelka-varscan-mutect MYO7B,missense_variant,p.His1640Gln,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.His1640Gln,ENST00000409816,;MYO7B,missense_variant,p.His493Gln,ENST00000409090,;RP11-286H15.1,upstream_gene_variant,,ENST00000609697,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,;MYO7B,upstream_gene_variant,,ENST00000494959,; A ENST00000428314 Transcript missense_variant 4973/6715 4920/6351 1640/2116 H/Q caC/caA COSM398554,COSM398555 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 tolerated(0.48) 36/47 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 127631266 127631266 C A 1 0 0 0 0 1 0 0 0 10084 506 18 2 2 MYO7B 2 127631266 Missense_Mutation SNP C C3N-01414_T 15300003 127631266 114562263 74 23274 POTEI 0 . GRCh38 2 130500593 130500593 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.860T>C p.Val287Ala p.V287A ENST00000451531 4/15 457 428 29 547 545 2 varscan-mutect POTEI,missense_variant,p.Val287Ala,ENST00000451531,NM_001277406.1;POTEI,missense_variant,p.Val287Ala,ENST00000631234,;POTEI,missense_variant,p.Val287Ala,ENST00000615053,;RNU6-473P,upstream_gene_variant,,ENST00000516164,; G ENST00000451531 Transcript missense_variant 1291/7020 860/3228 287/1075 V/A gTg/gCg 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0) 4/15 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 130500593 130500593 A G 1 0 0 0 0 1 0 0 0 12382 159 6 5 5 POTEI 2 130500593 Missense_Mutation SNP A C3N-01414_T 2869327 130500593 111692936 75 23275 POTEJ 0 . GRCh38 2 130620094 130620094 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.749T>C p.Val250Ala p.V250A ENST00000409602 4/15 122 112 10 142 142 0 varscan-mutect POTEJ,missense_variant,p.Val250Ala,ENST00000409602,NM_001277083.1;RNU6-848P,upstream_gene_variant,,ENST00000515948,; C ENST00000409602 Transcript missense_variant 801/3383 749/3117 250/1038 V/A gTg/gCg 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0) 4/15 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 130620094 130620094 T C 1 0 0 0 0 1 0 0 0 12383 1696 59 5 5 POTEJ 2 130620094 Missense_Mutation SNP T C3N-01414_T 119501 130620094 111573435 76 23276 GPR148 0 . GRCh38 2 130729690 130729690 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.539C>A p.Pro180His p.P180H ENST00000309926 1/1 202 162 40 239 239 0 strelka-varscan-mutect GPR148,missense_variant,p.Pro180His,ENST00000309926,NM_207364.2; A ENST00000309926 Transcript missense_variant 621/1267 539/1044 180/347 P/H cCc/cAc 1 1 GPR148 HGNC HGNC:23623 protein_coding YES CCDS2163.1 ENSP00000308908 Q8TDV2 UPI0000048E0D NM_207364.2 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243:SF114,hmmpanther:PTHR24243,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 130729690 130729690 C A 1 0 0 0 0 1 0 0 0 6539 623 22 2 2 GPR148 2 130729690 Missense_Mutation SNP C C3N-01414_T 109596 130729690 111463839 77 23277 LCT 0 . GRCh38 2 135804862 135804862 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.4369C>T p.Leu1457Phe p.L1457F ENST00000264162 10/17 274 228 46 346 346 0 strelka-varscan-mutect LCT,missense_variant,p.Leu1457Phe,ENST00000264162,NM_002299.2;LCT,missense_variant,p.Leu889Phe,ENST00000452974,; A ENST00000264162 Transcript missense_variant 4380/6279 4369/5784 1457/1927 L/F Ctc/Ttc 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 tolerated(0.19) 10/17 Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 135804862 135804862 G A 1 0 0 0 0 1 0 0 0 8599 1000 35 3 3 LCT 2 135804862 Missense_Mutation SNP G C3N-01414_T 5075172 135804862 106388667 78 23278 NXPH2 0 . GRCh38 2 138671433 138671433 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.284C>A p.Ala95Glu p.A95E ENST00000272641 2/2 133 113 20 153 152 1 strelka-varscan-mutect NXPH2,missense_variant,p.Ala95Glu,ENST00000272641,NM_007226.2; T ENST00000272641 Transcript missense_variant 391/1052 284/795 95/264 A/E gCa/gAa 1 -1 NXPH2 HGNC HGNC:8076 protein_coding YES CCDS46421.1 ENSP00000272641 O95156 UPI000023FCD4 NM_007226.2 tolerated(0.26) 2/2 Pfam_domain:PF06312,PIRSF_domain:PIRSF038019,hmmpanther:PTHR17103,hmmpanther:PTHR17103:SF11 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 138671433 138671433 G T 1 0 0 0 0 1 0 0 0 10867 1319 46 2 2 NXPH2 2 138671433 Missense_Mutation SNP G C3N-01414_T 2866571 138671433 103522096 79 23279 LRP1B 0 . GRCh38 2 141020043 141020043 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1849A>T p.Asn617Tyr p.N617Y ENST00000389484 12/91 146 100 46 191 191 0 strelka-varscan-mutect LRP1B,missense_variant,p.Asn617Tyr,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 2821/16535 1849/13800 617/4599 N/Y Aat/Tat 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 12/91 PROSITE_profiles:PS51120,Pfam_domain:PF00058,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 77 141020043 141020043 T A 1 0 0 0 0 1 0 0 0 8850 1812 63 4 4 LRP1B 2 141020043 Missense_Mutation SNP T C3N-01414_T 2348610 141020043 101173486 80 23280 LYPD6B 0 . GRCh38 2 149213050 149213050 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.387C>A p.= p.I129I ENST00000409642 6/7 223 183 40 295 295 0 strelka-varscan-mutect LYPD6B,synonymous_variant,p.=,ENST00000409642,NM_177964.3;LYPD6B,synonymous_variant,p.=,ENST00000409029,NM_001317004.1;LYPD6B,synonymous_variant,p.=,ENST00000409876,;LYPD6B,synonymous_variant,p.=,ENST00000280115,;LYPD6B,non_coding_transcript_exon_variant,,ENST00000498249,;LYPD6B,downstream_gene_variant,,ENST00000442722,; A ENST00000409642 Transcript synonymous_variant 788/1577 387/624 129/207 I atC/atA 1 1 LYPD6B HGNC HGNC:27018 protein_coding YES CCDS46423.1 ENSP00000387077 Q8NI32 UPI00001BDB14 NM_177964.3 6/7 Pfam_domain:PF16975,hmmpanther:PTHR31171,hmmpanther:PTHR31171:SF3,Superfamily_domains:SSF57302 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 149213050 149213050 C A 1 0 0 0 0 0 0 0 1 9026 816 29 2 2 LYPD6B 2 149213050 Silent SNP C C3N-01414_T 8193007 149213050 92980479 81 23281 TTC21B 0 . GRCh38 2 165949607 165949607 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.139A>G p.Thr47Ala p.T47A ENST00000243344 2/29 427 389 38 521 521 0 strelka-varscan-mutect TTC21B,missense_variant,p.Thr47Ala,ENST00000243344,NM_024753.4;TTC21B-AS1,non_coding_transcript_exon_variant,,ENST00000440322,;TTC21B-AS1,downstream_gene_variant,,ENST00000443032,;TTC21B,non_coding_transcript_exon_variant,,ENST00000464374,;TTC21B,non_coding_transcript_exon_variant,,ENST00000476227,;TTC21B-AS1,downstream_gene_variant,,ENST00000446624,; C ENST00000243344 Transcript missense_variant 277/5482 139/3951 47/1316 T/A Aca/Gca 1 -1 TTC21B HGNC HGNC:25660 protein_coding YES CCDS33315.1 ENSP00000243344 Q7Z4L5 UPI000020900A NM_024753.4 tolerated(0.47) 2/29 hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10 MODERATE 1 SNV 1 1 PASS rs1158269801 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 165949607 165949607 T C 1 0 0 0 0 1 0 0 0 17196 1696 59 5 5 TTC21B 2 165949607 Missense_Mutation SNP T C3N-01414_T 16736557 165949607 76243922 82 23282 PLEKHA3 0 . GRCh38 2 178495618 178495618 + Silent SNP G G T rs779469726 C3N-01414_T C3N-01414_N G G c.573G>T p.= p.P191P ENST00000234453 5/8 149 117 32 157 157 0 strelka-varscan-mutect PLEKHA3,synonymous_variant,p.=,ENST00000234453,NM_019091.3;PLEKHA3,upstream_gene_variant,,ENST00000421187,;PLEKHA3,downstream_gene_variant,,ENST00000461474,;PLEKHA3,downstream_gene_variant,,ENST00000453653,; T ENST00000234453 Transcript synonymous_variant 975/13880 573/903 191/300 P ccG/ccT rs779469726 1 1 PLEKHA3 HGNC HGNC:14338 protein_coding YES CCDS33336.1 ENSP00000234453 Q9HB20 UPI000000DA8A NM_019091.3 5/8 LOW 1 SNV 1 1 PASS rs779469726 . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 178495618 178495618 G T 1 0 0 0 0 0 0 0 1 12150 1103 39 1 1 PLEKHA3 2 178495618 Silent SNP G C3N-01414_T 12546011 178495618 63697911 83 23283 TTN 0 . GRCh38 2 178633295 178633295 + Silent SNP G G A rs369959066 C3N-01414_T C3N-01414_N G G c.42978C>T p.= p.Y14326Y ENST00000589042 233/363 204 167 37 236 236 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN,downstream_gene_variant,,ENST00000414766,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000630096,;TTN-AS1,downstream_gene_variant,,ENST00000626954,;TTN-AS1,upstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000418062,;TTN-AS1,downstream_gene_variant,,ENST00000628296,; A ENST00000589042 Transcript synonymous_variant 43203/109224 42978/107976 14326/35991 Y taC/taT rs369959066,COSM4088610,COSM4088611,COSM4088612,COSM4088613 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 233/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 likely_benign 0,1,1,1,1 LOW 1 SNV 5 1,1,1,1,1 1 PASS rs369959066 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 178633295 178633295 G A 1 0 0 0 0 0 0 0 1 17245 1140 40 1 1 TTN 2 178633295 Silent SNP G C3N-01414_T 137677 178633295 63560234 84 23284 PDE1A 0 . GRCh38 2 182188988 182188988 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.1246T>C p.Ser416Pro p.S416P ENST00000435564 11/15 137 110 27 226 226 0 strelka-varscan-mutect PDE1A,missense_variant,p.Ser416Pro,ENST00000435564,NM_005019.4,NM_001258312.1;PDE1A,missense_variant,p.Ser400Pro,ENST00000351439,NM_001258313.1;PDE1A,missense_variant,p.Ser400Pro,ENST00000409365,;PDE1A,missense_variant,p.Ser382Pro,ENST00000358139,NM_001258314.1;PDE1A,missense_variant,p.Ser416Pro,ENST00000410103,NM_001003683.2; G ENST00000435564 Transcript missense_variant 1447/4885 1246/1638 416/545 S/P Tca/Cca 1 -1 PDE1A HGNC HGNC:8774 protein_coding YES CCDS2285.1 ENSP00000410309 P54750 UPI0000001072 NM_005019.4,NM_001258312.1 deleterious(0) 11/15 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF32,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS rs1481121989 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 182188988 182188988 A G 1 0 0 0 0 1 0 0 0 11721 275 10 5 5 PDE1A 2 182188988 Missense_Mutation SNP A C3N-01414_T 3555693 182188988 60004541 85 23285 CD28 0 . GRCh38 2 203734902 203734902 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.653A>T p.Tyr218Phe p.Y218F ENST00000324106 4/4 220 172 48 249 248 1 strelka-varscan-mutect CD28,missense_variant,p.Tyr218Phe,ENST00000324106,NM_006139.3;CD28,missense_variant,p.Tyr99Phe,ENST00000374481,NM_001243078.1;CD28,missense_variant,p.Tyr232Phe,ENST00000458610,; T ENST00000324106 Transcript missense_variant 802/4812 653/663 218/220 Y/F tAt/tTt 1 1 CD28 HGNC HGNC:1653 protein_coding YES CCDS2361.1 ENSP00000324890 P10747 UPI0000043F4D NM_006139.3 deleterious(0) 4/4 hmmpanther:PTHR11494,hmmpanther:PTHR11494:SF7,Prints_domain:PR01717 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 203734902 203734902 A T 1 0 0 0 0 1 0 0 0 2697 449 16 4 4 CD28 2 203734902 Missense_Mutation SNP A C3N-01414_T 21545914 203734902 38458627 86 23286 ABCA12 0 . GRCh38 2 214983778 214983778 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.4251G>T p.= p.R1417R ENST00000272895 29/53 403 321 82 670 670 0 strelka-varscan-mutect ABCA12,synonymous_variant,p.=,ENST00000272895,NM_173076.2;ABCA12,synonymous_variant,p.=,ENST00000389661,NM_015657.3; A ENST00000272895 Transcript synonymous_variant 4471/9100 4251/7788 1417/2595 R cgG/cgT 1 -1 ABCA12 HGNC HGNC:14637 protein_coding YES CCDS33372.1 ENSP00000272895 Q86UK0 UPI000019AB7A NM_173076.2 29/53 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF29,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 214983778 214983778 C A 1 0 0 0 0 0 0 0 1 34 842 30 2 2 ABCA12 2 214983778 Silent SNP C C3N-01414_T 11248876 214983778 27209751 87 23287 NCL 0 . GRCh38 2 231455435 231455435 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.2022A>T p.= p.G674G ENST00000322723 13/14 363 281 82 461 461 0 strelka-varscan-mutect NCL,synonymous_variant,p.=,ENST00000322723,NM_005381.2;NCL,downstream_gene_variant,,ENST00000356936,;AC017104.2,downstream_gene_variant,,ENST00000370380,;SNORA75,downstream_gene_variant,,ENST00000384158,;SNORD20,downstream_gene_variant,,ENST00000384550,;SNORD82,downstream_gene_variant,,ENST00000365530,;NCL,non_coding_transcript_exon_variant,,ENST00000461347,;NCL,downstream_gene_variant,,ENST00000494618,;NCL,downstream_gene_variant,,ENST00000466274,; A ENST00000322723 Transcript synonymous_variant 2263/4034 2022/2133 674/710 G ggA/ggT 1 -1 NCL HGNC HGNC:7667 protein_coding YES CCDS33397.1 ENSP00000318195 P19338 A0A024R4A0 UPI0000456F25 NM_005381.2 13/14 hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF392,Low_complexity_(Seg):seg,Superfamily_domains:SSF54928 LOW 1 SNV 2 1 PASS rs1253091814 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 231455435 231455435 T A 1 0 0 0 0 0 0 0 1 10244 1538 54 4 4 NCL 2 231455435 Silent SNP T C3N-01414_T 16471657 231455435 10738094 88 23288 ECEL1 0 . GRCh38 2 232481796 232481796 + Missense_Mutation SNP C C T rs760929496 C3N-01414_T C3N-01414_N C C c.1850G>A p.Gly617Asp p.G617D ENST00000304546 13/18 141 127 14 185 185 0 strelka-varscan-mutect ECEL1,missense_variant,p.Gly617Asp,ENST00000304546,NM_004826.3;ECEL1,missense_variant,p.Gly615Asp,ENST00000409941,NM_001290787.1;ECEL1,missense_variant,p.Gly32Asp,ENST00000411860,;ECEL1,non_coding_transcript_exon_variant,,ENST00000482346,; T ENST00000304546 Transcript missense_variant 2061/2865 1850/2328 617/775 G/D gGc/gAc rs760929496 1 -1 ECEL1 HGNC HGNC:3147 protein_coding YES CCDS2493.1 ENSP00000302051 O95672 UPI000013E997 NM_004826.3 deleterious(0) 13/18 Gene3D:3.40.390.10,Pfam_domain:PF01431,Prints_domain:PR00786,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF108,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs760929496 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 232481796 232481796 C T 1 0 0 0 0 1 0 0 0 4717 739 26 3 3 ECEL1 2 232481796 Missense_Mutation SNP C C3N-01414_T 1026361 232481796 9711733 89 23289 DGKD 0 . GRCh38 2 233454824 233454824 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.2326A>T p.Ile776Leu p.I776L ENST00000264057 19/30 155 138 17 263 263 0 strelka-varscan-mutect DGKD,missense_variant,p.Ile776Leu,ENST00000264057,NM_152879.2;DGKD,missense_variant,p.Ile732Leu,ENST00000409813,NM_003648.2;DGKD,3_prime_UTR_variant,,ENST00000430834,;DGKD,non_coding_transcript_exon_variant,,ENST00000490764,;DGKD,upstream_gene_variant,,ENST00000471764,; T ENST00000264057 Transcript missense_variant 2338/6297 2326/3645 776/1214 I/L Ata/Tta 1 1 DGKD HGNC HGNC:2851 protein_coding YES CCDS2504.1 ENSP00000264057 Q16760 UPI000013D4AF NM_152879.2 deleterious(0) 19/30 hmmpanther:PTHR11255:SF30,hmmpanther:PTHR11255,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 233454824 233454824 A T 1 0 0 0 0 1 0 0 0 4273 333 12 4 4 DGKD 2 233454824 Missense_Mutation SNP A C3N-01414_T 973028 233454824 8738705 90 23290 SH3BP4 0 . GRCh38 2 235052741 235052741 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.2658G>A p.= p.V886V ENST00000409212 5/6 84 64 20 108 108 0 strelka-varscan-mutect SH3BP4,synonymous_variant,p.=,ENST00000409212,;SH3BP4,synonymous_variant,p.=,ENST00000392011,NM_014521.2;SH3BP4,synonymous_variant,p.=,ENST00000344528,; A ENST00000409212 Transcript synonymous_variant 3165/5231 2658/2892 886/963 V gtG/gtA 1 1 SH3BP4 HGNC HGNC:10826 protein_coding YES CCDS2513.1 ENSP00000386862 Q9P0V3 UPI000006DA47 5/6 hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF3 LOW 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999975 1 1 1 0 A 2 1 77 235052741 235052741 G A 1 0 0 0 0 0 0 0 1 14504 1335 47 3 3 SH3BP4 2 235052741 Silent SNP G C3N-01414_T 1597917 235052741 7140788 91 23291 HDAC4 0 . GRCh38 2 239066772 239066772 + Missense_Mutation SNP C C A rs761714997 C3N-01414_T C3N-01414_N C C c.2938G>T p.Ala980Ser p.A980S ENST00000345617 24/27 241 194 47 363 363 0 strelka-varscan-mutect HDAC4,missense_variant,p.Ala868Ser,ENST00000543185,;HDAC4,missense_variant,p.Ala980Ser,ENST00000345617,NM_006037.3;HDAC4,missense_variant,p.Ala71Ser,ENST00000430200,;MIR4440,downstream_gene_variant,,ENST00000583986,;HDAC4,non_coding_transcript_exon_variant,,ENST00000494800,; A ENST00000345617 Transcript missense_variant 3730/8976 2938/3255 980/1084 A/S Gcc/Tcc rs761714997,COSM4128244 1 -1 HDAC4 HGNC HGNC:14063 protein_coding YES CCDS2529.1 ENSP00000264606 P56524 UPI000013D541 NM_006037.3 deleterious(0.01) 24/27 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF100,Pfam_domain:PF00850,Gene3D:3.40.800.20,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761714997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 239066772 239066772 C A 1 0 0 0 0 1 0 0 0 6896 768 27 1 1 HDAC4 2 239066772 Missense_Mutation SNP C C3N-01414_T 4014031 239066772 3126757 92 23292 AGXT 0 . GRCh38 2 240875987 240875987 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.829G>T p.Ala277Ser p.A277S ENST00000307503 8/11 332 249 83 496 495 1 strelka-varscan-mutect AGXT,missense_variant,p.Ala277Ser,ENST00000307503,NM_000030.2;AGXT,non_coding_transcript_exon_variant,,ENST00000476698,;AGXT,upstream_gene_variant,,ENST00000470255,;AGXT,downstream_gene_variant,,ENST00000472436,; T ENST00000307503 Transcript missense_variant 1216/1865 829/1179 277/392 A/S Gcc/Tcc 1 1 AGXT HGNC HGNC:341 protein_coding YES CCDS2543.1 ENSP00000302620 P21549 UPI0000135E9B NM_000030.2 tolerated(0.1) 8/11 Gene3D:3.40.640.10,Pfam_domain:PF00266,PIRSF_domain:PIRSF000524,hmmpanther:PTHR21152,hmmpanther:PTHR21152:SF22,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS rs180177275 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 240875987 240875987 G T 1 0 0 0 0 1 0 0 0 483 1203 42 2 2 AGXT 2 240875987 Missense_Mutation SNP G C3N-01414_T 1809215 240875987 1317542 93 23293 BHLHE40 0 . GRCh38 3 4983160 4983160 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.707G>T p.Gly236Val p.G236V ENST00000256495 5/5 248 213 35 411 411 0 strelka-varscan-mutect BHLHE40,missense_variant,p.Gly236Val,ENST00000256495,NM_003670.2;BHLHE40-AS1,upstream_gene_variant,,ENST00000620618,;BHLHE40-AS1,upstream_gene_variant,,ENST00000615178,;BHLHE40-AS1,upstream_gene_variant,,ENST00000441386,;BHLHE40,non_coding_transcript_exon_variant,,ENST00000467610,;BHLHE40,downstream_gene_variant,,ENST00000460806,; T ENST00000256495 Transcript missense_variant 1310/3473 707/1239 236/412 G/V gGc/gTc 1 1 BHLHE40 HGNC HGNC:1046 protein_coding YES CCDS2565.1 ENSP00000256495 O14503 Q6IB83 UPI0000126923 NM_003670.2 deleterious(0.02) 5/5 hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 4983160 4983160 G T 1 0 0 0 0 1 0 0 0 1571 1203 42 2 2 BHLHE40 3 4983160 Missense_Mutation SNP G C3N-01414_T 4983160 193312399 94 23294 IQSEC1 0 . GRCh38 3 12935571 12935571 + Missense_Mutation SNP C C A rs760589697 C3N-01414_T C3N-01414_N C C c.1445G>T p.Arg482Leu p.R482L ENST00000613206 3/14 222 172 50 385 385 0 strelka-varscan-mutect IQSEC1,missense_variant,p.Arg496Leu,ENST00000273221,NM_014869.6;IQSEC1,missense_variant,p.Arg374Leu,ENST00000618604,;IQSEC1,missense_variant,p.Arg482Leu,ENST00000613206,NM_001134382.2;IQSEC1,downstream_gene_variant,,ENST00000473088,; A ENST00000613206 Transcript missense_variant 1548/3582 1445/3345 482/1114 R/L cGg/cTg rs760589697 1 -1 IQSEC1 HGNC HGNC:29112 protein_coding YES CCDS74902.1 ENSP00000480301 A0A087WWK8 UPI00017E10F8 NM_001134382.2 deleterious(0.01) 3/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663 MODERATE 1 SNV 2 1 PASS rs760589697 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 12935571 12935571 C A 1 0 0 0 0 1 0 0 0 7723 652 23 1 1 IQSEC1 3 12935571 Missense_Mutation SNP C C3N-01414_T 7952411 12935571 185359988 95 23295 GRIP2 0 . GRCh38 3 14520467 14520467 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.1074C>A p.= p.I358I ENST00000619221 9/25 268 240 28 403 402 1 strelka-varscan-mutect GRIP2,synonymous_variant,p.=,ENST00000619221,;GRIP2,synonymous_variant,p.=,ENST00000621039,NM_001080423.3;GRIP2,synonymous_variant,p.=,ENST00000637182,;GRIP2,downstream_gene_variant,,ENST00000637939,;GRIP2,downstream_gene_variant,,ENST00000422481,;GRIP2,downstream_gene_variant,,ENST00000413414,; T ENST00000619221 Transcript synonymous_variant 1074/7977 1074/3423 358/1140 I atC/atA 1 -1 GRIP2 HGNC HGNC:23841 protein_coding YES ENSP00000480660 A0A087WX15 UPI0001DD380B 9/25 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR10316,hmmpanther:PTHR10316:SF42,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 14520467 14520467 G T 1 0 0 0 0 0 0 0 1 6669 932 33 2 2 GRIP2 3 14520467 Silent SNP G C3N-01414_T 1584896 14520467 183775092 96 23296 FGD5 0 . GRCh38 3 14901039 14901039 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.3242C>A p.Ala1081Asp p.A1081D ENST00000285046 9/20 175 129 46 328 328 0 strelka-varscan-mutect FGD5,missense_variant,p.Ala840Asp,ENST00000543601,NM_001320276.1;FGD5,missense_variant,p.Ala1081Asp,ENST00000285046,NM_152536.3;FGD5,downstream_gene_variant,,ENST00000457774,;FGD5,non_coding_transcript_exon_variant,,ENST00000476851,;FGD5,non_coding_transcript_exon_variant,,ENST00000468662,; A ENST00000285046 Transcript missense_variant 3352/5720 3242/4389 1081/1462 A/D gCc/gAc 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 deleterious(0) 9/20 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF13,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS rs1474054082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 14901039 14901039 C A 1 0 0 0 0 1 0 0 0 5700 739 26 2 2 FGD5 3 14901039 Missense_Mutation SNP C C3N-01414_T 380572 14901039 183394520 97 23297 PLCL2 0 . GRCh38 3 17014837 17014837 + Nonsense_Mutation SNP G G T rs866276568 C3N-01414_T C3N-01414_N G G c.2944G>T p.Glu982Ter p.E982* ENST00000615277 3/6 295 218 77 423 422 1 strelka-varscan-mutect PLCL2,stop_gained,p.Glu982Ter,ENST00000615277,NM_001144382.1;PLCL2,stop_gained,p.Glu856Ter,ENST00000432376,NM_015184.5;PLCL2,stop_gained,p.Glu600Ter,ENST00000419842,;PLCL2,downstream_gene_variant,,ENST00000460467,; T ENST00000615277 Transcript stop_gained 3025/4147 2944/3384 982/1127 E/* Gag/Tag rs866276568,COSM1262429,COSM1692445 1 1 PLCL2 HGNC HGNC:9064 protein_coding YES CCDS74911.1 ENSP00000478458 Q9UPR0 UPI0000242D01 NM_001144382.1 3/6 hmmpanther:PTHR10336:SF84,hmmpanther:PTHR10336 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs866276568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 17014837 17014837 G T 1 0 0 0 0 0 1 0 0 12134 1059 37 1 1 PLCL2 3 17014837 Nonsense_Mutation SNP G C3N-01414_T 2113798 17014837 181280722 98 23298 TTC21A 0 . GRCh38 3 39131000 39131000 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.2488A>T p.Ile830Phe p.I830F ENST00000431162 19/29 113 98 15 185 185 0 strelka-varscan-mutect TTC21A,missense_variant,p.Ile830Phe,ENST00000431162,NM_145755.2;TTC21A,missense_variant,p.Ile782Phe,ENST00000440121,NM_001105513.2;TTC21A,upstream_gene_variant,,ENST00000493856,;TTC21A,upstream_gene_variant,,ENST00000472866,;TTC21A,upstream_gene_variant,,ENST00000481734,;TTC21A,downstream_gene_variant,,ENST00000466875,;TTC21A,downstream_gene_variant,,ENST00000471025,;TTC21A,missense_variant,p.Ile823Phe,ENST00000430597,;TTC21A,non_coding_transcript_exon_variant,,ENST00000473587,; T ENST00000431162 Transcript missense_variant 2622/4209 2488/3963 830/1320 I/F Atc/Ttc 1 1 TTC21A HGNC HGNC:30761 protein_coding YES CCDS46800.1 ENSP00000398211 Q8NDW8 UPI00015D46B9 NM_145755.2 deleterious(0.02) 19/29 PROSITE_profiles:PS50293,hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF2,Gene3D:1.25.40.10 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 39131000 39131000 A T 1 0 0 0 0 1 0 0 0 17195 217 8 4 4 TTC21A 3 39131000 Missense_Mutation SNP A C3N-01414_T 22116163 39131000 159164559 99 23299 SMARCC1 0 . GRCh38 3 47636034 47636034 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2479G>T p.Asp827Tyr p.D827Y ENST00000254480 23/28 103 74 29 187 187 0 strelka-varscan-mutect SMARCC1,missense_variant,p.Asp827Tyr,ENST00000254480,NM_003074.3;SMARCC1,non_coding_transcript_exon_variant,,ENST00000425518,; A ENST00000254480 Transcript missense_variant 2599/6375 2479/3318 827/1105 D/Y Gat/Tat 1 -1 SMARCC1 HGNC HGNC:11104 protein_coding YES CCDS2758.1 ENSP00000254480 Q92922 UPI000013CE3B NM_003074.3 deleterious(0) 23/28 Low_complexity_(Seg):seg,hmmpanther:PTHR12802,hmmpanther:PTHR12802:SF9 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 47636034 47636034 C A 1 0 0 0 0 1 0 0 0 15068 855 30 2 2 SMARCC1 3 47636034 Missense_Mutation SNP C C3N-01414_T 8505034 47636034 150659525 100 23300 TRAIP 0 . GRCh38 3 49832036 49832036 + Missense_Mutation SNP C C T rs368177362 C3N-01414_T C3N-01414_N C C c.917G>A p.Arg306His p.R306H ENST00000331456 11/15 59 53 6 101 100 1 strelka-varscan-mutect TRAIP,missense_variant,p.Arg306His,ENST00000331456,NM_005879.2;TRAIP,missense_variant,p.Arg151His,ENST00000469027,;TRAIP,non_coding_transcript_exon_variant,,ENST00000475495,;TRAIP,intron_variant,,ENST00000473195,;TRAIP,upstream_gene_variant,,ENST00000491060,; T ENST00000331456 Transcript missense_variant 1031/2028 917/1410 306/469 R/H cGc/cAc rs368177362,COSM5399616 1 -1 TRAIP HGNC HGNC:30764 protein_coding YES CCDS2806.1 ENSP00000328203 Q9BWF2 UPI000006FE67 NM_005879.2 tolerated(0.72) 11/15 hmmpanther:PTHR22937,hmmpanther:PTHR22937:SF52 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs368177362 . 0 201 9 0 0 0 0 0 -13.8013 0.9999859 1 1 1 0 T 3 4 77 49832036 49832036 C T 1 0 0 0 0 1 0 0 0 16931 768 27 1 1 TRAIP 3 49832036 Missense_Mutation SNP C C3N-01414_T 2196002 49832036 148463523 101 23301 TRAIP 0 . GRCh38 3 49841861 49841861 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.582G>A p.= p.V194V ENST00000331456 7/15 167 148 19 265 265 0 strelka-varscan-mutect TRAIP,synonymous_variant,p.=,ENST00000331456,NM_005879.2;TRAIP,synonymous_variant,p.=,ENST00000482582,;TRAIP,intron_variant,,ENST00000469027,;TRAIP,downstream_gene_variant,,ENST00000482243,;TRAIP,downstream_gene_variant,,ENST00000473863,;TRAIP,intron_variant,,ENST00000473195,;TRAIP,downstream_gene_variant,,ENST00000477546,;TRAIP,downstream_gene_variant,,ENST00000489948,;TRAIP,upstream_gene_variant,,ENST00000475495,;TRAIP,downstream_gene_variant,,ENST00000488860,; T ENST00000331456 Transcript synonymous_variant 696/2028 582/1410 194/469 V gtG/gtA 1 -1 TRAIP HGNC HGNC:30764 protein_coding YES CCDS2806.1 ENSP00000328203 Q9BWF2 UPI000006FE67 NM_005879.2 7/15 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22937,hmmpanther:PTHR22937:SF52,Superfamily_domains:SSF46579 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 49841861 49841861 C T 1 0 0 0 0 0 0 0 1 16931 581 21 3 3 TRAIP 3 49841861 Silent SNP C C3N-01414_T 9825 49841861 148453698 102 23302 GXYLT2 0 . GRCh38 3 72967660 72967660 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1090G>T p.Gly364Cys p.G364C ENST00000389617 6/7 193 166 27 322 322 0 strelka-varscan-mutect GXYLT2,missense_variant,p.Gly364Cys,ENST00000389617,NM_001080393.1;GXYLT2,missense_variant,p.Gly125Cys,ENST00000491839,; T ENST00000389617 Transcript missense_variant 1251/3260 1090/1332 364/443 G/C Ggc/Tgc 1 1 GXYLT2 HGNC HGNC:33383 protein_coding YES CCDS46870.1 ENSP00000374268 A0PJZ3 UPI00001D7E8F NM_001080393.1 deleterious(0) 6/7 hmmpanther:PTHR12270,hmmpanther:PTHR12270:SF15,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 72967660 72967660 G T 1 0 0 0 0 1 0 0 0 6787 1000 35 2 2 GXYLT2 3 72967660 Missense_Mutation SNP G C3N-01414_T 23125799 72967660 125327899 103 23303 PDZRN3 0 . GRCh38 3 73388054 73388054 + Missense_Mutation SNP C C A rs367867225 C3N-01414_T C3N-01414_N C C c.1432G>T p.Val478Leu p.V478L ENST00000263666 8/10 70 60 10 132 132 0 strelka-varscan-mutect PDZRN3,missense_variant,p.Val478Leu,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Val135Leu,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Val195Leu,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Val135Leu,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Val75Leu,ENST00000494559,;PDZRN3,missense_variant,p.Val176Leu,ENST00000492909,NM_001303139.1;PDZRN3,non_coding_transcript_exon_variant,,ENST00000466348,;PDZRN3,downstream_gene_variant,,ENST00000498048,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000478209,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000484487,;PDZRN3,downstream_gene_variant,,ENST00000477434,; A ENST00000263666 Transcript missense_variant 1547/4248 1432/3201 478/1066 V/L Gtg/Ttg rs367867225 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 8/10 PROSITE_profiles:PS50106,hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs367867225 . 0 201 9 0 0 0 0 0 -19.99551 0.999993 1 1 1 0 A 3 1 77 73388054 73388054 C A 1 0 0 0 0 1 0 0 0 11797 507 18 2 2 PDZRN3 3 73388054 Missense_Mutation SNP C C3N-01414_T 420394 73388054 124907505 104 23304 EPHA6 0 . GRCh38 3 96987662 96987662 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.783C>A p.= p.L261L ENST00000389672 3/18 70 51 19 120 120 0 strelka-varscan-mutect EPHA6,synonymous_variant,p.=,ENST00000389672,NM_001080448.2;EPHA6,synonymous_variant,p.=,ENST00000470610,;EPHA6,synonymous_variant,p.=,ENST00000506569,NM_001278301.1; A ENST00000389672 Transcript synonymous_variant 821/3971 783/3393 261/1130 L ctC/ctA 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 2 1 PASS rs1395356906 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 96987662 96987662 C A 1 0 0 0 0 0 0 0 1 5018 813 29 2 2 EPHA6 3 96987662 Silent SNP C C3N-01414_T 23599608 96987662 101307897 105 23305 ABI3BP 0 . GRCh38 3 100752866 100752866 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.2910G>A p.= p.R970R ENST00000284322 33/35 172 163 9 263 263 0 strelka-mutect ABI3BP,synonymous_variant,p.=,ENST00000471714,;ABI3BP,synonymous_variant,p.=,ENST00000284322,NM_015429.3;ABI3BP,synonymous_variant,p.=,ENST00000495591,;TFG,downstream_gene_variant,,ENST00000240851,NM_006070.5,NM_001195478.1;TFG,downstream_gene_variant,,ENST00000476228,NM_001195479.1;TFG,downstream_gene_variant,,ENST00000418917,;TFG,downstream_gene_variant,,ENST00000490574,NM_001007565.2;TFG,downstream_gene_variant,,ENST00000615993,;TFG,downstream_gene_variant,,ENST00000481203,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000470336,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000487012,;ABI3BP,non_coding_transcript_exon_variant,,ENST00000497021,; T ENST00000284322 Transcript synonymous_variant 3020/4498 2910/3228 970/1075 R agG/agA 1 -1 ABI3BP HGNC HGNC:17265 protein_coding YES CCDS46880.1 ENSP00000284322 Q7Z7G0 UPI000011C136 NM_015429.3 33/35 hmmpanther:PTHR23197:SF10,hmmpanther:PTHR23197 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -11.73734 0.9999993 1 1 1 0 T 2 4 77 100752866 100752866 C T 1 0 0 0 0 0 0 0 1 101 854 30 3 3 ABI3BP 3 100752866 Silent SNP C C3N-01414_T 3765204 100752866 97542693 106 23306 IMPG2 0 . GRCh38 3 101244609 101244609 + Silent SNP G G T C3N-01414_T C3N-01414_N G G c.1722C>A p.= p.S574S ENST00000193391 13/19 43 36 7 77 77 0 strelka-mutect IMPG2,synonymous_variant,p.=,ENST00000193391,NM_016247.3; T ENST00000193391 Transcript synonymous_variant 1910/8337 1722/3726 574/1241 S tcC/tcA COSM4471511 1 -1 IMPG2 HGNC HGNC:18362 protein_coding YES CCDS2940.1 ENSP00000193391 Q9BZV3 F1T0J3 UPI000013C605 NM_016247.3 13/19 hmmpanther:PTHR12199,hmmpanther:PTHR12199:SF4 1 LOW 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.38755 1 1 1 1 0 T 2 4 77 101244609 101244609 G T 1 0 0 0 0 0 0 0 1 7631 1335 47 2 2 IMPG2 3 101244609 Silent SNP G C3N-01414_T 491743 101244609 97050950 107 23307 HHLA2 0 . GRCh38 3 108362358 108362358 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.1020A>T p.= p.T340T ENST00000357759 7/10 139 106 33 193 192 1 strelka-mutect HHLA2,synonymous_variant,p.=,ENST00000357759,NM_007072.3;HHLA2,synonymous_variant,p.=,ENST00000482099,;HHLA2,synonymous_variant,p.=,ENST00000619531,NM_001282556.1;HHLA2,synonymous_variant,p.=,ENST00000489514,NM_001282557.1;HHLA2,synonymous_variant,p.=,ENST00000467761,;HHLA2,synonymous_variant,p.=,ENST00000467562,NM_001282559.1;HHLA2,synonymous_variant,p.=,ENST00000491820,NM_001282558.1; T ENST00000357759 Transcript synonymous_variant 1434/2666 1020/1245 340/414 T acA/acT 1 1 HHLA2 HGNC HGNC:4905 protein_coding YES CCDS46883.1 ENSP00000350402 Q9UM44 UPI0000073CD9 NM_007072.3 7/10 LOW 1 SNV 1 1 PASS . . 0 205 2 2 0 0 0 0 -20 0.9999992 1 1 1 0 T 2 4 77 108362358 108362358 A T 1 0 0 0 0 0 0 0 1 6981 175 7 4 4 HHLA2 3 108362358 Silent SNP A C3N-01414_T 7117749 108362358 89933201 108 23308 MORC1 0 . GRCh38 3 109059810 109059810 + Missense_Mutation SNP G G T rs551133230 C3N-01414_T C3N-01414_N G G c.1027C>A p.Gln343Lys p.Q343K ENST00000232603 12/28 105 83 22 194 194 0 strelka-varscan-mutect MORC1,missense_variant,p.Gln343Lys,ENST00000232603,NM_014429.3;MORC1,missense_variant,p.Gln343Lys,ENST00000483760,; T ENST00000232603 Transcript missense_variant 1110/3764 1027/2955 343/984 Q/K Caa/Aaa rs551133230 1 -1 MORC1 HGNC HGNC:7198 protein_coding YES CCDS2955.1 ENSP00000232603 Q86VD1 UPI000013C964 NM_014429.3 tolerated(0.16) 12/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23337:SF6,hmmpanther:PTHR23337 MODERATE 1 SNV 1 1 PASS rs551133230 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 109059810 109059810 G T 1 0 0 0 0 1 0 0 0 9665 1391 48 2 2 MORC1 3 109059810 Missense_Mutation SNP G C3N-01414_T 697452 109059810 89235749 109 23309 POPDC2 0 . GRCh38 3 119648359 119648359 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.910C>G p.Leu304Val p.L304V ENST00000264231 3/4 155 130 25 262 262 0 strelka-varscan-mutect POPDC2,missense_variant,p.Leu304Val,ENST00000493094,;POPDC2,missense_variant,p.Leu304Val,ENST00000264231,NM_022135.2;POPDC2,missense_variant,p.Leu304Val,ENST00000468801,NM_001308333.1;POPDC2,non_coding_transcript_exon_variant,,ENST00000474523,;POPDC2,downstream_gene_variant,,ENST00000468916,;POPDC2,downstream_gene_variant,,ENST00000463323,;POPDC2,missense_variant,p.Leu304Val,ENST00000341124,;POPDC2,downstream_gene_variant,,ENST00000476092,; C ENST00000264231 Transcript missense_variant 1077/1679 910/1095 304/364 L/V Ctc/Gtc 1 -1 POPDC2 HGNC HGNC:17648 protein_coding YES CCDS2992.1 ENSP00000264231 Q9HBU9 UPI000000DAC2 NM_022135.2 tolerated(1) 3/4 hmmpanther:PTHR12101,hmmpanther:PTHR12101:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 119648359 119648359 G C 1 0 0 0 0 1 0 0 0 12369 942 33 4 4 POPDC2 3 119648359 Missense_Mutation SNP G C3N-01414_T 10588549 119648359 78647200 110 23310 CFAP100 0 . GRCh38 3 126416403 126416403 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.313C>A p.Gln105Lys p.Q105K ENST00000352312 5/17 164 152 12 223 223 0 strelka-varscan-mutect CFAP100,missense_variant,p.Gln105Lys,ENST00000352312,NM_182628.2;CFAP100,missense_variant,p.Gln105Lys,ENST00000505024,;CFAP100,downstream_gene_variant,,ENST00000510833,;CFAP100,non_coding_transcript_exon_variant,,ENST00000533201,;CFAP100,upstream_gene_variant,,ENST00000507830,;CFAP100,upstream_gene_variant,,ENST00000503905,; A ENST00000352312 Transcript missense_variant 412/2086 313/1836 105/611 Q/K Cag/Aag 1 1 CFAP100 HGNC HGNC:26842 protein_coding YES CCDS3037.1 ENSP00000344749 Q494V2 UPI000013E315 NM_182628.2 tolerated(0.1) 5/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21683:SF5,hmmpanther:PTHR21683 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -16.18018 0.9999997 1 1 1 0 A 3 1 77 126416403 126416403 C A 1 0 0 0 0 1 0 0 0 3010 711 25 2 2 CFAP100 3 126416403 Missense_Mutation SNP C C3N-01414_T 6768044 126416403 71879156 111 23311 IL20RB 0 . GRCh38 3 136989526 136989526 + Missense_Mutation SNP G G T rs201605222 C3N-01414_T C3N-01414_N G G c.492G>T p.Glu164Asp p.E164D ENST00000329582 4/7 223 190 33 366 366 0 strelka-varscan-mutect IL20RB,missense_variant,p.Glu164Asp,ENST00000329582,NM_144717.3;IL20RB,downstream_gene_variant,,ENST00000484501,;IL20RB,3_prime_UTR_variant,,ENST00000469964,;IL20RB,3_prime_UTR_variant,,ENST00000475972,;IL20RB,3_prime_UTR_variant,,ENST00000491483,; T ENST00000329582 Transcript missense_variant 741/2047 492/936 164/311 E/D gaG/gaT rs201605222 1 1 IL20RB HGNC HGNC:6004 protein_coding YES CCDS3093.1 ENSP00000328133 Q6UXL0 UPI000003E7F6 NM_144717.3 tolerated(0.1) 4/7 hmmpanther:PTHR20859:SF48,hmmpanther:PTHR20859,Pfam_domain:PF09294,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs201605222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 136989526 136989526 G T 1 0 0 0 0 1 0 0 0 7572 1020 36 2 2 IL20RB 3 136989526 Missense_Mutation SNP G C3N-01414_T 10573123 136989526 61306033 112 23312 SPSB4 0 . GRCh38 3 141066388 141066388 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.284G>T p.Arg95Leu p.R95L ENST00000310546 2/3 57 43 14 97 97 0 strelka-varscan-mutect SPSB4,missense_variant,p.Arg95Leu,ENST00000310546,NM_080862.2;SPSB4,upstream_gene_variant,,ENST00000508126,; T ENST00000310546 Transcript missense_variant 1028/2908 284/822 95/273 R/L cGc/cTc 1 1 SPSB4 HGNC HGNC:30630 protein_coding YES CCDS3115.1 ENSP00000311609 Q96A44 UPI00000734A4 NM_080862.2 deleterious(0) 2/3 PROSITE_profiles:PS50188,hmmpanther:PTHR12245,hmmpanther:PTHR12245:SF3,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1457468003 . 0 198 12 0 0 0 0 0 -20 0.9999686 1 1 1 0 T 3 4 77 141066388 141066388 G T 1 0 0 0 0 1 0 0 0 15471 1087 38 1 1 SPSB4 3 141066388 Missense_Mutation SNP G C3N-01414_T 4076862 141066388 57229171 113 23313 MCF2L2 0 . GRCh38 3 183228320 183228320 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.2092C>T p.= p.L698L ENST00000328913 18/30 185 157 28 308 308 0 strelka-varscan-mutect MCF2L2,synonymous_variant,p.=,ENST00000328913,NM_015078.3;MCF2L2,synonymous_variant,p.=,ENST00000473233,;MCF2L2,synonymous_variant,p.=,ENST00000447025,;MCF2L2,non_coding_transcript_exon_variant,,ENST00000488149,; A ENST00000328913 Transcript synonymous_variant 2390/4980 2092/3345 698/1114 L Ctg/Ttg 1 -1 MCF2L2 HGNC HGNC:30319 protein_coding YES CCDS3243.1 ENSP00000328118 Q86YR7 UPI00001A962F NM_015078.3 18/30 PROSITE_profiles:PS50010,hmmpanther:PTHR22826:SF89,hmmpanther:PTHR22826,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 183228320 183228320 G A 1 0 0 0 0 0 0 0 1 9311 933 33 3 3 MCF2L2 3 183228320 Silent SNP G C3N-01414_T 42161932 183228320 15067239 114 23314 EHHADH 0 . GRCh38 3 185192557 185192557 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1841T>A p.Ile614Asn p.I614N ENST00000231887 7/7 156 134 22 297 297 0 strelka-varscan-mutect EHHADH,missense_variant,p.Ile614Asn,ENST00000231887,NM_001966.3;EHHADH,missense_variant,p.Ile518Asn,ENST00000456310,NM_001166415.1;EHHADH-AS1,downstream_gene_variant,,ENST00000417720,; T ENST00000231887 Transcript missense_variant 1917/3850 1841/2172 614/723 I/N aTt/aAt 1 -1 EHHADH HGNC HGNC:3247 protein_coding YES CCDS33901.1 ENSP00000231887 Q08426 UPI000013C959 NM_001966.3 deleterious(0) 7/7 hmmpanther:PTHR23309:SF9,hmmpanther:PTHR23309 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 185192557 185192557 A T 1 0 0 0 0 1 0 0 0 4818 101 4 4 4 EHHADH 3 185192557 Missense_Mutation SNP A C3N-01414_T 1964237 185192557 13103002 115 23315 RTP1 0 . GRCh38 3 187199988 187199988 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.710G>T p.Cys237Phe p.C237F ENST00000312295 2/2 24 20 4 37 37 0 strelka-varscan-mutect RTP1,missense_variant,p.Cys237Phe,ENST00000312295,NM_153708.2;RP11-208N14.4,non_coding_transcript_exon_variant,,ENST00000356133,; T ENST00000312295 Transcript missense_variant 740/2217 710/792 237/263 C/F tGc/tTc 1 1 RTP1 HGNC HGNC:28580 protein_coding YES CCDS3287.2 ENSP00000311712 P59025 UPI00004E18F3 NM_153708.2 tolerated(0.8) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR14402,hmmpanther:PTHR14402:SF19 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -11.82597 1 1 1 1 0 T 3 4 77 187199988 187199988 G T 1 0 0 0 0 1 0 0 0 13993 1319 46 2 2 RTP1 3 187199988 Missense_Mutation SNP G C3N-01414_T 2007431 187199988 11095571 116 23316 MASP1 0 . GRCh38 3 187256787 187256787 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.621C>A p.= p.P207P ENST00000296280 5/11 266 235 31 442 441 1 strelka-varscan-mutect MASP1,synonymous_variant,p.=,ENST00000337774,NM_001879.5;MASP1,synonymous_variant,p.=,ENST00000296280,NM_139125.3;MASP1,synonymous_variant,p.=,ENST00000392472,;MASP1,synonymous_variant,p.=,ENST00000169293,NM_001031849.2;MASP1,synonymous_variant,p.=,ENST00000392470,;MASP1,downstream_gene_variant,,ENST00000392475,;MASP1,intron_variant,,ENST00000495249,;MASP1,downstream_gene_variant,,ENST00000490558,;MASP1,downstream_gene_variant,,ENST00000465015,;MASP1,non_coding_transcript_exon_variant,,ENST00000460839,;MASP1,upstream_gene_variant,,ENST00000483719,; T ENST00000296280 Transcript synonymous_variant 847/4015 621/2187 207/728 P ccC/ccA 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 5/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS01180,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 187256787 187256787 G T 1 0 0 0 0 0 0 0 1 9248 1335 47 2 2 MASP1 3 187256787 Silent SNP G C3N-01414_T 56799 187256787 11038772 117 23317 TCTEX1D2 0 . GRCh38 3 196296020 196296020 + Missense_Mutation SNP C C A rs748477420 C3N-01414_T C3N-01414_N C C c.367G>T p.Asp123Tyr p.D123Y ENST00000325318 4/5 149 127 22 239 239 0 strelka-varscan-mutect TCTEX1D2,missense_variant,p.Asp123Tyr,ENST00000325318,NM_152773.4;TCTEX1D2,upstream_gene_variant,,ENST00000491186,;TCTEX1D2,3_prime_UTR_variant,,ENST00000446494,;TCTEX1D2,3_prime_UTR_variant,,ENST00000426563,;TCTEX1D2,non_coding_transcript_exon_variant,,ENST00000465757,;RP11-447L10.1,intron_variant,,ENST00000431391,;AC069257.6,downstream_gene_variant,,ENST00000441819,; A ENST00000325318 Transcript missense_variant 503/673 367/429 123/142 D/Y Gat/Tat rs748477420,COSM1043019,COSM479946 1 -1 TCTEX1D2 HGNC HGNC:28482 protein_coding YES CCDS33929.1 ENSP00000324323 Q8WW35 UPI000020AF09 NM_152773.4 deleterious(0) 4/5 Pfam_domain:PF03645,hmmpanther:PTHR21255,hmmpanther:PTHR21255:SF7 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs748477420 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 196296020 196296020 C A 1 0 0 0 0 1 0 0 0 16128 826 29 2 2 TCTEX1D2 3 196296020 Missense_Mutation SNP C C3N-01414_T 9039233 196296020 1999539 118 23318 PPARGC1A 0 . GRCh38 4 23802232 23802232 + Silent SNP C C G novel C3N-01414_T C3N-01414_N C C c.2133G>C p.= p.R711R ENST00000264867 11/13 174 140 34 267 267 0 strelka-varscan-mutect PPARGC1A,synonymous_variant,p.=,ENST00000264867,NM_013261.3;PPARGC1A,synonymous_variant,p.=,ENST00000613098,;PPARGC1A,non_coding_transcript_exon_variant,,ENST00000509702,;PPARGC1A,3_prime_UTR_variant,,ENST00000506055,; G ENST00000264867 Transcript synonymous_variant 2253/6318 2133/2397 711/798 R cgG/cgC 1 -1 PPARGC1A HGNC HGNC:9237 protein_coding YES CCDS3429.1 ENSP00000264867 Q9UBK2 A0A024R9Q9 UPI000004D072 NM_013261.3 11/13 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR15528,hmmpanther:PTHR15528:SF10,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 23802232 23802232 C G 1 0 0 0 0 0 0 0 1 12409 610 22 4 4 PPARGC1A 4 23802232 Silent SNP C C3N-01414_T 23802232 166412323 119 23319 SLC34A2 0 . GRCh38 4 25676282 25676282 + Missense_Mutation SNP T T A C3N-01414_T C3N-01414_N T T c.1606T>A p.Phe536Ile p.F536I ENST00000382051 13/13 453 383 70 671 670 1 strelka-varscan-mutect SLC34A2,missense_variant,p.Phe536Ile,ENST00000382051,NM_006424.2;SLC34A2,missense_variant,p.Phe535Ile,ENST00000503434,NM_001177999.1;SLC34A2,missense_variant,p.Phe535Ile,ENST00000504570,NM_001177998.1;RP11-302F12.1,upstream_gene_variant,,ENST00000496507,; A ENST00000382051 Transcript missense_variant 1656/4122 1606/2073 536/690 F/I Ttc/Atc COSM733650 1 1 SLC34A2 HGNC HGNC:11020 protein_coding YES CCDS3435.1 ENSP00000371483 O95436 UPI000013DF24 NM_006424.2 tolerated(0.06) 13/13 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10010,hmmpanther:PTHR10010:SF23,TIGRFAM_domain:TIGR01013 1 MODERATE 1 SNV 1 1 1 PASS rs1227346120 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 25676282 25676282 T A 1 0 0 0 0 1 0 0 0 14838 1609 56 4 4 SLC34A2 4 25676282 Missense_Mutation SNP T C3N-01414_T 1874050 25676282 164538273 120 23320 PDGFRA 0 . GRCh38 4 54290444 54290444 + Missense_Mutation SNP G G C C3N-01414_T C3N-01414_N G G c.3012G>C p.Glu1004Asp p.E1004D ENST00000257290 22/23 326 256 70 497 497 0 strelka-varscan-mutect PDGFRA,missense_variant,p.Glu1004Asp,ENST00000257290,NM_006206.4;RP11-231C18.3,missense_variant,p.Glu764Asp,ENST00000507166,; C ENST00000257290 Transcript missense_variant 3343/6576 3012/3270 1004/1089 E/D gaG/gaC COSM5004118 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 tolerated(0.06) 22/23 hmmpanther:PTHR24416:SF52,hmmpanther:PTHR24416,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615 1 MODERATE 1 SNV 1 1 1 PASS rs1224923673 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 54290444 54290444 G C 1 0 0 0 0 1 0 0 0 11749 991 35 4 4 PDGFRA 4 54290444 Missense_Mutation SNP G C3N-01414_T 28614162 54290444 135924111 121 23321 AASDH 0 . GRCh38 4 56378351 56378351 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.465A>T p.= p.L155L ENST00000205214 4/15 287 255 32 452 452 0 strelka-varscan-mutect AASDH,synonymous_variant,p.=,ENST00000205214,NM_181806.3;AASDH,synonymous_variant,p.=,ENST00000602986,NM_001286669.1;AASDH,synonymous_variant,p.=,ENST00000513376,NM_001286668.1;AASDH,synonymous_variant,p.=,ENST00000451613,NM_001286671.1;AASDH,synonymous_variant,p.=,ENST00000502617,NM_001286672.1;AASDH,non_coding_transcript_exon_variant,,ENST00000510762,;AASDH,3_prime_UTR_variant,,ENST00000503808,;AASDH,intron_variant,,ENST00000514745,NM_001286670.1;AASDH,downstream_gene_variant,,ENST00000510012,;AASDH,downstream_gene_variant,,ENST00000514796,; A ENST00000205214 Transcript synonymous_variant 646/3590 465/3297 155/1098 L ctA/ctT 1 -1 AASDH HGNC HGNC:23993 protein_coding YES CCDS3504.1 ENSP00000205214 Q4L235 UPI000020B8EF NM_181806.3 4/15 Pfam_domain:PF00501,Superfamily_domains:SSF56801 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 56378351 56378351 T A 1 0 0 0 0 0 0 0 1 26 1741 61 4 4 AASDH 4 56378351 Silent SNP T C3N-01414_T 2087907 56378351 133836204 122 23322 CSN2 0 . GRCh38 4 69956350 69956350 + Nonstop_Mutation SNP T T A rs762728005 C3N-01414_T C3N-01414_N T T c.681A>T p.Ter227TyrextTer14 p.*227Yext*14 ENST00000353151 6/7 52 47 5 108 108 0 strelka-varscan-mutect CSN2,stop_lost,p.Ter227TyrextTer14,ENST00000353151,NM_001302770.1,NM_001891.3; A ENST00000353151 Transcript stop_lost 693/1066 681/681 227/226 */Y taA/taT rs762728005 1 -1 CSN2 HGNC HGNC:2447 protein_coding YES CCDS3532.1 ENSP00000341030 P05814 W5RWE1 UPI0000126FDB NM_001302770.1,NM_001891.3 6/7 HIGH 1 SNV 1 1 PASS rs762728005 . 3 203 3 0 0 0 0 0 -12.50167 1 1 1 1 0 A 4 1 77 69956350 69956350 T A 1 0 0 0 0 0 0 0 0 3748 1623 56 4 4 CSN2 4 69956350 Nonstop_Mutation SNP T C3N-01414_T 13577999 69956350 120258205 123 23323 MUC7 0 . GRCh38 4 70480913 70480913 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.169C>A p.Pro57Thr p.P57T ENST00000413702 4/4 227 169 58 458 458 0 strelka-varscan-mutect MUC7,missense_variant,p.Pro57Thr,ENST00000413702,NM_001145006.1;MUC7,missense_variant,p.Pro57Thr,ENST00000456088,NM_001145007.1;MUC7,missense_variant,p.Pro57Thr,ENST00000304887,NM_152291.2;MUC7,missense_variant,p.Pro57Thr,ENST00000505411,;MUC7,non_coding_transcript_exon_variant,,ENST00000514512,;MUC7,non_coding_transcript_exon_variant,,ENST00000504482,; A ENST00000413702 Transcript missense_variant 457/2540 169/1134 57/377 P/T Ccg/Acg 1 1 MUC7 HGNC HGNC:7518 protein_coding YES CCDS3541.1 ENSP00000407422 Q8TAX7 UPI000013E9DD NM_001145006.1 tolerated(0.57) 4/4 hmmpanther:PTHR41683:SF1,hmmpanther:PTHR41683 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 70480913 70480913 C A 1 0 0 0 0 1 0 0 0 9981 739 26 2 2 MUC7 4 70480913 Missense_Mutation SNP C C3N-01414_T 524563 70480913 119733642 124 23324 FRAS1 0 . GRCh38 4 78479598 78479598 + Missense_Mutation SNP G G C C3N-01414_T C3N-01414_N G G c.8323G>C p.Asp2775His p.D2775H ENST00000512123 56/74 144 110 34 235 235 0 strelka-varscan-mutect FRAS1,missense_variant,p.Asp2775His,ENST00000512123,NM_025074.6; C ENST00000512123 Transcript missense_variant 8763/15624 8323/12039 2775/4012 D/H Gat/Cat COSM1310282,COSM1310283 1 1 FRAS1 HGNC HGNC:19185 protein_coding YES CCDS54771.1 ENSP00000422834 Q86XX4 UPI000021D4C2 NM_025074.6 deleterious(0.02) 56/74 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF29,Superfamily_domains:SSF141072 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 78479598 78479598 G C 1 0 0 0 0 1 0 0 0 5908 942 33 4 4 FRAS1 4 78479598 Missense_Mutation SNP G C3N-01414_T 7998685 78479598 111734957 125 23325 PTPN13 0 . GRCh38 4 86771513 86771513 + Missense_Mutation SNP A A T rs748061205 C3N-01414_T C3N-01414_N A A c.5161A>T p.Asn1721Tyr p.N1721Y ENST00000436978 31/48 71 47 24 105 105 0 strelka-varscan-mutect PTPN13,missense_variant,p.Asn1721Tyr,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Asn1697Tyr,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Asn1716Tyr,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Asn1721Tyr,ENST00000511467,;PTPN13,missense_variant,p.Asn1525Tyr,ENST00000316707,NM_080684.2;PTPN13,downstream_gene_variant,,ENST00000511105,; T ENST00000436978 Transcript missense_variant 5641/8573 5161/7473 1721/2490 N/Y Aat/Tat rs748061205 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0) 31/48 PIRSF_domain:PIRSF000933 MODERATE 1 SNV 5 1 PASS rs748061205 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 86771513 86771513 A T 1 0 0 0 0 1 0 0 0 12935 130 5 4 4 PTPN13 4 86771513 Missense_Mutation SNP A C3N-01414_T 8291915 86771513 103443042 126 23326 SPP1 0 . GRCh38 4 87981767 87981767 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.509A>T p.Lys170Ile p.K170I ENST00000395080 6/7 157 114 43 205 205 0 strelka-varscan-mutect SPP1,missense_variant,p.Lys156Ile,ENST00000237623,NM_000582.2;SPP1,missense_variant,p.Lys148Ile,ENST00000614857,NM_001251830.1;SPP1,missense_variant,p.Lys170Ile,ENST00000395080,NM_001040058.1;SPP1,missense_variant,p.Lys143Ile,ENST00000360804,NM_001040060.1;SPP1,missense_variant,p.Lys129Ile,ENST00000508233,NM_001251829.1;SPP1,non_coding_transcript_exon_variant,,ENST00000509659,;SPP1,downstream_gene_variant,,ENST00000509334,;SPP1,downstream_gene_variant,,ENST00000513981,;SPP1,downstream_gene_variant,,ENST00000508002,;SPP1,downstream_gene_variant,,ENST00000504310,;SPP1,downstream_gene_variant,,ENST00000505146,; T ENST00000395080 Transcript missense_variant 636/1473 509/945 170/314 K/I aAa/aTa 1 1 SPP1 HGNC HGNC:11255 protein_coding YES CCDS43250.1 ENSP00000378517 P10451 A0A024RDE2 UPI0000000E0B NM_001040058.1 deleterious(0) 6/7 hmmpanther:PTHR10607:SF1,hmmpanther:PTHR10607,Pfam_domain:PF00865,SMART_domains:SM00017 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 87981767 87981767 A T 1 0 0 0 0 1 0 0 0 15439 14 1 4 4 SPP1 4 87981767 Missense_Mutation SNP A C3N-01414_T 1210254 87981767 102232788 127 23327 PPM1K 0 . GRCh38 4 88262667 88262667 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.1047G>T p.Trp349Cys p.W349C ENST00000608933 7/7 222 187 35 329 329 0 strelka-varscan-mutect PPM1K,missense_variant,p.Trp349Cys,ENST00000608933,NM_152542.4;PPM1K,missense_variant,p.Trp304Cys,ENST00000295908,;PPM1K,missense_variant,p.Trp130Cys,ENST00000508256,; A ENST00000608933 Transcript missense_variant 1437/6484 1047/1119 349/372 W/C tgG/tgT COSM1541115 1 -1 PPM1K HGNC HGNC:25415 protein_coding YES CCDS3629.1 ENSP00000477341 Q8N3J5 UPI00000473F1 NM_152542.4 deleterious(0) 7/7 hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF267,Gene3D:3.60.40.10,Superfamily_domains:SSF81606 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 88262667 88262667 C A 1 0 0 0 0 1 0 0 0 12453 624 22 2 2 PPM1K 4 88262667 Missense_Mutation SNP C C3N-01414_T 280900 88262667 101951888 128 23328 GRID2 0 . GRCh38 4 93455700 93455700 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.1584A>T p.= p.P528P ENST00000282020 11/16 142 107 35 255 255 0 strelka-varscan-mutect GRID2,synonymous_variant,p.=,ENST00000282020,NM_001510.3;GRID2,synonymous_variant,p.=,ENST00000611049,;GRID2,synonymous_variant,p.=,ENST00000510992,NM_001286838.1; T ENST00000282020 Transcript synonymous_variant 2619/6117 1584/3024 528/1007 P ccA/ccT 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 11/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Pfam_domain:PF10613,Gene3D:3.40.190.10,SMART_domains:SM00079,Superfamily_domains:SSF53850 LOW 1 SNV 1 1 PASS rs1161815489 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 93455700 93455700 A T 1 0 0 0 0 0 0 0 1 6652 175 7 4 4 GRID2 4 93455700 Silent SNP A C3N-01414_T 5193033 93455700 96758855 129 23329 CENPE 0 . GRCh38 4 103141053 103141053 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.5515G>A p.Val1839Ile p.V1839I ENST00000265148 36/49 97 88 9 159 158 1 strelka-varscan-mutect CENPE,missense_variant,p.Val1839Ile,ENST00000265148,NM_001813.2;CENPE,missense_variant,p.Val1839Ile,ENST00000611174,;CENPE,missense_variant,p.Val1814Ile,ENST00000380026,NM_001286734.1;CENPE,downstream_gene_variant,,ENST00000515478,; T ENST00000265148 Transcript missense_variant 5605/8612 5515/8106 1839/2701 V/I Gtc/Atc 1 -1 CENPE HGNC HGNC:1856 protein_coding YES CCDS34042.1 ENSP00000265148 Q02224 UPI000020B28A NM_001813.2 tolerated(0.21) 36/49 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -18.71064 1 1 1 1 0 T 3 4 77 103141053 103141053 C T 1 0 0 0 0 1 0 0 0 2938 478 17 3 3 CENPE 4 103141053 Missense_Mutation SNP C C3N-01414_T 9685353 103141053 87073502 130 23330 GIMD1 0 . GRCh38 4 106367275 106367275 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.161A>T p.His54Leu p.H54L ENST00000507153 1/2 241 183 58 295 294 1 strelka-varscan-mutect GIMD1,missense_variant,p.His54Leu,ENST00000507153,NM_001195138.1; A ENST00000507153 Transcript missense_variant 161/654 161/654 54/217 H/L cAc/cTc 1 -1 GIMD1 HGNC HGNC:44141 protein_coding YES ENSP00000489975 P0DJR0 UPI0001E112A1 NM_001195138.1 tolerated(0.66) 1/2 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF40,hmmpanther:PTHR10903,Gene3D:3.40.50.300,Pfam_domain:PF04548,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 106367275 106367275 T A 1 0 0 0 0 1 0 0 0 6266 1696 59 4 4 GIMD1 4 106367275 Missense_Mutation SNP T C3N-01414_T 3226222 106367275 83847280 131 23331 ANK2 0 . GRCh38 4 113358634 113358634 + Missense_Mutation SNP C C A rs150437645 C3N-01414_T C3N-01414_N C C c.10016C>A p.Ala3339Glu p.A3339E ENST00000357077 38/46 262 215 47 442 442 0 strelka-varscan-mutect ANK2,missense_variant,p.Ala3339Glu,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala3306Glu,ENST00000264366,;ANK2,missense_variant,p.Ala349Glu,ENST00000505342,;ANK2,3_prime_UTR_variant,,ENST00000612754,;ANK2,intron_variant,,ENST00000506722,NM_001127493.1;ANK2,intron_variant,,ENST00000394537,NM_020977.3;ANK2,intron_variant,,ENST00000514960,;ANK2,intron_variant,,ENST00000509550,;ANK2,intron_variant,,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504454,;ANK2,downstream_gene_variant,,ENST00000503423,;ANK2,intron_variant,,ENST00000508007,; A ENST00000357077 Transcript missense_variant 10069/14196 10016/11874 3339/3957 A/E gCg/gAg rs150437645 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 tolerated_low_confidence(1) 38/46 hmmpanther:PTHR24123:SF17,hmmpanther:PTHR24123 MODERATE 1 SNV 1 1 PASS rs150437645 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 113358634 113358634 C A 1 0 0 0 0 1 0 0 0 721 768 27 1 1 ANK2 4 113358634 Missense_Mutation SNP C C3N-01414_T 6991359 113358634 76855921 132 23332 FAT4 0 . GRCh38 4 125490277 125490277 + Silent SNP G G T rs776669972 C3N-01414_T C3N-01414_N G G c.13455G>T p.= p.A4485A ENST00000394329 17/17 218 172 46 298 297 1 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,synonymous_variant,p.=,ENST00000335110,; T ENST00000394329 Transcript synonymous_variant 13468/16123 13455/14946 4485/4981 A gcG/gcT rs776669972,COSM1567023,COSM1567024 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 17/17 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs776669972 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 125490277 125490277 G T 1 0 0 0 0 0 0 0 1 5552 1103 39 1 1 FAT4 4 125490277 Silent SNP G C3N-01414_T 12131643 125490277 64724278 133 23333 PRMT9 0 . GRCh38 4 147673000 147673000 + Silent SNP C C A rs145578256 C3N-01414_T C3N-01414_N C C c.702G>T p.= p.T234T ENST00000322396 4/12 228 183 45 379 378 1 strelka-varscan-mutect PRMT9,synonymous_variant,p.=,ENST00000322396,NM_001304458.1,NM_138364.3;TMEM184C,downstream_gene_variant,,ENST00000508208,;PRMT9,3_prime_UTR_variant,,ENST00000514886,; A ENST00000322396 Transcript synonymous_variant 945/3528 702/2538 234/845 T acG/acT rs145578256,COSM1051860 1 -1 PRMT9 HGNC HGNC:25099 protein_coding YES CCDS3771.1 ENSP00000314396 Q6P2P2 UPI000004971D NM_001304458.1,NM_138364.3 4/12 PROSITE_profiles:PS51678,hmmpanther:PTHR11006,hmmpanther:PTHR11006:SF60,Gene3D:3.40.50.150,Superfamily_domains:SSF53335 0,1 LOW 1 SNV 1 0,1 1 PASS rs145578256 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 147673000 147673000 C A 1 0 0 0 0 0 0 0 1 12674 871 31 1 1 PRMT9 4 147673000 Silent SNP C C3N-01414_T 22182723 147673000 42541555 134 23334 DCHS2 0 . GRCh38 4 154304714 154304714 + Missense_Mutation SNP C C A rs761229608 C3N-01414_T C3N-01414_N C C c.4195G>T p.Asp1399Tyr p.D1399Y ENST00000623607 17/25 93 84 9 135 135 0 strelka-varscan-mutect DCHS2,missense_variant,p.Asp1399Tyr,ENST00000357232,;DCHS2,missense_variant,p.Asp1399Tyr,ENST00000623607,NM_017639.3; A ENST00000623607 Transcript missense_variant 4195/8912 4195/8751 1399/2916 D/Y Gat/Tat rs761229608 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 deleterious(0) 17/25 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs761229608 . 0 205 4 0 0 0 0 0 -18.7707 1 1 1 1 0 A 3 1 77 154304714 154304714 C A 1 0 0 0 0 1 0 0 0 4091 826 29 2 2 DCHS2 4 154304714 Missense_Mutation SNP C C3N-01414_T 6631714 154304714 35909841 135 23335 CENPU 0 . GRCh38 4 184734037 184734037 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.26C>A p.Pro9Gln p.P9Q ENST00000281453 1/13 179 162 17 304 304 0 strelka-varscan-mutect CENPU,missense_variant,p.Pro9Gln,ENST00000281453,NM_024629.3;CENPU,upstream_gene_variant,,ENST00000514781,;CENPU,missense_variant,p.Pro9Gln,ENST00000510146,; T ENST00000281453 Transcript missense_variant 97/1998 26/1257 9/418 P/Q cCg/cAg 1 -1 CENPU HGNC HGNC:21348 protein_coding YES CCDS3838.1 ENSP00000281453 Q71F23 UPI00001BFAF6 NM_024629.3 tolerated_low_confidence(0.21) 1/13 Low_complexity_(Seg):seg,hmmpanther:PTHR32222:SF1,hmmpanther:PTHR32222 MODERATE 1 SNV 1 1 PASS rs899831790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 184734037 184734037 G T 1 0 0 0 0 1 0 0 0 2951 1116 39 1 1 CENPU 4 184734037 Missense_Mutation SNP G C3N-01414_T 30429323 184734037 5480518 136 23336 FAT1 0 . GRCh38 4 186708182 186708182 + Missense_Mutation SNP C C A rs758383716 C3N-01414_T C3N-01414_N C C c.1646G>T p.Arg549Leu p.R549L ENST00000441802 2/27 170 131 39 297 297 0 strelka-varscan-mutect FAT1,missense_variant,p.Arg549Leu,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Arg549Leu,ENST00000614102,;FAT1,downstream_gene_variant,,ENST00000509647,; A ENST00000441802 Transcript missense_variant 1856/14786 1646/13767 549/4588 R/L cGg/cTg rs758383716 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0.04) 2/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs758383716 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 186708182 186708182 C A 1 0 0 0 0 1 0 0 0 5549 652 23 1 1 FAT1 4 186708182 Missense_Mutation SNP C C3N-01414_T 1974145 186708182 3506373 137 23337 ICE1 0 . GRCh38 5 5463093 5463093 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.3759G>T p.Gln1253His p.Q1253H ENST00000296564 13/19 161 129 32 321 321 0 strelka-varscan-mutect ICE1,missense_variant,p.Gln1253His,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 3981/7927 3759/6801 1253/2266 Q/H caG/caT 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 tolerated(0.08) 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 5463093 5463093 G T 1 0 0 0 0 1 0 0 0 7384 1020 36 2 2 ICE1 5 5463093 Missense_Mutation SNP G C3N-01414_T 5463093 176075166 138 23338 PAPD7 0 . GRCh38 5 6742568 6742568 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.337G>T p.Ala113Ser p.A113S ENST00000631941 5/13 251 208 43 357 356 1 strelka-varscan-mutect PAPD7,missense_variant,p.Ala363Ser,ENST00000230859,;PAPD7,missense_variant,p.Ala113Ser,ENST00000631941,NM_006999.4,NM_001171805.1;PAPD7,downstream_gene_variant,,ENST00000515721,;PAPD7,upstream_gene_variant,,ENST00000514697,;PAPD7,upstream_gene_variant,,ENST00000511764,; T ENST00000631941 Transcript missense_variant 525/1902 337/1629 113/542 A/S Gca/Tca 1 1 PAPD7 HGNC HGNC:16705 protein_coding YES CCDS3871.1 ENSP00000488642 Q5XG87 UPI0000071E30 NM_006999.4,NM_001171805.1 tolerated(0.44) 5/13 Gene3D:3.30.460.10,Pfam_domain:PF01909,hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF24,Superfamily_domains:SSF81301 MODERATE 1 SNV 5 1 PASS rs952798730 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 6742568 6742568 G T 1 0 0 0 0 1 0 0 0 11507 1203 42 2 2 PAPD7 5 6742568 Missense_Mutation SNP G C3N-01414_T 1279475 6742568 174795691 139 23339 ADCY2 0 . GRCh38 5 7707731 7707731 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1294C>G p.Leu432Val p.L432V ENST00000338316 9/25 184 161 23 323 323 0 strelka-mutect ADCY2,missense_variant,p.Leu432Val,ENST00000338316,NM_020546.2;RP11-711G10.1,downstream_gene_variant,,ENST00000514105,; G ENST00000338316 Transcript missense_variant 1383/6575 1294/3276 432/1091 L/V Ctg/Gtg 1 1 ADCY2 HGNC HGNC:233 protein_coding YES CCDS3872.2 ENSP00000342952 Q08462 UPI000066D9F2 NM_020546.2 deleterious(0) 9/25 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF253,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 7707731 7707731 C G 1 0 0 0 0 1 0 0 0 338 680 24 4 4 ADCY2 5 7707731 Missense_Mutation SNP C C3N-01414_T 965163 7707731 173830528 140 23340 CDH18 0 . GRCh38 5 19503035 19503035 + Missense_Mutation SNP T T G rs17852886 C3N-01414_T C3N-01414_N T T c.1587A>C p.Glu529Asp p.E529D ENST00000507958 13/15 204 193 11 345 345 0 strelka-varscan-mutect CDH18,missense_variant,p.Glu529Asp,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Glu529Asp,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Glu529Asp,ENST00000274170,;CDH18,missense_variant,p.Glu529Asp,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Glu529Asp,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Glu529Asp,ENST00000511273,;CDH18,intron_variant,,ENST00000515257,; G ENST00000507958 Transcript missense_variant 2578/3542 1587/2373 529/790 E/D gaA/gaC rs17852886 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0.02) 13/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS rs17852886 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 19503035 19503035 T G 1 0 0 0 0 1 0 0 0 2806 1722 60 5 5 CDH18 5 19503035 Missense_Mutation SNP T C3N-01414_T 11795304 19503035 162035224 141 23341 ADAMTS12 0 . GRCh38 5 33649697 33649697 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.1191C>G p.Ser397Arg p.S397R ENST00000504830 8/24 76 70 6 115 115 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Ser397Arg,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Ser397Arg,ENST00000352040,;ADAMTS12,splice_region_variant,,ENST00000504582,; C ENST00000504830 Transcript missense_variant,splice_region_variant 1527/8774 1191/4785 397/1594 S/R agC/agG 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0.01) 8/24 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.26877 1 1 1 1 0 C 3 2 77 33649697 33649697 G C 1 0 0 0 0 1 0 0 0 301 985 34 4 4 ADAMTS12 5 33649697 Missense_Mutation SNP G C3N-01414_T 14146662 33649697 147888562 142 23342 FYB 0 . GRCh38 5 39202703 39202703 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.288T>A p.= p.T96T ENST00000512982 2/19 406 319 87 645 645 0 strelka-varscan-mutect FYB,synonymous_variant,p.=,ENST00000351578,NM_199335.3;FYB,synonymous_variant,p.=,ENST00000505428,NM_001465.4;FYB,synonymous_variant,p.=,ENST00000512982,NM_001243093.1;FYB,synonymous_variant,p.=,ENST00000515010,;FYB,synonymous_variant,p.=,ENST00000510188,;FYB,synonymous_variant,p.=,ENST00000512138,;FYB,downstream_gene_variant,,ENST00000506557,;FYB,downstream_gene_variant,,ENST00000504542,;FYB,downstream_gene_variant,,ENST00000509072,; T ENST00000512982 Transcript synonymous_variant 374/2747 288/2520 96/839 T acT/acA 1 -1 FYB HGNC HGNC:4036 protein_coding YES CCDS58945.1 ENSP00000425845 O15117 UPI00017A75FB NM_001243093.1 2/19 hmmpanther:PTHR16830,hmmpanther:PTHR16830:SF13 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 39202703 39202703 A T 1 0 0 0 0 0 0 0 1 5995 175 7 4 4 FYB 5 39202703 Silent SNP A C3N-01414_T 5553006 39202703 142335556 143 23343 DIMT1 0 . GRCh38 5 62390964 62390964 + Missense_Mutation SNP T T G novel C3N-01414_T C3N-01414_N T T c.811A>C p.Ser271Arg p.S271R ENST00000199320 11/12 210 188 22 349 349 0 strelka-varscan-mutect DIMT1,missense_variant,p.Ser271Arg,ENST00000199320,NM_014473.2;KIF2A,downstream_gene_variant,,ENST00000381103,NM_001243952.1;DIMT1,downstream_gene_variant,,ENST00000506390,;KIF2A,intron_variant,,ENST00000509663,;DIMT1,non_coding_transcript_exon_variant,,ENST00000514605,;DIMT1,downstream_gene_variant,,ENST00000514911,;DIMT1,downstream_gene_variant,,ENST00000509182,; G ENST00000199320 Transcript missense_variant 972/2859 811/942 271/313 S/R Agc/Cgc 1 -1 DIMT1 HGNC HGNC:30217 protein_coding YES CCDS3981.1 ENSP00000199320 Q9UNQ2 UPI00001293E2 NM_014473.2 tolerated(0.2) 11/12 PROSITE_profiles:PS51689,hmmpanther:PTHR11727:SF7,hmmpanther:PTHR11727,TIGRFAM_domain:TIGR00755,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 62390964 62390964 T G 1 0 0 0 0 1 0 0 0 4328 1580 55 5 5 DIMT1 5 62390964 Missense_Mutation SNP T C3N-01414_T 23188261 62390964 119147295 144 23344 DIMT1 0 . GRCh38 5 62390980 62390980 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.795A>G p.Ile265Met p.I265M ENST00000199320 11/12 161 145 16 270 270 0 strelka-varscan-mutect DIMT1,missense_variant,p.Ile265Met,ENST00000199320,NM_014473.2;KIF2A,downstream_gene_variant,,ENST00000381103,NM_001243952.1;DIMT1,downstream_gene_variant,,ENST00000506390,;KIF2A,intron_variant,,ENST00000509663,;DIMT1,non_coding_transcript_exon_variant,,ENST00000514605,;DIMT1,downstream_gene_variant,,ENST00000514911,;DIMT1,downstream_gene_variant,,ENST00000509182,; C ENST00000199320 Transcript missense_variant,splice_region_variant 956/2859 795/942 265/313 I/M atA/atG 1 -1 DIMT1 HGNC HGNC:30217 protein_coding YES CCDS3981.1 ENSP00000199320 Q9UNQ2 UPI00001293E2 NM_014473.2 tolerated(0.13) 11/12 PROSITE_profiles:PS51689,hmmpanther:PTHR11727:SF7,hmmpanther:PTHR11727,TIGRFAM_domain:TIGR00755,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 62390980 62390980 T C 1 0 0 0 0 1 0 0 0 4328 1768 61 5 5 DIMT1 5 62390980 Missense_Mutation SNP T C3N-01414_T 16 62390980 119147279 145 23345 MAP1B 0 . GRCh38 5 72195957 72195957 + Nonsense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.2602A>T p.Lys868Ter p.K868* ENST00000296755 5/7 262 183 79 397 397 0 strelka-varscan-mutect MAP1B,stop_gained,p.Lys868Ter,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; T ENST00000296755 Transcript stop_gained 2900/12036 2602/7407 868/2468 K/* Aag/Tag 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 72195957 72195957 A T 1 0 0 0 0 0 1 0 0 9151 247 9 4 4 MAP1B 5 72195957 Nonsense_Mutation SNP A C3N-01414_T 9804977 72195957 109342302 146 23346 IQGAP2 0 . GRCh38 5 76589656 76589656 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.568G>C p.Gly190Arg p.G190R ENST00000274364 7/36 108 90 18 172 171 1 strelka-varscan-mutect IQGAP2,missense_variant,p.Gly190Arg,ENST00000274364,NM_006633.3;IQGAP2,missense_variant,p.Gly140Arg,ENST00000379730,NM_001285460.1;IQGAP2,missense_variant,p.Gly140Arg,ENST00000505766,;IQGAP2,missense_variant,p.Gly163Arg,ENST00000514350,; C ENST00000274364 Transcript missense_variant 865/5844 568/4728 190/1575 G/R Gga/Cga 1 1 IQGAP2 HGNC HGNC:6111 protein_coding YES CCDS34188.1 ENSP00000274364 Q13576 UPI000020CB2C NM_006633.3 deleterious(0) 7/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14149:SF12,hmmpanther:PTHR14149,Gene3D:1.10.418.10,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS rs1369697897 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 76589656 76589656 G C 1 0 0 0 0 1 0 0 0 7721 1349 47 4 4 IQGAP2 5 76589656 Missense_Mutation SNP G C3N-01414_T 4393699 76589656 104948603 147 23347 IQGAP2 0 . GRCh38 5 76693383 76693383 + Silent SNP C C A rs373730789 C3N-01414_T C3N-01414_N C C c.3934C>A p.= p.R1312R ENST00000274364 31/36 202 165 37 315 315 0 strelka-varscan-mutect IQGAP2,synonymous_variant,p.=,ENST00000274364,NM_006633.3;IQGAP2,synonymous_variant,p.=,ENST00000379730,NM_001285460.1;IQGAP2,synonymous_variant,p.=,ENST00000505766,;IQGAP2,synonymous_variant,p.=,ENST00000502745,NM_001285462.1;IQGAP2,synonymous_variant,p.=,ENST00000396234,NM_001285461.1;CTD-2384B11.2,intron_variant,,ENST00000507514,;IQGAP2,3_prime_UTR_variant,,ENST00000504477,;IQGAP2,non_coding_transcript_exon_variant,,ENST00000512256,; A ENST00000274364 Transcript synonymous_variant 4231/5844 3934/4728 1312/1575 R Cgg/Agg rs373730789 1 1 IQGAP2 HGNC HGNC:6111 protein_coding YES CCDS34188.1 ENSP00000274364 Q13576 UPI000020CB2C NM_006633.3 31/36 hmmpanther:PTHR14149:SF12,hmmpanther:PTHR14149 LOW 1 SNV 1 1 PASS rs373730789 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 76693383 76693383 C A 1 0 0 0 0 0 0 0 1 7721 643 23 1 1 IQGAP2 5 76693383 Silent SNP C C3N-01414_T 103727 76693383 104844876 148 23348 LVRN 0 . GRCh38 5 115993787 115993787 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1307T>A p.Leu436His p.L436H ENST00000357872 6/20 239 176 63 355 355 0 strelka-varscan-mutect LVRN,missense_variant,p.Leu436His,ENST00000357872,NM_173800.4;LVRN,missense_variant,p.Leu424His,ENST00000395528,;LVRN,missense_variant,p.Leu436His,ENST00000504467,;LVRN,upstream_gene_variant,,ENST00000503329,;LVRN,upstream_gene_variant,,ENST00000514509,;LVRN,upstream_gene_variant,,ENST00000512314,; A ENST00000357872 Transcript missense_variant 1431/4581 1307/2973 436/990 L/H cTc/cAc 1 1 LVRN HGNC HGNC:26904 protein_coding YES CCDS4124.1 ENSP00000350541 Q6Q4G3 A0A0A6YYA2 UPI0000457329 NM_173800.4 deleterious(0) 6/20 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF31,Gene3D:1.10.390.10,Pfam_domain:PF01433,Superfamily_domains:SSF55486,Prints_domain:PR00756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 115993787 115993787 T A 1 0 0 0 0 1 0 0 0 8998 1551 54 4 4 LVRN 5 115993787 Missense_Mutation SNP T C3N-01414_T 39300404 115993787 65544472 149 23349 DMXL1 0 . GRCh38 5 119177366 119177366 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.6768G>T p.Gln2256His p.Q2256H ENST00000539542 27/44 89 71 18 167 167 0 strelka-varscan-mutect DMXL1,missense_variant,p.Gln2256His,ENST00000539542,NM_001290321.2;DMXL1,missense_variant,p.Gln2256His,ENST00000311085,NM_001290322.2,NM_005509.5; T ENST00000539542 Transcript missense_variant 6949/11236 6768/9147 2256/3048 Q/H caG/caT 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 tolerated(0.38) 27/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 119177366 119177366 G T 1 0 0 0 0 1 0 0 0 4403 933 33 2 2 DMXL1 5 119177366 Missense_Mutation SNP G C3N-01414_T 3183579 119177366 62360893 150 23350 FBN2 0 . GRCh38 5 128345425 128345425 + Missense_Mutation SNP G G T rs150506063 C3N-01414_T C3N-01414_N G G c.3149C>A p.Thr1050Lys p.T1050K ENST00000508053 30/71 451 340 111 623 623 0 strelka-varscan-mutect FBN2,missense_variant,p.Thr1050Lys,ENST00000508053,;FBN2,missense_variant,p.Thr1050Lys,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Thr1049Lys,ENST00000619499,;FBN2,missense_variant,p.Thr1017Lys,ENST00000508989,; T ENST00000508053 Transcript missense_variant 4124/11132 3149/8739 1050/2912 T/K aCg/aAg rs150506063,COSM3849864,COSM50535 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.54) 30/71 Gene3D:3.90.290.10,PD968187,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 uncertain_significance 0,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS rs150506063 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 128345425 128345425 G T 1 0 0 0 0 1 0 0 0 5566 1145 40 1 1 FBN2 5 128345425 Missense_Mutation SNP G C3N-01414_T 9168059 128345425 53192834 151 23351 TRPC7 0 . GRCh38 5 136247600 136247600 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1715T>A p.Leu572Gln p.L572Q ENST00000513104 7/12 280 214 66 373 373 0 strelka-varscan-mutect TRPC7,missense_variant,p.Leu572Gln,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Leu517Gln,ENST00000502753,;TRPC7,missense_variant,p.Leu511Gln,ENST00000378459,NM_001167577.1;TRPC7,missense_variant,p.Leu456Gln,ENST00000352189,NM_001167576.1;TRPC7,3_prime_UTR_variant,,ENST00000503275,;TRPC7,3_prime_UTR_variant,,ENST00000514963,; T ENST00000513104 Transcript missense_variant 1998/2987 1715/2589 572/862 L/Q cTa/cAa 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 deleterious(0) 7/12 Pfam_domain:PF00520,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9,TIGRFAM_domain:TIGR00870 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 136247600 136247600 A T 1 0 0 0 0 1 0 0 0 17090 420 15 4 4 TRPC7 5 136247600 Missense_Mutation SNP A C3N-01414_T 7902175 136247600 45290659 152 23352 PCDHA7 0 . GRCh38 5 140836477 140836477 + Silent SNP G G C C3N-01414_T C3N-01414_N G G c.2094G>C p.= p.V698V ENST00000525929 1/4 362 322 40 569 569 0 strelka-varscan-mutect PCDHA7,synonymous_variant,p.=,ENST00000525929,NM_018910.2;PCDHA7,synonymous_variant,p.=,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA8,upstream_gene_variant,,ENST00000531613,NM_018911.2;PCDHA8,upstream_gene_variant,,ENST00000378123,NM_031856.1; C ENST00000525929 Transcript synonymous_variant 2094/5221 2094/2814 698/937 V gtG/gtC COSM3851008,COSM3851009 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 1/4 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 140836477 140836477 G C 1 0 0 0 0 0 0 0 1 11616 1364 48 4 4 PCDHA7 5 140836477 Silent SNP G C3N-01414_T 4588877 140836477 40701782 153 23353 PCDHB4 0 . GRCh38 5 141122149 141122149 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.151C>T p.= p.L51L ENST00000194152 1/1 241 179 62 336 336 0 strelka-varscan-mutect PCDHB4,synonymous_variant,p.=,ENST00000194152,NM_018938.3;AC005754.8,downstream_gene_variant,,ENST00000606030,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB4,intron_variant,,ENST00000623478,; T ENST00000194152 Transcript synonymous_variant 351/3825 151/2388 51/795 L Ctg/Ttg 1 1 PCDHB4 HGNC HGNC:8689 protein_coding YES CCDS4246.1 ENSP00000194152 Q9Y5E5 UPI00001273DF NM_018938.3 1/1 Gene3D:2.60.40.60,Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF55,Superfamily_domains:SSF49313 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 141122149 141122149 C T 1 0 0 0 0 0 0 0 1 11631 912 32 3 3 PCDHB4 5 141122149 Silent SNP C C3N-01414_T 285672 141122149 40416110 154 23354 PCDHB5 0 . GRCh38 5 141137459 141137459 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.2025G>T p.= p.A675A ENST00000231134 1/1 377 303 74 561 559 2 strelka-varscan-mutect PCDHB5,synonymous_variant,p.=,ENST00000231134,NM_015669.4;PCDHB5,downstream_gene_variant,,ENST00000623915,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; T ENST00000231134 Transcript synonymous_variant 2242/3408 2025/2388 675/795 A gcG/gcT 1 1 PCDHB5 HGNC HGNC:8690 protein_coding YES CCDS4247.1 ENSP00000231134 Q9Y5E4 UPI0000169DEA NM_015669.4 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF90,Low_complexity_(Seg):seg LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 141137459 141137459 G T 1 0 0 0 0 0 0 0 1 11632 1103 39 1 1 PCDHB5 5 141137459 Silent SNP G C3N-01414_T 15310 141137459 40400800 155 23355 PCDHB10 0 . GRCh38 5 141193223 141193223 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.671G>T p.Gly224Val p.G224V ENST00000239446 1/1 296 254 42 442 442 0 strelka-varscan-mutect PCDHB10,missense_variant,p.Gly224Val,ENST00000239446,NM_018930.3;PCDHB9,downstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.6,intron_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; T ENST00000239446 Transcript missense_variant 871/3290 671/2403 224/800 G/V gGg/gTg 1 1 PCDHB10 HGNC HGNC:8681 protein_coding YES CCDS4252.1 ENSP00000239446 Q9UN67 UPI0000048F2E NM_018930.3 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF54,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 141193223 141193223 G T 1 0 0 0 0 1 0 0 0 11622 1232 43 2 2 PCDHB10 5 141193223 Missense_Mutation SNP G C3N-01414_T 55764 141193223 40345036 156 23356 PCDHGA4 0 . GRCh38 5 141357141 141357141 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.2034G>T p.Gln678His p.Q678H ENST00000571252 1/4 135 108 27 217 217 0 strelka-varscan-mutect PCDHGA4,missense_variant,p.Gln678His,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Gln678His,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 2117/4778 2034/2889 678/962 Q/H caG/caT 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0.01) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 141357141 141357141 G T 1 0 0 0 0 1 0 0 0 11643 991 35 2 2 PCDHGA4 5 141357141 Missense_Mutation SNP G C3N-01414_T 163918 141357141 40181118 157 23357 PCDHGB3 0 . GRCh38 5 141370537 141370537 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.143G>T p.Gly48Val p.G48V ENST00000576222 1/4 150 110 40 221 220 1 strelka-varscan-mutect PCDHGB3,missense_variant,p.Gly48Val,ENST00000576222,NM_018924.4;PCDHGB3,missense_variant,p.Gly48Val,ENST00000618934,NM_032097.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,upstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGA6,upstream_gene_variant,,ENST00000517434,NM_018919.2;PCDHGA5,downstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000576222 Transcript missense_variant 274/4727 143/2790 48/929 G/V gGg/gTg 1 1 PCDHGB3 HGNC HGNC:8710 protein_coding YES CCDS58980.1 ENSP00000461862 Q9Y5G1 UPI0000EE35B5 NM_018924.4 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1484817452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 141370537 141370537 G T 1 0 0 0 0 1 0 0 0 11651 1232 43 2 2 PCDHGB3 5 141370537 Missense_Mutation SNP G C3N-01414_T 13396 141370537 40167722 158 23358 PCDHGB4 0 . GRCh38 5 141388655 141388655 + Silent SNP G G T rs375260597 C3N-01414_T C3N-01414_N G G c.771G>T p.= p.P257P ENST00000519479 1/4 248 175 73 402 402 0 strelka-varscan-mutect PCDHGB4,synonymous_variant,p.=,ENST00000615384,NM_032098.1;PCDHGB4,synonymous_variant,p.=,ENST00000519479,NM_003736.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA8,upstream_gene_variant,,ENST00000610569,NM_014004.2;PCDHGA8,upstream_gene_variant,,ENST00000398604,NM_032088.1;PCDHGA7,downstream_gene_variant,,ENST00000617050,NM_032087.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000519479 Transcript synonymous_variant 771/4578 771/2772 257/923 P ccG/ccT rs375260597 1 1 PCDHGB4 HGNC HGNC:8711 protein_coding YES CCDS54928.1 ENSP00000428288 Q9UN71 UPI000006F773 NM_003736.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF117,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 LOW 1 SNV 1 1 PASS rs375260597 . 0 207 0 0 3 0 0 0 -20 0.990084 1 1 1 0 T 2 4 77 141388655 141388655 G T 1 0 0 0 0 0 0 0 1 11652 1103 39 1 1 PCDHGB4 5 141388655 Silent SNP G C3N-01414_T 18118 141388655 40149604 159 23359 PCDHGA12 0 . GRCh38 5 141432363 141432363 + Frame_Shift_Del DEL G G - novel C3N-01414_T C3N-01414_N G G c.1606delG p.Asp536ThrfsTer13 p.D536Tfs*13 ENST00000252085 1/4 208 158 50 357 357 0 sindel-varindel-pindel PCDHGA12,frameshift_variant,p.Asp536ThrfsTer13,ENST00000252085,NM_003735.2;PCDHGA12,frameshift_variant,p.Asp536ThrfsTer13,ENST00000613314,NM_032094.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB7,intron_variant,,ENST00000398594,NM_018927.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA11,intron_variant,,ENST00000398587,NM_018914.2;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,intron_variant,,ENST00000518882,NM_032092.1;AC005618.9,upstream_gene_variant,,ENST00000624928,;PCDHGB8P,downstream_gene_variant,,ENST00000502926,;PCDHGA3,intron_variant,,ENST00000612467,;PCDHGB8P,downstream_gene_variant,,ENST00000507007,; - ENST00000252085 Transcript frameshift_variant 1746/4747 1604/2799 535/932 R/X cGg/cg 1 1 PCDHGA12 HGNC HGNC:8699 protein_coding YES CCDS4260.1 ENSP00000252085 O60330 UPI0000073EA1 NM_003735.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF109,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 141432363 141432363 G - 1 0 1 0 1 0 0 0 0 11640 1116 39 0 0 PCDHGA12 5 141432363 Frame_Shift_Del DEL G C3N-01414_T 43708 141432363 40105896 160 23360 FCHSD1 0 . GRCh38 5 141644349 141644349 + Silent SNP G G T rs766658544 C3N-01414_T C3N-01414_N G G c.1732C>A p.= p.R578R ENST00000435817 17/20 364 277 87 503 502 1 strelka-varscan-mutect FCHSD1,synonymous_variant,p.=,ENST00000435817,NM_033449.2;FCHSD1,synonymous_variant,p.=,ENST00000522783,;RELL2,downstream_gene_variant,,ENST00000297164,NM_173828.4;RELL2,downstream_gene_variant,,ENST00000444782,NM_001130029.1;RELL2,downstream_gene_variant,,ENST00000521367,;RELL2,downstream_gene_variant,,ENST00000518856,;FCHSD1,downstream_gene_variant,,ENST00000519800,;FCHSD1,downstream_gene_variant,,ENST00000518499,;FCHSD1,non_coding_transcript_exon_variant,,ENST00000523856,;RELL2,downstream_gene_variant,,ENST00000518025,;RELL2,downstream_gene_variant,,ENST00000520674,;RELL2,downstream_gene_variant,,ENST00000517794,;FCHSD1,upstream_gene_variant,,ENST00000518160,;FCHSD1,downstream_gene_variant,,ENST00000522386,;FCHSD1,downstream_gene_variant,,ENST00000522763,;FCHSD1,3_prime_UTR_variant,,ENST00000522126,;FCHSD1,upstream_gene_variant,,ENST00000520747,; T ENST00000435817 Transcript synonymous_variant 1783/4320 1732/2073 578/690 R Cgg/Agg rs766658544 1 -1 FCHSD1 HGNC HGNC:25463 protein_coding YES CCDS47295.1 ENSP00000399259 Q86WN1 UPI000000D903 NM_033449.2 17/20 PROSITE_profiles:PS50002,hmmpanther:PTHR15735:SF4,hmmpanther:PTHR15735,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS rs766658544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 141644349 141644349 G T 1 0 0 0 0 0 0 0 1 5651 1115 39 1 1 FCHSD1 5 141644349 Silent SNP G C3N-01414_T 211986 141644349 39893910 161 23361 PCDH1 0 . GRCh38 5 141864750 141864750 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.1581G>T p.Glu527Asp p.E527D ENST00000287008 3/5 249 183 66 365 364 1 strelka-varscan-mutect PCDH1,missense_variant,p.Glu527Asp,ENST00000287008,NM_032420.3;PCDH1,missense_variant,p.Glu527Asp,ENST00000394536,NM_001278613.1,NM_002587.4;PCDH1,3_prime_UTR_variant,,ENST00000515351,;PCDH1,intron_variant,,ENST00000503492,;PCDH1,downstream_gene_variant,,ENST00000514773,;PCDH1,non_coding_transcript_exon_variant,,ENST00000357517,;PCDH1,non_coding_transcript_exon_variant,,ENST00000511044,;PCDH1,downstream_gene_variant,,ENST00000505937,; A ENST00000287008 Transcript missense_variant 1729/4793 1581/3714 527/1237 E/D gaG/gaT COSM4529041,COSM4529042 1 -1 PCDH1 HGNC HGNC:8655 protein_coding YES CCDS4267.1 ENSP00000287008 Q08174 UPI000016158F NM_032420.3 tolerated(0.65) 3/5 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF326,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 141864750 141864750 C A 1 0 0 0 0 1 0 0 0 11593 912 32 2 2 PCDH1 5 141864750 Missense_Mutation SNP C C3N-01414_T 220401 141864750 39673509 162 23362 SPINK6 0 . GRCh38 5 148214937 148214937 + Missense_Mutation SNP C C G rs762291568 C3N-01414_T C3N-01414_N C C c.230C>G p.Pro77Arg p.P77R ENST00000325630 4/4 196 176 20 293 293 0 strelka-varscan-mutect SPINK6,missense_variant,p.Pro77Arg,ENST00000325630,NM_205841.3;SPINK6,missense_variant,p.Pro77Arg,ENST00000621437,NM_001195290.1;SPINK6,downstream_gene_variant,,ENST00000514389,; G ENST00000325630 Transcript missense_variant 486/686 230/243 77/80 P/R cCt/cGt rs762291568,COSM3612205 1 1 SPINK6 HGNC HGNC:29486 protein_coding YES CCDS34268.1 ENSP00000324870 Q6UWN8 UPI000004BA6C NM_205841.3 tolerated(0.49) 4/4 Gene3D:1.10.1890.10,Pfam_domain:PF00050,PROSITE_profiles:PS51465,hmmpanther:PTHR10913,SMART_domains:SM00280,Superfamily_domains:SSF100895 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762291568 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 148214937 148214937 C G 1 0 0 0 0 1 0 0 0 15416 681 24 4 4 SPINK6 5 148214937 Missense_Mutation SNP C C3N-01414_T 6350187 148214937 33323322 163 23363 HTR4 0 . GRCh38 5 148509532 148509532 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.1000T>C p.Tyr334His p.Y334H ENST00000360693 6/8 162 116 46 240 240 0 strelka-varscan-mutect HTR4,missense_variant,p.Tyr334His,ENST00000360693,;HTR4,missense_variant,p.Tyr334His,ENST00000362016,NM_001040173.2;HTR4,missense_variant,p.Tyr334His,ENST00000377888,NM_000870.6;HTR4,missense_variant,p.Tyr334His,ENST00000521530,NM_001040169.2;HTR4,missense_variant,p.Tyr334His,ENST00000521735,NM_199453.3;HTR4,missense_variant,p.Tyr334His,ENST00000520514,NM_001286410.1;HTR4,missense_variant,p.Tyr334His,ENST00000631296,;HTR4,missense_variant,p.Tyr334His,ENST00000517929,NM_001040172.2;HTR4,missense_variant,p.Tyr334His,ENST00000524063,;HTR4,missense_variant,p.Tyr334His,ENST00000522588,;HTR4,non_coding_transcript_exon_variant,,ENST00000521124,; G ENST00000360693 Transcript missense_variant 1139/3082 1000/1287 334/428 Y/H Tac/Cac 1 -1 HTR4 HGNC HGNC:5299 protein_coding YES CCDS34272.1 ENSP00000353915 Q13639 UPI00002323B1 deleterious(0.01) 6/8 hmmpanther:PTHR24249:SF33,hmmpanther:PTHR24249,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01059 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 148509532 148509532 A G 1 0 0 0 0 1 0 0 0 7345 420 15 5 5 HTR4 5 148509532 Missense_Mutation SNP A C3N-01414_T 294595 148509532 33028727 164 23364 SLC6A7 0 . GRCh38 5 150201206 150201206 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.841C>A p.His281Asn p.H281N ENST00000230671 6/14 99 81 18 120 120 0 strelka-varscan-mutect SLC6A7,missense_variant,p.His281Asn,ENST00000230671,NM_014228.3;SLC6A7,missense_variant,p.His281Asn,ENST00000524041,; A ENST00000230671 Transcript missense_variant 1212/3739 841/1911 281/636 H/N Cac/Aac COSM215970 1 1 SLC6A7 HGNC HGNC:11054 protein_coding YES CCDS4305.1 ENSP00000230671 Q99884 UPI000013C93C NM_014228.3 deleterious(0.04) 6/14 PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF35,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 1 MODERATE 1 SNV 1 1 1 PASS rs960870506 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 77 150201206 150201206 C A 1 0 0 0 0 1 0 0 0 14972 594 21 2 2 SLC6A7 5 150201206 Missense_Mutation SNP C C3N-01414_T 1691674 150201206 31337053 165 23365 PPP1R2P3 0 . GRCh38 5 156850962 156850962 + Missense_Mutation SNP C C G rs183405829 C3N-01414_T C3N-01414_N C C c.400C>G p.Arg134Gly p.R134G ENST00000522232 1/1 387 297 90 632 632 0 strelka-varscan-mutect PPP1R2P3,missense_variant,p.Arg134Gly,ENST00000522232,; G ENST00000522232 Transcript missense_variant 425/1991 400/618 134/205 R/G Cga/Gga rs183405829 1 1 PPP1R2P3 HGNC HGNC:16318 protein_coding YES ENSP00000490297 G1AUC5 UPI000013EC9E 1/1 Pfam_domain:PF04979,hmmpanther:PTHR12398,hmmpanther:PTHR12398:SF23 MODERATE 1 SNV 1 PASS rs183405829 . 0 125 0 0 84 0 0 0 -20 0 0 1 0 0 G 3 3 77 156850962 156850962 C G 1 0 0 0 0 1 0 0 0 12486 528 19 4 4 PPP1R2P3 5 156850962 Missense_Mutation SNP C C3N-01414_T 6649756 156850962 24687297 166 23366 EBF1 0 . GRCh38 5 158712188 158712188 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.1515C>A p.Phe505Leu p.F505L ENST00000313708 14/16 162 131 31 270 270 0 strelka-varscan-mutect EBF1,missense_variant,p.Phe505Leu,ENST00000313708,NM_001324107.1,NM_024007.3,NM_001290360.1;EBF1,missense_variant,p.Phe321Leu,ENST00000622875,;EBF1,missense_variant,p.Phe474Leu,ENST00000380654,NM_182708.1;EBF1,intron_variant,,ENST00000517373,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,upstream_gene_variant,,ENST00000518323,;EBF1,non_coding_transcript_exon_variant,,ENST00000519739,;EBF1,non_coding_transcript_exon_variant,,ENST00000519890,;EBF1,non_coding_transcript_exon_variant,,ENST00000522192,; T ENST00000313708 Transcript missense_variant 1798/5250 1515/1776 505/591 F/L ttC/ttA COSM5590713 1 -1 EBF1 HGNC HGNC:3126 protein_coding YES CCDS4343.1 ENSP00000322898 Q9UH73 UPI000000D95E NM_001324107.1,NM_024007.3,NM_001290360.1 tolerated_low_confidence(0.05) 14/16 hmmpanther:PTHR10747 1 MODERATE 1 SNV 1 1 1 PASS rs1211160649 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 158712188 158712188 G T 1 0 0 0 0 1 0 0 0 4704 1165 41 2 2 EBF1 5 158712188 Missense_Mutation SNP G C3N-01414_T 1861226 158712188 22826071 167 23367 GABRA1 0 . GRCh38 5 161882603 161882603 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.605C>A p.Pro202Gln p.P202Q ENST00000393943 7/10 346 306 40 557 556 1 strelka-varscan-mutect GABRA1,missense_variant,p.Pro202Gln,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,missense_variant,p.Pro202Gln,ENST00000428797,NM_001127643.1;GABRA1,missense_variant,p.Pro217Gln,ENST00000638159,;GABRA1,missense_variant,p.Pro202Gln,ENST00000437025,NM_001127645.1;GABRA1,missense_variant,p.Pro202Gln,ENST00000638112,;GABRA1,missense_variant,p.Pro202Gln,ENST00000636573,;GABRA1,missense_variant,p.Pro202Gln,ENST00000023897,NM_000806.5;GABRA1,missense_variant,p.Pro202Gln,ENST00000637827,;GABRA1,missense_variant,p.Pro202Gln,ENST00000635880,;GABRA1,missense_variant,p.Pro202Gln,ENST00000634335,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,downstream_gene_variant,,ENST00000635916,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,; A ENST00000393943 Transcript missense_variant 1388/4686 605/1371 202/456 P/Q cCa/cAa 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 deleterious(0.04) 7/10 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR01079,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs1442004290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 161882603 161882603 C A 1 0 0 0 0 1 0 0 0 6031 594 21 2 2 GABRA1 5 161882603 Missense_Mutation SNP C C3N-01414_T 3170415 161882603 19655656 168 23368 SLIT3 0 . GRCh38 5 168700679 168700679 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2866G>T p.Gly956Cys p.G956C ENST00000332966 27/36 158 117 41 256 256 0 strelka-varscan-mutect SLIT3,missense_variant,p.Gly949Cys,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Gly819Cys,ENST00000404867,;SLIT3,missense_variant,p.Gly956Cys,ENST00000332966,NM_001271946.1;SLIT3,upstream_gene_variant,,ENST00000518092,; A ENST00000332966 Transcript missense_variant,splice_region_variant 2939/4895 2866/4593 956/1530 G/C Ggc/Tgc 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 deleterious(0) 27/36 PROSITE_profiles:PS50026,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 168700679 168700679 C A 1 0 0 0 0 1 0 0 0 15032 637 22 2 2 SLIT3 5 168700679 Missense_Mutation SNP C C3N-01414_T 6818076 168700679 12837580 169 23369 TLX3 0 . GRCh38 5 171310199 171310199 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.471C>A p.= p.P157P ENST00000296921 2/3 233 184 49 293 293 0 strelka-varscan-mutect TLX3,synonymous_variant,p.=,ENST00000296921,NM_021025.2;RP11-546B8.6,upstream_gene_variant,,ENST00000619056,; A ENST00000296921 Transcript synonymous_variant 553/1493 471/876 157/291 P ccC/ccA 1 1 TLX3 HGNC HGNC:13532 protein_coding YES CCDS34288.1 ENSP00000296921 O43711 UPI000013E3AA NM_021025.2 2/3 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF154,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS rs1211964256 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 171310199 171310199 C A 1 0 0 0 0 0 0 0 1 16407 668 24 2 2 TLX3 5 171310199 Silent SNP C C3N-01414_T 2609520 171310199 10228060 170 23370 GRM6 0 . GRCh38 5 178994854 178994854 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.91G>T p.Gly31Cys p.G31C ENST00000231188 1/10 44 33 11 47 47 0 strelka-varscan-mutect GRM6,missense_variant,p.Gly31Cys,ENST00000231188,NM_000843.3;GRM6,missense_variant,p.Gly31Cys,ENST00000517717,;RP11-281O15.4,downstream_gene_variant,,ENST00000519491,;GRM6,downstream_gene_variant,,ENST00000519175,;RP11-281O15.5,downstream_gene_variant,,ENST00000521486,; A ENST00000231188 Transcript missense_variant 270/6143 91/2634 31/877 G/C Ggc/Tgc 1 -1 GRM6 HGNC HGNC:4598 protein_coding YES CCDS4442.1 ENSP00000231188 O15303 UPI000013C947 NM_000843.3 deleterious(0.05) 1/10 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF24,Prints_domain:PR01056 MODERATE 1 SNV 2 1 PASS . . 1 206 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 178994854 178994854 C A 1 0 0 0 0 1 0 0 0 6683 623 22 2 2 GRM6 5 178994854 Missense_Mutation SNP C C3N-01414_T 7684655 178994854 2543405 171 23371 DUSP22 0 . GRCh38 6 348263 348263 + Nonsense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.424G>T p.Glu142Ter p.E142* ENST00000419235 6/7 143 131 12 211 211 0 varscan-mutect DUSP22,stop_gained,p.Glu39Ter,ENST00000604971,;DUSP22,stop_gained,p.Glu142Ter,ENST00000419235,NM_001286555.1;DUSP22,stop_gained,p.Glu142Ter,ENST00000344450,NM_020185.4;DUSP22,stop_gained,p.Glu39Ter,ENST00000605035,;DUSP22,stop_gained,p.Glu39Ter,ENST00000605315,;DUSP22,stop_gained,p.Glu39Ter,ENST00000603453,;DUSP22,stop_gained,p.Glu39Ter,ENST00000605863,;DUSP22,downstream_gene_variant,,ENST00000603881,;DUSP22,downstream_gene_variant,,ENST00000603296,;DUSP22,non_coding_transcript_exon_variant,,ENST00000604914,;DUSP22,non_coding_transcript_exon_variant,,ENST00000604988,;DUSP22,non_coding_transcript_exon_variant,,ENST00000603005,;DUSP22,downstream_gene_variant,,ENST00000603290,;DUSP22,downstream_gene_variant,,ENST00000605391,;DUSP22,3_prime_UTR_variant,,ENST00000603795,;DUSP22,3_prime_UTR_variant,,ENST00000603726,; T ENST00000419235 Transcript stop_gained 502/3098 424/618 142/205 E/* Gag/Tag 1 1 DUSP22 HGNC HGNC:16077 protein_coding YES CCDS69035.1 ENSP00000397459 Q9NRW4 UPI000020E3B7 NM_001286555.1 6/7 Gene3D:3.90.190.10,PROSITE_profiles:PS50054,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF29 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 348263 348263 G T 1 0 0 0 0 0 1 0 0 4643 1291 45 2 2 DUSP22 6 348263 Nonsense_Mutation SNP G C3N-01414_T 348263 170457716 172 23372 WRNIP1 0 . GRCh38 6 2785099 2785099 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1815G>T p.Arg605Ser p.R605S ENST00000380773 7/7 395 291 104 661 661 0 strelka-varscan-mutect WRNIP1,missense_variant,p.Arg385Ser,ENST00000380769,;WRNIP1,missense_variant,p.Arg605Ser,ENST00000380773,;WRNIP1,missense_variant,p.Arg605Ser,ENST00000618555,NM_020135.2;WRNIP1,missense_variant,p.Arg580Ser,ENST00000380771,NM_130395.2;WRNIP1,missense_variant,p.Arg221Ser,ENST00000380764,; T ENST00000380773 Transcript missense_variant 2024/2670 1815/1998 605/665 R/S agG/agT 1 1 WRNIP1 HGNC HGNC:20876 protein_coding YES CCDS4475.1 ENSP00000370150 Q96S55 UPI000004A506 deleterious(0.02) 7/7 Gene3D:1.10.3710.10,Pfam_domain:PF12002,hmmpanther:PTHR13779,hmmpanther:PTHR13779:SF7,Superfamily_domains:SSF48019 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 2785099 2785099 G T 1 0 0 0 0 1 0 0 0 17960 1165 41 2 2 WRNIP1 6 2785099 Missense_Mutation SNP G C3N-01414_T 2436836 2785099 168020880 173 23373 LY86 0 . GRCh38 6 6624932 6624932 + Nonsense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.143T>A p.Leu48Ter p.L48* ENST00000379953 3/6 162 118 44 317 317 0 strelka-varscan-mutect LY86,stop_gained,p.Leu48Ter,ENST00000379953,;LY86,stop_gained,p.Leu48Ter,ENST00000230568,NM_004271.3;LY86-AS1,upstream_gene_variant,,ENST00000435641,;LY86-AS1,upstream_gene_variant,,ENST00000429345,;LY86-AS1,upstream_gene_variant,,ENST00000607278,;LY86-AS1,upstream_gene_variant,,ENST00000606044,; A ENST00000379953 Transcript stop_gained 495/1197 143/489 48/162 L/* tTa/tAa 1 1 LY86 HGNC HGNC:16837 protein_coding YES CCDS4498.1 ENSP00000369286 O95711 UPI0000001C73 3/6 Gene3D:2.60.40.770,hmmpanther:PTHR20838,hmmpanther:PTHR20838:SF0,SMART_domains:SM00737,Superfamily_domains:SSF81296 HIGH SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 6624932 6624932 T A 1 0 0 0 0 0 1 0 0 9011 1764 61 4 4 LY86 6 6624932 Nonsense_Mutation SNP T C3N-01414_T 3839833 6624932 164181047 174 23374 MCUR1 0 . GRCh38 6 13802300 13802300 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.582G>T p.Lys194Asn p.K194N ENST00000379170 3/9 202 149 53 334 334 0 strelka-varscan-mutect MCUR1,missense_variant,p.Lys194Asn,ENST00000379170,NM_001031713.3;MCUR1,upstream_gene_variant,,ENST00000607303,;MCUR1,3_prime_UTR_variant,,ENST00000488770,; A ENST00000379170 Transcript missense_variant 721/5471 582/1080 194/359 K/N aaG/aaT 1 -1 MCUR1 HGNC HGNC:21097 protein_coding YES CCDS35495.1 ENSP00000368468 Q96AQ8 UPI0000072AC6 NM_001031713.3 tolerated(0.18) 3/9 Pfam_domain:PF07798,hmmpanther:PTHR14360,hmmpanther:PTHR14360:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 13802300 13802300 C A 1 0 0 0 0 1 0 0 0 9340 912 32 2 2 MCUR1 6 13802300 Missense_Mutation SNP C C3N-01414_T 7177368 13802300 157003679 175 23375 JARID2 0 . GRCh38 6 15410222 15410222 + Splice_Site SNP A A G novel C3N-01414_T C3N-01414_N A A c.182-2A>G p.X61_splice ENST00000341776 90 67 23 182 182 0 strelka-varscan-mutect JARID2,splice_acceptor_variant,,ENST00000341776,NM_004973.3;JARID2,splice_acceptor_variant,,ENST00000397311,NM_001267040.1; G ENST00000341776 Transcript splice_acceptor_variant -/5755 182/3741 61/1246 1 1 JARID2 HGNC HGNC:6196 protein_coding YES CCDS4533.1 ENSP00000341280 Q92833 UPI0000161C67 NM_004973.3 2/17 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 77 15410222 15410222 A G 1 0 0 0 0 0 0 1 0 7859 434 15 5 5 JARID2 6 15410222 Splice_Site SNP A C3N-01414_T 1607922 15410222 155395757 176 23376 HIST1H2BB 0 . GRCh38 6 26043286 26043286 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.372C>T p.= p.S124S ENST00000615966 1/1 63 44 19 101 101 0 strelka-varscan-mutect HIST1H2BB,synonymous_variant,p.=,ENST00000615966,NM_021062.2;HIST1H3C,upstream_gene_variant,,ENST00000612966,NM_003531.2;U91328.2,upstream_gene_variant,,ENST00000454320,; A ENST00000615966 Transcript synonymous_variant 372/381 372/381 124/126 S agC/agT 1 -1 HIST1H2BB HGNC HGNC:4751 protein_coding YES CCDS4575.1 ENSP00000482674 P33778 UPI0000001BD2 NM_021062.2 1/1 hmmpanther:PTHR23428,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113 LOW 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 26043286 26043286 G A 1 0 0 0 0 0 0 0 1 7029 962 34 3 3 HIST1H2BB 6 26043286 Silent SNP G C3N-01414_T 10633064 26043286 144762693 177 23377 NOTCH4 0 . GRCh38 6 32219657 32219657 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1445A>T p.Gln482Leu p.Q482L ENST00000375023 8/30 183 153 30 306 306 0 strelka-varscan-mutect NOTCH4,missense_variant,p.Gln482Leu,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000473562,; A ENST00000375023 Transcript missense_variant 1584/6745 1445/6012 482/2003 Q/L cAg/cTg 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0.01) 8/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033:SF64,hmmpanther:PTHR24033,PROSITE_patterns:PS01187,Gene3D:2gy5A03,Pfam_domain:PF00008,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 32219657 32219657 T A 1 0 0 0 0 1 0 0 0 10596 1580 55 4 4 NOTCH4 6 32219657 Missense_Mutation SNP T C3N-01414_T 6176371 32219657 138586322 178 23378 HLA-DRB5 0 . GRCh38 6 32519526 32519526 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.496G>T p.Glu166Ter p.E166* ENST00000374975 3/6 226 214 12 470 470 0 varscan-mutect HLA-DRB5,stop_gained,p.Glu166Ter,ENST00000374975,NM_002125.3; A ENST00000374975 Transcript stop_gained 559/1260 496/801 166/266 E/* Gaa/Taa 1 -1 HLA-DRB5 HGNC HGNC:4953 protein_coding YES CCDS4751.1 ENSP00000364114 Q30154 UPI000008AF56 NM_002125.3 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19944:SF57,hmmpanther:PTHR19944,Gene3D:2.60.40.10,Pfam_domain:PF07654,SMART_domains:SM00407,Superfamily_domains:SSF48726 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 32519526 32519526 C A 1 0 0 0 0 0 1 0 0 7099 864 30 2 2 HLA-DRB5 6 32519526 Nonsense_Mutation SNP C C3N-01414_T 299869 32519526 138286453 179 23379 HLA-DRB1 0 . GRCh38 6 32581713 32581713 + Nonsense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.496G>T p.Glu166Ter p.E166* ENST00000360004 3/6 381 360 21 738 738 0 varscan-mutect HLA-DRB1,stop_gained,p.Glu166Ter,ENST00000360004,NM_002124.3;HLA-DRB1,stop_gained,p.Glu166Ter,ENST00000611060,; A ENST00000360004 Transcript stop_gained 602/1229 496/801 166/266 E/* Gaa/Taa COSM3625459 1 -1 HLA-DRB1 HGNC HGNC:4948 protein_coding YES CCDS47409.1 ENSP00000353099 P04229,Q9GIY3,P01911,Q29974 D7RIH8,X5DNQ0 UPI000008A1F7 NM_002124.3 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19944,hmmpanther:PTHR19944:SF57,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 1 HIGH 1 SNV 1 1 PASS rs1335525050 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 32581713 32581713 C A 1 0 0 0 0 0 1 0 0 7098 864 30 2 2 HLA-DRB1 6 32581713 Nonsense_Mutation SNP C C3N-01414_T 62187 32581713 138224266 180 23380 DAXX 0 . GRCh38 6 33320987 33320987 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.788G>T p.Arg263Leu p.R263L ENST00000374542 3/8 181 165 16 311 311 0 strelka-varscan-mutect DAXX,missense_variant,p.Arg263Leu,ENST00000374542,NM_001141969.1,NM_001141970.1,NM_001350.4;DAXX,missense_variant,p.Arg263Leu,ENST00000266000,;DAXX,missense_variant,p.Arg263Leu,ENST00000620164,;DAXX,missense_variant,p.Arg188Leu,ENST00000414083,NM_001254717.1;ZBTB22,upstream_gene_variant,,ENST00000431845,NM_005453.4;ZBTB22,upstream_gene_variant,,ENST00000418724,NM_001145338.1;DAXX,downstream_gene_variant,,ENST00000453407,;DAXX,downstream_gene_variant,,ENST00000446403,;ZBTB22,upstream_gene_variant,,ENST00000441117,;DAXX,downstream_gene_variant,,ENST00000446511,;DAXX,non_coding_transcript_exon_variant,,ENST00000477370,;DAXX,intron_variant,,ENST00000477162,;DAXX,intron_variant,,ENST00000468536,;DAXX,downstream_gene_variant,,ENST00000494082,;DAXX,upstream_gene_variant,,ENST00000490173,;DAXX,downstream_gene_variant,,ENST00000498030,; A ENST00000374542 Transcript missense_variant 993/2613 788/2223 263/740 R/L cGc/cTc COSM3349815 1 -1 DAXX HGNC HGNC:2681 protein_coding YES CCDS4776.1 ENSP00000363668 Q9UER7 A0A024RCS3 UPI0000128ED8 NM_001141969.1,NM_001141970.1,NM_001350.4 deleterious(0) 3/8 hmmpanther:PTHR12766 1 MODERATE 1 SNV 1 1 1 PASS rs1429735040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 33320987 33320987 C A 1 0 0 0 0 1 0 0 0 4044 768 27 1 1 DAXX 6 33320987 Missense_Mutation SNP C C3N-01414_T 739274 33320987 137484992 181 23381 RCAN2 0 . GRCh38 6 46456779 46456779 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.198G>T p.Gln66His p.Q66H ENST00000371374 2/5 179 155 24 296 294 2 strelka-varscan-mutect RCAN2,missense_variant,p.Gln66His,ENST00000371374,NM_001251974.1;RCAN2,missense_variant,p.Gln66His,ENST00000306764,NM_001251973.1; A ENST00000371374 Transcript missense_variant 390/3327 198/732 66/243 Q/H caG/caT 1 -1 RCAN2 HGNC HGNC:3041 protein_coding YES CCDS59023.1 ENSP00000360425 Q14206 UPI00001AEE48 NM_001251974.1 tolerated(0.1) 2/5 hmmpanther:PTHR10300,hmmpanther:PTHR10300:SF5,Gene3D:3.30.70.330,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS rs1040677659 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 46456779 46456779 C A 1 0 0 0 0 1 0 0 0 13338 564 20 2 2 RCAN2 6 46456779 Missense_Mutation SNP C C3N-01414_T 13135792 46456779 124349200 182 23382 FAM83B 0 . GRCh38 6 54940318 54940318 + Silent SNP G G T rs141100648 C3N-01414_T C3N-01414_N G G c.1347G>T p.= p.A449A ENST00000306858 5/5 268 203 65 441 441 0 strelka-varscan-mutect FAM83B,synonymous_variant,p.=,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; T ENST00000306858 Transcript synonymous_variant 1463/3167 1347/3036 449/1011 A gcG/gcT rs141100648,COSM1445234 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 0,1 LOW 1 SNV 1 0,1 1 PASS rs141100648 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 54940318 54940318 G T 1 0 0 0 0 0 0 0 1 5492 1074 38 1 1 FAM83B 6 54940318 Silent SNP G C3N-01414_T 8483539 54940318 115865661 183 23383 KHDRBS2 0 . GRCh38 6 61901308 61901308 + Missense_Mutation SNP C C A rs757121906 C3N-01414_T C3N-01414_N C C c.547G>T p.Asp183Tyr p.D183Y ENST00000281156 5/9 183 144 39 321 320 1 strelka-varscan-mutect KHDRBS2,missense_variant,p.Asp183Tyr,ENST00000281156,NM_152688.2; A ENST00000281156 Transcript missense_variant 826/2332 547/1050 183/349 D/Y Gac/Tac rs757121906 1 -1 KHDRBS2 HGNC HGNC:18114 protein_coding YES CCDS4963.1 ENSP00000281156 Q5VWX1 UPI000004D256 NM_152688.2 deleterious(0) 5/9 hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF34 MODERATE 1 SNV 1 1 PASS rs757121906 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 61901308 61901308 C A 1 0 0 0 0 1 0 0 0 8068 855 30 2 2 KHDRBS2 6 61901308 Missense_Mutation SNP C C3N-01414_T 6960990 61901308 108904671 184 23384 EYS 0 . GRCh38 6 64591429 64591429 + Silent SNP T T G rs753332937 C3N-01414_T C3N-01414_N T T c.4438A>C p.= p.R1480R ENST00000370621 26/44 306 208 98 554 553 1 strelka-varscan-mutect EYS,synonymous_variant,p.=,ENST00000503581,NM_001142800.1;EYS,synonymous_variant,p.=,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000330816,; G ENST00000370621 Transcript synonymous_variant 4965/10485 4438/9498 1480/3165 R Aga/Cga rs753332937 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 26/44 LOW 1 SNV 1 1 PASS rs753332937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 64591429 64591429 T G 1 0 0 0 0 0 0 0 1 5200 1617 56 5 5 EYS 6 64591429 Silent SNP T C3N-01414_T 2690121 64591429 106214550 185 23385 IMPG1 0 . GRCh38 6 75950742 75950742 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1644G>T p.Glu548Asp p.E548D ENST00000369950 13/17 200 141 59 355 355 0 strelka-varscan-mutect IMPG1,missense_variant,p.Glu548Asp,ENST00000369950,NM_001563.3;IMPG1,missense_variant,p.Glu470Asp,ENST00000611179,NM_001282368.1; A ENST00000369950 Transcript missense_variant 1834/3558 1644/2394 548/797 E/D gaG/gaT 1 -1 IMPG1 HGNC HGNC:6055 protein_coding YES CCDS4985.1 ENSP00000358966 Q17R60 UPI0000073F12 NM_001563.3 tolerated(0.1) 13/17 hmmpanther:PTHR12199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 75950742 75950742 C A 1 0 0 0 0 1 0 0 0 7630 680 24 2 2 IMPG1 6 75950742 Missense_Mutation SNP C C3N-01414_T 11359313 75950742 94855237 186 23386 BACH2 0 . GRCh38 6 89938209 89938209 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.1978G>T p.Ala660Ser p.A660S ENST00000257749 8/9 199 152 47 329 328 1 strelka-varscan-mutect BACH2,missense_variant,p.Ala660Ser,ENST00000257749,NM_021813.3;BACH2,missense_variant,p.Ala660Ser,ENST00000537989,NM_001170794.1;BACH2,missense_variant,p.Ala660Ser,ENST00000343122,; A ENST00000257749 Transcript missense_variant 2686/9113 1978/2526 660/841 A/S Gcc/Tcc COSM5266450,COSM5266451 1 -1 BACH2 HGNC HGNC:14078 protein_coding YES CCDS5026.1 ENSP00000257749 Q9BYV9 UPI000004F8AD NM_021813.3 deleterious(0.01) 8/9 Gene3D:1.10.880.10,Pfam_domain:PF03131,PROSITE_patterns:PS00036,PROSITE_profiles:PS50217,SMART_domains:SM00338,Superfamily_domains:SSF47454,Superfamily_domains:SSF57959 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 89938209 89938209 C A 1 0 0 0 0 1 0 0 0 1442 739 26 2 2 BACH2 6 89938209 Missense_Mutation SNP C C3N-01414_T 13987467 89938209 80867770 187 23387 GPR63 0 . GRCh38 6 96798550 96798550 + Silent SNP C C G rs377037155 C3N-01414_T C3N-01414_N C C c.1182G>C p.= p.P394P ENST00000229955 2/2 223 189 34 341 341 0 strelka-varscan-mutect GPR63,synonymous_variant,p.=,ENST00000229955,NM_030784.3,NM_001143957.2;RP3-417O22.3,downstream_gene_variant,,ENST00000442184,; G ENST00000229955 Transcript synonymous_variant 1528/5952 1182/1260 394/419 P ccG/ccC rs377037155 1 -1 GPR63 HGNC HGNC:13302 protein_coding YES CCDS5036.1 ENSP00000229955 Q9BZJ6 A8K1C4 UPI0000037594 NM_030784.3,NM_001143957.2 2/2 hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF1,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS rs377037155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 96798550 96798550 C G 1 0 0 0 0 0 0 0 1 6588 755 27 4 4 GPR63 6 96798550 Silent SNP C C3N-01414_T 6860341 96798550 74007429 188 23388 VGLL2 0 . GRCh38 6 117268408 117268408 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.308T>C p.Phe103Ser p.F103S ENST00000326274 2/4 212 193 19 330 330 0 strelka-varscan-mutect VGLL2,missense_variant,p.Phe103Ser,ENST00000326274,NM_182645.3;VGLL2,missense_variant,p.Phe103Ser,ENST00000352536,NM_153453.1; C ENST00000326274 Transcript missense_variant 498/2212 308/954 103/317 F/S tTc/tCc 1 1 VGLL2 HGNC HGNC:20232 protein_coding YES CCDS5115.1 ENSP00000320957 Q8N8G2 UPI000006FF57 NM_182645.3 deleterious(0) 2/4 hmmpanther:PTHR15950,hmmpanther:PTHR15950:SF17,Pfam_domain:PF07545 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 117268408 117268408 T C 1 0 0 0 0 1 0 0 0 17705 1783 62 5 5 VGLL2 6 117268408 Missense_Mutation SNP T C3N-01414_T 20469858 117268408 53537571 189 23389 EYA4 0 . GRCh38 6 133462679 133462679 + Silent SNP C C A C3N-01414_T C3N-01414_N C C c.639C>A p.= p.S213S ENST00000531901 9/20 244 212 32 347 347 0 strelka-varscan-mutect EYA4,synonymous_variant,p.=,ENST00000367895,NM_004100.4;EYA4,synonymous_variant,p.=,ENST00000355167,NM_172105.3;EYA4,synonymous_variant,p.=,ENST00000355286,NM_172103.3;EYA4,synonymous_variant,p.=,ENST00000525849,;EYA4,synonymous_variant,p.=,ENST00000531901,NM_001301013.1;EYA4,synonymous_variant,p.=,ENST00000452339,NM_001301012.1;EYA4,synonymous_variant,p.=,ENST00000430974,;EYA4,synonymous_variant,p.=,ENST00000431403,;EYA4,non_coding_transcript_exon_variant,,ENST00000531861,;EYA4,non_coding_transcript_exon_variant,,ENST00000421413,;EYA4,upstream_gene_variant,,ENST00000532518,;EYA4,downstream_gene_variant,,ENST00000525614,;EYA4,non_coding_transcript_exon_variant,,ENST00000497350,; A ENST00000531901 Transcript synonymous_variant 868/2892 639/1938 213/645 S tcC/tcA COSM4404265,COSM4404266 1 1 EYA4 HGNC HGNC:3522 protein_coding YES CCDS75521.1 ENSP00000432770 F2Z2Y1 UPI0001AE72E3 NM_001301013.1 9/20 hmmpanther:PTHR10190:SF17,hmmpanther:PTHR10190 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 133462679 133462679 C A 1 0 0 0 0 0 0 0 1 5199 610 22 2 2 EYA4 6 133462679 Silent SNP C C3N-01414_T 16194271 133462679 37343300 190 23390 MYCT1 0 . GRCh38 6 152697952 152697952 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.50C>A p.Ala17Asp p.A17D ENST00000367245 1/2 181 165 16 293 292 1 strelka-varscan-mutect MYCT1,missense_variant,p.Ala17Asp,ENST00000367245,NM_025107.2;MYCT1,missense_variant,p.Ala17Asp,ENST00000529453,;MYCT1,upstream_gene_variant,,ENST00000532295,; A ENST00000367245 Transcript missense_variant 58/3030 50/708 17/235 A/D gCt/gAt 1 1 MYCT1 HGNC HGNC:23172 protein_coding YES CCDS5239.1 ENSP00000356214 Q8N699 UPI0000073EDB NM_025107.2 deleterious_low_confidence(0.01) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 152697952 152697952 C A 1 0 0 0 0 1 0 0 0 10022 797 28 2 2 MYCT1 6 152697952 Missense_Mutation SNP C C3N-01414_T 19235273 152697952 18108027 191 23391 UNC93A 0 . GRCh38 6 167296244 167296244 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.482G>T p.Gly161Val p.G161V ENST00000230256 3/8 194 176 18 285 285 0 strelka-varscan-mutect UNC93A,missense_variant,p.Gly161Val,ENST00000230256,NM_018974.3;UNC93A,missense_variant,p.Gly161Val,ENST00000366829,NM_001143947.1;UNC93A,downstream_gene_variant,,ENST00000503433,;UNC93A,downstream_gene_variant,,ENST00000366830,;UNC93A,non_coding_transcript_exon_variant,,ENST00000504706,; T ENST00000230256 Transcript missense_variant 657/2116 482/1374 161/457 G/V gGc/gTc 1 1 UNC93A HGNC HGNC:12570 protein_coding YES CCDS5300.1 ENSP00000230256 Q86WB7 UPI0000062351 NM_018974.3 deleterious(0) 3/8 Gene3D:1.20.1250.20,Pfam_domain:PF05978,hmmpanther:PTHR19444,hmmpanther:PTHR19444:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 167296244 167296244 G T 1 0 0 0 0 1 0 0 0 17522 1203 42 2 2 UNC93A 6 167296244 Missense_Mutation SNP G C3N-01414_T 14598292 167296244 3509735 192 23392 MLLT4 0 . GRCh38 6 167870491 167870491 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.284C>T p.Pro95Leu p.P95L ENST00000366806 3/33 116 72 44 185 185 0 strelka-varscan-mutect MLLT4,missense_variant,p.Pro136Leu,ENST00000400822,;MLLT4,missense_variant,p.Pro136Leu,ENST00000392112,NM_001207008.1;MLLT4,missense_variant,p.Pro136Leu,ENST00000392108,NM_001040000.2;MLLT4,missense_variant,p.Pro95Leu,ENST00000366806,NM_001291964.1;MLLT4,missense_variant,p.Pro136Leu,ENST00000351017,;MLLT4,missense_variant,p.Pro136Leu,ENST00000447894,;MLLT4,missense_variant,p.Pro136Leu,ENST00000344191,;MLLT4,missense_variant,p.Pro137Leu,ENST00000400825,;MLLT4,missense_variant,p.Pro137Leu,ENST00000400824,;MLLT4,non_coding_transcript_exon_variant,,ENST00000366809,; T ENST00000366806 Transcript missense_variant 603/5962 284/5346 95/1781 P/L cCt/cTt 1 1 MLLT4 HGNC HGNC:7137 protein_coding YES CCDS78199.1 ENSP00000355771 A8MQ02 UPI00045D52FC NM_001291964.1 tolerated(0.22) 3/33 hmmpanther:PTHR10398,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS rs1180121039 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 167870491 167870491 C T 1 0 0 0 0 1 0 0 0 9592 681 24 3 3 MLLT4 6 167870491 Missense_Mutation SNP C C3N-01414_T 574247 167870491 2935488 193 23393 THBS2 0 . GRCh38 6 169228255 169228255 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.2286C>T p.= p.P762P ENST00000366787 16/23 171 155 16 251 250 1 strelka-varscan-mutect THBS2,synonymous_variant,p.=,ENST00000366787,NM_003247.3;THBS2,synonymous_variant,p.=,ENST00000617924,;XXyac-YX65C7_A.2,intron_variant,,ENST00000444188,;THBS2,upstream_gene_variant,,ENST00000488355,; A ENST00000366787 Transcript synonymous_variant 2536/5811 2286/3519 762/1172 P ccC/ccT 1 -1 THBS2 HGNC HGNC:11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 UPI0000231C7F NM_003247.3 16/23 PROSITE_profiles:PS51234,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF10,Gene3D:1ux6A01,Pfam_domain:PF02412,Superfamily_domains:0044556 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 169228255 169228255 G A 1 0 0 0 0 0 0 0 1 16287 1219 43 3 3 THBS2 6 169228255 Silent SNP G C3N-01414_T 1357764 169228255 1577724 194 23394 PRKAR1B 0 . GRCh38 7 579356 579356 + Missense_Mutation SNP C C A rs369460111 C3N-01414_T C3N-01414_N C C c.791G>T p.Arg264Leu p.R264L ENST00000406797 9/11 250 180 70 448 448 0 strelka-varscan-mutect PRKAR1B,missense_variant,p.Arg264Leu,ENST00000406797,NM_001164761.1;PRKAR1B,missense_variant,p.Arg264Leu,ENST00000537384,NM_001164760.1;PRKAR1B,missense_variant,p.Arg264Leu,ENST00000544935,NM_001164759.1,NM_001164762.1;PRKAR1B,missense_variant,p.Arg264Leu,ENST00000360274,NM_002735.2;PRKAR1B,missense_variant,p.Arg264Leu,ENST00000403562,NM_001164758.1;PRKAR1B,missense_variant,p.Arg264Leu,ENST00000430040,;PRKAR1B,missense_variant,p.Arg125Leu,ENST00000400758,; A ENST00000406797 Transcript missense_variant 966/2553 791/1146 264/381 R/L cGt/cTt rs369460111 1 -1 PRKAR1B HGNC HGNC:9390 protein_coding YES CCDS34579.1 ENSP00000385749 P31321 UPI000021C478 NM_001164761.1 deleterious(0.02) 9/11 Gene3D:2.60.120.10,PIRSF_domain:PIRSF000548,PROSITE_profiles:PS50042,hmmpanther:PTHR11635,hmmpanther:PTHR11635:SF126,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS rs369460111 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 579356 579356 C A 1 0 0 0 0 1 0 0 0 12637 536 19 1 1 PRKAR1B 7 579356 Missense_Mutation SNP C C3N-01414_T 579356 158766617 195 23395 PMS2 0 . GRCh38 7 5987084 5987084 + Missense_Mutation SNP T T G novel C3N-01414_T C3N-01414_N T T c.1681A>C p.Lys561Gln p.K561Q ENST00000265849 11/15 325 292 33 467 467 0 varscan-mutect PMS2,missense_variant,p.Lys561Gln,ENST00000265849,NM_000535.5;PMS2,missense_variant,p.Lys455Gln,ENST00000441476,;PMS2,intron_variant,,ENST00000382321,;PMS2,splice_region_variant,,ENST00000406569,;PMS2,intron_variant,,ENST00000469652,; G ENST00000265849 Transcript missense_variant 1787/2855 1681/2589 561/862 K/Q Aaa/Caa 1 -1 PMS2 HGNC HGNC:9122 protein_coding YES CCDS5343.1 ENSP00000265849 P54278 UPI000013D696 NM_000535.5 tolerated(0.26) 11/15 hmmpanther:PTHR10073,hmmpanther:PTHR10073:SF39 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 5987084 5987084 T G 1 0 0 0 0 1 0 0 0 12250 1763 61 5 5 PMS2 7 5987084 Missense_Mutation SNP T C3N-01414_T 5407728 5987084 153358889 196 23396 FAM221A 0 . GRCh38 7 23689426 23689426 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.397C>A p.His133Asn p.H133N ENST00000344962 3/7 43 37 6 72 72 0 strelka-mutect FAM221A,missense_variant,p.His133Asn,ENST00000344962,NM_199136.4;FAM221A,missense_variant,p.His75Asn,ENST00000409994,NM_001127365.2;FAM221A,missense_variant,p.His133Asn,ENST00000409192,NM_001127364.2;FAM221A,missense_variant,p.His75Asn,ENST00000409653,NM_001300932.1;FAM221A,3_prime_UTR_variant,,ENST00000429719,;FAM221A,3_prime_UTR_variant,,ENST00000446234,;FAM221A,non_coding_transcript_exon_variant,,ENST00000462546,; A ENST00000344962 Transcript missense_variant 486/1472 397/897 133/298 H/N Cac/Aac 1 1 FAM221A HGNC HGNC:27977 protein_coding YES CCDS5385.1 ENSP00000342576 A4D161 UPI0000199810 NM_199136.4 deleterious(0) 3/7 hmmpanther:PTHR31214,Pfam_domain:PF14753 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.05388 1 1 1 1 0 A 3 1 77 23689426 23689426 C A 1 0 0 0 0 1 0 0 0 5414 710 25 2 2 FAM221A 7 23689426 Missense_Mutation SNP C C3N-01414_T 17702342 23689426 135656547 197 23397 CAMK2B 0 . GRCh38 7 44229428 44229428 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.1299C>A p.= p.P433P ENST00000395749 18/24 30 25 5 47 47 0 strelka-varscan-mutect CAMK2B,synonymous_variant,p.=,ENST00000395749,NM_001220.4;CAMK2B,intron_variant,,ENST00000457475,NM_172079.2;CAMK2B,intron_variant,,ENST00000350811,NM_001293170.1;CAMK2B,intron_variant,,ENST00000440254,NM_172078.2;CAMK2B,intron_variant,,ENST00000358707,NM_172081.2;CAMK2B,intron_variant,,ENST00000258682,NM_172080.2;CAMK2B,intron_variant,,ENST00000353625,NM_172083.2;CAMK2B,intron_variant,,ENST00000347193,NM_172082.2;CAMK2B,intron_variant,,ENST00000395747,;CAMK2B,intron_variant,,ENST00000346990,NM_172084.2;CAMK2B,intron_variant,,ENST00000433930,;CAMK2B,upstream_gene_variant,,ENST00000425809,;CAMK2B,non_coding_transcript_exon_variant,,ENST00000489429,;CAMK2B,intron_variant,,ENST00000497584,;CAMK2B,intron_variant,,ENST00000523845,;CAMK2B,intron_variant,,ENST00000353185,; T ENST00000395749 Transcript synonymous_variant 1376/4447 1299/2001 433/666 P ccC/ccA 1 -1 CAMK2B HGNC HGNC:1461 protein_coding YES CCDS5483.1 ENSP00000379098 Q13554 A4D2J9 UPI0000164A3E NM_001220.4 18/24 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1177912237 . 0 205 5 0 0 0 0 0 -13.76551 1 1 1 1 0 T 2 4 77 44229428 44229428 G T 1 0 0 0 0 0 0 0 1 2291 987 35 2 2 CAMK2B 7 44229428 Silent SNP G C3N-01414_T 20540002 44229428 115116545 198 23398 CCM2 0 . GRCh38 7 45076052 45076052 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.1393G>A p.Ala465Thr p.A465T ENST00000381112 10/10 448 401 47 702 702 0 strelka-varscan-mutect CCM2,missense_variant,p.Ala438Thr,ENST00000475551,;CCM2,missense_variant,p.Ala444Thr,ENST00000258781,NM_031443.3;CCM2,missense_variant,p.Ala465Thr,ENST00000381112,NM_001029835.2;CCM2,missense_variant,p.Ala386Thr,ENST00000541586,NM_001167934.1;CCM2,missense_variant,p.Ala353Thr,ENST00000544363,NM_001167935.1;CCM2,missense_variant,p.Ala347Thr,ENST00000474617,;NACAD,downstream_gene_variant,,ENST00000490531,NM_001146334.1;CCM2,downstream_gene_variant,,ENST00000480382,;CCM2,non_coding_transcript_exon_variant,,ENST00000461377,;CCM2,downstream_gene_variant,,ENST00000482714,;CCM2,downstream_gene_variant,,ENST00000478582,;CCM2,3_prime_UTR_variant,,ENST00000488727,;CCM2,non_coding_transcript_exon_variant,,ENST00000481194,;CCM2,non_coding_transcript_exon_variant,,ENST00000477605,;CCM2,downstream_gene_variant,,ENST00000480658,;CCM2,downstream_gene_variant,,ENST00000492883,;CCM2,downstream_gene_variant,,ENST00000470837,;NACAD,downstream_gene_variant,,ENST00000460409,; A ENST00000381112 Transcript missense_variant 1464/1881 1393/1398 465/465 A/T Gca/Aca 1 1 CCM2 HGNC HGNC:21708 protein_coding YES CCDS34630.1 ENSP00000370503 Q9BSQ5 UPI0000563237 NM_001029835.2 deleterious_low_confidence(0) 10/10 hmmpanther:PTHR21642,hmmpanther:PTHR21642:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 45076052 45076052 G A 1 0 0 0 0 1 0 0 0 2606 971 34 3 3 CCM2 7 45076052 Missense_Mutation SNP G C3N-01414_T 846624 45076052 114269921 199 23399 DDC 0 . GRCh38 7 50543911 50543911 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.175G>T p.Asp59Tyr p.D59Y ENST00000444124 2/15 477 412 65 805 805 0 strelka-varscan-mutect DDC,missense_variant,p.Asp59Tyr,ENST00000444124,NM_001082971.1;DDC,missense_variant,p.Asp59Tyr,ENST00000357936,NM_000790.3;DDC,missense_variant,p.Asp59Tyr,ENST00000622873,NM_001242886.1;DDC,missense_variant,p.Asp59Tyr,ENST00000617822,NM_001242887.1;DDC,missense_variant,p.Asp59Tyr,ENST00000426377,NM_001242888.1;DDC,missense_variant,p.Asp59Tyr,ENST00000615193,NM_001242889.1;DDC,missense_variant,p.Asp59Tyr,ENST00000431062,;DDC,missense_variant,p.Asp25Tyr,ENST00000430300,;DDC,missense_variant,p.Asp59Tyr,ENST00000380984,NM_001242890.1;FIGNL1,upstream_gene_variant,,ENST00000613602,;DDC,downstream_gene_variant,,ENST00000420203,;DDC-AS1,downstream_gene_variant,,ENST00000454521,;DDC,upstream_gene_variant,,ENST00000489162,;DDC,missense_variant,p.Asp59Tyr,ENST00000444733,; A ENST00000444124 Transcript missense_variant 376/2041 175/1443 59/480 D/Y Gac/Tac COSM1090609,COSM1597046 1 -1 DDC HGNC HGNC:2719 protein_coding YES CCDS5511.1 ENSP00000403644 P20711 A0A0S2Z3N4 UPI000013F150 NM_001082971.1 deleterious(0) 2/15 Gene3D:3k40A01,Pfam_domain:PF00282,Prints_domain:PR00800,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF70,Superfamily_domains:SSF53383 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs931702374 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 50543911 50543911 C A 1 0 0 0 0 1 0 0 0 4128 884 31 1 1 DDC 7 50543911 Missense_Mutation SNP C C3N-01414_T 5467859 50543911 108802062 200 23400 WBSCR17 0 . GRCh38 7 71416043 71416043 + Missense_Mutation SNP C C A rs566090840 C3N-01414_T C3N-01414_N C C c.744C>A p.His248Gln p.H248Q ENST00000333538 4/11 72 61 11 106 106 0 strelka-varscan-mutect WBSCR17,missense_variant,p.His248Gln,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.His169Gln,ENST00000618959,;WBSCR17,downstream_gene_variant,,ENST00000447516,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; A ENST00000333538 Transcript missense_variant 1378/3884 744/1797 248/598 H/Q caC/caA rs566090840,COSM2151635 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 deleterious(0) 4/11 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs566090840 . 0 204 5 0 0 0 0 0 -19.99998 1 1 1 1 0 A 3 1 77 71416043 71416043 C A 1 0 0 0 0 1 0 0 0 17823 535 19 1 1 WBSCR17 7 71416043 Missense_Mutation SNP C C3N-01414_T 20872132 71416043 87929930 201 23401 WBSCR28 0 . GRCh38 7 73865741 73865741 + Silent SNP G G T rs782021022 C3N-01414_T C3N-01414_N G G c.666G>T p.= p.T222T ENST00000320531 3/3 372 272 100 431 431 0 strelka-varscan-mutect WBSCR28,synonymous_variant,p.=,ENST00000320531,NM_182504.3;WBSCR28,3_prime_UTR_variant,,ENST00000426490,; T ENST00000320531 Transcript synonymous_variant 702/854 666/798 222/265 T acG/acT rs782021022 1 1 WBSCR28 HGNC HGNC:23018 protein_coding YES CCDS43597.1 ENSP00000316775 Q6UE05 UPI00001408E5 NM_182504.3 3/3 hmmpanther:PTHR37369,Pfam_domain:PF15164 LOW 1 SNV 1 1 PASS rs782021022 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 73865741 73865741 G T 1 0 0 0 0 0 0 0 1 17826 1045 37 1 1 WBSCR28 7 73865741 Silent SNP G C3N-01414_T 2449698 73865741 85480232 202 23402 KIAA1324L 0 . GRCh38 7 86926826 86926826 + Frame_Shift_Del DEL C C - novel C3N-01414_T C3N-01414_N C C c.1180delG p.Asp394IlefsTer57 p.D394Ifs*57 ENST00000450689 9/22 136 110 26 174 174 0 sindel-varindel-pindel KIAA1324L,frameshift_variant,p.Asp394IlefsTer57,ENST00000450689,NM_001142749.2;KIAA1324L,frameshift_variant,p.Asp394IlefsTer57,ENST00000444627,;KIAA1324L,frameshift_variant,p.Asp227IlefsTer57,ENST00000416314,NM_152748.3,NM_001291990.1;KIAA1324L,frameshift_variant,p.Asp355IlefsTer57,ENST00000423294,;KIAA1324L,3_prime_UTR_variant,,ENST00000394714,; - ENST00000450689 Transcript frameshift_variant 1366/6841 1180/3090 394/1029 D/X Gat/at 1 -1 KIAA1324L HGNC HGNC:21945 protein_coding YES CCDS47632.1 ENSP00000413445 A8MWY0 UPI000173AA00 NM_001142749.2 9/22 hmmpanther:PTHR22727:SF3,hmmpanther:PTHR22727,Gene3D:2.10.50.10,Superfamily_domains:SSF57184 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 86926826 86926826 C - 1 0 1 0 1 0 0 0 0 8112 855 30 0 0 KIAA1324L 7 86926826 Frame_Shift_Del DEL C C3N-01414_T 13061085 86926826 72419147 203 23403 C7orf62 0 . GRCh38 7 88794249 88794249 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.694A>T p.Met232Leu p.M232L ENST00000297203 2/2 148 93 55 174 173 1 strelka-varscan-mutect C7orf62,missense_variant,p.Met232Leu,ENST00000297203,NM_152706.3;ZNF804B,intron_variant,,ENST00000333190,NM_181646.3; A ENST00000297203 Transcript missense_variant 880/1023 694/762 232/253 M/L Atg/Ttg 1 -1 C7orf62 HGNC HGNC:22402 protein_coding YES CCDS34678.1 ENSP00000297203 Q8TBZ9 UPI000005034C NM_152706.3 tolerated(0.17) 2/2 hmmpanther:PTHR34035,hmmpanther:PTHR34035:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 88794249 88794249 T A 1 0 0 0 0 1 0 0 0 2146 1464 51 4 4 C7orf62 7 88794249 Missense_Mutation SNP T C3N-01414_T 1867423 88794249 70551724 204 23404 ZNF804B 0 . GRCh38 7 89336085 89336085 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.3103A>G p.Thr1035Ala p.T1035A ENST00000333190 4/4 200 175 25 242 242 0 strelka-varscan-mutect ZNF804B,missense_variant,p.Thr1035Ala,ENST00000333190,NM_181646.3;ZNF804B,missense_variant,p.Thr952Ala,ENST00000611114,; G ENST00000333190 Transcript missense_variant 3712/4659 3103/4050 1035/1349 T/A Aca/Gca 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 tolerated(0.71) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 89336085 89336085 A G 1 0 0 0 0 1 0 0 0 18756 43 2 5 5 ZNF804B 7 89336085 Missense_Mutation SNP A C3N-01414_T 541836 89336085 70009888 205 23405 NPTX2 0 . GRCh38 7 98619814 98619814 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.598A>T p.Ser200Cys p.S200C ENST00000265634 2/5 270 218 52 335 335 0 strelka-varscan-mutect NPTX2,missense_variant,p.Ser200Cys,ENST00000265634,NM_002523.2;NPTX2,non_coding_transcript_exon_variant,,ENST00000466102,; T ENST00000265634 Transcript missense_variant 763/2700 598/1296 200/431 S/C Agc/Tgc 1 1 NPTX2 HGNC HGNC:7953 protein_coding YES CCDS5657.1 ENSP00000265634 P47972 UPI000013040F NM_002523.2 deleterious(0) 2/5 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF1 MODERATE 1 SNV 1 1 PASS rs1273647531 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 98619814 98619814 A T 1 0 0 0 0 1 0 0 0 10659 304 11 4 4 NPTX2 7 98619814 Missense_Mutation SNP A C3N-01414_T 9283729 98619814 60726159 206 23406 MUC17 0 . GRCh38 7 101034815 101034815 + Silent SNP C C G novel C3N-01414_T C3N-01414_N C C c.3399C>G p.= p.T1133T ENST00000306151 3/13 250 220 30 349 349 0 strelka-varscan-mutect MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; G ENST00000306151 Transcript synonymous_variant 3463/14247 3399/13482 1133/4493 T acC/acG 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 101034815 101034815 C G 1 0 0 0 0 0 0 0 1 9973 581 21 4 4 MUC17 7 101034815 Silent SNP C C3N-01414_T 2415001 101034815 58311158 207 23407 RELN 0 . GRCh38 7 103661410 103661410 + Silent SNP G G T rs574149208 C3N-01414_T C3N-01414_N G G c.1407C>A p.= p.T469T ENST00000428762 12/65 369 242 127 509 509 0 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript synonymous_variant 1567/11571 1407/10383 469/3460 T acC/acA rs574149208 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 12/65 hmmpanther:PTHR11841 LOW 1 SNV 5 1 PASS rs574149208 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 103661410 103661410 G T 1 0 0 0 0 0 0 0 1 13390 1103 39 1 1 RELN 7 103661410 Silent SNP G C3N-01414_T 2626595 103661410 55684563 208 23408 LAMB4 0 . GRCh38 7 108107813 108107813 + Missense_Mutation SNP G G A C3N-01414_T C3N-01414_N G G c.409C>T p.Arg137Trp p.R137W ENST00000388781 6/34 139 110 29 158 157 1 strelka-varscan-mutect LAMB4,missense_variant,p.Arg137Trp,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Arg137Trp,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Arg137Trp,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; A ENST00000388781 Transcript missense_variant 493/5858 409/5286 137/1761 R/W Cgg/Tgg COSM5406206,COSM5406207,COSM5406208 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0.03) 6/34 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00136 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1445033819 . 0 206 2 2 0 0 0 0 -20 0.999999 1 1 1 0 A 3 1 77 108107813 108107813 G A 1 0 0 0 0 1 0 0 0 8517 1057 37 1 1 LAMB4 7 108107813 Missense_Mutation SNP G C3N-01414_T 4446403 108107813 51238160 209 23409 GRM8 0 . GRCh38 7 126769883 126769883 + Missense_Mutation SNP G G A rs776267363 C3N-01414_T C3N-01414_N G G c.1339C>T p.Arg447Trp p.R447W ENST00000339582 7/11 150 141 9 211 211 0 strelka-varscan-mutect GRM8,missense_variant,p.Arg447Trp,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Arg447Trp,ENST00000358373,NM_001127323.1;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,downstream_gene_variant,,ENST00000448250,;GRM8,missense_variant,p.Arg447Trp,ENST00000472701,;GRM8,missense_variant,p.Arg447Trp,ENST00000341617,; A ENST00000339582 Transcript missense_variant 2148/4057 1339/2727 447/908 R/W Cgg/Tgg rs776267363,COSM4831477,COSM4831478,COSM4831479 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 deleterious(0.01) 7/11 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Superfamily_domains:SSF53822 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs776267363 . 0 207 0 3 0 0 0 0 -12.14308 0.9999571 1 1 1 0 A 3 1 77 126769883 126769883 G A 1 0 0 0 0 1 0 0 0 6685 1057 37 1 1 GRM8 7 126769883 Missense_Mutation SNP G C3N-01414_T 18662070 126769883 32576090 210 23410 NRF1 0 . GRCh38 7 129690514 129690514 + Nonsense_Mutation SNP G G T rs774042493 C3N-01414_T C3N-01414_N G G c.574G>T p.Gly192Ter p.G192* ENST00000353868 5/12 189 114 75 228 226 2 strelka-varscan-mutect NRF1,stop_gained,p.Gly192Ter,ENST00000353868,;NRF1,stop_gained,p.Gly192Ter,ENST00000393232,NM_005011.4,NM_001293164.1;NRF1,stop_gained,p.Gly192Ter,ENST00000393230,NM_001040110.1;NRF1,stop_gained,p.Gly192Ter,ENST00000311967,NM_001293163.1;NRF1,stop_gained,p.Gly192Ter,ENST00000223190,;NRF1,stop_gained,p.Gly192Ter,ENST00000454688,; T ENST00000353868 Transcript stop_gained 674/3568 574/1569 192/522 G/* Gga/Tga rs774042493 1 1 NRF1 HGNC HGNC:7996 protein_coding YES CCDS78273.1 ENSP00000342351 Q16656 A0A024R774 UPI0000072ED3 5/12 hmmpanther:PTHR20338,Pfam_domain:PF10491 HIGH 1 SNV 5 1 PASS rs774042493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 129690514 129690514 G T 1 0 0 0 0 0 1 0 0 10704 1117 39 1 1 NRF1 7 129690514 Nonsense_Mutation SNP G C3N-01414_T 2920631 129690514 29655459 211 23411 PLXNA4 0 . GRCh38 7 132507598 132507598 + Missense_Mutation SNP G G T rs748520326 C3N-01414_T C3N-01414_N G G c.1096C>A p.Arg366Ser p.R366S ENST00000359827 2/32 277 198 79 355 354 1 strelka-varscan-mutect PLXNA4,missense_variant,p.Arg366Ser,ENST00000359827,;PLXNA4,missense_variant,p.Arg366Ser,ENST00000321063,NM_020911.1;PLXNA4,missense_variant,p.Arg366Ser,ENST00000423507,NM_001105543.1;PLXNA4,missense_variant,p.Arg366Ser,ENST00000378539,NM_181775.3; T ENST00000359827 Transcript missense_variant 2059/13786 1096/5685 366/1894 R/S Cgc/Agc rs748520326,COSM1733143,COSM1733144,COSM1733145,COSM1733146 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B deleterious(0.01) 2/32 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs748520326 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 132507598 132507598 G T 1 0 0 0 0 1 0 0 0 12228 1116 39 1 1 PLXNA4 7 132507598 Missense_Mutation SNP G C3N-01414_T 2817084 132507598 26838375 212 23412 KDM7A 0 . GRCh38 7 140097628 140097628 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.1933G>T p.Val645Leu p.V645L ENST00000397560 15/20 125 107 18 168 168 0 strelka-varscan-mutect KDM7A,missense_variant,p.Val645Leu,ENST00000397560,NM_030647.1;Y_RNA,upstream_gene_variant,,ENST00000515919,;KDM7A,missense_variant,p.Val240Leu,ENST00000472616,; A ENST00000397560 Transcript missense_variant 2031/9272 1933/2826 645/941 V/L Gtg/Ttg COSM5662307 1 -1 KDM7A HGNC HGNC:22224 protein_coding YES CCDS43658.1 ENSP00000380692 Q6ZMT4 UPI000045761B NM_030647.1 tolerated(0.11) 15/20 hmmpanther:PTHR23123:SF15,hmmpanther:PTHR23123 1 MODERATE 1 SNV 2 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 140097628 140097628 C A 1 0 0 0 0 1 0 0 0 8057 478 17 2 2 KDM7A 7 140097628 Missense_Mutation SNP C C3N-01414_T 7590030 140097628 19248345 213 23413 TCAF2 0 . GRCh38 7 143703135 143703135 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.141G>T p.Gln47His p.Q47H ENST00000444908 2/7 90 75 15 100 99 1 varscan-mutect TCAF2,missense_variant,p.Gln47His,ENST00000441159,;TCAF2,missense_variant,p.Gln47His,ENST00000444908,NM_001130025.1;TCAF2,missense_variant,p.Gln47His,ENST00000357344,NM_173678.2;RP11-298A10.1,intron_variant,,ENST00000636919,;RP11-298A10.1,intron_variant,,ENST00000636123,;TCAF2,intron_variant,,ENST00000518791,; T ENST00000444908 Transcript missense_variant 226/2976 141/2538 47/845 Q/H caG/caT 1 1 TCAF2 HGNC HGNC:26878 protein_coding YES CCDS34769.1 ENSP00000412724 A6NFQ2 UPI00001AF3A8 NM_001130025.1 deleterious(0.01) 2/7 hmmpanther:PTHR15730,hmmpanther:PTHR15730:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 143703135 143703135 G T 1 0 0 0 0 1 0 0 0 16071 991 35 2 2 TCAF2 7 143703135 Missense_Mutation SNP G C3N-01414_T 3605507 143703135 15642838 214 23414 ATG9B 0 . GRCh38 7 151023723 151023723 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.558G>T p.Trp186Cys p.W186C ENST00000605952 2/17 280 208 72 398 398 0 strelka-varscan-mutect ATG9B,missense_variant,p.Trp186Cys,ENST00000469530,NM_173681.5;ABCB8,upstream_gene_variant,,ENST00000358849,NM_007188.4;ABCB8,upstream_gene_variant,,ENST00000542328,NM_001282293.1;ABCB8,upstream_gene_variant,,ENST00000297504,NM_001282291.1;ABCB8,upstream_gene_variant,,ENST00000498578,NM_001282292.1;ABCB8,upstream_gene_variant,,ENST00000477719,;ABCB8,upstream_gene_variant,,ENST00000477092,;ABCB8,upstream_gene_variant,,ENST00000461373,;ATG9B,non_coding_transcript_exon_variant,,ENST00000617967,;ATG9B,non_coding_transcript_exon_variant,,ENST00000473409,;ATG9B,non_coding_transcript_exon_variant,,ENST00000466157,;ATG9B,upstream_gene_variant,,ENST00000611177,;ABCB8,upstream_gene_variant,,ENST00000488370,;ABCB8,upstream_gene_variant,,ENST00000466956,;ABCB8,upstream_gene_variant,,ENST00000488826,;ABCB8,upstream_gene_variant,,ENST00000471796,;ABCB8,upstream_gene_variant,,ENST00000472698,;ABCB8,upstream_gene_variant,,ENST00000469410,;ATG9B,missense_variant,p.Trp186Cys,ENST00000605952,;ABCB8,upstream_gene_variant,,ENST00000466514,;ABCB8,upstream_gene_variant,,ENST00000482309,;ABCB8,upstream_gene_variant,,ENST00000470645,;ABCB8,upstream_gene_variant,,ENST00000489192,;ATG9B,upstream_gene_variant,,ENST00000473134,;ABCB8,upstream_gene_variant,,ENST00000462605,;ABCB8,upstream_gene_variant,,ENST00000488551,; A ENST00000605952 Transcript missense_variant,NMD_transcript_variant 634/4572 558/2775 186/924 W/C tgG/tgT 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 deleterious(0) 2/17 hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 151023723 151023723 C A 1 0 0 0 0 1 0 0 0 1255 740 26 2 2 ATG9B 7 151023723 Missense_Mutation SNP C C3N-01414_T 7320588 151023723 8322250 215 23415 VIPR2 0 . GRCh38 7 159103813 159103813 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.301A>T p.Thr101Ser p.T101S ENST00000262178 4/13 259 212 47 341 341 0 strelka-varscan-mutect VIPR2,missense_variant,p.Thr101Ser,ENST00000262178,NM_003382.4,NM_001304522.1;VIPR2,missense_variant,p.Thr242Ser,ENST00000402066,; A ENST00000262178 Transcript missense_variant 487/3944 301/1317 101/438 T/S Acg/Tcg 1 -1 VIPR2 HGNC HGNC:12695 protein_coding YES CCDS5950.1 ENSP00000262178 P41587 X5D7Q6 UPI0000055A9A NM_003382.4,NM_001304522.1 tolerated(0.09) 4/13 Pfam_domain:PF02793,Prints_domain:PR00491,PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF27,SMART_domains:SM00008,Superfamily_domains:SSF111418 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 159103813 159103813 T A 1 0 0 0 0 1 0 0 0 17717 1667 58 4 4 VIPR2 7 159103813 Missense_Mutation SNP T C3N-01414_T 8080090 159103813 242160 216 23416 DLGAP2 0 . GRCh38 8 1549314 1549314 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.621C>A p.= p.G207G ENST00000612087 2/11 225 134 91 240 239 1 strelka-varscan-mutect DLGAP2,synonymous_variant,p.=,ENST00000612087,NM_001277161.1;DLGAP2,synonymous_variant,p.=,ENST00000520901,;DLGAP2,synonymous_variant,p.=,ENST00000637795,;DLGAP2,synonymous_variant,p.=,ENST00000421627,;DLGAP2,synonymous_variant,p.=,ENST00000637152,NM_004745.4; A ENST00000612087 Transcript synonymous_variant 755/10088 621/2886 207/961 G ggC/ggA 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 2/11 Low_complexity_(Seg):seg,hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3 LOW 1 SNV 5 1 PASS rs973559824 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 1549314 1549314 C A 1 0 0 0 0 0 0 0 1 4367 697 25 2 2 DLGAP2 8 1549314 Silent SNP C C3N-01414_T 1549314 143589322 217 23417 ADRA1A 0 . GRCh38 8 26864682 26864682 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.288G>T p.Arg96Ser p.R96S ENST00000380586 1/3 442 283 159 470 470 0 strelka-varscan-mutect ADRA1A,missense_variant,p.Arg96Ser,ENST00000380573,;ADRA1A,missense_variant,p.Arg96Ser,ENST00000380586,NM_033303.3;ADRA1A,missense_variant,p.Arg96Ser,ENST00000276393,NM_000680.2;ADRA1A,missense_variant,p.Arg96Ser,ENST00000380582,NM_033302.2;ADRA1A,missense_variant,p.Arg96Ser,ENST00000519229,;ADRA1A,missense_variant,p.Arg96Ser,ENST00000354550,NM_033304.2;ADRA1A,missense_variant,p.Arg96Ser,ENST00000380572,;ADRA1A,missense_variant,p.Arg96Ser,ENST00000519096,;ADRA1A,missense_variant,p.Arg96Ser,ENST00000521711,; A ENST00000380586 Transcript missense_variant 724/2304 288/1428 96/475 R/S agG/agT 1 -1 ADRA1A HGNC HGNC:277 protein_coding YES CCDS34869.1 ENSP00000369960 P35348 B0ZBD3 UPI000066DA42 NM_033303.3 deleterious(0.01) 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF16,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 26864682 26864682 C A 1 0 0 0 0 1 0 0 0 410 622 22 2 2 ADRA1A 8 26864682 Missense_Mutation SNP C C3N-01414_T 25315368 26864682 118273954 218 23418 SNTG1 0 . GRCh38 8 50658660 50658660 + Silent SNP C C G C3N-01414_T C3N-01414_N C C c.1035C>G p.= p.L345L ENST00000522124 15/19 214 104 110 169 169 0 strelka-varscan-mutect SNTG1,synonymous_variant,p.=,ENST00000522124,NM_018967.3;SNTG1,synonymous_variant,p.=,ENST00000518864,NM_001287813.1;SNTG1,synonymous_variant,p.=,ENST00000517473,NM_001287814.1;SNTG1,synonymous_variant,p.=,ENST00000520825,;SNTG1,synonymous_variant,p.=,ENST00000524004,; G ENST00000522124 Transcript synonymous_variant 1696/3504 1035/1554 345/517 L ctC/ctG COSM121915,COSM121916 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 15/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 50658660 50658660 C G 1 0 0 0 0 0 0 0 1 15194 840 29 4 4 SNTG1 8 50658660 Silent SNP C C3N-01414_T 23793978 50658660 94479976 219 23419 YTHDF3 0 . GRCh38 8 63186397 63186397 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.395G>T p.Gly132Val p.G132V ENST00000621413 5/6 259 206 53 306 304 2 strelka-varscan-mutect YTHDF3,missense_variant,p.Gly78Val,ENST00000623280,NM_001277815.1,NM_001277817.1;YTHDF3,missense_variant,p.Gly129Val,ENST00000539294,NM_152758.5;YTHDF3,missense_variant,p.Gly78Val,ENST00000617200,NM_001277816.1;YTHDF3,missense_variant,p.Gly127Val,ENST00000621957,;YTHDF3,missense_variant,p.Gly132Val,ENST00000621413,NM_001277813.1;YTHDF3,missense_variant,p.Gly132Val,ENST00000621820,NM_001277814.1;YTHDF3,missense_variant,p.Gly78Val,ENST00000621890,NM_001277818.1;YTHDF3,missense_variant,p.Gly78Val,ENST00000612880,;YTHDF3,missense_variant,p.Gly78Val,ENST00000619337,;YTHDF3,intron_variant,,ENST00000517371,;YTHDF3,downstream_gene_variant,,ENST00000613853,;YTHDF3,downstream_gene_variant,,ENST00000617952,;YTHDF3,upstream_gene_variant,,ENST00000518373,;YTHDF3,3_prime_UTR_variant,,ENST00000615676,; T ENST00000621413 Transcript missense_variant 749/2370 395/1767 132/588 G/V gGt/gTt 1 1 YTHDF3 HGNC HGNC:26465 protein_coding YES CCDS75748.1 ENSP00000478490 A0A087WY31 UPI0002D13FA3 NM_001277813.1 tolerated(0.08) 5/6 hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF9 MODERATE 1 SNV 5 1 PASS . . 0 190 0 11 8 0 0 0 -20 0.1376488 1 1 0 0 T 3 4 77 63186397 63186397 G T 1 0 0 0 0 1 0 0 0 18061 1261 44 2 2 YTHDF3 8 63186397 Missense_Mutation SNP G C3N-01414_T 12527737 63186397 81952239 220 23420 C8orf34 0 . GRCh38 8 68533142 68533142 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1098A>T p.Glu366Asp p.E366D ENST00000518698 7/14 127 103 24 145 145 0 strelka-varscan-mutect C8orf34,missense_variant,p.Glu255Asp,ENST00000337103,;C8orf34,missense_variant,p.Glu280Asp,ENST00000348340,NM_001195639.1;C8orf34,missense_variant,p.Glu366Asp,ENST00000518698,NM_052958.2;C8orf34,non_coding_transcript_exon_variant,,ENST00000518515,;C8orf34,3_prime_UTR_variant,,ENST00000521406,; T ENST00000518698 Transcript missense_variant 1389/2223 1098/1617 366/538 E/D gaA/gaT 1 1 C8orf34 HGNC HGNC:30905 protein_coding YES CCDS6203.2 ENSP00000427820 Q49A92 UPI000021D12D NM_052958.2 tolerated(0.06) 7/14 hmmpanther:PTHR32000,hmmpanther:PTHR32000:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 68533142 68533142 A T 1 0 0 0 0 1 0 0 0 2155 98 4 4 4 C8orf34 8 68533142 Missense_Mutation SNP A C3N-01414_T 5346745 68533142 76605494 221 23421 ZFHX4 0 . GRCh38 8 76707767 76707767 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.2812G>A p.Val938Ile p.V938I ENST00000521891 3/11 388 309 79 329 329 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Val938Ile,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Val912Ile,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript missense_variant 3260/14019 2812/10851 938/3616 V/I Gta/Ata 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0.01) 3/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 76707767 76707767 G A 1 0 0 0 0 1 0 0 0 18213 1029 36 3 3 ZFHX4 8 76707767 Missense_Mutation SNP G C3N-01414_T 8174625 76707767 68430869 222 23422 ZFHX4 0 . GRCh38 8 76853091 76853091 + Missense_Mutation SNP C C T rs200704587 C3N-01414_T C3N-01414_N C C c.6170C>T p.Pro2057Leu p.P2057L ENST00000521891 10/11 158 135 23 146 146 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Pro2057Leu,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Pro2031Leu,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; T ENST00000521891 Transcript missense_variant 6618/14019 6170/10851 2057/3616 P/L cCa/cTa rs200704587 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated_low_confidence(0.31) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs200704587 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 77 76853091 76853091 C T 1 0 0 0 0 1 0 0 0 18213 594 21 3 3 ZFHX4 8 76853091 Missense_Mutation SNP C C3N-01414_T 145324 76853091 68285545 223 23423 RUNX1T1 0 . GRCh38 8 91975956 91975956 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.1474C>A p.Leu492Ile p.L492I ENST00000436581 10/12 229 193 36 270 270 0 strelka-varscan-mutect RUNX1T1,missense_variant,p.Leu433Ile,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.Leu433Ile,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.Leu433Ile,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.Leu433Ile,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.Leu492Ile,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.Leu406Ile,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.Leu413Ile,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.Leu433Ile,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.Leu406Ile,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.Leu406Ile,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.Leu396Ile,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.Leu396Ile,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.Leu444Ile,ENST00000520724,NM_001198634.1;GS1-5L10.1,non_coding_transcript_exon_variant,,ENST00000522980,;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,3_prime_UTR_variant,,ENST00000521751,;RUNX1T1,upstream_gene_variant,,ENST00000521078,; T ENST00000436581 Transcript missense_variant 1661/7454 1474/1992 492/663 L/I Ctt/Att COSM5597525,COSM5597526,COSM5597527,COSM606485,COSM606486,COSM606487 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 tolerated(0.44) 10/12 hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379 1,1,1,1,1,1 MODERATE SNV 5 1,1,1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 91975956 91975956 G T 1 0 0 0 0 1 0 0 0 14008 1000 35 2 2 RUNX1T1 8 91975956 Missense_Mutation SNP G C3N-01414_T 15122865 91975956 53162680 224 23424 RIMS2 0 . GRCh38 8 103885835 103885835 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1236G>T p.Met412Ile p.M412I ENST00000504942 4/24 304 153 151 297 297 0 strelka-varscan-mutect RIMS2,missense_variant,p.Met220Ile,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Met190Ile,ENST00000436393,;RIMS2,missense_variant,p.Met412Ile,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Met354Ile,ENST00000626043,;RIMS2,missense_variant,p.Met220Ile,ENST00000408894,;RIMS2,missense_variant,p.Met220Ile,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Met416Ile,ENST00000632716,;RIMS2,missense_variant,p.Met220Ile,ENST00000515551,; T ENST00000504942 Transcript missense_variant 1375/4228 1236/4050 412/1349 M/I atG/atT 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 tolerated_low_confidence(0.47) 4/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 103885835 103885835 G T 1 0 0 0 0 1 0 0 0 13543 1348 47 2 2 RIMS2 8 103885835 Missense_Mutation SNP G C3N-01414_T 11909879 103885835 41252801 225 23425 ZFPM2 0 . GRCh38 8 105318976 105318976 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.35T>A p.Ile12Asn p.I12N ENST00000407775 1/8 233 218 15 191 191 0 strelka-varscan-mutect ZFPM2,missense_variant,p.Ile12Asn,ENST00000407775,NM_012082.3;ZFPM2,upstream_gene_variant,,ENST00000520492,;ZFPM2,intron_variant,,ENST00000518180,; A ENST00000407775 Transcript missense_variant 285/4700 35/3456 12/1151 I/N aTc/aAc 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 deleterious(0) 1/8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 105318976 105318976 T A 1 0 0 0 0 1 0 0 0 18236 1449 50 4 4 ZFPM2 8 105318976 Missense_Mutation SNP T C3N-01414_T 1433141 105318976 39819660 226 23426 CSMD3 0 . GRCh38 8 112650219 112650219 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.3135A>T p.Glu1045Asp p.E1045D ENST00000297405 19/71 560 381 179 444 444 0 strelka-varscan-mutect CSMD3,missense_variant,p.Glu1045Asp,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Glu1005Asp,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Glu941Asp,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Glu385Asp,ENST00000339701,; A ENST00000297405 Transcript missense_variant 3380/13212 3135/11124 1045/3707 E/D gaA/gaT 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.54) 19/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs1157686539 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 112650219 112650219 T A 1 0 0 0 0 1 0 0 0 3747 1606 56 4 4 CSMD3 8 112650219 Missense_Mutation SNP T C3N-01414_T 7331243 112650219 32488417 227 23427 POU5F1B 0 . GRCh38 8 127416380 127416380 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.514G>T p.Gly172Trp p.G172W ENST00000465342 2/2 811 715 96 537 537 0 strelka-varscan-mutect POU5F1B,missense_variant,p.Gly172Trp,ENST00000465342,NM_001159542.1;CASC8,intron_variant,,ENST00000502082,;CASC8,intron_variant,,ENST00000501396,;CASC8,intron_variant,,ENST00000523825,; T ENST00000465342 Transcript missense_variant 1671/5360 514/1080 172/359 G/W Ggg/Tgg 1 1 POU5F1B HGNC HGNC:9223 protein_coding YES CCDS55274.1 ENSP00000419298 Q06416 UPI000013F18B NM_001159542.1 deleterious(0) 2/2 PROSITE_profiles:PS51179,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF86,Pfam_domain:PF00157,Gene3D:1.10.260.40,SMART_domains:SM00352,Superfamily_domains:SSF47413,Prints_domain:PR00028 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 127416380 127416380 G T 1 0 0 0 0 1 0 0 0 12398 1232 43 2 2 POU5F1B 8 127416380 Missense_Mutation SNP G C3N-01414_T 14766161 127416380 17722256 228 23428 NDRG1 0 . GRCh38 8 133264560 133264560 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.192C>A p.Asp64Glu p.D64E ENST00000414097 4/16 1115 1042 73 584 584 0 strelka-varscan-mutect NDRG1,missense_variant,p.Asp64Glu,ENST00000414097,NM_001135242.1;NDRG1,missense_variant,p.Asp64Glu,ENST00000323851,NM_006096.3;NDRG1,missense_variant,p.Asp64Glu,ENST00000519228,;NDRG1,missense_variant,p.Asp64Glu,ENST00000521544,;NDRG1,missense_variant,p.Asp81Glu,ENST00000520230,;NDRG1,missense_variant,p.Asp64Glu,ENST00000522890,;NDRG1,missense_variant,p.Asp64Glu,ENST00000519580,;NDRG1,missense_variant,p.Asp75Glu,ENST00000520943,;NDRG1,missense_variant,p.Asp118Glu,ENST00000522738,;NDRG1,5_prime_UTR_variant,,ENST00000522476,NM_001258432.1;NDRG1,5_prime_UTR_variant,,ENST00000523892,;NDRG1,5_prime_UTR_variant,,ENST00000518480,;NDRG1,intron_variant,,ENST00000537882,NM_001258433.1;NDRG1,intron_variant,,ENST00000518176,;NDRG1,intron_variant,,ENST00000518066,;NDRG1,non_coding_transcript_exon_variant,,ENST00000518010,;NDRG1,missense_variant,p.Asp64Glu,ENST00000522377,;NDRG1,non_coding_transcript_exon_variant,,ENST00000523931,;NDRG1,non_coding_transcript_exon_variant,,ENST00000517745,;NDRG1,intron_variant,,ENST00000517599,;NDRG1,upstream_gene_variant,,ENST00000518094,; T ENST00000414097 Transcript missense_variant 1060/3755 192/1185 64/394 D/E gaC/gaA 1 -1 NDRG1 HGNC HGNC:7679 protein_coding YES CCDS34945.1 ENSP00000404854 Q92597 UPI000012FEDD NM_001135242.1 deleterious(0.03) 4/16 hmmpanther:PTHR11034,hmmpanther:PTHR11034:SF18,Gene3D:3.40.50.1820,Pfam_domain:PF03096,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS rs1474130558 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 133264560 133264560 G T 1 0 0 0 0 1 0 0 0 10272 1368 48 2 2 NDRG1 8 133264560 Missense_Mutation SNP G C3N-01414_T 5848180 133264560 11874076 229 23429 KHDRBS3 0 . GRCh38 8 135542742 135542742 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.296G>C p.Gly99Ala p.G99A ENST00000355849 3/9 254 90 164 254 254 0 strelka-varscan-mutect KHDRBS3,missense_variant,p.Gly99Ala,ENST00000355849,NM_006558.2;KHDRBS3,missense_variant,p.Gly71Ala,ENST00000524199,;KHDRBS3,missense_variant,p.Gly72Ala,ENST00000517394,;KHDRBS3,missense_variant,p.Gly14Ala,ENST00000524282,;KHDRBS3,intron_variant,,ENST00000520981,;KHDRBS3,missense_variant,p.Gly24Ala,ENST00000517859,;KHDRBS3,non_coding_transcript_exon_variant,,ENST00000519600,; C ENST00000355849 Transcript missense_variant 706/1977 296/1041 99/346 G/A gGg/gCg 1 1 KHDRBS3 HGNC HGNC:18117 protein_coding YES CCDS6374.1 ENSP00000348108 O75525 UPI0000073E6F NM_006558.2 deleterious(0.02) 3/9 hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF29,Pfam_domain:PF00013,Gene3D:3.30.1370.10,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 135542742 135542742 G C 1 0 0 0 0 1 0 0 0 8069 1232 43 4 4 KHDRBS3 8 135542742 Missense_Mutation SNP G C3N-01414_T 2278182 135542742 9595894 230 23430 FAM135B 0 . GRCh38 8 138168010 138168010 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1143C>A p.Asn381Lys p.N381K ENST00000395297 12/20 243 202 41 185 185 0 strelka-varscan-mutect FAM135B,missense_variant,p.Asn381Lys,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Asn381Lys,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; T ENST00000395297 Transcript missense_variant 1314/6962 1143/4221 381/1406 N/K aaC/aaA 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0.03) 12/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 138168010 138168010 G T 1 0 0 0 0 1 0 0 0 5299 1020 36 2 2 FAM135B 8 138168010 Missense_Mutation SNP G C3N-01414_T 2625268 138168010 6970626 231 23431 COL22A1 0 . GRCh38 8 138722049 138722049 + Missense_Mutation SNP G G A rs114182767 C3N-01414_T C3N-01414_N G G c.2288C>T p.Pro763Leu p.P763L ENST00000303045 26/65 328 304 24 260 260 0 strelka-varscan-mutect COL22A1,missense_variant,p.Pro763Leu,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Pro476Leu,ENST00000435777,;COL22A1,intron_variant,,ENST00000341807,; A ENST00000303045 Transcript missense_variant 2735/6346 2288/4881 763/1626 P/L cCg/cTg rs114182767,COSM454082 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.74) 26/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391,Pfam_domain:PF01391 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs114182767 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 138722049 138722049 G A 1 0 0 0 0 1 0 0 0 3469 1116 39 1 1 COL22A1 8 138722049 Missense_Mutation SNP G C3N-01414_T 554039 138722049 6416587 232 23432 KCNK9 0 . GRCh38 8 139618587 139618587 + Missense_Mutation SNP C C T rs370302731 C3N-01414_T C3N-01414_N C C c.796G>A p.Gly266Arg p.G266R ENST00000520439 2/2 289 270 19 205 205 0 strelka-varscan-mutect KCNK9,missense_variant,p.Gly266Arg,ENST00000520439,NM_001282534.1;KCNK9,missense_variant,p.Gly266Arg,ENST00000303015,;KCNK9,upstream_gene_variant,,ENST00000523477,;KCNK9,upstream_gene_variant,,ENST00000519923,;KCNK9,missense_variant,p.Gly266Arg,ENST00000522317,; T ENST00000520439 Transcript missense_variant 860/1441 796/1125 266/374 G/R Gga/Aga rs370302731,COSM5238265,COSM5238266 1 -1 KCNK9 HGNC HGNC:6283 protein_coding YES CCDS6377.1 ENSP00000430676 Q9NPC2 A0A024R9H3 UPI000000D8AC NM_001282534.1 tolerated(0.84) 2/2 hmmpanther:PTHR11003:SF75,hmmpanther:PTHR11003,PIRSF_domain:PIRSF038061,Prints_domain:PR01585 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs370302731 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 139618587 139618587 C T 1 0 0 0 0 1 0 0 0 7989 661 23 1 1 KCNK9 8 139618587 Missense_Mutation SNP C C3N-01414_T 896538 139618587 5520049 233 23433 PTK2 0 . GRCh38 8 140846648 140846648 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.481G>T p.Asp161Tyr p.D161Y ENST00000340930 6/33 431 394 37 335 333 2 strelka-varscan-mutect PTK2,missense_variant,p.Asp161Tyr,ENST00000522684,NM_153831.3;PTK2,missense_variant,p.Asp205Tyr,ENST00000517887,;PTK2,missense_variant,p.Asp205Tyr,ENST00000519419,;PTK2,missense_variant,p.Asp161Tyr,ENST00000395218,;PTK2,missense_variant,p.Asp161Tyr,ENST00000340930,NM_001199649.1;PTK2,missense_variant,p.Asp161Tyr,ENST00000521059,NM_005607.4;PTK2,missense_variant,p.Asp172Tyr,ENST00000519654,;PTK2,missense_variant,p.Asp76Tyr,ENST00000524357,;PTK2,downstream_gene_variant,,ENST00000520828,;PTK2,downstream_gene_variant,,ENST00000520475,;PTK2,3_prime_UTR_variant,,ENST00000519993,NM_001316342.1;PTK2,3_prime_UTR_variant,,ENST00000521791,;PTK2,3_prime_UTR_variant,,ENST00000523067,;PTK2,upstream_gene_variant,,ENST00000524202,; A ENST00000340930 Transcript missense_variant 636/4414 481/3198 161/1065 D/Y Gat/Tat 1 -1 PTK2 HGNC HGNC:9611 protein_coding YES CCDS56557.1 ENSP00000341189 Q05397 UPI0001E8F57E NM_001199649.1 deleterious(0.01) 6/33 Pfam_domain:PF00373,SMART_domains:SM00295,Superfamily_domains:SSF47031,PROSITE_profiles:PS50057,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF78 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 140846648 140846648 C A 1 0 0 0 0 1 0 0 0 12918 826 29 2 2 PTK2 8 140846648 Missense_Mutation SNP C C3N-01414_T 1228061 140846648 4291988 234 23434 ARC 0 . GRCh38 8 142613353 142613353 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.919G>T p.Asp307Tyr p.D307Y ENST00000356613 1/3 267 236 31 186 186 0 strelka-varscan-mutect ARC,missense_variant,p.Asp307Tyr,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; A ENST00000356613 Transcript missense_variant 1120/2948 919/1191 307/396 D/Y Gac/Tac 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 tolerated(0.22) 1/3 Prints_domain:PR02027,hmmpanther:PTHR15962 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 142613353 142613353 C A 1 0 0 0 0 1 0 0 0 963 855 30 2 2 ARC 8 142613353 Missense_Mutation SNP C C3N-01414_T 1766705 142613353 2525283 235 23435 LY6K 0 . GRCh38 8 142703110 142703110 + Frame_Shift_Del DEL C C - C3N-01414_T C3N-01414_N C C c.237delC p.Phe79LeufsTer45 p.F79Lfs*45 ENST00000292430 3/3 201 100 101 211 211 0 sindel-varindel LY6K,frameshift_variant,p.Phe79LeufsTer45,ENST00000292430,NM_017527.3;LY6K,3_prime_UTR_variant,,ENST00000522591,;LY6K,intron_variant,,ENST00000519387,NM_001160355.1;LY6K,downstream_gene_variant,,ENST00000518841,;CTD-2292P10.4,non_coding_transcript_exon_variant,,ENST00000520572,;LY6K,non_coding_transcript_exon_variant,,ENST00000519390,; - ENST00000292430 Transcript frameshift_variant 654/2671 237/498 79/165 F/X ttC/tt COSM4768200 1 1 LY6K HGNC HGNC:24225 protein_coding YES CCDS6385.2 ENSP00000292430 Q17RY6 UPI0000071C96 NM_017527.3 3/3 Gene3D:2.10.60.10,hmmpanther:PTHR15049,hmmpanther:PTHR15049:SF1,Superfamily_domains:SSF57302 1 HIGH 1 deletion 1 1 1 PASS . . 0 172 0 23 15 0 0 0 -20 0.06341092 0 1 0 0 - 7 5 77 142703110 142703110 C - 1 0 1 0 1 0 0 0 0 9009 825 29 0 0 LY6K 8 142703110 Frame_Shift_Del DEL C C3N-01414_T 89757 142703110 2435526 236 23436 LYNX1 0 . GRCh38 8 142764624 142764624 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.377G>T p.Ser126Ile p.S126I ENST00000615007 5/5 204 169 35 212 212 0 strelka-varscan-mutect LYNX1,missense_variant,p.Ser126Ile,ENST00000615007,NM_023946.3;LYNX1,missense_variant,p.Ser92Ile,ENST00000317543,NM_177458.1;LYNX1,intron_variant,,ENST00000523332,;LYNX1,intron_variant,,ENST00000521396,;RP11-706C16.7,intron_variant,,ENST00000523657,; A ENST00000615007 Transcript missense_variant 1007/1293 377/396 126/131 S/I aGc/aTc 1 -1 LYNX1 HGNC HGNC:29604 protein_coding YES CCDS34951.1 ENSP00000479586 Q9BZG9 A0A140VJN6 UPI0000168665 NM_023946.3 deleterious(0) 5/5 Gene3D:2.10.60.10,Pfam_domain:PF00021,hmmpanther:PTHR16983,hmmpanther:PTHR16983:SF14,Superfamily_domains:SSF57302 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 142764624 142764624 C A 1 0 0 0 0 1 0 0 0 9019 797 28 2 2 LYNX1 8 142764624 Missense_Mutation SNP C C3N-01414_T 61514 142764624 2374012 237 23437 GLDC 0 . GRCh38 9 6553421 6553421 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2404G>T p.Ala802Ser p.A802S ENST00000321612 20/25 275 206 69 419 417 2 strelka-varscan-mutect GLDC,missense_variant,p.Ala802Ser,ENST00000321612,NM_000170.2;GLDC,downstream_gene_variant,,ENST00000460457,;GLDC,downstream_gene_variant,,ENST00000467946,; A ENST00000321612 Transcript missense_variant 2555/3767 2404/3063 802/1020 A/S Gcg/Tcg 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 tolerated(0.07) 20/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 6553421 6553421 C A 1 0 0 0 0 1 0 0 0 6311 710 25 2 2 GLDC 9 6553421 Missense_Mutation SNP C C3N-01414_T 6553421 131841296 238 23438 79 2 GLDC 0 . GRCh38 9 6553423 6553423 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2402G>T p.Ser801Ile p.S801I ENST00000321612 20/25 279 211 68 439 439 0 strelka-varscan-mutect GLDC,missense_variant,p.Ser801Ile,ENST00000321612,NM_000170.2;GLDC,downstream_gene_variant,,ENST00000460457,;GLDC,downstream_gene_variant,,ENST00000467946,; A ENST00000321612 Transcript missense_variant 2553/3767 2402/3063 801/1020 S/I aGt/aTt 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0) 20/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 6553423 6553423 C A 1 0 0 0 0 1 0 0 0 6311 565 20 2 2 GLDC 9 6553423 Missense_Mutation SNP C C3N-01414_T 2 6553423 131841294 239 23439 79 2 SH3GL2 0 . GRCh38 9 17795591 17795591 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.907C>T p.Pro303Ser p.P303S ENST00000380607 9/9 140 105 35 274 274 0 strelka-varscan-mutect SH3GL2,missense_variant,p.Pro303Ser,ENST00000380607,NM_003026.3; T ENST00000380607 Transcript missense_variant 1027/2565 907/1059 303/352 P/S Cct/Tct 1 1 SH3GL2 HGNC HGNC:10831 protein_coding YES CCDS6483.1 ENSP00000369981 Q99962 UPI0000135933 NM_003026.3 deleterious(0.04) 9/9 PROSITE_profiles:PS50002,hmmpanther:PTHR10663:SF205,hmmpanther:PTHR10663,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR01887,Prints_domain:PR00452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 17795591 17795591 C T 1 0 0 0 0 1 0 0 0 14510 507 18 3 3 SH3GL2 9 17795591 Missense_Mutation SNP C C3N-01414_T 11242168 17795591 120599126 240 23440 TEK 0 . GRCh38 9 27212756 27212756 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.2736C>T p.= p.D912D ENST00000380036 17/23 532 409 123 832 832 0 strelka-varscan-mutect TEK,synonymous_variant,p.=,ENST00000380036,NM_000459.4;TEK,synonymous_variant,p.=,ENST00000406359,NM_001290077.1;TEK,synonymous_variant,p.=,ENST00000519097,NM_001290078.1;TEK,3_prime_UTR_variant,,ENST00000615002,;RP11-179D22.1,downstream_gene_variant,,ENST00000422804,; T ENST00000380036 Transcript synonymous_variant 3178/4760 2736/3375 912/1124 D gaC/gaT 1 1 TEK HGNC HGNC:11724 protein_coding YES CCDS6519.1 ENSP00000369375 Q02763 UPI000021121E NM_000459.4 17/23 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF125,SMART_domains:SM00219,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 27212756 27212756 C T 1 0 0 0 0 0 0 0 1 16163 564 20 3 3 TEK 9 27212756 Silent SNP C C3N-01414_T 9417165 27212756 111181961 241 23441 C9orf131 0 . GRCh38 9 35043812 35043812 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1183C>A p.Leu395Met p.L395M ENST00000312292 2/2 222 165 57 346 346 0 strelka-varscan-mutect C9orf131,missense_variant,p.Leu395Met,ENST00000312292,NM_001287391.1,NM_203299.3,NM_001040410.2;C9orf131,missense_variant,p.Leu347Met,ENST00000421362,NM_001040412.2;C9orf131,missense_variant,p.Leu322Met,ENST00000354479,NM_001040411.2;C9orf131,downstream_gene_variant,,ENST00000378745,;C9orf131,downstream_gene_variant,,ENST00000534880,;C9orf131,downstream_gene_variant,,ENST00000537671,;RP11-182N22.9,non_coding_transcript_exon_variant,,ENST00000624351,;C9orf131,downstream_gene_variant,,ENST00000416537,; A ENST00000312292 Transcript missense_variant 1230/3409 1183/3240 395/1079 L/M Ctg/Atg 1 1 C9orf131 HGNC HGNC:31418 protein_coding YES CCDS6572.2 ENSP00000308279 Q5VYM1 UPI00001605AC NM_001287391.1,NM_203299.3,NM_001040410.2 tolerated(0.14) 2/2 hmmpanther:PTHR21777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 35043812 35043812 C A 1 0 0 0 0 1 0 0 0 2173 680 24 2 2 C9orf131 9 35043812 Missense_Mutation SNP C C3N-01414_T 7831056 35043812 103350905 242 23442 APBA1 0 . GRCh38 9 69516212 69516212 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.999G>T p.Glu333Asp p.E333D ENST00000265381 2/13 84 65 19 123 123 0 strelka-varscan-mutect APBA1,missense_variant,p.Glu333Asp,ENST00000265381,NM_001163.3; A ENST00000265381 Transcript missense_variant 1222/6534 999/2514 333/837 E/D gaG/gaT 1 -1 APBA1 HGNC HGNC:578 protein_coding YES CCDS6630.1 ENSP00000265381 Q02410 UPI000013D611 NM_001163.3 tolerated_low_confidence(0.19) 2/13 hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF14 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 69516212 69516212 C A 1 0 0 0 0 1 0 0 0 876 680 24 2 2 APBA1 9 69516212 Missense_Mutation SNP C C3N-01414_T 34472400 69516212 68878505 243 23443 GCNT1 0 . GRCh38 9 76502738 76502738 + Silent SNP G G A rs113228037 C3N-01414_T C3N-01414_N G G c.357G>A p.= p.A119A ENST00000442371 3/3 167 141 26 270 269 1 strelka-varscan-mutect GCNT1,synonymous_variant,p.=,ENST00000442371,NM_001097634.1;GCNT1,synonymous_variant,p.=,ENST00000376730,NM_001490.4;GCNT1,synonymous_variant,p.=,ENST00000444201,NM_001097633.1,NM_001097635.1,NM_001097636.1;GCNT1,downstream_gene_variant,,ENST00000488136,;GCNT1,downstream_gene_variant,,ENST00000480311,; A ENST00000442371 Transcript synonymous_variant 1296/5972 357/1287 119/428 A gcG/gcA rs113228037 1 1 GCNT1 HGNC HGNC:4203 protein_coding YES CCDS6653.1 ENSP00000415454 Q02742 UPI000013CF63 NM_001097634.1 3/3 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF81 LOW 1 SNV 1 1 PASS rs113228037 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 76502738 76502738 G A 1 0 0 0 0 0 0 0 1 6170 1103 39 1 1 GCNT1 9 76502738 Silent SNP G C3N-01414_T 6986526 76502738 61891979 244 23444 GCNT1 0 . GRCh38 9 76502957 76502957 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.576G>T p.= p.R192R ENST00000442371 3/3 141 112 29 217 217 0 strelka-varscan-mutect GCNT1,synonymous_variant,p.=,ENST00000442371,NM_001097634.1;GCNT1,synonymous_variant,p.=,ENST00000376730,NM_001490.4;GCNT1,synonymous_variant,p.=,ENST00000444201,NM_001097633.1,NM_001097635.1,NM_001097636.1;GCNT1,downstream_gene_variant,,ENST00000488136,;GCNT1,downstream_gene_variant,,ENST00000480311,; T ENST00000442371 Transcript synonymous_variant 1515/5972 576/1287 192/428 R cgG/cgT 1 1 GCNT1 HGNC HGNC:4203 protein_coding YES CCDS6653.1 ENSP00000415454 Q02742 UPI000013CF63 NM_001097634.1 3/3 Pfam_domain:PF02485,hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF81 LOW 1 SNV 1 1 PASS rs1334493217 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 76502957 76502957 G T 1 0 0 0 0 0 0 0 1 6170 1219 43 2 2 GCNT1 9 76502957 Silent SNP G C3N-01414_T 219 76502957 61891760 245 23445 SEMA4D 0 . GRCh38 9 89396832 89396832 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.319G>T p.Glu107Ter p.E107* ENST00000450295 6/16 164 128 36 240 240 0 strelka-varscan-mutect SEMA4D,stop_gained,p.Glu107Ter,ENST00000450295,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000438547,NM_006378.3;SEMA4D,stop_gained,p.Glu107Ter,ENST00000356444,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000422704,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000420987,NM_001142287.1;SEMA4D,stop_gained,p.Glu107Ter,ENST00000339861,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000455551,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000420681,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000429836,;SEMA4D,stop_gained,p.Glu107Ter,ENST00000537934,; A ENST00000450295 Transcript stop_gained 1096/5684 319/2589 107/862 E/* Gag/Tag 1 -1 SEMA4D HGNC HGNC:10732 protein_coding YES CCDS6685.1 ENSP00000416523 Q92854 UPI0000135A6C 6/16 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF18,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 89396832 89396832 C A 1 0 0 0 0 0 1 0 0 14310 927 32 2 2 SEMA4D 9 89396832 Nonsense_Mutation SNP C C3N-01414_T 12893875 89396832 48997885 246 23446 PHF2 0 . GRCh38 9 93676862 93676862 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.3101G>T p.Gly1034Val p.G1034V ENST00000359246 21/22 145 114 31 184 183 1 strelka-varscan-mutect PHF2,missense_variant,p.Gly1034Val,ENST00000359246,NM_005392.3;PHF2,missense_variant,p.Gly247Val,ENST00000375376,;PHF2,missense_variant,p.Gly266Val,ENST00000610682,; T ENST00000359246 Transcript missense_variant 3468/5569 3101/3291 1034/1096 G/V gGg/gTg 1 1 PHF2 HGNC HGNC:8920 protein_coding YES CCDS35069.1 ENSP00000352185 O75151 UPI0000211A97 NM_005392.3 tolerated(0.47) 21/22 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF14,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 93676862 93676862 G T 1 0 0 0 0 1 0 0 0 11916 1232 43 2 2 PHF2 9 93676862 Missense_Mutation SNP G C3N-01414_T 4280030 93676862 44717855 247 23447 LHX2 0 . GRCh38 9 124015380 124015380 + Silent SNP G G T rs760714480 C3N-01414_T C3N-01414_N G G c.582G>T p.= p.A194A ENST00000373615 3/5 112 80 32 160 160 0 varscan-mutect LHX2,synonymous_variant,p.=,ENST00000373615,NM_004789.3;LHX2,synonymous_variant,p.=,ENST00000446480,;LHX2,upstream_gene_variant,,ENST00000488674,;LHX2,downstream_gene_variant,,ENST00000560961,;RP11-85O21.4,downstream_gene_variant,,ENST00000421041,; T ENST00000373615 Transcript synonymous_variant 1321/2554 582/1221 194/406 A gcG/gcT rs760714480 1 1 LHX2 HGNC HGNC:6594 protein_coding YES CCDS6853.1 ENSP00000362717 P50458 UPI000012E659 NM_004789.3 3/5 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs760714480 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 124015380 124015380 G T 1 0 0 0 0 0 0 0 1 8680 1103 39 1 1 LHX2 9 124015380 Silent SNP G C3N-01414_T 30338518 124015380 14379337 248 23448 FUBP3 0 . GRCh38 9 130630749 130630749 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.1239G>C p.Gln413His p.Q413H ENST00000319725 13/19 52 40 12 53 53 0 strelka-varscan-mutect FUBP3,missense_variant,p.Gln413His,ENST00000319725,NM_003934.1;MIR6856,downstream_gene_variant,,ENST00000613330,;FUBP3,non_coding_transcript_exon_variant,,ENST00000487406,;FUBP3,upstream_gene_variant,,ENST00000472006,; C ENST00000319725 Transcript missense_variant 1314/3124 1239/1719 413/572 Q/H caG/caC 1 1 FUBP3 HGNC HGNC:4005 protein_coding YES CCDS43893.1 ENSP00000318177 Q96I24 A0A024R8A7 UPI00001C1EAA NM_003934.1 deleterious(0) 13/19 PROSITE_profiles:PS50084,hmmpanther:PTHR10288:SF100,hmmpanther:PTHR10288,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 130630749 130630749 G C 1 0 0 0 0 1 0 0 0 5964 933 33 4 4 FUBP3 9 130630749 Missense_Mutation SNP G C3N-01414_T 6615369 130630749 7763968 249 23449 ADAMTSL2 0 . GRCh38 9 133536755 133536755 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.43C>T p.= p.L15L ENST00000354484 2/19 219 175 44 303 303 0 strelka-varscan-mutect ADAMTSL2,synonymous_variant,p.=,ENST00000393061,;ADAMTSL2,synonymous_variant,p.=,ENST00000354484,NM_001145320.1;ADAMTSL2,synonymous_variant,p.=,ENST00000393060,NM_014694.3; T ENST00000354484 Transcript synonymous_variant 600/4068 43/2856 15/951 L Ctg/Ttg 1 1 ADAMTSL2 HGNC HGNC:14631 protein_coding YES CCDS6976.1 ENSP00000346478 Q86TH1 UPI000018CEA2 NM_001145320.1 2/19 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF147 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 133536755 133536755 C T 1 0 0 0 0 0 0 0 1 319 796 28 3 3 ADAMTSL2 9 133536755 Silent SNP C C3N-01414_T 2906006 133536755 4857962 250 23450 PNPLA7 0 . GRCh38 9 137497307 137497307 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1893G>T p.Gln631His p.Q631H ENST00000406427 18/35 71 49 22 108 108 0 strelka-varscan-mutect PNPLA7,missense_variant,p.Gln631His,ENST00000406427,NM_001098537.2;PNPLA7,missense_variant,p.Gln606His,ENST00000277531,NM_152286.4; A ENST00000406427 Transcript missense_variant 2230/4806 1893/4029 631/1342 Q/H caG/caT 1 -1 PNPLA7 HGNC HGNC:24768 protein_coding YES CCDS48070.1 ENSP00000384610 Q6ZV29 UPI000443805D NM_001098537.2 deleterious(0) 18/35 Gene3D:2.60.120.10,Pfam_domain:PF00027,PROSITE_profiles:PS50042,hmmpanther:PTHR14226,hmmpanther:PTHR14226:SF23,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 2 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999959 1 1 1 0 A 3 1 77 137497307 137497307 C A 1 0 0 0 0 1 0 0 0 12278 695 24 2 2 PNPLA7 9 137497307 Missense_Mutation SNP C C3N-01414_T 3960552 137497307 897410 251 23451 CACNA1B 0 . GRCh38 9 138118754 138118754 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.6016G>T p.Ala2006Ser p.A2006S ENST00000371372 44/47 188 147 41 251 251 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Ala2006Ser,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Ala2004Ser,ENST00000371363,;CACNA1B,missense_variant,p.Ala2007Ser,ENST00000371355,;CACNA1B,missense_variant,p.Ala2005Ser,ENST00000371357,;CACNA1B,missense_variant,p.Ala2006Ser,ENST00000277549,;CACNA1B,missense_variant,p.Ala2006Ser,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 6161/9790 6016/7020 2006/2339 A/S Gcg/Tcg 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 tolerated(0.39) 44/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 138118754 138118754 G T 1 0 0 0 0 1 0 0 0 2227 1319 46 2 2 CACNA1B 9 138118754 Missense_Mutation SNP G C3N-01414_T 621447 138118754 275963 252 23452 CELF2 0 . GRCh38 10 11314255 11314255 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.1093G>C p.Ala365Pro p.A365P ENST00000542579 10/14 355 274 81 515 515 0 strelka-varscan-mutect CELF2,missense_variant,p.Ala334Pro,ENST00000417956,NM_001025076.2;CELF2,missense_variant,p.Ala365Pro,ENST00000542579,NM_006561.3;CELF2,missense_variant,p.Ala334Pro,ENST00000399850,;CELF2,missense_variant,p.Ala358Pro,ENST00000416382,NM_001025077.2;CELF2,missense_variant,p.Ala358Pro,ENST00000631460,;CELF2,missense_variant,p.Ala370Pro,ENST00000636488,;CELF2,missense_variant,p.Ala334Pro,ENST00000632728,;CELF2,missense_variant,p.Ala370Pro,ENST00000637215,;CELF2,missense_variant,p.Ala334Pro,ENST00000609692,;CELF2,missense_variant,p.Ala365Pro,ENST00000632065,;CELF2,missense_variant,p.Ala334Pro,ENST00000608830,NM_001083591.1;CELF2,missense_variant,p.Ala334Pro,ENST00000638035,;CELF2,missense_variant,p.Ala358Pro,ENST00000631816,;CELF2,missense_variant,p.Ala334Pro,ENST00000354897,;CELF2,missense_variant,p.Ala365Pro,ENST00000633077,;CELF2-AS1,downstream_gene_variant,,ENST00000379256,;CELF2,3_prime_UTR_variant,,ENST00000609870,;CELF2,3_prime_UTR_variant,,ENST00000633200,; C ENST00000542579 Transcript missense_variant 1253/7982 1093/1566 365/521 A/P Gca/Cca 1 1 CELF2 HGNC HGNC:2550 protein_coding YES CCDS44355.1 ENSP00000443926 E9PC62 UPI0000F58F21 NM_006561.3 tolerated(0.39) 10/14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 11314255 11314255 G C 1 0 0 0 0 1 0 0 0 2923 985 34 4 4 CELF2 10 11314255 Missense_Mutation SNP G C3N-01414_T 11314255 122483167 253 23453 CUBN 0 . GRCh38 10 16869741 16869741 + Missense_Mutation SNP G G T rs375906166 C3N-01414_T C3N-01414_N G G c.9349C>A p.Arg3117Ser p.R3117S ENST00000377833 59/67 456 360 96 724 724 0 strelka-varscan-mutect CUBN,missense_variant,p.Arg3117Ser,ENST00000377833,NM_001081.3; T ENST00000377833 Transcript missense_variant 9415/11949 9349/10872 3117/3623 R/S Cgc/Agc rs375906166 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 tolerated(0.11) 59/67 PROSITE_profiles:PS01180,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs375906166 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 16869741 16869741 G T 1 0 0 0 0 1 0 0 0 3861 1087 38 1 1 CUBN 10 16869741 Missense_Mutation SNP G C3N-01414_T 5555486 16869741 116927681 254 23454 CUBN 0 . GRCh38 10 16916022 16916022 + Missense_Mutation SNP C C A rs775766640 C3N-01414_T C3N-01414_N C C c.7009G>T p.Gly2337Trp p.G2337W ENST00000377833 46/67 328 256 72 491 491 0 strelka-varscan-mutect CUBN,missense_variant,p.Gly2337Trp,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript missense_variant 7075/11949 7009/10872 2337/3623 G/W Ggg/Tgg rs775766640 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 deleterious(0) 46/67 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF645,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs775766640 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 16916022 16916022 C A 1 0 0 0 0 1 0 0 0 3861 594 21 2 2 CUBN 10 16916022 Missense_Mutation SNP C C3N-01414_T 46281 16916022 116881400 255 23455 CUBN 0 . GRCh38 10 16952339 16952339 + Missense_Mutation SNP G G A rs551594427 C3N-01414_T C3N-01414_N G G c.4906C>T p.Arg1636Trp p.R1636W ENST00000377833 33/67 436 383 53 615 615 0 strelka-varscan-mutect CUBN,missense_variant,p.Arg1636Trp,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript missense_variant 4972/11949 4906/10872 1636/3623 R/W Cgg/Tgg rs551594427,COSM1238618 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 tolerated(0.06) 33/67 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF645,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs551594427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 16952339 16952339 G A 1 0 0 0 0 1 0 0 0 3861 1144 40 1 1 CUBN 10 16952339 Missense_Mutation SNP G C3N-01414_T 36317 16952339 116845083 256 23456 SPAG6 0 . GRCh38 10 22368545 22368545 + Silent SNP T T C novel C3N-01414_T C3N-01414_N T T c.339T>C p.= p.H113H ENST00000376624 4/11 185 157 28 259 259 0 strelka-varscan-mutect SPAG6,synonymous_variant,p.=,ENST00000376603,NM_001253855.1;SPAG6,synonymous_variant,p.=,ENST00000376624,NM_012443.3;SPAG6,synonymous_variant,p.=,ENST00000313311,NM_172242.2;SPAG6,synonymous_variant,p.=,ENST00000538630,NM_001253854.1;SPAG6,synonymous_variant,p.=,ENST00000435326,;SPAG6,intron_variant,,ENST00000456231,;RP11-301N24.3,intron_variant,,ENST00000422675,;SPAG6,intron_variant,,ENST00000488555,; C ENST00000376624 Transcript synonymous_variant 481/2605 339/1530 113/509 H caT/caC 1 1 SPAG6 HGNC HGNC:11215 protein_coding YES CCDS7139.1 ENSP00000365811 O75602 A0A140VJU9 UPI0000073ED7 NM_012443.3 4/11 hmmpanther:PTHR23314:SF1,hmmpanther:PTHR23314,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 22368545 22368545 T C 1 0 0 0 0 0 0 0 1 15313 1490 52 5 5 SPAG6 10 22368545 Silent SNP T C3N-01414_T 5416206 22368545 111428877 257 23457 PARD3 0 . GRCh38 10 34111526 34111526 + Missense_Mutation SNP G G C C3N-01414_T C3N-01414_N G G c.3714C>G p.Asp1238Glu p.D1238E ENST00000374789 25/25 58 53 5 67 67 0 strelka-varscan-mutect PARD3,missense_variant,p.Asp1238Glu,ENST00000374789,NM_019619.3;PARD3,missense_variant,p.Asp1235Glu,ENST00000374788,NM_001184785.1;PARD3,missense_variant,p.Asp1222Glu,ENST00000545693,NM_001184786.1;PARD3,missense_variant,p.Asp1201Glu,ENST00000346874,NM_001184787.1;PARD3,missense_variant,p.Asp1192Glu,ENST00000350537,NM_001184789.1,NM_001184788.1;PARD3,missense_variant,p.Asp1178Glu,ENST00000374790,;PARD3,missense_variant,p.Asp1148Glu,ENST00000545260,NM_001184790.1;PARD3,missense_variant,p.Asp1126Glu,ENST00000374794,NM_001184791.1; C ENST00000374789 Transcript missense_variant 4040/6005 3714/4071 1238/1356 D/E gaC/gaG COSM427519 1 -1 PARD3 HGNC HGNC:16051 protein_coding YES CCDS7178.1 ENSP00000363921 Q8TEW0 UPI0000073A9F NM_019619.3 deleterious_low_confidence(0.04) 25/25 hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF10 1 MODERATE 1 SNV 1 1 1 PASS rs1228264244 . 0 204 6 0 0 0 0 0 -11.91003 0.9999998 1 1 1 0 C 3 2 77 34111526 34111526 G C 1 0 0 0 0 1 0 0 0 11523 1020 36 4 4 PARD3 10 34111526 Missense_Mutation SNP G C3N-01414_T 11742981 34111526 99685896 258 23458 ANKRD30A 0 . GRCh38 10 37166669 37166669 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1961T>A p.Ile654Lys p.I654K ENST00000361713 19/36 82 64 18 104 104 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Ile654Lys,ENST00000374660,;ANKRD30A,missense_variant,p.Ile710Lys,ENST00000611781,;ANKRD30A,missense_variant,p.Ile654Lys,ENST00000361713,NM_052997.2;ANKRD30A,intron_variant,,ENST00000602533,; A ENST00000361713 Transcript missense_variant 2060/4405 1961/4026 654/1341 I/K aTa/aAa 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.93) 19/36 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 37166669 37166669 T A 1 0 0 0 0 1 0 0 0 761 1406 49 4 4 ANKRD30A 10 37166669 Missense_Mutation SNP T C3N-01414_T 3055143 37166669 96630753 259 23459 ZNF22 0 . GRCh38 10 45004039 45004039 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.671G>T p.Arg224Leu p.R224L ENST00000298299 2/2 95 76 19 101 100 1 strelka-varscan-mutect ZNF22,missense_variant,p.Arg224Leu,ENST00000298299,NM_006963.4;C10orf25,upstream_gene_variant,,ENST00000625168,;CEP164P1,non_coding_transcript_exon_variant,,ENST00000456938,; T ENST00000298299 Transcript missense_variant 1264/2551 671/675 224/224 R/L cGt/cTt COSM5473015 1 1 ZNF22 HGNC HGNC:13012 protein_coding YES CCDS7211.1 ENSP00000298299 P17026 A0A024R7T4 UPI0000001C08 NM_006963.4 deleterious_low_confidence(0) 2/2 1 MODERATE 1 SNV 1 1 1 PASS rs1311422923 . 0 199 10 0 0 0 0 0 -20 0.99999 1 1 1 0 T 3 4 77 45004039 45004039 G T 1 0 0 0 0 1 0 0 0 18351 1145 40 1 1 ZNF22 10 45004039 Missense_Mutation SNP G C3N-01414_T 7837370 45004039 88793383 260 23460 ZFAND4 0 . GRCh38 10 45618147 45618147 + Missense_Mutation SNP C C G rs373664927 C3N-01414_T C3N-01414_N C C c.2041G>C p.Glu681Gln p.E681Q ENST00000344646 9/10 124 90 34 242 242 0 strelka-varscan-mutect ZFAND4,missense_variant,p.Glu607Gln,ENST00000374366,NM_001282906.1,NM_001282905.1;ZFAND4,missense_variant,p.Glu681Gln,ENST00000344646,NM_001128324.2,NM_174890.3;ZFAND4,3_prime_UTR_variant,,ENST00000374371,;ZFAND4,non_coding_transcript_exon_variant,,ENST00000374370,;ZFAND4,non_coding_transcript_exon_variant,,ENST00000484333,; G ENST00000344646 Transcript missense_variant 2257/3241 2041/2184 681/727 E/Q Gaa/Caa rs373664927 1 -1 ZFAND4 HGNC HGNC:23504 protein_coding YES CCDS7214.1 ENSP00000339484 Q86XD8 A0A024R7V9 UPI0000161363 NM_001128324.2,NM_174890.3 deleterious(0.03) 9/10 Gene3D:4.10.1110.10,Pfam_domain:PF01428,PROSITE_profiles:PS51039,hmmpanther:PTHR10666,hmmpanther:PTHR10666:SF109,SMART_domains:SM00154,Superfamily_domains:SSF118310 MODERATE 1 SNV 1 1 PASS rs373664927 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 45618147 45618147 C G 1 0 0 0 0 1 0 0 0 18206 893 31 4 4 ZFAND4 10 45618147 Missense_Mutation SNP C C3N-01414_T 614108 45618147 88179275 261 23461 WDFY4 0 . GRCh38 10 48786707 48786707 + Silent SNP T T C novel C3N-01414_T C3N-01414_N T T c.3645T>C p.= p.Y1215Y ENST00000325239 19/61 312 240 72 461 461 0 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1; C ENST00000325239 Transcript synonymous_variant 3645/9555 3645/9555 1215/3184 Y taT/taC 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 19/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 48786707 48786707 T C 1 0 0 0 0 0 0 0 1 17831 1471 51 5 5 WDFY4 10 48786707 Silent SNP T C3N-01414_T 3168560 48786707 85010715 262 23462 FAM170B 0 . GRCh38 10 49131955 49131955 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.510G>T p.Lys170Asn p.K170N ENST00000311787 2/2 266 204 62 392 392 0 strelka-varscan-mutect FAM170B,missense_variant,p.Lys170Asn,ENST00000311787,NM_001164484.1;FAM170B-AS1,intron_variant,,ENST00000442525,;FAM170B-AS1,intron_variant,,ENST00000443389,;FAM170B-AS1,intron_variant,,ENST00000435809,; A ENST00000311787 Transcript missense_variant 600/1401 510/852 170/283 K/N aaG/aaT 1 -1 FAM170B HGNC HGNC:19736 protein_coding YES CCDS53536.1 ENSP00000308292 A6NMN3 UPI00001C1ED8 NM_001164484.1 tolerated(0.09) 2/2 hmmpanther:PTHR33517,hmmpanther:PTHR33517:SF2 MODERATE 1 SNV 1 1 PASS rs1175942636 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 49131955 49131955 C A 1 0 0 0 0 1 0 0 0 5336 912 32 2 2 FAM170B 10 49131955 Missense_Mutation SNP C C3N-01414_T 345248 49131955 84665467 263 23463 PSAP 0 . GRCh38 10 71834380 71834380 + Missense_Mutation SNP G G T rs754702748 C3N-01414_T C3N-01414_N G G c.166C>A p.Pro56Thr p.P56T ENST00000394936 2/14 356 334 22 557 556 1 strelka-varscan-mutect PSAP,missense_variant,p.Pro56Thr,ENST00000394936,NM_002778.2,NM_001042465.1,NM_001042466.1;PSAP,missense_variant,p.Pro56Thr,ENST00000394934,;PSAP,missense_variant,p.Pro56Thr,ENST00000610929,; T ENST00000394936 Transcript missense_variant 320/2872 166/1575 56/524 P/T Cca/Aca rs754702748 1 -1 PSAP HGNC HGNC:9498 protein_coding YES CCDS7311.1 ENSP00000378394 P07602 A0A024QZQ2 UPI0000000DBF NM_002778.2,NM_001042465.1,NM_001042466.1 deleterious(0) 2/14 PROSITE_profiles:PS51110,hmmpanther:PTHR11480,hmmpanther:PTHR11480:SF36,PIRSF_domain:PIRSF002431,Prints_domain:PR01797 MODERATE 1 SNV 1 1 PASS rs754702748 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 71834380 71834380 G T 1 0 0 0 0 1 0 0 0 12793 1203 42 2 2 PSAP 10 71834380 Missense_Mutation SNP G C3N-01414_T 22702425 71834380 61963042 264 23464 FAM149B1 0 . GRCh38 10 73235205 73235205 + Missense_Mutation SNP G G A rs571636458 C3N-01414_T C3N-01414_N G G c.1489G>A p.Asp497Asn p.D497N ENST00000242505 12/14 182 167 15 281 281 0 strelka-varscan-mutect FAM149B1,missense_variant,p.Asp497Asn,ENST00000242505,NM_173348.1;FAM149B1,missense_variant,p.Asp430Asn,ENST00000372955,;FAM149B1,intron_variant,,ENST00000445951,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000470798,;DNAJC9,intron_variant,,ENST00000469143,;FAM149B1,downstream_gene_variant,,ENST00000607940,;DNAJC9,downstream_gene_variant,,ENST00000453189,;FAM149B1,3_prime_UTR_variant,,ENST00000475829,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000468462,;FAM149B1,non_coding_transcript_exon_variant,,ENST00000466261,; A ENST00000242505 Transcript missense_variant 1663/5408 1489/1749 497/582 D/N Gac/Aac rs571636458,COSM1206129 1 1 FAM149B1 HGNC HGNC:29162 protein_coding YES CCDS44435.1 ENSP00000242505 Q96BN6 UPI00001617A8 NM_173348.1 tolerated(0.7) 12/14 hmmpanther:PTHR31997,hmmpanther:PTHR31997:SF0 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs571636458 . 0 208 0 2 0 0 0 0 -19.70232 0.9999998 1 1 1 0 A 3 1 77 73235205 73235205 G A 1 0 0 0 0 1 0 0 0 5305 1058 37 1 1 FAM149B1 10 73235205 Missense_Mutation SNP G C3N-01414_T 1400825 73235205 60562217 265 23465 LRIT2 0 . GRCh38 10 84224869 84224869 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.356C>A p.Pro119Gln p.P119Q ENST00000538192 2/4 297 226 71 446 446 0 strelka-varscan-mutect LRIT2,missense_variant,p.Pro119Gln,ENST00000538192,NM_001284223.1;LRIT2,missense_variant,p.Pro119Gln,ENST00000372113,NM_001017924.3; T ENST00000538192 Transcript missense_variant 425/3177 356/1683 119/560 P/Q cCa/cAa 1 -1 LRIT2 HGNC HGNC:23443 protein_coding YES CCDS60581.1 ENSP00000438264 A6NDA9 UPI000189A8DA NM_001284223.1 deleterious(0) 2/4 PROSITE_profiles:PS51450,hmmpanther:PTHR24365:SF93,hmmpanther:PTHR24365,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 84224869 84224869 G T 1 0 0 0 0 1 0 0 0 8843 1348 47 2 2 LRIT2 10 84224869 Missense_Mutation SNP G C3N-01414_T 10989664 84224869 49572553 266 23466 TNKS2 0 . GRCh38 10 91840636 91840636 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1603G>T p.Gly535Trp p.G535W ENST00000371627 14/27 202 162 40 368 367 1 strelka-varscan-mutect TNKS2,missense_variant,p.Gly535Trp,ENST00000371627,NM_025235.3; T ENST00000371627 Transcript missense_variant 1982/6157 1603/3501 535/1166 G/W Ggg/Tgg 1 1 TNKS2 HGNC HGNC:15677 protein_coding YES CCDS7417.1 ENSP00000360689 Q9H2K2 UPI00000362BE NM_025235.3 deleterious(0.03) 14/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24180,hmmpanther:PTHR24180:SF11,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 91840636 91840636 G T 1 0 0 0 0 1 0 0 0 16794 1348 47 2 2 TNKS2 10 91840636 Missense_Mutation SNP G C3N-01414_T 7615767 91840636 41956786 267 23467 CYP2C18 0 . GRCh38 10 94735439 94735439 + Missense_Mutation SNP G G C rs764785028 C3N-01414_T C3N-01414_N G G c.1468G>C p.Val490Leu p.V490L ENST00000285979 9/9 134 105 29 186 186 0 strelka-varscan-mutect CYP2C18,missense_variant,p.Val490Leu,ENST00000285979,NM_000772.2;CYP2C18,missense_variant,p.Val431Leu,ENST00000339022,NM_001128925.1;RP11-400G3.5,intron_variant,,ENST00000464755,; C ENST00000285979 Transcript missense_variant 1667/2418 1468/1473 490/490 V/L Gtc/Ctc rs764785028 1 1 CYP2C18 HGNC HGNC:2620 protein_coding YES CCDS7435.1 ENSP00000285979 P33260 UPI000013DE1D NM_000772.2 tolerated_low_confidence(0.11) 9/9 hmmpanther:PTHR24300:SF123,hmmpanther:PTHR24300 MODERATE 1 SNV 1 1 PASS rs764785028 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 94735439 94735439 G C 1 0 0 0 0 1 0 0 0 3968 1377 48 4 4 CYP2C18 10 94735439 Missense_Mutation SNP G C3N-01414_T 2894803 94735439 39061983 268 23468 SORBS1 0 . GRCh38 10 95339134 95339134 + Missense_Mutation SNP T T A rs755805022 C3N-01414_T C3N-01414_N T T c.2864A>T p.Gln955Leu p.Q955L ENST00000371247 29/33 41 32 9 82 81 1 strelka-varscan-mutect SORBS1,missense_variant,p.Gln955Leu,ENST00000371247,;SORBS1,missense_variant,p.Gln909Leu,ENST00000371227,NM_001290294.1;SORBS1,missense_variant,p.Gln977Leu,ENST00000371246,;SORBS1,missense_variant,p.Gln737Leu,ENST00000371249,NM_015385.3;SORBS1,missense_variant,p.Gln702Leu,ENST00000306402,NM_024991.2,NM_001290295.1;SORBS1,missense_variant,p.Gln1215Leu,ENST00000607232,;SORBS1,missense_variant,p.Gln955Leu,ENST00000361941,NM_001034954.1;SORBS1,missense_variant,p.Gln977Leu,ENST00000277982,NM_001034955.1;SORBS1,missense_variant,p.Gln925Leu,ENST00000354106,NM_001290296.1,NM_001290298.1;SORBS1,missense_variant,p.Gln806Leu,ENST00000371245,NM_001034956.1;SORBS1,missense_variant,p.Gln732Leu,ENST00000371239,NM_001290297.1;SORBS1,missense_variant,p.Gln605Leu,ENST00000371241,NM_006434.2,NM_001034957.1;SORBS1,missense_variant,p.Gln428Leu,ENST00000634504,;SORBS1,downstream_gene_variant,,ENST00000371228,;SORBS1,downstream_gene_variant,,ENST00000474353,; A ENST00000371247 Transcript missense_variant,splice_region_variant 3054/7354 2864/3879 955/1292 Q/L cAg/cTg rs755805022 1 -1 SORBS1 HGNC HGNC:14565 protein_coding YES CCDS31255.1 ENSP00000360293 Q9BX66 UPI000013D6B7 deleterious(0) 29/33 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF202 MODERATE 1 SNV 5 1 PASS rs755805022 . 0 199 11 0 0 0 0 0 -19.99676 0.9999813 1 1 1 0 A 3 1 77 95339134 95339134 T A 1 0 0 0 0 1 0 0 0 15249 1594 55 4 4 SORBS1 10 95339134 Missense_Mutation SNP T C3N-01414_T 603695 95339134 38458288 269 23469 CPN1 0 . GRCh38 10 100069755 100069755 + Missense_Mutation SNP G G T rs754172095 C3N-01414_T C3N-01414_N G G c.535C>A p.Pro179Thr p.P179T ENST00000370418 3/9 344 244 100 488 487 1 strelka-varscan-mutect CPN1,missense_variant,p.Pro179Thr,ENST00000370418,NM_001308.2;CPN1,upstream_gene_variant,,ENST00000441382,; T ENST00000370418 Transcript missense_variant 787/1863 535/1377 179/458 P/T Ccc/Acc rs754172095 1 -1 CPN1 HGNC HGNC:2312 protein_coding YES CCDS7486.1 ENSP00000359446 P15169 UPI00000012AC NM_001308.2 tolerated(0.07) 3/9 hmmpanther:PTHR11532:SF7,hmmpanther:PTHR11532,Gene3D:3.40.630.10,Pfam_domain:PF00246,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs754172095 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 100069755 100069755 G T 1 0 0 0 0 1 0 0 0 3604 1232 43 2 2 CPN1 10 100069755 Missense_Mutation SNP G C3N-01414_T 4730621 100069755 33727667 270 23470 EBF3 0 . GRCh38 10 129963705 129963705 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.64A>T p.Ser22Cys p.S22C ENST00000368648 1/16 284 233 51 399 399 0 strelka-varscan-mutect EBF3,missense_variant,p.Ser22Cys,ENST00000368648,NM_001005463.2;EBF3,missense_variant,p.Ser22Cys,ENST00000355311,; A ENST00000368648 Transcript missense_variant 137/4375 64/1656 22/551 S/C Agc/Tgc 1 -1 EBF3 HGNC HGNC:19087 protein_coding YES CCDS31314.1 ENSP00000357637 Q9H4W6 UPI000002A6FB NM_001005463.2 deleterious_low_confidence(0) 1/16 Pfam_domain:PF16422,hmmpanther:PTHR10747 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 129963705 129963705 T A 1 0 0 0 0 1 0 0 0 4706 1580 55 4 4 EBF3 10 129963705 Missense_Mutation SNP T C3N-01414_T 29893950 129963705 3833717 271 23471 CFAP46 0 . GRCh38 10 132814907 132814907 + Silent SNP G G T rs777783771 C3N-01414_T C3N-01414_N G G c.7125C>A p.= p.G2375G ENST00000368586 51/58 158 127 31 235 233 2 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript synonymous_variant 7226/8278 7125/8148 2375/2715 G ggC/ggA rs777783771,COSM3769008,COSM3769009 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 51/58 Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs777783771 . 0 200 0 6 4 0 0 0 -18.49356 0.675531 1 1 1 0 T 2 4 77 132814907 132814907 G T 1 0 0 0 0 0 0 0 1 3021 1074 38 1 1 CFAP46 10 132814907 Silent SNP G C3N-01414_T 2851202 132814907 982515 272 23472 VENTX 0 . GRCh38 10 133238070 133238070 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.156C>A p.= p.S52S ENST00000325980 1/3 194 151 43 228 228 0 strelka-varscan-mutect VENTX,synonymous_variant,p.=,ENST00000325980,NM_014468.3; A ENST00000325980 Transcript synonymous_variant 667/2911 156/777 52/258 S tcC/tcA 1 1 VENTX HGNC HGNC:13639 protein_coding YES CCDS7675.1 ENSP00000357556 O95231 UPI0000070A25 NM_014468.3 1/3 LOW 1 SNV 1 1 PASS rs749870314 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 133238070 133238070 C A 1 0 0 0 0 0 0 0 1 17699 639 23 1 1 VENTX 10 133238070 Silent SNP C C3N-01414_T 423163 133238070 559352 273 23473 MUC5AC 0 . GRCh38 11 1163908 1163908 + Missense_Mutation SNP G G T rs775060592 C3N-01414_T C3N-01414_N G G c.706G>T p.Gly236Trp p.G236W ENST00000621226 7/49 260 174 86 368 367 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Gly236Trp,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript missense_variant 753/17448 706/16965 236/5654 G/W Ggg/Tgg rs775060592 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0) 7/49 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291 MODERATE 1 SNV 5 1 PASS rs775060592 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 1163908 1163908 G T 1 0 0 0 0 1 0 0 0 9978 1116 39 1 1 MUC5AC 11 1163908 Missense_Mutation SNP G C3N-01414_T 1163908 133922714 274 23474 MUC5B 0 . GRCh38 11 1225734 1225734 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.124G>A p.Gly42Ser p.G42S ENST00000529681 2/49 101 71 30 140 140 0 strelka-varscan-mutect MUC5B,missense_variant,p.Gly42Ser,ENST00000529681,NM_002458.2;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;MUC5B,upstream_gene_variant,,ENST00000531082,; A ENST00000529681 Transcript missense_variant 182/17911 124/17289 42/5762 G/S Ggc/Agc 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.39) 2/49 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 1225734 1225734 G A 1 0 0 0 0 1 0 0 0 9979 1362 47 3 3 MUC5B 11 1225734 Missense_Mutation SNP G C3N-01414_T 61826 1225734 133860888 275 23475 MUC5B 0 . GRCh38 11 1232461 1232461 + Silent SNP C C A rs56411917 C3N-01414_T C3N-01414_N C C c.1855C>A p.= p.R619R ENST00000529681 16/49 140 100 40 192 192 0 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;MUC5B,non_coding_transcript_exon_variant,,ENST00000525715,;MUC5B,downstream_gene_variant,,ENST00000531082,; A ENST00000529681 Transcript synonymous_variant 1913/17911 1855/17289 619/5762 R Cgg/Agg rs56411917 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 16/49 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF269,SMART_domains:SM00832 LOW 1 SNV 5 1 PASS rs56411917 . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 1232461 1232461 C A 1 0 0 0 0 0 0 0 1 9979 643 23 1 1 MUC5B 11 1232461 Silent SNP C C3N-01414_T 6727 1232461 133854161 276 23476 MUC5B 0 . GRCh38 11 1250376 1250376 + Missense_Mutation SNP C C G C3N-01414_T C3N-01414_N C C c.13496C>G p.Ser4499Cys p.S4499C ENST00000529681 31/49 613 550 63 772 772 0 strelka-varscan-mutect MUC5B,missense_variant,p.Ser4499Cys,ENST00000529681,NM_002458.2;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,; G ENST00000529681 Transcript missense_variant 13554/17911 13496/17289 4499/5762 S/C tCc/tGc COSM3967404,COSM3967405 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 deleterious(0.02) 31/49 Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 1250376 1250376 C G 1 0 0 0 0 1 0 0 0 9979 855 30 4 4 MUC5B 11 1250376 Missense_Mutation SNP C C3N-01414_T 17915 1250376 133836246 277 23477 OR51S1 0 . GRCh38 11 4848685 4848685 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.524C>A p.Pro175His p.P175H ENST00000322101 1/1 146 110 36 178 178 0 strelka-varscan-mutect OR51S1,missense_variant,p.Pro175His,ENST00000322101,NM_001004758.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322101 Transcript missense_variant 524/972 524/972 175/323 P/H cCc/cAc COSM3448151 1 -1 OR51S1 HGNC HGNC:15204 protein_coding YES CCDS31362.1 ENSP00000322754 Q8NGJ8 A0A126GWN3 UPI0000041C33 NM_001004758.1 tolerated(0.12) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF73,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 4848685 4848685 G T 1 0 0 0 0 1 0 0 0 11179 1232 43 2 2 OR51S1 11 4848685 Missense_Mutation SNP G C3N-01414_T 3598309 4848685 130237937 278 23478 OR52J3 0 . GRCh38 11 5046884 5046884 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.359T>C p.Met120Thr p.M120T ENST00000380370 1/1 191 121 70 265 265 0 strelka-varscan-mutect OR52J3,missense_variant,p.Met120Thr,ENST00000380370,NM_001001916.2; C ENST00000380370 Transcript missense_variant 359/936 359/936 120/311 M/T aTg/aCg 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 5046884 5046884 T C 1 0 0 0 0 1 0 0 0 11195 1464 51 5 5 OR52J3 11 5046884 Missense_Mutation SNP T C3N-01414_T 198199 5046884 130039738 279 23479 UBQLNL 0 . GRCh38 11 5516414 5516414 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.28A>T p.Arg10Trp p.R10W ENST00000380184 1/1 92 69 23 113 113 0 strelka-varscan-mutect UBQLNL,missense_variant,p.Arg10Trp,ENST00000380184,NM_145053.4;HBG2,intron_variant,,ENST00000380259,;OLFM5P,downstream_gene_variant,,ENST00000411807,; A ENST00000380184 Transcript missense_variant 292/2313 28/1428 10/475 R/W Agg/Tgg 1 -1 UBQLNL HGNC HGNC:28294 protein_coding YES CCDS31385.1 ENSP00000369531 Q8IYU4 UPI000066D8EC NM_145053.4 deleterious(0) 1/1 Superfamily_domains:SSF54236 MODERATE SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 5516414 5516414 T A 1 0 0 0 0 1 0 0 0 17424 1579 55 4 4 UBQLNL 11 5516414 Missense_Mutation SNP T C3N-01414_T 469530 5516414 129570208 280 23480 OR56A5 0 . GRCh38 11 5967633 5967633 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.862C>T p.Pro288Ser p.P288S ENST00000532411 1/1 148 107 41 253 253 0 strelka-varscan-mutect OR56A5,missense_variant,p.Pro288Ser,ENST00000532411,NM_001146033.1;OR56A5,missense_variant,p.Pro220Ser,ENST00000340110,; A ENST00000532411 Transcript missense_variant 862/942 862/942 288/313 P/S Cca/Tca 1 -1 OR56A5 HGNC HGNC:14792 protein_coding YES CCDS73248.1 ENSP00000481594 P0C7T3 A0A126GWP3 UPI00006C10F9 NM_001146033.1 deleterious(0.04) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF60,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 5967633 5967633 G A 1 0 0 0 0 1 0 0 0 11208 1232 43 3 3 OR56A5 11 5967633 Missense_Mutation SNP G C3N-01414_T 451219 5967633 129118989 281 23481 CCKBR 0 . GRCh38 11 6270698 6270698 + Missense_Mutation SNP G G A C3N-01414_T C3N-01414_N G G c.706G>A p.Val236Met p.V236M ENST00000334619 4/5 85 76 9 146 146 0 strelka-varscan-mutect CCKBR,missense_variant,p.Val236Met,ENST00000525462,;CCKBR,missense_variant,p.Val236Met,ENST00000334619,NM_176875.3;CCKBR,missense_variant,p.Val152Met,ENST00000532715,;CCKBR,downstream_gene_variant,,ENST00000525014,;CCKBR,downstream_gene_variant,,ENST00000531712,;CCKBR,upstream_gene_variant,,ENST00000532396,; A ENST00000334619 Transcript missense_variant 899/2121 706/1344 236/447 V/M Gtg/Atg COSM179422,COSM290358 1 1 CCKBR HGNC HGNC:1571 protein_coding YES CCDS7761.1 ENSP00000335544 P32239 UPI0000000C18 NM_176875.3 tolerated(0.05) 4/5 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF45,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 194 14 2 0 0 0 0 -14.79087 0.9940503 1 1 1 0 A 3 1 77 6270698 6270698 G A 1 0 0 0 0 1 0 0 0 2579 1145 40 1 1 CCKBR 11 6270698 Missense_Mutation SNP G C3N-01414_T 303065 6270698 128815924 282 23482 OR2AG1 0 . GRCh38 11 6785287 6785287 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.250G>A p.Asp84Asn p.D84N ENST00000307401 1/1 169 114 55 281 281 0 strelka-varscan-mutect OR2AG1,missense_variant,p.Asp84Asn,ENST00000307401,NM_001004489.2; A ENST00000307401 Transcript missense_variant 271/998 250/951 84/316 D/N Gac/Aac 1 1 OR2AG1 HGNC HGNC:15142 protein_coding YES CCDS31414.1 ENSP00000307447 Q9H205 A0A126GVD0 UPI00000015AF NM_001004489.2 tolerated(0.11) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF267,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 6785287 6785287 G A 1 0 0 0 0 1 0 0 0 11061 1174 41 3 3 OR2AG1 11 6785287 Missense_Mutation SNP G C3N-01414_T 514589 6785287 128301335 283 23483 ZNF214 0 . GRCh38 11 7000897 7000897 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.786G>T p.Leu262Phe p.L262F ENST00000278314 3/3 199 149 50 241 240 1 strelka-varscan-mutect ZNF214,missense_variant,p.Leu262Phe,ENST00000278314,NM_013249.2;ZNF214,missense_variant,p.Leu262Phe,ENST00000536068,;ZNF214,downstream_gene_variant,,ENST00000531083,;ZNF215,3_prime_UTR_variant,,ENST00000636606,; A ENST00000278314 Transcript missense_variant 1102/2681 786/1821 262/606 L/F ttG/ttT 1 -1 ZNF214 HGNC HGNC:13006 protein_coding YES CCDS31418.1 ENSP00000278314 Q9UL59 UPI000013DB6B NM_013249.2 tolerated(0.23) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF54,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 7000897 7000897 C A 1 0 0 0 0 1 0 0 0 18347 477 17 2 2 ZNF214 11 7000897 Missense_Mutation SNP C C3N-01414_T 215610 7000897 128085725 284 23484 NLRP14 0 . GRCh38 11 7049793 7049794 + Frame_Shift_Del DEL TG TG - novel C3N-01414_T C3N-01414_N TG TG c.2250_2251delTG p.Cys750Ter p.C750* ENST00000299481 6/12 358 242 116 479 479 0 sindel-varindel NLRP14,frameshift_variant,p.Cys750Ter,ENST00000299481,NM_176822.3; - ENST00000299481 Transcript frameshift_variant 2592-2593/3628 2246-2247/3282 749/1093 L/X tTG/t 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 6/12 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF154,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 HIGH 1 deletion 5 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 7049793 7049793 TG - 1 0 1 0 1 0 0 0 0 10513 1821 63 0 0 NLRP14 11 7049793 Frame_Shift_Del DEL TG C3N-01414_T 48896 7049793 128036829 285 23485 NLRP10 0 . GRCh38 11 7959879 7959879 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1733G>C p.Gly578Ala p.G578A ENST00000328600 2/2 220 177 43 355 355 0 strelka-varscan-mutect NLRP10,missense_variant,p.Gly578Ala,ENST00000328600,NM_176821.3;NLRP10,downstream_gene_variant,,ENST00000526590,; G ENST00000328600 Transcript missense_variant 1895/2350 1733/1968 578/655 G/A gGt/gCt 1 -1 NLRP10 HGNC HGNC:21464 protein_coding YES CCDS7784.1 ENSP00000327763 Q86W26 UPI0000167F6C NM_176821.3 tolerated(0.13) 2/2 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF142 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 7959879 7959879 C G 1 0 0 0 0 1 0 0 0 10509 507 18 4 4 NLRP10 11 7959879 Missense_Mutation SNP C C3N-01414_T 910086 7959879 127126743 286 23486 ST5 0 . GRCh38 11 8712678 8712678 + Missense_Mutation SNP C C T rs779020998 C3N-01414_T C3N-01414_N C C c.2045G>A p.Arg682His p.R682H ENST00000534127 12/23 136 129 7 177 177 0 strelka-varscan-mutect ST5,missense_variant,p.Arg682His,ENST00000534127,NM_005418.3;ST5,missense_variant,p.Arg682His,ENST00000313726,NM_213618.1;ST5,missense_variant,p.Arg154His,ENST00000530991,;ST5,missense_variant,p.Arg262His,ENST00000526757,NM_139157.2;ST5,missense_variant,p.Arg262His,ENST00000530438,;ST5,missense_variant,p.Arg195His,ENST00000526099,;ST5,missense_variant,p.Arg154His,ENST00000533020,;ST5,missense_variant,p.Arg292His,ENST00000626808,;ST5,missense_variant,p.Arg154His,ENST00000528527,;ST5,missense_variant,p.Arg139His,ENST00000530593,;ST5,upstream_gene_variant,,ENST00000534278,;ST5,downstream_gene_variant,,ENST00000526057,;ST5,downstream_gene_variant,,ENST00000528196,;ST5,downstream_gene_variant,,ENST00000530580,;ST5,downstream_gene_variant,,ENST00000527510,;ST5,downstream_gene_variant,,ENST00000531060,;RPL27A,intron_variant,,ENST00000531102,;ST5,downstream_gene_variant,,ENST00000533425,;ST5,upstream_gene_variant,,ENST00000526837,;ST5,missense_variant,p.Arg292His,ENST00000532734,;ST5,missense_variant,p.Arg15His,ENST00000530338,;ST5,intron_variant,,ENST00000530559,;ST5,upstream_gene_variant,,ENST00000526701,; T ENST00000534127 Transcript missense_variant 2431/4545 2045/3414 682/1137 R/H cGc/cAc rs779020998,COSM5485528 1 -1 ST5 HGNC HGNC:11350 protein_coding YES CCDS7791.1 ENSP00000433528 P78524 UPI00001AECB8 NM_005418.3 tolerated(0.12) 12/23 hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779020998 . 0 203 3 4 0 0 0 0 -9.654663 0.996317 1 1 1 0 T 3 4 77 8712678 8712678 C T 1 0 0 0 0 1 0 0 0 15598 768 27 1 1 ST5 11 8712678 Missense_Mutation SNP C C3N-01414_T 752799 8712678 126373944 287 23487 INSC 0 . GRCh38 11 15245942 15245942 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1642C>A p.Pro548Thr p.P548T ENST00000379554 13/13 172 139 33 232 231 1 strelka-varscan-mutect INSC,missense_variant,p.Pro548Thr,ENST00000379554,NM_001031853.4;INSC,missense_variant,p.Pro535Thr,ENST00000424273,NM_001278314.1;INSC,missense_variant,p.Pro501Thr,ENST00000379556,NM_001042536.2;INSC,missense_variant,p.Pro501Thr,ENST00000530161,NM_001278313.1;INSC,missense_variant,p.Pro459Thr,ENST00000525218,NM_001278316.1;INSC,3_prime_UTR_variant,,ENST00000528567,NM_001278315.1;INSC,non_coding_transcript_exon_variant,,ENST00000447214,;INSC,non_coding_transcript_exon_variant,,ENST00000526102,; A ENST00000379554 Transcript missense_variant 1688/2954 1642/1740 548/579 P/T Cct/Act 1 1 INSC HGNC HGNC:33116 protein_coding YES CCDS41621.1 ENSP00000368872 Q1MX18 UPI0000D63F1D NM_001031853.4 deleterious(0.02) 13/13 hmmpanther:PTHR21386:SF0,hmmpanther:PTHR21386,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 15245942 15245942 C A 1 0 0 0 0 1 0 0 0 7666 623 22 2 2 INSC 11 15245942 Missense_Mutation SNP C C3N-01414_T 6533264 15245942 119840680 288 23488 SAA2 0 . GRCh38 11 18245457 18245457 + Missense_Mutation SNP C C A rs373197707 C3N-01414_T C3N-01414_N C C c.289G>T p.Asp97Tyr p.D97Y ENST00000526900 4/4 217 179 38 343 343 0 strelka-varscan-mutect SAA2,missense_variant,p.Asp97Tyr,ENST00000526900,;SAA2,missense_variant,p.Asp97Tyr,ENST00000529528,;SAA2,missense_variant,p.Asp97Tyr,ENST00000256733,NM_030754.4;SAA2,intron_variant,,ENST00000414546,NM_001127380.2;SAA2,intron_variant,,ENST00000528349,;SAA2-SAA4,intron_variant,,ENST00000524555,NM_001199744.1;SAA2,intron_variant,,ENST00000530400,;RNA5SP333,downstream_gene_variant,,ENST00000363466,; A ENST00000526900 Transcript missense_variant 473/687 289/369 97/122 D/Y Gat/Tat rs373197707,COSM4031900 1 -1 SAA2 HGNC HGNC:10514 protein_coding YES CCDS7833.1 ENSP00000436126 P0DJI9 UPI000016A553 deleterious(0) 4/4 hmmpanther:PTHR23424:SF7,hmmpanther:PTHR23424,PIRSF_domain:PIRSF002472,Pfam_domain:PF00277,SMART_domains:SM00197 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs373197707 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 18245457 18245457 C A 1 0 0 0 0 1 0 0 0 14058 884 31 1 1 SAA2 11 18245457 Missense_Mutation SNP C C3N-01414_T 2999515 18245457 116841165 289 23489 SLC6A5 0 . GRCh38 11 20636307 20636307 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1625G>T p.Gly542Val p.G542V ENST00000525748 11/16 503 333 170 573 573 0 strelka-varscan-mutect SLC6A5,missense_variant,p.Gly542Val,ENST00000525748,NM_004211.3;SLC6A5,splice_region_variant,,ENST00000528440,;SLC6A5,splice_region_variant,,ENST00000298923,; T ENST00000525748 Transcript missense_variant,splice_region_variant 1898/7084 1625/2394 542/797 G/V gGg/gTg 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 tolerated(0.07) 11/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 20636307 20636307 G T 1 0 0 0 0 1 0 0 0 14970 1246 43 2 2 SLC6A5 11 20636307 Missense_Mutation SNP G C3N-01414_T 2390850 20636307 114450315 290 23490 ANO5 0 . GRCh38 11 22250368 22250368 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1010G>T p.Ser337Ile p.S337I ENST00000324559 10/22 182 128 54 268 268 0 strelka-varscan-mutect ANO5,missense_variant,p.Ser337Ile,ENST00000324559,NM_001142649.1,NM_213599.2; T ENST00000324559 Transcript missense_variant 1327/6651 1010/2742 337/913 S/I aGc/aTc 1 1 ANO5 HGNC HGNC:27337 protein_coding YES CCDS31444.1 ENSP00000315371 Q75V66 UPI000035B19B NM_001142649.1,NM_213599.2 tolerated(0.39) 10/22 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF04547 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 22250368 22250368 G T 1 0 0 0 0 1 0 0 0 807 985 34 2 2 ANO5 11 22250368 Missense_Mutation SNP G C3N-01414_T 1614061 22250368 112836254 291 23491 ANO5 0 . GRCh38 11 22272935 22272935 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.2181A>T p.= p.I727I ENST00000324559 19/22 330 246 84 483 483 0 strelka-varscan-mutect ANO5,synonymous_variant,p.=,ENST00000324559,NM_001142649.1,NM_213599.2;ANO5,non_coding_transcript_exon_variant,,ENST00000532043,; T ENST00000324559 Transcript synonymous_variant 2498/6651 2181/2742 727/913 I atA/atT 1 1 ANO5 HGNC HGNC:27337 protein_coding YES CCDS31444.1 ENSP00000315371 Q75V66 UPI000035B19B NM_001142649.1,NM_213599.2 19/22 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF23,Pfam_domain:PF04547 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 22272935 22272935 A T 1 0 0 0 0 0 0 0 1 807 410 15 4 4 ANO5 11 22272935 Silent SNP A C3N-01414_T 22567 22272935 112813687 292 23492 SLC17A6 0 . GRCh38 11 22374859 22374859 + Silent SNP G G C rs117003321 C3N-01414_T C3N-01414_N G G c.1146G>C p.= p.T382T ENST00000263160 9/12 109 93 16 193 193 0 strelka-varscan-mutect SLC17A6,synonymous_variant,p.=,ENST00000263160,NM_020346.2; C ENST00000263160 Transcript synonymous_variant 1583/3949 1146/1749 382/582 T acG/acC rs117003321 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 9/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS rs117003321 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 77 22374859 22374859 G C 1 0 0 0 0 0 0 0 1 14686 1045 37 4 4 SLC17A6 11 22374859 Silent SNP G C3N-01414_T 101924 22374859 112711763 293 23493 METTL15 0 . GRCh38 11 28330639 28330639 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1022G>T p.Arg341Ile p.R341I ENST00000407364 7/7 302 282 20 456 456 0 varscan-mutect METTL15,missense_variant,p.Arg341Ile,ENST00000407364,NM_001113528.1;METTL15,3_prime_UTR_variant,,ENST00000406787,NM_001297775.1;METTL15,3_prime_UTR_variant,,ENST00000303459,NM_152636.2;METTL15,3_prime_UTR_variant,,ENST00000451385,;METTL15,intron_variant,,ENST00000532947,;METTL15,intron_variant,,ENST00000634973,;METTL15,intron_variant,,ENST00000634627,;METTL15,downstream_gene_variant,,ENST00000468295,; T ENST00000407364 Transcript missense_variant 1374/4242 1022/1224 341/407 R/I aGa/aTa 1 1 METTL15 HGNC HGNC:26606 protein_coding YES CCDS44559.1 ENSP00000384369 A6NJ78 UPI0000DBEF34 NM_001113528.1 tolerated(0.07) 7/7 HAMAP:MF_01007,Pfam_domain:PF01795,hmmpanther:PTHR11265,hmmpanther:PTHR11265:SF0,TIGRFAM_domain:TIGR00006 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 28330639 28330639 G T 1 0 0 0 0 1 0 0 0 9441 942 33 2 2 METTL15 11 28330639 Missense_Mutation SNP G C3N-01414_T 5955780 28330639 106755983 294 23494 QSER1 0 . GRCh38 11 32933898 32933898 + Silent SNP T T G novel C3N-01414_T C3N-01414_N T T c.2253T>G p.= p.S751S ENST00000399302 4/13 182 139 43 239 238 1 strelka-varscan-mutect QSER1,synonymous_variant,p.=,ENST00000399302,NM_001076786.2;QSER1,synonymous_variant,p.=,ENST00000527788,;QSER1,upstream_gene_variant,,ENST00000524678,;QSER1,downstream_gene_variant,,ENST00000528155,;QSER1,downstream_gene_variant,,ENST00000527250,; G ENST00000399302 Transcript synonymous_variant 2588/9335 2253/5208 751/1735 S tcT/tcG 1 1 QSER1 HGNC HGNC:26154 protein_coding YES CCDS41631.1 ENSP00000382241 Q2KHR3 UPI0000E467AF NM_001076786.2 4/13 hmmpanther:PTHR14709:SF2,hmmpanther:PTHR14709 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 32933898 32933898 T G 1 0 0 0 0 0 0 0 1 13037 1596 56 5 5 QSER1 11 32933898 Silent SNP T C3N-01414_T 4603259 32933898 102152724 295 23495 LMO2 0 . GRCh38 11 33859550 33859550 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.490G>T p.Ala164Ser p.A164S ENST00000257818 6/6 246 196 50 320 320 0 strelka-varscan-mutect LMO2,missense_variant,p.Ala164Ser,ENST00000257818,NM_005574.3;LMO2,missense_variant,p.Ala95Ser,ENST00000395833,NM_001142315.1,NM_001142316.1;LMO2,3_prime_UTR_variant,,ENST00000411482,;LMO2,non_coding_transcript_exon_variant,,ENST00000464025,; A ENST00000257818 Transcript missense_variant 1320/2294 490/684 164/227 A/S Gca/Tca 1 -1 LMO2 HGNC HGNC:6642 protein_coding YES CCDS7888.2 ENSP00000257818 P25791 UPI00001F9F84 NM_005574.3 tolerated(0.23) 6/6 PROSITE_profiles:PS50023,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF109,PROSITE_patterns:PS00478,Pfam_domain:PF00412,Gene3D:2.10.110.10,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS rs1194594724 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 33859550 33859550 C A 1 0 0 0 0 1 0 0 0 8778 768 27 1 1 LMO2 11 33859550 Missense_Mutation SNP C C3N-01414_T 925652 33859550 101227072 296 23496 CHST1 0 . GRCh38 11 45650174 45650174 + Silent SNP C C T rs776340776 C3N-01414_T C3N-01414_N C C c.750G>A p.= p.T250T ENST00000308064 4/4 250 210 40 241 241 0 strelka-varscan-mutect CHST1,synonymous_variant,p.=,ENST00000308064,NM_003654.5;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,upstream_gene_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,; T ENST00000308064 Transcript synonymous_variant 1421/2718 750/1236 250/411 T acG/acA rs776340776 1 -1 CHST1 HGNC HGNC:1969 protein_coding YES CCDS7913.1 ENSP00000309270 O43916 UPI0000073EA0 NM_003654.5 4/4 hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF36,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs776340776 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 77 45650174 45650174 C T 1 0 0 0 0 0 0 0 1 3157 523 19 1 1 CHST1 11 45650174 Silent SNP C C3N-01414_T 11790624 45650174 89436448 297 23497 PHF21A 0 . GRCh38 11 46084197 46084197 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.23A>T p.Glu8Val p.E8V ENST00000418153 3/18 194 154 40 330 330 0 strelka-varscan-mutect PHF21A,missense_variant,p.Glu8Val,ENST00000323180,NM_016621.3;PHF21A,missense_variant,p.Glu8Val,ENST00000418153,NM_001101802.1;PHF21A,missense_variant,p.Glu8Val,ENST00000525438,;PHF21A,missense_variant,p.Glu8Val,ENST00000529734,;PHF21A,missense_variant,p.Glu8Val,ENST00000524497,;PHF21A,missense_variant,p.Glu8Val,ENST00000532010,;PHF21A,missense_variant,p.Glu8Val,ENST00000531959,;PHF21A,missense_variant,p.Glu8Val,ENST00000527782,;PHF21A,missense_variant,p.Glu8Val,ENST00000533757,;PHF21A,5_prime_UTR_variant,,ENST00000529782,;PHF21A,missense_variant,p.Glu8Val,ENST00000532883,; A ENST00000418153 Transcript missense_variant 223/2730 23/2043 8/680 E/V gAg/gTg 1 -1 PHF21A HGNC HGNC:24156 protein_coding YES CCDS44578.1 ENSP00000398824 Q96BD5 UPI000006E1CB NM_001101802.1 deleterious(0) 3/18 hmmpanther:PTHR24102:SF6,hmmpanther:PTHR24102 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 46084197 46084197 T A 1 0 0 0 0 1 0 0 0 11919 1551 54 4 4 PHF21A 11 46084197 Missense_Mutation SNP T C3N-01414_T 434023 46084197 89002425 298 23498 LRP4 0 . GRCh38 11 46899972 46899972 + Silent SNP G G C novel C3N-01414_T C3N-01414_N G G c.321C>G p.= p.P107P ENST00000378623 4/38 317 231 86 397 397 0 strelka-varscan-mutect LRP4,synonymous_variant,p.=,ENST00000378623,NM_002334.3;LRP4,synonymous_variant,p.=,ENST00000534404,; C ENST00000378623 Transcript synonymous_variant 564/8076 321/5718 107/1905 P ccC/ccG 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 4/38 hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF249,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 46899972 46899972 G C 1 0 0 0 0 0 0 0 1 8854 1246 43 4 4 LRP4 11 46899972 Silent SNP G C3N-01414_T 815775 46899972 88186650 299 23499 MTCH2 0 . GRCh38 11 47631704 47631704 + Missense_Mutation SNP C C A rs144753500 C3N-01414_T C3N-01414_N C C c.377G>T p.Arg126Leu p.R126L ENST00000302503 6/13 227 214 13 343 343 0 strelka-varscan-mutect MTCH2,missense_variant,p.Arg126Leu,ENST00000302503,NM_001317231.1,NM_014342.3;MTCH2,missense_variant,p.Arg117Leu,ENST00000530428,;MTCH2,non_coding_transcript_exon_variant,,ENST00000533571,;MTCH2,intron_variant,,ENST00000525649,;MTCH2,intron_variant,,ENST00000539759,;MTCH2,upstream_gene_variant,,ENST00000534074,; A ENST00000302503 Transcript missense_variant 535/2587 377/912 126/303 R/L cGa/cTa rs144753500,COSM3791530 1 -1 MTCH2 HGNC HGNC:17587 protein_coding YES CCDS7943.1 ENSP00000303222 Q9Y6C9 UPI000006E280 NM_001317231.1,NM_014342.3 deleterious(0.04) 6/13 Superfamily_domains:0048588,Gene3D:1okcA00,PROSITE_profiles:PS50920,hmmpanther:PTHR10780,hmmpanther:PTHR10780:SF20 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs144753500 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 47631704 47631704 C A 1 0 0 0 0 1 0 0 0 9899 884 31 1 1 MTCH2 11 47631704 Missense_Mutation SNP C C3N-01414_T 731732 47631704 87454918 300 23500 OR4C12 0 . GRCh38 11 49982202 49982202 + Nonsense_Mutation SNP A A C novel C3N-01414_T C3N-01414_N A A c.300T>G p.Tyr100Ter p.Y100* ENST00000335238 1/1 236 191 45 331 331 0 strelka-varscan-mutect OR4C12,stop_gained,p.Tyr100Ter,ENST00000335238,NM_001005270.4; C ENST00000335238 Transcript stop_gained 334/1063 300/930 100/309 Y/* taT/taG 1 -1 OR4C12 HGNC HGNC:15168 protein_coding YES CCDS31496.1 ENSP00000334418 Q96R67 UPI0000041E30 NM_001005270.4 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF353,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 77 49982202 49982202 A C 1 0 0 0 0 0 1 0 0 11123 224 8 5 5 OR4C12 11 49982202 Nonsense_Mutation SNP A C3N-01414_T 2350498 49982202 85104420 301 23501 OR4C6 0 . GRCh38 11 55665221 55665221 + Missense_Mutation SNP C C A rs773362372 C3N-01414_T C3N-01414_N C C c.55C>A p.Leu19Met p.L19M ENST00000314259 1/1 149 116 33 213 212 1 strelka-varscan-mutect OR4C6,missense_variant,p.Leu19Met,ENST00000314259,NM_001004704.1; A ENST00000314259 Transcript missense_variant 55/930 55/930 19/309 L/M Ctg/Atg rs773362372 1 1 OR4C6 HGNC HGNC:14743 protein_coding YES CCDS31506.1 ENSP00000324769 Q8NH72 A0A126GVN0 UPI0000041868 NM_001004704.1 deleterious_low_confidence(0.03) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF80,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs773362372 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 55665221 55665221 C A 1 0 0 0 0 1 0 0 0 11129 680 24 2 2 OR4C6 11 55665221 Missense_Mutation SNP C C3N-01414_T 5683019 55665221 79421401 302 23502 OR5W2 0 . GRCh38 11 55913719 55913719 + Silent SNP C C A C3N-01414_T C3N-01414_N C C c.864G>T p.= p.L288L ENST00000344514 1/1 196 175 21 282 281 1 strelka-varscan-mutect OR5W2,synonymous_variant,p.=,ENST00000344514,NM_001001960.1; A ENST00000344514 Transcript synonymous_variant 864/933 864/933 288/310 L ctG/ctT COSM4818025 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS rs1212274450 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 55913719 55913719 C A 1 0 0 0 0 0 0 0 1 11253 813 29 2 2 OR5W2 11 55913719 Silent SNP C C3N-01414_T 248498 55913719 79172903 303 23503 OR8H2 0 . GRCh38 11 56105732 56105732 + Silent SNP C C G C3N-01414_T C3N-01414_N C C c.690C>G p.= p.S230S ENST00000313503 1/1 210 173 37 303 303 0 strelka-varscan-mutect OR8H2,synonymous_variant,p.=,ENST00000618136,;OR8H2,synonymous_variant,p.=,ENST00000313503,NM_001005200.1; G ENST00000313503 Transcript synonymous_variant 690/939 690/939 230/312 S tcC/tcG COSM1354570 1 1 OR8H2 HGNC HGNC:15308 protein_coding YES CCDS31518.1 ENSP00000323982 Q8N162 UPI0000041D0C NM_001005200.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 56105732 56105732 C G 1 0 0 0 0 0 0 0 1 11306 581 21 4 4 OR8H2 11 56105732 Silent SNP C C3N-01414_T 192013 56105732 78980890 304 23504 OR8K5 0 . GRCh38 11 56160258 56160258 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.60G>T p.= p.R20R ENST00000313447 1/1 159 128 31 196 196 0 strelka-varscan-mutect OR8K5,synonymous_variant,p.=,ENST00000313447,NM_001004058.2; A ENST00000313447 Transcript synonymous_variant 60/924 60/924 20/307 R cgG/cgT 1 -1 OR8K5 HGNC HGNC:15315 protein_coding YES CCDS31521.1 ENSP00000323853 Q8NH50 UPI000004B231 NM_001004058.2 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 56160258 56160258 C A 1 0 0 0 0 0 0 0 1 11312 726 26 2 2 OR8K5 11 56160258 Silent SNP C C3N-01414_T 54526 56160258 78926364 305 23505 SLC22A9 0 . GRCh38 11 63408128 63408128 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.1305T>A p.= p.R435R ENST00000279178 8/10 174 127 47 171 171 0 strelka-varscan-mutect SLC22A9,synonymous_variant,p.=,ENST00000279178,NM_080866.2;SLC22A9,intron_variant,,ENST00000536333,; A ENST00000279178 Transcript synonymous_variant 1554/2343 1305/1662 435/553 R cgT/cgA 1 1 SLC22A9 HGNC HGNC:16261 protein_coding YES CCDS8043.1 ENSP00000279178 Q8IVM8 UPI00000745FF NM_080866.2 8/10 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF288,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 63408128 63408128 T A 1 0 0 0 0 0 0 0 1 14727 1683 59 4 4 SLC22A9 11 63408128 Silent SNP T C3N-01414_T 7247870 63408128 71678494 306 23506 MRGPRF 0 . GRCh38 11 69005339 69005339 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.971G>T p.Gly324Val p.G324V ENST00000309099 3/3 155 123 32 161 160 1 strelka-varscan-mutect MRGPRF,missense_variant,p.Gly324Val,ENST00000309099,NM_145015.4;MRGPRF,missense_variant,p.Gly324Val,ENST00000441623,NM_001098515.1;MRGPRF,downstream_gene_variant,,ENST00000320913,;RP11-554A11.4,upstream_gene_variant,,ENST00000562276,;RP11-554A11.5,downstream_gene_variant,,ENST00000562506,; A ENST00000309099 Transcript missense_variant 1354/2295 971/1032 324/343 G/V gGg/gTg 1 -1 MRGPRF HGNC HGNC:24828 protein_coding YES CCDS8188.1 ENSP00000309782 Q96AM1 A0A024R5F0 UPI000012F566 NM_145015.4 deleterious(0) 3/3 hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF3 MODERATE 1 SNV 1 1 PASS rs1179265574 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 69005339 69005339 C A 1 0 0 0 0 1 0 0 0 9731 623 22 2 2 MRGPRF 11 69005339 Missense_Mutation SNP C C3N-01414_T 5597211 69005339 66081283 307 23507 KRTAP5-7 0 . GRCh38 11 71527775 71527775 + Missense_Mutation SNP G G T rs200121713 C3N-01414_T C3N-01414_N G G c.475G>T p.Val159Leu p.V159L ENST00000398536 1/1 279 184 95 356 355 1 strelka-varscan-mutect KRTAP5-7,missense_variant,p.Val159Leu,ENST00000398536,NM_001012503.1;NADSYN1,downstream_gene_variant,,ENST00000527963,; T ENST00000398536 Transcript missense_variant 509/1408 475/498 159/165 V/L Gtg/Ttg rs200121713 1 1 KRTAP5-7 HGNC HGNC:23602 protein_coding YES CCDS41682.1 ENSP00000417330 Q6L8G8 UPI0000376061 NM_001012503.1 tolerated_low_confidence(0.13) 1/1 hmmpanther:PTHR23262,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS rs200121713 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 71527775 71527775 G T 1 0 0 0 0 1 0 0 0 8461 1145 40 1 1 KRTAP5-7 11 71527775 Missense_Mutation SNP G C3N-01414_T 2522436 71527775 63558847 308 23508 ARAP1 0 . GRCh38 11 72712481 72712481 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.835G>T p.Gly279Trp p.G279W ENST00000393609 6/35 105 80 25 99 99 0 strelka-varscan-mutect ARAP1,missense_variant,p.Gly279Trp,ENST00000359373,;ARAP1,missense_variant,p.Gly279Trp,ENST00000393609,NM_001040118.2;ARAP1,missense_variant,p.Gly34Trp,ENST00000334211,NM_015242.4;ARAP1,missense_variant,p.Gly39Trp,ENST00000393605,;ARAP1,missense_variant,p.Gly34Trp,ENST00000426523,;ARAP1,missense_variant,p.Gly34Trp,ENST00000429686,NM_001135190.1;ARAP1,upstream_gene_variant,,ENST00000542264,;ARAP1,non_coding_transcript_exon_variant,,ENST00000465814,;RPS12P20,downstream_gene_variant,,ENST00000464109,; A ENST00000393609 Transcript missense_variant 1038/5145 835/4353 279/1450 G/W Ggg/Tgg 1 -1 ARAP1 HGNC HGNC:16925 protein_coding YES CCDS41687.1 ENSP00000377233 Q96P48 UPI000053F81B NM_001040118.2 tolerated(0.2) 6/35 Low_complexity_(Seg):seg,hmmpanther:PTHR23180:SF195,hmmpanther:PTHR23180 MODERATE 1 SNV 2 1 PASS rs1370953930 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 72712481 72712481 C A 1 0 0 0 0 1 0 0 0 960 681 24 2 2 ARAP1 11 72712481 Missense_Mutation SNP C C3N-01414_T 1184706 72712481 62374141 309 23509 UVRAG 0 . GRCh38 11 75912024 75912024 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.578T>C p.Val193Ala p.V193A ENST00000356136 6/15 179 167 12 232 232 0 strelka-varscan-mutect UVRAG,missense_variant,p.Val193Ala,ENST00000356136,NM_003369.3;UVRAG,missense_variant,p.Val92Ala,ENST00000528420,;UVRAG,missense_variant,p.Val92Ala,ENST00000528264,;RP11-263C24.1,upstream_gene_variant,,ENST00000531215,;UVRAG,non_coding_transcript_exon_variant,,ENST00000525872,;PPP1R1AP1,upstream_gene_variant,,ENST00000525622,; C ENST00000356136 Transcript missense_variant 819/4123 578/2100 193/699 V/A gTc/gCc 1 1 UVRAG HGNC HGNC:12640 protein_coding YES CCDS8241.1 ENSP00000348455 Q9P2Y5 UPI0000137F03 NM_003369.3 deleterious(0.01) 6/15 hmmpanther:PTHR15157:SF5,hmmpanther:PTHR15157,Pfam_domain:PF10186 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 75912024 75912024 T C 1 0 0 0 0 1 0 0 0 17652 1667 58 5 5 UVRAG 11 75912024 Missense_Mutation SNP T C3N-01414_T 3199543 75912024 59174598 310 23510 UVRAG 0 . GRCh38 11 76140731 76140731 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1418G>T p.Ser473Ile p.S473I ENST00000356136 15/15 57 44 13 76 76 0 strelka-varscan-mutect UVRAG,missense_variant,p.Ser473Ile,ENST00000356136,NM_003369.3;UVRAG,missense_variant,p.Ser101Ile,ENST00000531818,;UVRAG,missense_variant,p.Ser372Ile,ENST00000528420,;UVRAG,missense_variant,p.Ser101Ile,ENST00000532130,;UVRAG,missense_variant,p.Ser101Ile,ENST00000533454,;CTD-2011F17.2,upstream_gene_variant,,ENST00000529298,;UVRAG,3_prime_UTR_variant,,ENST00000525183,; T ENST00000356136 Transcript missense_variant 1659/4123 1418/2100 473/699 S/I aGt/aTt 1 1 UVRAG HGNC HGNC:12640 protein_coding YES CCDS8241.1 ENSP00000348455 Q9P2Y5 UPI0000137F03 NM_003369.3 deleterious(0.04) 15/15 hmmpanther:PTHR15157:SF5,hmmpanther:PTHR15157 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 76140731 76140731 G T 1 0 0 0 0 1 0 0 0 17652 1029 36 2 2 UVRAG 11 76140731 Missense_Mutation SNP G C3N-01414_T 228707 76140731 58945891 311 23511 GRM5 0 . GRCh38 11 88567341 88567341 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.2342C>G p.Thr781Ser p.T781S ENST00000305447 7/9 184 129 55 306 306 0 strelka-varscan-mutect GRM5,missense_variant,p.Thr781Ser,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Thr781Ser,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Thr781Ser,ENST00000305432,; C ENST00000305447 Transcript missense_variant 2492/4571 2342/3639 781/1212 T/S aCc/aGc 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 7/9 Pfam_domain:PF00003,Prints_domain:PR00248,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 88567341 88567341 G C 1 0 0 0 0 1 0 0 0 6682 1261 44 4 4 GRM5 11 88567341 Missense_Mutation SNP G C3N-01414_T 12426610 88567341 46519281 312 23512 ATM 0 . GRCh38 11 108345909 108345909 + Splice_Site SNP G G T novel C3N-01414_T C3N-01414_N G G c.8584+1G>T p.X2862_splice ENST00000278616 346 257 89 476 476 0 strelka-varscan-mutect ATM,splice_donor_variant,,ENST00000278616,NM_000051.3;ATM,splice_donor_variant,,ENST00000452508,;C11orf65,intron_variant,,ENST00000615746,;C11orf65,intron_variant,,ENST00000525729,;C11orf65,intron_variant,,ENST00000524755,;C11orf65,intron_variant,,ENST00000526725,;ATM,upstream_gene_variant,,ENST00000525178,;ATM,splice_donor_variant,,ENST00000524792,;C11orf65,intron_variant,,ENST00000527531,; T ENST00000278616 Transcript splice_donor_variant -/13147 8584/9171 2862/3056 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 58/62 HIGH SNV 5 1 PASS rs876658182 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 77 108345909 108345909 G T 1 0 0 0 0 0 0 1 0 1261 1275 44 2 2 ATM 11 108345909 Splice_Site SNP G C3N-01414_T 19778568 108345909 26740713 313 23513 OR8G1 0 . GRCh38 11 124250345 124250345 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.670A>T p.Ser224Cys p.S224C ENST00000341493 1/1 295 199 96 329 329 0 strelka-varscan-mutect OR8G1,missense_variant,p.Ser224Cys,ENST00000341493,NM_001002905.1; T ENST00000341493 Transcript missense_variant 670/936 670/936 224/311 S/C Agc/Tgc 1 1 OR8G1 HGNC HGNC:8484 protein_coding YES CCDS73407.1 ENSP00000476313 Q15617 A0A126GVX6 UPI0000061EA7 NM_001002905.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF73,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 124250345 124250345 A T 1 0 0 0 0 1 0 0 0 11303 188 7 4 4 OR8G1 11 124250345 Missense_Mutation SNP A C3N-01414_T 15904436 124250345 10836277 314 23514 ROBO4 0 . GRCh38 11 124896205 124896205 + Silent SNP G G T C3N-01414_T C3N-01414_N G G c.672C>A p.= p.S224S ENST00000306534 4/18 126 78 48 192 192 0 strelka-varscan-mutect ROBO4,synonymous_variant,p.=,ENST00000306534,NM_019055.5;ROBO4,synonymous_variant,p.=,ENST00000533054,NM_001301088.1;RP11-664I21.6,downstream_gene_variant,,ENST00000524433,;ROBO4,non_coding_transcript_exon_variant,,ENST00000526899,;ROBO4,non_coding_transcript_exon_variant,,ENST00000527279,;ROBO4,downstream_gene_variant,,ENST00000529941,;ROBO4,non_coding_transcript_exon_variant,,ENST00000532300,;ROBO4,upstream_gene_variant,,ENST00000534407,;ROBO4,upstream_gene_variant,,ENST00000532216,;ROBO4,upstream_gene_variant,,ENST00000525182,;ROBO4,downstream_gene_variant,,ENST00000533337,; T ENST00000306534 Transcript synonymous_variant 1158/4710 672/3024 224/1007 S tcC/tcA COSM686543 1 -1 ROBO4 HGNC HGNC:17985 protein_coding YES CCDS8455.1 ENSP00000304945 Q8WZ75 UPI000004A023 NM_019055.5 4/18 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 LOW 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 124896205 124896205 G T 1 0 0 0 0 0 0 0 1 13694 1335 47 2 2 ROBO4 11 124896205 Silent SNP G C3N-01414_T 645860 124896205 10190417 315 23515 ACRV1 0 . GRCh38 11 125678051 125678051 + Missense_Mutation SNP G G T rs374663183 C3N-01414_T C3N-01414_N G G c.299C>A p.Ala100Glu p.A100E ENST00000533904 2/4 431 331 100 515 515 0 strelka-varscan-mutect ACRV1,missense_variant,p.Ala100Glu,ENST00000533904,NM_001612.5;ACRV1,missense_variant,p.Ala100Glu,ENST00000315608,NM_020069.4;ACRV1,missense_variant,p.Ala45Glu,ENST00000530048,NM_020107.4;ACRV1,intron_variant,,ENST00000527795,NM_020108.4;CHEK1,downstream_gene_variant,,ENST00000428830,NM_001114121.2;CHEK1,downstream_gene_variant,,ENST00000498122,; T ENST00000533904 Transcript missense_variant 642/2212 299/798 100/265 A/E gCg/gAg rs374663183,COSM5690032 1 -1 ACRV1 HGNC HGNC:127 protein_coding YES CCDS8460.1 ENSP00000432816 P26436 UPI000012615C NM_001612.5 tolerated(0.08) 2/4 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs374663183 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 125678051 125678051 G T 1 0 0 0 0 1 0 0 0 214 1087 38 1 1 ACRV1 11 125678051 Missense_Mutation SNP G C3N-01414_T 781846 125678051 9408571 316 23516 B3GAT1 0 . GRCh38 11 134387647 134387647 + Silent SNP G G T rs749052528 C3N-01414_T C3N-01414_N G G c.13C>A p.= p.R5R ENST00000524765 2/6 246 200 46 329 329 0 strelka-varscan-mutect B3GAT1,synonymous_variant,p.=,ENST00000524765,;B3GAT1,synonymous_variant,p.=,ENST00000312527,NM_054025.2;B3GAT1,synonymous_variant,p.=,ENST00000392580,NM_018644.3;B3GAT1,non_coding_transcript_exon_variant,,ENST00000531510,;B3GAT1,upstream_gene_variant,,ENST00000531778,; T ENST00000524765 Transcript synonymous_variant 4558/5737 13/1005 5/334 R Cgg/Agg rs749052528,COSM4019582,COSM4019583 1 -1 B3GAT1 HGNC HGNC:921 protein_coding YES CCDS8500.1 ENSP00000433847 Q9P2W7 UPI0000073281 2/6 hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF21 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs749052528 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 134387647 134387647 G T 1 0 0 0 0 0 0 0 1 1409 1144 40 1 1 B3GAT1 11 134387647 Silent SNP G C3N-01414_T 8709596 134387647 698975 317 23517 GDF3 0 . GRCh38 12 7690504 7690504 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.469G>T p.Gly157Cys p.G157C ENST00000329913 2/2 126 91 35 152 152 0 strelka-varscan-mutect GDF3,missense_variant,p.Gly157Cys,ENST00000329913,NM_020634.1; A ENST00000329913 Transcript missense_variant 517/1239 469/1095 157/364 G/C Ggc/Tgc COSM694987 1 -1 GDF3 HGNC HGNC:4218 protein_coding YES CCDS8581.1 ENSP00000331745 Q9NR23 UPI0000049E0E NM_020634.1 deleterious(0.01) 2/2 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF38,Pfam_domain:PF00688 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 7690504 7690504 C A 1 0 0 0 0 1 0 0 0 6187 623 22 2 2 GDF3 12 7690504 Missense_Mutation SNP C C3N-01414_T 7690504 125584805 318 23518 CLEC4E 0 . GRCh38 12 8537212 8537212 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.275A>T p.Tyr92Phe p.Y92F ENST00000299663 4/6 139 110 29 187 187 0 strelka-varscan-mutect CLEC4E,missense_variant,p.Tyr92Phe,ENST00000299663,NM_014358.3;CLEC4E,missense_variant,p.Tyr32Phe,ENST00000537698,;CLEC4E,intron_variant,,ENST00000545274,;CLEC4E,intron_variant,,ENST00000446457,;CLEC4E,intron_variant,,ENST00000450725,;CLEC4E,downstream_gene_variant,,ENST00000446809,; A ENST00000299663 Transcript missense_variant 441/2159 275/660 92/219 Y/F tAc/tTc 1 -1 CLEC4E HGNC HGNC:14555 protein_coding YES CCDS8594.1 ENSP00000299663 Q9ULY5 UPI0000037798 NM_014358.3 tolerated(0.08) 4/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF226,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 8537212 8537212 T A 1 0 0 0 0 1 0 0 0 3283 1638 57 4 4 CLEC4E 12 8537212 Missense_Mutation SNP T C3N-01414_T 846708 8537212 124738097 319 23519 A2ML1 0 . GRCh38 12 8848819 8848819 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.1933C>A p.Leu645Ile p.L645I ENST00000299698 16/36 307 231 76 386 386 0 strelka-varscan-mutect A2ML1,missense_variant,p.Leu645Ile,ENST00000299698,NM_144670.4;A2ML1,missense_variant,p.Leu154Ile,ENST00000539547,NM_001282424.1;A2ML1,missense_variant,p.Leu195Ile,ENST00000541459,;A2ML1,missense_variant,p.Leu157Ile,ENST00000545692,;A2ML1,downstream_gene_variant,,ENST00000536789,;A2ML1,downstream_gene_variant,,ENST00000540049,; A ENST00000299698 Transcript missense_variant 2113/5274 1933/4365 645/1454 L/I Ctc/Atc COSM1364784 1 1 A2ML1 HGNC HGNC:23336 protein_coding YES CCDS8596.2 ENSP00000299698 A8K2U0 UPI000022904E NM_144670.4 tolerated(0.21) 16/36 hmmpanther:PTHR11412:SF95,hmmpanther:PTHR11412 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 8848819 8848819 C A 1 0 0 0 0 1 0 0 0 4 681 24 2 2 A2ML1 12 8848819 Missense_Mutation SNP C C3N-01414_T 311607 8848819 124426490 320 23520 EIF2S3L 0 . GRCh38 12 10505922 10505922 + Missense_Mutation SNP G G T rs539272190 C3N-01414_T C3N-01414_N G G c.20G>T p.Gly7Val p.G7V ENST00000538173 1/1 330 233 97 426 426 0 strelka-varscan-mutect EIF2S3L,missense_variant,p.Gly7Val,ENST00000322446,;EIF2S3L,missense_variant,p.Gly7Val,ENST00000538173,; T ENST00000538173 Transcript missense_variant 33/1602 20/1419 7/472 G/V gGg/gTg rs539272190 1 1 EIF2S3L Clone_based_vega_gene protein_coding YES ENSP00000445077 Q2VIR3 UPI0000140E1D deleterious_low_confidence(0.02) 1/1 MODERATE 1 SNV 1 PASS rs539272190 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 10505922 10505922 G T 1 0 0 0 0 1 0 0 0 4845 1232 43 2 2 EIF2S3L 12 10505922 Missense_Mutation SNP G C3N-01414_T 1657103 10505922 122769387 321 23521 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3N-01414_T C3N-01414_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 384 279 105 477 477 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3N-01414_T 14739428 25245350 108029959 322 23522 TMPRSS12 0 . GRCh38 12 50842978 50842978 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.14T>A p.Leu5His p.L5H ENST00000398458 1/5 99 73 26 130 129 1 strelka-varscan-mutect TMPRSS12,missense_variant,p.Leu5His,ENST00000551456,;TMPRSS12,missense_variant,p.Leu5His,ENST00000398458,NM_182559.2;RN7SL519P,upstream_gene_variant,,ENST00000497925,;RP11-60E8.3,downstream_gene_variant,,ENST00000605614,; A ENST00000398458 Transcript missense_variant 46/1450 14/1047 5/348 L/H cTc/cAc 1 1 TMPRSS12 HGNC HGNC:28779 protein_coding YES CCDS44881.1 ENSP00000381476 Q86WS5 UPI000019741B NM_182559.2 deleterious_low_confidence(0) 1/5 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 50842978 50842978 T A 1 0 0 0 0 1 0 0 0 16720 1551 54 4 4 TMPRSS12 12 50842978 Missense_Mutation SNP T C3N-01414_T 25597628 50842978 82432331 323 23523 ITGA7 0 . GRCh38 12 55695533 55695533 + Missense_Mutation SNP T T G C3N-01414_T C3N-01414_N T T c.2004A>C p.Gln668His p.Q668H ENST00000553804 14/25 199 189 10 204 201 3 varscan-mutect ITGA7,missense_variant,p.Gln664His,ENST00000257879,NM_002206.2;ITGA7,missense_variant,p.Gln658His,ENST00000347027,;ITGA7,missense_variant,p.Gln668His,ENST00000553804,NM_001144996.1;ITGA7,missense_variant,p.Gln708His,ENST00000555728,;ITGA7,missense_variant,p.Gln571His,ENST00000452168,NM_001144997.1;ITGA7,downstream_gene_variant,,ENST00000557257,;ITGA7,missense_variant,p.Gln84His,ENST00000554327,;ITGA7,non_coding_transcript_exon_variant,,ENST00000557058,;ITGA7,downstream_gene_variant,,ENST00000553276,;ITGA7,downstream_gene_variant,,ENST00000554543,;ITGA7,downstream_gene_variant,,ENST00000555687,;ITGA7,downstream_gene_variant,,ENST00000556273,;ITGA7,downstream_gene_variant,,ENST00000557488,; G ENST00000553804 Transcript missense_variant 2023/3935 2004/3426 668/1141 Q/H caA/caC COSM4452615,COSM4452616,COSM4452617,COSM4452618 1 -1 ITGA7 HGNC HGNC:6143 protein_coding YES CCDS55832.1 ENSP00000452120 Q13683 UPI00003668CF NM_001144996.1 tolerated(0.16) 14/25 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF90,Pfam_domain:PF08441,Gene3D:2.60.40.1510,Superfamily_domains:SSF69179 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs1339387222 . 0 173 2 23 11 0 0 0 -2.677382 0 0 1 0 0 G 3 3 77 55695533 55695533 T G 1 0 0 0 0 1 0 0 0 7788 1722 60 5 5 ITGA7 12 55695533 Missense_Mutation SNP T C3N-01414_T 4852555 55695533 77579776 324 23524 LRP1 0 . GRCh38 12 57198221 57198221 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.9348G>A p.= p.L3116L ENST00000243077 59/89 217 147 70 245 245 0 strelka-varscan-mutect LRP1,synonymous_variant,p.=,ENST00000243077,NM_002332.2;LRP1,upstream_gene_variant,,ENST00000555124,;MIR1228,downstream_gene_variant,,ENST00000408438,;LRP1,upstream_gene_variant,,ENST00000556247,;LRP1,upstream_gene_variant,,ENST00000555941,; A ENST00000243077 Transcript synonymous_variant 9814/14897 9348/13635 3116/4544 L ctG/ctA 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 59/89 Gene3D:2.120.10.30,Pfam_domain:PF16472,PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF100,SMART_domains:SM00135,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 57198221 57198221 G A 1 0 0 0 0 0 0 0 1 8846 1364 48 3 3 LRP1 12 57198221 Silent SNP G C3N-01414_T 1502688 57198221 76077088 325 23525 C12orf66 0 . GRCh38 12 64222230 64222230 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.8A>T p.Glu3Val p.E3V ENST00000311915 1/4 161 114 47 204 204 0 strelka-varscan-mutect C12orf66,missense_variant,p.Glu3Val,ENST00000398055,NM_152440.4;C12orf66,missense_variant,p.Glu3Val,ENST00000311915,NM_001300940.1;C12orf66,missense_variant,p.Glu3Val,ENST00000544871,NM_001300941.1;C12orf66,non_coding_transcript_exon_variant,,ENST00000540673,;C12orf66,non_coding_transcript_exon_variant,,ENST00000615991,;RPS11P6,upstream_gene_variant,,ENST00000535684,; A ENST00000311915 Transcript missense_variant 36/2698 8/1407 3/468 E/V gAg/gTg 1 -1 C12orf66 HGNC HGNC:26517 protein_coding YES CCDS73490.1 ENSP00000311486 J3KNH0 UPI0003EAEA9B NM_001300940.1 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR31581,hmmpanther:PTHR31581:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 64222230 64222230 T A 1 0 0 0 0 1 0 0 0 1820 1551 54 4 4 C12orf66 12 64222230 Missense_Mutation SNP T C3N-01414_T 7024009 64222230 69053079 326 23526 PTPRB 0 . GRCh38 12 70555232 70555232 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.5071G>C p.Val1691Leu p.V1691L ENST00000334414 20/34 348 270 78 410 410 0 strelka-varscan-mutect PTPRB,missense_variant,p.Val1691Leu,ENST00000334414,NM_001109754.2;PTPRB,missense_variant,p.Val1603Leu,ENST00000550358,;PTPRB,missense_variant,p.Val1473Leu,ENST00000261266,NM_002837.4;PTPRB,missense_variant,p.Val1383Leu,ENST00000538708,NM_001206972.1;PTPRB,missense_variant,p.Val1383Leu,ENST00000550857,NM_001206971.1;PTPRB,downstream_gene_variant,,ENST00000551525,;PTPRB,downstream_gene_variant,,ENST00000548122,; G ENST00000334414 Transcript missense_variant 5116/12316 5071/6648 1691/2215 V/L Gtc/Ctc 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 deleterious(0.01) 20/34 PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 70555232 70555232 C G 1 0 0 0 0 1 0 0 0 12950 478 17 4 4 PTPRB 12 70555232 Missense_Mutation SNP C C3N-01414_T 6333002 70555232 62720077 327 23527 ANKS1B 0 . GRCh38 12 98798954 98798954 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.3247G>T p.Asp1083Tyr p.D1083Y ENST00000547776 21/26 163 127 36 208 208 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Asp1083Tyr,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Asp273Tyr,ENST00000550693,NM_001204069.1;ANKS1B,missense_variant,p.Asp333Tyr,ENST00000549493,NM_181670.3;ANKS1B,missense_variant,p.Asp181Tyr,ENST00000549025,NM_001204066.1;ANKS1B,missense_variant,p.Asp599Tyr,ENST00000547010,;ANKS1B,missense_variant,p.Asp249Tyr,ENST00000549558,NM_020140.3;ANKS1B,missense_variant,p.Asp89Tyr,ENST00000341752,NM_001204081.1;ANKS1B,missense_variant,p.Asp355Tyr,ENST00000550778,;ANKS1B,missense_variant,p.Asp218Tyr,ENST00000547446,NM_001204067.1;ANKS1B,missense_variant,p.Asp113Tyr,ENST00000333732,NM_001204079.1,NM_001204080.1,NM_001204065.1;ANKS1B,missense_variant,p.Asp309Tyr,ENST00000546960,NM_001204068.1;ANKS1B,missense_variant,p.Asp249Tyr,ENST00000546568,NM_001204070.1;ANKS1B,missense_variant,p.Asp113Tyr,ENST00000546364,;ANKS1B,missense_variant,p.Asp89Tyr,ENST00000549797,;ANKS1B,missense_variant,p.Asp89Tyr,ENST00000552407,;ANKS1B,missense_variant,p.Asp14Tyr,ENST00000551613,;ANKS1B,downstream_gene_variant,,ENST00000551560,;ANKS1B,downstream_gene_variant,,ENST00000552748,;ANKS1B,downstream_gene_variant,,ENST00000551830,;ANKS1B,missense_variant,p.Asp89Tyr,ENST00000547362,;RP11-90E9.1,downstream_gene_variant,,ENST00000549019,; A ENST00000547776 Transcript missense_variant 3247/3885 3247/3747 1083/1248 D/Y Gat/Tat 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 deleterious(0) 21/26 Gene3D:2.30.29.30,Pfam_domain:PF00640,PROSITE_profiles:PS01179,hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1161191193 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 98798954 98798954 C A 1 0 0 0 0 1 0 0 0 795 913 32 2 2 ANKS1B 12 98798954 Missense_Mutation SNP C C3N-01414_T 28243722 98798954 34476355 328 23528 SCYL2 0 . GRCh38 12 100315556 100315556 + Splice_Site SNP A A T novel C3N-01414_T C3N-01414_N A A c.1096-2A>T p.X366_splice ENST00000360820 120 85 35 123 123 0 strelka-varscan-mutect SCYL2,splice_acceptor_variant,,ENST00000360820,NM_001317784.1,NM_017988.4;SCYL2,splice_acceptor_variant,,ENST00000635101,;SCYL2,splice_acceptor_variant,,ENST00000549687,;SCYL2,downstream_gene_variant,,ENST00000548392,;SCYL2,upstream_gene_variant,,ENST00000553148,;SCYL2,upstream_gene_variant,,ENST00000550251,; T ENST00000360820 Transcript splice_acceptor_variant -/5779 1096/2790 366/929 1 1 SCYL2 HGNC HGNC:19286 protein_coding YES CCDS9076.1 ENSP00000354061 Q6P3W7 UPI000004FD59 NM_001317784.1,NM_017988.4 8/17 HIGH 1 SNV 1 1 PASS . . 0 194 16 0 0 0 0 0 -20 0.9997943 1 1 1 0 T 5 4 77 100315556 100315556 A T 1 0 0 0 0 0 0 1 0 14220 202 7 4 4 SCYL2 12 100315556 Splice_Site SNP A C3N-01414_T 1516602 100315556 32959753 329 23529 SLC17A8 0 . GRCh38 12 100419831 100419831 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1442A>T p.Gln481Leu p.Q481L ENST00000323346 12/12 279 197 82 387 387 0 strelka-varscan-mutect SLC17A8,missense_variant,p.Gln481Leu,ENST00000323346,NM_139319.2;SLC17A8,missense_variant,p.Gln431Leu,ENST00000392989,NM_001145288.1;SLC17A8,non_coding_transcript_exon_variant,,ENST00000552697,; T ENST00000323346 Transcript missense_variant 1755/3983 1442/1770 481/589 Q/L cAg/cTg 1 1 SLC17A8 HGNC HGNC:20151 protein_coding YES CCDS9077.1 ENSP00000316909 Q8NDX2 UPI0000073B9B NM_139319.2 deleterious(0.01) 12/12 Gene3D:1.20.1250.20,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF207,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 100419831 100419831 A T 1 0 0 0 0 1 0 0 0 14688 188 7 4 4 SLC17A8 12 100419831 Missense_Mutation SNP A C3N-01414_T 104275 100419831 32855478 330 23530 TXNRD1 0 . GRCh38 12 104325355 104325355 + Frame_Shift_Del DEL G G - novel C3N-01414_T C3N-01414_N G G c.1236delG p.Thr413HisfsTer7 p.T413Hfs*7 ENST00000525566 11/17 221 163 58 337 336 1 sindel-varindel-pindel TXNRD1,frameshift_variant,p.Thr313HisfsTer7,ENST00000388854,NM_001261445.1;TXNRD1,frameshift_variant,p.Thr263HisfsTer7,ENST00000354940,;TXNRD1,frameshift_variant,p.Thr315HisfsTer7,ENST00000526691,NM_003330.3;TXNRD1,frameshift_variant,p.Thr263HisfsTer7,ENST00000503506,NM_182743.2,NM_182729.2,NM_182742.2;TXNRD1,frameshift_variant,p.Thr413HisfsTer7,ENST00000429002,;TXNRD1,frameshift_variant,p.Thr413HisfsTer7,ENST00000525566,NM_001093771.2;TXNRD1,frameshift_variant,p.Thr225HisfsTer7,ENST00000397736,;TXNRD1,frameshift_variant,p.Thr307HisfsTer7,ENST00000526390,;TXNRD1,frameshift_variant,p.Thr225HisfsTer7,ENST00000529546,NM_001261446.1;TXNRD1,frameshift_variant,p.Thr263HisfsTer7,ENST00000524698,;TXNRD1,frameshift_variant,p.Thr332HisfsTer7,ENST00000526950,;TXNRD1,5_prime_UTR_variant,,ENST00000529751,;TXNRD1,frameshift_variant,p.Thr263HisfsTer7,ENST00000527688,; - ENST00000525566 Transcript frameshift_variant 1258/3836 1234/1950 412/649 G/X Ggg/gg 1 1 TXNRD1 HGNC HGNC:12437 protein_coding YES CCDS53820.1 ENSP00000434516 Q16881 UPI00015294EE NM_001093771.2 11/17 hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF129,Pfam_domain:PF07992,TIGRFAM_domain:TIGR01438,Gene3D:3.50.50.60,Superfamily_domains:SSF51905 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 104325355 104325355 G - 1 0 1 0 1 0 0 0 0 17321 1000 35 0 0 TXNRD1 12 104325355 Frame_Shift_Del DEL G C3N-01414_T 3905524 104325355 28949954 331 23531 DAO 0 . GRCh38 12 108885112 108885112 + Missense_Mutation SNP G G T rs551786568 C3N-01414_T C3N-01414_N G G c.106G>T p.Ala36Ser p.A36S ENST00000228476 2/11 91 57 34 99 99 0 strelka-varscan-mutect DAO,missense_variant,p.Ala36Ser,ENST00000228476,NM_001917.4;DAO,missense_variant,p.Ala36Ser,ENST00000551281,;DAO,missense_variant,p.Ala36Ser,ENST00000547166,;DAO,intron_variant,,ENST00000547768,;DAO,downstream_gene_variant,,ENST00000548052,;DAO,missense_variant,p.Ala36Ser,ENST00000549215,;DAO,missense_variant,p.Ala36Ser,ENST00000547122,; T ENST00000228476 Transcript missense_variant 310/1756 106/1044 36/347 A/S Gcg/Tcg rs551786568,COSM1202985 1 1 DAO HGNC HGNC:2671 protein_coding YES CCDS9122.1 ENSP00000228476 P14920 A0A024RBI1 UPI0000130F5F NM_001917.4 tolerated(0.43) 2/11 Gene3D:3.50.50.60,Pfam_domain:PF01266,PIRSF_domain:PIRSF000189,hmmpanther:PTHR11530,hmmpanther:PTHR11530:SF11,Superfamily_domains:SSF51971 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs551786568 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 108885112 108885112 G T 1 0 0 0 0 1 0 0 0 4032 1087 38 1 1 DAO 12 108885112 Missense_Mutation SNP G C3N-01414_T 4559757 108885112 24390197 332 23532 ACACB 0 . GRCh38 12 109191729 109191729 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.2261G>T p.Gly754Val p.G754V ENST00000338432 14/53 319 214 105 384 384 0 strelka-varscan-mutect ACACB,missense_variant,p.Gly754Val,ENST00000338432,;ACACB,missense_variant,p.Gly754Val,ENST00000377848,NM_001093.3;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,non_coding_transcript_exon_variant,,ENST00000544651,; T ENST00000338432 Transcript missense_variant 2380/9360 2261/7377 754/2458 G/V gGg/gTg 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB deleterious(0) 14/53 PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF02785,Gene3D:3.30.470.20,SMART_domains:SM00878,Superfamily_domains:SSF51246 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 109191729 109191729 G T 1 0 0 0 0 1 0 0 0 150 1232 43 2 2 ACACB 12 109191729 Missense_Mutation SNP G C3N-01414_T 306617 109191729 24083580 333 23533 OAS2 0 . GRCh38 12 113005023 113005023 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.1269C>T p.= p.S423S ENST00000342315 7/11 456 405 51 534 534 0 strelka-varscan-mutect OAS2,synonymous_variant,p.=,ENST00000392583,NM_002535.2;OAS2,synonymous_variant,p.=,ENST00000342315,NM_016817.2;OAS2,synonymous_variant,p.=,ENST00000620097,;OAS2,downstream_gene_variant,,ENST00000552756,;RP1-71H24.1,intron_variant,,ENST00000552784,;OAS2,non_coding_transcript_exon_variant,,ENST00000548941,; T ENST00000342315 Transcript synonymous_variant 1483/3613 1269/2160 423/719 S tcC/tcT 1 1 OAS2 HGNC HGNC:8087 protein_coding YES CCDS31906.1 ENSP00000342278 P29728 UPI000013CB0B NM_016817.2 7/11 PROSITE_profiles:PS50152,hmmpanther:PTHR11258,hmmpanther:PTHR11258:SF3,Pfam_domain:PF01909,Gene3D:3.30.460.10,Superfamily_domains:SSF81301 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 113005023 113005023 C T 1 0 0 0 0 0 0 0 1 10879 610 22 3 3 OAS2 12 113005023 Silent SNP C C3N-01414_T 3813294 113005023 20270286 334 23534 NOS1 0 . GRCh38 12 117265329 117265329 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.2123C>A p.Ser708Tyr p.S708Y ENST00000618760 12/30 38 31 7 40 40 0 strelka-varscan-mutect NOS1,missense_variant,p.Ser708Tyr,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Ser708Tyr,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Ser708Tyr,ENST00000338101,;NOS1,missense_variant,p.Ser707Tyr,ENST00000344089,; T ENST00000618760 Transcript missense_variant 2834/12283 2123/4407 708/1468 S/Y tCc/tAc 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 tolerated(0.1) 12/30 hmmpanther:PTHR19384:SF63,hmmpanther:PTHR19384,Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 117265329 117265329 G T 1 0 0 0 0 1 0 0 0 10586 1174 41 2 2 NOS1 12 117265329 Missense_Mutation SNP G C3N-01414_T 4260306 117265329 16009980 335 23535 NOS1 0 . GRCh38 12 117268078 117268078 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.1906G>A p.Val636Met p.V636M ENST00000618760 11/30 255 230 25 302 302 0 strelka-varscan-mutect NOS1,missense_variant,p.Val636Met,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Val636Met,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Val636Met,ENST00000338101,;NOS1,missense_variant,p.Val635Met,ENST00000344089,; T ENST00000618760 Transcript missense_variant 2617/12283 1906/4407 636/1468 V/M Gtg/Atg 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 deleterious(0.01) 11/30 hmmpanther:PTHR19384:SF63,hmmpanther:PTHR19384,Gene3D:3.90.1230.10,Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 117268078 117268078 C T 1 0 0 0 0 1 0 0 0 10586 507 18 3 3 NOS1 12 117268078 Missense_Mutation SNP C C3N-01414_T 2749 117268078 16007231 336 23536 KSR2 0 . GRCh38 12 117667630 117667630 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.928C>T p.Leu310Phe p.L310F ENST00000425217 5/20 105 74 31 123 122 1 varscan-mutect KSR2,missense_variant,p.Leu339Phe,ENST00000339824,;KSR2,missense_variant,p.Leu310Phe,ENST00000425217,NM_173598.4;KSR2,non_coding_transcript_exon_variant,,ENST00000545002,; A ENST00000425217 Transcript missense_variant 983/17008 928/2766 310/921 L/F Ctc/Ttc 1 -1 KSR2 HGNC HGNC:18610 protein_coding YES CCDS61250.1 ENSP00000389715 E9PB13 UPI000164FA1C NM_173598.4 tolerated(0.22) 5/20 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 117667630 117667630 G A 1 0 0 0 0 1 0 0 0 8481 1000 35 3 3 KSR2 12 117667630 Missense_Mutation SNP G C3N-01414_T 399552 117667630 15607679 337 23537 SBNO1 0 . GRCh38 12 123309730 123309730 + Missense_Mutation SNP C C A rs780127026 C3N-01414_T C3N-01414_N C C c.3422G>T p.Arg1141Ile p.R1141I ENST00000420886 25/31 165 107 58 219 218 1 strelka-varscan-mutect SBNO1,missense_variant,p.Arg1140Ile,ENST00000267176,NM_018183.3;SBNO1,missense_variant,p.Arg1141Ile,ENST00000420886,NM_001167856.1;SBNO1,missense_variant,p.Arg1141Ile,ENST00000602398,; A ENST00000420886 Transcript missense_variant 3422/10981 3422/4182 1141/1393 R/I aGa/aTa rs780127026 1 -1 SBNO1 HGNC HGNC:22973 protein_coding YES CCDS53844.1 ENSP00000387361 A3KN83 UPI00001FB922 NM_001167856.1 deleterious(0) 25/31 hmmpanther:PTHR12706:SF8,hmmpanther:PTHR12706,Pfam_domain:PF13871 MODERATE 1 SNV 1 1 PASS rs780127026 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 123309730 123309730 C A 1 0 0 0 0 1 0 0 0 14127 913 32 2 2 SBNO1 12 123309730 Missense_Mutation SNP C C3N-01414_T 5642100 123309730 9965579 338 23538 DNAH10 0 . GRCh38 12 123873655 123873655 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.7529G>T p.Gly2510Val p.G2510V ENST00000638045 45/78 261 209 52 304 304 0 strelka-varscan-mutect DNAH10,missense_variant,p.Gly2571Val,ENST00000409039,;DNAH10,missense_variant,p.Gly2510Val,ENST00000638045,NM_207437.3;DNAH10,intron_variant,,ENST00000497783,; T ENST00000638045 Transcript missense_variant 7554/13678 7529/13416 2510/4471 G/V gGc/gTc 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0) 45/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12775,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 123873655 123873655 G T 1 0 0 0 0 1 0 0 0 4411 1203 42 2 2 DNAH10 12 123873655 Missense_Mutation SNP G C3N-01414_T 563925 123873655 9401654 339 23539 PIWIL1 0 . GRCh38 12 130349937 130349937 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.1014T>A p.= p.S338S ENST00000245255 9/21 189 144 45 239 239 0 strelka-varscan-mutect PIWIL1,synonymous_variant,p.=,ENST00000245255,NM_004764.4,NM_001190971.1;PIWIL1,downstream_gene_variant,,ENST00000542723,;PIWIL1,downstream_gene_variant,,ENST00000546060,;PIWIL1,downstream_gene_variant,,ENST00000535956,;PIWIL1,downstream_gene_variant,,ENST00000539995,;PIWIL1,downstream_gene_variant,,ENST00000539400,;RP11-200K12.3,downstream_gene_variant,,ENST00000624997,;PIWIL1,downstream_gene_variant,,ENST00000540672,; A ENST00000245255 Transcript synonymous_variant 1286/3897 1014/2586 338/861 S tcT/tcA 1 1 PIWIL1 HGNC HGNC:9007 protein_coding YES CCDS9268.1 ENSP00000245255 Q96J94 A0A024RBS5 UPI000007059F NM_004764.4,NM_001190971.1 9/21 Gene3D:2.170.260.10,Pfam_domain:PF02170,PROSITE_profiles:PS50821,hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF46,SMART_domains:SM00949,Superfamily_domains:SSF101690 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 130349937 130349937 T A 1 0 0 0 0 0 0 0 1 12053 1567 55 4 4 PIWIL1 12 130349937 Silent SNP T C3N-01414_T 6476282 130349937 2925372 340 23540 GALNT9 0 . GRCh38 12 132261023 132261023 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.686G>T p.Arg229Leu p.R229L ENST00000328957 4/11 252 172 80 245 245 0 strelka-varscan-mutect GALNT9,missense_variant,p.Arg229Leu,ENST00000328957,;GALNT9,upstream_gene_variant,,ENST00000411988,;GALNT9,non_coding_transcript_exon_variant,,ENST00000535208,;GALNT9,non_coding_transcript_exon_variant,,ENST00000424720,; A ENST00000328957 Transcript missense_variant 686/2410 686/1812 229/603 R/L cGg/cTg 1 -1 GALNT9 HGNC HGNC:4131 protein_coding ENSP00000329846 J3KNN1 UPI00004566BE deleterious(0) 4/11 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF28,Gene3D:3.90.550.10,Pfam_domain:PF00535,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs908793467 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 132261023 132261023 C A 1 0 0 0 0 1 0 0 0 6091 652 23 1 1 GALNT9 12 132261023 Missense_Mutation SNP C C3N-01414_T 1911086 132261023 1014286 341 23541 LATS2 0 . GRCh38 13 20987915 20987915 + Missense_Mutation SNP T T G novel C3N-01414_T C3N-01414_N T T c.1865A>C p.Asn622Thr p.N622T ENST00000382592 4/8 152 126 26 249 249 0 strelka-varscan-mutect LATS2,missense_variant,p.Asn622Thr,ENST00000382592,NM_014572.2;LATS2,downstream_gene_variant,,ENST00000472754,; G ENST00000382592 Transcript missense_variant 2271/5511 1865/3267 622/1088 N/T aAc/aCc 1 -1 LATS2 HGNC HGNC:6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 A0A024RDM3 UPI000013DBF5 NM_014572.2 tolerated(0.26) 4/8 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24356:SF149,hmmpanther:PTHR24356 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 20987915 20987915 T G 1 0 0 0 0 1 0 0 0 8552 1725 60 5 5 LATS2 13 20987915 Missense_Mutation SNP T C3N-01414_T 20987915 93376413 342 23542 LNX2 0 . GRCh38 13 27581328 27581328 + Missense_Mutation SNP G G A C3N-01414_T C3N-01414_N G G c.376C>T p.Arg126Cys p.R126C ENST00000316334 2/10 20 13 7 34 34 0 strelka-varscan-mutect LNX2,missense_variant,p.Arg126Cys,ENST00000316334,NM_153371.3; A ENST00000316334 Transcript missense_variant 506/4627 376/2073 126/690 R/C Cgt/Tgt COSM946442 1 -1 LNX2 HGNC HGNC:20421 protein_coding YES CCDS9323.1 ENSP00000325929 Q8N448 UPI000012E7A7 NM_153371.3 deleterious(0) 2/10 hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF33 1 MODERATE 1 SNV 1 1 1 PASS rs963005282 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 27581328 27581328 G A 1 0 0 0 0 1 0 0 0 8793 1145 40 1 1 LNX2 13 27581328 Missense_Mutation SNP G C3N-01414_T 6593413 27581328 86783000 343 23543 NHLRC3 0 . GRCh38 13 39047803 39047803 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.921A>T p.Gln307His p.Q307H ENST00000379600 7/7 190 135 55 392 392 0 strelka-varscan-mutect NHLRC3,missense_variant,p.Gln307His,ENST00000379600,NM_001012754.3;NHLRC3,missense_variant,p.Gln110His,ENST00000470258,;NHLRC3,missense_variant,p.Gln240His,ENST00000379599,NM_001017370.2;NHLRC3,downstream_gene_variant,,ENST00000485407,; T ENST00000379600 Transcript missense_variant 1243/3549 921/1044 307/347 Q/H caA/caT 1 1 NHLRC3 HGNC HGNC:33751 protein_coding YES CCDS31961.1 ENSP00000368920 Q5JS37 UPI0000251E60 NM_001012754.3 tolerated(0.08) 7/7 hmmpanther:PTHR24104:SF8,hmmpanther:PTHR24104,Gene3D:2.120.10.30,Superfamily_domains:SSF101898 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 39047803 39047803 A T 1 0 0 0 0 1 0 0 0 10440 69 3 4 4 NHLRC3 13 39047803 Missense_Mutation SNP A C3N-01414_T 11466475 39047803 75316525 344 23544 ERICH6B 0 . GRCh38 13 45574841 45574841 + Splice_Site SNP C C A rs201946586 C3N-01414_T C3N-01414_N C C c.1050+1G>T p.X350_splice ENST00000298738 200 163 37 310 310 0 strelka-varscan-mutect ERICH6B,splice_donor_variant,,ENST00000298738,NM_182542.2;ERICH6B,splice_donor_variant,,ENST00000378977,; A ENST00000298738 Transcript splice_donor_variant -/2421 1050/2091 350/696 rs201946586 1 -1 ERICH6B HGNC HGNC:26523 protein_coding YES CCDS45045.1 ENSP00000298738 Q5W0A0 UPI000013E513 NM_182542.2 8/14 HIGH 1 SNV 2 1 PASS rs201946586 . 0 208 0 0 2 0 0 0 -19.93711 0.9978829 1 1 1 0 A 5 1 77 45574841 45574841 C A 1 0 0 0 0 0 0 1 0 5087 550 19 1 1 ERICH6B 13 45574841 Splice_Site SNP C C3N-01414_T 6527038 45574841 68789487 345 23545 SIAH3 0 . GRCh38 13 45783479 45783479 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.714C>A p.Asn238Lys p.N238K ENST00000400405 2/2 212 184 28 296 296 0 strelka-varscan-mutect SIAH3,missense_variant,p.Asn238Lys,ENST00000400405,NM_198849.2; T ENST00000400405 Transcript missense_variant 821/7057 714/810 238/269 N/K aaC/aaA 1 -1 SIAH3 HGNC HGNC:30553 protein_coding YES CCDS41883.1 ENSP00000383256 Q8IW03 UPI00001C1F5A NM_198849.2 deleterious(0) 2/2 hmmpanther:PTHR10315,hmmpanther:PTHR10315:SF21,Pfam_domain:PF03145,Gene3D:2.60.210.10,Superfamily_domains:SSF49599 MODERATE 1 SNV 1 1 PASS rs755151857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 45783479 45783479 G T 1 0 0 0 0 1 0 0 0 14565 1368 48 2 2 SIAH3 13 45783479 Missense_Mutation SNP G C3N-01414_T 208638 45783479 68580849 346 23546 THSD1 0 . GRCh38 13 52378774 52378774 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1196G>T p.Ser399Ile p.S399I ENST00000258613 5/5 75 63 12 99 98 1 strelka-varscan-mutect THSD1,missense_variant,p.Ser346Ile,ENST00000349258,NM_199263.2;THSD1,missense_variant,p.Ser399Ile,ENST00000258613,NM_018676.3; A ENST00000258613 Transcript missense_variant 1375/2962 1196/2559 399/852 S/I aGc/aTc 1 -1 THSD1 HGNC HGNC:17754 protein_coding YES CCDS9432.1 ENSP00000258613 Q9NS62 A0A024R064 UPI000007376D NM_018676.3 tolerated(0.08) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16311 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 52378774 52378774 C A 1 0 0 0 0 1 0 0 0 16311 797 28 2 2 THSD1 13 52378774 Missense_Mutation SNP C C3N-01414_T 6595295 52378774 61985554 347 23547 FARP1 0 . GRCh38 13 98440197 98440197 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.2684C>G p.Pro895Arg p.P895R ENST00000627049 24/28 242 164 78 349 349 0 strelka-varscan-mutect FARP1,missense_variant,p.Pro864Arg,ENST00000319562,NM_005766.3;FARP1,missense_variant,p.Pro895Arg,ENST00000627049,;FARP1,missense_variant,p.Pro895Arg,ENST00000595437,NM_001286839.1;FARP1,missense_variant,p.Pro194Arg,ENST00000596256,;STK24,downstream_gene_variant,,ENST00000539966,NM_001032296.3;FARP1,downstream_gene_variant,,ENST00000423063,;FARP1-AS1,upstream_gene_variant,,ENST00000432229,;FARP1,upstream_gene_variant,,ENST00000594346,; G ENST00000627049 Transcript missense_variant 3102/5103 2684/3231 895/1076 P/R cCc/cGc 1 1 FARP1 HGNC HGNC:3591 protein_coding YES CCDS66572.1 ENSP00000486285 C9JME2 UPI000041C6E3 tolerated(0.13) 24/28 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 98440197 98440197 C G 1 0 0 0 0 1 0 0 0 5536 623 22 4 4 FARP1 13 98440197 Missense_Mutation SNP C C3N-01414_T 46061423 98440197 15924131 348 23548 POTEM 0 . GRCh38 14 18967744 18967744 + Missense_Mutation SNP G G T rs764677157 C3N-01414_T C3N-01414_N G G c.259G>T p.Asp87Tyr p.D87Y ENST00000547889 1/11 647 588 59 926 925 1 varscan-mutect POTEM,missense_variant,p.Asp87Tyr,ENST00000547889,NM_001145442.1;POTEM,missense_variant,p.Asp87Tyr,ENST00000552966,;POTEM,missense_variant,p.Asp87Tyr,ENST00000616847,; T ENST00000547889 Transcript missense_variant 311/1817 259/1527 87/508 D/Y Gac/Tac rs764677157,COSM954028 1 1 POTEM HGNC HGNC:37096 protein_coding YES CCDS73609.1 ENSP00000448062 A6NI47 UPI00006C1407 NM_001145442.1 deleterious_low_confidence(0) 1/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764677157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 18967744 18967744 G T 1 0 0 0 0 1 0 0 0 12384 1058 37 1 1 POTEM 14 18967744 Missense_Mutation SNP G C3N-01414_T 18967744 88075974 349 23549 POTEG 0 . GRCh38 14 19434031 19434031 + Missense_Mutation SNP C C A rs369754554 C3N-01414_T C3N-01414_N C C c.259G>T p.Asp87Tyr p.D87Y ENST00000547848 1/11 111 96 15 218 218 0 varscan-mutect POTEG,missense_variant,p.Asp87Tyr,ENST00000547848,NM_001005356.2;POTEG,missense_variant,p.Asp87Tyr,ENST00000547722,;POTEG,missense_variant,p.Asp87Tyr,ENST00000622767,; A ENST00000547848 Transcript missense_variant 311/2204 259/1527 87/508 D/Y Gac/Tac rs369754554,COSM2028145,COSM2028146 1 -1 POTEG HGNC HGNC:33896 protein_coding YES CCDS73610.1 ENSP00000450853 Q6S5H5 UPI00004443FE NM_001005356.2 deleterious_low_confidence(0) 1/11 hmmpanther:PTHR24118:SF43,hmmpanther:PTHR24118 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs369754554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 19434031 19434031 C A 1 0 0 0 0 1 0 0 0 12380 884 31 1 1 POTEG 14 19434031 Missense_Mutation SNP C C3N-01414_T 466287 19434031 87609687 350 23550 OR11G2 0 . GRCh38 14 20197469 20197469 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.134G>T p.Ser45Ile p.S45I ENST00000357366 1/1 184 146 38 351 351 0 strelka-varscan-mutect OR11G2,missense_variant,p.Ser45Ile,ENST00000357366,NM_001005503.1; T ENST00000357366 Transcript missense_variant 134/1111 134/1038 45/345 S/I aGc/aTc 1 1 OR11G2 HGNC HGNC:15346 protein_coding YES CCDS32032.1 ENSP00000349930 Q8NGC1 UPI000015F241 NM_001005503.1 deleterious(0.05) 1/1 hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF183,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1302599281 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 20197469 20197469 G T 1 0 0 0 0 1 0 0 0 11001 971 34 2 2 OR11G2 14 20197469 Missense_Mutation SNP G C3N-01414_T 763438 20197469 86846249 351 23551 OR11H6 0 . GRCh38 14 20223901 20223901 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.192C>A p.= p.V64V ENST00000315519 1/1 183 153 30 270 269 1 strelka-varscan-mutect OR11H6,synonymous_variant,p.=,ENST00000315519,NM_001004480.1; A ENST00000315519 Transcript synonymous_variant 270/1174 192/993 64/330 V gtC/gtA 1 1 OR11H6 HGNC HGNC:15349 protein_coding YES CCDS32033.1 ENSP00000319071 Q8NGC7 A0A126GVP4 UPI000004B1F1 NM_001004480.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF90,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS rs1236938961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 20223901 20223901 C A 1 0 0 0 0 0 0 0 1 11006 900 32 2 2 OR11H6 14 20223901 Silent SNP C C3N-01414_T 26432 20223901 86819817 352 23552 ACIN1 0 . GRCh38 14 23059169 23059169 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.4005G>T p.= p.R1335R ENST00000262710 19/19 106 78 28 185 185 0 strelka-varscan-mutect ACIN1,synonymous_variant,p.=,ENST00000262710,NM_014977.3;ACIN1,synonymous_variant,p.=,ENST00000457657,NM_001164815.1;ACIN1,synonymous_variant,p.=,ENST00000605057,;ACIN1,synonymous_variant,p.=,ENST00000555053,NM_001164814.1;ACIN1,synonymous_variant,p.=,ENST00000557515,;ACIN1,synonymous_variant,p.=,ENST00000397341,;ACIN1,synonymous_variant,p.=,ENST00000357481,NM_001164817.1;ACIN1,synonymous_variant,p.=,ENST00000338631,NM_001164816.1;CDH24,upstream_gene_variant,,ENST00000397359,NM_022478.3;CDH24,upstream_gene_variant,,ENST00000487137,NM_144985.3;CDH24,upstream_gene_variant,,ENST00000267383,;CDH24,upstream_gene_variant,,ENST00000554034,;CDH24,upstream_gene_variant,,ENST00000610348,;ACIN1,downstream_gene_variant,,ENST00000555566,;ACIN1,3_prime_UTR_variant,,ENST00000473758,;ACIN1,downstream_gene_variant,,ENST00000555478,;ACIN1,downstream_gene_variant,,ENST00000555807,;ACIN1,downstream_gene_variant,,ENST00000554680,;ACIN1,downstream_gene_variant,,ENST00000553790,;ACIN1,downstream_gene_variant,,ENST00000556052,;ACIN1,downstream_gene_variant,,ENST00000557039,;ACIN1,downstream_gene_variant,,ENST00000555395,; A ENST00000262710 Transcript synonymous_variant 4333/4935 4005/4026 1335/1341 R cgG/cgT 1 -1 ACIN1 HGNC HGNC:17066 protein_coding YES CCDS9587.1 ENSP00000262710 Q9UKV3 UPI000013D308 NM_014977.3 19/19 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 23059169 23059169 C A 1 0 0 0 0 0 0 0 1 180 610 22 2 2 ACIN1 14 23059169 Silent SNP C C3N-01414_T 2835268 23059169 83984549 353 23553 RABGGTA 0 . GRCh38 14 24267773 24267773 + Missense_Mutation SNP C C A rs369378775 C3N-01414_T C3N-01414_N C C c.1240G>T p.Val414Leu p.V414L ENST00000399409 13/16 138 92 46 187 187 0 strelka-varscan-mutect RABGGTA,missense_variant,p.Val414Leu,ENST00000399409,NM_004581.5;RABGGTA,missense_variant,p.Val414Leu,ENST00000216840,NM_182836.2;RABGGTA,missense_variant,p.Val23Leu,ENST00000560777,;RABGGTA,missense_variant,p.Val50Leu,ENST00000560521,;TGM1,upstream_gene_variant,,ENST00000206765,NM_000359.2;TGM1,upstream_gene_variant,,ENST00000544573,;TGM1,upstream_gene_variant,,ENST00000560226,;TGM1,upstream_gene_variant,,ENST00000560478,;TGM1,upstream_gene_variant,,ENST00000558074,;TGM1,upstream_gene_variant,,ENST00000560443,;TGM1,upstream_gene_variant,,ENST00000561067,;RABGGTA,non_coding_transcript_exon_variant,,ENST00000560871,;RABGGTA,downstream_gene_variant,,ENST00000559586,;RABGGTA,downstream_gene_variant,,ENST00000560163,;RABGGTA,downstream_gene_variant,,ENST00000558534,;RABGGTA,downstream_gene_variant,,ENST00000558954,;RABGGTA,missense_variant,p.Arg415Leu,ENST00000559974,;RABGGTA,missense_variant,p.Arg415Leu,ENST00000558376,;RABGGTA,missense_variant,p.Val50Leu,ENST00000560243,;RABGGTA,non_coding_transcript_exon_variant,,ENST00000559551,;RABGGTA,non_coding_transcript_exon_variant,,ENST00000560998,;RABGGTA,non_coding_transcript_exon_variant,,ENST00000558649,;RABGGTA,non_coding_transcript_exon_variant,,ENST00000559850,;RABGGTA,downstream_gene_variant,,ENST00000543002,;RABGGTA,upstream_gene_variant,,ENST00000561055,;RABGGTA,downstream_gene_variant,,ENST00000560207,;RABGGTA,downstream_gene_variant,,ENST00000558936,;RABGGTA,downstream_gene_variant,,ENST00000560127,; A ENST00000399409 Transcript missense_variant 1724/2265 1240/1704 414/567 V/L Gtg/Ttg rs369378775 1 -1 RABGGTA HGNC HGNC:9795 protein_coding YES CCDS45088.1 ENSP00000382341 Q92696 UPI000013188E NM_004581.5 tolerated(0.17) 13/16 hmmpanther:PTHR11129,hmmpanther:PTHR11129:SF2,Gene3D:1.25.40.120,Superfamily_domains:SSF48439 MODERATE 1 SNV 1 1 PASS rs369378775 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 24267773 24267773 C A 1 0 0 0 0 1 0 0 0 13126 550 19 1 1 RABGGTA 14 24267773 Missense_Mutation SNP C C3N-01414_T 1208604 24267773 82775945 354 23554 CTSG 0 . GRCh38 14 24573657 24573657 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.748C>A p.Gln250Lys p.Q250K ENST00000216336 5/5 86 63 23 146 146 0 varscan-mutect CTSG,missense_variant,p.Gln250Lys,ENST00000216336,NM_001911.2;CTSG,non_coding_transcript_exon_variant,,ENST00000552252,; T ENST00000216336 Transcript missense_variant 785/886 748/768 250/255 Q/K Cag/Aag 1 -1 CTSG HGNC HGNC:2532 protein_coding YES CCDS9631.1 ENSP00000216336 P08311 UPI00001270AC NM_001911.2 tolerated(0.16) 5/5 hmmpanther:PTHR24271,hmmpanther:PTHR24271:SF13 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 24573657 24573657 G T 1 0 0 0 0 1 0 0 0 3844 1299 45 2 2 CTSG 14 24573657 Missense_Mutation SNP G C3N-01414_T 305884 24573657 82470061 355 23555 CLEC14A 0 . GRCh38 14 38255607 38255607 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.416C>A p.Thr139Asn p.T139N ENST00000342213 1/1 152 115 37 213 213 0 strelka-varscan-mutect CLEC14A,missense_variant,p.Thr139Asn,ENST00000342213,NM_175060.2; T ENST00000342213 Transcript missense_variant 763/2267 416/1473 139/490 T/N aCc/aAc 1 -1 CLEC14A HGNC HGNC:19832 protein_coding YES CCDS9667.1 ENSP00000353013 Q86T13 UPI000000CBD4 NM_175060.2 deleterious(0.01) 1/1 Gene3D:3.10.100.10,PROSITE_profiles:PS50041,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF285,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 38255607 38255607 G T 1 0 0 0 0 1 0 0 0 3265 1261 44 2 2 CLEC14A 14 38255607 Missense_Mutation SNP G C3N-01414_T 13681950 38255607 68788111 356 23556 TRAPPC6B 0 . GRCh38 14 39151808 39151808 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.383G>C p.Gly128Ala p.G128A ENST00000330149 5/6 153 121 32 270 270 0 strelka-varscan-mutect TRAPPC6B,missense_variant,p.Gly128Ala,ENST00000330149,NM_001079537.1;TRAPPC6B,missense_variant,p.Gly100Ala,ENST00000347691,NM_177452.3;TRAPPC6B,missense_variant,p.Gly99Ala,ENST00000554018,;TRAPPC6B,non_coding_transcript_exon_variant,,ENST00000557764,;TRAPPC6B,3_prime_UTR_variant,,ENST00000555269,;TRAPPC6B,non_coding_transcript_exon_variant,,ENST00000469361,;TRAPPC6B,downstream_gene_variant,,ENST00000556765,;RPL7AP2,upstream_gene_variant,,ENST00000496515,; G ENST00000330149 Transcript missense_variant 610/3242 383/477 128/158 G/A gGt/gCt 1 -1 TRAPPC6B HGNC HGNC:23066 protein_coding YES CCDS41947.1 ENSP00000330289 Q86SZ2 UPI000000CC28 NM_001079537.1 deleterious(0) 5/6 Gene3D:3.30.1380.20,Pfam_domain:PF04051,hmmpanther:PTHR12817,hmmpanther:PTHR12817:SF3,Superfamily_domains:SSF111126 MODERATE 1 SNV 1 1 PASS rs771251346 . 0 207 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 G 3 3 77 39151808 39151808 C G 1 0 0 0 0 1 0 0 0 16952 507 18 4 4 TRAPPC6B 14 39151808 Missense_Mutation SNP C C3N-01414_T 896201 39151808 67891910 357 23557 FANCM 0 . GRCh38 14 45164555 45164555 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.1778G>T p.Arg593Leu p.R593L ENST00000267430 10/23 230 178 52 331 330 1 strelka-varscan-mutect FANCM,missense_variant,p.Arg593Leu,ENST00000267430,NM_020937.2;FANCM,missense_variant,p.Arg567Leu,ENST00000542564,NM_001308133.1;FANCM,missense_variant,p.Arg593Leu,ENST00000556036,NM_001308134.1;FANCM,intron_variant,,ENST00000556250,; T ENST00000267430 Transcript missense_variant 1863/7111 1778/6147 593/2048 R/L cGa/cTa COSM553240 1 1 FANCM HGNC HGNC:23168 protein_coding YES CCDS32070.1 ENSP00000267430 Q8IYD8 UPI000059F032 NM_020937.2 deleterious(0) 10/23 PROSITE_profiles:PS51194,hmmpanther:PTHR14025:SF20,hmmpanther:PTHR14025,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 45164555 45164555 G T 1 0 0 0 0 1 0 0 0 5531 1058 37 1 1 FANCM 14 45164555 Missense_Mutation SNP G C3N-01414_T 6012747 45164555 61879163 358 23558 RPL10L 0 . GRCh38 14 46651305 46651305 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.432C>A p.Asn144Lys p.N144K ENST00000298283 1/1 307 237 70 491 491 0 strelka-varscan-mutect RPL10L,missense_variant,p.Asn144Lys,ENST00000298283,NM_080746.2; T ENST00000298283 Transcript missense_variant 517/812 432/645 144/214 N/K aaC/aaA 1 -1 RPL10L HGNC HGNC:17976 protein_coding YES CCDS32071.1 ENSP00000298283 Q96L21 UPI0000073CA8 NM_080746.2 deleterious(0.04) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11726:SF11,hmmpanther:PTHR11726,Pfam_domain:PF00252,TIGRFAM_domain:TIGR00279,Gene3D:3.90.1170.10,PIRSF_domain:PIRSF005590,Superfamily_domains:SSF54686 MODERATE 1 SNV 1 PASS rs1464110614 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 46651305 46651305 G T 1 0 0 0 0 1 0 0 0 13808 1136 40 1 1 RPL10L 14 46651305 Missense_Mutation SNP G C3N-01414_T 1486750 46651305 60392413 359 23559 TMEM260 0 . GRCh38 14 56647323 56647323 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1950G>T p.Met650Ile p.M650I ENST00000261556 16/16 370 287 83 515 515 0 strelka-varscan-mutect TMEM260,missense_variant,p.Met650Ile,ENST00000261556,NM_017799.3;TMEM260,intron_variant,,ENST00000555046,;RP11-1085N6.2,intron_variant,,ENST00000553800,;RP11-1085N6.2,intron_variant,,ENST00000555924,;RP11-1085N6.3,downstream_gene_variant,,ENST00000554597,;TMEM260,3_prime_UTR_variant,,ENST00000556422,;TMEM260,3_prime_UTR_variant,,ENST00000539559,;TMEM260,3_prime_UTR_variant,,ENST00000555497,;TMEM260,non_coding_transcript_exon_variant,,ENST00000556648,; T ENST00000261556 Transcript missense_variant 2072/4264 1950/2124 650/707 M/I atG/atT 1 1 TMEM260 HGNC HGNC:20185 protein_coding YES CCDS9727.2 ENSP00000261556 Q9NX78 UPI00001FD5D2 NM_017799.3 deleterious(0.04) 16/16 hmmpanther:PTHR16214,hmmpanther:PTHR16214:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 56647323 56647323 G T 1 0 0 0 0 1 0 0 0 16621 1319 46 2 2 TMEM260 14 56647323 Missense_Mutation SNP G C3N-01414_T 9996018 56647323 50396395 360 23560 KCNH5 0 . GRCh38 14 62707720 62707720 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2755G>T p.Glu919Ter p.E919* ENST00000322893 11/11 88 61 27 119 119 0 strelka-varscan-mutect KCNH5,stop_gained,p.Glu919Ter,ENST00000322893,NM_139318.4;KCNH5,3_prime_UTR_variant,,ENST00000420622,NM_172375.2;KCNH5,downstream_gene_variant,,ENST00000394968,; A ENST00000322893 Transcript stop_gained 3024/11290 2755/2967 919/988 E/* Gag/Tag 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 11/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10217:SF533,hmmpanther:PTHR10217 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 62707720 62707720 C A 1 0 0 0 0 0 1 0 0 7951 922 32 2 2 KCNH5 14 62707720 Nonsense_Mutation SNP C C3N-01414_T 6060397 62707720 44335998 361 23561 KCNH5 0 . GRCh38 14 62950181 62950181 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.1321A>G p.Thr441Ala p.T441A ENST00000322893 7/11 261 235 26 378 378 0 strelka-varscan-mutect KCNH5,missense_variant,p.Thr441Ala,ENST00000322893,NM_139318.4;KCNH5,missense_variant,p.Thr441Ala,ENST00000420622,NM_172375.2;KCNH5,missense_variant,p.Thr383Ala,ENST00000394968,;KCNH5,non_coding_transcript_exon_variant,,ENST00000394964,; C ENST00000322893 Transcript missense_variant 1590/11290 1321/2967 441/988 T/A Acc/Gcc 1 -1 KCNH5 HGNC HGNC:6254 protein_coding YES CCDS9756.1 ENSP00000321427 Q8NCM2 UPI0000039E2D NM_139318.4 tolerated(0.12) 7/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 62950181 62950181 T C 1 0 0 0 0 1 0 0 0 7951 1638 57 5 5 KCNH5 14 62950181 Missense_Mutation SNP T C3N-01414_T 242461 62950181 44093537 362 23562 SPTB 0 . GRCh38 14 64775155 64775155 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.4812G>C p.Glu1604Asp p.E1604D ENST00000556626 23/36 206 159 47 363 363 0 strelka-varscan-mutect SPTB,missense_variant,p.Glu1604Asp,ENST00000556626,;SPTB,missense_variant,p.Glu1604Asp,ENST00000389722,NM_001024858.2;SPTB,missense_variant,p.Glu1604Asp,ENST00000389721,NM_000347.5;SPTB,missense_variant,p.Glu1604Asp,ENST00000389720,;SPTB,missense_variant,p.Glu269Asp,ENST00000553938,; G ENST00000556626 Transcript missense_variant 4955/10153 4812/6987 1604/2328 E/D gaG/gaC 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D deleterious(0) 23/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 64775155 64775155 C G 1 0 0 0 0 1 0 0 0 15474 796 28 4 4 SPTB 14 64775155 Missense_Mutation SNP C C3N-01414_T 1824974 64775155 42268563 363 23563 SPTB 0 . GRCh38 14 64786847 64786847 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.3118G>T p.Glu1040Ter p.E1040* ENST00000556626 16/36 355 277 78 526 525 1 strelka-varscan-mutect SPTB,stop_gained,p.Glu1040Ter,ENST00000556626,;SPTB,stop_gained,p.Glu1040Ter,ENST00000389722,NM_001024858.2;SPTB,stop_gained,p.Glu1040Ter,ENST00000389721,NM_000347.5;SPTB,stop_gained,p.Glu1040Ter,ENST00000389720,;SPTB,upstream_gene_variant,,ENST00000553938,;SPTB,upstream_gene_variant,,ENST00000622027,; A ENST00000556626 Transcript stop_gained 3261/10153 3118/6987 1040/2328 E/* Gag/Tag 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D 16/36 Low_complexity_(Seg):seg,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 SNV 1 1 PASS rs1211615857 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 64786847 64786847 C A 1 0 0 0 0 0 1 0 0 15474 864 30 2 2 SPTB 14 64786847 Nonsense_Mutation SNP C C3N-01414_T 11692 64786847 42256871 364 23564 PLEKHD1 0 . GRCh38 14 69526786 69526786 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1013A>T p.Gln338Leu p.Q338L ENST00000322564 10/13 62 50 12 87 87 0 strelka-varscan-mutect PLEKHD1,missense_variant,p.Gln338Leu,ENST00000322564,NM_001161498.1; T ENST00000322564 Transcript missense_variant 1225/4865 1013/1521 338/506 Q/L cAg/cTg 1 1 PLEKHD1 HGNC HGNC:20148 protein_coding YES CCDS53903.1 ENSP00000317175 A6NEE1 UPI0000EE334F NM_001161498.1 tolerated(0.17) 10/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14383,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 69526786 69526786 A T 1 0 0 0 0 1 0 0 0 12158 188 7 4 4 PLEKHD1 14 69526786 Missense_Mutation SNP A C3N-01414_T 4739939 69526786 37516932 365 23565 MLH3 0 . GRCh38 14 75046629 75046629 + Silent SNP T T C novel C3N-01414_T C3N-01414_N T T c.3027A>G p.= p.V1009V ENST00000355774 2/13 410 333 77 716 716 0 strelka-varscan-mutect MLH3,synonymous_variant,p.=,ENST00000355774,NM_001040108.1;MLH3,synonymous_variant,p.=,ENST00000380968,NM_014381.2;MLH3,synonymous_variant,p.=,ENST00000556740,;MLH3,synonymous_variant,p.=,ENST00000556257,;MLH3,synonymous_variant,p.=,ENST00000553713,;MLH3,downstream_gene_variant,,ENST00000553263,;MLH3,downstream_gene_variant,,ENST00000557648,;MLH3,non_coding_transcript_exon_variant,,ENST00000555671,;MLH3,upstream_gene_variant,,ENST00000555499,;MLH3,synonymous_variant,p.=,ENST00000555144,;MLH3,upstream_gene_variant,,ENST00000556453,; C ENST00000355774 Transcript synonymous_variant 3243/7896 3027/4362 1009/1453 V gtA/gtG 1 -1 MLH3 HGNC HGNC:7128 protein_coding YES CCDS32123.1 ENSP00000348020 Q9UHC1 UPI00001AEEE0 NM_001040108.1 2/13 hmmpanther:PTHR10073:SF7,hmmpanther:PTHR10073 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 77 75046629 75046629 T C 1 0 0 0 0 0 0 0 1 9585 1509 53 5 5 MLH3 14 75046629 Silent SNP T C3N-01414_T 5519843 75046629 31997089 366 23566 LRRC74A 0 . GRCh38 14 76853345 76853345 + Missense_Mutation SNP G G A rs142713488,rs766259360 C3N-01414_T C3N-01414_N G G c.943G>A p.Gly315Ser p.G315S ENST00000393774 9/14 276 245 31 432 432 0 strelka-varscan-mutect LRRC74A,missense_variant,p.Gly315Ser,ENST00000393774,NM_194287.2;LRRC74A,3_prime_UTR_variant,,ENST00000484640,;LRRC74A,3_prime_UTR_variant,,ENST00000216450,; A ENST00000393774 Transcript missense_variant 1067/1648 943/1467 315/488 G/S Ggc/Agc rs142713488,rs766259360,COSM1198076 1 1 LRRC74A HGNC HGNC:23346 protein_coding YES CCDS9853.2 ENSP00000377369 Q0VAA2 UPI000155D520 NM_194287.2 tolerated(1) 9/14 hmmpanther:PTHR24114,Pfam_domain:PF13516,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 0,0,1 MODERATE 1 SNV 1 0,0,1 1 PASS rs142713488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 76853345 76853345 G A 1 0 0 0 0 1 0 0 0 8921 1116 39 1 1 LRRC74A 14 76853345 Missense_Mutation SNP G C3N-01414_T 1806716 76853345 30190373 367 23567 GPR65 0 . GRCh38 14 88011229 88011229 + Nonsense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.382A>T p.Arg128Ter p.R128* ENST00000267549 2/2 282 223 59 381 381 0 strelka-varscan-mutect GPR65,stop_gained,p.Arg128Ter,ENST00000267549,NM_003608.3;RP11-300J18.2,intron_variant,,ENST00000554433,; T ENST00000267549 Transcript stop_gained 940/4522 382/1014 128/337 R/* Aga/Tga 1 1 GPR65 HGNC HGNC:4517 protein_coding YES CCDS9879.1 ENSP00000267549 Q8IYL9 B5B0C2 UPI000007422C NM_003608.3 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01649,PROSITE_profiles:PS50262,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF49,Superfamily_domains:SSF81321 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 88011229 88011229 A T 1 0 0 0 0 0 1 0 0 6589 64 3 4 4 GPR65 14 88011229 Nonsense_Mutation SNP A C3N-01414_T 11157884 88011229 19032489 368 23568 MOAP1 0 . GRCh38 14 93184027 93184027 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.216G>T p.Glu72Asp p.E72D ENST00000556883 2/2 116 94 22 159 159 0 strelka-varscan-mutect MOAP1,missense_variant,p.Glu72Asp,ENST00000556883,;MOAP1,missense_variant,p.Glu72Asp,ENST00000298894,NM_022151.4;TMEM251,upstream_gene_variant,,ENST00000415050,NM_001098621.1;TMEM251,upstream_gene_variant,,ENST00000283534,NM_015676.1;RP11-371E8.4,upstream_gene_variant,,ENST00000557574,;RP11-371E8.4,upstream_gene_variant,,ENST00000557048,;RP11-371E8.4,upstream_gene_variant,,ENST00000554824,; A ENST00000556883 Transcript missense_variant 701/2529 216/1056 72/351 E/D gaG/gaT 1 -1 MOAP1 HGNC HGNC:16658 protein_coding YES CCDS9908.1 ENSP00000451594 Q96BY2 UPI0000037797 tolerated(0.65) 2/2 Pfam_domain:PF14893,hmmpanther:PTHR23095,hmmpanther:PTHR23095:SF14 MODERATE 1 SNV 2 1 PASS rs1298207409 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 93184027 93184027 C A 1 0 0 0 0 1 0 0 0 9644 912 32 2 2 MOAP1 14 93184027 Missense_Mutation SNP C C3N-01414_T 5172798 93184027 13859691 369 23569 UNC79 0 . GRCh38 14 93673405 93673405 + Missense_Mutation SNP C C G C3N-01414_T C3N-01414_N C C c.6277C>G p.Leu2093Val p.L2093V ENST00000256339 42/50 197 169 28 338 338 0 strelka-varscan-mutect UNC79,missense_variant,p.Leu2292Val,ENST00000553484,;UNC79,missense_variant,p.Leu2231Val,ENST00000555664,;UNC79,missense_variant,p.Leu2093Val,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Leu2270Val,ENST00000393151,;UNC79,missense_variant,p.Leu2093Val,ENST00000621021,; G ENST00000256339 Transcript missense_variant 6932/8400 6277/7377 2093/2458 L/V Cta/Gta COSM1516236,COSM1516237 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious(0.05) 42/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1371916622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 93673405 93673405 C G 1 0 0 0 0 1 0 0 0 17520 680 24 4 4 UNC79 14 93673405 Missense_Mutation SNP C C3N-01414_T 489378 93673405 13370313 370 23570 DDX24 0 . GRCh38 14 94062244 94062244 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.1096A>G p.Thr366Ala p.T366A ENST00000621632 3/9 289 229 60 464 464 0 strelka-varscan-mutect DDX24,missense_variant,p.Thr366Ala,ENST00000621632,NM_020414.3;DDX24,missense_variant,p.Thr323Ala,ENST00000555054,;DDX24,missense_variant,p.Thr311Ala,ENST00000330836,;DDX24,missense_variant,p.Thr116Ala,ENST00000544005,;DDX24,5_prime_UTR_variant,,ENST00000622786,;DDX24,non_coding_transcript_exon_variant,,ENST00000555762,; C ENST00000621632 Transcript missense_variant 1228/5612 1096/2580 366/859 T/A Act/Gct 1 -1 DDX24 HGNC HGNC:13266 protein_coding YES CCDS9918.1 ENSP00000481495 Q9GZR7 UPI0000129082 NM_020414.3 tolerated(0.83) 3/9 PROSITE_profiles:PS51192,Pfam_domain:PF00270,SMART_domains:SM00487 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 94062244 94062244 T C 1 0 0 0 0 1 0 0 0 4154 1667 58 5 5 DDX24 14 94062244 Missense_Mutation SNP T C3N-01414_T 388839 94062244 12981474 371 23571 SERPINA5 0 . GRCh38 14 94590756 94590756 + Nonsense_Mutation SNP G G T rs757910699 C3N-01414_T C3N-01414_N G G c.898G>T p.Glu300Ter p.E300* ENST00000329597 5/6 74 56 18 114 114 0 varscan-mutect SERPINA5,stop_gained,p.Glu300Ter,ENST00000329597,NM_000624.5;SERPINA5,stop_gained,p.Glu300Ter,ENST00000554866,;SERPINA5,stop_gained,p.Glu300Ter,ENST00000554276,;SERPINA5,stop_gained,p.Glu300Ter,ENST00000553780,;SERPINA5,downstream_gene_variant,,ENST00000554760,;SERPINA5,downstream_gene_variant,,ENST00000556775,;SERPINA5,downstream_gene_variant,,ENST00000555681,;SERPINA5,downstream_gene_variant,,ENST00000557598,;SERPINA5,downstream_gene_variant,,ENST00000554220,;SERPINA5,downstream_gene_variant,,ENST00000553511,;SERPINA5,downstream_gene_variant,,ENST00000554633,;SERPINA5,downstream_gene_variant,,ENST00000556064,;SERPINA5,non_coding_transcript_exon_variant,,ENST00000556730,;SERPINA3,upstream_gene_variant,,ENST00000553947,; T ENST00000329597 Transcript stop_gained 1133/2337 898/1221 300/406 E/* Gag/Tag rs757910699 1 1 SERPINA5 HGNC HGNC:8723 protein_coding YES CCDS9928.1 ENSP00000333203 P05154 A0A024R6N9 UPI000013E52C NM_000624.5 5/6 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF176,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 HIGH 1 SNV 1 1 PASS rs757910699 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 94590756 94590756 G T 1 0 0 0 0 0 1 0 0 14368 1059 37 1 1 SERPINA5 14 94590756 Nonsense_Mutation SNP G C3N-01414_T 528512 94590756 12452962 372 23572 EML1 0 . GRCh38 14 99914635 99914635 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.1747G>A p.Asp583Asn p.D583N ENST00000334192 16/23 180 156 24 239 239 0 strelka-varscan-mutect EML1,missense_variant,p.Asp564Asn,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Asp583Asn,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Asp552Asn,ENST00000327921,;EML1,downstream_gene_variant,,ENST00000554386,;EML1,downstream_gene_variant,,ENST00000555812,;EML1,missense_variant,p.Asp21Asn,ENST00000557313,;EML1,non_coding_transcript_exon_variant,,ENST00000554111,;EML1,downstream_gene_variant,,ENST00000554553,; A ENST00000334192 Transcript missense_variant 1881/4064 1747/2505 583/834 D/N Gac/Aac 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 deleterious(0.02) 16/23 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22,SMART_domains:SM00320,Superfamily_domains:SSF50998 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 99914635 99914635 G A 1 0 0 0 0 1 0 0 0 4939 1290 45 3 3 EML1 14 99914635 Missense_Mutation SNP G C3N-01414_T 5323879 99914635 7129083 373 23573 TECPR2 0 . GRCh38 14 102449656 102449656 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.3103G>C p.Asp1035His p.D1035H ENST00000359520 14/20 241 168 73 312 312 0 strelka-varscan-mutect TECPR2,missense_variant,p.Asp1035His,ENST00000359520,NM_014844.3;TECPR2,missense_variant,p.Asp1035His,ENST00000558678,NM_001172631.1;TECPR2,downstream_gene_variant,,ENST00000557786,; C ENST00000359520 Transcript missense_variant 3329/8686 3103/4236 1035/1411 D/H Gac/Cac 1 1 TECPR2 HGNC HGNC:19957 protein_coding YES CCDS32162.1 ENSP00000352510 O15040 UPI00001FDC38 NM_014844.3 deleterious(0) 14/20 hmmpanther:PTHR23287,hmmpanther:PTHR23287:SF16 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 102449656 102449656 G C 1 0 0 0 0 1 0 0 0 16155 1290 45 4 4 TECPR2 14 102449656 Missense_Mutation SNP G C3N-01414_T 2535021 102449656 4594062 374 23574 C14orf180 0 . GRCh38 14 104588690 104588690 + Missense_Mutation SNP G G T rs529444309 C3N-01414_T C3N-01414_N G G c.346G>T p.Gly116Cys p.G116C ENST00000331952 5/5 136 103 33 194 194 0 strelka-varscan-mutect C14orf180,missense_variant,p.Gly116Cys,ENST00000331952,NM_001286399.1;C14orf180,synonymous_variant,p.=,ENST00000557649,NM_001008404.2;C14orf180,synonymous_variant,p.=,ENST00000410013,NM_001286400.1;TMEM179,intron_variant,,ENST00000415614,;TMEM179,downstream_gene_variant,,ENST00000616017,;TMEM179,downstream_gene_variant,,ENST00000556573,NM_001286389.1;TMEM179,downstream_gene_variant,,ENST00000556320,;RP11-614O9.1,downstream_gene_variant,,ENST00000556073,; T ENST00000331952 Transcript missense_variant 602/1455 346/534 116/177 G/C Ggc/Tgc rs529444309 1 1 C14orf180 HGNC HGNC:33795 protein_coding YES CCDS66722.1 ENSP00000333041 J3KNP8 UPI00021CF38C NM_001286399.1 deleterious_low_confidence(0) 5/5 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs529444309 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 104588690 104588690 G T 1 0 0 0 0 1 0 0 0 1835 1103 39 1 1 C14orf180 14 104588690 Missense_Mutation SNP G C3N-01414_T 2139034 104588690 2455028 375 23575 AHNAK2 0 . GRCh38 14 104943841 104943841 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.11610A>T p.Lys3870Asn p.K3870N ENST00000333244 7/7 331 262 69 528 526 2 strelka-varscan-mutect AHNAK2,missense_variant,p.Lys3870Asn,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript missense_variant 11730/18254 11610/17388 3870/5795 K/N aaA/aaT 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 deleterious(0.01) 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 MODERATE 1 SNV 5 1 PASS rs1248596233 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 104943841 104943841 T A 1 0 0 0 0 1 0 0 0 492 1722 60 4 4 AHNAK2 14 104943841 Missense_Mutation SNP T C3N-01414_T 355151 104943841 2099877 376 23576 GOLGA6L2 0 . GRCh38 15 23440855 23440855 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.1620G>A p.= p.R540R ENST00000567107 8/8 321 290 31 554 553 1 varscan-mutect GOLGA6L2,synonymous_variant,p.=,ENST00000567107,NM_001304388.1;GOLGA6L2,synonymous_variant,p.=,ENST00000345070,;GOLGA6L2,intron_variant,,ENST00000312015,;GOLGA6L2,3_prime_UTR_variant,,ENST00000566571,; T ENST00000567107 Transcript synonymous_variant 1673/3030 1620/2730 540/909 R cgG/cgA 1 -1 GOLGA6L2 HGNC HGNC:26695 protein_coding YES CCDS76728.1 ENSP00000454407 H3BMJ4 UPI00024672CE NM_001304388.1 8/8 hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF11 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 23440855 23440855 C T 1 0 0 0 0 0 0 0 1 6440 610 22 3 3 GOLGA6L2 15 23440855 Silent SNP C C3N-01414_T 23440855 78550334 377 23577 NDN 0 . GRCh38 15 23687100 23687100 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.118G>T p.Glu40Ter p.E40* ENST00000331837 1/1 114 102 12 188 188 0 strelka-varscan-mutect NDN,stop_gained,p.Glu40Ter,ENST00000331837,NM_002487.2; A ENST00000331837 Transcript stop_gained 231/1931 118/966 40/321 E/* Gag/Tag 1 -1 NDN HGNC HGNC:7675 protein_coding YES CCDS10014.1 ENSP00000332643 Q99608 X5D982 UPI000012FEF1 NM_002487.2 1/1 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF10 HIGH 1 SNV 1 PASS rs1308499928 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 23687100 23687100 C A 1 0 0 0 0 0 1 0 0 10268 922 32 2 2 NDN 15 23687100 Nonsense_Mutation SNP C C3N-01414_T 246245 23687100 78304089 378 23578 GANC 0 . GRCh38 15 42306572 42306572 + Nonsense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.585G>A p.Trp195Ter p.W195* ENST00000318010 7/24 127 115 12 233 231 2 strelka-varscan-mutect GANC,stop_gained,p.Trp195Ter,ENST00000318010,NM_198141.2;GANC,stop_gained,p.Trp195Ter,ENST00000566442,NM_001301409.1;GANC,non_coding_transcript_exon_variant,,ENST00000567421,; A ENST00000318010 Transcript stop_gained 825/7781 585/2745 195/914 W/* tgG/tgA 1 1 GANC HGNC HGNC:4139 protein_coding YES CCDS10084.1 ENSP00000326227 Q8TET4 UPI00001FE303 NM_198141.2 7/24 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF60 HIGH 1 SNV 1 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 42306572 42306572 G A 1 0 0 0 0 0 1 0 0 6102 1241 43 3 3 GANC 15 42306572 Nonsense_Mutation SNP G C3N-01414_T 18619472 42306572 59684617 379 23579 DUOXA1 0 . GRCh38 15 45119264 45119264 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.874A>T p.Met292Leu p.M292L ENST00000267803 9/11 146 126 20 227 227 0 strelka-varscan-mutect DUOXA1,missense_variant,p.Met247Leu,ENST00000558996,NM_001276268.1;DUOXA1,missense_variant,p.Met292Leu,ENST00000267803,NM_144565.3;DUOXA1,missense_variant,p.Met292Leu,ENST00000559014,NM_001276264.1;DUOXA1,missense_variant,p.Met247Leu,ENST00000613425,;DUOXA1,missense_variant,p.Met247Leu,ENST00000558422,NM_001276267.1;DUOXA1,missense_variant,p.Met247Leu,ENST00000430224,NM_001276265.1;DUOXA1,missense_variant,p.Met292Leu,ENST00000560572,NM_001276266.1;DUOX2,upstream_gene_variant,,ENST00000389039,;DUOXA2,downstream_gene_variant,,ENST00000323030,NM_207581.3;DUOXA1,downstream_gene_variant,,ENST00000559644,;DUOXA1,downstream_gene_variant,,ENST00000558377,;DUOXA1,downstream_gene_variant,,ENST00000559226,;DUOXA1,downstream_gene_variant,,ENST00000558326,;DUOXA1,downstream_gene_variant,,ENST00000558851,;DUOXA1,downstream_gene_variant,,ENST00000559988,;DUOXA1,3_prime_UTR_variant,,ENST00000559013,;DUOXA2,downstream_gene_variant,,ENST00000491993,;DUOXA2,downstream_gene_variant,,ENST00000350243,; A ENST00000267803 Transcript missense_variant 1274/1996 874/1452 292/483 M/L Atg/Ttg 1 -1 DUOXA1 HGNC HGNC:26507 protein_coding YES CCDS10119.1 ENSP00000267803 Q1HG43 A8K9Q6 UPI000006D4D4 NM_144565.3 tolerated(0.43) 9/11 hmmpanther:PTHR31158,hmmpanther:PTHR31158:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 45119264 45119264 T A 1 0 0 0 0 1 0 0 0 4624 1464 51 4 4 DUOXA1 15 45119264 Missense_Mutation SNP T C3N-01414_T 2812692 45119264 56871925 380 23580 USP50 0 . GRCh38 15 50544634 50544635 + Frame_Shift_Ins INS - - A novel C3N-01414_T C3N-01414_N - - c.200_201insT p.Leu68AlafsTer20 p.L68Afs*20 ENST00000532404 2/7 161 139 22 270 270 0 sindel-pindel USP50,frameshift_variant,p.Leu68AlafsTer17,ENST00000616326,;USP50,frameshift_variant,p.Leu68AlafsTer20,ENST00000532404,NM_203494.4;USP50,intron_variant,,ENST00000530218,;USP50,intron_variant,,ENST00000559105,; A ENST00000532404 Transcript frameshift_variant 374-375/1386 200-201/1005 67/334 P/PX ccg/ccTg 1 -1 USP50 HGNC HGNC:20079 protein_coding YES CCDS53944.1 ENSP00000434676 Q70EL3 UPI0001CB7F8F NM_203494.4 2/7 PROSITE_profiles:PS50235,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 HIGH 1 insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 77 50544634 50544634 - A 1 0 1 1 0 0 0 0 0 17625 755 27 0 0 USP50 15 50544634 Frame_Shift_Ins INS - C3N-01414_T 5425370 50544634 51446555 381 23581 MYO5A 0 . GRCh38 15 52383134 52383134 + Missense_Mutation SNP A A C novel C3N-01414_T C3N-01414_N A A c.1969T>G p.Tyr657Asp p.Y657D ENST00000399231 16/41 349 330 19 587 586 1 strelka-varscan-mutect MYO5A,missense_variant,p.Tyr657Asp,ENST00000399231,NM_000259.3;MYO5A,missense_variant,p.Tyr657Asp,ENST00000358212,;MYO5A,missense_variant,p.Tyr657Asp,ENST00000399233,;MYO5A,missense_variant,p.Tyr657Asp,ENST00000613858,;MYO5A,missense_variant,p.Tyr657Asp,ENST00000356338,NM_001142495.1;MYO5A,missense_variant,p.Tyr657Asp,ENST00000553916,;MYO5A,3_prime_UTR_variant,,ENST00000556196,;MYO5A,downstream_gene_variant,,ENST00000469611,; C ENST00000399231 Transcript missense_variant 2213/12225 1969/5568 657/1855 Y/D Tat/Gat 1 -1 MYO5A HGNC HGNC:7602 protein_coding YES CCDS42037.1 ENSP00000382177 Q9Y4I1 UPI0000E445E1 NM_000259.3 deleterious(0.01) 16/41 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF273,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1393726283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 52383134 52383134 A C 1 0 0 0 0 1 0 0 0 10079 420 15 5 5 MYO5A 15 52383134 Missense_Mutation SNP A C3N-01414_T 1838500 52383134 49608055 382 23582 RFX7 0 . GRCh38 15 56093537 56093537 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.3900G>C p.Leu1300Phe p.L1300F ENST00000559447 9/9 110 84 26 176 176 0 strelka-varscan-mutect RFX7,missense_variant,p.Leu1300Phe,ENST00000559447,NM_022841.5;RFX7,intron_variant,,ENST00000559847,; G ENST00000559447 Transcript missense_variant 4172/10426 3900/4092 1300/1363 L/F ttG/ttC 1 -1 RFX7 HGNC HGNC:25777 protein_coding YES ENSP00000453281 Q2KHR2 UPI0000695D7E NM_022841.5 deleterious(0) 9/9 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF2 MODERATE 1 SNV 5 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 56093537 56093537 C G 1 0 0 0 0 1 0 0 0 13442 825 29 4 4 RFX7 15 56093537 Missense_Mutation SNP C C3N-01414_T 3710403 56093537 45897652 383 23583 CCNB2 0 . GRCh38 15 59114574 59114574 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.398A>T p.Asp133Val p.D133V ENST00000288207 4/9 60 47 13 102 102 0 strelka-varscan-mutect CCNB2,missense_variant,p.Asp133Val,ENST00000621385,;CCNB2,missense_variant,p.Asp133Val,ENST00000288207,NM_004701.3;CCNB2,missense_variant,p.Asp52Val,ENST00000559622,;RP11-59H7.4,downstream_gene_variant,,ENST00000619686,;CCNB2,non_coding_transcript_exon_variant,,ENST00000561077,;CCNB2,upstream_gene_variant,,ENST00000559301,; T ENST00000288207 Transcript missense_variant 589/1556 398/1197 133/398 D/V gAc/gTc 1 1 CCNB2 HGNC HGNC:1580 protein_coding YES CCDS10170.1 ENSP00000288207 O95067 UPI00001275B3 NM_004701.3 deleterious(0.02) 4/9 hmmpanther:PTHR10177:SF184,hmmpanther:PTHR10177,PIRSF_domain:PIRSF001771,Superfamily_domains:SSF47954 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 59114574 59114574 A T 1 0 0 0 0 1 0 0 0 2612 275 10 4 4 CCNB2 15 59114574 Missense_Mutation SNP A C3N-01414_T 3021037 59114574 42876615 384 23584 TLE3 0 . GRCh38 15 70096160 70096160 + Splice_Site SNP C C T novel C3N-01414_T C3N-01414_N C C c.125+1G>A p.X42_splice ENST00000558939 77 55 22 134 134 0 strelka-varscan-mutect TLE3,splice_donor_variant,,ENST00000558939,NM_005078.3;TLE3,splice_donor_variant,,ENST00000627388,;TLE3,splice_donor_variant,,ENST00000317509,NM_020908.2;TLE3,splice_donor_variant,,ENST00000557997,NM_001282979.1;TLE3,splice_donor_variant,,ENST00000559929,;TLE3,splice_donor_variant,,ENST00000560939,;TLE3,splice_donor_variant,,ENST00000559048,;TLE3,splice_donor_variant,,ENST00000558201,;TLE3,splice_donor_variant,,ENST00000440567,NM_001282981.1;TLE3,splice_donor_variant,,ENST00000451782,NM_001105192.2;TLE3,splice_donor_variant,,ENST00000558379,NM_001282980.1;TLE3,splice_donor_variant,,ENST00000557907,;TLE3,splice_donor_variant,,ENST00000560996,;TLE3,intron_variant,,ENST00000559191,;TLE3,upstream_gene_variant,,ENST00000560589,;TLE3,upstream_gene_variant,,ENST00000539550,NM_001282982.1;TLE3,upstream_gene_variant,,ENST00000557984,;TLE3,downstream_gene_variant,,ENST00000559574,;TLE3,splice_donor_variant,,ENST00000557919,;TLE3,splice_donor_variant,,ENST00000561453,;TLE3,splice_donor_variant,,ENST00000560525,; T ENST00000558939 Transcript splice_donor_variant -/6004 125/2319 42/772 1 -1 TLE3 HGNC HGNC:11839 protein_coding YES CCDS45293.1 ENSP00000452871 Q04726 UPI000013703A NM_005078.3 2/19 HIGH 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999888 1 1 1 0 T 5 4 77 70096160 70096160 C T 1 0 0 0 0 0 0 1 0 16386 521 18 3 3 TLE3 15 70096160 Splice_Site SNP C C3N-01414_T 10981586 70096160 31895029 385 23585 LARP6 0 . GRCh38 15 70832179 70832179 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1349C>A p.Thr450Lys p.T450K ENST00000299213 3/3 91 80 11 137 137 0 strelka-varscan-mutect LARP6,missense_variant,p.Thr450Lys,ENST00000299213,NM_018357.3;LARP6,downstream_gene_variant,,ENST00000559316,; T ENST00000299213 Transcript missense_variant 1420/4469 1349/1476 450/491 T/K aCg/aAg 1 -1 LARP6 HGNC HGNC:24012 protein_coding YES CCDS32281.1 ENSP00000299213 Q9BRS8 UPI0000073C63 NM_018357.3 tolerated(0.59) 3/3 hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF71 MODERATE 1 SNV 1 1 PASS rs1281107814 . 0 201 8 0 0 0 0 0 -19.99944 0.9999968 1 1 1 0 T 3 4 77 70832179 70832179 G T 1 0 0 0 0 1 0 0 0 8543 1145 40 1 1 LARP6 15 70832179 Missense_Mutation SNP G C3N-01414_T 736019 70832179 31159010 386 23586 THSD4 0 . GRCh38 15 71731141 71731141 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1554C>A p.Asn518Lys p.N518K ENST00000355327 10/18 221 200 21 340 339 1 strelka-varscan-mutect THSD4,missense_variant,p.Asn518Lys,ENST00000355327,NM_024817.2;THSD4,missense_variant,p.Asn158Lys,ENST00000357769,NM_001286429.1;THSD4,intron_variant,,ENST00000261862,;THSD4,non_coding_transcript_exon_variant,,ENST00000567838,;THSD4,non_coding_transcript_exon_variant,,ENST00000567776,;THSD4,non_coding_transcript_exon_variant,,ENST00000567745,; A ENST00000355327 Transcript missense_variant 1688/9200 1554/3057 518/1018 N/K aaC/aaA 1 1 THSD4 HGNC HGNC:25835 protein_coding YES CCDS10238.2 ENSP00000347484 Q6ZMP0 UPI00001A797D NM_024817.2 deleterious(0) 10/18 hmmpanther:PTHR13723,Pfam_domain:PF05986 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 71731141 71731141 C A 1 0 0 0 0 1 0 0 0 16312 506 18 2 2 THSD4 15 71731141 Missense_Mutation SNP C C3N-01414_T 898962 71731141 30260048 387 23587 REC114 0 . GRCh38 15 73443212 73443212 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.27G>C p.Leu9Phe p.L9F ENST00000331090 1/6 116 99 17 189 189 0 strelka-varscan-mutect REC114,missense_variant,p.Leu9Phe,ENST00000331090,NM_001042367.1;REC114,missense_variant,p.Leu9Phe,ENST00000560581,; C ENST00000331090 Transcript missense_variant 55/927 27/801 9/266 L/F ttG/ttC 1 1 REC114 HGNC HGNC:25065 protein_coding YES CCDS45296.1 ENSP00000328423 Q7Z4M0 UPI0000161A3A NM_001042367.1 tolerated(0.42) 1/6 hmmpanther:PTHR34921 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 73443212 73443212 G C 1 0 0 0 0 1 0 0 0 13368 1281 45 4 4 REC114 15 73443212 Missense_Mutation SNP G C3N-01414_T 1712071 73443212 28547977 388 23588 CYP11A1 0 . GRCh38 15 74338080 74338080 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.1458A>T p.Glu486Asp p.E486D ENST00000268053 9/9 349 304 45 624 624 0 strelka-varscan-mutect CYP11A1,missense_variant,p.Glu328Asp,ENST00000358632,NM_001099773.1;CYP11A1,missense_variant,p.Glu486Asp,ENST00000268053,NM_000781.2;CCDC33,downstream_gene_variant,,ENST00000398814,NM_025055.4;CCDC33,downstream_gene_variant,,ENST00000558659,;CCDC33,downstream_gene_variant,,ENST00000268082,NM_182791.3;CCDC33,downstream_gene_variant,,ENST00000558821,NM_001287181.1;CYP11A1,downstream_gene_variant,,ENST00000566674,;CYP11A1,3_prime_UTR_variant,,ENST00000435365,;CYP11A1,non_coding_transcript_exon_variant,,ENST00000498141,;CCDC33,downstream_gene_variant,,ENST00000321374,;CCDC33,downstream_gene_variant,,ENST00000560565,; A ENST00000268053 Transcript missense_variant 1613/1934 1458/1566 486/521 E/D gaA/gaT 1 -1 CYP11A1 HGNC HGNC:2590 protein_coding YES CCDS32291.1 ENSP00000268053 P05108 A0A0S2Z3R3 UPI00000725F7 NM_000781.2 tolerated(0.11) 9/9 hmmpanther:PTHR24279:SF3,hmmpanther:PTHR24279,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 74338080 74338080 T A 1 0 0 0 0 1 0 0 0 3947 1838 64 4 4 CYP11A1 15 74338080 Missense_Mutation SNP T C3N-01414_T 894868 74338080 27653109 389 23589 SCAMP5 0 . GRCh38 15 75018463 75018463 + Silent SNP G G T rs748929504 C3N-01414_T C3N-01414_N G G c.441G>T p.= p.S147S ENST00000361900 7/8 154 135 19 274 274 0 strelka-varscan-mutect SCAMP5,synonymous_variant,p.=,ENST00000361900,NM_001178111.1;SCAMP5,synonymous_variant,p.=,ENST00000425597,NM_138967.3,NM_001178112.1;SCAMP5,synonymous_variant,p.=,ENST00000562212,;SCAMP5,synonymous_variant,p.=,ENST00000568081,;SCAMP5,synonymous_variant,p.=,ENST00000564779,;SCAMP5,downstream_gene_variant,,ENST00000568018,;SCAMP5,downstream_gene_variant,,ENST00000567920,;SCAMP5,downstream_gene_variant,,ENST00000562327,;SCAMP5,downstream_gene_variant,,ENST00000566872,;SCAMP5,downstream_gene_variant,,ENST00000565989,;SCAMP5,downstream_gene_variant,,ENST00000565923,;SCAMP5,downstream_gene_variant,,ENST00000564141,;SCAMP5,3_prime_UTR_variant,,ENST00000562765,;SCAMP5,3_prime_UTR_variant,,ENST00000568423,;SCAMP5,3_prime_UTR_variant,,ENST00000567529,;SCAMP5,3_prime_UTR_variant,,ENST00000564491,;RP11-151H2.1,upstream_gene_variant,,ENST00000565251,; T ENST00000361900 Transcript synonymous_variant 648/3427 441/708 147/235 S tcG/tcT rs748929504 1 1 SCAMP5 HGNC HGNC:30386 protein_coding YES CCDS45306.1 ENSP00000355387 Q8TAC9 A0A0A8K8F5 UPI00000700E5 NM_001178111.1 7/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR10687:SF5,hmmpanther:PTHR10687,Pfam_domain:PF04144 LOW 1 SNV 2 1 PASS rs748929504 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 75018463 75018463 G T 1 0 0 0 0 0 0 0 1 14141 1103 39 1 1 SCAMP5 15 75018463 Silent SNP G C3N-01414_T 680383 75018463 26972726 390 23590 PEAK1 0 . GRCh38 15 77114253 77114253 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.5144G>T p.Gly1715Val p.G1715V ENST00000560626 7/7 240 181 59 440 439 1 strelka-varscan-mutect PEAK1,missense_variant,p.Gly1715Val,ENST00000560626,;PEAK1,missense_variant,p.Gly1715Val,ENST00000312493,NM_024776.3; A ENST00000560626 Transcript missense_variant 5620/19217 5144/5241 1715/1746 G/V gGt/gTt 1 -1 PEAK1 HGNC HGNC:29431 protein_coding YES CCDS42062.1 ENSP00000452796 Q9H792 UPI00002378D0 tolerated(0.51) 7/7 hmmpanther:PTHR22972,hmmpanther:PTHR22972:SF5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 77114253 77114253 C A 1 0 0 0 0 1 0 0 0 11800 507 18 2 2 PEAK1 15 77114253 Missense_Mutation SNP C C3N-01414_T 2095790 77114253 24876936 391 23591 ANKRD34C 0 . GRCh38 15 79293429 79293429 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.145A>T p.Met49Leu p.M49L ENST00000421388 1/1 139 103 36 236 236 0 strelka-varscan-mutect ANKRD34C,missense_variant,p.Met49Leu,ENST00000421388,NM_001146341.1; T ENST00000421388 Transcript missense_variant 145/4951 145/1608 49/535 M/L Atg/Ttg 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 deleterious(0.01) 1/1 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24157,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 79293429 79293429 A T 1 0 0 0 0 1 0 0 0 769 217 8 4 4 ANKRD34C 15 79293429 Missense_Mutation SNP A C3N-01414_T 2179176 79293429 22697760 392 23592 WHAMM 0 . GRCh38 15 82809943 82809943 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.217G>A p.Val73Ile p.V73I ENST00000286760 1/10 51 35 16 72 71 1 strelka-varscan-mutect WHAMM,missense_variant,p.Val73Ile,ENST00000286760,NM_001080435.2;FSD2,upstream_gene_variant,,ENST00000334574,NM_001007122.3;FSD2,upstream_gene_variant,,ENST00000541889,NM_001281806.1,NM_001281805.1;FSD2,upstream_gene_variant,,ENST00000561368,; A ENST00000286760 Transcript missense_variant 316/5101 217/2430 73/809 V/I Gtc/Atc 1 1 WHAMM HGNC HGNC:30493 protein_coding YES CCDS45333.1 ENSP00000286760 Q8TF30 UPI00001C1F94 NM_001080435.2 tolerated(0.21) 1/10 hmmpanther:PTHR23330,hmmpanther:PTHR23330:SF6 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 82809943 82809943 G A 1 0 0 0 0 1 0 0 0 17918 1145 40 1 1 WHAMM 15 82809943 Missense_Mutation SNP G C3N-01414_T 3516514 82809943 19181246 393 23593 KIF7 0 . GRCh38 15 89632888 89632888 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.2827C>A p.Leu943Met p.L943M ENST00000394412 14/19 362 263 99 591 591 0 strelka-varscan-mutect KIF7,missense_variant,p.Leu943Met,ENST00000394412,NM_198525.2;TICRR,downstream_gene_variant,,ENST00000268138,NM_152259.3;TICRR,downstream_gene_variant,,ENST00000560985,NM_001308025.1;KIF7,upstream_gene_variant,,ENST00000558928,;TICRR,downstream_gene_variant,,ENST00000561095,; T ENST00000394412 Transcript missense_variant 2904/4551 2827/4032 943/1343 L/M Ctg/Atg 1 -1 KIF7 HGNC HGNC:30497 protein_coding YES CCDS32325.2 ENSP00000377934 Q2M1P5 UPI00015F81C7 NM_198525.2 deleterious(0) 14/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF445 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 89632888 89632888 G T 1 0 0 0 0 1 0 0 0 8174 991 35 2 2 KIF7 15 89632888 Missense_Mutation SNP G C3N-01414_T 6822945 89632888 12358301 394 23594 AXIN1 0 . GRCh38 16 297735 297735 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1771G>T p.Gly591Cys p.G591C ENST00000262320 6/11 47 38 9 57 57 0 strelka-varscan-mutect AXIN1,missense_variant,p.Gly591Cys,ENST00000262320,NM_003502.3;AXIN1,missense_variant,p.Gly591Cys,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; A ENST00000262320 Transcript missense_variant 2143/3643 1771/2589 591/862 G/C Ggc/Tgc 1 -1 AXIN1 HGNC HGNC:903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 A0A0S2Z4R0 UPI000012669E NM_003502.3 deleterious(0.03) 6/11 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.9961 1 1 1 1 0 A 3 1 77 297735 297735 C A 1 0 0 0 0 1 0 0 0 1393 594 21 2 2 AXIN1 16 297735 Missense_Mutation SNP C C3N-01414_T 297735 90040610 395 23595 TPSAB1 0 . GRCh38 16 1240974 1240974 + Silent SNP G G C novel C3N-01414_T C3N-01414_N G G c.36G>C p.= p.L12L ENST00000338844 2/6 47 39 8 93 93 0 strelka-varscan-mutect TPSAB1,synonymous_variant,p.=,ENST00000461509,;TPSAB1,synonymous_variant,p.=,ENST00000338844,NM_003294.3;TPSAB1,upstream_gene_variant,,ENST00000561736,;TPSAB1,non_coding_transcript_exon_variant,,ENST00000562432,; C ENST00000338844 Transcript synonymous_variant 69/1175 36/828 12/275 L ctG/ctC 1 1 TPSAB1 HGNC HGNC:12019 protein_coding YES CCDS10431.1 ENSP00000343577 Q15661 UPI0000137302 NM_003294.3 2/6 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS rs1387570835 . 0 205 5 0 0 0 0 0 -19.31378 1 1 1 1 0 C 2 2 77 1240974 1240974 G C 1 0 0 0 0 0 0 0 1 16904 1335 47 4 4 TPSAB1 16 1240974 Silent SNP G C3N-01414_T 943239 1240974 89097371 396 23596 TSC2 0 . GRCh38 16 2079639 2079639 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.3367G>A p.Gly1123Arg p.G1123R ENST00000219476 29/42 184 132 52 204 204 0 strelka-varscan-mutect TSC2,missense_variant,p.Gly1123Arg,ENST00000219476,NM_000548.3;TSC2,missense_variant,p.Gly1123Arg,ENST00000350773,NM_001114382.1;TSC2,missense_variant,p.Gly1090Arg,ENST00000568454,NM_001318832.1;TSC2,missense_variant,p.Gly1079Arg,ENST00000401874,NM_001077183.1;TSC2,missense_variant,p.Gly1043Arg,ENST00000439673,NM_001318827.1;TSC2,missense_variant,p.Gly1031Arg,ENST00000382538,NM_001318829.1;TSC2,upstream_gene_variant,,ENST00000569110,;TSC2,non_coding_transcript_exon_variant,,ENST00000568366,;TSC2,3_prime_UTR_variant,,ENST00000439117,NM_001318831.1;TSC2,non_coding_transcript_exon_variant,,ENST00000497886,;TSC2,upstream_gene_variant,,ENST00000569930,;TSC2,downstream_gene_variant,,ENST00000463808,;TSC2,downstream_gene_variant,,ENST00000471143,;TSC2,downstream_gene_variant,,ENST00000483020,;TSC2,downstream_gene_variant,,ENST00000561695,; A ENST00000219476 Transcript missense_variant 3997/6156 3367/5424 1123/1807 G/R Ggg/Agg 1 1 TSC2 HGNC HGNC:12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 tolerated(0.23) 29/42 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 2079639 2079639 G A 1 0 0 0 0 1 0 0 0 17112 1348 47 3 3 TSC2 16 2079639 Missense_Mutation SNP G C3N-01414_T 838665 2079639 88258706 397 23597 TSC2 0 . GRCh38 16 2084629 2084629 + Frame_Shift_Del DEL A A - novel C3N-01414_T C3N-01414_N A A c.4407delA p.Arg1470AlafsTer6 p.R1470Afs*6 ENST00000219476 34/42 120 89 31 224 224 0 sindel-varindel TSC2,frameshift_variant,p.Arg1470AlafsTer6,ENST00000219476,NM_000548.3;TSC2,frameshift_variant,p.Arg1447AlafsTer6,ENST00000350773,NM_001114382.1;TSC2,frameshift_variant,p.Arg1414AlafsTer6,ENST00000568454,NM_001318832.1;TSC2,frameshift_variant,p.Arg1403AlafsTer6,ENST00000401874,NM_001077183.1;TSC2,frameshift_variant,p.Arg1367AlafsTer6,ENST00000439673,NM_001318827.1;TSC2,frameshift_variant,p.Arg1355AlafsTer6,ENST00000382538,NM_001318829.1;TSC2,frameshift_variant,p.Arg198AlafsTer6,ENST00000569110,;PKD1,downstream_gene_variant,,ENST00000262304,NM_001009944.2;PKD1,downstream_gene_variant,,ENST00000423118,NM_000296.3;TSC2,downstream_gene_variant,,ENST00000568366,;TSC2,3_prime_UTR_variant,,ENST00000439117,NM_001318831.1;TSC2,non_coding_transcript_exon_variant,,ENST00000497886,;TSC2,non_coding_transcript_exon_variant,,ENST00000569930,;PKD1,downstream_gene_variant,,ENST00000472577,; - ENST00000219476 Transcript frameshift_variant 5037/6156 4407/5424 1469/1807 S/X tcA/tc 1 1 TSC2 HGNC HGNC:12363 protein_coding YES CCDS10458.1 ENSP00000219476 P49815 UPI000013C781 NM_000548.3 34/42 Superfamily_domains:0043732 HIGH deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 2084629 2084629 A - 1 0 1 0 1 0 0 0 0 17112 146 6 0 0 TSC2 16 2084629 Frame_Shift_Del DEL A C3N-01414_T 4990 2084629 88253716 398 23598 RBFOX1 0 . GRCh38 16 7676804 7676804 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1090C>G p.Pro364Ala p.P364A ENST00000422070 14/16 144 117 27 212 212 0 strelka-varscan-mutect RBFOX1,missense_variant,p.Pro321Ala,ENST00000550418,NM_018723.3;RBFOX1,missense_variant,p.Pro326Ala,ENST00000340209,;RBFOX1,missense_variant,p.Pro299Ala,ENST00000620507,;RBFOX1,missense_variant,p.Pro364Ala,ENST00000547372,;RBFOX1,missense_variant,p.Pro342Ala,ENST00000355637,NM_145893.2;RBFOX1,missense_variant,p.Pro342Ala,ENST00000311745,NM_145891.2;RBFOX1,missense_variant,p.Pro294Ala,ENST00000553186,NM_001142333.1;RBFOX1,missense_variant,p.Pro364Ala,ENST00000422070,NM_001308117.1;RBFOX1,missense_variant,p.Pro278Ala,ENST00000535565,;RBFOX1,missense_variant,p.Pro342Ala,ENST00000436368,NM_145892.2;RBFOX1,missense_variant,p.Pro321Ala,ENST00000547338,NM_001142334.1;RBFOX1,missense_variant,p.Pro338Ala,ENST00000552089,;RBFOX1,missense_variant,p.Ser38Arg,ENST00000567470,;RBFOX1,non_coding_transcript_exon_variant,,ENST00000570188,; G ENST00000422070 Transcript missense_variant 1286/1684 1090/1278 364/425 P/A Cct/Gct 1 1 RBFOX1 HGNC HGNC:18222 protein_coding YES CCDS76818.1 ENSP00000391269 B7Z1U7 UPI0001914C99 NM_001308117.1 tolerated_low_confidence(0.12) 14/16 Low_complexity_(Seg):seg,hmmpanther:PTHR15597:SF26,hmmpanther:PTHR15597,PIRSF_domain:PIRSF037932,Pfam_domain:PF12414 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 7676804 7676804 C G 1 0 0 0 0 1 0 0 0 13271 739 26 4 4 RBFOX1 16 7676804 Missense_Mutation SNP C C3N-01414_T 5592175 7676804 82661541 399 23599 NOMO1 0 . GRCh38 16 14872321 14872321 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.2046G>T p.= p.V682V ENST00000287667 18/31 49 36 13 75 75 0 varscan-mutect NOMO1,synonymous_variant,p.=,ENST00000287667,NM_014287.3;NOMO1,synonymous_variant,p.=,ENST00000620755,;NOMO1,synonymous_variant,p.=,ENST00000610363,; T ENST00000287667 Transcript synonymous_variant 2217/4355 2046/3669 682/1222 V gtG/gtT 1 1 NOMO1 HGNC HGNC:30060 protein_coding YES CCDS10556.1 ENSP00000287667 Q15155 UPI000013D37E NM_014287.3 18/31 hmmpanther:PTHR23303 LOW 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 T 2 4 77 14872321 14872321 G T 1 0 0 0 0 0 0 0 1 10575 1277 45 2 2 NOMO1 16 14872321 Silent SNP G C3N-01414_T 7195517 14872321 75466024 400 23600 ACSM2A 0 . GRCh38 16 20465543 20465543 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.204C>A p.= p.A68A ENST00000573854 3/14 147 117 30 208 207 1 strelka-varscan-mutect ACSM2A,synonymous_variant,p.=,ENST00000573854,NM_001308172.1,NM_001010845.2;ACSM2A,synonymous_variant,p.=,ENST00000396104,;ACSM2A,synonymous_variant,p.=,ENST00000575690,;ACSM2A,synonymous_variant,p.=,ENST00000219054,;ACSM2A,synonymous_variant,p.=,ENST00000571894,;ACSM2A,synonymous_variant,p.=,ENST00000576361,;ACSM2A,5_prime_UTR_variant,,ENST00000417235,NM_001308169.1;ACSM2A,5_prime_UTR_variant,,ENST00000574251,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000575558,;ACSM2A,synonymous_variant,p.=,ENST00000574692,;ACSM2A,non_coding_transcript_exon_variant,,ENST00000570698,; A ENST00000573854 Transcript synonymous_variant 318/2837 204/1734 68/577 A gcC/gcA 1 1 ACSM2A HGNC HGNC:32017 protein_coding YES CCDS32401.1 ENSP00000459451 Q08AH3 UPI0000251E27 NM_001308172.1,NM_001010845.2 3/14 hmmpanther:PTHR24095:SF188,hmmpanther:PTHR24095,Gene3D:3.40.50.980,Superfamily_domains:SSF56801 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 20465543 20465543 C A 1 0 0 0 0 0 0 0 1 225 610 22 2 2 ACSM2A 16 20465543 Silent SNP C C3N-01414_T 5593222 20465543 69872802 401 23601 ACSM2B 0 . GRCh38 16 20546417 20546417 + Missense_Mutation SNP C C G rs768303608 C3N-01414_T C3N-01414_N C C c.1156G>C p.Ala386Pro p.A386P ENST00000329697 9/14 42 36 6 86 86 0 varscan-mutect ACSM2B,missense_variant,p.Ala386Pro,ENST00000329697,NM_001105069.1;ACSM2B,missense_variant,p.Ala386Pro,ENST00000414188,;ACSM2B,missense_variant,p.Ala386Pro,ENST00000565232,;ACSM2B,missense_variant,p.Ala386Pro,ENST00000567001,NM_182617.3;ACSM2B,missense_variant,p.Ala307Pro,ENST00000565322,;ACSM2B,missense_variant,p.Ala155Pro,ENST00000567288,;ACSM2B,downstream_gene_variant,,ENST00000569163,;ACSM2B,upstream_gene_variant,,ENST00000568098,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569131,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000566998,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,;ACSM2B,downstream_gene_variant,,ENST00000569327,; G ENST00000329697 Transcript missense_variant 1325/2935 1156/1734 386/577 A/P Gct/Cct rs768303608,COSM968090 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 tolerated(0.52) 9/14 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF188,Superfamily_domains:SSF56801 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768303608 . 0 202 7 0 0 0 0 0 -14.98262 0.9999995 1 1 1 0 G 3 3 77 20546417 20546417 C G 1 0 0 0 0 1 0 0 0 226 739 26 4 4 ACSM2B 16 20546417 Missense_Mutation SNP C C3N-01414_T 80874 20546417 69791928 402 23602 NPIPB4 0 . GRCh38 16 21837308 21837308 + Missense_Mutation SNP G G T rs777977460 C3N-01414_T C3N-01414_N G G c.1079C>A p.Pro360His p.P360H ENST00000415645 7/9 116 99 17 168 168 0 strelka-varscan-mutect NPIPB4,missense_variant,p.Pro360His,ENST00000415645,NM_130464.2;NPIPB4,missense_variant,p.Pro144His,ENST00000537951,;NPIPB4,downstream_gene_variant,,ENST00000614197,;NPIPB4,downstream_gene_variant,,ENST00000165086,;NPIPB4,downstream_gene_variant,,ENST00000541329,;NPIPB4,downstream_gene_variant,,ENST00000542133,;NPIPB4,downstream_gene_variant,,ENST00000545367,;NPIPB4,downstream_gene_variant,,ENST00000543660,;RP11-645C24.6,downstream_gene_variant,,ENST00000622730,; T ENST00000415645 Transcript missense_variant 1119/3606 1079/3417 360/1138 P/H cCc/cAc rs777977460 1 -1 NPIPB4 HGNC HGNC:41985 protein_coding YES ENSP00000404439 C9JG80 UPI00020651A0 NM_130464.2 7/9 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs777977460 . 15 195 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 21837308 21837308 G T 1 0 0 0 0 1 0 0 0 10638 1232 43 2 2 NPIPB4 16 21837308 Missense_Mutation SNP G C3N-01414_T 1290891 21837308 68501037 403 23603 PLK1 0 . GRCh38 16 23688676 23688676 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.1201G>A p.Glu401Lys p.E401K ENST00000300093 7/10 241 195 46 404 403 1 strelka-varscan-mutect PLK1,missense_variant,p.Glu401Lys,ENST00000300093,NM_005030.4;ERN2,downstream_gene_variant,,ENST00000634482,NM_033266.3;ERN2,downstream_gene_variant,,ENST00000256797,;ERN2,downstream_gene_variant,,ENST00000457008,NM_001308220.1;PLK1,downstream_gene_variant,,ENST00000567897,;PLK1,downstream_gene_variant,,ENST00000568568,;CTD-2196E14.5,upstream_gene_variant,,ENST00000566143,;PLK1,non_coding_transcript_exon_variant,,ENST00000562272,;PLK1,non_coding_transcript_exon_variant,,ENST00000564794,;PLK1,non_coding_transcript_exon_variant,,ENST00000564947,;ERN2,downstream_gene_variant,,ENST00000562458,;PLK1,downstream_gene_variant,,ENST00000562407,; A ENST00000300093 Transcript missense_variant 1312/2227 1201/1812 401/603 E/K Gag/Aag 1 1 PLK1 HGNC HGNC:9077 protein_coding YES CCDS10616.1 ENSP00000300093 P53350 UPI0000131BF9 NM_005030.4 tolerated(0.17) 7/10 hmmpanther:PTHR24345,Gene3D:3.30.1120.30,Superfamily_domains:SSF82615 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 23688676 23688676 G A 1 0 0 0 0 1 0 0 0 12190 1291 45 3 3 PLK1 16 23688676 Missense_Mutation SNP G C3N-01414_T 1851368 23688676 66649669 404 23604 ZKSCAN2 0 . GRCh38 16 25247141 25247141 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1055T>A p.Leu352Gln p.L352Q ENST00000328086 5/7 254 196 58 391 391 0 strelka-varscan-mutect ZKSCAN2,missense_variant,p.Leu352Gln,ENST00000328086,NM_001012981.4;ZKSCAN2,3_prime_UTR_variant,,ENST00000569150,;ZKSCAN2,non_coding_transcript_exon_variant,,ENST00000565590,; T ENST00000328086 Transcript missense_variant 1859/7523 1055/2904 352/967 L/Q cTg/cAg 1 -1 ZKSCAN2 HGNC HGNC:25677 protein_coding YES CCDS32410.1 ENSP00000331626 Q63HK3 UPI0000229E7F NM_001012981.4 deleterious(0) 5/7 hmmpanther:PTHR10032:SF206,hmmpanther:PTHR10032,Pfam_domain:PF13837 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 25247141 25247141 A T 1 0 0 0 0 1 0 0 0 18265 188 7 4 4 ZKSCAN2 16 25247141 Missense_Mutation SNP A C3N-01414_T 1558465 25247141 65091204 405 23605 SEZ6L2 0 . GRCh38 16 29896847 29896847 + Silent SNP A A T C3N-01414_T C3N-01414_N A A c.486T>A p.= p.T162T ENST00000617533 3/18 145 115 30 186 186 0 strelka-varscan-mutect SEZ6L2,synonymous_variant,p.=,ENST00000308713,NM_201575.3,NM_001114099.2;SEZ6L2,synonymous_variant,p.=,ENST00000617533,NM_001243332.1;SEZ6L2,synonymous_variant,p.=,ENST00000537485,NM_001243333.1;SEZ6L2,synonymous_variant,p.=,ENST00000350527,NM_012410.3;SEZ6L2,synonymous_variant,p.=,ENST00000346932,NM_001114100.2;ASPHD1,upstream_gene_variant,,ENST00000308748,NM_181718.3;ASPHD1,upstream_gene_variant,,ENST00000483405,;ASPHD1,upstream_gene_variant,,ENST00000563177,;SEZ6L2,downstream_gene_variant,,ENST00000568380,;SEZ6L2,non_coding_transcript_exon_variant,,ENST00000562159,;ASPHD1,upstream_gene_variant,,ENST00000566693,;ASPHD1,upstream_gene_variant,,ENST00000414952,; T ENST00000617533 Transcript synonymous_variant 731/3555 486/2772 162/923 T acT/acA COSM1588361,COSM969686 1 -1 SEZ6L2 HGNC HGNC:30844 protein_coding YES CCDS73865.1 ENSP00000481917 A0A087WYL5 UPI00001FFE46 NM_001243332.1 3/18 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF92,Low_complexity_(Seg):seg 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 29896847 29896847 A T 1 0 0 0 0 0 0 0 1 14423 175 7 4 4 SEZ6L2 16 29896847 Silent SNP A C3N-01414_T 4649706 29896847 60441498 406 23606 PRR14 0 . GRCh38 16 30653365 30653365 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.505G>A p.Gly169Ser p.G169S ENST00000542965 5/11 154 110 44 230 230 0 strelka-varscan-mutect PRR14,missense_variant,p.Gly169Ser,ENST00000542965,;PRR14,missense_variant,p.Gly169Ser,ENST00000300835,NM_024031.2;PRR14,missense_variant,p.Gly169Ser,ENST00000568754,;PRR14,downstream_gene_variant,,ENST00000569864,;PRR14,upstream_gene_variant,,ENST00000571654,;PRR14,splice_region_variant,,ENST00000287463,;PRR14,splice_region_variant,,ENST00000564946,;PRR14,upstream_gene_variant,,ENST00000567322,;PRR14,upstream_gene_variant,,ENST00000567989,;PRR14,downstream_gene_variant,,ENST00000563211,;PRR14,upstream_gene_variant,,ENST00000565977,;PRR14,downstream_gene_variant,,ENST00000565410,;PRR14,downstream_gene_variant,,ENST00000563399,; A ENST00000542965 Transcript missense_variant,splice_region_variant 961/2316 505/1758 169/585 G/S Ggc/Agc 1 1 PRR14 HGNC HGNC:28458 protein_coding YES CCDS10687.1 ENSP00000441641 Q9BWN1 A0A024QZB5 UPI000006F1D0 tolerated_low_confidence(0.13) 5/11 hmmpanther:PTHR14522 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 30653365 30653365 G A 1 0 0 0 0 1 0 0 0 12721 1246 43 3 3 PRR14 16 30653365 Missense_Mutation SNP G C3N-01414_T 756518 30653365 59684980 407 23607 ABCC11 0 . GRCh38 16 48178641 48178641 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.3304G>C p.Glu1102Gln p.E1102Q ENST00000394747 23/29 214 184 30 380 380 0 strelka-varscan-mutect ABCC11,missense_variant,p.Glu1102Gln,ENST00000394747,NM_033151.3;ABCC11,missense_variant,p.Glu1102Gln,ENST00000356608,;ABCC11,missense_variant,p.Glu1102Gln,ENST00000394748,NM_032583.3;ABCC11,missense_variant,p.Glu1102Gln,ENST00000353782,NM_145186.2;ABCC11,non_coding_transcript_exon_variant,,ENST00000565329,; G ENST00000394747 Transcript missense_variant 3654/4862 3304/4149 1102/1382 E/Q Gag/Cag 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 tolerated(0.3) 23/29 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Gene3D:2hydA01,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS rs1312037062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 48178641 48178641 C G 1 0 0 0 0 1 0 0 0 55 922 32 4 4 ABCC11 16 48178641 Missense_Mutation SNP C C3N-01414_T 17525276 48178641 42159704 408 23608 SALL1 0 . GRCh38 16 51141108 51141108 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1114T>A p.Ser372Thr p.S372T ENST00000251020 2/3 304 244 60 439 438 1 strelka-varscan-mutect SALL1,missense_variant,p.Ser275Thr,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Ser372Thr,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Ser275Thr,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; T ENST00000251020 Transcript missense_variant 1148/5146 1114/3975 372/1324 S/T Tca/Aca 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.43) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 51141108 51141108 A T 1 0 0 0 0 1 0 0 0 14069 333 12 4 4 SALL1 16 51141108 Missense_Mutation SNP A C3N-01414_T 2962467 51141108 39197237 409 23609 IRX5 0 . GRCh38 16 54932757 54932758 + In_Frame_Ins INS - - CCT novel C3N-01414_T C3N-01414_N - - c.511_513dupCTC p.Leu171dup p.L171dup ENST00000394636 2/3 308 280 28 516 515 1 sindel-varindel-pindel IRX5,inframe_insertion,p.Leu171dup,ENST00000394636,NM_005853.5;IRX5,inframe_insertion,p.Leu171dup,ENST00000320990,NM_001252197.1;IRX5,intron_variant,,ENST00000620085,;IRX5,intron_variant,,ENST00000560154,;CRNDE,upstream_gene_variant,,ENST00000560208,;CRNDE,upstream_gene_variant,,ENST00000559598,;CRNDE,upstream_gene_variant,,ENST00000502066,;CRNDE,upstream_gene_variant,,ENST00000501177,;CRNDE,upstream_gene_variant,,ENST00000558952,;CRNDE,upstream_gene_variant,,ENST00000559432,;CRNDE,upstream_gene_variant,,ENST00000557792,;CRNDE,upstream_gene_variant,,ENST00000560912,;CTD-3032H12.2,upstream_gene_variant,,ENST00000560487,;IRX5,non_coding_transcript_exon_variant,,ENST00000558597,; CCT ENST00000394636 Transcript inframe_insertion 846-847/2401 509-510/1452 170/483 R/RL cgc/cgCCTc 1 1 IRX5 HGNC HGNC:14361 protein_coding YES CCDS10751.1 ENSP00000378132 P78411 UPI00001FF1CD NM_005853.5 2/3 Gene3D:1.10.10.60,Pfam_domain:PF05920,PROSITE_patterns:PS00027,PROSITE_profiles:PS50071,hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF17,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 insertion 3 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 CCT 7 5 77 54932757 54932757 - CCT 1 0 1 1 0 0 0 0 0 7755 1087 38 0 0 IRX5 16 54932757 In_Frame_Ins INS - C3N-01414_T 3791649 54932757 35405588 410 23610 LPCAT2 0 . GRCh38 16 55529842 55529842 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.537A>T p.Leu179Phe p.L179F ENST00000262134 4/14 148 111 37 206 206 0 strelka-varscan-mutect LPCAT2,missense_variant,p.Leu179Phe,ENST00000262134,NM_017839.4;LPCAT2,missense_variant,p.Leu37Phe,ENST00000564084,;LPCAT2,upstream_gene_variant,,ENST00000566915,;LPCAT2,downstream_gene_variant,,ENST00000566911,; T ENST00000262134 Transcript missense_variant 721/5391 537/1635 179/544 L/F ttA/ttT 1 1 LPCAT2 HGNC HGNC:26032 protein_coding YES CCDS10753.1 ENSP00000262134 Q7L5N7 UPI00001BD900 NM_017839.4 deleterious(0.03) 4/14 hmmpanther:PTHR23063,hmmpanther:PTHR23063:SF21,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 55529842 55529842 A T 1 0 0 0 0 1 0 0 0 8814 388 14 4 4 LPCAT2 16 55529842 Missense_Mutation SNP A C3N-01414_T 597085 55529842 34808503 411 23611 80 2 LPCAT2 0 . GRCh38 16 55529844 55529844 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.539G>C p.Arg180Pro p.R180P ENST00000262134 4/14 157 118 39 218 218 0 strelka-varscan-mutect LPCAT2,missense_variant,p.Arg180Pro,ENST00000262134,NM_017839.4;LPCAT2,missense_variant,p.Arg38Pro,ENST00000564084,;LPCAT2,upstream_gene_variant,,ENST00000566915,;LPCAT2,downstream_gene_variant,,ENST00000566911,; C ENST00000262134 Transcript missense_variant 723/5391 539/1635 180/544 R/P cGg/cCg 1 1 LPCAT2 HGNC HGNC:26032 protein_coding YES CCDS10753.1 ENSP00000262134 Q7L5N7 UPI00001BD900 NM_017839.4 deleterious(0.04) 4/14 hmmpanther:PTHR23063,hmmpanther:PTHR23063:SF21,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877 MODERATE 1 SNV 1 1 PASS rs1263512562 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 55529844 55529844 G C 1 0 0 0 0 1 0 0 0 8814 1116 39 4 4 LPCAT2 16 55529844 Missense_Mutation SNP G C3N-01414_T 2 55529844 34808501 412 23612 80 2 AC027682.1 0 . GRCh38 16 67546390 67546390 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.3629G>A p.Arg1210Gln p.R1210Q ENST00000428437 22/22 167 141 26 261 261 0 strelka-varscan-mutect FAM65A,missense_variant,p.Arg1215Gln,ENST00000540839,;FAM65A,missense_variant,p.Arg1210Gln,ENST00000428437,NM_001193524.1;FAM65A,missense_variant,p.Arg1200Gln,ENST00000379312,NM_001193522.1;FAM65A,missense_variant,p.Arg1196Gln,ENST00000042381,NM_024519.3;AC027682.1,missense_variant,p.Arg1216Gln,ENST00000422602,NM_001193523.1;FAM65A,downstream_gene_variant,,ENST00000566559,;FAM65A,downstream_gene_variant,,ENST00000569253,;FAM65A,downstream_gene_variant,,ENST00000568959,;FAM65A,downstream_gene_variant,,ENST00000569179,;CTD-2012K14.6,downstream_gene_variant,,ENST00000605277,;CTD-2012K14.6,downstream_gene_variant,,ENST00000565929,;CTD-2012K14.3,upstream_gene_variant,,ENST00000563083,;CTD-2012K14.4,upstream_gene_variant,,ENST00000564717,;CTD-2012K14.5,downstream_gene_variant,,ENST00000623147,;FAM65A,non_coding_transcript_exon_variant,,ENST00000569733,;FAM65A,downstream_gene_variant,,ENST00000566815,;FAM65A,downstream_gene_variant,,ENST00000569474,;FAM65A,downstream_gene_variant,,ENST00000564616,;FAM65A,downstream_gene_variant,,ENST00000561534,;FAM65A,downstream_gene_variant,,ENST00000566730,;FAM65A,downstream_gene_variant,,ENST00000565190,;FAM65A,downstream_gene_variant,,ENST00000565679,; A ENST00000428437 Transcript missense_variant 3754/4152 3629/3702 1210/1233 R/Q cGa/cAa 1 1 FAM65A HGNC HGNC:25836 protein_coding YES CCDS54027.1 ENSP00000389456 Q6ZS17 UPI00017A7136 NM_001193524.1 deleterious(0) 22/22 hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF1,Gene3D:1.25.10.10,Pfam_domain:PF13646 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 67546390 67546390 G A 1 0 0 0 0 1 0 0 0 129 1058 37 1 1 AC027682.1 16 67546390 Missense_Mutation SNP G C3N-01414_T 12016546 67546390 22791955 413 23613 ZFP90 0 . GRCh38 16 68563663 68563663 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.876G>T p.Arg292Ser p.R292S ENST00000570495 5/5 231 182 49 339 338 1 strelka-varscan-mutect ZFP90,missense_variant,p.Arg292Ser,ENST00000570495,NM_001305203.1;ZFP90,missense_variant,p.Arg292Ser,ENST00000398253,NM_133458.2;ZFP90,missense_variant,p.Arg292Ser,ENST00000563169,;ZFP90,intron_variant,,ENST00000611381,NM_001305204.1;ZFP90,intron_variant,,ENST00000573113,;ZFP90,downstream_gene_variant,,ENST00000564323,;ZFP90,downstream_gene_variant,,ENST00000573685,;ZFP90,downstream_gene_variant,,ENST00000562156,;ZFP90,3_prime_UTR_variant,,ENST00000564558,;ZFP90,non_coding_transcript_exon_variant,,ENST00000571720,;ZFP90,downstream_gene_variant,,ENST00000571809,;ZFP90,downstream_gene_variant,,ENST00000576805,;ZFP90,downstream_gene_variant,,ENST00000569323,; T ENST00000570495 Transcript missense_variant 1168/4636 876/1911 292/636 R/S agG/agT 1 1 ZFP90 HGNC HGNC:23329 protein_coding YES CCDS42183.1 ENSP00000460547 Q8TF47 UPI000004C096 NM_001305203.1 tolerated(0.86) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF143,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 68563663 68563663 G T 1 0 0 0 0 1 0 0 0 18231 1194 42 2 2 ZFP90 16 68563663 Missense_Mutation SNP G C3N-01414_T 1017273 68563663 21774682 414 23614 COG8 0 . GRCh38 16 69331033 69331033 + Nonsense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.1645C>T p.Gln549Ter p.Q549* ENST00000306875 5/6 349 273 76 517 516 1 strelka-varscan-mutect COG8,stop_gained,p.Gln549Ter,ENST00000306875,NM_032382.4;COG8,intron_variant,,ENST00000562595,;COG8,intron_variant,,ENST00000562949,;VPS4A,downstream_gene_variant,,ENST00000254950,NM_013245.2;COG8,downstream_gene_variant,,ENST00000562081,;PDF,upstream_gene_variant,,ENST00000288022,NM_022341.1;COG8,downstream_gene_variant,,ENST00000567493,;RP11-343C2.9,downstream_gene_variant,,ENST00000563634,;COG8,upstream_gene_variant,,ENST00000564419,;RP11-343C2.7,downstream_gene_variant,,ENST00000564737,;RP11-343C2.7,downstream_gene_variant,,ENST00000570293,; A ENST00000306875 Transcript stop_gained 1760/4247 1645/1839 549/612 Q/* Cag/Tag 1 -1 COG8 HGNC HGNC:18623 protein_coding YES CCDS10876.1 ENSP00000305459 Q96MW5 A0A024R6Z6 UPI000013EBA1 NM_032382.4 5/6 hmmpanther:PTHR21311:SF0,hmmpanther:PTHR21311,PIRSF_domain:PIRSF015415 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 69331033 69331033 G A 1 0 0 0 0 0 1 0 0 3452 1299 45 3 3 COG8 16 69331033 Nonsense_Mutation SNP G C3N-01414_T 767370 69331033 21007312 415 23615 ATXN1L 0 . GRCh38 16 71851348 71851348 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.1608C>T p.= p.S536S ENST00000427980 3/3 287 236 51 525 525 0 strelka-varscan-mutect ATXN1L,synonymous_variant,p.=,ENST00000427980,NM_001137675.3;IST1,intron_variant,,ENST00000568581,;ATXN1L,intron_variant,,ENST00000569119,;ATXN1L,downstream_gene_variant,,ENST00000565676,; T ENST00000427980 Transcript synonymous_variant 1901/7886 1608/2070 536/689 S agC/agT 1 1 ATXN1L HGNC HGNC:33279 protein_coding YES CCDS45523.1 ENSP00000415822 P0C7T5 UPI0000198982 NM_001137675.3 3/3 Superfamily_domains:0041756,Gene3D:2.170.16.10,Pfam_domain:PF08517,PROSITE_profiles:PS51148,hmmpanther:PTHR13392,hmmpanther:PTHR13392:SF6,SMART_domains:SM00536 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 71851348 71851348 C T 1 0 0 0 0 0 0 0 1 1364 709 25 3 3 ATXN1L 16 71851348 Silent SNP C C3N-01414_T 2520315 71851348 18486997 416 23616 PMFBP1 0 . GRCh38 16 72140418 72140418 + Missense_Mutation SNP G G C rs139925979 C3N-01414_T C3N-01414_N G G c.801C>G p.Asn267Lys p.N267K ENST00000237353 6/21 106 74 32 168 168 0 strelka-varscan-mutect PMFBP1,missense_variant,p.Asn267Lys,ENST00000537465,;PMFBP1,missense_variant,p.Asn267Lys,ENST00000237353,NM_031293.2;PMFBP1,missense_variant,p.Asn122Lys,ENST00000355636,NM_001160213.1;PMFBP1,missense_variant,p.Asn70Lys,ENST00000537392,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,; C ENST00000237353 Transcript missense_variant 1063/3527 801/3024 267/1007 N/K aaC/aaG rs139925979 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 tolerated(0.2) 6/21 hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 MODERATE 1 SNV 1 1 PASS rs139925979 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 72140418 72140418 G C 1 0 0 0 0 1 0 0 0 12241 1136 40 4 4 PMFBP1 16 72140418 Missense_Mutation SNP G C3N-01414_T 289070 72140418 18197927 417 23617 SCARF1 0 . GRCh38 17 1634935 1634935 + Missense_Mutation SNP T T G novel C3N-01414_T C3N-01414_N T T c.2316A>C p.Arg772Ser p.R772S ENST00000263071 11/11 117 93 24 165 165 0 strelka-varscan-mutect SCARF1,missense_variant,p.Arg772Ser,ENST00000263071,NM_003693.3;SCARF1,missense_variant,p.Arg686Ser,ENST00000348987,;SCARF1,3_prime_UTR_variant,,ENST00000571272,NM_145350.2;SCARF1,3_prime_UTR_variant,,ENST00000434376,;SCARF1,3_prime_UTR_variant,,ENST00000573852,;SCARF1,non_coding_transcript_exon_variant,,ENST00000576012,;SCARF1,downstream_gene_variant,,ENST00000570902,; G ENST00000263071 Transcript missense_variant 2366/3443 2316/2493 772/830 R/S agA/agC 1 -1 SCARF1 HGNC HGNC:16820 protein_coding YES CCDS11007.1 ENSP00000263071 Q14162 UPI00001AE868 NM_003693.3 tolerated(0.52) 11/11 hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF0 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 1634935 1634935 T G 1 0 0 0 0 1 0 0 0 14149 1664 58 5 5 SCARF1 17 1634935 Missense_Mutation SNP T C3N-01414_T 1634935 81622506 418 23618 RPA1 0 . GRCh38 17 1883876 1883876 + Missense_Mutation SNP G G C rs771309470 C3N-01414_T C3N-01414_N G G c.1306G>C p.Gly436Arg p.G436R ENST00000254719 13/17 204 161 43 370 370 0 strelka-varscan-mutect RPA1,missense_variant,p.Gly436Arg,ENST00000254719,NM_002945.3;RPA1,missense_variant,p.Gly192Arg,ENST00000574049,;RPA1,downstream_gene_variant,,ENST00000573924,; C ENST00000254719 Transcript missense_variant 1416/4340 1306/1851 436/616 G/R Gga/Cga rs771309470 1 1 RPA1 HGNC HGNC:10289 protein_coding YES CCDS11014.1 ENSP00000254719 P27694 UPI000013379A NM_002945.3 tolerated(0.06) 13/17 hmmpanther:PTHR23273,hmmpanther:PTHR23273:SF6,TIGRFAM_domain:TIGR00617 MODERATE 1 SNV 1 1 PASS rs771309470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 1883876 1883876 G C 1 0 0 0 0 1 0 0 0 13788 1117 39 4 4 RPA1 17 1883876 Missense_Mutation SNP G C3N-01414_T 248941 1883876 81373565 419 23619 OR1A2 0 . GRCh38 17 3197966 3197966 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.448G>T p.Val150Leu p.V150L ENST00000381951 1/1 106 83 23 182 182 0 strelka-varscan-mutect OR1A2,missense_variant,p.Val150Leu,ENST00000381951,NM_012352.2; T ENST00000381951 Transcript missense_variant 448/930 448/930 150/309 V/L Gtg/Ttg COSM4065425 1 1 OR1A2 HGNC HGNC:8180 protein_coding YES CCDS11021.1 ENSP00000371377 Q9Y585 A0A126GVH4 UPI0000041E56 NM_012352.2 tolerated(0.11) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF319,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 3197966 3197966 G T 1 0 0 0 0 1 0 0 0 11028 1261 44 2 2 OR1A2 17 3197966 Missense_Mutation SNP G C3N-01414_T 1314090 3197966 80059475 420 23620 PER1 0 . GRCh38 17 8142270 8142270 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.3448A>T p.Arg1150Trp p.R1150W ENST00000317276 21/23 45 32 13 58 58 0 strelka-varscan-mutect PER1,missense_variant,p.Arg1150Trp,ENST00000317276,NM_002616.2;PER1,missense_variant,p.Arg1127Trp,ENST00000581082,;PER1,downstream_gene_variant,,ENST00000354903,;PER1,downstream_gene_variant,,ENST00000583559,;PER1,downstream_gene_variant,,ENST00000614952,;PER1,downstream_gene_variant,,ENST00000578089,;PER1,splice_region_variant,,ENST00000582719,;PER1,splice_region_variant,,ENST00000585284,;PER1,downstream_gene_variant,,ENST00000581395,;PER1,downstream_gene_variant,,ENST00000585095,;PER1,downstream_gene_variant,,ENST00000577424,;PER1,downstream_gene_variant,,ENST00000579203,;PER1,downstream_gene_variant,,ENST00000578950,;PER1,upstream_gene_variant,,ENST00000583677,;PER1,downstream_gene_variant,,ENST00000579098,; A ENST00000317276 Transcript missense_variant,splice_region_variant 3686/4707 3448/3873 1150/1290 R/W Agg/Tgg 1 -1 PER1 HGNC HGNC:8845 protein_coding YES CCDS11131.1 ENSP00000314420 O15534 UPI000013FFF5 NM_002616.2 deleterious(0) 21/23 hmmpanther:PTHR11269:SF8,hmmpanther:PTHR11269,Pfam_domain:PF12114 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 8142270 8142270 T A 1 0 0 0 0 1 0 0 0 11817 1594 55 4 4 PER1 17 8142270 Missense_Mutation SNP T C3N-01414_T 4944304 8142270 75115171 421 23621 GLP2R 0 . GRCh38 17 9860036 9860036 + Missense_Mutation SNP C C T rs145296340 C3N-01414_T C3N-01414_N C C c.860C>T p.Thr287Met p.T287M ENST00000262441 7/13 131 105 26 210 210 0 strelka-varscan-mutect GLP2R,missense_variant,p.Thr287Met,ENST00000262441,NM_004246.2;GLP2R,missense_variant,p.Thr107Met,ENST00000574745,;GLP2R,missense_variant,p.Thr107Met,ENST00000304773,;GLP2R,3_prime_UTR_variant,,ENST00000458005,; T ENST00000262441 Transcript missense_variant 1373/4572 860/1662 287/553 T/M aCg/aTg rs145296340,COSM1208321 1 1 GLP2R HGNC HGNC:4325 protein_coding YES CCDS11150.1 ENSP00000262441 O95838 UPI0000050469 NM_004246.2 deleterious(0) 7/13 PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF269,Pfam_domain:PF00002,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs145296340 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 9860036 9860036 C T 1 0 0 0 0 1 0 0 0 6332 536 19 1 1 GLP2R 17 9860036 Missense_Mutation SNP C C3N-01414_T 1717766 9860036 73397405 422 23622 MYH8 0 . GRCh38 17 10398632 10398632 + Silent SNP G G A rs199830005 C3N-01414_T C3N-01414_N G G c.3990C>T p.= p.N1330N ENST00000403437 30/40 481 437 44 639 638 1 strelka-varscan-mutect MYH8,synonymous_variant,p.=,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript synonymous_variant 4085/6041 3990/5814 1330/1937 N aaC/aaT rs199830005,COSM1479205 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 30/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Superfamily_domains:SSF90257 0,1 LOW SNV 5 0,1 1 PASS rs199830005 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 10398632 10398632 G A 1 0 0 0 0 0 0 0 1 10041 1136 40 1 1 MYH8 17 10398632 Silent SNP G C3N-01414_T 538596 10398632 72858809 423 23623 MYH8 0 . GRCh38 17 10401123 10401123 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.3177G>T p.Glu1059Asp p.E1059D ENST00000403437 25/40 324 243 81 468 468 0 strelka-varscan-mutect MYH8,missense_variant,p.Glu1059Asp,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript missense_variant 3272/6041 3177/5814 1059/1937 E/D gaG/gaT 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0.02) 25/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 10401123 10401123 C A 1 0 0 0 0 1 0 0 0 10041 680 24 2 2 MYH8 17 10401123 Missense_Mutation SNP C C3N-01414_T 2491 10401123 72856318 424 23624 GID4 0 . GRCh38 17 18054158 18054158 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.530G>T p.Gly177Val p.G177V ENST00000268719 3/6 144 119 25 160 159 1 strelka-varscan-mutect GID4,missense_variant,p.Gly177Val,ENST00000268719,NM_024052.4;GID4,missense_variant,p.Gly177Val,ENST00000376345,;GID4,missense_variant,p.Gly8Val,ENST00000459843,;GID4,missense_variant,p.Gly4Val,ENST00000481836,; T ENST00000268719 Transcript missense_variant 703/4237 530/903 177/300 G/V gGa/gTa 1 1 GID4 HGNC HGNC:28453 protein_coding YES CCDS11190.1 ENSP00000268719 Q8IVV7 UPI00000745B4 NM_024052.4 deleterious(0) 3/6 Pfam_domain:PF09783,hmmpanther:PTHR15898 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 18054158 18054158 G T 1 0 0 0 0 1 0 0 0 6254 1174 41 2 2 GID4 17 18054158 Missense_Mutation SNP G C3N-01414_T 7653035 18054158 65203283 425 23625 KIAA0100 0 . GRCh38 17 28635499 28635499 + Silent SNP C C T novel C3N-01414_T C3N-01414_N C C c.2088G>A p.= p.V696V ENST00000528896 16/39 405 363 42 389 389 0 strelka-varscan-mutect KIAA0100,synonymous_variant,p.=,ENST00000528896,NM_014680.3;KIAA0100,synonymous_variant,p.=,ENST00000544884,;KIAA0100,synonymous_variant,p.=,ENST00000389003,;KIAA0100,upstream_gene_variant,,ENST00000577261,;RP11-192H23.7,non_coding_transcript_exon_variant,,ENST00000577814,;RP11-192H23.7,downstream_gene_variant,,ENST00000583787,;KIAA0100,downstream_gene_variant,,ENST00000577417,;KIAA0100,downstream_gene_variant,,ENST00000580882,;KIAA0100,downstream_gene_variant,,ENST00000583403,;KIAA0100,downstream_gene_variant,,ENST00000577580,;KIAA0100,upstream_gene_variant,,ENST00000582417,;KIAA0100,upstream_gene_variant,,ENST00000581064,;KIAA0100,downstream_gene_variant,,ENST00000581267,;KIAA0100,downstream_gene_variant,,ENST00000579253,; T ENST00000528896 Transcript synonymous_variant 2163/7407 2088/6708 696/2235 V gtG/gtA 1 -1 KIAA0100 HGNC HGNC:28960 protein_coding YES CCDS32595.1 ENSP00000436773 Q14667 UPI00004B4130 NM_014680.3 16/39 hmmpanther:PTHR15678 LOW 1 SNV 1 1 PASS rs1217756749 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 28635499 28635499 C T 1 0 0 0 0 0 0 0 1 8074 465 17 3 3 KIAA0100 17 28635499 Silent SNP C C3N-01414_T 10581341 28635499 54621942 426 23626 TLCD1 0 . GRCh38 17 28724613 28724613 + Missense_Mutation SNP A A C novel C3N-01414_T C3N-01414_N A A c.641T>G p.Leu214Arg p.L214R ENST00000292090 4/4 504 415 89 480 480 0 strelka-varscan-mutect TLCD1,missense_variant,p.Leu214Arg,ENST00000292090,NM_138463.3;TLCD1,missense_variant,p.Leu167Arg,ENST00000394933,NM_001160407.1;TLCD1,missense_variant,p.Leu143Arg,ENST00000580518,;TLCD1,missense_variant,p.Trp52Gly,ENST00000581236,;NEK8,upstream_gene_variant,,ENST00000268766,NM_178170.2;RPL23A,downstream_gene_variant,,ENST00000422514,NM_000984.5;RPL23A,downstream_gene_variant,,ENST00000394938,;NEK8,upstream_gene_variant,,ENST00000579060,;NEK8,upstream_gene_variant,,ENST00000579671,;RPL23A,downstream_gene_variant,,ENST00000472628,;RPL23A,downstream_gene_variant,,ENST00000496182,;RPL23A,downstream_gene_variant,,ENST00000578181,;RPL23A,downstream_gene_variant,,ENST00000355731,;RPL23A,downstream_gene_variant,,ENST00000394935,;SNORD4B,downstream_gene_variant,,ENST00000459083,;SNORD4A,downstream_gene_variant,,ENST00000459174,;SNORD42B,downstream_gene_variant,,ENST00000458893,;SNORD42A,downstream_gene_variant,,ENST00000459584,;AC010761.8,upstream_gene_variant,,ENST00000582718,;AC010761.14,upstream_gene_variant,,ENST00000587898,;NEK8,upstream_gene_variant,,ENST00000593261,;NEK8,upstream_gene_variant,,ENST00000543014,;NEK8,upstream_gene_variant,,ENST00000584342,;RPL23A,downstream_gene_variant,,ENST00000582736,;NEK8,upstream_gene_variant,,ENST00000581000,;RPL23A,downstream_gene_variant,,ENST00000580755,; C ENST00000292090 Transcript missense_variant 752/1017 641/744 214/247 L/R cTg/cGg 1 -1 TLCD1 HGNC HGNC:25177 protein_coding YES CCDS11242.1 ENSP00000292090 Q96CP7 UPI000006DF3D NM_138463.3 deleterious(0) 4/4 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50922,hmmpanther:PTHR13439,hmmpanther:PTHR13439:SF5,Pfam_domain:PF03798,SMART_domains:SM00724 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 28724613 28724613 A C 1 0 0 0 0 1 0 0 0 16380 188 7 5 5 TLCD1 17 28724613 Missense_Mutation SNP A C3N-01414_T 89114 28724613 54532828 427 23627 TADA2A 0 . GRCh38 17 37465567 37465567 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.849G>T p.Gln283His p.Q283H ENST00000620367 11/11 220 179 41 331 330 1 strelka-varscan-mutect TADA2A,missense_variant,p.Gln283His,ENST00000620367,NM_001291918.1,NM_133439.3;TADA2A,intron_variant,,ENST00000615182,NM_001166105.2;TADA2A,intron_variant,,ENST00000612272,NM_001488.4;TADA2A,downstream_gene_variant,,ENST00000615328,;TADA2A,intron_variant,,ENST00000620086,;TADA2A,intron_variant,,ENST00000619335,;TADA2A,intron_variant,,ENST00000620628,;TADA2A,intron_variant,,ENST00000619777,;TADA2A,intron_variant,,ENST00000616284,;TADA2A,downstream_gene_variant,,ENST00000614122,; T ENST00000620367 Transcript missense_variant 957/1043 849/918 283/305 Q/H caG/caT 1 1 TADA2A HGNC HGNC:11531 protein_coding CCDS45656.1 ENSP00000480446 A0A087WWR4 UPI0000161F3F NM_001291918.1,NM_133439.3 tolerated_low_confidence(0.14) 11/11 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 37465567 37465567 G T 1 0 0 0 0 1 0 0 0 15906 1020 36 2 2 TADA2A 17 37465567 Missense_Mutation SNP G C3N-01414_T 8740954 37465567 45791874 428 23628 ACLY 0 . GRCh38 17 41869589 41869589 + Splice_Site SNP T T C novel C3N-01414_T C3N-01414_N T T c.2938-2A>G p.X980_splice ENST00000352035 123 94 29 123 123 0 strelka-varscan-mutect ACLY,splice_acceptor_variant,,ENST00000352035,NM_001303274.1,NM_001096.2;ACLY,splice_acceptor_variant,,ENST00000353196,NM_001303275.1,NM_198830.1;ACLY,splice_acceptor_variant,,ENST00000590151,;ACLY,splice_acceptor_variant,,ENST00000393896,;ACLY,splice_acceptor_variant,,ENST00000537919,;KLHL11,upstream_gene_variant,,ENST00000319121,NM_018143.2;RP11-229E13.4,downstream_gene_variant,,ENST00000619176,;ACLY,splice_acceptor_variant,,ENST00000588779,; C ENST00000352035 Transcript splice_acceptor_variant -/4339 2938/3306 980/1101 1 -1 ACLY HGNC HGNC:115 protein_coding YES CCDS11412.1 ENSP00000253792 P53396 A0A024R1T9 UPI000013CDF3 NM_001303274.1,NM_001096.2 25/28 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 77 41869589 41869589 T C 1 0 0 0 0 0 0 1 0 185 1536 53 5 5 ACLY 17 41869589 Splice_Site SNP T C3N-01414_T 4404022 41869589 41387852 429 23629 CACNA1G 0 . GRCh38 17 50607974 50607974 + Silent SNP C C A rs751708640 C3N-01414_T C3N-01414_N C C c.4660C>A p.= p.R1554R ENST00000359106 25/38 227 150 77 306 306 0 strelka-varscan-mutect CACNA1G,synonymous_variant,p.=,ENST00000354983,NM_198396.2;CACNA1G,synonymous_variant,p.=,ENST00000352832,NM_198387.2;CACNA1G,synonymous_variant,p.=,ENST00000359106,NM_018896.4;CACNA1G,synonymous_variant,p.=,ENST00000360761,NM_198382.2;CACNA1G,synonymous_variant,p.=,ENST00000442258,NM_198388.2;CACNA1G,synonymous_variant,p.=,ENST00000429973,NM_198386.2;CACNA1G,synonymous_variant,p.=,ENST00000507336,NM_198377.2;CACNA1G,synonymous_variant,p.=,ENST00000358244,NM_198376.2;CACNA1G,synonymous_variant,p.=,ENST00000507510,NM_198385.2;CACNA1G,synonymous_variant,p.=,ENST00000515765,NM_198380.2;CACNA1G,synonymous_variant,p.=,ENST00000515411,NM_001256324.1;CACNA1G,synonymous_variant,p.=,ENST00000502264,NM_198383.2;CACNA1G,synonymous_variant,p.=,ENST00000510115,NM_198379.2;CACNA1G,synonymous_variant,p.=,ENST00000514079,NM_001256325.1;CACNA1G,synonymous_variant,p.=,ENST00000513689,NM_001256326.1;CACNA1G,synonymous_variant,p.=,ENST00000515165,NM_198384.2;CACNA1G,synonymous_variant,p.=,ENST00000507609,NM_001256327.1;CACNA1G,synonymous_variant,p.=,ENST00000512389,NM_198378.2;CACNA1G,synonymous_variant,p.=,ENST00000514181,NM_001256328.1;CACNA1G,synonymous_variant,p.=,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,synonymous_variant,p.=,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,synonymous_variant,p.=,ENST00000510366,NM_001256331.1;CACNA1G,synonymous_variant,p.=,ENST00000514717,NM_001256332.1;CACNA1G,synonymous_variant,p.=,ENST00000505165,NM_001256333.1;CACNA1G,synonymous_variant,p.=,ENST00000507896,NM_001256334.1;CACNA1G,downstream_gene_variant,,ENST00000416767,;CACNA1G,downstream_gene_variant,,ENST00000506520,;CACNA1G,synonymous_variant,p.=,ENST00000506406,;CACNA1G,synonymous_variant,p.=,ENST00000504076,;CACNA1G,synonymous_variant,p.=,ENST00000511765,;CACNA1G,synonymous_variant,p.=,ENST00000503436,;CACNA1G,synonymous_variant,p.=,ENST00000511768,;CACNA1G,synonymous_variant,p.=,ENST00000503607,; A ENST00000359106 Transcript synonymous_variant 4660/7648 4660/7134 1554/2377 R Cgg/Agg rs751708640 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 25/38 Coiled-coils_(Ncoils):Coil,Prints_domain:PR01629,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs751708640 . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 A 2 1 77 50607974 50607974 C A 1 0 0 0 0 0 0 0 1 2232 759 27 1 1 CACNA1G 17 50607974 Silent SNP C C3N-01414_T 8738385 50607974 32649467 430 23630 SPAG9 0 . GRCh38 17 51046610 51046610 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.51G>T p.= p.A17A ENST00000510283 1/27 233 215 18 350 349 1 strelka-varscan-mutect SPAG9,synonymous_variant,p.=,ENST00000510283,NM_001251971.1;SPAG9,synonymous_variant,p.=,ENST00000510855,;SPAG9,intron_variant,,ENST00000262013,NM_001130528.2;SPAG9,intron_variant,,ENST00000618113,;SPAG9,intron_variant,,ENST00000357122,NM_003971.5;SPAG9,intron_variant,,ENST00000505279,NM_001130527.2;RP11-481C4.1,intron_variant,,ENST00000509833,;SPAG9,non_coding_transcript_exon_variant,,ENST00000511987,;SPAG9,intron_variant,,ENST00000514613,;SPAG9,intron_variant,,ENST00000505173,;SPAG9,intron_variant,,ENST00000502329,; A ENST00000510283 Transcript synonymous_variant 269/4949 51/3534 17/1177 A gcG/gcT 1 -1 SPAG9 HGNC HGNC:14524 protein_coding CCDS58577.1 ENSP00000423165 O60271 UPI0001D3B84D NM_001251971.1 1/27 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS rs922410087 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 51046610 51046610 C A 1 0 0 0 0 0 0 0 1 15316 639 23 1 1 SPAG9 17 51046610 Silent SNP C C3N-01414_T 438636 51046610 32210831 431 23631 KIF2B 0 . GRCh38 17 53824820 53824820 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.1787A>T p.Glu596Val p.E596V ENST00000268919 1/1 142 103 39 216 216 0 strelka-varscan-mutect KIF2B,missense_variant,p.Glu596Val,ENST00000268919,NM_032559.4; T ENST00000268919 Transcript missense_variant 1920/2313 1787/2022 596/673 E/V gAa/gTa 1 1 KIF2B HGNC HGNC:29443 protein_coding YES CCDS32685.1 ENSP00000268919 Q8N4N8 A0A140VKG5 UPI000013D7E6 NM_032559.4 tolerated(0.07) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF524 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 53824820 53824820 A T 1 0 0 0 0 1 0 0 0 8163 246 9 4 4 KIF2B 17 53824820 Missense_Mutation SNP A C3N-01414_T 2778210 53824820 29432621 432 23632 USP32 0 . GRCh38 17 60181485 60181485 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.4387G>T p.Asp1463Tyr p.D1463Y ENST00000300896 32/34 256 207 49 430 430 0 strelka-varscan-mutect USP32,missense_variant,p.Asp1463Tyr,ENST00000300896,NM_032582.3;USP32,missense_variant,p.Asp1133Tyr,ENST00000592339,;USP32,missense_variant,p.Asp64Tyr,ENST00000593071,;USP32,downstream_gene_variant,,ENST00000586238,; A ENST00000300896 Transcript missense_variant 4582/5171 4387/4815 1463/1604 D/Y Gac/Tac 1 -1 USP32 HGNC HGNC:19143 protein_coding YES CCDS32697.1 ENSP00000300896 Q8NFA0 UPI0000047AF8 NM_032582.3 deleterious_low_confidence(0.01) 32/34 PROSITE_profiles:PS50235,Pfam_domain:PF00443 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 60181485 60181485 C A 1 0 0 0 0 1 0 0 0 17605 855 30 2 2 USP32 17 60181485 Missense_Mutation SNP C C3N-01414_T 6356665 60181485 23075956 433 23633 CCDC47 0 . GRCh38 17 63751876 63751876 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1435G>C p.Gly479Arg p.G479R ENST00000582252 12/12 223 159 64 287 287 0 strelka-varscan-mutect CCDC47,missense_variant,p.Gly479Arg,ENST00000582252,;CCDC47,intron_variant,,ENST00000225726,NM_020198.2;CCDC47,intron_variant,,ENST00000403162,;CCDC47,intron_variant,,ENST00000612558,;RP11-51F16.8,intron_variant,,ENST00000580553,;CCDC47,downstream_gene_variant,,ENST00000582331,; G ENST00000582252 Transcript missense_variant 1613/1719 1435/1443 479/480 G/R Ggt/Cgt 1 -1 CCDC47 HGNC HGNC:24856 protein_coding ENSP00000463577 Q96A33 UPI000007108D 12/12 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 63751876 63751876 C G 1 0 0 0 0 1 0 0 0 2524 594 21 4 4 CCDC47 17 63751876 Missense_Mutation SNP C C3N-01414_T 3570391 63751876 19505565 434 23634 LRRC37A3 0 . GRCh38 17 64894968 64894968 + Nonsense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.2290G>T p.Gly764Ter p.G764* ENST00000584306 3/14 422 330 92 576 576 0 strelka-varscan-mutect LRRC37A3,stop_gained,p.Gly764Ter,ENST00000584306,NM_199340.3;LRRC37A3,stop_gained,p.Gly764Ter,ENST00000319651,;LRRC37A3,stop_gained,p.Gly31Ter,ENST00000580464,;LRRC37A3,intron_variant,,ENST00000400877,;LRRC37A3,intron_variant,,ENST00000339474,NM_001303255.1;LRRC37A3,intron_variant,,ENST00000581368,;LRRC37A3,upstream_gene_variant,,ENST00000584788,;RP11-927P21.1,intron_variant,,ENST00000584959,;RP11-927P21.1,intron_variant,,ENST00000577938,;RP11-927P21.1,intron_variant,,ENST00000584131,;RP11-927P21.2,upstream_gene_variant,,ENST00000581622,;LRRC37A3,downstream_gene_variant,,ENST00000577487,;LRRC37A3,downstream_gene_variant,,ENST00000580439,;RP11-927P21.9,downstream_gene_variant,,ENST00000607347,; A ENST00000584306 Transcript stop_gained 2821/5665 2290/4905 764/1634 G/* Gga/Tga 1 -1 LRRC37A3 HGNC HGNC:32427 protein_coding YES CCDS32708.1 ENSP00000464535 O60309 UPI00005B2F0A NM_199340.3 3/14 hmmpanther:PTHR23045,hmmpanther:PTHR23045:SF7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 64894968 64894968 C A 1 0 0 0 0 0 1 0 0 8887 603 21 2 2 LRRC37A3 17 64894968 Nonsense_Mutation SNP C C3N-01414_T 1143092 64894968 18362473 435 23635 SDK2 0 . GRCh38 17 73365287 73365287 + Missense_Mutation SNP A A C novel C3N-01414_T C3N-01414_N A A c.5276T>G p.Leu1759Arg p.L1759R ENST00000392650 38/45 96 74 22 130 129 1 strelka-varscan-mutect SDK2,missense_variant,p.Leu1759Arg,ENST00000392650,NM_001144952.1;SDK2,missense_variant,p.Leu916Arg,ENST00000424778,;SDK2,non_coding_transcript_exon_variant,,ENST00000410094,;SDK2,non_coding_transcript_exon_variant,,ENST00000479356,; C ENST00000392650 Transcript missense_variant 5277/10723 5276/6519 1759/2172 L/R cTg/cGg 1 -1 SDK2 HGNC HGNC:19308 protein_coding YES CCDS45769.1 ENSP00000376421 Q58EX2 UPI0000E5A088 NM_001144952.1 deleterious(0) 38/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF37,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 73365287 73365287 A C 1 0 0 0 0 1 0 0 0 14244 188 7 5 5 SDK2 17 73365287 Missense_Mutation SNP A C3N-01414_T 8470319 73365287 9892154 436 23636 CD300LD 0 . GRCh38 17 74588850 74588850 + Splice_Site SNP C C A novel C3N-01414_T C3N-01414_N C C c.41-1G>T p.X14_splice ENST00000375352 53 41 12 89 89 0 strelka-varscan-mutect CD300LD,splice_acceptor_variant,,ENST00000375352,NM_001115152.1;C17orf77,intron_variant,,ENST00000392620,;C17orf77,intron_variant,,ENST00000524389,;C17orf77,upstream_gene_variant,,ENST00000328023,; A ENST00000375352 Transcript splice_acceptor_variant -/1303 41/585 14/194 1 -1 CD300LD HGNC HGNC:16848 protein_coding YES CCDS42379.1 ENSP00000364501 Q6UXZ3 UPI00001D6916 NM_001115152.1 1/3 HIGH 1 SNV 1 1 PASS rs1432871816 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 77 74588850 74588850 C A 1 0 0 0 0 0 0 1 0 2704 695 24 2 2 CD300LD 17 74588850 Splice_Site SNP C C3N-01414_T 1223563 74588850 8668591 437 23637 SLC9A3R1 0 . GRCh38 17 74763409 74763409 + Missense_Mutation SNP G G A novel C3N-01414_T C3N-01414_N G G c.646G>A p.Val216Met p.V216M ENST00000262613 3/6 123 115 8 179 179 0 strelka-mutect SLC9A3R1,missense_variant,p.Val216Met,ENST00000262613,NM_004252.4;SLC9A3R1,missense_variant,p.Val60Met,ENST00000413388,;SLC9A3R1,intron_variant,,ENST00000583369,;SLC9A3R1,non_coding_transcript_exon_variant,,ENST00000578958,;SLC9A3R1,upstream_gene_variant,,ENST00000581356,; A ENST00000262613 Transcript missense_variant 841/1969 646/1077 216/358 V/M Gtg/Atg 1 1 SLC9A3R1 HGNC HGNC:11075 protein_coding YES CCDS11705.1 ENSP00000262613 O14745 UPI0000072521 NM_004252.4 deleterious(0) 3/6 Gene3D:2.30.42.10,Pfam_domain:PF00595,PIRSF_domain:PIRSF037866,PROSITE_profiles:PS50106,hmmpanther:PTHR14191,hmmpanther:PTHR14191:SF7,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -11.70995 0.9999887 1 1 1 0 A 3 1 77 74763409 74763409 G A 1 0 0 0 0 1 0 0 0 14996 1261 44 3 3 SLC9A3R1 17 74763409 Missense_Mutation SNP G C3N-01414_T 174559 74763409 8494032 438 23638 FN3KRP 0 . GRCh38 17 82716770 82716770 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.15G>T p.= p.L5L ENST00000269373 1/6 119 95 24 147 147 0 strelka-varscan-mutect FN3KRP,synonymous_variant,p.=,ENST00000269373,NM_024619.3;FN3KRP,upstream_gene_variant,,ENST00000573158,;FN3KRP,upstream_gene_variant,,ENST00000577128,;AC024361.1,downstream_gene_variant,,ENST00000629043,;RP11-388C12.1,upstream_gene_variant,,ENST00000574471,;FN3KRP,synonymous_variant,p.=,ENST00000574832,;FN3KRP,synonymous_variant,p.=,ENST00000574356,;FN3KRP,synonymous_variant,p.=,ENST00000574206,;FN3KRP,upstream_gene_variant,,ENST00000571482,; T ENST00000269373 Transcript synonymous_variant 88/1849 15/930 5/309 L ctG/ctT 1 1 FN3KRP HGNC HGNC:25700 protein_coding YES CCDS11817.1 ENSP00000269373 Q9HA64 A0A140VK84 UPI000006F7D6 NM_024619.3 1/6 PIRSF_domain:PIRSF006221,hmmpanther:PTHR12149,hmmpanther:PTHR12149:SF10,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs953911562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 82716770 82716770 G T 1 0 0 0 0 0 0 0 1 5820 1277 45 2 2 FN3KRP 17 82716770 Silent SNP G C3N-01414_T 7953361 82716770 540671 439 23639 PIEZO2 0 . GRCh38 18 10702021 10702021 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.6070C>A p.Leu2024Met p.L2024M ENST00000503781 39/52 122 89 33 189 189 0 strelka-varscan-mutect PIEZO2,missense_variant,p.Leu1975Met,ENST00000383408,;PIEZO2,missense_variant,p.Leu2024Met,ENST00000302079,;PIEZO2,missense_variant,p.Leu2049Met,ENST00000580640,;PIEZO2,missense_variant,p.Leu2024Met,ENST00000503781,NM_022068.3;PIEZO2,upstream_gene_variant,,ENST00000538948,;RP11-856M7.2,upstream_gene_variant,,ENST00000584167,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; T ENST00000503781 Transcript missense_variant 6070/8259 6070/8259 2024/2752 L/M Ctg/Atg 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 tolerated(0.21) 39/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 10702021 10702021 G T 1 0 0 0 0 1 0 0 0 11975 991 35 2 2 PIEZO2 18 10702021 Missense_Mutation SNP G C3N-01414_T 10702021 69671264 440 23640 PIEZO2 0 . GRCh38 18 10714843 10714843 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.5170G>T p.Asp1724Tyr p.D1724Y ENST00000503781 36/52 231 188 43 413 410 3 strelka-varscan-mutect PIEZO2,missense_variant,p.Asp1675Tyr,ENST00000383408,;PIEZO2,missense_variant,p.Asp1724Tyr,ENST00000302079,;PIEZO2,missense_variant,p.Asp1749Tyr,ENST00000580640,;PIEZO2,missense_variant,p.Asp1724Tyr,ENST00000503781,NM_022068.3;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; A ENST00000503781 Transcript missense_variant 5170/8259 5170/8259 1724/2752 D/Y Gac/Tac 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 deleterious(0.05) 36/52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 10714843 10714843 C A 1 0 0 0 0 1 0 0 0 11975 826 29 2 2 PIEZO2 18 10714843 Missense_Mutation SNP C C3N-01414_T 12822 10714843 69658442 441 23641 CEP192 0 . GRCh38 18 13056362 13056362 + Missense_Mutation SNP G G T rs546992868 C3N-01414_T C3N-01414_N G G c.3772G>T p.Ala1258Ser p.A1258S ENST00000506447 19/45 275 209 66 414 413 1 strelka-varscan-mutect CEP192,missense_variant,p.Ala1258Ser,ENST00000506447,NM_032142.3;CEP192,missense_variant,p.Ala783Ser,ENST00000325971,;CEP192,missense_variant,p.Ala797Ser,ENST00000511820,;CEP192,missense_variant,p.Ala999Ser,ENST00000589596,;CEP192,upstream_gene_variant,,ENST00000430049,;CEP192,missense_variant,p.Ala858Ser,ENST00000510237,;CEP192,3_prime_UTR_variant,,ENST00000513432,;CEP192,upstream_gene_variant,,ENST00000589993,;CEP192,upstream_gene_variant,,ENST00000585938,; T ENST00000506447 Transcript missense_variant 3852/7960 3772/7614 1258/2537 A/S Gct/Tct rs546992868,COSM708405,COSM708406 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 deleterious(0.04) 19/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs546992868 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 13056362 13056362 G T 1 0 0 0 0 1 0 0 0 2967 1087 38 1 1 CEP192 18 13056362 Missense_Mutation SNP G C3N-01414_T 2341519 13056362 67316923 442 23642 NPC1 0 . GRCh38 18 23568910 23568910 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.376A>T p.Thr126Ser p.T126S ENST00000269228 4/25 355 283 72 573 573 0 strelka-varscan-mutect NPC1,missense_variant,p.Thr126Ser,ENST00000269228,NM_000271.4;NPC1,non_coding_transcript_exon_variant,,ENST00000540608,;NPC1,downstream_gene_variant,,ENST00000587223,; A ENST00000269228 Transcript missense_variant 931/5157 376/3837 126/1278 T/S Act/Tct 1 -1 NPC1 HGNC HGNC:7897 protein_coding YES CCDS11878.1 ENSP00000269228 O15118 UPI000013D80F NM_000271.4 tolerated(0.06) 4/25 hmmpanther:PTHR10796:SF116,hmmpanther:PTHR10796,TIGRFAM_domain:TIGR00917,Pfam_domain:PF16414 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 23568910 23568910 T A 1 0 0 0 0 1 0 0 0 10618 1638 57 4 4 NPC1 18 23568910 Missense_Mutation SNP T C3N-01414_T 10512548 23568910 56804375 443 23643 TAF4B 0 . GRCh38 18 26227258 26227258 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.325A>T p.Asn109Tyr p.N109Y ENST00000578121 1/15 338 258 80 502 502 0 strelka-varscan-mutect TAF4B,missense_variant,p.Asn109Tyr,ENST00000269142,NM_005640.2;TAF4B,missense_variant,p.Asn109Tyr,ENST00000578121,NM_001293725.1;TAF4B,missense_variant,p.Asn109Tyr,ENST00000418698,; T ENST00000578121 Transcript missense_variant 773/3204 325/2604 109/867 N/Y Aat/Tat 1 1 TAF4B HGNC HGNC:11538 protein_coding YES CCDS77170.1 ENSP00000462980 J3KTH2 UPI0000EE54F8 NM_001293725.1 deleterious(0) 1/15 hmmpanther:PTHR15138,hmmpanther:PTHR15138:SF17 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 26227258 26227258 A T 1 0 0 0 0 1 0 0 0 15923 362 13 4 4 TAF4B 18 26227258 Missense_Mutation SNP A C3N-01414_T 2658348 26227258 54146027 444 23644 DSG1 0 . GRCh38 18 31333639 31333639 + Silent SNP G G T C3N-01414_T C3N-01414_N G G c.735G>T p.= p.G245G ENST00000257192 7/15 418 321 97 601 599 2 strelka-varscan-mutect DSG1,synonymous_variant,p.=,ENST00000257192,NM_001942.3; T ENST00000257192 Transcript synonymous_variant 947/5045 735/3150 245/1049 G ggG/ggT COSM347897 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 7/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 LOW 1 SNV 1 1 1 PASS rs1449413200 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 31333639 31333639 G T 1 0 0 0 0 0 0 0 1 4597 1219 43 2 2 DSG1 18 31333639 Silent SNP G C3N-01414_T 5106381 31333639 49039646 445 23645 ELP2 0 . GRCh38 18 36142305 36142305 + Nonsense_Mutation SNP G G T rs772323657 C3N-01414_T C3N-01414_N G G c.808G>T p.Gly270Ter p.G270* ENST00000442325 8/23 355 286 69 534 534 0 strelka-varscan-mutect ELP2,stop_gained,p.Gly205Ter,ENST00000358232,NM_018255.2;ELP2,stop_gained,p.Gly270Ter,ENST00000442325,NM_001242875.1;ELP2,stop_gained,p.Gly244Ter,ENST00000350494,NM_001242876.1;ELP2,stop_gained,p.Gly179Ter,ENST00000351393,NM_001242877.1;ELP2,stop_gained,p.Gly179Ter,ENST00000542824,NM_001242878.1;ELP2,stop_gained,p.Gly56Ter,ENST00000543127,;ELP2,intron_variant,,ENST00000423854,NM_001242879.1;ELP2,non_coding_transcript_exon_variant,,ENST00000535093,;ELP2,non_coding_transcript_exon_variant,,ENST00000540730,;ELP2,non_coding_transcript_exon_variant,,ENST00000543439,;ELP2,downstream_gene_variant,,ENST00000540135,;ELP2,stop_gained,p.Gly205Ter,ENST00000539560,;ELP2,3_prime_UTR_variant,,ENST00000542430,;ELP2,3_prime_UTR_variant,,ENST00000545632,;ELP2,non_coding_transcript_exon_variant,,ENST00000536373,;ELP2,non_coding_transcript_exon_variant,,ENST00000540323,;ELP2,intron_variant,,ENST00000540799,;ELP2,downstream_gene_variant,,ENST00000535488,;ELP2,downstream_gene_variant,,ENST00000544267,; T ENST00000442325 Transcript stop_gained 844/2722 808/2676 270/891 G/* Gga/Tga rs772323657 1 1 ELP2 HGNC HGNC:18248 protein_coding YES CCDS56065.1 ENSP00000414851 Q6IA86 UPI0000E03DE9 NM_001242875.1 8/23 PROSITE_profiles:PS50082,hmmpanther:PTHR22847:SF471,hmmpanther:PTHR22847,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50998 HIGH 1 SNV 2 1 PASS rs772323657 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 36142305 36142305 G T 1 0 0 0 0 0 1 0 0 4914 1349 47 2 2 ELP2 18 36142305 Nonsense_Mutation SNP G C3N-01414_T 4808666 36142305 44230980 446 23646 ST8SIA5 0 . GRCh38 18 46686248 46686248 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.603T>A p.= p.A201A ENST00000538168 6/8 284 212 72 407 407 0 strelka-varscan-mutect ST8SIA5,synonymous_variant,p.=,ENST00000538168,NM_001307986.1;ST8SIA5,synonymous_variant,p.=,ENST00000315087,NM_013305.4;ST8SIA5,synonymous_variant,p.=,ENST00000536490,NM_001307987.1;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000590497,;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000589088,;ST8SIA5,non_coding_transcript_exon_variant,,ENST00000587428,;ST8SIA5,downstream_gene_variant,,ENST00000591375,; T ENST00000538168 Transcript synonymous_variant 904/13761 603/1239 201/412 A gcT/gcA 1 -1 ST8SIA5 HGNC HGNC:17827 protein_coding YES CCDS77184.1 ENSP00000445492 O15466 UPI0000E03E3B NM_001307986.1 6/8 hmmpanther:PTHR11987:SF4,hmmpanther:PTHR11987,PIRSF_domain:PIRSF005557,Pfam_domain:PF00777 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 46686248 46686248 A T 1 0 0 0 0 0 0 0 1 15613 175 7 4 4 ST8SIA5 18 46686248 Silent SNP A C3N-01414_T 10543943 46686248 33687037 447 23647 CTIF 0 . GRCh38 18 48817240 48817240 + Missense_Mutation SNP A A G novel C3N-01414_T C3N-01414_N A A c.1397A>G p.Glu466Gly p.E466G ENST00000382998 11/13 128 118 10 162 162 0 strelka-varscan-mutect CTIF,missense_variant,p.Glu464Gly,ENST00000256413,NM_014772.2;CTIF,missense_variant,p.Glu466Gly,ENST00000382998,NM_001142397.1;CTIF,non_coding_transcript_exon_variant,,ENST00000587860,; G ENST00000382998 Transcript missense_variant 1654/4407 1397/1803 466/600 E/G gAg/gGg 1 1 CTIF HGNC HGNC:23925 protein_coding YES CCDS45864.1 ENSP00000372459 O43310 UPI0000074650 NM_001142397.1 deleterious(0.04) 11/13 hmmpanther:PTHR23254,Gene3D:1.25.40.180,Pfam_domain:PF02854,SMART_domains:SM00543,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 48817240 48817240 A G 1 0 0 0 0 1 0 0 0 3819 304 11 5 5 CTIF 18 48817240 Missense_Mutation SNP A C3N-01414_T 2130992 48817240 31556045 448 23648 MBD1 0 . GRCh38 18 50275384 50275384 + Missense_Mutation SNP C C G C3N-01414_T C3N-01414_N C C c.853G>C p.Val285Leu p.V285L ENST00000457839 9/17 149 112 37 204 204 0 strelka-varscan-mutect MBD1,missense_variant,p.Val285Leu,ENST00000457839,NM_001204137.1,NM_001204138.1;MBD1,missense_variant,p.Val285Leu,ENST00000585595,;MBD1,missense_variant,p.Val285Leu,ENST00000398495,NM_001204140.1;MBD1,missense_variant,p.Val161Leu,ENST00000592060,;MBD1,intron_variant,,ENST00000591416,;MBD1,intron_variant,,ENST00000269468,NM_015846.3;MBD1,intron_variant,,ENST00000347968,NM_015844.2;MBD1,intron_variant,,ENST00000269471,NM_015845.3;MBD1,intron_variant,,ENST00000339998,NM_001204142.1;MBD1,intron_variant,,ENST00000590208,NM_001204136.1;MBD1,intron_variant,,ENST00000353909,NM_015847.3;MBD1,intron_variant,,ENST00000585672,NM_001204141.1;MBD1,intron_variant,,ENST00000382948,NM_001204139.1;MBD1,intron_variant,,ENST00000587605,NM_001204143.1;MBD1,intron_variant,,ENST00000398493,;MBD1,intron_variant,,ENST00000588937,;MBD1,intron_variant,,ENST00000591535,NM_001204151.1;MBD1,intron_variant,,ENST00000398488,NM_002384.2;MBD1,intron_variant,,ENST00000589733,;MBD1,upstream_gene_variant,,ENST00000589541,;MBD1,intron_variant,,ENST00000586679,;MBD1,intron_variant,,ENST00000591661,;MBD1,downstream_gene_variant,,ENST00000586118,;MBD1,downstream_gene_variant,,ENST00000590215,;MBD1,downstream_gene_variant,,ENST00000589867,;MBD1,upstream_gene_variant,,ENST00000586884,;MBD1,downstream_gene_variant,,ENST00000589758,; G ENST00000457839 Transcript missense_variant 982/2473 853/1893 285/630 V/L Gtg/Ctg COSM4411307 1 -1 MBD1 HGNC HGNC:6916 protein_coding CCDS56073.1 ENSP00000405268 Q9UIS9 UPI0000151F37 NM_001204137.1,NM_001204138.1 tolerated(0.19) 9/17 hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF8 1 MODERATE SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 50275384 50275384 C G 1 0 0 0 0 1 0 0 0 9271 478 17 4 4 MBD1 18 50275384 Missense_Mutation SNP C C3N-01414_T 1458144 50275384 30097901 449 23649 C18orf54 0 . GRCh38 18 54362838 54362838 + Silent SNP A A G novel C3N-01414_T C3N-01414_N A A c.1140A>G p.= p.P380P ENST00000620105 5/9 253 189 64 450 450 0 strelka-varscan-mutect C18orf54,synonymous_variant,p.=,ENST00000620105,NM_001288981.1,NM_001288980.1;C18orf54,synonymous_variant,p.=,ENST00000300091,NM_173529.5,NM_001288982.1;C18orf54,synonymous_variant,p.=,ENST00000382911,;C18orf54,5_prime_UTR_variant,,ENST00000578138,;STARD6,upstream_gene_variant,,ENST00000581310,;STARD6,upstream_gene_variant,,ENST00000577499,;STARD6,upstream_gene_variant,,ENST00000584040,;C18orf54,upstream_gene_variant,,ENST00000582188,; G ENST00000620105 Transcript synonymous_variant 1442/5693 1140/1602 380/533 P ccA/ccG 1 1 C18orf54 HGNC HGNC:13796 protein_coding YES CCDS74223.1 ENSP00000477654 Q8IYD9 UPI000022A74A NM_001288981.1,NM_001288980.1 5/9 hmmpanther:PTHR35079:SF1,hmmpanther:PTHR35079,Pfam_domain:PF15792 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 54362838 54362838 A G 1 0 0 0 0 0 0 0 1 1900 117 5 5 5 C18orf54 18 54362838 Silent SNP A C3N-01414_T 4087454 54362838 26010447 450 23650 TIMM21 0 . GRCh38 18 74155346 74155346 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.405A>T p.= p.S135S ENST00000169551 3/6 147 113 34 297 297 0 strelka-varscan-mutect TIMM21,synonymous_variant,p.=,ENST00000169551,NM_014177.2;TIMM21,synonymous_variant,p.=,ENST00000580087,;TIMM21,synonymous_variant,p.=,ENST00000579071,;TIMM21,non_coding_transcript_exon_variant,,ENST00000577952,;TIMM21,non_coding_transcript_exon_variant,,ENST00000584925,;TIMM21,non_coding_transcript_exon_variant,,ENST00000581467,; T ENST00000169551 Transcript synonymous_variant 703/3095 405/747 135/248 S tcA/tcT 1 1 TIMM21 HGNC HGNC:25010 protein_coding YES CCDS12003.1 ENSP00000169551 Q9BVV7 A8K1K8 UPI0000073827 NM_014177.2 3/6 Pfam_domain:PF08294,hmmpanther:PTHR13032 LOW 1 SNV 1 1 PASS rs1020281964 . 0 204 2 4 0 0 0 0 -20 0.9998811 1 1 1 0 T 2 4 77 74155346 74155346 A T 1 0 0 0 0 0 0 0 1 16348 204 8 4 4 TIMM21 18 74155346 Silent SNP A C3N-01414_T 19792508 74155346 6217939 451 23651 KISS1R 0 . GRCh38 19 919564 919564 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.444G>A p.= p.L148L ENST00000234371 3/5 415 371 44 560 560 0 strelka-varscan-mutect KISS1R,synonymous_variant,p.=,ENST00000234371,NM_032551.4;KISS1R,synonymous_variant,p.=,ENST00000606939,;KISS1R,downstream_gene_variant,,ENST00000592648,; A ENST00000234371 Transcript synonymous_variant 605/1625 444/1197 148/398 L ttG/ttA 1 1 KISS1R HGNC HGNC:4510 protein_coding YES CCDS12049.1 ENSP00000234371 Q969F8 UPI0000070700 NM_032551.4 3/5 PROSITE_profiles:PS50262,hmmpanther:PTHR24230:SF78,hmmpanther:PTHR24230,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR01728 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 919564 919564 G A 1 0 0 0 0 0 0 0 1 8192 1310 46 3 3 KISS1R 19 919564 Silent SNP G C3N-01414_T 919564 57698052 452 23652 STK11 0 . GRCh38 19 1223052 1223053 + Frame_Shift_Ins INS - - T rs786200991 C3N-01414_T C3N-01414_N - - c.988_989insT p.Asp330ValfsTer30 p.D330Vfs*30 ENST00000326873 8/10 97 39 58 168 168 0 sindel-varindel-pindel STK11,frameshift_variant,p.Asp330ValfsTer30,ENST00000586243,;STK11,frameshift_variant,p.Asp330ValfsTer30,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript frameshift_variant 1438-1439/2611 988-989/1302 330/433 D/VX gac/gTac rs786200991 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 8/10 Gene3D:1.10.510.10,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,Superfamily_domains:SSF56112 pathogenic HIGH 1 insertion 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 77 1223052 1223052 - T 1 0 1 1 0 0 0 0 0 15664 1174 41 0 0 STK11 19 1223052 Frame_Shift_Ins INS - C3N-01414_T 303488 1223052 57394564 453 23653 ANKRD24 0 . GRCh38 19 4216029 4216029 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1249G>T p.Gly417Cys p.G417C ENST00000600132 16/22 186 144 42 257 257 0 strelka-varscan-mutect ANKRD24,missense_variant,p.Gly417Cys,ENST00000600132,NM_133475.1;ANKRD24,missense_variant,p.Gly417Cys,ENST00000318934,;ANKRD24,missense_variant,p.Gly507Cys,ENST00000262970,;ANKRD24,missense_variant,p.Gly388Cys,ENST00000597689,;ANKRD24,non_coding_transcript_exon_variant,,ENST00000595096,; T ENST00000600132 Transcript missense_variant 1525/4026 1249/3441 417/1146 G/C Ggt/Tgt 1 1 ANKRD24 HGNC HGNC:29424 protein_coding YES CCDS45925.1 ENSP00000471252 Q8TF21 UPI000041F5A9 NM_133475.1 deleterious(0) 16/22 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF16 MODERATE 1 SNV 5 1 PASS rs1394473184 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 4216029 4216029 G T 1 0 0 0 0 1 0 0 0 756 1232 43 2 2 ANKRD24 19 4216029 Missense_Mutation SNP G C3N-01414_T 2992977 4216029 54401587 454 23654 FBN3 0 . GRCh38 19 8110953 8110953 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.4225G>T p.Ala1409Ser p.A1409S ENST00000600128 34/64 188 137 51 280 280 0 strelka-varscan-mutect FBN3,missense_variant,p.Ala1409Ser,ENST00000600128,;FBN3,missense_variant,p.Ala1409Ser,ENST00000270509,NM_032447.3;FBN3,missense_variant,p.Ala1409Ser,ENST00000601739,NM_001321431.1;FBN3,non_coding_transcript_exon_variant,,ENST00000594331,; A ENST00000600128 Transcript missense_variant 4640/9362 4225/8430 1409/2809 A/S Gcg/Tcg 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F tolerated(1) 34/64 PROSITE_profiles:PS50026,hmmpanther:PTHR24039:SF0,hmmpanther:PTHR24039,PROSITE_patterns:PS01187,PIRSF_domain:PIRSF036312,Gene3D:2.10.25.10,Pfam_domain:PF07645,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 8110953 8110953 C A 1 0 0 0 0 1 0 0 0 5567 710 25 2 2 FBN3 19 8110953 Missense_Mutation SNP C C3N-01414_T 3894924 8110953 50506663 455 23655 MUC16 0 . GRCh38 19 8855995 8855995 + Missense_Mutation SNP T T A C3N-01414_T C3N-01414_N T T c.43282A>T p.Arg14428Trp p.R14428W ENST00000397910 81/84 193 157 36 262 262 0 strelka-varscan-mutect MUC16,missense_variant,p.Arg14428Trp,ENST00000397910,NM_024690.2;MUC16,missense_variant,p.Arg1251Trp,ENST00000599436,;MUC16,3_prime_UTR_variant,,ENST00000601404,;MUC16,3_prime_UTR_variant,,ENST00000596768,; A ENST00000397910 Transcript missense_variant 43486/43816 43282/43524 14428/14507 R/W Agg/Tgg COSM715583 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 81/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,SMART_domains:SM00200,Superfamily_domains:0047452 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 8855995 8855995 T A 1 0 0 0 0 1 0 0 0 9972 1579 55 4 4 MUC16 19 8855995 Missense_Mutation SNP T C3N-01414_T 745042 8855995 49761621 456 23656 WDR83 0 . GRCh38 19 12673302 12673302 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.784T>A p.Trp262Arg p.W262R ENST00000418543 10/11 137 101 36 167 167 0 strelka-varscan-mutect WDR83,missense_variant,p.Trp262Arg,ENST00000418543,NM_001099737.2,NM_032332.3;WDR83,missense_variant,p.Trp194Arg,ENST00000547797,;WDR83OS,upstream_gene_variant,,ENST00000596731,NM_016145.3;DHPS,downstream_gene_variant,,ENST00000210060,NM_001930.3;DHPS,downstream_gene_variant,,ENST00000594424,NM_001206974.1;DHPS,downstream_gene_variant,,ENST00000614126,;DHPS,downstream_gene_variant,,ENST00000351660,NM_013406.2;WDR83OS,upstream_gene_variant,,ENST00000598732,;DHPS,downstream_gene_variant,,ENST00000597152,;WDR83OS,upstream_gene_variant,,ENST00000222190,;DHPS,downstream_gene_variant,,ENST00000596162,;CTD-2192J16.24,upstream_gene_variant,,ENST00000597961,;DHPS,downstream_gene_variant,,ENST00000598246,;DHPS,downstream_gene_variant,,ENST00000600864,;DHPS,downstream_gene_variant,,ENST00000600639,;WDR83OS,upstream_gene_variant,,ENST00000600694,;WDR83,3_prime_UTR_variant,,ENST00000548381,;WDR83,3_prime_UTR_variant,,ENST00000425834,;WDR83,non_coding_transcript_exon_variant,,ENST00000546754,;WDR83,non_coding_transcript_exon_variant,,ENST00000547255,;WDR83,non_coding_transcript_exon_variant,,ENST00000552700,;DHPS,downstream_gene_variant,,ENST00000601537,;DHPS,downstream_gene_variant,,ENST00000601639,;DHPS,downstream_gene_variant,,ENST00000600510,;WDR83,downstream_gene_variant,,ENST00000553179,;DHPS,downstream_gene_variant,,ENST00000595844,;DHPS,downstream_gene_variant,,ENST00000595912,;WDR83,downstream_gene_variant,,ENST00000547481,;DHPS,downstream_gene_variant,,ENST00000598850,;DHPS,downstream_gene_variant,,ENST00000596847,;WDR83,downstream_gene_variant,,ENST00000551329,;WDR83,downstream_gene_variant,,ENST00000550939,;DHPS,downstream_gene_variant,,ENST00000593400,;DHPS,downstream_gene_variant,,ENST00000600451,; A ENST00000418543 Transcript missense_variant 1133/1457 784/948 262/315 W/R Tgg/Agg 1 1 WDR83 HGNC HGNC:32672 protein_coding YES CCDS12275.1 ENSP00000402653 Q9BRX9 UPI000006DE5C NM_001099737.2,NM_032332.3 deleterious(0) 10/11 PROSITE_profiles:PS50294,hmmpanther:PTHR22842,PROSITE_patterns:PS00678,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 12673302 12673302 T A 1 0 0 0 0 1 0 0 0 17887 1580 55 4 4 WDR83 19 12673302 Missense_Mutation SNP T C3N-01414_T 3817307 12673302 45944314 457 23657 NOTCH3 0 . GRCh38 19 15177547 15177547 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.4381G>T p.Gly1461Cys p.G1461C ENST00000263388 24/33 326 263 63 483 483 0 strelka-varscan-mutect NOTCH3,missense_variant,p.Gly1461Cys,ENST00000263388,NM_000435.2;NOTCH3,downstream_gene_variant,,ENST00000601011,;MIR6795,downstream_gene_variant,,ENST00000620824,;NOTCH3,downstream_gene_variant,,ENST00000600841,;NOTCH3,downstream_gene_variant,,ENST00000595045,; A ENST00000263388 Transcript missense_variant 4457/8666 4381/6966 1461/2321 G/C Ggt/Tgt 1 -1 NOTCH3 HGNC HGNC:7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 deleterious(0.01) 24/33 hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF57,SMART_domains:SM00004 MODERATE 1 SNV 1 1 PASS rs1309726793 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 15177547 15177547 C A 1 0 0 0 0 1 0 0 0 10595 652 23 1 1 NOTCH3 19 15177547 Missense_Mutation SNP C C3N-01414_T 2504245 15177547 43440069 458 23658 NWD1 0 . GRCh38 19 16765153 16765171 + Frame_Shift_Del DEL CTCCAGCTCTGCCGCCCTG CTCCAGCTCTGCCGCCCTG - novel C3N-01414_T C3N-01414_N CTCCAGCTCTGCCGCCCTG CTCCAGCTCTGCCGCCCTG c.2373_2391delCCAGCTCTGCCGCCCTGCT p.Gln792TrpfsTer87 p.Q792Wfs*87 ENST00000524140 10/19 216 185 31 329 329 0 sindel-pindel NWD1,frameshift_variant,p.Gln792TrpfsTer87,ENST00000524140,NM_001007525.3;NWD1,frameshift_variant,p.Gln792TrpfsTer87,ENST00000379808,;NWD1,frameshift_variant,p.Gln792TrpfsTer87,ENST00000552788,NM_001290355.1;NWD1,frameshift_variant,p.Gln792TrpfsTer87,ENST00000549814,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; - ENST00000524140 Transcript frameshift_variant 2789-2807/7641 2371-2389/4299 791-797/1432 LQLCRPA/X CTCCAGCTCTGCCGCCCTGct/ct 1 1 NWD1 HGNC HGNC:27619 protein_coding YES CCDS32945.2 ENSP00000428579 Q149M9 UPI0000D6173E NM_001007525.3 10/19 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF472 HIGH 1 deletion 1 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 77 16765153 16765153 CTCCAGCTCTGCCGCCCTG - 1 0 1 0 1 0 0 0 0 10854 681 24 0 0 NWD1 19 16765153 Frame_Shift_Del DEL CTCCAGCTCTGCCGCCCTG C3N-01414_T 1587606 16765153 41852463 459 23659 CPAMD8 0 . GRCh38 19 16947202 16947202 + Missense_Mutation SNP T T A C3N-01414_T C3N-01414_N T T c.2675A>T p.Lys892Met p.K892M ENST00000443236 21/42 73 59 14 106 106 0 strelka-varscan-mutect CPAMD8,missense_variant,p.Lys892Met,ENST00000443236,NM_015692.2;CPAMD8,3_prime_UTR_variant,,ENST00000388925,;CPAMD8,non_coding_transcript_exon_variant,,ENST00000593420,;CPAMD8,downstream_gene_variant,,ENST00000602159,; A ENST00000443236 Transcript missense_variant 2707/5992 2675/5799 892/1932 K/M aAg/aTg COSM50638 1 -1 CPAMD8 HGNC HGNC:23228 protein_coding YES CCDS42519.1 ENSP00000402505 Q8IZJ3 UPI0000E8AC99 NM_015692.2 deleterious(0.01) 21/42 hmmpanther:PTHR11412:SF84,hmmpanther:PTHR11412,Superfamily_domains:SSF81296 1 MODERATE 1 SNV 1 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 77 16947202 16947202 T A 1 0 0 0 0 1 0 0 0 3589 1609 56 4 4 CPAMD8 19 16947202 Missense_Mutation SNP T C3N-01414_T 182049 16947202 41670414 460 23660 CRLF1 0 . GRCh38 19 18596984 18596984 + Missense_Mutation SNP C C T rs756906640 C3N-01414_T C3N-01414_N C C c.763G>A p.Val255Met p.V255M ENST00000392386 5/9 190 177 13 223 223 0 strelka-varscan-mutect CRLF1,missense_variant,p.Val255Met,ENST00000392386,NM_004750.4;CRLF1,missense_variant,p.Val77Met,ENST00000597131,;C19orf60,downstream_gene_variant,,ENST00000358607,NM_001100418.1;C19orf60,downstream_gene_variant,,ENST00000450195,NM_001100419.1;C19orf60,downstream_gene_variant,,ENST00000595490,;CRLF1,upstream_gene_variant,,ENST00000594325,;CRLF1,downstream_gene_variant,,ENST00000593286,;C19orf60,downstream_gene_variant,,ENST00000595077,;C19orf60,downstream_gene_variant,,ENST00000600997,;C19orf60,downstream_gene_variant,,ENST00000598375,;C19orf60,downstream_gene_variant,,ENST00000597371,;C19orf60,downstream_gene_variant,,ENST00000601736,;CRLF1,upstream_gene_variant,,ENST00000596360,; T ENST00000392386 Transcript missense_variant 957/1792 763/1269 255/422 V/M Gtg/Atg rs756906640 1 -1 CRLF1 HGNC HGNC:2364 protein_coding YES CCDS32962.1 ENSP00000376188 O75462 UPI000000DA9E NM_004750.4 deleterious(0.02) 5/9 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF100,hmmpanther:PTHR23036,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs756906640 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 18596984 18596984 C T 1 0 0 0 0 1 0 0 0 3687 536 19 1 1 CRLF1 19 18596984 Missense_Mutation SNP C C3N-01414_T 1649782 18596984 40020632 461 23661 ZNF626 0 . GRCh38 19 20625108 20625108 + Missense_Mutation SNP A A T rs782685901 C3N-01414_T C3N-01414_N A A c.769T>A p.Tyr257Asn p.Y257N ENST00000601440 4/4 202 154 48 321 321 0 strelka-varscan-mutect ZNF626,missense_variant,p.Tyr257Asn,ENST00000601440,NM_001076675.2;ZNF626,missense_variant,p.Tyr257Asn,ENST00000612591,;ZNF626,downstream_gene_variant,,ENST00000595405,;CTC-513N18.7,intron_variant,,ENST00000595094,; T ENST00000601440 Transcript missense_variant 916/5963 769/1587 257/528 Y/N Tac/Aac rs782685901,COSM4744480 1 -1 ZNF626 HGNC HGNC:30461 protein_coding YES CCDS42535.1 ENSP00000469958 Q68DY1 UPI000035E843 NM_001076675.2 deleterious(0.02) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384:SF129,hmmpanther:PTHR24384,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 4 0,1 1 PASS rs782685901 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 20625108 20625108 A T 1 0 0 0 0 1 0 0 0 18625 420 15 4 4 ZNF626 19 20625108 Missense_Mutation SNP A C3N-01414_T 2028124 20625108 37992508 462 23662 ZNF98 0 . GRCh38 19 22392948 22392948 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.287C>A p.Pro96Gln p.P96Q ENST00000357774 4/4 54 46 8 98 97 1 strelka-varscan-mutect ZNF98,missense_variant,p.Pro96Gln,ENST00000357774,NM_001098626.1;ZNF98,missense_variant,p.Pro55Gln,ENST00000593657,; T ENST00000357774 Transcript missense_variant 409/2338 287/1719 96/572 P/Q cCa/cAa 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 tolerated(0.06) 4/4 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108 MODERATE 1 SNV 3 1 PASS rs948277901 . 2 206 2 0 0 0 0 0 -19.16685 1 1 1 1 0 T 3 4 77 22392948 22392948 G T 1 0 0 0 0 1 0 0 0 18796 1348 47 2 2 ZNF98 19 22392948 Missense_Mutation SNP G C3N-01414_T 1767840 22392948 36224668 463 23663 ZNF728 0 . GRCh38 19 22976569 22976569 + Nonsense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.768C>A p.Tyr256Ter p.Y256* ENST00000594710 4/4 405 360 45 587 587 0 strelka-varscan-mutect ZNF728,stop_gained,p.Tyr256Ter,ENST00000594710,NM_001267716.1;ZNF728,downstream_gene_variant,,ENST00000599851,; T ENST00000594710 Transcript stop_gained 914/2015 768/1869 256/622 Y/* taC/taA 1 -1 ZNF728 HGNC HGNC:32463 protein_coding YES CCDS59370.1 ENSP00000471593 P0DKX0 UPI0002656E4B NM_001267716.1 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF239,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 22976569 22976569 G T 1 0 0 0 0 0 1 0 0 18702 1372 48 2 2 ZNF728 19 22976569 Nonsense_Mutation SNP G C3N-01414_T 583621 22976569 35641047 464 23664 ZNF91 0 . GRCh38 19 23374717 23374717 + Missense_Mutation SNP C C A rs369467332 C3N-01414_T C3N-01414_N C C c.78G>T p.Glu26Asp p.E26D ENST00000300619 2/4 235 184 51 387 387 0 strelka-varscan-mutect ZNF91,missense_variant,p.Glu26Asp,ENST00000300619,NM_003430.3;ZNF91,missense_variant,p.Glu26Asp,ENST00000397082,NM_001300951.1;ZNF91,missense_variant,p.Glu26Asp,ENST00000599743,;ZNF91,intron_variant,,ENST00000595533,;ZNF91,non_coding_transcript_exon_variant,,ENST00000596989,; A ENST00000300619 Transcript missense_variant 284/5489 78/3576 26/1191 E/D gaG/gaT rs369467332 1 -1 ZNF91 HGNC HGNC:13166 protein_coding YES CCDS42541.1 ENSP00000300619 Q05481 UPI00002038F9 NM_003430.3 deleterious(0) 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF195,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS rs369467332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 23374717 23374717 C A 1 0 0 0 0 1 0 0 0 18793 564 20 2 2 ZNF91 19 23374717 Missense_Mutation SNP C C3N-01414_T 398148 23374717 35242899 465 23665 HSPB6 0 . GRCh38 19 35755602 35755602 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.403G>A p.Ala135Thr p.A135T ENST00000592984 4/4 125 106 19 196 196 0 strelka-varscan-mutect HSPB6,missense_variant,p.Ala135Thr,ENST00000592984,;HSPB6,missense_variant,p.Ala135Thr,ENST00000004982,NM_144617.2;HSPB6,3_prime_UTR_variant,,ENST00000587965,;PROSER3,upstream_gene_variant,,ENST00000396908,NM_001039887.2;PROSER3,upstream_gene_variant,,ENST00000536950,;LIN37,downstream_gene_variant,,ENST00000301159,NM_019104.2;PROSER3,upstream_gene_variant,,ENST00000301165,;PROSER3,upstream_gene_variant,,ENST00000537459,;PROSER3,upstream_gene_variant,,ENST00000421853,;PROSER3,upstream_gene_variant,,ENST00000545674,;PROSER3,upstream_gene_variant,,ENST00000444637,;LIN37,downstream_gene_variant,,ENST00000591163,;PROSER3,upstream_gene_variant,,ENST00000542134,;LIN37,downstream_gene_variant,,ENST00000587751,;AC002398.11,upstream_gene_variant,,ENST00000591091,;AC002398.12,downstream_gene_variant,,ENST00000587767,;PROSER3,upstream_gene_variant,,ENST00000544876,;LIN37,downstream_gene_variant,,ENST00000591076,;PROSER3,upstream_gene_variant,,ENST00000620918,;PROSER3,upstream_gene_variant,,ENST00000600988,;LIN37,downstream_gene_variant,,ENST00000595455,;LIN37,downstream_gene_variant,,ENST00000587108,;LIN37,downstream_gene_variant,,ENST00000590706,;AC002398.9,downstream_gene_variant,,ENST00000591613,;PROSER3,upstream_gene_variant,,ENST00000601095,;LIN37,downstream_gene_variant,,ENST00000590890,;LIN37,downstream_gene_variant,,ENST00000592871,;PROSER3,upstream_gene_variant,,ENST00000539771,; T ENST00000592984 Transcript missense_variant 600/1634 403/483 135/160 A/T Gcg/Acg 1 -1 HSPB6 HGNC HGNC:26511 protein_coding YES CCDS12475.1 ENSP00000468057 O14558 V9HWB6 UPI000012CCD5 tolerated(0.1) 4/4 Gene3D:2.60.40.790,Pfam_domain:PF00011,Prints_domain:PR00299,PROSITE_profiles:PS01031,hmmpanther:PTHR11527,hmmpanther:PTHR11527:SF109,Superfamily_domains:SSF49764 MODERATE SNV 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 35755602 35755602 C T 1 0 0 0 0 1 0 0 0 7318 768 27 1 1 HSPB6 19 35755602 Missense_Mutation SNP C C3N-01414_T 12380885 35755602 22862014 466 23666 NFKBID 0 . GRCh38 19 35896119 35896119 + Missense_Mutation SNP G G A C3N-01414_T C3N-01414_N G G c.467C>T p.Pro156Leu p.P156L ENST00000396901 9/12 158 109 49 223 223 0 strelka-varscan-mutect NFKBID,missense_variant,p.Pro156Leu,ENST00000396901,NM_139239.1;NFKBID,missense_variant,p.Pro156Leu,ENST00000606253,;NFKBID,downstream_gene_variant,,ENST00000585925,;NFKBID,downstream_gene_variant,,ENST00000585544,;NFKBID,missense_variant,p.Pro18Leu,ENST00000590828,;NFKBID,non_coding_transcript_exon_variant,,ENST00000586361,;NFKBID,non_coding_transcript_exon_variant,,ENST00000588497,;NFKBID,downstream_gene_variant,,ENST00000591730,;NFKBID,downstream_gene_variant,,ENST00000590094,;NFKBID,downstream_gene_variant,,ENST00000588039,; A ENST00000396901 Transcript missense_variant 1041/1834 467/942 156/313 P/L cCg/cTg COSM3371274,COSM3371275,COSM5244793,COSM5244794 1 -1 NFKBID HGNC HGNC:15671 protein_coding YES CCDS42552.1 ENSP00000380109 Q8NI38 UPI000006EE99 NM_139239.1 deleterious(0) 9/12 PROSITE_profiles:PS50297,hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF7,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs1440823199 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 35896119 35896119 G A 1 0 0 0 0 1 0 0 0 10416 1116 39 1 1 NFKBID 19 35896119 Missense_Mutation SNP G C3N-01414_T 140517 35896119 22721497 467 23667 ZNF585B 0 . GRCh38 19 37186879 37186879 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.658G>T p.Gly220Trp p.G220W ENST00000532828 5/5 148 104 44 210 210 0 strelka-varscan-mutect ZNF585B,missense_variant,p.Gly220Trp,ENST00000532828,NM_152279.3;ZNF585B,missense_variant,p.Gly165Trp,ENST00000531805,;ZNF585B,3_prime_UTR_variant,,ENST00000527838,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585B,downstream_gene_variant,,ENST00000591492,;ZNF585B,downstream_gene_variant,,ENST00000586320,;CTC-454I21.3,intron_variant,,ENST00000585860,;CTC-454I21.3,intron_variant,,ENST00000590245,;ZNF585B,downstream_gene_variant,,ENST00000392156,;ZNF585B,downstream_gene_variant,,ENST00000591273,;ZNF585B,downstream_gene_variant,,ENST00000526705,; A ENST00000532828 Transcript missense_variant 910/6210 658/2310 220/769 G/W Ggg/Tgg 1 -1 ZNF585B HGNC HGNC:30948 protein_coding YES CCDS12500.1 ENSP00000433773 Q52M93 UPI00001AF01B NM_152279.3 deleterious(0) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF105,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 37186879 37186879 C A 1 0 0 0 0 1 0 0 0 18592 594 21 2 2 ZNF585B 19 37186879 Missense_Mutation SNP C C3N-01414_T 1290760 37186879 21430737 468 23668 PSMD8 0 . GRCh38 19 38374806 38374806 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.205G>T p.Val69Leu p.V69L ENST00000215071 1/7 172 118 54 249 249 0 strelka-varscan-mutect PSMD8,missense_variant,p.Val69Leu,ENST00000215071,;PSMD8,missense_variant,p.Val69Leu,ENST00000620216,NM_002812.4;PSMD8,missense_variant,p.Val6Leu,ENST00000602911,;PSMD8,missense_variant,p.Val6Leu,ENST00000592561,;PSMD8,missense_variant,p.Val6Leu,ENST00000585598,;CATSPERG,downstream_gene_variant,,ENST00000409235,NM_021185.4;CATSPERG,downstream_gene_variant,,ENST00000410018,;PSMD8,upstream_gene_variant,,ENST00000592035,;PSMD8,upstream_gene_variant,,ENST00000591250,;PSMD8,non_coding_transcript_exon_variant,,ENST00000592001,;PSMD8,non_coding_transcript_exon_variant,,ENST00000591216,;CATSPERG,downstream_gene_variant,,ENST00000471517,;CATSPERG,downstream_gene_variant,,ENST00000492088,;CATSPERG,downstream_gene_variant,,ENST00000312265,;CATSPERG,downstream_gene_variant,,ENST00000412458,; T ENST00000215071 Transcript missense_variant 271/1553 205/1053 69/350 V/L Gtg/Ttg 1 1 PSMD8 HGNC HGNC:9566 protein_coding YES CCDS12515.2 ENSP00000215071 P48556 V9HW09 UPI000059D712 tolerated_low_confidence(0.09) 1/7 hmmpanther:PTHR12387,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 38374806 38374806 G T 1 0 0 0 0 1 0 0 0 12855 1261 44 2 2 PSMD8 19 38374806 Missense_Mutation SNP G C3N-01414_T 1187927 38374806 20242810 469 23669 ACP7 0 . GRCh38 19 39098598 39098598 + Missense_Mutation SNP C C G rs761395482 C3N-01414_T C3N-01414_N C C c.262C>G p.Arg88Gly p.R88G ENST00000331256 3/13 95 89 6 160 160 0 strelka-varscan-mutect ACP7,missense_variant,p.Arg88Gly,ENST00000331256,NM_001004318.2;ACP7,missense_variant,p.Arg88Gly,ENST00000594229,;ACP7,upstream_gene_variant,,ENST00000601531,;ACP7,missense_variant,p.Arg88Gly,ENST00000601575,; G ENST00000331256 Transcript missense_variant 536/2966 262/1317 88/438 R/G Cgg/Ggg rs761395482 1 1 ACP7 HGNC HGNC:33781 protein_coding YES CCDS33018.1 ENSP00000327557 Q6ZNF0 UPI000041AA68 NM_001004318.2 tolerated(0.16) 3/13 Gene3D:2qfpA01,Pfam_domain:PF16656,hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF9,Superfamily_domains:SSF49363 MODERATE 1 SNV 2 1 PASS rs761395482 . 0 206 3 0 0 0 0 0 -12.80267 1 1 1 1 0 G 3 3 77 39098598 39098598 C G 1 0 0 0 0 1 0 0 0 208 643 23 4 4 ACP7 19 39098598 Missense_Mutation SNP C C3N-01414_T 723792 39098598 19519018 470 23670 IFNL1 0 . GRCh38 19 39298481 39298481 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.568T>A p.Cys190Ser p.C190S ENST00000333625 5/5 186 137 49 282 282 0 strelka-varscan-mutect IFNL1,missense_variant,p.Cys190Ser,ENST00000333625,NM_172140.1; A ENST00000333625 Transcript missense_variant 665/857 568/603 190/200 C/S Tgt/Agt 1 1 IFNL1 HGNC HGNC:18363 protein_coding YES CCDS12531.1 ENSP00000329991 Q8IU54 UPI00000474AE NM_172140.1 deleterious(0) 5/5 PD856660,hmmpanther:PTHR31943,hmmpanther:PTHR31943:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 39298481 39298481 T A 1 0 0 0 0 1 0 0 0 7452 1696 59 4 4 IFNL1 19 39298481 Missense_Mutation SNP T C3N-01414_T 199883 39298481 19319135 471 23671 AXL 0 . GRCh38 19 41222002 41222003 + In_Frame_Ins INS - - TTT novel C3N-01414_T C3N-01414_N - - c.533_534insTTT p.Val178_Pro179insPhe p.V178_P179insF ENST00000301178 4/20 121 83 38 152 152 0 sindel-varindel AXL,inframe_insertion,p.Val178_Pro179insPhe,ENST00000301178,NM_021913.4;AXL,inframe_insertion,p.Val178_Pro179insPhe,ENST00000359092,NM_001699.5;AXL,upstream_gene_variant,,ENST00000593513,NM_001278599.1;CTD-2195B23.3,non_coding_transcript_exon_variant,,ENST00000598541,;AXL,downstream_gene_variant,,ENST00000594880,;AXL,non_coding_transcript_exon_variant,,ENST00000599659,; TTT ENST00000301178 Transcript inframe_insertion 722-723/4737 532-533/2685 178/894 V/VF gtc/gTTTtc 1 1 AXL HGNC HGNC:905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 UPI000014319B NM_021913.4 4/20 PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF323,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 insertion 1 1 1 PASS . . 0 200 4 6 0 0 0 0 -20 0.9985179 1 1 1 0 TTT 7 5 77 41222002 41222002 - TTT 1 0 1 1 0 0 0 0 0 1395 1377 48 0 0 AXL 19 41222002 In_Frame_Ins INS - C3N-01414_T 1923521 41222002 17395614 472 23672 ZNF180 0 . GRCh38 19 44476585 44476585 + Silent SNP T T G novel C3N-01414_T C3N-01414_N T T c.1896A>C p.= p.P632P ENST00000221327 5/5 187 164 23 272 272 0 strelka-varscan-mutect ZNF180,synonymous_variant,p.=,ENST00000221327,NM_013256.5,NM_001288759.2;ZNF180,synonymous_variant,p.=,ENST00000391956,NM_001278508.2;ZNF180,synonymous_variant,p.=,ENST00000592529,NM_001278509.2,NM_001291633.1;ZNF180,downstream_gene_variant,,ENST00000586637,;ZNF180,downstream_gene_variant,,ENST00000591064,;ZNF180,downstream_gene_variant,,ENST00000587047,;ZNF180,downstream_gene_variant,,ENST00000585514,;ZNF180,3_prime_UTR_variant,,ENST00000592095,;ZNF180,3_prime_UTR_variant,,ENST00000590088,;ZNF285B,downstream_gene_variant,,ENST00000561698,; G ENST00000221327 Transcript synonymous_variant 2178/4335 1896/2079 632/692 P ccA/ccC 1 -1 ZNF180 HGNC HGNC:12970 protein_coding YES CCDS12639.1 ENSP00000221327 Q9UJW8 UPI000013C30E NM_013256.5,NM_001288759.2 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF27,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 44476585 44476585 T G 1 0 0 0 0 0 0 0 1 18328 1451 51 5 5 ZNF180 19 44476585 Silent SNP T C3N-01414_T 3254583 44476585 14141031 473 23673 PNMAL2 0 . GRCh38 19 46493840 46493840 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.1626C>A p.= p.P542P ENST00000599531 1/1 31 26 5 37 37 0 strelka-varscan-mutect PNMAL2,synonymous_variant,p.=,ENST00000599531,NM_020709.2;PPP5D1,intron_variant,,ENST00000602017,NM_001205281.1;CTB-158D10.3,upstream_gene_variant,,ENST00000377652,;PNMAL2,intron_variant,,ENST00000594749,;PPP5D1,upstream_gene_variant,,ENST00000595691,; T ENST00000599531 Transcript synonymous_variant 2659/5308 1626/1908 542/635 P ccC/ccA 1 -1 PNMAL2 HGNC HGNC:29206 protein_coding YES CCDS59400.1 ENSP00000473036 Q9ULN7 UPI0000237925 NM_020709.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23095:SF25,hmmpanther:PTHR23095 LOW SNV 1 PASS rs1220510406 . 0 204 6 0 0 0 0 0 -13.59653 0.9999999 1 1 1 0 T 2 4 77 46493840 46493840 G T 1 0 0 0 0 0 0 0 1 12266 1335 47 2 2 PNMAL2 19 46493840 Silent SNP G C3N-01414_T 2017255 46493840 12123776 474 23674 FPR1 0 . GRCh38 19 51746356 51746356 + Silent SNP G G T rs141229910 C3N-01414_T C3N-01414_N G G c.639C>A p.= p.P213P ENST00000595042 3/3 296 224 72 426 425 1 strelka-varscan-mutect FPR1,synonymous_variant,p.=,ENST00000595042,NM_001193306.1;FPR1,synonymous_variant,p.=,ENST00000304748,NM_002029.3;FPR1,downstream_gene_variant,,ENST00000600815,;FPR1,downstream_gene_variant,,ENST00000594900,; T ENST00000595042 Transcript synonymous_variant 781/1965 639/1053 213/350 P ccC/ccA rs141229910 1 -1 FPR1 HGNC HGNC:3826 protein_coding YES CCDS12839.1 ENSP00000471493 P21462 UPI0000050484 NM_001193306.1 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF15,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 2 1 PASS rs141229910 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 51746356 51746356 G T 1 0 0 0 0 0 0 0 1 5904 1335 47 2 2 FPR1 19 51746356 Silent SNP G C3N-01414_T 5252516 51746356 6871260 475 23675 ZNF880 0 . GRCh38 19 52385264 52385264 + Missense_Mutation SNP A A T C3N-01414_T C3N-01414_N A A c.1684A>T p.Asn562Tyr p.N562Y ENST00000422689 4/4 131 118 13 198 198 0 strelka-varscan-mutect ZNF880,missense_variant,p.Asn562Tyr,ENST00000422689,NM_001145434.1;ZNF880,downstream_gene_variant,,ENST00000424032,;ZNF528-AS1,downstream_gene_variant,,ENST00000601562,;ZNF528-AS1,downstream_gene_variant,,ENST00000594119,; T ENST00000422689 Transcript missense_variant 1699/2230 1684/1734 562/577 N/Y Aac/Tac COSM1197042 1 1 ZNF880 HGNC HGNC:37249 protein_coding YES CCDS46164.1 ENSP00000406318 Q6PDB4 UPI00001D818D NM_001145434.1 tolerated(0.54) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF335,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 52385264 52385264 A T 1 0 0 0 0 1 0 0 0 18789 14 1 4 4 ZNF880 19 52385264 Missense_Mutation SNP A C3N-01414_T 638908 52385264 6232352 476 23676 ZNF528 0 . GRCh38 19 52415832 52415832 + Missense_Mutation SNP G G T rs767287723 C3N-01414_T C3N-01414_N G G c.980G>T p.Cys327Phe p.C327F ENST00000360465 7/7 160 146 14 188 187 1 strelka-varscan-mutect ZNF528,missense_variant,p.Cys327Phe,ENST00000360465,NM_032423.2;ZNF528,3_prime_UTR_variant,,ENST00000391788,;ZNF528,downstream_gene_variant,,ENST00000448954,;ZNF528,non_coding_transcript_exon_variant,,ENST00000598479,;ZNF528,downstream_gene_variant,,ENST00000479718,; T ENST00000360465 Transcript missense_variant 1406/3978 980/1887 327/628 C/F tGt/tTt rs767287723 1 1 ZNF528 HGNC HGNC:29384 protein_coding YES CCDS33091.1 ENSP00000353652 Q3MIS6 UPI00001B6535 NM_032423.2 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF143,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs767287723 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 52415832 52415832 G T 1 0 0 0 0 1 0 0 0 18542 1377 48 2 2 ZNF528 19 52415832 Missense_Mutation SNP G C3N-01414_T 30568 52415832 6201784 477 23677 ZNF808 0 . GRCh38 19 52553511 52553511 + Missense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.595A>T p.Arg199Trp p.R199W ENST00000359798 5/5 216 167 49 342 342 0 strelka-varscan-mutect ZNF808,missense_variant,p.Arg199Trp,ENST00000359798,NM_001321424.1,NM_001039886.3;ZNF808,upstream_gene_variant,,ENST00000611267,;ZNF808,downstream_gene_variant,,ENST00000465448,;ZNF808,downstream_gene_variant,,ENST00000461321,;ZNF808,downstream_gene_variant,,ENST00000461779,;ZNF808,downstream_gene_variant,,ENST00000486474,;ZNF701,upstream_gene_variant,,ENST00000478039,;ZNF808,missense_variant,p.Arg130Trp,ENST00000487863,; T ENST00000359798 Transcript missense_variant 775/3600 595/2712 199/903 R/W Agg/Tgg 1 1 ZNF808 HGNC HGNC:33230 protein_coding YES CCDS46167.1 ENSP00000352846 Q8N4W9 UPI000041AA80 NM_001321424.1,NM_001039886.3 deleterious(0.02) 5/5 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 52553511 52553511 A T 1 0 0 0 0 1 0 0 0 18758 411 15 4 4 ZNF808 19 52553511 Missense_Mutation SNP A C3N-01414_T 137679 52553511 6064105 478 23678 ZNF83 0 . GRCh38 19 52613238 52613238 + Missense_Mutation SNP A A C novel C3N-01414_T C3N-01414_N A A c.1327T>G p.Ser443Ala p.S443A ENST00000597597 2/2 133 120 13 194 193 1 strelka-varscan-mutect ZNF83,missense_variant,p.Ser443Ala,ENST00000597597,NM_001277946.1;ZNF83,missense_variant,p.Ser443Ala,ENST00000541777,;ZNF83,missense_variant,p.Ser443Ala,ENST00000536937,NM_001105550.1,NM_001105552.1,NM_001277948.1,NM_001105551.1,NM_001277945.1,NM_001277952.1,NM_001277949.1,NM_001105549.1;ZNF83,missense_variant,p.Ser443Ala,ENST00000545872,NM_001277951.1;ZNF83,missense_variant,p.Ser443Ala,ENST00000301096,NM_001277947.1,NM_018300.3;ZNF83,3_prime_UTR_variant,,ENST00000594682,;ZNF83,intron_variant,,ENST00000600714,;ZNF83,intron_variant,,ENST00000601257,;ZNF83,downstream_gene_variant,,ENST00000596930,;ZNF83,downstream_gene_variant,,ENST00000598536,;ZNF83,downstream_gene_variant,,ENST00000597161,;ZNF83,downstream_gene_variant,,ENST00000595171,;ZNF83,downstream_gene_variant,,ENST00000595939,;ZNF83,downstream_gene_variant,,ENST00000601140,; C ENST00000597597 Transcript missense_variant 3581/4442 1327/1551 443/516 S/A Tcc/Gcc 1 -1 ZNF83 HGNC HGNC:13158 protein_coding YES CCDS12854.1 ENSP00000472619 P51522 A0A024R4L3 UPI000013E6CF NM_001277946.1 tolerated(0.53) 2/2 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1322585859 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 52613238 52613238 A C 1 0 0 0 0 1 0 0 0 18768 333 12 5 5 ZNF83 19 52613238 Missense_Mutation SNP A C3N-01414_T 59727 52613238 6004378 479 23679 ERVV-1 0 . GRCh38 19 53015333 53015333 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1243G>T p.Ala415Ser p.A415S ENST00000602168 1/1 240 192 48 358 356 2 strelka-varscan-mutect ERVV-1,missense_variant,p.Ala415Ser,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; T ENST00000602168 Transcript missense_variant 1413/2202 1243/1434 415/477 A/S Gcg/Tcg 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 tolerated(0.73) 1/1 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424,Pfam_domain:PF00429,Gene3D:1.10.287.210,Superfamily_domains:SSF58069 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 53015333 53015333 G T 1 0 0 0 0 1 0 0 0 5106 1203 42 2 2 ERVV-1 19 53015333 Missense_Mutation SNP G C3N-01414_T 402095 53015333 5602283 480 23680 ZNF415 0 . GRCh38 19 53109401 53109401 + Missense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.644C>A p.Pro215His p.P215H ENST00000500065 4/4 151 124 27 210 209 1 strelka-varscan-mutect ZNF415,missense_variant,p.Pro215His,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Pro215His,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Pro215His,ENST00000243643,NM_018355.3;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,5_prime_UTR_variant,,ENST00000601493,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; T ENST00000500065 Transcript missense_variant 978/2496 644/1668 215/555 P/H cCt/cAt COSM3707359,COSM4781253 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 deleterious(0.04) 4/4 hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 4 1,1 1 PASS rs1213586457 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 53109401 53109401 G T 1 0 0 0 0 1 0 0 0 18464 1000 35 2 2 ZNF415 19 53109401 Missense_Mutation SNP G C3N-01414_T 94068 53109401 5508215 481 23681 LILRA5 0 . GRCh38 19 54311999 54311999 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.274C>A p.Pro92Thr p.P92T ENST00000432233 4/7 498 398 100 646 646 0 strelka-varscan-mutect LILRA5,missense_variant,p.Pro92Thr,ENST00000432233,NM_021250.3;LILRA5,missense_variant,p.Pro80Thr,ENST00000486742,NM_181985.3;AC008984.2,intron_variant,,ENST00000616950,;LILRA5,non_coding_transcript_exon_variant,,ENST00000489504,;LILRA5,non_coding_transcript_exon_variant,,ENST00000446712,;LILRA5,upstream_gene_variant,,ENST00000477720,; T ENST00000432233 Transcript missense_variant 394/1363 274/900 92/299 P/T Cca/Aca 1 -1 LILRA5 HGNC HGNC:16309 protein_coding YES CCDS12888.1 ENSP00000404236 A6NI73 UPI0000034C06 NM_021250.3 tolerated(0.15) 4/7 hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 54311999 54311999 G T 1 0 0 0 0 1 0 0 0 8696 1232 43 2 2 LILRA5 19 54311999 Missense_Mutation SNP G C3N-01414_T 1202598 54311999 4305617 482 23682 FAM71E2 0 . GRCh38 19 55358901 55358901 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1967C>A p.Pro656Gln p.P656Q ENST00000424985 9/11 106 85 21 128 128 0 strelka-varscan-mutect FAM71E2,missense_variant,p.Pro656Gln,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;CTD-2105E13.6,missense_variant,p.Pro206Gln,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; T ENST00000424985 Transcript missense_variant 2161/3191 1967/2769 656/922 P/Q cCg/cAg 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 deleterious(0) 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 MODERATE SNV 5 1 PASS rs1166784749 . 0 195 10 5 0 0 0 0 -20 0.9928332 1 1 1 0 T 3 4 77 55358901 55358901 G T 1 0 0 0 0 1 0 0 0 5476 1116 39 1 1 FAM71E2 19 55358901 Missense_Mutation SNP G C3N-01414_T 1046902 55358901 3258715 483 23683 SSC5D 0 . GRCh38 19 55499939 55499939 + Missense_Mutation SNP C C G novel C3N-01414_T C3N-01414_N C C c.1829C>G p.Ala610Gly p.A610G ENST00000389623 10/14 422 354 68 575 575 0 strelka-varscan-mutect SSC5D,missense_variant,p.Ala610Gly,ENST00000389623,NM_001144950.1;SSC5D,missense_variant,p.Ala610Gly,ENST00000587166,NM_001195267.1;SSC5D,missense_variant,p.Ala107Gly,ENST00000589020,; G ENST00000389623 Transcript missense_variant 1852/4845 1829/4722 610/1573 A/G gCc/gGc 1 1 SSC5D HGNC HGNC:26641 protein_coding YES CCDS46196.1 ENSP00000374274 A1L4H1 UPI000192952A NM_001144950.1 tolerated(0.34) 10/14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 77 55499939 55499939 C G 1 0 0 0 0 1 0 0 0 15558 739 26 4 4 SSC5D 19 55499939 Missense_Mutation SNP C C3N-01414_T 141038 55499939 3117677 484 23684 SBK3 0 . GRCh38 19 55540959 55540959 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.967G>T p.Ala323Ser p.A323S ENST00000612221 4/4 127 86 41 126 126 0 strelka-varscan-mutect SBK3,missense_variant,p.Ala323Ser,ENST00000612221,NM_001199824.2;SBK2,upstream_gene_variant,,ENST00000413299,NM_001101401.2;SBK2,upstream_gene_variant,,ENST00000344158,;SBK3,downstream_gene_variant,,ENST00000592464,; A ENST00000612221 Transcript missense_variant 967/1270 967/1080 323/359 A/S Gcc/Tcc 1 -1 SBK3 HGNC HGNC:44121 protein_coding YES CCDS74457.1 ENSP00000483467 P0C264 UPI00004FF064 NM_001199824.2 tolerated_low_confidence(0.75) 4/4 hmmpanther:PTHR24363,hmmpanther:PTHR24363:SF6 MODERATE 1 SNV 5 1 PASS rs1338883622 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 55540959 55540959 C A 1 0 0 0 0 1 0 0 0 14126 768 27 1 1 SBK3 19 55540959 Missense_Mutation SNP C C3N-01414_T 41020 55540959 3076657 485 23685 RFPL4A 0 . GRCh38 19 55763015 55763015 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.704G>T p.Gly235Val p.G235V ENST00000434937 3/3 1394 1259 135 1967 1967 0 varscan-mutect RFPL4A,missense_variant,p.Gly235Val,ENST00000434937,NM_001145014.1; T ENST00000434937 Transcript missense_variant 875/1035 704/864 235/287 G/V gGg/gTg 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 deleterious(0) 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 55763015 55763015 G T 1 0 0 0 0 1 0 0 0 13428 1232 43 2 2 RFPL4A 19 55763015 Missense_Mutation SNP G C3N-01414_T 222056 55763015 2854601 486 23686 RFPL4AL1 0 . GRCh38 19 55773019 55773019 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.704G>T p.Gly235Val p.G235V ENST00000341750 3/3 464 425 39 604 604 0 varscan-mutect RFPL4AL1,missense_variant,p.Gly235Val,ENST00000341750,NM_001277397.1;RFPL4AP1,upstream_gene_variant,,ENST00000530883,; T ENST00000341750 Transcript missense_variant 748/908 704/864 235/287 G/V gGg/gTg 1 1 RFPL4AL1 HGNC HGNC:45147 protein_coding YES CCDS59425.1 ENSP00000345151 F8VTS6 UPI000015FD78 NM_001277397.1 deleterious(0) 3/3 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 55773019 55773019 G T 1 0 0 0 0 1 0 0 0 13429 1232 43 2 2 RFPL4AL1 19 55773019 Missense_Mutation SNP G C3N-01414_T 10004 55773019 2844597 487 23687 NLRP13 0 . GRCh38 19 55932164 55932164 + Missense_Mutation SNP C C A C3N-01414_T C3N-01414_N C C c.148G>T p.Gly50Trp p.G50W ENST00000342929 1/11 289 217 72 372 372 0 strelka-varscan-mutect NLRP13,missense_variant,p.Gly50Trp,ENST00000588751,NM_001321057.1;NLRP13,missense_variant,p.Gly50Trp,ENST00000342929,NM_176810.2; A ENST00000342929 Transcript missense_variant 148/3132 148/3132 50/1043 G/W Ggg/Tgg COSM5543183 1 -1 NLRP13 HGNC HGNC:22937 protein_coding YES CCDS33119.1 ENSP00000343891 Q86W25 UPI00001AEEC8 NM_176810.2 deleterious(0.01) 1/11 Gene3D:1.10.533.10,Pfam_domain:PF02758,PROSITE_profiles:PS50824,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,SMART_domains:SM01289,Superfamily_domains:SSF47986 1 MODERATE 1 SNV 1 1 1 PASS rs1310852384 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 55932164 55932164 C A 1 0 0 0 0 1 0 0 0 10512 623 22 2 2 NLRP13 19 55932164 Missense_Mutation SNP C C3N-01414_T 159145 55932164 2685452 488 23688 NLRP5 0 . GRCh38 19 56027061 56027061 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.828C>A p.= p.G276G ENST00000390649 7/15 272 219 53 365 365 0 strelka-varscan-mutect NLRP5,synonymous_variant,p.=,ENST00000390649,NM_153447.4;NLRP5,synonymous_variant,p.=,ENST00000621651,; A ENST00000390649 Transcript synonymous_variant 828/3888 828/3603 276/1200 G ggC/ggA 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 7/15 hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 56027061 56027061 C A 1 0 0 0 0 0 0 0 1 10518 784 28 2 2 NLRP5 19 56027061 Silent SNP C C3N-01414_T 94897 56027061 2590555 489 23689 ZNF667 0 . GRCh38 19 56442324 56442324 + Missense_Mutation SNP C C A rs748880533 C3N-01414_T C3N-01414_N C C c.671G>T p.Gly224Val p.G224V ENST00000504904 7/7 109 87 22 152 152 0 strelka-varscan-mutect ZNF667,missense_variant,p.Gly224Val,ENST00000504904,NM_001321356.1;ZNF667,missense_variant,p.Gly224Val,ENST00000292069,NM_022103.3;ZNF667,missense_variant,p.Gly6Val,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; A ENST00000504904 Transcript missense_variant 1391/4390 671/1833 224/610 G/V gGa/gTa rs748880533 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 deleterious(0) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs748880533 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 56442324 56442324 C A 1 0 0 0 0 1 0 0 0 18648 855 30 2 2 ZNF667 19 56442324 Missense_Mutation SNP C C3N-01414_T 415263 56442324 2175292 490 23690 PEG3 0 . GRCh38 19 56814119 56814119 + Silent SNP T T A novel C3N-01414_T C3N-01414_N T T c.4323A>T p.= p.G1441G ENST00000326441 10/10 368 294 74 496 496 0 strelka-varscan-mutect PEG3,synonymous_variant,p.=,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,synonymous_variant,p.=,ENST00000598410,NM_001146187.1;PEG3,synonymous_variant,p.=,ENST00000599534,;PEG3,synonymous_variant,p.=,ENST00000599577,;PEG3,synonymous_variant,p.=,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;PEG3,upstream_gene_variant,,ENST00000599565,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript synonymous_variant 4687/8723 4323/4767 1441/1588 G ggA/ggT 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 10/10 LOW 1 SNV 1 1 PASS rs1202053429 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 56814119 56814119 T A 1 0 0 0 0 0 0 0 1 11808 1538 54 4 4 PEG3 19 56814119 Silent SNP T C3N-01414_T 371795 56814119 1803497 491 23691 ZNF264 0 . GRCh38 19 57194002 57194002 + Splice_Site SNP G G T novel C3N-01414_T C3N-01414_N G G c.160+1G>T p.X54_splice ENST00000263095 68 46 22 103 103 0 strelka-varscan-mutect ZNF264,splice_donor_variant,,ENST00000263095,NM_003417.4;ZNF264,splice_donor_variant,,ENST00000536056,;ZNF264,splice_donor_variant,,ENST00000600531,;ZNF264,splice_donor_variant,,ENST00000597447,;ZNF264,missense_variant,p.Gly54Val,ENST00000599653,;ZNF264,downstream_gene_variant,,ENST00000594126,; T ENST00000263095 Transcript splice_donor_variant -/12163 160/1884 54/627 1 1 ZNF264 HGNC HGNC:13057 protein_coding YES CCDS33127.1 ENSP00000263095 O43296 UPI000013C33B NM_003417.4 2/3 HIGH 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 77 57194002 57194002 G T 1 0 0 0 0 0 0 1 0 18380 1275 44 2 2 ZNF264 19 57194002 Splice_Site SNP G C3N-01414_T 379883 57194002 1423614 492 23692 ZIK1 0 . GRCh38 19 57590853 57590853 + Nonsense_Mutation SNP G G T C3N-01414_T C3N-01414_N G G c.1042G>T p.Glu348Ter p.E348* ENST00000597850 4/4 219 195 24 347 347 0 strelka-varscan-mutect ZIK1,stop_gained,p.Glu348Ter,ENST00000597850,NM_001010879.2;ZIK1,stop_gained,p.Glu335Ter,ENST00000536878,NM_001321145.1;ZIK1,stop_gained,p.Glu293Ter,ENST00000599456,;ZIK1,3_prime_UTR_variant,,ENST00000307468,;ZIK1,downstream_gene_variant,,ENST00000600053,;ZIK1,downstream_gene_variant,,ENST00000597219,;ZIK1,downstream_gene_variant,,ENST00000598689,;ZIK1,downstream_gene_variant,,ENST00000598726,; T ENST00000597850 Transcript stop_gained 1257/4181 1042/1464 348/487 E/* Gaa/Taa COSM327551 1 1 ZIK1 HGNC HGNC:33104 protein_coding YES CCDS33135.1 ENSP00000472867 Q3SY52 UPI00001609B2 NM_001010879.2 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF219,Superfamily_domains:SSF57667 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 57590853 57590853 G T 1 0 0 0 0 0 1 0 0 18261 943 33 2 2 ZIK1 19 57590853 Nonsense_Mutation SNP G C3N-01414_T 396851 57590853 1026763 493 23693 ZSCAN4 0 . GRCh38 19 57676481 57676481 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.336C>A p.= p.G112G ENST00000318203 3/5 118 91 27 189 188 1 strelka-varscan-mutect ZSCAN4,synonymous_variant,p.=,ENST00000318203,NM_152677.2;ZSCAN4,synonymous_variant,p.=,ENST00000612521,; A ENST00000318203 Transcript synonymous_variant 1033/2246 336/1302 112/433 G ggC/ggA 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 3/5 Pfam_domain:PF02023,PROSITE_profiles:PS50804,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,SMART_domains:SM00431,Superfamily_domains:SSF47353 LOW 1 SNV 2 1 PASS rs1435378174 . 0 183 7 15 4 0 0 0 -18.37881 0.2890632 0 1 0 0 A 2 1 77 57676481 57676481 C A 1 0 0 0 0 0 0 0 1 18836 697 25 2 2 ZSCAN4 19 57676481 Silent SNP C C3N-01414_T 85628 57676481 941135 494 23694 ZNF587B 0 . GRCh38 19 57839084 57839084 + Missense_Mutation SNP G G T rs535519327 C3N-01414_T C3N-01414_N G G c.98G>T p.Ser33Ile p.S33I ENST00000442832 2/4 161 138 23 212 211 1 strelka-varscan-mutect ZNF587B,missense_variant,p.Ser33Ile,ENST00000442832,NM_001204818.1;ZNF587B,missense_variant,p.Ser33Ile,ENST00000594901,;ZNF587B,5_prime_UTR_variant,,ENST00000594328,;CTD-2583A14.10,5_prime_UTR_variant,,ENST00000597134,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000598031,;CTD-2583A14.10,intron_variant,,ENST00000603271,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,missense_variant,p.Ser33Ile,ENST00000604231,; T ENST00000442832 Transcript missense_variant 332/3339 98/1209 33/402 S/I aGt/aTt rs535519327 1 1 ZNF587B HGNC HGNC:37142 protein_coding YES CCDS56109.1 ENSP00000392410 E7ETH6 UPI0001AE657B NM_001204818.1 deleterious(0) 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF191,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 2 1 PASS rs535519327 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 57839084 57839084 G T 1 0 0 0 0 1 0 0 0 18595 1029 36 2 2 ZNF587B 19 57839084 Missense_Mutation SNP G C3N-01414_T 162603 57839084 778532 495 23695 81 2 ZNF587B 0 . GRCh38 19 57839086 57839086 + Nonsense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.100G>T p.Glu34Ter p.E34* ENST00000442832 2/4 163 140 23 216 216 0 strelka-varscan-mutect ZNF587B,stop_gained,p.Glu34Ter,ENST00000442832,NM_001204818.1;ZNF587B,stop_gained,p.Glu34Ter,ENST00000594901,;ZNF587B,5_prime_UTR_variant,,ENST00000594328,;CTD-2583A14.10,5_prime_UTR_variant,,ENST00000597134,;CTD-2583A14.10,intron_variant,,ENST00000596498,;CTD-2583A14.10,intron_variant,,ENST00000598031,;CTD-2583A14.10,intron_variant,,ENST00000603271,;CTD-2583A14.10,intron_variant,,ENST00000593873,;CTD-2583A14.10,stop_gained,p.Glu34Ter,ENST00000604231,; T ENST00000442832 Transcript stop_gained 334/3339 100/1209 34/402 E/* Gag/Tag 1 1 ZNF587B HGNC HGNC:37142 protein_coding YES CCDS56109.1 ENSP00000392410 E7ETH6 UPI0001AE657B NM_001204818.1 2/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF191,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 57839086 57839086 G T 1 0 0 0 0 0 1 0 0 18595 1291 45 2 2 ZNF587B 19 57839086 Nonsense_Mutation SNP G C3N-01414_T 2 57839086 778530 496 23696 81 2 ZNF418 0 . GRCh38 19 57927690 57927690 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.491G>T p.Ser164Ile p.S164I ENST00000396147 4/6 146 120 26 222 222 0 strelka-varscan-mutect ZNF418,missense_variant,p.Ser164Ile,ENST00000396147,NM_001317028.1,NM_133460.1;ZNF418,missense_variant,p.Ser185Ile,ENST00000425570,;ZNF418,missense_variant,p.Ser164Ile,ENST00000595830,NM_001317029.1,NM_001317030.1;ZNF418,missense_variant,p.Ser79Ile,ENST00000599852,;ZNF418,missense_variant,p.Ser164Ile,ENST00000616958,;ZNF418,intron_variant,,ENST00000600989,;ZNF418,downstream_gene_variant,,ENST00000595569,;ZNF418,downstream_gene_variant,,ENST00000593296,;ZNF418,downstream_gene_variant,,ENST00000601593,;ZNF418,intron_variant,,ENST00000598213,;ZNF418,upstream_gene_variant,,ENST00000599086,; A ENST00000396147 Transcript missense_variant 783/3694 491/2031 164/676 S/I aGt/aTt 1 -1 ZNF418 HGNC HGNC:20647 protein_coding YES CCDS42642.1 ENSP00000379451 Q8TF45 UPI000013B4C8 NM_001317028.1,NM_133460.1 tolerated(0.31) 4/6 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF192 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 57927690 57927690 C A 1 0 0 0 0 1 0 0 0 18467 565 20 2 2 ZNF418 19 57927690 Missense_Mutation SNP C C3N-01414_T 88604 57927690 689926 497 23697 TRMT6 0 . GRCh38 20 5941242 5941242 + Splice_Site SNP C C T novel C3N-01414_T C3N-01414_N C C c.1215+1G>A p.X405_splice ENST00000203001 193 133 60 148 148 0 strelka-varscan-mutect TRMT6,splice_donor_variant,,ENST00000203001,NM_015939.4;TRMT6,splice_donor_variant,,ENST00000453074,NM_001281467.1;TRMT6,splice_donor_variant,,ENST00000473131,;TRMT6,non_coding_transcript_exon_variant,,ENST00000466974,;TRMT6,downstream_gene_variant,,ENST00000493972,; T ENST00000203001 Transcript splice_donor_variant -/2327 1215/1494 405/497 1 -1 TRMT6 HGNC HGNC:20900 protein_coding YES CCDS13093.1 ENSP00000203001 Q9UJA5 UPI000006D9E4 NM_015939.4 9/10 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 77 5941242 5941242 C T 1 0 0 0 0 0 0 1 0 17073 521 18 3 3 TRMT6 20 5941242 Splice_Site SNP C C3N-01414_T 5941242 58502925 498 23698 POLR3F 0 . GRCh38 20 18475126 18475126 + Missense_Mutation SNP T T C novel C3N-01414_T C3N-01414_N T T c.368T>C p.Ile123Thr p.I123T ENST00000377603 5/9 200 141 59 249 249 0 strelka-varscan-mutect POLR3F,missense_variant,p.Ile123Thr,ENST00000377603,NM_006466.3,NM_001282526.1;MIR3192,downstream_gene_variant,,ENST00000584920,;POLR3F,non_coding_transcript_exon_variant,,ENST00000462997,;POLR3F,non_coding_transcript_exon_variant,,ENST00000489753,;POLR3F,intron_variant,,ENST00000497333,;POLR3F,downstream_gene_variant,,ENST00000475192,; C ENST00000377603 Transcript missense_variant 748/2416 368/951 123/316 I/T aTc/aCc 1 1 POLR3F HGNC HGNC:15763 protein_coding YES CCDS13135.1 ENSP00000366828 Q9H1D9 UPI0000134605 NM_006466.3,NM_001282526.1 deleterious(0) 5/9 Gene3D:1.10.10.10,Pfam_domain:PF05158,PIRSF_domain:PIRSF028763,hmmpanther:PTHR12780,hmmpanther:PTHR12780:SF1,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 18475126 18475126 T C 1 0 0 0 0 1 0 0 0 12344 1435 50 5 5 POLR3F 20 18475126 Missense_Mutation SNP T C3N-01414_T 12533884 18475126 45969041 499 23699 DLGAP4 0 . GRCh38 20 36431769 36431769 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.52C>A p.Pro18Thr p.P18T ENST00000373913 3/13 186 117 69 152 152 0 strelka-varscan-mutect DLGAP4,missense_variant,p.Pro18Thr,ENST00000373913,NM_014902.5;DLGAP4,missense_variant,p.Pro18Thr,ENST00000339266,;DLGAP4,missense_variant,p.Pro18Thr,ENST00000401952,;DLGAP4,missense_variant,p.Pro18Thr,ENST00000373907,; A ENST00000373913 Transcript missense_variant 532/5056 52/2970 18/989 P/T Cca/Aca 1 1 DLGAP4 HGNC HGNC:24476 protein_coding YES CCDS13274.1 ENSP00000363023 Q9Y2H0 UPI000013D34B NM_014902.5 deleterious(0.03) 3/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 36431769 36431769 C A 1 0 0 0 0 1 0 0 0 4369 623 22 2 2 DLGAP4 20 36431769 Missense_Mutation SNP C C3N-01414_T 17956643 36431769 28012398 500 23700 HNF4A 0 . GRCh38 20 44428453 44428453 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.1248G>A p.= p.Q416Q ENST00000316099 9/10 552 276 276 732 732 0 strelka-varscan-mutect HNF4A,synonymous_variant,p.=,ENST00000316099,NM_001258355.1,NM_000457.4;HNF4A,synonymous_variant,p.=,ENST00000619550,NM_001287182.1,NM_001287183.1;HNF4A,synonymous_variant,p.=,ENST00000415691,NM_178849.2;HNF4A,synonymous_variant,p.=,ENST00000316673,NM_175914.4;HNF4A,synonymous_variant,p.=,ENST00000457232,NM_001030003.2;HNF4A,downstream_gene_variant,,ENST00000443598,NM_178850.2;HNF4A,downstream_gene_variant,,ENST00000609795,NM_001030004.2,NM_001287184.1;HNF4A,3_prime_UTR_variant,,ENST00000372920,; A ENST00000316099 Transcript synonymous_variant 1337/6445 1248/1425 416/474 Q caG/caA 1 1 HNF4A HGNC HGNC:5024 protein_coding YES CCDS13330.1 ENSP00000312987 P41235 F1D8T1 UPI000016A0BA NM_001258355.1,NM_000457.4 9/10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 44428453 44428453 G A 1 0 0 0 0 0 0 0 1 7144 956 33 3 3 HNF4A 20 44428453 Silent SNP G C3N-01414_T 7996684 44428453 20015714 501 23701 BMP7 0 . GRCh38 20 57171064 57171064 + Silent SNP C C G rs200826465 C3N-01414_T C3N-01414_N C C c.1191G>C p.= p.A397A ENST00000395863 7/7 595 478 117 773 773 0 strelka-varscan-mutect BMP7,synonymous_variant,p.=,ENST00000395863,NM_001719.2;BMP7,synonymous_variant,p.=,ENST00000395864,;BMP7,downstream_gene_variant,,ENST00000450594,;BMP7,downstream_gene_variant,,ENST00000433911,;BMP7,non_coding_transcript_exon_variant,,ENST00000460817,;BMP7,non_coding_transcript_exon_variant,,ENST00000476877,; G ENST00000395863 Transcript synonymous_variant 1697/4013 1191/1296 397/431 A gcG/gcC rs200826465 1 -1 BMP7 HGNC HGNC:1074 protein_coding YES CCDS13455.1 ENSP00000379204 P18075 A8K571 UPI00000349AD NM_001719.2 7/7 Gene3D:2.10.90.10,Pfam_domain:PF00019,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF135,SMART_domains:SM00204,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS rs200826465 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 57171064 57171064 C G 1 0 0 0 0 0 0 0 1 1620 755 27 4 4 BMP7 20 57171064 Silent SNP C C3N-01414_T 12742611 57171064 7273103 502 23702 DIDO1 0 . GRCh38 20 62911136 62911136 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.477G>T p.= p.L159L ENST00000266070 3/16 581 451 130 540 540 0 strelka-varscan-mutect DIDO1,synonymous_variant,p.=,ENST00000266070,NM_033081.2;DIDO1,synonymous_variant,p.=,ENST00000395343,NM_001193369.1;DIDO1,synonymous_variant,p.=,ENST00000395340,NM_080797.3,NM_001193370.1;DIDO1,synonymous_variant,p.=,ENST00000370371,NM_022105.4;DIDO1,synonymous_variant,p.=,ENST00000354665,NM_080796.3;DIDO1,synonymous_variant,p.=,ENST00000370368,;DIDO1,synonymous_variant,p.=,ENST00000370366,; A ENST00000266070 Transcript synonymous_variant 833/8574 477/6723 159/2240 L ctG/ctT 1 -1 DIDO1 HGNC HGNC:2680 protein_coding YES CCDS33506.1 ENSP00000266070 Q9BTC0 UPI0000206380 NM_033081.2 3/16 hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF13 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 62911136 62911136 C A 1 0 0 0 0 0 0 0 1 4326 813 29 2 2 DIDO1 20 62911136 Silent SNP C C3N-01414_T 5740072 62911136 1533031 503 23703 KCNQ2 0 . GRCh38 20 63424203 63424203 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1221G>T p.Lys407Asn p.K407N ENST00000359125 11/17 428 234 194 301 301 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Lys407Asn,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Lys407Asn,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Lys397Asn,ENST00000370224,;KCNQ2,missense_variant,p.Lys224Asn,ENST00000637193,;KCNQ2,missense_variant,p.Lys397Asn,ENST00000625514,;KCNQ2,missense_variant,p.Lys397Asn,ENST00000629241,;KCNQ2,missense_variant,p.Lys397Asn,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Lys407Asn,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Lys293Asn,ENST00000357249,;KCNQ2,missense_variant,p.Lys397Asn,ENST00000629676,;KCNQ2,missense_variant,p.Lys112Asn,ENST00000627221,;RP11-358D14.3,intron_variant,,ENST00000629794,;KCNQ2,non_coding_transcript_exon_variant,,ENST00000637632,;KCNQ2,upstream_gene_variant,,ENST00000635867,;KCNQ2,downstream_gene_variant,,ENST00000636638,;KCNQ2,upstream_gene_variant,,ENST00000637584,;KCNQ2,non_coding_transcript_exon_variant,,ENST00000370221,; A ENST00000359125 Transcript missense_variant 1348/3253 1221/2619 407/872 K/N aaG/aaT 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious(0.04) 11/17 hmmpanther:PTHR11537:SF6,hmmpanther:PTHR11537 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 63424203 63424203 C A 1 0 0 0 0 1 0 0 0 7999 695 24 2 2 KCNQ2 20 63424203 Missense_Mutation SNP C C3N-01414_T 513067 63424203 1019964 504 23704 GABPA 0 . GRCh38 21 25764711 25764711 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.1060G>C p.Glu354Gln p.E354Q ENST00000354828 9/10 213 176 37 302 302 0 strelka-varscan-mutect GABPA,missense_variant,p.Glu354Gln,ENST00000354828,NM_001197297.1;GABPA,missense_variant,p.Glu354Gln,ENST00000400075,NM_002040.3;LLPHP2,upstream_gene_variant,,ENST00000436405,; C ENST00000354828 Transcript missense_variant 1587/5120 1060/1365 354/454 E/Q Gaa/Caa 1 1 GABPA HGNC HGNC:4071 protein_coding YES CCDS13575.1 ENSP00000346886 Q06546 A8IE48 UPI000012AFB2 NM_001197297.1 deleterious(0.01) 9/10 Gene3D:1.10.10.10,Pfam_domain:PF00178,PIRSF_domain:PIRSF001703,Prints_domain:PR00454,PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF195,SMART_domains:SM00413,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 25764711 25764711 G C 1 0 0 0 0 1 0 0 0 6028 1291 45 4 4 GABPA 21 25764711 Missense_Mutation SNP G C3N-01414_T 25764711 20945272 505 23705 ADAMTS5 0 . GRCh38 21 26924083 26924083 + Silent SNP C C T rs146590255 C3N-01414_T C3N-01414_N C C c.2763G>A p.= p.A921A ENST00000284987 8/8 52 40 12 66 66 0 strelka-varscan-mutect ADAMTS5,synonymous_variant,p.=,ENST00000284987,NM_007038.3;AP001601.2,intron_variant,,ENST00000426771,; T ENST00000284987 Transcript synonymous_variant 2885/9056 2763/2793 921/930 A gcG/gcA rs146590255 1 -1 ADAMTS5 HGNC HGNC:221 protein_coding YES CCDS13579.1 ENSP00000284987 Q9UNA0 UPI00001AEAC2 NM_007038.3 8/8 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF37,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS rs146590255 . 0 196 14 0 0 0 0 0 -20 0.9998806 1 1 1 0 T 2 4 77 26924083 26924083 C T 1 0 0 0 0 0 0 0 1 313 523 19 1 1 ADAMTS5 21 26924083 Silent SNP C C3N-01414_T 1159372 26924083 19785900 506 23706 LTN1 0 . GRCh38 21 28992915 28992915 + Missense_Mutation SNP G G T rs770980232 C3N-01414_T C3N-01414_N G G c.29C>A p.Pro10His p.P10H ENST00000614971 1/30 101 73 28 149 149 0 strelka-varscan-mutect LTN1,missense_variant,p.Pro10His,ENST00000614971,NM_015565.2;LTN1,missense_variant,p.Pro10His,ENST00000389194,;LTN1,missense_variant,p.Pro10His,ENST00000389195,;LTN1,upstream_gene_variant,,ENST00000361371,;RPL23P2,downstream_gene_variant,,ENST00000320371,; T ENST00000614971 Transcript missense_variant 42/7756 29/5439 10/1812 P/H cCc/cAc rs770980232 1 -1 LTN1 HGNC HGNC:13082 protein_coding YES CCDS33527.2 ENSP00000478783 O94822 UPI000049DF6C NM_015565.2 deleterious_low_confidence(0) 1/30 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs770980232 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 28992915 28992915 G T 1 0 0 0 0 1 0 0 0 8987 1232 43 2 2 LTN1 21 28992915 Missense_Mutation SNP G C3N-01414_T 2068832 28992915 17717068 507 23707 USP16 0 . GRCh38 21 29040669 29040669 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1012C>A p.Leu338Ile p.L338I ENST00000334352 11/19 40 36 4 114 114 0 varscan-mutect USP16,missense_variant,p.Leu338Ile,ENST00000334352,NM_001032410.1;USP16,missense_variant,p.Leu338Ile,ENST00000399976,NM_006447.2;USP16,missense_variant,p.Leu337Ile,ENST00000399975,NM_001001992.1;USP16,non_coding_transcript_exon_variant,,ENST00000474835,; A ENST00000334352 Transcript missense_variant 1243/3004 1012/2472 338/823 L/I Cta/Ata 1 1 USP16 HGNC HGNC:12614 protein_coding YES CCDS13583.1 ENSP00000334808 Q9Y5T5 UPI00001379FA NM_001032410.1 tolerated(0.17) 11/19 PROSITE_profiles:PS50235,HAMAP:MF_03062,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 5 1 PASS rs1188724092 . 1 192 14 3 0 0 0 0 -8.616962 0.9843305 1 1 1 0 A 3 1 77 29040669 29040669 C A 1 0 0 0 0 1 0 0 0 17581 564 20 2 2 USP16 21 29040669 Missense_Mutation SNP C C3N-01414_T 47754 29040669 17669314 508 23708 URB1 0 . GRCh38 21 32383442 32383442 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.547G>T p.Val183Leu p.V183L ENST00000382751 4/39 93 81 12 159 159 0 strelka-varscan-mutect URB1,missense_variant,p.Val183Leu,ENST00000382751,NM_014825.2; A ENST00000382751 Transcript missense_variant 663/10832 547/6816 183/2271 V/L Gtg/Ttg 1 -1 URB1 HGNC HGNC:17344 protein_coding YES CCDS46645.1 ENSP00000372199 O60287 UPI0000185F65 NM_014825.2 tolerated(0.36) 4/39 hmmpanther:PTHR13500,Pfam_domain:PF11707 MODERATE 1 SNV 1 1 PASS rs1264629474 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 32383442 32383442 C A 1 0 0 0 0 1 0 0 0 17554 507 18 2 2 URB1 21 32383442 Missense_Mutation SNP C C3N-01414_T 3342773 32383442 14326541 509 23709 SON 0 . GRCh38 21 33550915 33550915 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1684G>T p.Gly562Trp p.G562W ENST00000356577 3/12 64 46 18 116 116 0 strelka-varscan-mutect SON,missense_variant,p.Gly562Trp,ENST00000356577,NM_138927.2;SON,missense_variant,p.Gly562Trp,ENST00000381679,NM_001291411.1;SON,missense_variant,p.Gly562Trp,ENST00000300278,NM_032195.2;SON,intron_variant,,ENST00000381692,NM_001291412.1;SON,upstream_gene_variant,,ENST00000436227,;SON,upstream_gene_variant,,ENST00000421541,;SON,downstream_gene_variant,,ENST00000290239,;SON,downstream_gene_variant,,ENST00000492229,;SON,missense_variant,p.Gly562Trp,ENST00000455528,;SON,downstream_gene_variant,,ENST00000475072,; T ENST00000356577 Transcript missense_variant 2159/8813 1684/7281 562/2426 G/W Ggg/Tgg 1 1 SON HGNC HGNC:11183 protein_coding YES CCDS13629.1 ENSP00000348984 P18583 UPI0000140BFD NM_138927.2 deleterious_low_confidence(0) 3/12 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 77 33550915 33550915 G T 1 0 0 0 0 1 0 0 0 15248 1232 43 2 2 SON 21 33550915 Missense_Mutation SNP G C3N-01414_T 1167473 33550915 13159068 510 23710 AGPAT3 0 . GRCh38 21 43969193 43969193 + Missense_Mutation SNP G G C novel C3N-01414_T C3N-01414_N G G c.424G>C p.Val142Leu p.V142L ENST00000398063 4/9 207 163 44 340 340 0 strelka-varscan-mutect AGPAT3,missense_variant,p.Val142Leu,ENST00000398063,NM_001037553.1;AGPAT3,missense_variant,p.Val142Leu,ENST00000291572,NM_020132.4;AGPAT3,missense_variant,p.Val142Leu,ENST00000398058,;AGPAT3,missense_variant,p.Val142Leu,ENST00000398061,;AGPAT3,missense_variant,p.Val142Leu,ENST00000327505,;AGPAT3,missense_variant,p.Val142Leu,ENST00000546158,;AGPAT3,missense_variant,p.Val142Leu,ENST00000422850,;AGPAT3,missense_variant,p.Val142Leu,ENST00000457068,;AGPAT3,downstream_gene_variant,,ENST00000445582,;AGPAT3,downstream_gene_variant,,ENST00000448287,;AGPAT3,non_coding_transcript_exon_variant,,ENST00000479117,;AGPAT3,non_coding_transcript_exon_variant,,ENST00000481319,;AGPAT3,non_coding_transcript_exon_variant,,ENST00000467358,;AGPAT3,upstream_gene_variant,,ENST00000484865,; C ENST00000398063 Transcript missense_variant 916/5767 424/1131 142/376 V/L Gtg/Ctg 1 1 AGPAT3 HGNC HGNC:326 protein_coding YES CCDS13703.1 ENSP00000381140 Q9NRZ7 UPI000004616E NM_001037553.1 deleterious(0.04) 4/9 hmmpanther:PTHR10983:SF9,hmmpanther:PTHR10983,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 43969193 43969193 G C 1 0 0 0 0 1 0 0 0 470 1377 48 4 4 AGPAT3 21 43969193 Missense_Mutation SNP G C3N-01414_T 10418278 43969193 2740790 511 23711 AIRE 0 . GRCh38 21 44287591 44287591 + Missense_Mutation SNP G G T rs200899780 C3N-01414_T C3N-01414_N G G c.538G>T p.Gly180Trp p.G180W ENST00000291582 4/14 190 162 28 323 323 0 strelka-varscan-mutect AIRE,missense_variant,p.Gly180Trp,ENST00000291582,NM_000383.3;AIRE,splice_region_variant,,ENST00000530812,;AIRE,splice_region_variant,,ENST00000527919,;AIRE,upstream_gene_variant,,ENST00000337909,;AIRE,upstream_gene_variant,,ENST00000397994,; T ENST00000291582 Transcript missense_variant,splice_region_variant 665/2257 538/1638 180/545 G/W Ggg/Tgg rs200899780,COSM5661260 1 1 AIRE HGNC HGNC:360 protein_coding YES CCDS13706.1 ENSP00000291582 O43918 UPI0000030FA6 NM_000383.3 deleterious(0) 4/14 Prints_domain:PR01711,hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF15 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200899780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 44287591 44287591 G T 1 0 0 0 0 1 0 0 0 514 1130 39 1 1 AIRE 21 44287591 Missense_Mutation SNP G C3N-01414_T 318398 44287591 2422392 512 23712 KRTAP10-1 0 . GRCh38 21 44539530 44539530 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.621C>A p.= p.S207S ENST00000400375 1/1 457 393 64 738 738 0 strelka-varscan-mutect KRTAP10-1,synonymous_variant,p.=,ENST00000400375,NM_198691.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,intron_variant,,ENST00000397916,; T ENST00000400375 Transcript synonymous_variant 666/1215 621/849 207/282 S tcC/tcA 1 -1 KRTAP10-1 HGNC HGNC:22966 protein_coding YES CCDS42954.1 ENSP00000383226 P60331 UPI00003D4D6C NM_198691.2 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72,Low_complexity_(Seg):seg LOW SNV 1 PASS rs1258170802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 44539530 44539530 G T 1 0 0 0 0 0 0 0 1 8388 1335 47 2 2 KRTAP10-1 21 44539530 Silent SNP G C3N-01414_T 251939 44539530 2170453 513 23713 COL18A1 0 . GRCh38 21 45468711 45468711 + Silent SNP A A T novel C3N-01414_T C3N-01414_N A A c.1821A>T p.= p.S607S ENST00000359759 2/41 138 105 33 266 266 0 strelka-varscan-mutect COL18A1,synonymous_variant,p.=,ENST00000359759,NM_130444.2;COL18A1,synonymous_variant,p.=,ENST00000355480,NM_030582.3;COL18A1,synonymous_variant,p.=,ENST00000400337,NM_130445.3; T ENST00000359759 Transcript synonymous_variant 1821/6586 1821/5265 607/1754 S tcA/tcT 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 2/41 Pfam_domain:PF13385,SMART_domains:SM00210,Superfamily_domains:SSF49899 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 45468711 45468711 A T 1 0 0 0 0 0 0 0 1 3463 146 6 4 4 COL18A1 21 45468711 Silent SNP A C3N-01414_T 929181 45468711 1241272 514 23714 LSS 0 . GRCh38 21 46215705 46215705 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.872G>T p.Trp291Leu p.W291L ENST00000397728 8/22 73 56 17 97 97 0 strelka-varscan-mutect LSS,missense_variant,p.Trp291Leu,ENST00000397728,NM_002340.5;LSS,missense_variant,p.Trp211Leu,ENST00000457828,NM_001145437.1;LSS,missense_variant,p.Trp291Leu,ENST00000356396,NM_001001438.2;LSS,missense_variant,p.Trp280Leu,ENST00000522411,NM_001145436.1;LSS,downstream_gene_variant,,ENST00000450351,;AP001469.5,upstream_gene_variant,,ENST00000418029,;AP001469.5,upstream_gene_variant,,ENST00000626933,;LSS,non_coding_transcript_exon_variant,,ENST00000464357,; A ENST00000397728 Transcript missense_variant 951/4936 872/2199 291/732 W/L tGg/tTg 1 -1 LSS HGNC HGNC:6708 protein_coding YES CCDS13733.1 ENSP00000380837 P48449 UPI000012A14D NM_002340.5 tolerated(0.33) 8/22 Gene3D:1.50.10.20,Pfam_domain:PF13249,hmmpanther:PTHR11764,hmmpanther:PTHR11764:SF20,Superfamily_domains:SSF48239,TIGRFAM_domain:TIGR01787 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 46215705 46215705 C A 1 0 0 0 0 1 0 0 0 8972 595 21 2 2 LSS 21 46215705 Missense_Mutation SNP C C3N-01414_T 746994 46215705 494278 515 23715 ATP6V1E1 0 . GRCh38 22 17612875 17612875 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.213G>T p.Gln71His p.Q71H ENST00000253413 4/9 76 66 10 191 190 1 strelka-varscan-mutect ATP6V1E1,missense_variant,p.Gln71His,ENST00000253413,NM_001696.3;ATP6V1E1,missense_variant,p.Gln71His,ENST00000399796,NM_001039367.1;ATP6V1E1,missense_variant,p.Gln49His,ENST00000399798,NM_001039366.1;ATP6V1E1,missense_variant,p.Gln72His,ENST00000413576,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000478963,;ATP6V1E1,downstream_gene_variant,,ENST00000460085,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000484653,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000481365,; A ENST00000253413 Transcript missense_variant 396/1402 213/681 71/226 Q/H caG/caT 1 -1 ATP6V1E1 HGNC HGNC:857 protein_coding YES CCDS13745.1 ENSP00000253413 P36543 Q53Y06 UPI0000000C60 NM_001696.3 deleterious(0.01) 4/9 Low_complexity_(Seg):seg,HAMAP:MF_00311,hmmpanther:PTHR12317:SF20,hmmpanther:PTHR12317,Pfam_domain:PF01991 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 17612875 17612875 C A 1 0 0 0 0 1 0 0 0 1336 927 32 2 2 ATP6V1E1 22 17612875 Missense_Mutation SNP C C3N-01414_T 17612875 33205593 516 23716 CLTCL1 0 . GRCh38 22 19226325 19226325 + Missense_Mutation SNP G G A rs782573395 C3N-01414_T C3N-01414_N G G c.1841C>T p.Ala614Val p.A614V ENST00000427926 12/33 206 146 60 335 335 0 strelka-varscan-mutect CLTCL1,missense_variant,p.Ala614Val,ENST00000427926,NM_007098.3;CLTCL1,missense_variant,p.Ala614Val,ENST00000621271,NM_001835.3;CLTCL1,missense_variant,p.Ala614Val,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,upstream_gene_variant,,ENST00000458188,;CLTCL1,downstream_gene_variant,,ENST00000540896,; A ENST00000427926 Transcript missense_variant 1914/5513 1841/4923 614/1640 A/V gCc/gTc rs782573395 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 deleterious(0) 12/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs782573395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 19226325 19226325 G A 1 0 0 0 0 1 0 0 0 3339 1203 42 3 3 CLTCL1 22 19226325 Missense_Mutation SNP G C3N-01414_T 1613450 19226325 31592143 517 23717 PRAME 0 . GRCh38 22 22549742 22549742 + Silent SNP G G A novel C3N-01414_T C3N-01414_N G G c.937C>T p.= p.L313L ENST00000543184 4/5 50 37 13 111 111 0 strelka-varscan-mutect PRAME,synonymous_variant,p.=,ENST00000543184,NM_206953.2;PRAME,synonymous_variant,p.=,ENST00000398741,NM_206955.2;PRAME,synonymous_variant,p.=,ENST00000398743,NM_206954.2,NM_001291715.1,NM_006115.4;PRAME,synonymous_variant,p.=,ENST00000405655,NM_206956.2,NM_001291716.1;PRAME,synonymous_variant,p.=,ENST00000402697,;PRAME,downstream_gene_variant,,ENST00000439106,;PRAME,downstream_gene_variant,,ENST00000406503,;PRAME,downstream_gene_variant,,ENST00000420709,;PRAME,downstream_gene_variant,,ENST00000403441,;PRAME,downstream_gene_variant,,ENST00000438888,;PRAME,downstream_gene_variant,,ENST00000485532,;PRAME,downstream_gene_variant,,ENST00000476336,;PRAME,non_coding_transcript_exon_variant,,ENST00000492657,;PRAME,downstream_gene_variant,,ENST00000442481,; A ENST00000543184 Transcript synonymous_variant 1800/2758 937/1530 313/509 L Ctg/Ttg 1 -1 PRAME HGNC HGNC:9336 protein_coding YES CCDS13801.1 ENSP00000445675 P78395 A0A024R1E6 UPI0000000DDA NM_206953.2 4/5 hmmpanther:PTHR14224:SF4,hmmpanther:PTHR14224,Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 22549742 22549742 G A 1 0 0 0 0 0 0 0 1 12553 991 35 3 3 PRAME 22 22549742 Silent SNP G C3N-01414_T 3323417 22549742 28268726 518 23718 SPECC1L 0 . GRCh38 22 24313349 24313349 + Nonsense_Mutation SNP G G T rs548017612 C3N-01414_T C3N-01414_N G G c.190G>T p.Gly64Ter p.G64* ENST00000314328 4/17 308 239 69 574 573 1 strelka-varscan-mutect SPECC1L,stop_gained,p.Gly64Ter,ENST00000314328,NM_015330.4;SPECC1L,stop_gained,p.Gly64Ter,ENST00000437398,NM_001145468.3;SPECC1L,stop_gained,p.Gly64Ter,ENST00000541492,NM_001254732.2;SPECC1L,stop_gained,p.Gly64Ter,ENST00000421374,;SPECC1L,stop_gained,p.Gly3Ter,ENST00000440893,;SPECC1L,non_coding_transcript_exon_variant,,ENST00000416735,;SPECC1L-ADORA2A,stop_gained,p.Gly64Ter,ENST00000358654,; T ENST00000314328 Transcript stop_gained 475/6756 190/3354 64/1117 G/* Gga/Tga rs548017612,COSM4998544 1 1 SPECC1L HGNC HGNC:29022 protein_coding YES CCDS33619.1 ENSP00000325785 Q69YQ0 UPI0004620B3B NM_015330.4 4/17 hmmpanther:PTHR23167,hmmpanther:PTHR23167:SF18,Low_complexity_(Seg):seg 0,1 HIGH 1 SNV 1 0,1 1 PASS rs548017612 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 24313349 24313349 G T 1 0 0 0 0 0 1 0 0 15384 1117 39 1 1 SPECC1L 22 24313349 Nonsense_Mutation SNP G C3N-01414_T 1763607 24313349 26505119 519 23719 CRYBB2 0 . GRCh38 22 25231742 25231752 + Frame_Shift_Del DEL CCAACGTGGTG CCAACGTGGTG - novel C3N-01414_T C3N-01414_N CCAACGTGGTG CCAACGTGGTG c.590_600delAACGTGGTGCC p.Gln197LeufsTer35 p.Q197Lfs*35 ENST00000398215 6/6 138 103 35 277 277 0 sindel-varindel-pindel CRYBB2,frameshift_variant,p.Gln197LeufsTer35,ENST00000398215,NM_000496.2; - ENST00000398215 Transcript frameshift_variant 759-769/886 588-598/618 196-200/205 HQRGA/HX caCCAACGTGGTGcc/cacc 1 1 CRYBB2 HGNC HGNC:2398 protein_coding YES CCDS13831.1 ENSP00000381273 P43320 R4UMM2 UPI000013C6A2 NM_000496.2 6/6 hmmpanther:PTHR11818:SF11,hmmpanther:PTHR11818,Gene3D:2.60.20.10 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 25231742 25231742 CCAACGTGGTG - 1 0 1 0 1 0 0 0 0 3713 506 18 0 0 CRYBB2 22 25231742 Frame_Shift_Del DEL CCAACGTGGTG C3N-01414_T 918393 25231742 25586726 520 23720 MYO18B 0 . GRCh38 22 25898403 25898403 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.4765T>A p.Cys1589Ser p.C1589S ENST00000335473 29/44 194 170 24 357 357 0 strelka-varscan-mutect MYO18B,missense_variant,p.Cys1589Ser,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Cys1590Ser,ENST00000407587,;MYO18B,missense_variant,p.Cys1589Ser,ENST00000536101,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000609275,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000597284,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000609157,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000608507,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000608115,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000595102,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000594856,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000594542,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000609889,;CTA-125H2.2,non_coding_transcript_exon_variant,,ENST00000600903,;CTA-125H2.2,intron_variant,,ENST00000453457,;CTA-125H2.2,intron_variant,,ENST00000600211,;CTA-125H2.2,intron_variant,,ENST00000597548,;CTA-125H2.2,intron_variant,,ENST00000594585,;CTA-125H2.2,intron_variant,,ENST00000599080,;CTA-125H2.2,intron_variant,,ENST00000600269,;CTA-125H2.2,intron_variant,,ENST00000609570,;CTA-125H2.2,intron_variant,,ENST00000608257,;CTA-125H2.2,intron_variant,,ENST00000599792,;CTA-125H2.2,intron_variant,,ENST00000609823,;CTA-125H2.2,intron_variant,,ENST00000607895,;CTA-125H2.2,upstream_gene_variant,,ENST00000608921,;CTA-125H2.2,upstream_gene_variant,,ENST00000609820,;CTA-125H2.2,upstream_gene_variant,,ENST00000597614,;CTA-125H2.2,upstream_gene_variant,,ENST00000609809,;CTA-125H2.2,downstream_gene_variant,,ENST00000595093,;CTA-125H2.2,upstream_gene_variant,,ENST00000596813,;CTA-125H2.2,upstream_gene_variant,,ENST00000593715,;MYO18B,upstream_gene_variant,,ENST00000536204,;MYO18B,upstream_gene_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript missense_variant 5015/8565 4765/7704 1589/2567 C/S Tgc/Agc 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0) 29/44 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 25898403 25898403 T A 1 0 0 0 0 1 0 0 0 10067 1580 55 4 4 MYO18B 22 25898403 Missense_Mutation SNP T C3N-01414_T 666661 25898403 24920065 521 23721 DNAL4 0 . GRCh38 22 38782721 38782721 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.11C>A p.Thr4Lys p.T4K ENST00000216068 2/4 111 105 6 162 162 0 strelka-varscan-mutect DNAL4,missense_variant,p.Thr4Lys,ENST00000216068,NM_005740.2;DNAL4,missense_variant,p.Thr4Lys,ENST00000406199,;SUN2,intron_variant,,ENST00000406622,;DNAL4,intron_variant,,ENST00000486019,;DNAL4,downstream_gene_variant,,ENST00000475512,; T ENST00000216068 Transcript missense_variant 256/1504 11/318 4/105 T/K aCa/aAa 1 -1 DNAL4 HGNC HGNC:2955 protein_coding YES CCDS13979.1 ENSP00000216068 O96015 UPI0000129452 NM_005740.2 tolerated(0.92) 2/4 hmmpanther:PTHR11886 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.50204 1 1 1 1 0 T 3 4 77 38782721 38782721 G T 1 0 0 0 0 1 0 0 0 4471 1377 48 2 2 DNAL4 22 38782721 Missense_Mutation SNP G C3N-01414_T 12884318 38782721 12035747 522 23722 CACNA1I 0 . GRCh38 22 39619346 39619346 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.519C>A p.Asn173Lys p.N173K ENST00000402142 4/37 222 199 23 370 370 0 strelka-varscan-mutect CACNA1I,missense_variant,p.Asn173Lys,ENST00000402142,NM_021096.3;CACNA1I,missense_variant,p.Asn173Lys,ENST00000404898,NM_001003406.1;CACNA1I,missense_variant,p.Asn173Lys,ENST00000401624,;CACNA1I,missense_variant,p.Asn173Lys,ENST00000407673,; A ENST00000402142 Transcript missense_variant 519/10004 519/6672 173/2223 N/K aaC/aaA 1 1 CACNA1I HGNC HGNC:1396 protein_coding YES CCDS46710.1 ENSP00000385019 Q9P0X4 UPI000012727D NM_021096.3 deleterious(0.01) 4/37 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF209,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 39619346 39619346 C A 1 0 0 0 0 1 0 0 0 2234 506 18 2 2 CACNA1I 22 39619346 Missense_Mutation SNP C C3N-01414_T 836625 39619346 11199122 523 23723 VCX3B 0 . GRCh38 X 8465956 8465956 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.314G>T p.Ser105Ile p.S105I ENST00000381032 3/3 37 19 18 41 41 0 strelka-varscan-mutect VCX3B,missense_variant,p.Ser105Ile,ENST00000381032,NM_001001888.3;VCX3B,missense_variant,p.Ser105Ile,ENST00000453306,;VCX3B,missense_variant,p.Ser105Ile,ENST00000444481,;VCX3B,intron_variant,,ENST00000381029,; T ENST00000381032 Transcript missense_variant 621/1171 314/741 105/246 S/I aGt/aTt 1 1 VCX3B HGNC HGNC:31838 protein_coding YES CCDS48077.2 ENSP00000370420 Q9H321 UPI000057A469 NM_001001888.3 deleterious(0.02) 3/3 Pfam_domain:PF15231,hmmpanther:PTHR15251,hmmpanther:PTHR15251:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1217126065 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 8465956 8465956 G T 1 0 0 0 0 1 0 0 0 17690 1029 36 2 2 VCX3B 23 8465956 Missense_Mutation SNP G C3N-01414_T 8465956 147574939 524 23724 CLCN4 0 . GRCh38 X 10194970 10194970 + Missense_Mutation SNP G G C rs760253224 C3N-01414_T C3N-01414_N G G c.304G>C p.Val102Leu p.V102L ENST00000380833 5/13 143 121 22 185 185 0 strelka-varscan-mutect CLCN4,missense_variant,p.Val102Leu,ENST00000380833,NM_001830.3;CLCN4,missense_variant,p.Val8Leu,ENST00000421085,NM_001256944.1;CLCN4,missense_variant,p.Val102Leu,ENST00000380829,;CLCN4,missense_variant,p.Val102Leu,ENST00000454850,; C ENST00000380833 Transcript missense_variant 695/6750 304/2283 102/760 V/L Gtc/Ctc rs760253224 1 1 CLCN4 HGNC HGNC:2022 protein_coding YES CCDS14137.1 ENSP00000370213 P51793 UPI0000127A99 NM_001830.3 tolerated(0.06) 5/13 Gene3D:1otsB00,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF18,Superfamily_domains:SSF81340 MODERATE 1 SNV 1 1 PASS rs760253224 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 77 10194970 10194970 G C 1 0 0 0 0 1 0 0 0 3229 1261 44 4 4 CLCN4 23 10194970 Missense_Mutation SNP G C3N-01414_T 1729014 10194970 145845925 525 23725 FANCB 0 . GRCh38 X 14864999 14864999 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.512A>T p.Gln171Leu p.Q171L ENST00000398334 3/10 116 45 71 185 185 0 strelka-varscan-mutect FANCB,missense_variant,p.Gln171Leu,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Gln171Leu,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Gln171Leu,ENST00000452869,;FANCB,downstream_gene_variant,,ENST00000489126,; A ENST00000398334 Transcript missense_variant 780/3008 512/2580 171/859 Q/L cAg/cTg 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 tolerated(0.2) 3/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 14864999 14864999 T A 1 0 0 0 0 1 0 0 0 5522 1580 55 4 4 FANCB 23 14864999 Missense_Mutation SNP T C3N-01414_T 4670029 14864999 141175896 526 23726 MAP3K15 0 . GRCh38 X 19515036 19515036 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.226G>T p.Ala76Ser p.A76S ENST00000338883 1/29 111 103 8 105 105 0 strelka-mutect MAP3K15,missense_variant,p.Ala76Ser,ENST00000338883,NM_001001671.3; A ENST00000338883 Transcript missense_variant 226/4012 226/3942 76/1313 A/S Gcc/Tcc 1 -1 MAP3K15 HGNC HGNC:31689 protein_coding YES CCDS35212.2 ENSP00000345629 Q6ZN16 UPI0000E444D0 NM_001001671.3 tolerated(0.3) 1/29 Low_complexity_(Seg):seg,hmmpanther:PTHR11584,hmmpanther:PTHR11584:SF363 MODERATE 1 SNV 5 1 PASS . . 0 200 7 3 0 0 0 0 -11.93181 0.9970689 1 1 1 0 A 3 1 77 19515036 19515036 C A 1 0 0 0 0 1 0 0 0 9171 739 26 2 2 MAP3K15 23 19515036 Missense_Mutation SNP C C3N-01414_T 4650037 19515036 136525859 527 23727 CNKSR2 0 . GRCh38 X 21609080 21609080 + Missense_Mutation SNP G G T rs768216123 C3N-01414_T C3N-01414_N G G c.2155G>T p.Ala719Ser p.A719S ENST00000379510 20/22 41 16 25 47 47 0 strelka-varscan-mutect CNKSR2,missense_variant,p.Ala689Ser,ENST00000425654,NM_001168647.1;CNKSR2,missense_variant,p.Ala719Ser,ENST00000379510,NM_014927.3;CNKSR2,missense_variant,p.Ala719Ser,ENST00000279451,NM_001168648.1;CNKSR2,missense_variant,p.Ala670Ser,ENST00000543067,NM_001168649.1; T ENST00000379510 Transcript missense_variant 2191/5315 2155/3105 719/1034 A/S Gcc/Tcc rs768216123,COSM1119162 1 1 CNKSR2 HGNC HGNC:19701 protein_coding YES CCDS14198.1 ENSP00000368824 Q8WXI2 UPI0000070D72 NM_014927.3 tolerated(1) 20/22 hmmpanther:PTHR12844:SF21,hmmpanther:PTHR12844 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs768216123 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 21609080 21609080 G T 1 0 0 0 0 1 0 0 0 3387 1087 38 1 1 CNKSR2 23 21609080 Missense_Mutation SNP G C3N-01414_T 2094044 21609080 134431815 528 23728 RP5-972B16.2 0 . GRCh38 X 38674250 38674250 + Silent SNP G G T rs11541004 C3N-01414_T C3N-01414_N G G c.375G>T p.= p.T125T ENST00000378482 4/8 241 108 133 307 307 0 strelka-varscan-mutect TSPAN7,synonymous_variant,p.=,ENST00000378482,NM_004615.3;TSPAN7,synonymous_variant,p.=,ENST00000286824,;RP5-972B16.2,synonymous_variant,p.=,ENST00000465127,;TSPAN7,non_coding_transcript_exon_variant,,ENST00000488893,;TSPAN7,downstream_gene_variant,,ENST00000494037,;TSPAN7,3_prime_UTR_variant,,ENST00000475216,;TSPAN7,3_prime_UTR_variant,,ENST00000471410,;TSPAN7,3_prime_UTR_variant,,ENST00000480976,;TSPAN7,non_coding_transcript_exon_variant,,ENST00000419600,; T ENST00000378482 Transcript synonymous_variant 552/1909 375/750 125/249 T acG/acT rs11541004 1 1 TSPAN7 HGNC HGNC:11854 protein_coding YES CCDS14248.1 ENSP00000367743 P41732 UPI000013683C NM_004615.3 4/8 Superfamily_domains:0037997,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,hmmpanther:PTHR19282,hmmpanther:PTHR19282:SF257 LOW 1 SNV 1 1 PASS rs11541004 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 38674250 38674250 G T 1 0 0 0 0 0 0 0 1 13785 1103 39 1 1 RP5-972B16.2 23 38674250 Silent SNP G C3N-01414_T 17065170 38674250 117366645 529 23729 MED14 0 . GRCh38 X 40697132 40697132 + Silent SNP C C A rs867624763 C3N-01414_T C3N-01414_N C C c.1542G>T p.= p.T514T ENST00000324817 13/31 116 51 65 123 123 0 strelka-varscan-mutect MED14,synonymous_variant,p.=,ENST00000324817,NM_004229.3; A ENST00000324817 Transcript synonymous_variant 1661/7984 1542/4365 514/1454 T acG/acT rs867624763 1 -1 MED14 HGNC HGNC:2370 protein_coding YES CCDS14254.1 ENSP00000323720 O60244 UPI00001414B1 NM_004229.3 13/31 hmmpanther:PTHR12809 LOW 1 SNV 1 1 PASS rs867624763 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 40697132 40697132 C A 1 0 0 0 0 0 0 0 1 9371 871 31 1 1 MED14 23 40697132 Silent SNP C C3N-01414_T 2022882 40697132 115343763 530 23730 USP9X 0 . GRCh38 X 41123656 41123656 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.28G>T p.Val10Phe p.V10F ENST00000324545 2/45 125 62 63 171 171 0 strelka-varscan-mutect USP9X,missense_variant,p.Val10Phe,ENST00000324545,NM_001039590.2;USP9X,missense_variant,p.Val10Phe,ENST00000378308,NM_001039591.2; T ENST00000324545 Transcript missense_variant 661/12401 28/7713 10/2570 V/F Gtc/Ttc 1 1 USP9X HGNC HGNC:12632 protein_coding YES CCDS43930.1 ENSP00000316357 Q93008 UPI00001AF419 NM_001039590.2 deleterious_low_confidence(0.01) 2/45 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 41123656 41123656 G T 1 0 0 0 0 1 0 0 0 17633 1261 44 2 2 USP9X 23 41123656 Missense_Mutation SNP G C3N-01414_T 426524 41123656 114917239 531 23731 EFHC2 0 . GRCh38 X 44272776 44272776 + Nonsense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.292A>T p.Arg98Ter p.R98* ENST00000420999 3/15 169 137 32 251 251 0 strelka-varscan-mutect EFHC2,stop_gained,p.Arg98Ter,ENST00000420999,NM_025184.3; A ENST00000420999 Transcript stop_gained 376/2464 292/2250 98/749 R/* Aga/Tga 1 -1 EFHC2 HGNC HGNC:26233 protein_coding YES CCDS55405.1 ENSP00000404232 Q5JST6 UPI00000717F2 NM_025184.3 3/15 PROSITE_profiles:PS51336,hmmpanther:PTHR12086,hmmpanther:PTHR12086:SF11,SMART_domains:SM00676 HIGH 1 SNV 1 1 PASS rs1323183173 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 77 44272776 44272776 T A 1 0 0 0 0 0 1 0 0 4782 1588 55 4 4 EFHC2 23 44272776 Nonsense_Mutation SNP T C3N-01414_T 3149120 44272776 111768119 532 23732 KDM5C 0 . GRCh38 X 53220916 53220916 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.151G>T p.Asp51Tyr p.D51Y ENST00000375401 2/26 233 120 113 264 263 1 strelka-varscan-mutect KDM5C,missense_variant,p.Asp51Tyr,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Asp51Tyr,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Asp51Tyr,ENST00000375379,;KDM5C,missense_variant,p.Asp51Tyr,ENST00000375383,;KDM5C,intron_variant,,ENST00000452825,NM_001146702.1;KDM5C,splice_region_variant,,ENST00000467093,;KDM5C,upstream_gene_variant,,ENST00000495519,;KDM5C,missense_variant,p.Asp51Tyr,ENST00000428012,;KDM5C,splice_region_variant,,ENST00000429877,;KDM5C,downstream_gene_variant,,ENST00000349663,;KDM5C,upstream_gene_variant,,ENST00000497995,; A ENST00000375401 Transcript missense_variant,splice_region_variant 684/6031 151/4683 51/1560 D/Y Gac/Tac 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 deleterious(0) 2/26 PROSITE_profiles:PS51183,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43,SMART_domains:SM00545 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 53220916 53220916 C A 1 0 0 0 0 1 0 0 0 8053 869 30 2 2 KDM5C 23 53220916 Missense_Mutation SNP C C3N-01414_T 8948140 53220916 102819979 533 23733 MAGEH1 0 . GRCh38 X 55452638 55452638 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.264G>T p.Lys88Asn p.K88N ENST00000342972 1/1 156 130 26 203 202 1 strelka-varscan-mutect MAGEH1,missense_variant,p.Lys88Asn,ENST00000342972,NM_014061.4;hsa-mir-4536-1,downstream_gene_variant,,ENST00000583537,;MIR4536-2,upstream_gene_variant,,ENST00000636519,; T ENST00000342972 Transcript missense_variant 534/1462 264/660 88/219 K/N aaG/aaT 1 1 MAGEH1 HGNC HGNC:24092 protein_coding YES CCDS14369.1 ENSP00000343706 Q9H213 UPI0000038A64 NM_014061.4 deleterious_low_confidence(0.01) 1/1 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF8,SMART_domains:SM01373 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 55452638 55452638 G T 1 0 0 0 0 1 0 0 0 9106 933 33 2 2 MAGEH1 23 55452638 Missense_Mutation SNP G C3N-01414_T 2231722 55452638 100588257 534 23734 ABCB7 0 . GRCh38 X 75069369 75069369 + Frame_Shift_Del DEL C C - novel C3N-01414_T C3N-01414_N C C c.1454delG p.Gly485AlafsTer21 p.G485Afs*21 ENST00000253577 11/16 195 156 39 305 305 0 sindel-varindel-pindel ABCB7,frameshift_variant,p.Gly445AlafsTer21,ENST00000620875,NM_001271699.1;ABCB7,frameshift_variant,p.Gly485AlafsTer21,ENST00000253577,NM_004299.4;ABCB7,frameshift_variant,p.Gly484AlafsTer21,ENST00000373394,NM_001271696.1;ABCB7,frameshift_variant,p.Gly444AlafsTer21,ENST00000339447,NM_001271697.1;ABCB7,frameshift_variant,p.Gly458AlafsTer21,ENST00000529949,NM_001271698.1;ABCB7,non_coding_transcript_exon_variant,,ENST00000534570,;ABCB7,non_coding_transcript_exon_variant,,ENST00000469368,; - ENST00000253577 Transcript frameshift_variant 1479/2377 1454/2262 485/753 G/X gGc/gc 1 -1 ABCB7 HGNC HGNC:48 protein_coding YES CCDS14428.1 ENSP00000253577 O75027 A0A0S2Z2Z3 UPI0000169E78 NM_004299.4 11/16 PROSITE_profiles:PS50893,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF187,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 77 75069369 75069369 C - 1 0 1 0 1 0 0 0 0 50 739 26 0 0 ABCB7 23 75069369 Frame_Shift_Del DEL C C3N-01414_T 19616731 75069369 80971526 535 23735 MAGEE1 0 . GRCh38 X 76428272 76428272 + Silent SNP C C G novel C3N-01414_T C3N-01414_N C C c.342C>G p.= p.T114T ENST00000361470 1/1 113 100 13 194 194 0 strelka-varscan-mutect MAGEE1,synonymous_variant,p.=,ENST00000361470,NM_020932.2; G ENST00000361470 Transcript synonymous_variant 549/3630 342/2874 114/957 T acC/acG 1 1 MAGEE1 HGNC HGNC:24934 protein_coding YES CCDS14433.1 ENSP00000354912 Q9HCI5 UPI000006F138 NM_020932.2 1/1 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 77 76428272 76428272 C G 1 0 0 0 0 0 0 0 1 9103 668 24 4 4 MAGEE1 23 76428272 Silent SNP C C3N-01414_T 1358903 76428272 79612623 536 23736 PCDH11X 0 . GRCh38 X 92618894 92618894 + Missense_Mutation SNP G G A C3N-01414_T C3N-01414_N G G c.3998G>A p.Arg1333Lys p.R1333K ENST00000373094 7/7 249 125 124 383 383 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Arg1333Lys,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Arg1323Lys,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Arg1325Lys,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Arg1315Lys,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Arg1296Lys,ENST00000373088,NM_001168362.1;PCDH11X,3_prime_UTR_variant,,ENST00000504220,NM_001168361.1; A ENST00000373094 Transcript missense_variant 4843/9179 3998/4044 1333/1347 R/K aGa/aAa COSM5048771,COSM5048772 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious_low_confidence(0) 7/7 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 92618894 92618894 G A 1 0 0 0 0 1 0 0 0 11595 942 33 3 3 PCDH11X 23 92618894 Missense_Mutation SNP G C3N-01414_T 16190622 92618894 63422001 537 23737 NRK 0 . GRCh38 X 105949614 105949614 + Missense_Mutation SNP C C T novel C3N-01414_T C3N-01414_N C C c.4393C>T p.Pro1465Ser p.P1465S ENST00000243300 27/29 93 88 5 125 125 0 strelka-varscan-mutect NRK,missense_variant,p.Pro1465Ser,ENST00000243300,NM_198465.3;NRK,missense_variant,p.Pro46Ser,ENST00000540278,; T ENST00000243300 Transcript missense_variant 4696/8062 4393/4749 1465/1582 P/S Cct/Tct 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 deleterious(0) 27/29 Low_complexity_(Seg):seg,PROSITE_profiles:PS50219,Pfam_domain:PF00780,SMART_domains:SM00036 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 105949614 105949614 C T 1 0 0 0 0 1 0 0 0 10713 507 18 3 3 NRK 23 105949614 Missense_Mutation SNP C C3N-01414_T 13330720 105949614 50091281 538 23738 NUP62CL 0 . GRCh38 X 107153493 107153493 + Nonsense_Mutation SNP A A T novel C3N-01414_T C3N-01414_N A A c.356T>A p.Leu119Ter p.L119* ENST00000372466 6/9 31 14 17 44 44 0 strelka-varscan-mutect NUP62CL,stop_gained,p.Leu119Ter,ENST00000372466,NM_017681.2;NUP62CL,stop_gained,p.Leu51Ter,ENST00000432145,;NUP62CL,stop_gained,p.Leu119Ter,ENST00000421752,;NUP62CL,missense_variant,p.Tyr69Asn,ENST00000484614,; T ENST00000372466 Transcript stop_gained 608/1755 356/555 119/184 L/* tTa/tAa 1 -1 NUP62CL HGNC HGNC:25960 protein_coding YES CCDS14527.1 ENSP00000361544 Q9H1M0 A0A0S2Z5E8 UPI0000071522 NM_017681.2 6/9 hmmpanther:PTHR12084,hmmpanther:PTHR12084:SF3,Pfam_domain:PF05064 HIGH 1 SNV 1 1 PASS . . 3 204 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 77 107153493 107153493 A T 1 0 0 0 0 0 1 0 0 10835 372 13 4 4 NUP62CL 23 107153493 Nonsense_Mutation SNP A C3N-01414_T 1203879 107153493 48887402 539 23739 THOC2 0 . GRCh38 X 123644811 123644811 + Missense_Mutation SNP C C A novel C3N-01414_T C3N-01414_N C C c.1527G>T p.Trp509Cys p.W509C ENST00000245838 14/39 79 29 50 109 109 0 strelka-varscan-mutect THOC2,missense_variant,p.Trp509Cys,ENST00000245838,NM_001081550.1;THOC2,missense_variant,p.Trp509Cys,ENST00000355725,;THOC2,missense_variant,p.Trp394Cys,ENST00000491737,; A ENST00000245838 Transcript missense_variant 1559/5609 1527/4782 509/1593 W/C tgG/tgT 1 -1 THOC2 HGNC HGNC:19073 protein_coding YES CCDS43988.1 ENSP00000245838 Q8NI27 UPI00001D7C42 NM_001081550.1 deleterious(0.01) 14/39 hmmpanther:PTHR21597,hmmpanther:PTHR21597:SF1,Pfam_domain:PF16134 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 123644811 123644811 C A 1 0 0 0 0 1 0 0 0 16300 624 22 2 2 THOC2 23 123644811 Missense_Mutation SNP C C3N-01414_T 16491318 123644811 32396084 540 23740 SASH3 0 . GRCh38 X 129793104 129793104 + Missense_Mutation SNP T T A novel C3N-01414_T C3N-01414_N T T c.917T>A p.Leu306Gln p.L306Q ENST00000356892 7/8 134 59 75 151 151 0 strelka-varscan-mutect SASH3,missense_variant,p.Leu306Gln,ENST00000356892,NM_018990.3;RP4-753P9.3,upstream_gene_variant,,ENST00000432513,;Metazoa_SRP,downstream_gene_variant,,ENST00000614439,;SASH3,downstream_gene_variant,,ENST00000476532,; A ENST00000356892 Transcript missense_variant 1031/2626 917/1143 306/380 L/Q cTg/cAg 1 1 SASH3 HGNC HGNC:15975 protein_coding YES CCDS14614.1 ENSP00000349359 O75995 UPI000006EC21 NM_018990.3 deleterious(0) 7/8 PROSITE_profiles:PS50105,hmmpanther:PTHR12301,Pfam_domain:PF07647,Gene3D:1.10.150.50,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 77 129793104 129793104 T A 1 0 0 0 0 1 0 0 0 14110 1580 55 4 4 SASH3 23 129793104 Missense_Mutation SNP T C3N-01414_T 6148293 129793104 26247791 541 23741 ADGRG4 0 . GRCh38 X 136345170 136345170 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1464G>T p.Gln488His p.Q488H ENST00000394143 6/26 137 52 85 143 143 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Gln488His,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Gln488His,ENST00000370652,;ADGRG4,missense_variant,p.Gln283His,ENST00000394141,; T ENST00000394143 Transcript missense_variant 1755/9931 1464/9243 488/3080 Q/H caG/caT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 tolerated(0.09) 6/26 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 136345170 136345170 G T 1 0 0 0 0 1 0 0 0 371 933 33 2 2 ADGRG4 23 136345170 Missense_Mutation SNP G C3N-01414_T 6552066 136345170 19695725 542 23742 ADGRG4 0 . GRCh38 X 136345350 136345350 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.1644G>T p.Met548Ile p.M548I ENST00000394143 6/26 147 67 80 185 185 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Met548Ile,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Met548Ile,ENST00000370652,;ADGRG4,missense_variant,p.Met343Ile,ENST00000394141,; T ENST00000394143 Transcript missense_variant 1935/9931 1644/9243 548/3080 M/I atG/atT 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 tolerated(0.22) 6/26 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 136345350 136345350 G T 1 0 0 0 0 1 0 0 0 371 1377 48 2 2 ADGRG4 23 136345350 Missense_Mutation SNP G C3N-01414_T 180 136345350 19695545 543 23743 ADGRG4 0 . GRCh38 X 136361486 136361486 + Silent SNP C C A novel C3N-01414_T C3N-01414_N C C c.7176C>A p.= p.A2392A ENST00000394143 12/26 76 32 44 115 115 0 strelka-varscan-mutect ADGRG4,synonymous_variant,p.=,ENST00000394143,NM_153834.3;ADGRG4,synonymous_variant,p.=,ENST00000370652,;ADGRG4,synonymous_variant,p.=,ENST00000394141,; A ENST00000394143 Transcript synonymous_variant 7467/9931 7176/9243 2392/3080 A gcC/gcA 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 12/26 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 77 136361486 136361486 C A 1 0 0 0 0 0 0 0 1 371 668 24 2 2 ADGRG4 23 136361486 Silent SNP C C3N-01414_T 16136 136361486 19679409 544 23744 TMEM185A 0 . GRCh38 X 149599557 149599557 + Missense_Mutation SNP G G T novel C3N-01414_T C3N-01414_N G G c.805C>A p.His269Asn p.H269N ENST00000600449 6/7 116 89 27 157 157 0 strelka-varscan-mutect TMEM185A,missense_variant,p.His269Asn,ENST00000600449,NM_032508.3;TMEM185A,missense_variant,p.His210Asn,ENST00000611119,NM_001174092.2;TMEM185A,missense_variant,p.His91Asn,ENST00000613273,;TMEM185A,missense_variant,p.His142Asn,ENST00000502858,;HSFX2,upstream_gene_variant,,ENST00000598963,NM_001164415.2;TMEM185A,downstream_gene_variant,,ENST00000507237,NM_001282302.1;TMEM185A,3_prime_UTR_variant,,ENST00000612022,;TMEM185A,non_coding_transcript_exon_variant,,ENST00000616857,;TMEM185A,downstream_gene_variant,,ENST00000502618,; T ENST00000600449 Transcript missense_variant 1137/2840 805/1053 269/350 H/N Cac/Aac 1 -1 TMEM185A HGNC HGNC:17125 protein_coding YES CCDS14689.1 ENSP00000471932 Q8NFB2 UPI0000049DA9 NM_032508.3 tolerated(0.08) 6/7 hmmpanther:PTHR13568,hmmpanther:PTHR13568:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 77 149599557 149599557 G T 1 0 0 0 0 1 0 0 0 16550 1362 47 2 2 TMEM185A 23 149599557 Missense_Mutation SNP G C3N-01414_T 13238071 149599557 6441338 545 23745 BGN 0 . GRCh38 X 153508396 153508396 + Missense_Mutation SNP G G A rs368783683 C3N-01414_T C3N-01414_N G G c.1058G>A p.Arg353His p.R353H ENST00000331595 8/8 153 129 24 183 183 0 strelka-varscan-mutect BGN,missense_variant,p.Arg353His,ENST00000331595,NM_001711.4;BGN,downstream_gene_variant,,ENST00000431891,;BGN,non_coding_transcript_exon_variant,,ENST00000480756,;BGN,non_coding_transcript_exon_variant,,ENST00000472615,;BGN,intron_variant,,ENST00000492658,; A ENST00000331595 Transcript missense_variant 1244/2402 1058/1107 353/368 R/H cGc/cAc rs368783683,COSM3694416 1 1 BGN HGNC HGNC:1044 protein_coding YES CCDS14721.1 ENSP00000327336 P21810 UPI000003BDBA NM_001711.4 deleterious(0) 8/8 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF6,PIRSF_domain:PIRSF002490 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs368783683 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 77 153508396 153508396 G A 1 0 0 0 0 1 0 0 0 1566 1087 38 1 1 BGN 23 153508396 Missense_Mutation SNP G C3N-01414_T 3908839 153508396 2532499 546 23746 DKC1 0 . GRCh38 X 154766294 154766294 + Silent SNP G G T novel C3N-01414_T C3N-01414_N G G c.342G>T p.= p.R114R ENST00000369550 5/15 116 51 65 163 163 0 strelka-varscan-mutect DKC1,synonymous_variant,p.=,ENST00000620277,NM_001288747.1;DKC1,synonymous_variant,p.=,ENST00000369550,NM_001142463.2,NM_001363.4;DKC1,synonymous_variant,p.=,ENST00000413910,;DKC1,synonymous_variant,p.=,ENST00000437719,;SNORA36A,upstream_gene_variant,,ENST00000384221,;DKC1,upstream_gene_variant,,ENST00000626756,;DKC1,non_coding_transcript_exon_variant,,ENST00000473552,;DKC1,upstream_gene_variant,,ENST00000475966,;DKC1,synonymous_variant,p.=,ENST00000452771,;DKC1,upstream_gene_variant,,ENST00000426673,;DKC1,upstream_gene_variant,,ENST00000484317,;DKC1,upstream_gene_variant,,ENST00000412124,;DKC1,downstream_gene_variant,,ENST00000475423,; T ENST00000369550 Transcript synonymous_variant 552/2577 342/1545 114/514 R cgG/cgT 1 1 DKC1 HGNC HGNC:2890 protein_coding YES CCDS14761.1 ENSP00000358563 O60832 UPI00000325ED NM_001142463.2,NM_001363.4 5/15 hmmpanther:PTHR23127,Pfam_domain:PF01509,TIGRFAM_domain:TIGR00425,Superfamily_domains:SSF55120 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 77 154766294 154766294 G T 1 0 0 0 0 0 0 0 1 4349 1219 43 2 2 DKC1 23 154766294 Silent SNP G C3N-01414_T 1257898 154766294 1274601 547 23747 SSU72 0 . GRCh38 1 1543967 1543967 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.385G>T p.Glu129Ter p.E129* ENST00000291386 4/5 157 142 15 151 151 0 strelka-varscan-mutect SSU72,stop_gained,p.Glu129Ter,ENST00000291386,NM_014188.2;TMEM240,upstream_gene_variant,,ENST00000624426,;TMEM240,upstream_gene_variant,,ENST00000378733,NM_001114748.1;TMEM240,upstream_gene_variant,,ENST00000425828,;SSU72,non_coding_transcript_exon_variant,,ENST00000378726,;SSU72,downstream_gene_variant,,ENST00000378725,; A ENST00000291386 Transcript stop_gained 697/1290 385/585 129/194 E/* Gag/Tag 1 -1 SSU72 HGNC HGNC:25016 protein_coding YES CCDS32.1 ENSP00000291386 Q9NP77 UPI00000437EE NM_014188.2 4/5 hmmpanther:PTHR20383:SF11,hmmpanther:PTHR20383,Pfam_domain:PF04722 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 1543967 1543967 C A 1 0 0 0 0 0 1 0 0 15579 864 30 2 2 SSU72 1 1543967 Nonsense_Mutation SNP C C3N-01415_T 1543967 247412455 1 23748 MMEL1 0 . GRCh38 1 2592684 2592684 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.2038G>T p.Asp680Tyr p.D680Y ENST00000378412 21/24 139 121 18 117 117 0 strelka-mutect MMEL1,missense_variant,p.Asp680Tyr,ENST00000378412,NM_033467.3;MMEL1,missense_variant,p.Asp523Tyr,ENST00000502556,;FAM213B,downstream_gene_variant,,ENST00000444521,NM_001195736.1;FAM213B,downstream_gene_variant,,ENST00000378424,;FAM213B,downstream_gene_variant,,ENST00000419916,NM_152371.3,NM_001195737.1;FAM213B,downstream_gene_variant,,ENST00000378427,NM_001195738.1;FAM213B,downstream_gene_variant,,ENST00000378425,NM_001195740.1;FAM213B,downstream_gene_variant,,ENST00000537325,NM_001195741.1;FAM213B,downstream_gene_variant,,ENST00000465233,;MMEL1,upstream_gene_variant,,ENST00000471840,;FAM213B,downstream_gene_variant,,ENST00000498083,;FAM213B,downstream_gene_variant,,ENST00000484099,;FAM213B,downstream_gene_variant,,ENST00000464043,;FAM213B,downstream_gene_variant,,ENST00000493183,;FAM213B,downstream_gene_variant,,ENST00000474659,;FAM213B,downstream_gene_variant,,ENST00000481683,;MMEL1,3_prime_UTR_variant,,ENST00000504800,;MMEL1,non_coding_transcript_exon_variant,,ENST00000464195,;MMEL1,non_coding_transcript_exon_variant,,ENST00000469962,;MMEL1,intron_variant,,ENST00000491941,;FAM213B,downstream_gene_variant,,ENST00000476686,;FAM213B,downstream_gene_variant,,ENST00000477045,; A ENST00000378412 Transcript missense_variant 2200/2849 2038/2340 680/779 D/Y Gac/Tac 1 -1 MMEL1 HGNC HGNC:14668 protein_coding YES CCDS30569.2 ENSP00000367668 Q495T6 UPI0000047596 NM_033467.3 deleterious(0) 21/24 Gene3D:3.40.390.10,Pfam_domain:PF01431,Prints_domain:PR00786,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF141,Superfamily_domains:SSF55486 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 2592684 2592684 C A 1 0 0 0 0 1 0 0 0 9609 826 29 2 2 MMEL1 1 2592684 Missense_Mutation SNP C C3N-01415_T 1048717 2592684 246363738 2 23749 CCDC27 0 . GRCh38 1 3752792 3752792 + Missense_Mutation SNP G G T rs76597070 C3N-01415_T C3N-01415_N G G c.311G>T p.Arg104Met p.R104M ENST00000294600 1/12 140 124 16 182 182 0 strelka-varscan-mutect CCDC27,missense_variant,p.Arg104Met,ENST00000294600,NM_152492.2;CCDC27,missense_variant,p.Arg104Met,ENST00000462521,;CCDC27,non_coding_transcript_exon_variant,,ENST00000636250,; T ENST00000294600 Transcript missense_variant 395/2176 311/1971 104/656 R/M aGg/aTg rs76597070 1 1 CCDC27 HGNC HGNC:26546 protein_coding YES CCDS50.1 ENSP00000294600 Q2M243 UPI000013E186 NM_152492.2 deleterious(0.01) 1/12 hmmpanther:PTHR18853:SF8,hmmpanther:PTHR18853 23251661 MODERATE 1 SNV 1 1 1 PASS rs76597070 . 0 202 5 0 0 0 0 3 -4.176534 0 0 1 0 0 T 3 4 78 3752792 3752792 G T 1 0 0 0 0 1 0 0 0 2511 1000 35 2 2 CCDC27 1 3752792 Missense_Mutation SNP G C3N-01415_T 1160108 3752792 245203630 3 23750 AJAP1 0 . GRCh38 1 4769933 4769933 + Missense_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.910A>C p.Lys304Gln p.K304Q ENST00000378191 3/6 337 307 30 342 340 2 strelka-varscan-mutect AJAP1,missense_variant,p.Lys304Gln,ENST00000378191,NM_018836.3;AJAP1,missense_variant,p.Lys304Gln,ENST00000378190,NM_001042478.1; C ENST00000378191 Transcript missense_variant 1291/11666 910/1236 304/411 K/Q Aaa/Caa 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 deleterious(0) 3/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR32422,Pfam_domain:PF15298 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 4769933 4769933 A C 1 0 0 0 0 1 0 0 0 516 15 1 5 5 AJAP1 1 4769933 Missense_Mutation SNP A C3N-01415_T 1017141 4769933 244186489 4 23751 GPR153 0 . GRCh38 1 6254830 6254830 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.76G>T p.Ala26Ser p.A26S ENST00000377893 2/6 96 82 14 110 110 0 strelka-varscan-mutect GPR153,missense_variant,p.Ala26Ser,ENST00000377893,NM_207370.2; A ENST00000377893 Transcript missense_variant 336/4082 76/1830 26/609 A/S Gcc/Tcc 1 -1 GPR153 HGNC HGNC:23618 protein_coding YES CCDS64.1 ENSP00000367125 Q6NV75 A0A0I9QQ03 UPI000040E9D7 NM_207370.2 tolerated(0.19) 2/6 Gene3D:1.20.1070.10,Prints_domain:PR01991,PROSITE_profiles:PS50262,hmmpanther:PTHR16518,hmmpanther:PTHR16518:SF5,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999812 1 1 1 0 A 3 1 78 6254830 6254830 C A 1 0 0 0 0 1 0 0 0 6545 710 25 2 2 GPR153 1 6254830 Missense_Mutation SNP C C3N-01415_T 1484897 6254830 242701592 5 23752 PRAMEF6 0 . GRCh38 1 12939094 12939094 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1012C>A p.Leu338Ile p.L338I ENST00000376189 4/4 81 63 18 95 95 0 varscan-mutect PRAMEF6,missense_variant,p.Leu338Ile,ENST00000376189,NM_001010889.2;PRAMEF6,missense_variant,p.Leu338Ile,ENST00000415464,; T ENST00000376189 Transcript missense_variant 1098/1720 1012/1431 338/476 L/I Ctt/Att 1 -1 PRAMEF6 HGNC HGNC:30583 protein_coding YES CCDS30594.1 ENSP00000365360 Q5VXH4 UPI0000418E57 NM_001010889.2 tolerated(0.26) 4/4 Gene3D:3.80.10.10,PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 2 203 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 12939094 12939094 G T 1 0 0 0 0 1 0 0 0 12568 942 33 2 2 PRAMEF6 1 12939094 Missense_Mutation SNP G C3N-01415_T 6684264 12939094 236017328 6 23753 PRAMEF19 0 . GRCh38 1 13371197 13371197 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.111G>T p.= p.R37R ENST00000376101 2/3 699 642 57 729 729 0 varscan-mutect PRAMEF19,synonymous_variant,p.=,ENST00000376101,; A ENST00000376101 Transcript synonymous_variant 111/1233 111/1233 37/410 R cgG/cgT 1 -1 PRAMEF19 HGNC HGNC:24908 protein_coding YES ENSP00000365269 Q5SWL8 UPI0001661E5E 2/3 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF5,PIRSF_domain:PIRSF038286 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 13371197 13371197 C A 1 0 0 0 0 0 0 0 1 12561 610 22 2 2 PRAMEF19 1 13371197 Silent SNP C C3N-01415_T 432103 13371197 235585225 7 23754 COL16A1 0 . GRCh38 1 31689074 31689074 + Silent SNP G G C novel C3N-01415_T C3N-01415_N G G c.1632C>G p.= p.G544G ENST00000373672 24/71 283 224 59 269 269 0 strelka-varscan-mutect COL16A1,synonymous_variant,p.=,ENST00000373672,NM_001856.3;COL16A1,synonymous_variant,p.=,ENST00000373668,;COL16A1,synonymous_variant,p.=,ENST00000373667,;COL16A1,non_coding_transcript_exon_variant,,ENST00000482478,;COL16A1,non_coding_transcript_exon_variant,,ENST00000474000,;COL16A1,non_coding_transcript_exon_variant,,ENST00000529928,; C ENST00000373672 Transcript synonymous_variant 2149/5736 1632/4815 544/1604 G ggC/ggG 1 -1 COL16A1 HGNC HGNC:2193 protein_coding YES CCDS41297.1 ENSP00000362776 Q07092 UPI0000203DD1 NM_001856.3 24/71 hmmpanther:PTHR24023:SF372,hmmpanther:PTHR24023 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 78 31689074 31689074 G C 1 0 0 0 0 0 0 0 1 3461 1306 46 4 4 COL16A1 1 31689074 Silent SNP G C3N-01415_T 18317877 31689074 217267348 8 23755 CSMD2 0 . GRCh38 1 33540581 33540581 + Missense_Mutation SNP G G A rs146014963 C3N-01415_T C3N-01415_N G G c.9575C>T p.Ala3192Val p.A3192V ENST00000373381 60/71 277 239 38 329 329 0 strelka-varscan-mutect CSMD2,missense_variant,p.Ala3192Val,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Ala3152Val,ENST00000619121,;CSMD2,missense_variant,p.Ala3048Val,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Ala3048Val,ENST00000241312,; A ENST00000373381 Transcript missense_variant 9752/13698 9575/10896 3192/3631 A/V gCg/gTg rs146014963 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 deleterious(0) 60/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF371,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs146014963 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 33540581 33540581 G A 1 0 0 0 0 1 0 0 0 3746 1087 38 1 1 CSMD2 1 33540581 Missense_Mutation SNP G C3N-01415_T 1851507 33540581 215415841 9 23756 PSMB2 0 . GRCh38 1 35609300 35609300 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.394C>T p.His132Tyr p.H132Y ENST00000373237 4/6 141 120 21 144 144 0 strelka-varscan-mutect PSMB2,missense_variant,p.His15Tyr,ENST00000621781,NM_001199780.1;PSMB2,missense_variant,p.His132Tyr,ENST00000373237,NM_001199779.1,NM_002794.4;PSMB2,non_coding_transcript_exon_variant,,ENST00000630477,; A ENST00000373237 Transcript missense_variant 806/2701 394/606 132/201 H/Y Cac/Tac 1 -1 PSMB2 HGNC HGNC:9539 protein_coding YES CCDS394.1 ENSP00000362334 P49721 A0A140VJS6 UPI0000111E4C NM_001199779.1,NM_002794.4 deleterious(0) 4/6 Gene3D:3.60.20.10,Pfam_domain:PF00227,PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF6,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 35609300 35609300 G A 1 0 0 0 0 1 0 0 0 12828 1348 47 3 3 PSMB2 1 35609300 Missense_Mutation SNP G C3N-01415_T 2068719 35609300 213347122 10 23757 NASP 0 . GRCh38 1 45607473 45607473 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.562A>T p.Ile188Leu p.I188L ENST00000350030 6/15 210 180 30 234 234 0 strelka-varscan-mutect NASP,missense_variant,p.Ile188Leu,ENST00000350030,NM_002482.3;NASP,missense_variant,p.Ile124Leu,ENST00000537798,NM_001195193.1;NASP,missense_variant,p.Ile151Leu,ENST00000470768,;NASP,missense_variant,p.Ile124Leu,ENST00000527470,;NASP,intron_variant,,ENST00000351223,NM_152298.3;NASP,intron_variant,,ENST00000372052,;NASP,intron_variant,,ENST00000528238,;NASP,intron_variant,,ENST00000437901,;NASP,intron_variant,,ENST00000525515,;NASP,non_coding_transcript_exon_variant,,ENST00000534101,;NASP,upstream_gene_variant,,ENST00000530073,;NASP,3_prime_UTR_variant,,ENST00000453748,;NASP,3_prime_UTR_variant,,ENST00000529333,;NASP,intron_variant,,ENST00000437362,;NASP,intron_variant,,ENST00000527359,;NASP,upstream_gene_variant,,ENST00000481782,;NASP,downstream_gene_variant,,ENST00000464190,;NASP,downstream_gene_variant,,ENST00000531532,;NASP,downstream_gene_variant,,ENST00000528084,;AL355480.4,upstream_gene_variant,,ENST00000626823,; T ENST00000350030 Transcript missense_variant 649/3207 562/2367 188/788 I/L Ata/Tta 1 1 NASP HGNC HGNC:7644 protein_coding YES CCDS524.1 ENSP00000255120 P49321 UPI000012FDA0 NM_002482.3 tolerated_low_confidence(0.17) 6/15 hmmpanther:PTHR15081,hmmpanther:PTHR15081:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 45607473 45607473 A T 1 0 0 0 0 1 0 0 0 10181 449 16 4 4 NASP 1 45607473 Missense_Mutation SNP A C3N-01415_T 9998173 45607473 203348949 11 23758 GLIS1 0 . GRCh38 1 53529932 53529932 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.816C>A p.= p.A272A ENST00000312233 4/10 176 142 34 143 142 1 strelka-varscan-mutect GLIS1,synonymous_variant,p.=,ENST00000312233,NM_147193.2;GLIS1,synonymous_variant,p.=,ENST00000628545,; T ENST00000312233 Transcript synonymous_variant 1383/2812 816/1863 272/620 A gcC/gcA 1 -1 GLIS1 HGNC HGNC:29525 protein_coding YES CCDS582.1 ENSP00000309653 Q8NBF1 UPI000013F293 NM_147193.2 4/10 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF93,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 53529932 53529932 G T 1 0 0 0 0 0 0 0 1 6323 987 35 2 2 GLIS1 1 53529932 Silent SNP G C3N-01415_T 7922459 53529932 195426490 12 23759 MROH7 0 . GRCh38 1 54653756 54653756 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.830A>T p.Asn277Ile p.N277I ENST00000421030 3/24 302 240 62 380 379 1 strelka-varscan-mutect MROH7,missense_variant,p.Asn277Ile,ENST00000421030,NM_001039464.3;MROH7,missense_variant,p.Asn277Ile,ENST00000339553,;MROH7,missense_variant,p.Asn277Ile,ENST00000395690,;MROH7,intron_variant,,ENST00000409996,NM_001291332.1;MROH7,non_coding_transcript_exon_variant,,ENST00000472987,;MROH7,intron_variant,,ENST00000478097,;MROH7-TTC4,missense_variant,p.Asn277Ile,ENST00000425300,;MROH7-TTC4,missense_variant,p.Asn277Ile,ENST00000414150,;MROH7-TTC4,missense_variant,p.Asn277Ile,ENST00000606515,;MROH7,missense_variant,p.Asn277Ile,ENST00000413188,;MROH7,missense_variant,p.Asn277Ile,ENST00000422659,;MROH7,missense_variant,p.Asn277Ile,ENST00000440047,;MROH7,missense_variant,p.Asn277Ile,ENST00000438846,;MROH7,upstream_gene_variant,,ENST00000440217,; T ENST00000421030 Transcript missense_variant 1115/4329 830/3972 277/1323 N/I aAt/aTt 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 deleterious_low_confidence(0) 3/24 MODERATE 1 SNV 2 1 PASS rs1044440310 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 54653756 54653756 A T 1 0 0 0 0 1 0 0 0 9747 101 4 4 4 MROH7 1 54653756 Missense_Mutation SNP A C3N-01415_T 1123824 54653756 194302666 13 23760 HOOK1 0 . GRCh38 1 59872819 59872819 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.2041A>T p.Met681Leu p.M681L ENST00000371208 22/22 63 57 6 62 62 0 strelka-mutect HOOK1,missense_variant,p.Met681Leu,ENST00000371208,NM_015888.4;HOOK1,non_coding_transcript_exon_variant,,ENST00000465876,;HOOK1,non_coding_transcript_exon_variant,,ENST00000466803,;HOOK1,non_coding_transcript_exon_variant,,ENST00000491135,; T ENST00000371208 Transcript missense_variant 2298/5857 2041/2187 681/728 M/L Atg/Ttg 1 1 HOOK1 HGNC HGNC:19884 protein_coding YES CCDS612.1 ENSP00000360252 Q9UJC3 UPI0000071E61 NM_015888.4 tolerated(0.2) 22/22 Pfam_domain:PF05622,hmmpanther:PTHR18947,hmmpanther:PTHR18947:SF36 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -13.70554 0.9999988 1 1 1 0 T 3 4 78 59872819 59872819 A T 1 0 0 0 0 1 0 0 0 7176 333 12 4 4 HOOK1 1 59872819 Missense_Mutation SNP A C3N-01415_T 5219063 59872819 189083603 14 23761 LEPR 0 . GRCh38 1 65601549 65601549 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.1152G>T p.= p.V384V ENST00000349533 9/20 548 466 82 569 569 0 strelka-varscan-mutect LEPR,synonymous_variant,p.=,ENST00000349533,NM_002303.5;LEPR,synonymous_variant,p.=,ENST00000371060,NM_001003679.3;LEPR,synonymous_variant,p.=,ENST00000616738,NM_001198689.1;LEPR,synonymous_variant,p.=,ENST00000371059,NM_001003680.3,NM_001198687.1;LEPR,synonymous_variant,p.=,ENST00000344610,NM_001198688.1;LEPR,synonymous_variant,p.=,ENST00000371058,;LEPR,intron_variant,,ENST00000406510,;LEPR,non_coding_transcript_exon_variant,,ENST00000462765,; T ENST00000349533 Transcript synonymous_variant 1337/8227 1152/3498 384/1165 V gtG/gtT 1 1 LEPR HGNC HGNC:6554 protein_coding YES CCDS631.1 ENSP00000330393 P48357 UPI000014C37B NM_002303.5 9/20 PROSITE_profiles:PS50835,Pfam_domain:PF06328,Gene3D:2.60.40.10 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 65601549 65601549 G T 1 0 0 0 0 0 0 0 1 8636 1277 45 2 2 LEPR 1 65601549 Silent SNP G C3N-01415_T 5728730 65601549 183354873 15 23762 FPGT 0 . GRCh38 1 74204973 74204973 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.965G>T p.Gly322Val p.G322V ENST00000370898 4/4 305 283 22 392 392 0 strelka-varscan-mutect FPGT,missense_variant,p.Gly322Val,ENST00000370898,NM_003838.4;FPGT-TNNI3K,intron_variant,,ENST00000370895,;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,intron_variant,,ENST00000370899,NM_001199327.1;FPGT,intron_variant,,ENST00000534056,NM_001199328.2;FPGT,intron_variant,,ENST00000370894,NM_001199329.2;FPGT-TNNI3K,intron_variant,,ENST00000370893,;FPGT-TNNI3K,intron_variant,,ENST00000534632,;FPGT,downstream_gene_variant,,ENST00000467578,;FPGT,downstream_gene_variant,,ENST00000482102,;FPGT,downstream_gene_variant,,ENST00000472069,;FPGT,intron_variant,,ENST00000524915,;FPGT-TNNI3K,intron_variant,,ENST00000533006,;FPGT,downstream_gene_variant,,ENST00000529485,; T ENST00000370898 Transcript missense_variant 993/3254 965/1824 322/607 G/V gGa/gTa 1 1 FPGT HGNC HGNC:3825 protein_coding YES CCDS663.2 ENSP00000359935 A0A0A0MRP2 UPI0003348FC3 NM_003838.4 deleterious(0) 4/4 Pfam_domain:PF07959,PIRSF_domain:PIRSF036640,hmmpanther:PTHR15045 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 74204973 74204973 G T 1 0 0 0 0 1 0 0 0 5903 1174 41 2 2 FPGT 1 74204973 Missense_Mutation SNP G C3N-01415_T 8603424 74204973 174751449 16 23763 CRYZ 0 . GRCh38 1 74724767 74724767 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.55C>T p.Pro19Ser p.P19S ENST00000417775 3/10 259 235 24 305 303 2 strelka-varscan-mutect CRYZ,missense_variant,p.Pro19Ser,ENST00000417775,NM_001130042.1;CRYZ,missense_variant,p.Pro19Ser,ENST00000340866,NM_001889.3;CRYZ,missense_variant,p.Pro19Ser,ENST00000370871,NM_001130043.1;CRYZ,missense_variant,p.Pro19Ser,ENST00000370870,;CRYZ,missense_variant,p.Pro19Ser,ENST00000441120,;CRYZ,intron_variant,,ENST00000370872,NM_001134759.1; A ENST00000417775 Transcript missense_variant 560/2301 55/990 19/329 P/S Cca/Tca 1 -1 CRYZ HGNC HGNC:2419 protein_coding YES CCDS665.1 ENSP00000399805 Q08257 UPI0000001C81 NM_001130042.1 deleterious(0) 3/10 Gene3D:3.90.180.10,SMART_domains:SM00829,Superfamily_domains:SSF50129 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 74724767 74724767 G A 1 0 0 0 0 1 0 0 0 3724 1203 42 3 3 CRYZ 1 74724767 Missense_Mutation SNP G C3N-01415_T 519794 74724767 174231655 17 23764 ADGRL4 0 . GRCh38 1 79005120 79005120 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.122C>G p.Ala41Gly p.A41G ENST00000370742 2/15 210 174 36 259 259 0 strelka-varscan-mutect ADGRL4,missense_variant,p.Ala41Gly,ENST00000370742,NM_022159.3; C ENST00000370742 Transcript missense_variant 186/3527 122/2073 41/690 A/G gCc/gGc 1 -1 ADGRL4 HGNC HGNC:20822 protein_coding YES CCDS41352.1 ENSP00000359778 Q9HBW9 UPI00004561FF NM_022159.3 tolerated_low_confidence(0.74) 2/15 PROSITE_profiles:PS50026,hmmpanther:PTHR12011:SF59,hmmpanther:PTHR12011,Gene3D:2.10.25.10,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 79005120 79005120 G C 1 0 0 0 0 1 0 0 0 378 1203 42 4 4 ADGRL4 1 79005120 Missense_Mutation SNP G C3N-01415_T 4280353 79005120 169951302 18 23765 BARHL2 0 . GRCh38 1 90716879 90716879 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.317A>C p.Gln106Pro p.Q106P ENST00000370445 1/3 269 248 21 303 303 0 strelka-varscan-mutect BARHL2,missense_variant,p.Gln106Pro,ENST00000370445,NM_020063.1; G ENST00000370445 Transcript missense_variant 359/1979 317/1164 106/387 Q/P cAg/cCg 1 -1 BARHL2 HGNC HGNC:954 protein_coding YES CCDS730.1 ENSP00000359474 Q9NY43 UPI00001B50ED NM_020063.1 tolerated_low_confidence(0.41) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24330:SF4,hmmpanther:PTHR24330 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 90716879 90716879 T G 1 0 0 0 0 1 0 0 0 1466 1580 55 5 5 BARHL2 1 90716879 Missense_Mutation SNP T C3N-01415_T 11711759 90716879 158239543 19 23766 DPYD 0 . GRCh38 1 97691760 97691760 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.719T>A p.Val240Glu p.V240E ENST00000370192 7/23 503 441 62 532 532 0 strelka-varscan-mutect DPYD,missense_variant,p.Val240Glu,ENST00000370192,NM_000110.3;DPYD,non_coding_transcript_exon_variant,,ENST00000474241,; T ENST00000370192 Transcript missense_variant 820/4412 719/3078 240/1025 V/E gTa/gAa 1 -1 DPYD HGNC HGNC:3012 protein_coding YES CCDS30777.1 ENSP00000359211 Q12882 UPI00000727C7 NM_000110.3 tolerated(0.17) 7/23 hmmpanther:PTHR11938,hmmpanther:PTHR11938:SF5,Gene3D:3.50.50.60,Pfam_domain:PF07992,Superfamily_domains:SSF51971 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 97691760 97691760 A T 1 0 0 0 0 1 0 0 0 4560 391 14 4 4 DPYD 1 97691760 Missense_Mutation SNP A C3N-01415_T 6974881 97691760 151264662 20 23767 PLPPR5 0 . GRCh38 1 99004595 99004595 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.77T>C p.Leu26Pro p.L26P ENST00000263177 1/6 375 337 38 310 310 0 strelka-varscan-mutect PLPPR5,missense_variant,p.Leu26Pro,ENST00000370188,NM_001010861.2;PLPPR5,missense_variant,p.Leu26Pro,ENST00000263177,NM_001037317.1;RP5-896L10.1,non_coding_transcript_exon_variant,,ENST00000425113,;PLPPR5,upstream_gene_variant,,ENST00000534652,;RP11-234N17.1,upstream_gene_variant,,ENST00000457507,; G ENST00000263177 Transcript missense_variant 299/3288 77/966 26/321 L/P cTg/cCg 1 -1 PLPPR5 HGNC HGNC:31703 protein_coding YES CCDS30778.1 ENSP00000263177 Q32ZL2 UPI0000048D53 NM_001037317.1 deleterious(0) 1/6 hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF17,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs757739352 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 99004595 99004595 A G 1 0 0 0 0 1 0 0 0 12213 188 7 5 5 PLPPR5 1 99004595 Missense_Mutation SNP A C3N-01415_T 1312835 99004595 149951827 21 23768 GDAP2 0 . GRCh38 1 117920329 117920329 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.29T>C p.Phe10Ser p.F10S ENST00000369443 2/14 169 149 20 161 161 0 strelka-varscan-mutect GDAP2,missense_variant,p.Phe10Ser,ENST00000369443,NM_017686.3;GDAP2,missense_variant,p.Phe10Ser,ENST00000369442,NM_001135589.2;GDAP2,non_coding_transcript_exon_variant,,ENST00000494224,;GDAP2,upstream_gene_variant,,ENST00000493555,; G ENST00000369443 Transcript missense_variant 279/8828 29/1494 10/497 F/S tTt/tCt 1 -1 GDAP2 HGNC HGNC:18010 protein_coding YES CCDS897.1 ENSP00000358451 Q9NXN4 UPI0000071019 NM_017686.3 deleterious(0.04) 2/14 hmmpanther:PTHR11106,hmmpanther:PTHR11106:SF72 MODERATE 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 117920329 117920329 A G 1 0 0 0 0 1 0 0 0 6181 14 1 5 5 GDAP2 1 117920329 Missense_Mutation SNP A C3N-01415_T 18915734 117920329 131036093 22 23769 BCL9 0 . GRCh38 1 147613047 147613047 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.218C>T p.Pro73Leu p.P73L ENST00000234739 5/10 142 114 28 118 118 0 strelka-varscan-mutect BCL9,missense_variant,p.Pro73Leu,ENST00000234739,NM_004326.3;BCL9,intron_variant,,ENST00000473292,;BCL9,downstream_gene_variant,,ENST00000497938,; T ENST00000234739 Transcript missense_variant 958/6278 218/4281 73/1426 P/L cCt/cTt 1 1 BCL9 HGNC HGNC:1008 protein_coding YES CCDS30833.1 ENSP00000234739 O00512 A0A024QYY4 UPI000013C9B9 NM_004326.3 deleterious(0.03) 5/10 hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 78 147613047 147613047 C T 1 0 0 0 0 1 0 0 0 1528 681 24 3 3 BCL9 1 147613047 Missense_Mutation SNP C C3N-01415_T 29692718 147613047 101343375 23 23770 HIST2H2BE 0 . GRCh38 1 149886273 149886273 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.368C>A p.Thr123Asn p.T123N ENST00000369155 1/1 574 498 76 528 528 0 strelka-varscan-mutect HIST2H2BE,missense_variant,p.Thr123Asn,ENST00000369155,NM_003528.2;BOLA1,upstream_gene_variant,,ENST00000369153,;HIST2H2AB,downstream_gene_variant,,ENST00000331128,NM_175065.2;HIST2H2AC,upstream_gene_variant,,ENST00000331380,NM_003517.2; T ENST00000369155 Transcript missense_variant 380/2194 368/381 123/126 T/N aCc/aAc 1 -1 HIST2H2BE HGNC HGNC:4760 protein_coding YES CCDS936.1 ENSP00000358151 Q16778 UPI0000000C6F NM_003528.2 deleterious_low_confidence(0.02) 1/1 hmmpanther:PTHR23428,Gene3D:1.10.20.10,SMART_domains:SM00427,Superfamily_domains:SSF47113 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 149886273 149886273 G T 1 0 0 0 0 1 0 0 0 7067 1261 44 2 2 HIST2H2BE 1 149886273 Missense_Mutation SNP G C3N-01415_T 2273226 149886273 99070149 24 23771 TDRKH 0 . GRCh38 1 151778961 151778961 + Frame_Shift_Del DEL T T - novel C3N-01415_T C3N-01415_N T T c.607delA p.Arg203GlufsTer18 p.R203Efs*18 ENST00000368822 6/14 222 176 46 341 341 0 sindel-varindel TDRKH,frameshift_variant,p.Arg203GlufsTer18,ENST00000368822,;TDRKH,frameshift_variant,p.Arg203GlufsTer18,ENST00000368824,NM_001083965.1;TDRKH,frameshift_variant,p.Arg203GlufsTer18,ENST00000458431,NM_001083963.1;TDRKH,frameshift_variant,p.Arg199GlufsTer18,ENST00000368823,;TDRKH,frameshift_variant,p.Arg158GlufsTer18,ENST00000368825,NM_001083964.1;TDRKH,frameshift_variant,p.Arg203GlufsTer18,ENST00000368827,NM_006862.3;TDRKH,frameshift_variant,p.Arg203GlufsTer18,ENST00000440583,;TDRKH,downstream_gene_variant,,ENST00000526378,;TDRKH,non_coding_transcript_exon_variant,,ENST00000484421,;TDRKH,3_prime_UTR_variant,,ENST00000525790,;TDRKH,3_prime_UTR_variant,,ENST00000526413,;TDRKH,downstream_gene_variant,,ENST00000486986,;TDRKH,downstream_gene_variant,,ENST00000494725,;TDRKH,downstream_gene_variant,,ENST00000530202,;TDRKH,downstream_gene_variant,,ENST00000463553,; - ENST00000368822 Transcript frameshift_variant 1241/3093 607/1686 203/561 R/X Aga/ga 1 -1 TDRKH HGNC HGNC:11713 protein_coding YES CCDS41394.1 ENSP00000357812 Q9Y2W6 UPI0000204267 6/14 hmmpanther:PTHR22948,Gene3D:3.30.1370.10,Superfamily_domains:SSF54791 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 151778961 151778961 T - 1 0 1 0 1 0 0 0 0 16147 1559 54 0 0 TDRKH 1 151778961 Frame_Shift_Del DEL T C3N-01415_T 1892688 151778961 97177461 25 23772 FLG 0 . GRCh38 1 152308746 152308746 + Missense_Mutation SNP C C T rs758506209 C3N-01415_T C3N-01415_N C C c.6140G>A p.Ser2047Asn p.S2047N ENST00000368799 3/3 1277 1186 91 1284 1283 1 varscan-mutect FLG,missense_variant,p.Ser2047Asn,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 6176/12747 6140/12186 2047/4061 S/N aGt/aAt rs758506209 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.04) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 PASS rs758506209 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 152308746 152308746 C T 1 0 0 0 0 1 0 0 0 5784 565 20 3 3 FLG 1 152308746 Missense_Mutation SNP C C3N-01415_T 529785 152308746 96647676 26 23773 IVL 0 . GRCh38 1 152910326 152910326 + Nonsense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.529G>T p.Glu177Ter p.E177* ENST00000368764 2/2 192 173 19 189 189 0 varscan-mutect IVL,stop_gained,p.Glu177Ter,ENST00000368764,NM_005547.2; T ENST00000368764 Transcript stop_gained 593/2153 529/1758 177/585 E/* Gag/Tag 1 1 IVL HGNC HGNC:6187 protein_coding YES CCDS1030.1 ENSP00000357753 P07476 UPI000013E24A NM_005547.2 2/2 Pfam_domain:PF00904,Low_complexity_(Seg):seg HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 152910326 152910326 G T 1 0 0 0 0 0 1 0 0 7835 1175 41 2 2 IVL 1 152910326 Nonsense_Mutation SNP G C3N-01415_T 601580 152910326 96046096 27 23774 CHRNB2 0 . GRCh38 1 154571351 154571351 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.528G>C p.Trp176Cys p.W176C ENST00000368476 5/6 666 587 79 603 603 0 strelka-varscan-mutect CHRNB2,missense_variant,p.Trp176Cys,ENST00000368476,NM_000748.2;CHRNB2,missense_variant,p.Trp178Cys,ENST00000637900,;CHRNB2,missense_variant,p.Trp176Cys,ENST00000636034,;CHRNB2,downstream_gene_variant,,ENST00000636695,; C ENST00000368476 Transcript missense_variant 792/5867 528/1509 176/502 W/C tgG/tgC 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 deleterious(0.01) 5/6 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF80,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 154571351 154571351 G C 1 0 0 0 0 1 0 0 0 3151 1183 41 4 4 CHRNB2 1 154571351 Missense_Mutation SNP G C3N-01415_T 1661025 154571351 94385071 28 23775 CD1D 0 . GRCh38 1 158181540 158181540 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.147G>C p.Trp49Cys p.W49C ENST00000368171 3/7 419 378 41 339 339 0 strelka-mutect CD1D,missense_variant,p.Trp49Cys,ENST00000368171,NM_001766.3;ELL2P1,upstream_gene_variant,,ENST00000413990,; C ENST00000368171 Transcript missense_variant 646/2253 147/1008 49/335 W/C tgG/tgC 1 1 CD1D HGNC HGNC:1637 protein_coding YES CCDS1173.1 ENSP00000357153 P15813 UPI00000012B1 NM_001766.3 deleterious(0) 3/7 Gene3D:3.30.500.10,Pfam_domain:PF16497,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF175,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 158181540 158181540 G C 1 0 0 0 0 1 0 0 0 2680 1212 42 4 4 CD1D 1 158181540 Missense_Mutation SNP G C3N-01415_T 3610189 158181540 90774882 29 23776 OR6P1 0 . GRCh38 1 158563544 158563544 + Missense_Mutation SNP G G T rs373879280 C3N-01415_T C3N-01415_N G G c.61C>A p.Pro21Thr p.P21T ENST00000334632 1/1 337 295 42 347 347 0 strelka-varscan-mutect OR6P1,missense_variant,p.Pro21Thr,ENST00000334632,NM_001160325.1; T ENST00000334632 Transcript missense_variant 61/954 61/954 21/317 P/T Cct/Act rs373879280 1 -1 OR6P1 HGNC HGNC:15036 protein_coding YES CCDS53391.1 ENSP00000334721 Q8NGX9 A0A126GV72 UPI000004B1FF NM_001160325.1 tolerated(0.43) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs373879280 . 0 204 0 4 2 0 0 0 -16.5569 0.9401791 1 1 1 0 T 3 4 78 158563544 158563544 G T 1 0 0 0 0 1 0 0 0 11277 1203 42 2 2 OR6P1 1 158563544 Missense_Mutation SNP G C3N-01415_T 382004 158563544 90392878 30 23777 SPTA1 0 . GRCh38 1 158626941 158626941 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.5731C>A p.Pro1911Thr p.P1911T ENST00000368147 41/52 538 412 126 524 524 0 strelka-varscan-mutect SPTA1,missense_variant,p.Pro1911Thr,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,; T ENST00000368147 Transcript missense_variant 5912/7999 5731/7260 1911/2419 P/T Cct/Act 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.42) 41/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs1355504062 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 158626941 158626941 G T 1 0 0 0 0 1 0 0 0 15472 1232 43 2 2 SPTA1 1 158626941 Missense_Mutation SNP G C3N-01415_T 63397 158626941 90329481 31 23778 PYHIN1 0 . GRCh38 1 158939183 158939183 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.515C>A p.Ala172Asp p.A172D ENST00000368140 4/9 174 137 37 163 163 0 strelka-varscan-mutect PYHIN1,missense_variant,p.Ala172Asp,ENST00000368140,NM_152501.4;PYHIN1,missense_variant,p.Ala163Asp,ENST00000368138,NM_198928.4;PYHIN1,missense_variant,p.Ala172Asp,ENST00000368135,;PYHIN1,missense_variant,p.Ala172Asp,ENST00000392254,NM_198929.4;PYHIN1,missense_variant,p.Ala163Asp,ENST00000392252,NM_198930.3;PYHIN1,downstream_gene_variant,,ENST00000458222,;PYHIN1,upstream_gene_variant,,ENST00000485134,; A ENST00000368140 Transcript missense_variant 760/2083 515/1479 172/492 A/D gCc/gAc 1 1 PYHIN1 HGNC HGNC:28894 protein_coding YES CCDS1178.1 ENSP00000357122 Q6K0P9 UPI0000225618 NM_152501.4 deleterious(0.04) 4/9 hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF14 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999969 1 1 1 0 A 3 1 78 158939183 158939183 C A 1 0 0 0 0 1 0 0 0 13019 739 26 2 2 PYHIN1 1 158939183 Missense_Mutation SNP C C3N-01415_T 312242 158939183 90017239 32 23779 APCS 0 . GRCh38 1 159588614 159588614 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.578A>T p.Gln193Leu p.Q193L ENST00000255040 2/2 295 210 85 325 325 0 strelka-varscan-mutect APCS,missense_variant,p.Gln193Leu,ENST00000255040,NM_001639.3; T ENST00000255040 Transcript missense_variant 675/926 578/672 193/223 Q/L cAg/cTg 1 1 APCS HGNC HGNC:584 protein_coding YES CCDS1186.1 ENSP00000255040 P02743 V9HWP0 UPI0000135533 NM_001639.3 tolerated(0.72) 2/2 hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF99,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 159588614 159588614 A T 1 0 0 0 0 1 0 0 0 887 188 7 4 4 APCS 1 159588614 Missense_Mutation SNP A C3N-01415_T 649431 159588614 89367808 33 23780 IGSF9 0 . GRCh38 1 159929649 159929649 + Missense_Mutation SNP C C T C3N-01415_T C3N-01415_N C C c.2315G>A p.Arg772His p.R772H ENST00000368094 17/21 108 92 16 96 96 0 strelka-varscan-mutect IGSF9,missense_variant,p.Arg772His,ENST00000368094,NM_001135050.1;IGSF9,missense_variant,p.Arg756His,ENST00000361509,NM_020789.3;IGSF9,intron_variant,,ENST00000611023,;TAGLN2,upstream_gene_variant,,ENST00000368097,NM_003564.2;TAGLN2,upstream_gene_variant,,ENST00000397334,;IGSF9,non_coding_transcript_exon_variant,,ENST00000493195,;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102,;IGSF9,non_coding_transcript_exon_variant,,ENST00000496645,;TAGLN2,upstream_gene_variant,,ENST00000478033,; T ENST00000368094 Transcript missense_variant 2513/4044 2315/3540 772/1179 R/H cGc/cAc COSM4864722,COSM898103 1 -1 IGSF9 HGNC HGNC:18132 protein_coding YES CCDS44254.1 ENSP00000357073 Q9P2J2 UPI000004A10B NM_001135050.1 tolerated(0.07) 17/21 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF708,Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1340975643 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 159929649 159929649 C T 1 0 0 0 0 1 0 0 0 7513 768 27 1 1 IGSF9 1 159929649 Missense_Mutation SNP C C3N-01415_T 341035 159929649 89026773 34 23781 ILDR2 0 . GRCh38 1 166921216 166921216 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.1375C>G p.Arg459Gly p.R459G ENST00000271417 9/10 151 102 49 147 146 1 strelka-varscan ILDR2,missense_variant,p.Arg459Gly,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Arg440Gly,ENST00000529071,;ILDR2,missense_variant,p.Arg400Gly,ENST00000528703,;ILDR2,missense_variant,p.Arg351Gly,ENST00000526687,;ILDR2,missense_variant,p.Arg332Gly,ENST00000525740,;ILDR2,intron_variant,,ENST00000469934,;ILDR2,intron_variant,,ENST00000529387,;ILDR2,upstream_gene_variant,,ENST00000614979,; C ENST00000271417 Transcript missense_variant 1431/13140 1375/1920 459/639 R/G Cgc/Ggc 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 deleterious(0.03) 9/10 hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 166921216 166921216 G C 1 0 0 0 0 1 0 0 0 7613 1087 38 4 4 ILDR2 1 166921216 Missense_Mutation SNP G C3N-01415_T 6991567 166921216 82035206 35 23782 F5 0 . GRCh38 1 169540392 169540392 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.4698C>A p.Asn1566Lys p.N1566K ENST00000367797 13/25 385 316 69 425 425 0 strelka-varscan-mutect F5,missense_variant,p.Asn1571Lys,ENST00000367796,;F5,missense_variant,p.Asn1566Lys,ENST00000367797,NM_000130.4; T ENST00000367797 Transcript missense_variant 4900/7024 4698/6675 1566/2224 N/K aaC/aaA 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 tolerated(0.13) 13/25 PIRSF_domain:PIRSF000354 MODERATE 1 SNV 1 1 PASS rs921390554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 169540392 169540392 G T 1 0 0 0 0 1 0 0 0 5216 1368 48 2 2 F5 1 169540392 Missense_Mutation SNP G C3N-01415_T 2619176 169540392 79416030 36 23783 TNN 0 . GRCh38 1 175083770 175083770 + Missense_Mutation SNP G G T rs777266284 C3N-01415_T C3N-01415_N G G c.1069G>T p.Ala357Ser p.A357S ENST00000239462 5/19 160 139 21 162 162 0 strelka-varscan-mutect TNN,missense_variant,p.Ala357Ser,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Ala357Ser,ENST00000621086,;TNN,missense_variant,p.Ala357Ser,ENST00000622870,; T ENST00000239462 Transcript missense_variant 1182/5008 1069/3900 357/1299 A/S Gcc/Tcc rs777266284 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 tolerated(0.47) 5/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS rs777266284 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 175083770 175083770 G T 1 0 0 0 0 1 0 0 0 16796 1319 46 2 2 TNN 1 175083770 Missense_Mutation SNP G C3N-01415_T 5543378 175083770 73872652 37 23784 TNN 0 . GRCh38 1 175083842 175083842 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.1141T>A p.Tyr381Asn p.Y381N ENST00000239462 5/19 336 297 39 289 288 1 strelka-varscan-mutect TNN,missense_variant,p.Tyr381Asn,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Tyr381Asn,ENST00000621086,;TNN,missense_variant,p.Tyr381Asn,ENST00000622870,; A ENST00000239462 Transcript missense_variant 1254/5008 1141/3900 381/1299 Y/N Tac/Aac 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 deleterious(0) 5/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 175083842 175083842 T A 1 0 0 0 0 1 0 0 0 16796 1522 53 4 4 TNN 1 175083842 Missense_Mutation SNP T C3N-01415_T 72 175083842 73872580 38 23785 TNN 0 . GRCh38 1 175136907 175136907 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.3514T>A p.Tyr1172Asn p.Y1172N ENST00000239462 17/19 319 283 36 291 291 0 strelka-varscan-mutect TNN,missense_variant,p.Tyr1172Asn,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Tyr995Asn,ENST00000621086,;TNN,missense_variant,p.Tyr995Asn,ENST00000622870,; A ENST00000239462 Transcript missense_variant 3627/5008 3514/3900 1172/1299 Y/N Tat/Aat 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 deleterious(0) 17/19 PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Pfam_domain:PF00147,Gene3D:3.90.215.10,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 2 1 PASS rs1227376424 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 175136907 175136907 T A 1 0 0 0 0 1 0 0 0 16796 1522 53 4 4 TNN 1 175136907 Missense_Mutation SNP T C3N-01415_T 53065 175136907 73819515 39 23786 TNR 0 . GRCh38 1 175367254 175367254 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.2007C>A p.= p.V669V ENST00000367674 10/23 309 290 19 308 308 0 strelka-varscan-mutect TNR,synonymous_variant,p.=,ENST00000367674,;TNR,synonymous_variant,p.=,ENST00000263525,NM_003285.2; T ENST00000367674 Transcript synonymous_variant 2716/12949 2007/4077 669/1358 V gtC/gtA 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 10/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 175367254 175367254 G T 1 0 0 0 0 0 0 0 1 16811 1277 45 2 2 TNR 1 175367254 Silent SNP G C3N-01415_T 230347 175367254 73589168 40 23787 CEP350 0 . GRCh38 1 180092903 180092903 + Missense_Mutation SNP G G C rs532994014 C3N-01415_T C3N-01415_N G G c.6798G>C p.Leu2266Phe p.L2266F ENST00000367607 34/38 287 243 44 281 281 0 strelka-varscan-mutect CEP350,missense_variant,p.Leu2266Phe,ENST00000367607,NM_014810.4;CEP350,missense_variant,p.Leu441Phe,ENST00000429851,;CEP350,upstream_gene_variant,,ENST00000417046,;CEP350,non_coding_transcript_exon_variant,,ENST00000490141,;CEP350,upstream_gene_variant,,ENST00000496440,;CEP350,downstream_gene_variant,,ENST00000484356,; C ENST00000367607 Transcript missense_variant 7216/13491 6798/9354 2266/3117 L/F ttG/ttC rs532994014 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 tolerated(0.68) 34/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS rs532994014 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 180092903 180092903 G C 1 0 0 0 0 1 0 0 0 2972 1281 45 4 4 CEP350 1 180092903 Missense_Mutation SNP G C3N-01415_T 4725649 180092903 68863519 41 23788 DHX9 0 . GRCh38 1 182858814 182858814 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.982G>T p.Gly328Cys p.G328C ENST00000367549 10/28 347 314 33 378 378 0 strelka-varscan-mutect DHX9,missense_variant,p.Gly328Cys,ENST00000367549,NM_001357.4;DHX9,downstream_gene_variant,,ENST00000483416,;DHX9,upstream_gene_variant,,ENST00000477802,;DHX9,downstream_gene_variant,,ENST00000479271,; T ENST00000367549 Transcript missense_variant 1092/4240 982/3813 328/1270 G/C Ggt/Tgt 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 deleterious(0.03) 10/28 hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF119 MODERATE 1 SNV 1 1 PASS rs1359583792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 182858814 182858814 G T 1 0 0 0 0 1 0 0 0 4320 1232 43 2 2 DHX9 1 182858814 Missense_Mutation SNP G C3N-01415_T 2765911 182858814 66097608 42 23789 LGR6 0 . GRCh38 1 202310239 202310239 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.1449G>T p.= p.G483G ENST00000367278 16/18 243 186 57 225 224 1 strelka-varscan LGR6,synonymous_variant,p.=,ENST00000367278,NM_001017403.1;LGR6,synonymous_variant,p.=,ENST00000255432,NM_021636.2;LGR6,synonymous_variant,p.=,ENST00000439764,NM_001017404.1;LGR6,downstream_gene_variant,,ENST00000423542,;LGR6,downstream_gene_variant,,ENST00000308543,;LGR6,3_prime_UTR_variant,,ENST00000487787,; T ENST00000367278 Transcript synonymous_variant 1538/3567 1449/2904 483/967 G ggG/ggT 1 1 LGR6 HGNC HGNC:19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 16/18 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 202310239 202310239 G T 1 0 0 0 0 0 0 0 1 8668 1161 41 2 2 LGR6 1 202310239 Silent SNP G C3N-01415_T 19451425 202310239 46646183 43 23790 SERTAD4 0 . GRCh38 1 210237986 210237986 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.26G>A p.Arg9Lys p.R9K ENST00000367012 2/4 344 250 94 331 331 0 strelka-varscan SERTAD4,missense_variant,p.Arg9Lys,ENST00000367012,NM_019605.3;SERTAD4-AS1,upstream_gene_variant,,ENST00000437764,;SERTAD4-AS1,upstream_gene_variant,,ENST00000480052,;SERTAD4,non_coding_transcript_exon_variant,,ENST00000490620,;SERTAD4,non_coding_transcript_exon_variant,,ENST00000482421,;SERTAD4,non_coding_transcript_exon_variant,,ENST00000483884,; A ENST00000367012 Transcript missense_variant 256/5219 26/1071 9/356 R/K aGa/aAa 1 1 SERTAD4 HGNC HGNC:25236 protein_coding YES CCDS1494.1 ENSP00000355979 Q9NUC0 UPI0000070BBE NM_019605.3 tolerated(0.17) 2/4 hmmpanther:PTHR14272,hmmpanther:PTHR14272:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 210237986 210237986 G A 1 0 0 0 0 1 0 0 0 14399 942 33 3 3 SERTAD4 1 210237986 Missense_Mutation SNP G C3N-01415_T 7927747 210237986 38718436 44 23791 PPP2R5A 0 . GRCh38 1 212329213 212329213 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.260C>G p.Ser87Cys p.S87C ENST00000261461 2/13 191 169 22 215 215 0 strelka-varscan PPP2R5A,missense_variant,p.Ser87Cys,ENST00000261461,NM_006243.3;PPP2R5A,missense_variant,p.Ser30Cys,ENST00000537030,NM_001199756.1;RP11-384C4.7,intron_variant,,ENST00000442146,;PPP2R5A,non_coding_transcript_exon_variant,,ENST00000498129,;PPP2R5A,non_coding_transcript_exon_variant,,ENST00000479259,; G ENST00000261461 Transcript missense_variant 834/3128 260/1461 87/486 S/C tCt/tGt 1 1 PPP2R5A HGNC HGNC:9309 protein_coding YES CCDS1503.1 ENSP00000261461 Q15172 UPI0000124E90 NM_006243.3 tolerated(0.12) 2/13 hmmpanther:PTHR10257,hmmpanther:PTHR10257:SF6,Pfam_domain:PF01603,PIRSF_domain:PIRSF028043,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 212329213 212329213 C G 1 0 0 0 0 1 0 0 0 12514 913 32 4 4 PPP2R5A 1 212329213 Missense_Mutation SNP C C3N-01415_T 2091227 212329213 36627209 45 23792 USH2A 0 . GRCh38 1 216327596 216327596 + Silent SNP T T A rs759081029 C3N-01415_T C3N-01415_N T T c.843A>T p.= p.T281T ENST00000307340 5/72 445 393 52 488 488 0 strelka-varscan USH2A,synonymous_variant,p.=,ENST00000307340,NM_206933.2;USH2A,synonymous_variant,p.=,ENST00000366942,NM_007123.5; A ENST00000307340 Transcript synonymous_variant 1230/18883 843/15609 281/5202 T acA/acT rs759081029 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 5/72 Gene3D:2.60.120.200,Pfam_domain:PF13385,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00136,SMART_domains:SM00560,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 216327596 216327596 T A 1 0 0 0 0 0 0 0 1 17570 1826 63 4 4 USH2A 1 216327596 Silent SNP T C3N-01415_T 3998383 216327596 32628826 46 23793 USH2A 0 . GRCh38 1 216422242 216422242 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.95A>T p.Glu32Val p.E32V ENST00000307340 2/72 164 141 23 211 211 0 strelka-varscan USH2A,missense_variant,p.Glu32Val,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Glu32Val,ENST00000366942,NM_007123.5; A ENST00000307340 Transcript missense_variant 482/18883 95/15609 32/5202 E/V gAg/gTg 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.29) 2/72 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 216422242 216422242 T A 1 0 0 0 0 1 0 0 0 17570 1551 54 4 4 USH2A 1 216422242 Missense_Mutation SNP T C3N-01415_T 94646 216422242 32534180 47 23794 LEFTY1 0 . GRCh38 1 225888965 225888965 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.102G>T p.Gln34His p.Q34H ENST00000272134 1/4 121 104 17 109 109 0 strelka-varscan LEFTY1,missense_variant,p.Gln34His,ENST00000272134,NM_020997.3;RP4-559A3.7,intron_variant,,ENST00000432920,;LEFTY1,intron_variant,,ENST00000492457,; A ENST00000272134 Transcript missense_variant 182/1626 102/1101 34/366 Q/H caG/caT 1 -1 LEFTY1 HGNC HGNC:6552 protein_coding YES CCDS1548.1 ENSP00000272134 O75610 UPI000003721B NM_020997.3 tolerated(0.05) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11848:SF167,hmmpanther:PTHR11848,PIRSF_domain:PIRSF037402,Prints_domain:PR01427 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 78 225888965 225888965 C A 1 0 0 0 0 1 0 0 0 8623 796 28 2 2 LEFTY1 1 225888965 Missense_Mutation SNP C C3N-01415_T 9466723 225888965 23067457 48 23795 SDE2 0 . GRCh38 1 225999303 225999303 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.10G>A p.Ala4Thr p.A4T ENST00000272091 1/7 144 109 35 104 103 1 strelka-varscan SDE2,missense_variant,p.Ala4Thr,ENST00000272091,NM_152608.3; T ENST00000272091 Transcript missense_variant 29/3975 10/1356 4/451 A/T Gcc/Acc 1 -1 SDE2 HGNC HGNC:26643 protein_coding YES CCDS41473.1 ENSP00000272091 Q6IQ49 UPI0000204007 NM_152608.3 tolerated_low_confidence(0.36) 1/7 hmmpanther:PTHR12786:SF1,hmmpanther:PTHR12786 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 225999303 225999303 C T 1 0 0 0 0 1 0 0 0 14231 739 26 3 3 SDE2 1 225999303 Missense_Mutation SNP C C3N-01415_T 110338 225999303 22957119 49 23796 NID1 0 . GRCh38 1 236025894 236025894 + Splice_Site SNP A A T rs756600846 C3N-01415_T C3N-01415_N A A c.1984+2T>A p.X662_splice ENST00000264187 210 181 29 212 212 0 strelka-varscan NID1,splice_donor_variant,,ENST00000264187,NM_002508.2;NID1,splice_donor_variant,,ENST00000366595,; T ENST00000264187 Transcript splice_donor_variant -/5864 1984/3744 662/1247 rs756600846 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 8/19 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 78 236025894 236025894 A T 1 0 0 0 0 0 0 1 0 10447 405 14 4 4 NID1 1 236025894 Splice_Site SNP A C3N-01415_T 10026591 236025894 12930528 50 23797 MTR 0 . GRCh38 1 236825351 236825352 + Frame_Shift_Ins INS - - T novel C3N-01415_T C3N-01415_N - - c.882dupT p.Gly295TrpfsTer2 p.G295Wfs*2 ENST00000366577 10/33 451 404 47 432 432 0 sindel-varindel-pindel MTR,frameshift_variant,p.Gly295TrpfsTer2,ENST00000366577,NM_000254.2;MTR,frameshift_variant,p.Gly295TrpfsTer2,ENST00000535889,NM_001291939.1;MTR,non_coding_transcript_exon_variant,,ENST00000463959,;RPSAP21,downstream_gene_variant,,ENST00000414293,; T ENST00000366577 Transcript frameshift_variant 1273-1274/10529 879-880/3798 293-294/1265 -/X -/T 1 1 MTR HGNC HGNC:7468 protein_coding YES CCDS1614.1 ENSP00000355536 Q99707 UPI0000036BC4 NM_000254.2 10/33 PROSITE_profiles:PS50970,hmmpanther:PTHR21091,hmmpanther:PTHR21091:SF112,Pfam_domain:PF02574,TIGRFAM_domain:TIGR02082,PIRSF_domain:PIRSF000381,Gene3D:3.20.20.330,Superfamily_domains:SSF82282 HIGH 1 insertion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 78 236825351 236825351 - T 1 0 1 1 0 0 0 0 0 9944 668 24 0 0 MTR 1 236825351 Frame_Shift_Ins INS - C3N-01415_T 799457 236825351 12131071 51 23798 RGS7 0 . GRCh38 1 240813690 240813690 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.884C>T p.Pro295Leu p.P295L ENST00000366565 13/18 648 563 85 617 617 0 strelka-varscan RGS7,missense_variant,p.Pro295Leu,ENST00000366565,NM_002924.5;RGS7,missense_variant,p.Pro295Leu,ENST00000366564,NM_001282778.1;RGS7,missense_variant,p.Pro295Leu,ENST00000366563,NM_001282775.1;RGS7,missense_variant,p.Pro242Leu,ENST00000348120,NM_001282773.1;RGS7,missense_variant,p.Pro126Leu,ENST00000440928,; A ENST00000366565 Transcript missense_variant 1266/2494 884/1464 295/487 P/L cCg/cTg COSM1668605,COSM1668606,COSM1668607 1 -1 RGS7 HGNC HGNC:10003 protein_coding YES CCDS31071.1 ENSP00000355523 P49802 UPI000040E182 NM_002924.5 tolerated(0.06) 13/18 hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF26,Pfam_domain:PF00631,Gene3D:4.10.260.10,SMART_domains:SM00224,SMART_domains:SM01224,Superfamily_domains:SSF48670 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 240813690 240813690 G A 1 0 0 0 0 1 0 0 0 13481 1116 39 1 1 RGS7 1 240813690 Missense_Mutation SNP G C3N-01415_T 3988339 240813690 8142732 52 23799 OR14K1 0 . GRCh38 1 247739332 247739332 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.718G>T p.Val240Leu p.V240L ENST00000283225 1/1 341 248 93 412 411 1 strelka-varscan OR14K1,missense_variant,p.Val240Leu,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; T ENST00000283225 Transcript missense_variant 718/945 718/945 240/314 V/L Gtg/Ttg COSM5296434 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 247739332 247739332 G T 1 0 0 0 0 1 0 0 0 11026 1377 48 2 2 OR14K1 1 247739332 Missense_Mutation SNP G C3N-01415_T 6925642 247739332 1217090 53 23800 OR2M3 0 . GRCh38 1 248203988 248203988 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.921G>T p.Lys307Asn p.K307N ENST00000456743 1/1 318 285 33 356 355 1 strelka-varscan OR2M3,missense_variant,p.Lys307Asn,ENST00000456743,NM_001004689.1; T ENST00000456743 Transcript missense_variant 921/939 921/939 307/312 K/N aaG/aaT 1 1 OR2M3 HGNC HGNC:8269 protein_coding YES CCDS31107.1 ENSP00000389625 Q8NG83 A0A126GV67 UPI000004B234 NM_001004689.1 deleterious(0.05) 1/1 hmmpanther:PTHR26453:SF28,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 248203988 248203988 G T 1 0 0 0 0 1 0 0 0 11089 991 35 2 2 OR2M3 1 248203988 Missense_Mutation SNP G C3N-01415_T 464656 248203988 752434 54 23801 OR2G6 0 . GRCh38 1 248521838 248521838 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.192C>A p.Ser64Arg p.S64R ENST00000343414 1/1 423 369 54 427 427 0 strelka-varscan OR2G6,missense_variant,p.Ser64Arg,ENST00000343414,NM_001013355.1; A ENST00000343414 Transcript missense_variant 192/951 192/951 64/316 S/R agC/agA 1 1 OR2G6 HGNC HGNC:27019 protein_coding YES CCDS31119.1 ENSP00000341291 Q5TZ20 A0A126GW53 UPI0000237253 NM_001013355.1 tolerated(0.09) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF110,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 248521838 248521838 C A 1 0 0 0 0 1 0 0 0 11078 709 25 2 2 OR2G6 1 248521838 Missense_Mutation SNP C C3N-01415_T 317850 248521838 434584 55 23802 DDX1 0 . GRCh38 2 15617267 15617267 + Silent SNP G G T rs150852999 C3N-01415_T C3N-01415_N G G c.1041G>T p.= p.P347P ENST00000381341 16/27 191 170 21 238 238 0 strelka-varscan DDX1,synonymous_variant,p.=,ENST00000381341,;DDX1,synonymous_variant,p.=,ENST00000233084,NM_004939.2;DDX1,synonymous_variant,p.=,ENST00000617198,;DDX1,synonymous_variant,p.=,ENST00000621973,;DDX1,upstream_gene_variant,,ENST00000459706,;DDX1,upstream_gene_variant,,ENST00000470674,; T ENST00000381341 Transcript synonymous_variant 1430/2817 1041/2223 347/740 P ccG/ccT rs150852999 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 16/27 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF307,hmmpanther:PTHR24031,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 15617267 15617267 G T 1 0 0 0 0 0 0 0 1 4145 1103 39 1 1 DDX1 2 15617267 Silent SNP G C3N-01415_T 15617267 226576262 56 23803 NT5C1B 0 . GRCh38 2 18584863 18584863 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.554T>A p.Leu185Gln p.L185Q ENST00000359846 5/10 107 74 33 109 109 0 strelka-varscan NT5C1B,missense_variant,p.Leu125Gln,ENST00000304081,NM_033253.3;NT5C1B,missense_variant,p.Leu185Gln,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Leu185Gln,ENST00000532967,NM_001199104.1;NT5C1B-RDH14,missense_variant,p.Leu127Gln,ENST00000444297,NM_001199103.1;NT5C1B,missense_variant,p.Leu202Gln,ENST00000416783,;NT5C1B,upstream_gene_variant,,ENST00000418427,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,missense_variant,p.Cys103Ser,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,; T ENST00000359846 Transcript missense_variant 632/2475 554/1833 185/610 L/Q cTg/cAg 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 tolerated_low_confidence(0.36) 5/10 hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 18584863 18584863 A T 1 0 0 0 0 1 0 0 0 10749 188 7 4 4 NT5C1B 2 18584863 Missense_Mutation SNP A C3N-01415_T 2967596 18584863 223608666 57 23804 EMILIN1 0 . GRCh38 2 27082918 27082918 + Frame_Shift_Del DEL G G - rs557123421 C3N-01415_T C3N-01415_N G G c.1353delG p.Leu452CysfsTer5 p.L452Cfs*5 ENST00000380320 4/8 85 65 20 89 89 0 sindel-varindel-pindel EMILIN1,frameshift_variant,p.Leu452CysfsTer5,ENST00000380320,NM_007046.3;KHK,upstream_gene_variant,,ENST00000260599,NM_000221.2;KHK,upstream_gene_variant,,ENST00000260598,NM_006488.2;EMILIN1,upstream_gene_variant,,ENST00000433140,;KHK,upstream_gene_variant,,ENST00000429697,;KHK,upstream_gene_variant,,ENST00000490823,; - ENST00000380320 Transcript frameshift_variant 1846/3943 1347/3051 449/1016 L/X ttG/tt rs557123421,COSM2913095,COSM368731 1 1 EMILIN1 HGNC HGNC:19880 protein_coding YES CCDS1733.1 ENSP00000369677 A0A0C4DFX3 UPI0000073B0E NM_007046.3 4/8 0,1,1 HIGH 1 deletion 1 6 0,1,1 1 PASS . . 0 158 39 13 0 0 0 0 -20 0.4512338 0 1 0 0 - 7 5 78 27082918 27082918 G - 1 0 1 0 1 0 0 0 0 4936 1339 47 0 0 EMILIN1 2 27082918 Frame_Shift_Del DEL G C3N-01415_T 8498055 27082918 215110611 58 23805 SLC5A6 0 . GRCh38 2 27201003 27201003 + Missense_Mutation SNP C C A rs764448030 C3N-01415_T C3N-01415_N C C c.1759G>T p.Gly587Cys p.G587C ENST00000310574 16/17 68 48 20 59 59 0 strelka-varscan SLC5A6,missense_variant,p.Gly587Cys,ENST00000310574,NM_021095.2;SLC5A6,missense_variant,p.Gly587Cys,ENST00000408041,;SLC5A6,downstream_gene_variant,,ENST00000461319,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000488743,;SLC5A6,non_coding_transcript_exon_variant,,ENST00000461757,;SLC5A6,downstream_gene_variant,,ENST00000445802,;SLC5A6,downstream_gene_variant,,ENST00000476319,;SLC5A6,downstream_gene_variant,,ENST00000492069,;SLC5A6,downstream_gene_variant,,ENST00000464538,;SLC5A6,downstream_gene_variant,,ENST00000481751,; A ENST00000310574 Transcript missense_variant 2233/3231 1759/1908 587/635 G/C Ggc/Tgc rs764448030 1 -1 SLC5A6 HGNC HGNC:11041 protein_coding YES CCDS1740.1 ENSP00000310208 Q9Y289 UPI000006DE33 NM_021095.2 tolerated(0.06) 16/17 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF140 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 27201003 27201003 C A 1 0 0 0 0 1 0 0 0 14952 666 23 1 1 SLC5A6 2 27201003 Missense_Mutation SNP C C3N-01415_T 118085 27201003 214992526 59 23806 SPAST 0 . GRCh38 2 32098842 32098842 + Silent SNP C C G novel C3N-01415_T C3N-01415_N C C c.633C>G p.= p.V211V ENST00000615843 4/17 556 524 32 525 525 0 strelka-varscan SPAST,synonymous_variant,p.=,ENST00000615843,NM_014946.3;SPAST,synonymous_variant,p.=,ENST00000315285,;SPAST,synonymous_variant,p.=,ENST00000621856,;SPAST,intron_variant,,ENST00000345662,NM_199436.1; G ENST00000615843 Transcript synonymous_variant 854/5212 633/1851 211/616 V gtC/gtG 1 1 SPAST HGNC HGNC:11233 protein_coding YES CCDS1778.1 ENSP00000480893 Q9UBP0 E5KRP5 UPI0000038A6B NM_014946.3 4/17 HAMAP:MF_03021,PIRSF_domain:PIRSF037338,hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF86 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 32098842 32098842 C G 1 0 0 0 0 0 0 0 1 15328 900 32 4 4 SPAST 2 32098842 Silent SNP C C3N-01415_T 4897839 32098842 210094687 60 23807 NRXN1 0 . GRCh38 2 51028088 51028088 + Silent SNP G G A C3N-01415_T C3N-01415_N G G c.186C>T p.= p.S62S ENST00000404971 2/24 89 77 12 90 90 0 strelka-varscan NRXN1,synonymous_variant,p.=,ENST00000406316,NM_004801.4;NRXN1,synonymous_variant,p.=,ENST00000625672,;NRXN1,synonymous_variant,p.=,ENST00000404971,NM_001135659.1;NRXN1,synonymous_variant,p.=,ENST00000401669,;NRXN1,synonymous_variant,p.=,ENST00000405472,;NRXN1,synonymous_variant,p.=,ENST00000405581,;NRXN1,synonymous_variant,p.=,ENST00000630543,;NRXN1,synonymous_variant,p.=,ENST00000637511,;NRXN1,synonymous_variant,p.=,ENST00000628515,;NRXN1,synonymous_variant,p.=,ENST00000626899,;NRXN1,upstream_gene_variant,,ENST00000636066,;NRXN1,upstream_gene_variant,,ENST00000627198,;NRXN1,upstream_gene_variant,,ENST00000496792,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000635126,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,upstream_gene_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; A ENST00000404971 Transcript synonymous_variant 1526/7578 186/4644 62/1547 S agC/agT COSM1130765,COSM1130766,COSM4876256,COSM4876257 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 2/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1,1 LOW 1 SNV 1 1,1,1,1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999491 1 1 1 0 A 2 1 78 51028088 51028088 G A 1 0 0 0 0 0 0 0 1 10724 1078 38 1 1 NRXN1 2 51028088 Silent SNP G C3N-01415_T 18929246 51028088 191165441 61 23808 UGP2 0 . GRCh38 2 63882522 63882522 + Silent SNP G G T rs779321630 C3N-01415_T C3N-01415_N G G c.312G>T p.= p.V104V ENST00000337130 4/10 118 106 12 136 136 0 strelka-varscan UGP2,synonymous_variant,p.=,ENST00000337130,NM_006759.3;UGP2,synonymous_variant,p.=,ENST00000394417,NM_001001521.1;UGP2,synonymous_variant,p.=,ENST00000467648,;UGP2,synonymous_variant,p.=,ENST00000445915,;UGP2,synonymous_variant,p.=,ENST00000613823,;UGP2,synonymous_variant,p.=,ENST00000488245,;UGP2,synonymous_variant,p.=,ENST00000491621,;UGP2,synonymous_variant,p.=,ENST00000482668,;UGP2,synonymous_variant,p.=,ENST00000497883,;UGP2,synonymous_variant,p.=,ENST00000475462,;UGP2,synonymous_variant,p.=,ENST00000472047,;ACA59,downstream_gene_variant,,ENST00000515966,;UGP2,non_coding_transcript_exon_variant,,ENST00000487469,;UGP2,non_coding_transcript_exon_variant,,ENST00000495020,;UGP2,3_prime_UTR_variant,,ENST00000466642,;UGP2,3_prime_UTR_variant,,ENST00000487042,;UGP2,3_prime_UTR_variant,,ENST00000493222,;UGP2,3_prime_UTR_variant,,ENST00000467999,;UGP2,3_prime_UTR_variant,,ENST00000497510,;UGP2,3_prime_UTR_variant,,ENST00000467400,;UGP2,3_prime_UTR_variant,,ENST00000496334,;UGP2,non_coding_transcript_exon_variant,,ENST00000475550,;UGP2,non_coding_transcript_exon_variant,,ENST00000494536,;UGP2,non_coding_transcript_exon_variant,,ENST00000483461,;UGP2,downstream_gene_variant,,ENST00000483108,; T ENST00000337130 Transcript synonymous_variant 788/2338 312/1527 104/508 V gtG/gtT rs779321630 1 1 UGP2 HGNC HGNC:12527 protein_coding YES CCDS1875.1 ENSP00000338703 Q16851 UPI000000DB95 NM_006759.3 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR11952,Pfam_domain:PF01704,Gene3D:3.90.550.10,PIRSF_domain:PIRSF000806,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 63882522 63882522 G T 1 0 0 0 0 0 0 0 1 17468 1364 48 2 2 UGP2 2 63882522 Silent SNP G C3N-01415_T 12854434 63882522 178311007 62 23809 ANXA4 0 . GRCh38 2 69810623 69810623 + Missense_Mutation SNP C C T rs755577388 C3N-01415_T C3N-01415_N C C c.427C>T p.Arg143Cys p.R143C ENST00000394295 7/13 241 225 16 273 273 0 strelka-varscan ANXA4,missense_variant,p.Arg143Cys,ENST00000394295,NM_001153.3;ANXA4,missense_variant,p.Arg121Cys,ENST00000409920,;ANXA4,downstream_gene_variant,,ENST00000460942,;ANXA4,downstream_gene_variant,,ENST00000460439,;ANXA4,missense_variant,p.Arg121Cys,ENST00000635311,;ANXA4,3_prime_UTR_variant,,ENST00000468815,;ANXA4,3_prime_UTR_variant,,ENST00000472124,;ANXA4,non_coding_transcript_exon_variant,,ENST00000477632,;ANXA4,non_coding_transcript_exon_variant,,ENST00000487351,;ANXA4,upstream_gene_variant,,ENST00000471395,; T ENST00000394295 Transcript missense_variant 675/2799 427/966 143/321 R/C Cgc/Tgc rs755577388,COSM3582769 1 1 ANXA4 HGNC HGNC:542 protein_coding YES CCDS1894.1 ENSP00000377833 P09525 Q6LES2 UPI000013D51A NM_001153.3 tolerated(0.11) 7/13 hmmpanther:PTHR10502,hmmpanther:PTHR10502:SF28,PROSITE_patterns:PS00223,Pfam_domain:PF00191,Gene3D:1.10.220.10,SMART_domains:SM00335,Superfamily_domains:SSF47874 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 69810623 69810623 C T 1 0 0 0 0 1 0 0 0 828 884 31 1 1 ANXA4 2 69810623 Missense_Mutation SNP C C3N-01415_T 5928101 69810623 172382906 63 23810 REG3A 0 . GRCh38 2 79158417 79158417 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.242G>T p.Ser81Ile p.S81I ENST00000393878 3/5 284 252 32 286 286 0 strelka-varscan-mutect REG3A,missense_variant,p.Ser81Ile,ENST00000393878,NM_138938.2;REG3A,missense_variant,p.Ser81Ile,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,missense_variant,p.Ser81Ile,ENST00000305165,;AC011754.1,non_coding_transcript_exon_variant,,ENST00000415201,;REG3A,downstream_gene_variant,,ENST00000464746,;REG3A,downstream_gene_variant,,ENST00000490901,; A ENST00000393878 Transcript missense_variant 590/1095 242/528 81/175 S/I aGt/aTt 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 deleterious(0) 3/5 PROSITE_profiles:PS50041,hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 79158417 79158417 C A 1 0 0 0 0 1 0 0 0 13382 565 20 2 2 REG3A 2 79158417 Missense_Mutation SNP C C3N-01415_T 9347794 79158417 163035112 64 23811 IMMT 0 . GRCh38 2 86159586 86159586 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.982G>A p.Glu328Lys p.E328K ENST00000410111 9/15 231 210 21 264 264 0 strelka-varscan-mutect IMMT,missense_variant,p.Glu328Lys,ENST00000410111,NM_006839.2;IMMT,missense_variant,p.Glu317Lys,ENST00000449247,NM_001100170.1;IMMT,missense_variant,p.Glu327Lys,ENST00000442664,NM_001100169.1;IMMT,missense_variant,p.Glu229Lys,ENST00000254636,;IMMT,missense_variant,p.Glu281Lys,ENST00000409051,;IMMT,missense_variant,p.Glu183Lys,ENST00000419070,;IMMT,intron_variant,,ENST00000620815,;Y_RNA,downstream_gene_variant,,ENST00000363371,;IMMT,non_coding_transcript_exon_variant,,ENST00000490238,;IMMT,3_prime_UTR_variant,,ENST00000409258,;IMMT,non_coding_transcript_exon_variant,,ENST00000474969,; T ENST00000410111 Transcript missense_variant 1370/3001 982/2277 328/758 E/K Gag/Aag 1 -1 IMMT HGNC HGNC:6047 protein_coding YES CCDS46355.1 ENSP00000387262 Q16891 UPI0000073828 NM_006839.2 deleterious(0.01) 9/15 hmmpanther:PTHR15415:SF7,hmmpanther:PTHR15415,Pfam_domain:PF09731 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 86159586 86159586 C T 1 0 0 0 0 1 0 0 0 7621 922 32 3 3 IMMT 2 86159586 Missense_Mutation SNP C C3N-01415_T 7001169 86159586 156033943 65 23812 SMYD1 0 . GRCh38 2 88108410 88108410 + Silent SNP C C A rs113530320 C3N-01415_T C3N-01415_N C C c.1185C>A p.= p.A395A ENST00000419482 9/10 141 94 47 142 142 0 strelka-varscan-mutect SMYD1,synonymous_variant,p.=,ENST00000419482,NM_198274.3;SMYD1,synonymous_variant,p.=,ENST00000444564,;SMYD1,intron_variant,,ENST00000438570,; A ENST00000419482 Transcript synonymous_variant 1270/4433 1185/1473 395/490 A gcC/gcA rs113530320,COSM3758407 1 1 SMYD1 HGNC HGNC:20986 protein_coding YES CCDS33240.1 ENSP00000393453 Q8NB12 A0A0A6YYB2 UPI000006EB68 NM_198274.3 9/10 hmmpanther:PTHR12197,hmmpanther:PTHR12197:SF184 0,1 LOW 1 SNV 1 0,1 1 PASS rs113530320 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 78 88108410 88108410 C A 1 0 0 0 0 0 0 0 1 15142 639 23 1 1 SMYD1 2 88108410 Silent SNP C C3N-01415_T 1948824 88108410 154085119 66 23813 TEKT4 0 . GRCh38 2 94874920 94874920 + Missense_Mutation SNP C C A rs782775406 C3N-01415_T C3N-01415_N C C c.858C>A p.Asp286Glu p.D286E ENST00000295201 4/6 318 242 76 262 262 0 strelka-varscan-mutect TEKT4,missense_variant,p.Asp286Glu,ENST00000295201,NM_144705.3,NM_001286559.1;AC097374.2,intron_variant,,ENST00000568768,;AC097374.2,intron_variant,,ENST00000582835,;TEKT4,non_coding_transcript_exon_variant,,ENST00000468063,; A ENST00000295201 Transcript missense_variant 995/1505 858/1308 286/435 D/E gaC/gaA rs782775406 1 1 TEKT4 HGNC HGNC:31012 protein_coding YES CCDS2005.1 ENSP00000295201 Q8WW24 UPI00000730A8 NM_144705.3,NM_001286559.1 tolerated(0.05) 4/6 hmmpanther:PTHR19960,hmmpanther:PTHR19960:SF26,Pfam_domain:PF03148 MODERATE 1 SNV 1 1 PASS rs782775406 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 94874920 94874920 C A 1 0 0 0 0 1 0 0 0 16167 535 19 1 1 TEKT4 2 94874920 Missense_Mutation SNP C C3N-01415_T 6766510 94874920 147318609 67 23814 SNRNP200 0 . GRCh38 2 96301614 96301614 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.484G>T p.Gly162Cys p.G162C ENST00000323853 4/45 617 434 183 531 531 0 strelka-varscan-mutect SNRNP200,missense_variant,p.Gly162Cys,ENST00000323853,NM_014014.4; A ENST00000323853 Transcript missense_variant 562/7165 484/6411 162/2136 G/C Ggt/Tgt 1 -1 SNRNP200 HGNC HGNC:30859 protein_coding YES CCDS2020.1 ENSP00000317123 O75643 UPI0000207C53 NM_014014.4 deleterious(0) 4/45 PIRSF_domain:PIRSF039073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 96301614 96301614 C A 1 0 0 0 0 1 0 0 0 15172 623 22 2 2 SNRNP200 2 96301614 Missense_Mutation SNP C C3N-01415_T 1426694 96301614 145891915 68 23815 FAHD2B 0 . GRCh38 2 97086139 97086139 + Missense_Mutation SNP C C A rs760450683 C3N-01415_T C3N-01415_N C C c.522G>T p.Lys174Asn p.K174N ENST00000414820 5/9 424 400 24 204 203 1 varscan-mutect FAHD2B,missense_variant,p.Lys174Asn,ENST00000414820,NM_001320848.1;FAHD2B,missense_variant,p.Lys174Asn,ENST00000272610,NM_199336.1;FAHD2B,downstream_gene_variant,,ENST00000468548,;FAHD2B,non_coding_transcript_exon_variant,,ENST00000463096,;FAHD2B,intron_variant,,ENST00000474849,;FAHD2B,downstream_gene_variant,,ENST00000483657,;AC018892.9,downstream_gene_variant,,ENST00000445404,; A ENST00000414820 Transcript missense_variant,splice_region_variant 793/1388 522/945 174/314 K/N aaG/aaT rs760450683 1 -1 FAHD2B HGNC HGNC:25318 protein_coding YES CCDS2030.1 ENSP00000410470 Q6P2I3 UPI000004D29E NM_001320848.1 tolerated(0.18) 5/9 hmmpanther:PTHR11820:SF84,hmmpanther:PTHR11820,Gene3D:3.90.850.10,Pfam_domain:PF01557,Superfamily_domains:SSF56529 MODERATE 1 SNV 5 1 PASS rs760450683 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 97086139 97086139 C A 1 0 0 0 0 1 0 0 0 5246 695 24 2 2 FAHD2B 2 97086139 Missense_Mutation SNP C C3N-01415_T 784525 97086139 145107390 69 23816 VWA3B 0 . GRCh38 2 98290536 98290536 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.3071C>A p.Thr1024Lys p.T1024K ENST00000477737 23/28 309 237 72 332 332 0 strelka-varscan-mutect VWA3B,missense_variant,p.Thr1024Lys,ENST00000477737,NM_144992.4;VWA3B,missense_variant,p.Thr435Lys,ENST00000473149,;VWA3B,missense_variant,p.Thr146Lys,ENST00000614454,;VWA3B,non_coding_transcript_exon_variant,,ENST00000490947,;VWA3B,3_prime_UTR_variant,,ENST00000432242,;VWA3B,3_prime_UTR_variant,,ENST00000495571,;VWA3B,3_prime_UTR_variant,,ENST00000489630,;VWA3B,non_coding_transcript_exon_variant,,ENST00000409460,; A ENST00000477737 Transcript missense_variant 3275/4454 3071/3885 1024/1294 T/K aCa/aAa 1 1 VWA3B HGNC HGNC:28385 protein_coding YES CCDS42718.1 ENSP00000417955 Q502W6 UPI0000E9B173 NM_144992.4 tolerated(0.4) 23/28 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF111 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 98290536 98290536 C A 1 0 0 0 0 1 0 0 0 17795 478 17 2 2 VWA3B 2 98290536 Missense_Mutation SNP C C3N-01415_T 1204397 98290536 143902993 70 23817 IL1R1 0 . GRCh38 2 102176654 102176654 + Missense_Mutation SNP G G T rs141357524 C3N-01415_T C3N-01415_N G G c.1605G>T p.Arg535Ser p.R535S ENST00000410023 12/12 321 301 20 328 327 1 strelka-varscan-mutect IL1R1,missense_variant,p.Arg535Ser,ENST00000410023,NM_001320978.1,NM_001320980.1,NM_001320981.1,NM_001320982.1,NM_001320983.1,NM_000877.3;IL1R1,missense_variant,p.Arg504Ser,ENST00000409929,NM_001288706.1;IL1R1,3_prime_UTR_variant,,ENST00000424272,;IL1R1,intron_variant,,ENST00000409589,;IL1R1,downstream_gene_variant,,ENST00000409329,;IL1R1,downstream_gene_variant,,ENST00000409288,;IL1R1,downstream_gene_variant,,ENST00000428279,;AC007271.3,intron_variant,,ENST00000428188,;IL1R1,3_prime_UTR_variant,,ENST00000413623,;IL1R1,downstream_gene_variant,,ENST00000422532,; T ENST00000410023 Transcript missense_variant 1923/5143 1605/1710 535/569 R/S agG/agT rs141357524 1 1 IL1R1 HGNC HGNC:5993 protein_coding YES CCDS2055.1 ENSP00000386380 P14778 UPI0000034759 NM_001320978.1,NM_001320980.1,NM_001320981.1,NM_001320982.1,NM_001320983.1,NM_000877.3 deleterious(0) 12/12 Gene3D:3.40.50.10140,Pfam_domain:PF01582,Prints_domain:PR01537,PROSITE_profiles:PS50104,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF26,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS rs141357524 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 102176654 102176654 G T 1 0 0 0 0 1 0 0 0 7561 1252 44 2 2 IL1R1 2 102176654 Missense_Mutation SNP G C3N-01415_T 3886118 102176654 140016875 71 23818 IL1RL1 0 . GRCh38 2 102349131 102349131 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.1170T>A p.Ser390Arg p.S390R ENST00000233954 10/11 279 245 34 351 351 0 strelka-varscan-mutect IL1RL1,missense_variant,p.Ser390Arg,ENST00000233954,NM_016232.4;IL18R1,intron_variant,,ENST00000410040,;IL1RL1,downstream_gene_variant,,ENST00000311734,NM_003856.3;IL1RL1,downstream_gene_variant,,ENST00000404917,NM_001282408.1;IL1RL1,downstream_gene_variant,,ENST00000409584,; A ENST00000233954 Transcript missense_variant 1441/2058 1170/1671 390/556 S/R agT/agA 1 1 IL1RL1 HGNC HGNC:5998 protein_coding YES CCDS2057.1 ENSP00000233954 Q01638 UPI000013C992 NM_016232.4 tolerated(0.52) 10/11 Gene3D:3.40.50.10140,Pfam_domain:PF01582,PROSITE_profiles:PS50104,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF7,SMART_domains:SM00255,Superfamily_domains:SSF52200 MODERATE 1 SNV 1 1 PASS rs1229510770 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 102349131 102349131 T A 1 0 0 0 0 1 0 0 0 7566 1635 57 4 4 IL1RL1 2 102349131 Missense_Mutation SNP T C3N-01415_T 172477 102349131 139844398 72 23819 SLC35F5 0 . GRCh38 2 113725394 113725394 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1234G>T p.Glu412Ter p.E412* ENST00000245680 12/16 361 274 87 267 267 0 strelka-varscan-mutect SLC35F5,stop_gained,p.Glu412Ter,ENST00000245680,NM_025181.3;SLC35F5,stop_gained,p.Glu175Ter,ENST00000447673,;MIR4782,upstream_gene_variant,,ENST00000577987,;SLC35F5,non_coding_transcript_exon_variant,,ENST00000470204,;SLC35F5,stop_gained,p.Glu406Ter,ENST00000409106,;SLC35F5,non_coding_transcript_exon_variant,,ENST00000459683,;SLC35F5,non_coding_transcript_exon_variant,,ENST00000485214,;SLC35F5,upstream_gene_variant,,ENST00000469702,; A ENST00000245680 Transcript stop_gained 1648/4412 1234/1572 412/523 E/* Gag/Tag 1 -1 SLC35F5 HGNC HGNC:23617 protein_coding YES CCDS2119.1 ENSP00000245680 Q8WV83 A0A024RAD4 UPI000004C648 NM_025181.3 12/16 hmmpanther:PTHR23051,hmmpanther:PTHR23051:SF0,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS rs1438483695 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 113725394 113725394 C A 1 0 0 0 0 0 1 0 0 14863 922 32 2 2 SLC35F5 2 113725394 Nonsense_Mutation SNP C C3N-01415_T 11376263 113725394 128468135 73 23820 PROC 0 . GRCh38 2 127423152 127423153 + Frame_Shift_Ins INS - - CTCCC novel C3N-01415_T C3N-01415_N - - c.381_382insCTCCC p.Gly128LeufsTer10 p.G128Lfs*10 ENST00000234071 5/9 133 105 28 162 162 0 sindel-varindel-pindel PROC,frameshift_variant,p.Gly128LeufsTer10,ENST00000234071,NM_000312.3;PROC,frameshift_variant,p.Gly128LeufsTer44,ENST00000409048,;PROC,frameshift_variant,p.Gly128LeufsTer35,ENST00000442644,;PROC,upstream_gene_variant,,ENST00000402125,;PROC,downstream_gene_variant,,ENST00000427769,;PROC,downstream_gene_variant,,ENST00000429925,;MIR4783,downstream_gene_variant,,ENST00000580343,;PROC,3_prime_UTR_variant,,ENST00000419985,;PROC,downstream_gene_variant,,ENST00000431364,;PROC,upstream_gene_variant,,ENST00000464089,;PROC,downstream_gene_variant,,ENST00000474030,; CTCCC ENST00000234071 Transcript frameshift_variant 468-469/1773 381-382/1386 127-128/461 -/LX -/CTCCC 1 1 PROC HGNC HGNC:9451 protein_coding YES CCDS2145.1 ENSP00000234071 P04070 UPI0000001646 NM_000312.3 5/9 PROSITE_profiles:PS50026,hmmpanther:PTHR24278,hmmpanther:PTHR24278:SF0,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Pfam_domain:PF00008,Gene3D:2.10.25.10,PIRSF_domain:PIRSF001143,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 HIGH 1 insertion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 CTCCC 7 5 78 127423152 127423152 - CTCCC 1 0 1 1 0 0 0 0 0 12679 991 35 0 0 PROC 2 127423152 Frame_Shift_Ins INS - C3N-01415_T 13697758 127423152 114770377 74 23821 POTEI 0 . GRCh38 2 130509158 130509158 + Missense_Mutation SNP C C A rs745983020 C3N-01415_T C3N-01415_N C C c.78G>T p.Lys26Asn p.K26N ENST00000451531 1/15 185 158 27 242 242 0 strelka-varscan-mutect POTEI,missense_variant,p.Lys26Asn,ENST00000451531,NM_001277406.1;POTEI,missense_variant,p.Lys26Asn,ENST00000631234,;POTEI,missense_variant,p.Lys26Asn,ENST00000615053,; A ENST00000451531 Transcript missense_variant 509/7020 78/3228 26/1075 K/N aaG/aaT rs745983020 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0) 1/15 MODERATE 1 SNV 1 1 PASS rs745983020 . 3 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 130509158 130509158 C A 1 0 0 0 0 1 0 0 0 12382 564 20 2 2 POTEI 2 130509158 Missense_Mutation SNP C C3N-01415_T 3086006 130509158 111684371 75 23822 LCT 0 . GRCh38 2 135817939 135817939 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1109C>A p.Ser370Tyr p.S370Y ENST00000264162 6/17 485 407 78 640 640 0 strelka-varscan-mutect LCT,missense_variant,p.Ser370Tyr,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; T ENST00000264162 Transcript missense_variant 1120/6279 1109/5784 370/1927 S/Y tCc/tAc 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 deleterious(0) 6/17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 135817939 135817939 G T 1 0 0 0 0 1 0 0 0 8599 1174 41 2 2 LCT 2 135817939 Missense_Mutation SNP G C3N-01415_T 5308781 135817939 106375590 76 23823 RPRM 0 . GRCh38 2 153478440 153478440 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.126G>A p.= p.A42A ENST00000325926 1/1 244 188 56 274 274 0 strelka-varscan-mutect RPRM,synonymous_variant,p.=,ENST00000325926,NM_019845.2;AC012501.2,intron_variant,,ENST00000424322,; T ENST00000325926 Transcript synonymous_variant 369/1471 126/330 42/109 A gcG/gcA 1 -1 RPRM HGNC HGNC:24201 protein_coding YES CCDS2198.1 ENSP00000314946 Q9NS64 UPI0000072BEC NM_019845.2 1/1 hmmpanther:PTHR28649,hmmpanther:PTHR28649:SF2 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 153478440 153478440 C T 1 0 0 0 0 0 0 0 1 13872 639 23 1 1 RPRM 2 153478440 Silent SNP C C3N-01415_T 17660501 153478440 88715089 77 23824 PKP4 0 . GRCh38 2 158577348 158577348 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.210G>C p.Arg70Ser p.R70S ENST00000389759 3/22 200 174 26 265 265 0 strelka-varscan-mutect PKP4,missense_variant,p.Arg70Ser,ENST00000389757,NM_001005476.2;PKP4,missense_variant,p.Arg70Ser,ENST00000389759,NM_001304970.1,NM_003628.4,NM_001304969.1;PKP4,missense_variant,p.Arg70Ser,ENST00000628904,;PKP4,non_coding_transcript_exon_variant,,ENST00000462335,;PKP4,missense_variant,p.Arg70Ser,ENST00000426248,;PKP4,missense_variant,p.Arg70Ser,ENST00000421462,;PKP4,missense_variant,p.Arg3Ser,ENST00000481115,;PKP4,missense_variant,p.Arg70Ser,ENST00000411900,;PKP4,3_prime_UTR_variant,,ENST00000457109,;PKP4,intron_variant,,ENST00000452162,; C ENST00000389759 Transcript missense_variant 322/4443 210/3579 70/1192 R/S agG/agC 1 1 PKP4 HGNC HGNC:9026 protein_coding YES CCDS33305.1 ENSP00000374409 Q99569 UPI000044D379 NM_001304970.1,NM_003628.4,NM_001304969.1 deleterious(0.03) 3/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF8 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 78 158577348 158577348 G C 1 0 0 0 0 1 0 0 0 12083 1194 42 4 4 PKP4 2 158577348 Missense_Mutation SNP G C3N-01415_T 5098908 158577348 83616181 78 23825 PLA2R1 0 . GRCh38 2 160020153 160020153 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1405C>A p.His469Asn p.H469N ENST00000283243 8/30 223 182 41 272 271 1 strelka-varscan-mutect PLA2R1,missense_variant,p.His469Asn,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.His469Asn,ENST00000392771,NM_001007267.2; T ENST00000283243 Transcript missense_variant 1612/14371 1405/4392 469/1463 H/N Cac/Aac 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 tolerated(0.74) 8/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 160020153 160020153 G T 1 0 0 0 0 1 0 0 0 12106 1348 47 2 2 PLA2R1 2 160020153 Missense_Mutation SNP G C3N-01415_T 1442805 160020153 82173376 79 23826 DPP4 0 . GRCh38 2 162020640 162020640 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.1117A>C p.Lys373Gln p.K373Q ENST00000360534 13/26 270 255 15 322 322 0 strelka-varscan-mutect DPP4,missense_variant,p.Lys373Gln,ENST00000360534,NM_001935.3;DPP4,non_coding_transcript_exon_variant,,ENST00000468903,;DPP4,upstream_gene_variant,,ENST00000491591,;DPP4,3_prime_UTR_variant,,ENST00000434918,;DPP4,non_coding_transcript_exon_variant,,ENST00000490286,; G ENST00000360534 Transcript missense_variant 1678/3904 1117/2301 373/766 K/Q Aag/Cag 1 -1 DPP4 HGNC HGNC:3009 protein_coding YES CCDS2216.1 ENSP00000353731 P27487 UPI000004F7BF NM_001935.3 tolerated(0.15) 13/26 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF128,Pfam_domain:PF00930,Gene3D:2.140.10.30,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 162020640 162020640 T G 1 0 0 0 0 1 0 0 0 4544 1821 63 5 5 DPP4 2 162020640 Missense_Mutation SNP T C3N-01415_T 2000487 162020640 80172889 80 23827 SCN3A 0 . GRCh38 2 165090492 165090492 + Silent SNP A A T novel C3N-01415_T C3N-01415_N A A c.5661T>A p.= p.S1887S ENST00000283254 28/28 540 469 71 675 674 1 strelka-varscan-mutect SCN3A,synonymous_variant,p.=,ENST00000360093,;SCN3A,synonymous_variant,p.=,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,synonymous_variant,p.=,ENST00000409101,NM_001081677.1;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000431341,;AC013463.2,upstream_gene_variant,,ENST00000625505,;SCN3A,downstream_gene_variant,,ENST00000465043,; T ENST00000283254 Transcript synonymous_variant 6129/9091 5661/6003 1887/2000 S tcT/tcA 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 28/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 165090492 165090492 A T 1 0 0 0 0 0 0 0 1 14187 59 3 4 4 SCN3A 2 165090492 Silent SNP A C3N-01415_T 3069852 165090492 77103037 81 23828 TTN 0 . GRCh38 2 178582207 178582207 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.66162C>A p.Asp22054Glu p.D22054E ENST00000589042 315/363 292 267 25 353 353 0 strelka-varscan-mutect TTN,missense_variant,p.Asp22054Glu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Asp20413Glu,ENST00000591111,;TTN,missense_variant,p.Asp20413Glu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Asp19486Glu,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Asp12989Glu,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Asp13181Glu,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Asp13114Glu,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-171I2.2,downstream_gene_variant,,ENST00000603521,;TTN-AS1,upstream_gene_variant,,ENST00000590743,;TTN-AS1,upstream_gene_variant,,ENST00000629117,;TTN-AS1,upstream_gene_variant,,ENST00000589907,;RP11-171I2.5,downstream_gene_variant,,ENST00000604215,;TTN-AS1,upstream_gene_variant,,ENST00000626517,; T ENST00000589042 Transcript missense_variant,splice_region_variant 66387/109224 66162/107976 22054/35991 D/E gaC/gaA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 315/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS rs1328861562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 178582207 178582207 G T 1 0 0 0 0 1 0 0 0 17245 1275 44 2 2 TTN 2 178582207 Missense_Mutation SNP G C3N-01415_T 13491715 178582207 63611322 82 23829 TTN 0 . GRCh38 2 178732298 178732298 + Missense_Mutation SNP C C A rs765248071 C3N-01415_T C3N-01415_N C C c.16671G>T p.Lys5557Asn p.K5557N ENST00000589042 57/363 113 96 17 141 140 1 strelka-varscan-mutect TTN,missense_variant,p.Lys5557Asn,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Lys5240Asn,ENST00000591111,;TTN,missense_variant,p.Lys5240Asn,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Lys4313Asn,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,upstream_gene_variant,,ENST00000582847,; A ENST00000589042 Transcript missense_variant 16896/109224 16671/107976 5557/35991 K/N aaG/aaT rs765248071,COSM1529828,COSM5272941 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 57/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs765248071 . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 78 178732298 178732298 C A 1 0 0 0 0 1 0 0 0 17245 680 24 2 2 TTN 2 178732298 Missense_Mutation SNP C C3N-01415_T 150091 178732298 63461231 83 23830 ZNF385B 0 . GRCh38 2 179769551 179769551 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.205C>A p.Gln69Lys p.Q69K ENST00000410066 3/10 269 231 38 319 319 0 strelka-varscan-mutect ZNF385B,missense_variant,p.Gln69Lys,ENST00000410066,NM_152520.4;ZNF385B,missense_variant,p.Gln69Lys,ENST00000451732,;ZNF385B,downstream_gene_variant,,ENST00000438871,; T ENST00000410066 Transcript missense_variant 809/3288 205/1416 69/471 Q/K Cag/Aag 1 -1 ZNF385B HGNC HGNC:26332 protein_coding YES CCDS33339.1 ENSP00000386845 Q569K4 UPI00004F9C24 NM_152520.4 tolerated(1) 3/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 179769551 179769551 G T 1 0 0 0 0 1 0 0 0 18449 1328 46 2 2 ZNF385B 2 179769551 Missense_Mutation SNP G C3N-01415_T 1037253 179769551 62423978 84 23831 COL3A1 0 . GRCh38 2 188991514 188991514 + Nonsense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.880G>T p.Gly294Ter p.G294* ENST00000304636 12/51 285 233 52 431 430 1 strelka-mutect COL3A1,stop_gained,p.Gly294Ter,ENST00000304636,NM_000090.3;COL3A1,stop_gained,p.Gly294Ter,ENST00000317840,;COL3A1,upstream_gene_variant,,ENST00000450867,;COL3A1,upstream_gene_variant,,ENST00000637672,; T ENST00000304636 Transcript stop_gained 1050/5543 880/4401 294/1466 G/* Gga/Tga 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 12/51 Low_complexity_(Seg):seg,Pfam_domain:PF01391 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 188991514 188991514 G T 1 0 0 0 0 0 1 0 0 3477 1349 47 2 2 COL3A1 2 188991514 Nonsense_Mutation SNP G C3N-01415_T 9221963 188991514 53202015 85 23832 ZDBF2 0 . GRCh38 2 206309288 206309288 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.4760A>G p.Lys1587Arg p.K1587R ENST00000374423 5/5 272 249 23 323 322 1 strelka-varscan-mutect ZDBF2,missense_variant,p.Lys1587Arg,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Lys1585Arg,ENST00000611847,NM_001285549.1; G ENST00000374423 Transcript missense_variant 5146/10286 4760/7065 1587/2354 K/R aAa/aGa 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.05) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 206309288 206309288 A G 1 0 0 0 0 1 0 0 0 18174 14 1 5 5 ZDBF2 2 206309288 Missense_Mutation SNP A C3N-01415_T 17317774 206309288 35884241 86 23833 DES 0 . GRCh38 2 219418568 219418568 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.106C>A p.Pro36Thr p.P36T ENST00000373960 1/9 136 115 21 166 166 0 strelka-varscan-mutect DES,missense_variant,p.Pro36Thr,ENST00000373960,NM_001927.3;DES,upstream_gene_variant,,ENST00000477226,;DES,upstream_gene_variant,,ENST00000492726,; A ENST00000373960 Transcript missense_variant 192/2248 106/1413 36/470 P/T Ccg/Acg 1 1 DES HGNC HGNC:2770 protein_coding YES CCDS33383.1 ENSP00000363071 P17661 Q53SB5 UPI0000001603 NM_001927.3 tolerated(0.42) 1/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF28,Pfam_domain:PF04732 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 219418568 219418568 C A 1 0 0 0 0 1 0 0 0 4255 623 22 2 2 DES 2 219418568 Missense_Mutation SNP C C3N-01415_T 13109280 219418568 22774961 87 23834 SPEG 0 . GRCh38 2 219464548 219464548 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.2821A>G p.Thr941Ala p.T941A ENST00000312358 9/41 232 202 30 247 247 0 strelka-varscan-mutect SPEG,missense_variant,p.Thr941Ala,ENST00000312358,NM_005876.4;SPEG,missense_variant,p.Thr837Ala,ENST00000396698,;SPEG,missense_variant,p.Thr92Ala,ENST00000396688,NM_001173476.1;SPEG,missense_variant,p.Thr92Ala,ENST00000396689,;SPEG,missense_variant,p.Thr92Ala,ENST00000396686,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,;SPEG,non_coding_transcript_exon_variant,,ENST00000498378,;SPEG,non_coding_transcript_exon_variant,,ENST00000462545,;SPEG,non_coding_transcript_exon_variant,,ENST00000463218,;SPEG,non_coding_transcript_exon_variant,,ENST00000496786,;SPEG,non_coding_transcript_exon_variant,,ENST00000464989,;SPEG,non_coding_transcript_exon_variant,,ENST00000475921,; G ENST00000312358 Transcript missense_variant 2953/10782 2821/9804 941/3267 T/A Act/Gct 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 tolerated(0.18) 9/41 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1339089426 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 219464548 219464548 A G 1 0 0 0 0 1 0 0 0 15387 159 6 5 5 SPEG 2 219464548 Missense_Mutation SNP A C3N-01415_T 45980 219464548 22728981 88 23835 SPEG 0 . GRCh38 2 219483170 219483170 + Missense_Mutation SNP C C T rs762000831 C3N-01415_T C3N-01415_N C C c.5707C>T p.Arg1903Trp p.R1903W ENST00000312358 30/41 200 173 27 194 194 0 strelka-varscan-mutect SPEG,missense_variant,p.Arg1903Trp,ENST00000312358,NM_005876.4;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript missense_variant 5839/10782 5707/9804 1903/3267 R/W Cgg/Tgg rs762000831,COSM20704,COSM5427678 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 30/41 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs762000831 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 219483170 219483170 C T 1 0 0 0 0 1 0 0 0 15387 759 27 1 1 SPEG 2 219483170 Missense_Mutation SNP C C3N-01415_T 18622 219483170 22710359 89 23836 SPHKAP 0 . GRCh38 2 228020094 228020094 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.760C>A p.Gln254Lys p.Q254K ENST00000392056 7/12 192 167 25 249 248 1 strelka-varscan-mutect SPHKAP,missense_variant,p.Gln254Lys,ENST00000392056,NM_001142644.1;SPHKAP,missense_variant,p.Gln254Lys,ENST00000344657,NM_030623.3; T ENST00000392056 Transcript missense_variant 807/6917 760/5103 254/1700 Q/K Cag/Aag 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 tolerated(0.37) 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 228020094 228020094 G T 1 0 0 0 0 1 0 0 0 15399 1357 47 2 2 SPHKAP 2 228020094 Missense_Mutation SNP G C3N-01415_T 8536924 228020094 14173435 90 23837 COPS7B 0 . GRCh38 2 231807580 231807580 + Silent SNP G G C rs762906824 C3N-01415_T C3N-01415_N G G c.798G>C p.= p.T266T ENST00000410017 8/8 194 179 15 177 177 0 strelka-varscan-mutect COPS7B,missense_variant,p.Ala244Pro,ENST00000350033,NM_022730.2;COPS7B,missense_variant,p.Ala137Pro,ENST00000620578,NM_001282952.1;COPS7B,missense_variant,p.Ala189Pro,ENST00000611614,NM_001282951.1;COPS7B,missense_variant,p.Ala244Pro,ENST00000410024,;COPS7B,missense_variant,p.Ala210Pro,ENST00000409295,NM_001282949.1;COPS7B,missense_variant,p.Ala137Pro,ENST00000409091,;COPS7B,missense_variant,p.Ala108Pro,ENST00000449174,;COPS7B,synonymous_variant,p.=,ENST00000373608,NM_001282950.1;COPS7B,synonymous_variant,p.=,ENST00000410017,NM_001308381.1;RP11-690I21.2,upstream_gene_variant,,ENST00000563949,;COPS7B,3_prime_UTR_variant,,ENST00000413197,;COPS7B,3_prime_UTR_variant,,ENST00000412922,;COPS7B,non_coding_transcript_exon_variant,,ENST00000461350,;COPS7B,non_coding_transcript_exon_variant,,ENST00000488111,;COPS7B,non_coding_transcript_exon_variant,,ENST00000474042,;RP11-690I21.3,downstream_gene_variant,,ENST00000569668,; C ENST00000410017 Transcript synonymous_variant 908/2051 798/837 266/278 T acG/acC rs762906824 1 1 COPS7B HGNC HGNC:16760 protein_coding YES CCDS77539.1 ENSP00000386880 J3KQ41 UPI0000E1FA1C NM_001308381.1 8/8 LOW 1 SNV 3 1 PASS rs762906824 . 0 207 0 3 0 0 0 0 -19.29103 0.999975 1 1 1 0 C 2 2 78 231807580 231807580 G C 1 0 0 0 0 0 0 0 1 3532 1087 38 4 4 COPS7B 2 231807580 Silent SNP G C3N-01415_T 3787486 231807580 10385949 91 23838 NGEF 0 . GRCh38 2 232883447 232883447 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.1621G>A p.Asp541Asn p.D541N ENST00000264051 12/15 77 67 10 96 96 0 strelka-varscan-mutect NGEF,missense_variant,p.Asp541Asn,ENST00000264051,NM_019850.2;NGEF,missense_variant,p.Asp449Asn,ENST00000373552,NM_001114090.1;NGEF,missense_variant,p.Asp93Asn,ENST00000424488,;NGEF,downstream_gene_variant,,ENST00000416114,;C2orf82,downstream_gene_variant,,ENST00000481155,;NGEF,non_coding_transcript_exon_variant,,ENST00000489127,;C2orf82,downstream_gene_variant,,ENST00000467665,;NGEF,downstream_gene_variant,,ENST00000461944,; T ENST00000264051 Transcript missense_variant 1900/3215 1621/2133 541/710 D/N Gac/Aac 1 -1 NGEF HGNC HGNC:7807 protein_coding YES CCDS2500.1 ENSP00000264051 Q8N5V2 UPI000013D4AE NM_019850.2 deleterious(0.03) 12/15 PROSITE_profiles:PS50003,hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845,Gene3D:2.30.29.30,Pfam_domain:PF00169,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99399 1 1 1 1 0 T 3 4 78 232883447 232883447 C T 1 0 0 0 0 1 0 0 0 10430 826 29 3 3 NGEF 2 232883447 Missense_Mutation SNP C C3N-01415_T 1075867 232883447 9310082 92 23839 NGEF 0 . GRCh38 2 232892909 232892909 + Nonsense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.1131T>A p.Tyr377Ter p.Y377* ENST00000264051 7/15 132 117 15 108 108 0 strelka-varscan-mutect NGEF,stop_gained,p.Tyr377Ter,ENST00000264051,NM_019850.2;NGEF,stop_gained,p.Tyr285Ter,ENST00000373552,NM_001114090.1;NGEF,stop_gained,p.Tyr100Ter,ENST00000416114,;NGEF,downstream_gene_variant,,ENST00000409079,;NGEF,upstream_gene_variant,,ENST00000424488,;NGEF,non_coding_transcript_exon_variant,,ENST00000420650,;NGEF,upstream_gene_variant,,ENST00000461944,; T ENST00000264051 Transcript stop_gained 1410/3215 1131/2133 377/710 Y/* taT/taA 1 -1 NGEF HGNC HGNC:7807 protein_coding YES CCDS2500.1 ENSP00000264051 Q8N5V2 UPI000013D4AE NM_019850.2 7/15 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 HIGH 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -19.99772 0.9999312 1 1 1 0 T 4 4 78 232892909 232892909 A T 1 0 0 0 0 0 1 0 0 10430 456 16 4 4 NGEF 2 232892909 Nonsense_Mutation SNP A C3N-01415_T 9462 232892909 9300620 93 23840 NGEF 0 . GRCh38 2 232920374 232920374 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.738C>A p.His246Gln p.H246Q ENST00000264051 5/15 143 126 17 147 147 0 strelka-varscan-mutect NGEF,missense_variant,p.His246Gln,ENST00000264051,NM_019850.2;NGEF,missense_variant,p.His154Gln,ENST00000373552,NM_001114090.1;NGEF,missense_variant,p.His154Gln,ENST00000409079,; T ENST00000264051 Transcript missense_variant 1017/3215 738/2133 246/710 H/Q caC/caA 1 -1 NGEF HGNC HGNC:7807 protein_coding YES CCDS2500.1 ENSP00000264051 Q8N5V2 UPI000013D4AE NM_019850.2 tolerated(0.24) 5/15 hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 232920374 232920374 G T 1 0 0 0 0 1 0 0 0 10430 1020 36 2 2 NGEF 2 232920374 Missense_Mutation SNP G C3N-01415_T 27465 232920374 9273155 94 23841 INPP5D 0 . GRCh38 2 233147529 233147529 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.965C>G p.Ser322Cys p.S322C ENST00000445964 9/27 283 256 27 308 308 0 strelka-varscan-mutect INPP5D,missense_variant,p.Ser321Cys,ENST00000359570,NM_005541.4;INPP5D,missense_variant,p.Ser322Cys,ENST00000445964,NM_001017915.2; G ENST00000445964 Transcript missense_variant 1046/4845 965/3570 322/1189 S/C tCt/tGt 1 1 INPP5D HGNC HGNC:6079 protein_coding YES CCDS74672.1 ENSP00000405338 Q92835 UPI000006FD6D NM_001017915.2 deleterious(0.01) 9/27 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF69 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 233147529 233147529 C G 1 0 0 0 0 1 0 0 0 7659 913 32 4 4 INPP5D 2 233147529 Missense_Mutation SNP C C3N-01415_T 227155 233147529 9046000 95 23842 MROH2A 0 . GRCh38 2 233832214 233832214 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.4814T>A p.Leu1605Gln p.L1605Q ENST00000610772 40/42 353 332 21 329 328 1 strelka-varscan-mutect MROH2A,missense_variant,p.Leu1591Gln,ENST00000389758,;MROH2A,missense_variant,p.Leu1605Gln,ENST00000610772,NM_001287395.1;HJURP,downstream_gene_variant,,ENST00000411486,NM_018410.4;HJURP,downstream_gene_variant,,ENST00000432087,NM_001282962.1;HJURP,downstream_gene_variant,,ENST00000441687,NM_001282963.1;MROH2A,non_coding_transcript_exon_variant,,ENST00000487979,;HJURP,downstream_gene_variant,,ENST00000433484,; A ENST00000610772 Transcript missense_variant 4907/5324 4814/5067 1605/1688 L/Q cTa/cAa 1 1 MROH2A HGNC HGNC:27936 protein_coding YES CCDS74674.1 ENSP00000477597 A0A087WT58 UPI00021AED4F NM_001287395.1 deleterious(0.03) 40/42 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF14,Superfamily_domains:SSF48371 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 233832214 233832214 T A 1 0 0 0 0 1 0 0 0 9744 1522 53 4 4 MROH2A 2 233832214 Missense_Mutation SNP T C3N-01415_T 684685 233832214 8361315 96 23843 ESPNL 0 . GRCh38 2 238130540 238130540 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1826G>T p.Gly609Val p.G609V ENST00000343063 9/9 164 140 24 204 204 0 strelka-mutect ESPNL,missense_variant,p.Gly609Val,ENST00000343063,NM_194312.2;ESPNL,missense_variant,p.Gly565Val,ENST00000409169,;ESPNL,missense_variant,p.Gly241Val,ENST00000409506,NM_001308370.1;ESPNL,5_prime_UTR_variant,,ENST00000612395,;ESPNL,downstream_gene_variant,,ENST00000423032,;ESPNL,non_coding_transcript_exon_variant,,ENST00000477241,; T ENST00000343063 Transcript missense_variant 2089/4836 1826/3018 609/1005 G/V gGc/gTc 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 deleterious(0) 9/9 hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153 MODERATE 1 SNV 2 1 PASS rs1472528769 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 238130540 238130540 G T 1 0 0 0 0 1 0 0 0 5117 1203 42 2 2 ESPNL 2 238130540 Missense_Mutation SNP G C3N-01415_T 4298326 238130540 4062989 97 23844 D2HGDH 0 . GRCh38 2 241751299 241751299 + Missense_Mutation SNP G G T rs772618143 C3N-01415_T C3N-01415_N G G c.1051G>T p.Ala351Ser p.A351S ENST00000321264 8/10 380 329 51 403 402 1 strelka-varscan-mutect D2HGDH,missense_variant,p.Ala351Ser,ENST00000321264,NM_152783.4;D2HGDH,missense_variant,p.Ala217Ser,ENST00000403782,NM_001287249.1;D2HGDH,missense_variant,p.Ala105Ser,ENST00000432449,;D2HGDH,missense_variant,p.Ala52Ser,ENST00000454048,;D2HGDH,upstream_gene_variant,,ENST00000445308,;D2HGDH,downstream_gene_variant,,ENST00000417686,;D2HGDH,downstream_gene_variant,,ENST00000437164,;AC114730.7,downstream_gene_variant,,ENST00000417267,;D2HGDH,non_coding_transcript_exon_variant,,ENST00000496252,;D2HGDH,intron_variant,,ENST00000486953,;D2HGDH,intron_variant,,ENST00000467427,;D2HGDH,3_prime_UTR_variant,,ENST00000436747,;D2HGDH,non_coding_transcript_exon_variant,,ENST00000473126,;D2HGDH,non_coding_transcript_exon_variant,,ENST00000470343,;D2HGDH,intron_variant,,ENST00000400769,;D2HGDH,upstream_gene_variant,,ENST00000468064,; T ENST00000321264 Transcript missense_variant 1260/2617 1051/1566 351/521 A/S Gct/Tct rs772618143 1 1 D2HGDH HGNC HGNC:28358 protein_coding YES CCDS33426.1 ENSP00000315351 Q8N465 UPI0000456F51 NM_152783.4 tolerated(0.53) 8/10 Pfam_domain:PF02913,hmmpanther:PTHR11748,hmmpanther:PTHR11748:SF90,Superfamily_domains:SSF55103 MODERATE 1 SNV 1 1 PASS rs772618143 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 241751299 241751299 G T 1 0 0 0 0 1 0 0 0 4015 1087 38 1 1 D2HGDH 2 241751299 Missense_Mutation SNP G C3N-01415_T 3620759 241751299 442230 98 23845 RAD18 0 . GRCh38 3 8947282 8947282 + Silent SNP T T G rs761228149 C3N-01415_T C3N-01415_N T T c.204A>C p.= p.T68T ENST00000264926 4/13 169 134 35 227 227 0 strelka-varscan-mutect RAD18,synonymous_variant,p.=,ENST00000264926,NM_020165.3;RAD18,synonymous_variant,p.=,ENST00000421052,;RAD18,synonymous_variant,p.=,ENST00000413832,;RAD18,synonymous_variant,p.=,ENST00000418463,;RAD18,non_coding_transcript_exon_variant,,ENST00000495087,;RAD18,synonymous_variant,p.=,ENST00000415439,;RAD18,non_coding_transcript_exon_variant,,ENST00000469793,; G ENST00000264926 Transcript synonymous_variant 321/5886 204/1488 68/495 T acA/acC rs761228149 1 -1 RAD18 HGNC HGNC:18278 protein_coding YES CCDS2571.1 ENSP00000264926 Q9NS91 UPI000013D592 NM_020165.3 4/13 Gene3D:3.30.40.10,hmmpanther:PTHR14134,hmmpanther:PTHR14134:SF2,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS rs761228149 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 8947282 8947282 T G 1 0 0 0 0 0 0 0 1 13140 1588 55 5 5 RAD18 3 8947282 Silent SNP T C3N-01415_T 8947282 189348277 99 23846 FGD5 0 . GRCh38 3 14821387 14821387 + Silent SNP A A G novel C3N-01415_T C3N-01415_N A A c.2316A>G p.= p.S772S ENST00000285046 1/20 185 150 35 226 226 0 strelka-varscan-mutect FGD5,synonymous_variant,p.=,ENST00000543601,NM_001320276.1;FGD5,synonymous_variant,p.=,ENST00000285046,NM_152536.3;FGD5,upstream_gene_variant,,ENST00000457774,; G ENST00000285046 Transcript synonymous_variant 2426/5720 2316/4389 772/1462 S tcA/tcG 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 1/20 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF13 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 14821387 14821387 A G 1 0 0 0 0 0 0 0 1 5700 175 7 5 5 FGD5 3 14821387 Silent SNP A C3N-01415_T 5874105 14821387 183474172 100 23847 TRAK1 0 . GRCh38 3 42223418 42223418 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2543G>T p.Arg848Met p.R848M ENST00000327628 16/16 390 317 73 430 430 0 strelka-varscan TRAK1,missense_variant,p.Arg744Met,ENST00000487159,;TRAK1,missense_variant,p.Arg848Met,ENST00000327628,NM_001042646.2,NM_001265608.1;TRAK1,missense_variant,p.Arg790Met,ENST00000396175,;RNU4-78P,downstream_gene_variant,,ENST00000410940,; T ENST00000327628 Transcript missense_variant 2943/5293 2543/2862 848/953 R/M aGg/aTg 1 1 TRAK1 HGNC HGNC:29947 protein_coding YES CCDS43072.1 ENSP00000328998 Q9UPV9 A0A024R2M0 UPI0000139F52 NM_001042646.2,NM_001265608.1 deleterious(0) 16/16 hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 42223418 42223418 G T 1 0 0 0 0 1 0 0 0 16932 1000 35 2 2 TRAK1 3 42223418 Missense_Mutation SNP G C3N-01415_T 27402031 42223418 156072141 101 23848 SLC6A20 0 . GRCh38 3 45772537 45772537 + Missense_Mutation SNP T T C C3N-01415_T C3N-01415_N T T c.661A>G p.Thr221Ala p.T221A ENST00000358525 5/11 150 136 14 225 224 1 strelka-varscan SLC6A20,missense_variant,p.Thr221Ala,ENST00000358525,NM_020208.3;SLC6A20,missense_variant,p.Thr221Ala,ENST00000456124,;SLC6A20,missense_variant,p.Thr174Ala,ENST00000413781,;SLC6A20,intron_variant,,ENST00000353278,NM_022405.3;SLC6A20,upstream_gene_variant,,ENST00000473146,; C ENST00000358525 Transcript missense_variant 777/5423 661/1779 221/592 T/A Acc/Gcc COSM144089 1 -1 SLC6A20 HGNC HGNC:30927 protein_coding YES CCDS43077.1 ENSP00000346298 Q9NP91 UPI0000046064 NM_020208.3 tolerated(0.21) 5/11 PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF44,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 45772537 45772537 T C 1 0 0 0 0 1 0 0 0 14967 1696 59 5 5 SLC6A20 3 45772537 Missense_Mutation SNP T C3N-01415_T 3549119 45772537 152523022 102 23849 CCR9 0 . GRCh38 3 45901136 45901136 + Silent SNP C C A rs72890686 C3N-01415_T C3N-01415_N C C c.348C>A p.= p.T116T ENST00000357632 3/3 240 208 32 291 291 0 strelka-varscan CCR9,synonymous_variant,p.=,ENST00000355983,NM_001256369.1;CCR9,synonymous_variant,p.=,ENST00000357632,NM_031200.2;CCR9,synonymous_variant,p.=,ENST00000395963,NM_006641.3;CCR9,3_prime_UTR_variant,,ENST00000422395,;LZTFL1,intron_variant,,ENST00000536047,NM_001276378.1;LZTFL1,intron_variant,,ENST00000539217,NM_001276379.1;Y_RNA,upstream_gene_variant,,ENST00000364765,;LZTFL1,intron_variant,,ENST00000483279,;LZTFL1,intron_variant,,ENST00000472635,;LZTFL1,intron_variant,,ENST00000492333,;LZTFL1,intron_variant,,ENST00000418700,;LZTFL1,intron_variant,,ENST00000448111,; A ENST00000357632 Transcript synonymous_variant 528/2569 348/1110 116/369 T acC/acA rs72890686 1 1 CCR9 HGNC HGNC:1610 protein_coding YES CCDS2732.1 ENSP00000350256 P51686 UPI0000039DBB NM_031200.2 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR10489,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 45901136 45901136 C A 1 0 0 0 0 0 0 0 1 2648 668 24 2 2 CCR9 3 45901136 Silent SNP C C3N-01415_T 128599 45901136 152394423 103 23850 WDR6 0 . GRCh38 3 49011470 49011470 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.150G>T p.= p.P50P ENST00000438660 2/3 151 129 22 195 195 0 strelka-varscan WDR6,synonymous_variant,p.=,ENST00000438660,;WDR6,synonymous_variant,p.=,ENST00000627177,;WDR6,5_prime_UTR_variant,,ENST00000429900,;WDR6,5_prime_UTR_variant,,ENST00000419837,;WDR6,intron_variant,,ENST00000395474,;WDR6,intron_variant,,ENST00000610967,NM_001320547.1,NM_018031.3;WDR6,intron_variant,,ENST00000608424,NM_001320547.1;WDR6,intron_variant,,ENST00000448293,;WDR6,intron_variant,,ENST00000415265,;WDR6,intron_variant,,ENST00000489427,;WDR6,intron_variant,,ENST00000491365,;P4HTM,downstream_gene_variant,,ENST00000343546,NM_177938.2;P4HTM,downstream_gene_variant,,ENST00000383729,NM_177939.2;DALRD3,downstream_gene_variant,,ENST00000440857,;DALRD3,downstream_gene_variant,,ENST00000313778,NM_018114.5;WDR6,upstream_gene_variant,,ENST00000615452,;DALRD3,downstream_gene_variant,,ENST00000341949,NM_001009996.2;DALRD3,downstream_gene_variant,,ENST00000441576,NM_001276405.1;P4HTM,downstream_gene_variant,,ENST00000491739,;DALRD3,downstream_gene_variant,,ENST00000438585,;WDR6,intron_variant,,ENST00000489684,;WDR6,intron_variant,,ENST00000488572,;WDR6,intron_variant,,ENST00000462064,;WDR6,intron_variant,,ENST00000473238,;WDR6,intron_variant,,ENST00000472878,;WDR6,intron_variant,,ENST00000461687,;WDR6,synonymous_variant,p.=,ENST00000452875,;WDR6,intron_variant,,ENST00000420783,;WDR6,intron_variant,,ENST00000471162,;P4HTM,downstream_gene_variant,,ENST00000484115,;DALRD3,downstream_gene_variant,,ENST00000498794,;P4HTM,downstream_gene_variant,,ENST00000472301,;DALRD3,downstream_gene_variant,,ENST00000460505,;DALRD3,downstream_gene_variant,,ENST00000484831,;DALRD3,downstream_gene_variant,,ENST00000467457,;DALRD3,downstream_gene_variant,,ENST00000498498,;DALRD3,downstream_gene_variant,,ENST00000472331,;DALRD3,downstream_gene_variant,,ENST00000481001,;WDR6,upstream_gene_variant,,ENST00000498023,;WDR6,upstream_gene_variant,,ENST00000492780,; T ENST00000438660 Transcript synonymous_variant 189/852 150/813 50/271 P ccG/ccT 1 1 WDR6 HGNC HGNC:12758 protein_coding ENSP00000387692 C9K020 UPI000198CA5F 2/3 LOW SNV 5 1 PASS . . 0 203 0 6 0 0 0 0 -20 0.9982771 1 1 1 0 T 2 4 78 49011470 49011470 G T 1 0 0 0 0 0 0 0 1 17869 1074 38 1 1 WDR6 3 49011470 Silent SNP G C3N-01415_T 3110334 49011470 149284089 104 23851 MON1A 0 . GRCh38 3 49911882 49911882 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.548A>T p.Asp183Val p.D183V ENST00000296473 3/6 211 192 19 249 249 0 strelka-varscan MON1A,missense_variant,p.Asp94Val,ENST00000417270,;MON1A,missense_variant,p.Asp183Val,ENST00000296473,NM_032355.3;MON1A,intron_variant,,ENST00000455683,NM_001142501.1;CTD-2330K9.3,intron_variant,,ENST00000419183,;MON1A,non_coding_transcript_exon_variant,,ENST00000483022,;MON1A,non_coding_transcript_exon_variant,,ENST00000484985,;MON1A,non_coding_transcript_exon_variant,,ENST00000493206,;MON1A,intron_variant,,ENST00000486107,;MON1A,downstream_gene_variant,,ENST00000473451,; A ENST00000296473 Transcript missense_variant 807/2370 548/1959 183/652 D/V gAc/gTc 1 -1 MON1A HGNC HGNC:28207 protein_coding YES CCDS2808.2 ENSP00000296473 X6R3V9 UPI0000EE2989 NM_032355.3 tolerated(0.07) 3/6 hmmpanther:PTHR13027,hmmpanther:PTHR13027:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 49911882 49911882 T A 1 0 0 0 0 1 0 0 0 9662 1667 58 4 4 MON1A 3 49911882 Missense_Mutation SNP T C3N-01415_T 900412 49911882 148383677 105 23852 WNT5A 0 . GRCh38 3 55470532 55470532 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.703G>A p.Asp235Asn p.D235N ENST00000264634 5/5 51 40 11 72 72 0 strelka-varscan WNT5A,missense_variant,p.Asp235Asn,ENST00000264634,NM_003392.4;WNT5A,missense_variant,p.Asp235Asn,ENST00000474267,;WNT5A,missense_variant,p.Asp220Asn,ENST00000497027,NM_001256105.1;WNT5A,intron_variant,,ENST00000614415,;WNT5A,downstream_gene_variant,,ENST00000482079,;WNT5A,upstream_gene_variant,,ENST00000493406,; T ENST00000264634 Transcript missense_variant 1360/6176 703/1143 235/380 D/N Gat/Aat 1 -1 WNT5A HGNC HGNC:12784 protein_coding YES CCDS46850.1 ENSP00000264634 P41221 UPI0000231C66 NM_003392.4 tolerated(0.18) 5/5 hmmpanther:PTHR12027:SF33,hmmpanther:PTHR12027,Pfam_domain:PF00110,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 55470532 55470532 C T 1 0 0 0 0 1 0 0 0 17947 826 29 3 3 WNT5A 3 55470532 Missense_Mutation SNP C C3N-01415_T 5558650 55470532 142825027 106 23853 C3orf67 0 . GRCh38 3 58867917 58867917 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.660G>T p.Met220Ile p.M220I ENST00000295966 10/16 107 83 24 143 143 0 strelka-varscan C3orf67,missense_variant,p.Met220Ile,ENST00000295966,NM_198463.2;C3orf67,missense_variant,p.Met220Ile,ENST00000482387,;C3orf67,intron_variant,,ENST00000472469,;C3orf67-AS1,intron_variant,,ENST00000482372,;C3orf67-AS1,intron_variant,,ENST00000493123,;C3orf67-AS1,intron_variant,,ENST00000492031,;C3orf67-AS1,intron_variant,,ENST00000463703,;C3orf67,3_prime_UTR_variant,,ENST00000468415,; A ENST00000295966 Transcript missense_variant 1164/2650 660/1692 220/563 M/I atG/atT 1 -1 C3orf67 HGNC HGNC:24763 protein_coding YES CCDS33776.1 ENSP00000295966 Q6ZVT6 UPI00001C098C NM_198463.2 tolerated(0.34) 10/16 hmmpanther:PTHR12458 MODERATE 1 SNV 2 1 PASS . . 0 200 8 2 0 0 0 0 -20 0.999874 1 1 1 0 A 3 1 78 58867917 58867917 C A 1 0 0 0 0 1 0 0 0 2071 710 25 2 2 C3orf67 3 58867917 Missense_Mutation SNP C C3N-01415_T 3397385 58867917 139427642 107 23854 CCDC80 0 . GRCh38 3 112616716 112616716 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.2315T>C p.Leu772Pro p.L772P ENST00000206423 5/8 239 181 58 211 211 0 strelka-varscan CCDC80,missense_variant,p.Leu772Pro,ENST00000206423,NM_199511.2;CCDC80,missense_variant,p.Leu772Pro,ENST00000439685,NM_199512.2;CCDC80,missense_variant,p.Leu170Pro,ENST00000461431,; G ENST00000206423 Transcript missense_variant 3269/12430 2315/2853 772/950 L/P cTa/cCa 1 -1 CCDC80 HGNC HGNC:30649 protein_coding YES CCDS2968.1 ENSP00000206423 Q76M96 UPI000004EE7F NM_199511.2 deleterious(0) 5/8 Pfam_domain:PF13778,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 112616716 112616716 A G 1 0 0 0 0 1 0 0 0 2552 420 15 5 5 CCDC80 3 112616716 Missense_Mutation SNP A C3N-01415_T 53748799 112616716 85678843 108 23855 SPICE1 0 . GRCh38 3 113453951 113453951 + Splice_Site SNP C C G novel C3N-01415_T C3N-01415_N C C c.1658-1G>C p.X553_splice ENST00000295872 126 118 8 140 140 0 strelka-varscan SPICE1,splice_acceptor_variant,,ENST00000295872,NM_144718.3;SPICE1,intron_variant,,ENST00000467618,;SPICE1,splice_acceptor_variant,,ENST00000496105,; G ENST00000295872 Transcript splice_acceptor_variant -/5417 1658/2568 553/855 1 -1 SPICE1 HGNC HGNC:25083 protein_coding YES CCDS2973.1 ENSP00000295872 Q8N0Z3 UPI000007328D NM_144718.3 13/17 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -15.34166 0.9999996 1 1 1 0 G 5 3 78 113453951 113453951 C G 1 0 0 0 0 0 0 1 0 15403 579 20 4 4 SPICE1 3 113453951 Splice_Site SNP C C3N-01415_T 837235 113453951 84841608 109 23856 PARP14 0 . GRCh38 3 122727852 122727852 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.4982A>T p.Gln1661Leu p.Q1661L ENST00000474629 16/17 105 77 28 86 86 0 strelka-varscan PARP14,missense_variant,p.Gln1661Leu,ENST00000474629,NM_017554.2;PARP14,3_prime_UTR_variant,,ENST00000460683,; T ENST00000474629 Transcript missense_variant 5248/7915 4982/5406 1661/1801 Q/L cAg/cTg 1 1 PARP14 HGNC HGNC:29232 protein_coding YES CCDS46894.1 ENSP00000418194 Q460N5 UPI00015A20AB NM_017554.2 deleterious(0) 16/17 PROSITE_profiles:PS51059,hmmpanther:PTHR14453:SF65,hmmpanther:PTHR14453,Gene3D:3.90.228.10,Pfam_domain:PF00644,Superfamily_domains:SSF56399 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 122727852 122727852 A T 1 0 0 0 0 1 0 0 0 11538 188 7 4 4 PARP14 3 122727852 Missense_Mutation SNP A C3N-01415_T 9273901 122727852 75567707 110 23857 ALDH1L1 0 . GRCh38 3 126136778 126136778 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1360C>A p.Pro454Thr p.P454T ENST00000273450 11/23 265 234 31 238 238 0 strelka-varscan ALDH1L1,missense_variant,p.Pro444Thr,ENST00000393434,NM_012190.3;ALDH1L1,missense_variant,p.Pro454Thr,ENST00000273450,NM_001270364.1;ALDH1L1,missense_variant,p.Pro444Thr,ENST00000472186,;ALDH1L1,missense_variant,p.Pro444Thr,ENST00000455064,;ALDH1L1,missense_variant,p.Pro444Thr,ENST00000393431,;ALDH1L1,missense_variant,p.Pro343Thr,ENST00000452905,NM_001270365.1;ALDH1L1,3_prime_UTR_variant,,ENST00000473607,;ALDH1L1,non_coding_transcript_exon_variant,,ENST00000476245,; T ENST00000273450 Transcript missense_variant 1578/3179 1360/2739 454/912 P/T Ccc/Acc 1 -1 ALDH1L1 HGNC HGNC:3978 protein_coding YES CCDS58851.1 ENSP00000273450 O75891 UPI0000425C57 NM_001270364.1 deleterious(0.01) 11/23 Gene3D:3.40.605.10,Pfam_domain:PF00171,PIRSF_domain:PIRSF036489,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF120,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 126136778 126136778 G T 1 0 0 0 0 1 0 0 0 594 1174 41 2 2 ALDH1L1 3 126136778 Missense_Mutation SNP G C3N-01415_T 3408926 126136778 72158781 111 23858 ACAD9 0 . GRCh38 3 128908204 128908204 + Missense_Mutation SNP G G A rs781156571 C3N-01415_T C3N-01415_N G G c.1298G>A p.Arg433Gln p.R433Q ENST00000308982 13/18 472 358 114 424 424 0 strelka-varscan ACAD9,missense_variant,p.Arg433Gln,ENST00000308982,NM_014049.4;KIAA1257,downstream_gene_variant,,ENST00000511438,;RP11-723O4.6,downstream_gene_variant,,ENST00000508239,;ACAD9,non_coding_transcript_exon_variant,,ENST00000511526,;ACAD9,missense_variant,p.Arg196Gln,ENST00000508971,;ACAD9,3_prime_UTR_variant,,ENST00000511227,;ACAD9,3_prime_UTR_variant,,ENST00000505867,;ACAD9,3_prime_UTR_variant,,ENST00000505192,;ACAD9,non_coding_transcript_exon_variant,,ENST00000511325,; A ENST00000308982 Transcript missense_variant 1379/2454 1298/1866 433/621 R/Q cGg/cAg rs781156571,COSM1418781 1 1 ACAD9 HGNC HGNC:21497 protein_coding YES CCDS3053.1 ENSP00000312618 Q9H845 UPI00000498C3 NM_014049.4 deleterious(0) 13/18 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF121,Gene3D:1.20.140.10,Pfam_domain:PF00441,Superfamily_domains:SSF47203 pathogenic 0,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 128908204 128908204 G A 1 0 0 0 0 1 0 0 0 154 1116 39 1 1 ACAD9 3 128908204 Missense_Mutation SNP G C3N-01415_T 2771426 128908204 69387355 112 23859 IFT122 0 . GRCh38 3 129502731 129502731 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.2549A>G p.Lys850Arg p.K850R ENST00000296266 21/31 639 484 155 527 526 1 strelka-varscan IFT122,missense_variant,p.Lys649Arg,ENST00000431818,NM_001280545.1;IFT122,missense_variant,p.Lys850Arg,ENST00000296266,NM_052985.3;IFT122,missense_variant,p.Lys590Arg,ENST00000440957,NM_001280546.1;IFT122,missense_variant,p.Lys799Arg,ENST00000348417,NM_052989.2;IFT122,missense_variant,p.Lys740Arg,ENST00000347300,NM_018262.3;IFT122,missense_variant,p.Lys791Arg,ENST00000507564,NM_001280541.1;IFT122,missense_variant,p.Lys688Arg,ENST00000349441,NM_052990.2;IFT122,missense_variant,p.Lys675Arg,ENST00000504021,;IFT122,missense_variant,p.Lys296Arg,ENST00000509522,;IFT122,missense_variant,p.Lys161Arg,ENST00000507221,;IFT122,non_coding_transcript_exon_variant,,ENST00000513932,;IFT122,3_prime_UTR_variant,,ENST00000512220,;IFT122,non_coding_transcript_exon_variant,,ENST00000506507,;IFT122,non_coding_transcript_exon_variant,,ENST00000511425,; G ENST00000296266 Transcript missense_variant 2741/4151 2549/3879 850/1292 K/R aAa/aGa 1 1 IFT122 HGNC HGNC:13556 protein_coding YES CCDS3060.1 ENSP00000296266 Q9HBG6 UPI0000141042 NM_052985.3 tolerated(0.48) 21/31 hmmpanther:PTHR12764,hmmpanther:PTHR12764:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 129502731 129502731 A G 1 0 0 0 0 1 0 0 0 7459 14 1 5 5 IFT122 3 129502731 Missense_Mutation SNP A C3N-01415_T 594527 129502731 68792828 113 23860 COL6A5 0 . GRCh38 3 130469065 130469065 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.7049C>A p.Pro2350His p.P2350H ENST00000265379 39/43 497 453 44 518 517 1 strelka-varscan COL6A5,missense_variant,p.Pro2350His,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Pro606His,ENST00000512836,;COL6A5,missense_variant,p.Pro189His,ENST00000512482,;COL6A5,missense_variant,p.Pro297His,ENST00000373157,;COL6A5,missense_variant,p.Pro2354His,ENST00000312481,; A ENST00000265379 Transcript missense_variant 7543/9214 7049/7836 2350/2611 P/H cCt/cAt 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0) 39/43 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 130469065 130469065 C A 1 0 0 0 0 1 0 0 0 3491 681 24 2 2 COL6A5 3 130469065 Missense_Mutation SNP C C3N-01415_T 966334 130469065 67826494 114 23861 SLCO2A1 0 . GRCh38 3 133948568 133948568 + Frame_Shift_Del DEL C C - novel C3N-01415_T C3N-01415_N C C c.1073delG p.Gly358AlafsTer14 p.G358Afs*14 ENST00000310926 8/14 145 110 35 149 149 0 sindel-varindel-pindel SLCO2A1,frameshift_variant,p.Gly358AlafsTer14,ENST00000310926,NM_005630.2;SLCO2A1,frameshift_variant,p.Gly282AlafsTer14,ENST00000493729,;SLCO2A1,frameshift_variant,p.Gly358AlafsTer156,ENST00000481359,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000462770,;SLCO2A1,downstream_gene_variant,,ENST00000464676,;SLCO2A1,downstream_gene_variant,,ENST00000477061,; - ENST00000310926 Transcript frameshift_variant 1347/4223 1073/1932 358/643 G/X gGc/gc 1 -1 SLCO2A1 HGNC HGNC:10955 protein_coding YES CCDS3084.1 ENSP00000311291 Q92959 UPI000013F0AD NM_005630.2 8/14 PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF14,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 HIGH 1 deletion 1 1 PASS . . 0 203 4 3 0 0 0 0 -20 0.9999382 1 1 1 0 - 7 5 78 133948568 133948568 C - 1 0 1 0 1 0 0 0 0 15013 739 26 0 0 SLCO2A1 3 133948568 Frame_Shift_Del DEL C C3N-01415_T 3479503 133948568 64346991 115 23862 SLC35G2 0 . GRCh38 3 136855044 136855048 + Frame_Shift_Del DEL CCACT CCACT - novel C3N-01415_T C3N-01415_N CCACT CCACT c.584_588delCCACT p.Thr195AsnfsTer20 p.T195Nfs*20 ENST00000446465 2/2 526 469 57 565 565 0 sindel-varindel-pindel SLC35G2,frameshift_variant,p.Thr195AsnfsTer20,ENST00000446465,NM_001097599.1,NM_025246.2;SLC35G2,frameshift_variant,p.Thr195AsnfsTer20,ENST00000393079,NM_001097600.1;NCK1-AS1,intron_variant,,ENST00000461864,;NCK1-AS1,intron_variant,,ENST00000474250,;NCK1-AS1,intron_variant,,ENST00000470236,; - ENST00000446465 Transcript frameshift_variant 1212-1216/2060 584-588/1239 195-196/412 TT/X aCCACT/a 1 1 SLC35G2 HGNC HGNC:28480 protein_coding YES CCDS3091.1 ENSP00000400839 Q8TBE7 UPI000013EB08 NM_001097599.1,NM_025246.2 2/2 hmmpanther:PTHR22911,hmmpanther:PTHR22911:SF52,Pfam_domain:PF00892,Superfamily_domains:0043518,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 136855044 136855044 CCACT - 1 0 1 0 1 0 0 0 0 14866 507 18 0 0 SLC35G2 3 136855044 Frame_Shift_Del DEL CCACT C3N-01415_T 2906476 136855044 61440515 116 23863 CLSTN2 0 . GRCh38 3 140175970 140175970 + Nonsense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.129G>A p.Trp43Ter p.W43* ENST00000458420 2/17 160 132 28 170 170 0 strelka-varscan CLSTN2,stop_gained,p.Trp43Ter,ENST00000458420,NM_022131.2;CLSTN2,non_coding_transcript_exon_variant,,ENST00000511524,; A ENST00000458420 Transcript stop_gained 319/14202 129/2868 43/955 W/* tgG/tgA 1 1 CLSTN2 HGNC HGNC:17448 protein_coding YES CCDS3112.1 ENSP00000402460 Q9H4D0 UPI00001B0051 NM_022131.2 2/17 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF3,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 140175970 140175970 G A 1 0 0 0 0 0 1 0 0 3334 1183 41 3 3 CLSTN2 3 140175970 Nonsense_Mutation SNP G C3N-01415_T 3320926 140175970 58119589 117 23864 PLOD2 0 . GRCh38 3 146070776 146070776 + Nonsense_Mutation SNP C C A C3N-01415_T C3N-01415_N C C c.2218G>T p.Glu740Ter p.E740* ENST00000282903 20/20 326 288 38 343 342 1 strelka-varscan PLOD2,stop_gained,p.Glu740Ter,ENST00000282903,NM_182943.2;PLOD2,stop_gained,p.Glu719Ter,ENST00000360060,NM_000935.2;PLOD2,stop_gained,p.Glu400Ter,ENST00000461497,;PLOD2,stop_gained,p.Glu685Ter,ENST00000494950,;RP11-274H2.2,intron_variant,,ENST00000480247,;RP11-274H2.3,upstream_gene_variant,,ENST00000490375,;RP11-274H2.2,downstream_gene_variant,,ENST00000494745,;PLOD2,non_coding_transcript_exon_variant,,ENST00000495700,;PLOD2,downstream_gene_variant,,ENST00000475505,; A ENST00000282903 Transcript stop_gained 2396/3732 2218/2277 740/758 E/* Gaa/Taa COSM4802559 1 -1 PLOD2 HGNC HGNC:9082 protein_coding YES CCDS3132.1 ENSP00000282903 O00469 UPI0000049C44 NM_182943.2 20/20 PROSITE_profiles:PS51471,hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF6,Pfam_domain:PF03171,SMART_domains:SM00702 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 146070776 146070776 C A 1 0 0 0 0 0 1 0 0 12198 835 29 2 2 PLOD2 3 146070776 Nonsense_Mutation SNP C C3N-01415_T 5894806 146070776 52224783 118 23865 P2RY1 0 . GRCh38 3 152836264 152836264 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.482G>T p.Gly161Val p.G161V ENST00000305097 1/1 340 293 47 311 311 0 strelka-varscan P2RY1,missense_variant,p.Gly161Val,ENST00000305097,NM_002563.3; T ENST00000305097 Transcript missense_variant 1572/6747 482/1122 161/373 G/V gGc/gTc 1 1 P2RY1 HGNC HGNC:8539 protein_coding YES CCDS3169.1 ENSP00000304767 P47900 UPI0000001C06 NM_002563.3 tolerated(0.26) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF2,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 152836264 152836264 G T 1 0 0 0 0 1 0 0 0 11419 1203 42 2 2 P2RY1 3 152836264 Missense_Mutation SNP G C3N-01415_T 6765488 152836264 45459295 119 23866 MME 0 . GRCh38 3 155172546 155172546 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2087G>T p.Gly696Val p.G696V ENST00000460393 22/23 636 475 161 604 604 0 strelka-varscan MME,missense_variant,p.Gly696Val,ENST00000460393,NM_000902.3;MME,missense_variant,p.Gly696Val,ENST00000615825,NM_007287.2,NM_007289.2;MME,missense_variant,p.Gly696Val,ENST00000462745,NM_007288.2;MME,missense_variant,p.Gly696Val,ENST00000492661,;MME,missense_variant,p.Gly696Val,ENST00000493237,;MME,missense_variant,p.Gly696Val,ENST00000360490,;MME-AS1,intron_variant,,ENST00000484721,;MME,non_coding_transcript_exon_variant,,ENST00000493888,;MME,downstream_gene_variant,,ENST00000495577,; T ENST00000460393 Transcript missense_variant 2207/5622 2087/2253 696/750 G/V gGa/gTa 1 1 MME HGNC HGNC:7154 protein_coding YES CCDS3172.1 ENSP00000418525 P08473 UPI0000033C41 NM_000902.3 deleterious(0) 22/23 hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF114,Gene3D:3.40.390.10,Pfam_domain:PF01431,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 155172546 155172546 G T 1 0 0 0 0 1 0 0 0 9608 1174 41 2 2 MME 3 155172546 Missense_Mutation SNP G C3N-01415_T 2336282 155172546 43123013 120 23867 TNIK 0 . GRCh38 3 171085168 171085168 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.2948A>G p.Gln983Arg p.Q983R ENST00000436636 25/33 185 171 14 207 207 0 strelka-varscan TNIK,missense_variant,p.Gln983Arg,ENST00000436636,NM_015028.2;TNIK,missense_variant,p.Gln899Arg,ENST00000341852,NM_001161565.1;TNIK,missense_variant,p.Gln975Arg,ENST00000284483,NM_001161560.1;TNIK,missense_variant,p.Gln954Arg,ENST00000357327,NM_001161561.1;TNIK,missense_variant,p.Gln946Arg,ENST00000470834,NM_001161562.1;TNIK,missense_variant,p.Gln928Arg,ENST00000488470,NM_001161563.1;TNIK,missense_variant,p.Gln920Arg,ENST00000460047,NM_001161564.1;TNIK,missense_variant,p.Gln891Arg,ENST00000475336,NM_001161566.1;TNIK,non_coding_transcript_exon_variant,,ENST00000496492,;TNIK,upstream_gene_variant,,ENST00000484051,; C ENST00000436636 Transcript missense_variant 3293/6970 2948/4083 983/1360 Q/R cAg/cGg 1 -1 TNIK HGNC HGNC:30765 protein_coding YES CCDS46956.1 ENSP00000399511 Q9UKE5 UPI000003ABDF NM_015028.2 deleterious(0.02) 25/33 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.38819 0.9999997 1 1 1 0 C 3 2 78 171085168 171085168 T C 1 0 0 0 0 1 0 0 0 16786 1580 55 5 5 TNIK 3 171085168 Missense_Mutation SNP T C3N-01415_T 15912622 171085168 27210391 121 23868 FBXO45 0 . GRCh38 3 196584314 196584314 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.857G>C p.Gly286Ala p.G286A ENST00000311630 3/3 136 112 24 138 138 0 strelka-varscan FBXO45,missense_variant,p.Gly286Ala,ENST00000311630,NM_001105573.1;FBXO45,missense_variant,p.Gly107Ala,ENST00000440469,; C ENST00000311630 Transcript missense_variant 1154/5899 857/861 286/286 G/A gGa/gCa 1 1 FBXO45 HGNC HGNC:29148 protein_coding YES CCDS46985.1 ENSP00000310332 P0C2W1 UPI00001602EC NM_001105573.1 deleterious(0) 3/3 hmmpanther:PTHR12245:SF7,hmmpanther:PTHR12245 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 196584314 196584314 G C 1 0 0 0 0 1 0 0 0 5617 1174 41 4 4 FBXO45 3 196584314 Missense_Mutation SNP G C3N-01415_T 25499146 196584314 1711245 122 23869 PDE6B 0 . GRCh38 4 634817 634817 + Missense_Mutation SNP C C G rs762366124 C3N-01415_T C3N-01415_N C C c.609C>G p.Ser203Arg p.S203R ENST00000496514 2/22 328 298 30 257 257 0 strelka-varscan-mutect PDE6B,missense_variant,p.Ser203Arg,ENST00000255622,NM_001145291.1;PDE6B,missense_variant,p.Ser203Arg,ENST00000496514,NM_000283.3; G ENST00000496514 Transcript missense_variant 630/3232 609/2565 203/854 S/R agC/agG rs762366124 1 1 PDE6B HGNC HGNC:8786 protein_coding YES CCDS33932.1 ENSP00000420295 P35913 UPI0000DBEE72 NM_000283.3 tolerated(0.13) 2/22 Gene3D:3.30.450.40,Pfam_domain:PF01590,SMART_domains:SM00065,Superfamily_domains:SSF55781 MODERATE 1 SNV 1 1 PASS rs762366124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 634817 634817 C G 1 0 0 0 0 1 0 0 0 11734 767 27 4 4 PDE6B 4 634817 Missense_Mutation SNP C C3N-01415_T 634817 189579738 123 23870 MXD4 0 . GRCh38 4 2252409 2252409 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.308A>T p.Lys103Met p.K103M ENST00000337190 4/6 357 326 31 297 297 0 strelka-varscan-mutect MXD4,missense_variant,p.Lys103Met,ENST00000337190,NM_006454.2;MXD4,upstream_gene_variant,,ENST00000537353,;MXD4,downstream_gene_variant,,ENST00000515378,;MXD4,splice_region_variant,,ENST00000513372,;MXD4,splice_region_variant,,ENST00000513380,;MXD4,downstream_gene_variant,,ENST00000510822,; A ENST00000337190 Transcript missense_variant,splice_region_variant 622/4056 308/630 103/209 K/M aAg/aTg 1 -1 MXD4 HGNC HGNC:13906 protein_coding YES CCDS3361.1 ENSP00000337889 Q14582 UPI000012EB1A NM_006454.2 deleterious(0) 4/6 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS50888,hmmpanther:PTHR11969:SF4,hmmpanther:PTHR11969,Gene3D:4.10.280.10,Pfam_domain:PF00010,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 2252409 2252409 T A 1 0 0 0 0 1 0 0 0 10000 1623 56 4 4 MXD4 4 2252409 Missense_Mutation SNP T C3N-01415_T 1617592 2252409 187962146 124 23871 JAKMIP1 0 . GRCh38 4 6040651 6040651 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2163C>A p.Asp721Glu p.D721E ENST00000409021 18/21 561 510 51 482 482 0 strelka-varscan-mutect JAKMIP1,missense_variant,p.Asp721Glu,ENST00000409021,NM_001099433.1;JAKMIP1,missense_variant,p.Asp536Glu,ENST00000409371,;JAKMIP1,missense_variant,p.Asp289Glu,ENST00000637373,; T ENST00000409021 Transcript missense_variant 2613/2975 2163/2496 721/831 D/E gaC/gaA 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 deleterious(0) 18/21 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 6040651 6040651 G T 1 0 0 0 0 1 0 0 0 7853 1252 44 2 2 JAKMIP1 4 6040651 Missense_Mutation SNP G C3N-01415_T 3788242 6040651 184173904 125 23872 DRD5 0 . GRCh38 4 9782414 9782414 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.385C>G p.Leu129Val p.L129V ENST00000304374 1/1 240 165 75 240 240 0 strelka-varscan DRD5,missense_variant,p.Leu129Val,ENST00000304374,NM_000798.4;SLC2A9,intron_variant,,ENST00000503803,;SLC2A9,intron_variant,,ENST00000508585,; G ENST00000304374 Transcript missense_variant 735/2330 385/1434 129/477 L/V Ctg/Gtg 1 1 DRD5 HGNC HGNC:3026 protein_coding YES CCDS3405.1 ENSP00000306129 P21918 UPI000004E905 NM_000798.4 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF295,hmmpanther:PTHR24249,PROSITE_patterns:PS00237,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 9782414 9782414 C G 1 0 0 0 0 1 0 0 0 4579 680 24 4 4 DRD5 4 9782414 Missense_Mutation SNP C C3N-01415_T 3741763 9782414 180432141 126 23873 CPEB2 0 . GRCh38 4 15002686 15002686 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.13G>T p.Gly5Trp p.G5W ENST00000538197 1/12 100 72 28 99 99 0 strelka-varscan CPEB2,missense_variant,p.Gly5Trp,ENST00000538197,NM_001177382.1;CPEB2,missense_variant,p.Gly5Trp,ENST00000442003,NM_001177383.1,NM_001177381.1;CPEB2,upstream_gene_variant,,ENST00000259997,;CPEB2,upstream_gene_variant,,ENST00000382395,;CPEB2,upstream_gene_variant,,ENST00000382401,NM_001177384.1;CPEB2,upstream_gene_variant,,ENST00000507071,NM_182485.2;CPEB2,upstream_gene_variant,,ENST00000345451,NM_182646.2;CPEB2-AS1,upstream_gene_variant,,ENST00000500394,;RP11-665G4.1,downstream_gene_variant,,ENST00000502344,;RP11-665G4.1,downstream_gene_variant,,ENST00000513384,;CPEB2,upstream_gene_variant,,ENST00000503926,; T ENST00000538197 Transcript missense_variant 13/6878 13/3105 5/1034 G/W Ggg/Tgg 1 1 CPEB2 HGNC HGNC:21745 protein_coding YES CCDS56325.1 ENSP00000443985 Q7Z5Q1 UPI0001D0434B NM_001177382.1 deleterious_low_confidence(0) 1/12 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 15002686 15002686 G T 1 0 0 0 0 1 0 0 0 3595 1116 39 1 1 CPEB2 4 15002686 Missense_Mutation SNP G C3N-01415_T 5220272 15002686 175211869 127 23874 QDPR 0 . GRCh38 4 17492256 17492256 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.521G>T p.Gly174Val p.G174V ENST00000281243 5/7 153 134 19 184 183 1 strelka-varscan QDPR,missense_variant,p.Gly174Val,ENST00000281243,NM_000320.2;QDPR,missense_variant,p.Gly143Val,ENST00000428702,NM_001306140.1;QDPR,intron_variant,,ENST00000513615,;QDPR,intron_variant,,ENST00000505710,;QDPR,intron_variant,,ENST00000508623,;QDPR,non_coding_transcript_exon_variant,,ENST00000501943,;QDPR,non_coding_transcript_exon_variant,,ENST00000511609,;QDPR,intron_variant,,ENST00000507439,;QDPR,intron_variant,,ENST00000514300,; A ENST00000281243 Transcript missense_variant 701/1648 521/735 174/244 G/V gGg/gTg 1 -1 QDPR HGNC HGNC:9752 protein_coding YES CCDS3421.1 ENSP00000281243 P09417 A0A140VKA9 UPI0000111B0A NM_000320.2 deleterious(0.01) 5/7 hmmpanther:PTHR15104:SF0,hmmpanther:PTHR15104,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 17492256 17492256 C A 1 0 0 0 0 1 0 0 0 13027 623 22 2 2 QDPR 4 17492256 Missense_Mutation SNP C C3N-01415_T 2489570 17492256 172722299 128 23875 ADGRA3 0 . GRCh38 4 22388290 22388290 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.3381C>T p.= p.A1127A ENST00000334304 19/19 145 107 38 164 163 1 strelka-varscan ADGRA3,synonymous_variant,p.=,ENST00000334304,NM_145290.3;ADGRA3,non_coding_transcript_exon_variant,,ENST00000282943,;ADGRA3,downstream_gene_variant,,ENST00000504617,;ADGRA3,non_coding_transcript_exon_variant,,ENST00000499527,;ADGRA3,intron_variant,,ENST00000511051,; A ENST00000334304 Transcript synonymous_variant 3651/4566 3381/3966 1127/1321 A gcC/gcT 1 -1 ADGRA3 HGNC HGNC:13839 protein_coding YES CCDS33964.1 ENSP00000334952 Q8IWK6 UPI00001D7735 NM_145290.3 19/19 hmmpanther:PTHR12011:SF35,hmmpanther:PTHR12011 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 22388290 22388290 G A 1 0 0 0 0 0 0 0 1 354 1335 47 3 3 ADGRA3 4 22388290 Silent SNP G C3N-01415_T 4896034 22388290 167826265 129 23876 CORIN 0 . GRCh38 4 47744481 47744481 + Nonsense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.720C>A p.Cys240Ter p.C240* ENST00000273857 5/22 264 238 26 292 292 0 strelka-varscan CORIN,stop_gained,p.Cys240Ter,ENST00000273857,NM_006587.3;CORIN,stop_gained,p.Cys173Ter,ENST00000610355,NM_001278585.1;CORIN,stop_gained,p.Cys101Ter,ENST00000508498,;CORIN,stop_gained,p.Cys173Ter,ENST00000502252,;CORIN,stop_gained,p.Cys240Ter,ENST00000505909,;CORIN,stop_gained,p.Cys240Ter,ENST00000504584,NM_001278586.1;CORIN,non_coding_transcript_exon_variant,,ENST00000502726,;CORIN,non_coding_transcript_exon_variant,,ENST00000503821,; T ENST00000273857 Transcript stop_gained 720/4852 720/3129 240/1042 C/* tgC/tgA 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 5/22 Gene3D:1ijyA00,Pfam_domain:PF01392,PIRSF_domain:PIRSF036376,PROSITE_profiles:PS50038,hmmpanther:PTHR24270,SMART_domains:SM00063,Superfamily_domains:SSF63501 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 47744481 47744481 G T 1 0 0 0 0 0 1 0 0 3546 963 34 2 2 CORIN 4 47744481 Nonsense_Mutation SNP G C3N-01415_T 25356191 47744481 142470074 130 23877 FIP1L1 0 . GRCh38 4 53391059 53391059 + Frame_Shift_Del DEL A A - novel C3N-01415_T C3N-01415_N A A c.558delA p.Ala187LeufsTer18 p.A187Lfs*18 ENST00000507166 8/24 153 136 17 215 214 1 sindel-varindel-pindel RP11-231C18.3,frameshift_variant,p.Ala187LeufsTer18,ENST00000507166,;FIP1L1,frameshift_variant,p.Ala187LeufsTer18,ENST00000337488,NM_030917.3;FIP1L1,frameshift_variant,p.Ala172LeufsTer18,ENST00000358575,NM_001134937.1;FIP1L1,frameshift_variant,p.Ala172LeufsTer18,ENST00000306932,NM_001134938.1;FIP1L1,frameshift_variant,p.Ala172LeufsTer18,ENST00000507922,;FIP1L1,downstream_gene_variant,,ENST00000510668,;FIP1L1,downstream_gene_variant,,ENST00000511376,;FIP1L1,3_prime_UTR_variant,,ENST00000514543,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000505125,;FIP1L1,non_coding_transcript_exon_variant,,ENST00000513975,; - ENST00000507166 Transcript frameshift_variant 556/2550 556/2550 186/849 K/X Aaa/aa 1 1 RP11-231C18.3 Clone_based_vega_gene protein_coding YES ENSP00000423325 A0A0B4J203 UPI00001AA722 8/24 Pfam_domain:PF05182 HIGH deletion 2 2 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 53391059 53391059 A - 1 0 1 0 1 0 0 0 0 5759 247 9 0 0 FIP1L1 4 53391059 Frame_Shift_Del DEL A C3N-01415_T 5646578 53391059 136823496 131 23878 EPHA5 0 . GRCh38 4 65365028 65365028 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.2228T>A p.Val743Glu p.V743E ENST00000622150 12/18 142 125 17 225 225 0 strelka-varscan EPHA5,missense_variant,p.Val743Glu,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Val721Glu,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Val742Glu,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Val743Glu,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Val579Glu,ENST00000432638,;EPHA5,missense_variant,p.Val720Glu,ENST00000354839,NM_182472.3; T ENST00000622150 Transcript missense_variant 2981/8421 2228/3117 743/1038 V/E gTg/gAg 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 12/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 65365028 65365028 A T 1 0 0 0 0 1 0 0 0 5017 159 6 4 4 EPHA5 4 65365028 Missense_Mutation SNP A C3N-01415_T 11973969 65365028 124849527 132 23879 EPHA5 0 . GRCh38 4 65601872 65601872 + Missense_Mutation SNP G G C rs746706656 C3N-01415_T C3N-01415_N G G c.679C>G p.Arg227Gly p.R227G ENST00000622150 3/18 259 229 30 370 370 0 strelka-varscan EPHA5,missense_variant,p.Arg227Gly,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Arg227Gly,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Arg227Gly,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Arg227Gly,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Arg227Gly,ENST00000432638,;EPHA5,missense_variant,p.Arg227Gly,ENST00000354839,NM_182472.3; C ENST00000622150 Transcript missense_variant 1432/8421 679/3117 227/1038 R/G Cgt/Ggt rs746706656 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PIRSF_domain:PIRSF000666,PROSITE_patterns:PS00790,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 65601872 65601872 G C 1 0 0 0 0 1 0 0 0 5017 1087 38 4 4 EPHA5 4 65601872 Missense_Mutation SNP G C3N-01415_T 236844 65601872 124612683 133 23880 AMTN 0 . GRCh38 4 70528758 70528758 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.330G>T p.Gln110His p.Q110H ENST00000339336 6/9 102 84 18 138 138 0 strelka-varscan AMTN,missense_variant,p.Gln110His,ENST00000339336,NM_212557.3;AMTN,missense_variant,p.Gln109His,ENST00000504451,NM_001286731.1; T ENST00000339336 Transcript missense_variant,splice_region_variant 460/1037 330/630 110/209 Q/H caG/caT 1 1 AMTN HGNC HGNC:33188 protein_coding YES CCDS3542.1 ENSP00000341013 Q6UX39 F1T0L8 UPI00000389F3 NM_212557.3 tolerated(0.06) 6/9 PD400414,Pfam_domain:PF15757,hmmpanther:PTHR36858,hmmpanther:PTHR36858:SF1 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 70528758 70528758 G T 1 0 0 0 0 1 0 0 0 688 1014 35 2 2 AMTN 4 70528758 Missense_Mutation SNP G C3N-01415_T 4926886 70528758 119685797 134 23881 PTPN13 0 . GRCh38 4 86762928 86762928 + Missense_Mutation SNP A A C rs539162204 C3N-01415_T C3N-01415_N A A c.3755A>C p.Glu1252Ala p.E1252A ENST00000436978 24/48 236 193 43 296 295 1 strelka-varscan PTPN13,missense_variant,p.Glu1252Ala,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Glu1233Ala,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Glu1252Ala,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Glu1252Ala,ENST00000511467,;PTPN13,missense_variant,p.Glu1061Ala,ENST00000316707,NM_080684.2;PTPN13,non_coding_transcript_exon_variant,,ENST00000508063,;PTPN13,upstream_gene_variant,,ENST00000511105,; C ENST00000436978 Transcript missense_variant 4235/8573 3755/7473 1252/2490 E/A gAg/gCg rs539162204 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0.04) 24/48 PIRSF_domain:PIRSF000933,Pfam_domain:PF16599 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 86762928 86762928 A C 1 0 0 0 0 1 0 0 0 12935 304 11 5 5 PTPN13 4 86762928 Missense_Mutation SNP A C3N-01415_T 16234170 86762928 103451627 135 23882 PKD2 0 . GRCh38 4 88074919 88074919 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.2630G>C p.Arg877Thr p.R877T ENST00000237596 14/15 447 364 83 508 508 0 strelka-varscan PKD2,missense_variant,p.Arg877Thr,ENST00000237596,NM_000297.3;PKD2,missense_variant,p.Arg295Thr,ENST00000508588,;PKD2,missense_variant,p.Arg295Thr,ENST00000502363,;PKD2,non_coding_transcript_exon_variant,,ENST00000511337,;PKD2,non_coding_transcript_exon_variant,,ENST00000512858,; C ENST00000237596 Transcript missense_variant 2696/5056 2630/2907 877/968 R/T aGg/aCg 1 1 PKD2 HGNC HGNC:9009 protein_coding YES CCDS3627.1 ENSP00000237596 Q13563 UPI000013CA1D NM_000297.3 deleterious(0) 14/15 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF114 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 88074919 88074919 G C 1 0 0 0 0 1 0 0 0 12062 1000 35 4 4 PKD2 4 88074919 Missense_Mutation SNP G C3N-01415_T 1311991 88074919 102139636 136 23883 RAP1GDS1 0 . GRCh38 4 98343159 98343159 + Missense_Mutation SNP A A T rs765486837 C3N-01415_T C3N-01415_N A A c.136A>T p.Ile46Phe p.I46F ENST00000339360 3/15 167 128 39 239 239 0 strelka-varscan RAP1GDS1,missense_variant,p.Ile45Phe,ENST00000408927,NM_001100427.1;RAP1GDS1,missense_variant,p.Ile46Phe,ENST00000453712,NM_021159.4;RAP1GDS1,missense_variant,p.Ile46Phe,ENST00000339360,NM_001100426.1;RAP1GDS1,missense_variant,p.Ile46Phe,ENST00000380158,NM_001100428.1;RAP1GDS1,missense_variant,p.Ile45Phe,ENST00000408900,NM_001100429.1;RAP1GDS1,missense_variant,p.Ile46Phe,ENST00000264572,NM_001100430.1;RAP1GDS1,missense_variant,p.Ile45Phe,ENST00000514122,;RAP1GDS1,missense_variant,p.Ile46Phe,ENST00000511212,;RAP1GDS1,intron_variant,,ENST00000508213,;RAP1GDS1,intron_variant,,ENST00000509011,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000512857,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000515187,;RAP1GDS1,missense_variant,p.Ile45Phe,ENST00000510870,;RAP1GDS1,3_prime_UTR_variant,,ENST00000503667,;RAP1GDS1,3_prime_UTR_variant,,ENST00000508490,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000511379,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000505378,;RAP1GDS1,non_coding_transcript_exon_variant,,ENST00000507303,; T ENST00000339360 Transcript missense_variant 184/2092 136/1827 46/608 I/F Atc/Ttc rs765486837 1 1 RAP1GDS1 HGNC HGNC:9859 protein_coding YES CCDS47105.1 ENSP00000340454 P52306 UPI000004A01F NM_001100426.1 deleterious(0.01) 3/15 Gene3D:1.25.10.10,hmmpanther:PTHR10957,hmmpanther:PTHR10957:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 98343159 98343159 A T 1 0 0 0 0 1 0 0 0 13198 101 4 4 4 RAP1GDS1 4 98343159 Missense_Mutation SNP A C3N-01415_T 10268240 98343159 91871396 137 23884 MTTP 0 . GRCh38 4 99613067 99613067 + Missense_Mutation SNP C C A rs149228079 C3N-01415_T C3N-01415_N C C c.2225C>A p.Ser742Tyr p.S742Y ENST00000511045 15/18 540 441 99 660 659 1 strelka-varscan MTTP,missense_variant,p.Ser715Tyr,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Ser715Tyr,ENST00000265517,;MTTP,missense_variant,p.Ser742Tyr,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; A ENST00000511045 Transcript missense_variant 2238/3154 2225/2766 742/921 S/Y tCc/tAc rs149228079 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 deleterious(0) 15/18 hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 99613067 99613067 C A 1 0 0 0 0 1 0 0 0 9961 855 30 2 2 MTTP 4 99613067 Missense_Mutation SNP C C3N-01415_T 1269908 99613067 90601488 138 23885 DKK2 0 . GRCh38 4 106924189 106924189 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.545C>A p.Pro182His p.P182H ENST00000285311 4/4 169 144 25 258 255 3 strelka-varscan DKK2,missense_variant,p.Pro182His,ENST00000285311,NM_014421.2;DKK2,missense_variant,p.Pro82His,ENST00000513208,;DKK2,missense_variant,p.Pro136His,ENST00000510463,;DKK2,non_coding_transcript_exon_variant,,ENST00000510534,; T ENST00000285311 Transcript missense_variant 1251/3638 545/780 182/259 P/H cCc/cAc COSM4121196 1 -1 DKK2 HGNC HGNC:2892 protein_coding YES CCDS3675.1 ENSP00000285311 Q9UBU2 UPI0000048EF2 NM_014421.2 deleterious(0.02) 4/4 hmmpanther:PTHR12113:SF12,hmmpanther:PTHR12113,Gene3D:2.10.80.10 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 106924189 106924189 G T 1 0 0 0 0 1 0 0 0 4351 1232 43 2 2 DKK2 4 106924189 Missense_Mutation SNP G C3N-01415_T 7311122 106924189 83290366 139 23886 NDNF 0 . GRCh38 4 121037120 121037120 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.851C>T p.Pro284Leu p.P284L ENST00000379692 4/4 234 198 36 306 304 2 strelka-varscan NDNF,missense_variant,p.Pro284Leu,ENST00000379692,NM_024574.3;NDNF,downstream_gene_variant,,ENST00000515757,;NDNF,downstream_gene_variant,,ENST00000511408,;NDNF,non_coding_transcript_exon_variant,,ENST00000506900,; A ENST00000379692 Transcript missense_variant 1378/2885 851/1707 284/568 P/L cCc/cTc 1 -1 NDNF HGNC HGNC:26256 protein_coding YES CCDS3717.2 ENSP00000369014 Q8TB73 UPI00001D6985 NM_024574.3 tolerated(0.07) 4/4 hmmpanther:PTHR14619,hmmpanther:PTHR14619:SF1,Gene3D:2.60.40.10,SMART_domains:SM00060 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 121037120 121037120 G A 1 0 0 0 0 1 0 0 0 10269 1232 43 3 3 NDNF 4 121037120 Missense_Mutation SNP G C3N-01415_T 14112931 121037120 69177435 140 23887 KIAA1109 0 . GRCh38 4 122353814 122353814 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.14102G>T p.Gly4701Val p.G4701V ENST00000264501 82/86 196 169 27 252 252 0 strelka-varscan KIAA1109,missense_variant,p.Gly4701Val,ENST00000264501,;KIAA1109,missense_variant,p.Gly4701Val,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Gly1370Val,ENST00000438707,;KIAA1109,missense_variant,p.Gly1077Val,ENST00000306802,;KIAA1109,downstream_gene_variant,,ENST00000491933,; T ENST00000264501 Transcript missense_variant,splice_region_variant 14475/15896 14102/15018 4701/5005 G/V gGc/gTc 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 deleterious(0.01) 82/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640,Pfam_domain:PF10479,SMART_domains:SM01220 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 122353814 122353814 G T 1 0 0 0 0 1 0 0 0 8101 1217 42 2 2 KIAA1109 4 122353814 Missense_Mutation SNP G C3N-01415_T 1316694 122353814 67860741 141 23888 FAT4 0 . GRCh38 4 125321020 125321020 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.4609G>T p.Ala1537Ser p.A1537S ENST00000394329 1/17 204 166 38 275 275 0 strelka-varscan-mutect FAT4,missense_variant,p.Ala1537Ser,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; T ENST00000394329 Transcript missense_variant 4622/16123 4609/14946 1537/4981 A/S Gca/Tca 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.45) 1/17 Gene3D:2.60.40.60,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 125321020 125321020 G T 1 0 0 0 0 1 0 0 0 5552 1319 46 2 2 FAT4 4 125321020 Missense_Mutation SNP G C3N-01415_T 2967206 125321020 64893535 142 23889 FAT4 0 . GRCh38 4 125451055 125451055 + Missense_Mutation SNP C C A C3N-01415_T C3N-01415_N C C c.10039C>A p.Gln3347Lys p.Q3347K ENST00000394329 9/17 269 215 54 381 381 0 strelka-varscan-mutect FAT4,missense_variant,p.Gln3347Lys,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Gln1645Lys,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; A ENST00000394329 Transcript missense_variant 10052/16123 10039/14946 3347/4981 Q/K Cag/Aag COSM4122035,COSM4122036 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 tolerated(0.46) 9/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 125451055 125451055 C A 1 0 0 0 0 1 0 0 0 5552 595 21 2 2 FAT4 4 125451055 Missense_Mutation SNP C C3N-01415_T 130035 125451055 64763500 143 23890 TBC1D9 0 . GRCh38 4 140686454 140686454 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.250A>G p.Arg84Gly p.R84G ENST00000442267 3/21 211 179 32 223 223 0 strelka-varscan-mutect TBC1D9,missense_variant,p.Arg84Gly,ENST00000442267,NM_015130.2; C ENST00000442267 Transcript missense_variant 325/5306 250/3801 84/1266 R/G Agg/Ggg 1 -1 TBC1D9 HGNC HGNC:21710 protein_coding YES CCDS47136.1 ENSP00000411197 Q6ZT07 UPI00001C1E18 NM_015130.2 deleterious(0.03) 3/21 hmmpanther:PTHR22957:SF190,hmmpanther:PTHR22957 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 140686454 140686454 T C 1 0 0 0 0 1 0 0 0 16032 1579 55 5 5 TBC1D9 4 140686454 Missense_Mutation SNP T C3N-01415_T 15235399 140686454 49528101 144 23891 FSTL5 0 . GRCh38 4 161455080 161455080 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1765C>A p.Gln589Lys p.Q589K ENST00000306100 15/16 138 124 14 192 192 0 strelka-varscan FSTL5,missense_variant,p.Gln589Lys,ENST00000306100,NM_020116.4;FSTL5,missense_variant,p.Gln588Lys,ENST00000379164,NM_001128427.2;FSTL5,missense_variant,p.Gln579Lys,ENST00000427802,NM_001128428.2; T ENST00000306100 Transcript missense_variant 2202/4831 1765/2544 589/847 Q/K Caa/Aaa 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 deleterious(0.02) 15/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44,Gene3D:2.130.10.10,Superfamily_domains:0047643 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 161455080 161455080 G T 1 0 0 0 0 1 0 0 0 5954 1357 47 2 2 FSTL5 4 161455080 Missense_Mutation SNP G C3N-01415_T 20768626 161455080 28759475 145 23892 NPY5R 0 . GRCh38 4 163350780 163350780 + Silent SNP C C G C3N-01415_T C3N-01415_N C C c.507C>G p.= p.A169A ENST00000515560 4/4 204 175 29 270 270 0 strelka-varscan NPY5R,synonymous_variant,p.=,ENST00000515560,NM_001317091.1;NPY5R,synonymous_variant,p.=,ENST00000338566,NM_006174.2;NPY5R,synonymous_variant,p.=,ENST00000506953,; G ENST00000515560 Transcript synonymous_variant 2029/3183 507/1338 169/445 A gcC/gcG COSM3601580 1 1 NPY5R HGNC HGNC:7958 protein_coding YES CCDS3804.1 ENSP00000423917 Q15761 UPI000000D9D7 NM_001317091.1 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF217,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01016,Prints_domain:PR00237 1 LOW 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 163350780 163350780 C G 1 0 0 0 0 0 0 0 1 10666 581 21 4 4 NPY5R 4 163350780 Silent SNP C C3N-01415_T 1895700 163350780 26863775 146 23893 SPOCK3 0 . GRCh38 4 166889132 166889132 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.596G>T p.Arg199Ile p.R199I ENST00000357154 7/12 243 204 39 326 324 2 strelka-varscan SPOCK3,missense_variant,p.Arg148Ile,ENST00000421836,NM_001204352.1;SPOCK3,missense_variant,p.Arg199Ile,ENST00000357154,NM_016950.2;SPOCK3,missense_variant,p.Arg199Ile,ENST00000506886,;SPOCK3,missense_variant,p.Arg196Ile,ENST00000357545,NM_001040159.1;SPOCK3,missense_variant,p.Arg199Ile,ENST00000511531,;SPOCK3,missense_variant,p.Arg196Ile,ENST00000504953,;SPOCK3,missense_variant,p.Arg79Ile,ENST00000541354,NM_001204355.1,NM_001204353.1;SPOCK3,missense_variant,p.Arg199Ile,ENST00000502330,;SPOCK3,missense_variant,p.Arg107Ile,ENST00000535728,NM_001204354.1;SPOCK3,missense_variant,p.Arg196Ile,ENST00000510741,NM_001204356.1;SPOCK3,missense_variant,p.Arg196Ile,ENST00000511269,;SPOCK3,missense_variant,p.Arg101Ile,ENST00000512681,NM_001251967.1;SPOCK3,missense_variant,p.Arg196Ile,ENST00000512648,NM_001204358.1;SPOCK3,intron_variant,,ENST00000510403,;SPOCK3,downstream_gene_variant,,ENST00000509854,;SPOCK3,splice_region_variant,,ENST00000502821,;SPOCK3,splice_region_variant,,ENST00000511905,;SPOCK3,splice_region_variant,,ENST00000505187,;SPOCK3,splice_region_variant,,ENST00000507370,;SPOCK3,splice_region_variant,,ENST00000502741,;SPOCK3,splice_region_variant,,ENST00000507086,;SPOCK3,splice_region_variant,,ENST00000511226,;SPOCK3,splice_region_variant,,ENST00000515143,; A ENST00000357154 Transcript missense_variant,splice_region_variant 734/2986 596/1311 199/436 R/I aGa/aTa 1 -1 SPOCK3 HGNC HGNC:13565 protein_coding YES CCDS54817.1 ENSP00000349677 Q9BQ16 UPI000004BA60 NM_016950.2 deleterious(0.02) 7/12 hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF10,Pfam_domain:PF10591 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 166889132 166889132 C A 1 0 0 0 0 1 0 0 0 15434 927 32 2 2 SPOCK3 4 166889132 Missense_Mutation SNP C C3N-01415_T 3538352 166889132 23325423 147 23894 NEK1 0 . GRCh38 4 169400288 169400288 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.3784G>A p.Glu1262Lys p.E1262K ENST00000507142 35/36 158 144 14 195 195 0 strelka-varscan NEK1,missense_variant,p.Glu1234Lys,ENST00000439128,NM_012224.2;NEK1,missense_variant,p.Glu1262Lys,ENST00000507142,NM_001199397.1;NEK1,missense_variant,p.Glu1218Lys,ENST00000511633,NM_001199398.1;NEK1,missense_variant,p.Glu1190Lys,ENST00000510533,NM_001199400.1;NEK1,missense_variant,p.Glu1165Lys,ENST00000512193,NM_001199399.1; T ENST00000507142 Transcript missense_variant 4364/5556 3784/3861 1262/1286 E/K Gaa/Aaa 1 -1 NEK1 HGNC HGNC:7744 protein_coding YES CCDS56351.1 ENSP00000424757 Q96PY6 UPI00001D76CA NM_001199397.1 tolerated(0.06) 35/36 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 169400288 169400288 C T 1 0 0 0 0 1 0 0 0 10349 835 29 3 3 NEK1 4 169400288 Missense_Mutation SNP C C3N-01415_T 2511156 169400288 20814267 148 23895 ADAM29 0 . GRCh38 4 174975939 174975939 + Silent SNP C C A rs200900534 C3N-01415_T C3N-01415_N C C c.414C>A p.= p.P138P ENST00000615367 6/6 208 177 31 314 314 0 strelka-varscan ADAM29,synonymous_variant,p.=,ENST00000615367,NM_001278125.1;ADAM29,synonymous_variant,p.=,ENST00000359240,NM_014269.4,NM_001278126.1;ADAM29,synonymous_variant,p.=,ENST00000445694,NM_001130703.1;ADAM29,synonymous_variant,p.=,ENST00000404450,NM_001130704.1;ADAM29,synonymous_variant,p.=,ENST00000514159,NM_001130705.1;ADAM29,synonymous_variant,p.=,ENST00000618444,NM_001278127.1;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000505141,;ADAM29,downstream_gene_variant,,ENST00000502940,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,; A ENST00000615367 Transcript synonymous_variant 1145/3386 414/2463 138/820 P ccC/ccA rs200900534 1 1 ADAM29 HGNC HGNC:207 protein_coding YES CCDS3823.1 ENSP00000484862 Q9UKF5 A0A140VJD8 UPI000013E9DE NM_001278125.1 6/6 hmmpanther:PTHR11905:SF34,hmmpanther:PTHR11905,Pfam_domain:PF01562 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 174975939 174975939 C A 1 0 0 0 0 0 0 0 1 291 610 22 2 2 ADAM29 4 174975939 Silent SNP C C3N-01415_T 5575651 174975939 15238616 149 23896 ASB5 0 . GRCh38 4 176221555 176221555 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.430T>A p.Cys144Ser p.C144S ENST00000296525 4/7 132 104 28 141 141 0 strelka-varscan ASB5,missense_variant,p.Cys144Ser,ENST00000296525,NM_080874.3;ASB5,missense_variant,p.Cys91Ser,ENST00000512254,;ASB5,non_coding_transcript_exon_variant,,ENST00000511879,;ASB5,downstream_gene_variant,,ENST00000510578,; T ENST00000296525 Transcript missense_variant 544/3031 430/990 144/329 C/S Tgc/Agc 1 -1 ASB5 HGNC HGNC:17180 protein_coding YES CCDS3827.1 ENSP00000296525 Q8WWX0 Q5HYF3 UPI00000015CF NM_080874.3 deleterious(0.04) 4/7 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24136,hmmpanther:PTHR24136:SF18,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403,Prints_domain:PR01415 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 176221555 176221555 A T 1 0 0 0 0 1 0 0 0 1168 217 8 4 4 ASB5 4 176221555 Missense_Mutation SNP A C3N-01415_T 1245616 176221555 13993000 150 23897 TRAPPC11 0 . GRCh38 4 183697677 183697677 + Splice_Site SNP A A T novel C3N-01415_T C3N-01415_N A A c.2695-2A>T p.X899_splice ENST00000334690 124 99 25 150 150 0 strelka-varscan TRAPPC11,splice_acceptor_variant,,ENST00000334690,NM_021942.5;TRAPPC11,splice_acceptor_variant,,ENST00000357207,NM_199053.2;TRAPPC11,splice_acceptor_variant,,ENST00000512476,;TRAPPC11,splice_acceptor_variant,,ENST00000505676,;TRAPPC11,upstream_gene_variant,,ENST00000511955,;TRAPPC11,upstream_gene_variant,,ENST00000506426,; T ENST00000334690 Transcript splice_acceptor_variant -/4552 2695/3402 899/1133 1 1 TRAPPC11 HGNC HGNC:25751 protein_coding YES CCDS34112.1 ENSP00000335371 Q7Z392 UPI000020B774 NM_021942.5 24/29 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 78 183697677 183697677 A T 1 0 0 0 0 0 0 1 0 16941 202 7 4 4 TRAPPC11 4 183697677 Splice_Site SNP A C3N-01415_T 7476122 183697677 6516878 151 23898 TRIML1 0 . GRCh38 4 188142418 188142418 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.671G>T p.Ser224Ile p.S224I ENST00000332517 3/6 329 266 63 365 365 0 strelka-varscan TRIML1,missense_variant,p.Ser224Ile,ENST00000332517,NM_178556.3;RP11-366H4.3,intron_variant,,ENST00000501322,;TRIML1,upstream_gene_variant,,ENST00000507581,;TRIML1,upstream_gene_variant,,ENST00000512233,; T ENST00000332517 Transcript missense_variant 811/1797 671/1407 224/468 S/I aGc/aTc 1 1 TRIML1 HGNC HGNC:26698 protein_coding YES CCDS3851.1 ENSP00000327738 Q8N9V2 UPI000006FC8A NM_178556.3 deleterious(0.03) 3/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 188142418 188142418 G T 1 0 0 0 0 1 0 0 0 17047 971 34 2 2 TRIML1 4 188142418 Missense_Mutation SNP G C3N-01415_T 4444741 188142418 2072137 152 23899 ZDHHC11B 0 . GRCh38 5 756093 756093 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.307T>C p.Cys103Arg p.C103R ENST00000508859 2/11 72 64 8 71 71 0 varscan-mutect ZDHHC11B,missense_variant,p.Cys103Arg,ENST00000508859,;ZDHHC11B,missense_variant,p.Cys92Arg,ENST00000382776,;ZDHHC11B,upstream_gene_variant,,ENST00000622126,; G ENST00000508859 Transcript missense_variant 307/1631 307/1149 103/382 C/R Tgc/Cgc 1 -1 ZDHHC11B HGNC HGNC:32962 protein_coding YES ENSP00000442373 F5H7P5 UPI000204A7C8 deleterious(0.01) 2/11 Transmembrane_helices:TMhelix,hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF83 MODERATE 1 SNV 5 1 PASS . . 1 202 7 0 0 0 0 0 -17.51358 0.9999991 1 1 1 0 G 3 3 78 756093 756093 A G 1 0 0 0 0 1 0 0 0 18177 188 7 5 5 ZDHHC11B 5 756093 Missense_Mutation SNP A C3N-01415_T 756093 180782166 153 23900 ZDHHC11 0 . GRCh38 5 848609 848609 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.274T>C p.Cys92Arg p.C92R ENST00000283441 2/13 119 112 7 89 89 0 varscan-mutect ZDHHC11,missense_variant,p.Cys92Arg,ENST00000283441,NM_024786.2;ZDHHC11,intron_variant,,ENST00000511193,;ZDHHC11,upstream_gene_variant,,ENST00000511539,;ZDHHC11,non_coding_transcript_exon_variant,,ENST00000512775,;ZDHHC11,intron_variant,,ENST00000508951,;ZDHHC11,upstream_gene_variant,,ENST00000507800,;BRD9,downstream_gene_variant,,ENST00000493082,;ZDHHC11,upstream_gene_variant,,ENST00000503880,;ZDHHC11,upstream_gene_variant,,ENST00000505815,;ZDHHC11,upstream_gene_variant,,ENST00000512190,; G ENST00000283441 Transcript missense_variant 658/2604 274/1239 92/412 C/R Tgc/Cgc 1 -1 ZDHHC11 HGNC HGNC:19158 protein_coding YES CCDS3857.1 ENSP00000283441 Q9H8X9 UPI000013C384 NM_024786.2 deleterious(0.01) 2/13 hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF83,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 199 11 0 0 0 0 0 -13.39964 0.9997347 1 1 1 0 G 3 3 78 848609 848609 A G 1 0 0 0 0 1 0 0 0 18176 188 7 5 5 ZDHHC11 5 848609 Missense_Mutation SNP A C3N-01415_T 92516 848609 180689650 154 23901 CLPTM1L 0 . GRCh38 5 1338996 1338996 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.463G>T p.Ala155Ser p.A155S ENST00000320895 4/17 161 139 22 108 108 0 strelka-varscan-mutect CLPTM1L,missense_variant,p.Ala155Ser,ENST00000320895,NM_030782.3;CLPTM1L,missense_variant,p.Ala22Ser,ENST00000630539,;CLPTM1L,missense_variant,p.Ala22Ser,ENST00000507807,;CLPTM1L,upstream_gene_variant,,ENST00000508765,;CLPTM1L,upstream_gene_variant,,ENST00000503151,;CLPTM1L,upstream_gene_variant,,ENST00000511786,; A ENST00000320895 Transcript missense_variant 721/2500 463/1617 155/538 A/S Gcg/Tcg 1 -1 CLPTM1L HGNC HGNC:24308 protein_coding YES CCDS3862.1 ENSP00000313854 Q96KA5 UPI00000707DF NM_030782.3 tolerated(0.4) 4/17 hmmpanther:PTHR21347:SF1,hmmpanther:PTHR21347,Pfam_domain:PF05602 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 1338996 1338996 C A 1 0 0 0 0 1 0 0 0 3327 739 26 2 2 CLPTM1L 5 1338996 Missense_Mutation SNP C C3N-01415_T 490387 1338996 180199263 155 23902 IRX1 0 . GRCh38 5 3601028 3601028 + Silent SNP C C G novel C3N-01415_T C3N-01415_N C C c.1431C>G p.= p.L477L ENST00000302006 4/4 683 645 38 376 376 0 strelka-varscan-mutect IRX1,synonymous_variant,p.=,ENST00000302006,NM_024337.3;CTD-2012M11.3,upstream_gene_variant,,ENST00000559410,; G ENST00000302006 Transcript synonymous_variant 1483/1858 1431/1443 477/480 L ctC/ctG 1 1 IRX1 HGNC HGNC:14358 protein_coding YES CCDS34132.1 ENSP00000305244 P78414 UPI00001B6455 NM_024337.3 4/4 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 3601028 3601028 C G 1 0 0 0 0 0 0 0 1 7751 842 30 4 4 IRX1 5 3601028 Silent SNP C C3N-01415_T 2262032 3601028 177937231 156 23903 CTNND2 0 . GRCh38 5 11384858 11384858 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.984G>A p.= p.P328P ENST00000304623 7/22 495 429 66 295 295 0 strelka-varscan-mutect CTNND2,synonymous_variant,p.=,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,synonymous_variant,p.=,ENST00000511377,NM_001288715.1;CTNND2,intron_variant,,ENST00000503622,NM_001288716.1;CTNND2,intron_variant,,ENST00000502551,;CTNND2,downstream_gene_variant,,ENST00000513598,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506735,;CTNND2,intron_variant,,ENST00000504354,;CTNND2,intron_variant,,ENST00000511278,;CTNND2,upstream_gene_variant,,ENST00000495388,;CTNND2,downstream_gene_variant,,ENST00000514132,;CTNND2,non_coding_transcript_exon_variant,,ENST00000507430,;CTNND2,intron_variant,,ENST00000513588,;CTNND2,intron_variant,,ENST00000504499,; T ENST00000304623 Transcript synonymous_variant 1174/5481 984/3678 328/1225 P ccG/ccA 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 7/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 11384858 11384858 C T 1 0 0 0 0 0 0 0 1 3829 871 31 1 1 CTNND2 5 11384858 Silent SNP C C3N-01415_T 7783830 11384858 170153401 157 23904 FBXL7 0 . GRCh38 5 15928079 15928079 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.317G>T p.Arg106Ile p.R106I ENST00000504595 3/4 204 168 36 132 132 0 strelka-varscan-mutect FBXL7,missense_variant,p.Arg106Ile,ENST00000504595,NM_012304.4;FBXL7,missense_variant,p.Arg64Ile,ENST00000329673,;FBXL7,missense_variant,p.Arg59Ile,ENST00000510662,NM_001278317.1; T ENST00000504595 Transcript missense_variant 798/4562 317/1476 106/491 R/I aGa/aTa 1 1 FBXL7 HGNC HGNC:13604 protein_coding YES CCDS54833.1 ENSP00000423630 Q9UJT9 UPI00000724E0 NM_012304.4 tolerated(0.06) 3/4 hmmpanther:PTHR24006 MODERATE 1 SNV 1 1 PASS rs1293082391 . 0 201 8 0 0 0 0 0 -20 0.9999986 1 1 1 0 T 3 4 78 15928079 15928079 G T 1 0 0 0 0 1 0 0 0 5587 942 33 2 2 FBXL7 5 15928079 Missense_Mutation SNP G C3N-01415_T 4543221 15928079 165610180 158 23905 PRDM9 0 . GRCh38 5 23527703 23527703 + Missense_Mutation SNP G G T rs762274382 C3N-01415_T C3N-01415_N G G c.2615G>T p.Arg872Met p.R872M ENST00000296682 11/11 433 365 68 357 354 3 strelka-varscan PRDM9,missense_variant,p.Arg872Met,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; T ENST00000296682 Transcript missense_variant 2797/3691 2615/2685 872/894 R/M aGg/aTg rs762274382 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0.03) 11/11 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 188 0 5 17 0 0 0 -20 0.01996588 0 1 0 0 T 3 4 78 23527703 23527703 G T 1 0 0 0 0 1 0 0 0 12595 1000 35 2 2 PRDM9 5 23527703 Missense_Mutation SNP G C3N-01415_T 7599624 23527703 158010556 159 23906 CDH9 0 . GRCh38 5 26906829 26906829 + Missense_Mutation SNP A A T C3N-01415_T C3N-01415_N A A c.533T>A p.Val178Asp p.V178D ENST00000231021 4/12 207 120 87 138 137 1 strelka-varscan CDH9,missense_variant,p.Val178Asp,ENST00000231021,NM_016279.3;CDH9,non_coding_transcript_exon_variant,,ENST00000505045,; T ENST00000231021 Transcript missense_variant 706/3079 533/2370 178/789 V/D gTt/gAt COSM3854629 1 -1 CDH9 HGNC HGNC:1768 protein_coding YES CCDS3893.1 ENSP00000231021 Q9ULB4 UPI000013C945 NM_016279.3 deleterious(0) 4/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF99,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313,Prints_domain:PR00205 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 26906829 26906829 A T 1 0 0 0 0 1 0 0 0 2820 43 2 4 4 CDH9 5 26906829 Missense_Mutation SNP A C3N-01415_T 3379126 26906829 154631430 160 23907 TARS 0 . GRCh38 5 33461292 33461292 + Missense_Mutation SNP G G C C3N-01415_T C3N-01415_N G G c.1647G>C p.Glu549Asp p.E549D ENST00000455217 14/20 149 140 9 106 106 0 strelka-varscan TARS,missense_variant,p.Glu516Asp,ENST00000265112,NM_152295.4;TARS,missense_variant,p.Glu516Asp,ENST00000502553,NM_001258437.1;TARS,missense_variant,p.Glu549Asp,ENST00000455217,NM_001258438.1;TARS,non_coding_transcript_exon_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,downstream_gene_variant,,ENST00000504698,; C ENST00000455217 Transcript missense_variant 1769/2523 1647/2271 549/756 E/D gaG/gaC COSM5695189 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 deleterious(0) 14/20 PROSITE_profiles:PS50862,HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF36,TIGRFAM_domain:TIGR00418,Gene3D:3.30.930.10,Pfam_domain:PF00587,Superfamily_domains:SSF55681 1 MODERATE 1 SNV 2 1 1 PASS . . 0 204 6 0 0 0 0 0 -16.53117 0.9999995 1 1 1 0 C 3 2 78 33461292 33461292 G C 1 0 0 0 0 1 0 0 0 15958 956 33 4 4 TARS 5 33461292 Missense_Mutation SNP G C3N-01415_T 6554463 33461292 148076967 161 23908 ADAMTS12 0 . GRCh38 5 33527231 33527231 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.4742G>C p.Arg1581Thr p.R1581T ENST00000504830 24/24 494 465 29 299 299 0 strelka-varscan ADAMTS12,missense_variant,p.Arg1581Thr,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Arg1496Thr,ENST00000352040,; G ENST00000504830 Transcript missense_variant 5078/8774 4742/4785 1581/1594 R/T aGg/aCg 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0.01) 24/24 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999995 1 1 1 0 G 3 3 78 33527231 33527231 C G 1 0 0 0 0 1 0 0 0 301 681 24 4 4 ADAMTS12 5 33527231 Missense_Mutation SNP C C3N-01415_T 65939 33527231 148011028 162 23909 FGF10 0 . GRCh38 5 44388404 44388404 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.279G>T p.Glu93Asp p.E93D ENST00000264664 1/3 684 638 46 520 519 1 strelka-varscan FGF10,missense_variant,p.Glu93Asp,ENST00000264664,NM_004465.1;FGF10,downstream_gene_variant,,ENST00000513107,;FGF10-AS1,upstream_gene_variant,,ENST00000502457,; A ENST00000264664 Transcript missense_variant 394/2193 279/627 93/208 E/D gaG/gaT 1 -1 FGF10 HGNC HGNC:3666 protein_coding YES CCDS3950.1 ENSP00000264664 O15520 UPI000004065F NM_004465.1 tolerated(1) 1/3 hmmpanther:PTHR11486:SF21,hmmpanther:PTHR11486,Gene3D:2.80.10.50,Pfam_domain:PF00167,SMART_domains:SM00442,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 44388404 44388404 C A 1 0 0 0 0 1 0 0 0 5703 912 32 2 2 FGF10 5 44388404 Missense_Mutation SNP C C3N-01415_T 10861173 44388404 137149855 163 23910 ITGA2 0 . GRCh38 5 53055620 53055620 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.862G>T p.Asp288Tyr p.D288Y ENST00000296585 8/30 934 877 57 653 653 0 strelka-varscan-mutect ITGA2,missense_variant,p.Asp288Tyr,ENST00000296585,NM_002203.3;ITGA2,missense_variant,p.Asp288Tyr,ENST00000509960,;ITGA2,missense_variant,p.Asp288Tyr,ENST00000510722,;ITGA2,missense_variant,p.Asp288Tyr,ENST00000509814,;ITGA2,3_prime_UTR_variant,,ENST00000503810,;ITGA2,3_prime_UTR_variant,,ENST00000513685,; T ENST00000296585 Transcript missense_variant 1005/7869 862/3546 288/1181 D/Y Gat/Tat 1 1 ITGA2 HGNC HGNC:6137 protein_coding YES CCDS3957.1 ENSP00000296585 P17301 UPI0000169C36 NM_002203.3 deleterious(0) 8/30 PROSITE_profiles:PS50234,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs1187559883 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 53055620 53055620 G T 1 0 0 0 0 1 0 0 0 7782 1290 45 2 2 ITGA2 5 53055620 Missense_Mutation SNP G C3N-01415_T 8667216 53055620 128482639 164 23911 ARL15 0 . GRCh38 5 54171862 54171862 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.115G>C p.Gly39Arg p.G39R ENST00000504924 2/5 280 164 116 211 211 0 strelka-varscan-mutect ARL15,missense_variant,p.Gly39Arg,ENST00000504924,NM_019087.2;ARL15,missense_variant,p.Gly39Arg,ENST00000620747,;ARL15,missense_variant,p.Gly39Arg,ENST00000507646,;ARL15,intron_variant,,ENST00000502271,;ARL15,non_coding_transcript_exon_variant,,ENST00000510591,;ARL15,non_coding_transcript_exon_variant,,ENST00000505630,;ARL15,non_coding_transcript_exon_variant,,ENST00000505383,; G ENST00000504924 Transcript missense_variant 209/2486 115/615 39/204 G/R Ggc/Cgc 1 -1 ARL15 HGNC HGNC:25945 protein_coding YES CCDS54850.1 ENSP00000433427 Q9NXU5 UPI000006D66A NM_019087.2 deleterious(0) 2/5 Gene3D:3.40.50.300,Pfam_domain:PF00025,Prints_domain:PR00328,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF192,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 54171862 54171862 C G 1 0 0 0 0 1 0 0 0 1070 681 24 4 4 ARL15 5 54171862 Missense_Mutation SNP C C3N-01415_T 1116242 54171862 127366397 165 23912 RNF180 0 . GRCh38 5 64212109 64212109 + Missense_Mutation SNP G G T rs765050615 C3N-01415_T C3N-01415_N G G c.180G>T p.Trp60Cys p.W60C ENST00000389100 3/8 232 214 18 285 285 0 strelka-varscan RNF180,missense_variant,p.Trp60Cys,ENST00000389100,NM_001113561.1;RNF180,missense_variant,p.Trp60Cys,ENST00000296615,NM_178532.3;RNF180,missense_variant,p.Trp60Cys,ENST00000504296,; T ENST00000389100 Transcript missense_variant 252/4906 180/1779 60/592 W/C tgG/tgT rs765050615 1 1 RNF180 HGNC HGNC:27752 protein_coding YES CCDS47219.1 ENSP00000373752 Q86T96 UPI0000141201 NM_001113561.1 deleterious(0) 3/8 hmmpanther:PTHR23327,hmmpanther:PTHR23327:SF18 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99904 0.9999997 1 1 1 0 T 3 4 78 64212109 64212109 G T 1 0 0 0 0 1 0 0 0 13641 1212 42 2 2 RNF180 5 64212109 Missense_Mutation SNP G C3N-01415_T 10040247 64212109 117326150 166 23913 TRIM23 0 . GRCh38 5 65591803 65591803 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.1691A>G p.Gln564Arg p.Q564R ENST00000231524 11/11 179 124 55 238 238 0 strelka-varscan TRIM23,missense_variant,p.Gln564Arg,ENST00000231524,NM_001656.3;TRIM23,intron_variant,,ENST00000381018,NM_033227.2;TRIM23,intron_variant,,ENST00000274327,NM_033228.2;PPWD1,downstream_gene_variant,,ENST00000535264,NM_001278926.1;PPWD1,downstream_gene_variant,,ENST00000261308,NM_015342.3,NM_001278927.1;PPWD1,downstream_gene_variant,,ENST00000538977,NM_001278929.1;PPWD1,downstream_gene_variant,,ENST00000510930,;PPWD1,downstream_gene_variant,,ENST00000511908,;PPWD1,downstream_gene_variant,,ENST00000513773,; C ENST00000231524 Transcript missense_variant 2063/4186 1691/1725 564/574 Q/R cAa/cGa 1 -1 TRIM23 HGNC HGNC:660 protein_coding YES CCDS3987.1 ENSP00000231524 P36406 UPI0000125DB3 NM_001656.3 deleterious(0.02) 11/11 Gene3D:3.40.50.300,Pfam_domain:PF00025,PROSITE_profiles:PS51417,hmmpanther:PTHR11711,SMART_domains:SM00175,SMART_domains:SM00177,SMART_domains:SM00178,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 65591803 65591803 T C 1 0 0 0 0 1 0 0 0 16986 1812 63 5 5 TRIM23 5 65591803 Missense_Mutation SNP T C3N-01415_T 1379694 65591803 115946456 167 23914 MAP1B 0 . GRCh38 5 72196463 72196463 + Silent SNP G G A rs150527364 C3N-01415_T C3N-01415_N G G c.3108G>A p.= p.P1036P ENST00000296755 5/7 297 270 27 393 389 4 strelka-varscan MAP1B,synonymous_variant,p.=,ENST00000296755,NM_001324255.1,NM_005909.3;MAP1B,downstream_gene_variant,,ENST00000504492,;MAP1B,downstream_gene_variant,,ENST00000511641,;MAP1B,downstream_gene_variant,,ENST00000513526,; A ENST00000296755 Transcript synonymous_variant 3406/12036 3108/7407 1036/2468 P ccG/ccA rs150527364,COSM288063 1 1 MAP1B HGNC HGNC:6836 protein_coding YES CCDS4012.1 ENSP00000296755 P46821 UPI000013E382 NM_001324255.1,NM_005909.3 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR13843:SF5,hmmpanther:PTHR13843 0,1 LOW 1 SNV 2 0,1 1 PASS . . 0 206 0 0 4 0 0 0 -8.562107 0.7477283 1 1 1 0 A 2 1 78 72196463 72196463 G A 1 0 0 0 0 0 0 0 1 9151 1103 39 1 1 MAP1B 5 72196463 Silent SNP G C3N-01415_T 6604660 72196463 109341796 168 23915 TMEM171 0 . GRCh38 5 73131579 73131579 + Missense_Mutation SNP G G T rs371795452 C3N-01415_T C3N-01415_N G G c.824G>T p.Cys275Phe p.C275F ENST00000454765 4/4 131 113 18 177 177 0 strelka-varscan TMEM171,missense_variant,p.Cys275Phe,ENST00000454765,NM_173490.7;TMEM171,missense_variant,p.Cys274Phe,ENST00000287773,NM_001161342.2;RP11-232L2.2,downstream_gene_variant,,ENST00000508255,; T ENST00000454765 Transcript missense_variant 1297/1535 824/975 275/324 C/F tGt/tTt rs371795452 1 1 TMEM171 HGNC HGNC:27031 protein_coding YES CCDS4017.1 ENSP00000415030 Q8WVE6 UPI000020CAC5 NM_173490.7 tolerated(0.7) 4/4 hmmpanther:PTHR31617:SF0,hmmpanther:PTHR31617,Pfam_domain:PF15471 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 73131579 73131579 G T 1 0 0 0 0 1 0 0 0 16532 1377 48 2 2 TMEM171 5 73131579 Missense_Mutation SNP G C3N-01415_T 935116 73131579 108406680 169 23916 TMEM174 0 . GRCh38 5 73173865 73173865 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.622C>A p.His208Asn p.H208N ENST00000296776 1/2 80 61 19 127 127 0 strelka-varscan TMEM174,missense_variant,p.His208Asn,ENST00000296776,NM_153217.2;TMEM174,intron_variant,,ENST00000511737,; A ENST00000296776 Transcript missense_variant 671/1759 622/732 208/243 H/N Cac/Aac 1 1 TMEM174 HGNC HGNC:28187 protein_coding YES CCDS4018.1 ENSP00000296776 Q8WUU8 A0A024RAN0 UPI0000037779 NM_153217.2 tolerated(0.54) 1/2 hmmpanther:PTHR31020,Pfam_domain:PF15029 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 73173865 73173865 C A 1 0 0 0 0 1 0 0 0 16534 840 29 2 2 TMEM174 5 73173865 Missense_Mutation SNP C C3N-01415_T 42286 73173865 108364394 170 23917 ANKRD31 0 . GRCh38 5 75196200 75196200 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.448G>T p.Glu150Ter p.E150* ENST00000274361 7/25 58 46 12 83 83 0 strelka-varscan ANKRD31,stop_gained,p.Glu150Ter,ENST00000506364,;ANKRD31,stop_gained,p.Glu150Ter,ENST00000274361,NM_001164443.1; A ENST00000274361 Transcript stop_gained,splice_region_variant 640/6036 448/5622 150/1873 E/* Gaa/Taa 1 -1 ANKRD31 HGNC HGNC:26853 protein_coding YES CCDS47233.1 ENSP00000274361 Q8N7Z5 UPI00001D7FAE NM_001164443.1 7/25 HIGH 1 SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 75196200 75196200 C A 1 0 0 0 0 0 1 0 0 764 869 30 2 2 ANKRD31 5 75196200 Nonsense_Mutation SNP C C3N-01415_T 2022335 75196200 106342059 171 23918 GPR150 0 . GRCh38 5 95621516 95621516 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1241G>A p.Gly414Asp p.G414D ENST00000380007 1/1 292 203 89 356 356 0 strelka-varscan GPR150,missense_variant,p.Gly414Asp,ENST00000380007,NM_199243.1; A ENST00000380007 Transcript missense_variant 1439/2065 1241/1305 414/434 G/D gGc/gAc 1 1 GPR150 HGNC HGNC:23628 protein_coding YES CCDS4074.1 ENSP00000369344 Q8NGU9 G4XH61 UPI000003BCD0 NM_199243.1 tolerated(0.08) 1/1 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF650 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 95621516 95621516 G A 1 0 0 0 0 1 0 0 0 6542 1203 42 3 3 GPR150 5 95621516 Missense_Mutation SNP G C3N-01415_T 20425316 95621516 85916743 172 23919 KCNN2 0 . GRCh38 5 114463126 114463126 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1079G>A p.Gly360Asp p.G360D ENST00000512097 5/9 200 164 36 233 233 0 strelka-varscan KCNN2,missense_variant,p.Gly360Asp,ENST00000512097,;KCNN2,missense_variant,p.Gly360Asp,ENST00000264773,NM_021614.3;KCNN2,missense_variant,p.Gly360Asp,ENST00000631899,;KCNN2,missense_variant,p.Gly12Asp,ENST00000610748,NM_001278204.1;KCNN2,missense_variant,p.Gly12Asp,ENST00000503706,NM_170775.2;KCNN2,non_coding_transcript_exon_variant,,ENST00000507750,;KCNN2,missense_variant,p.Gly12Asp,ENST00000505491,; A ENST00000512097 Transcript missense_variant 2097/3076 1079/1740 360/579 G/D gGt/gAt 1 1 KCNN2 HGNC HGNC:6291 protein_coding YES CCDS4114.1 ENSP00000427120 Q9H2S1 UPI000013D56A deleterious(0) 5/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR10153,hmmpanther:PTHR10153:SF43,Gene3D:1.10.287.70,Pfam_domain:PF07885,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 114463126 114463126 G A 1 0 0 0 0 1 0 0 0 7995 1261 44 3 3 KCNN2 5 114463126 Missense_Mutation SNP G C3N-01415_T 18841610 114463126 67075133 173 23920 FBN2 0 . GRCh38 5 128263512 128263512 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.8105C>A p.Ser2702Tyr p.S2702Y ENST00000508053 69/71 477 349 128 601 601 0 strelka-varscan-mutect FBN2,missense_variant,p.Ser2702Tyr,ENST00000508053,;FBN2,missense_variant,p.Ser2702Tyr,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Ser2701Tyr,ENST00000619499,; T ENST00000508053 Transcript missense_variant 9080/11132 8105/8739 2702/2912 S/Y tCc/tAc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(1) 69/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 128263512 128263512 G T 1 0 0 0 0 1 0 0 0 5566 1174 41 2 2 FBN2 5 128263512 Missense_Mutation SNP G C3N-01415_T 13800386 128263512 53274747 174 23921 FBN2 0 . GRCh38 5 128291564 128291564 + Frame_Shift_Del DEL C C - novel C3N-01415_T C3N-01415_N C C c.6257delG p.Gly2086AlafsTer163 p.G2086Afs*163 ENST00000508053 55/71 312 280 32 430 430 0 sindel-varindel-pindel FBN2,frameshift_variant,p.Gly2086AlafsTer163,ENST00000508053,;FBN2,frameshift_variant,p.Gly2086AlafsTer163,ENST00000262464,NM_001999.3;FBN2,frameshift_variant,p.Gly2085AlafsTer163,ENST00000619499,; - ENST00000508053 Transcript frameshift_variant 7232/11132 6257/8739 2086/2912 G/X gGc/gc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 55/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 128291564 128291564 C - 1 0 1 0 1 0 0 0 0 5566 739 26 0 0 FBN2 5 128291564 Frame_Shift_Del DEL C C3N-01415_T 28052 128291564 53246695 175 23922 TRPC7 0 . GRCh38 5 136213449 136213449 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.2575G>A p.Gly859Ser p.G859S ENST00000513104 12/12 145 104 41 198 198 0 strelka-varscan-mutect TRPC7,missense_variant,p.Gly859Ser,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Gly804Ser,ENST00000502753,;TRPC7,missense_variant,p.Gly798Ser,ENST00000378459,NM_001167577.1;TRPC7,missense_variant,p.Gly743Ser,ENST00000352189,NM_001167576.1;TRPC7-AS1,upstream_gene_variant,,ENST00000514459,;TRPC7,3_prime_UTR_variant,,ENST00000503275,;TRPC7,3_prime_UTR_variant,,ENST00000514963,;TRPC7,non_coding_transcript_exon_variant,,ENST00000509288,; T ENST00000513104 Transcript missense_variant 2858/2987 2575/2589 859/862 G/S Ggc/Agc 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 deleterious_low_confidence(0.03) 12/12 Prints_domain:PR01648,hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 136213449 136213449 C T 1 0 0 0 0 1 0 0 0 17090 623 22 3 3 TRPC7 5 136213449 Missense_Mutation SNP C C3N-01415_T 7921885 136213449 45324810 176 23923 PCDHA8 0 . GRCh38 5 140841829 140841829 + Missense_Mutation SNP T T A C3N-01415_T C3N-01415_N T T c.508T>A p.Tyr170Asn p.Y170N ENST00000531613 1/4 274 231 43 412 412 0 strelka-varscan-mutect PCDHA8,missense_variant,p.Tyr170Asn,ENST00000531613,NM_018911.2;PCDHA8,missense_variant,p.Tyr170Asn,ENST00000378123,NM_031856.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA7,downstream_gene_variant,,ENST00000356878,NM_031852.1; A ENST00000531613 Transcript missense_variant 508/5260 508/2853 170/950 Y/N Tac/Aac COSM736204 1 1 PCDHA8 HGNC HGNC:8674 protein_coding YES CCDS54919.1 ENSP00000434655 Q9Y5H6 UPI00001273D0 NM_018911.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF125,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS rs1470654104 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 140841829 140841829 T A 1 0 0 0 0 1 0 0 0 11617 1522 53 4 4 PCDHA8 5 140841829 Missense_Mutation SNP T C3N-01415_T 4628380 140841829 40696430 177 23924 PCDHB11 0 . GRCh38 5 141201787 141201787 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.2013G>T p.= p.L671L ENST00000354757 1/1 438 313 125 588 587 1 strelka-varscan-mutect PCDHB11,synonymous_variant,p.=,ENST00000354757,NM_018931.2;PCDHB11,synonymous_variant,p.=,ENST00000624887,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624549,; T ENST00000354757 Transcript synonymous_variant 2206/4198 2013/2394 671/797 L ctG/ctT 1 1 PCDHB11 HGNC HGNC:8682 protein_coding YES CCDS4253.1 ENSP00000346802 Q9Y5F2 UPI00001273E6 NM_018931.2 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF91,Low_complexity_(Seg):seg LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 141201787 141201787 G T 1 0 0 0 0 0 0 0 1 11623 1306 46 2 2 PCDHB11 5 141201787 Silent SNP G C3N-01415_T 359958 141201787 40336472 178 23925 PCDHGB2 0 . GRCh38 5 141360257 141360257 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.122T>A p.Leu41Gln p.L41Q ENST00000522605 1/4 232 165 67 336 334 2 strelka-varscan-mutect PCDHGB2,missense_variant,p.Leu41Gln,ENST00000522605,NM_018923.2;PCDHGB2,missense_variant,p.Leu41Gln,ENST00000622527,NM_032096.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA5,upstream_gene_variant,,ENST00000518069,NM_018918.2;PCDHGA5,upstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA4,downstream_gene_variant,,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000522605 Transcript missense_variant 122/4602 122/2796 41/931 L/Q cTg/cAg 1 1 PCDHGB2 HGNC HGNC:8709 protein_coding YES CCDS54924.1 ENSP00000429018 Q9Y5G2 UPI000006EE67 NM_018923.2 deleterious(0.03) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF73,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF08266,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 141360257 141360257 T A 1 0 0 0 0 1 0 0 0 11650 1580 55 4 4 PCDHGB2 5 141360257 Missense_Mutation SNP T C3N-01415_T 158470 141360257 40178002 179 23926 PCDHGA6 0 . GRCh38 5 141374603 141374603 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.520G>T p.Gly174Cys p.G174C ENST00000517434 1/4 161 132 29 227 227 0 strelka-varscan-mutect PCDHGA6,missense_variant,p.Gly174Cys,ENST00000610583,NM_032086.1;PCDHGA6,missense_variant,p.Gly174Cys,ENST00000517434,NM_018919.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB3,downstream_gene_variant,,ENST00000618934,NM_032097.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000517434 Transcript missense_variant 690/4775 520/2799 174/932 G/C Ggt/Tgt COSM1186856 1 1 PCDHGA6 HGNC HGNC:8704 protein_coding YES CCDS54926.1 ENSP00000429601 Q9Y5G7 UPI00000715C8 NM_018919.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF107,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 141374603 141374603 G T 1 0 0 0 0 1 0 0 0 11645 1348 47 2 2 PCDHGA6 5 141374603 Missense_Mutation SNP G C3N-01415_T 14346 141374603 40163656 180 23927 FAM114A2 0 . GRCh38 5 153994957 153994957 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1345G>T p.Asp449Tyr p.D449Y ENST00000351797 13/14 297 252 45 224 224 0 strelka-varscan-mutect FAM114A2,missense_variant,p.Asp449Tyr,ENST00000351797,NM_001317993.1,NM_001317995.1,NM_018691.2;FAM114A2,missense_variant,p.Asp449Tyr,ENST00000522858,;FAM114A2,missense_variant,p.Asp449Tyr,ENST00000520667,;FAM114A2,missense_variant,p.Asp379Tyr,ENST00000520313,;FAM114A2,non_coding_transcript_exon_variant,,ENST00000518946,;FAM114A2,non_coding_transcript_exon_variant,,ENST00000518914,; A ENST00000351797 Transcript missense_variant 1422/4443 1345/1518 449/505 D/Y Gat/Tat 1 -1 FAM114A2 HGNC HGNC:1333 protein_coding YES CCDS4323.1 ENSP00000341597 Q9NRY5 A0A140VKG4 UPI000013D5DA NM_001317993.1,NM_001317995.1,NM_018691.2 deleterious(0) 13/14 hmmpanther:PTHR12842:SF3,hmmpanther:PTHR12842 MODERATE 1 SNV 1 1 PASS rs1206151581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 153994957 153994957 C A 1 0 0 0 0 1 0 0 0 5267 913 32 2 2 FAM114A2 5 153994957 Missense_Mutation SNP C C3N-01415_T 12620354 153994957 27543302 181 23928 CCNJL 0 . GRCh38 5 160253571 160253571 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1115G>T p.Gly372Val p.G372V ENST00000393977 7/7 264 241 23 178 178 0 strelka-varscan-mutect CCNJL,missense_variant,p.Gly372Val,ENST00000393977,NM_024565.5;CCNJL,missense_variant,p.Gly353Val,ENST00000541762,;CCNJL,missense_variant,p.Gly324Val,ENST00000257536,NM_001308173.1;CCNJL,downstream_gene_variant,,ENST00000519673,;CCNJL,non_coding_transcript_exon_variant,,ENST00000377503,;RP11-34P1.2,upstream_gene_variant,,ENST00000522428,; A ENST00000393977 Transcript missense_variant 1401/3320 1115/1308 372/435 G/V gGg/gTg 1 -1 CCNJL HGNC HGNC:25876 protein_coding YES CCDS4350.2 ENSP00000377547 Q8IV13 UPI000020C075 NM_024565.5 deleterious(0) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 160253571 160253571 C A 1 0 0 0 0 1 0 0 0 2628 623 22 2 2 CCNJL 5 160253571 Missense_Mutation SNP C C3N-01415_T 6258614 160253571 21284688 182 23929 HMMR 0 . GRCh38 5 163475667 163475667 + Silent SNP G G A rs766280399 C3N-01415_T C3N-01415_N G G c.1263G>A p.= p.L421L ENST00000393915 11/18 180 168 12 167 167 0 strelka-varscan-mutect HMMR,synonymous_variant,p.=,ENST00000393915,NM_001142556.1;HMMR,synonymous_variant,p.=,ENST00000358715,NM_012484.2;HMMR,synonymous_variant,p.=,ENST00000353866,NM_012485.2;HMMR,synonymous_variant,p.=,ENST00000432118,NM_001142557.1;HMMR,downstream_gene_variant,,ENST00000520345,;HMMR,downstream_gene_variant,,ENST00000522094,; A ENST00000393915 Transcript synonymous_variant 1406/3102 1263/2178 421/725 L ctG/ctA rs766280399,COSM462019 1 1 HMMR HGNC HGNC:5012 protein_coding YES CCDS47334.1 ENSP00000377492 O75330 UPI00001AE676 NM_001142556.1 11/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18956,Low_complexity_(Seg):seg 0,1 LOW 1 SNV 1 0,1 1 PASS rs766280399 . 0 208 2 0 0 0 0 0 -19.9919 1 1 1 1 0 A 2 1 78 163475667 163475667 G A 1 0 0 0 0 0 0 0 1 7133 1304 45 3 3 HMMR 5 163475667 Silent SNP G C3N-01415_T 3222096 163475667 18062592 183 23930 TENM2 0 . GRCh38 5 168218348 168218348 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.4457G>T p.Gly1486Val p.G1486V ENST00000518659 23/29 396 282 114 336 336 0 strelka-varscan-mutect TENM2,missense_variant,p.Gly1365Val,ENST00000519204,;TENM2,missense_variant,p.Gly1486Val,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Gly1247Val,ENST00000520394,; T ENST00000518659 Transcript missense_variant 4496/8550 4457/8325 1486/2774 G/V gGg/gTg 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 23/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2.120.10.30,Superfamily_domains:SSF101898,Superfamily_domains:SSF50969 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 168218348 168218348 G T 1 0 0 0 0 1 0 0 0 16172 1232 43 2 2 TENM2 5 168218348 Missense_Mutation SNP G C3N-01415_T 4742681 168218348 13319911 184 23931 FGF18 0 . GRCh38 5 171456696 171456696 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.515T>C p.Val172Ala p.V172A ENST00000274625 5/5 676 625 51 437 437 0 strelka-varscan-mutect FGF18,missense_variant,p.Val172Ala,ENST00000274625,NM_003862.2; C ENST00000274625 Transcript missense_variant 1059/1986 515/624 172/207 V/A gTg/gCg 1 1 FGF18 HGNC HGNC:3674 protein_coding YES CCDS4378.1 ENSP00000274625 O76093 UPI000003C116 NM_003862.2 tolerated(0.2) 5/5 Gene3D:2.80.10.50,Pfam_domain:PF00167,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF4,SMART_domains:SM00442,Superfamily_domains:SSF50353 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 171456696 171456696 T C 1 0 0 0 0 1 0 0 0 5710 1696 59 5 5 FGF18 5 171456696 Missense_Mutation SNP T C3N-01415_T 3238348 171456696 10081563 185 23932 NEURL1B 0 . GRCh38 5 172669926 172669926 + Frame_Shift_Del DEL G G - novel C3N-01415_T C3N-01415_N G G c.175delG p.Ala59ProfsTer51 p.A59Pfs*51 ENST00000369800 2/5 146 134 12 69 69 0 varindel-pindel NEURL1B,frameshift_variant,p.Ala59ProfsTer51,ENST00000369800,NM_001142651.1;NEURL1B,frameshift_variant,p.Ala59ProfsTer51,ENST00000520919,NM_001308178.1;NEURL1B,intron_variant,,ENST00000522853,; - ENST00000369800 Transcript frameshift_variant 314/6424 173/1668 58/555 R/X cGg/cg 1 1 NEURL1B HGNC HGNC:35422 protein_coding YES CCDS47342.1 ENSP00000358815 A8MQ27 UPI0000D6E5EA NM_001142651.1 2/5 PROSITE_profiles:PS51065,hmmpanther:PTHR12429,Pfam_domain:PF07177,SMART_domains:SM00588 HIGH 1 deletion 1 2 1 PASS . . 0 204 6 0 0 0 0 0 -19.99848 0.9999998 1 1 1 0 - 7 5 78 172669926 172669926 G - 1 0 1 0 1 0 0 0 0 10381 1116 39 0 0 NEURL1B 5 172669926 Frame_Shift_Del DEL G C3N-01415_T 1213230 172669926 8868333 186 23933 C5orf47 0 . GRCh38 5 173989404 173989404 + Silent SNP A A T novel C3N-01415_T C3N-01415_N A A c.141A>T p.= p.A47A ENST00000340147 1/5 96 63 33 59 59 0 strelka-varscan-mutect C5orf47,synonymous_variant,p.=,ENST00000340147,NM_001144954.1;C5orf47,intron_variant,,ENST00000522195,; T ENST00000340147 Transcript synonymous_variant 246/2522 141/531 47/176 A gcA/gcT 1 1 C5orf47 HGNC HGNC:27026 protein_coding YES CCDS47343.1 ENSP00000340887 Q569G3 UPI00001603F7 NM_001144954.1 1/5 Pfam_domain:PF15730,hmmpanther:PTHR38655,hmmpanther:PTHR38655:SF1,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 173989404 173989404 A T 1 0 0 0 0 0 0 0 1 2103 175 7 4 4 C5orf47 5 173989404 Silent SNP A C3N-01415_T 1319478 173989404 7548855 187 23934 C5orf47 0 . GRCh38 5 173998194 173998194 + Missense_Mutation SNP A A T rs553250617 C3N-01415_T C3N-01415_N A A c.367A>T p.Ile123Leu p.I123L ENST00000340147 2/5 347 228 119 233 232 1 strelka-varscan-mutect C5orf47,missense_variant,p.Ile123Leu,ENST00000340147,NM_001144954.1;C5orf47,intron_variant,,ENST00000522195,; T ENST00000340147 Transcript missense_variant 472/2522 367/531 123/176 I/L Ata/Tta rs553250617 1 1 C5orf47 HGNC HGNC:27026 protein_coding YES CCDS47343.1 ENSP00000340887 Q569G3 UPI00001603F7 NM_001144954.1 deleterious(0.02) 2/5 Pfam_domain:PF15730,hmmpanther:PTHR38655,hmmpanther:PTHR38655:SF1 MODERATE 1 SNV 1 1 PASS rs553250617 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 173998194 173998194 A T 1 0 0 0 0 1 0 0 0 2103 217 8 4 4 C5orf47 5 173998194 Missense_Mutation SNP A C3N-01415_T 8790 173998194 7540065 188 23935 HK3 0 . GRCh38 5 176889495 176889495 + Missense_Mutation SNP C C A rs545419310 C3N-01415_T C3N-01415_N C C c.800G>T p.Arg267Leu p.R267L ENST00000292432 8/19 512 484 28 310 309 1 strelka-varscan-mutect HK3,missense_variant,p.Arg267Leu,ENST00000292432,NM_002115.2;HK3,intron_variant,,ENST00000509717,;HK3,upstream_gene_variant,,ENST00000506834,;HK3,downstream_gene_variant,,ENST00000504910,; A ENST00000292432 Transcript missense_variant 892/3066 800/2772 267/923 R/L cGc/cTc rs545419310 1 -1 HK3 HGNC HGNC:4925 protein_coding YES CCDS4407.1 ENSP00000292432 P52790 A0A024R7R1 UPI000006E237 NM_002115.2 deleterious(0) 8/19 PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF1,Gene3D:3.40.367.20,Pfam_domain:PF03727,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs545419310 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 176889495 176889495 C A 1 0 0 0 0 1 0 0 0 7081 768 27 1 1 HK3 5 176889495 Missense_Mutation SNP C C3N-01415_T 2891301 176889495 4648764 189 23936 ADAMTS2 0 . GRCh38 5 179345232 179345232 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.97C>A p.Pro33Thr p.P33T ENST00000251582 1/22 68 50 18 32 32 0 strelka-varscan-mutect ADAMTS2,missense_variant,p.Pro33Thr,ENST00000251582,NM_014244.4;ADAMTS2,missense_variant,p.Pro33Thr,ENST00000274609,NM_021599.2; T ENST00000251582 Transcript missense_variant 199/6754 97/3636 33/1211 P/T Ccg/Acg 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 tolerated_low_confidence(0.13) 1/22 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 17 187 3 3 0 0 0 0 -20 0.9999463 1 1 1 0 T 3 4 78 179345232 179345232 G T 1 0 0 0 0 1 0 0 0 309 1203 42 2 2 ADAMTS2 5 179345232 Missense_Mutation SNP G C3N-01415_T 2455737 179345232 2193027 190 23937 LTC4S 0 . GRCh38 5 179796014 179796014 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.303G>A p.= p.A101A ENST00000292596 4/5 420 393 27 287 287 0 strelka-varscan-mutect LTC4S,synonymous_variant,p.=,ENST00000292596,NM_145867.1;LTC4S,synonymous_variant,p.=,ENST00000401985,;MGAT4B,downstream_gene_variant,,ENST00000337755,NM_054013.3;MGAT4B,downstream_gene_variant,,ENST00000292591,NM_014275.4;MGAT4B,downstream_gene_variant,,ENST00000519836,;MGAT4B,downstream_gene_variant,,ENST00000518778,;MGAT4B,downstream_gene_variant,,ENST00000520969,;MGAT4B,downstream_gene_variant,,ENST00000523108,;MGAT4B,downstream_gene_variant,,ENST00000518980,;MGAT4B,downstream_gene_variant,,ENST00000520875,;MGAT4B,downstream_gene_variant,,ENST00000518867,;MIR1229,downstream_gene_variant,,ENST00000408467,;MAML1,non_coding_transcript_exon_variant,,ENST00000503050,;MGAT4B,downstream_gene_variant,,ENST00000521305,;MGAT4B,downstream_gene_variant,,ENST00000523382,;MGAT4B,downstream_gene_variant,,ENST00000522293,;LTC4S,3_prime_UTR_variant,,ENST00000505170,;LTC4S,non_coding_transcript_exon_variant,,ENST00000465572,;LTC4S,non_coding_transcript_exon_variant,,ENST00000466071,;LTC4S,non_coding_transcript_exon_variant,,ENST00000509898,;LTC4S,non_coding_transcript_exon_variant,,ENST00000486713,;LTC4S,non_coding_transcript_exon_variant,,ENST00000510544,;MGAT4B,downstream_gene_variant,,ENST00000520918,;MGAT4B,downstream_gene_variant,,ENST00000520822,;MGAT4B,downstream_gene_variant,,ENST00000521855,;MGAT4B,downstream_gene_variant,,ENST00000522451,;MGAT4B,downstream_gene_variant,,ENST00000523329,;MGAT4B,downstream_gene_variant,,ENST00000518702,; A ENST00000292596 Transcript synonymous_variant 398/666 303/453 101/150 A gcG/gcA 1 1 LTC4S HGNC HGNC:6719 protein_coding YES CCDS34316.1 ENSP00000292596 Q16873 UPI0000043F83 NM_145867.1 4/5 hmmpanther:PTHR10250:SF4,hmmpanther:PTHR10250,Gene3D:1.20.120.550,Pfam_domain:PF01124,Superfamily_domains:SSF161084,Prints_domain:PR00488 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 179796014 179796014 G A 1 0 0 0 0 0 0 0 1 8984 1074 38 1 1 LTC4S 5 179796014 Silent SNP G C3N-01415_T 450782 179796014 1742245 191 23938 GFPT2 0 . GRCh38 5 180335921 180335921 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.247G>C p.Glu83Gln p.E83Q ENST00000253778 4/19 142 133 9 89 89 0 strelka-mutect GFPT2,missense_variant,p.Glu83Gln,ENST00000253778,NM_005110.2;GFPT2,upstream_gene_variant,,ENST00000518906,;GFPT2,downstream_gene_variant,,ENST00000503228,;GFPT2,upstream_gene_variant,,ENST00000518185,;GFPT2,non_coding_transcript_exon_variant,,ENST00000503546,;GFPT2,non_coding_transcript_exon_variant,,ENST00000518158,; G ENST00000253778 Transcript missense_variant 417/3093 247/2049 83/682 E/Q Gag/Cag 1 -1 GFPT2 HGNC HGNC:4242 protein_coding YES CCDS43411.1 ENSP00000253778 O94808 A0A0S2Z4X9 UPI000014F5AC NM_005110.2 tolerated(0.45) 4/19 Gene3D:3.60.20.10,Pfam_domain:PF13522,PROSITE_profiles:PS51278,hmmpanther:PTHR10937,hmmpanther:PTHR10937:SF10,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS rs902531269 . 0 206 4 0 0 0 0 0 -16.91851 1 1 1 1 0 G 3 3 78 180335921 180335921 C G 1 0 0 0 0 1 0 0 0 6220 835 29 4 4 GFPT2 5 180335921 Missense_Mutation SNP C C3N-01415_T 539907 180335921 1202338 192 23939 BTNL9 0 . GRCh38 5 181059653 181059653 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1399G>T p.Asp467Tyr p.D467Y ENST00000327705 11/11 626 543 83 442 441 1 strelka-varscan-mutect BTNL9,missense_variant,p.Asp467Tyr,ENST00000327705,NM_152547.4;BTNL9,downstream_gene_variant,,ENST00000376841,NM_001308245.1;BTNL9,downstream_gene_variant,,ENST00000491209,;BTNL9,downstream_gene_variant,,ENST00000512570,;BTNL9,downstream_gene_variant,,ENST00000506782,;BTNL9,downstream_gene_variant,,ENST00000511056,; T ENST00000327705 Transcript missense_variant 1630/3500 1399/1608 467/535 D/Y Gac/Tac 1 1 BTNL9 HGNC HGNC:24176 protein_coding YES CCDS4460.2 ENSP00000330200 Q6UXG8 UPI000004C620 NM_152547.4 deleterious(0) 11/11 PROSITE_profiles:PS50188,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF62,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1295595400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 181059653 181059653 G T 1 0 0 0 0 1 0 0 0 1744 1058 37 1 1 BTNL9 5 181059653 Missense_Mutation SNP G C3N-01415_T 723732 181059653 478606 193 23940 IRF4 0 . GRCh38 6 395910 395910 + Missense_Mutation SNP C C T rs755460615 C3N-01415_T C3N-01415_N C C c.467C>T p.Thr156Met p.T156M ENST00000380956 4/9 377 295 82 352 351 1 strelka-varscan-mutect IRF4,missense_variant,p.Thr156Met,ENST00000380956,NM_002460.3,NM_001195286.1;IRF4,non_coding_transcript_exon_variant,,ENST00000495137,;IRF4,non_coding_transcript_exon_variant,,ENST00000468485,;IRF4,non_coding_transcript_exon_variant,,ENST00000469834,;IRF4,missense_variant,p.Thr156Met,ENST00000493114,; T ENST00000380956 Transcript missense_variant 593/5331 467/1356 156/451 T/M aCg/aTg rs755460615 1 1 IRF4 HGNC HGNC:6119 protein_coding YES CCDS4469.1 ENSP00000370343 Q15306 UPI000012D88B NM_002460.3,NM_001195286.1 tolerated(0.08) 4/9 hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF6 MODERATE 1 SNV 1 1 PASS rs755460615 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 395910 395910 C T 1 0 0 0 0 1 0 0 0 7739 536 19 1 1 IRF4 6 395910 Missense_Mutation SNP C C3N-01415_T 395910 170410069 194 23941 MYLK4 0 . GRCh38 6 2685488 2685488 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.430G>T p.Asp144Tyr p.D144Y ENST00000274643 5/13 226 201 25 236 236 0 strelka-varscan-mutect MYLK4,missense_variant,p.Asp144Tyr,ENST00000274643,NM_001012418.3; A ENST00000274643 Transcript missense_variant 773/5806 430/1167 144/388 D/Y Gac/Tac 1 -1 MYLK4 HGNC HGNC:27972 protein_coding YES CCDS34330.1 ENSP00000274643 Q86YV6 UPI00000498AE NM_001012418.3 deleterious(0) 5/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF119,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 2685488 2685488 C A 1 0 0 0 0 1 0 0 0 10059 869 30 2 2 MYLK4 6 2685488 Missense_Mutation SNP C C3N-01415_T 2289578 2685488 168120491 195 23942 SLC22A23 0 . GRCh38 6 3283926 3283926 + Silent SNP C C T rs566206184 C3N-01415_T C3N-01415_N C C c.1629G>A p.= p.V543V ENST00000406686 9/10 143 126 17 166 166 0 strelka-varscan-mutect SLC22A23,synonymous_variant,p.=,ENST00000436008,;SLC22A23,synonymous_variant,p.=,ENST00000406686,NM_015482.1;SLC22A23,synonymous_variant,p.=,ENST00000380302,NM_001286455.1;SLC22A23,synonymous_variant,p.=,ENST00000490273,NM_021945.6;SLC22A23,synonymous_variant,p.=,ENST00000485307,;SLC22A23,synonymous_variant,p.=,ENST00000467177,;PSMG4,intron_variant,,ENST00000454610,;PSMG4,intron_variant,,ENST00000451246,;SLC22A23,downstream_gene_variant,,ENST00000467144,;SLC22A23,3_prime_UTR_variant,,ENST00000497691,;SLC22A23,non_coding_transcript_exon_variant,,ENST00000482874,; T ENST00000406686 Transcript synonymous_variant 1629/5658 1629/2061 543/686 V gtG/gtA rs566206184 1 -1 SLC22A23 HGNC HGNC:21106 protein_coding YES CCDS47363.1 ENSP00000385028 A1A5C7 UPI0000EE5391 NM_015482.1 9/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF192,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS rs566206184 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 3283926 3283926 C T 1 0 0 0 0 0 0 0 1 14717 581 21 3 3 SLC22A23 6 3283926 Silent SNP C C3N-01415_T 598438 3283926 167522053 196 23943 FAM217A 0 . GRCh38 6 4074662 4074662 + Splice_Site SNP C C G C3N-01415_T C3N-01415_N C C c.61-1G>C p.X21_splice ENST00000274673 181 160 21 201 201 0 strelka-varscan-mutect FAM217A,splice_acceptor_variant,,ENST00000274673,NM_173563.2;FAM217A,splice_acceptor_variant,,ENST00000492651,;FAM217A,intron_variant,,ENST00000498677,;C6orf201,upstream_gene_variant,,ENST00000380175,NM_001085401.2;FAM217A,splice_acceptor_variant,,ENST00000478714,;FAM217A,intron_variant,,ENST00000380188,;FAM217A,intron_variant,,ENST00000469157,;C6orf201,upstream_gene_variant,,ENST00000427996,; G ENST00000274673 Transcript splice_acceptor_variant -/2265 61/1527 21/508 COSM1079140 1 -1 FAM217A HGNC HGNC:21362 protein_coding YES CCDS4489.1 ENSP00000274673 Q8IXS0 UPI0000160AA7 NM_173563.2 2/6 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 78 4074662 4074662 C G 1 0 0 0 0 0 0 1 0 5406 927 32 4 4 FAM217A 6 4074662 Splice_Site SNP C C3N-01415_T 790736 4074662 166731317 197 23944 DSP 0 . GRCh38 6 7577804 7577804 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.2903A>G p.Tyr968Cys p.Y968C ENST00000379802 21/24 440 399 41 452 452 0 strelka-varscan-mutect DSP,missense_variant,p.Tyr968Cys,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Tyr968Cys,ENST00000418664,NM_001008844.1; G ENST00000379802 Transcript missense_variant 3244/9796 2903/8616 968/2871 Y/C tAc/tGc 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 deleterious(0) 21/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,SMART_domains:SM00150 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 7577804 7577804 A G 1 0 0 0 0 1 0 0 0 4602 391 14 5 5 DSP 6 7577804 Missense_Mutation SNP A C3N-01415_T 3503142 7577804 163228175 198 23945 SLC17A3 0 . GRCh38 6 25861960 25861960 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.373C>A p.Leu125Met p.L125M ENST00000397060 4/13 227 200 27 218 218 0 strelka-varscan-mutect SLC17A3,missense_variant,p.Leu125Met,ENST00000397060,NM_001098486.1;SLC17A3,intron_variant,,ENST00000360657,;SLC17A3,intron_variant,,ENST00000361703,NM_006632.3;SLC17A3,non_coding_transcript_exon_variant,,ENST00000308453,;SLC17A3,intron_variant,,ENST00000509714,;SLC17A3,intron_variant,,ENST00000506105,;SLC17A3,intron_variant,,ENST00000503922,;SLC17A3,intron_variant,,ENST00000449356,; T ENST00000397060 Transcript missense_variant 483/2052 373/1497 125/498 L/M Ctg/Atg 1 -1 SLC17A3 HGNC HGNC:10931 protein_coding YES CCDS47385.1 ENSP00000380250 O00476 UPI0001536779 NM_001098486.1 deleterious(0.02) 4/13 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF134,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS rs1400780544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 25861960 25861960 G T 1 0 0 0 0 1 0 0 0 14683 1020 36 2 2 SLC17A3 6 25861960 Missense_Mutation SNP G C3N-01415_T 18284156 25861960 144944019 199 23946 HIST1H2AE 0 . GRCh38 6 26217333 26217333 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.359A>G p.Lys120Arg p.K120R ENST00000303910 1/1 310 290 20 283 283 0 strelka-varscan-mutect HIST1H2AE,missense_variant,p.Lys120Arg,ENST00000303910,NM_021052.2;HIST1H2BG,upstream_gene_variant,,ENST00000541790,NM_003518.3;RP1-34B20.19,upstream_gene_variant,,ENST00000611953,; G ENST00000303910 Transcript missense_variant 359/509 359/393 120/130 K/R aAg/aGg 1 1 HIST1H2AE HGNC HGNC:4724 protein_coding YES CCDS4595.1 ENSP00000303373 P04908 Q08AJ9 UPI00000007AF NM_021052.2 deleterious_low_confidence(0.02) 1/1 hmmpanther:PTHR23430,Pfam_domain:PF16211,Gene3D:1.10.20.10,SMART_domains:SM00414,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 26217333 26217333 A G 1 0 0 0 0 1 0 0 0 7020 72 3 5 5 HIST1H2AE 6 26217333 Missense_Mutation SNP A C3N-01415_T 355373 26217333 144588646 200 23947 HIST1H3I 0 . GRCh38 6 27872163 27872163 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.153G>T p.Glu51Asp p.E51D ENST00000616365 1/1 278 251 27 317 317 0 strelka-varscan-mutect HIST1H3I,missense_variant,p.Glu51Asp,ENST00000616365,NM_003533.2;HIST1H1B,upstream_gene_variant,,ENST00000331442,NM_005322.2;HIST1H4L,downstream_gene_variant,,ENST00000618305,NM_003546.2; A ENST00000616365 Transcript missense_variant 153/411 153/411 51/136 E/D gaG/gaT 1 -1 HIST1H3I HGNC HGNC:4771 protein_coding YES CCDS4636.1 ENSP00000483283 P68431 UPI00000003C7 NM_003533.2 deleterious_low_confidence(0.03) 1/1 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 27872163 27872163 C A 1 0 0 0 0 1 0 0 0 7051 912 32 2 2 HIST1H3I 6 27872163 Missense_Mutation SNP C C3N-01415_T 1654830 27872163 142933816 201 23948 ZBED9 0 . GRCh38 6 28573320 28573320 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.2569G>T p.Gly857Cys p.G857C ENST00000452236 4/4 680 514 166 688 688 0 strelka-varscan-mutect ZBED9,missense_variant,p.Gly857Cys,ENST00000452236,NM_052923.1;ZBED9,downstream_gene_variant,,ENST00000530247,; A ENST00000452236 Transcript missense_variant 3187/4877 2569/3978 857/1325 G/C Ggt/Tgt 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 deleterious(0.01) 4/4 hmmpanther:PTHR11697:SF108,hmmpanther:PTHR11697 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 28573320 28573320 C A 1 0 0 0 0 1 0 0 0 18086 623 22 2 2 ZBED9 6 28573320 Missense_Mutation SNP C C3N-01415_T 701157 28573320 142232659 202 23949 OR10C1 0 . GRCh38 6 29440133 29440133 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.118G>T p.Gly40Cys p.G40C ENST00000444197 1/1 468 396 72 422 422 0 strelka-varscan-mutect OR10C1,missense_variant,p.Gly40Cys,ENST00000444197,NM_013941.3;OR10C1,missense_variant,p.Gly42Cys,ENST00000622521,;OR11A1,intron_variant,,ENST00000377149,; T ENST00000444197 Transcript missense_variant 828/1649 118/939 40/312 G/C Ggc/Tgc 1 1 OR10C1 HGNC HGNC:8165 protein_coding YES CCDS34364.1 ENSP00000419119 Q96KK4 A0A126GV80 UPI000014068E NM_013941.3 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF191,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 29440133 29440133 G T 1 0 0 0 0 1 0 0 0 10973 1000 35 2 2 OR10C1 6 29440133 Missense_Mutation SNP G C3N-01415_T 866813 29440133 141365846 203 23950 OR2H2 0 . GRCh38 6 29588053 29588053 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.109C>A p.Leu37Ile p.L37I ENST00000383640 1/1 302 283 19 311 311 0 strelka-varscan-mutect OR2H2,missense_variant,p.Leu37Ile,ENST00000383640,NM_007160.3;GABBR1,intron_variant,,ENST00000355973,; A ENST00000383640 Transcript missense_variant 599/1584 109/939 37/312 L/I Cta/Ata 1 1 OR2H2 HGNC HGNC:8253 protein_coding YES CCDS34365.1 ENSP00000373136 O95918 UPI00001404DC NM_007160.3 tolerated(0.27) 1/1 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF199,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 29588053 29588053 C A 1 0 0 0 0 1 0 0 0 11080 680 24 2 2 OR2H2 6 29588053 Missense_Mutation SNP C C3N-01415_T 147920 29588053 141217926 204 23951 TRIM26 0 . GRCh38 6 30198721 30198721 + Missense_Mutation SNP C C A C3N-01415_T C3N-01415_N C C c.383G>T p.Arg128Leu p.R128L ENST00000454678 4/10 165 152 13 168 168 0 strelka-varscan-mutect TRIM26,missense_variant,p.Arg128Leu,ENST00000454678,NM_003449.4;TRIM26,missense_variant,p.Arg128Leu,ENST00000453195,NM_001242783.1;TRIM26,missense_variant,p.Arg128Leu,ENST00000437089,;TRIM26,missense_variant,p.Arg128Leu,ENST00000416596,;TRIM26,missense_variant,p.Arg128Leu,ENST00000418026,;TRIM26,downstream_gene_variant,,ENST00000434785,;TRIM26,downstream_gene_variant,,ENST00000487829,; A ENST00000454678 Transcript missense_variant 820/3478 383/1620 128/539 R/L cGg/cTg COSM1739215,COSM1739216 1 -1 TRIM26 HGNC HGNC:12962 protein_coding YES CCDS4678.1 ENSP00000410446 Q12899 A0A024RCP3 UPI0000001C20 NM_003449.4 tolerated(0.2) 4/10 PROSITE_profiles:PS50119,hmmpanther:PTHR24103:SF369,hmmpanther:PTHR24103,Gene3D:1freA00,Pfam_domain:PF00643,SMART_domains:SM00336,Superfamily_domains:SSF57845 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 30198721 30198721 C A 1 0 0 0 0 1 0 0 0 16989 652 23 1 1 TRIM26 6 30198721 Missense_Mutation SNP C C3N-01415_T 610668 30198721 140607258 205 23952 ITPR3 0 . GRCh38 6 33688757 33688757 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.6670C>T p.Pro2224Ser p.P2224S ENST00000374316 50/59 351 325 26 345 345 0 strelka-varscan-mutect ITPR3,missense_variant,p.Pro2224Ser,ENST00000374316,;ITPR3,missense_variant,p.Pro2224Ser,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript missense_variant 7730/9870 6670/8016 2224/2671 P/S Cct/Tct 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 deleterious(0) 50/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS rs1426232454 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 33688757 33688757 C T 1 0 0 0 0 1 0 0 0 7828 623 22 3 3 ITPR3 6 33688757 Missense_Mutation SNP C C3N-01415_T 3490036 33688757 137117222 206 23953 PACSIN1 0 . GRCh38 6 34528719 34528719 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.298G>A p.Glu100Lys p.E100K ENST00000620693 4/10 543 388 155 496 496 0 strelka-varscan-mutect PACSIN1,missense_variant,p.Glu100Lys,ENST00000620693,NM_020804.4;PACSIN1,missense_variant,p.Glu100Lys,ENST00000538621,NM_001199583.2;PACSIN1,missense_variant,p.Glu100Lys,ENST00000244458,;PACSIN1,missense_variant,p.Glu58Lys,ENST00000374043,;PACSIN1,non_coding_transcript_exon_variant,,ENST00000486120,;PACSIN1,downstream_gene_variant,,ENST00000487760,;PACSIN1,downstream_gene_variant,,ENST00000493633,; A ENST00000620693 Transcript missense_variant 571/4299 298/1335 100/444 E/K Gag/Aag COSM1219104 1 1 PACSIN1 HGNC HGNC:8570 protein_coding YES CCDS4793.1 ENSP00000484060 Q9BY11 Q5TZC3 UPI000000D983 NM_020804.4 tolerated(0.18) 4/10 PROSITE_profiles:PS51741,hmmpanther:PTHR23065:SF16,hmmpanther:PTHR23065,SMART_domains:SM00055,Superfamily_domains:SSF103657 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 34528719 34528719 G A 1 0 0 0 0 1 0 0 0 11452 1175 41 3 3 PACSIN1 6 34528719 Missense_Mutation SNP G C3N-01415_T 839962 34528719 136277260 207 23954 SNRPC 0 . GRCh38 6 34767924 34767924 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.177A>T p.Gln59His p.Q59H ENST00000244520 4/6 228 165 63 233 233 0 strelka-varscan-mutect SNRPC,missense_variant,p.Gln80His,ENST00000374017,;SNRPC,missense_variant,p.Gln59His,ENST00000244520,NM_003093.2;SNRPC,missense_variant,p.Gln18His,ENST00000374018,;SNRPC,non_coding_transcript_exon_variant,,ENST00000474635,; T ENST00000244520 Transcript missense_variant 315/842 177/480 59/159 Q/H caA/caT 1 1 SNRPC HGNC HGNC:11157 protein_coding YES CCDS34436.1 ENSP00000244520 P09234 Q5TAL4 UPI00001352E7 NM_003093.2 tolerated(0.05) 4/6 HAMAP:MF_03153,PIRSF_domain:PIRSF037969,hmmpanther:PTHR31148,hmmpanther:PTHR31148:SF3,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 34767924 34767924 A T 1 0 0 0 0 1 0 0 0 15183 69 3 4 4 SNRPC 6 34767924 Missense_Mutation SNP A C3N-01415_T 239205 34767924 136038055 208 23955 PPARD 0 . GRCh38 6 35424725 35424725 + Nonsense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1024G>T p.Glu342Ter p.E342* ENST00000311565 8/9 254 215 39 251 250 1 strelka-varscan-mutect PPARD,stop_gained,p.Glu342Ter,ENST00000311565,NM_001171818.1;PPARD,stop_gained,p.Glu342Ter,ENST00000360694,NM_006238.4;PPARD,stop_gained,p.Glu303Ter,ENST00000448077,NM_001171819.1;PPARD,stop_gained,p.Glu244Ter,ENST00000418635,NM_001171820.1;PPARD,stop_gained,p.Glu342Ter,ENST00000337400,NM_177435.2; T ENST00000311565 Transcript stop_gained 1373/3774 1024/1326 342/441 E/* Gaa/Taa 1 1 PPARD HGNC HGNC:9235 protein_coding YES CCDS4803.1 ENSP00000310928 Q03181 A0A024RCW6 UPI000004EF98 NM_001171818.1 8/9 Gene3D:1.10.565.10,Pfam_domain:PF00104,Prints_domain:PR00398,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF15,SMART_domains:SM00430,Superfamily_domains:SSF48508 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 35424725 35424725 G T 1 0 0 0 0 0 1 0 0 12407 1175 41 2 2 PPARD 6 35424725 Nonsense_Mutation SNP G C3N-01415_T 656801 35424725 135381254 209 23956 CPNE5 0 . GRCh38 6 36794626 36794626 + Missense_Mutation SNP G G T rs142540878 C3N-01415_T C3N-01415_N G G c.428C>A p.Ser143Tyr p.S143Y ENST00000244751 7/21 396 366 30 309 309 0 strelka-varscan-mutect CPNE5,missense_variant,p.Ser143Tyr,ENST00000244751,NM_020939.1;CPNE5,missense_variant,p.Ser127Tyr,ENST00000633136,;CPNE5,missense_variant,p.Ser143Tyr,ENST00000633280,; T ENST00000244751 Transcript missense_variant 1053/3897 428/1782 143/593 S/Y tCc/tAc rs142540878 1 -1 CPNE5 HGNC HGNC:2318 protein_coding YES CCDS4825.1 ENSP00000244751 Q9HCH3 UPI0000127C15 NM_020939.1 tolerated(0.17) 7/21 MODERATE 1 SNV 1 1 PASS rs142540878 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 36794626 36794626 G T 1 0 0 0 0 1 0 0 0 3610 1174 41 2 2 CPNE5 6 36794626 Missense_Mutation SNP G C3N-01415_T 1369901 36794626 134011353 210 23957 DNAH8 0 . GRCh38 6 38882988 38882988 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.7937T>C p.Leu2646Ser p.L2646S ENST00000327475 54/93 188 157 31 190 190 0 strelka-varscan-mutect DNAH8,missense_variant,p.Leu2646Ser,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Leu2429Ser,ENST00000359357,;DNAH8,missense_variant,p.Leu2646Ser,ENST00000449981,; C ENST00000327475 Transcript missense_variant 8046/14360 7937/14124 2646/4707 L/S tTg/tCg 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 54/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF12775 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 38882988 38882988 T C 1 0 0 0 0 1 0 0 0 4422 1821 63 5 5 DNAH8 6 38882988 Missense_Mutation SNP T C3N-01415_T 2088362 38882988 131922991 211 23958 TREM1 0 . GRCh38 6 41281135 41281135 + Missense_Mutation SNP C C A rs372884401 C3N-01415_T C3N-01415_N C C c.425G>T p.Gly142Val p.G142V ENST00000244709 3/4 223 170 53 223 223 0 strelka-varscan-mutect TREM1,missense_variant,p.Gly142Val,ENST00000591620,NM_001242589.1;TREM1,missense_variant,p.Gly142Val,ENST00000244709,NM_018643.3;TREM1,missense_variant,p.Gly142Val,ENST00000589614,;TREM1,intron_variant,,ENST00000334475,NM_001242590.1;TREM1,non_coding_transcript_exon_variant,,ENST00000589882,;TREM1,non_coding_transcript_exon_variant,,ENST00000589695,;TREM1,downstream_gene_variant,,ENST00000586287,; A ENST00000244709 Transcript missense_variant 489/1690 425/705 142/234 G/V gGc/gTc rs372884401 1 -1 TREM1 HGNC HGNC:17760 protein_coding YES CCDS4854.1 ENSP00000244709 Q9NP99 Q38L15 UPI0000047FA9 NM_018643.3 tolerated(0.48) 3/4 hmmpanther:PTHR19357,hmmpanther:PTHR19357:SF0 MODERATE 1 SNV 1 1 PASS rs372884401 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 41281135 41281135 C A 1 0 0 0 0 1 0 0 0 16959 739 26 2 2 TREM1 6 41281135 Missense_Mutation SNP C C3N-01415_T 2398147 41281135 129524844 212 23959 PEX6 0 . GRCh38 6 42966431 42966431 + Missense_Mutation SNP C C A rs774799323 C3N-01415_T C3N-01415_N C C c.2111G>T p.Trp704Leu p.W704L ENST00000304611 11/17 747 562 185 798 795 3 strelka-varscan-mutect PEX6,missense_variant,p.Trp704Leu,ENST00000304611,NM_000287.3;PEX6,intron_variant,,ENST00000244546,;GNMT,downstream_gene_variant,,ENST00000372808,NM_018960.4; A ENST00000304611 Transcript missense_variant 2181/3478 2111/2943 704/980 W/L tGg/tTg rs774799323 1 -1 PEX6 HGNC HGNC:8859 protein_coding YES CCDS4877.1 ENSP00000303511 Q13608 A0A024RD09 UPI00001316EC NM_000287.3 deleterious(0) 11/17 Gene3D:3.40.50.300,hmmpanther:PTHR23077,hmmpanther:PTHR23077:SF9,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs774799323 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 42966431 42966431 C A 1 0 0 0 0 1 0 0 0 11840 595 21 2 2 PEX6 6 42966431 Missense_Mutation SNP C C3N-01415_T 1685296 42966431 127839548 213 23960 KLC4 0 . GRCh38 6 43063102 43063102 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.498G>A p.= p.E166E ENST00000259708 3/16 177 144 33 188 188 0 strelka-varscan-mutect KLC4,synonymous_variant,p.=,ENST00000394056,NM_201522.2;KLC4,synonymous_variant,p.=,ENST00000259708,NM_201523.2;KLC4,synonymous_variant,p.=,ENST00000479388,NM_001289034.1;KLC4,synonymous_variant,p.=,ENST00000347162,NM_201521.2;KLC4,synonymous_variant,p.=,ENST00000458460,NM_138343.3;KLC4,synonymous_variant,p.=,ENST00000470728,;KLC4,synonymous_variant,p.=,ENST00000479632,;KLC4,intron_variant,,ENST00000453940,NM_001289035.1;MRPL2,upstream_gene_variant,,ENST00000388752,NM_015950.4;MRPL2,upstream_gene_variant,,ENST00000487429,;MRPL2,upstream_gene_variant,,ENST00000230413,NM_001300848.1;MRPL2,upstream_gene_variant,,ENST00000468957,;KLC4,downstream_gene_variant,,ENST00000472792,;MRPL2,upstream_gene_variant,,ENST00000489623,;KLC4,downstream_gene_variant,,ENST00000460283,;KLC4,downstream_gene_variant,,ENST00000481888,;KLC4,3_prime_UTR_variant,,ENST00000467906,;KLC4,3_prime_UTR_variant,,ENST00000481499,;KLC4,non_coding_transcript_exon_variant,,ENST00000472172,;MRPL2,upstream_gene_variant,,ENST00000491898,;KLC4,upstream_gene_variant,,ENST00000469987,;MRPL2,upstream_gene_variant,,ENST00000470667,;MRPL2,upstream_gene_variant,,ENST00000480286,;KLC4,upstream_gene_variant,,ENST00000468114,; A ENST00000259708 Transcript synonymous_variant 851/2688 498/1914 166/637 E gaG/gaA 1 1 KLC4 HGNC HGNC:21624 protein_coding YES CCDS4882.1 ENSP00000259708 Q9NSK0 UPI000023C3DA NM_201523.2 3/16 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19959:SF139,hmmpanther:PTHR19959 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 43063102 43063102 G A 1 0 0 0 0 0 0 0 1 8201 1020 36 3 3 KLC4 6 43063102 Silent SNP G C3N-01415_T 96671 43063102 127742877 214 23961 TFAP2D 0 . GRCh38 6 50772825 50772825 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.1320G>A p.= p.E440E ENST00000008391 8/8 387 346 41 353 353 0 strelka-varscan-mutect TFAP2D,synonymous_variant,p.=,ENST00000008391,NM_172238.3; A ENST00000008391 Transcript synonymous_variant 1548/1711 1320/1359 440/452 E gaG/gaA 1 1 TFAP2D HGNC HGNC:15581 protein_coding YES CCDS4933.1 ENSP00000008391 Q7Z6R9 UPI00001A3A89 NM_172238.3 8/8 hmmpanther:PTHR10812:SF5,hmmpanther:PTHR10812 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 50772825 50772825 G A 1 0 0 0 0 0 0 0 1 16223 991 35 3 3 TFAP2D 6 50772825 Silent SNP G C3N-01415_T 7709723 50772825 120033154 215 23962 PKHD1 0 . GRCh38 6 51887247 51887247 + Splice_Site SNP T T A novel C3N-01415_T C3N-01415_N T T c.6997-2A>T p.X2333_splice ENST00000371117 556 425 131 575 575 0 strelka-varscan-mutect PKHD1,splice_acceptor_variant,,ENST00000371117,NM_138694.3;PKHD1,splice_acceptor_variant,,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript splice_acceptor_variant -/16282 6997/12225 2333/4074 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 43/66 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 78 51887247 51887247 T A 1 0 0 0 0 0 0 1 0 12067 1536 53 4 4 PKHD1 6 51887247 Splice_Site SNP T C3N-01415_T 1114422 51887247 118918732 216 23963 DST 0 . GRCh38 6 56704304 56704304 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.339A>T p.Leu113Phe p.L113F ENST00000312431 4/95 252 212 40 258 258 0 strelka-mutect DST,missense_variant,p.Leu73Phe,ENST00000361203,;DST,missense_variant,p.Leu73Phe,ENST00000421834,NM_183380.3;DST,missense_variant,p.Leu113Phe,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Leu73Phe,ENST00000370788,;DST,missense_variant,p.Leu113Phe,ENST00000520645,;DST,missense_variant,p.Leu251Phe,ENST00000449297,;DST,missense_variant,p.Leu24Phe,ENST00000522538,;DST,missense_variant,p.Leu66Phe,ENST00000523817,;DST,non_coding_transcript_exon_variant,,ENST00000523967,;DST,non_coding_transcript_exon_variant,,ENST00000521821,; A ENST00000312431 Transcript missense_variant 465/17756 339/16614 113/5537 L/F ttA/ttT 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 deleterious(0) 4/95 PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 56704304 56704304 T A 1 0 0 0 0 1 0 0 0 4604 1519 53 4 4 DST 6 56704304 Missense_Mutation SNP T C3N-01415_T 4817057 56704304 114101675 217 23964 PRIM2 0 . GRCh38 6 57325954 57325954 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.368A>T p.Gln123Leu p.Q123L ENST00000615550 5/14 279 257 22 312 311 1 strelka-varscan-mutect PRIM2,missense_variant,p.Gln123Leu,ENST00000615550,NM_000947.4;PRIM2,missense_variant,p.Gln123Leu,ENST00000370687,NM_001282488.1;PRIM2,missense_variant,p.Gln123Leu,ENST00000274891,NM_001282487.1;PRIM2,non_coding_transcript_exon_variant,,ENST00000419977,; T ENST00000615550 Transcript missense_variant 455/2308 368/1530 123/509 Q/L cAa/cTa 1 1 PRIM2 HGNC HGNC:9370 protein_coding YES CCDS75476.1 ENSP00000484105 P49643 UPI0000232A3A NM_000947.4 deleterious(0) 5/14 Superfamily_domains:0051637,PIRSF_domain:PIRSF009449,hmmpanther:PTHR10537,hmmpanther:PTHR10537:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 57325954 57325954 A T 1 0 0 0 0 1 0 0 0 12623 130 5 4 4 PRIM2 6 57325954 Missense_Mutation SNP A C3N-01415_T 621650 57325954 113480025 218 23965 OOEP 0 . GRCh38 6 73369336 73369336 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.240G>T p.= p.L80L ENST00000370359 2/3 181 124 57 175 175 0 strelka-varscan-mutect OOEP,synonymous_variant,p.=,ENST00000370363,;OOEP,synonymous_variant,p.=,ENST00000441145,;OOEP,synonymous_variant,p.=,ENST00000370359,NM_001080507.2;OOEP-AS1,upstream_gene_variant,,ENST00000445350,;RPL39P3,downstream_gene_variant,,ENST00000424573,; A ENST00000370359 Transcript synonymous_variant 240/478 240/450 80/149 L ctG/ctT 1 -1 OOEP HGNC HGNC:21382 protein_coding YES CCDS47451.1 ENSP00000359384 A6NGQ2 UPI00001D8132 NM_001080507.2 2/3 hmmpanther:PTHR19447:SF14,hmmpanther:PTHR19447,Pfam_domain:PF16005 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 73369336 73369336 C A 1 0 0 0 0 0 0 0 1 10946 697 25 2 2 OOEP 6 73369336 Silent SNP C C3N-01415_T 16043382 73369336 97436643 219 23966 SIM1 0 . GRCh38 6 100393792 100393792 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1265C>A p.Pro422His p.P422H ENST00000369208 11/12 159 146 13 145 144 1 strelka-varscan-mutect SIM1,missense_variant,p.Pro422His,ENST00000369208,;SIM1,missense_variant,p.Pro422His,ENST00000262901,NM_005068.2;SIM1,non_coding_transcript_exon_variant,,ENST00000505753,; T ENST00000369208 Transcript missense_variant 2048/8430 1265/2301 422/766 P/H cCc/cAc 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 deleterious(0.03) 11/12 Pfam_domain:PF06621,PROSITE_profiles:PS51302,hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 100393792 100393792 G T 1 0 0 0 0 1 0 0 0 14586 1232 43 2 2 SIM1 6 100393792 Missense_Mutation SNP G C3N-01415_T 27024456 100393792 70412187 220 23967 LAMA4 0 . GRCh38 6 112191803 112191803 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.551G>T p.Cys184Phe p.C184F ENST00000230538 6/39 495 437 58 506 506 0 strelka-varscan-mutect LAMA4,missense_variant,p.Cys184Phe,ENST00000230538,NM_001105206.2;LAMA4,missense_variant,p.Cys184Phe,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,missense_variant,p.Cys184Phe,ENST00000389463,;LAMA4,missense_variant,p.Cys184Phe,ENST00000424408,;LAMA4,missense_variant,p.Cys184Phe,ENST00000521398,;LAMA4,missense_variant,p.Cys4Phe,ENST00000521732,;LAMA4,upstream_gene_variant,,ENST00000368640,;RNU6-1226P,downstream_gene_variant,,ENST00000384317,;LAMA4,non_coding_transcript_exon_variant,,ENST00000524032,;LAMA4,upstream_gene_variant,,ENST00000518842,; A ENST00000230538 Transcript missense_variant 949/6547 551/5472 184/1823 C/F tGt/tTt 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 deleterious(0) 6/39 PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF277,PROSITE_patterns:PS01248,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00181,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 112191803 112191803 C A 1 0 0 0 0 1 0 0 0 8512 478 17 2 2 LAMA4 6 112191803 Missense_Mutation SNP C C3N-01415_T 11798011 112191803 58614176 221 23968 LAMA2 0 . GRCh38 6 129287910 129287910 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.2601C>G p.Cys867Trp p.C867W ENST00000421865 19/65 540 486 54 610 610 0 strelka-varscan-mutect LAMA2,missense_variant,p.Cys867Trp,ENST00000618192,;LAMA2,missense_variant,p.Cys867Trp,ENST00000617695,;LAMA2,missense_variant,p.Cys867Trp,ENST00000421865,NM_001079823.1,NM_000426.3; G ENST00000421865 Transcript missense_variant 2650/9640 2601/9369 867/3122 C/W tgC/tgG 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 deleterious(0) 19/65 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF291,SMART_domains:SM00180,Superfamily_domains:SSF57196,Superfamily_domains:SSF57196 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 129287910 129287910 C G 1 0 0 0 0 1 0 0 0 8510 718 25 4 4 LAMA2 6 129287910 Missense_Mutation SNP C C3N-01415_T 17096107 129287910 41518069 222 23969 TMEM244 0 . GRCh38 6 129831370 129831370 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.336C>T p.= p.P112P ENST00000368143 5/5 300 277 23 314 314 0 strelka-varscan-mutect TMEM244,synonymous_variant,p.=,ENST00000438392,;TMEM244,synonymous_variant,p.=,ENST00000368143,NM_001010876.1; A ENST00000368143 Transcript synonymous_variant 419/545 336/387 112/128 P ccC/ccT 1 -1 TMEM244 HGNC HGNC:21571 protein_coding YES CCDS34536.1 ENSP00000357125 Q5VVB8 UPI0000161685 NM_001010876.1 5/5 hmmpanther:PTHR12952,hmmpanther:PTHR12952:SF1,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 129831370 129831370 G A 1 0 0 0 0 0 0 0 1 16604 987 35 3 3 TMEM244 6 129831370 Silent SNP G C3N-01415_T 543460 129831370 40974609 223 23970 REPS1 0 . GRCh38 6 138912914 138912914 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1822G>T p.Asp608Tyr p.D608Y ENST00000450536 16/20 168 157 11 175 175 0 strelka-varscan-mutect REPS1,missense_variant,p.Asp608Tyr,ENST00000450536,NM_001286611.1;REPS1,missense_variant,p.Asp607Tyr,ENST00000258062,NM_031922.4;REPS1,missense_variant,p.Asp581Tyr,ENST00000367663,NM_001128617.2;REPS1,missense_variant,p.Asp517Tyr,ENST00000409812,NM_001286612.1;REPS1,missense_variant,p.Asp566Tyr,ENST00000529597,;REPS1,missense_variant,p.Asp581Tyr,ENST00000415951,;REPS1,missense_variant,p.Asp131Tyr,ENST00000530255,;REPS1,3_prime_UTR_variant,,ENST00000626459,;REPS1,upstream_gene_variant,,ENST00000478483,;REPS1,upstream_gene_variant,,ENST00000526022,;REPS1,3_prime_UTR_variant,,ENST00000483468,;REPS1,3_prime_UTR_variant,,ENST00000445570,;REPS1,non_coding_transcript_exon_variant,,ENST00000484164,;REPS1,non_coding_transcript_exon_variant,,ENST00000492787,;REPS1,non_coding_transcript_exon_variant,,ENST00000529423,;REPS1,upstream_gene_variant,,ENST00000530370,;REPS1,upstream_gene_variant,,ENST00000526244,; A ENST00000450536 Transcript missense_variant 2397/4537 1822/2391 608/796 D/Y Gat/Tat 1 -1 REPS1 HGNC HGNC:15578 protein_coding YES CCDS69213.1 ENSP00000392065 Q96D71 UPI000020E300 NM_001286611.1 deleterious(0.01) 16/20 MODERATE 1 SNV 1 1 PASS rs1274364851 . 0 207 0 3 0 0 0 0 -14.42776 0.9999644 1 1 1 0 A 3 1 78 138912914 138912914 C A 1 0 0 0 0 1 0 0 0 13398 884 31 1 1 REPS1 6 138912914 Missense_Mutation SNP C C3N-01415_T 9081544 138912914 31893065 224 23971 MTHFD1L 0 . GRCh38 6 151092495 151092495 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2879G>T p.Arg960Leu p.R960L ENST00000611279 27/28 252 224 28 243 243 0 strelka-varscan-mutect MTHFD1L,missense_variant,p.Arg959Leu,ENST00000367321,NM_015440.4;MTHFD1L,missense_variant,p.Arg960Leu,ENST00000611279,NM_001242767.1;MTHFD1L,missense_variant,p.Arg894Leu,ENST00000618312,NM_001242768.1;RP1-292B18.4,intron_variant,,ENST00000415477,; T ENST00000611279 Transcript missense_variant 3023/3475 2879/2940 960/979 R/L cGg/cTg 1 1 MTHFD1L HGNC HGNC:21055 protein_coding YES CCDS75535.1 ENSP00000478253 B7ZM99 UPI000166C73D NM_001242767.1 deleterious(0.01) 27/28 HAMAP:MF_01543,hmmpanther:PTHR10025,hmmpanther:PTHR10025:SF14,Pfam_domain:PF01268,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 151092495 151092495 G T 1 0 0 0 0 1 0 0 0 9917 1116 39 1 1 MTHFD1L 6 151092495 Missense_Mutation SNP G C3N-01415_T 12179581 151092495 19713484 225 23972 MAS1 0 . GRCh38 6 159907384 159907384 + Silent SNP T T C novel C3N-01415_T C3N-01415_N T T c.429T>C p.= p.H143H ENST00000252660 1/1 415 374 41 405 405 0 strelka-varscan-mutect MAS1,synonymous_variant,p.=,ENST00000252660,NM_002377.2;RP1-249F5.3,downstream_gene_variant,,ENST00000434562,; C ENST00000252660 Transcript synonymous_variant 695/9841 429/978 143/325 H caT/caC 1 1 MAS1 HGNC HGNC:6899 protein_coding YES CCDS5272.1 ENSP00000252660 P04201 W8W3P4 UPI0000050458 NM_002377.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF30,hmmpanther:PTHR11334,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 78 159907384 159907384 T C 1 0 0 0 0 0 0 0 1 9246 1432 50 5 5 MAS1 6 159907384 Silent SNP T C3N-01415_T 8814889 159907384 10898595 226 23973 TCP10 0 . GRCh38 6 167377963 167377963 + Missense_Mutation SNP G G C rs563134633 C3N-01415_T C3N-01415_N G G c.409C>G p.Pro137Ala p.P137A ENST00000397829 4/8 302 271 31 337 337 0 varscan-mutect TCP10,missense_variant,p.Pro133Ala,ENST00000460930,;TCP10,missense_variant,p.Pro137Ala,ENST00000366827,;TCP10,missense_variant,p.Pro163Ala,ENST00000617120,;TCP10,missense_variant,p.Pro137Ala,ENST00000397829,NM_004610.3;TCP10,downstream_gene_variant,,ENST00000476779,;TCP10,downstream_gene_variant,,ENST00000485157,;TCP10,non_coding_transcript_exon_variant,,ENST00000508373,;TCP10,non_coding_transcript_exon_variant,,ENST00000463894,;TCP10,non_coding_transcript_exon_variant,,ENST00000491085,;TCP10,upstream_gene_variant,,ENST00000514083,; C ENST00000397829 Transcript missense_variant 577/2141 409/981 137/326 P/A Cct/Gct rs563134633 1 -1 TCP10 HGNC HGNC:11656 protein_coding YES CCDS43527.1 ENSP00000380929 D1MPS5 UPI0000D820CE NM_004610.3 tolerated(0.32) 4/8 hmmpanther:PTHR10331 MODERATE 1 SNV 1 1 PASS rs563134633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 167377963 167377963 G C 1 0 0 0 0 1 0 0 0 16117 1174 41 4 4 TCP10 6 167377963 Missense_Mutation SNP G C3N-01415_T 7470579 167377963 3428016 227 23974 VWDE 0 . GRCh38 7 12383602 12383602 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.476-1G>T p.X159_splice ENST00000275358 303 230 73 319 317 2 strelka-varscan-mutect VWDE,splice_acceptor_variant,,ENST00000275358,NM_001135924.1;VWDE,splice_acceptor_variant,,ENST00000614403,;VWDE,splice_acceptor_variant,,ENST00000452576,;VWDE,splice_acceptor_variant,,ENST00000521169,;VWDE,splice_acceptor_variant,,ENST00000326715,; A ENST00000275358 Transcript splice_acceptor_variant -/5260 476/4773 159/1590 1 -1 VWDE HGNC HGNC:21897 protein_coding YES CCDS47544.1 ENSP00000275358 Q8N2E2 UPI00006C0B98 NM_001135924.1 3/28 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 78 12383602 12383602 C A 1 0 0 0 0 0 0 1 0 17805 811 28 2 2 VWDE 7 12383602 Splice_Site SNP C C3N-01415_T 12383602 146962371 228 23975 ABCB5 0 . GRCh38 7 20650092 20650092 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1277G>T p.Gly426Val p.G426V ENST00000404938 12/28 369 344 25 331 330 1 strelka-varscan-mutect ABCB5,missense_variant,p.Gly426Val,ENST00000404938,NM_001163941.1;ABCB5,5_prime_UTR_variant,,ENST00000258738,NM_178559.5;ABCB5,5_prime_UTR_variant,,ENST00000443026,NM_001163942.1;ABCB5,5_prime_UTR_variant,,ENST00000406935,NM_001163993.2;ABCB5,non_coding_transcript_exon_variant,,ENST00000477094,; T ENST00000404938 Transcript missense_variant 1929/5811 1277/3774 426/1257 G/V gGg/gTg 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 deleterious(0) 12/28 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 20650092 20650092 G T 1 0 0 0 0 1 0 0 0 48 1232 43 2 2 ABCB5 7 20650092 Missense_Mutation SNP G C3N-01415_T 8266490 20650092 138695881 229 23976 NFE2L3 0 . GRCh38 7 26185062 26185062 + Missense_Mutation SNP C C G rs771810558 C3N-01415_T C3N-01415_N C C c.1364C>G p.Ser455Cys p.S455C ENST00000056233 4/4 347 306 41 332 332 0 strelka-varscan-mutect NFE2L3,missense_variant,p.Ser455Cys,ENST00000056233,NM_004289.6;HNRNPA2B1,downstream_gene_variant,,ENST00000354667,NM_031243.2;HNRNPA2B1,downstream_gene_variant,,ENST00000618183,;NFE2L3,downstream_gene_variant,,ENST00000607375,;HNRNPA2B1,downstream_gene_variant,,ENST00000476233,;NFE2L3,non_coding_transcript_exon_variant,,ENST00000606261,; G ENST00000056233 Transcript missense_variant 1623/3686 1364/2085 455/694 S/C tCt/tGt rs771810558,COSM5634034 1 1 NFE2L3 HGNC HGNC:7783 protein_coding YES CCDS5396.1 ENSP00000056233 Q9Y4A8 UPI000007206C NM_004289.6 deleterious(0.02) 4/4 hmmpanther:PTHR24411,hmmpanther:PTHR24411:SF8 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771810558 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 26185062 26185062 C G 1 0 0 0 0 1 0 0 0 10406 913 32 4 4 NFE2L3 7 26185062 Missense_Mutation SNP C C3N-01415_T 5534970 26185062 133160911 230 23977 TRIL 0 . GRCh38 7 28956170 28956170 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1877G>T p.Arg626Leu p.R626L ENST00000539664 1/1 121 114 7 142 142 0 strelka-varscan-mutect TRIL,missense_variant,p.Arg626Leu,ENST00000539664,NM_014817.3;AC005013.5,upstream_gene_variant,,ENST00000436594,; A ENST00000539664 Transcript missense_variant 2123/4935 1877/2436 626/811 R/L cGc/cTc 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 deleterious(0) 1/1 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263 MODERATE SNV 1 PASS . . 0 204 6 0 0 0 0 0 -13.60449 0.9999995 1 1 1 0 A 3 1 78 28956170 28956170 C A 1 0 0 0 0 1 0 0 0 16974 768 27 1 1 TRIL 7 28956170 Missense_Mutation SNP C C3N-01415_T 2771108 28956170 130389803 231 23978 ELMO1 0 . GRCh38 7 36887572 36887572 + Silent SNP G G T C3N-01415_T C3N-01415_N G G c.1702C>A p.= p.R568R ENST00000310758 18/22 251 213 38 222 222 0 strelka-varscan-mutect ELMO1,synonymous_variant,p.=,ENST00000310758,NM_001206480.2,NM_014800.10;ELMO1,synonymous_variant,p.=,ENST00000442504,NM_001206482.1;ELMO1,synonymous_variant,p.=,ENST00000448602,;ELMO1,synonymous_variant,p.=,ENST00000396045,NM_130442.3;ELMO1,synonymous_variant,p.=,ENST00000396040,NM_001039459.2;ELMO1,intron_variant,,ENST00000487843,;ELMO1,intron_variant,,ENST00000464262,; T ENST00000310758 Transcript synonymous_variant 2350/4022 1702/2184 568/727 R Cgg/Agg COSM362534 1 -1 ELMO1 HGNC HGNC:16286 protein_coding YES CCDS5449.1 ENSP00000312185 Q92556 A4D1X5 UPI000006F687 NM_001206480.2,NM_014800.10 18/22 Gene3D:2.30.29.30,Pfam_domain:PF16457,hmmpanther:PTHR12771,hmmpanther:PTHR12771:SF23,Superfamily_domains:SSF50729 1 LOW 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999938 1 1 1 0 T 2 4 78 36887572 36887572 G T 1 0 0 0 0 0 0 0 1 4899 1115 39 1 1 ELMO1 7 36887572 Silent SNP G C3N-01415_T 7931402 36887572 122458401 232 23979 SUGCT 0 . GRCh38 7 40496369 40496369 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1093G>T p.Val365Leu p.V365L ENST00000628514 12/15 369 344 25 369 369 0 strelka-varscan-mutect SUGCT,missense_variant,p.Val365Leu,ENST00000335693,NM_001193313.1;SUGCT,missense_variant,p.Val360Leu,ENST00000416370,;SUGCT,missense_variant,p.Val365Leu,ENST00000628514,NM_024728.2,NM_001193311.1;SUGCT,missense_variant,p.Val317Leu,ENST00000401647,NM_001193312.1; T ENST00000628514 Transcript missense_variant 1116/1591 1093/1416 365/471 V/L Gta/Tta 1 1 SUGCT HGNC HGNC:16001 protein_coding YES CCDS55104.1 ENSP00000486291 Q9HAC7 UPI000013EF6B NM_024728.2,NM_001193311.1 deleterious(0.01) 12/15 Gene3D:3.40.50.10540,Pfam_domain:PF02515,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF593,Superfamily_domains:SSF89796 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 40496369 40496369 G T 1 0 0 0 0 1 0 0 0 15754 1377 48 2 2 SUGCT 7 40496369 Missense_Mutation SNP G C3N-01415_T 3608797 40496369 118849604 233 23980 PGAM2 0 . GRCh38 7 44064889 44064892 + Frame_Shift_Del DEL GCTT GCTT - novel C3N-01415_T C3N-01415_N GCTT GCTT c.535_538delAAGC p.Lys179GlufsTer29 p.K179Efs*29 ENST00000297283 2/3 241 204 37 215 215 0 sindel-varindel-pindel PGAM2,frameshift_variant,p.Lys179GlufsTer29,ENST00000297283,NM_000290.3;DBNL,3_prime_UTR_variant,,ENST00000432854,;DBNL,downstream_gene_variant,,ENST00000494774,NM_014063.6;DBNL,downstream_gene_variant,,ENST00000468694,NM_001122956.1;DBNL,downstream_gene_variant,,ENST00000490734,NM_001284315.1;DBNL,downstream_gene_variant,,ENST00000448521,NM_001014436.2;DBNL,downstream_gene_variant,,ENST00000452943,;DBNL,downstream_gene_variant,,ENST00000440166,NM_001284313.1;DBNL,downstream_gene_variant,,ENST00000456905,;DBNL,downstream_gene_variant,,ENST00000452661,;AC017116.11,upstream_gene_variant,,ENST00000445938,;AC017116.11,upstream_gene_variant,,ENST00000425727,;DBNL,downstream_gene_variant,,ENST00000497184,;DBNL,downstream_gene_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000441840,;DBNL,downstream_gene_variant,,ENST00000429716,;DBNL,downstream_gene_variant,,ENST00000411855,;DBNL,downstream_gene_variant,,ENST00000498733,; - ENST00000297283 Transcript frameshift_variant 593-596/857 535-538/762 179-180/253 KR/X AAGCga/ga 1 -1 PGAM2 HGNC HGNC:8889 protein_coding YES CCDS34624.1 ENSP00000297283 P15259 UPI000013E3E8 NM_000290.3 2/3 Gene3D:3.40.50.1240,HAMAP:MF_01039,Pfam_domain:PF00300,hmmpanther:PTHR11931,hmmpanther:PTHR11931:SF8,SMART_domains:SM00855,Superfamily_domains:SSF53254,TIGRFAM_domain:TIGR01258 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 44064889 44064889 GCTT - 1 0 1 0 1 0 0 0 0 11864 1095 38 0 0 PGAM2 7 44064889 Frame_Shift_Del DEL GCTT C3N-01415_T 3568520 44064889 115281084 234 23981 ABCA13 0 . GRCh38 7 48274574 48274574 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.4908G>T p.Arg1636Ser p.R1636S ENST00000435803 17/62 689 509 180 594 593 1 strelka-varscan-mutect ABCA13,missense_variant,p.Arg1636Ser,ENST00000435803,NM_152701.4;ABCA13,upstream_gene_variant,,ENST00000544596,;ABCA13,upstream_gene_variant,,ENST00000611776,;ABCA13,downstream_gene_variant,,ENST00000417403,; T ENST00000435803 Transcript missense_variant 4932/17184 4908/15177 1636/5058 R/S agG/agT 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0) 17/62 MODERATE 1 SNV 1 1 PASS rs1290234871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 48274574 48274574 G T 1 0 0 0 0 1 0 0 0 35 1223 43 2 2 ABCA13 7 48274574 Missense_Mutation SNP G C3N-01415_T 4209685 48274574 111071399 235 23982 ABCA13 0 . GRCh38 7 48427865 48427865 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.12559G>T p.Gly4187Cys p.G4187C ENST00000435803 42/62 92 77 15 77 77 0 strelka-varscan-mutect ABCA13,missense_variant,p.Gly4187Cys,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Gly1494Cys,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,missense_variant,p.Gly453Cys,ENST00000453246,; T ENST00000435803 Transcript missense_variant 12583/17184 12559/15177 4187/5058 G/C Ggc/Tgc 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0.01) 42/62 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 48427865 48427865 G T 1 0 0 0 0 1 0 0 0 35 1348 47 2 2 ABCA13 7 48427865 Missense_Mutation SNP G C3N-01415_T 153291 48427865 110918108 236 23983 VSTM2A 0 . GRCh38 7 54550034 54550034 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.498G>T p.Trp166Cys p.W166C ENST00000402613 4/5 492 388 104 251 250 1 strelka-varscan-mutect VSTM2A,missense_variant,p.Trp166Cys,ENST00000302287,NM_001317843.1;VSTM2A,missense_variant,p.Trp166Cys,ENST00000407838,NM_182546.3;VSTM2A,missense_variant,p.Trp166Cys,ENST00000404951,;VSTM2A,missense_variant,p.Trp166Cys,ENST00000402613,NM_001301009.1;VSTM2A,non_coding_transcript_exon_variant,,ENST00000498834,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000466888,;VSTM2A,non_coding_transcript_exon_variant,,ENST00000469952,;VSTM2A,downstream_gene_variant,,ENST00000495904,; T ENST00000402613 Transcript missense_variant 624/1076 498/723 166/240 W/C tgG/tgT 1 1 VSTM2A HGNC HGNC:28499 protein_coding YES CCDS75604.1 ENSP00000384103 F8W8J5 UPI00003E58E7 NM_001301009.1 deleterious(0.05) 4/5 hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF23 MODERATE 1 SNV 2 1 PASS rs1463999118 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 54550034 54550034 G T 1 0 0 0 0 1 0 0 0 17780 1212 42 2 2 VSTM2A 7 54550034 Missense_Mutation SNP G C3N-01415_T 6122169 54550034 104795939 237 23984 EGFR 0 . GRCh38 7 55205437 55205437 + Silent SNP C C T C3N-01415_T C3N-01415_N C C c.3453C>T p.= p.F1151F ENST00000275493 28/28 717 674 43 348 348 0 strelka-varscan-mutect EGFR,synonymous_variant,p.=,ENST00000275493,NM_005228.3;EGFR,synonymous_variant,p.=,ENST00000454757,;EGFR,downstream_gene_variant,,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000485503,; T ENST00000275493 Transcript synonymous_variant 3630/9821 3453/3633 1151/1210 F ttC/ttT COSM3266666 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 28/28 1 LOW 1 SNV 1 1 1 PASS rs1040652650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 55205437 55205437 C T 1 0 0 0 0 0 0 0 1 4803 883 31 1 1 EGFR 7 55205437 Silent SNP C C3N-01415_T 655403 55205437 104140536 238 23985 ZNF479 0 . GRCh38 7 57120420 57120420 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.995A>G p.Lys332Arg p.K332R ENST00000331162 5/5 267 240 27 264 264 0 varscan-mutect ZNF479,missense_variant,p.Lys332Arg,ENST00000331162,NM_033273.2;ZNF479,missense_variant,p.Lys332Arg,ENST00000319636,;ZNF479,missense_variant,p.Lys248Arg,ENST00000620639,; C ENST00000331162 Transcript missense_variant 1266/2072 995/1575 332/524 K/R aAa/aGa 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 deleterious(0.02) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 57120420 57120420 T C 1 0 0 0 0 1 0 0 0 18505 1841 64 5 5 ZNF479 7 57120420 Missense_Mutation SNP T C3N-01415_T 1914983 57120420 102225553 239 23986 GUSB 0 . GRCh38 7 65970286 65970286 + Missense_Mutation SNP T T A rs771250055 C3N-01415_T C3N-01415_N T T c.1472A>T p.Lys491Met p.K491M ENST00000304895 9/12 495 459 36 434 434 0 varscan-mutect GUSB,missense_variant,p.Lys491Met,ENST00000304895,NM_001293105.1,NM_001293104.1,NM_000181.3;GUSB,missense_variant,p.Lys345Met,ENST00000421103,NM_001284290.1;GUSB,downstream_gene_variant,,ENST00000476486,;GUSB,downstream_gene_variant,,ENST00000465785,;GUSB,downstream_gene_variant,,ENST00000475316,;GUSB,downstream_gene_variant,,ENST00000479038,;GUSB,3_prime_UTR_variant,,ENST00000447929,;GUSB,3_prime_UTR_variant,,ENST00000430730,;GUSB,non_coding_transcript_exon_variant,,ENST00000462371,;GUSB,intron_variant,,ENST00000466883,;GUSB,downstream_gene_variant,,ENST00000489482,;GUSB,upstream_gene_variant,,ENST00000461622,; A ENST00000304895 Transcript missense_variant 1603/2300 1472/1956 491/651 K/M aAg/aTg rs771250055 1 -1 GUSB HGNC HGNC:4696 protein_coding YES CCDS5530.1 ENSP00000302728 P08236 UPI000013E9E0 NM_001293105.1,NM_001293104.1,NM_000181.3 tolerated(0.18) 9/12 Gene3D:3.20.20.80,Pfam_domain:PF02836,hmmpanther:PTHR10066,hmmpanther:PTHR10066:SF67,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 65970286 65970286 T A 1 0 0 0 0 1 0 0 0 6784 1623 56 4 4 GUSB 7 65970286 Missense_Mutation SNP T C3N-01415_T 8849866 65970286 93375687 240 23987 RHBDD2 0 . GRCh38 7 75888349 75888349 + Nonstop_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.1095A>C p.Ter365CysextTer4 p.*365Cext*4 ENST00000006777 4/4 134 101 33 121 121 0 strelka-varscan-mutect RHBDD2,stop_lost,p.Ter224CysextTer4,ENST00000318622,NM_001040457.1;RHBDD2,stop_lost,p.Ter365CysextTer4,ENST00000006777,NM_001040456.1;RHBDD2,stop_lost,p.Ter224CysextTer4,ENST00000428119,;RHBDD2,non_coding_transcript_exon_variant,,ENST00000468304,;RHBDD2,downstream_gene_variant,,ENST00000467406,;RHBDD2,3_prime_UTR_variant,,ENST00000454791,; C ENST00000006777 Transcript stop_lost 1230/1802 1095/1095 365/364 */C tgA/tgC 1 1 RHBDD2 HGNC HGNC:23082 protein_coding YES CCDS43602.1 ENSP00000006777 Q6NTF9 UPI0000072213 NM_001040456.1 4/4 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 78 75888349 75888349 A C 1 0 0 0 0 0 0 0 0 13489 317 11 5 5 RHBDD2 7 75888349 Nonstop_Mutation SNP A C3N-01415_T 9918063 75888349 83457624 241 23988 PCLO 0 . GRCh38 7 82954765 82954765 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.6188C>G p.Ala2063Gly p.A2063G ENST00000333891 5/25 257 236 21 286 286 0 strelka-varscan-mutect PCLO,missense_variant,p.Ala2063Gly,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Ala2063Gly,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; C ENST00000333891 Transcript missense_variant 6526/20329 6188/15429 2063/5142 A/G gCt/gGt 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0) 5/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 82954765 82954765 G C 1 0 0 0 0 1 0 0 0 11671 971 34 4 4 PCLO 7 82954765 Missense_Mutation SNP G C3N-01415_T 7066416 82954765 76391208 242 23989 SEMA3A 0 . GRCh38 7 84046344 84046344 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.647A>C p.His216Pro p.H216P ENST00000265362 6/17 292 266 26 250 250 0 strelka-varscan-mutect SEMA3A,missense_variant,p.His216Pro,ENST00000265362,NM_006080.2;SEMA3A,missense_variant,p.His216Pro,ENST00000436949,; G ENST00000265362 Transcript missense_variant 962/8225 647/2316 216/771 H/P cAt/cCt 1 -1 SEMA3A HGNC HGNC:10723 protein_coding YES CCDS5599.1 ENSP00000265362 Q14563 UPI0000135A60 NM_006080.2 tolerated(0.05) 6/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF23,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 84046344 84046344 T G 1 0 0 0 0 1 0 0 0 14300 1464 51 5 5 SEMA3A 7 84046344 Missense_Mutation SNP T C3N-01415_T 1091579 84046344 75299629 243 23990 ZNF804B 0 . GRCh38 7 89333708 89333708 + Silent SNP A A T novel C3N-01415_T C3N-01415_N A A c.726A>T p.= p.T242T ENST00000333190 4/4 306 288 18 332 332 0 strelka-varscan-mutect ZNF804B,synonymous_variant,p.=,ENST00000333190,NM_181646.3;ZNF804B,synonymous_variant,p.=,ENST00000611114,; T ENST00000333190 Transcript synonymous_variant 1335/4659 726/4050 242/1349 T acA/acT 1 1 ZNF804B HGNC HGNC:21958 protein_coding YES CCDS5613.1 ENSP00000329638 A4D1E1 UPI00001A92D2 NM_181646.3 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF12 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 89333708 89333708 A T 1 0 0 0 0 0 0 0 1 18756 175 7 4 4 ZNF804B 7 89333708 Silent SNP A C3N-01415_T 5287364 89333708 70012265 244 23991 DYNC1I1 0 . GRCh38 7 95995956 95995956 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.903G>A p.= p.E301E ENST00000324972 10/17 144 135 9 155 155 0 strelka-varscan-mutect DYNC1I1,synonymous_variant,p.=,ENST00000324972,NM_004411.4;DYNC1I1,synonymous_variant,p.=,ENST00000447467,NM_001135556.1;DYNC1I1,synonymous_variant,p.=,ENST00000437599,NM_001278421.1;DYNC1I1,synonymous_variant,p.=,ENST00000359388,NM_001135557.1;DYNC1I1,synonymous_variant,p.=,ENST00000457059,;DYNC1I1,synonymous_variant,p.=,ENST00000630942,NM_001278422.1;DYNC1I1,synonymous_variant,p.=,ENST00000537881,;DYNC1I1,non_coding_transcript_exon_variant,,ENST00000519371,; A ENST00000324972 Transcript synonymous_variant 1096/2950 903/1938 301/645 E gaG/gaA 1 1 DYNC1I1 HGNC HGNC:2963 protein_coding YES CCDS5644.1 ENSP00000320130 O14576 A4D1I7 UPI0000129A01 NM_004411.4 10/17 hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -17.15777 1 1 1 1 0 A 2 1 78 95995956 95995956 G A 1 0 0 0 0 0 0 0 1 4666 962 34 3 3 DYNC1I1 7 95995956 Silent SNP G C3N-01415_T 6662248 95995956 63350017 245 23992 TRRAP 0 . GRCh38 7 98899467 98899467 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.679G>A p.Glu227Lys p.E227K ENST00000359863 9/72 349 319 30 260 260 0 strelka-varscan-mutect TRRAP,missense_variant,p.Glu227Lys,ENST00000359863,NM_001244580.1;TRRAP,missense_variant,p.Glu227Lys,ENST00000628380,;TRRAP,missense_variant,p.Glu227Lys,ENST00000355540,NM_003496.3;TRRAP,missense_variant,p.Glu227Lys,ENST00000446306,;TRRAP,upstream_gene_variant,,ENST00000456197,; A ENST00000359863 Transcript missense_variant 888/12677 679/11580 227/3859 E/K Gaa/Aaa COSM1268754,COSM1268755,COSM4820286,COSM4820287 1 1 TRRAP HGNC HGNC:12347 protein_coding YES CCDS59066.1 ENSP00000352925 Q9Y4A5 UPI00004575B4 NM_001244580.1 deleterious(0.01) 9/72 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF1 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 78 98899467 98899467 G A 1 0 0 0 0 1 0 0 0 17107 943 33 3 3 TRRAP 7 98899467 Missense_Mutation SNP G C3N-01415_T 2903511 98899467 60446506 246 23993 ARPC1B 0 . GRCh38 7 99392876 99392876 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.989G>T p.Ser330Ile p.S330I ENST00000451682 10/12 121 98 23 93 93 0 strelka-varscan-mutect ARPC1B,missense_variant,p.Ser330Ile,ENST00000451682,;ARPC1B,missense_variant,p.Ser330Ile,ENST00000252725,NM_005720.3;PDAP1,downstream_gene_variant,,ENST00000350498,NM_014891.6;ARPC1B,downstream_gene_variant,,ENST00000443222,;ARPC1B,downstream_gene_variant,,ENST00000431816,;ARPC1B,downstream_gene_variant,,ENST00000455009,;ARPC1B,downstream_gene_variant,,ENST00000414376,;ARPC1B,downstream_gene_variant,,ENST00000418347,;ARPC1B,downstream_gene_variant,,ENST00000458033,;ARPC1B,downstream_gene_variant,,ENST00000417330,;ARPC1B,downstream_gene_variant,,ENST00000427217,;PDAP1,intron_variant,,ENST00000496335,;ARPC1B,downstream_gene_variant,,ENST00000474880,;ARPC1B,upstream_gene_variant,,ENST00000463078,;ARPC1B,downstream_gene_variant,,ENST00000493403,;ARPC1B,splice_region_variant,,ENST00000491294,;ARPC1B,splice_region_variant,,ENST00000481997,;ARPC1A,downstream_gene_variant,,ENST00000441989,;ARPC1B,downstream_gene_variant,,ENST00000468337,;ARPC1B,downstream_gene_variant,,ENST00000432343,;ARPC1B,downstream_gene_variant,,ENST00000484375,;PDAP1,downstream_gene_variant,,ENST00000426447,;ARPC1B,downstream_gene_variant,,ENST00000445924,;ARPC1B,downstream_gene_variant,,ENST00000484600,; T ENST00000451682 Transcript missense_variant,splice_region_variant 1298/1715 989/1119 330/372 S/I aGc/aTc 1 1 ARPC1B HGNC HGNC:704 protein_coding YES CCDS5661.1 ENSP00000389631 O15143 A4D275 UPI0000125D33 deleterious(0.04) 10/12 Gene3D:2.130.10.10,PIRSF_domain:PIRSF038093,hmmpanther:PTHR10709,hmmpanther:PTHR10709:SF10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 99392876 99392876 G T 1 0 0 0 0 1 0 0 0 1112 1014 35 2 2 ARPC1B 7 99392876 Missense_Mutation SNP G C3N-01415_T 493409 99392876 59953097 247 23994 MUC17 0 . GRCh38 7 101033661 101033661 + Missense_Mutation SNP T T A rs71557224 C3N-01415_T C3N-01415_N T T c.2245T>A p.Leu749Ile p.L749I ENST00000306151 3/13 255 204 51 275 274 1 strelka-varscan-mutect MUC17,missense_variant,p.Leu749Ile,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Leu749Ile,ENST00000379439,; A ENST00000306151 Transcript missense_variant 2309/14247 2245/13482 749/4493 L/I Tta/Ata rs71557224,COSM743581 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.22) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs71557224 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 101033661 101033661 T A 1 0 0 0 0 1 0 0 0 9973 1490 52 4 4 MUC17 7 101033661 Missense_Mutation SNP T C3N-01415_T 1640785 101033661 58312312 248 23995 MUC17 0 . GRCh38 7 101037251 101037251 + Silent SNP C C A rs200579827 C3N-01415_T C3N-01415_N C C c.5835C>A p.= p.T1945T ENST00000306151 3/13 100 85 15 127 127 0 strelka-varscan-mutect MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; A ENST00000306151 Transcript synonymous_variant 5899/14247 5835/13482 1945/4493 T acC/acA rs200579827,COSM3922360 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 0,1 LOW 1 SNV 1 0,1 1 PASS rs200579827 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 101037251 101037251 C A 1 0 0 0 0 0 0 0 1 9973 610 22 2 2 MUC17 7 101037251 Silent SNP C C3N-01415_T 3590 101037251 58308722 249 23996 MUC17 0 . GRCh38 7 101058013 101058013 + Missense_Mutation SNP A A C rs754600840 C3N-01415_T C3N-01415_N A A c.13451A>C p.Gln4484Pro p.Q4484P ENST00000306151 13/13 192 147 45 153 153 0 strelka-varscan-mutect MUC17,missense_variant,p.Gln4484Pro,ENST00000306151,NM_001040105.1;RN7SKP54,upstream_gene_variant,,ENST00000410704,;MUC17,3_prime_UTR_variant,,ENST00000379439,;MUC17,downstream_gene_variant,,ENST00000497859,; C ENST00000306151 Transcript missense_variant 13515/14247 13451/13482 4484/4493 Q/P cAg/cCg rs754600840 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious_low_confidence(0) 13/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 MODERATE 1 SNV 1 1 PASS rs754600840 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 101058013 101058013 A C 1 0 0 0 0 1 0 0 0 9973 188 7 5 5 MUC17 7 101058013 Missense_Mutation SNP A C3N-01415_T 20762 101058013 58287960 250 23997 RELN 0 . GRCh38 7 103749479 103749479 + Silent SNP G G T C3N-01415_T C3N-01415_N G G c.603C>A p.= p.I201I ENST00000428762 6/65 448 417 31 482 482 0 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript synonymous_variant 763/11571 603/10383 201/3460 I atC/atA COSM4502050 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 6/65 hmmpanther:PTHR11841 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 103749479 103749479 G T 1 0 0 0 0 0 0 0 1 13390 1164 41 2 2 RELN 7 103749479 Silent SNP G C3N-01415_T 2691466 103749479 55596494 251 23998 SND1 0 . GRCh38 7 128089624 128089624 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.2554G>A p.Gly852Arg p.G852R ENST00000354725 22/24 329 291 38 318 318 0 strelka-varscan-mutect SND1,missense_variant,p.Gly852Arg,ENST00000354725,NM_014390.2;SND1,downstream_gene_variant,,ENST00000486037,;SND1,non_coding_transcript_exon_variant,,ENST00000485871,;SND1,downstream_gene_variant,,ENST00000470463,;SND1,non_coding_transcript_exon_variant,,ENST00000489417,; A ENST00000354725 Transcript missense_variant 2748/3476 2554/2733 852/910 G/R Ggg/Agg COSM1548348 1 1 SND1 HGNC HGNC:30646 protein_coding YES CCDS34747.1 ENSP00000346762 Q7KZF4 A0A140VK49 UPI00000727E5 NM_014390.2 deleterious(0.02) 22/24 Superfamily_domains:0047647,Gene3D:2.40.50.90,Pfam_domain:PF00565,PIRSF_domain:PIRSF017179,hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 128089624 128089624 G A 1 0 0 0 0 1 0 0 0 15165 1232 43 3 3 SND1 7 128089624 Missense_Mutation SNP G C3N-01415_T 24340145 128089624 31256349 252 23999 FLNC 0 . GRCh38 7 128849337 128849337 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.4958G>T p.Cys1653Phe p.C1653F ENST00000325888 30/48 493 397 96 467 467 0 strelka-varscan-mutect FLNC,missense_variant,p.Cys1653Phe,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Cys1653Phe,ENST00000346177,NM_001127487.1;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,; T ENST00000325888 Transcript missense_variant 5219/9188 4958/8178 1653/2725 C/F tGc/tTc 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.24) 30/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 128849337 128849337 G T 1 0 0 0 0 1 0 0 0 5791 1319 46 2 2 FLNC 7 128849337 Missense_Mutation SNP G C3N-01415_T 759713 128849337 30496636 253 24000 WDR91 0 . GRCh38 7 135209718 135209718 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.161A>C p.Gln54Pro p.Q54P ENST00000354475 2/15 120 105 15 111 111 0 strelka-varscan-mutect WDR91,missense_variant,p.Gln54Pro,ENST00000354475,NM_014149.3;WDR91,missense_variant,p.Gln19Pro,ENST00000423565,;MIR6509,upstream_gene_variant,,ENST00000614603,;AC009542.2,non_coding_transcript_exon_variant,,ENST00000628498,;AC009542.2,downstream_gene_variant,,ENST00000631295,;WDR91,upstream_gene_variant,,ENST00000485942,;WDR91,non_coding_transcript_exon_variant,,ENST00000466182,; G ENST00000354475 Transcript missense_variant 193/4588 161/2244 54/747 Q/P cAg/cCg 1 -1 WDR91 HGNC HGNC:24997 protein_coding YES CCDS34758.1 ENSP00000346466 A4D1P6 UPI000006F2DE NM_014149.3 tolerated(0.12) 2/15 hmmpanther:PTHR13083 MODERATE 1 SNV 1 1 PASS rs1375077753 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 135209718 135209718 T G 1 0 0 0 0 1 0 0 0 17894 1580 55 5 5 WDR91 7 135209718 Missense_Mutation SNP T C3N-01415_T 6360381 135209718 24136255 254 24001 MTPN 0 . GRCh38 7 135929943 135929943 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.340A>G p.Lys114Glu p.K114E ENST00000393085 4/4 301 229 72 329 328 1 strelka-varscan-mutect MTPN,missense_variant,p.Lys114Glu,ENST00000393085,NM_145808.3;MTPN,missense_variant,p.Lys48Glu,ENST00000435723,;LUZP6,upstream_gene_variant,,ENST00000589735,NM_001128619.2;AC015987.1,intron_variant,,ENST00000419211,; C ENST00000393085 Transcript missense_variant 556/3738 340/357 114/118 K/E Aaa/Gaa 1 -1 MTPN HGNC HGNC:15667 protein_coding YES CCDS5842.1 ENSP00000376800 P58546 Q69YG1 UPI00000012BC NM_145808.3 deleterious(0) 4/4 hmmpanther:PTHR24189:SF26,hmmpanther:PTHR24189,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 135929943 135929943 T C 1 0 0 0 0 1 0 0 0 9943 1821 63 5 5 MTPN 7 135929943 Missense_Mutation SNP T C3N-01415_T 720225 135929943 23416030 255 24002 PTN 0 . GRCh38 7 137253597 137253597 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.156G>T p.Trp52Cys p.W52C ENST00000348225 3/5 102 83 19 112 112 0 strelka-varscan-mutect PTN,missense_variant,p.Trp52Cys,ENST00000348225,NM_001321387.1,NM_002825.5;PTN,missense_variant,p.Trp52Cys,ENST00000393083,; A ENST00000348225 Transcript missense_variant 584/1614 156/507 52/168 W/C tgG/tgT 1 -1 PTN HGNC HGNC:9630 protein_coding YES CCDS5844.1 ENSP00000341170 P21246 A0A024R778 UPI000013297B NM_001321387.1,NM_002825.5 deleterious(0) 3/5 Gene3D:1mknA00,PD005592,Pfam_domain:PF05196,Prints_domain:PR00269,PROSITE_patterns:PS00619,hmmpanther:PTHR13850,SMART_domains:SM00193,Superfamily_domains:SSF57288 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 137253597 137253597 C A 1 0 0 0 0 1 0 0 0 12924 856 30 2 2 PTN 7 137253597 Missense_Mutation SNP C C3N-01415_T 1323654 137253597 22092376 256 24003 MGAM 0 . GRCh38 7 142034774 142034774 + Missense_Mutation SNP C C A rs782592725 C3N-01415_T C3N-01415_N C C c.1892C>A p.Ala631Asp p.A631D ENST00000549489 16/48 185 143 42 240 240 0 strelka-varscan-mutect MGAM,missense_variant,p.Ala631Asp,ENST00000475668,;MGAM,missense_variant,p.Ala631Asp,ENST00000549489,NM_004668.2;MGAM,missense_variant,p.Ala631Asp,ENST00000620571,;MGAM,downstream_gene_variant,,ENST00000495045,;MGAM,upstream_gene_variant,,ENST00000490593,; A ENST00000549489 Transcript missense_variant 1987/6525 1892/5574 631/1857 A/D gCc/gAc rs782592725,COSM2862017,COSM2862018,COSM2862019 1 1 MGAM HGNC HGNC:7043 protein_coding YES CCDS47727.1 ENSP00000447378 O43451 UPI000183CB7B NM_004668.2 deleterious(0) 16/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF63,Pfam_domain:PF01055,Superfamily_domains:SSF51445 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs782592725 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 142034774 142034774 C A 1 0 0 0 0 1 0 0 0 9499 739 26 2 2 MGAM 7 142034774 Missense_Mutation SNP C C3N-01415_T 4781177 142034774 17311199 257 24004 TRPV6 0 . GRCh38 7 142875536 142875536 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1174C>A p.Leu392Ile p.L392I ENST00000359396 8/15 107 97 10 113 113 0 strelka-varscan-mutect TRPV6,missense_variant,p.Leu392Ile,ENST00000359396,NM_018646.5;TRPV6,intron_variant,,ENST00000436401,;EPHB6,downstream_gene_variant,,ENST00000619012,;EPHB6,downstream_gene_variant,,ENST00000422643,NM_004445.5;EPHB6,downstream_gene_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000476059,;TRPV6,downstream_gene_variant,,ENST00000431833,;RP11-114L10.2,upstream_gene_variant,,ENST00000438839,;EPHB6,downstream_gene_variant,,ENST00000617632,;TRPV6,non_coding_transcript_exon_variant,,ENST00000615386,;TRPV6,non_coding_transcript_exon_variant,,ENST00000485138,;TRPV6,non_coding_transcript_exon_variant,,ENST00000619250,;EPHB6,downstream_gene_variant,,ENST00000616380,;EPHB6,downstream_gene_variant,,ENST00000614832,;EPHB6,downstream_gene_variant,,ENST00000611578,;EPHB6,downstream_gene_variant,,ENST00000486511,;TRPV6,downstream_gene_variant,,ENST00000489123,;TRPV6,downstream_gene_variant,,ENST00000474388,;EPHB6,downstream_gene_variant,,ENST00000471581,; T ENST00000359396 Transcript missense_variant 1300/2928 1174/2298 392/765 L/I Ctc/Atc 1 -1 TRPV6 HGNC HGNC:14006 protein_coding YES ENSP00000352358 Q9H1D0 UPI00064546CC NM_018646.5 deleterious(0.04) 8/15 hmmpanther:PTHR10582:SF25,hmmpanther:PTHR10582,TIGRFAM_domain:TIGR00870,Pfam_domain:PF00520,Prints_domain:PR01765 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -19.72084 0.9999998 1 1 1 0 T 3 4 78 142875536 142875536 G T 1 0 0 0 0 1 0 0 0 17106 1000 35 2 2 TRPV6 7 142875536 Missense_Mutation SNP G C3N-01415_T 840762 142875536 16470437 258 24005 ARHGEF35 0 . GRCh38 7 144187399 144187399 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.985G>T p.Glu329Ter p.E329* ENST00000378115 2/2 170 118 52 178 177 1 strelka-varscan-mutect ARHGEF35,stop_gained,p.Glu329Ter,ENST00000378115,NM_001003702.2;CTAGE4,downstream_gene_variant,,ENST00000486333,NM_198495.2; A ENST00000378115 Transcript stop_gained 1115/2431 985/1455 329/484 E/* Gag/Tag 1 -1 ARHGEF35 HGNC HGNC:33846 protein_coding YES CCDS34770.1 ENSP00000367355 A5YM69 UPI00002373BE NM_001003702.2 2/2 Pfam_domain:PF15441,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF2 HIGH 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 144187399 144187399 C A 1 0 0 0 0 0 1 0 0 1039 864 30 2 2 ARHGEF35 7 144187399 Nonsense_Mutation SNP C C3N-01415_T 1311863 144187399 15158574 259 24006 SSPO 0 . GRCh38 7 149776353 149776353 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.58T>C p.Cys20Arg p.C20R ENST00000378016 2/107 129 113 16 110 110 0 varscan-mutect SSPO,missense_variant,p.Cys20Arg,ENST00000378016,NM_198455.2;ZNF467,upstream_gene_variant,,ENST00000302017,NM_207336.1;ZNF467,upstream_gene_variant,,ENST00000484747,;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,upstream_gene_variant,,ENST00000486824,; C ENST00000378016 Transcript missense_variant 58/15589 58/15453 20/5150 C/R Tgt/Cgt 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 2/107 MODERATE SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 78 149776353 149776353 T C 1 0 0 0 0 1 0 0 0 15566 1696 59 5 5 SSPO 7 149776353 Missense_Mutation SNP T C3N-01415_T 5588954 149776353 9569620 260 24007 ZNF775 0 . GRCh38 7 150397128 150397128 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.647A>G p.Asp216Gly p.D216G ENST00000329630 3/3 138 126 12 143 143 0 strelka-varscan-mutect ZNF775,missense_variant,p.Asp216Gly,ENST00000329630,NM_173680.3;ZNF775,downstream_gene_variant,,ENST00000490973,;ZNF775,downstream_gene_variant,,ENST00000478789,;ZNF775,intron_variant,,ENST00000486297,;ZNF775,intron_variant,,ENST00000483664,; G ENST00000329630 Transcript missense_variant 754/2257 647/1614 216/537 D/G gAc/gGc 1 1 ZNF775 HGNC HGNC:28501 protein_coding YES CCDS43678.1 ENSP00000330838 Q96BV0 UPI00001BDA25 NM_173680.3 tolerated(0.08) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24409 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99952 1 1 1 1 0 G 3 3 78 150397128 150397128 A G 1 0 0 0 0 1 0 0 0 18731 275 10 5 5 ZNF775 7 150397128 Missense_Mutation SNP A C3N-01415_T 620775 150397128 8948845 261 24008 GIMAP7 0 . GRCh38 7 150520645 150520645 + Missense_Mutation SNP A A G novel C3N-01415_T C3N-01415_N A A c.671A>G p.Tyr224Cys p.Y224C ENST00000313543 2/2 268 207 61 291 291 0 strelka-varscan-mutect GIMAP7,missense_variant,p.Tyr224Cys,ENST00000313543,NM_153236.3; G ENST00000313543 Transcript missense_variant 828/1256 671/903 224/300 Y/C tAc/tGc 1 1 GIMAP7 HGNC HGNC:22404 protein_coding YES CCDS5903.1 ENSP00000315474 Q8NHV1 A0A090N8P8 UPI0000036B86 NM_153236.3 deleterious(0.03) 2/2 hmmpanther:PTHR10903,hmmpanther:PTHR10903:SF63,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 150520645 150520645 A G 1 0 0 0 0 1 0 0 0 6264 391 14 5 5 GIMAP7 7 150520645 Missense_Mutation SNP A C3N-01415_T 123517 150520645 8825328 262 24009 RBM33 0 . GRCh38 7 155774558 155774558 + Splice_Site SNP G G T novel C3N-01415_T C3N-01415_N G G c.3376-1G>T p.X1126_splice ENST00000401878 236 187 49 200 200 0 strelka-varscan-mutect RBM33,splice_acceptor_variant,,ENST00000401878,NM_053043.2;RBM33,splice_acceptor_variant,,ENST00000341148,;RBM33,splice_acceptor_variant,,ENST00000392755,; T ENST00000401878 Transcript splice_acceptor_variant -/10149 3376/3513 1126/1170 1 1 RBM33 HGNC HGNC:27223 protein_coding YES CCDS5941.2 ENSP00000384160 Q96EV2 UPI00015743D7 NM_053043.2 16/17 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 78 155774558 155774558 G T 1 0 0 0 0 0 0 1 0 13296 956 33 2 2 RBM33 7 155774558 Splice_Site SNP G C3N-01415_T 5253913 155774558 3571415 263 24010 UBE3C 0 . GRCh38 7 157267677 157267677 + Silent SNP C C T rs147977568 C3N-01415_T C3N-01415_N C C c.3174C>T p.= p.P1058P ENST00000348165 23/23 243 201 42 230 230 0 strelka-varscan-mutect UBE3C,synonymous_variant,p.=,ENST00000348165,NM_014671.2;UBE3C,non_coding_transcript_exon_variant,,ENST00000470408,;UBE3C,downstream_gene_variant,,ENST00000474153,;RP5-1142J19.2,upstream_gene_variant,,ENST00000428733,; T ENST00000348165 Transcript synonymous_variant 3534/5229 3174/3252 1058/1083 P ccC/ccT rs147977568,COSM3305937 1 1 UBE3C HGNC HGNC:16803 protein_coding YES CCDS34789.1 ENSP00000309198 Q15386 UPI000020E72A NM_014671.2 23/23 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF336,SMART_domains:SM00119,Superfamily_domains:SSF56204 0,1 LOW 1 SNV 1 0,1 1 PASS rs147977568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 157267677 157267677 C T 1 0 0 0 0 0 0 0 1 17404 639 23 1 1 UBE3C 7 157267677 Silent SNP C C3N-01415_T 1493119 157267677 2078296 264 24011 RP1L1 0 . GRCh38 8 10612663 10612663 + Missense_Mutation SNP C C A rs773293580 C3N-01415_T C3N-01415_N C C c.1435G>T p.Gly479Trp p.G479W ENST00000382483 4/4 85 70 15 125 124 1 strelka-varscan-mutect RP1L1,missense_variant,p.Gly479Trp,ENST00000382483,NM_178857.5; A ENST00000382483 Transcript missense_variant 1659/7973 1435/7203 479/2400 G/W Ggg/Tgg rs773293580 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 deleterious(0) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 MODERATE 1 SNV 1 1 PASS rs773293580 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 10612663 10612663 C A 1 0 0 0 0 1 0 0 0 13773 652 23 1 1 RP1L1 8 10612663 Missense_Mutation SNP C C3N-01415_T 10612663 134525973 265 24012 EXTL3 0 . GRCh38 8 28717343 28717343 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.1284C>T p.= p.S428S ENST00000220562 3/7 316 267 49 471 471 0 strelka-varscan-mutect EXTL3,synonymous_variant,p.=,ENST00000220562,NM_001440.3;EXTL3,synonymous_variant,p.=,ENST00000523149,;EXTL3,intron_variant,,ENST00000521532,;EXTL3,upstream_gene_variant,,ENST00000521473,;EXTL3,intron_variant,,ENST00000519886,;EXTL3,downstream_gene_variant,,ENST00000518223,;EXTL3,downstream_gene_variant,,ENST00000522725,;EXTL3,downstream_gene_variant,,ENST00000520940,;EXTL3,downstream_gene_variant,,ENST00000454906,;EXTL3,downstream_gene_variant,,ENST00000519288,;EXTL3,intron_variant,,ENST00000522698,; T ENST00000220562 Transcript synonymous_variant 2186/6483 1284/2760 428/919 S tcC/tcT 1 1 EXTL3 HGNC HGNC:3518 protein_coding YES CCDS6070.1 ENSP00000220562 O43909 UPI000012A35D NM_001440.3 3/7 hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF73,Pfam_domain:PF03016 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 28717343 28717343 C T 1 0 0 0 0 0 0 0 1 5195 581 21 3 3 EXTL3 8 28717343 Silent SNP C C3N-01415_T 18104680 28717343 116421293 266 24013 ANK1 0 . GRCh38 8 41704110 41704110 + Silent SNP G G A C3N-01415_T C3N-01415_N G G c.2325C>T p.= p.A775A ENST00000265709 20/43 631 569 62 488 488 0 strelka-varscan-mutect ANK1,synonymous_variant,p.=,ENST00000289734,NM_000037.3;ANK1,synonymous_variant,p.=,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,synonymous_variant,p.=,ENST00000265709,NM_001142446.1;ANK1,synonymous_variant,p.=,ENST00000520299,; A ENST00000265709 Transcript synonymous_variant 2607/6379 2325/5694 775/1897 A gcC/gcT COSM3649239,COSM3649240 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 20/43 Gene3D:1.25.40.20,Pfam_domain:PF13637,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 41704110 41704110 G A 1 0 0 0 0 0 0 0 1 720 1219 43 3 3 ANK1 8 41704110 Silent SNP G C3N-01415_T 12986767 41704110 103434526 267 24014 ANK1 0 . GRCh38 8 41723591 41723591 + Missense_Mutation SNP C C G rs140138043 C3N-01415_T C3N-01415_N C C c.853G>C p.Val285Leu p.V285L ENST00000265709 8/43 565 457 108 422 422 0 strelka-varscan-mutect ANK1,missense_variant,p.Val252Leu,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Val252Leu,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Val285Leu,ENST00000265709,NM_001142446.1; G ENST00000265709 Transcript missense_variant 1135/6379 853/5694 285/1897 V/L Gtg/Ctg rs140138043 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 tolerated(0.15) 8/43 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs140138043 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 41723591 41723591 C G 1 0 0 0 0 1 0 0 0 720 536 19 4 4 ANK1 8 41723591 Missense_Mutation SNP C C3N-01415_T 19481 41723591 103415045 268 24015 DKK4 0 . GRCh38 8 42377018 42377018 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.28A>T p.Ser10Cys p.S10C ENST00000220812 1/4 281 213 68 243 243 0 strelka-varscan-mutect DKK4,missense_variant,p.Ser10Cys,ENST00000220812,NM_014420.2; A ENST00000220812 Transcript missense_variant 215/894 28/675 10/224 S/C Agc/Tgc 1 -1 DKK4 HGNC HGNC:2894 protein_coding YES CCDS6130.1 ENSP00000220812 Q9UBT3 UPI0000051057 NM_014420.2 tolerated(0.12) 1/4 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12113,hmmpanther:PTHR12113:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 42377018 42377018 T A 1 0 0 0 0 1 0 0 0 4353 1551 54 4 4 DKK4 8 42377018 Missense_Mutation SNP T C3N-01415_T 653427 42377018 102761618 269 24016 RUNX1T1 0 . GRCh38 8 91991740 91991740 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1067C>T p.Pro356Leu p.P356L ENST00000436581 7/12 420 396 24 366 366 0 strelka-varscan-mutect RUNX1T1,missense_variant,p.Pro297Leu,ENST00000613302,NM_001198630.1,NM_001198627.1;RUNX1T1,missense_variant,p.Pro297Leu,ENST00000617740,NM_001198629.1,NM_001198626.1;RUNX1T1,missense_variant,p.Pro297Leu,ENST00000523629,NM_175634.2;RUNX1T1,missense_variant,p.Pro297Leu,ENST00000614812,NM_001198631.1;RUNX1T1,missense_variant,p.Pro356Leu,ENST00000436581,NM_001198679.1;RUNX1T1,missense_variant,p.Pro270Leu,ENST00000613886,NM_001198632.1;RUNX1T1,missense_variant,p.Pro277Leu,ENST00000615601,NM_001198633.1;RUNX1T1,missense_variant,p.Pro297Leu,ENST00000265814,NM_001198628.1;RUNX1T1,missense_variant,p.Pro270Leu,ENST00000396218,NM_004349.3;RUNX1T1,missense_variant,p.Pro270Leu,ENST00000518844,NM_001198625.1;RUNX1T1,missense_variant,p.Pro260Leu,ENST00000422361,NM_175636.2;RUNX1T1,missense_variant,p.Pro260Leu,ENST00000360348,NM_175635.2;RUNX1T1,missense_variant,p.Pro308Leu,ENST00000520724,NM_001198634.1;RUNX1T1,3_prime_UTR_variant,,ENST00000520978,;RUNX1T1,3_prime_UTR_variant,,ENST00000518361,;RUNX1T1,non_coding_transcript_exon_variant,,ENST00000520047,;RUNX1T1,upstream_gene_variant,,ENST00000521751,; A ENST00000436581 Transcript missense_variant 1254/7454 1067/1992 356/663 P/L cCt/cTt 1 -1 RUNX1T1 HGNC HGNC:1535 protein_coding YES CCDS75766.1 ENSP00000402257 A0A0A0MSU1 UPI0001E7B0BD NM_001198679.1 tolerated(0.53) 7/12 Low_complexity_(Seg):seg,hmmpanther:PTHR10379:SF5,hmmpanther:PTHR10379 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 91991740 91991740 G A 1 0 0 0 0 1 0 0 0 14008 1000 35 3 3 RUNX1T1 8 91991740 Missense_Mutation SNP G C3N-01415_T 49614722 91991740 53146896 270 24017 CDH17 0 . GRCh38 8 94151951 94151951 + Missense_Mutation SNP G G C C3N-01415_T C3N-01415_N G G c.1713C>G p.Phe571Leu p.F571L ENST00000027335 13/18 572 523 49 582 582 0 strelka-varscan-mutect CDH17,missense_variant,p.Phe571Leu,ENST00000027335,NM_004063.3;CDH17,missense_variant,p.Phe571Leu,ENST00000450165,NM_001144663.1;CDH17,missense_variant,p.Phe357Leu,ENST00000441892,;CDH17,intron_variant,,ENST00000520952,; C ENST00000027335 Transcript missense_variant 1838/3693 1713/2499 571/832 F/L ttC/ttG COSM3651876 1 -1 CDH17 HGNC HGNC:1756 protein_coding YES CCDS6260.1 ENSP00000027335 Q12864 UPI000013C546 NM_004063.3 tolerated(0.27) 13/18 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF292,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 94151951 94151951 G C 1 0 0 0 0 1 0 0 0 2805 1165 41 4 4 CDH17 8 94151951 Missense_Mutation SNP G C3N-01415_T 2160211 94151951 50986685 271 24018 CPQ 0 . GRCh38 8 96879805 96879805 + Missense_Mutation SNP A A C rs147764297 C3N-01415_T C3N-01415_N A A c.649A>C p.Thr217Pro p.T217P ENST00000220763 4/8 281 256 25 287 287 0 strelka-varscan-mutect CPQ,missense_variant,p.Thr217Pro,ENST00000220763,NM_016134.3; C ENST00000220763 Transcript missense_variant 859/1947 649/1419 217/472 T/P Aca/Cca rs147764297 1 1 CPQ HGNC HGNC:16910 protein_coding YES CCDS6273.1 ENSP00000220763 Q9Y646 A0A024R9B8 UPI00000706B8 NM_016134.3 deleterious(0) 4/8 hmmpanther:PTHR12053,hmmpanther:PTHR12053:SF3,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS rs147764297 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 96879805 96879805 A C 1 0 0 0 0 1 0 0 0 3618 159 6 5 5 CPQ 8 96879805 Missense_Mutation SNP A C3N-01415_T 2727854 96879805 48258831 272 24019 KCNS2 0 . GRCh38 8 98428432 98428432 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.453C>A p.= p.I151I ENST00000287042 2/2 524 478 46 491 490 1 strelka-varscan-mutect KCNS2,synonymous_variant,p.=,ENST00000287042,NM_020697.2;KCNS2,synonymous_variant,p.=,ENST00000521839,;STK3,intron_variant,,ENST00000517832,; A ENST00000287042 Transcript synonymous_variant 803/5219 453/1434 151/477 I atC/atA 1 1 KCNS2 HGNC HGNC:6301 protein_coding YES CCDS6279.1 ENSP00000287042 Q9ULS6 UPI0000001653 NM_020697.2 2/2 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF60 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 98428432 98428432 C A 1 0 0 0 0 0 0 0 1 8005 845 30 2 2 KCNS2 8 98428432 Silent SNP C C3N-01415_T 1548627 98428432 46710204 273 24020 RIMS2 0 . GRCh38 8 103936688 103936688 + Missense_Mutation SNP G G T rs766328696 C3N-01415_T C3N-01415_N G G c.2513G>T p.Arg838Leu p.R838L ENST00000504942 13/24 154 140 14 158 158 0 strelka-varscan-mutect RIMS2,missense_variant,p.Arg630Leu,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Arg616Leu,ENST00000436393,;RIMS2,missense_variant,p.Arg838Leu,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Arg780Leu,ENST00000626043,;RIMS2,missense_variant,p.Arg630Leu,ENST00000408894,;RIMS2,missense_variant,p.Arg677Leu,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Arg826Leu,ENST00000632716,;RIMS2,missense_variant,p.Arg232Leu,ENST00000507677,;RIMS2,missense_variant,p.Arg630Leu,ENST00000515551,; T ENST00000504942 Transcript missense_variant 2652/4228 2513/4050 838/1349 R/L cGt/cTt rs766328696,COSM3395036,COSM3395037,COSM3395038,COSM3395039,COSM3395040 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 13/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1,1,1,1,1 MODERATE 1 SNV 2 0,1,1,1,1,1 1 PASS rs766328696 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 103936688 103936688 G T 1 0 0 0 0 1 0 0 0 13543 1145 40 1 1 RIMS2 8 103936688 Missense_Mutation SNP G C3N-01415_T 5508256 103936688 41201948 274 24021 82 2 RIMS2 0 . GRCh38 8 103936690 103936690 + Missense_Mutation SNP G G T rs774233059 C3N-01415_T C3N-01415_N G G c.2515G>T p.Val839Phe p.V839F ENST00000504942 13/24 156 142 14 152 152 0 strelka-varscan-mutect RIMS2,missense_variant,p.Val631Phe,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Val617Phe,ENST00000436393,;RIMS2,missense_variant,p.Val839Phe,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Val781Phe,ENST00000626043,;RIMS2,missense_variant,p.Val631Phe,ENST00000408894,;RIMS2,missense_variant,p.Val678Phe,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Val827Phe,ENST00000632716,;RIMS2,missense_variant,p.Val233Phe,ENST00000507677,;RIMS2,missense_variant,p.Val631Phe,ENST00000515551,; T ENST00000504942 Transcript missense_variant 2654/4228 2515/4050 839/1349 V/F Gtt/Ttt rs774233059 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 13/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS rs774233059 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 103936690 103936690 G T 1 0 0 0 0 1 0 0 0 13543 1377 48 2 2 RIMS2 8 103936690 Missense_Mutation SNP G C3N-01415_T 2 103936690 41201946 275 24022 82 2 RIMS2 0 . GRCh38 8 104251818 104251818 + Nonstop_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.4048T>C p.Ter1350GlnextTer3 p.*1350Qext*3 ENST00000504942 24/24 160 111 49 175 175 0 strelka-varscan-mutect RIMS2,stop_lost,p.Ter1164GlnextTer3,ENST00000507740,NM_014677.4;RIMS2,stop_lost,p.Ter1368GlnextTer3,ENST00000436393,;RIMS2,stop_lost,p.Ter1350GlnextTer3,ENST00000504942,NM_001100117.2;RIMS2,stop_lost,p.Ter1189GlnextTer3,ENST00000262231,NM_001282881.1;RIMS2,stop_lost,p.Ter286GlnextTer3,ENST00000339750,NM_001282882.1;RIMS2,downstream_gene_variant,,ENST00000626043,;RIMS2,downstream_gene_variant,,ENST00000408894,;RIMS2,downstream_gene_variant,,ENST00000523362,; C ENST00000504942 Transcript stop_lost 4187/4228 4048/4050 1350/1349 */Q Tag/Cag 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 24/24 HIGH 1 SNV 2 1 PASS rs766810783 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 78 104251818 104251818 T C 1 0 0 0 0 0 0 0 0 13543 1419 49 5 5 RIMS2 8 104251818 Nonstop_Mutation SNP T C3N-01415_T 315128 104251818 40886818 276 24023 TRPS1 0 . GRCh38 8 115587392 115587392 + Missense_Mutation SNP C C G C3N-01415_T C3N-01415_N C C c.2309G>C p.Gly770Ala p.G770A ENST00000395715 5/7 798 753 45 775 775 0 strelka-varscan-mutect TRPS1,missense_variant,p.Gly770Ala,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Gly757Ala,ENST00000220888,;TRPS1,missense_variant,p.Gly761Ala,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Gly511Ala,ENST00000519076,;TRPS1,missense_variant,p.Gly757Ala,ENST00000519674,;TRPS1,missense_variant,p.Gly561Ala,ENST00000517323,; G ENST00000395715 Transcript missense_variant 2887/9990 2309/3885 770/1294 G/A gGa/gCa COSM3663523,COSM3663524 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 tolerated_low_confidence(0.81) 5/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 115587392 115587392 C G 1 0 0 0 0 1 0 0 0 17099 855 30 4 4 TRPS1 8 115587392 Missense_Mutation SNP C C3N-01415_T 11335574 115587392 29551244 277 24024 NOV 0 . GRCh38 8 119418191 119418191 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.444G>T p.= p.V148V ENST00000259526 3/5 428 400 28 442 442 0 strelka-varscan-mutect NOV,synonymous_variant,p.=,ENST00000259526,NM_002514.3;RP11-775B15.2,downstream_gene_variant,,ENST00000519786,;NOV,downstream_gene_variant,,ENST00000520082,; T ENST00000259526 Transcript synonymous_variant 671/2522 444/1074 148/357 V gtG/gtT 1 1 NOV HGNC HGNC:7885 protein_coding YES CCDS6328.1 ENSP00000259526 P48745 A0A024R9J4 UPI00001303BE NM_002514.3 3/5 PROSITE_profiles:PS50184,hmmpanther:PTHR11348:SF8,hmmpanther:PTHR11348,PROSITE_patterns:PS01208,PIRSF_domain:PIRSF036495,Pfam_domain:PF00093,SMART_domains:SM00214,Superfamily_domains:SSF57603 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 119418191 119418191 G T 1 0 0 0 0 0 0 0 1 10599 1306 46 2 2 NOV 8 119418191 Silent SNP G C3N-01415_T 3830799 119418191 25720445 278 24025 TMEM65 0 . GRCh38 8 124320103 124320103 + Missense_Mutation SNP G G A rs779556138 C3N-01415_T C3N-01415_N G G c.604C>T p.Arg202Cys p.R202C ENST00000297632 6/7 274 251 23 221 221 0 strelka-varscan-mutect TMEM65,missense_variant,p.Arg202Cys,ENST00000297632,NM_194291.2; A ENST00000297632 Transcript missense_variant 1139/9029 604/723 202/240 R/C Cgt/Tgt rs779556138,COSM247904 1 -1 TMEM65 HGNC HGNC:25203 protein_coding YES CCDS6348.1 ENSP00000297632 Q6PI78 UPI00003675D1 NM_194291.2 deleterious(0) 6/7 Pfam_domain:PF10507,hmmpanther:PTHR21706 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779556138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 124320103 124320103 G A 1 0 0 0 0 1 0 0 0 16670 1145 40 1 1 TMEM65 8 124320103 Missense_Mutation SNP G C3N-01415_T 4901912 124320103 20818533 279 24026 SLC45A4 0 . GRCh38 8 141215822 141215822 + Silent SNP G G A C3N-01415_T C3N-01415_N G G c.1878C>T p.= p.I626I ENST00000517878 6/8 674 634 40 500 500 0 strelka-varscan-mutect SLC45A4,synonymous_variant,p.=,ENST00000519067,NM_001286648.1;SLC45A4,synonymous_variant,p.=,ENST00000024061,NM_001080431.2;SLC45A4,synonymous_variant,p.=,ENST00000517878,NM_001286646.1;SLC45A4,downstream_gene_variant,,ENST00000520137,;SLC45A4,downstream_gene_variant,,ENST00000519986,; A ENST00000517878 Transcript synonymous_variant 1878/3470 1878/2427 626/808 I atC/atT COSM377312 1 -1 SLC45A4 HGNC HGNC:29196 protein_coding YES CCDS75795.1 ENSP00000428137 E7EV90 UPI0001E8F5C7 NM_001286646.1 6/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF7,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 1 LOW 1 SNV 1 1 1 PASS rs1418560621 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 141215822 141215822 G A 1 0 0 0 0 0 0 0 1 14920 1048 37 1 1 SLC45A4 8 141215822 Silent SNP G C3N-01415_T 16895719 141215822 3922814 280 24027 TSNARE1 0 . GRCh38 8 142314383 142314383 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.1131+1G>T p.X377_splice ENST00000524325 284 257 27 243 242 1 strelka-varscan-mutect TSNARE1,splice_donor_variant,,ENST00000519651,NM_001291931.1;TSNARE1,splice_donor_variant,,ENST00000524325,NM_145003.4;TSNARE1,splice_donor_variant,,ENST00000307180,;TSNARE1,splice_donor_variant,,ENST00000520166,;TSNARE1,splice_donor_variant,,ENST00000518928,; A ENST00000524325 Transcript splice_donor_variant -/1963 1131/1542 377/513 1 -1 TSNARE1 HGNC HGNC:26437 protein_coding YES CCDS6384.1 ENSP00000428763 Q96NA8 UPI00001AEE5E NM_145003.4 9/13 HIGH 1 SNV 2 1 PASS rs1241789175 . 0 207 0 3 0 0 0 0 -20 0.9999838 1 1 1 0 A 5 1 78 142314383 142314383 C A 1 0 0 0 0 0 0 1 0 17135 521 18 2 2 TSNARE1 8 142314383 Splice_Site SNP C C3N-01415_T 1098561 142314383 2824253 281 24028 CYP11B1 0 . GRCh38 8 142875124 142875124 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.1231G>C p.Gly411Arg p.G411R ENST00000292427 8/9 604 549 55 558 558 0 strelka-varscan-mutect CYP11B1,missense_variant,p.Gly411Arg,ENST00000292427,NM_000497.3;CYP11B1,missense_variant,p.Gly89Arg,ENST00000519285,;CYP11B1,missense_variant,p.Gly482Arg,ENST00000377675,;CYP11B1,intron_variant,,ENST00000517471,NM_001026213.1;GML,intron_variant,,ENST00000522728,;CYP11B1,intron_variant,,ENST00000314111,; G ENST00000292427 Transcript missense_variant 1264/2664 1231/1512 411/503 G/R Ggt/Cgt 1 -1 CYP11B1 HGNC HGNC:2591 protein_coding YES CCDS6392.1 ENSP00000292427 P15538 UPI000013E0BA NM_000497.3 deleterious(0) 8/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 142875124 142875124 C G 1 0 0 0 0 1 0 0 0 3948 623 22 4 4 CYP11B1 8 142875124 Missense_Mutation SNP C C3N-01415_T 560741 142875124 2263512 282 24029 MROH1 0 . GRCh38 8 144261684 144261711 + Frame_Shift_Del DEL CCCGAGGTGCGGACGAGGGCTGCTGAGG CCCGAGGTGCGGACGAGGGCTGCTGAGG - novel C3N-01415_T C3N-01415_N CCCGAGGTGCGGACGAGGGCTGCTGAGG CCCGAGGTGCGGACGAGGGCTGCTGAGG c.4873_4900delGAGGTGCGGACGAGGGCTGCTGAGGCCC p.Glu1625TrpfsTer5 p.E1625Wfs*5 ENST00000528919 43/43 593 456 137 540 540 0 sindel-varindel-pindel MROH1,frameshift_variant,p.Glu1625TrpfsTer5,ENST00000528919,NM_032450.2;MROH1,frameshift_variant,p.Glu1625TrpfsTer5,ENST00000326134,;MROH1,frameshift_variant,p.Glu1616TrpfsTer5,ENST00000534366,NM_001288814.1;MROH1,coding_sequence_variant,,ENST00000544576,;BOP1,downstream_gene_variant,,ENST00000569669,NM_015201.4;SCX,upstream_gene_variant,,ENST00000567180,NM_001080514.2;BOP1,downstream_gene_variant,,ENST00000569403,;BOP1,downstream_gene_variant,,ENST00000616126,;BOP1,downstream_gene_variant,,ENST00000563210,;BOP1,downstream_gene_variant,,ENST00000568812,;BOP1,downstream_gene_variant,,ENST00000569160,; - ENST00000528919 Transcript frameshift_variant 4991-5018/5234 4870-4897/4926 1624-1633/1641 PEVRTRAAEA/X CCCGAGGTGCGGACGAGGGCTGCTGAGGcc/cc 1 1 MROH1 HGNC HGNC:26958 protein_coding YES CCDS47938.1 ENSP00000435565 Q8NDA8 UPI0001AE6FA6 NM_032450.2 43/43 PROSITE_profiles:PS50077,hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Pfam_domain:PF02985,Superfamily_domains:SSF48371 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 144261684 144261684 CCCGAGGTGCGGACGAGGGCTGCTGAGG - 1 0 1 0 1 0 0 0 0 9743 623 22 0 0 MROH1 8 144261684 Frame_Shift_Del DEL CCCGAGGTGCGGACGAGGGCTGCTGAGG C3N-01415_T 1386560 144261684 876952 283 24030 RPL8 0 . GRCh38 8 144791801 144791801 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.252G>T p.= p.T84T ENST00000262584 3/6 315 270 45 250 249 1 strelka-varscan-mutect RPL8,synonymous_variant,p.=,ENST00000262584,NM_000973.3;RPL8,synonymous_variant,p.=,ENST00000528957,NM_001317782.1;RPL8,synonymous_variant,p.=,ENST00000394920,NM_001317771.1,NM_033301.1;RPL8,synonymous_variant,p.=,ENST00000532702,;RPL8,synonymous_variant,p.=,ENST00000533397,;RPL8,intron_variant,,ENST00000527914,;ZNF34,upstream_gene_variant,,ENST00000429371,NM_001286769.1;ZNF34,upstream_gene_variant,,ENST00000343459,NM_030580.4;ZNF34,upstream_gene_variant,,ENST00000534445,NM_001286770.1;RPL8,downstream_gene_variant,,ENST00000612162,;RPL8,intron_variant,,ENST00000529163,;RPL8,intron_variant,,ENST00000528296,;RPL8,missense_variant,p.Arg47Leu,ENST00000531975,;RPL8,synonymous_variant,p.=,ENST00000529920,;RPL8,non_coding_transcript_exon_variant,,ENST00000525232,;RPL8,non_coding_transcript_exon_variant,,ENST00000526668,;RPL8,non_coding_transcript_exon_variant,,ENST00000531767,;ZNF34,upstream_gene_variant,,ENST00000527740,;RPL8,upstream_gene_variant,,ENST00000534781,; A ENST00000262584 Transcript synonymous_variant 485/1041 252/774 84/257 T acG/acT 1 -1 RPL8 HGNC HGNC:10368 protein_coding YES CCDS6433.1 ENSP00000262584 P62917 UPI000000419E NM_000973.3 3/6 Gene3D:2.40.50.140,HAMAP:MF_01320_A,Pfam_domain:PF00181,PIRSF_domain:PIRSF002158,hmmpanther:PTHR13691,hmmpanther:PTHR13691:SF16,SMART_domains:SM01383,Superfamily_domains:SSF50249 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 144791801 144791801 C A 1 0 0 0 0 0 0 0 1 13855 639 23 1 1 RPL8 8 144791801 Silent SNP C C3N-01415_T 530117 144791801 346835 284 24031 CCDC171 0 . GRCh38 9 15623349 15623349 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.758G>T p.Arg253Leu p.R253L ENST00000380701 7/26 164 136 28 253 253 0 strelka-varscan-mutect CCDC171,missense_variant,p.Arg253Leu,ENST00000380701,NM_173550.2;CCDC171,missense_variant,p.Arg253Leu,ENST00000535968,; T ENST00000380701 Transcript missense_variant 1086/6512 758/3981 253/1326 R/L cGg/cTg 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 tolerated(0.06) 7/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 MODERATE 1 SNV 1 1 PASS rs1014327388 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 15623349 15623349 G T 1 0 0 0 0 1 0 0 0 2488 1116 39 1 1 CCDC171 9 15623349 Missense_Mutation SNP G C3N-01415_T 15623349 122771368 285 24032 BNC2 0 . GRCh38 9 16436298 16436298 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1896G>T p.Lys632Asn p.K632N ENST00000380672 6/7 370 294 76 546 546 0 strelka-varscan-mutect BNC2,missense_variant,p.Lys632Asn,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,missense_variant,p.Lys458Asn,ENST00000545497,;BNC2,missense_variant,p.Lys589Asn,ENST00000418777,;BNC2,missense_variant,p.Lys565Asn,ENST00000380667,;BNC2,missense_variant,p.Lys25Asn,ENST00000411752,;BNC2,downstream_gene_variant,,ENST00000380666,;BNC2,downstream_gene_variant,,ENST00000603713,;BNC2,missense_variant,p.Lys632Asn,ENST00000484726,; A ENST00000380672 Transcript missense_variant 1954/12844 1896/3300 632/1099 K/N aaG/aaT 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 deleterious(0) 6/7 hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 16436298 16436298 C A 1 0 0 0 0 1 0 0 0 1631 796 28 2 2 BNC2 9 16436298 Missense_Mutation SNP C C3N-01415_T 812949 16436298 121958419 286 24033 SPATA31A3 0 . GRCh38 9 66988397 66988397 + Silent SNP A A G novel C3N-01415_T C3N-01415_N A A c.2101T>C p.= p.L701L ENST00000428649 4/4 388 319 69 509 509 0 strelka-varscan-mutect SPATA31A3,synonymous_variant,p.=,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; G ENST00000428649 Transcript synonymous_variant 2163/4256 2101/4044 701/1347 L Ttg/Ctg 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 4/4 Pfam_domain:PF14650,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 66988397 66988397 A G 1 0 0 0 0 0 0 0 1 15344 40 2 5 5 SPATA31A3 9 66988397 Silent SNP A C3N-01415_T 50552099 66988397 71406320 287 24034 SPATA31A3 0 . GRCh38 9 66990092 66990092 + Nonsense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.406C>T p.Gln136Ter p.Q136* ENST00000428649 4/4 1021 908 113 1260 1260 0 varscan-mutect SPATA31A3,stop_gained,p.Gln136Ter,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; A ENST00000428649 Transcript stop_gained 468/4256 406/4044 136/1347 Q/* Cag/Tag 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 4/4 Pfam_domain:PF15371,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 66990092 66990092 G A 1 0 0 0 0 0 1 0 0 15344 1357 47 3 3 SPATA31A3 9 66990092 Nonsense_Mutation SNP G C3N-01415_T 1695 66990092 71404625 288 24035 NTRK2 0 . GRCh38 9 85021432 85021432 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2512G>T p.Gly838Cys p.G838C ENST00000277120 19/19 514 455 59 621 621 0 strelka-varscan-mutect NTRK2,missense_variant,p.Gly838Cys,ENST00000277120,;NTRK2,missense_variant,p.Gly838Cys,ENST00000376214,NM_006180.4;NTRK2,missense_variant,p.Gly822Cys,ENST00000376213,;NTRK2,missense_variant,p.Gly822Cys,ENST00000323115,NM_001018064.2; T ENST00000277120 Transcript missense_variant 2995/8633 2512/2517 838/838 G/C Ggc/Tgc 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D deleterious(0) 19/19 MODERATE 1 SNV 1 1 PASS rs1229826541 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 85021432 85021432 G T 1 0 0 0 0 1 0 0 0 10773 1000 35 2 2 NTRK2 9 85021432 Missense_Mutation SNP G C3N-01415_T 18031340 85021432 53373285 289 24036 CDK20 0 . GRCh38 9 87970810 87970810 + Missense_Mutation SNP C C A rs141798102 C3N-01415_T C3N-01415_N C C c.466G>T p.Gly156Cys p.G156C ENST00000325303 4/8 233 209 24 246 246 0 strelka-varscan-mutect CDK20,missense_variant,p.Gly156Cys,ENST00000375883,NM_012119.4;CDK20,missense_variant,p.Gly169Cys,ENST00000336654,NM_178432.3;CDK20,missense_variant,p.Gly156Cys,ENST00000325303,NM_001039803.2;CDK20,missense_variant,p.Gly156Cys,ENST00000375871,NM_001170640.1;CDK20,missense_variant,p.Gly156Cys,ENST00000605159,NM_001170639.1;CDK20,non_coding_transcript_exon_variant,,ENST00000603475,;CDK20,non_coding_transcript_exon_variant,,ENST00000459720,;CDK20,non_coding_transcript_exon_variant,,ENST00000486228,;CDK20,non_coding_transcript_exon_variant,,ENST00000604175,;CDK20,downstream_gene_variant,,ENST00000605591,; A ENST00000325303 Transcript missense_variant 772/2175 466/1041 156/346 G/C Ggc/Tgc rs141798102 1 -1 CDK20 HGNC HGNC:21420 protein_coding YES CCDS35060.1 ENSP00000322343 Q8IZL9 UPI00000740E8 NM_001039803.2 deleterious(0.02) 4/8 PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF171,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs141798102 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 87970810 87970810 C A 1 0 0 0 0 1 0 0 0 2841 652 23 1 1 CDK20 9 87970810 Missense_Mutation SNP C C3N-01415_T 2949378 87970810 50423907 290 24037 CYLC2 0 . GRCh38 9 103004770 103004770 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.256G>A p.Glu86Lys p.E86K ENST00000374798 4/8 272 251 21 351 351 0 strelka-varscan-mutect CYLC2,missense_variant,p.Glu86Lys,ENST00000374798,NM_001340.4;CYLC2,missense_variant,p.Glu86Lys,ENST00000487798,;CYLC2,missense_variant,p.Glu86Lys,ENST00000612124,; A ENST00000374798 Transcript missense_variant 326/2171 256/1047 86/348 E/K Gag/Aag 1 1 CYLC2 HGNC HGNC:2583 protein_coding YES CCDS35085.1 ENSP00000420256 Q14093 A0A024R146 UPI0000128C36 NM_001340.4 deleterious(0) 4/8 Pfam_domain:PF15241,hmmpanther:PTHR16742 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 103004770 103004770 G A 1 0 0 0 0 1 0 0 0 3945 1291 45 3 3 CYLC2 9 103004770 Missense_Mutation SNP G C3N-01415_T 15033960 103004770 35389947 291 24038 RC3H2 0 . GRCh38 9 122859103 122859103 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.1850-1G>T p.X617_splice ENST00000373670 42 35 7 89 89 0 strelka-varscan-mutect RC3H2,splice_acceptor_variant,,ENST00000373670,;RC3H2,splice_acceptor_variant,,ENST00000357244,NM_001100588.1;RC3H2,splice_acceptor_variant,,ENST00000423239,NM_018835.2;RC3H2,upstream_gene_variant,,ENST00000454740,;RC3H2,upstream_gene_variant,,ENST00000398671,;RC3H2,splice_acceptor_variant,,ENST00000498479,; A ENST00000373670 Transcript splice_acceptor_variant -/9248 1850/3576 617/1191 1 -1 RC3H2 HGNC HGNC:21461 protein_coding YES CCDS43874.1 ENSP00000362774 Q9HBD1 A0A024R899 UPI0000048D91 10/19 HIGH 1 SNV 5 1 PASS . . 2 205 3 0 0 0 0 0 -17.69506 1 1 1 1 0 A 5 1 78 122859103 122859103 C A 1 0 0 0 0 0 0 1 0 13336 695 24 2 2 RC3H2 9 122859103 Splice_Site SNP C C3N-01415_T 19854333 122859103 15535614 292 24039 SNAPC4 0 . GRCh38 9 136383368 136383368 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1801C>T p.Pro601Ser p.P601S ENST00000298532 15/23 188 132 56 198 197 1 strelka-varscan-mutect SNAPC4,missense_variant,p.Pro601Ser,ENST00000298532,NM_003086.2;SNAPC4,downstream_gene_variant,,ENST00000637388,; A ENST00000298532 Transcript missense_variant 2170/5010 1801/4410 601/1469 P/S Ccc/Tcc 1 -1 SNAPC4 HGNC HGNC:11137 protein_coding YES CCDS6998.1 ENSP00000298532 Q5SXM2 A0A024R8F4 UPI000013E4EC NM_003086.2 tolerated(0.3) 15/23 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 136383368 136383368 G A 1 0 0 0 0 1 0 0 0 15158 1174 41 3 3 SNAPC4 9 136383368 Missense_Mutation SNP G C3N-01415_T 13524265 136383368 2011349 293 24040 LARP4B 0 . GRCh38 10 864215 864215 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.197C>T p.Pro66Leu p.P66L ENST00000612396 4/18 364 301 63 411 411 0 strelka-varscan-mutect LARP4B,missense_variant,p.Pro66Leu,ENST00000612396,NM_015155.2;LARP4B,missense_variant,p.Pro66Leu,ENST00000316157,;LARP4B,missense_variant,p.Pro66Leu,ENST00000406525,;LARP4B,downstream_gene_variant,,ENST00000412411,;LARP4B,non_coding_transcript_exon_variant,,ENST00000481118,;LARP4B,3_prime_UTR_variant,,ENST00000476529,; A ENST00000612396 Transcript missense_variant 514/8546 197/2217 66/738 P/L cCt/cTt 1 -1 LARP4B HGNC HGNC:28987 protein_coding YES CCDS31131.1 ENSP00000482767 Q92615 UPI00001F8C87 NM_015155.2 tolerated(0.12) 4/18 hmmpanther:PTHR22792,hmmpanther:PTHR22792:SF43 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 864215 864215 G A 1 0 0 0 0 1 0 0 0 8542 1000 35 3 3 LARP4B 10 864215 Missense_Mutation SNP G C3N-01415_T 864215 132933207 294 24041 DNAJC1 0 . GRCh38 10 21759496 21759496 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1270G>T p.Glu424Ter p.E424* ENST00000376980 11/12 389 316 73 540 540 0 strelka-varscan-mutect DNAJC1,stop_gained,p.Glu424Ter,ENST00000376980,NM_022365.3;DNAJC1,downstream_gene_variant,,ENST00000483085,; A ENST00000376980 Transcript stop_gained 1561/2106 1270/1665 424/554 E/* Gag/Tag 1 -1 DNAJC1 HGNC HGNC:20090 protein_coding YES CCDS7136.1 ENSP00000366179 Q96KC8 UPI0000049FEF NM_022365.3 11/12 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 21759496 21759496 C A 1 0 0 0 0 0 1 0 0 4442 864 30 2 2 DNAJC1 10 21759496 Nonsense_Mutation SNP C C3N-01415_T 20895281 21759496 112037926 295 24042 KIAA1217 0 . GRCh38 10 24545083 24545083 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.5314G>T p.Asp1772Tyr p.D1772Y ENST00000376454 20/21 170 141 29 194 192 2 strelka-varscan-mutect KIAA1217,missense_variant,p.Asp1455Tyr,ENST00000376451,;KIAA1217,missense_variant,p.Asp1772Tyr,ENST00000376454,NM_019590.4;KIAA1217,missense_variant,p.Asp1093Tyr,ENST00000376462,NM_001098500.2;KIAA1217,missense_variant,p.Asp1203Tyr,ENST00000376452,NM_001282767.1;KIAA1217,missense_variant,p.Asp1178Tyr,ENST00000458595,NM_001282768.1;KIAA1217,missense_variant,p.Asp1093Tyr,ENST00000430453,;KIAA1217,missense_variant,p.Asp896Tyr,ENST00000396445,;KIAA1217,missense_variant,p.Asp922Tyr,ENST00000307544,NM_001282769.1;KIAA1217,missense_variant,p.Asp856Tyr,ENST00000396446,NM_001282770.1;KIAA1217,downstream_gene_variant,,ENST00000635163,;KIAA1217,downstream_gene_variant,,ENST00000492009,; T ENST00000376454 Transcript missense_variant 5344/7381 5314/5832 1772/1943 D/Y Gat/Tat 1 1 KIAA1217 HGNC HGNC:25428 protein_coding YES CCDS31165.1 ENSP00000365637 Q5T5P2 UPI000013EC2A NM_019590.4 deleterious(0) 20/21 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 24545083 24545083 G T 1 0 0 0 0 1 0 0 0 8109 1174 41 2 2 KIAA1217 10 24545083 Missense_Mutation SNP G C3N-01415_T 2785587 24545083 109252339 296 24043 KIAA1462 0 . GRCh38 10 30029205 30029205 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.943G>T p.Asp315Tyr p.D315Y ENST00000375377 3/4 467 383 84 527 526 1 strelka-varscan-mutect KIAA1462,missense_variant,p.Asp315Tyr,ENST00000375377,NM_020848.2; A ENST00000375377 Transcript missense_variant 1045/9265 943/4080 315/1359 D/Y Gac/Tac 1 -1 KIAA1462 HGNC HGNC:29283 protein_coding YES CCDS41500.1 ENSP00000364526 Q9P266 UPI00001D8117 NM_020848.2 deleterious(0.01) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR34757,hmmpanther:PTHR34757:SF1,Pfam_domain:PF15351 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 30029205 30029205 C A 1 0 0 0 0 1 0 0 0 8116 855 30 2 2 KIAA1462 10 30029205 Missense_Mutation SNP C C3N-01415_T 5484122 30029205 103768217 297 24044 ZNF33B 0 . GRCh38 10 42593560 42593560 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.1390A>C p.Thr464Pro p.T464P ENST00000359467 5/5 213 173 40 302 302 0 strelka-varscan-mutect ZNF33B,missense_variant,p.Thr464Pro,ENST00000359467,NM_001305036.1,NM_001305033.1,NM_006955.1;ZNF33B,missense_variant,p.Thr464Pro,ENST00000613419,;ZNF33B,intron_variant,,ENST00000465206,;ZNF33B,intron_variant,,ENST00000462075,;ZNF33B,intron_variant,,ENST00000486187,; G ENST00000359467 Transcript missense_variant 1505/5958 1390/2337 464/778 T/P Aca/Cca 1 -1 ZNF33B HGNC HGNC:13097 protein_coding YES CCDS7198.1 ENSP00000352444 Q06732 UPI000007257B NM_001305036.1,NM_001305033.1,NM_006955.1 deleterious(0) 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF204,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 42593560 42593560 T G 1 0 0 0 0 1 0 0 0 18427 1696 59 5 5 ZNF33B 10 42593560 Missense_Mutation SNP T C3N-01415_T 12564355 42593560 91203862 298 24045 FAM21C 0 . GRCh38 10 45787112 45787112 + Silent SNP A A T rs782720298 C3N-01415_T C3N-01415_N A A c.2889A>T p.= p.P963P ENST00000374362 27/30 153 128 25 208 208 0 strelka-varscan-mutect FAM21C,synonymous_variant,p.=,ENST00000336378,;FAM21C,synonymous_variant,p.=,ENST00000374362,NM_015262.2;FAM21C,synonymous_variant,p.=,ENST00000623400,;FAM21C,synonymous_variant,p.=,ENST00000540872,NM_001169106.1;FAM21C,synonymous_variant,p.=,ENST00000359860,;FAM21C,synonymous_variant,p.=,ENST00000537517,NM_001169107.1;FAM21C,non_coding_transcript_exon_variant,,ENST00000471102,;FAM21C,downstream_gene_variant,,ENST00000374359,; T ENST00000374362 Transcript synonymous_variant 2988/4623 2889/3963 963/1320 P ccA/ccT rs782720298 1 1 FAM21C HGNC HGNC:23414 protein_coding YES CCDS44374.2 ENSP00000363482 Q9Y4E1 UPI0000551BE9 NM_015262.2 27/30 hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669,Pfam_domain:PF15255 LOW 1 SNV 1 1 PASS rs782720298 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 45787112 45787112 A T 1 0 0 0 0 0 0 0 1 5412 175 7 4 4 FAM21C 10 45787112 Silent SNP A C3N-01415_T 3193552 45787112 88010310 299 24046 C10orf71 0 . GRCh38 10 49326482 49326482 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.3937C>A p.Pro1313Thr p.P1313T ENST00000374144 3/3 201 155 46 203 203 0 strelka-varscan-mutect C10orf71,missense_variant,p.Pro1313Thr,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript missense_variant 4225/5230 3937/4308 1313/1435 P/T Ccg/Acg 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 deleterious(0.01) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR33775,Pfam_domain:PF15232 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 49326482 49326482 C A 1 0 0 0 0 1 0 0 0 1769 623 22 2 2 C10orf71 10 49326482 Missense_Mutation SNP C C3N-01415_T 3539370 49326482 84470940 300 24047 KAT6B 0 . GRCh38 10 74975737 74975737 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.1400A>T p.Lys467Met p.K467M ENST00000287239 8/18 800 691 109 964 964 0 strelka-varscan-mutect KAT6B,missense_variant,p.Lys467Met,ENST00000287239,NM_012330.3;KAT6B,missense_variant,p.Lys467Met,ENST00000372711,NM_001256468.1;KAT6B,intron_variant,,ENST00000372724,NM_001256469.1;KAT6B,intron_variant,,ENST00000372725,;KAT6B,intron_variant,,ENST00000372714,;KAT6B,upstream_gene_variant,,ENST00000490365,; T ENST00000287239 Transcript missense_variant 1889/8287 1400/6222 467/2073 K/M aAg/aTg 1 1 KAT6B HGNC HGNC:17582 protein_coding YES CCDS7345.1 ENSP00000287239 Q8WYB5 UPI000013DEA0 NM_012330.3 tolerated(0.06) 8/18 hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF73 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 74975737 74975737 A T 1 0 0 0 0 1 0 0 0 7899 72 3 4 4 KAT6B 10 74975737 Missense_Mutation SNP A C3N-01415_T 25649255 74975737 58821685 301 24048 DLG5 0 . GRCh38 10 77809607 77809607 + Silent SNP C C G novel C3N-01415_T C3N-01415_N C C c.4587G>C p.= p.V1529V ENST00000372391 24/32 257 217 40 225 225 0 strelka-varscan-mutect DLG5,synonymous_variant,p.=,ENST00000372391,NM_004747.3;DLG5,synonymous_variant,p.=,ENST00000424842,;DLG5,non_coding_transcript_exon_variant,,ENST00000459739,;DLG5,non_coding_transcript_exon_variant,,ENST00000489547,;DLG5,upstream_gene_variant,,ENST00000484525,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;DLG5,non_coding_transcript_exon_variant,,ENST00000463362,; G ENST00000372391 Transcript synonymous_variant 4593/7415 4587/5760 1529/1919 V gtG/gtC 1 -1 DLG5 HGNC HGNC:2904 protein_coding YES CCDS7353.2 ENSP00000361467 Q8TDM6 UPI0000470041 NM_004747.3 24/32 PROSITE_profiles:PS50106,hmmpanther:PTHR13865:SF31,hmmpanther:PTHR13865,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 LOW 1 SNV 1 1 PASS rs1199958729 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 77809607 77809607 C G 1 0 0 0 0 0 0 0 1 4365 581 21 4 4 DLG5 10 77809607 Silent SNP C C3N-01415_T 2833870 77809607 55987815 302 24049 LRIT1 0 . GRCh38 10 84234316 84234316 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.652G>T p.Gly218Cys p.G218C ENST00000372105 3/4 80 66 14 90 90 0 strelka-varscan-mutect LRIT1,missense_variant,p.Gly218Cys,ENST00000372105,NM_015613.2; A ENST00000372105 Transcript missense_variant 674/2228 652/1872 218/623 G/C Ggc/Tgc 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 tolerated(0.18) 3/4 Gene3D:3.80.10.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 84234316 84234316 C A 1 0 0 0 0 1 0 0 0 8842 594 21 2 2 LRIT1 10 84234316 Missense_Mutation SNP C C3N-01415_T 6424709 84234316 49563106 303 24050 LIPK 0 . GRCh38 10 88752625 88752625 + Missense_Mutation SNP C C G rs752619939 C3N-01415_T C3N-01415_N C C c.1069C>G p.Gln357Glu p.Q357E ENST00000404190 9/9 299 265 34 356 356 0 strelka-varscan-mutect LIPK,missense_variant,p.Gln357Glu,ENST00000404190,NM_001080518.1; G ENST00000404190 Transcript missense_variant 1069/1230 1069/1200 357/399 Q/E Caa/Gaa rs752619939 1 1 LIPK HGNC HGNC:23444 protein_coding YES CCDS44455.1 ENSP00000383900 Q5VXJ0 UPI00000497BC NM_001080518.1 tolerated(0.36) 9/9 hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF45,PIRSF_domain:PIRSF000862,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs752619939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 88752625 88752625 C G 1 0 0 0 0 1 0 0 0 8748 827 29 4 4 LIPK 10 88752625 Missense_Mutation SNP C C3N-01415_T 4518309 88752625 45044797 304 24051 LIPN 0 . GRCh38 10 88778012 88778012 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.967C>A p.His323Asn p.H323N ENST00000404459 9/9 108 89 19 177 177 0 strelka-varscan-mutect LIPN,missense_variant,p.His323Asn,ENST00000404459,NM_001102469.1; A ENST00000404459 Transcript missense_variant 967/1197 967/1197 323/398 H/N Cat/Aat 1 1 LIPN HGNC HGNC:23452 protein_coding YES CCDS44456.1 ENSP00000383923 Q5VXI9 UPI000150AF6A NM_001102469.1 deleterious(0.05) 9/9 hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF16,Gene3D:3.40.50.1820,PIRSF_domain:PIRSF000862,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 88778012 88778012 C A 1 0 0 0 0 1 0 0 0 8750 840 29 2 2 LIPN 10 88778012 Missense_Mutation SNP C C3N-01415_T 25387 88778012 45019410 305 24052 PNLIP 0 . GRCh38 10 116559220 116559220 + Frame_Shift_Del DEL G G - C3N-01415_T C3N-01415_N G G c.999delG p.Thr335GlnfsTer10 p.T335Qfs*10 ENST00000369221 10/13 267 241 26 327 327 0 sindel-varindel-pindel PNLIP,frameshift_variant,p.Thr335GlnfsTer10,ENST00000369221,NM_000936.2; - ENST00000369221 Transcript frameshift_variant 1025/1483 997/1398 333/465 G/X Ggg/gg COSM1287272,COSM1287273 1 1 PNLIP HGNC HGNC:9155 protein_coding YES CCDS7594.1 ENSP00000358223 P16233 UPI000004F1A0 NM_000936.2 10/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF85,Superfamily_domains:SSF53474 1,1 HIGH 1 deletion 1 2 1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 116559220 116559220 G - 1 0 1 0 1 0 0 0 0 12257 1348 47 0 0 PNLIP 10 116559220 Frame_Shift_Del DEL G C3N-01415_T 27781208 116559220 17238202 306 24053 ACADSB 0 . GRCh38 10 123041287 123041287 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.589G>T p.Asp197Tyr p.D197Y ENST00000358776 5/11 486 406 80 529 528 1 strelka-varscan-mutect ACADSB,missense_variant,p.Asp197Tyr,ENST00000358776,NM_001609.3;ACADSB,missense_variant,p.Asp95Tyr,ENST00000368869,;ACADSB,downstream_gene_variant,,ENST00000411816,; T ENST00000358776 Transcript missense_variant 603/5859 589/1299 197/432 D/Y Gat/Tat 1 1 ACADSB HGNC HGNC:91 protein_coding YES CCDS7634.1 ENSP00000357873 P45954 A0A0S2Z3P9 UPI00001251DF NM_001609.3 deleterious(0.01) 5/11 Gene3D:2.40.110.10,Pfam_domain:PF02770,hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF10,Superfamily_domains:SSF56645 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 123041287 123041287 G T 1 0 0 0 0 1 0 0 0 158 942 33 2 2 ACADSB 10 123041287 Missense_Mutation SNP G C3N-01415_T 6482067 123041287 10756135 307 24054 TEX36 0 . GRCh38 10 125656172 125656172 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.289C>G p.Pro97Ala p.P97A ENST00000368821 4/4 91 65 26 120 120 0 strelka-varscan-mutect TEX36,missense_variant,p.Pro97Ala,ENST00000368821,NM_001128202.1;TEX36,intron_variant,,ENST00000532135,NM_001318133.1;TEX36,intron_variant,,ENST00000526819,; C ENST00000368821 Transcript missense_variant 444/922 289/561 97/186 P/A Cca/Gca 1 -1 TEX36 HGNC HGNC:31653 protein_coding YES CCDS44493.1 ENSP00000357811 Q5VZQ5 UPI00001D808E NM_001128202.1 deleterious(0.01) 4/4 Pfam_domain:PF15115,hmmpanther:PTHR35440,hmmpanther:PTHR35440:SF1 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 125656172 125656172 G C 1 0 0 0 0 1 0 0 0 16212 1174 41 4 4 TEX36 10 125656172 Missense_Mutation SNP G C3N-01415_T 2614885 125656172 8141250 308 24055 LRRC27 0 . GRCh38 10 132342262 132342262 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.391G>T p.Val131Leu p.V131L ENST00000368614 4/11 245 228 17 219 219 0 strelka-varscan-mutect LRRC27,missense_variant,p.Val131Leu,ENST00000368614,NM_030626.2;LRRC27,missense_variant,p.Val131Leu,ENST00000368613,NM_001143757.1;LRRC27,missense_variant,p.Val131Leu,ENST00000344079,NM_001143759.1;LRRC27,missense_variant,p.Val69Leu,ENST00000368612,;LRRC27,missense_variant,p.Val131Leu,ENST00000625755,NM_001143758.1;LRRC27,non_coding_transcript_exon_variant,,ENST00000450442,;LRRC27,non_coding_transcript_exon_variant,,ENST00000490055,;LRRC27,non_coding_transcript_exon_variant,,ENST00000489204,;LRRC27,intron_variant,,ENST00000462656,; T ENST00000368614 Transcript missense_variant 496/6374 391/1593 131/530 V/L Gtg/Ttg 1 1 LRRC27 HGNC HGNC:29346 protein_coding YES CCDS31316.1 ENSP00000357603 Q9C0I9 A0A140VJN2 UPI0000141386 NM_030626.2 deleterious(0.04) 4/11 PROSITE_profiles:PS51450,hmmpanther:PTHR23155,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 132342262 132342262 G T 1 0 0 0 0 1 0 0 0 8876 1377 48 2 2 LRRC27 10 132342262 Missense_Mutation SNP G C3N-01415_T 6686090 132342262 1455160 309 24056 PAOX 0 . GRCh38 10 133380462 133380462 + Silent SNP G G T rs769816764 C3N-01415_T C3N-01415_N G G c.645G>T p.= p.P215P ENST00000278060 2/7 204 175 29 218 218 0 strelka-varscan-mutect PAOX,synonymous_variant,p.=,ENST00000278060,NM_152911.3;PAOX,synonymous_variant,p.=,ENST00000357296,NM_207128.2;PAOX,synonymous_variant,p.=,ENST00000480071,NM_207127.2;PAOX,intron_variant,,ENST00000368539,;PAOX,non_coding_transcript_exon_variant,,ENST00000368535,;PAOX,downstream_gene_variant,,ENST00000528127,;PAOX,synonymous_variant,p.=,ENST00000356306,;PAOX,intron_variant,,ENST00000476834,;PAOX,intron_variant,,ENST00000483211,;PAOX,intron_variant,,ENST00000529585,; T ENST00000278060 Transcript synonymous_variant 728/1858 645/1536 215/511 P ccG/ccT rs769816764 1 1 PAOX HGNC HGNC:20837 protein_coding YES CCDS7683.1 ENSP00000278060 Q6QHF9 UPI000000D787 NM_152911.3 2/7 hmmpanther:PTHR10742:SF43,hmmpanther:PTHR10742,Gene3D:3.90.660.10,Pfam_domain:PF01593,Superfamily_domains:SSF51905 LOW 1 SNV 1 1 PASS rs769816764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 133380462 133380462 G T 1 0 0 0 0 0 0 0 1 11504 1103 39 1 1 PAOX 10 133380462 Silent SNP G C3N-01415_T 1038200 133380462 416960 310 24057 MUC5AC 0 . GRCh38 11 1187781 1187781 + Silent SNP A A G novel C3N-01415_T C3N-01415_N A A c.9636A>G p.= p.T3212T ENST00000621226 31/49 230 213 17 242 242 0 varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; G ENST00000621226 Transcript synonymous_variant 9683/17448 9636/16965 3212/5654 T acA/acG 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 31/49 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 1187781 1187781 A G 1 0 0 0 0 0 0 0 1 9978 117 5 5 5 MUC5AC 11 1187781 Silent SNP A C3N-01415_T 1187781 133898841 311 24058 LSP1 0 . GRCh38 11 1887556 1887556 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1397C>A p.Ala466Asp p.A466D ENST00000381775 11/12 205 157 48 175 175 0 strelka-varscan-mutect LSP1,missense_variant,p.Ala276Asp,ENST00000406638,NM_001013254.1,NM_001013255.1;LSP1,missense_variant,p.Ala466Asp,ENST00000381775,NM_001242932.1;LSP1,missense_variant,p.Ala276Asp,ENST00000612798,NM_001289005.1;LSP1,missense_variant,p.Ala276Asp,ENST00000405957,NM_001013253.1;LSP1,missense_variant,p.Ala338Asp,ENST00000311604,NM_002339.2;LSP1,downstream_gene_variant,,ENST00000432093,;LSP1,downstream_gene_variant,,ENST00000417766,;LSP1,downstream_gene_variant,,ENST00000457279,;LSP1,downstream_gene_variant,,ENST00000421485,;LSP1,downstream_gene_variant,,ENST00000429923,;LSP1,downstream_gene_variant,,ENST00000446808,;LSP1,downstream_gene_variant,,ENST00000451814,;LSP1,non_coding_transcript_exon_variant,,ENST00000485341,;LSP1,non_coding_transcript_exon_variant,,ENST00000472974,;LSP1,downstream_gene_variant,,ENST00000484895,;LSP1,downstream_gene_variant,,ENST00000464670,; A ENST00000381775 Transcript missense_variant 1505/2016 1397/1404 466/467 A/D gCt/gAt 1 1 LSP1 HGNC HGNC:6707 protein_coding YES CCDS58110.1 ENSP00000371194 P33241 UPI000013F8D0 NM_001242932.1 deleterious_low_confidence(0) 11/12 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 1887556 1887556 C A 1 0 0 0 0 1 0 0 0 8970 797 28 2 2 LSP1 11 1887556 Missense_Mutation SNP C C3N-01415_T 699775 1887556 133199066 312 24059 TRPM5 0 . GRCh38 11 2418573 2418573 + Frame_Shift_Del DEL A A - novel C3N-01415_T C3N-01415_N A A c.668delT p.Ile223ThrfsTer29 p.I223Tfs*29 ENST00000155858 5/24 191 177 14 193 193 0 sindel-varindel-pindel TRPM5,frameshift_variant,p.Ile223ThrfsTer29,ENST00000155858,NM_014555.3;TRPM5,frameshift_variant,p.Ile217ThrfsTer29,ENST00000533881,;TRPM5,frameshift_variant,p.Ile223ThrfsTer29,ENST00000533060,;TRPM5,frameshift_variant,p.Ile223ThrfsTer29,ENST00000528453,; - ENST00000155858 Transcript frameshift_variant 677/3929 668/3498 223/1165 I/X aTc/ac 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 5/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.18466 0.9999997 1 1 1 0 - 7 5 78 2418573 2418573 A - 1 0 1 0 1 0 0 0 0 17095 333 12 0 0 TRPM5 11 2418573 Frame_Shift_Del DEL A C3N-01415_T 531017 2418573 132668049 313 24060 OSBPL5 0 . GRCh38 11 3103319 3103319 + Frame_Shift_Del DEL C C - novel C3N-01415_T C3N-01415_N C C c.1246delG p.Ala416LeufsTer11 p.A416Lfs*11 ENST00000263650 11/22 128 114 14 145 145 0 sindel-varindel-pindel OSBPL5,frameshift_variant,p.Ala416LeufsTer11,ENST00000263650,NM_020896.3;OSBPL5,frameshift_variant,p.Ala348LeufsTer11,ENST00000389989,NM_145638.2,NM_001144063.1;OSBPL5,frameshift_variant,p.Ala348LeufsTer11,ENST00000348039,;OSBPL5,frameshift_variant,p.Ala327LeufsTer11,ENST00000525498,;OSBPL5,upstream_gene_variant,,ENST00000534454,;OSBPL5,splice_region_variant,,ENST00000534491,;OSBPL5,splice_region_variant,,ENST00000471998,;OSBPL5,downstream_gene_variant,,ENST00000532951,; - ENST00000263650 Transcript frameshift_variant,splice_region_variant 1406/3889 1246/2640 416/879 A/X Gct/ct 1 -1 OSBPL5 HGNC HGNC:16392 protein_coding YES CCDS31344.1 ENSP00000263650 Q9H0X9 UPI000000D722 NM_020896.3 11/22 hmmpanther:PTHR10972:SF94,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579 HIGH 1 deletion 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 3103319 3103319 C - 1 0 1 0 1 0 0 0 0 11346 753 26 0 0 OSBPL5 11 3103319 Frame_Shift_Del DEL C C3N-01415_T 684746 3103319 131983303 314 24061 UBQLN3 0 . GRCh38 11 5508330 5508330 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.1229C>T p.Pro410Leu p.P410L ENST00000311659 2/2 135 104 31 149 148 1 strelka-varscan-mutect UBQLN3,missense_variant,p.Pro410Leu,ENST00000311659,NM_017481.2;HBG2,intron_variant,,ENST00000380259,;HBE1,upstream_gene_variant,,ENST00000380237,;UBQLN3,downstream_gene_variant,,ENST00000445998,;HBG2,upstream_gene_variant,,ENST00000380252,;HBE1,upstream_gene_variant,,ENST00000396895,;AC104389.28,upstream_gene_variant,,ENST00000415970,;AC104389.28,upstream_gene_variant,,ENST00000418729,;AC104389.28,upstream_gene_variant,,ENST00000420465,;AC104389.28,upstream_gene_variant,,ENST00000420726,; A ENST00000311659 Transcript missense_variant 1377/2407 1229/1968 410/655 P/L cCa/cTa COSM3448827 1 -1 UBQLN3 HGNC HGNC:12510 protein_coding YES CCDS7758.1 ENSP00000347997 Q9H347 A0A140VJZ3 UPI000006E3A0 NM_017481.2 deleterious(0) 2/2 1 MODERATE 1 SNV 1 1 1 PASS rs999501348 . 0 201 9 0 0 0 0 0 -20 0.9999973 1 1 1 0 A 3 1 78 5508330 5508330 G A 1 0 0 0 0 1 0 0 0 17422 1348 47 3 3 UBQLN3 11 5508330 Missense_Mutation SNP G C3N-01415_T 2405011 5508330 129578292 315 24062 OR52N1 0 . GRCh38 11 5788519 5788519 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.298C>A p.Leu100Ile p.L100I ENST00000317078 1/1 496 414 82 586 586 0 strelka-varscan-mutect OR52N1,missense_variant,p.Leu100Ile,ENST00000317078,NM_001001913.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000317078 Transcript missense_variant 298/963 298/963 100/320 L/I Ctc/Atc 1 -1 OR52N1 HGNC HGNC:14853 protein_coding YES CCDS31398.1 ENSP00000322823 Q8NH53 UPI0000041BDD NM_001001913.1 deleterious(0.03) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF145,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 5788519 5788519 G T 1 0 0 0 0 1 0 0 0 11200 1000 35 2 2 OR52N1 11 5788519 Missense_Mutation SNP G C3N-01415_T 280189 5788519 129298103 316 24063 OR2D2 0 . GRCh38 11 6891798 6891798 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.703C>A p.Leu235Ile p.L235I ENST00000299459 1/1 222 204 18 270 270 0 strelka-varscan-mutect OR2D2,missense_variant,p.Leu235Ile,ENST00000299459,NM_003700.1;RP11-413N10.3,intron_variant,,ENST00000637205,; T ENST00000299459 Transcript missense_variant 802/1110 703/927 235/308 L/I Ctc/Atc 1 -1 OR2D2 HGNC HGNC:8244 protein_coding YES CCDS31416.1 ENSP00000299459 Q9H210 A0A126GVN9 UPI0000061F0B NM_003700.1 tolerated(0.34) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF156,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 6891798 6891798 G T 1 0 0 0 0 1 0 0 0 11073 942 33 2 2 OR2D2 11 6891798 Missense_Mutation SNP G C3N-01415_T 1103279 6891798 128194824 317 24064 RBMXL2 0 . GRCh38 11 7089685 7089685 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.565G>C p.Gly189Arg p.G189R ENST00000306904 1/1 99 85 14 82 82 0 strelka-varscan-mutect RBMXL2,missense_variant,p.Gly189Arg,ENST00000306904,NM_014469.4; C ENST00000306904 Transcript missense_variant 659/1874 565/1179 189/392 G/R Ggc/Cgc 1 1 RBMXL2 HGNC HGNC:17886 protein_coding YES CCDS7777.1 ENSP00000304139 O75526 UPI000013EBA5 NM_014469.4 deleterious(0.03) 1/1 Pfam_domain:PF08081 MODERATE 1 SNV 1 PASS rs1443508314 . 0 202 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 C 3 2 78 7089685 7089685 G C 1 0 0 0 0 1 0 0 0 13320 1116 39 4 4 RBMXL2 11 7089685 Missense_Mutation SNP G C3N-01415_T 197887 7089685 127996937 318 24065 NLRP10 0 . GRCh38 11 7961091 7961091 + Missense_Mutation SNP G G A C3N-01415_T C3N-01415_N G G c.521C>T p.Ser174Leu p.S174L ENST00000328600 2/2 240 224 16 259 259 0 strelka-varscan-mutect NLRP10,missense_variant,p.Ser174Leu,ENST00000328600,NM_176821.3;NLRP10,downstream_gene_variant,,ENST00000526590,; A ENST00000328600 Transcript missense_variant 683/2350 521/1968 174/655 S/L tCg/tTg COSM429951 1 -1 NLRP10 HGNC HGNC:21464 protein_coding YES CCDS7784.1 ENSP00000327763 Q86W26 UPI0000167F6C NM_176821.3 tolerated(0.06) 2/2 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF142,Pfam_domain:PF05729,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS rs1186100956 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 7961091 7961091 G A 1 0 0 0 0 1 0 0 0 10509 1059 37 1 1 NLRP10 11 7961091 Missense_Mutation SNP G C3N-01415_T 871406 7961091 127125531 319 24066 ST5 0 . GRCh38 11 8730770 8730770 + Missense_Mutation SNP G G A rs149905155 C3N-01415_T C3N-01415_N G G c.520C>T p.Arg174Cys p.R174C ENST00000534127 6/23 386 331 55 421 420 1 strelka-varscan-mutect ST5,missense_variant,p.Arg174Cys,ENST00000534127,NM_005418.3;ST5,missense_variant,p.Arg174Cys,ENST00000313726,NM_213618.1;ST5,intron_variant,,ENST00000526757,NM_139157.2;ST5,intron_variant,,ENST00000530438,;ST5,intron_variant,,ENST00000626808,;ST5,intron_variant,,ENST00000528527,;ST5,intron_variant,,ENST00000526057,;ST5,intron_variant,,ENST00000528196,;ST5,intron_variant,,ENST00000530580,;ST5,intron_variant,,ENST00000533225,;ST5,intron_variant,,ENST00000527510,;ST5,intron_variant,,ENST00000526126,;ST5,intron_variant,,ENST00000531093,;ST5,downstream_gene_variant,,ENST00000526155,;ST5,upstream_gene_variant,,ENST00000530593,;ST5,downstream_gene_variant,,ENST00000533016,;ST5,downstream_gene_variant,,ENST00000530959,;ST5,downstream_gene_variant,,ENST00000534665,;ST5,downstream_gene_variant,,ENST00000533681,;ST5,downstream_gene_variant,,ENST00000527516,;ST5,downstream_gene_variant,,ENST00000524757,;ST5,downstream_gene_variant,,ENST00000525169,;ST5,downstream_gene_variant,,ENST00000527392,;ST5,downstream_gene_variant,,ENST00000527347,;ST5,downstream_gene_variant,,ENST00000534248,;ST5,downstream_gene_variant,,ENST00000527930,;ST5,downstream_gene_variant,,ENST00000528523,;ST5,downstream_gene_variant,,ENST00000533471,;ST5,downstream_gene_variant,,ENST00000526828,;ST5,downstream_gene_variant,,ENST00000533580,;ST5,downstream_gene_variant,,ENST00000530938,;ST5,downstream_gene_variant,,ENST00000526241,;ST5,downstream_gene_variant,,ENST00000527473,;ST5,intron_variant,,ENST00000533425,;ST5,intron_variant,,ENST00000532651,;ST5,intron_variant,,ENST00000526221,;ST5,downstream_gene_variant,,ENST00000534783,;ST5,downstream_gene_variant,,ENST00000529940,;ST5,intron_variant,,ENST00000532734,;ST5,upstream_gene_variant,,ENST00000527870,; A ENST00000534127 Transcript missense_variant 906/4545 520/3414 174/1137 R/C Cgc/Tgc rs149905155 1 -1 ST5 HGNC HGNC:11350 protein_coding YES CCDS7791.1 ENSP00000433528 P78524 UPI00001AECB8 NM_005418.3 deleterious(0) 6/23 hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF5 MODERATE 1 SNV 1 1 PASS rs149905155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 8730770 8730770 G A 1 0 0 0 0 1 0 0 0 15598 1058 37 1 1 ST5 11 8730770 Missense_Mutation SNP G C3N-01415_T 769679 8730770 126355852 320 24067 AMPD3 0 . GRCh38 11 10494952 10494952 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.1215G>T p.= p.V405V ENST00000396554 8/15 595 444 151 572 571 1 strelka-varscan-mutect AMPD3,synonymous_variant,p.=,ENST00000444303,NM_001172431.1;AMPD3,synonymous_variant,p.=,ENST00000396554,NM_000480.2;AMPD3,synonymous_variant,p.=,ENST00000396553,NM_001025389.1;AMPD3,synonymous_variant,p.=,ENST00000529507,NM_001172430.1;AMPD3,synonymous_variant,p.=,ENST00000528723,NM_001025390.1;AMPD3,upstream_gene_variant,,ENST00000530864,;AMPD3,synonymous_variant,p.=,ENST00000529834,;AMPD3,3_prime_UTR_variant,,ENST00000534047,;AMPD3,3_prime_UTR_variant,,ENST00000533116,; T ENST00000396554 Transcript synonymous_variant 1556/3806 1215/2331 405/776 V gtG/gtT 1 1 AMPD3 HGNC HGNC:470 protein_coding YES CCDS7802.1 ENSP00000379802 Q01432 UPI0000161AFD NM_000480.2 8/15 hmmpanther:PTHR11359,hmmpanther:PTHR11359:SF2,PIRSF_domain:PIRSF001251,Pfam_domain:PF00962,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR01429,Superfamily_domains:SSF51556 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 10494952 10494952 G T 1 0 0 0 0 0 0 0 1 685 1335 47 2 2 AMPD3 11 10494952 Silent SNP G C3N-01415_T 1764182 10494952 124591670 321 24068 OTOG 0 . GRCh38 11 17572158 17572158 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.2070G>T p.= p.L690L ENST00000399391 17/55 260 221 39 264 263 1 strelka-varscan-mutect OTOG,synonymous_variant,p.=,ENST00000399397,NM_001292063.1;OTOG,synonymous_variant,p.=,ENST00000399391,NM_001277269.1;OTOG,downstream_gene_variant,,ENST00000498332,; T ENST00000399391 Transcript synonymous_variant 2070/8778 2070/8778 690/2925 L ctG/ctT 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 17/55 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 17572158 17572158 G T 1 0 0 0 0 0 0 0 1 11370 1335 47 2 2 OTOG 11 17572158 Silent SNP G C3N-01415_T 7077206 17572158 117514464 322 24069 MRGPRX4 0 . GRCh38 11 18173464 18173464 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.208G>T p.Ala70Ser p.A70S ENST00000314254 1/1 203 189 14 240 240 0 varscan-mutect MRGPRX4,missense_variant,p.Ala70Ser,ENST00000314254,NM_054032.3;MRGPRX4,missense_variant,p.Ala70Ser,ENST00000618161,;RP11-113D6.6,intron_variant,,ENST00000527671,; T ENST00000314254 Transcript missense_variant 628/1444 208/969 70/322 A/S Gca/Tca COSM687016 1 1 MRGPRX4 HGNC HGNC:17617 protein_coding YES CCDS7831.1 ENSP00000314042 Q96LA9 UPI0000061F60 NM_054032.3 tolerated(0.18) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR11334:SF23,hmmpanther:PTHR11334,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS rs1043434232 . 0 206 0 2 0 0 0 0 -17.79367 0.9999996 1 1 1 0 T 3 4 78 18173464 18173464 G T 1 0 0 0 0 1 0 0 0 9736 1087 38 1 1 MRGPRX4 11 18173464 Missense_Mutation SNP G C3N-01415_T 601306 18173464 116913158 323 24070 UEVLD 0 . GRCh38 11 18578805 18578805 + Nonsense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.46A>T p.Lys16Ter p.K16* ENST00000396197 2/12 246 214 32 256 256 0 strelka-varscan-mutect UEVLD,stop_gained,p.Lys16Ter,ENST00000396197,NM_001040697.2;UEVLD,stop_gained,p.Lys16Ter,ENST00000543987,NM_018314.4;UEVLD,stop_gained,p.Lys16Ter,ENST00000379387,NM_001261382.1;UEVLD,stop_gained,p.Lys16Ter,ENST00000320750,NM_001261383.1;UEVLD,stop_gained,p.Lys16Ter,ENST00000300038,NM_001297771.1;UEVLD,stop_gained,p.Lys16Ter,ENST00000541984,NM_001261386.1;UEVLD,5_prime_UTR_variant,,ENST00000535484,NM_001261385.1;UEVLD,non_coding_transcript_exon_variant,,ENST00000490736,;UEVLD,intron_variant,,ENST00000540666,;UEVLD,intron_variant,,ENST00000540917,;UEVLD,stop_gained,p.Lys16Ter,ENST00000396196,;UEVLD,non_coding_transcript_exon_variant,,ENST00000535340,; A ENST00000396197 Transcript stop_gained 75/4156 46/1416 16/471 K/* Aag/Tag 1 -1 UEVLD HGNC HGNC:30866 protein_coding YES CCDS41624.1 ENSP00000379500 Q8IX04 UPI00001AF2D2 NM_001040697.2 2/12 PROSITE_profiles:PS51322,hmmpanther:PTHR23306:SF18,hmmpanther:PTHR23306,Gene3D:3.10.110.10,Superfamily_domains:SSF54495 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 18578805 18578805 T A 1 0 0 0 0 0 1 0 0 17457 1826 63 4 4 UEVLD 11 18578805 Nonsense_Mutation SNP T C3N-01415_T 405341 18578805 116507817 324 24071 SPTY2D1 0 . GRCh38 11 18612455 18612455 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.1745A>G p.Lys582Arg p.K582R ENST00000336349 4/6 147 132 15 181 181 0 strelka-varscan-mutect SPTY2D1,missense_variant,p.Lys582Arg,ENST00000336349,NM_194285.2;SPTY2D1-AS1,downstream_gene_variant,,ENST00000636011,;SPTY2D1,downstream_gene_variant,,ENST00000543776,;SPTY2D1,non_coding_transcript_exon_variant,,ENST00000536336,;SPTY2D1-AS1,downstream_gene_variant,,ENST00000501599,; C ENST00000336349 Transcript missense_variant 1981/5754 1745/2058 582/685 K/R aAa/aGa 1 -1 SPTY2D1 HGNC HGNC:26818 protein_coding YES CCDS31441.1 ENSP00000337991 Q68D10 UPI00001607F0 NM_194285.2 tolerated(0.08) 4/6 Pfam_domain:PF08243,hmmpanther:PTHR22691,hmmpanther:PTHR22691:SF8,SMART_domains:SM00784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 18612455 18612455 T C 1 0 0 0 0 1 0 0 0 15484 1841 64 5 5 SPTY2D1 11 18612455 Missense_Mutation SNP T C3N-01415_T 33650 18612455 116474167 325 24072 GAS2 0 . GRCh38 11 22755914 22755914 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.684A>T p.Gln228His p.Q228H ENST00000454584 7/8 299 234 65 325 325 0 strelka-varscan-mutect GAS2,missense_variant,p.Gln228His,ENST00000454584,NM_001143830.1;GAS2,missense_variant,p.Gln228His,ENST00000278187,NM_177553.2,NM_005256.3;GAS2,non_coding_transcript_exon_variant,,ENST00000526665,;GAS2,3_prime_UTR_variant,,ENST00000524701,; T ENST00000454584 Transcript missense_variant 989/2286 684/942 228/313 Q/H caA/caT 1 1 GAS2 HGNC HGNC:4167 protein_coding YES CCDS7858.1 ENSP00000401145 O43903 UPI000000D98C NM_001143830.1 deleterious(0.01) 7/8 PROSITE_profiles:PS51460,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF298,Gene3D:1v5rA00,Pfam_domain:PF02187,SMART_domains:SM00243,Superfamily_domains:0050058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 22755914 22755914 A T 1 0 0 0 0 1 0 0 0 6115 69 3 4 4 GAS2 11 22755914 Missense_Mutation SNP A C3N-01415_T 4143459 22755914 112330708 326 24073 METTL15 0 . GRCh38 11 28330409 28330409 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.792C>T p.= p.P264P ENST00000407364 7/7 141 108 33 153 153 0 strelka-varscan-mutect METTL15,missense_variant,p.Leu250Phe,ENST00000406787,NM_001297775.1;METTL15,synonymous_variant,p.=,ENST00000407364,NM_001113528.1;METTL15,3_prime_UTR_variant,,ENST00000303459,NM_152636.2;METTL15,3_prime_UTR_variant,,ENST00000451385,;METTL15,non_coding_transcript_exon_variant,,ENST00000468295,;METTL15,intron_variant,,ENST00000532947,;METTL15,intron_variant,,ENST00000634973,;METTL15,intron_variant,,ENST00000634627,; T ENST00000407364 Transcript synonymous_variant 1144/4242 792/1224 264/407 P ccC/ccT 1 1 METTL15 HGNC HGNC:26606 protein_coding YES CCDS44559.1 ENSP00000384369 A6NJ78 UPI0000DBEF34 NM_001113528.1 7/7 Gene3D:1m6yA02,HAMAP:MF_01007,Pfam_domain:PF01795,hmmpanther:PTHR11265,hmmpanther:PTHR11265:SF0,Superfamily_domains:SSF81799,TIGRFAM_domain:TIGR00006 LOW 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 78 28330409 28330409 C T 1 0 0 0 0 0 0 0 1 9441 681 24 3 3 METTL15 11 28330409 Silent SNP C C3N-01415_T 5574495 28330409 106756213 327 24074 ELP4 0 . GRCh38 11 31594876 31594876 + Missense_Mutation SNP G G T rs199901084 C3N-01415_T C3N-01415_N G G c.488G>T p.Arg163Leu p.R163L ENST00000395934 4/12 207 168 39 262 261 1 strelka-varscan-mutect ELP4,missense_variant,p.Arg163Leu,ENST00000395934,NM_001288726.1;ELP4,missense_variant,p.Arg163Leu,ENST00000350638,NM_019040.4;ELP4,missense_variant,p.Arg163Leu,ENST00000379163,NM_001288725.1;ELP4,missense_variant,p.Arg163Leu,ENST00000474374,; T ENST00000395934 Transcript missense_variant 495/1961 488/1608 163/535 R/L cGt/cTt rs199901084 1 1 ELP4 HGNC HGNC:1171 protein_coding YES CCDS73272.1 ENSP00000379267 G5E9D4 UPI000013FA14 NM_001288726.1 deleterious(0.01) 4/12 hmmpanther:PTHR12896,Pfam_domain:PF05625 MODERATE 1 SNV 1 1 PASS rs199901084 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 31594876 31594876 G T 1 0 0 0 0 1 0 0 0 4916 1145 40 1 1 ELP4 11 31594876 Missense_Mutation SNP G C3N-01415_T 3264467 31594876 103491746 328 24075 RAG1 0 . GRCh38 11 36574245 36574245 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.941G>T p.Arg314Leu p.R314L ENST00000299440 2/2 468 424 44 543 542 1 strelka-varscan-mutect RAG1,missense_variant,p.Arg314Leu,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Arg314Leu,ENST00000534663,; T ENST00000299440 Transcript missense_variant 1053/6564 941/3132 314/1043 R/L cGg/cTg 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 deleterious_low_confidence(0) 2/2 Gene3D:3.30.40.10,Pfam_domain:PF00097,PROSITE_patterns:PS00518,PROSITE_profiles:PS50089,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs1206270386 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 36574245 36574245 G T 1 0 0 0 0 1 0 0 0 13164 1116 39 1 1 RAG1 11 36574245 Missense_Mutation SNP G C3N-01415_T 4979369 36574245 98512377 329 24076 RAG1 0 . GRCh38 11 36575434 36575434 + Silent SNP T T C novel C3N-01415_T C3N-01415_N T T c.2130T>C p.= p.Y710Y ENST00000299440 2/2 222 179 43 307 307 0 strelka-varscan-mutect RAG1,synonymous_variant,p.=,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,synonymous_variant,p.=,ENST00000534663,; C ENST00000299440 Transcript synonymous_variant 2242/6564 2130/3132 710/1043 Y taT/taC 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 2/2 Pfam_domain:PF12940,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 78 36575434 36575434 T C 1 0 0 0 0 0 0 0 1 13164 1471 51 5 5 RAG1 11 36575434 Silent SNP T C3N-01415_T 1189 36575434 98511188 330 24077 RAG1 0 . GRCh38 11 36575483 36575483 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2179G>T p.Val727Phe p.V727F ENST00000299440 2/2 304 259 45 367 367 0 strelka-varscan-mutect RAG1,missense_variant,p.Val727Phe,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Val727Phe,ENST00000534663,; T ENST00000299440 Transcript missense_variant 2291/6564 2179/3132 727/1043 V/F Gtc/Ttc 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 deleterious_low_confidence(0) 2/2 Pfam_domain:PF12940,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 36575483 36575483 G T 1 0 0 0 0 1 0 0 0 13164 1029 36 2 2 RAG1 11 36575483 Missense_Mutation SNP G C3N-01415_T 49 36575483 98511139 331 24078 LRRC4C 0 . GRCh38 11 40115138 40115138 + Silent SNP A A T novel C3N-01415_T C3N-01415_N A A c.1155T>A p.= p.S385S ENST00000278198 2/2 310 283 27 335 335 0 strelka-varscan-mutect LRRC4C,synonymous_variant,p.=,ENST00000278198,;LRRC4C,synonymous_variant,p.=,ENST00000527150,;LRRC4C,synonymous_variant,p.=,ENST00000530763,NM_020929.2;LRRC4C,synonymous_variant,p.=,ENST00000528697,NM_001258419.1;LRRC4C,synonymous_variant,p.=,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; T ENST00000278198 Transcript synonymous_variant 3119/4054 1155/1923 385/640 S tcT/tcA 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 2/2 PROSITE_profiles:PS50835,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 40115138 40115138 A T 1 0 0 0 0 0 0 0 1 8903 59 3 4 4 LRRC4C 11 40115138 Silent SNP A C3N-01415_T 3539655 40115138 94971484 332 24079 OR4C6 0 . GRCh38 11 55665576 55665576 + Missense_Mutation SNP G G T rs759529017 C3N-01415_T C3N-01415_N G G c.410G>T p.Arg137Leu p.R137L ENST00000314259 1/1 275 210 65 335 334 1 strelka-varscan-mutect OR4C6,missense_variant,p.Arg137Leu,ENST00000314259,NM_001004704.1; T ENST00000314259 Transcript missense_variant 410/930 410/930 137/309 R/L cGg/cTg rs759529017,COSM3953272,COSM5664821 1 1 OR4C6 HGNC HGNC:14743 protein_coding YES CCDS31506.1 ENSP00000324769 Q8NH72 A0A126GVN0 UPI0000041868 NM_001004704.1 deleterious_low_confidence(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF80,Superfamily_domains:SSF81321 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs759529017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 55665576 55665576 G T 1 0 0 0 0 1 0 0 0 11129 1116 39 1 1 OR4C6 11 55665576 Missense_Mutation SNP G C3N-01415_T 15550438 55665576 79421046 333 24080 OR5D18 0 . GRCh38 11 55820457 55820457 + Silent SNP T T C novel C3N-01415_T C3N-01415_N T T c.828T>C p.= p.S276S ENST00000333976 1/1 310 278 32 372 372 0 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; C ENST00000333976 Transcript synonymous_variant 828/942 828/942 276/313 S tcT/tcC 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 78 55820457 55820457 T C 1 0 0 0 0 0 0 0 1 11227 1567 55 5 5 OR5D18 11 55820457 Silent SNP T C3N-01415_T 154881 55820457 79266165 334 24081 OR5I1 0 . GRCh38 11 55935831 55935831 + Silent SNP G G T rs758297822 C3N-01415_T C3N-01415_N G G c.570C>A p.= p.S190S ENST00000301532 1/1 226 207 19 294 294 0 strelka-varscan-mutect OR5I1,synonymous_variant,p.=,ENST00000301532,NM_006637.1; T ENST00000301532 Transcript synonymous_variant 570/945 570/945 190/314 S tcC/tcA rs758297822 1 -1 OR5I1 HGNC HGNC:8347 protein_coding YES CCDS7949.1 ENSP00000301532 Q13606 A0A126GVE5 UPI00000405D5 NM_006637.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF69,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS rs758297822 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 55935831 55935831 G T 1 0 0 0 0 0 0 0 1 11234 987 35 2 2 OR5I1 11 55935831 Silent SNP G C3N-01415_T 115374 55935831 79150791 335 24082 OR5F1 0 . GRCh38 11 55994046 55994046 + Silent SNP G G A rs752470605 C3N-01415_T C3N-01415_N G G c.580C>T p.= p.L194L ENST00000278409 1/1 309 279 30 340 340 0 strelka-varscan-mutect OR5F1,synonymous_variant,p.=,ENST00000278409,NM_003697.1; A ENST00000278409 Transcript synonymous_variant 580/945 580/945 194/314 L Ctg/Ttg rs752470605 1 -1 OR5F1 HGNC HGNC:8343 protein_coding YES CCDS31515.1 ENSP00000278409 O95221 UPI0000041D19 NM_003697.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF168,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs752470605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 55994046 55994046 G A 1 0 0 0 0 0 0 0 1 11228 991 35 3 3 OR5F1 11 55994046 Silent SNP G C3N-01415_T 58215 55994046 79092576 336 24083 OR8I2 0 . GRCh38 11 56093713 56093713 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.406A>T p.Met136Leu p.M136L ENST00000302124 1/1 245 220 25 284 283 1 strelka-varscan-mutect OR8I2,missense_variant,p.Met136Leu,ENST00000302124,NM_001003750.1;OR8I4P,downstream_gene_variant,,ENST00000526965,; T ENST00000302124 Transcript missense_variant 406/933 406/933 136/310 M/L Atg/Ttg 1 1 OR8I2 HGNC HGNC:15310 protein_coding YES CCDS31517.1 ENSP00000303864 Q8N0Y5 UPI0000041D16 NM_001003750.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF207,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs1207549624 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 56093713 56093713 A T 1 0 0 0 0 1 0 0 0 11308 217 8 4 4 OR8I2 11 56093713 Missense_Mutation SNP A C3N-01415_T 99667 56093713 78992909 337 24084 OR8J3 0 . GRCh38 11 56136859 56136859 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.860C>A p.Pro287His p.P287H ENST00000301529 1/1 182 151 31 212 212 0 strelka-varscan-mutect OR8J3,missense_variant,p.Pro287His,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; T ENST00000301529 Transcript missense_variant 860/948 860/948 287/315 P/H cCc/cAc 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 56136859 56136859 G T 1 0 0 0 0 1 0 0 0 11310 1232 43 2 2 OR8J3 11 56136859 Missense_Mutation SNP G C3N-01415_T 43146 56136859 78949763 338 24085 OR8H1 0 . GRCh38 11 56290699 56290699 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.364T>A p.Tyr122Asn p.Y122N ENST00000313022 1/1 218 169 49 308 308 0 strelka-varscan-mutect OR8H1,missense_variant,p.Tyr122Asn,ENST00000313022,NM_001005199.1;OR8H1,missense_variant,p.Tyr118Asn,ENST00000610894,; T ENST00000313022 Transcript missense_variant 392/1038 364/936 122/311 Y/N Tac/Aac 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1402858145 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 56290699 56290699 A T 1 0 0 0 0 1 0 0 0 11305 420 15 4 4 OR8H1 11 56290699 Missense_Mutation SNP A C3N-01415_T 153840 56290699 78795923 339 24086 OR10Q1 0 . GRCh38 11 58228632 58228632 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.244G>T p.Val82Leu p.V82L ENST00000316770 1/1 320 247 73 344 344 0 strelka-varscan-mutect OR10Q1,missense_variant,p.Val82Leu,ENST00000316770,NM_001004471.2; A ENST00000316770 Transcript missense_variant 287/1037 244/960 82/319 V/L Gta/Tta 1 -1 OR10Q1 HGNC HGNC:15134 protein_coding YES CCDS31547.1 ENSP00000314324 Q8NGQ4 UPI0000041C4C NM_001004471.2 tolerated(0.06) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF253,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 58228632 58228632 C A 1 0 0 0 0 1 0 0 0 10993 565 20 2 2 OR10Q1 11 58228632 Missense_Mutation SNP C C3N-01415_T 1937933 58228632 76857990 340 24087 OR5AN1 0 . GRCh38 11 59364905 59364905 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.447C>A p.= p.A149A ENST00000313940 1/1 196 183 13 225 225 0 strelka-varscan-mutect OR5AN1,synonymous_variant,p.=,ENST00000313940,NM_001004729.1; A ENST00000313940 Transcript synonymous_variant 494/1037 447/936 149/311 A gcC/gcA 1 1 OR5AN1 HGNC HGNC:15255 protein_coding YES CCDS31559.1 ENSP00000320302 Q8NGI8 A0A126GVP9 UPI000004B1FD NM_001004729.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF262,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -19.99967 1 1 1 1 0 A 2 1 78 59364905 59364905 C A 1 0 0 0 0 0 0 0 1 11215 668 24 2 2 OR5AN1 11 59364905 Silent SNP C C3N-01415_T 1136273 59364905 75721717 341 24088 AHNAK 0 . GRCh38 11 62532183 62532183 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.2234G>T p.Trp745Leu p.W745L ENST00000378024 5/5 412 318 94 480 480 0 strelka-varscan-mutect AHNAK,missense_variant,p.Trp745Leu,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000531324,;AHNAK,downstream_gene_variant,,ENST00000528508,; A ENST00000378024 Transcript missense_variant 2509/18787 2234/17673 745/5890 W/L tGg/tTg 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 tolerated(0.65) 5/5 hmmpanther:PTHR23348:SF41,hmmpanther:PTHR23348 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 62532183 62532183 C A 1 0 0 0 0 1 0 0 0 491 595 21 2 2 AHNAK 11 62532183 Missense_Mutation SNP C C3N-01415_T 3167278 62532183 72554439 342 24089 DNAJC4 0 . GRCh38 11 64232744 64232744 + Missense_Mutation SNP C C G C3N-01415_T C3N-01415_N C C c.409C>G p.His137Asp p.H137D ENST00000321460 4/5 63 57 6 55 55 0 strelka-varscan-mutect DNAJC4,missense_variant,p.His136Asp,ENST00000321685,NM_005528.3;DNAJC4,missense_variant,p.His137Asp,ENST00000321460,NM_001307980.1;DNAJC4,missense_variant,p.His74Asp,ENST00000535246,;DNAJC4,intron_variant,,ENST00000628077,;DNAJC4,intron_variant,,ENST00000355040,;VEGFB,upstream_gene_variant,,ENST00000309422,NM_003377.4;NUDT22,downstream_gene_variant,,ENST00000279206,NM_001128612.2,NM_032344.3;NUDT22,downstream_gene_variant,,ENST00000441250,NM_001271831.1,NM_001128613.2;VEGFB,upstream_gene_variant,,ENST00000426086,NM_001243733.1;NUDT22,downstream_gene_variant,,ENST00000428347,;VEGFB,upstream_gene_variant,,ENST00000541681,;RP11-783K16.14,intron_variant,,ENST00000534988,;RP11-783K16.14,intron_variant,,ENST00000539963,;DNAJC4,non_coding_transcript_exon_variant,,ENST00000537109,;DNAJC4,non_coding_transcript_exon_variant,,ENST00000542376,;DNAJC4,non_coding_transcript_exon_variant,,ENST00000538961,;DNAJC4,non_coding_transcript_exon_variant,,ENST00000543791,;NUDT22,downstream_gene_variant,,ENST00000422364,;NUDT22,downstream_gene_variant,,ENST00000535000,;DNAJC4,upstream_gene_variant,,ENST00000540945,;DNAJC4,downstream_gene_variant,,ENST00000536006,;VEGFB,upstream_gene_variant,,ENST00000543462,;NUDT22,downstream_gene_variant,,ENST00000543358,;NUDT22,downstream_gene_variant,,ENST00000534929,;NUDT22,downstream_gene_variant,,ENST00000545184,;NUDT22,downstream_gene_variant,,ENST00000537094,;NUDT22,downstream_gene_variant,,ENST00000543501,;DNAJC4,downstream_gene_variant,,ENST00000543685,; G ENST00000321460 Transcript missense_variant 506/1015 409/750 137/249 H/D Cac/Gac COSM4830683,COSM4830684 1 1 DNAJC4 HGNC HGNC:5271 protein_coding YES CCDS76424.1 ENSP00000320548 J3KNJ8 UPI0000140B66 NM_001307980.1 deleterious(0) 4/5 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -14.24961 1 1 1 1 0 G 3 3 78 64232744 64232744 C G 1 0 0 0 0 1 0 0 0 4462 826 29 4 4 DNAJC4 11 64232744 Missense_Mutation SNP C C3N-01415_T 1700561 64232744 70853878 343 24090 CATSPER1 0 . GRCh38 11 66025651 66025651 + Missense_Mutation SNP G G T rs753126981 C3N-01415_T C3N-01415_N G G c.729C>A p.His243Gln p.H243Q ENST00000312106 1/12 386 359 27 399 399 0 strelka-varscan-mutect CATSPER1,missense_variant,p.His243Gln,ENST00000312106,NM_053054.3;CATSPER1,upstream_gene_variant,,ENST00000529244,; T ENST00000312106 Transcript missense_variant 867/2619 729/2343 243/780 H/Q caC/caA rs753126981,COSM5516567 1 -1 CATSPER1 HGNC HGNC:17116 protein_coding YES CCDS8127.1 ENSP00000309052 Q8NEC5 UPI000045651C NM_053054.3 tolerated(0.09) 1/12 hmmpanther:PTHR10037:SF216,hmmpanther:PTHR10037 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753126981 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 66025651 66025651 G T 1 0 0 0 0 1 0 0 0 2387 1136 40 1 1 CATSPER1 11 66025651 Missense_Mutation SNP G C3N-01415_T 1792907 66025651 69060971 344 24091 GAL3ST3 0 . GRCh38 11 66042567 66042567 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.1236C>A p.= p.V412V ENST00000312006 3/3 147 130 17 136 136 0 strelka-varscan-mutect GAL3ST3,synonymous_variant,p.=,ENST00000312006,NM_033036.2;GAL3ST3,synonymous_variant,p.=,ENST00000527878,;GAL3ST3,downstream_gene_variant,,ENST00000527048,; T ENST00000312006 Transcript synonymous_variant 1518/2133 1236/1296 412/431 V gtC/gtA 1 -1 GAL3ST3 HGNC HGNC:24144 protein_coding YES CCDS8128.1 ENSP00000308591 Q96A11 UPI0000071842 NM_033036.2 3/3 hmmpanther:PTHR14647:SF1,hmmpanther:PTHR14647 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 66042567 66042567 G T 1 0 0 0 0 0 0 0 1 6067 1161 41 2 2 GAL3ST3 11 66042567 Silent SNP G C3N-01415_T 16916 66042567 69044055 345 24092 TBC1D10C 0 . GRCh38 11 67405095 67405095 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.163C>G p.Pro55Ala p.P55A ENST00000542590 2/9 146 134 12 80 80 0 strelka-varscan-mutect TBC1D10C,missense_variant,p.Pro55Ala,ENST00000542590,NM_198517.3;TBC1D10C,missense_variant,p.Pro55Ala,ENST00000526387,NM_001256508.1;TBC1D10C,missense_variant,p.Pro55Ala,ENST00000312390,;PPP1CA,intron_variant,,ENST00000542876,;PPP1CA,intron_variant,,ENST00000546202,;PPP1CA,upstream_gene_variant,,ENST00000376745,NM_002708.3;PPP1CA,upstream_gene_variant,,ENST00000312989,NM_001008709.1;PPP1CA,upstream_gene_variant,,ENST00000358239,NM_206873.1;PPP1CA,upstream_gene_variant,,ENST00000527663,;PPP1CA,intron_variant,,ENST00000537694,;PPP1CA,upstream_gene_variant,,ENST00000532446,;PPP1CA,upstream_gene_variant,,ENST00000529724,;TBC1D10C,missense_variant,p.Pro55Ala,ENST00000529635,;TBC1D10C,non_coding_transcript_exon_variant,,ENST00000530967,;TBC1D10C,non_coding_transcript_exon_variant,,ENST00000529132,;TBC1D10C,non_coding_transcript_exon_variant,,ENST00000533745,;TBC1D10C,upstream_gene_variant,,ENST00000526474,;PPP1CA,upstream_gene_variant,,ENST00000526510,;TBC1D10C,upstream_gene_variant,,ENST00000524662,; G ENST00000542590 Transcript missense_variant 177/1659 163/1341 55/446 P/A Cca/Gca 1 1 TBC1D10C HGNC HGNC:24702 protein_coding YES CCDS8162.1 ENSP00000443654 Q8IV04 UPI00000746CA NM_198517.3 tolerated(0.58) 2/9 hmmpanther:PTHR22957:SF324,hmmpanther:PTHR22957 MODERATE 1 SNV 1 1 PASS rs1369480489 . 0 202 6 2 0 0 0 0 -16.83692 0.9997291 1 1 1 0 G 3 3 78 67405095 67405095 C G 1 0 0 0 0 1 0 0 0 16000 623 22 4 4 TBC1D10C 11 67405095 Missense_Mutation SNP C C3N-01415_T 1362528 67405095 67681527 346 24093 PPP6R3 0 . GRCh38 11 68596187 68596187 + Silent SNP G G T rs369801611 C3N-01415_T C3N-01415_N G G c.2007G>T p.= p.T669T ENST00000393801 19/25 369 320 49 285 285 0 strelka-varscan-mutect PPP6R3,synonymous_variant,p.=,ENST00000393800,NM_001164161.1;PPP6R3,synonymous_variant,p.=,ENST00000393801,NM_001164160.1;PPP6R3,synonymous_variant,p.=,ENST00000527403,;PPP6R3,synonymous_variant,p.=,ENST00000265636,NM_018312.4;PPP6R3,synonymous_variant,p.=,ENST00000265637,;PPP6R3,synonymous_variant,p.=,ENST00000524904,NM_001164162.1;PPP6R3,synonymous_variant,p.=,ENST00000529710,NM_001164164.1;PPP6R3,synonymous_variant,p.=,ENST00000534534,;PPP6R3,synonymous_variant,p.=,ENST00000524845,NM_001164163.1;PPP6R3,synonymous_variant,p.=,ENST00000534190,;PPP6R3,3_prime_UTR_variant,,ENST00000525421,;PPP6R3,non_coding_transcript_exon_variant,,ENST00000526307,; T ENST00000393801 Transcript synonymous_variant 2222/5069 2007/2640 669/879 T acG/acT rs369801611 1 1 PPP6R3 HGNC HGNC:1173 protein_coding YES CCDS53671.1 ENSP00000377390 Q5H9R7 UPI0000688150 NM_001164160.1 19/25 hmmpanther:PTHR12634:SF12,hmmpanther:PTHR12634 LOW 1 SNV 1 1 PASS rs369801611 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 68596187 68596187 G T 1 0 0 0 0 0 0 0 1 12536 1103 39 1 1 PPP6R3 11 68596187 Silent SNP G C3N-01415_T 1191092 68596187 66490435 347 24094 DGAT2 0 . GRCh38 11 75796464 75796464 + Missense_Mutation SNP G G T rs770570893 C3N-01415_T C3N-01415_N G G c.566G>T p.Arg189Leu p.R189L ENST00000228027 5/8 284 206 78 253 253 0 strelka-varscan-mutect DGAT2,missense_variant,p.Arg189Leu,ENST00000228027,NM_032564.4;DGAT2,missense_variant,p.Arg146Leu,ENST00000376262,NM_001253891.1;DGAT2,missense_variant,p.Arg143Leu,ENST00000604733,;DGAT2,missense_variant,p.Arg98Leu,ENST00000603276,;DGAT2,missense_variant,p.Arg98Leu,ENST00000604935,;DGAT2,missense_variant,p.Arg98Leu,ENST00000605099,;RP11-535A19.1,downstream_gene_variant,,ENST00000534354,;DGAT2,non_coding_transcript_exon_variant,,ENST00000603363,;DGAT2,non_coding_transcript_exon_variant,,ENST00000603865,; T ENST00000228027 Transcript missense_variant 826/2453 566/1167 189/388 R/L cGg/cTg rs770570893 1 1 DGAT2 HGNC HGNC:16940 protein_coding YES CCDS31642.1 ENSP00000228027 Q96PD7 UPI0000048F05 NM_032564.4 deleterious(0.03) 5/8 hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF14,Pfam_domain:PF03982 MODERATE 1 SNV 1 1 PASS rs770570893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 75796464 75796464 G T 1 0 0 0 0 1 0 0 0 4265 1116 39 1 1 DGAT2 11 75796464 Missense_Mutation SNP G C3N-01415_T 7200277 75796464 59290158 348 24095 TRIM49 0 . GRCh38 11 89798424 89798424 + Missense_Mutation SNP A A T rs752461771,rs760863845 C3N-01415_T C3N-01415_N A A c.1065T>A p.Phe355Leu p.F355L ENST00000329758 8/8 425 290 135 535 534 1 strelka-varscan-mutect TRIM49,missense_variant,p.Phe355Leu,ENST00000329758,NM_020358.2;TRIM49,missense_variant,p.Phe278Leu,ENST00000532501,; T ENST00000329758 Transcript missense_variant 1394/2163 1065/1359 355/452 F/L ttT/ttA rs752461771,rs760863845,COSM4004548 1 -1 TRIM49 HGNC HGNC:13431 protein_coding YES CCDS8287.1 ENSP00000327604 P0CI25 UPI000013431B NM_020358.2 tolerated(0.78) 8/8 Pfam_domain:PF00622,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,SMART_domains:SM00449,Superfamily_domains:SSF49899 0,0,1 MODERATE 1 SNV 1 0,0,1 1 PASS rs760863845 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 89798424 89798424 A T 1 0 0 0 0 1 0 0 0 17014 127 5 4 4 TRIM49 11 89798424 Missense_Mutation SNP A C3N-01415_T 14001960 89798424 45288198 349 24096 POU2AF1 0 . GRCh38 11 111358907 111358907 + Missense_Mutation SNP C C G rs755989118 C3N-01415_T C3N-01415_N C C c.28G>C p.Glu10Gln p.E10Q ENST00000393067 2/5 117 77 40 166 165 1 strelka-varscan-mutect POU2AF1,missense_variant,p.Glu10Gln,ENST00000393067,NM_006235.2;POU2AF1,missense_variant,p.Glu12Gln,ENST00000531398,;POU2AF1,non_coding_transcript_exon_variant,,ENST00000525584,;POU2AF1,non_coding_transcript_exon_variant,,ENST00000525662,;POU2AF1,non_coding_transcript_exon_variant,,ENST00000530793,;POU2AF1,downstream_gene_variant,,ENST00000526535,;POU2AF1,downstream_gene_variant,,ENST00000525499,; G ENST00000393067 Transcript missense_variant 543/3295 28/771 10/256 E/Q Gag/Cag rs755989118 1 -1 POU2AF1 HGNC HGNC:9211 protein_coding YES CCDS31675.1 ENSP00000376786 Q16633 UPI000011D77C NM_006235.2 tolerated(0.12) 2/5 hmmpanther:PTHR15363,Pfam_domain:PF09310 MODERATE 1 SNV 1 1 PASS rs755989118 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 111358907 111358907 C G 1 0 0 0 0 1 0 0 0 12386 864 30 4 4 POU2AF1 11 111358907 Missense_Mutation SNP C C3N-01415_T 21560483 111358907 23727715 350 24097 SIDT2 0 . GRCh38 11 117184121 117184121 + Missense_Mutation SNP G G T rs767955020 C3N-01415_T C3N-01415_N G G c.850G>T p.Val284Leu p.V284L ENST00000324225 8/26 197 158 39 199 199 0 strelka-varscan-mutect SIDT2,missense_variant,p.Val284Leu,ENST00000324225,NM_001040455.1;SIDT2,missense_variant,p.Val284Leu,ENST00000620360,;SIDT2,missense_variant,p.Val284Leu,ENST00000431081,;SIDT2,missense_variant,p.Val284Leu,ENST00000278951,;SIDT2,missense_variant,p.Val284Leu,ENST00000628876,;SIDT2,missense_variant,p.Val134Leu,ENST00000524842,;SIDT2,downstream_gene_variant,,ENST00000531353,;SIDT2,downstream_gene_variant,,ENST00000532960,;SIDT2,non_coding_transcript_exon_variant,,ENST00000530948,;SIDT2,intron_variant,,ENST00000525339,;SIDT2,upstream_gene_variant,,ENST00000526813,;SIDT2,upstream_gene_variant,,ENST00000529441,;SIDT2,downstream_gene_variant,,ENST00000531255,;SIDT2,downstream_gene_variant,,ENST00000528397,;SIDT2,upstream_gene_variant,,ENST00000524988,;SIDT2,upstream_gene_variant,,ENST00000527654,; T ENST00000324225 Transcript missense_variant 1381/4406 850/2499 284/832 V/L Gtg/Ttg rs767955020 1 1 SIDT2 HGNC HGNC:24272 protein_coding YES CCDS31682.1 ENSP00000314023 Q8NBJ9 UPI000004BA68 NM_001040455.1 tolerated(0.14) 8/26 hmmpanther:PTHR12185,hmmpanther:PTHR12185:SF16,Pfam_domain:PF13965 MODERATE 1 SNV 1 1 PASS rs767955020 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 117184121 117184121 G T 1 0 0 0 0 1 0 0 0 14567 1261 44 2 2 SIDT2 11 117184121 Missense_Mutation SNP G C3N-01415_T 5825214 117184121 17902501 351 24098 FOXR1 0 . GRCh38 11 118979479 118979479 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.422G>A p.Ser141Asn p.S141N ENST00000317011 4/6 149 95 54 123 123 0 strelka-mutect FOXR1,missense_variant,p.Ser141Asn,ENST00000317011,NM_181721.2;FOXR1,intron_variant,,ENST00000533282,;FOXR1,intron_variant,,ENST00000531539,; A ENST00000317011 Transcript missense_variant 647/1159 422/879 141/292 S/N aGc/aAc 1 1 FOXR1 HGNC HGNC:29980 protein_coding YES CCDS31688.1 ENSP00000314806 Q6PIV2 UPI0000192103 NM_181721.2 tolerated(0.47) 4/6 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF152,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999989 1 1 1 0 A 3 1 78 118979479 118979479 G A 1 0 0 0 0 1 0 0 0 5896 971 34 3 3 FOXR1 11 118979479 Missense_Mutation SNP G C3N-01415_T 1795358 118979479 16107143 352 24099 NECTIN1 0 . GRCh38 11 119665053 119665053 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.1248G>T p.= p.L416L ENST00000264025 6/6 430 281 149 441 441 0 strelka-varscan-mutect NECTIN1,synonymous_variant,p.=,ENST00000264025,NM_002855.4;NECTIN1,intron_variant,,ENST00000341398,NM_203285.1; A ENST00000264025 Transcript synonymous_variant 1779/5840 1248/1554 416/517 L ctG/ctT 1 -1 NECTIN1 HGNC HGNC:9706 protein_coding YES CCDS8426.1 ENSP00000264025 Q15223 UPI000004A2BE NM_002855.4 6/6 hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF69 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 119665053 119665053 C A 1 0 0 0 0 0 0 0 1 10333 697 25 2 2 NECTIN1 11 119665053 Silent SNP C C3N-01415_T 685574 119665053 15421569 353 24100 NECTIN1 0 . GRCh38 11 119675274 119675274 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.888G>A p.= p.Q296Q ENST00000264025 5/6 449 399 50 438 438 0 strelka-varscan-mutect NECTIN1,synonymous_variant,p.=,ENST00000264025,NM_002855.4;NECTIN1,synonymous_variant,p.=,ENST00000341398,NM_203285.1;NECTIN1,synonymous_variant,p.=,ENST00000340882,NM_203286.1;NECTIN1,downstream_gene_variant,,ENST00000524510,;NECTIN1,non_coding_transcript_exon_variant,,ENST00000524429,;NECTIN1,downstream_gene_variant,,ENST00000532197,; T ENST00000264025 Transcript synonymous_variant 1419/5840 888/1554 296/517 Q caG/caA 1 -1 NECTIN1 HGNC HGNC:9706 protein_coding YES CCDS8426.1 ENSP00000264025 Q15223 UPI000004A2BE NM_002855.4 5/6 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF69,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 119675274 119675274 C T 1 0 0 0 0 0 0 0 1 10333 912 32 3 3 NECTIN1 11 119675274 Silent SNP C C3N-01415_T 10221 119675274 15411348 354 24101 HEPACAM 0 . GRCh38 11 124921280 124921280 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1109C>A p.Ala370Asp p.A370D ENST00000298251 7/7 42 37 5 51 51 0 strelka-varscan-mutect HEPACAM,missense_variant,p.Ala370Asp,ENST00000298251,NM_152722.4;HEPN1,downstream_gene_variant,,ENST00000408930,NM_001037558.2;HEPACAM,downstream_gene_variant,,ENST00000528971,;HEPACAM,downstream_gene_variant,,ENST00000526273,; T ENST00000298251 Transcript missense_variant 1515/3602 1109/1251 370/416 A/D gCc/gAc 1 -1 HEPACAM HGNC HGNC:26361 protein_coding YES CCDS8456.1 ENSP00000298251 Q14CZ8 UPI000013E4B5 NM_152722.4 tolerated_low_confidence(0.21) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -12.70582 0.9999993 1 1 1 0 T 3 4 78 124921280 124921280 G T 1 0 0 0 0 1 0 0 0 6936 1203 42 2 2 HEPACAM 11 124921280 Missense_Mutation SNP G C3N-01415_T 5246006 124921280 10165342 355 24102 KDM5A 0 . GRCh38 12 388950 388959 + Frame_Shift_Del DEL TGCCGGTTTT TGCCGGTTTT - novel C3N-01415_T C3N-01415_N TGCCGGTTTT TGCCGGTTTT c.133_142delAAAACCGGCA p.Lys45SerfsTer18 p.K45Sfs*18 ENST00000399788 1/28 380 356 24 412 411 1 varindel-pindel KDM5A,frameshift_variant,p.Lys45SerfsTer18,ENST00000399788,NM_001042603.2;KDM5A,frameshift_variant,p.Lys45SerfsTer17,ENST00000544760,;KDM5A,frameshift_variant,p.Lys45SerfsTer27,ENST00000543507,;KDM5A,frameshift_variant,p.Lys45SerfsTer18,ENST00000535014,;CCDC77,upstream_gene_variant,,ENST00000422000,NM_001130147.1;CCDC77,upstream_gene_variant,,ENST00000540180,NM_001130148.1;CCDC77,upstream_gene_variant,,ENST00000543504,;KDM5A,upstream_gene_variant,,ENST00000536014,;CCDC77,upstream_gene_variant,,ENST00000535052,;CCDC77,upstream_gene_variant,,ENST00000540344,;CCDC77,upstream_gene_variant,,ENST00000537453,; - ENST00000399788 Transcript frameshift_variant 496-505/10763 133-142/5073 45-48/1690 KTGI/X AAAACCGGCAtc/tc 1 -1 KDM5A HGNC HGNC:9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.2 1/28 PROSITE_profiles:PS51183,hmmpanther:PTHR10694:SF17,hmmpanther:PTHR10694,Pfam_domain:PF02375,SMART_domains:SM00545 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 388950 388950 TGCCGGTTTT - 1 0 1 0 1 0 0 0 0 8051 1464 51 0 0 KDM5A 12 388950 Frame_Shift_Del DEL TGCCGGTTTT C3N-01415_T 388950 132886359 356 24103 CACNA2D4 0 . GRCh38 12 1858599 1858599 + Silent SNP C C G rs764496676 C3N-01415_T C3N-01415_N C C c.1986G>C p.= p.L662L ENST00000382722 20/38 173 139 34 152 152 0 strelka-varscan-mutect CACNA2D4,synonymous_variant,p.=,ENST00000382722,NM_172364.4;CACNA2D4,synonymous_variant,p.=,ENST00000587995,;CACNA2D4,synonymous_variant,p.=,ENST00000586184,;CACNA2D4,synonymous_variant,p.=,ENST00000588077,;CACNA2D4,synonymous_variant,p.=,ENST00000585708,;CACNA2D4,synonymous_variant,p.=,ENST00000585732,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000539048,;CACNA2D4,3_prime_UTR_variant,,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,;CACNA2D4,upstream_gene_variant,,ENST00000537784,; G ENST00000382722 Transcript synonymous_variant 2349/5475 1986/3414 662/1137 L ctG/ctC rs764496676 1 -1 CACNA2D4 HGNC HGNC:20202 protein_coding YES CCDS44785.1 ENSP00000372169 Q7Z3S7 UPI0000E593D9 NM_172364.4 20/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF26 LOW 1 SNV 1 1 PASS rs764496676 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 1858599 1858599 C G 1 0 0 0 0 0 0 0 1 2239 581 21 4 4 CACNA2D4 12 1858599 Silent SNP C C3N-01415_T 1469649 1858599 131416710 357 24104 CD163L1 0 . GRCh38 12 7369369 7369369 + Missense_Mutation SNP C C G rs367598769 C3N-01415_T C3N-01415_N C C c.4057G>C p.Val1353Leu p.V1353L ENST00000416109 15/20 142 118 24 192 192 0 strelka-varscan-mutect CD163L1,missense_variant,p.Val1343Leu,ENST00000313599,NM_174941.5;CD163L1,missense_variant,p.Val1353Leu,ENST00000416109,NM_001297650.1;CD163L1,upstream_gene_variant,,ENST00000539726,;CD163L1,non_coding_transcript_exon_variant,,ENST00000545597,;CD163L1,upstream_gene_variant,,ENST00000543841,;CD163L1,upstream_gene_variant,,ENST00000546182,; G ENST00000416109 Transcript missense_variant 4076/4603 4057/4392 1353/1463 V/L Gtg/Ctg rs367598769 1 -1 CD163L1 HGNC HGNC:30375 protein_coding YES CCDS73434.1 ENSP00000393474 Q9NR16 UPI0001AE6A76 NM_001297650.1 deleterious(0) 15/20 PROSITE_profiles:PS50287,hmmpanther:PTHR19331:SF260,hmmpanther:PTHR19331,Gene3D:3.10.250.10,Pfam_domain:PF00530,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 2 1 PASS rs367598769 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 7369369 7369369 C G 1 0 0 0 0 1 0 0 0 2671 536 19 4 4 CD163L1 12 7369369 Missense_Mutation SNP C C3N-01415_T 5510770 7369369 125905940 358 24105 SLCO1B1 0 . GRCh38 12 21224720 21224720 + Splice_Site SNP A A T novel C3N-01415_T C3N-01415_N A A c.1748-2A>T p.X583_splice ENST00000256958 293 246 47 317 317 0 strelka-varscan-mutect SLCO1B1,splice_acceptor_variant,,ENST00000256958,NM_006446.4; T ENST00000256958 Transcript splice_acceptor_variant -/2229 1748/2076 583/691 1 1 SLCO1B1 HGNC HGNC:10959 protein_coding YES CCDS8685.1 ENSP00000256958 Q9Y6L6 A0A024RAU7 UPI0000043BED NM_006446.4 13/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 78 21224720 21224720 A T 1 0 0 0 0 0 0 1 0 15009 202 7 4 4 SLCO1B1 12 21224720 Splice_Site SNP A C3N-01415_T 13855351 21224720 112050589 359 24106 GOLT1B 0 . GRCh38 12 21508383 21508383 + Missense_Mutation SNP G G C rs200318646 C3N-01415_T C3N-01415_N G G c.118G>C p.Val40Leu p.V40L ENST00000229314 3/5 120 106 14 168 168 0 strelka-varscan-mutect GOLT1B,missense_variant,p.Val40Leu,ENST00000229314,NM_016072.4;GOLT1B,missense_variant,p.Val40Leu,ENST00000540141,;GOLT1B,splice_region_variant,,ENST00000542038,;GOLT1B,downstream_gene_variant,,ENST00000631252,;GOLT1B,intron_variant,,ENST00000535593,;GOLT1B,intron_variant,,ENST00000545093,;GOLT1B,splice_region_variant,,ENST00000539025,;GOLT1B,splice_region_variant,,ENST00000539663,;GOLT1B,splice_region_variant,,ENST00000542194,;GOLT1B,downstream_gene_variant,,ENST00000545113,; C ENST00000229314 Transcript missense_variant,splice_region_variant 227/3227 118/417 40/138 V/L Gtt/Ctt rs200318646 1 1 GOLT1B HGNC HGNC:20175 protein_coding YES CCDS8689.1 ENSP00000229314 Q9Y3E0 UPI0000048ED8 NM_016072.4 tolerated(0.59) 3/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR21493,Pfam_domain:PF04178 MODERATE 1 SNV 1 1 PASS rs200318646 . 0 203 7 0 0 0 0 0 -20 0.9999993 1 1 1 0 C 3 2 78 21508383 21508383 G C 1 0 0 0 0 1 0 0 0 6465 1275 44 4 4 GOLT1B 12 21508383 Missense_Mutation SNP G C3N-01415_T 283663 21508383 111766926 360 24107 GYS2 0 . GRCh38 12 21580478 21580478 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.167C>A p.Ala56Glu p.A56E ENST00000261195 2/16 512 449 63 652 651 1 strelka-varscan-mutect GYS2,missense_variant,p.Ala56Glu,ENST00000261195,NM_021957.3; T ENST00000261195 Transcript missense_variant 422/3132 167/2112 56/703 A/E gCa/gAa 1 -1 GYS2 HGNC HGNC:4707 protein_coding YES CCDS8690.1 ENSP00000261195 P54840 UPI000013D13D NM_021957.3 deleterious(0.04) 2/16 hmmpanther:PTHR10176:SF1,hmmpanther:PTHR10176,Pfam_domain:PF05693 MODERATE 1 SNV 1 1 PASS rs778914111 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 21580478 21580478 G T 1 0 0 0 0 1 0 0 0 6795 1319 46 2 2 GYS2 12 21580478 Missense_Mutation SNP G C3N-01415_T 72095 21580478 111694831 361 24108 SMCO2 0 . GRCh38 12 27495760 27495760 + Missense_Mutation SNP T T A novel C3N-01415_T C3N-01415_N T T c.738T>A p.Ser246Arg p.S246R ENST00000416383 8/9 94 87 7 112 111 1 strelka-varscan-mutect SMCO2,missense_variant,p.Ser246Arg,ENST00000416383,NM_001145010.1;SMCO2,missense_variant,p.Ser196Arg,ENST00000298876,;SMCO2,missense_variant,p.Ser246Arg,ENST00000535986,;SMCO2,non_coding_transcript_exon_variant,,ENST00000538647,;SMCO2,non_coding_transcript_exon_variant,,ENST00000541168,;RARSP1,upstream_gene_variant,,ENST00000542842,; A ENST00000416383 Transcript missense_variant 914/1272 738/1032 246/343 S/R agT/agA 1 1 SMCO2 HGNC HGNC:34448 protein_coding YES CCDS44852.1 ENSP00000387617 A6NFE2 UPI000166275D NM_001145010.1 deleterious(0.03) 8/9 hmmpanther:PTHR22422:SF5,hmmpanther:PTHR22422,Pfam_domain:PF14992 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -14.66898 1 1 1 1 0 A 3 1 78 27495760 27495760 T A 1 0 0 0 0 1 0 0 0 15083 1722 60 4 4 SMCO2 12 27495760 Missense_Mutation SNP T C3N-01415_T 5915282 27495760 105779549 362 24109 TMTC1 0 . GRCh38 12 29514584 29514584 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.2328G>T p.Lys776Asn p.K776N ENST00000539277 16/18 153 113 40 188 188 0 strelka-varscan-mutect TMTC1,missense_variant,p.Lys668Asn,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Lys838Asn,ENST00000551659,;TMTC1,missense_variant,p.Lys800Asn,ENST00000552618,;TMTC1,missense_variant,p.Lys776Asn,ENST00000539277,NM_001193451.1;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,non_coding_transcript_exon_variant,,ENST00000552925,; A ENST00000539277 Transcript missense_variant 2387/2758 2328/2649 776/882 K/N aaG/aaT 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 deleterious(0.02) 16/18 Gene3D:1.25.40.10,Pfam_domain:PF13181,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 29514584 29514584 C A 1 0 0 0 0 1 0 0 0 16734 680 24 2 2 TMTC1 12 29514584 Missense_Mutation SNP C C3N-01415_T 2018824 29514584 103760725 363 24110 ANO6 0 . GRCh38 12 45348072 45348072 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.453G>T p.Trp151Cys p.W151C ENST00000423947 6/21 293 237 56 310 310 0 strelka-varscan-mutect ANO6,missense_variant,p.Trp130Cys,ENST00000320560,NM_001025356.2;ANO6,missense_variant,p.Trp112Cys,ENST00000441606,NM_001142678.1;ANO6,missense_variant,p.Trp151Cys,ENST00000423947,NM_001204803.1;ANO6,missense_variant,p.Trp130Cys,ENST00000425752,NM_001142679.1;ANO6,non_coding_transcript_exon_variant,,ENST00000426898,;ANO6,downstream_gene_variant,,ENST00000551667,; T ENST00000423947 Transcript missense_variant 690/5504 453/2796 151/931 W/C tgG/tgT 1 1 ANO6 HGNC HGNC:25240 protein_coding YES CCDS55819.1 ENSP00000409126 Q4KMQ2 UPI000022935A NM_001204803.1 deleterious(0.01) 6/21 hmmpanther:PTHR12308:SF21,hmmpanther:PTHR12308,Pfam_domain:PF16178 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 45348072 45348072 G T 1 0 0 0 0 1 0 0 0 808 1241 43 2 2 ANO6 12 45348072 Missense_Mutation SNP G C3N-01415_T 15833488 45348072 87927237 364 24111 KMT2D 0 . GRCh38 12 49052005 49052005 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1678G>T p.Glu560Ter p.E560* ENST00000301067 10/54 281 261 20 273 273 0 strelka-varscan-mutect KMT2D,stop_gained,p.Glu560Ter,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000547610,; A ENST00000301067 Transcript stop_gained 1678/19419 1678/16614 560/5537 E/* Gaa/Taa 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 10/54 Low_complexity_(Seg):seg HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 49052005 49052005 C A 1 0 0 0 0 0 1 0 0 8298 864 30 2 2 KMT2D 12 49052005 Nonsense_Mutation SNP C C3N-01415_T 3703933 49052005 84223304 365 24112 ACVRL1 0 . GRCh38 12 51913581 51913581 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.336G>T p.Gln112His p.Q112H ENST00000388922 4/10 448 359 89 366 366 0 strelka-varscan-mutect ACVRL1,missense_variant,p.Gln126His,ENST00000550683,;ACVRL1,missense_variant,p.Gln112His,ENST00000388922,NM_000020.2,NM_001077401.1;ACVRL1,intron_variant,,ENST00000419526,;ACVRL1,intron_variant,,ENST00000547400,;ACVRL1,upstream_gene_variant,,ENST00000552678,;ACVRL1,downstream_gene_variant,,ENST00000551576,;ACVRL1,upstream_gene_variant,,ENST00000547632,; T ENST00000388922 Transcript missense_variant 619/1971 336/1512 112/503 Q/H caG/caT 1 1 ACVRL1 HGNC HGNC:175 protein_coding YES CCDS31804.1 ENSP00000373574 P37023 A0A0S2Z310 UPI000000D9F4 NM_000020.2,NM_001077401.1 tolerated(0.18) 4/10 hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF66 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 51913581 51913581 G T 1 0 0 0 0 1 0 0 0 269 962 34 2 2 ACVRL1 12 51913581 Missense_Mutation SNP G C3N-01415_T 2861576 51913581 81361728 366 24113 AAAS 0 . GRCh38 12 53308973 53308973 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.983C>T p.Ser328Leu p.S328L ENST00000209873 10/16 816 754 62 744 743 1 strelka-varscan-mutect AAAS,missense_variant,p.Ser328Leu,ENST00000209873,NM_015665.5;AAAS,missense_variant,p.Ser295Leu,ENST00000394384,NM_001173466.1;AAAS,missense_variant,p.Ser204Leu,ENST00000550286,;AAAS,missense_variant,p.Ser168Leu,ENST00000548931,;C12orf10,downstream_gene_variant,,ENST00000267103,NM_021640.3;C12orf10,downstream_gene_variant,,ENST00000548632,;AAAS,downstream_gene_variant,,ENST00000547757,;C12orf10,downstream_gene_variant,,ENST00000549488,;C12orf10,downstream_gene_variant,,ENST00000547864,;AAAS,downstream_gene_variant,,ENST00000549983,;AAAS,downstream_gene_variant,,ENST00000547761,;AAAS,non_coding_transcript_exon_variant,,ENST00000552876,;AAAS,non_coding_transcript_exon_variant,,ENST00000550033,;AAAS,non_coding_transcript_exon_variant,,ENST00000547520,;AAAS,non_coding_transcript_exon_variant,,ENST00000546572,;C12orf10,downstream_gene_variant,,ENST00000548845,;AAAS,downstream_gene_variant,,ENST00000547238,;AAAS,downstream_gene_variant,,ENST00000546393,;C12orf10,downstream_gene_variant,,ENST00000550199,;C12orf10,downstream_gene_variant,,ENST00000549177,;C12orf10,downstream_gene_variant,,ENST00000547490,; A ENST00000209873 Transcript missense_variant 1149/1840 983/1641 328/546 S/L tCa/tTa 1 -1 AAAS HGNC HGNC:13666 protein_coding YES CCDS8856.1 ENSP00000209873 Q9NRG9 UPI0000039E40 NM_015665.5 tolerated(0.11) 10/16 hmmpanther:PTHR14494,hmmpanther:PTHR14494:SF0,Gene3D:2.130.10.10,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 53308973 53308973 G A 1 0 0 0 0 1 0 0 0 8 1294 45 3 3 AAAS 12 53308973 Missense_Mutation SNP G C3N-01415_T 1395392 53308973 79966336 367 24114 OR6C3 0 . GRCh38 12 55332046 55332046 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.346T>C p.Ser116Pro p.S116P ENST00000379667 1/1 277 256 21 339 339 0 strelka-varscan-mutect OR6C3,missense_variant,p.Ser116Pro,ENST00000379667,NM_054104.1; C ENST00000379667 Transcript missense_variant 346/936 346/936 116/311 S/P Tcc/Ccc 1 1 OR6C3 HGNC HGNC:15437 protein_coding YES CCDS31819.1 ENSP00000368989 Q9NZP0 A0A126GW44 UPI000016150E NM_054104.1 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF39,hmmpanther:PTHR26454,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 55332046 55332046 T C 1 0 0 0 0 1 0 0 0 11260 1667 58 5 5 OR6C3 12 55332046 Missense_Mutation SNP T C3N-01415_T 2023073 55332046 77943263 368 24115 PTPRQ 0 . GRCh38 12 80496049 80496050 + Frame_Shift_Ins INS - - A novel C3N-01415_T C3N-01415_N - - c.1933_1934insA p.Val645AspfsTer8 p.V645Dfs*8 ENST00000614701 13/45 231 215 16 247 247 0 varindel-pindel PTPRQ,frameshift_variant,p.Val645AspfsTer8,ENST00000614701,NM_001145026.1;PTPRQ,frameshift_variant,p.Val687AspfsTer8,ENST00000616559,; A ENST00000614701 Transcript frameshift_variant 2111-2112/8289 1933-1934/6900 645/2299 V/DX gtt/gAtt 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 13/45 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF414,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 insertion 5 1 PASS . . 0 31 0 0 0 0 0 179 -7.740987 0 0 1 0 0 A 7 5 78 80496049 80496049 - A 1 0 1 1 0 0 0 0 0 12964 1145 40 0 0 PTPRQ 12 80496049 Frame_Shift_Ins INS - C3N-01415_T 25164003 80496049 52779260 369 24116 PPFIA2 0 . GRCh38 12 81353136 81353136 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.1977C>A p.= p.A659A ENST00000549396 17/33 274 225 49 316 316 0 strelka-varscan-mutect PPFIA2,synonymous_variant,p.=,ENST00000333447,NM_001220478.2;PPFIA2,synonymous_variant,p.=,ENST00000550584,NM_001220473.2;PPFIA2,synonymous_variant,p.=,ENST00000549396,NM_003625.4;PPFIA2,synonymous_variant,p.=,ENST00000549325,NM_001220474.2;PPFIA2,synonymous_variant,p.=,ENST00000548586,NM_001220476.2;PPFIA2,synonymous_variant,p.=,ENST00000552948,NM_001220475.2;PPFIA2,synonymous_variant,p.=,ENST00000407050,NM_001220477.2;PPFIA2,synonymous_variant,p.=,ENST00000550359,NM_001282536.1;PPFIA2,synonymous_variant,p.=,ENST00000443686,;PPFIA2,synonymous_variant,p.=,ENST00000541570,NM_001220479.2;PPFIA2,synonymous_variant,p.=,ENST00000553058,;PPFIA2,5_prime_UTR_variant,,ENST00000541017,NM_001220480.2;PPFIA2,intron_variant,,ENST00000545296,;PPFIA2,upstream_gene_variant,,ENST00000549917,;PPFIA2,3_prime_UTR_variant,,ENST00000551461,; T ENST00000549396 Transcript synonymous_variant 2138/5363 1977/3774 659/1257 A gcC/gcA 1 -1 PPFIA2 HGNC HGNC:9246 protein_coding YES CCDS55857.1 ENSP00000450337 O75334 UPI0000168655 NM_003625.4 17/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587:SF6,hmmpanther:PTHR12587 LOW 1 SNV 1 1 PASS rs1172602266 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 81353136 81353136 G T 1 0 0 0 0 0 0 0 1 12419 1335 47 2 2 PPFIA2 12 81353136 Silent SNP G C3N-01415_T 857087 81353136 51922173 370 24117 POC1B 0 . GRCh38 12 89497270 89497270 + Frame_Shift_Del DEL C C - novel C3N-01415_T C3N-01415_N C C c.173delG p.Gly58ValfsTer6 p.G58Vfs*6 ENST00000313546 3/12 228 189 39 293 293 0 sindel-varindel-pindel POC1B,frameshift_variant,p.Gly58ValfsTer6,ENST00000313546,NM_172240.2;POC1B,frameshift_variant,p.Gly16ValfsTer6,ENST00000549035,NM_001199777.1;POC1B,intron_variant,,ENST00000393179,;POC1B,intron_variant,,ENST00000549504,;POC1B,frameshift_variant,p.Gly58ValfsTer6,ENST00000546830,;POC1B,non_coding_transcript_exon_variant,,ENST00000539190,;POC1B,intron_variant,,ENST00000547496,;POC1B,intron_variant,,ENST00000548715,;POC1B,intron_variant,,ENST00000552563,;POC1B,intron_variant,,ENST00000547274,;CENPCP1,upstream_gene_variant,,ENST00000533085,; - ENST00000313546 Transcript frameshift_variant 302/3001 173/1437 58/478 G/X gGt/gt 1 -1 POC1B HGNC HGNC:30836 protein_coding YES CCDS31869.1 ENSP00000323302 Q8TC44 A0MNP0 UPI000006E6B9 NM_172240.2 3/12 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 89497270 89497270 C - 1 0 1 0 1 0 0 0 0 12285 507 18 0 0 POC1B 12 89497270 Frame_Shift_Del DEL C C3N-01415_T 8144134 89497270 43778039 371 24118 EPYC 0 . GRCh38 12 90971940 90971940 + Silent SNP G G T rs143768297 C3N-01415_T C3N-01415_N G G c.562C>A p.= p.R188R ENST00000261172 5/7 295 226 69 313 312 1 strelka-varscan-mutect EPYC,synonymous_variant,p.=,ENST00000261172,NM_004950.4;EPYC,synonymous_variant,p.=,ENST00000551767,;EPYC,downstream_gene_variant,,ENST00000550203,; T ENST00000261172 Transcript synonymous_variant 655/1539 562/969 188/322 R Cga/Aga rs143768297 1 -1 EPYC HGNC HGNC:3053 protein_coding YES CCDS31870.1 ENSP00000261172 Q99645 A0A024RBC3 UPI000013D136 NM_004950.4 5/7 PROSITE_profiles:PS51450,hmmpanther:PTHR24373:SF123,hmmpanther:PTHR24373,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs143768297 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 90971940 90971940 G T 1 0 0 0 0 0 0 0 1 5049 1124 39 1 1 EPYC 12 90971940 Silent SNP G C3N-01415_T 1474670 90971940 42303369 372 24119 CFAP54 0 . GRCh38 12 96743439 96743439 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.7257A>T p.Glu2419Asp p.E2419D ENST00000524981 53/68 344 264 80 355 354 1 strelka-varscan-mutect CFAP54,missense_variant,p.Glu2419Asp,ENST00000524981,NM_001306084.1;CFAP54,missense_variant,p.Glu1390Asp,ENST00000637336,;CFAP54,non_coding_transcript_exon_variant,,ENST00000342887,; T ENST00000524981 Transcript missense_variant 7280/9766 7257/9291 2419/3096 E/D gaA/gaT 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 deleterious(0.03) 53/68 hmmpanther:PTHR33487,hmmpanther:PTHR33487:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 96743439 96743439 A T 1 0 0 0 0 1 0 0 0 3025 69 3 4 4 CFAP54 12 96743439 Missense_Mutation SNP A C3N-01415_T 5771499 96743439 36531870 373 24120 TMPO 0 . GRCh38 12 98527964 98527964 + Missense_Mutation SNP C C G rs200420073 C3N-01415_T C3N-01415_N C C c.358C>G p.Leu120Val p.L120V ENST00000266732 2/4 523 464 59 495 495 0 strelka-varscan-mutect TMPO,missense_variant,p.Leu120Val,ENST00000556029,NM_001032283.2;TMPO,missense_variant,p.Leu120Val,ENST00000266732,NM_003276.2;TMPO,missense_variant,p.Leu120Val,ENST00000343315,NM_001307975.1;TMPO,missense_variant,p.Leu120Val,ENST00000393053,NM_001032284.2;TMPO,missense_variant,p.Leu120Val,ENST00000261210,;TMPO,missense_variant,p.Leu27Val,ENST00000556678,;TMPO,non_coding_transcript_exon_variant,,ENST00000547214,;TMPO,non_coding_transcript_exon_variant,,ENST00000549938,;TMPO,non_coding_transcript_exon_variant,,ENST00000546828,;TMPO,non_coding_transcript_exon_variant,,ENST00000548911,;TMPO,non_coding_transcript_exon_variant,,ENST00000552831,; G ENST00000266732 Transcript missense_variant 596/3615 358/2085 120/694 L/V Ctt/Gtt rs200420073 1 1 TMPO HGNC HGNC:11875 protein_coding YES CCDS9064.1 ENSP00000266732 P42166 UPI000013D709 NM_003276.2 deleterious_low_confidence(0) 2/4 PROSITE_profiles:PS50954,hmmpanther:PTHR12019:SF10,hmmpanther:PTHR12019,Gene3D:1.10.720.40,Pfam_domain:PF03020,SMART_domains:SM00540,Superfamily_domains:SSF63451 uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs200420073 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 98527964 98527964 C G 1 0 0 0 0 1 0 0 0 16713 913 32 4 4 TMPO 12 98527964 Missense_Mutation SNP C C3N-01415_T 1784525 98527964 34747345 374 24121 CKAP4 0 . GRCh38 12 106247556 106247556 + Missense_Mutation SNP G G T rs575354598 C3N-01415_T C3N-01415_N G G c.296C>A p.Ser99Tyr p.S99Y ENST00000378026 1/2 160 135 25 174 174 0 strelka-varscan-mutect CKAP4,missense_variant,p.Ser99Tyr,ENST00000378026,NM_006825.3;CKAP4,intron_variant,,ENST00000553039,;RP11-651L5.3,upstream_gene_variant,,ENST00000611145,;RP11-651L5.2,upstream_gene_variant,,ENST00000552486,;CKAP4,intron_variant,,ENST00000552828,; T ENST00000378026 Transcript missense_variant 433/3093 296/1809 99/602 S/Y tCc/tAc rs575354598 1 -1 CKAP4 HGNC HGNC:16991 protein_coding YES CCDS9103.1 ENSP00000367265 Q07065 A0A024RBH2 UPI00000723B9 NM_006825.3 deleterious(0) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs575354598 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 106247556 106247556 G T 1 0 0 0 0 1 0 0 0 3207 1174 41 2 2 CKAP4 12 106247556 Missense_Mutation SNP G C3N-01415_T 7719592 106247556 27027753 375 24122 NAA25 0 . GRCh38 12 112054505 112054505 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.1511C>G p.Ser504Cys p.S504C ENST00000261745 14/24 348 277 71 320 320 0 strelka-varscan-mutect NAA25,missense_variant,p.Ser504Cys,ENST00000261745,NM_024953.3;NAA25,3_prime_UTR_variant,,ENST00000549711,;NAA25,3_prime_UTR_variant,,ENST00000551858,;NAA25,non_coding_transcript_exon_variant,,ENST00000552527,; C ENST00000261745 Transcript missense_variant 1760/6010 1511/2919 504/972 S/C tCc/tGc 1 -1 NAA25 HGNC HGNC:25783 protein_coding YES CCDS9159.1 ENSP00000261745 Q14CX7 UPI00001FBB50 NM_024953.3 deleterious(0) 14/24 Gene3D:1.25.40.10,Pfam_domain:PF09797,hmmpanther:PTHR22767,hmmpanther:PTHR22767:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 112054505 112054505 G C 1 0 0 0 0 1 0 0 0 10124 1174 41 4 4 NAA25 12 112054505 Missense_Mutation SNP G C3N-01415_T 5806949 112054505 21220804 376 24123 RPH3A 0 . GRCh38 12 112865515 112865515 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.332C>T p.Ala111Val p.A111V ENST00000389385 6/22 275 220 55 262 260 2 strelka-varscan-mutect RPH3A,missense_variant,p.Ala111Val,ENST00000389385,NM_001143854.1;RPH3A,missense_variant,p.Ala111Val,ENST00000415485,;RPH3A,missense_variant,p.Ala107Val,ENST00000551052,NM_014954.3;RPH3A,missense_variant,p.Ala111Val,ENST00000543106,;RPH3A,missense_variant,p.Ala62Val,ENST00000548866,;RPH3A,missense_variant,p.Ala111Val,ENST00000551593,;RPH3A,missense_variant,p.Ala111Val,ENST00000547728,;RPH3A,missense_variant,p.Ala44Val,ENST00000550901,;RPH3A,missense_variant,p.Ala111Val,ENST00000551198,;RPH3A,missense_variant,p.Ala111Val,ENST00000552667,;RPH3A,missense_variant,p.Ala111Val,ENST00000553114,;RPH3A,missense_variant,p.Ala111Val,ENST00000547840,;RPH3A,missense_variant,p.Ala111Val,ENST00000549769,;RPH3A,downstream_gene_variant,,ENST00000548197,;RPH3A,downstream_gene_variant,,ENST00000546703,;RPH3A,downstream_gene_variant,,ENST00000551748,;RPH3A,downstream_gene_variant,,ENST00000547686,;RPH3A,non_coding_transcript_exon_variant,,ENST00000547222,;RPH3A,non_coding_transcript_exon_variant,,ENST00000552679,;RPH3A,upstream_gene_variant,,ENST00000549913,;RPH3A,3_prime_UTR_variant,,ENST00000547099,; T ENST00000389385 Transcript missense_variant 829/4679 332/2085 111/694 A/V gCc/gTc 1 1 RPH3A HGNC HGNC:17056 protein_coding YES CCDS44979.1 ENSP00000374036 Q9Y2J0 UPI000013456D NM_001143854.1 deleterious(0.01) 6/22 PROSITE_profiles:PS50178,PROSITE_profiles:PS50916,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118,Gene3D:3.30.40.10,Pfam_domain:PF02318,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 112865515 112865515 C T 1 0 0 0 0 1 0 0 0 13803 739 26 3 3 RPH3A 12 112865515 Missense_Mutation SNP C C3N-01415_T 811010 112865515 20409794 377 24124 NOS1 0 . GRCh38 12 117234591 117234591 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.3311T>A p.Leu1104Gln p.L1104Q ENST00000618760 22/30 115 101 14 134 134 0 strelka-varscan-mutect NOS1,missense_variant,p.Leu1104Gln,ENST00000618760,NM_001204218.1;NOS1,missense_variant,p.Leu1070Gln,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,missense_variant,p.Leu1104Gln,ENST00000338101,;NOS1,missense_variant,p.Leu1069Gln,ENST00000344089,; T ENST00000618760 Transcript missense_variant 4022/12283 3311/4407 1104/1468 L/Q cTg/cAg 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 tolerated(0.21) 22/30 PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Gene3D:1.20.990.10,Pfam_domain:PF00667,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF63380 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.999997 1 1 1 0 T 3 4 78 117234591 117234591 A T 1 0 0 0 0 1 0 0 0 10586 188 7 4 4 NOS1 12 117234591 Missense_Mutation SNP A C3N-01415_T 4369076 117234591 16040718 378 24125 GCN1 0 . GRCh38 12 120129493 120129493 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.7673G>T p.Cys2558Phe p.C2558F ENST00000300648 57/58 214 157 57 218 217 1 strelka-varscan-mutect GCN1,missense_variant,p.Cys2558Phe,ENST00000300648,NM_006836.1; A ENST00000300648 Transcript missense_variant,splice_region_variant 7686/8675 7673/8016 2558/2671 C/F tGt/tTt 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 deleterious(0.05) 57/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 120129493 120129493 C A 1 0 0 0 0 1 0 0 0 6169 492 17 2 2 GCN1 12 120129493 Missense_Mutation SNP C C3N-01415_T 2894902 120129493 13145816 379 24126 SBNO1 0 . GRCh38 12 123341081 123341081 + Silent SNP T T A novel C3N-01415_T C3N-01415_N T T c.558A>T p.= p.V186V ENST00000420886 4/31 174 128 46 238 238 0 strelka-varscan-mutect SBNO1,synonymous_variant,p.=,ENST00000267176,NM_018183.3;SBNO1,synonymous_variant,p.=,ENST00000420886,NM_001167856.1;SBNO1,synonymous_variant,p.=,ENST00000602398,; A ENST00000420886 Transcript synonymous_variant 558/10981 558/4182 186/1393 V gtA/gtT 1 -1 SBNO1 HGNC HGNC:22973 protein_coding YES CCDS53844.1 ENSP00000387361 A3KN83 UPI00001FB922 NM_001167856.1 4/31 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 123341081 123341081 T A 1 0 0 0 0 0 0 0 1 14127 1741 61 4 4 SBNO1 12 123341081 Silent SNP T C3N-01415_T 3211588 123341081 9934228 380 24127 RNF17 0 . GRCh38 13 24764331 24764331 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.128C>A p.Ser43Tyr p.S43Y ENST00000255324 1/36 55 49 6 56 56 0 strelka-varscan-mutect RNF17,missense_variant,p.Ser43Tyr,ENST00000255324,NM_031277.2,NM_001184993.1;RNF17,missense_variant,p.Ser43Tyr,ENST00000255325,;RNF17,splice_region_variant,,ENST00000255326,; A ENST00000255324 Transcript missense_variant,splice_region_variant 180/5119 128/4872 43/1623 S/Y tCc/tAc 1 1 RNF17 HGNC HGNC:10060 protein_coding YES CCDS9308.2 ENSP00000255324 Q9BXT8 UPI00001FC8BA NM_031277.2,NM_001184993.1 deleterious_low_confidence(0) 1/36 PROSITE_profiles:PS50089,hmmpanther:PTHR16442,Superfamily_domains:SSF57850 MODERATE 1 SNV 2 1 PASS rs1037705532 . 0 203 7 0 0 0 0 0 -14.13041 0.9999991 1 1 1 0 A 3 1 78 24764331 24764331 C A 1 0 0 0 0 1 0 0 0 13638 869 30 2 2 RNF17 13 24764331 Missense_Mutation SNP C C3N-01415_T 24764331 89599997 381 24128 ZAR1L 0 . GRCh38 13 32311545 32311545 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.381G>T p.= p.L127L ENST00000533490 3/6 97 85 12 166 166 0 strelka-varscan-mutect ZAR1L,synonymous_variant,p.=,ENST00000533490,;ZAR1L,synonymous_variant,p.=,ENST00000345108,NM_001136571.1;BRCA2,upstream_gene_variant,,ENST00000380152,;BRCA2,upstream_gene_variant,,ENST00000544455,NM_000059.3;BRCA2,upstream_gene_variant,,ENST00000614259,;BRCA2,upstream_gene_variant,,ENST00000530893,; A ENST00000533490 Transcript synonymous_variant 800/1564 381/966 127/321 L ctG/ctT 1 -1 ZAR1L HGNC HGNC:37116 protein_coding YES CCDS45023.1 ENSP00000437289 A6NP61 UPI00006C1387 3/6 hmmpanther:PTHR31054:SF5,hmmpanther:PTHR31054 LOW 1 SNV 5 1 PASS rs1480808783 . 0 203 7 0 0 0 0 0 -19.99999 0.9999994 1 1 1 0 A 2 1 78 32311545 32311545 C A 1 0 0 0 0 0 0 0 1 18077 697 25 2 2 ZAR1L 13 32311545 Silent SNP C C3N-01415_T 7547214 32311545 82052783 382 24129 KBTBD6 0 . GRCh38 13 41131338 41131338 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1174G>T p.Asp392Tyr p.D392Y ENST00000379485 1/1 319 275 44 438 438 0 strelka-varscan-mutect KBTBD6,missense_variant,p.Asp392Tyr,ENST00000379485,NM_152903.4;RP11-74J13.8,upstream_gene_variant,,ENST00000619407,;RP11-74J13.8,upstream_gene_variant,,ENST00000620300,;RP11-74J13.8,upstream_gene_variant,,ENST00000616251,;RP11-74J13.8,upstream_gene_variant,,ENST00000615685,; A ENST00000379485 Transcript missense_variant 1409/5178 1174/2025 392/674 D/Y Gac/Tac 1 -1 KBTBD6 HGNC HGNC:25340 protein_coding YES CCDS9376.1 ENSP00000368799 Q86V97 UPI00001969BB NM_152903.4 deleterious(0) 1/1 hmmpanther:PTHR24412:SF132,hmmpanther:PTHR24412,Gene3D:1zgkA00,Superfamily_domains:0052715 MODERATE SNV 1 PASS rs1245106912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 41131338 41131338 C A 1 0 0 0 0 1 0 0 0 7913 826 29 2 2 KBTBD6 13 41131338 Missense_Mutation SNP C C3N-01415_T 8819793 41131338 73232990 383 24130 TEX30 0 . GRCh38 13 102768275 102768275 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.283G>T p.Gly95Cys p.G95C ENST00000376032 4/6 174 153 21 252 252 0 strelka-varscan-mutect TEX30,missense_variant,p.Gly54Cys,ENST00000376019,;TEX30,missense_variant,p.Gly95Cys,ENST00000376032,NM_138779.4;TEX30,missense_variant,p.Gly95Cys,ENST00000376027,;TEX30,missense_variant,p.Gly54Cys,ENST00000376021,NM_001286776.1;TEX30,missense_variant,p.Gly95Cys,ENST00000376029,NM_001286775.1;TEX30,missense_variant,p.Gly54Cys,ENST00000376022,;TEX30,downstream_gene_variant,,ENST00000487260,; A ENST00000376032 Transcript missense_variant 473/1165 283/684 95/227 G/C Ggt/Tgt 1 -1 TEX30 HGNC HGNC:25188 protein_coding YES CCDS9503.2 ENSP00000365200 Q5JUR7 A0A024RDZ1 UPI0000070F4A NM_138779.4 deleterious(0.01) 4/6 hmmpanther:PTHR13136,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs1260559320 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 102768275 102768275 C A 1 0 0 0 0 1 0 0 0 16209 681 24 2 2 TEX30 13 102768275 Missense_Mutation SNP C C3N-01415_T 61636937 102768275 11596053 384 24131 TEP1 0 . GRCh38 14 20368893 20368893 + Missense_Mutation SNP C C A rs772873649 C3N-01415_T C3N-01415_N C C c.7666G>T p.Gly2556Cys p.G2556C ENST00000262715 54/55 163 117 46 224 224 0 strelka-varscan-mutect TEP1,missense_variant,p.Gly2556Cys,ENST00000262715,NM_007110.4;TEP1,missense_variant,p.Gly2448Cys,ENST00000556935,;TEP1,downstream_gene_variant,,ENST00000553984,;TEP1,3_prime_UTR_variant,,ENST00000555727,;TEP1,3_prime_UTR_variant,,ENST00000553365,;TEP1,intron_variant,,ENST00000555008,;TEP1,downstream_gene_variant,,ENST00000557314,;TEP1,downstream_gene_variant,,ENST00000556488,;TEP1,downstream_gene_variant,,ENST00000471684,; A ENST00000262715 Transcript missense_variant 7707/10695 7666/7884 2556/2627 G/C Ggc/Tgc rs772873649 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 deleterious(0) 54/55 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF448,hmmpanther:PTHR22847,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs772873649 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 20368893 20368893 C A 1 0 0 0 0 1 0 0 0 16175 623 22 2 2 TEP1 14 20368893 Missense_Mutation SNP C C3N-01415_T 20368893 86674825 385 24132 INSM2 0 . GRCh38 14 35534853 35534853 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.601G>T p.Gly201Cys p.G201C ENST00000307169 1/1 78 71 7 101 101 0 strelka-varscan-mutect INSM2,missense_variant,p.Gly201Cys,ENST00000307169,NM_032594.3;RALGAPA1,downstream_gene_variant,,ENST00000637992,;RALGAPA1,downstream_gene_variant,,ENST00000307138,NM_194301.2;RALGAPA1,downstream_gene_variant,,ENST00000389698,NM_014990.1;RALGAPA1,downstream_gene_variant,,ENST00000382366,NM_001283043.1;RALGAPA1,downstream_gene_variant,,ENST00000554259,;RALGAPA1,downstream_gene_variant,,ENST00000554573,;RALGAPA1,downstream_gene_variant,,ENST00000556106,; T ENST00000307169 Transcript missense_variant 812/3013 601/1701 201/566 G/C Ggc/Tgc 1 1 INSM2 HGNC HGNC:17539 protein_coding YES CCDS9657.1 ENSP00000306523 Q96T92 UPI000013EBD6 NM_032594.3 deleterious(0.02) 1/1 hmmpanther:PTHR15065,hmmpanther:PTHR15065:SF6 MODERATE SNV 1 PASS rs1241978074 . 0 208 2 0 0 0 0 0 -15.63213 1 1 1 1 0 T 3 4 78 35534853 35534853 G T 1 0 0 0 0 1 0 0 0 7674 1116 39 1 1 INSM2 14 35534853 Missense_Mutation SNP G C3N-01415_T 15165960 35534853 71508865 386 24133 GPR65 0 . GRCh38 14 88010890 88010890 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.43T>C p.Tyr15His p.Y15H ENST00000267549 2/2 175 161 14 240 240 0 strelka-varscan-mutect GPR65,missense_variant,p.Tyr15His,ENST00000267549,NM_003608.3;RP11-300J18.2,non_coding_transcript_exon_variant,,ENST00000554433,; C ENST00000267549 Transcript missense_variant 601/4522 43/1014 15/337 Y/H Tat/Cat 1 1 GPR65 HGNC HGNC:4517 protein_coding YES CCDS9879.1 ENSP00000267549 Q8IYL9 B5B0C2 UPI000007422C NM_003608.3 tolerated(0.06) 2/2 Gene3D:1.20.1070.10,Prints_domain:PR01649,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF49,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 88010890 88010890 T C 1 0 0 0 0 1 0 0 0 6589 1522 53 5 5 GPR65 14 88010890 Missense_Mutation SNP T C3N-01415_T 52476037 88010890 19032828 387 24134 TTC7B 0 . GRCh38 14 90593627 90593627 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.1967-1G>T p.X656_splice ENST00000328459 40 29 11 51 51 0 strelka-varscan-mutect TTC7B,splice_acceptor_variant,,ENST00000328459,NM_001010854.1;TTC7B,splice_acceptor_variant,,ENST00000553972,;TTC7B,splice_acceptor_variant,,ENST00000557292,;TTC7B,splice_acceptor_variant,,ENST00000555894,;TTC7B,splice_acceptor_variant,,ENST00000554654,;TTC7B,splice_acceptor_variant,,ENST00000555005,;TTC7B,non_coding_transcript_exon_variant,,ENST00000557059,; A ENST00000328459 Transcript splice_acceptor_variant -/19458 1967/2532 656/843 1 -1 TTC7B HGNC HGNC:19858 protein_coding YES CCDS32140.1 ENSP00000336127 Q86TV6 UPI00001FD9F0 NM_001010854.1 17/19 HIGH 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 78 90593627 90593627 C A 1 0 0 0 0 0 0 1 0 17223 695 24 2 2 TTC7B 14 90593627 Splice_Site SNP C C3N-01415_T 2582737 90593627 16450091 388 24135 UNC79 0 . GRCh38 14 93577842 93577842 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.1681G>T p.Val561Leu p.V561L ENST00000256339 18/50 219 201 18 238 238 0 strelka-varscan-mutect UNC79,missense_variant,p.Val738Leu,ENST00000553484,;UNC79,missense_variant,p.Val738Leu,ENST00000555664,;UNC79,missense_variant,p.Val561Leu,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Val738Leu,ENST00000393151,;UNC79,missense_variant,p.Val561Leu,ENST00000621021,; T ENST00000256339 Transcript missense_variant,splice_region_variant 2336/8400 1681/7377 561/2458 V/L Gtg/Ttg COSM5292867,COSM5292868 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated(0.15) 18/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 93577842 93577842 G T 1 0 0 0 0 1 0 0 0 17520 1275 44 2 2 UNC79 14 93577842 Missense_Mutation SNP G C3N-01415_T 2984215 93577842 13465876 389 24136 SERPINA11 0 . GRCh38 14 94448400 94448400 + Silent SNP G G T rs769649474 C3N-01415_T C3N-01415_N G G c.375C>A p.= p.T125T ENST00000334708 2/5 385 348 37 416 415 1 strelka-varscan-mutect SERPINA11,synonymous_variant,p.=,ENST00000334708,NM_001080451.1;RP11-349I1.2,intron_variant,,ENST00000536735,; T ENST00000334708 Transcript synonymous_variant 440/1476 375/1269 125/422 T acC/acA rs769649474 1 -1 SERPINA11 HGNC HGNC:19193 protein_coding YES CCDS32149.1 ENSP00000335024 Q86U17 UPI000015DA3A NM_001080451.1 2/5 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF154,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS rs769649474 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 94448400 94448400 G T 1 0 0 0 0 0 0 0 1 14364 1219 43 2 2 SERPINA11 14 94448400 Silent SNP G C3N-01415_T 870558 94448400 12595318 390 24137 PAPOLA 0 . GRCh38 14 96535954 96535954 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.985G>T p.Val329Leu p.V329L ENST00000216277 11/22 108 93 15 145 145 0 strelka-varscan-mutect PAPOLA,missense_variant,p.Val329Leu,ENST00000216277,NM_032632.4,NM_001293627.1;PAPOLA,missense_variant,p.Val329Leu,ENST00000392990,;PAPOLA,missense_variant,p.Val79Leu,ENST00000555626,NM_001293632.1,NM_001293628.1;PAPOLA,downstream_gene_variant,,ENST00000557320,NM_001252006.1;PAPOLA,downstream_gene_variant,,ENST00000557471,NM_001252007.1;PAPOLA,downstream_gene_variant,,ENST00000553461,;RP11-872J21.5,upstream_gene_variant,,ENST00000618976,;PAPOLA,downstream_gene_variant,,ENST00000554130,;PAPOLA,3_prime_UTR_variant,,ENST00000553689,;PAPOLA,non_coding_transcript_exon_variant,,ENST00000555021,;PAPOLA,non_coding_transcript_exon_variant,,ENST00000555131,;PAPOLA,downstream_gene_variant,,ENST00000555912,;PAPOLA,downstream_gene_variant,,ENST00000553357,;PAPOLA,upstream_gene_variant,,ENST00000554666,;PAPOLA,downstream_gene_variant,,ENST00000555224,;PAPOLA,downstream_gene_variant,,ENST00000557406,; T ENST00000216277 Transcript missense_variant 1205/4519 985/2238 329/745 V/L Gtg/Ttg 1 1 PAPOLA HGNC HGNC:14981 protein_coding YES CCDS9946.1 ENSP00000216277 P51003 A0A024R6M3 UPI0000074269 NM_032632.4,NM_001293627.1 deleterious(0.02) 11/22 hmmpanther:PTHR10682:SF9,hmmpanther:PTHR10682,Pfam_domain:PF04928,PIRSF_domain:PIRSF018425,Gene3D:2q66A01,Superfamily_domains:SSF81631 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 96535954 96535954 G T 1 0 0 0 0 1 0 0 0 11509 1377 48 2 2 PAPOLA 14 96535954 Missense_Mutation SNP G C3N-01415_T 2087554 96535954 10507764 391 24138 TDRD9 0 . GRCh38 14 104042145 104042145 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.3932G>T p.Arg1311Ile p.R1311I ENST00000409874 34/36 143 109 34 145 145 0 strelka-varscan-mutect TDRD9,missense_variant,p.Arg1311Ile,ENST00000409874,NM_153046.2;TDRD9,missense_variant,p.Arg847Ile,ENST00000557332,;TDRD9,3_prime_UTR_variant,,ENST00000339063,; T ENST00000409874 Transcript missense_variant 3980/4782 3932/4149 1311/1382 R/I aGa/aTa 1 1 TDRD9 HGNC HGNC:20122 protein_coding YES CCDS9987.2 ENSP00000387303 Q8NDG6 UPI0001642306 NM_153046.2 tolerated(0.06) 34/36 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 104042145 104042145 G T 1 0 0 0 0 1 0 0 0 16146 942 33 2 2 TDRD9 14 104042145 Missense_Mutation SNP G C3N-01415_T 7506191 104042145 3001573 392 24139 KIF26A 0 . GRCh38 14 104152061 104152061 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.335G>T p.Gly112Val p.G112V ENST00000423312 3/15 710 532 178 683 680 3 strelka-varscan-mutect KIF26A,missense_variant,p.Gly112Val,ENST00000423312,NM_015656.1;KIF26A,5_prime_UTR_variant,,ENST00000315264,; T ENST00000423312 Transcript missense_variant 335/5649 335/5649 112/1882 G/V gGg/gTg 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 deleterious(0) 3/15 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 104152061 104152061 G T 1 0 0 0 0 1 0 0 0 8159 1232 43 2 2 KIF26A 14 104152061 Missense_Mutation SNP G C3N-01415_T 109916 104152061 2891657 393 24140 KIF26A 0 . GRCh38 14 104175304 104175304 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2516G>T p.Ser839Ile p.S839I ENST00000423312 12/15 307 277 30 325 325 0 strelka-varscan-mutect KIF26A,missense_variant,p.Ser700Ile,ENST00000315264,;KIF26A,missense_variant,p.Ser839Ile,ENST00000423312,NM_015656.1; T ENST00000423312 Transcript missense_variant 2516/5649 2516/5649 839/1882 S/I aGc/aTc 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 deleterious(0) 12/15 MODERATE 1 SNV 5 1 PASS rs1196175799 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 104175304 104175304 G T 1 0 0 0 0 1 0 0 0 8159 971 34 2 2 KIF26A 14 104175304 Missense_Mutation SNP G C3N-01415_T 23243 104175304 2868414 394 24141 KIF26A 0 . GRCh38 14 104177235 104177235 + Missense_Mutation SNP G G A rs775132075 C3N-01415_T C3N-01415_N G G c.4447G>A p.Gly1483Ser p.G1483S ENST00000423312 12/15 129 115 14 113 113 0 strelka-varscan-mutect KIF26A,missense_variant,p.Gly1344Ser,ENST00000315264,;KIF26A,missense_variant,p.Gly1483Ser,ENST00000423312,NM_015656.1; A ENST00000423312 Transcript missense_variant 4447/5649 4447/5649 1483/1882 G/S Ggc/Agc rs775132075,COSM1368485 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 tolerated(1) 12/15 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs775132075 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 104177235 104177235 G A 1 0 0 0 0 1 0 0 0 8159 1116 39 1 1 KIF26A 14 104177235 Missense_Mutation SNP G C3N-01415_T 1931 104177235 2866483 395 24142 AHNAK2 0 . GRCh38 14 104946532 104946532 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.8919C>T p.= p.A2973A ENST00000333244 7/7 627 575 52 683 683 0 varscan-mutect AHNAK2,synonymous_variant,p.=,ENST00000333244,NM_138420.2;AHNAK2,intron_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,; A ENST00000333244 Transcript synonymous_variant 9039/18254 8919/17388 2973/5795 A gcC/gcT 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 7/7 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF37 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 104946532 104946532 G A 1 0 0 0 0 0 0 0 1 492 1335 47 3 3 AHNAK2 14 104946532 Silent SNP G C3N-01415_T 769297 104946532 2097186 396 24143 GOLGA6L2 0 . GRCh38 15 23440703 23440703 + Missense_Mutation SNP C C A rs373079057 C3N-01415_T C3N-01415_N C C c.1772G>T p.Gly591Val p.G591V ENST00000567107 8/8 606 561 45 751 750 1 varscan-mutect GOLGA6L2,missense_variant,p.Gly591Val,ENST00000567107,NM_001304388.1;GOLGA6L2,intron_variant,,ENST00000345070,;GOLGA6L2,intron_variant,,ENST00000312015,;GOLGA6L2,3_prime_UTR_variant,,ENST00000566571,; A ENST00000567107 Transcript missense_variant 1825/3030 1772/2730 591/909 G/V gGa/gTa rs373079057 1 -1 GOLGA6L2 HGNC HGNC:26695 protein_coding YES CCDS76728.1 ENSP00000454407 H3BMJ4 UPI00024672CE NM_001304388.1 deleterious_low_confidence(0.01) 8/8 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 23440703 23440703 C A 1 0 0 0 0 1 0 0 0 6440 855 30 2 2 GOLGA6L2 15 23440703 Missense_Mutation SNP C C3N-01415_T 23440703 78550486 397 24144 GJD2 0 . GRCh38 15 34753025 34753025 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.419G>T p.Arg140Leu p.R140L ENST00000290374 2/2 232 202 30 375 373 2 strelka-varscan-mutect GJD2,missense_variant,p.Arg140Leu,ENST00000290374,NM_020660.2;RP11-814P5.1,upstream_gene_variant,,ENST00000503496,;RP11-814P5.1,upstream_gene_variant,,ENST00000558707,; A ENST00000290374 Transcript missense_variant 896/2889 419/966 140/321 R/L cGa/cTa 1 -1 GJD2 HGNC HGNC:19154 protein_coding YES CCDS10040.1 ENSP00000290374 Q9UKL4 UPI00001287E3 NM_020660.2 tolerated(0.16) 2/2 Pfam_domain:PF00029 MODERATE 1 SNV 1 1 PASS rs969962661 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 34753025 34753025 C A 1 0 0 0 0 1 0 0 0 6294 884 31 1 1 GJD2 15 34753025 Missense_Mutation SNP C C3N-01415_T 11312322 34753025 67238164 398 24145 LTK 0 . GRCh38 15 41507626 41507626 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.1281G>T p.= p.L427L ENST00000263800 10/20 191 171 20 235 235 0 strelka-varscan-mutect LTK,synonymous_variant,p.=,ENST00000263800,NM_002344.5;LTK,synonymous_variant,p.=,ENST00000355166,NM_206961.3;LTK,synonymous_variant,p.=,ENST00000453182,NM_001135685.1;LTK,synonymous_variant,p.=,ENST00000561619,;ITPKA,downstream_gene_variant,,ENST00000260386,NM_002220.2;LTK,non_coding_transcript_exon_variant,,ENST00000563518,;LTK,intron_variant,,ENST00000569283,;ITPKA,downstream_gene_variant,,ENST00000462816,;ITPKA,downstream_gene_variant,,ENST00000491007,; A ENST00000263800 Transcript synonymous_variant 1378/3046 1281/2595 427/864 L ctG/ctT 1 -1 LTK HGNC HGNC:6721 protein_coding YES CCDS10077.1 ENSP00000263800 P29376 UPI000013D463 NM_002344.5 10/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF294 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 41507626 41507626 C A 1 0 0 0 0 0 0 0 1 8986 813 29 2 2 LTK 15 41507626 Silent SNP C C3N-01415_T 6754601 41507626 60483563 399 24146 ZNF106 0 . GRCh38 15 42442277 42442278 + Frame_Shift_Ins INS - - CT novel C3N-01415_T C3N-01415_N - - c.3489_3490insAG p.Ser1165LeufsTer15 p.S1165Lfs*15 ENST00000263805 7/19 331 301 30 466 466 0 varindel-pindel ZNF106,frameshift_variant,p.Ser1165LeufsTer15,ENST00000263805,NM_022473.2;ZNF106,frameshift_variant,p.Ser393LeufsTer15,ENST00000565380,NM_001284307.1;ZNF106,frameshift_variant,p.Ser350LeufsTer15,ENST00000565611,NM_001284306.1;ZNF106,frameshift_variant,p.Ser219LeufsTer15,ENST00000565500,;ZNF106,frameshift_variant,p.Ser123LeufsTer15,ENST00000567772,;ZNF106,downstream_gene_variant,,ENST00000565948,; CT ENST00000263805 Transcript frameshift_variant 3816-3817/10460 3489-3490/5652 1163-1164/1883 -/X -/AG 1 -1 ZNF106 HGNC HGNC:12886 protein_coding YES CCDS32208.1 ENSP00000263805 Q9H2Y7 UPI000006D6CC NM_022473.2 7/19 hmmpanther:PTHR14435 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 CT 7 5 78 42442277 42442277 - CT 1 0 1 1 0 0 0 0 0 18294 333 12 0 0 ZNF106 15 42442277 Frame_Shift_Ins INS - C3N-01415_T 934651 42442277 59548912 400 24147 TGM5 0 . GRCh38 15 43235684 43235684 + Missense_Mutation SNP C C A rs768303078 C3N-01415_T C3N-01415_N C C c.1499G>T p.Arg500Leu p.R500L ENST00000220420 10/13 354 301 53 419 418 1 strelka-varscan-mutect TGM5,missense_variant,p.Arg500Leu,ENST00000220420,NM_201631.3;TGM5,missense_variant,p.Arg499Leu,ENST00000610827,;TGM5,missense_variant,p.Arg417Leu,ENST00000611276,;TGM5,missense_variant,p.Arg501Leu,ENST00000622115,;TGM5,missense_variant,p.Arg418Leu,ENST00000349114,NM_004245.3;TGM5,non_coding_transcript_exon_variant,,ENST00000396996,;TGM5,downstream_gene_variant,,ENST00000635871,;TGM5,downstream_gene_variant,,ENST00000563838,; A ENST00000220420 Transcript missense_variant 1507/2767 1499/2163 500/720 R/L cGa/cTa rs768303078 1 -1 TGM5 HGNC HGNC:11781 protein_coding YES CCDS32212.1 ENSP00000220420 O43548 UPI0000136CCF NM_201631.3 deleterious(0.04) 10/13 PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF38 MODERATE 1 SNV 1 1 PASS rs768303078 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 43235684 43235684 C A 1 0 0 0 0 1 0 0 0 16266 884 31 1 1 TGM5 15 43235684 Missense_Mutation SNP C C3N-01415_T 793407 43235684 58755505 401 24148 TGM5 0 . GRCh38 15 43253549 43253549 + Missense_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.641T>G p.Leu214Arg p.L214R ENST00000220420 5/13 451 396 55 550 546 4 strelka-varscan-mutect TGM5,missense_variant,p.Leu214Arg,ENST00000220420,NM_201631.3;TGM5,missense_variant,p.Leu213Arg,ENST00000610827,;TGM5,missense_variant,p.Leu131Arg,ENST00000611276,;TGM5,missense_variant,p.Leu215Arg,ENST00000622115,;TGM5,missense_variant,p.Leu132Arg,ENST00000349114,NM_004245.3;TGM5,non_coding_transcript_exon_variant,,ENST00000635871,; C ENST00000220420 Transcript missense_variant 649/2767 641/2163 214/720 L/R cTg/cGg 1 -1 TGM5 HGNC HGNC:11781 protein_coding YES CCDS32212.1 ENSP00000220420 O43548 UPI0000136CCF NM_201631.3 tolerated(0.94) 5/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF38,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs606231277 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 43253549 43253549 A C 1 0 0 0 0 1 0 0 0 16266 188 7 5 5 TGM5 15 43253549 Missense_Mutation SNP A C3N-01415_T 17865 43253549 58737640 402 24149 STRC 0 . GRCh38 15 43600611 43600611 + Missense_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.4916T>G p.Leu1639Arg p.L1639R ENST00000450892 26/29 451 401 50 527 527 0 strelka-varscan-mutect STRC,missense_variant,p.Leu1639Arg,ENST00000450892,NM_153700.2;STRC,missense_variant,p.Leu866Arg,ENST00000541030,;CKMT1B,downstream_gene_variant,,ENST00000300283,NM_020990.3;CKMT1B,downstream_gene_variant,,ENST00000441322,;CKMT1B,downstream_gene_variant,,ENST00000453782,;CKMT1B,downstream_gene_variant,,ENST00000627381,;CKMT1B,downstream_gene_variant,,ENST00000453733,;RNU6-554P,upstream_gene_variant,,ENST00000410466,;CKMT1B,intron_variant,,ENST00000411560,;CKMT1B,downstream_gene_variant,,ENST00000498538,;STRC,3_prime_UTR_variant,,ENST00000428650,;STRC,3_prime_UTR_variant,,ENST00000440125,;STRC,non_coding_transcript_exon_variant,,ENST00000485556,;STRC,non_coding_transcript_exon_variant,,ENST00000471703,;STRC,non_coding_transcript_exon_variant,,ENST00000448437,;STRC,non_coding_transcript_exon_variant,,ENST00000460952,;CKMT1B,downstream_gene_variant,,ENST00000437534,;STRC,downstream_gene_variant,,ENST00000455136,;CKMT1B,downstream_gene_variant,,ENST00000428981,;STRC,downstream_gene_variant,,ENST00000493750,; C ENST00000450892 Transcript missense_variant 4994/5680 4916/5328 1639/1775 L/R cTa/cGa 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 tolerated(0.56) 26/29 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF14 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 43600611 43600611 A C 1 0 0 0 0 1 0 0 0 15709 420 15 5 5 STRC 15 43600611 Missense_Mutation SNP A C3N-01415_T 347062 43600611 58390578 403 24150 NEDD4 0 . GRCh38 15 55860553 55860553 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.2071G>A p.Asp691Asn p.D691N ENST00000508342 7/25 135 117 18 216 216 0 strelka-varscan-mutect NEDD4,missense_variant,p.Asp691Asn,ENST00000508342,NM_001284338.1;NEDD4,missense_variant,p.Asp619Asn,ENST00000338963,NM_198400.3;NEDD4,missense_variant,p.Asp675Asn,ENST00000506154,NM_001284339.1;NEDD4,missense_variant,p.Asp272Asn,ENST00000435532,NM_006154.3;NEDD4,missense_variant,p.Asp282Asn,ENST00000508871,NM_001284340.1;NEDD4,downstream_gene_variant,,ENST00000514893,;NEDD4,3_prime_UTR_variant,,ENST00000503468,;NEDD4,downstream_gene_variant,,ENST00000502612,;NEDD4,downstream_gene_variant,,ENST00000507063,; T ENST00000508342 Transcript missense_variant 2371/7235 2071/3960 691/1319 D/N Gat/Aat 1 -1 NEDD4 HGNC HGNC:7727 protein_coding YES CCDS61644.1 ENSP00000424827 P46934 UPI00001FE52D NM_001284338.1 deleterious(0) 7/25 hmmpanther:PTHR11254:SF282,hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 55860553 55860553 C T 1 0 0 0 0 1 0 0 0 10338 913 32 3 3 NEDD4 15 55860553 Missense_Mutation SNP C C3N-01415_T 12259942 55860553 46130636 404 24151 VPS13C 0 . GRCh38 15 61951917 61951917 + Silent SNP G G A rs769215114 C3N-01415_T C3N-01415_N G G c.4363C>T p.= p.L1455L ENST00000261517 39/85 200 182 18 296 295 1 strelka-varscan-mutect VPS13C,synonymous_variant,p.=,ENST00000395896,NM_001018088.2;VPS13C,synonymous_variant,p.=,ENST00000261517,NM_020821.2;VPS13C,synonymous_variant,p.=,ENST00000249837,NM_017684.4;VPS13C,synonymous_variant,p.=,ENST00000395898,NM_018080.3;VPS13C,non_coding_transcript_exon_variant,,ENST00000558088,; A ENST00000261517 Transcript synonymous_variant 4437/13400 4363/11262 1455/3753 L Ctg/Ttg rs769215114 1 -1 VPS13C HGNC HGNC:23594 protein_coding YES CCDS32257.1 ENSP00000261517 Q709C8 UPI000023B7D3 NM_020821.2 39/85 hmmpanther:PTHR16166,hmmpanther:PTHR16166:SF69 LOW 1 SNV 1 1 PASS rs769215114 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 61951917 61951917 G A 1 0 0 0 0 0 0 0 1 17738 991 35 3 3 VPS13C 15 61951917 Silent SNP G C3N-01415_T 6091364 61951917 40039272 405 24152 STRA6 0 . GRCh38 15 74182205 74182205 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1593G>T p.Trp531Cys p.W531C ENST00000563965 16/19 590 525 65 708 707 1 strelka-varscan-mutect STRA6,missense_variant,p.Trp492Cys,ENST00000323940,NM_001142617.1;STRA6,missense_variant,p.Trp492Cys,ENST00000616000,NM_001142618.1;STRA6,missense_variant,p.Trp492Cys,ENST00000395105,NM_022369.3;STRA6,missense_variant,p.Trp483Cys,ENST00000423167,NM_001142619.1;STRA6,missense_variant,p.Trp484Cys,ENST00000416286,;STRA6,missense_variant,p.Trp492Cys,ENST00000449139,;STRA6,missense_variant,p.Trp529Cys,ENST00000535552,NM_001199040.1;STRA6,missense_variant,p.Trp531Cys,ENST00000563965,NM_001199042.1;STRA6,missense_variant,p.Trp507Cys,ENST00000574278,NM_001199041.1;STRA6,missense_variant,p.Trp111Cys,ENST00000572785,;RP11-665J16.1,upstream_gene_variant,,ENST00000561647,;STRA6,non_coding_transcript_exon_variant,,ENST00000574439,;STRA6,non_coding_transcript_exon_variant,,ENST00000545137,;STRA6,downstream_gene_variant,,ENST00000569936,;STRA6,downstream_gene_variant,,ENST00000575272,; A ENST00000563965 Transcript missense_variant 1932/2565 1593/2121 531/706 W/C tgG/tgT 1 -1 STRA6 HGNC HGNC:30650 protein_coding YES CCDS55973.1 ENSP00000456609 Q9BX79 UPI00015F460B NM_001199042.1 deleterious(0.02) 16/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR21444:SF16,hmmpanther:PTHR21444,Pfam_domain:PF14752 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 74182205 74182205 C A 1 0 0 0 0 1 0 0 0 15703 624 22 2 2 STRA6 15 74182205 Missense_Mutation SNP C C3N-01415_T 12230288 74182205 27808984 406 24153 TICRR 0 . GRCh38 15 89575806 89575806 + Nonsense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.220G>T p.Glu74Ter p.E74* ENST00000268138 1/22 310 277 33 364 364 0 strelka-varscan-mutect TICRR,stop_gained,p.Glu74Ter,ENST00000268138,NM_152259.3;TICRR,stop_gained,p.Glu74Ter,ENST00000560985,NM_001308025.1;RP11-429B14.1,intron_variant,,ENST00000559041,;RP11-429B14.3,downstream_gene_variant,,ENST00000560477,; T ENST00000268138 Transcript stop_gained 325/6775 220/5733 74/1910 E/* Gag/Tag 1 1 TICRR HGNC HGNC:28704 protein_coding YES CCDS10352.2 ENSP00000268138 Q7Z2Z1 UPI0000D61399 NM_152259.3 1/22 Low_complexity_(Seg):seg,hmmpanther:PTHR21556 HIGH SNV 5 1 PASS rs1364894231 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 89575806 89575806 G T 1 0 0 0 0 0 1 0 0 16328 1175 41 2 2 TICRR 15 89575806 Nonsense_Mutation SNP G C3N-01415_T 15393601 89575806 12415383 407 24154 PCSK6 0 . GRCh38 15 101313441 101313441 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.2634G>T p.= p.V878V ENST00000611716 20/22 240 210 30 250 250 0 strelka-varscan-mutect PCSK6,synonymous_variant,p.=,ENST00000611716,NM_002570.4;PCSK6,synonymous_variant,p.=,ENST00000618548,NM_138319.3;PCSK6,synonymous_variant,p.=,ENST00000398185,NM_001291309.1;PCSK6,synonymous_variant,p.=,ENST00000622483,;PCSK6,synonymous_variant,p.=,ENST00000619160,;PCSK6,synonymous_variant,p.=,ENST00000632686,;PCSK6,intron_variant,,ENST00000558951,;PCSK6,upstream_gene_variant,,ENST00000558864,;PCSK6,non_coding_transcript_exon_variant,,ENST00000557794,;PCSK6,non_coding_transcript_exon_variant,,ENST00000558433,;PCSK6,upstream_gene_variant,,ENST00000559430,;PCSK6,non_coding_transcript_exon_variant,,ENST00000560785,;PCSK6,upstream_gene_variant,,ENST00000559499,; A ENST00000611716 Transcript synonymous_variant 2803/4409 2634/2910 878/969 V gtG/gtT 1 -1 PCSK6 HGNC HGNC:8569 protein_coding YES CCDS73790.1 ENSP00000482760 P29122 UPI00001311D0 NM_002570.4 20/22 hmmpanther:PTHR10795:SF345,hmmpanther:PTHR10795,Gene3D:2.10.220.10,SMART_domains:SM00181,SMART_domains:SM00261,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 101313441 101313441 C A 1 0 0 0 0 0 0 0 1 11692 697 25 2 2 PCSK6 15 101313441 Silent SNP C C3N-01415_T 11737635 101313441 677748 408 24155 SSTR5 0 . GRCh38 16 1079124 1079124 + Missense_Mutation SNP G G C rs771072236 C3N-01415_T C3N-01415_N G G c.256G>C p.Asp86His p.D86H ENST00000293897 1/1 824 672 152 685 685 0 strelka-varscan-mutect SSTR5,missense_variant,p.Asp86His,ENST00000293897,NM_001172560.1,NM_001053.3;SSTR5-AS1,upstream_gene_variant,,ENST00000569832,;SSTR5-AS1,upstream_gene_variant,,ENST00000566499,;SSTR5-AS1,upstream_gene_variant,,ENST00000624643,; C ENST00000293897 Transcript missense_variant 344/1362 256/1095 86/364 D/H Gac/Cac rs771072236 1 1 SSTR5 HGNC HGNC:11334 protein_coding YES CCDS10429.1 ENSP00000293897 P35346 UPI00000015DC NM_001172560.1,NM_001053.3 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF20,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs771072236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 1079124 1079124 G C 1 0 0 0 0 1 0 0 0 15578 1058 37 4 4 SSTR5 16 1079124 Missense_Mutation SNP G C3N-01415_T 1079124 89259221 409 24156 ZNF597 0 . GRCh38 16 3436906 3436906 + Nonsense_Mutation SNP C C A rs143250831 C3N-01415_T C3N-01415_N C C c.793G>T p.Glu265Ter p.E265* ENST00000301744 4/4 293 275 18 303 303 0 strelka-varscan-mutect ZNF597,stop_gained,p.Glu265Ter,ENST00000301744,NM_152457.2;LA16c-306E5.2,intron_variant,,ENST00000575785,; A ENST00000301744 Transcript stop_gained 1029/5513 793/1275 265/424 E/* Gaa/Taa rs143250831 1 -1 ZNF597 HGNC HGNC:26573 protein_coding YES CCDS10505.1 ENSP00000301744 Q96LX8 UPI0000070B73 NM_152457.2 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF219,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS rs143250831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 3436906 3436906 C A 1 0 0 0 0 0 1 0 0 18602 835 29 2 2 ZNF597 16 3436906 Nonsense_Mutation SNP C C3N-01415_T 2357782 3436906 86901439 410 24157 XYLT1 0 . GRCh38 16 17127759 17127759 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.2130C>A p.Ser710Arg p.S710R ENST00000261381 10/12 505 476 29 391 387 4 strelka-varscan-mutect XYLT1,missense_variant,p.Ser710Arg,ENST00000261381,NM_022166.3; T ENST00000261381 Transcript missense_variant 2215/9891 2130/2880 710/959 S/R agC/agA 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 tolerated(0.52) 10/12 hmmpanther:PTHR19297:SF91,hmmpanther:PTHR19297,Pfam_domain:PF12529 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 17127759 17127759 G T 1 0 0 0 0 1 0 0 0 18022 1310 46 2 2 XYLT1 16 17127759 Missense_Mutation SNP G C3N-01415_T 13690853 17127759 73210586 411 24158 XYLT1 0 . GRCh38 16 17134693 17134693 + Missense_Mutation SNP C C A rs187270026 C3N-01415_T C3N-01415_N C C c.1807G>T p.Val603Leu p.V603L ENST00000261381 9/12 328 304 24 292 292 0 strelka-varscan-mutect XYLT1,missense_variant,p.Val603Leu,ENST00000261381,NM_022166.3;CTD-2576D5.4,intron_variant,,ENST00000567344,; A ENST00000261381 Transcript missense_variant 1892/9891 1807/2880 603/959 V/L Gtg/Ttg rs187270026 1 -1 XYLT1 HGNC HGNC:15516 protein_coding YES CCDS10569.1 ENSP00000261381 Q86Y38 UPI000000DCCE NM_022166.3 tolerated(0.28) 9/12 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF91 MODERATE 1 SNV 1 1 PASS rs187270026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 17134693 17134693 C A 1 0 0 0 0 1 0 0 0 18022 536 19 1 1 XYLT1 16 17134693 Missense_Mutation SNP C C3N-01415_T 6934 17134693 73203652 412 24159 SMG1 0 . GRCh38 16 18896138 18896138 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.326G>T p.Arg109Met p.R109M ENST00000446231 3/63 366 269 97 341 339 2 strelka-varscan-mutect SMG1,missense_variant,p.Arg109Met,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Arg83Met,ENST00000565224,;SMG1,missense_variant,p.Arg83Met,ENST00000532700,;SMG1,5_prime_UTR_variant,,ENST00000569122,;SMG1,intron_variant,,ENST00000565324,;SMG1,intron_variant,,ENST00000561947,;SMG1,intron_variant,,ENST00000330588,;SMG1,downstream_gene_variant,,ENST00000563836,; A ENST00000446231 Transcript missense_variant 739/16115 326/10986 109/3661 R/M aGg/aTg 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 deleterious_low_confidence(0) 3/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF71 MODERATE 1 SNV 1 1 PASS rs1285650069 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 18896138 18896138 C A 1 0 0 0 0 1 0 0 0 15089 681 24 2 2 SMG1 16 18896138 Missense_Mutation SNP C C3N-01415_T 1761445 18896138 71442207 413 24160 UMOD 0 . GRCh38 16 20337367 20337367 + Missense_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.1763T>G p.Phe588Cys p.F588C ENST00000396134 9/12 481 440 41 382 382 0 strelka-varscan-mutect UMOD,missense_variant,p.Phe555Cys,ENST00000302509,NM_001008389.2,NM_003361.3;UMOD,missense_variant,p.Phe588Cys,ENST00000396134,NM_001278614.1;UMOD,missense_variant,p.Phe604Cys,ENST00000396138,;UMOD,missense_variant,p.Phe555Cys,ENST00000570689,;UMOD,non_coding_transcript_exon_variant,,ENST00000570331,; C ENST00000396134 Transcript missense_variant 1887/2408 1763/2022 588/673 F/C tTt/tGt 1 -1 UMOD HGNC HGNC:12559 protein_coding YES CCDS61876.1 ENSP00000379438 P07911 UPI000059D336 NM_001278614.1 deleterious(0) 9/12 PROSITE_profiles:PS51034,hmmpanther:PTHR24044:SF263,hmmpanther:PTHR24044,Pfam_domain:PF00100,SMART_domains:SM00241 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 20337367 20337367 A C 1 0 0 0 0 1 0 0 0 17503 14 1 5 5 UMOD 16 20337367 Missense_Mutation SNP A C3N-01415_T 1441229 20337367 70000978 414 24161 EEF2K 0 . GRCh38 16 22264876 22264876 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1436G>A p.Gly479Glu p.G479E ENST00000263026 13/18 248 225 23 166 166 0 strelka-varscan-mutect EEF2K,missense_variant,p.Gly479Glu,ENST00000263026,NM_013302.3;EEF2K,3_prime_UTR_variant,,ENST00000568269,;EEF2K,downstream_gene_variant,,ENST00000563555,; A ENST00000263026 Transcript missense_variant 1910/7388 1436/2178 479/725 G/E gGa/gAa 1 1 EEF2K HGNC HGNC:24615 protein_coding YES CCDS10604.1 ENSP00000263026 O00418 UPI000013D387 NM_013302.3 tolerated(0.71) 13/18 hmmpanther:PTHR14187,PIRSF_domain:PIRSF038139 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 78 22264876 22264876 G A 1 0 0 0 0 1 0 0 0 4760 1188 41 3 3 EEF2K 16 22264876 Missense_Mutation SNP G C3N-01415_T 1927509 22264876 68073469 415 24162 SCNN1B 0 . GRCh38 16 23355329 23355329 + Missense_Mutation SNP C C T rs756809433 C3N-01415_T C3N-01415_N C C c.616C>T p.Arg206Trp p.R206W ENST00000343070 4/13 850 668 182 632 632 0 strelka-varscan-mutect SCNN1B,missense_variant,p.Arg206Trp,ENST00000343070,NM_000336.2;SCNN1B,missense_variant,p.Arg251Trp,ENST00000307331,;SCNN1B,missense_variant,p.Arg206Trp,ENST00000568085,;SCNN1B,intron_variant,,ENST00000568923,;SCNN1B,upstream_gene_variant,,ENST00000566441,;SCNN1B,downstream_gene_variant,,ENST00000569789,;SCNN1B,upstream_gene_variant,,ENST00000566647,;SCNN1B,missense_variant,p.Arg206Trp,ENST00000564275,;SCNN1B,downstream_gene_variant,,ENST00000566870,; T ENST00000343070 Transcript missense_variant 792/2597 616/1923 206/640 R/W Cgg/Tgg rs756809433 1 1 SCNN1B HGNC HGNC:10600 protein_coding YES CCDS10609.1 ENSP00000345751 P51168 B2R812 UPI0000135616 NM_000336.2 tolerated(0.12) 4/13 Pfam_domain:PF00858,hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF18,TIGRFAM_domain:TIGR00859 MODERATE 1 SNV 1 1 PASS rs756809433 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 23355329 23355329 C T 1 0 0 0 0 1 0 0 0 14197 643 23 1 1 SCNN1B 16 23355329 Missense_Mutation SNP C C3N-01415_T 1090453 23355329 66983016 416 24163 PALB2 0 . GRCh38 16 23630090 23630090 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.2064C>T p.= p.N688N ENST00000261584 5/13 509 472 37 473 472 1 strelka-varscan-mutect PALB2,synonymous_variant,p.=,ENST00000261584,NM_024675.3;PALB2,synonymous_variant,p.=,ENST00000568219,;PALB2,intron_variant,,ENST00000565038,; A ENST00000261584 Transcript synonymous_variant 2217/4003 2064/3561 688/1186 N aaC/aaT 1 -1 PALB2 HGNC HGNC:26144 protein_coding YES CCDS32406.1 ENSP00000261584 Q86YC2 UPI000000DA86 NM_024675.3 5/13 hmmpanther:PTHR14662,hmmpanther:PTHR14662:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 23630090 23630090 G A 1 0 0 0 0 0 0 0 1 11485 1020 36 3 3 PALB2 16 23630090 Silent SNP G C3N-01415_T 274761 23630090 66708255 417 24164 CD2BP2 0 . GRCh38 16 30353735 30353735 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.441G>C p.Leu147Phe p.L147F ENST00000305596 5/7 189 176 13 159 159 0 strelka-varscan-mutect CD2BP2,missense_variant,p.Leu147Phe,ENST00000305596,NM_006110.2;CD2BP2,missense_variant,p.Leu147Phe,ENST00000569466,NM_001243646.1;TBC1D10B,downstream_gene_variant,,ENST00000409939,NM_015527.3;TBC1D10B,downstream_gene_variant,,ENST00000490703,;RP11-347C12.10,upstream_gene_variant,,ENST00000563252,;TBC1D10B,downstream_gene_variant,,ENST00000478158,;TBC1D10B,downstream_gene_variant,,ENST00000475650,;CD2BP2,downstream_gene_variant,,ENST00000564525,; G ENST00000305596 Transcript missense_variant 617/3421 441/1026 147/341 L/F ttG/ttC 1 -1 CD2BP2 HGNC HGNC:1656 protein_coding YES CCDS10675.1 ENSP00000304903 O95400 A0A024QZC1 UPI000006D625 NM_006110.2 tolerated(0.7) 5/7 hmmpanther:PTHR13138,hmmpanther:PTHR13138:SF3 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.99961 1 1 1 1 0 G 3 3 78 30353735 30353735 C G 1 0 0 0 0 1 0 0 0 2699 593 21 4 4 CD2BP2 16 30353735 Missense_Mutation SNP C C3N-01415_T 6723645 30353735 59984610 418 24165 ZNF48 0 . GRCh38 16 30398315 30398315 + Silent SNP C C T rs143156281 C3N-01415_T C3N-01415_N C C c.1065C>T p.= p.G355G ENST00000613509 3/3 343 323 20 267 266 1 strelka-varscan-mutect ZNF48,synonymous_variant,p.=,ENST00000613509,NM_001214906.1,NM_001214909.1;ZNF48,synonymous_variant,p.=,ENST00000320159,NM_152652.2;ZNF48,synonymous_variant,p.=,ENST00000622647,NM_001214907.1;ZNF48,downstream_gene_variant,,ENST00000524644,;ZNF48,downstream_gene_variant,,ENST00000528032,;ZNF48,downstream_gene_variant,,ENST00000495929,;SEPT1,upstream_gene_variant,,ENST00000570039,;SEPT1,upstream_gene_variant,,ENST00000567783,; T ENST00000613509 Transcript synonymous_variant 1547/3339 1065/1857 355/618 G ggC/ggT rs143156281,COSM969829 1 1 ZNF48 HGNC HGNC:13114 protein_coding YES CCDS10679.1 ENSP00000480262 Q96MX3 UPI000013E982 NM_001214906.1,NM_001214909.1 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF199,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 0,1 LOW 1 SNV 2 0,1 1 PASS rs143156281 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 30398315 30398315 C T 1 0 0 0 0 0 0 0 1 18506 755 27 1 1 ZNF48 16 30398315 Silent SNP C C3N-01415_T 44580 30398315 59940030 419 24166 ZNF423 0 . GRCh38 16 49525374 49525374 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.3698T>A p.Val1233Glu p.V1233E ENST00000561648 7/9 147 125 22 132 132 0 strelka-varscan-mutect ZNF423,missense_variant,p.Val1233Glu,ENST00000561648,;ZNF423,missense_variant,p.Val1173Glu,ENST00000563137,;ZNF423,missense_variant,p.Val1233Glu,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Val1173Glu,ENST00000562871,;ZNF423,missense_variant,p.Val1116Glu,ENST00000535559,;ZNF423,missense_variant,p.Val1173Glu,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Val1116Glu,ENST00000567169,; T ENST00000561648 Transcript missense_variant 3999/7907 3698/3855 1233/1284 V/E gTg/gAg 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC deleterious(0) 7/9 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 49525374 49525374 A T 1 0 0 0 0 1 0 0 0 18470 159 6 4 4 ZNF423 16 49525374 Missense_Mutation SNP A C3N-01415_T 19127059 49525374 40812971 420 24167 DDX19B 0 . GRCh38 16 70317505 70317505 + Missense_Mutation SNP G G T rs143996882 C3N-01415_T C3N-01415_N G G c.306G>T p.Gln102His p.Q102H ENST00000288071 5/12 161 101 60 215 215 0 strelka-varscan-mutect DDX19B,missense_variant,p.Gln102His,ENST00000288071,NM_007242.5;DDX19B,missense_variant,p.Gln107His,ENST00000563206,;RP11-529K1.3,missense_variant,p.Gln102His,ENST00000567706,;DDX19B,missense_variant,p.Gln89His,ENST00000566216,;DDX19B,5_prime_UTR_variant,,ENST00000563392,NM_001257174.1;DDX19B,5_prime_UTR_variant,,ENST00000393657,NM_001257175.1,NM_001014449.2;DDX19B,5_prime_UTR_variant,,ENST00000568625,NM_001257173.1;RP11-529K1.3,intron_variant,,ENST00000443119,;DDX19B,intron_variant,,ENST00000355992,NM_001014451.2;DDX19B,intron_variant,,ENST00000451014,NM_001257172.1;RP11-529K1.2,intron_variant,,ENST00000562077,;DDX19B,non_coding_transcript_exon_variant,,ENST00000570055,;DDX19B,non_coding_transcript_exon_variant,,ENST00000569099,;DDX19B,3_prime_UTR_variant,,ENST00000568460,;DDX19B,3_prime_UTR_variant,,ENST00000562912,;DDX19B,non_coding_transcript_exon_variant,,ENST00000569224,;DDX19B,intron_variant,,ENST00000562519,;DDX19B,intron_variant,,ENST00000568408,;DDX19B,intron_variant,,ENST00000568008,;RP11-529K1.3,intron_variant,,ENST00000565116,; T ENST00000288071 Transcript missense_variant 551/3386 306/1440 102/479 Q/H caG/caT rs143996882 1 1 DDX19B HGNC HGNC:2742 protein_coding YES CCDS10888.1 ENSP00000288071 Q9UMR2 A0A0U4B4U6 UPI000012907F NM_007242.5 deleterious(0) 5/12 Gene3D:3.40.50.300,PROSITE_profiles:PS51195,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF323 MODERATE 1 SNV 1 1 PASS rs143996882 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 70317505 70317505 G T 1 0 0 0 0 1 0 0 0 4150 962 34 2 2 DDX19B 16 70317505 Missense_Mutation SNP G C3N-01415_T 20792131 70317505 20020840 421 24168 CDH13 0 . GRCh38 16 82627083 82627083 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.26G>A p.Ser9Asn p.S9N ENST00000268613 1/15 525 463 62 543 543 0 strelka-varscan-mutect CDH13,missense_variant,p.Ser9Asn,ENST00000268613,NM_001220488.1;CDH13,5_prime_UTR_variant,,ENST00000567109,NM_001220490.1,NM_001257.4;CDH13,5_prime_UTR_variant,,ENST00000428848,NM_001220489.1;CDH13,5_prime_UTR_variant,,ENST00000567445,;CDH13,5_prime_UTR_variant,,ENST00000431540,NM_001220491.1;CDH13,5_prime_UTR_variant,,ENST00000565636,NM_001220492.1;CDH13,non_coding_transcript_exon_variant,,ENST00000569455,;CDH13,5_prime_UTR_variant,,ENST00000539548,;CDH13,5_prime_UTR_variant,,ENST00000568770,;CDH13,5_prime_UTR_variant,,ENST00000569144,;CDH13,5_prime_UTR_variant,,ENST00000562601,;CDH13,non_coding_transcript_exon_variant,,ENST00000566333,; A ENST00000268613 Transcript missense_variant 119/2722 26/2283 9/760 S/N aGt/aAt 1 1 CDH13 HGNC HGNC:1753 protein_coding YES CCDS58485.1 ENSP00000268613 P55290 UPI00020E71A6 NM_001220488.1 deleterious_low_confidence(0) 1/15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 82627083 82627083 G A 1 0 0 0 0 1 0 0 0 2802 1029 36 3 3 CDH13 16 82627083 Missense_Mutation SNP G C3N-01415_T 12309578 82627083 7711262 422 24169 IRF8 0 . GRCh38 16 85914475 85914475 + Missense_Mutation SNP G G T rs767204633 C3N-01415_T C3N-01415_N G G c.556G>T p.Val186Leu p.V186L ENST00000268638 6/9 531 482 49 535 535 0 strelka-varscan-mutect IRF8,missense_variant,p.Val186Leu,ENST00000268638,NM_002163.2;IRF8,missense_variant,p.Val186Leu,ENST00000564803,;IRF8,splice_region_variant,,ENST00000562492,;IRF8,splice_region_variant,,ENST00000569145,;IRF8,5_prime_UTR_variant,,ENST00000569607,;IRF8,intron_variant,,ENST00000566369,;IRF8,downstream_gene_variant,,ENST00000563180,;IRF8,downstream_gene_variant,,ENST00000564617,;MIR6774,upstream_gene_variant,,ENST00000614651,;IRF8,downstream_gene_variant,,ENST00000564056,; T ENST00000268638 Transcript missense_variant,splice_region_variant 978/3030 556/1281 186/426 V/L Gtg/Ttg rs767204633 1 1 IRF8 HGNC HGNC:5358 protein_coding YES CCDS10956.1 ENSP00000268638 Q02556 UPI000012D188 NM_002163.2 tolerated(1) 6/9 hmmpanther:PTHR11949,hmmpanther:PTHR11949:SF7 MODERATE 1 SNV 1 1 PASS rs767204633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 85914475 85914475 G T 1 0 0 0 0 1 0 0 0 7743 1159 40 1 1 IRF8 16 85914475 Missense_Mutation SNP G C3N-01415_T 3287392 85914475 4423870 423 24170 ZNF469 0 . GRCh38 16 88428182 88428182 + Missense_Mutation SNP G G C rs748253495 C3N-01415_T C3N-01415_N G G c.712G>C p.Ala238Pro p.A238P ENST00000437464 1/2 506 457 49 547 547 0 strelka-varscan-mutect ZNF469,missense_variant,p.Ala238Pro,ENST00000565624,;ZNF469,missense_variant,p.Ala238Pro,ENST00000437464,NM_001127464.2; C ENST00000437464 Transcript missense_variant 712/13203 712/11778 238/3925 A/P Gct/Cct rs748253495 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.14) 1/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS rs748253495 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 88428182 88428182 G C 1 0 0 0 0 1 0 0 0 18500 1087 38 4 4 ZNF469 16 88428182 Missense_Mutation SNP G C3N-01415_T 2513707 88428182 1910163 424 24171 ZNF276 0 . GRCh38 16 89734015 89734015 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.1451G>A p.Arg484His p.R484H ENST00000443381 9/11 188 124 64 185 185 0 strelka-varscan-mutect ZNF276,missense_variant,p.Arg409His,ENST00000289816,NM_152287.3;ZNF276,missense_variant,p.Arg484His,ENST00000443381,NM_001113525.1;ZNF276,missense_variant,p.Arg392His,ENST00000568064,;FANCA,downstream_gene_variant,,ENST00000389301,NM_000135.2;FANCA,downstream_gene_variant,,ENST00000568369,NM_001286167.1;FANCA,downstream_gene_variant,,ENST00000564475,;FANCA,downstream_gene_variant,,ENST00000567879,;FANCA,downstream_gene_variant,,ENST00000561722,;FANCA,downstream_gene_variant,,ENST00000564870,;ZNF276,3_prime_UTR_variant,,ENST00000568295,;ZNF276,3_prime_UTR_variant,,ENST00000562530,;ZNF276,non_coding_transcript_exon_variant,,ENST00000563983,;ZNF276,non_coding_transcript_exon_variant,,ENST00000564004,;ZNF276,non_coding_transcript_exon_variant,,ENST00000561536,;ZNF276,non_coding_transcript_exon_variant,,ENST00000569582,;FANCA,downstream_gene_variant,,ENST00000562424,;ZNF276,downstream_gene_variant,,ENST00000563541,;ZNF276,upstream_gene_variant,,ENST00000569901,;ZNF276,downstream_gene_variant,,ENST00000569426,; A ENST00000443381 Transcript missense_variant 1548/2267 1451/1845 484/614 R/H cGc/cAc 1 1 ZNF276 HGNC HGNC:23330 protein_coding YES CCDS45554.1 ENSP00000415836 Q8N554 UPI0000EE7D9C NM_001113525.1 deleterious(0) 9/11 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF56,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1395828475 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 89734015 89734015 G A 1 0 0 0 0 1 0 0 0 18387 1087 38 1 1 ZNF276 16 89734015 Missense_Mutation SNP G C3N-01415_T 1305833 89734015 604330 425 24172 SLC43A2 0 . GRCh38 17 1591604 1591604 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.690C>T p.= p.P230P ENST00000571650 7/15 196 175 21 286 286 0 strelka-varscan-mutect SLC43A2,synonymous_variant,p.=,ENST00000301335,NM_001321364.1,NM_001321365.1,NM_152346.2;SLC43A2,synonymous_variant,p.=,ENST00000571650,NM_001284498.1;SLC43A2,synonymous_variant,p.=,ENST00000412517,NM_001284499.1;SLC43A2,non_coding_transcript_exon_variant,,ENST00000574274,;SLC43A2,3_prime_UTR_variant,,ENST00000572801,;SLC43A2,3_prime_UTR_variant,,ENST00000576721,;SLC43A2,non_coding_transcript_exon_variant,,ENST00000572135,;SLC43A2,non_coding_transcript_exon_variant,,ENST00000574743,;SLC43A2,downstream_gene_variant,,ENST00000571376,; A ENST00000571650 Transcript synonymous_variant 997/3261 690/1722 230/573 P ccC/ccT 1 -1 SLC43A2 HGNC HGNC:23087 protein_coding YES CCDS67108.1 ENSP00000461382 Q8N370 UPI00004EAF8C NM_001284498.1 7/15 hmmpanther:PTHR20766,hmmpanther:PTHR20766:SF2,Gene3D:1.20.1250.20,Pfam_domain:PF07690,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS rs1180235106 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 1591604 1591604 G A 1 0 0 0 0 0 0 0 1 14911 1219 43 3 3 SLC43A2 17 1591604 Silent SNP G C3N-01415_T 1591604 81665837 426 24173 WSCD1 0 . GRCh38 17 6120496 6120496 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.1563G>A p.= p.E521E ENST00000574946 9/9 356 307 49 396 395 1 strelka-varscan-mutect WSCD1,synonymous_variant,p.=,ENST00000574946,;WSCD1,synonymous_variant,p.=,ENST00000317744,NM_015253.1;WSCD1,synonymous_variant,p.=,ENST00000539421,;WSCD1,synonymous_variant,p.=,ENST00000574232,;WSCD1,synonymous_variant,p.=,ENST00000573634,;WSCD1,3_prime_UTR_variant,,ENST00000571494,; A ENST00000574946 Transcript synonymous_variant 1953/5884 1563/1728 521/575 E gaG/gaA 1 1 WSCD1 HGNC HGNC:29060 protein_coding YES CCDS32538.1 ENSP00000460825 Q658N2 UPI0000197208 9/9 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF90,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS rs747881273 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 6120496 6120496 G A 1 0 0 0 0 0 0 0 1 17963 933 33 3 3 WSCD1 17 6120496 Silent SNP G C3N-01415_T 4528892 6120496 77136945 427 24174 TP53 0 . GRCh38 17 7674220 7674220 + Missense_Mutation SNP C C A rs11540652 C3N-01415_T C3N-01415_N C C c.743G>T p.Arg248Leu p.R248L ENST00000269305 7/11 280 241 39 365 365 0 strelka-varscan-mutect TP53,missense_variant,p.Arg248Leu,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg248Leu,ENST00000420246,;TP53,missense_variant,p.Arg209Leu,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg209Leu,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg248Leu,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg209Leu,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg248Leu,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg209Leu,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg248Leu,ENST00000445888,;TP53,missense_variant,p.Arg209Leu,ENST00000619485,;TP53,missense_variant,p.Arg116Leu,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg89Leu,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg116Leu,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg89Leu,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg116Leu,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg89Leu,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg248Leu,ENST00000359597,;TP53,missense_variant,p.Arg237Leu,ENST00000615910,;TP53,missense_variant,p.Arg248Leu,ENST00000413465,;TP53,missense_variant,p.Arg116Leu,ENST00000509690,;TP53,missense_variant,p.Arg155Leu,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Arg209Leu,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 933/2579 743/1182 248/393 R/L cGg/cTg rs11540652,CM920675,TP53_g.13380G>A,TP53_g.13380G>C,TP53_g.13380G>T,TP53_g.13380del,COSM10662,COSM11491,COSM1640830,COSM1646857,COSM1646858,COSM241994,COSM241995,COSM241996,COSM3356964,COSM3378346,COSM340105,COSM340106,COSM340107,COSM3726799,COSM46135,COSM6549,COSM99020,COSM99021,COSM99602 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 2.50327002037787e+47 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs11540652 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 7674220 7674220 C A 1 0 0 0 0 1 0 0 0 16859 652 23 1 1 TP53 17 7674220 Missense_Mutation SNP C C3N-01415_T 1553724 7674220 75583221 428 24175 KCNJ18 0 . GRCh38 17 21703355 21703355 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.569G>T p.Arg190Leu p.R190L ENST00000567955 3/3 104 94 10 112 112 0 varscan-mutect KCNJ18,missense_variant,p.Arg190Leu,ENST00000567955,NM_001194958.2; T ENST00000567955 Transcript missense_variant 939/2196 569/1302 190/433 R/L cGg/cTg 1 1 KCNJ18 HGNC HGNC:39080 protein_coding YES CCDS74015.1 ENSP00000457807 B7U540 UPI0002064ECF NM_001194958.2 deleterious(0) 3/3 Gene3D:2.60.40.1400,Pfam_domain:PF01007,hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs1259420942 . 0 206 4 0 0 0 0 0 -19.84303 1 1 1 1 0 T 3 4 78 21703355 21703355 G T 1 0 0 0 0 1 0 0 0 7967 1116 39 1 1 KCNJ18 17 21703355 Missense_Mutation SNP G C3N-01415_T 14029135 21703355 61554086 429 24176 PSMB3 0 . GRCh38 17 38755937 38755937 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.243G>C p.Gln81His p.Q81H ENST00000619426 3/6 338 300 38 279 279 0 strelka-varscan-mutect PSMB3,missense_variant,p.Gln81His,ENST00000619426,NM_002795.3;PSMB3,missense_variant,p.Gln78His,ENST00000610434,;RNU6-866P,upstream_gene_variant,,ENST00000613402,;CTB-58E17.5,downstream_gene_variant,,ENST00000610658,;PSMB3,missense_variant,p.Gln81His,ENST00000613870,;PSMB3,missense_variant,p.Gln81His,ENST00000620309,;PSMB3,upstream_gene_variant,,ENST00000614132,; C ENST00000619426 Transcript missense_variant 334/773 243/618 81/205 Q/H caG/caC 1 1 PSMB3 HGNC HGNC:9540 protein_coding YES CCDS11328.1 ENSP00000483688 P49720 UPI00001325B3 NM_002795.3 tolerated(0.1) 3/6 PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF62,Pfam_domain:PF00227,Gene3D:3.60.20.10,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 38755937 38755937 G C 1 0 0 0 0 1 0 0 0 12829 933 33 4 4 PSMB3 17 38755937 Missense_Mutation SNP G C3N-01415_T 17052582 38755937 44501504 430 24177 KRTAP4-8 0 . GRCh38 17 41098058 41098058 + Silent SNP C C G C3N-01415_T C3N-01415_N C C c.27G>C p.= p.V9V ENST00000333822 1/1 132 101 31 183 183 0 strelka-varscan-mutect KRTAP4-8,synonymous_variant,p.=,ENST00000333822,NM_031960.2;KRTAP4-8,synonymous_variant,p.=,ENST00000318329,;KRTAP4-7,intron_variant,,ENST00000612231,;KRTAP4-16,downstream_gene_variant,,ENST00000440582,; G ENST00000333822 Transcript synonymous_variant 84/1161 27/558 9/185 V gtG/gtC COSM4919081 1 -1 KRTAP4-8 HGNC HGNC:17230 protein_coding YES CCDS45674.1 ENSP00000328444 Q9BYQ9 UPI0000366BFD NM_031960.2 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF67 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 41098058 41098058 C G 1 0 0 0 0 0 0 0 1 8451 465 17 4 4 KRTAP4-8 17 41098058 Silent SNP C C3N-01415_T 2342121 41098058 42159383 431 24178 DHX58 0 . GRCh38 17 42111814 42111814 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.79G>T p.Gly27Cys p.G27C ENST00000251642 3/14 154 128 26 169 169 0 strelka-varscan-mutect DHX58,missense_variant,p.Gly27Cys,ENST00000251642,NM_024119.2;DHX58,missense_variant,p.Gly27Cys,ENST00000413196,;DHX58,missense_variant,p.Gly27Cys,ENST00000430773,;DHX58,intron_variant,,ENST00000591220,;KAT2A,downstream_gene_variant,,ENST00000225916,NM_021078.2;DHX58,non_coding_transcript_exon_variant,,ENST00000586522,;KAT2A,downstream_gene_variant,,ENST00000465682,;KAT2A,downstream_gene_variant,,ENST00000586972,;DHX58,upstream_gene_variant,,ENST00000590637,;KAT2A,downstream_gene_variant,,ENST00000592310,;KAT2A,downstream_gene_variant,,ENST00000588759,; A ENST00000251642 Transcript missense_variant 302/2617 79/2037 27/678 G/C Ggt/Tgt 1 -1 DHX58 HGNC HGNC:29517 protein_coding YES CCDS11416.1 ENSP00000251642 Q96C10 A0A024R1Y5 UPI000006ED88 NM_024119.2 deleterious(0) 3/14 PROSITE_profiles:PS51192,hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF7,Pfam_domain:PF04851,Gene3D:3.40.50.300,SMART_domains:SM00487 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 42111814 42111814 C A 1 0 0 0 0 1 0 0 0 4318 623 22 2 2 DHX58 17 42111814 Missense_Mutation SNP C C3N-01415_T 1013756 42111814 41145627 432 24179 STAT5B 0 . GRCh38 17 42212096 42212096 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1568G>T p.Arg523Leu p.R523L ENST00000293328 13/19 657 551 106 706 705 1 strelka-varscan-mutect STAT5B,missense_variant,p.Arg523Leu,ENST00000293328,NM_012448.3;STAT5B,non_coding_transcript_exon_variant,,ENST00000481517,;STAT5B,non_coding_transcript_exon_variant,,ENST00000468496,;STAT5B,upstream_gene_variant,,ENST00000481253,; A ENST00000293328 Transcript missense_variant 1737/5103 1568/2364 523/787 R/L cGg/cTg 1 -1 STAT5B HGNC HGNC:11367 protein_coding YES CCDS11423.1 ENSP00000293328 P51692 UPI000006F059 NM_012448.3 tolerated(0.07) 13/19 Gene3D:1.10.238.10,Pfam_domain:PF02864,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF39,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 42212096 42212096 C A 1 0 0 0 0 1 0 0 0 15645 652 23 1 1 STAT5B 17 42212096 Missense_Mutation SNP C C3N-01415_T 100282 42212096 41045345 433 24180 RUNDC3A 0 . GRCh38 17 44316449 44316449 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.1018C>T p.= p.L340L ENST00000426726 9/11 218 173 45 164 164 0 strelka-varscan-mutect RUNDC3A,synonymous_variant,p.=,ENST00000426726,NM_001144825.1;RUNDC3A,synonymous_variant,p.=,ENST00000225441,NM_006695.4;RUNDC3A,synonymous_variant,p.=,ENST00000590941,NM_001144826.1;RUNDC3A,synonymous_variant,p.=,ENST00000612735,;SLC25A39,downstream_gene_variant,,ENST00000225308,NM_001321241.1,NM_016016.2;SLC25A39,downstream_gene_variant,,ENST00000377095,NM_001143780.1;SLC25A39,downstream_gene_variant,,ENST00000590194,;SLC25A39,downstream_gene_variant,,ENST00000537904,;SLC25A39,downstream_gene_variant,,ENST00000586016,;SLC25A39,downstream_gene_variant,,ENST00000588049,;SLC25A39,downstream_gene_variant,,ENST00000588767,;RUNDC3A-AS1,upstream_gene_variant,,ENST00000588097,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000587483,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000590834,;SLC25A39,downstream_gene_variant,,ENST00000591006,;SLC25A39,downstream_gene_variant,,ENST00000588315,;SLC25A39,downstream_gene_variant,,ENST00000585695,;SLC25A39,downstream_gene_variant,,ENST00000592372,;SLC25A39,downstream_gene_variant,,ENST00000593166,;RUNDC3A,upstream_gene_variant,,ENST00000588564,;RUNDC3A,downstream_gene_variant,,ENST00000593079,; T ENST00000426726 Transcript synonymous_variant 1292/2048 1018/1341 340/446 L Ctg/Ttg 1 1 RUNDC3A HGNC HGNC:16984 protein_coding YES CCDS45698.1 ENSP00000410862 Q59EK9 UPI0000EE7B82 NM_001144825.1 9/11 hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF38 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 44316449 44316449 C T 1 0 0 0 0 0 0 0 1 14005 680 24 3 3 RUNDC3A 17 44316449 Silent SNP C C3N-01415_T 2104353 44316449 38940992 434 24181 PLEKHM1 0 . GRCh38 17 45453952 45453952 + Nonsense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1900G>T p.Glu634Ter p.E634* ENST00000430334 7/12 382 274 108 359 359 0 strelka-varscan-mutect PLEKHM1,stop_gained,p.Glu634Ter,ENST00000430334,NM_014798.2;AC091132.1,intron_variant,,ENST00000433601,;PLEKHM1,non_coding_transcript_exon_variant,,ENST00000580205,;PLEKHM1,3_prime_UTR_variant,,ENST00000579197,;PLEKHM1,3_prime_UTR_variant,,ENST00000581448,;PLEKHM1,3_prime_UTR_variant,,ENST00000446609,;PLEKHM1,non_coding_transcript_exon_variant,,ENST00000582035,; A ENST00000430334 Transcript stop_gained 2034/5263 1900/3171 634/1056 E/* Gag/Tag 1 -1 PLEKHM1 HGNC HGNC:29017 protein_coding YES CCDS32671.1 ENSP00000389913 Q9Y4G2 UPI00001C1FC4 NM_014798.2 7/12 hmmpanther:PTHR12326,hmmpanther:PTHR12326:SF5,Superfamily_domains:SSF50729 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 78 45453952 45453952 C A 1 0 0 0 0 0 1 0 0 12173 835 29 2 2 PLEKHM1 17 45453952 Nonsense_Mutation SNP C C3N-01415_T 1137503 45453952 37803489 435 24182 WNT9B 0 . GRCh38 17 46872682 46872682 + Silent SNP T T A novel C3N-01415_T C3N-01415_N T T c.243T>A p.= p.A81A ENST00000290015 2/4 192 170 22 191 191 0 strelka-varscan-mutect WNT9B,synonymous_variant,p.=,ENST00000393461,NM_001320458.1;WNT9B,synonymous_variant,p.=,ENST00000290015,NM_003396.1;WNT9B,synonymous_variant,p.=,ENST00000575372,; A ENST00000290015 Transcript synonymous_variant 296/1376 243/1074 81/357 A gcT/gcA 1 1 WNT9B HGNC HGNC:12779 protein_coding YES CCDS11506.1 ENSP00000290015 O14905 UPI000013DFB5 NM_003396.1 2/4 Pfam_domain:PF00110,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF84,SMART_domains:SM00097 LOW 1 SNV 1 1 PASS rs1040778099 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 46872682 46872682 T A 1 0 0 0 0 0 0 0 1 17955 1567 55 4 4 WNT9B 17 46872682 Silent SNP T C3N-01415_T 1418730 46872682 36384759 436 24183 LUC7L3 0 . GRCh38 17 50746545 50746545 + Missense_Mutation SNP T T G novel C3N-01415_T C3N-01415_N T T c.981T>G p.Ser327Arg p.S327R ENST00000505658 9/10 159 141 18 155 155 0 strelka-varscan-mutect LUC7L3,missense_variant,p.Ser327Arg,ENST00000505658,NM_016424.4;LUC7L3,missense_variant,p.Ser327Arg,ENST00000393227,;LUC7L3,missense_variant,p.Ser327Arg,ENST00000240304,NM_006107.3;LUC7L3,upstream_gene_variant,,ENST00000503728,;LUC7L3,downstream_gene_variant,,ENST00000505619,;LUC7L3,downstream_gene_variant,,ENST00000513025,;LUC7L3,upstream_gene_variant,,ENST00000511974,;LUC7L3,upstream_gene_variant,,ENST00000513969,;LUC7L3,upstream_gene_variant,,ENST00000503798,;LUC7L3,upstream_gene_variant,,ENST00000512549,;LUC7L3,missense_variant,p.Ser147Arg,ENST00000504065,;LUC7L3,missense_variant,p.Ser34Arg,ENST00000509487,;LUC7L3,3_prime_UTR_variant,,ENST00000508482,;LUC7L3,downstream_gene_variant,,ENST00000508045,;LUC7L3,downstream_gene_variant,,ENST00000504563,;LUC7L3,downstream_gene_variant,,ENST00000507503,;LUC7L3,downstream_gene_variant,,ENST00000507200,;LUC7L3,downstream_gene_variant,,ENST00000511068,; G ENST00000505658 Transcript missense_variant 1170/7040 981/1299 327/432 S/R agT/agG 1 1 LUC7L3 HGNC HGNC:24309 protein_coding YES CCDS11573.1 ENSP00000425092 O95232 UPI00000736F2 NM_016424.4 deleterious(0.05) 9/10 hmmpanther:PTHR12375,hmmpanther:PTHR12375:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 50746545 50746545 T G 1 0 0 0 0 1 0 0 0 8991 1652 57 5 5 LUC7L3 17 50746545 Missense_Mutation SNP T C3N-01415_T 3873863 50746545 32510896 437 24184 INTS2 0 . GRCh38 17 61875039 61875039 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.2481-1G>T p.X827_splice ENST00000444766 127 93 34 122 122 0 strelka-varscan-mutect INTS2,splice_acceptor_variant,,ENST00000444766,NM_020748.2;INTS2,splice_acceptor_variant,,ENST00000617492,;INTS2,splice_acceptor_variant,,ENST00000251334,;Y_RNA,upstream_gene_variant,,ENST00000365491,;INTS2,splice_acceptor_variant,,ENST00000583822,;INTS2,downstream_gene_variant,,ENST00000584967,; A ENST00000444766 Transcript splice_acceptor_variant -/5878 2481/3615 827/1204 1 -1 INTS2 HGNC HGNC:29241 protein_coding YES CCDS45750.1 ENSP00000414237 Q9H0H0 UPI0000E5A03A NM_020748.2 18/24 HIGH 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999868 1 1 1 0 A 5 1 78 61875039 61875039 C A 1 0 0 0 0 0 0 1 0 7680 695 24 2 2 INTS2 17 61875039 Splice_Site SNP C C3N-01415_T 11128494 61875039 21382402 438 24185 ABCA6 0 . GRCh38 17 69081114 69081114 + Missense_Mutation SNP C C A rs148075714 C3N-01415_T C3N-01415_N C C c.4648G>T p.Val1550Leu p.V1550L ENST00000284425 37/39 207 185 22 209 209 0 strelka-varscan-mutect ABCA6,missense_variant,p.Val1550Leu,ENST00000284425,NM_080284.2;ABCA6,non_coding_transcript_exon_variant,,ENST00000446604,;ABCA6,downstream_gene_variant,,ENST00000589482,; A ENST00000284425 Transcript missense_variant 4823/5300 4648/4854 1550/1617 V/L Gtg/Ttg rs148075714 1 -1 ABCA6 HGNC HGNC:36 protein_coding YES CCDS11683.1 ENSP00000284425 Q8N139 UPI000013DD9D NM_080284.2 tolerated(0.29) 37/39 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF13 MODERATE 1 SNV 1 1 PASS rs148075714 . 0 206 0 3 0 0 0 0 -20 0.9999865 1 1 1 0 A 3 1 78 69081114 69081114 C A 1 0 0 0 0 1 0 0 0 40 536 19 1 1 ABCA6 17 69081114 Missense_Mutation SNP C C3N-01415_T 7206075 69081114 14176327 439 24186 ABCA6 0 . GRCh38 17 69083242 69083242 + Missense_Mutation SNP C C A rs200105664 C3N-01415_T C3N-01415_N C C c.4445G>T p.Arg1482Leu p.R1482L ENST00000284425 35/39 100 73 27 124 124 0 strelka-varscan-mutect ABCA6,missense_variant,p.Arg1482Leu,ENST00000284425,NM_080284.2;ABCA6,non_coding_transcript_exon_variant,,ENST00000446604,;ABCA6,downstream_gene_variant,,ENST00000589482,; A ENST00000284425 Transcript missense_variant 4620/5300 4445/4854 1482/1617 R/L cGt/cTt rs200105664 1 -1 ABCA6 HGNC HGNC:36 protein_coding YES CCDS11683.1 ENSP00000284425 Q8N139 UPI000013DD9D NM_080284.2 deleterious(0.01) 35/39 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF13,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1470401286 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 69083242 69083242 C A 1 0 0 0 0 1 0 0 0 40 536 19 1 1 ABCA6 17 69083242 Missense_Mutation SNP C C3N-01415_T 2128 69083242 14174199 440 24187 DNAI2 0 . GRCh38 17 74299806 74299806 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.813G>T p.Trp271Cys p.W271C ENST00000446837 6/13 514 433 81 441 440 1 strelka-varscan-mutect DNAI2,missense_variant,p.Trp328Cys,ENST00000579490,;DNAI2,missense_variant,p.Trp271Cys,ENST00000446837,;DNAI2,missense_variant,p.Trp271Cys,ENST00000582036,NM_001172810.1;DNAI2,missense_variant,p.Trp271Cys,ENST00000311014,NM_023036.4;DNAI2,3_prime_UTR_variant,,ENST00000579055,; T ENST00000446837 Transcript missense_variant 1119/2474 813/1818 271/605 W/C tgG/tgT 1 1 DNAI2 HGNC HGNC:18744 protein_coding YES CCDS11697.1 ENSP00000400252 Q9GZS0 UPI000013EC1D deleterious(0) 6/13 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF7,hmmpanther:PTHR12442,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 74299806 74299806 G T 1 0 0 0 0 1 0 0 0 4425 1212 42 2 2 DNAI2 17 74299806 Missense_Mutation SNP G C3N-01415_T 5216564 74299806 8957635 441 24188 EVPL 0 . GRCh38 17 76018478 76018478 + Silent SNP T T A novel C3N-01415_T C3N-01415_N T T c.1407A>T p.= p.A469A ENST00000301607 12/22 286 205 81 226 226 0 strelka-varscan-mutect EVPL,synonymous_variant,p.=,ENST00000301607,NM_001988.2;EVPL,synonymous_variant,p.=,ENST00000586740,NM_001320747.1;EVPL,non_coding_transcript_exon_variant,,ENST00000587569,; A ENST00000301607 Transcript synonymous_variant 1661/6614 1407/6102 469/2033 A gcA/gcT 1 -1 EVPL HGNC HGNC:3503 protein_coding YES CCDS11737.1 ENSP00000301607 Q92817 UPI000013E730 NM_001988.2 12/22 hmmpanther:PTHR23169,hmmpanther:PTHR23169:SF7 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 76018478 76018478 T A 1 0 0 0 0 0 0 0 1 5159 1683 59 4 4 EVPL 17 76018478 Silent SNP T C3N-01415_T 1718672 76018478 7238963 442 24189 CARD14 0 . GRCh38 17 80201839 80201839 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.1947C>T p.= p.F649F ENST00000573882 16/23 199 168 31 156 156 0 strelka-varscan-mutect CARD14,synonymous_variant,p.=,ENST00000573882,;CARD14,synonymous_variant,p.=,ENST00000344227,NM_024110.4;CARD14,synonymous_variant,p.=,ENST00000570421,NM_001257970.1;RP11-334C17.5,non_coding_transcript_exon_variant,,ENST00000570309,;RP11-334C17.5,non_coding_transcript_exon_variant,,ENST00000576824,;RP11-334C17.5,non_coding_transcript_exon_variant,,ENST00000573346,;RP11-334C17.5,non_coding_transcript_exon_variant,,ENST00000573935,;RP11-334C17.5,downstream_gene_variant,,ENST00000572730,;CARD14,downstream_gene_variant,,ENST00000573754,;SGSH,downstream_gene_variant,,ENST00000575484,;CARD14,downstream_gene_variant,,ENST00000574148,;CARD14,3_prime_UTR_variant,,ENST00000575500,;CARD14,intron_variant,,ENST00000571450,;CARD14,downstream_gene_variant,,ENST00000575666,; T ENST00000573882 Transcript synonymous_variant 2483/4537 1947/3015 649/1004 F ttC/ttT 1 1 CARD14 HGNC HGNC:16446 protein_coding YES CCDS11768.1 ENSP00000458715 Q9BXL6 UPI000013D81B 16/23 PROSITE_profiles:PS50106,hmmpanther:PTHR14559:SF1,hmmpanther:PTHR14559,Gene3D:2.30.42.10,Superfamily_domains:SSF50156 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 80201839 80201839 C T 1 0 0 0 0 0 0 0 1 2341 912 32 3 3 CARD14 17 80201839 Silent SNP C C3N-01415_T 4183361 80201839 3055602 443 24190 BAHCC1 0 . GRCh38 17 81447149 81447149 + Missense_Mutation SNP G G T C3N-01415_T C3N-01415_N G G c.3370G>T p.Ala1124Ser p.A1124S ENST00000584436 12/29 169 118 51 161 161 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Ala1124Ser,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Ala1093Ser,ENST00000307745,;MIR3186,downstream_gene_variant,,ENST00000577404,;BAHCC1,downstream_gene_variant,,ENST00000585224,; T ENST00000584436 Transcript missense_variant 3737/10801 3370/7920 1124/2639 A/S Gcc/Tcc COSM4912807 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 tolerated(0.07) 12/29 hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505 1 MODERATE 1 SNV 5 1 1 PASS rs1363829397 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 81447149 81447149 G T 1 0 0 0 0 1 0 0 0 1451 1203 42 2 2 BAHCC1 17 81447149 Missense_Mutation SNP G C3N-01415_T 1245310 81447149 1810292 444 24191 ZNF519 0 . GRCh38 18 14105210 14105210 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1330G>T p.Gly444Cys p.G444C ENST00000590202 3/3 116 102 14 192 192 0 strelka-varscan-mutect ZNF519,missense_variant,p.Gly444Cys,ENST00000590202,NM_145287.3;ZNF519,intron_variant,,ENST00000589498,;RP11-411B10.3,non_coding_transcript_exon_variant,,ENST00000592926,;ZNF519,intron_variant,,ENST00000589203,;ZNF519,intron_variant,,ENST00000591393,;ZNF519,intron_variant,,ENST00000592345,;ZNF519,intron_variant,,ENST00000592411,;ZNF519,intron_variant,,ENST00000592049,;ZNF519,downstream_gene_variant,,ENST00000588435,;ZNF519,non_coding_transcript_exon_variant,,ENST00000624133,;ZNF519,intron_variant,,ENST00000587419,; A ENST00000590202 Transcript missense_variant 1483/2830 1330/1623 444/540 G/C Ggc/Tgc 1 -1 ZNF519 HGNC HGNC:30574 protein_coding YES CCDS32797.1 ENSP00000464872 Q8TB69 UPI0000201A41 NM_145287.3 tolerated(0.14) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF97,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999968 1 1 1 0 A 3 1 78 14105210 14105210 C A 1 0 0 0 0 1 0 0 0 18536 623 22 2 2 ZNF519 18 14105210 Missense_Mutation SNP C C3N-01415_T 14105210 66268075 445 24192 IMPACT 0 . GRCh38 18 24437982 24437982 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.309C>T p.= p.Y103Y ENST00000284202 5/11 220 192 28 281 281 0 strelka-varscan-mutect IMPACT,synonymous_variant,p.=,ENST00000284202,NM_018439.3;IMPACT,synonymous_variant,p.=,ENST00000585067,;IMPACT,synonymous_variant,p.=,ENST00000578221,;RP11-178F10.1,intron_variant,,ENST00000579049,;IMPACT,non_coding_transcript_exon_variant,,ENST00000580706,; T ENST00000284202 Transcript synonymous_variant 450/3792 309/963 103/320 Y taC/taT 1 1 IMPACT HGNC HGNC:20387 protein_coding YES CCDS11886.1 ENSP00000284202 Q9P2X3 UPI000007006B NM_018439.3 5/11 Gene3D:3.10.110.10,Pfam_domain:PF05773,PROSITE_profiles:PS50908,hmmpanther:PTHR16301,hmmpanther:PTHR16301:SF6,SMART_domains:SM00591,Superfamily_domains:SSF54495 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 24437982 24437982 C T 1 0 0 0 0 0 0 0 1 7626 518 18 3 3 IMPACT 18 24437982 Silent SNP C C3N-01415_T 10332772 24437982 55935303 446 24193 SETBP1 0 . GRCh38 18 44952638 44952638 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.3298C>A p.His1100Asn p.H1100N ENST00000282030 4/6 132 104 28 214 213 1 strelka-varscan-mutect SETBP1,missense_variant,p.His1100Asn,ENST00000282030,NM_015559.2; A ENST00000282030 Transcript missense_variant 3594/9899 3298/4791 1100/1596 H/N Cac/Aac 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 deleterious(0) 4/6 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF342 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 44952638 44952638 C A 1 0 0 0 0 1 0 0 0 14406 594 21 2 2 SETBP1 18 44952638 Missense_Mutation SNP C C3N-01415_T 20514656 44952638 35420647 447 24194 SMAD4 0 . GRCh38 18 51054904 51054904 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.578A>T p.Glu193Val p.E193V ENST00000342988 5/12 363 311 52 629 626 3 strelka-varscan-mutect SMAD4,missense_variant,p.Glu193Val,ENST00000342988,NM_005359.5;SMAD4,missense_variant,p.Glu193Val,ENST00000398417,;SMAD4,missense_variant,p.Glu193Val,ENST00000588745,;SMAD4,non_coding_transcript_exon_variant,,ENST00000592911,;SMAD4,missense_variant,p.Glu193Val,ENST00000592186,;RP11-729L2.2,3_prime_UTR_variant,,ENST00000590722,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,non_coding_transcript_exon_variant,,ENST00000585448,;SMAD4,upstream_gene_variant,,ENST00000611848,; T ENST00000342988 Transcript missense_variant 1116/8769 578/1659 193/552 E/V gAg/gTg 1 1 SMAD4 HGNC HGNC:6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 A0A024R274 UPI0000053431 NM_005359.5 tolerated(0.28) 5/12 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 51054904 51054904 A T 1 0 0 0 0 1 0 0 0 15053 304 11 4 4 SMAD4 18 51054904 Missense_Mutation SNP A C3N-01415_T 6102266 51054904 29318381 448 24195 ZNF236 0 . GRCh38 18 76881432 76881432 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.1337A>T p.Gln446Leu p.Q446L ENST00000320610 9/31 299 262 37 457 457 0 strelka-varscan-mutect ZNF236,missense_variant,p.Gln444Leu,ENST00000253159,NM_007345.3;ZNF236,missense_variant,p.Gln446Leu,ENST00000320610,NM_001306089.1;ZNF236,missense_variant,p.Gln444Leu,ENST00000579322,;ZNF236,missense_variant,p.Gln444Leu,ENST00000543926,;ZNF236,non_coding_transcript_exon_variant,,ENST00000583488,;RP11-162A12.3,downstream_gene_variant,,ENST00000583058,; T ENST00000320610 Transcript missense_variant 1338/7124 1337/5544 446/1847 Q/L cAa/cTa 1 1 ZNF236 HGNC HGNC:13028 protein_coding YES CCDS77201.1 ENSP00000322361 J9JID5 UPI000268B415 NM_001306089.1 tolerated(0.34) 9/31 hmmpanther:PTHR24396:SF21,hmmpanther:PTHR24396 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 76881432 76881432 A T 1 0 0 0 0 1 0 0 0 18366 130 5 4 4 ZNF236 18 76881432 Missense_Mutation SNP A C3N-01415_T 25826528 76881432 3491853 449 24196 GALR1 0 . GRCh38 18 77268772 77268772 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.920C>A p.Ser307Tyr p.S307Y ENST00000299727 3/3 353 288 65 517 516 1 strelka-varscan-mutect GALR1,missense_variant,p.Ser307Tyr,ENST00000299727,NM_001480.3; A ENST00000299727 Transcript missense_variant 920/10044 920/1050 307/349 S/Y tCt/tAt 1 1 GALR1 HGNC HGNC:4132 protein_coding YES CCDS12012.1 ENSP00000299727 P47211 UPI000013E5DE NM_001480.3 deleterious(0) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR24230:SF31,hmmpanther:PTHR24230,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS rs1485699296 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 77268772 77268772 C A 1 0 0 0 0 1 0 0 0 6095 913 32 2 2 GALR1 18 77268772 Missense_Mutation SNP C C3N-01415_T 387340 77268772 3104513 450 24197 ADNP2 0 . GRCh38 18 80136362 80136362 + Frame_Shift_Del DEL G G - C3N-01415_T C3N-01415_N G G c.950delG p.Gly317GlufsTer15 p.G317Efs*15 ENST00000262198 4/4 109 96 13 166 166 0 sindel-varindel-pindel ADNP2,frameshift_variant,p.Gly317GlufsTer15,ENST00000262198,NM_014913.3;ADNP2,intron_variant,,ENST00000561195,;ADNP2,downstream_gene_variant,,ENST00000560752,;ADNP2,downstream_gene_variant,,ENST00000559951,;ADNP2,downstream_gene_variant,,ENST00000560561,; - ENST00000262198 Transcript frameshift_variant 1404/5393 949/3396 317/1131 G/X Gga/ga COSM564347 1 1 ADNP2 HGNC HGNC:23803 protein_coding YES CCDS32853.1 ENSP00000262198 Q6IQ32 A0A024R377 UPI0000071DEA NM_014913.3 4/4 hmmpanther:PTHR15740 1 HIGH 1 deletion 1 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 80136362 80136362 G - 1 0 1 0 1 0 0 0 0 399 1349 47 0 0 ADNP2 18 80136362 Frame_Shift_Del DEL G C3N-01415_T 2867590 80136362 236923 451 24198 CACTIN 0 . GRCh38 19 3623773 3623773 + Missense_Mutation SNP C C G C3N-01415_T C3N-01415_N C C c.557G>C p.Gly186Ala p.G186A ENST00000429344 2/10 399 337 62 298 298 0 strelka-varscan-mutect CACTIN,missense_variant,p.Gly186Ala,ENST00000429344,NM_001080543.1;CACTIN,missense_variant,p.Gly186Ala,ENST00000221899,;CACTIN,missense_variant,p.Gly186Ala,ENST00000248420,NM_021231.1;CACTIN,upstream_gene_variant,,ENST00000588749,;CACTIN,missense_variant,p.Gly186Ala,ENST00000585942,;CACTIN,upstream_gene_variant,,ENST00000587175,;CACTIN,upstream_gene_variant,,ENST00000589321,; G ENST00000429344 Transcript missense_variant 610/3612 557/2277 186/758 G/A gGc/gCc COSM4921949,COSM4921950 1 -1 CACTIN HGNC HGNC:29938 protein_coding YES CCDS45920.1 ENSP00000415078 Q8WUQ7 UPI00006C1962 NM_001080543.1 deleterious(0.04) 2/10 hmmpanther:PTHR21737,hmmpanther:PTHR21737:SF6 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 3623773 3623773 C G 1 0 0 0 0 1 0 0 0 2252 739 26 4 4 CACTIN 19 3623773 Missense_Mutation SNP C C3N-01415_T 3623773 54993843 452 24199 DAPK3 0 . GRCh38 19 3964934 3964934 + Silent SNP T T A novel C3N-01415_T C3N-01415_N T T c.120A>T p.= p.A40A ENST00000545797 3/9 204 170 34 192 192 0 strelka-varscan-mutect DAPK3,synonymous_variant,p.=,ENST00000545797,NM_001348.2;DAPK3,synonymous_variant,p.=,ENST00000301264,;DAPK3,synonymous_variant,p.=,ENST00000596311,;DAPK3,synonymous_variant,p.=,ENST00000593844,;DAPK3,synonymous_variant,p.=,ENST00000601824,;DAPK3,upstream_gene_variant,,ENST00000594894,;DAPK3,upstream_gene_variant,,ENST00000385000,;DAPK3,upstream_gene_variant,,ENST00000595279,; A ENST00000545797 Transcript synonymous_variant 364/2257 120/1365 40/454 A gcA/gcT 1 -1 DAPK3 HGNC HGNC:2676 protein_coding YES CCDS12116.1 ENSP00000442973 O43293 UPI000006F7FA NM_001348.2 3/9 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,PROSITE_patterns:PS00107,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 3964934 3964934 T A 1 0 0 0 0 0 0 0 1 4038 1567 55 4 4 DAPK3 19 3964934 Silent SNP T C3N-01415_T 341161 3964934 54652682 453 24200 ZNRF4 0 . GRCh38 19 5455635 5455635 + Frame_Shift_Del DEL C C - rs376298220 C3N-01415_T C3N-01415_N C C c.146delC p.Pro49GlnfsTer21 p.P49Qfs*21 ENST00000222033 1/1 210 177 33 240 240 0 sindel-varindel-pindel ZNRF4,frameshift_variant,p.Pro49GlnfsTer21,ENST00000222033,NM_181710.3; - ENST00000222033 Transcript frameshift_variant 205/1426 144/1290 48/429 C/X tgC/tg rs376298220 1 1 ZNRF4 HGNC HGNC:17726 protein_coding YES CCDS42475.1 ENSP00000222033 Q8WWF5 UPI0000366CF5 NM_181710.3 1/1 hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF49 HIGH 1 deletion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 78 5455635 5455635 C - 1 0 1 0 1 0 0 0 0 18806 747 26 0 0 ZNRF4 19 5455635 Frame_Shift_Del DEL C C3N-01415_T 1490701 5455635 53161981 454 24201 C3 0 . GRCh38 19 6686818 6686818 + Missense_Mutation SNP C C A rs375011405 C3N-01415_T C3N-01415_N C C c.3574G>T p.Ala1192Ser p.A1192S ENST00000245907 28/41 519 438 81 495 495 0 strelka-varscan-mutect C3,missense_variant,p.Ala1192Ser,ENST00000245907,NM_000064.3;C3,missense_variant,p.Ala57Ser,ENST00000601008,;C3,upstream_gene_variant,,ENST00000596548,;C3,non_coding_transcript_exon_variant,,ENST00000598805,;C3,upstream_gene_variant,,ENST00000599899,;C3,upstream_gene_variant,,ENST00000596238,;C3,upstream_gene_variant,,ENST00000596179,; A ENST00000245907 Transcript missense_variant 3667/5263 3574/4992 1192/1663 A/S Gct/Tct rs375011405 1 -1 C3 HGNC HGNC:1318 protein_coding YES CCDS32883.1 ENSP00000245907 P01024 V9HWA9 UPI000013EC9B NM_000064.3 tolerated(0.09) 28/41 hmmpanther:PTHR11412:SF90,hmmpanther:PTHR11412,Gene3D:1.50.10.20,Pfam_domain:PF07678,Superfamily_domains:SSF48239 MODERATE 1 SNV 1 1 PASS rs375011405 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 6686818 6686818 C A 1 0 0 0 0 1 0 0 0 2057 710 25 2 2 C3 19 6686818 Missense_Mutation SNP C C3N-01415_T 1231183 6686818 51930798 455 24202 ADGRE1 0 . GRCh38 19 6916352 6916352 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.1404G>C p.Glu468Asp p.E468D ENST00000312053 12/21 117 111 6 157 157 0 strelka-varscan-mutect ADGRE1,missense_variant,p.Glu468Asp,ENST00000312053,NM_001974.4;ADGRE1,missense_variant,p.Glu416Asp,ENST00000381404,NM_001256252.1;ADGRE1,missense_variant,p.Glu468Asp,ENST00000250572,NM_001256253.1;ADGRE1,missense_variant,p.Glu327Asp,ENST00000381407,NM_001256254.1;ADGRE1,missense_variant,p.Glu291Asp,ENST00000450315,NM_001256255.1;ADGRE1,downstream_gene_variant,,ENST00000595026,; C ENST00000312053 Transcript missense_variant 1441/3128 1404/2661 468/886 E/D gaG/gaC 1 1 ADGRE1 HGNC HGNC:3336 protein_coding YES CCDS12175.1 ENSP00000311545 Q14246 UPI0000203241 NM_001974.4 tolerated(0.14) 12/21 Low_complexity_(Seg):seg,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF303 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -11.7393 0.9999811 1 1 1 0 C 3 2 78 6916352 6916352 G C 1 0 0 0 0 1 0 0 0 359 991 35 4 4 ADGRE1 19 6916352 Missense_Mutation SNP G C3N-01415_T 229534 6916352 51701264 456 24203 INSR 0 . GRCh38 19 7184584 7184584 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.706C>T p.His236Tyr p.H236Y ENST00000302850 3/22 169 151 18 234 234 0 strelka-varscan-mutect INSR,missense_variant,p.His236Tyr,ENST00000341500,NM_001079817.1;INSR,missense_variant,p.His236Tyr,ENST00000302850,NM_000208.2;INSR,non_coding_transcript_exon_variant,,ENST00000598216,; A ENST00000302850 Transcript missense_variant 849/4721 706/4149 236/1382 H/Y Cac/Tac 1 -1 INSR HGNC HGNC:6091 protein_coding YES CCDS12176.1 ENSP00000303830 P06213 UPI000020324D NM_000208.2 deleterious(0.02) 3/22 Gene3D:3.80.20.20,Pfam_domain:PF00757,PIRSF_domain:PIRSF000620,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF325,SMART_domains:SM00261,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 7184584 7184584 G A 1 0 0 0 0 1 0 0 0 7675 1348 47 3 3 INSR 19 7184584 Missense_Mutation SNP G C3N-01415_T 268232 7184584 51433032 457 24204 MYO1F 0 . GRCh38 19 8554692 8554692 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.193T>A p.Tyr65Asn p.Y65N ENST00000338257 3/28 523 479 44 524 524 0 strelka-varscan-mutect MYO1F,missense_variant,p.Tyr65Asn,ENST00000338257,NM_012335.3;MYO1F,missense_variant,p.Tyr65Asn,ENST00000613525,;MYO1F,missense_variant,p.Tyr61Asn,ENST00000596675,;AC092316.1,downstream_gene_variant,,ENST00000598703,;MYO1F,missense_variant,p.Leu72Gln,ENST00000598321,;MYO1F,non_coding_transcript_exon_variant,,ENST00000594977,;MYO1F,non_coding_transcript_exon_variant,,ENST00000595325,;MYO1F,non_coding_transcript_exon_variant,,ENST00000594774,;MYO1F,non_coding_transcript_exon_variant,,ENST00000599123,;MYO1F,upstream_gene_variant,,ENST00000595191,;MYO1F,upstream_gene_variant,,ENST00000598529,;MYO1F,downstream_gene_variant,,ENST00000596645,;MYO1F,upstream_gene_variant,,ENST00000600825,;MYO1F,upstream_gene_variant,,ENST00000596937,; T ENST00000338257 Transcript missense_variant 461/4303 193/3297 65/1098 Y/N Tac/Aac 1 -1 MYO1F HGNC HGNC:7600 protein_coding YES CCDS42494.1 ENSP00000344871 O00160 UPI00001678F0 NM_012335.3 tolerated(0.06) 3/28 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF288,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 8554692 8554692 A T 1 0 0 0 0 1 0 0 0 10074 420 15 4 4 MYO1F 19 8554692 Missense_Mutation SNP A C3N-01415_T 1370108 8554692 50062924 458 24205 ACTL9 0 . GRCh38 19 8698158 8698158 + Missense_Mutation SNP C C A rs781941982 C3N-01415_T C3N-01415_N C C c.544G>T p.Val182Leu p.V182L ENST00000324436 1/1 152 130 22 158 158 0 strelka-varscan-mutect ACTL9,missense_variant,p.Val182Leu,ENST00000324436,NM_178525.4;ACTL9,missense_variant,p.Val182Leu,ENST00000612068,;AC093230.2,upstream_gene_variant,,ENST00000623340,; A ENST00000324436 Transcript missense_variant 665/1426 544/1251 182/416 V/L Gtg/Ttg rs781941982,COSM1751283 1 -1 ACTL9 HGNC HGNC:28494 protein_coding YES CCDS12207.1 ENSP00000316674 Q8TC94 UPI000000DB15 NM_178525.4 tolerated(0.14) 1/1 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF194,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 0,1 MODERATE 1 SNV 0,1 1 PASS rs781941982 . 0 207 0 3 0 0 0 0 -20 0.9999932 1 1 1 0 A 3 1 78 8698158 8698158 C A 1 0 0 0 0 1 0 0 0 247 507 18 2 2 ACTL9 19 8698158 Missense_Mutation SNP C C3N-01415_T 143466 8698158 49919458 459 24206 MUC16 0 . GRCh38 19 8901827 8901827 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.38703C>A p.= p.G12901G ENST00000397910 35/84 280 233 47 325 325 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript synonymous_variant 38907/43816 38703/43524 12901/14507 G ggC/ggA 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 35/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,SMART_domains:SM00200,Superfamily_domains:0047452 LOW 1 SNV 5 1 PASS rs922032342 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 8901827 8901827 G T 1 0 0 0 0 0 0 0 1 9972 1190 42 2 2 MUC16 19 8901827 Silent SNP G C3N-01415_T 203669 8901827 49715789 460 24207 EPOR 0 . GRCh38 19 11381119 11381119 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.676G>A p.Glu226Lys p.E226K ENST00000222139 5/8 318 290 28 360 360 0 strelka-varscan-mutect EPOR,missense_variant,p.Glu226Lys,ENST00000222139,NM_000121.3;EPOR,missense_variant,p.Glu226Lys,ENST00000592375,;SWSAP1,downstream_gene_variant,,ENST00000312423,NM_175871.3;EPOR,3_prime_UTR_variant,,ENST00000591958,;EPOR,3_prime_UTR_variant,,ENST00000586890,;EPOR,3_prime_UTR_variant,,ENST00000588859,;EPOR,non_coding_transcript_exon_variant,,ENST00000588681,;EPOR,non_coding_transcript_exon_variant,,ENST00000589402,;EPOR,non_coding_transcript_exon_variant,,ENST00000590927,;RGL3,downstream_gene_variant,,ENST00000563726,;RGL3,downstream_gene_variant,,ENST00000562663,; T ENST00000222139 Transcript missense_variant 781/2411 676/1527 226/508 E/K Gag/Aag 1 -1 EPOR HGNC HGNC:3416 protein_coding YES CCDS12260.1 ENSP00000222139 P19235 UPI000012A0AD NM_000121.3 tolerated(0.17) 5/8 PROSITE_profiles:PS50853,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF28,PROSITE_patterns:PS01352,Gene3D:2.60.40.10,PIRSF_domain:PIRSF001959,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 11381119 11381119 C T 1 0 0 0 0 1 0 0 0 5036 835 29 3 3 EPOR 19 11381119 Missense_Mutation SNP C C3N-01415_T 2479292 11381119 47236497 461 24208 ILVBL 0 . GRCh38 19 15125029 15125029 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.31G>T p.Gly11Trp p.G11W ENST00000263383 2/16 180 150 30 182 182 0 strelka-varscan-mutect ILVBL,missense_variant,p.Gly11Trp,ENST00000263383,NM_006844.4;ILVBL,missense_variant,p.Gly11Trp,ENST00000527093,;ILVBL,missense_variant,p.Gly11Trp,ENST00000533747,;ILVBL,intron_variant,,ENST00000534378,;ILVBL,intron_variant,,ENST00000598709,;ILVBL,intron_variant,,ENST00000600984,;AC003956.1,intron_variant,,ENST00000598450,;ILVBL,intron_variant,,ENST00000531635,;ILVBL,missense_variant,p.Gly11Trp,ENST00000533148,;ILVBL,non_coding_transcript_exon_variant,,ENST00000599324,;ILVBL,upstream_gene_variant,,ENST00000533086,; A ENST00000263383 Transcript missense_variant 171/2304 31/1899 11/632 G/W Ggg/Tgg 1 -1 ILVBL HGNC HGNC:6041 protein_coding YES CCDS12325.1 ENSP00000263383 A1L0T0 UPI000007055E NM_006844.4 tolerated_low_confidence(0.15) 2/16 MODERATE 1 SNV 1 1 PASS rs1397568008 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 15125029 15125029 C A 1 0 0 0 0 1 0 0 0 7618 594 21 2 2 ILVBL 19 15125029 Missense_Mutation SNP C C3N-01415_T 3743910 15125029 43492587 462 24209 CYP4F3 0 . GRCh38 19 15641584 15641584 + Silent SNP C C A rs138587161 C3N-01415_T C3N-01415_N C C c.169C>A p.= p.R57R ENST00000221307 2/13 355 270 85 356 356 0 strelka-varscan-mutect CYP4F3,synonymous_variant,p.=,ENST00000221307,NM_000896.2;CYP4F3,synonymous_variant,p.=,ENST00000591058,NM_001199208.1;CYP4F3,synonymous_variant,p.=,ENST00000586182,NM_001199209.1;CYP4F3,synonymous_variant,p.=,ENST00000585846,;CYP4F3,intron_variant,,ENST00000620621,;CYP4F3,synonymous_variant,p.=,ENST00000587360,;CYP4F3,non_coding_transcript_exon_variant,,ENST00000592279,;CYP4F3,upstream_gene_variant,,ENST00000609670,; A ENST00000221307 Transcript synonymous_variant 216/5050 169/1563 57/520 R Cgg/Agg rs138587161,COSM3970777,COSM3970778 1 1 CYP4F3 HGNC HGNC:2646 protein_coding YES CCDS12332.1 ENSP00000221307 Q08477 A0A024R7J8 UPI0000052BE3 NM_000896.2 2/13 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF25,Superfamily_domains:SSF48264 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs138587161 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 15641584 15641584 C A 1 0 0 0 0 0 0 0 1 3993 527 19 1 1 CYP4F3 19 15641584 Silent SNP C C3N-01415_T 516555 15641584 42976032 463 24210 CYP4F3 0 . GRCh38 19 15650016 15650016 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.751C>T p.Pro251Ser p.P251S ENST00000221307 7/13 366 302 64 446 446 0 strelka-varscan-mutect CYP4F3,missense_variant,p.Pro251Ser,ENST00000221307,NM_000896.2;CYP4F3,missense_variant,p.Pro251Ser,ENST00000591058,NM_001199208.1;CYP4F3,missense_variant,p.Pro251Ser,ENST00000586182,NM_001199209.1;CYP4F3,missense_variant,p.Pro251Ser,ENST00000585846,;CYP4F3,missense_variant,p.Pro251Ser,ENST00000620621,;CYP4F3,missense_variant,p.Pro13Ser,ENST00000592424,;CYP4F3,non_coding_transcript_exon_variant,,ENST00000592279,;CYP4F3,downstream_gene_variant,,ENST00000587360,;CYP4F3,downstream_gene_variant,,ENST00000609670,; T ENST00000221307 Transcript missense_variant 798/5050 751/1563 251/520 P/S Cct/Tct 1 1 CYP4F3 HGNC HGNC:2646 protein_coding YES CCDS12332.1 ENSP00000221307 Q08477 A0A024R7J8 UPI0000052BE3 NM_000896.2 tolerated(0.29) 7/13 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF25,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 15650016 15650016 C T 1 0 0 0 0 1 0 0 0 3993 623 22 3 3 CYP4F3 19 15650016 Missense_Mutation SNP C C3N-01415_T 8432 15650016 42967600 464 24211 FAM32A 0 . GRCh38 19 16185766 16185766 + Splice_Site SNP G G T novel C3N-01415_T C3N-01415_N G G c.216+1G>T p.X72_splice ENST00000263384 105 99 6 97 97 0 strelka-varscan-mutect FAM32A,splice_donor_variant,,ENST00000263384,NM_014077.3;FAM32A,splice_donor_variant,,ENST00000589852,;FAM32A,splice_donor_variant,,ENST00000588367,;FAM32A,splice_donor_variant,,ENST00000587351,;CTD-2562J15.4,downstream_gene_variant,,ENST00000591038,;Metazoa_SRP,upstream_gene_variant,,ENST00000621370,;FAM32A,splice_donor_variant,,ENST00000585831,; T ENST00000263384 Transcript splice_donor_variant -/1455 216/339 72/112 1 1 FAM32A HGNC HGNC:24563 protein_coding YES CCDS12341.1 ENSP00000263384 Q9Y421 A0A024R7I4 UPI0000073135 NM_014077.3 2/3 HIGH 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -12.12788 0.9999965 1 1 1 0 T 5 4 78 16185766 16185766 G T 1 0 0 0 0 0 0 1 0 5434 1275 44 2 2 FAM32A 19 16185766 Splice_Site SNP G C3N-01415_T 535750 16185766 42431850 465 24212 SLC5A5 0 . GRCh38 19 17882199 17882199 + Missense_Mutation SNP C C A rs755539179 C3N-01415_T C3N-01415_N C C c.1222C>A p.Leu408Ile p.L408I ENST00000222248 10/15 602 526 76 587 586 1 strelka-varscan-mutect SLC5A5,missense_variant,p.Leu408Ile,ENST00000222248,NM_000453.2;SLC5A5,non_coding_transcript_exon_variant,,ENST00000597109,; A ENST00000222248 Transcript missense_variant 1569/3576 1222/1932 408/643 L/I Ctc/Atc rs755539179 1 1 SLC5A5 HGNC HGNC:11040 protein_coding YES CCDS12368.1 ENSP00000222248 Q92911 UPI00001359F6 NM_000453.2 deleterious(0.01) 10/15 Low_complexity_(Seg):seg,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF18,Pfam_domain:PF00474,TIGRFAM_domain:TIGR00813 MODERATE 1 SNV 1 1 PASS rs755539179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 17882199 17882199 C A 1 0 0 0 0 1 0 0 0 14951 797 28 2 2 SLC5A5 19 17882199 Missense_Mutation SNP C C3N-01415_T 1696433 17882199 40735417 466 24213 IL12RB1 0 . GRCh38 19 18069670 18069670 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.1065C>T p.= p.T355T ENST00000600835 11/18 289 263 26 315 315 0 strelka-varscan-mutect IL12RB1,synonymous_variant,p.=,ENST00000600835,NM_001290024.1;IL12RB1,synonymous_variant,p.=,ENST00000593993,NM_001290023.1,NM_005535.2;IL12RB1,downstream_gene_variant,,ENST00000322153,NM_153701.2; A ENST00000600835 Transcript synonymous_variant 1364/2901 1065/1989 355/662 T acC/acT 1 -1 IL12RB1 HGNC HGNC:5971 protein_coding YES CCDS54232.1 ENSP00000470788 P42701 UPI00000502CE NM_001290024.1 11/18 hmmpanther:PTHR23036:SF51,hmmpanther:PTHR23036,PROSITE_patterns:PS01353 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 18069670 18069670 G A 1 0 0 0 0 0 0 0 1 7534 1335 47 3 3 IL12RB1 19 18069670 Silent SNP G C3N-01415_T 187471 18069670 40547946 467 24214 CILP2 0 . GRCh38 19 19544955 19544955 + Missense_Mutation SNP G G T rs368883992 C3N-01415_T C3N-01415_N G G c.2410G>T p.Ala804Ser p.A804S ENST00000291495 8/8 169 147 22 207 207 0 strelka-varscan-mutect CILP2,missense_variant,p.Ala810Ser,ENST00000586018,;CILP2,missense_variant,p.Ala804Ser,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; T ENST00000291495 Transcript missense_variant 2495/4199 2410/3471 804/1156 A/S Gcc/Tcc rs368883992 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 tolerated(0.05) 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 MODERATE 1 SNV 1 1 PASS rs368883992 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 19544955 19544955 G T 1 0 0 0 0 1 0 0 0 3192 1087 38 1 1 CILP2 19 19544955 Missense_Mutation SNP G C3N-01415_T 1475285 19544955 39072661 468 24215 ZNF85 0 . GRCh38 19 20949379 20949379 + Missense_Mutation SNP A A G rs775582693 C3N-01415_T C3N-01415_N A A c.865A>G p.Lys289Glu p.K289E ENST00000328178 4/4 222 193 29 334 332 2 strelka-varscan-mutect ZNF85,missense_variant,p.Lys289Glu,ENST00000328178,NM_003429.4;ZNF85,missense_variant,p.Lys256Glu,ENST00000345030,;ZNF85,missense_variant,p.Lys237Glu,ENST00000596534,;ZNF85,missense_variant,p.Lys212Glu,ENST00000599064,;ZNF85,downstream_gene_variant,,ENST00000595742,;ZNF85,downstream_gene_variant,,ENST00000598862,;ZNF85,downstream_gene_variant,,ENST00000597314,;ZNF85,downstream_gene_variant,,ENST00000595854,;ZNF85,downstream_gene_variant,,ENST00000599885,;ZNF85,downstream_gene_variant,,ENST00000601924,;ZNF85,downstream_gene_variant,,ENST00000601284,NM_001256171.1;ZNF85,non_coding_transcript_exon_variant,,ENST00000601023,; G ENST00000328178 Transcript missense_variant 978/2296 865/1788 289/595 K/E Aaa/Gaa rs775582693,COSM349533 1 1 ZNF85 HGNC HGNC:13160 protein_coding YES CCDS32977.1 ENSP00000329793 Q03923 UPI0000203897 NM_003429.4 tolerated(1) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF88,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775582693 . 0 203 3 3 0 0 0 0 -20 0.9998886 1 1 1 0 G 3 3 78 20949379 20949379 A G 1 0 0 0 0 1 0 0 0 18781 363 13 5 5 ZNF85 19 20949379 Missense_Mutation SNP A C3N-01415_T 1404424 20949379 37668237 469 24216 CD22 0 . GRCh38 19 35341576 35341576 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1741G>T p.Ala581Ser p.A581S ENST00000085219 8/14 118 102 16 152 152 0 strelka-varscan-mutect CD22,missense_variant,p.Ala581Ser,ENST00000085219,NM_001771.3;CD22,missense_variant,p.Ala493Ser,ENST00000536635,NM_001185099.1;CD22,missense_variant,p.Ala404Ser,ENST00000341773,NM_001185101.1;CD22,missense_variant,p.Ala581Ser,ENST00000544992,NM_001185100.1;CD22,missense_variant,p.Ala409Ser,ENST00000419549,NM_001278417.1;CD22,missense_variant,p.Ala404Ser,ENST00000594250,;CD22,downstream_gene_variant,,ENST00000613136,;CD22,downstream_gene_variant,,ENST00000599811,;CD22,downstream_gene_variant,,ENST00000600424,;CD22,upstream_gene_variant,,ENST00000578146,;CD22,non_coding_transcript_exon_variant,,ENST00000598815,;CD22,downstream_gene_variant,,ENST00000597433,;CD22,downstream_gene_variant,,ENST00000598028,;CD22,downstream_gene_variant,,ENST00000601732,;CD22,downstream_gene_variant,,ENST00000601329,;CD22,3_prime_UTR_variant,,ENST00000601769,;CD22,3_prime_UTR_variant,,ENST00000594125,;CD22,non_coding_transcript_exon_variant,,ENST00000600655,;CD22,non_coding_transcript_exon_variant,,ENST00000602123,;CD22,downstream_gene_variant,,ENST00000594349,;CD22,upstream_gene_variant,,ENST00000593704,; T ENST00000085219 Transcript missense_variant 1807/3268 1741/2544 581/847 A/S Gcg/Tcg 1 1 CD22 HGNC HGNC:1643 protein_coding YES CCDS12457.1 ENSP00000085219 P20273 Q0EAF5 UPI000012733D NM_001771.3 tolerated(0.66) 8/14 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF60,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF13895,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 35341576 35341576 G T 1 0 0 0 0 1 0 0 0 2688 971 34 2 2 CD22 19 35341576 Missense_Mutation SNP G C3N-01415_T 14392197 35341576 23276040 470 24217 CAPNS1 0 . GRCh38 19 36146025 36146025 + Missense_Mutation SNP G G T rs550791287 C3N-01415_T C3N-01415_N G G c.575G>T p.Ser192Ile p.S192I ENST00000246533 8/11 450 407 43 504 504 0 strelka-varscan-mutect CAPNS1,missense_variant,p.Ser192Ile,ENST00000246533,NM_001749.3,NM_001003962.2;CAPNS1,missense_variant,p.Ser192Ile,ENST00000587718,;CAPNS1,missense_variant,p.Ser202Ile,ENST00000628018,;CAPNS1,missense_variant,p.Ser192Ile,ENST00000588815,NM_001302632.1;CAPNS1,missense_variant,p.Ser162Ile,ENST00000628306,;CAPNS1,missense_variant,p.Ser202Ile,ENST00000588780,;CAPNS1,missense_variant,p.Ser162Ile,ENST00000590874,;CAPNS1,missense_variant,p.Ser80Ile,ENST00000592354,;CAPNS1,missense_variant,p.Ser137Ile,ENST00000586851,;CAPNS1,missense_variant,p.Ser124Ile,ENST00000586963,;CAPNS1,intron_variant,,ENST00000629983,;CAPNS1,intron_variant,,ENST00000589146,;CAPNS1,intron_variant,,ENST00000590211,;CAPNS1,downstream_gene_variant,,ENST00000591041,;COX7A1,downstream_gene_variant,,ENST00000292907,NM_001864.3;CAPNS1,downstream_gene_variant,,ENST00000592483,;COX7A1,downstream_gene_variant,,ENST00000437291,;COX7A1,downstream_gene_variant,,ENST00000589154,;AD001527.7,intron_variant,,ENST00000604228,;CAPNS1,missense_variant,p.Ser143Ile,ENST00000590049,;CAPNS1,non_coding_transcript_exon_variant,,ENST00000589162,;COX7A1,downstream_gene_variant,,ENST00000481297,; T ENST00000246533 Transcript missense_variant 1173/1918 575/807 192/268 S/I aGt/aTt rs550791287 1 1 CAPNS1 HGNC HGNC:1481 protein_coding YES CCDS12489.1 ENSP00000246533 P04632 UPI0000000E07 NM_001749.3,NM_001003962.2 tolerated(0.29) 8/11 PROSITE_profiles:PS50222,hmmpanther:PTHR10183:SF38,hmmpanther:PTHR10183,PROSITE_patterns:PS00018,Gene3D:1.10.238.10,Pfam_domain:PF13202,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs550791287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 36146025 36146025 G T 1 0 0 0 0 1 0 0 0 2328 1029 36 2 2 CAPNS1 19 36146025 Missense_Mutation SNP G C3N-01415_T 804449 36146025 22471591 471 24218 ZNF420 0 . GRCh38 19 37127490 37127490 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.499T>C p.Tyr167His p.Y167H ENST00000337995 5/5 142 129 13 184 184 0 strelka-varscan-mutect ZNF420,missense_variant,p.Tyr167His,ENST00000337995,NM_144689.3;ZNF420,missense_variant,p.Tyr167His,ENST00000304239,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,downstream_gene_variant,,ENST00000589245,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000590332,;ZNF420,upstream_gene_variant,,ENST00000585862,;CTC-454I21.4,downstream_gene_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,upstream_gene_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,; C ENST00000337995 Transcript missense_variant 714/3535 499/2067 167/688 Y/H Tat/Cat 1 1 ZNF420 HGNC HGNC:20649 protein_coding YES CCDS12498.1 ENSP00000338770 Q8TAQ5 UPI000007049F NM_144689.3 deleterious(0.05) 5/5 PROSITE_profiles:PS50157,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 37127490 37127490 T C 1 0 0 0 0 1 0 0 0 18469 1522 53 5 5 ZNF420 19 37127490 Missense_Mutation SNP T C3N-01415_T 981465 37127490 21490126 472 24219 TTC9B 0 . GRCh38 19 40218264 40218264 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.118G>A p.Gly40Ser p.G40S ENST00000311308 1/3 124 109 15 130 130 0 strelka-varscan-mutect TTC9B,missense_variant,p.Gly40Ser,ENST00000311308,NM_152479.5;MAP3K10,downstream_gene_variant,,ENST00000253055,NM_002446.3;CNTD2,downstream_gene_variant,,ENST00000430325,NM_024877.3;CNTD2,downstream_gene_variant,,ENST00000513948,;CNTD2,downstream_gene_variant,,ENST00000599263,;TTC9B,non_coding_transcript_exon_variant,,ENST00000593586,;MAP3K10,downstream_gene_variant,,ENST00000597986,;CNTD2,downstream_gene_variant,,ENST00000221818,;MAP3K10,downstream_gene_variant,,ENST00000594791,;CNTD2,downstream_gene_variant,,ENST00000593335,; T ENST00000311308 Transcript missense_variant 136/843 118/720 40/239 G/S Ggc/Agc 1 -1 TTC9B HGNC HGNC:26395 protein_coding YES CCDS12550.1 ENSP00000311760 Q8N6N2 UPI000006E8C1 NM_152479.5 tolerated(0.14) 1/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 40218264 40218264 C T 1 0 0 0 0 1 0 0 0 17226 594 21 3 3 TTC9B 19 40218264 Missense_Mutation SNP C C3N-01415_T 3090774 40218264 18399352 473 24220 DMRTC2 0 . GRCh38 19 41849256 41849256 + Missense_Mutation SNP C C A rs781913731 C3N-01415_T C3N-01415_N C C c.755C>A p.Thr252Lys p.T252K ENST00000269945 6/9 148 132 16 169 169 0 strelka-varscan-mutect DMRTC2,missense_variant,p.Thr252Lys,ENST00000269945,NM_001040283.2;DMRTC2,missense_variant,p.Thr252Lys,ENST00000596827,;LYPD4,upstream_gene_variant,,ENST00000609812,NM_173506.6;LYPD4,upstream_gene_variant,,ENST00000601246,;DMRTC2,downstream_gene_variant,,ENST00000596660,;DMRTC2,downstream_gene_variant,,ENST00000600017,;DMRTC2,downstream_gene_variant,,ENST00000596258,;DMRTC2,downstream_gene_variant,,ENST00000602098,;DMRTC2,splice_region_variant,,ENST00000601660,;DMRTC2,upstream_gene_variant,,ENST00000599022,; A ENST00000269945 Transcript missense_variant,splice_region_variant 806/1792 755/1104 252/367 T/K aCa/aAa rs781913731 1 1 DMRTC2 HGNC HGNC:13911 protein_coding YES CCDS33034.1 ENSP00000269945 Q8IXT2 UPI0000071B2A NM_001040283.2 tolerated(0.08) 6/9 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF15,Pfam_domain:PF15791 MODERATE 1 SNV 1 1 PASS rs781913731 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 41849256 41849256 C A 1 0 0 0 0 1 0 0 0 4399 550 19 1 1 DMRTC2 19 41849256 Missense_Mutation SNP C C3N-01415_T 1630992 41849256 16768360 474 24221 ZNF574 0 . GRCh38 19 42078799 42078799 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.193G>T p.Gly65Cys p.G65C ENST00000600245 2/2 198 165 33 232 232 0 strelka-varscan-mutect ZNF574,missense_variant,p.Gly65Cys,ENST00000600245,;ZNF574,missense_variant,p.Gly155Cys,ENST00000222339,;ZNF574,missense_variant,p.Gly65Cys,ENST00000359044,NM_022752.5;ZNF574,missense_variant,p.Gly65Cys,ENST00000597391,; T ENST00000600245 Transcript missense_variant 848/3598 193/2691 65/896 G/C Ggc/Tgc 1 1 ZNF574 HGNC HGNC:26166 protein_coding YES CCDS12596.1 ENSP00000469029 Q6ZN55 UPI00001AE536 tolerated(0.06) 2/2 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF38 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 42078799 42078799 G T 1 0 0 0 0 1 0 0 0 18580 1232 43 2 2 ZNF574 19 42078799 Missense_Mutation SNP G C3N-01415_T 229543 42078799 16538817 475 24222 ZNF45 0 . GRCh38 19 43919576 43919576 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.139G>T p.Val47Leu p.V47L ENST00000269973 8/10 147 130 17 161 161 0 varscan-mutect ZNF45,missense_variant,p.Val47Leu,ENST00000269973,NM_003425.3;ZNF45,missense_variant,p.Val47Leu,ENST00000615985,;ZNF45,missense_variant,p.Val47Leu,ENST00000589703,;ZNF45,missense_variant,p.Val11Leu,ENST00000588140,;RP11-15A1.2,intron_variant,,ENST00000586247,; A ENST00000269973 Transcript missense_variant 1230/3898 139/2049 47/682 V/L Gtg/Ttg 1 -1 ZNF45 HGNC HGNC:13111 protein_coding YES CCDS12632.1 ENSP00000269973 Q02386 UPI0000001C64 NM_003425.3 tolerated(0.13) 8/10 PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF174,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 43919576 43919576 C A 1 0 0 0 0 1 0 0 0 18492 579 20 2 2 ZNF45 19 43919576 Missense_Mutation SNP C C3N-01415_T 1840777 43919576 14698040 476 24223 INAFM1 0 . GRCh38 19 47275084 47275084 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.165G>T p.Trp55Cys p.W55C ENST00000552360 1/1 362 316 46 378 377 1 strelka-varscan-mutect INAFM1,missense_variant,p.Trp55Cys,ENST00000552360,NM_178511.5;CCDC9,downstream_gene_variant,,ENST00000221922,NM_015603.2;CCDC9,downstream_gene_variant,,ENST00000600117,; T ENST00000552360 Transcript missense_variant 632/1255 165/429 55/142 W/C tgG/tgT 1 1 INAFM1 HGNC HGNC:27406 protein_coding YES CCDS46131.1 ENSP00000447679 C9JVW0 UPI0000070F52 NM_178511.5 deleterious_low_confidence(0) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR34929:SF1,hmmpanther:PTHR34929,Pfam_domain:PF15018 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 47275084 47275084 G T 1 0 0 0 0 1 0 0 0 7633 1241 43 2 2 INAFM1 19 47275084 Missense_Mutation SNP G C3N-01415_T 3355508 47275084 11342532 477 24224 ZNF541 0 . GRCh38 19 47544393 47544393 + Frame_Shift_Del DEL C C - novel C3N-01415_T C3N-01415_N C C c.2136delG p.Leu713CysfsTer63 p.L713Cfs*63 ENST00000391901 3/15 259 235 24 323 323 0 varindel-pindel ZNF541,frameshift_variant,p.Leu713CysfsTer63,ENST00000314121,;ZNF541,frameshift_variant,p.Leu713CysfsTer63,ENST00000391901,NM_001277075.1;ZNF541,frameshift_variant,p.Leu291CysfsTer63,ENST00000595558,;ZNF541,frameshift_variant,p.Leu304CysfsTer63,ENST00000263351,;ZNF541,upstream_gene_variant,,ENST00000487275,; - ENST00000391901 Transcript frameshift_variant 2136/4580 2136/4041 712/1346 S/X tcG/tc 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 3/15 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 - 7 5 78 47544393 47544393 C - 1 0 1 0 1 0 0 0 0 18549 755 27 0 0 ZNF541 19 47544393 Frame_Shift_Del DEL C C3N-01415_T 269309 47544393 11073223 478 24225 ALDH16A1 0 . GRCh38 19 49466091 49466091 + Silent SNP C C T novel C3N-01415_T C3N-01415_N C C c.1746C>T p.= p.G582G ENST00000293350 14/17 120 114 6 139 139 0 strelka-mutect ALDH16A1,synonymous_variant,p.=,ENST00000293350,NM_153329.3;ALDH16A1,synonymous_variant,p.=,ENST00000455361,NM_001145396.1;ALDH16A1,synonymous_variant,p.=,ENST00000540132,;ALDH16A1,missense_variant,p.Ala120Val,ENST00000600265,;ALDH16A1,3_prime_UTR_variant,,ENST00000593417,;ALDH16A1,non_coding_transcript_exon_variant,,ENST00000599652,;CTD-3148I10.9,intron_variant,,ENST00000599536,;ALDH16A1,upstream_gene_variant,,ENST00000594549,; T ENST00000293350 Transcript synonymous_variant 1909/3153 1746/2409 582/802 G ggC/ggT 1 1 ALDH16A1 HGNC HGNC:28114 protein_coding YES CCDS12766.1 ENSP00000293350 Q8IZ83 UPI000013E0FF NM_153329.3 14/17 Gene3D:3.40.605.10,PIRSF_domain:PIRSF036490,Pfam_domain:PF00171,Superfamily_domains:SSF53720 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -9.011097 0.9999993 1 1 1 0 T 2 4 78 49466091 49466091 C T 1 0 0 0 0 0 0 0 1 588 726 26 3 3 ALDH16A1 19 49466091 Silent SNP C C3N-01415_T 1921698 49466091 9151525 479 24226 LRRC4B 0 . GRCh38 19 50548832 50548832 + Missense_Mutation SNP G G T rs779023193 C3N-01415_T C3N-01415_N G G c.7C>A p.Arg3Ser p.R3S ENST00000599957 2/3 63 48 15 67 67 0 strelka-varscan-mutect LRRC4B,missense_variant,p.Arg3Ser,ENST00000599957,;LRRC4B,missense_variant,p.Arg3Ser,ENST00000389201,NM_001080457.1;LRRC4B,missense_variant,p.Arg3Ser,ENST00000600381,; T ENST00000599957 Transcript missense_variant 205/3019 7/2142 3/713 R/S Cgt/Agt rs779023193 1 -1 LRRC4B HGNC HGNC:25042 protein_coding YES CCDS42595.1 ENSP00000471502 Q9NT99 A0A024R4I8 UPI00000497E7 tolerated_low_confidence(0.1) 2/3 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 3 1 PASS rs779023193 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 50548832 50548832 G T 1 0 0 0 0 1 0 0 0 8902 1087 38 1 1 LRRC4B 19 50548832 Missense_Mutation SNP G C3N-01415_T 1082741 50548832 8068784 480 24227 KLK1 0 . GRCh38 19 50821828 50821828 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.90G>T p.Glu30Asp p.E30D ENST00000301420 2/5 122 110 12 98 98 0 strelka-varscan-mutect KLK1,missense_variant,p.Glu30Asp,ENST00000301420,NM_002257.3;KLK15,downstream_gene_variant,,ENST00000326856,NM_001277081.1;KLK15,downstream_gene_variant,,ENST00000598239,NM_017509.3;KLK15,downstream_gene_variant,,ENST00000596931,NM_001277082.1;MGC45922,downstream_gene_variant,,ENST00000635639,;MGC45922,downstream_gene_variant,,ENST00000634979,;MGC45922,downstream_gene_variant,,ENST00000326989,;MGC45922,downstream_gene_variant,,ENST00000593632,;KLK1,3_prime_UTR_variant,,ENST00000593325,;KLK1,non_coding_transcript_exon_variant,,ENST00000593859,;KLK15,downstream_gene_variant,,ENST00000596531,;KLK15,downstream_gene_variant,,ENST00000601680,;KLK1,upstream_gene_variant,,ENST00000596300,;KLK15,downstream_gene_variant,,ENST00000602114,; A ENST00000301420 Transcript missense_variant 126/866 90/789 30/262 E/D gaG/gaT 1 -1 KLK1 HGNC HGNC:6357 protein_coding YES CCDS12804.1 ENSP00000301420 P06870 UPI000004CA0D NM_002257.3 tolerated(0.1) 2/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF111,hmmpanther:PTHR24256,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs1487017655 . 0 205 4 0 0 0 0 0 -19.99991 1 1 1 1 0 A 3 1 78 50821828 50821828 C A 1 0 0 0 0 1 0 0 0 8266 564 20 2 2 KLK1 19 50821828 Missense_Mutation SNP C C3N-01415_T 272996 50821828 7795788 481 24228 KLK7 0 . GRCh38 19 50981852 50981852 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.136G>C p.Ala46Pro p.A46P ENST00000391807 3/6 254 209 45 273 273 0 strelka-varscan-mutect KLK7,missense_variant,p.Ala46Pro,ENST00000391807,NM_139277.2;KLK7,missense_variant,p.Ala46Pro,ENST00000595820,NM_005046.3;KLK7,5_prime_UTR_variant,,ENST00000597707,NM_001207053.1;KLK7,5_prime_UTR_variant,,ENST00000593904,;CTB-147C22.9,intron_variant,,ENST00000594512,;KLK7,downstream_gene_variant,,ENST00000595638,;KLK7,intron_variant,,ENST00000304045,NM_001243126.1; G ENST00000391807 Transcript missense_variant 238/1912 136/762 46/253 A/P Gcc/Ccc 1 -1 KLK7 HGNC HGNC:6368 protein_coding YES CCDS12812.1 ENSP00000375683 P49862 A0A024R4H6 UPI0000001BC4 NM_139277.2 deleterious(0) 3/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF231,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 50981852 50981852 C G 1 0 0 0 0 1 0 0 0 8278 739 26 4 4 KLK7 19 50981852 Missense_Mutation SNP C C3N-01415_T 160024 50981852 7635764 482 24229 VN1R4 0 . GRCh38 19 53267433 53267433 + Missense_Mutation SNP A A G rs753112793 C3N-01415_T C3N-01415_N A A c.233T>C p.Leu78Pro p.L78P ENST00000311170 1/1 424 372 52 489 489 0 varscan-mutect VN1R4,missense_variant,p.Leu78Pro,ENST00000311170,NM_173857.2;CTD-2245F17.9,downstream_gene_variant,,ENST00000599803,; G ENST00000311170 Transcript missense_variant 291/1048 233/906 78/301 L/P cTt/cCt rs753112793 1 -1 VN1R4 HGNC HGNC:19871 protein_coding YES CCDS33099.1 ENSP00000310856 Q7Z5H5 UPI000004B23A NM_173857.2 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF03402,Prints_domain:PR01534,PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF80,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs753112793 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 53267433 53267433 A G 1 0 0 0 0 1 0 0 0 17728 72 3 5 5 VN1R4 19 53267433 Missense_Mutation SNP A C3N-01415_T 2285581 53267433 5350183 483 24230 ZNF331 0 . GRCh38 19 53577235 53577235 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.675G>T p.= p.R225R ENST00000253144 7/7 206 179 27 238 237 1 strelka-varscan-mutect ZNF331,synonymous_variant,p.=,ENST00000253144,NM_018555.5;ZNF331,synonymous_variant,p.=,ENST00000449416,NM_001317115.1,NM_001317117.1,NM_001317118.1;ZNF331,synonymous_variant,p.=,ENST00000411977,NM_001079906.1,NM_001253799.1,NM_001253798.1;ZNF331,synonymous_variant,p.=,ENST00000512387,NM_001253801.1;ZNF331,synonymous_variant,p.=,ENST00000511154,;ZNF331,synonymous_variant,p.=,ENST00000511593,NM_001079907.1;ZNF331,synonymous_variant,p.=,ENST00000513999,NM_001253800.1;ZNF331,intron_variant,,ENST00000513265,;ZNF331,downstream_gene_variant,,ENST00000514022,;ZNF331,downstream_gene_variant,,ENST00000505949,;ZNF331,downstream_gene_variant,,ENST00000505426,;ZNF331,downstream_gene_variant,,ENST00000502248,;ZNF331,downstream_gene_variant,,ENST00000509047,;ZNF331,downstream_gene_variant,,ENST00000504493,;ZNF331,downstream_gene_variant,,ENST00000514374,;ZNF331,downstream_gene_variant,,ENST00000502616,;ZNF331,downstream_gene_variant,,ENST00000509585,;ZNF331,downstream_gene_variant,,ENST00000511567,; T ENST00000253144 Transcript synonymous_variant 2008/5042 675/1392 225/463 R cgG/cgT 1 1 ZNF331 HGNC HGNC:15489 protein_coding YES CCDS33102.1 ENSP00000253144 Q9NQX6 A0A024R4J5 UPI0000039DC3 NM_018555.5 7/7 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF13,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 53577235 53577235 G T 1 0 0 0 0 0 0 0 1 18421 1190 42 2 2 ZNF331 19 53577235 Silent SNP G C3N-01415_T 309802 53577235 5040381 484 24231 DPRX 0 . GRCh38 19 53636650 53636650 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.238C>G p.His80Asp p.H80D ENST00000376650 3/3 140 106 34 172 172 0 strelka-varscan-mutect DPRX,missense_variant,p.His80Asp,ENST00000376650,NM_001012728.1; G ENST00000376650 Transcript missense_variant 289/648 238/576 80/191 H/D Cat/Gat 1 1 DPRX HGNC HGNC:32166 protein_coding YES CCDS33103.1 ENSP00000365838 A6NFQ7 UPI00004ED62B NM_001012728.1 tolerated(0.5) 3/3 hmmpanther:PTHR24329:SF299,hmmpanther:PTHR24329 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 53636650 53636650 C G 1 0 0 0 0 1 0 0 0 4553 826 29 4 4 DPRX 19 53636650 Missense_Mutation SNP C C3N-01415_T 59415 53636650 4980966 485 24232 LAIR1 0 . GRCh38 19 54355288 54355288 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.844G>T p.Ala282Ser p.A282S ENST00000391742 10/10 108 81 27 101 101 0 strelka-varscan-mutect LAIR1,missense_variant,p.Ala282Ser,ENST00000391742,NM_002287.5;LAIR1,missense_variant,p.Ala264Ser,ENST00000391743,NM_001289026.2,NM_001289027.2;LAIR1,missense_variant,p.Ala281Ser,ENST00000434277,NM_001289025.2;LAIR1,missense_variant,p.Ala265Ser,ENST00000348231,NM_021706.4;LAIR1,missense_variant,p.Ala264Ser,ENST00000474878,NM_001289023.2;LAIR1,downstream_gene_variant,,ENST00000622064,;LAIR1,downstream_gene_variant,,ENST00000440716,;LAIR1,downstream_gene_variant,,ENST00000463489,;LAIR1,downstream_gene_variant,,ENST00000468656,;LAIR1,3_prime_UTR_variant,,ENST00000391741,;LAIR1,non_coding_transcript_exon_variant,,ENST00000475389,;LAIR1,non_coding_transcript_exon_variant,,ENST00000467269,;LAIR1,non_coding_transcript_exon_variant,,ENST00000498511,;LAIR1,downstream_gene_variant,,ENST00000460312,;LAIR1,downstream_gene_variant,,ENST00000418556,;LAIR1,downstream_gene_variant,,ENST00000436513,;LAIR1,downstream_gene_variant,,ENST00000420483,; A ENST00000391742 Transcript missense_variant 997/4901 844/864 282/287 A/S Gca/Tca 1 -1 LAIR1 HGNC HGNC:6477 protein_coding YES CCDS12891.1 ENSP00000375622 Q6GTX8 UPI00034F23B9 NM_002287.5 deleterious(0) 10/10 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF122 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 78 54355288 54355288 C A 1 0 0 0 0 1 0 0 0 8506 710 25 2 2 LAIR1 19 54355288 Missense_Mutation SNP C C3N-01415_T 718638 54355288 4262328 486 24233 LILRB1 0 . GRCh38 19 54636637 54636637 + Missense_Mutation SNP G G T rs756832533 C3N-01415_T C3N-01415_N G G c.1797G>T p.Arg599Ser p.R599S ENST00000324602 14/15 350 305 45 425 425 0 strelka-varscan-mutect LILRB1,missense_variant,p.Arg597Ser,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Arg598Ser,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Arg598Ser,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Arg599Ser,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Arg648Ser,ENST00000427581,;LILRB1,missense_variant,p.Arg599Ser,ENST00000396315,;LILRB1,missense_variant,p.Arg581Ser,ENST00000396317,NM_001278398.2;AC009892.10,intron_variant,,ENST00000456337,;LILRB1,non_coding_transcript_exon_variant,,ENST00000462628,;LILRB1,downstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,3_prime_UTR_variant,,ENST00000421584,;LILRB1,downstream_gene_variant,,ENST00000480375,;LILRB1,downstream_gene_variant,,ENST00000487425,; T ENST00000324602 Transcript missense_variant 1962/2774 1797/1959 599/652 R/S agG/agT rs756832533,COSM1481496 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 tolerated(0.05) 14/15 0,1 MODERATE SNV 5 0,1 1 PASS rs756832533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 54636637 54636637 G T 1 0 0 0 0 1 0 0 0 8698 1194 42 2 2 LILRB1 19 54636637 Missense_Mutation SNP G C3N-01415_T 281349 54636637 3980979 487 24234 LILRB4 0 . GRCh38 19 54663992 54663992 + Silent SNP T T A novel C3N-01415_T C3N-01415_N T T c.309T>A p.= p.P103P ENST00000391736 5/14 239 209 30 373 373 0 strelka-varscan-mutect LILRB4,synonymous_variant,p.=,ENST00000391736,NM_001278426.3;LILRB4,synonymous_variant,p.=,ENST00000430952,NM_001278427.3;LILRB4,synonymous_variant,p.=,ENST00000391733,NM_001278429.3,NM_001278428.3;LILRB4,synonymous_variant,p.=,ENST00000391734,;LILRB4,synonymous_variant,p.=,ENST00000434286,;LILRB4,downstream_gene_variant,,ENST00000270452,;LILRB4,upstream_gene_variant,,ENST00000461262,;LILRB4,3_prime_UTR_variant,,ENST00000494796,;LILRB4,upstream_gene_variant,,ENST00000470943,; A ENST00000391736 Transcript synonymous_variant 624/4002 309/1347 103/448 P ccT/ccA 1 1 LILRB4 HGNC HGNC:6608 protein_coding YES CCDS12902.1 ENSP00000375616 Q8NHJ6 UPI0000034C02 NM_001278426.3 5/14 PROSITE_profiles:PS50835,hmmpanther:PTHR11738:SF30,hmmpanther:PTHR11738,Pfam_domain:PF13895,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 54663992 54663992 T A 1 0 0 0 0 0 0 0 1 8701 1567 55 4 4 LILRB4 19 54663992 Silent SNP T C3N-01415_T 27355 54663992 3953624 488 24235 SYT5 0 . GRCh38 19 55178971 55178972 + Frame_Shift_Ins INS - - G novel C3N-01415_T C3N-01415_N - - c.70dupC p.His24ProfsTer85 p.H24Pfs*85 ENST00000354308 2/9 60 52 8 52 52 0 sindel-varindel SYT5,frameshift_variant,p.His24ProfsTer85,ENST00000354308,NM_003180.2;SYT5,frameshift_variant,p.Thr79HisfsTer27,ENST00000590851,NM_001297774.1;SYT5,frameshift_variant,p.His24ProfsTer85,ENST00000537500,;SYT5,frameshift_variant,p.His24ProfsTer85,ENST00000592470,;SYT5,frameshift_variant,p.His24ProfsTer85,ENST00000589172,;PTPRH,downstream_gene_variant,,ENST00000376350,NM_002842.4;PTPRH,downstream_gene_variant,,ENST00000263434,NM_001161440.2;SYT5,upstream_gene_variant,,ENST00000590859,;SYT5,upstream_gene_variant,,ENST00000587067,;CTD-2587H24.5,downstream_gene_variant,,ENST00000591665,;SYT5,frameshift_variant,p.His24ProfsTer9,ENST00000585461,;SYT5,upstream_gene_variant,,ENST00000588305,;SYT5,upstream_gene_variant,,ENST00000592956,; G ENST00000354308 Transcript frameshift_variant 440-441/3792 70-71/1161 24/386 H/PX cac/cCac 1 -1 SYT5 HGNC HGNC:11513 protein_coding YES CCDS12919.1 ENSP00000346265 O00445 A0A024R4N8 UPI000013C56F NM_003180.2 2/9 hmmpanther:PTHR10024:SF227,hmmpanther:PTHR10024 HIGH 1 insertion 1 1 PASS . . 0 198 12 0 0 0 0 0 -18.01971 0.999897 1 1 1 0 G 7 5 78 55178971 55178971 - G 1 0 1 1 0 0 0 0 0 15871 1696 59 0 0 SYT5 19 55178971 Frame_Shift_Ins INS - C3N-01415_T 514979 55178971 3438645 489 24236 ZNF543 0 . GRCh38 19 57327893 57327893 + Missense_Mutation SNP G G T rs748458287 C3N-01415_T C3N-01415_N G G c.431G>T p.Gly144Val p.G144V ENST00000321545 4/4 219 177 42 246 246 0 strelka-varscan-mutect ZNF543,missense_variant,p.Gly144Val,ENST00000321545,NM_213598.3; T ENST00000321545 Transcript missense_variant 776/3659 431/1803 144/600 G/V gGg/gTg rs748458287 1 1 ZNF543 HGNC HGNC:25281 protein_coding YES CCDS33130.1 ENSP00000322545 Q08ER8 UPI00001D8197 NM_213598.3 deleterious(0.01) 4/4 MODERATE 1 SNV 1 1 PASS rs748458287 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 57327893 57327893 G T 1 0 0 0 0 1 0 0 0 18550 1232 43 2 2 ZNF543 19 57327893 Missense_Mutation SNP G C3N-01415_T 2148922 57327893 1289723 490 24237 ZNF606 0 . GRCh38 19 57979838 57979838 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.842G>A p.Arg281Lys p.R281K ENST00000341164 7/7 238 217 21 324 324 0 strelka-varscan-mutect ZNF606,missense_variant,p.Arg281Lys,ENST00000341164,NM_025027.3;ZNF606,missense_variant,p.Arg281Lys,ENST00000551380,;ZNF606,3_prime_UTR_variant,,ENST00000550599,; T ENST00000341164 Transcript missense_variant 1463/4248 842/2379 281/792 R/K aGa/aAa 1 -1 ZNF606 HGNC HGNC:25879 protein_coding YES CCDS12968.1 ENSP00000343617 Q8WXB4 A0A024R4S7 UPI000013C35B NM_025027.3 tolerated(0.08) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 57979838 57979838 C T 1 0 0 0 0 1 0 0 0 18607 913 32 3 3 ZNF606 19 57979838 Missense_Mutation SNP C C3N-01415_T 651945 57979838 637778 491 24238 ZSCAN1 0 . GRCh38 19 58037968 58037968 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.132C>A p.Phe44Leu p.F44L ENST00000282326 3/6 174 159 15 200 199 1 strelka-varscan-mutect ZSCAN1,missense_variant,p.Phe44Leu,ENST00000282326,NM_182572.3;ZSCAN1,missense_variant,p.Phe44Leu,ENST00000391700,;ZSCAN1,missense_variant,p.Phe44Leu,ENST00000601162,; A ENST00000282326 Transcript missense_variant 379/2054 132/1227 44/408 F/L ttC/ttA 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 deleterious(0) 3/6 PROSITE_profiles:PS50804,hmmpanther:PTHR10032:SF187,hmmpanther:PTHR10032,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -19.83058 0.9999998 1 1 1 0 A 3 1 78 58037968 58037968 C A 1 0 0 0 0 1 0 0 0 18820 854 30 2 2 ZSCAN1 19 58037968 Missense_Mutation SNP C C3N-01415_T 58130 58037968 579648 492 24239 ZNF497 0 . GRCh38 19 58357540 58357540 + Silent SNP C C A rs148878757 C3N-01415_T C3N-01415_N C C c.96G>T p.= p.G32G ENST00000311044 3/3 83 68 15 104 104 0 strelka-varscan-mutect ZNF497,synonymous_variant,p.=,ENST00000311044,NM_198458.2;ZNF497,synonymous_variant,p.=,ENST00000425453,NM_001207009.1;ZNF497,synonymous_variant,p.=,ENST00000595763,;A1BG,upstream_gene_variant,,ENST00000263100,NM_130786.3;A1BG,upstream_gene_variant,,ENST00000600966,;A1BG-AS1,downstream_gene_variant,,ENST00000595302,;A1BG-AS1,downstream_gene_variant,,ENST00000594950,;CTD-2619J13.9,upstream_gene_variant,,ENST00000599952,;A1BG-AS1,downstream_gene_variant,,ENST00000600686,;A1BG-AS1,downstream_gene_variant,,ENST00000593960,;A1BG-AS1,downstream_gene_variant,,ENST00000593374,;A1BG-AS1,downstream_gene_variant,,ENST00000600379,;A1BG-AS1,downstream_gene_variant,,ENST00000599728,;CTD-2619J13.8,intron_variant,,ENST00000599109,;CTD-2619J13.8,upstream_gene_variant,,ENST00000600123,;CTD-2619J13.8,upstream_gene_variant,,ENST00000596636,;A1BG,upstream_gene_variant,,ENST00000595014,; A ENST00000311044 Transcript synonymous_variant 285/3468 96/1497 32/498 G ggG/ggT rs148878757,COSM1613000 1 -1 ZNF497 HGNC HGNC:23714 protein_coding YES CCDS12977.1 ENSP00000311183 Q6ZNH5 UPI00001D819C NM_198458.2 3/3 0,1 LOW SNV 2 0,1 1 PASS rs148878757 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 58357540 58357540 C A 1 0 0 0 0 0 0 0 1 18519 610 22 2 2 ZNF497 19 58357540 Silent SNP C C3N-01415_T 319572 58357540 260076 493 24240 SIRPB1 0 . GRCh38 20 1578383 1578383 + Missense_Mutation SNP C C T rs572529769,rs866668053 C3N-01415_T C3N-01415_N C C c.388G>A p.Asp130Asn p.D130N ENST00000381605 2/6 447 424 23 399 398 1 varscan-mutect SIRPB1,missense_variant,p.Asp130Asn,ENST00000381605,NM_006065.3;SIRPB1,missense_variant,p.Asp130Asn,ENST00000381603,NM_001083910.2;SIRPB1,missense_variant,p.Asp129Asn,ENST00000262929,;RP4-576H24.4,missense_variant,p.Asp130Asn,ENST00000564763,;SIRPB1,missense_variant,p.Asp129Asn,ENST00000563840,;RP4-576H24.4,missense_variant,p.Asp129Asn,ENST00000567028,;RP4-576H24.4,intron_variant,,ENST00000566961,;SIRPB1,intron_variant,,ENST00000569629,;SIRPB1,non_coding_transcript_exon_variant,,ENST00000565775,; T ENST00000381605 Transcript missense_variant 453/3241 388/1197 130/398 D/N Gac/Aac rs572529769,rs866668053,COSM1724829 1 -1 SIRPB1 HGNC HGNC:15928 protein_coding YES CCDS13019.1 ENSP00000371018 O00241 UPI000036700F NM_006065.3 tolerated(0.17) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,0,1 MODERATE 1 SNV 1 0,0,1 1 PASS rs572529769 . 0 205 0 0 5 0 0 0 -3.909878 0.2788344 1 1 0 0 T 3 4 78 1578383 1578383 C T 1 0 0 0 0 1 0 0 0 14596 884 31 1 1 SIRPB1 20 1578383 Missense_Mutation SNP C C3N-01415_T 1578383 62865784 494 24241 PROKR2 0 . GRCh38 20 5302345 5302345 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.850T>A p.Tyr284Asn p.Y284N ENST00000217270 2/2 824 749 75 830 829 1 strelka-varscan-mutect PROKR2,missense_variant,p.Tyr284Asn,ENST00000217270,NM_144773.2; T ENST00000217270 Transcript missense_variant 850/1155 850/1155 284/384 Y/N Tat/Aat 1 -1 PROKR2 HGNC HGNC:15836 protein_coding YES CCDS13089.1 ENSP00000217270 Q8NFJ6 UPI000003BCC6 NM_144773.2 deleterious(0) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF234,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 5302345 5302345 A T 1 0 0 0 0 1 0 0 0 12686 420 15 4 4 PROKR2 20 5302345 Missense_Mutation SNP A C3N-01415_T 3723962 5302345 59141822 495 24242 CFAP61 0 . GRCh38 20 20251680 20251680 + Missense_Mutation SNP C C G C3N-01415_T C3N-01415_N C C c.2245C>G p.Arg749Gly p.R749G ENST00000245957 20/27 403 326 77 426 426 0 strelka-varscan-mutect CFAP61,missense_variant,p.Arg749Gly,ENST00000245957,NM_015585.3;CFAP61,missense_variant,p.Arg105Gly,ENST00000377293,;CFAP61,missense_variant,p.Arg105Gly,ENST00000389656,;CFAP61,non_coding_transcript_exon_variant,,ENST00000476414,;CFAP61,non_coding_transcript_exon_variant,,ENST00000468719,;CFAP61,missense_variant,p.Arg105Gly,ENST00000377308,;RPL17P1,downstream_gene_variant,,ENST00000445304,; G ENST00000245957 Transcript missense_variant 2321/4082 2245/3714 749/1237 R/G Cga/Gga COSM3544555,COSM3544556 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 deleterious(0) 20/27 Gene3D:3.50.50.60,hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8,Superfamily_domains:SSF51905 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs984625585 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 20251680 20251680 C G 1 0 0 0 0 1 0 0 0 3028 644 23 4 4 CFAP61 20 20251680 Missense_Mutation SNP C C3N-01415_T 14949335 20251680 44192487 496 24243 RALGAPA2 0 . GRCh38 20 20620603 20620603 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1261G>T p.Ala421Ser p.A421S ENST00000202677 11/40 127 118 9 154 154 0 strelka-varscan-mutect RALGAPA2,missense_variant,p.Ala238Ser,ENST00000430436,;RALGAPA2,missense_variant,p.Ala421Ser,ENST00000202677,NM_020343.3; A ENST00000202677 Transcript missense_variant 1269/6152 1261/5622 421/1873 A/S Gct/Tct 1 -1 RALGAPA2 HGNC HGNC:16207 protein_coding YES CCDS46584.1 ENSP00000202677 Q2PPJ7 UPI000040F987 NM_020343.3 tolerated(0.85) 11/40 hmmpanther:PTHR10063,hmmpanther:PTHR10063:SF2 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -17.53447 1 1 1 1 0 A 3 1 78 20620603 20620603 C A 1 0 0 0 0 1 0 0 0 13173 797 28 2 2 RALGAPA2 20 20620603 Missense_Mutation SNP C C3N-01415_T 368923 20620603 43823564 497 24244 PAX1 0 . GRCh38 20 21708669 21708669 + Missense_Mutation SNP C C A novel C3N-01415_T C3N-01415_N C C c.1028C>A p.Pro343His p.P343H ENST00000398485 3/5 768 598 170 716 716 0 strelka-varscan-mutect PAX1,missense_variant,p.Pro343His,ENST00000613128,NM_001257096.1;PAX1,missense_variant,p.Pro343His,ENST00000398485,NM_006192.4;PAX1,missense_variant,p.Pro319His,ENST00000444366,;PAX1,non_coding_transcript_exon_variant,,ENST00000460221,;PAX1,non_coding_transcript_exon_variant,,ENST00000485038,; A ENST00000398485 Transcript missense_variant 1082/2838 1028/1605 343/534 P/H cCt/cAt 1 1 PAX1 HGNC HGNC:8615 protein_coding YES CCDS13146.2 ENSP00000381499 P15863 UPI000179A786 NM_006192.4 deleterious_low_confidence(0) 3/5 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF262 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 21708669 21708669 C A 1 0 0 0 0 1 0 0 0 11563 681 24 2 2 PAX1 20 21708669 Missense_Mutation SNP C C3N-01415_T 1088066 21708669 42735498 498 24245 SYNDIG1 0 . GRCh38 20 24543540 24543540 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.443A>T p.Tyr148Phe p.Y148F ENST00000376862 2/4 168 128 40 168 167 1 strelka-varscan-mutect SYNDIG1,missense_variant,p.Tyr148Phe,ENST00000376862,NM_024893.2; T ENST00000376862 Transcript missense_variant 1076/2522 443/777 148/258 Y/F tAc/tTc 1 1 SYNDIG1 HGNC HGNC:15885 protein_coding YES CCDS13164.1 ENSP00000366058 Q9H7V2 UPI00001285DC NM_024893.2 tolerated(0.08) 2/4 hmmpanther:PTHR14768,hmmpanther:PTHR14768:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 24543540 24543540 A T 1 0 0 0 0 1 0 0 0 15835 391 14 4 4 SYNDIG1 20 24543540 Missense_Mutation SNP A C3N-01415_T 2834871 24543540 39900627 499 24246 TM9SF4 0 . GRCh38 20 32157905 32157905 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1441G>T p.Val481Leu p.V481L ENST00000398022 14/18 404 348 56 377 377 0 strelka-varscan-mutect TM9SF4,missense_variant,p.Val464Leu,ENST00000217315,;TM9SF4,missense_variant,p.Val481Leu,ENST00000398022,NM_014742.3;TM9SF4,upstream_gene_variant,,ENST00000495749,;TM9SF4,upstream_gene_variant,,ENST00000479591,; T ENST00000398022 Transcript missense_variant 1676/3978 1441/1929 481/642 V/L Gtg/Ttg 1 1 TM9SF4 HGNC HGNC:30797 protein_coding YES CCDS13196.2 ENSP00000381104 Q92544 A0A024QYR3 UPI0000206163 NM_014742.3 deleterious(0) 14/18 Pfam_domain:PF02990,hmmpanther:PTHR10766,hmmpanther:PTHR10766:SF55 MODERATE 1 SNV 1 1 PASS rs1315178656 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 32157905 32157905 G T 1 0 0 0 0 1 0 0 0 16424 1377 48 2 2 TM9SF4 20 32157905 Missense_Mutation SNP G C3N-01415_T 7614365 32157905 32286262 500 24247 ZNF335 0 . GRCh38 20 45953749 45953749 + Missense_Mutation SNP T T C novel C3N-01415_T C3N-01415_N T T c.2642A>G p.Tyr881Cys p.Y881C ENST00000322927 18/28 386 291 95 350 350 0 strelka-varscan-mutect ZNF335,missense_variant,p.Tyr881Cys,ENST00000322927,NM_022095.3; C ENST00000322927 Transcript missense_variant 2743/4430 2642/4029 881/1342 Y/C tAc/tGc 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 deleterious(0.01) 18/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 45953749 45953749 T C 1 0 0 0 0 1 0 0 0 18424 1638 57 5 5 ZNF335 20 45953749 Missense_Mutation SNP T C3N-01415_T 13795844 45953749 18490418 501 24248 CDH22 0 . GRCh38 20 46174991 46174991 + Missense_Mutation SNP T T C rs773793973 C3N-01415_T C3N-01415_N T T c.2002A>G p.Ile668Val p.I668V ENST00000537909 12/12 324 296 28 288 288 0 strelka-varscan-mutect CDH22,missense_variant,p.Ile668Val,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Ile668Val,ENST00000372262,;RP5-998H6.2,upstream_gene_variant,,ENST00000450586,; C ENST00000537909 Transcript missense_variant 2645/3902 2002/2487 668/828 I/V Atc/Gtc rs773793973 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 tolerated(1) 12/12 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF01049 MODERATE 1 SNV 2 1 PASS rs773793973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 46174991 46174991 T C 1 0 0 0 0 1 0 0 0 2810 1464 51 5 5 CDH22 20 46174991 Missense_Mutation SNP T C3N-01415_T 221242 46174991 18269176 502 24249 NCOA3 0 . GRCh38 20 47649047 47649047 + Missense_Mutation SNP A A T novel C3N-01415_T C3N-01415_N A A c.3589A>T p.Asn1197Tyr p.N1197Y ENST00000371998 19/23 188 169 19 188 188 0 strelka-varscan-mutect NCOA3,missense_variant,p.Asn1197Tyr,ENST00000372004,NM_006534.3;NCOA3,missense_variant,p.Asn1192Tyr,ENST00000371997,NM_001174088.1;NCOA3,missense_variant,p.Asn1197Tyr,ENST00000371998,NM_001174087.1,NM_181659.2; T ENST00000371998 Transcript missense_variant 3780/4668 3589/4275 1197/1424 N/Y Aac/Tac 1 1 NCOA3 HGNC HGNC:7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 UPI000012FE45 NM_001174087.1,NM_181659.2 deleterious(0) 19/23 hmmpanther:PTHR10684:SF3,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 47649047 47649047 A T 1 0 0 0 0 1 0 0 0 10249 14 1 4 4 NCOA3 20 47649047 Missense_Mutation SNP A C3N-01415_T 1474056 47649047 16795120 503 24250 KCNB1 0 . GRCh38 20 49482274 49482274 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.207G>T p.= p.L69L ENST00000371741 1/2 160 139 21 165 165 0 strelka-varscan-mutect KCNB1,synonymous_variant,p.=,ENST00000371741,NM_004975.2;KCNB1,synonymous_variant,p.=,ENST00000635465,;KCNB1,upstream_gene_variant,,ENST00000635878,;KCNB1,upstream_gene_variant,,ENST00000637357,;KCNB1,upstream_gene_variant,,ENST00000636950,;KCNB1,downstream_gene_variant,,ENST00000635809,; A ENST00000371741 Transcript synonymous_variant 403/11879 207/2577 69/858 L ctG/ctT 1 -1 KCNB1 HGNC HGNC:6231 protein_coding YES CCDS13418.1 ENSP00000360806 Q14721 UPI000012DC80 NM_004975.2 1/2 hmmpanther:PTHR11537:SF134,hmmpanther:PTHR11537,Gene3D:3.30.710.10,Pfam_domain:PF02214,SMART_domains:SM00225,Superfamily_domains:SSF54695 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 49482274 49482274 C A 1 0 0 0 0 0 0 0 1 7928 697 25 2 2 KCNB1 20 49482274 Silent SNP C C3N-01415_T 1833227 49482274 14961893 504 24251 ZFP64 0 . GRCh38 20 52160309 52160309 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.577C>T p.His193Tyr p.H193Y ENST00000216923 5/6 264 238 26 261 261 0 strelka-varscan-mutect ZFP64,missense_variant,p.His193Tyr,ENST00000216923,NM_018197.2;ZFP64,missense_variant,p.His191Tyr,ENST00000371515,NM_199426.1;ZFP64,missense_variant,p.His139Tyr,ENST00000346617,NM_022088.4;ZFP64,missense_variant,p.His193Tyr,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.His193Tyr,ENST00000371518,;ZFP64,non_coding_transcript_exon_variant,,ENST00000477786,;ZFP64,non_coding_transcript_exon_variant,,ENST00000461898,; A ENST00000216923 Transcript missense_variant 927/3264 577/2046 193/681 H/Y Cac/Tac 1 -1 ZFP64 HGNC HGNC:15940 protein_coding YES CCDS13440.1 ENSP00000216923 Q9NPA5 UPI000006D699 NM_018197.2 deleterious(0) 5/6 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF41,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 52160309 52160309 G A 1 0 0 0 0 1 0 0 0 18228 1290 45 3 3 ZFP64 20 52160309 Missense_Mutation SNP G C3N-01415_T 2678035 52160309 12283858 505 24252 TSHZ2 0 . GRCh38 20 53254426 53254426 + Missense_Mutation SNP G G T rs772219519 C3N-01415_T C3N-01415_N G G c.968G>T p.Arg323Leu p.R323L ENST00000371497 2/3 124 90 34 172 171 1 strelka-varscan-mutect TSHZ2,missense_variant,p.Arg323Leu,ENST00000371497,NM_173485.5;TSHZ2,missense_variant,p.Arg320Leu,ENST00000603338,NM_001193421.1;TSHZ2,missense_variant,p.Arg320Leu,ENST00000329613,;RP4-678D15.1,downstream_gene_variant,,ENST00000606932,;TSHZ2,upstream_gene_variant,,ENST00000605656,; T ENST00000371497 Transcript missense_variant 1855/12187 968/3105 323/1034 R/L cGc/cTc rs772219519,COSM5187566 1 1 TSHZ2 HGNC HGNC:13010 protein_coding YES CCDS33490.1 ENSP00000360552 Q9NRE2 UPI0000206747 NM_173485.5 deleterious(0) 2/3 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF3 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772219519 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 53254426 53254426 G T 1 0 0 0 0 1 0 0 0 17129 1087 38 1 1 TSHZ2 20 53254426 Missense_Mutation SNP G C3N-01415_T 1094117 53254426 11189741 506 24253 CASS4 0 . GRCh38 20 56453034 56453034 + Nonsense_Mutation SNP G G T rs770674921 C3N-01415_T C3N-01415_N G G c.1858G>T p.Glu620Ter p.E620* ENST00000360314 6/7 366 340 26 385 384 1 strelka-varscan-mutect CASS4,stop_gained,p.Glu620Ter,ENST00000360314,NM_001164116.1,NM_020356.3,NM_001164114.1;CASS4,intron_variant,,ENST00000434344,NM_001164115.1;CASS4,non_coding_transcript_exon_variant,,ENST00000497244,; T ENST00000360314 Transcript stop_gained 2083/2619 1858/2361 620/786 E/* Gaa/Taa rs770674921 1 1 CASS4 HGNC HGNC:15878 protein_coding YES CCDS33492.1 ENSP00000353462 Q9NQ75 UPI00001285DB NM_001164116.1,NM_020356.3,NM_001164114.1 6/7 hmmpanther:PTHR10654:SF19,hmmpanther:PTHR10654,Pfam_domain:PF12026 HIGH 1 SNV 1 1 PASS rs770674921 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 78 56453034 56453034 G T 1 0 0 0 0 0 1 0 0 2382 1291 45 2 2 CASS4 20 56453034 Nonsense_Mutation SNP G C3N-01415_T 3198608 56453034 7991133 507 24254 NPEPL1 0 . GRCh38 20 58699276 58699276 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.677G>T p.Gly226Val p.G226V ENST00000356091 5/12 124 97 27 95 95 0 strelka-varscan-mutect NPEPL1,missense_variant,p.Gly226Val,ENST00000356091,NM_024663.3;NPEPL1,missense_variant,p.Gly198Val,ENST00000525967,NM_001204872.1;NPEPL1,missense_variant,p.Gly178Val,ENST00000525817,NM_001204873.1;NPEPL1,missense_variant,p.Gly115Val,ENST00000533788,;NPEPL1,splice_region_variant,,ENST00000529976,;NPEPL1,splice_region_variant,,ENST00000527587,;STX16-NPEPL1,splice_region_variant,,ENST00000530122,; T ENST00000356091 Transcript missense_variant,splice_region_variant 965/2378 677/1572 226/523 G/V gGa/gTa 1 1 NPEPL1 HGNC HGNC:16244 protein_coding YES CCDS46621.1 ENSP00000348395 Q8NDH3 UPI000036789E NM_024663.3 deleterious(0) 5/12 hmmpanther:PTHR11963:SF4,hmmpanther:PTHR11963,Pfam_domain:PF00883,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 58699276 58699276 G T 1 0 0 0 0 1 0 0 0 10622 1188 41 2 2 NPEPL1 20 58699276 Missense_Mutation SNP G C3N-01415_T 2246242 58699276 5744891 508 24255 COL9A3 0 . GRCh38 20 62828922 62828922 + Splice_Site SNP G G T novel C3N-01415_T C3N-01415_N G G c.955-1G>T p.X319_splice ENST00000343916 394 354 40 387 387 0 strelka-varscan-mutect COL9A3,splice_acceptor_variant,,ENST00000343916,NM_001853.3;COL9A3,downstream_gene_variant,,ENST00000452372,;COL9A3,splice_acceptor_variant,,ENST00000463487,;COL9A3,upstream_gene_variant,,ENST00000462700,;COL9A3,downstream_gene_variant,,ENST00000489045,;COL9A3,downstream_gene_variant,,ENST00000477612,;COL9A3,upstream_gene_variant,,ENST00000466192,;COL9A3,upstream_gene_variant,,ENST00000472880,;COL9A3,upstream_gene_variant,,ENST00000469852,;COL9A3,upstream_gene_variant,,ENST00000469802,;COL9A3,upstream_gene_variant,,ENST00000481800,;COL9A3,upstream_gene_variant,,ENST00000490398,; T ENST00000343916 Transcript splice_acceptor_variant -/2485 955/2055 319/684 1 1 COL9A3 HGNC HGNC:2219 protein_coding YES CCDS13505.1 ENSP00000341640 Q14050 UPI0000126D51 NM_001853.3 18/31 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 78 62828922 62828922 G T 1 0 0 0 0 0 0 1 0 3498 1014 35 2 2 COL9A3 20 62828922 Splice_Site SNP G C3N-01415_T 4129646 62828922 1615245 509 24256 TPTE 0 . GRCh38 21 10543353 10543353 + Silent SNP A A T novel C3N-01415_T C3N-01415_N A A c.144A>T p.= p.G48G ENST00000618007 7/24 439 414 25 485 485 0 varscan-mutect TPTE,synonymous_variant,p.=,ENST00000618007,NM_199261.3;TPTE,synonymous_variant,p.=,ENST00000612957,;TPTE,intron_variant,,ENST00000622113,NM_199259.3;TPTE,intron_variant,,ENST00000427445,NM_199260.3;TPTE,intron_variant,,ENST00000612746,NM_001290224.1;AL078471.5,intron_variant,,ENST00000612267,; T ENST00000618007 Transcript synonymous_variant 474/2150 144/1656 48/551 G ggA/ggT 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 7/24 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 10543353 10543353 A T 1 0 0 0 0 0 0 0 1 16911 291 11 4 4 TPTE 21 10543353 Silent SNP A C3N-01415_T 10543353 36166630 510 24257 IFNAR2 0 . GRCh38 21 33263022 33263022 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.1070C>T p.Ser357Phe p.S357F ENST00000342136 9/9 291 231 60 323 323 0 strelka-varscan-mutect IFNAR2,missense_variant,p.Ser357Phe,ENST00000342136,NM_001289125.1,NM_207585.2;IFNAR2,3_prime_UTR_variant,,ENST00000404220,;IFNAR2,3_prime_UTR_variant,,ENST00000342101,NM_001289126.1,NM_001289128.1;AP000295.9,intron_variant,,ENST00000433395,;IL10RB,upstream_gene_variant,,ENST00000290200,NM_000628.4;IFNAR2,downstream_gene_variant,,ENST00000382264,NM_207584.2,NM_000874.4;IFNAR2,downstream_gene_variant,,ENST00000443073,;IFNAR2,downstream_gene_variant,,ENST00000413881,;IL10RB-AS1,downstream_gene_variant,,ENST00000411998,;AP000295.9,intron_variant,,ENST00000432231,;IL10RB,upstream_gene_variant,,ENST00000493295,;IFNAR2,downstream_gene_variant,,ENST00000382238,;IL10RB,upstream_gene_variant,,ENST00000422891,;IFNAR2,downstream_gene_variant,,ENST00000417007,; T ENST00000342136 Transcript missense_variant 1396/2899 1070/1548 357/515 S/F tCc/tTc 1 1 IFNAR2 HGNC HGNC:5433 protein_coding YES CCDS13621.1 ENSP00000343957 P48551 UPI000012D69B NM_001289125.1,NM_207585.2 deleterious(0.05) 9/9 hmmpanther:PTHR20859:SF53,hmmpanther:PTHR20859 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 33263022 33263022 C T 1 0 0 0 0 1 0 0 0 7445 855 30 3 3 IFNAR2 21 33263022 Missense_Mutation SNP C C3N-01415_T 22719669 33263022 13446961 511 24258 DOPEY2 0 . GRCh38 21 36239856 36239856 + Missense_Mutation SNP G G T rs748499096 C3N-01415_T C3N-01415_N G G c.2968G>T p.Gly990Trp p.G990W ENST00000399151 18/37 202 165 37 216 215 1 strelka-varscan-mutect DOPEY2,missense_variant,p.Gly990Trp,ENST00000399151,NM_001320714.1,NM_005128.3; T ENST00000399151 Transcript missense_variant 3053/7685 2968/6897 990/2298 G/W Ggg/Tgg rs748499096 1 1 DOPEY2 HGNC HGNC:1291 protein_coding YES CCDS13643.1 ENSP00000382104 Q9Y3R5 UPI000013D876 NM_001320714.1,NM_005128.3 deleterious(0.01) 18/37 hmmpanther:PTHR14042,hmmpanther:PTHR14042:SF23 MODERATE 1 SNV 1 1 PASS rs748499096 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 36239856 36239856 G T 1 0 0 0 0 1 0 0 0 4522 1116 39 1 1 DOPEY2 21 36239856 Missense_Mutation SNP G C3N-01415_T 2976834 36239856 10470127 512 24259 DSCAM 0 . GRCh38 21 40013246 40013246 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.5827C>G p.Leu1943Val p.L1943V ENST00000400454 33/33 220 183 37 191 191 0 strelka-varscan-mutect DSCAM,missense_variant,p.Leu1943Val,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Leu1778Val,ENST00000617870,;DSCAM,missense_variant,p.Leu1677Val,ENST00000404019,; C ENST00000400454 Transcript missense_variant 6305/8552 5827/6039 1943/2012 L/V Ctg/Gtg 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 tolerated_low_confidence(0.08) 33/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 40013246 40013246 G C 1 0 0 0 0 1 0 0 0 4589 991 35 4 4 DSCAM 21 40013246 Missense_Mutation SNP G C3N-01415_T 3773390 40013246 6696737 513 24260 TFF2 0 . GRCh38 21 42346547 42346547 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.377-1G>T p.X126_splice ENST00000291526 135 121 14 164 164 0 strelka-varscan-mutect TFF2,splice_acceptor_variant,,ENST00000291526,NM_005423.4;TFF2,splice_acceptor_variant,,ENST00000475297,;TFF2,splice_acceptor_variant,,ENST00000463771,; A ENST00000291526 Transcript splice_acceptor_variant -/737 377/390 126/129 1 -1 TFF2 HGNC HGNC:11756 protein_coding YES CCDS13684.1 ENSP00000291526 Q03403 UPI0000001632 NM_005423.4 3/3 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 78 42346547 42346547 C A 1 0 0 0 0 0 0 1 0 16237 927 32 2 2 TFF2 21 42346547 Splice_Site SNP C C3N-01415_T 2333301 42346547 4363436 514 24261 POTEH 0 . GRCh38 22 15690397 15690397 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.320C>G p.Pro107Arg p.P107R ENST00000343518 1/11 988 918 70 1024 1022 2 varscan-mutect POTEH,missense_variant,p.Pro107Arg,ENST00000343518,NM_001136213.1;POTEH,intron_variant,,ENST00000621704,;POTEH,missense_variant,p.Pro51Arg,ENST00000452800,; G ENST00000343518 Transcript missense_variant 372/1928 320/1638 107/545 P/R cCc/cGc 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 deleterious_low_confidence(0) 1/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 15690397 15690397 C G 1 0 0 0 0 1 0 0 0 12381 623 22 4 4 POTEH 22 15690397 Missense_Mutation SNP C C3N-01415_T 15690397 35128071 515 24262 POTEH 0 . GRCh38 22 15690456 15690456 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.379G>T p.Ala127Ser p.A127S ENST00000343518 1/11 458 373 85 419 419 0 strelka-varscan-mutect POTEH,missense_variant,p.Ala127Ser,ENST00000343518,NM_001136213.1;POTEH,missense_variant,p.Ala90Ser,ENST00000621704,;POTEH,missense_variant,p.Ala71Ser,ENST00000452800,; T ENST00000343518 Transcript missense_variant 431/1928 379/1638 127/545 A/S Gct/Tct 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 tolerated_low_confidence(0.12) 1/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 15690456 15690456 G T 1 0 0 0 0 1 0 0 0 12381 1319 46 2 2 POTEH 22 15690456 Missense_Mutation SNP G C3N-01415_T 59 15690456 35128012 516 24263 GAB4 0 . GRCh38 22 16965257 16965257 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1300C>A p.Pro434Thr p.P434T ENST00000400588 7/10 258 191 67 288 288 0 strelka-varscan-mutect GAB4,missense_variant,p.Pro434Thr,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,downstream_gene_variant,,ENST00000523144,;GAB4,downstream_gene_variant,,ENST00000520505,;GAB4,3_prime_UTR_variant,,ENST00000465611,; T ENST00000400588 Transcript missense_variant 1408/2630 1300/1725 434/574 P/T Ccg/Acg 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 deleterious(0.03) 7/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 16965257 16965257 G T 1 0 0 0 0 1 0 0 0 6022 1261 44 2 2 GAB4 22 16965257 Missense_Mutation SNP G C3N-01415_T 1274801 16965257 33853211 517 24264 CCDC188 0 . GRCh38 22 20150175 20150175 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.595C>A p.Pro199Thr p.P199T ENST00000439765 2/9 135 124 11 134 134 0 varscan-mutect CCDC188,missense_variant,p.Pro199Thr,ENST00000439765,;ZDHHC8,downstream_gene_variant,,ENST00000334554,NM_013373.3;ZDHHC8,downstream_gene_variant,,ENST00000405930,NM_001185024.1;ZDHHC8,downstream_gene_variant,,ENST00000320602,;CCDC188,upstream_gene_variant,,ENST00000444532,; T ENST00000439765 Transcript missense_variant 674/1475 595/1209 199/402 P/T Ccc/Acc 1 -1 CCDC188 HGNC HGNC:51899 protein_coding YES ENSP00000409542 H7C350 UPI000387C900 tolerated_low_confidence(0.34) 2/9 hmmpanther:PTHR22422:SF6,hmmpanther:PTHR22422 MODERATE SNV 5 1 PASS rs1419351679 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 20150175 20150175 G T 1 0 0 0 0 1 0 0 0 2503 1174 41 2 2 CCDC188 22 20150175 Missense_Mutation SNP G C3N-01415_T 3184918 20150175 30668293 518 24265 P2RX6 0 . GRCh38 22 21015999 21015999 + Silent SNP C C A novel C3N-01415_T C3N-01415_N C C c.222C>A p.= p.S74S ENST00000413302 2/12 232 215 17 249 248 1 strelka-varscan-mutect P2RX6,synonymous_variant,p.=,ENST00000413302,NM_005446.3;P2RX6,synonymous_variant,p.=,ENST00000401443,NM_001159554.1;P2RX6,non_coding_transcript_exon_variant,,ENST00000591411,;TUBA3FP,upstream_gene_variant,,ENST00000422086,;TUBA3FP,upstream_gene_variant,,ENST00000292748,;P2RX6,missense_variant,p.His69Asn,ENST00000432930,;P2RX6,synonymous_variant,p.=,ENST00000442475,;P2RX6,synonymous_variant,p.=,ENST00000422210,;P2RX6,synonymous_variant,p.=,ENST00000452228,;P2RX6,non_coding_transcript_exon_variant,,ENST00000469722,; A ENST00000413302 Transcript synonymous_variant 370/3687 222/1326 74/441 S tcC/tcA 1 1 P2RX6 HGNC HGNC:8538 protein_coding YES CCDS13788.2 ENSP00000416193 O15547 UPI000013C698 NM_005446.3 2/12 Gene3D:3h9vA02,Pfam_domain:PF00864,PIRSF_domain:PIRSF005713,hmmpanther:PTHR10125,hmmpanther:PTHR10125:SF21,TIGRFAM_domain:TIGR00863 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 21015999 21015999 C A 1 0 0 0 0 0 0 0 1 11417 581 21 2 2 P2RX6 22 21015999 Silent SNP C C3N-01415_T 865824 21015999 29802469 519 24266 GGT2 0 . GRCh38 22 21208703 21208703 + Splice_Site SNP C C A novel C3N-01415_T C3N-01415_N C C c.1450-1G>T p.X484_splice ENST00000401924 21 9 12 11 11 0 varscan-mutect GGT2,splice_acceptor_variant,,ENST00000401924,;GGT2,splice_acceptor_variant,,ENST00000424627,;GGT2,splice_acceptor_variant,,ENST00000405188,;FAM230B,intron_variant,,ENST00000440315,; A ENST00000401924 Transcript splice_acceptor_variant -/2366 1450/1710 484/569 1 -1 GGT2 HGNC HGNC:4251 protein_coding YES ENSP00000385721 P36268 UPI00004DE9E9 13/14 HIGH 1 SNV 5 1 PASS . . 41 167 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 78 21208703 21208703 C A 1 0 0 0 0 0 0 1 0 6238 695 24 2 2 GGT2 22 21208703 Splice_Site SNP C C3N-01415_T 192704 21208703 29609765 520 24267 MYO18B 0 . GRCh38 22 25903769 25903769 + Missense_Mutation SNP A A C novel C3N-01415_T C3N-01415_N A A c.5086A>C p.Ser1696Arg p.S1696R ENST00000335473 31/44 285 251 34 335 335 0 strelka-varscan-mutect MYO18B,missense_variant,p.Ser1696Arg,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Ser1697Arg,ENST00000407587,;MYO18B,missense_variant,p.Ser1696Arg,ENST00000536101,;CTA-125H2.2,upstream_gene_variant,,ENST00000453457,;CTA-125H2.2,upstream_gene_variant,,ENST00000600211,;CTA-125H2.2,upstream_gene_variant,,ENST00000609275,;CTA-125H2.2,upstream_gene_variant,,ENST00000597284,;CTA-125H2.2,upstream_gene_variant,,ENST00000609157,;CTA-125H2.2,upstream_gene_variant,,ENST00000608507,;CTA-125H2.2,upstream_gene_variant,,ENST00000595093,;CTA-125H2.2,upstream_gene_variant,,ENST00000608115,;CTA-125H2.2,upstream_gene_variant,,ENST00000597548,;CTA-125H2.2,upstream_gene_variant,,ENST00000594585,;CTA-125H2.2,upstream_gene_variant,,ENST00000595102,;CTA-125H2.2,upstream_gene_variant,,ENST00000599080,;CTA-125H2.2,upstream_gene_variant,,ENST00000594542,;CTA-125H2.2,upstream_gene_variant,,ENST00000609889,;CTA-125H2.2,upstream_gene_variant,,ENST00000600269,;CTA-125H2.2,upstream_gene_variant,,ENST00000609570,;CTA-125H2.2,upstream_gene_variant,,ENST00000608257,;CTA-125H2.2,upstream_gene_variant,,ENST00000599792,;CTA-125H2.2,upstream_gene_variant,,ENST00000609823,;CTA-125H2.2,upstream_gene_variant,,ENST00000607895,;MYO18B,non_coding_transcript_exon_variant,,ENST00000536204,;MYO18B,downstream_gene_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; C ENST00000335473 Transcript missense_variant 5336/8565 5086/7704 1696/2567 S/R Agc/Cgc 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 tolerated(0.25) 31/44 hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 25903769 25903769 A C 1 0 0 0 0 1 0 0 0 10067 188 7 5 5 MYO18B 22 25903769 Missense_Mutation SNP A C3N-01415_T 4695066 25903769 24914699 521 24268 DEPDC5 0 . GRCh38 22 31845210 31845210 + Missense_Mutation SNP G G C novel C3N-01415_T C3N-01415_N G G c.2994G>C p.Arg998Ser p.R998S ENST00000400246 30/43 318 288 30 403 403 0 strelka-varscan-mutect DEPDC5,missense_variant,p.Arg998Ser,ENST00000400246,NM_001242896.1;DEPDC5,missense_variant,p.Arg989Ser,ENST00000400249,;DEPDC5,missense_variant,p.Arg989Ser,ENST00000382112,NM_001136029.2;DEPDC5,missense_variant,p.Arg989Ser,ENST00000400248,NM_014662.4;DEPDC5,missense_variant,p.Arg998Ser,ENST00000382111,;DEPDC5,missense_variant,p.Arg920Ser,ENST00000535622,NM_001242897.1;DEPDC5,missense_variant,p.Arg396Ser,ENST00000433147,;DEPDC5,upstream_gene_variant,,ENST00000494060,;DEPDC5,missense_variant,p.Arg350Ser,ENST00000448753,;DEPDC5,downstream_gene_variant,,ENST00000490731,;DEPDC5,downstream_gene_variant,,ENST00000471914,; C ENST00000400246 Transcript missense_variant 3196/5551 2994/4812 998/1603 R/S agG/agC 1 1 DEPDC5 HGNC HGNC:18423 protein_coding YES CCDS74849.1 ENSP00000383105 O75140 UPI000192C426 NM_001242896.1 deleterious(0.03) 30/43 Low_complexity_(Seg):seg,hmmpanther:PTHR13179 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 31845210 31845210 G C 1 0 0 0 0 1 0 0 0 4248 1194 42 4 4 DEPDC5 22 31845210 Missense_Mutation SNP G C3N-01415_T 5941441 31845210 18973258 522 24269 SYN3 0 . GRCh38 22 32513809 32513809 + Silent SNP C C G novel C3N-01415_T C3N-01415_N C C c.1626G>C p.= p.L542L ENST00000358763 14/14 160 149 11 171 171 0 strelka-varscan-mutect SYN3,synonymous_variant,p.=,ENST00000358763,NM_001135774.1,NM_003490.3,NM_133633.2;SYN3,synonymous_variant,p.=,ENST00000332840,;SYN3,non_coding_transcript_exon_variant,,ENST00000467095,;SYN3,downstream_gene_variant,,ENST00000459990,;SYN3,downstream_gene_variant,,ENST00000468922,;SYN3,non_coding_transcript_exon_variant,,ENST00000483062,;SYN3,downstream_gene_variant,,ENST00000461446,; G ENST00000358763 Transcript synonymous_variant 1869/3126 1626/1743 542/580 L ctG/ctC 1 -1 SYN3 HGNC HGNC:11496 protein_coding YES CCDS13908.1 ENSP00000351614 O14994 A0A024R1I8 UPI00001365D3 NM_001135774.1,NM_003490.3,NM_133633.2 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10841 LOW 1 SNV 5 1 PASS rs1175943424 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 78 32513809 32513809 C G 1 0 0 0 0 0 0 0 1 15832 813 29 4 4 SYN3 22 32513809 Silent SNP C C3N-01415_T 668599 32513809 18304659 523 24270 APOBEC3H 0 . GRCh38 22 39102010 39102010 + Silent SNP C C A rs200960035 C3N-01415_T C3N-01415_N C C c.511C>A p.= p.R171R ENST00000401756 4/6 228 212 16 251 251 0 strelka-varscan-mutect APOBEC3H,synonymous_variant,p.=,ENST00000348946,NM_001166002.2;APOBEC3H,synonymous_variant,p.=,ENST00000401756,NM_001166003.2;APOBEC3H,synonymous_variant,p.=,ENST00000442487,NM_181773.4;APOBEC3H,synonymous_variant,p.=,ENST00000613677,;APOBEC3H,intron_variant,,ENST00000421988,NM_001166004.2;APOBEC3H,intron_variant,,ENST00000613996,;APOBEC3H,downstream_gene_variant,,ENST00000474235,; A ENST00000401756 Transcript synonymous_variant 587/1023 511/603 171/200 R Cga/Aga rs200960035 1 1 APOBEC3H HGNC HGNC:24100 protein_coding YES CCDS54530.1 ENSP00000385741 Q6NTF7 UPI000188E67A NM_001166003.2 4/6 hmmpanther:PTHR13857,hmmpanther:PTHR13857:SF25,Pfam_domain:PF08210 LOW 1 SNV 3 1 PASS rs200960035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 39102010 39102010 C A 1 0 0 0 0 0 0 0 1 916 876 31 1 1 APOBEC3H 22 39102010 Silent SNP C C3N-01415_T 6588201 39102010 11716458 524 24271 FBLN1 0 . GRCh38 22 45548620 45548620 + Missense_Mutation SNP C C A rs553677396 C3N-01415_T C3N-01415_N C C c.1449C>A p.Asp483Glu p.D483E ENST00000327858 13/17 254 194 60 288 288 0 strelka-varscan-mutect FBLN1,missense_variant,p.Asp483Glu,ENST00000327858,NM_006486.2;FBLN1,missense_variant,p.Asp483Glu,ENST00000442170,NM_006485.3;FBLN1,missense_variant,p.Asp521Glu,ENST00000402984,;FBLN1,missense_variant,p.Asp483Glu,ENST00000340923,NM_006487.2;FBLN1,missense_variant,p.Asp483Glu,ENST00000262722,NM_001996.3;FBLN1,intron_variant,,ENST00000476366,; A ENST00000327858 Transcript missense_variant 1544/2896 1449/2112 483/703 D/E gaC/gaA rs553677396 1 1 FBLN1 HGNC HGNC:3600 protein_coding YES CCDS14067.1 ENSP00000331544 P23142 UPI00001AE84C NM_006486.2 deleterious(0) 13/17 Gene3D:2.10.25.10,Pfam_domain:PF12662,PIRSF_domain:PIRSF036313,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF272,SMART_domains:SM00179,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs553677396 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 45548620 45548620 C A 1 0 0 0 0 1 0 0 0 5561 535 19 1 1 FBLN1 22 45548620 Missense_Mutation SNP C C3N-01415_T 6446610 45548620 5269848 525 24272 PLXNB2 0 . GRCh38 22 50278691 50278691 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.4552C>T p.Arg1518Cys p.R1518C ENST00000449103 29/37 274 245 29 267 267 0 strelka-varscan-mutect PLXNB2,missense_variant,p.Arg1518Cys,ENST00000449103,;PLXNB2,missense_variant,p.Arg1518Cys,ENST00000359337,NM_012401.3;PLXNB2,missense_variant,p.Arg70Cys,ENST00000411680,;PLXNB2,synonymous_variant,p.=,ENST00000614805,;PLXNB2,5_prime_UTR_variant,,ENST00000610984,;PLXNB2,downstream_gene_variant,,ENST00000427829,;PLXNB2,downstream_gene_variant,,ENST00000496720,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479818,;PLXNB2,downstream_gene_variant,,ENST00000492578,; A ENST00000449103 Transcript missense_variant 4693/6383 4552/5517 1518/1838 R/C Cgt/Tgt 1 -1 PLXNB2 HGNC HGNC:9104 protein_coding YES CCDS43035.1 ENSP00000409171 O15031 UPI000003812D deleterious(0) 29/37 hmmpanther:PTHR22625:SF9,hmmpanther:PTHR22625,Pfam_domain:PF08337,Gene3D:3.10.20.90 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 78 50278691 50278691 G A 1 0 0 0 0 1 0 0 0 12230 1101 38 1 1 PLXNB2 22 50278691 Missense_Mutation SNP G C3N-01415_T 4730071 50278691 539777 526 24273 SHANK3 0 . GRCh38 22 50711627 50711627 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.2120G>A p.Arg707Lys p.R707K ENST00000262795 21/25 236 212 24 246 246 0 strelka-varscan-mutect SHANK3,missense_variant,p.Arg707Lys,ENST00000262795,;SHANK3,missense_variant,p.Arg701Lys,ENST00000445220,NM_033517.1;SHANK3,non_coding_transcript_exon_variant,,ENST00000414786,; A ENST00000262795 Transcript missense_variant 2120/7091 2120/5193 707/1730 R/K aGa/aAa 1 1 SHANK3 HGNC HGNC:14294 protein_coding YES ENSP00000489147 A0A0U1RQS4 UPI00071AFB18 tolerated(0.96) 21/25 hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 50711627 50711627 G A 1 0 0 0 0 1 0 0 0 14525 942 33 3 3 SHANK3 22 50711627 Missense_Mutation SNP G C3N-01415_T 432936 50711627 106841 527 24274 PRKX 0 . GRCh38 X 3713222 3713222 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.32C>T p.Ala11Val p.A11V ENST00000262848 1/9 42 36 6 48 48 0 strelka-varscan-mutect PRKX,missense_variant,p.Ala11Val,ENST00000262848,NM_005044.4;RP11-558O12.1,upstream_gene_variant,,ENST00000329806,; A ENST00000262848 Transcript missense_variant 387/6031 32/1077 11/358 A/V gCg/gTg 1 -1 PRKX HGNC HGNC:9441 protein_coding YES CCDS14125.1 ENSP00000262848 P51817 A0A024RBU5 UPI000000D998 NM_005044.4 tolerated(0.25) 1/9 hmmpanther:PTHR24353,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -14.82772 0.9999812 1 1 1 0 A 3 1 78 3713222 3713222 G A 1 0 0 0 0 1 0 0 0 12659 1087 38 1 1 PRKX 23 3713222 Missense_Mutation SNP G C3N-01415_T 3713222 152327673 528 24275 FRMPD4 0 . GRCh38 X 12717838 12717838 + Silent SNP T T A rs779754245 C3N-01415_T C3N-01415_N T T c.3012T>A p.= p.T1004T ENST00000380682 16/17 159 114 45 213 213 0 strelka-varscan-mutect FRMPD4,synonymous_variant,p.=,ENST00000380682,NM_014728.3;FRMPD4,synonymous_variant,p.=,ENST00000616992,; A ENST00000380682 Transcript synonymous_variant 3518/8465 3012/3969 1004/1322 T acT/acA rs779754245 1 1 FRMPD4 HGNC HGNC:29007 protein_coding YES CCDS35201.1 ENSP00000370057 Q14CM0 UPI00001C2066 NM_014728.3 16/17 LOW 1 SNV 1 1 PASS rs779754245 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 12717838 12717838 T A 1 0 0 0 0 0 0 0 1 5930 1509 53 4 4 FRMPD4 23 12717838 Silent SNP T C3N-01415_T 9004616 12717838 143323057 529 24276 WAS 0 . GRCh38 X 48683879 48683879 + Missense_Mutation SNP G G A novel C3N-01415_T C3N-01415_N G G c.26G>A p.Arg9Lys p.R9K ENST00000376701 1/12 147 103 44 138 138 0 strelka-varscan-mutect WAS,missense_variant,p.Arg9Lys,ENST00000376701,NM_000377.2;WAS,missense_variant,p.Arg9Lys,ENST00000450772,;WAS,non_coding_transcript_exon_variant,,ENST00000483750,;WAS,non_coding_transcript_exon_variant,,ENST00000465982,;WAS,upstream_gene_variant,,ENST00000474174,;WAS,upstream_gene_variant,,ENST00000490627,; A ENST00000376701 Transcript missense_variant 101/1849 26/1509 9/502 R/K aGg/aAg 1 1 WAS HGNC HGNC:12731 protein_coding YES CCDS14303.1 ENSP00000365891 P42768 A0A024QYX8 UPI000003CA0A NM_000377.2 tolerated_low_confidence(0.24) 1/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23202,hmmpanther:PTHR23202:SF35 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999995 1 1 1 0 A 3 1 78 48683879 48683879 G A 1 0 0 0 0 1 0 0 0 17811 1000 35 3 3 WAS 23 48683879 Missense_Mutation SNP G C3N-01415_T 35966041 48683879 107357016 530 24277 AWAT1 0 . GRCh38 X 70239835 70239835 + Missense_Mutation SNP C C A rs766687052 C3N-01415_T C3N-01415_N C C c.733C>A p.Arg245Ser p.R245S ENST00000374521 6/7 381 184 197 298 298 0 strelka-varscan-mutect AWAT1,missense_variant,p.Arg245Ser,ENST00000374521,NM_001013579.2;AWAT1,downstream_gene_variant,,ENST00000480702,; A ENST00000374521 Transcript missense_variant 774/1365 733/987 245/328 R/S Cgc/Agc rs766687052 1 1 AWAT1 HGNC HGNC:23252 protein_coding YES CCDS35321.1 ENSP00000363645 Q58HT5 UPI00002122D8 NM_001013579.2 deleterious(0.01) 6/7 hmmpanther:PTHR12317:SF16,hmmpanther:PTHR12317,Pfam_domain:PF03982 MODERATE 1 SNV 1 1 PASS rs766687052 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 78 70239835 70239835 C A 1 0 0 0 0 1 0 0 0 1390 652 23 1 1 AWAT1 23 70239835 Missense_Mutation SNP C C3N-01415_T 21555956 70239835 85801060 531 24278 NLGN3 0 . GRCh38 X 71167278 71167278 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.1181G>T p.Gly394Val p.G394V ENST00000358741 7/8 354 310 44 249 249 0 strelka-varscan-mutect NLGN3,missense_variant,p.Gly374Val,ENST00000374051,NM_018977.3;NLGN3,missense_variant,p.Gly354Val,ENST00000536169,NM_001166660.1;NLGN3,missense_variant,p.Gly257Val,ENST00000612180,NM_001321276.1;NLGN3,missense_variant,p.Gly394Val,ENST00000358741,NM_181303.1;NLGN3,missense_variant,p.Gly354Val,ENST00000395855,;NLGN3,non_coding_transcript_exon_variant,,ENST00000476589,; T ENST00000358741 Transcript missense_variant 1484/3046 1181/2547 394/848 G/V gGc/gTc 1 1 NLGN3 HGNC HGNC:14289 protein_coding YES CCDS55441.1 ENSP00000351591 Q9NZ94 X5DNV3 UPI000006FCBB NM_181303.1 deleterious(0) 7/8 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF145,Gene3D:3.40.50.1820,Pfam_domain:PF00135,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 78 71167278 71167278 G T 1 0 0 0 0 1 0 0 0 10500 1203 42 2 2 NLGN3 23 71167278 Missense_Mutation SNP G C3N-01415_T 927443 71167278 84873617 532 24279 PHKA1 0 . GRCh38 X 72581099 72581099 + Missense_Mutation SNP G G C rs782205805 C3N-01415_T C3N-01415_N G G c.3575C>G p.Ala1192Gly p.A1192G ENST00000373542 32/32 210 166 44 201 201 0 strelka-varscan-mutect PHKA1,missense_variant,p.Ala1150Gly,ENST00000373545,;PHKA1,missense_variant,p.Ala1179Gly,ENST00000339490,NM_001122670.1;PHKA1,missense_variant,p.Ala1192Gly,ENST00000373542,NM_002637.3;PHKA1,missense_variant,p.Ala1120Gly,ENST00000541944,NM_001172436.1;PHKA1,missense_variant,p.Ala1209Gly,ENST00000373539,; C ENST00000373542 Transcript missense_variant 3735/6020 3575/3672 1192/1223 A/G gCa/gGa rs782205805 1 -1 PHKA1 HGNC HGNC:8925 protein_coding YES CCDS14421.1 ENSP00000362643 P46020 UPI000013D340 NM_002637.3 deleterious(0) 32/32 hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF4 MODERATE 1 SNV 1 1 PASS rs782205805 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 78 72581099 72581099 G C 1 0 0 0 0 1 0 0 0 11931 1319 46 4 4 PHKA1 23 72581099 Missense_Mutation SNP G C3N-01415_T 1413821 72581099 83459796 533 24280 BRWD3 0 . GRCh38 X 80676903 80676903 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.5115G>C p.Arg1705Ser p.R1705S ENST00000373275 41/41 287 134 153 263 263 0 strelka-varscan-mutect BRWD3,missense_variant,p.Arg1705Ser,ENST00000373275,NM_153252.4;BRWD3,downstream_gene_variant,,ENST00000473691,; G ENST00000373275 Transcript missense_variant 5332/11381 5115/5409 1705/1802 R/S agG/agC 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 deleterious_low_confidence(0) 41/41 Low_complexity_(Seg):seg,hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 80676903 80676903 C G 1 0 0 0 0 1 0 0 0 1700 622 22 4 4 BRWD3 23 80676903 Missense_Mutation SNP C C3N-01415_T 8095804 80676903 75363992 534 24281 CYLC1 0 . GRCh38 X 83874204 83874204 + Nonsense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.1496C>G p.Ser499Ter p.S499* ENST00000329312 4/5 208 98 110 180 179 1 strelka-varscan-mutect CYLC1,stop_gained,p.Ser499Ter,ENST00000329312,NM_021118.2;CYLC1,intron_variant,,ENST00000621735,NM_001271680.1; G ENST00000329312 Transcript stop_gained 1533/2106 1496/1956 499/651 S/* tCa/tGa 1 1 CYLC1 HGNC HGNC:2582 protein_coding YES CCDS35341.1 ENSP00000331556 P35663 UPI0000251E1D NM_021118.2 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16742,hmmpanther:PTHR16742:SF1 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 78 83874204 83874204 C G 1 0 0 0 0 0 1 0 0 3944 838 29 4 4 CYLC1 23 83874204 Nonsense_Mutation SNP C C3N-01415_T 3197301 83874204 72166691 535 24282 CYLC1 0 . GRCh38 X 83886559 83886559 + Missense_Mutation SNP C C T novel C3N-01415_T C3N-01415_N C C c.1931C>T p.Ala644Val p.A644V ENST00000329312 5/5 213 180 33 172 172 0 strelka-varscan-mutect CYLC1,missense_variant,p.Ala644Val,ENST00000329312,NM_021118.2;CYLC1,missense_variant,p.Ala61Val,ENST00000621735,NM_001271680.1; T ENST00000329312 Transcript missense_variant 1968/2106 1931/1956 644/651 A/V gCa/gTa 1 1 CYLC1 HGNC HGNC:2582 protein_coding YES CCDS35341.1 ENSP00000331556 P35663 UPI0000251E1D NM_021118.2 tolerated(0.85) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16742,hmmpanther:PTHR16742:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 83886559 83886559 C T 1 0 0 0 0 1 0 0 0 3944 710 25 3 3 CYLC1 23 83886559 Missense_Mutation SNP C C3N-01415_T 12355 83886559 72154336 536 24283 TGIF2LX 0 . GRCh38 X 89922118 89922118 + Silent SNP C C T rs750966074 C3N-01415_T C3N-01415_N C C c.33C>T p.= p.T11T ENST00000561129 1/1 370 317 53 279 279 0 strelka-varscan-mutect TGIF2LX,synonymous_variant,p.=,ENST00000561129,;TGIF2LX,synonymous_variant,p.=,ENST00000283891,NM_138960.3; T ENST00000561129 Transcript synonymous_variant 163/928 33/726 11/241 T acC/acT rs750966074 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 1/1 LOW 1 SNV 1 PASS rs750966074 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 89922118 89922118 C T 1 0 0 0 0 0 0 0 1 16260 610 22 3 3 TGIF2LX 23 89922118 Silent SNP C C3N-01415_T 6035559 89922118 66118777 537 24284 TSC22D3 0 . GRCh38 X 107714639 107714639 + Silent SNP G G T novel C3N-01415_T C3N-01415_N G G c.483C>A p.= p.T161T ENST00000372383 3/3 254 95 159 258 256 2 strelka-varscan-mutect TSC22D3,synonymous_variant,p.=,ENST00000372383,NM_198057.2;TSC22D3,synonymous_variant,p.=,ENST00000315660,NM_001318468.1;TSC22D3,synonymous_variant,p.=,ENST00000372384,NM_001318470.1;TSC22D3,synonymous_variant,p.=,ENST00000372397,NM_004089.3;TSC22D3,synonymous_variant,p.=,ENST00000372390,NM_001015881.1;TSC22D3,synonymous_variant,p.=,ENST00000372382,;TSC22D3,synonymous_variant,p.=,ENST00000506081,;TSC22D3,synonymous_variant,p.=,ENST00000514426,;TSC22D3,downstream_gene_variant,,ENST00000514897,;TSC22D3,downstream_gene_variant,,ENST00000510887,;TSC22D3,downstream_gene_variant,,ENST00000486554,;TSC22D3,downstream_gene_variant,,ENST00000502650,;TSC22D3,downstream_gene_variant,,ENST00000503515,;TSC22D3,downstream_gene_variant,,ENST00000480691,; T ENST00000372383 Transcript synonymous_variant 851/2266 483/603 161/200 T acC/acA 1 -1 TSC22D3 HGNC HGNC:3051 protein_coding YES CCDS14530.1 ENSP00000361458 Q99576 UPI000006DE94 NM_198057.2 3/3 Superfamily_domains:0053404,Gene3D:1.20.5.490,Coiled-coils_(Ncoils):Coil,PD007152,Pfam_domain:PF01166,hmmpanther:PTHR12348 LOW 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 107714639 107714639 G T 1 0 0 0 0 0 0 0 1 17115 1219 43 2 2 TSC22D3 23 107714639 Silent SNP G C3N-01415_T 17792521 107714639 48326256 538 24285 ATP11C 0 . GRCh38 X 139826746 139826746 + Silent SNP G G A novel C3N-01415_T C3N-01415_N G G c.114C>T p.= p.Y38Y ENST00000327569 2/30 123 105 18 120 120 0 strelka-varscan-mutect ATP11C,synonymous_variant,p.=,ENST00000370557,;ATP11C,synonymous_variant,p.=,ENST00000327569,NM_173694.4;ATP11C,synonymous_variant,p.=,ENST00000361648,NM_001010986.2;ATP11C,non_coding_transcript_exon_variant,,ENST00000485626,; A ENST00000327569 Transcript synonymous_variant 213/6115 114/3399 38/1132 Y taC/taT 1 -1 ATP11C HGNC HGNC:13554 protein_coding YES CCDS14668.1 ENSP00000332756 Q8NB49 UPI000036777E NM_173694.4 2/30 hmmpanther:PTHR24092:SF38,hmmpanther:PTHR24092 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 78 139826746 139826746 G A 1 0 0 0 0 0 0 0 1 1273 1372 48 3 3 ATP11C 23 139826746 Silent SNP G C3N-01415_T 32112107 139826746 16214149 539 24286 ZNF275 0 . GRCh38 X 153347764 153347764 + Missense_Mutation SNP G G T novel C3N-01415_T C3N-01415_N G G c.981G>T p.Trp327Cys p.W327C ENST00000370251 5/5 95 81 14 72 72 0 strelka-varscan-mutect ZNF275,missense_variant,p.Trp327Cys,ENST00000370251,NM_001080485.3;ZNF275,missense_variant,p.Gly307Val,ENST00000370249,;ZNF275,upstream_gene_variant,,ENST00000438239,; T ENST00000370251 Transcript missense_variant 1158/6320 981/990 327/329 W/C tgG/tgT 1 1 ZNF275 HGNC HGNC:13069 protein_coding YES ENSP00000359271 A6NFS0 UPI000059DBB5 NM_001080485.3 5/5 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 78 153347764 153347764 G T 1 0 0 0 0 1 0 0 0 18386 1241 43 2 2 ZNF275 23 153347764 Missense_Mutation SNP G C3N-01415_T 13521018 153347764 2693131 540 24287 F8A1 0 . GRCh38 X 154887338 154887338 + Missense_Mutation SNP C C G novel C3N-01415_T C3N-01415_N C C c.964C>G p.Leu322Val p.L322V ENST00000610495 1/1 154 134 20 116 116 0 varscan-mutect F8A1,missense_variant,p.Leu322Val,ENST00000610495,NM_012151.3;F8,intron_variant,,ENST00000360256,NM_000132.3;F8,upstream_gene_variant,,ENST00000330287,NM_019863.2;H2AFB1,downstream_gene_variant,,ENST00000620016,NM_001017990.1;MIR1184-1,downstream_gene_variant,,ENST00000408606,; G ENST00000610495 Transcript missense_variant 990/1713 964/1116 322/371 L/V Ctc/Gtc 1 1 F8A1 HGNC HGNC:3547 protein_coding YES CCDS35459.1 ENSP00000479624 P23610 UPI0000074369 NM_012151.3 deleterious(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR16797 MODERATE SNV 1 PASS . . 47 161 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 78 154887338 154887338 C G 1 0 0 0 0 1 0 0 0 5219 797 28 4 4 F8A1 23 154887338 Missense_Mutation SNP C C3N-01415_T 1539574 154887338 1153557 541 24288 PCDH11Y 0 . GRCh38 Y 5100050 5100050 + Silent SNP A A T C3N-01415_T C3N-01415_N A A c.2472A>T p.= p.A824A ENST00000362095 2/3 311 192 119 385 385 0 strelka-varscan-mutect PCDH11Y,synonymous_variant,p.=,ENST00000400457,NM_032973.2;PCDH11Y,synonymous_variant,p.=,ENST00000622698,NM_001278619.1;PCDH11Y,synonymous_variant,p.=,ENST00000333703,NM_032971.2;PCDH11Y,synonymous_variant,p.=,ENST00000215473,;PCDH11Y,synonymous_variant,p.=,ENST00000362095,NM_032972.2; T ENST00000362095 Transcript synonymous_variant 3206/4220 2472/3147 824/1048 A gcA/gcT COSM5504806,COSM5504807,COSM5504808 1 1 PCDH11Y HGNC HGNC:15813 protein_coding YES CCDS14777.1 ENSP00000355419 Q9BZA8 UPI000006EF4D NM_032972.2 2/3 Pfam_domain:PF08374,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 78 5100050 5100050 A T 1 0 0 0 0 0 0 0 1 11596 146 6 4 4 PCDH11Y 24 5100050 Silent SNP A C3N-01415_T 5100050 52127365 542 24289 PRAMEF11 0 . GRCh38 1 12824987 12824987 + Silent SNP G G A rs758547297 C3N-01416_T C3N-01416_N G G c.1392C>T p.= p.G464G ENST00000619922 4/4 255 234 21 375 374 1 varscan-mutect PRAMEF11,synonymous_variant,p.=,ENST00000619922,NM_001146344.2;RP5-845O24.8,upstream_gene_variant,,ENST00000438401,; A ENST00000619922 Transcript synonymous_variant 1463/1845 1392/1437 464/478 G ggC/ggT rs758547297,COSM894918 1 -1 PRAMEF11 HGNC HGNC:14086 protein_coding YES CCDS53268.2 ENSP00000480027 A0A087WW85 UPI0003EAF149 NM_001146344.2 4/4 hmmpanther:PTHR14224:SF19,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 0,1 LOW 1 SNV 1 0,1 1 PASS rs758547297 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 12824987 12824987 G A 1 0 0 0 0 0 0 0 1 12556 1074 38 1 1 PRAMEF11 1 12824987 Silent SNP G C3N-01416_T 12824987 236131435 1 24290 KIRREL 0 . GRCh38 1 158078124 158078124 + Silent SNP C C T novel C3N-01416_T C3N-01416_N C C c.336C>T p.= p.A112A ENST00000359209 3/15 161 121 40 140 140 0 strelka-varscan-mutect KIRREL,synonymous_variant,p.=,ENST00000360089,;KIRREL,synonymous_variant,p.=,ENST00000359209,NM_018240.6;KIRREL,intron_variant,,ENST00000368173,NM_001286349.1; T ENST00000359209 Transcript synonymous_variant 403/2874 336/2274 112/757 A gcC/gcT 1 1 KIRREL HGNC HGNC:15734 protein_coding YES CCDS1172.2 ENSP00000352138 Q96J84 UPI0000443FBD NM_018240.6 3/15 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF14,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 79 158078124 158078124 C T 1 0 0 0 0 0 0 0 1 8188 581 21 3 3 KIRREL 1 158078124 Silent SNP C C3N-01416_T 145253137 158078124 90878298 2 24291 ADAMTS4 0 . GRCh38 1 161193727 161193727 + Missense_Mutation SNP G G T novel C3N-01416_T C3N-01416_N G G c.1648C>A p.Pro550Thr p.P550T ENST00000367996 6/9 167 154 13 181 181 0 strelka-varscan-mutect ADAMTS4,missense_variant,p.Pro550Thr,ENST00000367996,NM_005099.4;ADAMTS4,downstream_gene_variant,,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000496133,;NDUFS2,upstream_gene_variant,,ENST00000479948,;ADAMTS4,downstream_gene_variant,,ENST00000478394,; T ENST00000367996 Transcript missense_variant 2077/9773 1648/2514 550/837 P/T Cct/Act 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 deleterious(0) 6/9 PROSITE_profiles:PS50092,hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 161193727 161193727 G T 1 0 0 0 0 1 0 0 0 312 1203 42 2 2 ADAMTS4 1 161193727 Missense_Mutation SNP G C3N-01416_T 3115603 161193727 87762695 3 24292 KIFAP3 0 . GRCh38 1 169954089 169954089 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.2195G>A p.Gly732Glu p.G732E ENST00000361580 19/20 229 210 19 275 275 0 strelka-varscan-mutect KIFAP3,missense_variant,p.Gly692Glu,ENST00000367765,NM_001204517.1;KIFAP3,missense_variant,p.Gly654Glu,ENST00000538366,NM_001204514.1;KIFAP3,missense_variant,p.Gly732Glu,ENST00000361580,NM_014970.3;KIFAP3,missense_variant,p.Gly688Glu,ENST00000367767,NM_001204516.1;RN7SL269P,downstream_gene_variant,,ENST00000467795,; T ENST00000361580 Transcript missense_variant 2423/2957 2195/2379 732/792 G/E gGa/gAa 1 -1 KIFAP3 HGNC HGNC:17060 protein_coding YES CCDS1288.1 ENSP00000354560 Q92845 UPI000006CD6C NM_014970.3 tolerated(0.26) 19/20 hmmpanther:PTHR15605 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 169954089 169954089 C T 1 0 0 0 0 1 0 0 0 8176 855 30 3 3 KIFAP3 1 169954089 Missense_Mutation SNP C C3N-01416_T 8760362 169954089 79002333 4 24293 TRMT1L 0 . GRCh38 1 185137712 185137712 + Missense_Mutation SNP C C G novel C3N-01416_T C3N-01416_N C C c.1407G>C p.Leu469Phe p.L469F ENST00000367506 10/15 258 244 14 250 250 0 strelka-varscan-mutect TRMT1L,missense_variant,p.Leu469Phe,ENST00000367506,NM_030934.4,NM_001202423.1;TRMT1L,missense_variant,p.Leu93Phe,ENST00000458395,; G ENST00000367506 Transcript missense_variant 1676/4392 1407/2202 469/733 L/F ttG/ttC 1 -1 TRMT1L HGNC HGNC:16782 protein_coding YES CCDS1366.1 ENSP00000356476 Q7Z2T5 UPI000000DADB NM_030934.4,NM_001202423.1 tolerated(0.05) 10/15 Pfam_domain:PF02005,PROSITE_profiles:PS51626,hmmpanther:PTHR10631,hmmpanther:PTHR10631:SF1,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 185137712 185137712 C G 1 0 0 0 0 1 0 0 0 17068 825 29 4 4 TRMT1L 1 185137712 Missense_Mutation SNP C C3N-01416_T 15183623 185137712 63818710 5 24294 PRG4 0 . GRCh38 1 186307723 186307723 + Silent SNP T T C novel C3N-01416_T C3N-01416_N T T c.2004T>C p.= p.T668T ENST00000445192 7/13 262 245 17 299 294 5 strelka-mutect PRG4,synonymous_variant,p.=,ENST00000445192,NM_005807.4;PRG4,synonymous_variant,p.=,ENST00000367483,NM_001127708.2;PRG4,synonymous_variant,p.=,ENST00000635041,NM_001303232.1;PRG4,synonymous_variant,p.=,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,synonymous_variant,p.=,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; C ENST00000445192 Transcript synonymous_variant 2049/5044 2004/4215 668/1404 T acT/acC 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 7/13 Low_complexity_(Seg):seg,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1 LOW SNV 5 1 PASS rs1157327525 . 0 143 0 20 46 0 0 0 -3.605606 0 0 1 0 0 C 2 2 79 186307723 186307723 T C 1 0 0 0 0 0 0 0 1 12615 1538 54 5 5 PRG4 1 186307723 Silent SNP T C3N-01416_T 1170011 186307723 62648699 6 24295 ADCY3 0 . GRCh38 2 24834894 24834894 + Silent SNP G G A C3N-01416_T C3N-01416_N G G c.1705C>T p.= p.L569L ENST00000260600 9/21 138 109 29 174 174 0 strelka-varscan-mutect ADCY3,synonymous_variant,p.=,ENST00000260600,NM_004036.3;ADCY3,synonymous_variant,p.=,ENST00000405392,NM_001320613.1;ADCY3,synonymous_variant,p.=,ENST00000606682,;ADCY3,downstream_gene_variant,,ENST00000435135,;ADCY3,downstream_gene_variant,,ENST00000427849,;ADCY3,upstream_gene_variant,,ENST00000455323,;ADCY3,upstream_gene_variant,,ENST00000450524,;ADCY3,downstream_gene_variant,,ENST00000454027,; A ENST00000260600 Transcript synonymous_variant 2557/5050 1705/3435 569/1144 L Ctg/Ttg COSM5265969 1 -1 ADCY3 HGNC HGNC:234 protein_coding YES CCDS1715.1 ENSP00000260600 O60266 UPI000013D0ED NM_004036.3 9/21 Low_complexity_(Seg):seg,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF291,PIRSF_domain:PIRSF039050 1 LOW 1 SNV 1 1 1 PASS rs1327311702 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 24834894 24834894 G A 1 0 0 0 0 0 0 0 1 339 991 35 3 3 ADCY3 2 24834894 Silent SNP G C3N-01416_T 24834894 217358635 7 24296 EPT1 0 . GRCh38 2 26386464 26386464 + Nonsense_Mutation SNP C C A rs749959444 C3N-01416_T C3N-01416_N C C c.1023C>A p.Tyr341Ter p.Y341* ENST00000260585 9/10 155 133 22 296 296 0 strelka-varscan-mutect EPT1,stop_gained,p.Tyr341Ter,ENST00000613142,;EPT1,stop_gained,p.Tyr341Ter,ENST00000260585,NM_033505.2;EPT1,downstream_gene_variant,,ENST00000447170,; A ENST00000260585 Transcript stop_gained 1142/8101 1023/1194 341/397 Y/* taC/taA rs749959444 1 1 EPT1 HGNC HGNC:29361 protein_coding YES CCDS46240.1 ENSP00000260585 Q9C0D9 UPI00003CE422 NM_033505.2 9/10 PIRSF_domain:PIRSF015665,hmmpanther:PTHR10414,hmmpanther:PTHR10414:SF47 HIGH 1 SNV 1 1 PASS rs749959444 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 79 26386464 26386464 C A 1 0 0 0 0 0 1 0 0 5047 547 19 1 1 EPT1 2 26386464 Nonsense_Mutation SNP C C3N-01416_T 1551570 26386464 215807065 8 24297 LOXL3 0 . GRCh38 2 74549414 74549414 + Missense_Mutation SNP A A T novel C3N-01416_T C3N-01416_N A A c.647T>A p.Met216Lys p.M216K ENST00000264094 4/14 104 85 19 157 157 0 strelka-varscan LOXL3,missense_variant,p.Met216Lys,ENST00000264094,NM_032603.3;LOXL3,missense_variant,p.Met216Lys,ENST00000409549,;LOXL3,missense_variant,p.Met216Lys,ENST00000409249,;LOXL3,missense_variant,p.Met216Lys,ENST00000413469,;LOXL3,missense_variant,p.Asp16Glu,ENST00000420535,;LOXL3,intron_variant,,ENST00000393937,NM_001289164.1;LOXL3,intron_variant,,ENST00000409986,;DOK1,intron_variant,,ENST00000409429,NM_001197260.1;DOK1,upstream_gene_variant,,ENST00000233668,NM_001318866.1,NM_001381.3;DOK1,splice_region_variant,,ENST00000485132,;LOXL3,non_coding_transcript_exon_variant,,ENST00000484369,;LOXL3,non_coding_transcript_exon_variant,,ENST00000481835,;DOK1,upstream_gene_variant,,ENST00000488613,;LOXL3,non_coding_transcript_exon_variant,,ENST00000470907,; T ENST00000264094 Transcript missense_variant 719/3502 647/2262 216/753 M/K aTg/aAg 1 -1 LOXL3 HGNC HGNC:13869 protein_coding YES CCDS1953.1 ENSP00000264094 P58215 UPI0000044959 NM_032603.3 deleterious(0) 4/14 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF305,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 74549414 74549414 A T 1 0 0 0 0 1 0 0 0 8804 217 8 4 4 LOXL3 2 74549414 Missense_Mutation SNP A C3N-01416_T 48162950 74549414 167644115 9 24298 ZAP70 0 . GRCh38 2 97725095 97725095 + Missense_Mutation SNP G G A C3N-01416_T C3N-01416_N G G c.406G>A p.Glu136Lys p.E136K ENST00000264972 4/14 292 269 23 350 349 1 strelka-varscan ZAP70,missense_variant,p.Glu136Lys,ENST00000264972,NM_001079.3;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000483781,; A ENST00000264972 Transcript missense_variant 621/2437 406/1860 136/619 E/K Gag/Aag COSM3584184 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 tolerated(0.14) 4/14 Gene3D:2oq1A02,PIRSF_domain:PIRSF000604,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 97725095 97725095 G A 1 0 0 0 0 1 0 0 0 18075 1072 37 1 1 ZAP70 2 97725095 Missense_Mutation SNP G C3N-01416_T 23175681 97725095 144468434 10 24299 TTN 0 . GRCh38 2 178560056 178560056 + Silent SNP T T C novel C3N-01416_T C3N-01416_N T T c.86076A>G p.= p.K28692K ENST00000589042 326/363 265 228 37 372 372 0 strelka-varscan TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.3,downstream_gene_variant,,ENST00000624360,; C ENST00000589042 Transcript synonymous_variant 86301/109224 86076/107976 28692/35991 K aaA/aaG 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 79 178560056 178560056 T C 1 0 0 0 0 0 0 0 1 17245 1490 52 5 5 TTN 2 178560056 Silent SNP T C3N-01416_T 80834961 178560056 63633473 11 24300 ZNF804A 0 . GRCh38 2 184936720 184936720 + Missense_Mutation SNP G G A novel C3N-01416_T C3N-01416_N G G c.1324G>A p.Glu442Lys p.E442K ENST00000302277 4/4 116 109 7 164 163 1 strelka-varscan ZNF804A,missense_variant,p.Glu442Lys,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Glu357Lys,ENST00000613975,; A ENST00000302277 Transcript missense_variant 1918/4690 1324/3630 442/1209 E/K Gaa/Aaa 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 deleterious(0.01) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -10.49673 0.9999995 1 1 1 0 A 3 1 79 184936720 184936720 G A 1 0 0 0 0 1 0 0 0 18755 943 33 3 3 ZNF804A 2 184936720 Missense_Mutation SNP G C3N-01416_T 6376664 184936720 57256809 12 24301 UNC80 0 . GRCh38 2 209937528 209937528 + Splice_Site SNP G G A novel C3N-01416_T C3N-01416_N G G c.6166-1G>A p.X2056_splice ENST00000439458 106 97 9 191 191 0 strelka-varscan UNC80,splice_acceptor_variant,,ENST00000439458,NM_032504.1;UNC80,splice_acceptor_variant,,ENST00000272845,NM_182587.3;UNC80,splice_acceptor_variant,,ENST00000489023,; A ENST00000439458 Transcript splice_acceptor_variant -/13562 6166/9777 2056/3258 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 40/63 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 79 209937528 209937528 G A 1 0 0 0 0 0 0 1 0 17521 956 33 3 3 UNC80 2 209937528 Splice_Site SNP G C3N-01416_T 25000808 209937528 32256001 13 24302 PLCD4 0 . GRCh38 2 218634619 218634619 + Missense_Mutation SNP C C G rs558899268 C3N-01416_T C3N-01416_N C C c.1885C>G p.Leu629Val p.L629V ENST00000450993 13/16 115 106 9 103 103 0 strelka-varscan-mutect PLCD4,missense_variant,p.Leu629Val,ENST00000450993,NM_032726.3;PLCD4,missense_variant,p.Leu661Val,ENST00000432688,;PLCD4,missense_variant,p.Leu629Val,ENST00000417849,;ZNF142,downstream_gene_variant,,ENST00000411696,;ZNF142,downstream_gene_variant,,ENST00000449707,NM_001105537.2;PLCD4,upstream_gene_variant,,ENST00000457773,;RP11-548H3.1,upstream_gene_variant,,ENST00000607946,;PLCD4,non_coding_transcript_exon_variant,,ENST00000459791,;PLCD4,non_coding_transcript_exon_variant,,ENST00000473443,;PLCD4,non_coding_transcript_exon_variant,,ENST00000483685,;PLCD4,non_coding_transcript_exon_variant,,ENST00000484718,;ZNF142,downstream_gene_variant,,ENST00000450765,;ZNF142,downstream_gene_variant,,ENST00000433921,;PLCD4,downstream_gene_variant,,ENST00000465713,;PLCD4,downstream_gene_variant,,ENST00000497482,;PLCD4,downstream_gene_variant,,ENST00000458239,; G ENST00000450993 Transcript missense_variant 2224/3232 1885/2289 629/762 L/V Ctc/Gtc rs558899268 1 1 PLCD4 HGNC HGNC:9062 protein_coding YES CCDS46516.1 ENSP00000388631 Q9BRC7 UPI0000044279 NM_032726.3 deleterious(0.01) 13/16 PROSITE_profiles:PS50004,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF31,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs558899268 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 218634619 218634619 C G 1 0 0 0 0 1 0 0 0 12127 913 32 4 4 PLCD4 2 218634619 Missense_Mutation SNP C C3N-01416_T 8697091 218634619 23558910 14 24303 STT3B 0 . GRCh38 3 31623735 31623735 + Missense_Mutation SNP A A T novel C3N-01416_T C3N-01416_N A A c.1601A>T p.Asn534Ile p.N534I ENST00000295770 11/16 86 75 11 186 186 0 strelka-varscan-mutect STT3B,missense_variant,p.Asn534Ile,ENST00000295770,NM_178862.2;STT3B,downstream_gene_variant,,ENST00000453168,;STT3B,downstream_gene_variant,,ENST00000423527,;STT3B,upstream_gene_variant,,ENST00000463044,;STT3B,downstream_gene_variant,,ENST00000436236,; T ENST00000295770 Transcript missense_variant 1810/4248 1601/2481 534/826 N/I aAt/aTt 1 1 STT3B HGNC HGNC:30611 protein_coding YES CCDS2650.1 ENSP00000295770 Q8TCJ2 UPI000006D7FB NM_178862.2 tolerated(0.16) 11/16 hmmpanther:PTHR13872,hmmpanther:PTHR13872:SF25,Pfam_domain:PF02516 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 31623735 31623735 A T 1 0 0 0 0 1 0 0 0 15717 101 4 4 4 STT3B 3 31623735 Missense_Mutation SNP A C3N-01416_T 31623735 166671824 15 24304 CACNA1D 0 . GRCh38 3 53726982 53726989 + Frame_Shift_Del DEL TCTTCATT TCTTCATT - novel C3N-01416_T C3N-01416_N TCTTCATT TCTTCATT c.2265_2272delCTTCATTT p.Phe756TrpfsTer2 p.F756Wfs*2 ENST00000288139 16/49 283 268 15 464 464 0 varindel-pindel CACNA1D,frameshift_variant,p.Phe756TrpfsTer2,ENST00000288139,NM_000720.3;CACNA1D,frameshift_variant,p.Phe736TrpfsTer2,ENST00000350061,NM_001128840.2;CACNA1D,frameshift_variant,p.Phe736TrpfsTer2,ENST00000636938,;CACNA1D,frameshift_variant,p.Phe760TrpfsTer2,ENST00000637424,;CACNA1D,frameshift_variant,p.Phe736TrpfsTer2,ENST00000636570,;CACNA1D,frameshift_variant,p.Phe736TrpfsTer2,ENST00000422281,NM_001128839.2;CACNA1D,frameshift_variant,p.Phe429TrpfsTer2,ENST00000481478,;CACNA1D,frameshift_variant,p.Phe503TrpfsTer2,ENST00000636627,;CACNA1D,upstream_gene_variant,,ENST00000637714,;CACNA1D,downstream_gene_variant,,ENST00000481085,;CACNA1D,upstream_gene_variant,,ENST00000636138,;CACNA1D,upstream_gene_variant,,ENST00000637078,; - ENST00000288139 Transcript frameshift_variant 2732-2739/9341 2264-2271/6546 755-757/2181 LFI/X cTCTTCATT/c 1 1 CACNA1D HGNC HGNC:1391 protein_coding YES CCDS2872.1 ENSP00000288139 Q01668 UPI000005031A NM_000720.3 16/49 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF139,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 79 53726982 53726982 TCTTCATT - 1 0 1 0 1 0 0 0 0 2229 1551 54 0 0 CACNA1D 3 53726982 Frame_Shift_Del DEL TCTTCATT C3N-01416_T 22103247 53726982 144568577 16 24305 PRSS48 0 . GRCh38 4 151282286 151282286 + Silent SNP G G A novel C3N-01416_T C3N-01416_N G G c.354G>A p.= p.L118L ENST00000455694 3/5 290 270 20 453 453 0 strelka-varscan PRSS48,synonymous_variant,p.=,ENST00000455694,NM_183375.2;SH3D19,intron_variant,,ENST00000604030,;PRSS48,intron_variant,,ENST00000441586,;RP11-731D1.3,upstream_gene_variant,,ENST00000507181,; A ENST00000455694 Transcript synonymous_variant 356/989 354/987 118/328 L ttG/ttA 1 1 PRSS48 HGNC HGNC:24635 protein_coding YES CCDS47145.1 ENSP00000401328 Q7RTY5 A0A140VJJ1 UPI0000047B08 NM_183375.2 3/5 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF120,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 151282286 151282286 G A 1 0 0 0 0 0 0 0 1 12778 1281 45 3 3 PRSS48 4 151282286 Silent SNP G C3N-01416_T 151282286 38932269 17 24306 C5orf42 0 . GRCh38 5 37153979 37153979 + Nonsense_Mutation SNP C C A novel C3N-01416_T C3N-01416_N C C c.7972G>T p.Glu2658Ter p.E2658* ENST00000425232 41/52 81 66 15 120 120 0 strelka-varscan-mutect C5orf42,stop_gained,p.Glu2658Ter,ENST00000425232,NM_023073.3;C5orf42,stop_gained,p.Glu2658Ter,ENST00000508244,;C5orf42,stop_gained,p.Glu1724Ter,ENST00000514429,;C5orf42,stop_gained,p.Glu417Ter,ENST00000511824,;C5orf42,non_coding_transcript_exon_variant,,ENST00000511210,;C5orf42,upstream_gene_variant,,ENST00000508405,;C5orf42,stop_gained,p.Glu1716Ter,ENST00000509849,;C5orf42,non_coding_transcript_exon_variant,,ENST00000509957,;C5orf42,non_coding_transcript_exon_variant,,ENST00000515380,;C5orf42,downstream_gene_variant,,ENST00000510830,; A ENST00000425232 Transcript stop_gained 8203/11199 7972/9594 2658/3197 E/* Gag/Tag 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 41/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 79 37153979 37153979 C A 1 0 0 0 0 0 1 0 0 2100 922 32 2 2 C5orf42 5 37153979 Nonsense_Mutation SNP C C3N-01416_T 37153979 144384280 18 24307 PCDHA3 0 . GRCh38 5 140802293 140802293 + Missense_Mutation SNP A A T novel C3N-01416_T C3N-01416_N A A c.1096A>T p.Ser366Cys p.S366C ENST00000522353 1/4 340 279 61 512 512 0 strelka-varscan-mutect PCDHA3,missense_variant,p.Ser366Cys,ENST00000522353,NM_018906.2;PCDHA3,missense_variant,p.Ser366Cys,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000530339,NM_018907.3;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; T ENST00000522353 Transcript missense_variant 1096/5260 1096/2853 366/950 S/C Agc/Tgc 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 140802293 140802293 A T 1 0 0 0 0 1 0 0 0 11612 420 15 4 4 PCDHA3 5 140802293 Missense_Mutation SNP A C3N-01416_T 103648314 140802293 40735966 19 24308 FCHSD1 0 . GRCh38 5 141651021 141651021 + Missense_Mutation SNP T T C novel C3N-01416_T C3N-01416_N T T c.118A>G p.Arg40Gly p.R40G ENST00000435817 2/20 149 127 22 233 233 0 strelka-varscan-mutect FCHSD1,missense_variant,p.Arg40Gly,ENST00000435817,NM_033449.2;FCHSD1,missense_variant,p.Arg40Gly,ENST00000522783,;FCHSD1,missense_variant,p.Arg40Gly,ENST00000519800,;ARAP3,downstream_gene_variant,,ENST00000239440,NM_022481.5;ARAP3,downstream_gene_variant,,ENST00000626478,;ARAP3,downstream_gene_variant,,ENST00000508305,;ARAP3,downstream_gene_variant,,ENST00000513878,;FCHSD1,upstream_gene_variant,,ENST00000518499,;FCHSD1,upstream_gene_variant,,ENST00000523856,;ARAP3,downstream_gene_variant,,ENST00000512390,;FCHSD1,upstream_gene_variant,,ENST00000522386,;FCHSD1,upstream_gene_variant,,ENST00000522763,;FCHSD1,splice_region_variant,,ENST00000522126,; C ENST00000435817 Transcript missense_variant,splice_region_variant 169/4320 118/2073 40/690 R/G Aga/Gga 1 -1 FCHSD1 HGNC HGNC:25463 protein_coding YES CCDS47295.1 ENSP00000399259 Q86WN1 UPI000000D903 NM_033449.2 deleterious(0) 2/20 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51741,hmmpanther:PTHR15735:SF4,hmmpanther:PTHR15735,Pfam_domain:PF00611,SMART_domains:SM00055,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 141651021 141651021 T C 1 0 0 0 0 1 0 0 0 5651 1594 55 5 5 FCHSD1 5 141651021 Missense_Mutation SNP T C3N-01416_T 848728 141651021 39887238 20 24309 ZFP57 0 . GRCh38 6 29672890 29672890 + Silent SNP G G C novel C3N-01416_T C3N-01416_N G G c.1221C>G p.= p.L407L ENST00000488757 4/4 596 541 55 735 735 0 strelka-varscan-mutect ZFP57,synonymous_variant,p.=,ENST00000376883,;ZFP57,synonymous_variant,p.=,ENST00000488757,NM_001109809.2;ZFP57,synonymous_variant,p.=,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.3;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.3;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.5;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.4;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.3;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.3;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.2;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.2;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.1;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,; C ENST00000488757 Transcript synonymous_variant 1372/1870 1221/1611 407/536 L ctC/ctG 1 -1 ZFP57 HGNC HGNC:18791 protein_coding YES CCDS43436.2 ENSP00000418259 Q9NU63 UPI0001951170 NM_001109809.2 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF179,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 79 29672890 29672890 G C 1 0 0 0 0 0 0 0 1 18226 1277 45 4 4 ZFP57 6 29672890 Silent SNP G C3N-01416_T 29672890 141133089 21 24310 ZFP57 0 . GRCh38 6 29672975 29672975 + Nonsense_Mutation SNP G G C rs781584552 C3N-01416_T C3N-01416_N G G c.1136C>G p.Ser379Ter p.S379* ENST00000488757 4/4 569 503 66 713 713 0 strelka-varscan-mutect ZFP57,stop_gained,p.Ser359Ter,ENST00000376883,;ZFP57,stop_gained,p.Ser379Ter,ENST00000488757,NM_001109809.2;ZFP57,stop_gained,p.Ser295Ter,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.3;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.3;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.5;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.4;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.3;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.3;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.2;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.2;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.1;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,; C ENST00000488757 Transcript stop_gained 1287/1870 1136/1611 379/536 S/* tCa/tGa rs781584552 1 -1 ZFP57 HGNC HGNC:18791 protein_coding YES CCDS43436.2 ENSP00000418259 Q9NU63 UPI0001951170 NM_001109809.2 4/4 HIGH 1 SNV 1 1 PASS rs781584552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 79 29672975 29672975 G C 1 0 0 0 0 0 1 0 0 18226 1294 45 4 4 ZFP57 6 29672975 Nonsense_Mutation SNP G C3N-01416_T 85 29672975 141133004 22 24311 BAK1 0 . GRCh38 6 33575377 33575377 + Missense_Mutation SNP A A G novel C3N-01416_T C3N-01416_N A A c.271T>C p.Ser91Pro p.S91P ENST00000374467 4/6 330 283 47 399 398 1 strelka-varscan BAK1,missense_variant,p.Ser91Pro,ENST00000442998,;BAK1,missense_variant,p.Ser91Pro,ENST00000374467,NM_001188.3;BAK1,missense_variant,p.Ser71Pro,ENST00000360661,;GGNBP1,non_coding_transcript_exon_variant,,ENST00000612409,; G ENST00000374467 Transcript missense_variant 520/2136 271/636 91/211 S/P Tca/Cca 1 -1 BAK1 HGNC HGNC:949 protein_coding YES CCDS4781.1 ENSP00000363591 Q16611 A0A0S2Z391 UPI0000126777 NM_001188.3 tolerated(0.31) 4/6 Gene3D:1.10.437.10,Pfam_domain:PF00452,PROSITE_profiles:PS50062,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF41,SMART_domains:SM00337,Superfamily_domains:SSF56854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 33575377 33575377 A G 1 0 0 0 0 1 0 0 0 1457 304 11 5 5 BAK1 6 33575377 Missense_Mutation SNP A C3N-01416_T 3902402 33575377 137230602 23 24312 MOCS1 0 . GRCh38 6 39934298 39934298 + Silent SNP C C T novel C3N-01416_T C3N-01416_N C C c.120G>A p.= p.S40S ENST00000373188 1/11 82 77 5 130 129 1 strelka-varscan MOCS1,synonymous_variant,p.=,ENST00000373188,NM_001075098.3;MOCS1,synonymous_variant,p.=,ENST00000340692,;MOCS1,5_prime_UTR_variant,,ENST00000373195,;MOCS1,synonymous_variant,p.=,ENST00000487924,;MOCS1,non_coding_transcript_exon_variant,,ENST00000473742,;MOCS1,upstream_gene_variant,,ENST00000373181,; T ENST00000373188 Transcript synonymous_variant 254/3358 120/1158 40/385 S tcG/tcA 1 -1 MOCS1 HGNC HGNC:7190 protein_coding CCDS43460.1 ENSP00000362284 Q9NZB8 A0A024RD17 UPI000013DA31 NM_001075098.3 1/11 Low_complexity_(Seg):seg,hmmpanther:PTHR22960:SF0,hmmpanther:PTHR22960 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -11.07505 1 1 1 1 0 T 2 4 79 39934298 39934298 C T 1 0 0 0 0 0 0 0 1 9653 666 23 1 1 MOCS1 6 39934298 Silent SNP C C3N-01416_T 6358921 39934298 130871681 24 24313 DST 0 . GRCh38 6 56648601 56648601 + Missense_Mutation SNP C C G novel C3N-01416_T C3N-01416_N C C c.1010G>C p.Arg337Thr p.R337T ENST00000312431 10/95 134 124 10 167 167 0 strelka-varscan DST,missense_variant,p.Arg297Thr,ENST00000361203,;DST,missense_variant,p.Arg297Thr,ENST00000421834,NM_183380.3;DST,missense_variant,p.Arg337Thr,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Arg297Thr,ENST00000370788,;DST,missense_variant,p.Arg337Thr,ENST00000520645,;DST,missense_variant,p.Arg475Thr,ENST00000449297,;DST,non_coding_transcript_exon_variant,,ENST00000521104,;DST,non_coding_transcript_exon_variant,,ENST00000523967,; G ENST00000312431 Transcript missense_variant 1136/17756 1010/16614 337/5537 R/T aGa/aCa 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.06) 10/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 56648601 56648601 C G 1 0 0 0 0 1 0 0 0 4604 913 32 4 4 DST 6 56648601 Missense_Mutation SNP C C3N-01416_T 16714303 56648601 114157378 25 24314 AIM1 0 . GRCh38 6 106520809 106520809 + Nonsense_Mutation SNP A A T novel C3N-01416_T C3N-01416_N A A c.2377A>T p.Lys793Ter p.K793* ENST00000369066 2/20 154 113 41 287 287 0 strelka-varscan-mutect AIM1,stop_gained,p.Lys1201Ter,ENST00000633556,;AIM1,stop_gained,p.Lys793Ter,ENST00000369066,NM_001624.3; T ENST00000369066 Transcript stop_gained 2864/7553 2377/5172 793/1723 K/* Aag/Tag 1 1 AIM1 HGNC HGNC:356 protein_coding YES CCDS34506.1 ENSP00000358062 Q9Y4K1 UPI000013C91D NM_001624.3 2/20 hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF2 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 79 106520809 106520809 A T 1 0 0 0 0 0 1 0 0 507 131 5 4 4 AIM1 6 106520809 Nonsense_Mutation SNP A C3N-01416_T 49872208 106520809 64285170 26 24315 ROS1 0 . GRCh38 6 117386903 117386903 + Missense_Mutation SNP A A T rs758536297 C3N-01416_T C3N-01416_N A A c.2111T>A p.Ile704Lys p.I704K ENST00000368508 14/43 75 59 16 142 142 0 strelka-varscan-mutect ROS1,missense_variant,p.Ile704Lys,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Ile699Lys,ENST00000368507,;RP1-179P9.3,intron_variant,,ENST00000467125,; T ENST00000368508 Transcript missense_variant 2310/7435 2111/7044 704/2347 I/K aTa/aAa rs758536297 1 -1 ROS1 HGNC HGNC:10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 deleterious(0) 14/43 Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS rs758536297 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 117386903 117386903 A T 1 0 0 0 0 1 0 0 0 13708 449 16 4 4 ROS1 6 117386903 Missense_Mutation SNP A C3N-01416_T 10866094 117386903 53419076 27 24316 GRM1 0 . GRCh38 6 146029947 146029947 + Missense_Mutation SNP G G A C3N-01416_T C3N-01416_N G G c.430G>A p.Gly144Ser p.G144S ENST00000361719 2/9 268 203 65 465 464 1 strelka-varscan-mutect GRM1,missense_variant,p.Gly144Ser,ENST00000492807,NM_001278065.1,NM_001278066.1;GRM1,missense_variant,p.Gly144Ser,ENST00000361719,;GRM1,missense_variant,p.Gly144Ser,ENST00000282753,NM_001278064.1;GRM1,missense_variant,p.Gly144Ser,ENST00000355289,NM_001278067.1;GRM1,missense_variant,p.Gly144Ser,ENST00000507907,;GRM1,non_coding_transcript_exon_variant,,ENST00000502405,;GRM1,non_coding_transcript_exon_variant,,ENST00000507005,; A ENST00000361719 Transcript missense_variant 797/6754 430/3585 144/1194 G/S Ggc/Agc COSM236749,COSM740710,COSM740711 1 1 GRM1 HGNC HGNC:4593 protein_coding YES CCDS5209.1 ENSP00000354896 Q13255 UPI000013DCFD tolerated(0.75) 2/9 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF29,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR01051 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 146029947 146029947 G A 1 0 0 0 0 1 0 0 0 6678 1116 39 1 1 GRM1 6 146029947 Missense_Mutation SNP G C3N-01416_T 28643044 146029947 24776032 28 24317 RNF216 0 . GRCh38 7 5721158 5721158 + Nonsense_Mutation SNP C C A novel C3N-01416_T C3N-01416_N C C c.1519G>T p.Glu507Ter p.E507* ENST00000389902 9/17 136 110 26 133 133 0 strelka-varscan-mutect RNF216,stop_gained,p.Glu450Ter,ENST00000425013,NM_207116.2;RNF216,stop_gained,p.Glu507Ter,ENST00000389902,NM_207111.3;RNF216,3_prime_UTR_variant,,ENST00000389900,; A ENST00000389902 Transcript stop_gained 1787/3293 1519/2772 507/923 E/* Gaa/Taa 1 -1 RNF216 HGNC HGNC:21698 protein_coding YES CCDS34594.1 ENSP00000374552 Q9NWF9 UPI000013F5B3 NM_207111.3 9/17 hmmpanther:PTHR22770,hmmpanther:PTHR22770:SF13 HIGH 1 SNV 1 1 PASS rs1398849784 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 79 5721158 5721158 C A 1 0 0 0 0 0 1 0 0 13659 922 32 2 2 RNF216 7 5721158 Nonsense_Mutation SNP C C3N-01416_T 5721158 153624815 29 24318 STK31 0 . GRCh38 7 23783654 23783654 + Silent SNP C C T novel C3N-01416_T C3N-01416_N C C c.2139C>T p.= p.L713L ENST00000355870 17/24 130 100 30 207 207 0 strelka-varscan-mutect STK31,synonymous_variant,p.=,ENST00000354639,NM_032944.3,NM_001260504.1;STK31,synonymous_variant,p.=,ENST00000355870,NM_031414.4;STK31,synonymous_variant,p.=,ENST00000433467,NM_001260505.1;STK31,non_coding_transcript_exon_variant,,ENST00000405627,;STK31,downstream_gene_variant,,ENST00000476399,; T ENST00000355870 Transcript synonymous_variant 2258/3326 2139/3060 713/1019 L ctC/ctT 1 1 STK31 HGNC HGNC:11407 protein_coding YES CCDS5386.1 ENSP00000348132 Q9BXU1 UPI0000167B73 NM_031414.4 17/24 PROSITE_profiles:PS50011,hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 79 23783654 23783654 C T 1 0 0 0 0 0 0 0 1 15673 813 29 3 3 STK31 7 23783654 Silent SNP C C3N-01416_T 18062496 23783654 135562319 30 24319 HOXA4 0 . GRCh38 7 27129344 27129344 + Nonsense_Mutation SNP G G A C3N-01416_T C3N-01416_N G G c.844C>T p.Arg282Ter p.R282* ENST00000360046 2/2 468 386 82 489 485 4 strelka-varscan-mutect HOXA4,stop_gained,p.Arg282Ter,ENST00000360046,;HOXA4,stop_gained,p.Arg282Ter,ENST00000610970,NM_002141.4;HOXA4,stop_gained,p.Arg282Ter,ENST00000428284,;HOXA4,stop_gained,p.Arg102Ter,ENST00000511914,;HOXA3,intron_variant,,ENST00000317201,;HOXA3,intron_variant,,ENST00000522788,;HOXA3,upstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA-AS2,intron_variant,,ENST00000521159,;HOXA-AS2,downstream_gene_variant,,ENST00000517550,;HOXA-AS2,downstream_gene_variant,,ENST00000521687,;HOXA-AS3,upstream_gene_variant,,ENST00000518848,;RP1-170O19.22,non_coding_transcript_exon_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000521401,;HOXA3,intron_variant,,ENST00000518451,; A ENST00000360046 Transcript stop_gained 910/1747 844/963 282/320 R/* Cga/Tga COSM184290 1 -1 HOXA4 HGNC HGNC:5105 protein_coding YES CCDS5405.1 ENSP00000353151 Q00056 UPI000013C810 2/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF211 1 HIGH 1 SNV 2 1 1 PASS rs1383100158 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 79 27129344 27129344 G A 1 0 0 0 0 0 1 0 0 7188 1095 38 1 1 HOXA4 7 27129344 Nonsense_Mutation SNP G C3N-01416_T 3345690 27129344 132216629 31 24320 HECW1 0 . GRCh38 7 43445405 43445405 + Missense_Mutation SNP G G A rs762002584 C3N-01416_T C3N-01416_N G G c.2233G>A p.Ala745Thr p.A745T ENST00000395891 11/30 164 135 29 145 144 1 strelka-varscan-mutect HECW1,missense_variant,p.Ala745Thr,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Ala745Thr,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,; A ENST00000395891 Transcript missense_variant 2838/9501 2233/4821 745/1606 A/T Gcg/Acg rs762002584,COSM1254084,COSM1254085,COSM325484 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious_low_confidence(0.02) 11/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs762002584 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 43445405 43445405 G A 1 0 0 0 0 1 0 0 0 6924 1087 38 1 1 HECW1 7 43445405 Missense_Mutation SNP G C3N-01416_T 16316061 43445405 115900568 32 24321 URGCP 0 . GRCh38 7 43878650 43878650 + Silent SNP A A G novel C3N-01416_T C3N-01416_N A A c.813T>C p.= p.S271S ENST00000453200 6/6 403 358 45 467 465 2 strelka-varscan-mutect URGCP,synonymous_variant,p.=,ENST00000336086,;URGCP,synonymous_variant,p.=,ENST00000453200,NM_001077663.2;URGCP,synonymous_variant,p.=,ENST00000443736,NM_001077664.2,NM_001290075.1,NM_001290076.1;URGCP,synonymous_variant,p.=,ENST00000402306,NM_017920.4;URGCP-MRPS24,intron_variant,,ENST00000603700,NM_001204871.1;URGCP,downstream_gene_variant,,ENST00000426198,;URGCP,downstream_gene_variant,,ENST00000439702,;URGCP,downstream_gene_variant,,ENST00000455877,;URGCP,downstream_gene_variant,,ENST00000446958,;URGCP,non_coding_transcript_exon_variant,,ENST00000497914,;URGCP,downstream_gene_variant,,ENST00000467410,;URGCP,downstream_gene_variant,,ENST00000474376,; G ENST00000453200 Transcript synonymous_variant 1307/4042 813/2796 271/931 S agT/agC 1 -1 URGCP HGNC HGNC:30890 protein_coding YES CCDS47578.1 ENSP00000396918 Q8TCY9 UPI000020EE9D NM_001077663.2 6/6 hmmpanther:PTHR22796 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 79 43878650 43878650 A G 1 0 0 0 0 0 0 0 1 17556 388 14 5 5 URGCP 7 43878650 Silent SNP A C3N-01416_T 433245 43878650 115467323 33 24322 ZPBP 0 . GRCh38 7 50031143 50031143 + Missense_Mutation SNP C C T rs776265657 C3N-01416_T C3N-01416_N C C c.655G>A p.Val219Ile p.V219I ENST00000046087 5/8 272 210 62 365 365 0 strelka-varscan-mutect ZPBP,missense_variant,p.Val219Ile,ENST00000046087,NM_007009.2;ZPBP,missense_variant,p.Val218Ile,ENST00000419417,NM_001159878.1;ZPBP,intron_variant,,ENST00000491129,; T ENST00000046087 Transcript missense_variant 725/1213 655/1056 219/351 V/I Gtt/Att rs776265657,COSM1090559 1 -1 ZPBP HGNC HGNC:15662 protein_coding YES CCDS5509.1 ENSP00000046087 Q9BS86 UPI0000073BD0 NM_007009.2 tolerated(0.12) 5/8 Pfam_domain:PF07354,hmmpanther:PTHR15443,hmmpanther:PTHR15443:SF5 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776265657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 50031143 50031143 C T 1 0 0 0 0 1 0 0 0 18811 536 19 1 1 ZPBP 7 50031143 Missense_Mutation SNP C C3N-01416_T 6152493 50031143 109314830 34 24323 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-01416_T C3N-01416_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 427 359 68 514 514 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 79 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-01416_T 5143629 55174772 104171201 35 24324 MUC17 0 . GRCh38 7 101043717 101043717 + Missense_Mutation SNP C C T rs368040615 C3N-01416_T C3N-01416_N C C c.12301C>T p.Arg4101Trp p.R4101W ENST00000306151 3/13 162 149 13 195 195 0 strelka-varscan MUC17,missense_variant,p.Arg4101Trp,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Arg4101Trp,ENST00000379439,;MUC17,non_coding_transcript_exon_variant,,ENST00000470303,; T ENST00000306151 Transcript missense_variant 12365/14247 12301/13482 4101/4493 R/W Cgg/Tgg rs368040615,COSM1312528 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999:SF1,hmmpanther:PTHR37999 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 101043717 101043717 C T 1 0 0 0 0 1 0 0 0 9973 527 19 1 1 MUC17 7 101043717 Missense_Mutation SNP C C3N-01416_T 45868945 101043717 58302256 36 24325 HR 0 . GRCh38 8 22116946 22116946 + Missense_Mutation SNP C C A novel C3N-01416_T C3N-01416_N C C c.3307G>T p.Gly1103Cys p.G1103C ENST00000381418 17/19 168 135 33 153 153 0 strelka-varscan-mutect HR,missense_variant,p.Gly1103Cys,ENST00000381418,NM_005144.4;HR,intron_variant,,ENST00000312841,NM_018411.4;HR,non_coding_transcript_exon_variant,,ENST00000522016,;HR,downstream_gene_variant,,ENST00000517699,;HR,downstream_gene_variant,,ENST00000522039,;HR,downstream_gene_variant,,ENST00000518461,; A ENST00000381418 Transcript missense_variant 4788/6336 3307/3570 1103/1189 G/C Ggc/Tgc 1 -1 HR HGNC HGNC:5172 protein_coding YES CCDS6022.1 ENSP00000370826 O43593 UPI000013EB0B NM_005144.4 deleterious(0) 17/19 PROSITE_profiles:PS51184,hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF4,Pfam_domain:PF02373,SMART_domains:SM00558,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 22116946 22116946 C A 1 0 0 0 0 1 0 0 0 7242 623 22 2 2 HR 8 22116946 Missense_Mutation SNP C C3N-01416_T 22116946 123021690 37 24326 ZNF7 0 . GRCh38 8 144842755 144842755 + Missense_Mutation SNP G G C novel C3N-01416_T C3N-01416_N G G c.1681G>C p.Glu561Gln p.E561Q ENST00000446747 5/5 130 123 7 199 199 0 strelka-varscan-mutect ZNF7,missense_variant,p.Glu550Gln,ENST00000528372,NM_003416.3;ZNF7,missense_variant,p.Glu561Gln,ENST00000446747,NM_001282795.1;ZNF7,missense_variant,p.Glu454Gln,ENST00000544249,NM_001282797.1;ZNF7,intron_variant,,ENST00000525266,NM_001282796.1;ZNF7,intron_variant,,ENST00000325217,;ZNF7,downstream_gene_variant,,ENST00000528130,;ZNF7,downstream_gene_variant,,ENST00000532777,;ZNF7,downstream_gene_variant,,ENST00000527218,;ZNF7,downstream_gene_variant,,ENST00000533314,;ZNF7,downstream_gene_variant,,ENST00000529819,;ZNF7,downstream_gene_variant,,ENST00000532393,;ZNF7,downstream_gene_variant,,ENST00000530776,;ZNF7,downstream_gene_variant,,ENST00000532051,;ZNF7,non_coding_transcript_exon_variant,,ENST00000528017,;COMMD5,intron_variant,,ENST00000530332,;ZNF7,downstream_gene_variant,,ENST00000532382,;ZNF7,downstream_gene_variant,,ENST00000530082,;ZNF7,downstream_gene_variant,,ENST00000529767,; C ENST00000446747 Transcript missense_variant 1777/2242 1681/2094 561/697 E/Q Gag/Cag 1 1 ZNF7 HGNC HGNC:13139 protein_coding YES CCDS64996.1 ENSP00000393260 P17097 UPI00017A7AA1 NM_001282795.1 deleterious(0.03) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF189,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 144842755 144842755 G C 1 0 0 0 0 1 0 0 0 18675 943 33 4 4 ZNF7 8 144842755 Missense_Mutation SNP G C3N-01416_T 122725809 144842755 295881 38 24327 ZNF462 0 . GRCh38 9 106924596 106924596 + Silent SNP C C T novel C3N-01416_T C3N-01416_N C C c.684C>T p.= p.I228I ENST00000277225 3/13 193 161 32 327 327 0 strelka-varscan-mutect ZNF462,synonymous_variant,p.=,ENST00000277225,NM_021224.4;ZNF462,intron_variant,,ENST00000472574,;ZNF462,upstream_gene_variant,,ENST00000374686,;ZNF462,upstream_gene_variant,,ENST00000441147,;ZNF462,upstream_gene_variant,,ENST00000480607,; T ENST00000277225 Transcript synonymous_variant 973/10414 684/7521 228/2506 I atC/atT 1 1 ZNF462 HGNC HGNC:21684 protein_coding YES CCDS35096.1 ENSP00000277225 Q96JM2 UPI0000470106 NM_021224.4 3/13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 79 106924596 106924596 C T 1 0 0 0 0 0 0 0 1 18497 903 32 3 3 ZNF462 9 106924596 Silent SNP C C3N-01416_T 106924596 31470121 39 24328 NDOR1 0 . GRCh38 9 137212579 137212579 + Silent SNP C C T rs750433403 C3N-01416_T C3N-01416_N C C c.291C>T p.= p.L97L ENST00000371521 3/14 241 225 16 242 241 1 strelka-varscan-mutect NDOR1,synonymous_variant,p.=,ENST00000371521,NM_001144026.2;NDOR1,synonymous_variant,p.=,ENST00000427047,NM_001144027.2;NDOR1,synonymous_variant,p.=,ENST00000458322,NM_001144028.2;NDOR1,synonymous_variant,p.=,ENST00000344894,NM_014434.3;NDOR1,non_coding_transcript_exon_variant,,ENST00000613750,;NDOR1,non_coding_transcript_exon_variant,,ENST00000612145,; T ENST00000371521 Transcript synonymous_variant 374/2497 291/1821 97/606 L ctC/ctT rs750433403,COSM1461342,COSM1461343 1 1 NDOR1 HGNC HGNC:29838 protein_coding YES CCDS48061.1 ENSP00000360576 Q9UHB4 UPI0000190A69 NM_001144026.2 3/14 Gene3D:3.40.50.360,HAMAP:MF_03178,Pfam_domain:PF00258,Prints_domain:PR00369,PROSITE_profiles:PS50902,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF10,Superfamily_domains:SSF52218 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs750433403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 79 137212579 137212579 C T 1 0 0 0 0 0 0 0 1 10270 871 31 1 1 NDOR1 9 137212579 Silent SNP C C3N-01416_T 30287983 137212579 1182138 40 24329 C10orf71 0 . GRCh38 10 49325934 49325934 + Missense_Mutation SNP C C T C3N-01416_T C3N-01416_N C C c.3389C>T p.Ser1130Leu p.S1130L ENST00000374144 3/3 68 64 4 122 122 0 varscan-mutect C10orf71,missense_variant,p.Ser1130Leu,ENST00000374144,NM_001135196.1; T ENST00000374144 Transcript missense_variant 3677/5230 3389/4308 1130/1435 S/L tCg/tTg COSM5628222 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 tolerated(0.3) 3/3 hmmpanther:PTHR33775 1 MODERATE 1 SNV 1 1 1 PASS rs1471758251 . 0 205 4 0 0 0 0 0 -9.692605 1 1 1 1 0 T 3 4 79 49325934 49325934 C T 1 0 0 0 0 1 0 0 0 1769 893 31 1 1 C10orf71 10 49325934 Missense_Mutation SNP C C3N-01416_T 49325934 84471488 41 24330 HECTD2 0 . GRCh38 10 91500595 91500595 + Missense_Mutation SNP G G A novel C3N-01416_T C3N-01416_N G G c.2056G>A p.Ala686Thr p.A686T ENST00000446394 20/22 161 145 16 216 216 0 strelka-varscan-mutect HECTD2,missense_variant,p.Ala686Thr,ENST00000446394,NM_001284274.1;HECTD2,missense_variant,p.Ala682Thr,ENST00000298068,NM_182765.4;HECTD2,missense_variant,p.Ala332Thr,ENST00000371667,; A ENST00000446394 Transcript missense_variant 2210/4939 2056/2343 686/780 A/T Gca/Aca 1 1 HECTD2 HGNC HGNC:26736 protein_coding YES CCDS60591.1 ENSP00000401023 E7ERR3 UPI0001AE6DAB NM_001284274.1 tolerated(0.58) 20/22 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF301,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 2 1 PASS . . 0 200 0 9 0 0 0 0 -19.99321 0.9616823 1 1 1 0 A 3 1 79 91500595 91500595 G A 1 0 0 0 0 1 0 0 0 6921 1319 46 3 3 HECTD2 10 91500595 Missense_Mutation SNP G C3N-01416_T 42174661 91500595 42296827 42 24331 MYOF 0 . GRCh38 10 93366427 93366427 + Silent SNP T T C rs770387435 C3N-01416_T C3N-01416_N T T c.2718A>G p.= p.E906E ENST00000359263 26/54 94 80 14 236 236 0 strelka-varscan-mutect MYOF,synonymous_variant,p.=,ENST00000359263,NM_013451.3;MYOF,synonymous_variant,p.=,ENST00000358334,NM_133337.2;MYOF,synonymous_variant,p.=,ENST00000463743,; C ENST00000359263 Transcript synonymous_variant 2718/6719 2718/6186 906/2061 E gaA/gaG rs770387435 1 -1 MYOF HGNC HGNC:3656 protein_coding YES CCDS41551.1 ENSP00000352208 Q9NZM1 UPI000012FBA1 NM_013451.3 26/54 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF40,SMART_domains:SM00693 LOW 1 SNV 1 1 PASS rs770387435 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 79 93366427 93366427 T C 1 0 0 0 0 0 0 0 1 10090 1490 52 5 5 MYOF 10 93366427 Silent SNP T C3N-01416_T 1865832 93366427 40430995 43 24332 MTG1 0 . GRCh38 10 133420043 133420043 + Nonsense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.898C>T p.Gln300Ter p.Q300* ENST00000468317 12/12 37 31 6 53 53 0 strelka-varscan-mutect RP11-108K14.8,stop_gained,p.Gln300Ter,ENST00000468317,;MTG1,stop_gained,p.Gln295Ter,ENST00000317502,NM_138384.2;MTG1,stop_gained,p.Gln254Ter,ENST00000477902,;MTG1,stop_gained,p.Gln244Ter,ENST00000432508,;SPRN,downstream_gene_variant,,ENST00000414069,NM_001012508.3;MTG1,non_coding_transcript_exon_variant,,ENST00000460848,;MTG1,non_coding_transcript_exon_variant,,ENST00000473735,; T ENST00000468317 Transcript stop_gained 1153/1605 898/1020 300/339 Q/* Cag/Tag 1 1 RP11-108K14.8 Clone_based_vega_gene protein_coding YES ENSP00000436767 E9PI62 UPI0000D4C5CD 12/12 hmmpanther:PTHR11089,Gene3D:1pujA02,PIRSF_domain:PIRSF006230 HIGH SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -15.23293 0.9999854 1 1 1 0 T 4 4 79 133420043 133420043 C T 1 0 0 0 0 0 1 0 0 9914 827 29 3 3 MTG1 10 133420043 Nonsense_Mutation SNP C C3N-01416_T 40053616 133420043 377379 44 24333 COPB1 0 . GRCh38 11 14468785 14468785 + Missense_Mutation SNP C C T C3N-01416_T C3N-01416_N C C c.2041G>A p.Glu681Lys p.E681K ENST00000249923 16/22 162 150 12 276 276 0 strelka-varscan-mutect COPB1,missense_variant,p.Glu681Lys,ENST00000249923,NM_016451.4;COPB1,missense_variant,p.Glu681Lys,ENST00000439561,NM_001144061.1,NM_001144062.1; T ENST00000249923 Transcript missense_variant 2342/3481 2041/2862 681/953 E/K Gaa/Aaa COSM147148 1 -1 COPB1 HGNC HGNC:2231 protein_coding YES CCDS7815.1 ENSP00000249923 P53618 UPI000000103D NM_016451.4 tolerated(0.36) 16/22 hmmpanther:PTHR10635,Pfam_domain:PF07718,PIRSF_domain:PIRSF005727 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 14468785 14468785 C T 1 0 0 0 0 1 0 0 0 3520 835 29 3 3 COPB1 11 14468785 Missense_Mutation SNP C C3N-01416_T 14468785 120617837 45 24334 SORL1 0 . GRCh38 11 121554018 121554018 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.2348C>T p.Pro783Leu p.P783L ENST00000260197 17/48 184 159 25 297 297 0 strelka-varscan-mutect SORL1,missense_variant,p.Pro783Leu,ENST00000260197,NM_003105.5;SORL1,upstream_gene_variant,,ENST00000529445,;SORL1,upstream_gene_variant,,ENST00000524873,; T ENST00000260197 Transcript missense_variant 2477/10904 2348/6645 783/2214 P/L cCt/cTt 1 1 SORL1 HGNC HGNC:11185 protein_coding YES CCDS8436.1 ENSP00000260197 Q92673 UPI000013D0B1 NM_003105.5 tolerated(0.07) 17/48 Gene3D:2.120.10.30,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF20,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 121554018 121554018 C T 1 0 0 0 0 1 0 0 0 15256 681 24 3 3 SORL1 11 121554018 Missense_Mutation SNP C C3N-01416_T 107085233 121554018 13532604 46 24335 OVOS2 0 . GRCh38 12 31148114 31148114 + Nonsense_Mutation SNP A A T rs757342956 C3N-01416_T C3N-01416_N A A c.1212T>A p.Tyr404Ter p.Y404* ENST00000632817 11/34 122 108 14 186 185 1 strelka-mutect OVOS2,stop_gained,p.Tyr404Ter,ENST00000398963,;OVOS2,stop_gained,p.Tyr404Ter,ENST00000632817,; T ENST00000632817 Transcript stop_gained 1212/4299 1212/4299 404/1432 Y/* taT/taA rs757342956 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 11/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 HIGH 1 SNV 5 1 PASS rs757342956 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 79 31148114 31148114 A T 1 0 0 0 0 0 1 0 0 11399 224 8 4 4 OVOS2 12 31148114 Nonsense_Mutation SNP A C3N-01416_T 31148114 102127195 47 24336 KRT1 0 . GRCh38 12 52677695 52677695 + Missense_Mutation SNP G G T novel C3N-01416_T C3N-01416_N G G c.918C>A p.Asp306Glu p.D306E ENST00000252244 4/9 222 180 42 440 439 1 strelka-varscan-mutect KRT1,missense_variant,p.Asp306Glu,ENST00000252244,NM_006121.3;KRT1,upstream_gene_variant,,ENST00000548765,; T ENST00000252244 Transcript missense_variant 977/2451 918/1935 306/644 D/E gaC/gaA 1 -1 KRT1 HGNC HGNC:6412 protein_coding YES CCDS8836.1 ENSP00000252244 P04264 UPI000013CD4D NM_006121.3 deleterious(0.04) 4/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF95,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 52677695 52677695 G T 1 0 0 0 0 1 0 0 0 8329 1368 48 2 2 KRT1 12 52677695 Missense_Mutation SNP G C3N-01416_T 21529581 52677695 80597614 48 24337 SP1 0 . GRCh38 12 53382835 53382835 + Silent SNP A A G novel C3N-01416_T C3N-01416_N A A c.888A>G p.= p.S296S ENST00000327443 3/6 275 219 56 381 381 0 strelka-varscan-mutect SP1,synonymous_variant,p.=,ENST00000426431,NM_003109.1;SP1,synonymous_variant,p.=,ENST00000327443,NM_138473.2,NM_001251825.1;SP1,downstream_gene_variant,,ENST00000548560,;SP1,downstream_gene_variant,,ENST00000551969,; G ENST00000327443 Transcript synonymous_variant 986/2846 888/2358 296/785 S tcA/tcG 1 1 SP1 HGNC HGNC:11205 protein_coding YES CCDS8857.1 ENSP00000329357 P08047 UPI0000135D4E NM_138473.2,NM_001251825.1 3/6 hmmpanther:PTHR23235,hmmpanther:PTHR23235:SF16,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 79 53382835 53382835 A G 1 0 0 0 0 0 0 0 1 15285 146 6 5 5 SP1 12 53382835 Silent SNP A C3N-01416_T 705140 53382835 79892474 49 24338 OTOGL 0 . GRCh38 12 80377861 80377861 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.6848C>T p.Ser2283Phe p.S2283F ENST00000458043 58/58 461 287 174 196 195 1 strelka-varscan-mutect OTOGL,missense_variant,p.Ser2283Phe,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Ser2271Phe,ENST00000547103,;OTOGL,missense_variant,p.Ser691Phe,ENST00000298820,;OTOGL,3_prime_UTR_variant,,ENST00000551340,;OTOGL,non_coding_transcript_exon_variant,,ENST00000546620,; T ENST00000458043 Transcript missense_variant 6854/8083 6848/7035 2283/2344 S/F tCt/tTt 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 58/58 PROSITE_profiles:PS01225,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,SMART_domains:SM00041 MODERATE 1 SNV 5 1 PASS rs1474633778 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 80377861 80377861 C T 1 0 0 0 0 1 0 0 0 11371 913 32 3 3 OTOGL 12 80377861 Missense_Mutation SNP C C3N-01416_T 26995026 80377861 52897448 50 24339 1 15 2 2 22 C 5.643785e-05 OTOGL 0 . GRCh38 12 80377882 80377882 + Nonsense_Mutation SNP C C G novel C3N-01416_T C3N-01416_N C C c.6869C>G p.Ser2290Ter p.S2290* ENST00000458043 58/58 564 341 223 258 258 0 strelka-varscan-mutect OTOGL,stop_gained,p.Ser2290Ter,ENST00000458043,NM_173591.3;OTOGL,stop_gained,p.Ser2278Ter,ENST00000547103,;OTOGL,stop_gained,p.Ser698Ter,ENST00000298820,;OTOGL,3_prime_UTR_variant,,ENST00000551340,;OTOGL,non_coding_transcript_exon_variant,,ENST00000546620,; G ENST00000458043 Transcript stop_gained 6875/8083 6869/7035 2290/2344 S/* tCa/tGa 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 58/58 PROSITE_profiles:PS01225,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,SMART_domains:SM00041 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 4 3 79 80377882 80377882 C G 1 0 0 0 0 0 1 0 0 11371 838 29 4 4 OTOGL 12 80377882 Nonsense_Mutation SNP C C3N-01416_T 21 80377882 52897427 51 24340 1 15 2 2 22 C 5.643785e-05 RASSF9 0 . GRCh38 12 85805191 85805191 + Silent SNP C C A C3N-01416_T C3N-01416_N C C c.819G>T p.= p.L273L ENST00000361228 2/2 106 97 9 229 229 0 strelka-varscan-mutect RASSF9,synonymous_variant,p.=,ENST00000361228,NM_005447.3; A ENST00000361228 Transcript synonymous_variant 1188/5682 819/1308 273/435 L ctG/ctT COSM3872656,COSM3872657 1 -1 RASSF9 HGNC HGNC:15739 protein_coding YES CCDS44950.1 ENSP00000354884 O75901 UPI000003E7E4 NM_005447.3 2/2 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF10 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 85805191 85805191 C A 1 0 0 0 0 0 0 0 1 13254 813 29 2 2 RASSF9 12 85805191 Silent SNP C C3N-01416_T 5427309 85805191 47470118 52 24341 RB1 0 . GRCh38 13 48368549 48368549 + Nonsense_Mutation SNP C C T rs121913301 C3N-01416_T C3N-01416_N C C c.1072C>T p.Arg358Ter p.R358* ENST00000267163 11/27 182 159 23 347 347 0 strelka-varscan-mutect RB1,stop_gained,p.Arg358Ter,ENST00000267163,NM_000321.2; T ENST00000267163 Transcript stop_gained 1210/4840 1072/2787 358/928 R/* Cga/Tga rs121913301,CM951105,CM961226,COSM4776098,COSM879 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 11/27 hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21 pathogenic 0,0,0,1,1 HIGH 1 SNV 1 1,1,1,1,1 1 PASS rs121913301 . 0 208 0 0 2 0 0 0 -10.75843 0.9957245 1 1 1 0 T 4 4 79 48368549 48368549 C T 1 0 0 0 0 0 1 0 0 13259 528 19 1 1 RB1 13 48368549 Nonsense_Mutation SNP C C3N-01416_T 48368549 65995779 53 24342 RNASEH2B 0 . GRCh38 13 50927476 50927476 + Missense_Mutation SNP C C T rs575985863 C3N-01416_T C3N-01416_N C C c.134C>T p.Ser45Leu p.S45L ENST00000336617 2/11 234 221 13 453 453 0 strelka-varscan-mutect RNASEH2B,missense_variant,p.Ser45Leu,ENST00000422660,NM_001142279.2;RNASEH2B,missense_variant,p.Ser45Leu,ENST00000336617,NM_024570.3;RNASEH2B,missense_variant,p.Ser15Leu,ENST00000611510,;RNASEH2B,missense_variant,p.Ser15Leu,ENST00000636524,;RNASEH2B,downstream_gene_variant,,ENST00000637648,;RNASEH2B,upstream_gene_variant,,ENST00000495244,;RNASEH2B,upstream_gene_variant,,ENST00000459681,; T ENST00000336617 Transcript missense_variant,splice_region_variant 533/1629 134/939 45/312 S/L tCa/tTa rs575985863,COSM696439 1 1 RNASEH2B HGNC HGNC:25671 protein_coding YES CCDS9425.1 ENSP00000337623 Q5TBB1 UPI000013CFE7 NM_024570.3 deleterious(0.01) 2/11 hmmpanther:PTHR13383:SF11,hmmpanther:PTHR13383,Pfam_domain:PF09468 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs575985863 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 50927476 50927476 C T 1 0 0 0 0 1 0 0 0 13592 840 29 3 3 RNASEH2B 13 50927476 Missense_Mutation SNP C C3N-01416_T 2558927 50927476 63436852 54 24343 GABRB3 0 . GRCh38 15 26621483 26621483 + Missense_Mutation SNP C C T rs756369937 C3N-01416_T C3N-01416_N C C c.292G>A p.Ala98Thr p.A98T ENST00000311550 4/9 183 169 14 279 279 0 strelka-varscan-mutect GABRB3,missense_variant,p.Ala154Thr,ENST00000541819,;GABRB3,missense_variant,p.Ala13Thr,ENST00000622697,NM_001278631.1;GABRB3,missense_variant,p.Ala98Thr,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Ala13Thr,ENST00000628124,NM_001191320.1;GABRB3,missense_variant,p.Ala13Thr,ENST00000636466,;GABRB3,missense_variant,p.Ala98Thr,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Ala65Thr,ENST00000638099,;GABRB3,missense_variant,p.Ala27Thr,ENST00000400188,NM_001191321.2;GABRB3,missense_variant,p.Ala13Thr,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000556166,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,upstream_gene_variant,,ENST00000636690,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;GABRB3,intron_variant,,ENST00000554556,;GABRB3,upstream_gene_variant,,ENST00000635994,;GABRB3,upstream_gene_variant,,ENST00000556636,; T ENST00000311550 Transcript missense_variant 404/5781 292/1422 98/473 A/T Gcc/Acc rs756369937,COSM1372173,COSM1372174,COSM1372175 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 tolerated(0.06) 4/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932,Prints_domain:PR00252,Prints_domain:PR01160 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs756369937 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 26621483 26621483 C T 1 0 0 0 0 1 0 0 0 6039 768 27 1 1 GABRB3 15 26621483 Missense_Mutation SNP C C3N-01416_T 26621483 75369706 55 24344 TP53BP1 0 . GRCh38 15 43407960 43407960 + Nonsense_Mutation SNP G G C novel C3N-01416_T C3N-01416_N G G c.5729C>G p.Ser1910Ter p.S1910* ENST00000382044 27/28 50 43 7 113 113 0 strelka-varscan-mutect TP53BP1,stop_gained,p.Ser1910Ter,ENST00000382044,NM_001141980.1;TP53BP1,stop_gained,p.Ser1905Ter,ENST00000263801,NM_005657.2;TP53BP1,stop_gained,p.Ser1908Ter,ENST00000450115,NM_001141979.1;TP53BP1,stop_gained,p.Ser1860Ter,ENST00000382039,;TUBGCP4,3_prime_UTR_variant,,ENST00000564079,NM_014444.3;TUBGCP4,downstream_gene_variant,,ENST00000260383,NM_001286414.1;TUBGCP4,downstream_gene_variant,,ENST00000563147,;TUBGCP4,downstream_gene_variant,,ENST00000565548,;TP53BP1,downstream_gene_variant,,ENST00000434595,;TP53BP1,3_prime_UTR_variant,,ENST00000411772,;TP53BP1,non_coding_transcript_exon_variant,,ENST00000476454,;TUBGCP4,downstream_gene_variant,,ENST00000563963,;TUBGCP4,downstream_gene_variant,,ENST00000561691,;TUBGCP4,downstream_gene_variant,,ENST00000566251,; C ENST00000382044 Transcript stop_gained 5857/10384 5729/5934 1910/1977 S/* tCa/tGa 1 -1 TP53BP1 HGNC HGNC:11999 protein_coding YES CCDS45250.1 ENSP00000371475 Q12888 UPI0000D720ED NM_001141980.1 27/28 PROSITE_profiles:PS50172,hmmpanther:PTHR15321,hmmpanther:PTHR15321:SF3,Gene3D:3.40.50.10190,SMART_domains:SM00292,Superfamily_domains:SSF52113 HIGH 1 SNV 1 1 PASS . . 0 200 8 2 0 0 0 0 -13.44986 0.9996899 1 1 1 0 C 4 2 79 43407960 43407960 G C 1 0 0 0 0 0 1 0 0 16861 1294 45 4 4 TP53BP1 15 43407960 Nonsense_Mutation SNP G C3N-01416_T 16786477 43407960 58583229 56 24345 PDIA3 0 . GRCh38 15 43761497 43761497 + Silent SNP G G A novel C3N-01416_T C3N-01416_N G G c.438G>A p.= p.K146K ENST00000300289 4/13 86 76 10 172 172 0 strelka-varscan-mutect PDIA3,synonymous_variant,p.=,ENST00000300289,NM_005313.4;PDIA3,downstream_gene_variant,,ENST00000469684,;PDIA3,3_prime_UTR_variant,,ENST00000434494,;PDIA3,intron_variant,,ENST00000455250,;PDIA3,downstream_gene_variant,,ENST00000446523,; A ENST00000300289 Transcript synonymous_variant 586/3727 438/1518 146/505 K aaG/aaA 1 1 PDIA3 HGNC HGNC:4606 protein_coding YES CCDS10101.1 ENSP00000300289 P30101 V9HVY3 UPI0000052A4F NM_005313.4 4/13 hmmpanther:PTHR18929:SF60,hmmpanther:PTHR18929,TIGRFAM_domain:TIGR01130,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 LOW 1 SNV 1 1 PASS rs1240705929 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 43761497 43761497 G A 1 0 0 0 0 0 0 0 1 11757 933 33 3 3 PDIA3 15 43761497 Silent SNP G C3N-01416_T 353537 43761497 58229692 57 24346 WDR72 0 . GRCh38 15 53712822 53712822 + Missense_Mutation SNP A A G C3N-01416_T C3N-01416_N A A c.661T>C p.Cys221Arg p.C221R ENST00000396328 7/20 229 192 37 372 372 0 strelka-varscan-mutect WDR72,missense_variant,p.Cys221Arg,ENST00000396328,;WDR72,missense_variant,p.Cys220Arg,ENST00000557913,;WDR72,missense_variant,p.Cys221Arg,ENST00000360509,NM_182758.3;WDR72,missense_variant,p.Cys221Arg,ENST00000559418,;WDR72,missense_variant,p.Cys221Arg,ENST00000560036,; G ENST00000396328 Transcript missense_variant 901/7507 661/3309 221/1102 C/R Tgc/Cgc COSM4055616 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D deleterious(0) 7/20 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF408,Superfamily_domains:SSF50978 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 53712822 53712822 A G 1 0 0 0 0 1 0 0 0 17878 130 5 5 5 WDR72 15 53712822 Missense_Mutation SNP A C3N-01416_T 9951325 53712822 48278367 58 24347 FAM173A 0 . GRCh38 16 721799 721799 + Splice_Site SNP A A T novel C3N-01416_T C3N-01416_N A A c.268-2A>T p.X90_splice ENST00000569529 73 64 9 97 97 0 strelka-varscan-mutect FAM173A,splice_acceptor_variant,,ENST00000564000,;FAM173A,splice_acceptor_variant,,ENST00000569529,NM_023933.2;FAM173A,splice_acceptor_variant,,ENST00000219535,NM_001271285.1;FAM173A,splice_acceptor_variant,,ENST00000568916,;METRN,downstream_gene_variant,,ENST00000568223,NM_024042.2;CCDC78,downstream_gene_variant,,ENST00000293889,NM_001031737.2;CCDC78,downstream_gene_variant,,ENST00000345165,;METRN,downstream_gene_variant,,ENST00000219542,;CCDC78,downstream_gene_variant,,ENST00000423653,;METRN,downstream_gene_variant,,ENST00000568415,;METRN,downstream_gene_variant,,ENST00000567076,;FAM173A,splice_acceptor_variant,,ENST00000566525,;FAM173A,splice_acceptor_variant,,ENST00000564640,;FAM173A,splice_acceptor_variant,,ENST00000566437,;CCDC78,downstream_gene_variant,,ENST00000482878,;CCDC78,downstream_gene_variant,,ENST00000481804,;CCDC78,downstream_gene_variant,,ENST00000478979,;CCDC78,downstream_gene_variant,,ENST00000466708,;CCDC78,downstream_gene_variant,,ENST00000463539,;CCDC78,downstream_gene_variant,,ENST00000485091,;METRN,downstream_gene_variant,,ENST00000564661,;CCDC78,downstream_gene_variant,,ENST00000538176,;CCDC78,downstream_gene_variant,,ENST00000439619,;CCDC78,downstream_gene_variant,,ENST00000482152,;CCDC78,downstream_gene_variant,,ENST00000460023,;CCDC78,downstream_gene_variant,,ENST00000471861,;CCDC78,downstream_gene_variant,,ENST00000544996,;CCDC78,downstream_gene_variant,,ENST00000474647,;METRN,downstream_gene_variant,,ENST00000570132,;FAM173A,upstream_gene_variant,,ENST00000570237,; T ENST00000569529 Transcript splice_acceptor_variant -/1052 268/708 90/235 1 1 FAM173A HGNC HGNC:14152 protein_coding YES CCDS10423.1 ENSP00000454380 Q9BQD7 UPI000006E1B7 NM_023933.2 2/4 HIGH 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -19.37391 0.9999735 1 1 1 0 T 5 4 79 721799 721799 A T 1 0 0 0 0 0 0 1 0 5341 202 7 4 4 FAM173A 16 721799 Splice_Site SNP A C3N-01416_T 721799 89616546 59 24348 CACNA1H 0 . GRCh38 16 1202406 1202406 + Missense_Mutation SNP C C G novel C3N-01416_T C3N-01416_N C C c.1956C>G p.Asn652Lys p.N652K ENST00000348261 9/35 28 25 3 40 40 0 strelka-mutect CACNA1H,missense_variant,p.Asn652Lys,ENST00000348261,NM_021098.2;CACNA1H,missense_variant,p.Asn652Lys,ENST00000358590,NM_001005407.1;CACNA1H,missense_variant,p.Asn652Lys,ENST00000565831,;RP11-616M22.3,downstream_gene_variant,,ENST00000564700,;CACNA1H,downstream_gene_variant,,ENST00000564954,; G ENST00000348261 Transcript missense_variant 2324/8208 1956/7062 652/2353 N/K aaC/aaG 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 tolerated(0.23) 9/35 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -9.353163 1 1 1 1 0 G 3 3 79 1202406 1202406 C G 1 0 0 0 0 1 0 0 0 2233 477 17 4 4 CACNA1H 16 1202406 Missense_Mutation SNP C C3N-01416_T 480607 1202406 89135939 60 24349 MMP2 0 . GRCh38 16 55489658 55489658 + Silent SNP C C T C3N-01416_T C3N-01416_N C C c.1014C>T p.= p.S338S ENST00000219070 7/13 385 339 46 564 564 0 strelka-varscan-mutect MMP2,synonymous_variant,p.=,ENST00000219070,NM_004530.5;MMP2,synonymous_variant,p.=,ENST00000570308,;MMP2,synonymous_variant,p.=,ENST00000437642,NM_001127891.2;MMP2,synonymous_variant,p.=,ENST00000543485,NM_001302508.1,NM_001302510.1,NM_001302509.1;MMP2,intron_variant,,ENST00000570283,;MMP2,downstream_gene_variant,,ENST00000564864,;MMP2,downstream_gene_variant,,ENST00000568715,;RP11-212I21.3,downstream_gene_variant,,ENST00000623886,; T ENST00000219070 Transcript synonymous_variant 1523/3741 1014/1983 338/660 S tcC/tcT COSM5339173 1 1 MMP2 HGNC HGNC:7166 protein_coding YES CCDS10752.1 ENSP00000219070 P08253 A0A024R6R4 UPI00000422C4 NM_004530.5 7/13 Gene3D:2.10.10.10,Pfam_domain:PF00413,SMART_domains:SM00235,Superfamily_domains:SSF57440 1 LOW 1 SNV 1 1 1 PASS rs1265010226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 79 55489658 55489658 C T 1 0 0 0 0 0 0 0 1 9621 581 21 3 3 MMP2 16 55489658 Silent SNP C C3N-01416_T 54287252 55489658 34848687 61 24350 FUK 0 . GRCh38 16 70463677 70463677 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.137C>T p.Ala46Val p.A46V ENST00000288078 3/24 180 160 20 227 227 0 strelka-varscan-mutect FUK,missense_variant,p.Ala46Val,ENST00000288078,NM_145059.2;FUK,missense_variant,p.Ala46Val,ENST00000378912,;FUK,missense_variant,p.Ala46Val,ENST00000574784,;FUK,missense_variant,p.Ala46Val,ENST00000573352,;FUK,missense_variant,p.Ala46Val,ENST00000576453,;FUK,missense_variant,p.Ala46Val,ENST00000572784,;FUK,intron_variant,,ENST00000571514,;FUK,non_coding_transcript_exon_variant,,ENST00000464499,;FUK,non_coding_transcript_exon_variant,,ENST00000571487,;FUK,non_coding_transcript_exon_variant,,ENST00000576107,; T ENST00000288078 Transcript missense_variant 369/4081 137/3255 46/1084 A/V gCc/gTc 1 1 FUK HGNC HGNC:29500 protein_coding YES CCDS10891.2 ENSP00000288078 Q8N0W3 UPI000013DEF1 NM_145059.2 tolerated(0.34) 3/24 hmmpanther:PTHR32463 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 70463677 70463677 C T 1 0 0 0 0 1 0 0 0 5967 739 26 3 3 FUK 16 70463677 Missense_Mutation SNP C C3N-01416_T 14974019 70463677 19874668 62 24351 OR3A3 0 . GRCh38 17 3420791 3420791 + Missense_Mutation SNP T T C novel C3N-01416_T C3N-01416_N T T c.224T>C p.Leu75Pro p.L75P ENST00000291231 1/1 30 26 4 55 55 0 varscan-mutect OR3A3,missense_variant,p.Leu75Pro,ENST00000291231,NM_012373.2; C ENST00000291231 Transcript missense_variant 224/966 224/966 75/321 L/P cTg/cCg 1 1 OR3A3 HGNC HGNC:8284 protein_coding YES CCDS11025.1 ENSP00000291231 P47888 UPI000013E033 NM_012373.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 3420791 3420791 T C 1 0 0 0 0 1 0 0 0 11116 1580 55 5 5 OR3A3 17 3420791 Missense_Mutation SNP T C3N-01416_T 3420791 79836650 63 24352 ATP2A3 0 . GRCh38 17 3925423 3925423 + Nonstop_Mutation SNP C C G novel C3N-01416_T C3N-01416_N C C c.3158G>C p.Ter1053SerextTer42 p.*1053Sext*42 ENST00000359983 23/23 223 211 12 285 285 0 strelka-varscan-mutect ATP2A3,stop_lost,p.Ter1000SerextTer42,ENST00000397041,NM_005173.3;ATP2A3,stop_lost,p.Ter1053SerextTer42,ENST00000359983,NM_174953.2,NM_174954.2;ATP2A3,stop_lost,p.Ter999SerextTer?,ENST00000397043,NM_174957.2;ATP2A3,synonymous_variant,p.=,ENST00000352011,NM_174955.2;ATP2A3,synonymous_variant,p.=,ENST00000572116,;ATP2A3,3_prime_UTR_variant,,ENST00000309890,NM_174956.2;ATP2A3,3_prime_UTR_variant,,ENST00000397035,NM_174958.2;ATP2A3,3_prime_UTR_variant,,ENST00000570845,;ATP2A3,non_coding_transcript_exon_variant,,ENST00000570773,;ATP2A3,non_coding_transcript_exon_variant,,ENST00000574999,;ATP2A3,downstream_gene_variant,,ENST00000576957,;ATP2A3,downstream_gene_variant,,ENST00000571245,; G ENST00000359983 Transcript stop_lost 3158/3290 3158/3159 1053/1052 */S tGa/tCa 1 -1 ATP2A3 HGNC HGNC:813 protein_coding YES CCDS11042.1 ENSP00000353072 Q93084 UPI0000161584 NM_174953.2,NM_174954.2 23/23 HIGH 1 SNV 5 1 PASS rs1246664144 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 79 3925423 3925423 C G 1 0 0 0 0 0 0 0 0 1291 837 29 4 4 ATP2A3 17 3925423 Nonstop_Mutation SNP C C3N-01416_T 504632 3925423 79332018 64 24353 GUCY2D 0 . GRCh38 17 8013918 8013918 + Silent SNP C C A rs61750168 C3N-01416_T C3N-01416_N C C c.2302C>A p.= p.R768R ENST00000254854 12/20 244 229 15 322 322 0 strelka-varscan-mutect GUCY2D,synonymous_variant,p.=,ENST00000254854,NM_000180.3;RP11-1099M24.9,non_coding_transcript_exon_variant,,ENST00000623126,;GUCY2D,upstream_gene_variant,,ENST00000574510,; A ENST00000254854 Transcript synonymous_variant 2452/3698 2302/3312 768/1103 R Cgg/Agg rs61750168,CM004764,RISN_GC1:c.2302C>T,KinMutBase_AJ222657:g.9875C>T 1 1 GUCY2D HGNC HGNC:4689 protein_coding YES CCDS11127.1 ENSP00000254854 Q02846 UPI0000128C1C NM_000180.3 12/20 PROSITE_profiles:PS50011,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF228,Pfam_domain:PF07714,Gene3D:1.10.510.10,Superfamily_domains:SSF56112 not_provided LOW 1 SNV 1 1,1,0,0 1 PASS rs61750168 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 8013918 8013918 C A 1 0 0 0 0 0 0 0 1 6779 875 31 1 1 GUCY2D 17 8013918 Silent SNP C C3N-01416_T 4088495 8013918 75243523 65 24354 FAM83G 0 . GRCh38 17 18971738 18971738 + Missense_Mutation SNP A A C novel C3N-01416_T C3N-01416_N A A c.2093T>G p.Phe698Cys p.F698C ENST00000388995 6/6 17 13 4 39 39 0 strelka-varscan-mutect FAM83G,missense_variant,p.Phe698Cys,ENST00000388995,NM_001039999.2;FAM83G,missense_variant,p.Phe698Cys,ENST00000345041,;SLC5A10,intron_variant,,ENST00000317977,NM_001282417.1;SLC5A10,intron_variant,,ENST00000395647,NM_152351.4;SLC5A10,intron_variant,,ENST00000395645,NM_001042450.2;SLC5A10,intron_variant,,ENST00000417251,NM_001270649.1;SLC5A10,intron_variant,,ENST00000395643,NM_001270648.1;FAM83G,downstream_gene_variant,,ENST00000399096,; C ENST00000388995 Transcript missense_variant 2317/5266 2093/2472 698/823 F/C tTt/tGt 1 -1 FAM83G HGNC HGNC:32554 protein_coding YES CCDS42276.1 ENSP00000373647 A6ND36 UPI0000E03260 NM_001039999.2 deleterious(0) 6/6 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF5 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -12.91692 1 1 1 1 0 C 3 2 79 18971738 18971738 A C 1 0 0 0 0 1 0 0 0 5497 14 1 5 5 FAM83G 17 18971738 Missense_Mutation SNP A C3N-01416_T 10957820 18971738 64285703 66 24355 AARSD1 0 . GRCh38 17 42956318 42956319 + Frame_Shift_Ins INS - - A novel C3N-01416_T C3N-01416_N - - c.1070dupT p.Ser358GlufsTer7 p.S358Efs*7 ENST00000421990 11/17 108 87 21 203 203 0 sindel-varindel-pindel PTGES3L-AARSD1,frameshift_variant,p.Ser358GlufsTer7,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,frameshift_variant,p.Ser358GlufsTer7,ENST00000409399,;PTGES3L-AARSD1,frameshift_variant,p.Ser297GlufsTer7,ENST00000360221,NM_025267.3;PTGES3L-AARSD1,frameshift_variant,p.Ser267GlufsTer7,ENST00000409103,;AARSD1,frameshift_variant,p.Ser184GlufsTer7,ENST00000427569,NM_001261434.1;AARSD1,frameshift_variant,p.Ser79GlufsTer7,ENST00000430739,;PTGES3L-AARSD1,downstream_gene_variant,,ENST00000452752,;AARSD1,downstream_gene_variant,,ENST00000416949,;AARSD1,splice_region_variant,,ENST00000441280,;AARSD1,splice_region_variant,,ENST00000450475,;AARSD1,splice_region_variant,,ENST00000491665,;AARSD1,splice_region_variant,,ENST00000591910,;AARSD1,splice_region_variant,,ENST00000486664,;PTGES3L-AARSD1,splice_region_variant,,ENST00000423601,;AARSD1,non_coding_transcript_exon_variant,,ENST00000483774,;AARSD1,non_coding_transcript_exon_variant,,ENST00000478040,;AARSD1,downstream_gene_variant,,ENST00000436545,;AARSD1,upstream_gene_variant,,ENST00000593123,;AARSD1,upstream_gene_variant,,ENST00000474578,;AARSD1,downstream_gene_variant,,ENST00000492036,;AARSD1,upstream_gene_variant,,ENST00000591096,;AARSD1,upstream_gene_variant,,ENST00000587023,;AARSD1,upstream_gene_variant,,ENST00000592136,;AARSD1,upstream_gene_variant,,ENST00000483535,;AARSD1,upstream_gene_variant,,ENST00000486493,; A ENST00000421990 Transcript frameshift_variant,splice_region_variant 1416-1417/2150 1070-1071/1761 357/586 V/VX gtg/gtTg 1 -1 PTGES3L-AARSD1 HGNC HGNC:43946 protein_coding YES CCDS45691.1 ENSP00000409924 Q9BTE6 UPI0000D4E5DF NM_001136042.2 11/17 PROSITE_profiles:PS50860,hmmpanther:PTHR11777,Superfamily_domains:SSF55186 HIGH 1 insertion 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 79 42956318 42956318 - A 1 0 1 1 0 0 0 0 0 25 840 29 0 0 AARSD1 17 42956318 Frame_Shift_Ins INS - C3N-01416_T 23984580 42956318 40301123 67 24356 SMAD4 0 . GRCh38 18 51065549 51065549 + Missense_Mutation SNP G G A rs377767347 C3N-01416_T C3N-01416_N G G c.1082G>A p.Arg361His p.R361H ENST00000342988 9/12 174 135 39 301 301 0 strelka-varscan-mutect SMAD4,missense_variant,p.Arg361His,ENST00000342988,NM_005359.5;SMAD4,missense_variant,p.Arg361His,ENST00000398417,;SMAD4,missense_variant,p.Arg265His,ENST00000588745,;SMAD4,upstream_gene_variant,,ENST00000593223,;SMAD4,missense_variant,p.Arg95His,ENST00000611848,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,intron_variant,,ENST00000592186,;SMAD4,upstream_gene_variant,,ENST00000590499,; A ENST00000342988 Transcript missense_variant 1620/8769 1082/1659 361/552 R/H cGc/cAc rs377767347,CM004254,CM100519,COSM14122,COSM4072505 1 1 SMAD4 HGNC HGNC:6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 A0A024R274 UPI0000053431 NM_005359.5 deleterious(0.03) 9/12 Gene3D:2.60.200.10,Pfam_domain:PF03166,PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF39,SMART_domains:SM00524,Superfamily_domains:SSF49879 pathogenic 0,0,0,1,1 2010169710797267 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs377767347 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 51065549 51065549 G A 1 0 0 0 0 1 0 0 0 15053 1087 38 1 1 SMAD4 18 51065549 Missense_Mutation SNP G C3N-01416_T 51065549 29307736 68 24357 MBD3 0 . GRCh38 19 1578414 1578414 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.802G>A p.Glu268Lys p.E268K ENST00000434436 6/7 282 264 18 315 315 0 strelka-varscan-mutect MBD3,missense_variant,p.Glu236Lys,ENST00000156825,NM_001281454.1;MBD3,missense_variant,p.Glu212Lys,ENST00000590550,;MBD3,missense_variant,p.Glu268Lys,ENST00000434436,NM_001281453.1;MBD3,downstream_gene_variant,,ENST00000592361,;MBD3,downstream_gene_variant,,ENST00000585967,;MBD3,non_coding_transcript_exon_variant,,ENST00000589064,;AC005943.6,downstream_gene_variant,,ENST00000624421,;MBD3,3_prime_UTR_variant,,ENST00000592012,;AC005943.2,3_prime_UTR_variant,,ENST00000585937,;MBD3,non_coding_transcript_exon_variant,,ENST00000590830,;MBD3,downstream_gene_variant,,ENST00000589901,;MBD3,downstream_gene_variant,,ENST00000585903,; T ENST00000434436 Transcript missense_variant 879/2439 802/876 268/291 E/K Gag/Aag 1 -1 MBD3 HGNC HGNC:6918 protein_coding YES CCDS12072.1 ENSP00000412302 O95983 UPI000003166B NM_001281453.1 deleterious_low_confidence(0.03) 6/7 hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF12,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 1578414 1578414 C T 1 0 0 0 0 1 0 0 0 9273 835 29 3 3 MBD3 19 1578414 Missense_Mutation SNP C C3N-01416_T 1578414 57039202 69 24358 ZNF91 0 . GRCh38 19 23361925 23361925 + Missense_Mutation SNP A A T rs753123290 C3N-01416_T C3N-01416_N A A c.1054T>A p.Cys352Ser p.C352S ENST00000300619 4/4 161 142 19 295 295 0 varscan-mutect ZNF91,missense_variant,p.Cys352Ser,ENST00000300619,NM_003430.3;ZNF91,missense_variant,p.Cys320Ser,ENST00000397082,NM_001300951.1;ZNF91,intron_variant,,ENST00000599743,;ZNF91,downstream_gene_variant,,ENST00000595533,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000596528,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000593341,; T ENST00000300619 Transcript missense_variant 1260/5489 1054/3576 352/1191 C/S Tgt/Agt rs753123290 1 -1 ZNF91 HGNC HGNC:13166 protein_coding YES CCDS42541.1 ENSP00000300619 Q05481 UPI00002038F9 NM_003430.3 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF195,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs753123290 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 23361925 23361925 A T 1 0 0 0 0 1 0 0 0 18793 217 8 4 4 ZNF91 19 23361925 Missense_Mutation SNP A C3N-01416_T 21783511 23361925 35255691 70 24359 RHPN2 0 . GRCh38 19 33011719 33011719 + Missense_Mutation SNP A A G novel C3N-01416_T C3N-01416_N A A c.553T>C p.Phe185Leu p.F185L ENST00000254260 6/15 477 384 93 594 594 0 strelka-varscan-mutect RHPN2,missense_variant,p.Phe185Leu,ENST00000254260,NM_033103.4;RHPN2,3_prime_UTR_variant,,ENST00000588388,;RHPN2,intron_variant,,ENST00000544458,; G ENST00000254260 Transcript missense_variant 589/3500 553/2061 185/686 F/L Ttc/Ctc 1 -1 RHPN2 HGNC HGNC:19974 protein_coding YES CCDS12427.1 ENSP00000254260 Q8IUC4 UPI00000747A3 NM_033103.4 deleterious(0.02) 6/15 PROSITE_profiles:PS51180,hmmpanther:PTHR23031,hmmpanther:PTHR23031:SF5,Pfam_domain:PF03097,Gene3D:2xs1A01,SMART_domains:SM01041 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 33011719 33011719 A G 1 0 0 0 0 1 0 0 0 13524 101 4 5 5 RHPN2 19 33011719 Missense_Mutation SNP A C3N-01416_T 9649794 33011719 25605897 71 24360 RYR1 0 . GRCh38 19 38486032 38486032 + Missense_Mutation SNP G G C novel C3N-01416_T C3N-01416_N G G c.5377G>C p.Glu1793Gln p.E1793Q ENST00000359596 34/106 162 152 10 192 192 0 strelka-varscan-mutect RYR1,missense_variant,p.Glu1793Gln,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Glu1793Gln,ENST00000359596,NM_000540.2; C ENST00000359596 Transcript missense_variant 5377/15117 5377/15117 1793/5038 E/Q Gag/Cag 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 tolerated(0.14) 34/106 Low_complexity_(Seg):seg,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 38486032 38486032 G C 1 0 0 0 0 1 0 0 0 14028 943 33 4 4 RYR1 19 38486032 Missense_Mutation SNP G C3N-01416_T 5474313 38486032 20131584 72 24361 SPTBN4 0 . GRCh38 19 40556162 40556162 + Silent SNP G G A novel C3N-01416_T C3N-01416_N G G c.5163G>A p.= p.V1721V ENST00000352632 25/36 118 93 25 132 132 0 strelka-mutect SPTBN4,synonymous_variant,p.=,ENST00000338932,;SPTBN4,synonymous_variant,p.=,ENST00000352632,;SPTBN4,synonymous_variant,p.=,ENST00000392025,;SPTBN4,synonymous_variant,p.=,ENST00000598249,NM_020971.2;SPTBN4,synonymous_variant,p.=,ENST00000595535,;SPTBN4,synonymous_variant,p.=,ENST00000392023,NM_025213.2;SPTBN4,3_prime_UTR_variant,,ENST00000597389,;SPTBN4,downstream_gene_variant,,ENST00000596900,; A ENST00000352632 Transcript synonymous_variant 5249/8676 5163/7695 1721/2564 V gtG/gtA 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB 25/36 Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 79 40556162 40556162 G A 1 0 0 0 0 0 0 0 1 15477 1335 47 3 3 SPTBN4 19 40556162 Silent SNP G C3N-01416_T 2070130 40556162 18061454 73 24362 CBFA2T2 0 . GRCh38 20 33623873 33623873 + Missense_Mutation SNP G G C novel C3N-01416_T C3N-01416_N G G c.733G>C p.Glu245Gln p.E245Q ENST00000344201 6/6 147 138 9 225 225 0 strelka-varscan-mutect CBFA2T2,missense_variant,p.Glu245Gln,ENST00000344201,;CBFA2T2,intron_variant,,ENST00000492345,;CBFA2T2,intron_variant,,ENST00000346541,NM_005093.3;CBFA2T2,intron_variant,,ENST00000375279,;CBFA2T2,intron_variant,,ENST00000397800,NM_001039709.1;CBFA2T2,intron_variant,,ENST00000359606,;CBFA2T2,intron_variant,,ENST00000342704,NM_001032999.2;CBFA2T2,intron_variant,,ENST00000491618,; C ENST00000344201 Transcript missense_variant 1100/1181 733/792 245/263 E/Q Gag/Cag 1 1 CBFA2T2 HGNC HGNC:1536 protein_coding ENSP00000341865 O43439 UPI000013E65D deleterious_low_confidence(0) 6/6 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 33623873 33623873 G C 1 0 0 0 0 1 0 0 0 2398 943 33 4 4 CBFA2T2 20 33623873 Missense_Mutation SNP G C3N-01416_T 33623873 30820294 74 24363 CBFA2T2 0 . GRCh38 20 33624783 33624783 + Missense_Mutation SNP G G C novel C3N-01416_T C3N-01416_N G G c.739G>C p.Asp247His p.D247H ENST00000346541 7/12 158 148 10 197 197 0 strelka-varscan-mutect CBFA2T2,missense_variant,p.Asp218His,ENST00000492345,;CBFA2T2,missense_variant,p.Asp247His,ENST00000346541,NM_005093.3;CBFA2T2,missense_variant,p.Asp247His,ENST00000375279,;CBFA2T2,missense_variant,p.Asp218His,ENST00000397800,NM_001039709.1;CBFA2T2,missense_variant,p.Asp257His,ENST00000359606,;CBFA2T2,missense_variant,p.Asp238His,ENST00000342704,NM_001032999.2;CBFA2T2,downstream_gene_variant,,ENST00000344201,;CBFA2T2,non_coding_transcript_exon_variant,,ENST00000491618,; C ENST00000346541 Transcript missense_variant 1276/7737 739/1815 247/604 D/H Gat/Cat 1 1 CBFA2T2 HGNC HGNC:1536 protein_coding YES CCDS13221.1 ENSP00000262653 O43439 UPI0000073E07 NM_005093.3 tolerated(0.09) 7/12 hmmpanther:PTHR10379:SF13,hmmpanther:PTHR10379 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 79 33624783 33624783 G C 1 0 0 0 0 1 0 0 0 2398 1290 45 4 4 CBFA2T2 20 33624783 Missense_Mutation SNP G C3N-01416_T 910 33624783 30819384 75 24364 83 2 CBFA2T2 0 . GRCh38 20 33624787 33624787 + Missense_Mutation SNP G G A novel C3N-01416_T C3N-01416_N G G c.743G>A p.Arg248Lys p.R248K ENST00000346541 7/12 170 160 10 214 213 1 strelka-varscan-mutect CBFA2T2,missense_variant,p.Arg219Lys,ENST00000492345,;CBFA2T2,missense_variant,p.Arg248Lys,ENST00000346541,NM_005093.3;CBFA2T2,missense_variant,p.Arg248Lys,ENST00000375279,;CBFA2T2,missense_variant,p.Arg219Lys,ENST00000397800,NM_001039709.1;CBFA2T2,missense_variant,p.Arg258Lys,ENST00000359606,;CBFA2T2,missense_variant,p.Arg239Lys,ENST00000342704,NM_001032999.2;CBFA2T2,downstream_gene_variant,,ENST00000344201,;CBFA2T2,non_coding_transcript_exon_variant,,ENST00000491618,; A ENST00000346541 Transcript missense_variant 1280/7737 743/1815 248/604 R/K aGa/aAa 1 1 CBFA2T2 HGNC HGNC:1536 protein_coding YES CCDS13221.1 ENSP00000262653 O43439 UPI0000073E07 NM_005093.3 tolerated(0.13) 7/12 hmmpanther:PTHR10379:SF13,hmmpanther:PTHR10379 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 79 33624787 33624787 G A 1 0 0 0 0 1 0 0 0 2398 942 33 3 3 CBFA2T2 20 33624787 Missense_Mutation SNP G C3N-01416_T 4 33624787 30819380 76 24365 83 2 CEP250 0 . GRCh38 20 35490728 35490728 + Missense_Mutation SNP A A T novel C3N-01416_T C3N-01416_N A A c.2678A>T p.Glu893Val p.E893V ENST00000397527 21/35 216 153 63 283 283 0 strelka-varscan-mutect CEP250,missense_variant,p.Glu893Val,ENST00000397527,NM_007186.4;RP3-477O4.14,intron_variant,,ENST00000453914,;RP3-477O4.14,intron_variant,,ENST00000416260,;RP3-477O4.14,intron_variant,,ENST00000444933,;CEP250,upstream_gene_variant,,ENST00000487467,; T ENST00000397527 Transcript missense_variant 3398/15703 2678/7329 893/2442 E/V gAg/gTg 1 1 CEP250 HGNC HGNC:1859 protein_coding YES CCDS13255.1 ENSP00000380661 Q9BV73 UPI000006FE8F NM_007186.4 deleterious(0) 21/35 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF1,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 35490728 35490728 A T 1 0 0 0 0 1 0 0 0 2968 304 11 4 4 CEP250 20 35490728 Missense_Mutation SNP A C3N-01416_T 1865941 35490728 28953439 77 24366 GID8 0 . GRCh38 20 62943606 62943606 + Missense_Mutation SNP A A G novel C3N-01416_T C3N-01416_N A A c.427A>G p.Met143Val p.M143V ENST00000266069 4/5 265 219 46 299 299 0 strelka-varscan-mutect GID8,missense_variant,p.Met143Val,ENST00000266069,NM_017896.2;GID8,downstream_gene_variant,,ENST00000497101,; G ENST00000266069 Transcript missense_variant 574/4397 427/687 143/228 M/V Atg/Gtg 1 1 GID8 HGNC HGNC:15857 protein_coding YES CCDS13510.1 ENSP00000266069 Q9NWU2 UPI0000034E17 NM_017896.2 deleterious(0.04) 4/5 Pfam_domain:PF10607,hmmpanther:PTHR12864,SMART_domains:SM00757 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 62943606 62943606 A G 1 0 0 0 0 1 0 0 0 6255 333 12 5 5 GID8 20 62943606 Missense_Mutation SNP A C3N-01416_T 27452878 62943606 1500561 78 24367 DSCAM 0 . GRCh38 21 40142687 40142687 + Missense_Mutation SNP C C T rs759720915 C3N-01416_T C3N-01416_N C C c.3277G>A p.Glu1093Lys p.E1093K ENST00000400454 18/33 100 83 17 137 137 0 strelka-varscan-mutect DSCAM,missense_variant,p.Glu1093Lys,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Glu928Lys,ENST00000617870,;DSCAM,missense_variant,p.Glu845Lys,ENST00000404019,; T ENST00000400454 Transcript missense_variant 3755/8552 3277/6039 1093/2012 E/K Gaa/Aaa rs759720915 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 deleterious(0.01) 18/33 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs759720915 . 0 196 6 6 2 0 0 0 -10.89667 0.8495977 1 1 1 0 T 3 4 79 40142687 40142687 C T 1 0 0 0 0 1 0 0 0 4589 893 31 1 1 DSCAM 21 40142687 Missense_Mutation SNP C C3N-01416_T 40142687 6567296 79 24368 XPNPEP3 0 . GRCh38 22 40924437 40924437 + Missense_Mutation SNP C C G rs374335250 C3N-01416_T C3N-01416_N C C c.1312C>G p.Arg438Gly p.R438G ENST00000357137 9/10 469 425 44 668 667 1 strelka-varscan-mutect XPNPEP3,missense_variant,p.Arg438Gly,ENST00000357137,NM_022098.3;XPNPEP3,3_prime_UTR_variant,,ENST00000428799,; G ENST00000357137 Transcript missense_variant 1396/7988 1312/1524 438/507 R/G Cgt/Ggt rs374335250 1 1 XPNPEP3 HGNC HGNC:28052 protein_coding YES CCDS14007.1 ENSP00000349658 Q9NQH7 UPI00000401E0 NM_022098.3 deleterious(0) 9/10 Gene3D:3.90.230.10,Pfam_domain:PF00557,hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF17,Superfamily_domains:SSF55920 MODERATE 1 SNV 1 1 PASS rs374335250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 79 40924437 40924437 C G 1 0 0 0 0 1 0 0 0 18003 652 23 4 4 XPNPEP3 22 40924437 Missense_Mutation SNP C C3N-01416_T 40924437 9894031 80 24369 MXRA5 0 . GRCh38 X 3310414 3310414 + Missense_Mutation SNP C C T novel C3N-01416_T C3N-01416_N C C c.7789G>A p.Ala2597Thr p.A2597T ENST00000217939 7/7 374 314 60 352 352 0 strelka-varscan-mutect MXRA5,missense_variant,p.Ala2597Thr,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 7944/9793 7789/8487 2597/2828 A/T Gct/Act 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.55) 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 79 3310414 3310414 C T 1 0 0 0 0 1 0 0 0 10002 739 26 3 3 MXRA5 23 3310414 Missense_Mutation SNP C C3N-01416_T 3310414 152730481 81 24370 KLHL34 0 . GRCh38 X 21656493 21656493 + Silent SNP G G A novel C3N-01416_T C3N-01416_N G G c.1296C>T p.= p.G432G ENST00000379499 1/1 215 189 26 259 259 0 strelka-varscan-mutect KLHL34,synonymous_variant,p.=,ENST00000379499,NM_153270.2;CNKSR2,downstream_gene_variant,,ENST00000425654,NM_001168647.1;CNKSR2,downstream_gene_variant,,ENST00000379510,NM_014927.3; A ENST00000379499 Transcript synonymous_variant 1838/3641 1296/1935 432/644 G ggC/ggT 1 -1 KLHL34 HGNC HGNC:26634 protein_coding YES CCDS14199.1 ENSP00000368813 Q8N239 UPI0000072CC4 NM_153270.2 1/1 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF199,Low_complexity_(Seg):seg,SMART_domains:SM00612 LOW SNV 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999902 1 1 1 0 A 2 1 79 21656493 21656493 G A 1 0 0 0 0 0 0 0 1 8253 1190 42 3 3 KLHL34 23 21656493 Silent SNP G C3N-01416_T 18346079 21656493 134384402 82 24371 84 2 KLHL34 0 . GRCh38 X 21656496 21656496 + Silent SNP C C G novel C3N-01416_T C3N-01416_N C C c.1293G>C p.= p.G431G ENST00000379499 1/1 214 186 28 258 258 0 strelka-varscan-mutect KLHL34,synonymous_variant,p.=,ENST00000379499,NM_153270.2;CNKSR2,downstream_gene_variant,,ENST00000425654,NM_001168647.1;CNKSR2,downstream_gene_variant,,ENST00000379510,NM_014927.3; G ENST00000379499 Transcript synonymous_variant 1835/3641 1293/1935 431/644 G ggG/ggC 1 -1 KLHL34 HGNC HGNC:26634 protein_coding YES CCDS14199.1 ENSP00000368813 Q8N239 UPI0000072CC4 NM_153270.2 1/1 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF199,Low_complexity_(Seg):seg,SMART_domains:SM00612 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 79 21656496 21656496 C G 1 0 0 0 0 0 0 0 1 8253 610 22 4 4 KLHL34 23 21656496 Silent SNP C C3N-01416_T 3 21656496 134384399 83 24372 84 2 RAB40AL 0 . GRCh38 X 102937895 102937895 + Nonsense_Mutation SNP C C T rs780011542 C3N-01416_T C3N-01416_N C C c.577C>T p.Gln193Ter p.Q193* ENST00000218249 1/1 255 217 38 372 372 0 strelka-varscan-mutect RAB40AL,stop_gained,p.Gln193Ter,ENST00000218249,NM_001031834.1;LL0XNC01-237H1.3,non_coding_transcript_exon_variant,,ENST00000413528,; T ENST00000218249 Transcript stop_gained 624/1029 577/837 193/278 Q/* Caa/Taa rs780011542 1 1 RAB40AL HGNC HGNC:25410 protein_coding YES CCDS35353.1 ENSP00000218249 P0C0E4 UPI000013C751 NM_001031834.1 1/1 PROSITE_profiles:PS50225,PROSITE_profiles:PS51419,Pfam_domain:PF07525,SMART_domains:SM00253,SMART_domains:SM00969,SMART_domains:SM00176,Superfamily_domains:SSF158235 HIGH SNV 1 PASS rs780011542 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 79 102937895 102937895 C T 1 0 0 0 0 0 1 0 0 13099 711 25 3 3 RAB40AL 23 102937895 Nonsense_Mutation SNP C C3N-01416_T 81281399 102937895 53103000 84 24373 NRK 0 . GRCh38 X 105912653 105912653 + Missense_Mutation SNP A A T rs764035983 C3N-01416_T C3N-01416_N A A c.2247A>T p.Lys749Asn p.K749N ENST00000243300 14/29 93 83 10 153 153 0 strelka-varscan-mutect NRK,missense_variant,p.Lys749Asn,ENST00000243300,NM_198465.3;NRK,3_prime_UTR_variant,,ENST00000428173,; T ENST00000243300 Transcript missense_variant 2550/8062 2247/4749 749/1582 K/N aaA/aaT rs764035983 1 1 NRK HGNC HGNC:25391 protein_coding YES CCDS65305.1 ENSP00000434830 Q7Z2Y5 UPI0000418886 NM_198465.3 tolerated(0.1) 14/29 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS rs764035983 . 0 206 3 0 0 0 0 0 -19.96201 1 1 1 1 0 T 3 4 79 105912653 105912653 A T 1 0 0 0 0 1 0 0 0 10713 86 3 4 4 NRK 23 105912653 Missense_Mutation SNP A C3N-01416_T 2974758 105912653 50128242 85 24374 AJAP1 0 . GRCh38 1 4712545 4712545 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.675G>T p.= p.T225T ENST00000378191 2/6 125 110 15 141 141 0 strelka-varscan-mutect AJAP1,synonymous_variant,p.=,ENST00000378191,NM_018836.3;AJAP1,synonymous_variant,p.=,ENST00000378190,NM_001042478.1;AJAP1,downstream_gene_variant,,ENST00000466761,; T ENST00000378191 Transcript synonymous_variant 1056/11666 675/1236 225/411 T acG/acT 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR32422,Pfam_domain:PF15298 LOW 1 SNV 1 1 PASS rs1459076033 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 4712545 4712545 G T 1 0 0 0 0 0 0 0 1 516 1103 39 1 1 AJAP1 1 4712545 Silent SNP G C3N-01488_T 4712545 244243877 1 24375 CHD5 0 . GRCh38 1 6106455 6106455 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.5797G>A p.Gly1933Ser p.G1933S ENST00000262450 40/42 321 254 67 404 403 1 strelka-varscan-mutect CHD5,missense_variant,p.Gly1933Ser,ENST00000262450,NM_015557.2;CHD5,intron_variant,,ENST00000475121,;CHD5,3_prime_UTR_variant,,ENST00000496404,;CHD5,intron_variant,,ENST00000462991,;CHD5,intron_variant,,ENST00000377999,; T ENST00000262450 Transcript missense_variant 5897/9646 5797/5865 1933/1954 G/S Ggc/Agc 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 tolerated_low_confidence(0.14) 40/42 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 6106455 6106455 C T 1 0 0 0 0 1 0 0 0 3087 623 22 3 3 CHD5 1 6106455 Missense_Mutation SNP C C3N-01488_T 1393910 6106455 242849967 2 24376 C1orf127 0 . GRCh38 1 10969972 10969972 + Frame_Shift_Del DEL G G - novel C3N-01488_T C3N-01488_N G G c.245delC p.Pro82GlnfsTer58 p.P82Qfs*58 ENST00000377004 3/13 77 62 15 118 118 0 sindel-varindel-pindel C1orf127,frameshift_variant,p.Pro82GlnfsTer58,ENST00000377004,NM_001170754.1;C1orf127,frameshift_variant,p.Pro60GlnfsTer58,ENST00000520253,; - ENST00000377004 Transcript frameshift_variant,splice_region_variant 245/2761 245/2472 82/823 P/X cCa/ca 1 -1 C1orf127 HGNC HGNC:26730 protein_coding YES CCDS53267.1 ENSP00000366203 G8JLG8 UPI0001C0B385 NM_001170754.1 3/13 hmmpanther:PTHR38653 HIGH 1 deletion 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 - 7 5 80 10969972 10969972 G - 1 0 1 0 1 0 0 0 0 1964 1362 47 0 0 C1orf127 1 10969972 Frame_Shift_Del DEL G C3N-01488_T 4863517 10969972 237986450 3 24377 CLCN6 0 . GRCh38 1 11819523 11819523 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.315C>A p.Phe105Leu p.F105L ENST00000346436 5/23 272 251 21 362 362 0 strelka-varscan-mutect CLCN6,missense_variant,p.Phe83Leu,ENST00000312413,NM_001256959.1;CLCN6,missense_variant,p.Phe105Leu,ENST00000346436,NM_001286.3;CLCN6,missense_variant,p.Phe105Leu,ENST00000376496,;CLCN6,missense_variant,p.Phe105Leu,ENST00000376497,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376492,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376490,;CLCN6,non_coding_transcript_exon_variant,,ENST00000376491,; A ENST00000346436 Transcript missense_variant 367/5583 315/2610 105/869 F/L ttC/ttA 1 1 CLCN6 HGNC HGNC:2024 protein_coding YES CCDS138.1 ENSP00000234488 P51797 UPI000013F2D3 NM_001286.3 tolerated(1) 5/23 Gene3D:1otsB00,Prints_domain:PR01117,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF59,Superfamily_domains:SSF81340 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 11819523 11819523 C A 1 0 0 0 0 1 0 0 0 3231 825 29 2 2 CLCN6 1 11819523 Missense_Mutation SNP C C3N-01488_T 849551 11819523 237136899 4 24378 PRAMEF15 0 . GRCh38 1 13318430 13318430 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.23C>A p.Pro8Gln p.P8Q ENST00000376152 2/4 631 576 55 905 905 0 varscan-mutect PRAMEF15,missense_variant,p.Pro8Gln,ENST00000376152,NM_001098376.2;PRAMEF15,missense_variant,p.Pro6Gln,ENST00000613530,; A ENST00000376152 Transcript missense_variant 117/1865 23/1437 8/478 P/Q cCa/cAa 1 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES CCDS44059.1 ENSP00000365322 Q5VWM5 UPI0000199BA7 NM_001098376.2 deleterious(0) 2/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 13318430 13318430 C A 1 0 0 0 0 1 0 0 0 12559 594 21 2 2 PRAMEF15 1 13318430 Missense_Mutation SNP C C3N-01488_T 1498907 13318430 235637992 5 24379 PRAMEF15 0 . GRCh38 1 13318481 13318481 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.74T>C p.Leu25Ser p.L25S ENST00000376152 2/4 897 845 52 1334 1334 0 varscan-mutect PRAMEF15,missense_variant,p.Leu25Ser,ENST00000376152,NM_001098376.2;PRAMEF15,missense_variant,p.Leu23Ser,ENST00000613530,; C ENST00000376152 Transcript missense_variant 168/1865 74/1437 25/478 L/S tTg/tCg 1 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES CCDS44059.1 ENSP00000365322 Q5VWM5 UPI0000199BA7 NM_001098376.2 tolerated(0.31) 2/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF19,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 13318481 13318481 T C 1 0 0 0 0 1 0 0 0 12559 1821 63 5 5 PRAMEF15 1 13318481 Missense_Mutation SNP T C3N-01488_T 51 13318481 235637941 6 24380 CLCNKB 0 . GRCh38 1 16056491 16056491 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1999T>A p.Cys667Ser p.C667S ENST00000375679 19/20 157 139 18 229 229 0 strelka-varscan-mutect CLCNKB,missense_variant,p.Cys667Ser,ENST00000375679,NM_000085.4;CLCNKB,missense_variant,p.Cys497Ser,ENST00000375667,NM_001165945.2;CLCNKB,intron_variant,,ENST00000619181,;CLCNKB,intron_variant,,ENST00000431772,;FAM131C,downstream_gene_variant,,ENST00000375662,NM_182623.2;FAM131C,downstream_gene_variant,,ENST00000494078,; A ENST00000375679 Transcript missense_variant 2110/2567 1999/2064 667/687 C/S Tgc/Agc 1 1 CLCNKB HGNC HGNC:2027 protein_coding YES CCDS168.1 ENSP00000364831 P51801 UPI000040E261 NM_000085.4 tolerated(0.56) 19/20 PROSITE_profiles:PS51371,hmmpanther:PTHR11689:SF95,hmmpanther:PTHR11689,Gene3D:3.10.580.10,SMART_domains:SM00116,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 16056491 16056491 T A 1 0 0 0 0 1 0 0 0 3234 1580 55 4 4 CLCNKB 1 16056491 Missense_Mutation SNP T C3N-01488_T 2738010 16056491 232899931 7 24381 AIM1L 0 . GRCh38 1 26346572 26346572 + Missense_Mutation SNP T T G novel C3N-01488_T C3N-01488_N T T c.86A>C p.Gln29Pro p.Q29P ENST00000308182 2/20 120 112 8 187 187 0 strelka-varscan-mutect AIM1L,missense_variant,p.Gln29Pro,ENST00000308182,NM_001039775.3;AIM1L,missense_variant,p.Gln29Pro,ENST00000475866,;AIM1L,upstream_gene_variant,,ENST00000527815,;AIM1L,intron_variant,,ENST00000374207,; G ENST00000308182 Transcript missense_variant 236/5245 86/4986 29/1661 Q/P cAg/cCg 1 -1 AIM1L HGNC HGNC:17295 protein_coding YES ENSP00000310435 Q8N1P7 UPI0001DD21C3 NM_001039775.3 tolerated_low_confidence(0.07) 2/20 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 26346572 26346572 T G 1 0 0 0 0 1 0 0 0 508 1580 55 5 5 AIM1L 1 26346572 Missense_Mutation SNP T C3N-01488_T 10290081 26346572 222609850 8 24382 LIN28A 0 . GRCh38 1 26411449 26411449 + Missense_Mutation SNP C C A rs372648933 C3N-01488_T C3N-01488_N C C c.95C>A p.Ala32Glu p.A32E ENST00000326279 2/4 179 142 37 211 211 0 strelka-varscan-mutect LIN28A,missense_variant,p.Ala32Glu,ENST00000326279,NM_024674.4;LIN28A,missense_variant,p.Ala32Glu,ENST00000254231,; A ENST00000326279 Transcript missense_variant 209/4008 95/630 32/209 A/E gCg/gAg rs372648933 1 1 LIN28A HGNC HGNC:15986 protein_coding YES CCDS280.1 ENSP00000363314 Q9H9Z2 UPI000006F0DA NM_024674.4 tolerated(1) 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR11544,hmmpanther:PTHR11544:SF31 MODERATE 1 SNV 1 1 PASS rs372648933 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 26411449 26411449 C A 1 0 0 0 0 1 0 0 0 8713 768 27 1 1 LIN28A 1 26411449 Missense_Mutation SNP C C3N-01488_T 64877 26411449 222544973 9 24383 ARID1A 0 . GRCh38 1 26779116 26779116 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.5218G>T p.Gly1740Ter p.G1740* ENST00000324856 20/20 24 20 4 51 51 0 strelka-varscan-mutect ARID1A,stop_gained,p.Gly1740Ter,ENST00000324856,NM_006015.4;ARID1A,stop_gained,p.Gly1358Ter,ENST00000636219,;ARID1A,stop_gained,p.Gly1356Ter,ENST00000430799,;ARID1A,stop_gained,p.Gly1357Ter,ENST00000374152,;ARID1A,stop_gained,p.Gly1523Ter,ENST00000457599,NM_139135.2;ARID1A,downstream_gene_variant,,ENST00000615191,;ARID1A,downstream_gene_variant,,ENST00000636794,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,;ARID1A,non_coding_transcript_exon_variant,,ENST00000637788,;ARID1A,downstream_gene_variant,,ENST00000636072,; T ENST00000324856 Transcript stop_gained 5589/8577 5218/6858 1740/2285 G/* Gga/Tga 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 20/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.127 1 1 1 1 0 T 4 4 80 26779116 26779116 G T 1 0 0 0 0 0 1 0 0 1049 1001 35 2 2 ARID1A 1 26779116 Nonsense_Mutation SNP G C3N-01488_T 367667 26779116 222177306 10 24384 DLGAP3 0 . GRCh38 1 34905098 34905098 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.286C>A p.Gln96Lys p.Q96K ENST00000373347 3/12 149 126 23 239 239 0 strelka-varscan-mutect DLGAP3,missense_variant,p.Gln96Lys,ENST00000373347,NM_001080418.2;DLGAP3,missense_variant,p.Gln96Lys,ENST00000235180,;DLGAP3,downstream_gene_variant,,ENST00000495979,; T ENST00000373347 Transcript missense_variant 555/3856 286/2940 96/979 Q/K Cag/Aag 1 -1 DLGAP3 HGNC HGNC:30368 protein_coding YES CCDS30670.1 ENSP00000362444 O95886 UPI00003D4D81 NM_001080418.2 tolerated(0.21) 3/12 hmmpanther:PTHR12353:SF4,hmmpanther:PTHR12353 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 34905098 34905098 G T 1 0 0 0 0 1 0 0 0 4368 1357 47 2 2 DLGAP3 1 34905098 Missense_Mutation SNP G C3N-01488_T 8125982 34905098 214051324 11 24385 SLFNL1 0 . GRCh38 1 41020431 41020431 + Missense_Mutation SNP G G T rs141843089 C3N-01488_T C3N-01488_N G G c.230C>A p.Pro77Gln p.P77Q ENST00000359345 1/4 260 227 33 372 372 0 strelka-varscan-mutect SLFNL1,missense_variant,p.Pro77Gln,ENST00000359345,NM_144990.3;SLFNL1,missense_variant,p.Pro77Gln,ENST00000372613,;SLFNL1,missense_variant,p.Pro77Gln,ENST00000439569,NM_001168247.2;SLFNL1,missense_variant,p.Pro77Gln,ENST00000302946,;SLFNL1,missense_variant,p.Pro77Gln,ENST00000372611,NM_001300859.1;SLFNL1-AS1,intron_variant,,ENST00000626479,; T ENST00000359345 Transcript missense_variant 2807/4310 230/1224 77/407 P/Q cCg/cAg rs141843089 1 -1 SLFNL1 HGNC HGNC:26313 protein_coding YES CCDS460.1 ENSP00000352299 Q499Z3 A0A140VJU6 UPI000013E83F NM_144990.3 deleterious(0.01) 1/4 hmmpanther:PTHR12155,hmmpanther:PTHR12155:SF29 MODERATE SNV 2 1 PASS rs141843089 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 41020431 41020431 G T 1 0 0 0 0 1 0 0 0 15028 1116 39 1 1 SLFNL1 1 41020431 Missense_Mutation SNP G C3N-01488_T 6115333 41020431 207935991 12 24386 STIL 0 . GRCh38 1 47251688 47251688 + Silent SNP T T A rs748226209 C3N-01488_T C3N-01488_N T T c.3315A>T p.= p.T1105T ENST00000371877 17/17 156 134 22 279 279 0 strelka-varscan-mutect STIL,synonymous_variant,p.=,ENST00000360380,NM_001282936.1,NM_003035.2;STIL,synonymous_variant,p.=,ENST00000337817,NM_001282939.1,NM_001282938.1;STIL,synonymous_variant,p.=,ENST00000371877,NM_001048166.1;STIL,synonymous_variant,p.=,ENST00000396221,NM_001282937.1; A ENST00000371877 Transcript synonymous_variant 3463/5009 3315/3867 1105/1288 T acA/acT rs748226209 1 -1 STIL HGNC HGNC:10879 protein_coding YES CCDS41329.1 ENSP00000360944 Q15468 UPI00002042D5 NM_001048166.1 17/17 hmmpanther:PTHR15128,hmmpanther:PTHR15128:SF0 LOW 1 SNV 1 1 PASS rs748226209 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 47251688 47251688 T A 1 0 0 0 0 0 0 0 1 15659 1567 55 4 4 STIL 1 47251688 Silent SNP T C3N-01488_T 6231257 47251688 201704734 13 24387 ROR1 0 . GRCh38 1 64178790 64178790 + Missense_Mutation SNP G G T rs776286055 C3N-01488_T C3N-01488_N G G c.2749G>T p.Ala917Ser p.A917S ENST00000371079 9/9 155 143 12 239 239 0 strelka-varscan-mutect ROR1,missense_variant,p.Ala917Ser,ENST00000371079,NM_005012.3;ROR1,missense_variant,p.Ala862Ser,ENST00000545203,; T ENST00000371079 Transcript missense_variant 3124/5832 2749/2814 917/937 A/S Gca/Tca rs776286055 1 1 ROR1 HGNC HGNC:10256 protein_coding YES CCDS626.1 ENSP00000360120 Q01973 UPI00001AF82C NM_005012.3 tolerated_low_confidence(0.74) 9/9 MODERATE 1 SNV 1 1 PASS rs776286055 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 64178790 64178790 G T 1 0 0 0 0 1 0 0 0 13703 971 34 2 2 ROR1 1 64178790 Missense_Mutation SNP G C3N-01488_T 16927102 64178790 184777632 14 24388 SGIP1 0 . GRCh38 1 66682023 66682023 + Silent SNP T T G novel C3N-01488_T C3N-01488_N T T c.969T>G p.= p.V323V ENST00000371037 15/25 212 195 17 318 317 1 strelka-varscan-mutect SGIP1,synonymous_variant,p.=,ENST00000371037,NM_032291.2;SGIP1,synonymous_variant,p.=,ENST00000237247,;SGIP1,intron_variant,,ENST00000371039,NM_001308203.1;SGIP1,downstream_gene_variant,,ENST00000424320,;RP4-598P13.1,upstream_gene_variant,,ENST00000502413,;SGIP1,intron_variant,,ENST00000480548,;SGIP1,downstream_gene_variant,,ENST00000468286,;SGIP1,upstream_gene_variant,,ENST00000487507,; G ENST00000371037 Transcript synonymous_variant 1046/7768 969/2487 323/828 V gtT/gtG 1 1 SGIP1 HGNC HGNC:25412 protein_coding YES CCDS30744.1 ENSP00000360076 Q9BQI5 UPI000045891B NM_032291.2 15/25 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 66682023 66682023 T G 1 0 0 0 0 0 0 0 1 14466 1741 61 5 5 SGIP1 1 66682023 Silent SNP T C3N-01488_T 2503233 66682023 182274399 15 24389 C1orf141 0 . GRCh38 1 67115465 67115465 + Splice_Site SNP C C A novel C3N-01488_T C3N-01488_N C C c.234-1G>T p.X78_splice ENST00000371007 103 82 21 164 164 0 strelka-varscan-mutect C1orf141,splice_acceptor_variant,,ENST00000371007,NM_001276351.1;C1orf141,splice_acceptor_variant,,ENST00000475209,NM_001276352.1;C1orf141,splice_acceptor_variant,,ENST00000371006,;C1orf141,splice_acceptor_variant,,ENST00000448166,;C1orf141,splice_acceptor_variant,,ENST00000603691,;C1orf141,intron_variant,,ENST00000621590,;C1orf141,splice_acceptor_variant,,ENST00000544837,;C1orf141,intron_variant,,ENST00000371004,; A ENST00000371007 Transcript splice_acceptor_variant -/2153 234/1203 78/400 1 -1 C1orf141 HGNC HGNC:32044 protein_coding YES CCDS30745.1 ENSP00000360046 Q5JVX7 UPI0000470AFA NM_001276351.1 4/7 HIGH 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 5 1 80 67115465 67115465 C A 1 0 0 0 0 0 0 1 0 1966 695 24 2 2 C1orf141 1 67115465 Splice_Site SNP C C3N-01488_T 433442 67115465 181840957 16 24390 TNNI3K 0 . GRCh38 1 74369052 74369052 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1694G>T p.Gly565Val p.G565V ENST00000557284 16/27 74 62 12 195 195 0 strelka-varscan-mutect FPGT-TNNI3K,missense_variant,p.Gly552Val,ENST00000370895,;TNNI3K,missense_variant,p.Gly451Val,ENST00000326637,NM_015978.2;FPGT-TNNI3K,missense_variant,p.Gly565Val,ENST00000557284,NM_001112808.2;FPGT-TNNI3K,missense_variant,p.Gly552Val,ENST00000370899,NM_001199327.1;TNNI3K,upstream_gene_variant,,ENST00000526236,;TNNI3K,upstream_gene_variant,,ENST00000534020,;FPGT-TNNI3K,downstream_gene_variant,,ENST00000534632,;TNNI3K,upstream_gene_variant,,ENST00000525480,;RP11-439H8.4,non_coding_transcript_exon_variant,,ENST00000415549,;TNNI3K,non_coding_transcript_exon_variant,,ENST00000497284,; T ENST00000557284 Transcript missense_variant 1699/2855 1694/2850 565/949 G/V gGa/gTa 1 1 FPGT-TNNI3K HGNC HGNC:42952 protein_coding YES CCDS44161.2 ENSP00000450895 V9GXZ4 UPI0001EECC26 NM_001112808.2 deleterious(0.03) 16/27 hmmpanther:PTHR23257:SF477,hmmpanther:PTHR23257 MODERATE SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 74369052 74369052 G T 1 0 0 0 0 1 0 0 0 16802 1174 41 2 2 TNNI3K 1 74369052 Missense_Mutation SNP G C3N-01488_T 7253587 74369052 174587370 17 24391 ABCA4 0 . GRCh38 1 94031993 94031993 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.3913G>T p.Gly1305Cys p.G1305C ENST00000370225 27/50 230 212 18 291 289 2 strelka-varscan-mutect ABCA4,missense_variant,p.Gly1305Cys,ENST00000370225,NM_000350.2;ABCA4,missense_variant,p.Gly97Cys,ENST00000536513,; A ENST00000370225 Transcript missense_variant 4000/7309 3913/6822 1305/2273 G/C Ggt/Tgt COSM361384 1 -1 ABCA4 HGNC HGNC:34 protein_coding YES CCDS747.1 ENSP00000359245 P78363 UPI000012511C NM_000350.2 deleterious(0.03) 27/50 TIGRFAM_domain:TIGR01257 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 94031993 94031993 C A 1 0 0 0 0 1 0 0 0 38 623 22 2 2 ABCA4 1 94031993 Missense_Mutation SNP C C3N-01488_T 19662941 94031993 154924429 18 24392 PLPPR4 0 . GRCh38 1 99288103 99288103 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.361C>A p.Pro121Thr p.P121T ENST00000370185 2/7 183 160 23 260 260 0 strelka-varscan-mutect PLPPR4,missense_variant,p.Pro121Thr,ENST00000370185,NM_014839.4;PLPPR4,missense_variant,p.Pro121Thr,ENST00000457765,NM_001166252.1; A ENST00000370185 Transcript missense_variant 858/5369 361/2292 121/763 P/T Cca/Aca 1 1 PLPPR4 HGNC HGNC:23496 protein_coding YES CCDS757.1 ENSP00000359204 Q7Z2D5 UPI0000161229 NM_014839.4 deleterious(0.01) 2/7 hmmpanther:PTHR10165:SF13,hmmpanther:PTHR10165 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 99288103 99288103 C A 1 0 0 0 0 1 0 0 0 12212 855 30 2 2 PLPPR4 1 99288103 Missense_Mutation SNP C C3N-01488_T 5256110 99288103 149668319 19 24393 NTNG1 0 . GRCh38 1 107436746 107436746 + Missense_Mutation SNP G G T rs778962536 C3N-01488_T C3N-01488_N G G c.1337G>T p.Gly446Val p.G446V ENST00000370068 7/8 160 136 24 263 262 1 strelka-varscan-mutect NTNG1,missense_variant,p.Gly446Val,ENST00000370068,;NTNG1,missense_variant,p.Gly446Val,ENST00000370073,NM_001113226.1;NTNG1,intron_variant,,ENST00000370067,;NTNG1,intron_variant,,ENST00000370071,NM_001113228.1;NTNG1,intron_variant,,ENST00000370074,NM_014917.2;NTNG1,intron_variant,,ENST00000370065,;NTNG1,intron_variant,,ENST00000370066,; T ENST00000370068 Transcript missense_variant 2183/4034 1337/1620 446/539 G/V gGg/gTg rs778962536,COSM5326094,COSM5326095 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0.01) 7/8 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs778962536 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 107436746 107436746 G T 1 0 0 0 0 1 0 0 0 10769 1232 43 2 2 NTNG1 1 107436746 Missense_Mutation SNP G C3N-01488_T 8148643 107436746 141519676 20 24394 FNDC7 0 . GRCh38 1 108717910 108717910 + Silent SNP G G T rs754855969 C3N-01488_T C3N-01488_N G G c.216G>T p.= p.T72T ENST00000370017 3/13 411 354 57 541 541 0 strelka-varscan-mutect FNDC7,synonymous_variant,p.=,ENST00000370017,NM_001144937.1;FNDC7,upstream_gene_variant,,ENST00000445274,; T ENST00000370017 Transcript synonymous_variant 493/3332 216/2202 72/733 T acG/acT rs754855969 1 1 FNDC7 HGNC HGNC:26668 protein_coding YES CCDS44185.1 ENSP00000359034 Q5VTL7 UPI000187497A NM_001144937.1 3/13 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF204,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs754855969 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 108717910 108717910 G T 1 0 0 0 0 0 0 0 1 5830 1103 39 1 1 FNDC7 1 108717910 Silent SNP G C3N-01488_T 1281164 108717910 140238512 21 24395 FNDC7 0 . GRCh38 1 108725929 108725929 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1036A>T p.Thr346Ser p.T346S ENST00000370017 6/13 298 260 38 460 460 0 strelka-varscan-mutect FNDC7,missense_variant,p.Thr346Ser,ENST00000370017,NM_001144937.1;FNDC7,missense_variant,p.Thr122Ser,ENST00000445274,; T ENST00000370017 Transcript missense_variant 1313/3332 1036/2202 346/733 T/S Act/Tct 1 1 FNDC7 HGNC HGNC:26668 protein_coding YES CCDS44185.1 ENSP00000359034 Q5VTL7 UPI000187497A NM_001144937.1 tolerated(0.06) 6/13 PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF204,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 108725929 108725929 A T 1 0 0 0 0 1 0 0 0 5830 159 6 4 4 FNDC7 1 108725929 Missense_Mutation SNP A C3N-01488_T 8019 108725929 140230493 22 24396 MAGI3 0 . GRCh38 1 113585428 113585428 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.595C>A p.Pro199Thr p.P199T ENST00000307546 4/21 269 242 27 482 479 3 strelka-varscan-mutect MAGI3,missense_variant,p.Pro199Thr,ENST00000369615,NM_152900.2;MAGI3,missense_variant,p.Pro199Thr,ENST00000307546,NM_001142782.1;MAGI3,missense_variant,p.Pro199Thr,ENST00000369617,;MAGI3,missense_variant,p.Pro199Thr,ENST00000369611,;MAGI3,downstream_gene_variant,,ENST00000486456,; A ENST00000307546 Transcript missense_variant 670/6430 595/4446 199/1481 P/T Cct/Act 1 1 MAGI3 HGNC HGNC:29647 protein_coding YES CCDS44196.1 ENSP00000304604 Q5TCQ9 UPI00004589AE NM_001142782.1 deleterious(0.05) 4/21 hmmpanther:PTHR10316:SF10,hmmpanther:PTHR10316,SMART_domains:SM00072 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 113585428 113585428 C A 1 0 0 0 0 1 0 0 0 9110 623 22 2 2 MAGI3 1 113585428 Missense_Mutation SNP C C3N-01488_T 4859499 113585428 135370994 23 24397 CASQ2 0 . GRCh38 1 115744862 115744862 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.285T>A p.Asp95Glu p.D95E ENST00000261448 2/11 432 396 36 632 632 0 strelka-varscan-mutect CASQ2,missense_variant,p.Asp95Glu,ENST00000261448,NM_001232.3; T ENST00000261448 Transcript missense_variant 525/2674 285/1200 95/399 D/E gaT/gaA 1 -1 CASQ2 HGNC HGNC:1513 protein_coding YES CCDS884.1 ENSP00000261448 O14958 UPI0000126F16 NM_001232.3 deleterious(0) 2/11 Gene3D:3.40.30.10,Pfam_domain:PF01216,Prints_domain:PR00312,hmmpanther:PTHR10033,hmmpanther:PTHR10033:SF15,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 115744862 115744862 A T 1 0 0 0 0 1 0 0 0 2380 214 8 4 4 CASQ2 1 115744862 Missense_Mutation SNP A C3N-01488_T 2159434 115744862 133211560 24 24398 SPAG17 0 . GRCh38 1 117996628 117996628 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.4892A>T p.His1631Leu p.H1631L ENST00000336338 33/49 126 100 26 210 210 0 strelka-varscan-mutect SPAG17,missense_variant,p.His1631Leu,ENST00000336338,NM_206996.2;SPAG17,missense_variant,p.His111Leu,ENST00000437255,; A ENST00000336338 Transcript missense_variant 4958/6924 4892/6672 1631/2223 H/L cAt/cTt 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 tolerated(0.42) 33/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 117996628 117996628 T A 1 0 0 0 0 1 0 0 0 15310 1464 51 4 4 SPAG17 1 117996628 Missense_Mutation SNP T C3N-01488_T 2251766 117996628 130959794 25 24399 HSD3B2 0 . GRCh38 1 119422043 119422043 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.542C>G p.Thr181Ser p.T181S ENST00000543831 4/4 437 366 71 727 727 0 strelka-varscan-mutect HSD3B2,missense_variant,p.Thr181Ser,ENST00000543831,NM_001166120.1;HSD3B2,missense_variant,p.Thr181Ser,ENST00000369416,NM_000198.3;HSD3B2,missense_variant,p.Thr181Ser,ENST00000433745,;HSD3B2,downstream_gene_variant,,ENST00000471656,;HSD3B2,downstream_gene_variant,,ENST00000443865,;HSD3B2,downstream_gene_variant,,ENST00000448448,; G ENST00000543831 Transcript missense_variant 791/1783 542/1119 181/372 T/S aCt/aGt 1 1 HSD3B2 HGNC HGNC:5218 protein_coding YES CCDS902.1 ENSP00000445122 P26439 A0A024R0F9 UPI0000001C6C NM_001166120.1 deleterious(0.01) 4/4 Gene3D:3.40.50.720,Pfam_domain:PF01073,hmmpanther:PTHR10366,hmmpanther:PTHR10366:SF444,Superfamily_domains:SSF51735 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 119422043 119422043 C G 1 0 0 0 0 1 0 0 0 7285 565 20 4 4 HSD3B2 1 119422043 Missense_Mutation SNP C C3N-01488_T 1425415 119422043 129534379 26 24400 LCE2D 0 . GRCh38 1 152664355 152664355 + Missense_Mutation SNP C C G C3N-01488_T C3N-01488_N C C c.250C>G p.Arg84Gly p.R84G ENST00000368784 2/2 223 137 86 297 297 0 strelka-varscan-mutect LCE2D,missense_variant,p.Arg84Gly,ENST00000368784,NM_178430.3; G ENST00000368784 Transcript missense_variant 305/609 250/333 84/110 R/G Cgc/Ggc COSM5185099 1 1 LCE2D HGNC HGNC:16518 protein_coding YES CCDS1018.1 ENSP00000357773 Q5TA82 UPI00001927D4 NM_178430.3 tolerated_low_confidence(0.33) 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,hmmpanther:PTHR23263:SF51,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 152664355 152664355 C G 1 0 0 0 0 1 0 0 0 8573 768 27 4 4 LCE2D 1 152664355 Missense_Mutation SNP C C3N-01488_T 33242312 152664355 96292067 27 24401 SNAPIN 0 . GRCh38 1 153659165 153659165 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.171A>T p.Gln57His p.Q57H ENST00000368685 2/4 231 148 83 251 251 0 strelka-varscan-mutect SNAPIN,missense_variant,p.Gln57His,ENST00000368685,NM_012437.5;ILF2,downstream_gene_variant,,ENST00000615950,NM_001267809.1;ILF2,downstream_gene_variant,,ENST00000361891,NM_004515.3;SNAPIN,non_coding_transcript_exon_variant,,ENST00000478558,;SNAPIN,non_coding_transcript_exon_variant,,ENST00000474959,;SNAPIN,intron_variant,,ENST00000462880,;ILF2,downstream_gene_variant,,ENST00000480213,; T ENST00000368685 Transcript missense_variant 261/1030 171/411 57/136 Q/H caA/caT 1 1 SNAPIN HGNC HGNC:17145 protein_coding YES CCDS1049.1 ENSP00000357674 O95295 UPI000003E7DC NM_012437.5 tolerated(0.44) 2/4 hmmpanther:PTHR31305,PIRSF_domain:PIRSF037631,Pfam_domain:PF14712 MODERATE 1 SNV 1 1 PASS rs934510807 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 153659165 153659165 A T 1 0 0 0 0 1 0 0 0 15160 11 1 4 4 SNAPIN 1 153659165 Missense_Mutation SNP A C3N-01488_T 994810 153659165 95297257 28 24402 CLK2 0 . GRCh38 1 155269634 155269634 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.253G>T p.Asp85Tyr p.D85Y ENST00000368361 3/13 693 642 51 630 629 1 strelka-varscan-mutect CLK2,missense_variant,p.Asp85Tyr,ENST00000368361,NM_001294338.1,NM_001294339.1;CLK2,missense_variant,p.Asp84Tyr,ENST00000355560,;CLK2,missense_variant,p.Asp85Tyr,ENST00000361168,NM_003993.3;CLK2,non_coding_transcript_exon_variant,,ENST00000476983,;CLK2,non_coding_transcript_exon_variant,,ENST00000471047,;CLK2,non_coding_transcript_exon_variant,,ENST00000484699,;CLK2,upstream_gene_variant,,ENST00000497188,; A ENST00000368361 Transcript missense_variant 569/2166 253/1500 85/499 D/Y Gat/Tat 1 -1 CLK2 HGNC HGNC:2069 protein_coding YES CCDS72939.1 ENSP00000357345 P49760 A8K7I0 UPI0000127AD2 NM_001294338.1,NM_001294339.1 deleterious(0.02) 3/13 hmmpanther:PTHR24058,hmmpanther:PTHR24058:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 155269634 155269634 C A 1 0 0 0 0 1 0 0 0 3306 855 30 2 2 CLK2 1 155269634 Missense_Mutation SNP C C3N-01488_T 1610469 155269634 93686788 29 24403 SEMA4A 0 . GRCh38 1 156154718 156154718 + Splice_Site SNP G G T rs770789701 C3N-01488_T C3N-01488_N G G c.139+1G>T p.X47_splice ENST00000368285 288 266 22 299 299 0 varscan-mutect SEMA4A,splice_donor_variant,,ENST00000368285,NM_001193300.1,NM_022367.3;SEMA4A,splice_donor_variant,,ENST00000368282,;SEMA4A,splice_donor_variant,,ENST00000355014,NM_001193301.1;SEMA4A,splice_donor_variant,,ENST00000368286,;SEMA4A,splice_donor_variant,,ENST00000435124,;SEMA4A,splice_donor_variant,,ENST00000438830,;SEMA4A,splice_donor_variant,,ENST00000633494,;SEMA4A,intron_variant,,ENST00000368284,NM_001193302.1;SEMA4A,intron_variant,,ENST00000414683,;SEMA4A,non_coding_transcript_exon_variant,,ENST00000485575,;SEMA4A,upstream_gene_variant,,ENST00000487358,;SEMA4A,upstream_gene_variant,,ENST00000470306,; T ENST00000368285 Transcript splice_donor_variant -/3300 139/2286 47/761 rs770789701 1 1 SEMA4A HGNC HGNC:10729 protein_coding YES CCDS1132.1 ENSP00000357268 Q9H3S1 UPI000007217A NM_001193300.1,NM_022367.3 2/14 HIGH 1 SNV 1 1 PASS rs770789701 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 80 156154718 156154718 G T 1 0 0 0 0 0 0 1 0 14307 1275 44 2 2 SEMA4A 1 156154718 Splice_Site SNP G C3N-01488_T 885084 156154718 92801704 30 24404 CD1A 0 . GRCh38 1 158257439 158257439 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.902G>T p.Gly301Val p.G301V ENST00000289429 5/6 358 278 80 361 360 1 strelka-varscan-mutect CD1A,missense_variant,p.Gly301Val,ENST00000289429,NM_001763.2; T ENST00000289429 Transcript missense_variant 1435/2096 902/984 301/327 G/V gGc/gTc 1 1 CD1A HGNC HGNC:1634 protein_coding YES CCDS1174.1 ENSP00000289429 P06126 UPI0000161A54 NM_001763.2 tolerated(0.07) 5/6 Gene3D:2.60.40.10,hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF160,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 158257439 158257439 G T 1 0 0 0 0 1 0 0 0 2677 1203 42 2 2 CD1A 1 158257439 Missense_Mutation SNP G C3N-01488_T 2102721 158257439 90698983 31 24405 SPTA1 0 . GRCh38 1 158649937 158649937 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.3488C>A p.Ser1163Tyr p.S1163Y ENST00000368147 25/52 355 329 26 373 372 1 strelka-varscan-mutect SPTA1,missense_variant,p.Ser1163Tyr,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 3669/7999 3488/7260 1163/2419 S/Y tCc/tAc 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.02) 25/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 158649937 158649937 G T 1 0 0 0 0 1 0 0 0 15472 1174 41 2 2 SPTA1 1 158649937 Missense_Mutation SNP G C3N-01488_T 392498 158649937 90306485 32 24406 SPTA1 0 . GRCh38 1 158678462 158678462 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.751G>A p.Gly251Ser p.G251S ENST00000368147 6/52 580 546 34 565 565 0 strelka-varscan-mutect SPTA1,missense_variant,p.Gly251Ser,ENST00000368147,NM_003126.2;SPTA1,missense_variant,p.Gly69Ser,ENST00000467387,; T ENST00000368147 Transcript missense_variant 932/7999 751/7260 251/2419 G/S Ggt/Agt 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.9) 6/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 158678462 158678462 C T 1 0 0 0 0 1 0 0 0 15472 594 21 3 3 SPTA1 1 158678462 Missense_Mutation SNP C C3N-01488_T 28525 158678462 90277960 33 24407 OR6K6 0 . GRCh38 1 158755364 158755364 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.549T>A p.= p.L183L ENST00000368144 1/1 229 206 23 300 300 0 strelka-varscan-mutect OR6K6,synonymous_variant,p.=,ENST00000368144,NM_001005184.1; A ENST00000368144 Transcript synonymous_variant 645/1172 549/1032 183/343 L ctT/ctA 1 1 OR6K6 HGNC HGNC:15033 protein_coding YES CCDS30904.1 ENSP00000357126 Q8NGW6 UPI000015F229 NM_001005184.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1229290149 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 80 158755364 158755364 T A 1 0 0 0 0 0 0 0 1 11273 1799 63 4 4 OR6K6 1 158755364 Silent SNP T C3N-01488_T 76902 158755364 90201058 34 24408 CADM3 0 . GRCh38 1 159192032 159192032 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.287G>T p.Trp96Leu p.W96L ENST00000368124 3/10 379 229 150 344 342 2 strelka-varscan-mutect CADM3,missense_variant,p.Trp62Leu,ENST00000368125,NM_001127173.1;CADM3,missense_variant,p.Trp96Leu,ENST00000368124,NM_021189.3;CADM3,missense_variant,p.Trp62Leu,ENST00000416746,;CADM3-AS1,downstream_gene_variant,,ENST00000415675,; T ENST00000368124 Transcript missense_variant 444/2546 287/1299 96/432 W/L tGg/tTg COSM1499015 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 tolerated(0.72) 3/10 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 159192032 159192032 G T 1 0 0 0 0 1 0 0 0 2258 1357 47 2 2 CADM3 1 159192032 Missense_Mutation SNP G C3N-01488_T 436668 159192032 89764390 35 24409 IGSF8 0 . GRCh38 1 160095083 160095083 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.228G>T p.= p.L76L ENST00000368086 2/7 366 305 61 292 292 0 strelka-varscan-mutect IGSF8,synonymous_variant,p.=,ENST00000368086,NM_001320247.1;IGSF8,synonymous_variant,p.=,ENST00000314485,NM_052868.4;IGSF8,synonymous_variant,p.=,ENST00000614243,NM_001206665.2;IGSF8,synonymous_variant,p.=,ENST00000448417,;KCNJ9,downstream_gene_variant,,ENST00000368088,NM_004983.2;IGSF8,non_coding_transcript_exon_variant,,ENST00000460351,; A ENST00000368086 Transcript synonymous_variant 445/2366 228/1842 76/613 L ctG/ctT 1 -1 IGSF8 HGNC HGNC:17813 protein_coding YES CCDS1195.1 ENSP00000357065 Q969P0 UPI0000073CBA NM_001320247.1 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12207:SF22,hmmpanther:PTHR12207,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 160095083 160095083 C A 1 0 0 0 0 0 0 0 1 7512 581 21 2 2 IGSF8 1 160095083 Silent SNP C C3N-01488_T 903051 160095083 88861339 36 24410 SLAMF6 0 . GRCh38 1 160486752 160486752 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.954T>A p.Ser318Arg p.S318R ENST00000368057 8/8 306 211 95 399 399 0 strelka-varscan-mutect SLAMF6,missense_variant,p.Ser317Arg,ENST00000368059,NM_052931.4,NM_001184715.1;SLAMF6,missense_variant,p.Ser318Arg,ENST00000368057,NM_001184714.1;SLAMF6,missense_variant,p.Ser207Arg,ENST00000368055,NM_001184716.1; T ENST00000368057 Transcript missense_variant,splice_region_variant 1015/2712 954/999 318/332 S/R agT/agA 1 -1 SLAMF6 HGNC HGNC:21392 protein_coding YES CCDS53394.1 ENSP00000357036 Q96DU3 UPI0000051E34 NM_001184714.1 tolerated(0.35) 8/8 hmmpanther:PTHR12080:SF16,hmmpanther:PTHR12080 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 160486752 160486752 A T 1 0 0 0 0 1 0 0 0 14633 405 14 4 4 SLAMF6 1 160486752 Missense_Mutation SNP A C3N-01488_T 391669 160486752 88469670 37 24411 PBX1 0 . GRCh38 1 164821586 164821586 + Missense_Mutation SNP G G T rs201029742 C3N-01488_T C3N-01488_N G G c.1160G>T p.Gly387Val p.G387V ENST00000420696 8/9 383 236 147 396 396 0 strelka-varscan-mutect PBX1,missense_variant,p.Gly387Val,ENST00000420696,NM_002585.3;PBX1,missense_variant,p.Gly299Val,ENST00000540236,;PBX1,missense_variant,p.Gly282Val,ENST00000560641,;PBX1,missense_variant,p.Gly296Val,ENST00000559240,;PBX1,missense_variant,p.Gly387Val,ENST00000627490,NM_001204963.1;PBX1,3_prime_UTR_variant,,ENST00000612123,;PBX1,3_prime_UTR_variant,,ENST00000367897,NM_001204961.1;PBX1,non_coding_transcript_exon_variant,,ENST00000468104,;PBX1,non_coding_transcript_exon_variant,,ENST00000560469,;PBX1,non_coding_transcript_exon_variant,,ENST00000496120,;PBX1,intron_variant,,ENST00000558796,;PBX1,non_coding_transcript_exon_variant,,ENST00000465089,; T ENST00000420696 Transcript missense_variant 1348/6636 1160/1293 387/430 G/V gGa/gTa rs201029742,COSM1335884,COSM4711409,COSM4711410,COSM5140886 1 1 PBX1 HGNC HGNC:8632 protein_coding YES CCDS1246.1 ENSP00000405890 P40424 A0A024R919 UPI00000213E1 NM_002585.3 deleterious(0.03) 8/9 hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF89 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs201029742 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 164821586 164821586 G T 1 0 0 0 0 1 0 0 0 11579 1174 41 2 2 PBX1 1 164821586 Missense_Mutation SNP G C3N-01488_T 4334834 164821586 84134836 38 24412 ILDR2 0 . GRCh38 1 166936636 166936636 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.658G>T p.Val220Phe p.V220F ENST00000271417 5/10 389 369 20 382 382 0 strelka-varscan ILDR2,missense_variant,p.Val220Phe,ENST00000271417,NM_199351.2;ILDR2,missense_variant,p.Val201Phe,ENST00000529071,;ILDR2,missense_variant,p.Val220Phe,ENST00000528703,;ILDR2,missense_variant,p.Val220Phe,ENST00000469934,;ILDR2,intron_variant,,ENST00000526687,;ILDR2,intron_variant,,ENST00000525740,;ILDR2,intron_variant,,ENST00000529387,; A ENST00000271417 Transcript missense_variant 714/13140 658/1920 220/639 V/F Gtc/Ttc 1 -1 ILDR2 HGNC HGNC:18131 protein_coding YES CCDS1256.1 ENSP00000271417 Q71H61 UPI00002317DF NM_199351.2 deleterious(0) 5/10 Pfam_domain:PF05624,hmmpanther:PTHR15923,hmmpanther:PTHR15923:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 166936636 166936636 C A 1 0 0 0 0 1 0 0 0 7613 478 17 2 2 ILDR2 1 166936636 Missense_Mutation SNP C C3N-01488_T 2115050 166936636 82019786 39 24413 TIPRL 0 . GRCh38 1 168198947 168198947 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.641A>G p.Tyr214Cys p.Y214C ENST00000367833 6/7 197 172 25 203 203 0 strelka-varscan TIPRL,missense_variant,p.Tyr214Cys,ENST00000367833,NM_152902.4; G ENST00000367833 Transcript missense_variant 786/3032 641/819 214/272 Y/C tAt/tGt 1 1 TIPRL HGNC HGNC:30231 protein_coding YES CCDS1270.1 ENSP00000356807 O75663 UPI0000071605 NM_152902.4 deleterious(0) 6/7 hmmpanther:PTHR21021:SF16,hmmpanther:PTHR21021,Pfam_domain:PF04176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 168198947 168198947 A G 1 0 0 0 0 1 0 0 0 16367 449 16 5 5 TIPRL 1 168198947 Missense_Mutation SNP A C3N-01488_T 1262311 168198947 80757475 40 24414 F5 0 . GRCh38 1 169549973 169549973 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.1439C>A p.Thr480Asn p.T480N ENST00000367797 10/25 484 268 216 527 527 0 strelka-varscan F5,missense_variant,p.Thr480Asn,ENST00000367796,;F5,missense_variant,p.Thr480Asn,ENST00000367797,NM_000130.4; T ENST00000367797 Transcript missense_variant 1641/7024 1439/6675 480/2224 T/N aCc/aAc COSM4763492 1 -1 F5 HGNC HGNC:3542 protein_coding YES CCDS1281.1 ENSP00000356771 P12259 UPI000016A8CE NM_000130.4 deleterious(0.01) 10/25 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF597,PIRSF_domain:PIRSF000354,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 169549973 169549973 G T 1 0 0 0 0 1 0 0 0 5216 1261 44 2 2 F5 1 169549973 Missense_Mutation SNP G C3N-01488_T 1351026 169549973 79406449 41 24415 PRRC2C 0 . GRCh38 1 171532613 171532613 + Missense_Mutation SNP A A T rs139508183 C3N-01488_T C3N-01488_N A A c.1519A>T p.Arg507Trp p.R507W ENST00000338920 12/34 333 306 27 412 412 0 strelka-varscan PRRC2C,missense_variant,p.Arg509Trp,ENST00000367742,;PRRC2C,missense_variant,p.Arg507Trp,ENST00000338920,NM_015172.3;PRRC2C,missense_variant,p.Arg507Trp,ENST00000426496,;PRRC2C,missense_variant,p.Arg264Trp,ENST00000392078,;PRRC2C,non_coding_transcript_exon_variant,,ENST00000476522,; T ENST00000338920 Transcript missense_variant 1756/10355 1519/8454 507/2817 R/W Agg/Tgg rs139508183 1 1 PRRC2C HGNC HGNC:24903 protein_coding YES CCDS1296.2 ENSP00000343629 Q9Y520 UPI0000E265EC NM_015172.3 tolerated_low_confidence(0.06) 12/34 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14038,hmmpanther:PTHR14038:SF6 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 171532613 171532613 A T 1 0 0 0 0 1 0 0 0 12750 63 3 4 4 PRRC2C 1 171532613 Missense_Mutation SNP A C3N-01488_T 1982640 171532613 77423809 42 24416 PAPPA2 0 . GRCh38 1 176594784 176594784 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1180C>A p.Pro394Thr p.P394T ENST00000367662 3/23 347 325 22 380 379 1 strelka-varscan-mutect PAPPA2,missense_variant,p.Pro394Thr,ENST00000367662,NM_020318.2;PAPPA2,missense_variant,p.Pro394Thr,ENST00000367661,NM_021936.2; A ENST00000367662 Transcript missense_variant 2344/9691 1180/5376 394/1791 P/T Ccc/Acc 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 tolerated(0.1) 3/23 Gene3D:2.60.120.200,Pfam_domain:PF13385,SMART_domains:SM00560,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1255241135 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 176594784 176594784 C A 1 0 0 0 0 1 0 0 0 11513 855 30 2 2 PAPPA2 1 176594784 Missense_Mutation SNP C C3N-01488_T 5062171 176594784 72361638 43 24417 PAPPA2 0 . GRCh38 1 176771050 176771050 + Missense_Mutation SNP C C A rs866010097 C3N-01488_T C3N-01488_N C C c.4585C>A p.Pro1529Thr p.P1529T ENST00000367662 17/23 556 513 43 618 618 0 strelka-varscan-mutect PAPPA2,missense_variant,p.Pro1529Thr,ENST00000367662,NM_020318.2; A ENST00000367662 Transcript missense_variant 5749/9691 4585/5376 1529/1791 P/T Cct/Act rs866010097 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 deleterious(0) 17/23 Low_complexity_(Seg):seg,PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs866010097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 176771050 176771050 C A 1 0 0 0 0 1 0 0 0 11513 623 22 2 2 PAPPA2 1 176771050 Missense_Mutation SNP C C3N-01488_T 176266 176771050 72185372 44 24418 PAPPA2 0 . GRCh38 1 176789867 176789867 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.4774C>T p.Pro1592Ser p.P1592S ENST00000367662 18/23 437 268 169 562 561 1 strelka-varscan-mutect PAPPA2,missense_variant,p.Pro1592Ser,ENST00000367662,NM_020318.2;PAPPA2,upstream_gene_variant,,ENST00000479836,; T ENST00000367662 Transcript missense_variant 5938/9691 4774/5376 1592/1791 P/S Cct/Tct 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 deleterious(0.03) 18/23 Low_complexity_(Seg):seg,PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 176789867 176789867 C T 1 0 0 0 0 1 0 0 0 11513 855 30 3 3 PAPPA2 1 176789867 Missense_Mutation SNP C C3N-01488_T 18817 176789867 72166555 45 24419 BRINP2 0 . GRCh38 1 177229925 177229925 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.49G>T p.Ala17Ser p.A17S ENST00000361539 2/8 100 87 13 109 109 0 strelka-varscan-mutect BRINP2,missense_variant,p.Ala17Ser,ENST00000361539,NM_021165.3; T ENST00000361539 Transcript missense_variant 361/3558 49/2352 17/783 A/S Gcc/Tcc 1 1 BRINP2 HGNC HGNC:13746 protein_coding YES CCDS1320.1 ENSP00000354481 Q9C0B6 UPI000006DF55 NM_021165.3 tolerated_low_confidence(0.43) 2/8 Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF8 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 80 177229925 177229925 G T 1 0 0 0 0 1 0 0 0 1686 1203 42 2 2 BRINP2 1 177229925 Missense_Mutation SNP G C3N-01488_T 440058 177229925 71726497 46 24420 CACNA1E 0 . GRCh38 1 181798563 181798563 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.6671C>T p.Pro2224Leu p.P2224L ENST00000367573 48/48 301 277 24 277 277 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Pro2162Leu,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Pro2224Leu,ENST00000621551,;CACNA1E,missense_variant,p.Pro2181Leu,ENST00000367567,;CACNA1E,missense_variant,p.Pro2162Leu,ENST00000358338,;CACNA1E,missense_variant,p.Pro2181Leu,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Pro2224Leu,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Pro2223Leu,ENST00000357570,;CACNA1E,missense_variant,p.Pro2205Leu,ENST00000360108,; T ENST00000367573 Transcript missense_variant 6671/7067 6671/6942 2224/2313 P/L cCa/cTa 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0.02) 48/48 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 181798563 181798563 C T 1 0 0 0 0 1 0 0 0 2230 594 21 3 3 CACNA1E 1 181798563 Missense_Mutation SNP C C3N-01488_T 4568638 181798563 67157859 47 24421 NPL 0 . GRCh38 1 182806494 182806494 + Missense_Mutation SNP G G T rs868407257 C3N-01488_T C3N-01488_N G G c.136G>T p.Ala46Ser p.A46S ENST00000367554 3/11 218 198 20 210 209 1 strelka-varscan-mutect NPL,missense_variant,p.Ala46Ser,ENST00000367554,NM_001200050.1;NPL,intron_variant,,ENST00000258317,;NPL,intron_variant,,ENST00000614468,NM_001200052.1;NPL,intron_variant,,ENST00000367553,NM_001200056.1,NM_030769.2;NPL,intron_variant,,ENST00000367555,NM_001200051.1;NPL,intron_variant,,ENST00000367552,;NPL,non_coding_transcript_exon_variant,,ENST00000471010,;NPL,intron_variant,,ENST00000463899,;NPL,intron_variant,,ENST00000488424,;NPL,intron_variant,,ENST00000460690,;NPL,intron_variant,,ENST00000479721,; T ENST00000367554 Transcript missense_variant 781/3027 136/906 46/301 A/S Gcc/Tcc rs868407257 1 1 NPL HGNC HGNC:16781 protein_coding CCDS55667.1 ENSP00000356525 Q9BXD5 UPI000043F347 NM_001200050.1 deleterious_low_confidence(0.02) 3/11 SMART_domains:SM01130 MODERATE SNV 1 1 PASS rs868407257 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 182806494 182806494 G T 1 0 0 0 0 1 0 0 0 10641 1203 42 2 2 NPL 1 182806494 Missense_Mutation SNP G C3N-01488_T 1007931 182806494 66149928 48 24422 CRB1 0 . GRCh38 1 197347420 197347420 + Missense_Mutation SNP G G T rs779835125 C3N-01488_T C3N-01488_N G G c.929G>T p.Cys310Phe p.C310F ENST00000367400 4/12 427 403 24 429 429 0 strelka-varscan-mutect CRB1,missense_variant,p.Cys241Phe,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Cys310Phe,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Cys310Phe,ENST00000538660,NM_001257966.1;CRB1,intron_variant,,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Cys310Phe,ENST00000484075,;CRB1,non_coding_transcript_exon_variant,,ENST00000475659,; T ENST00000367400 Transcript missense_variant 1064/4932 929/4221 310/1406 C/F tGt/tTt rs779835125,CM106993 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0) 4/12 Gene3D:2gy5A03,Pfam_domain:PF00008,PROSITE_profiles:PS50026,hmmpanther:PTHR24049,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 0,1 1 PASS rs779835125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 197347420 197347420 G T 1 0 0 0 0 1 0 0 0 3648 1377 48 2 2 CRB1 1 197347420 Missense_Mutation SNP G C3N-01488_T 14540926 197347420 51609002 49 24423 IGFN1 0 . GRCh38 1 201206323 201206323 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1430G>T p.Gly477Val p.G477V ENST00000335211 12/24 187 117 70 211 211 0 strelka-varscan IGFN1,missense_variant,p.Gly477Val,ENST00000335211,NM_001164586.1;IGFN1,intron_variant,,ENST00000295591,;IGFN1,non_coding_transcript_exon_variant,,ENST00000444705,;IGFN1,intron_variant,,ENST00000437879,; T ENST00000335211 Transcript missense_variant 1560/11810 1430/11127 477/3708 G/V gGg/gTg 1 1 IGFN1 HGNC HGNC:24607 protein_coding YES CCDS53455.1 ENSP00000334714 Q86VF2 UPI0001B300F4 NM_001164586.1 deleterious(0.03) 12/24 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 201206323 201206323 G T 1 0 0 0 0 1 0 0 0 7497 1232 43 2 2 IGFN1 1 201206323 Missense_Mutation SNP G C3N-01488_T 3858903 201206323 47750099 50 24424 MDM4 0 . GRCh38 1 204530687 204530687 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.157A>G p.Met53Val p.M53V ENST00000367182 4/11 200 170 30 239 239 0 strelka-varscan MDM4,missense_variant,p.Met53Val,ENST00000367182,NM_002393.4;MDM4,missense_variant,p.Met53Val,ENST00000391947,NM_001278516.1;MDM4,missense_variant,p.Met53Val,ENST00000454264,NM_001204171.1;MDM4,missense_variant,p.Met53Val,ENST00000616250,NM_001278518.1;MDM4,missense_variant,p.Met53Val,ENST00000621032,;MDM4,missense_variant,p.Met53Val,ENST00000367180,;MDM4,missense_variant,p.Met53Val,ENST00000507825,;MDM4,intron_variant,,ENST00000614459,NM_001278517.1;MDM4,intron_variant,,ENST00000612738,NM_001278519.1;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,non_coding_transcript_exon_variant,,ENST00000463049,;MDM4,non_coding_transcript_exon_variant,,ENST00000470797,;MDM4,non_coding_transcript_exon_variant,,ENST00000470908,;MDM4,intron_variant,,ENST00000471783,;RP11-430C7.2,upstream_gene_variant,,ENST00000432698,; G ENST00000367182 Transcript missense_variant 319/10073 157/1473 53/490 M/V Atg/Gtg 1 1 MDM4 HGNC HGNC:6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 A0A024R990 UPI000007467F NM_002393.4 deleterious(0.01) 4/11 hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF20,PIRSF_domain:PIRSF006748,Pfam_domain:PF02201,Gene3D:1.10.245.10,PIRSF_domain:PIRSF500699,Superfamily_domains:SSF47592 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 80 204530687 204530687 A G 1 0 0 0 0 1 0 0 0 9352 231 8 5 5 MDM4 1 204530687 Missense_Mutation SNP A C3N-01488_T 3324364 204530687 44425735 51 24425 CNTN2 0 . GRCh38 1 205064747 205064747 + Missense_Mutation SNP C C G rs114903768 C3N-01488_T C3N-01488_N C C c.1516C>G p.Arg506Gly p.R506G ENST00000331830 12/23 139 120 19 124 124 0 strelka-varscan CNTN2,missense_variant,p.Arg506Gly,ENST00000331830,NM_005076.3;CNTN2,upstream_gene_variant,,ENST00000636641,;CNTN2,non_coding_transcript_exon_variant,,ENST00000481872,;CNTN2,non_coding_transcript_exon_variant,,ENST00000636809,;CNTN2,downstream_gene_variant,,ENST00000530117,;CNTN2,upstream_gene_variant,,ENST00000638050,;CNTN2,downstream_gene_variant,,ENST00000527340,;CNTN2,upstream_gene_variant,,ENST00000530594,; G ENST00000331830 Transcript missense_variant 1873/8214 1516/3123 506/1040 R/G Cga/Gga rs114903768 1 1 CNTN2 HGNC HGNC:2172 protein_coding YES CCDS1449.1 ENSP00000330633 Q02246 A0A024R9B4 UPI00001266A5 NM_005076.3 tolerated(0.11) 12/23 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF50,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 201 5 4 0 0 0 0 -20 0.9987139 1 1 1 0 G 3 3 80 205064747 205064747 C G 1 0 0 0 0 1 0 0 0 3422 782 27 4 4 CNTN2 1 205064747 Missense_Mutation SNP C C3N-01488_T 534060 205064747 43891675 52 24426 C1orf186 0 . GRCh38 1 206101796 206101796 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.363T>A p.= p.P121P ENST00000331555 6/6 299 190 109 338 338 0 strelka-varscan C1orf186,synonymous_variant,p.=,ENST00000331555,NM_001007544.3;C1orf186,synonymous_variant,p.=,ENST00000582070,;C1orf186,synonymous_variant,p.=,ENST00000603488,;C1orf186,synonymous_variant,p.=,ENST00000603378,;C1orf186,downstream_gene_variant,,ENST00000604112,; A ENST00000331555 Transcript synonymous_variant 1002/1665 363/519 121/172 P ccT/ccA 1 1 C1orf186 HGNC HGNC:25341 protein_coding YES CCDS73014.1 ENSP00000356093 Q6ZWK4 UPI0000039E60 NM_001007544.3 6/6 Pfam_domain:PF15763,hmmpanther:PTHR38491,hmmpanther:PTHR38491:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 206101796 206101796 T A 1 0 0 0 0 0 0 0 1 1976 1567 55 4 4 C1orf186 1 206101796 Silent SNP T C3N-01488_T 1037049 206101796 42854626 53 24427 TRAF3IP3 0 . GRCh38 1 209775617 209775617 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.934G>A p.Glu312Lys p.E312K ENST00000367024 11/17 144 99 45 174 174 0 strelka-varscan TRAF3IP3,missense_variant,p.Glu312Lys,ENST00000367024,NM_001320143.1;TRAF3IP3,missense_variant,p.Glu312Lys,ENST00000367025,NM_025228.3;TRAF3IP3,missense_variant,p.Glu292Lys,ENST00000367026,NM_001320144.1;TRAF3IP3,missense_variant,p.Glu292Lys,ENST00000400959,;TRAF3IP3,missense_variant,p.Glu48Lys,ENST00000367023,NM_001287754.1;TRAF3IP3,missense_variant,p.Glu48Lys,ENST00000477431,;TRAF3IP3,missense_variant,p.Glu48Lys,ENST00000487271,;C1orf74,downstream_gene_variant,,ENST00000294811,NM_152485.2;TRAF3IP3,upstream_gene_variant,,ENST00000488702,;TRAF3IP3,missense_variant,p.Glu312Lys,ENST00000478359,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000476050,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000474496,;TRAF3IP3,upstream_gene_variant,,ENST00000460314,;TRAF3IP3,upstream_gene_variant,,ENST00000471368,; A ENST00000367024 Transcript missense_variant 1450/2331 934/1656 312/551 E/K Gag/Aag 1 1 TRAF3IP3 HGNC HGNC:30766 protein_coding YES CCDS1490.2 ENSP00000355991 Q9Y228 UPI00005190E1 NM_001320143.1 tolerated(0.15) 11/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15715:SF21,hmmpanther:PTHR15715,Superfamily_domains:SSF57997 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 209775617 209775617 G A 1 0 0 0 0 1 0 0 0 16925 943 33 3 3 TRAF3IP3 1 209775617 Missense_Mutation SNP G C3N-01488_T 3673821 209775617 39180805 54 24428 TRAF3IP3 0 . GRCh38 1 209782076 209782076 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.1584C>T p.= p.L528L ENST00000367024 17/17 280 262 18 342 342 0 strelka-varscan TRAF3IP3,missense_variant,p.Pro140Ser,ENST00000477431,;TRAF3IP3,synonymous_variant,p.=,ENST00000367024,NM_001320143.1;TRAF3IP3,synonymous_variant,p.=,ENST00000367025,NM_025228.3;TRAF3IP3,synonymous_variant,p.=,ENST00000367026,NM_001320144.1;C1orf74,3_prime_UTR_variant,,ENST00000294811,NM_152485.2;IRF6,downstream_gene_variant,,ENST00000367021,NM_006147.3;IRF6,downstream_gene_variant,,ENST00000542854,NM_001206696.1;TRAF3IP3,downstream_gene_variant,,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000367023,NM_001287754.1;TRAF3IP3,downstream_gene_variant,,ENST00000487271,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000467830,;TRAF3IP3,downstream_gene_variant,,ENST00000488702,;TRAF3IP3,3_prime_UTR_variant,,ENST00000471368,;TRAF3IP3,non_coding_transcript_exon_variant,,ENST00000460314,;TRAF3IP3,downstream_gene_variant,,ENST00000476050,;TRAF3IP3,downstream_gene_variant,,ENST00000478359,;TRAF3IP3,downstream_gene_variant,,ENST00000474496,; T ENST00000367024 Transcript synonymous_variant 2100/2331 1584/1656 528/551 L ctC/ctT 1 1 TRAF3IP3 HGNC HGNC:30766 protein_coding YES CCDS1490.2 ENSP00000355991 Q9Y228 UPI00005190E1 NM_001320143.1 17/17 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR15715:SF21,hmmpanther:PTHR15715 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 209782076 209782076 C T 1 0 0 0 0 0 0 0 1 16925 842 30 3 3 TRAF3IP3 1 209782076 Silent SNP C C3N-01488_T 6459 209782076 39174346 55 24429 C1orf74 0 . GRCh38 1 209783195 209783195 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.440A>T p.Gln147Leu p.Q147L ENST00000294811 2/2 425 238 187 438 438 0 strelka-varscan C1orf74,missense_variant,p.Gln147Leu,ENST00000294811,NM_152485.2;IRF6,downstream_gene_variant,,ENST00000367021,NM_006147.3;IRF6,downstream_gene_variant,,ENST00000542854,NM_001206696.1;TRAF3IP3,downstream_gene_variant,,ENST00000367024,NM_001320143.1;TRAF3IP3,downstream_gene_variant,,ENST00000367025,NM_025228.3;TRAF3IP3,downstream_gene_variant,,ENST00000367026,NM_001320144.1;TRAF3IP3,downstream_gene_variant,,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000367023,NM_001287754.1;TRAF3IP3,downstream_gene_variant,,ENST00000477431,;TRAF3IP3,downstream_gene_variant,,ENST00000467830,;TRAF3IP3,downstream_gene_variant,,ENST00000488702,;TRAF3IP3,downstream_gene_variant,,ENST00000476050,;TRAF3IP3,downstream_gene_variant,,ENST00000460314,;TRAF3IP3,downstream_gene_variant,,ENST00000478359,;TRAF3IP3,downstream_gene_variant,,ENST00000471368,; A ENST00000294811 Transcript missense_variant 697/4684 440/810 147/269 Q/L cAg/cTg 1 -1 C1orf74 HGNC HGNC:26319 protein_coding YES CCDS1491.1 ENSP00000294811 Q96LT6 A0A0A8K8E6 UPI0000073C4E NM_152485.2 deleterious(0.03) 2/2 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14953,hmmpanther:PTHR31366 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 209783195 209783195 T A 1 0 0 0 0 1 0 0 0 1998 1580 55 4 4 C1orf74 1 209783195 Missense_Mutation SNP T C3N-01488_T 1119 209783195 39173227 56 24430 NEK2 0 . GRCh38 1 211669333 211669333 + Splice_Site SNP C C G novel C3N-01488_T C3N-01488_N C C c.766-1G>C p.X256_splice ENST00000366999 189 170 19 245 245 0 strelka-varscan NEK2,splice_acceptor_variant,,ENST00000366999,NM_002497.3;NEK2,splice_acceptor_variant,,ENST00000366998,NM_001204183.1;NEK2,splice_acceptor_variant,,ENST00000540251,NM_001204182.1;NEK2,splice_acceptor_variant,,ENST00000462283,;NEK2,non_coding_transcript_exon_variant,,ENST00000489633,; G ENST00000366999 Transcript splice_acceptor_variant -/2131 766/1338 256/445 1 -1 NEK2 HGNC HGNC:7745 protein_coding YES CCDS1500.1 ENSP00000355966 P51955 UPI000012FF27 NM_002497.3 5/7 HIGH 1 SNV 1 1 PASS . . 0 147 0 31 31 0 0 0 -6.67541 0 0 1 0 0 G 5 3 80 211669333 211669333 C G 1 0 0 0 0 0 0 1 0 10352 695 24 4 4 NEK2 1 211669333 Splice_Site SNP C C3N-01488_T 1886138 211669333 37287089 57 24431 USH2A 0 . GRCh38 1 215782145 215782145 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.10637G>T p.Gly3546Val p.G3546V ENST00000307340 54/72 378 355 23 536 535 1 strelka-varscan USH2A,missense_variant,p.Gly3546Val,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 11024/18883 10637/15609 3546/5202 G/V gGa/gTa COSM3864471,COSM3864472 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 54/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 215782145 215782145 C A 1 0 0 0 0 1 0 0 0 17570 855 30 2 2 USH2A 1 215782145 Missense_Mutation SNP C C3N-01488_T 4112812 215782145 33174277 58 24432 USH2A 0 . GRCh38 1 216048581 216048581 + Missense_Mutation SNP C C G rs771891583 C3N-01488_T C3N-01488_N C C c.6116G>C p.Gly2039Ala p.G2039A ENST00000307340 31/72 507 480 27 545 545 0 strelka-varscan USH2A,missense_variant,p.Gly2039Ala,ENST00000307340,NM_206933.2; G ENST00000307340 Transcript missense_variant 6503/18883 6116/15609 2039/5202 G/A gGc/gCc rs771891583 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 31/72 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 216048581 216048581 C G 1 0 0 0 0 1 0 0 0 17570 739 26 4 4 USH2A 1 216048581 Missense_Mutation SNP C C3N-01488_T 266436 216048581 32907841 59 24433 GPATCH2 0 . GRCh38 1 217491714 217491714 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.1243C>T p.His415Tyr p.H415Y ENST00000366935 8/10 273 255 18 274 274 0 strelka-varscan GPATCH2,missense_variant,p.His415Tyr,ENST00000366935,NM_018040.3;GPATCH2,non_coding_transcript_exon_variant,,ENST00000489246,;GPATCH2,downstream_gene_variant,,ENST00000470014,; A ENST00000366935 Transcript missense_variant 1354/5851 1243/1587 415/528 H/Y Cac/Tac 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 tolerated(0.11) 8/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4 MODERATE 1 SNV 2 1 PASS . . 0 203 0 6 0 0 0 0 -19.94133 0.9921808 1 1 1 0 A 3 1 80 217491714 217491714 G A 1 0 0 0 0 1 0 0 0 6491 1377 48 3 3 GPATCH2 1 217491714 Missense_Mutation SNP G C3N-01488_T 1443133 217491714 31464708 60 24434 RAB3GAP2 0 . GRCh38 1 220210954 220210954 + Splice_Site SNP C C A novel C3N-01488_T C3N-01488_N C C c.434+1G>T p.X145_splice ENST00000358951 518 460 58 622 619 3 strelka-varscan RAB3GAP2,splice_donor_variant,,ENST00000358951,NM_012414.3;RAB3GAP2,splice_donor_variant,,ENST00000484658,;RAB3GAP2,intron_variant,,ENST00000478976,;RAB3GAP2,splice_donor_variant,,ENST00000237724,;RAB3GAP2,splice_donor_variant,,ENST00000474178,;RP11-568G11.4,downstream_gene_variant,,ENST00000604232,; A ENST00000358951 Transcript splice_donor_variant -/7257 434/4182 145/1393 1 -1 RAB3GAP2 HGNC HGNC:17168 protein_coding YES CCDS31028.1 ENSP00000351832 Q9H2M9 UPI0000072269 NM_012414.3 5/34 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 80 220210954 220210954 C A 1 0 0 0 0 0 0 1 0 13095 521 18 2 2 RAB3GAP2 1 220210954 Splice_Site SNP C C3N-01488_T 2719240 220210954 28745468 61 24435 RBM34 0 . GRCh38 1 235160995 235160995 + Silent SNP T T C novel C3N-01488_T C3N-01488_N T T c.126A>G p.= p.L42L ENST00000408888 2/11 281 208 73 266 265 1 strelka-varscan RBM34,synonymous_variant,p.=,ENST00000408888,NM_015014.2;RBM34,synonymous_variant,p.=,ENST00000447801,;RBM34,synonymous_variant,p.=,ENST00000429912,;RBM34,non_coding_transcript_exon_variant,,ENST00000485019,;RBM34,synonymous_variant,p.=,ENST00000474086,;ARID4B,3_prime_UTR_variant,,ENST00000474953,;RBM34,non_coding_transcript_exon_variant,,ENST00000476261,;RBM34,non_coding_transcript_exon_variant,,ENST00000486751,;RBM34,non_coding_transcript_exon_variant,,ENST00000468751,;RBM34,upstream_gene_variant,,ENST00000475960,; C ENST00000408888 Transcript synonymous_variant 357/2054 126/1293 42/430 L ttA/ttG 1 -1 RBM34 HGNC HGNC:28965 protein_coding YES CCDS41477.2 ENSP00000386226 P42696 UPI00001D7E4C NM_015014.2 2/11 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 235160995 235160995 T C 1 0 0 0 0 0 0 0 1 13297 1403 49 5 5 RBM34 1 235160995 Silent SNP T C3N-01488_T 14950041 235160995 13795427 62 24436 HEATR1 0 . GRCh38 1 236597962 236597962 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.519A>T p.Leu173Phe p.L173F ENST00000366582 5/45 150 106 44 226 226 0 strelka-varscan HEATR1,missense_variant,p.Leu173Phe,ENST00000366582,NM_018072.5;HEATR1,missense_variant,p.Leu173Phe,ENST00000366581,;HEATR1,downstream_gene_variant,,ENST00000366579,;HEATR1,non_coding_transcript_exon_variant,,ENST00000483073,; A ENST00000366582 Transcript missense_variant 634/8447 519/6435 173/2144 L/F ttA/ttT 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 deleterious(0) 5/45 hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 236597962 236597962 T A 1 0 0 0 0 1 0 0 0 6910 1519 53 4 4 HEATR1 1 236597962 Missense_Mutation SNP T C3N-01488_T 1436967 236597962 12358460 63 24437 ACTN2 0 . GRCh38 1 236762602 236762602 + Missense_Mutation SNP G G T rs536297856 C3N-01488_T C3N-01488_N G G c.2668G>T p.Gly890Trp p.G890W ENST00000542672 21/21 561 336 225 589 587 2 strelka-varscan ACTN2,missense_variant,p.Gly682Trp,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Gly890Trp,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Gly890Trp,ENST00000366578,NM_001103.3;ACTN2,downstream_gene_variant,,ENST00000461367,; T ENST00000542672 Transcript missense_variant 2888/4906 2668/2685 890/894 G/W Ggg/Tgg rs536297856,COSM5131258,COSM5131259,COSM5556126,COSM5556127 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0) 21/21 Gene3D:1.10.238.10,Pfam_domain:PF08726,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM01184 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 236762602 236762602 G T 1 0 0 0 0 1 0 0 0 249 1116 39 1 1 ACTN2 1 236762602 Missense_Mutation SNP G C3N-01488_T 164640 236762602 12193820 64 24438 RYR2 0 . GRCh38 1 237783742 237783742 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.12030G>A p.= p.V4010V ENST00000366574 90/105 189 160 29 230 230 0 strelka-varscan RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; A ENST00000366574 Transcript synonymous_variant 12347/16562 12030/14904 4010/4967 V gtG/gtA 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 90/105 Gene3D:1.10.238.10,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 237783742 237783742 G A 1 0 0 0 0 0 0 0 1 14029 1335 47 3 3 RYR2 1 237783742 Silent SNP G C3N-01488_T 1021140 237783742 11172680 65 24439 FH 0 . GRCh38 1 241504217 241504217 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.933A>T p.Lys311Asn p.K311N ENST00000366560 7/10 376 301 75 530 530 0 strelka-varscan FH,missense_variant,p.Lys311Asn,ENST00000366560,NM_000143.3; A ENST00000366560 Transcript missense_variant 972/1797 933/1533 311/510 K/N aaA/aaT 1 -1 FH HGNC HGNC:3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 A0A0S2Z4C3 UPI000012AD6A NM_000143.3 deleterious(0) 7/10 HAMAP:MF_00743,hmmpanther:PTHR11444:SF1,hmmpanther:PTHR11444,TIGRFAM_domain:TIGR00979,Gene3D:1.20.200.10,Pfam_domain:PF00206,Superfamily_domains:SSF48557 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 241504217 241504217 T A 1 0 0 0 0 1 0 0 0 5739 1490 52 4 4 FH 1 241504217 Missense_Mutation SNP T C3N-01488_T 3720475 241504217 7452205 66 24440 85 2 FH 0 . GRCh38 1 241504220 241504220 + Missense_Mutation SNP A A T rs549087719 C3N-01488_T C3N-01488_N A A c.930T>A p.Asn310Lys p.N310K ENST00000366560 7/10 381 300 81 524 523 1 strelka-varscan FH,missense_variant,p.Asn310Lys,ENST00000366560,NM_000143.3; T ENST00000366560 Transcript missense_variant 969/1797 930/1533 310/510 N/K aaT/aaA rs549087719 1 -1 FH HGNC HGNC:3700 protein_coding YES CCDS1617.1 ENSP00000355518 P07954 A0A0S2Z4C3 UPI000012AD6A NM_000143.3 deleterious(0) 7/10 HAMAP:MF_00743,hmmpanther:PTHR11444:SF1,hmmpanther:PTHR11444,TIGRFAM_domain:TIGR00979,Gene3D:1.20.200.10,Pfam_domain:PF00206,Superfamily_domains:SSF48557 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 241504220 241504220 A T 1 0 0 0 0 1 0 0 0 5739 446 16 4 4 FH 1 241504220 Missense_Mutation SNP A C3N-01488_T 3 241504220 7452202 67 24441 85 2 ADSS 0 . GRCh38 1 244432583 244432583 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.368G>T p.Trp123Leu p.W123L ENST00000366535 4/13 174 154 20 256 255 1 strelka-varscan ADSS,missense_variant,p.Trp123Leu,ENST00000366535,NM_001126.3; A ENST00000366535 Transcript missense_variant 685/2780 368/1371 123/456 W/L tGg/tTg 1 -1 ADSS HGNC HGNC:292 protein_coding YES CCDS1624.1 ENSP00000355493 P30520 A0A024R5Q7 UPI0000132AF5 NM_001126.3 tolerated(0.12) 4/13 HAMAP:MF_00011,HAMAP:MF_03127,hmmpanther:PTHR11846:SF1,hmmpanther:PTHR11846,Pfam_domain:PF00709,TIGRFAM_domain:TIGR00184,SMART_domains:SM00788,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 197 0 10 2 0 0 0 -9.081728 0.6118737 1 1 1 0 A 3 1 80 244432583 244432583 C A 1 0 0 0 0 1 0 0 0 421 595 21 2 2 ADSS 1 244432583 Missense_Mutation SNP C C3N-01488_T 2928363 244432583 4523839 68 24442 KIF26B 0 . GRCh38 1 245687550 245687550 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.4567C>A p.Gln1523Lys p.Q1523K ENST00000407071 12/15 449 265 184 460 460 0 strelka-varscan KIF26B,missense_variant,p.Gln1142Lys,ENST00000366518,;KIF26B,missense_variant,p.Gln1523Lys,ENST00000407071,NM_018012.3;KIF26B,downstream_gene_variant,,ENST00000483253,; A ENST00000407071 Transcript missense_variant 5007/7287 4567/6327 1523/2108 Q/K Cag/Aag 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 tolerated(0.74) 12/15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 245687550 245687550 C A 1 0 0 0 0 1 0 0 0 8160 595 21 2 2 KIF26B 1 245687550 Missense_Mutation SNP C C3N-01488_T 1254967 245687550 3268872 69 24443 KIF26B 0 . GRCh38 1 245688805 245688805 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.5822C>A p.Pro1941Gln p.P1941Q ENST00000407071 12/15 58 53 5 64 64 0 strelka-varscan KIF26B,missense_variant,p.Pro1560Gln,ENST00000366518,;KIF26B,missense_variant,p.Pro1941Gln,ENST00000407071,NM_018012.3;KIF26B,downstream_gene_variant,,ENST00000483253,; A ENST00000407071 Transcript missense_variant,splice_region_variant 6262/7287 5822/6327 1941/2108 P/Q cCa/cAa 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 tolerated(0.29) 12/15 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.38715 1 1 1 1 0 A 3 1 80 245688805 245688805 C A 1 0 0 0 0 1 0 0 0 8160 608 21 2 2 KIF26B 1 245688805 Missense_Mutation SNP C C3N-01488_T 1255 245688805 3267617 70 24444 OR14A2 0 . GRCh38 1 247723555 247723555 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.489C>A p.= p.S163S ENST00000366485 1/1 259 244 15 320 320 0 strelka-varscan OR14A2,synonymous_variant,p.=,ENST00000366485,;RP11-634B7.5,intron_variant,,ENST00000426444,;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; T ENST00000366485 Transcript synonymous_variant 489/945 489/945 163/314 S tcC/tcA 1 -1 OR14A2 HGNC HGNC:15024 protein_coding YES ENSP00000355441 Q96R54 A0A126GWG8 UPI000004A5E7 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF346,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 247723555 247723555 G T 1 0 0 0 0 0 0 0 1 11022 1335 47 2 2 OR14A2 1 247723555 Silent SNP G C3N-01488_T 2034750 247723555 1232867 71 24445 OR14K1 0 . GRCh38 1 247739045 247739045 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.431C>A p.Ala144Asp p.A144D ENST00000283225 1/1 261 231 30 291 291 0 strelka-varscan OR14K1,missense_variant,p.Ala144Asp,ENST00000283225,;RP11-634B7.4,intron_variant,,ENST00000449298,; A ENST00000283225 Transcript missense_variant 431/945 431/945 144/314 A/D gCt/gAt 1 1 OR14K1 HGNC HGNC:15025 protein_coding YES ENSP00000283225 Q8NGZ2 UPI0000041CBA deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF51,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 247739045 247739045 C A 1 0 0 0 0 1 0 0 0 11026 797 28 2 2 OR14K1 1 247739045 Missense_Mutation SNP C C3N-01488_T 15490 247739045 1217377 72 24446 OR1C1 0 . GRCh38 1 247758132 247758132 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.275T>A p.Ile92Asn p.I92N ENST00000408896 1/1 253 231 22 293 292 1 strelka-varscan OR1C1,missense_variant,p.Ile92Asn,ENST00000408896,NM_012353.2; T ENST00000408896 Transcript missense_variant 275/945 275/945 92/314 I/N aTc/aAc 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 247758132 247758132 A T 1 0 0 0 0 1 0 0 0 11029 333 12 4 4 OR1C1 1 247758132 Missense_Mutation SNP A C3N-01488_T 19087 247758132 1198290 73 24447 OR11L1 0 . GRCh38 1 247841414 247841414 + Silent SNP C C G novel C3N-01488_T C3N-01488_N C C c.483G>C p.= p.L161L ENST00000355784 1/1 412 376 36 427 427 0 strelka-varscan OR11L1,synonymous_variant,p.=,ENST00000355784,NM_001001959.1; G ENST00000355784 Transcript synonymous_variant 483/969 483/969 161/322 L ctG/ctC 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 247841414 247841414 C G 1 0 0 0 0 0 0 0 1 11007 813 29 4 4 OR11L1 1 247841414 Silent SNP C C3N-01488_T 83282 247841414 1115008 74 24448 OR2W3 0 . GRCh38 1 247896171 247896171 + Silent SNP C C T rs376214113 C3N-01488_T C3N-01488_N C C c.585C>T p.= p.I195I ENST00000360358 1/1 253 228 25 269 269 0 strelka-varscan OR2W3,synonymous_variant,p.=,ENST00000360358,NM_001001957.2; T ENST00000360358 Transcript synonymous_variant 585/945 585/945 195/314 I atC/atT rs376214113,COSM2232622 1 1 OR2W3 HGNC HGNC:15021 protein_coding YES CCDS31099.1 ENSP00000353516 Q7Z3T1 UPI0000061EA8 NM_001001957.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF223,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 LOW 1 SNV 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 247896171 247896171 C T 1 0 0 0 0 0 0 0 1 11111 874 31 1 1 OR2W3 1 247896171 Silent SNP C C3N-01488_T 54757 247896171 1060251 75 24449 OR2M4 0 . GRCh38 1 248239160 248239160 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.232C>A p.Leu78Ile p.L78I ENST00000306687 1/1 142 121 21 212 212 0 strelka-varscan OR2M4,missense_variant,p.Leu78Ile,ENST00000306687,NM_017504.1; A ENST00000306687 Transcript missense_variant 232/936 232/936 78/311 L/I Cta/Ata 1 1 OR2M4 HGNC HGNC:8270 protein_coding YES CCDS31108.1 ENSP00000306688 Q96R27 A0A126GV73 UPI000004B233 NM_017504.1 tolerated(0.07) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF91,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 248239160 248239160 C A 1 0 0 0 0 1 0 0 0 11090 912 32 2 2 OR2M4 1 248239160 Missense_Mutation SNP C C3N-01488_T 342989 248239160 717262 76 24450 OR14C36 0 . GRCh38 1 248349688 248349688 + Missense_Mutation SNP G G A rs74467694 C3N-01488_T C3N-01488_N G G c.914G>A p.Arg305Lys p.R305K ENST00000317861 1/1 102 96 6 137 137 0 strelka-varscan OR14C36,missense_variant,p.Arg305Lys,ENST00000317861,NM_001001918.1; A ENST00000317861 Transcript missense_variant 914/939 914/939 305/312 R/K aGa/aAa rs74467694 1 1 OR14C36 HGNC HGNC:15026 protein_coding YES CCDS31112.1 ENSP00000324534 Q8NHC7 UPI0000041CB1 NM_001001918.1 tolerated(0.27) 1/1 hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF180,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 202 7 0 0 0 0 0 -12.21663 0.9999965 1 1 1 0 A 3 1 80 248349688 248349688 G A 1 0 0 0 0 1 0 0 0 11023 942 33 3 3 OR14C36 1 248349688 Missense_Mutation SNP G C3N-01488_T 110528 248349688 606734 77 24451 OR2T1 0 . GRCh38 1 248406067 248406067 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.73C>A p.His25Asn p.H25N ENST00000366474 1/1 235 207 28 264 264 0 strelka-varscan OR2T1,missense_variant,p.His25Asn,ENST00000366474,NM_030904.1; A ENST00000366474 Transcript missense_variant 73/1110 73/1110 25/369 H/N Cat/Aat COSM4030760 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 tolerated_low_confidence(0.14) 1/1 Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 248406067 248406067 C A 1 0 0 0 0 1 0 0 0 11094 478 17 2 2 OR2T1 1 248406067 Missense_Mutation SNP C C3N-01488_T 56379 248406067 550355 78 24452 SNTG2 0 . GRCh38 2 1247363 1247363 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.925G>T p.Gly309Ter p.G309* ENST00000308624 12/17 272 234 38 323 323 0 strelka-varscan-mutect SNTG2,stop_gained,p.Gly309Ter,ENST00000308624,NM_018968.3;SNTG2,stop_gained,p.Gly182Ter,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000489646,;SNTG2,downstream_gene_variant,,ENST00000494178,; T ENST00000308624 Transcript stop_gained 1054/1888 925/1620 309/539 G/* Gga/Tga 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 12/17 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,Superfamily_domains:SSF50729 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 1247363 1247363 G T 1 0 0 0 0 0 1 0 0 15195 1001 35 2 2 SNTG2 2 1247363 Nonsense_Mutation SNP G C3N-01488_T 1247363 240946166 79 24453 TDRD15 0 . GRCh38 2 21138420 21138420 + Missense_Mutation SNP A A C novel C3N-01488_T C3N-01488_N A A c.953A>C p.Gln318Pro p.Q318P ENST00000405799 4/4 103 90 13 166 166 0 strelka-varscan TDRD15,missense_variant,p.Gln318Pro,ENST00000405799,;TDRD15,missense_variant,p.Gln318Pro,ENST00000622654,; C ENST00000405799 Transcript missense_variant 1283/6135 953/5805 318/1934 Q/P cAa/cCa 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 deleterious(0.03) 4/4 Gene3D:2.30.30.140,Pfam_domain:PF00567,PROSITE_profiles:PS50304,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7,SMART_domains:SM00333,Superfamily_domains:SSF63748 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 21138420 21138420 A C 1 0 0 0 0 1 0 0 0 16141 130 5 5 5 TDRD15 2 21138420 Missense_Mutation SNP A C3N-01488_T 19891057 21138420 221055109 80 24454 ABCG8 0 . GRCh38 2 43877690 43877690 + Splice_Site SNP T T C novel C3N-01488_T C3N-01488_N T T c.1884+2T>C p.X628_splice ENST00000272286 474 393 81 634 634 0 strelka-varscan ABCG8,splice_donor_variant,,ENST00000272286,NM_022437.2; C ENST00000272286 Transcript splice_donor_variant -/2665 1884/2022 628/673 1 1 ABCG8 HGNC HGNC:13887 protein_coding YES CCDS1815.1 ENSP00000272286 Q9H221 UPI000004C4CD NM_022437.2 12/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 80 43877690 43877690 T C 1 0 0 0 0 0 0 1 0 76 1652 57 5 5 ABCG8 2 43877690 Splice_Site SNP T C3N-01488_T 22739270 43877690 198315839 81 24455 NRXN1 0 . GRCh38 2 50053285 50053285 + Nonsense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.4234G>T p.Glu1412Ter p.E1412* ENST00000404971 22/24 234 189 45 352 350 2 strelka-varscan NRXN1,stop_gained,p.Glu1342Ter,ENST00000406316,NM_004801.4;NRXN1,stop_gained,p.Glu1364Ter,ENST00000625672,;NRXN1,stop_gained,p.Glu1412Ter,ENST00000404971,NM_001135659.1;NRXN1,stop_gained,p.Glu1372Ter,ENST00000401669,;NRXN1,stop_gained,p.Glu1360Ter,ENST00000405472,;NRXN1,stop_gained,p.Glu1364Ter,ENST00000630543,;NRXN1,stop_gained,p.Glu307Ter,ENST00000342183,NM_138735.2;NRXN1,stop_gained,p.Glu337Ter,ENST00000401710,;NRXN1,stop_gained,p.Glu337Ter,ENST00000628364,;NRXN1,stop_gained,p.Glu63Ter,ENST00000611589,;NRXN1,non_coding_transcript_exon_variant,,ENST00000637889,;NRXN1,non_coding_transcript_exon_variant,,ENST00000635264,;NRXN1,3_prime_UTR_variant,,ENST00000637906,; A ENST00000404971 Transcript stop_gained 5574/7578 4234/4644 1412/1547 E/* Gaa/Taa COSM3582024,COSM3582025,COSM3582026,COSM3582027,COSM3582028 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 22/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565 1,1,1,1,1 HIGH 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 80 50053285 50053285 C A 1 0 0 0 0 0 1 0 0 10724 922 32 2 2 NRXN1 2 50053285 Nonsense_Mutation SNP C C3N-01488_T 6175595 50053285 192140244 82 24456 M1AP 0 . GRCh38 2 74562222 74562222 + Missense_Mutation SNP C C A rs143680043 C3N-01488_T C3N-01488_N C C c.1276G>T p.Val426Leu p.V426L ENST00000290536 8/11 61 50 11 116 116 0 strelka-varscan M1AP,missense_variant,p.Val426Leu,ENST00000290536,NM_138804.4;M1AP,missense_variant,p.Val426Leu,ENST00000536235,NM_001321739.1,NM_001281296.1;M1AP,missense_variant,p.Val426Leu,ENST00000409585,;DOK1,downstream_gene_variant,,ENST00000233668,NM_001318866.1,NM_001381.3;DOK1,downstream_gene_variant,,ENST00000409429,NM_001197260.1;DOK1,downstream_gene_variant,,ENST00000340004,;M1AP,non_coding_transcript_exon_variant,,ENST00000464686,;M1AP,intron_variant,,ENST00000485997,;DOK1,downstream_gene_variant,,ENST00000464613,; A ENST00000290536 Transcript missense_variant 1393/2543 1276/1593 426/530 V/L Gtg/Ttg rs143680043 1 -1 M1AP HGNC HGNC:25183 protein_coding YES CCDS33229.1 ENSP00000290536 Q8TC57 UPI0000072570 NM_138804.4 deleterious(0.01) 8/11 hmmpanther:PTHR28642,hmmpanther:PTHR28642:SF1 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 80 74562222 74562222 C A 1 0 0 0 0 1 0 0 0 9053 492 17 2 2 M1AP 2 74562222 Missense_Mutation SNP C C3N-01488_T 24508937 74562222 167631307 83 24457 REG1B 0 . GRCh38 2 79087557 79087557 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.56T>A p.Leu19Gln p.L19Q ENST00000305089 2/6 152 118 34 190 190 0 strelka-varscan REG1B,missense_variant,p.Leu19Gln,ENST00000305089,NM_006507.3;REG1B,upstream_gene_variant,,ENST00000454188,;REG1B,non_coding_transcript_exon_variant,,ENST00000479258,;REG1B,non_coding_transcript_exon_variant,,ENST00000476554,;REG1B,non_coding_transcript_exon_variant,,ENST00000469052,; T ENST00000305089 Transcript missense_variant 137/767 56/501 19/166 L/Q cTg/cAg 1 -1 REG1B HGNC HGNC:9952 protein_coding YES CCDS1963.1 ENSP00000303206 P48304 Q6ICS1 UPI00000012AB NM_006507.3 tolerated(0.44) 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR22801:SF55,hmmpanther:PTHR22801,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 79087557 79087557 A T 1 0 0 0 0 1 0 0 0 13381 188 7 4 4 REG1B 2 79087557 Missense_Mutation SNP A C3N-01488_T 4525335 79087557 163105972 84 24458 CTNNA2 0 . GRCh38 2 79874300 79874300 + Missense_Mutation SNP C C A rs756399817 C3N-01488_T C3N-01488_N C C c.810C>A p.His270Gln p.H270Q ENST00000402739 5/18 215 179 36 299 299 0 strelka-varscan CTNNA2,missense_variant,p.His270Gln,ENST00000466387,;CTNNA2,missense_variant,p.His270Gln,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.His270Gln,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.His270Gln,ENST00000629316,NM_001164883.1; A ENST00000402739 Transcript missense_variant 815/3684 810/2862 270/953 H/Q caC/caA rs756399817 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 tolerated(0.36) 5/18 Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 79874300 79874300 C A 1 0 0 0 0 1 0 0 0 3822 477 17 2 2 CTNNA2 2 79874300 Missense_Mutation SNP C C3N-01488_T 786743 79874300 162319229 85 24459 LRRTM1 0 . GRCh38 2 80303177 80303177 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.643C>A p.His215Asn p.H215N ENST00000295057 2/2 211 170 41 283 283 0 strelka-varscan LRRTM1,missense_variant,p.His215Asn,ENST00000295057,;LRRTM1,missense_variant,p.His215Asn,ENST00000409148,NM_178839.4;LRRTM1,missense_variant,p.His215Asn,ENST00000416268,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.His215Asn,ENST00000433224,;LRRTM1,missense_variant,p.His215Asn,ENST00000417012,; T ENST00000295057 Transcript missense_variant 1300/2599 643/1569 215/522 H/N Cac/Aac 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE deleterious(0) 2/2 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 80303177 80303177 G T 1 0 0 0 0 1 0 0 0 8945 1319 46 2 2 LRRTM1 2 80303177 Missense_Mutation SNP G C3N-01488_T 428877 80303177 161890352 86 24460 LRRTM1 0 . GRCh38 2 80303607 80303607 + Silent SNP G G A rs149452279 C3N-01488_T C3N-01488_N G G c.213C>T p.= p.S71S ENST00000295057 2/2 121 99 22 188 188 0 strelka-varscan LRRTM1,synonymous_variant,p.=,ENST00000295057,;LRRTM1,synonymous_variant,p.=,ENST00000409148,NM_178839.4;LRRTM1,synonymous_variant,p.=,ENST00000416268,;LRRTM1,synonymous_variant,p.=,ENST00000452811,;LRRTM1,synonymous_variant,p.=,ENST00000415098,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.=,ENST00000433224,;LRRTM1,synonymous_variant,p.=,ENST00000417012,; A ENST00000295057 Transcript synonymous_variant 870/2599 213/1569 71/522 S tcC/tcT rs149452279 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 80303607 80303607 G A 1 0 0 0 0 0 0 0 1 8945 1219 43 3 3 LRRTM1 2 80303607 Silent SNP G C3N-01488_T 430 80303607 161889922 87 24461 RPIA 0 . GRCh38 2 88736573 88736573 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.635G>T p.Gly212Val p.G212V ENST00000283646 7/9 215 193 22 347 346 1 strelka-varscan RPIA,missense_variant,p.Gly212Val,ENST00000283646,NM_144563.2; T ENST00000283646 Transcript missense_variant 690/1848 635/936 212/311 G/V gGa/gTa COSM576275 1 1 RPIA HGNC HGNC:10297 protein_coding YES CCDS2004.2 ENSP00000283646 P49247 UPI0000037A98 NM_144563.2 deleterious(0) 7/9 Gene3D:3.40.50.1360,HAMAP:MF_00170,Pfam_domain:PF06026,hmmpanther:PTHR11934,hmmpanther:PTHR11934:SF0,Superfamily_domains:SSF100950,Superfamily_domains:SSF75445,TIGRFAM_domain:TIGR00021 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 88736573 88736573 G T 1 0 0 0 0 1 0 0 0 13805 1174 41 2 2 RPIA 2 88736573 Missense_Mutation SNP G C3N-01488_T 8432966 88736573 153456956 88 24462 ZNF2 0 . GRCh38 2 95181432 95181432 + Missense_Mutation SNP G G T rs551623974 C3N-01488_T C3N-01488_N G G c.643G>T p.Asp215Tyr p.D215Y ENST00000611147 5/5 162 133 29 195 195 0 strelka-varscan-mutect ZNF2,missense_variant,p.Asp160Tyr,ENST00000617923,NM_001017396.2;ZNF2,missense_variant,p.Asp122Tyr,ENST00000611463,NM_001291604.1;ZNF2,missense_variant,p.Asp202Tyr,ENST00000614034,NM_021088.3;ZNF2,missense_variant,p.Asp164Tyr,ENST00000622059,NM_001282398.1;ZNF2,missense_variant,p.Asp215Tyr,ENST00000611147,NM_001291605.1; T ENST00000611147 Transcript missense_variant 726/1465 643/1317 215/438 D/Y Gac/Tac rs551623974 1 1 ZNF2 HGNC HGNC:12991 protein_coding YES CCDS77434.1 ENSP00000482030 A0A087WYR5 UPI0004438063 NM_001291605.1 deleterious(0.01) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF364,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs551623974 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 95181432 95181432 G T 1 0 0 0 0 1 0 0 0 18337 1058 37 1 1 ZNF2 2 95181432 Missense_Mutation SNP G C3N-01488_T 6444859 95181432 147012097 89 24463 ANKRD36 0 . GRCh38 2 97164403 97164403 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.1465G>A p.Val489Met p.V489M ENST00000420699 20/76 281 250 31 444 444 0 varscan-mutect ANKRD36,missense_variant,p.Val489Met,ENST00000420699,NM_001164315.1;ANKRD36,missense_variant,p.Val489Met,ENST00000461153,;ANKRD36,intron_variant,,ENST00000620383,; A ENST00000420699 Transcript missense_variant 1709/6269 1465/5826 489/1941 V/M Gtg/Atg 1 1 ANKRD36 HGNC HGNC:24079 protein_coding YES CCDS54379.1 ENSP00000391950 A6QL64 UPI0001B23BB4 NM_001164315.1 tolerated_low_confidence(0.15) 20/76 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 97164403 97164403 G A 1 0 0 0 0 1 0 0 0 771 1261 44 3 3 ANKRD36 2 97164403 Missense_Mutation SNP G C3N-01488_T 1982971 97164403 145029126 90 24464 ZAP70 0 . GRCh38 2 97725140 97725140 + Nonsense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.451A>T p.Lys151Ter p.K151* ENST00000264972 4/14 348 321 27 355 355 0 strelka-varscan-mutect ZAP70,stop_gained,p.Lys151Ter,ENST00000264972,NM_001079.3;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000483781,; T ENST00000264972 Transcript stop_gained 666/2437 451/1860 151/619 K/* Aag/Tag 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 4/14 Gene3D:2oq1A02,PIRSF_domain:PIRSF000604,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262,Superfamily_domains:SSF55550 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 97725140 97725140 A T 1 0 0 0 0 0 1 0 0 18075 247 9 4 4 ZAP70 2 97725140 Nonsense_Mutation SNP A C3N-01488_T 560737 97725140 144468389 91 24465 TMEM131 0 . GRCh38 2 97759747 97759747 + Missense_Mutation SNP G G C rs747733812 C3N-01488_T C3N-01488_N G G c.5111C>G p.Ser1704Trp p.S1704W ENST00000186436 39/41 153 111 42 188 188 0 strelka-varscan-mutect TMEM131,missense_variant,p.Ser1704Trp,ENST00000186436,NM_015348.1;TMEM131,splice_region_variant,,ENST00000465767,;TMEM131,non_coding_transcript_exon_variant,,ENST00000485245,;TMEM131,non_coding_transcript_exon_variant,,ENST00000469447,; C ENST00000186436 Transcript missense_variant,splice_region_variant 5340/6640 5111/5652 1704/1883 S/W tCg/tGg rs747733812 1 -1 TMEM131 HGNC HGNC:30366 protein_coding YES CCDS46368.1 ENSP00000186436 Q92545 UPI00006C0498 NM_015348.1 deleterious_low_confidence(0) 39/41 Low_complexity_(Seg):seg,hmmpanther:PTHR22050:SF1,hmmpanther:PTHR22050 MODERATE 1 SNV 5 1 PASS rs747733812 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 97759747 97759747 G C 1 0 0 0 0 1 0 0 0 16488 1072 37 4 4 TMEM131 2 97759747 Missense_Mutation SNP G C3N-01488_T 34607 97759747 144433782 92 24466 INPP4A 0 . GRCh38 2 98554293 98554293 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.1385G>A p.Cys462Tyr p.C462Y ENST00000074304 16/26 124 102 22 136 135 1 strelka-varscan-mutect INPP4A,missense_variant,p.Cys462Tyr,ENST00000409016,NM_004027.2;INPP4A,missense_variant,p.Cys462Tyr,ENST00000074304,NM_001134224.1;INPP4A,missense_variant,p.Cys457Tyr,ENST00000409851,NM_001134225.1;INPP4A,missense_variant,p.Cys462Tyr,ENST00000409540,NM_001566.2;INPP4A,missense_variant,p.Cys462Tyr,ENST00000523221,;INPP4A,intron_variant,,ENST00000409463,;INPP4A,upstream_gene_variant,,ENST00000468638,; A ENST00000074304 Transcript missense_variant 1778/6752 1385/2934 462/977 C/Y tGc/tAc 1 1 INPP4A HGNC HGNC:6074 protein_coding YES CCDS46369.1 ENSP00000074304 Q96PE3 UPI000006CD60 NM_001134224.1 deleterious(0.02) 16/26 hmmpanther:PTHR12187,hmmpanther:PTHR12187:SF4 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 98554293 98554293 G A 1 0 0 0 0 1 0 0 0 7655 1319 46 3 3 INPP4A 2 98554293 Missense_Mutation SNP G C3N-01488_T 794546 98554293 143639236 93 24467 RGPD4 0 . GRCh38 2 107871820 107871820 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.3816A>T p.= p.P1272P ENST00000408999 20/23 533 437 96 773 773 0 strelka-varscan-mutect RGPD4,synonymous_variant,p.=,ENST00000408999,NM_182588.2; T ENST00000408999 Transcript synonymous_variant 3893/5464 3816/5277 1272/1758 P ccA/ccT 1 1 RGPD4 HGNC HGNC:32417 protein_coding YES CCDS46381.1 ENSP00000386810 Q7Z3J3 UPI0000418FF7 NM_182588.2 20/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23138:SF86,hmmpanther:PTHR23138 LOW 1 SNV 1 1 PASS rs772961976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 107871820 107871820 A T 1 0 0 0 0 0 0 0 1 13460 204 8 4 4 RGPD4 2 107871820 Silent SNP A C3N-01488_T 9317527 107871820 134321709 94 24468 GLI2 0 . GRCh38 2 120970511 120970511 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.964A>T p.Thr322Ser p.T322S ENST00000452319 7/14 290 228 62 362 361 1 strelka-varscan-mutect GLI2,missense_variant,p.Thr322Ser,ENST00000452319,;GLI2,missense_variant,p.Thr322Ser,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000360874,;GLI2,non_coding_transcript_exon_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,3_prime_UTR_variant,,ENST00000438299,;GLI2,3_prime_UTR_variant,,ENST00000452692,;GLI2,3_prime_UTR_variant,,ENST00000437950,;GLI2,3_prime_UTR_variant,,ENST00000433812,; T ENST00000452319 Transcript missense_variant 1024/6799 964/4761 322/1586 T/S Acc/Tcc 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 tolerated(0.13) 7/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 120970511 120970511 A T 1 0 0 0 0 1 0 0 0 6316 159 6 4 4 GLI2 2 120970511 Missense_Mutation SNP A C3N-01488_T 13098691 120970511 121223018 95 24469 POTEF 0 . GRCh38 2 130075235 130075235 + Frame_Shift_Del DEL C C - rs760191584 C3N-01488_T C3N-01488_N C C c.2237delG p.Gly746AlafsTer20 p.G746Afs*20 ENST00000409914 17/17 572 496 76 790 789 1 sindel-varindel POTEF,frameshift_variant,p.Gly746AlafsTer20,ENST00000409914,NM_001099771.2; - ENST00000409914 Transcript frameshift_variant 2637/3842 2237/3228 746/1075 G/X gGc/gc rs760191584,COSM4747878 1 -1 POTEF HGNC HGNC:33905 protein_coding YES CCDS46409.1 ENSP00000386786 A5A3E0 UPI0000418FEA NM_001099771.2 17/17 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Low_complexity_(Seg):seg,SMART_domains:SM00268,Superfamily_domains:SSF53067 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 130075235 130075235 C - 1 0 1 0 1 0 0 0 0 12379 739 26 0 0 POTEF 2 130075235 Frame_Shift_Del DEL C C3N-01488_T 9104724 130075235 112118294 96 24470 CFC1 0 . GRCh38 2 130598725 130598725 + Missense_Mutation SNP G G T rs777951243 C3N-01488_T C3N-01488_N G G c.164C>A p.Ser55Tyr p.S55Y ENST00000259216 3/6 200 186 14 255 255 0 varscan-mutect CFC1,missense_variant,p.Ser55Tyr,ENST00000615342,NM_001270420.1;CFC1,missense_variant,p.Ser55Tyr,ENST00000621673,NM_001270421.1;CFC1,missense_variant,p.Ser55Tyr,ENST00000259216,NM_032545.3;Metazoa_SRP,upstream_gene_variant,,ENST00000621608,; T ENST00000259216 Transcript missense_variant 427/1046 164/672 55/223 S/Y tCc/tAc rs777951243 1 -1 CFC1 HGNC HGNC:18292 protein_coding YES CCDS2162.1 ENSP00000259216 P0CG37 UPI0000070FF1 NM_032545.3 tolerated(0.65) 3/6 hmmpanther:PTHR14949,hmmpanther:PTHR14949:SF25 MODERATE 1 SNV 1 1 PASS rs777951243 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 130598725 130598725 G T 1 0 0 0 0 1 0 0 0 3038 1174 41 2 2 CFC1 2 130598725 Missense_Mutation SNP G C3N-01488_T 523490 130598725 111594804 97 24471 POTEJ 0 . GRCh38 2 130657103 130657103 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2343G>T p.Lys781Asn p.K781N ENST00000409602 15/15 409 380 29 578 578 0 varscan-mutect POTEJ,missense_variant,p.Lys781Asn,ENST00000409602,NM_001277083.1; T ENST00000409602 Transcript missense_variant 2395/3383 2343/3117 781/1038 K/N aaG/aaT 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0.01) 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 130657103 130657103 G T 1 0 0 0 0 1 0 0 0 12383 933 33 2 2 POTEJ 2 130657103 Missense_Mutation SNP G C3N-01488_T 58378 130657103 111536426 98 24472 POTEJ 0 . GRCh38 2 130657118 130657118 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.2358G>A p.Met786Ile p.M786I ENST00000409602 15/15 260 242 18 384 384 0 varscan-mutect POTEJ,missense_variant,p.Met786Ile,ENST00000409602,NM_001277083.1; A ENST00000409602 Transcript missense_variant 2410/3383 2358/3117 786/1038 M/I atG/atA 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 deleterious_low_confidence(0.01) 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,Prints_domain:PR00190,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 5 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 130657118 130657118 G A 1 0 0 0 0 1 0 0 0 12383 1377 48 3 3 POTEJ 2 130657118 Missense_Mutation SNP G C3N-01488_T 15 130657118 111536411 99 24473 POTEE 0 . GRCh38 2 131264113 131264113 + Silent SNP T T G novel C3N-01488_T C3N-01488_N T T c.2658T>G p.= p.P886P ENST00000356920 15/15 598 499 99 775 774 1 strelka-varscan-mutect POTEE,synonymous_variant,p.=,ENST00000356920,NM_001083538.1;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000613282,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; G ENST00000356920 Transcript synonymous_variant 2994/4159 2658/3228 886/1075 P ccT/ccG 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 15/15 Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS rs1396559721 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 131264113 131264113 T G 1 0 0 0 0 0 0 0 1 12378 1567 55 5 5 POTEE 2 131264113 Silent SNP T C3N-01488_T 606995 131264113 110929416 100 24474 POTEE 0 . GRCh38 2 131264520 131264520 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3065C>A p.Pro1022His p.P1022H ENST00000356920 15/15 61 56 5 143 142 1 varscan-mutect POTEE,missense_variant,p.Pro1022His,ENST00000356920,NM_001083538.1;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000613282,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; A ENST00000356920 Transcript missense_variant 3401/4159 3065/3228 1022/1075 P/H cCt/cAt 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 deleterious_low_confidence(0) 15/15 Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.95231 1 1 1 1 0 A 3 1 80 131264520 131264520 C A 1 0 0 0 0 1 0 0 0 12378 681 24 2 2 POTEE 2 131264520 Missense_Mutation SNP C C3N-01488_T 407 131264520 110929009 101 24475 LRP1B 0 . GRCh38 2 140923050 140923050 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.3234C>G p.Asp1078Glu p.D1078E ENST00000389484 21/91 212 173 39 338 338 0 strelka-varscan-mutect LRP1B,missense_variant,p.Asp1078Glu,ENST00000389484,NM_018557.2;LRP1B,missense_variant,p.Asp223Glu,ENST00000434794,; C ENST00000389484 Transcript missense_variant 4206/16535 3234/13800 1078/4599 D/E gaC/gaG 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 21/91 PROSITE_profiles:PS50068,hmmpanther:PTHR10529:SF105,hmmpanther:PTHR10529,PROSITE_patterns:PS01209,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424,Prints_domain:PR00261 MODERATE 1 SNV 1 1 PASS rs1367877453 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 140923050 140923050 G C 1 0 0 0 0 1 0 0 0 8850 1020 36 4 4 LRP1B 2 140923050 Missense_Mutation SNP G C3N-01488_T 9658530 140923050 101270479 102 24476 FMNL2 0 . GRCh38 2 152611578 152611578 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.1035C>T p.= p.T345T ENST00000288670 11/26 153 135 18 201 201 0 strelka-varscan-mutect FMNL2,synonymous_variant,p.=,ENST00000288670,NM_052905.3;FMNL2,downstream_gene_variant,,ENST00000492942,; T ENST00000288670 Transcript synonymous_variant 1402/5575 1035/3279 345/1092 T acC/acT 1 1 FMNL2 HGNC HGNC:18267 protein_coding YES CCDS46429.1 ENSP00000288670 Q96PY5 UPI0000441EF9 NM_052905.3 11/26 Pfam_domain:PF06367,PROSITE_profiles:PS51232,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF180,SMART_domains:SM01139,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 152611578 152611578 C T 1 0 0 0 0 0 0 0 1 5808 581 21 3 3 FMNL2 2 152611578 Silent SNP C C3N-01488_T 11688528 152611578 89581951 103 24477 SCN1A 0 . GRCh38 2 166039451 166039451 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.2561G>T p.Gly854Val p.G854V ENST00000303395 16/28 205 164 41 327 327 0 strelka-varscan-mutect SCN1A,missense_variant,p.Gly843Val,ENST00000635776,;SCN1A,missense_variant,p.Gly843Val,ENST00000637988,;SCN1A,missense_variant,p.Gly854Val,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Gly843Val,ENST00000635750,;SCN1A,missense_variant,p.Gly854Val,ENST00000423058,;SCN1A,missense_variant,p.Gly843Val,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Gly826Val,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;AC010127.3,downstream_gene_variant,,ENST00000597623,;SCN1A,3_prime_UTR_variant,,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000636759,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,;SCN1A,upstream_gene_variant,,ENST00000637038,; A ENST00000303395 Transcript missense_variant 2979/8533 2561/6030 854/2009 G/V gGa/gTa CD061467 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 deleterious(0) 16/28 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Superfamily_domains:SSF81324 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 166039451 166039451 C A 1 0 0 0 0 1 0 0 0 14183 855 30 2 2 SCN1A 2 166039451 Missense_Mutation SNP C C3N-01488_T 13427873 166039451 76154078 104 24478 RAPGEF4 0 . GRCh38 2 172988809 172988809 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.1344A>G p.= p.V448V ENST00000397081 14/31 190 152 38 253 252 1 strelka-varscan-mutect RAPGEF4,synonymous_variant,p.=,ENST00000397081,NM_007023.3;RAPGEF4,synonymous_variant,p.=,ENST00000397087,NM_001100397.1;RAPGEF4,synonymous_variant,p.=,ENST00000409036,;RAPGEF4,synonymous_variant,p.=,ENST00000540783,NM_001282899.1;RAPGEF4,synonymous_variant,p.=,ENST00000538974,NM_001282900.1;RAPGEF4,synonymous_variant,p.=,ENST00000535187,NM_001282901.1;RAPGEF4,non_coding_transcript_exon_variant,,ENST00000473043,;RAPGEF4,downstream_gene_variant,,ENST00000459852,; G ENST00000397081 Transcript synonymous_variant 1487/4299 1344/3036 448/1011 V gtA/gtG 1 1 RAPGEF4 HGNC HGNC:16626 protein_coding YES CCDS42775.1 ENSP00000380271 Q8WZA2 UPI000006D4C7 NM_007023.3 14/31 Gene3D:2.60.120.10,Pfam_domain:PF00027,PROSITE_profiles:PS50042,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF175,SMART_domains:SM00100,Superfamily_domains:SSF51206 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 172988809 172988809 A G 1 0 0 0 0 0 0 0 1 13205 407 15 5 5 RAPGEF4 2 172988809 Silent SNP A C3N-01488_T 6949358 172988809 69204720 105 24479 TTN 0 . GRCh38 2 178636155 178636155 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.41416A>G p.Lys13806Glu p.K13806E ENST00000589042 226/363 107 90 17 154 153 1 strelka-varscan-mutect TTN,missense_variant,p.Lys13806Glu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Lys12165Glu,ENST00000591111,;TTN,missense_variant,p.Lys12165Glu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Lys11238Glu,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Lys4741Glu,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Lys4933Glu,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Lys4866Glu,ENST00000359218,NM_133432.3;TTN,downstream_gene_variant,,ENST00000414766,;TTN,downstream_gene_variant,,ENST00000446966,;TTN,downstream_gene_variant,,ENST00000426232,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000626954,;TTN-AS1,upstream_gene_variant,,ENST00000431752,;TTN-AS1,downstream_gene_variant,,ENST00000589907,;TTN-AS1,upstream_gene_variant,,ENST00000418062,;TTN-AS1,downstream_gene_variant,,ENST00000628296,; C ENST00000589042 Transcript missense_variant 41641/109224 41416/107976 13806/35991 K/E Aaa/Gaa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 226/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 178636155 178636155 T C 1 0 0 0 0 1 0 0 0 17245 1821 63 5 5 TTN 2 178636155 Missense_Mutation SNP T C3N-01488_T 5647346 178636155 63557374 106 24480 TTN 0 . GRCh38 2 178728652 178728652 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.19274T>C p.Ile6425Thr p.I6425T ENST00000589042 66/363 164 136 28 253 253 0 strelka-varscan-mutect TTN,missense_variant,p.Ile6425Thr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ile6108Thr,ENST00000591111,;TTN,missense_variant,p.Ile6108Thr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ile5181Thr,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,;RP11-171I2.1,downstream_gene_variant,,ENST00000590024,;TTN-AS1,upstream_gene_variant,,ENST00000582847,; G ENST00000589042 Transcript missense_variant 19499/109224 19274/107976 6425/35991 I/T aTa/aCa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 66/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 178728652 178728652 A G 1 0 0 0 0 1 0 0 0 17245 449 16 5 5 TTN 2 178728652 Missense_Mutation SNP A C3N-01488_T 92497 178728652 63464877 107 24481 ZNF385B 0 . GRCh38 2 179446747 179446747 + Missense_Mutation SNP T T G novel C3N-01488_T C3N-01488_N T T c.694A>C p.Ser232Arg p.S232R ENST00000410066 7/10 114 106 8 163 163 0 strelka-varscan-mutect ZNF385B,missense_variant,p.Ser232Arg,ENST00000410066,NM_152520.4;ZNF385B,missense_variant,p.Ser156Arg,ENST00000409343,NM_001113397.1;ZNF385B,missense_variant,p.Ser130Arg,ENST00000336917,NM_001113398.1;ZNF385B,missense_variant,p.Ser130Arg,ENST00000409692,NM_001282725.1;ZNF385B,missense_variant,p.Ser130Arg,ENST00000457304,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000466398,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000469551,;ZNF385B,non_coding_transcript_exon_variant,,ENST00000475539,; G ENST00000410066 Transcript missense_variant 1298/3288 694/1416 232/471 S/R Agc/Cgc 1 -1 ZNF385B HGNC HGNC:26332 protein_coding YES CCDS33339.1 ENSP00000386845 Q569K4 UPI00004F9C24 NM_152520.4 tolerated(0.51) 7/10 Low_complexity_(Seg):seg,hmmpanther:PTHR23067:SF8,hmmpanther:PTHR23067 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.21546 1 1 1 1 0 G 3 3 80 179446747 179446747 T G 1 0 0 0 0 1 0 0 0 18449 1580 55 5 5 ZNF385B 2 179446747 Missense_Mutation SNP T C3N-01488_T 718095 179446747 62746782 108 24482 PLCL1 0 . GRCh38 2 198084768 198084768 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.1251A>T p.= p.L417L ENST00000428675 2/6 156 131 25 240 240 0 strelka-varscan-mutect PLCL1,synonymous_variant,p.=,ENST00000437704,;PLCL1,synonymous_variant,p.=,ENST00000428675,NM_006226.3;PLCL1,synonymous_variant,p.=,ENST00000487695,;PLCL1,3_prime_UTR_variant,,ENST00000435320,; T ENST00000428675 Transcript synonymous_variant 1649/5125 1251/3288 417/1095 L ctA/ctT 1 1 PLCL1 HGNC HGNC:9063 protein_coding YES CCDS2326.2 ENSP00000402861 Q15111 UPI000165BCF5 NM_006226.3 2/6 PROSITE_profiles:PS50007,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF102,Pfam_domain:PF00388,Gene3D:3.20.20.190,SMART_domains:SM00148,Superfamily_domains:SSF51695,Prints_domain:PR00390 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 198084768 198084768 A T 1 0 0 0 0 0 0 0 1 12133 349 13 4 4 PLCL1 2 198084768 Silent SNP A C3N-01488_T 18638021 198084768 44108761 109 24483 MAP2 0 . GRCh38 2 209693684 209693684 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1514A>T p.Gln505Leu p.Q505L ENST00000360351 7/15 148 114 34 211 211 0 strelka-varscan-mutect MAP2,missense_variant,p.Gln505Leu,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Gln501Leu,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; T ENST00000360351 Transcript missense_variant 2020/9711 1514/5484 505/1827 Q/L cAa/cTa 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious_low_confidence(0.01) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 209693684 209693684 A T 1 0 0 0 0 1 0 0 0 9157 130 5 4 4 MAP2 2 209693684 Missense_Mutation SNP A C3N-01488_T 11608916 209693684 32499845 110 24484 SPAG16 0 . GRCh38 2 214014003 214014003 + Nonsense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.1453G>T p.Glu485Ter p.E485* ENST00000331683 13/16 205 189 16 252 252 0 strelka-varscan-mutect SPAG16,stop_gained,p.Glu485Ter,ENST00000331683,NM_024532.4;SPAG16,stop_gained,p.Glu109Ter,ENST00000451561,;SPAG16,non_coding_transcript_exon_variant,,ENST00000480494,;SPAG16,3_prime_UTR_variant,,ENST00000452556,;SPAG16,3_prime_UTR_variant,,ENST00000406979,; T ENST00000331683 Transcript stop_gained 1548/2177 1453/1896 485/631 E/* Gag/Tag COSM4624556,COSM5517311 1 1 SPAG16 HGNC HGNC:23225 protein_coding YES CCDS2396.1 ENSP00000332592 Q8N0X2 UPI00001AFF12 NM_024532.4 13/16 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR14604:SF3,hmmpanther:PTHR14604,Pfam_domain:PF00400,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 214014003 214014003 G T 1 0 0 0 0 0 1 0 0 15309 1291 45 2 2 SPAG16 2 214014003 Nonsense_Mutation SNP G C3N-01488_T 4320319 214014003 28179526 111 24485 CFAP65 0 . GRCh38 2 219010554 219010554 + Missense_Mutation SNP G G C C3N-01488_T C3N-01488_N G G c.4300C>G p.Pro1434Ala p.P1434A ENST00000341552 26/35 200 173 27 281 280 1 strelka-varscan-mutect CFAP65,missense_variant,p.Pro1434Ala,ENST00000341552,NM_194302.3;CFAP65,missense_variant,p.Pro1434Ala,ENST00000453220,;AC097468.4,intron_variant,,ENST00000441450,; C ENST00000341552 Transcript missense_variant 4384/5953 4300/5778 1434/1925 P/A Cct/Gct COSM1016539 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 deleterious(0.02) 26/35 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF223 1 MODERATE SNV 5 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 80 219010554 219010554 G C 1 0 0 0 0 1 0 0 0 3029 1203 42 4 4 CFAP65 2 219010554 Missense_Mutation SNP G C3N-01488_T 4996551 219010554 23182975 112 24486 DAW1 0 . GRCh38 2 227885349 227885349 + Splice_Site SNP A A T novel C3N-01488_T C3N-01488_N A A c.41-2A>T p.X14_splice ENST00000309931 100 90 10 146 146 0 strelka-mutect DAW1,splice_acceptor_variant,,ENST00000373666,;DAW1,splice_acceptor_variant,,ENST00000309931,NM_178821.1;DAW1,splice_acceptor_variant,,ENST00000440997,;SNORA25,upstream_gene_variant,,ENST00000607153,;DAW1,upstream_gene_variant,,ENST00000472604,;DAW1,splice_acceptor_variant,,ENST00000454999,; T ENST00000309931 Transcript splice_acceptor_variant -/1704 41/1248 14/415 1 1 DAW1 HGNC HGNC:26383 protein_coding YES CCDS2470.1 ENSP00000311899 Q8N136 A0A140VKH6 UPI000006EAC6 NM_178821.1 1/12 HIGH 1 SNV 1 1 PASS rs974168180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 80 227885349 227885349 A T 1 0 0 0 0 0 0 1 0 4043 434 15 4 4 DAW1 2 227885349 Splice_Site SNP A C3N-01488_T 8874795 227885349 14308180 113 24487 SPHKAP 0 . GRCh38 2 228017187 228017187 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.3667C>A p.Leu1223Met p.L1223M ENST00000392056 7/12 169 146 23 212 212 0 strelka-varscan-mutect SPHKAP,missense_variant,p.Leu1223Met,ENST00000392056,NM_001142644.1;SPHKAP,missense_variant,p.Leu1223Met,ENST00000344657,NM_030623.3; T ENST00000392056 Transcript missense_variant 3714/6917 3667/5103 1223/1700 L/M Ctg/Atg COSM5261127,COSM5261128 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 deleterious(0) 7/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 228017187 228017187 G T 1 0 0 0 0 1 0 0 0 15399 991 35 2 2 SPHKAP 2 228017187 Missense_Mutation SNP G C3N-01488_T 131838 228017187 14176342 114 24488 COPS7B 0 . GRCh38 2 231794302 231794302 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.278A>G p.Gln93Arg p.Q93R ENST00000410017 4/8 185 154 31 257 257 0 strelka-varscan-mutect COPS7B,missense_variant,p.Gln93Arg,ENST00000373608,NM_001282950.1;COPS7B,missense_variant,p.Gln93Arg,ENST00000350033,NM_022730.2;COPS7B,missense_variant,p.Gln93Arg,ENST00000410017,NM_001308381.1;COPS7B,missense_variant,p.Gln93Arg,ENST00000410024,;COPS7B,missense_variant,p.Gln59Arg,ENST00000409295,NM_001282949.1;COPS7B,5_prime_UTR_variant,,ENST00000620578,NM_001282952.1;COPS7B,5_prime_UTR_variant,,ENST00000409091,;COPS7B,intron_variant,,ENST00000611614,NM_001282951.1;COPS7B,intron_variant,,ENST00000412591,;COPS7B,upstream_gene_variant,,ENST00000449174,;COPS7B,downstream_gene_variant,,ENST00000631349,;COPS7B,3_prime_UTR_variant,,ENST00000413197,;COPS7B,3_prime_UTR_variant,,ENST00000449784,;COPS7B,3_prime_UTR_variant,,ENST00000436564,;COPS7B,non_coding_transcript_exon_variant,,ENST00000461350,;COPS7B,non_coding_transcript_exon_variant,,ENST00000488111,;COPS7B,non_coding_transcript_exon_variant,,ENST00000474042,;COPS7B,intron_variant,,ENST00000412922,;COPS7B,downstream_gene_variant,,ENST00000452375,;COPS7B,downstream_gene_variant,,ENST00000466901,;COPS7B,downstream_gene_variant,,ENST00000432387,;COPS7B,downstream_gene_variant,,ENST00000357490,;COPS7B,downstream_gene_variant,,ENST00000450501,;RP11-690I21.1,upstream_gene_variant,,ENST00000452854,; G ENST00000410017 Transcript missense_variant 388/2051 278/837 93/278 Q/R cAg/cGg 1 1 COPS7B HGNC HGNC:16760 protein_coding YES CCDS77539.1 ENSP00000386880 J3KQ41 UPI0000E1FA1C NM_001308381.1 tolerated(0.55) 4/8 Pfam_domain:PF01399,hmmpanther:PTHR15350,hmmpanther:PTHR15350:SF8,SMART_domains:SM00088,SMART_domains:SM00753 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 231794302 231794302 A G 1 0 0 0 0 1 0 0 0 3532 188 7 5 5 COPS7B 2 231794302 Missense_Mutation SNP A C3N-01488_T 3777115 231794302 10399227 115 24489 USP40 0 . GRCh38 2 233549173 233549173 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.930A>T p.Lys310Asn p.K310N ENST00000450966 7/31 154 145 9 241 241 0 strelka-varscan-mutect USP40,missense_variant,p.Lys298Asn,ENST00000251722,;USP40,missense_variant,p.Lys310Asn,ENST00000450966,NM_018218.2;USP40,missense_variant,p.Lys298Asn,ENST00000427112,;RP11-289A15.1,downstream_gene_variant,,ENST00000604535,; A ENST00000450966 Transcript missense_variant 930/5616 930/3744 310/1247 K/N aaA/aaT 1 -1 USP40 HGNC HGNC:20069 protein_coding YES CCDS46547.1 ENSP00000415434 Q9NVE5 UPI0000232F06 NM_018218.2 deleterious(0) 7/31 Pfam_domain:PF00443,PROSITE_patterns:PS00973,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF514,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 233549173 233549173 T A 1 0 0 0 0 1 0 0 0 17614 1606 56 4 4 USP40 2 233549173 Missense_Mutation SNP T C3N-01488_T 1754871 233549173 8644356 116 24490 TRAF3IP1 0 . GRCh38 2 238328935 238328935 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.508G>A p.Asp170Asn p.D170N ENST00000373327 5/17 57 43 14 110 109 1 strelka-mutect TRAF3IP1,missense_variant,p.Asp170Asn,ENST00000373327,NM_015650.3;TRAF3IP1,missense_variant,p.Asp170Asn,ENST00000391993,NM_001139490.1;TRAF3IP1,3_prime_UTR_variant,,ENST00000409739,; A ENST00000373327 Transcript missense_variant 730/4279 508/2076 170/691 D/N Gac/Aac 1 1 TRAF3IP1 HGNC HGNC:17861 protein_coding YES CCDS33415.1 ENSP00000362424 Q8TDR0 UPI0000070E5D NM_015650.3 tolerated(0.97) 5/17 Pfam_domain:PF10243,hmmpanther:PTHR31363,hmmpanther:PTHR31363:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 238328935 238328935 G A 1 0 0 0 0 1 0 0 0 16923 942 33 3 3 TRAF3IP1 2 238328935 Missense_Mutation SNP G C3N-01488_T 4779762 238328935 3864594 117 24491 KIF1A 0 . GRCh38 2 240737090 240737090 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3980G>T p.Gly1327Val p.G1327V ENST00000498729 38/49 128 111 17 174 173 1 strelka-varscan-mutect KIF1A,missense_variant,p.Gly1327Val,ENST00000498729,NM_001244008.1;KIF1A,missense_variant,p.Gly1226Val,ENST00000320389,NM_004321.6;KIF1A,missense_variant,p.Gly1327Val,ENST00000404283,;KIF1A,missense_variant,p.Gly150Val,ENST00000431776,;KIF1A,non_coding_transcript_exon_variant,,ENST00000494452,; A ENST00000498729 Transcript missense_variant 4227/9223 3980/5376 1327/1791 G/V gGa/gTa 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 tolerated(0.13) 38/49 Pfam_domain:PF12473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 240737090 240737090 C A 1 0 0 0 0 1 0 0 0 8147 855 30 2 2 KIF1A 2 240737090 Missense_Mutation SNP C C3N-01488_T 2408155 240737090 1456439 118 24492 CROCC2 0 . GRCh38 2 240946180 240946180 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2290G>T p.Ala764Ser p.A764S ENST00000443866 15/32 94 84 10 96 96 0 strelka-varscan-mutect CROCC2,missense_variant,p.Ala764Ser,ENST00000443866,;CROCC2,upstream_gene_variant,,ENST00000480779,; T ENST00000443866 Transcript missense_variant 2474/5382 2290/4968 764/1655 A/S Gcc/Tcc 1 1 CROCC2 HGNC HGNC:51677 protein_coding YES ENSP00000397968 H7BZ55 UPI0004F2364A tolerated(0.11) 15/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159:SF16,hmmpanther:PTHR23159 MODERATE 1 SNV 5 1 PASS . . 0 203 5 2 0 0 0 0 -15.98063 0.9999214 1 1 1 0 T 3 4 80 240946180 240946180 G T 1 0 0 0 0 1 0 0 0 3695 1203 42 2 2 CROCC2 2 240946180 Missense_Mutation SNP G C3N-01488_T 209090 240946180 1247349 119 24493 CHL1 0 . GRCh38 3 377870 377870 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1804C>A p.Gln602Lys p.Q602K ENST00000256509 16/28 138 117 21 270 269 1 strelka-varscan-mutect CHL1,missense_variant,p.Gln602Lys,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Gln602Lys,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Gln586Lys,ENST00000397491,NM_001253387.1;CHL1-AS1,intron_variant,,ENST00000417612,;CHL1-AS1,upstream_gene_variant,,ENST00000608098,;CHL1,non_coding_transcript_exon_variant,,ENST00000470880,;CHL1,upstream_gene_variant,,ENST00000470005,;CHL1,3_prime_UTR_variant,,ENST00000453040,; A ENST00000256509 Transcript missense_variant 2446/8023 1804/3675 602/1224 Q/K Caa/Aaa 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(0.07) 16/28 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 377870 377870 C A 1 0 0 0 0 1 0 0 0 3108 595 21 2 2 CHL1 3 377870 Missense_Mutation SNP C C3N-01488_T 377870 197917689 120 24494 CNTN4 0 . GRCh38 3 3043070 3043070 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2605G>T p.Gly869Cys p.G869C ENST00000397461 21/24 419 339 80 656 656 0 strelka-varscan-mutect CNTN4,missense_variant,p.Gly869Cys,ENST00000397461,NM_001206955.1;CNTN4,missense_variant,p.Gly869Cys,ENST00000418658,NM_175607.2;CNTN4,missense_variant,p.Gly869Cys,ENST00000427331,;CNTN4,missense_variant,p.Gly541Cys,ENST00000397459,NM_001206956.1,NM_175613.2;CNTN4-AS1,intron_variant,,ENST00000442749,;CNTN4-AS1,intron_variant,,ENST00000629672,;CNTN4,non_coding_transcript_exon_variant,,ENST00000484686,;CNTN4,downstream_gene_variant,,ENST00000427741,; T ENST00000397461 Transcript missense_variant 2989/5198 2605/3081 869/1026 G/C Ggc/Tgc 1 1 CNTN4 HGNC HGNC:2174 protein_coding YES CCDS43041.1 ENSP00000380602 Q8IWV2 A0A024R2E5 UPI000007446C NM_001206955.1 deleterious(0) 21/24 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF568,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS rs1194216177 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 3043070 3043070 G T 1 0 0 0 0 1 0 0 0 3424 1000 35 2 2 CNTN4 3 3043070 Missense_Mutation SNP G C3N-01488_T 2665200 3043070 195252489 121 24495 SRGAP3 0 . GRCh38 3 9025264 9025264 + Missense_Mutation SNP T T C C3N-01488_T C3N-01488_N T T c.1675A>G p.Arg559Gly p.R559G ENST00000383836 14/22 398 327 71 530 530 0 strelka-varscan-mutect SRGAP3,missense_variant,p.Arg559Gly,ENST00000383836,NM_014850.3;SRGAP3,missense_variant,p.Arg535Gly,ENST00000360413,NM_001033117.2;SRGAP3,3_prime_UTR_variant,,ENST00000618999,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000433332,;SRGAP3,non_coding_transcript_exon_variant,,ENST00000475560,; C ENST00000383836 Transcript missense_variant 2103/8656 1675/3300 559/1099 R/G Aga/Gga COSM328515 1 -1 SRGAP3 HGNC HGNC:19744 protein_coding YES CCDS2572.1 ENSP00000373347 O43295 UPI0000074099 NM_014850.3 deleterious(0) 14/22 PROSITE_profiles:PS50238,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF8,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 9025264 9025264 T C 1 0 0 0 0 1 0 0 0 15508 1565 54 5 5 SRGAP3 3 9025264 Missense_Mutation SNP T C3N-01488_T 5982194 9025264 189270295 122 24496 MKRN2OS 0 . GRCh38 3 12545455 12545455 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.10G>T p.Ala4Ser p.A4S ENST00000564146 1/4 75 52 23 120 120 0 strelka-varscan-mutect MKRN2OS,missense_variant,p.Ala4Ser,ENST00000564146,NM_001195279.1;MKRN2OS,intron_variant,,ENST00000567514,;MKRN2OS,missense_variant,p.Ala4Ser,ENST00000561645,; A ENST00000564146 Transcript missense_variant 102/985 10/672 4/223 A/S Gca/Tca 1 -1 MKRN2OS HGNC HGNC:40375 protein_coding YES CCDS58816.1 ENSP00000455385 H3BPM6 UPI0001E13BF6 NM_001195279.1 tolerated_low_confidence(0.83) 1/4 MODERATE 1 SNV 5 1 PASS rs1235025623 . 0 198 12 0 0 0 0 0 -20 0.9999795 1 1 1 0 A 3 1 80 12545455 12545455 C A 1 0 0 0 0 1 0 0 0 9575 768 27 1 1 MKRN2OS 3 12545455 Missense_Mutation SNP C C3N-01488_T 3520191 12545455 185750104 123 24497 CCDC174 0 . GRCh38 3 14651853 14651853 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.17A>T p.Lys6Met p.K6M ENST00000383794 1/11 314 272 42 384 384 0 strelka-varscan-mutect CCDC174,missense_variant,p.Lys6Met,ENST00000383794,NM_016474.4;CCDC174,missense_variant,p.Lys6Met,ENST00000303688,;CCDC174,5_prime_UTR_variant,,ENST00000611584,;AC090952.5,upstream_gene_variant,,ENST00000424242,;CCDC174,non_coding_transcript_exon_variant,,ENST00000465759,;CCDC174,non_coding_transcript_exon_variant,,ENST00000463438,; T ENST00000383794 Transcript missense_variant 90/2942 17/1404 6/467 K/M aAg/aTg 1 1 CCDC174 HGNC HGNC:28033 protein_coding YES CCDS2620.2 ENSP00000373304 Q6PII3 UPI00004120DD NM_016474.4 deleterious(0) 1/11 hmmpanther:PTHR15885 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 14651853 14651853 A T 1 0 0 0 0 1 0 0 0 2491 72 3 4 4 CCDC174 3 14651853 Missense_Mutation SNP A C3N-01488_T 2106398 14651853 183643706 124 24498 RARB 0 . GRCh38 3 25569760 25569760 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.451G>T p.Val151Phe p.V151F ENST00000330688 4/8 78 66 12 127 127 0 strelka-varscan-mutect RARB,missense_variant,p.Val151Phe,ENST00000330688,NM_001290266.1,NM_001290277.1,NM_000965.4;RARB,missense_variant,p.Val39Phe,ENST00000437042,NM_001290276.1,NM_016152.3;RARB,missense_variant,p.Val39Phe,ENST00000458646,NM_001290217.1;RARB,missense_variant,p.Val158Phe,ENST00000383772,NM_001290216.1;RARB,splice_region_variant,,ENST00000462272,;RARB,splice_region_variant,,ENST00000480001,;RARB,intron_variant,,ENST00000479097,; T ENST00000330688 Transcript missense_variant,splice_region_variant 872/3084 451/1347 151/448 V/F Gtc/Ttc 1 1 RARB HGNC HGNC:9865 protein_coding YES CCDS2642.1 ENSP00000332296 P10826 F1D8S6 UPI000002B2CB NM_001290266.1,NM_001290277.1,NM_000965.4 deleterious(0) 4/8 Gene3D:3.30.50.10,Prints_domain:PR00398,Prints_domain:PR01292,PROSITE_profiles:PS51030,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF115,Superfamily_domains:SSF48508,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 80 25569760 25569760 G T 1 0 0 0 0 1 0 0 0 13212 1391 48 2 2 RARB 3 25569760 Missense_Mutation SNP G C3N-01488_T 10917907 25569760 172725799 125 24499 NEK10 0 . GRCh38 3 27119847 27119847 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.3274C>A p.Pro1092Thr p.P1092T ENST00000429845 36/39 240 202 38 348 348 0 strelka-varscan-mutect NEK10,missense_variant,p.Pro1092Thr,ENST00000429845,NM_152534.4;NEK10,missense_variant,p.Pro404Thr,ENST00000295720,NM_001304384.1;NEK10,missense_variant,p.Pro394Thr,ENST00000383771,NM_001031741.3;NEK10,missense_variant,p.Pro338Thr,ENST00000383770,; T ENST00000429845 Transcript missense_variant 3637/4250 3274/3519 1092/1172 P/T Ccg/Acg 1 -1 NEK10 HGNC HGNC:18592 protein_coding ENSP00000395849 Q6ZWH5 UPI0000EE2A86 NM_152534.4 tolerated(0.31) 36/39 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 27119847 27119847 G T 1 0 0 0 0 1 0 0 0 10350 1261 44 2 2 NEK10 3 27119847 Missense_Mutation SNP G C3N-01488_T 1550087 27119847 171175712 126 24500 TGFBR2 0 . GRCh38 3 30672214 30672214 + Frame_Shift_Del DEL G G - novel C3N-01488_T C3N-01488_N G G c.1108delG p.Glu370ArgfsTer43 p.E370Rfs*43 ENST00000359013 5/8 80 67 13 141 141 0 sindel-varindel-pindel TGFBR2,frameshift_variant,p.Glu345ArgfsTer43,ENST00000295754,NM_003242.5;TGFBR2,frameshift_variant,p.Glu370ArgfsTer43,ENST00000359013,NM_001024847.2; - ENST00000359013 Transcript frameshift_variant 1389/4605 1106/1779 369/592 W/X tGg/tg 1 1 TGFBR2 HGNC HGNC:11773 protein_coding YES CCDS33727.1 ENSP00000351905 P37173 D2JYI1 UPI000053030E NM_001024847.2 5/8 PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF55,PIRSF_domain:PIRSF037393,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 deletion 1 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 - 7 5 80 30672214 30672214 G - 1 0 1 0 1 0 0 0 0 16255 1357 47 0 0 TGFBR2 3 30672214 Frame_Shift_Del DEL G C3N-01488_T 3552367 30672214 167623345 127 24501 TMPPE 0 . GRCh38 3 33093636 33093636 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.560C>T p.Pro187Leu p.P187L ENST00000342462 2/2 152 141 11 204 203 1 strelka-varscan-mutect TMPPE,missense_variant,p.Pro187Leu,ENST00000342462,NM_001039770.2;TMPPE,missense_variant,p.Pro50Leu,ENST00000416695,NM_001136238.1;GLB1,intron_variant,,ENST00000307363,NM_000404.2;GLB1,intron_variant,,ENST00000399402,NM_001079811.1;GLB1,intron_variant,,ENST00000307377,NM_001135602.1;GLB1,intron_variant,,ENST00000440656,;GLB1,intron_variant,,ENST00000415454,;GLB1,intron_variant,,ENST00000436768,;GLB1,intron_variant,,ENST00000450835,;GLB1,intron_variant,,ENST00000498537,;GLB1,intron_variant,,ENST00000464355,;GLB1,intron_variant,,ENST00000485698,;GLB1,intron_variant,,ENST00000482097,;GLB1,intron_variant,,ENST00000438227,; A ENST00000342462 Transcript missense_variant 751/3962 560/1362 187/453 P/L cCc/cTc 1 -1 TMPPE HGNC HGNC:33865 protein_coding YES CCDS33732.1 ENSP00000343398 Q6ZT21 UPI000022BF97 NM_001039770.2 deleterious(0) 2/2 hmmpanther:PTHR31302,hmmpanther:PTHR31302:SF7 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 33093636 33093636 G A 1 0 0 0 0 1 0 0 0 16714 1232 43 3 3 TMPPE 3 33093636 Missense_Mutation SNP G C3N-01488_T 2421422 33093636 165201923 128 24502 XYLB 0 . GRCh38 3 38362956 38362956 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.230A>G p.Glu77Gly p.E77G ENST00000207870 4/19 77 67 10 64 64 0 strelka-varscan-mutect XYLB,missense_variant,p.Glu77Gly,ENST00000207870,NM_005108.3;XYLB,upstream_gene_variant,,ENST00000487569,;XYLB,intron_variant,,ENST00000424034,; G ENST00000207870 Transcript missense_variant 320/3664 230/1611 77/536 E/G gAg/gGg 1 1 XYLB HGNC HGNC:12839 protein_coding YES CCDS2678.1 ENSP00000207870 O75191 UPI0000160544 NM_005108.3 tolerated(0.13) 4/19 hmmpanther:PTHR10196,hmmpanther:PTHR10196:SF57,Gene3D:3.30.420.40,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -16.96163 0.9999974 1 1 1 0 G 3 3 80 38362956 38362956 A G 1 0 0 0 0 1 0 0 0 18021 304 11 5 5 XYLB 3 38362956 Missense_Mutation SNP A C3N-01488_T 5269320 38362956 159932603 129 24503 ZNF35 0 . GRCh38 3 44658882 44658882 + Silent SNP T T C novel C3N-01488_T C3N-01488_N T T c.519T>C p.= p.D173D ENST00000396056 4/4 164 155 9 277 277 0 strelka-varscan-mutect ZNF35,synonymous_variant,p.=,ENST00000396056,NM_003420.3;ZNF35,3_prime_UTR_variant,,ENST00000296092,;ZNF35,3_prime_UTR_variant,,ENST00000453164,;ZNF35,downstream_gene_variant,,ENST00000415571,;ZNF35,downstream_gene_variant,,ENST00000399560,;RP11-944L7.4,intron_variant,,ENST00000457331,; C ENST00000396056 Transcript synonymous_variant 754/2661 519/1584 173/527 D gaT/gaC 1 1 ZNF35 HGNC HGNC:13099 protein_coding YES CCDS2718.2 ENSP00000379368 P13682 UPI000020A5BF NM_003420.3 4/4 hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF60 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 44658882 44658882 T C 1 0 0 0 0 0 0 0 1 18434 1490 52 5 5 ZNF35 3 44658882 Silent SNP T C3N-01488_T 6295926 44658882 153636677 130 24504 CELSR3 0 . GRCh38 3 48656788 48656788 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.4309G>T p.Asp1437Tyr p.D1437Y ENST00000164024 2/35 80 68 12 95 94 1 strelka-varscan CELSR3,missense_variant,p.Asp1437Tyr,ENST00000164024,NM_001407.2; A ENST00000164024 Transcript missense_variant 4590/11956 4309/9939 1437/3312 D/Y Gac/Tac 1 -1 CELSR3 HGNC HGNC:3230 protein_coding YES CCDS2775.1 ENSP00000164024 Q9NYQ7 UPI00001AE5A6 NM_001407.2 deleterious(0) 2/35 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF38,SMART_domains:SM00179,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 48656788 48656788 C A 1 0 0 0 0 1 0 0 0 2930 884 31 1 1 CELSR3 3 48656788 Missense_Mutation SNP C C3N-01488_T 3997906 48656788 149638771 131 24505 LRTM1 0 . GRCh38 3 54918732 54918732 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.765G>T p.= p.L255L ENST00000273286 3/3 142 122 20 221 220 1 strelka-varscan LRTM1,synonymous_variant,p.=,ENST00000273286,NM_020678.3;LRTM1,synonymous_variant,p.=,ENST00000493075,NM_001304389.1;CACNA2D3,intron_variant,,ENST00000474759,NM_018398.2;CACNA2D3,intron_variant,,ENST00000288197,;CACNA2D3,intron_variant,,ENST00000415676,;CACNA2D3,intron_variant,,ENST00000490478,;CACNA2D3,intron_variant,,ENST00000620722,;CACNA2D3,intron_variant,,ENST00000471363,; A ENST00000273286 Transcript synonymous_variant 928/1423 765/1038 255/345 L ctG/ctT 1 -1 LRTM1 HGNC HGNC:25023 protein_coding YES CCDS2876.1 ENSP00000273286 Q9HBL6 UPI000006CEEC NM_020678.3 3/3 hmmpanther:PTHR24369:SF18,hmmpanther:PTHR24369 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 54918732 54918732 C A 1 0 0 0 0 0 0 0 1 8950 813 29 2 2 LRTM1 3 54918732 Silent SNP C C3N-01488_T 6261944 54918732 143376827 132 24506 ERC2 0 . GRCh38 3 56434994 56434994 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.14C>A p.Ala5Glu p.A5E ENST00000288221 2/18 90 72 18 147 147 0 strelka-varscan ERC2,missense_variant,p.Ala5Glu,ENST00000288221,NM_015576.1;ERC2,missense_variant,p.Ala5Glu,ENST00000612797,;ERC2,non_coding_transcript_exon_variant,,ENST00000472917,;ERC2,upstream_gene_variant,,ENST00000477381,;ERC2,missense_variant,p.Ala5Glu,ENST00000460849,; T ENST00000288221 Transcript missense_variant 270/6138 14/2874 5/957 A/E gCa/gAa 1 -1 ERC2 HGNC HGNC:31922 protein_coding YES CCDS46851.1 ENSP00000288221 O15083 UPI00001C1572 NM_015576.1 deleterious_low_confidence(0) 2/18 hmmpanther:PTHR18861 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 56434994 56434994 G T 1 0 0 0 0 1 0 0 0 5060 1319 46 2 2 ERC2 3 56434994 Missense_Mutation SNP G C3N-01488_T 1516262 56434994 141860565 133 24507 CADPS 0 . GRCh38 3 62753639 62753639 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.690G>T p.Lys230Asn p.K230N ENST00000383710 3/30 330 286 44 430 430 0 strelka-varscan CADPS,missense_variant,p.Lys230Asn,ENST00000383710,NM_003716.3;CADPS,missense_variant,p.Lys230Asn,ENST00000612439,;CADPS,missense_variant,p.Lys230Asn,ENST00000357948,NM_183393.2;CADPS,missense_variant,p.Lys230Asn,ENST00000283269,NM_183394.2;CADPS,missense_variant,p.Lys230Asn,ENST00000490353,; A ENST00000383710 Transcript missense_variant 1040/5471 690/4062 230/1353 K/N aaG/aaT COSM4556410,COSM4556411 1 -1 CADPS HGNC HGNC:1426 protein_coding YES CCDS46858.1 ENSP00000373215 Q9ULU8 UPI00001C036A NM_003716.3 deleterious(0.01) 3/30 hmmpanther:PTHR12166:SF6,hmmpanther:PTHR12166 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 62753639 62753639 C A 1 0 0 0 0 1 0 0 0 2260 680 24 2 2 CADPS 3 62753639 Missense_Mutation SNP C C3N-01488_T 6318645 62753639 135541920 134 24508 CNTN3 0 . GRCh38 3 74299887 74299887 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.2147A>G p.Glu716Gly p.E716G ENST00000263665 16/22 108 97 11 150 150 0 strelka-varscan CNTN3,missense_variant,p.Glu716Gly,ENST00000263665,NM_020872.2; C ENST00000263665 Transcript missense_variant 2175/4948 2147/3087 716/1028 E/G gAa/gGa 1 -1 CNTN3 HGNC HGNC:2173 protein_coding YES CCDS33790.1 ENSP00000263665 Q9P232 UPI00001A7974 NM_020872.2 deleterious(0) 16/22 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF695,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99882 1 1 1 1 0 C 3 2 80 74299887 74299887 T C 1 0 0 0 0 1 0 0 0 3423 1783 62 5 5 CNTN3 3 74299887 Missense_Mutation SNP T C3N-01488_T 11546248 74299887 123995672 135 24509 CGGBP1 0 . GRCh38 3 88055641 88055641 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.336G>T p.= p.L112L ENST00000398392 1/1 170 143 27 203 202 1 strelka-varscan CGGBP1,synonymous_variant,p.=,ENST00000398392,;CGGBP1,synonymous_variant,p.=,ENST00000309534,NM_003663.3;CGGBP1,synonymous_variant,p.=,ENST00000482016,NM_001008390.1;CGGBP1,synonymous_variant,p.=,ENST00000462901,NM_001195308.1;ZNF654,upstream_gene_variant,,ENST00000636215,;CGGBP1,downstream_gene_variant,,ENST00000467332,;CGGBP1,downstream_gene_variant,,ENST00000474441,;ZNF654,upstream_gene_variant,,ENST00000473136,; A ENST00000398392 Transcript synonymous_variant 1669/5298 336/504 112/167 L ctG/ctT 1 -1 CGGBP1 HGNC HGNC:1888 protein_coding YES CCDS43111.1 ENSP00000381429 Q9UFW8 UPI000006DF25 1/1 hmmpanther:PTHR32344:SF1,hmmpanther:PTHR32344 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 88055641 88055641 C A 1 0 0 0 0 0 0 0 1 3060 581 21 2 2 CGGBP1 3 88055641 Silent SNP C C3N-01488_T 13755754 88055641 110239918 136 24510 PROS1 0 . GRCh38 3 93886404 93886404 + Nonsense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1255G>T p.Gly419Ter p.G419* ENST00000394236 11/15 204 180 24 323 321 2 strelka-varscan PROS1,stop_gained,p.Gly419Ter,ENST00000394236,NM_000313.3;PROS1,stop_gained,p.Gly288Ter,ENST00000407433,; A ENST00000394236 Transcript stop_gained 1572/3560 1255/2031 419/676 G/* Gga/Tga 1 -1 PROS1 HGNC HGNC:9456 protein_coding YES CCDS2923.1 ENSP00000377783 P07225 A0A0S2Z4K3 UPI00001323E8 NM_000313.3 11/15 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR24040,hmmpanther:PTHR24040:SF0,SMART_domains:SM00282,Superfamily_domains:SSF49899 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 80 93886404 93886404 C A 1 0 0 0 0 0 1 0 0 12691 603 21 2 2 PROS1 3 93886404 Nonsense_Mutation SNP C C3N-01488_T 5830763 93886404 104409155 137 24511 CBLB 0 . GRCh38 3 105704087 105704087 + Missense_Mutation SNP C C A rs779328589 C3N-01488_T C3N-01488_N C C c.1494G>T p.Gln498His p.Q498H ENST00000264122 11/19 178 145 33 282 282 0 strelka-varscan CBLB,missense_variant,p.Gln498His,ENST00000264122,NM_001321786.1,NM_001321788.1,NM_170662.3;CBLB,missense_variant,p.Gln498His,ENST00000403724,;CBLB,missense_variant,p.Gln498His,ENST00000405772,;CBLB,upstream_gene_variant,,ENST00000394030,; A ENST00000264122 Transcript missense_variant 1816/6780 1494/2949 498/982 Q/H caG/caT rs779328589 1 -1 CBLB HGNC HGNC:1542 protein_coding YES CCDS2948.1 ENSP00000264122 Q13191 UPI00001AE89F NM_001321786.1,NM_001321788.1,NM_170662.3 tolerated(0.35) 11/19 hmmpanther:PTHR23007:SF3,hmmpanther:PTHR23007 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 105704087 105704087 C A 1 0 0 0 0 1 0 0 0 2402 912 32 2 2 CBLB 3 105704087 Missense_Mutation SNP C C3N-01488_T 11817683 105704087 92591472 138 24512 ARHGAP31 0 . GRCh38 3 119416141 119416141 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.4212A>T p.= p.T1404T ENST00000264245 12/12 499 417 82 618 617 1 strelka-varscan ARHGAP31,synonymous_variant,p.=,ENST00000264245,NM_020754.3; T ENST00000264245 Transcript synonymous_variant 4744/9317 4212/4335 1404/1444 T acA/acT 1 1 ARHGAP31 HGNC HGNC:29216 protein_coding YES CCDS43135.1 ENSP00000264245 Q2M1Z3 UPI00001C1DFD NM_020754.3 12/12 hmmpanther:PTHR15729:SF3,hmmpanther:PTHR15729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 119416141 119416141 A T 1 0 0 0 0 0 0 0 1 1005 146 6 4 4 ARHGAP31 3 119416141 Silent SNP A C3N-01488_T 13712054 119416141 78879418 139 24513 POLQ 0 . GRCh38 3 121433006 121433006 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.7571G>T p.Gly2524Val p.G2524V ENST00000264233 29/30 275 260 15 365 365 0 strelka-varscan POLQ,missense_variant,p.Gly2659Val,ENST00000621776,;POLQ,missense_variant,p.Gly2524Val,ENST00000264233,NM_199420.3; A ENST00000264233 Transcript missense_variant 7700/8775 7571/7773 2524/2590 G/V gGg/gTg COSM5298938 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious(0.01) 29/30 Pfam_domain:PF00476,SMART_domains:SM00482 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 121433006 121433006 C A 1 0 0 0 0 1 0 0 0 12318 623 22 2 2 POLQ 3 121433006 Missense_Mutation SNP C C3N-01488_T 2016865 121433006 76862553 140 24514 H1FOO 0 . GRCh38 3 129547453 129547453 + Missense_Mutation SNP C C A rs773156190 C3N-01488_T C3N-01488_N C C c.151C>A p.Arg51Ser p.R51S ENST00000324382 2/5 134 116 18 197 197 0 strelka-varscan H1FOO,missense_variant,p.Arg51Ser,ENST00000324382,NM_153833.1;H1FOO,upstream_gene_variant,,ENST00000503977,NM_001308262.1; A ENST00000324382 Transcript missense_variant 156/1067 151/1041 51/346 R/S Cgc/Agc rs773156190 1 1 H1FOO HGNC HGNC:18463 protein_coding YES CCDS3064.1 ENSP00000319799 Q8IZA3 UPI000007414E NM_153833.1 deleterious(0.01) 2/5 Gene3D:1.10.10.10,PROSITE_profiles:PS51504,hmmpanther:PTHR11467,hmmpanther:PTHR11467:SF42,SMART_domains:SM00526,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 129547453 129547453 C A 1 0 0 0 0 1 0 0 0 6804 652 23 1 1 H1FOO 3 129547453 Missense_Mutation SNP C C3N-01488_T 8114447 129547453 68748106 141 24515 SLCO2A1 0 . GRCh38 3 133973717 133973717 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.343C>A p.Leu115Ile p.L115I ENST00000310926 3/14 295 248 47 331 331 0 strelka-varscan SLCO2A1,missense_variant,p.Leu115Ile,ENST00000310926,NM_005630.2;SLCO2A1,missense_variant,p.Leu115Ile,ENST00000493729,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000478651,;SLCO2A1,missense_variant,p.Leu115Ile,ENST00000481359,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000462770,;SLCO2A1,non_coding_transcript_exon_variant,,ENST00000464676,; T ENST00000310926 Transcript missense_variant 617/4223 343/1932 115/643 L/I Ctc/Atc COSM1038605 1 -1 SLCO2A1 HGNC HGNC:10955 protein_coding YES CCDS3084.1 ENSP00000311291 Q92959 UPI000013F0AD NM_005630.2 tolerated(0.12) 3/14 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF14,TIGRFAM_domain:TIGR00805,Pfam_domain:PF03137,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 133973717 133973717 G T 1 0 0 0 0 1 0 0 0 15013 1000 35 2 2 SLCO2A1 3 133973717 Missense_Mutation SNP G C3N-01488_T 4426264 133973717 64321842 142 24516 ZBTB38 0 . GRCh38 3 141444372 141444372 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.1984A>G p.Met662Val p.M662V ENST00000514251 4/4 140 112 28 241 241 0 strelka-varscan ZBTB38,missense_variant,p.Met662Val,ENST00000514251,;ZBTB38,missense_variant,p.Met662Val,ENST00000637056,NM_001080412.2;ZBTB38,missense_variant,p.Met662Val,ENST00000441582,;ZBTB38,missense_variant,p.Met662Val,ENST00000321464,;ZBTB38,missense_variant,p.Met662Val,ENST00000636289,;ZBTB38,missense_variant,p.Met662Val,ENST00000509883,;ZBTB38,downstream_gene_variant,,ENST00000509842,;ZBTB38,downstream_gene_variant,,ENST00000510726,;ZBTB38,downstream_gene_variant,,ENST00000509813,;ZBTB38,downstream_gene_variant,,ENST00000513570,;ZBTB38,downstream_gene_variant,,ENST00000510338,;ZBTB38,downstream_gene_variant,,ENST00000507722,;ZBTB38,downstream_gene_variant,,ENST00000513258,;ZBTB38,downstream_gene_variant,,ENST00000504673,;ZBTB38,downstream_gene_variant,,ENST00000503809,;ZBTB38,upstream_gene_variant,,ENST00000512769,; G ENST00000514251 Transcript missense_variant 2263/7683 1984/3588 662/1195 M/V Atg/Gtg 1 1 ZBTB38 HGNC HGNC:26636 protein_coding YES CCDS43157.1 ENSP00000426387 Q8NAP3 UPI000020A364 tolerated(1) 4/4 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF267 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 141444372 141444372 A G 1 0 0 0 0 1 0 0 0 18108 101 4 5 5 ZBTB38 3 141444372 Missense_Mutation SNP A C3N-01488_T 7470655 141444372 56851187 143 24517 LEKR1 0 . GRCh38 3 157045448 157045448 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.865G>T p.Gly289Ter p.G289* ENST00000470811 14/14 213 191 22 309 308 1 strelka-varscan LEKR1,stop_gained,p.Gly289Ter,ENST00000470811,;LEKR1,stop_gained,p.Gly593Ter,ENST00000356539,NM_001004316.2; T ENST00000470811 Transcript stop_gained 2200/2881 865/1167 289/388 G/* Gga/Tga 1 1 LEKR1 HGNC HGNC:33765 protein_coding ENSP00000418214 Q6ZMV7 UPI0000425F3D 14/14 hmmpanther:PTHR34251 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 157045448 157045448 G T 1 0 0 0 0 0 1 0 0 8625 1349 47 2 2 LEKR1 3 157045448 Nonsense_Mutation SNP G C3N-01488_T 15601076 157045448 41250111 144 24518 SI 0 . GRCh38 3 165049865 165049865 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1523A>T p.Glu508Val p.E508V ENST00000264382 14/48 175 139 36 334 334 0 strelka-varscan SI,missense_variant,p.Glu508Val,ENST00000264382,NM_001041.3; A ENST00000264382 Transcript missense_variant 1586/6011 1523/5484 508/1827 E/V gAa/gTa 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 14/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,PROSITE_patterns:PS00129,Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 165049865 165049865 T A 1 0 0 0 0 1 0 0 0 14561 1783 62 4 4 SI 3 165049865 Missense_Mutation SNP T C3N-01488_T 8004417 165049865 33245694 145 24519 SI 0 . GRCh38 3 165065407 165065407 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.661G>T p.Val221Leu p.V221L ENST00000264382 7/48 165 141 24 270 270 0 strelka-varscan SI,missense_variant,p.Val221Leu,ENST00000264382,NM_001041.3;SI,downstream_gene_variant,,ENST00000476593,; A ENST00000264382 Transcript missense_variant 724/6011 661/5484 221/1827 V/L Gtg/Ttg 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.77) 7/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF16863,Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 165065407 165065407 C A 1 0 0 0 0 1 0 0 0 14561 565 20 2 2 SI 3 165065407 Missense_Mutation SNP C C3N-01488_T 15542 165065407 33230152 146 24520 SI 0 . GRCh38 3 165067382 165067382 + Missense_Mutation SNP G G C rs142923909 C3N-01488_T C3N-01488_N G G c.593C>G p.Pro198Arg p.P198R ENST00000264382 6/48 232 178 54 365 365 0 strelka-varscan SI,missense_variant,p.Pro198Arg,ENST00000264382,NM_001041.3;SI,downstream_gene_variant,,ENST00000476593,; C ENST00000264382 Transcript missense_variant 656/6011 593/5484 198/1827 P/R cCa/cGa rs142923909 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 deleterious(0) 6/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF66,Pfam_domain:PF16863,Superfamily_domains:SSF74650 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 165067382 165067382 G C 1 0 0 0 0 1 0 0 0 14561 1348 47 4 4 SI 3 165067382 Missense_Mutation SNP G C3N-01488_T 1975 165067382 33228177 147 24521 ZBBX 0 . GRCh38 3 167333965 167333965 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.549C>A p.Phe183Leu p.F183L ENST00000455345 9/21 54 42 12 108 108 0 strelka-varscan ZBBX,missense_variant,p.Phe183Leu,ENST00000392766,NM_024687.3;ZBBX,missense_variant,p.Phe183Leu,ENST00000455345,NM_001199201.1;ZBBX,missense_variant,p.Phe183Leu,ENST00000307529,;ZBBX,missense_variant,p.Phe154Leu,ENST00000392767,;ZBBX,missense_variant,p.Phe154Leu,ENST00000392764,NM_001199202.1;ZBBX,intron_variant,,ENST00000469220,; T ENST00000455345 Transcript missense_variant 833/3185 549/2520 183/839 F/L ttC/ttA 1 -1 ZBBX HGNC HGNC:26245 protein_coding YES CCDS56296.1 ENSP00000390232 A8MT70 UPI000020A746 NM_001199201.1 tolerated(0.06) 9/21 hmmpanther:PTHR28634 MODERATE 1 SNV 1 1 PASS . . 1 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 80 167333965 167333965 G T 1 0 0 0 0 1 0 0 0 18078 1281 45 2 2 ZBBX 3 167333965 Missense_Mutation SNP G C3N-01488_T 2266583 167333965 30961594 148 24522 MAP3K13 0 . GRCh38 3 185443564 185443564 + Frame_Shift_Del DEL C C - novel C3N-01488_T C3N-01488_N C C c.780delC p.Thr261GlnfsTer7 p.T261Qfs*7 ENST00000265026 4/14 152 129 23 208 208 0 sindel-varindel-pindel MAP3K13,frameshift_variant,p.Thr261GlnfsTer7,ENST00000265026,NM_004721.4;MAP3K13,frameshift_variant,p.Thr261GlnfsTer7,ENST00000424227,NM_001242314.1;MAP3K13,frameshift_variant,p.Thr117GlnfsTer7,ENST00000443863,;MAP3K13,frameshift_variant,p.Thr54GlnfsTer7,ENST00000446828,NM_001242317.1;MAP3K13,intron_variant,,ENST00000420577,;MAP3K13,3_prime_UTR_variant,,ENST00000433092,;MAP3K13,3_prime_UTR_variant,,ENST00000439882,;MAP3K13,non_coding_transcript_exon_variant,,ENST00000477582,;MAP3K13,intron_variant,,ENST00000438053,; - ENST00000265026 Transcript frameshift_variant 1113/9876 779/2901 260/966 S/X tCc/tc 1 1 MAP3K13 HGNC HGNC:6852 protein_coding YES CCDS3270.1 ENSP00000265026 O43283 UPI000006CF91 NM_004721.4 4/14 PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF336,PIRSF_domain:PIRSF038165,Pfam_domain:PF07714,PIRSF_domain:PIRSF500742,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 80 185443564 185443564 C - 1 0 1 0 1 0 0 0 0 9169 855 30 0 0 MAP3K13 3 185443564 Frame_Shift_Del DEL C C3N-01488_T 18109599 185443564 12851995 149 24523 MASP1 0 . GRCh38 3 187251663 187251663 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.982A>T p.Ser328Cys p.S328C ENST00000296280 7/11 315 247 68 405 405 0 strelka-varscan MASP1,missense_variant,p.Ser328Cys,ENST00000337774,NM_001879.5;MASP1,missense_variant,p.Ser328Cys,ENST00000296280,NM_139125.3;MASP1,missense_variant,p.Ser215Cys,ENST00000392472,;MASP1,missense_variant,p.Ser328Cys,ENST00000169293,NM_001031849.2;MASP1,missense_variant,p.Ser302Cys,ENST00000392470,;MASP1,intron_variant,,ENST00000495249,;MASP1,non_coding_transcript_exon_variant,,ENST00000483719,;MASP1,downstream_gene_variant,,ENST00000460839,; A ENST00000296280 Transcript missense_variant 1208/4015 982/2187 328/728 S/C Agc/Tgc 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 deleterious(0.02) 7/11 Gene3D:2.10.70.10,Pfam_domain:PF00084,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS50923,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 187251663 187251663 T A 1 0 0 0 0 1 0 0 0 9248 1580 55 4 4 MASP1 3 187251663 Missense_Mutation SNP T C3N-01488_T 1808099 187251663 11043896 150 24524 ACOX3 0 . GRCh38 4 8389628 8389628 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.1407G>A p.= p.L469L ENST00000356406 12/18 185 146 39 228 228 0 strelka-varscan-mutect ACOX3,synonymous_variant,p.=,ENST00000356406,NM_003501.2;ACOX3,synonymous_variant,p.=,ENST00000413009,NM_001101667.1;ACOX3,synonymous_variant,p.=,ENST00000503233,;RNA5SP152,upstream_gene_variant,,ENST00000365184,;ACOX3,non_coding_transcript_exon_variant,,ENST00000508302,;ACOX3,non_coding_transcript_exon_variant,,ENST00000510365,; T ENST00000356406 Transcript synonymous_variant 1485/2860 1407/2103 469/700 L ctG/ctA 1 -1 ACOX3 HGNC HGNC:121 protein_coding YES CCDS3401.1 ENSP00000348775 O15254 UPI000013EEE2 NM_003501.2 12/18 hmmpanther:PTHR10909:SF315,hmmpanther:PTHR10909,PIRSF_domain:PIRSF000168,Gene3D:1.20.140.10,Superfamily_domains:SSF47203 LOW 1 SNV 1 1 PASS rs1028393578 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 8389628 8389628 C T 1 0 0 0 0 0 0 0 1 202 581 21 3 3 ACOX3 4 8389628 Silent SNP C C3N-01488_T 8389628 181824927 151 24525 EPHA5 0 . GRCh38 4 65490432 65490432 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1347C>A p.Asp449Glu p.D449E ENST00000622150 5/18 196 156 40 273 273 0 strelka-varscan EPHA5,missense_variant,p.Asp449Glu,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Asp449Glu,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Asp449Glu,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Asp449Glu,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Asp449Glu,ENST00000354839,NM_182472.3;EPHA5,intron_variant,,ENST00000432638,; T ENST00000622150 Transcript missense_variant 2100/8421 1347/3117 449/1038 D/E gaC/gaA 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 tolerated(0.65) 5/18 Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 65490432 65490432 G T 1 0 0 0 0 1 0 0 0 5017 1020 36 2 2 EPHA5 4 65490432 Missense_Mutation SNP G C3N-01488_T 57100804 65490432 124724123 152 24526 STAP1 0 . GRCh38 4 67581339 67581339 + Missense_Mutation SNP G G T rs202106508 C3N-01488_T C3N-01488_N G G c.398G>T p.Gly133Val p.G133V ENST00000265404 5/9 128 107 21 188 188 0 strelka-varscan STAP1,missense_variant,p.Gly133Val,ENST00000265404,NM_012108.2;STAP1,missense_variant,p.Gly133Val,ENST00000396225,NM_001317769.1; T ENST00000265404 Transcript missense_variant 480/1511 398/888 133/295 G/V gGg/gTg rs202106508 1 1 STAP1 HGNC HGNC:24133 protein_coding YES CCDS3515.1 ENSP00000265404 Q9ULZ2 A0A024RD91 UPI0000073E6C NM_012108.2 deleterious(0) 5/9 hmmpanther:PTHR16186,hmmpanther:PTHR16186:SF10,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 67581339 67581339 G T 1 0 0 0 0 1 0 0 0 15627 1232 43 2 2 STAP1 4 67581339 Missense_Mutation SNP G C3N-01488_T 2090907 67581339 122633216 153 24527 CSN2 0 . GRCh38 4 69957418 69957418 + Silent SNP C C A rs202159563 C3N-01488_T C3N-01488_N C C c.531G>T p.= p.L177L ENST00000353151 5/7 101 80 21 180 180 0 strelka-varscan CSN2,synonymous_variant,p.=,ENST00000353151,NM_001302770.1,NM_001891.3; A ENST00000353151 Transcript synonymous_variant 543/1066 531/681 177/226 L ctG/ctT rs202159563 1 -1 CSN2 HGNC HGNC:2447 protein_coding YES CCDS3532.1 ENSP00000341030 P05814 W5RWE1 UPI0000126FDB NM_001302770.1,NM_001891.3 5/7 hmmpanther:PTHR11500:SF0,hmmpanther:PTHR11500,Pfam_domain:PF00363,PIRSF_domain:PIRSF002372 LOW 1 SNV 1 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999568 1 1 1 0 A 2 1 80 69957418 69957418 C A 1 0 0 0 0 0 0 0 1 3748 697 25 2 2 CSN2 4 69957418 Silent SNP C C3N-01488_T 2376079 69957418 120257137 154 24528 OPRPN 0 . GRCh38 4 70409741 70409741 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.413C>T p.Ser138Phe p.S138F ENST00000399575 3/3 160 136 24 252 252 0 strelka-varscan OPRPN,missense_variant,p.Ser138Phe,ENST00000399575,NM_021225.4;OPRPN,non_coding_transcript_exon_variant,,ENST00000514338,;OPRPN,non_coding_transcript_exon_variant,,ENST00000505023,; T ENST00000399575 Transcript missense_variant 587/1040 413/747 138/248 S/F tCt/tTt 1 1 OPRPN HGNC HGNC:17279 protein_coding YES CCDS43235.1 ENSP00000382485 Q99935 UPI000020BE52 NM_021225.4 tolerated_low_confidence(0.91) 3/3 hmmpanther:PTHR14179,hmmpanther:PTHR14179:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 70409741 70409741 C T 1 0 0 0 0 1 0 0 0 10963 913 32 3 3 OPRPN 4 70409741 Missense_Mutation SNP C C3N-01488_T 452323 70409741 119804814 155 24529 C4orf22 0 . GRCh38 4 80870026 80870026 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.418G>T p.Gly140Trp p.G140W ENST00000508675 5/7 138 130 8 146 146 0 strelka-varscan C4orf22,missense_variant,p.Gly123Trp,ENST00000358105,NM_152770.2;C4orf22,missense_variant,p.Gly140Trp,ENST00000508675,NM_001206997.1;C4orf22,upstream_gene_variant,,ENST00000508314,;C4orf22,3_prime_UTR_variant,,ENST00000513920,; T ENST00000508675 Transcript missense_variant 418/753 418/753 140/250 G/W Ggg/Tgg 1 1 C4orf22 HGNC HGNC:28554 protein_coding YES CCDS56336.1 ENSP00000425786 Q6V702 UPI0000D61589 NM_001206997.1 deleterious(0) 5/7 Pfam_domain:PF14713,hmmpanther:PTHR33588,hmmpanther:PTHR33588:SF1 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -15.06152 1 1 1 1 0 T 3 4 80 80870026 80870026 G T 1 0 0 0 0 1 0 0 0 2080 1348 47 2 2 C4orf22 4 80870026 Missense_Mutation SNP G C3N-01488_T 10460285 80870026 109344529 156 24530 RASGEF1B 0 . GRCh38 4 81456710 81456710 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.379G>C p.Asp127His p.D127H ENST00000264400 4/14 243 205 38 372 372 0 strelka-varscan RASGEF1B,missense_variant,p.Asp127His,ENST00000436139,;RASGEF1B,missense_variant,p.Asp127His,ENST00000613784,;RASGEF1B,missense_variant,p.Asp127His,ENST00000509081,NM_001300735.1;RASGEF1B,missense_variant,p.Asp214His,ENST00000638048,;RASGEF1B,missense_variant,p.Asp127His,ENST00000264400,NM_152545.2;RASGEF1B,missense_variant,p.Asp86His,ENST00000335927,NM_001300736.1;RASGEF1B,intron_variant,,ENST00000504863,;RASGEF1B,non_coding_transcript_exon_variant,,ENST00000514889,;RASGEF1B,downstream_gene_variant,,ENST00000507538,;RASGEF1B,downstream_gene_variant,,ENST00000512716,; G ENST00000264400 Transcript missense_variant 531/2277 379/1422 127/473 D/H Gat/Cat 1 -1 RASGEF1B HGNC HGNC:24881 protein_coding YES CCDS34022.1 ENSP00000264400 Q0VAM2 UPI0000044685 NM_152545.2 deleterious(0) 4/14 PROSITE_profiles:PS50212,hmmpanther:PTHR23113:SF197,hmmpanther:PTHR23113,Gene3D:2ii0A01,Pfam_domain:PF00618,SMART_domains:SM00229,Superfamily_domains:0041591 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 81456710 81456710 C G 1 0 0 0 0 1 0 0 0 13231 855 30 4 4 RASGEF1B 4 81456710 Missense_Mutation SNP C C3N-01488_T 586684 81456710 108757845 157 24531 RP11-766F14.2 0 . GRCh38 4 99651090 99651090 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.3559T>A p.Ser1187Thr p.S1187T ENST00000511828 1/2 240 219 21 368 368 0 strelka-varscan RP11-766F14.2,missense_variant,p.Ser1187Thr,ENST00000511828,; T ENST00000511828 Transcript missense_variant 3559/10086 3559/5382 1187/1793 S/T Tcc/Acc 1 -1 RP11-766F14.2 Clone_based_vega_gene protein_coding YES ENSP00000427555 D6RIA3 UPI0001D3B6FE tolerated(0.08) 1/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 99651090 99651090 A T 1 0 0 0 0 1 0 0 0 13762 304 11 4 4 RP11-766F14.2 4 99651090 Missense_Mutation SNP A C3N-01488_T 18194380 99651090 90563465 158 24532 LRIT3 0 . GRCh38 4 109870111 109870111 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.1362G>T p.= p.V454V ENST00000594814 4/4 141 124 17 293 292 1 strelka-varscan LRIT3,synonymous_variant,p.=,ENST00000327908,;LRIT3,synonymous_variant,p.=,ENST00000594814,NM_198506.4; T ENST00000594814 Transcript synonymous_variant 1362/3566 1362/2040 454/679 V gtG/gtT 1 1 LRIT3 HGNC HGNC:24783 protein_coding YES CCDS3688.3 ENSP00000469759 Q3SXY7 UPI0000F07E94 NM_198506.4 4/4 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF236 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 109870111 109870111 G T 1 0 0 0 0 0 0 0 1 8844 1335 47 2 2 LRIT3 4 109870111 Silent SNP G C3N-01488_T 10219021 109870111 80344444 159 24533 ANK2 0 . GRCh38 4 113199086 113199086 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.361G>T p.Ala121Ser p.A121S ENST00000357077 4/46 288 243 45 394 393 1 strelka-varscan ANK2,missense_variant,p.Ala121Ser,ENST00000357077,NM_001148.4;ANK2,missense_variant,p.Ala121Ser,ENST00000264366,;ANK2,missense_variant,p.Ala100Ser,ENST00000506722,NM_001127493.1;ANK2,missense_variant,p.Ala121Ser,ENST00000394537,NM_020977.3;ANK2,missense_variant,p.Ala136Ser,ENST00000504454,;ANK2,missense_variant,p.Ala100Ser,ENST00000503423,;ANK2,missense_variant,p.Ala93Ser,ENST00000634436,;ANK2,missense_variant,p.Ala100Ser,ENST00000503271,;ANK2,missense_variant,p.Ala136Ser,ENST00000508613,;ANK2,5_prime_UTR_variant,,ENST00000515034,;ANK2,downstream_gene_variant,,ENST00000511380,; T ENST00000357077 Transcript missense_variant 414/14196 361/11874 121/3957 A/S Gcc/Tcc 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 deleterious(0.03) 4/46 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 113199086 113199086 G T 1 0 0 0 0 1 0 0 0 721 971 34 2 2 ANK2 4 113199086 Missense_Mutation SNP G C3N-01488_T 3328975 113199086 77015469 160 24534 ANK2 0 . GRCh38 4 113343130 113343130 + Silent SNP T T A C3N-01488_T C3N-01488_N T T c.4236T>A p.= p.P1412P ENST00000357077 34/46 227 183 44 395 395 0 strelka-varscan ANK2,synonymous_variant,p.=,ENST00000357077,NM_001148.4;ANK2,synonymous_variant,p.=,ENST00000264366,;ANK2,synonymous_variant,p.=,ENST00000506722,NM_001127493.1;ANK2,synonymous_variant,p.=,ENST00000394537,NM_020977.3;ANK2,synonymous_variant,p.=,ENST00000504454,;ANK2,synonymous_variant,p.=,ENST00000514960,;ANK2,synonymous_variant,p.=,ENST00000503423,;ANK2,synonymous_variant,p.=,ENST00000509550,;ANK2,synonymous_variant,p.=,ENST00000510275,;ANK2,intron_variant,,ENST00000504415,;ANK2,downstream_gene_variant,,ENST00000504887,;ANK2,upstream_gene_variant,,ENST00000508007,; A ENST00000357077 Transcript synonymous_variant 4289/14196 4236/11874 1412/3957 P ccT/ccA COSM5167337,COSM5167338 1 1 ANK2 HGNC HGNC:493 protein_coding YES CCDS3702.1 ENSP00000349588 Q01484 UPI0000441EF3 NM_001148.4 34/46 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF17 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 113343130 113343130 T A 1 0 0 0 0 0 0 0 1 721 1538 54 4 4 ANK2 4 113343130 Silent SNP T C3N-01488_T 144044 113343130 76871425 161 24535 TRPC3 0 . GRCh38 4 121932696 121932696 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.562G>T p.Val188Leu p.V188L ENST00000379645 2/12 104 91 13 179 179 0 strelka-varscan TRPC3,missense_variant,p.Val115Leu,ENST00000264811,NM_003305.2;TRPC3,missense_variant,p.Val188Leu,ENST00000379645,NM_001130698.1;TRPC3,missense_variant,p.Val115Leu,ENST00000513531,;TRPC3,downstream_gene_variant,,ENST00000502968,;TRPC3,missense_variant,p.Val115Leu,ENST00000506449,; A ENST00000379645 Transcript missense_variant 636/3548 562/2766 188/921 V/L Gtg/Ttg 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 tolerated(0.13) 2/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Gene3D:1.25.40.20,Pfam_domain:PF12796,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 121932696 121932696 C A 1 0 0 0 0 1 0 0 0 17084 536 19 1 1 TRPC3 4 121932696 Missense_Mutation SNP C C3N-01488_T 8589566 121932696 68281859 162 24536 FAM198B 0 . GRCh38 4 158127552 158127552 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.1439C>G p.Ser480Cys p.S480C ENST00000393807 6/6 241 220 21 352 352 0 strelka-varscan FAM198B,missense_variant,p.Ser472Cys,ENST00000296530,NM_016613.6;FAM198B,missense_variant,p.Ser472Cys,ENST00000585682,NM_001128424.1;FAM198B,missense_variant,p.Ser480Cys,ENST00000393807,NM_001031700.2;FAM198B,missense_variant,p.Ser178Cys,ENST00000590648,;FAM198B,missense_variant,p.Ser106Cys,ENST00000592586,;FAM198B,downstream_gene_variant,,ENST00000593260,;FAM198B,downstream_gene_variant,,ENST00000589306,; C ENST00000393807 Transcript missense_variant 1846/4544 1439/1584 480/527 S/C tCt/tGt 1 -1 FAM198B HGNC HGNC:25312 protein_coding YES CCDS34087.1 ENSP00000377396 Q6UWH4 UPI00003672A2 NM_001031700.2 deleterious(0) 6/6 Pfam_domain:PF15051,hmmpanther:PTHR15905,hmmpanther:PTHR15905:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 158127552 158127552 G C 1 0 0 0 0 1 0 0 0 5376 942 33 4 4 FAM198B 4 158127552 Missense_Mutation SNP G C3N-01488_T 36194856 158127552 32087003 163 24537 RAPGEF2 0 . GRCh38 4 159343116 159343116 + Missense_Mutation SNP A A G rs766326195 C3N-01488_T C3N-01488_N A A c.2573A>G p.Asn858Ser p.N858S ENST00000264431 15/24 304 255 49 453 453 0 strelka-varscan RAPGEF2,missense_variant,p.Asn858Ser,ENST00000264431,NM_014247.2;RAPGEF2,upstream_gene_variant,,ENST00000510253,;RAPGEF2,upstream_gene_variant,,ENST00000502485,; G ENST00000264431 Transcript missense_variant 2992/6949 2573/4500 858/1499 N/S aAt/aGt rs766326195 1 1 RAPGEF2 HGNC HGNC:16854 protein_coding YES CCDS43277.1 ENSP00000264431 Q9Y4G8 UPI0000033783 NM_014247.2 tolerated(1) 15/24 PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF217,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 159343116 159343116 A G 1 0 0 0 0 1 0 0 0 13203 101 4 5 5 RAPGEF2 4 159343116 Missense_Mutation SNP A C3N-01488_T 1215564 159343116 30871439 164 24538 GALNTL6 0 . GRCh38 4 172052519 172052519 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.75G>T p.Glu25Asp p.E25D ENST00000508122 1/12 142 118 24 181 181 0 strelka-varscan GALNTL6,missense_variant,p.Glu25Asp,ENST00000508122,;GALNTL6,intron_variant,,ENST00000506823,NM_001034845.2; T ENST00000508122 Transcript missense_variant 75/1755 75/1755 25/584 E/D gaG/gaT 1 1 GALNTL6 HGNC HGNC:33844 protein_coding ENSP00000423827 Q49A17 UPI0000695D6D tolerated_low_confidence(0.44) 1/12 hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF40 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 172052519 172052519 G T 1 0 0 0 0 1 0 0 0 6093 962 34 2 2 GALNTL6 4 172052519 Missense_Mutation SNP G C3N-01488_T 12709403 172052519 18162036 165 24539 TENM3 0 . GRCh38 4 182775075 182775075 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.5226C>A p.Asn1742Lys p.N1742K ENST00000511685 24/28 402 340 62 443 441 2 strelka-varscan TENM3,missense_variant,p.Asn1742Lys,ENST00000511685,NM_001080477.2;RP11-18D7.2,upstream_gene_variant,,ENST00000513255,; A ENST00000511685 Transcript missense_variant 5349/10896 5226/8100 1742/2699 N/K aaC/aaA COSM3337961 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 tolerated(0.11) 24/28 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 182775075 182775075 C A 1 0 0 0 0 1 0 0 0 16173 535 19 1 1 TENM3 4 182775075 Missense_Mutation SNP C C3N-01488_T 10722556 182775075 7439480 166 24540 CYP4V2 0 . GRCh38 4 186197533 186197533 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.605A>T p.Glu202Val p.E202V ENST00000378802 5/11 336 279 57 487 487 0 strelka-varscan CYP4V2,missense_variant,p.Glu202Val,ENST00000378802,NM_207352.3;CYP4V2,non_coding_transcript_exon_variant,,ENST00000507209,; T ENST00000378802 Transcript missense_variant,splice_region_variant 909/2042 605/1578 202/525 E/V gAa/gTa 1 1 CYP4V2 HGNC HGNC:23198 protein_coding YES CCDS34119.1 ENSP00000368079 Q6ZWL3 UPI00002372FE NM_207352.3 deleterious(0) 5/11 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF56,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 186197533 186197533 A T 1 0 0 0 0 1 0 0 0 3995 260 9 4 4 CYP4V2 4 186197533 Missense_Mutation SNP A C3N-01488_T 3422458 186197533 4017022 167 24541 FAT1 0 . GRCh38 4 186617130 186617130 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.8950C>T p.= p.L2984L ENST00000441802 11/27 223 208 15 359 359 0 strelka-varscan FAT1,synonymous_variant,p.=,ENST00000441802,NM_005245.3;FAT1,synonymous_variant,p.=,ENST00000614102,; A ENST00000441802 Transcript synonymous_variant 9160/14786 8950/13767 2984/4588 L Cta/Tta 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 11/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 186617130 186617130 G A 1 0 0 0 0 0 0 0 1 5549 933 33 3 3 FAT1 4 186617130 Silent SNP G C3N-01488_T 419597 186617130 3597425 168 24542 CDH18 0 . GRCh38 5 19612464 19612464 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.781G>T p.Val261Phe p.V261F ENST00000507958 8/15 210 174 36 275 274 1 strelka-varscan CDH18,missense_variant,p.Val261Phe,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Val261Phe,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Val261Phe,ENST00000274170,;CDH18,missense_variant,p.Val261Phe,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Val261Phe,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Val261Phe,ENST00000511273,;CDH18,missense_variant,p.Val207Phe,ENST00000515257,; A ENST00000507958 Transcript missense_variant 1772/3542 781/2373 261/790 V/F Gtc/Ttc 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 8/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 19612464 19612464 C A 1 0 0 0 0 1 0 0 0 2806 478 17 2 2 CDH18 5 19612464 Missense_Mutation SNP C C3N-01488_T 19612464 161925795 169 24543 SUB1 0 . GRCh38 5 32599028 32599028 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.263A>T p.Tyr88Phe p.Y88F ENST00000265073 4/5 211 181 30 360 360 0 strelka-varscan SUB1,missense_variant,p.Tyr88Phe,ENST00000265073,NM_006713.3;SUB1,missense_variant,p.Tyr88Phe,ENST00000506237,;SUB1,missense_variant,p.Tyr88Phe,ENST00000515355,;SUB1,missense_variant,p.Tyr88Phe,ENST00000512913,;SUB1,missense_variant,p.Tyr88Phe,ENST00000502897,;SUB1,non_coding_transcript_exon_variant,,ENST00000504789,;SUB1,non_coding_transcript_exon_variant,,ENST00000513013,;SUB1,intron_variant,,ENST00000504016,;SUB1,3_prime_UTR_variant,,ENST00000511615,;SUB1,non_coding_transcript_exon_variant,,ENST00000502453,;SUB1,non_coding_transcript_exon_variant,,ENST00000511175,; T ENST00000265073 Transcript missense_variant 391/3507 263/384 88/127 Y/F tAt/tTt 1 1 SUB1 HGNC HGNC:19985 protein_coding YES CCDS3897.1 ENSP00000265073 P53999 Q6IBA2 UPI0000044938 NM_006713.3 tolerated(0.41) 4/5 hmmpanther:PTHR13215:SF7,hmmpanther:PTHR13215,Pfam_domain:PF02229,Gene3D:2.30.31.10,Superfamily_domains:SSF54447 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 32599028 32599028 A T 1 0 0 0 0 1 0 0 0 15746 449 16 4 4 SUB1 5 32599028 Missense_Mutation SNP A C3N-01488_T 12986564 32599028 148939231 170 24544 ADAMTS12 0 . GRCh38 5 33576060 33576060 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3966G>T p.Trp1322Cys p.W1322C ENST00000504830 19/24 96 87 9 148 147 1 strelka-varscan ADAMTS12,missense_variant,p.Trp1322Cys,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Trp1237Cys,ENST00000352040,;ADAMTS12,downstream_gene_variant,,ENST00000504582,; A ENST00000504830 Transcript missense_variant 4302/8774 3966/4785 1322/1594 W/C tgG/tgT 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 19/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -18.54262 1 1 1 1 0 A 3 1 80 33576060 33576060 C A 1 0 0 0 0 1 0 0 0 301 856 30 2 2 ADAMTS12 5 33576060 Missense_Mutation SNP C C3N-01488_T 977032 33576060 147962199 171 24545 NNT 0 . GRCh38 5 43615955 43615955 + Missense_Mutation SNP G G T rs765251374 C3N-01488_T C3N-01488_N G G c.489G>T p.Leu163Phe p.L163F ENST00000264663 4/22 318 273 45 402 400 2 strelka-varscan NNT,missense_variant,p.Leu163Phe,ENST00000264663,NM_012343.3;NNT,missense_variant,p.Leu163Phe,ENST00000344920,NM_182977.2;NNT,missense_variant,p.Leu32Phe,ENST00000512996,;NNT,missense_variant,p.Leu163Phe,ENST00000512422,;NNT,missense_variant,p.Leu32Phe,ENST00000515208,;NNT,missense_variant,p.Leu163Phe,ENST00000505678,; T ENST00000264663 Transcript missense_variant 710/6483 489/3261 163/1086 L/F ttG/ttT rs765251374 1 1 NNT HGNC HGNC:7863 protein_coding YES CCDS3949.1 ENSP00000264663 Q13423 A0A024R0C3 UPI000013D54F NM_012343.3 deleterious(0) 4/22 Gene3D:3.40.50.1770,Pfam_domain:PF05222,hmmpanther:PTHR10160,hmmpanther:PTHR10160:SF22,SMART_domains:SM01003,Superfamily_domains:SSF52283,TIGRFAM_domain:TIGR00561 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 43615955 43615955 G T 1 0 0 0 0 1 0 0 0 10551 1310 46 2 2 NNT 5 43615955 Missense_Mutation SNP G C3N-01488_T 10039895 43615955 137922304 172 24546 ACTBL2 0 . GRCh38 5 57482582 57482582 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.126G>C p.Gln42His p.Q42H ENST00000423391 1/1 353 293 60 460 459 1 strelka-varscan-mutect ACTBL2,missense_variant,p.Gln42His,ENST00000423391,NM_001017992.3;CTD-2023N9.1,intron_variant,,ENST00000506106,; G ENST00000423391 Transcript missense_variant 228/2794 126/1131 42/376 Q/H caG/caC 1 -1 ACTBL2 HGNC HGNC:17780 protein_coding YES CCDS34163.1 ENSP00000416706 Q562R1 UPI000013EB83 NM_001017992.3 tolerated_low_confidence(0.12) 1/1 hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF168,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE SNV 1 PASS rs1421001463 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 57482582 57482582 C G 1 0 0 0 0 1 0 0 0 237 680 24 4 4 ACTBL2 5 57482582 Missense_Mutation SNP C C3N-01488_T 13866627 57482582 124055677 173 24547 SLCO4C1 0 . GRCh38 5 102247338 102247338 + Silent SNP C C A rs574597658 C3N-01488_T C3N-01488_N C C c.1725G>T p.= p.A575A ENST00000310954 10/13 56 48 8 122 122 0 strelka-varscan SLCO4C1,synonymous_variant,p.=,ENST00000310954,NM_180991.4; A ENST00000310954 Transcript synonymous_variant 2012/5334 1725/2175 575/724 A gcG/gcT rs574597658,COSM1642543 1 -1 SLCO4C1 HGNC HGNC:23612 protein_coding YES CCDS34205.1 ENSP00000309741 Q6ZQN7 UPI00001C10B6 NM_180991.4 10/13 Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF103,TIGRFAM_domain:TIGR00805 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 203 5 2 0 0 0 0 -14.82931 0.9999565 1 1 1 0 A 2 1 80 102247338 102247338 C A 1 0 0 0 0 0 0 0 1 15017 871 31 1 1 SLCO4C1 5 102247338 Silent SNP C C3N-01488_T 44764756 102247338 79290921 174 24548 GRAMD3 0 . GRCh38 5 126473296 126473296 + Silent SNP A A G rs759689240 C3N-01488_T C3N-01488_N A A c.459A>G p.= p.L153L ENST00000513040 5/14 69 59 10 91 91 0 strelka-varscan GRAMD3,synonymous_variant,p.=,ENST00000285689,NM_023927.2;GRAMD3,synonymous_variant,p.=,ENST00000515200,;GRAMD3,synonymous_variant,p.=,ENST00000542322,NM_001146321.1;GRAMD3,synonymous_variant,p.=,ENST00000544396,NM_001146320.1;GRAMD3,synonymous_variant,p.=,ENST00000513040,NM_001146319.1;GRAMD3,synonymous_variant,p.=,ENST00000511134,NM_001146322.1;GRAMD3,synonymous_variant,p.=,ENST00000502348,;GRAMD3,synonymous_variant,p.=,ENST00000506445,;RP11-517I3.1,intron_variant,,ENST00000515808,;GRAMD3,non_coding_transcript_exon_variant,,ENST00000509882,;GRAMD3,downstream_gene_variant,,ENST00000514932,;GRAMD3,downstream_gene_variant,,ENST00000513913,;GRAMD3,downstream_gene_variant,,ENST00000505720,;GRAMD3,3_prime_UTR_variant,,ENST00000513978,;GRAMD3,3_prime_UTR_variant,,ENST00000514099,;GRAMD3,non_coding_transcript_exon_variant,,ENST00000504859,;GRAMD3,downstream_gene_variant,,ENST00000505441,; G ENST00000513040 Transcript synonymous_variant 659/2196 459/1344 153/447 L ctA/ctG rs759689240 1 1 GRAMD3 HGNC HGNC:24911 protein_coding YES CCDS54891.1 ENSP00000426120 Q96HH9 UPI0001914E8F NM_001146319.1 5/14 Pfam_domain:PF02893,hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF5,SMART_domains:SM00568 LOW 1 SNV 2 1 PASS . . 0 201 9 0 0 0 0 0 -19.9962 0.9999932 1 1 1 0 G 2 3 80 126473296 126473296 A G 1 0 0 0 0 0 0 0 1 6630 436 16 5 5 GRAMD3 5 126473296 Silent SNP A C3N-01488_T 24225958 126473296 55064963 175 24549 ADAMTS19 0 . GRCh38 5 129526416 129526416 + Missense_Mutation SNP C C A rs770860264 C3N-01488_T C3N-01488_N C C c.1028C>A p.Ala343Glu p.A343E ENST00000274487 4/23 237 204 33 359 359 0 strelka-varscan ADAMTS19,missense_variant,p.Ala343Glu,ENST00000274487,NM_133638.3;CTC-575N7.1,intron_variant,,ENST00000503616,;ADAMTS19,missense_variant,p.Ala128Glu,ENST00000502709,;ADAMTS19,3_prime_UTR_variant,,ENST00000505791,; A ENST00000274487 Transcript missense_variant 1173/5234 1028/3624 343/1207 A/E gCa/gAa rs770860264 1 1 ADAMTS19 HGNC HGNC:17111 protein_coding YES CCDS4146.1 ENSP00000274487 Q8TE59 UPI000013DA0D NM_133638.3 deleterious(0.04) 4/23 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF197,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 129526416 129526416 C A 1 0 0 0 0 1 0 0 0 308 710 25 2 2 ADAMTS19 5 129526416 Missense_Mutation SNP C C3N-01488_T 3053120 129526416 52011843 176 24550 RAD50 0 . GRCh38 5 132559359 132559359 + Missense_Mutation SNP G G T rs370769989 C3N-01488_T C3N-01488_N G G c.205G>T p.Asp69Tyr p.D69Y ENST00000378823 2/25 190 161 29 271 271 0 strelka-varscan RAD50,missense_variant,p.Asp69Tyr,ENST00000378823,NM_005732.3;RAD50,missense_variant,p.Asp69Tyr,ENST00000453394,;RAD50,5_prime_UTR_variant,,ENST00000416135,;IL5,upstream_gene_variant,,ENST00000450655,;RAD50,missense_variant,p.Asp69Tyr,ENST00000533482,;RAD50,missense_variant,p.Asp69Tyr,ENST00000423956,; T ENST00000378823 Transcript missense_variant 592/8306 205/3939 69/1312 D/Y Gat/Tat rs370769989,COSM332051,COSM420422 1 1 RAD50 HGNC HGNC:9816 protein_coding YES CCDS34233.1 ENSP00000368100 Q92878 UPI000006E9ED NM_005732.3 deleterious(0) 2/25 Gene3D:3.40.50.300,Pfam_domain:PF13476,hmmpanther:PTHR18867,hmmpanther:PTHR18867:SF12,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00606 uncertain_significance 0,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 132559359 132559359 G T 1 0 0 0 0 1 0 0 0 13145 1058 37 1 1 RAD50 5 132559359 Missense_Mutation SNP G C3N-01488_T 3032943 132559359 48978900 177 24551 RAD50 0 . GRCh38 5 132595584 132595584 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1981G>T p.Gly661Ter p.G661* ENST00000378823 13/25 239 199 40 334 333 1 strelka-varscan RAD50,stop_gained,p.Gly661Ter,ENST00000378823,NM_005732.3;RAD50,stop_gained,p.Gly600Ter,ENST00000453394,;RAD50,downstream_gene_variant,,ENST00000434288,;RAD50,non_coding_transcript_exon_variant,,ENST00000496204,;RAD50,3_prime_UTR_variant,,ENST00000533482,;RAD50,3_prime_UTR_variant,,ENST00000423956,; T ENST00000378823 Transcript stop_gained 2368/8306 1981/3939 661/1312 G/* Gga/Tga 1 1 RAD50 HGNC HGNC:9816 protein_coding YES CCDS34233.1 ENSP00000368100 Q92878 UPI000006E9ED NM_005732.3 13/25 Superfamily_domains:0053474,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF04423,PROSITE_profiles:PS51131,hmmpanther:PTHR18867,hmmpanther:PTHR18867:SF12,TIGRFAM_domain:TIGR00606 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 132595584 132595584 G T 1 0 0 0 0 0 1 0 0 13145 1349 47 2 2 RAD50 5 132595584 Nonsense_Mutation SNP G C3N-01488_T 36225 132595584 48942675 178 24552 SCGB3A2 0 . GRCh38 5 147881614 147881614 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.224G>C p.Gly75Ala p.G75A ENST00000296694 2/3 160 134 26 243 243 0 strelka-varscan SCGB3A2,missense_variant,p.Gly75Ala,ENST00000296694,NM_054023.4;SCGB3A2,missense_variant,p.Gly30Ala,ENST00000504320,;CTC-327F10.5,downstream_gene_variant,,ENST00000512300,;SCGB3A2,non_coding_transcript_exon_variant,,ENST00000514688,;SCGB3A2,non_coding_transcript_exon_variant,,ENST00000507160,;C5orf46,intron_variant,,ENST00000510432,; C ENST00000296694 Transcript missense_variant 317/515 224/282 75/93 G/A gGa/gCa 1 1 SCGB3A2 HGNC HGNC:18391 protein_coding YES CCDS4287.1 ENSP00000296694 Q96PL1 Q2L6B3 UPI0000001278 NM_054023.4 deleterious(0.02) 2/3 hmmpanther:PTHR34829,hmmpanther:PTHR34829:SF2,Pfam_domain:PF01099,PD586436 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 147881614 147881614 G C 1 0 0 0 0 1 0 0 0 14170 1174 41 4 4 SCGB3A2 5 147881614 Missense_Mutation SNP G C3N-01488_T 15286030 147881614 33656645 179 24553 FBXO38 0 . GRCh38 5 148406265 148406265 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.739A>T p.Asn247Tyr p.N247Y ENST00000394370 7/22 78 57 21 109 109 0 strelka-varscan FBXO38,missense_variant,p.Asn247Tyr,ENST00000340253,;FBXO38,missense_variant,p.Asn247Tyr,ENST00000394370,NM_030793.4;FBXO38,missense_variant,p.Asn247Tyr,ENST00000296701,NM_001271723.1;FBXO38,missense_variant,p.Asn247Tyr,ENST00000513826,;FBXO38,non_coding_transcript_exon_variant,,ENST00000509699,;FBXO38,intron_variant,,ENST00000511080,;FBXO38,downstream_gene_variant,,ENST00000503613,;FBXO38,downstream_gene_variant,,ENST00000521160,;FBXO38,non_coding_transcript_exon_variant,,ENST00000502571,;FBXO38,downstream_gene_variant,,ENST00000508326,;FBXO38,upstream_gene_variant,,ENST00000508670,;FBXO38,downstream_gene_variant,,ENST00000502629,; T ENST00000394370 Transcript missense_variant 840/4132 739/3342 247/1113 N/Y Aat/Tat 1 1 FBXO38 HGNC HGNC:28844 protein_coding YES CCDS43384.1 ENSP00000377895 Q6PIJ6 UPI000034ECEB NM_030793.4 deleterious(0) 7/22 hmmpanther:PTHR14753,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 148406265 148406265 A T 1 0 0 0 0 1 0 0 0 5609 14 1 4 4 FBXO38 5 148406265 Missense_Mutation SNP A C3N-01488_T 524651 148406265 33131994 180 24554 ATP10B 0 . GRCh38 5 160606839 160606839 + Missense_Mutation SNP C C A rs200782414 C3N-01488_T C3N-01488_N C C c.3086G>T p.Arg1029Leu p.R1029L ENST00000327245 19/26 282 239 43 357 356 1 strelka-varscan ATP10B,missense_variant,p.Arg1029Leu,ENST00000327245,NM_025153.2;ATP10B,upstream_gene_variant,,ENST00000523758,;ATP10B,downstream_gene_variant,,ENST00000522169,;ATP10B,non_coding_transcript_exon_variant,,ENST00000517815,; A ENST00000327245 Transcript missense_variant 3933/7566 3086/4386 1029/1461 R/L cGc/cTc rs200782414,COSM3853354 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0.01) 19/26 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF79,Gene3D:3.40.50.1000,TIGRFAM_domain:TIGR01652,TIGRFAM_domain:TIGR01494,Superfamily_domains:SSF56784 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 160606839 160606839 C A 1 0 0 0 0 1 0 0 0 1269 768 27 1 1 ATP10B 5 160606839 Missense_Mutation SNP C C3N-01488_T 12200574 160606839 20931420 181 24555 MAT2B 0 . GRCh38 5 163517675 163517675 + Splice_Site SNP G G T novel C3N-01488_T C3N-01488_N G G c.834+1G>T p.X278_splice ENST00000321757 109 81 28 150 150 0 strelka-varscan MAT2B,splice_donor_variant,,ENST00000280969,NM_182796.2;MAT2B,splice_donor_variant,,ENST00000321757,NM_013283.4;MAT2B,3_prime_UTR_variant,,ENST00000518095,;MAT2B,downstream_gene_variant,,ENST00000421814,;MAT2B,splice_donor_variant,,ENST00000521838,;MAT2B,splice_donor_variant,,ENST00000523606,;MAT2B,downstream_gene_variant,,ENST00000520449,; T ENST00000321757 Transcript splice_donor_variant -/2103 834/1005 278/334 1 1 MAT2B HGNC HGNC:6905 protein_coding YES CCDS4365.1 ENSP00000325425 Q9NZL9 A0A140VJP2 UPI0000037B81 NM_013283.4 6/6 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 80 163517675 163517675 G T 1 0 0 0 0 0 0 1 0 9257 1391 48 2 2 MAT2B 5 163517675 Splice_Site SNP G C3N-01488_T 2910836 163517675 18020584 182 24556 TENM2 0 . GRCh38 5 168126857 168126857 + Frame_Shift_Del DEL C C - novel C3N-01488_T C3N-01488_N C C c.2317delC p.Arg773AlafsTer127 p.R773Afs*127 ENST00000518659 12/29 224 178 46 302 301 1 sindel-varindel-pindel TENM2,frameshift_variant,p.Arg652AlafsTer127,ENST00000519204,;TENM2,frameshift_variant,p.Arg773AlafsTer127,ENST00000518659,NM_001122679.1;TENM2,frameshift_variant,p.Arg541AlafsTer127,ENST00000520394,;CTB-178M22.1,intron_variant,,ENST00000517408,;CTB-105N12.2,upstream_gene_variant,,ENST00000624423,; - ENST00000518659 Transcript frameshift_variant 2352/8550 2313/8325 771/2774 H/X caC/ca 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 12/29 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2gy5A03,SMART_domains:SM00181 HIGH deletion 5 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 168126857 168126857 C - 1 0 1 0 1 0 0 0 0 16172 506 18 0 0 TENM2 5 168126857 Frame_Shift_Del DEL C C3N-01488_T 4609182 168126857 13411402 183 24557 TENM2 0 . GRCh38 5 168218497 168218497 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.4606G>T p.Ala1536Ser p.A1536S ENST00000518659 23/29 268 219 49 358 358 0 strelka-varscan TENM2,missense_variant,p.Ala1415Ser,ENST00000519204,;TENM2,missense_variant,p.Ala1536Ser,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Ala1297Ser,ENST00000520394,; T ENST00000518659 Transcript missense_variant 4645/8550 4606/8325 1536/2774 A/S Gcc/Tcc 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 tolerated(0.06) 23/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8,Gene3D:2.120.10.30,Superfamily_domains:SSF101898 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 168218497 168218497 G T 1 0 0 0 0 1 0 0 0 16172 1319 46 2 2 TENM2 5 168218497 Missense_Mutation SNP G C3N-01488_T 91640 168218497 13319762 184 24558 DOCK2 0 . GRCh38 5 169716224 169716224 + Silent SNP T T C novel C3N-01488_T C3N-01488_N T T c.1953T>C p.= p.D651D ENST00000256935 20/52 144 107 37 187 187 0 strelka-varscan DOCK2,synonymous_variant,p.=,ENST00000256935,NM_004946.2;DOCK2,synonymous_variant,p.=,ENST00000520908,;DOCK2,intron_variant,,ENST00000540750,;DOCK2,upstream_gene_variant,,ENST00000520836,;DOCK2,synonymous_variant,p.=,ENST00000524185,; C ENST00000256935 Transcript synonymous_variant 2033/6097 1953/5493 651/1830 D gaT/gaC 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 20/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 169716224 169716224 T C 1 0 0 0 0 0 0 0 1 4502 1403 49 5 5 DOCK2 5 169716224 Silent SNP T C3N-01488_T 1497727 169716224 11822035 185 24559 STC2 0 . GRCh38 5 173318018 173318018 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.738C>A p.= p.L246L ENST00000265087 4/4 72 58 14 89 89 0 strelka-varscan STC2,synonymous_variant,p.=,ENST00000265087,NM_003714.2;STC2,downstream_gene_variant,,ENST00000520648,;STC2,downstream_gene_variant,,ENST00000520593,; T ENST00000265087 Transcript synonymous_variant 2048/5353 738/909 246/302 L ctC/ctA 1 -1 STC2 HGNC HGNC:11374 protein_coding YES CCDS4388.1 ENSP00000265087 O76061 Q6FHC9 UPI00001360B8 NM_003714.2 4/4 hmmpanther:PTHR11245:SF2,hmmpanther:PTHR11245 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 173318018 173318018 G T 1 0 0 0 0 0 0 0 1 15652 1161 41 2 2 STC2 5 173318018 Silent SNP G C3N-01488_T 3601794 173318018 8220241 186 24560 DBN1 0 . GRCh38 5 177466947 177466947 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.677G>T p.Arg226Leu p.R226L ENST00000292385 8/15 244 199 45 293 293 0 strelka-varscan-mutect DBN1,missense_variant,p.Arg226Leu,ENST00000292385,NM_080881.2;DBN1,missense_variant,p.Arg224Leu,ENST00000309007,NM_004395.3;DBN1,missense_variant,p.Arg224Leu,ENST00000393565,;DBN1,missense_variant,p.Arg223Leu,ENST00000477391,;DBN1,upstream_gene_variant,,ENST00000512501,;DBN1,downstream_gene_variant,,ENST00000506117,;DBN1,downstream_gene_variant,,ENST00000514833,;DBN1,non_coding_transcript_exon_variant,,ENST00000472831,;DBN1,non_coding_transcript_exon_variant,,ENST00000471767,;DBN1,downstream_gene_variant,,ENST00000505550,; A ENST00000292385 Transcript missense_variant 1287/3072 677/1956 226/651 R/L cGc/cTc 1 -1 DBN1 HGNC HGNC:2695 protein_coding YES CCDS4421.1 ENSP00000292385 Q16643 UPI0000457395 NM_080881.2 deleterious(0.02) 8/15 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10829:SF1,hmmpanther:PTHR10829 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 177466947 177466947 C A 1 0 0 0 0 1 0 0 0 4052 768 27 1 1 DBN1 5 177466947 Missense_Mutation SNP C C3N-01488_T 4148929 177466947 4071312 187 24561 ZNF354B 0 . GRCh38 5 178883561 178883561 + Missense_Mutation SNP G G T rs570095961 C3N-01488_T C3N-01488_N G G c.1109G>T p.Arg370Leu p.R370L ENST00000322434 5/5 188 152 36 289 288 1 strelka-varscan-mutect ZNF354B,missense_variant,p.Arg370Leu,ENST00000322434,NM_058230.2;ZNF354B,downstream_gene_variant,,ENST00000520377,;RNU1-39P,upstream_gene_variant,,ENST00000383897,;ZNF354B,upstream_gene_variant,,ENST00000522714,;ZNF354B,upstream_gene_variant,,ENST00000522624,; T ENST00000322434 Transcript missense_variant 1335/2802 1109/1839 370/612 R/L cGt/cTt rs570095961,COSM4159788 1 1 ZNF354B HGNC HGNC:17197 protein_coding YES CCDS4439.1 ENSP00000327143 Q96LW1 UPI0000071A24 NM_058230.2 tolerated(0.08) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF87,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs570095961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 178883561 178883561 G T 1 0 0 0 0 1 0 0 0 18437 1145 40 1 1 ZNF354B 5 178883561 Missense_Mutation SNP G C3N-01488_T 1416614 178883561 2654698 188 24562 SERPINB9 0 . GRCh38 6 2896144 2896144 + Missense_Mutation SNP G G C rs555422802 C3N-01488_T C3N-01488_N G G c.215C>G p.Ser72Trp p.S72W ENST00000380698 3/7 171 150 21 248 248 0 strelka-varscan-mutect SERPINB9,missense_variant,p.Ser72Trp,ENST00000380698,NM_004155.5; C ENST00000380698 Transcript missense_variant 305/4118 215/1131 72/376 S/W tCg/tGg rs555422802,COSM277223 1 -1 SERPINB9 HGNC HGNC:8955 protein_coding YES CCDS4478.1 ENSP00000370074 P50453 A0A024QZT4 UPI000000121F NM_004155.5 deleterious(0.04) 3/7 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF67,SMART_domains:SM00093,Superfamily_domains:SSF56574 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs555422802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 2896144 2896144 G C 1 0 0 0 0 1 0 0 0 14384 1059 37 4 4 SERPINB9 6 2896144 Missense_Mutation SNP G C3N-01488_T 2896144 167909835 189 24563 AL078584.1 0 . GRCh38 6 24849925 24849925 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.824C>G p.Thr275Ser p.T275S ENST00000613507 11/23 106 91 15 139 139 0 strelka-varscan-mutect FAM65B,missense_variant,p.Thr275Ser,ENST00000613507,;FAM65B,missense_variant,p.Thr275Ser,ENST00000259698,NM_014722.3;FAM65B,missense_variant,p.Thr304Ser,ENST00000538035,NM_001286445.1;FAM65B,missense_variant,p.Thr275Ser,ENST00000540914,NM_001286447.1;FAM65B,missense_variant,p.Thr275Ser,ENST00000378023,NM_015864.3;AL078584.1,missense_variant,p.Thr309Ser,ENST00000510784,NM_001286446.1; C ENST00000613507 Transcript missense_variant 1065/5539 824/3207 275/1068 T/S aCt/aGt 1 -1 FAM65B HGNC HGNC:13872 protein_coding YES CCDS47383.1 ENSP00000482957 Q9Y4F9 A0A024QZY9 UPI0000EE554D tolerated(0.37) 11/23 Pfam_domain:PF15903,hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF2 MODERATE SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 24849925 24849925 G C 1 0 0 0 0 1 0 0 0 571 1029 36 4 4 AL078584.1 6 24849925 Missense_Mutation SNP G C3N-01488_T 21953781 24849925 145956054 190 24564 SLC17A4 0 . GRCh38 6 25770985 25770985 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.679G>T p.Gly227Ter p.G227* ENST00000377905 6/12 229 205 24 320 320 0 strelka-varscan-mutect SLC17A4,stop_gained,p.Gly173Ter,ENST00000439485,NM_001286121.1;SLC17A4,stop_gained,p.Gly227Ter,ENST00000377905,NM_005495.2;SLC17A4,intron_variant,,ENST00000397076,; T ENST00000377905 Transcript stop_gained 798/3616 679/1494 227/497 G/* Gga/Tga 1 1 SLC17A4 HGNC HGNC:10932 protein_coding YES CCDS4564.1 ENSP00000367137 Q9Y2C5 A0A024R013 UPI0000073585 NM_005495.2 6/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF284,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 25770985 25770985 G T 1 0 0 0 0 0 1 0 0 14684 1001 35 2 2 SLC17A4 6 25770985 Nonsense_Mutation SNP G C3N-01488_T 921060 25770985 145034994 191 24565 SLC17A1 0 . GRCh38 6 25798866 25798866 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.1323G>T p.= p.V441V ENST00000244527 12/13 107 95 12 170 170 0 strelka-varscan-mutect SLC17A1,synonymous_variant,p.=,ENST00000244527,NM_005074.3;SLC17A1,synonymous_variant,p.=,ENST00000476801,;SLC17A1,synonymous_variant,p.=,ENST00000468082,;SLC17A1,3_prime_UTR_variant,,ENST00000377886,; A ENST00000244527 Transcript synonymous_variant 1439/1844 1323/1404 441/467 V gtG/gtT 1 -1 SLC17A1 HGNC HGNC:10929 protein_coding YES CCDS4565.1 ENSP00000244527 Q14916 UPI00000719C0 NM_005074.3 12/13 Gene3D:1.20.1250.20,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF26,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00894,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 25798866 25798866 C A 1 0 0 0 0 0 0 0 1 14681 813 29 2 2 SLC17A1 6 25798866 Silent SNP C C3N-01488_T 27881 25798866 145007113 192 24566 MAS1L 0 . GRCh38 6 29487612 29487612 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.291C>A p.Phe97Leu p.F97L ENST00000377127 1/1 318 288 30 404 402 2 strelka-varscan-mutect MAS1L,missense_variant,p.Phe97Leu,ENST00000377127,NM_052967.1;RPS17P1,downstream_gene_variant,,ENST00000396783,; T ENST00000377127 Transcript missense_variant 345/1260 291/1137 97/378 F/L ttC/ttA 1 -1 MAS1L HGNC HGNC:13961 protein_coding YES CCDS4661.1 ENSP00000366331 P35410 W8W3J1 UPI000003B44C NM_052967.1 tolerated(1) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF12,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 29487612 29487612 G T 1 0 0 0 0 1 0 0 0 9247 933 33 2 2 MAS1L 6 29487612 Missense_Mutation SNP G C3N-01488_T 3688746 29487612 141318367 193 24567 PPP1R10 0 . GRCh38 6 30604624 30604624 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.1066G>C p.Val356Leu p.V356L ENST00000376511 12/20 208 161 47 289 289 0 strelka-varscan-mutect PPP1R10,missense_variant,p.Val356Leu,ENST00000376511,NM_002714.3;PPP1R10,non_coding_transcript_exon_variant,,ENST00000476704,;PPP1R10,downstream_gene_variant,,ENST00000461593,;PPP1R10,upstream_gene_variant,,ENST00000496955,;PPP1R10,downstream_gene_variant,,ENST00000468181,; G ENST00000376511 Transcript missense_variant 1619/4525 1066/2823 356/940 V/L Gtt/Ctt 1 -1 PPP1R10 HGNC HGNC:9284 protein_coding YES CCDS4681.1 ENSP00000365694 Q96QC0 Q2L6I0 UPI000000D73C NM_002714.3 tolerated(0.07) 12/20 hmmpanther:PTHR12506,hmmpanther:PTHR12506:SF18,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 30604624 30604624 C G 1 0 0 0 0 1 0 0 0 12462 507 18 4 4 PPP1R10 6 30604624 Missense_Mutation SNP C C3N-01488_T 1117012 30604624 140201355 194 24568 CDC5L 0 . GRCh38 6 44445779 44445779 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2216G>T p.Trp739Leu p.W739L ENST00000371477 15/16 331 301 30 501 500 1 strelka-varscan-mutect CDC5L,missense_variant,p.Trp739Leu,ENST00000371477,NM_001253.3; T ENST00000371477 Transcript missense_variant 2515/6423 2216/2409 739/802 W/L tGg/tTg 1 1 CDC5L HGNC HGNC:1743 protein_coding YES CCDS4912.1 ENSP00000360532 Q99459 UPI000006EE42 NM_001253.3 tolerated(0.59) 15/16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 44445779 44445779 G T 1 0 0 0 0 1 0 0 0 2785 1357 47 2 2 CDC5L 6 44445779 Missense_Mutation SNP G C3N-01488_T 13841155 44445779 126360200 195 24569 ADGRF2 0 . GRCh38 6 47681993 47681993 + Silent SNP A A C novel C3N-01488_T C3N-01488_N A A c.1434A>C p.= p.T478T ENST00000296862 6/6 240 217 23 312 311 1 strelka-varscan-mutect ADGRF2,synonymous_variant,p.=,ENST00000398742,NM_153839.6;ADGRF2,synonymous_variant,p.=,ENST00000507065,;ADGRF2,synonymous_variant,p.=,ENST00000296862,;ADGRF4,upstream_gene_variant,,ENST00000371220,;ADGRF2,synonymous_variant,p.=,ENST00000467205,; C ENST00000296862 Transcript synonymous_variant 1434/2127 1434/2127 478/708 T acA/acC 1 1 ADGRF2 HGNC HGNC:18991 protein_coding YES ENSP00000296862 Q8IZF7 UPI000007411C 6/6 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF54 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 47681993 47681993 A C 1 0 0 0 0 0 0 0 1 364 175 7 5 5 ADGRF2 6 47681993 Silent SNP A C3N-01488_T 3236214 47681993 123123986 196 24570 PTCHD4 0 . GRCh38 6 47878459 47878459 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.2385A>T p.= p.T795T ENST00000339488 3/3 146 116 30 248 248 0 strelka-varscan-mutect PTCHD4,synonymous_variant,p.=,ENST00000339488,NM_001013732.3; A ENST00000339488 Transcript synonymous_variant 2419/2850 2385/2541 795/846 T acA/acT 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 3/3 Gene3D:2j8sB01,Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15,Low_complexity_(Seg):seg,Superfamily_domains:SSF82866,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 47878459 47878459 T A 1 0 0 0 0 0 0 0 1 12887 1683 59 4 4 PTCHD4 6 47878459 Silent SNP T C3N-01488_T 196466 47878459 122927520 197 24571 PTCHD4 0 . GRCh38 6 47879162 47879162 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1682G>T p.Ser561Ile p.S561I ENST00000339488 3/3 201 169 32 334 334 0 strelka-varscan-mutect PTCHD4,missense_variant,p.Ser561Ile,ENST00000339488,NM_001013732.3; A ENST00000339488 Transcript missense_variant 1716/2850 1682/2541 561/846 S/I aGc/aTc 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 tolerated(0.43) 3/3 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 47879162 47879162 C A 1 0 0 0 0 1 0 0 0 12887 797 28 2 2 PTCHD4 6 47879162 Missense_Mutation SNP C C3N-01488_T 703 47879162 122926817 198 24572 GFRAL 0 . GRCh38 6 55333911 55333911 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.283A>G p.Lys95Glu p.K95E ENST00000340465 3/9 66 57 9 124 124 0 strelka-varscan-mutect GFRAL,missense_variant,p.Lys95Glu,ENST00000340465,NM_207410.2; G ENST00000340465 Transcript missense_variant 369/1911 283/1185 95/394 K/E Aaa/Gaa 1 1 GFRAL HGNC HGNC:32789 protein_coding YES CCDS4957.1 ENSP00000343636 Q6UXV0 UPI000023780D NM_207410.2 tolerated(0.11) 3/9 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF1,SMART_domains:SM00907 MODERATE 1 SNV 1 1 PASS rs925064576 . 0 208 2 0 0 0 0 0 -19.91213 1 1 1 1 0 G 3 3 80 55333911 55333911 A G 1 0 0 0 0 1 0 0 0 6225 131 5 5 5 GFRAL 6 55333911 Missense_Mutation SNP A C3N-01488_T 7454749 55333911 115472068 199 24573 EYS 0 . GRCh38 6 65494800 65494800 + Missense_Mutation SNP G G A C3N-01488_T C3N-01488_N G G c.611C>T p.Pro204Leu p.P204L ENST00000370621 4/44 155 130 25 329 329 0 strelka-varscan-mutect EYS,missense_variant,p.Pro204Leu,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Pro204Leu,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Pro204Leu,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Pro204Leu,ENST00000342421,NM_198283.1;EYS,missense_variant,p.Pro101Leu,ENST00000471279,;EYS,non_coding_transcript_exon_variant,,ENST00000489873,; A ENST00000370621 Transcript missense_variant 1138/10485 611/9498 204/3165 P/L cCt/cTt COSM451726,COSM451727 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.18) 4/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 65494800 65494800 G A 1 0 0 0 0 1 0 0 0 5200 1000 35 3 3 EYS 6 65494800 Missense_Mutation SNP G C3N-01488_T 10160889 65494800 105311179 200 24574 MTFR2 0 . GRCh38 6 136239637 136239637 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.698C>A p.Ser233Tyr p.S233Y ENST00000420702 6/8 180 150 30 403 403 0 strelka-varscan-mutect MTFR2,missense_variant,p.Ser233Tyr,ENST00000420702,NM_001099286.1;MTFR2,missense_variant,p.Ser233Tyr,ENST00000451457,NM_138419.3;MTFR2,missense_variant,p.Ser190Tyr,ENST00000418509,;MTFR2,upstream_gene_variant,,ENST00000532958,;MTFR2,3_prime_UTR_variant,,ENST00000367784,NM_001318738.1; T ENST00000420702 Transcript missense_variant 1088/1793 698/1158 233/385 S/Y tCt/tAt 1 -1 MTFR2 HGNC HGNC:21115 protein_coding YES CCDS5176.1 ENSP00000395232 Q6P444 UPI000004FA2A NM_001099286.1 tolerated(0.31) 6/8 Pfam_domain:PF05308,hmmpanther:PTHR14215,hmmpanther:PTHR14215:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 136239637 136239637 G T 1 0 0 0 0 1 0 0 0 9913 942 33 2 2 MTFR2 6 136239637 Missense_Mutation SNP G C3N-01488_T 70744837 136239637 34566342 201 24575 HIVEP2 0 . GRCh38 6 142764809 142764809 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.5508C>T p.= p.F1836F ENST00000367603 7/10 142 121 21 259 259 0 strelka-varscan-mutect HIVEP2,synonymous_variant,p.=,ENST00000367603,NM_006734.3;HIVEP2,synonymous_variant,p.=,ENST00000367604,;HIVEP2,synonymous_variant,p.=,ENST00000012134,; A ENST00000367603 Transcript synonymous_variant 6251/9723 5508/7341 1836/2446 F ttC/ttT 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 7/10 PROSITE_profiles:PS50157,hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 142764809 142764809 G A 1 0 0 0 0 0 0 0 1 7076 1281 45 3 3 HIVEP2 6 142764809 Silent SNP G C3N-01488_T 6525172 142764809 28041170 202 24576 TIAM2 0 . GRCh38 6 155256650 155256650 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.4635T>A p.= p.S1545S ENST00000461783 29/29 304 250 54 508 508 0 strelka-varscan-mutect TIAM2,synonymous_variant,p.=,ENST00000461783,;TIAM2,synonymous_variant,p.=,ENST00000318981,NM_012454.3;TIAM2,synonymous_variant,p.=,ENST00000360366,;TIAM2,synonymous_variant,p.=,ENST00000529824,;TIAM2,synonymous_variant,p.=,ENST00000528391,;TIAM2,synonymous_variant,p.=,ENST00000456877,;TIAM2,synonymous_variant,p.=,ENST00000275246,NM_001010927.2;TIAM2,downstream_gene_variant,,ENST00000528535,;TFB1M,downstream_gene_variant,,ENST00000367166,NM_016020.3;RP11-477D19.2,non_coding_transcript_exon_variant,,ENST00000435295,;TFB1M,downstream_gene_variant,,ENST00000468889,;TFB1M,downstream_gene_variant,,ENST00000489874,;TFB1M,downstream_gene_variant,,ENST00000495806,;TFB1M,downstream_gene_variant,,ENST00000470239,;TIAM2,non_coding_transcript_exon_variant,,ENST00000537845,; A ENST00000461783 Transcript synonymous_variant 5908/6981 4635/5106 1545/1701 S tcT/tcA 1 1 TIAM2 HGNC HGNC:11806 protein_coding YES CCDS34558.1 ENSP00000437188 Q8IVF5 UPI00004DF8BE 29/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF118 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 155256650 155256650 T A 1 0 0 0 0 0 0 0 1 16325 1538 54 4 4 TIAM2 6 155256650 Silent SNP T C3N-01488_T 12491841 155256650 15549329 203 24577 MAP3K4 0 . GRCh38 6 161092043 161092043 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.3169G>C p.Glu1057Gln p.E1057Q ENST00000392142 13/27 137 123 14 294 294 0 strelka-varscan-mutect MAP3K4,missense_variant,p.Glu1057Gln,ENST00000392142,NM_005922.3,NM_001291958.1;MAP3K4,missense_variant,p.Glu1057Gln,ENST00000366920,NM_001301072.1;MAP3K4,missense_variant,p.Glu1057Gln,ENST00000366919,NM_006724.3;MAP3K4,missense_variant,p.Glu1057Gln,ENST00000348824,;MAP3K4,missense_variant,p.Glu1057Gln,ENST00000544041,;MAP3K4,3_prime_UTR_variant,,ENST00000490904,;MAP3K4,upstream_gene_variant,,ENST00000543421,; C ENST00000392142 Transcript missense_variant 3317/5490 3169/4827 1057/1608 E/Q Gag/Cag 1 1 MAP3K4 HGNC HGNC:6856 protein_coding YES CCDS34565.1 ENSP00000375986 Q9Y6R4 UPI00004574E1 NM_005922.3,NM_001291958.1 deleterious(0.01) 13/27 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 161092043 161092043 G C 1 0 0 0 0 1 0 0 0 9175 1175 41 4 4 MAP3K4 6 161092043 Missense_Mutation SNP G C3N-01488_T 5835393 161092043 9713936 204 24578 SFT2D1 0 . GRCh38 6 166330180 166330180 + Missense_Mutation SNP C C A rs772038544 C3N-01488_T C3N-01488_N C C c.131G>T p.Gly44Val p.G44V ENST00000361731 2/8 102 87 15 167 167 0 strelka-mutect SFT2D1,missense_variant,p.Gly44Val,ENST00000361731,NM_145169.2;SFT2D1,non_coding_transcript_exon_variant,,ENST00000487841,;SFT2D1,non_coding_transcript_exon_variant,,ENST00000478705,;SFT2D1,non_coding_transcript_exon_variant,,ENST00000488773,;SFT2D1,upstream_gene_variant,,ENST00000494682,;HNRNPA1P49,upstream_gene_variant,,ENST00000421336,; A ENST00000361731 Transcript missense_variant 241/1079 131/480 44/159 G/V gGc/gTc rs772038544 1 -1 SFT2D1 HGNC HGNC:21102 protein_coding YES CCDS5292.1 ENSP00000354590 Q8WV19 UPI00000722B1 NM_145169.2 deleterious(0) 2/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR23137:SF7,hmmpanther:PTHR23137,Pfam_domain:PF04178 MODERATE 1 SNV 1 1 PASS rs772038544 . 0 208 0 2 0 0 0 0 -19.99997 0.9999999 1 1 1 0 A 3 1 80 166330180 166330180 C A 1 0 0 0 0 1 0 0 0 14445 739 26 2 2 SFT2D1 6 166330180 Missense_Mutation SNP C C3N-01488_T 5238137 166330180 4475799 205 24579 CYP2W1 0 . GRCh38 7 984512 984512 + Missense_Mutation SNP C C A rs749614470 C3N-01488_T C3N-01488_N C C c.275C>A p.Pro92His p.P92H ENST00000308919 2/9 180 146 34 221 221 0 strelka-varscan-mutect CYP2W1,missense_variant,p.Pro36His,ENST00000340150,;CYP2W1,missense_variant,p.Pro92His,ENST00000308919,NM_017781.2;CYP2W1,upstream_gene_variant,,ENST00000415893,;CYP2W1,upstream_gene_variant,,ENST00000462453,;CYP2W1,upstream_gene_variant,,ENST00000468456,; A ENST00000308919 Transcript missense_variant 288/2304 275/1473 92/490 P/H cCc/cAc rs749614470 1 1 CYP2W1 HGNC HGNC:20243 protein_coding YES CCDS5319.2 ENSP00000310149 Q8TAV3 UPI000013C59A NM_017781.2 tolerated(0.55) 2/9 hmmpanther:PTHR24300:SF183,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS rs749614470 . 0 207 0 3 0 0 0 0 -20 0.999996 1 1 1 0 A 3 1 80 984512 984512 C A 1 0 0 0 0 1 0 0 0 3979 623 22 2 2 CYP2W1 7 984512 Missense_Mutation SNP C C3N-01488_T 984512 158361461 206 24580 AP5Z1 0 . GRCh38 7 4790569 4790569 + Missense_Mutation SNP G G T rs201798269 C3N-01488_T C3N-01488_N G G c.1916G>T p.Arg639Met p.R639M ENST00000348624 15/17 173 139 34 232 232 0 strelka-varscan-mutect AP5Z1,missense_variant,p.Arg639Met,ENST00000348624,NM_014855.2;MIR4656,upstream_gene_variant,,ENST00000579503,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000490487,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000496303,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000477680,;AP5Z1,non_coding_transcript_exon_variant,,ENST00000469614,;AP5Z1,downstream_gene_variant,,ENST00000477454,; T ENST00000348624 Transcript missense_variant 2010/2901 1916/2424 639/807 R/M aGg/aTg rs201798269 1 1 AP5Z1 HGNC HGNC:22197 protein_coding YES CCDS47528.1 ENSP00000297562 O43299 UPI00003E5903 NM_014855.2 deleterious(0) 15/17 hmmpanther:PTHR12181:SF29,hmmpanther:PTHR12181,Gene3D:1.25.10.10 MODERATE 1 SNV 5 1 PASS rs201798269 . 0 207 0 3 0 0 0 0 -20 0.9999963 1 1 1 0 T 3 4 80 4790569 4790569 G T 1 0 0 0 0 1 0 0 0 874 1000 35 2 2 AP5Z1 7 4790569 Missense_Mutation SNP G C3N-01488_T 3806057 4790569 154555404 207 24581 AGMO 0 . GRCh38 7 15544814 15544814 + Nonsense_Mutation SNP C C A rs188343828 C3N-01488_T C3N-01488_N C C c.367G>T p.Gly123Ter p.G123* ENST00000342526 3/13 149 133 16 180 180 0 strelka-varscan-mutect AGMO,stop_gained,p.Gly123Ter,ENST00000342526,NM_001004320.1; A ENST00000342526 Transcript stop_gained 537/2475 367/1338 123/445 G/* Gga/Tga rs188343828 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 3/13 Pfam_domain:PF04116,hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 HIGH 1 SNV 1 1 PASS rs188343828 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 80 15544814 15544814 C A 1 0 0 0 0 0 1 0 0 463 690 24 2 2 AGMO 7 15544814 Nonsense_Mutation SNP C C3N-01488_T 10754245 15544814 143801159 208 24582 EVX1 0 . GRCh38 7 27246170 27246170 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.969G>T p.= p.L323L ENST00000496902 3/3 313 240 73 366 365 1 strelka-varscan-mutect EVX1,synonymous_variant,p.=,ENST00000496902,NM_001989.4,NM_001304519.1;EVX1,3_prime_UTR_variant,,ENST00000580535,;EVX1,3_prime_UTR_variant,,ENST00000222761,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1-AS,upstream_gene_variant,,ENST00000519218,;EVX1,upstream_gene_variant,,ENST00000518886,; T ENST00000496902 Transcript synonymous_variant 1300/2955 969/1224 323/407 L ctG/ctT 1 1 EVX1 HGNC HGNC:3506 protein_coding YES CCDS5413.1 ENSP00000419266 P49640 UPI000012A2AD NM_001989.4,NM_001304519.1 3/3 hmmpanther:PTHR24329:SF246,hmmpanther:PTHR24329 LOW 1 SNV 1 1 PASS rs996765710 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 27246170 27246170 G T 1 0 0 0 0 0 0 0 1 5161 1364 48 2 2 EVX1 7 27246170 Silent SNP G C3N-01488_T 11701356 27246170 132099803 209 24583 TBX20 0 . GRCh38 7 35253585 35253585 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.36C>A p.= p.S12S ENST00000408931 1/8 205 160 45 235 235 0 strelka-varscan-mutect TBX20,synonymous_variant,p.=,ENST00000408931,NM_001077653.2;AC009531.2,downstream_gene_variant,,ENST00000442323,;TBX20,non_coding_transcript_exon_variant,,ENST00000492961,; T ENST00000408931 Transcript synonymous_variant 563/1871 36/1344 12/447 S tcC/tcA 1 -1 TBX20 HGNC HGNC:11598 protein_coding YES CCDS43568.1 ENSP00000386170 Q9UMR3 UPI00004B23D3 NM_001077653.2 1/8 hmmpanther:PTHR11267 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 35253585 35253585 G T 1 0 0 0 0 0 0 0 1 16061 987 35 2 2 TBX20 7 35253585 Silent SNP G C3N-01488_T 8007415 35253585 124092388 210 24584 OGDH 0 . GRCh38 7 44696112 44696112 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1756G>T p.Asp586Tyr p.D586Y ENST00000222673 13/23 171 135 36 199 198 1 strelka-varscan-mutect OGDH,missense_variant,p.Asp586Tyr,ENST00000222673,NM_002541.3;OGDH,missense_variant,p.Asp586Tyr,ENST00000631326,;OGDH,missense_variant,p.Asp582Tyr,ENST00000449767,NM_001165036.1;OGDH,missense_variant,p.Asp597Tyr,ENST00000447398,;OGDH,missense_variant,p.Asp601Tyr,ENST00000444676,;OGDH,missense_variant,p.Asp436Tyr,ENST00000439616,; T ENST00000222673 Transcript missense_variant 1798/4181 1756/3072 586/1023 D/Y Gac/Tac 1 1 OGDH HGNC HGNC:8124 protein_coding YES CCDS34627.1 ENSP00000222673 Q02218 UPI000006D5FE NM_002541.3 deleterious(0) 13/23 Gene3D:3.40.50.970,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF7,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999968 1 1 1 0 T 3 4 80 44696112 44696112 G T 1 0 0 0 0 1 0 0 0 10913 1174 41 2 2 OGDH 7 44696112 Missense_Mutation SNP G C3N-01488_T 9442527 44696112 114649861 211 24585 COBL 0 . GRCh38 7 51043491 51043491 + Missense_Mutation SNP G G T rs758890126 C3N-01488_T C3N-01488_N G G c.1469C>A p.Ala490Asp p.A490D ENST00000395542 9/14 494 418 76 565 565 0 strelka-varscan-mutect COBL,missense_variant,p.Ala490Asp,ENST00000395542,NM_001287436.1;COBL,missense_variant,p.Ala433Asp,ENST00000265136,NM_015198.3;COBL,missense_variant,p.Ala318Asp,ENST00000431948,;COBL,missense_variant,p.Ala325Asp,ENST00000445054,;COBL,missense_variant,p.Ala409Asp,ENST00000452534,; T ENST00000395542 Transcript missense_variant 1654/5339 1469/3816 490/1271 A/D gCc/gAc rs758890126 1 -1 COBL HGNC HGNC:22199 protein_coding YES CCDS75602.1 ENSP00000378912 O75128 UPI0001F992C3 NM_001287436.1 deleterious(0) 9/14 hmmpanther:PTHR21557,hmmpanther:PTHR21557:SF1 MODERATE 1 SNV 1 1 PASS rs758890126 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 51043491 51043491 G T 1 0 0 0 0 1 0 0 0 3442 1203 42 2 2 COBL 7 51043491 Missense_Mutation SNP G C3N-01488_T 6347379 51043491 108302482 212 24586 POM121L12 0 . GRCh38 7 53035687 53035687 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.16C>A p.Pro6Thr p.P6T ENST00000408890 1/1 66 50 16 101 100 1 strelka-varscan-mutect POM121L12,missense_variant,p.Pro6Thr,ENST00000408890,NM_182595.3; A ENST00000408890 Transcript missense_variant 46/1283 16/891 6/296 P/T Ccg/Acg 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated_low_confidence(0.39) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS rs1481598999 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 53035687 53035687 C A 1 0 0 0 0 1 0 0 0 12352 855 30 2 2 POM121L12 7 53035687 Missense_Mutation SNP C C3N-01488_T 1992196 53035687 106310286 213 24587 ZNF713 0 . GRCh38 7 55939953 55939953 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1279G>T p.Glu427Ter p.E427* ENST00000429591 7/7 83 60 23 124 124 0 strelka-varscan-mutect ZNF713,stop_gained,p.Glu427Ter,ENST00000429591,NM_182633.2;ZNF713,stop_gained,p.Glu414Ter,ENST00000633730,;RP11-15K19.2,intron_variant,,ENST00000426595,; T ENST00000429591 Transcript stop_gained 2067/4339 1279/1332 427/443 E/* Gaa/Taa 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 7/7 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80 HIGH 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 55939953 55939953 G T 1 0 0 0 0 0 1 0 0 18692 1291 45 2 2 ZNF713 7 55939953 Nonsense_Mutation SNP G C3N-01488_T 2904266 55939953 103406020 214 24588 ZNF727 0 . GRCh38 7 64069516 64069516 + Missense_Mutation SNP C C T rs762329481 C3N-01488_T C3N-01488_N C C c.133C>T p.Leu45Phe p.L45F ENST00000456806 3/4 259 217 42 363 363 0 strelka-varscan-mutect ZNF727,missense_variant,p.Leu45Phe,ENST00000456806,NM_001159522.1; T ENST00000456806 Transcript missense_variant,splice_region_variant 312/1679 133/1500 45/499 L/F Ctt/Ttt rs762329481,COSM5672944 1 1 ZNF727 HGNC HGNC:22785 protein_coding YES CCDS55113.1 ENSP00000485448 A8MUV8 UPI0001A23134 NM_001159522.1 deleterious(0.04) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24384:SF98,hmmpanther:PTHR24384,SMART_domains:SM00349,Superfamily_domains:0044637 0,1 MODERATE 1 SNV 4 0,1 1 PASS rs762329481 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 64069516 64069516 C T 1 0 0 0 0 1 0 0 0 18701 927 32 3 3 ZNF727 7 64069516 Missense_Mutation SNP C C3N-01488_T 8129563 64069516 95276457 215 24589 VKORC1L1 0 . GRCh38 7 65954121 65954121 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.242A>G p.His81Arg p.H81R ENST00000434382 2/2 73 59 14 118 118 0 strelka-varscan-mutect VKORC1L1,missense_variant,p.Ile118Val,ENST00000360768,NM_173517.4;VKORC1L1,missense_variant,p.His81Arg,ENST00000434382,NM_001284342.1; G ENST00000434382 Transcript missense_variant 245/1541 242/534 81/177 H/R cAt/cGt 1 1 VKORC1L1 HGNC HGNC:21492 protein_coding YES CCDS64663.1 ENSP00000403077 Q8N0U8 UPI0000423DF4 NM_001284342.1 tolerated_low_confidence(0.34) 2/2 MODERATE 1 SNV 2 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999962 1 1 1 0 G 3 3 80 65954121 65954121 A G 1 0 0 0 0 1 0 0 0 17720 217 8 5 5 VKORC1L1 7 65954121 Missense_Mutation SNP A C3N-01488_T 1884605 65954121 93391852 216 24590 TYW1 0 . GRCh38 7 67098693 67098693 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1537A>T p.Asn513Tyr p.N513Y ENST00000359626 12/16 127 95 32 157 157 0 strelka-varscan-mutect TYW1,missense_variant,p.Asn513Tyr,ENST00000359626,NM_018264.3;TYW1,missense_variant,p.Asn449Tyr,ENST00000615572,;TYW1,3_prime_UTR_variant,,ENST00000361660,;TYW1,non_coding_transcript_exon_variant,,ENST00000495971,; T ENST00000359626 Transcript missense_variant 1701/3348 1537/2199 513/732 N/Y Aac/Tac 1 1 TYW1 HGNC HGNC:25598 protein_coding YES CCDS5538.1 ENSP00000352645 Q9NV66 UPI00003674A9 NM_018264.3 deleterious(0) 12/16 Gene3D:3.20.20.70,Pfam_domain:PF04055,hmmpanther:PTHR13930,hmmpanther:PTHR13930:SF0,Superfamily_domains:SSF102114 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 67098693 67098693 A T 1 0 0 0 0 1 0 0 0 17333 14 1 4 4 TYW1 7 67098693 Missense_Mutation SNP A C3N-01488_T 1144572 67098693 92247280 217 24591 CALN1 0 . GRCh38 7 72106184 72106184 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.355C>A p.Leu119Met p.L119M ENST00000395275 4/7 215 180 35 184 184 0 strelka-varscan-mutect CALN1,missense_variant,p.Leu119Met,ENST00000395275,NM_031468.3;CALN1,missense_variant,p.Leu77Met,ENST00000329008,NM_001017440.2;CALN1,missense_variant,p.Leu77Met,ENST00000395276,;CALN1,missense_variant,p.Leu77Met,ENST00000431984,;CALN1,missense_variant,p.Leu77Met,ENST00000446128,;ABCF2P2,downstream_gene_variant,,ENST00000450549,; T ENST00000395275 Transcript missense_variant 744/9459 355/786 119/261 L/M Ctg/Atg 1 -1 CALN1 HGNC HGNC:13248 protein_coding YES CCDS47603.1 ENSP00000378690 Q9BXU9 UPI0000D4B903 NM_031468.3 deleterious(0) 4/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23050,hmmpanther:PTHR23050:SF51,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 72106184 72106184 G T 1 0 0 0 0 1 0 0 0 2282 962 34 2 2 CALN1 7 72106184 Missense_Mutation SNP G C3N-01488_T 5007491 72106184 87239789 218 24592 CACNA2D1 0 . GRCh38 7 81984666 81984666 + Silent SNP G G C novel C3N-01488_T C3N-01488_N G G c.1842C>G p.= p.A614A ENST00000356860 22/39 338 261 77 463 463 0 strelka-varscan-mutect CACNA2D1,synonymous_variant,p.=,ENST00000356860,NM_000722.3;CACNA2D1,synonymous_variant,p.=,ENST00000356253,;CACNA2D1,synonymous_variant,p.=,ENST00000443883,; C ENST00000356860 Transcript synonymous_variant 2181/7563 1842/3276 614/1091 A gcC/gcG 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 22/39 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 81984666 81984666 G C 1 0 0 0 0 0 0 0 1 2236 1335 47 4 4 CACNA2D1 7 81984666 Silent SNP G C3N-01488_T 9878482 81984666 77361307 219 24593 CDK14 0 . GRCh38 7 90984157 90984157 + Silent SNP T T C novel C3N-01488_T C3N-01488_N T T c.957T>C p.= p.G319G ENST00000380050 10/15 178 154 24 247 247 0 strelka-mutect CDK14,synonymous_variant,p.=,ENST00000406263,NM_001287136.1;CDK14,synonymous_variant,p.=,ENST00000380050,NM_001287135.1;CDK14,synonymous_variant,p.=,ENST00000265741,NM_012395.3;CDK14,synonymous_variant,p.=,ENST00000436577,NM_001287137.1;CDK14,downstream_gene_variant,,ENST00000460493,; C ENST00000380050 Transcript synonymous_variant 1088/4995 957/1410 319/469 G ggT/ggC 1 1 CDK14 HGNC HGNC:8883 protein_coding YES CCDS75626.1 ENSP00000369390 O94921 UPI000013EAF4 NM_001287135.1 10/15 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF154,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 90984157 90984157 T C 1 0 0 0 0 0 0 0 1 2834 1712 60 5 5 CDK14 7 90984157 Silent SNP T C3N-01488_T 8999491 90984157 68361816 220 24594 SAMD9L 0 . GRCh38 7 93133613 93133613 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.2359T>A p.Tyr787Asn p.Y787N ENST00000318238 5/5 206 152 54 272 271 1 strelka-varscan-mutect SAMD9L,missense_variant,p.Tyr787Asn,ENST00000318238,NM_001303500.1,NM_152703.3;SAMD9L,missense_variant,p.Tyr787Asn,ENST00000411955,NM_001303496.1,NM_001303498.1;SAMD9L,missense_variant,p.Tyr787Asn,ENST00000437805,NM_001303497.1;SAMD9L,intron_variant,,ENST00000610760,;SAMD9L,downstream_gene_variant,,ENST00000446033,;SAMD9L,downstream_gene_variant,,ENST00000446959,;SAMD9L,downstream_gene_variant,,ENST00000439952,;SAMD9L,downstream_gene_variant,,ENST00000414791,; T ENST00000318238 Transcript missense_variant 3576/7134 2359/4755 787/1584 Y/N Tat/Aat 1 -1 SAMD9L HGNC HGNC:1349 protein_coding YES CCDS34681.1 ENSP00000326247 Q8IVG5 UPI000020F567 NM_001303500.1,NM_152703.3 deleterious(0.01) 5/5 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF18,Gene3D:3.40.50.300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 93133613 93133613 A T 1 0 0 0 0 1 0 0 0 14087 420 15 4 4 SAMD9L 7 93133613 Missense_Mutation SNP A C3N-01488_T 2149456 93133613 66212360 221 24595 NPTX2 0 . GRCh38 7 98627310 98627310 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1034A>T p.Lys345Met p.K345M ENST00000265634 4/5 179 154 25 226 226 0 strelka-varscan-mutect NPTX2,missense_variant,p.Lys345Met,ENST00000265634,NM_002523.2;NPTX2,downstream_gene_variant,,ENST00000466102,; T ENST00000265634 Transcript missense_variant 1199/2700 1034/1296 345/431 K/M aAg/aTg 1 1 NPTX2 HGNC HGNC:7953 protein_coding YES CCDS5657.1 ENSP00000265634 P47972 UPI000013040F NM_002523.2 deleterious(0) 4/5 Gene3D:2.60.120.200,Pfam_domain:PF00354,Prints_domain:PR00895,hmmpanther:PTHR19277,hmmpanther:PTHR19277:SF1,SMART_domains:SM00159,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs1424885365 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 98627310 98627310 A T 1 0 0 0 0 1 0 0 0 10659 72 3 4 4 NPTX2 7 98627310 Missense_Mutation SNP A C3N-01488_T 5493697 98627310 60718663 222 24596 RELN 0 . GRCh38 7 103491999 103491999 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.9397T>A p.Cys3133Ser p.C3133S ENST00000428762 58/65 390 336 54 482 482 0 strelka-varscan-mutect RELN,missense_variant,p.Cys3133Ser,ENST00000424685,;RELN,missense_variant,p.Cys3133Ser,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Cys3133Ser,ENST00000343529,NM_173054.2;CTB-107G13.1,intron_variant,,ENST00000422488,; T ENST00000428762 Transcript missense_variant 9557/11571 9397/10383 3133/3460 C/S Tgt/Agt 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.1) 58/65 hmmpanther:PTHR11841 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 103491999 103491999 A T 1 0 0 0 0 1 0 0 0 13390 130 5 4 4 RELN 7 103491999 Missense_Mutation SNP A C3N-01488_T 4864689 103491999 55853974 223 24597 COG5 0 . GRCh38 7 107256767 107256767 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.1807C>T p.= p.L603L ENST00000297135 16/22 330 263 67 381 380 1 strelka-varscan-mutect COG5,synonymous_variant,p.=,ENST00000393603,NM_001161520.1;COG5,synonymous_variant,p.=,ENST00000297135,NM_006348.3;COG5,intron_variant,,ENST00000347053,NM_181733.2;COG5,non_coding_transcript_exon_variant,,ENST00000468350,;COG5,non_coding_transcript_exon_variant,,ENST00000462342,;COG5,upstream_gene_variant,,ENST00000464542,; A ENST00000297135 Transcript synonymous_variant 2332/4060 1807/2583 603/860 L Ctg/Ttg 1 -1 COG5 HGNC HGNC:14857 protein_coding YES CCDS5742.1 ENSP00000297135 Q9UP83 UPI0000246D05 NM_006348.3 16/22 hmmpanther:PTHR13228,hmmpanther:PTHR13228:SF3 LOW 1 SNV 1 1 PASS rs1173422961 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 107256767 107256767 G A 1 0 0 0 0 0 0 0 1 3449 1020 36 3 3 COG5 7 107256767 Silent SNP G C3N-01488_T 3764768 107256767 52089206 224 24598 DOCK4 0 . GRCh38 7 111994153 111994153 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.297G>T p.Met99Ile p.M99I ENST00000437633 5/52 101 68 33 166 166 0 strelka-varscan-mutect DOCK4,missense_variant,p.Met99Ile,ENST00000428084,;DOCK4,missense_variant,p.Met99Ile,ENST00000437633,NM_014705.3;DOCK4,missense_variant,p.Met87Ile,ENST00000445943,;DOCK4,missense_variant,p.Met87Ile,ENST00000494651,;DOCK4,non_coding_transcript_exon_variant,,ENST00000476846,;DOCK4,non_coding_transcript_exon_variant,,ENST00000468571,; A ENST00000437633 Transcript missense_variant 554/6212 297/5901 99/1966 M/I atG/atT 1 -1 DOCK4 HGNC HGNC:19192 protein_coding YES CCDS47688.1 ENSP00000404179 Q8N1I0 UPI0000D5BB0D NM_014705.3 tolerated(0.94) 5/52 hmmpanther:PTHR23317:SF75,hmmpanther:PTHR23317,Pfam_domain:PF16172 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 111994153 111994153 C A 1 0 0 0 0 1 0 0 0 4504 478 17 2 2 DOCK4 7 111994153 Missense_Mutation SNP C C3N-01488_T 4737386 111994153 47351820 225 24599 PPP1R3A 0 . GRCh38 7 113879718 113879718 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.1374A>T p.= p.S458S ENST00000284601 4/4 188 142 46 274 273 1 strelka-varscan-mutect PPP1R3A,synonymous_variant,p.=,ENST00000284601,NM_002711.3;PPP1R3A,synonymous_variant,p.=,ENST00000449795,;PPP1R3A,downstream_gene_variant,,ENST00000284602,; A ENST00000284601 Transcript synonymous_variant 1443/4384 1374/3369 458/1122 S tcA/tcT 1 -1 PPP1R3A HGNC HGNC:9291 protein_coding YES CCDS5759.1 ENSP00000284601 Q16821 UPI000013DDAA NM_002711.3 4/4 LOW 1 SNV 1 1 PASS rs775908707 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 113879718 113879718 T A 1 0 0 0 0 0 0 0 1 12492 1567 55 4 4 PPP1R3A 7 113879718 Silent SNP T C3N-01488_T 1885565 113879718 45466255 226 24600 ING3 0 . GRCh38 7 120969106 120969106 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.810G>C p.Arg270Ser p.R270S ENST00000315870 9/12 216 172 44 272 272 0 strelka-varscan-mutect ING3,missense_variant,p.Arg270Ser,ENST00000315870,NM_019071.2;ING3,missense_variant,p.Arg255Ser,ENST00000431467,;ING3,3_prime_UTR_variant,,ENST00000427726,;ING3,non_coding_transcript_exon_variant,,ENST00000497502,; C ENST00000315870 Transcript missense_variant 958/3777 810/1257 270/418 R/S agG/agC 1 1 ING3 HGNC HGNC:14587 protein_coding YES CCDS5778.1 ENSP00000320566 Q9NXR8 UPI00000373B3 NM_019071.2 tolerated(0.24) 9/12 hmmpanther:PTHR10333:SF65,hmmpanther:PTHR10333 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 120969106 120969106 G C 1 0 0 0 0 1 0 0 0 7639 1223 43 4 4 ING3 7 120969106 Missense_Mutation SNP G C3N-01488_T 7089388 120969106 38376867 227 24601 GRM8 0 . GRCh38 7 126532952 126532952 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.2430G>T p.Lys810Asn p.K810N ENST00000339582 9/11 58 47 11 89 89 0 strelka-varscan-mutect GRM8,missense_variant,p.Lys810Asn,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Lys810Asn,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Lys318Asn,ENST00000444921,;GRM8,downstream_gene_variant,,ENST00000480995,;GRM8,missense_variant,p.Lys810Asn,ENST00000472701,;GRM8,splice_region_variant,,ENST00000341617,; A ENST00000339582 Transcript missense_variant,splice_region_variant 3239/4057 2430/2727 810/908 K/N aaG/aaT COSM3662898,COSM3662899 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.06) 9/11 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1343682343 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 80 126532952 126532952 C A 1 0 0 0 0 1 0 0 0 6685 695 24 2 2 GRM8 7 126532952 Missense_Mutation SNP C C3N-01488_T 5563846 126532952 32813021 228 24602 CEP41 0 . GRCh38 7 130398910 130398910 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1103A>T p.Gln368Leu p.Q368L ENST00000223208 11/11 432 361 71 571 570 1 strelka-varscan-mutect CEP41,missense_variant,p.Gln368Leu,ENST00000223208,NM_018718.2;CEP41,missense_variant,p.Gln280Leu,ENST00000541543,NM_001257159.1;CEP41,missense_variant,p.Gln296Leu,ENST00000343969,NM_001257158.1;CEP41,downstream_gene_variant,,ENST00000472739,;CEP41,downstream_gene_variant,,ENST00000492389,;CEP41,downstream_gene_variant,,ENST00000475282,;CEP41,downstream_gene_variant,,ENST00000477003,;CEP41,3_prime_UTR_variant,,ENST00000484549,;CEP41,non_coding_transcript_exon_variant,,ENST00000603513,;CEP41,non_coding_transcript_exon_variant,,ENST00000485736,;CEP41,downstream_gene_variant,,ENST00000480206,; A ENST00000223208 Transcript missense_variant 1374/6513 1103/1122 368/373 Q/L cAa/cTa 1 -1 CEP41 HGNC HGNC:12370 protein_coding YES CCDS5821.1 ENSP00000223208 Q9BYV8 UPI000006D546 NM_018718.2 tolerated(0.05) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 130398910 130398910 T A 1 0 0 0 0 1 0 0 0 2973 1812 63 4 4 CEP41 7 130398910 Missense_Mutation SNP T C3N-01488_T 3865958 130398910 28947063 229 24603 PLXNA4 0 . GRCh38 7 132179736 132179736 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3825G>T p.Gln1275His p.Q1275H ENST00000359827 20/32 161 129 32 176 176 0 strelka-varscan-mutect PLXNA4,missense_variant,p.Gln1275His,ENST00000359827,;PLXNA4,missense_variant,p.Gln1275His,ENST00000321063,NM_020911.1; A ENST00000359827 Transcript missense_variant 4788/13786 3825/5685 1275/1894 Q/H caG/caT 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B deleterious(0) 20/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 132179736 132179736 C A 1 0 0 0 0 1 0 0 0 12228 912 32 2 2 PLXNA4 7 132179736 Missense_Mutation SNP C C3N-01488_T 1780826 132179736 27166237 230 24604 UBN2 0 . GRCh38 7 139283784 139283784 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.2879A>G p.Asn960Ser p.N960S ENST00000473989 15/18 341 315 26 453 453 0 strelka-varscan-mutect UBN2,missense_variant,p.Asn960Ser,ENST00000473989,NM_173569.3; G ENST00000473989 Transcript missense_variant 2879/14444 2879/4044 960/1347 N/S aAt/aGt 1 1 UBN2 HGNC HGNC:21931 protein_coding YES CCDS43655.2 ENSP00000418648 Q6ZU65 UPI00001D74DF NM_173569.3 tolerated_low_confidence(1) 15/18 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 139283784 139283784 A G 1 0 0 0 0 1 0 0 0 17417 101 4 5 5 UBN2 7 139283784 Missense_Mutation SNP A C3N-01488_T 7104048 139283784 20062189 231 24605 MGAM2 0 . GRCh38 7 142183295 142183295 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.3846G>T p.Gln1282His p.Q1282H ENST00000477922 33/48 187 144 43 225 225 0 strelka-varscan-mutect MGAM2,missense_variant,p.Gln1282His,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; T ENST00000477922 Transcript missense_variant 3900/7867 3846/7548 1282/2515 Q/H caG/caT 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated(0.29) 33/48 Pfam_domain:PF01055,Superfamily_domains:SSF51445 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 142183295 142183295 G T 1 0 0 0 0 1 0 0 0 9500 1020 36 2 2 MGAM2 7 142183295 Missense_Mutation SNP G C3N-01488_T 2899511 142183295 17162678 232 24606 MGAM2 0 . GRCh38 7 142196197 142196197 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.4390C>A p.Arg1464Ser p.R1464S ENST00000477922 38/48 272 235 37 357 357 0 strelka-varscan-mutect MGAM2,missense_variant,p.Arg1464Ser,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript missense_variant 4444/7867 4390/7548 1464/2515 R/S Cgc/Agc COSM3745580 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0.01) 38/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Superfamily_domains:SSF51445 1 MODERATE 1 SNV 5 1 1 PASS rs1416070278 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 142196197 142196197 C A 1 0 0 0 0 1 0 0 0 9500 652 23 1 1 MGAM2 7 142196197 Missense_Mutation SNP C C3N-01488_T 12902 142196197 17149776 233 24607 TAS2R41 0 . GRCh38 7 143478632 143478632 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.760G>A p.Ala254Thr p.A254T ENST00000408916 1/1 189 153 36 307 307 0 strelka-varscan-mutect TAS2R41,missense_variant,p.Ala254Thr,ENST00000408916,NM_176883.2;EPHA1-AS1,intron_variant,,ENST00000429289,; A ENST00000408916 Transcript missense_variant 760/924 760/924 254/307 A/T Gcc/Acc 1 1 TAS2R41 HGNC HGNC:18883 protein_coding YES CCDS43663.1 ENSP00000386201 P59536 UPI000000D823 NM_176883.2 tolerated(0.1) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR11394:SF73,hmmpanther:PTHR11394,Pfam_domain:PF05296,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 143478632 143478632 G A 1 0 0 0 0 1 0 0 0 15978 1319 46 3 3 TAS2R41 7 143478632 Missense_Mutation SNP G C3N-01488_T 1282435 143478632 15867341 234 24608 CNTNAP2 0 . GRCh38 7 147562231 147562231 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1871C>A p.Pro624His p.P624H ENST00000361727 12/24 408 304 104 557 557 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Pro624His,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,; A ENST00000361727 Transcript missense_variant 2389/9896 1871/3996 624/1331 P/H cCt/cAt 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 12/24 PROSITE_profiles:PS51406,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 147562231 147562231 C A 1 0 0 0 0 1 0 0 0 3428 681 24 2 2 CNTNAP2 7 147562231 Missense_Mutation SNP C C3N-01488_T 4083599 147562231 11783742 235 24609 KCNH2 0 . GRCh38 7 150977855 150977855 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.59G>T p.Arg20Leu p.R20L ENST00000262186 1/15 181 158 23 165 165 0 strelka-varscan-mutect KCNH2,missense_variant,p.Arg20Leu,ENST00000262186,NM_000238.3;KCNH2,5_prime_UTR_variant,,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,; A ENST00000262186 Transcript missense_variant 461/4286 59/3480 20/1159 R/L cGc/cTc 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0.02) 1/15 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 150977855 150977855 C A 1 0 0 0 0 1 0 0 0 7948 768 27 1 1 KCNH2 7 150977855 Missense_Mutation SNP C C3N-01488_T 3415624 150977855 8368118 236 24610 AGAP3 0 . GRCh38 7 151114863 151114863 + Silent SNP G G C novel C3N-01488_T C3N-01488_N G G c.93G>C p.= p.L31L ENST00000335367 1/9 43 33 10 23 23 0 strelka-mutect AGAP3,synonymous_variant,p.=,ENST00000335367,NM_001308305.1;AGAP3,intron_variant,,ENST00000397238,NM_031946.5;AGAP3,intron_variant,,ENST00000622464,;AGAP3,intron_variant,,ENST00000463381,NM_001281300.1;AGAP3,intron_variant,,ENST00000473312,NM_001042535.2;AGAP3,intron_variant,,ENST00000479901,;AGAP3,intron_variant,,ENST00000469901,;AGAP3,upstream_gene_variant,,ENST00000468796,;AGAP3,intron_variant,,ENST00000476375,;AGAP3,intron_variant,,ENST00000490097,;AGAP3,intron_variant,,ENST00000492234,;AGAP3,upstream_gene_variant,,ENST00000486946,;AGAP3,upstream_gene_variant,,ENST00000480106,;AGAP3,upstream_gene_variant,,ENST00000467724,;AGAP3,upstream_gene_variant,,ENST00000473140,;AGAP3,upstream_gene_variant,,ENST00000490839,;AGAP3,upstream_gene_variant,,ENST00000498559,; C ENST00000335367 Transcript synonymous_variant 186/2675 93/1731 31/576 L ctG/ctC 1 1 AGAP3 HGNC HGNC:16923 protein_coding CCDS78287.1 ENSP00000335589 E7ESL9 UPI0000246FFA NM_001308305.1 1/9 LOW SNV 1 1 PASS rs1385529763 . 2 205 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 151114863 151114863 G C 1 0 0 0 0 0 0 0 1 446 1306 46 4 4 AGAP3 7 151114863 Silent SNP G C3N-01488_T 137008 151114863 8231110 237 24611 UBE3C 0 . GRCh38 7 157186951 157186951 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.1261G>C p.Val421Leu p.V421L ENST00000348165 10/23 185 144 41 265 265 0 strelka-varscan-mutect UBE3C,missense_variant,p.Val421Leu,ENST00000348165,NM_014671.2;UBE3C,missense_variant,p.Val378Leu,ENST00000611269,;UBE3C,missense_variant,p.Val378Leu,ENST00000389103,; C ENST00000348165 Transcript missense_variant 1621/5229 1261/3252 421/1083 V/L Gtc/Ctc 1 1 UBE3C HGNC HGNC:16803 protein_coding YES CCDS34789.1 ENSP00000309198 Q15386 UPI000020E72A NM_014671.2 tolerated(0.18) 10/23 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF336 MODERATE 1 SNV 1 1 PASS rs994274762 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 157186951 157186951 G C 1 0 0 0 0 1 0 0 0 17404 1261 44 4 4 UBE3C 7 157186951 Missense_Mutation SNP G C3N-01488_T 6072088 157186951 2159022 238 24612 CSMD1 0 . GRCh38 8 2973127 2973128 + Frame_Shift_Ins INS - - A novel C3N-01488_T C3N-01488_N - - c.8915_8916insT p.Val2973GlyfsTer3 p.V2973Gfs*3 ENST00000520002 58/71 102 80 22 148 148 0 sindel-varindel-pindel CSMD1,frameshift_variant,p.Val2834GlyfsTer3,ENST00000537824,;CSMD1,frameshift_variant,p.Val2390GlyfsTer3,ENST00000335551,;CSMD1,frameshift_variant,p.Val2973GlyfsTer3,ENST00000520002,;CSMD1,frameshift_variant,p.Val2973GlyfsTer3,ENST00000602557,;CSMD1,frameshift_variant,p.Val2972GlyfsTer3,ENST00000635120,NM_033225.5;CSMD1,frameshift_variant,p.Val2915GlyfsTer3,ENST00000400186,;CSMD1,frameshift_variant,p.Val2915GlyfsTer3,ENST00000602723,; A ENST00000520002 Transcript frameshift_variant 9471-9472/11740 8915-8916/10698 2972/3565 P/PX ccg/ccTg 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 58/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 insertion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 80 2973127 2973127 - A 1 0 1 1 0 0 0 0 0 3745 639 23 0 0 CSMD1 8 2973127 Frame_Shift_Ins INS - C3N-01488_T 2973127 142165509 239 24613 CSMD1 0 . GRCh38 8 3409504 3409504 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1666G>T p.Ala556Ser p.A556S ENST00000520002 14/71 212 188 24 271 271 0 strelka-varscan-mutect CSMD1,missense_variant,p.Ala417Ser,ENST00000537824,;CSMD1,missense_variant,p.Ala36Ser,ENST00000335551,;CSMD1,missense_variant,p.Ala556Ser,ENST00000520002,;CSMD1,missense_variant,p.Ala556Ser,ENST00000602557,;CSMD1,missense_variant,p.Ala555Ser,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Ala556Ser,ENST00000400186,;CSMD1,missense_variant,p.Ala556Ser,ENST00000602723,; A ENST00000520002 Transcript missense_variant 2222/11740 1666/10698 556/3565 A/S Gcg/Tcg 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.54) 14/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs891274894 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 3409504 3409504 C A 1 0 0 0 0 1 0 0 0 3745 739 26 2 2 CSMD1 8 3409504 Missense_Mutation SNP C C3N-01488_T 436377 3409504 141729132 240 24614 SFTPC 0 . GRCh38 8 22163453 22163453 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.342G>T p.Lys114Asn p.K114N ENST00000318561 4/6 455 382 73 513 513 0 strelka-varscan-mutect SFTPC,missense_variant,p.Lys114Asn,ENST00000521315,NM_001172357.1;SFTPC,missense_variant,p.Lys114Asn,ENST00000318561,NM_001317778.1,NM_001317780.1,NM_003018.3,NM_001172410.1;SFTPC,missense_variant,p.Lys114Asn,ENST00000522109,;SFTPC,missense_variant,p.Lys114Asn,ENST00000437090,;SFTPC,missense_variant,p.Lys61Asn,ENST00000524255,;SFTPC,missense_variant,p.Lys61Asn,ENST00000520605,;SFTPC,missense_variant,p.Lys61Asn,ENST00000523296,;BMP1,upstream_gene_variant,,ENST00000306385,NM_006129.4;BMP1,upstream_gene_variant,,ENST00000354870,;BMP1,upstream_gene_variant,,ENST00000306349,NM_001199.3;BMP1,upstream_gene_variant,,ENST00000397814,;SFTPC,downstream_gene_variant,,ENST00000522880,;SFTPC,downstream_gene_variant,,ENST00000524318,;SFTPC,downstream_gene_variant,,ENST00000524350,;SFTPC,non_coding_transcript_exon_variant,,ENST00000522630,;BMP1,upstream_gene_variant,,ENST00000520970,;BMP1,upstream_gene_variant,,ENST00000520626,;BMP1,upstream_gene_variant,,ENST00000520982,;BMP1,upstream_gene_variant,,ENST00000471755,;BMP1,upstream_gene_variant,,ENST00000518913,;BMP1,upstream_gene_variant,,ENST00000483364,;BMP1,upstream_gene_variant,,ENST00000521385,;BMP1,upstream_gene_variant,,ENST00000518656,;SFTPC,downstream_gene_variant,,ENST00000518615,; T ENST00000318561 Transcript missense_variant 516/997 342/594 114/197 K/N aaG/aaT 1 1 SFTPC HGNC HGNC:10802 protein_coding YES CCDS43722.1 ENSP00000316152 P11686 A0A0S2Z4Q0 UPI0000140371 NM_001317778.1,NM_001317780.1,NM_003018.3,NM_001172410.1 deleterious(0) 4/6 PROSITE_profiles:PS50869,hmmpanther:PTHR10800,Pfam_domain:PF04089,SMART_domains:SM00019,SMART_domains:SM01039 MODERATE 1 SNV 1 1 PASS rs1318655449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 22163453 22163453 G T 1 0 0 0 0 1 0 0 0 14452 962 34 2 2 SFTPC 8 22163453 Missense_Mutation SNP G C3N-01488_T 18753949 22163453 122975183 241 24615 TNFRSF10A 0 . GRCh38 8 23199436 23199436 + Missense_Mutation SNP G G A rs759566687 C3N-01488_T C3N-01488_N G G c.844C>T p.Arg282Cys p.R282C ENST00000221132 8/10 82 61 21 102 102 0 strelka-varscan-mutect TNFRSF10A,missense_variant,p.Arg282Cys,ENST00000221132,NM_003844.3;TNFRSF10A,missense_variant,p.Arg124Cys,ENST00000613472,;TNFRSF10A,downstream_gene_variant,,ENST00000524158,;TNFRSF10A,upstream_gene_variant,,ENST00000519862,; A ENST00000221132 Transcript missense_variant 909/2714 844/1407 282/468 R/C Cgc/Tgc rs759566687,COSM1229865 1 -1 TNFRSF10A HGNC HGNC:11904 protein_coding YES CCDS6039.1 ENSP00000221132 O00220 UPI000013C7A8 NM_003844.3 tolerated(0.29) 8/10 hmmpanther:PTHR23097:SF113,hmmpanther:PTHR23097,PIRSF_domain:PIRSF037867 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759566687 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 23199436 23199436 G A 1 0 0 0 0 1 0 0 0 16754 1087 38 1 1 TNFRSF10A 8 23199436 Missense_Mutation SNP G C3N-01488_T 1035983 23199436 121939200 242 24616 FGFR1 0 . GRCh38 8 38418333 38418333 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.1418T>C p.Leu473Pro p.L473P ENST00000425967 11/19 385 361 24 421 421 0 strelka-varscan-mutect FGFR1,missense_variant,p.Leu442Pro,ENST00000447712,NM_023110.2;FGFR1,missense_variant,p.Leu440Pro,ENST00000397091,NM_015850.3;FGFR1,missense_variant,p.Leu440Pro,ENST00000532791,NM_001174063.1;FGFR1,missense_variant,p.Leu473Pro,ENST00000425967,NM_001174067.1;FGFR1,missense_variant,p.Leu432Pro,ENST00000335922,NM_001174064.1;FGFR1,missense_variant,p.Leu353Pro,ENST00000356207,NM_023105.2,NM_001174066.1;FGFR1,missense_variant,p.Leu351Pro,ENST00000326324,NM_023106.2;FGFR1,missense_variant,p.Leu440Pro,ENST00000397113,NM_001174065.1;FGFR1,missense_variant,p.Leu353Pro,ENST00000397103,;FGFR1,missense_variant,p.Leu440Pro,ENST00000397108,;FGFR1,3_prime_UTR_variant,,ENST00000341462,;FGFR1,3_prime_UTR_variant,,ENST00000619564,;RP11-350N15.4,upstream_gene_variant,,ENST00000528407,;FGFR1,upstream_gene_variant,,ENST00000526688,;FGFR1,downstream_gene_variant,,ENST00000530701,;FGFR1,3_prime_UTR_variant,,ENST00000487647,;FGFR1,non_coding_transcript_exon_variant,,ENST00000526570,;FGFR1,non_coding_transcript_exon_variant,,ENST00000527114,;FGFR1,non_coding_transcript_exon_variant,,ENST00000466021,;FGFR1,non_coding_transcript_exon_variant,,ENST00000527745,;FGFR1,non_coding_transcript_exon_variant,,ENST00000524528,;FGFR1,downstream_gene_variant,,ENST00000470826,;FGFR1,upstream_gene_variant,,ENST00000531196,;FGFR1,downstream_gene_variant,,ENST00000464163,;FGFR1,upstream_gene_variant,,ENST00000533619,;FGFR1,downstream_gene_variant,,ENST00000475621,; G ENST00000425967 Transcript missense_variant 1741/5375 1418/2562 473/853 L/P cTt/cCt 1 -1 FGFR1 HGNC HGNC:3688 protein_coding YES CCDS55223.1 ENSP00000393312 P11362 UPI0001CE06A3 NM_001174067.1 tolerated(0.25) 11/19 PIRSF_domain:PIRSF000628,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF131,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 38418333 38418333 A G 1 0 0 0 0 1 0 0 0 5727 72 3 5 5 FGFR1 8 38418333 Missense_Mutation SNP A C3N-01488_T 15218897 38418333 106720303 243 24617 ADAM18 0 . GRCh38 8 39648353 39648353 + Silent SNP T T C C3N-01488_T C3N-01488_N T T c.1056T>C p.= p.S352S ENST00000265707 12/20 53 43 10 91 91 0 strelka-varscan-mutect ADAM18,synonymous_variant,p.=,ENST00000265707,NM_014237.2;ADAM18,synonymous_variant,p.=,ENST00000379866,NM_001320313.1;ADAM18,intron_variant,,ENST00000520087,; C ENST00000265707 Transcript synonymous_variant 1101/2388 1056/2220 352/739 S agT/agC COSM1330990 1 1 ADAM18 HGNC HGNC:196 protein_coding YES CCDS6113.1 ENSP00000265707 Q9Y3Q7 UPI00001254D7 NM_014237.2 12/20 Gene3D:3.40.390.10,Pfam_domain:PF01421,PROSITE_profiles:PS50215,hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF158,Superfamily_domains:SSF55486 1 LOW 1 SNV 1 1 1 PASS rs1474693878 . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 C 2 2 80 39648353 39648353 T C 1 0 0 0 0 0 0 0 1 283 1693 59 5 5 ADAM18 8 39648353 Silent SNP T C3N-01488_T 1230020 39648353 105490283 244 24618 SNTG1 0 . GRCh38 8 50792749 50792749 + Missense_Mutation SNP C C A rs759531781 C3N-01488_T C3N-01488_N C C c.1474C>A p.Pro492Thr p.P492T ENST00000522124 19/19 192 160 32 350 348 2 strelka-varscan-mutect SNTG1,missense_variant,p.Pro492Thr,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Pro492Thr,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Pro455Thr,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,; A ENST00000522124 Transcript missense_variant 2135/3504 1474/1554 492/517 P/T Cct/Act rs759531781 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 19/19 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2 MODERATE 1 SNV 1 1 PASS rs759531781 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 50792749 50792749 C A 1 0 0 0 0 1 0 0 0 15194 623 22 2 2 SNTG1 8 50792749 Missense_Mutation SNP C C3N-01488_T 11144396 50792749 94345887 245 24619 XKR4 0 . GRCh38 8 55523752 55523752 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1478G>T p.Cys493Phe p.C493F ENST00000327381 3/3 315 275 40 419 417 2 strelka-varscan-mutect XKR4,missense_variant,p.Cys493Phe,ENST00000327381,NM_052898.1;XKR4,missense_variant,p.Cys493Phe,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; T ENST00000327381 Transcript missense_variant 1578/19880 1478/1953 493/650 C/F tGt/tTt 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 deleterious(0) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14,Pfam_domain:PF09815 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 55523752 55523752 G T 1 0 0 0 0 1 0 0 0 17992 1377 48 2 2 XKR4 8 55523752 Missense_Mutation SNP G C3N-01488_T 4731003 55523752 89614884 246 24620 SLCO5A1 0 . GRCh38 8 69682264 69682264 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1702C>A p.Pro568Thr p.P568T ENST00000260126 7/10 152 125 27 231 230 1 strelka-varscan-mutect SLCO5A1,missense_variant,p.Pro568Thr,ENST00000260126,NM_030958.2;SLCO5A1,missense_variant,p.Pro568Thr,ENST00000524945,NM_001146008.1;SLCO5A1,missense_variant,p.Pro513Thr,ENST00000530307,NM_001146009.1;SLCO5A1,3_prime_UTR_variant,,ENST00000526750,; T ENST00000260126 Transcript missense_variant 2409/9076 1702/2547 568/848 P/T Cca/Aca 1 -1 SLCO5A1 HGNC HGNC:19046 protein_coding YES CCDS6205.1 ENSP00000260126 Q9H2Y9 UPI0000140F53 NM_030958.2 deleterious(0) 7/10 PROSITE_profiles:PS51465,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF91,Pfam_domain:PF03137,Gene3D:3.30.60.30,TIGRFAM_domain:TIGR00805,Pfam_domain:PF07648,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 69682264 69682264 G T 1 0 0 0 0 1 0 0 0 15018 1203 42 2 2 SLCO5A1 8 69682264 Missense_Mutation SNP G C3N-01488_T 14158512 69682264 75456372 247 24621 ZFHX4 0 . GRCh38 8 76842772 76842772 + Splice_Site SNP G G T novel C3N-01488_T C3N-01488_N G G c.3511+1G>T p.X1171_splice ENST00000521891 109 87 22 123 123 0 strelka-varscan-mutect ZFHX4,splice_donor_variant,,ENST00000521891,NM_024721.4;ZFHX4,splice_donor_variant,,ENST00000518282,;ZFHX4,splice_donor_variant,,ENST00000523625,;ZFHX4,splice_donor_variant,,ENST00000519536,; T ENST00000521891 Transcript splice_donor_variant -/14019 3511/10851 1171/3616 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 6/10 HIGH 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999965 1 1 1 0 T 5 4 80 76842772 76842772 G T 1 0 0 0 0 0 0 1 0 18213 1275 44 2 2 ZFHX4 8 76842772 Splice_Site SNP G C3N-01488_T 7160508 76842772 68295864 248 24622 ZFHX4 0 . GRCh38 8 76854715 76854715 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.7794C>A p.Ser2598Arg p.S2598R ENST00000521891 10/11 125 91 34 146 145 1 strelka-varscan-mutect ZFHX4,missense_variant,p.Ser2598Arg,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Ser2572Arg,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; A ENST00000521891 Transcript missense_variant 8242/14019 7794/10851 2598/3616 S/R agC/agA 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 tolerated(0.13) 10/11 Gene3D:1.10.10.60,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,Superfamily_domains:SSF46689 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 76854715 76854715 C A 1 0 0 0 0 1 0 0 0 18213 767 27 1 1 ZFHX4 8 76854715 Missense_Mutation SNP C C3N-01488_T 11943 76854715 68283921 249 24623 SLC7A13 0 . GRCh38 8 86229641 86229641 + Frame_Shift_Del DEL G G - novel C3N-01488_T C3N-01488_N G G c.637delC p.Gln213LysfsTer15 p.Q213Kfs*15 ENST00000297524 1/4 147 122 25 200 199 1 sindel-varindel-pindel SLC7A13,frameshift_variant,p.Gln213LysfsTer15,ENST00000297524,NM_138817.2;SLC7A13,frameshift_variant,p.Gln213LysfsTer10,ENST00000419776,;SLC7A13,intron_variant,,ENST00000520624,; - ENST00000297524 Transcript frameshift_variant 741/1878 637/1413 213/470 Q/X Caa/aa 1 -1 SLC7A13 HGNC HGNC:23092 protein_coding YES CCDS34917.1 ENSP00000297524 Q8TCU3 UPI000006DF39 NM_138817.2 1/4 Transmembrane_helices:TMhelix,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF238,Pfam_domain:PF13520,PIRSF_domain:PIRSF006060 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 86229641 86229641 G - 1 0 1 0 1 0 0 0 0 14978 1357 47 0 0 SLC7A13 8 86229641 Frame_Shift_Del DEL G C3N-01488_T 9374926 86229641 58908995 250 24624 WWP1 0 . GRCh38 8 86374057 86374057 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.7A>G p.Thr3Ala p.T3A ENST00000517970 3/25 178 134 44 239 239 0 strelka-varscan-mutect WWP1,missense_variant,p.Thr3Ala,ENST00000517970,NM_007013.3;WWP1,missense_variant,p.Thr3Ala,ENST00000265428,;WWP1,non_coding_transcript_exon_variant,,ENST00000523863,; G ENST00000517970 Transcript missense_variant 314/4686 7/2769 3/922 T/A Act/Gct 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 tolerated_low_confidence(0.46) 3/25 hmmpanther:PTHR11254:SF299,hmmpanther:PTHR11254,PIRSF_domain:PIRSF001569 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 86374057 86374057 A G 1 0 0 0 0 1 0 0 0 17973 159 6 5 5 WWP1 8 86374057 Missense_Mutation SNP A C3N-01488_T 144416 86374057 58764579 251 24625 DCAF4L2 0 . GRCh38 8 87873452 87873452 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.520C>A p.Pro174Thr p.P174T ENST00000319675 1/1 428 333 95 537 537 0 strelka-varscan-mutect DCAF4L2,missense_variant,p.Pro174Thr,ENST00000319675,NM_152418.3;CTB-118P15.3,downstream_gene_variant,,ENST00000613582,; T ENST00000319675 Transcript missense_variant 617/3326 520/1188 174/395 P/T Cct/Act 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 tolerated(0.18) 1/1 hmmpanther:PTHR22847:SF457,hmmpanther:PTHR22847,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 87873452 87873452 G T 1 0 0 0 0 1 0 0 0 4073 1203 42 2 2 DCAF4L2 8 87873452 Missense_Mutation SNP G C3N-01488_T 1499395 87873452 57265184 252 24626 DPYS 0 . GRCh38 8 104392878 104392878 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1349C>A p.Ala450Asp p.A450D ENST00000351513 8/10 527 450 77 740 740 0 strelka-varscan-mutect DPYS,missense_variant,p.Ala450Asp,ENST00000351513,NM_001385.2;DPYS,upstream_gene_variant,,ENST00000533874,;DPYS,non_coding_transcript_exon_variant,,ENST00000521372,;DPYS,intron_variant,,ENST00000521601,;DPYS,non_coding_transcript_exon_variant,,ENST00000520483,; T ENST00000351513 Transcript missense_variant 1482/2127 1349/1560 450/519 A/D gCc/gAc 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 tolerated(1) 8/10 hmmpanther:PTHR11647:SF50,hmmpanther:PTHR11647,TIGRFAM_domain:TIGR02033,Gene3D:2.30.40.10,Superfamily_domains:SSF51338 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 104392878 104392878 G T 1 0 0 0 0 1 0 0 0 4561 1203 42 2 2 DPYS 8 104392878 Missense_Mutation SNP G C3N-01488_T 16519426 104392878 40745758 253 24627 TRPS1 0 . GRCh38 8 115619824 115619824 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.274G>T p.Val92Phe p.V92F ENST00000395715 3/7 447 332 115 693 692 1 strelka-varscan-mutect TRPS1,missense_variant,p.Val92Phe,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Val79Phe,ENST00000220888,;TRPS1,missense_variant,p.Val83Phe,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Val79Phe,ENST00000519674,;TRPS1,missense_variant,p.Val83Phe,ENST00000517323,;TRPS1,missense_variant,p.Val92Phe,ENST00000519815,;TRPS1,missense_variant,p.Val92Phe,ENST00000395713,;TRPS1,intron_variant,,ENST00000519076,;TRPS1,downstream_gene_variant,,ENST00000422939,;TRPS1,downstream_gene_variant,,ENST00000451156,; A ENST00000395715 Transcript missense_variant 852/9990 274/3885 92/1294 V/F Gtt/Ttt 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 deleterious_low_confidence(0.01) 3/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 115619824 115619824 C A 1 0 0 0 0 1 0 0 0 17099 565 20 2 2 TRPS1 8 115619824 Missense_Mutation SNP C C3N-01488_T 11226946 115619824 29518812 254 24628 TMEM65 0 . GRCh38 8 124372026 124372026 + Frame_Shift_Del DEL G G - rs778670441 C3N-01488_T C3N-01488_N G G c.132delC p.Gly45AlafsTer22 p.G45Afs*22 ENST00000297632 1/7 46 33 13 53 53 0 sindel-varindel-pindel TMEM65,frameshift_variant,p.Gly45AlafsTer22,ENST00000297632,NM_194291.2; - ENST00000297632 Transcript frameshift_variant 667/9029 132/723 44/240 P/X ccC/cc rs778670441 1 -1 TMEM65 HGNC HGNC:25203 protein_coding YES CCDS6348.1 ENSP00000297632 Q6PI78 UPI00003675D1 NM_194291.2 1/7 hmmpanther:PTHR21706,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 194 15 0 0 0 0 0 -20 0.9998584 1 1 1 0 - 7 5 80 124372026 124372026 G - 1 0 1 0 1 0 0 0 0 16670 1103 39 0 0 TMEM65 8 124372026 Frame_Shift_Del DEL G C3N-01488_T 8752202 124372026 20766610 255 24629 OC90 0 . GRCh38 8 132041543 132041543 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.914C>G p.Pro305Arg p.P305R ENST00000262283 8/18 100 77 23 130 130 0 strelka-varscan-mutect RP11-240B13.2,missense_variant,p.Pro305Arg,ENST00000262283,;OC90,missense_variant,p.Pro109Arg,ENST00000254627,NM_001080399.2; C ENST00000262283 Transcript missense_variant 1014/2413 914/2070 305/689 P/R cCt/cGt 1 -1 RP11-240B13.2 Clone_based_vega_gene protein_coding YES ENSP00000262283 I6L893 UPI0000E5AF6B deleterious(0) 8/18 Gene3D:1.20.90.10,Pfam_domain:PF00068,Prints_domain:PR00389,hmmpanther:PTHR11716,hmmpanther:PTHR11716:SF1,SMART_domains:SM00085,Superfamily_domains:SSF48619 MODERATE 1 SNV 1 1 PASS rs764580544 . 0 204 4 2 0 0 0 0 -20 0.9999927 1 1 1 0 C 3 2 80 132041543 132041543 G C 1 0 0 0 0 1 0 0 0 10891 1000 35 4 4 OC90 8 132041543 Missense_Mutation SNP G C3N-01488_T 7669517 132041543 13097093 256 24630 KCNQ3 0 . GRCh38 8 132480327 132480327 + Missense_Mutation SNP A A T rs763182139 C3N-01488_T C3N-01488_N A A c.206T>A p.Leu69Gln p.L69Q ENST00000388996 1/15 145 124 21 155 155 0 strelka-varscan-mutect KCNQ3,missense_variant,p.Leu69Gln,ENST00000388996,NM_004519.3;KCNQ3,missense_variant,p.Leu69Gln,ENST00000519445,;KCNQ3,upstream_gene_variant,,ENST00000519589,; T ENST00000388996 Transcript missense_variant 627/11441 206/2619 69/872 L/Q cTg/cAg rs763182139 1 -1 KCNQ3 HGNC HGNC:6297 protein_coding YES CCDS34943.1 ENSP00000373648 O43525 UPI00001279F0 NM_004519.3 deleterious(0.01) 1/15 MODERATE 1 SNV 1 1 PASS rs763182139 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 132480327 132480327 A T 1 0 0 0 0 1 0 0 0 8000 188 7 4 4 KCNQ3 8 132480327 Missense_Mutation SNP A C3N-01488_T 438784 132480327 12658309 257 24631 FAM135B 0 . GRCh38 8 138132676 138132676 + Silent SNP G G T rs750596567 C3N-01488_T C3N-01488_N G G c.4138C>A p.= p.R1380R ENST00000395297 20/20 471 394 77 508 507 1 strelka-varscan-mutect FAM135B,synonymous_variant,p.=,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,3_prime_UTR_variant,,ENST00000276737,; T ENST00000395297 Transcript synonymous_variant 4309/6962 4138/4221 1380/1406 R Cga/Aga rs750596567 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 20/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 LOW 1 SNV 5 1 PASS rs750596567 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 138132676 138132676 G T 1 0 0 0 0 0 0 0 1 5299 1124 39 1 1 FAM135B 8 138132676 Silent SNP G C3N-01488_T 5652349 138132676 7005960 258 24632 FAM135B 0 . GRCh38 8 138151233 138151233 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.3242C>T p.Ser1081Phe p.S1081F ENST00000395297 13/20 60 48 12 106 106 0 strelka-varscan-mutect FAM135B,missense_variant,p.Ser1081Phe,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Ser1081Phe,ENST00000276737,;FAM135B,missense_variant,p.Ser391Phe,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 3413/6962 3242/4221 1081/1406 S/F tCc/tTc 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.16) 13/20 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 138151233 138151233 G A 1 0 0 0 0 1 0 0 0 5299 1174 41 3 3 FAM135B 8 138151233 Missense_Mutation SNP G C3N-01488_T 18557 138151233 6987403 259 24633 COL22A1 0 . GRCh38 8 138594168 138594168 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.4464C>A p.= p.P1488P ENST00000303045 63/65 238 189 49 301 301 0 strelka-varscan-mutect COL22A1,synonymous_variant,p.=,ENST00000303045,NM_152888.2;COL22A1,synonymous_variant,p.=,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; T ENST00000303045 Transcript synonymous_variant 4911/6346 4464/4881 1488/1626 P ccC/ccA 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 63/65 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 138594168 138594168 G T 1 0 0 0 0 0 0 0 1 3469 1219 43 2 2 COL22A1 8 138594168 Silent SNP G C3N-01488_T 442935 138594168 6544468 260 24634 SLC45A4 0 . GRCh38 8 141254097 141254097 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.133G>T p.Asp45Tyr p.D45Y ENST00000517878 1/8 396 319 77 409 409 0 strelka-varscan-mutect SLC45A4,missense_variant,p.Asp45Tyr,ENST00000517878,NM_001286646.1;SLC45A4,intron_variant,,ENST00000520137,;RP11-10J21.3,upstream_gene_variant,,ENST00000518520,;RP11-10J21.4,upstream_gene_variant,,ENST00000517658,;SLC45A4,downstream_gene_variant,,ENST00000521804,; A ENST00000517878 Transcript missense_variant 133/3470 133/2427 45/808 D/Y Gac/Tac 1 -1 SLC45A4 HGNC HGNC:29196 protein_coding YES CCDS75795.1 ENSP00000428137 E7EV90 UPI0001E8F5C7 NM_001286646.1 deleterious(0) 1/8 hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 141254097 141254097 C A 1 0 0 0 0 1 0 0 0 14920 913 32 2 2 SLC45A4 8 141254097 Missense_Mutation SNP C C3N-01488_T 2659929 141254097 3884539 261 24635 CYP11B2 0 . GRCh38 8 142912029 142912029 + Missense_Mutation SNP A A C novel C3N-01488_T C3N-01488_N A A c.1463T>G p.Ile488Arg p.I488R ENST00000323110 9/9 326 280 46 426 426 0 strelka-varscan-mutect CYP11B2,missense_variant,p.Ile488Arg,ENST00000323110,NM_000498.3;GML,intron_variant,,ENST00000522728,; C ENST00000323110 Transcript missense_variant 1466/2936 1463/1512 488/503 I/R aTa/aGa 1 -1 CYP11B2 HGNC HGNC:2592 protein_coding YES CCDS6393.1 ENSP00000325822 P19099 UPI00001282CF NM_000498.3 deleterious(0) 9/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs1425460719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 142912029 142912029 A C 1 0 0 0 0 1 0 0 0 3949 449 16 5 5 CYP11B2 8 142912029 Missense_Mutation SNP A C3N-01488_T 1657932 142912029 2226607 262 24636 GPIHBP1 0 . GRCh38 8 143215412 143215412 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.449C>A p.Thr150Lys p.T150K ENST00000622500 4/4 329 271 58 374 374 0 strelka-varscan-mutect GPIHBP1,missense_variant,p.Thr150Lys,ENST00000622500,NM_001301772.1,NM_178172.5; A ENST00000622500 Transcript missense_variant 524/2282 449/555 150/184 T/K aCa/aAa 1 1 GPIHBP1 HGNC HGNC:24945 protein_coding YES CCDS34954.1 ENSP00000480053 Q8IV16 UPI00002283CA NM_001301772.1,NM_178172.5 tolerated(0.76) 4/4 hmmpanther:PTHR16983,hmmpanther:PTHR16983:SF12 MODERATE 1 SNV 1 1 PASS rs1216010165 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 143215412 143215412 C A 1 0 0 0 0 1 0 0 0 6514 478 17 2 2 GPIHBP1 8 143215412 Missense_Mutation SNP C C3N-01488_T 303383 143215412 1923224 263 24637 HGH1 0 . GRCh38 8 144138238 144138238 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.403C>A p.Pro135Thr p.P135T ENST00000347708 1/6 161 131 30 207 206 1 strelka-varscan-mutect HGH1,missense_variant,p.Pro135Thr,ENST00000347708,NM_016458.3;HGH1,intron_variant,,ENST00000628266,;HGH1,non_coding_transcript_exon_variant,,ENST00000530074,;HGH1,intron_variant,,ENST00000533266,;HGH1,upstream_gene_variant,,ENST00000534255,;HGH1,upstream_gene_variant,,ENST00000525101,;HGH1,upstream_gene_variant,,ENST00000530409,;TSSK5P,downstream_gene_variant,,ENST00000423978,; A ENST00000347708 Transcript missense_variant 470/2531 403/1173 135/390 P/T Ccg/Acg 1 1 HGH1 HGNC HGNC:24161 protein_coding YES CCDS6417.1 ENSP00000321320 Q9BTY7 UPI0000073A95 NM_016458.3 tolerated(0.26) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR13387,Pfam_domain:PF04063,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999743 1 1 1 0 A 3 1 80 144138238 144138238 C A 1 0 0 0 0 1 0 0 0 6971 739 26 2 2 HGH1 8 144138238 Missense_Mutation SNP C C3N-01488_T 922826 144138238 1000398 264 24638 DMRT1 0 . GRCh38 9 847013 847013 + Silent SNP C C A rs372939169 C3N-01488_T C3N-01488_N C C c.408C>A p.= p.P136P ENST00000382276 2/5 217 171 46 319 318 1 strelka-varscan-mutect DMRT1,synonymous_variant,p.=,ENST00000382276,NM_021951.2;DMRT1,5_prime_UTR_variant,,ENST00000569227,;DMRT1,non_coding_transcript_exon_variant,,ENST00000564322,; A ENST00000382276 Transcript synonymous_variant 557/2222 408/1122 136/373 P ccC/ccA rs372939169 1 1 DMRT1 HGNC HGNC:2934 protein_coding YES CCDS6442.1 ENSP00000371711 Q9Y5R6 UPI00000008AC NM_021951.2 2/5 Pfam_domain:PF12374,hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF70 LOW 1 SNV 1 1 PASS rs372939169 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 847013 847013 C A 1 0 0 0 0 0 0 0 1 4392 581 21 2 2 DMRT1 9 847013 Silent SNP C C3N-01488_T 847013 137547704 265 24639 SMARCA2 0 . GRCh38 9 2032995 2032995 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.269A>G p.His90Arg p.H90R ENST00000382203 3/34 159 134 25 244 244 0 strelka-varscan-mutect SMARCA2,missense_variant,p.His90Arg,ENST00000637806,;SMARCA2,missense_variant,p.His90Arg,ENST00000636559,;SMARCA2,missense_variant,p.His90Arg,ENST00000382203,NM_001289396.1;SMARCA2,missense_variant,p.His90Arg,ENST00000357248,NM_139045.3;SMARCA2,missense_variant,p.His90Arg,ENST00000349721,NM_003070.4;SMARCA2,missense_variant,p.His90Arg,ENST00000382194,;SMARCA2,missense_variant,p.His90Arg,ENST00000637103,;SMARCA2,missense_variant,p.His90Arg,ENST00000450198,NM_001289397.1;SMARCA2,missense_variant,p.His90Arg,ENST00000636903,;SMARCA2,missense_variant,p.His90Arg,ENST00000439732,;SMARCA2,missense_variant,p.His90Arg,ENST00000457226,;SMARCA2,5_prime_UTR_variant,,ENST00000634287,;SMARCA2,downstream_gene_variant,,ENST00000637383,;SMARCA2,downstream_gene_variant,,ENST00000637352,;SMARCA2,downstream_gene_variant,,ENST00000636221,;SMARCA2,downstream_gene_variant,,ENST00000637097,;SMARCA2,downstream_gene_variant,,ENST00000637134,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000491574,;SMARCA2,missense_variant,p.His90Arg,ENST00000634760,;SMARCA2,non_coding_transcript_exon_variant,,ENST00000634536,; G ENST00000382203 Transcript missense_variant 478/5867 269/4773 90/1590 H/R cAt/cGt 1 1 SMARCA2 HGNC HGNC:11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 UPI00001AE8EB NM_001289396.1 tolerated_low_confidence(1) 3/34 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 2032995 2032995 A G 1 0 0 0 0 1 0 0 0 15062 217 8 5 5 SMARCA2 9 2032995 Missense_Mutation SNP A C3N-01488_T 1185982 2032995 136361722 266 24640 PTPRD 0 . GRCh38 9 8485811 8485811 + Silent SNP G G T rs148110842 C3N-01488_T C3N-01488_N G G c.3006C>A p.= p.P1002P ENST00000381196 25/43 145 117 28 218 218 0 strelka-varscan-mutect PTPRD,synonymous_variant,p.=,ENST00000381196,NM_002839.3;PTPRD,synonymous_variant,p.=,ENST00000356435,;PTPRD,synonymous_variant,p.=,ENST00000540109,;PTPRD,intron_variant,,ENST00000355233,NM_130392.3;PTPRD,intron_variant,,ENST00000397617,;PTPRD,intron_variant,,ENST00000397611,NM_001040712.2;PTPRD,intron_variant,,ENST00000537002,NM_130393.3;PTPRD,intron_variant,,ENST00000486161,NM_130391.3;PTPRD,intron_variant,,ENST00000397606,NM_001171025.1;PTPRD,upstream_gene_variant,,ENST00000637354,;PTPRD,non_coding_transcript_exon_variant,,ENST00000471274,;PTPRD,upstream_gene_variant,,ENST00000477552,; T ENST00000381196 Transcript synonymous_variant 3550/9911 3006/5739 1002/1912 P ccC/ccA rs148110842 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 25/43 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs148110842 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 8485811 8485811 G T 1 0 0 0 0 0 0 0 1 12953 1103 39 1 1 PTPRD 9 8485811 Silent SNP G C3N-01488_T 6452816 8485811 129908906 267 24641 FAM205A 0 . GRCh38 9 34723470 34723470 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.3770C>G p.Ala1257Gly p.A1257G ENST00000378788 4/4 254 224 30 379 379 0 strelka-varscan-mutect FAM205A,missense_variant,p.Ala1257Gly,ENST00000378788,NM_001141917.1; C ENST00000378788 Transcript missense_variant 3810/4225 3770/4008 1257/1335 A/G gCc/gGc 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 deleterious(0.03) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 34723470 34723470 G C 1 0 0 0 0 1 0 0 0 5386 1203 42 4 4 FAM205A 9 34723470 Missense_Mutation SNP G C3N-01488_T 26237659 34723470 103671247 268 24642 FAM205A 0 . GRCh38 9 34724437 34724437 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2803C>A p.His935Asn p.H935N ENST00000378788 4/4 121 110 11 219 219 0 varscan-mutect FAM205A,missense_variant,p.His935Asn,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript missense_variant 2843/4225 2803/4008 935/1335 H/N Cac/Aac 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 tolerated(1) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 34724437 34724437 G T 1 0 0 0 0 1 0 0 0 5386 1348 47 2 2 FAM205A 9 34724437 Missense_Mutation SNP G C3N-01488_T 967 34724437 103670280 269 24643 CCIN 0 . GRCh38 9 36169785 36169785 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.283G>T p.Val95Leu p.V95L ENST00000335119 1/1 386 307 79 573 573 0 strelka-varscan-mutect CCIN,missense_variant,p.Val95Leu,ENST00000335119,NM_005893.2; T ENST00000335119 Transcript missense_variant 392/1941 283/1767 95/588 V/L Gtg/Ttg 1 1 CCIN HGNC HGNC:1568 protein_coding YES CCDS6599.1 ENSP00000334996 Q13939 Q8WX35 UPI000006EB8E NM_005893.2 tolerated(0.31) 1/1 PROSITE_profiles:PS50097,hmmpanther:PTHR24412:SF163,hmmpanther:PTHR24412,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 36169785 36169785 G T 1 0 0 0 0 1 0 0 0 2576 1261 44 2 2 CCIN 9 36169785 Missense_Mutation SNP G C3N-01488_T 1445348 36169785 102224932 270 24644 SPATA31A6 0 . GRCh38 9 42188923 42188923 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3221C>A p.Ala1074Asp p.A1074D ENST00000332857 4/4 515 468 47 821 821 0 varscan-mutect SPATA31A6,missense_variant,p.Ala1074Asp,ENST00000332857,NM_001145196.1;SPATA31A6,downstream_gene_variant,,ENST00000496386,; A ENST00000332857 Transcript missense_variant 3250/4209 3221/4032 1074/1343 A/D gCc/gAc 1 1 SPATA31A6 HGNC HGNC:32006 protein_coding YES CCDS75837.1 ENSP00000329825 Q5VVP1 UPI0000197F6E NM_001145196.1 tolerated(0.88) 4/4 hmmpanther:PTHR21859:SF18,hmmpanther:PTHR21859 MODERATE 1 SNV 5 1 PASS . . 11 199 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 42188923 42188923 C A 1 0 0 0 0 1 0 0 0 15345 739 26 2 2 SPATA31A6 9 42188923 Missense_Mutation SNP C C3N-01488_T 6019138 42188923 96205794 271 24645 SPATA31A3 0 . GRCh38 9 66990037 66990037 + Missense_Mutation SNP G G T rs762767425 C3N-01488_T C3N-01488_N G G c.461C>A p.Ser154Tyr p.S154Y ENST00000428649 4/4 737 677 60 1185 1184 1 varscan-mutect SPATA31A3,missense_variant,p.Ser154Tyr,ENST00000428649,NM_001083124.1;RP11-395E19.2,downstream_gene_variant,,ENST00000616253,; T ENST00000428649 Transcript missense_variant 523/4256 461/4044 154/1347 S/Y tCc/tAc rs762767425 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 deleterious(0.01) 4/4 Pfam_domain:PF15371,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS rs762767425 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 66990037 66990037 G T 1 0 0 0 0 1 0 0 0 15344 1174 41 2 2 SPATA31A3 9 66990037 Missense_Mutation SNP G C3N-01488_T 24801114 66990037 71404680 272 24646 VPS13A 0 . GRCh38 9 77407565 77407565 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.9432G>C p.Glu3144Asp p.E3144D ENST00000360280 71/72 241 188 53 382 382 0 strelka-varscan-mutect VPS13A,missense_variant,p.Glu3144Asp,ENST00000360280,NM_033305.2;VPS13A,missense_variant,p.Glu3105Asp,ENST00000376636,NM_001018037.1;VPS13A,missense_variant,p.Glu80Asp,ENST00000376646,;VPS13A,missense_variant,p.Glu80Asp,ENST00000484581,;VPS13A,missense_variant,p.Glu18Asp,ENST00000467124,; C ENST00000360280 Transcript missense_variant 9692/15320 9432/9525 3144/3174 E/D gaG/gaC 1 1 VPS13A HGNC HGNC:1908 protein_coding YES CCDS6655.1 ENSP00000353422 Q96RL7 UPI0000210B7A NM_033305.2 tolerated(0.28) 71/72 hmmpanther:PTHR16166:SF22,hmmpanther:PTHR16166 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 77407565 77407565 G C 1 0 0 0 0 1 0 0 0 17736 1020 36 4 4 VPS13A 9 77407565 Missense_Mutation SNP G C3N-01488_T 10417528 77407565 60987152 273 24647 RASEF 0 . GRCh38 9 83000477 83000477 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.1531A>G p.Ile511Val p.I511V ENST00000376447 11/17 139 130 9 227 227 0 strelka-varscan-mutect RASEF,missense_variant,p.Ile511Val,ENST00000376447,NM_152573.3; C ENST00000376447 Transcript missense_variant 1792/5576 1531/2223 511/740 I/V Att/Gtt 1 -1 RASEF HGNC HGNC:26464 protein_coding YES CCDS6662.1 ENSP00000365630 Q8IZ41 UPI0000074189 NM_152573.3 tolerated(0.63) 11/17 Low_complexity_(Seg):seg,hmmpanther:PTHR22621:SF4,hmmpanther:PTHR22621 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 83000477 83000477 T C 1 0 0 0 0 1 0 0 0 13229 1464 51 5 5 RASEF 9 83000477 Missense_Mutation SNP T C3N-01488_T 5592912 83000477 55394240 274 24648 WNK2 0 . GRCh38 9 93317559 93317559 + Frame_Shift_Del DEL C C - rs767273259 C3N-01488_T C3N-01488_N C C c.6671delC p.Pro2224GlnfsTer92 p.P2224Qfs*92 ENST00000297954 29/30 281 248 33 384 383 1 sindel-varindel-pindel WNK2,frameshift_variant,p.Pro2183GlnfsTer55,ENST00000432730,;WNK2,frameshift_variant,p.Pro2224GlnfsTer92,ENST00000297954,NM_001282394.1;WNK2,frameshift_variant,p.Pro2187GlnfsTer35,ENST00000395477,NM_006648.3;WNK2,frameshift_variant,p.Pro1679GlnfsTer155,ENST00000411624,;WNK2,frameshift_variant,p.Pro984GlnfsTer35,ENST00000448251,;C9orf129,downstream_gene_variant,,ENST00000375419,NM_001098808.1;WNK2,non_coding_transcript_exon_variant,,ENST00000471076,;WNK2,non_coding_transcript_exon_variant,,ENST00000467401,; - ENST00000297954 Transcript frameshift_variant 6667/7138 6667/6894 2223/2297 P/X Ccc/cc rs767273259 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 29/30 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 93317559 93317559 C - 1 0 1 0 1 0 0 0 0 17934 739 26 0 0 WNK2 9 93317559 Frame_Shift_Del DEL C C3N-01488_T 10317082 93317559 45077158 275 24649 NUTM2F 0 . GRCh38 9 94325727 94325727 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.224G>T p.Gly75Val p.G75V ENST00000253262 2/7 243 217 26 388 388 0 strelka-varscan-mutect NUTM2F,missense_variant,p.Gly75Val,ENST00000253262,NM_017561.1;NUTM2F,missense_variant,p.Gly75Val,ENST00000341207,; A ENST00000253262 Transcript missense_variant 245/2561 224/2271 75/756 G/V gGg/gTg 1 -1 NUTM2F HGNC HGNC:23450 protein_coding YES CCDS47994.1 ENSP00000253262 A1L443 UPI00001D771D NM_017561.1 deleterious(0.01) 2/7 Pfam_domain:PF12881,hmmpanther:PTHR22879,hmmpanther:PTHR22879:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 94325727 94325727 C A 1 0 0 0 0 1 0 0 0 10851 623 22 2 2 NUTM2F 9 94325727 Missense_Mutation SNP C C3N-01488_T 1008168 94325727 44068990 276 24650 FKBP15 0 . GRCh38 9 113184706 113184706 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.1597C>T p.Leu533Phe p.L533F ENST00000238256 16/28 159 132 27 226 226 0 strelka-varscan-mutect FKBP15,missense_variant,p.Leu558Phe,ENST00000446284,;FKBP15,missense_variant,p.Leu533Phe,ENST00000238256,NM_015258.1;FKBP15,downstream_gene_variant,,ENST00000414250,;FKBP15,non_coding_transcript_exon_variant,,ENST00000489645,; A ENST00000238256 Transcript missense_variant 1715/4336 1597/3660 533/1219 L/F Ctc/Ttc 1 -1 FKBP15 HGNC HGNC:23397 protein_coding YES CCDS48007.1 ENSP00000238256 Q5T1M5 UPI000022D996 NM_015258.1 deleterious(0) 16/28 hmmpanther:PTHR18937:SF256,hmmpanther:PTHR18937 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 113184706 113184706 G A 1 0 0 0 0 1 0 0 0 5768 942 33 3 3 FKBP15 9 113184706 Missense_Mutation SNP G C3N-01488_T 18858979 113184706 25210011 277 24651 ODF2 0 . GRCh38 9 128471441 128471441 + Missense_Mutation SNP G G T rs780846935 C3N-01488_T C3N-01488_N G G c.554G>T p.Arg185Leu p.R185L ENST00000434106 6/21 367 296 71 440 440 0 strelka-varscan-mutect ODF2,missense_variant,p.Arg180Leu,ENST00000351030,NM_001242352.1;ODF2,missense_variant,p.Arg185Leu,ENST00000434106,NM_153433.1;ODF2,missense_variant,p.Arg161Leu,ENST00000393527,NM_002540.4,NM_153435.1;ODF2,missense_variant,p.Arg185Leu,ENST00000604420,NM_001242353.1;ODF2,missense_variant,p.Arg180Leu,ENST00000372807,;ODF2,missense_variant,p.Arg161Leu,ENST00000444119,;ODF2,missense_variant,p.Arg166Leu,ENST00000372791,NM_153437.2;ODF2,missense_variant,p.Arg229Leu,ENST00000372814,NM_153432.1,NM_153439.1;ODF2,missense_variant,p.Arg166Leu,ENST00000546203,NM_153440.1;ODF2,missense_variant,p.Arg185Leu,ENST00000393533,NM_153436.1;ODF2,missense_variant,p.Arg104Leu,ENST00000448249,NM_001242354.1;ODF2,missense_variant,p.Arg128Leu,ENST00000421776,;ODF2,missense_variant,p.Arg109Leu,ENST00000432065,;ODF2,downstream_gene_variant,,ENST00000446274,;ODF2,downstream_gene_variant,,ENST00000470061,;ODF2,downstream_gene_variant,,ENST00000497812,;ODF2-AS1,intron_variant,,ENST00000420801,;ODF2,downstream_gene_variant,,ENST00000469582,; T ENST00000434106 Transcript missense_variant 917/3890 554/2490 185/829 R/L cGc/cTc rs780846935 1 1 ODF2 HGNC HGNC:8114 protein_coding YES CCDS56588.1 ENSP00000403453 Q5BJF6 UPI0000211922 NM_153433.1 deleterious(0.04) 6/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23162,hmmpanther:PTHR23162:SF8 MODERATE 1 SNV 1 1 PASS rs780846935 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 128471441 128471441 G T 1 0 0 0 0 1 0 0 0 10905 1087 38 1 1 ODF2 9 128471441 Missense_Mutation SNP G C3N-01488_T 15286735 128471441 9923276 278 24652 HMCN2 0 . GRCh38 9 130386485 130386485 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.9349G>A p.Ala3117Thr p.A3117T ENST00000624552 61/98 121 111 10 167 167 0 strelka-varscan-mutect HMCN2,missense_variant,p.Ala3117Thr,ENST00000624552,NM_001291815.1;HMCN2,missense_variant,p.Ala150Thr,ENST00000487727,; A ENST00000624552 Transcript missense_variant 9349/15610 9349/15180 3117/5059 A/T Gct/Act 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0) 61/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1286631968 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 130386485 130386485 G A 1 0 0 0 0 1 0 0 0 7112 1203 42 3 3 HMCN2 9 130386485 Missense_Mutation SNP G C3N-01488_T 1915044 130386485 8008232 279 24653 LAMC3 0 . GRCh38 9 131057069 131057069 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.2080G>C p.Glu694Gln p.E694Q ENST00000361069 12/28 436 345 91 630 630 0 strelka-varscan-mutect LAMC3,missense_variant,p.Glu694Gln,ENST00000361069,NM_006059.3;LAMC3,intron_variant,,ENST00000480883,; C ENST00000361069 Transcript missense_variant 2213/6133 2080/4728 694/1575 E/Q Gag/Cag 1 1 LAMC3 HGNC HGNC:6494 protein_coding YES CCDS6938.1 ENSP00000354360 Q9Y6N6 UPI000013D6D3 NM_006059.3 deleterious(0.04) 12/28 Pfam_domain:PF00053,PROSITE_patterns:PS01248,SMART_domains:SM00180 MODERATE 1 SNV 2 1 PASS rs1328441247 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 131057069 131057069 G C 1 0 0 0 0 1 0 0 0 8520 1175 41 4 4 LAMC3 9 131057069 Missense_Mutation SNP G C3N-01488_T 670584 131057069 7337648 280 24654 ABO 0 . GRCh38 9 133256128 133256128 + Silent SNP G G C novel C3N-01488_T C3N-01488_N G G c.600C>G p.= p.L200L ENST00000538324 8/9 429 360 69 572 571 1 strelka-varscan-mutect ABO,synonymous_variant,p.=,ENST00000611156,NM_020469.2;ABO,synonymous_variant,p.=,ENST00000538324,;ABO,non_coding_transcript_exon_variant,,ENST00000453660,; C ENST00000538324 Transcript synonymous_variant 625/1147 600/1122 200/373 L ctC/ctG 1 -1 ABO HGNC HGNC:79 protein_coding YES ENSP00000483018 A0A087X009 UPI0004E4CBD3 8/9 hmmpanther:PTHR10462,hmmpanther:PTHR10462:SF31,Pfam_domain:PF03414,Gene3D:3.90.550.10,Superfamily_domains:SSF53448 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 133256128 133256128 G C 1 0 0 0 0 0 0 0 1 107 1277 45 4 4 ABO 9 133256128 Silent SNP G C3N-01488_T 2199059 133256128 5138589 281 24655 PNPLA7 0 . GRCh38 9 137501716 137501716 + Silent SNP C C A rs533121955 C3N-01488_T C3N-01488_N C C c.1485G>T p.= p.L495L ENST00000406427 15/35 160 150 10 208 208 0 strelka-varscan-mutect PNPLA7,synonymous_variant,p.=,ENST00000406427,NM_001098537.2;PNPLA7,synonymous_variant,p.=,ENST00000277531,NM_152286.4; A ENST00000406427 Transcript synonymous_variant 1822/4806 1485/4029 495/1342 L ctG/ctT rs533121955 1 -1 PNPLA7 HGNC HGNC:24768 protein_coding YES CCDS48070.1 ENSP00000384610 Q6ZV29 UPI000443805D NM_001098537.2 15/35 PROSITE_profiles:PS50042,hmmpanther:PTHR14226,hmmpanther:PTHR14226:SF23,SMART_domains:SM00100,Superfamily_domains:SSF51206 LOW 1 SNV 2 1 PASS rs533121955 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 137501716 137501716 C A 1 0 0 0 0 0 0 0 1 12278 465 17 2 2 PNPLA7 9 137501716 Silent SNP C C3N-01488_T 4245588 137501716 893001 282 24656 EHMT1 0 . GRCh38 9 137743489 137743489 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.942G>T p.Glu314Asp p.E314D ENST00000460843 5/27 213 186 27 308 303 5 strelka-varscan-mutect EHMT1,missense_variant,p.Glu314Asp,ENST00000460843,NM_024757.4;EHMT1,missense_variant,p.Glu283Asp,ENST00000637161,;EHMT1,missense_variant,p.Glu314Asp,ENST00000629335,;EHMT1,missense_variant,p.Glu276Asp,ENST00000636027,;EHMT1,missense_variant,p.Glu22Asp,ENST00000637318,;EHMT1,missense_variant,p.Glu314Asp,ENST00000462484,NM_001145527.1;EHMT1,missense_variant,p.Glu296Asp,ENST00000637977,;EHMT1,missense_variant,p.Glu282Asp,ENST00000626066,;EHMT1,missense_variant,p.Glu38Asp,ENST00000629808,;EHMT1,missense_variant,p.Glu22Asp,ENST00000478940,;EHMT1,non_coding_transcript_exon_variant,,ENST00000495657,;EHMT1,3_prime_UTR_variant,,ENST00000637261,;EHMT1,3_prime_UTR_variant,,ENST00000371394,;EHMT1,3_prime_UTR_variant,,ENST00000638071,;EHMT1,upstream_gene_variant,,ENST00000462942,; T ENST00000460843 Transcript missense_variant 1008/5137 942/3897 314/1298 E/D gaG/gaT 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 deleterious_low_confidence(0.01) 5/27 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF364 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 137743489 137743489 G T 1 0 0 0 0 1 0 0 0 4819 933 33 2 2 EHMT1 9 137743489 Missense_Mutation SNP G C3N-01488_T 241773 137743489 651228 283 24657 UCN3 0 . GRCh38 10 5374205 5374205 + Nonstop_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.485A>G p.Ter162TrpextTer49 p.*162Wext*49 ENST00000380433 2/2 76 63 13 72 71 1 strelka-varscan-mutect UCN3,stop_lost,p.Ter162TrpextTer49,ENST00000380433,NM_053049.2; G ENST00000380433 Transcript stop_lost 713/1200 485/486 162/161 */W tAg/tGg 1 1 UCN3 HGNC HGNC:17781 protein_coding YES CCDS7065.1 ENSP00000369798 Q969E3 UPI000013FC64 NM_053049.2 2/2 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 80 5374205 5374205 A G 1 0 0 0 0 0 0 0 0 17453 433 15 5 5 UCN3 10 5374205 Nonstop_Mutation SNP A C3N-01488_T 5374205 128423217 284 24658 PHYH 0 . GRCh38 10 13281078 13281089 + In_Frame_Del DEL GCAATCGGCACT GCAATCGGCACT - novel C3N-01488_T C3N-01488_N GCAATCGGCACT GCAATCGGCACT c.850_861delAGTGCCGATTGC p.Ser284_Cys287del p.S284_C287del ENST00000263038 8/9 446 385 61 639 639 0 sindel-varindel-pindel PHYH,inframe_deletion,p.Ser267_Cys270del,ENST00000396920,;PHYH,inframe_deletion,p.Ser184_Cys187del,ENST00000396913,NM_001323084.1,NM_001037537.1;PHYH,inframe_deletion,p.Ser284_Cys287del,ENST00000263038,NM_001323082.1,NM_006214.3;PHYH,downstream_gene_variant,,ENST00000453759,; - ENST00000263038 Transcript inframe_deletion 909-920/1577 850-861/1017 284-287/338 SADC/- AGTGCCGATTGC/- 1 -1 PHYH HGNC HGNC:8940 protein_coding YES CCDS7097.1 ENSP00000263038 O14832 UPI0000131215 NM_001323082.1,NM_006214.3 8/9 hmmpanther:PTHR21308:SF1,hmmpanther:PTHR21308,Gene3D:2.60.120.620,Superfamily_domains:SSF51197 MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 13281078 13281078 GCAATCGGCACT - 1 0 1 0 1 0 0 0 0 11952 1195 42 0 0 PHYH 10 13281078 In_Frame_Del DEL GCAATCGGCACT C3N-01488_T 7906873 13281078 120516344 285 24659 FAM107B 0 . GRCh38 10 14774506 14774506 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.158G>T p.Arg53Leu p.R53L ENST00000181796 1/5 262 204 58 303 303 0 strelka-varscan-mutect FAM107B,missense_variant,p.Arg53Leu,ENST00000181796,NM_031453.3;FAM107B,missense_variant,p.Arg53Leu,ENST00000487335,; A ENST00000181796 Transcript missense_variant 392/3785 158/921 53/306 R/L cGt/cTt 1 -1 FAM107B HGNC HGNC:23726 protein_coding YES CCDS7102.1 ENSP00000181796 Q9H098 UPI00001C0E1E NM_031453.3 tolerated_low_confidence(0.49) 1/5 MODERATE 1 SNV 2 1 PASS rs1238674134 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 14774506 14774506 C A 1 0 0 0 0 1 0 0 0 5258 536 19 1 1 FAM107B 10 14774506 Missense_Mutation SNP C C3N-01488_T 1493428 14774506 119022916 286 24660 ITGA8 0 . GRCh38 10 15718900 15718900 + Splice_Site SNP C C A C3N-01488_T C3N-01488_N C C c.210-1G>T p.X70_splice ENST00000378076 146 115 31 175 175 0 strelka-varscan-mutect ITGA8,splice_acceptor_variant,,ENST00000378076,NM_003638.2,NM_001291494.1; A ENST00000378076 Transcript splice_acceptor_variant -/6755 210/3192 70/1063 COSM1297139 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 1/29 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 80 15718900 15718900 C A 1 0 0 0 0 0 0 1 0 7789 927 32 2 2 ITGA8 10 15718900 Splice_Site SNP C C3N-01488_T 944394 15718900 118078522 287 24661 CUBN 0 . GRCh38 10 16948491 16948491 + Silent SNP G G A rs182162293 C3N-01488_T C3N-01488_N G G c.5196C>T p.= p.T1732T ENST00000377833 35/67 385 310 75 553 553 0 strelka-varscan-mutect CUBN,synonymous_variant,p.=,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript synonymous_variant 5262/11949 5196/10872 1732/3623 T acC/acT rs182162293,COSM1560854 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 35/67 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF645,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1 LOW 1 SNV 1 0,1 1 PASS rs182162293 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 16948491 16948491 G A 1 0 0 0 0 0 0 0 1 3861 1103 39 1 1 CUBN 10 16948491 Silent SNP G C3N-01488_T 1229591 16948491 116848931 288 24662 MRC1 0 . GRCh38 10 17906960 17906960 + Frame_Shift_Del DEL A A - novel C3N-01488_T C3N-01488_N A A c.3877delA p.Thr1293ProfsTer5 p.T1293Pfs*5 ENST00000569591 27/30 291 240 51 394 394 0 sindel-varindel-pindel MRC1,frameshift_variant,p.Thr1293ProfsTer5,ENST00000569591,NM_002438.3; - ENST00000569591 Transcript frameshift_variant 3996/5198 3874/4371 1292/1456 K/X Aaa/aa 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 27/30 PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 17906960 17906960 A - 1 0 1 0 1 0 0 0 0 9722 363 13 0 0 MRC1 10 17906960 Frame_Shift_Del DEL A C3N-01488_T 958469 17906960 115890462 289 24663 ARHGAP21 0 . GRCh38 10 24597998 24597998 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.3144C>A p.= p.V1048V ENST00000396432 15/26 116 103 13 178 177 1 strelka-varscan-mutect ARHGAP21,synonymous_variant,p.=,ENST00000396432,NM_020824.3;ARHGAP21,synonymous_variant,p.=,ENST00000636789,;ARHGAP21,synonymous_variant,p.=,ENST00000446003,;ARHGAP21,synonymous_variant,p.=,ENST00000376410,;ARHGAP21,intron_variant,,ENST00000612832,;ARHGAP21,intron_variant,,ENST00000320481,;ARHGAP21,upstream_gene_variant,,ENST00000418033,;ARHGAP21,upstream_gene_variant,,ENST00000418325,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000493154,;ARHGAP21,synonymous_variant,p.=,ENST00000638156,;ARHGAP21,non_coding_transcript_exon_variant,,ENST00000486374,;ARHGAP21,upstream_gene_variant,,ENST00000482792,; T ENST00000396432 Transcript synonymous_variant 3631/7167 3144/5877 1048/1958 V gtC/gtA 1 -1 ARHGAP21 HGNC HGNC:23725 protein_coding YES CCDS7144.2 ENSP00000379709 Q5T5U3 UPI0001639C78 NM_020824.3 15/26 hmmpanther:PTHR23175:SF16,hmmpanther:PTHR23175,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 24597998 24597998 G T 1 0 0 0 0 0 0 0 1 995 1277 45 2 2 ARHGAP21 10 24597998 Silent SNP G C3N-01488_T 6691038 24597998 109199424 290 24664 ANKRD26 0 . GRCh38 10 27035531 27035531 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.2919G>C p.Gln973His p.Q973H ENST00000376087 24/34 286 259 27 397 397 0 strelka-varscan-mutect ANKRD26,missense_variant,p.Gln989His,ENST00000436985,;ANKRD26,missense_variant,p.Gln973His,ENST00000376087,NM_014915.2,NM_001256053.1;ANKRD26,downstream_gene_variant,,ENST00000490015,; G ENST00000376087 Transcript missense_variant 3085/6591 2919/5133 973/1710 Q/H caG/caC 1 -1 ANKRD26 HGNC HGNC:29186 protein_coding YES CCDS41499.1 ENSP00000365255 Q9UPS8 UPI000006FC41 NM_014915.2,NM_001256053.1 deleterious(0.01) 24/34 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF24 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 27035531 27035531 C G 1 0 0 0 0 1 0 0 0 757 564 20 4 4 ANKRD26 10 27035531 Missense_Mutation SNP C C3N-01488_T 2437533 27035531 106761891 291 24665 ARHGAP12 0 . GRCh38 10 31908324 31908324 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.532G>A p.Gly178Ser p.G178S ENST00000344936 3/20 187 154 33 293 293 0 strelka-varscan-mutect ARHGAP12,missense_variant,p.Gly178Ser,ENST00000396144,NM_001270695.1;ARHGAP12,missense_variant,p.Gly178Ser,ENST00000375245,NM_001270697.1;ARHGAP12,missense_variant,p.Gly178Ser,ENST00000375250,NM_001270696.1,NM_001270698.1;ARHGAP12,missense_variant,p.Gly178Ser,ENST00000311380,NM_001270699.1;ARHGAP12,missense_variant,p.Gly178Ser,ENST00000344936,NM_018287.6;HMGB1P7,upstream_gene_variant,,ENST00000450921,; T ENST00000344936 Transcript missense_variant 767/4128 532/2541 178/846 G/S Ggt/Agt 1 -1 ARHGAP12 HGNC HGNC:16348 protein_coding YES CCDS7170.1 ENSP00000345808 Q8IWW6 UPI000007445E NM_018287.6 tolerated(0.2) 3/20 hmmpanther:PTHR23181,hmmpanther:PTHR23181:SF3,Pfam_domain:PF16618 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 31908324 31908324 C T 1 0 0 0 0 1 0 0 0 989 594 21 3 3 ARHGAP12 10 31908324 Missense_Mutation SNP C C3N-01488_T 4872793 31908324 101889098 292 24666 AGAP4 0 . GRCh38 10 45827238 45827238 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.669G>T p.= p.R223R ENST00000448048 7/7 79 67 12 104 104 0 varscan-mutect AGAP4,synonymous_variant,p.=,ENST00000616763,;AGAP4,synonymous_variant,p.=,ENST00000311652,;AGAP4,synonymous_variant,p.=,ENST00000448048,NM_133446.3;AGAP4,synonymous_variant,p.=,ENST00000618171,NM_001276343.2;AGAP4,downstream_gene_variant,,ENST00000492347,;AGAP4,downstream_gene_variant,,ENST00000430779,; A ENST00000448048 Transcript synonymous_variant 795/2439 669/1992 223/663 R cgG/cgT 1 -1 AGAP4 HGNC HGNC:23459 protein_coding YES CCDS7215.1 ENSP00000392513 Q96P64 UPI000013ED67 NM_133446.3 7/7 hmmpanther:PTHR23180:SF213,hmmpanther:PTHR23180 LOW 1 SNV 1 1 PASS . . 2 206 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 45827238 45827238 C A 1 0 0 0 0 0 0 0 1 447 494 18 2 2 AGAP4 10 45827238 Silent SNP C C3N-01488_T 13918914 45827238 87970184 293 24667 AGAP14P 0 . GRCh38 10 46358124 46358124 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1468A>T p.Ser490Cys p.S490C ENST00000624701 9/9 935 884 51 1178 1178 0 varscan-mutect AGAP14P,missense_variant,p.Ser490Cys,ENST00000624701,; T ENST00000624701 Transcript missense_variant 1468/2058 1468/2058 490/685 S/C Agt/Tgt 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF deleterious(0) 9/9 PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,Pfam_domain:PF01412,SMART_domains:SM00105,Superfamily_domains:SSF57863,Prints_domain:PR00405 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 46358124 46358124 A T 1 0 0 0 0 1 0 0 0 444 188 7 4 4 AGAP14P 10 46358124 Missense_Mutation SNP A C3N-01488_T 530886 46358124 87439298 294 24668 GDF10 0 . GRCh38 10 47310436 47310436 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.960G>T p.Lys320Asn p.K320N ENST00000580279 2/3 162 137 25 193 193 0 strelka-varscan-mutect GDF10,missense_variant,p.Lys320Asn,ENST00000580279,NM_004962.3; T ENST00000580279 Transcript missense_variant 1226/2458 960/1437 320/478 K/N aaG/aaT 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 tolerated(0.23) 2/3 PIRSF_domain:PIRSF037403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 47310436 47310436 G T 1 0 0 0 0 1 0 0 0 6184 962 34 2 2 GDF10 10 47310436 Missense_Mutation SNP G C3N-01488_T 952312 47310436 86486986 295 24669 ADAMTS14 0 . GRCh38 10 70735264 70735264 + Missense_Mutation SNP G G T rs781417210 C3N-01488_T C3N-01488_N G G c.1457G>T p.Arg486Leu p.R486L ENST00000373208 9/22 183 157 26 211 211 0 strelka-varscan-mutect ADAMTS14,missense_variant,p.Arg486Leu,ENST00000373208,NM_139155.2;ADAMTS14,missense_variant,p.Arg483Leu,ENST00000373207,NM_080722.3; T ENST00000373208 Transcript missense_variant 1457/5269 1457/3681 486/1226 R/L cGc/cTc rs781417210 1 1 ADAMTS14 HGNC HGNC:14899 protein_coding YES CCDS7307.1 ENSP00000362304 Q8WXS8 UPI000013E57B NM_139155.2 deleterious(0) 9/22 hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723,SMART_domains:SM00608 MODERATE 1 SNV 2 1 PASS rs781417210 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 80 70735264 70735264 G T 1 0 0 0 0 1 0 0 0 303 1087 38 1 1 ADAMTS14 10 70735264 Missense_Mutation SNP G C3N-01488_T 23424828 70735264 63062158 296 24670 ADAMTS14 0 . GRCh38 10 70745260 70745260 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.2226C>A p.= p.A742A ENST00000373208 15/22 153 124 29 230 230 0 strelka-varscan-mutect ADAMTS14,synonymous_variant,p.=,ENST00000373208,NM_139155.2;ADAMTS14,synonymous_variant,p.=,ENST00000373207,NM_080722.3; A ENST00000373208 Transcript synonymous_variant 2226/5269 2226/3681 742/1226 A gcC/gcA 1 1 ADAMTS14 HGNC HGNC:14899 protein_coding YES CCDS7307.1 ENSP00000362304 Q8WXS8 UPI000013E57B NM_139155.2 15/22 hmmpanther:PTHR13723:SF24,hmmpanther:PTHR13723,Pfam_domain:PF05986 LOW 1 SNV 2 1 PASS rs957360888 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 70745260 70745260 C A 1 0 0 0 0 0 0 0 1 303 581 21 2 2 ADAMTS14 10 70745260 Silent SNP C C3N-01488_T 9996 70745260 63052162 297 24671 HHEX 0 . GRCh38 10 92690260 92690260 + Missense_Mutation SNP G G A rs867605493 C3N-01488_T C3N-01488_N G G c.274G>A p.Gly92Arg p.G92R ENST00000282728 1/4 261 228 33 342 342 0 strelka-varscan-mutect HHEX,missense_variant,p.Gly92Arg,ENST00000282728,NM_002729.4;HHEX,upstream_gene_variant,,ENST00000472590,;HHEX,upstream_gene_variant,,ENST00000492654,;HHEX,non_coding_transcript_exon_variant,,ENST00000551454,; A ENST00000282728 Transcript missense_variant 310/1727 274/813 92/270 G/R Gga/Aga rs867605493,COSM1741957 1 1 HHEX HGNC HGNC:4901 protein_coding YES CCDS7423.1 ENSP00000282728 Q03014 UPI000012CA59 NM_002729.4 deleterious(0.03) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs867605493 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 92690260 92690260 G A 1 0 0 0 0 1 0 0 0 6976 1117 39 1 1 HHEX 10 92690260 Missense_Mutation SNP G C3N-01488_T 21945000 92690260 41107162 298 24672 SLIT1 0 . GRCh38 10 97066050 97066050 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.450G>T p.Arg150Ser p.R150S ENST00000266058 5/37 282 237 45 361 360 1 strelka-varscan-mutect SLIT1,missense_variant,p.Arg150Ser,ENST00000266058,NM_003061.2;SLIT1,missense_variant,p.Arg150Ser,ENST00000371070,;SLIT1,missense_variant,p.Arg133Ser,ENST00000314867,;SLIT1,missense_variant,p.Arg150Ser,ENST00000371041,;SLIT1,non_coding_transcript_exon_variant,,ENST00000497714,; A ENST00000266058 Transcript missense_variant 696/7925 450/4605 150/1534 R/S agG/agT 1 -1 SLIT1 HGNC HGNC:11085 protein_coding YES CCDS7453.1 ENSP00000266058 O75093 UPI00001F9491 NM_003061.2 deleterious(0.01) 5/37 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 97066050 97066050 C A 1 0 0 0 0 1 0 0 0 15030 854 30 2 2 SLIT1 10 97066050 Missense_Mutation SNP C C3N-01488_T 4375790 97066050 36731372 299 24673 PDCD11 0 . GRCh38 10 103406692 103406692 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.772G>T p.Gly258Cys p.G258C ENST00000369797 7/36 303 259 44 385 385 0 strelka-varscan-mutect PDCD11,missense_variant,p.Gly258Cys,ENST00000369797,NM_014976.1;PDCD11,downstream_gene_variant,,ENST00000493610,;PDCD11,downstream_gene_variant,,ENST00000471061,; T ENST00000369797 Transcript missense_variant 866/6453 772/5616 258/1871 G/C Ggt/Tgt 1 1 PDCD11 HGNC HGNC:13408 protein_coding YES CCDS31276.1 ENSP00000358812 Q14690 UPI00001C1ED1 NM_014976.1 tolerated(0.06) 7/36 PROSITE_profiles:PS50126,hmmpanther:PTHR23270,hmmpanther:PTHR23270:SF10,Gene3D:2.40.50.140,SMART_domains:SM00316,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 103406692 103406692 G T 1 0 0 0 0 1 0 0 0 11705 1348 47 2 2 PDCD11 10 103406692 Missense_Mutation SNP G C3N-01488_T 6340642 103406692 30390730 300 24674 SORCS3 0 . GRCh38 10 105211158 105211158 + Frame_Shift_Del DEL T T - novel C3N-01488_T C3N-01488_N T T c.2283delT p.His761GlnfsTer45 p.H761Qfs*45 ENST00000369701 17/27 172 139 33 261 261 0 sindel-varindel SORCS3,frameshift_variant,p.His761GlnfsTer45,ENST00000369701,NM_014978.2;SORCS3,frameshift_variant,p.His761GlnfsTer45,ENST00000369699,;SORCS3,frameshift_variant,p.His122GlnfsTer?,ENST00000393176,; - ENST00000369701 Transcript frameshift_variant 2510/5757 2283/3669 761/1222 H/X caT/ca 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 17/27 Pfam_domain:PF15901,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,SMART_domains:SM00602 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 105211158 105211158 T - 1 0 1 0 1 0 0 0 0 15254 1461 51 0 0 SORCS3 10 105211158 Frame_Shift_Del DEL T C3N-01488_T 1804466 105211158 28586264 301 24675 SORCS3 0 . GRCh38 10 105255801 105255801 + Missense_Mutation SNP G G T rs755605384 C3N-01488_T C3N-01488_N G G c.3337G>T p.Ala1113Ser p.A1113S ENST00000369701 24/27 79 71 8 111 110 1 strelka-varscan-mutect SORCS3,missense_variant,p.Ala1113Ser,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Ala1113Ser,ENST00000369699,; T ENST00000369701 Transcript missense_variant,splice_region_variant 3564/5757 3337/3669 1113/1222 A/S Gct/Tct rs755605384,COSM427049 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 tolerated(0.13) 24/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs755605384 . 0 202 8 0 0 0 0 0 -17.08106 0.9999956 1 1 1 0 T 3 4 80 105255801 105255801 G T 1 0 0 0 0 1 0 0 0 15254 1014 35 2 2 SORCS3 10 105255801 Missense_Mutation SNP G C3N-01488_T 44643 105255801 28541621 302 24676 SORCS1 0 . GRCh38 10 106652472 106652472 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.2385A>T p.Lys795Asn p.K795N ENST00000263054 18/26 223 184 39 269 269 0 strelka-varscan-mutect SORCS1,missense_variant,p.Lys795Asn,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,missense_variant,p.Lys553Asn,ENST00000612154,;SORCS1,missense_variant,p.Lys553Asn,ENST00000622431,;SORCS1,missense_variant,p.Lys553Asn,ENST00000344440,;SORCS1,missense_variant,p.Lys330Asn,ENST00000369698,; A ENST00000263054 Transcript missense_variant 2393/7272 2385/3507 795/1168 K/N aaA/aaT 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 tolerated(0.19) 18/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8,SMART_domains:SM00602,Superfamily_domains:SSF49299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 106652472 106652472 T A 1 0 0 0 0 1 0 0 0 15252 1606 56 4 4 SORCS1 10 106652472 Missense_Mutation SNP T C3N-01488_T 1396671 106652472 27144950 303 24677 SORCS1 0 . GRCh38 10 106688218 106688218 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1534A>T p.Arg512Trp p.R512W ENST00000263054 10/26 195 156 39 204 204 0 strelka-varscan-mutect SORCS1,missense_variant,p.Arg512Trp,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,missense_variant,p.Arg270Trp,ENST00000612154,;SORCS1,missense_variant,p.Arg270Trp,ENST00000622431,;SORCS1,missense_variant,p.Arg270Trp,ENST00000344440,;SORCS1,missense_variant,p.Arg47Trp,ENST00000369698,; A ENST00000263054 Transcript missense_variant 1542/7272 1534/3507 512/1168 R/W Agg/Tgg 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 deleterious(0.01) 10/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8,Gene3D:2.130.10.140,Pfam_domain:PF15902,SMART_domains:SM00602,Superfamily_domains:SSF110296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 106688218 106688218 T A 1 0 0 0 0 1 0 0 0 15252 1608 56 4 4 SORCS1 10 106688218 Missense_Mutation SNP T C3N-01488_T 35746 106688218 27109204 304 24678 AFAP1L2 0 . GRCh38 10 114300318 114300318 + Silent SNP G G T C3N-01488_T C3N-01488_N G G c.1833C>A p.= p.T611T ENST00000304129 15/19 224 186 38 310 310 0 strelka-varscan-mutect AFAP1L2,synonymous_variant,p.=,ENST00000369271,NM_032550.3;AFAP1L2,synonymous_variant,p.=,ENST00000304129,NM_001287824.1,NM_001001936.2;AFAP1L2,non_coding_transcript_exon_variant,,ENST00000491814,;AFAP1L2,downstream_gene_variant,,ENST00000486300,; T ENST00000304129 Transcript synonymous_variant 1863/3705 1833/2457 611/818 T acC/acA COSM5570214,COSM5570215 1 -1 AFAP1L2 HGNC HGNC:25901 protein_coding YES CCDS31286.1 ENSP00000303042 Q8N4X5 UPI0000071FAF NM_001287824.1,NM_001001936.2 15/19 hmmpanther:PTHR14338:SF4,hmmpanther:PTHR14338 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 114300318 114300318 G T 1 0 0 0 0 0 0 0 1 432 1335 47 2 2 AFAP1L2 10 114300318 Silent SNP G C3N-01488_T 7612100 114300318 19497104 305 24679 PNLIPRP3 0 . GRCh38 10 116466145 116466145 + Nonsense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.904A>T p.Arg302Ter p.R302* ENST00000369230 8/12 181 150 31 263 263 0 strelka-varscan-mutect PNLIPRP3,stop_gained,p.Arg302Ter,ENST00000369230,NM_001011709.2; T ENST00000369230 Transcript stop_gained 1050/2354 904/1404 302/467 R/* Aga/Tga 1 1 PNLIPRP3 HGNC HGNC:23492 protein_coding YES CCDS31292.1 ENSP00000358232 Q17RR3 UPI000013DB40 NM_001011709.2 8/12 hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF100,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 116466145 116466145 A T 1 0 0 0 0 0 1 0 0 12259 412 15 4 4 PNLIPRP3 10 116466145 Nonsense_Mutation SNP A C3N-01488_T 2165827 116466145 17331277 306 24680 PRLHR 0 . GRCh38 10 118594167 118594167 + Missense_Mutation SNP G G T rs200268174 C3N-01488_T C3N-01488_N G G c.1078C>A p.His360Asn p.H360N ENST00000239032 2/2 18 14 4 26 26 0 strelka-varscan-mutect PRLHR,missense_variant,p.His360Asn,ENST00000239032,NM_004248.2;PRLHR,missense_variant,p.His360Asn,ENST00000636925,; T ENST00000239032 Transcript missense_variant 1268/5446 1078/1113 360/370 H/N Cat/Aat rs200268174,COSM1346076 1 -1 PRLHR HGNC HGNC:4464 protein_coding YES CCDS7606.1 ENSP00000239032 P49683 UPI000013CA6F NM_004248.2 tolerated(0.46) 2/2 Prints_domain:PR01018,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF194 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200268174 . 5 201 4 0 0 0 0 0 -12.65972 1 1 1 1 0 T 3 4 80 118594167 118594167 G T 1 0 0 0 0 1 0 0 0 12662 1348 47 2 2 PRLHR 10 118594167 Missense_Mutation SNP G C3N-01488_T 2128022 118594167 15203255 307 24681 CPXM2 0 . GRCh38 10 123746765 123746765 + Nonstop_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.2270G>T p.Ter757LeuextTer19 p.*757Lext*19 ENST00000241305 14/14 135 110 25 214 210 4 strelka-varscan-mutect CPXM2,stop_lost,p.Ter757LeuextTer19,ENST00000241305,NM_198148.2;CPXM2,intron_variant,,ENST00000615851,;CPXM2,intron_variant,,ENST00000368854,; A ENST00000241305 Transcript stop_lost 2425/3554 2270/2271 757/756 */L tGa/tTa COSM4834564 1 -1 CPXM2 HGNC HGNC:26977 protein_coding YES CCDS7637.1 ENSP00000241305 Q8N436 UPI00001AE6BE NM_198148.2 14/14 1 HIGH 1 SNV 1 1 1 PASS rs1464713173 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 80 123746765 123746765 C A 1 0 0 0 0 0 0 0 0 3636 837 29 2 2 CPXM2 10 123746765 Nonstop_Mutation SNP C C3N-01488_T 5152598 123746765 10050657 308 24682 MKI67 0 . GRCh38 10 128103254 128103254 + Silent SNP T T C novel C3N-01488_T C3N-01488_N T T c.8586A>G p.= p.T2862T ENST00000368654 13/15 418 345 73 503 503 0 strelka-varscan-mutect MKI67,synonymous_variant,p.=,ENST00000368654,NM_002417.4;MKI67,synonymous_variant,p.=,ENST00000368653,NM_001145966.1;MKI67,upstream_gene_variant,,ENST00000464771,; C ENST00000368654 Transcript synonymous_variant 8962/12678 8586/9771 2862/3256 T acA/acG 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 13/15 Pfam_domain:PF08065,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM01295 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 128103254 128103254 T C 1 0 0 0 0 0 0 0 1 9566 1683 59 5 5 MKI67 10 128103254 Silent SNP T C3N-01488_T 4356489 128103254 5694168 309 24683 CFAP46 0 . GRCh38 10 132847300 132847300 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.5974C>A p.Leu1992Ile p.L1992I ENST00000368586 42/58 107 84 23 142 142 0 strelka-varscan-mutect CFAP46,missense_variant,p.Leu1992Ile,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript missense_variant 6075/8278 5974/8148 1992/2715 L/I Ctc/Atc 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 tolerated(0.17) 42/58 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 132847300 132847300 G T 1 0 0 0 0 1 0 0 0 3021 1000 35 2 2 CFAP46 10 132847300 Missense_Mutation SNP G C3N-01488_T 4744046 132847300 950122 310 24684 NLRP6 0 . GRCh38 11 284575 284581 + Frame_Shift_Del DEL CCCGCCC CCCGCCC - novel C3N-01488_T C3N-01488_N CCCGCCC CCCGCCC c.2475_2481delCGCCCCC p.Ala826TrpfsTer2 p.A826Wfs*2 ENST00000312165 7/8 209 191 18 265 265 0 sindel-varindel-pindel NLRP6,frameshift_variant,p.Ala825TrpfsTer2,ENST00000534750,NM_001276700.1;NLRP6,frameshift_variant,p.Ala826TrpfsTer2,ENST00000312165,NM_138329.2;ATHL1,upstream_gene_variant,,ENST00000409548,NM_025092.4;ATHL1,upstream_gene_variant,,ENST00000409479,;ATHL1,upstream_gene_variant,,ENST00000409655,;RP11-326C3.2,upstream_gene_variant,,ENST00000534742,;RP11-326C3.2,upstream_gene_variant,,ENST00000525217,;RP11-326C3.2,upstream_gene_variant,,ENST00000533924,;ATHL1,upstream_gene_variant,,ENST00000474221,;ATHL1,upstream_gene_variant,,ENST00000529087,;NLRP6,downstream_gene_variant,,ENST00000527946,; - ENST00000312165 Transcript frameshift_variant 2473-2479/2679 2473-2479/2679 825-827/892 PAP/X CCCGCCCcc/cc 1 1 NLRP6 HGNC HGNC:22944 protein_coding YES CCDS7693.1 ENSP00000309767 P59044 UPI00001AEFE1 NM_138329.2 7/8 hmmpanther:PTHR24106:SF3,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 284575 284575 CCCGCCC - 1 0 1 0 1 0 0 0 0 10519 739 26 0 0 NLRP6 11 284575 Frame_Shift_Del DEL CCCGCCC C3N-01488_T 284575 134802047 311 24685 CDHR5 0 . GRCh38 11 621374 621374 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.589C>A p.Pro197Thr p.P197T ENST00000358353 7/16 211 171 40 259 258 1 strelka-varscan-mutect CDHR5,missense_variant,p.Pro197Thr,ENST00000358353,;CDHR5,missense_variant,p.Pro197Thr,ENST00000397542,NM_001171968.1,NM_021924.4;CDHR5,missense_variant,p.Pro197Thr,ENST00000349570,NM_031264.3;CDHR5,missense_variant,p.Pro166Thr,ENST00000526077,;CDHR5,downstream_gene_variant,,ENST00000534311,;CDHR5,downstream_gene_variant,,ENST00000531088,;CDHR5,downstream_gene_variant,,ENST00000529337,;CDHR5,upstream_gene_variant,,ENST00000532949,;CDHR5,3_prime_UTR_variant,,ENST00000531177,;CDHR5,non_coding_transcript_exon_variant,,ENST00000531899,; T ENST00000358353 Transcript missense_variant 912/3635 589/2538 197/845 P/T Ccg/Acg 1 -1 CDHR5 HGNC HGNC:7521 protein_coding YES CCDS7707.1 ENSP00000351118 Q9HBB8 UPI0000456444 tolerated(0.32) 7/16 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF313,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 621374 621374 G T 1 0 0 0 0 1 0 0 0 2825 1203 42 2 2 CDHR5 11 621374 Missense_Mutation SNP G C3N-01488_T 336799 621374 134465248 312 24686 MUC5AC 0 . GRCh38 11 1162011 1162011 + Missense_Mutation SNP G G C rs371261781 C3N-01488_T C3N-01488_N G G c.316G>C p.Val106Leu p.V106L ENST00000621226 4/49 382 321 61 426 426 0 strelka-varscan-mutect MUC5AC,missense_variant,p.Val106Leu,ENST00000621226,NM_001304359.1; C ENST00000621226 Transcript missense_variant 363/17448 316/16965 106/5654 V/L Gtg/Ctg rs371261781 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0.01) 4/49 Pfam_domain:PF00094,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS rs371261781 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 1162011 1162011 G C 1 0 0 0 0 1 0 0 0 9978 1145 40 4 4 MUC5AC 11 1162011 Missense_Mutation SNP G C3N-01488_T 540637 1162011 133924611 313 24687 DUSP8 0 . GRCh38 11 1557793 1557793 + Splice_Site SNP C C A novel C3N-01488_T C3N-01488_N C C c.821+1G>T p.X274_splice ENST00000397374 156 131 25 187 187 0 strelka-varscan-mutect DUSP8,splice_donor_variant,,ENST00000397374,NM_004420.2;DUSP8,splice_donor_variant,,ENST00000331588,;DUSP8,splice_donor_variant,,ENST00000528778,; A ENST00000397374 Transcript splice_donor_variant -/4480 821/1878 274/625 1 -1 DUSP8 HGNC HGNC:3074 protein_coding YES CCDS7724.1 ENSP00000380530 Q13202 UPI000000DAD1 NM_004420.2 6/6 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 80 1557793 1557793 C A 1 0 0 0 0 0 0 1 0 4653 521 18 2 2 DUSP8 11 1557793 Splice_Site SNP C C3N-01488_T 395782 1557793 133528829 314 24688 DUSP8 0 . GRCh38 11 1565734 1565734 + Missense_Mutation SNP G G T rs61732130 C3N-01488_T C3N-01488_N G G c.93C>A p.Asp31Glu p.D31E ENST00000397374 2/7 205 164 41 236 236 0 strelka-varscan-mutect DUSP8,missense_variant,p.Asp31Glu,ENST00000397374,NM_004420.2;DUSP8,missense_variant,p.Asp31Glu,ENST00000331588,; T ENST00000397374 Transcript missense_variant 221/4480 93/1878 31/625 D/E gaC/gaA rs61732130 1 -1 DUSP8 HGNC HGNC:3074 protein_coding YES CCDS7724.1 ENSP00000380530 Q13202 UPI000000DAD1 NM_004420.2 deleterious(0) 2/7 PROSITE_profiles:PS50206,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF108,Pfam_domain:PF00581,Gene3D:3.40.250.10,SMART_domains:SM00450,Superfamily_domains:SSF52821,Prints_domain:PR01764 MODERATE 1 SNV 1 1 PASS rs61732130 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 1565734 1565734 G T 1 0 0 0 0 1 0 0 0 4653 1368 48 2 2 DUSP8 11 1565734 Missense_Mutation SNP G C3N-01488_T 7941 1565734 133520888 315 24689 OR51H1 0 . GRCh38 11 4860352 4860352 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.213T>A p.= p.T71T ENST00000322059 1/1 159 122 37 239 239 0 strelka-varscan-mutect OR51H1,synonymous_variant,p.=,ENST00000322059,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322059 Transcript synonymous_variant 213/909 213/909 71/302 T acT/acA 1 -1 OR51H1 HGNC HGNC:14833 protein_coding YES ENSP00000322724 Q8NH63 A0A126GVH7 UPI0000061F03 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF53,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 4860352 4860352 A T 1 0 0 0 0 0 0 0 1 11172 175 7 4 4 OR51H1 11 4860352 Silent SNP A C3N-01488_T 3294618 4860352 130226270 316 24690 OR51G2 0 . GRCh38 11 4915156 4915156 + Missense_Mutation SNP T T C C3N-01488_T C3N-01488_N T T c.508A>G p.Arg170Gly p.R170G ENST00000322013 1/1 259 223 36 369 369 0 strelka-varscan-mutect OR51G2,missense_variant,p.Arg170Gly,ENST00000322013,NM_001005238.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; C ENST00000322013 Transcript missense_variant 508/945 508/945 170/314 R/G Aga/Gga COSM4192742 1 -1 OR51G2 HGNC HGNC:15198 protein_coding YES CCDS31365.1 ENSP00000322593 Q8NGK0 UPI0000041C2F NM_001005238.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF133,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 4915156 4915156 T C 1 0 0 0 0 1 0 0 0 11171 1617 56 5 5 OR51G2 11 4915156 Missense_Mutation SNP T C3N-01488_T 54804 4915156 130171466 317 24691 OR51B4 0 . GRCh38 11 5301230 5301230 + Frame_Shift_Del DEL G G - rs375187554 C3N-01488_T C3N-01488_N G G c.717delC p.Ser240ProfsTer7 p.S240Pfs*7 ENST00000380224 1/1 129 108 21 261 261 0 sindel-varindel-pindel OR51B4,frameshift_variant,p.Ser240ProfsTer7,ENST00000380224,NM_033179.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,downstream_gene_variant,,ENST00000420465,; - ENST00000380224 Transcript frameshift_variant 767/983 717/933 239/310 V/X gtC/gt rs375187554 1 -1 OR51B4 HGNC HGNC:14708 protein_coding YES CCDS7757.1 ENSP00000369573 Q9Y5P0 UPI0000041B31 NM_033179.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF154,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 5301230 5301230 G - 1 0 1 0 1 0 0 0 0 11164 929 33 0 0 OR51B4 11 5301230 Frame_Shift_Del DEL G C3N-01488_T 386074 5301230 129785392 318 24692 SBF2 0 . GRCh38 11 10002640 10002640 + Missense_Mutation SNP C C A rs778821017 C3N-01488_T C3N-01488_N C C c.669G>T p.Lys223Asn p.K223N ENST00000256190 7/40 299 248 51 480 479 1 strelka-varscan-mutect SBF2,missense_variant,p.Lys223Asn,ENST00000256190,NM_030962.3;SBF2,non_coding_transcript_exon_variant,,ENST00000527019,;SBF2,non_coding_transcript_exon_variant,,ENST00000533770,; A ENST00000256190 Transcript missense_variant 807/7439 669/5550 223/1849 K/N aaG/aaT rs778821017 1 -1 SBF2 HGNC HGNC:2135 protein_coding YES CCDS31427.1 ENSP00000256190 Q86WG5 UPI00000622D5 NM_030962.3 deleterious(0) 7/40 Pfam_domain:PF02141,PROSITE_profiles:PS50211,SMART_domains:SM00799 MODERATE 1 SNV 1 1 PASS rs778821017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 10002640 10002640 C A 1 0 0 0 0 1 0 0 0 14123 680 24 2 2 SBF2 11 10002640 Missense_Mutation SNP C C3N-01488_T 4701410 10002640 125083982 319 24693 DKK3 0 . GRCh38 11 11965946 11965946 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.693C>A p.Cys231Ter p.C231* ENST00000396505 7/8 110 89 21 120 120 0 strelka-varscan-mutect DKK3,stop_gained,p.Cys231Ter,ENST00000396505,NM_015881.5;DKK3,stop_gained,p.Cys231Ter,ENST00000326932,NM_001018057.1,NM_013253.4;DKK3,stop_gained,p.Cys231Ter,ENST00000525493,;DKK3,stop_gained,p.Cys231Ter,ENST00000533813,;DKK3,downstream_gene_variant,,ENST00000534511,;DKK3,downstream_gene_variant,,ENST00000529338,;DKK3,non_coding_transcript_exon_variant,,ENST00000532873,;DKK3,non_coding_transcript_exon_variant,,ENST00000528188,;DKK3,non_coding_transcript_exon_variant,,ENST00000525927,;DKK3,intron_variant,,ENST00000527132,;DKK3,non_coding_transcript_exon_variant,,ENST00000532372,; T ENST00000396505 Transcript stop_gained 932/2650 693/1053 231/350 C/* tgC/tgA 1 -1 DKK3 HGNC HGNC:2893 protein_coding YES CCDS7808.1 ENSP00000379762 Q9UBP4 UPI00001694CA NM_015881.5 7/8 hmmpanther:PTHR12113:SF8,hmmpanther:PTHR12113,Gene3D:2.10.80.10 HIGH 1 SNV 1 1 PASS rs946901457 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 11965946 11965946 G T 1 0 0 0 0 0 1 0 0 4352 1311 46 2 2 DKK3 11 11965946 Nonsense_Mutation SNP G C3N-01488_T 1963306 11965946 123120676 320 24694 KCNA4 0 . GRCh38 11 30011802 30011802 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.877A>T p.Ile293Phe p.I293F ENST00000328224 2/2 179 166 13 231 231 0 strelka-varscan-mutect KCNA4,missense_variant,p.Ile293Phe,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript missense_variant 2111/4172 877/1962 293/653 I/F Att/Ttt 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 tolerated(0.19) 2/2 Gene3D:1.20.120.350,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 30011802 30011802 T A 1 0 0 0 0 1 0 0 0 7921 1435 50 4 4 KCNA4 11 30011802 Missense_Mutation SNP T C3N-01488_T 18045856 30011802 105074820 321 24695 KCNA4 0 . GRCh38 11 30012115 30012115 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.564G>T p.Glu188Asp p.E188D ENST00000328224 2/2 217 184 33 258 258 0 strelka-varscan-mutect KCNA4,missense_variant,p.Glu188Asp,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript missense_variant 1798/4172 564/1962 188/653 E/D gaG/gaT 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 deleterious(0) 2/2 Gene3D:3.30.710.10,Pfam_domain:PF02214,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS rs1358787949 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 30012115 30012115 C A 1 0 0 0 0 1 0 0 0 7921 912 32 2 2 KCNA4 11 30012115 Missense_Mutation SNP C C3N-01488_T 313 30012115 105074507 322 24696 QSER1 0 . GRCh38 11 32935316 32935316 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.3671A>T p.Glu1224Val p.E1224V ENST00000399302 4/13 149 128 21 237 237 0 strelka-varscan-mutect QSER1,missense_variant,p.Glu1224Val,ENST00000399302,NM_001076786.2;QSER1,missense_variant,p.Glu985Val,ENST00000527788,;QSER1,missense_variant,p.Glu245Val,ENST00000524678,;QSER1,downstream_gene_variant,,ENST00000528155,;QSER1,downstream_gene_variant,,ENST00000527250,; T ENST00000399302 Transcript missense_variant 4006/9335 3671/5208 1224/1735 E/V gAa/gTa 1 1 QSER1 HGNC HGNC:26154 protein_coding YES CCDS41631.1 ENSP00000382241 Q2KHR3 UPI0000E467AF NM_001076786.2 deleterious(0) 4/13 hmmpanther:PTHR14709:SF2,hmmpanther:PTHR14709 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 32935316 32935316 A T 1 0 0 0 0 1 0 0 0 13037 246 9 4 4 QSER1 11 32935316 Missense_Mutation SNP A C3N-01488_T 2923201 32935316 102151306 323 24697 TTC17 0 . GRCh38 11 43391481 43391481 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.436G>T p.Asp146Tyr p.D146Y ENST00000039989 4/24 187 156 31 279 279 0 strelka-varscan-mutect TTC17,missense_variant,p.Asp146Tyr,ENST00000039989,NM_018259.5;TTC17,missense_variant,p.Asp146Tyr,ENST00000299240,NM_001307943.1;RP11-484D2.4,intron_variant,,ENST00000394183,;TTC17,upstream_gene_variant,,ENST00000526774,;TTC17,3_prime_UTR_variant,,ENST00000534347,;TTC17,non_coding_transcript_exon_variant,,ENST00000530469,; T ENST00000039989 Transcript missense_variant 450/4469 436/3426 146/1141 D/Y Gac/Tac 1 1 TTC17 HGNC HGNC:25596 protein_coding YES CCDS31466.1 ENSP00000039989 Q96AE7 UPI000006E6C7 NM_018259.5 deleterious(0) 4/24 hmmpanther:PTHR16091 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 43391481 43391481 G T 1 0 0 0 0 1 0 0 0 17193 942 33 2 2 TTC17 11 43391481 Missense_Mutation SNP G C3N-01488_T 10456165 43391481 91695141 324 24698 DGKZ 0 . GRCh38 11 46377183 46377183 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.2877C>T p.= p.L959L ENST00000454345 26/32 91 70 21 88 88 0 strelka-varscan-mutect DGKZ,synonymous_variant,p.=,ENST00000454345,NM_001105540.1;DGKZ,synonymous_variant,p.=,ENST00000343674,NM_201532.2;DGKZ,synonymous_variant,p.=,ENST00000456247,NM_001199267.1;DGKZ,synonymous_variant,p.=,ENST00000527911,NM_001199266.1;DGKZ,synonymous_variant,p.=,ENST00000318201,NM_001199268.1;DGKZ,synonymous_variant,p.=,ENST00000532868,NM_201533.3;DGKZ,synonymous_variant,p.=,ENST00000421244,NM_003646.3;DGKZ,synonymous_variant,p.=,ENST00000528615,;MDK,upstream_gene_variant,,ENST00000405308,NM_001270550.1;MDK,upstream_gene_variant,,ENST00000407067,NM_001270551.1;MDK,upstream_gene_variant,,ENST00000359803,NM_001012334.2;MDK,upstream_gene_variant,,ENST00000395565,NM_001012333.2;MDK,upstream_gene_variant,,ENST00000395566,NM_002391.4;MDK,upstream_gene_variant,,ENST00000395569,NM_001270552.1;MDK,upstream_gene_variant,,ENST00000617138,;DGKZ,downstream_gene_variant,,ENST00000524869,;MDK,upstream_gene_variant,,ENST00000441869,;MDK,upstream_gene_variant,,ENST00000533952,;MIR4688,downstream_gene_variant,,ENST00000577966,;DGKZ,non_coding_transcript_exon_variant,,ENST00000529660,;MDK,upstream_gene_variant,,ENST00000533283,;DGKZ,3_prime_UTR_variant,,ENST00000524984,;DGKZ,non_coding_transcript_exon_variant,,ENST00000528173,;DGKZ,non_coding_transcript_exon_variant,,ENST00000527211,;DGKZ,non_coding_transcript_exon_variant,,ENST00000531879,;DGKZ,non_coding_transcript_exon_variant,,ENST00000529698,;DGKZ,upstream_gene_variant,,ENST00000534802,;MDK,upstream_gene_variant,,ENST00000489525,;MDK,upstream_gene_variant,,ENST00000481047,;DGKZ,upstream_gene_variant,,ENST00000532941,;DGKZ,downstream_gene_variant,,ENST00000527903,;MDK,upstream_gene_variant,,ENST00000490240,; T ENST00000454345 Transcript synonymous_variant 3002/4086 2877/3354 959/1117 L ctC/ctT 1 1 DGKZ HGNC HGNC:2857 protein_coding YES CCDS41640.1 ENSP00000412178 Q13574 UPI000013DB71 NM_001105540.1 26/32 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF43,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1156856577 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 46377183 46377183 C T 1 0 0 0 0 0 0 0 1 4280 842 30 3 3 DGKZ 11 46377183 Silent SNP C C3N-01488_T 2985702 46377183 88709439 325 24699 TRIM49B 0 . GRCh38 11 49031999 49031999 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.400G>T p.Glu134Ter p.E134* ENST00000622138 3/8 268 224 44 377 376 1 strelka-varscan-mutect TRIM49B,stop_gained,p.Glu134Ter,ENST00000622138,;TRIM49B,stop_gained,p.Glu134Ter,ENST00000332682,NM_001206626.1; T ENST00000622138 Transcript stop_gained 729/2162 400/1359 134/452 E/* Gag/Tag 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 3/8 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Superfamily_domains:SSF57845 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 49031999 49031999 G T 1 0 0 0 0 0 1 0 0 17015 1291 45 2 2 TRIM49B 11 49031999 Nonsense_Mutation SNP G C3N-01488_T 2654816 49031999 86054623 326 24700 TRIM49B 0 . GRCh38 11 49037910 49037910 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.1292T>C p.Ile431Thr p.I431T ENST00000622138 8/8 159 132 27 265 265 0 strelka-varscan-mutect TRIM49B,missense_variant,p.Ile431Thr,ENST00000622138,;TRIM49B,missense_variant,p.Ile431Thr,ENST00000332682,NM_001206626.1; C ENST00000622138 Transcript missense_variant 1621/2162 1292/1359 431/452 I/T aTa/aCa 1 1 TRIM49B HGNC HGNC:42955 protein_coding YES CCDS55762.1 ENSP00000481457 A6NDI0 UPI000013EEA1 deleterious(0) 8/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 49037910 49037910 T C 1 0 0 0 0 1 0 0 0 17015 1406 49 5 5 TRIM49B 11 49037910 Missense_Mutation SNP T C3N-01488_T 5911 49037910 86048712 327 24701 OR4A5 0 . GRCh38 11 54707692 54707692 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.808G>T p.Val270Leu p.V270L ENST00000319760 1/1 132 115 17 179 179 0 strelka-varscan-mutect OR4A5,missense_variant,p.Val270Leu,ENST00000319760,NM_001005272.3; T ENST00000319760 Transcript missense_variant 808/948 808/948 270/315 V/L Gtg/Ttg 1 1 OR4A5 HGNC HGNC:15162 protein_coding YES CCDS73289.1 ENSP00000367664 Q8NH83 A0A126GWJ2 UPI0000041D58 NM_001005272.3 tolerated_low_confidence(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF306,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 54707692 54707692 G T 1 0 0 0 0 1 0 0 0 11120 1377 48 2 2 OR4A5 11 54707692 Missense_Mutation SNP G C3N-01488_T 5669782 54707692 80378930 328 24702 OR5L2 0 . GRCh38 11 55827389 55827389 + Silent SNP C C A C3N-01488_T C3N-01488_N C C c.171C>A p.= p.T57T ENST00000378397 1/1 191 147 44 299 299 0 strelka-varscan-mutect OR5L2,synonymous_variant,p.=,ENST00000378397,NM_001004739.1; A ENST00000378397 Transcript synonymous_variant 171/936 171/936 57/311 T acC/acA COSM3449048 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9985795 1 1 1 0 A 2 1 80 55827389 55827389 C A 1 0 0 0 0 0 0 0 1 11240 610 22 2 2 OR5L2 11 55827389 Silent SNP C C3N-01488_T 1119697 55827389 79259233 329 24703 OR5L2 0 . GRCh38 11 55827562 55827562 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.344T>A p.Leu115Gln p.L115Q ENST00000378397 1/1 233 196 37 359 359 0 strelka-varscan-mutect OR5L2,missense_variant,p.Leu115Gln,ENST00000378397,NM_001004739.1; A ENST00000378397 Transcript missense_variant 344/936 344/936 115/311 L/Q cTg/cAg 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 55827562 55827562 T A 1 0 0 0 0 1 0 0 0 11240 1580 55 4 4 OR5L2 11 55827562 Missense_Mutation SNP T C3N-01488_T 173 55827562 79259060 330 24704 OR5W2 0 . GRCh38 11 55913792 55913792 + Missense_Mutation SNP G G A rs754041941 C3N-01488_T C3N-01488_N G G c.791C>T p.Ser264Phe p.S264F ENST00000344514 1/1 240 201 39 363 362 1 strelka-varscan-mutect OR5W2,missense_variant,p.Ser264Phe,ENST00000344514,NM_001001960.1; A ENST00000344514 Transcript missense_variant 791/933 791/933 264/310 S/F tCt/tTt rs754041941,COSM543350 1 -1 OR5W2 HGNC HGNC:15299 protein_coding YES CCDS31513.1 ENSP00000342448 Q8NH69 UPI0000061E8D NM_001001960.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF58,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs754041941 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 55913792 55913792 G A 1 0 0 0 0 1 0 0 0 11253 942 33 3 3 OR5W2 11 55913792 Missense_Mutation SNP G C3N-01488_T 86230 55913792 79172830 331 24705 OR5T2 0 . GRCh38 11 56232645 56232645 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.541A>T p.Met181Leu p.M181L ENST00000313264 1/1 127 107 20 190 190 0 strelka-varscan-mutect OR5T2,missense_variant,p.Met181Leu,ENST00000313264,NM_001004746.1; A ENST00000313264 Transcript missense_variant 541/1080 541/1080 181/359 M/L Atg/Ttg 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 tolerated(0.19) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1435243679 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 56232645 56232645 T A 1 0 0 0 0 1 0 0 0 11250 1464 51 4 4 OR5T2 11 56232645 Missense_Mutation SNP T C3N-01488_T 318853 56232645 78853977 332 24706 OR5M11 0 . GRCh38 11 56542937 56542937 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.321A>T p.= p.L107L ENST00000528616 1/1 197 162 35 286 282 4 strelka-varscan-mutect OR5M11,synonymous_variant,p.=,ENST00000528616,NM_001005245.1; A ENST00000528616 Transcript synonymous_variant 321/918 321/918 107/305 L ctA/ctT 1 -1 OR5M11 HGNC HGNC:15291 protein_coding YES CCDS53629.1 ENSP00000432417 Q96RB7 A0A126GVL9 UPI00000405CF NM_001005245.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF97,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 56542937 56542937 T A 1 0 0 0 0 0 0 0 1 11243 1625 57 4 4 OR5M11 11 56542937 Silent SNP T C3N-01488_T 310292 56542937 78543685 333 24707 CLP1 0 . GRCh38 11 57660981 57660981 + Missense_Mutation SNP C C T rs539245351 C3N-01488_T C3N-01488_N C C c.823C>T p.Arg275Cys p.R275C ENST00000533682 3/3 209 163 46 247 247 0 strelka-varscan-mutect CLP1,missense_variant,p.Arg275Cys,ENST00000533682,;CLP1,missense_variant,p.Arg286Cys,ENST00000529430,;CLP1,missense_variant,p.Arg211Cys,ENST00000302731,NM_001142597.1;CLP1,missense_variant,p.Arg275Cys,ENST00000525602,NM_006831.2;CLP1,downstream_gene_variant,,ENST00000529773,;CLP1,downstream_gene_variant,,ENST00000533905,; T ENST00000533682 Transcript missense_variant 1548/2435 823/1278 275/425 R/C Cgc/Tgc rs539245351 1 1 CLP1 HGNC HGNC:16999 protein_coding YES CCDS7964.1 ENSP00000434995 Q92989 UPI000012754A deleterious(0) 3/3 HAMAP:MF_03035,hmmpanther:PTHR12755,Gene3D:3.40.50.300,Pfam_domain:PF16575,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs539245351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 57660981 57660981 C T 1 0 0 0 0 1 0 0 0 3320 536 19 1 1 CLP1 11 57660981 Missense_Mutation SNP C C3N-01488_T 1118044 57660981 77425641 334 24708 SLC22A10 0 . GRCh38 11 63302521 63302521 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1263G>T p.Leu421Phe p.L421F ENST00000332793 7/10 210 171 39 320 319 1 strelka-varscan-mutect SLC22A10,missense_variant,p.Leu421Phe,ENST00000332793,NM_001039752.3;SLC22A10,intron_variant,,ENST00000526800,;SLC22A10,intron_variant,,ENST00000525620,;SLC22A10,intron_variant,,ENST00000533483,;SLC22A10,intron_variant,,ENST00000532724,; T ENST00000332793 Transcript missense_variant 1265/2026 1263/1626 421/541 L/F ttG/ttT 1 1 SLC22A10 HGNC HGNC:18057 protein_coding YES CCDS41661.1 ENSP00000327569 Q63ZE4 UPI0000D62620 NM_001039752.3 deleterious(0.02) 7/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF217,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 63302521 63302521 G T 1 0 0 0 0 1 0 0 0 14707 1339 47 2 2 SLC22A10 11 63302521 Missense_Mutation SNP G C3N-01488_T 5641540 63302521 71784101 335 24709 FLRT1 0 . GRCh38 11 64117690 64117690 + Missense_Mutation SNP C C A rs771778580 C3N-01488_T C3N-01488_N C C c.1423C>A p.Pro475Thr p.P475T ENST00000246841 2/2 96 74 22 136 135 1 strelka-varscan-mutect FLRT1,missense_variant,p.Pro475Thr,ENST00000246841,NM_013280.4;MACROD1,intron_variant,,ENST00000255681,NM_014067.3;RP11-21A7A.3,downstream_gene_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000545464,; A ENST00000246841 Transcript missense_variant 2466/3949 1423/2025 475/674 P/T Cca/Aca rs771778580 1 1 FLRT1 HGNC HGNC:3760 protein_coding YES CCDS8057.1 ENSP00000246841 Q9NZU1 UPI0000039F94 NM_013280.4 tolerated(1) 2/2 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF30,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs771778580 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 64117690 64117690 C A 1 0 0 0 0 1 0 0 0 5794 623 22 2 2 FLRT1 11 64117690 Missense_Mutation SNP C C3N-01488_T 815169 64117690 70968932 336 24710 CABP2 0 . GRCh38 11 67520153 67520153 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.387A>T p.= p.G129G ENST00000294288 5/7 97 77 20 124 124 0 strelka-varscan-mutect CABP2,synonymous_variant,p.=,ENST00000636477,;CABP2,synonymous_variant,p.=,ENST00000294288,NM_016366.2;CABP2,synonymous_variant,p.=,ENST00000353903,;CABP2,3_prime_UTR_variant,,ENST00000545205,NM_001318496.1; A ENST00000294288 Transcript synonymous_variant 457/925 387/663 129/220 G ggA/ggT 1 -1 CABP2 HGNC HGNC:1385 protein_coding YES CCDS8170.1 ENSP00000294288 Q9NPB3 UPI000013E147 NM_016366.2 5/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23050:SF21,hmmpanther:PTHR23050,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999967 1 1 1 0 A 2 1 80 67520153 67520153 T A 1 0 0 0 0 0 0 0 1 2218 1770 62 4 4 CABP2 11 67520153 Silent SNP T C3N-01488_T 3402463 67520153 67566469 337 24711 EMSY 0 . GRCh38 11 76544272 76544272 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.2768A>T p.His923Leu p.H923L ENST00000524767 19/21 53 41 12 128 128 0 strelka-varscan-mutect EMSY,missense_variant,p.His908Leu,ENST00000529032,;EMSY,missense_variant,p.His908Leu,ENST00000334736,NM_020193.4;EMSY,missense_variant,p.His909Leu,ENST00000525038,NM_001300944.1;EMSY,missense_variant,p.His923Leu,ENST00000524767,NM_001300942.1;EMSY,missense_variant,p.His909Leu,ENST00000525919,NM_001300943.1;EMSY,missense_variant,p.His810Leu,ENST00000524490,;EMSY,missense_variant,p.His817Leu,ENST00000533248,;EMSY,missense_variant,p.His48Leu,ENST00000532719,;EMSY,missense_variant,p.His180Leu,ENST00000524451,;EMSY,upstream_gene_variant,,ENST00000531793,;EMSY,non_coding_transcript_exon_variant,,ENST00000531641,;EMSY,non_coding_transcript_exon_variant,,ENST00000534573,; T ENST00000524767 Transcript missense_variant 2807/4116 2768/4014 923/1337 H/L cAc/cTc 1 1 EMSY HGNC HGNC:18071 protein_coding YES CCDS73349.1 ENSP00000433205 Q7Z589 UPI000191704B NM_001300942.1 deleterious_low_confidence(0.01) 19/21 hmmpanther:PTHR16500,hmmpanther:PTHR16500:SF3 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 80 76544272 76544272 A T 1 0 0 0 0 1 0 0 0 4948 159 6 4 4 EMSY 11 76544272 Missense_Mutation SNP A C3N-01488_T 9024119 76544272 58542350 338 24712 B3GNT6 0 . GRCh38 11 77040111 77040111 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.560A>T p.Gln187Leu p.Q187L ENST00000622824 2/2 202 153 49 264 264 0 strelka-varscan-mutect B3GNT6,missense_variant,p.Gln187Leu,ENST00000622824,NM_138706.4;B3GNT6,downstream_gene_variant,,ENST00000528622,; T ENST00000622824 Transcript missense_variant 641/2503 560/1155 187/384 Q/L cAg/cTg 1 1 B3GNT6 HGNC HGNC:24141 protein_coding YES CCDS53681.1 ENSP00000484640 Q6ZMB0 A8K9Q8 UPI000006D55A NM_138706.4 deleterious(0.02) 2/2 Pfam_domain:PF01762,hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 77040111 77040111 A T 1 0 0 0 0 1 0 0 0 1417 188 7 4 4 B3GNT6 11 77040111 Missense_Mutation SNP A C3N-01488_T 495839 77040111 58046511 339 24713 TENM4 0 . GRCh38 11 78701921 78701921 + Frame_Shift_Del DEL C C - novel C3N-01488_T C3N-01488_N C C c.4692delG p.Lys1565ArgfsTer65 p.K1565Rfs*65 ENST00000278550 28/34 226 179 47 325 325 0 sindel-varindel-pindel TENM4,frameshift_variant,p.Lys1565ArgfsTer65,ENST00000278550,NM_001098816.2;TENM4,frameshift_variant,p.Lys29ArgfsTer65,ENST00000530738,; - ENST00000278550 Transcript frameshift_variant 5155/14000 4692/8310 1564/2769 R/X cgG/cg 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 28/34 Gene3D:2.120.10.30,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9,Superfamily_domains:SSF101898,Superfamily_domains:SSF63829 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 78701921 78701921 C - 1 0 1 0 1 0 0 0 0 16174 842 30 0 0 TENM4 11 78701921 Frame_Shift_Del DEL C C3N-01488_T 1661810 78701921 56384701 340 24714 FAM181B 0 . GRCh38 11 82732631 82732631 + Silent SNP G G T C3N-01488_T C3N-01488_N G G c.1099C>A p.= p.R367R ENST00000329203 1/1 76 58 18 92 92 0 strelka-varscan-mutect FAM181B,synonymous_variant,p.=,ENST00000329203,NM_175885.3; T ENST00000329203 Transcript synonymous_variant 1234/3924 1099/1281 367/426 R Cgg/Agg COSM5565798 1 -1 FAM181B HGNC HGNC:28512 protein_coding YES CCDS31648.1 ENSP00000365295 A6NEQ2 UPI000015FCC7 NM_175885.3 1/1 hmmpanther:PTHR33766,hmmpanther:PTHR33766:SF2 1 LOW 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 80 82732631 82732631 G T 1 0 0 0 0 0 0 0 1 5355 1086 38 1 1 FAM181B 11 82732631 Silent SNP G C3N-01488_T 4030710 82732631 52353991 341 24715 FAT3 0 . GRCh38 11 92789989 92789989 + Missense_Mutation SNP C C G C3N-01488_T C3N-01488_N C C c.3932C>G p.Ser1311Cys p.S1311C ENST00000525166 7/27 164 151 13 285 285 0 strelka-varscan-mutect FAT3,missense_variant,p.Ser1461Cys,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Ser1311Cys,ENST00000525166,; G ENST00000525166 Transcript missense_variant 3954/18699 3932/13320 1311/4439 S/C tCt/tGt COSM1206610,COSM1206611,COSM4494684,COSM4494685 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 deleterious(0.02) 7/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 1,1,1,1 MODERATE 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 92789989 92789989 C G 1 0 0 0 0 1 0 0 0 5551 913 32 4 4 FAT3 11 92789989 Missense_Mutation SNP C C3N-01488_T 10057358 92789989 42296633 342 24716 DDI1 0 . GRCh38 11 104037551 104037551 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.729G>T p.Met243Ile p.M243I ENST00000302259 1/1 352 305 47 466 464 2 strelka-varscan-mutect DDI1,missense_variant,p.Met243Ile,ENST00000302259,NM_001001711.2;PDGFD,intron_variant,,ENST00000302251,NM_033135.3;PDGFD,intron_variant,,ENST00000393158,NM_025208.4;PDGFD,upstream_gene_variant,,ENST00000529268,; T ENST00000302259 Transcript missense_variant 972/2609 729/1191 243/396 M/I atG/atT 1 1 DDI1 HGNC HGNC:18961 protein_coding YES CCDS31660.1 ENSP00000302805 Q8WTU0 UPI0000047AEA NM_001001711.2 deleterious(0) 1/1 Pfam_domain:PF09668,hmmpanther:PTHR12917,hmmpanther:PTHR12917:SF15,Superfamily_domains:SSF50630 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 104037551 104037551 G T 1 0 0 0 0 1 0 0 0 4131 1319 46 2 2 DDI1 11 104037551 Missense_Mutation SNP G C3N-01488_T 11247562 104037551 31049071 343 24717 ARHGAP20 0 . GRCh38 11 110580940 110580940 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.2006C>T p.Pro669Leu p.P669L ENST00000260283 16/16 138 119 19 217 217 0 strelka-varscan-mutect ARHGAP20,missense_variant,p.Pro669Leu,ENST00000260283,NM_020809.3;ARHGAP20,missense_variant,p.Pro646Leu,ENST00000524756,NM_001258415.1;ARHGAP20,missense_variant,p.Pro643Leu,ENST00000533353,NM_001258416.1;ARHGAP20,missense_variant,p.Pro633Leu,ENST00000527598,NM_001258418.1;ARHGAP20,missense_variant,p.Pro633Leu,ENST00000528829,NM_001258417.1;ARHGAP20,missense_variant,p.Pro212Leu,ENST00000529591,; A ENST00000260283 Transcript missense_variant 2291/6189 2006/3576 669/1191 P/L cCa/cTa 1 -1 ARHGAP20 HGNC HGNC:18357 protein_coding YES CCDS31673.1 ENSP00000260283 Q9P2F6 UPI000013D0BA NM_020809.3 tolerated(0.08) 16/16 hmmpanther:PTHR23179,hmmpanther:PTHR23179:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 110580940 110580940 G A 1 0 0 0 0 1 0 0 0 994 1348 47 3 3 ARHGAP20 11 110580940 Missense_Mutation SNP G C3N-01488_T 6543389 110580940 24505682 344 24718 NCAM1 0 . GRCh38 11 113233260 113233260 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.1714G>A p.Glu572Lys p.E572K ENST00000619839 14/21 205 172 33 251 250 1 strelka-varscan-mutect NCAM1,missense_variant,p.Glu572Lys,ENST00000615285,;NCAM1,missense_variant,p.Glu546Lys,ENST00000615112,;NCAM1,missense_variant,p.Glu536Lys,ENST00000618266,;NCAM1,missense_variant,p.Glu546Lys,ENST00000316851,NM_181351.4;NCAM1,missense_variant,p.Glu536Lys,ENST00000621518,;NCAM1,missense_variant,p.Glu536Lys,ENST00000621128,NM_001242608.1;NCAM1,missense_variant,p.Glu572Lys,ENST00000619839,NM_001242607.1;NCAM1,missense_variant,p.Glu536Lys,ENST00000531044,NM_000615.6;NCAM1,missense_variant,p.Glu536Lys,ENST00000621850,NM_001076682.3;NCAM1,missense_variant,p.Glu536Lys,ENST00000401611,;NCAM1,missense_variant,p.Glu46Lys,ENST00000533073,;NCAM1,missense_variant,p.Glu81Lys,ENST00000526322,;NCAM1,missense_variant,p.Glu39Lys,ENST00000528590,;NCAM1,missense_variant,p.Glu102Lys,ENST00000530543,;NCAM1,intron_variant,,ENST00000620046,;NCAM1,downstream_gene_variant,,ENST00000613217,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,missense_variant,p.Glu46Lys,ENST00000531817,;NCAM1,non_coding_transcript_exon_variant,,ENST00000525355,;NCAM1,downstream_gene_variant,,ENST00000534046,; A ENST00000619839 Transcript missense_variant 2052/2993 1714/2655 572/884 E/K Gag/Aag 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 deleterious(0.04) 14/21 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 113233260 113233260 G A 1 0 0 0 0 1 0 0 0 10218 1291 45 3 3 NCAM1 11 113233260 Missense_Mutation SNP G C3N-01488_T 2652320 113233260 21853362 345 24719 DSCAML1 0 . GRCh38 11 117503899 117503899 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.2485G>A p.Ala829Thr p.A829T ENST00000321322 11/33 198 166 32 263 262 1 strelka-varscan-mutect DSCAML1,missense_variant,p.Ala829Thr,ENST00000321322,NM_020693.3;DSCAML1,missense_variant,p.Ala559Thr,ENST00000527706,; T ENST00000321322 Transcript missense_variant 2487/6899 2485/6342 829/2113 A/T Gcc/Acc 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 deleterious(0.02) 11/33 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999946 1 1 1 0 T 3 4 80 117503899 117503899 C T 1 0 0 0 0 1 0 0 0 4590 739 26 3 3 DSCAML1 11 117503899 Missense_Mutation SNP C C3N-01488_T 4270639 117503899 17582723 346 24720 OR6M1 0 . GRCh38 11 123805779 123805779 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.571C>A p.Leu191Ile p.L191I ENST00000309154 1/1 151 126 25 259 259 0 strelka-varscan-mutect OR6M1,missense_variant,p.Leu191Ile,ENST00000309154,NM_001005325.1; T ENST00000309154 Transcript missense_variant 609/1053 571/942 191/313 L/I Ctc/Atc 1 -1 OR6M1 HGNC HGNC:14711 protein_coding YES CCDS31696.1 ENSP00000311038 Q8NGM8 A0A126GVK2 UPI000003FE18 NM_001005325.1 tolerated(0.09) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF51,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs748844391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 123805779 123805779 G T 1 0 0 0 0 1 0 0 0 11274 1000 35 2 2 OR6M1 11 123805779 Missense_Mutation SNP G C3N-01488_T 6301880 123805779 11280843 347 24721 OR10S1 0 . GRCh38 11 123976894 123976894 + Nonsense_Mutation SNP G G T rs758385131 C3N-01488_T C3N-01488_N G G c.798C>A p.Tyr266Ter p.Y266* ENST00000531945 1/1 172 153 19 204 204 0 strelka-varscan-mutect OR10S1,stop_gained,p.Tyr266Ter,ENST00000531945,NM_001004474.1; T ENST00000531945 Transcript stop_gained 888/1121 798/996 266/331 Y/* taC/taA rs758385131 1 -1 OR10S1 HGNC HGNC:14807 protein_coding YES CCDS31701.1 ENSP00000431914 Q8NGN2 UPI00001A7787 NM_001004474.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF205,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS rs758385131 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 123976894 123976894 G T 1 0 0 0 0 0 1 0 0 10995 1140 40 1 1 OR10S1 11 123976894 Nonsense_Mutation SNP G C3N-01488_T 171115 123976894 11109728 348 24722 ROBO3 0 . GRCh38 11 124870668 124870668 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.973A>T p.Thr325Ser p.T325S ENST00000397801 6/28 311 260 51 424 424 0 strelka-varscan-mutect ROBO3,missense_variant,p.Thr325Ser,ENST00000397801,NM_022370.3;ROBO3,missense_variant,p.Thr303Ser,ENST00000538940,; T ENST00000397801 Transcript missense_variant 1165/4569 973/4161 325/1386 T/S Acc/Tcc 1 1 ROBO3 HGNC HGNC:13433 protein_coding YES CCDS44755.1 ENSP00000380903 Q96MS0 UPI000035AA82 NM_022370.3 deleterious(0.02) 6/28 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF724,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 124870668 124870668 A T 1 0 0 0 0 1 0 0 0 13693 159 6 4 4 ROBO3 11 124870668 Missense_Mutation SNP A C3N-01488_T 893774 124870668 10215954 349 24723 FLI1 0 . GRCh38 11 128810889 128810889 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.1260A>T p.= p.S420S ENST00000527786 9/9 403 334 69 609 608 1 strelka-varscan-mutect FLI1,synonymous_variant,p.=,ENST00000281428,NM_001271010.1;FLI1,synonymous_variant,p.=,ENST00000527786,NM_002017.4;FLI1,synonymous_variant,p.=,ENST00000534087,NM_001167681.2;FLI1,synonymous_variant,p.=,ENST00000344954,NM_001271012.1;FLI1,3_prime_UTR_variant,,ENST00000429175,;FLI1,3_prime_UTR_variant,,ENST00000608303,;FLI1,non_coding_transcript_exon_variant,,ENST00000528790,; T ENST00000527786 Transcript synonymous_variant 1749/4127 1260/1359 420/452 S tcA/tcT 1 1 FLI1 HGNC HGNC:3749 protein_coding YES CCDS44768.1 ENSP00000433488 Q01543 A0A024R3M5 UPI000012A972 NM_002017.4 9/9 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF161 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 128810889 128810889 A T 1 0 0 0 0 0 0 0 1 5786 146 6 4 4 FLI1 11 128810889 Silent SNP A C3N-01488_T 3940221 128810889 6275733 350 24724 PRDM10 0 . GRCh38 11 129914986 129914986 + Missense_Mutation SNP A A T rs763285097 C3N-01488_T C3N-01488_N A A c.2571T>A p.His857Gln p.H857Q ENST00000358825 18/22 120 99 21 203 202 1 strelka-varscan-mutect PRDM10,missense_variant,p.His857Gln,ENST00000358825,NM_020228.2;PRDM10,missense_variant,p.His853Gln,ENST00000360871,NM_199437.1;PRDM10,missense_variant,p.His827Gln,ENST00000528746,;PRDM10,missense_variant,p.His771Gln,ENST00000423662,NM_199438.1;PRDM10,missense_variant,p.His767Gln,ENST00000304538,NM_199439.1;PRDM10,missense_variant,p.His771Gln,ENST00000526082,;PRDM10,missense_variant,p.His570Gln,ENST00000533431,; T ENST00000358825 Transcript missense_variant 2803/6322 2571/3483 857/1160 H/Q caT/caA rs763285097 1 -1 PRDM10 HGNC HGNC:13995 protein_coding YES CCDS44771.1 ENSP00000351686 Q9NQV6 UPI00002371B3 NM_020228.2 deleterious(0) 18/22 PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF30,PROSITE_patterns:PS00028,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS rs763285097 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 129914986 129914986 A T 1 0 0 0 0 1 0 0 0 12582 330 12 4 4 PRDM10 11 129914986 Missense_Mutation SNP A C3N-01488_T 1104097 129914986 5171636 351 24725 IGSF9B 0 . GRCh38 11 133921066 133921066 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.2659C>T p.Pro887Ser p.P887S ENST00000533871 18/20 186 163 23 237 237 0 strelka-varscan-mutect IGSF9B,missense_variant,p.Pro887Ser,ENST00000533871,NM_001277285.1;IGSF9B,missense_variant,p.Pro887Ser,ENST00000321016,;IGSF9B,downstream_gene_variant,,ENST00000527648,; A ENST00000533871 Transcript missense_variant 2890/5050 2659/4314 887/1437 P/S Ccc/Tcc 1 -1 IGSF9B HGNC HGNC:32326 protein_coding YES CCDS61010.1 ENSP00000436552 Q9UPX0 UPI0002C439DB NM_001277285.1 deleterious(0.01) 18/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF681 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 80 133921066 133921066 G A 1 0 0 0 0 1 0 0 0 7514 1232 43 3 3 IGSF9B 11 133921066 Missense_Mutation SNP G C3N-01488_T 4006080 133921066 1165556 352 24726 IQSEC3 0 . GRCh38 12 161965 161965 + Missense_Mutation SNP T T A rs782198288 C3N-01488_T C3N-01488_N T T c.2483T>A p.Val828Glu p.V828E ENST00000538872 8/14 322 231 91 275 275 0 strelka-varscan-mutect IQSEC3,missense_variant,p.Val828Glu,ENST00000538872,NM_001170738.1;IQSEC3,missense_variant,p.Val525Glu,ENST00000382841,NM_015232.1;RP11-598F7.6,downstream_gene_variant,,ENST00000537295,;RP11-598F7.5,downstream_gene_variant,,ENST00000540136,; A ENST00000538872 Transcript missense_variant 2601/7094 2483/3549 828/1182 V/E gTa/gAa rs782198288 1 1 IQSEC3 HGNC HGNC:29193 protein_coding YES CCDS53728.1 ENSP00000437554 Q9UPP2 UPI0000DBEEF0 NM_001170738.1 deleterious(0) 8/14 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF62,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE SNV 5 1 PASS rs782198288 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 161965 161965 T A 1 0 0 0 0 1 0 0 0 7725 1638 57 4 4 IQSEC3 12 161965 Missense_Mutation SNP T C3N-01488_T 161965 133113344 353 24727 DYRK4 0 . GRCh38 12 4599167 4599167 + Splice_Site SNP G G T rs185807035 C3N-01488_T C3N-01488_N G G c.699+1G>T p.X233_splice ENST00000540757 142 105 37 159 159 0 strelka-varscan-mutect DYRK4,splice_donor_variant,,ENST00000540757,NM_003845.2;DYRK4,splice_donor_variant,,ENST00000543431,;DYRK4,splice_donor_variant,,ENST00000010132,;DYRK4,downstream_gene_variant,,ENST00000536157,;DYRK4,upstream_gene_variant,,ENST00000540644,;RP11-234B24.5,downstream_gene_variant,,ENST00000538921,; T ENST00000540757 Transcript splice_donor_variant -/3272 699/1563 233/520 rs185807035 1 1 DYRK4 HGNC HGNC:3095 protein_coding YES CCDS8530.1 ENSP00000441755 Q9NR20 UPI000006E05C NM_003845.2 7/12 HIGH 1 SNV 1 1 PASS rs185807035 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 80 4599167 4599167 G T 1 0 0 0 0 0 0 1 0 4682 1159 40 1 1 DYRK4 12 4599167 Splice_Site SNP G C3N-01488_T 4437202 4599167 128676142 354 24728 ATF7IP 0 . GRCh38 12 14424162 14424162 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.271G>T p.Gly91Ter p.G91* ENST00000544627 2/15 184 144 40 345 344 1 strelka-varscan-mutect ATF7IP,stop_gained,p.Gly83Ter,ENST00000261168,NM_018179.4;ATF7IP,stop_gained,p.Gly83Ter,ENST00000536444,NM_001286514.1;ATF7IP,stop_gained,p.Gly83Ter,ENST00000543189,NM_001286515.1;ATF7IP,stop_gained,p.Gly91Ter,ENST00000544627,NM_181352.1;ATF7IP,stop_gained,p.Gly83Ter,ENST00000540793,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000396279,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000545723,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000542514,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000539057,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000535132,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000536279,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000541056,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000545769,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000542967,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000428217,;ATF7IP,stop_gained,p.Gly83Ter,ENST00000534828,;ATF7IP,intron_variant,,ENST00000538511,;ATF7IP,downstream_gene_variant,,ENST00000542508,;ATF7IP,downstream_gene_variant,,ENST00000542991,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000541654,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000539659,;ATF7IP,non_coding_transcript_exon_variant,,ENST00000537653,; T ENST00000544627 Transcript stop_gained 591/4847 271/3837 91/1278 G/* Gga/Tga 1 1 ATF7IP HGNC HGNC:20092 protein_coding YES CCDS66326.1 ENSP00000440440 Q6VMQ6 UPI0001EE42CD NM_181352.1 2/15 hmmpanther:PTHR23210,hmmpanther:PTHR23210:SF22 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 14424162 14424162 G T 1 0 0 0 0 0 1 0 0 1236 1001 35 2 2 ATF7IP 12 14424162 Nonsense_Mutation SNP G C3N-01488_T 9824995 14424162 118851147 355 24729 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C T rs121913529 C3N-01488_T C3N-01488_N C C c.35G>A p.Gly12Asp p.G12D ENST00000256078 2/6 258 194 64 440 440 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Asp,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Asp,ENST00000556131,;KRAS,missense_variant,p.Gly12Asp,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Asp,ENST00000557334,; T ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/D gGt/gAt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 25245350 25245350 C T 1 0 0 0 0 1 0 0 0 8318 507 18 3 3 KRAS 12 25245350 Missense_Mutation SNP C C3N-01488_T 10821188 25245350 108029959 356 24730 ASUN 0 . GRCh38 12 26928833 26928833 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.373G>C p.Gly125Arg p.G125R ENST00000261191 4/17 248 209 39 447 447 0 strelka-varscan-mutect ASUN,missense_variant,p.Gly125Arg,ENST00000261191,NM_018164.2;ASUN,missense_variant,p.Gly125Arg,ENST00000544548,;ASUN,missense_variant,p.Gly125Arg,ENST00000537336,;ASUN,missense_variant,p.Gly24Arg,ENST00000538727,;ASUN,upstream_gene_variant,,ENST00000536232,;ASUN,non_coding_transcript_exon_variant,,ENST00000538748,; G ENST00000261191 Transcript missense_variant 910/2974 373/2121 125/706 G/R Ggc/Cgc 1 -1 ASUN HGNC HGNC:20174 protein_coding YES CCDS8708.1 ENSP00000261191 Q9NVM9 UPI0000044950 NM_018164.2 deleterious(0) 4/17 hmmpanther:PTHR12955,hmmpanther:PTHR12955:SF1,Pfam_domain:PF10221 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 26928833 26928833 C G 1 0 0 0 0 1 0 0 0 1213 594 21 4 4 ASUN 12 26928833 Missense_Mutation SNP C C3N-01488_T 1683483 26928833 106346476 357 24731 OVCH1 0 . GRCh38 12 29451383 29451383 + Missense_Mutation SNP A A T C3N-01488_T C3N-01488_N A A c.2717T>A p.Ile906Asn p.I906N ENST00000318184 22/28 208 157 51 344 344 0 strelka-varscan-mutect OVCH1,missense_variant,p.Ile906Asn,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,;OVCH1-AS1,intron_variant,,ENST00000550906,; T ENST00000318184 Transcript missense_variant 2717/3405 2717/3405 906/1134 I/N aTt/aAt COSM938569 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 tolerated(0.16) 22/28 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 29451383 29451383 A T 1 0 0 0 0 1 0 0 0 11393 101 4 4 4 OVCH1 12 29451383 Missense_Mutation SNP A C3N-01488_T 2522550 29451383 103823926 358 24732 BICD1 0 . GRCh38 12 32107612 32107612 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.281G>A p.= p.*94* ENST00000551848 1/1 218 199 19 264 264 0 strelka-varscan-mutect BICD1,stop_retained_variant,p.=,ENST00000551848,;BICD1,intron_variant,,ENST00000548411,NM_001003398.1;BICD1,intron_variant,,ENST00000281474,NM_001714.2;BICD1,intron_variant,,ENST00000550207,;BICD1,intron_variant,,ENST00000551086,;RP11-843B15.4,upstream_gene_variant,,ENST00000619744,;RP11-843B15.2,upstream_gene_variant,,ENST00000551974,;BICD1,intron_variant,,ENST00000395758,; A ENST00000551848 Transcript stop_retained_variant 778/1962 281/282 94/93 * tGa/tAa 1 1 BICD1 HGNC HGNC:1049 protein_coding ENSP00000448933 Q96G01 UPI0000073646 1/1 LOW SNV 1 PASS rs1412114406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 32107612 32107612 G A 1 0 0 0 0 0 0 0 1 1577 1285 45 3 3 BICD1 12 32107612 Silent SNP G C3N-01488_T 2656229 32107612 101167697 359 24733 ADAMTS20 0 . GRCh38 12 43431355 43431355 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.3238T>A p.Trp1080Arg p.W1080R ENST00000389420 22/39 199 178 21 289 289 0 strelka-varscan-mutect ADAMTS20,missense_variant,p.Trp1080Arg,ENST00000389420,NM_025003.3;ADAMTS20,missense_variant,p.Trp1080Arg,ENST00000395541,;ADAMTS20,missense_variant,p.Trp1080Arg,ENST00000553158,;ADAMTS20,missense_variant,p.Trp246Arg,ENST00000549670,; T ENST00000389420 Transcript missense_variant 3238/6076 3238/5733 1080/1910 W/R Tgg/Agg 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 deleterious(0) 22/39 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 43431355 43431355 A T 1 0 0 0 0 1 0 0 0 310 188 7 4 4 ADAMTS20 12 43431355 Missense_Mutation SNP A C3N-01488_T 11323743 43431355 89843954 360 24734 PUS7L 0 . GRCh38 12 43730396 43730396 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.2086A>T p.Ile696Leu p.I696L ENST00000344862 9/9 89 77 12 188 188 0 strelka-varscan-mutect PUS7L,missense_variant,p.Ile696Leu,ENST00000344862,NM_031292.4;PUS7L,missense_variant,p.Ile696Leu,ENST00000416848,NM_001098615.1;PUS7L,missense_variant,p.Ile696Leu,ENST00000551923,NM_001098614.2;PUS7L,missense_variant,p.Ile383Leu,ENST00000431332,NM_001271826.1; A ENST00000344862 Transcript missense_variant 2190/13593 2086/2106 696/701 I/L Ata/Tta 1 -1 PUS7L HGNC HGNC:25276 protein_coding YES CCDS8743.1 ENSP00000343081 Q9H0K6 UPI0000037C53 NM_031292.4 deleterious(0.01) 9/9 Pfam_domain:PF01142,PIRSF_domain:PIRSF037016,hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF5,Superfamily_domains:SSF55120,TIGRFAM_domain:TIGR00094 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 43730396 43730396 T A 1 0 0 0 0 1 0 0 0 12992 1493 52 4 4 PUS7L 12 43730396 Missense_Mutation SNP T C3N-01488_T 299041 43730396 89544913 361 24735 PUS7L 0 . GRCh38 12 43746074 43746074 + Missense_Mutation SNP C C G rs777009297 C3N-01488_T C3N-01488_N C C c.1235G>C p.Arg412Thr p.R412T ENST00000344862 4/9 176 137 39 317 317 0 strelka-varscan-mutect PUS7L,missense_variant,p.Arg412Thr,ENST00000344862,NM_031292.4;PUS7L,missense_variant,p.Arg412Thr,ENST00000416848,NM_001098615.1;PUS7L,missense_variant,p.Arg412Thr,ENST00000551923,NM_001098614.2;PUS7L,missense_variant,p.Arg99Thr,ENST00000431332,NM_001271826.1;PUS7L,missense_variant,p.Arg99Thr,ENST00000550784,;PUS7L,missense_variant,p.Arg99Thr,ENST00000547156,;PUS7L,downstream_gene_variant,,ENST00000553166,; G ENST00000344862 Transcript missense_variant 1339/13593 1235/2106 412/701 R/T aGa/aCa rs777009297,COSM284402 1 -1 PUS7L HGNC HGNC:25276 protein_coding YES CCDS8743.1 ENSP00000343081 Q9H0K6 UPI0000037C53 NM_031292.4 tolerated(0.08) 4/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01142,PIRSF_domain:PIRSF037016,hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF5,Superfamily_domains:SSF55120,TIGRFAM_domain:TIGR00094 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777009297 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 43746074 43746074 C G 1 0 0 0 0 1 0 0 0 12992 913 32 4 4 PUS7L 12 43746074 Missense_Mutation SNP C C3N-01488_T 15678 43746074 89529235 362 24736 IRAK4 0 . GRCh38 12 43768212 43768212 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.101A>T p.Lys34Met p.K34M ENST00000613694 2/12 141 121 20 221 221 0 strelka-varscan-mutect IRAK4,missense_variant,p.Lys34Met,ENST00000613694,NM_016123.3;IRAK4,missense_variant,p.Lys34Met,ENST00000551736,NM_001114182.2;IRAK4,missense_variant,p.Lys34Met,ENST00000448290,;IRAK4,missense_variant,p.Lys34Met,ENST00000550616,;IRAK4,5_prime_UTR_variant,,ENST00000431837,NM_001145257.1,NM_001145256.1;IRAK4,intron_variant,,ENST00000440781,NM_001145258.1;IRAK4,missense_variant,p.Lys34Met,ENST00000547521,;IRAK4,missense_variant,p.Lys34Met,ENST00000550386,;IRAK4,missense_variant,p.Lys34Met,ENST00000547101,;IRAK4,missense_variant,p.Lys34Met,ENST00000550615,;IRAK4,missense_variant,p.Lys34Met,ENST00000552309,;IRAK4,missense_variant,p.Lys34Met,ENST00000550361,;IRAK4,non_coding_transcript_exon_variant,,ENST00000546780,; T ENST00000613694 Transcript missense_variant 172/4280 101/1383 34/460 K/M aAg/aTg 1 1 IRAK4 HGNC HGNC:17967 protein_coding YES CCDS8744.1 ENSP00000479889 Q9NWZ3 Q69FE3 UPI000004ABE6 NM_016123.3 deleterious(0.02) 2/12 hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF22,PIRSF_domain:PIRSF038189,Gene3D:1.10.533.10,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999979 1 1 1 0 T 3 4 80 43768212 43768212 A T 1 0 0 0 0 1 0 0 0 7731 72 3 4 4 IRAK4 12 43768212 Missense_Mutation SNP A C3N-01488_T 22138 43768212 89507097 363 24737 KMT2D 0 . GRCh38 12 49040924 49040924 + Silent SNP C C A rs371474793 C3N-01488_T C3N-01488_N C C c.6846G>T p.= p.R2282R ENST00000301067 31/54 119 93 26 191 191 0 strelka-varscan-mutect KMT2D,synonymous_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,upstream_gene_variant,,ENST00000549799,;KMT2D,downstream_gene_variant,,ENST00000550356,; A ENST00000301067 Transcript synonymous_variant 6846/19419 6846/16614 2282/5537 R cgG/cgT rs371474793 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 31/54 LOW 1 SNV 5 1 PASS rs371474793 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 49040924 49040924 C A 1 0 0 0 0 0 0 0 1 8298 842 30 2 2 KMT2D 12 49040924 Silent SNP C C3N-01488_T 5272712 49040924 84234385 364 24738 SCN8A 0 . GRCh38 12 51765743 51765743 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.2617G>T p.Gly873Cys p.G873C ENST00000354534 16/27 82 68 14 164 164 0 strelka-varscan-mutect SCN8A,missense_variant,p.Gly873Cys,ENST00000354534,NM_014191.3;SCN8A,missense_variant,p.Gly873Cys,ENST00000545061,NM_001177984.2;SCN8A,missense_variant,p.Gly884Cys,ENST00000599343,;SCN8A,missense_variant,p.Gly873Cys,ENST00000627620,;SCN8A,missense_variant,p.Gly873Cys,ENST00000355133,;SCN8A,upstream_gene_variant,,ENST00000636458,;SCN8A,missense_variant,p.Gly208Cys,ENST00000636945,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,non_coding_transcript_exon_variant,,ENST00000550891,;SCN8A,upstream_gene_variant,,ENST00000627665,; T ENST00000354534 Transcript missense_variant 2795/11556 2617/5943 873/1980 G/C Ggt/Tgt 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 deleterious(0.01) 16/27 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 51765743 51765743 G T 1 0 0 0 0 1 0 0 0 14193 1232 43 2 2 SCN8A 12 51765743 Missense_Mutation SNP G C3N-01488_T 2724819 51765743 81509566 365 24739 HOXC10 0 . GRCh38 12 53989195 53989195 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.778G>T p.Gly260Ter p.G260* ENST00000303460 2/2 110 77 33 178 178 0 strelka-varscan-mutect HOXC10,stop_gained,p.Gly260Ter,ENST00000303460,NM_017409.3;RP11-834C11.12,intron_variant,,ENST00000513209,;HOXC6,upstream_gene_variant,,ENST00000504315,;HOXC10,downstream_gene_variant,,ENST00000515593,;MIR196A2,upstream_gene_variant,,ENST00000385189,;HOXC-AS3,upstream_gene_variant,,ENST00000509870,;HOXC-AS3,upstream_gene_variant,,ENST00000513165,;HOXC-AS3,upstream_gene_variant,,ENST00000514702,;HOXC10,non_coding_transcript_exon_variant,,ENST00000511575,;HOXC10,non_coding_transcript_exon_variant,,ENST00000513413,;HOXC10,non_coding_transcript_exon_variant,,ENST00000514415,;HOXC-AS3,upstream_gene_variant,,ENST00000567780,;HOXC-AS2,downstream_gene_variant,,ENST00000604081,; T ENST00000303460 Transcript stop_gained 852/1936 778/1029 260/342 G/* Gga/Tga 1 1 HOXC10 HGNC HGNC:5122 protein_coding YES CCDS8868.1 ENSP00000307321 Q9NYD6 Q53XI4 UPI000012CF7C NM_017409.3 2/2 hmmpanther:PTHR24326:SF135,hmmpanther:PTHR24326,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 53989195 53989195 G T 1 0 0 0 0 0 1 0 0 7203 1001 35 2 2 HOXC10 12 53989195 Nonsense_Mutation SNP G C3N-01488_T 2223452 53989195 79286114 366 24740 BAZ2A 0 . GRCh38 12 56615129 56615129 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.621G>T p.Gln207His p.Q207H ENST00000551812 3/29 159 134 25 265 264 1 strelka-varscan-mutect BAZ2A,splice_acceptor_variant,,ENST00000379441,;BAZ2A,missense_variant,p.Gln207His,ENST00000551812,NM_013449.3;BAZ2A,missense_variant,p.Gln205His,ENST00000549884,NM_001300905.1;BAZ2A,upstream_gene_variant,,ENST00000551996,;BAZ2A,downstream_gene_variant,,ENST00000546695,;BAZ2A,upstream_gene_variant,,ENST00000547650,;BAZ2A,downstream_gene_variant,,ENST00000549506,;BAZ2A,upstream_gene_variant,,ENST00000547647,;BAZ2A,downstream_gene_variant,,ENST00000550730,;BAZ2A,downstream_gene_variant,,ENST00000551959,;BAZ2A,upstream_gene_variant,,ENST00000549327,; A ENST00000551812 Transcript missense_variant 815/8600 621/5718 207/1905 Q/H caG/caT 1 -1 BAZ2A HGNC HGNC:962 protein_coding YES CCDS44924.1 ENSP00000446880 Q9UIF9 UPI0000D4FED1 NM_013449.3 deleterious(0.01) 3/29 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF141 MODERATE 1 SNV 1 1 PASS rs1357249498 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 56615129 56615129 C A 1 0 0 0 0 1 0 0 0 1476 680 24 2 2 BAZ2A 12 56615129 Missense_Mutation SNP C C3N-01488_T 2625934 56615129 76660180 367 24741 C12orf56 0 . GRCh38 12 64275344 64275344 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.1463A>G p.Asn488Ser p.N488S ENST00000543942 10/13 94 88 6 87 87 0 strelka-varscan-mutect C12orf56,missense_variant,p.Asn328Ser,ENST00000333722,NM_001099676.2;C12orf56,missense_variant,p.Asn488Ser,ENST00000543942,NM_001170633.1;C12orf56,non_coding_transcript_exon_variant,,ENST00000536975,;C12orf56,non_coding_transcript_exon_variant,,ENST00000542397,;RPS11P6,intron_variant,,ENST00000535684,;C12orf56,upstream_gene_variant,,ENST00000535515,;C12orf56,non_coding_transcript_exon_variant,,ENST00000541802,; C ENST00000543942 Transcript missense_variant 2090/3242 1463/1869 488/622 N/S aAt/aGt 1 -1 C12orf56 HGNC HGNC:26967 protein_coding YES CCDS61182.1 ENSP00000446101 Q8IXR9 UPI0001C0B37D NM_001170633.1 deleterious(0) 10/13 Pfam_domain:PF15087,hmmpanther:PTHR35354 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 64275344 64275344 T C 1 0 0 0 0 1 0 0 0 1816 1493 52 5 5 C12orf56 12 64275344 Missense_Mutation SNP T C3N-01488_T 7660215 64275344 68999965 368 24742 SYT1 0 . GRCh38 12 79299406 79299406 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.665G>T p.Gly222Val p.G222V ENST00000261205 8/11 297 200 97 362 362 0 strelka-varscan-mutect SYT1,missense_variant,p.Gly222Val,ENST00000261205,NM_005639.2;SYT1,missense_variant,p.Gly219Val,ENST00000457153,NM_001291901.1;SYT1,missense_variant,p.Gly222Val,ENST00000393240,NM_001135805.1;SYT1,missense_variant,p.Gly222Val,ENST00000552744,NM_001135806.1;SYT1,downstream_gene_variant,,ENST00000446242,;SYT1,downstream_gene_variant,,ENST00000552624,;SYT1,non_coding_transcript_exon_variant,,ENST00000549559,; T ENST00000261205 Transcript missense_variant 1322/4808 665/1269 222/422 G/V gGc/gTc 1 1 SYT1 HGNC HGNC:11509 protein_coding YES CCDS9017.1 ENSP00000261205 P21579 A0A024RBE9 UPI000013669A NM_005639.2 deleterious(0.01) 8/11 PROSITE_profiles:PS50004,hmmpanther:PTHR10024:SF239,hmmpanther:PTHR10024,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 79299406 79299406 G T 1 0 0 0 0 1 0 0 0 15859 1203 42 2 2 SYT1 12 79299406 Missense_Mutation SNP G C3N-01488_T 15024062 79299406 53975903 369 24743 OTOGL 0 . GRCh38 12 80318705 80318705 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.3767A>T p.Lys1256Met p.K1256M ENST00000458043 32/58 42 28 14 44 44 0 strelka-varscan-mutect OTOGL,missense_variant,p.Lys1256Met,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Lys1256Met,ENST00000547103,; T ENST00000458043 Transcript missense_variant 3773/8083 3767/7035 1256/2344 K/M aAg/aTg 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 32/58 Low_complexity_(Seg):seg,Pfam_domain:PF05270,Gene3D:2.80.10.50,Superfamily_domains:0050434 MODERATE 1 SNV 5 1 PASS rs1490972201 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 80318705 80318705 A T 1 0 0 0 0 1 0 0 0 11371 72 3 4 4 OTOGL 12 80318705 Missense_Mutation SNP A C3N-01488_T 1019299 80318705 52956604 370 24744 DAO 0 . GRCh38 12 108887513 108887513 + Silent SNP C C T rs762709353 C3N-01488_T C3N-01488_N C C c.258C>T p.= p.N86N ENST00000228476 3/11 412 388 24 448 448 0 strelka-varscan-mutect DAO,synonymous_variant,p.=,ENST00000228476,NM_001917.4;DAO,synonymous_variant,p.=,ENST00000551281,;DAO,synonymous_variant,p.=,ENST00000547166,;DAO,intron_variant,,ENST00000547768,;DAO,downstream_gene_variant,,ENST00000548052,;DAO,synonymous_variant,p.=,ENST00000549215,;DAO,intron_variant,,ENST00000547122,; T ENST00000228476 Transcript synonymous_variant 462/1756 258/1044 86/347 N aaC/aaT rs762709353 1 1 DAO HGNC HGNC:2671 protein_coding YES CCDS9122.1 ENSP00000228476 P14920 A0A024RBI1 UPI0000130F5F NM_001917.4 3/11 Pfam_domain:PF01266,PIRSF_domain:PIRSF000189,hmmpanther:PTHR11530,hmmpanther:PTHR11530:SF11,Superfamily_domains:SSF51971 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 108887513 108887513 C T 1 0 0 0 0 0 0 0 1 4032 506 18 3 3 DAO 12 108887513 Silent SNP C C3N-01488_T 28568808 108887513 24387796 371 24745 RBM19 0 . GRCh38 12 113959231 113959231 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.552A>T p.= p.G184G ENST00000545145 5/25 64 45 19 63 63 0 strelka-varscan-mutect RBM19,synonymous_variant,p.=,ENST00000545145,NM_001146699.1;RBM19,synonymous_variant,p.=,ENST00000261741,NM_016196.3;RBM19,synonymous_variant,p.=,ENST00000392561,NM_001146698.1;RBM19,intron_variant,,ENST00000546876,; A ENST00000545145 Transcript synonymous_variant 631/4422 552/2883 184/960 G ggA/ggT 1 -1 RBM19 HGNC HGNC:29098 protein_coding YES CCDS9172.1 ENSP00000442053 Q9Y4C8 UPI000013D1EC NM_001146699.1 5/25 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 113959231 113959231 T A 1 0 0 0 0 0 0 0 1 13286 1538 54 4 4 RBM19 12 113959231 Silent SNP T C3N-01488_T 5071718 113959231 19316078 372 24746 SRRM4 0 . GRCh38 12 119156719 119156719 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1757G>T p.Arg586Met p.R586M ENST00000267260 13/13 211 179 32 288 286 2 strelka-varscan-mutect SRRM4,missense_variant,p.Arg586Met,ENST00000267260,NM_194286.3; T ENST00000267260 Transcript missense_variant 2145/8477 1757/1836 586/611 R/M aGg/aTg 1 1 SRRM4 HGNC HGNC:29389 protein_coding YES CCDS44994.1 ENSP00000267260 A7MD48 V5T9A0 UPI00001FBC3F NM_194286.3 deleterious_low_confidence(0) 13/13 hmmpanther:PTHR34755,hmmpanther:PTHR34755:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -15.87856 0.9969504 1 1 1 0 T 3 4 80 119156719 119156719 G T 1 0 0 0 0 1 0 0 0 15532 1000 35 2 2 SRRM4 12 119156719 Missense_Mutation SNP G C3N-01488_T 5197488 119156719 14118590 373 24747 NCOR2 0 . GRCh38 12 124346636 124346636 + Silent SNP C C A rs759702301 C3N-01488_T C3N-01488_N C C c.4287G>T p.= p.P1429P ENST00000405201 31/47 149 126 23 164 164 0 strelka-mutect NCOR2,synonymous_variant,p.=,ENST00000405201,NM_006312.5;NCOR2,synonymous_variant,p.=,ENST00000404621,NM_001077261.3;NCOR2,synonymous_variant,p.=,ENST00000429285,NM_001206654.1;NCOR2,synonymous_variant,p.=,ENST00000356219,;NCOR2,synonymous_variant,p.=,ENST00000404121,;NCOR2,synonymous_variant,p.=,ENST00000458234,;NCOR2,upstream_gene_variant,,ENST00000453428,;NCOR2,upstream_gene_variant,,ENST00000440187,;NCOR2,downstream_gene_variant,,ENST00000473999,; A ENST00000405201 Transcript synonymous_variant 4288/8533 4287/7545 1429/2514 P ccG/ccT rs759702301 1 -1 NCOR2 HGNC HGNC:7673 protein_coding YES CCDS41858.2 ENSP00000384018 C9JFD3 UPI000013D737 NM_006312.5 31/47 hmmpanther:PTHR13992,hmmpanther:PTHR13992:SF21 LOW 1 SNV 1 1 PASS rs759702301 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 124346636 124346636 C A 1 0 0 0 0 0 0 0 1 10255 755 27 1 1 NCOR2 12 124346636 Silent SNP C C3N-01488_T 5189917 124346636 8928673 374 24748 RIMBP2 0 . GRCh38 12 130422556 130422556 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.2367A>T p.Leu789Phe p.L789F ENST00000261655 13/19 72 56 16 103 103 0 strelka-varscan-mutect RIMBP2,missense_variant,p.Leu789Phe,ENST00000261655,NM_015347.4;RP11-117L5.4,upstream_gene_variant,,ENST00000539532,;RP11-117L5.1,upstream_gene_variant,,ENST00000624734,; A ENST00000261655 Transcript missense_variant 2531/6321 2367/3159 789/1052 L/F ttA/ttT 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 tolerated(0.06) 13/19 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 80 130422556 130422556 T A 1 0 0 0 0 1 0 0 0 13538 1536 53 4 4 RIMBP2 12 130422556 Missense_Mutation SNP T C3N-01488_T 6075920 130422556 2852753 375 24749 EP400 0 . GRCh38 12 132077554 132077554 + Missense_Mutation SNP G G C rs752334163 C3N-01488_T C3N-01488_N G G c.9253G>C p.Gly3085Arg p.G3085R ENST00000389562 52/52 276 237 39 347 346 1 strelka-varscan-mutect EP400,missense_variant,p.Gly3085Arg,ENST00000389562,;EP400,missense_variant,p.Gly3085Arg,ENST00000389561,NM_015409.4;EP400,missense_variant,p.Gly336Arg,ENST00000330386,;RP13-820C6.2,downstream_gene_variant,,ENST00000542422,;EP400,non_coding_transcript_exon_variant,,ENST00000611739,;EP400,non_coding_transcript_exon_variant,,ENST00000616136,;EP400,non_coding_transcript_exon_variant,,ENST00000611118,; C ENST00000389562 Transcript missense_variant 9288/12836 9253/9372 3085/3123 G/R Ggc/Cgc rs752334163 1 1 EP400 HGNC HGNC:11958 protein_coding YES CCDS31929.2 ENSP00000374213 Q96L91 UPI00004566BC deleterious_low_confidence(0.01) 52/52 MODERATE 1 SNV 1 1 PASS rs752334163 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 132077554 132077554 G C 1 0 0 0 0 1 0 0 0 4995 1000 35 4 4 EP400 12 132077554 Missense_Mutation SNP G C3N-01488_T 1654998 132077554 1197755 376 24750 CENPJ 0 . GRCh38 13 24906230 24906230 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.1808G>C p.Arg603Thr p.R603T ENST00000381884 7/17 63 58 5 107 107 0 strelka-varscan-mutect CENPJ,missense_variant,p.Arg603Thr,ENST00000616936,;CENPJ,missense_variant,p.Arg603Thr,ENST00000381884,NM_018451.4;CENPJ,missense_variant,p.Arg603Thr,ENST00000545981,;CENPJ,upstream_gene_variant,,ENST00000418179,; G ENST00000381884 Transcript missense_variant 1994/4347 1808/4017 603/1338 R/T aGg/aCg 1 -1 CENPJ HGNC HGNC:17272 protein_coding YES CCDS9310.1 ENSP00000371308 Q9HC77 UPI000013DC8A NM_018451.4 deleterious(0) 7/17 hmmpanther:PTHR10331,hmmpanther:PTHR10331:SF23 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -12.16787 1 1 1 1 0 G 3 3 80 24906230 24906230 C G 1 0 0 0 0 1 0 0 0 2942 681 24 4 4 CENPJ 13 24906230 Missense_Mutation SNP C C3N-01488_T 24906230 89458098 377 24751 OLFM4 0 . GRCh38 13 53049989 53049989 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.751G>C p.Val251Leu p.V251L ENST00000219022 5/5 76 47 29 147 147 0 strelka-varscan-mutect OLFM4,missense_variant,p.Val251Leu,ENST00000219022,NM_006418.4; C ENST00000219022 Transcript missense_variant 829/2897 751/1533 251/510 V/L Gtg/Ctg 1 1 OLFM4 HGNC HGNC:17190 protein_coding YES CCDS9440.1 ENSP00000219022 Q6UX06 A0A024QZ95 UPI00000359F0 NM_006418.4 tolerated(1) 5/5 PROSITE_profiles:PS51132,hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF7,SMART_domains:SM00284 MODERATE 1 SNV 1 1 PASS rs1373398655 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 53049989 53049989 G C 1 0 0 0 0 1 0 0 0 10930 1377 48 4 4 OLFM4 13 53049989 Missense_Mutation SNP G C3N-01488_T 28143759 53049989 61314339 378 24752 KLHL1 0 . GRCh38 13 69796765 69796765 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1612C>A p.Pro538Thr p.P538T ENST00000377844 7/11 197 137 60 312 311 1 strelka-varscan-mutect KLHL1,missense_variant,p.Pro538Thr,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Pro477Thr,ENST00000545028,NM_001286725.1; T ENST00000377844 Transcript missense_variant 2372/4115 1612/2247 538/748 P/T Cca/Aca 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 deleterious(0) 7/11 hmmpanther:PTHR24412:SF75,hmmpanther:PTHR24412,Pfam_domain:PF01344,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 69796765 69796765 G T 1 0 0 0 0 1 0 0 0 8229 1261 44 2 2 KLHL1 13 69796765 Missense_Mutation SNP G C3N-01488_T 16746776 69796765 44567563 379 24753 SLITRK1 0 . GRCh38 13 83880447 83880447 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1061G>T p.Gly354Val p.G354V ENST00000377084 1/1 252 234 18 359 358 1 strelka-varscan-mutect SLITRK1,missense_variant,p.Gly354Val,ENST00000377084,NM_052910.2,NM_001281503.1; A ENST00000377084 Transcript missense_variant 1947/5189 1061/2091 354/696 G/V gGt/gTt 1 -1 SLITRK1 HGNC HGNC:20297 protein_coding YES CCDS9464.1 ENSP00000366288 Q96PX8 UPI0000035971 NM_052910.2,NM_001281503.1 deleterious(0) 1/1 MODERATE 1 SNV 1 PASS rs1410216234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 83880447 83880447 C A 1 0 0 0 0 1 0 0 0 15033 507 18 2 2 SLITRK1 13 83880447 Missense_Mutation SNP C C3N-01488_T 14083682 83880447 30483881 380 24754 TM9SF2 0 . GRCh38 13 99554451 99554451 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.1636A>G p.Ile546Val p.I546V ENST00000376387 14/17 98 86 12 143 143 0 varscan-mutect TM9SF2,missense_variant,p.Ile546Val,ENST00000376387,NM_004800.2; G ENST00000376387 Transcript missense_variant 1826/3430 1636/1992 546/663 I/V Att/Gtt 1 1 TM9SF2 HGNC HGNC:11865 protein_coding YES CCDS9493.1 ENSP00000365567 Q99805 A0A024QYR8 UPI000013684D NM_004800.2 deleterious(0.02) 14/17 hmmpanther:PTHR10766,hmmpanther:PTHR10766:SF36,Pfam_domain:PF02990 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 99554451 99554451 A G 1 0 0 0 0 1 0 0 0 16422 463 16 5 5 TM9SF2 13 99554451 Missense_Mutation SNP A C3N-01488_T 15674004 99554451 14809877 381 24755 BIVM 0 . GRCh38 13 102839607 102839607 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.1168G>C p.Gln390His p.Q390H ENST00000602836 9/21 173 142 31 256 256 0 strelka-varscan-mutect BIVM-ERCC5,missense_variant,p.Gln390His,ENST00000602836,NM_001204425.1;BIVM,missense_variant,p.Gln418His,ENST00000257336,NM_017693.3;BIVM,missense_variant,p.Gln196His,ENST00000448849,NM_001159596.1;BIVM,non_coding_transcript_exon_variant,,ENST00000490317,; C ENST00000602836 Transcript missense_variant 1168/4155 1170/4157 390/1385 Q/H caG/caC 1 1 BIVM-ERCC5 HGNC HGNC:43690 protein_coding YES ENSP00000473384 R4GMW8 UPI0002B83330 NM_001204425.1 deleterious_low_confidence(0) 9/21 hmmpanther:PTHR16171:SF5,hmmpanther:PTHR16171 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 102839607 102839607 G C 1 0 0 0 0 1 0 0 0 1592 933 33 4 4 BIVM 13 102839607 Missense_Mutation SNP G C3N-01488_T 3285156 102839607 11524721 382 24756 SLC10A2 0 . GRCh38 13 103066154 103066154 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.96G>T p.= p.V32V ENST00000245312 1/6 178 124 54 229 228 1 strelka-varscan-mutect SLC10A2,synonymous_variant,p.=,ENST00000245312,NM_000452.2; A ENST00000245312 Transcript synonymous_variant 693/3779 96/1047 32/348 V gtG/gtT 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 1/6 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 103066154 103066154 C A 1 0 0 0 0 0 0 0 1 14639 581 21 2 2 SLC10A2 13 103066154 Silent SNP C C3N-01488_T 226547 103066154 11298174 383 24757 NDRG2 0 . GRCh38 14 21022182 21022182 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.224A>G p.Tyr75Cys p.Y75C ENST00000556147 5/16 159 132 27 248 248 0 strelka-varscan-mutect NDRG2,missense_variant,p.Tyr75Cys,ENST00000556147,NM_001320329.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000555158,NM_001282214.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000553503,NM_001282213.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000350792,NM_016250.2;NDRG2,missense_variant,p.Tyr75Cys,ENST00000298687,NM_201535.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000397844,NM_001282212.1;NDRG2,missense_variant,p.Tyr75Cys,ENST00000397847,NM_001282215.1;NDRG2,missense_variant,p.Tyr75Cys,ENST00000397853,NM_201540.1;NDRG2,missense_variant,p.Tyr75Cys,ENST00000397858,NM_201537.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000360463,NM_201536.1;NDRG2,missense_variant,p.Tyr75Cys,ENST00000397851,NM_201539.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554143,NM_201541.1,NM_201538.1;NDRG2,missense_variant,p.Tyr61Cys,ENST00000298684,;NDRG2,missense_variant,p.Tyr71Cys,ENST00000403829,NM_001282211.1;NDRG2,missense_variant,p.Tyr60Cys,ENST00000397856,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000555026,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000556008,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000556974,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000553784,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000555733,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000555869,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557169,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000553867,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000555384,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000556420,;NDRG2,missense_variant,p.Tyr64Cys,ENST00000554531,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000553442,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000556457,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557676,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554561,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000555142,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000556329,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000556924,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554094,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557264,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000554472,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000554419,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000556688,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557149,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000556561,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554893,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000555657,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554489,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000554833,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557274,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000554398,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554483,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000554415,;NDRG2,missense_variant,p.Tyr36Cys,ENST00000449431,;NDRG2,missense_variant,p.Tyr18Cys,ENST00000557633,;NDRG2,splice_region_variant,,ENST00000554104,NM_001282216.1;NDRG2,coding_sequence_variant,p.=,ENST00000635386,;NDRG2,5_prime_UTR_variant,,ENST00000556366,;NDRG2,intron_variant,,ENST00000557182,;NDRG2,intron_variant,,ENST00000553563,;NDRG2,upstream_gene_variant,,ENST00000553593,;AL161668.5,upstream_gene_variant,,ENST00000533984,;AL161668.5,upstream_gene_variant,,ENST00000532213,;NDRG2,downstream_gene_variant,,ENST00000622747,;NDRG2,upstream_gene_variant,,ENST00000554277,;NDRG2,missense_variant,p.Tyr75Cys,ENST00000555695,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000557616,;NDRG2,missense_variant,p.Ile26Val,ENST00000555767,;NDRG2,missense_variant,p.Tyr61Cys,ENST00000554379,;NDRG2,splice_region_variant,,ENST00000553741,;NDRG2,splice_region_variant,,ENST00000557669,;NDRG2,splice_region_variant,,ENST00000557198,;NDRG2,splice_region_variant,,ENST00000553900,;NDRG2,splice_region_variant,,ENST00000557113,;NDRG2,splice_region_variant,,ENST00000557318,;NDRG2,non_coding_transcript_exon_variant,,ENST00000553862,;NDRG2,non_coding_transcript_exon_variant,,ENST00000557728,;NDRG2,intron_variant,,ENST00000557353,;NDRG2,upstream_gene_variant,,ENST00000556716,;NDRG2,upstream_gene_variant,,ENST00000555650,;TPPP2,upstream_gene_variant,,ENST00000533755,;NDRG2,upstream_gene_variant,,ENST00000553793,;NDRG2,upstream_gene_variant,,ENST00000557305,;NDRG2,upstream_gene_variant,,ENST00000366204,;NDRG2,downstream_gene_variant,,ENST00000557167,;NDRG2,upstream_gene_variant,,ENST00000557416,;NDRG2,upstream_gene_variant,,ENST00000553567,; C ENST00000556147 Transcript missense_variant,splice_region_variant 1165/2880 224/1116 75/371 Y/C tAt/tGt 1 -1 NDRG2 HGNC HGNC:14460 protein_coding YES CCDS9565.1 ENSP00000451712 Q9UN36 UPI000012FEDE NM_001320329.1 deleterious(0.03) 5/16 Gene3D:3.40.50.1820,Pfam_domain:PF03096,hmmpanther:PTHR11034,hmmpanther:PTHR11034:SF17,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 21022182 21022182 T C 1 0 0 0 0 1 0 0 0 10273 1449 50 5 5 NDRG2 14 21022182 Missense_Mutation SNP T C3N-01488_T 21022182 86021536 384 24758 CLEC14A 0 . GRCh38 14 38255266 38255266 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.757G>A p.Ala253Thr p.A253T ENST00000342213 1/1 185 140 45 306 306 0 strelka-varscan-mutect CLEC14A,missense_variant,p.Ala253Thr,ENST00000342213,NM_175060.2; T ENST00000342213 Transcript missense_variant 1104/2267 757/1473 253/490 A/T Gct/Act 1 -1 CLEC14A HGNC HGNC:19832 protein_coding YES CCDS9667.1 ENSP00000353013 Q86T13 UPI000000CBD4 NM_175060.2 tolerated(0.4) 1/1 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF285 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 38255266 38255266 C T 1 0 0 0 0 1 0 0 0 3265 710 25 3 3 CLEC14A 14 38255266 Missense_Mutation SNP C C3N-01488_T 17233084 38255266 68788452 385 24759 SOS2 0 . GRCh38 14 50199747 50199747 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.454A>T p.Ile152Phe p.I152F ENST00000216373 4/23 104 97 7 196 196 0 strelka-varscan-mutect SOS2,missense_variant,p.Ile152Phe,ENST00000216373,NM_006939.2;SOS2,missense_variant,p.Ile152Phe,ENST00000543680,;SOS2,non_coding_transcript_exon_variant,,ENST00000555666,;SOS2,non_coding_transcript_exon_variant,,ENST00000556469,;SOS2,downstream_gene_variant,,ENST00000556452,; A ENST00000216373 Transcript missense_variant 729/5498 454/3999 152/1332 I/F Atc/Ttc 1 -1 SOS2 HGNC HGNC:11188 protein_coding YES CCDS9697.1 ENSP00000216373 Q07890 UPI000013C6E8 NM_006939.2 deleterious(0) 4/23 hmmpanther:PTHR23113:SF150,hmmpanther:PTHR23113,Pfam_domain:PF00125,Gene3D:1.10.20.10,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 50199747 50199747 T A 1 0 0 0 0 1 0 0 0 15259 1406 49 4 4 SOS2 14 50199747 Missense_Mutation SNP T C3N-01488_T 11944481 50199747 56843971 386 24760 TXNDC16 0 . GRCh38 14 52511392 52511392 + Splice_Site SNP T T A novel C3N-01488_T C3N-01488_N T T c.606-2A>T p.X202_splice ENST00000281741 45 39 6 68 68 0 strelka-varscan-mutect TXNDC16,splice_acceptor_variant,,ENST00000281741,NM_001160047.1,NM_020784.2;TXNDC16,intron_variant,,ENST00000557374,;TXNDC16,intron_variant,,ENST00000554399,; A ENST00000281741 Transcript splice_acceptor_variant -/4564 606/2478 202/825 1 -1 TXNDC16 HGNC HGNC:19965 protein_coding YES CCDS32083.1 ENSP00000281741 Q9P2K2 UPI000059D245 NM_001160047.1,NM_020784.2 8/20 HIGH 1 SNV 1 1 PASS . . 1 200 9 0 0 0 0 0 -14.65424 0.9999916 1 1 1 0 A 5 1 80 52511392 52511392 T A 1 0 0 0 0 0 0 1 0 17311 1536 53 4 4 TXNDC16 14 52511392 Splice_Site SNP T C3N-01488_T 2311645 52511392 54532326 387 24761 RTN1 0 . GRCh38 14 59727044 59727044 + Missense_Mutation SNP G G T rs776096398 C3N-01488_T C3N-01488_N G G c.1640C>A p.Thr547Lys p.T547K ENST00000267484 3/9 323 268 55 344 344 0 strelka-varscan-mutect RTN1,missense_variant,p.Thr547Lys,ENST00000267484,NM_021136.2;RTN1,missense_variant,p.Thr473Lys,ENST00000611068,;RTN1,non_coding_transcript_exon_variant,,ENST00000432103,; T ENST00000267484 Transcript missense_variant 1976/3435 1640/2331 547/776 T/K aCg/aAg rs776096398 1 -1 RTN1 HGNC HGNC:10467 protein_coding YES CCDS9740.1 ENSP00000267484 Q16799 UPI00001352DA NM_021136.2 tolerated(0.87) 3/9 hmmpanther:PTHR10994:SF26,hmmpanther:PTHR10994 MODERATE 1 SNV 1 1 PASS rs776096398 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 59727044 59727044 G T 1 0 0 0 0 1 0 0 0 13985 1145 40 1 1 RTN1 14 59727044 Missense_Mutation SNP G C3N-01488_T 7215652 59727044 47316674 388 24762 HIF1A 0 . GRCh38 14 61738268 61738268 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.1503A>G p.= p.K501K ENST00000539097 10/15 235 218 17 296 296 0 strelka-varscan-mutect HIF1A,synonymous_variant,p.=,ENST00000539097,NM_001243084.1;HIF1A,synonymous_variant,p.=,ENST00000394997,;HIF1A,synonymous_variant,p.=,ENST00000337138,NM_001530.3;HIF1A,synonymous_variant,p.=,ENST00000323441,NM_181054.2;HIF1A,synonymous_variant,p.=,ENST00000557538,;HIF1A-AS2,intron_variant,,ENST00000554254,;HIF1A,intron_variant,,ENST00000555014,;RP11-618G20.1,intron_variant,,ENST00000555937,;HIF1A,upstream_gene_variant,,ENST00000547430,; G ENST00000539097 Transcript synonymous_variant 1732/3956 1503/2553 501/850 K aaA/aaG 1 1 HIF1A HGNC HGNC:4910 protein_coding YES CCDS58324.1 ENSP00000437955 Q16665 UPI0001982748 NM_001243084.1 10/15 hmmpanther:PTHR23043:SF7,hmmpanther:PTHR23043,Prints_domain:PR01080 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 61738268 61738268 A G 1 0 0 0 0 0 0 0 1 6988 98 4 5 5 HIF1A 14 61738268 Silent SNP A C3N-01488_T 2011224 61738268 45305450 389 24763 SLC8A3 0 . GRCh38 14 70168207 70168207 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.216C>A p.Asp72Glu p.D72E ENST00000381269 2/8 239 192 47 334 334 0 strelka-varscan-mutect SLC8A3,missense_variant,p.Asp72Glu,ENST00000381269,NM_183002.2;SLC8A3,missense_variant,p.Asp72Glu,ENST00000357887,NM_033262.4;SLC8A3,missense_variant,p.Asp72Glu,ENST00000356921,NM_182932.2;SLC8A3,missense_variant,p.Asp72Glu,ENST00000528359,;SLC8A3,missense_variant,p.Asp72Glu,ENST00000534137,NM_058240.3;SLC8A3,missense_variant,p.Asp72Glu,ENST00000494208,; T ENST00000381269 Transcript missense_variant 970/5268 216/2784 72/927 D/E gaC/gaA COSM1158461,COSM216329 1 -1 SLC8A3 HGNC HGNC:11070 protein_coding YES CCDS35498.1 ENSP00000370669 P57103 UPI0000073C9A NM_183002.2 tolerated(0.11) 2/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF7,TIGRFAM_domain:TIGR00845 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs912657750 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 70168207 70168207 G T 1 0 0 0 0 1 0 0 0 14991 1368 48 2 2 SLC8A3 14 70168207 Missense_Mutation SNP G C3N-01488_T 8429939 70168207 36875511 390 24764 VSX2 0 . GRCh38 14 74239662 74239662 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.101T>A p.Ile34Asn p.I34N ENST00000261980 1/5 385 321 64 459 459 0 strelka-varscan-mutect VSX2,missense_variant,p.Ile34Asn,ENST00000261980,NM_182894.2; A ENST00000261980 Transcript missense_variant 191/2995 101/1086 34/361 I/N aTc/aAc 1 1 VSX2 HGNC HGNC:1975 protein_coding YES CCDS9827.1 ENSP00000261980 P58304 UPI0000128755 NM_182894.2 deleterious(0) 1/5 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF330 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 74239662 74239662 T A 1 0 0 0 0 1 0 0 0 17786 1435 50 4 4 VSX2 14 74239662 Missense_Mutation SNP T C3N-01488_T 4071455 74239662 32804056 391 24765 VIPAS39 0 . GRCh38 14 77453312 77453312 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.183G>A p.= p.G61G ENST00000553888 3/20 490 398 92 608 607 1 strelka-varscan-mutect VIPAS39,synonymous_variant,p.=,ENST00000553888,NM_022067.3,NM_001193314.1,NM_001193317.1;VIPAS39,synonymous_variant,p.=,ENST00000343765,;VIPAS39,synonymous_variant,p.=,ENST00000327028,;VIPAS39,synonymous_variant,p.=,ENST00000557658,NM_001193315.1;VIPAS39,synonymous_variant,p.=,ENST00000556412,;VIPAS39,synonymous_variant,p.=,ENST00000448935,NM_001193316.1;AHSA1,upstream_gene_variant,,ENST00000216479,NM_012111.2;AHSA1,upstream_gene_variant,,ENST00000535854,;AHSA1,upstream_gene_variant,,ENST00000555133,;AHSA1,upstream_gene_variant,,ENST00000555517,;VIPAS39,downstream_gene_variant,,ENST00000557466,;VIPAS39,downstream_gene_variant,,ENST00000556909,;VIPAS39,non_coding_transcript_exon_variant,,ENST00000553691,;AHSA1,upstream_gene_variant,,ENST00000556963,;AHSA1,upstream_gene_variant,,ENST00000554156,; T ENST00000553888 Transcript synonymous_variant 694/2934 183/1482 61/493 G ggG/ggA 1 -1 VIPAS39 HGNC HGNC:20347 protein_coding YES CCDS9862.1 ENSP00000452181 Q9H9C1 Q6IA61 UPI00000735EF NM_022067.3,NM_001193314.1,NM_001193317.1 3/20 hmmpanther:PTHR13364,hmmpanther:PTHR13364:SF6 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 77453312 77453312 C T 1 0 0 0 0 0 0 0 1 17715 610 22 3 3 VIPAS39 14 77453312 Silent SNP C C3N-01488_T 3213650 77453312 29590406 392 24766 NRXN3 0 . GRCh38 14 78967235 78967235 + Silent SNP A A T novel C3N-01488_T C3N-01488_N A A c.1686A>T p.= p.G562G ENST00000554719 10/17 147 121 26 187 187 0 strelka-varscan-mutect NRXN3,synonymous_variant,p.=,ENST00000634499,;NRXN3,synonymous_variant,p.=,ENST00000635466,;NRXN3,synonymous_variant,p.=,ENST00000554719,NM_004796.5;NRXN3,synonymous_variant,p.=,ENST00000335750,;NRXN3,non_coding_transcript_exon_variant,,ENST00000634266,;NRXN3,synonymous_variant,p.=,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,; T ENST00000554719 Transcript synonymous_variant 2177/4156 1686/3186 562/1061 G ggA/ggT 1 1 NRXN3 HGNC HGNC:8010 protein_coding YES CCDS9870.1 ENSP00000451648 Q9Y4C0 UPI0000167BBA NM_004796.5 10/17 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 78967235 78967235 A T 1 0 0 0 0 0 0 0 1 10726 233 9 4 4 NRXN3 14 78967235 Silent SNP A C3N-01488_T 1513923 78967235 28076483 393 24767 TSHR 0 . GRCh38 14 81143160 81143160 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1102C>A p.Gln368Lys p.Q368K ENST00000541158 11/11 611 505 106 850 847 3 strelka-varscan-mutect TSHR,missense_variant,p.Gln368Lys,ENST00000541158,;TSHR,missense_variant,p.Gln368Lys,ENST00000298171,NM_000369.2;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,non_coding_transcript_exon_variant,,ENST00000636454,;TSHR,missense_variant,p.Gln3Lys,ENST00000637447,; A ENST00000541158 Transcript missense_variant 1424/4566 1102/2295 368/764 Q/K Cag/Aag 1 1 TSHR HGNC HGNC:12373 protein_coding YES CCDS9872.1 ENSP00000441235 A0A0A0MTJ0 UPI000013E4A2 tolerated(0.21) 11/11 Prints_domain:PR01145,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 81143160 81143160 C A 1 0 0 0 0 1 0 0 0 17127 595 21 2 2 TSHR 14 81143160 Missense_Mutation SNP C C3N-01488_T 2175925 81143160 25900558 394 24768 SEL1L 0 . GRCh38 14 81499609 81499609 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.831G>T p.Lys277Asn p.K277N ENST00000336735 7/21 127 110 17 206 206 0 strelka-varscan-mutect SEL1L,missense_variant,p.Lys277Asn,ENST00000336735,NM_005065.5;SEL1L,missense_variant,p.Lys277Asn,ENST00000555824,NM_001244984.1;SEL1L,downstream_gene_variant,,ENST00000557372,;SEL1L,splice_region_variant,,ENST00000554744,; A ENST00000336735 Transcript missense_variant,splice_region_variant 948/7925 831/2385 277/794 K/N aaG/aaT 1 -1 SEL1L HGNC HGNC:10717 protein_coding YES CCDS9876.1 ENSP00000337053 Q9UBV2 UPI0000135746 NM_005065.5 deleterious(0) 7/21 Gene3D:1.25.40.10,Pfam_domain:PF08238,hmmpanther:PTHR11102,hmmpanther:PTHR11102:SF70,SMART_domains:SM00671,Superfamily_domains:SSF81901 MODERATE 1 SNV 1 1 PASS rs1292032705 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 81499609 81499609 C A 1 0 0 0 0 1 0 0 0 14287 695 24 2 2 SEL1L 14 81499609 Missense_Mutation SNP C C3N-01488_T 356449 81499609 25544109 395 24769 AHNAK2 0 . GRCh38 14 104954030 104954030 + Missense_Mutation SNP C C A rs770634629 C3N-01488_T C3N-01488_N C C c.1421G>T p.Gly474Val p.G474V ENST00000333244 7/7 110 84 26 198 197 1 strelka-varscan-mutect AHNAK2,missense_variant,p.Gly474Val,ENST00000333244,NM_138420.2;AHNAK2,upstream_gene_variant,,ENST00000557457,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555544,; A ENST00000333244 Transcript missense_variant 1541/18254 1421/17388 474/5795 G/V gGc/gTc rs770634629 1 -1 AHNAK2 HGNC HGNC:20125 protein_coding YES CCDS45177.1 ENSP00000353114 Q8IVF2 UPI00015BB2CA NM_138420.2 tolerated(0.09) 7/7 MODERATE 1 SNV 5 1 PASS rs770634629 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 104954030 104954030 C A 1 0 0 0 0 1 0 0 0 492 739 26 2 2 AHNAK2 14 104954030 Missense_Mutation SNP C C3N-01488_T 23454421 104954030 2089688 396 24770 POTEB3 0 . GRCh38 15 21430307 21430307 + Nonsense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1012G>T p.Gly338Ter p.G338* ENST00000611217 5/11 145 132 13 244 244 0 varscan-mutect POTEB3,stop_gained,p.Gly338Ter,ENST00000611217,NM_207355.3;U6,upstream_gene_variant,,ENST00000612037,;POTEB3,stop_gained,p.Gly338Ter,ENST00000624267,;POTEB3,stop_gained,p.Gly338Ter,ENST00000612601,; A ENST00000611217 Transcript stop_gained 1060/1813 1012/1746 338/581 G/* Gga/Tga 1 -1 POTEB3 HGNC HGNC:51240 protein_coding YES CCDS73690.1 ENSP00000483103 A0JP26,Q6S5H4 UPI0000197FCA NM_207355.3 5/11 PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF38,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH 1 SNV 1 1 PASS rs1341991927 . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 80 21430307 21430307 C A 1 0 0 0 0 0 1 0 0 12375 603 21 2 2 POTEB3 15 21430307 Nonsense_Mutation SNP C C3N-01488_T 21430307 80560882 397 24771 KLF13 0 . GRCh38 15 31372213 31372213 + Missense_Mutation SNP G G T rs766830250 C3N-01488_T C3N-01488_N G G c.781G>T p.Gly261Cys p.G261C ENST00000307145 2/2 82 64 18 137 137 0 strelka-varscan-mutect KLF13,missense_variant,p.Gly261Cys,ENST00000307145,NM_015995.3;KLF13,missense_variant,p.Gly73Cys,ENST00000560473,;KLF13,downstream_gene_variant,,ENST00000558844,;KLF13,intron_variant,,ENST00000558921,;KLF13,upstream_gene_variant,,ENST00000558673,; T ENST00000307145 Transcript missense_variant 1139/6825 781/867 261/288 G/C Ggc/Tgc rs766830250 1 1 KLF13 HGNC HGNC:13672 protein_coding YES CCDS10025.1 ENSP00000302456 Q9Y2Y9 X5DNR2 UPI000012DEDC NM_015995.3 deleterious(0.01) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs766830250 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 31372213 31372213 G T 1 0 0 0 0 1 0 0 0 8206 1116 39 1 1 KLF13 15 31372213 Missense_Mutation SNP G C3N-01488_T 9941906 31372213 70618976 398 24772 KATNBL1 0 . GRCh38 15 34146770 34146770 + Missense_Mutation SNP A A C novel C3N-01488_T C3N-01488_N A A c.779T>G p.Ile260Arg p.I260R ENST00000256544 8/10 175 144 31 277 277 0 strelka-varscan-mutect KATNBL1,missense_variant,p.Ile260Arg,ENST00000256544,NM_024713.2;KATNBL1,missense_variant,p.Ile114Arg,ENST00000559760,;KATNBL1,missense_variant,p.Ile33Arg,ENST00000561371,;KATNBL1,intron_variant,,ENST00000561270,;KATNBL1,downstream_gene_variant,,ENST00000560108,;KATNBL1,downstream_gene_variant,,ENST00000557877,;KATNBL1,downstream_gene_variant,,ENST00000560310,;KATNBL1,downstream_gene_variant,,ENST00000559462,;KATNBL1,non_coding_transcript_exon_variant,,ENST00000560247,;KATNBL1,non_coding_transcript_exon_variant,,ENST00000540594,;KATNBL1,downstream_gene_variant,,ENST00000560671,;KATNBL1,upstream_gene_variant,,ENST00000558681,;KATNBL1,downstream_gene_variant,,ENST00000560308,;KATNBL1,downstream_gene_variant,,ENST00000558473,; C ENST00000256544 Transcript missense_variant 922/2723 779/915 260/304 I/R aTa/aGa 1 -1 KATNBL1 HGNC HGNC:26199 protein_coding YES CCDS10034.1 ENSP00000256544 Q9H079 A0A024R9P5 UPI0000037DAE NM_024713.2 tolerated(0.4) 8/10 hmmpanther:PTHR14682,Pfam_domain:PF13925 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 34146770 34146770 A C 1 0 0 0 0 1 0 0 0 7905 449 16 5 5 KATNBL1 15 34146770 Missense_Mutation SNP A C3N-01488_T 2774557 34146770 67844419 399 24773 FAM98B 0 . GRCh38 15 38470331 38470331 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.457A>G p.Met153Val p.M153V ENST00000397609 4/8 120 101 19 185 184 1 strelka-varscan-mutect FAM98B,missense_variant,p.Met153Val,ENST00000397609,NM_173611.3;FAM98B,missense_variant,p.Met153Val,ENST00000491535,;FAM98B,missense_variant,p.Met55Val,ENST00000559431,;FAM98B,non_coding_transcript_exon_variant,,ENST00000305752,; G ENST00000397609 Transcript missense_variant 492/4388 457/1302 153/433 M/V Atg/Gtg 1 1 FAM98B HGNC HGNC:26773 protein_coding YES CCDS10047.2 ENSP00000380734 Q52LJ0 UPI0000DA182F NM_173611.3 tolerated(0.12) 4/8 hmmpanther:PTHR31353,hmmpanther:PTHR31353:SF11,Pfam_domain:PF10239 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 38470331 38470331 A G 1 0 0 0 0 1 0 0 0 5515 449 16 5 5 FAM98B 15 38470331 Missense_Mutation SNP A C3N-01488_T 4323561 38470331 63520858 400 24774 CASC5 0 . GRCh38 15 40624779 40624779 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.4593A>G p.= p.K1531K ENST00000346991 11/27 194 183 11 259 258 1 strelka-varscan-mutect CASC5,synonymous_variant,p.=,ENST00000346991,NM_170589.4;CASC5,synonymous_variant,p.=,ENST00000399668,NM_144508.4;CASC5,synonymous_variant,p.=,ENST00000527044,;CASC5,upstream_gene_variant,,ENST00000532406,;CASC5,downstream_gene_variant,,ENST00000614337,;CASC5,synonymous_variant,p.=,ENST00000526913,;CASC5,non_coding_transcript_exon_variant,,ENST00000533001,;CASC5,intron_variant,,ENST00000534204,; G ENST00000346991 Transcript synonymous_variant 4983/9573 4593/7029 1531/2342 K aaA/aaG 1 1 CASC5 HGNC HGNC:24054 protein_coding YES CCDS42023.1 ENSP00000335463 Q8NG31 UPI0000E59BD3 NM_170589.4 11/27 hmmpanther:PTHR16520,hmmpanther:PTHR16520:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 40624779 40624779 A G 1 0 0 0 0 0 0 0 1 2363 69 3 5 5 CASC5 15 40624779 Silent SNP A C3N-01488_T 2154448 40624779 61366410 401 24775 MGA 0 . GRCh38 15 41749539 41749539 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.5932A>G p.Lys1978Glu p.K1978E ENST00000219905 17/24 171 162 9 372 372 0 strelka-varscan-mutect MGA,missense_variant,p.Lys1769Glu,ENST00000566586,;MGA,missense_variant,p.Lys1978Glu,ENST00000219905,NM_001164273.1;MGA,missense_variant,p.Lys1978Glu,ENST00000570161,;MGA,missense_variant,p.Lys1769Glu,ENST00000545763,NM_001080541.2;MGA,missense_variant,p.Lys626Glu,ENST00000564190,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,; G ENST00000219905 Transcript missense_variant 6113/12042 5932/9198 1978/3065 K/E Aaa/Gaa 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 deleterious_low_confidence(0.02) 17/24 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 41749539 41749539 A G 1 0 0 0 0 1 0 0 0 9498 247 9 5 5 MGA 15 41749539 Missense_Mutation SNP A C3N-01488_T 1124760 41749539 60241650 402 24776 STRC 0 . GRCh38 15 43618017 43618017 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.404G>T p.Gly135Val p.G135V ENST00000450892 2/29 231 212 19 321 321 0 varscan-mutect STRC,missense_variant,p.Gly135Val,ENST00000450892,NM_153700.2;STRC,missense_variant,p.Gly75Val,ENST00000432436,;STRC,5_prime_UTR_variant,,ENST00000541030,;STRC,missense_variant,p.Gly135Val,ENST00000428650,;STRC,missense_variant,p.Gly135Val,ENST00000440125,;STRC,upstream_gene_variant,,ENST00000485556,;STRC,upstream_gene_variant,,ENST00000471703,;STRC,upstream_gene_variant,,ENST00000448437,;STRC,upstream_gene_variant,,ENST00000455136,;STRC,upstream_gene_variant,,ENST00000483250,;STRC,upstream_gene_variant,,ENST00000470279,; A ENST00000450892 Transcript missense_variant 482/5680 404/5328 135/1775 G/V gGg/gTg 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 tolerated(0.2) 2/29 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 43618017 43618017 C A 1 0 0 0 0 1 0 0 0 15709 623 22 2 2 STRC 15 43618017 Missense_Mutation SNP C C3N-01488_T 1868478 43618017 58373172 403 24777 FBN1 0 . GRCh38 15 48412719 48412719 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.8076G>T p.Met2692Ile p.M2692I ENST00000316623 65/66 586 479 107 788 786 2 strelka-varscan-mutect FBN1,missense_variant,p.Met2692Ile,ENST00000316623,NM_000138.4;FBN1,non_coding_transcript_exon_variant,,ENST00000561429,;FBN1,3_prime_UTR_variant,,ENST00000559133,; A ENST00000316623 Transcript missense_variant 8532/11756 8076/8616 2692/2871 M/I atG/atT 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 tolerated(0.12) 65/66 PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 48412719 48412719 C A 1 0 0 0 0 1 0 0 0 5565 594 21 2 2 FBN1 15 48412719 Missense_Mutation SNP C C3N-01488_T 4794702 48412719 53578470 404 24778 AP4E1 0 . GRCh38 15 50929125 50929125 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.659G>T p.Gly220Val p.G220V ENST00000261842 6/21 300 254 46 469 469 0 strelka-varscan-mutect AP4E1,missense_variant,p.Gly220Val,ENST00000261842,NM_007347.4;AP4E1,missense_variant,p.Gly145Val,ENST00000560508,NM_001252127.1;AP4E1,missense_variant,p.Gly220Val,ENST00000558439,;AP4E1,missense_variant,p.Gly145Val,ENST00000561393,;AP4E1,missense_variant,p.Gly220Val,ENST00000561441,; T ENST00000261842 Transcript missense_variant 765/6758 659/3414 220/1137 G/V gGg/gTg 1 1 AP4E1 HGNC HGNC:573 protein_coding YES CCDS32240.1 ENSP00000261842 Q9UPM8 UPI00001D89D8 NM_007347.4 deleterious(0) 6/21 hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF13,Pfam_domain:PF01602,PIRSF_domain:PIRSF037097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 50929125 50929125 G T 1 0 0 0 0 1 0 0 0 868 1232 43 2 2 AP4E1 15 50929125 Missense_Mutation SNP G C3N-01488_T 2516406 50929125 51062064 405 24779 MYO5C 0 . GRCh38 15 52272720 52272720 + Missense_Mutation SNP C C A rs368931124 C3N-01488_T C3N-01488_N C C c.610G>T p.Val204Phe p.V204F ENST00000261839 6/41 162 125 37 220 220 0 strelka-varscan-mutect MYO5C,missense_variant,p.Val204Phe,ENST00000261839,NM_018728.3;MYO5C,missense_variant,p.Val97Phe,ENST00000558479,;MIR1266,downstream_gene_variant,,ENST00000408125,;MYO5C,non_coding_transcript_exon_variant,,ENST00000541028,;MYO5C,missense_variant,p.Val204Phe,ENST00000560809,;MYO5C,missense_variant,p.Val204Phe,ENST00000559459,;MYO5C,3_prime_UTR_variant,,ENST00000558902,; A ENST00000261839 Transcript missense_variant 772/6971 610/5229 204/1742 V/F Gtt/Ttt rs368931124 1 -1 MYO5C HGNC HGNC:7604 protein_coding YES CCDS42036.1 ENSP00000261839 Q9NQX4 UPI000013D20E NM_018728.3 tolerated(0.26) 6/41 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF313,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540,Prints_domain:PR00193 MODERATE 1 SNV 1 1 PASS rs368931124 . 0 187 0 15 7 0 0 0 -19.9999 0.1511738 0 1 0 0 A 3 1 80 52272720 52272720 C A 1 0 0 0 0 1 0 0 0 10081 550 19 1 1 MYO5C 15 52272720 Missense_Mutation SNP C C3N-01488_T 1343595 52272720 49718469 406 24780 UNC13C 0 . GRCh38 15 54414990 54414990 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.4856A>T p.Gln1619Leu p.Q1619L ENST00000260323 18/32 118 107 11 198 197 1 strelka-varscan-mutect UNC13C,missense_variant,p.Gln1619Leu,ENST00000260323,NM_001080534.1;UNC13C,non_coding_transcript_exon_variant,,ENST00000561210,; T ENST00000260323 Transcript missense_variant 4856/12946 4856/6645 1619/2214 Q/L cAa/cTa 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0) 18/32 Pfam_domain:PF06292,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2,SMART_domains:SM01145 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 54414990 54414990 A T 1 0 0 0 0 1 0 0 0 17510 130 5 4 4 UNC13C 15 54414990 Missense_Mutation SNP A C3N-01488_T 2142270 54414990 47576199 407 24781 UNC13C 0 . GRCh38 15 54555466 54555466 + Missense_Mutation SNP C C G rs186728296 C3N-01488_T C3N-01488_N C C c.5912C>G p.Thr1971Arg p.T1971R ENST00000260323 28/32 240 206 34 336 335 1 strelka-varscan-mutect UNC13C,missense_variant,p.Thr1971Arg,ENST00000260323,NM_001080534.1; G ENST00000260323 Transcript missense_variant 5912/12946 5912/6645 1971/2214 T/R aCg/aGg rs186728296,COSM3816370,COSM3816371,COSM3816372 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0) 28/32 Pfam_domain:PF10540,PROSITE_profiles:PS51259,hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs186728296 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 54555466 54555466 C G 1 0 0 0 0 1 0 0 0 17510 536 19 4 4 UNC13C 15 54555466 Missense_Mutation SNP C C3N-01488_T 140476 54555466 47435723 408 24782 FBXL22 0 . GRCh38 15 63597466 63597466 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.74A>G p.Asp25Gly p.D25G ENST00000360587 1/2 157 127 30 172 172 0 strelka-varscan-mutect FBXL22,missense_variant,p.Asp25Gly,ENST00000534939,;FBXL22,missense_variant,p.Asp25Gly,ENST00000360587,NM_203373.2;USP3,downstream_gene_variant,,ENST00000540797,NM_001256702.1;USP3,downstream_gene_variant,,ENST00000268049,;FBXL22,upstream_gene_variant,,ENST00000560325,;USP3-AS1,intron_variant,,ENST00000560962,;USP3-AS1,intron_variant,,ENST00000558831,;USP3-AS1,intron_variant,,ENST00000559737,;USP3-AS1,intron_variant,,ENST00000561191,;USP3-AS1,intron_variant,,ENST00000561256,;USP3-AS1,intron_variant,,ENST00000560622,;USP3-AS1,upstream_gene_variant,,ENST00000559861,;USP3,downstream_gene_variant,,ENST00000559192,;USP3,downstream_gene_variant,,ENST00000559257,;USP3,downstream_gene_variant,,ENST00000560202,; G ENST00000360587 Transcript missense_variant 114/1526 74/744 25/247 D/G gAc/gGc 1 1 FBXL22 HGNC HGNC:27537 protein_coding YES CCDS10187.2 ENSP00000353794 Q6P050 UPI0000408A7A NM_203373.2 deleterious_low_confidence(0.03) 1/2 Pfam_domain:PF12937,Gene3D:1.20.1280.50,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 63597466 63597466 A G 1 0 0 0 0 1 0 0 0 5582 275 10 5 5 FBXL22 15 63597466 Missense_Mutation SNP A C3N-01488_T 9042000 63597466 38393723 409 24783 FAM96A 0 . GRCh38 15 64075527 64075527 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.350A>T p.Tyr117Phe p.Y117F ENST00000300030 4/5 145 128 17 231 229 2 strelka-varscan-mutect FAM96A,missense_variant,p.Tyr117Phe,ENST00000300030,NM_032231.5;FAM96A,missense_variant,p.Tyr117Phe,ENST00000559950,;FAM96A,synonymous_variant,p.=,ENST00000557835,NM_001289108.1;FAM96A,synonymous_variant,p.=,ENST00000380290,NM_001014812.2;DAPK2,upstream_gene_variant,,ENST00000559306,;FAM96A,upstream_gene_variant,,ENST00000558779,;FAM96A,3_prime_UTR_variant,,ENST00000559705,; A ENST00000300030 Transcript missense_variant 600/1105 350/483 117/160 Y/F tAc/tTc 1 -1 FAM96A HGNC HGNC:26235 protein_coding YES CCDS10189.1 ENSP00000300030 Q9H5X1 UPI0000137917 NM_032231.5 tolerated(0.48) 4/5 hmmpanther:PTHR12377,hmmpanther:PTHR12377:SF2,Superfamily_domains:SSF117916 MODERATE 1 SNV 1 1 PASS rs1238811900 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 64075527 64075527 T A 1 0 0 0 0 1 0 0 0 5512 1638 57 4 4 FAM96A 15 64075527 Missense_Mutation SNP T C3N-01488_T 478061 64075527 37915662 410 24784 PML 0 . GRCh38 15 74044450 74044450 + Silent SNP G G T rs756674362 C3N-01488_T C3N-01488_N G G c.2091G>T p.= p.L697L ENST00000268058 9/9 627 532 95 720 719 1 strelka-varscan-mutect PML,synonymous_variant,p.=,ENST00000565898,;PML,synonymous_variant,p.=,ENST00000268058,NM_033238.2;PML,downstream_gene_variant,,ENST00000395135,NM_002675.3;PML,downstream_gene_variant,,ENST00000569965,;PML,downstream_gene_variant,,ENST00000564428,NM_033249.2;PML,downstream_gene_variant,,ENST00000359928,NM_033246.2;PML,downstream_gene_variant,,ENST00000565317,; T ENST00000268058 Transcript synonymous_variant 2187/4508 2091/2649 697/882 L ctG/ctT rs756674362 1 1 PML HGNC HGNC:9113 protein_coding YES CCDS10255.1 ENSP00000268058 P29590 UPI000013D78F NM_033238.2 9/9 LOW 1 SNV 1 1 PASS rs756674362 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 74044450 74044450 G T 1 0 0 0 0 0 0 0 1 12242 1364 48 2 2 PML 15 74044450 Silent SNP G C3N-01488_T 9968923 74044450 27946739 411 24785 ALPK3 0 . GRCh38 15 84860063 84860063 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.4726G>T p.Glu1576Ter p.E1576* ENST00000258888 9/14 201 174 27 303 303 0 strelka-varscan-mutect ALPK3,stop_gained,p.Glu1576Ter,ENST00000258888,NM_020778.4;ALPK3,upstream_gene_variant,,ENST00000558077,; T ENST00000258888 Transcript stop_gained 4893/10917 4726/5724 1576/1907 E/* Gaa/Taa 1 1 ALPK3 HGNC HGNC:17574 protein_coding YES CCDS10333.1 ENSP00000258888 Q96L96 UPI000013D013 NM_020778.4 9/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF667,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 84860063 84860063 G T 1 0 0 0 0 0 1 0 0 646 943 33 2 2 ALPK3 15 84860063 Nonsense_Mutation SNP G C3N-01488_T 10815613 84860063 17131126 412 24786 AKAP13 0 . GRCh38 15 85575177 85575177 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.709A>G p.Ile237Val p.I237V ENST00000361243 6/37 345 321 24 413 412 1 strelka-varscan-mutect AKAP13,missense_variant,p.Ile237Val,ENST00000394518,NM_007200.4;AKAP13,missense_variant,p.Ile237Val,ENST00000361243,NM_006738.5;AKAP13,missense_variant,p.Ile237Val,ENST00000559362,;AKAP13,missense_variant,p.Ile29Val,ENST00000558811,;AKAP13,5_prime_UTR_variant,,ENST00000558166,;RP11-815J21.2,downstream_gene_variant,,ENST00000561409,; G ENST00000361243 Transcript missense_variant 790/9468 709/8454 237/2817 I/V Ata/Gta 1 1 AKAP13 HGNC HGNC:371 protein_coding YES CCDS32320.1 ENSP00000354718 Q12802 UPI00001A8BEB NM_006738.5 tolerated(0.38) 6/37 hmmpanther:PTHR13944,hmmpanther:PTHR13944:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 85575177 85575177 A G 1 0 0 0 0 1 0 0 0 532 101 4 5 5 AKAP13 15 85575177 Missense_Mutation SNP A C3N-01488_T 715114 85575177 16416012 413 24787 AGBL1 0 . GRCh38 15 86269942 86269942 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1862A>T p.Asn621Ile p.N621I ENST00000441037 14/25 159 134 25 188 187 1 strelka-varscan-mutect AGBL1,missense_variant,p.Asn621Ile,ENST00000441037,;AGBL1,missense_variant,p.Asn575Ile,ENST00000635782,NM_152336.2;AGBL1,missense_variant,p.Asn575Ile,ENST00000421325,;AGBL1,non_coding_transcript_exon_variant,,ENST00000567715,;AGBL1,non_coding_transcript_exon_variant,,ENST00000568785,; T ENST00000441037 Transcript missense_variant 1862/3551 1862/3339 621/1112 N/I aAc/aTc 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 deleterious(0) 14/25 hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 86269942 86269942 A T 1 0 0 0 0 1 0 0 0 451 43 2 4 4 AGBL1 15 86269942 Missense_Mutation SNP A C3N-01488_T 694765 86269942 15721247 414 24788 DET1 0 . GRCh38 15 88530764 88530764 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.975G>T p.Met325Ile p.M325I ENST00000564406 3/6 229 199 30 309 309 0 strelka-varscan-mutect DET1,missense_variant,p.Met325Ile,ENST00000564406,NM_001321596.1,NM_017996.3;DET1,missense_variant,p.Met314Ile,ENST00000268148,NM_001321596.1,NM_001144074.1;DET1,missense_variant,p.Met325Ile,ENST00000444300,NM_001321596.1;DET1,downstream_gene_variant,,ENST00000558413,;DET1,downstream_gene_variant,,ENST00000559656,;DET1,3_prime_UTR_variant,,ENST00000557842,;DET1,3_prime_UTR_variant,,ENST00000557837,; A ENST00000564406 Transcript missense_variant 1136/2315 975/1686 325/561 M/I atG/atT 1 -1 DET1 HGNC HGNC:25477 protein_coding YES CCDS45343.1 ENSP00000456340 Q7L5Y6 UPI00001A8183 NM_001321596.1,NM_017996.3 tolerated(0.42) 3/6 hmmpanther:PTHR13374,Pfam_domain:PF09737 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 88530764 88530764 C A 1 0 0 0 0 1 0 0 0 4258 594 21 2 2 DET1 15 88530764 Missense_Mutation SNP C C3N-01488_T 2260822 88530764 13460425 415 24789 IGF1R 0 . GRCh38 15 98913135 98913135 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1681G>T p.Asp561Tyr p.D561Y ENST00000268035 8/21 293 275 18 365 365 0 strelka-varscan-mutect IGF1R,missense_variant,p.Asp561Tyr,ENST00000268035,NM_000875.4;IGF1R,missense_variant,p.Asp561Tyr,ENST00000558762,NM_001291858.1;IGF1R,downstream_gene_variant,,ENST00000558898,;IGF1R,downstream_gene_variant,,ENST00000559582,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,;IGF1R,upstream_gene_variant,,ENST00000561049,;IGF1R,upstream_gene_variant,,ENST00000560144,; T ENST00000268035 Transcript missense_variant 2292/11803 1681/4104 561/1367 D/Y Gac/Tac 1 1 IGF1R HGNC HGNC:5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 UPI000012D3EA NM_000875.4 deleterious(0.01) 8/21 PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF106,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000620,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 98913135 98913135 G T 1 0 0 0 0 1 0 0 0 7477 1174 41 2 2 IGF1R 15 98913135 Missense_Mutation SNP G C3N-01488_T 10382371 98913135 3078054 416 24790 LRRK1 0 . GRCh38 15 101022525 101022525 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1995G>T p.Gln665His p.Q665H ENST00000388948 15/34 240 203 37 274 274 0 strelka-varscan-mutect LRRK1,missense_variant,p.Gln665His,ENST00000388948,NM_024652.4;LRRK1,missense_variant,p.Gln665His,ENST00000525284,;LRRK1,non_coding_transcript_exon_variant,,ENST00000525617,;LRRK1,non_coding_transcript_exon_variant,,ENST00000538064,;LRRK1,intron_variant,,ENST00000531270,; T ENST00000388948 Transcript missense_variant 2354/7671 1995/6048 665/2015 Q/H caG/caT 1 1 LRRK1 HGNC HGNC:18608 protein_coding YES CCDS42086.1 ENSP00000373600 Q38SD2 UPI0000D4FE63 NM_024652.4 tolerated(0.13) 15/34 Gene3D:2zejA01,Pfam_domain:PF08477,PROSITE_profiles:PS51424,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 101022525 101022525 G T 1 0 0 0 0 1 0 0 0 8938 991 35 2 2 LRRK1 15 101022525 Missense_Mutation SNP G C3N-01488_T 2109390 101022525 968664 417 24791 RPUSD1 0 . GRCh38 16 787643 787643 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.95A>T p.Lys32Met p.K32M ENST00000561734 1/5 343 321 22 411 410 1 strelka-varscan-mutect RPUSD1,missense_variant,p.Lys32Met,ENST00000561734,;RPUSD1,missense_variant,p.Lys32Met,ENST00000007264,NM_001324415.1,NM_001324086.1,NM_058192.2;RPUSD1,missense_variant,p.Lys32Met,ENST00000565809,NM_001324411.1;RPUSD1,missense_variant,p.Lys32Met,ENST00000563560,;RPUSD1,splice_region_variant,,ENST00000565377,;RPUSD1,splice_region_variant,,ENST00000569601,;RPUSD1,intron_variant,,ENST00000567114,NM_001324412.1;CHTF18,upstream_gene_variant,,ENST00000631357,;CHTF18,upstream_gene_variant,,ENST00000455171,;CHTF18,upstream_gene_variant,,ENST00000262315,NM_022092.2;CHTF18,upstream_gene_variant,,ENST00000317063,;MSLNL,upstream_gene_variant,,ENST00000442466,;RPUSD1,upstream_gene_variant,,ENST00000562070,;CHTF18,upstream_gene_variant,,ENST00000426047,;CHTF18,upstream_gene_variant,,ENST00000491530,;CHTF18,upstream_gene_variant,,ENST00000461268,;CHTF18,upstream_gene_variant,,ENST00000570058,;RPUSD1,missense_variant,p.Lys32Met,ENST00000567283,;RPUSD1,missense_variant,p.Lys32Met,ENST00000565503,;CHTF18,upstream_gene_variant,,ENST00000471202,;CHTF18,upstream_gene_variant,,ENST00000464728,;CHTF18,upstream_gene_variant,,ENST00000440239,;CHTF18,upstream_gene_variant,,ENST00000479976,;CHTF18,upstream_gene_variant,,ENST00000569270,;CHTF18,upstream_gene_variant,,ENST00000567620,;CHTF18,upstream_gene_variant,,ENST00000565787,;CHTF18,upstream_gene_variant,,ENST00000563545,;CHTF18,upstream_gene_variant,,ENST00000484349,; A ENST00000561734 Transcript missense_variant 339/2159 95/939 32/312 K/M aAg/aTg 1 -1 RPUSD1 HGNC HGNC:14173 protein_coding YES CCDS10426.1 ENSP00000455026 Q9UJJ7 UPI0000073C11 deleterious(0) 1/5 Pfam_domain:PF00849,hmmpanther:PTHR11079,hmmpanther:PTHR11079:SF64,Superfamily_domains:SSF55120 MODERATE 1 SNV 1 1 PASS rs1222000832 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 787643 787643 T A 1 0 0 0 0 1 0 0 0 13921 1609 56 4 4 RPUSD1 16 787643 Missense_Mutation SNP T C3N-01488_T 787643 89550702 418 24792 CACNA1H 0 . GRCh38 16 1208073 1208073 + Missense_Mutation SNP T T A rs769013395 C3N-01488_T C3N-01488_N T T c.3215T>A p.Leu1072Gln p.L1072Q ENST00000348261 16/35 339 274 65 374 374 0 strelka-varscan-mutect CACNA1H,missense_variant,p.Leu1072Gln,ENST00000348261,NM_021098.2;CACNA1H,missense_variant,p.Leu1072Gln,ENST00000358590,NM_001005407.1;CACNA1H,missense_variant,p.Leu1072Gln,ENST00000565831,;CACNA1H,upstream_gene_variant,,ENST00000569107,;CACNA1H,upstream_gene_variant,,ENST00000564231,;CACNA1H,upstream_gene_variant,,ENST00000562079,;RP11-616M22.3,upstream_gene_variant,,ENST00000564700,;CACNA1H,upstream_gene_variant,,ENST00000637236,;CACNA1H,upstream_gene_variant,,ENST00000569953,; A ENST00000348261 Transcript missense_variant 3583/8208 3215/7062 1072/2353 L/Q cTg/cAg rs769013395 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 deleterious(0.01) 16/35 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192 MODERATE 1 SNV 1 1 PASS rs769013395 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 1208073 1208073 T A 1 0 0 0 0 1 0 0 0 2233 1580 55 4 4 CACNA1H 16 1208073 Missense_Mutation SNP T C3N-01488_T 420430 1208073 89130272 419 24793 CACNA1H 0 . GRCh38 16 1217973 1217973 + Missense_Mutation SNP A A T rs72552051 C3N-01488_T C3N-01488_N A A c.5378A>T p.Asn1793Ile p.N1793I ENST00000348261 32/35 166 142 24 203 203 0 strelka-varscan-mutect CACNA1H,missense_variant,p.Asn1793Ile,ENST00000348261,NM_021098.2;CACNA1H,missense_variant,p.Asn1787Ile,ENST00000358590,NM_001005407.1;CACNA1H,missense_variant,p.Asn1787Ile,ENST00000565831,;CACNA1H,missense_variant,p.Asn540Ile,ENST00000569107,;CACNA1H,missense_variant,p.Asn535Ile,ENST00000564231,;CACNA1H,missense_variant,p.Asn529Ile,ENST00000562079,;TPSG1,downstream_gene_variant,,ENST00000234798,NM_012467.3;TPSG1,downstream_gene_variant,,ENST00000564684,; T ENST00000348261 Transcript missense_variant 5746/8208 5378/7062 1793/2353 N/I aAc/aTc rs72552051 1 1 CACNA1H HGNC HGNC:1395 protein_coding YES CCDS45375.1 ENSP00000334198 O95180 UPI000012727B NM_021098.2 deleterious(0) 32/35 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF192,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs72552051 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 1217973 1217973 A T 1 0 0 0 0 1 0 0 0 2233 43 2 4 4 CACNA1H 16 1217973 Missense_Mutation SNP A C3N-01488_T 9900 1217973 89120372 420 24794 ABCA3 0 . GRCh38 16 2277881 2277881 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.4907C>T p.Pro1636Leu p.P1636L ENST00000301732 31/33 357 294 63 425 424 1 strelka-varscan-mutect ABCA3,missense_variant,p.Pro1636Leu,ENST00000301732,NM_001089.2;ABCA3,missense_variant,p.Pro1578Leu,ENST00000382381,;MIR940,downstream_gene_variant,,ENST00000563734,;MIR940,downstream_gene_variant,,ENST00000562838,;MIR940,downstream_gene_variant,,ENST00000567888,;MIR4717,downstream_gene_variant,,ENST00000584656,;ABCA3,downstream_gene_variant,,ENST00000566200,;ABCA3,downstream_gene_variant,,ENST00000569062,; A ENST00000301732 Transcript missense_variant,splice_region_variant 5608/6609 4907/5115 1636/1704 P/L cCa/cTa 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 deleterious(0) 31/33 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 2277881 2277881 G A 1 0 0 0 0 1 0 0 0 37 1362 47 3 3 ABCA3 16 2277881 Missense_Mutation SNP G C3N-01488_T 1059908 2277881 88060464 421 24795 CREBBP 0 . GRCh38 16 3731269 3731269 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.5095G>T p.Gly1699Cys p.G1699C ENST00000262367 30/31 331 264 67 399 398 1 strelka-varscan-mutect CREBBP,missense_variant,p.Gly1699Cys,ENST00000262367,NM_004380.2;CREBBP,missense_variant,p.Gly1661Cys,ENST00000382070,NM_001079846.1;CREBBP,downstream_gene_variant,,ENST00000570939,;CREBBP,upstream_gene_variant,,ENST00000637492,;CREBBP,downstream_gene_variant,,ENST00000576720,;CREBBP,downstream_gene_variant,,ENST00000571763,; A ENST00000262367 Transcript missense_variant 5905/10803 5095/7329 1699/2442 G/C Ggc/Tgc 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 deleterious(0.01) 30/31 PROSITE_profiles:PS51727,hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 3731269 3731269 C A 1 0 0 0 0 1 0 0 0 3661 623 22 2 2 CREBBP 16 3731269 Missense_Mutation SNP C C3N-01488_T 1453388 3731269 86607076 422 24796 NUDT16L1 0 . GRCh38 16 4694219 4694219 + Nonsense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.395C>A p.Ser132Ter p.S132* ENST00000304301 2/3 93 83 10 107 107 0 strelka-varscan-mutect NUDT16L1,stop_gained,p.Ser132Ter,ENST00000405142,;NUDT16L1,stop_gained,p.Ser132Ter,ENST00000586536,NM_001193452.1;NUDT16L1,stop_gained,p.Ser132Ter,ENST00000304301,NM_032349.3;NUDT16L1,stop_gained,p.Ser132Ter,ENST00000586252,;NUDT16L1,stop_gained,p.Ser119Ter,ENST00000590460,;MGRN1,downstream_gene_variant,,ENST00000399577,NM_001142290.2;MGRN1,downstream_gene_variant,,ENST00000415496,NM_001142291.2;MGRN1,downstream_gene_variant,,ENST00000262370,NM_015246.3;ANKS3,downstream_gene_variant,,ENST00000304283,NM_133450.3;ANKS3,downstream_gene_variant,,ENST00000614075,;ANKS3,downstream_gene_variant,,ENST00000450067,NM_001242929.1;ANKS3,downstream_gene_variant,,ENST00000446014,NM_001308089.1;ANKS3,downstream_gene_variant,,ENST00000585773,;ANKS3,downstream_gene_variant,,ENST00000588513,;ANKS3,downstream_gene_variant,,ENST00000591653,;ANKS3,downstream_gene_variant,,ENST00000590803,;ANKS3,downstream_gene_variant,,ENST00000592077,;ANKS3,downstream_gene_variant,,ENST00000590193,;ANKS3,downstream_gene_variant,,ENST00000589035,;ANKS3,downstream_gene_variant,,ENST00000591185,;ANKS3,downstream_gene_variant,,ENST00000588398,; A ENST00000304301 Transcript stop_gained 428/1349 395/636 132/211 S/* tCg/tAg 1 1 NUDT16L1 HGNC HGNC:28154 protein_coding YES CCDS10519.1 ENSP00000306670 Q9BRJ7 UPI0000071EB2 NM_032349.3 2/3 Gene3D:3.90.79.10,hmmpanther:PTHR31699,hmmpanther:PTHR31699:SF6,Superfamily_domains:SSF55811 HIGH 1 SNV 1 1 PASS rs1387387964 . 0 207 3 0 0 0 0 0 -19.96201 1 1 1 1 0 A 4 1 80 4694219 4694219 C A 1 0 0 0 0 0 1 0 0 10797 893 31 1 1 NUDT16L1 16 4694219 Nonsense_Mutation SNP C C3N-01488_T 962950 4694219 85644126 423 24797 GRIN2A 0 . GRCh38 16 9938393 9938393 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.573G>A p.= p.V191V ENST00000396573 4/14 219 174 45 305 305 0 strelka-varscan-mutect GRIN2A,synonymous_variant,p.=,ENST00000396573,NM_000833.4;GRIN2A,synonymous_variant,p.=,ENST00000396575,;GRIN2A,synonymous_variant,p.=,ENST00000330684,NM_001134407.2;GRIN2A,synonymous_variant,p.=,ENST00000562109,NM_001134408.2;GRIN2A,synonymous_variant,p.=,ENST00000535259,;GRIN2A,synonymous_variant,p.=,ENST00000637393,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000568247,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000566670,;GRIN2A,intron_variant,,ENST00000566683,; T ENST00000396573 Transcript synonymous_variant 883/14450 573/4395 191/1464 V gtG/gtA 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 4/14 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF16,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 9938393 9938393 C T 1 0 0 0 0 0 0 0 1 6661 581 21 3 3 GRIN2A 16 9938393 Silent SNP C C3N-01488_T 5244174 9938393 80399952 424 24798 MYH11 0 . GRCh38 16 15756455 15756455 + Silent SNP C C T rs773802963 C3N-01488_T C3N-01488_N C C c.1656G>A p.= p.T552T ENST00000396324 15/42 316 241 75 340 339 1 strelka-varscan-mutect MYH11,synonymous_variant,p.=,ENST00000452625,NM_001040113.1;MYH11,synonymous_variant,p.=,ENST00000396324,NM_001040114.1;MYH11,synonymous_variant,p.=,ENST00000576790,NM_022844.2;MYH11,synonymous_variant,p.=,ENST00000300036,NM_002474.2;MYH11,non_coding_transcript_exon_variant,,ENST00000570785,; T ENST00000396324 Transcript synonymous_variant 1744/6847 1656/5940 552/1979 T acG/acA rs773802963,COSM283014,COSM283015 1 -1 MYH11 HGNC HGNC:7569 protein_coding YES CCDS45423.1 ENSP00000379616 P35749 UPI00005B7237 NM_001040114.1 15/42 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF335,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs773802963 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 15756455 15756455 C T 1 0 0 0 0 0 0 0 1 10031 639 23 1 1 MYH11 16 15756455 Silent SNP C C3N-01488_T 5818062 15756455 74581890 425 24799 ACSM2B 0 . GRCh38 16 20545226 20545226 + Silent SNP G G T rs367747928,rs758760721 C3N-01488_T C3N-01488_N G G c.1212C>A p.= p.P404P ENST00000329697 10/14 101 90 11 106 106 0 varscan-mutect ACSM2B,synonymous_variant,p.=,ENST00000329697,NM_001105069.1;ACSM2B,synonymous_variant,p.=,ENST00000414188,;ACSM2B,synonymous_variant,p.=,ENST00000565232,;ACSM2B,synonymous_variant,p.=,ENST00000567001,NM_182617.3;ACSM2B,synonymous_variant,p.=,ENST00000565322,;ACSM2B,synonymous_variant,p.=,ENST00000567288,;ACSM2B,downstream_gene_variant,,ENST00000569163,;ACSM2B,upstream_gene_variant,,ENST00000568098,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569131,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000566998,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000569364,;ACSM2B,non_coding_transcript_exon_variant,,ENST00000563943,;ACSM2B,downstream_gene_variant,,ENST00000569327,;ACSM2B,upstream_gene_variant,,ENST00000564849,; T ENST00000329697 Transcript synonymous_variant 1381/2935 1212/1734 404/577 P ccC/ccA rs367747928,rs758760721,COSM1717948 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 10/14 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR24095,hmmpanther:PTHR24095:SF188,Superfamily_domains:SSF56801 0,0,1 LOW 1 SNV 1 0,0,1 1 PASS rs367747928 . 0 193 10 5 0 0 0 0 -16.87512 0.9779528 1 1 1 0 T 2 4 80 20545226 20545226 G T 1 0 0 0 0 0 0 0 1 226 1103 39 1 1 ACSM2B 16 20545226 Silent SNP G C3N-01488_T 4788771 20545226 69793119 426 24800 USP31 0 . GRCh38 16 23085584 23085584 + Splice_Site SNP C C A novel C3N-01488_T C3N-01488_N C C c.1700+1G>T p.X567_splice ENST00000219689 172 151 21 242 242 0 strelka-varscan-mutect USP31,splice_donor_variant,,ENST00000219689,NM_020718.3;USP31,splice_donor_variant,,ENST00000563525,; A ENST00000219689 Transcript splice_donor_variant -/10699 1700/4059 567/1352 1 -1 USP31 HGNC HGNC:20060 protein_coding YES CCDS10607.1 ENSP00000219689 Q70CQ4 UPI0000366B06 NM_020718.3 10/15 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 80 23085584 23085584 C A 1 0 0 0 0 0 0 1 0 17604 492 17 2 2 USP31 16 23085584 Splice_Site SNP C C3N-01488_T 2540358 23085584 67252761 427 24801 COG7 0 . GRCh38 16 23442636 23442636 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.445G>C p.Val149Leu p.V149L ENST00000307149 4/17 490 372 118 595 593 2 strelka-varscan-mutect COG7,missense_variant,p.Val149Leu,ENST00000307149,NM_153603.3;SNORA75,downstream_gene_variant,,ENST00000391291,;CTD-2270L9.2,downstream_gene_variant,,ENST00000561624,; G ENST00000307149 Transcript missense_variant 631/2926 445/2313 149/770 V/L Gtg/Ctg 1 -1 COG7 HGNC HGNC:18622 protein_coding YES CCDS10610.1 ENSP00000305442 P83436 A0A0S2Z652 UPI0000127E42 NM_153603.3 tolerated(0.37) 4/17 hmmpanther:PTHR21443,Pfam_domain:PF10191 MODERATE 1 SNV 1 1 PASS rs1441413236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 23442636 23442636 C G 1 0 0 0 0 1 0 0 0 3451 478 17 4 4 COG7 16 23442636 Missense_Mutation SNP C C3N-01488_T 357052 23442636 66895709 428 24802 CHP2 0 . GRCh38 16 23757201 23757201 + Missense_Mutation SNP G G T rs35717824 C3N-01488_T C3N-01488_N G G c.415G>T p.Val139Phe p.V139F ENST00000300113 6/7 317 241 76 407 407 0 strelka-varscan-mutect CHP2,missense_variant,p.Val139Phe,ENST00000300113,NM_022097.3;CTD-2385L22.2,upstream_gene_variant,,ENST00000623305,; T ENST00000300113 Transcript missense_variant,splice_region_variant 838/2382 415/591 139/196 V/F Gtt/Ttt rs35717824 1 1 CHP2 HGNC HGNC:24927 protein_coding YES CCDS10617.1 ENSP00000300113 O43745 UPI000013E626 NM_022097.3 deleterious(0) 6/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23056,hmmpanther:PTHR23056:SF49,Gene3D:1.10.238.10,Pfam_domain:PF13499,SMART_domains:SM00054,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS rs1453864245 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 23757201 23757201 G T 1 0 0 0 0 1 0 0 0 3127 1275 44 2 2 CHP2 16 23757201 Missense_Mutation SNP G C3N-01488_T 314565 23757201 66581144 429 24803 TNRC6A 0 . GRCh38 16 24789834 24789834 + Missense_Mutation SNP A A G rs764455500 C3N-01488_T C3N-01488_N A A c.1192A>G p.Ile398Val p.I398V ENST00000395799 6/25 213 194 19 270 270 0 strelka-varscan-mutect TNRC6A,missense_variant,p.Ile398Val,ENST00000395799,NM_014494.2;TNRC6A,missense_variant,p.Ile398Val,ENST00000315183,;TNRC6A,upstream_gene_variant,,ENST00000450465,;TNRC6A,3_prime_UTR_variant,,ENST00000491718,;TNRC6A,upstream_gene_variant,,ENST00000568903,;TNRC6A,upstream_gene_variant,,ENST00000567232,; G ENST00000395799 Transcript missense_variant 1321/8438 1192/5889 398/1962 I/V Ata/Gta rs764455500,COSM4428425 1 1 TNRC6A HGNC HGNC:11969 protein_coding YES CCDS10624.2 ENSP00000379144 Q8NDV7 UPI000059D33E NM_014494.2 tolerated(0.11) 6/25 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF28 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs764455500 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 24789834 24789834 A G 1 0 0 0 0 1 0 0 0 16813 449 16 5 5 TNRC6A 16 24789834 Missense_Mutation SNP A C3N-01488_T 1032633 24789834 65548511 430 24804 HS3ST4 0 . GRCh38 16 26135901 26135901 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1024A>T p.Asn342Tyr p.N342Y ENST00000331351 2/2 465 370 95 535 534 1 strelka-varscan-mutect HS3ST4,missense_variant,p.Asn342Tyr,ENST00000331351,NM_006040.2;HS3ST4,non_coding_transcript_exon_variant,,ENST00000475436,; T ENST00000331351 Transcript missense_variant 1416/3203 1024/1371 342/456 N/Y Aac/Tac 1 1 HS3ST4 HGNC HGNC:5200 protein_coding YES CCDS53995.1 ENSP00000330606 Q9Y661 UPI000040938A NM_006040.2 deleterious(0.02) 2/2 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF11,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 26135901 26135901 A T 1 0 0 0 0 1 0 0 0 7261 14 1 4 4 HS3ST4 16 26135901 Missense_Mutation SNP A C3N-01488_T 1346067 26135901 64202444 431 24805 IL21R 0 . GRCh38 16 27430079 27430079 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.8G>T p.Arg3Leu p.R3L ENST00000337929 2/9 190 166 24 205 205 0 strelka-varscan-mutect IL21R,missense_variant,p.Arg3Leu,ENST00000337929,NM_181078.2;IL21R,missense_variant,p.Arg3Leu,ENST00000564089,NM_181079.4;IL21R,missense_variant,p.Arg3Leu,ENST00000395754,NM_021798.3; T ENST00000337929 Transcript missense_variant 481/4849 8/1617 3/538 R/L cGt/cTt COSM702831 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 tolerated_low_confidence(0.09) 2/9 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7,Cleavage_site_(Signalp):SignalP-noTM 1 MODERATE 1 SNV 1 1 1 PASS rs913538510 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 27430079 27430079 G T 1 0 0 0 0 1 0 0 0 7574 1145 40 1 1 IL21R 16 27430079 Missense_Mutation SNP G C3N-01488_T 1294178 27430079 62908266 432 24806 GSG1L 0 . GRCh38 16 27828804 27828804 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.815A>T p.Lys272Met p.K272M ENST00000447459 5/7 121 97 24 133 133 0 varscan-mutect GSG1L,missense_variant,p.Lys272Met,ENST00000447459,NM_001109763.1;GSG1L,missense_variant,p.Lys221Met,ENST00000395724,;GSG1L,missense_variant,p.Lys117Met,ENST00000380897,NM_144675.2;GSG1L,missense_variant,p.Lys117Met,ENST00000569166,;GSG1L,3_prime_UTR_variant,,ENST00000562611,; A ENST00000447459 Transcript missense_variant 900/4916 815/996 272/331 K/M aAg/aTg 1 -1 GSG1L HGNC HGNC:28283 protein_coding YES CCDS45450.1 ENSP00000394954 Q6UXU4 UPI0000EE765B NM_001109763.1 deleterious(0.02) 5/7 hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF35 MODERATE 1 SNV 2 1 PASS rs1336722013 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 27828804 27828804 T A 1 0 0 0 0 1 0 0 0 6704 1609 56 4 4 GSG1L 16 27828804 Missense_Mutation SNP T C3N-01488_T 398725 27828804 62509541 433 24807 NFATC2IP 0 . GRCh38 16 28963825 28963825 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1222G>T p.Gly408Cys p.G408C ENST00000320805 8/8 175 144 31 237 235 2 strelka-varscan-mutect NFATC2IP,missense_variant,p.Gly408Cys,ENST00000320805,NM_032815.3;NFATC2IP,missense_variant,p.Gly129Cys,ENST00000564978,;NFATC2IP,missense_variant,p.Gly116Cys,ENST00000568148,;RP11-264B17.2,intron_variant,,ENST00000569974,;NFATC2IP,downstream_gene_variant,,ENST00000562977,; T ENST00000320805 Transcript missense_variant 1297/4569 1222/1260 408/419 G/C Ggc/Tgc 1 1 NFATC2IP HGNC HGNC:25906 protein_coding YES CCDS10645.1 ENSP00000324792 Q8NCF5 UPI00000316E2 NM_032815.3 deleterious(0) 8/8 Gene3D:3.10.20.90,Pfam_domain:PF11976,PROSITE_profiles:PS50053,hmmpanther:PTHR10562,hmmpanther:PTHR10562:SF28,SMART_domains:SM00213,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 28963825 28963825 G T 1 0 0 0 0 1 0 0 0 10400 1232 43 2 2 NFATC2IP 16 28963825 Missense_Mutation SNP G C3N-01488_T 1135021 28963825 61374520 434 24808 ZNF768 0 . GRCh38 16 30524961 30524961 + Missense_Mutation SNP C C A rs780124084 C3N-01488_T C3N-01488_N C C c.1179G>T p.Arg393Ser p.R393S ENST00000380412 2/2 358 288 70 425 425 0 strelka-varscan-mutect ZNF768,missense_variant,p.Arg393Ser,ENST00000380412,NM_024671.3;ZNF768,missense_variant,p.Arg362Ser,ENST00000562803,;ITGAL,downstream_gene_variant,,ENST00000356798,NM_002209.2;ITGAL,downstream_gene_variant,,ENST00000358164,NM_001114380.1;ITGAL,downstream_gene_variant,,ENST00000433423,;AC002310.14,upstream_gene_variant,,ENST00000624451,;AC002310.11,downstream_gene_variant,,ENST00000569360,;ITGAL,downstream_gene_variant,,ENST00000564632,; A ENST00000380412 Transcript missense_variant 1355/2315 1179/1623 393/540 R/S agG/agT rs780124084 1 -1 ZNF768 HGNC HGNC:26273 protein_coding YES CCDS10681.2 ENSP00000369777 Q9H5H4 A0A024QZC8 UPI00001FFEED NM_024671.3 deleterious_low_confidence(0.02) 2/2 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF208,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs780124084 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 30524961 30524961 C A 1 0 0 0 0 1 0 0 0 18724 622 22 2 2 ZNF768 16 30524961 Missense_Mutation SNP C C3N-01488_T 1561136 30524961 59813384 435 24809 FBRS 0 . GRCh38 16 30669368 30669368 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.1106C>T p.Pro369Leu p.P369L ENST00000287468 12/12 398 291 107 384 384 0 strelka-varscan-mutect FBRS,missense_variant,p.Pro889Leu,ENST00000356166,;FBRS,missense_variant,p.Pro369Leu,ENST00000287468,NM_001105079.1;FBRS,downstream_gene_variant,,ENST00000482749,;FBRS,3_prime_UTR_variant,,ENST00000543786,;FBRS,non_coding_transcript_exon_variant,,ENST00000494101,;FBRS,downstream_gene_variant,,ENST00000570170,; T ENST00000287468 Transcript missense_variant 1369/2811 1106/1383 369/460 P/L cCa/cTa 1 1 FBRS HGNC HGNC:20442 protein_coding YES CCDS45462.1 ENSP00000287468 Q9HAH7 UPI000059D366 NM_001105079.1 tolerated(0.11) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR14429,hmmpanther:PTHR14429:SF24 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 30669368 30669368 C T 1 0 0 0 0 1 0 0 0 5570 594 21 3 3 FBRS 16 30669368 Missense_Mutation SNP C C3N-01488_T 144407 30669368 59668977 436 24810 AC007906.1 0 . GRCh38 16 53209657 53209657 + Missense_Mutation SNP G G T rs777290043 C3N-01488_T C3N-01488_N G G c.1628G>T p.Arg543Leu p.R543L ENST00000447540 3/39 365 289 76 492 492 0 strelka-varscan-mutect CHD9,missense_variant,p.Arg543Leu,ENST00000566029,NM_025134.4;CHD9,missense_variant,p.Arg543Leu,ENST00000447540,NM_001308319.1;CHD9,missense_variant,p.Arg543Leu,ENST00000564845,;CHD9,missense_variant,p.Arg543Leu,ENST00000398510,;CHD9,missense_variant,p.Arg69Leu,ENST00000565803,;CHD9,missense_variant,p.Arg543Leu,ENST00000565832,;AC007906.1,missense_variant,p.Arg56Ser,ENST00000624244,;CHD9,missense_variant,p.Arg36Leu,ENST00000565442,;CHD9,5_prime_UTR_variant,,ENST00000615216,;CHD9,intron_variant,,ENST00000622617,;CHD9,intron_variant,,ENST00000569794,;CHD9,upstream_gene_variant,,ENST00000562791,;CHD9,non_coding_transcript_exon_variant,,ENST00000564255,; T ENST00000447540 Transcript missense_variant 1837/11509 1628/8694 543/2897 R/L cGc/cTc rs777290043,COSM4672107 1 1 CHD9 HGNC HGNC:25701 protein_coding YES CCDS76865.1 ENSP00000396345 Q3L8U1 UPI0000E02AC8 NM_001308319.1 deleterious(0.04) 3/39 0,1 MODERATE SNV 5 0,1 1 PASS rs777290043 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 53209657 53209657 G T 1 0 0 0 0 1 0 0 0 117 1087 38 1 1 AC007906.1 16 53209657 Missense_Mutation SNP G C3N-01488_T 22540289 53209657 37128688 437 24811 RP11-457D20.2 0 . GRCh38 16 60359157 60359157 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.324A>T p.Glu108Asp p.E108D ENST00000614215 1/1 100 70 30 130 130 0 strelka-varscan-mutect RP11-457D20.2,missense_variant,p.Glu108Asp,ENST00000614215,NM_001282301.1;RP11-354I13.2,upstream_gene_variant,,ENST00000565506,;RP11-354I13.2,upstream_gene_variant,,ENST00000565133,;RP11-457D20.1,downstream_gene_variant,,ENST00000563482,; A ENST00000614215 Transcript missense_variant 324/1026 324/1026 108/341 E/D gaA/gaT 1 -1 RP11-457D20.2 Clone_based_vega_gene protein_coding YES ENSP00000482925 A8MU76 UPI00017616FE NM_001282301.1 tolerated(0.61) 1/1 Pfam_domain:PF15229 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 60359157 60359157 T A 1 0 0 0 0 1 0 0 0 13744 1606 56 4 4 RP11-457D20.2 16 60359157 Missense_Mutation SNP T C3N-01488_T 7149500 60359157 29979188 438 24812 FUK 0 . GRCh38 16 70463707 70463707 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.167G>T p.Ser56Ile p.S56I ENST00000288078 3/24 211 174 37 249 249 0 strelka-varscan-mutect FUK,missense_variant,p.Ser56Ile,ENST00000288078,NM_145059.2;FUK,missense_variant,p.Ser56Ile,ENST00000378912,;FUK,missense_variant,p.Ser56Ile,ENST00000574784,;FUK,missense_variant,p.Ser56Ile,ENST00000573352,;FUK,missense_variant,p.Ser56Ile,ENST00000576453,;FUK,missense_variant,p.Ser56Ile,ENST00000572784,;FUK,intron_variant,,ENST00000571514,;FUK,non_coding_transcript_exon_variant,,ENST00000464499,;FUK,non_coding_transcript_exon_variant,,ENST00000571487,;FUK,non_coding_transcript_exon_variant,,ENST00000576107,; T ENST00000288078 Transcript missense_variant 399/4081 167/3255 56/1084 S/I aGc/aTc COSM4798265,COSM4798266,COSM4798267 1 1 FUK HGNC HGNC:29500 protein_coding YES CCDS10891.2 ENSP00000288078 Q8N0W3 UPI000013DEF1 NM_145059.2 deleterious(0) 3/24 hmmpanther:PTHR32463 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 70463707 70463707 G T 1 0 0 0 0 1 0 0 0 5967 971 34 2 2 FUK 16 70463707 Missense_Mutation SNP G C3N-01488_T 10104550 70463707 19874638 439 24813 KLHL36 0 . GRCh38 16 84661726 84661727 + Frame_Shift_Del DEL GC GC - C3N-01488_T C3N-01488_N GC GC c.1449_1450delCG p.Gly484LeufsTer9 p.G484Lfs*9 ENST00000564996 5/5 129 109 20 136 136 0 sindel-varindel-pindel KLHL36,frameshift_variant,p.Gly484LeufsTer9,ENST00000564996,NM_024731.3;KLHL36,frameshift_variant,p.Gly421LeufsTer9,ENST00000258157,NM_001303451.1;KLHL36,downstream_gene_variant,,ENST00000567410,;KLHL36,downstream_gene_variant,,ENST00000565743,;KLHL36,downstream_gene_variant,,ENST00000569472,;KLHL36,non_coding_transcript_exon_variant,,ENST00000325279,;KLHL36,non_coding_transcript_exon_variant,,ENST00000564159,; - ENST00000564996 Transcript frameshift_variant 1585-1586/2173 1444-1445/1851 482/616 A/X GCg/g COSM391738 1 1 KLHL36 HGNC HGNC:17844 protein_coding YES CCDS10948.1 ENSP00000456743 Q8N4N3 UPI000006F9CF NM_024731.3 5/5 Superfamily_domains:0052715,Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF246,SMART_domains:SM00612 1 HIGH 1 deletion 1 5 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 84661726 84661726 GC - 1 0 1 0 1 0 0 0 0 8255 1203 42 0 0 KLHL36 16 84661726 Frame_Shift_Del DEL GC C3N-01488_T 14198019 84661726 5676619 440 24814 BANP 0 . GRCh38 16 88037996 88037996 + Silent SNP G G T rs772483207 C3N-01488_T C3N-01488_N G G c.1263G>T p.= p.V421V ENST00000393207 11/14 273 224 49 386 386 0 strelka-varscan-mutect BANP,synonymous_variant,p.=,ENST00000393207,NM_001173543.1;BANP,synonymous_variant,p.=,ENST00000538234,NM_001173539.1,NM_001173542.1;BANP,synonymous_variant,p.=,ENST00000286122,;BANP,synonymous_variant,p.=,ENST00000393208,NM_079837.2;BANP,synonymous_variant,p.=,ENST00000355022,NM_017869.3;BANP,synonymous_variant,p.=,ENST00000626016,NM_001173540.1;BANP,synonymous_variant,p.=,ENST00000479780,NM_001173541.1;BANP,downstream_gene_variant,,ENST00000497491,;BANP,non_coding_transcript_exon_variant,,ENST00000565242,;BANP,non_coding_transcript_exon_variant,,ENST00000466847,; T ENST00000393207 Transcript synonymous_variant 1484/2438 1263/1560 421/519 V gtG/gtT rs772483207 1 1 BANP HGNC HGNC:13450 protein_coding YES CCDS54054.1 ENSP00000376902 Q8N9N5 UPI0000E59DA3 NM_001173543.1 11/14 hmmpanther:PTHR16243 LOW 1 SNV 2 1 PASS rs772483207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 88037996 88037996 G T 1 0 0 0 0 0 0 0 1 1462 1335 47 2 2 BANP 16 88037996 Silent SNP G C3N-01488_T 3376270 88037996 2300349 441 24815 FAM57A 0 . GRCh38 17 737960 737960 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.321C>A p.= p.S107S ENST00000308278 3/5 400 308 92 559 559 0 strelka-varscan-mutect FAM57A,synonymous_variant,p.=,ENST00000308278,NM_024792.1;FAM57A,synonymous_variant,p.=,ENST00000301324,NM_001318006.1;FAM57A,intron_variant,,ENST00000577008,;FAM57A,intron_variant,,ENST00000572018,;FAM57A,upstream_gene_variant,,ENST00000570892,;FAM57A,3_prime_UTR_variant,,ENST00000570699,;FAM57A,intron_variant,,ENST00000574327,; A ENST00000308278 Transcript synonymous_variant 557/2412 321/774 107/257 S tcC/tcA 1 1 FAM57A HGNC HGNC:29646 protein_coding YES CCDS10996.1 ENSP00000312017 Q8TBR7 UPI000006F9B9 NM_024792.1 3/5 Pfam_domain:PF03798,PROSITE_profiles:PS50922,hmmpanther:PTHR13439,hmmpanther:PTHR13439:SF20,SMART_domains:SM00724 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 737960 737960 C A 1 0 0 0 0 0 0 0 1 5458 610 22 2 2 FAM57A 17 737960 Silent SNP C C3N-01488_T 737960 82519481 442 24816 CLUH 0 . GRCh38 17 2698373 2698373 + Missense_Mutation SNP C C A rs748257674 C3N-01488_T C3N-01488_N C C c.1370G>T p.Arg457Leu p.R457L ENST00000570628 10/26 150 118 32 219 218 1 strelka-varscan-mutect CLUH,missense_variant,p.Arg457Leu,ENST00000570628,;CLUH,missense_variant,p.Arg457Leu,ENST00000435359,NM_015229.3;CLUH,missense_variant,p.Arg398Leu,ENST00000575014,;CLUH,missense_variant,p.Arg495Leu,ENST00000574426,;CLUH,downstream_gene_variant,,ENST00000576885,;CLUH,downstream_gene_variant,,ENST00000572129,;CLUH,upstream_gene_variant,,ENST00000574210,;CLUH,upstream_gene_variant,,ENST00000575624,;CLUH,upstream_gene_variant,,ENST00000574166,;CLUH,upstream_gene_variant,,ENST00000573641,;CLUH,upstream_gene_variant,,ENST00000572014,;CLUH,downstream_gene_variant,,ENST00000571539,; A ENST00000570628 Transcript missense_variant 1476/5244 1370/3930 457/1309 R/L cGc/cTc rs748257674 1 -1 CLUH HGNC HGNC:29094 protein_coding YES CCDS45572.1 ENSP00000458986 O75153 UPI00004C8042 deleterious(0) 10/26 HAMAP:MF_03013,Pfam_domain:PF13236,hmmpanther:PTHR12601,hmmpanther:PTHR12601:SF10 MODERATE 1 SNV 2 1 PASS rs748257674 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 2698373 2698373 C A 1 0 0 0 0 1 0 0 0 3342 768 27 1 1 CLUH 17 2698373 Missense_Mutation SNP C C3N-01488_T 1960413 2698373 80559068 443 24817 TMEM256 0 . GRCh38 17 7403326 7403326 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.182G>T p.Cys61Phe p.C61F ENST00000302422 3/4 265 239 26 338 338 0 strelka-varscan-mutect TMEM256,missense_variant,p.Cys61Phe,ENST00000302422,NM_152766.3;TMEM256,3_prime_UTR_variant,,ENST00000576017,;NLGN2,upstream_gene_variant,,ENST00000302926,NM_020795.3;NLGN2,upstream_gene_variant,,ENST00000575301,;NLGN2,upstream_gene_variant,,ENST00000572893,;TMEM256-PLSCR3,missense_variant,p.Cys61Phe,ENST00000573331,;TMEM256-PLSCR3,missense_variant,p.Cys21Phe,ENST00000571125,;TMEM256-PLSCR3,missense_variant,p.Cys61Phe,ENST00000570569,;TMEM256,non_coding_transcript_exon_variant,,ENST00000575427,;TMEM256-PLSCR3,intron_variant,,ENST00000570600,; A ENST00000302422 Transcript missense_variant 235/486 182/342 61/113 C/F tGc/tTc 1 -1 TMEM256 HGNC HGNC:28618 protein_coding YES CCDS11102.1 ENSP00000301939 Q8N2U0 UPI0000049DA7 NM_152766.3 deleterious(0) 3/4 Pfam_domain:PF04241,hmmpanther:PTHR10584 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 7403326 7403326 C A 1 0 0 0 0 1 0 0 0 16616 710 25 2 2 TMEM256 17 7403326 Missense_Mutation SNP C C3N-01488_T 4704953 7403326 75854115 444 24818 NTN1 0 . GRCh38 17 9022585 9022585 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.212G>T p.Gly71Val p.G71V ENST00000173229 2/7 83 69 14 104 104 0 strelka-varscan-mutect NTN1,missense_variant,p.Gly71Val,ENST00000173229,NM_004822.2; T ENST00000173229 Transcript missense_variant 319/5954 212/1815 71/604 G/V gGc/gTc 1 1 NTN1 HGNC HGNC:8029 protein_coding YES CCDS11148.1 ENSP00000173229 O95631 UPI000013C5C7 NM_004822.2 deleterious(0) 2/7 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF278,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 9022585 9022585 G T 1 0 0 0 0 1 0 0 0 10765 1203 42 2 2 NTN1 17 9022585 Missense_Mutation SNP G C3N-01488_T 1619259 9022585 74234856 445 24819 MYH8 0 . GRCh38 17 10393110 10393110 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.5267A>G p.Glu1756Gly p.E1756G ENST00000403437 36/40 405 369 36 609 609 0 strelka-varscan-mutect MYH8,missense_variant,p.Glu1756Gly,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; C ENST00000403437 Transcript missense_variant 5362/6041 5267/5814 1756/1937 E/G gAg/gGg 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0) 36/40 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF57997 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 10393110 10393110 T C 1 0 0 0 0 1 0 0 0 10041 1551 54 5 5 MYH8 17 10393110 Missense_Mutation SNP T C3N-01488_T 1370525 10393110 72864331 446 24820 MYH8 0 . GRCh38 17 10396988 10396988 + Splice_Site SNP T T A novel C3N-01488_T C3N-01488_N T T c.4179-2A>T p.X1393_splice ENST00000403437 280 253 27 414 414 0 strelka-varscan-mutect MYH8,splice_acceptor_variant,,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000403437 Transcript splice_acceptor_variant -/6041 4179/5814 1393/1937 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 30/39 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 80 10396988 10396988 T A 1 0 0 0 0 0 0 1 0 10041 1594 55 4 4 MYH8 17 10396988 Splice_Site SNP T C3N-01488_T 3878 10396988 72860453 447 24821 MYH4 0 . GRCh38 17 10450564 10450564 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.4070C>A p.Ala1357Asp p.A1357D ENST00000255381 30/40 240 200 40 335 335 0 strelka-varscan-mutect MYH4,missense_variant,p.Ala1357Asp,ENST00000255381,NM_017533.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000255381 Transcript missense_variant 4181/6016 4070/5820 1357/1939 A/D gCc/gAc 1 -1 MYH4 HGNC HGNC:7574 protein_coding YES CCDS11154.1 ENSP00000255381 Q9Y623 UPI000013CEAB NM_017533.2 deleterious(0.01) 30/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1208775437 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 10450564 10450564 G T 1 0 0 0 0 1 0 0 0 10037 1203 42 2 2 MYH4 17 10450564 Missense_Mutation SNP G C3N-01488_T 53576 10450564 72806877 448 24822 MYH1 0 . GRCh38 17 10496414 10496414 + Missense_Mutation SNP C C A rs150456818 C3N-01488_T C3N-01488_N C C c.4792G>T p.Val1598Leu p.V1598L ENST00000226207 34/40 409 332 77 684 683 1 strelka-varscan-mutect MYH1,missense_variant,p.Val1598Leu,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 4887/6024 4792/5820 1598/1939 V/L Gtg/Ttg rs150456818,COSM33235,COSM4579422 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 tolerated(0.35) 34/40 Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs150456818 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 10496414 10496414 C A 1 0 0 0 0 1 0 0 0 10029 536 19 1 1 MYH1 17 10496414 Missense_Mutation SNP C C3N-01488_T 45850 10496414 72761027 449 24823 MYH1 0 . GRCh38 17 10501901 10501901 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.3122C>T p.Ser1041Phe p.S1041F ENST00000226207 25/40 98 91 7 184 184 0 strelka-varscan-mutect MYH1,missense_variant,p.Ser1041Phe,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 3217/6024 3122/5820 1041/1939 S/F tCt/tTt 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 25/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,Superfamily_domains:SSF90257 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -14.64672 1 1 1 1 0 A 3 1 80 10501901 10501901 G A 1 0 0 0 0 1 0 0 0 10029 942 33 3 3 MYH1 17 10501901 Missense_Mutation SNP G C3N-01488_T 5487 10501901 72755540 450 24824 DNAH9 0 . GRCh38 17 11690333 11690333 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.4511C>A p.Thr1504Lys p.T1504K ENST00000262442 20/69 314 275 39 515 515 0 strelka-varscan-mutect DNAH9,missense_variant,p.Thr1504Lys,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Thr1504Lys,ENST00000454412,; A ENST00000262442 Transcript missense_variant 4579/13750 4511/13461 1504/4486 T/K aCa/aAa 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 tolerated(0.07) 20/69 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 11690333 11690333 C A 1 0 0 0 0 1 0 0 0 4423 478 17 2 2 DNAH9 17 11690333 Missense_Mutation SNP C C3N-01488_T 1188432 11690333 71567108 451 24825 MFAP4 0 . GRCh38 17 19385420 19385420 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.347T>C p.Phe116Ser p.F116S ENST00000395592 4/6 332 283 49 448 448 0 strelka-varscan-mutect MFAP4,missense_variant,p.Phe116Ser,ENST00000395592,NM_001198695.1;MFAP4,missense_variant,p.Phe117Ser,ENST00000497081,;MFAP4,missense_variant,p.Phe92Ser,ENST00000299610,NM_002404.2;MAPK7,downstream_gene_variant,,ENST00000308406,NM_139033.2;MAPK7,downstream_gene_variant,,ENST00000395604,NM_002749.3;MAPK7,downstream_gene_variant,,ENST00000395602,NM_139034.2;MAPK7,downstream_gene_variant,,ENST00000299612,NM_139032.2;MAPK7,downstream_gene_variant,,ENST00000443215,;MAPK7,downstream_gene_variant,,ENST00000482850,;MAPK7,downstream_gene_variant,,ENST00000579284,;MAPK7,downstream_gene_variant,,ENST00000603493,;MAPK7,downstream_gene_variant,,ENST00000571657,;MFAP4,upstream_gene_variant,,ENST00000574313,;MAPK7,downstream_gene_variant,,ENST00000572968,;MAPK7,downstream_gene_variant,,ENST00000573417,;MFAP4,non_coding_transcript_exon_variant,,ENST00000571210,;MAPK7,downstream_gene_variant,,ENST00000570306,;MAPK7,downstream_gene_variant,,ENST00000490660,;MAPK7,downstream_gene_variant,,ENST00000572716,;MAPK7,downstream_gene_variant,,ENST00000581260,; G ENST00000395592 Transcript missense_variant 419/1932 347/840 116/279 F/S tTc/tCc 1 -1 MFAP4 HGNC HGNC:7035 protein_coding YES CCDS56023.1 ENSP00000378957 P55083 A0A024QZ34 UPI000014C39C NM_001198695.1 deleterious(0) 4/6 Gene3D:3.90.215.10,Pfam_domain:PF00147,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 19385420 19385420 A G 1 0 0 0 0 1 0 0 0 9470 246 9 5 5 MFAP4 17 19385420 Missense_Mutation SNP A C3N-01488_T 7695087 19385420 63872021 452 24826 EFCAB5 0 . GRCh38 17 30091898 30091898 + Missense_Mutation SNP G G T rs762793386 C3N-01488_T C3N-01488_N G G c.3965G>T p.Arg1322Leu p.R1322L ENST00000394835 21/23 104 97 7 164 164 0 strelka-varscan-mutect EFCAB5,missense_variant,p.Arg1322Leu,ENST00000394835,NM_198529.3;EFCAB5,missense_variant,p.Arg1004Leu,ENST00000419434,;EFCAB5,intron_variant,,ENST00000588978,;RP11-1148O4.2,intron_variant,,ENST00000582938,;EFCAB5,non_coding_transcript_exon_variant,,ENST00000582953,; T ENST00000394835 Transcript missense_variant 4157/5132 3965/4512 1322/1503 R/L cGg/cTg rs762793386 1 1 EFCAB5 HGNC HGNC:24801 protein_coding YES CCDS11254.2 ENSP00000378312 A4FU69 UPI0000E59EF5 NM_198529.3 deleterious(0) 21/23 hmmpanther:PTHR31938,hmmpanther:PTHR31938:SF6 MODERATE 1 SNV 1 1 PASS rs762793386 . 0 205 3 2 0 0 0 0 -10.87116 0.9999664 1 1 1 0 T 3 4 80 30091898 30091898 G T 1 0 0 0 0 1 0 0 0 4772 1116 39 1 1 EFCAB5 17 30091898 Missense_Mutation SNP G C3N-01488_T 10706478 30091898 53165543 453 24827 TOP2A 0 . GRCh38 17 40408122 40408122 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1345G>T p.Gly449Cys p.G449C ENST00000423485 12/35 78 70 8 105 105 0 strelka-varscan-mutect TOP2A,missense_variant,p.Gly449Cys,ENST00000423485,NM_001067.3; A ENST00000423485 Transcript missense_variant,splice_region_variant 1504/5758 1345/4596 449/1531 G/C Ggc/Tgc 1 -1 TOP2A HGNC HGNC:11989 protein_coding YES CCDS45672.1 ENSP00000411532 P11388 UPI0000137195 NM_001067.3 deleterious(0.05) 12/35 Gene3D:3.40.50.670,Prints_domain:PR01158,hmmpanther:PTHR10169,hmmpanther:PTHR10169:SF46,SMART_domains:SM00433,Superfamily_domains:SSF56719 MODERATE 1 SNV 1 1 PASS . . 0 199 10 0 0 0 0 0 -17.03564 0.9999615 1 1 1 0 A 3 1 80 40408122 40408122 C A 1 0 0 0 0 1 0 0 0 16841 637 22 2 2 TOP2A 17 40408122 Missense_Mutation SNP C C3N-01488_T 10316224 40408122 42849319 454 24828 COASY 0 . GRCh38 17 42565711 42565711 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1625G>T p.Ser542Ile p.S542I ENST00000590958 10/11 269 245 24 360 360 0 strelka-varscan-mutect COASY,missense_variant,p.Ser513Ile,ENST00000393818,NM_025233.6;COASY,missense_variant,p.Ser513Ile,ENST00000421097,NM_001042529.2;COASY,missense_variant,p.Ser542Ile,ENST00000590958,NM_001042532.3;MLX,upstream_gene_variant,,ENST00000246912,NM_170607.2;MLX,upstream_gene_variant,,ENST00000435881,NM_198204.1;MLX,upstream_gene_variant,,ENST00000346833,NM_198205.1;COASY,downstream_gene_variant,,ENST00000591779,;MLX,upstream_gene_variant,,ENST00000591024,;COASY,downstream_gene_variant,,ENST00000586771,;COASY,downstream_gene_variant,,ENST00000585811,;COASY,downstream_gene_variant,,ENST00000585909,;COASY,downstream_gene_variant,,ENST00000587858,;COASY,downstream_gene_variant,,ENST00000587157,;COASY,downstream_gene_variant,,ENST00000587214,;RP11-400F19.8,downstream_gene_variant,,ENST00000585572,;COASY,downstream_gene_variant,,ENST00000588757,;COASY,non_coding_transcript_exon_variant,,ENST00000591753,;COASY,non_coding_transcript_exon_variant,,ENST00000591583,;MLX,upstream_gene_variant,,ENST00000590050,;MLX,upstream_gene_variant,,ENST00000588320,;MLX,upstream_gene_variant,,ENST00000585403,;MLX,upstream_gene_variant,,ENST00000586393,;MLX,upstream_gene_variant,,ENST00000590084,;MLX,upstream_gene_variant,,ENST00000592717,;MLX,upstream_gene_variant,,ENST00000591195,;COASY,downstream_gene_variant,,ENST00000588353,; T ENST00000590958 Transcript missense_variant 1750/1976 1625/1782 542/593 S/I aGc/aTc 1 1 COASY HGNC HGNC:29932 protein_coding YES CCDS45685.1 ENSP00000464814 Q13057 UPI00018131ED NM_001042532.3 tolerated(0.08) 10/11 PROSITE_profiles:PS51219,HAMAP:MF_00376,hmmpanther:PTHR10695,hmmpanther:PTHR10695:SF20,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00152,Pfam_domain:PF01121,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 42565711 42565711 G T 1 0 0 0 0 1 0 0 0 3441 971 34 2 2 COASY 17 42565711 Missense_Mutation SNP G C3N-01488_T 2157589 42565711 40691730 455 24829 CACNA1G 0 . GRCh38 17 50618941 50618941 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.5714A>T p.Lys1905Met p.K1905M ENST00000359106 33/38 59 29 30 73 73 0 strelka-varscan-mutect CACNA1G,missense_variant,p.Lys1871Met,ENST00000354983,NM_198396.2;CACNA1G,missense_variant,p.Lys1871Met,ENST00000352832,NM_198387.2;CACNA1G,missense_variant,p.Lys1905Met,ENST00000359106,NM_018896.4;CACNA1G,missense_variant,p.Lys1882Met,ENST00000360761,NM_198382.2;CACNA1G,missense_variant,p.Lys1864Met,ENST00000442258,NM_198388.2;CACNA1G,missense_variant,p.Lys1887Met,ENST00000429973,NM_198386.2;CACNA1G,missense_variant,p.Lys1894Met,ENST00000507336,NM_198377.2;CACNA1G,missense_variant,p.Lys1871Met,ENST00000358244,NM_198376.2;CACNA1G,missense_variant,p.Lys1905Met,ENST00000507510,NM_198385.2;CACNA1G,missense_variant,p.Lys1894Met,ENST00000515765,NM_198380.2;CACNA1G,missense_variant,p.Lys1887Met,ENST00000515411,NM_001256324.1;CACNA1G,missense_variant,p.Lys1882Met,ENST00000502264,NM_198383.2;CACNA1G,missense_variant,p.Lys1871Met,ENST00000510115,NM_198379.2;CACNA1G,missense_variant,p.Lys1912Met,ENST00000514079,NM_001256325.1;CACNA1G,missense_variant,p.Lys1860Met,ENST00000513689,NM_001256326.1;CACNA1G,missense_variant,p.Lys1905Met,ENST00000515165,NM_198384.2;CACNA1G,missense_variant,p.Lys1898Met,ENST00000507609,NM_001256327.1;CACNA1G,missense_variant,p.Lys1894Met,ENST00000512389,NM_198378.2;CACNA1G,missense_variant,p.Lys1880Met,ENST00000514181,NM_001256328.1;CACNA1G,missense_variant,p.Lys1871Met,ENST00000503485,NM_001256359.1,NM_001256329.1;CACNA1G,missense_variant,p.Lys1860Met,ENST00000513964,NM_001256360.1,NM_001256361.1,NM_001256330.1;CACNA1G,missense_variant,p.Lys1853Met,ENST00000510366,NM_001256331.1;CACNA1G,missense_variant,p.Lys1848Met,ENST00000514717,NM_001256332.1;CACNA1G,missense_variant,p.Lys1905Met,ENST00000505165,NM_001256333.1;CACNA1G,missense_variant,p.Lys1894Met,ENST00000507896,NM_001256334.1;CACNA1G,3_prime_UTR_variant,,ENST00000506406,;CACNA1G,3_prime_UTR_variant,,ENST00000504076,;CACNA1G,3_prime_UTR_variant,,ENST00000511765,;CACNA1G,3_prime_UTR_variant,,ENST00000503436,;CACNA1G,3_prime_UTR_variant,,ENST00000511768,;CACNA1G,3_prime_UTR_variant,,ENST00000503607,; T ENST00000359106 Transcript missense_variant 5714/7648 5714/7134 1905/2377 K/M aAg/aTg 1 1 CACNA1G HGNC HGNC:1394 protein_coding YES CCDS45730.1 ENSP00000352011 O43497 UPI000012727A NM_018896.4 tolerated(0.06) 33/38 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF137 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 50618941 50618941 A T 1 0 0 0 0 1 0 0 0 2232 72 3 4 4 CACNA1G 17 50618941 Missense_Mutation SNP A C3N-01488_T 8053230 50618941 32638500 456 24830 SPAG9 0 . GRCh38 17 50990505 50990505 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.2562A>T p.= p.G854G ENST00000262013 20/30 607 370 237 544 544 0 strelka-varscan-mutect SPAG9,synonymous_variant,p.=,ENST00000262013,NM_001130528.2;SPAG9,synonymous_variant,p.=,ENST00000618113,;SPAG9,synonymous_variant,p.=,ENST00000510283,NM_001251971.1;SPAG9,synonymous_variant,p.=,ENST00000357122,NM_003971.5;SPAG9,synonymous_variant,p.=,ENST00000505279,NM_001130527.2;SPAG9,synonymous_variant,p.=,ENST00000513906,;SPAG9,synonymous_variant,p.=,ENST00000513746,;SPAG9,non_coding_transcript_exon_variant,,ENST00000514613,;SPAG9,non_coding_transcript_exon_variant,,ENST00000505173,;SPAG9,non_coding_transcript_exon_variant,,ENST00000514205,;SPAG9,downstream_gene_variant,,ENST00000506483,; A ENST00000262013 Transcript synonymous_variant 2771/8273 2562/3966 854/1321 G ggA/ggT 1 -1 SPAG9 HGNC HGNC:14524 protein_coding YES CCDS45740.1 ENSP00000262013 O60271 UPI0000D60DF7 NM_001130528.2 20/30 hmmpanther:PTHR13886,hmmpanther:PTHR13886:SF2 LOW 1 SNV 1 1 PASS rs1430051962 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 50990505 50990505 T A 1 0 0 0 0 0 0 0 1 15316 1538 54 4 4 SPAG9 17 50990505 Silent SNP T C3N-01488_T 371564 50990505 32266936 457 24831 C17orf67 0 . GRCh38 17 56795118 56795118 + Missense_Mutation SNP C C A rs771245835 C3N-01488_T C3N-01488_N C C c.219G>T p.Trp73Cys p.W73C ENST00000397861 7/8 381 336 45 362 360 2 strelka-varscan-mutect C17orf67,missense_variant,p.Trp73Cys,ENST00000397861,NM_001085430.2;C17orf67,non_coding_transcript_exon_variant,,ENST00000570754,; A ENST00000397861 Transcript missense_variant 1499/2013 219/273 73/90 W/C tgG/tgT rs771245835 1 -1 C17orf67 HGNC HGNC:27900 protein_coding YES CCDS42364.2 ENSP00000380959 Q0P5P2 UPI000015F12E NM_001085430.2 deleterious_low_confidence(0.03) 7/8 hmmpanther:PTHR35971,Pfam_domain:PF15076 MODERATE 1 SNV 1 1 PASS rs771245835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 56795118 56795118 C A 1 0 0 0 0 1 0 0 0 1887 740 26 2 2 C17orf67 17 56795118 Missense_Mutation SNP C C3N-01488_T 5804613 56795118 26462323 458 24832 EPX 0 . GRCh38 17 58197211 58197211 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.1074C>A p.= p.P358P ENST00000225371 7/13 309 271 38 303 303 0 strelka-varscan-mutect EPX,synonymous_variant,p.=,ENST00000225371,NM_000502.4; A ENST00000225371 Transcript synonymous_variant 1184/2708 1074/2148 358/715 P ccC/ccA 1 1 EPX HGNC HGNC:3423 protein_coding YES CCDS11602.1 ENSP00000225371 P11678 UPI0000131629 NM_000502.4 7/13 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF63,hmmpanther:PTHR11475,Pfam_domain:PF03098,Gene3D:1.10.640.10,Superfamily_domains:SSF48113 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 58197211 58197211 C A 1 0 0 0 0 0 0 0 1 5048 668 24 2 2 EPX 17 58197211 Silent SNP C C3N-01488_T 1402093 58197211 25060230 459 24833 EFCAB3 0 . GRCh38 17 62391848 62391848 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.334T>C p.Tyr112His p.Y112H ENST00000450662 6/12 214 128 86 210 210 0 strelka-varscan-mutect EFCAB3,missense_variant,p.Tyr112His,ENST00000450662,NM_001144933.1;EFCAB3,missense_variant,p.Tyr60His,ENST00000305286,NM_173503.3;EFCAB3,missense_variant,p.Tyr60His,ENST00000518576,;EFCAB3,missense_variant,p.Tyr60His,ENST00000520404,;EFCAB3,non_coding_transcript_exon_variant,,ENST00000636041,; C ENST00000450662 Transcript missense_variant 405/1694 334/1473 112/490 Y/H Tac/Cac 1 1 EFCAB3 HGNC HGNC:26379 protein_coding YES CCDS45751.1 ENSP00000403932 Q8N7B9 UPI0001929531 NM_001144933.1 tolerated(0.16) 6/12 PROSITE_profiles:PS50222,hmmpanther:PTHR23050:SF158,hmmpanther:PTHR23050,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 62391848 62391848 T C 1 0 0 0 0 1 0 0 0 4771 1522 53 5 5 EFCAB3 17 62391848 Missense_Mutation SNP T C3N-01488_T 4194637 62391848 20865593 460 24834 TANC2 0 . GRCh38 17 63421349 63421349 + Silent SNP C C A rs200558942 C3N-01488_T C3N-01488_N C C c.5367C>A p.= p.I1789I ENST00000424789 25/25 322 287 35 335 334 1 strelka-varscan-mutect TANC2,synonymous_variant,p.=,ENST00000424789,NM_025185.3;TANC2,synonymous_variant,p.=,ENST00000389520,;TANC2,synonymous_variant,p.=,ENST00000613171,;TANC2,3_prime_UTR_variant,,ENST00000583356,;RP11-269G24.3,intron_variant,,ENST00000583552,; A ENST00000424789 Transcript synonymous_variant 5371/11721 5367/5973 1789/1990 I atC/atA rs200558942 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 25/25 hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs200558942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 63421349 63421349 C A 1 0 0 0 0 0 0 0 1 15942 903 32 2 2 TANC2 17 63421349 Silent SNP C C3N-01488_T 1029501 63421349 19836092 461 24835 LRRC37A3 0 . GRCh38 17 64860117 64860117 + Silent SNP C C T rs555242552 C3N-01488_T C3N-01488_N C C c.4029G>A p.= p.P1343P ENST00000584306 11/14 675 599 76 680 679 1 strelka-varscan-mutect LRRC37A3,synonymous_variant,p.=,ENST00000584306,NM_199340.3;LRRC37A3,synonymous_variant,p.=,ENST00000319651,;LRRC37A3,synonymous_variant,p.=,ENST00000400877,;LRRC37A3,synonymous_variant,p.=,ENST00000334962,;LRRC37A3,synonymous_variant,p.=,ENST00000339474,NM_001303255.1;LRRC37A3,downstream_gene_variant,,ENST00000581368,;LRRC37A3,downstream_gene_variant,,ENST00000584788,;LRRC37A3,upstream_gene_variant,,ENST00000583510,;LRRC37A3,downstream_gene_variant,,ENST00000579305,; T ENST00000584306 Transcript synonymous_variant 4560/5665 4029/4905 1343/1634 P ccG/ccA rs555242552,COSM1522010 1 -1 LRRC37A3 HGNC HGNC:32427 protein_coding YES CCDS32708.1 ENSP00000464535 O60309 UPI00005B2F0A NM_199340.3 11/14 hmmpanther:PTHR23045,hmmpanther:PTHR23045:SF7 0,1 LOW 1 SNV 1 0,1 1 PASS rs555242552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 64860117 64860117 C T 1 0 0 0 0 0 0 0 1 8887 523 19 1 1 LRRC37A3 17 64860117 Silent SNP C C3N-01488_T 1438768 64860117 18397324 462 24836 HELZ 0 . GRCh38 17 67188455 67188455 + Missense_Mutation SNP T T G novel C3N-01488_T C3N-01488_N T T c.1026A>C p.Leu342Phe p.L342F ENST00000358691 12/33 396 356 40 444 444 0 strelka-varscan-mutect HELZ,missense_variant,p.Leu342Phe,ENST00000358691,NM_014877.3;HELZ,missense_variant,p.Leu342Phe,ENST00000580168,;HELZ,upstream_gene_variant,,ENST00000578783,;HELZ,downstream_gene_variant,,ENST00000580662,;HELZ,upstream_gene_variant,,ENST00000578938,;HELZ,missense_variant,p.Leu342Phe,ENST00000579953,;HELZ,missense_variant,p.Leu342Phe,ENST00000417253,;HELZ,non_coding_transcript_exon_variant,,ENST00000582864,; G ENST00000358691 Transcript missense_variant 1193/13810 1026/5829 342/1942 L/F ttA/ttC 1 -1 HELZ HGNC HGNC:16878 protein_coding YES CCDS42374.1 ENSP00000351524 P42694 UPI000013D7F5 NM_014877.3 tolerated(0.08) 12/33 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF365 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 67188455 67188455 T G 1 0 0 0 0 1 0 0 0 6931 1519 53 5 5 HELZ 17 67188455 Missense_Mutation SNP T C3N-01488_T 2328338 67188455 16068986 463 24837 BPTF 0 . GRCh38 17 67903805 67903805 + Missense_Mutation SNP T T G novel C3N-01488_T C3N-01488_N T T c.2560T>G p.Ser854Ala p.S854A ENST00000306378 8/28 76 72 4 106 106 0 varscan-mutect BPTF,missense_variant,p.Ser980Ala,ENST00000321892,NM_004459.6;BPTF,missense_variant,p.Ser854Ala,ENST00000306378,NM_182641.3;BPTF,missense_variant,p.Ser841Ala,ENST00000424123,;BPTF,missense_variant,p.Ser917Ala,ENST00000544778,;BPTF,3_prime_UTR_variant,,ENST00000335221,; G ENST00000306378 Transcript missense_variant 2620/9688 2560/8763 854/2920 S/A Tca/Gca 1 1 BPTF HGNC HGNC:3581 protein_coding YES CCDS11673.1 ENSP00000307208 Q12830 UPI00002263BF NM_182641.3 tolerated(0.65) 8/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF5 MODERATE 1 SNV 1 1 PASS . . 1 201 7 0 0 0 0 0 -9.207429 0.9999953 1 1 1 0 G 3 3 80 67903805 67903805 T G 1 0 0 0 0 1 0 0 0 1664 1435 50 5 5 BPTF 17 67903805 Missense_Mutation SNP T C3N-01488_T 715350 67903805 15353636 464 24838 BPTF 0 . GRCh38 17 67945940 67945940 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.7232A>G p.Asn2411Ser p.N2411S ENST00000306378 21/28 481 423 58 486 485 1 strelka-varscan-mutect BPTF,missense_variant,p.Asn2537Ser,ENST00000321892,NM_004459.6;BPTF,missense_variant,p.Asn2411Ser,ENST00000306378,NM_182641.3;BPTF,intron_variant,,ENST00000424123,;BPTF,intron_variant,,ENST00000342579,;BPTF,intron_variant,,ENST00000580465,;BPTF,downstream_gene_variant,,ENST00000544778,;BPTF,upstream_gene_variant,,ENST00000581258,;RP11-855A2.3,downstream_gene_variant,,ENST00000577385,;BPTF,downstream_gene_variant,,ENST00000577770,;BPTF,downstream_gene_variant,,ENST00000582406,;BPTF,downstream_gene_variant,,ENST00000584931,; G ENST00000306378 Transcript missense_variant 7292/9688 7232/8763 2411/2920 N/S aAt/aGt 1 1 BPTF HGNC HGNC:3581 protein_coding YES CCDS11673.1 ENSP00000307208 Q12830 UPI00002263BF NM_182641.3 tolerated_low_confidence(0.64) 21/28 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 67945940 67945940 A G 1 0 0 0 0 1 0 0 0 1664 101 4 5 5 BPTF 17 67945940 Missense_Mutation SNP A C3N-01488_T 42135 67945940 15311501 465 24839 KIF19 0 . GRCh38 17 74351918 74351918 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1639G>T p.Glu547Ter p.E547* ENST00000389916 13/20 141 96 45 128 128 0 strelka-mutect KIF19,stop_gained,p.Glu547Ter,ENST00000389916,NM_153209.3;KIF19,stop_gained,p.Glu505Ter,ENST00000551294,;BTBD17,downstream_gene_variant,,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000547389,;KIF19,downstream_gene_variant,,ENST00000359939,;KIF19,downstream_gene_variant,,ENST00000549637,; T ENST00000389916 Transcript stop_gained 1777/3643 1639/2997 547/998 E/* Gag/Tag 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 13/20 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF434 HIGH SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 74351918 74351918 G T 1 0 0 0 0 0 1 0 0 8146 1175 41 2 2 KIF19 17 74351918 Nonsense_Mutation SNP G C3N-01488_T 6405978 74351918 8905523 466 24840 MYO15B 0 . GRCh38 17 75592493 75592493 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.2592G>T p.= p.R864R ENST00000610510 6/63 21 17 4 32 32 0 strelka-varscan-mutect MYO15B,synonymous_variant,p.=,ENST00000610510,;MYO15B,upstream_gene_variant,,ENST00000633867,;MYO15B,upstream_gene_variant,,ENST00000584762,;MYO15B,downstream_gene_variant,,ENST00000582561,;MYO15B,downstream_gene_variant,,ENST00000578564,;MYO15B,synonymous_variant,p.=,ENST00000621743,;MYO15B,3_prime_UTR_variant,,ENST00000584516,;MYO15B,non_coding_transcript_exon_variant,,ENST00000581866,;MYO15B,intron_variant,,ENST00000619501,;MYO15B,downstream_gene_variant,,ENST00000581612,;MYO15B,upstream_gene_variant,,ENST00000580701,; T ENST00000610510 Transcript synonymous_variant 2592/9195 2592/9195 864/3064 R cgG/cgT 1 1 MYO15B HGNC HGNC:14083 protein_coding YES ENSP00000488624 A0A0J9YY01 UPI00064546F0 6/63 PROSITE_profiles:PS51456,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs1222752755 . 6 199 5 0 0 0 0 0 -12.20889 1 1 1 1 0 T 2 4 80 75592493 75592493 G T 1 0 0 0 0 0 0 0 1 10064 1219 43 2 2 MYO15B 17 75592493 Silent SNP G C3N-01488_T 1240575 75592493 7664948 467 24841 LGALS3BP 0 . GRCh38 17 78972541 78972542 + Frame_Shift_Ins INS - - A novel C3N-01488_T C3N-01488_N - - c.792dupT p.Ala265CysfsTer73 p.A265Cfs*73 ENST00000262776 6/6 97 85 12 117 117 0 sindel-varindel-pindel LGALS3BP,frameshift_variant,p.Ala265CysfsTer73,ENST00000262776,NM_005567.3;LGALS3BP,frameshift_variant,p.Met180IlefsTer323,ENST00000591778,;LGALS3BP,downstream_gene_variant,,ENST00000585407,;LGALS3BP,downstream_gene_variant,,ENST00000589775,;LGALS3BP,downstream_gene_variant,,ENST00000589527,;LGALS3BP,downstream_gene_variant,,ENST00000589906,;LGALS3BP,downstream_gene_variant,,ENST00000591274,;LGALS3BP,3_prime_UTR_variant,,ENST00000587251,;LGALS3BP,3_prime_UTR_variant,,ENST00000587311,;LGALS3BP,3_prime_UTR_variant,,ENST00000586720,;LGALS3BP,3_prime_UTR_variant,,ENST00000588198,;LGALS3BP,non_coding_transcript_exon_variant,,ENST00000588508,;LGALS3BP,downstream_gene_variant,,ENST00000588587,;LGALS3BP,downstream_gene_variant,,ENST00000587310,;LGALS3BP,downstream_gene_variant,,ENST00000588899,;LGALS3BP,downstream_gene_variant,,ENST00000588990,;LGALS3BP,downstream_gene_variant,,ENST00000588205,;LGALS3BP,downstream_gene_variant,,ENST00000592255,;LGALS3BP,downstream_gene_variant,,ENST00000586300,; A ENST00000262776 Transcript frameshift_variant 1101-1102/2405 792-793/1758 264-265/585 -/X -/T 1 -1 LGALS3BP HGNC HGNC:6564 protein_coding YES CCDS11759.1 ENSP00000262776 Q08380 A0A0S2Z3Y1 UPI000006E64A NM_005567.3 6/6 hmmpanther:PTHR24410,hmmpanther:PTHR24410:SF13,Pfam_domain:PF07707,SMART_domains:SM00875 HIGH 1 insertion 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.99999 0.9999971 1 1 1 0 A 7 5 80 78972541 78972541 - A 1 0 1 1 0 0 0 0 0 8652 710 25 0 0 LGALS3BP 17 78972541 Frame_Shift_Ins INS - C3N-01488_T 3380048 78972541 4284900 468 24842 ENPP7 0 . GRCh38 17 79735557 79735557 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.914C>A p.Pro305His p.P305H ENST00000328313 3/6 470 283 187 401 401 0 strelka-varscan-mutect ENPP7,missense_variant,p.Pro305His,ENST00000328313,NM_178543.4;ENPP7,missense_variant,p.Pro6His,ENST00000576512,; A ENST00000328313 Transcript missense_variant 1135/2043 914/1377 305/458 P/H cCc/cAc 1 1 ENPP7 HGNC HGNC:23764 protein_coding YES CCDS11763.1 ENSP00000332656 Q6UWV6 UPI000019219F NM_178543.4 deleterious(0.02) 3/6 Gene3D:3.40.720.10,Pfam_domain:PF01663,hmmpanther:PTHR10151,hmmpanther:PTHR10151:SF63,Superfamily_domains:SSF53649 MODERATE 1 SNV 1 1 PASS rs1263330435 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 79735557 79735557 C A 1 0 0 0 0 1 0 0 0 4980 623 22 2 2 ENPP7 17 79735557 Missense_Mutation SNP C C3N-01488_T 763016 79735557 3521884 469 24843 CCDC57 0 . GRCh38 17 82101742 82101742 + Silent SNP A A G rs771727603 C3N-01488_T C3N-01488_N A A c.2691T>C p.= p.P897P ENST00000389641 18/18 171 146 25 166 165 1 strelka-varscan-mutect CCDC57,missense_variant,p.Cys210Arg,ENST00000392345,;CCDC57,synonymous_variant,p.=,ENST00000389641,;CCDC57,synonymous_variant,p.=,ENST00000392347,NM_198082.2;CCDC57,intron_variant,,ENST00000583053,;FASN,upstream_gene_variant,,ENST00000306749,NM_004104.4;FASN,upstream_gene_variant,,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000635197,;FASN,upstream_gene_variant,,ENST00000636968,;FASN,upstream_gene_variant,,ENST00000637026,;CCDC57,non_coding_transcript_exon_variant,,ENST00000584717,;CCDC57,downstream_gene_variant,,ENST00000582100,;FASN,upstream_gene_variant,,ENST00000635733,;FASN,upstream_gene_variant,,ENST00000637693,;CCDC57,downstream_gene_variant,,ENST00000583593,; G ENST00000389641 Transcript synonymous_variant 2728/3000 2691/2751 897/916 P ccT/ccC rs771727603 1 -1 CCDC57 HGNC HGNC:27564 protein_coding YES ENSP00000374292 Q2TAC2 UPI000155D557 18/18 LOW SNV 5 1 PASS rs771727603 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 82101742 82101742 A G 1 0 0 0 0 0 0 0 1 2529 175 7 5 5 CCDC57 17 82101742 Silent SNP A C3N-01488_T 2366185 82101742 1155699 470 24844 TGIF1 0 . GRCh38 18 3457438 3457438 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.704A>G p.Asn235Ser p.N235S ENST00000330513 3/3 433 399 34 604 604 0 strelka-varscan-mutect TGIF1,missense_variant,p.Asn120Ser,ENST00000618001,NM_173207.2;TGIF1,missense_variant,p.Asn86Ser,ENST00000472042,;TGIF1,missense_variant,p.Asn106Ser,ENST00000343820,NM_001278684.1,NM_173208.2,NM_003244.3;TGIF1,missense_variant,p.Asn235Ser,ENST00000330513,NM_170695.3;TGIF1,missense_variant,p.Asn86Ser,ENST00000405385,NM_173209.2;TGIF1,missense_variant,p.Asn86Ser,ENST00000401449,NM_174886.2;TGIF1,missense_variant,p.Asn106Ser,ENST00000407501,;TGIF1,missense_variant,p.Asn86Ser,ENST00000548489,NM_001278686.1;TGIF1,missense_variant,p.Asn86Ser,ENST00000400167,NM_173211.1;TGIF1,missense_variant,p.Asn86Ser,ENST00000552383,;TGIF1,missense_variant,p.Asn86Ser,ENST00000345133,;TGIF1,missense_variant,p.Asn86Ser,ENST00000551541,NM_173210.2;TGIF1,missense_variant,p.Asn86Ser,ENST00000549546,;TGIF1,missense_variant,p.Asn86Ser,ENST00000549780,;TGIF1,missense_variant,p.Asn86Ser,ENST00000550958,;TGIF1,missense_variant,p.Asn86Ser,ENST00000551333,;TGIF1,missense_variant,p.Asn86Ser,ENST00000549253,;TGIF1,missense_variant,p.Asn106Ser,ENST00000546979,;TGIF1,missense_variant,p.Asn86Ser,ENST00000549468,;TGIF1,3_prime_UTR_variant,,ENST00000577543,;TGIF1,downstream_gene_variant,,ENST00000551402,; G ENST00000330513 Transcript missense_variant 1007/1980 704/1206 235/401 N/S aAt/aGt 1 1 TGIF1 HGNC HGNC:11776 protein_coding YES CCDS11834.1 ENSP00000327959 Q15583 UPI0000140386 NM_170695.3 deleterious(0.02) 3/3 hmmpanther:PTHR11850,hmmpanther:PTHR11850:SF59,Gene3D:1.10.10.60,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 3457438 3457438 A G 1 0 0 0 0 1 0 0 0 16258 101 4 5 5 TGIF1 18 3457438 Missense_Mutation SNP A C3N-01488_T 3457438 76915847 471 24845 PTPRM 0 . GRCh38 18 8113647 8113647 + Missense_Mutation SNP C C G rs770279168 C3N-01488_T C3N-01488_N C C c.2018C>G p.Ala673Gly p.A673G ENST00000580170 12/33 297 239 58 454 454 0 strelka-varscan-mutect PTPRM,missense_variant,p.Ala673Gly,ENST00000332175,NM_002845.3;PTPRM,missense_variant,p.Ala673Gly,ENST00000580170,NM_001105244.1;PTPRM,missense_variant,p.Ala611Gly,ENST00000400053,;PTPRM,missense_variant,p.Ala146Gly,ENST00000583289,;PTPRM,missense_variant,p.Ala26Gly,ENST00000577468,;PTPRM,5_prime_UTR_variant,,ENST00000400060,;PTPRM,downstream_gene_variant,,ENST00000578571,; G ENST00000580170 Transcript missense_variant 3055/5941 2018/4398 673/1465 A/G gCg/gGg rs770279168,COSM167690,COSM4409859 1 1 PTPRM HGNC HGNC:9675 protein_coding YES CCDS58613.1 ENSP00000463325 P28827 UPI00015CFC03 NM_001105244.1 tolerated(0.07) 12/33 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF206,SMART_domains:SM00060 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs770279168 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 8113647 8113647 C G 1 0 0 0 0 1 0 0 0 12960 768 27 4 4 PTPRM 18 8113647 Missense_Mutation SNP C C3N-01488_T 4656209 8113647 72259638 472 24846 SLC35G4 0 . GRCh38 18 11609630 11609630 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.35A>T p.Asp12Val p.D12V ENST00000636911 1/2 65 55 10 115 115 0 strelka-varscan-mutect SLC35G4,missense_variant,p.Asp12Val,ENST00000636911,;SLC35G4,missense_variant,p.Asp12Val,ENST00000588001,NM_001282300.1; T ENST00000636911 Transcript missense_variant 156/1201 35/1017 12/338 D/V gAc/gTc 1 1 SLC35G4 HGNC HGNC:31043 protein_coding YES ENSP00000489773 UPI0001AE65E0 deleterious(0) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 205 4 0 0 0 0 0 -19.99916 1 1 1 1 0 T 3 4 80 11609630 11609630 A T 1 0 0 0 0 1 0 0 0 14868 275 10 4 4 SLC35G4 18 11609630 Missense_Mutation SNP A C3N-01488_T 3495983 11609630 68763655 473 24847 ZNF519 0 . GRCh38 18 14106110 14106110 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.430A>G p.Lys144Glu p.K144E ENST00000590202 3/3 111 87 24 190 190 0 strelka-varscan-mutect ZNF519,missense_variant,p.Lys144Glu,ENST00000590202,NM_145287.3;ZNF519,intron_variant,,ENST00000589498,;RP11-411B10.3,downstream_gene_variant,,ENST00000592926,;ZNF519,non_coding_transcript_exon_variant,,ENST00000588435,;ZNF519,intron_variant,,ENST00000589203,;ZNF519,intron_variant,,ENST00000591393,;ZNF519,intron_variant,,ENST00000592345,;ZNF519,intron_variant,,ENST00000592411,;ZNF519,intron_variant,,ENST00000592049,;ZNF519,non_coding_transcript_exon_variant,,ENST00000624133,;ZNF519,intron_variant,,ENST00000587419,; C ENST00000590202 Transcript missense_variant 583/2830 430/1623 144/540 K/E Aaa/Gaa 1 -1 ZNF519 HGNC HGNC:30574 protein_coding YES CCDS32797.1 ENSP00000464872 Q8TB69 UPI0000201A41 NM_145287.3 tolerated(0.28) 3/3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 14106110 14106110 T C 1 0 0 0 0 1 0 0 0 18536 1763 61 5 5 ZNF519 18 14106110 Missense_Mutation SNP T C3N-01488_T 2496480 14106110 66267175 474 24848 TCEB3B 0 . GRCh38 18 47033455 47033455 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1810T>A p.Trp604Arg p.W604R ENST00000332567 1/1 276 257 19 409 409 0 strelka-varscan-mutect TCEB3B,missense_variant,p.Trp604Arg,ENST00000332567,NM_016427.2;TCEB3B,missense_variant,p.Trp412Arg,ENST00000620522,;KATNAL2,intron_variant,,ENST00000245121,NM_031303.2;KATNAL2,intron_variant,,ENST00000356157,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,intron_variant,,ENST00000585469,;TCEB3C,upstream_gene_variant,,ENST00000330682,NM_145653.3; T ENST00000332567 Transcript missense_variant 2167/3050 1810/2262 604/753 W/R Tgg/Agg 1 -1 TCEB3B HGNC HGNC:30771 protein_coding YES CCDS11932.1 ENSP00000331302 Q8IYF1 UPI0000140A82 NM_016427.2 deleterious(0) 1/1 hmmpanther:PTHR15141:SF7,hmmpanther:PTHR15141,Pfam_domain:PF06881 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 47033455 47033455 A T 1 0 0 0 0 1 0 0 0 16089 130 5 4 4 TCEB3B 18 47033455 Missense_Mutation SNP A C3N-01488_T 32927345 47033455 33339830 475 24849 TCEB3B 0 . GRCh38 18 47035257 47035257 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.8C>A p.Ala3Glu p.A3E ENST00000332567 1/1 343 279 64 429 428 1 strelka-varscan-mutect TCEB3B,missense_variant,p.Ala3Glu,ENST00000332567,NM_016427.2;TCEB3B,missense_variant,p.Ala3Glu,ENST00000620522,;KATNAL2,intron_variant,,ENST00000245121,NM_031303.2;KATNAL2,intron_variant,,ENST00000356157,;KATNAL2,intron_variant,,ENST00000592005,;KATNAL2,intron_variant,,ENST00000585469,; T ENST00000332567 Transcript missense_variant 365/3050 8/2262 3/753 A/E gCa/gAa 1 -1 TCEB3B HGNC HGNC:30771 protein_coding YES CCDS11932.1 ENSP00000331302 Q8IYF1 UPI0000140A82 NM_016427.2 tolerated(0.07) 1/1 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 47035257 47035257 G T 1 0 0 0 0 1 0 0 0 16089 1319 46 2 2 TCEB3B 18 47035257 Missense_Mutation SNP G C3N-01488_T 1802 47035257 33338028 476 24850 DYM 0 . GRCh38 18 49286544 49286544 + Missense_Mutation SNP G G A C3N-01488_T C3N-01488_N G G c.836C>T p.Pro279Leu p.P279L ENST00000269445 9/17 222 183 39 293 293 0 strelka-varscan-mutect DYM,missense_variant,p.Pro279Leu,ENST00000269445,NM_017653.3;DYM,missense_variant,p.Pro89Leu,ENST00000442713,;DYM,missense_variant,p.Pro124Leu,ENST00000583280,;DYM,missense_variant,p.Pro124Leu,ENST00000584983,;DYM,missense_variant,p.Pro124Leu,ENST00000581738,;DYM,missense_variant,p.Pro123Leu,ENST00000583225,;DYM,non_coding_transcript_exon_variant,,ENST00000580615,;DYM,3_prime_UTR_variant,,ENST00000418472,; A ENST00000269445 Transcript missense_variant 1294/5049 836/2010 279/669 P/L cCt/cTt COSM1388931 1 -1 DYM HGNC HGNC:21317 protein_coding YES CCDS11937.1 ENSP00000269445 Q7RTS9 UPI00001AE953 NM_017653.3 tolerated(0.1) 9/17 Low_complexity_(Seg):seg,hmmpanther:PTHR12895:SF9,hmmpanther:PTHR12895,Pfam_domain:PF09742 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 49286544 49286544 G A 1 0 0 0 0 1 0 0 0 4663 1000 35 3 3 DYM 18 49286544 Missense_Mutation SNP G C3N-01488_T 2251287 49286544 31086741 477 24851 MEX3C 0 . GRCh38 18 51177180 51177180 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1151G>T p.Arg384Leu p.R384L ENST00000406189 2/2 165 150 15 311 310 1 strelka-varscan-mutect MEX3C,missense_variant,p.Arg384Leu,ENST00000406189,NM_016626.4;MEX3C,missense_variant,p.Arg214Leu,ENST00000616921,;MEX3C,non_coding_transcript_exon_variant,,ENST00000591040,; A ENST00000406189 Transcript missense_variant 1151/3781 1151/1980 384/659 R/L cGg/cTg 1 -1 MEX3C HGNC HGNC:28040 protein_coding YES CCDS11951.2 ENSP00000385610 Q5U5Q3 UPI00005956CD NM_016626.4 deleterious(0) 2/2 PROSITE_profiles:PS50084,hmmpanther:PTHR23285:SF8,hmmpanther:PTHR23285,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS rs1211176379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 51177180 51177180 C A 1 0 0 0 0 1 0 0 0 9464 652 23 1 1 MEX3C 18 51177180 Missense_Mutation SNP C C3N-01488_T 1890636 51177180 29196105 478 24852 ALPK2 0 . GRCh38 18 58580408 58580408 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.368G>A p.Arg123Lys p.R123K ENST00000361673 4/13 300 280 20 469 468 1 strelka-varscan-mutect ALPK2,missense_variant,p.Arg123Lys,ENST00000361673,NM_052947.3;ALPK2,non_coding_transcript_exon_variant,,ENST00000590642,;ALPK2,upstream_gene_variant,,ENST00000587399,;ALPK2,upstream_gene_variant,,ENST00000587842,;ALPK2,upstream_gene_variant,,ENST00000590662,; T ENST00000361673 Transcript missense_variant 582/7303 368/6513 123/2170 R/K aGg/aAg 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(0.11) 4/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 58580408 58580408 C T 1 0 0 0 0 1 0 0 0 645 681 24 3 3 ALPK2 18 58580408 Missense_Mutation SNP C C3N-01488_T 7403228 58580408 21792877 479 24853 CDH20 0 . GRCh38 18 61549979 61549979 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1650T>A p.Asp550Glu p.D550E ENST00000262717 11/12 97 80 17 133 133 0 strelka-varscan-mutect CDH20,missense_variant,p.Asp550Glu,ENST00000262717,;CDH20,missense_variant,p.Asp550Glu,ENST00000536675,NM_031891.2;CDH20,missense_variant,p.Asp550Glu,ENST00000538374,;CDH20,non_coding_transcript_exon_variant,,ENST00000587582,; A ENST00000262717 Transcript missense_variant,splice_region_variant 2048/3882 1650/2406 550/801 D/E gaT/gaA 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D deleterious(0.02) 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 61549979 61549979 T A 1 0 0 0 0 1 0 0 0 2809 1420 49 4 4 CDH20 18 61549979 Missense_Mutation SNP T C3N-01488_T 2969571 61549979 18823306 480 24854 SERPINB10 0 . GRCh38 18 63919898 63919898 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.483G>A p.= p.Q161Q ENST00000238508 5/8 127 116 11 176 176 0 strelka-varscan-mutect SERPINB10,synonymous_variant,p.=,ENST00000238508,;SERPINB10,synonymous_variant,p.=,ENST00000619595,NM_005024.1;SERPINB10,downstream_gene_variant,,ENST00000397996,;SERPINB10,downstream_gene_variant,,ENST00000418725,; A ENST00000238508 Transcript synonymous_variant 542/2122 483/1194 161/397 Q caG/caA 1 1 SERPINB10 HGNC HGNC:8942 protein_coding YES CCDS11990.1 ENSP00000238508 P48595 UPI000013558E 5/8 Gene3D:3.30.497.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF175,SMART_domains:SM00093,Superfamily_domains:SSF56574 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 63919898 63919898 G A 1 0 0 0 0 0 0 0 1 14373 933 33 3 3 SERPINB10 18 63919898 Silent SNP G C3N-01488_T 2369919 63919898 16453387 481 24855 SALL3 0 . GRCh38 18 78994247 78994247 + Silent SNP G G T rs112670102 C3N-01488_T C3N-01488_N G G c.2256G>T p.= p.V752V ENST00000537592 2/3 192 179 13 286 286 0 strelka-varscan-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000536229,;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,synonymous_variant,p.=,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript synonymous_variant 2256/6555 2256/3903 752/1300 V gtG/gtT rs112670102 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46,PROSITE_patterns:PS00028,Pfam_domain:PF12874,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS rs112670102 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 78994247 78994247 G T 1 0 0 0 0 0 0 0 1 14071 1335 47 2 2 SALL3 18 78994247 Silent SNP G C3N-01488_T 15074349 78994247 1379038 482 24856 SALL3 0 . GRCh38 18 78994697 78994697 + Silent SNP G G T rs763229465 C3N-01488_T C3N-01488_N G G c.2706G>T p.= p.S902S ENST00000537592 2/3 201 185 16 240 238 2 strelka-varscan-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000536229,;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,synonymous_variant,p.=,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; T ENST00000537592 Transcript synonymous_variant 2706/6555 2706/3903 902/1300 S tcG/tcT rs763229465,COSM5056143 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 0,1 LOW 1 SNV 5 0,1 1 PASS rs763229465 . 0 206 0 4 0 0 0 0 -19.88011 0.999711 1 1 1 0 T 2 4 80 78994697 78994697 G T 1 0 0 0 0 0 0 0 1 14071 1074 38 1 1 SALL3 18 78994697 Silent SNP G C3N-01488_T 450 78994697 1378588 483 24857 HCN2 0 . GRCh38 19 590399 590399 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.454G>C p.Ala152Pro p.A152P ENST00000251287 1/8 60 32 28 61 61 0 strelka-varscan-mutect HCN2,missense_variant,p.Ala152Pro,ENST00000251287,NM_001194.3;AC005559.3,downstream_gene_variant,,ENST00000589661,; C ENST00000251287 Transcript missense_variant 507/3408 454/2670 152/889 A/P Gcg/Ccg 1 1 HCN2 HGNC HGNC:4846 protein_coding YES CCDS12035.1 ENSP00000251287 Q9UL51 UPI000013CCF6 NM_001194.3 tolerated(0.2) 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF372 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 590399 590399 G C 1 0 0 0 0 1 0 0 0 6884 1203 42 4 4 HCN2 19 590399 Missense_Mutation SNP G C3N-01488_T 590399 58027217 484 24858 SBNO2 0 . GRCh38 19 1117441 1117441 + Missense_Mutation SNP C C A rs770290202 C3N-01488_T C3N-01488_N C C c.1586G>T p.Arg529Leu p.R529L ENST00000361757 15/32 248 231 17 259 259 0 strelka-varscan-mutect SBNO2,missense_variant,p.Arg529Leu,ENST00000361757,NM_014963.2;SBNO2,missense_variant,p.Arg519Leu,ENST00000587024,;SBNO2,missense_variant,p.Arg472Leu,ENST00000438103,NM_001100122.1;SBNO2,non_coding_transcript_exon_variant,,ENST00000592222,;SBNO2,non_coding_transcript_exon_variant,,ENST00000590446,; A ENST00000361757 Transcript missense_variant 1824/4923 1586/4101 529/1366 R/L cGc/cTc rs770290202 1 -1 SBNO2 HGNC HGNC:29158 protein_coding YES CCDS45894.1 ENSP00000354733 Q9Y2G9 UPI0000140680 NM_014963.2 deleterious(0) 15/32 hmmpanther:PTHR12706,hmmpanther:PTHR12706:SF5 MODERATE 1 SNV 1 1 PASS rs770290202 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 1117441 1117441 C A 1 0 0 0 0 1 0 0 0 14128 768 27 1 1 SBNO2 19 1117441 Missense_Mutation SNP C C3N-01488_T 527042 1117441 57500175 485 24859 ADAMTSL5 0 . GRCh38 19 1510911 1510911 + Silent SNP G G A novel C3N-01488_T C3N-01488_N G G c.33C>T p.= p.H11H ENST00000330475 2/12 35 31 4 35 35 0 strelka-mutect ADAMTSL5,synonymous_variant,p.=,ENST00000330475,NM_213604.2;ADAMTSL5,synonymous_variant,p.=,ENST00000586272,;ADAMTSL5,synonymous_variant,p.=,ENST00000585804,;ADAMTSL5,synonymous_variant,p.=,ENST00000590562,;ADAMTSL5,5_prime_UTR_variant,,ENST00000395467,;ADAMTSL5,upstream_gene_variant,,ENST00000590090,;CTB-25B13.9,downstream_gene_variant,,ENST00000590252,;ADAMTSL5,non_coding_transcript_exon_variant,,ENST00000590440,;ADAMTSL5,non_coding_transcript_exon_variant,,ENST00000585700,;ADAMTSL5,non_coding_transcript_exon_variant,,ENST00000589839,;ADAMTSL5,upstream_gene_variant,,ENST00000591077,;ADAMTSL5,upstream_gene_variant,,ENST00000590682,; A ENST00000330475 Transcript synonymous_variant 477/2857 33/1416 11/471 H caC/caT 1 -1 ADAMTSL5 HGNC HGNC:27912 protein_coding YES CCDS12071.1 ENSP00000327608 X6R4H8 UPI00001D8216 NM_213604.2 2/12 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 2 1 PASS rs1264249475 . 0 203 6 0 0 0 0 0 -10.97896 0.9999999 1 1 1 0 A 2 1 80 1510911 1510911 G A 1 0 0 0 0 0 0 0 1 322 1252 44 3 3 ADAMTSL5 19 1510911 Silent SNP G C3N-01488_T 393470 1510911 57106705 486 24860 KLF16 0 . GRCh38 19 1854486 1854486 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.732G>T p.= p.A244A ENST00000250916 2/2 50 46 4 78 78 0 varscan-mutect KLF16,synonymous_variant,p.=,ENST00000250916,NM_031918.3;KLF16,synonymous_variant,p.=,ENST00000617223,;KLF16,synonymous_variant,p.=,ENST00000592313,;CTB-31O20.6,downstream_gene_variant,,ENST00000592884,;KLF16,synonymous_variant,p.=,ENST00000541015,; A ENST00000250916 Transcript synonymous_variant 803/2890 732/759 244/252 A gcG/gcT 1 -1 KLF16 HGNC HGNC:16857 protein_coding YES CCDS12075.1 ENSP00000250916 Q9BXK1 UPI0000126B0D NM_031918.3 2/2 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs971035483 . 0 200 8 2 0 0 0 0 -8.308864 0.9990711 1 1 1 0 A 2 1 80 1854486 1854486 C A 1 0 0 0 0 0 0 0 1 8209 755 27 1 1 KLF16 19 1854486 Silent SNP C C3N-01488_T 343575 1854486 56763130 487 24861 AP3D1 0 . GRCh38 19 2111287 2111287 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.2983A>G p.Met995Val p.M995V ENST00000355272 26/32 180 145 35 206 206 0 strelka-varscan-mutect AP3D1,missense_variant,p.Met995Val,ENST00000355272,NM_001261826.1;AP3D1,missense_variant,p.Met933Val,ENST00000345016,NM_003938.6;AP3D1,upstream_gene_variant,,ENST00000586370,;AP3D1,upstream_gene_variant,,ENST00000589369,;AP3D1,downstream_gene_variant,,ENST00000591631,;AP3D1,splice_region_variant,,ENST00000591650,;AP3D1,non_coding_transcript_exon_variant,,ENST00000585652,;AP3D1,non_coding_transcript_exon_variant,,ENST00000589223,;AP3D1,downstream_gene_variant,,ENST00000592488,; C ENST00000355272 Transcript missense_variant,splice_region_variant 3190/5034 2983/3648 995/1215 M/V Atg/Gtg 1 -1 AP3D1 HGNC HGNC:568 protein_coding YES CCDS58638.1 ENSP00000347416 O14617 UPI0000202F99 NM_001261826.1 tolerated(0.28) 26/32 hmmpanther:PTHR22781 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 2111287 2111287 T C 1 0 0 0 0 1 0 0 0 862 1507 52 5 5 AP3D1 19 2111287 Missense_Mutation SNP T C3N-01488_T 256801 2111287 56506329 488 24862 ATCAY 0 . GRCh38 19 3907790 3907790 + Frame_Shift_Del DEL G G - rs761078143 C3N-01488_T C3N-01488_N G G c.418delG p.Asp140ThrfsTer18 p.D140Tfs*18 ENST00000450849 5/13 516 311 205 594 592 2 sindel-varindel-pindel ATCAY,frameshift_variant,p.Asp140ThrfsTer18,ENST00000450849,NM_033064.4;ATCAY,frameshift_variant,p.Asp140ThrfsTer18,ENST00000600960,;ATCAY,downstream_gene_variant,,ENST00000598136,;ATCAY,3_prime_UTR_variant,,ENST00000597739,; - ENST00000450849 Transcript frameshift_variant 882/5070 415/1116 139/371 G/X Ggg/gg rs761078143 1 1 ATCAY HGNC HGNC:779 protein_coding YES CCDS45923.1 ENSP00000390941 Q86WG3 A0A0S2Z5T8 UPI000006DE3B NM_033064.4 5/13 Pfam_domain:PF12496,hmmpanther:PTHR12112,hmmpanther:PTHR12112:SF9 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 3907790 3907790 G - 1 0 1 0 1 0 0 0 0 1226 1348 47 0 0 ATCAY 19 3907790 Frame_Shift_Del DEL G C3N-01488_T 1796503 3907790 54709826 489 24863 OR2Z1 0 . GRCh38 19 8731102 8731102 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.74A>T p.Gln25Leu p.Q25L ENST00000324060 1/1 342 316 26 390 390 0 strelka-varscan-mutect OR2Z1,missense_variant,p.Gln25Leu,ENST00000324060,NM_001004699.2;RPL23AP78,upstream_gene_variant,,ENST00000599928,; T ENST00000324060 Transcript missense_variant 149/1056 74/945 25/314 Q/L cAg/cTg 1 1 OR2Z1 HGNC HGNC:15391 protein_coding YES CCDS32895.1 ENSP00000316284 Q8NG97 A0A126GVT8 UPI000003F225 NM_001004699.2 tolerated(0.98) 1/1 hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF96,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 8731102 8731102 A T 1 0 0 0 0 1 0 0 0 11113 188 7 4 4 OR2Z1 19 8731102 Missense_Mutation SNP A C3N-01488_T 4823312 8731102 49886514 490 24864 MUC16 0 . GRCh38 19 8945898 8945898 + Missense_Mutation SNP G G T rs749147041 C3N-01488_T C3N-01488_N G G c.30872C>A p.Thr10291Asn p.T10291N ENST00000397910 3/84 81 54 27 103 102 1 strelka-varscan-mutect MUC16,missense_variant,p.Thr10291Asn,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 31076/43816 30872/43524 10291/14507 T/N aCc/aAc rs749147041,COSM3542138,COSM3542139 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs749147041 . 0 201 9 0 0 0 0 0 -20 0.9999987 1 1 1 0 T 3 4 80 8945898 8945898 G T 1 0 0 0 0 1 0 0 0 9972 1261 44 2 2 MUC16 19 8945898 Missense_Mutation SNP G C3N-01488_T 214796 8945898 49671718 491 24865 MUC16 0 . GRCh38 19 8947546 8947546 + Missense_Mutation SNP C C A rs765870616 C3N-01488_T C3N-01488_N C C c.29224G>T p.Val9742Leu p.V9742L ENST00000397910 3/84 200 133 67 274 273 1 strelka-varscan-mutect MUC16,missense_variant,p.Val9742Leu,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 29428/43816 29224/43524 9742/14507 V/L Gtg/Ttg rs765870616 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs765870616 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 8947546 8947546 C A 1 0 0 0 0 1 0 0 0 9972 478 17 2 2 MUC16 19 8947546 Missense_Mutation SNP C C3N-01488_T 1648 8947546 49670070 492 24866 COL5A3 0 . GRCh38 19 9977266 9977266 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.3251C>A p.Pro1084His p.P1084H ENST00000264828 44/67 245 171 74 240 240 0 strelka-varscan-mutect COL5A3,missense_variant,p.Pro1084His,ENST00000264828,NM_015719.3; T ENST00000264828 Transcript missense_variant 3337/6174 3251/5238 1084/1745 P/H cCc/cAc 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 deleterious(0.03) 44/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 9977266 9977266 G T 1 0 0 0 0 1 0 0 0 3487 1232 43 2 2 COL5A3 19 9977266 Missense_Mutation SNP G C3N-01488_T 1029720 9977266 48640350 493 24867 ICAM5 0 . GRCh38 19 10291303 10291303 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.314G>T p.Arg105Leu p.R105L ENST00000221980 2/11 192 174 18 207 205 2 strelka-varscan-mutect ICAM5,missense_variant,p.Arg105Leu,ENST00000221980,NM_003259.3;ICAM5,5_prime_UTR_variant,,ENST00000587398,;ICAM1,downstream_gene_variant,,ENST00000264832,NM_000201.2;ICAM4,downstream_gene_variant,,ENST00000393717,NM_022377.3;ICAM4,downstream_gene_variant,,ENST00000380770,NM_001544.4;ICAM4,downstream_gene_variant,,ENST00000340992,NM_001039132.2;CTD-2369P2.8,upstream_gene_variant,,ENST00000589379,;ICAM5,non_coding_transcript_exon_variant,,ENST00000586004,;ICAM5,upstream_gene_variant,,ENST00000586480,;ICAM5,downstream_gene_variant,,ENST00000588912,; T ENST00000221980 Transcript missense_variant 377/3000 314/2775 105/924 R/L cGg/cTg 1 1 ICAM5 HGNC HGNC:5348 protein_coding YES CCDS12233.1 ENSP00000221980 Q9UMF0 UPI000013C7E4 NM_003259.3 tolerated(0.24) 2/11 Gene3D:2.60.40.10,Pfam_domain:PF03921,hmmpanther:PTHR13771,hmmpanther:PTHR13771:SF9,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1184663874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 10291303 10291303 G T 1 0 0 0 0 1 0 0 0 7383 1116 39 1 1 ICAM5 19 10291303 Missense_Mutation SNP G C3N-01488_T 314037 10291303 48326313 494 24868 CACNA1A 0 . GRCh38 19 13214303 13214303 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.5870C>A p.Ala1957Glu p.A1957E ENST00000360228 40/47 313 232 81 363 363 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Ala1958Glu,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000635895,;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000637769,;CACNA1A,missense_variant,p.Ala1957Glu,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Ala1963Glu,ENST00000614285,;CACNA1A,missense_variant,p.Ala1911Glu,ENST00000637736,;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000636389,;CACNA1A,missense_variant,p.Ala1963Glu,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Ala1963Glu,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Ala1959Glu,ENST00000573710,;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000635727,;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000636012,;CACNA1A,missense_variant,p.Ala1958Glu,ENST00000637276,;CACNA1A,missense_variant,p.Ala1959Glu,ENST00000637927,;CACNA1A,missense_variant,p.Ala1960Glu,ENST00000636549,NM_001174080.1;CACNA1A,missense_variant,p.Ala444Glu,ENST00000587525,;CACNA1A,missense_variant,p.Ala344Glu,ENST00000585802,;CACNA1A,missense_variant,p.Ala247Glu,ENST00000636473,;CACNA1A,missense_variant,p.Ala425Glu,ENST00000637819,;CACNA1A,3_prime_UTR_variant,,ENST00000636768,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636610,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635988,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000636074,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000638114,;CACNA1A,downstream_gene_variant,,ENST00000586190,; T ENST00000360228 Transcript missense_variant 6105/8627 5870/7521 1957/2506 A/E gCa/gAa 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0.01) 40/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF08763,SMART_domains:SM01062 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 13214303 13214303 G T 1 0 0 0 0 1 0 0 0 2226 1319 46 2 2 CACNA1A 19 13214303 Missense_Mutation SNP G C3N-01488_T 2923000 13214303 45403313 495 24869 NOTCH3 0 . GRCh38 19 15170344 15170344 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.5101G>T p.Ala1701Ser p.A1701S ENST00000263388 27/33 293 191 102 285 285 0 strelka-varscan-mutect NOTCH3,missense_variant,p.Ala1701Ser,ENST00000263388,NM_000435.2;NOTCH3,upstream_gene_variant,,ENST00000597756,;NOTCH3,upstream_gene_variant,,ENST00000595514,; A ENST00000263388 Transcript missense_variant 5177/8666 5101/6966 1701/2321 A/S Gcg/Tcg COSM5454696,COSM5454697 1 -1 NOTCH3 HGNC HGNC:7883 protein_coding YES CCDS12326.1 ENSP00000263388 Q9UM47 UPI000013D3FA NM_000435.2 tolerated(0.84) 27/33 hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF57 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 15170344 15170344 C A 1 0 0 0 0 1 0 0 0 10595 768 27 1 1 NOTCH3 19 15170344 Missense_Mutation SNP C C3N-01488_T 1956041 15170344 43447272 496 24870 TMEM59L 0 . GRCh38 19 18617069 18617069 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.631G>T p.Gly211Cys p.G211C ENST00000600490 6/9 231 142 89 234 234 0 strelka-varscan-mutect TMEM59L,missense_variant,p.Gly211Cys,ENST00000600490,;TMEM59L,missense_variant,p.Gly211Cys,ENST00000262817,NM_012109.2;TMEM59L,missense_variant,p.Gly75Cys,ENST00000594709,;TMEM59L,non_coding_transcript_exon_variant,,ENST00000598660,;TMEM59L,non_coding_transcript_exon_variant,,ENST00000594859,; T ENST00000600490 Transcript missense_variant 816/1717 631/1029 211/342 G/C Ggc/Tgc 1 1 TMEM59L HGNC HGNC:13237 protein_coding YES CCDS12383.1 ENSP00000470879 Q9UK28 A0A024R7L4 UPI0000034024 deleterious(0.03) 6/9 hmmpanther:PTHR28652:SF1,hmmpanther:PTHR28652,Pfam_domain:PF12280 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 18617069 18617069 G T 1 0 0 0 0 1 0 0 0 16662 1000 35 2 2 TMEM59L 19 18617069 Missense_Mutation SNP G C3N-01488_T 3446725 18617069 40000547 497 24871 ZNF729 0 . GRCh38 19 22316927 22316927 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3510C>A p.Asn1170Lys p.N1170K ENST00000601693 4/4 348 216 132 554 554 0 strelka-varscan-mutect ZNF729,missense_variant,p.Asn1170Lys,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript missense_variant 3628/3877 3510/3759 1170/1252 N/K aaC/aaA 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 tolerated(0.67) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS rs1248180516 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 22316927 22316927 C A 1 0 0 0 0 1 0 0 0 18703 506 18 2 2 ZNF729 19 22316927 Missense_Mutation SNP C C3N-01488_T 3699858 22316927 36300689 498 24872 ZNF98 0 . GRCh38 19 22422214 22422214 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.11C>A p.Pro4His p.P4H ENST00000357774 1/4 314 211 103 414 414 0 strelka-varscan-mutect ZNF98,missense_variant,p.Pro4His,ENST00000357774,NM_001098626.1;ZNF98,missense_variant,p.Pro4His,ENST00000601553,;ZNF98,intron_variant,,ENST00000593657,;ZNF98,intron_variant,,ENST00000593802,;AC011516.1,upstream_gene_variant,,ENST00000599129,; T ENST00000357774 Transcript missense_variant 133/2338 11/1719 4/572 P/H cCc/cAc 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 tolerated_low_confidence(0.19) 1/4 MODERATE 1 SNV 3 1 PASS rs1232951359 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 22422214 22422214 G T 1 0 0 0 0 1 0 0 0 18796 1232 43 2 2 ZNF98 19 22422214 Missense_Mutation SNP G C3N-01488_T 105287 22422214 36195402 499 24873 ZNF536 0 . GRCh38 19 30548245 30548245 + Missense_Mutation SNP A A T rs779112682 C3N-01488_T C3N-01488_N A A c.2626A>T p.Met876Leu p.M876L ENST00000355537 4/5 155 141 14 214 214 0 strelka-varscan-mutect ZNF536,missense_variant,p.Met876Leu,ENST00000355537,NM_014717.1;ZNF536,missense_variant,p.Met876Leu,ENST00000585628,;ZNF536,upstream_gene_variant,,ENST00000592773,; T ENST00000355537 Transcript missense_variant 2773/4945 2626/3903 876/1300 M/L Atg/Ttg rs779112682 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 tolerated(0.66) 4/5 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5 MODERATE 1 SNV 1 1 PASS rs779112682 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 30548245 30548245 A T 1 0 0 0 0 1 0 0 0 18547 217 8 4 4 ZNF536 19 30548245 Missense_Mutation SNP A C3N-01488_T 8126031 30548245 28069371 500 24874 PEPD 0 . GRCh38 19 33413599 33413599 + Missense_Mutation SNP C C T novel C3N-01488_T C3N-01488_N C C c.716G>A p.Ser239Asn p.S239N ENST00000244137 10/15 312 260 52 294 294 0 strelka-varscan-mutect PEPD,missense_variant,p.Ser239Asn,ENST00000244137,NM_000285.3;PEPD,missense_variant,p.Ser198Asn,ENST00000397032,NM_001166056.1;PEPD,missense_variant,p.Ser175Asn,ENST00000436370,NM_001166057.1;PEPD,missense_variant,p.Ser70Asn,ENST00000588328,;PEPD,missense_variant,p.Ser50Asn,ENST00000609145,;PEPD,non_coding_transcript_exon_variant,,ENST00000590731,;PEPD,non_coding_transcript_exon_variant,,ENST00000588719,;PEPD,non_coding_transcript_exon_variant,,ENST00000593163,; T ENST00000244137 Transcript missense_variant 750/1910 716/1482 239/493 S/N aGc/aAc 1 -1 PEPD HGNC HGNC:8840 protein_coding YES CCDS42544.1 ENSP00000244137 P12955 A0A140VJR2 UPI000006F8BF NM_000285.3 tolerated(0.17) 10/15 hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF100,Pfam_domain:PF00557,Gene3D:3.90.230.10,Superfamily_domains:SSF55920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 33413599 33413599 C T 1 0 0 0 0 1 0 0 0 11816 797 28 3 3 PEPD 19 33413599 Missense_Mutation SNP C C3N-01488_T 2865354 33413599 25204017 501 24875 KMT2B 0 . GRCh38 19 35720951 35720951 + Missense_Mutation SNP G G T rs527331134 C3N-01488_T C3N-01488_N G G c.1604G>T p.Arg535Leu p.R535L ENST00000420124 3/37 206 181 25 265 265 0 strelka-varscan-mutect KMT2B,missense_variant,p.Arg535Leu,ENST00000420124,NM_014727.2;ZBTB32,downstream_gene_variant,,ENST00000392197,;ZBTB32,downstream_gene_variant,,ENST00000262630,NM_014383.1;ZBTB32,downstream_gene_variant,,ENST00000426659,;KMT2B,intron_variant,,ENST00000606995,;ZBTB32,downstream_gene_variant,,ENST00000481182,; T ENST00000420124 Transcript missense_variant 1604/8469 1604/8148 535/2715 R/L cGc/cTc rs527331134 1 1 KMT2B HGNC HGNC:15840 protein_coding YES CCDS46055.1 ENSP00000398837 Q9UMN6 UPI00001376B5 NM_014727.2 deleterious(0.05) 3/37 MODERATE 1 SNV 1 1 PASS rs527331134 . 0 205 0 3 2 0 0 0 -11.01273 0.9617861 1 1 1 0 T 3 4 80 35720951 35720951 G T 1 0 0 0 0 1 0 0 0 8296 1087 38 1 1 KMT2B 19 35720951 Missense_Mutation SNP G C3N-01488_T 2307352 35720951 22896665 502 24876 SPTBN4 0 . GRCh38 19 40556167 40556167 + Missense_Mutation SNP T T C novel C3N-01488_T C3N-01488_N T T c.5168T>C p.Leu1723Pro p.L1723P ENST00000352632 25/36 136 124 12 169 169 0 strelka-mutect SPTBN4,missense_variant,p.Leu1723Pro,ENST00000338932,;SPTBN4,missense_variant,p.Leu1723Pro,ENST00000352632,;SPTBN4,missense_variant,p.Leu1723Pro,ENST00000392025,;SPTBN4,missense_variant,p.Leu1723Pro,ENST00000598249,NM_020971.2;SPTBN4,missense_variant,p.Leu1723Pro,ENST00000595535,;SPTBN4,missense_variant,p.Leu399Pro,ENST00000392023,NM_025213.2;SPTBN4,3_prime_UTR_variant,,ENST00000597389,;SPTBN4,downstream_gene_variant,,ENST00000596900,; C ENST00000352632 Transcript missense_variant 5254/8676 5168/7695 1723/2564 L/P cTg/cCg 1 1 SPTBN4 HGNC HGNC:14896 protein_coding YES CCDS12559.1 ENSP00000263373 Q9H254 UPI0000135DBB deleterious(0) 25/36 Gene3D:1.20.58.60,Pfam_domain:PF00435,PIRSF_domain:PIRSF002297,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF232,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 40556167 40556167 T C 1 0 0 0 0 1 0 0 0 15477 1580 55 5 5 SPTBN4 19 40556167 Missense_Mutation SNP T C3N-01488_T 4835216 40556167 18061449 503 24877 CYP2F1 0 . GRCh38 19 41127957 41127957 + Missense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.1351A>T p.Thr451Ser p.T451S ENST00000331105 10/10 123 113 10 174 173 1 varscan-mutect CYP2F1,missense_variant,p.Thr451Ser,ENST00000331105,NM_000774.3;CYP2F1,3_prime_UTR_variant,,ENST00000439903,;CYP2F1,3_prime_UTR_variant,,ENST00000532164,;CYP2F1,downstream_gene_variant,,ENST00000531409,;CYP2F1,downstream_gene_variant,,ENST00000526093,;CYP2F1,downstream_gene_variant,,ENST00000534009,; T ENST00000331105 Transcript missense_variant 1423/1720 1351/1476 451/491 T/S Acc/Tcc 1 1 CYP2F1 HGNC HGNC:2632 protein_coding YES CCDS12572.1 ENSP00000333534 P24903 UPI000013C622 NM_000774.3 tolerated(0.05) 10/10 hmmpanther:PTHR24300:SF163,hmmpanther:PTHR24300,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 41127957 41127957 A T 1 0 0 0 0 1 0 0 0 3974 159 6 4 4 CYP2F1 19 41127957 Missense_Mutation SNP A C3N-01488_T 571790 41127957 17489659 504 24878 HIF3A 0 . GRCh38 19 46312601 46312601 + Missense_Mutation SNP G G A rs747603903 C3N-01488_T C3N-01488_N G G c.973G>A p.Gly325Arg p.G325R ENST00000377670 8/15 65 48 17 98 98 0 strelka-varscan-mutect HIF3A,missense_variant,p.Gly325Arg,ENST00000377670,NM_152795.3;HIF3A,missense_variant,p.Gly323Arg,ENST00000300862,NM_152794.3;HIF3A,missense_variant,p.Gly256Arg,ENST00000244303,NM_022462.4;HIF3A,missense_variant,p.Gly256Arg,ENST00000600383,;HIF3A,missense_variant,p.Gly256Arg,ENST00000472815,NM_152796.2;HIF3A,downstream_gene_variant,,ENST00000533145,;HIF3A,downstream_gene_variant,,ENST00000525854,;HIF3A,3_prime_UTR_variant,,ENST00000528563,;HIF3A,3_prime_UTR_variant,,ENST00000531043,;HIF3A,non_coding_transcript_exon_variant,,ENST00000244302,;HIF3A,non_coding_transcript_exon_variant,,ENST00000291300,;HIF3A,non_coding_transcript_exon_variant,,ENST00000475432,;HIF3A,downstream_gene_variant,,ENST00000600879,;HIF3A,downstream_gene_variant,,ENST00000533789,;HIF3A,downstream_gene_variant,,ENST00000529205,;HIF3A,downstream_gene_variant,,ENST00000526506,; A ENST00000377670 Transcript missense_variant 1004/5852 973/2010 325/669 G/R Ggg/Agg rs747603903,COSM296914 1 1 HIF3A HGNC HGNC:15825 protein_coding YES CCDS12681.2 ENSP00000366898 Q9Y2N7 UPI00002026E2 NM_152795.3 deleterious(0.01) 8/15 hmmpanther:PTHR23043:SF18,hmmpanther:PTHR23043,Gene3D:3.30.450.20,Pfam_domain:PF14598,SMART_domains:SM00086,Superfamily_domains:SSF55785 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs747603903 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 46312601 46312601 G A 1 0 0 0 0 1 0 0 0 6990 1000 35 3 3 HIF3A 19 46312601 Missense_Mutation SNP G C3N-01488_T 5184644 46312601 12305015 505 24879 PPP5D1 0 . GRCh38 19 46526988 46526988 + Missense_Mutation SNP G G A rs754415342 C3N-01488_T C3N-01488_N G G c.135C>T p.Arg46Trp p.R46W ENST00000602017 2/4 243 223 20 271 270 1 varscan-mutect PPP5D1,missense_variant,p.Arg58Trp,ENST00000414155,;PPP5D1,missense_variant,p.Arg46Trp,ENST00000602017,NM_001205281.1;PPP5D1,missense_variant,p.Arg46Trp,ENST00000593359,; A ENST00000602017 Transcript missense_variant 135/965 136/378 46/125 R/W Cgg/Tgg rs754415342,COSM3105494,COSM3105495 1 -1 PPP5D1 HGNC HGNC:44209 protein_coding YES ENSP00000471730 M0R196 UPI0002A471E1 NM_001205281.1 deleterious(0) 2/4 Pfam_domain:PF08321 0,1,1 MODERATE 1 SNV 3 0,1,1 1 PASS rs754415342 . 0 207 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 80 46526988 46526988 G A 1 0 0 0 0 1 0 0 0 12532 1086 38 1 1 PPP5D1 19 46526988 Missense_Mutation SNP G C3N-01488_T 214387 46526988 12090628 506 24880 MYH14 0 . GRCh38 19 50257359 50257359 + Missense_Mutation SNP G G C rs775328084 C3N-01488_T C3N-01488_N G G c.2105G>C p.Arg702Pro p.R702P ENST00000601313 18/43 115 94 21 142 142 0 strelka-varscan-mutect MYH14,missense_variant,p.Arg702Pro,ENST00000601313,NM_001145809.1;MYH14,missense_variant,p.Arg669Pro,ENST00000425460,NM_001077186.1;MYH14,missense_variant,p.Arg661Pro,ENST00000376970,NM_024729.3;MYH14,missense_variant,p.Arg669Pro,ENST00000598205,;MYH14,missense_variant,p.Arg661Pro,ENST00000596571,;MYH14,missense_variant,p.Arg669Pro,ENST00000599920,;MYH14,intron_variant,,ENST00000440075,;Metazoa_SRP,upstream_gene_variant,,ENST00000622099,; C ENST00000601313 Transcript missense_variant 2135/6896 2105/6111 702/2036 R/P cGc/cCc rs775328084,COSM3960307,COSM3960308,COSM3960309 1 1 MYH14 HGNC HGNC:23212 protein_coding YES CCDS54295.1 ENSP00000470298 Q7Z406 UPI0001641C2F NM_001145809.1 deleterious(0.02) 18/43 Low_complexity_(Seg):seg,PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF462,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs775328084 . 0 198 6 6 0 0 0 0 -20 0.993454 1 1 1 0 C 3 2 80 50257359 50257359 G C 1 0 0 0 0 1 0 0 0 10033 1087 38 4 4 MYH14 19 50257359 Missense_Mutation SNP G C3N-01488_T 3730371 50257359 8360257 507 24881 LRRC4B 0 . GRCh38 19 50519062 50519062 + Nonsense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.651C>A p.Cys217Ter p.C217* ENST00000599957 3/3 279 253 26 378 378 0 strelka-varscan-mutect LRRC4B,stop_gained,p.Cys217Ter,ENST00000599957,;LRRC4B,stop_gained,p.Cys217Ter,ENST00000389201,NM_001080457.1;LRRC4B,stop_gained,p.Cys217Ter,ENST00000600381,;ASPDH,upstream_gene_variant,,ENST00000376916,NM_001024656.2;ASPDH,upstream_gene_variant,,ENST00000601207,;ASPDH,upstream_gene_variant,,ENST00000598657,;ASPDH,upstream_gene_variant,,ENST00000597030,;ASPDH,upstream_gene_variant,,ENST00000601287,;ASPDH,upstream_gene_variant,,ENST00000593569,; T ENST00000599957 Transcript stop_gained 849/3019 651/2142 217/713 C/* tgC/tgA 1 -1 LRRC4B HGNC HGNC:25042 protein_coding YES CCDS42595.1 ENSP00000471502 Q9NT99 A0A024R4I8 UPI00000497E7 3/3 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF66,SMART_domains:SM00369,Superfamily_domains:SSF52058 HIGH 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 50519062 50519062 G T 1 0 0 0 0 0 1 0 0 8902 1311 46 2 2 LRRC4B 19 50519062 Nonsense_Mutation SNP G C3N-01488_T 261703 50519062 8098554 508 24882 LILRA1 0 . GRCh38 19 54596476 54596476 + Missense_Mutation SNP G G C rs777824206 C3N-01488_T C3N-01488_N G G c.1246G>C p.Glu416Gln p.E416Q ENST00000251372 7/10 249 196 53 381 381 0 strelka-varscan-mutect LILRA1,missense_variant,p.Glu416Gln,ENST00000251372,NM_006863.3;LILRA1,missense_variant,p.Glu416Gln,ENST00000618665,;LILRA1,intron_variant,,ENST00000453777,NM_001278318.1;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,non_coding_transcript_exon_variant,,ENST00000495417,;LILRA1,non_coding_transcript_exon_variant,,ENST00000477255,; C ENST00000251372 Transcript missense_variant 1428/1910 1246/1470 416/489 E/Q Gag/Cag rs777824206,COSM4523994 1 1 LILRA1 HGNC HGNC:6602 protein_coding YES CCDS12901.1 ENSP00000251372 O75019 UPI0000034C00 NM_006863.3 tolerated(0.05) 7/10 Gene3D:2.60.40.10,Pfam_domain:PF13895,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777824206 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 54596476 54596476 G C 1 0 0 0 0 1 0 0 0 8693 1175 41 4 4 LILRA1 19 54596476 Missense_Mutation SNP G C3N-01488_T 4077414 54596476 4021140 509 24883 FAM71E2 0 . GRCh38 19 55359314 55359314 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.1554G>T p.Lys518Asn p.K518N ENST00000424985 9/11 236 206 30 299 298 1 strelka-varscan-mutect FAM71E2,missense_variant,p.Lys518Asn,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;CTD-2105E13.6,missense_variant,p.Lys68Asn,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; A ENST00000424985 Transcript missense_variant 1748/3191 1554/2769 518/922 K/N aaG/aaT COSM5595796,COSM5595797 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 deleterious(0.03) 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 1,1 MODERATE SNV 5 1,1 1 PASS rs918673377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 55359314 55359314 C A 1 0 0 0 0 1 0 0 0 5476 680 24 2 2 FAM71E2 19 55359314 Missense_Mutation SNP C C3N-01488_T 762838 55359314 3258302 510 24884 NLRP4 0 . GRCh38 19 55857754 55857754 + Missense_Mutation SNP C C A rs767957395 C3N-01488_T C3N-01488_N C C c.361C>A p.Leu121Ile p.L121I ENST00000301295 3/10 279 244 35 418 417 1 strelka-varscan-mutect NLRP4,missense_variant,p.Leu121Ile,ENST00000301295,NM_134444.4;NLRP4,missense_variant,p.Leu46Ile,ENST00000587891,;NLRP4,missense_variant,p.Leu121Ile,ENST00000587464,;NLRP4,upstream_gene_variant,,ENST00000589437,; A ENST00000301295 Transcript missense_variant 783/3670 361/2985 121/994 L/I Cta/Ata rs767957395,COSM1647007,COSM5233551,COSM568022,COSM714566 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 tolerated(0.13) 3/10 hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs767957395 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 55857754 55857754 C A 1 0 0 0 0 1 0 0 0 10517 680 24 2 2 NLRP4 19 55857754 Missense_Mutation SNP C C3N-01488_T 498440 55857754 2759862 511 24885 ZSCAN1 0 . GRCh38 19 58037953 58037953 + Silent SNP G G C C3N-01488_T C3N-01488_N G G c.117G>C p.= p.L39L ENST00000282326 3/6 144 130 14 187 187 0 strelka-varscan-mutect ZSCAN1,synonymous_variant,p.=,ENST00000282326,NM_182572.3;ZSCAN1,synonymous_variant,p.=,ENST00000391700,;ZSCAN1,synonymous_variant,p.=,ENST00000601162,; C ENST00000282326 Transcript synonymous_variant 364/2054 117/1227 39/408 L ctG/ctC COSM4745389,COSM4745390 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 3/6 PROSITE_profiles:PS50804,hmmpanther:PTHR10032:SF187,hmmpanther:PTHR10032,Pfam_domain:PF02023,SMART_domains:SM00431,Superfamily_domains:SSF47353 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 80 58037953 58037953 G C 1 0 0 0 0 0 0 0 1 18820 1306 46 4 4 ZSCAN1 19 58037953 Silent SNP G C3N-01488_T 2180199 58037953 579663 512 24886 SNPH 0 . GRCh38 20 1297147 1297147 + Missense_Mutation SNP G G T rs567531133 C3N-01488_T C3N-01488_N G G c.53G>T p.Arg18Leu p.R18L ENST00000381873 4/6 87 78 9 106 106 0 strelka-mutect SNPH,missense_variant,p.Arg62Leu,ENST00000381867,NM_001318234.1;SNPH,missense_variant,p.Arg62Leu,ENST00000614659,;SNPH,missense_variant,p.Arg18Leu,ENST00000381873,NM_014723.2;RAD21L1,downstream_gene_variant,,ENST00000402452,; T ENST00000381873 Transcript missense_variant,splice_region_variant 289/4995 53/1485 18/494 R/L cGc/cTc rs567531133,COSM722662,COSM722663 1 1 SNPH HGNC HGNC:15931 protein_coding YES CCDS13012.1 ENSP00000371297 O15079 UPI000007424E NM_014723.2 deleterious(0) 4/6 Low_complexity_(Seg):seg,hmmpanther:PTHR16208:SF1,hmmpanther:PTHR16208 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs567531133 . 0 200 10 0 0 0 0 0 -18.67732 0.9999638 1 1 1 0 T 3 4 80 1297147 1297147 G T 1 0 0 0 0 1 0 0 0 15170 1101 38 1 1 SNPH 20 1297147 Missense_Mutation SNP G C3N-01488_T 1297147 63147020 513 24887 PDYN 0 . GRCh38 20 1980406 1980406 + Missense_Mutation SNP C C A rs763424462 C3N-01488_T C3N-01488_N C C c.682G>T p.Gly228Cys p.G228C ENST00000539905 3/3 236 217 19 340 340 0 strelka-varscan-mutect PDYN,missense_variant,p.Gly228Cys,ENST00000539905,NM_001190899.2;PDYN,missense_variant,p.Gly228Cys,ENST00000217305,NM_024411.4,NM_001190898.2;PDYN,missense_variant,p.Gly228Cys,ENST00000540134,NM_001190892.1,NM_001190900.1;RP4-684O24.5,intron_variant,,ENST00000446562,; A ENST00000539905 Transcript missense_variant 1076/2725 682/765 228/254 G/C Ggt/Tgt rs763424462,COSM4096935 1 -1 PDYN HGNC HGNC:8820 protein_coding YES CCDS13023.1 ENSP00000440185 P01213 UPI000012FE6A NM_001190899.2 deleterious(0) 3/3 hmmpanther:PTHR11438,hmmpanther:PTHR11438:SF4 0,1 MODERATE SNV 4 0,1 1 PASS rs763424462 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 1980406 1980406 C A 1 0 0 0 0 1 0 0 0 11787 652 23 1 1 PDYN 20 1980406 Missense_Mutation SNP C C3N-01488_T 683259 1980406 62463761 514 24888 ZNF343 0 . GRCh38 20 2483561 2483561 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1523G>T p.Cys508Phe p.C508F ENST00000612935 8/8 334 224 110 477 476 1 strelka-varscan-mutect ZNF343,missense_variant,p.Cys508Phe,ENST00000612935,NM_001321803.1,NM_001321801.1,NM_001321802.1,NM_001282497.1;ZNF343,missense_variant,p.Cys467Phe,ENST00000278772,NM_001321805.1,NM_001321800.1,NM_001282496.1,NM_001282495.1,NM_024325.5;ZNF343,missense_variant,p.Cys377Phe,ENST00000617391,NM_001282498.1;ZNF343,downstream_gene_variant,,ENST00000445484,;ZNF343,non_coding_transcript_exon_variant,,ENST00000465019,;RP4-734P14.4,intron_variant,,ENST00000461548,; A ENST00000612935 Transcript missense_variant 1937/3675 1523/1923 508/640 C/F tGt/tTt 1 -1 ZNF343 HGNC HGNC:16017 protein_coding YES CCDS74693.1 ENSP00000482819 A0A087WZQ2 UPI00002068B7 NM_001321803.1,NM_001321801.1,NM_001321802.1,NM_001282497.1 deleterious(0.01) 8/8 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF97,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 2483561 2483561 C A 1 0 0 0 0 1 0 0 0 18430 478 17 2 2 ZNF343 20 2483561 Missense_Mutation SNP C C3N-01488_T 503155 2483561 61960606 515 24889 TMC2 0 . GRCh38 20 2536631 2536631 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.10C>A p.Gln4Lys p.Q4K ENST00000358864 1/20 295 272 23 418 418 0 strelka-varscan-mutect TMC2,missense_variant,p.Gln4Lys,ENST00000358864,NM_080751.2; A ENST00000358864 Transcript missense_variant 25/3169 10/2721 4/906 Q/K Cag/Aag 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 tolerated_low_confidence(0.16) 1/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 2536631 2536631 C A 1 0 0 0 0 1 0 0 0 16431 595 21 2 2 TMC2 20 2536631 Missense_Mutation SNP C C3N-01488_T 53070 2536631 61907536 516 24890 PCSK2 0 . GRCh38 20 17429517 17429517 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.703G>T p.Val235Phe p.V235F ENST00000262545 7/12 139 80 59 170 170 0 strelka-varscan-mutect PCSK2,missense_variant,p.Val235Phe,ENST00000262545,NM_002594.4;PCSK2,missense_variant,p.Val216Phe,ENST00000377899,NM_001201528.1;PCSK2,missense_variant,p.Val200Phe,ENST00000536609,NM_001201529.2; T ENST00000262545 Transcript missense_variant 1018/4740 703/1917 235/638 V/F Gtt/Ttt 1 1 PCSK2 HGNC HGNC:8744 protein_coding YES CCDS13125.1 ENSP00000262545 P16519 UPI0000000C6E NM_002594.4 deleterious(0.01) 7/12 Gene3D:3.40.50.200,Pfam_domain:PF00082,hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF11,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 17429517 17429517 G T 1 0 0 0 0 1 0 0 0 11689 1261 44 2 2 PCSK2 20 17429517 Missense_Mutation SNP G C3N-01488_T 14892886 17429517 47014650 517 24891 EMILIN3 0 . GRCh38 20 41362075 41362075 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.1494A>T p.= p.S498S ENST00000332312 4/4 78 60 18 97 97 0 strelka-varscan-mutect EMILIN3,synonymous_variant,p.=,ENST00000332312,NM_052846.1;LPIN3,downstream_gene_variant,,ENST00000373257,;LPIN3,downstream_gene_variant,,ENST00000632009,NM_001301860.1;LPIN3,downstream_gene_variant,,ENST00000445975,;LPIN3,downstream_gene_variant,,ENST00000491528,;LPIN3,downstream_gene_variant,,ENST00000496565,; A ENST00000332312 Transcript synonymous_variant 1687/3796 1494/2301 498/766 S tcA/tcT 1 -1 EMILIN3 HGNC HGNC:16123 protein_coding YES CCDS13316.1 ENSP00000332806 Q9NT22 UPI00001D82E8 NM_052846.1 4/4 hmmpanther:PTHR15427:SF2,hmmpanther:PTHR15427,PD968187 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 41362075 41362075 T A 1 0 0 0 0 0 0 0 1 4938 1567 55 4 4 EMILIN3 20 41362075 Silent SNP T C3N-01488_T 23932558 41362075 23082092 518 24892 KCNK15 0 . GRCh38 20 44750778 44750778 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.933C>G p.Ser311Arg p.S311R ENST00000372861 2/2 101 90 11 112 112 0 strelka-varscan-mutect KCNK15,missense_variant,p.Ser311Arg,ENST00000372861,NM_022358.3;RIMS4,downstream_gene_variant,,ENST00000372851,NM_182970.3;RP4-781B1.5,downstream_gene_variant,,ENST00000611368,;KCNK15-AS1,upstream_gene_variant,,ENST00000427303,;KCNK15-AS1,upstream_gene_variant,,ENST00000445420,; G ENST00000372861 Transcript missense_variant 1064/2599 933/993 311/330 S/R agC/agG 1 1 KCNK15 HGNC HGNC:13814 protein_coding YES CCDS13337.1 ENSP00000361952 Q9H427 UPI000003EA1C NM_022358.3 deleterious_low_confidence(0) 2/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF18,Prints_domain:PR01690 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -19.99769 0.9999878 1 1 1 0 G 3 3 80 44750778 44750778 C G 1 0 0 0 0 1 0 0 0 7979 738 26 4 4 KCNK15 20 44750778 Missense_Mutation SNP C C3N-01488_T 3388703 44750778 19693389 519 24893 TP53TG5 0 . GRCh38 20 45375319 45375319 + Nonsense_Mutation SNP G G T rs374959663 C3N-01488_T C3N-01488_N G G c.488C>A p.Ser163Ter p.S163* ENST00000372726 4/5 551 520 31 658 656 2 strelka-varscan-mutect TP53TG5,stop_gained,p.Ser163Ter,ENST00000372726,NM_014477.2;SYS1,3_prime_UTR_variant,,ENST00000426004,NM_001099791.2;SYS1-DBNDD2,intron_variant,,ENST00000475242,;TP53TG5,downstream_gene_variant,,ENST00000494455,;TP53TG5,downstream_gene_variant,,ENST00000488588,;SYS1-DBNDD2,intron_variant,,ENST00000419593,;SYS1-DBNDD2,intron_variant,,ENST00000452133,;SYS1-DBNDD2,intron_variant,,ENST00000458187,; T ENST00000372726 Transcript stop_gained 645/2374 488/873 163/290 S/* tCg/tAg rs374959663 1 -1 TP53TG5 HGNC HGNC:15856 protein_coding YES CCDS13352.1 ENSP00000361811 Q9Y2B4 UPI000000165C NM_014477.2 4/5 hmmpanther:PTHR15562,hmmpanther:PTHR15562:SF0,Pfam_domain:PF15331 HIGH 1 SNV 1 1 PASS rs374959663 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 45375319 45375319 G T 1 0 0 0 0 0 1 0 0 16870 1059 37 1 1 TP53TG5 20 45375319 Nonsense_Mutation SNP G C3N-01488_T 624541 45375319 19068848 520 24894 ZNFX1 0 . GRCh38 20 49247487 49247487 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.5537G>T p.Trp1846Leu p.W1846L ENST00000396105 14/14 201 167 34 225 224 1 strelka-varscan-mutect ZNFX1,missense_variant,p.Trp1846Leu,ENST00000396105,NM_021035.2;ZNFX1,missense_variant,p.Trp1846Leu,ENST00000371752,;ZNFX1,intron_variant,,ENST00000371754,;DDX27,downstream_gene_variant,,ENST00000622530,NM_017895.7;DDX27,downstream_gene_variant,,ENST00000371764,;DDX27,downstream_gene_variant,,ENST00000618172,;ZNFX1,upstream_gene_variant,,ENST00000469991,;DDX27,downstream_gene_variant,,ENST00000484427,;DDX27,downstream_gene_variant,,ENST00000471144,; A ENST00000396105 Transcript missense_variant 5784/7371 5537/5757 1846/1918 W/L tGg/tTg 1 -1 ZNFX1 HGNC HGNC:29271 protein_coding YES CCDS13417.1 ENSP00000379412 Q9P2E3 UPI000012DD83 NM_021035.2 deleterious(0) 14/14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 49247487 49247487 C A 1 0 0 0 0 1 0 0 0 18798 595 21 2 2 ZNFX1 20 49247487 Missense_Mutation SNP C C3N-01488_T 3872168 49247487 15196680 521 24895 CTCFL 0 . GRCh38 20 57498614 57498614 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.1928G>T p.Arg643Ile p.R643I ENST00000423479 11/12 207 180 27 247 246 1 strelka-varscan-mutect CTCFL,missense_variant,p.Arg643Ile,ENST00000608263,NM_001269041.1;CTCFL,missense_variant,p.Arg593Ile,ENST00000429804,NM_001269046.1;CTCFL,missense_variant,p.Arg643Ile,ENST00000609232,NM_080618.3;CTCFL,missense_variant,p.Arg643Ile,ENST00000243914,;CTCFL,missense_variant,p.Arg643Ile,ENST00000371196,NM_001269042.1,NM_001269040.1;CTCFL,missense_variant,p.Arg643Ile,ENST00000423479,NM_001269043.1;CTCFL,downstream_gene_variant,,ENST00000608440,NM_001269044.1;CTCFL,downstream_gene_variant,,ENST00000433949,NM_001269049.1;CTCFL,downstream_gene_variant,,ENST00000502686,NM_001269054.1;CTCFL,downstream_gene_variant,,ENST00000426658,;CTCFL,downstream_gene_variant,,ENST00000422109,; A ENST00000423479 Transcript missense_variant 2019/2478 1928/2103 643/700 R/I aGa/aTa 1 -1 CTCFL HGNC HGNC:16234 protein_coding YES CCDS58780.1 ENSP00000415579 Q8NI51 UPI000157860F NM_001269043.1 tolerated(0.18) 11/12 hmmpanther:PTHR24375:SF96,hmmpanther:PTHR24375 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 57498614 57498614 C A 1 0 0 0 0 1 0 0 0 3808 913 32 2 2 CTCFL 20 57498614 Missense_Mutation SNP C C3N-01488_T 8251127 57498614 6945553 522 24896 COL9A3 0 . GRCh38 20 62829793 62829793 + Missense_Mutation SNP G G C rs201250184 C3N-01488_T C3N-01488_N G G c.1135G>C p.Gly379Arg p.G379R ENST00000343916 22/32 348 285 63 400 400 0 strelka-varscan-mutect COL9A3,missense_variant,p.Gly379Arg,ENST00000343916,NM_001853.3;COL9A3,downstream_gene_variant,,ENST00000452372,;COL9A3,upstream_gene_variant,,ENST00000462700,;COL9A3,downstream_gene_variant,,ENST00000489045,;COL9A3,downstream_gene_variant,,ENST00000463487,;COL9A3,downstream_gene_variant,,ENST00000477612,;COL9A3,upstream_gene_variant,,ENST00000466192,;COL9A3,upstream_gene_variant,,ENST00000472880,;COL9A3,upstream_gene_variant,,ENST00000469852,;COL9A3,upstream_gene_variant,,ENST00000469802,;COL9A3,upstream_gene_variant,,ENST00000481800,;COL9A3,upstream_gene_variant,,ENST00000490398,; C ENST00000343916 Transcript missense_variant 1138/2485 1135/2055 379/684 G/R Ggt/Cgt rs201250184 1 1 COL9A3 HGNC HGNC:2219 protein_coding YES CCDS13505.1 ENSP00000341640 Q14050 UPI0000126D51 NM_001853.3 deleterious(0) 22/32 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF529 MODERATE 1 SNV 1 1 PASS rs201250184 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 62829793 62829793 G C 1 0 0 0 0 1 0 0 0 3498 1116 39 4 4 COL9A3 20 62829793 Missense_Mutation SNP G C3N-01488_T 5331179 62829793 1614374 523 24897 CHRNA4 0 . GRCh38 20 63350569 63350569 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.842T>C p.Val281Ala p.V281A ENST00000370263 5/6 701 599 102 749 749 0 strelka-varscan-mutect CHRNA4,missense_variant,p.Val210Ala,ENST00000615287,;CHRNA4,missense_variant,p.Val281Ala,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,non_coding_transcript_exon_variant,,ENST00000463705,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,downstream_gene_variant,,ENST00000628665,;CHRNA4,downstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000637628,;CHRNA4,downstream_gene_variant,,ENST00000637243,;CHRNA4,3_prime_UTR_variant,,ENST00000627000,;CHRNA4,3_prime_UTR_variant,,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000630240,;CHRNA4,upstream_gene_variant,,ENST00000631289,; G ENST00000370263 Transcript missense_variant 1020/5577 842/1884 281/627 V/A gTg/gCg 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 deleterious(0) 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,Low_complexity_(Seg):seg,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 63350569 63350569 A G 1 0 0 0 0 1 0 0 0 3145 159 6 5 5 CHRNA4 20 63350569 Missense_Mutation SNP A C3N-01488_T 520776 63350569 1093598 524 24898 SOX18 0 . GRCh38 20 64048833 64048833 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.488G>T p.Arg163Leu p.R163L ENST00000340356 2/2 164 105 59 141 141 0 strelka-varscan-mutect SOX18,missense_variant,p.Arg163Leu,ENST00000340356,NM_018419.2;TCEA2,upstream_gene_variant,,ENST00000475792,; A ENST00000340356 Transcript missense_variant 613/1864 488/1155 163/384 R/L cGc/cTc COSM4802022 1 -1 SOX18 HGNC HGNC:11194 protein_coding YES CCDS13552.1 ENSP00000341815 P35713 UPI0000001C70 NM_018419.2 deleterious(0) 2/2 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF204,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 64048833 64048833 C A 1 0 0 0 0 1 0 0 0 15274 768 27 1 1 SOX18 20 64048833 Missense_Mutation SNP C C3N-01488_T 698264 64048833 395334 525 24899 86 2 SOX18 0 . GRCh38 20 64048838 64048838 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.483G>C p.Gln161His p.Q161H ENST00000340356 2/2 171 111 60 148 148 0 strelka-varscan-mutect SOX18,missense_variant,p.Gln161His,ENST00000340356,NM_018419.2;TCEA2,upstream_gene_variant,,ENST00000475792,; G ENST00000340356 Transcript missense_variant 608/1864 483/1155 161/384 Q/H caG/caC 1 -1 SOX18 HGNC HGNC:11194 protein_coding YES CCDS13552.1 ENSP00000341815 P35713 UPI0000001C70 NM_018419.2 deleterious(0) 2/2 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF204,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 64048838 64048838 C G 1 0 0 0 0 1 0 0 0 15274 680 24 4 4 SOX18 20 64048838 Missense_Mutation SNP C C3N-01488_T 5 64048838 395329 526 24900 86 2 CHODL 0 . GRCh38 21 18260286 18260286 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.634G>T p.Gly212Cys p.G212C ENST00000299295 4/6 219 156 63 254 254 0 strelka-varscan-mutect CHODL,missense_variant,p.Gly212Cys,ENST00000299295,NM_024944.2;CHODL,missense_variant,p.Gly171Cys,ENST00000400128,;CHODL,missense_variant,p.Gly171Cys,ENST00000400127,NM_001204176.1,NM_001204175.1;CHODL,missense_variant,p.Val171Leu,ENST00000400135,NM_001204178.1;CHODL,missense_variant,p.Val171Leu,ENST00000400131,NM_001204177.1;CHODL,missense_variant,p.Val171Leu,ENST00000338326,;CHODL,missense_variant,p.Gly193Cys,ENST00000543733,NM_001204174.1; T ENST00000299295 Transcript missense_variant,splice_region_variant 1025/2548 634/822 212/273 G/C Ggt/Tgt 1 1 CHODL HGNC HGNC:17807 protein_coding YES CCDS13570.1 ENSP00000299295 Q9H9P2 UPI0000037746 NM_024944.2 deleterious(0) 4/6 hmmpanther:PTHR14789 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 18260286 18260286 G T 1 0 0 0 0 1 0 0 0 3124 1014 35 2 2 CHODL 21 18260286 Missense_Mutation SNP G C3N-01488_T 18260286 28449697 527 24901 NCAM2 0 . GRCh38 21 21324429 21324429 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.666A>G p.= p.A222A ENST00000400546 6/18 193 181 12 205 204 1 strelka-varscan-mutect NCAM2,synonymous_variant,p.=,ENST00000400546,NM_004540.3;NCAM2,synonymous_variant,p.=,ENST00000284894,;NCAM2,non_coding_transcript_exon_variant,,ENST00000461281,; G ENST00000400546 Transcript synonymous_variant 915/8135 666/2514 222/837 A gcA/gcG 1 1 NCAM2 HGNC HGNC:7657 protein_coding YES CCDS42910.1 ENSP00000383392 O15394 UPI00001A3703 NM_004540.3 6/18 Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF35,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -4.233889 0.9831946 1 1 1 0 G 2 3 80 21324429 21324429 A G 1 0 0 0 0 0 0 0 1 10219 175 7 5 5 NCAM2 21 21324429 Silent SNP A C3N-01488_T 3064143 21324429 25385554 528 24902 BACH1 0 . GRCh38 21 29342662 29342662 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.2040G>T p.= p.L680L ENST00000399921 5/5 202 157 45 193 193 0 strelka-varscan-mutect BACH1,synonymous_variant,p.=,ENST00000399921,NM_206866.2;BACH1,synonymous_variant,p.=,ENST00000286800,NM_001186.3;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; T ENST00000399921 Transcript synonymous_variant 2283/5769 2040/2211 680/736 L ctG/ctT 1 1 BACH1 HGNC HGNC:935 protein_coding YES CCDS13585.1 ENSP00000382805 O14867 UPI000012673F NM_206866.2 5/5 LOW 1 SNV 1 1 PASS rs1232540697 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 29342662 29342662 G T 1 0 0 0 0 0 0 0 1 1441 1306 46 2 2 BACH1 21 29342662 Silent SNP G C3N-01488_T 8018233 29342662 17367321 529 24903 ITSN1 0 . GRCh38 21 33761967 33761967 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.769G>A p.Ala257Thr p.A257T ENST00000381318 9/40 274 217 57 298 298 0 strelka-varscan-mutect ITSN1,missense_variant,p.Ala257Thr,ENST00000381318,NM_003024.2;ITSN1,missense_variant,p.Ala220Thr,ENST00000381285,;ITSN1,missense_variant,p.Ala257Thr,ENST00000399367,;ITSN1,missense_variant,p.Ala257Thr,ENST00000381291,NM_001001132.1;ITSN1,missense_variant,p.Ala257Thr,ENST00000399352,;ITSN1,missense_variant,p.Ala257Thr,ENST00000399349,;ITSN1,missense_variant,p.Ala257Thr,ENST00000399355,;ITSN1,missense_variant,p.Ala220Thr,ENST00000399353,;ITSN1,missense_variant,p.Ala257Thr,ENST00000399338,;ITSN1,missense_variant,p.Ala141Thr,ENST00000379960,;ITSN1,missense_variant,p.Ala197Thr,ENST00000381283,;AP000304.12,intron_variant,,ENST00000429238,;ITSN1,non_coding_transcript_exon_variant,,ENST00000488166,; A ENST00000381318 Transcript missense_variant 1057/17015 769/5166 257/1721 A/T Gct/Act 1 1 ITSN1 HGNC HGNC:6183 protein_coding YES CCDS33545.1 ENSP00000370719 Q15811 UPI00001403C6 NM_003024.2 tolerated(1) 9/40 PROSITE_profiles:PS50031,PROSITE_profiles:PS50222,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF68,Pfam_domain:PF12763,Gene3D:1.10.238.10,SMART_domains:SM00027,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 33761967 33761967 G A 1 0 0 0 0 1 0 0 0 7832 1203 42 3 3 ITSN1 21 33761967 Missense_Mutation SNP G C3N-01488_T 4419305 33761967 12948016 530 24904 TTC3 0 . GRCh38 21 37126104 37126104 + Missense_Mutation SNP G G T novel C3N-01488_T C3N-01488_N G G c.1258G>T p.Asp420Tyr p.D420Y ENST00000399017 15/46 220 185 35 275 273 2 strelka-mutect TTC3,missense_variant,p.Asp420Tyr,ENST00000399017,NM_003316.3;TTC3,missense_variant,p.Asp420Tyr,ENST00000354749,;TTC3,missense_variant,p.Asp420Tyr,ENST00000355666,NM_001001894.1;TTC3,missense_variant,p.Asp420Tyr,ENST00000418766,;TTC3,missense_variant,p.Asp402Tyr,ENST00000438055,;TTC3,missense_variant,p.Asp420Tyr,ENST00000450533,;TTC3,missense_variant,p.Asp110Tyr,ENST00000540756,;TTC3,non_coding_transcript_exon_variant,,ENST00000479930,;TTC3,non_coding_transcript_exon_variant,,ENST00000485402,;TTC3,non_coding_transcript_exon_variant,,ENST00000481605,;TTC3,non_coding_transcript_exon_variant,,ENST00000494243,;TTC3,non_coding_transcript_exon_variant,,ENST00000463216,;TTC3,non_coding_transcript_exon_variant,,ENST00000492275,;TTC3,non_coding_transcript_exon_variant,,ENST00000476784,; T ENST00000399017 Transcript missense_variant 4005/10363 1258/6078 420/2025 D/Y Gat/Tat 1 1 TTC3 HGNC HGNC:12393 protein_coding YES CCDS13651.1 ENSP00000381981 P53804 UPI00001B043E NM_003316.3 deleterious(0) 15/46 hmmpanther:PTHR17550,hmmpanther:PTHR17550:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 37126104 37126104 G T 1 0 0 0 0 1 0 0 0 17206 942 33 2 2 TTC3 21 37126104 Missense_Mutation SNP G C3N-01488_T 3364137 37126104 9583879 531 24905 ABCG1 0 . GRCh38 21 42294607 42294607 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.1755C>G p.Ser585Arg p.S585R ENST00000361802 14/15 397 358 39 458 458 0 strelka-varscan-mutect ABCG1,missense_variant,p.Ser731Arg,ENST00000398437,;ABCG1,missense_variant,p.Ser575Arg,ENST00000398457,NM_207627.1,NM_207628.1;ABCG1,missense_variant,p.Ser584Arg,ENST00000343687,NM_207174.1;ABCG1,missense_variant,p.Ser585Arg,ENST00000361802,NM_004915.3;ABCG1,missense_variant,p.Ser573Arg,ENST00000398449,NM_016818.2;ABCG1,missense_variant,p.Ser570Arg,ENST00000347800,NM_207629.1;ABCG1,non_coding_transcript_exon_variant,,ENST00000462050,;ABCG1,non_coding_transcript_exon_variant,,ENST00000472587,;ABCG1,non_coding_transcript_exon_variant,,ENST00000496783,; G ENST00000361802 Transcript missense_variant 1900/3034 1755/2037 585/678 S/R agC/agG 1 1 ABCG1 HGNC HGNC:73 protein_coding YES CCDS13682.1 ENSP00000354995 P45844 UPI0000125130 NM_004915.3 tolerated(0.19) 14/15 Transmembrane_helices:TMhelix,hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF177,TIGRFAM_domain:TIGR00955,Pfam_domain:PF01061 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 42294607 42294607 C G 1 0 0 0 0 1 0 0 0 72 796 28 4 4 ABCG1 21 42294607 Missense_Mutation SNP C C3N-01488_T 5168503 42294607 4415376 532 24906 TRPM2 0 . GRCh38 21 44418472 44418472 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.3378C>A p.= p.I1126I ENST00000397928 22/32 236 199 37 231 230 1 strelka-varscan-mutect TRPM2,synonymous_variant,p.=,ENST00000397928,NM_003307.3;TRPM2,synonymous_variant,p.=,ENST00000300482,;TRPM2,synonymous_variant,p.=,ENST00000300481,;TRPM2,synonymous_variant,p.=,ENST00000397932,;TRPM2-AS,intron_variant,,ENST00000423310,;TRPM2-AS,upstream_gene_variant,,ENST00000456880,;TRPM2,non_coding_transcript_exon_variant,,ENST00000498430,; A ENST00000397928 Transcript synonymous_variant 3823/6221 3378/4512 1126/1503 I atC/atA 1 1 TRPM2 HGNC HGNC:12339 protein_coding YES CCDS13710.1 ENSP00000381023 O94759 UPI0000169D60 NM_003307.3 22/32 hmmpanther:PTHR13800:SF2,hmmpanther:PTHR13800 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 44418472 44418472 C A 1 0 0 0 0 0 0 0 1 17092 903 32 2 2 TRPM2 21 44418472 Silent SNP C C3N-01488_T 2123865 44418472 2291511 533 24907 KRTAP10-4 0 . GRCh38 21 44573904 44573904 + Missense_Mutation SNP C C A rs587701380 C3N-01488_T C3N-01488_N C C c.146C>A p.Pro49Gln p.P49Q ENST00000400374 1/1 534 461 73 589 588 1 strelka-varscan-mutect KRTAP10-4,missense_variant,p.Pro49Gln,ENST00000400374,NM_198687.2;TSPEAR,intron_variant,,ENST00000614657,NM_001272037.1;TSPEAR,intron_variant,,ENST00000323084,NM_144991.2;TSPEAR,intron_variant,,ENST00000613245,;TSPEAR,upstream_gene_variant,,ENST00000397916,; A ENST00000400374 Transcript missense_variant 176/1643 146/1206 49/401 P/Q cCg/cAg rs587701380 1 1 KRTAP10-4 HGNC HGNC:20521 protein_coding YES CCDS42957.1 ENSP00000383225 P60372 UPI00003D4D6E NM_198687.2 deleterious(0.01) 1/1 hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF72,Low_complexity_(Seg):seg MODERATE SNV 1 PASS rs587701380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 44573904 44573904 C A 1 0 0 0 0 1 0 0 0 8394 652 23 1 1 KRTAP10-4 21 44573904 Missense_Mutation SNP C C3N-01488_T 155432 44573904 2136079 534 24908 COL18A1 0 . GRCh38 21 45486969 45486969 + Missense_Mutation SNP G G A novel C3N-01488_T C3N-01488_N G G c.3055G>A p.Gly1019Arg p.G1019R ENST00000359759 15/41 48 42 6 42 42 0 strelka-varscan-mutect COL18A1,missense_variant,p.Gly1019Arg,ENST00000359759,NM_130444.2;COL18A1,missense_variant,p.Gly784Arg,ENST00000355480,NM_030582.3;COL18A1,missense_variant,p.Gly604Arg,ENST00000400337,NM_130445.3;COL18A1,upstream_gene_variant,,ENST00000342220,; A ENST00000359759 Transcript missense_variant 3055/6586 3055/5265 1019/1754 G/R Gga/Aga 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 deleterious(0) 15/41 hmmpanther:PTHR24023,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -14.70521 1 1 1 1 0 A 3 1 80 45486969 45486969 G A 1 0 0 0 0 1 0 0 0 3463 1001 35 3 3 COL18A1 21 45486969 Missense_Mutation SNP G C3N-01488_T 913065 45486969 1223014 535 24909 GAB4 0 . GRCh38 22 17008041 17008041 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.74G>T p.Trp25Leu p.W25L ENST00000400588 1/10 134 117 17 158 158 0 strelka-varscan-mutect GAB4,missense_variant,p.Trp25Leu,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,upstream_gene_variant,,ENST00000523144,;GAB4,upstream_gene_variant,,ENST00000465611,;AC006548.26,upstream_gene_variant,,ENST00000605217,; A ENST00000400588 Transcript missense_variant 182/2630 74/1725 25/574 W/L tGg/tTg 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 tolerated_low_confidence(0.07) 1/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20,Low_complexity_(Seg):seg,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999973 1 1 1 0 A 3 1 80 17008041 17008041 C A 1 0 0 0 0 1 0 0 0 6022 595 21 2 2 GAB4 22 17008041 Missense_Mutation SNP C C3N-01488_T 17008041 33810427 536 24910 GAB4 0 . GRCh38 22 17008053 17008053 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.62C>G p.Pro21Arg p.P21R ENST00000400588 1/10 128 112 16 154 154 0 strelka-varscan-mutect GAB4,missense_variant,p.Pro21Arg,ENST00000400588,NM_001037814.1;AC006548.28,non_coding_transcript_exon_variant,,ENST00000623130,;GAB4,upstream_gene_variant,,ENST00000523144,;GAB4,upstream_gene_variant,,ENST00000465611,;AC006548.26,upstream_gene_variant,,ENST00000605217,; C ENST00000400588 Transcript missense_variant 170/2630 62/1725 21/574 P/R cCt/cGt 1 -1 GAB4 HGNC HGNC:18325 protein_coding YES CCDS42976.1 ENSP00000383431 Q2WGN9 UPI00002326B5 NM_001037814.1 deleterious_low_confidence(0) 1/10 hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF20,Low_complexity_(Seg):seg,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs1227455985 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 17008053 17008053 G C 1 0 0 0 0 1 0 0 0 6022 1000 35 4 4 GAB4 22 17008053 Missense_Mutation SNP G C3N-01488_T 12 17008053 33810415 537 24911 MED15 0 . GRCh38 22 20584899 20584899 + Silent SNP C C T novel C3N-01488_T C3N-01488_N C C c.1848C>T p.= p.Y616Y ENST00000263205 15/18 274 225 49 380 380 0 strelka-varscan-mutect MED15,synonymous_variant,p.=,ENST00000263205,NM_001003891.2;MED15,synonymous_variant,p.=,ENST00000292733,NM_001293234.1,NM_015889.4;MED15,synonymous_variant,p.=,ENST00000406969,NM_001293235.1,NM_001293237.1;MED15,synonymous_variant,p.=,ENST00000382974,NM_001293236.1;MED15,downstream_gene_variant,,ENST00000478831,;MED15,3_prime_UTR_variant,,ENST00000433831,;MED15,non_coding_transcript_exon_variant,,ENST00000493216,;MED15,non_coding_transcript_exon_variant,,ENST00000492381,;MED15,non_coding_transcript_exon_variant,,ENST00000489651,;MED15,non_coding_transcript_exon_variant,,ENST00000473244,;MED15,intron_variant,,ENST00000461076,;MED15,downstream_gene_variant,,ENST00000476187,;MED15,upstream_gene_variant,,ENST00000436496,;CCDC74BP1,downstream_gene_variant,,ENST00000508880,; T ENST00000263205 Transcript synonymous_variant 1917/3351 1848/2367 616/788 Y taC/taT 1 1 MED15 HGNC HGNC:14248 protein_coding YES CCDS33602.1 ENSP00000263205 Q96RN5 UPI00001313C4 NM_001003891.2 15/18 Pfam_domain:PF09606,hmmpanther:PTHR31804,hmmpanther:PTHR31804:SF2 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 20584899 20584899 C T 1 0 0 0 0 0 0 0 1 9372 518 18 3 3 MED15 22 20584899 Silent SNP C C3N-01488_T 3576846 20584899 30233569 538 24912 ZNF280A 0 . GRCh38 22 22515067 22515067 + Silent SNP T T A novel C3N-01488_T C3N-01488_N T T c.564A>T p.= p.P188P ENST00000302097 2/2 208 174 34 381 381 0 strelka-varscan-mutect ZNF280A,synonymous_variant,p.=,ENST00000302097,NM_080740.4; A ENST00000302097 Transcript synonymous_variant 817/2148 564/1629 188/542 P ccA/ccT 1 -1 ZNF280A HGNC HGNC:18597 protein_coding YES CCDS13800.1 ENSP00000302855 P59817 UPI000011B50C NM_080740.4 2/2 Pfam_domain:PF13836 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 22515067 22515067 T A 1 0 0 0 0 0 0 0 1 18390 1567 55 4 4 ZNF280A 22 22515067 Silent SNP T C3N-01488_T 1930168 22515067 28303401 539 24913 NCF4 0 . GRCh38 22 36870453 36870453 + Missense_Mutation SNP G G C novel C3N-01488_T C3N-01488_N G G c.381G>C p.Glu127Asp p.E127D ENST00000397147 5/9 562 509 53 695 695 0 strelka-varscan-mutect NCF4,missense_variant,p.Glu127Asp,ENST00000397147,NM_013416.3;NCF4,missense_variant,p.Glu127Asp,ENST00000248899,NM_000631.4;NCF4,missense_variant,p.Glu24Asp,ENST00000447071,;CTA-833B7.2,upstream_gene_variant,,ENST00000619915,;CTA-833B7.2,upstream_gene_variant,,ENST00000431290,;NCF4,upstream_gene_variant,,ENST00000415063,; C ENST00000397147 Transcript missense_variant 565/1641 381/1047 127/348 E/D gaG/gaC 1 1 NCF4 HGNC HGNC:7662 protein_coding YES CCDS13935.1 ENSP00000380334 Q15080 UPI000013CC59 NM_013416.3 tolerated(0.23) 5/9 PROSITE_profiles:PS50195,hmmpanther:PTHR10663:SF209,hmmpanther:PTHR10663,Gene3D:3.30.1520.10,Pfam_domain:PF00787,SMART_domains:SM00312,Superfamily_domains:SSF64268 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 80 36870453 36870453 G C 1 0 0 0 0 1 0 0 0 10236 991 35 4 4 NCF4 22 36870453 Missense_Mutation SNP G C3N-01488_T 14355386 36870453 13948015 540 24914 SULT4A1 0 . GRCh38 22 43838904 43838904 + Silent SNP G G T novel C3N-01488_T C3N-01488_N G G c.471C>A p.= p.T157T ENST00000330884 4/7 208 180 28 307 307 0 strelka-varscan-mutect SULT4A1,synonymous_variant,p.=,ENST00000330884,NM_014351.3;SULT4A1,synonymous_variant,p.=,ENST00000422525,;SULT4A1,3_prime_UTR_variant,,ENST00000432404,;SULT4A1,non_coding_transcript_exon_variant,,ENST00000475131,; T ENST00000330884 Transcript synonymous_variant 592/2468 471/855 157/284 T acC/acA 1 -1 SULT4A1 HGNC HGNC:14903 protein_coding YES CCDS14051.1 ENSP00000332565 Q9BR01 UPI0000135477 NM_014351.3 4/7 hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF76,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs1169389768 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 80 43838904 43838904 G T 1 0 0 0 0 0 0 0 1 15769 987 35 2 2 SULT4A1 22 43838904 Silent SNP G C3N-01488_T 6968451 43838904 6979564 541 24915 TBC1D22A 0 . GRCh38 22 46878712 46878712 + Nonsense_Mutation SNP A A T novel C3N-01488_T C3N-01488_N A A c.697A>T p.Lys233Ter p.K233* ENST00000337137 5/13 151 126 25 239 238 1 strelka-varscan-mutect TBC1D22A,stop_gained,p.Lys203Ter,ENST00000380995,NM_001284304.1;TBC1D22A,stop_gained,p.Lys233Ter,ENST00000337137,NM_014346.3;TBC1D22A,stop_gained,p.Lys186Ter,ENST00000406733,NM_001284305.1;TBC1D22A,stop_gained,p.Lys174Ter,ENST00000407381,;TBC1D22A,stop_gained,p.Lys155Ter,ENST00000355704,NM_001284303.1;TBC1D22A,stop_gained,p.Lys186Ter,ENST00000441162,;TBC1D22A,intron_variant,,ENST00000394449,; T ENST00000337137 Transcript stop_gained 863/3787 697/1554 233/517 K/* Aag/Tag 1 1 TBC1D22A HGNC HGNC:1309 protein_coding YES CCDS14078.1 ENSP00000336724 Q8WUA7 UPI0000128722 NM_014346.3 5/13 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF255,Gene3D:2qq8A02,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 80 46878712 46878712 A T 1 0 0 0 0 0 1 0 0 16011 247 9 4 4 TBC1D22A 22 46878712 Nonsense_Mutation SNP A C3N-01488_T 3039808 46878712 3939756 542 24916 MAGEB6P1 0 . GRCh38 X 26161447 26161447 + Frame_Shift_Del DEL C C - novel C3N-01488_T C3N-01488_N C C c.848delC p.Pro283ArgfsTer6 p.P283Rfs*6 ENST00000416929 1/1 107 73 34 171 171 0 sindel-varindel-pindel MAGEB6P1,frameshift_variant,p.Pro283ArgfsTer6,ENST00000416929,; - ENST00000416929 Transcript frameshift_variant 847/1224 847/1224 283/407 P/X Ccg/cg 1 1 MAGEB6P1 HGNC HGNC:28824 protein_coding YES ENSP00000488257 A0A0J9YX57 UPI0000237759 1/1 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,Pfam_domain:PF01454,SMART_domains:SM01373 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 80 26161447 26161447 C - 1 0 1 0 1 0 0 0 0 9097 739 26 0 0 MAGEB6P1 23 26161447 Frame_Shift_Del DEL C C3N-01488_T 26161447 129879448 543 24917 FAM47A 0 . GRCh38 X 34131532 34131532 + Silent SNP C C A novel C3N-01488_T C3N-01488_N C C c.747G>T p.= p.P249P ENST00000346193 1/1 111 70 41 184 184 0 strelka-varscan-mutect FAM47A,synonymous_variant,p.=,ENST00000346193,NM_203408.3;FAM47A,synonymous_variant,p.=,ENST00000613251,; A ENST00000346193 Transcript synonymous_variant 780/2556 747/2376 249/791 P ccG/ccT 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 LOW 1 SNV 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 80 34131532 34131532 C A 1 0 0 0 0 0 0 0 1 5447 639 23 1 1 FAM47A 23 34131532 Silent SNP C C3N-01488_T 7970085 34131532 121909363 544 24918 CFAP47 0 . GRCh38 X 36104633 36104633 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.5262T>A p.Ser1754Arg p.S1754R ENST00000378653 33/64 25 17 8 41 41 0 strelka-varscan-mutect CFAP47,missense_variant,p.Ser1754Arg,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Ser329Arg,ENST00000313548,;CFAP47,non_coding_transcript_exon_variant,,ENST00000378660,; A ENST00000378653 Transcript missense_variant 5328/9943 5262/9564 1754/3187 S/R agT/agA 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 tolerated(0.08) 33/64 PROSITE_profiles:PS50021,hmmpanther:PTHR23053,Gene3D:1.10.418.10,Superfamily_domains:SSF47576 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -19.99746 1 1 1 1 0 A 3 1 80 36104633 36104633 T A 1 0 0 0 0 1 0 0 0 3022 1722 60 4 4 CFAP47 23 36104633 Missense_Mutation SNP T C3N-01488_T 1973101 36104633 119936262 545 24919 SYN1 0 . GRCh38 X 47574256 47574256 + Missense_Mutation SNP C C G novel C3N-01488_T C3N-01488_N C C c.1728G>C p.Lys576Asn p.K576N ENST00000295987 12/13 80 55 25 104 104 0 strelka-varscan-mutect SYN1,missense_variant,p.Lys576Asn,ENST00000295987,NM_006950.3;SYN1,missense_variant,p.Lys576Asn,ENST00000340666,NM_133499.2;ARAF,downstream_gene_variant,,ENST00000290277,NM_001256196.1;ARAF,downstream_gene_variant,,ENST00000377045,NM_001654.4;ARAF,downstream_gene_variant,,ENST00000470206,;ARAF,downstream_gene_variant,,ENST00000469505,; G ENST00000295987 Transcript missense_variant 1853/3209 1728/2118 576/705 K/N aaG/aaC 1 -1 SYN1 HGNC HGNC:11494 protein_coding YES CCDS14280.1 ENSP00000295987 P17600 UPI0000167B47 NM_006950.3 tolerated(0.22) 12/13 Low_complexity_(Seg):seg,hmmpanther:PTHR10841:SF22,hmmpanther:PTHR10841 MODERATE SNV 2 1 PASS rs1230257627 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 47574256 47574256 C G 1 0 0 0 0 1 0 0 0 15830 680 24 4 4 SYN1 23 47574256 Missense_Mutation SNP C C3N-01488_T 11469623 47574256 108466639 546 24920 PIN4 0 . GRCh38 X 72197523 72197523 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.468A>G p.= p.K156K ENST00000373669 4/4 43 37 6 71 71 0 strelka-varscan-mutect PIN4,synonymous_variant,p.=,ENST00000373669,NM_006223.3;PIN4,3_prime_UTR_variant,,ENST00000218432,;PIN4,intron_variant,,ENST00000423432,NM_001170747.1;PIN4,intron_variant,,ENST00000496835,;PIN4,downstream_gene_variant,,ENST00000446576,;RN7SL388P,upstream_gene_variant,,ENST00000498736,;PIN4,intron_variant,,ENST00000439980,;PIN4,downstream_gene_variant,,ENST00000373662,; G ENST00000373669 Transcript synonymous_variant 500/1321 468/471 156/156 K aaA/aaG 1 1 PIN4 HGNC HGNC:8992 protein_coding YES CCDS14417.1 ENSP00000362773 Q9Y237 UPI00002263A9 NM_006223.3 4/4 Gene3D:3.10.50.40,hmmpanther:PTHR10657 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.15078 1 1 1 1 0 G 2 3 80 72197523 72197523 A G 1 0 0 0 0 0 0 0 1 12026 98 4 5 5 PIN4 23 72197523 Silent SNP A C3N-01488_T 24623267 72197523 83843372 547 24921 UPRT 0 . GRCh38 X 75300876 75300876 + Missense_Mutation SNP A A G novel C3N-01488_T C3N-01488_N A A c.734A>G p.Asn245Ser p.N245S ENST00000373383 6/7 54 30 24 75 75 0 strelka-mutect UPRT,missense_variant,p.Asn245Ser,ENST00000373379,NM_001307944.1;UPRT,missense_variant,p.Asn245Ser,ENST00000373383,NM_145052.3;UPRT,missense_variant,p.Asn109Ser,ENST00000530743,;UPRT,non_coding_transcript_exon_variant,,ENST00000474175,;UPRT,non_coding_transcript_exon_variant,,ENST00000526850,;UPRT,downstream_gene_variant,,ENST00000531704,;UPRT,3_prime_UTR_variant,,ENST00000462237,; G ENST00000373383 Transcript missense_variant 901/2186 734/930 245/309 N/S aAt/aGt 1 1 UPRT HGNC HGNC:28334 protein_coding YES CCDS14429.1 ENSP00000362481 Q96BW1 A8KAF9 UPI000004B62E NM_145052.3 deleterious(0.02) 6/7 Gene3D:3.40.50.2020,Pfam_domain:PF14681,hmmpanther:PTHR10285,Superfamily_domains:SSF53271 MODERATE 1 SNV 1 1 PASS . . 0 201 7 2 0 0 0 0 -20 0.9999803 1 1 1 0 G 3 3 80 75300876 75300876 A G 1 0 0 0 0 1 0 0 0 17540 101 4 5 5 UPRT 23 75300876 Missense_Mutation SNP A C3N-01488_T 3103353 75300876 80740019 548 24922 GLRA4 0 . GRCh38 X 103724541 103724541 + Missense_Mutation SNP C C G C3N-01488_T C3N-01488_N C C c.270G>C p.Met90Ile p.M90I ENST00000372617 3/9 66 50 16 103 103 0 strelka-varscan-mutect GLRA4,missense_variant,p.Met90Ile,ENST00000372617,NM_001024452.2;GLRA4,upstream_gene_variant,,ENST00000469567,;GLRA4,splice_region_variant,,ENST00000480725,;GLRA4,splice_region_variant,,ENST00000436213,; G ENST00000372617 Transcript missense_variant,splice_region_variant 691/1795 270/1254 90/417 M/I atG/atC COSM462350,COSM462351 1 -1 GLRA4 HGNC HGNC:31715 protein_coding YES CCDS43980.2 ENSP00000361700 Q5JXX5 UPI000188140C NM_001024452.2 deleterious(0) 3/9 hmmpanther:PTHR18945:SF211,hmmpanther:PTHR18945,TIGRFAM_domain:TIGR00860,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1300011619 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 80 103724541 103724541 C G 1 0 0 0 0 1 0 0 0 6336 608 21 4 4 GLRA4 23 103724541 Missense_Mutation SNP C C3N-01488_T 28423665 103724541 52316354 549 24923 TBC1D8B 0 . GRCh38 X 106827182 106827182 + Missense_Mutation SNP G G T C3N-01488_T C3N-01488_N G G c.1048G>T p.Asp350Tyr p.D350Y ENST00000357242 7/21 69 43 26 114 113 1 strelka-varscan-mutect TBC1D8B,missense_variant,p.Asp350Tyr,ENST00000357242,NM_017752.2;TBC1D8B,missense_variant,p.Asp350Tyr,ENST00000481617,;TBC1D8B,missense_variant,p.Asp350Tyr,ENST00000276175,;TBC1D8B,missense_variant,p.Asp350Tyr,ENST00000310452,NM_198881.1;MORC4,intron_variant,,ENST00000604604,; T ENST00000357242 Transcript missense_variant 1222/5717 1048/3363 350/1120 D/Y Gat/Tat COSM164815 1 1 TBC1D8B HGNC HGNC:24715 protein_coding YES CCDS14522.1 ENSP00000349781 Q0IIM8 UPI0000225CD5 NM_017752.2 deleterious(0) 7/21 hmmpanther:PTHR22957:SF320,hmmpanther:PTHR22957,Pfam_domain:PF02893,SMART_domains:SM00568 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 80 106827182 106827182 G T 1 0 0 0 0 1 0 0 0 16031 942 33 2 2 TBC1D8B 23 106827182 Missense_Mutation SNP G C3N-01488_T 3102641 106827182 49213713 550 24924 TRPC5 0 . GRCh38 X 111952136 111952136 + Silent SNP A A G novel C3N-01488_T C3N-01488_N A A c.285T>C p.= p.Y95Y ENST00000262839 2/11 134 87 47 152 152 0 strelka-varscan-mutect TRPC5,synonymous_variant,p.=,ENST00000262839,NM_012471.2; G ENST00000262839 Transcript synonymous_variant 1204/5839 285/2922 95/973 Y taT/taC 1 -1 TRPC5 HGNC HGNC:12337 protein_coding YES CCDS14561.1 ENSP00000262839 Q9UL62 UPI00001374B6 NM_012471.2 2/11 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF24,Pfam_domain:PF12796,Gene3D:1.25.40.20,TIGRFAM_domain:TIGR00870,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 80 111952136 111952136 A G 1 0 0 0 0 0 0 0 1 17087 224 8 5 5 TRPC5 23 111952136 Silent SNP A C3N-01488_T 5124954 111952136 44088759 551 24925 KLHL13 0 . GRCh38 X 117909673 117909673 + Missense_Mutation SNP T T A novel C3N-01488_T C3N-01488_N T T c.1003A>T p.Arg335Trp p.R335W ENST00000539496 6/8 147 96 51 210 209 1 strelka-varscan-mutect KLHL13,missense_variant,p.Arg281Trp,ENST00000371876,;KLHL13,missense_variant,p.Arg332Trp,ENST00000262820,NM_033495.3;KLHL13,missense_variant,p.Arg281Trp,ENST00000447671,;KLHL13,missense_variant,p.Arg316Trp,ENST00000540167,NM_001168302.1;KLHL13,missense_variant,p.Arg290Trp,ENST00000545703,NM_001168303.1,NM_001168300.1;KLHL13,missense_variant,p.Arg281Trp,ENST00000371882,;KLHL13,missense_variant,p.Arg281Trp,ENST00000371878,;KLHL13,missense_variant,p.Arg316Trp,ENST00000541812,NM_001168301.1;KLHL13,missense_variant,p.Arg335Trp,ENST00000539496,NM_001168299.1;KLHL13,missense_variant,p.Arg281Trp,ENST00000469946,;Y_RNA,downstream_gene_variant,,ENST00000363421,; A ENST00000539496 Transcript missense_variant 1003/3071 1003/1977 335/658 R/W Agg/Tgg 1 -1 KLHL13 HGNC HGNC:22931 protein_coding YES CCDS55480.1 ENSP00000443191 Q9P2N7 UPI0001914B0F NM_001168299.1 deleterious(0) 6/8 Gene3D:1k3iA02,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF68 MODERATE 1 SNV 2 1 PASS rs1336320983 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 117909673 117909673 T A 1 0 0 0 0 1 0 0 0 8233 1579 55 4 4 KLHL13 23 117909673 Missense_Mutation SNP T C3N-01488_T 5957537 117909673 38131222 552 24926 RHOXF2B 0 . GRCh38 X 120077098 120077098 + Missense_Mutation SNP C C A rs782408568 C3N-01488_T C3N-01488_N C C c.270G>T p.Trp90Cys p.W90C ENST00000371402 2/4 354 231 123 427 425 2 strelka-varscan-mutect RHOXF2B,missense_variant,p.Trp90Cys,ENST00000371402,NM_001099685.1;RHOXF1-AS1,intron_variant,,ENST00000553843,; A ENST00000371402 Transcript missense_variant 423/2864 270/867 90/288 W/C tgG/tgT rs782408568 1 -1 RHOXF2B HGNC HGNC:33519 protein_coding YES CCDS43985.1 ENSP00000360455 P0C7M4 UPI000006D753 NM_001099685.1 tolerated(0.18) 2/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF327 MODERATE 1 SNV 1 1 PASS rs782408568 . 60 150 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 120077098 120077098 C A 1 0 0 0 0 1 0 0 0 13522 624 22 2 2 RHOXF2B 23 120077098 Missense_Mutation SNP C C3N-01488_T 2167425 120077098 35963797 553 24927 CD40LG 0 . GRCh38 X 136659156 136659156 + Missense_Mutation SNP C C A C3N-01488_T C3N-01488_N C C c.527C>A p.Thr176Asn p.T176N ENST00000370629 5/5 175 130 45 276 275 1 strelka-varscan-mutect CD40LG,missense_variant,p.Thr176Asn,ENST00000370629,NM_000074.2;CD40LG,missense_variant,p.Thr155Asn,ENST00000370628,; A ENST00000370629 Transcript missense_variant 583/1817 527/786 176/261 T/N aCc/aAc CM011012,CD40Lbase_D0015:g.11963C>T 1 1 CD40LG HGNC HGNC:11935 protein_coding YES CCDS14659.1 ENSP00000359663 P29965 UPI00000315E7 NM_000074.2 deleterious(0.01) 5/5 PROSITE_profiles:PS50049,hmmpanther:PTHR11471:SF5,hmmpanther:PTHR11471,PROSITE_patterns:PS00251,Pfam_domain:PF00229,PIRSF_domain:PIRSF016527,Gene3D:2.60.120.40,SMART_domains:SM00207,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1,0 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 136659156 136659156 C A 1 0 0 0 0 1 0 0 0 2720 507 18 2 2 CD40LG 23 136659156 Missense_Mutation SNP C C3N-01488_T 16582058 136659156 19381739 554 24928 FGF13 0 . GRCh38 X 138635544 138635544 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.544G>T p.Gly182Cys p.G182C ENST00000436198 6/7 180 131 49 292 292 0 strelka-varscan-mutect FGF13,missense_variant,p.Gly172Cys,ENST00000315930,NM_004114.3;FGF13,missense_variant,p.Gly119Cys,ENST00000305414,NM_033642.2;FGF13,missense_variant,p.Gly182Cys,ENST00000436198,NM_001139500.1;FGF13,missense_variant,p.Gly126Cys,ENST00000626909,NM_001139498.1;FGF13,missense_variant,p.Gly188Cys,ENST00000455663,;Z83313.1,missense_variant,p.Gly153Cys,ENST00000441825,NM_001139501.1,NM_001139502.1; A ENST00000436198 Transcript missense_variant 794/1165 544/768 182/255 G/C Ggt/Tgt 1 -1 FGF13 HGNC HGNC:3670 protein_coding YES CCDS55513.1 ENSP00000396198 Q92913 UPI00001484B4 NM_001139500.1 deleterious(0) 6/7 Gene3D:2.80.10.50,Pfam_domain:PF00167,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF77,SMART_domains:SM00442,Superfamily_domains:SSF50353 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 138635544 138635544 C A 1 0 0 0 0 1 0 0 0 5706 623 22 2 2 FGF13 23 138635544 Missense_Mutation SNP C C3N-01488_T 1976388 138635544 17405351 555 24929 HCFC1 0 . GRCh38 X 153955069 153955069 + Missense_Mutation SNP C C A novel C3N-01488_T C3N-01488_N C C c.3330G>T p.Glu1110Asp p.E1110D ENST00000310441 17/26 86 56 30 114 114 0 strelka-varscan-mutect HCFC1,missense_variant,p.Glu1110Asp,ENST00000310441,NM_005334.2;HCFC1,missense_variant,p.Glu1110Asp,ENST00000369984,;HCFC1,upstream_gene_variant,,ENST00000444191,;HCFC1,downstream_gene_variant,,ENST00000461098,; A ENST00000310441 Transcript missense_variant 4297/8869 3330/6108 1110/2035 E/D gaG/gaT 1 -1 HCFC1 HGNC HGNC:4839 protein_coding YES CCDS44020.1 ENSP00000309555 P51610 UPI0000142F1F NM_005334.2 deleterious_low_confidence(0.01) 17/26 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 80 153955069 153955069 C A 1 0 0 0 0 1 0 0 0 6879 912 32 2 2 HCFC1 23 153955069 Missense_Mutation SNP C C3N-01488_T 15319525 153955069 2085826 556 24930 PLEKHN1 0 . GRCh38 1 974474 974474 + Missense_Mutation SNP G G T rs765491496 C3N-01489_T C3N-01489_N G G c.1735G>T p.Gly579Cys p.G579C ENST00000379410 16/16 148 127 21 222 221 1 strelka-varscan-mutect PLEKHN1,missense_variant,p.Gly631Cys,ENST00000379409,;PLEKHN1,missense_variant,p.Gly579Cys,ENST00000379410,NM_032129.2;PLEKHN1,missense_variant,p.Gly544Cys,ENST00000379407,NM_001160184.1;PLEKHN1,missense_variant,p.Gly144Cys,ENST00000491024,;PERM1,downstream_gene_variant,,ENST00000433179,NM_001291366.1;PERM1,downstream_gene_variant,,ENST00000341290,NM_001291367.1;PERM1,downstream_gene_variant,,ENST00000479361,;PLEKHN1,downstream_gene_variant,,ENST00000480267,; T ENST00000379410 Transcript missense_variant 1770/2404 1735/1836 579/611 G/C Ggc/Tgc rs765491496,COSM4530870,COSM4530871 1 1 PLEKHN1 HGNC HGNC:25284 protein_coding YES CCDS4.1 ENSP00000368720 Q494U1 UPI00001416D8 NM_032129.2 deleterious_low_confidence(0.02) 16/16 hmmpanther:PTHR22826:SF139,hmmpanther:PTHR22826 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs765491496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 974474 974474 G T 1 0 0 0 0 1 0 0 0 12176 1116 39 1 1 PLEKHN1 1 974474 Missense_Mutation SNP G C3N-01489_T 974474 247981948 1 24931 TTLL10 0 . GRCh38 1 1180057 1180057 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.223G>C p.Gly75Arg p.G75R ENST00000379290 6/16 34 28 6 62 62 0 strelka-mutect TTLL10,missense_variant,p.Gly75Arg,ENST00000379290,;TTLL10,missense_variant,p.Gly75Arg,ENST00000379289,NM_001130045.1;TTLL10,missense_variant,p.Gly2Arg,ENST00000379288,NM_153254.2;TTLL10-AS1,upstream_gene_variant,,ENST00000379317,;TTLL10,upstream_gene_variant,,ENST00000460998,;TTLL10,upstream_gene_variant,,ENST00000486379,;TTLL10,upstream_gene_variant,,ENST00000514695,; C ENST00000379290 Transcript missense_variant 396/2283 223/2022 75/673 G/R Ggg/Cgg 1 1 TTLL10 HGNC HGNC:26693 protein_coding YES CCDS44036.1 ENSP00000368592 Q6ZVT0 UPI0000205ADB deleterious_low_confidence(0.04) 6/16 hmmpanther:PTHR12241,hmmpanther:PTHR12241:SF110 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 1180057 1180057 G C 1 0 0 0 0 1 0 0 0 17235 1232 43 4 4 TTLL10 1 1180057 Missense_Mutation SNP G C3N-01489_T 205583 1180057 247776365 2 24932 CHD5 0 . GRCh38 1 6142293 6142293 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.2271C>A p.= p.P757P ENST00000262450 15/42 61 54 7 92 92 0 strelka-mutect CHD5,synonymous_variant,p.=,ENST00000262450,NM_015557.2;CHD5,synonymous_variant,p.=,ENST00000496404,;CHD5,synonymous_variant,p.=,ENST00000462991,; T ENST00000262450 Transcript synonymous_variant 2371/9646 2271/5865 757/1954 P ccC/ccA 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 15/42 Gene3D:3.40.50.300,Pfam_domain:PF00176,PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF583,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.3368 1 1 1 1 0 T 2 4 81 6142293 6142293 G T 1 0 0 0 0 0 0 0 1 3087 1219 43 2 2 CHD5 1 6142293 Silent SNP G C3N-01489_T 4962236 6142293 242814129 3 24933 HES2 0 . GRCh38 1 6419277 6419277 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.205G>A p.Glu69Lys p.E69K ENST00000377834 3/4 253 229 24 360 359 1 strelka-varscan-mutect HES2,missense_variant,p.Glu69Lys,ENST00000377834,NM_019089.4;HES2,missense_variant,p.Glu69Lys,ENST00000489730,;HES2,intron_variant,,ENST00000377837,;HES2,intron_variant,,ENST00000487437,;HES2,intron_variant,,ENST00000377836,;HES2,upstream_gene_variant,,ENST00000471190,; T ENST00000377834 Transcript missense_variant 304/4262 205/522 69/173 E/K Gag/Aag 1 -1 HES2 HGNC HGNC:16005 protein_coding YES CCDS30574.1 ENSP00000367065 Q9Y543 UPI000012C617 NM_019089.4 deleterious(0.01) 3/4 Gene3D:4.10.280.10,Pfam_domain:PF00010,PROSITE_profiles:PS50888,hmmpanther:PTHR10985,hmmpanther:PTHR10985:SF15,SMART_domains:SM00353,Superfamily_domains:SSF47459 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 6419277 6419277 C T 1 0 0 0 0 1 0 0 0 6950 864 30 3 3 HES2 1 6419277 Missense_Mutation SNP C C3N-01489_T 276984 6419277 242537145 4 24934 PRAMEF2 0 . GRCh38 1 12859152 12859152 + Missense_Mutation SNP A A C novel C3N-01489_T C3N-01489_N A A c.143A>C p.His48Pro p.H48P ENST00000240189 2/4 530 501 29 892 891 1 varscan-mutect PRAMEF2,missense_variant,p.His48Pro,ENST00000240189,NM_023014.1; C ENST00000240189 Transcript missense_variant 230/1642 143/1425 48/474 H/P cAc/cCc 1 1 PRAMEF2 HGNC HGNC:28841 protein_coding YES CCDS149.1 ENSP00000240189 O60811 UPI0000139EF9 NM_023014.1 deleterious(0.04) 2/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 12859152 12859152 A C 1 0 0 0 0 1 0 0 0 12562 159 6 5 5 PRAMEF2 1 12859152 Missense_Mutation SNP A C3N-01489_T 6439875 12859152 236097270 5 24935 ATP13A2 0 . GRCh38 1 16990171 16990171 + Nonsense_Mutation SNP C C A rs754208001 C3N-01489_T C3N-01489_N C C c.2368G>T p.Glu790Ter p.E790* ENST00000326735 21/29 116 107 9 183 183 0 strelka-varscan-mutect ATP13A2,stop_gained,p.Glu785Ter,ENST00000452699,NM_001141973.2;ATP13A2,stop_gained,p.Glu790Ter,ENST00000326735,NM_022089.3;ATP13A2,stop_gained,p.Glu785Ter,ENST00000341676,NM_001141974.2;ATP13A2,upstream_gene_variant,,ENST00000502418,;ATP13A2,downstream_gene_variant,,ENST00000503552,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000466561,; A ENST00000326735 Transcript stop_gained 2402/3840 2368/3543 790/1180 E/* Gag/Tag rs754208001,COSM3802889,COSM3802890 1 -1 ATP13A2 HGNC HGNC:30213 protein_coding YES CCDS175.1 ENSP00000327214 Q9NQ11 UPI0000049724 NM_022089.3 21/29 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF86,TIGRFAM_domain:TIGR01657 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs754208001 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 16990171 16990171 C A 1 0 0 0 0 0 1 0 0 1276 893 31 1 1 ATP13A2 1 16990171 Nonsense_Mutation SNP C C3N-01489_T 4131019 16990171 231966251 6 24936 ATP13A2 0 . GRCh38 1 17000053 17000053 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.997C>T p.= p.L333L ENST00000326735 11/29 104 95 9 110 110 0 strelka-varscan-mutect ATP13A2,synonymous_variant,p.=,ENST00000452699,NM_001141973.2;ATP13A2,synonymous_variant,p.=,ENST00000326735,NM_022089.3;ATP13A2,synonymous_variant,p.=,ENST00000341676,NM_001141974.2;ATP13A2,synonymous_variant,p.=,ENST00000617114,;ATP13A2,synonymous_variant,p.=,ENST00000510069,;ATP13A2,synonymous_variant,p.=,ENST00000506174,;ATP13A2,upstream_gene_variant,,ENST00000503552,;ATP13A2,downstream_gene_variant,,ENST00000509619,;ATP13A2,downstream_gene_variant,,ENST00000511957,;ATP13A2,downstream_gene_variant,,ENST00000508222,;RP1-37C10.3,intron_variant,,ENST00000446261,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000463860,;ATP13A2,non_coding_transcript_exon_variant,,ENST00000502860,;ATP13A2,upstream_gene_variant,,ENST00000509392,; A ENST00000326735 Transcript synonymous_variant 1031/3840 997/3543 333/1180 L Ctg/Ttg 1 -1 ATP13A2 HGNC HGNC:30213 protein_coding YES CCDS175.1 ENSP00000327214 Q9NQ11 UPI0000049724 NM_022089.3 11/29 Superfamily_domains:0049471,Gene3D:2.70.150.10,Pfam_domain:PF00122,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF86,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01657 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.58168 1 1 1 1 0 A 2 1 81 17000053 17000053 G A 1 0 0 0 0 0 0 0 1 1276 991 35 3 3 ATP13A2 1 17000053 Silent SNP G C3N-01489_T 9882 17000053 231956369 7 24937 PADI6 0 . GRCh38 1 17394025 17394025 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1125G>T p.Leu375Phe p.L375F ENST00000619609 10/16 262 235 27 358 358 0 strelka-varscan-mutect PADI6,missense_variant,p.Leu375Phe,ENST00000619609,NM_207421.4; T ENST00000619609 Transcript missense_variant 1175/2396 1125/2085 375/694 L/F ttG/ttT 1 1 PADI6 HGNC HGNC:20449 protein_coding YES CCDS72715.1 ENSP00000483125 Q6TGC4 UPI0000253BE7 NM_207421.4 tolerated(0.09) 10/16 hmmpanther:PTHR10837:SF4,hmmpanther:PTHR10837,PIRSF_domain:PIRSF001247,Pfam_domain:PF03068,Superfamily_domains:SSF55909 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 17394025 17394025 G T 1 0 0 0 0 1 0 0 0 11459 1281 45 2 2 PADI6 1 17394025 Missense_Mutation SNP G C3N-01489_T 393972 17394025 231562397 8 24938 ALDH4A1 0 . GRCh38 1 18889382 18889382 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.229G>T p.Asp77Tyr p.D77Y ENST00000375341 3/15 221 198 23 315 315 0 strelka-varscan-mutect ALDH4A1,missense_variant,p.Asp77Tyr,ENST00000375341,NM_003748.3;ALDH4A1,missense_variant,p.Asp77Tyr,ENST00000538839,NM_001319218.1;ALDH4A1,missense_variant,p.Asp77Tyr,ENST00000290597,NM_170726.2;ALDH4A1,missense_variant,p.Asp17Tyr,ENST00000538309,NM_001161504.1;ALDH4A1,missense_variant,p.Asp77Tyr,ENST00000432718,;ALDH4A1,upstream_gene_variant,,ENST00000454547,;RP13-279N23.2,3_prime_UTR_variant,,ENST00000494072,; A ENST00000375341 Transcript missense_variant 487/3363 229/1692 77/563 D/Y Gac/Tac 1 -1 ALDH4A1 HGNC HGNC:406 protein_coding YES CCDS188.1 ENSP00000364490 P30038 A0A024RAD8 UPI000007418C NM_003748.3 deleterious(0.01) 3/15 hmmpanther:PTHR14516,hmmpanther:PTHR14516:SF1,Gene3D:3.40.605.10,TIGRFAM_domain:TIGR01236,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 18889382 18889382 C A 1 0 0 0 0 1 0 0 0 601 855 30 2 2 ALDH4A1 1 18889382 Missense_Mutation SNP C C3N-01489_T 1495357 18889382 230067040 9 24939 ARID1A 0 . GRCh38 1 26731326 26731326 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1525C>T p.Pro509Ser p.P509S ENST00000324856 3/20 491 458 33 729 729 0 strelka-varscan-mutect ARID1A,missense_variant,p.Pro509Ser,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Pro128Ser,ENST00000636219,;ARID1A,missense_variant,p.Pro126Ser,ENST00000430799,;ARID1A,missense_variant,p.Pro126Ser,ENST00000374152,;ARID1A,missense_variant,p.Pro509Ser,ENST00000457599,NM_139135.2;ARID1A,missense_variant,p.Pro126Ser,ENST00000615191,;ARID1A,missense_variant,p.Pro126Ser,ENST00000637465,;ARID1A,downstream_gene_variant,,ENST00000524572,; T ENST00000324856 Transcript missense_variant 1896/8577 1525/6858 509/2285 P/S Cca/Tca 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 deleterious_low_confidence(0.03) 3/20 Low_complexity_(Seg):seg,hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 MODERATE 1 SNV 1 1 PASS rs1453816622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 26731326 26731326 C T 1 0 0 0 0 1 0 0 0 1049 507 18 3 3 ARID1A 1 26731326 Missense_Mutation SNP C C3N-01489_T 7841944 26731326 222225096 10 24940 ARID1A 0 . GRCh38 1 26779444 26779444 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.5546G>T p.Gly1849Val p.G1849V ENST00000324856 20/20 211 183 28 316 316 0 strelka-varscan-mutect ARID1A,missense_variant,p.Gly1849Val,ENST00000324856,NM_006015.4;ARID1A,missense_variant,p.Gly1467Val,ENST00000636219,;ARID1A,missense_variant,p.Gly1465Val,ENST00000430799,;ARID1A,missense_variant,p.Gly1466Val,ENST00000374152,;ARID1A,missense_variant,p.Gly1632Val,ENST00000457599,NM_139135.2;ARID1A,downstream_gene_variant,,ENST00000615191,;ARID1A,downstream_gene_variant,,ENST00000636794,;ARID1A,3_prime_UTR_variant,,ENST00000466382,;ARID1A,3_prime_UTR_variant,,ENST00000532781,;ARID1A,non_coding_transcript_exon_variant,,ENST00000637788,;ARID1A,downstream_gene_variant,,ENST00000636072,; T ENST00000324856 Transcript missense_variant 5917/8577 5546/6858 1849/2285 G/V gGg/gTg 1 1 ARID1A HGNC HGNC:11110 protein_coding YES CCDS285.1 ENSP00000320485 O14497 UPI0000167B91 NM_006015.4 deleterious(0) 20/20 hmmpanther:PTHR12656,hmmpanther:PTHR12656:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 26779444 26779444 G T 1 0 0 0 0 1 0 0 0 1049 1232 43 2 2 ARID1A 1 26779444 Missense_Mutation SNP G C3N-01489_T 48118 26779444 222176978 11 24941 WDTC1 0 . GRCh38 1 27305091 27305091 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1734G>T p.= p.G578G ENST00000319394 15/16 185 150 35 221 221 0 strelka-varscan-mutect WDTC1,synonymous_variant,p.=,ENST00000319394,NM_001276252.1;WDTC1,synonymous_variant,p.=,ENST00000361771,NM_015023.4;WDTC1,missense_variant,p.Gly559Val,ENST00000447062,;WDTC1,synonymous_variant,p.=,ENST00000472249,;WDTC1,non_coding_transcript_exon_variant,,ENST00000491239,; T ENST00000319394 Transcript synonymous_variant 2269/4819 1734/2034 578/677 G ggG/ggT 1 1 WDTC1 HGNC HGNC:29175 protein_coding YES CCDS60044.1 ENSP00000317971 Q8N5D0 UPI000004814E NM_001276252.1 15/16 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF40,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 27305091 27305091 G T 1 0 0 0 0 0 0 0 1 17899 1219 43 2 2 WDTC1 1 27305091 Silent SNP G C3N-01489_T 525647 27305091 221651331 12 24942 FCN3 0 . GRCh38 1 27369357 27369357 + Missense_Mutation SNP C C A rs143244488 C3N-01489_T C3N-01489_N C C c.779G>T p.Arg260Leu p.R260L ENST00000270879 8/8 382 320 62 551 551 0 strelka-varscan-mutect FCN3,missense_variant,p.Arg260Leu,ENST00000270879,NM_003665.2;FCN3,missense_variant,p.Arg249Leu,ENST00000354982,NM_173452.1;MAP3K6,upstream_gene_variant,,ENST00000374040,NM_001297609.1;MAP3K6,upstream_gene_variant,,ENST00000493901,NM_004672.4;MAP3K6,upstream_gene_variant,,ENST00000357582,;FCN3,downstream_gene_variant,,ENST00000481748,;FCN3,downstream_gene_variant,,ENST00000498393,; A ENST00000270879 Transcript missense_variant 785/1030 779/900 260/299 R/L cGa/cTa rs143244488,COSM1502553,COSM907868 1 -1 FCN3 HGNC HGNC:3625 protein_coding YES CCDS300.1 ENSP00000270879 O75636 UPI00000343FF NM_003665.2 tolerated(0.67) 8/8 PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF215,PROSITE_patterns:PS00514,Pfam_domain:PF00147,Gene3D:4.10.530.10,SMART_domains:SM00186,Superfamily_domains:SSF56496 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs143244488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 27369357 27369357 C A 1 0 0 0 0 1 0 0 0 5656 884 31 1 1 FCN3 1 27369357 Missense_Mutation SNP C C3N-01489_T 64266 27369357 221587065 13 24943 RCC1 0 . GRCh38 1 28532234 28532234 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.418G>A p.Glu140Lys p.E140K ENST00000373831 5/11 217 191 26 351 351 0 strelka-varscan-mutect RCC1,missense_variant,p.Glu109Lys,ENST00000373833,;RCC1,missense_variant,p.Glu109Lys,ENST00000398958,NM_001048199.2;RCC1,missense_variant,p.Glu109Lys,ENST00000373832,NM_001269.4;RCC1,missense_variant,p.Glu140Lys,ENST00000373831,NM_001048195.2,NM_001048194.2;RCC1,missense_variant,p.Glu126Lys,ENST00000411533,;RCC1,missense_variant,p.Glu109Lys,ENST00000430407,;RCC1,missense_variant,p.Glu117Lys,ENST00000434290,;RCC1,missense_variant,p.Glu109Lys,ENST00000419074,;RCC1,missense_variant,p.Glu109Lys,ENST00000427469,;RCC1,downstream_gene_variant,,ENST00000486790,;RCC1,non_coding_transcript_exon_variant,,ENST00000429051,;RCC1,upstream_gene_variant,,ENST00000478232,; A ENST00000373831 Transcript missense_variant 479/1577 418/1359 140/452 E/K Gag/Aag 1 1 RCC1 HGNC HGNC:1913 protein_coding YES CCDS41295.1 ENSP00000362937 P18754 A0A0S2Z404 UPI0000204066 NM_001048195.2,NM_001048194.2 deleterious(0.03) 5/11 Gene3D:2.130.10.30,Pfam_domain:PF00415,PROSITE_profiles:PS50012,hmmpanther:PTHR22870,hmmpanther:PTHR22870:SF179,Superfamily_domains:SSF50985 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 28532234 28532234 G A 1 0 0 0 0 1 0 0 0 13342 1175 41 3 3 RCC1 1 28532234 Missense_Mutation SNP G C3N-01489_T 1162877 28532234 220424188 14 24944 ADGRB2 0 . GRCh38 1 31740121 31740121 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.2047G>T p.Asp683Tyr p.D683Y ENST00000373655 13/33 289 268 21 390 388 2 strelka-varscan-mutect ADGRB2,missense_variant,p.Asp683Tyr,ENST00000373658,;ADGRB2,missense_variant,p.Asp683Tyr,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.Asp616Tyr,ENST00000398542,;ADGRB2,missense_variant,p.Asp683Tyr,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.Asp631Tyr,ENST00000398556,;ADGRB2,missense_variant,p.Asp616Tyr,ENST00000398547,;ADGRB2,missense_variant,p.Asp671Tyr,ENST00000398538,;ADGRB2,missense_variant,p.Asp621Tyr,ENST00000420125,;ADGRB2,downstream_gene_variant,,ENST00000533175,;ADGRB2,intron_variant,,ENST00000530134,;ADGRB2,downstream_gene_variant,,ENST00000468430,;ADGRB2,upstream_gene_variant,,ENST00000465256,;ADGRB2,upstream_gene_variant,,ENST00000530999,;ADGRB2,upstream_gene_variant,,ENST00000466109,; A ENST00000373655 Transcript missense_variant 2389/5400 2047/4755 683/1584 D/Y Gat/Tat COSM4168571 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 deleterious(0) 13/33 hmmpanther:PTHR12011:SF41,hmmpanther:PTHR12011,Pfam_domain:PF16489,Prints_domain:PR01694 1 MODERATE 1 SNV 1 1 1 PASS rs1471496906 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 31740121 31740121 C A 1 0 0 0 0 1 0 0 0 356 884 31 1 1 ADGRB2 1 31740121 Missense_Mutation SNP C C3N-01489_T 3207887 31740121 217216301 15 24945 TRIM62 0 . GRCh38 1 33165561 33165561 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.414G>A p.= p.E138E ENST00000291416 2/5 38 31 7 77 77 0 strelka-varscan-mutect TRIM62,synonymous_variant,p.=,ENST00000291416,NM_018207.2;TRIM62,synonymous_variant,p.=,ENST00000543586,;RP11-131M11.3,non_coding_transcript_exon_variant,,ENST00000624339,;TRIM62,non_coding_transcript_exon_variant,,ENST00000485148,; T ENST00000291416 Transcript synonymous_variant 648/3437 414/1428 138/475 E gaG/gaA 1 -1 TRIM62 HGNC HGNC:25574 protein_coding YES CCDS376.1 ENSP00000291416 Q9BVG3 UPI000004E050 NM_018207.2 2/5 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF30,Superfamily_domains:SSF57845,Coiled-coils_(Ncoils):Coil LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -17.84314 1 1 1 1 0 T 2 4 81 33165561 33165561 C T 1 0 0 0 0 0 0 0 1 17029 811 28 3 3 TRIM62 1 33165561 Silent SNP C C3N-01489_T 1425440 33165561 215790861 16 24946 RSPO1 0 . GRCh38 1 37616662 37616662 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.108G>A p.= p.G36G ENST00000356545 4/7 181 158 23 262 261 1 strelka-varscan-mutect RSPO1,synonymous_variant,p.=,ENST00000356545,NM_001242908.1;RSPO1,synonymous_variant,p.=,ENST00000612451,NM_001242910.1;RSPO1,synonymous_variant,p.=,ENST00000615459,NM_001242909.1;RSPO1,synonymous_variant,p.=,ENST00000401068,NM_001038633.3; T ENST00000356545 Transcript synonymous_variant 821/2621 108/792 36/263 G ggG/ggA 1 -1 RSPO1 HGNC HGNC:21679 protein_coding YES CCDS41304.1 ENSP00000348944 Q2MKA7 UPI0000674A16 NM_001242908.1 4/7 hmmpanther:PTHR23275,hmmpanther:PTHR23275:SF44,SMART_domains:SM00261 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 37616662 37616662 C T 1 0 0 0 0 0 0 0 1 13967 842 30 3 3 RSPO1 1 37616662 Silent SNP C C3N-01489_T 4451101 37616662 211339760 17 24947 EPHA10 0 . GRCh38 1 37761481 37761481 + Silent SNP G G C novel C3N-01489_T C3N-01489_N G G c.774C>G p.= p.A258A ENST00000373048 3/17 136 128 8 232 232 0 strelka-varscan-mutect EPHA10,synonymous_variant,p.=,ENST00000373048,NM_001099439.1;EPHA10,synonymous_variant,p.=,ENST00000427468,;EPHA10,synonymous_variant,p.=,ENST00000319637,NM_173641.2;EPHA10,upstream_gene_variant,,ENST00000446149,; C ENST00000373048 Transcript synonymous_variant 774/5425 774/3027 258/1008 A gcC/gcG 1 -1 EPHA10 HGNC HGNC:19987 protein_coding YES CCDS41305.1 ENSP00000362139 Q5JZY3 UPI00001A41BD NM_001099439.1 3/17 Gene3D:2gy5A03,PIRSF_domain:PIRSF000666,PROSITE_patterns:PS00791,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF258 LOW 1 SNV 5 1 PASS rs1221302559 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 37761481 37761481 G C 1 0 0 0 0 0 0 0 1 5013 1103 39 4 4 EPHA10 1 37761481 Silent SNP G C3N-01489_T 144819 37761481 211194941 18 24948 AGBL4 0 . GRCh38 1 48634561 48634561 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.883C>A p.Pro295Thr p.P295T ENST00000371839 9/14 134 124 10 191 191 0 strelka-varscan-mutect AGBL4,missense_variant,p.Pro141Thr,ENST00000416121,;AGBL4,missense_variant,p.Pro295Thr,ENST00000371839,NM_032785.3;AGBL4,missense_variant,p.Pro295Thr,ENST00000371838,;AGBL4,missense_variant,p.Pro84Thr,ENST00000334103,; T ENST00000371839 Transcript missense_variant 1000/2947 883/1512 295/503 P/T Ccc/Acc 1 -1 AGBL4 HGNC HGNC:25892 protein_coding YES CCDS44137.1 ENSP00000360905 Q5VU57 UPI00002042F9 NM_032785.3 tolerated(0.08) 9/14 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR12756,SMART_domains:SM00631,Superfamily_domains:SSF53187 MODERATE 1 SNV 2 1 PASS rs1352783869 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 48634561 48634561 G T 1 0 0 0 0 1 0 0 0 454 1174 41 2 2 AGBL4 1 48634561 Missense_Mutation SNP G C3N-01489_T 10873080 48634561 200321861 19 24949 ZFYVE9 0 . GRCh38 1 52239586 52239586 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.2169A>T p.= p.A723A ENST00000287727 4/19 65 57 8 117 117 0 strelka-varscan-mutect ZFYVE9,synonymous_variant,p.=,ENST00000287727,NM_004799.3;ZFYVE9,synonymous_variant,p.=,ENST00000371591,;ZFYVE9,synonymous_variant,p.=,ENST00000357206,NM_007324.3;ZFYVE9,non_coding_transcript_exon_variant,,ENST00000361625,; T ENST00000287727 Transcript synonymous_variant 2621/5194 2169/4278 723/1425 A gcA/gcT 1 1 ZFYVE9 HGNC HGNC:6775 protein_coding YES CCDS563.1 ENSP00000287727 O95405 UPI0000001620 NM_004799.3 4/19 PROSITE_profiles:PS50178,hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF265,Pfam_domain:PF01363,Gene3D:3.30.40.10,SMART_domains:SM00064,Superfamily_domains:SSF57903 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -18.16764 1 1 1 1 0 T 2 4 81 52239586 52239586 A T 1 0 0 0 0 0 0 0 1 18248 204 8 4 4 ZFYVE9 1 52239586 Silent SNP A C3N-01489_T 3605025 52239586 196716836 20 24950 PODN 0 . GRCh38 1 53082140 53082140 + Missense_Mutation SNP G G T rs756994868 C3N-01489_T C3N-01489_N G G c.1965G>T p.Glu655Asp p.E655D ENST00000312553 10/11 73 65 8 104 104 0 strelka-varscan-mutect PODN,missense_variant,p.Glu636Asp,ENST00000371500,NM_001199080.1;PODN,missense_variant,p.Glu636Asp,ENST00000618387,NM_001199081.1;PODN,missense_variant,p.Glu655Asp,ENST00000312553,NM_153703.4;PODN,missense_variant,p.Glu513Asp,ENST00000395871,NM_001199082.1;RP11-334A14.5,intron_variant,,ENST00000447867,;PODN,non_coding_transcript_exon_variant,,ENST00000490650,;PODN,downstream_gene_variant,,ENST00000471285,; T ENST00000312553 Transcript missense_variant 1972/3010 1965/1986 655/661 E/D gaG/gaT rs756994868 1 1 PODN HGNC HGNC:23174 protein_coding YES CCDS573.1 ENSP00000308315 Q7Z5L7 UPI000034ECE9 NM_153703.4 deleterious_low_confidence(0) 10/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF12,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs756994868 . 0 199 10 0 0 0 0 0 -17.3033 0.9999664 1 1 1 0 T 3 4 81 53082140 53082140 G T 1 0 0 0 0 1 0 0 0 12287 991 35 2 2 PODN 1 53082140 Missense_Mutation SNP G C3N-01489_T 842554 53082140 195874282 21 24951 SLC1A7 0 . GRCh38 1 53105754 53105754 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.452T>A p.Leu151Gln p.L151Q ENST00000620347 4/11 230 200 30 326 325 1 strelka-varscan-mutect SLC1A7,missense_variant,p.Leu151Gln,ENST00000620288,;SLC1A7,missense_variant,p.Leu151Gln,ENST00000620347,NM_001287595.1;SLC1A7,missense_variant,p.Leu151Gln,ENST00000371494,NM_006671.5;SLC1A7,missense_variant,p.Leu79Gln,ENST00000611397,NM_001287597.1;SLC1A7,downstream_gene_variant,,ENST00000371491,NM_001287596.1; T ENST00000620347 Transcript missense_variant 635/2873 452/1860 151/619 L/Q cTa/cAa 1 -1 SLC1A7 HGNC HGNC:10945 protein_coding YES CCDS72797.1 ENSP00000478639 A0A087WUF9 UPI000387D8A4 NM_001287595.1 deleterious(0) 4/11 hmmpanther:PTHR11958,hmmpanther:PTHR11958:SF22,Gene3D:2nwlC00,Pfam_domain:PF00375,Superfamily_domains:0053221 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 53105754 53105754 A T 1 0 0 0 0 1 0 0 0 14703 420 15 4 4 SLC1A7 1 53105754 Missense_Mutation SNP A C3N-01489_T 23614 53105754 195850668 22 24952 NDC1 0 . GRCh38 1 53825862 53825862 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.530G>T p.Gly177Val p.G177V ENST00000371429 5/18 168 152 16 232 231 1 strelka-varscan-mutect NDC1,missense_variant,p.Gly177Val,ENST00000371429,NM_001168551.1,NM_018087.4;NDC1,non_coding_transcript_exon_variant,,ENST00000480952,; A ENST00000371429 Transcript missense_variant 1129/5134 530/2025 177/674 G/V gGc/gTc COSM4879885 1 -1 NDC1 HGNC HGNC:25525 protein_coding YES CCDS583.1 ENSP00000360483 Q9BTX1 UPI000006D8F7 NM_001168551.1,NM_018087.4 deleterious(0) 5/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR13269:SF6,hmmpanther:PTHR13269,Pfam_domain:PF09531 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 53825862 53825862 C A 1 0 0 0 0 1 0 0 0 10262 739 26 2 2 NDC1 1 53825862 Missense_Mutation SNP C C3N-01489_T 720108 53825862 195130560 23 24953 MROH7 0 . GRCh38 1 54686393 54686393 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2656G>T p.Ala886Ser p.A886S ENST00000421030 15/24 237 214 23 274 274 0 strelka-varscan-mutect MROH7,missense_variant,p.Ala886Ser,ENST00000421030,NM_001039464.3;MROH7,missense_variant,p.Ala886Ser,ENST00000339553,;MROH7,missense_variant,p.Ala886Ser,ENST00000395690,;MROH7,missense_variant,p.Ala454Ser,ENST00000409996,NM_001291332.1;MROH7-TTC4,missense_variant,p.Ala886Ser,ENST00000414150,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000425300,;MROH7-TTC4,3_prime_UTR_variant,,ENST00000606515,;MROH7,3_prime_UTR_variant,,ENST00000422659,;MROH7,3_prime_UTR_variant,,ENST00000440047,;MROH7,3_prime_UTR_variant,,ENST00000438846,;MROH7,3_prime_UTR_variant,,ENST00000440217,;MROH7,non_coding_transcript_exon_variant,,ENST00000493533,;MROH7,intron_variant,,ENST00000413188,; T ENST00000421030 Transcript missense_variant 2941/4329 2656/3972 886/1323 A/S Gct/Tct 1 1 MROH7 HGNC HGNC:24802 protein_coding YES CCDS41342.2 ENSP00000396622 Q68CQ1 UPI000198C4E2 NM_001039464.3 tolerated(0.46) 15/24 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF17 MODERATE 1 SNV 2 1 PASS rs1330756620 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 81 54686393 54686393 G T 1 0 0 0 0 1 0 0 0 9747 1203 42 2 2 MROH7 1 54686393 Missense_Mutation SNP G C3N-01489_T 860531 54686393 194270029 24 24954 PARS2 0 . GRCh38 1 54758991 54758991 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.171C>A p.= p.L57L ENST00000371279 2/2 89 82 7 113 113 0 strelka-varscan-mutect PARS2,synonymous_variant,p.=,ENST00000371279,NM_152268.3; T ENST00000371279 Transcript synonymous_variant 254/2347 171/1428 57/475 L ctC/ctA 1 -1 PARS2 HGNC HGNC:30563 protein_coding YES CCDS597.1 ENSP00000360327 Q7L3T8 UPI00000492D2 NM_152268.3 2/2 PROSITE_profiles:PS50862 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 54758991 54758991 G T 1 0 0 0 0 0 0 0 1 11548 929 33 2 2 PARS2 1 54758991 Silent SNP G C3N-01489_T 72598 54758991 194197431 25 24955 AK4 0 . GRCh38 1 65224782 65224782 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.469G>A p.Val157Ile p.V157I ENST00000395334 5/6 122 109 13 212 212 0 strelka-varscan-mutect AK4,missense_variant,p.Val157Ile,ENST00000395334,NM_001005353.2;AK4,missense_variant,p.Val157Ile,ENST00000545314,NM_203464.2;AK4,missense_variant,p.Val157Ile,ENST00000327299,NM_013410.3;AK4,missense_variant,p.Val105Ile,ENST00000546702,;AK4,non_coding_transcript_exon_variant,,ENST00000470888,;AK4,non_coding_transcript_exon_variant,,ENST00000474968,;AK4,non_coding_transcript_exon_variant,,ENST00000479060,;AK4,non_coding_transcript_exon_variant,,ENST00000497030,; A ENST00000395334 Transcript missense_variant 827/6998 469/672 157/223 V/I Gtc/Atc 1 1 AK4 HGNC HGNC:363 protein_coding YES CCDS629.1 ENSP00000378743 P27144 UPI000011E13C NM_001005353.2 tolerated(0.57) 5/6 HAMAP:MF_03169,HAMAP:MF_03170,HAMAP:MF_00235,hmmpanther:PTHR23359,hmmpanther:PTHR23359:SF58,TIGRFAM_domain:TIGR01351,Gene3D:3.40.50.300,Pfam_domain:PF00406,Pfam_domain:PF05191,Superfamily_domains:SSF57774 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 65224782 65224782 G A 1 0 0 0 0 1 0 0 0 521 1029 36 3 3 AK4 1 65224782 Missense_Mutation SNP G C3N-01489_T 10465791 65224782 183731640 26 24956 INSL5 0 . GRCh38 1 66798126 66798126 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.295C>A p.Pro99Thr p.P99T ENST00000304526 2/2 259 238 21 409 409 0 strelka-varscan-mutect INSL5,missense_variant,p.Pro99Thr,ENST00000304526,NM_005478.4; T ENST00000304526 Transcript missense_variant 330/715 295/408 99/135 P/T Ccc/Acc 1 -1 INSL5 HGNC HGNC:6088 protein_coding YES CCDS634.1 ENSP00000302724 Q9Y5Q6 UPI000013E991 NM_005478.4 deleterious(0.01) 2/2 Pfam_domain:PF00049,hmmpanther:PTHR20968,hmmpanther:PTHR20968:SF2,SMART_domains:SM00078 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 66798126 66798126 G T 1 0 0 0 0 1 0 0 0 7671 1203 42 2 2 INSL5 1 66798126 Missense_Mutation SNP G C3N-01489_T 1573344 66798126 182158296 27 24957 LRRC53 0 . GRCh38 1 74480825 74480825 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.232C>A p.His78Asn p.H78N ENST00000294635 3/5 344 320 24 462 461 1 strelka-varscan-mutect LRRC53,missense_variant,p.His78Asn,ENST00000294635,;TNNI3K,intron_variant,,ENST00000326637,NM_015978.2;FPGT-TNNI3K,intron_variant,,ENST00000557284,NM_001112808.2; T ENST00000294635 Transcript missense_variant 347/3859 232/3744 78/1247 H/N Cat/Aat 1 -1 LRRC53 HGNC HGNC:25255 protein_coding YES ENSP00000294635 A6NM62 UPI000178DEDE tolerated(0.23) 3/5 Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF379,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 74480825 74480825 G T 1 0 0 0 0 1 0 0 0 8905 1319 46 2 2 LRRC53 1 74480825 Missense_Mutation SNP G C3N-01489_T 7682699 74480825 174475597 28 24958 ST6GALNAC3 0 . GRCh38 1 76412077 76412077 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.283G>T p.Gly95Ter p.G95* ENST00000328299 3/5 207 187 20 286 286 0 strelka-varscan-mutect ST6GALNAC3,stop_gained,p.Gly95Ter,ENST00000328299,NM_152996.2;ST6GALNAC3,stop_gained,p.Gly24Ter,ENST00000621530,;ST6GALNAC3,non_coding_transcript_exon_variant,,ENST00000464140,; T ENST00000328299 Transcript stop_gained 431/6861 283/918 95/305 G/* Gga/Tga 1 1 ST6GALNAC3 HGNC HGNC:19343 protein_coding YES CCDS672.1 ENSP00000329214 Q8NDV1 UPI000006F75A NM_152996.2 3/5 Pfam_domain:PF00777,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF49 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 76412077 76412077 G T 1 0 0 0 0 0 1 0 0 15603 1233 43 2 2 ST6GALNAC3 1 76412077 Nonsense_Mutation SNP G C3N-01489_T 1931252 76412077 172544345 29 24959 AK5 0 . GRCh38 1 77340517 77340517 + Missense_Mutation SNP G G T rs777885275 C3N-01489_T C3N-01489_N G G c.840G>T p.Gln280His p.Q280H ENST00000354567 6/14 173 157 16 262 262 0 strelka-varscan-mutect AK5,missense_variant,p.Gln254His,ENST00000344720,NM_012093.3;AK5,missense_variant,p.Gln280His,ENST00000354567,NM_174858.2;AK5,non_coding_transcript_exon_variant,,ENST00000524494,;AK5,non_coding_transcript_exon_variant,,ENST00000465146,; T ENST00000354567 Transcript missense_variant 1103/3251 840/1689 280/562 Q/H caG/caT rs777885275,COSM4560372 1 1 AK5 HGNC HGNC:365 protein_coding YES CCDS675.1 ENSP00000346577 Q9Y6K8 UPI0000167E20 NM_174858.2 deleterious(0.04) 6/14 HAMAP:MF_00235,hmmpanther:PTHR23359:SF79,hmmpanther:PTHR23359,Pfam_domain:PF00406,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777885275 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 77340517 77340517 G T 1 0 0 0 0 1 0 0 0 522 933 33 2 2 AK5 1 77340517 Missense_Mutation SNP G C3N-01489_T 928440 77340517 171615905 30 24960 CLCA4 0 . GRCh38 1 86560240 86560240 + Silent SNP C C A C3N-01489_T C3N-01489_N C C c.330C>A p.= p.L110L ENST00000370563 3/14 135 126 9 203 202 1 strelka-varscan-mutect CLCA4,synonymous_variant,p.=,ENST00000370563,NM_012128.3; A ENST00000370563 Transcript synonymous_variant 372/3211 330/2760 110/919 L ctC/ctA COSM4488326 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 3/14 hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 1 LOW 1 SNV 1 1 1 PASS rs1343178324 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 86560240 86560240 C A 1 0 0 0 0 0 0 0 1 3223 842 30 2 2 CLCA4 1 86560240 Silent SNP C C3N-01489_T 9219723 86560240 162396182 31 24961 AC096949.1 0 . GRCh38 1 99864435 99864435 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.510G>A p.= p.R170R ENST00000294724 5/34 347 312 35 498 498 0 strelka-varscan-mutect AGL,synonymous_variant,p.=,ENST00000294724,NM_000028.2;AGL,synonymous_variant,p.=,ENST00000361915,NM_000642.2;AGL,synonymous_variant,p.=,ENST00000370163,NM_000643.2;AGL,synonymous_variant,p.=,ENST00000370165,NM_000644.2;AGL,synonymous_variant,p.=,ENST00000370161,NM_000646.2;AC096949.1,synonymous_variant,p.=,ENST00000361522,NM_000645.2;AGL,3_prime_UTR_variant,,ENST00000361302,;AGL,non_coding_transcript_exon_variant,,ENST00000637337,; A ENST00000294724 Transcript synonymous_variant 988/7446 510/4599 170/1532 R agG/agA 1 1 AGL HGNC HGNC:321 protein_coding YES CCDS759.1 ENSP00000294724 P35573 A0A0S2A4E4 UPI00001694CB NM_000028.2 5/34 hmmpanther:PTHR10569,TIGRFAM_domain:TIGR01531,Pfam_domain:PF14701,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 99864435 99864435 G A 1 0 0 0 0 0 0 0 1 135 1252 44 3 3 AC096949.1 1 99864435 Silent SNP G C3N-01489_T 13304195 99864435 149091987 32 24962 RNPC3 0 . GRCh38 1 103534799 103534799 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.385A>G p.Lys129Glu p.K129E ENST00000533099 5/16 131 123 8 233 233 0 strelka-varscan-mutect RNPC3,missense_variant,p.Lys129Glu,ENST00000533099,;RNPC3,missense_variant,p.Lys129Glu,ENST00000524631,;RNPC3,missense_variant,p.Lys129Glu,ENST00000423855,NM_017619.3;RNPC3,missense_variant,p.Lys129Glu,ENST00000531883,;RNPC3,5_prime_UTR_variant,,ENST00000527062,;RNPC3,upstream_gene_variant,,ENST00000533834,; G ENST00000533099 Transcript missense_variant 621/3641 385/1554 129/517 K/E Aaa/Gaa 1 1 RNPC3 HGNC HGNC:18666 protein_coding YES CCDS781.1 ENSP00000432886 Q96LT9 UPI000006E703 tolerated(0.16) 5/16 Low_complexity_(Seg):seg,hmmpanther:PTHR16105,hmmpanther:PTHR16105:SF0 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 103534799 103534799 A G 1 0 0 0 0 1 0 0 0 13687 363 13 5 5 RNPC3 1 103534799 Missense_Mutation SNP A C3N-01489_T 3670364 103534799 145421623 33 24963 AMY2B 0 . GRCh38 1 103573216 103573216 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.469A>G p.Lys157Glu p.K157E ENST00000361355 5/12 208 187 21 345 345 0 varscan-mutect AMY2B,missense_variant,p.Lys157Glu,ENST00000361355,NM_020978.4;AMY2B,missense_variant,p.Lys157Glu,ENST00000610648,;AMY2B,downstream_gene_variant,,ENST00000453959,;AMY2B,downstream_gene_variant,,ENST00000435302,;AMY2B,non_coding_transcript_exon_variant,,ENST00000491397,;AMY2B,upstream_gene_variant,,ENST00000481821,;AMY2B,upstream_gene_variant,,ENST00000462971,;AMY2B,missense_variant,p.Lys157Glu,ENST00000477657,;ACTG1P4,downstream_gene_variant,,ENST00000425123,; G ENST00000361355 Transcript missense_variant 1085/2181 469/1536 157/511 K/E Aaa/Gaa 1 1 AMY2B HGNC HGNC:478 protein_coding YES CCDS782.1 ENSP00000354610 P19961 UPI0000000CB1 NM_020978.4 tolerated(0.76) 5/12 hmmpanther:PTHR10357:SF105,hmmpanther:PTHR10357,Gene3D:3.20.20.80,Pfam_domain:PF00128,SMART_domains:SM00642,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 103573216 103573216 A G 1 0 0 0 0 1 0 0 0 692 363 13 5 5 AMY2B 1 103573216 Missense_Mutation SNP A C3N-01489_T 38417 103573216 145383206 34 24964 NTNG1 0 . GRCh38 1 107324349 107324349 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.314T>A p.Leu105Gln p.L105Q ENST00000370068 3/8 172 146 26 282 281 1 strelka-varscan-mutect NTNG1,missense_variant,p.Leu105Gln,ENST00000370067,;NTNG1,missense_variant,p.Leu105Gln,ENST00000370068,;NTNG1,missense_variant,p.Leu105Gln,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Leu105Gln,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Leu105Gln,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Leu105Gln,ENST00000370065,;NTNG1,missense_variant,p.Leu105Gln,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; A ENST00000370068 Transcript missense_variant 1160/4034 314/1620 105/539 L/Q cTg/cAg 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.60.120.260,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 107324349 107324349 T A 1 0 0 0 0 1 0 0 0 10769 1580 55 4 4 NTNG1 1 107324349 Missense_Mutation SNP T C3N-01489_T 3751133 107324349 141632073 35 24965 NTNG1 0 . GRCh38 1 107324505 107324505 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.470C>A p.Pro157Gln p.P157Q ENST00000370068 3/8 219 204 15 368 367 1 strelka-varscan-mutect NTNG1,missense_variant,p.Pro157Gln,ENST00000370067,;NTNG1,missense_variant,p.Pro157Gln,ENST00000370068,;NTNG1,missense_variant,p.Pro157Gln,ENST00000370073,NM_001113226.1;NTNG1,missense_variant,p.Pro157Gln,ENST00000370071,NM_001113228.1;NTNG1,missense_variant,p.Pro157Gln,ENST00000370074,NM_014917.2;NTNG1,missense_variant,p.Pro157Gln,ENST00000370065,;NTNG1,missense_variant,p.Pro157Gln,ENST00000370066,;NTNG1,non_coding_transcript_exon_variant,,ENST00000477948,;NTNG1,non_coding_transcript_exon_variant,,ENST00000294649,; A ENST00000370068 Transcript missense_variant 1316/4034 470/1620 157/539 P/Q cCa/cAa 1 1 NTNG1 HGNC HGNC:23319 protein_coding YES CCDS44180.1 ENSP00000359085 Q9Y2I2 UPI0000458A3E deleterious(0.01) 3/8 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF28,hmmpanther:PTHR10574,Gene3D:2.60.120.260,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 107324505 107324505 C A 1 0 0 0 0 1 0 0 0 10769 594 21 2 2 NTNG1 1 107324505 Missense_Mutation SNP C C3N-01489_T 156 107324505 141631917 36 24966 AKNAD1 0 . GRCh38 1 108849568 108849568 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1002C>A p.= p.P334P ENST00000370001 3/16 157 149 8 243 243 0 strelka-varscan-mutect AKNAD1,synonymous_variant,p.=,ENST00000370001,NM_152763.4;AKNAD1,synonymous_variant,p.=,ENST00000369995,;AKNAD1,synonymous_variant,p.=,ENST00000369994,;RP11-475E11.9,synonymous_variant,p.=,ENST00000357393,;AKNAD1,synonymous_variant,p.=,ENST00000474186,;AKNAD1,synonymous_variant,p.=,ENST00000461774,;AKNAD1,synonymous_variant,p.=,ENST00000472781,; T ENST00000370001 Transcript synonymous_variant 1271/3053 1002/2511 334/836 P ccC/ccA 1 -1 AKNAD1 HGNC HGNC:28398 protein_coding YES CCDS791.2 ENSP00000359018 Q5T1N1 UPI00004700A0 NM_152763.4 3/16 Pfam_domain:PF12443,hmmpanther:PTHR21510,hmmpanther:PTHR21510:SF16 LOW 1 SNV 1 1 PASS rs1475665025 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 108849568 108849568 G T 1 0 0 0 0 0 0 0 1 548 1335 47 2 2 AKNAD1 1 108849568 Silent SNP G C3N-01489_T 1525063 108849568 140106854 37 24967 GNAT2 0 . GRCh38 1 109608723 109608723 + Silent SNP G G T rs12046787 C3N-01489_T C3N-01489_N G G c.369C>A p.= p.L123L ENST00000351050 4/8 354 310 44 549 549 0 strelka-varscan-mutect GNAT2,synonymous_variant,p.=,ENST00000351050,NM_005272.3;GNAT2,synonymous_variant,p.=,ENST00000622865,;GNAI3,3_prime_UTR_variant,,ENST00000369851,NM_006496.3; T ENST00000351050 Transcript synonymous_variant 556/1339 369/1065 123/354 L ctC/ctA rs12046787 1 -1 GNAT2 HGNC HGNC:4394 protein_coding YES CCDS803.1 ENSP00000251337 P19087 Q5T697 UPI000000124D NM_005272.3 4/8 Gene3D:1.10.400.10,Pfam_domain:PF00503,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF68,SMART_domains:SM00275,Superfamily_domains:SSF47895 LOW 1 SNV 1 1 PASS rs12046787 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 109608723 109608723 G T 1 0 0 0 0 0 0 0 1 6392 1045 37 1 1 GNAT2 1 109608723 Silent SNP G C3N-01489_T 759155 109608723 139347699 38 24968 ANKRD35 0 . GRCh38 1 145872785 145872785 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1984G>T p.Ala662Ser p.A662S ENST00000355594 10/14 154 132 22 215 215 0 strelka-varscan-mutect ANKRD35,missense_variant,p.Ala662Ser,ENST00000355594,NM_144698.4;ANKRD35,missense_variant,p.Ala572Ser,ENST00000544626,NM_001280799.1; A ENST00000355594 Transcript missense_variant 2071/3342 1984/3006 662/1001 A/S Gcg/Tcg 1 -1 ANKRD35 HGNC HGNC:26323 protein_coding YES CCDS72867.1 ENSP00000347802 Q8N283 UPI0002747112 NM_144698.4 tolerated(0.14) 10/14 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 145872785 145872785 C A 1 0 0 0 0 1 0 0 0 770 739 26 2 2 ANKRD35 1 145872785 Missense_Mutation SNP C C3N-01489_T 36264062 145872785 103083637 39 24969 BCL9 0 . GRCh38 1 147622288 147622288 + Missense_Mutation SNP A A T rs587754307 C3N-01489_T C3N-01489_N A A c.2920A>T p.Thr974Ser p.T974S ENST00000234739 9/10 145 123 22 236 236 0 strelka-varscan-mutect BCL9,missense_variant,p.Thr974Ser,ENST00000234739,NM_004326.3; T ENST00000234739 Transcript missense_variant 3660/6278 2920/4281 974/1426 T/S Aca/Tca rs587754307 1 1 BCL9 HGNC HGNC:1008 protein_coding YES CCDS30833.1 ENSP00000234739 O00512 A0A024QYY4 UPI000013C9B9 NM_004326.3 tolerated(1) 9/10 hmmpanther:PTHR15185,hmmpanther:PTHR15185:SF5 MODERATE 1 SNV 1 1 PASS rs587754307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 147622288 147622288 A T 1 0 0 0 0 1 0 0 0 1528 391 14 4 4 BCL9 1 147622288 Missense_Mutation SNP A C3N-01489_T 1749503 147622288 101334134 40 24970 NBPF11 0 . GRCh38 1 148117644 148117644 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1234G>T p.Gly412Trp p.G412W ENST00000615281 12/24 60 50 10 63 63 0 varscan-mutect NBPF11,missense_variant,p.Gly412Trp,ENST00000615281,NM_183372.5;NBPF11,missense_variant,p.Gly412Trp,ENST00000614015,NM_001101663.4;NBPF11,missense_variant,p.Gly377Trp,ENST00000614785,;NBPF11,missense_variant,p.Gly337Trp,ENST00000613531,;NBPF11,missense_variant,p.Gly337Trp,ENST00000614506,; A ENST00000615281 Transcript missense_variant 2385/5494 1234/2598 412/865 G/W Ggg/Tgg 1 -1 NBPF11 HGNC HGNC:31993 protein_coding YES CCDS41381.2 ENSP00000477509 Q86T75 UPI0000198783 NM_183372.5 tolerated(0.06) 12/24 hmmpanther:PTHR14199,hmmpanther:PTHR14199:SF20 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99959 1 1 1 1 0 A 3 1 81 148117644 148117644 C A 1 0 0 0 0 1 0 0 0 10205 623 22 2 2 NBPF11 1 148117644 Missense_Mutation SNP C C3N-01489_T 495356 148117644 100838778 41 24971 SV2A 0 . GRCh38 1 149909873 149909873 + Missense_Mutation SNP C C A rs782252414 C3N-01489_T C3N-01489_N C C c.1107G>T p.Glu369Asp p.E369D ENST00000369146 6/13 237 210 27 319 318 1 strelka-varscan-mutect SV2A,missense_variant,p.Glu369Asp,ENST00000369146,NM_014849.4;SV2A,missense_variant,p.Glu369Asp,ENST00000369145,; A ENST00000369146 Transcript missense_variant 1598/4416 1107/2229 369/742 E/D gaG/gaT rs782252414 1 -1 SV2A HGNC HGNC:20566 protein_coding YES CCDS940.1 ENSP00000358142 Q7L0J3 UPI000000DAD2 NM_014849.4 deleterious(0.02) 6/13 Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23511,hmmpanther:PTHR23511:SF11,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR01299 MODERATE 1 SNV 1 1 PASS rs782252414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 149909873 149909873 C A 1 0 0 0 0 1 0 0 0 15801 680 24 2 2 SV2A 1 149909873 Missense_Mutation SNP C C3N-01489_T 1792229 149909873 99046549 42 24972 CIART 0 . GRCh38 1 150283384 150283384 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.117G>T p.Lys39Asn p.K39N ENST00000290363 1/5 81 68 13 129 129 0 strelka-varscan-mutect CIART,missense_variant,p.Lys39Asn,ENST00000290363,NM_144697.3;CIART,missense_variant,p.Lys39Asn,ENST00000369095,NM_001300838.1;CIART,intron_variant,,ENST00000369094,NM_001300840.1,NM_001300839.1,NM_001300841.1;CIART,intron_variant,,ENST00000417398,;CIART,intron_variant,,ENST00000447007,;C1orf54,downstream_gene_variant,,ENST00000369102,NM_001301040.1,NM_001301039.1;C1orf54,downstream_gene_variant,,ENST00000369099,NM_024579.3;C1orf54,downstream_gene_variant,,ENST00000369098,NM_001301042.1;CIART,upstream_gene_variant,,ENST00000497211,;CIART,non_coding_transcript_exon_variant,,ENST00000469255,; T ENST00000290363 Transcript missense_variant 566/1746 117/1158 39/385 K/N aaG/aaT 1 1 CIART HGNC HGNC:25200 protein_coding YES CCDS949.1 ENSP00000290363 Q8N365 UPI000000DBBF NM_144697.3 deleterious_low_confidence(0.04) 1/5 hmmpanther:PTHR35441 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 81 150283384 150283384 G T 1 0 0 0 0 1 0 0 0 3181 991 35 2 2 CIART 1 150283384 Missense_Mutation SNP G C3N-01489_T 373511 150283384 98673038 43 24973 OAZ3 0 . GRCh38 1 151767261 151767261 + Nonsense_Mutation SNP G G T rs755505565 C3N-01489_T C3N-01489_N G G c.169G>T p.Glu57Ter p.E57* ENST00000453029 3/6 214 184 30 197 196 1 strelka-varscan-mutect OAZ3,stop_gained,p.Glu89Ter,ENST00000479764,;OAZ3,stop_gained,p.Glu89Ter,ENST00000400999,NM_016178.2;OAZ3,stop_gained,p.Glu44Ter,ENST00000321531,NM_001134939.1;OAZ3,stop_gained,p.Glu44Ter,ENST00000627780,;OAZ3,stop_gained,p.Glu44Ter,ENST00000635322,;OAZ3,stop_gained,p.Glu57Ter,ENST00000453029,NM_001301371.1;OAZ3,stop_gained,p.Glu23Ter,ENST00000635374,;OAZ3,stop_gained,p.Glu6Ter,ENST00000582415,;TDRKH,downstream_gene_variant,,ENST00000368827,NM_006862.3;TDRKH,downstream_gene_variant,,ENST00000440583,;MRPL9,upstream_gene_variant,,ENST00000368830,NM_031420.3;MRPL9,upstream_gene_variant,,ENST00000368829,NM_001300733.1;RP11-98D18.3,intron_variant,,ENST00000512280,;RP11-98D18.16,upstream_gene_variant,,ENST00000596133,;RP11-98D18.2,downstream_gene_variant,,ENST00000420382,;OAZ3,non_coding_transcript_exon_variant,,ENST00000577465,;MRPL9,upstream_gene_variant,,ENST00000467306,;MRPL9,upstream_gene_variant,,ENST00000462783,;MRPL9,upstream_gene_variant,,ENST00000478926,;MRPL9,upstream_gene_variant,,ENST00000486707,;MRPL9,upstream_gene_variant,,ENST00000481777,;MRPL9,upstream_gene_variant,,ENST00000492684,;MRPL9,upstream_gene_variant,,ENST00000461182,;OAZ3,non_coding_transcript_exon_variant,,ENST00000635179,;TDRKH,downstream_gene_variant,,ENST00000525790,; T ENST00000453029 Transcript stop_gained 184/729 169/612 57/203 E/* Gag/Tag rs755505565,COSM3722844,COSM3722845 1 1 OAZ3 HGNC HGNC:8097 protein_coding YES CCDS76216.1 ENSP00000415904 H0Y7Y4 UPI000268AE32 NM_001301371.1 3/6 hmmpanther:PTHR10279,hmmpanther:PTHR10279:SF9 0,1,1 HIGH SNV 5 0,1,1 1 PASS rs755505565 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 151767261 151767261 G T 1 0 0 0 0 0 1 0 0 10885 1059 37 1 1 OAZ3 1 151767261 Nonsense_Mutation SNP G C3N-01489_T 1483877 151767261 97189161 44 24974 FLG 0 . GRCh38 1 152307357 152307357 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.7529C>A p.Ser2510Tyr p.S2510Y ENST00000368799 3/3 514 410 104 647 647 0 strelka-varscan-mutect FLG,missense_variant,p.Ser2510Tyr,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 7565/12747 7529/12186 2510/4061 S/Y tCc/tAc 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 152307357 152307357 G T 1 0 0 0 0 1 0 0 0 5784 1174 41 2 2 FLG 1 152307357 Missense_Mutation SNP G C3N-01489_T 540096 152307357 96649065 45 24975 FLG 0 . GRCh38 1 152313535 152313535 + Missense_Mutation SNP G G T rs748669946 C3N-01489_T C3N-01489_N G G c.1351C>A p.Gln451Lys p.Q451K ENST00000368799 3/3 308 270 38 465 463 2 strelka-varscan-mutect FLG,missense_variant,p.Gln451Lys,ENST00000368799,NM_002016.1;FLG-AS1,non_coding_transcript_exon_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368799 Transcript missense_variant 1387/12747 1351/12186 451/4061 Q/K Caa/Aaa rs748669946 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.46) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571 MODERATE 1 SNV 1 1 PASS rs748669946 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 152313535 152313535 G T 1 0 0 0 0 1 0 0 0 5784 1357 47 2 2 FLG 1 152313535 Missense_Mutation SNP G C3N-01489_T 6178 152313535 96642887 46 24976 FLG2 0 . GRCh38 1 152357310 152357310 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.476C>A p.Ser159Tyr p.S159Y ENST00000388718 3/3 227 202 25 274 274 0 strelka-varscan-mutect FLG2,missense_variant,p.Ser159Tyr,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; T ENST00000388718 Transcript missense_variant 549/9124 476/7176 159/2391 S/Y tCc/tAc 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 deleterious(0) 3/3 hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 152357310 152357310 G T 1 0 0 0 0 1 0 0 0 5785 1174 41 2 2 FLG2 1 152357310 Missense_Mutation SNP G C3N-01489_T 43775 152357310 96599112 47 24977 CHRNB2 0 . GRCh38 1 154571660 154571660 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.837C>A p.Phe279Leu p.F279L ENST00000368476 5/6 218 176 42 309 309 0 strelka-varscan-mutect CHRNB2,missense_variant,p.Phe279Leu,ENST00000368476,NM_000748.2;CHRNB2,missense_variant,p.Phe281Leu,ENST00000637900,;CHRNB2,missense_variant,p.Phe279Leu,ENST00000636034,;CHRNB2,downstream_gene_variant,,ENST00000636695,; A ENST00000368476 Transcript missense_variant 1101/5867 837/1509 279/502 F/L ttC/ttA 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 deleterious(0) 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF80,Low_complexity_(Seg):seg,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 154571660 154571660 C A 1 0 0 0 0 1 0 0 0 3151 854 30 2 2 CHRNB2 1 154571660 Missense_Mutation SNP C C3N-01489_T 2214350 154571660 94384762 48 24978 RHBG 0 . GRCh38 1 156384781 156384781 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1313C>A p.Pro438His p.P438H ENST00000537040 10/10 94 78 16 125 124 1 strelka-varscan-mutect RHBG,missense_variant,p.Pro438His,ENST00000537040,NM_001256395.1,NM_020407.4,NM_001256396.1;RP11-139I14.2,upstream_gene_variant,,ENST00000451362,;RHBG,non_coding_transcript_exon_variant,,ENST00000494874,;RHBG,3_prime_UTR_variant,,ENST00000620376,;RHBG,3_prime_UTR_variant,,ENST00000451864,;RHBG,3_prime_UTR_variant,,ENST00000613460,;RHBG,3_prime_UTR_variant,,ENST00000612897,;RHBG,non_coding_transcript_exon_variant,,ENST00000618120,;RHBG,downstream_gene_variant,,ENST00000622297,; A ENST00000537040 Transcript missense_variant 1351/1789 1313/1377 438/458 P/H cCt/cAt 1 1 RHBG HGNC HGNC:14572 protein_coding YES ENSP00000441197 Q9H310 UPI000004F267 NM_001256395.1,NM_020407.4,NM_001256396.1 deleterious(0.01) 10/10 Gene3D:1.10.3430.10,hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF42 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 156384781 156384781 C A 1 0 0 0 0 1 0 0 0 13496 695 24 2 2 RHBG 1 156384781 Missense_Mutation SNP C C3N-01489_T 1813121 156384781 92571641 49 24979 INSRR 0 . GRCh38 1 156851425 156851425 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1094A>T p.Glu365Val p.E365V ENST00000368195 5/22 225 188 37 280 280 0 strelka-varscan-mutect INSRR,missense_variant,p.Glu365Val,ENST00000368195,NM_014215.2;NTRK1,intron_variant,,ENST00000392302,NM_001007792.1;NTRK1,intron_variant,,ENST00000489021,;NTRK1,intron_variant,,ENST00000530298,;NTRK1,intron_variant,,ENST00000497019,; A ENST00000368195 Transcript missense_variant 1491/5101 1094/3894 365/1297 E/V gAg/gTg 1 -1 INSRR HGNC HGNC:6093 protein_coding YES CCDS1160.1 ENSP00000357178 P14616 UPI000012D8BD NM_014215.2 tolerated(0.4) 5/22 hmmpanther:PTHR24416:SF338,hmmpanther:PTHR24416,Pfam_domain:PF01030,PIRSF_domain:PIRSF000620,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 156851425 156851425 T A 1 0 0 0 0 1 0 0 0 7676 1551 54 4 4 INSRR 1 156851425 Missense_Mutation SNP T C3N-01489_T 466644 156851425 92104997 50 24980 FCRL5 0 . GRCh38 1 157521052 157521052 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2480C>A p.Ala827Asp p.A827D ENST00000361835 11/17 87 75 12 123 123 0 strelka-varscan-mutect FCRL5,missense_variant,p.Ala827Asp,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,downstream_gene_variant,,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000461387,;FCRL5,non_coding_transcript_exon_variant,,ENST00000497286,;FCRL5,upstream_gene_variant,,ENST00000462218,;FCRL5,upstream_gene_variant,,ENST00000483875,; T ENST00000361835 Transcript missense_variant 2638/5390 2480/2934 827/977 A/D gCc/gAc 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(0.06) 11/17 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF68,hmmpanther:PTHR11481,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs770580193 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 157521052 157521052 G T 1 0 0 0 0 1 0 0 0 5660 1203 42 2 2 FCRL5 1 157521052 Missense_Mutation SNP G C3N-01489_T 669627 157521052 91435370 51 24981 FCRL5 0 . GRCh38 1 157544432 157544432 + Missense_Mutation SNP C C T rs138632023 C3N-01489_T C3N-01489_N C C c.674G>A p.Arg225Gln p.R225Q ENST00000361835 5/17 365 333 32 532 530 2 strelka-varscan-mutect FCRL5,missense_variant,p.Arg225Gln,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,missense_variant,p.Arg225Gln,ENST00000368189,;FCRL5,missense_variant,p.Arg225Gln,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000481082,; T ENST00000361835 Transcript missense_variant 832/5390 674/2934 225/977 R/Q cGg/cAg rs138632023,COSM400855 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(1) 5/17 PROSITE_profiles:PS50835,hmmpanther:PTHR11481:SF68,hmmpanther:PTHR11481,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs138632023 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 157544432 157544432 C T 1 0 0 0 0 1 0 0 0 5660 652 23 1 1 FCRL5 1 157544432 Missense_Mutation SNP C C3N-01489_T 23380 157544432 91411990 52 24982 FCRL1 0 . GRCh38 1 157802179 157802179 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.622C>A p.Pro208Thr p.P208T ENST00000368176 5/11 78 64 14 139 139 0 strelka-varscan-mutect FCRL1,missense_variant,p.Pro208Thr,ENST00000358292,NM_001159397.1;FCRL1,missense_variant,p.Pro208Thr,ENST00000368176,NM_052938.4;FCRL1,missense_variant,p.Pro208Thr,ENST00000491942,NM_001159398.1;FCRL1,non_coding_transcript_exon_variant,,ENST00000489998,;FCRL1,intron_variant,,ENST00000368175,;FCRL1,upstream_gene_variant,,ENST00000463001,;FCRL1,upstream_gene_variant,,ENST00000495126,;FCRL1,downstream_gene_variant,,ENST00000480310,; T ENST00000368176 Transcript missense_variant 690/2596 622/1290 208/429 P/T Cca/Aca 1 -1 FCRL1 HGNC HGNC:18509 protein_coding YES CCDS1170.1 ENSP00000357158 Q96LA6 UPI000006E5BD NM_052938.4 deleterious(0) 5/11 PROSITE_profiles:PS50835,hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF49,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 157802179 157802179 G T 1 0 0 0 0 1 0 0 0 5657 1232 43 2 2 FCRL1 1 157802179 Missense_Mutation SNP G C3N-01489_T 257747 157802179 91154243 53 24983 OR10T2 0 . GRCh38 1 158398814 158398814 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.653C>A p.Ser218Tyr p.S218Y ENST00000334438 1/1 158 144 14 217 217 0 strelka-varscan-mutect OR10T2,missense_variant,p.Ser218Tyr,ENST00000334438,NM_001004475.1; T ENST00000334438 Transcript missense_variant 653/945 653/945 218/314 S/Y tCc/tAc COSM1668091 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS rs1212822908 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 158398814 158398814 G T 1 0 0 0 0 1 0 0 0 10996 1174 41 2 2 OR10T2 1 158398814 Missense_Mutation SNP G C3N-01489_T 596635 158398814 90557608 54 24984 SPTA1 0 . GRCh38 1 158636736 158636736 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.5215C>A p.Gln1739Lys p.Q1739K ENST00000368147 37/52 376 317 59 513 513 0 strelka-varscan-mutect SPTA1,missense_variant,p.Gln1739Lys,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000461624,;SPTA1,downstream_gene_variant,,ENST00000465741,; T ENST00000368147 Transcript missense_variant 5396/7999 5215/7260 1739/2419 Q/K Cag/Aag 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 tolerated(0.08) 37/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 158636736 158636736 G T 1 0 0 0 0 1 0 0 0 15472 1357 47 2 2 SPTA1 1 158636736 Missense_Mutation SNP G C3N-01489_T 237922 158636736 90319686 55 24985 IFI16 0 . GRCh38 1 159032672 159032672 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.1310C>A p.Ser437Tyr p.S437Y ENST00000368131 7/11 65 58 7 129 129 0 strelka-varscan-mutect IFI16,missense_variant,p.Ser437Tyr,ENST00000295809,;IFI16,missense_variant,p.Ser437Tyr,ENST00000368131,NM_005531.2;IFI16,missense_variant,p.Ser437Tyr,ENST00000368132,;IFI16,missense_variant,p.Ser381Tyr,ENST00000359709,NM_001206567.1;IFI16,missense_variant,p.Ser437Tyr,ENST00000448393,;IFI16,5_prime_UTR_variant,,ENST00000340979,;IFI16,non_coding_transcript_exon_variant,,ENST00000483916,;IFI16,non_coding_transcript_exon_variant,,ENST00000493884,;IFI16,non_coding_transcript_exon_variant,,ENST00000562225,; A ENST00000368131 Transcript missense_variant 1600/2734 1310/2190 437/729 S/Y tCc/tAc COSM4463919,COSM4463920 1 1 IFI16 HGNC HGNC:5395 protein_coding YES CCDS1180.3 ENSP00000357113 Q16666 UPI00001412C9 NM_005531.2 deleterious(0.03) 7/11 Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 203 7 0 0 0 0 0 -15.74031 0.9999991 1 1 1 0 A 3 1 81 159032672 159032672 C A 1 0 0 0 0 1 0 0 0 7412 855 30 2 2 IFI16 1 159032672 Missense_Mutation SNP C C3N-01489_T 395936 159032672 89923750 56 24986 FCER1A 0 . GRCh38 1 159302379 159302379 + Missense_Mutation SNP G G T rs142102904 C3N-01489_T C3N-01489_N G G c.15G>T p.Met5Ile p.M5I ENST00000368115 2/6 197 173 24 270 269 1 strelka-varscan-mutect FCER1A,missense_variant,p.Met5Ile,ENST00000368115,NM_002001.3;FCER1A,missense_variant,p.Met5Ile,ENST00000368114,; T ENST00000368115 Transcript missense_variant 114/1165 15/774 5/257 M/I atG/atT rs142102904,COSM109802 1 1 FCER1A HGNC HGNC:3609 protein_coding YES CCDS1184.1 ENSP00000357097 P12319 UPI000002CFDB NM_002001.3 tolerated(0.07) 2/6 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF12,Cleavage_site_(Signalp):SignalP-noTM 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs142102904 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 159302379 159302379 G T 1 0 0 0 0 1 0 0 0 5637 1348 47 2 2 FCER1A 1 159302379 Missense_Mutation SNP G C3N-01489_T 269707 159302379 89654043 57 24987 CRP 0 . GRCh38 1 159713650 159713650 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.550C>T p.= p.L184L ENST00000255030 2/2 253 230 23 359 358 1 strelka-varscan-mutect CRP,synonymous_variant,p.=,ENST00000255030,NM_000567.2;CRP,synonymous_variant,p.=,ENST00000437342,;CRP,intron_variant,,ENST00000368112,;CRP,intron_variant,,ENST00000368110,;CRP,intron_variant,,ENST00000368111,;CRP,non_coding_transcript_exon_variant,,ENST00000473196,;CRP,intron_variant,,ENST00000489317,; A ENST00000255030 Transcript synonymous_variant 654/2015 550/675 184/224 L Ctg/Ttg 1 -1 CRP HGNC HGNC:2367 protein_coding YES CCDS30911.1 ENSP00000255030 P02741 UPI0000128478 NM_000567.2 2/2 hmmpanther:PTHR19277:SF119,hmmpanther:PTHR19277,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899,Prints_domain:PR00895 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 159713650 159713650 G A 1 0 0 0 0 0 0 0 1 3697 962 34 3 3 CRP 1 159713650 Silent SNP G C3N-01489_T 411271 159713650 89242772 58 24988 IGSF8 0 . GRCh38 1 160092467 160092467 + Missense_Mutation SNP C C T C3N-01489_T C3N-01489_N C C c.1541G>A p.Gly514Glu p.G514E ENST00000368086 5/7 118 101 17 167 167 0 strelka-varscan-mutect IGSF8,missense_variant,p.Gly514Glu,ENST00000368086,NM_001320247.1;IGSF8,missense_variant,p.Gly514Glu,ENST00000314485,NM_052868.4;IGSF8,missense_variant,p.Gly514Glu,ENST00000614243,NM_001206665.2;KCNJ9,downstream_gene_variant,,ENST00000368088,NM_004983.2;IGSF8,downstream_gene_variant,,ENST00000448417,;IGSF8,downstream_gene_variant,,ENST00000460351,; T ENST00000368086 Transcript missense_variant 1758/2366 1541/1842 514/613 G/E gGa/gAa COSM4852267 1 -1 IGSF8 HGNC HGNC:17813 protein_coding YES CCDS1195.1 ENSP00000357065 Q969P0 UPI0000073CBA NM_001320247.1 deleterious(0.01) 5/7 hmmpanther:PTHR12207:SF22,hmmpanther:PTHR12207,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 160092467 160092467 C T 1 0 0 0 0 1 0 0 0 7512 855 30 3 3 IGSF8 1 160092467 Missense_Mutation SNP C C3N-01489_T 378817 160092467 88863955 59 24989 ATP1A4 0 . GRCh38 1 160186301 160186301 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2995C>A p.Pro999Thr p.P999T ENST00000368081 21/22 270 239 31 341 341 0 strelka-varscan-mutect ATP1A4,missense_variant,p.Pro999Thr,ENST00000368081,NM_144699.3;ATP1A4,missense_variant,p.Pro135Thr,ENST00000470705,NM_001001734.1;CASQ1,upstream_gene_variant,,ENST00000368078,NM_001231.4;ATP1A4,downstream_gene_variant,,ENST00000418334,;ATP1A4,downstream_gene_variant,,ENST00000466526,;ATP1A4,3_prime_UTR_variant,,ENST00000477338,;ATP1A4,non_coding_transcript_exon_variant,,ENST00000469023,; A ENST00000368081 Transcript missense_variant 3466/3839 2995/3090 999/1029 P/T Ccc/Acc 1 1 ATP1A4 HGNC HGNC:14073 protein_coding YES CCDS1197.1 ENSP00000357060 Q13733 UPI0000124FC5 NM_144699.3 deleterious(0) 21/22 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF309,TIGRFAM_domain:TIGR01106,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 160186301 160186301 C A 1 0 0 0 0 1 0 0 0 1283 855 30 2 2 ATP1A4 1 160186301 Missense_Mutation SNP C C3N-01489_T 93834 160186301 88770121 60 24990 DDR2 0 . GRCh38 1 162766023 162766023 + Silent SNP T T A novel C3N-01489_T C3N-01489_N T T c.1122T>A p.= p.S374S ENST00000367922 11/19 433 381 52 596 596 0 strelka-varscan-mutect DDR2,synonymous_variant,p.=,ENST00000367922,NM_001014796.1;DDR2,synonymous_variant,p.=,ENST00000367921,NM_006182.2;DDR2,upstream_gene_variant,,ENST00000433757,;DDR2,upstream_gene_variant,,ENST00000458105,; A ENST00000367922 Transcript synonymous_variant 1560/10160 1122/2568 374/855 S tcT/tcA 1 1 DDR2 HGNC HGNC:2731 protein_coding YES CCDS1241.1 ENSP00000356899 Q16832 A0A024R906 UPI000013E1B4 NM_001014796.1 11/19 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF295 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 162766023 162766023 T A 1 0 0 0 0 0 0 0 1 4141 1567 55 4 4 DDR2 1 162766023 Silent SNP T C3N-01489_T 2579722 162766023 86190399 61 24991 RGS4 0 . GRCh38 1 163069456 163069456 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.263T>C p.Leu88Pro p.L88P ENST00000421743 2/6 294 272 22 352 351 1 strelka-varscan-mutect RGS4,missense_variant,p.Leu88Pro,ENST00000421743,NM_001102445.2;RGS4,5_prime_UTR_variant,,ENST00000367909,NM_005613.5;RGS4,5_prime_UTR_variant,,ENST00000367908,NM_001113381.1;RGS4,5_prime_UTR_variant,,ENST00000531057,;RGS4,intron_variant,,ENST00000527809,;RGS4,upstream_gene_variant,,ENST00000367906,NM_001113380.1;RGS4,upstream_gene_variant,,ENST00000528938,;RGS4,non_coding_transcript_exon_variant,,ENST00000491263,;RGS4,non_coding_transcript_exon_variant,,ENST00000527393,;RGS4,upstream_gene_variant,,ENST00000533019,; C ENST00000421743 Transcript missense_variant 423/3311 263/909 88/302 L/P cTg/cCg 1 1 RGS4 HGNC HGNC:10000 protein_coding YES CCDS44270.1 ENSP00000397181 P49798 UPI0000E1EDBA NM_001102445.2 deleterious_low_confidence(0.01) 2/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 163069456 163069456 T C 1 0 0 0 0 1 0 0 0 13478 1580 55 5 5 RGS4 1 163069456 Missense_Mutation SNP T C3N-01489_T 303433 163069456 85886966 62 24992 SFT2D2 0 . GRCh38 1 168242501 168242501 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.444G>T p.Arg148Ser p.R148S ENST00000271375 8/8 247 216 31 389 388 1 strelka-varscan-mutect SFT2D2,missense_variant,p.Arg148Ser,ENST00000271375,NM_199344.2;SFT2D2,splice_region_variant,,ENST00000630869,;SFT2D2,downstream_gene_variant,,ENST00000367829,;ANKRD36BP1,downstream_gene_variant,,ENST00000358576,;ANKRD36BP1,downstream_gene_variant,,ENST00000604892,; T ENST00000271375 Transcript missense_variant,splice_region_variant 516/11040 444/483 148/160 R/S agG/agT 1 1 SFT2D2 HGNC HGNC:25140 protein_coding YES CCDS1271.1 ENSP00000271375 O95562 UPI0000072549 NM_199344.2 deleterious(0) 8/8 hmmpanther:PTHR23137,hmmpanther:PTHR23137:SF1,Pfam_domain:PF04178 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 168242501 168242501 G T 1 0 0 0 0 1 0 0 0 14446 1246 43 2 2 SFT2D2 1 168242501 Missense_Mutation SNP G C3N-01489_T 5173045 168242501 80713921 63 24993 TNR 0 . GRCh38 1 175365215 175365215 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.2382G>C p.Trp794Cys p.W794C ENST00000367674 12/23 94 85 9 143 143 0 strelka-varscan-mutect TNR,missense_variant,p.Trp794Cys,ENST00000367674,;TNR,missense_variant,p.Trp794Cys,ENST00000263525,NM_003285.2; G ENST00000367674 Transcript missense_variant 3091/12949 2382/4077 794/1358 W/C tgG/tgC 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C deleterious(0) 12/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -19.00401 1 1 1 1 0 G 3 3 81 175365215 175365215 C G 1 0 0 0 0 1 0 0 0 16811 856 30 4 4 TNR 1 175365215 Missense_Mutation SNP C C3N-01489_T 7122714 175365215 73591207 64 24994 TNR 0 . GRCh38 1 175396775 175396775 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.1009A>G p.Ile337Val p.I337V ENST00000367674 5/23 117 107 10 160 160 0 strelka-varscan-mutect TNR,missense_variant,p.Ile337Val,ENST00000367674,;TNR,missense_variant,p.Ile337Val,ENST00000263525,NM_003285.2;TNR,missense_variant,p.Ile62Val,ENST00000422274,; C ENST00000367674 Transcript missense_variant 1718/12949 1009/4077 337/1358 I/V Atc/Gtc 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C tolerated(1) 5/23 Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 175396775 175396775 T C 1 0 0 0 0 1 0 0 0 16811 1406 49 5 5 TNR 1 175396775 Missense_Mutation SNP T C3N-01489_T 31560 175396775 73559647 65 24995 ASTN1 0 . GRCh38 1 177164486 177164486 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.191C>A p.Pro64His p.P64H ENST00000361833 1/23 143 126 17 212 212 0 strelka-varscan-mutect ASTN1,missense_variant,p.Pro64His,ENST00000361833,NM_004319.2;ASTN1,missense_variant,p.Pro64His,ENST00000367657,NM_001286164.1;ASTN1,missense_variant,p.Pro64His,ENST00000424564,NM_207108.2;ASTN1,non_coding_transcript_exon_variant,,ENST00000281881,; T ENST00000361833 Transcript missense_variant 205/7116 191/3885 64/1294 P/H cCc/cAc 1 -1 ASTN1 HGNC HGNC:773 protein_coding YES CCDS1319.1 ENSP00000354536 O14525 UPI0000160388 NM_004319.2 deleterious_low_confidence(0) 1/23 hmmpanther:PTHR16592:SF8,hmmpanther:PTHR16592 MODERATE 1 SNV 1 1 PASS rs1259045452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 177164486 177164486 G T 1 0 0 0 0 1 0 0 0 1211 1232 43 2 2 ASTN1 1 177164486 Missense_Mutation SNP G C3N-01489_T 1767711 177164486 71791936 66 24996 CACNA1E 0 . GRCh38 1 181718123 181718123 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1594C>T p.Pro532Ser p.P532S ENST00000367573 12/48 164 150 14 242 242 0 strelka-varscan-mutect CACNA1E,missense_variant,p.Pro532Ser,ENST00000621791,NM_001205294.1;CACNA1E,missense_variant,p.Pro532Ser,ENST00000621551,;CACNA1E,missense_variant,p.Pro532Ser,ENST00000367567,;CACNA1E,missense_variant,p.Pro532Ser,ENST00000358338,;CACNA1E,missense_variant,p.Pro532Ser,ENST00000367570,NM_000721.3;CACNA1E,missense_variant,p.Pro532Ser,ENST00000367573,NM_001205293.1;CACNA1E,missense_variant,p.Pro532Ser,ENST00000357570,;CACNA1E,missense_variant,p.Pro532Ser,ENST00000360108,;CACNA1E,downstream_gene_variant,,ENST00000524607,; T ENST00000367573 Transcript missense_variant 1594/7067 1594/6942 532/2313 P/S Cct/Tct 1 1 CACNA1E HGNC HGNC:1392 protein_coding YES CCDS55664.1 ENSP00000356545 Q15878 UPI00004588C2 NM_001205293.1 deleterious(0.03) 12/48 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF57,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -18.96831 0.9999797 1 1 1 0 T 3 4 81 181718123 181718123 C T 1 0 0 0 0 1 0 0 0 2230 739 26 3 3 CACNA1E 1 181718123 Missense_Mutation SNP C C3N-01489_T 4553637 181718123 67238299 67 24997 DHX9 0 . GRCh38 1 182843342 182843342 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.160A>G p.Lys54Glu p.K54E ENST00000367549 3/28 141 124 17 192 192 0 strelka-mutect DHX9,missense_variant,p.Lys54Glu,ENST00000367549,NM_001357.4;DHX9,non_coding_transcript_exon_variant,,ENST00000483416,; G ENST00000367549 Transcript missense_variant 270/4240 160/3813 54/1270 K/E Aaa/Gaa 1 1 DHX9 HGNC HGNC:2750 protein_coding YES CCDS41444.1 ENSP00000356520 Q08211 UPI00001AEF15 NM_001357.4 deleterious(0) 3/28 Gene3D:3.30.160.20,Pfam_domain:PF00035,PROSITE_profiles:PS50137,SMART_domains:SM00358,Superfamily_domains:SSF54768 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 182843342 182843342 A G 1 0 0 0 0 1 0 0 0 4320 363 13 5 5 DHX9 1 182843342 Missense_Mutation SNP A C3N-01489_T 1125219 182843342 66113080 68 24998 HMCN1 0 . GRCh38 1 186093203 186093203 + Nonsense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.9957T>A p.Cys3319Ter p.C3319* ENST00000271588 65/107 369 311 58 487 487 0 strelka-varscan-mutect HMCN1,stop_gained,p.Cys3319Ter,ENST00000271588,NM_031935.2; A ENST00000271588 Transcript stop_gained 10186/18208 9957/16908 3319/5635 C/* tgT/tgA 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 65/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 186093203 186093203 T A 1 0 0 0 0 0 1 0 0 7111 1702 59 4 4 HMCN1 1 186093203 Nonsense_Mutation SNP T C3N-01489_T 3249861 186093203 62863219 69 24999 RGS21 0 . GRCh38 1 192365936 192365936 + Missense_Mutation SNP G G T rs370485345 C3N-01489_T C3N-01489_N G G c.271G>T p.Gly91Cys p.G91C ENST00000417209 5/5 199 175 24 281 280 1 strelka-varscan-mutect RGS21,missense_variant,p.Gly91Cys,ENST00000417209,NM_001039152.3; T ENST00000417209 Transcript missense_variant 445/1794 271/459 91/152 G/C Ggt/Tgt rs370485345,COSM531447 1 1 RGS21 HGNC HGNC:26839 protein_coding YES CCDS41448.1 ENSP00000428343 Q2M5E4 UPI0000682FB1 NM_001039152.3 tolerated(0.26) 5/5 Gene3D:1.10.167.10,Pfam_domain:PF00615,Prints_domain:PR01301,PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF160,SMART_domains:SM00315,Superfamily_domains:SSF48097 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs370485345 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 192365936 192365936 G T 1 0 0 0 0 1 0 0 0 13475 1116 39 1 1 RGS21 1 192365936 Missense_Mutation SNP G C3N-01489_T 6272733 192365936 56590486 70 25000 GPR25 0 . GRCh38 1 200873531 200873531 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.494C>T p.Ala165Val p.A165V ENST00000304244 1/1 103 95 8 101 101 0 strelka-varscan GPR25,missense_variant,p.Ala165Val,ENST00000304244,NM_005298.3; T ENST00000304244 Transcript missense_variant 577/1224 494/1086 165/361 A/V gCc/gTc 1 1 GPR25 HGNC HGNC:4480 protein_coding YES CCDS1405.1 ENSP00000301917 O00155 UPI000013E957 NM_005298.3 tolerated(0.67) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF9,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 201 9 0 0 0 0 0 -15.96614 0.9999752 1 1 1 0 T 3 4 81 200873531 200873531 C T 1 0 0 0 0 1 0 0 0 6567 739 26 3 3 GPR25 1 200873531 Missense_Mutation SNP C C3N-01489_T 8507595 200873531 48082891 71 25001 PPFIA4 0 . GRCh38 1 203061030 203061030 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.2779A>T p.Thr927Ser p.T927S ENST00000447715 28/35 224 198 26 285 285 0 strelka-varscan PPFIA4,missense_variant,p.Thr928Ser,ENST00000367240,NM_001304331.1,NM_001304332.1;PPFIA4,missense_variant,p.Thr443Ser,ENST00000295706,;PPFIA4,missense_variant,p.Thr927Ser,ENST00000447715,;PPFIA4,missense_variant,p.Thr443Ser,ENST00000272198,;PPFIA4,missense_variant,p.Thr443Ser,ENST00000599966,;PPFIA4,missense_variant,p.Thr695Ser,ENST00000600426,;PPFIA4,downstream_gene_variant,,ENST00000599514,;PPFIA4,upstream_gene_variant,,ENST00000486360,;PPFIA4,upstream_gene_variant,,ENST00000594656,; T ENST00000447715 Transcript missense_variant,splice_region_variant 3220/6349 2779/3558 927/1185 T/S Aca/Tca 1 1 PPFIA4 HGNC HGNC:9248 protein_coding YES ENSP00000402576 O75335 UPI0001661778 tolerated(0.17) 28/35 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 203061030 203061030 A T 1 0 0 0 0 1 0 0 0 12421 57 2 4 4 PPFIA4 1 203061030 Missense_Mutation SNP A C3N-01489_T 2187499 203061030 45895392 72 25002 RBBP5 0 . GRCh38 1 205099943 205099943 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.874G>T p.Gly292Trp p.G292W ENST00000264515 8/14 140 122 18 162 162 0 strelka-varscan RBBP5,missense_variant,p.Gly292Trp,ENST00000264515,NM_001193273.1,NM_005057.3;RBBP5,missense_variant,p.Gly292Trp,ENST00000367164,NM_001193272.1; A ENST00000264515 Transcript missense_variant 1016/4404 874/1617 292/538 G/W Ggg/Tgg 1 -1 RBBP5 HGNC HGNC:9888 protein_coding YES CCDS30983.1 ENSP00000264515 Q15291 A0A024R9B5 UPI00001A9CA5 NM_001193273.1,NM_005057.3 deleterious(0) 8/14 Gene3D:2.130.10.10,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF433,SMART_domains:SM00320,Superfamily_domains:SSF117289 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 205099943 205099943 C A 1 0 0 0 0 1 0 0 0 13263 594 21 2 2 RBBP5 1 205099943 Missense_Mutation SNP C C3N-01489_T 2038913 205099943 43856479 73 25003 SLC41A1 0 . GRCh38 1 205810280 205810280 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.162G>T p.= p.R54R ENST00000367137 2/11 267 234 33 333 332 1 strelka-varscan-mutect SLC41A1,synonymous_variant,p.=,ENST00000367137,NM_173854.5;SLC41A1,downstream_gene_variant,,ENST00000484000,; A ENST00000367137 Transcript synonymous_variant 1177/4997 162/1542 54/513 R cgG/cgT 1 -1 SLC41A1 HGNC HGNC:19429 protein_coding YES CCDS30988.1 ENSP00000356105 Q8IVJ1 B2RMP2 UPI000013E1E6 NM_173854.5 2/11 hmmpanther:PTHR16228,hmmpanther:PTHR16228:SF23 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 205810280 205810280 C A 1 0 0 0 0 0 0 0 1 14907 610 22 2 2 SLC41A1 1 205810280 Silent SNP C C3N-01489_T 710337 205810280 43146142 74 25004 CR1 0 . GRCh38 1 207580349 207580349 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.5046C>T p.= p.L1682L ENST00000367049 30/47 194 163 31 257 257 0 strelka-varscan-mutect CR1,synonymous_variant,p.=,ENST00000367049,NM_000651.4;CR1,synonymous_variant,p.=,ENST00000367051,;CR1,synonymous_variant,p.=,ENST00000367052,;CR1,synonymous_variant,p.=,ENST00000367053,;CR1,synonymous_variant,p.=,ENST00000400960,NM_000573.3;CR1,intron_variant,,ENST00000529814,;RP11-78B10.2,intron_variant,,ENST00000623503,;RP11-78B10.2,intron_variant,,ENST00000597497,;RP11-78B10.2,intron_variant,,ENST00000596003,;CR1,3_prime_UTR_variant,,ENST00000534202,; T ENST00000367049 Transcript synonymous_variant 5046/7470 5046/7470 1682/2489 L ctC/ctT 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 30/47 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF354,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 207580349 207580349 C T 1 0 0 0 0 0 0 0 1 3638 813 29 3 3 CR1 1 207580349 Silent SNP C C3N-01489_T 1770069 207580349 41376073 75 25005 KCNH1 0 . GRCh38 1 211082825 211082825 + Missense_Mutation SNP G G T rs771777021 C3N-01489_T C3N-01489_N G G c.513C>A p.Ser171Arg p.S171R ENST00000271751 5/11 144 128 16 213 213 0 strelka-varscan-mutect KCNH1,missense_variant,p.Ser171Arg,ENST00000271751,NM_172362.2;KCNH1,missense_variant,p.Ser171Arg,ENST00000367007,NM_002238.3; T ENST00000271751 Transcript missense_variant 541/7964 513/2970 171/989 S/R agC/agA rs771777021 1 -1 KCNH1 HGNC HGNC:6250 protein_coding YES CCDS1496.1 ENSP00000271751 O95259 UPI000003230D NM_172362.2 tolerated(0.48) 5/11 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF533 MODERATE 1 SNV 2 1 PASS rs771777021 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 211082825 211082825 G T 1 0 0 0 0 1 0 0 0 7947 1078 38 1 1 KCNH1 1 211082825 Missense_Mutation SNP G C3N-01489_T 3502476 211082825 37873597 76 25006 TATDN3 0 . GRCh38 1 212795126 212795126 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.98A>T p.Lys33Met p.K33M ENST00000532324 2/10 154 128 26 250 249 1 strelka-varscan-mutect TATDN3,missense_variant,p.Lys33Met,ENST00000366974,NM_001042552.2;TATDN3,missense_variant,p.Lys33Met,ENST00000366973,NM_001042553.2;TATDN3,missense_variant,p.Lys33Met,ENST00000532324,NM_001146171.1;TATDN3,missense_variant,p.Lys33Met,ENST00000531963,NM_001146169.1;TATDN3,missense_variant,p.Lys33Met,ENST00000526641,NM_001146170.1;TATDN3,missense_variant,p.Lys33Met,ENST00000526997,;TATDN3,missense_variant,p.Lys32Met,ENST00000530399,;TATDN3,missense_variant,p.Lys33Met,ENST00000488246,;TATDN3,missense_variant,p.Lys33Met,ENST00000530441,;NSL1,upstream_gene_variant,,ENST00000366977,NM_015471.3;NSL1,upstream_gene_variant,,ENST00000366978,NM_001297739.1;NSL1,upstream_gene_variant,,ENST00000626725,NM_001042549.1;NSL1,upstream_gene_variant,,ENST00000366976,NM_001297737.1;TATDN3,upstream_gene_variant,,ENST00000606486,;TATDN3,splice_region_variant,,ENST00000525569,;TATDN3,splice_region_variant,,ENST00000530392,;TATDN3,splice_region_variant,,ENST00000497768,;NSL1,upstream_gene_variant,,ENST00000473995,;NSL1,upstream_gene_variant,,ENST00000487995,;TATDN3,missense_variant,p.Lys32Met,ENST00000525574,;TATDN3,missense_variant,p.Lys33Met,ENST00000533650,;TATDN3,splice_region_variant,,ENST00000532433,; T ENST00000532324 Transcript missense_variant,splice_region_variant 192/1381 98/846 33/281 K/M aAg/aTg 1 1 TATDN3 HGNC HGNC:27010 protein_coding YES CCDS53475.1 ENSP00000431376 Q17R31 UPI0000205E43 NM_001146171.1 deleterious(0.01) 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR10060,hmmpanther:PTHR10060:SF25,Gene3D:3.20.20.140,Pfam_domain:PF01026,PIRSF_domain:PIRSF005902,Superfamily_domains:SSF51556 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 212795126 212795126 A T 1 0 0 0 0 1 0 0 0 15992 86 3 4 4 TATDN3 1 212795126 Missense_Mutation SNP A C3N-01489_T 1712301 212795126 36161296 77 25007 USH2A 0 . GRCh38 1 215993077 215993077 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.6748C>T p.His2250Tyr p.H2250Y ENST00000307340 35/72 290 254 36 414 414 0 strelka-varscan-mutect USH2A,missense_variant,p.His2250Tyr,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 7135/18883 6748/15609 2250/5202 H/Y Cac/Tac 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.83) 35/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 215993077 215993077 G A 1 0 0 0 0 1 0 0 0 17570 1348 47 3 3 USH2A 1 215993077 Missense_Mutation SNP G C3N-01489_T 3197951 215993077 32963345 78 25008 USH2A 0 . GRCh38 1 216323672 216323672 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1352A>T p.Asn451Ile p.N451I ENST00000307340 8/72 301 270 31 423 423 0 strelka-varscan-mutect USH2A,missense_variant,p.Asn451Ile,ENST00000307340,NM_206933.2;USH2A,missense_variant,p.Asn451Ile,ENST00000366942,NM_007123.5; A ENST00000307340 Transcript missense_variant 1739/18883 1352/15609 451/5202 N/I aAt/aTt 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 8/72 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 216323672 216323672 T A 1 0 0 0 0 1 0 0 0 17570 1493 52 4 4 USH2A 1 216323672 Missense_Mutation SNP T C3N-01489_T 330595 216323672 32632750 79 25009 HHIPL2 0 . GRCh38 1 222540237 222540237 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.1223G>C p.Gly408Ala p.G408A ENST00000343410 4/9 306 253 53 471 471 0 strelka-varscan-mutect HHIPL2,missense_variant,p.Gly408Ala,ENST00000343410,NM_024746.3;HHIPL2,upstream_gene_variant,,ENST00000468172,;HHIPL2,upstream_gene_variant,,ENST00000494899,; G ENST00000343410 Transcript missense_variant 1282/2575 1223/2175 408/724 G/A gGg/gCg 1 -1 HHIPL2 HGNC HGNC:25842 protein_coding YES CCDS1530.2 ENSP00000342118 Q6UWX4 UPI000004C60D NM_024746.3 tolerated(0.32) 4/9 hmmpanther:PTHR19328:SF31,hmmpanther:PTHR19328,Gene3D:2.120.10.30,Pfam_domain:PF07995,Superfamily_domains:0046203 MODERATE 1 SNV 1 1 PASS rs913036719 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 222540237 222540237 C G 1 0 0 0 0 1 0 0 0 6979 623 22 4 4 HHIPL2 1 222540237 Missense_Mutation SNP C C3N-01489_T 6216565 222540237 26416185 80 25010 MIA3 0 . GRCh38 1 222618163 222618163 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.53G>T p.Trp18Leu p.W18L ENST00000344922 1/28 147 124 23 149 148 1 strelka-varscan-mutect MIA3,missense_variant,p.Trp18Leu,ENST00000344922,NM_001324064.1,NM_198551.3;MIA3,missense_variant,p.Trp18Leu,ENST00000344507,;MIA3,non_coding_transcript_exon_variant,,ENST00000470521,; T ENST00000344922 Transcript missense_variant 78/8142 53/5724 18/1907 W/L tGg/tTg 1 1 MIA3 HGNC HGNC:24008 protein_coding YES CCDS41470.1 ENSP00000340900 Q5JRA6 UPI00001D75B3 NM_001324064.1,NM_198551.3 tolerated_low_confidence(0.16) 1/28 Low_complexity_(Seg):seg,hmmpanther:PTHR23158,hmmpanther:PTHR23158:SF37,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 222618163 222618163 G T 1 0 0 0 0 1 0 0 0 9522 1357 47 2 2 MIA3 1 222618163 Missense_Mutation SNP G C3N-01489_T 77926 222618163 26338259 81 25011 DNAH14 0 . GRCh38 1 225085763 225085763 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.3547G>C p.Gly1183Arg p.G1183R ENST00000430092 21/84 152 141 11 257 257 0 strelka-varscan-mutect DNAH14,missense_variant,p.Gly1183Arg,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Gly1183Arg,ENST00000439375,;DNAH14,missense_variant,p.Gly1009Arg,ENST00000445597,; C ENST00000430092 Transcript missense_variant 3762/13763 3547/13548 1183/4515 G/R Gga/Cga 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 deleterious(0) 21/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254,Pfam_domain:PF08393 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 225085763 225085763 G C 1 0 0 0 0 1 0 0 0 4415 1001 35 4 4 DNAH14 1 225085763 Missense_Mutation SNP G C3N-01489_T 2467600 225085763 23870659 82 25012 DNAH14 0 . GRCh38 1 225185410 225185410 + Silent SNP A A G novel C3N-01489_T C3N-01489_N A A c.5589A>G p.= p.R1863R ENST00000430092 36/84 170 155 15 229 229 0 strelka-varscan-mutect DNAH14,synonymous_variant,p.=,ENST00000430092,NM_001373.1;DNAH14,synonymous_variant,p.=,ENST00000439375,;DNAH14,synonymous_variant,p.=,ENST00000445597,; G ENST00000430092 Transcript synonymous_variant 5804/13763 5589/13548 1863/4515 R agA/agG 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 36/84 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF254,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 225185410 225185410 A G 1 0 0 0 0 0 0 0 1 4415 243 9 5 5 DNAH14 1 225185410 Silent SNP A C3N-01489_T 99647 225185410 23771012 83 25013 LEFTY2 0 . GRCh38 1 225940975 225940975 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.166C>A p.His56Asn p.H56N ENST00000366820 1/4 263 244 19 333 332 1 strelka-varscan-mutect LEFTY2,missense_variant,p.His56Asn,ENST00000366820,NM_003240.3;LEFTY2,missense_variant,p.His56Asn,ENST00000420304,NM_001172425.1;RP4-559A3.6,upstream_gene_variant,,ENST00000513672,;LEFTY2,upstream_gene_variant,,ENST00000474493,; T ENST00000366820 Transcript missense_variant 515/2287 166/1101 56/366 H/N Cac/Aac 1 -1 LEFTY2 HGNC HGNC:3122 protein_coding YES CCDS1549.1 ENSP00000355785 O00292 A0A024R3P5 UPI0000136CBB NM_003240.3 deleterious(0.05) 1/4 PIRSF_domain:PIRSF037402,Prints_domain:PR01427,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF167 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 225940975 225940975 G T 1 0 0 0 0 1 0 0 0 8624 1348 47 2 2 LEFTY2 1 225940975 Missense_Mutation SNP G C3N-01489_T 755565 225940975 23015447 84 25014 AGT 0 . GRCh38 1 230706164 230706164 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.893A>T p.Gln298Leu p.Q298L ENST00000366667 3/5 165 131 34 223 223 0 strelka-varscan-mutect AGT,missense_variant,p.Gln298Leu,ENST00000366667,NM_000029.3;RP11-99J16__A.2,downstream_gene_variant,,ENST00000412344,; A ENST00000366667 Transcript missense_variant 1108/2291 893/1458 298/485 Q/L cAg/cTg 1 -1 AGT HGNC HGNC:333 protein_coding YES CCDS1585.1 ENSP00000355627 P01019 B0ZBE2 UPI0000125B13 NM_000029.3 deleterious(0) 3/5 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF13,Gene3D:2.30.39.10,Pfam_domain:PF00079,SMART_domains:SM00093,Superfamily_domains:SSF56574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 230706164 230706164 T A 1 0 0 0 0 1 0 0 0 478 1580 55 4 4 AGT 1 230706164 Missense_Mutation SNP T C3N-01489_T 4765189 230706164 18250258 85 25015 TRIM67 0 . GRCh38 1 231163844 231163844 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.875C>G p.Thr292Ser p.T292S ENST00000366653 1/10 168 148 20 211 211 0 strelka-mutect TRIM67,missense_variant,p.Thr292Ser,ENST00000444294,;TRIM67,missense_variant,p.Thr292Ser,ENST00000366653,NM_001004342.3;TRIM67,missense_variant,p.Thr230Ser,ENST00000449018,NM_001300889.1; G ENST00000366653 Transcript missense_variant 875/3936 875/2352 292/783 T/S aCt/aGt 1 1 TRIM67 HGNC HGNC:31859 protein_coding YES CCDS44333.1 ENSP00000355613 Q6ZTA4 UPI0000418F23 NM_001004342.3 tolerated(0.79) 1/10 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 231163844 231163844 C G 1 0 0 0 0 1 0 0 0 17036 565 20 4 4 TRIM67 1 231163844 Missense_Mutation SNP C C3N-01489_T 457680 231163844 17792578 86 25016 NID1 0 . GRCh38 1 236024185 236024185 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.2013C>A p.= p.P671P ENST00000264187 9/20 216 181 35 289 288 1 strelka-varscan NID1,synonymous_variant,p.=,ENST00000264187,NM_002508.2;NID1,synonymous_variant,p.=,ENST00000366595,; T ENST00000264187 Transcript synonymous_variant 2096/5864 2013/3744 671/1247 P ccC/ccA 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 9/20 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 236024185 236024185 G T 1 0 0 0 0 0 0 0 1 10447 987 35 2 2 NID1 1 236024185 Silent SNP G C3N-01489_T 4860341 236024185 12932237 87 25017 MTR 0 . GRCh38 1 236853078 236853078 + Missense_Mutation SNP G G T rs751565093 C3N-01489_T C3N-01489_N G G c.1943G>T p.Arg648Leu p.R648L ENST00000366577 18/33 453 392 61 600 599 1 strelka-varscan MTR,missense_variant,p.Arg648Leu,ENST00000366577,NM_000254.2;MTR,missense_variant,p.Arg648Leu,ENST00000535889,NM_001291939.1;MTR,missense_variant,p.Arg202Leu,ENST00000366576,NM_001291940.1;MTR,non_coding_transcript_exon_variant,,ENST00000463959,; T ENST00000366577 Transcript missense_variant 2337/10529 1943/3798 648/1265 R/L cGt/cTt rs751565093 1 1 MTR HGNC HGNC:7468 protein_coding YES CCDS1614.1 ENSP00000355536 Q99707 UPI0000036BC4 NM_000254.2 tolerated(0.13) 18/33 TIGRFAM_domain:TIGR02082,Gene3D:3.20.20.20,PIRSF_domain:PIRSF000381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 236853078 236853078 G T 1 0 0 0 0 1 0 0 0 9944 1145 40 1 1 MTR 1 236853078 Missense_Mutation SNP G C3N-01489_T 828893 236853078 12103344 88 25018 RYR2 0 . GRCh38 1 237655830 237655830 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.7975C>A p.Gln2659Lys p.Q2659K ENST00000366574 53/105 157 144 13 258 258 0 strelka-varscan RYR2,missense_variant,p.Gln2659Lys,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gln2643Lys,ENST00000360064,; A ENST00000366574 Transcript missense_variant 8292/16562 7975/14904 2659/4967 Q/K Caa/Aaa 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.04) 53/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.92976 0.9999998 1 1 1 0 A 3 1 81 237655830 237655830 C A 1 0 0 0 0 1 0 0 0 14029 479 17 2 2 RYR2 1 237655830 Missense_Mutation SNP C C3N-01489_T 802752 237655830 11300592 89 25019 RYR2 0 . GRCh38 1 237819150 237819150 + Missense_Mutation SNP T T G novel C3N-01489_T C3N-01489_N T T c.14548T>G p.Phe4850Val p.F4850V ENST00000366574 101/105 153 137 16 273 272 1 strelka-varscan RYR2,missense_variant,p.Phe4850Val,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Phe4833Val,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000608590,; G ENST00000366574 Transcript missense_variant 14865/16562 14548/14904 4850/4967 F/V Ttc/Gtc 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 101/105 Pfam_domain:PF00520,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 237819150 237819150 T G 1 0 0 0 0 1 0 0 0 14029 1841 64 5 5 RYR2 1 237819150 Missense_Mutation SNP T C3N-01489_T 163320 237819150 11137272 90 25020 HNRNPU 0 . GRCh38 1 244863733 244863733 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.575C>T p.Ser192Leu p.S192L ENST00000283179 1/14 226 189 37 309 309 0 strelka-varscan HNRNPU,missense_variant,p.Ser192Leu,ENST00000444376,NM_004501.3;HNRNPU,missense_variant,p.Ser192Leu,ENST00000283179,NM_031844.2;HNRNPU,upstream_gene_variant,,ENST00000440865,;RP11-11N7.4,upstream_gene_variant,,ENST00000610145,;HNRNPU,non_coding_transcript_exon_variant,,ENST00000476241,;HNRNPU,upstream_gene_variant,,ENST00000366525,;HNRNPU,upstream_gene_variant,,ENST00000465881,; A ENST00000283179 Transcript missense_variant 739/3704 575/2478 192/825 S/L tCg/tTg 1 -1 HNRNPU HGNC HGNC:5048 protein_coding YES CCDS41479.1 ENSP00000283179 Q00839 UPI000040E1C8 NM_031844.2 tolerated(0.32) 1/14 hmmpanther:PTHR12381,hmmpanther:PTHR12381:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 244863733 244863733 G A 1 0 0 0 0 1 0 0 0 7168 1059 37 1 1 HNRNPU 1 244863733 Missense_Mutation SNP G C3N-01489_T 7044583 244863733 4092689 91 25021 KIF26B 0 . GRCh38 1 245688800 245688800 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.5817C>A p.= p.S1939S ENST00000407071 12/15 27 23 4 54 54 0 strelka-varscan KIF26B,synonymous_variant,p.=,ENST00000366518,;KIF26B,synonymous_variant,p.=,ENST00000407071,NM_018012.3;KIF26B,downstream_gene_variant,,ENST00000483253,; A ENST00000407071 Transcript synonymous_variant 6257/7287 5817/6327 1939/2108 S tcC/tcA 1 1 KIF26B HGNC HGNC:25484 protein_coding YES CCDS44342.1 ENSP00000385545 Q2KJY2 UPI0000695D71 NM_018012.3 12/15 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.73602 1 1 1 1 0 A 2 1 81 245688800 245688800 C A 1 0 0 0 0 0 0 0 1 8160 581 21 2 2 KIF26B 1 245688800 Silent SNP C C3N-01489_T 825067 245688800 3267622 92 25022 CNST 0 . GRCh38 1 246665840 246665840 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2113G>T p.Asp705Tyr p.D705Y ENST00000366513 11/11 179 158 21 246 245 1 strelka-varscan CNST,missense_variant,p.Asp705Tyr,ENST00000366513,NM_152609.2; T ENST00000366513 Transcript missense_variant 2382/5126 2113/2178 705/725 D/Y Gac/Tac 1 1 CNST HGNC HGNC:26486 protein_coding YES CCDS1628.1 ENSP00000355470 Q6PJW8 UPI000013E1DF NM_152609.2 deleterious(0) 11/11 Pfam_domain:PF15281,hmmpanther:PTHR28581 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 246665840 246665840 G T 1 0 0 0 0 1 0 0 0 3416 1174 41 2 2 CNST 1 246665840 Missense_Mutation SNP G C3N-01489_T 977040 246665840 2290582 93 25023 OR2C3 0 . GRCh38 1 247532338 247532338 + Silent SNP T T A novel C3N-01489_T C3N-01489_N T T c.174A>T p.= p.T58T ENST00000366487 2/2 287 253 34 419 419 0 strelka-varscan OR2C3,synonymous_variant,p.=,ENST00000366487,NM_198074.4;OR2C3,synonymous_variant,p.=,ENST00000617752,;GCSAML,intron_variant,,ENST00000366491,NM_001281834.1;GCSAML,intron_variant,,ENST00000536561,NM_001281853.1;GCSAML,intron_variant,,ENST00000366489,NM_001281835.1;GCSAML,intron_variant,,ENST00000623578,NM_001281837.1;GCSAML,intron_variant,,ENST00000463359,;GCSAML,intron_variant,,ENST00000527084,NM_001281836.1;GCSAML,intron_variant,,ENST00000527541,NM_001281838.1;GCSAML,intron_variant,,ENST00000529512,;GCSAML,intron_variant,,ENST00000526896,;GCSAML,intron_variant,,ENST00000531662,; A ENST00000366487 Transcript synonymous_variant 536/2742 174/963 58/320 T acA/acT 1 -1 OR2C3 HGNC HGNC:15005 protein_coding YES CCDS1634.2 ENSP00000355443 Q8N628 UPI0000061EBD NM_198074.4 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF117,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 247532338 247532338 T A 1 0 0 0 0 0 0 0 1 11072 1683 59 4 4 OR2C3 1 247532338 Silent SNP T C3N-01489_T 866498 247532338 1424084 94 25024 TRIM58 0 . GRCh38 1 247876370 247876370 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1342T>A p.Phe448Ile p.F448I ENST00000366481 6/6 274 244 30 383 383 0 strelka-varscan TRIM58,missense_variant,p.Phe448Ile,ENST00000366481,NM_015431.3; A ENST00000366481 Transcript missense_variant 1390/3225 1342/1461 448/486 F/I Ttt/Att 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0) 6/6 PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899,Prints_domain:PR01407 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 247876370 247876370 T A 1 0 0 0 0 1 0 0 0 17024 1609 56 4 4 TRIM58 1 247876370 Missense_Mutation SNP T C3N-01489_T 344032 247876370 1080052 95 25025 TSSC1 0 . GRCh38 2 3338083 3338083 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.193G>T p.Gly65Cys p.G65C ENST00000382125 3/9 171 149 22 241 241 0 strelka-varscan-mutect TSSC1,missense_variant,p.Gly65Cys,ENST00000398659,;TSSC1,missense_variant,p.Gly65Cys,ENST00000443925,;TSSC1,missense_variant,p.Gly65Cys,ENST00000382125,NM_003310.2;TSSC1,missense_variant,p.Gly65Cys,ENST00000444776,;TSSC1,intron_variant,,ENST00000441271,;TSSC1,non_coding_transcript_exon_variant,,ENST00000463662,;TSSC1,missense_variant,p.Gly65Cys,ENST00000435721,;TSSC1,3_prime_UTR_variant,,ENST00000406835,;TSSC1,intron_variant,,ENST00000455162,; A ENST00000382125 Transcript missense_variant 386/1766 193/1164 65/387 G/C Ggt/Tgt 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 deleterious(0) 3/9 hmmpanther:PTHR14205:SF15,hmmpanther:PTHR14205,Gene3D:2.130.10.10,Superfamily_domains:0049172 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 3338083 3338083 C A 1 0 0 0 0 1 0 0 0 17174 623 22 2 2 TSSC1 2 3338083 Missense_Mutation SNP C C3N-01489_T 3338083 238855446 96 25026 MYCN 0 . GRCh38 2 15945586 15945586 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.884C>A p.Thr295Asn p.T295N ENST00000281043 3/3 256 239 17 357 357 0 strelka-varscan-mutect MYCN,missense_variant,p.Thr295Asn,ENST00000281043,NM_001293233.1,NM_001293228.1,NM_005378.5;MYCNOS,upstream_gene_variant,,ENST00000420452,;MYCNOS,upstream_gene_variant,,ENST00000419083,;MYCNOS,upstream_gene_variant,,ENST00000453400,;MYCNOS,upstream_gene_variant,,ENST00000439180,;MYCNOS,upstream_gene_variant,,ENST00000448719,; A ENST00000281043 Transcript missense_variant 1181/2602 884/1395 295/464 T/N aCc/aAc 1 1 MYCN HGNC HGNC:7559 protein_coding YES CCDS1687.1 ENSP00000281043 P04198 UPI000012FAF8 NM_001293233.1,NM_001293228.1,NM_005378.5 tolerated(0.1) 3/3 Pfam_domain:PF01056,PIRSF_domain:PIRSF001705,hmmpanther:PTHR11514,hmmpanther:PTHR11514:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 15945586 15945586 C A 1 0 0 0 0 1 0 0 0 10021 507 18 2 2 MYCN 2 15945586 Missense_Mutation SNP C C3N-01489_T 12607503 15945586 226247943 97 25027 APOB 0 . GRCh38 2 21012095 21012095 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.4773C>A p.Phe1591Leu p.F1591L ENST00000233242 26/29 85 74 11 135 134 1 strelka-varscan-mutect APOB,missense_variant,p.Phe1591Leu,ENST00000233242,NM_000384.2; T ENST00000233242 Transcript missense_variant 4901/14121 4773/13692 1591/4563 F/L ttC/ttA 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 tolerated(1) 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99994 1 1 1 1 0 T 3 4 81 21012095 21012095 G T 1 0 0 0 0 1 0 0 0 907 933 33 2 2 APOB 2 21012095 Missense_Mutation SNP G C3N-01489_T 5066509 21012095 221181434 98 25028 APOB 0 . GRCh38 2 21019884 21019884 + Silent SNP A A G novel C3N-01489_T C3N-01489_N A A c.2838T>C p.= p.S946S ENST00000233242 19/29 436 400 36 585 585 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;APOB,downstream_gene_variant,,ENST00000399256,;AC010872.1,upstream_gene_variant,,ENST00000624225,; G ENST00000233242 Transcript synonymous_variant 2966/14121 2838/13692 946/4563 S tcT/tcC 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 19/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Gene3D:1lshA04,Superfamily_domains:SSF56968 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 21019884 21019884 A G 1 0 0 0 0 0 0 0 1 907 407 15 5 5 APOB 2 21019884 Silent SNP A C3N-01489_T 7789 21019884 221173645 99 25029 ASXL2 0 . GRCh38 2 25750206 25750206 + Silent SNP T T C novel C3N-01489_T C3N-01489_N T T c.570A>G p.= p.Q190Q ENST00000404843 8/10 186 168 18 315 315 0 strelka-varscan ASXL2,synonymous_variant,p.=,ENST00000435504,NM_018263.4;ASXL2,synonymous_variant,p.=,ENST00000336112,;ASXL2,synonymous_variant,p.=,ENST00000404843,; C ENST00000404843 Transcript synonymous_variant 1008/3299 570/2757 190/918 Q caA/caG 1 -1 ASXL2 HGNC HGNC:23805 protein_coding YES ENSP00000383920 Q76L83 UPI0000246C78 8/10 hmmpanther:PTHR13578:SF11,hmmpanther:PTHR13578 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 25750206 25750206 T C 1 0 0 0 0 0 0 0 1 1215 1606 56 5 5 ASXL2 2 25750206 Silent SNP T C3N-01489_T 4730322 25750206 216443323 100 25030 OTOF 0 . GRCh38 2 26458074 26458074 + Missense_Mutation SNP G G T rs121908598 C3N-01489_T C3N-01489_N G G c.5960C>A p.Pro1987His p.P1987H ENST00000403946 46/46 127 113 14 168 168 0 strelka-varscan OTOF,missense_variant,p.Pro1987His,ENST00000403946,NM_001287489.1;OTOF,missense_variant,p.Pro1220His,ENST00000339598,NM_194323.2;OTOF,3_prime_UTR_variant,,ENST00000272371,NM_194248.2;OTOF,3_prime_UTR_variant,,ENST00000402415,NM_194322.2;OTOF,3_prime_UTR_variant,,ENST00000338581,NM_004802.3;DRC1,downstream_gene_variant,,ENST00000288710,NM_145038.3;DRC1,downstream_gene_variant,,ENST00000439066,; T ENST00000403946 Transcript missense_variant 6067/6937 5960/5994 1987/1997 P/H cCt/cAt rs121908598 1 -1 OTOF HGNC HGNC:8515 protein_coding CCDS74497.1 ENSP00000385255 Q9HC10 UPI000173A4A0 NM_001287489.1 deleterious(0) 46/46 Low_complexity_(Seg):seg,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Pfam_domain:PF16165 pathogenic MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 26458074 26458074 G T 1 0 0 0 0 1 0 0 0 11369 1000 35 2 2 OTOF 2 26458074 Missense_Mutation SNP G C3N-01489_T 707868 26458074 215735455 101 25031 FAM179A 0 . GRCh38 2 29003536 29003536 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.684G>T p.Met228Ile p.M228I ENST00000379558 6/20 81 68 13 121 121 0 strelka-varscan FAM179A,missense_variant,p.Met228Ile,ENST00000379558,NM_199280.2;FAM179A,intron_variant,,ENST00000401723,;FAM179A,downstream_gene_variant,,ENST00000420297,; T ENST00000379558 Transcript missense_variant 1035/12691 684/3060 228/1019 M/I atG/atT 1 1 FAM179A HGNC HGNC:33715 protein_coding YES CCDS1769.2 ENSP00000368876 Q6ZUX3 UPI00014F7B81 NM_199280.2 tolerated(0.28) 6/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF42 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 29003536 29003536 G T 1 0 0 0 0 1 0 0 0 5350 1319 46 2 2 FAM179A 2 29003536 Missense_Mutation SNP G C3N-01489_T 2545462 29003536 213189993 102 25032 ALK 0 . GRCh38 2 29320882 29320882 + Missense_Mutation SNP C C T C3N-01489_T C3N-01489_N C C c.1415G>A p.Arg472Gln p.R472Q ENST00000389048 7/29 355 300 55 496 496 0 strelka-varscan ALK,missense_variant,p.Arg472Gln,ENST00000389048,NM_004304.4;ALK,missense_variant,p.Arg95Gln,ENST00000618119,;ALK,upstream_gene_variant,,ENST00000498037,; T ENST00000389048 Transcript missense_variant,splice_region_variant 2322/6220 1415/4863 472/1620 R/Q cGg/cAg COSM4526739 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 tolerated(0.47) 7/29 SMART_domains:SM00192 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 29320882 29320882 C T 1 0 0 0 0 1 0 0 0 625 637 22 3 3 ALK 2 29320882 Missense_Mutation SNP C C3N-01489_T 317346 29320882 212872647 103 25033 XDH 0 . GRCh38 2 31381639 31381639 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.1126T>C p.Ser376Pro p.S376P ENST00000379416 12/36 416 371 45 548 548 0 strelka-varscan XDH,missense_variant,p.Ser376Pro,ENST00000379416,NM_000379.3;XDH,downstream_gene_variant,,ENST00000491727,;XDH,downstream_gene_variant,,ENST00000476043,; G ENST00000379416 Transcript missense_variant 1175/5688 1126/4002 376/1333 S/P Tcc/Ccc 1 -1 XDH HGNC HGNC:12805 protein_coding YES CCDS1775.1 ENSP00000368727 P47989 UPI0000036BC9 NM_000379.3 deleterious(0) 12/36 PROSITE_profiles:PS51387,hmmpanther:PTHR11908,hmmpanther:PTHR11908:SF78,Gene3D:3.30.465.10,TIGRFAM_domain:TIGR02963,Pfam_domain:PF00941,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF56176 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 31381639 31381639 A G 1 0 0 0 0 1 0 0 0 17985 275 10 5 5 XDH 2 31381639 Missense_Mutation SNP A C3N-01489_T 2060757 31381639 210811890 104 25034 LTBP1 0 . GRCh38 2 33217640 33217641 + Frame_Shift_Ins INS - - C novel C3N-01489_T C3N-01489_N - - c.1794dupC p.Lys599GlnfsTer19 p.K599Qfs*19 ENST00000404816 8/34 128 115 13 197 197 0 sindel-varindel-pindel LTBP1,frameshift_variant,p.Lys599GlnfsTer19,ENST00000404816,NM_206943.2;LTBP1,frameshift_variant,p.Lys273GlnfsTer19,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,frameshift_variant,p.Lys273GlnfsTer19,ENST00000404525,NM_001166265.1;LTBP1,frameshift_variant,p.Lys273GlnfsTer19,ENST00000407925,NM_000627.3;LTBP1,frameshift_variant,p.Lys273GlnfsTer19,ENST00000402934,; C ENST00000404816 Transcript frameshift_variant 2143-2144/6333 1790-1791/5166 597/1721 C/CX tgc/tgCc 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 8/34 Gene3D:3.90.290.10,Pfam_domain:PF00683,PROSITE_profiles:PS51364,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,Superfamily_domains:SSF57581 HIGH 1 insertion 5 4 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 81 33217640 33217640 - C 1 0 1 1 0 0 0 0 0 8979 1319 46 0 0 LTBP1 2 33217640 Frame_Shift_Ins INS - C3N-01489_T 1836001 33217640 208975889 105 25035 EIF2AK2 0 . GRCh38 2 37122570 37122570 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1003G>T p.Glu335Ter p.E335* ENST00000233057 12/17 247 217 30 343 343 0 strelka-varscan EIF2AK2,stop_gained,p.Glu335Ter,ENST00000233057,;EIF2AK2,stop_gained,p.Glu335Ter,ENST00000395127,NM_001135651.2,NM_002759.3;EIF2AK2,stop_gained,p.Glu294Ter,ENST00000405334,NM_001135652.2; A ENST00000233057 Transcript stop_gained 1326/10042 1003/1656 335/551 E/* Gag/Tag 1 -1 EIF2AK2 HGNC HGNC:9437 protein_coding YES CCDS1786.1 ENSP00000233057 P19525 UPI000000D925 12/17 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF102,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 37122570 37122570 C A 1 0 0 0 0 0 1 0 0 4833 835 29 2 2 EIF2AK2 2 37122570 Nonsense_Mutation SNP C C3N-01489_T 3904930 37122570 205070959 106 25036 EML4 0 . GRCh38 2 42264704 42264704 + Splice_Site SNP A A T novel C3N-01489_T C3N-01489_N A A c.642-2A>T p.X214_splice ENST00000318522 95 87 8 146 146 0 strelka-varscan EML4,splice_acceptor_variant,,ENST00000318522,NM_019063.4;EML4,splice_acceptor_variant,,ENST00000401738,;EML4,splice_acceptor_variant,,ENST00000402711,NM_001145076.2;EML4,downstream_gene_variant,,ENST00000409040,; T ENST00000318522 Transcript splice_acceptor_variant -/5549 642/2946 214/981 1 1 EML4 HGNC HGNC:1316 protein_coding YES CCDS1807.1 ENSP00000320663 Q9HC35 UPI0000140350 NM_019063.4 5/22 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 81 42264704 42264704 A T 1 0 0 0 0 0 0 1 0 4942 434 15 4 4 EML4 2 42264704 Splice_Site SNP A C3N-01489_T 5142134 42264704 199928825 107 25037 PLEKHH2 0 . GRCh38 2 43700339 43700339 + Missense_Mutation SNP C C T rs150493851 C3N-01489_T C3N-01489_N C C c.1381C>T p.Pro461Ser p.P461S ENST00000282406 8/30 308 279 29 503 503 0 strelka-varscan PLEKHH2,missense_variant,p.Pro461Ser,ENST00000282406,NM_172069.3;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405000,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405223,;PLEKHH2,downstream_gene_variant,,ENST00000491692,; T ENST00000282406 Transcript missense_variant 1491/6981 1381/4482 461/1493 P/S Cca/Tca rs150493851 1 1 PLEKHH2 HGNC HGNC:30506 protein_coding YES CCDS1812.1 ENSP00000282406 Q8IVE3 UPI000016021B NM_172069.3 deleterious(0) 8/30 hmmpanther:PTHR22903,hmmpanther:PTHR22903:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 43700339 43700339 C T 1 0 0 0 0 1 0 0 0 12170 739 26 3 3 PLEKHH2 2 43700339 Missense_Mutation SNP C C3N-01489_T 1435635 43700339 198493190 108 25038 ABCG8 0 . GRCh38 2 43877684 43877684 + Missense_Mutation SNP A A T rs768950847 C3N-01489_T C3N-01489_N A A c.1880A>T p.Asp627Val p.D627V ENST00000272286 12/13 421 371 50 622 621 1 strelka-varscan ABCG8,missense_variant,p.Asp627Val,ENST00000272286,NM_022437.2; T ENST00000272286 Transcript missense_variant 1970/2665 1880/2022 627/673 D/V gAt/gTt rs768950847 1 1 ABCG8 HGNC HGNC:13887 protein_coding YES CCDS1815.1 ENSP00000272286 Q9H221 UPI000004C4CD NM_022437.2 tolerated(0.09) 12/13 hmmpanther:PTHR19241,hmmpanther:PTHR19241:SF239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 43877684 43877684 A T 1 0 0 0 0 1 0 0 0 76 347 12 4 4 ABCG8 2 43877684 Missense_Mutation SNP A C3N-01489_T 177345 43877684 198315845 109 25039 NRXN1 0 . GRCh38 2 50620149 50620149 + Missense_Mutation SNP G G T rs147400611 C3N-01489_T C3N-01489_N G G c.1313C>A p.Thr438Lys p.T438K ENST00000404971 9/24 146 128 18 239 239 0 strelka-varscan NRXN1,missense_variant,p.Thr398Lys,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Thr390Lys,ENST00000625672,;NRXN1,missense_variant,p.Thr438Lys,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Thr398Lys,ENST00000401669,;NRXN1,missense_variant,p.Thr386Lys,ENST00000405472,;NRXN1,missense_variant,p.Thr390Lys,ENST00000630543,;NRXN1,missense_variant,p.Thr370Lys,ENST00000628515,;NRXN1,missense_variant,p.Thr128Lys,ENST00000406859,;NRXN1,missense_variant,p.Thr113Lys,ENST00000402717,;NRXN1,missense_variant,p.Thr125Lys,ENST00000625891,;NRXN1,upstream_gene_variant,,ENST00000495871,;RP11-358H12.1,upstream_gene_variant,,ENST00000634985,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000628761,;NRXN1,downstream_gene_variant,,ENST00000630431,;NRXN1,upstream_gene_variant,,ENST00000637605,;NRXN1,missense_variant,p.Thr125Lys,ENST00000331040,;NRXN1,3_prime_UTR_variant,,ENST00000626249,; T ENST00000404971 Transcript missense_variant 2653/7578 1313/4644 438/1547 T/K aCg/aAg rs147400611 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0.03) 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 81 50620149 50620149 G T 1 0 0 0 0 1 0 0 0 10724 1145 40 1 1 NRXN1 2 50620149 Missense_Mutation SNP G C3N-01489_T 6742465 50620149 191573380 110 25040 EML6 0 . GRCh38 2 54950748 54950748 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.4182A>T p.= p.A1394A ENST00000356458 29/41 158 147 11 205 203 2 strelka-varscan EML6,synonymous_variant,p.=,ENST00000356458,NM_001039753.2;EML6,non_coding_transcript_exon_variant,,ENST00000481376,;EML6,upstream_gene_variant,,ENST00000490828,; T ENST00000356458 Transcript synonymous_variant 4702/8320 4182/5877 1394/1958 A gcA/gcT 1 1 EML6 HGNC HGNC:35412 protein_coding YES CCDS46286.1 ENSP00000348842 Q6ZMW3 UPI00006C0432 NM_001039753.2 29/41 Pfam_domain:PF03451 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 54950748 54950748 A T 1 0 0 0 0 0 0 0 1 4944 175 7 4 4 EML6 2 54950748 Silent SNP A C3N-01489_T 4330599 54950748 187242781 111 25041 VRK2 0 . GRCh38 2 58089633 58089633 + Frame_Shift_Del DEL G G - rs772465160 C3N-01489_T C3N-01489_N G G c.454delG p.Asp152MetfsTer16 p.D152Mfs*16 ENST00000435505 10/16 60 55 5 131 131 0 varindel-pindel VRK2,frameshift_variant,p.Asp152MetfsTer16,ENST00000435505,NM_001288837.1;VRK2,frameshift_variant,p.Asp152MetfsTer16,ENST00000417641,NM_001288838.1,NM_001130483.2;VRK2,frameshift_variant,p.Asp34MetfsTer16,ENST00000412104,NM_001288839.1,NM_001288836.1;VRK2,frameshift_variant,p.Asp152MetfsTer16,ENST00000340157,NM_001130480.2,NM_006296.6,NM_001130481.2;VRK2,frameshift_variant,p.Asp129MetfsTer16,ENST00000440705,NM_001130482.2;VRK2,downstream_gene_variant,,ENST00000428021,;VRK2,splice_region_variant,,ENST00000432057,; - ENST00000435505 Transcript frameshift_variant,splice_region_variant 1198/2446 453/1527 151/508 L/X ttG/tt rs772465160 1 1 VRK2 HGNC HGNC:12719 protein_coding YES CCDS1859.1 ENSP00000408002 Q86Y07 UPI000013D498 NM_001288837.1 10/16 PROSITE_profiles:PS50011,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF100,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 HIGH 1 deletion 1 1 1 PASS . . 1 207 2 0 0 0 0 0 -12.29717 1 1 1 1 0 - 7 5 81 58089633 58089633 G - 1 0 1 0 1 0 0 0 0 17769 1362 47 0 0 VRK2 2 58089633 Frame_Shift_Del DEL G C3N-01489_T 3138885 58089633 184103896 112 25042 VRK2 0 . GRCh38 2 58123209 58123209 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.652A>T p.Ser218Cys p.S218C ENST00000435505 11/16 196 175 21 319 318 1 strelka-varscan VRK2,missense_variant,p.Ser218Cys,ENST00000435505,NM_001288837.1;VRK2,missense_variant,p.Ser218Cys,ENST00000417641,NM_001288838.1,NM_001130483.2;VRK2,missense_variant,p.Ser100Cys,ENST00000412104,NM_001288839.1,NM_001288836.1;VRK2,missense_variant,p.Ser218Cys,ENST00000340157,NM_001130480.2,NM_006296.6,NM_001130481.2;VRK2,missense_variant,p.Ser195Cys,ENST00000440705,NM_001130482.2;VRK2,3_prime_UTR_variant,,ENST00000432057,; T ENST00000435505 Transcript missense_variant 1397/2446 652/1527 218/508 S/C Agc/Tgc 1 1 VRK2 HGNC HGNC:12719 protein_coding YES CCDS1859.1 ENSP00000408002 Q86Y07 UPI000013D498 NM_001288837.1 deleterious(0) 11/16 PROSITE_profiles:PS50011,hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF100,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 58123209 58123209 A T 1 0 0 0 0 1 0 0 0 17769 188 7 4 4 VRK2 2 58123209 Missense_Mutation SNP A C3N-01489_T 33576 58123209 184070320 113 25043 WDPCP 0 . GRCh38 2 63404288 63404288 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1195G>T p.Gly399Trp p.G399W ENST00000272321 10/18 139 117 22 179 179 0 strelka-varscan WDPCP,missense_variant,p.Gly207Trp,ENST00000409120,;WDPCP,missense_variant,p.Gly399Trp,ENST00000409562,;WDPCP,missense_variant,p.Gly399Trp,ENST00000272321,NM_015910.5;WDPCP,missense_variant,p.Gly207Trp,ENST00000409199,;WDPCP,missense_variant,p.Gly240Trp,ENST00000398544,NM_001042692.2;WDPCP,non_coding_transcript_exon_variant,,ENST00000409835,;WDPCP,missense_variant,p.Gly186Trp,ENST00000409354,;WDPCP,3_prime_UTR_variant,,ENST00000417238,;WDPCP,non_coding_transcript_exon_variant,,ENST00000493315,; A ENST00000272321 Transcript missense_variant 1723/3392 1195/2241 399/746 G/W Ggg/Tgg 1 -1 WDPCP HGNC HGNC:28027 protein_coding YES CCDS42688.1 ENSP00000272321 O95876 UPI000013D946 NM_015910.5 deleterious(0) 10/18 hmmpanther:PTHR13667:SF5,hmmpanther:PTHR13667,Pfam_domain:PF11768,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 63404288 63404288 C A 1 0 0 0 0 1 0 0 0 17833 681 24 2 2 WDPCP 2 63404288 Missense_Mutation SNP C C3N-01489_T 5281079 63404288 178789241 114 25044 BMP10 0 . GRCh38 2 68871071 68871071 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.288G>T p.= p.R96R ENST00000295379 1/2 148 131 17 205 205 0 strelka-varscan BMP10,synonymous_variant,p.=,ENST00000295379,NM_014482.1; A ENST00000295379 Transcript synonymous_variant 447/1584 288/1275 96/424 R cgG/cgT 1 -1 BMP10 HGNC HGNC:20869 protein_coding YES CCDS1890.1 ENSP00000295379 O95393 UPI0000126A11 NM_014482.1 1/2 hmmpanther:PTHR11848:SF39,hmmpanther:PTHR11848,Pfam_domain:PF00688 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 68871071 68871071 C A 1 0 0 0 0 0 0 0 1 1612 842 30 2 2 BMP10 2 68871071 Silent SNP C C3N-01489_T 5466783 68871071 173322458 115 25045 ADD2 0 . GRCh38 2 70663527 70663527 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.2079C>A p.= p.S693S ENST00000264436 16/16 289 255 34 428 427 1 strelka-varscan ADD2,synonymous_variant,p.=,ENST00000264436,NM_001617.3;ADD2,synonymous_variant,p.=,ENST00000407644,NM_001185054.1;ADD2,3_prime_UTR_variant,,ENST00000355733,NM_017488.3;ADD2,synonymous_variant,p.=,ENST00000403045,;ADD2,non_coding_transcript_exon_variant,,ENST00000481675,; T ENST00000264436 Transcript synonymous_variant 2524/9267 2079/2181 693/726 S tcC/tcA 1 -1 ADD2 HGNC HGNC:244 protein_coding YES CCDS1906.1 ENSP00000264436 P35612 UPI0000125503 NM_001617.3 16/16 Low_complexity_(Seg):seg,hmmpanther:PTHR10672,hmmpanther:PTHR10672:SF6 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 70663527 70663527 G T 1 0 0 0 0 0 0 0 1 349 1219 43 2 2 ADD2 2 70663527 Silent SNP G C3N-01489_T 1792456 70663527 171530002 116 25046 EMX1 0 . GRCh38 2 72924323 72924323 + Nonsense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.535C>T p.Gln179Ter p.Q179* ENST00000258106 2/3 365 331 34 428 427 1 strelka-varscan EMX1,stop_gained,p.Gln179Ter,ENST00000258106,NM_004097.2;EMX1,stop_gained,p.Gln57Ter,ENST00000473732,;EMX1,missense_variant,p.Pro131Leu,ENST00000394111,;EMX1,non_coding_transcript_exon_variant,,ENST00000491023,;EMX1,non_coding_transcript_exon_variant,,ENST00000464675,; T ENST00000258106 Transcript stop_gained 913/2188 535/873 179/290 Q/* Cag/Tag 1 1 EMX1 HGNC HGNC:3340 protein_coding YES CCDS1921.2 ENSP00000258106 Q04741 UPI0000D47CF7 NM_004097.2 2/3 hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF26,Superfamily_domains:SSF46689 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 72924323 72924323 C T 1 0 0 0 0 0 1 0 0 4949 595 21 3 3 EMX1 2 72924323 Nonsense_Mutation SNP C C3N-01489_T 2260796 72924323 169269206 117 25047 ALMS1 0 . GRCh38 2 73450824 73450824 + Nonsense_Mutation SNP G G T rs577224267 C3N-01489_T C3N-01489_N G G c.4297G>T p.Glu1433Ter p.E1433* ENST00000613296 8/23 144 132 12 249 249 0 strelka-varscan ALMS1,stop_gained,p.Glu1433Ter,ENST00000613296,NM_015120.4;ALMS1,stop_gained,p.Glu1391Ter,ENST00000484298,;ALMS1,stop_gained,p.Glu1433Ter,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; T ENST00000613296 Transcript stop_gained 4408/12925 4297/12507 1433/4168 E/* Gag/Tag rs577224267 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 8/23 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 73450824 73450824 G T 1 0 0 0 0 0 1 0 0 635 943 33 2 2 ALMS1 2 73450824 Nonsense_Mutation SNP G C3N-01489_T 526501 73450824 168742705 118 25048 LRRTM1 0 . GRCh38 2 80302562 80302562 + Nonsense_Mutation SNP C C A rs200735251 C3N-01489_T C3N-01489_N C C c.1258G>T p.Glu420Ter p.E420* ENST00000295057 2/2 171 157 14 222 222 0 strelka-varscan LRRTM1,stop_gained,p.Glu420Ter,ENST00000295057,;LRRTM1,stop_gained,p.Glu420Ter,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,stop_gained,p.Glu420Ter,ENST00000433224,;LRRTM1,stop_gained,p.Glu420Ter,ENST00000417012,; A ENST00000295057 Transcript stop_gained 1915/2599 1258/1569 420/522 E/* Gag/Tag rs200735251,COSM226504,COSM226505 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 80302562 80302562 C A 1 0 0 0 0 0 1 0 0 8945 893 31 1 1 LRRTM1 2 80302562 Nonsense_Mutation SNP C C3N-01489_T 6851738 80302562 161890967 119 25049 SFTPB 0 . GRCh38 2 85663492 85663492 + Splice_Site SNP C C T novel C3N-01489_T C3N-01489_N C C c.893-1G>A p.X298_splice ENST00000409383 497 437 60 662 661 1 strelka-varscan SFTPB,splice_acceptor_variant,,ENST00000393822,;SFTPB,splice_acceptor_variant,,ENST00000519937,;SFTPB,splice_acceptor_variant,,ENST00000409383,NM_198843.2,NM_000542.3;SFTPB,intron_variant,,ENST00000428225,;SFTPB,upstream_gene_variant,,ENST00000494165,;SFTPB,non_coding_transcript_exon_variant,,ENST00000491167,;SFTPB,downstream_gene_variant,,ENST00000473692,; T ENST00000409383 Transcript splice_acceptor_variant -/1867 893/1182 298/393 1 -1 SFTPB HGNC HGNC:10801 protein_coding YES CCDS1983.2 ENSP00000386346 D6W5L6 UPI0000421A06 NM_198843.2,NM_000542.3 8/11 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 81 85663492 85663492 C T 1 0 0 0 0 0 0 1 0 14451 695 24 3 3 SFTPB 2 85663492 Splice_Site SNP C C3N-01489_T 5360930 85663492 156530037 120 25050 RNF103 0 . GRCh38 2 86604582 86604582 + Missense_Mutation SNP C C A rs375282269 C3N-01489_T C3N-01489_N C C c.1319G>T p.Arg440Leu p.R440L ENST00000237455 4/4 162 144 18 229 229 0 strelka-varscan RNF103,missense_variant,p.Arg440Leu,ENST00000237455,NM_005667.3;RNF103-CHMP3,intron_variant,,ENST00000604011,NM_001198954.1;RNF103-CHMP3,intron_variant,,ENST00000440757,;AC015971.2,intron_variant,,ENST00000426549,;AC015971.2,intron_variant,,ENST00000424788,;AC015971.2,intron_variant,,ENST00000597638,;AC015971.2,intron_variant,,ENST00000439077,;RNF103,intron_variant,,ENST00000463333,;RNF103,downstream_gene_variant,,ENST00000477307,;RNF103,non_coding_transcript_exon_variant,,ENST00000472030,; A ENST00000237455 Transcript missense_variant 2288/3477 1319/2058 440/685 R/L cGc/cTc rs375282269 1 -1 RNF103 HGNC HGNC:12859 protein_coding YES CCDS33237.1 ENSP00000237455 O00237 UPI0000073F2A NM_005667.3 tolerated(0.68) 4/4 hmmpanther:PTHR15302,hmmpanther:PTHR15302:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999883 1 1 1 0 A 3 1 81 86604582 86604582 C A 1 0 0 0 0 1 0 0 0 13601 768 27 1 1 RNF103 2 86604582 Missense_Mutation SNP C C3N-01489_T 941090 86604582 155588947 121 25051 ASTL 0 . GRCh38 2 96132622 96132622 + Frame_Shift_Del DEL C C - novel C3N-01489_T C3N-01489_N C C c.555delG p.Met185IlefsTer43 p.M185Ifs*43 ENST00000342380 6/9 106 95 11 130 130 0 sindel-varindel-pindel ASTL,frameshift_variant,p.Met185IlefsTer43,ENST00000342380,NM_001002036.3;ASTL,downstream_gene_variant,,ENST00000470582,; - ENST00000342380 Transcript frameshift_variant 555/1296 555/1296 185/431 M/X atG/at 1 -1 ASTL HGNC HGNC:31704 protein_coding YES CCDS33249.1 ENSP00000343674 Q6HA08 UPI0000161978 NM_001002036.3 6/9 Gene3D:3.40.390.10,Pfam_domain:PF01400,Prints_domain:PR00480,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF649,SMART_domains:SM00235,Superfamily_domains:SSF55486 HIGH 1 deletion 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99859 1 1 1 1 0 - 7 5 81 96132622 96132622 C - 1 0 1 0 1 0 0 0 0 1210 710 25 0 0 ASTL 2 96132622 Frame_Shift_Del DEL C C3N-01489_T 9528040 96132622 146060907 122 25052 NCAPH 0 . GRCh38 2 96343256 96343256 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.547C>T p.= p.L183L ENST00000240423 5/18 117 105 12 152 152 0 strelka-varscan NCAPH,synonymous_variant,p.=,ENST00000455200,;NCAPH,synonymous_variant,p.=,ENST00000240423,NM_015341.4,NM_001281710.1,NM_001281711.1;NCAPH,synonymous_variant,p.=,ENST00000427946,NM_001281712.1;NCAPH,synonymous_variant,p.=,ENST00000435975,;NCAPH,intron_variant,,ENST00000456906,;NCAPH,non_coding_transcript_exon_variant,,ENST00000477409,; T ENST00000240423 Transcript synonymous_variant 590/2763 547/2226 183/741 L Ctg/Ttg 1 1 NCAPH HGNC HGNC:1112 protein_coding YES CCDS2021.1 ENSP00000240423 Q15003 UPI0000163F72 NM_015341.4,NM_001281710.1,NM_001281711.1 5/18 hmmpanther:PTHR13108,Pfam_domain:PF05786,PIRSF_domain:PIRSF017126 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -18.09785 0.9999998 1 1 1 0 T 2 4 81 96343256 96343256 C T 1 0 0 0 0 0 0 0 1 10225 796 28 3 3 NCAPH 2 96343256 Silent SNP C C3N-01489_T 210634 96343256 145850273 123 25053 RFX8 0 . GRCh38 2 101402557 101402557 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1124C>A p.Pro375His p.P375H ENST00000428343 11/12 261 234 27 348 348 0 strelka-varscan RFX8,missense_variant,p.Pro375His,ENST00000428343,NM_001145664.1;RFX8,3_prime_UTR_variant,,ENST00000481179,; T ENST00000428343 Transcript missense_variant 1244/1686 1124/1422 375/473 P/H cCc/cAc 1 -1 RFX8 HGNC HGNC:37253 protein_coding YES CCDS46376.1 ENSP00000401536 Q6ZV50 UPI0001AE76D5 NM_001145664.1 deleterious(0.04) 11/12 hmmpanther:PTHR12619:SF24,hmmpanther:PTHR12619 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 101402557 101402557 G T 1 0 0 0 0 1 0 0 0 13443 1232 43 2 2 RFX8 2 101402557 Missense_Mutation SNP G C3N-01489_T 5059301 101402557 140790972 124 25054 IL18RAP 0 . GRCh38 2 102424385 102424385 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.550G>T p.Ala184Ser p.A184S ENST00000264260 5/12 123 102 21 185 185 0 strelka-varscan IL18RAP,missense_variant,p.Ala184Ser,ENST00000264260,NM_003853.3;IL18RAP,missense_variant,p.Ala42Ser,ENST00000409369,;IL18RAP,downstream_gene_variant,,ENST00000450855,;IL18RAP,downstream_gene_variant,,ENST00000497795,; T ENST00000264260 Transcript missense_variant 1139/2773 550/1800 184/599 A/S Gca/Tca 1 1 IL18RAP HGNC HGNC:5989 protein_coding YES CCDS2061.1 ENSP00000264260 O95256 UPI0000071CAF NM_003853.3 tolerated(0.1) 5/12 Gene3D:2.60.40.10,Pfam_domain:PF13895,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF23,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 102424385 102424385 G T 1 0 0 0 0 1 0 0 0 7556 1319 46 2 2 IL18RAP 2 102424385 Missense_Mutation SNP G C3N-01489_T 1021828 102424385 139769144 125 25055 NCK2 0 . GRCh38 2 105881657 105881657 + Missense_Mutation SNP G G A rs755385208 C3N-01489_T C3N-01489_N G G c.556G>A p.Ala186Thr p.A186T ENST00000233154 4/5 67 55 12 133 133 0 strelka-varscan NCK2,missense_variant,p.Ala186Thr,ENST00000233154,NM_003581.4;NCK2,missense_variant,p.Ala186Thr,ENST00000393349,NM_001004720.2;NCK2,intron_variant,,ENST00000451463,NM_001004722.3;NCK2,intron_variant,,ENST00000522586,;NCK2,downstream_gene_variant,,ENST00000393348,;NCK2,downstream_gene_variant,,ENST00000425756,; A ENST00000233154 Transcript missense_variant 998/2683 556/1143 186/380 A/T Gcc/Acc rs755385208,COSM5511752,COSM5511753 1 1 NCK2 HGNC HGNC:7665 protein_coding YES CCDS33266.1 ENSP00000233154 O43639 A0A0S2Z4M6 UPI000012FE3F NM_003581.4 tolerated(0.17) 4/5 PIRSF_domain:PIRSF037874,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF159 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 105881657 105881657 G A 1 0 0 0 0 1 0 0 0 10238 1087 38 1 1 NCK2 2 105881657 Missense_Mutation SNP G C3N-01489_T 3457272 105881657 136311872 126 25056 SH3RF3 0 . GRCh38 2 109129641 109129641 + Missense_Mutation SNP G G T rs549801912 C3N-01489_T C3N-01489_N G G c.101G>T p.Arg34Leu p.R34L ENST00000309415 1/10 108 100 8 159 159 0 strelka-varscan SH3RF3,missense_variant,p.Arg34Leu,ENST00000309415,NM_001099289.2;SH3RF3-AS1,upstream_gene_variant,,ENST00000567491,; T ENST00000309415 Transcript missense_variant 294/5803 101/2649 34/882 R/L cGg/cTg rs549801912 1 1 SH3RF3 HGNC HGNC:24699 protein_coding YES CCDS74557.1 ENSP00000309186 Q8TEJ3 UPI0000DD7AEA NM_001099289.2 tolerated_low_confidence(0.07) 1/10 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -16.25435 1 1 1 1 0 T 3 4 81 109129641 109129641 G T 1 0 0 0 0 1 0 0 0 14519 1116 39 1 1 SH3RF3 2 109129641 Missense_Mutation SNP G C3N-01489_T 3247984 109129641 133063888 127 25057 PAX8 0 . GRCh38 2 113235423 113235423 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1058G>A p.Gly353Glu p.G353E ENST00000263334 9/12 118 97 21 160 160 0 strelka-varscan PAX8,missense_variant,p.Gly353Glu,ENST00000263334,;PAX8,missense_variant,p.Gly353Glu,ENST00000429538,NM_003466.3;PAX8,missense_variant,p.Gly327Ser,ENST00000348715,NM_013952.3;PAX8,missense_variant,p.Gly8Glu,ENST00000465084,;PAX8,5_prime_UTR_variant,,ENST00000497038,;PAX8,intron_variant,,ENST00000263335,NM_013953.3;PAX8,intron_variant,,ENST00000397647,NM_013992.3;PAX8,intron_variant,,ENST00000468980,;PAX8-AS1,intron_variant,,ENST00000456685,;PAX8-AS1,upstream_gene_variant,,ENST00000422956,;PAX8-AS1,upstream_gene_variant,,ENST00000436293,;PAX8-AS1,upstream_gene_variant,,ENST00000445745,;PAX8-AS1,upstream_gene_variant,,ENST00000437551,;PAX8-AS1,upstream_gene_variant,,ENST00000333145,;PAX8-AS1,upstream_gene_variant,,ENST00000451179,;PAX8-AS1,upstream_gene_variant,,ENST00000623306,;PAX8-AS1,upstream_gene_variant,,ENST00000617509,;PAX8-AS1,upstream_gene_variant,,ENST00000431844,;PAX8-AS1,upstream_gene_variant,,ENST00000556070,;PAX8-AS1,upstream_gene_variant,,ENST00000553869,;PAX8-AS1,upstream_gene_variant,,ENST00000616073,;PAX8-AS1,upstream_gene_variant,,ENST00000624706,;PAX8,non_coding_transcript_exon_variant,,ENST00000485840,;PAX8,non_coding_transcript_exon_variant,,ENST00000554352,;PAX8-AS1,upstream_gene_variant,,ENST00000613966,;PAX8-AS1,upstream_gene_variant,,ENST00000555766,; T ENST00000263334 Transcript missense_variant 1321/4152 1058/1353 353/450 G/E gGg/gAg 1 -1 PAX8 HGNC HGNC:8622 protein_coding YES CCDS46398.1 ENSP00000263334 Q06710 R9W7C9 UPI0000071DEC deleterious(0.01) 9/12 Pfam_domain:PF12403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 113235423 113235423 C T 1 0 0 0 0 1 0 0 0 11570 623 22 3 3 PAX8 2 113235423 Missense_Mutation SNP C C3N-01489_T 4105782 113235423 128958106 128 25058 GLI2 0 . GRCh38 2 120989871 120989871 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.3957G>T p.Gln1319His p.Q1319H ENST00000452319 14/14 106 98 8 169 169 0 strelka-varscan GLI2,missense_variant,p.Gln1319His,ENST00000452319,;GLI2,missense_variant,p.Gln1319His,ENST00000361492,NM_005270.4;GLI2,downstream_gene_variant,,ENST00000435313,;GLI2,3_prime_UTR_variant,,ENST00000445186,;GLI2,3_prime_UTR_variant,,ENST00000341310,;GLI2,intron_variant,,ENST00000438299,;GLI2,intron_variant,,ENST00000452692,;GLI2,downstream_gene_variant,,ENST00000437950,; T ENST00000452319 Transcript missense_variant 4017/6799 3957/4761 1319/1586 Q/H caG/caT 1 1 GLI2 HGNC HGNC:4318 protein_coding YES CCDS33283.1 ENSP00000390436 P10070 UPI000053FCB4 tolerated_low_confidence(0.05) 14/14 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF73 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 120989871 120989871 G T 1 0 0 0 0 1 0 0 0 6316 933 33 2 2 GLI2 2 120989871 Missense_Mutation SNP G C3N-01489_T 7754448 120989871 121203658 129 25059 ZRANB3 0 . GRCh38 2 135390808 135390808 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.174T>A p.= p.A58A ENST00000264159 3/21 90 81 9 136 136 0 strelka-varscan ZRANB3,synonymous_variant,p.=,ENST00000401392,NM_001286568.1;ZRANB3,synonymous_variant,p.=,ENST00000264159,NM_032143.3;ZRANB3,5_prime_UTR_variant,,ENST00000536680,NM_001286569.1;ZRANB3,intron_variant,,ENST00000452187,;ZRANB3,synonymous_variant,p.=,ENST00000403017,;ZRANB3,non_coding_transcript_exon_variant,,ENST00000492193,; T ENST00000264159 Transcript synonymous_variant 291/4046 174/3240 58/1079 A gcT/gcA 1 -1 ZRANB3 HGNC HGNC:25249 protein_coding YES CCDS46419.1 ENSP00000264159 Q5FWF4 UPI0000509F0C NM_032143.3 3/21 PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF731,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.02093 1 1 1 1 0 T 2 4 81 135390808 135390808 A T 1 0 0 0 0 0 0 0 1 18817 175 7 4 4 ZRANB3 2 135390808 Silent SNP A C3N-01489_T 14400937 135390808 106802721 130 25060 ZEB2 0 . GRCh38 2 144398839 144398839 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2348C>A p.Pro783His p.P783H ENST00000637267 9/11 343 308 35 547 546 1 strelka-varscan ZEB2,missense_variant,p.Pro783His,ENST00000637267,;ZEB2,missense_variant,p.Pro808His,ENST00000636471,;ZEB2,missense_variant,p.Pro783His,ENST00000627532,NM_014795.3;ZEB2,missense_variant,p.Pro783His,ENST00000636026,;ZEB2,missense_variant,p.Pro671His,ENST00000638087,;ZEB2,missense_variant,p.Pro671His,ENST00000637304,;ZEB2,missense_variant,p.Pro671His,ENST00000638007,;ZEB2,missense_variant,p.Pro671His,ENST00000637045,;ZEB2,missense_variant,p.Pro671His,ENST00000636413,;ZEB2,missense_variant,p.Pro524His,ENST00000638128,;ZEB2,missense_variant,p.Pro783His,ENST00000409487,;ZEB2,missense_variant,p.Pro759His,ENST00000539609,NM_001171653.1;ZEB2,missense_variant,p.Pro783His,ENST00000558170,;ZEB2,missense_variant,p.Pro782His,ENST00000303660,;ZEB2,intron_variant,,ENST00000440875,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,upstream_gene_variant,,ENST00000637873,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,3_prime_UTR_variant,,ENST00000636732,; T ENST00000637267 Transcript missense_variant 3189/9856 2348/3645 783/1214 P/H cCt/cAt 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 deleterious(0) 9/11 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 144398839 144398839 G T 1 0 0 0 0 1 0 0 0 18200 1000 35 2 2 ZEB2 2 144398839 Missense_Mutation SNP G C3N-01489_T 9008031 144398839 97794690 131 25061 BAZ2B 0 . GRCh38 2 159429202 159429202 + Nonsense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.2253T>A p.Tyr751Ter p.Y751* ENST00000392783 11/37 68 60 8 95 95 0 strelka-varscan BAZ2B,stop_gained,p.Tyr751Ter,ENST00000392783,NM_013450.3;BAZ2B,stop_gained,p.Tyr749Ter,ENST00000392782,NM_001289975.1;BAZ2B,stop_gained,p.Tyr457Ter,ENST00000343439,;BAZ2B,stop_gained,p.Tyr85Ter,ENST00000441143,;BAZ2B,splice_region_variant,,ENST00000472953,; T ENST00000392783 Transcript stop_gained,splice_region_variant 2749/8289 2253/6507 751/2168 Y/* taT/taA 1 -1 BAZ2B HGNC HGNC:963 protein_coding YES CCDS2209.2 ENSP00000376534 Q9UIF8 UPI0000D74C4A NM_013450.3 11/37 Gene3D:3.30.890.10,Pfam_domain:PF01429,PROSITE_profiles:PS50982,hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF154,SMART_domains:SM00391,Superfamily_domains:SSF54171 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -17.81133 0.9999999 1 1 1 0 T 4 4 81 159429202 159429202 A T 1 0 0 0 0 0 1 0 0 1477 231 8 4 4 BAZ2B 2 159429202 Nonsense_Mutation SNP A C3N-01489_T 15030363 159429202 82764327 132 25062 SCN2A 0 . GRCh38 2 165389497 165389497 + Silent SNP G G A rs780700291 C3N-01489_T C3N-01489_N G G c.5691G>A p.= p.T1897T ENST00000636071 28/28 387 341 46 567 566 1 strelka-varscan SCN2A,synonymous_variant,p.=,ENST00000636071,;SCN2A,synonymous_variant,p.=,ENST00000636985,;SCN2A,synonymous_variant,p.=,ENST00000637266,;SCN2A,synonymous_variant,p.=,ENST00000375437,NM_001040142.1;SCN2A,synonymous_variant,p.=,ENST00000283256,NM_021007.2;SCN2A,synonymous_variant,p.=,ENST00000375427,NM_001040143.1;SCN2A,synonymous_variant,p.=,ENST00000631182,;SCN2A,3_prime_UTR_variant,,ENST00000636662,;SCN2A,3_prime_UTR_variant,,ENST00000636384,;SCN2A,3_prime_UTR_variant,,ENST00000636769,;SCN2A,3_prime_UTR_variant,,ENST00000636135,;SCN2A,non_coding_transcript_exon_variant,,ENST00000480032,; A ENST00000636071 Transcript synonymous_variant 6068/9303 5691/6018 1897/2005 T acG/acA rs780700291,COSM359552,COSM359553,COSM3895163,COSM3895164 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 28/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 0,1,1,1,1 LOW 1 SNV 0,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 165389497 165389497 G A 1 0 0 0 0 0 0 0 1 14185 1045 37 1 1 SCN2A 2 165389497 Silent SNP G C3N-01489_T 5960295 165389497 76804032 133 25063 GALNT3 0 . GRCh38 2 165770427 165770427 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.274G>T p.Ala92Ser p.A92S ENST00000392701 2/11 300 261 39 468 468 0 strelka-varscan GALNT3,missense_variant,p.Ala92Ser,ENST00000392701,NM_004482.3;GALNT3,missense_variant,p.Ala92Ser,ENST00000412248,;GALNT3,downstream_gene_variant,,ENST00000447156,;GALNT3,downstream_gene_variant,,ENST00000414977,;GALNT3,downstream_gene_variant,,ENST00000431484,;GALNT3,downstream_gene_variant,,ENST00000422973,; A ENST00000392701 Transcript missense_variant 1050/3868 274/1902 92/633 A/S Gct/Tct 1 -1 GALNT3 HGNC HGNC:4125 protein_coding YES CCDS2226.1 ENSP00000376465 Q14435 UPI000013C989 NM_004482.3 tolerated(0.87) 2/11 hmmpanther:PTHR11675:SF33,hmmpanther:PTHR11675 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 165770427 165770427 C A 1 0 0 0 0 1 0 0 0 6085 710 25 2 2 GALNT3 2 165770427 Missense_Mutation SNP C C3N-01489_T 380930 165770427 76423102 134 25064 TTC21B 0 . GRCh38 2 165941165 165941165 + Missense_Mutation SNP C C A rs778525866,rs781486283 C3N-01489_T C3N-01489_N C C c.572G>T p.Arg191Leu p.R191L ENST00000243344 6/29 358 326 32 558 556 2 strelka-varscan TTC21B,missense_variant,p.Arg191Leu,ENST00000243344,NM_024753.4;TTC21B-AS1,intron_variant,,ENST00000440322,;TTC21B-AS1,intron_variant,,ENST00000443032,;TTC21B,non_coding_transcript_exon_variant,,ENST00000464374,;TTC21B-AS1,intron_variant,,ENST00000446624,; A ENST00000243344 Transcript missense_variant 710/5482 572/3951 191/1316 R/L cGc/cTc rs778525866,rs781486283,COSM268204 1 -1 TTC21B HGNC HGNC:25660 protein_coding YES CCDS33315.1 ENSP00000243344 Q7Z4L5 UPI000020900A NM_024753.4 tolerated(0.08) 6/29 hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF81901,Superfamily_domains:SSF48452 0,0,1 MODERATE 1 SNV 1 0,0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 165941165 165941165 C A 1 0 0 0 0 1 0 0 0 17196 768 27 1 1 TTC21B 2 165941165 Missense_Mutation SNP C C3N-01489_T 170738 165941165 76252364 135 25065 STK39 0 . GRCh38 2 168075183 168075183 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1138G>T p.Gly380Trp p.G380W ENST00000355999 11/18 255 228 27 379 377 2 strelka-varscan-mutect STK39,missense_variant,p.Gly380Trp,ENST00000355999,NM_013233.2;STK39,non_coding_transcript_exon_variant,,ENST00000487143,; A ENST00000355999 Transcript missense_variant 1844/3820 1138/1638 380/545 G/W Ggg/Tgg 1 -1 STK39 HGNC HGNC:17717 protein_coding YES CCDS42770.1 ENSP00000348278 Q9UEW8 UPI000013D46D NM_013233.2 deleterious(0.01) 11/18 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF330 MODERATE 1 SNV 1 1 PASS rs1362104547 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 168075183 168075183 C A 1 0 0 0 0 1 0 0 0 15682 652 23 1 1 STK39 2 168075183 Missense_Mutation SNP C C3N-01489_T 2134018 168075183 74118346 136 25066 COL3A1 0 . GRCh38 2 188999855 188999855 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.2243G>T p.Gly748Val p.G748V ENST00000304636 32/51 295 268 27 388 387 1 strelka-varscan-mutect COL3A1,missense_variant,p.Gly748Val,ENST00000304636,NM_000090.3;COL3A1,missense_variant,p.Gly748Val,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000637672,;COL3A1,upstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript missense_variant 2413/5543 2243/4401 748/1466 G/V gGt/gTt COSM3575394,COSM3575395 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 tolerated(0.61) 32/51 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 188999855 188999855 G T 1 0 0 0 0 1 0 0 0 3477 1261 44 2 2 COL3A1 2 188999855 Missense_Mutation SNP G C3N-01489_T 20924672 188999855 53193674 137 25067 MSTN 0 . GRCh38 2 190057624 190057624 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.762G>T p.Glu254Asp p.E254D ENST00000260950 3/3 180 159 21 319 319 0 strelka-varscan-mutect MSTN,missense_variant,p.Glu254Asp,ENST00000260950,NM_005259.2;C2orf88,intron_variant,,ENST00000478197,;C2orf88,intron_variant,,ENST00000495546,; A ENST00000260950 Transcript missense_variant 895/2822 762/1128 254/375 E/D gaG/gaT 1 -1 MSTN HGNC HGNC:4223 protein_coding YES CCDS2303.1 ENSP00000260950 O14793 Q53S46 UPI0000037254 NM_005259.2 deleterious(0.01) 3/3 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 190057624 190057624 C A 1 0 0 0 0 1 0 0 0 9877 680 24 2 2 MSTN 2 190057624 Missense_Mutation SNP C C3N-01489_T 1057769 190057624 52135905 138 25068 SATB2 0 . GRCh38 2 199368671 199368671 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.634G>T p.Ala212Ser p.A212S ENST00000417098 6/11 276 254 22 393 393 0 strelka-varscan-mutect SATB2,missense_variant,p.Ala153Ser,ENST00000443023,;SATB2,missense_variant,p.Ala212Ser,ENST00000417098,NM_001172509.1;SATB2,missense_variant,p.Ala212Ser,ENST00000260926,NM_001172517.1;SATB2,missense_variant,p.Ala212Ser,ENST00000457245,NM_015265.3;SATB2,intron_variant,,ENST00000614512,;SATB2,intron_variant,,ENST00000428695,;SATB2,non_coding_transcript_exon_variant,,ENST00000484124,;SATB2,non_coding_transcript_exon_variant,,ENST00000483346,; A ENST00000417098 Transcript missense_variant 1451/5730 634/2202 212/733 A/S Gcc/Tcc 1 -1 SATB2 HGNC HGNC:21637 protein_coding YES CCDS2327.1 ENSP00000401112 Q9UPW6 A0A024R3U6 UPI00000336B1 NM_001172509.1 deleterious(0.04) 6/11 hmmpanther:PTHR15116:SF15,hmmpanther:PTHR15116,Pfam_domain:PF16557 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 199368671 199368671 C A 1 0 0 0 0 1 0 0 0 14115 710 25 2 2 SATB2 2 199368671 Missense_Mutation SNP C C3N-01489_T 9311047 199368671 42824858 139 25069 AOX1 0 . GRCh38 2 200641163 200641163 + Silent SNP C C A rs768503886 C3N-01489_T C3N-01489_N C C c.2634C>A p.= p.A878A ENST00000374700 24/35 104 98 6 104 104 0 strelka-mutect AOX1,synonymous_variant,p.=,ENST00000374700,NM_001159.3;AOX1,non_coding_transcript_exon_variant,,ENST00000485106,;AOX1,non_coding_transcript_exon_variant,,ENST00000465297,;AOX1,non_coding_transcript_exon_variant,,ENST00000472553,; A ENST00000374700 Transcript synonymous_variant 2875/5074 2634/4017 878/1338 A gcC/gcA rs768503886 1 1 AOX1 HGNC HGNC:553 protein_coding YES CCDS33360.1 ENSP00000363832 Q06278 UPI0000071863 NM_001159.3 24/35 hmmpanther:PTHR11908:SF86,hmmpanther:PTHR11908,Pfam_domain:PF02738,Gene3D:3.30.365.10,PIRSF_domain:PIRSF000127,TIGRFAM_domain:TIGR02969,Superfamily_domains:SSF56003 LOW 1 SNV 1 1 PASS rs768503886 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 200641163 200641163 C A 1 0 0 0 0 0 0 0 1 839 668 24 2 2 AOX1 2 200641163 Silent SNP C C3N-01489_T 1272492 200641163 41552366 140 25070 CASP8 0 . GRCh38 2 201258300 201258300 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.69C>T p.= p.P23P ENST00000358485 1/9 408 358 50 581 581 0 strelka-varscan-mutect CASP8,synonymous_variant,p.=,ENST00000358485,NM_001080125.1;CASP8,intron_variant,,ENST00000264274,;CASP8,intron_variant,,ENST00000264275,NM_001228.4;CASP8,intron_variant,,ENST00000392263,NM_001080124.1;CASP8,intron_variant,,ENST00000432109,NM_033355.3;CASP8,intron_variant,,ENST00000392266,;CASP8,intron_variant,,ENST00000392258,NM_033358.3;CASP8,intron_variant,,ENST00000447616,;CASP8,intron_variant,,ENST00000450491,;CASP8,intron_variant,,ENST00000413726,;CASP8,intron_variant,,ENST00000440732,;CASP8,upstream_gene_variant,,ENST00000323492,NM_033356.3;CASP8,upstream_gene_variant,,ENST00000429881,;CASP8,intron_variant,,ENST00000490412,;CASP8,synonymous_variant,p.=,ENST00000437283,;CASP8,intron_variant,,ENST00000471383,;CASP8,upstream_gene_variant,,ENST00000339403,; T ENST00000358485 Transcript synonymous_variant 265/2930 69/1617 23/538 P ccC/ccT 1 1 CASP8 HGNC HGNC:1509 protein_coding YES CCDS42798.1 ENSP00000351273 Q14790 UPI0000456ECD NM_001080125.1 1/9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 201258300 201258300 C T 1 0 0 0 0 0 0 0 1 2377 581 21 3 3 CASP8 2 201258300 Silent SNP C C3N-01489_T 617137 201258300 40935229 141 25071 KIAA2012 0 . GRCh38 2 202099760 202099760 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.976G>T p.Gly326Ter p.G326* ENST00000498697 6/24 132 116 16 201 201 0 strelka-mutect KIAA2012,stop_gained,p.Gly326Ter,ENST00000498697,;KIAA2012,stop_gained,p.Gly326Ter,ENST00000541917,NM_001277372.1;KIAA2012,stop_gained,p.Gly382Ter,ENST00000459709,;KIAA2012,non_coding_transcript_exon_variant,,ENST00000409515,; T ENST00000498697 Transcript stop_gained 976/3772 976/3546 326/1181 G/* Gga/Tga 1 1 KIAA2012 HGNC HGNC:51250 protein_coding YES ENSP00000419834 H7C5G6 UPI0005D0279F 6/24 hmmpanther:PTHR21937,hmmpanther:PTHR21937:SF3 HIGH SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.99995 0.9999999 1 1 1 0 T 4 4 81 202099760 202099760 G T 1 0 0 0 0 0 1 0 0 8131 1349 47 2 2 KIAA2012 2 202099760 Nonsense_Mutation SNP G C3N-01489_T 841460 202099760 40093769 142 25072 ZDBF2 0 . GRCh38 2 206305659 206305659 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.1131G>C p.Gln377His p.Q377H ENST00000374423 5/5 96 88 8 177 177 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Gln377His,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Gln375His,ENST00000611847,NM_001285549.1; C ENST00000374423 Transcript missense_variant 1517/10286 1131/7065 377/2354 Q/H caG/caC 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.3) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 206305659 206305659 G C 1 0 0 0 0 1 0 0 0 18174 962 34 4 4 ZDBF2 2 206305659 Missense_Mutation SNP G C3N-01489_T 4205899 206305659 35887870 143 25073 CRYGA 0 . GRCh38 2 208163293 208163293 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.163C>A p.Gln55Lys p.Q55K ENST00000304502 2/3 277 243 34 422 422 0 strelka-varscan-mutect CRYGA,missense_variant,p.Gln55Lys,ENST00000304502,NM_014617.3;C2orf80,downstream_gene_variant,,ENST00000341287,NM_001099334.2;C2orf80,downstream_gene_variant,,ENST00000451346,;C2orf80,downstream_gene_variant,,ENST00000451342,;C2orf80,downstream_gene_variant,,ENST00000428015,;C2orf80,downstream_gene_variant,,ENST00000453017,; T ENST00000304502 Transcript missense_variant 183/609 163/525 55/174 Q/K Cag/Aag 1 -1 CRYGA HGNC HGNC:2408 protein_coding YES CCDS33367.1 ENSP00000302105 P11844 A0A0S2A4T3 UPI000049DF32 NM_014617.3 deleterious(0) 2/3 PROSITE_profiles:PS50915,hmmpanther:PTHR11818,hmmpanther:PTHR11818:SF28,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695,Prints_domain:PR01367 MODERATE 1 SNV 1 1 PASS rs902028178 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 208163293 208163293 G T 1 0 0 0 0 1 0 0 0 3716 1357 47 2 2 CRYGA 2 208163293 Missense_Mutation SNP G C3N-01489_T 1857634 208163293 34030236 144 25074 PIKFYVE 0 . GRCh38 2 208285811 208285811 + Missense_Mutation SNP G G T rs777357869 C3N-01489_T C3N-01489_N G G c.699G>T p.Leu233Phe p.L233F ENST00000264380 6/42 338 316 22 443 442 1 strelka-varscan-mutect PIKFYVE,missense_variant,p.Leu233Phe,ENST00000264380,NM_015040.3;PIKFYVE,missense_variant,p.Leu233Phe,ENST00000452564,;PIKFYVE,missense_variant,p.Leu136Phe,ENST00000392202,NM_152671.3;PIKFYVE,missense_variant,p.Leu233Phe,ENST00000407449,NM_001178000.1;PIKFYVE,missense_variant,p.Leu147Phe,ENST00000308862,;PIKFYVE,downstream_gene_variant,,ENST00000422495,;PIKFYVE,3_prime_UTR_variant,,ENST00000443896,; T ENST00000264380 Transcript missense_variant 857/9901 699/6297 233/2098 L/F ttG/ttT rs777357869 1 1 PIKFYVE HGNC HGNC:23785 protein_coding YES CCDS2382.1 ENSP00000264380 Q9Y2I7 UPI0000366FD6 NM_015040.3 deleterious(0.01) 6/42 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF57 MODERATE 1 SNV 1 1 PASS rs777357869 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 208285811 208285811 G T 1 0 0 0 0 1 0 0 0 12019 1281 45 2 2 PIKFYVE 2 208285811 Missense_Mutation SNP G C3N-01489_T 122518 208285811 33907718 145 25075 CPS1 0 . GRCh38 2 210612229 210612229 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2522C>A p.Ser841Tyr p.S841Y ENST00000430249 21/39 384 349 35 518 518 0 strelka-varscan-mutect CPS1,missense_variant,p.Ser835Tyr,ENST00000233072,NM_001875.4;CPS1,missense_variant,p.Ser841Tyr,ENST00000430249,NM_001122633.2;CPS1,missense_variant,p.Ser384Tyr,ENST00000451903,NM_001122634.3; A ENST00000430249 Transcript missense_variant 2577/5698 2522/4521 841/1506 S/Y tCt/tAt 1 1 CPS1 HGNC HGNC:2323 protein_coding YES CCDS46505.1 ENSP00000402608 P31327 UPI000166C19F NM_001122633.2 deleterious(0.03) 21/39 hmmpanther:PTHR11405:SF38,hmmpanther:PTHR11405,TIGRFAM_domain:TIGR01369,Gene3D:1.10.1030.10,Superfamily_domains:0034967 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 210612229 210612229 C A 1 0 0 0 0 1 0 0 0 3619 913 32 2 2 CPS1 2 210612229 Missense_Mutation SNP C C3N-01489_T 2326418 210612229 31581300 146 25076 TNS1 0 . GRCh38 2 217836088 217836088 + Missense_Mutation SNP C C A rs777917136 C3N-01489_T C3N-01489_N C C c.2756G>T p.Arg919Leu p.R919L ENST00000171887 18/33 123 109 14 196 195 1 strelka-varscan-mutect TNS1,missense_variant,p.Arg919Leu,ENST00000171887,NM_022648.4;TNS1,missense_variant,p.Arg919Leu,ENST00000611415,;TNS1,missense_variant,p.Arg570Leu,ENST00000615025,;TNS1,missense_variant,p.Arg919Leu,ENST00000419504,;TNS1,missense_variant,p.Arg919Leu,ENST00000430930,NM_001308023.1;TNS1,missense_variant,p.Arg51Leu,ENST00000446688,; A ENST00000171887 Transcript missense_variant 3209/10331 2756/5208 919/1735 R/L cGc/cTc rs777917136,COSM4583169 1 -1 TNS1 HGNC HGNC:11973 protein_coding YES CCDS2407.1 ENSP00000171887 Q9HBL0 UPI0000456EEB NM_022648.4 tolerated(0.06) 18/33 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777917136 . 0 202 0 6 2 0 0 0 -7.303602 0.8496897 1 1 1 0 A 3 1 81 217836088 217836088 C A 1 0 0 0 0 1 0 0 0 16816 768 27 1 1 TNS1 2 217836088 Missense_Mutation SNP C C3N-01489_T 7223859 217836088 24357441 147 25077 CFAP65 0 . GRCh38 2 219010022 219010022 + Missense_Mutation SNP G G T rs760792718 C3N-01489_T C3N-01489_N G G c.4372C>A p.Arg1458Ser p.R1458S ENST00000341552 27/35 82 73 9 143 143 0 strelka-varscan-mutect CFAP65,missense_variant,p.Arg1458Ser,ENST00000341552,NM_194302.3;CFAP65,missense_variant,p.Arg1458Ser,ENST00000453220,;AC097468.4,non_coding_transcript_exon_variant,,ENST00000441450,; T ENST00000341552 Transcript missense_variant 4456/5953 4372/5778 1458/1925 R/S Cgc/Agc rs760792718 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 deleterious(0) 27/35 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF223 MODERATE SNV 5 1 PASS rs760792718 . 0 206 4 0 0 0 0 0 -19.27283 1 1 1 1 0 T 3 4 81 219010022 219010022 G T 1 0 0 0 0 1 0 0 0 3029 1116 39 1 1 CFAP65 2 219010022 Missense_Mutation SNP G C3N-01489_T 1173934 219010022 23183507 148 25078 KCNE4 0 . GRCh38 2 223052867 223052867 + Missense_Mutation SNP G G T rs777074947 C3N-01489_T C3N-01489_N G G c.190G>T p.Gly64Cys p.G64C ENST00000281830 2/2 250 229 21 365 364 1 strelka-varscan-mutect KCNE4,missense_variant,p.Gly64Cys,ENST00000281830,NM_080671.3;KCNE4,intron_variant,,ENST00000488477,; T ENST00000281830 Transcript missense_variant 521/3291 190/666 64/221 G/C Ggc/Tgc rs777074947 1 1 KCNE4 HGNC HGNC:6244 protein_coding YES CCDS2456.2 ENSP00000281830 Q8WWG9 UPI00002096C1 NM_080671.3 tolerated(0.12) 2/2 hmmpanther:PTHR15282,hmmpanther:PTHR15282:SF9 MODERATE 1 SNV 1 1 PASS rs777074947 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 223052867 223052867 G T 1 0 0 0 0 1 0 0 0 7941 1116 39 1 1 KCNE4 2 223052867 Missense_Mutation SNP G C3N-01489_T 4042845 223052867 19140662 149 25079 DOCK10 0 . GRCh38 2 224775056 224775056 + Silent SNP C C A rs367785024 C3N-01489_T C3N-01489_N C C c.5862G>T p.= p.P1954P ENST00000258390 52/56 309 277 32 462 462 0 strelka-varscan-mutect DOCK10,synonymous_variant,p.=,ENST00000409592,NM_001290263.1;DOCK10,synonymous_variant,p.=,ENST00000258390,NM_014689.2;DOCK10,synonymous_variant,p.=,ENST00000535663,; A ENST00000258390 Transcript synonymous_variant 5930/7260 5862/6561 1954/2186 P ccG/ccT rs367785024 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 52/56 Pfam_domain:PF06920,PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 LOW 1 SNV 5 1 PASS rs367785024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 224775056 224775056 C A 1 0 0 0 0 0 0 0 1 4500 523 19 1 1 DOCK10 2 224775056 Silent SNP C C3N-01489_T 1722189 224775056 17418473 150 25080 DOCK10 0 . GRCh38 2 224796991 224796991 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.4800G>T p.Gln1600His p.Q1600H ENST00000258390 43/56 64 60 4 111 111 0 varscan-mutect DOCK10,missense_variant,p.Gln1594His,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Gln1600His,ENST00000258390,NM_014689.2;DOCK10,downstream_gene_variant,,ENST00000422684,;DOCK10,upstream_gene_variant,,ENST00000492251,; A ENST00000258390 Transcript missense_variant 4868/7260 4800/6561 1600/2186 Q/H caG/caT 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 deleterious(0.03) 43/56 Pfam_domain:PF06920,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -9.727984 1 1 1 1 0 A 3 1 81 224796991 224796991 C A 1 0 0 0 0 1 0 0 0 4500 912 32 2 2 DOCK10 2 224796991 Missense_Mutation SNP C C3N-01489_T 21935 224796991 17396538 151 25081 NYAP2 0 . GRCh38 2 225651482 225651482 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1879C>A p.Pro627Thr p.P627T ENST00000636099 7/7 272 250 22 405 405 0 strelka-varscan-mutect NYAP2,missense_variant,p.Pro627Thr,ENST00000636099,;NYAP2,missense_variant,p.Pro627Thr,ENST00000272907,NM_020864.1; A ENST00000636099 Transcript missense_variant 2925/5461 1879/1962 627/653 P/T Cct/Act 1 1 NYAP2 HGNC HGNC:29291 protein_coding YES CCDS46529.1 ENSP00000490942 UPI00001C1DB6 deleterious_low_confidence(0) 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF1,Pfam_domain:PF15452 MODERATE 1 SNV 1 PASS rs1216355535 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 225651482 225651482 C A 1 0 0 0 0 1 0 0 0 10873 739 26 2 2 NYAP2 2 225651482 Missense_Mutation SNP C C3N-01489_T 854491 225651482 16542047 152 25082 SP140 0 . GRCh38 2 230248006 230248006 + Missense_Mutation SNP C C A rs756153976 C3N-01489_T C3N-01489_N C C c.833C>A p.Pro278His p.P278H ENST00000392045 8/27 183 172 11 292 292 0 strelka-varscan-mutect SP140,missense_variant,p.Pro278His,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Pro278His,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Pro252His,ENST00000343805,NM_001278452.1;SP140,intron_variant,,ENST00000417495,NM_001278453.1; A ENST00000392045 Transcript missense_variant 947/3246 833/2604 278/867 P/H cCc/cAc rs756153976 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 tolerated(0.32) 8/27 MODERATE 1 SNV 2 1 PASS rs756153976 . 0 207 0 0 2 0 0 0 -4.016963 0.9820705 1 1 1 0 A 3 1 81 230248006 230248006 C A 1 0 0 0 0 1 0 0 0 15288 623 22 2 2 SP140 2 230248006 Missense_Mutation SNP C C3N-01489_T 4596524 230248006 11945523 153 25083 SP140 0 . GRCh38 2 230310807 230310807 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.2239G>A p.Glu747Lys p.E747K ENST00000392045 24/27 43 37 6 82 82 0 varscan-mutect SP140,missense_variant,p.Glu747Lys,ENST00000392045,NM_007237.4;SP140,missense_variant,p.Glu720Lys,ENST00000420434,NM_001278451.1;SP140,missense_variant,p.Glu687Lys,ENST00000343805,NM_001278452.1;SP140,missense_variant,p.Glu633Lys,ENST00000417495,NM_001278453.1;SP140,non_coding_transcript_exon_variant,,ENST00000479539,;SP140,downstream_gene_variant,,ENST00000486750,; A ENST00000392045 Transcript missense_variant 2353/3246 2239/2604 747/867 E/K Gaa/Aaa 1 1 SP140 HGNC HGNC:17133 protein_coding YES CCDS42831.1 ENSP00000375899 Q13342 UPI0000209746 NM_007237.4 deleterious(0) 24/27 hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF45 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -15.27572 1 1 1 1 0 A 3 1 81 230310807 230310807 G A 1 0 0 0 0 1 0 0 0 15288 1175 41 3 3 SP140 2 230310807 Missense_Mutation SNP G C3N-01489_T 62801 230310807 11882722 154 25084 NEU4 0 . GRCh38 2 241816361 241816361 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.807G>T p.Glu269Asp p.E269D ENST00000325935 4/4 188 177 11 266 266 0 strelka-varscan-mutect NEU4,missense_variant,p.Glu256Asp,ENST00000391969,NM_001167602.2;NEU4,missense_variant,p.Glu268Asp,ENST00000404257,NM_080741.3;NEU4,missense_variant,p.Glu269Asp,ENST00000325935,NM_001167599.2;NEU4,missense_variant,p.Glu256Asp,ENST00000407683,NM_001167601.2,NM_001167600.2;NEU4,missense_variant,p.Glu256Asp,ENST00000405370,;NEU4,missense_variant,p.Arg171Met,ENST00000415936,;NEU4,missense_variant,p.Glu256Asp,ENST00000420288,;NEU4,missense_variant,p.Arg183Met,ENST00000426032,;NEU4,downstream_gene_variant,,ENST00000423583,;NEU4,downstream_gene_variant,,ENST00000428592,;NEU4,downstream_gene_variant,,ENST00000435894,;NEU4,downstream_gene_variant,,ENST00000435934,;AC114730.3,upstream_gene_variant,,ENST00000420272,;NEU4,non_coding_transcript_exon_variant,,ENST00000618597,;NEU4,intron_variant,,ENST00000435855,;NEU4,downstream_gene_variant,,ENST00000488997,;NEU4,downstream_gene_variant,,ENST00000476542,;NEU4,downstream_gene_variant,,ENST00000494678,; T ENST00000325935 Transcript missense_variant 1236/2288 807/1494 269/497 E/D gaG/gaT 1 1 NEU4 HGNC HGNC:21328 protein_coding YES CCDS54441.1 ENSP00000320318 Q8WWR8 UPI0000EE378E NM_001167599.2 tolerated(1) 4/4 Gene3D:2.120.10.10,Pfam_domain:PF13088,hmmpanther:PTHR10628,hmmpanther:PTHR10628:SF22,Superfamily_domains:SSF50939 MODERATE 1 SNV 1 1 PASS rs1352716991 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 241816361 241816361 G T 1 0 0 0 0 1 0 0 0 10379 991 35 2 2 NEU4 2 241816361 Missense_Mutation SNP G C3N-01489_T 11505554 241816361 377168 155 25085 CHL1 0 . GRCh38 3 340840 340840 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.432G>T p.Glu144Asp p.E144D ENST00000256509 6/28 212 196 16 340 340 0 strelka-varscan-mutect CHL1,missense_variant,p.Glu144Asp,ENST00000256509,NM_006614.3;CHL1,missense_variant,p.Glu144Asp,ENST00000620033,NM_001253388.1;CHL1,missense_variant,p.Glu144Asp,ENST00000397491,NM_001253387.1;CHL1,missense_variant,p.Glu144Asp,ENST00000435603,;CHL1,3_prime_UTR_variant,,ENST00000453040,; T ENST00000256509 Transcript missense_variant 1074/8023 432/3675 144/1224 E/D gaG/gaT 1 1 CHL1 HGNC HGNC:1939 protein_coding YES CCDS2556.1 ENSP00000256509 O00533 UPI000013CF0F NM_006614.3 tolerated(0.16) 6/28 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF653,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 340840 340840 G T 1 0 0 0 0 1 0 0 0 3108 991 35 2 2 CHL1 3 340840 Missense_Mutation SNP G C3N-01489_T 340840 197954719 156 25086 ITPR1 0 . GRCh38 3 4673280 4673280 + Nonsense_Mutation SNP C C A rs770093543 C3N-01489_T C3N-01489_N C C c.2304C>A p.Cys768Ter p.C768* ENST00000302640 20/61 184 170 14 242 242 0 strelka-varscan-mutect ITPR1,stop_gained,p.Cys783Ter,ENST00000354582,;ITPR1,stop_gained,p.Cys768Ter,ENST00000302640,NM_001168272.1;ITPR1,stop_gained,p.Cys783Ter,ENST00000357086,NM_001099952.2;ITPR1,stop_gained,p.Cys768Ter,ENST00000456211,NM_002222.5;ITPR1,stop_gained,p.Cys768Ter,ENST00000443694,;ITPR1,intron_variant,,ENST00000544951,;ITPR1,downstream_gene_variant,,ENST00000477577,; A ENST00000302640 Transcript stop_gained 2654/10197 2304/8232 768/2743 C/* tgC/tgA rs770093543 1 1 ITPR1 HGNC HGNC:6180 protein_coding YES CCDS54551.1 ENSP00000306253 Q14643 UPI0000E5A461 NM_001168272.1 20/61 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF52,Prints_domain:PR00779 HIGH 1 SNV 5 1 PASS rs770093543 . 0 205 0 5 0 0 0 0 -18.0316 0.9983156 1 1 1 0 A 4 1 81 4673280 4673280 C A 1 0 0 0 0 0 1 0 0 7826 747 26 2 2 ITPR1 3 4673280 Nonsense_Mutation SNP C C3N-01489_T 4332440 4673280 193622279 157 25087 SLC6A1 0 . GRCh38 3 11029284 11029284 + Missense_Mutation SNP C C G C3N-01489_T C3N-01489_N C C c.1255C>G p.Arg419Gly p.R419G ENST00000287766 12/16 181 169 12 304 304 0 strelka-varscan-mutect SLC6A1,missense_variant,p.Arg419Gly,ENST00000287766,NM_003042.3;SLC6A1,upstream_gene_variant,,ENST00000495636,; G ENST00000287766 Transcript missense_variant 1676/4502 1255/1800 419/599 R/G Cgc/Ggc COSM4112136 1 1 SLC6A1 HGNC HGNC:11042 protein_coding YES CCDS2603.1 ENSP00000287766 P30531 A0A024R2G0 UPI000013DECF NM_003042.3 deleterious(0.02) 12/16 PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF138,Pfam_domain:PF00209,Superfamily_domains:0053687 1 MODERATE 1 SNV 1 1 1 PASS rs910130675 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 11029284 11029284 C G 1 0 0 0 0 1 0 0 0 14956 652 23 4 4 SLC6A1 3 11029284 Missense_Mutation SNP C C3N-01489_T 6356004 11029284 187266275 158 25088 XPC 0 . GRCh38 3 14148890 14148890 + Missense_Mutation SNP C C A rs567932695 C3N-01489_T C3N-01489_N C C c.2174G>T p.Arg725Leu p.R725L ENST00000285021 12/16 193 169 24 274 274 0 strelka-varscan-mutect XPC,missense_variant,p.Arg725Leu,ENST00000285021,NM_004628.4;AC093495.4,intron_variant,,ENST00000628785,;AC093495.4,intron_variant,,ENST00000630173,;AC093495.4,intron_variant,,ENST00000629301,;AC093495.4,intron_variant,,ENST00000626655,;AC093495.4,intron_variant,,ENST00000630772,;AC093495.4,intron_variant,,ENST00000629796,;AC093495.4,intron_variant,,ENST00000628760,;AC093495.4,intron_variant,,ENST00000627116,;AC093495.4,intron_variant,,ENST00000627997,;AC093495.4,intron_variant,,ENST00000628978,;AC093495.4,downstream_gene_variant,,ENST00000420253,;AC093495.4,upstream_gene_variant,,ENST00000628791,;AC093495.4,downstream_gene_variant,,ENST00000428681,;AC093495.4,downstream_gene_variant,,ENST00000628412,;AC093495.4,downstream_gene_variant,,ENST00000629708,;AC093495.4,downstream_gene_variant,,ENST00000628446,;AC093495.4,upstream_gene_variant,,ENST00000627385,;RP11-434D12.1,downstream_gene_variant,,ENST00000626721,;RP11-434D12.1,downstream_gene_variant,,ENST00000601399,;XPC,3_prime_UTR_variant,,ENST00000476581,;XPC,non_coding_transcript_exon_variant,,ENST00000427795,;RP11-434D12.1,downstream_gene_variant,,ENST00000608606,; A ENST00000285021 Transcript missense_variant 2389/3832 2174/2823 725/940 R/L cGg/cTg rs567932695 1 -1 XPC HGNC HGNC:12816 protein_coding YES CCDS46763.1 ENSP00000285021 Q01831 X5DRB1 UPI000196375E NM_004628.4 deleterious(0.01) 12/16 hmmpanther:PTHR12135:SF0,hmmpanther:PTHR12135,Pfam_domain:PF10404,TIGRFAM_domain:TIGR00605,SMART_domains:SM01031 MODERATE 1 SNV 1 1 PASS rs567932695 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 14148890 14148890 C A 1 0 0 0 0 1 0 0 0 18000 652 23 1 1 XPC 3 14148890 Missense_Mutation SNP C C3N-01489_T 3119606 14148890 184146669 159 25089 SATB1 0 . GRCh38 3 18394702 18394702 + Silent SNP C C G novel C3N-01489_T C3N-01489_N C C c.966G>C p.= p.V322V ENST00000417717 7/12 204 192 12 312 312 0 strelka-varscan-mutect SATB1,synonymous_variant,p.=,ENST00000338745,NM_002971.4;SATB1,synonymous_variant,p.=,ENST00000417717,NM_001195470.1;SATB1,synonymous_variant,p.=,ENST00000454909,NM_001131010.2;SATB1,downstream_gene_variant,,ENST00000440737,;SATB1,downstream_gene_variant,,ENST00000475083,;TBC1D5,intron_variant,,ENST00000414318,; G ENST00000417717 Transcript synonymous_variant 1937/4589 966/2388 322/795 V gtG/gtC 1 -1 SATB1 HGNC HGNC:10541 protein_coding YES CCDS56242.1 ENSP00000399518 Q01826 UPI0000E1FB67 NM_001195470.1 7/12 hmmpanther:PTHR15116,hmmpanther:PTHR15116:SF14 LOW 1 SNV 1 1 PASS rs764675060 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 18394702 18394702 C G 1 0 0 0 0 0 0 0 1 14114 813 29 4 4 SATB1 3 18394702 Silent SNP C C3N-01489_T 4245812 18394702 179900857 160 25090 PP2D1 0 . GRCh38 3 20001957 20001957 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.163G>T p.Glu55Ter p.E55* ENST00000389050 2/3 289 271 18 405 405 0 strelka-varscan-mutect PP2D1,stop_gained,p.Glu55Ter,ENST00000389050,NM_001252657.1;PP2D1,stop_gained,p.Glu55Ter,ENST00000333083,;PP2D1,non_coding_transcript_exon_variant,,ENST00000461033,; A ENST00000389050 Transcript stop_gained 421/2151 163/1893 55/630 E/* Gag/Tag 1 -1 PP2D1 HGNC HGNC:28406 protein_coding YES CCDS58817.1 ENSP00000373702 A8MPX8 UPI000164284E NM_001252657.1 2/3 hmmpanther:PTHR13832:SF245,hmmpanther:PTHR13832 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 20001957 20001957 C A 1 0 0 0 0 0 1 0 0 12402 864 30 2 2 PP2D1 3 20001957 Nonsense_Mutation SNP C C3N-01489_T 1607255 20001957 178293602 161 25091 SLC4A7 0 . GRCh38 3 27394580 27394580 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.3028G>T p.Val1010Phe p.V1010F ENST00000295736 20/25 238 218 20 370 369 1 strelka-varscan-mutect SLC4A7,missense_variant,p.Val995Phe,ENST00000425128,NM_001321105.1,NM_001321106.1;SLC4A7,missense_variant,p.Val1010Phe,ENST00000295736,NM_003615.4;SLC4A7,missense_variant,p.Val886Phe,ENST00000428386,NM_001321107.1,NM_001258380.1;SLC4A7,missense_variant,p.Val561Phe,ENST00000419036,;SLC4A7,missense_variant,p.Val1019Phe,ENST00000454389,;SLC4A7,missense_variant,p.Val1006Phe,ENST00000440156,;SLC4A7,missense_variant,p.Val1006Phe,ENST00000445684,;SLC4A7,missense_variant,p.Val1002Phe,ENST00000446700,;SLC4A7,missense_variant,p.Val891Phe,ENST00000455077,NM_001258379.1;SLC4A7,missense_variant,p.Val891Phe,ENST00000437179,;SLC4A7,missense_variant,p.Val906Phe,ENST00000428179,;SLC4A7,3_prime_UTR_variant,,ENST00000438530,;SLC4A7,3_prime_UTR_variant,,ENST00000457377,;SLC4A7,3_prime_UTR_variant,,ENST00000437266,;SLC4A7,downstream_gene_variant,,ENST00000475120,;SLC4A7,upstream_gene_variant,,ENST00000465487,; A ENST00000295736 Transcript missense_variant 3099/7757 3028/3645 1010/1214 V/F Gtt/Ttt 1 -1 SLC4A7 HGNC HGNC:11033 protein_coding YES CCDS33721.1 ENSP00000295736 Q9Y6M7 UPI0000DBEEB7 NM_003615.4 tolerated(0.06) 20/25 Pfam_domain:PF00955,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF36,TIGRFAM_domain:TIGR00834,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 27394580 27394580 C A 1 0 0 0 0 1 0 0 0 14935 507 18 2 2 SLC4A7 3 27394580 Missense_Mutation SNP C C3N-01489_T 7392623 27394580 170900979 162 25092 SLC4A7 0 . GRCh38 3 27420763 27420763 + Silent SNP T T A novel C3N-01489_T C3N-01489_N T T c.1422A>T p.= p.P474P ENST00000295736 10/25 159 141 18 253 253 0 strelka-varscan-mutect SLC4A7,synonymous_variant,p.=,ENST00000425128,NM_001321105.1,NM_001321106.1;SLC4A7,synonymous_variant,p.=,ENST00000295736,NM_003615.4;SLC4A7,synonymous_variant,p.=,ENST00000428386,NM_001321107.1,NM_001258380.1;SLC4A7,synonymous_variant,p.=,ENST00000419036,;SLC4A7,synonymous_variant,p.=,ENST00000454389,;SLC4A7,synonymous_variant,p.=,ENST00000440156,;SLC4A7,synonymous_variant,p.=,ENST00000445684,;SLC4A7,synonymous_variant,p.=,ENST00000446700,;SLC4A7,synonymous_variant,p.=,ENST00000455077,NM_001258379.1;SLC4A7,synonymous_variant,p.=,ENST00000437179,;SLC4A7,synonymous_variant,p.=,ENST00000428179,;SLC4A7,synonymous_variant,p.=,ENST00000438530,;SLC4A7,synonymous_variant,p.=,ENST00000457377,;SLC4A7,synonymous_variant,p.=,ENST00000437266,;SLC4A7,downstream_gene_variant,,ENST00000428005,;SLC4A7,downstream_gene_variant,,ENST00000491211,; A ENST00000295736 Transcript synonymous_variant 1493/7757 1422/3645 474/1214 P ccA/ccT 1 -1 SLC4A7 HGNC HGNC:11033 protein_coding YES CCDS33721.1 ENSP00000295736 Q9Y6M7 UPI0000DBEEB7 NM_003615.4 10/25 Gene3D:1hynR00,Pfam_domain:PF07565,Prints_domain:PR01231,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF36,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 27420763 27420763 T A 1 0 0 0 0 0 0 0 1 14935 1567 55 4 4 SLC4A7 3 27420763 Silent SNP T C3N-01489_T 26183 27420763 170874796 163 25093 GADL1 0 . GRCh38 3 30728328 30728328 + Missense_Mutation SNP G G T rs750604147 C3N-01489_T C3N-01489_N G G c.1480C>A p.Arg494Ser p.R494S ENST00000282538 15/15 224 209 15 312 312 0 strelka-varscan-mutect GADL1,missense_variant,p.Arg494Ser,ENST00000282538,NM_207359.2;GADL1,non_coding_transcript_exon_variant,,ENST00000498387,; T ENST00000282538 Transcript missense_variant 1631/3759 1480/1566 494/521 R/S Cgc/Agc rs750604147,COSM325380 1 -1 GADL1 HGNC HGNC:27949 protein_coding YES CCDS2649.2 ENSP00000282538 Q6ZQY3 UPI000022BF90 NM_207359.2 deleterious(0) 15/15 hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF95,Gene3D:3.90.1150.10,Superfamily_domains:SSF53383 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs750604147 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 30728328 30728328 G T 1 0 0 0 0 1 0 0 0 6056 1116 39 1 1 GADL1 3 30728328 Missense_Mutation SNP G C3N-01489_T 3307565 30728328 167567231 164 25094 SCN5A 0 . GRCh38 3 38603901 38603901 + Silent SNP C C G novel C3N-01489_T C3N-01489_N C C c.1701G>C p.= p.L567L ENST00000413689 12/28 201 186 15 296 296 0 strelka-varscan-mutect SCN5A,synonymous_variant,p.=,ENST00000413689,NM_001099404.1;SCN5A,synonymous_variant,p.=,ENST00000333535,NM_198056.2;SCN5A,synonymous_variant,p.=,ENST00000425664,NM_001099405.1;SCN5A,synonymous_variant,p.=,ENST00000423572,NM_000335.4;SCN5A,synonymous_variant,p.=,ENST00000451551,NM_001160161.1;SCN5A,synonymous_variant,p.=,ENST00000414099,;SCN5A,synonymous_variant,p.=,ENST00000455624,NM_001160160.1;SCN5A,synonymous_variant,p.=,ENST00000450102,;SCN5A,synonymous_variant,p.=,ENST00000449557,; G ENST00000413689 Transcript synonymous_variant 1895/8504 1701/6051 567/2016 L ctG/ctC 1 -1 SCN5A HGNC HGNC:10593 protein_coding YES CCDS46799.1 ENSP00000410257 H9KVD2 UPI0001572CC8 NM_001099404.1 12/28 Pfam_domain:PF11933,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF206 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 38603901 38603901 C G 1 0 0 0 0 0 0 0 1 14191 697 25 4 4 SCN5A 3 38603901 Silent SNP C C3N-01489_T 7875573 38603901 159691658 165 25095 SNRK 0 . GRCh38 3 43347454 43347454 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1195C>A p.Leu399Ile p.L399I ENST00000296088 7/7 127 111 16 146 146 0 strelka-varscan-mutect SNRK,missense_variant,p.Leu399Ile,ENST00000296088,NM_017719.4;SNRK,missense_variant,p.Leu399Ile,ENST00000429705,NM_001100594.1;SNRK,missense_variant,p.Leu399Ile,ENST00000454177,;SNRK,missense_variant,p.Leu193Ile,ENST00000437827,;RP11-188P20.3,non_coding_transcript_exon_variant,,ENST00000607513,;SNRK-AS1,downstream_gene_variant,,ENST00000422681,;SNRK,intron_variant,,ENST00000468628,;SNRK,non_coding_transcript_exon_variant,,ENST00000481892,; A ENST00000296088 Transcript missense_variant 1499/5183 1195/2298 399/765 L/I Ctc/Atc 1 1 SNRK HGNC HGNC:30598 protein_coding YES CCDS43075.1 ENSP00000296088 Q9NRH2 A0A024R2Y6 UPI00000558E4 NM_017719.4 tolerated(0.07) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 43347454 43347454 C A 1 0 0 0 0 1 0 0 0 15171 681 24 2 2 SNRK 3 43347454 Missense_Mutation SNP C C3N-01489_T 4743553 43347454 154948105 166 25096 TOPAZ1 0 . GRCh38 3 44244487 44244487 + Silent SNP C C A rs776686174 C3N-01489_T C3N-01489_N C C c.1981C>A p.= p.R661R ENST00000309765 2/20 173 164 9 331 331 0 strelka-varscan-mutect TOPAZ1,synonymous_variant,p.=,ENST00000309765,NM_001145030.1; A ENST00000309765 Transcript synonymous_variant 2149/5334 1981/5079 661/1692 R Cga/Aga rs776686174 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 2/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1 LOW 1 SNV 5 1 PASS rs776686174 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 44244487 44244487 C A 1 0 0 0 0 0 0 0 1 16845 876 31 1 1 TOPAZ1 3 44244487 Silent SNP C C3N-01489_T 897033 44244487 154051072 167 25097 TOPAZ1 0 . GRCh38 3 44267067 44267067 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.3091T>A p.Cys1031Ser p.C1031S ENST00000309765 6/20 186 175 11 287 287 0 strelka-varscan-mutect TOPAZ1,missense_variant,p.Cys1031Ser,ENST00000309765,NM_001145030.1; A ENST00000309765 Transcript missense_variant 3259/5334 3091/5079 1031/1692 C/S Tgt/Agt 1 1 TOPAZ1 HGNC HGNC:24746 protein_coding YES CCDS46809.1 ENSP00000310303 Q8N9V7 UPI000047FF75 NM_001145030.1 tolerated(0.32) 6/20 hmmpanther:PTHR35671,hmmpanther:PTHR35671:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 44267067 44267067 T A 1 0 0 0 0 1 0 0 0 16845 1696 59 4 4 TOPAZ1 3 44267067 Missense_Mutation SNP T C3N-01489_T 22580 44267067 154028492 168 25098 ZNF197 0 . GRCh38 3 44642298 44642298 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.1168A>G p.Arg390Gly p.R390G ENST00000396058 5/5 140 129 11 271 271 0 strelka-varscan-mutect ZNF197,missense_variant,p.Arg390Gly,ENST00000396058,;ZNF197,missense_variant,p.Arg390Gly,ENST00000344387,NM_006991.3;ZNF197,intron_variant,,ENST00000383745,NM_001024855.1;ZNF197,intron_variant,,ENST00000383744,;RP11-944L7.4,intron_variant,,ENST00000457331,;ZNF197,intron_variant,,ENST00000334075,; G ENST00000396058 Transcript missense_variant 1335/4299 1168/3090 390/1029 R/G Aga/Gga 1 1 ZNF197 HGNC HGNC:12988 protein_coding YES CCDS2717.1 ENSP00000379370 O14709 UPI000013C317 deleterious(0.01) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF280,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1352212940 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 44642298 44642298 A G 1 0 0 0 0 1 0 0 0 18336 296 11 5 5 ZNF197 3 44642298 Missense_Mutation SNP A C3N-01489_T 375231 44642298 153653261 169 25099 SETD2 0 . GRCh38 3 47120357 47120357 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.4279G>T p.Val1427Phe p.V1427F ENST00000409792 3/21 60 49 11 87 87 0 strelka-varscan-mutect SETD2,missense_variant,p.Val1427Phe,ENST00000409792,NM_014159.6;SETD2,downstream_gene_variant,,ENST00000412450,;SETD2,missense_variant,p.Val1299Phe,ENST00000330022,;SETD2,missense_variant,p.Val1145Phe,ENST00000431180,;SETD2,missense_variant,p.Val1061Phe,ENST00000445387,; A ENST00000409792 Transcript missense_variant 4322/8142 4279/7695 1427/2564 V/F Gtt/Ttt 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 deleterious(0.04) 3/21 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF344 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 47120357 47120357 C A 1 0 0 0 0 1 0 0 0 14409 565 20 2 2 SETD2 3 47120357 Missense_Mutation SNP C C3N-01489_T 2478059 47120357 151175202 170 25100 RBM6 0 . GRCh38 3 49968083 49968083 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.658G>T p.Val220Leu p.V220L ENST00000266022 3/21 177 168 9 315 315 0 strelka-varscan RBM6,missense_variant,p.Val88Leu,ENST00000443081,;RBM6,missense_variant,p.Val220Leu,ENST00000266022,NM_005777.2;RBM6,intron_variant,,ENST00000422955,;RBM6,intron_variant,,ENST00000442092,NM_001167582.1;RBM6,downstream_gene_variant,,ENST00000433811,;RBM6,intron_variant,,ENST00000441115,;RBM6,downstream_gene_variant,,ENST00000488807,;RBM6,downstream_gene_variant,,ENST00000491874,;RBM6,missense_variant,p.Val88Leu,ENST00000454079,;RBM6,missense_variant,p.Val220Leu,ENST00000425608,;RBM6,intron_variant,,ENST00000434592,;RBM6,intron_variant,,ENST00000419610,; T ENST00000266022 Transcript missense_variant 917/3750 658/3372 220/1123 V/L Gta/Tta 1 1 RBM6 HGNC HGNC:9903 protein_coding YES CCDS2809.1 ENSP00000266022 P78332 UPI000013D6C0 NM_005777.2 tolerated(0.15) 3/21 hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF22,Superfamily_domains:SSF141571 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 49968083 49968083 G T 1 0 0 0 0 1 0 0 0 13311 1377 48 2 2 RBM6 3 49968083 Missense_Mutation SNP G C3N-01489_T 2847726 49968083 148327476 171 25101 DOCK3 0 . GRCh38 3 51277688 51277688 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2757G>T p.Met919Ile p.M919I ENST00000266037 26/53 107 94 13 137 137 0 strelka-varscan-mutect DOCK3,missense_variant,p.Met919Ile,ENST00000266037,NM_004947.4; T ENST00000266037 Transcript missense_variant 2780/8755 2757/6093 919/2030 M/I atG/atT 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 tolerated(0.57) 26/53 hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 51277688 51277688 G T 1 0 0 0 0 1 0 0 0 4503 1290 45 2 2 DOCK3 3 51277688 Missense_Mutation SNP G C3N-01489_T 1309605 51277688 147017871 172 25102 RAD54L2 0 . GRCh38 3 51630896 51630896 + Missense_Mutation SNP G G T rs781070262 C3N-01489_T C3N-01489_N G G c.790G>T p.Ala264Ser p.A264S ENST00000409535 6/22 154 146 8 219 219 0 strelka-varscan-mutect RAD54L2,missense_variant,p.Ala264Ser,ENST00000409535,NM_001322253.1,NM_001322256.1,NM_015106.2;RAD54L2,missense_variant,p.Ala93Ser,ENST00000432863,;RAD54L2,non_coding_transcript_exon_variant,,ENST00000461680,;RAD54L2,non_coding_transcript_exon_variant,,ENST00000487093,;RAD54L2,non_coding_transcript_exon_variant,,ENST00000462377,; T ENST00000409535 Transcript missense_variant 915/9776 790/4404 264/1467 A/S Gcc/Tcc rs781070262 1 1 RAD54L2 HGNC HGNC:29123 protein_coding YES CCDS33765.2 ENSP00000386520 Q9Y4B4 UPI000022C0AA NM_001322253.1,NM_001322256.1,NM_015106.2 tolerated(0.25) 6/22 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF350,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs781070262 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 51630896 51630896 G T 1 0 0 0 0 1 0 0 0 13155 1319 46 2 2 RAD54L2 3 51630896 Missense_Mutation SNP G C3N-01489_T 353208 51630896 146664663 173 25103 GRM2 0 . GRCh38 3 51713059 51713059 + Missense_Mutation SNP G G C rs200432452 C3N-01489_T C3N-01489_N G G c.1037G>C p.Arg346Pro p.R346P ENST00000395052 3/6 224 210 14 354 354 0 strelka-varscan-mutect GRM2,missense_variant,p.Arg346Pro,ENST00000395052,NM_000839.3;GRM2,missense_variant,p.Arg346Pro,ENST00000442933,;GRM2,downstream_gene_variant,,ENST00000419928,;GRM2,non_coding_transcript_exon_variant,,ENST00000496661,;GRM2,intron_variant,,ENST00000475478,;GRM2,downstream_gene_variant,,ENST00000477330,;GRM2,missense_variant,p.Arg346Pro,ENST00000296479,;GRM2,non_coding_transcript_exon_variant,,ENST00000464585,; C ENST00000395052 Transcript missense_variant 1271/3151 1037/2619 346/872 R/P cGt/cCt rs200432452,COSM1424297 1 1 GRM2 HGNC HGNC:4594 protein_coding YES CCDS2834.1 ENSP00000378492 Q14416 UPI000013E346 NM_000839.3 tolerated(0.16) 3/6 hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF111,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs200432452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 51713059 51713059 G C 1 0 0 0 0 1 0 0 0 6679 1145 40 4 4 GRM2 3 51713059 Missense_Mutation SNP G C3N-01489_T 82163 51713059 146582500 174 25104 IQCF5 0 . GRCh38 3 51874126 51874126 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.54C>A p.= p.I18I ENST00000446461 2/2 125 111 14 223 222 1 strelka-varscan-mutect IQCF5,synonymous_variant,p.=,ENST00000446461,NM_001145059.1;IQCF5-AS1,non_coding_transcript_exon_variant,,ENST00000440723,;RN7SL504P,downstream_gene_variant,,ENST00000494496,; T ENST00000446461 Transcript synonymous_variant 107/512 54/447 18/148 I atC/atA 1 -1 IQCF5 HGNC HGNC:35159 protein_coding YES CCDS46838.1 ENSP00000394653 A8MTL0 UPI00002377DA NM_001145059.1 2/2 Pfam_domain:PF00612,PROSITE_profiles:PS50096,hmmpanther:PTHR21633,hmmpanther:PTHR21633:SF11,SMART_domains:SM00015 LOW SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 51874126 51874126 G T 1 0 0 0 0 0 0 0 1 7714 1164 41 2 2 IQCF5 3 51874126 Silent SNP G C3N-01489_T 161067 51874126 146421433 175 25105 RFT1 0 . GRCh38 3 53103980 53103980 + Missense_Mutation SNP C C G rs201876415 C3N-01489_T C3N-01489_N C C c.1075G>C p.Gly359Arg p.G359R ENST00000296292 10/13 363 337 26 523 523 0 strelka-varscan-mutect RFT1,missense_variant,p.Gly359Arg,ENST00000296292,NM_052859.3;RFT1,missense_variant,p.Gly320Arg,ENST00000394738,;RFT1,downstream_gene_variant,,ENST00000467048,;RFT1,non_coding_transcript_exon_variant,,ENST00000471158,;RP11-894J14.5,upstream_gene_variant,,ENST00000607495,;RP11-894J14.5,upstream_gene_variant,,ENST00000607203,;RP11-894J14.5,upstream_gene_variant,,ENST00000607283,; G ENST00000296292 Transcript missense_variant 1137/5108 1075/1626 359/541 G/R Gga/Cga rs201876415 1 -1 RFT1 HGNC HGNC:30220 protein_coding YES CCDS2869.1 ENSP00000296292 Q96AA3 UPI000000DA67 NM_052859.3 deleterious(0) 10/13 Pfam_domain:PF04506,hmmpanther:PTHR13117 MODERATE 1 SNV 1 1 PASS rs201876415 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 53103980 53103980 C G 1 0 0 0 0 1 0 0 0 13431 661 23 4 4 RFT1 3 53103980 Missense_Mutation SNP C C3N-01489_T 1229854 53103980 145191579 176 25106 CACNA2D3 0 . GRCh38 3 54891408 54891408 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.2204C>A p.Ser735Tyr p.S735Y ENST00000474759 25/38 205 186 19 230 228 2 strelka-varscan-mutect CACNA2D3,missense_variant,p.Ser735Tyr,ENST00000474759,NM_018398.2;CACNA2D3,missense_variant,p.Ser735Tyr,ENST00000288197,;CACNA2D3,missense_variant,p.Ser735Tyr,ENST00000415676,;CACNA2D3,missense_variant,p.Ser641Tyr,ENST00000490478,;CACNA2D3,3_prime_UTR_variant,,ENST00000620722,;CACNA2D3-AS1,intron_variant,,ENST00000471265,;CACNA2D3,3_prime_UTR_variant,,ENST00000471363,;CACNA2D3,downstream_gene_variant,,ENST00000477024,; A ENST00000474759 Transcript missense_variant 2252/3675 2204/3276 735/1091 S/Y tCc/tAc COSM340674 1 1 CACNA2D3 HGNC HGNC:15460 protein_coding YES CCDS54598.1 ENSP00000419101 Q8IZS8 UPI000004A7BF NM_018398.2 deleterious(0.03) 25/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF25,Pfam_domain:PF08473 1 MODERATE 1 SNV 1 1 1 PASS rs1326937537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 54891408 54891408 C A 1 0 0 0 0 1 0 0 0 2238 855 30 2 2 CACNA2D3 3 54891408 Missense_Mutation SNP C C3N-01489_T 1787428 54891408 143404151 177 25107 ERC2 0 . GRCh38 3 55683851 55683851 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.2856G>A p.= p.E952E ENST00000288221 17/18 117 111 6 178 178 0 varscan-mutect ERC2,synonymous_variant,p.=,ENST00000288221,NM_015576.1;ERC2,synonymous_variant,p.=,ENST00000612797,;ERC2,non_coding_transcript_exon_variant,,ENST00000468118,;ERC2,intron_variant,,ENST00000487287,;ERC2,synonymous_variant,p.=,ENST00000460849,; T ENST00000288221 Transcript synonymous_variant 3112/6138 2856/2874 952/957 E gaG/gaA 1 -1 ERC2 HGNC HGNC:31922 protein_coding YES CCDS46851.1 ENSP00000288221 O15083 UPI00001C1572 NM_015576.1 17/18 hmmpanther:PTHR18861 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 55683851 55683851 C T 1 0 0 0 0 0 0 0 1 5060 680 24 3 3 ERC2 3 55683851 Silent SNP C C3N-01489_T 792443 55683851 142611708 178 25108 EPHA3 0 . GRCh38 3 89341072 89341072 + Splice_Site SNP G G A rs754818412 C3N-01489_T C3N-01489_N G G c.970+1G>A p.X324_splice ENST00000336596 88 77 11 139 139 0 strelka-varscan-mutect EPHA3,splice_donor_variant,,ENST00000336596,NM_005233.5;EPHA3,splice_donor_variant,,ENST00000494014,;EPHA3,splice_donor_variant,,ENST00000452448,NM_182644.2; A ENST00000336596 Transcript splice_donor_variant -/5809 970/2952 324/983 rs754818412,COSM387341,COSM387342,COSM584798,COSM584799 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 4/16 0,1,1,1,1 HIGH 1 SNV 1 0,1,1,1,1 1 PASS rs754818412 . 0 204 6 0 0 0 0 0 -19.99973 0.9999999 1 1 1 0 A 5 1 81 89341072 89341072 G A 1 0 0 0 0 0 0 1 0 5015 1159 40 1 1 EPHA3 3 89341072 Splice_Site SNP G C3N-01489_T 33657221 89341072 108954487 179 25109 CEP97 0 . GRCh38 3 101765220 101765220 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2267G>T p.Gly756Val p.G756V ENST00000341893 11/11 146 124 22 238 238 0 strelka-varscan-mutect CEP97,missense_variant,p.Gly756Val,ENST00000341893,NM_024548.3;CEP97,missense_variant,p.Gly697Val,ENST00000494050,NM_001303401.1;CEP97,downstream_gene_variant,,ENST00000467655,; T ENST00000341893 Transcript missense_variant 3019/8361 2267/2598 756/865 G/V gGt/gTt 1 1 CEP97 HGNC HGNC:26244 protein_coding YES CCDS2944.1 ENSP00000342510 Q8IW35 UPI0000074569 NM_024548.3 deleterious(0.01) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 101765220 101765220 G T 1 0 0 0 0 1 0 0 0 2989 1261 44 2 2 CEP97 3 101765220 Missense_Mutation SNP G C3N-01489_T 12424148 101765220 96530339 180 25110 CD200R1 0 . GRCh38 3 112929321 112929321 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.389G>T p.Trp130Leu p.W130L ENST00000308611 4/8 275 254 21 485 485 0 varscan-mutect CD200R1,missense_variant,p.Trp107Leu,ENST00000471858,NM_170780.2;CD200R1,missense_variant,p.Trp130Leu,ENST00000308611,NM_138806.3;CD200R1,missense_variant,p.Trp85Leu,ENST00000295863,;CD200R1,missense_variant,p.Trp130Leu,ENST00000440122,NM_138939.2;CD200R1,missense_variant,p.Trp107Leu,ENST00000490004,NM_138940.2; A ENST00000308611 Transcript missense_variant 654/2299 389/1047 130/348 W/L tGg/tTg 1 -1 CD200R1 HGNC HGNC:24235 protein_coding YES CCDS2969.1 ENSP00000311035 Q8TD46 UPI000013E2BD NM_138806.3 deleterious(0) 4/8 hmmpanther:PTHR21462,hmmpanther:PTHR21462:SF2,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 112929321 112929321 C A 1 0 0 0 0 1 0 0 0 2684 595 21 2 2 CD200R1 3 112929321 Missense_Mutation SNP C C3N-01489_T 11164101 112929321 85366238 181 25111 GAP43 0 . GRCh38 3 115676447 115676447 + Silent SNP G G A C3N-01489_T C3N-01489_N G G c.573G>A p.= p.K191K ENST00000393780 3/4 110 89 21 146 146 0 strelka-varscan-mutect GAP43,synonymous_variant,p.=,ENST00000393780,NM_001130064.1;GAP43,synonymous_variant,p.=,ENST00000305124,NM_002045.3; A ENST00000393780 Transcript synonymous_variant 1041/1901 573/825 191/274 K aaG/aaA COSM1207911,COSM1207912 1 1 GAP43 HGNC HGNC:4140 protein_coding YES CCDS46890.1 ENSP00000377372 P17677 UPI0000209FC5 NM_001130064.1 3/4 hmmpanther:PTHR10699:SF15,hmmpanther:PTHR10699,Pfam_domain:PF06614 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 115676447 115676447 G A 1 0 0 0 0 0 0 0 1 6103 991 35 3 3 GAP43 3 115676447 Silent SNP G C3N-01489_T 2747126 115676447 82619112 182 25112 LSAMP 0 . GRCh38 3 115810343 115810343 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.991C>A p.Leu331Met p.L331M ENST00000490035 7/7 223 197 26 289 288 1 strelka-varscan-mutect LSAMP,missense_variant,p.Leu331Met,ENST00000490035,NM_002338.3;LSAMP,missense_variant,p.Leu281Met,ENST00000539563,;LSAMP,missense_variant,p.Leu338Met,ENST00000333617,;LSAMP,non_coding_transcript_exon_variant,,ENST00000475403,; T ENST00000490035 Transcript missense_variant 1491/9446 991/1017 331/338 L/M Ctg/Atg 1 -1 LSAMP HGNC HGNC:6705 protein_coding YES CCDS2982.1 ENSP00000419000 Q13449 UPI00000746A0 NM_002338.3 deleterious(0.02) 7/7 hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF118,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 115810343 115810343 G T 1 0 0 0 0 1 0 0 0 8954 933 33 2 2 LSAMP 3 115810343 Missense_Mutation SNP G C3N-01489_T 133896 115810343 82485216 183 25113 STXBP5L 0 . GRCh38 3 121259074 121259074 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1864G>T p.Gly622Ter p.G622* ENST00000273666 18/28 154 128 26 169 169 0 strelka-varscan-mutect STXBP5L,stop_gained,p.Gly622Ter,ENST00000273666,NM_014980.2;STXBP5L,stop_gained,p.Gly622Ter,ENST00000471454,NM_001308330.1;STXBP5L,stop_gained,p.Gly622Ter,ENST00000471262,;STXBP5L,stop_gained,p.Gly622Ter,ENST00000492541,;STXBP5L,stop_gained,p.Gly622Ter,ENST00000472879,;STXBP5L,stop_gained,p.Gly622Ter,ENST00000497029,; T ENST00000273666 Transcript stop_gained 2135/9496 1864/3561 622/1186 G/* Gga/Tga 1 1 STXBP5L HGNC HGNC:30757 protein_coding YES CCDS43137.1 ENSP00000273666 Q9Y2K9 UPI00001C1DEA NM_014980.2 18/28 hmmpanther:PTHR10241:SF19,hmmpanther:PTHR10241 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 121259074 121259074 G T 1 0 0 0 0 0 1 0 0 15741 1001 35 2 2 STXBP5L 3 121259074 Nonsense_Mutation SNP G C3N-01489_T 5448731 121259074 77036485 184 25114 POLQ 0 . GRCh38 3 121529741 121529741 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1012C>T p.His338Tyr p.H338Y ENST00000264233 7/30 203 180 23 320 320 0 strelka-varscan-mutect POLQ,missense_variant,p.His471Tyr,ENST00000621776,;POLQ,missense_variant,p.His338Tyr,ENST00000264233,NM_199420.3;POLQ,non_coding_transcript_exon_variant,,ENST00000488282,; A ENST00000264233 Transcript missense_variant 1141/8775 1012/7773 338/2590 H/Y Cat/Tat 1 -1 POLQ HGNC HGNC:9186 protein_coding YES CCDS33833.1 ENSP00000264233 O75417 UPI0000D61B5F NM_199420.3 deleterious(0.03) 7/30 PROSITE_profiles:PS51194,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 121529741 121529741 G A 1 0 0 0 0 1 0 0 0 12318 1348 47 3 3 POLQ 3 121529741 Missense_Mutation SNP G C3N-01489_T 270667 121529741 76765818 185 25115 FBXO40 0 . GRCh38 3 121622257 121622257 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.828G>T p.Gln276His p.Q276H ENST00000338040 3/4 225 185 40 336 336 0 strelka-varscan-mutect FBXO40,missense_variant,p.Gln276His,ENST00000338040,NM_016298.3; T ENST00000338040 Transcript missense_variant 1242/5929 828/2130 276/709 Q/H caG/caT 1 1 FBXO40 HGNC HGNC:29816 protein_coding YES CCDS33835.1 ENSP00000337510 Q9UH90 UPI000020A046 NM_016298.3 tolerated(0.13) 3/4 hmmpanther:PTHR15933,hmmpanther:PTHR15933:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 121622257 121622257 G T 1 0 0 0 0 1 0 0 0 5612 991 35 2 2 FBXO40 3 121622257 Missense_Mutation SNP G C3N-01489_T 92516 121622257 76673302 186 25116 ADCY5 0 . GRCh38 3 123327704 123327704 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1861G>T p.Glu621Ter p.E621* ENST00000462833 7/21 204 192 12 315 315 0 strelka-varscan-mutect ADCY5,stop_gained,p.Glu621Ter,ENST00000462833,NM_183357.2;ADCY5,stop_gained,p.Glu254Ter,ENST00000491190,;ADCY5,stop_gained,p.Glu271Ter,ENST00000309879,NM_001199642.1;ADCY5,stop_gained,p.Glu180Ter,ENST00000466617,;ADCY5,downstream_gene_variant,,ENST00000483566,;ADCY5,downstream_gene_variant,,ENST00000476455,; A ENST00000462833 Transcript stop_gained 3074/7311 1861/3786 621/1261 E/* Gag/Tag 1 -1 ADCY5 HGNC HGNC:236 protein_coding YES CCDS3022.1 ENSP00000419361 O95622 UPI000015E262 NM_183357.2 7/21 Gene3D:3.30.70.1230,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF332,SMART_domains:SM00044,Superfamily_domains:SSF55073 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 123327704 123327704 C A 1 0 0 0 0 0 1 0 0 341 864 30 2 2 ADCY5 3 123327704 Nonsense_Mutation SNP C C3N-01489_T 1705447 123327704 74967855 187 25117 UROC1 0 . GRCh38 3 126508467 126508467 + Silent SNP C C T C3N-01489_T C3N-01489_N C C c.360G>A p.= p.Q120Q ENST00000383579 4/21 242 225 17 355 355 0 strelka-varscan-mutect UROC1,synonymous_variant,p.=,ENST00000290868,NM_144639.2;UROC1,synonymous_variant,p.=,ENST00000383579,NM_001165974.1; T ENST00000383579 Transcript synonymous_variant 394/2735 360/2211 120/736 Q caG/caA COSM3058812,COSM3058813 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 4/21 Gene3D:1x87B01,HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 126508467 126508467 C T 1 0 0 0 0 0 0 0 1 17560 680 24 3 3 UROC1 3 126508467 Silent SNP C C3N-01489_T 3180763 126508467 71787092 188 25118 COL6A5 0 . GRCh38 3 130415694 130415694 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.4811A>T p.Gln1604Leu p.Q1604L ENST00000265379 23/43 156 125 31 202 202 0 strelka-varscan-mutect COL6A5,missense_variant,p.Gln1604Leu,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Gln1604Leu,ENST00000312481,; T ENST00000265379 Transcript missense_variant 5305/9214 4811/7836 1604/2611 Q/L cAg/cTg 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 tolerated(0.69) 23/43 Low_complexity_(Seg):seg,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF01391 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 130415694 130415694 A T 1 0 0 0 0 1 0 0 0 3491 188 7 4 4 COL6A5 3 130415694 Missense_Mutation SNP A C3N-01489_T 3907227 130415694 67879865 189 25119 COL6A6 0 . GRCh38 3 130570891 130570891 + Nonsense_Mutation SNP T T A C3N-01489_T C3N-01489_N T T c.2475T>A p.Tyr825Ter p.Y825* ENST00000358511 6/36 152 140 12 219 219 0 strelka-mutect COL6A6,stop_gained,p.Tyr825Ter,ENST00000358511,NM_001102608.1; A ENST00000358511 Transcript stop_gained 2506/9581 2475/6792 825/2263 Y/* taT/taA COSM5344348,COSM5344349 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 6/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,SMART_domains:SM00327,Superfamily_domains:SSF53300 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 130570891 130570891 T A 1 0 0 0 0 0 1 0 0 3492 1413 49 4 4 COL6A6 3 130570891 Nonsense_Mutation SNP T C3N-01489_T 155197 130570891 67724668 190 25120 PRR23A 0 . GRCh38 3 139006053 139006053 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.216C>A p.= p.P72P ENST00000383163 1/1 108 91 17 171 171 0 strelka-varscan-mutect PRR23A,synonymous_variant,p.=,ENST00000383163,NM_001134659.1;MRPS22,5_prime_UTR_variant,,ENST00000495075,; T ENST00000383163 Transcript synonymous_variant 216/801 216/801 72/266 P ccC/ccA 1 -1 PRR23A HGNC HGNC:37172 protein_coding YES CCDS46923.1 ENSP00000372649 A6NEV1 UPI00003671C1 NM_001134659.1 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR31813:SF7,hmmpanther:PTHR31813,Pfam_domain:PF10630 LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 139006053 139006053 G T 1 0 0 0 0 0 0 0 1 12729 1219 43 2 2 PRR23A 3 139006053 Silent SNP G C3N-01489_T 8435162 139006053 59289506 191 25121 ANKUB1 0 . GRCh38 3 149767807 149767807 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.855G>T p.Lys285Asn p.K285N ENST00000446160 5/6 141 132 9 210 210 0 strelka-varscan-mutect ANKUB1,missense_variant,p.Lys285Asn,ENST00000446160,NM_001144960.1;ANKUB1,missense_variant,p.Lys285Asn,ENST00000462519,NM_001315506.1;ANKUB1,3_prime_UTR_variant,,ENST00000484019,NM_001315505.1; A ENST00000446160 Transcript missense_variant 1312/2471 855/1635 285/544 K/N aaG/aaT 1 -1 ANKUB1 HGNC HGNC:29642 protein_coding YES ENSP00000387907 E9PHT4 UPI0000DD7B6F NM_001144960.1 deleterious(0.04) 5/6 hmmpanther:PTHR10666,hmmpanther:PTHR10666:SF111,Pfam_domain:PF13637,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 149767807 149767807 C A 1 0 0 0 0 1 0 0 0 799 796 28 2 2 ANKUB1 3 149767807 Missense_Mutation SNP C C3N-01489_T 10761754 149767807 48527752 192 25122 IGSF10 0 . GRCh38 3 151447221 151447221 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.2760C>A p.= p.P920P ENST00000282466 4/6 259 217 42 426 426 0 strelka-varscan-mutect IGSF10,synonymous_variant,p.=,ENST00000282466,NM_178822.4;IGSF10,upstream_gene_variant,,ENST00000489791,; T ENST00000282466 Transcript synonymous_variant 2760/11067 2760/7872 920/2623 P ccC/ccA 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 4/6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 151447221 151447221 G T 1 0 0 0 0 0 0 0 1 7504 1219 43 2 2 IGSF10 3 151447221 Silent SNP G C3N-01489_T 1679414 151447221 46848338 193 25123 SHOX2 0 . GRCh38 3 158099877 158099877 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.757A>T p.Arg253Trp p.R253W ENST00000389589 5/6 162 146 16 211 210 1 strelka-varscan-mutect SHOX2,missense_variant,p.Arg229Trp,ENST00000441443,NM_006884.3;SHOX2,missense_variant,p.Arg253Trp,ENST00000389589,NM_003030.4;SHOX2,missense_variant,p.Arg229Trp,ENST00000483851,NM_001163678.1;SHOX2,missense_variant,p.Arg100Trp,ENST00000425436,;SHOX2,downstream_gene_variant,,ENST00000554685,;SHOX2,non_coding_transcript_exon_variant,,ENST00000490689,; A ENST00000389589 Transcript missense_variant 893/2072 757/1068 253/355 R/W Agg/Tgg 1 -1 SHOX2 HGNC HGNC:10854 protein_coding YES CCDS33884.2 ENSP00000374240 O60902 UPI0000169EC9 NM_003030.4 deleterious(0) 5/6 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF290 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 158099877 158099877 T A 1 0 0 0 0 1 0 0 0 14552 1608 56 4 4 SHOX2 3 158099877 Missense_Mutation SNP T C3N-01489_T 6652656 158099877 40195682 194 25124 FNDC3B 0 . GRCh38 3 172112541 172112541 + Missense_Mutation SNP G G T rs771905097 C3N-01489_T C3N-01489_N G G c.62G>T p.Gly21Val p.G21V ENST00000336824 2/26 357 307 50 479 479 0 strelka-varscan-mutect FNDC3B,missense_variant,p.Gly21Val,ENST00000336824,NM_001135095.1;FNDC3B,missense_variant,p.Gly21Val,ENST00000415807,NM_022763.3;FNDC3B,missense_variant,p.Gly21Val,ENST00000416957,;FNDC3B,missense_variant,p.Gly21Val,ENST00000421757,;FNDC3B,missense_variant,p.Gly21Val,ENST00000423424,;FNDC3B,non_coding_transcript_exon_variant,,ENST00000469491,; T ENST00000336824 Transcript missense_variant 161/7904 62/3615 21/1204 G/V gGa/gTa rs771905097 1 1 FNDC3B HGNC HGNC:24670 protein_coding YES CCDS3217.1 ENSP00000338523 Q53EP0 UPI00001AE8B2 NM_001135095.1 tolerated(0.08) 2/26 MODERATE 1 SNV 1 1 PASS rs771905097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 172112541 172112541 G T 1 0 0 0 0 1 0 0 0 5827 1174 41 2 2 FNDC3B 3 172112541 Missense_Mutation SNP G C3N-01489_T 14012664 172112541 26183018 195 25125 NLGN1 0 . GRCh38 3 174279176 174279176 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1175G>T p.Gly392Val p.G392V ENST00000457714 6/7 148 125 23 219 219 0 strelka-varscan-mutect NLGN1,missense_variant,p.Gly392Val,ENST00000457714,NM_014932.3;NLGN1,missense_variant,p.Gly392Val,ENST00000361589,;NLGN1,missense_variant,p.Gly177Val,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,non_coding_transcript_exon_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,;NLGN1,downstream_gene_variant,,ENST00000490929,; T ENST00000457714 Transcript missense_variant 1604/8242 1175/2472 392/823 G/V gGg/gTg 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 deleterious(0) 6/7 hmmpanther:PTHR11559:SF52,hmmpanther:PTHR11559,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 81 174279176 174279176 G T 1 0 0 0 0 1 0 0 0 10498 1232 43 2 2 NLGN1 3 174279176 Missense_Mutation SNP G C3N-01489_T 2166635 174279176 24016383 196 25126 ABCC5 0 . GRCh38 3 183978526 183978526 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.1273G>T p.Gly425Cys p.G425C ENST00000334444 9/30 139 116 23 193 191 2 strelka-varscan-mutect ABCC5,missense_variant,p.Gly425Cys,ENST00000334444,NM_005688.2;ABCC5,missense_variant,p.Gly425Cys,ENST00000265586,;ABCC5,non_coding_transcript_exon_variant,,ENST00000492216,;ABCC5,missense_variant,p.Gly425Cys,ENST00000437205,NM_001320032.1; A ENST00000334444 Transcript missense_variant 1514/5921 1273/4314 425/1437 G/C Ggc/Tgc COSM3590596 1 -1 ABCC5 HGNC HGNC:56 protein_coding YES CCDS43176.1 ENSP00000333926 O15440 UPI000004A33C NM_005688.2 deleterious(0) 9/30 PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF196,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 183978526 183978526 C A 1 0 0 0 0 1 0 0 0 60 623 22 2 2 ABCC5 3 183978526 Missense_Mutation SNP C C3N-01489_T 9699350 183978526 14317033 197 25127 POLR2H 0 . GRCh38 3 184368202 184368202 + Missense_Mutation SNP C C G C3N-01489_T C3N-01489_N C C c.425C>G p.Pro142Arg p.P142R ENST00000429568 5/5 139 132 7 219 219 0 strelka-varscan-mutect POLR2H,missense_variant,p.Leu121Val,ENST00000456318,NM_006232.3;POLR2H,missense_variant,p.Leu93Val,ENST00000430783,NM_001278714.1;POLR2H,missense_variant,p.Leu85Val,ENST00000438240,NM_001278700.1;POLR2H,missense_variant,p.Pro142Arg,ENST00000429568,NM_001278698.1;POLR2H,missense_variant,p.Leu121Val,ENST00000455712,;POLR2H,missense_variant,p.Leu57Val,ENST00000443489,NM_001278715.1;POLR2H,missense_variant,p.Leu85Val,ENST00000452961,NM_001278699.1;THPO,downstream_gene_variant,,ENST00000204615,NM_000460.3,NM_001289998.1,NM_001290028.1;THPO,downstream_gene_variant,,ENST00000445696,NM_001177598.2,NM_001290022.1,NM_001177597.2,NM_001290026.1;THPO,downstream_gene_variant,,ENST00000421442,NM_001289997.1,NM_001290027.1;POLR2H,downstream_gene_variant,,ENST00000412877,;POLR2H,downstream_gene_variant,,ENST00000460083,;THPO,downstream_gene_variant,,ENST00000477594,;POLR2H,non_coding_transcript_exon_variant,,ENST00000488213,;POLR2H,non_coding_transcript_exon_variant,,ENST00000476003,;POLR2H,non_coding_transcript_exon_variant,,ENST00000489043,;POLR2H,downstream_gene_variant,,ENST00000490958,; G ENST00000429568 Transcript missense_variant 484/878 425/528 142/175 P/R cCt/cGt COSM4424676 1 1 POLR2H HGNC HGNC:9195 protein_coding YES CCDS63859.1 ENSP00000415536 P52434 UPI000198CBDF NM_001278698.1 deleterious_low_confidence(0) 5/5 1 MODERATE SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 184368202 184368202 C G 1 0 0 0 0 1 0 0 0 12331 681 24 4 4 POLR2H 3 184368202 Missense_Mutation SNP C C3N-01489_T 389676 184368202 13927357 198 25128 TMEM207 0 . GRCh38 3 190440373 190440373 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.175G>C p.Val59Leu p.V59L ENST00000354905 4/5 93 84 9 108 108 0 strelka-varscan-mutect TMEM207,missense_variant,p.Val59Leu,ENST00000354905,NM_207316.1; G ENST00000354905 Transcript missense_variant 242/1448 175/441 59/146 V/L Gtt/Ctt 1 -1 TMEM207 HGNC HGNC:33705 protein_coding YES CCDS3297.1 ENSP00000346981 Q6UWW9 UPI0000048F12 NM_207316.1 tolerated(0.21) 4/5 hmmpanther:PTHR36467,hmmpanther:PTHR36467:SF1,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1176326813 . 0 204 6 0 0 0 0 0 -18.60323 0.9999998 1 1 1 0 G 3 3 81 190440373 190440373 C G 1 0 0 0 0 1 0 0 0 16571 507 18 4 4 TMEM207 3 190440373 Missense_Mutation SNP C C3N-01489_T 6072171 190440373 7855186 199 25129 MUC4 0 . GRCh38 3 195791289 195791289 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.291G>A p.Met97Ile p.M97I ENST00000463781 2/25 183 136 47 236 236 0 strelka-varscan-mutect MUC4,missense_variant,p.Met97Ile,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Met97Ile,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Met97Ile,ENST00000478156,;MUC4,missense_variant,p.Met97Ile,ENST00000466475,;MUC4,missense_variant,p.Met97Ile,ENST00000477756,;MUC4,missense_variant,p.Met97Ile,ENST00000477086,;MUC4,missense_variant,p.Met97Ile,ENST00000480843,;MUC4,missense_variant,p.Met97Ile,ENST00000462323,;MUC4,missense_variant,p.Met97Ile,ENST00000470451,;MUC4,missense_variant,p.Met97Ile,ENST00000479406,; T ENST00000463781 Transcript missense_variant 751/17110 291/16239 97/5412 M/I atG/atA 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 tolerated_low_confidence(0.43) 2/25 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 195791289 195791289 C T 1 0 0 0 0 1 0 0 0 9977 826 29 3 3 MUC4 3 195791289 Missense_Mutation SNP C C3N-01489_T 5350916 195791289 2504270 200 25130 CLRN2 0 . GRCh38 4 17526897 17526897 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.514C>A p.Gln172Lys p.Q172K ENST00000511148 3/3 294 251 43 468 467 1 strelka-varscan-mutect CLRN2,missense_variant,p.Gln172Lys,ENST00000511148,NM_001079827.2; A ENST00000511148 Transcript missense_variant 616/823 514/699 172/232 Q/K Cag/Aag 1 1 CLRN2 HGNC HGNC:33939 protein_coding YES CCDS47032.1 ENSP00000424711 A0PK11 UPI0000D6154A NM_001079827.2 tolerated(1) 3/3 hmmpanther:PTHR31548,hmmpanther:PTHR31548:SF5,PD525711 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 17526897 17526897 C A 1 0 0 0 0 1 0 0 0 3330 827 29 2 2 CLRN2 4 17526897 Missense_Mutation SNP C C3N-01489_T 17526897 172687658 201 25131 GABRG1 0 . GRCh38 4 46065558 46065558 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.348C>A p.= p.A116A ENST00000295452 4/9 155 98 57 176 176 0 strelka-varscan-mutect GABRG1,synonymous_variant,p.=,ENST00000295452,NM_173536.3; T ENST00000295452 Transcript synonymous_variant 516/6785 348/1398 116/465 A gcC/gcA 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 4/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,Prints_domain:PR00252,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,TIGRFAM_domain:TIGR00860 LOW 1 SNV 1 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999855 1 1 1 0 T 2 4 81 46065558 46065558 G T 1 0 0 0 0 0 0 0 1 6042 1219 43 2 2 GABRG1 4 46065558 Silent SNP G C3N-01489_T 28538661 46065558 144148997 202 25132 GABRA2 0 . GRCh38 4 46303560 46303560 + Nonsense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.756T>A p.Tyr252Ter p.Y252* ENST00000510861 8/10 236 211 25 271 271 0 strelka-varscan-mutect GABRA2,stop_gained,p.Tyr252Ter,ENST00000510861,;GABRA2,stop_gained,p.Tyr252Ter,ENST00000514090,;GABRA2,stop_gained,p.Tyr252Ter,ENST00000356504,NM_001114175.1;GABRA2,stop_gained,p.Tyr168Ter,ENST00000540012,NM_001286827.1;GABRA2,stop_gained,p.Tyr252Ter,ENST00000381620,NM_000807.2;GABRA2,stop_gained,p.Tyr252Ter,ENST00000515082,;GABRA2,stop_gained,p.Tyr252Ter,ENST00000507069,;GABRA2,stop_gained,p.Tyr21Ter,ENST00000514236,;GABRA2,3_prime_UTR_variant,,ENST00000630416,;GABRA2,3_prime_UTR_variant,,ENST00000510233,;GABRA2,intron_variant,,ENST00000513005,;GABRA2,downstream_gene_variant,,ENST00000514193,; T ENST00000510861 Transcript stop_gained 930/3411 756/1356 252/451 Y/* taT/taA 1 -1 GABRA2 HGNC HGNC:4076 protein_coding YES CCDS3471.1 ENSP00000421828 P47869 A0A024R9X6 UPI000013DC88 8/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF218,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:SSF90112,Prints_domain:PR00252 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 46303560 46303560 A T 1 0 0 0 0 0 1 0 0 6032 108 4 4 4 GABRA2 4 46303560 Nonsense_Mutation SNP A C3N-01489_T 238002 46303560 143910995 203 25133 GABRA4 0 . GRCh38 4 46928582 46928582 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1308C>A p.Phe436Leu p.F436L ENST00000264318 9/9 249 217 32 322 322 0 strelka-varscan-mutect GABRA4,missense_variant,p.Phe436Leu,ENST00000264318,NM_000809.3,NM_001204266.1;GABRA4,3_prime_UTR_variant,,ENST00000508560,;GABRA4,3_prime_UTR_variant,,ENST00000511523,; T ENST00000264318 Transcript missense_variant 2291/11973 1308/1665 436/554 F/L ttC/ttA 1 -1 GABRA4 HGNC HGNC:4078 protein_coding YES CCDS3473.1 ENSP00000264318 P48169 X5D7F5 UPI0000074200 NM_000809.3,NM_001204266.1 tolerated_low_confidence(0.3) 9/9 TIGRFAM_domain:TIGR00860,Pfam_domain:PF02932,Prints_domain:PR01617 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 46928582 46928582 G T 1 0 0 0 0 1 0 0 0 6034 1281 45 2 2 GABRA4 4 46928582 Missense_Mutation SNP G C3N-01489_T 625022 46928582 143285973 204 25134 CORIN 0 . GRCh38 4 47744470 47744470 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.731G>A p.Arg244Lys p.R244K ENST00000273857 5/22 232 207 25 256 256 0 strelka-varscan-mutect CORIN,missense_variant,p.Arg244Lys,ENST00000273857,NM_006587.3;CORIN,missense_variant,p.Arg177Lys,ENST00000610355,NM_001278585.1;CORIN,missense_variant,p.Arg105Lys,ENST00000508498,;CORIN,missense_variant,p.Arg177Lys,ENST00000502252,;CORIN,missense_variant,p.Arg244Lys,ENST00000505909,;CORIN,missense_variant,p.Arg244Lys,ENST00000504584,NM_001278586.1;CORIN,non_coding_transcript_exon_variant,,ENST00000502726,;CORIN,non_coding_transcript_exon_variant,,ENST00000503821,; T ENST00000273857 Transcript missense_variant 731/4852 731/3129 244/1042 R/K aGa/aAa 1 -1 CORIN HGNC HGNC:19012 protein_coding YES CCDS3477.1 ENSP00000273857 Q9Y5Q5 UPI0000168657 NM_006587.3 tolerated(0.61) 5/22 Gene3D:1ijyA00,Pfam_domain:PF01392,PIRSF_domain:PIRSF036376,PROSITE_profiles:PS50038,hmmpanther:PTHR24270,SMART_domains:SM00063,Superfamily_domains:SSF63501 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 47744470 47744470 C T 1 0 0 0 0 1 0 0 0 3546 913 32 3 3 CORIN 4 47744470 Missense_Mutation SNP C C3N-01489_T 815888 47744470 142470085 205 25135 LRRC66 0 . GRCh38 4 51994518 51994518 + Missense_Mutation SNP G G C rs758354405 C3N-01489_T C3N-01489_N G G c.2504C>G p.Ala835Gly p.A835G ENST00000343457 4/4 469 440 29 416 416 0 strelka-varscan-mutect LRRC66,missense_variant,p.Ala835Gly,ENST00000343457,NM_001024611.1; C ENST00000343457 Transcript missense_variant 2511/3327 2504/2643 835/880 A/G gCa/gGa rs758354405 1 -1 LRRC66 HGNC HGNC:34299 protein_coding YES CCDS43229.1 ENSP00000341944 Q68CR7 UPI0000425C5B NM_001024611.1 deleterious(0.03) 4/4 MODERATE 1 SNV 1 1 PASS rs758354405 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 51994518 51994518 G C 1 0 0 0 0 1 0 0 0 8914 1319 46 4 4 LRRC66 4 51994518 Missense_Mutation SNP G C3N-01489_T 4250048 51994518 138220037 206 25136 SULT1E1 0 . GRCh38 4 69847712 69847712 + Missense_Mutation SNP C C T rs769456468 C3N-01489_T C3N-01489_N C C c.577G>A p.Glu193Lys p.E193K ENST00000226444 6/8 88 82 6 155 155 0 strelka-varscan-mutect SULT1E1,missense_variant,p.Glu193Lys,ENST00000226444,NM_005420.2;SULT1E1,missense_variant,p.Glu26Lys,ENST00000506796,;SULT1E1,downstream_gene_variant,,ENST00000504002,; T ENST00000226444 Transcript missense_variant 690/1780 577/885 193/294 E/K Gaa/Aaa rs769456468,COSM1671053 1 -1 SULT1E1 HGNC HGNC:11377 protein_coding YES CCDS3531.1 ENSP00000226444 P49888 Q53X91 UPI00000623C8 NM_005420.2 deleterious(0) 6/8 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF53,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769456468 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 69847712 69847712 C T 1 0 0 0 0 1 0 0 0 15766 893 31 1 1 SULT1E1 4 69847712 Missense_Mutation SNP C C3N-01489_T 17853194 69847712 120366843 207 25137 PPEF2 0 . GRCh38 4 75876364 75876364 + Nonsense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.1243G>T p.Glu415Ter p.E415* ENST00000286719 11/17 95 79 16 170 169 1 strelka-mutect PPEF2,stop_gained,p.Glu415Ter,ENST00000286719,NM_006239.2;PPEF2,stop_gained,p.Glu415Ter,ENST00000621010,;PPEF2,3_prime_UTR_variant,,ENST00000511880,; A ENST00000286719 Transcript stop_gained 1600/3414 1243/2262 415/753 E/* Gag/Tag COSM588553 1 -1 PPEF2 HGNC HGNC:9244 protein_coding YES CCDS34013.1 ENSP00000286719 O14830 UPI0000163923 NM_006239.2 11/17 PIRSF_domain:PIRSF000912,SMART_domains:SM00156 1 HIGH 1 SNV 1 1 1 PASS rs1450302356 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 75876364 75876364 C A 1 0 0 0 0 0 1 0 0 12417 864 30 2 2 PPEF2 4 75876364 Nonsense_Mutation SNP C C3N-01489_T 6028652 75876364 114338191 208 25138 PRDM8 0 . GRCh38 4 80200216 80200216 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.136C>A p.Leu46Met p.L46M ENST00000339711 8/10 282 246 36 539 539 0 strelka-varscan-mutect PRDM8,missense_variant,p.Leu46Met,ENST00000339711,NM_020226.3;PRDM8,missense_variant,p.Leu46Met,ENST00000504452,;PRDM8,missense_variant,p.Leu46Met,ENST00000415738,NM_001099403.1;PRDM8,missense_variant,p.Leu46Met,ENST00000515013,;PRDM8,downstream_gene_variant,,ENST00000508061,;PRDM8,downstream_gene_variant,,ENST00000511825,;PRDM8,downstream_gene_variant,,ENST00000508965,;PRDM8,downstream_gene_variant,,ENST00000507025,;PRDM8,downstream_gene_variant,,ENST00000509375,;PRDM8,downstream_gene_variant,,ENST00000506547,; A ENST00000339711 Transcript missense_variant 1367/4095 136/2070 46/689 L/M Ctg/Atg 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 deleterious(0) 8/10 Gene3D:2.170.270.10,PROSITE_profiles:PS50280,hmmpanther:PTHR16516,hmmpanther:PTHR16516:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 80200216 80200216 C A 1 0 0 0 0 1 0 0 0 12594 680 24 2 2 PRDM8 4 80200216 Missense_Mutation SNP C C3N-01489_T 4323852 80200216 110014339 209 25139 HERC3 0 . GRCh38 4 88654133 88654133 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.777G>T p.Lys259Asn p.K259N ENST00000402738 7/26 98 83 15 141 141 0 strelka-varscan-mutect HERC3,missense_variant,p.Lys259Asn,ENST00000402738,NM_014606.2,NM_001271602.1;HERC3,missense_variant,p.Lys259Asn,ENST00000264345,;HERC3,missense_variant,p.Lys259Asn,ENST00000407637,NM_001318505.1;HERC3,downstream_gene_variant,,ENST00000452979,;HERC3,downstream_gene_variant,,ENST00000431413,;HERC3,downstream_gene_variant,,ENST00000513325,;HERC3,downstream_gene_variant,,ENST00000422770,;HERC3,downstream_gene_variant,,ENST00000426683,;HERC3,upstream_gene_variant,,ENST00000470815,; T ENST00000402738 Transcript missense_variant,splice_region_variant 1016/4974 777/3153 259/1050 K/N aaG/aaT 1 1 HERC3 HGNC HGNC:4876 protein_coding YES CCDS34028.1 ENSP00000385684 Q15034 UPI000012C614 NM_014606.2,NM_001271602.1 tolerated(0.16) 7/26 PROSITE_profiles:PS50012,hmmpanther:PTHR11254:SF335,hmmpanther:PTHR11254,Gene3D:2.130.10.30,Superfamily_domains:SSF50985,Prints_domain:PR00633 MODERATE 1 SNV 1 1 PASS rs1334614738 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 88654133 88654133 G T 1 0 0 0 0 1 0 0 0 6943 1014 35 2 2 HERC3 4 88654133 Missense_Mutation SNP G C3N-01489_T 8453917 88654133 101560422 210 25140 TIGD2 0 . GRCh38 4 89113853 89113853 + Silent SNP C C T rs754328555 C3N-01489_T C3N-01489_N C C c.879C>T p.= p.F293F ENST00000603357 2/2 139 122 17 262 262 0 strelka-varscan-mutect TIGD2,synonymous_variant,p.=,ENST00000603357,;TIGD2,synonymous_variant,p.=,ENST00000317005,NM_145715.2;FAM13A,upstream_gene_variant,,ENST00000502459,; T ENST00000603357 Transcript synonymous_variant 2171/3217 879/1578 293/525 F ttC/ttT rs754328555,COSM3918341 1 1 TIGD2 HGNC HGNC:18333 protein_coding YES CCDS3633.1 ENSP00000486687 Q4W5G0 V9HWD1 UPI000013FF3C 2/2 hmmpanther:PTHR19303:SF220,hmmpanther:PTHR19303,Pfam_domain:PF03184 0,1 LOW 1 SNV 4 0,1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.9998731 1 1 1 0 T 2 4 81 89113853 89113853 C T 1 0 0 0 0 0 0 0 1 16334 854 30 3 3 TIGD2 4 89113853 Silent SNP C C3N-01489_T 459720 89113853 101100702 211 25141 UNC5C 0 . GRCh38 4 95169391 95169391 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.2639A>G p.Asn880Ser p.N880S ENST00000453304 16/16 62 58 4 112 112 0 varscan-mutect UNC5C,missense_variant,p.Asn880Ser,ENST00000453304,NM_003728.3;UNC5C,missense_variant,p.Asn839Ser,ENST00000610318,; C ENST00000453304 Transcript missense_variant 2988/9875 2639/2796 880/931 N/S aAt/aGt 1 -1 UNC5C HGNC HGNC:12569 protein_coding YES CCDS3643.1 ENSP00000406022 O95185 UPI000004E6A5 NM_003728.3 tolerated(0.79) 16/16 Gene3D:1.10.533.10,Pfam_domain:PF00531,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF7,SMART_domains:SM00005,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.19529 1 1 1 1 0 C 3 2 81 95169391 95169391 T C 1 0 0 0 0 1 0 0 0 17517 1493 52 5 5 UNC5C 4 95169391 Missense_Mutation SNP T C3N-01489_T 6055538 95169391 95045164 212 25142 C4orf17 0 . GRCh38 4 99522652 99522652 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.280G>T p.Val94Leu p.V94L ENST00000326581 3/9 224 185 39 392 390 2 strelka-varscan-mutect C4orf17,missense_variant,p.Val94Leu,ENST00000514652,;C4orf17,missense_variant,p.Val94Leu,ENST00000326581,NM_032149.2;C4orf17,non_coding_transcript_exon_variant,,ENST00000503257,;C4orf17,missense_variant,p.Val94Leu,ENST00000477187,; T ENST00000326581 Transcript missense_variant 642/1636 280/1080 94/359 V/L Gta/Tta 1 1 C4orf17 HGNC HGNC:25274 protein_coding YES CCDS3649.1 ENSP00000322582 Q53FE4 UPI0000141987 NM_032149.2 tolerated(0.18) 3/9 Pfam_domain:PF15256,hmmpanther:PTHR33772,hmmpanther:PTHR33772:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 99522652 99522652 G T 1 0 0 0 0 1 0 0 0 2078 1377 48 2 2 C4orf17 4 99522652 Missense_Mutation SNP G C3N-01489_T 4353261 99522652 90691903 213 25143 DKK2 0 . GRCh38 4 106924179 106924179 + Silent SNP T T C novel C3N-01489_T C3N-01489_N T T c.555A>G p.= p.R185R ENST00000285311 4/4 157 147 10 278 278 0 strelka-varscan-mutect DKK2,synonymous_variant,p.=,ENST00000285311,NM_014421.2;DKK2,synonymous_variant,p.=,ENST00000513208,;DKK2,synonymous_variant,p.=,ENST00000510463,;DKK2,non_coding_transcript_exon_variant,,ENST00000510534,; C ENST00000285311 Transcript synonymous_variant 1261/3638 555/780 185/259 R cgA/cgG 1 -1 DKK2 HGNC HGNC:2892 protein_coding YES CCDS3675.1 ENSP00000285311 Q9UBU2 UPI0000048EF2 NM_014421.2 4/4 hmmpanther:PTHR12113:SF12,hmmpanther:PTHR12113,Gene3D:2.10.80.10 LOW 1 SNV 1 1 PASS rs1405642897 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 106924179 106924179 T C 1 0 0 0 0 0 0 0 1 4351 1422 50 5 5 DKK2 4 106924179 Silent SNP T C3N-01489_T 7401527 106924179 83290376 214 25144 NDST4 0 . GRCh38 4 114970571 114970571 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1080A>T p.Glu360Asp p.E360D ENST00000264363 4/14 80 75 5 133 133 0 varscan-mutect NDST4,missense_variant,p.Glu360Asp,ENST00000264363,NM_022569.1;NDST4,5_prime_UTR_variant,,ENST00000613194,;NDST4,5_prime_UTR_variant,,ENST00000504854,;NDST4,non_coding_transcript_exon_variant,,ENST00000514570,; A ENST00000264363 Transcript missense_variant 1759/3351 1080/2619 360/872 E/D gaA/gaT 1 -1 NDST4 HGNC HGNC:20779 protein_coding YES CCDS3706.1 ENSP00000264363 Q9H3R1 UPI000006CED7 NM_022569.1 deleterious(0) 4/14 Pfam_domain:PF12062,hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF45,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1376335163 . 0 208 2 0 0 0 0 0 -11.53783 1 1 1 1 0 A 3 1 81 114970571 114970571 T A 1 0 0 0 0 1 0 0 0 10279 1606 56 4 4 NDST4 4 114970571 Missense_Mutation SNP T C3N-01489_T 8046392 114970571 75243984 215 25145 TRPC3 0 . GRCh38 4 121932326 121932326 + Missense_Mutation SNP G G C C3N-01489_T C3N-01489_N G G c.932C>G p.Ala311Gly p.A311G ENST00000379645 2/12 147 137 10 254 254 0 strelka-varscan-mutect TRPC3,missense_variant,p.Ala238Gly,ENST00000264811,NM_003305.2;TRPC3,missense_variant,p.Ala311Gly,ENST00000379645,NM_001130698.1;TRPC3,missense_variant,p.Ala238Gly,ENST00000513531,;TRPC3,downstream_gene_variant,,ENST00000502968,;TRPC3,missense_variant,p.Ala238Gly,ENST00000506449,; C ENST00000379645 Transcript missense_variant 1006/3548 932/2766 311/921 A/G gCc/gGc COSM3599665,COSM3599666 1 -1 TRPC3 HGNC HGNC:12335 protein_coding YES CCDS47130.1 ENSP00000368966 Q13507 UPI00004C6F61 NM_001130698.1 deleterious(0) 2/12 hmmpanther:PTHR10117:SF8,hmmpanther:PTHR10117,TIGRFAM_domain:TIGR00870,Pfam_domain:PF08344 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 121932326 121932326 G C 1 0 0 0 0 1 0 0 0 17084 1203 42 4 4 TRPC3 4 121932326 Missense_Mutation SNP G C3N-01489_T 6961755 121932326 68282229 216 25146 FAT4 0 . GRCh38 4 125319839 125319839 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.3428A>T p.Gln1143Leu p.Q1143L ENST00000394329 1/17 113 97 16 173 173 0 strelka-varscan-mutect FAT4,missense_variant,p.Gln1143Leu,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; T ENST00000394329 Transcript missense_variant 3441/16123 3428/14946 1143/4981 Q/L cAg/cTg 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.03) 1/17 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 125319839 125319839 A T 1 0 0 0 0 1 0 0 0 5552 188 7 4 4 FAT4 4 125319839 Missense_Mutation SNP A C3N-01489_T 3387513 125319839 64894716 217 25147 GAB1 0 . GRCh38 4 143460434 143460434 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1840G>T p.Asp614Tyr p.D614Y ENST00000262995 9/11 247 229 18 326 326 0 strelka-varscan-mutect GAB1,missense_variant,p.Asp614Tyr,ENST00000262995,NM_207123.2;GAB1,missense_variant,p.Asp584Tyr,ENST00000262994,NM_002039.3;GAB1,missense_variant,p.Asp481Tyr,ENST00000505913,;GAB1,intron_variant,,ENST00000512843,;GAB1,non_coding_transcript_exon_variant,,ENST00000508833,;GAB1,downstream_gene_variant,,ENST00000507070,;GAB1,downstream_gene_variant,,ENST00000510615,; T ENST00000262995 Transcript missense_variant 2267/7981 1840/2175 614/724 D/Y Gac/Tac 1 1 GAB1 HGNC HGNC:4066 protein_coding YES CCDS3760.1 ENSP00000262995 Q13480 UPI0000232A33 NM_207123.2 deleterious(0) 9/11 Low_complexity_(Seg):seg,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF18 MODERATE 1 SNV 1 1 PASS rs1294424013 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 143460434 143460434 G T 1 0 0 0 0 1 0 0 0 6019 1058 37 1 1 GAB1 4 143460434 Missense_Mutation SNP G C3N-01489_T 18140595 143460434 46754121 218 25148 ZNF827 0 . GRCh38 4 145774641 145774641 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.2725A>T p.Asn909Tyr p.N909Y ENST00000508784 11/15 114 98 16 177 177 0 strelka-varscan-mutect ZNF827,missense_variant,p.Asn909Tyr,ENST00000508784,NM_001306215.1;ZNF827,missense_variant,p.Asn909Tyr,ENST00000379448,NM_178835.3;ZNF827,missense_variant,p.Asn559Tyr,ENST00000513320,;ZNF827,missense_variant,p.Asn10Tyr,ENST00000511659,;C4orf51,downstream_gene_variant,,ENST00000510096,;ZNF827,upstream_gene_variant,,ENST00000515386,; A ENST00000508784 Transcript missense_variant 2953/7463 2725/3246 909/1081 N/Y Aat/Tat 1 -1 ZNF827 HGNC HGNC:27193 protein_coding YES CCDS77968.1 ENSP00000421863 Q17R98 UPI0000DA58F8 NM_001306215.1 deleterious(0.01) 11/15 hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF4,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 145774641 145774641 T A 1 0 0 0 0 1 0 0 0 18766 1812 63 4 4 ZNF827 4 145774641 Missense_Mutation SNP T C3N-01489_T 2314207 145774641 44439914 219 25149 SLC10A7 0 . GRCh38 4 146517107 146517107 + Silent SNP T T A novel C3N-01489_T C3N-01489_N T T c.114A>T p.= p.P38P ENST00000507030 2/13 78 69 9 129 129 0 strelka-varscan-mutect SLC10A7,synonymous_variant,p.=,ENST00000432059,NM_001317816.1;SLC10A7,synonymous_variant,p.=,ENST00000335472,NM_001029998.4;SLC10A7,synonymous_variant,p.=,ENST00000394059,NM_032128.3;SLC10A7,synonymous_variant,p.=,ENST00000502607,NM_001317818.1;SLC10A7,synonymous_variant,p.=,ENST00000507030,NM_001300842.1;SLC10A7,synonymous_variant,p.=,ENST00000511374,;SLC10A7,non_coding_transcript_exon_variant,,ENST00000511315,;SLC10A7,non_coding_transcript_exon_variant,,ENST00000507560,; A ENST00000507030 Transcript synonymous_variant 114/1134 114/1077 38/358 P ccA/ccT 1 -1 SLC10A7 HGNC HGNC:23088 protein_coding YES CCDS75198.1 ENSP00000421275 Q0GE19 UPI0000DD5C53 NM_001300842.1 2/13 hmmpanther:PTHR18640,PIRSF_domain:PIRSF026166,Pfam_domain:PF13593 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 146517107 146517107 T A 1 0 0 0 0 0 0 0 1 14644 1567 55 4 4 SLC10A7 4 146517107 Silent SNP T C3N-01489_T 742466 146517107 43697448 220 25150 POU4F2 0 . GRCh38 4 146640206 146640206 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.628G>T p.Gly210Cys p.G210C ENST00000281321 2/2 111 101 10 185 184 1 strelka-varscan-mutect POU4F2,missense_variant,p.Gly210Cys,ENST00000281321,NM_004575.2; T ENST00000281321 Transcript missense_variant 876/3144 628/1230 210/409 G/C Ggc/Tgc 1 1 POU4F2 HGNC HGNC:9219 protein_coding YES CCDS34074.1 ENSP00000281321 Q12837 UPI000013DC6C NM_004575.2 deleterious(0.01) 2/2 hmmpanther:PTHR11636:SF41,hmmpanther:PTHR11636 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 146640206 146640206 G T 1 0 0 0 0 1 0 0 0 12395 1116 39 1 1 POU4F2 4 146640206 Missense_Mutation SNP G C3N-01489_T 123099 146640206 43574349 221 25151 DCLK2 0 . GRCh38 4 150102785 150102785 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.729G>T p.Lys243Asn p.K243N ENST00000302176 2/17 71 60 11 129 129 0 strelka-varscan-mutect DCLK2,missense_variant,p.Lys243Asn,ENST00000296550,NM_001040260.3;DCLK2,missense_variant,p.Lys243Asn,ENST00000302176,NM_001040261.4;DCLK2,missense_variant,p.Lys243Asn,ENST00000506325,;DCLK2,missense_variant,p.Lys243Asn,ENST00000635524,;DCLK2,missense_variant,p.Lys243Asn,ENST00000411937,; T ENST00000302176 Transcript missense_variant 729/3543 729/2352 243/783 K/N aaG/aaT COSM3127429,COSM3127430 1 1 DCLK2 HGNC HGNC:19002 protein_coding YES CCDS47142.2 ENSP00000303887 Q8N568 UPI0000D615C9 NM_001040261.4 deleterious(0) 2/17 PROSITE_profiles:PS50309,hmmpanther:PTHR24347:SF122,hmmpanther:PTHR24347,Pfam_domain:PF03607,Gene3D:1mfwA00,SMART_domains:SM00537,Superfamily_domains:SSF89837 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1009660569 . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 3 4 81 150102785 150102785 G T 1 0 0 0 0 1 0 0 0 4094 933 33 2 2 DCLK2 4 150102785 Missense_Mutation SNP G C3N-01489_T 3462579 150102785 40111770 222 25152 FBXW7 0 . GRCh38 4 152411569 152411569 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.235G>T p.Glu79Ter p.E79* ENST00000281708 2/12 179 158 21 289 289 0 strelka-varscan-mutect FBXW7,stop_gained,p.Glu79Ter,ENST00000281708,NM_033632.3;FBXW7,stop_gained,p.Glu79Ter,ENST00000603548,;FBXW7,stop_gained,p.Glu79Ter,ENST00000603841,;FBXW7,stop_gained,p.Glu79Ter,ENST00000604872,NM_001257069.1;FBXW7,stop_gained,p.Glu79Ter,ENST00000605042,; A ENST00000281708 Transcript stop_gained 1465/4976 235/2124 79/707 E/* Gaa/Taa 1 -1 FBXW7 HGNC HGNC:16712 protein_coding YES CCDS3777.1 ENSP00000281708 Q969H0 UPI000007007E NM_033632.3 2/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 152411569 152411569 C A 1 0 0 0 0 0 1 0 0 5632 922 32 2 2 FBXW7 4 152411569 Nonsense_Mutation SNP C C3N-01489_T 2308784 152411569 37802986 223 25153 TIGD4 0 . GRCh38 4 152770251 152770251 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.754T>C p.Tyr252His p.Y252H ENST00000304337 2/2 156 145 11 317 317 0 strelka-varscan-mutect TIGD4,missense_variant,p.Tyr252His,ENST00000304337,NM_145720.3; G ENST00000304337 Transcript missense_variant 1575/2472 754/1539 252/512 Y/H Tat/Cat 1 -1 TIGD4 HGNC HGNC:18335 protein_coding YES CCDS34079.1 ENSP00000355162 Q8IY51 UPI000013E966 NM_145720.3 deleterious(0) 2/2 hmmpanther:PTHR19303:SF204,hmmpanther:PTHR19303,Pfam_domain:PF03184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 152770251 152770251 A G 1 0 0 0 0 1 0 0 0 16336 362 13 5 5 TIGD4 4 152770251 Missense_Mutation SNP A C3N-01489_T 358682 152770251 37444304 224 25154 DCHS2 0 . GRCh38 4 154255570 154255570 + Missense_Mutation SNP C C A rs116814307 C3N-01489_T C3N-01489_N C C c.5525G>T p.Gly1842Val p.G1842V ENST00000623607 21/25 194 177 17 269 269 0 strelka-varscan-mutect DCHS2,missense_variant,p.Gly1842Val,ENST00000357232,;DCHS2,missense_variant,p.Gly1842Val,ENST00000623607,NM_017639.3;RP11-290O12.2,intron_variant,,ENST00000624941,;RP11-290O12.2,intron_variant,,ENST00000623325,;DCHS2,downstream_gene_variant,,ENST00000623568,; A ENST00000623607 Transcript missense_variant 5525/8912 5525/8751 1842/2916 G/V gGt/gTt rs116814307 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 deleterious(0) 21/25 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs116814307 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 154255570 154255570 C A 1 0 0 0 0 1 0 0 0 4091 507 18 2 2 DCHS2 4 154255570 Missense_Mutation SNP C C3N-01489_T 1485319 154255570 35958985 225 25155 GLRB 0 . GRCh38 4 157138892 157138892 + Missense_Mutation SNP G G A rs866839956 C3N-01489_T C3N-01489_N G G c.694G>A p.Asp232Asn p.D232N ENST00000264428 7/10 112 102 10 196 195 1 strelka-varscan GLRB,missense_variant,p.Asp232Asn,ENST00000264428,NM_000824.4;GLRB,missense_variant,p.Asp232Asn,ENST00000541722,NM_001166061.1;GLRB,missense_variant,p.Asp232Asn,ENST00000509282,NM_001166060.1;GLRB,intron_variant,,ENST00000512619,;GLRB,non_coding_transcript_exon_variant,,ENST00000510970,;GLRB,downstream_gene_variant,,ENST00000506411,;GLRB,downstream_gene_variant,,ENST00000515642,; A ENST00000264428 Transcript missense_variant 964/3126 694/1494 232/497 D/N Gat/Aat rs866839956,COSM1695149 1 1 GLRB HGNC HGNC:4329 protein_coding YES CCDS3796.1 ENSP00000264428 P48167 UPI000000161E NM_000824.4 tolerated(0.37) 7/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF29,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 157138892 157138892 G A 1 0 0 0 0 1 0 0 0 6337 1290 45 3 3 GLRB 4 157138892 Missense_Mutation SNP G C3N-01489_T 2883322 157138892 33075663 226 25156 WWC2 0 . GRCh38 4 183253972 183253972 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1169G>T p.Gly390Val p.G390V ENST00000403733 9/23 98 89 9 157 157 0 strelka-varscan-mutect WWC2,missense_variant,p.Gly390Val,ENST00000403733,NM_024949.5;WWC2,missense_variant,p.Gly390Val,ENST00000448232,;WWC2,missense_variant,p.Gly72Val,ENST00000504005,;WWC2,missense_variant,p.Gly390Val,ENST00000513834,;WWC2,missense_variant,p.Gly292Val,ENST00000438543,;WWC2,3_prime_UTR_variant,,ENST00000427431,; T ENST00000403733 Transcript missense_variant 1368/8826 1169/3579 390/1192 G/V gGa/gTa 1 1 WWC2 HGNC HGNC:24148 protein_coding YES CCDS34109.2 ENSP00000384222 Q6AWC2 UPI000022C4C2 NM_024949.5 deleterious(0.04) 9/23 hmmpanther:PTHR14791:SF26,hmmpanther:PTHR14791,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 183253972 183253972 G T 1 0 0 0 0 1 0 0 0 17970 1174 41 2 2 WWC2 4 183253972 Missense_Mutation SNP G C3N-01489_T 26115080 183253972 6960583 227 25157 PLEKHG4B 0 . GRCh38 5 143218 143218 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.581G>C p.Ser194Thr p.S194T ENST00000283426 2/18 299 202 97 299 299 0 strelka-varscan-mutect PLEKHG4B,missense_variant,p.Ser550Thr,ENST00000637938,;PLEKHG4B,missense_variant,p.Ser194Thr,ENST00000283426,NM_052909.3;PLEKHG4B,missense_variant,p.Ser108Thr,ENST00000502646,;Y_RNA,downstream_gene_variant,,ENST00000362670,; C ENST00000283426 Transcript missense_variant 631/11515 581/3816 194/1271 S/T aGt/aCt 1 1 PLEKHG4B HGNC HGNC:29399 protein_coding YES CCDS34124.1 ENSP00000283426 Q96PX9 UPI0000D615EE NM_052909.3 tolerated(0.06) 2/18 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF119 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 143218 143218 G C 1 0 0 0 0 1 0 0 0 12165 1029 36 4 4 PLEKHG4B 5 143218 Missense_Mutation SNP G C3N-01489_T 143218 181395041 228 25158 SLC9A3 0 . GRCh38 5 484583 484583 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.869T>C p.Val290Ala p.V290A ENST00000264938 5/17 322 241 81 322 322 0 strelka-varscan-mutect SLC9A3,missense_variant,p.Val290Ala,ENST00000264938,NM_004174.2;SLC9A3,missense_variant,p.Val290Ala,ENST00000514375,NM_001284351.1;CTD-2228K2.7,downstream_gene_variant,,ENST00000607286,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606288,;CTD-2228K2.7,downstream_gene_variant,,ENST00000607005,;CTD-2228K2.7,downstream_gene_variant,,ENST00000534918,;CTD-2228K2.7,downstream_gene_variant,,ENST00000606107,;SLC9A3,upstream_gene_variant,,ENST00000507407,; G ENST00000264938 Transcript missense_variant 879/2584 869/2505 290/834 V/A gTg/gCg 1 -1 SLC9A3 HGNC HGNC:11073 protein_coding YES CCDS3855.1 ENSP00000264938 P48764 UPI000013D597 NM_004174.2 deleterious(0) 5/17 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF90,TIGRFAM_domain:TIGR00840,Pfam_domain:PF00999 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 484583 484583 A G 1 0 0 0 0 1 0 0 0 14995 159 6 5 5 SLC9A3 5 484583 Missense_Mutation SNP A C3N-01489_T 341365 484583 181053676 229 25159 TPPP 0 . GRCh38 5 666002 666002 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.433G>T p.Glu145Ter p.E145* ENST00000360578 3/4 160 113 47 216 216 0 strelka-varscan-mutect TPPP,stop_gained,p.Glu145Ter,ENST00000360578,NM_007030.2;CEP72,non_coding_transcript_exon_variant,,ENST00000514507,; A ENST00000360578 Transcript stop_gained 555/6022 433/660 145/219 E/* Gag/Tag 1 -1 TPPP HGNC HGNC:24164 protein_coding YES CCDS3856.1 ENSP00000353785 O94811 Q4L233 UPI0000130FB2 NM_007030.2 3/4 hmmpanther:PTHR12932:SF18,hmmpanther:PTHR12932,Pfam_domain:PF05517,Superfamily_domains:SSF47473 HIGH 1 SNV 1 1 PASS rs1248170111 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 666002 666002 C A 1 0 0 0 0 0 1 0 0 16894 893 31 1 1 TPPP 5 666002 Nonsense_Mutation SNP C C3N-01489_T 181419 666002 180872257 230 25160 IRX2 0 . GRCh38 5 2748659 2748659 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1049G>T p.Gly350Val p.G350V ENST00000382611 3/5 200 182 18 190 190 0 strelka-varscan-mutect IRX2,missense_variant,p.Gly350Val,ENST00000382611,NM_001134222.1;IRX2,missense_variant,p.Gly350Val,ENST00000302057,NM_033267.4;C5orf38,upstream_gene_variant,,ENST00000515640,NM_001306150.1;C5orf38,upstream_gene_variant,,ENST00000334000,NM_001306149.1,NM_178569.3;C5orf38,upstream_gene_variant,,ENST00000397835,;C5orf38,upstream_gene_variant,,ENST00000505778,;C5orf38,upstream_gene_variant,,ENST00000457752,NM_001294337.1;C5orf38,upstream_gene_variant,,ENST00000503940,;C5orf38,upstream_gene_variant,,ENST00000505106,; A ENST00000382611 Transcript missense_variant 1298/2630 1049/1416 350/471 G/V gGg/gTg 1 -1 IRX2 HGNC HGNC:14359 protein_coding YES CCDS3868.1 ENSP00000372056 Q9BZI1 UPI00001B6456 NM_001134222.1 tolerated(0.25) 3/5 Low_complexity_(Seg):seg,hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 2748659 2748659 C A 1 0 0 0 0 1 0 0 0 7752 623 22 2 2 IRX2 5 2748659 Missense_Mutation SNP C C3N-01489_T 2082657 2748659 178789600 231 25161 IRX1 0 . GRCh38 5 3599347 3599347 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.399C>T p.= p.N133N ENST00000302006 2/4 427 388 39 471 471 0 strelka-mutect IRX1,synonymous_variant,p.=,ENST00000302006,NM_024337.3;CTD-2012M11.3,intron_variant,,ENST00000559410,; T ENST00000302006 Transcript synonymous_variant 451/1858 399/1443 133/480 N aaC/aaT 1 1 IRX1 HGNC HGNC:14358 protein_coding YES CCDS34132.1 ENSP00000305244 P78414 UPI00001B6455 NM_024337.3 2/4 Gene3D:1.10.10.60,hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF13,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS rs1185415252 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 3599347 3599347 C T 1 0 0 0 0 0 0 0 1 7751 535 19 1 1 IRX1 5 3599347 Silent SNP C C3N-01489_T 850688 3599347 177938912 232 25162 ADAMTS16 0 . GRCh38 5 5303455 5303455 + Missense_Mutation SNP G G T rs780516913 C3N-01489_T C3N-01489_N G G c.2977G>T p.Gly993Trp p.G993W ENST00000274181 19/23 89 76 13 101 101 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.Gly993Trp,ENST00000274181,NM_139056.2;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 3115/4979 2977/3675 993/1224 G/W Ggg/Tgg rs780516913,COSM1181862,COSM1181863 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 19/23 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs780516913 . 0 201 8 0 0 0 0 0 -20 0.9999979 1 1 1 0 T 3 4 81 5303455 5303455 G T 1 0 0 0 0 1 0 0 0 305 1116 39 1 1 ADAMTS16 5 5303455 Missense_Mutation SNP G C3N-01489_T 1704108 5303455 176234804 233 25163 ICE1 0 . GRCh38 5 5461606 5461606 + Nonsense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.2272A>T p.Arg758Ter p.R758* ENST00000296564 13/19 200 171 29 248 248 0 strelka-varscan-mutect ICE1,stop_gained,p.Arg758Ter,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript stop_gained 2494/7927 2272/6801 758/2266 R/* Aga/Tga 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 5461606 5461606 A T 1 0 0 0 0 0 1 0 0 7384 64 3 4 4 ICE1 5 5461606 Nonsense_Mutation SNP A C3N-01489_T 158151 5461606 176076653 234 25164 PAPD7 0 . GRCh38 5 6742495 6742495 + Silent SNP A A T rs752659073 C3N-01489_T C3N-01489_N A A c.264A>T p.= p.P88P ENST00000631941 5/13 199 183 16 206 206 0 strelka-varscan-mutect PAPD7,synonymous_variant,p.=,ENST00000230859,;PAPD7,synonymous_variant,p.=,ENST00000631941,NM_006999.4,NM_001171805.1;PAPD7,downstream_gene_variant,,ENST00000515721,;PAPD7,upstream_gene_variant,,ENST00000514697,;PAPD7,upstream_gene_variant,,ENST00000511764,; T ENST00000631941 Transcript synonymous_variant 452/1902 264/1629 88/542 P ccA/ccT rs752659073 1 1 PAPD7 HGNC HGNC:16705 protein_coding YES CCDS3871.1 ENSP00000488642 Q5XG87 UPI0000071E30 NM_006999.4,NM_001171805.1 5/13 Gene3D:3.30.460.10,Pfam_domain:PF01909,hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF24,Superfamily_domains:SSF81301 LOW 1 SNV 5 1 PASS rs752659073 . 0 205 0 5 0 0 0 0 -19.87449 0.9984896 1 1 1 0 T 2 4 81 6742495 6742495 A T 1 0 0 0 0 0 0 0 1 11507 144 5 4 4 PAPD7 5 6742495 Silent SNP A C3N-01489_T 1280889 6742495 174795764 235 25165 MTRR 0 . GRCh38 5 7885707 7885707 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.991G>A p.Asp331Asn p.D331N ENST00000264668 7/15 276 213 63 349 347 2 strelka-varscan-mutect MTRR,missense_variant,p.Asp331Asn,ENST00000264668,NM_024010.2;MTRR,missense_variant,p.Asp304Asn,ENST00000440940,NM_002454.2;MTRR,non_coding_transcript_exon_variant,,ENST00000508101,;MTRR,upstream_gene_variant,,ENST00000509961,;MTRR,upstream_gene_variant,,ENST00000507414,;MTRR,missense_variant,p.Asp313Asn,ENST00000510525,;MTRR,3_prime_UTR_variant,,ENST00000511461,;MTRR,3_prime_UTR_variant,,ENST00000513439,;MTRR,downstream_gene_variant,,ENST00000514369,;MTRR,upstream_gene_variant,,ENST00000512311,; A ENST00000264668 Transcript missense_variant 1021/3274 991/2178 331/725 D/N Gac/Aac 1 1 MTRR HGNC HGNC:7473 protein_coding YES CCDS3874.1 ENSP00000264668 Q9UBK8 UPI000013D550 NM_024010.2 tolerated(0.48) 7/15 Gene3D:2.40.30.10,Pfam_domain:PF00667,PROSITE_profiles:PS51384,hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF84,Superfamily_domains:SSF63380 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 7885707 7885707 G A 1 0 0 0 0 1 0 0 0 9958 942 33 3 3 MTRR 5 7885707 Missense_Mutation SNP G C3N-01489_T 1143212 7885707 173652552 236 25166 SEMA5A 0 . GRCh38 5 9054155 9054155 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2621C>A p.Ala874Asp p.A874D ENST00000382496 19/23 237 159 78 261 261 0 strelka-varscan-mutect SEMA5A,missense_variant,p.Ala874Asp,ENST00000382496,NM_003966.2;MIR4636,upstream_gene_variant,,ENST00000582271,; T ENST00000382496 Transcript missense_variant 3287/11762 2621/3225 874/1074 A/D gCc/gAc 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 tolerated(0.06) 19/23 PROSITE_profiles:PS50092,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 9054155 9054155 G T 1 0 0 0 0 1 0 0 0 14313 1203 42 2 2 SEMA5A 5 9054155 Missense_Mutation SNP G C3N-01489_T 1168448 9054155 172484104 237 25167 SEMA5A 0 . GRCh38 5 9119087 9119087 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.1836G>T p.= p.G612G ENST00000382496 15/23 302 207 95 363 362 1 strelka-varscan-mutect SEMA5A,synonymous_variant,p.=,ENST00000382496,NM_003966.2; A ENST00000382496 Transcript synonymous_variant 2502/11762 1836/3225 612/1074 G ggG/ggT 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 15/23 PROSITE_profiles:PS50092,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS rs1415296325 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 9119087 9119087 C A 1 0 0 0 0 0 0 0 1 14313 842 30 2 2 SEMA5A 5 9119087 Silent SNP C C3N-01489_T 64932 9119087 172419172 238 25168 TRIO 0 . GRCh38 5 14504398 14504398 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.8417G>T p.Arg2806Ile p.R2806I ENST00000344204 55/57 240 162 78 265 265 0 strelka-varscan-mutect TRIO,missense_variant,p.Arg2806Ile,ENST00000344204,NM_007118.2;TRIO,missense_variant,p.Arg305Ile,ENST00000344135,;TRIO,intron_variant,,ENST00000513206,;TRIO,intron_variant,,ENST00000620511,;TRIO,3_prime_UTR_variant,,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000508717,;TRIO,non_coding_transcript_exon_variant,,ENST00000508283,; T ENST00000344204 Transcript missense_variant 8441/11100 8417/9294 2806/3097 R/I aGa/aTa 1 1 TRIO HGNC HGNC:12303 protein_coding YES CCDS3883.1 ENSP00000339299 O75962 UPI000034ECE6 NM_007118.2 deleterious(0) 55/57 PROSITE_profiles:PS50011,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 14504398 14504398 G T 1 0 0 0 0 1 0 0 0 17049 956 33 2 2 TRIO 5 14504398 Missense_Mutation SNP G C3N-01489_T 5385311 14504398 167033861 239 25169 MARCH11 0 . GRCh38 5 16067636 16067636 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.1044G>C p.Leu348Phe p.L348F ENST00000332432 4/4 567 404 163 648 648 0 strelka-varscan-mutect MARCH11,missense_variant,p.Leu348Phe,ENST00000332432,NM_001102562.1;MARCH11,3_prime_UTR_variant,,ENST00000507111,; G ENST00000332432 Transcript missense_variant 1244/1741 1044/1209 348/402 L/F ttG/ttC 1 -1 MARCH11 HGNC HGNC:33609 protein_coding YES CCDS47192.1 ENSP00000333181 A6NNE9 UPI00015B3D4A NM_001102562.1 tolerated(0.14) 4/4 hmmpanther:PTHR23012:SF67,hmmpanther:PTHR23012 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 16067636 16067636 C G 1 0 0 0 0 1 0 0 0 9225 825 29 4 4 MARCH11 5 16067636 Missense_Mutation SNP C C3N-01489_T 1563238 16067636 165470623 240 25170 DROSHA 0 . GRCh38 5 31405687 31405687 + Silent SNP C C A rs776295904 C3N-01489_T C3N-01489_N C C c.3984G>T p.= p.A1328A ENST00000511367 34/35 153 102 51 190 190 0 strelka-varscan-mutect DROSHA,synonymous_variant,p.=,ENST00000511367,NM_013235.4;DROSHA,synonymous_variant,p.=,ENST00000344624,;DROSHA,synonymous_variant,p.=,ENST00000442743,;DROSHA,synonymous_variant,p.=,ENST00000513349,NM_001100412.1;DROSHA,non_coding_transcript_exon_variant,,ENST00000511778,;DROSHA,non_coding_transcript_exon_variant,,ENST00000514927,;DROSHA,non_coding_transcript_exon_variant,,ENST00000512166,;DROSHA,downstream_gene_variant,,ENST00000509067,; A ENST00000511367 Transcript synonymous_variant 4229/5305 3984/4125 1328/1374 A gcG/gcT rs776295904 1 -1 DROSHA HGNC HGNC:17904 protein_coding YES CCDS47195.1 ENSP00000425979 Q9NRR4 UPI0000134351 NM_013235.4 34/35 Gene3D:3.30.160.20,HAMAP:MF_00104,Pfam_domain:PF00035,PROSITE_profiles:PS50137,hmmpanther:PTHR11207,SMART_domains:SM00358,Superfamily_domains:SSF54768 LOW 1 SNV 1 1 PASS rs776295904 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 31405687 31405687 C A 1 0 0 0 0 0 0 0 1 4584 755 27 1 1 DROSHA 5 31405687 Silent SNP C C3N-01489_T 15338051 31405687 150132572 241 25171 NNT 0 . GRCh38 5 43653152 43653152 + Frame_Shift_Del DEL A A - rs147914179 C3N-01489_T C3N-01489_N A A c.2001delA p.Lys667AsnfsTer7 p.K667Nfs*7 ENST00000264663 14/22 141 97 44 195 195 0 sindel-varindel-pindel NNT,frameshift_variant,p.Lys667AsnfsTer7,ENST00000264663,NM_012343.3;NNT,frameshift_variant,p.Lys667AsnfsTer7,ENST00000344920,NM_182977.2;NNT,frameshift_variant,p.Lys536AsnfsTer7,ENST00000512996,;NNT,downstream_gene_variant,,ENST00000503651,;NNT,non_coding_transcript_exon_variant,,ENST00000513390,; - ENST00000264663 Transcript frameshift_variant 2219/6483 1998/3261 666/1086 L/X ctA/ct rs147914179 1 1 NNT HGNC HGNC:7863 protein_coding YES CCDS3949.1 ENSP00000264663 Q13423 A0A024R0C3 UPI000013D54F NM_012343.3 14/22 Pfam_domain:PF02233,hmmpanther:PTHR10160,hmmpanther:PTHR10160:SF22,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix HIGH 1 deletion 1 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 81 43653152 43653152 A - 1 0 1 0 1 0 0 0 0 10551 349 13 0 0 NNT 5 43653152 Frame_Shift_Del DEL A C3N-01489_T 12247465 43653152 137885107 242 25172 DDX4 0 . GRCh38 5 55760256 55760256 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.184G>T p.Gly62Trp p.G62W ENST00000505374 4/22 88 79 9 149 149 0 strelka-varscan-mutect DDX4,missense_variant,p.Gly62Trp,ENST00000505374,NM_024415.2;DDX4,missense_variant,p.Gly62Trp,ENST00000353507,NM_001142549.1;DDX4,missense_variant,p.Gly62Trp,ENST00000514278,NM_001166533.1;DDX4,missense_variant,p.Gly62Trp,ENST00000354991,;DDX4,missense_variant,p.Gly62Trp,ENST00000506511,;DDX4,missense_variant,p.Gly62Trp,ENST00000506848,;DDX4,missense_variant,p.Gly62Trp,ENST00000514679,;DDX4,missense_variant,p.Gly62Trp,ENST00000511491,;DDX4,intron_variant,,ENST00000515709,;DDX4,non_coding_transcript_exon_variant,,ENST00000508580,;SLC38A9,intron_variant,,ENST00000504880,;DDX4,upstream_gene_variant,,ENST00000503129,; T ENST00000505374 Transcript missense_variant 276/2884 184/2175 62/724 G/W Ggg/Tgg 1 1 DDX4 HGNC HGNC:18700 protein_coding YES CCDS3969.1 ENSP00000424838 Q9NQI0 UPI00001290D3 NM_024415.2 deleterious_low_confidence(0) 4/22 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.25907 1 1 1 1 0 T 3 4 81 55760256 55760256 G T 1 0 0 0 0 1 0 0 0 4163 1348 47 2 2 DDX4 5 55760256 Missense_Mutation SNP G C3N-01489_T 12107104 55760256 125778003 243 25173 CMYA5 0 . GRCh38 5 79736937 79736937 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.8172G>T p.= p.L2724L ENST00000446378 2/13 200 172 28 319 319 0 strelka-varscan-mutect CMYA5,synonymous_variant,p.=,ENST00000446378,NM_153610.4;CMYA5,upstream_gene_variant,,ENST00000506603,; T ENST00000446378 Transcript synonymous_variant 8203/12847 8172/12210 2724/4069 L ctG/ctT 1 1 CMYA5 HGNC HGNC:14305 protein_coding YES CCDS47238.1 ENSP00000394770 Q8N3K9 UPI00004F9478 NM_153610.4 2/13 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 79736937 79736937 G T 1 0 0 0 0 0 0 0 1 3368 1306 46 2 2 CMYA5 5 79736937 Silent SNP G C3N-01489_T 23976681 79736937 101801322 244 25174 FAM81B 0 . GRCh38 5 95450262 95450262 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1339G>T p.Val447Leu p.V447L ENST00000283357 10/10 298 252 46 445 443 2 strelka-varscan-mutect FAM81B,missense_variant,p.Val447Leu,ENST00000283357,NM_152548.2;FAM81B,missense_variant,p.Val122Leu,ENST00000512365,;FAM81B,3_prime_UTR_variant,,ENST00000507832,;FAM81B,3_prime_UTR_variant,,ENST00000513110,;FAM81B,downstream_gene_variant,,ENST00000503361,; T ENST00000283357 Transcript missense_variant 1385/1560 1339/1359 447/452 V/L Gtg/Ttg 1 1 FAM81B HGNC HGNC:26335 protein_coding YES CCDS43341.1 ENSP00000283357 Q96LP2 UPI00005A8996 NM_152548.2 deleterious(0.01) 10/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22420,hmmpanther:PTHR22420:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 95450262 95450262 G T 1 0 0 0 0 1 0 0 0 5490 1029 36 2 2 FAM81B 5 95450262 Missense_Mutation SNP G C3N-01489_T 15713325 95450262 86087997 245 25175 SEMA6A 0 . GRCh38 5 116447260 116447260 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.2497G>A p.Val833Met p.V833M ENST00000257414 20/20 201 153 48 305 305 0 strelka-varscan-mutect SEMA6A,missense_variant,p.Val816Met,ENST00000343348,NM_020796.4;SEMA6A,missense_variant,p.Val833Met,ENST00000257414,NM_001300780.1;SEMA6A,missense_variant,p.Val243Met,ENST00000513137,;SEMA6A,missense_variant,p.Val816Met,ENST00000510263,;SEMA6A,missense_variant,p.Val331Met,ENST00000515129,;SEMA6A,missense_variant,p.Val195Met,ENST00000503865,;SEMA6A-AS1,upstream_gene_variant,,ENST00000508424,;SEMA6A-AS1,upstream_gene_variant,,ENST00000514214,;SEMA6A-AS1,upstream_gene_variant,,ENST00000508640,;SEMA6A-AS1,upstream_gene_variant,,ENST00000510682,;SEMA6A-AS1,upstream_gene_variant,,ENST00000512128,;SEMA6A,downstream_gene_variant,,ENST00000506114,; T ENST00000257414 Transcript missense_variant 2746/4256 2497/3144 833/1047 V/M Gtg/Atg 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 tolerated(0.14) 20/20 hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 116447260 116447260 C T 1 0 0 0 0 1 0 0 0 14315 507 18 3 3 SEMA6A 5 116447260 Missense_Mutation SNP C C3N-01489_T 20996998 116447260 65090999 246 25176 SEMA6A 0 . GRCh38 5 116482447 116482447 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1091C>T p.Pro364Leu p.P364L ENST00000257414 11/20 111 84 27 156 156 0 strelka-varscan-mutect SEMA6A,missense_variant,p.Pro364Leu,ENST00000343348,NM_020796.4;SEMA6A,missense_variant,p.Pro364Leu,ENST00000257414,NM_001300780.1;SEMA6A,missense_variant,p.Pro364Leu,ENST00000510263,;SEMA6A,upstream_gene_variant,,ENST00000515129,;SEMA6A-AS1,intron_variant,,ENST00000514214,;SEMA6A-AS1,intron_variant,,ENST00000508640,;SEMA6A-AS1,intron_variant,,ENST00000510682,;SEMA6A,upstream_gene_variant,,ENST00000506114,;SEMA6A,downstream_gene_variant,,ENST00000502996,;SEMA6A,upstream_gene_variant,,ENST00000514316,;SEMA6A,downstream_gene_variant,,ENST00000503402,;SEMA6A,downstream_gene_variant,,ENST00000510024,; A ENST00000257414 Transcript missense_variant 1340/4256 1091/3144 364/1047 P/L cCc/cTc 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 deleterious(0.01) 11/20 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 116482447 116482447 G A 1 0 0 0 0 1 0 0 0 14315 1246 43 3 3 SEMA6A 5 116482447 Missense_Mutation SNP G C3N-01489_T 35187 116482447 65055812 247 25177 MEGF10 0 . GRCh38 5 127410480 127410480 + Missense_Mutation SNP G G T rs779799530 C3N-01489_T C3N-01489_N G G c.1009G>T p.Gly337Cys p.G337C ENST00000274473 10/26 409 328 81 537 537 0 strelka-varscan-mutect MEGF10,missense_variant,p.Gly337Cys,ENST00000274473,NM_032446.2;MEGF10,missense_variant,p.Gly337Cys,ENST00000503335,NM_001256545.1;MEGF10,missense_variant,p.Gly337Cys,ENST00000508365,NM_001308121.1;MEGF10,missense_variant,p.Gly337Cys,ENST00000418761,;MEGF10,non_coding_transcript_exon_variant,,ENST00000515002,; T ENST00000274473 Transcript missense_variant 1276/7594 1009/3423 337/1140 G/C Ggc/Tgc rs779799530 1 1 MEGF10 HGNC HGNC:29634 protein_coding YES CCDS4142.1 ENSP00000274473 Q96KG7 UPI000006F868 NM_032446.2 deleterious(0) 10/26 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,SMART_domains:SM00180,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS rs779799530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 127410480 127410480 G T 1 0 0 0 0 1 0 0 0 9400 1116 39 1 1 MEGF10 5 127410480 Missense_Mutation SNP G C3N-01489_T 10928033 127410480 54127779 248 25178 TRPC7 0 . GRCh38 5 136315747 136315747 + Missense_Mutation SNP C C A rs183133343 C3N-01489_T C3N-01489_N C C c.813G>T p.Lys271Asn p.K271N ENST00000513104 3/12 126 103 23 175 175 0 strelka-varscan-mutect TRPC7,missense_variant,p.Lys271Asn,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Lys271Asn,ENST00000502753,;TRPC7,intron_variant,,ENST00000378459,NM_001167577.1;TRPC7,intron_variant,,ENST00000352189,NM_001167576.1;TRPC7-AS2,non_coding_transcript_exon_variant,,ENST00000513958,;TRPC7,missense_variant,p.Lys271Asn,ENST00000503275,;TRPC7,intron_variant,,ENST00000514963,; A ENST00000513104 Transcript missense_variant 1096/2987 813/2589 271/862 K/N aaG/aaT rs183133343,COSM364672,COSM364673 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 deleterious(0) 3/12 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9,TIGRFAM_domain:TIGR00870 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs183133343 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 136315747 136315747 C A 1 0 0 0 0 1 0 0 0 17090 680 24 2 2 TRPC7 5 136315747 Missense_Mutation SNP C C3N-01489_T 8905267 136315747 45222512 249 25179 BRD8 0 . GRCh38 5 138145192 138145192 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.3422A>T p.Lys1141Met p.K1141M ENST00000254900 25/27 222 188 34 333 333 0 strelka-varscan-mutect BRD8,missense_variant,p.Lys1141Met,ENST00000254900,NM_139199.1;BRD8,missense_variant,p.Lys247Met,ENST00000427976,; A ENST00000254900 Transcript missense_variant 3794/4388 3422/3708 1141/1235 K/M aAg/aTg 1 -1 BRD8 HGNC HGNC:19874 protein_coding YES CCDS4198.1 ENSP00000254900 Q9H0E9 UPI0000246C01 NM_139199.1 deleterious(0.05) 25/27 PROSITE_profiles:PS50014,Gene3D:1.20.920.10,Pfam_domain:PF00439,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 138145192 138145192 T A 1 0 0 0 0 1 0 0 0 1676 1609 56 4 4 BRD8 5 138145192 Missense_Mutation SNP T C3N-01489_T 1829445 138145192 43393067 250 25180 PCDHA1 0 . GRCh38 5 140788591 140788591 + Silent SNP C C A rs781992120 C3N-01489_T C3N-01489_N C C c.2301C>A p.= p.T767T ENST00000504120 1/4 161 146 15 217 217 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,non_coding_transcript_exon_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; A ENST00000504120 Transcript synonymous_variant 2301/5263 2301/2853 767/950 T acC/acA rs781992120 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92 LOW 1 SNV 1 1 PASS rs781992120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 140788591 140788591 C A 1 0 0 0 0 0 0 0 1 11606 639 23 1 1 PCDHA1 5 140788591 Silent SNP C C3N-01489_T 2643399 140788591 40749668 251 25181 PCDHA3 0 . GRCh38 5 140802739 140802739 + Missense_Mutation SNP C C G C3N-01489_T C3N-01489_N C C c.1542C>G p.Ser514Arg p.S514R ENST00000522353 1/4 644 566 78 790 790 0 strelka-varscan-mutect PCDHA3,missense_variant,p.Ser514Arg,ENST00000522353,NM_018906.2;PCDHA3,missense_variant,p.Ser514Arg,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA4,upstream_gene_variant,,ENST00000530339,NM_018907.3;PCDHA4,upstream_gene_variant,,ENST00000512229,;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; G ENST00000522353 Transcript missense_variant 1542/5260 1542/2853 514/950 S/R agC/agG COSM1567468,COSM1567469 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 140802739 140802739 C G 1 0 0 0 0 1 0 0 0 11612 767 27 4 4 PCDHA3 5 140802739 Missense_Mutation SNP C C3N-01489_T 14148 140802739 40735520 252 25182 PCDHA7 0 . GRCh38 5 140836406 140836406 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.2023G>A p.Ala675Thr p.A675T ENST00000525929 1/4 342 272 70 496 495 1 strelka-varscan-mutect PCDHA7,missense_variant,p.Ala675Thr,ENST00000525929,NM_018910.2;PCDHA7,missense_variant,p.Ala675Thr,ENST00000356878,NM_031852.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA8,upstream_gene_variant,,ENST00000531613,NM_018911.2;PCDHA8,upstream_gene_variant,,ENST00000378123,NM_031856.1; A ENST00000525929 Transcript missense_variant 2023/5221 2023/2814 675/937 A/T Gca/Aca 1 1 PCDHA7 HGNC HGNC:8673 protein_coding YES CCDS54918.1 ENSP00000436426 Q9UN72 UPI00001273CF NM_018910.2 tolerated_low_confidence(0.21) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 140836406 140836406 G A 1 0 0 0 0 1 0 0 0 11616 1203 42 3 3 PCDHA7 5 140836406 Missense_Mutation SNP G C3N-01489_T 33667 140836406 40701853 253 25183 PCDHA13 0 . GRCh38 5 140884016 140884016 + Missense_Mutation SNP G G T rs143828814 C3N-01489_T C3N-01489_N G G c.1748G>T p.Arg583Leu p.R583L ENST00000289272 1/4 341 296 45 482 482 0 strelka-varscan-mutect PCDHA13,missense_variant,p.Arg583Leu,ENST00000289272,NM_018904.2;PCDHA13,missense_variant,p.Arg583Leu,ENST00000409494,;PCDHA13,missense_variant,p.Arg583Leu,ENST00000617769,NM_031865.1;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;AC005609.17,upstream_gene_variant,,ENST00000625195,; T ENST00000289272 Transcript missense_variant 1748/5260 1748/2853 583/950 R/L cGg/cTg rs143828814 1 1 PCDHA13 HGNC HGNC:8667 protein_coding YES CCDS4240.1 ENSP00000289272 Q9Y5I0 UPI00001273D6 NM_018904.2 tolerated_low_confidence(0.08) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs143828814 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 140884016 140884016 G T 1 0 0 0 0 1 0 0 0 11610 1116 39 1 1 PCDHA13 5 140884016 Missense_Mutation SNP G C3N-01489_T 47610 140884016 40654243 254 25184 PCDHB8 0 . GRCh38 5 141179771 141179771 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1737G>T p.= p.R579R ENST00000239444 1/1 534 441 93 723 722 1 strelka-varscan-mutect PCDHB8,synonymous_variant,p.=,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; T ENST00000239444 Transcript synonymous_variant 1982/2740 1737/2406 579/801 R cgG/cgT 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 141179771 141179771 G T 1 0 0 0 0 0 0 0 1 11635 1219 43 2 2 PCDHB8 5 141179771 Silent SNP G C3N-01489_T 295755 141179771 40358488 255 25185 PCDHB11 0 . GRCh38 5 141202099 141202099 + Silent SNP G G A C3N-01489_T C3N-01489_N G G c.2325G>A p.= p.Q775Q ENST00000354757 1/1 129 119 10 227 227 0 strelka-varscan-mutect PCDHB11,synonymous_variant,p.=,ENST00000354757,NM_018931.2;PCDHB11,synonymous_variant,p.=,ENST00000624887,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624549,; A ENST00000354757 Transcript synonymous_variant 2518/4198 2325/2394 775/797 Q caG/caA COSM5330094 1 1 PCDHB11 HGNC HGNC:8682 protein_coding YES CCDS4253.1 ENSP00000346802 Q9Y5F2 UPI00001273E6 NM_018931.2 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF91 1 LOW SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 141202099 141202099 G A 1 0 0 0 0 0 0 0 1 11623 991 35 3 3 PCDHB11 5 141202099 Silent SNP G C3N-01489_T 22328 141202099 40336160 256 25186 PCDHB15 0 . GRCh38 5 141247309 141247309 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.1731C>A p.= p.P577P ENST00000231173 1/1 344 312 32 507 505 2 varscan-mutect PCDHB15,synonymous_variant,p.=,ENST00000231173,NM_018935.3;PCDHB15,downstream_gene_variant,,ENST00000623671,;CH17-140K24.8,downstream_gene_variant,,ENST00000624396,;CH17-140K24.2,upstream_gene_variant,,ENST00000624560,;PCDHB19P,downstream_gene_variant,,ENST00000625133,; A ENST00000231173 Transcript synonymous_variant 1961/4017 1731/2364 577/787 P ccC/ccA 1 1 PCDHB15 HGNC HGNC:8686 protein_coding YES CCDS4257.1 ENSP00000231173 Q9Y5E8 UPI00001273E8 NM_018935.3 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF97,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 141247309 141247309 C A 1 0 0 0 0 0 0 0 1 11627 610 22 2 2 PCDHB15 5 141247309 Silent SNP C C3N-01489_T 45210 141247309 40290950 257 25187 PCDHGB7 0 . GRCh38 5 141419293 141419293 + Silent SNP C C T rs748856660 C3N-01489_T C3N-01489_N C C c.1434C>T p.= p.D478D ENST00000398594 1/4 210 165 45 300 300 0 strelka-varscan-mutect PCDHGB7,synonymous_variant,p.=,ENST00000398594,NM_018927.3;PCDHGB7,synonymous_variant,p.=,ENST00000612073,NM_032101.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,upstream_gene_variant,,ENST00000398587,NM_018914.2;PCDHGA10,downstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA11,upstream_gene_variant,,ENST00000622044,NM_032091.1;PCDHGA11,upstream_gene_variant,,ENST00000518882,NM_032092.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398594 Transcript synonymous_variant 1603/4765 1434/2790 478/929 D gaC/gaT rs748856660,COSM5368136 1 1 PCDHGB7 HGNC HGNC:8714 protein_coding YES CCDS47293.1 ENSP00000381594 Q9Y5F8 UPI000007141F NM_018927.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF113,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 LOW 1 SNV 1 0,1 1 PASS rs748856660 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 141419293 141419293 C T 1 0 0 0 0 0 0 0 1 11655 506 18 3 3 PCDHGB7 5 141419293 Silent SNP C C3N-01489_T 171984 141419293 40118966 258 25188 SH3TC2 0 . GRCh38 5 149047958 149047958 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.183C>A p.= p.R61R ENST00000515425 3/17 385 303 82 575 575 0 strelka-varscan-mutect SH3TC2,synonymous_variant,p.=,ENST00000515425,NM_024577.3;SH3TC2,synonymous_variant,p.=,ENST00000512049,;SH3TC2,synonymous_variant,p.=,ENST00000323829,;SH3TC2,synonymous_variant,p.=,ENST00000504690,;SH3TC2,synonymous_variant,p.=,ENST00000513604,;SH3TC2,synonymous_variant,p.=,ENST00000511307,;SH3TC2,non_coding_transcript_exon_variant,,ENST00000504091,;SH3TC2,non_coding_transcript_exon_variant,,ENST00000511949,; T ENST00000515425 Transcript synonymous_variant 285/4059 183/3867 61/1288 R cgC/cgA 1 -1 SH3TC2 HGNC HGNC:29427 protein_coding YES CCDS4293.1 ENSP00000423660 Q8TF17 UPI00001DFBEE NM_024577.3 3/17 hmmpanther:PTHR22647,hmmpanther:PTHR22647:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 149047958 149047958 G T 1 0 0 0 0 0 0 0 1 14521 958 34 2 2 SH3TC2 5 149047958 Silent SNP G C3N-01489_T 7628665 149047958 32490301 259 25189 ARHGEF37 0 . GRCh38 5 149597822 149597822 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.53G>T p.Arg18Met p.R18M ENST00000333677 2/13 100 81 19 139 138 1 strelka-varscan-mutect ARHGEF37,missense_variant,p.Arg18Met,ENST00000333677,NM_001001669.2;ARHGEF37,missense_variant,p.Arg18Met,ENST00000505810,; T ENST00000333677 Transcript missense_variant 216/4968 53/2028 18/675 R/M aGg/aTg 1 1 ARHGEF37 HGNC HGNC:34430 protein_coding YES CCDS43385.1 ENSP00000328083 A1IGU5 UPI00001D7F04 NM_001001669.2 tolerated_low_confidence(0.13) 2/13 hmmpanther:PTHR22834,Gene3D:1.20.900.10,Superfamily_domains:SSF48065 MODERATE 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 149597822 149597822 G T 1 0 0 0 0 1 0 0 0 1040 1000 35 2 2 ARHGEF37 5 149597822 Missense_Mutation SNP G C3N-01489_T 549864 149597822 31940437 260 25190 ARHGEF37 0 . GRCh38 5 149627156 149627156 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1545C>A p.Ser515Arg p.S515R ENST00000333677 11/13 140 123 17 237 236 1 strelka-varscan-mutect ARHGEF37,missense_variant,p.Ser515Arg,ENST00000333677,NM_001001669.2;ARHGEF37,non_coding_transcript_exon_variant,,ENST00000509831,; A ENST00000333677 Transcript missense_variant 1708/4968 1545/2028 515/675 S/R agC/agA 1 1 ARHGEF37 HGNC HGNC:34430 protein_coding YES CCDS43385.1 ENSP00000328083 A1IGU5 UPI00001D7F04 NM_001001669.2 deleterious(0) 11/13 hmmpanther:PTHR22834,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 149627156 149627156 C A 1 0 0 0 0 1 0 0 0 1040 709 25 2 2 ARHGEF37 5 149627156 Missense_Mutation SNP C C3N-01489_T 29334 149627156 31911103 261 25191 ZBED8 0 . GRCh38 5 160394493 160394493 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.998G>T p.Trp333Leu p.W333L ENST00000408953 2/2 275 229 46 459 459 0 strelka-varscan-mutect ZBED8,missense_variant,p.Trp333Leu,ENST00000408953,NM_022090.4;ZBED8,missense_variant,p.Trp333Leu,ENST00000523213,NM_001303251.1; A ENST00000408953 Transcript missense_variant 1506/2851 998/1785 333/594 W/L tGg/tTg 1 -1 ZBED8 HGNC HGNC:30804 protein_coding YES CCDS34283.1 ENSP00000386184 Q8IZ13 UPI00000741A3 NM_022090.4 deleterious(0) 2/2 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF102,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS rs1215029406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 160394493 160394493 C A 1 0 0 0 0 1 0 0 0 18085 595 21 2 2 ZBED8 5 160394493 Missense_Mutation SNP C C3N-01489_T 10767337 160394493 21143766 262 25192 DOCK2 0 . GRCh38 5 170050276 170050276 + Silent SNP C C A rs142465529 C3N-01489_T C3N-01489_N C C c.4092C>A p.= p.R1364R ENST00000256935 41/52 120 98 22 196 196 0 strelka-varscan-mutect DOCK2,synonymous_variant,p.=,ENST00000256935,NM_004946.2;DOCK2,synonymous_variant,p.=,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,; A ENST00000256935 Transcript synonymous_variant 4172/6097 4092/5493 1364/1830 R cgC/cgA rs142465529,COSM127833 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 41/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF06920 0,1 LOW 1 SNV 1 0,1 1 PASS rs142465529 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 170050276 170050276 C A 1 0 0 0 0 0 0 0 1 4502 755 27 1 1 DOCK2 5 170050276 Silent SNP C C3N-01489_T 9655783 170050276 11487983 263 25193 NSD1 0 . GRCh38 5 177210711 177210711 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2312G>T p.Gly771Val p.G771V ENST00000439151 5/23 335 262 73 508 507 1 strelka-varscan-mutect NSD1,missense_variant,p.Gly771Val,ENST00000439151,NM_022455.4;NSD1,missense_variant,p.Gly502Val,ENST00000354179,NM_172349.2;NSD1,missense_variant,p.Gly502Val,ENST00000347982,;NSD1,downstream_gene_variant,,ENST00000508896,;NSD1,upstream_gene_variant,,ENST00000375350,; T ENST00000439151 Transcript missense_variant 2357/12892 2312/8091 771/2696 G/V gGg/gTg 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 deleterious_low_confidence(0.02) 5/23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 177210711 177210711 G T 1 0 0 0 0 1 0 0 0 10728 1232 43 2 2 NSD1 5 177210711 Missense_Mutation SNP G C3N-01489_T 7160435 177210711 4327548 264 25194 BTNL8 0 . GRCh38 5 180948942 180948942 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.831G>T p.Gln277His p.Q277H ENST00000340184 6/8 25 21 4 71 71 0 varscan-mutect BTNL8,missense_variant,p.Gly321Cys,ENST00000231229,NM_024850.2;BTNL8,missense_variant,p.Gln277His,ENST00000340184,NM_001040462.2;BTNL8,missense_variant,p.Gly314Cys,ENST00000508408,NM_001159708.1;BTNL8,missense_variant,p.Gln93His,ENST00000533815,NM_001159710.1;BTNL8,missense_variant,p.Gln152His,ENST00000400707,NM_001159709.1;BTNL8,missense_variant,p.Gln152His,ENST00000610640,;BTNL8,missense_variant,p.Gln70His,ENST00000505126,;BTNL8,missense_variant,p.Gln161His,ENST00000511704,NM_001159707.1;BTNL8,3_prime_UTR_variant,,ENST00000503543,;BTNL8,downstream_gene_variant,,ENST00000514448,;BTNL8,downstream_gene_variant,,ENST00000513442,;RPS29P12,downstream_gene_variant,,ENST00000460178,; T ENST00000340184 Transcript missense_variant 1037/2071 831/1503 277/500 Q/H caG/caT 1 1 BTNL8 HGNC HGNC:26131 protein_coding YES CCDS43413.1 ENSP00000342197 Q6UX41 UPI00000389ED NM_001040462.2 deleterious(0.04) 6/8 PROSITE_profiles:PS50188,hmmpanther:PTHR24100:SF73,hmmpanther:PTHR24100 MODERATE 1 SNV 1 1 PASS . . 35 174 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 180948942 180948942 G T 1 0 0 0 0 1 0 0 0 1743 1014 35 2 2 BTNL8 5 180948942 Missense_Mutation SNP G C3N-01489_T 3738231 180948942 589317 265 25195 TRIM7 0 . GRCh38 5 181204690 181204690 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.421T>A p.Cys141Ser p.C141S ENST00000274773 1/7 121 102 19 151 151 0 strelka-varscan-mutect TRIM7,missense_variant,p.Cys141Ser,ENST00000274773,NM_203293.2;TRIM7,missense_variant,p.Cys141Ser,ENST00000334421,NM_033342.3;TRIM7,upstream_gene_variant,,ENST00000393315,NM_203294.1,NM_203296.1;TRIM7,upstream_gene_variant,,ENST00000393319,NM_203297.1;TRIM7,upstream_gene_variant,,ENST00000422067,NM_203295.1;CTC-338M12.6,downstream_gene_variant,,ENST00000511517,;CTC-338M12.6,downstream_gene_variant,,ENST00000514784,;CTC-338M12.6,downstream_gene_variant,,ENST00000509080,;CTC-338M12.6,downstream_gene_variant,,ENST00000502812,;CTC-338M12.6,downstream_gene_variant,,ENST00000512508,;CTC-338M12.1,downstream_gene_variant,,ENST00000503314,;CTC-338M12.6,downstream_gene_variant,,ENST00000419707,;TRIM7,upstream_gene_variant,,ENST00000509199,; T ENST00000274773 Transcript missense_variant 483/2840 421/1536 141/511 C/S Tgc/Agc 1 -1 TRIM7 HGNC HGNC:16278 protein_coding YES CCDS4462.1 ENSP00000274773 Q9C029 UPI000006D24A NM_203293.2 deleterious(0) 1/7 PROSITE_profiles:PS50119,hmmpanther:PTHR24103:SF361,hmmpanther:PTHR24103,Gene3D:1freA00,Pfam_domain:PF00643,SMART_domains:SM00336,Superfamily_domains:SSF57845,Prints_domain:PR01406 MODERATE 1 SNV 1 1 PASS rs1334651364 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 81 181204690 181204690 A T 1 0 0 0 0 1 0 0 0 17039 188 7 4 4 TRIM7 5 181204690 Missense_Mutation SNP A C3N-01489_T 255748 181204690 333569 266 25196 FAM50B 0 . GRCh38 6 3849879 3849879 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.68G>T p.Arg23Met p.R23M ENST00000380274 1/1 110 102 8 181 181 0 strelka-mutect FAM50B,missense_variant,p.Arg23Met,ENST00000380274,;FAM50B,missense_variant,p.Arg23Met,ENST00000380272,NM_012135.1;RP11-420L9.4,intron_variant,,ENST00000454396,; T ENST00000380274 Transcript missense_variant 494/1932 68/978 23/325 R/M aGg/aTg 1 1 FAM50B HGNC HGNC:18789 protein_coding YES CCDS4487.1 ENSP00000369627 Q9Y247 A0A024QZY3 UPI000003373E deleterious(0) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12722,hmmpanther:PTHR12722:SF1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 3849879 3849879 G T 1 0 0 0 0 1 0 0 0 5454 1000 35 2 2 FAM50B 6 3849879 Missense_Mutation SNP G C3N-01489_T 3849879 166956100 267 25197 F13A1 0 . GRCh38 6 6167518 6167518 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1848C>A p.= p.T616T ENST00000264870 13/15 456 355 101 620 617 3 strelka-varscan-mutect F13A1,synonymous_variant,p.=,ENST00000264870,NM_000129.3;MIR7853,downstream_gene_variant,,ENST00000584820,;MIR5683,upstream_gene_variant,,ENST00000636514,; T ENST00000264870 Transcript synonymous_variant 2114/3999 1848/2199 616/732 T acC/acA 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 13/15 Gene3D:2.60.40.10,Pfam_domain:PF00927,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF42,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 6167518 6167518 G T 1 0 0 0 0 0 0 0 1 5208 1335 47 2 2 F13A1 6 6167518 Silent SNP G C3N-01489_T 2317639 6167518 164638461 268 25198 DSP 0 . GRCh38 6 7584809 7584809 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.7547G>T p.Arg2516Met p.R2516M ENST00000379802 24/24 376 301 75 581 581 0 strelka-varscan-mutect DSP,missense_variant,p.Arg2516Met,ENST00000379802,NM_004415.2;DSP,missense_variant,p.Arg1917Met,ENST00000418664,NM_001008844.1; T ENST00000379802 Transcript missense_variant 7888/9796 7547/8616 2516/2871 R/M aGg/aTg 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 deleterious(0) 24/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,Gene3D:3.90.1290.10,SMART_domains:SM00250 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 7584809 7584809 G T 1 0 0 0 0 1 0 0 0 4602 1000 35 2 2 DSP 6 7584809 Missense_Mutation SNP G C3N-01489_T 1417291 7584809 163221170 269 25199 TXNDC5 0 . GRCh38 6 7899603 7899603 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.492G>T p.Met164Ile p.M164I ENST00000379757 3/10 144 114 30 203 202 1 strelka-varscan-mutect TXNDC5,missense_variant,p.Met164Ile,ENST00000379757,NM_030810.3;TXNDC5,missense_variant,p.Met56Ile,ENST00000473453,NM_001145549.2;BLOC1S5-TXNDC5,3_prime_UTR_variant,,ENST00000439343,;TXNDC5,non_coding_transcript_exon_variant,,ENST00000469459,; A ENST00000379757 Transcript missense_variant 530/2964 492/1299 164/432 M/I atG/atT 1 -1 TXNDC5 HGNC HGNC:21073 protein_coding YES CCDS4505.1 ENSP00000369081 Q8NBS9 UPI0000048EC3 NM_030810.3 tolerated(0.48) 3/10 Gene3D:3.40.30.10,Pfam_domain:PF00085,PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF43,Superfamily_domains:SSF52833 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 7899603 7899603 C A 1 0 0 0 0 1 0 0 0 17314 710 25 2 2 TXNDC5 6 7899603 Missense_Mutation SNP C C3N-01489_T 314794 7899603 162906376 270 25200 GMPR 0 . GRCh38 6 16250352 16250352 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.276C>G p.His92Gln p.H92Q ENST00000259727 3/9 236 196 40 369 369 0 strelka-varscan-mutect GMPR,missense_variant,p.His92Gln,ENST00000259727,NM_006877.3; G ENST00000259727 Transcript missense_variant 390/1515 276/1038 92/345 H/Q caC/caG 1 1 GMPR HGNC HGNC:4376 protein_coding YES CCDS4537.1 ENSP00000259727 P36959 UPI000012B8B2 NM_006877.3 tolerated(0.51) 3/9 Gene3D:3.20.20.70,HAMAP:MF_00596,Pfam_domain:PF00478,PIRSF_domain:PIRSF000235,hmmpanther:PTHR11911,hmmpanther:PTHR11911:SF61,SMART_domains:SM01240,Superfamily_domains:SSF51412,TIGRFAM_domain:TIGR01305 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 16250352 16250352 C G 1 0 0 0 0 1 0 0 0 6376 506 18 4 4 GMPR 6 16250352 Missense_Mutation SNP C C3N-01489_T 8350749 16250352 154555627 271 25201 ZSCAN9 0 . GRCh38 6 28227117 28227117 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.33G>T p.= p.L11L ENST00000425468 2/5 119 97 22 162 162 0 strelka-varscan ZSCAN9,synonymous_variant,p.=,ENST00000527436,;ZSCAN9,synonymous_variant,p.=,ENST00000425468,NM_001199479.1;ZSCAN9,synonymous_variant,p.=,ENST00000252207,NM_006299.4;ZSCAN9,synonymous_variant,p.=,ENST00000531979,NM_001199480.1;ZSCAN9,synonymous_variant,p.=,ENST00000527844,;ZSCAN9,synonymous_variant,p.=,ENST00000531981,;ZSCAN9,synonymous_variant,p.=,ENST00000526391,;ZSCAN9,synonymous_variant,p.=,ENST00000531941,; T ENST00000425468 Transcript synonymous_variant 198/1791 33/1338 11/445 L ctG/ctT 1 1 ZSCAN9 HGNC HGNC:12984 protein_coding YES CCDS56407.1 ENSP00000404074 O15535 UPI0000E09E19 NM_001199479.1 2/5 hmmpanther:PTHR23226:SF15,hmmpanther:PTHR23226 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 28227117 28227117 G T 1 0 0 0 0 0 0 0 1 18840 1335 47 2 2 ZSCAN9 6 28227117 Silent SNP G C3N-01489_T 11976765 28227117 142578862 272 25202 C6orf10 0 . GRCh38 6 32293212 32293212 + Missense_Mutation SNP T T A C3N-01489_T C3N-01489_N T T c.1461A>T p.Gln487His p.Q487H ENST00000447241 23/23 294 224 70 499 499 0 strelka-varscan-mutect C6orf10,missense_variant,p.Gln487His,ENST00000612031,;C6orf10,missense_variant,p.Gln486His,ENST00000375015,;C6orf10,missense_variant,p.Gln485His,ENST00000533191,NM_001286474.1;C6orf10,missense_variant,p.Gln487His,ENST00000447241,NM_006781.4;C6orf10,missense_variant,p.Gln485His,ENST00000375007,;C6orf10,missense_variant,p.Gln471His,ENST00000527965,NM_001286475.1;C6orf10,missense_variant,p.Gln482His,ENST00000617061,;C6orf10,intron_variant,,ENST00000442822,;XXbac-BPG154L12.5,intron_variant,,ENST00000611838,; A ENST00000447241 Transcript missense_variant 1634/2148 1461/1692 487/563 Q/H caA/caT COSM1496351 1 -1 C6orf10 HGNC HGNC:13922 protein_coding YES CCDS34422.1 ENSP00000415517 Q5SRN2 UPI0000470279 NM_006781.4 deleterious(0) 23/23 hmmpanther:PTHR14368 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 32293212 32293212 T A 1 0 0 0 0 1 0 0 0 2113 1606 56 4 4 C6orf10 6 32293212 Missense_Mutation SNP T C3N-01489_T 4066095 32293212 138512767 273 25203 ITPR3 0 . GRCh38 6 33679972 33679972 + Missense_Mutation SNP G G T rs537066535 C3N-01489_T C3N-01489_N G G c.4063G>T p.Gly1355Cys p.G1355C ENST00000374316 32/59 287 218 69 393 392 1 strelka-varscan-mutect ITPR3,missense_variant,p.Gly1355Cys,ENST00000374316,;ITPR3,missense_variant,p.Gly1355Cys,ENST00000605930,NM_002224.3; T ENST00000374316 Transcript missense_variant 5123/9870 4063/8016 1355/2671 G/C Ggc/Tgc rs537066535 1 1 ITPR3 HGNC HGNC:6182 protein_coding YES CCDS4783.1 ENSP00000363435 Q14573 UPI000013CB74 tolerated(0.08) 32/59 hmmpanther:PTHR13715:SF51,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS rs537066535 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 33679972 33679972 G T 1 0 0 0 0 1 0 0 0 7828 1116 39 1 1 ITPR3 6 33679972 Missense_Mutation SNP G C3N-01489_T 1386760 33679972 137126007 274 25204 GRM4 0 . GRCh38 6 34058977 34058977 + Nonsense_Mutation SNP G G A rs751686429 C3N-01489_T C3N-01489_N G G c.1024C>T p.Arg342Ter p.R342* ENST00000538487 5/11 96 86 10 137 137 0 strelka-varscan-mutect GRM4,stop_gained,p.Arg342Ter,ENST00000374181,NM_001256811.2;GRM4,stop_gained,p.Arg209Ter,ENST00000535756,NM_001256813.2;GRM4,stop_gained,p.Arg342Ter,ENST00000538487,NM_000841.3;GRM4,stop_gained,p.Arg273Ter,ENST00000374177,NM_001256809.2;GRM4,stop_gained,p.Arg209Ter,ENST00000609222,;GRM4,stop_gained,p.Arg173Ter,ENST00000544773,NM_001256812.2;GRM4,stop_gained,p.Arg202Ter,ENST00000455714,;GRM4,stop_gained,p.Arg34Ter,ENST00000609443,;GRM4,non_coding_transcript_exon_variant,,ENST00000545715,;GRM4,upstream_gene_variant,,ENST00000609915,;GRM4,3_prime_UTR_variant,,ENST00000609278,;GRM4,non_coding_transcript_exon_variant,,ENST00000609973,;GRM4,non_coding_transcript_exon_variant,,ENST00000609860,; A ENST00000538487 Transcript stop_gained 1468/4153 1024/2739 342/912 R/* Cga/Tga rs751686429,COSM4430245,COSM4430246,COSM4430247 1 -1 GRM4 HGNC HGNC:4596 protein_coding YES CCDS4787.1 ENSP00000440556 Q14833 A1L4F9 UPI000004A7DE NM_000841.3 5/11 Pfam_domain:PF01094,Prints_domain:PR00593,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF23,Superfamily_domains:SSF53822 0,1,1,1 HIGH 1 SNV 2 0,1,1,1 1 PASS rs751686429 . 0 207 2 0 0 0 0 0 -19.96355 1 1 1 1 0 A 4 1 81 34058977 34058977 G A 1 0 0 0 0 0 1 0 0 6681 1159 40 1 1 GRM4 6 34058977 Nonsense_Mutation SNP G C3N-01489_T 379005 34058977 136747002 275 25205 DNAH8 0 . GRCh38 6 38837985 38837985 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.4409C>A p.Ser1470Tyr p.S1470Y ENST00000327475 33/93 275 216 59 295 295 0 strelka-varscan-mutect DNAH8,missense_variant,p.Ser1470Tyr,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Ser1253Tyr,ENST00000359357,;DNAH8,missense_variant,p.Ser1470Tyr,ENST00000449981,; A ENST00000327475 Transcript missense_variant 4518/14360 4409/14124 1470/4707 S/Y tCt/tAt 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 33/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 38837985 38837985 C A 1 0 0 0 0 1 0 0 0 4422 913 32 2 2 DNAH8 6 38837985 Missense_Mutation SNP C C3N-01489_T 4779008 38837985 131967994 276 25206 KLC4 0 . GRCh38 6 43071864 43071864 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.1375G>C p.Glu459Gln p.E459Q ENST00000259708 11/16 118 111 7 178 178 0 strelka-varscan-mutect KLC4,missense_variant,p.Glu441Gln,ENST00000394056,NM_201522.2;KLC4,missense_variant,p.Glu459Gln,ENST00000259708,NM_201523.2;KLC4,missense_variant,p.Glu441Gln,ENST00000479388,NM_001289034.1;KLC4,missense_variant,p.Glu441Gln,ENST00000347162,NM_201521.2;KLC4,missense_variant,p.Glu364Gln,ENST00000453940,NM_001289035.1;PTK7,upstream_gene_variant,,ENST00000230419,NM_002821.4;PTK7,upstream_gene_variant,,ENST00000345201,NM_152880.3;PTK7,upstream_gene_variant,,ENST00000352931,NM_152882.3;PTK7,upstream_gene_variant,,ENST00000349241,NM_152881.3;PTK7,upstream_gene_variant,,ENST00000481273,NM_001270398.1;PTK7,upstream_gene_variant,,ENST00000471863,;KLC4,downstream_gene_variant,,ENST00000458460,NM_138343.3;PTK7,upstream_gene_variant,,ENST00000476760,;KLC4,downstream_gene_variant,,ENST00000470728,;RP11-387M24.5,downstream_gene_variant,,ENST00000606123,;KLC4,3_prime_UTR_variant,,ENST00000467906,;KLC4,non_coding_transcript_exon_variant,,ENST00000463063,;KLC4,intron_variant,,ENST00000469987,;PTK7,upstream_gene_variant,,ENST00000487673,;PTK7,upstream_gene_variant,,ENST00000470019,;PTK7,upstream_gene_variant,,ENST00000230418,;KLC4,upstream_gene_variant,,ENST00000486439,;KLC4,upstream_gene_variant,,ENST00000463168,; C ENST00000259708 Transcript missense_variant 1728/2688 1375/1914 459/637 E/Q Gag/Cag 1 1 KLC4 HGNC HGNC:21624 protein_coding YES CCDS4882.1 ENSP00000259708 Q9NSK0 UPI000023C3DA NM_201523.2 tolerated(0.17) 11/16 hmmpanther:PTHR19959:SF139,hmmpanther:PTHR19959 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 43071864 43071864 G C 1 0 0 0 0 1 0 0 0 8201 1291 45 4 4 KLC4 6 43071864 Missense_Mutation SNP G C3N-01489_T 4233879 43071864 127734115 277 25207 VEGFA 0 . GRCh38 6 43784545 43784545 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1222G>T p.Asp408Tyr p.D408Y ENST00000611736 8/8 528 429 99 679 679 0 strelka-varscan-mutect VEGFA,stop_lost,p.Ter355LeuextTer?,ENST00000417285,NM_001025369.2;VEGFA,stop_lost,p.Ter175LeuextTer?,ENST00000523125,NM_001171627.1;VEGFA,missense_variant,p.Asp408Tyr,ENST00000611736,NM_001025366.2;VEGFA,missense_variant,p.Asp367Tyr,ENST00000621747,NM_001317010.1,NM_001025368.2;VEGFA,missense_variant,p.Asp367Tyr,ENST00000372067,;VEGFA,missense_variant,p.Asp323Tyr,ENST00000615393,NM_001025370.2;VEGFA,missense_variant,p.Asp313Tyr,ENST00000617771,NM_001171622.1;VEGFA,missense_variant,p.Asp323Tyr,ENST00000372064,;VEGFA,missense_variant,p.Asp143Tyr,ENST00000372077,NM_001171628.1;VEGFA,missense_variant,p.Asp391Tyr,ENST00000425836,NM_003376.5;VEGFA,missense_variant,p.Asp408Tyr,ENST00000372055,;VEGFA,missense_variant,p.Asp211Tyr,ENST00000520948,NM_001171624.1;VEGFA,missense_variant,p.Asp385Tyr,ENST00000413642,NM_001025367.2;VEGFA,missense_variant,p.Asp159Tyr,ENST00000230480,NM_001287044.1;VEGFA,missense_variant,p.Asp319Tyr,ENST00000519767,NM_001204384.1,NM_001204385.1;VEGFA,missense_variant,p.Asp313Tyr,ENST00000324450,;VEGFA,missense_variant,p.Asp187Tyr,ENST00000523950,NM_001171626.1;VEGFA,missense_variant,p.Asp228Tyr,ENST00000523873,NM_001171623.1;VEGFA,missense_variant,p.Asp205Tyr,ENST00000518689,NM_001171625.1;VEGFA,missense_variant,p.Asp133Tyr,ENST00000457104,NM_001171630.1;VEGFA,missense_variant,p.Asp107Tyr,ENST00000520265,;VEGFA,intron_variant,,ENST00000482630,NM_001033756.2;VEGFA,intron_variant,,ENST00000518824,NM_001171629.1;VEGFA,non_coding_transcript_exon_variant,,ENST00000480614,;VEGFA,non_coding_transcript_exon_variant,,ENST00000497139,;VEGFA,non_coding_transcript_exon_variant,,ENST00000493786,; T ENST00000611736 Transcript missense_variant 1720/3659 1222/1239 408/412 D/Y Gac/Tac 1 1 VEGFA HGNC HGNC:12680 protein_coding YES CCDS34457.1 ENSP00000478570 J3KPA4 UPI0000D61463 NM_001025366.2 deleterious(0) 8/8 hmmpanther:PTHR12025:SF5,hmmpanther:PTHR12025,Pfam_domain:PF14554,Gene3D:1kmxA00,Superfamily_domains:0044742 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 43784545 43784545 G T 1 0 0 0 0 1 0 0 0 17695 1304 45 2 2 VEGFA 6 43784545 Missense_Mutation SNP G C3N-01489_T 712681 43784545 127021434 278 25208 RHAG 0 . GRCh38 6 49612444 49612444 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.898G>C p.Gly300Arg p.G300R ENST00000371175 6/10 401 362 39 537 537 0 strelka-varscan-mutect RHAG,missense_variant,p.Gly300Arg,ENST00000371175,NM_000324.2;RHAG,missense_variant,p.Gly300Arg,ENST00000229810,;RHAG,missense_variant,p.Gly300Arg,ENST00000618248,; G ENST00000371175 Transcript missense_variant 925/1912 898/1230 300/409 G/R Ggg/Cgg 1 -1 RHAG HGNC HGNC:10006 protein_coding YES CCDS4927.1 ENSP00000360217 Q02094 UPI000006D18F NM_000324.2 deleterious(0) 6/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11730:SF32,hmmpanther:PTHR11730,Pfam_domain:PF00909,Gene3D:1.10.3430.10,Superfamily_domains:0044218,Prints_domain:PR00342 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 49612444 49612444 C G 1 0 0 0 0 1 0 0 0 13487 594 21 4 4 RHAG 6 49612444 Missense_Mutation SNP C C3N-01489_T 5827899 49612444 121193535 279 25209 PKHD1 0 . GRCh38 6 51934122 51934122 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.6109C>T p.Leu2037Phe p.L2037F ENST00000371117 37/67 430 376 54 623 623 0 strelka-varscan-mutect PKHD1,missense_variant,p.Leu2037Phe,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Leu2037Phe,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 6385/16282 6109/12225 2037/4074 L/F Ctt/Ttt 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.02) 37/67 PROSITE_profiles:PS51484,Pfam_domain:PF10162,SMART_domains:SM01225 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 51934122 51934122 G A 1 0 0 0 0 1 0 0 0 12067 942 33 3 3 PKHD1 6 51934122 Missense_Mutation SNP G C3N-01489_T 2321678 51934122 118871857 280 25210 DST 0 . GRCh38 6 56471209 56471209 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.15447G>T p.Met5149Ile p.M5149I ENST00000312431 87/95 173 153 20 252 252 0 strelka-varscan-mutect DST,missense_variant,p.Met7086Ile,ENST00000361203,;DST,missense_variant,p.Met5109Ile,ENST00000421834,NM_183380.3;DST,missense_variant,p.Met5149Ile,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Met5000Ile,ENST00000370788,;DST,missense_variant,p.Met4783Ile,ENST00000244364,NM_015548.4;DST,upstream_gene_variant,,ENST00000523292,;DST,downstream_gene_variant,,ENST00000523943,;DST,upstream_gene_variant,,ENST00000523597,;DST,upstream_gene_variant,,ENST00000482156,;DST,downstream_gene_variant,,ENST00000517840,;DST,downstream_gene_variant,,ENST00000492944,; A ENST00000312431 Transcript missense_variant 15573/17756 15447/16614 5149/5537 M/I atG/atT 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 deleterious(0) 87/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 56471209 56471209 C A 1 0 0 0 0 1 0 0 0 4604 826 29 2 2 DST 6 56471209 Missense_Mutation SNP C C3N-01489_T 4537087 56471209 114334770 281 25211 DST 0 . GRCh38 6 56634861 56634861 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.2766T>A p.= p.S922S ENST00000312431 22/95 268 237 31 393 393 0 strelka-varscan-mutect DST,synonymous_variant,p.=,ENST00000361203,;DST,synonymous_variant,p.=,ENST00000421834,NM_183380.3;DST,synonymous_variant,p.=,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,synonymous_variant,p.=,ENST00000370788,;DST,synonymous_variant,p.=,ENST00000244364,NM_015548.4;DST,synonymous_variant,p.=,ENST00000439203,;DST,synonymous_variant,p.=,ENST00000370765,NM_001723.5;DST,synonymous_variant,p.=,ENST00000520645,;DST,synonymous_variant,p.=,ENST00000518935,;DST,downstream_gene_variant,,ENST00000521104,;DST,downstream_gene_variant,,ENST00000523967,; T ENST00000312431 Transcript synonymous_variant 2892/17756 2766/16614 922/5537 S tcT/tcA 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 22/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Superfamily_domains:SSF46966 LOW 1 SNV 5 1 PASS rs928254579 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 56634861 56634861 A T 1 0 0 0 0 0 0 0 1 4604 175 7 4 4 DST 6 56634861 Silent SNP A C3N-01489_T 163652 56634861 114171118 282 25212 KHDC1L 0 . GRCh38 6 73224335 73224335 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.126G>T p.= p.T42T ENST00000370388 2/3 61 52 9 83 82 1 strelka-varscan KHDC1L,synonymous_variant,p.=,ENST00000370388,NM_001126063.2;KHDC1L,non_coding_transcript_exon_variant,,ENST00000471312,;RP11-257K9.8,missense_variant,p.Arg145Leu,ENST00000423730,; A ENST00000370388 Transcript synonymous_variant 170/635 126/387 42/128 T acG/acT 1 -1 KHDC1L HGNC HGNC:37274 protein_coding YES CCDS47450.1 ENSP00000359415 Q5JSQ8 UPI0000070CED NM_001126063.2 2/3 Pfam_domain:PF16005,hmmpanther:PTHR31368,hmmpanther:PTHR31368:SF5 LOW 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -19.78652 0.9998407 1 1 1 0 A 2 1 81 73224335 73224335 C A 1 0 0 0 0 0 0 0 1 8065 523 19 1 1 KHDC1L 6 73224335 Silent SNP C C3N-01489_T 16589474 73224335 97581644 283 25213 PHIP 0 . GRCh38 6 78997599 78997599 + Splice_Site SNP T T C novel C3N-01489_T C3N-01489_N T T c.2018-2A>G p.X673_splice ENST00000275034 86 71 15 130 130 0 strelka-varscan PHIP,splice_acceptor_variant,,ENST00000275034,NM_017934.5; C ENST00000275034 Transcript splice_acceptor_variant -/10460 2018/5466 673/1821 1 -1 PHIP HGNC HGNC:15673 protein_coding YES CCDS4987.1 ENSP00000275034 Q8WWQ0 UPI000013DA40 NM_017934.5 18/39 HIGH 1 SNV 1 1 PASS . . 0 194 13 3 0 0 0 0 -20 0.9957545 1 1 1 0 C 5 2 81 78997599 78997599 T C 1 0 0 0 0 0 0 1 0 11930 1536 53 5 5 PHIP 6 78997599 Splice_Site SNP T C3N-01489_T 5773264 78997599 91808380 284 25214 MDN1 0 . GRCh38 6 89794795 89794795 + Silent SNP G G A C3N-01489_T C3N-01489_N G G c.336C>T p.= p.A112A ENST00000369393 3/102 119 104 15 185 185 0 strelka-varscan-mutect MDN1,synonymous_variant,p.=,ENST00000369393,NM_014611.2;MDN1,synonymous_variant,p.=,ENST00000629399,;MDN1,synonymous_variant,p.=,ENST00000439638,;DNAJC19P6,upstream_gene_variant,,ENST00000401853,; A ENST00000369393 Transcript synonymous_variant 452/18413 336/16791 112/5596 A gcC/gcT COSM1622033 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 3/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 89794795 89794795 G A 1 0 0 0 0 0 0 0 1 9353 1219 43 3 3 MDN1 6 89794795 Silent SNP G C3N-01489_T 10797196 89794795 81011184 285 25215 GPR63 0 . GRCh38 6 96799581 96799581 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.151A>T p.Met51Leu p.M51L ENST00000229955 2/2 187 163 24 340 339 1 strelka-varscan-mutect GPR63,missense_variant,p.Met51Leu,ENST00000229955,NM_030784.3,NM_001143957.2;RP3-417O22.3,downstream_gene_variant,,ENST00000442184,; A ENST00000229955 Transcript missense_variant 497/5952 151/1260 51/419 M/L Atg/Ttg 1 -1 GPR63 HGNC HGNC:13302 protein_coding YES CCDS5036.1 ENSP00000229955 Q9BZJ6 A8K1C4 UPI0000037594 NM_030784.3,NM_001143957.2 tolerated_low_confidence(0.81) 2/2 hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF1 MODERATE 1 SNV 1 1 PASS rs1214668880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 96799581 96799581 T A 1 0 0 0 0 1 0 0 0 6588 1464 51 4 4 GPR63 6 96799581 Missense_Mutation SNP T C3N-01489_T 7004786 96799581 74006398 286 25216 GJA1 0 . GRCh38 6 121447764 121447764 + Missense_Mutation SNP G G A C3N-01489_T C3N-01489_N G G c.917G>A p.Ser306Asn p.S306N ENST00000282561 2/2 324 284 40 551 551 0 strelka-varscan-mutect GJA1,missense_variant,p.Ser306Asn,ENST00000282561,NM_000165.4; A ENST00000282561 Transcript missense_variant 1074/3037 917/1149 306/382 S/N aGt/aAt COSM5300405 1 1 GJA1 HGNC HGNC:4274 protein_coding YES CCDS5123.1 ENSP00000282561 P17302 UPI000013DCEC NM_000165.4 tolerated(0.4) 2/2 hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF33,Pfam_domain:PF03508,Superfamily_domains:0049114,Prints_domain:PR01132 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 121447764 121447764 G A 1 0 0 0 0 1 0 0 0 6280 1029 36 3 3 GJA1 6 121447764 Missense_Mutation SNP G C3N-01489_T 24648183 121447764 49358215 287 25217 TAAR2 0 . GRCh38 6 132617653 132617653 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.553G>T p.Ala185Ser p.A185S ENST00000367931 2/2 160 137 23 273 273 0 strelka-varscan TAAR2,missense_variant,p.Ala140Ser,ENST00000275191,NM_014626.3;TAAR2,missense_variant,p.Ala185Ser,ENST00000367931,NM_001033080.1; A ENST00000367931 Transcript missense_variant 553/1056 553/1056 185/351 A/S Gca/Tca 1 -1 TAAR2 HGNC HGNC:4514 protein_coding YES CCDS34541.1 ENSP00000356908 Q9P1P5 UPI000048F3E6 NM_001033080.1 tolerated(0.41) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF30,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 132617653 132617653 C A 1 0 0 0 0 1 0 0 0 15886 710 25 2 2 TAAR2 6 132617653 Missense_Mutation SNP C C3N-01489_T 11169889 132617653 38188326 288 25218 FBXO30 0 . GRCh38 6 145806278 145806278 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.128C>T p.Ser43Phe p.S43F ENST00000237281 2/3 192 167 25 307 307 0 strelka-varscan FBXO30,missense_variant,p.Ser43Phe,ENST00000237281,NM_032145.4;RP11-545I5.3,intron_variant,,ENST00000629681,; A ENST00000237281 Transcript missense_variant 295/9009 128/2238 43/745 S/F tCt/tTt 1 -1 FBXO30 HGNC HGNC:15600 protein_coding YES CCDS5208.1 ENSP00000237281 Q8TB52 UPI0000071E84 NM_032145.4 deleterious(0.03) 2/3 Pfam_domain:PF15965,hmmpanther:PTHR15933,hmmpanther:PTHR15933:SF13,Superfamily_domains:SSF49599 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 145806278 145806278 G A 1 0 0 0 0 1 0 0 0 5603 942 33 3 3 FBXO30 6 145806278 Missense_Mutation SNP G C3N-01489_T 13188625 145806278 24999701 289 25219 EIF3B 0 . GRCh38 7 2379172 2379172 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.2271C>T p.= p.F757F ENST00000360876 17/19 173 118 55 215 215 0 strelka-varscan-mutect EIF3B,synonymous_variant,p.=,ENST00000360876,NM_001037283.1;EIF3B,synonymous_variant,p.=,ENST00000397011,NM_003751.3;AC004840.8,upstream_gene_variant,,ENST00000443103,;EIF3B,non_coding_transcript_exon_variant,,ENST00000475415,;EIF3B,non_coding_transcript_exon_variant,,ENST00000465670,;EIF3B,non_coding_transcript_exon_variant,,ENST00000468611,;EIF3B,non_coding_transcript_exon_variant,,ENST00000494658,;AC004840.8,upstream_gene_variant,,ENST00000636359,; T ENST00000360876 Transcript synonymous_variant 2327/3055 2271/2445 757/814 F ttC/ttT 1 1 EIF3B HGNC HGNC:3280 protein_coding YES CCDS5332.1 ENSP00000354125 P55884 A0A024R821 UPI000013F934 NM_001037283.1 17/19 HAMAP:MF_03001,hmmpanther:PTHR14068:SF0,hmmpanther:PTHR14068,PIRSF_domain:PIRSF036424 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 2379172 2379172 C T 1 0 0 0 0 0 0 0 1 4847 854 30 3 3 EIF3B 7 2379172 Silent SNP C C3N-01489_T 2379172 156966801 290 25220 MMD2 0 . GRCh38 7 4907582 4907582 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.627C>G p.Ile209Met p.I209M ENST00000404774 7/7 232 177 55 295 295 0 strelka-varscan-mutect MMD2,missense_variant,p.Ile209Met,ENST00000404774,NM_001100600.1;MMD2,missense_variant,p.Ile185Met,ENST00000401401,NM_198403.3;MMD2,3_prime_UTR_variant,,ENST00000406755,NM_001270375.1;MMD2,downstream_gene_variant,,ENST00000612910,; C ENST00000404774 Transcript missense_variant 822/2415 627/813 209/270 I/M atC/atG 1 -1 MMD2 HGNC HGNC:30133 protein_coding YES CCDS47529.1 ENSP00000384690 Q8IY49 UPI000016199F NM_001100600.1 tolerated(0.25) 7/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR20855:SF21,hmmpanther:PTHR20855,Pfam_domain:PF03006 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 4907582 4907582 G C 1 0 0 0 0 1 0 0 0 9607 932 33 4 4 MMD2 7 4907582 Missense_Mutation SNP G C3N-01489_T 2528410 4907582 154438391 291 25221 COL28A1 0 . GRCh38 7 7456087 7456087 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.1328A>G p.Gln443Arg p.Q443R ENST00000399429 16/35 224 210 14 277 277 0 strelka-varscan-mutect COL28A1,missense_variant,p.Gln443Arg,ENST00000399429,NM_001037763.2;COL28A1,3_prime_UTR_variant,,ENST00000444268,; C ENST00000399429 Transcript missense_variant 1469/4277 1328/3378 443/1125 Q/R cAa/cGa 1 -1 COL28A1 HGNC HGNC:22442 protein_coding YES CCDS43553.1 ENSP00000382356 Q2UY09 UPI000155D64E NM_001037763.2 tolerated(0.78) 16/35 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF578 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 7456087 7456087 T C 1 0 0 0 0 1 0 0 0 3475 1812 63 5 5 COL28A1 7 7456087 Missense_Mutation SNP T C3N-01489_T 2548505 7456087 151889886 292 25222 ICA1 0 . GRCh38 7 8218392 8218392 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.492G>T p.= p.T164T ENST00000402384 6/14 432 396 36 563 563 0 strelka-varscan-mutect ICA1,synonymous_variant,p.=,ENST00000402384,NM_001136020.2;ICA1,synonymous_variant,p.=,ENST00000406470,NM_004968.3;ICA1,synonymous_variant,p.=,ENST00000265577,NM_001276478.1;ICA1,synonymous_variant,p.=,ENST00000396675,NM_022307.2;ICA1,synonymous_variant,p.=,ENST00000401396,;ICA1,synonymous_variant,p.=,ENST00000407906,;ICA1,synonymous_variant,p.=,ENST00000422063,;ICA1,synonymous_variant,p.=,ENST00000317367,;ICA1,downstream_gene_variant,,ENST00000447326,;ICA1,downstream_gene_variant,,ENST00000430867,;ICA1,intron_variant,,ENST00000486677,;ICA1,downstream_gene_variant,,ENST00000476942,;ICA1,synonymous_variant,p.=,ENST00000339809,;ICA1,3_prime_UTR_variant,,ENST00000455539,;ICA1,non_coding_transcript_exon_variant,,ENST00000490041,;ICA1,downstream_gene_variant,,ENST00000457755,; A ENST00000402384 Transcript synonymous_variant 759/2458 492/1452 164/483 T acG/acT 1 -1 ICA1 HGNC HGNC:5343 protein_coding YES CCDS34602.1 ENSP00000385570 Q05084 A0A024RA29 UPI000012D139 NM_001136020.2 6/14 Gene3D:1.20.1270.60,Pfam_domain:PF06456,PROSITE_profiles:PS50870,hmmpanther:PTHR10164,hmmpanther:PTHR10164:SF3,SMART_domains:SM01015,Superfamily_domains:SSF103657 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 8218392 8218392 C A 1 0 0 0 0 0 0 0 1 7377 639 23 1 1 ICA1 7 8218392 Silent SNP C C3N-01489_T 762305 8218392 151127581 293 25223 HDAC9 0 . GRCh38 7 18835991 18835991 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.2678C>G p.Ala893Gly p.A893G ENST00000441542 20/25 132 118 14 157 157 0 strelka-varscan HDAC9,missense_variant,p.Ala890Gly,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Ala849Gly,ENST00000401921,;HDAC9,missense_variant,p.Ala893Gly,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Ala890Gly,ENST00000432645,NM_058176.2;HDAC9,non_coding_transcript_exon_variant,,ENST00000483142,;HDAC9,non_coding_transcript_exon_variant,,ENST00000490851,;HDAC9,downstream_gene_variant,,ENST00000523867,; G ENST00000441542 Transcript missense_variant 2678/3210 2678/3210 893/1069 A/G gCa/gGa 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0) 20/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,Gene3D:3.40.800.20,Pfam_domain:PF00850,PIRSF_domain:PIRSF037911,Superfamily_domains:SSF52768 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 18835991 18835991 C G 1 0 0 0 0 1 0 0 0 6901 710 25 4 4 HDAC9 7 18835991 Missense_Mutation SNP C C3N-01489_T 10617599 18835991 140509982 294 25224 HOXA7 0 . GRCh38 7 27156195 27156195 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.351C>A p.Phe117Leu p.F117L ENST00000242159 1/2 74 58 16 80 80 0 strelka-varscan HOXA7,missense_variant,p.Phe117Leu,ENST00000242159,NM_006896.3;HOXA7,downstream_gene_variant,,ENST00000519842,;HOXA-AS3,downstream_gene_variant,,ENST00000518947,;HOXA-AS3,downstream_gene_variant,,ENST00000524304,;HOXA-AS3,downstream_gene_variant,,ENST00000521197,;RP1-170O19.24,upstream_gene_variant,,ENST00000602610,;HOXA-AS3,downstream_gene_variant,,ENST00000521231,;HOXA-AS3,downstream_gene_variant,,ENST00000518848,;RP1-170O19.22,upstream_gene_variant,,ENST00000467897,;HOXA3,upstream_gene_variant,,ENST00000518451,;HOXA7,upstream_gene_variant,,ENST00000523796,;RP1-170O19.23,upstream_gene_variant,,ENST00000498652,; T ENST00000242159 Transcript missense_variant 483/2018 351/693 117/230 F/L ttC/ttA 1 -1 HOXA7 HGNC HGNC:5108 protein_coding YES CCDS5408.1 ENSP00000242159 P31268 UPI000013CAF3 NM_006896.3 tolerated(0.44) 1/2 hmmpanther:PTHR24326:SF293,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 27156195 27156195 G T 1 0 0 0 0 1 0 0 0 7191 1165 41 2 2 HOXA7 7 27156195 Missense_Mutation SNP G C3N-01489_T 8320204 27156195 132189778 295 25225 BMPER 0 . GRCh38 7 34085904 34085904 + Silent SNP G G T rs868718269 C3N-01489_T C3N-01489_N G G c.1557G>T p.= p.V519V ENST00000297161 14/16 337 266 71 501 500 1 strelka-varscan BMPER,synonymous_variant,p.=,ENST00000297161,NM_133468.4;BMPER,non_coding_transcript_exon_variant,,ENST00000476525,; T ENST00000297161 Transcript synonymous_variant 1931/5031 1557/2058 519/685 V gtG/gtT rs868718269,COSM3638240 1 1 BMPER HGNC HGNC:24154 protein_coding YES CCDS5442.1 ENSP00000297161 Q8N8U9 A0A090N7U6 UPI000006D462 NM_133468.4 14/16 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF272 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 34085904 34085904 G T 1 0 0 0 0 0 0 0 1 1623 1335 47 2 2 BMPER 7 34085904 Silent SNP G C3N-01489_T 6929709 34085904 125260069 296 25226 AOAH 0 . GRCh38 7 36618336 36618336 + Missense_Mutation SNP G G A rs756559735 C3N-01489_T C3N-01489_N G G c.712C>T p.Pro238Ser p.P238S ENST00000617267 10/22 122 107 15 170 170 0 strelka-varscan AOAH,missense_variant,p.Pro238Ser,ENST00000617267,NM_001177506.1;AOAH,missense_variant,p.Pro238Ser,ENST00000617537,NM_001637.3;AOAH,missense_variant,p.Pro206Ser,ENST00000612871,NM_001177507.1;AOAH,downstream_gene_variant,,ENST00000543742,; A ENST00000617267 Transcript missense_variant 1013/2398 712/2067 238/688 P/S Cca/Tca rs756559735,COSM3638472 1 -1 AOAH HGNC HGNC:548 protein_coding YES CCDS75584.1 ENSP00000479664 A0A087WVT3 UPI0001D043BB NM_001177506.1 tolerated(0.08) 10/22 hmmpanther:PTHR15010 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 36618336 36618336 G A 1 0 0 0 0 1 0 0 0 835 1174 41 3 3 AOAH 7 36618336 Missense_Mutation SNP G C3N-01489_T 2532432 36618336 122727637 297 25227 MYL7 0 . GRCh38 7 44140420 44140420 + Silent SNP C C G novel C3N-01489_T C3N-01489_N C C c.201G>C p.= p.V67V ENST00000223364 4/7 124 114 10 172 172 0 strelka-varscan MYL7,synonymous_variant,p.=,ENST00000458240,;MYL7,synonymous_variant,p.=,ENST00000457314,;MYL7,synonymous_variant,p.=,ENST00000223364,NM_021223.2;MYL7,synonymous_variant,p.=,ENST00000447951,;MYL7,synonymous_variant,p.=,ENST00000431007,;GCK,downstream_gene_variant,,ENST00000403799,NM_000162.3;GCK,downstream_gene_variant,,ENST00000395796,NM_033508.1;GCK,downstream_gene_variant,,ENST00000345378,NM_033507.1;GCK,downstream_gene_variant,,ENST00000616242,;GCK,downstream_gene_variant,,ENST00000437084,;GCK,downstream_gene_variant,,ENST00000336642,;MYL7,upstream_gene_variant,,ENST00000446581,;MYL7,non_coding_transcript_exon_variant,,ENST00000434895,;MYL7,stop_lost,p.Ter39SerextTer41,ENST00000431289,;MYL7,non_coding_transcript_exon_variant,,ENST00000476118,;GCK,downstream_gene_variant,,ENST00000459642,;MYL7,downstream_gene_variant,,ENST00000457910,; G ENST00000223364 Transcript synonymous_variant 228/612 201/528 67/175 V gtG/gtC 1 -1 MYL7 HGNC HGNC:21719 protein_coding YES CCDS5478.1 ENSP00000223364 Q01449 UPI000006FF43 NM_021223.2 4/7 PROSITE_profiles:PS50222,hmmpanther:PTHR23049,hmmpanther:PTHR23049:SF39,Pfam_domain:PF13499,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -14.64087 0.9999997 1 1 1 0 G 2 3 81 44140420 44140420 C G 1 0 0 0 0 0 0 0 1 10053 813 29 4 4 MYL7 7 44140420 Silent SNP C C3N-01489_T 7522084 44140420 115205553 298 25228 DDX56 0 . GRCh38 7 44570840 44570840 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.928G>T p.Asp310Tyr p.D310Y ENST00000258772 7/14 164 141 23 169 167 2 strelka-varscan DDX56,missense_variant,p.Asp310Tyr,ENST00000258772,NM_019082.3;DDX56,intron_variant,,ENST00000431640,NM_001257189.1;DDX56,upstream_gene_variant,,ENST00000448192,;DDX56,non_coding_transcript_exon_variant,,ENST00000485367,;DDX56,non_coding_transcript_exon_variant,,ENST00000467318,;DDX56,upstream_gene_variant,,ENST00000479602,;DDX56,missense_variant,p.Asp310Tyr,ENST00000421223,;DDX56,missense_variant,p.Asp264Tyr,ENST00000433257,;DDX56,3_prime_UTR_variant,,ENST00000446987,;DDX56,3_prime_UTR_variant,,ENST00000415758,;DDX56,downstream_gene_variant,,ENST00000479440,;DDX56,upstream_gene_variant,,ENST00000473924,; A ENST00000258772 Transcript missense_variant 1035/2336 928/1644 310/547 D/Y Gac/Tac 1 -1 DDX56 HGNC HGNC:18193 protein_coding YES CCDS5492.1 ENSP00000258772 Q9NY93 UPI0000037BB1 NM_019082.3 deleterious(0) 7/14 Gene3D:3.40.50.300,Pfam_domain:PF00271,PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF96,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 81 44570840 44570840 C A 1 0 0 0 0 1 0 0 0 4177 884 31 1 1 DDX56 7 44570840 Missense_Mutation SNP C C3N-01489_T 430420 44570840 114775133 299 25229 ABCA13 0 . GRCh38 7 48524402 48524402 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.14206G>T p.Ala4736Ser p.A4736S ENST00000435803 54/62 207 190 17 277 277 0 strelka-varscan ABCA13,missense_variant,p.Ala4736Ser,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Ala2044Ser,ENST00000544596,;ABCA13,missense_variant,p.Ala509Ser,ENST00000411975,;ABCA13,downstream_gene_variant,,ENST00000435451,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,missense_variant,p.Ala1002Ser,ENST00000453246,; T ENST00000435803 Transcript missense_variant 14230/17184 14206/15177 4736/5058 A/S Gct/Tct 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 deleterious(0.04) 54/62 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 48524402 48524402 G T 1 0 0 0 0 1 0 0 0 35 1319 46 2 2 ABCA13 7 48524402 Missense_Mutation SNP G C3N-01489_T 3953562 48524402 110821571 300 25230 IKZF1 0 . GRCh38 7 50387392 50387392 + Silent SNP C C A C3N-01489_T C3N-01489_N C C c.637C>A p.= p.R213R ENST00000331340 6/8 183 170 13 250 250 0 strelka-varscan IKZF1,synonymous_variant,p.=,ENST00000331340,NM_006060.5;IKZF1,synonymous_variant,p.=,ENST00000343574,NM_001291839.1,NM_001220767.2,NM_001291841.1;IKZF1,synonymous_variant,p.=,ENST00000615491,;IKZF1,synonymous_variant,p.=,ENST00000438033,NM_001291838.1;IKZF1,intron_variant,,ENST00000357364,NM_001220768.2;IKZF1,intron_variant,,ENST00000349824,NM_001220771.2;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000439701,NM_001291837.1;IKZF1,intron_variant,,ENST00000359197,NM_001220765.2;IKZF1,intron_variant,,ENST00000612658,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,non_coding_transcript_exon_variant,,ENST00000471793,; A ENST00000331340 Transcript synonymous_variant 792/6189 637/1560 213/519 R Cga/Aga COSM1210465 1 1 IKZF1 HGNC HGNC:13176 protein_coding YES CCDS75596.1 ENSP00000331614 Q13422 UPI000012D465 NM_006060.5 6/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF36,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 50387392 50387392 C A 1 0 0 0 0 0 0 0 1 7522 760 27 1 1 IKZF1 7 50387392 Silent SNP C C3N-01489_T 1862990 50387392 108958581 301 25231 POM121L12 0 . GRCh38 7 53035886 53035886 + Missense_Mutation SNP T T G novel C3N-01489_T C3N-01489_N T T c.215T>G p.Val72Gly p.V72G ENST00000408890 1/1 172 141 31 217 217 0 strelka-varscan POM121L12,missense_variant,p.Val72Gly,ENST00000408890,NM_182595.3; G ENST00000408890 Transcript missense_variant 245/1283 215/891 72/296 V/G gTg/gGg 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.21) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 53035886 53035886 T G 1 0 0 0 0 1 0 0 0 12352 1696 59 5 5 POM121L12 7 53035886 Missense_Mutation SNP T C3N-01489_T 2648494 53035886 106310087 302 25232 POM121L12 0 . GRCh38 7 53036228 53036228 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.557C>G p.Pro186Arg p.P186R ENST00000408890 1/1 236 184 52 327 327 0 strelka-varscan POM121L12,missense_variant,p.Pro186Arg,ENST00000408890,NM_182595.3; G ENST00000408890 Transcript missense_variant 587/1283 557/891 186/296 P/R cCc/cGc 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.82) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 53036228 53036228 C G 1 0 0 0 0 1 0 0 0 12352 623 22 4 4 POM121L12 7 53036228 Missense_Mutation SNP C C3N-01489_T 342 53036228 106309745 303 25233 GBAS 0 . GRCh38 7 55984866 55984866 + Frame_Shift_Del DEL G G - novel C3N-01489_T C3N-01489_N G G c.608delG p.Gly203AlafsTer75 p.G203Afs*75 ENST00000322090 7/10 145 135 10 222 222 0 varindel-pindel GBAS,frameshift_variant,p.Gly203AlafsTer75,ENST00000322090,NM_001483.2;GBAS,frameshift_variant,p.Gly164AlafsTer75,ENST00000446778,NM_001202469.1;GBAS,frameshift_variant,p.Gly63AlafsTer?,ENST00000437587,;GBAS,frameshift_variant,p.Gly63AlafsTer?,ENST00000446692,;GBAS,downstream_gene_variant,,ENST00000487370,;GBAS,downstream_gene_variant,,ENST00000472404,;GBAS,frameshift_variant,p.Gly111AlafsTer6,ENST00000415967,;GBAS,non_coding_transcript_exon_variant,,ENST00000497279,;GBAS,downstream_gene_variant,,ENST00000456204,;GBAS,downstream_gene_variant,,ENST00000464772,; - ENST00000322090 Transcript frameshift_variant 634/1999 605/861 202/286 W/X tGg/tg 1 1 GBAS HGNC HGNC:4179 protein_coding YES CCDS5521.1 ENSP00000313050 O75323 UPI00000015EB NM_001483.2 7/10 Gene3D:3.30.70.900,Pfam_domain:PF07978,hmmpanther:PTHR21017,hmmpanther:PTHR21017:SF14,Superfamily_domains:SSF54909 HIGH 1 deletion 1 3 1 PASS . . 0 208 0 2 0 0 0 0 -13.89505 0.9999997 1 1 1 0 - 7 5 81 55984866 55984866 G - 1 0 1 0 1 0 0 0 0 6140 1357 47 0 0 GBAS 7 55984866 Frame_Shift_Del DEL G C3N-01489_T 2948638 55984866 103361107 304 25234 TBL2 0 . GRCh38 7 73571310 73571310 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.757G>T p.Val253Leu p.V253L ENST00000305632 6/7 200 180 20 298 298 0 strelka-varscan-mutect TBL2,missense_variant,p.Val253Leu,ENST00000305632,NM_012453.2;TBL2,missense_variant,p.Val253Leu,ENST00000610724,;TBL2,missense_variant,p.Val217Leu,ENST00000432538,;TBL2,downstream_gene_variant,,ENST00000479892,;TBL2,non_coding_transcript_exon_variant,,ENST00000459913,;TBL2,downstream_gene_variant,,ENST00000452475,;TBL2,downstream_gene_variant,,ENST00000465279,;TBL2,downstream_gene_variant,,ENST00000468669,;TBL2,downstream_gene_variant,,ENST00000476136,;TBL2,3_prime_UTR_variant,,ENST00000424598,;TBL2,3_prime_UTR_variant,,ENST00000450285,;TBL2,3_prime_UTR_variant,,ENST00000417008,;TBL2,3_prime_UTR_variant,,ENST00000433464,;TBL2,3_prime_UTR_variant,,ENST00000426966,;TBL2,non_coding_transcript_exon_variant,,ENST00000488915,;TBL2,downstream_gene_variant,,ENST00000435792,;TBL2,downstream_gene_variant,,ENST00000437521,;TBL2,downstream_gene_variant,,ENST00000458466,;TBL2,downstream_gene_variant,,ENST00000469518,;TBL2,downstream_gene_variant,,ENST00000496056,;TBL2,downstream_gene_variant,,ENST00000452125,;TBL2,downstream_gene_variant,,ENST00000495885,; A ENST00000305632 Transcript missense_variant 999/3161 757/1344 253/447 V/L Gtg/Ttg 1 -1 TBL2 HGNC HGNC:11586 protein_coding YES CCDS5551.1 ENSP00000307260 Q9Y4P3 UPI0000048EF4 NM_012453.2 deleterious(0) 6/7 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF358,hmmpanther:PTHR22847,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 73571310 73571310 C A 1 0 0 0 0 1 0 0 0 16047 478 17 2 2 TBL2 7 73571310 Missense_Mutation SNP C C3N-01489_T 17586444 73571310 85774663 305 25235 CLIP2 0 . GRCh38 7 74338642 74338642 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.316G>T p.Gly106Cys p.G106C ENST00000223398 3/17 402 366 36 467 466 1 strelka-varscan-mutect CLIP2,missense_variant,p.Gly106Cys,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Gly106Cys,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Gly106Cys,ENST00000395060,; T ENST00000223398 Transcript missense_variant 643/5563 316/3141 106/1046 G/C Ggc/Tgc 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 deleterious(0) 3/17 Gene3D:2.30.30.190,Pfam_domain:PF01302,PROSITE_patterns:PS00845,PROSITE_profiles:PS50245,hmmpanther:PTHR18916,hmmpanther:PTHR18916:SF10,SMART_domains:SM01052,Superfamily_domains:SSF74924 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 74338642 74338642 G T 1 0 0 0 0 1 0 0 0 3302 1232 43 2 2 CLIP2 7 74338642 Missense_Mutation SNP G C3N-01489_T 767332 74338642 85007331 306 25236 SEMA3E 0 . GRCh38 7 83407116 83407116 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.794G>C p.Arg265Thr p.R265T ENST00000307792 7/17 330 303 27 411 411 0 strelka-mutect SEMA3E,missense_variant,p.Arg265Thr,ENST00000307792,NM_012431.2;SEMA3E,missense_variant,p.Arg205Thr,ENST00000427262,NM_001178129.1;SEMA3E,downstream_gene_variant,,ENST00000442159,; G ENST00000307792 Transcript missense_variant 1262/6476 794/2328 265/775 R/T aGg/aCg 1 -1 SEMA3E HGNC HGNC:10727 protein_coding YES CCDS34674.1 ENSP00000303212 O15041 UPI0000135A68 NM_012431.2 deleterious(0) 7/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF22,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 83407116 83407116 C G 1 0 0 0 0 1 0 0 0 14304 681 24 4 4 SEMA3E 7 83407116 Missense_Mutation SNP C C3N-01489_T 9068474 83407116 75938857 307 25237 SLC25A13 0 . GRCh38 7 96121852 96121852 + Nonsense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1740G>A p.Trp580Ter p.W580* ENST00000416240 16/18 419 363 56 677 676 1 strelka-varscan-mutect SLC25A13,stop_gained,p.Trp580Ter,ENST00000416240,NM_001160210.1;SLC25A13,stop_gained,p.Trp579Ter,ENST00000265631,NM_014251.2;SLC25A13,non_coding_transcript_exon_variant,,ENST00000494085,;GS1-25M2.1,downstream_gene_variant,,ENST00000625023,; T ENST00000416240 Transcript stop_gained 1931/3192 1740/2031 580/676 W/* tgG/tgA 1 -1 SLC25A13 HGNC HGNC:10983 protein_coding YES CCDS55130.1 ENSP00000400101 Q9UJS0 UPI0000001663 NM_001160210.1 16/18 PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF265,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 96121852 96121852 C T 1 0 0 0 0 0 1 0 0 14740 856 30 3 3 SLC25A13 7 96121852 Nonsense_Mutation SNP C C3N-01489_T 12714736 96121852 63224121 308 25238 LMTK2 0 . GRCh38 7 98193721 98193721 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.3256G>T p.Glu1086Ter p.E1086* ENST00000297293 11/14 181 161 20 304 303 1 strelka-varscan-mutect LMTK2,stop_gained,p.Glu1086Ter,ENST00000297293,NM_014916.3; T ENST00000297293 Transcript stop_gained 3549/8946 3256/4512 1086/1503 E/* Gaa/Taa 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 11/14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 98193721 98193721 G T 1 0 0 0 0 0 1 0 0 8786 943 33 2 2 LMTK2 7 98193721 Nonsense_Mutation SNP G C3N-01489_T 2071869 98193721 61152252 309 25239 TECPR1 0 . GRCh38 7 98243563 98243563 + Silent SNP C C G novel C3N-01489_T C3N-01489_N C C c.561G>C p.= p.L187L ENST00000447648 6/26 129 117 12 162 162 0 strelka-varscan-mutect TECPR1,synonymous_variant,p.=,ENST00000447648,NM_015395.2;TECPR1,downstream_gene_variant,,ENST00000420697,;TECPR1,downstream_gene_variant,,ENST00000423128,;TECPR1,downstream_gene_variant,,ENST00000415086,;TECPR1,intron_variant,,ENST00000471397,;TECPR1,downstream_gene_variant,,ENST00000472845,;TECPR1,non_coding_transcript_exon_variant,,ENST00000463648,; G ENST00000447648 Transcript synonymous_variant 861/6564 561/3498 187/1165 L ctG/ctC 1 -1 TECPR1 HGNC HGNC:22214 protein_coding YES CCDS47648.1 ENSP00000404923 Q7Z6L1 UPI0000161940 NM_015395.2 6/26 hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 98243563 98243563 C G 1 0 0 0 0 0 0 0 1 16154 697 25 4 4 TECPR1 7 98243563 Silent SNP C C3N-01489_T 49842 98243563 61102410 310 25240 MUC17 0 . GRCh38 7 101035947 101035947 + Missense_Mutation SNP G G A C3N-01489_T C3N-01489_N G G c.4531G>A p.Glu1511Lys p.E1511K ENST00000306151 3/13 82 73 9 128 128 0 strelka-varscan-mutect MUC17,missense_variant,p.Glu1511Lys,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Glu1511Lys,ENST00000379439,; A ENST00000306151 Transcript missense_variant 4595/14247 4531/13482 1511/4493 E/K Gaa/Aaa COSM5601856 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.1) 3/13 hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.27283 1 1 1 1 0 A 3 1 81 101035947 101035947 G A 1 0 0 0 0 1 0 0 0 9973 1291 45 3 3 MUC17 7 101035947 Missense_Mutation SNP G C3N-01489_T 2792384 101035947 58310026 311 25241 RELN 0 . GRCh38 7 103917155 103917155 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.257G>T p.Gly86Val p.G86V ENST00000428762 2/65 307 280 27 496 489 7 strelka-varscan RELN,missense_variant,p.Gly86Val,ENST00000424685,;RELN,missense_variant,p.Gly86Val,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Gly86Val,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 417/11571 257/10383 86/3460 G/V gGc/gTc COSM1446998 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 deleterious(0) 2/65 PROSITE_profiles:PS51019,Pfam_domain:PF02014 1 MODERATE 1 SNV 5 1 1 PASS . . 0 202 0 0 8 0 0 0 -7.966641 0.1280544 1 1 0 0 A 3 1 81 103917155 103917155 C A 1 0 0 0 0 1 0 0 0 13390 739 26 2 2 RELN 7 103917155 Missense_Mutation SNP C C3N-01489_T 2881208 103917155 55428818 312 25242 RELN 0 . GRCh38 7 103989147 103989147 + Silent SNP C C T rs770473518 C3N-01489_T C3N-01489_N C C c.210G>A p.= p.P70P ENST00000428762 1/65 213 196 17 316 316 0 strelka-varscan-mutect RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript synonymous_variant 370/11571 210/10383 70/3460 P ccG/ccA rs770473518 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 1/65 PROSITE_profiles:PS51019,Pfam_domain:PF02014 LOW 1 SNV 5 1 PASS rs770473518 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 103989147 103989147 C T 1 0 0 0 0 0 0 0 1 13390 639 23 1 1 RELN 7 103989147 Silent SNP C C3N-01489_T 71992 103989147 55356826 313 25243 LAMB1 0 . GRCh38 7 107959823 107959823 + Missense_Mutation SNP C C A rs755423167 C3N-01489_T C3N-01489_N C C c.2326G>T p.Asp776Tyr p.D776Y ENST00000222399 19/34 100 85 15 148 148 0 strelka-varscan-mutect LAMB1,missense_variant,p.Asp800Tyr,ENST00000393561,;LAMB1,missense_variant,p.Asp776Tyr,ENST00000222399,NM_002291.2;LAMB1,missense_variant,p.Asp776Tyr,ENST00000393560,; A ENST00000222399 Transcript missense_variant 2557/5725 2326/5361 776/1786 D/Y Gac/Tac rs755423167 1 -1 LAMB1 HGNC HGNC:6486 protein_coding YES CCDS5750.1 ENSP00000222399 P07942 UPI00001AE63F NM_002291.2 deleterious(0) 19/34 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF233,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs755423167 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 107959823 107959823 C A 1 0 0 0 0 1 0 0 0 8514 884 31 1 1 LAMB1 7 107959823 Missense_Mutation SNP C C3N-01489_T 3970676 107959823 51386150 314 25244 AKR1B1 0 . GRCh38 7 134442755 134442755 + Missense_Mutation SNP C C A rs780078330 C3N-01489_T C3N-01489_N C C c.924G>T p.Lys308Asn p.K308N ENST00000285930 10/10 249 220 29 354 353 1 strelka-varscan-mutect AKR1B1,missense_variant,p.Lys308Asn,ENST00000285930,NM_001628.2;AKR1B1,3_prime_UTR_variant,,ENST00000434222,;AKR1B1,non_coding_transcript_exon_variant,,ENST00000465351,;AKR1B1,downstream_gene_variant,,ENST00000467251,; A ENST00000285930 Transcript missense_variant 1004/1409 924/951 308/316 K/N aaG/aaT rs780078330 1 -1 AKR1B1 HGNC HGNC:381 protein_coding YES CCDS5831.1 ENSP00000285930 P15121 A0A024R7A8 UPI000000D78E NM_001628.2 deleterious(0.02) 10/10 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF233,Gene3D:3.20.20.100,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430 MODERATE 1 SNV 1 1 PASS rs780078330 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 134442755 134442755 C A 1 0 0 0 0 1 0 0 0 550 680 24 2 2 AKR1B1 7 134442755 Missense_Mutation SNP C C3N-01489_T 26482932 134442755 24903218 315 25245 SLC13A4 0 . GRCh38 7 135721447 135721447 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.176C>A p.Ala59Asp p.A59D ENST00000354042 2/16 259 224 35 276 276 0 strelka-varscan-mutect SLC13A4,missense_variant,p.Ala59Asp,ENST00000354042,NM_001318192.1,NM_012450.2;SLC13A4,missense_variant,p.Ala59Asp,ENST00000378428,;SLC13A4,missense_variant,p.Ala59Asp,ENST00000422620,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000471405,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000478310,; T ENST00000354042 Transcript missense_variant 866/2897 176/1881 59/626 A/D gCc/gAc 1 -1 SLC13A4 HGNC HGNC:15827 protein_coding YES CCDS5840.1 ENSP00000297282 Q9UKG4 UPI00000343D9 NM_001318192.1,NM_012450.2 deleterious(0) 2/16 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF63,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1408601893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 135721447 135721447 G T 1 0 0 0 0 1 0 0 0 14659 1203 42 2 2 SLC13A4 7 135721447 Missense_Mutation SNP G C3N-01489_T 1278692 135721447 23624526 316 25246 MGAM2 0 . GRCh38 7 142220588 142220588 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.6077C>A p.Ala2026Glu p.A2026E ENST00000477922 48/48 248 214 34 411 411 0 strelka-varscan-mutect MGAM2,missense_variant,p.Ala2026Glu,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript missense_variant 6131/7867 6077/7548 2026/2515 A/E gCa/gAa 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated_low_confidence(0.73) 48/48 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs922535377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 142220588 142220588 C A 1 0 0 0 0 1 0 0 0 9500 710 25 2 2 MGAM2 7 142220588 Missense_Mutation SNP C C3N-01489_T 6499141 142220588 17125385 317 25247 ZNF746 0 . GRCh38 7 149477591 149477591 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.685G>T p.Gly229Ter p.G229* ENST00000458143 5/7 50 43 7 80 80 0 strelka-varscan-mutect ZNF746,stop_gained,p.Gly229Ter,ENST00000340622,NM_152557.4;ZNF746,stop_gained,p.Gly229Ter,ENST00000458143,NM_001163474.1;ZNF746,non_coding_transcript_exon_variant,,ENST00000471735,; A ENST00000458143 Transcript stop_gained 956/3797 685/1938 229/645 G/* Gga/Tga 1 -1 ZNF746 HGNC HGNC:21948 protein_coding YES CCDS55180.1 ENSP00000395007 Q6NUN9 UPI00015DA840 NM_001163474.1 5/7 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF13 HIGH 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -16.83558 1 1 1 1 0 A 4 1 81 149477591 149477591 C A 1 0 0 0 0 0 1 0 0 18712 690 24 2 2 ZNF746 7 149477591 Nonsense_Mutation SNP C C3N-01489_T 7257003 149477591 9868382 318 25248 SSPO 0 . GRCh38 7 149785597 149785597 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.3104G>T p.Gly1035Val p.G1035V ENST00000378016 21/107 411 362 49 584 582 2 strelka-varscan-mutect SSPO,missense_variant,p.Gly1035Val,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,downstream_gene_variant,,ENST00000486824,;SSPO,upstream_gene_variant,,ENST00000475488,;SSPO,downstream_gene_variant,,ENST00000493502,; T ENST00000378016 Transcript missense_variant 3104/15589 3104/15453 1035/5150 G/V gGg/gTg 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 21/107 Pfam_domain:PF00094,SMART_domains:SM00216,SMART_domains:SM00215,PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 149785597 149785597 G T 1 0 0 0 0 1 0 0 0 15566 1232 43 2 2 SSPO 7 149785597 Missense_Mutation SNP G C3N-01489_T 308006 149785597 9560376 319 25249 SSPO 0 . GRCh38 7 149796433 149796433 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.6600G>C p.Gln2200His p.Q2200H ENST00000378016 43/107 344 297 47 382 382 0 strelka-varscan-mutect SSPO,missense_variant,p.Gln2200His,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,; C ENST00000378016 Transcript missense_variant 6600/15589 6600/15453 2200/5150 Q/H caG/caC 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0.02) 43/107 Pfam_domain:PF00754,Gene3D:2.60.120.260,SMART_domains:SM00231,Superfamily_domains:SSF49785,PROSITE_profiles:PS50022,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 149796433 149796433 G C 1 0 0 0 0 1 0 0 0 15566 991 35 4 4 SSPO 7 149796433 Missense_Mutation SNP G C3N-01489_T 10836 149796433 9549540 320 25250 CNPY1 0 . GRCh38 7 155509077 155509077 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.120G>T p.Glu40Asp p.E40D ENST00000636372 3/6 57 49 8 121 121 0 strelka-varscan-mutect CNPY1,missense_variant,p.Glu40Asp,ENST00000636372,;CNPY1,missense_variant,p.Glu40Asp,ENST00000636446,;CNPY1,5_prime_UTR_variant,,ENST00000321736,NM_001103176.1;CNPY1,5_prime_UTR_variant,,ENST00000406197,;AC008060.5,upstream_gene_variant,,ENST00000415333,;RP5-912I13.2,non_coding_transcript_exon_variant,,ENST00000636307,;RP5-912I13.2,non_coding_transcript_exon_variant,,ENST00000635770,;RP5-912I13.2,non_coding_transcript_exon_variant,,ENST00000637398,;RP5-912I13.2,non_coding_transcript_exon_variant,,ENST00000635903,; A ENST00000636372 Transcript missense_variant 1032/2259 120/438 40/145 E/D gaG/gaT 1 -1 CNPY1 HGNC HGNC:27786 protein_coding ENSP00000490060 3/6 hmmpanther:PTHR13341:SF4,hmmpanther:PTHR13341,Pfam_domain:PF11938 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -18.97045 1 1 1 1 0 A 3 1 81 155509077 155509077 C A 1 0 0 0 0 1 0 0 0 3409 680 24 2 2 CNPY1 7 155509077 Missense_Mutation SNP C C3N-01489_T 5712644 155509077 3836896 321 25251 CSMD1 0 . GRCh38 8 3998008 3998008 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.713T>C p.Ile238Thr p.I238T ENST00000520002 5/71 208 195 13 287 287 0 strelka-varscan-mutect CSMD1,missense_variant,p.Ile100Thr,ENST00000537824,;CSMD1,missense_variant,p.Ile238Thr,ENST00000520002,;CSMD1,missense_variant,p.Ile238Thr,ENST00000602557,;CSMD1,missense_variant,p.Ile238Thr,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Ile238Thr,ENST00000400186,;CSMD1,missense_variant,p.Ile238Thr,ENST00000602723,; G ENST00000520002 Transcript missense_variant 1269/11740 713/10698 238/3565 I/T aTt/aCt 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 5/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 3998008 3998008 A G 1 0 0 0 0 1 0 0 0 3745 101 4 5 5 CSMD1 8 3998008 Missense_Mutation SNP A C3N-01489_T 3998008 141140628 322 25252 RP1L1 0 . GRCh38 8 10608194 10608194 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.5904G>T p.Glu1968Asp p.E1968D ENST00000382483 4/4 302 269 33 467 466 1 strelka-varscan-mutect RP1L1,missense_variant,p.Glu1968Asp,ENST00000382483,NM_178857.5; A ENST00000382483 Transcript missense_variant 6128/7973 5904/7203 1968/2400 E/D gaG/gaT 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 tolerated_low_confidence(0.5) 4/4 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1409852774 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 10608194 10608194 C A 1 0 0 0 0 1 0 0 0 13773 680 24 2 2 RP1L1 8 10608194 Missense_Mutation SNP C C3N-01489_T 6610186 10608194 134530442 323 25253 GATA4 0 . GRCh38 8 11708913 11708913 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.601C>A p.= p.R201R ENST00000532059 1/6 90 78 12 104 104 0 strelka-varscan-mutect GATA4,synonymous_variant,p.=,ENST00000335135,NM_002052.3;GATA4,synonymous_variant,p.=,ENST00000622443,;GATA4,synonymous_variant,p.=,ENST00000532059,NM_001308093.1;GATA4,intron_variant,,ENST00000528712,NM_001308094.1;GATA4,intron_variant,,ENST00000526716,;GATA4,downstream_gene_variant,,ENST00000528027,;GATA4,downstream_gene_variant,,ENST00000532977,;GATA4,downstream_gene_variant,,ENST00000526974,; A ENST00000532059 Transcript synonymous_variant 681/1459 601/1332 201/443 R Cga/Aga 1 1 GATA4 HGNC HGNC:4173 protein_coding YES CCDS78303.1 ENSP00000435712 P43694 UPI0000210221 NM_001308093.1 1/6 Pfam_domain:PF05349,PIRSF_domain:PIRSF003028,hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF154 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 11708913 11708913 C A 1 0 0 0 0 0 0 0 1 6126 644 23 1 1 GATA4 8 11708913 Silent SNP C C3N-01489_T 1100719 11708913 133429723 324 25254 MSR1 0 . GRCh38 8 16150312 16150312 + Splice_Site SNP C C G novel C3N-01489_T C3N-01489_N C C c.899-1G>C p.X300_splice ENST00000262101 86 78 8 167 167 0 strelka-varscan-mutect MSR1,splice_acceptor_variant,,ENST00000350896,NM_138716.2;MSR1,splice_acceptor_variant,,ENST00000381998,NM_002445.3;MSR1,splice_acceptor_variant,,ENST00000262101,NM_138715.2;MSR1,splice_acceptor_variant,,ENST00000445506,;MSR1,splice_acceptor_variant,,ENST00000355282,;MSR1,splice_acceptor_variant,,ENST00000522672,;MSR1,splice_acceptor_variant,,ENST00000519060,; G ENST00000262101 Transcript splice_acceptor_variant -/2132 899/1356 300/451 1 -1 MSR1 HGNC HGNC:7376 protein_coding YES CCDS5995.1 ENSP00000262101 P21757 UPI000012F686 NM_138715.2 6/9 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.10856 0.9999998 1 1 1 0 G 5 3 81 16150312 16150312 C G 1 0 0 0 0 0 0 1 0 9869 695 24 4 4 MSR1 8 16150312 Splice_Site SNP C C3N-01489_T 4441399 16150312 128988324 325 25255 MSR1 0 . GRCh38 8 16164220 16164220 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.662A>G p.Asn221Ser p.N221S ENST00000262101 5/10 215 197 18 281 281 0 strelka-varscan-mutect MSR1,missense_variant,p.Asn221Ser,ENST00000350896,NM_138716.2;MSR1,missense_variant,p.Asn221Ser,ENST00000381998,NM_002445.3;MSR1,missense_variant,p.Asn221Ser,ENST00000262101,NM_138715.2;MSR1,missense_variant,p.Asn239Ser,ENST00000445506,;MSR1,missense_variant,p.Asn221Ser,ENST00000355282,;MSR1,missense_variant,p.Asn11Ser,ENST00000522672,;MSR1,3_prime_UTR_variant,,ENST00000519060,; C ENST00000262101 Transcript missense_variant 784/2132 662/1356 221/451 N/S aAt/aGt 1 -1 MSR1 HGNC HGNC:7376 protein_coding YES CCDS5995.1 ENSP00000262101 P21757 UPI000012F686 NM_138715.2 deleterious(0.01) 5/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24023:SF603,hmmpanther:PTHR24023,Prints_domain:PR01408 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 16164220 16164220 T C 1 0 0 0 0 1 0 0 0 9869 1493 52 5 5 MSR1 8 16164220 Missense_Mutation SNP T C3N-01489_T 13908 16164220 128974416 326 25256 HR 0 . GRCh38 8 22127135 22127135 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1307C>A p.Pro436Gln p.P436Q ENST00000381418 3/19 78 70 8 121 121 0 strelka-varscan-mutect HR,missense_variant,p.Pro436Gln,ENST00000381418,NM_005144.4;HR,missense_variant,p.Pro436Gln,ENST00000312841,NM_018411.4;HR,downstream_gene_variant,,ENST00000518377,;HR,downstream_gene_variant,,ENST00000519619,;HR,downstream_gene_variant,,ENST00000522759,;HR,upstream_gene_variant,,ENST00000517699,;HR,upstream_gene_variant,,ENST00000518461,; T ENST00000381418 Transcript missense_variant 2788/6336 1307/3570 436/1189 P/Q cCa/cAa 1 -1 HR HGNC HGNC:5172 protein_coding YES CCDS6022.1 ENSP00000370826 O43593 UPI000013EB0B NM_005144.4 deleterious(0.03) 3/19 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF4 MODERATE 1 SNV 1 1 PASS rs1278767455 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 22127135 22127135 G T 1 0 0 0 0 1 0 0 0 7242 1348 47 2 2 HR 8 22127135 Missense_Mutation SNP G C3N-01489_T 5962915 22127135 123011501 327 25257 ANK1 0 . GRCh38 8 41668513 41668513 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.5271T>A p.= p.A1757A ENST00000265709 40/43 106 91 15 188 187 1 strelka-varscan-mutect ANK1,synonymous_variant,p.=,ENST00000289734,NM_000037.3;ANK1,synonymous_variant,p.=,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,synonymous_variant,p.=,ENST00000265709,NM_001142446.1;ANK1,synonymous_variant,p.=,ENST00000520299,;ANK1,upstream_gene_variant,,ENST00000314214,NM_020478.4;ANK1,upstream_gene_variant,,ENST00000522543,NM_001142445.1;ANK1,upstream_gene_variant,,ENST00000522231,;ANK1,upstream_gene_variant,,ENST00000348036,NM_020480.4;ANK1,upstream_gene_variant,,ENST00000335651,;RP11-930P14.1,downstream_gene_variant,,ENST00000522388,;RP11-930P14.1,downstream_gene_variant,,ENST00000520418,;RP11-930P14.1,downstream_gene_variant,,ENST00000585088,;ANK1,3_prime_UTR_variant,,ENST00000518061,;ANK1,non_coding_transcript_exon_variant,,ENST00000524227,;ANK1,upstream_gene_variant,,ENST00000518715,; T ENST00000265709 Transcript synonymous_variant 5553/6379 5271/5694 1757/1897 A gcT/gcA 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 40/43 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 41668513 41668513 A T 1 0 0 0 0 0 0 0 1 720 175 7 4 4 ANK1 8 41668513 Silent SNP A C3N-01489_T 19541378 41668513 103470123 328 25258 CHRNB3 0 . GRCh38 8 42731956 42731956 + Missense_Mutation SNP G G C rs760859517 C3N-01489_T C3N-01489_N G G c.649G>C p.Val217Leu p.V217L ENST00000289957 5/6 180 147 33 311 311 0 strelka-varscan-mutect CHRNB3,missense_variant,p.Val217Leu,ENST00000289957,NM_000749.3; C ENST00000289957 Transcript missense_variant 777/2294 649/1377 217/458 V/L Gtg/Ctg rs760859517 1 1 CHRNB3 HGNC HGNC:1963 protein_coding YES CCDS6134.1 ENSP00000289957 Q05901 UPI0000125272 NM_000749.3 tolerated(0.14) 5/6 hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945,Pfam_domain:PF02931,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE 1 SNV 1 1 PASS rs760859517 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 42731956 42731956 G C 1 0 0 0 0 1 0 0 0 3152 1145 40 4 4 CHRNB3 8 42731956 Missense_Mutation SNP G C3N-01489_T 1063443 42731956 102406680 329 25259 NPBWR1 0 . GRCh38 8 52940396 52940396 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.489G>T p.Trp163Cys p.W163C ENST00000331251 1/1 130 105 25 245 245 0 strelka-varscan-mutect NPBWR1,missense_variant,p.Trp163Cys,ENST00000331251,NM_005285.3; T ENST00000331251 Transcript missense_variant 1966/2687 489/987 163/328 W/C tgG/tgT 1 1 NPBWR1 HGNC HGNC:4522 protein_coding YES CCDS6151.1 ENSP00000330284 P48145 H9NIL7 UPI000013EEF3 NM_005285.3 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR01855,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF47,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs1395346192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 52940396 52940396 G T 1 0 0 0 0 1 0 0 0 10616 1241 43 2 2 NPBWR1 8 52940396 Missense_Mutation SNP G C3N-01489_T 10208440 52940396 92198240 330 25260 PDE7A 0 . GRCh38 8 65782841 65782841 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.141G>T p.Arg47Ser p.R47S ENST00000401827 2/13 100 79 21 170 169 1 strelka-varscan-mutect PDE7A,missense_variant,p.Arg47Ser,ENST00000401827,NM_001242318.2;PDE7A,missense_variant,p.Arg47Ser,ENST00000396642,;PDE7A,missense_variant,p.Arg21Ser,ENST00000379419,NM_002603.3;PDE7A,missense_variant,p.Arg21Ser,ENST00000523253,;PDE7A,splice_region_variant,,ENST00000519231,;PDE7A,splice_region_variant,,ENST00000519626,; A ENST00000401827 Transcript missense_variant,splice_region_variant 585/3673 141/1449 47/482 R/S agG/agT 1 -1 PDE7A HGNC HGNC:8791 protein_coding YES CCDS56538.1 ENSP00000385632 Q13946 UPI0000127BFD NM_001242318.2 deleterious(0.01) 2/13 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF96 MODERATE 1 SNV 1 1 PASS . . 0 193 10 7 0 0 0 0 -20 0.9790044 1 1 1 0 A 3 1 81 65782841 65782841 C A 1 0 0 0 0 1 0 0 0 11739 753 26 2 2 PDE7A 8 65782841 Missense_Mutation SNP C C3N-01489_T 12842445 65782841 79355795 331 25261 DCAF4L2 0 . GRCh38 8 87873490 87873490 + Missense_Mutation SNP G G T rs367683322 C3N-01489_T C3N-01489_N G G c.482C>A p.Ala161Glu p.A161E ENST00000319675 1/1 241 195 46 406 405 1 strelka-varscan-mutect DCAF4L2,missense_variant,p.Ala161Glu,ENST00000319675,NM_152418.3;CTB-118P15.3,downstream_gene_variant,,ENST00000613582,; T ENST00000319675 Transcript missense_variant 579/3326 482/1188 161/395 A/E gCg/gAg rs367683322,COSM160338 1 -1 DCAF4L2 HGNC HGNC:26657 protein_coding YES CCDS6245.1 ENSP00000316496 Q8NA75 UPI0000072860 NM_152418.3 deleterious(0) 1/1 hmmpanther:PTHR22847:SF457,hmmpanther:PTHR22847,Superfamily_domains:SSF50978 0,1 MODERATE 1 SNV 0,1 1 PASS rs367683322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 87873490 87873490 G T 1 0 0 0 0 1 0 0 0 4073 1087 38 1 1 DCAF4L2 8 87873490 Missense_Mutation SNP G C3N-01489_T 22090649 87873490 57265146 332 25262 ESRP1 0 . GRCh38 8 94662322 94662322 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.541G>T p.Val181Phe p.V181F ENST00000433389 5/16 169 143 26 221 221 0 strelka-varscan-mutect ESRP1,missense_variant,p.Val181Phe,ENST00000433389,NM_017697.3;ESRP1,missense_variant,p.Val181Phe,ENST00000358397,NM_001034915.2;ESRP1,missense_variant,p.Val181Phe,ENST00000423620,NM_001122826.1;ESRP1,missense_variant,p.Val181Phe,ENST00000454170,NM_001122825.1,NM_001122827.1;ESRP1,missense_variant,p.Val47Phe,ENST00000519505,;ESRP1,missense_variant,p.Val40Phe,ENST00000517610,;ESRP1,missense_variant,p.Val21Phe,ENST00000520385,;ESRP1,intron_variant,,ENST00000522756,;ESRP1,upstream_gene_variant,,ENST00000517556,; T ENST00000433389 Transcript missense_variant 731/3770 541/2046 181/681 V/F Gtt/Ttt 1 1 ESRP1 HGNC HGNC:25966 protein_coding YES CCDS47897.1 ENSP00000405738 Q6NXG1 UPI0000210327 NM_017697.3 deleterious(0) 5/16 hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF37,Gene3D:3.30.420.10,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS rs772343882 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 94662322 94662322 G T 1 0 0 0 0 1 0 0 0 5120 1029 36 2 2 ESRP1 8 94662322 Missense_Mutation SNP G C3N-01489_T 6788832 94662322 50476314 333 25263 NDUFAF6 0 . GRCh38 8 95032036 95032036 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.239C>T p.Pro80Leu p.P80L ENST00000396124 2/9 434 381 53 559 559 0 strelka-varscan-mutect NDUFAF6,missense_variant,p.Pro80Leu,ENST00000396124,NM_152416.3;NDUFAF6,5_prime_UTR_variant,,ENST00000396113,;NDUFAF6,5_prime_UTR_variant,,ENST00000396111,;NDUFAF6,5_prime_UTR_variant,,ENST00000523378,;NDUFAF6,5_prime_UTR_variant,,ENST00000519136,;NDUFAF6,upstream_gene_variant,,ENST00000519804,;NDUFAF6,missense_variant,p.Pro61Leu,ENST00000520757,;NDUFAF6,missense_variant,p.Pro80Leu,ENST00000518258,;NDUFAF6,missense_variant,p.Pro76Leu,ENST00000517976,;NDUFAF6,missense_variant,p.Pro61Leu,ENST00000454358,;NDUFAF6,missense_variant,p.Pro72Leu,ENST00000520632,;NDUFAF6,missense_variant,p.Pro80Leu,ENST00000523337,;NDUFAF6,missense_variant,p.Pro61Leu,ENST00000522683,;NDUFAF6,intron_variant,,ENST00000518608,; T ENST00000396124 Transcript missense_variant 262/1798 239/1002 80/333 P/L cCt/cTt 1 1 NDUFAF6 HGNC HGNC:28625 protein_coding YES CCDS6266.2 ENSP00000379430 Q330K2 UPI0000F0A5CF NM_152416.3 deleterious(0) 2/9 hmmpanther:PTHR21181,hmmpanther:PTHR21181:SF13,Gene3D:1.10.600.10,Pfam_domain:PF00494,Superfamily_domains:SSF48576 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 95032036 95032036 C T 1 0 0 0 0 1 0 0 0 10300 681 24 3 3 NDUFAF6 8 95032036 Missense_Mutation SNP C C3N-01489_T 369714 95032036 50106600 334 25264 UBR5 0 . GRCh38 8 102285722 102285722 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.5275A>T p.Ser1759Cys p.S1759C ENST00000520539 39/59 177 157 20 234 234 0 varscan-mutect UBR5,missense_variant,p.Ser1759Cys,ENST00000520539,NM_015902.5;UBR5,missense_variant,p.Ser1759Cys,ENST00000220959,NM_001282873.1;UBR5,missense_variant,p.Ser1753Cys,ENST00000521922,;UBR5,downstream_gene_variant,,ENST00000519528,; A ENST00000520539 Transcript missense_variant 5882/10297 5275/8400 1759/2799 S/C Agt/Tgt 1 -1 UBR5 HGNC HGNC:16806 protein_coding YES CCDS34933.1 ENSP00000429084 O95071 UPI0000129BCB NM_015902.5 deleterious(0.02) 39/59 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF337,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 102285722 102285722 T A 1 0 0 0 0 1 0 0 0 17429 1580 55 4 4 UBR5 8 102285722 Missense_Mutation SNP T C3N-01489_T 7253686 102285722 42852914 335 25265 AZIN1 0 . GRCh38 8 102839771 102839771 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.155A>T p.His52Leu p.H52L ENST00000337198 4/12 127 115 12 143 143 0 strelka-varscan-mutect AZIN1,missense_variant,p.His52Leu,ENST00000337198,NM_001301668.1,NM_148174.3;AZIN1,missense_variant,p.His52Leu,ENST00000347770,NM_015878.5;AZIN1,missense_variant,p.His52Leu,ENST00000520402,;AZIN1,intron_variant,,ENST00000521536,;AZIN1,downstream_gene_variant,,ENST00000518353,;AZIN1,non_coding_transcript_exon_variant,,ENST00000522311,;AZIN1,upstream_gene_variant,,ENST00000523071,;AZIN1,downstream_gene_variant,,ENST00000518940,; A ENST00000337198 Transcript missense_variant 1319/4721 155/1347 52/448 H/L cAc/cTc 1 -1 AZIN1 HGNC HGNC:16432 protein_coding YES CCDS6295.1 ENSP00000337180 O14977 A0A024R9C7 UPI00000722AD NM_001301668.1,NM_148174.3 deleterious(0) 4/12 Gene3D:3.20.20.10,Pfam_domain:PF02784,Prints_domain:PR01182,hmmpanther:PTHR11482,hmmpanther:PTHR11482:SF7,Superfamily_domains:SSF51419 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 102839771 102839771 T A 1 0 0 0 0 1 0 0 0 1398 1696 59 4 4 AZIN1 8 102839771 Missense_Mutation SNP T C3N-01489_T 554049 102839771 42298865 336 25266 PKHD1L1 0 . GRCh38 8 109452766 109452766 + Missense_Mutation SNP T T A rs376573811 C3N-01489_T C3N-01489_N T T c.6556T>A p.Trp2186Arg p.W2186R ENST00000378402 43/78 133 109 24 169 169 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Trp2186Arg,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 6660/13076 6556/12732 2186/4243 W/R Tgg/Agg rs376573811 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 43/78 Pfam_domain:PF10162,PROSITE_profiles:PS51484,SMART_domains:SM01225 MODERATE 1 SNV 1 1 PASS rs376573811 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 109452766 109452766 T A 1 0 0 0 0 1 0 0 0 12068 1464 51 4 4 PKHD1L1 8 109452766 Missense_Mutation SNP T C3N-01489_T 6612995 109452766 35685870 337 25267 PKHD1L1 0 . GRCh38 8 109464843 109464843 + Missense_Mutation SNP C C A rs761865905 C3N-01489_T C3N-01489_N C C c.8011C>A p.His2671Asn p.H2671N ENST00000378402 49/78 261 228 33 372 370 2 strelka-varscan-mutect PKHD1L1,missense_variant,p.His2671Asn,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 8115/13076 8011/12732 2671/4243 H/N Cat/Aat rs761865905 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 tolerated(0.15) 49/78 SMART_domains:SM00710 MODERATE 1 SNV 1 1 PASS rs761865905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 109464843 109464843 C A 1 0 0 0 0 1 0 0 0 12068 594 21 2 2 PKHD1L1 8 109464843 Missense_Mutation SNP C C3N-01489_T 12077 109464843 35673793 338 25268 CSMD3 0 . GRCh38 8 113314694 113314694 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.278G>T p.Trp93Leu p.W93L ENST00000297405 2/71 276 250 26 421 420 1 strelka-varscan-mutect CSMD3,missense_variant,p.Trp93Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Trp53Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Trp93Leu,ENST00000455883,NM_052900.2;CSMD3,non_coding_transcript_exon_variant,,ENST00000493303,;CSMD3,non_coding_transcript_exon_variant,,ENST00000497026,; A ENST00000297405 Transcript missense_variant 523/13212 278/11124 93/3707 W/L tGg/tTg COSM1151010,COSM748570 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 2/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 113314694 113314694 C A 1 0 0 0 0 1 0 0 0 3747 595 21 2 2 CSMD3 8 113314694 Missense_Mutation SNP C C3N-01489_T 3849851 113314694 31823942 339 25269 MTBP 0 . GRCh38 8 120488181 120488181 + Silent SNP A A G novel C3N-01489_T C3N-01489_N A A c.1188A>G p.= p.G396G ENST00000305949 12/22 134 121 13 194 194 0 strelka-varscan-mutect MTBP,synonymous_variant,p.=,ENST00000305949,NM_022045.4;MTBP,non_coding_transcript_exon_variant,,ENST00000519188,; G ENST00000305949 Transcript synonymous_variant 1233/3059 1188/2715 396/904 G ggA/ggG 1 1 MTBP HGNC HGNC:7417 protein_coding YES CCDS6333.1 ENSP00000303398 Q96DY7 UPI00000703F0 NM_022045.4 12/22 Pfam_domain:PF14919,hmmpanther:PTHR14382,hmmpanther:PTHR14382:SF1 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.87373 0.9999998 1 1 1 0 G 2 3 81 120488181 120488181 A G 1 0 0 0 0 0 0 0 1 9897 291 11 5 5 MTBP 8 120488181 Silent SNP A C3N-01489_T 7173487 120488181 24650455 340 25270 POU5F1B 0 . GRCh38 8 127416098 127416098 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.232C>T p.Pro78Ser p.P78S ENST00000465342 2/2 268 243 25 324 324 0 strelka-varscan-mutect POU5F1B,missense_variant,p.Pro78Ser,ENST00000465342,NM_001159542.1;CASC8,intron_variant,,ENST00000502082,;CASC8,intron_variant,,ENST00000501396,;CASC8,intron_variant,,ENST00000523825,; T ENST00000465342 Transcript missense_variant 1389/5360 232/1080 78/359 P/S Cct/Tct 1 1 POU5F1B HGNC HGNC:9223 protein_coding YES CCDS55274.1 ENSP00000419298 Q06416 UPI000013F18B NM_001159542.1 tolerated(0.11) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF86 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 127416098 127416098 C T 1 0 0 0 0 1 0 0 0 12398 739 26 3 3 POU5F1B 8 127416098 Missense_Mutation SNP C C3N-01489_T 6927917 127416098 17722538 341 25271 POU5F1B 0 . GRCh38 8 127416687 127416687 + Missense_Mutation SNP G G C rs759719679 C3N-01489_T C3N-01489_N G G c.821G>C p.Arg274Pro p.R274P ENST00000465342 2/2 534 478 56 649 649 0 strelka-varscan-mutect POU5F1B,missense_variant,p.Arg274Pro,ENST00000465342,NM_001159542.1;CASC8,intron_variant,,ENST00000502082,;CASC8,intron_variant,,ENST00000501396,;CASC8,intron_variant,,ENST00000523825,; C ENST00000465342 Transcript missense_variant 1978/5360 821/1080 274/359 R/P cGa/cCa rs759719679 1 1 POU5F1B HGNC HGNC:9223 protein_coding YES CCDS55274.1 ENSP00000419298 Q06416 UPI000013F18B NM_001159542.1 deleterious(0.04) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF86,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00028 MODERATE SNV 3 1 PASS rs759719679 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 127416687 127416687 G C 1 0 0 0 0 1 0 0 0 12398 1058 37 4 4 POU5F1B 8 127416687 Missense_Mutation SNP G C3N-01489_T 589 127416687 17721949 342 25272 GSDMC 0 . GRCh38 8 129765633 129765633 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.565G>T p.Gly189Cys p.G189C ENST00000276708 4/14 268 222 46 357 357 0 strelka-varscan-mutect GSDMC,missense_variant,p.Gly189Cys,ENST00000276708,NM_031415.2;GSDMC,missense_variant,p.Gly189Cys,ENST00000619643,; A ENST00000276708 Transcript missense_variant 1447/2714 565/1527 189/508 G/C Ggc/Tgc 1 -1 GSDMC HGNC HGNC:7151 protein_coding YES CCDS6360.1 ENSP00000276708 Q9BYG8 UPI0000071445 NM_031415.2 tolerated(0.05) 4/14 Pfam_domain:PF04598,hmmpanther:PTHR16399,hmmpanther:PTHR16399:SF21 MODERATE 1 SNV 1 1 PASS rs1300580183 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 129765633 129765633 C A 1 0 0 0 0 1 0 0 0 6700 608 21 2 2 GSDMC 8 129765633 Missense_Mutation SNP C C3N-01489_T 2348946 129765633 15373003 343 25273 TG 0 . GRCh38 8 133022041 133022041 + Missense_Mutation SNP G G T rs777482713 C3N-01489_T C3N-01489_N G G c.6927G>T p.Glu2309Asp p.E2309D ENST00000220616 40/48 412 342 70 517 517 0 strelka-varscan-mutect TG,missense_variant,p.Glu2309Asp,ENST00000220616,NM_003235.4;TG,missense_variant,p.Glu765Asp,ENST00000519178,;TG,missense_variant,p.Glu442Asp,ENST00000519543,;TG,missense_variant,p.Glu105Asp,ENST00000518108,;TG,downstream_gene_variant,,ENST00000522523,;TG,3_prime_UTR_variant,,ENST00000523756,; T ENST00000220616 Transcript missense_variant 6967/8450 6927/8307 2309/2768 E/D gaG/gaT rs777482713 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 tolerated(0.6) 40/48 Gene3D:3.40.50.1820,Pfam_domain:PF00135,PIRSF_domain:PIRSF001831,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs777482713 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 133022041 133022041 G T 1 0 0 0 0 1 0 0 0 16246 991 35 2 2 TG 8 133022041 Missense_Mutation SNP G C3N-01489_T 3256408 133022041 12116595 344 25274 WISP1 0 . GRCh38 8 133212900 133212900 + Missense_Mutation SNP C C A rs759578017 C3N-01489_T C3N-01489_N C C c.106C>A p.Pro36Thr p.P36T ENST00000250160 2/5 62 43 19 80 80 0 strelka-varscan-mutect WISP1,missense_variant,p.Pro36Thr,ENST00000250160,NM_003882.3;WISP1,missense_variant,p.Pro36Thr,ENST00000220856,NM_080838.2;WISP1,missense_variant,p.Pro36Thr,ENST00000517423,NM_001204869.1;WISP1,intron_variant,,ENST00000519433,NM_001204870.1;WISP1,intron_variant,,ENST00000377862,; A ENST00000250160 Transcript missense_variant 212/3844 106/1104 36/367 P/T Cca/Aca rs759578017 1 1 WISP1 HGNC HGNC:12769 protein_coding YES CCDS6371.1 ENSP00000250160 O95388 UPI00000359FE NM_003882.3 tolerated(0.08) 2/5 hmmpanther:PTHR11348:SF4,hmmpanther:PTHR11348,PIRSF_domain:PIRSF036495 MODERATE 1 SNV 1 1 PASS rs759578017 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 133212900 133212900 C A 1 0 0 0 0 1 0 0 0 17928 623 22 2 2 WISP1 8 133212900 Missense_Mutation SNP C C3N-01489_T 190859 133212900 11925736 345 25275 FAM135B 0 . GRCh38 8 138151291 138151291 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.3184A>T p.Thr1062Ser p.T1062S ENST00000395297 13/20 118 100 18 152 152 0 strelka-varscan-mutect FAM135B,missense_variant,p.Thr1062Ser,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Thr1062Ser,ENST00000276737,;FAM135B,missense_variant,p.Thr372Ser,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript missense_variant 3355/6962 3184/4221 1062/1406 T/S Acc/Tcc 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.14) 13/20 MODERATE 1 SNV 5 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999835 1 1 1 0 A 3 1 81 138151291 138151291 T A 1 0 0 0 0 1 0 0 0 5299 1667 58 4 4 FAM135B 8 138151291 Missense_Mutation SNP T C3N-01489_T 4938391 138151291 6987345 346 25276 COL22A1 0 . GRCh38 8 138636789 138636789 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.3508C>A p.Gln1170Lys p.Q1170K ENST00000303045 48/65 243 211 32 335 334 1 strelka-varscan-mutect COL22A1,missense_variant,p.Gln1170Lys,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Gln863Lys,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; T ENST00000303045 Transcript missense_variant 3955/6346 3508/4881 1170/1626 Q/K Caa/Aaa COSM340292 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(1) 48/65 hmmpanther:PTHR24023,Pfam_domain:PF01391,Pfam_domain:PF01391 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 138636789 138636789 G T 1 0 0 0 0 1 0 0 0 3469 1299 45 2 2 COL22A1 8 138636789 Missense_Mutation SNP G C3N-01489_T 485498 138636789 6501847 347 25277 COL22A1 0 . GRCh38 8 138685305 138685305 + Missense_Mutation SNP G G C C3N-01489_T C3N-01489_N G G c.2870C>G p.Ala957Gly p.A957G ENST00000303045 38/65 219 201 18 338 338 0 strelka-mutect COL22A1,missense_variant,p.Ala957Gly,ENST00000303045,NM_152888.2;COL22A1,missense_variant,p.Ala670Gly,ENST00000435777,;COL22A1,non_coding_transcript_exon_variant,,ENST00000341807,; C ENST00000303045 Transcript missense_variant 3317/6346 2870/4881 957/1626 A/G gCg/gGg COSM5225899 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 tolerated(0.17) 38/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023 1 MODERATE 1 SNV 1 1 1 PASS rs1269287631 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 138685305 138685305 G C 1 0 0 0 0 1 0 0 0 3469 1087 38 4 4 COL22A1 8 138685305 Missense_Mutation SNP G C3N-01489_T 48516 138685305 6453331 348 25278 TRAPPC9 0 . GRCh38 8 140023947 140023947 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2983C>A p.Pro995Thr p.P995T ENST00000389328 18/23 448 404 44 505 504 1 strelka-varscan-mutect TRAPPC9,missense_variant,p.Pro995Thr,ENST00000389328,NM_031466.6;TRAPPC9,missense_variant,p.Pro897Thr,ENST00000438773,NM_001160372.2;TRAPPC9,missense_variant,p.Pro741Thr,ENST00000520857,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000521667,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000523777,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000520532,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000517667,; T ENST00000389328 Transcript missense_variant 2998/4474 2983/3741 995/1246 P/T Cca/Aca 1 -1 TRAPPC9 HGNC HGNC:30832 protein_coding YES CCDS34946.1 ENSP00000373979 Q96Q05 UPI0000DBEF2B NM_031466.6 deleterious(0) 18/23 Pfam_domain:PF08626,hmmpanther:PTHR21512,hmmpanther:PTHR21512:SF5 MODERATE 1 SNV 2 1 PASS rs1056486718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 140023947 140023947 G T 1 0 0 0 0 1 0 0 0 16954 1232 43 2 2 TRAPPC9 8 140023947 Missense_Mutation SNP G C3N-01489_T 1338642 140023947 5114689 349 25279 TOP1MT 0 . GRCh38 8 143321307 143321307 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.1040A>G p.His347Arg p.H347R ENST00000329245 8/14 105 93 12 163 163 0 strelka-varscan-mutect TOP1MT,missense_variant,p.His249Arg,ENST00000523676,;TOP1MT,missense_variant,p.His249Arg,ENST00000521193,NM_001258446.1;TOP1MT,missense_variant,p.His347Arg,ENST00000329245,NM_052963.2;TOP1MT,missense_variant,p.His249Arg,ENST00000519148,NM_001258447.1;TOP1MT,missense_variant,p.His249Arg,ENST00000519139,;TOP1MT,downstream_gene_variant,,ENST00000519591,;TOP1MT,downstream_gene_variant,,ENST00000522041,;TOP1MT,downstream_gene_variant,,ENST00000518760,;TOP1MT,downstream_gene_variant,,ENST00000518007,;TOP1MT,3_prime_UTR_variant,,ENST00000518951,;TOP1MT,downstream_gene_variant,,ENST00000522121,;TOP1MT,downstream_gene_variant,,ENST00000523417,; C ENST00000329245 Transcript missense_variant 1075/1958 1040/1806 347/601 H/R cAc/cGc 1 -1 TOP1MT HGNC HGNC:29787 protein_coding YES CCDS6400.1 ENSP00000328835 Q969P6 E5KMK7 UPI000013716D NM_052963.2 deleterious(0) 8/14 Gene3D:3.90.15.10,Pfam_domain:PF01028,Prints_domain:PR00416,hmmpanther:PTHR10290,hmmpanther:PTHR10290:SF1,SMART_domains:SM00435,Superfamily_domains:SSF56349 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 143321307 143321307 T C 1 0 0 0 0 1 0 0 0 16840 1696 59 5 5 TOP1MT 8 143321307 Missense_Mutation SNP T C3N-01489_T 3297360 143321307 1817329 350 25280 ZNF623 0 . GRCh38 8 143650879 143650879 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.1007A>T p.Gln336Leu p.Q336L ENST00000501748 1/1 291 257 34 351 350 1 strelka-varscan-mutect ZNF623,missense_variant,p.Gln336Leu,ENST00000501748,NM_014789.3;ZNF623,missense_variant,p.Gln296Leu,ENST00000458270,NM_001082480.2;ZNF623,missense_variant,p.Gln296Leu,ENST00000526926,NM_001261843.1; T ENST00000501748 Transcript missense_variant 1220/6759 1007/1611 336/536 Q/L cAg/cTg 1 1 ZNF623 HGNC HGNC:29084 protein_coding YES CCDS34957.1 ENSP00000445979 O75123 UPI0000139B4D NM_014789.3 tolerated(0.28) 1/1 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF244,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 143650879 143650879 A T 1 0 0 0 0 1 0 0 0 18622 188 7 4 4 ZNF623 8 143650879 Missense_Mutation SNP A C3N-01489_T 329572 143650879 1487757 351 25281 EPPK1 0 . GRCh38 8 143870896 143870896 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.2358G>T p.= p.V786V ENST00000615648 2/2 199 161 38 210 209 1 strelka-varscan-mutect EPPK1,synonymous_variant,p.=,ENST00000615648,NM_031308.3;EPPK1,synonymous_variant,p.=,ENST00000568225,; A ENST00000615648 Transcript synonymous_variant 2430/16002 2358/15267 786/5088 V gtG/gtT 1 -1 EPPK1 HGNC HGNC:15577 protein_coding YES CCDS75800.1 ENSP00000484472 A0A087X1U6 UPI0002065B93 NM_031308.3 2/2 Gene3D:3.90.1290.10,SMART_domains:SM00250,Superfamily_domains:SSF75399 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 143870896 143870896 C A 1 0 0 0 0 0 0 0 1 5038 697 25 2 2 EPPK1 8 143870896 Silent SNP C C3N-01489_T 220017 143870896 1267740 352 25282 TONSL 0 . GRCh38 8 144436126 144436126 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.2307G>T p.= p.V769V ENST00000409379 17/26 84 74 10 103 103 0 strelka-varscan-mutect TONSL,synonymous_variant,p.=,ENST00000409379,NM_013432.4;TONSL,downstream_gene_variant,,ENST00000613741,;MIR6893,upstream_gene_variant,,ENST00000613458,;TONSL-AS1,upstream_gene_variant,,ENST00000442850,;TONSL,non_coding_transcript_exon_variant,,ENST00000497613,; A ENST00000409379 Transcript synonymous_variant 2337/4502 2307/4137 769/1378 V gtG/gtT 1 -1 TONSL HGNC HGNC:7801 protein_coding YES CCDS34968.2 ENSP00000386239 Q96HA7 UPI0000424A3B NM_013432.4 17/26 hmmpanther:PTHR24139,hmmpanther:PTHR24139:SF31 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99183 1 1 1 1 0 A 2 1 81 144436126 144436126 C A 1 0 0 0 0 0 0 0 1 16838 581 21 2 2 TONSL 8 144436126 Silent SNP C C3N-01489_T 565230 144436126 702510 353 25283 JAK2 0 . GRCh38 9 5064930 5064930 + Missense_Mutation SNP A A C novel C3N-01489_T C3N-01489_N A A c.1104A>C p.Leu368Phe p.L368F ENST00000381652 9/25 93 77 16 129 129 0 strelka-varscan-mutect JAK2,missense_variant,p.Leu368Phe,ENST00000381652,NM_001322195.1,NM_001322194.1,NM_001322196.1,NM_004972.3;JAK2,missense_variant,p.Leu368Phe,ENST00000636127,; C ENST00000381652 Transcript missense_variant 1598/5285 1104/3399 368/1132 L/F ttA/ttC 1 1 JAK2 HGNC HGNC:6192 protein_coding YES CCDS6457.1 ENSP00000371067 O60674 UPI000012DA9E NM_001322195.1,NM_001322194.1,NM_001322196.1,NM_004972.3 deleterious(0) 9/25 PROSITE_profiles:PS50057,hmmpanther:PTHR24418:SF179,hmmpanther:PTHR24418,PIRSF_domain:PIRSF000636,Superfamily_domains:SSF50729,Prints_domain:PR01823 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 5064930 5064930 A C 1 0 0 0 0 1 0 0 0 7851 359 13 5 5 JAK2 9 5064930 Missense_Mutation SNP A C3N-01489_T 5064930 133329787 354 25284 RIC1 0 . GRCh38 9 5720216 5720216 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.475A>T p.Thr159Ser p.T159S ENST00000414202 5/26 109 102 7 169 169 0 strelka-varscan-mutect RIC1,missense_variant,p.Thr159Ser,ENST00000414202,NM_020829.3;RIC1,missense_variant,p.Thr159Ser,ENST00000418622,NM_001206557.1;RIC1,missense_variant,p.Thr159Ser,ENST00000251879,NM_001135920.2;RIC1,missense_variant,p.Thr88Ser,ENST00000545641,;RP11-207C16.4,non_coding_transcript_exon_variant,,ENST00000426764,;RIC1,non_coding_transcript_exon_variant,,ENST00000276898,; T ENST00000414202 Transcript missense_variant 666/6774 475/4272 159/1423 T/S Act/Tct 1 1 RIC1 HGNC HGNC:17686 protein_coding YES CCDS34982.2 ENSP00000416696 Q4ADV7 UPI00002110DE NM_020829.3 tolerated(0.05) 5/26 Gene3D:2.130.10.10,hmmpanther:PTHR22746,hmmpanther:PTHR22746:SF10,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 5720216 5720216 A T 1 0 0 0 0 1 0 0 0 13527 391 14 4 4 RIC1 9 5720216 Missense_Mutation SNP A C3N-01489_T 655286 5720216 132674501 355 25285 KIAA2026 0 . GRCh38 9 5968640 5968640 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1591C>A p.Leu531Met p.L531M ENST00000399933 3/8 138 122 16 244 243 1 strelka-varscan-mutect KIAA2026,missense_variant,p.Leu531Met,ENST00000399933,NM_001017969.2;KIAA2026,missense_variant,p.Leu531Met,ENST00000381461,;KIAA2026,missense_variant,p.Leu464Met,ENST00000513355,;KIAA2026,upstream_gene_variant,,ENST00000540714,; T ENST00000399933 Transcript missense_variant 1591/6988 1591/6312 531/2103 L/M Ctg/Atg 1 -1 KIAA2026 HGNC HGNC:23378 protein_coding YES ENSP00000382815 Q5HYC2 UPI0001533DB0 NM_001017969.2 deleterious(0.01) 3/8 hmmpanther:PTHR31095,hmmpanther:PTHR31095:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 5968640 5968640 G T 1 0 0 0 0 1 0 0 0 8134 991 35 2 2 KIAA2026 9 5968640 Missense_Mutation SNP G C3N-01489_T 248424 5968640 132426077 356 25286 PTPRD 0 . GRCh38 9 8319908 8319908 + Nonsense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.5593A>T p.Arg1865Ter p.R1865* ENST00000381196 42/43 160 142 18 282 282 0 strelka-varscan-mutect PTPRD,stop_gained,p.Arg1865Ter,ENST00000381196,NM_002839.3;PTPRD,stop_gained,p.Arg1865Ter,ENST00000356435,;PTPRD,stop_gained,p.Arg1459Ter,ENST00000355233,NM_130392.3;PTPRD,stop_gained,p.Arg1458Ter,ENST00000397617,;PTPRD,stop_gained,p.Arg1455Ter,ENST00000397611,NM_001040712.2;PTPRD,stop_gained,p.Arg1449Ter,ENST00000537002,NM_130393.3;PTPRD,stop_gained,p.Arg1865Ter,ENST00000540109,;PTPRD,stop_gained,p.Arg1458Ter,ENST00000486161,NM_130391.3;PTPRD,stop_gained,p.Arg1458Ter,ENST00000397606,NM_001171025.1; A ENST00000381196 Transcript stop_gained 6137/9911 5593/5739 1865/1912 R/* Aga/Tga 1 -1 PTPRD HGNC HGNC:9668 protein_coding YES CCDS43786.1 ENSP00000370593 P23468 UPI0000132990 NM_002839.3 42/43 Gene3D:3.90.190.10,Pfam_domain:PF00102,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF313,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 HIGH 1 SNV 5 1 PASS . . 0 207 0 0 2 0 0 0 -8.363811 0.9945295 1 1 1 0 A 4 1 81 8319908 8319908 T A 1 0 0 0 0 0 1 0 0 12953 1559 54 4 4 PTPRD 9 8319908 Nonsense_Mutation SNP T C3N-01489_T 2351268 8319908 130074809 357 25287 TAF1L 0 . GRCh38 9 32632391 32632391 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.3189G>T p.Met1063Ile p.M1063I ENST00000242310 1/1 258 231 27 397 397 0 varscan-mutect TAF1L,missense_variant,p.Met1063Ile,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; A ENST00000242310 Transcript missense_variant 3279/6216 3189/5481 1063/1826 M/I atG/atT 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0.05) 1/1 PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS rs1320786616 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 32632391 32632391 C A 1 0 0 0 0 1 0 0 0 15919 826 29 2 2 TAF1L 9 32632391 Missense_Mutation SNP C C3N-01489_T 24312483 32632391 105762326 358 25288 SMU1 0 . GRCh38 9 33056845 33056845 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.987G>A p.= p.Q329Q ENST00000397149 8/12 107 90 17 133 133 0 varscan-mutect SMU1,synonymous_variant,p.=,ENST00000397149,NM_018225.2; T ENST00000397149 Transcript synonymous_variant 1038/7122 987/1542 329/513 Q caG/caA 1 -1 SMU1 HGNC HGNC:18247 protein_coding YES CCDS6534.1 ENSP00000380336 Q2TAY7 A0MNN4 UPI0000022E9B NM_018225.2 8/12 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22848,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 33056845 33056845 C T 1 0 0 0 0 0 0 0 1 15138 912 32 3 3 SMU1 9 33056845 Silent SNP C C3N-01489_T 424454 33056845 105337872 359 25289 FAM205A 0 . GRCh38 9 34726598 34726598 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.642C>A p.= p.L214L ENST00000378788 4/4 153 142 11 234 234 0 varscan-mutect FAM205A,synonymous_variant,p.=,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript synonymous_variant 682/4225 642/4008 214/1335 L ctC/ctA 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 34726598 34726598 G T 1 0 0 0 0 0 0 0 1 5386 1161 41 2 2 FAM205A 9 34726598 Silent SNP G C3N-01489_T 1669753 34726598 103668119 360 25290 TLN1 0 . GRCh38 9 35699056 35699056 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.6975G>T p.Gln2325His p.Q2325H ENST00000314888 52/57 68 60 8 95 95 0 strelka-varscan-mutect TLN1,missense_variant,p.Gln2325His,ENST00000314888,NM_006289.3;TLN1,non_coding_transcript_exon_variant,,ENST00000489255,;TLN1,downstream_gene_variant,,ENST00000464379,;TLN1,downstream_gene_variant,,ENST00000465002,;TLN1,downstream_gene_variant,,ENST00000466916,; A ENST00000314888 Transcript missense_variant 7329/8823 6975/7626 2325/2541 Q/H caG/caT 1 -1 TLN1 HGNC HGNC:11845 protein_coding YES CCDS35009.1 ENSP00000316029 Q9Y490 UPI0000211375 NM_006289.3 deleterious(0.01) 52/57 Low_complexity_(Seg):seg,PROSITE_profiles:PS50945,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF7,Gene3D:1r0dB00,Superfamily_domains:SSF109885 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -17.6871 0.9999967 1 1 1 0 A 3 1 81 35699056 35699056 C A 1 0 0 0 0 1 0 0 0 16393 796 28 2 2 TLN1 9 35699056 Missense_Mutation SNP C C3N-01489_T 972458 35699056 102695661 361 25291 OR2S2 0 . GRCh38 9 35958083 35958083 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.16G>C p.Glu6Gln p.E6Q ENST00000341959 1/1 79 69 10 109 109 0 strelka-varscan-mutect OR2S2,missense_variant,p.Glu6Gln,ENST00000341959,NM_019897.2; G ENST00000341959 Transcript missense_variant 72/1047 16/960 6/319 E/Q Gag/Cag 1 -1 OR2S2 HGNC HGNC:8276 protein_coding YES CCDS6596.2 ENSP00000344040 Q9NQN1 UPI000003FF74 NM_019897.2 tolerated(1) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF176,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 205 5 0 0 0 0 0 -19.98995 1 1 1 1 0 G 3 3 81 35958083 35958083 C G 1 0 0 0 0 1 0 0 0 11093 835 29 4 4 OR2S2 9 35958083 Missense_Mutation SNP C C3N-01489_T 259027 35958083 102436634 362 25292 CARNMT1 0 . GRCh38 9 74984909 74984909 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1126G>T p.Glu376Ter p.E376* ENST00000376834 7/8 88 74 14 123 123 0 strelka-varscan-mutect CARNMT1,stop_gained,p.Glu376Ter,ENST00000376834,NM_001320497.1,NM_152420.1;C9orf41-AS1,intron_variant,,ENST00000455609,; A ENST00000376834 Transcript stop_gained,splice_region_variant 1279/4130 1126/1230 376/409 E/* Gag/Tag 1 -1 CARNMT1 HGNC HGNC:23435 protein_coding YES CCDS6649.1 ENSP00000366030 Q8N4J0 UPI000006D991 NM_001320497.1,NM_152420.1 7/8 hmmpanther:PTHR12303:SF6,hmmpanther:PTHR12303,Gene3D:3.40.50.150,Pfam_domain:PF07942,SMART_domains:SM01296,Superfamily_domains:SSF53335 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 74984909 74984909 C A 1 0 0 0 0 0 1 0 0 2354 927 32 2 2 CARNMT1 9 74984909 Nonsense_Mutation SNP C C3N-01489_T 39026826 74984909 63409808 363 25293 SPATA31D1 0 . GRCh38 9 81988862 81988862 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.44G>T p.Gly15Val p.G15V ENST00000344803 1/4 187 158 29 377 376 1 strelka-varscan-mutect SPATA31D1,missense_variant,p.Gly15Val,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,non_coding_transcript_exon_variant,,ENST00000603921,; T ENST00000344803 Transcript missense_variant 91/4833 44/4731 15/1576 G/V gGg/gTg 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 tolerated_low_confidence(0.32) 1/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 81988862 81988862 G T 1 0 0 0 0 1 0 0 0 15347 1232 43 2 2 SPATA31D1 9 81988862 Missense_Mutation SNP G C3N-01489_T 7003953 81988862 56405855 364 25294 NUTM2F 0 . GRCh38 9 94325617 94325617 + Missense_Mutation SNP G G C rs774933572 C3N-01489_T C3N-01489_N G G c.334C>G p.Pro112Ala p.P112A ENST00000253262 2/7 91 81 10 153 153 0 varscan-mutect NUTM2F,missense_variant,p.Pro112Ala,ENST00000253262,NM_017561.1;NUTM2F,missense_variant,p.Pro112Ala,ENST00000341207,; C ENST00000253262 Transcript missense_variant 355/2561 334/2271 112/756 P/A Cca/Gca rs774933572 1 -1 NUTM2F HGNC HGNC:23450 protein_coding YES CCDS47994.1 ENSP00000253262 A1L443 UPI00001D771D NM_017561.1 tolerated(0.11) 2/7 Pfam_domain:PF12881,hmmpanther:PTHR22879,hmmpanther:PTHR22879:SF12 MODERATE 1 SNV 1 1 PASS rs774933572 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 94325617 94325617 G C 1 0 0 0 0 1 0 0 0 10851 1174 41 4 4 NUTM2F 9 94325617 Missense_Mutation SNP G C3N-01489_T 12336755 94325617 44069100 365 25295 PAPPA 0 . GRCh38 9 116332372 116332372 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.3301G>A p.Val1101Ile p.V1101I ENST00000328252 12/22 99 86 13 133 133 0 strelka-varscan-mutect PAPPA,missense_variant,p.Val1101Ile,ENST00000328252,NM_002581.3;PAPPA,upstream_gene_variant,,ENST00000460463,; A ENST00000328252 Transcript missense_variant 3670/10959 3301/4884 1101/1627 V/I Gtc/Atc 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 tolerated(1) 12/22 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 116332372 116332372 G A 1 0 0 0 0 1 0 0 0 11512 1377 48 3 3 PAPPA 9 116332372 Missense_Mutation SNP G C3N-01489_T 22006755 116332372 22062345 366 25296 C9orf78 0 . GRCh38 9 129829295 129829295 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.688G>C p.Glu230Gln p.E230Q ENST00000372447 8/9 48 43 5 113 113 0 strelka-varscan-mutect C9orf78,missense_variant,p.Glu230Gln,ENST00000372447,NM_016520.2;C9orf78,non_coding_transcript_exon_variant,,ENST00000461762,;C9orf78,non_coding_transcript_exon_variant,,ENST00000480023,;C9orf78,non_coding_transcript_exon_variant,,ENST00000461349,;C9orf78,non_coding_transcript_exon_variant,,ENST00000461539,;C9orf78,downstream_gene_variant,,ENST00000492991,;C9orf78,downstream_gene_variant,,ENST00000495934,; G ENST00000372447 Transcript missense_variant 742/1795 688/870 230/289 E/Q Gag/Cag 1 -1 C9orf78 HGNC HGNC:24932 protein_coding YES CCDS6931.1 ENSP00000361524 Q9NZ63 UPI000006F0CA NM_016520.2 deleterious(0.02) 8/9 hmmpanther:PTHR13486:SF2,hmmpanther:PTHR13486 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.59054 1 1 1 1 0 G 3 3 81 129829295 129829295 C G 1 0 0 0 0 1 0 0 0 2191 835 29 4 4 C9orf78 9 129829295 Missense_Mutation SNP C C3N-01489_T 13496923 129829295 8565422 367 25297 GFI1B 0 . GRCh38 9 132986775 132986775 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.97C>A p.Pro33Thr p.P33T ENST00000339463 6/11 140 124 16 240 240 0 strelka-varscan-mutect GFI1B,missense_variant,p.Pro33Thr,ENST00000339463,NM_004188.5;GFI1B,missense_variant,p.Pro33Thr,ENST00000636137,;GFI1B,missense_variant,p.Pro33Thr,ENST00000372122,;GFI1B,missense_variant,p.Pro33Thr,ENST00000636263,;GFI1B,missense_variant,p.Pro33Thr,ENST00000372123,NM_001135031.1; A ENST00000339463 Transcript missense_variant 916/2449 97/993 33/330 P/T Ccg/Acg 1 1 GFI1B HGNC HGNC:4238 protein_coding YES CCDS6957.1 ENSP00000344782 Q5VTD9 UPI000013E4EE NM_004188.5 tolerated(0.24) 6/11 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99987 0.9999999 1 1 1 0 A 3 1 81 132986775 132986775 C A 1 0 0 0 0 1 0 0 0 6214 637 22 2 2 GFI1B 9 132986775 Missense_Mutation SNP C C3N-01489_T 3157480 132986775 5407942 368 25298 PPP1R26 0 . GRCh38 9 135484902 135484902 + Frame_Shift_Del DEL G G - novel C3N-01489_T C3N-01489_N G G c.394delG p.Asp132ThrfsTer10 p.D132Tfs*10 ENST00000356818 4/4 34 26 8 51 51 0 sindel-varindel-pindel PPP1R26,frameshift_variant,p.Asp132ThrfsTer10,ENST00000356818,NM_014811.3;PPP1R26,frameshift_variant,p.Asp132ThrfsTer10,ENST00000401470,;PPP1R26,frameshift_variant,p.Asp132ThrfsTer10,ENST00000605286,;PPP1R26,frameshift_variant,p.Asp132ThrfsTer10,ENST00000604351,;PPP1R26,frameshift_variant,p.Asp132ThrfsTer10,ENST00000605660,;PPP1R26-AS1,upstream_gene_variant,,ENST00000455039,;PPP1R26-AS1,upstream_gene_variant,,ENST00000603893,;PPP1R26-AS1,upstream_gene_variant,,ENST00000605260,;PPP1R26,intron_variant,,ENST00000602993,; - ENST00000356818 Transcript frameshift_variant 941/4932 392/3630 131/1209 R/X aGg/ag 1 1 PPP1R26 HGNC HGNC:29089 protein_coding YES CCDS6988.1 ENSP00000349274 Q5T8A7 UPI000013DB17 NM_014811.3 4/4 Pfam_domain:PF15740,hmmpanther:PTHR15724 HIGH 1 deletion 1 2 1 PASS . . 0 203 7 0 0 0 0 0 -19.91013 0.9999998 1 1 1 0 - 7 5 81 135484902 135484902 G - 1 0 1 0 1 0 0 0 0 12484 1000 35 0 0 PPP1R26 9 135484902 Frame_Shift_Del DEL G C3N-01489_T 2498127 135484902 2909815 369 25299 ABCA2 0 . GRCh38 9 137016958 137016958 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.2720A>G p.Tyr907Cys p.Y907C ENST00000341511 19/49 189 161 28 252 252 0 strelka-varscan-mutect ABCA2,missense_variant,p.Tyr907Cys,ENST00000265662,;ABCA2,missense_variant,p.Tyr906Cys,ENST00000371605,;ABCA2,missense_variant,p.Tyr937Cys,ENST00000614293,;ABCA2,missense_variant,p.Tyr907Cys,ENST00000341511,NM_001606.4,NM_212533.2;ABCA2,missense_variant,p.Tyr936Cys,ENST00000487109,;ABCA2,missense_variant,p.Tyr257Cys,ENST00000479446,;ABCA2,missense_variant,p.Tyr254Cys,ENST00000488535,;ABCA2,non_coding_transcript_exon_variant,,ENST00000459850,;ABCA2,downstream_gene_variant,,ENST00000464876,;ABCA2,downstream_gene_variant,,ENST00000492260,;ABCA2,downstream_gene_variant,,ENST00000494046,;ABCA2,downstream_gene_variant,,ENST00000476211,;ABCA2,upstream_gene_variant,,ENST00000431584,;ABCA2,downstream_gene_variant,,ENST00000398207,;ABCA2,downstream_gene_variant,,ENST00000470535,;ABCA2,downstream_gene_variant,,ENST00000466707,;ABCA2,downstream_gene_variant,,ENST00000467624,; C ENST00000341511 Transcript missense_variant 2770/8063 2720/7311 907/2436 Y/C tAt/tGt 1 -1 ABCA2 HGNC HGNC:32 protein_coding YES CCDS43909.1 ENSP00000344155 Q9BZC7 UPI0000049F97 NM_001606.4,NM_212533.2 deleterious(0) 19/49 Transmembrane_helices:TMhelix,hmmpanther:PTHR19229:SF116,hmmpanther:PTHR19229,Pfam_domain:PF12698 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 137016958 137016958 T C 1 0 0 0 0 1 0 0 0 36 1406 49 5 5 ABCA2 9 137016958 Missense_Mutation SNP T C3N-01489_T 1532056 137016958 1377759 370 25300 TPRN 0 . GRCh38 9 137199598 137199598 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1114G>T p.Val372Leu p.V372L ENST00000409012 1/4 172 153 19 263 263 0 strelka-varscan-mutect TPRN,missense_variant,p.Val372Leu,ENST00000409012,NM_001128228.2;TPRN,missense_variant,p.Val170Leu,ENST00000333046,;TMEM203,downstream_gene_variant,,ENST00000343666,NM_053045.1;TPRN,intron_variant,,ENST00000541945,;TPRN,upstream_gene_variant,,ENST00000477345,; A ENST00000409012 Transcript missense_variant 1201/2718 1114/2136 372/711 V/L Gtg/Ttg 1 -1 TPRN HGNC HGNC:26894 protein_coding YES CCDS56594.1 ENSP00000387100 Q4KMQ1 UPI0001722188 NM_001128228.2 tolerated(0.23) 1/4 hmmpanther:PTHR21685:SF1,hmmpanther:PTHR21685 MODERATE 1 SNV 1 1 PASS rs1440793236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 137199598 137199598 C A 1 0 0 0 0 1 0 0 0 16902 507 18 2 2 TPRN 9 137199598 Missense_Mutation SNP C C3N-01489_T 182640 137199598 1195119 371 25301 EXD3 0 . GRCh38 9 137349525 137349525 + Missense_Mutation SNP C C A rs551667120 C3N-01489_T C3N-01489_N C C c.1501G>T p.Val501Leu p.V501L ENST00000340951 15/22 38 32 6 61 61 0 strelka-varscan-mutect EXD3,missense_variant,p.Val501Leu,ENST00000340951,NM_017820.4;EXD3,non_coding_transcript_exon_variant,,ENST00000484392,;EXD3,downstream_gene_variant,,ENST00000490886,;EXD3,downstream_gene_variant,,ENST00000478350,;EXD3,3_prime_UTR_variant,,ENST00000478344,;EXD3,3_prime_UTR_variant,,ENST00000491734,;EXD3,non_coding_transcript_exon_variant,,ENST00000487745,;EXD3,downstream_gene_variant,,ENST00000472958,; A ENST00000340951 Transcript missense_variant 1697/2872 1501/2631 501/876 V/L Gtg/Ttg rs551667120 1 -1 EXD3 HGNC HGNC:26023 protein_coding YES CCDS48066.1 ENSP00000340474 Q8N9H8 A0A140VJP9 UPI00003676BC NM_017820.4 tolerated(0.37) 15/22 hmmpanther:PTHR13620:SF10,hmmpanther:PTHR13620,Pfam_domain:PF01612,SMART_domains:SM00474,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS rs551667120 . 0 208 2 0 0 0 0 0 -15.84634 1 1 1 1 0 A 3 1 81 137349525 137349525 C A 1 0 0 0 0 1 0 0 0 5166 507 18 2 2 EXD3 9 137349525 Missense_Mutation SNP C C3N-01489_T 149927 137349525 1045192 372 25302 GDI2 0 . GRCh38 10 5800707 5800707 + Splice_Site SNP T T A novel C3N-01489_T C3N-01489_N T T c.46-2A>T p.X16_splice ENST00000380191 152 138 14 190 190 0 strelka-mutect GDI2,splice_acceptor_variant,,ENST00000380191,NM_001494.3;GDI2,splice_acceptor_variant,,ENST00000380181,NM_001115156.1;GDI2,splice_acceptor_variant,,ENST00000456041,;GDI2,splice_acceptor_variant,,ENST00000608581,;GDI2,splice_acceptor_variant,,ENST00000609712,;GDI2,splice_acceptor_variant,,ENST00000380127,;GDI2,intron_variant,,ENST00000418688,; A ENST00000380191 Transcript splice_acceptor_variant -/2412 46/1338 16/445 1 -1 GDI2 HGNC HGNC:4227 protein_coding YES CCDS7071.1 ENSP00000369538 P50395 Q6IAT1 UPI000012B39E NM_001494.3 1/10 HIGH 1 SNV 1 1 PASS . . 0 202 2 5 0 0 0 0 -19.21193 0.9971786 1 1 1 0 A 5 1 81 5800707 5800707 T A 1 0 0 0 0 0 0 1 0 6194 1536 53 4 4 GDI2 10 5800707 Splice_Site SNP T C3N-01489_T 5800707 127996715 373 25303 PRKCQ 0 . GRCh38 10 6456731 6456731 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1590G>T p.Met530Ile p.M530I ENST00000263125 15/18 245 217 28 326 325 1 strelka-varscan-mutect PRKCQ,missense_variant,p.Met530Ile,ENST00000263125,NM_001323265.1,NM_006257.4,NM_001282644.1;PRKCQ,missense_variant,p.Met405Ile,ENST00000539722,NM_001323266.1,NM_001282645.1;PRKCQ,missense_variant,p.Met530Ile,ENST00000397176,NM_001242413.2;PRKCQ,missense_variant,p.Met494Ile,ENST00000610727,; A ENST00000263125 Transcript missense_variant 1690/3285 1590/2121 530/706 M/I atG/atT 1 -1 PRKCQ HGNC HGNC:9410 protein_coding YES CCDS7079.1 ENSP00000263125 Q04759 UPI000012DF74 NM_001323265.1,NM_006257.4,NM_001282644.1 tolerated(1) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000551,PIRSF_domain:PIRSF501105,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF181,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 6456731 6456731 C A 1 0 0 0 0 1 0 0 0 12648 478 17 2 2 PRKCQ 10 6456731 Missense_Mutation SNP C C3N-01489_T 656024 6456731 127340691 374 25304 DHTKD1 0 . GRCh38 10 12084575 12084575 + Nonsense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.346G>T p.Glu116Ter p.E116* ENST00000263035 3/17 211 180 31 320 320 0 strelka-varscan-mutect DHTKD1,stop_gained,p.Glu116Ter,ENST00000263035,NM_018706.6;DHTKD1,stop_gained,p.Glu116Ter,ENST00000437298,;DHTKD1,upstream_gene_variant,,ENST00000415935,;DHTKD1,intron_variant,,ENST00000465617,; T ENST00000263035 Transcript stop_gained 408/5159 346/2760 116/919 E/* Gag/Tag COSM5094920 1 1 DHTKD1 HGNC HGNC:23537 protein_coding YES CCDS7087.1 ENSP00000263035 Q96HY7 UPI000013D38C NM_018706.6 3/17 hmmpanther:PTHR23152:SF11,hmmpanther:PTHR23152,PIRSF_domain:PIRSF000157,TIGRFAM_domain:TIGR00239,Superfamily_domains:SSF52518 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 12084575 12084575 G T 1 0 0 0 0 0 1 0 0 4304 1291 45 2 2 DHTKD1 10 12084575 Nonsense_Mutation SNP G C3N-01489_T 5627844 12084575 121712847 375 25305 APBB1IP 0 . GRCh38 10 26496326 26496326 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.95C>G p.Pro32Arg p.P32R ENST00000376236 4/15 168 155 13 276 276 0 strelka-varscan-mutect APBB1IP,missense_variant,p.Pro32Arg,ENST00000376236,NM_019043.3;APBB1IP,missense_variant,p.Pro32Arg,ENST00000356785,; G ENST00000376236 Transcript missense_variant 550/2771 95/2001 32/666 P/R cCt/cGt 1 1 APBB1IP HGNC HGNC:17379 protein_coding YES CCDS31167.1 ENSP00000365411 Q7Z5R6 UPI00001AF165 NM_019043.3 tolerated(0.13) 4/15 hmmpanther:PTHR11243,hmmpanther:PTHR11243:SF14,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 26496326 26496326 C G 1 0 0 0 0 1 0 0 0 880 681 24 4 4 APBB1IP 10 26496326 Missense_Mutation SNP C C3N-01489_T 14411751 26496326 107301096 376 25306 PARD3 0 . GRCh38 10 34119714 34119714 + Missense_Mutation SNP G G T rs745473559 C3N-01489_T C3N-01489_N G G c.3576C>A p.Ser1192Arg p.S1192R ENST00000374789 24/25 115 105 10 170 170 0 strelka-varscan-mutect PARD3,missense_variant,p.Ser1192Arg,ENST00000374789,NM_019619.3;PARD3,missense_variant,p.Ser1189Arg,ENST00000374788,NM_001184785.1;PARD3,missense_variant,p.Ser1176Arg,ENST00000545693,NM_001184786.1;PARD3,missense_variant,p.Ser1155Arg,ENST00000346874,NM_001184787.1;PARD3,missense_variant,p.Ser1146Arg,ENST00000350537,NM_001184789.1,NM_001184788.1;PARD3,missense_variant,p.Ser1132Arg,ENST00000374790,;PARD3,missense_variant,p.Ser1102Arg,ENST00000545260,NM_001184790.1;PARD3,missense_variant,p.Ser1080Arg,ENST00000374794,NM_001184791.1; T ENST00000374789 Transcript missense_variant 3902/6005 3576/4071 1192/1356 S/R agC/agA rs745473559 1 -1 PARD3 HGNC HGNC:16051 protein_coding YES CCDS7178.1 ENSP00000363921 Q8TEW0 UPI0000073A9F NM_019619.3 deleterious_low_confidence(0.02) 24/25 hmmpanther:PTHR16484,hmmpanther:PTHR16484:SF10 MODERATE 1 SNV 1 1 PASS rs745473559 . 0 205 2 2 0 0 0 0 -15.00284 0.9999937 1 1 1 0 T 3 4 81 34119714 34119714 G T 1 0 0 0 0 1 0 0 0 11523 1078 38 1 1 PARD3 10 34119714 Missense_Mutation SNP G C3N-01489_T 7623388 34119714 99677708 377 25307 ZNF37A 0 . GRCh38 10 38117467 38117467 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.316G>A p.Glu106Lys p.E106K ENST00000361085 7/7 77 66 11 132 132 0 strelka-varscan-mutect ZNF37A,missense_variant,p.Glu106Lys,ENST00000361085,NM_001178101.1,NM_003421.2;ZNF37A,missense_variant,p.Glu106Lys,ENST00000351773,NM_001324248.1,NM_001324246.1,NM_001324249.1,NM_001007094.2;ZNF37A,intron_variant,,ENST00000638053,NM_001324256.1;ZNF37A,downstream_gene_variant,,ENST00000479469,;ZNF37A,downstream_gene_variant,,ENST00000477790,; A ENST00000361085 Transcript missense_variant 661/8738 316/1686 106/561 E/K Gaa/Aaa 1 1 ZNF37A HGNC HGNC:13102 protein_coding YES CCDS31183.1 ENSP00000354377 P17032 UPI000006E045 NM_001178101.1,NM_003421.2 tolerated(0.89) 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR24377:SF188,hmmpanther:PTHR24377 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.99998 1 1 1 1 0 A 3 1 81 38117467 38117467 G A 1 0 0 0 0 1 0 0 0 18444 1291 45 3 3 ZNF37A 10 38117467 Missense_Mutation SNP G C3N-01489_T 3997753 38117467 95679955 378 25308 RET 0 . GRCh38 10 43100653 43100653 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.268G>T p.Glu90Ter p.E90* ENST00000355710 2/20 377 337 40 487 486 1 strelka-varscan-mutect RET,stop_gained,p.Glu90Ter,ENST00000355710,NM_020975.4;RET,stop_gained,p.Glu90Ter,ENST00000615310,;RET,stop_gained,p.Glu90Ter,ENST00000340058,NM_020630.4;RET,intron_variant,,ENST00000498820,;RET,upstream_gene_variant,,ENST00000479913,; T ENST00000355710 Transcript stop_gained 500/5659 268/3345 90/1114 E/* Gag/Tag 1 1 RET HGNC HGNC:9967 protein_coding YES CCDS7200.1 ENSP00000347942 P07949 A0A024R7T2 UPI00001336E1 NM_020975.4 2/20 PIRSF_domain:PIRSF000631 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 43100653 43100653 G T 1 0 0 0 0 0 1 0 0 13406 1175 41 2 2 RET 10 43100653 Nonsense_Mutation SNP G C3N-01489_T 4983186 43100653 90696769 379 25309 ANTXRL 0 . GRCh38 10 46311650 46311650 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.1314G>A p.= p.G438G ENST00000620264 15/17 109 94 15 153 153 0 strelka-varscan-mutect ANTXRL,synonymous_variant,p.=,ENST00000620264,NM_001278688.2;ANTXRL,synonymous_variant,p.=,ENST00000622632,;ANTXRL,3_prime_UTR_variant,,ENST00000617088,;ANTXRL,downstream_gene_variant,,ENST00000614267,; A ENST00000620264 Transcript synonymous_variant 1579/2206 1314/1896 438/631 G ggG/ggA 1 1 ANTXRL HGNC HGNC:27277 protein_coding YES CCDS60524.1 ENSP00000480615 A6NF34 UPI00015B6A6A NM_001278688.2 15/17 Low_complexity_(Seg):seg,hmmpanther:PTHR16059:SF10,hmmpanther:PTHR16059 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 46311650 46311650 G A 1 0 0 0 0 0 0 0 1 820 1161 41 3 3 ANTXRL 10 46311650 Silent SNP G C3N-01489_T 3210997 46311650 87485772 380 25310 RBP3 0 . GRCh38 10 47349265 47349265 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.781G>C p.Gly261Arg p.G261R ENST00000584701 1/4 260 233 27 384 384 0 strelka-varscan-mutect RBP3,missense_variant,p.Gly261Arg,ENST00000584701,NM_002900.2; C ENST00000584701 Transcript missense_variant 895/4276 781/3744 261/1247 G/R Gga/Cga 1 1 RBP3 HGNC HGNC:9921 protein_coding YES CCDS73119.1 ENSP00000463151 P10745 UPI000012D87A NM_002900.2 deleterious(0) 1/4 Gene3D:3.90.226.10,Pfam_domain:PF03572,hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF3,SMART_domains:SM00245,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 47349265 47349265 G C 1 0 0 0 0 1 0 0 0 13325 1233 43 4 4 RBP3 10 47349265 Missense_Mutation SNP G C3N-01489_T 1037615 47349265 86448157 381 25311 FAM25C 0 . GRCh38 10 47997700 47997700 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.113A>T p.His38Leu p.H38L ENST00000617224 2/3 199 179 20 289 289 0 varscan-mutect FAM25C,missense_variant,p.His38Leu,ENST00000617224,NM_001137548.2; A ENST00000617224 Transcript missense_variant 139/319 113/270 38/89 H/L cAt/cTt 1 -1 FAM25C HGNC HGNC:23586 protein_coding YES CCDS76299.1 ENSP00000485370 B3EWG5,B3EWG4 UPI00003666A7 NM_001137548.2 deleterious_low_confidence(0) 2/3 hmmpanther:PTHR34994,hmmpanther:PTHR34994:SF1,Pfam_domain:PF15825,Prints_domain:PR02048 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 47997700 47997700 T A 1 0 0 0 0 1 0 0 0 5429 1464 51 4 4 FAM25C 10 47997700 Missense_Mutation SNP T C3N-01489_T 648435 47997700 85799722 382 25312 C10orf71 0 . GRCh38 10 49323158 49323158 + Missense_Mutation SNP A A C novel C3N-01489_T C3N-01489_N A A c.613A>C p.Thr205Pro p.T205P ENST00000374144 3/3 215 180 35 310 310 0 strelka-varscan-mutect C10orf71,missense_variant,p.Thr205Pro,ENST00000374144,NM_001135196.1; C ENST00000374144 Transcript missense_variant 901/5230 613/4308 205/1435 T/P Acc/Ccc 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 tolerated(0.18) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 49323158 49323158 A C 1 0 0 0 0 1 0 0 0 1769 159 6 5 5 C10orf71 10 49323158 Missense_Mutation SNP A C3N-01489_T 1325458 49323158 84474264 383 25313 C10orf53 0 . GRCh38 10 49708493 49708493 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.350G>T p.Cys117Phe p.C117F ENST00000374112 3/3 347 312 35 519 519 0 strelka-varscan-mutect C10orf53,missense_variant,p.Cys117Phe,ENST00000374112,NM_182554.2;C10orf53,missense_variant,p.Cys117Phe,ENST00000535836,; T ENST00000374112 Transcript missense_variant 362/2130 350/474 117/157 C/F tGt/tTt 1 1 C10orf53 HGNC HGNC:27421 protein_coding YES CCDS31202.1 ENSP00000363226 Q8N6V4 UPI00001406B3 NM_182554.2 deleterious_low_confidence(0) 3/3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 49708493 49708493 G T 1 0 0 0 0 1 0 0 0 1764 1377 48 2 2 C10orf53 10 49708493 Missense_Mutation SNP G C3N-01489_T 385335 49708493 84088929 384 25314 OGDHL 0 . GRCh38 10 49745437 49745437 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.1536C>T p.= p.L512L ENST00000374103 12/23 249 234 15 351 351 0 strelka-varscan-mutect OGDHL,synonymous_variant,p.=,ENST00000374103,NM_018245.2;OGDHL,synonymous_variant,p.=,ENST00000419399,NM_001143996.1;OGDHL,synonymous_variant,p.=,ENST00000432695,NM_001143997.1;OGDHL,upstream_gene_variant,,ENST00000496884,; A ENST00000374103 Transcript synonymous_variant 1622/3704 1536/3033 512/1010 L ctC/ctT 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 12/23 Gene3D:3.40.50.970,Pfam_domain:PF00676,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 LOW 1 SNV 1 1 PASS rs997298253 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 49745437 49745437 G A 1 0 0 0 0 0 0 0 1 10914 1277 45 3 3 OGDHL 10 49745437 Silent SNP G C3N-01489_T 36944 49745437 84051985 385 25315 DNA2 0 . GRCh38 10 68450115 68450115 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.852A>G p.Ile284Met p.I284M ENST00000358410 6/21 242 220 22 314 314 0 strelka-varscan-mutect DNA2,missense_variant,p.Ile284Met,ENST00000358410,NM_001080449.2;DNA2,missense_variant,p.Ile284Met,ENST00000551118,;DNA2,missense_variant,p.Ile284Met,ENST00000399180,;DNA2,missense_variant,p.Ile284Met,ENST00000399179,; C ENST00000358410 Transcript missense_variant 903/4208 852/3183 284/1060 I/M atA/atG 1 -1 DNA2 HGNC HGNC:2939 protein_coding YES CCDS44415.2 ENSP00000351185 P51530 UPI00001C1EDB NM_001080449.2 tolerated(0.2) 6/21 hmmpanther:PTHR10887:SF14,hmmpanther:PTHR10887 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 68450115 68450115 T C 1 0 0 0 0 1 0 0 0 4405 1628 57 5 5 DNA2 10 68450115 Missense_Mutation SNP T C3N-01489_T 18704678 68450115 65347307 386 25316 KCNMA1 0 . GRCh38 10 77637450 77637450 + Nonsense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.193A>T p.Lys65Ter p.K65* ENST00000286628 1/28 325 295 30 446 446 0 strelka-varscan-mutect KCNMA1,stop_gained,p.Lys65Ter,ENST00000286627,NM_002247.3;KCNMA1,stop_gained,p.Lys65Ter,ENST00000286628,NM_001161352.1;KCNMA1,stop_gained,p.Lys65Ter,ENST00000372443,;KCNMA1,stop_gained,p.Lys65Ter,ENST00000372440,NM_001014797.2;KCNMA1,stop_gained,p.Lys65Ter,ENST00000404771,;KCNMA1,stop_gained,p.Lys39Ter,ENST00000457953,;KCNMA1,stop_gained,p.Lys65Ter,ENST00000626620,NM_001161353.1;KCNMA1,stop_gained,p.Lys39Ter,ENST00000372421,;KCNMA1,stop_gained,p.Lys2Ter,ENST00000372408,;KCNMA1,stop_gained,p.Lys16Ter,ENST00000372403,;KCNMA1,stop_gained,p.Lys65Ter,ENST00000618048,NM_001271520.1;KCNMA1,stop_gained,p.Lys65Ter,ENST00000480683,NM_001271522.1;KCNMA1,stop_gained,p.Lys65Ter,ENST00000481070,NM_001271521.1;KCNMA1,upstream_gene_variant,,ENST00000372437,; A ENST00000286628 Transcript stop_gained 193/6100 193/3711 65/1236 K/* Aag/Tag 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 1/28 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 77637450 77637450 T A 1 0 0 0 0 0 1 0 0 7990 1821 63 4 4 KCNMA1 10 77637450 Nonsense_Mutation SNP T C3N-01489_T 9187335 77637450 56159972 387 25317 DLG5 0 . GRCh38 10 77811192 77811192 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.4365C>T p.= p.G1455G ENST00000372391 23/32 159 146 13 228 228 0 strelka-varscan-mutect DLG5,synonymous_variant,p.=,ENST00000372391,NM_004747.3;DLG5,synonymous_variant,p.=,ENST00000424842,;DLG5,non_coding_transcript_exon_variant,,ENST00000459739,;DLG5,non_coding_transcript_exon_variant,,ENST00000489547,;DLG5,upstream_gene_variant,,ENST00000484525,;DLG5,3_prime_UTR_variant,,ENST00000468332,;DLG5,non_coding_transcript_exon_variant,,ENST00000475613,;DLG5,non_coding_transcript_exon_variant,,ENST00000463362,;DLG5,downstream_gene_variant,,ENST00000476354,; A ENST00000372391 Transcript synonymous_variant 4371/7415 4365/5760 1455/1919 G ggC/ggT 1 -1 DLG5 HGNC HGNC:2904 protein_coding YES CCDS7353.2 ENSP00000361467 Q8TDM6 UPI0000470041 NM_004747.3 23/32 hmmpanther:PTHR13865:SF31,hmmpanther:PTHR13865,Pfam_domain:PF16610 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 77811192 77811192 G A 1 0 0 0 0 0 0 0 1 4365 1306 46 3 3 DLG5 10 77811192 Silent SNP G C3N-01489_T 173742 77811192 55986230 388 25318 SFTPA2 0 . GRCh38 10 79558076 79558076 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.346C>T p.His116Tyr p.H116Y ENST00000372325 5/6 278 255 23 382 381 1 varscan-mutect SFTPA2,missense_variant,p.His116Tyr,ENST00000372325,NM_001320813.1,NM_001320814.1,NM_001098668.2;SFTPA2,missense_variant,p.His116Tyr,ENST00000372327,;SFTPA2,missense_variant,p.His116Tyr,ENST00000417041,;SFTPA2,downstream_gene_variant,,ENST00000492049,; A ENST00000372325 Transcript missense_variant 431/2189 346/747 116/248 H/Y Cat/Tat 1 -1 SFTPA2 HGNC HGNC:10799 protein_coding YES CCDS41540.1 ENSP00000361400 Q8IWL1 UPI000013CAFF NM_001320813.1,NM_001320814.1,NM_001098668.2 tolerated(0.05) 5/6 hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF21,Gene3D:3.10.100.10,Superfamily_domains:SSF57944 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 79558076 79558076 G A 1 0 0 0 0 1 0 0 0 14450 1377 48 3 3 SFTPA2 10 79558076 Missense_Mutation SNP G C3N-01489_T 1746884 79558076 54239346 389 25319 PLAC9 0 . GRCh38 10 80144334 80144334 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.274C>A p.Leu92Ile p.L92I ENST00000372263 3/4 98 92 6 136 136 0 strelka-varscan-mutect PLAC9,missense_variant,p.Leu92Ile,ENST00000372263,NM_001012973.1;PLAC9,missense_variant,p.Leu50Ile,ENST00000372270,;PLAC9,intron_variant,,ENST00000372267,;PLAC9,non_coding_transcript_exon_variant,,ENST00000465660,; A ENST00000372263 Transcript missense_variant 316/785 274/294 92/97 L/I Ctt/Att 1 1 PLAC9 HGNC HGNC:19255 protein_coding YES CCDS31232.1 ENSP00000361337 Q5JTB6 UPI0000161743 NM_001012973.1 tolerated(0.44) 3/4 Pfam_domain:PF15205,hmmpanther:PTHR37355 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -12.70724 1 1 1 1 0 A 3 1 81 80144334 80144334 C A 1 0 0 0 0 1 0 0 0 12111 681 24 2 2 PLAC9 10 80144334 Missense_Mutation SNP C C3N-01489_T 586258 80144334 53653088 390 25320 MYOF 0 . GRCh38 10 93351434 93351434 + Silent SNP T T G novel C3N-01489_T C3N-01489_N T T c.3801A>C p.= p.A1267A ENST00000359263 34/54 112 99 13 197 197 0 strelka-mutect MYOF,synonymous_variant,p.=,ENST00000359263,NM_013451.3;MYOF,synonymous_variant,p.=,ENST00000358334,NM_133337.2;MYOF,synonymous_variant,p.=,ENST00000463743,; G ENST00000359263 Transcript synonymous_variant 3801/6719 3801/6186 1267/2061 A gcA/gcC 1 -1 MYOF HGNC HGNC:3656 protein_coding YES CCDS41551.1 ENSP00000352208 Q9NZM1 UPI000012FBA1 NM_013451.3 34/54 Gene3D:2.60.40.150,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF40,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 93351434 93351434 T G 1 0 0 0 0 0 0 0 1 10090 1567 55 5 5 MYOF 10 93351434 Silent SNP T C3N-01489_T 13207100 93351434 40445988 391 25321 COL17A1 0 . GRCh38 10 104047774 104047774 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2300G>T p.Gly767Val p.G767V ENST00000353479 31/56 436 396 40 657 656 1 strelka-varscan-mutect COL17A1,missense_variant,p.Gly767Val,ENST00000353479,NM_000494.3;COL17A1,missense_variant,p.Gly767Val,ENST00000369733,;COL17A1,downstream_gene_variant,,ENST00000401264,; A ENST00000353479 Transcript missense_variant 2591/5734 2300/4494 767/1497 G/V gGc/gTc 1 -1 COL17A1 HGNC HGNC:2194 protein_coding YES CCDS7554.1 ENSP00000340937 Q9UMD9 UPI000006DB58 NM_000494.3 deleterious(0) 31/56 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 104047774 104047774 C A 1 0 0 0 0 1 0 0 0 3462 739 26 2 2 COL17A1 10 104047774 Missense_Mutation SNP C C3N-01489_T 10696340 104047774 29749648 392 25322 SORCS3 0 . GRCh38 10 104641371 104641371 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.44C>G p.Ala15Gly p.A15G ENST00000369701 1/27 76 68 8 137 137 0 strelka-varscan-mutect SORCS3,missense_variant,p.Ala15Gly,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Ala15Gly,ENST00000369699,; G ENST00000369701 Transcript missense_variant 271/5757 44/3669 15/1222 A/G gCg/gGg 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious_low_confidence(0.04) 1/27 Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1250863365 . 0 201 7 2 0 0 0 0 -13.59911 0.999691 1 1 1 0 G 3 3 81 104641371 104641371 C G 1 0 0 0 0 1 0 0 0 15254 768 27 4 4 SORCS3 10 104641371 Missense_Mutation SNP C C3N-01489_T 593597 104641371 29156051 393 25323 SORCS3 0 . GRCh38 10 104641551 104641551 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.224C>A p.Ala75Glu p.A75E ENST00000369701 1/27 120 107 13 183 183 0 strelka-varscan-mutect SORCS3,missense_variant,p.Ala75Glu,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Ala75Glu,ENST00000369699,; A ENST00000369701 Transcript missense_variant 451/5757 224/3669 75/1222 A/E gCg/gAg 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious_low_confidence(0.02) 1/27 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 104641551 104641551 C A 1 0 0 0 0 1 0 0 0 15254 768 27 1 1 SORCS3 10 104641551 Missense_Mutation SNP C C3N-01489_T 180 104641551 29155871 394 25324 SORCS3 0 . GRCh38 10 105245609 105245609 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.2936T>A p.Val979Asp p.V979D ENST00000369701 21/27 159 149 10 197 197 0 strelka-varscan-mutect SORCS3,missense_variant,p.Val979Asp,ENST00000369701,NM_014978.2;SORCS3,missense_variant,p.Val979Asp,ENST00000369699,; A ENST00000369701 Transcript missense_variant 3163/5757 2936/3669 979/1222 V/D gTc/gAc 1 1 SORCS3 HGNC HGNC:16699 protein_coding YES CCDS7558.1 ENSP00000358715 Q9UPU3 UPI0000135CE1 NM_014978.2 deleterious(0) 21/27 Gene3D:2.60.40.670,hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF10,Superfamily_domains:SSF49299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 105245609 105245609 T A 1 0 0 0 0 1 0 0 0 15254 1667 58 4 4 SORCS3 10 105245609 Missense_Mutation SNP T C3N-01489_T 604058 105245609 28551813 395 25325 SORCS1 0 . GRCh38 10 106709263 106709263 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.1103C>G p.Pro368Arg p.P368R ENST00000263054 7/26 220 205 15 309 309 0 strelka-varscan-mutect SORCS1,missense_variant,p.Pro368Arg,ENST00000263054,NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1;SORCS1,missense_variant,p.Pro126Arg,ENST00000612154,;SORCS1,missense_variant,p.Pro126Arg,ENST00000622431,;SORCS1,missense_variant,p.Pro126Arg,ENST00000344440,; C ENST00000263054 Transcript missense_variant 1111/7272 1103/3507 368/1168 P/R cCa/cGa 1 -1 SORCS1 HGNC HGNC:16697 protein_coding YES CCDS7559.1 ENSP00000263054 Q8WY21 UPI00001AE866 NM_052918.4,NM_001206570.1,NM_001013031.2,NM_001206572.1,NM_001206571.1,NM_001206569.1 tolerated(0.79) 7/26 hmmpanther:PTHR12106,hmmpanther:PTHR12106:SF8,Pfam_domain:PF15902,SMART_domains:SM00602 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 106709263 106709263 G C 1 0 0 0 0 1 0 0 0 15252 1348 47 4 4 SORCS1 10 106709263 Missense_Mutation SNP G C3N-01489_T 1463654 106709263 27088159 396 25326 RBM20 0 . GRCh38 10 110812415 110812415 + Missense_Mutation SNP G G T rs138926584 C3N-01489_T C3N-01489_N G G c.2018G>T p.Arg673Leu p.R673L ENST00000369519 9/14 259 236 23 298 297 1 strelka-varscan-mutect RBM20,missense_variant,p.Arg673Leu,ENST00000369519,NM_001134363.2; T ENST00000369519 Transcript missense_variant 2076/7233 2018/3684 673/1227 R/L cGg/cTg rs138926584,COSM3978082 1 1 RBM20 HGNC HGNC:27424 protein_coding YES CCDS44477.1 ENSP00000358532 Q5T481 UPI00044338F1 NM_001134363.2 deleterious(0) 9/14 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs138926584 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 110812415 110812415 G T 1 0 0 0 0 1 0 0 0 13287 1116 39 1 1 RBM20 10 110812415 Missense_Mutation SNP G C3N-01489_T 4103152 110812415 22985007 397 25327 GFRA1 0 . GRCh38 10 116125540 116125540 + Missense_Mutation SNP C C A rs758642456 C3N-01489_T C3N-01489_N C C c.451G>T p.Gly151Trp p.G151W ENST00000355422 6/11 177 162 15 353 353 0 strelka-varscan-mutect GFRA1,missense_variant,p.Gly146Trp,ENST00000439649,NM_001145453.1;GFRA1,missense_variant,p.Gly146Trp,ENST00000369236,NM_145793.3;GFRA1,missense_variant,p.Gly151Trp,ENST00000355422,NM_005264.4;GFRA1,missense_variant,p.Gly151Trp,ENST00000369234,; A ENST00000355422 Transcript missense_variant 1002/2583 451/1398 151/465 G/W Ggg/Tgg rs758642456 1 -1 GFRA1 HGNC HGNC:4243 protein_coding YES CCDS44481.1 ENSP00000347591 P56159 UPI000012B3A8 NM_005264.4 deleterious(0.01) 6/11 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF3,PIRSF_domain:PIRSF038071 MODERATE 1 SNV 5 1 PASS rs758642456 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 116125540 116125540 C A 1 0 0 0 0 1 0 0 0 6221 681 24 2 2 GFRA1 10 116125540 Missense_Mutation SNP C C3N-01489_T 5313125 116125540 17671882 398 25328 EMX2 0 . GRCh38 10 117543436 117543436 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.169G>T p.Ala57Ser p.A57S ENST00000553456 1/3 264 235 29 377 377 0 strelka-varscan-mutect EMX2,missense_variant,p.Ala57Ser,ENST00000553456,NM_004098.3;EMX2,missense_variant,p.Ala57Ser,ENST00000442245,NM_001165924.1;EMX2,upstream_gene_variant,,ENST00000616794,;EMX2OS,intron_variant,,ENST00000551288,;EMX2OS,upstream_gene_variant,,ENST00000440007,;EMX2OS,upstream_gene_variant,,ENST00000450314,;EMX2,upstream_gene_variant,,ENST00000546446,; T ENST00000553456 Transcript missense_variant 993/2897 169/759 57/252 A/S Gcc/Tcc 1 1 EMX2 HGNC HGNC:3341 protein_coding YES CCDS7601.1 ENSP00000450962 Q04743 UPI000004CC07 NM_004098.3 tolerated(0.33) 1/3 hmmpanther:PTHR24339,hmmpanther:PTHR24339:SF25,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 117543436 117543436 G T 1 0 0 0 0 1 0 0 0 4950 1087 38 1 1 EMX2 10 117543436 Missense_Mutation SNP G C3N-01489_T 1417896 117543436 16253986 399 25329 CFAP46 0 . GRCh38 10 132808655 132808655 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.7914C>A p.= p.G2638G ENST00000368586 58/58 102 91 11 139 138 1 strelka-varscan-mutect CFAP46,synonymous_variant,p.=,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript synonymous_variant 8015/8278 7914/8148 2638/2715 G ggC/ggA 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 58/58 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99942 1 1 1 1 0 T 2 4 81 132808655 132808655 G T 1 0 0 0 0 0 0 0 1 3021 1190 42 2 2 CFAP46 10 132808655 Silent SNP G C3N-01489_T 15265219 132808655 988767 400 25330 CFAP46 0 . GRCh38 10 132847244 132847244 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.6030C>A p.Asp2010Glu p.D2010E ENST00000368586 42/58 117 106 11 168 168 0 strelka-varscan-mutect CFAP46,missense_variant,p.Asp2010Glu,ENST00000368586,NM_001200049.2; T ENST00000368586 Transcript missense_variant 6131/8278 6030/8148 2010/2715 D/E gaC/gaA 1 -1 CFAP46 HGNC HGNC:25247 protein_coding YES CCDS58101.1 ENSP00000357575 Q8IYW2 UPI0001B79116 NM_001200049.2 tolerated(0.23) 42/58 hmmpanther:PTHR15977,hmmpanther:PTHR15977:SF15 MODERATE 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -16.49211 0.9999949 1 1 1 0 T 3 4 81 132847244 132847244 G T 1 0 0 0 0 1 0 0 0 3021 1252 44 2 2 CFAP46 10 132847244 Missense_Mutation SNP G C3N-01489_T 38589 132847244 950178 401 25331 B4GALNT4 0 . GRCh38 11 375892 375892 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1031G>T p.Cys344Phe p.C344F ENST00000329962 11/20 216 193 23 278 278 0 strelka-varscan-mutect B4GALNT4,missense_variant,p.Cys344Phe,ENST00000329962,NM_178537.4;B4GALNT4,non_coding_transcript_exon_variant,,ENST00000524443,;B4GALNT4,upstream_gene_variant,,ENST00000534778,;B4GALNT4,upstream_gene_variant,,ENST00000526584,;B4GALNT4,downstream_gene_variant,,ENST00000530717,; T ENST00000329962 Transcript missense_variant 1031/3444 1031/3120 344/1039 C/F tGc/tTc 1 1 B4GALNT4 HGNC HGNC:26315 protein_coding YES CCDS7694.1 ENSP00000328277 Q76KP1 UPI00002326B6 NM_178537.4 deleterious(0.03) 11/20 hmmpanther:PTHR12369,hmmpanther:PTHR12369:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 375892 375892 G T 1 0 0 0 0 1 0 0 0 1425 1319 46 2 2 B4GALNT4 11 375892 Missense_Mutation SNP G C3N-01489_T 375892 134710730 402 25332 MUC6 0 . GRCh38 11 1027992 1027992 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.1821C>T p.= p.A607A ENST00000421673 15/33 135 125 10 208 208 0 strelka-varscan-mutect MUC6,synonymous_variant,p.=,ENST00000421673,NM_005961.2;MUC6,downstream_gene_variant,,ENST00000525923,; A ENST00000421673 Transcript synonymous_variant 1872/8006 1821/7320 607/2439 A gcC/gcT 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 15/33 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF264,hmmpanther:PTHR11339,Pfam_domain:PF08742,SMART_domains:SM00832 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 1027992 1027992 G A 1 0 0 0 0 0 0 0 1 9980 1335 47 3 3 MUC6 11 1027992 Silent SNP G C3N-01489_T 652100 1027992 134058630 403 25333 TNNT3 0 . GRCh38 11 1934857 1934857 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.619C>A p.Leu207Met p.L207M ENST00000278317 14/16 432 372 60 655 655 0 strelka-varscan-mutect TNNT3,missense_variant,p.Leu199Met,ENST00000381558,NM_001042782.2,NM_001297646.1;TNNT3,missense_variant,p.Leu207Met,ENST00000278317,NM_006757.3;TNNT3,missense_variant,p.Leu205Met,ENST00000381589,NM_001042781.2;TNNT3,missense_variant,p.Leu199Met,ENST00000381579,NM_001042780.2;TNNT3,missense_variant,p.Leu193Met,ENST00000381557,;TNNT3,missense_variant,p.Leu210Met,ENST00000381563,;TNNT3,missense_variant,p.Leu218Met,ENST00000397301,;TNNT3,missense_variant,p.Leu194Met,ENST00000344578,;TNNT3,missense_variant,p.Leu188Met,ENST00000397304,;TNNT3,missense_variant,p.Leu188Met,ENST00000446240,;TNNT3,missense_variant,p.Leu188Met,ENST00000453458,;TNNT3,non_coding_transcript_exon_variant,,ENST00000493234,;TNNT3,downstream_gene_variant,,ENST00000492075,;TNNT3,upstream_gene_variant,,ENST00000473100,; A ENST00000278317 Transcript missense_variant 838/1210 619/777 207/258 L/M Ctg/Atg 1 1 TNNT3 HGNC HGNC:11950 protein_coding YES CCDS7727.1 ENSP00000278317 P45378 UPI000013DB6C NM_006757.3 tolerated(0.32) 14/16 Gene3D:1.20.5.350,hmmpanther:PTHR11521,hmmpanther:PTHR11521:SF4,Superfamily_domains:SSF90250 MODERATE 1 SNV 5 1 PASS rs985064835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 1934857 1934857 C A 1 0 0 0 0 1 0 0 0 16805 680 24 2 2 TNNT3 11 1934857 Missense_Mutation SNP C C3N-01489_T 906865 1934857 133151765 404 25334 OR51E1 0 . GRCh38 11 4652951 4652951 + Missense_Mutation SNP C C A rs565904107 C3N-01489_T C3N-01489_N C C c.425C>A p.Pro142His p.P142H ENST00000396952 2/2 41 29 12 94 94 0 strelka-varscan-mutect OR51E1,missense_variant,p.Pro142His,ENST00000396952,NM_152430.3;OR51E1,intron_variant,,ENST00000530215,; A ENST00000396952 Transcript missense_variant 1075/3612 425/957 142/318 P/H cCt/cAt rs565904107,COSM4494054 1 1 OR51E1 HGNC HGNC:15194 protein_coding YES CCDS31358.2 ENSP00000380155 Q8TCB6 A0A126GVF8 UPI000003ACE2 NM_152430.3 deleterious(0.04) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF167,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 0,1 MODERATE 1 SNV 0,1 1 PASS rs565904107 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 4652951 4652951 C A 1 0 0 0 0 1 0 0 0 11168 681 24 2 2 OR51E1 11 4652951 Missense_Mutation SNP C C3N-01489_T 2718094 4652951 130433671 405 25335 OR51E2 0 . GRCh38 11 4682101 4682101 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.611T>A p.Leu204Gln p.L204Q ENST00000396950 2/2 294 245 49 508 508 0 strelka-varscan-mutect OR51E2,missense_variant,p.Leu204Gln,ENST00000396950,NM_030774.3;OR51E2,downstream_gene_variant,,ENST00000532598,; T ENST00000396950 Transcript missense_variant 851/2781 611/963 204/320 L/Q cTg/cAg 1 -1 OR51E2 HGNC HGNC:15195 protein_coding YES CCDS7751.1 ENSP00000380153 Q9H255 A0A126GVK0 UPI000003B49B NM_030774.3 tolerated(0.13) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 4682101 4682101 A T 1 0 0 0 0 1 0 0 0 11169 188 7 4 4 OR51E2 11 4682101 Missense_Mutation SNP A C3N-01489_T 29150 4682101 130404521 406 25336 OR51S1 0 . GRCh38 11 4848665 4848665 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.544C>A p.Leu182Ile p.L182I ENST00000322101 1/1 82 69 13 126 125 1 strelka-varscan-mutect OR51S1,missense_variant,p.Leu182Ile,ENST00000322101,NM_001004758.1;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; T ENST00000322101 Transcript missense_variant 544/972 544/972 182/323 L/I Cta/Ata 1 -1 OR51S1 HGNC HGNC:15204 protein_coding YES CCDS31362.1 ENSP00000322754 Q8NGJ8 A0A126GWN3 UPI0000041C33 NM_001004758.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF73,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 4848665 4848665 G T 1 0 0 0 0 1 0 0 0 11179 991 35 2 2 OR51S1 11 4848665 Missense_Mutation SNP G C3N-01489_T 166564 4848665 130237957 407 25337 OR51M1 0 . GRCh38 11 5389522 5389522 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.124C>A p.Pro42Thr p.P42T ENST00000328611 1/1 318 274 44 518 518 0 strelka-varscan-mutect OR51M1,missense_variant,p.Pro42Thr,ENST00000328611,NM_001004756.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000328611 Transcript missense_variant 124/981 124/981 42/326 P/T Ccc/Acc COSM3448665 1 1 OR51M1 HGNC HGNC:14847 protein_coding YES CCDS53596.1 ENSP00000333196 Q9H341 UPI000066D8EB NM_001004756.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26450:SF44,hmmpanther:PTHR26450,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 5389522 5389522 C A 1 0 0 0 0 1 0 0 0 11177 623 22 2 2 OR51M1 11 5389522 Missense_Mutation SNP C C3N-01489_T 540857 5389522 129697100 408 25338 OR56B4 0 . GRCh38 11 6107836 6107836 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.58C>G p.Leu20Val p.L20V ENST00000316529 1/1 72 58 14 142 142 0 strelka-varscan-mutect OR56B4,missense_variant,p.Leu20Val,ENST00000316529,NM_001005181.2;RP11-290F24.3,downstream_gene_variant,,ENST00000529961,; G ENST00000316529 Transcript missense_variant 153/1152 58/960 20/319 L/V Ctg/Gtg 1 1 OR56B4 HGNC HGNC:15248 protein_coding YES CCDS31406.1 ENSP00000321196 Q8NH76 UPI000004B214 NM_001005181.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF142,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 6107836 6107836 C G 1 0 0 0 0 1 0 0 0 11210 680 24 4 4 OR56B4 11 6107836 Missense_Mutation SNP C C3N-01489_T 718314 6107836 128978786 409 25339 ARFIP2 0 . GRCh38 11 6479268 6479268 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.286G>A p.Asp96Asn p.D96N ENST00000614314 4/8 278 236 42 417 417 0 strelka-varscan-mutect ARFIP2,missense_variant,p.Asp96Asn,ENST00000614314,NM_001242854.1;ARFIP2,intron_variant,,ENST00000254584,NM_012402.3;ARFIP2,intron_variant,,ENST00000396777,;ARFIP2,intron_variant,,ENST00000423813,NM_001242855.1;ARFIP2,intron_variant,,ENST00000445086,NM_001242856.1;ARFIP2,intron_variant,,ENST00000525235,;TRIM3,upstream_gene_variant,,ENST00000525074,NM_001248006.1;TIMM10B,upstream_gene_variant,,ENST00000254616,NM_012192.3;TIMM10B,upstream_gene_variant,,ENST00000530751,;TRIM3,upstream_gene_variant,,ENST00000529529,;ARFIP2,intron_variant,,ENST00000531037,;ARFIP2,downstream_gene_variant,,ENST00000530410,;ARFIP2,downstream_gene_variant,,ENST00000529847,;TIMM10B,upstream_gene_variant,,ENST00000533379,;TIMM10B,upstream_gene_variant,,ENST00000528908,;ARFIP2,downstream_gene_variant,,ENST00000525329,;TIMM10B,upstream_gene_variant,,ENST00000531462,; T ENST00000614314 Transcript missense_variant 577/3846 286/1125 96/374 D/N Gat/Aat 1 -1 ARFIP2 HGNC HGNC:17160 protein_coding YES CCDS73250.1 ENSP00000484121 A0A087X1E4 UPI0002176A53 NM_001242854.1 tolerated(0.5) 4/8 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 6479268 6479268 C T 1 0 0 0 0 1 0 0 0 979 826 29 3 3 ARFIP2 11 6479268 Missense_Mutation SNP C C3N-01489_T 371432 6479268 128607354 410 25340 WEE1 0 . GRCh38 11 9574349 9574349 + Missense_Mutation SNP C C T rs866472787 C3N-01489_T C3N-01489_N C C c.416C>T p.Ser139Leu p.S139L ENST00000450114 1/11 45 41 4 39 39 0 strelka-mutect WEE1,missense_variant,p.Ser139Leu,ENST00000450114,NM_003390.3;WEE1,upstream_gene_variant,,ENST00000299613,NM_001143976.1;WEE1,upstream_gene_variant,,ENST00000524612,;snoU13,upstream_gene_variant,,ENST00000458785,;WEE1,upstream_gene_variant,,ENST00000524549,; T ENST00000450114 Transcript missense_variant 669/2799 416/1941 139/646 S/L tCg/tTg rs866472787 1 1 WEE1 HGNC HGNC:12761 protein_coding YES CCDS7800.1 ENSP00000402084 P30291 UPI0000138EF4 NM_003390.3 deleterious(0.01) 1/11 hmmpanther:PTHR11042:SF72,hmmpanther:PTHR11042,PIRSF_domain:PIRSF037281 MODERATE 1 SNV 1 1 PASS rs866472787 . 0 205 5 0 0 0 0 0 -10.50113 1 1 1 1 0 T 3 4 81 9574349 9574349 C T 1 0 0 0 0 1 0 0 0 17901 893 31 1 1 WEE1 11 9574349 Missense_Mutation SNP C C3N-01489_T 3095081 9574349 125512273 411 25341 OTOG 0 . GRCh38 11 17612281 17612281 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.6279C>A p.= p.L2093L ENST00000399391 36/55 86 80 6 149 149 0 strelka-mutect OTOG,synonymous_variant,p.=,ENST00000399397,NM_001292063.1;OTOG,synonymous_variant,p.=,ENST00000399391,NM_001277269.1;OTOG,synonymous_variant,p.=,ENST00000342528,; A ENST00000399391 Transcript synonymous_variant 6279/8778 6279/8778 2093/2925 L ctC/ctA 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 36/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 LOW 1 SNV 5 1 PASS rs1016887523 . 0 207 3 0 0 0 0 0 -13.10883 1 1 1 1 0 A 2 1 81 17612281 17612281 C A 1 0 0 0 0 0 0 0 1 11370 871 31 1 1 OTOG 11 17612281 Silent SNP C C3N-01489_T 8037932 17612281 117474341 412 25342 LIN7C 0 . GRCh38 11 27499403 27499403 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.394G>A p.Gly132Arg p.G132R ENST00000278193 4/5 212 183 29 388 388 0 strelka-mutect LIN7C,missense_variant,p.Gly132Arg,ENST00000278193,NM_018362.3;LIN7C,missense_variant,p.Gly108Arg,ENST00000524596,; T ENST00000278193 Transcript missense_variant 415/4688 394/594 132/197 G/R Ggg/Agg 1 -1 LIN7C HGNC HGNC:17789 protein_coding YES CCDS7864.1 ENSP00000278193 Q9NUP9 UPI000000BB45 NM_018362.3 deleterious(0) 4/5 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR14063,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 27499403 27499403 C T 1 0 0 0 0 1 0 0 0 8720 594 21 3 3 LIN7C 11 27499403 Missense_Mutation SNP C C3N-01489_T 9887122 27499403 107587219 413 25343 LRRC4C 0 . GRCh38 11 40115276 40115276 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.1017G>C p.Arg339Ser p.R339S ENST00000278198 2/2 216 194 22 433 433 0 strelka-varscan-mutect LRRC4C,missense_variant,p.Arg339Ser,ENST00000278198,;LRRC4C,missense_variant,p.Arg339Ser,ENST00000527150,;LRRC4C,missense_variant,p.Arg339Ser,ENST00000530763,NM_020929.2;LRRC4C,missense_variant,p.Arg339Ser,ENST00000528697,NM_001258419.1;LRRC4C,missense_variant,p.Arg339Ser,ENST00000619527,;LRRC4C,downstream_gene_variant,,ENST00000533474,;RP11-454H19.2,upstream_gene_variant,,ENST00000624239,; G ENST00000278198 Transcript missense_variant 2981/4054 1017/1923 339/640 R/S agG/agC 1 -1 LRRC4C HGNC HGNC:29317 protein_coding YES CCDS31464.1 ENSP00000278198 Q9HCJ2 UPI000000D9A7 deleterious(0.03) 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF8,Gene3D:3.80.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 40115276 40115276 C G 1 0 0 0 0 1 0 0 0 8903 506 18 4 4 LRRC4C 11 40115276 Missense_Mutation SNP C C3N-01489_T 12615873 40115276 94971346 414 25344 TTC17 0 . GRCh38 11 43407410 43407410 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1897G>T p.Gly633Ter p.G633* ENST00000039989 15/24 181 154 27 324 323 1 strelka-varscan-mutect TTC17,stop_gained,p.Gly633Ter,ENST00000039989,NM_018259.5;TTC17,stop_gained,p.Gly633Ter,ENST00000299240,NM_001307943.1;TTC17,non_coding_transcript_exon_variant,,ENST00000526774,;TTC17,downstream_gene_variant,,ENST00000530483,; T ENST00000039989 Transcript stop_gained 1911/4469 1897/3426 633/1141 G/* Gga/Tga 1 1 TTC17 HGNC HGNC:25596 protein_coding YES CCDS31466.1 ENSP00000039989 Q96AE7 UPI000006E6C7 NM_018259.5 15/24 Gene3D:1.25.40.10,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR16091,SMART_domains:SM00028,Superfamily_domains:SSF48452 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 43407410 43407410 G T 1 0 0 0 0 0 1 0 0 17193 1001 35 2 2 TTC17 11 43407410 Nonsense_Mutation SNP G C3N-01489_T 3292134 43407410 91679212 415 25345 LRP4 0 . GRCh38 11 46886380 46886380 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2369C>A p.Thr790Lys p.T790K ENST00000378623 17/38 354 288 66 535 535 0 strelka-varscan-mutect LRP4,missense_variant,p.Thr790Lys,ENST00000378623,NM_002334.3;LRP4,non_coding_transcript_exon_variant,,ENST00000529921,; T ENST00000378623 Transcript missense_variant 2612/8076 2369/5718 790/1905 T/K aCa/aAa 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 deleterious(0) 17/38 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF249,Gene3D:2.120.10.30,Pfam_domain:PF00058,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 46886380 46886380 G T 1 0 0 0 0 1 0 0 0 8854 1377 48 2 2 LRP4 11 46886380 Missense_Mutation SNP G C3N-01489_T 3478970 46886380 88200242 416 25346 OR4C3 0 . GRCh38 11 48325710 48325710 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.770G>T p.Gly257Val p.G257V ENST00000319856 1/1 109 92 17 212 211 1 strelka-varscan-mutect OR4C3,missense_variant,p.Gly257Val,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.Gly120Val,ENST00000611380,; T ENST00000319856 Transcript missense_variant 791/1036 770/990 257/329 G/V gGg/gTg 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs974667078 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 48325710 48325710 G T 1 0 0 0 0 1 0 0 0 11126 1232 43 2 2 OR4C3 11 48325710 Missense_Mutation SNP G C3N-01489_T 1439330 48325710 86760912 417 25347 OR4C5 0 . GRCh38 11 48365952 48365952 + Missense_Mutation SNP C C G rs777300947 C3N-01489_T C3N-01489_N C C c.514G>C p.Gly172Arg p.G172R ENST00000319813 1/1 212 179 33 346 346 0 strelka-varscan-mutect OR4C5,missense_variant,p.Gly172Arg,ENST00000319813,; G ENST00000319813 Transcript missense_variant 514/981 514/981 172/326 G/R Ggg/Cgg rs777300947 1 -1 OR4C5 HGNC HGNC:14702 protein_coding YES ENSP00000321338 Q8NGB2 UPI0000061EE9 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF9,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs777300947 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 48365952 48365952 C G 1 0 0 0 0 1 0 0 0 11128 652 23 4 4 OR4C5 11 48365952 Missense_Mutation SNP C C3N-01489_T 40242 48365952 86720670 418 25348 OR4P4 0 . GRCh38 11 55638489 55638489 + Missense_Mutation SNP G G T rs865781161 C3N-01489_T C3N-01489_N G G c.132G>T p.Met44Ile p.M44I ENST00000314612 1/1 130 123 7 203 203 0 strelka-varscan-mutect OR4P4,missense_variant,p.Met44Ile,ENST00000314612,NM_001004124.2; T ENST00000314612 Transcript missense_variant 132/939 132/939 44/312 M/I atG/atT rs865781161,COSM5545485 1 1 OR4P4 HGNC HGNC:15180 protein_coding YES CCDS31504.1 ENSP00000324831 Q8NGL7 UPI0000061E8A NM_001004124.2 tolerated(0.5) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF386,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs865781161 . 23 184 0 2 0 0 0 0 -10.10864 0.9999973 1 1 1 0 T 3 4 81 55638489 55638489 G T 1 0 0 0 0 1 0 0 0 11156 1290 45 2 2 OR4P4 11 55638489 Missense_Mutation SNP G C3N-01489_T 7272537 55638489 79448133 419 25349 OR4S2 0 . GRCh38 11 55651711 55651711 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.808G>T p.Ala270Ser p.A270S ENST00000312422 1/1 203 180 23 290 290 0 strelka-varscan-mutect OR4S2,missense_variant,p.Ala270Ser,ENST00000312422,NM_001004059.2; T ENST00000312422 Transcript missense_variant 808/936 808/936 270/311 A/S Gct/Tct 1 1 OR4S2 HGNC HGNC:15183 protein_coding YES CCDS31505.1 ENSP00000310337 Q8NH73 A0A126GVG1 UPI00001D77D2 NM_001004059.2 tolerated(0.16) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF110,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 23 185 0 2 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 81 55651711 55651711 G T 1 0 0 0 0 1 0 0 0 11159 1203 42 2 2 OR4S2 11 55651711 Missense_Mutation SNP G C3N-01489_T 13222 55651711 79434911 420 25350 OR5M9 0 . GRCh38 11 56463358 56463358 + Missense_Mutation SNP A A C novel C3N-01489_T C3N-01489_N A A c.44T>G p.Leu15Arg p.L15R ENST00000279791 1/1 89 77 12 136 136 0 strelka-varscan-mutect OR5M9,missense_variant,p.Leu15Arg,ENST00000279791,NM_001004743.1; C ENST00000279791 Transcript missense_variant 44/933 44/933 15/310 L/R cTg/cGg 1 -1 OR5M9 HGNC HGNC:15294 protein_coding YES CCDS31531.1 ENSP00000279791 Q8NGP3 A0A126GVK6 UPI0000061E81 NM_001004743.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF13,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 56463358 56463358 A C 1 0 0 0 0 1 0 0 0 11246 188 7 5 5 OR5M9 11 56463358 Missense_Mutation SNP A C3N-01489_T 811647 56463358 78623264 421 25351 OR5M1 0 . GRCh38 11 56613188 56613188 + Missense_Mutation SNP G G C rs755863011 C3N-01489_T C3N-01489_N G G c.315C>G p.Ile105Met p.I105M ENST00000526538 1/1 180 152 28 302 302 0 strelka-varscan-mutect OR5M1,missense_variant,p.Ile105Met,ENST00000526538,NM_001004740.1; C ENST00000526538 Transcript missense_variant 315/948 315/948 105/315 I/M atC/atG rs755863011,COSM3953402 1 -1 OR5M1 HGNC HGNC:8352 protein_coding YES CCDS53631.1 ENSP00000435416 Q8NGP8 UPI0000041C9B NM_001004740.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF98,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs755863011 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 56613188 56613188 G C 1 0 0 0 0 1 0 0 0 11241 1048 37 4 4 OR5M1 11 56613188 Missense_Mutation SNP G C3N-01489_T 149830 56613188 78473434 422 25352 TNKS1BP1 0 . GRCh38 11 57313625 57313625 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1063G>T p.Gly355Trp p.G355W ENST00000532437 4/11 84 75 9 170 169 1 strelka-varscan-mutect TNKS1BP1,missense_variant,p.Gly355Trp,ENST00000532437,;TNKS1BP1,missense_variant,p.Gly355Trp,ENST00000358252,NM_033396.2;TNKS1BP1,upstream_gene_variant,,ENST00000530920,;TNKS1BP1,3_prime_UTR_variant,,ENST00000528882,; A ENST00000532437 Transcript missense_variant 1375/5952 1063/5190 355/1729 G/W Ggg/Tgg 1 -1 TNKS1BP1 HGNC HGNC:19081 protein_coding YES CCDS7951.1 ENSP00000437271 Q9C0C2 A0A024R542 UPI000013DB72 deleterious(0) 4/11 Low_complexity_(Seg):seg,hmmpanther:PTHR22042,hmmpanther:PTHR22042:SF2 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.42208 1 1 1 1 0 A 3 1 81 57313625 57313625 C A 1 0 0 0 0 1 0 0 0 16793 623 22 2 2 TNKS1BP1 11 57313625 Missense_Mutation SNP C C3N-01489_T 700437 57313625 77772997 423 25353 OR6Q1 0 . GRCh38 11 58031027 58031027 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.75A>T p.= p.A25A ENST00000302622 1/1 159 137 22 262 262 0 strelka-varscan-mutect OR6Q1,synonymous_variant,p.=,ENST00000302622,NM_001005186.2;OR9Q1,intron_variant,,ENST00000335397,NM_001005212.3;RNU6-899P,upstream_gene_variant,,ENST00000363947,; T ENST00000302622 Transcript synonymous_variant 98/1002 75/954 25/317 A gcA/gcT 1 1 OR6Q1 HGNC HGNC:15302 protein_coding YES CCDS31541.1 ENSP00000307734 Q8NGQ2 A0A126GVP6 UPI000013E7FD NM_001005186.2 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF140,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 58031027 58031027 A T 1 0 0 0 0 0 0 0 1 11278 146 6 4 4 OR6Q1 11 58031027 Silent SNP A C3N-01489_T 717402 58031027 77055595 424 25354 MS4A14 0 . GRCh38 11 60402926 60402926 + Silent SNP G G T rs371907012 C3N-01489_T C3N-01489_N G G c.333G>T p.= p.T111T ENST00000531783 4/6 130 108 22 248 248 0 strelka-varscan-mutect MS4A14,synonymous_variant,p.=,ENST00000395001,NM_001261827.1;MS4A14,synonymous_variant,p.=,ENST00000300187,NM_032597.4;MS4A14,synonymous_variant,p.=,ENST00000531783,NM_001261828.1;MS4A14,synonymous_variant,p.=,ENST00000395005,NM_001079692.2;MS4A14,synonymous_variant,p.=,ENST00000526375,;MS4A14,synonymous_variant,p.=,ENST00000534688,;MS4A14,5_prime_UTR_variant,,ENST00000531787,;MS4A14,synonymous_variant,p.=,ENST00000530662,;MS4A14,synonymous_variant,p.=,ENST00000527841,;MS4A14,synonymous_variant,p.=,ENST00000525397,;MS4A14,downstream_gene_variant,,ENST00000531949,; T ENST00000531783 Transcript synonymous_variant 424/2910 333/2139 111/712 T acG/acT rs371907012 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 4/6 Pfam_domain:PF04103,hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF10,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS rs371907012 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 60402926 60402926 G T 1 0 0 0 0 0 0 0 1 9835 1103 39 1 1 MS4A14 11 60402926 Silent SNP G C3N-01489_T 2371899 60402926 74683696 425 25355 VWCE 0 . GRCh38 11 61273290 61273290 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1608G>T p.Met536Ile p.M536I ENST00000335613 13/20 81 68 13 111 111 0 strelka-varscan-mutect VWCE,start_lost,p.Met1?,ENST00000535710,;VWCE,missense_variant,p.Met536Ile,ENST00000335613,NM_152718.2;VWCE,missense_variant,p.Met253Ile,ENST00000613271,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,non_coding_transcript_exon_variant,,ENST00000398808,;VWCE,upstream_gene_variant,,ENST00000538438,; A ENST00000335613 Transcript missense_variant 1995/3640 1608/2868 536/955 M/I atG/atT 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 tolerated(0.22) 13/20 Pfam_domain:PF00093,PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF250,SMART_domains:SM00214,SMART_domains:SM00215,Superfamily_domains:SSF57603 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 61273290 61273290 C A 1 0 0 0 0 1 0 0 0 17804 710 25 2 2 VWCE 11 61273290 Missense_Mutation SNP C C3N-01489_T 870364 61273290 73813332 426 25356 SYT7 0 . GRCh38 11 61546253 61546253 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.218G>T p.Gly73Val p.G73V ENST00000540677 4/10 42 35 7 57 57 0 strelka-varscan-mutect SYT7,missense_variant,p.Gly117Val,ENST00000539008,;SYT7,missense_variant,p.Gly73Val,ENST00000540677,NM_001252065.1;SYT7,missense_variant,p.Gly117Val,ENST00000535826,;SYT7,intron_variant,,ENST00000263846,NM_004200.3;SYT7,intron_variant,,ENST00000542670,;SYT7,intron_variant,,ENST00000542836,NM_001300773.1;SYT7,intron_variant,,ENST00000545053,;RP11-794G24.1,upstream_gene_variant,,ENST00000540906,;SYT7,splice_region_variant,,ENST00000539468,;SYT7,intron_variant,,ENST00000539246,; A ENST00000540677 Transcript missense_variant,splice_region_variant 224/2013 218/1437 73/478 G/V gGc/gTc 1 -1 SYT7 HGNC HGNC:11514 protein_coding YES CCDS58139.1 ENSP00000444201 O43581 UPI0001639ECE NM_001252065.1 tolerated_low_confidence(0.1) 4/10 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF230 MODERATE 1 SNV 1 1 PASS rs989409706 . 0 197 13 0 0 0 0 0 -17.0599 0.9998742 1 1 1 0 A 3 1 81 61546253 61546253 C A 1 0 0 0 0 1 0 0 0 15873 753 26 2 2 SYT7 11 61546253 Missense_Mutation SNP C C3N-01489_T 272963 61546253 73540369 427 25357 INTS5 0 . GRCh38 11 62647177 62647177 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.2903G>T p.Arg968Leu p.R968L ENST00000330574 2/2 246 211 35 336 336 0 strelka-varscan-mutect INTS5,missense_variant,p.Arg968Leu,ENST00000330574,NM_030628.1;GANAB,upstream_gene_variant,,ENST00000346178,NM_198335.3;GANAB,upstream_gene_variant,,ENST00000540933,NM_001278194.1;GANAB,upstream_gene_variant,,ENST00000356638,NM_198334.2;GANAB,upstream_gene_variant,,ENST00000534779,NM_001278192.1,NM_001278193.1;RP11-831H9.11,downstream_gene_variant,,ENST00000528405,;GANAB,upstream_gene_variant,,ENST00000525994,;GANAB,upstream_gene_variant,,ENST00000534419,;GANAB,upstream_gene_variant,,ENST00000532402,;GANAB,upstream_gene_variant,,ENST00000534613,;GANAB,upstream_gene_variant,,ENST00000529737,;GANAB,upstream_gene_variant,,ENST00000526210,;GANAB,upstream_gene_variant,,ENST00000526392,; A ENST00000330574 Transcript missense_variant 2956/3285 2903/3060 968/1019 R/L cGc/cTc COSM4692752 1 -1 INTS5 HGNC HGNC:29352 protein_coding YES CCDS8027.1 ENSP00000327889 Q6P9B9 UPI0000161948 NM_030628.1 tolerated(1) 2/2 hmmpanther:PTHR31697:SF2,hmmpanther:PTHR31697,Pfam_domain:PF14838 1 MODERATE 1 SNV 1 1 1 PASS rs1471548435 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 62647177 62647177 C A 1 0 0 0 0 1 0 0 0 7683 768 27 1 1 INTS5 11 62647177 Missense_Mutation SNP C C3N-01489_T 1100924 62647177 72439445 428 25358 OVOL1 0 . GRCh38 11 65794674 65794674 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.455G>T p.Gly152Val p.G152V ENST00000335987 3/4 203 172 31 280 280 0 strelka-varscan-mutect OVOL1,missense_variant,p.Gly152Val,ENST00000335987,NM_004561.3;OVOL1,missense_variant,p.Gly90Val,ENST00000532448,;RP11-770G2.5,downstream_gene_variant,,ENST00000531155,;OVOL1-AS1,upstream_gene_variant,,ENST00000532454,;OVOL1-AS1,upstream_gene_variant,,ENST00000534178,;OVOL1-AS1,upstream_gene_variant,,ENST00000527453,;OVOL1,downstream_gene_variant,,ENST00000531907,; T ENST00000335987 Transcript missense_variant 807/3034 455/804 152/267 G/V gGg/gTg 1 1 OVOL1 HGNC HGNC:8525 protein_coding YES CCDS8112.1 ENSP00000337862 O14753 UPI00001D70C0 NM_004561.3 deleterious(0) 3/4 PROSITE_profiles:PS50157,hmmpanther:PTHR10032:SF193,hmmpanther:PTHR10032,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 65794674 65794674 G T 1 0 0 0 0 1 0 0 0 11396 1232 43 2 2 OVOL1 11 65794674 Missense_Mutation SNP G C3N-01489_T 3147497 65794674 69291948 429 25359 TENM4 0 . GRCh38 11 78805392 78805392 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2079G>T p.Arg693Ser p.R693S ENST00000278550 15/34 190 164 26 289 288 1 strelka-varscan-mutect TENM4,missense_variant,p.Arg693Ser,ENST00000278550,NM_001098816.2;TENM4,missense_variant,p.Arg7Ser,ENST00000533525,; A ENST00000278550 Transcript missense_variant 2542/14000 2079/8310 693/2769 R/S agG/agT 1 -1 TENM4 HGNC HGNC:29945 protein_coding YES CCDS44688.1 ENSP00000278550 Q6N022 UPI0000DD8112 NM_001098816.2 tolerated(0.42) 15/34 PROSITE_profiles:PS50026,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF9 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 78805392 78805392 C A 1 0 0 0 0 1 0 0 0 16174 622 22 2 2 TENM4 11 78805392 Missense_Mutation SNP C C3N-01489_T 13010718 78805392 56281230 430 25360 POU2AF1 0 . GRCh38 11 111358794 111358794 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.141T>A p.= p.P47P ENST00000393067 2/5 305 269 36 425 425 0 strelka-varscan-mutect POU2AF1,synonymous_variant,p.=,ENST00000393067,NM_006235.2;POU2AF1,synonymous_variant,p.=,ENST00000531398,;POU2AF1,non_coding_transcript_exon_variant,,ENST00000525584,;POU2AF1,downstream_gene_variant,,ENST00000526535,;POU2AF1,downstream_gene_variant,,ENST00000525499,;POU2AF1,downstream_gene_variant,,ENST00000525662,;POU2AF1,downstream_gene_variant,,ENST00000530793,; T ENST00000393067 Transcript synonymous_variant 656/3295 141/771 47/256 P ccT/ccA 1 -1 POU2AF1 HGNC HGNC:9211 protein_coding YES CCDS31675.1 ENSP00000376786 Q16633 UPI000011D77C NM_006235.2 2/5 hmmpanther:PTHR15363,Pfam_domain:PF09310 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 111358794 111358794 A T 1 0 0 0 0 0 0 0 1 12386 407 15 4 4 POU2AF1 11 111358794 Silent SNP A C3N-01489_T 32553402 111358794 23727828 431 25361 NCAM1 0 . GRCh38 11 113232214 113232214 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1363G>T p.Gly455Trp p.G455W ENST00000619839 12/21 82 72 10 118 118 0 strelka-varscan-mutect NCAM1,missense_variant,p.Gly455Trp,ENST00000615285,;NCAM1,missense_variant,p.Gly429Trp,ENST00000615112,;NCAM1,missense_variant,p.Gly419Trp,ENST00000618266,;NCAM1,missense_variant,p.Gly429Trp,ENST00000316851,NM_181351.4;NCAM1,missense_variant,p.Gly419Trp,ENST00000621518,;NCAM1,missense_variant,p.Gly419Trp,ENST00000621128,NM_001242608.1;NCAM1,missense_variant,p.Gly455Trp,ENST00000619839,NM_001242607.1;NCAM1,missense_variant,p.Gly419Trp,ENST00000531044,NM_000615.6;NCAM1,missense_variant,p.Gly419Trp,ENST00000621850,NM_001076682.3;NCAM1,missense_variant,p.Gly419Trp,ENST00000401611,;NCAM1,missense_variant,p.Gly131Trp,ENST00000613217,;NCAM1,intron_variant,,ENST00000620046,;NCAM1,upstream_gene_variant,,ENST00000533073,;NCAM1,upstream_gene_variant,,ENST00000526322,;NCAM1,upstream_gene_variant,,ENST00000528590,;NCAM1,upstream_gene_variant,,ENST00000530543,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,non_coding_transcript_exon_variant,,ENST00000534046,;NCAM1,upstream_gene_variant,,ENST00000531817,;NCAM1,upstream_gene_variant,,ENST00000525355,; T ENST00000619839 Transcript missense_variant 1701/2993 1363/2655 455/884 G/W Ggg/Tgg 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 deleterious(0.01) 12/21 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF34,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -16.65076 0.9999999 1 1 1 0 T 3 4 81 113232214 113232214 G T 1 0 0 0 0 1 0 0 0 10218 1232 43 2 2 NCAM1 11 113232214 Missense_Mutation SNP G C3N-01489_T 1873420 113232214 21854408 432 25362 TMPRSS13 0 . GRCh38 11 117908757 117908757 + Missense_Mutation SNP C C G rs767233672 C3N-01489_T C3N-01489_N C C c.1137G>C p.Trp379Cys p.W379C ENST00000524993 9/13 96 81 15 137 137 0 strelka-varscan-mutect TMPRSS13,missense_variant,p.Trp344Cys,ENST00000528626,NM_001206789.1;TMPRSS13,missense_variant,p.Trp379Cys,ENST00000526090,NM_001206790.1;TMPRSS13,missense_variant,p.Trp379Cys,ENST00000445164,;TMPRSS13,missense_variant,p.Trp379Cys,ENST00000430170,NM_001244995.1;TMPRSS13,missense_variant,p.Trp379Cys,ENST00000524993,NM_001077263.2;TMPRSS13,downstream_gene_variant,,ENST00000528135,; G ENST00000524993 Transcript missense_variant 1195/1950 1137/1704 379/567 W/C tgG/tgC rs767233672 1 -1 TMPRSS13 HGNC HGNC:29808 protein_coding YES CCDS41721.1 ENSP00000434279 E9PRA0 UPI0000E5923F NM_001077263.2 deleterious(0) 9/13 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF153,hmmpanther:PTHR24256,PIRSF_domain:PIRSF037935,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs767233672 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 117908757 117908757 C G 1 0 0 0 0 1 0 0 0 16721 856 30 4 4 TMPRSS13 11 117908757 Missense_Mutation SNP C C3N-01489_T 4676543 117908757 17177865 433 25363 TMPRSS13 0 . GRCh38 11 117918702 117918702 + Missense_Mutation SNP C C A rs769945026 C3N-01489_T C3N-01489_N C C c.158G>T p.Arg53Leu p.R53L ENST00000524993 2/13 470 396 74 660 659 1 strelka-varscan-mutect TMPRSS13,missense_variant,p.Arg53Leu,ENST00000528626,NM_001206789.1;TMPRSS13,missense_variant,p.Arg53Leu,ENST00000526090,NM_001206790.1;TMPRSS13,missense_variant,p.Arg53Leu,ENST00000445164,;TMPRSS13,missense_variant,p.Arg53Leu,ENST00000430170,NM_001244995.1;TMPRSS13,missense_variant,p.Arg53Leu,ENST00000524993,NM_001077263.2;TMPRSS13,non_coding_transcript_exon_variant,,ENST00000525794,;TMPRSS13,intron_variant,,ENST00000528135,; A ENST00000524993 Transcript missense_variant 216/1950 158/1704 53/567 R/L cGg/cTg rs769945026 1 -1 TMPRSS13 HGNC HGNC:29808 protein_coding YES CCDS41721.1 ENSP00000434279 E9PRA0 UPI0000E5923F NM_001077263.2 deleterious_low_confidence(0.03) 2/13 PIRSF_domain:PIRSF037935 MODERATE 1 SNV 1 1 PASS rs769945026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 117918702 117918702 C A 1 0 0 0 0 1 0 0 0 16721 652 23 1 1 TMPRSS13 11 117918702 Missense_Mutation SNP C C3N-01489_T 9945 117918702 17167920 434 25364 TMPRSS4 0 . GRCh38 11 118111750 118111750 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.593A>T p.Lys198Met p.K198M ENST00000618855 8/13 53 42 11 86 86 0 strelka-varscan-mutect TMPRSS4,missense_variant,p.Lys196Met,ENST00000534111,NM_001173551.1;TMPRSS4,missense_variant,p.Lys198Met,ENST00000618855,NM_019894.3,NM_001290094.1;TMPRSS4,missense_variant,p.Lys160Met,ENST00000616579,;TMPRSS4,missense_variant,p.Lys198Met,ENST00000437212,;TMPRSS4,missense_variant,p.Lys193Met,ENST00000522824,NM_001083947.1;TMPRSS4,missense_variant,p.Lys158Met,ENST00000523251,NM_001173552.1;TMPRSS4,missense_variant,p.Lys51Met,ENST00000522307,NM_001290096.1;TMPRSS4,missense_variant,p.Lys145Met,ENST00000522151,;TMPRSS4,downstream_gene_variant,,ENST00000517544,;TMPRSS4,upstream_gene_variant,,ENST00000524218,;TMPRSS4,upstream_gene_variant,,ENST00000518413,;TMPRSS4,missense_variant,p.Lys196Met,ENST00000519236,;TMPRSS4,3_prime_UTR_variant,,ENST00000517483,;TMPRSS4,non_coding_transcript_exon_variant,,ENST00000528118,;TMPRSS4,downstream_gene_variant,,ENST00000519813,;TMPRSS4,upstream_gene_variant,,ENST00000523770,;TMPRSS4,downstream_gene_variant,,ENST00000522462,;TMPRSS4,upstream_gene_variant,,ENST00000518610,; T ENST00000618855 Transcript missense_variant 884/3531 593/1314 198/437 K/M aAg/aTg 1 1 TMPRSS4 HGNC HGNC:11878 protein_coding YES CCDS31684.1 ENSP00000477949 Q9NRS4 UPI00001FA467 NM_019894.3,NM_001290094.1 deleterious(0.02) 8/13 hmmpanther:PTHR24256:SF228,hmmpanther:PTHR24256,Pfam_domain:PF15494,Superfamily_domains:SSF56487,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 196 14 0 0 0 0 0 -20 0.9998541 1 1 1 0 T 3 4 81 118111750 118111750 A T 1 0 0 0 0 1 0 0 0 16725 72 3 4 4 TMPRSS4 11 118111750 Missense_Mutation SNP A C3N-01489_T 193048 118111750 16974872 435 25365 ERC1 0 . GRCh38 12 1083571 1083571 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1077G>T p.Met359Ile p.M359I ENST00000589028 2/18 64 59 5 102 102 0 strelka-varscan-mutect ERC1,missense_variant,p.Met359Ile,ENST00000543086,NM_178039.3;ERC1,missense_variant,p.Met359Ile,ENST00000589028,NM_178040.3;ERC1,missense_variant,p.Met359Ile,ENST00000397203,;ERC1,missense_variant,p.Met359Ile,ENST00000355446,NM_001301248.1;ERC1,missense_variant,p.Met359Ile,ENST00000360905,;ERC1,missense_variant,p.Met359Ile,ENST00000546231,;ERC1,missense_variant,p.Met208Ile,ENST00000592048,;ERC1,intron_variant,,ENST00000611180,;ERC1,upstream_gene_variant,,ENST00000536573,;ERC1,missense_variant,p.Met359Ile,ENST00000440394,;ERC1,missense_variant,p.Met359Ile,ENST00000347735,;ERC1,missense_variant,p.Met359Ile,ENST00000542302,;ERC1,non_coding_transcript_exon_variant,,ENST00000538971,;ERC1,non_coding_transcript_exon_variant,,ENST00000539007,;ERC1,intron_variant,,ENST00000545948,; T ENST00000589028 Transcript missense_variant 1234/9202 1077/3351 359/1116 M/I atG/atT 1 1 ERC1 HGNC HGNC:17072 protein_coding YES CCDS8508.1 ENSP00000468263 Q8IUD2 UPI000007479C NM_178040.3 tolerated(0.32) 2/18 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10174,hmmpanther:PTHR18861,hmmpanther:PTHR18861:SF1 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -11.82515 1 1 1 1 0 T 3 4 81 1083571 1083571 G T 1 0 0 0 0 1 0 0 0 5059 1377 48 2 2 ERC1 12 1083571 Missense_Mutation SNP G C3N-01489_T 1083571 132191738 436 25366 LRRC23 0 . GRCh38 12 6906576 6906576 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.404A>T p.Tyr135Phe p.Y135F ENST00000443597 4/8 298 255 43 479 477 2 strelka-varscan-mutect LRRC23,missense_variant,p.Tyr135Phe,ENST00000443597,NM_001135217.1;LRRC23,missense_variant,p.Tyr135Phe,ENST00000007969,NM_201650.2;LRRC23,missense_variant,p.Tyr135Phe,ENST00000433346,;LRRC23,missense_variant,p.Tyr135Phe,ENST00000323702,NM_006992.3;LRRC23,missense_variant,p.Tyr135Phe,ENST00000622489,;LRRC23,missense_variant,p.Tyr135Phe,ENST00000436789,;LRRC23,missense_variant,p.Tyr135Phe,ENST00000429740,;LRRC23,downstream_gene_variant,,ENST00000415834,;LRRC23,non_coding_transcript_exon_variant,,ENST00000457146,;LRRC23,downstream_gene_variant,,ENST00000449039,;LRRC23,3_prime_UTR_variant,,ENST00000451681,;LRRC23,3_prime_UTR_variant,,ENST00000431207,;LRRC23,3_prime_UTR_variant,,ENST00000428946,;LRRC23,non_coding_transcript_exon_variant,,ENST00000486401,; T ENST00000443597 Transcript missense_variant 623/1628 404/1032 135/343 Y/F tAc/tTc 1 1 LRRC23 HGNC HGNC:19138 protein_coding YES CCDS8569.1 ENSP00000390932 Q53EV4 UPI000013C506 NM_001135217.1 tolerated(0.18) 4/8 PROSITE_profiles:PS51450,hmmpanther:PTHR24365:SF298,hmmpanther:PTHR24365,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 6906576 6906576 A T 1 0 0 0 0 1 0 0 0 8873 391 14 4 4 LRRC23 12 6906576 Missense_Mutation SNP A C3N-01489_T 5823005 6906576 126368733 437 25367 CLEC4E 0 . GRCh38 12 8534719 8534719 + Silent SNP A A G novel C3N-01489_T C3N-01489_N A A c.579T>C p.= p.N193N ENST00000299663 6/6 185 164 21 346 345 1 strelka-varscan-mutect CLEC4E,stop_lost,p.Ter95ArgextTer12,ENST00000537698,;CLEC4E,synonymous_variant,p.=,ENST00000299663,NM_014358.3;CLEC4E,synonymous_variant,p.=,ENST00000545274,;CLEC4E,3_prime_UTR_variant,,ENST00000446457,;CLEC4E,downstream_gene_variant,,ENST00000446809,;CLEC4E,downstream_gene_variant,,ENST00000450725,; G ENST00000299663 Transcript synonymous_variant 745/2159 579/660 193/219 N aaT/aaC 1 -1 CLEC4E HGNC HGNC:14555 protein_coding YES CCDS8594.1 ENSP00000299663 Q9ULY5 UPI0000037798 NM_014358.3 6/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF226,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 8534719 8534719 A G 1 0 0 0 0 0 0 0 1 3283 214 8 5 5 CLEC4E 12 8534719 Silent SNP A C3N-01489_T 1628143 8534719 124740590 438 25368 PZP 0 . GRCh38 12 9166060 9166060 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.2250G>T p.= p.V750V ENST00000261336 18/36 85 73 12 148 147 1 strelka-varscan-mutect PZP,synonymous_variant,p.=,ENST00000261336,NM_002864.2;PZP,non_coding_transcript_exon_variant,,ENST00000539983,;PZP,non_coding_transcript_exon_variant,,ENST00000546197,;PZP,non_coding_transcript_exon_variant,,ENST00000543108,;PZP,non_coding_transcript_exon_variant,,ENST00000540995,;PZP,downstream_gene_variant,,ENST00000546116,;PZP,3_prime_UTR_variant,,ENST00000535230,; A ENST00000261336 Transcript synonymous_variant 2279/4610 2250/4449 750/1482 V gtG/gtT 1 -1 PZP HGNC HGNC:9750 protein_coding YES CCDS8600.1 ENSP00000261336 P20742 UPI000013D168 NM_002864.2 18/36 Pfam_domain:PF00207,hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF92,SMART_domains:SM01360 LOW 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -19.68231 0.9999807 1 1 1 0 A 2 1 81 9166060 9166060 C A 1 0 0 0 0 0 0 0 1 13025 581 21 2 2 PZP 12 9166060 Silent SNP C C3N-01489_T 631341 9166060 124109249 439 25369 SLCO1B1 0 . GRCh38 12 21178960 21178960 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.667G>T p.Gly223Cys p.G223C ENST00000256958 7/15 264 246 18 318 318 0 strelka-varscan-mutect SLCO1B1,missense_variant,p.Gly223Cys,ENST00000256958,NM_006446.4;RP11-125O5.2,downstream_gene_variant,,ENST00000543498,; T ENST00000256958 Transcript missense_variant 763/2229 667/2076 223/691 G/C Ggc/Tgc 1 1 SLCO1B1 HGNC HGNC:10959 protein_coding YES CCDS8685.1 ENSP00000256958 Q9Y6L6 A0A024RAU7 UPI0000043BED NM_006446.4 deleterious(0) 7/15 Gene3D:1.20.1250.20,Pfam_domain:PF03137,PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF82,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 21178960 21178960 G T 1 0 0 0 0 1 0 0 0 15009 1348 47 2 2 SLCO1B1 12 21178960 Missense_Mutation SNP G C3N-01489_T 12012900 21178960 112096349 440 25370 KRAS 0 . GRCh38 12 25245350 25245350 + Missense_Mutation SNP C C A rs121913529 C3N-01489_T C3N-01489_N C C c.35G>T p.Gly12Val p.G12V ENST00000256078 2/6 262 233 29 436 436 0 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Val,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Val,ENST00000556131,;KRAS,missense_variant,p.Gly12Val,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Val,ENST00000557334,; A ENST00000256078 Transcript missense_variant 99/1119 35/570 12/189 G/V gGt/gTt rs121913529,CM087372,COSM1135366,COSM1140133,COSM1140134,COSM12657,COSM49168,COSM520,COSM521,COSM522 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 pathogenic 0,0,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1,1,1 1 PASS rs121913529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 25245350 25245350 C A 1 0 0 0 0 1 0 0 0 8318 507 18 2 2 KRAS 12 25245350 Missense_Mutation SNP C C3N-01489_T 4066390 25245350 108029959 441 25371 OVCH1 0 . GRCh38 12 29461853 29461853 + Splice_Site SNP C C A novel C3N-01489_T C3N-01489_N C C c.2280+1G>T p.X760_splice ENST00000318184 251 228 23 456 456 0 strelka-varscan-mutect OVCH1,splice_donor_variant,,ENST00000318184,NM_183378.2;OVCH1-AS1,non_coding_transcript_exon_variant,,ENST00000550906,;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; A ENST00000318184 Transcript splice_donor_variant -/3405 2280/3405 760/1134 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 19/27 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 81 29461853 29461853 C A 1 0 0 0 0 0 0 1 0 11393 521 18 2 2 OVCH1 12 29461853 Splice_Site SNP C C3N-01489_T 4216503 29461853 103813456 442 25372 OVOS2 0 . GRCh38 12 31132245 31132245 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2818G>T p.Gly940Trp p.G940W ENST00000632817 21/34 191 171 20 315 315 0 strelka-varscan-mutect OVOS2,missense_variant,p.Gly940Trp,ENST00000398963,;OVOS2,missense_variant,p.Gly940Trp,ENST00000632817,; A ENST00000632817 Transcript missense_variant,splice_region_variant 2818/4299 2818/4299 940/1432 G/W Ggg/Tgg 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 deleterious(0) 21/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 31132245 31132245 C A 1 0 0 0 0 1 0 0 0 11399 637 22 2 2 OVOS2 12 31132245 Missense_Mutation SNP C C3N-01489_T 1670392 31132245 102143064 443 25373 FAM60A 0 . GRCh38 12 31282715 31282715 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.663G>T p.Trp221Cys p.W221C ENST00000337682 6/6 56 48 8 104 104 0 strelka-varscan-mutect FAM60A,missense_variant,p.Trp221Cys,ENST00000337682,NM_021238.2,NM_001135811.1,NM_001135812.1;FAM60A,missense_variant,p.Trp73Cys,ENST00000539409,;FAM60A,missense_variant,p.Trp221Cys,ENST00000454658,;FAM60A,missense_variant,p.Trp73Cys,ENST00000542983,;RP11-627K11.6,upstream_gene_variant,,ENST00000622889,;FAM60A,3_prime_UTR_variant,,ENST00000544921,;FAM60A,non_coding_transcript_exon_variant,,ENST00000448582,; A ENST00000337682 Transcript missense_variant 1032/3163 663/666 221/221 W/C tgG/tgT 1 -1 FAM60A HGNC HGNC:30702 protein_coding YES CCDS8723.1 ENSP00000337477 Q9NP50 UPI00000373C6 NM_021238.2,NM_001135811.1,NM_001135812.1 deleterious_low_confidence(0) 6/6 hmmpanther:PTHR13422,hmmpanther:PTHR13422:SF12 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -18.299 0.9999101 1 1 1 0 A 3 1 81 31282715 31282715 C A 1 0 0 0 0 1 0 0 0 5461 508 18 2 2 FAM60A 12 31282715 Missense_Mutation SNP C C3N-01489_T 150470 31282715 101992594 444 25374 C12orf40 0 . GRCh38 12 39716804 39716804 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1460C>A p.Pro487Gln p.P487Q ENST00000324616 12/13 147 128 19 232 231 1 strelka-varscan-mutect C12orf40,missense_variant,p.Pro487Gln,ENST00000324616,NM_001031748.2;C12orf40,3_prime_UTR_variant,,ENST00000468200,; A ENST00000324616 Transcript missense_variant 1614/2776 1460/1959 487/652 P/Q cCa/cAa 1 1 C12orf40 HGNC HGNC:26846 protein_coding YES CCDS41770.1 ENSP00000317671 Q86WS4 UPI000069A925 NM_001031748.2 tolerated(0.32) 12/13 Low_complexity_(Seg):seg,hmmpanther:PTHR35158:SF1,hmmpanther:PTHR35158,Pfam_domain:PF15089 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 39716804 39716804 C A 1 0 0 0 0 1 0 0 0 1809 594 21 2 2 C12orf40 12 39716804 Missense_Mutation SNP C C3N-01489_T 8434089 39716804 93558505 445 25375 ADAMTS20 0 . GRCh38 12 43462976 43462976 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1533C>A p.Cys511Ter p.C511* ENST00000389420 11/39 149 140 9 224 224 0 strelka-varscan-mutect ADAMTS20,stop_gained,p.Cys511Ter,ENST00000389420,NM_025003.3;ADAMTS20,stop_gained,p.Cys511Ter,ENST00000395541,;ADAMTS20,stop_gained,p.Cys511Ter,ENST00000553158,; T ENST00000389420 Transcript stop_gained 1533/6076 1533/5733 511/1910 C/* tgC/tgA 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 11/39 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 43462976 43462976 G T 1 0 0 0 0 0 1 0 0 310 1311 46 2 2 ADAMTS20 12 43462976 Nonsense_Mutation SNP G C3N-01489_T 3746172 43462976 89812333 446 25376 KRT6B 0 . GRCh38 12 52447981 52447981 + Silent SNP G G A rs388626 C3N-01489_T C3N-01489_N G G c.1221C>T p.= p.A407A ENST00000252252 7/9 419 385 34 581 580 1 varscan-mutect KRT6B,synonymous_variant,p.=,ENST00000252252,NM_005555.3; A ENST00000252252 Transcript synonymous_variant 1269/2282 1221/1695 407/564 A gcC/gcT rs388626 1 -1 KRT6B HGNC HGNC:6444 protein_coding YES CCDS8828.1 ENSP00000252252 P04259 UPI000013CD50 NM_005555.3 7/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,Gene3D:1.20.5.170,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS rs388626 . 0 61 0 0 5 0 0 144 -8.676797 0 0 1 0 0 A 2 1 81 52447981 52447981 G A 1 0 0 0 0 0 0 0 1 8363 1103 39 1 1 KRT6B 12 52447981 Silent SNP G C3N-01489_T 8985005 52447981 80827328 447 25377 KRT6C 0 . GRCh38 12 52472248 52472248 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.573G>T p.= p.L191L ENST00000252250 2/9 325 288 37 491 491 0 varscan-mutect KRT6C,synonymous_variant,p.=,ENST00000252250,NM_173086.4;KRT6C,upstream_gene_variant,,ENST00000553087,; A ENST00000252250 Transcript synonymous_variant 621/2289 573/1695 191/564 L ctG/ctT 1 -1 KRT6C HGNC HGNC:20406 protein_coding YES CCDS8829.1 ENSP00000252250 P48668 UPI00001AE73F NM_173086.4 2/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF141,SMART_domains:SM01391,Superfamily_domains:SSF64593 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 52472248 52472248 C A 1 0 0 0 0 0 0 0 1 8364 581 21 2 2 KRT6C 12 52472248 Silent SNP C C3N-01489_T 24267 52472248 80803061 448 25378 KRT76 0 . GRCh38 12 52768942 52768942 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.1688G>C p.Ser563Thr p.S563T ENST00000332411 9/9 92 79 13 149 149 0 strelka-varscan-mutect KRT76,missense_variant,p.Ser563Thr,ENST00000332411,NM_015848.4; G ENST00000332411 Transcript missense_variant 1742/2529 1688/1917 563/638 S/T aGc/aCc 1 -1 KRT76 HGNC HGNC:24430 protein_coding YES CCDS8838.1 ENSP00000330101 Q01546 UPI000019B3C1 NM_015848.4 tolerated(0.16) 9/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF199,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 52768942 52768942 C G 1 0 0 0 0 1 0 0 0 8371 797 28 4 4 KRT76 12 52768942 Missense_Mutation SNP C C3N-01489_T 296694 52768942 80506367 449 25379 MFSD5 0 . GRCh38 12 53253548 53253548 + Missense_Mutation SNP G G C rs778246487 C3N-01489_T C3N-01489_N G G c.1034G>C p.Gly345Ala p.G345A ENST00000534842 2/2 220 191 29 321 321 0 strelka-varscan-mutect MFSD5,missense_variant,p.Gly345Ala,ENST00000534842,NM_001170790.1;MFSD5,missense_variant,p.Gly238Ala,ENST00000329548,NM_032889.4;MFSD5,missense_variant,p.Gly345Ala,ENST00000551660,;MFSD5,downstream_gene_variant,,ENST00000546655,;MFSD5,downstream_gene_variant,,ENST00000552097,; C ENST00000534842 Transcript missense_variant 1181/2038 1034/1674 345/557 G/A gGa/gCa rs778246487 1 1 MFSD5 HGNC HGNC:28156 protein_coding YES CCDS53796.1 ENSP00000442688 Q6N075 UPI0000EE2648 NM_001170790.1 tolerated(0.32) 2/2 hmmpanther:PTHR23516:SF1,hmmpanther:PTHR23516,Pfam_domain:PF05631,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS rs778246487 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 53253548 53253548 G C 1 0 0 0 0 1 0 0 0 9492 1174 41 4 4 MFSD5 12 53253548 Missense_Mutation SNP G C3N-01489_T 484606 53253548 80021761 450 25380 HOXC10 0 . GRCh38 12 53985683 53985683 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.424G>C p.Glu142Gln p.E142Q ENST00000303460 1/2 73 68 5 128 128 0 strelka-varscan-mutect HOXC10,missense_variant,p.Glu142Gln,ENST00000303460,NM_017409.3;HOXC10,missense_variant,p.Glu30Gln,ENST00000515593,;RP11-834C11.12,upstream_gene_variant,,ENST00000513209,;HOXC6,upstream_gene_variant,,ENST00000504315,;HOXC-AS3,upstream_gene_variant,,ENST00000509870,;HOXC-AS3,upstream_gene_variant,,ENST00000513165,;HOXC-AS3,upstream_gene_variant,,ENST00000514702,;HOXC10,upstream_gene_variant,,ENST00000511575,;HOXC10,upstream_gene_variant,,ENST00000513413,;HOXC10,upstream_gene_variant,,ENST00000514415,;HOXC-AS3,upstream_gene_variant,,ENST00000567780,; C ENST00000303460 Transcript missense_variant 498/1936 424/1029 142/342 E/Q Gag/Cag 1 1 HOXC10 HGNC HGNC:5122 protein_coding YES CCDS8868.1 ENSP00000307321 Q9NYD6 Q53XI4 UPI000012CF7C NM_017409.3 deleterious(0.02) 1/2 hmmpanther:PTHR24326:SF135,hmmpanther:PTHR24326 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -11.23467 0.9999976 1 1 1 0 C 3 2 81 53985683 53985683 G C 1 0 0 0 0 1 0 0 0 7203 1059 37 4 4 HOXC10 12 53985683 Missense_Mutation SNP G C3N-01489_T 732135 53985683 79289626 451 25381 OR6C70 0 . GRCh38 12 55469880 55469880 + Frame_Shift_Del DEL C C - rs767288966 C3N-01489_T C3N-01489_N C C c.259delG p.Glu87LysfsTer27 p.E87Kfs*27 ENST00000327335 1/1 110 103 7 197 197 0 varindel-pindel OR6C70,frameshift_variant,p.Glu87LysfsTer27,ENST00000327335,NM_001005499.1;RP11-110A12.2,intron_variant,,ENST00000556750,;RP11-110A12.2,intron_variant,,ENST00000555146,;RP11-110A12.2,intron_variant,,ENST00000554049,;RP11-110A12.2,intron_variant,,ENST00000555138,; - ENST00000327335 Transcript frameshift_variant 259/939 259/939 87/312 E/X Gaa/aa rs767288966,COSM3463100 1 -1 OR6C70 HGNC HGNC:31299 protein_coding YES CCDS31825.1 ENSP00000329153 A6NIJ9 UPI000044D40E NM_001005499.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454:SF17,hmmpanther:PTHR26454,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 HIGH deletion 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 81 55469880 55469880 C - 1 0 1 0 1 0 0 0 0 11265 864 30 0 0 OR6C70 12 55469880 Frame_Shift_Del DEL C C3N-01489_T 1484197 55469880 77805429 452 25382 BEST3 0 . GRCh38 12 69655688 69655688 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.1226G>C p.Arg409Thr p.R409T ENST00000330891 10/10 172 161 11 246 246 0 strelka-varscan-mutect BEST3,missense_variant,p.Arg409Thr,ENST00000330891,NM_032735.2;BEST3,missense_variant,p.Arg303Thr,ENST00000553096,NM_001282613.1;BEST3,missense_variant,p.Arg196Thr,ENST00000488961,NM_152439.3;BEST3,intron_variant,,ENST00000331471,NM_001282614.1;RP11-588G21.1,downstream_gene_variant,,ENST00000622965,;BEST3,intron_variant,,ENST00000547208,; G ENST00000330891 Transcript missense_variant 1453/3532 1226/2007 409/668 R/T aGa/aCa 1 -1 BEST3 HGNC HGNC:17105 protein_coding YES CCDS8992.2 ENSP00000332413 Q8N1M1 UPI000006E397 NM_032735.2 tolerated(0.76) 10/10 hmmpanther:PTHR10736,hmmpanther:PTHR10736:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 69655688 69655688 C G 1 0 0 0 0 1 0 0 0 1554 913 32 4 4 BEST3 12 69655688 Missense_Mutation SNP C C3N-01489_T 14185808 69655688 63619621 453 25383 PTPRR 0 . GRCh38 12 70701219 70701219 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.1112T>A p.Leu371Gln p.L371Q ENST00000283228 7/14 244 220 24 370 370 0 strelka-varscan-mutect PTPRR,missense_variant,p.Leu371Gln,ENST00000283228,NM_002849.3;PTPRR,missense_variant,p.Leu126Gln,ENST00000440835,NM_130846.2;PTPRR,missense_variant,p.Leu165Gln,ENST00000378778,NM_001207016.1;PTPRR,missense_variant,p.Leu259Gln,ENST00000342084,NM_001207015.1;PTPRR,missense_variant,p.Leu126Gln,ENST00000549308,;PTPRR,missense_variant,p.Leu126Gln,ENST00000550661,;PTPRR,non_coding_transcript_exon_variant,,ENST00000548220,;PTPRR,intron_variant,,ENST00000551219,; T ENST00000283228 Transcript missense_variant 1565/3529 1112/1974 371/657 L/Q cTg/cAg 1 -1 PTPRR HGNC HGNC:9680 protein_coding YES CCDS8998.1 ENSP00000283228 Q15256 UPI000013DD2F NM_002849.3 deleterious(0) 7/14 hmmpanther:PTHR19134:SF264,hmmpanther:PTHR19134,PIRSF_domain:PIRSF001997,Superfamily_domains:SSF52799,Prints_domain:PR01778 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 70701219 70701219 A T 1 0 0 0 0 1 0 0 0 12965 188 7 4 4 PTPRR 12 70701219 Missense_Mutation SNP A C3N-01489_T 1045531 70701219 62574090 454 25384 TRHDE 0 . GRCh38 12 72618905 72618905 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.2201C>T p.Pro734Leu p.P734L ENST00000261180 13/19 65 56 9 55 55 0 varscan-mutect TRHDE,missense_variant,p.Pro734Leu,ENST00000261180,NM_013381.2;TRHDE,non_coding_transcript_exon_variant,,ENST00000549138,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549922,; T ENST00000261180 Transcript missense_variant 2297/10733 2201/3075 734/1024 P/L cCt/cTt 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0.03) 13/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 MODERATE 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -19.64951 0.9998197 1 1 1 0 T 3 4 81 72618905 72618905 C T 1 0 0 0 0 1 0 0 0 16968 681 24 3 3 TRHDE 12 72618905 Missense_Mutation SNP C C3N-01489_T 1917686 72618905 60656404 455 25385 NAV3 0 . GRCh38 12 78050878 78050878 + Silent SNP G G C rs367740483 C3N-01489_T C3N-01489_N G G c.2247G>C p.= p.P749P ENST00000397909 11/40 148 136 12 200 200 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,downstream_gene_variant,,ENST00000549464,;RP11-136F16.1,downstream_gene_variant,,ENST00000549103,; C ENST00000397909 Transcript synonymous_variant 2420/9821 2247/7158 749/2385 P ccG/ccC rs367740483,COSM196552 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 11/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 0,1 LOW 1 SNV 1 0,1 1 PASS rs367740483 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 78050878 78050878 G C 1 0 0 0 0 0 0 0 1 10194 1074 38 4 4 NAV3 12 78050878 Silent SNP G C3N-01489_T 5431973 78050878 55224431 456 25386 TMTC3 0 . GRCh38 12 88148496 88148496 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.181A>G p.Met61Val p.M61V ENST00000266712 2/14 73 68 5 85 85 0 strelka-varscan-mutect TMTC3,missense_variant,p.Met61Val,ENST00000266712,NM_181783.3;TMTC3,missense_variant,p.Met61Val,ENST00000551088,;TMTC3,missense_variant,p.Met61Val,ENST00000549011,;TMTC3,missense_variant,p.Met61Val,ENST00000547034,; G ENST00000266712 Transcript missense_variant 401/7203 181/2745 61/914 M/V Atg/Gtg 1 1 TMTC3 HGNC HGNC:26899 protein_coding YES CCDS9032.1 ENSP00000266712 Q6ZXV5 UPI000004D255 NM_181783.3 deleterious(0) 2/14 hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF419 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 88148496 88148496 A G 1 0 0 0 0 1 0 0 0 16736 449 16 5 5 TMTC3 12 88148496 Missense_Mutation SNP A C3N-01489_T 10097618 88148496 45126813 457 25387 ANO4 0 . GRCh38 12 101126905 101126905 + Frame_Shift_Del DEL C C - novel C3N-01489_T C3N-01489_N C C c.2703delC p.Ile902PhefsTer4 p.I902Ffs*4 ENST00000392977 27/28 76 64 12 127 127 0 sindel-varindel-pindel ANO4,frameshift_variant,p.Ile867PhefsTer4,ENST00000392979,NM_178826.3;ANO4,frameshift_variant,p.Ile902PhefsTer4,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,frameshift_variant,p.Ile422PhefsTer4,ENST00000550015,; - ENST00000392977 Transcript frameshift_variant 2913/3509 2703/2868 901/955 L/X ctC/ct 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 27/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547 HIGH 1 deletion 2 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 81 101126905 101126905 C - 1 0 1 0 1 0 0 0 0 806 813 29 0 0 ANO4 12 101126905 Frame_Shift_Del DEL C C3N-01489_T 12978409 101126905 32148404 458 25388 CKAP4 0 . GRCh38 12 106247504 106247504 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.348G>T p.= p.L116L ENST00000378026 1/2 199 188 11 246 244 2 strelka-varscan-mutect CKAP4,synonymous_variant,p.=,ENST00000378026,NM_006825.3;CKAP4,intron_variant,,ENST00000553039,;RP11-651L5.3,upstream_gene_variant,,ENST00000611145,;RP11-651L5.2,upstream_gene_variant,,ENST00000552486,;CKAP4,intron_variant,,ENST00000552828,; A ENST00000378026 Transcript synonymous_variant 485/3093 348/1809 116/602 L ctG/ctT 1 -1 CKAP4 HGNC HGNC:16991 protein_coding YES CCDS9103.1 ENSP00000367265 Q07065 A0A024RBH2 UPI00000723B9 NM_006825.3 1/2 hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF243,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 106247504 106247504 C A 1 0 0 0 0 0 0 0 1 3207 581 21 2 2 CKAP4 12 106247504 Silent SNP C C3N-01489_T 5120599 106247504 27027805 459 25389 DTX1 0 . GRCh38 12 113077907 113077907 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.743G>T p.Arg248Leu p.R248L ENST00000257600 2/9 31 20 11 29 29 0 strelka-varscan-mutect DTX1,missense_variant,p.Arg248Leu,ENST00000257600,NM_004416.2; T ENST00000257600 Transcript missense_variant 1246/3455 743/1863 248/620 R/L cGc/cTc 1 1 DTX1 HGNC HGNC:3060 protein_coding YES CCDS9164.1 ENSP00000257600 Q86Y01 UPI000013CF71 NM_004416.2 tolerated(0.33) 2/9 hmmpanther:PTHR12622:SF7,hmmpanther:PTHR12622 MODERATE 1 SNV 1 1 PASS rs1291880499 . 14 194 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 113077907 113077907 G T 1 0 0 0 0 1 0 0 0 4616 1087 38 1 1 DTX1 12 113077907 Missense_Mutation SNP G C3N-01489_T 6830403 113077907 20197402 460 25390 NOC4L 0 . GRCh38 12 132152096 132152096 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1330C>A p.His444Asn p.H444N ENST00000330579 14/15 137 122 15 183 183 0 strelka-mutect NOC4L,missense_variant,p.His444Asn,ENST00000330579,NM_024078.2;NOC4L,downstream_gene_variant,,ENST00000541954,;NOC4L,downstream_gene_variant,,ENST00000535343,;NOC4L,non_coding_transcript_exon_variant,,ENST00000538784,; A ENST00000330579 Transcript missense_variant 1371/1632 1330/1551 444/516 H/N Cac/Aac 1 1 NOC4L HGNC HGNC:28461 protein_coding YES CCDS9277.1 ENSP00000328854 Q9BVI4 UPI00000723C4 NM_024078.2 deleterious(0) 14/15 Pfam_domain:PF03914,hmmpanther:PTHR12455,hmmpanther:PTHR12455:SF0,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 132152096 132152096 C A 1 0 0 0 0 1 0 0 0 10557 594 21 2 2 NOC4L 12 132152096 Missense_Mutation SNP C C3N-01489_T 19074189 132152096 1123213 461 25391 PARP4 0 . GRCh38 13 24434697 24434697 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.4444G>T p.Ala1482Ser p.A1482S ENST00000381989 31/34 147 130 17 192 190 2 strelka-varscan-mutect PARP4,missense_variant,p.Ala1482Ser,ENST00000381989,NM_006437.3;TPTE2P6,intron_variant,,ENST00000445572,; A ENST00000381989 Transcript missense_variant 4550/5474 4444/5175 1482/1724 A/S Gct/Tct 1 -1 PARP4 HGNC HGNC:271 protein_coding YES CCDS9307.1 ENSP00000371419 Q9UKK3 UPI000013C76E NM_006437.3 tolerated(0.53) 31/34 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF112 MODERATE 1 SNV 1 1 PASS rs1451443767 . 0 208 0 2 0 0 0 0 -19.99999 0.9999999 1 1 1 0 A 3 1 81 24434697 24434697 C A 1 0 0 0 0 1 0 0 0 11543 710 25 2 2 PARP4 13 24434697 Missense_Mutation SNP C C3N-01489_T 24434697 89929631 462 25392 TEX26 0 . GRCh38 13 30952698 30952698 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.185T>A p.Leu62His p.L62H ENST00000380473 3/7 106 89 17 211 211 0 strelka-varscan-mutect TEX26,missense_variant,p.Leu62His,ENST00000380473,NM_152325.1;TEX26,upstream_gene_variant,,ENST00000530916,;TEX26,intron_variant,,ENST00000531960,; A ENST00000380473 Transcript missense_variant 198/1478 185/870 62/289 L/H cTt/cAt 1 1 TEX26 HGNC HGNC:28622 protein_coding YES CCDS9339.1 ENSP00000369840 Q8N6G2 UPI0000070D41 NM_152325.1 deleterious(0) 3/7 hmmpanther:PTHR33769:SF1,hmmpanther:PTHR33769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 30952698 30952698 T A 1 0 0 0 0 1 0 0 0 16205 1609 56 4 4 TEX26 13 30952698 Missense_Mutation SNP T C3N-01489_T 6518001 30952698 83411630 463 25393 DCLK1 0 . GRCh38 13 35836121 35836121 + Nonsense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1141C>T p.Gln381Ter p.Q381* ENST00000255448 8/18 137 120 17 222 221 1 strelka-varscan-mutect DCLK1,stop_gained,p.Gln381Ter,ENST00000360631,;DCLK1,stop_gained,p.Gln74Ter,ENST00000615680,NM_001195415.1;DCLK1,stop_gained,p.Gln381Ter,ENST00000255448,NM_004734.4;DCLK1,stop_gained,p.Gln74Ter,ENST00000379893,NM_001195416.1; A ENST00000255448 Transcript stop_gained 1353/5703 1141/2190 381/729 Q/* Cag/Tag 1 -1 DCLK1 HGNC HGNC:2700 protein_coding YES CCDS9354.1 ENSP00000255448 O15075 UPI000002A7C2 NM_004734.4 8/18 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF122,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9998813 1 1 1 0 A 4 1 81 35836121 35836121 G A 1 0 0 0 0 0 1 0 0 4093 1357 47 3 3 DCLK1 13 35836121 Nonsense_Mutation SNP G C3N-01489_T 4883423 35836121 78528207 464 25394 RCBTB1 0 . GRCh38 13 49560085 49560085 + Splice_Site SNP C C G novel C3N-01489_T C3N-01489_N C C c.278-1G>C p.X93_splice ENST00000378302 54 48 6 116 116 0 strelka-varscan-mutect RCBTB1,splice_acceptor_variant,,ENST00000378302,NM_018191.3;RCBTB1,splice_acceptor_variant,,ENST00000258646,; G ENST00000378302 Transcript splice_acceptor_variant -/4033 278/1596 93/531 1 -1 RCBTB1 HGNC HGNC:18243 protein_coding YES CCDS9418.1 ENSP00000367552 Q8NDN9 UPI000007181F NM_018191.3 4/12 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 81 49560085 49560085 C G 1 0 0 0 0 0 0 1 0 13340 927 32 4 4 RCBTB1 13 49560085 Splice_Site SNP C C3N-01489_T 13723964 49560085 64804243 465 25395 THSD1 0 . GRCh38 13 52378523 52378523 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1447G>T p.Asp483Tyr p.D483Y ENST00000258613 5/5 239 217 22 369 369 0 strelka-varscan-mutect THSD1,missense_variant,p.Asp430Tyr,ENST00000349258,NM_199263.2;THSD1,missense_variant,p.Asp483Tyr,ENST00000258613,NM_018676.3; A ENST00000258613 Transcript missense_variant 1626/2962 1447/2559 483/852 D/Y Gac/Tac 1 -1 THSD1 HGNC HGNC:17754 protein_coding YES CCDS9432.1 ENSP00000258613 Q9NS62 A0A024R064 UPI000007376D NM_018676.3 deleterious(0) 5/5 Low_complexity_(Seg):seg,hmmpanther:PTHR16311 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 52378523 52378523 C A 1 0 0 0 0 1 0 0 0 16311 913 32 2 2 THSD1 13 52378523 Missense_Mutation SNP C C3N-01489_T 2818438 52378523 61985805 466 25396 PCDH17 0 . GRCh38 13 57633451 57633451 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.905T>A p.Leu302Gln p.L302Q ENST00000377918 1/4 302 266 36 563 563 0 strelka-varscan-mutect PCDH17,missense_variant,p.Leu302Gln,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,non_coding_transcript_exon_variant,,ENST00000610846,;PCDH17,missense_variant,p.Leu302Gln,ENST00000484979,; A ENST00000377918 Transcript missense_variant 1640/8232 905/3480 302/1159 L/Q cTa/cAa 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.08) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 57633451 57633451 T A 1 0 0 0 0 1 0 0 0 11599 1522 53 4 4 PCDH17 13 57633451 Missense_Mutation SNP T C3N-01489_T 5254928 57633451 56730877 467 25397 PCDH17 0 . GRCh38 13 57633560 57633560 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1014G>T p.= p.T338T ENST00000377918 1/4 244 226 18 469 466 3 strelka-varscan-mutect PCDH17,synonymous_variant,p.=,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,non_coding_transcript_exon_variant,,ENST00000610846,;PCDH17,synonymous_variant,p.=,ENST00000484979,; T ENST00000377918 Transcript synonymous_variant 1749/8232 1014/3480 338/1159 T acG/acT 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 57633560 57633560 G T 1 0 0 0 0 0 0 0 1 11599 1103 39 1 1 PCDH17 13 57633560 Silent SNP G C3N-01489_T 109 57633560 56730768 468 25398 RBM26 0 . GRCh38 13 79371850 79371850 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.408G>T p.Arg136Ser p.R136S ENST00000622611 4/22 127 110 17 190 188 2 strelka-varscan-mutect RBM26,missense_variant,p.Arg136Ser,ENST00000622611,NM_001286631.1;RBM26,missense_variant,p.Arg136Ser,ENST00000438724,NM_001286632.1;RBM26,missense_variant,p.Arg136Ser,ENST00000438737,;RBM26,missense_variant,p.Arg136Ser,ENST00000267229,NM_022118.4;RBM26,downstream_gene_variant,,ENST00000472143,; A ENST00000622611 Transcript missense_variant 855/5230 408/3030 136/1009 R/S agG/agT 1 -1 RBM26 HGNC HGNC:20327 protein_coding YES CCDS73591.1 ENSP00000483408 A0A087X0H9 UPI00016378C8 NM_001286631.1 tolerated(1) 4/22 hmmpanther:PTHR14398,hmmpanther:PTHR14398:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 79371850 79371850 C A 1 0 0 0 0 1 0 0 0 13292 622 22 2 2 RBM26 13 79371850 Missense_Mutation SNP C C3N-01489_T 21738290 79371850 34992478 469 25399 GPC6 0 . GRCh38 13 94027831 94027831 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.814A>G p.Asn272Asp p.N272D ENST00000377047 4/9 279 237 42 443 443 0 strelka-varscan-mutect GPC6,missense_variant,p.Asn272Asp,ENST00000377047,NM_005708.3;RNA5SP35,upstream_gene_variant,,ENST00000391257,; G ENST00000377047 Transcript missense_variant 1429/6467 814/1668 272/555 N/D Aac/Gac 1 1 GPC6 HGNC HGNC:4454 protein_coding YES CCDS9469.1 ENSP00000366246 Q9Y625 UPI0000032F5B NM_005708.3 deleterious(0) 4/9 Pfam_domain:PF01153,PROSITE_patterns:PS01207,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 94027831 94027831 A G 1 0 0 0 0 1 0 0 0 6504 130 5 5 5 GPC6 13 94027831 Missense_Mutation SNP A C3N-01489_T 14655981 94027831 20336497 470 25400 UBAC2 0 . GRCh38 13 99244554 99244554 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.319G>T p.Asp107Tyr p.D107Y ENST00000403766 4/9 197 164 33 347 344 3 strelka-varscan-mutect UBAC2,missense_variant,p.Asp107Tyr,ENST00000403766,NM_001144072.1;UBAC2,missense_variant,p.Asp113Tyr,ENST00000457666,;UBAC2,intron_variant,,ENST00000376440,NM_177967.3;UBAC2,intron_variant,,ENST00000355700,;UBAC2,non_coding_transcript_exon_variant,,ENST00000494576,;UBAC2,non_coding_transcript_exon_variant,,ENST00000468067,;UBAC2,non_coding_transcript_exon_variant,,ENST00000473091,; T ENST00000403766 Transcript missense_variant 454/1375 319/1035 107/344 D/Y Gac/Tac 1 1 UBAC2 HGNC HGNC:20486 protein_coding YES CCDS45064.1 ENSP00000383911 Q8NBM4 A0A024RE02 UPI000003B0B4 NM_001144072.1 deleterious(0) 4/9 hmmpanther:PTHR12917:SF22,hmmpanther:PTHR12917,Superfamily_domains:SSF144091,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 99244554 99244554 G T 1 0 0 0 0 1 0 0 0 17354 1290 45 2 2 UBAC2 13 99244554 Missense_Mutation SNP G C3N-01489_T 5216723 99244554 15119774 471 25401 CCDC168 0 . GRCh38 13 102746833 102746833 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.3864A>T p.Lys1288Asn p.K1288N ENST00000322527 4/4 190 172 18 332 332 0 strelka-varscan-mutect CCDC168,missense_variant,p.Lys1288Asn,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; A ENST00000322527 Transcript missense_variant 4002/21466 3864/21246 1288/7081 K/N aaA/aaT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.06) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 102746833 102746833 T A 1 0 0 0 0 1 0 0 0 2484 1490 52 4 4 CCDC168 13 102746833 Missense_Mutation SNP T C3N-01489_T 3502279 102746833 11617495 472 25402 SLC10A2 0 . GRCh38 13 103051326 103051326 + Missense_Mutation SNP G G C C3N-01489_T C3N-01489_N G G c.692C>G p.Thr231Arg p.T231R ENST00000245312 4/6 322 288 34 464 464 0 strelka-varscan-mutect SLC10A2,missense_variant,p.Thr231Arg,ENST00000245312,NM_000452.2; C ENST00000245312 Transcript missense_variant 1289/3779 692/1047 231/348 T/R aCa/aGa COSM696098 1 -1 SLC10A2 HGNC HGNC:10906 protein_coding YES CCDS9506.1 ENSP00000245312 Q12908 UPI000013CB9B NM_000452.2 deleterious(0.04) 4/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR10361,hmmpanther:PTHR10361:SF19,TIGRFAM_domain:TIGR00841 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 103051326 103051326 G C 1 0 0 0 0 1 0 0 0 14639 1377 48 4 4 SLC10A2 13 103051326 Missense_Mutation SNP G C3N-01489_T 304493 103051326 11313002 473 25403 COL4A1 0 . GRCh38 13 110170556 110170556 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.3733G>T p.Gly1245Cys p.G1245C ENST00000375820 42/52 222 189 33 374 374 0 strelka-varscan-mutect COL4A1,missense_variant,p.Gly1245Cys,ENST00000375820,NM_001845.5; A ENST00000375820 Transcript missense_variant 3855/6532 3733/5010 1245/1669 G/C Ggc/Tgc 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0) 42/52 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 110170556 110170556 C A 1 0 0 0 0 1 0 0 0 3478 594 21 2 2 COL4A1 13 110170556 Missense_Mutation SNP C C3N-01489_T 7119230 110170556 4193772 474 25404 OXA1L 0 . GRCh38 14 22770276 22770276 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.847C>A p.Gln283Lys p.Q283K ENST00000612549 5/10 171 157 14 263 263 0 strelka-mutect OXA1L,missense_variant,p.Gln283Lys,ENST00000612549,;OXA1L,missense_variant,p.Gln207Lys,ENST00000358043,;OXA1L,missense_variant,p.Gln283Lys,ENST00000285848,NM_005015.3;OXA1L,missense_variant,p.Gln223Lys,ENST00000604262,;OXA1L,missense_variant,p.Gln223Lys,ENST00000412791,;OXA1L,missense_variant,p.Gln92Lys,ENST00000431881,;SLC7A7,downstream_gene_variant,,ENST00000397532,;SLC7A7,downstream_gene_variant,,ENST00000555702,NM_001126106.2;SLC7A7,downstream_gene_variant,,ENST00000285850,;SLC7A7,downstream_gene_variant,,ENST00000397528,NM_001126105.2;SLC7A7,downstream_gene_variant,,ENST00000397529,;SLC7A7,downstream_gene_variant,,ENST00000554517,;SLC7A7,downstream_gene_variant,,ENST00000556350,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554857,;CTD-2555K7.2,upstream_gene_variant,,ENST00000553792,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554730,;SLC7A7,downstream_gene_variant,,ENST00000554061,;OXA1L,splice_region_variant,,ENST00000442110,;OXA1L,non_coding_transcript_exon_variant,,ENST00000495424,;OXA1L,non_coding_transcript_exon_variant,,ENST00000481218,;OXA1L,non_coding_transcript_exon_variant,,ENST00000473744,;SLC7A7,downstream_gene_variant,,ENST00000556287,;OXA1L,downstream_gene_variant,,ENST00000483939,;SLC7A7,downstream_gene_variant,,ENST00000555678,;OXA1L,downstream_gene_variant,,ENST00000556473,;CTD-2555K7.2,upstream_gene_variant,,ENST00000554194,;OXA1L,downstream_gene_variant,,ENST00000557299,; A ENST00000612549 Transcript missense_variant,splice_region_variant 847/2971 847/1488 283/495 Q/K Cag/Aag 1 1 OXA1L HGNC HGNC:8526 protein_coding YES CCDS9573.1 ENSP00000483491 J3KNA0 UPI000013DE11 deleterious(0) 5/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR12428:SF14,hmmpanther:PTHR12428,TIGRFAM_domain:TIGR03592,Pfam_domain:PF02096 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.87857 0.9999998 1 1 1 0 A 3 1 81 22770276 22770276 C A 1 0 0 0 0 1 0 0 0 11400 840 29 2 2 OXA1L 14 22770276 Missense_Mutation SNP C C3N-01489_T 22770276 84273442 475 25405 STXBP6 0 . GRCh38 14 24856092 24856092 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.295G>A p.Glu99Lys p.E99K ENST00000323944 4/6 52 45 7 94 94 0 strelka-varscan-mutect STXBP6,missense_variant,p.Glu99Lys,ENST00000323944,;STXBP6,missense_variant,p.Glu99Lys,ENST00000396700,NM_001304476.1;STXBP6,missense_variant,p.Glu99Lys,ENST00000419632,NM_014178.7;STXBP6,missense_variant,p.Glu99Lys,ENST00000550887,;STXBP6,missense_variant,p.Glu99Lys,ENST00000546511,NM_001304477.1;STXBP6,3_prime_UTR_variant,,ENST00000548182,; T ENST00000323944 Transcript missense_variant 747/4132 295/633 99/210 E/K Gag/Aag 1 -1 STXBP6 HGNC HGNC:19666 protein_coding YES CCDS9634.1 ENSP00000324302 Q8NFX7 UPI000006DD7D deleterious(0.05) 4/6 Pfam_domain:PF15277,hmmpanther:PTHR16092,SMART_domains:SM01313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 24856092 24856092 C T 1 0 0 0 0 1 0 0 0 15742 922 32 3 3 STXBP6 14 24856092 Missense_Mutation SNP C C3N-01489_T 2085816 24856092 82187626 476 25406 NOVA1 0 . GRCh38 14 26448087 26448087 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1396G>T p.Gly466Cys p.G466C ENST00000539517 5/5 359 330 29 522 521 1 strelka-varscan-mutect NOVA1,missense_variant,p.Gly466Cys,ENST00000539517,NM_002515.2;NOVA1,missense_variant,p.Gly442Cys,ENST00000465357,NM_006489.2;NOVA1,downstream_gene_variant,,ENST00000549571,;NOVA1,downstream_gene_variant,,ENST00000449198,;NOVA1,downstream_gene_variant,,ENST00000549146,;NOVA1,downstream_gene_variant,,ENST00000347476,;NOVA1,3_prime_UTR_variant,,ENST00000483536,;NOVA1,downstream_gene_variant,,ENST00000546546,; A ENST00000539517 Transcript missense_variant 1714/3912 1396/1524 466/507 G/C Ggc/Tgc 1 -1 NOVA1 HGNC HGNC:7886 protein_coding YES CCDS32061.1 ENSP00000438875 P51513 UPI000013D74E NM_002515.2 deleterious(0.02) 5/5 PROSITE_profiles:PS50084,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF150,Gene3D:3.30.1370.10,Pfam_domain:PF00013,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 26448087 26448087 C A 1 0 0 0 0 1 0 0 0 10600 594 21 2 2 NOVA1 14 26448087 Missense_Mutation SNP C C3N-01489_T 1591995 26448087 80595631 477 25407 PAX9 0 . GRCh38 14 36676322 36676322 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.896G>T p.Gly299Val p.G299V ENST00000361487 4/4 440 389 51 568 568 0 strelka-varscan-mutect PAX9,missense_variant,p.Gly299Val,ENST00000361487,;PAX9,missense_variant,p.Gly299Val,ENST00000402703,NM_006194.3;PAX9,3_prime_UTR_variant,,ENST00000554201,;SLC25A21,downstream_gene_variant,,ENST00000331299,NM_030631.3;SLC25A21,downstream_gene_variant,,ENST00000555449,NM_001171170.1;PAX9,non_coding_transcript_exon_variant,,ENST00000557107,; T ENST00000361487 Transcript missense_variant 1121/4514 896/1026 299/341 G/V gGa/gTa 1 1 PAX9 HGNC HGNC:8623 protein_coding YES CCDS9662.1 ENSP00000355245 P55771 Q2L4T1 UPI0000131377 deleterious_low_confidence(0) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 36676322 36676322 G T 1 0 0 0 0 1 0 0 0 11571 1174 41 2 2 PAX9 14 36676322 Missense_Mutation SNP G C3N-01489_T 10228235 36676322 70367396 478 25408 FANCM 0 . GRCh38 14 45159138 45159138 + Missense_Mutation SNP T T C rs776804525 C3N-01489_T C3N-01489_N T T c.1439T>C p.Met480Thr p.M480T ENST00000267430 9/23 155 141 14 248 248 0 strelka-varscan-mutect FANCM,missense_variant,p.Met480Thr,ENST00000267430,NM_020937.2;FANCM,missense_variant,p.Met454Thr,ENST00000542564,NM_001308133.1;FANCM,missense_variant,p.Met65Thr,ENST00000556250,;FANCM,missense_variant,p.Met480Thr,ENST00000556036,NM_001308134.1; C ENST00000267430 Transcript missense_variant 1524/7111 1439/6147 480/2048 M/T aTg/aCg rs776804525,COSM4569002 1 1 FANCM HGNC HGNC:23168 protein_coding YES CCDS32070.1 ENSP00000267430 Q8IYD8 UPI000059F032 NM_020937.2 deleterious(0) 9/23 PROSITE_profiles:PS51194,hmmpanther:PTHR14025:SF20,hmmpanther:PTHR14025,Pfam_domain:PF00271,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs776804525 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 45159138 45159138 T C 1 0 0 0 0 1 0 0 0 5531 1464 51 5 5 FANCM 14 45159138 Missense_Mutation SNP T C3N-01489_T 8482816 45159138 61884580 479 25409 PYGL 0 . GRCh38 14 50910044 50910044 + Silent SNP C C G rs772998983 C3N-01489_T C3N-01489_N C C c.2028G>C p.= p.G676G ENST00000216392 17/20 329 305 24 458 458 0 strelka-varscan-mutect PYGL,synonymous_variant,p.=,ENST00000216392,NM_002863.4;PYGL,synonymous_variant,p.=,ENST00000532462,;PYGL,synonymous_variant,p.=,ENST00000544180,NM_001163940.1;RP11-218E20.5,upstream_gene_variant,,ENST00000557343,;PYGL,non_coding_transcript_exon_variant,,ENST00000532107,; G ENST00000216392 Transcript synonymous_variant 2361/3048 2028/2544 676/847 G ggG/ggC rs772998983,COSM5126032 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 17/20 hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF12,PROSITE_patterns:PS00102,TIGRFAM_domain:TIGR02093,Gene3D:3.40.50.2000,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 50910044 50910044 C G 1 0 0 0 0 0 0 0 1 13015 842 30 4 4 PYGL 14 50910044 Silent SNP C C3N-01489_T 5750906 50910044 56133674 480 25410 PYGL 0 . GRCh38 14 50915936 50915936 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1128C>A p.= p.T376T ENST00000216392 10/20 199 168 31 296 296 0 strelka-varscan-mutect PYGL,synonymous_variant,p.=,ENST00000216392,NM_002863.4;PYGL,synonymous_variant,p.=,ENST00000532462,;PYGL,synonymous_variant,p.=,ENST00000544180,NM_001163940.1;RP11-218E20.5,downstream_gene_variant,,ENST00000557343,;PYGL,non_coding_transcript_exon_variant,,ENST00000528757,;PYGL,downstream_gene_variant,,ENST00000553872,;PYGL,upstream_gene_variant,,ENST00000532107,; T ENST00000216392 Transcript synonymous_variant 1461/3048 1128/2544 376/847 T acC/acA 1 -1 PYGL HGNC HGNC:9725 protein_coding YES CCDS32080.1 ENSP00000216392 P06737 UPI000011136E NM_002863.4 10/20 hmmpanther:PTHR11468,hmmpanther:PTHR11468:SF12,TIGRFAM_domain:TIGR02093,Gene3D:3.40.50.2000,Pfam_domain:PF00343,PIRSF_domain:PIRSF000460,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 50915936 50915936 G T 1 0 0 0 0 0 0 0 1 13015 1335 47 2 2 PYGL 14 50915936 Silent SNP G C3N-01489_T 5892 50915936 56127782 481 25411 NID2 0 . GRCh38 14 52068025 52068025 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.367C>A p.Leu123Met p.L123M ENST00000216286 2/22 110 104 6 180 180 0 strelka-varscan-mutect NID2,missense_variant,p.Leu123Met,ENST00000216286,NM_007361.3;NID2,missense_variant,p.Leu123Met,ENST00000617139,; T ENST00000216286 Transcript missense_variant 367/4811 367/4128 123/1375 L/M Ctg/Atg 1 -1 NID2 HGNC HGNC:13389 protein_coding YES CCDS9706.1 ENSP00000216286 Q14112 UPI000013C6E1 NM_007361.3 deleterious(0.03) 2/22 PROSITE_profiles:PS51220,SMART_domains:SM00539 MODERATE 1 SNV 1 1 PASS rs1344195019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 52068025 52068025 G T 1 0 0 0 0 1 0 0 0 10448 1014 35 2 2 NID2 14 52068025 Missense_Mutation SNP G C3N-01489_T 1152089 52068025 54975693 482 25412 C14orf37 0 . GRCh38 14 58138739 58138739 + Nonsense_Mutation SNP G G T rs762869222 C3N-01489_T C3N-01489_N G G c.620C>A p.Ser207Ter p.S207* ENST00000267485 2/8 226 211 15 376 375 1 strelka-varscan-mutect C14orf37,stop_gained,p.Ser207Ter,ENST00000267485,NM_001001872.2;C14orf37,non_coding_transcript_exon_variant,,ENST00000334342,;C14orf37,non_coding_transcript_exon_variant,,ENST00000557175,;C14orf37,downstream_gene_variant,,ENST00000554218,;UBA52P3,upstream_gene_variant,,ENST00000491303,; T ENST00000267485 Transcript stop_gained 815/6495 620/2325 207/774 S/* tCa/tAa rs762869222 1 -1 C14orf37 HGNC HGNC:19846 protein_coding YES CCDS32089.1 ENSP00000267485 Q86TY3 UPI000000CC37 NM_001001872.2 2/8 hmmpanther:PTHR21585,hmmpanther:PTHR21585:SF0,Pfam_domain:PF15767 HIGH 1 SNV 1 1 PASS rs762869222 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 58138739 58138739 G T 1 0 0 0 0 0 1 0 0 1838 1294 45 2 2 C14orf37 14 58138739 Nonsense_Mutation SNP G C3N-01489_T 6070714 58138739 48904979 483 25413 SYNE2 0 . GRCh38 14 63949853 63949853 + Missense_Mutation SNP G G T rs762685285 C3N-01489_T C3N-01489_N G G c.437G>T p.Cys146Phe p.C146F ENST00000358025 7/116 260 230 30 395 395 0 strelka-varscan-mutect SYNE2,missense_variant,p.Cys146Phe,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Cys146Phe,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Cys146Phe,ENST00000357395,;SYNE2,missense_variant,p.Cys146Phe,ENST00000554584,;SYNE2,missense_variant,p.Cys146Phe,ENST00000341472,; T ENST00000358025 Transcript missense_variant 649/21842 437/20724 146/6907 C/F tGc/tTc rs762685285 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(0.12) 7/116 hmmpanther:PTHR11915:SF317,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS rs762685285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 63949853 63949853 G T 1 0 0 0 0 1 0 0 0 15838 1319 46 2 2 SYNE2 14 63949853 Missense_Mutation SNP G C3N-01489_T 5811114 63949853 43093865 484 25414 SPTB 0 . GRCh38 14 64793503 64793503 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.2160G>T p.Glu720Asp p.E720D ENST00000556626 14/36 433 393 40 703 703 0 strelka-varscan-mutect SPTB,missense_variant,p.Glu720Asp,ENST00000556626,;SPTB,missense_variant,p.Glu720Asp,ENST00000389722,NM_001024858.2;SPTB,missense_variant,p.Glu720Asp,ENST00000389721,NM_000347.5;SPTB,missense_variant,p.Glu720Asp,ENST00000389720,; A ENST00000556626 Transcript missense_variant 2303/10153 2160/6987 720/2328 E/D gaG/gaT COSM4535158,COSM4535159 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D tolerated(0.47) 14/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 64793503 64793503 C A 1 0 0 0 0 1 0 0 0 15474 680 24 2 2 SPTB 14 64793503 Missense_Mutation SNP C C3N-01489_T 843650 64793503 42250215 485 25415 GPHN 0 . GRCh38 14 66776472 66776472 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.152G>T p.Gly51Val p.G51V ENST00000478722 3/23 180 165 15 265 265 0 strelka-varscan-mutect GPHN,missense_variant,p.Gly51Val,ENST00000478722,NM_020806.4;GPHN,missense_variant,p.Gly51Val,ENST00000315266,NM_001024218.1;GPHN,missense_variant,p.Gly51Val,ENST00000543237,;GPHN,missense_variant,p.Gly51Val,ENST00000459628,;GPHN,non_coding_transcript_exon_variant,,ENST00000556020,;GPHN,3_prime_UTR_variant,,ENST00000553936,;GPHN,3_prime_UTR_variant,,ENST00000555668,;GPHN,3_prime_UTR_variant,,ENST00000557654,;GPHN,intron_variant,,ENST00000556633,; T ENST00000478722 Transcript missense_variant 1273/4297 152/2310 51/769 G/V gGg/gTg 1 1 GPHN HGNC HGNC:15465 protein_coding YES CCDS9777.1 ENSP00000417901 Q9NQX3 UPI0000072592 NM_020806.4 tolerated(0.28) 3/23 Gene3D:3.40.980.10,Pfam_domain:PF00994,hmmpanther:PTHR10192,SMART_domains:SM00852,Superfamily_domains:SSF53218,TIGRFAM_domain:TIGR00177 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 66776472 66776472 G T 1 0 0 0 0 1 0 0 0 6512 1232 43 2 2 GPHN 14 66776472 Missense_Mutation SNP G C3N-01489_T 1982969 66776472 40267246 486 25416 GALNT16 0 . GRCh38 14 69260395 69260395 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.105C>T p.= p.S35S ENST00000337827 1/16 309 278 31 420 420 0 strelka-varscan-mutect GALNT16,synonymous_variant,p.=,ENST00000337827,NM_001168368.1,NM_020692.2;GALNT16,synonymous_variant,p.=,ENST00000448469,;GALNT16,synonymous_variant,p.=,ENST00000553669,;RP11-363J20.2,non_coding_transcript_exon_variant,,ENST00000556316,;GALNT16,non_coding_transcript_exon_variant,,ENST00000555920,;GALNT16,non_coding_transcript_exon_variant,,ENST00000554317,;GALNT16,downstream_gene_variant,,ENST00000554858,;GALNT16,synonymous_variant,p.=,ENST00000553471,; T ENST00000337827 Transcript synonymous_variant 432/5708 105/1677 35/558 S tcC/tcT 1 1 GALNT16 HGNC HGNC:23233 protein_coding YES CCDS32107.1 ENSP00000336729 Q8N428 Q68VJ8 UPI000004D296 NM_001168368.1,NM_020692.2 1/16 Low_complexity_(Seg):seg,hmmpanther:PTHR11675:SF3,hmmpanther:PTHR11675 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 69260395 69260395 C T 1 0 0 0 0 0 0 0 1 6082 639 23 1 1 GALNT16 14 69260395 Silent SNP C C3N-01489_T 2483923 69260395 37783323 487 25417 SIPA1L1 0 . GRCh38 14 71588566 71588566 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.694G>T p.Asp232Tyr p.D232Y ENST00000555818 2/22 251 233 18 424 423 1 strelka-varscan-mutect SIPA1L1,missense_variant,p.Asp232Tyr,ENST00000555818,NM_015556.2,NM_001284247.1;SIPA1L1,missense_variant,p.Asp232Tyr,ENST00000358550,NM_001284246.1;SIPA1L1,missense_variant,p.Asp232Tyr,ENST00000381232,NM_001284245.1;SIPA1L1,downstream_gene_variant,,ENST00000557151,;SIPA1L1,downstream_gene_variant,,ENST00000555989,;SIPA1L1,downstream_gene_variant,,ENST00000554362,;SIPA1L1,downstream_gene_variant,,ENST00000555652,; T ENST00000555818 Transcript missense_variant 1042/7831 694/5415 232/1804 D/Y Gac/Tac 1 1 SIPA1L1 HGNC HGNC:20284 protein_coding YES CCDS9807.1 ENSP00000450832 O43166 UPI00000443CB NM_015556.2,NM_001284247.1 deleterious(0.01) 2/22 hmmpanther:PTHR15711,hmmpanther:PTHR15711:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 71588566 71588566 G T 1 0 0 0 0 1 0 0 0 14592 1290 45 2 2 SIPA1L1 14 71588566 Missense_Mutation SNP G C3N-01489_T 2328171 71588566 35455152 488 25418 ESRRB 0 . GRCh38 14 76482048 76482048 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.547C>A p.Gln183Lys p.Q183K ENST00000509242 4/9 396 350 46 669 665 4 strelka-varscan-mutect ESRRB,missense_variant,p.Gln183Lys,ENST00000509242,;ESRRB,missense_variant,p.Gln183Lys,ENST00000380887,NM_004452.3;ESRRB,missense_variant,p.Gln188Lys,ENST00000512784,;ESRRB,missense_variant,p.Gln183Lys,ENST00000556177,;ESRRB,non_coding_transcript_exon_variant,,ENST00000507951,;ESRRB,missense_variant,p.Gln183Lys,ENST00000505752,; A ENST00000509242 Transcript missense_variant 755/2849 547/1527 183/508 Q/K Cag/Aag 1 1 ESRRB HGNC HGNC:3473 protein_coding YES CCDS9850.2 ENSP00000422488 O95718 UPI000003157B deleterious(0) 4/9 Gene3D:1.10.565.10,PIRSF_domain:PIRSF002527,PIRSF_domain:PIRSF500939,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF23,Superfamily_domains:SSF48508,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 76482048 76482048 C A 1 0 0 0 0 1 0 0 0 5123 827 29 2 2 ESRRB 14 76482048 Missense_Mutation SNP C C3N-01489_T 4893482 76482048 30561670 489 25419 TMEM63C 0 . GRCh38 14 77253377 77253377 + Splice_Site SNP G G T novel C3N-01489_T C3N-01489_N G G c.2220+1G>T p.X740_splice ENST00000298351 208 180 28 277 277 0 strelka-varscan-mutect TMEM63C,splice_donor_variant,,ENST00000298351,NM_020431.3;TMEM63C,splice_donor_variant,,ENST00000557504,; T ENST00000298351 Transcript splice_donor_variant -/5334 2220/2421 740/806 1 1 TMEM63C HGNC HGNC:23787 protein_coding YES CCDS45141.1 ENSP00000298351 Q9P1W3 A0A024R6B3 UPI0000049C5C NM_020431.3 23/23 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 81 77253377 77253377 G T 1 0 0 0 0 0 0 1 0 16668 1159 40 1 1 TMEM63C 14 77253377 Splice_Site SNP G C3N-01489_T 771329 77253377 29790341 490 25420 ADCK1 0 . GRCh38 14 77899230 77899230 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.713A>T p.Gln238Leu p.Q238L ENST00000238561 6/11 119 104 15 214 214 0 strelka-varscan-mutect ADCK1,missense_variant,p.Gln238Leu,ENST00000238561,NM_020421.3;ADCK1,missense_variant,p.Gln170Leu,ENST00000341211,NM_001142545.1;ADCK1,missense_variant,p.Gln238Leu,ENST00000557501,;ADCK1,upstream_gene_variant,,ENST00000555333,;ADCK1,missense_variant,p.Gln185Leu,ENST00000393639,; T ENST00000238561 Transcript missense_variant 812/2234 713/1572 238/523 Q/L cAg/cTg 1 1 ADCK1 HGNC HGNC:19038 protein_coding YES CCDS9869.1 ENSP00000238561 Q86TW2 UPI000014035F NM_020421.3 tolerated(0.07) 6/11 Gene3D:3.90.1200.10,Pfam_domain:PF03109,hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF58,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 77899230 77899230 A T 1 0 0 0 0 1 0 0 0 331 188 7 4 4 ADCK1 14 77899230 Missense_Mutation SNP A C3N-01489_T 645853 77899230 29144488 491 25421 GOLGA5 0 . GRCh38 14 92833208 92833208 + Missense_Mutation SNP G G C C3N-01489_T C3N-01489_N G G c.1806G>C p.Gln602His p.Q602H ENST00000163416 10/13 312 285 27 429 429 0 strelka-varscan-mutect GOLGA5,missense_variant,p.Gln602His,ENST00000163416,NM_005113.3;GOLGA5,missense_variant,p.Gln28His,ENST00000554700,; C ENST00000163416 Transcript missense_variant 2062/2969 1806/2196 602/731 Q/H caG/caC COSM5382894 1 1 GOLGA5 HGNC HGNC:4428 protein_coding YES CCDS9905.1 ENSP00000163416 Q8TBA6 UPI000013C5AA NM_005113.3 deleterious(0) 10/13 Pfam_domain:PF09787,hmmpanther:PTHR13815,hmmpanther:PTHR13815:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 92833208 92833208 G C 1 0 0 0 0 1 0 0 0 6434 933 33 4 4 GOLGA5 14 92833208 Missense_Mutation SNP G C3N-01489_T 14933978 92833208 14210510 492 25422 DICER1 0 . GRCh38 14 95105100 95105101 + Frame_Shift_Ins INS - - A novel C3N-01489_T C3N-01489_N - - c.3239dupT p.Val1082SerfsTer9 p.V1082Sfs*9 ENST00000526495 22/29 189 175 14 310 309 1 varindel-pindel DICER1,frameshift_variant,p.Val1082SerfsTer9,ENST00000526495,NM_030621.4,NM_001291628.1;DICER1,frameshift_variant,p.Val1082SerfsTer9,ENST00000343455,NM_177438.2;DICER1,frameshift_variant,p.Val1082SerfsTer9,ENST00000393063,;DICER1,frameshift_variant,p.Val1082SerfsTer9,ENST00000527414,NM_001271282.2;DICER1,frameshift_variant,p.Val1082SerfsTer9,ENST00000541352,NM_001195573.1;DICER1,frameshift_variant,p.Trp4LeufsTer12,ENST00000556045,;DICER1,upstream_gene_variant,,ENST00000532939,;DICER1,non_coding_transcript_exon_variant,,ENST00000554367,;DICER1,downstream_gene_variant,,ENST00000556681,; A ENST00000526495 Transcript frameshift_variant 3531-3532/10331 3239-3240/5769 1080/1922 V/VX gtg/gtTg 1 -1 DICER1 HGNC HGNC:17098 protein_coding YES CCDS9931.1 ENSP00000437256 Q9UPY3 UPI0000168662 NM_030621.4,NM_001291628.1 22/29 hmmpanther:PTHR14950,hmmpanther:PTHR14950:SF26 HIGH 1 insertion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 81 95105100 95105100 - A 1 0 1 1 0 0 0 0 0 4325 595 21 0 0 DICER1 14 95105100 Frame_Shift_Ins INS - C3N-01489_T 2271892 95105100 11938618 493 25423 CLMN 0 . GRCh38 14 95203457 95203457 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1892C>T p.Pro631Leu p.P631L ENST00000298912 9/13 236 219 17 366 366 0 strelka-varscan-mutect CLMN,missense_variant,p.Pro631Leu,ENST00000298912,NM_024734.3;CLMN,non_coding_transcript_exon_variant,,ENST00000556454,;RP11-725G5.3,downstream_gene_variant,,ENST00000555482,; A ENST00000298912 Transcript missense_variant 2006/12747 1892/3009 631/1002 P/L cCt/cTt 1 -1 CLMN HGNC HGNC:19972 protein_coding YES CCDS9933.1 ENSP00000298912 Q96JQ2 UPI000006DB99 NM_024734.3 tolerated_low_confidence(0.08) 9/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 95203457 95203457 G A 1 0 0 0 0 1 0 0 0 3311 1000 35 3 3 CLMN 14 95203457 Missense_Mutation SNP G C3N-01489_T 98357 95203457 11840261 494 25424 SYNE3 0 . GRCh38 14 95439711 95439711 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.2147A>T p.Glu716Val p.E716V ENST00000334258 12/17 188 171 17 296 296 0 strelka-varscan-mutect SYNE3,missense_variant,p.Glu716Val,ENST00000557275,;SYNE3,missense_variant,p.Glu716Val,ENST00000334258,NM_152592.3;SYNE3,missense_variant,p.Glu473Val,ENST00000554873,;SYNE3,downstream_gene_variant,,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,; A ENST00000334258 Transcript missense_variant 2162/3275 2147/2928 716/975 E/V gAg/gTg 1 -1 SYNE3 HGNC HGNC:19861 protein_coding YES CCDS9935.1 ENSP00000334308 Q6ZMZ3 UPI0000246F54 NM_152592.3 deleterious(0.01) 12/17 Pfam_domain:PF00435,hmmpanther:PTHR11915,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 95439711 95439711 T A 1 0 0 0 0 1 0 0 0 15839 1551 54 4 4 SYNE3 14 95439711 Missense_Mutation SNP T C3N-01489_T 236254 95439711 11604007 495 25425 SYNE3 0 . GRCh38 14 95466010 95466010 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.548G>T p.Arg183Met p.R183M ENST00000334258 3/17 79 71 8 105 105 0 strelka-varscan-mutect SYNE3,missense_variant,p.Arg183Met,ENST00000557275,;SYNE3,missense_variant,p.Arg183Met,ENST00000334258,NM_152592.3;SYNE3,missense_variant,p.Arg183Met,ENST00000553340,;SYNE3,non_coding_transcript_exon_variant,,ENST00000555759,; A ENST00000334258 Transcript missense_variant 563/3275 548/2928 183/975 R/M aGg/aTg 1 -1 SYNE3 HGNC HGNC:19861 protein_coding YES CCDS9935.1 ENSP00000334308 Q6ZMZ3 UPI0000246F54 NM_152592.3 deleterious(0.02) 3/17 Gene3D:1.20.58.60,hmmpanther:PTHR11915,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -17.28487 1 1 1 1 0 A 3 1 81 95466010 95466010 C A 1 0 0 0 0 1 0 0 0 15839 681 24 2 2 SYNE3 14 95466010 Missense_Mutation SNP C C3N-01489_T 26299 95466010 11577708 496 25426 BDKRB1 0 . GRCh38 14 96264336 96264336 + Silent SNP C C T rs753420449 C3N-01489_T C3N-01489_N C C c.654C>T p.= p.I218I ENST00000216629 3/3 284 251 33 448 448 0 strelka-varscan-mutect BDKRB1,synonymous_variant,p.=,ENST00000216629,NM_000710.3;BDKRB1,synonymous_variant,p.=,ENST00000553356,;BDKRB1,synonymous_variant,p.=,ENST00000611804,;RP11-404P21.8,downstream_gene_variant,,ENST00000553811,;RP11-404P21.3,intron_variant,,ENST00000553638,;BDKRB1,upstream_gene_variant,,ENST00000557122,;RP11-404P21.8,downstream_gene_variant,,ENST00000555847,; T ENST00000216629 Transcript synonymous_variant 1260/1687 654/1062 218/353 I atC/atT rs753420449,COSM3886668 1 1 BDKRB1 HGNC HGNC:1029 protein_coding YES CCDS9943.1 ENSP00000216629 P46663 UPI0000000348 NM_000710.3 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF28,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00425,Prints_domain:PR00237 0,1 LOW 1 SNV 1 0,1 1 PASS rs753420449 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 96264336 96264336 C T 1 0 0 0 0 0 0 0 1 1539 874 31 1 1 BDKRB1 14 96264336 Silent SNP C C3N-01489_T 798326 96264336 10779382 497 25427 DYNC1H1 0 . GRCh38 14 102002876 102002876 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.4794G>A p.= p.Q1598Q ENST00000360184 23/78 233 205 28 418 418 0 strelka-varscan-mutect DYNC1H1,synonymous_variant,p.=,ENST00000360184,NM_001376.4; A ENST00000360184 Transcript synonymous_variant 4958/14333 4794/13941 1598/4646 Q caG/caA 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 23/78 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 102002876 102002876 G A 1 0 0 0 0 0 0 0 1 4665 933 33 3 3 DYNC1H1 14 102002876 Silent SNP G C3N-01489_T 5738540 102002876 5040842 498 25428 DYNC1H1 0 . GRCh38 14 102016072 102016072 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.7459G>T p.Glu2487Ter p.E2487* ENST00000360184 36/78 165 145 20 222 222 0 strelka-varscan-mutect DYNC1H1,stop_gained,p.Glu2487Ter,ENST00000360184,NM_001376.4;DYNC1H1,upstream_gene_variant,,ENST00000555204,; T ENST00000360184 Transcript stop_gained 7623/14333 7459/13941 2487/4646 E/* Gag/Tag 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 36/78 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 102016072 102016072 G T 1 0 0 0 0 0 1 0 0 4665 1175 41 2 2 DYNC1H1 14 102016072 Nonsense_Mutation SNP G C3N-01489_T 13196 102016072 5027646 499 25429 MTA1 0 . GRCh38 14 105469492 105469492 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1839G>T p.Arg613Ser p.R613S ENST00000331320 19/21 184 174 10 278 278 0 strelka-varscan-mutect MTA1,missense_variant,p.Arg153Ser,ENST00000435036,;MTA1,missense_variant,p.Arg613Ser,ENST00000331320,NM_004689.3;MTA1,missense_variant,p.Arg601Ser,ENST00000406191,NM_001203258.1;MTA1,missense_variant,p.Arg596Ser,ENST00000405646,;MTA1,missense_variant,p.Arg409Ser,ENST00000434050,;CRIP2,upstream_gene_variant,,ENST00000329146,NM_001312.3;CRIP2,upstream_gene_variant,,ENST00000483017,NM_001270837.1;RP11-521B24.5,intron_variant,,ENST00000552675,;MTA1,non_coding_transcript_exon_variant,,ENST00000494981,;MTA1,downstream_gene_variant,,ENST00000550551,;MTA1,3_prime_UTR_variant,,ENST00000438610,;MTA1,non_coding_transcript_exon_variant,,ENST00000552286,;MTA1,non_coding_transcript_exon_variant,,ENST00000481206,;MTA1,non_coding_transcript_exon_variant,,ENST00000481635,;MTA1,non_coding_transcript_exon_variant,,ENST00000426567,;MTA1,downstream_gene_variant,,ENST00000469140,;MTA1,downstream_gene_variant,,ENST00000490198,;MTA1,downstream_gene_variant,,ENST00000550808,; T ENST00000331320 Transcript missense_variant 2053/2876 1839/2148 613/715 R/S agG/agT 1 1 MTA1 HGNC HGNC:7410 protein_coding YES CCDS32169.1 ENSP00000333633 Q13330 UPI00003669FD NM_004689.3 tolerated(0.2) 19/21 hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF5 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -3.628046 0.978246 1 1 1 0 T 3 4 81 105469492 105469492 G T 1 0 0 0 0 1 0 0 0 9893 1194 42 2 2 MTA1 14 105469492 Missense_Mutation SNP G C3N-01489_T 3453420 105469492 1574226 500 25430 GOLGA8S 0 . GRCh38 15 23364727 23364727 + Missense_Mutation SNP G G T rs761643345 C3N-01489_T C3N-01489_N G G c.1555G>T p.Ala519Ser p.A519S ENST00000562295 18/19 454 417 37 619 618 1 varscan-mutect GOLGA8S,missense_variant,p.Ala519Ser,ENST00000562295,;RN7SL536P,downstream_gene_variant,,ENST00000612366,;GOLGA8S,non_coding_transcript_exon_variant,,ENST00000604046,; T ENST00000562295 Transcript missense_variant 1555/1878 1555/1878 519/625 A/S Gct/Tct rs761643345 1 1 GOLGA8S HGNC HGNC:44409 protein_coding YES ENSP00000455298 H3BPF8 UPI00024672CC tolerated(0.22) 18/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs761643345 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 23364727 23364727 G T 1 0 0 0 0 1 0 0 0 6457 1319 46 2 2 GOLGA8S 15 23364727 Missense_Mutation SNP G C3N-01489_T 23364727 78626462 501 25431 MKRN3 0 . GRCh38 15 23566917 23566917 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1135G>T p.Glu379Ter p.E379* ENST00000314520 1/1 289 264 25 489 488 1 strelka-varscan-mutect MKRN3,stop_gained,p.Glu379Ter,ENST00000314520,NM_005664.3;MKRN3,stop_gained,p.Glu139Ter,ENST00000564592,;MKRN3,intron_variant,,ENST00000568252,;AC126407.1,upstream_gene_variant,,ENST00000626930,;MIR4508,upstream_gene_variant,,ENST00000584178,;MKRN3-AS1,downstream_gene_variant,,ENST00000563044,;MKRN3,non_coding_transcript_exon_variant,,ENST00000568945,;MKRN3,3_prime_UTR_variant,,ENST00000570112,; T ENST00000314520 Transcript stop_gained 1234/2337 1135/1524 379/507 E/* Gag/Tag 1 1 MKRN3 HGNC HGNC:7114 protein_coding YES CCDS10013.1 ENSP00000313881 Q13064 UPI000000DAA1 NM_005664.3 1/1 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11224:SF38,hmmpanther:PTHR11224 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 23566917 23566917 G T 1 0 0 0 0 0 1 0 0 9576 1175 41 2 2 MKRN3 15 23566917 Nonsense_Mutation SNP G C3N-01489_T 202190 23566917 78424272 502 25432 MAGEL2 0 . GRCh38 15 23646070 23646070 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1673G>T p.Gly558Val p.G558V ENST00000532292 1/1 36 32 4 87 87 0 strelka-varscan-mutect MAGEL2,missense_variant,p.Gly558Val,ENST00000532292,NM_019066.4; A ENST00000532292 Transcript missense_variant 1772/4298 1673/3750 558/1249 G/V gGc/gTc 1 -1 MAGEL2 HGNC HGNC:6814 protein_coding YES CCDS73700.1 ENSP00000433433 Q9UJ55 UPI0001B3CB28 NM_019066.4 tolerated_low_confidence(0.11) 1/1 Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 199 11 0 0 0 0 0 -10.65302 0.999928 1 1 1 0 A 3 1 81 23646070 23646070 C A 1 0 0 0 0 1 0 0 0 9107 739 26 2 2 MAGEL2 15 23646070 Missense_Mutation SNP C C3N-01489_T 79153 23646070 78345119 503 25433 GABRB3 0 . GRCh38 15 26583347 26583347 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.529C>A p.Leu177Met p.L177M ENST00000311550 5/9 411 379 32 576 576 0 strelka-varscan-mutect GABRB3,missense_variant,p.Leu233Met,ENST00000541819,;GABRB3,missense_variant,p.Leu92Met,ENST00000622697,NM_001278631.1;GABRB3,missense_variant,p.Leu177Met,ENST00000311550,NM_000814.5;GABRB3,missense_variant,p.Leu92Met,ENST00000628124,NM_001191320.1;GABRB3,missense_variant,p.Leu92Met,ENST00000636466,;GABRB3,missense_variant,p.Leu177Met,ENST00000299267,NM_021912.4;GABRB3,missense_variant,p.Leu144Met,ENST00000638099,;GABRB3,missense_variant,p.Leu106Met,ENST00000400188,NM_001191321.2;GABRB3,missense_variant,p.Leu92Met,ENST00000545868,;GABRB3,non_coding_transcript_exon_variant,,ENST00000635832,;GABRB3,non_coding_transcript_exon_variant,,ENST00000555094,;GABRB3,non_coding_transcript_exon_variant,,ENST00000636512,;GABRB3,missense_variant,p.Leu72Met,ENST00000635994,;GABRB3,missense_variant,p.Ser103Tyr,ENST00000554556,;GABRB3,3_prime_UTR_variant,,ENST00000555632,;GABRB3,upstream_gene_variant,,ENST00000557765,; T ENST00000311550 Transcript missense_variant 641/5781 529/1422 177/473 L/M Ctg/Atg COSM4826130,COSM4826131,COSM4826132 1 -1 GABRB3 HGNC HGNC:4083 protein_coding YES CCDS10019.1 ENSP00000308725 P28472 UPI000012AFB0 NM_000814.5 deleterious(0) 5/9 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF571,TIGRFAM_domain:TIGR00860,Gene3D:2.70.170.10,Pfam_domain:PF02931,Superfamily_domains:0038932 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 26583347 26583347 G T 1 0 0 0 0 1 0 0 0 6039 933 33 2 2 GABRB3 15 26583347 Missense_Mutation SNP G C3N-01489_T 2937277 26583347 75407842 504 25434 HERC2 0 . GRCh38 15 28218628 28218628 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.5889G>T p.Met1963Ile p.M1963I ENST00000261609 38/93 235 215 20 358 358 0 varscan-mutect HERC2,missense_variant,p.Met1963Ile,ENST00000261609,NM_004667.5;HERC2,downstream_gene_variant,,ENST00000569335,; A ENST00000261609 Transcript missense_variant 5998/15337 5889/14505 1963/4834 M/I atG/atT 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 tolerated(0.26) 38/93 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 28218628 28218628 C A 1 0 0 0 0 1 0 0 0 6942 478 17 2 2 HERC2 15 28218628 Missense_Mutation SNP C C3N-01489_T 1635281 28218628 73772561 505 25435 THBS1 0 . GRCh38 15 39591221 39591221 + Missense_Mutation SNP C C G rs778071185 C3N-01489_T C3N-01489_N C C c.2284C>G p.Gln762Glu p.Q762E ENST00000260356 15/22 89 80 9 145 145 0 strelka-varscan-mutect THBS1,missense_variant,p.Gln762Glu,ENST00000260356,NM_003246.2;CTD-2033D15.2,downstream_gene_variant,,ENST00000478845,;CTD-2033D15.3,upstream_gene_variant,,ENST00000616754,;CTD-2033D15.1,downstream_gene_variant,,ENST00000560769,;THBS1,non_coding_transcript_exon_variant,,ENST00000560894,;THBS1,upstream_gene_variant,,ENST00000484734,;THBS1,upstream_gene_variant,,ENST00000559746,;THBS1,downstream_gene_variant,,ENST00000497720,;THBS1,downstream_gene_variant,,ENST00000466755,;THBS1,downstream_gene_variant,,ENST00000490247,; G ENST00000260356 Transcript missense_variant 2449/7775 2284/3513 762/1170 Q/E Cag/Gag rs778071185 1 1 THBS1 HGNC HGNC:11785 protein_coding YES CCDS32194.1 ENSP00000260356 P07996 UPI00001FE219 NM_003246.2 deleterious(0) 15/22 PROSITE_profiles:PS51234,hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF78,Gene3D:1ux6A01,Pfam_domain:PF02412,Superfamily_domains:0044556 MODERATE 1 SNV 1 1 PASS rs778071185 . 0 208 2 0 0 0 0 0 -19.2171 1 1 1 1 0 G 3 3 81 39591221 39591221 C G 1 0 0 0 0 1 0 0 0 16286 827 29 4 4 THBS1 15 39591221 Missense_Mutation SNP C C3N-01489_T 11372593 39591221 62399968 506 25436 STRC 0 . GRCh38 15 43603352 43603352 + Missense_Mutation SNP G G T rs200086657 C3N-01489_T C3N-01489_N G G c.4435C>A p.Gln1479Lys p.Q1479K ENST00000450892 23/29 347 323 24 527 527 0 varscan-mutect STRC,missense_variant,p.Gln1479Lys,ENST00000450892,NM_153700.2;STRC,missense_variant,p.Gln706Lys,ENST00000541030,;CKMT1B,downstream_gene_variant,,ENST00000300283,NM_020990.3;CKMT1B,downstream_gene_variant,,ENST00000441322,;RNU6-554P,downstream_gene_variant,,ENST00000410466,;CKMT1B,intron_variant,,ENST00000411560,;STRC,3_prime_UTR_variant,,ENST00000440125,;STRC,non_coding_transcript_exon_variant,,ENST00000485556,;STRC,non_coding_transcript_exon_variant,,ENST00000471703,;STRC,non_coding_transcript_exon_variant,,ENST00000493750,;STRC,intron_variant,,ENST00000428650,;STRC,intron_variant,,ENST00000448437,;CKMT1B,downstream_gene_variant,,ENST00000437534,;STRC,downstream_gene_variant,,ENST00000455136,;STRC,upstream_gene_variant,,ENST00000460952,; T ENST00000450892 Transcript missense_variant 4513/5680 4435/5328 1479/1775 Q/K Cag/Aag rs200086657 1 -1 STRC HGNC HGNC:16035 protein_coding YES CCDS10098.1 ENSP00000401513 Q7RTU9 UPI000013E60F NM_153700.2 deleterious(0) 23/29 hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF14 MODERATE 1 SNV 5 1 PASS rs200086657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 43603352 43603352 G T 1 0 0 0 0 1 0 0 0 15709 1357 47 2 2 STRC 15 43603352 Missense_Mutation SNP G C3N-01489_T 4012131 43603352 58387837 507 25437 AQP9 0 . GRCh38 15 58173082 58173082 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.253C>A p.Pro85Thr p.P85T ENST00000219919 3/6 118 109 9 196 195 1 strelka-mutect AQP9,missense_variant,p.Pro85Thr,ENST00000219919,NM_020980.3;AQP9,missense_variant,p.Pro85Thr,ENST00000536493,;AQP9,missense_variant,p.Pro20Thr,ENST00000558772,;ALDH1A2,intron_variant,,ENST00000558231,;ALDH1A2,intron_variant,,ENST00000558239,;ALDH1A2,intron_variant,,ENST00000560863,;ALDH1A2,intron_variant,,ENST00000558073,;ALDH1A2,intron_variant,,ENST00000560122,;ALDH1A2,intron_variant,,ENST00000559297,;ALDH1A2,intron_variant,,ENST00000558504,; A ENST00000219919 Transcript missense_variant 623/3034 253/888 85/295 P/T Cca/Aca 1 1 AQP9 HGNC HGNC:643 protein_coding YES CCDS10165.1 ENSP00000219919 O43315 UPI000013C796 NM_020980.3 deleterious(0.02) 3/6 hmmpanther:PTHR19139:SF149,hmmpanther:PTHR19139,PROSITE_patterns:PS00221,TIGRFAM_domain:TIGR00861,Gene3D:1.20.1080.10,Pfam_domain:PF00230,Superfamily_domains:SSF81338,Prints_domain:PR00783 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 58173082 58173082 C A 1 0 0 0 0 1 0 0 0 956 623 22 2 2 AQP9 15 58173082 Missense_Mutation SNP C C3N-01489_T 14569730 58173082 43818107 508 25438 HERC1 0 . GRCh38 15 63641558 63641558 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.11519G>T p.Gly3840Val p.G3840V ENST00000443617 60/78 165 151 14 219 219 0 strelka-varscan-mutect HERC1,missense_variant,p.Gly3840Val,ENST00000443617,NM_003922.3;HERC1,upstream_gene_variant,,ENST00000560897,; A ENST00000443617 Transcript missense_variant 11607/15137 11519/14586 3840/4861 G/V gGt/gTt 1 -1 HERC1 HGNC HGNC:4867 protein_coding YES CCDS45277.1 ENSP00000390158 Q15751 A0A024R5W0 UPI0000212760 NM_003922.3 deleterious(0) 60/78 hmmpanther:PTHR22870:SF188,hmmpanther:PTHR22870 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 63641558 63641558 C A 1 0 0 0 0 1 0 0 0 6941 507 18 2 2 HERC1 15 63641558 Missense_Mutation SNP C C3N-01489_T 5468476 63641558 38349631 509 25439 IGDCC3 0 . GRCh38 15 65331098 65331098 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.1513G>T p.Gly505Trp p.G505W ENST00000327987 9/14 220 201 19 306 306 0 strelka-varscan-mutect IGDCC3,missense_variant,p.Gly505Trp,ENST00000327987,NM_004884.3;IGDCC3,missense_variant,p.Gly368Trp,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559058,;IGDCC3,downstream_gene_variant,,ENST00000559231,; A ENST00000327987 Transcript missense_variant 1765/4479 1513/2445 505/814 G/W Ggg/Tgg COSM4151002 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 deleterious(0) 9/14 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF106,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 65331098 65331098 C A 1 0 0 0 0 1 0 0 0 7474 623 22 2 2 IGDCC3 15 65331098 Missense_Mutation SNP C C3N-01489_T 1689540 65331098 36660091 510 25440 FEM1B 0 . GRCh38 15 68289997 68289997 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.639A>T p.= p.I213I ENST00000306917 2/2 124 110 14 186 186 0 strelka-varscan-mutect FEM1B,synonymous_variant,p.=,ENST00000306917,NM_015322.4;FEM1B,synonymous_variant,p.=,ENST00000566739,;FEM1B,upstream_gene_variant,,ENST00000566008,;FEM1B,downstream_gene_variant,,ENST00000570067,; T ENST00000306917 Transcript synonymous_variant 1254/7122 639/1884 213/627 I atA/atT 1 1 FEM1B HGNC HGNC:3649 protein_coding YES CCDS10228.1 ENSP00000307298 Q9UK73 UPI00000011FB NM_015322.4 2/2 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24173:SF18,hmmpanther:PTHR24173,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 68289997 68289997 A T 1 0 0 0 0 0 0 0 1 5673 410 15 4 4 FEM1B 15 68289997 Silent SNP A C3N-01489_T 2958899 68289997 33701192 511 25441 ISLR2 0 . GRCh38 15 74134630 74134630 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1876C>T p.Arg626Cys p.R626C ENST00000361742 4/4 190 170 20 243 243 0 strelka-varscan-mutect ISLR2,missense_variant,p.Arg626Cys,ENST00000361742,NM_001130136.1;ISLR2,missense_variant,p.Arg626Cys,ENST00000435464,NM_001130138.1;ISLR2,missense_variant,p.Arg626Cys,ENST00000565159,NM_001130137.1;ISLR2,missense_variant,p.Arg626Cys,ENST00000453268,NM_020851.2;ISLR2,missense_variant,p.Arg626Cys,ENST00000565540,;ISLR2,missense_variant,p.Arg215Cys,ENST00000419208,;ISLR2,downstream_gene_variant,,ENST00000569886,;ISLR2,downstream_gene_variant,,ENST00000561740,;ISLR2,downstream_gene_variant,,ENST00000567206,;ISLR2,downstream_gene_variant,,ENST00000565332,;ISLR2,intron_variant,,ENST00000561975,;ISLR2,downstream_gene_variant,,ENST00000565068,; T ENST00000361742 Transcript missense_variant 2645/4817 1876/2238 626/745 R/C Cgt/Tgt 1 1 ISLR2 HGNC HGNC:29286 protein_coding YES CCDS10259.1 ENSP00000355402 Q6UXK2 UPI000004C60F NM_001130136.1 deleterious(0) 4/4 hmmpanther:PTHR24366,hmmpanther:PTHR24366:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 74134630 74134630 C T 1 0 0 0 0 1 0 0 0 7766 652 23 1 1 ISLR2 15 74134630 Missense_Mutation SNP C C3N-01489_T 5844633 74134630 27856559 512 25442 LMAN1L 0 . GRCh38 15 74816685 74816685 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.492G>T p.Gln164His p.Q164H ENST00000309664 4/14 83 76 7 139 139 0 strelka-varscan-mutect LMAN1L,missense_variant,p.Gln164His,ENST00000309664,NM_021819.2;LMAN1L,missense_variant,p.Gln164His,ENST00000379709,;LMAN1L,downstream_gene_variant,,ENST00000562810,;LMAN1L,upstream_gene_variant,,ENST00000567848,;RP11-414J4.2,non_coding_transcript_exon_variant,,ENST00000488000,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000470711,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000456603,;RP11-414J4.2,upstream_gene_variant,,ENST00000564823,;LMAN1L,upstream_gene_variant,,ENST00000565585,;LMAN1L,downstream_gene_variant,,ENST00000568467,;LMAN1L,downstream_gene_variant,,ENST00000570147,; T ENST00000309664 Transcript missense_variant 631/1873 492/1581 164/526 Q/H caG/caT 1 1 LMAN1L HGNC HGNC:6632 protein_coding YES CCDS10270.1 ENSP00000310431 Q9HAT1 UPI00001AEF1F NM_021819.2 tolerated(1) 4/14 Gene3D:2.60.120.200,Pfam_domain:PF03388,PROSITE_profiles:PS51328,hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF31,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -15.23499 1 1 1 1 0 T 3 4 81 74816685 74816685 G T 1 0 0 0 0 1 0 0 0 8761 985 34 2 2 LMAN1L 15 74816685 Missense_Mutation SNP G C3N-01489_T 682055 74816685 27174504 513 25443 ANKRD34C 0 . GRCh38 15 79294086 79294086 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.802C>A p.Arg268Ser p.R268S ENST00000421388 1/1 143 130 13 232 232 0 strelka-varscan-mutect ANKRD34C,missense_variant,p.Arg268Ser,ENST00000421388,NM_001146341.1; A ENST00000421388 Transcript missense_variant 802/4951 802/1608 268/535 R/S Cgt/Agt 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 tolerated(0.54) 1/1 hmmpanther:PTHR24157 MODERATE 1 SNV 1 PASS rs927055082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 79294086 79294086 C A 1 0 0 0 0 1 0 0 0 769 768 27 1 1 ANKRD34C 15 79294086 Missense_Mutation SNP C C3N-01489_T 4477401 79294086 22697103 514 25444 ANKRD34C 0 . GRCh38 15 79294280 79294280 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.996C>A p.= p.A332A ENST00000421388 1/1 141 121 20 283 283 0 strelka-varscan-mutect ANKRD34C,synonymous_variant,p.=,ENST00000421388,NM_001146341.1; A ENST00000421388 Transcript synonymous_variant 996/4951 996/1608 332/535 A gcC/gcA 1 1 ANKRD34C HGNC HGNC:33888 protein_coding YES CCDS53965.1 ENSP00000401089 P0C6C1 UPI0000160A7F NM_001146341.1 1/1 hmmpanther:PTHR24157 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 79294280 79294280 C A 1 0 0 0 0 0 0 0 1 769 668 24 2 2 ANKRD34C 15 79294280 Silent SNP C C3N-01489_T 194 79294280 22696909 515 25445 ALPK3 0 . GRCh38 15 84857762 84857762 + Silent SNP C C T rs755638287 C3N-01489_T C3N-01489_N C C c.3630C>T p.= p.P1210P ENST00000258888 6/14 76 71 5 125 125 0 varscan-mutect ALPK3,synonymous_variant,p.=,ENST00000258888,NM_020778.4; T ENST00000258888 Transcript synonymous_variant 3797/10917 3630/5724 1210/1907 P ccC/ccT rs755638287 1 1 ALPK3 HGNC HGNC:17574 protein_coding YES CCDS10333.1 ENSP00000258888 Q96L96 UPI000013D013 NM_020778.4 6/14 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF667 LOW 1 SNV 1 1 PASS rs755638287 . 0 207 3 0 0 0 0 0 -11.4966 1 1 1 1 0 T 2 4 81 84857762 84857762 C T 1 0 0 0 0 0 0 0 1 646 610 22 3 3 ALPK3 15 84857762 Silent SNP C C3N-01489_T 5563482 84857762 17133427 516 25446 NTRK3 0 . GRCh38 15 87933067 87933067 + Missense_Mutation SNP G G T rs373273419 C3N-01489_T C3N-01489_N G G c.1834C>A p.Pro612Thr p.P612T ENST00000360948 16/20 267 235 32 469 469 0 strelka-varscan-mutect NTRK3,missense_variant,p.Pro612Thr,ENST00000394480,NM_002530.3;NTRK3,missense_variant,p.Pro604Thr,ENST00000558676,;NTRK3,missense_variant,p.Pro612Thr,ENST00000360948,NM_001012338.2;NTRK3,missense_variant,p.Pro604Thr,ENST00000357724,;NTRK3,missense_variant,p.Pro604Thr,ENST00000355254,NM_001243101.1;NTRK3,missense_variant,p.Pro612Thr,ENST00000626019,;NTRK3,missense_variant,p.Pro612Thr,ENST00000629765,;NTRK3,missense_variant,p.Pro604Thr,ENST00000557856,;NTRK3,missense_variant,p.Pro514Thr,ENST00000542733,NM_001320135.1;NTRK3,missense_variant,p.Pro9Thr,ENST00000558576,;NTRK3,non_coding_transcript_exon_variant,,ENST00000559680,; T ENST00000360948 Transcript missense_variant 2140/3004 1834/2520 612/839 P/T Ccc/Acc rs373273419,COSM702264,COSM702265 1 -1 NTRK3 HGNC HGNC:8033 protein_coding YES CCDS32322.1 ENSP00000354207 Q16288 X5D2R1 UPI000006DC82 NM_001012338.2 deleterious(0) 16/20 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF66,SMART_domains:SM00219,Superfamily_domains:SSF56112 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs373273419 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 87933067 87933067 G T 1 0 0 0 0 1 0 0 0 10774 1232 43 2 2 NTRK3 15 87933067 Missense_Mutation SNP G C3N-01489_T 3075305 87933067 14058122 517 25447 IGF1R 0 . GRCh38 15 98916815 98916815 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2140G>T p.Glu714Ter p.E714* ENST00000268035 10/21 469 439 30 622 621 1 strelka-varscan-mutect IGF1R,stop_gained,p.Glu714Ter,ENST00000268035,NM_000875.4;IGF1R,stop_gained,p.Glu714Ter,ENST00000558762,NM_001291858.1;IGF1R,downstream_gene_variant,,ENST00000559582,;IGF1R,3_prime_UTR_variant,,ENST00000560144,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,;IGF1R,non_coding_transcript_exon_variant,,ENST00000561049,; T ENST00000268035 Transcript stop_gained 2751/11803 2140/4104 714/1367 E/* Gag/Tag 1 1 IGF1R HGNC HGNC:5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 UPI000012D3EA NM_000875.4 10/21 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF000620,SMART_domains:SM00060 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 98916815 98916815 G T 1 0 0 0 0 0 1 0 0 7477 1175 41 2 2 IGF1R 15 98916815 Nonsense_Mutation SNP G C3N-01489_T 10983748 98916815 3074374 518 25448 ALDH1A3 0 . GRCh38 15 100898112 100898112 + Silent SNP C C T C3N-01489_T C3N-01489_N C C c.810C>T p.= p.S270S ENST00000329841 8/13 134 126 8 179 179 0 strelka-varscan-mutect ALDH1A3,synonymous_variant,p.=,ENST00000329841,NM_000693.3;ALDH1A3,synonymous_variant,p.=,ENST00000346623,NM_001293815.1;RP11-66B24.4,intron_variant,,ENST00000560351,;ALDH1A3,non_coding_transcript_exon_variant,,ENST00000558869,;ALDH1A3,downstream_gene_variant,,ENST00000558033,; T ENST00000329841 Transcript synonymous_variant 1342/3924 810/1539 270/512 S tcC/tcT COSM3815662 1 1 ALDH1A3 HGNC HGNC:409 protein_coding YES CCDS10389.1 ENSP00000332256 P47895 A0A024RC95 UPI00001AFAF8 NM_000693.3 8/13 Gene3D:3.40.605.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF209,Superfamily_domains:SSF53720 1 LOW 1 SNV 1 1 1 PASS . . 0 206 2 2 0 0 0 0 -11.37987 0.9999864 1 1 1 0 T 2 4 81 100898112 100898112 C T 1 0 0 0 0 0 0 0 1 592 610 22 3 3 ALDH1A3 15 100898112 Silent SNP C C3N-01489_T 1981297 100898112 1093077 519 25449 PCSK6 0 . GRCh38 15 101430036 101430036 + Missense_Mutation SNP C C A rs757548126 C3N-01489_T C3N-01489_N C C c.685G>T p.Gly229Cys p.G229C ENST00000611716 5/22 325 305 20 527 527 0 strelka-varscan-mutect PCSK6,missense_variant,p.Gly229Cys,ENST00000611716,NM_002570.4;PCSK6,missense_variant,p.Gly229Cys,ENST00000618548,NM_138319.3;PCSK6,missense_variant,p.Gly131Cys,ENST00000398185,NM_001291309.1;PCSK6,missense_variant,p.Gly229Cys,ENST00000611967,NM_138324.2;PCSK6,missense_variant,p.Gly229Cys,ENST00000622483,;PCSK6,missense_variant,p.Gly229Cys,ENST00000619160,;PCSK6,missense_variant,p.Gly229Cys,ENST00000615296,NM_138323.2;PCSK6,missense_variant,p.Gly229Cys,ENST00000331826,NM_138325.3;PCSK6,missense_variant,p.Gly103Cys,ENST00000559417,;PCSK6,intron_variant,,ENST00000557794,; A ENST00000611716 Transcript missense_variant 854/4409 685/2910 229/969 G/C Ggc/Tgc rs757548126 1 -1 PCSK6 HGNC HGNC:8569 protein_coding YES CCDS73790.1 ENSP00000482760 P29122 UPI00001311D0 NM_002570.4 deleterious(0) 5/22 hmmpanther:PTHR10795:SF345,hmmpanther:PTHR10795,Pfam_domain:PF00082,Gene3D:3.40.50.200,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS rs757548126 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 101430036 101430036 C A 1 0 0 0 0 1 0 0 0 11692 652 23 1 1 PCSK6 15 101430036 Missense_Mutation SNP C C3N-01489_T 531924 101430036 561153 520 25450 HAGHL 0 . GRCh38 16 727591 727591 + Missense_Mutation SNP G G A rs777098321 C3N-01489_T C3N-01489_N G G c.82G>A p.Val28Met p.V28M ENST00000389703 1/8 159 129 30 170 170 0 strelka-varscan-mutect HAGHL,missense_variant,p.Val28Met,ENST00000549114,;HAGHL,missense_variant,p.Val28Met,ENST00000341413,;HAGHL,missense_variant,p.Val28Met,ENST00000564537,;HAGHL,missense_variant,p.Val28Met,ENST00000389703,NM_001290137.1,NM_001290139.1,NM_032304.3;HAGHL,missense_variant,p.Val28Met,ENST00000561546,;HAGHL,missense_variant,p.Val28Met,ENST00000568141,;HAGHL,missense_variant,p.Val28Met,ENST00000567414,;HAGHL,missense_variant,p.Val28Met,ENST00000564545,;HAGHL,missense_variant,p.Val28Met,ENST00000562141,;NARFL,downstream_gene_variant,,ENST00000540986,NM_001304799.1;NARFL,downstream_gene_variant,,ENST00000568545,;NARFL,downstream_gene_variant,,ENST00000251588,NM_022493.2;CCDC78,upstream_gene_variant,,ENST00000293889,NM_001031737.2;CCDC78,upstream_gene_variant,,ENST00000345165,;FAM173A,downstream_gene_variant,,ENST00000569529,NM_023933.2;NARFL,downstream_gene_variant,,ENST00000562421,;CCDC78,upstream_gene_variant,,ENST00000423653,;HAGHL,upstream_gene_variant,,ENST00000563792,;HAGHL,downstream_gene_variant,,ENST00000562187,;NARFL,downstream_gene_variant,,ENST00000562862,;HAGHL,upstream_gene_variant,,ENST00000563156,;HAGHL,non_coding_transcript_exon_variant,,ENST00000567696,;HAGHL,non_coding_transcript_exon_variant,,ENST00000389701,;HAGHL,non_coding_transcript_exon_variant,,ENST00000561750,;HAGHL,non_coding_transcript_exon_variant,,ENST00000569143,;CCDC78,upstream_gene_variant,,ENST00000482878,;CCDC78,upstream_gene_variant,,ENST00000481804,;CCDC78,upstream_gene_variant,,ENST00000478979,;NARFL,downstream_gene_variant,,ENST00000563051,;NARFL,downstream_gene_variant,,ENST00000566650,;NARFL,downstream_gene_variant,,ENST00000565425,;CCDC78,upstream_gene_variant,,ENST00000466708,;CCDC78,upstream_gene_variant,,ENST00000463539,;CCDC78,upstream_gene_variant,,ENST00000485091,;NARFL,downstream_gene_variant,,ENST00000564285,;CCDC78,upstream_gene_variant,,ENST00000538176,;CCDC78,upstream_gene_variant,,ENST00000439619,;CCDC78,upstream_gene_variant,,ENST00000482152,;CCDC78,upstream_gene_variant,,ENST00000460023,;CCDC78,upstream_gene_variant,,ENST00000471861,;CCDC78,upstream_gene_variant,,ENST00000544996,;CCDC78,upstream_gene_variant,,ENST00000474647,;HAGHL,upstream_gene_variant,,ENST00000569385,;HAGHL,upstream_gene_variant,,ENST00000561561,; A ENST00000389703 Transcript missense_variant 321/1347 82/849 28/282 V/M Gtg/Atg rs777098321 1 1 HAGHL HGNC HGNC:14177 protein_coding YES CCDS32354.1 ENSP00000374353 Q6PII5 UPI00000498AB NM_001290137.1,NM_001290139.1,NM_032304.3 deleterious(0) 1/8 HAMAP:MF_01374,hmmpanther:PTHR11935:SF77,hmmpanther:PTHR11935,TIGRFAM_domain:TIGR03413,Gene3D:3.60.15.10,SMART_domains:SM00849,Superfamily_domains:SSF56281 MODERATE 1 SNV 1 1 PASS rs777098321 . 0 206 0 3 0 0 0 0 -20 0.9999958 1 1 1 0 A 3 1 81 727591 727591 G A 1 0 0 0 0 1 0 0 0 6832 1145 40 1 1 HAGHL 16 727591 Missense_Mutation SNP G C3N-01489_T 727591 89610754 521 25451 C1QTNF8 0 . GRCh38 16 1093958 1093958 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.302A>T p.Gln101Leu p.Q101L ENST00000328449 4/5 80 68 12 128 128 0 strelka-varscan-mutect C1QTNF8,missense_variant,p.Gln101Leu,ENST00000328449,NM_207419.3;C1QTNF8,intron_variant,,ENST00000621771,; A ENST00000328449 Transcript missense_variant 576/1627 302/759 101/252 Q/L cAg/cTg 1 -1 C1QTNF8 HGNC HGNC:31374 protein_coding YES CCDS32358.1 ENSP00000330426 P60827 UPI0000049307 NM_207419.3 tolerated(0.05) 4/5 Low_complexity_(Seg):seg,Pfam_domain:PF01391 MODERATE 1 SNV 5 1 PASS rs1294796320 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 1093958 1093958 T A 1 0 0 0 0 1 0 0 0 1947 1580 55 4 4 C1QTNF8 16 1093958 Missense_Mutation SNP T C3N-01489_T 366367 1093958 89244387 522 25452 NOXO1 0 . GRCh38 16 1979513 1979513 + Missense_Mutation SNP C C T C3N-01489_T C3N-01489_N C C c.745G>A p.Glu249Lys p.E249K ENST00000397280 7/8 105 94 11 196 196 0 strelka-varscan-mutect NOXO1,missense_variant,p.Glu243Lys,ENST00000354249,NM_144603.3;NOXO1,missense_variant,p.Glu244Lys,ENST00000356120,NM_172167.2;NOXO1,missense_variant,p.Glu249Lys,ENST00000397280,NM_172168.2;NOXO1,missense_variant,p.Glu248Lys,ENST00000566005,NM_001267721.1;TBL3,3_prime_UTR_variant,,ENST00000568546,NM_006453.2;TBL3,downstream_gene_variant,,ENST00000615855,;GFER,upstream_gene_variant,,ENST00000248114,NM_005262.2;TBL3,downstream_gene_variant,,ENST00000332704,;NOXO1,downstream_gene_variant,,ENST00000567471,;GFER,upstream_gene_variant,,ENST00000569451,;GFER,upstream_gene_variant,,ENST00000561710,;NOXO1,non_coding_transcript_exon_variant,,ENST00000569739,;TBL3,downstream_gene_variant,,ENST00000569628,;GFER,upstream_gene_variant,,ENST00000565658,;NOXO1,downstream_gene_variant,,ENST00000563181,;TBL3,downstream_gene_variant,,ENST00000567615,;TBL3,downstream_gene_variant,,ENST00000564171,;TBL3,downstream_gene_variant,,ENST00000569792,;TBL3,downstream_gene_variant,,ENST00000561907,; T ENST00000397280 Transcript missense_variant 749/1147 745/1131 249/376 E/K Gag/Aag COSM4845869 1 -1 NOXO1 HGNC HGNC:19404 protein_coding YES CCDS42101.1 ENSP00000380450 Q8NFA2 UPI000006E194 NM_172168.2 tolerated(0.1) 7/8 PROSITE_profiles:PS50002,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF10,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 1 MODERATE 1 SNV 1 1 1 PASS rs1264960922 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 1979513 1979513 C T 1 0 0 0 0 1 0 0 0 10607 893 31 1 1 NOXO1 16 1979513 Missense_Mutation SNP C C3N-01489_T 885555 1979513 88358832 523 25453 ZNF200 0 . GRCh38 16 3232532 3232532 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.355G>C p.Glu119Gln p.E119Q ENST00000431561 4/5 126 119 7 215 215 0 strelka-varscan-mutect ZNF200,missense_variant,p.Glu119Gln,ENST00000431561,NM_003454.3;ZNF200,missense_variant,p.Glu119Gln,ENST00000414144,NM_198088.2;ZNF200,missense_variant,p.Glu119Gln,ENST00000396871,NM_001145446.1,NM_001145448.1;ZNF200,missense_variant,p.Glu118Gln,ENST00000396868,NM_198087.2;ZNF200,missense_variant,p.Glu119Gln,ENST00000396870,NM_001145447.1;ZNF200,missense_variant,p.Glu119Gln,ENST00000575948,;ZNF200,downstream_gene_variant,,ENST00000575617,;ZNF200,non_coding_transcript_exon_variant,,ENST00000575630,;ZNF200,upstream_gene_variant,,ENST00000575285,;ZNF200,downstream_gene_variant,,ENST00000577015,; G ENST00000431561 Transcript missense_variant 968/3348 355/1188 119/395 E/Q Gag/Cag 1 -1 ZNF200 HGNC HGNC:12993 protein_coding YES CCDS10497.1 ENSP00000395723 P98182 UPI00001D89D6 NM_003454.3 deleterious(0.02) 4/5 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF156 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 3232532 3232532 C G 1 0 0 0 0 1 0 0 0 18339 835 29 4 4 ZNF200 16 3232532 Missense_Mutation SNP C C3N-01489_T 1253019 3232532 87105813 524 25454 SLX4 0 . GRCh38 16 3602264 3602264 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.804G>T p.= p.V268V ENST00000294008 4/15 192 169 23 295 295 0 strelka-varscan-mutect SLX4,synonymous_variant,p.=,ENST00000294008,NM_032444.2;SLX4,non_coding_transcript_exon_variant,,ENST00000466154,;SLX4,non_coding_transcript_exon_variant,,ENST00000486524,; A ENST00000294008 Transcript synonymous_variant 1445/7307 804/5505 268/1834 V gtG/gtT 1 -1 SLX4 HGNC HGNC:23845 protein_coding YES CCDS10506.2 ENSP00000294008 Q8IY92 UPI000050D2C5 NM_032444.2 4/15 hmmpanther:PTHR21541,hmmpanther:PTHR21541:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 3602264 3602264 C A 1 0 0 0 0 0 0 0 1 15048 581 21 2 2 SLX4 16 3602264 Silent SNP C C3N-01489_T 369732 3602264 86736081 525 25455 SHISA9 0 . GRCh38 16 12902219 12902219 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.155G>T p.Gly52Val p.G52V ENST00000558583 1/5 134 114 20 243 243 0 strelka-varscan-mutect SHISA9,missense_variant,p.Gly52Val,ENST00000558583,NM_001145204.2;SHISA9,missense_variant,p.Gly52Val,ENST00000423335,NM_001145205.1;SHISA9,upstream_gene_variant,,ENST00000482916,; T ENST00000558583 Transcript missense_variant 600/6724 155/1275 52/424 G/V gGa/gTa 1 1 SHISA9 HGNC HGNC:37231 protein_coding YES CCDS45417.2 ENSP00000454014 B4DS77 UPI0001CE6F1C NM_001145204.2 tolerated(0.2) 1/5 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 12902219 12902219 G T 1 0 0 0 0 1 0 0 0 14546 1174 41 2 2 SHISA9 16 12902219 Missense_Mutation SNP G C3N-01489_T 9299955 12902219 77436126 526 25456 MKL2 0 . GRCh38 16 14246818 14246818 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.1558A>G p.Thr520Ala p.T520A ENST00000571589 12/17 274 235 39 497 497 0 strelka-varscan-mutect MKL2,missense_variant,p.Thr520Ala,ENST00000571589,NM_001308142.1;MKL2,missense_variant,p.Thr520Ala,ENST00000318282,;MKL2,missense_variant,p.Thr520Ala,ENST00000574045,NM_014048.3;MKL2,upstream_gene_variant,,ENST00000572588,; G ENST00000571589 Transcript missense_variant 1730/8799 1558/3300 520/1099 T/A Aca/Gca 1 1 MKL2 HGNC HGNC:29819 protein_coding YES CCDS76823.1 ENSP00000459626 Q9ULH7 UPI00001FEE5A NM_001308142.1 tolerated(0.25) 12/17 hmmpanther:PTHR22793:SF5,hmmpanther:PTHR22793 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 14246818 14246818 A G 1 0 0 0 0 1 0 0 0 9569 159 6 5 5 MKL2 16 14246818 Missense_Mutation SNP A C3N-01489_T 1344599 14246818 76091527 527 25457 NOMO2 0 . GRCh38 16 18520821 18520821 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2217G>T p.Gln739His p.Q739H ENST00000621364 19/32 685 625 60 1130 1130 0 varscan-mutect NOMO2,missense_variant,p.Gln739His,ENST00000330537,;NOMO2,missense_variant,p.Gln739His,ENST00000622306,NM_173614.2;NOMO2,missense_variant,p.Gln739His,ENST00000621364,NM_001004060.1;NOMO2,missense_variant,p.Gln739His,ENST00000381474,;NOMO2,missense_variant,p.Gln572His,ENST00000543392,;NOMO2,3_prime_UTR_variant,,ENST00000564991,;NOMO2,3_prime_UTR_variant,,ENST00000567831,;NOMO2,downstream_gene_variant,,ENST00000569051,; A ENST00000621364 Transcript missense_variant 2289/3921 2217/3804 739/1267 Q/H caG/caT 1 -1 NOMO2 HGNC HGNC:22652 protein_coding YES CCDS32394.1 ENSP00000477502 Q5JPE7 UPI00001AFC79 NM_001004060.1 deleterious(0.01) 19/32 hmmpanther:PTHR23303 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 18520821 18520821 C A 1 0 0 0 0 1 0 0 0 10576 680 24 2 2 NOMO2 16 18520821 Missense_Mutation SNP C C3N-01489_T 4274003 18520821 71817524 528 25458 DNAH3 0 . GRCh38 16 21051795 21051795 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.4113G>A p.= p.L1371L ENST00000261383 29/62 407 357 50 576 576 0 strelka-varscan-mutect DNAH3,synonymous_variant,p.=,ENST00000261383,NM_017539.2;DNAH3,non_coding_transcript_exon_variant,,ENST00000572640,; T ENST00000261383 Transcript synonymous_variant 4113/12394 4113/12351 1371/4116 L ctG/ctA 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 29/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 21051795 21051795 C T 1 0 0 0 0 0 0 0 1 4418 697 25 3 3 DNAH3 16 21051795 Silent SNP C C3N-01489_T 2530974 21051795 69286550 529 25459 IL21R 0 . GRCh38 16 27449181 27449181 + Nonsense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1515T>A p.Cys505Ter p.C505* ENST00000337929 9/9 184 170 14 281 281 0 strelka-varscan-mutect IL21R,stop_gained,p.Cys505Ter,ENST00000337929,NM_181078.2;IL21R,stop_gained,p.Cys505Ter,ENST00000564089,NM_181079.4;IL21R,stop_gained,p.Cys505Ter,ENST00000395754,NM_021798.3;IL21R-AS1,non_coding_transcript_exon_variant,,ENST00000563191,;IL21R,downstream_gene_variant,,ENST00000564583,;IL21R,downstream_gene_variant,,ENST00000561953,; A ENST00000337929 Transcript stop_gained 1988/4849 1515/1617 505/538 C/* tgT/tgA 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 9/9 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 27449181 27449181 T A 1 0 0 0 0 0 1 0 0 7574 1702 59 4 4 IL21R 16 27449181 Nonsense_Mutation SNP T C3N-01489_T 6397386 27449181 62889164 530 25460 KIAA0556 0 . GRCh38 16 27740723 27740723 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.2426G>T p.Arg809Leu p.R809L ENST00000261588 15/28 205 171 34 362 362 0 strelka-varscan-mutect KIAA0556,missense_variant,p.Arg809Leu,ENST00000261588,NM_015202.2;KIAA0556,intron_variant,,ENST00000573850,; T ENST00000261588 Transcript missense_variant 2445/6616 2426/4857 809/1618 R/L cGg/cTg COSM3741868,COSM3741869 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 tolerated(0.07) 15/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1286736049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 27740723 27740723 G T 1 0 0 0 0 1 0 0 0 8088 1116 39 1 1 KIAA0556 16 27740723 Missense_Mutation SNP G C3N-01489_T 291542 27740723 62597622 531 25461 QPRT 0 . GRCh38 16 29695010 29695010 + Silent SNP T T G novel C3N-01489_T C3N-01489_N T T c.360T>G p.= p.A120A ENST00000395384 2/4 158 125 33 236 235 1 strelka-varscan-mutect QPRT,synonymous_variant,p.=,ENST00000395384,NM_014298.3;AC009133.22,synonymous_variant,p.=,ENST00000449759,;QPRT,intron_variant,,ENST00000562473,;QPRT,intron_variant,,ENST00000219771,;QPRT,upstream_gene_variant,,ENST00000564967,; G ENST00000395384 Transcript synonymous_variant 521/2343 360/894 120/297 A gcT/gcG 1 1 QPRT HGNC HGNC:9755 protein_coding YES CCDS10651.1 ENSP00000378782 Q15274 UPI000013C78C NM_014298.3 2/4 Low_complexity_(Seg):seg,hmmpanther:PTHR32179,PIRSF_domain:PIRSF006250,TIGRFAM_domain:TIGR00078,Pfam_domain:PF01729,Gene3D:3.90.1170.20,Superfamily_domains:SSF51690 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 29695010 29695010 T G 1 0 0 0 0 0 0 0 1 13031 1567 55 5 5 QPRT 16 29695010 Silent SNP T C3N-01489_T 1954287 29695010 60643335 532 25462 SALL1 0 . GRCh38 16 51141590 51141590 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.632C>T p.Ser211Phe p.S211F ENST00000251020 2/3 192 171 21 337 337 0 strelka-varscan-mutect SALL1,missense_variant,p.Ser114Phe,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Ser211Phe,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Ser114Phe,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; A ENST00000251020 Transcript missense_variant 666/5146 632/3975 211/1324 S/F tCc/tTc 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 deleterious(0) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS rs1174750691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 51141590 51141590 G A 1 0 0 0 0 1 0 0 0 14069 1174 41 3 3 SALL1 16 51141590 Missense_Mutation SNP G C3N-01489_T 21446580 51141590 39196755 533 25463 GOT2 0 . GRCh38 16 58716033 58716033 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.1000C>G p.Pro334Ala p.P334A ENST00000245206 8/10 93 78 15 183 183 0 strelka-varscan-mutect GOT2,missense_variant,p.Pro334Ala,ENST00000245206,NM_002080.3;GOT2,missense_variant,p.Pro291Ala,ENST00000434819,NM_001286220.1;GOT2,non_coding_transcript_exon_variant,,ENST00000564400,;GOT2,non_coding_transcript_exon_variant,,ENST00000494627,;GOT2,downstream_gene_variant,,ENST00000496461,;GOT2,downstream_gene_variant,,ENST00000568368,; C ENST00000245206 Transcript missense_variant 1129/2462 1000/1293 334/430 P/A Cca/Gca 1 -1 GOT2 HGNC HGNC:4433 protein_coding YES CCDS10801.1 ENSP00000245206 P00505 UPI000013CB99 NM_002080.3 tolerated(0.13) 8/10 hmmpanther:PTHR11879,Pfam_domain:PF00155,Gene3D:3.40.640.10,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 58716033 58716033 G C 1 0 0 0 0 1 0 0 0 6475 1232 43 4 4 GOT2 16 58716033 Missense_Mutation SNP G C3N-01489_T 7574443 58716033 31622312 534 25464 CARMIL2 0 . GRCh38 16 67656834 67656834 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.4070G>A p.Gly1357Glu p.G1357E ENST00000334583 36/38 79 63 16 119 119 0 strelka-varscan-mutect CARMIL2,missense_variant,p.Gly1357Glu,ENST00000334583,NM_001013838.1;CARMIL2,intron_variant,,ENST00000545661,NM_001317026.1;ACD,downstream_gene_variant,,ENST00000620338,NM_001082486.1;ACD,downstream_gene_variant,,ENST00000219251,NM_001082487.1,NM_022914.2;ACD,downstream_gene_variant,,ENST00000393919,;ACD,downstream_gene_variant,,ENST00000620761,;ACD,downstream_gene_variant,,ENST00000602320,;PARD6A,upstream_gene_variant,,ENST00000458121,NM_001037281.1;PARD6A,upstream_gene_variant,,ENST00000219255,NM_016948.2;PARD6A,upstream_gene_variant,,ENST00000602551,;ACD,downstream_gene_variant,,ENST00000602382,;CARMIL2,splice_region_variant,,ENST00000602368,;CARMIL2,downstream_gene_variant,,ENST00000602321,;ACD,downstream_gene_variant,,ENST00000602622,;ACD,downstream_gene_variant,,ENST00000602860,;PARD6A,upstream_gene_variant,,ENST00000602727,;ACD,downstream_gene_variant,,ENST00000602519,;CARMIL2,downstream_gene_variant,,ENST00000602633,;ACD,downstream_gene_variant,,ENST00000602850,;ACD,downstream_gene_variant,,ENST00000602945,;ACD,downstream_gene_variant,,ENST00000602656,;CARMIL2,upstream_gene_variant,,ENST00000602705,;ACD,downstream_gene_variant,,ENST00000602780,;ACD,downstream_gene_variant,,ENST00000602821,;CARMIL2,downstream_gene_variant,,ENST00000602931,;CARMIL2,downstream_gene_variant,,ENST00000602924,;ACD,downstream_gene_variant,,ENST00000602423,; A ENST00000334583 Transcript missense_variant 4398/4687 4070/4308 1357/1435 G/E gGg/gAg 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 deleterious(0.02) 36/38 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 67656834 67656834 G A 1 0 0 0 0 1 0 0 0 2352 1232 43 3 3 CARMIL2 16 67656834 Missense_Mutation SNP G C3N-01489_T 8940801 67656834 22681511 535 25465 GAN 0 . GRCh38 16 81363909 81363909 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.1202G>C p.Trp401Ser p.W401S ENST00000568107 7/11 333 293 40 594 594 0 strelka-varscan-mutect GAN,missense_variant,p.Trp401Ser,ENST00000568107,NM_022041.3;GAN,upstream_gene_variant,,ENST00000567335,; C ENST00000568107 Transcript missense_variant 1364/15244 1202/1794 401/597 W/S tGg/tCg 1 1 GAN HGNC HGNC:4137 protein_coding YES CCDS10935.1 ENSP00000476795 Q9H2C0 A0A0S2Z4W2 UPI000000DAB6 NM_022041.3 deleterious(0) 7/11 Superfamily_domains:0052715,Gene3D:1zgkA00,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF232,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 81363909 81363909 G C 1 0 0 0 0 1 0 0 0 6100 1357 47 4 4 GAN 16 81363909 Missense_Mutation SNP G C3N-01489_T 13707075 81363909 8974436 536 25466 ADAD2 0 . GRCh38 16 84191491 84191491 + Frame_Shift_Del DEL G G - novel C3N-01489_T C3N-01489_N G G c.265delG p.Glu89AsnfsTer65 p.E89Nfs*65 ENST00000268624 1/11 85 74 11 141 141 0 sindel-varindel-pindel ADAD2,frameshift_variant,p.Glu89AsnfsTer65,ENST00000268624,NM_139174.3;ADAD2,frameshift_variant,p.Glu89AsnfsTer59,ENST00000315906,NM_001145400.1;ADAD2,frameshift_variant,p.Glu14AsnfsTer59,ENST00000567685,;TAF1C,upstream_gene_variant,,ENST00000567759,NM_005679.3,NM_001243159.1;TAF1C,upstream_gene_variant,,ENST00000341690,NM_139353.2;TAF1C,upstream_gene_variant,,ENST00000541676,NM_001243157.1;TAF1C,upstream_gene_variant,,ENST00000566732,NM_001243156.1;TAF1C,upstream_gene_variant,,ENST00000570117,NM_001243158.1;TAF1C,upstream_gene_variant,,ENST00000564345,;TAF1C,upstream_gene_variant,,ENST00000561955,;TAF1C,upstream_gene_variant,,ENST00000564454,;RP11-486L19.2,downstream_gene_variant,,ENST00000536986,;RP11-486L19.2,downstream_gene_variant,,ENST00000565643,;RP11-486L19.2,downstream_gene_variant,,ENST00000569834,;RP11-486L19.2,downstream_gene_variant,,ENST00000561900,;ADAD2,non_coding_transcript_exon_variant,,ENST00000567413,;TAF1C,upstream_gene_variant,,ENST00000565544,;TAF1C,upstream_gene_variant,,ENST00000564774,;TAF1C,upstream_gene_variant,,ENST00000564208,;TAF1C,upstream_gene_variant,,ENST00000544090,;TAF1C,upstream_gene_variant,,ENST00000566903,;ADAD2,upstream_gene_variant,,ENST00000564430,;ADAD2,upstream_gene_variant,,ENST00000566526,;TAF1C,upstream_gene_variant,,ENST00000563428,;TAF1C,upstream_gene_variant,,ENST00000537450,;TAF1C,upstream_gene_variant,,ENST00000565279,;ADAD2,upstream_gene_variant,,ENST00000564169,;TAF1C,upstream_gene_variant,,ENST00000569505,;TAF1C,upstream_gene_variant,,ENST00000569609,;ADAD2,upstream_gene_variant,,ENST00000569221,; - ENST00000268624 Transcript frameshift_variant 354/2283 261/1998 87/665 L/X ttG/tt 1 1 ADAD2 HGNC HGNC:30714 protein_coding YES CCDS10944.1 ENSP00000268624 Q8NCV1 UPI000013D7CA NM_139174.3 1/11 HIGH 1 deletion 2 4 1 PASS . . 0 207 2 0 0 0 0 0 -19.99994 1 1 1 1 0 - 7 5 81 84191491 84191491 G - 1 0 1 0 1 0 0 0 0 276 1339 47 0 0 ADAD2 16 84191491 Frame_Shift_Del DEL G C3N-01489_T 2827582 84191491 6146854 537 25467 FOXC2 0 . GRCh38 16 86568752 86568752 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1417G>T p.Gly473Cys p.G473C ENST00000320354 1/1 422 359 63 562 562 0 strelka-varscan-mutect FOXC2,missense_variant,p.Gly473Cys,ENST00000320354,NM_005251.2;FOXC2-AS1,upstream_gene_variant,,ENST00000563280,; T ENST00000320354 Transcript missense_variant 1502/2478 1417/1506 473/501 G/C Ggc/Tgc 1 1 FOXC2 HGNC HGNC:3801 protein_coding YES CCDS10958.1 ENSP00000326371 Q99958 UPI000012ADC6 NM_005251.2 deleterious(0) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF189 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 86568752 86568752 G T 1 0 0 0 0 1 0 0 0 5855 1348 47 2 2 FOXC2 16 86568752 Missense_Mutation SNP G C3N-01489_T 2377261 86568752 3769593 538 25468 ZNF469 0 . GRCh38 16 88434998 88434998 + Silent SNP T T C novel C3N-01489_T C3N-01489_N T T c.7444T>C p.= p.L2482L ENST00000437464 2/2 254 214 40 450 450 0 strelka-varscan-mutect ZNF469,synonymous_variant,p.=,ENST00000565624,;ZNF469,synonymous_variant,p.=,ENST00000437464,NM_001127464.2; C ENST00000437464 Transcript synonymous_variant 7444/13203 7444/11778 2482/3925 L Ttg/Ctg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 88434998 88434998 T C 1 0 0 0 0 0 0 0 1 18500 1606 56 5 5 ZNF469 16 88434998 Silent SNP T C3N-01489_T 1866246 88434998 1903347 539 25469 ZZEF1 0 . GRCh38 17 4072649 4072649 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.3793G>T p.Glu1265Ter p.E1265* ENST00000381638 25/55 108 81 27 192 192 0 strelka-varscan-mutect ZZEF1,stop_gained,p.Glu1265Ter,ENST00000381638,NM_015113.3;ZZEF1,downstream_gene_variant,,ENST00000574474,;ZZEF1,stop_gained,p.Glu132Ter,ENST00000572699,;ZZEF1,non_coding_transcript_exon_variant,,ENST00000570365,;ZZEF1,upstream_gene_variant,,ENST00000572426,; A ENST00000381638 Transcript stop_gained 3918/11456 3793/8886 1265/2961 E/* Gaa/Taa 1 -1 ZZEF1 HGNC HGNC:29027 protein_coding YES CCDS11043.1 ENSP00000371051 O43149 UPI00004569F7 NM_015113.3 25/55 hmmpanther:PTHR22772:SF4,hmmpanther:PTHR22772 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 4072649 4072649 C A 1 0 0 0 0 0 1 0 0 18859 922 32 2 2 ZZEF1 17 4072649 Nonsense_Mutation SNP C C3N-01489_T 4072649 79184792 540 25470 SLC16A11 0 . GRCh38 17 7042405 7042405 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.777C>T p.= p.F259F ENST00000308009 3/4 152 124 28 216 216 0 strelka-varscan-mutect SLC16A11,synonymous_variant,p.=,ENST00000308009,NM_153357.1;SLC16A11,synonymous_variant,p.=,ENST00000447225,;SLC16A13,downstream_gene_variant,,ENST00000308027,NM_201566.2;SLC16A11,downstream_gene_variant,,ENST00000574600,;SLC16A11,intron_variant,,ENST00000573338,; A ENST00000308009 Transcript synonymous_variant 1115/1803 777/1416 259/471 F ttC/ttT 1 -1 SLC16A11 HGNC HGNC:23093 protein_coding YES CCDS11086.1 ENSP00000310490 Q8NCK7 UPI000006F985 NM_153357.1 3/4 PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF80,hmmpanther:PTHR11360,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 7042405 7042405 G A 1 0 0 0 0 0 0 0 1 14670 1049 37 1 1 SLC16A11 17 7042405 Silent SNP G C3N-01489_T 2969756 7042405 76215036 541 25471 ACAP1 0 . GRCh38 17 7346889 7346889 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1089C>A p.Phe363Leu p.F363L ENST00000158762 13/22 79 72 7 101 101 0 strelka-varscan-mutect ACAP1,missense_variant,p.Phe363Leu,ENST00000158762,NM_014716.3;ACAP1,downstream_gene_variant,,ENST00000570457,;ACAP1,downstream_gene_variant,,ENST00000575425,;ACAP1,upstream_gene_variant,,ENST00000574499,;ACAP1,upstream_gene_variant,,ENST00000571471,;ACAP1,upstream_gene_variant,,ENST00000575415,;ACAP1,upstream_gene_variant,,ENST00000570504,;KCTD11,upstream_gene_variant,,ENST00000576980,;ACAP1,downstream_gene_variant,,ENST00000573893,;ACAP1,non_coding_transcript_exon_variant,,ENST00000570439,;ACAP1,downstream_gene_variant,,ENST00000571220,;ACAP1,downstream_gene_variant,,ENST00000576628,;ACAP1,upstream_gene_variant,,ENST00000576594,; A ENST00000158762 Transcript missense_variant 1295/2512 1089/2223 363/740 F/L ttC/ttA 1 1 ACAP1 HGNC HGNC:16467 protein_coding YES CCDS11101.1 ENSP00000158762 Q15027 UPI000012749A NM_014716.3 tolerated(0.06) 13/22 hmmpanther:PTHR23180:SF197,hmmpanther:PTHR23180,Gene3D:2.30.29.30 MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -11.8254 0.9999942 1 1 1 0 A 3 1 81 7346889 7346889 C A 1 0 0 0 0 1 0 0 0 161 825 29 2 2 ACAP1 17 7346889 Missense_Mutation SNP C C3N-01489_T 304484 7346889 75910552 542 25472 MYH2 0 . GRCh38 17 10544100 10544100 + Missense_Mutation SNP G G T rs756953958 C3N-01489_T C3N-01489_N G G c.533C>A p.Thr178Asn p.T178N ENST00000245503 6/40 331 281 50 558 557 1 strelka-varscan-mutect MYH2,missense_variant,p.Thr178Asn,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.Thr178Asn,ENST00000397183,NM_001100112.1;MYH2,missense_variant,p.Thr178Asn,ENST00000532183,;MYH2,missense_variant,p.Thr178Asn,ENST00000622564,;MYH2,missense_variant,p.Thr178Asn,ENST00000420805,;MYH2,missense_variant,p.Thr99Asn,ENST00000578017,;MYHAS,intron_variant,,ENST00000587182,; T ENST00000245503 Transcript missense_variant,splice_region_variant 918/6339 533/5826 178/1941 T/N aCt/aAt rs756953958,COSM4141978 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 deleterious(0) 6/40 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,SMART_domains:SM00242,Superfamily_domains:SSF52540 pathogenic 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs756953958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 10544100 10544100 G T 1 0 0 0 0 1 0 0 0 10035 1159 40 1 1 MYH2 17 10544100 Missense_Mutation SNP G C3N-01489_T 3197211 10544100 72713341 543 25473 UBB 0 . GRCh38 17 16382584 16382584 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.677G>T p.Arg226Met p.R226M ENST00000302182 2/2 166 143 23 227 227 0 strelka-varscan-mutect UBB,missense_variant,p.Arg226Met,ENST00000302182,NM_001281716.1,NM_018955.3,NM_001281720.1;UBB,missense_variant,p.Arg226Met,ENST00000614404,NM_001281717.1;UBB,missense_variant,p.Arg226Met,ENST00000395837,NM_001281718.1;UBB,missense_variant,p.Arg226Met,ENST00000395839,NM_001281719.1;UBB,missense_variant,p.Arg150Met,ENST00000535788,;UBB,downstream_gene_variant,,ENST00000577640,;UBB,downstream_gene_variant,,ENST00000578706,;UBB,downstream_gene_variant,,ENST00000577958,;RP11-138I1.4,non_coding_transcript_exon_variant,,ENST00000583934,;UBB,non_coding_transcript_exon_variant,,ENST00000578649,; T ENST00000302182 Transcript missense_variant 1069/1225 677/690 226/229 R/M aGg/aTg COSM2739149 1 1 UBB HGNC HGNC:12463 protein_coding YES CCDS11177.1 ENSP00000304697 P0CG47 Q5U5U6 UPI0000002146 NM_001281716.1,NM_018955.3,NM_001281720.1 tolerated(0.13) 2/2 PROSITE_profiles:PS50053,hmmpanther:PTHR10666,Pfam_domain:PF00240,Gene3D:3.10.20.90,Superfamily_domains:SSF54236 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 16382584 16382584 G T 1 0 0 0 0 1 0 0 0 17363 1000 35 2 2 UBB 17 16382584 Missense_Mutation SNP G C3N-01489_T 5838484 16382584 66874857 544 25474 CCDC144A 0 . GRCh38 17 16705282 16705282 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.547C>A p.Gln183Lys p.Q183K ENST00000360524 3/18 62 56 6 136 136 0 varscan-mutect CCDC144A,missense_variant,p.Gln183Lys,ENST00000399273,;CCDC144A,missense_variant,p.Gln183Lys,ENST00000360524,NM_014695.2;CCDC144A,missense_variant,p.Gln183Lys,ENST00000456009,;CCDC144A,missense_variant,p.Gln183Lys,ENST00000340621,;CCDC144A,missense_variant,p.Gln80Lys,ENST00000420937,;RN7SL620P,upstream_gene_variant,,ENST00000610816,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000436374,;CCDC144A,upstream_gene_variant,,ENST00000428950,;RP11-219A15.1,missense_variant,p.Gln183Lys,ENST00000448331,;CCDC144A,missense_variant,p.Gln183Lys,ENST00000360495,;CCDC144A,non_coding_transcript_exon_variant,,ENST00000399264,;CCDC144A,upstream_gene_variant,,ENST00000328495,; A ENST00000360524 Transcript missense_variant 623/5830 547/4284 183/1427 Q/K Cag/Aag 1 1 CCDC144A HGNC HGNC:29072 protein_coding YES CCDS45621.1 ENSP00000353717 A2RUR9 UPI0000F095D0 NM_014695.2 tolerated_low_confidence(0.1) 3/18 hmmpanther:PTHR22245,hmmpanther:PTHR22245:SF0 MODERATE 1 SNV 1 1 PASS rs1039413018 . 0 208 2 0 0 0 0 0 -14.29953 1 1 1 1 0 A 3 1 81 16705282 16705282 C A 1 0 0 0 0 1 0 0 0 2465 479 17 2 2 CCDC144A 17 16705282 Missense_Mutation SNP C C3N-01489_T 322698 16705282 66552159 545 25475 SLC13A2 0 . GRCh38 17 28495775 28495775 + Missense_Mutation SNP G G C rs11568476 C3N-01489_T C3N-01489_N G G c.1576G>C p.Val526Leu p.V526L ENST00000444914 10/12 158 135 23 198 198 0 strelka-varscan-mutect SLC13A2,missense_variant,p.Val526Leu,ENST00000444914,NM_001145975.1;SLC13A2,missense_variant,p.Val477Leu,ENST00000314669,NM_003984.3;SLC13A2,downstream_gene_variant,,ENST00000545060,;SLC13A2,3_prime_UTR_variant,,ENST00000459818,;SLC13A2,3_prime_UTR_variant,,ENST00000579281,;SLC13A2,3_prime_UTR_variant,,ENST00000577903,;RP11-192H23.4,intron_variant,,ENST00000481916,;SLC13A2,downstream_gene_variant,,ENST00000541739,; C ENST00000444914 Transcript missense_variant 1996/2855 1576/1926 526/641 V/L Gtg/Ctg rs11568476,CM109406,COSM1141097,COSM560128 1 1 SLC13A2 HGNC HGNC:10917 protein_coding YES CCDS54098.1 ENSP00000392411 Q13183 UPI0001986446 NM_001145975.1 deleterious(0.04) 10/12 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF66 0,0,1,1 20610529 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs11568476 . 0 205 0 3 0 0 0 2 -3.358924 0 0 1 0 0 C 3 2 81 28495775 28495775 G C 1 0 0 0 0 1 0 0 0 14657 1145 40 4 4 SLC13A2 17 28495775 Missense_Mutation SNP G C3N-01489_T 11790493 28495775 54761666 546 25476 ERAL1 0 . GRCh38 17 28858182 28858182 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.573G>T p.Trp191Cys p.W191C ENST00000254928 5/10 296 261 35 433 433 0 strelka-varscan-mutect ERAL1,missense_variant,p.Trp191Cys,ENST00000254928,NM_001317985.1,NM_005702.2;ERAL1,missense_variant,p.Trp188Cys,ENST00000580917,;FAM222B,upstream_gene_variant,,ENST00000577513,;ERAL1,upstream_gene_variant,,ENST00000583487,;FAM222B,upstream_gene_variant,,ENST00000583953,;MIR4732,downstream_gene_variant,,ENST00000582320,;MIR4732,downstream_gene_variant,,ENST00000384886,;MIR4732,downstream_gene_variant,,ENST00000581873,;MIR4732,downstream_gene_variant,,ENST00000385059,;MIR451B,upstream_gene_variant,,ENST00000636285,;ERAL1,non_coding_transcript_exon_variant,,ENST00000578001,;ERAL1,missense_variant,p.Trp191Cys,ENST00000461894,;ERAL1,3_prime_UTR_variant,,ENST00000412138,;ERAL1,non_coding_transcript_exon_variant,,ENST00000471992,;ERAL1,non_coding_transcript_exon_variant,,ENST00000577942,; T ENST00000254928 Transcript missense_variant 670/1925 573/1314 191/437 W/C tgG/tgT 1 1 ERAL1 HGNC HGNC:3424 protein_coding YES CCDS11244.1 ENSP00000254928 O75616 UPI000006DECC NM_001317985.1,NM_005702.2 deleterious(0.01) 5/10 PROSITE_profiles:PS51713,HAMAP:MF_00367,hmmpanther:PTHR11649:SF3,hmmpanther:PTHR11649,TIGRFAM_domain:TIGR00231,Gene3D:3.40.50.300,Pfam_domain:PF01926,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 28858182 28858182 G T 1 0 0 0 0 1 0 0 0 5051 1183 41 2 2 ERAL1 17 28858182 Missense_Mutation SNP G C3N-01489_T 362407 28858182 54399259 547 25477 PHF12 0 . GRCh38 17 28913257 28913257 + Silent SNP C C A rs764914317 C3N-01489_T C3N-01489_N C C c.1314G>T p.= p.A438A ENST00000332830 9/15 72 63 9 94 94 0 strelka-varscan-mutect PHF12,synonymous_variant,p.=,ENST00000577226,NM_001290131.1;PHF12,synonymous_variant,p.=,ENST00000332830,NM_001033561.1;PHF12,synonymous_variant,p.=,ENST00000268756,NM_020889.2;PHF12,upstream_gene_variant,,ENST00000579036,;PHF12,non_coding_transcript_exon_variant,,ENST00000582655,;PHF12,upstream_gene_variant,,ENST00000579563,;PHF12,synonymous_variant,p.=,ENST00000378879,;PHF12,3_prime_UTR_variant,,ENST00000583524,;PHF12,3_prime_UTR_variant,,ENST00000584822,;PHF12,non_coding_transcript_exon_variant,,ENST00000582436,;PHF12,intron_variant,,ENST00000589176,; A ENST00000332830 Transcript synonymous_variant 2125/4759 1314/3015 438/1004 A gcG/gcT rs764914317,COSM977055 1 -1 PHF12 HGNC HGNC:20816 protein_coding YES CCDS32598.1 ENSP00000329933 Q96QT6 UPI0000197E05 NM_001033561.1 9/15 hmmpanther:PTHR24102,hmmpanther:PTHR24102:SF17 0,1 LOW 1 SNV 2 0,1 1 PASS rs764914317 . 0 201 9 0 0 0 0 0 -19.45413 0.9999908 1 1 1 0 A 2 1 81 28913257 28913257 C A 1 0 0 0 0 0 0 0 1 11912 755 27 1 1 PHF12 17 28913257 Silent SNP C C3N-01489_T 55075 28913257 54344184 548 25478 SLC6A4 0 . GRCh38 17 30209188 30209188 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1504C>A p.Leu502Ile p.L502I ENST00000261707 12/15 181 167 14 242 242 0 strelka-varscan-mutect SLC6A4,missense_variant,p.Leu502Ile,ENST00000261707,NM_001045.5;SLC6A4,missense_variant,p.Leu502Ile,ENST00000401766,;SLC6A4,missense_variant,p.Leu502Ile,ENST00000394821,;RP11-354P11.4,downstream_gene_variant,,ENST00000581633,;SLC6A4,intron_variant,,ENST00000579221,; T ENST00000261707 Transcript missense_variant 2080/6604 1504/1893 502/630 L/I Ctc/Atc 1 -1 SLC6A4 HGNC HGNC:11050 protein_coding YES CCDS11256.1 ENSP00000261707 P31645 UPI0000135493 NM_001045.5 tolerated(0.11) 12/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF105,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 30209188 30209188 G T 1 0 0 0 0 1 0 0 0 14969 971 34 2 2 SLC6A4 17 30209188 Missense_Mutation SNP G C3N-01489_T 1295931 30209188 53048253 549 25479 CPD 0 . GRCh38 17 30379572 30379572 + Frame_Shift_Del DEL G G - novel C3N-01489_T C3N-01489_N G G c.593delG p.Gly198AlafsTer65 p.G198Afs*65 ENST00000225719 1/21 79 71 8 117 117 0 sindel-varindel-pindel CPD,frameshift_variant,p.Gly198AlafsTer65,ENST00000225719,NM_001304.4;CPD,upstream_gene_variant,,ENST00000543464,NM_001199775.1;CPD,upstream_gene_variant,,ENST00000583275,; - ENST00000225719 Transcript frameshift_variant 668/9394 592/4143 198/1380 G/X Ggc/gc 1 1 CPD HGNC HGNC:2301 protein_coding YES CCDS11257.1 ENSP00000225719 O75976 UPI000000DAF7 NM_001304.4 1/21 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF50,Low_complexity_(Seg):seg,SMART_domains:SM00631,Superfamily_domains:SSF53187 HIGH 1 deletion 1 1 1 PASS . . 0 204 5 0 0 0 0 0 -17.28487 1 1 1 1 0 - 7 5 81 30379572 30379572 G - 1 0 1 0 1 0 0 0 0 3592 1116 39 0 0 CPD 17 30379572 Frame_Shift_Del DEL G C3N-01489_T 170384 30379572 52877869 550 25480 CPD 0 . GRCh38 17 30445728 30445728 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.2581G>A p.Glu861Lys p.E861K ENST00000225719 12/21 93 78 15 140 140 0 strelka-varscan-mutect CPD,missense_variant,p.Glu861Lys,ENST00000225719,NM_001304.4;CPD,missense_variant,p.Glu614Lys,ENST00000543464,NM_001199775.1;CPD,missense_variant,p.Glu70Lys,ENST00000584221,;CPD,non_coding_transcript_exon_variant,,ENST00000588977,;CPD,upstream_gene_variant,,ENST00000584051,;CPD,downstream_gene_variant,,ENST00000581826,;CPD,upstream_gene_variant,,ENST00000584050,; A ENST00000225719 Transcript missense_variant 2657/9394 2581/4143 861/1380 E/K Gaa/Aaa 1 1 CPD HGNC HGNC:2301 protein_coding YES CCDS11257.1 ENSP00000225719 O75976 UPI000000DAF7 NM_001304.4 tolerated(0.72) 12/21 Gene3D:2.60.40.1120,Pfam_domain:PF13620,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF50,SMART_domains:SM00631,Superfamily_domains:SSF49464 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 30445728 30445728 G A 1 0 0 0 0 1 0 0 0 3592 1291 45 3 3 CPD 17 30445728 Missense_Mutation SNP G C3N-01489_T 66156 30445728 52811713 551 25481 NF1 0 . GRCh38 17 31181426 31181426 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.591A>T p.= p.T197T ENST00000358273 6/58 191 160 31 242 242 0 strelka-varscan-mutect NF1,synonymous_variant,p.=,ENST00000358273,NM_001042492.2;NF1,synonymous_variant,p.=,ENST00000356175,NM_000267.3;NF1,synonymous_variant,p.=,ENST00000431387,NM_001128147.2;NF1,missense_variant,p.Ser123Cys,ENST00000495910,;NF1,synonymous_variant,p.=,ENST00000579081,;NF1,non_coding_transcript_exon_variant,,ENST00000487476,;NF1,non_coding_transcript_exon_variant,,ENST00000490416,; T ENST00000358273 Transcript synonymous_variant 974/12425 591/8520 197/2839 T acA/acT 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 6/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 31181426 31181426 A T 1 0 0 0 0 0 0 0 1 10393 202 7 4 4 NF1 17 31181426 Silent SNP A C3N-01489_T 735698 31181426 52076015 552 25482 NF1 0 . GRCh38 17 31349187 31349187 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.7257G>T p.= p.L2419L ENST00000358273 49/58 219 187 32 363 363 0 strelka-varscan-mutect NF1,synonymous_variant,p.=,ENST00000358273,NM_001042492.2;NF1,synonymous_variant,p.=,ENST00000356175,NM_000267.3;NF1,synonymous_variant,p.=,ENST00000456735,;NF1,synonymous_variant,p.=,ENST00000471572,;NF1,synonymous_variant,p.=,ENST00000581790,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,downstream_gene_variant,,ENST00000582892,;AK4P1,downstream_gene_variant,,ENST00000581275,; T ENST00000358273 Transcript synonymous_variant 7640/12425 7257/8520 2419/2839 L ctG/ctT 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 49/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs1373033155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 31349187 31349187 G T 1 0 0 0 0 0 0 0 1 10393 1335 47 2 2 NF1 17 31349187 Silent SNP G C3N-01489_T 167761 31349187 51908254 553 25483 ASIC2 0 . GRCh38 17 33291937 33291937 + Nonsense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.179C>A p.Ser60Ter p.S60* ENST00000225823 1/10 75 65 10 112 112 0 strelka-varscan-mutect ASIC2,stop_gained,p.Ser60Ter,ENST00000225823,NM_183377.1;ASIC2,intron_variant,,ENST00000359872,NM_001094.4;ASIC2,upstream_gene_variant,,ENST00000448983,;ASIC2,upstream_gene_variant,,ENST00000579816,; T ENST00000225823 Transcript stop_gained 1052/3443 179/1692 60/563 S/* tCg/tAg COSM4842094 1 -1 ASIC2 HGNC HGNC:99 protein_coding YES CCDS11276.1 ENSP00000225823 Q16515 UPI000013C881 NM_183377.1 1/10 hmmpanther:PTHR11690:SF128,hmmpanther:PTHR11690 1 HIGH 1 SNV 1 1 1 PASS rs1253695117 . 0 206 4 0 0 0 0 0 -19.99556 1 1 1 1 0 T 4 4 81 33291937 33291937 G T 1 0 0 0 0 0 1 0 0 1186 1059 37 1 1 ASIC2 17 33291937 Nonsense_Mutation SNP G C3N-01489_T 1942750 33291937 49965504 554 25484 C17orf96 0 . GRCh38 17 38674171 38674171 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.325G>A p.Asp109Asn p.D109N ENST00000621654 1/1 40 35 5 73 73 0 strelka-mutect C17orf96,missense_variant,p.Asp109Asn,ENST00000621654,NM_001130677.1; T ENST00000621654 Transcript missense_variant 1251/3719 325/1140 109/379 D/N Gac/Aac 1 -1 C17orf96 HGNC HGNC:34493 protein_coding YES CCDS45661.1 ENSP00000484710 A6NHQ4 UPI0000198ACE NM_001130677.1 tolerated_low_confidence(0.09) 1/1 hmmpanther:PTHR23187,hmmpanther:PTHR23187:SF1 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 38674171 38674171 C T 1 0 0 0 0 1 0 0 0 1893 855 30 3 3 C17orf96 17 38674171 Missense_Mutation SNP C C3N-01489_T 5382234 38674171 44583270 555 25485 CACNB1 0 . GRCh38 17 39175516 39175516 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1474C>T p.Arg492Trp p.R492W ENST00000394303 14/14 158 140 18 225 224 1 strelka-varscan-mutect CACNB1,missense_variant,p.Arg492Trp,ENST00000394303,NM_000723.4;CACNB1,3_prime_UTR_variant,,ENST00000622445,;CACNB1,downstream_gene_variant,,ENST00000344140,NM_199247.2;CACNB1,downstream_gene_variant,,ENST00000394310,NM_199248.2;RP5-906A24.2,intron_variant,,ENST00000579256,;CACNB1,non_coding_transcript_exon_variant,,ENST00000539338,;CACNB1,downstream_gene_variant,,ENST00000582544,; A ENST00000394303 Transcript missense_variant 1682/3742 1474/1797 492/598 R/W Cgg/Tgg 1 -1 CACNB1 HGNC HGNC:1401 protein_coding YES CCDS42311.1 ENSP00000377840 Q02641 UPI0000127290 NM_000723.4 deleterious_low_confidence(0) 14/14 hmmpanther:PTHR11824,hmmpanther:PTHR11824:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 81 39175516 39175516 G A 1 0 0 0 0 1 0 0 0 2240 1144 40 1 1 CACNB1 17 39175516 Missense_Mutation SNP G C3N-01489_T 501345 39175516 44081925 556 25486 KRT9 0 . GRCh38 17 41571647 41571647 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.346G>C p.Gly116Arg p.G116R ENST00000246662 1/8 62 53 9 97 97 0 strelka-varscan-mutect KRT9,missense_variant,p.Gly116Arg,ENST00000246662,NM_000226.3;KRT9,intron_variant,,ENST00000588431,; G ENST00000246662 Transcript missense_variant 412/2290 346/1872 116/623 G/R Ggt/Cgt 1 -1 KRT9 HGNC HGNC:6447 protein_coding YES CCDS32654.1 ENSP00000246662 P35527 UPI00001AE6F7 NM_000226.3 deleterious_low_confidence(0.04) 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR23239:SF96,hmmpanther:PTHR23239 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.95234 1 1 1 1 0 G 3 3 81 41571647 41571647 C G 1 0 0 0 0 1 0 0 0 8383 594 21 4 4 KRT9 17 41571647 Missense_Mutation SNP C C3N-01489_T 2396131 41571647 41685794 557 25487 EFTUD2 0 . GRCh38 17 44859151 44859151 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1891G>T p.Gly631Cys p.G631C ENST00000426333 19/28 266 225 41 331 331 0 strelka-varscan-mutect EFTUD2,missense_variant,p.Gly631Cys,ENST00000426333,NM_004247.3;EFTUD2,missense_variant,p.Gly631Cys,ENST00000591382,NM_001258353.1;EFTUD2,missense_variant,p.Gly621Cys,ENST00000592576,NM_001258354.1;EFTUD2,missense_variant,p.Gly596Cys,ENST00000402521,NM_001142605.1;EFTUD2,upstream_gene_variant,,ENST00000590124,;EFTUD2,downstream_gene_variant,,ENST00000585616,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000586276,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590367,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590977,;EFTUD2,upstream_gene_variant,,ENST00000589769,;EFTUD2,upstream_gene_variant,,ENST00000588340,;EFTUD2,downstream_gene_variant,,ENST00000586654,;EFTUD2,downstream_gene_variant,,ENST00000585794,;EFTUD2,downstream_gene_variant,,ENST00000587914,; A ENST00000426333 Transcript missense_variant 2189/4548 1891/2919 631/972 G/C Ggc/Tgc 1 -1 EFTUD2 HGNC HGNC:30858 protein_coding YES CCDS11489.1 ENSP00000392094 Q15029 UPI0000137931 NM_004247.3 deleterious(0.04) 19/28 hmmpanther:PTHR23115:SF5,hmmpanther:PTHR23115,Gene3D:3.30.70.870,Pfam_domain:PF14492,Superfamily_domains:SSF54980 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 44859151 44859151 C A 1 0 0 0 0 1 0 0 0 4797 623 22 2 2 EFTUD2 17 44859151 Missense_Mutation SNP C C3N-01489_T 3287504 44859151 38398290 558 25488 KIF18B 0 . GRCh38 17 44928317 44928317 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.1985C>T p.Ser662Phe p.S662F ENST00000593135 13/16 275 228 47 410 410 0 strelka-varscan-mutect KIF18B,missense_variant,p.Ser674Phe,ENST00000587309,NM_001264573.1;KIF18B,missense_variant,p.Ser662Phe,ENST00000593135,NM_001265577.1;KIF18B,missense_variant,p.Ser683Phe,ENST00000590129,;KIF18B,downstream_gene_variant,,ENST00000585687,; A ENST00000593135 Transcript missense_variant 2083/2745 1985/2559 662/852 S/F tCt/tTt 1 -1 KIF18B HGNC HGNC:27102 protein_coding YES CCDS45709.2 ENSP00000465992 A0A0C4DGP5 UPI000192C418 NM_001265577.1 deleterious(0) 13/16 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 44928317 44928317 G A 1 0 0 0 0 1 0 0 0 8145 942 33 3 3 KIF18B 17 44928317 Missense_Mutation SNP G C3N-01489_T 69166 44928317 38329124 559 25489 SPAG9 0 . GRCh38 17 51120436 51120442 + Frame_Shift_Del DEL TCCACCT TCCACCT - novel C3N-01489_T C3N-01489_N TCCACCT TCCACCT c.215_221delAGGTGGA p.Gln72ArgfsTer51 p.Q72Rfs*51 ENST00000262013 1/30 219 192 27 322 322 0 sindel-varindel-pindel SPAG9,frameshift_variant,p.Gln72ArgfsTer51,ENST00000262013,NM_001130528.2;SPAG9,frameshift_variant,p.Gln72ArgfsTer51,ENST00000618113,;SPAG9,frameshift_variant,p.Gln72ArgfsTer51,ENST00000357122,NM_003971.5;SPAG9,frameshift_variant,p.Gln72ArgfsTer51,ENST00000505279,NM_001130527.2; - ENST00000262013 Transcript frameshift_variant 424-430/8273 215-221/3966 72-74/1321 QVE/X cAGGTGGAg/cg 1 -1 SPAG9 HGNC HGNC:14524 protein_coding YES CCDS45740.1 ENSP00000262013 O60271 UPI0000D60DF7 NM_001130528.2 1/30 hmmpanther:PTHR13886:SF2,hmmpanther:PTHR13886,Pfam_domain:PF09744 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 81 51120436 51120436 TCCACCT - 1 0 1 0 1 0 0 0 0 15316 1551 54 0 0 SPAG9 17 51120436 Frame_Shift_Del DEL TCCACCT C3N-01489_T 6192119 51120436 32137005 560 25490 MPO 0 . GRCh38 17 58273572 58273572 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1463C>A p.Pro488Gln p.P488Q ENST00000225275 9/12 451 403 48 574 574 0 strelka-varscan-mutect MPO,missense_variant,p.Pro488Gln,ENST00000225275,NM_000250.1;MPO,upstream_gene_variant,,ENST00000577220,;MPO,downstream_gene_variant,,ENST00000578493,; T ENST00000225275 Transcript missense_variant 1640/3215 1463/2238 488/745 P/Q cCa/cAa 1 -1 MPO HGNC HGNC:7218 protein_coding YES CCDS11604.1 ENSP00000225275 P05164 UPI0000131634 NM_000250.1 deleterious(0) 9/12 PROSITE_profiles:PS50292,hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF49,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 58273572 58273572 G T 1 0 0 0 0 1 0 0 0 9698 1348 47 2 2 MPO 17 58273572 Missense_Mutation SNP G C3N-01489_T 7153136 58273572 24983869 561 25491 MRC2 0 . GRCh38 17 62664892 62664892 + Missense_Mutation SNP A A C novel C3N-01489_T C3N-01489_N A A c.463A>C p.Ser155Arg p.S155R ENST00000303375 2/30 98 88 10 175 175 0 strelka-varscan-mutect MRC2,missense_variant,p.Ser155Arg,ENST00000303375,NM_006039.4;Y_RNA,upstream_gene_variant,,ENST00000384652,;MRC2,non_coding_transcript_exon_variant,,ENST00000584265,; C ENST00000303375 Transcript missense_variant 865/5988 463/4440 155/1479 S/R Agt/Cgt 1 1 MRC2 HGNC HGNC:16875 protein_coding YES CCDS11634.1 ENSP00000307513 Q9UBG0 UPI000013E895 NM_006039.4 tolerated(0.3) 2/30 Gene3D:2.80.10.50,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF69,SMART_domains:SM00458,Superfamily_domains:SSF50370 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 62664892 62664892 A C 1 0 0 0 0 1 0 0 0 9723 188 7 5 5 MRC2 17 62664892 Missense_Mutation SNP A C3N-01489_T 4391320 62664892 20592549 562 25492 ACE 0 . GRCh38 17 63494431 63494431 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.3341G>T p.Gly1114Val p.G1114V ENST00000290866 22/25 501 433 68 629 629 0 strelka-varscan-mutect ACE,missense_variant,p.Gly1114Val,ENST00000428043,;ACE,missense_variant,p.Gly1114Val,ENST00000290866,NM_000789.3;ACE,missense_variant,p.Gly540Val,ENST00000290863,NM_152830.2;ACE,missense_variant,p.Gly540Val,ENST00000413513,NM_001178057.1;ACE,missense_variant,p.Gly10Val,ENST00000579409,;ACE,downstream_gene_variant,,ENST00000582761,;ACE,non_coding_transcript_exon_variant,,ENST00000577418,;CTD-2501B8.1,missense_variant,p.Gly540Val,ENST00000577647,;ACE,3_prime_UTR_variant,,ENST00000579314,;ACE,3_prime_UTR_variant,,ENST00000578839,;ACE,non_coding_transcript_exon_variant,,ENST00000578679,;ACE,downstream_gene_variant,,ENST00000584865,;ACE,downstream_gene_variant,,ENST00000583645,;ACE,upstream_gene_variant,,ENST00000582244,; T ENST00000290866 Transcript missense_variant 3365/4959 3341/3921 1114/1306 G/V gGg/gTg 1 1 ACE HGNC HGNC:2707 protein_coding YES CCDS11637.1 ENSP00000290866 P12821 UPI000002B8AD NM_000789.3 deleterious(0) 22/25 hmmpanther:PTHR10514:SF19,hmmpanther:PTHR10514,Pfam_domain:PF01401,Superfamily_domains:SSF55486,Prints_domain:PR00791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 63494431 63494431 G T 1 0 0 0 0 1 0 0 0 174 1232 43 2 2 ACE 17 63494431 Missense_Mutation SNP G C3N-01489_T 829539 63494431 19763010 563 25493 PRKCA 0 . GRCh38 17 66788855 66788855 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1730C>T p.Pro577Leu p.P577L ENST00000413366 16/17 135 125 10 208 208 0 strelka-varscan-mutect PRKCA,missense_variant,p.Pro577Leu,ENST00000413366,NM_002737.2;MIR634,downstream_gene_variant,,ENST00000385208,; T ENST00000413366 Transcript missense_variant 1756/8751 1730/2019 577/672 P/L cCa/cTa 1 1 PRKCA HGNC HGNC:9393 protein_coding YES CCDS11664.1 ENSP00000408695 P17252 L7RSM7 UPI000013DD98 NM_002737.2 deleterious(0) 16/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF193,Pfam_domain:PF00069,PIRSF_domain:PIRSF000550,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 66788855 66788855 C T 1 0 0 0 0 1 0 0 0 12640 594 21 3 3 PRKCA 17 66788855 Missense_Mutation SNP C C3N-01489_T 3294424 66788855 16468586 564 25494 DNAI2 0 . GRCh38 17 74309355 74309355 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1314G>T p.Met438Ile p.M438I ENST00000446837 9/13 441 390 51 597 597 0 strelka-varscan-mutect DNAI2,missense_variant,p.Met495Ile,ENST00000579490,;DNAI2,missense_variant,p.Met438Ile,ENST00000446837,;DNAI2,missense_variant,p.Met438Ile,ENST00000582036,NM_001172810.1;DNAI2,missense_variant,p.Met438Ile,ENST00000311014,NM_023036.4;RP11-647F2.2,non_coding_transcript_exon_variant,,ENST00000585167,;DNAI2,3_prime_UTR_variant,,ENST00000579055,;DNAI2,upstream_gene_variant,,ENST00000579312,; T ENST00000446837 Transcript missense_variant 1620/2474 1314/1818 438/605 M/I atG/atT 1 1 DNAI2 HGNC HGNC:18744 protein_coding YES CCDS11697.1 ENSP00000400252 Q9GZS0 UPI000013EC1D tolerated(0.11) 9/13 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF7,hmmpanther:PTHR12442,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs1448018393 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 74309355 74309355 G T 1 0 0 0 0 1 0 0 0 4425 1377 48 2 2 DNAI2 17 74309355 Missense_Mutation SNP G C3N-01489_T 7520500 74309355 8948086 565 25495 BTBD17 0 . GRCh38 17 74360191 74360191 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.140A>T p.Gln47Leu p.Q47L ENST00000375366 2/3 126 101 25 169 169 0 strelka-varscan-mutect BTBD17,missense_variant,p.Gln47Leu,ENST00000375366,NM_001080466.1;KIF19,downstream_gene_variant,,ENST00000389916,NM_153209.3; A ENST00000375366 Transcript missense_variant 267/1805 140/1437 47/478 Q/L cAg/cTg 1 -1 BTBD17 HGNC HGNC:33758 protein_coding YES CCDS32719.1 ENSP00000364515 A6NE02 UPI00001D7961 NM_001080466.1 tolerated(1) 2/3 hmmpanther:PTHR24410:SF12,hmmpanther:PTHR24410,Gene3D:3.30.710.10,Superfamily_domains:SSF54695 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 74360191 74360191 T A 1 0 0 0 0 1 0 0 0 1716 1580 55 4 4 BTBD17 17 74360191 Missense_Mutation SNP T C3N-01489_T 50836 74360191 8897250 566 25496 RNF157 0 . GRCh38 17 76167760 76167760 + Missense_Mutation SNP T T A rs146324319 C3N-01489_T C3N-01489_N T T c.334A>T p.Ser112Cys p.S112C ENST00000269391 4/19 203 176 27 295 295 0 strelka-varscan-mutect RNF157,missense_variant,p.Ser112Cys,ENST00000269391,NM_052916.2;RNF157,missense_variant,p.Ser112Cys,ENST00000319945,;RNF157,upstream_gene_variant,,ENST00000591615,; A ENST00000269391 Transcript missense_variant 467/4955 334/2040 112/679 S/C Agt/Tgt rs146324319 1 -1 RNF157 HGNC HGNC:29402 protein_coding YES CCDS32740.1 ENSP00000269391 Q96PX1 UPI00001C1FDD NM_052916.2 deleterious(0.01) 4/19 hmmpanther:PTHR22996:SF1,hmmpanther:PTHR22996 MODERATE 1 SNV 1 1 PASS rs146324319 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 76167760 76167760 T A 1 0 0 0 0 1 0 0 0 13632 1580 55 4 4 RNF157 17 76167760 Missense_Mutation SNP T C3N-01489_T 1807569 76167760 7089681 567 25497 RPTOR 0 . GRCh38 17 80822231 80822231 + Silent SNP G G T rs751529541 C3N-01489_T C3N-01489_N G G c.921G>T p.= p.T307T ENST00000306801 8/34 227 187 40 278 277 1 strelka-varscan-mutect RPTOR,synonymous_variant,p.=,ENST00000306801,NM_020761.2;RPTOR,synonymous_variant,p.=,ENST00000544334,NM_001163034.1;RPTOR,synonymous_variant,p.=,ENST00000570891,;RPTOR,non_coding_transcript_exon_variant,,ENST00000575542,;RPTOR,non_coding_transcript_exon_variant,,ENST00000577161,;RPTOR,3_prime_UTR_variant,,ENST00000574767,; T ENST00000306801 Transcript synonymous_variant 1283/6408 921/4008 307/1335 T acG/acT rs751529541,COSM1659113 1 1 RPTOR HGNC HGNC:30287 protein_coding YES CCDS11773.1 ENSP00000307272 Q8N122 UPI000007000F NM_020761.2 8/34 Prints_domain:PR01547,hmmpanther:PTHR12848 0,1 LOW 1 SNV 1 0,1 1 PASS rs751529541 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 80822231 80822231 G T 1 0 0 0 0 0 0 0 1 13920 1074 38 1 1 RPTOR 17 80822231 Silent SNP G C3N-01489_T 4654471 80822231 2435210 568 25498 BAHCC1 0 . GRCh38 17 81462861 81462861 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.7598A>T p.Tyr2533Phe p.Y2533F ENST00000584436 28/29 207 188 19 295 295 0 strelka-varscan-mutect BAHCC1,missense_variant,p.Tyr2533Phe,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.Tyr2502Phe,ENST00000307745,;RP11-1055B8.8,upstream_gene_variant,,ENST00000572590,;BAHCC1,non_coding_transcript_exon_variant,,ENST00000582709,;BAHCC1,downstream_gene_variant,,ENST00000578541,;BAHCC1,downstream_gene_variant,,ENST00000584330,; T ENST00000584436 Transcript missense_variant 7965/10801 7598/7920 2533/2639 Y/F tAc/tTc 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 tolerated(0.05) 28/29 PROSITE_profiles:PS51038,hmmpanther:PTHR12505:SF22,hmmpanther:PTHR12505,Pfam_domain:PF01426,SMART_domains:SM00439 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 81462861 81462861 A T 1 0 0 0 0 1 0 0 0 1451 391 14 4 4 BAHCC1 17 81462861 Missense_Mutation SNP A C3N-01489_T 640630 81462861 1794580 569 25499 FOXK2 0 . GRCh38 17 82571810 82571810 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.849G>T p.= p.G283G ENST00000335255 4/9 107 99 8 130 130 0 strelka-varscan-mutect FOXK2,synonymous_variant,p.=,ENST00000335255,NM_004514.3;FOXK2,synonymous_variant,p.=,ENST00000531030,;FOXK2,synonymous_variant,p.=,ENST00000526383,;FOXK2,synonymous_variant,p.=,ENST00000473637,;FOXK2,non_coding_transcript_exon_variant,,ENST00000527313,;FOXK2,non_coding_transcript_exon_variant,,ENST00000570585,;RP13-638C3.6,downstream_gene_variant,,ENST00000581815,; T ENST00000335255 Transcript synonymous_variant 1023/5265 849/1983 283/660 G ggG/ggT 1 1 FOXK2 HGNC HGNC:6036 protein_coding YES CCDS11813.1 ENSP00000335677 Q01167 UPI00001A8BEE NM_004514.3 4/9 Gene3D:1.10.10.10,Pfam_domain:PF00250,Prints_domain:PR00053,PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF106,SMART_domains:SM00339,Superfamily_domains:SSF46785 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 82571810 82571810 G T 1 0 0 0 0 0 0 0 1 5878 1161 41 2 2 FOXK2 17 82571810 Silent SNP G C3N-01489_T 1108949 82571810 685631 570 25500 ROCK1 0 . GRCh38 18 20970417 20970417 + Silent SNP C C G rs761231638 C3N-01489_T C3N-01489_N C C c.2751G>C p.= p.T917T ENST00000399799 23/33 172 142 30 265 265 0 strelka-varscan-mutect ROCK1,synonymous_variant,p.=,ENST00000399799,NM_005406.2;ROCK1,synonymous_variant,p.=,ENST00000635540,;ROCK1,non_coding_transcript_exon_variant,,ENST00000583556,;ROCK1,upstream_gene_variant,,ENST00000584875,; G ENST00000399799 Transcript synonymous_variant 3692/9484 2751/4065 917/1354 T acG/acC rs761231638 1 -1 ROCK1 HGNC HGNC:10251 protein_coding YES CCDS11870.2 ENSP00000382697 Q13464 UPI000006F0A4 NM_005406.2 23/33 hmmpanther:PTHR22988:SF33,hmmpanther:PTHR22988,PIRSF_domain:PIRSF037568,PD936484 LOW 1 SNV 1 1 PASS rs761231638 . 0 208 0 0 2 0 0 0 -16.82313 0.9976419 1 1 1 0 G 2 3 81 20970417 20970417 C G 1 0 0 0 0 0 0 0 1 13695 755 27 4 4 ROCK1 18 20970417 Silent SNP C C3N-01489_T 20970417 59402868 571 25501 ABHD3 0 . GRCh38 18 21704573 21704573 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.93G>T p.= p.G31G ENST00000289119 1/9 163 153 10 192 192 0 strelka-varscan-mutect ABHD3,synonymous_variant,p.=,ENST00000289119,NM_138340.4;ABHD3,synonymous_variant,p.=,ENST00000580981,NM_001308256.1;ABHD3,upstream_gene_variant,,ENST00000578270,NM_001308257.1;ABHD3,upstream_gene_variant,,ENST00000584464,;ABHD3,non_coding_transcript_exon_variant,,ENST00000579875,;MIB1,upstream_gene_variant,,ENST00000578646,;ABHD3,synonymous_variant,p.=,ENST00000577891,;ABHD3,non_coding_transcript_exon_variant,,ENST00000579982,;ABHD3,non_coding_transcript_exon_variant,,ENST00000577928,; A ENST00000289119 Transcript synonymous_variant 233/2064 93/1230 31/409 G ggG/ggT 1 -1 ABHD3 HGNC HGNC:18718 protein_coding YES CCDS32802.1 ENSP00000289119 Q8WU67 UPI0000163938 NM_138340.4 1/9 Transmembrane_helices:TMhelix,hmmpanther:PTHR10794,hmmpanther:PTHR10794:SF50,PIRSF_domain:PIRSF005211 LOW 1 SNV 1 1 PASS rs1205956355 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 21704573 21704573 C A 1 0 0 0 0 0 0 0 1 93 610 22 2 2 ABHD3 18 21704573 Silent SNP C C3N-01489_T 734156 21704573 58668712 572 25502 NPC1 0 . GRCh38 18 23561455 23561455 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.536A>G p.Lys179Arg p.K179R ENST00000269228 5/25 200 166 34 339 339 0 strelka-varscan-mutect NPC1,missense_variant,p.Lys179Arg,ENST00000269228,NM_000271.4;NPC1,upstream_gene_variant,,ENST00000591051,;NPC1,non_coding_transcript_exon_variant,,ENST00000540608,; C ENST00000269228 Transcript missense_variant 1091/5157 536/3837 179/1278 K/R aAg/aGg 1 -1 NPC1 HGNC HGNC:7897 protein_coding YES CCDS11878.1 ENSP00000269228 O15118 UPI000013D80F NM_000271.4 tolerated(0.38) 5/25 hmmpanther:PTHR10796:SF116,hmmpanther:PTHR10796,TIGRFAM_domain:TIGR00917,Pfam_domain:PF16414 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 23561455 23561455 T C 1 0 0 0 0 1 0 0 0 10618 1609 56 5 5 NPC1 18 23561455 Missense_Mutation SNP T C3N-01489_T 1856882 23561455 56811830 573 25503 NOL4 0 . GRCh38 18 33958367 33958367 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1108G>T p.Asp370Tyr p.D370Y ENST00000261592 7/11 123 93 30 169 169 0 strelka-varscan-mutect NOL4,missense_variant,p.Asp370Tyr,ENST00000261592,NM_003787.4;NOL4,missense_variant,p.Asp370Tyr,ENST00000589544,NM_001198548.1;NOL4,missense_variant,p.Asp296Tyr,ENST00000538587,NM_001198547.1;NOL4,missense_variant,p.Asp354Tyr,ENST00000590712,NM_001198546.1;NOL4,missense_variant,p.Asp85Tyr,ENST00000535384,NM_001198549.1;NOL4,missense_variant,p.Asp119Tyr,ENST00000586553,;NOL4,3_prime_UTR_variant,,ENST00000586314,; A ENST00000261592 Transcript missense_variant 1406/3957 1108/1917 370/638 D/Y Gac/Tac 1 -1 NOL4 HGNC HGNC:7870 protein_coding YES CCDS11907.2 ENSP00000261592 O94818 UPI000059D504 NM_003787.4 deleterious(0.05) 7/11 hmmpanther:PTHR12449,hmmpanther:PTHR12449:SF17 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 33958367 33958367 C A 1 0 0 0 0 1 0 0 0 10567 913 32 2 2 NOL4 18 33958367 Missense_Mutation SNP C C3N-01489_T 10396912 33958367 46414918 574 25504 FHOD3 0 . GRCh38 18 36779516 36779516 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.4855G>A p.Glu1619Lys p.E1619K ENST00000590592 29/29 202 191 11 279 279 0 strelka-varscan-mutect FHOD3,missense_variant,p.Glu1436Lys,ENST00000257209,NM_025135.3;FHOD3,missense_variant,p.Glu1619Lys,ENST00000590592,NM_001281740.1;FHOD3,missense_variant,p.Glu1419Lys,ENST00000359247,NM_001281739.1;FHOD3,missense_variant,p.Glu1197Lys,ENST00000592930,;FHOD3,missense_variant,p.Glu632Lys,ENST00000591635,;FHOD3,missense_variant,p.Glu525Lys,ENST00000592128,;TPGS2,3_prime_UTR_variant,,ENST00000590258,;FHOD3,3_prime_UTR_variant,,ENST00000585579,;TPGS2,downstream_gene_variant,,ENST00000614939,NM_001271956.1;TPGS2,downstream_gene_variant,,ENST00000587129,;TPGS2,downstream_gene_variant,,ENST00000590652,; A ENST00000590592 Transcript missense_variant 4855/4869 4855/4869 1619/1622 E/K Gag/Aag 1 1 FHOD3 HGNC HGNC:26178 protein_coding YES CCDS62418.1 ENSP00000466937 Q2V2M9 UPI0002840E0A NM_001281740.1 deleterious_low_confidence(0) 29/29 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 36779516 36779516 G A 1 0 0 0 0 1 0 0 0 5748 1175 41 3 3 FHOD3 18 36779516 Missense_Mutation SNP G C3N-01489_T 2821149 36779516 43593769 575 25505 PIK3C3 0 . GRCh38 18 42064830 42064830 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.2523G>C p.Lys841Asn p.K841N ENST00000262039 23/25 89 81 8 107 107 0 strelka-varscan-mutect PIK3C3,missense_variant,p.Lys841Asn,ENST00000262039,NM_002647.2;PIK3C3,missense_variant,p.Lys778Asn,ENST00000398870,NM_001308020.1;PIK3C3,splice_region_variant,,ENST00000593098,;PIK3C3,splice_region_variant,,ENST00000588156,;PIK3C3,splice_region_variant,,ENST00000587261,;PIK3C3,splice_region_variant,,ENST00000588631,;PIK3C3,splice_region_variant,,ENST00000587328,; C ENST00000262039 Transcript missense_variant,splice_region_variant 2609/9443 2523/2664 841/887 K/N aaG/aaC 1 1 PIK3C3 HGNC HGNC:8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 UPI00000708CE NM_002647.2 deleterious(0) 23/25 Gene3D:1.10.1070.11,PIRSF_domain:PIRSF000587,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -17.2032 1 1 1 1 0 C 3 2 81 42064830 42064830 G C 1 0 0 0 0 1 0 0 0 12007 1014 35 4 4 PIK3C3 18 42064830 Missense_Mutation SNP G C3N-01489_T 5285314 42064830 38308455 576 25506 SMAD2 0 . GRCh38 18 47848483 47848483 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.989G>T p.Arg330Met p.R330M ENST00000262160 8/11 265 249 16 416 415 1 strelka-varscan-mutect SMAD2,missense_variant,p.Arg330Met,ENST00000262160,NM_005901.5;SMAD2,missense_variant,p.Arg330Met,ENST00000402690,NM_001003652.3;SMAD2,missense_variant,p.Arg300Met,ENST00000356825,NM_001135937.2;SMAD2,missense_variant,p.Arg300Met,ENST00000586040,;SMAD2,missense_variant,p.Arg300Met,ENST00000591214,;MTCO2P2,downstream_gene_variant,,ENST00000591258,; A ENST00000262160 Transcript missense_variant 1241/34526 989/1404 330/467 R/M aGg/aTg 1 -1 SMAD2 HGNC HGNC:6768 protein_coding YES CCDS11934.1 ENSP00000262160 Q15796 Q53XR6 UPI0000032EE7 NM_005901.5 deleterious(0) 8/11 PROSITE_profiles:PS51076,hmmpanther:PTHR13703:SF42,hmmpanther:PTHR13703,Gene3D:2.60.200.10,Pfam_domain:PF03166,SMART_domains:SM00524,Superfamily_domains:SSF49879 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 47848483 47848483 C A 1 0 0 0 0 1 0 0 0 15051 681 24 2 2 SMAD2 18 47848483 Missense_Mutation SNP C C3N-01489_T 5783653 47848483 32524802 577 25507 MRO 0 . GRCh38 18 50800044 50800044 + Nonsense_Mutation SNP G G A C3N-01489_T C3N-01489_N G G c.727C>T p.Gln243Ter p.Q243* ENST00000436348 6/7 106 98 8 188 188 0 strelka-varscan-mutect MRO,stop_gained,p.Gln229Ter,ENST00000610511,NM_031939.3;MRO,stop_gained,p.Gln229Ter,ENST00000256425,;MRO,stop_gained,p.Gln229Ter,ENST00000428869,;MRO,stop_gained,p.Gln191Ter,ENST00000431965,NM_001127175.1;MRO,stop_gained,p.Gln243Ter,ENST00000436348,NM_001127176.1;MRO,stop_gained,p.Gln229Ter,ENST00000398439,;MRO,stop_gained,p.Gln177Ter,ENST00000588444,NM_001127174.1;MRO,stop_gained,p.Gln177Ter,ENST00000592966,;MRO,downstream_gene_variant,,ENST00000587291,;MRO,3_prime_UTR_variant,,ENST00000585524,;MRO,downstream_gene_variant,,ENST00000590988,; A ENST00000436348 Transcript stop_gained 876/1125 727/789 243/262 Q/* Cag/Tag COSM5388214,COSM5388215 1 -1 MRO HGNC HGNC:24121 protein_coding YES CCDS45868.1 ENSP00000397900 Q9BYG7 UPI000174C6BE NM_001127176.1 6/7 hmmpanther:PTHR23120:SF2,hmmpanther:PTHR23120 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 50800044 50800044 G A 1 0 0 0 0 0 1 0 0 9742 1357 47 3 3 MRO 18 50800044 Nonsense_Mutation SNP G C3N-01489_T 2951561 50800044 29573241 578 25508 TCF4 0 . GRCh38 18 55228884 55228884 + Silent SNP C C A rs369262048 C3N-01489_T C3N-01489_N C C c.2148G>T p.= p.A716A ENST00000398339 19/21 394 364 30 623 621 2 strelka-varscan-mutect TCF4,synonymous_variant,p.=,ENST00000636400,;TCF4,synonymous_variant,p.=,ENST00000356073,NM_003199.2;TCF4,synonymous_variant,p.=,ENST00000616053,;TCF4,synonymous_variant,p.=,ENST00000635822,;TCF4,synonymous_variant,p.=,ENST00000638154,;TCF4,synonymous_variant,p.=,ENST00000636822,;TCF4,synonymous_variant,p.=,ENST00000637169,;TCF4,synonymous_variant,p.=,ENST00000629387,;TCF4,synonymous_variant,p.=,ENST00000564999,;TCF4,synonymous_variant,p.=,ENST00000354452,NM_001083962.1;TCF4,synonymous_variant,p.=,ENST00000570287,NM_001243235.1;TCF4,synonymous_variant,p.=,ENST00000537578,NM_001243227.1;TCF4,synonymous_variant,p.=,ENST00000564403,NM_001243228.1;TCF4,synonymous_variant,p.=,ENST00000568740,;TCF4,synonymous_variant,p.=,ENST00000540999,NM_001306207.1;TCF4,synonymous_variant,p.=,ENST00000398339,NM_001243226.2;TCF4,synonymous_variant,p.=,ENST00000543082,NM_001243231.1;TCF4,synonymous_variant,p.=,ENST00000568673,;TCF4,synonymous_variant,p.=,ENST00000457482,NM_001243234.1;TCF4,synonymous_variant,p.=,ENST00000565018,;TCF4,synonymous_variant,p.=,ENST00000544241,NM_001243232.1;TCF4,synonymous_variant,p.=,ENST00000561992,NM_001243233.1;TCF4,synonymous_variant,p.=,ENST00000566279,;TCF4,synonymous_variant,p.=,ENST00000566286,NM_001243230.1;TCF4,synonymous_variant,p.=,ENST00000537856,;TCF4,synonymous_variant,p.=,ENST00000567880,;TCF4,synonymous_variant,p.=,ENST00000564228,NM_001306208.1;TCF4,synonymous_variant,p.=,ENST00000570177,;TCF4,synonymous_variant,p.=,ENST00000561831,NM_001243236.1;TCF4,synonymous_variant,p.=,ENST00000626584,;TCF4,synonymous_variant,p.=,ENST00000626631,;TCF4,non_coding_transcript_exon_variant,,ENST00000637239,;TCF4,non_coding_transcript_exon_variant,,ENST00000637250,;TCF4,non_coding_transcript_exon_variant,,ENST00000635990,;TCF4,3_prime_UTR_variant,,ENST00000636751,;TCF4,3_prime_UTR_variant,,ENST00000637115,;TCF4,3_prime_UTR_variant,,ENST00000637923,;TCF4,non_coding_transcript_exon_variant,,ENST00000562680,;TCF4,non_coding_transcript_exon_variant,,ENST00000626466,; A ENST00000398339 Transcript synonymous_variant 2278/2551 2148/2322 716/773 A gcG/gcT rs369262048 1 -1 TCF4 HGNC HGNC:11634 protein_coding YES CCDS58631.1 ENSP00000381382 E9PH57 UPI0000EE5B9B NM_001243226.2 19/21 PROSITE_profiles:PS50888,hmmpanther:PTHR11793:SF10,hmmpanther:PTHR11793,Pfam_domain:PF00010,Gene3D:4.10.280.10,SMART_domains:SM00353,Superfamily_domains:SSF47459 LOW 1 SNV 1 1 PASS rs369262048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 55228884 55228884 C A 1 0 0 0 0 0 0 0 1 16102 639 23 1 1 TCF4 18 55228884 Silent SNP C C3N-01489_T 4428840 55228884 25144401 579 25509 ALPK2 0 . GRCh38 18 58536839 58536839 + Missense_Mutation SNP T T G novel C3N-01489_T C3N-01489_N T T c.3348A>C p.Arg1116Ser p.R1116S ENST00000361673 5/13 187 174 13 365 363 2 strelka-varscan-mutect ALPK2,missense_variant,p.Arg1116Ser,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; G ENST00000361673 Transcript missense_variant 3562/7303 3348/6513 1116/2170 R/S agA/agC 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(0.43) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 58536839 58536839 T G 1 0 0 0 0 1 0 0 0 645 1548 54 5 5 ALPK2 18 58536839 Missense_Mutation SNP T C3N-01489_T 3307955 58536839 21836446 580 25510 ALPK2 0 . GRCh38 18 58536855 58536855 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.3332G>T p.Ser1111Ile p.S1111I ENST00000361673 5/13 204 192 12 386 385 1 strelka-varscan-mutect ALPK2,missense_variant,p.Ser1111Ile,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; A ENST00000361673 Transcript missense_variant 3546/7303 3332/6513 1111/2170 S/I aGc/aTc 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(0.06) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 58536855 58536855 C A 1 0 0 0 0 1 0 0 0 645 797 28 2 2 ALPK2 18 58536855 Missense_Mutation SNP C C3N-01489_T 16 58536855 21836430 581 25511 ZNF532 0 . GRCh38 18 58918613 58918613 + Missense_Mutation SNP C C A rs776628824 C3N-01489_T C3N-01489_N C C c.326C>A p.Ser109Tyr p.S109Y ENST00000336078 4/11 260 239 21 449 449 0 strelka-varscan-mutect ZNF532,missense_variant,p.Ser109Tyr,ENST00000336078,NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4;ZNF532,missense_variant,p.Ser109Tyr,ENST00000589288,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000591083,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000591808,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000591230,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000589481,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000592452,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000591049,;ZNF532,missense_variant,p.Ser109Tyr,ENST00000588456,;ZNF532,downstream_gene_variant,,ENST00000588601,;ZNF532,downstream_gene_variant,,ENST00000590285,;ZNF532,downstream_gene_variant,,ENST00000590287,;ZNF532,downstream_gene_variant,,ENST00000587755,;ZNF532,downstream_gene_variant,,ENST00000586085,;ZNF532,downstream_gene_variant,,ENST00000588543,;ZNF532,upstream_gene_variant,,ENST00000586997,;ZNF532,upstream_gene_variant,,ENST00000590157,;ZNF532,upstream_gene_variant,,ENST00000589156,; A ENST00000336078 Transcript missense_variant 1102/6696 326/3906 109/1301 S/Y tCc/tAc rs776628824 1 1 ZNF532 HGNC HGNC:30940 protein_coding YES CCDS11969.1 ENSP00000338217 Q9HCE3 A0A024R283 UPI000013D30C NM_001318726.1,NM_001318727.1,NM_001318728.1,NM_018181.4 tolerated(0.84) 4/11 hmmpanther:PTHR26374,hmmpanther:PTHR26374:SF204 MODERATE 1 SNV 1 1 PASS rs776628824 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 58918613 58918613 C A 1 0 0 0 0 1 0 0 0 18545 855 30 2 2 ZNF532 18 58918613 Missense_Mutation SNP C C3N-01489_T 381758 58918613 21454672 582 25512 HMSD 0 . GRCh38 18 63960266 63960266 + Nonsense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.331A>T p.Lys111Ter p.K111* ENST00000408945 4/4 207 182 25 339 339 0 strelka-varscan-mutect HMSD,stop_gained,p.Lys111Ter,ENST00000408945,NM_001123366.1;HMSD,downstream_gene_variant,,ENST00000526932,;HMSD,non_coding_transcript_exon_variant,,ENST00000481726,;HMSD,non_coding_transcript_exon_variant,,ENST00000498680,; T ENST00000408945 Transcript stop_gained 533/2101 331/420 111/139 K/* Aaa/Taa 1 1 HMSD HGNC HGNC:23037 protein_coding YES CCDS42441.1 ENSP00000386207 A8MTL9 UPI00001609A8 NM_001123366.1 4/4 hmmpanther:PTHR11461:SF168,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:3.30.497.10,Superfamily_domains:SSF56574 HIGH 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 63960266 63960266 A T 1 0 0 0 0 0 1 0 0 7137 363 13 4 4 HMSD 18 63960266 Nonsense_Mutation SNP A C3N-01489_T 5041653 63960266 16413019 583 25513 DOK6 0 . GRCh38 18 69739099 69739099 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.734C>A p.Ala245Asp p.A245D ENST00000382713 6/8 89 82 7 128 128 0 strelka-mutect DOK6,missense_variant,p.Ala245Asp,ENST00000382713,NM_152721.5;DOK6,missense_variant,p.Ala149Asp,ENST00000582992,;DOK6,non_coding_transcript_exon_variant,,ENST00000577609,;DOK6,downstream_gene_variant,,ENST00000584435,; A ENST00000382713 Transcript missense_variant 924/8890 734/996 245/331 A/D gCc/gAc 1 1 DOK6 HGNC HGNC:28301 protein_coding YES CCDS32841.1 ENSP00000372160 Q6PKX4 UPI000035EC7C NM_152721.5 tolerated(0.12) 6/8 hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF43,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 69739099 69739099 C A 1 0 0 0 0 1 0 0 0 4516 753 26 2 2 DOK6 18 69739099 Missense_Mutation SNP C C3N-01489_T 5778833 69739099 10634186 584 25514 CTDP1 0 . GRCh38 18 79680174 79680174 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.227C>T p.Pro76Leu p.P76L ENST00000613122 1/13 65 60 5 79 79 0 strelka-varscan-mutect CTDP1,missense_variant,p.Pro76Leu,ENST00000613122,NM_004715.4;CTDP1,missense_variant,p.Pro76Leu,ENST00000075430,NM_048368.3;CTDP1,missense_variant,p.Pro8Leu,ENST00000591598,;CTDP1,upstream_gene_variant,,ENST00000299543,NM_001202504.1;CTDP1,upstream_gene_variant,,ENST00000590635,;RP11-567M16.6,upstream_gene_variant,,ENST00000616428,;RP11-567M16.3,upstream_gene_variant,,ENST00000317008,;CTDP1,upstream_gene_variant,,ENST00000587623,; T ENST00000613122 Transcript missense_variant 374/5866 227/2886 76/961 P/L cCc/cTc 1 1 CTDP1 HGNC HGNC:2498 protein_coding YES CCDS12017.1 ENSP00000484525 Q9Y5B0 UPI000013C57B NM_004715.4 tolerated(0.05) 1/13 Gene3D:2.40.50.100,hmmpanther:PTHR23081,hmmpanther:PTHR23081:SF0 MODERATE 1 SNV 1 1 PASS rs1379116232 . 0 206 4 0 0 0 0 0 -11.78413 1 1 1 1 0 T 3 4 81 79680174 79680174 C T 1 0 0 0 0 1 0 0 0 3810 623 22 3 3 CTDP1 18 79680174 Missense_Mutation SNP C C3N-01489_T 9941075 79680174 693111 585 25515 CTDP1 0 . GRCh38 18 79715469 79715469 + Missense_Mutation SNP G G T rs752664929 C3N-01489_T C3N-01489_N G G c.2009G>T p.Arg670Leu p.R670L ENST00000613122 8/13 145 137 8 236 234 2 strelka-varscan-mutect CTDP1,missense_variant,p.Arg670Leu,ENST00000613122,NM_004715.4;CTDP1,missense_variant,p.Arg670Leu,ENST00000075430,NM_048368.3;CTDP1,missense_variant,p.Arg551Leu,ENST00000299543,NM_001202504.1;CTDP1,missense_variant,p.Arg602Leu,ENST00000591598,; T ENST00000613122 Transcript missense_variant 2156/5866 2009/2886 670/961 R/L cGg/cTg rs752664929 1 1 CTDP1 HGNC HGNC:2498 protein_coding YES CCDS12017.1 ENSP00000484525 Q9Y5B0 UPI000013C57B NM_004715.4 deleterious(0.02) 8/13 Gene3D:3.40.50.10190,PROSITE_profiles:PS50172,hmmpanther:PTHR23081,hmmpanther:PTHR23081:SF0,SMART_domains:SM00292,Superfamily_domains:SSF52113 MODERATE 1 SNV 1 1 PASS rs752664929 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 79715469 79715469 G T 1 0 0 0 0 1 0 0 0 3810 1116 39 1 1 CTDP1 18 79715469 Missense_Mutation SNP G C3N-01489_T 35295 79715469 657816 586 25516 PLPP2 0 . GRCh38 19 282216 282216 + Missense_Mutation SNP T T A C3N-01489_T C3N-01489_N T T c.698A>T p.Tyr233Phe p.Y233F ENST00000327790 5/6 257 239 18 379 379 0 strelka-varscan-mutect PLPP2,missense_variant,p.Tyr233Phe,ENST00000327790,NM_177543.2;PLPP2,missense_variant,p.Tyr212Phe,ENST00000434325,NM_003712.3;PLPP2,missense_variant,p.Tyr156Phe,ENST00000269812,NM_177526.2;PLPP2,missense_variant,p.Tyr156Phe,ENST00000633125,;PLPP2,missense_variant,p.Tyr106Phe,ENST00000586998,;PLPP2,downstream_gene_variant,,ENST00000591572,;PLPP2,non_coding_transcript_exon_variant,,ENST00000621795,; A ENST00000327790 Transcript missense_variant 817/1397 698/930 233/309 Y/F tAc/tTc COSM3531909,COSM3531910 1 -1 PLPP2 HGNC HGNC:9230 protein_coding YES CCDS12024.1 ENSP00000329697 O43688 UPI0000168654 NM_177543.2 tolerated(0.09) 5/6 Gene3D:1.20.144.10,Pfam_domain:PF01569,hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF25,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 282216 282216 T A 1 0 0 0 0 1 0 0 0 12203 1638 57 4 4 PLPP2 19 282216 Missense_Mutation SNP T C3N-01489_T 282216 58335400 587 25517 POLRMT 0 . GRCh38 19 619963 619963 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2881G>T p.Ala961Ser p.A961S ENST00000588649 12/21 120 106 14 197 197 0 strelka-mutect POLRMT,missense_variant,p.Ala961Ser,ENST00000588649,NM_005035.3;HCN2,downstream_gene_variant,,ENST00000251287,NM_001194.3;POLRMT,downstream_gene_variant,,ENST00000590573,;POLRMT,upstream_gene_variant,,ENST00000590336,;POLRMT,upstream_gene_variant,,ENST00000587057,;POLRMT,downstream_gene_variant,,ENST00000590709,;POLRMT,upstream_gene_variant,,ENST00000589961,;POLRMT,upstream_gene_variant,,ENST00000592633,; A ENST00000588649 Transcript missense_variant 2973/3835 2881/3693 961/1230 A/S Gcg/Tcg 1 -1 POLRMT HGNC HGNC:9200 protein_coding YES CCDS12036.1 ENSP00000465759 O00411 UPI000013C68E NM_005035.3 tolerated(0.06) 12/21 hmmpanther:PTHR10102:SF0,hmmpanther:PTHR10102,Gene3D:1.10.150.20,Pfam_domain:PF00940,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 619963 619963 C A 1 0 0 0 0 1 0 0 0 12349 782 27 1 1 POLRMT 19 619963 Missense_Mutation SNP C C3N-01489_T 337747 619963 57997653 588 25518 UQCR11 0 . GRCh38 19 1599560 1599560 + Missense_Mutation SNP C C A rs758492664 C3N-01489_T C3N-01489_N C C c.51G>T p.Trp17Cys p.W17C ENST00000591899 2/3 89 70 19 183 183 0 strelka-varscan-mutect UQCR11,missense_variant,p.Trp17Cys,ENST00000591899,NM_006830.3;UQCR11,missense_variant,p.Trp17Cys,ENST00000585671,;UQCR11,missense_variant,p.Trp17Cys,ENST00000589880,;UQCR11,splice_region_variant,,ENST00000593029,;UQCR11,splice_region_variant,,ENST00000593264,;AC005943.2,missense_variant,p.Trp17Cys,ENST00000585937,; A ENST00000591899 Transcript missense_variant,splice_region_variant 132/1324 51/171 17/56 W/C tgG/tgT rs758492664 1 -1 UQCR11 HGNC HGNC:30862 protein_coding YES CCDS12073.1 ENSP00000467262 O14957 UPI0000137A81 NM_006830.3 deleterious(0) 2/3 hmmpanther:PTHR15420,Gene3D:1.20.5.220,Pfam_domain:PF08997,Superfamily_domains:SSF81518,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs758492664 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 1599560 1599560 C A 1 0 0 0 0 1 0 0 0 17545 637 22 2 2 UQCR11 19 1599560 Missense_Mutation SNP C C3N-01489_T 979597 1599560 57018056 589 25519 S1PR4 0 . GRCh38 19 3179822 3179822 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1030G>T p.Ala344Ser p.A344S ENST00000246115 1/1 48 36 12 86 86 0 strelka-varscan-mutect S1PR4,missense_variant,p.Ala344Ser,ENST00000246115,NM_003775.3;S1PR4,downstream_gene_variant,,ENST00000591346,; T ENST00000246115 Transcript missense_variant 1055/1565 1030/1155 344/384 A/S Gct/Tct 1 1 S1PR4 HGNC HGNC:3170 protein_coding YES CCDS12105.1 ENSP00000246115 O95977 UPI0000050462 NM_003775.3 tolerated(0.66) 1/1 hmmpanther:PTHR22750:SF13,hmmpanther:PTHR22750,Prints_domain:PR01526 MODERATE 1 SNV 1 PASS rs935970379 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 3179822 3179822 G T 1 0 0 0 0 1 0 0 0 14055 1203 42 2 2 S1PR4 19 3179822 Missense_Mutation SNP G C3N-01489_T 1580262 3179822 55437794 590 25520 ARRDC5 0 . GRCh38 19 4891096 4891096 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.979C>A p.Gln327Lys p.Q327K ENST00000381781 3/3 127 107 20 227 227 0 strelka-varscan-mutect ARRDC5,missense_variant,p.Gln327Lys,ENST00000381781,NM_001080523.1; T ENST00000381781 Transcript missense_variant 979/1638 979/1029 327/342 Q/K Cag/Aag 1 -1 ARRDC5 HGNC HGNC:31407 protein_coding YES CCDS45929.1 ENSP00000371200 A6NEK1 UPI0000DD84C9 NM_001080523.1 tolerated_low_confidence(0.61) 3/3 hmmpanther:PTHR11188,hmmpanther:PTHR11188:SF56 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 4891096 4891096 G T 1 0 0 0 0 1 0 0 0 1129 1357 47 2 2 ARRDC5 19 4891096 Missense_Mutation SNP G C3N-01489_T 1711274 4891096 53726520 591 25521 MUC16 0 . GRCh38 19 8961549 8961549 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.15221C>G p.Ser5074Cys p.S5074C ENST00000397910 3/84 88 79 9 171 171 0 strelka-varscan-mutect MUC16,missense_variant,p.Ser5074Cys,ENST00000397910,NM_024690.2; C ENST00000397910 Transcript missense_variant 15425/43816 15221/43524 5074/14507 S/C tCt/tGt 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 8961549 8961549 G C 1 0 0 0 0 1 0 0 0 9972 942 33 4 4 MUC16 19 8961549 Missense_Mutation SNP G C3N-01489_T 4070453 8961549 49656067 592 25522 ZGLP1 0 . GRCh38 19 10308310 10308310 + Missense_Mutation SNP C C G C3N-01489_T C3N-01489_N C C c.372G>C p.Gln124His p.Q124H ENST00000403903 1/4 82 71 11 102 102 0 strelka-varscan-mutect ZGLP1,missense_variant,p.Gln124His,ENST00000403903,NM_001103167.1;ZGLP1,missense_variant,p.Gln40His,ENST00000403352,;FDX2,downstream_gene_variant,,ENST00000393708,NM_001031734.3;FDX2,downstream_gene_variant,,ENST00000492239,;FDX2,downstream_gene_variant,,ENST00000494368,;CTD-2369P2.10,3_prime_UTR_variant,,ENST00000452032,;CTD-2369P2.10,downstream_gene_variant,,ENST00000493771,;FDX2,downstream_gene_variant,,ENST00000460631,;FDX2,downstream_gene_variant,,ENST00000453681,;ZGLP1,upstream_gene_variant,,ENST00000480726,;FDX2,downstream_gene_variant,,ENST00000343376,; G ENST00000403903 Transcript missense_variant 1571/2303 372/816 124/271 Q/H caG/caC COSM3528156,COSM3528157 1 -1 ZGLP1 HGNC HGNC:37245 protein_coding YES CCDS45959.1 ENSP00000384434 P0C6A0 UPI00001D8262 NM_001103167.1 deleterious(0.01) 1/4 hmmpanther:PTHR10071:SF185,hmmpanther:PTHR10071 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -19.99991 1 1 1 1 0 G 3 3 81 10308310 10308310 C G 1 0 0 0 0 1 0 0 0 18251 912 32 4 4 ZGLP1 19 10308310 Missense_Mutation SNP C C3N-01489_T 1346761 10308310 48309306 593 25523 ZGLP1 0 . GRCh38 19 10308487 10308487 + Missense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.195G>C p.Glu65Asp p.E65D ENST00000403903 1/4 67 57 10 100 100 0 strelka-varscan-mutect ZGLP1,missense_variant,p.Glu65Asp,ENST00000403903,NM_001103167.1;ZGLP1,5_prime_UTR_variant,,ENST00000403352,;FDX2,downstream_gene_variant,,ENST00000393708,NM_001031734.3;FDX2,downstream_gene_variant,,ENST00000492239,;FDX2,downstream_gene_variant,,ENST00000494368,;CTD-2369P2.10,3_prime_UTR_variant,,ENST00000452032,;CTD-2369P2.10,non_coding_transcript_exon_variant,,ENST00000493771,;FDX2,downstream_gene_variant,,ENST00000460631,;FDX2,downstream_gene_variant,,ENST00000453681,;ZGLP1,upstream_gene_variant,,ENST00000480726,;FDX2,downstream_gene_variant,,ENST00000343376,; G ENST00000403903 Transcript missense_variant 1394/2303 195/816 65/271 E/D gaG/gaC 1 -1 ZGLP1 HGNC HGNC:37245 protein_coding YES CCDS45959.1 ENSP00000384434 P0C6A0 UPI00001D8262 NM_001103167.1 deleterious(0.04) 1/4 hmmpanther:PTHR10071:SF185,hmmpanther:PTHR10071 MODERATE 1 SNV 1 1 PASS rs1333824260 . 0 205 5 0 0 0 0 0 -19.9985 1 1 1 1 0 G 3 3 81 10308487 10308487 C G 1 0 0 0 0 1 0 0 0 18251 912 32 4 4 ZGLP1 19 10308487 Missense_Mutation SNP C C3N-01489_T 177 10308487 48309129 594 25524 GCDH 0 . GRCh38 19 12891928 12891928 + Frame_Shift_Del DEL C C - novel C3N-01489_T C3N-01489_N C C c.226delC p.Gln76ArgfsTer66 p.Q76Rfs*66 ENST00000222214 4/12 443 385 58 736 736 0 sindel-varindel-pindel GCDH,frameshift_variant,p.Gln76ArgfsTer66,ENST00000222214,NM_000159.3,NM_013976.3;GCDH,frameshift_variant,p.Gln76ArgfsTer66,ENST00000591470,;GCDH,frameshift_variant,p.Gln64ArgfsTer66,ENST00000588905,;GCDH,frameshift_variant,p.Gln76ArgfsTer45,ENST00000589039,;GCDH,frameshift_variant,p.Gln76ArgfsTer47,ENST00000587072,;KLF1,upstream_gene_variant,,ENST00000264834,NM_006563.3;GCDH,frameshift_variant,p.Gln76ArgfsTer382,ENST00000590530,;GCDH,3_prime_UTR_variant,,ENST00000590445,;GCDH,non_coding_transcript_exon_variant,,ENST00000591043,;GCDH,non_coding_transcript_exon_variant,,ENST00000585420,;GCDH,non_coding_transcript_exon_variant,,ENST00000421816,;GCDH,non_coding_transcript_exon_variant,,ENST00000590627,;GCDH,non_coding_transcript_exon_variant,,ENST00000587832,;GCDH,non_coding_transcript_exon_variant,,ENST00000585760,;RPS6P25,upstream_gene_variant,,ENST00000464444,; - ENST00000222214 Transcript frameshift_variant 436/1956 225/1317 75/438 C/X tgC/tg 1 1 GCDH HGNC HGNC:4189 protein_coding YES CCDS12286.1 ENSP00000222214 Q92947 A0A024R7F9 UPI000012B292 NM_000159.3,NM_013976.3 4/12 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF307,Pfam_domain:PF02771,Gene3D:1.10.540.10,Superfamily_domains:SSF56645 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 81 12891928 12891928 C - 1 0 1 0 1 0 0 0 0 6157 747 26 0 0 GCDH 19 12891928 Frame_Shift_Del DEL C C3N-01489_T 2583441 12891928 45725688 595 25525 ADGRL1 0 . GRCh38 19 14152142 14152142 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.3673C>T p.Arg1225Trp p.R1225W ENST00000340736 23/24 235 200 35 366 362 4 strelka-varscan-mutect ADGRL1,missense_variant,p.Arg1225Trp,ENST00000340736,NM_001008701.2;ADGRL1,missense_variant,p.Arg1220Trp,ENST00000361434,NM_014921.4;ADGRL1,missense_variant,p.Arg126Trp,ENST00000592164,;ADGRL1,intron_variant,,ENST00000593005,;CTB-55O6.12,intron_variant,,ENST00000588387,;CTB-55O6.12,intron_variant,,ENST00000588658,;CTB-55O6.12,upstream_gene_variant,,ENST00000592086,; A ENST00000340736 Transcript missense_variant 3971/7853 3673/4425 1225/1474 R/W Cgg/Tgg 1 -1 ADGRL1 HGNC HGNC:20973 protein_coding YES CCDS32928.1 ENSP00000340688 O94910 UPI000005046A NM_001008701.2 deleterious(0.01) 23/24 Pfam_domain:PF02354 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 14152142 14152142 G A 1 0 0 0 0 1 0 0 0 375 1115 39 1 1 ADGRL1 19 14152142 Missense_Mutation SNP G C3N-01489_T 1260214 14152142 44465474 596 25526 OR10H1 0 . GRCh38 19 15807640 15807640 + Missense_Mutation SNP T T G rs551484315 C3N-01489_T C3N-01489_N T T c.398A>C p.Asn133Thr p.N133T ENST00000334920 1/1 111 89 22 194 194 0 strelka-varscan-mutect OR10H1,missense_variant,p.Asn133Thr,ENST00000334920,NM_013940.2; G ENST00000334920 Transcript missense_variant 487/1124 398/957 133/318 N/T aAc/aCc rs551484315 1 -1 OR10H1 HGNC HGNC:8172 protein_coding YES CCDS12335.1 ENSP00000335596 Q9Y4A9 A0A126GVU5 UPI000004CA3D NM_013940.2 tolerated(0.57) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF122,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs551484315 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 15807640 15807640 T G 1 0 0 0 0 1 0 0 0 10982 1725 60 5 5 OR10H1 19 15807640 Missense_Mutation SNP T C3N-01489_T 1655498 15807640 42809976 597 25527 MYO9B 0 . GRCh38 19 17195244 17195244 + Nonsense_Mutation SNP G G T rs777317964 C3N-01489_T C3N-01489_N G G c.3817G>T p.Glu1273Ter p.E1273* ENST00000595618 22/40 448 406 42 698 697 1 strelka-varscan-mutect MYO9B,stop_gained,p.Glu1273Ter,ENST00000595618,NM_001130065.1;MYO9B,stop_gained,p.Glu1273Ter,ENST00000594824,NM_004145.3;MYO9B,stop_gained,p.Glu1273Ter,ENST00000397274,;MYO9B,stop_gained,p.Glu1273Ter,ENST00000595641,;MYO9B,upstream_gene_variant,,ENST00000593533,; T ENST00000595618 Transcript stop_gained 3969/7623 3817/6069 1273/2022 E/* Gag/Tag rs777317964 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 22/40 HIGH 1 SNV 1 1 PASS rs777317964 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 17195244 17195244 G T 1 0 0 0 0 0 1 0 0 10086 1059 37 1 1 MYO9B 19 17195244 Nonsense_Mutation SNP G C3N-01489_T 1387604 17195244 41422372 598 25528 MYO9B 0 . GRCh38 19 17195319 17195319 + Nonsense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.3892C>T p.Gln1298Ter p.Q1298* ENST00000595618 22/40 495 424 71 669 668 1 strelka-varscan-mutect MYO9B,stop_gained,p.Gln1298Ter,ENST00000595618,NM_001130065.1;MYO9B,stop_gained,p.Gln1298Ter,ENST00000594824,NM_004145.3;MYO9B,stop_gained,p.Gln1298Ter,ENST00000397274,;MYO9B,stop_gained,p.Gln1298Ter,ENST00000595641,;MYO9B,upstream_gene_variant,,ENST00000593533,; T ENST00000595618 Transcript stop_gained 4044/7623 3892/6069 1298/2022 Q/* Cag/Tag 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 22/40 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 17195319 17195319 C T 1 0 0 0 0 0 1 0 0 10086 595 21 3 3 MYO9B 19 17195319 Nonsense_Mutation SNP C C3N-01489_T 75 17195319 41422297 599 25529 FCHO1 0 . GRCh38 19 17774419 17774419 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.861G>T p.Lys287Asn p.K287N ENST00000594202 13/29 122 99 23 185 185 0 strelka-varscan-mutect FCHO1,missense_variant,p.Lys287Asn,ENST00000594202,NM_001161357.1;FCHO1,missense_variant,p.Lys287Asn,ENST00000596536,NM_015122.2;FCHO1,missense_variant,p.Lys287Asn,ENST00000252771,;FCHO1,missense_variant,p.Lys287Asn,ENST00000600676,NM_001161358.1;FCHO1,missense_variant,p.Lys287Asn,ENST00000596951,;FCHO1,missense_variant,p.Lys294Asn,ENST00000597512,;FCHO1,missense_variant,p.Lys237Asn,ENST00000595033,NM_001161359.1;FCHO1,downstream_gene_variant,,ENST00000595023,;FCHO1,downstream_gene_variant,,ENST00000596507,;FCHO1,downstream_gene_variant,,ENST00000597718,;FCHO1,downstream_gene_variant,,ENST00000600209,;FCHO1,downstream_gene_variant,,ENST00000594068,;FCHO1,downstream_gene_variant,,ENST00000595549,;FCHO1,downstream_gene_variant,,ENST00000593833,;FCHO1,downstream_gene_variant,,ENST00000597474,;FCHO1,non_coding_transcript_exon_variant,,ENST00000600393,;FCHO1,non_coding_transcript_exon_variant,,ENST00000597076,;FCHO1,upstream_gene_variant,,ENST00000600058,;FCHO1,upstream_gene_variant,,ENST00000595594,;FCHO1,upstream_gene_variant,,ENST00000602111,;FCHO1,upstream_gene_variant,,ENST00000599766,;FCHO1,upstream_gene_variant,,ENST00000596522,; T ENST00000594202 Transcript missense_variant 1140/3214 861/2676 287/891 K/N aaG/aaT COSM992893 1 1 FCHO1 HGNC HGNC:29002 protein_coding YES CCDS59365.1 ENSP00000473001 A0A0C3SFZ9 UPI000059D6B0 NM_001161357.1 deleterious(0.01) 13/29 hmmpanther:PTHR23065,hmmpanther:PTHR23065:SF6 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 17774419 17774419 G T 1 0 0 0 0 1 0 0 0 5649 991 35 2 2 FCHO1 19 17774419 Missense_Mutation SNP G C3N-01489_T 579100 17774419 40843197 600 25530 HAPLN4 0 . GRCh38 19 19260876 19260876 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.421T>C p.Tyr141His p.Y141H ENST00000291481 3/5 176 148 28 228 228 0 strelka-varscan-mutect HAPLN4,missense_variant,p.Tyr141His,ENST00000291481,NM_023002.2;TM6SF2,downstream_gene_variant,,ENST00000389363,NM_001001524.2;LLNLR-259H9.1,downstream_gene_variant,,ENST00000624068,;AC138430.4,non_coding_transcript_exon_variant,,ENST00000586064,;HAPLN4,non_coding_transcript_exon_variant,,ENST00000592862,;TM6SF2,downstream_gene_variant,,ENST00000431465,;TM6SF2,downstream_gene_variant,,ENST00000591001,;TM6SF2,downstream_gene_variant,,ENST00000590431,; G ENST00000291481 Transcript missense_variant 485/3449 421/1209 141/402 Y/H Tat/Cat 1 -1 HAPLN4 HGNC HGNC:31357 protein_coding YES CCDS12398.1 ENSP00000291481 Q86UW8 UPI00000496C7 NM_023002.2 deleterious(0) 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF11,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,SMART_domains:SM00408,SMART_domains:SM00406,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 81 19260876 19260876 A G 1 0 0 0 0 1 0 0 0 6843 420 15 5 5 HAPLN4 19 19260876 Missense_Mutation SNP A C3N-01489_T 1486457 19260876 39356740 601 25531 CILP2 0 . GRCh38 19 19545299 19545299 + Silent SNP A A T novel C3N-01489_T C3N-01489_N A A c.2754A>T p.= p.T918T ENST00000291495 8/8 130 112 18 229 228 1 strelka-varscan-mutect CILP2,synonymous_variant,p.=,ENST00000586018,;CILP2,synonymous_variant,p.=,ENST00000291495,NM_153221.2;CILP2,downstream_gene_variant,,ENST00000588333,; T ENST00000291495 Transcript synonymous_variant 2839/4199 2754/3471 918/1156 T acA/acT 1 1 CILP2 HGNC HGNC:24213 protein_coding YES CCDS12405.1 ENSP00000291495 Q8IUL8 UPI000013E04D NM_153221.2 8/8 hmmpanther:PTHR15031,hmmpanther:PTHR15031:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 19545299 19545299 A T 1 0 0 0 0 0 0 0 1 3192 146 6 4 4 CILP2 19 19545299 Silent SNP A C3N-01489_T 284423 19545299 39072317 602 25532 ZNF729 0 . GRCh38 19 22316567 22316567 + Nonsense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.3150T>A p.Cys1050Ter p.C1050* ENST00000601693 4/4 156 133 23 312 312 0 strelka-varscan-mutect ZNF729,stop_gained,p.Cys1050Ter,ENST00000601693,NM_001242680.1; A ENST00000601693 Transcript stop_gained 3268/3877 3150/3759 1050/1252 C/* tgT/tgA 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 22316567 22316567 T A 1 0 0 0 0 0 1 0 0 18703 1702 59 4 4 ZNF729 19 22316567 Nonsense_Mutation SNP T C3N-01489_T 2771268 22316567 36301049 603 25533 ZNF729 0 . GRCh38 19 22316929 22316929 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.3512A>T p.Gln1171Leu p.Q1171L ENST00000601693 4/4 251 221 30 421 421 0 strelka-varscan-mutect ZNF729,missense_variant,p.Gln1171Leu,ENST00000601693,NM_001242680.1; T ENST00000601693 Transcript missense_variant 3630/3877 3512/3759 1171/1252 Q/L cAg/cTg 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 tolerated(0.34) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 22316929 22316929 A T 1 0 0 0 0 1 0 0 0 18703 188 7 4 4 ZNF729 19 22316929 Missense_Mutation SNP A C3N-01489_T 362 22316929 36300687 604 25534 ANKRD27 0 . GRCh38 19 32619273 32619273 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1994A>T p.Lys665Met p.K665M ENST00000306065 20/29 60 56 4 108 108 0 varscan-mutect ANKRD27,missense_variant,p.Lys665Met,ENST00000306065,NM_032139.2; A ENST00000306065 Transcript missense_variant 2153/4450 1994/3153 665/1050 K/M aAg/aTg 1 -1 ANKRD27 HGNC HGNC:25310 protein_coding YES CCDS32986.1 ENSP00000304292 Q96NW4 UPI000004FDE9 NM_032139.2 deleterious(0.04) 20/29 PROSITE_profiles:PS50297,hmmpanther:PTHR24170,hmmpanther:PTHR24170:SF1,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 32619273 32619273 T A 1 0 0 0 0 1 0 0 0 758 1609 56 4 4 ANKRD27 19 32619273 Missense_Mutation SNP T C3N-01489_T 10302344 32619273 25998343 605 25535 PDCD2L 0 . GRCh38 19 34413838 34413838 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.788A>T p.Gln263Leu p.Q263L ENST00000246535 5/7 100 85 15 165 165 0 strelka-varscan-mutect PDCD2L,missense_variant,p.Gln263Leu,ENST00000246535,NM_032346.1;PDCD2L,intron_variant,,ENST00000587065,;RP11-618P17.4,downstream_gene_variant,,ENST00000606020,;RP11-618P17.4,downstream_gene_variant,,ENST00000592740,;PDCD2L,non_coding_transcript_exon_variant,,ENST00000587385,;PDCD2L,non_coding_transcript_exon_variant,,ENST00000585821,; T ENST00000246535 Transcript missense_variant 835/1171 788/1077 263/358 Q/L cAg/cTg 1 1 PDCD2L HGNC HGNC:28194 protein_coding YES CCDS12438.1 ENSP00000246535 Q9BRP1 UPI0000038A65 NM_032346.1 deleterious(0) 5/7 Pfam_domain:PF04194,hmmpanther:PTHR12298 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 34413838 34413838 A T 1 0 0 0 0 1 0 0 0 11708 188 7 4 4 PDCD2L 19 34413838 Missense_Mutation SNP A C3N-01489_T 1794565 34413838 24203778 606 25536 GRAMD1A 0 . GRCh38 19 35019249 35019249 + Silent SNP G G T rs777595203 C3N-01489_T C3N-01489_N G G c.1272G>T p.= p.T424T ENST00000317991 12/20 59 51 8 112 112 0 strelka-varscan-mutect GRAMD1A,synonymous_variant,p.=,ENST00000599564,NM_001320036.1;GRAMD1A,synonymous_variant,p.=,ENST00000317991,NM_001320034.1,NM_020895.3;GRAMD1A,synonymous_variant,p.=,ENST00000411896,NM_001136199.1;CTD-2527I21.14,intron_variant,,ENST00000605640,;GRAMD1A,3_prime_UTR_variant,,ENST00000600231,NM_001320035.1;GRAMD1A,non_coding_transcript_exon_variant,,ENST00000598118,;GRAMD1A,downstream_gene_variant,,ENST00000595596,;GRAMD1A,downstream_gene_variant,,ENST00000598362,;GRAMD1A,upstream_gene_variant,,ENST00000603907,; T ENST00000317991 Transcript synonymous_variant 1464/2695 1272/2175 424/724 T acG/acT rs777595203,COSM5480118 1 1 GRAMD1A HGNC HGNC:29305 protein_coding YES CCDS42546.1 ENSP00000441032 Q96CP6 UPI00000377B4 NM_001320034.1,NM_020895.3 12/20 Pfam_domain:PF16016,hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF8 0,1 LOW 1 SNV 1 0,1 1 PASS rs777595203 . 0 206 4 0 0 0 0 0 -18.55448 1 1 1 1 0 T 2 4 81 35019249 35019249 G T 1 0 0 0 0 0 0 0 1 6626 1132 40 1 1 GRAMD1A 19 35019249 Silent SNP G C3N-01489_T 605411 35019249 23598367 607 25537 GPR42 0 . GRCh38 19 35372290 35372290 + Nonsense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.931G>T p.Glu311Ter p.E311* ENST00000597214 1/1 117 103 14 163 163 0 varscan-mutect GPR42,stop_gained,p.Glu311Ter,ENST00000454971,;GPR42,stop_gained,p.Glu311Ter,ENST00000597214,; T ENST00000597214 Transcript stop_gained 1001/1182 931/1041 311/346 E/* Gag/Tag 1 1 GPR42 HGNC HGNC:4500 protein_coding YES ENSP00000473212 O15529 A0A0K0PUY3 UPI0000040740 1/1 hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40 HIGH 1 SNV 1 PASS . . 8 200 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 35372290 35372290 G T 1 0 0 0 0 0 1 0 0 6580 1175 41 2 2 GPR42 19 35372290 Nonsense_Mutation SNP G C3N-01489_T 353041 35372290 23245326 608 25538 ATP4A 0 . GRCh38 19 35562506 35562506 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.349G>T p.Val117Phe p.V117F ENST00000262623 4/22 186 170 16 296 296 0 strelka-varscan-mutect ATP4A,missense_variant,p.Val117Phe,ENST00000262623,NM_000704.2;ATP4A,non_coding_transcript_exon_variant,,ENST00000590916,;ATP4A,upstream_gene_variant,,ENST00000592131,;ATP4A,upstream_gene_variant,,ENST00000592767,; A ENST00000262623 Transcript missense_variant 378/3709 349/3108 117/1035 V/F Gtt/Ttt 1 -1 ATP4A HGNC HGNC:819 protein_coding YES CCDS12467.1 ENSP00000262623 P20648 UPI000016A49B NM_000704.2 deleterious(0.04) 4/22 Transmembrane_helices:TMhelix,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF251,TIGRFAM_domain:TIGR01106,Pfam_domain:PF00690,SMART_domains:SM00831,Superfamily_domains:0049473,Prints_domain:PR00121 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 35562506 35562506 C A 1 0 0 0 0 1 0 0 0 1298 507 18 2 2 ATP4A 19 35562506 Missense_Mutation SNP C C3N-01489_T 190216 35562506 23055110 609 25539 PRODH2 0 . GRCh38 19 35803023 35803023 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.1285T>A p.Cys429Ser p.C429S ENST00000301175 9/11 78 73 5 79 79 0 strelka-varscan-mutect PRODH2,missense_variant,p.Cys429Ser,ENST00000301175,NM_021232.1;PRODH2,missense_variant,p.Cys25Ser,ENST00000589835,;PRODH2,missense_variant,p.Cys94Ser,ENST00000588266,;PRODH2,non_coding_transcript_exon_variant,,ENST00000587695,;PRODH2,upstream_gene_variant,,ENST00000587808,; T ENST00000301175 Transcript missense_variant 1303/1677 1285/1611 429/536 C/S Tgc/Agc 1 -1 PRODH2 HGNC HGNC:17325 protein_coding YES CCDS12478.1 ENSP00000301175 Q9UF12 UPI000006EE59 NM_021232.1 tolerated(0.14) 9/11 hmmpanther:PTHR13914,hmmpanther:PTHR13914:SF5,Pfam_domain:PF01619,Gene3D:3.20.20.220,Superfamily_domains:SSF51730 MODERATE 1 SNV 1 1 PASS rs1436746097 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 35803023 35803023 A T 1 0 0 0 0 1 0 0 0 12682 159 6 4 4 PRODH2 19 35803023 Missense_Mutation SNP A C3N-01489_T 240517 35803023 22814593 610 25540 KIRREL2 0 . GRCh38 19 35857144 35857144 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.25C>T p.Leu9Phe p.L9F ENST00000360202 1/15 178 158 20 260 260 0 strelka-varscan-mutect KIRREL2,missense_variant,p.Leu9Phe,ENST00000360202,NM_199180.3;KIRREL2,missense_variant,p.Leu9Phe,ENST00000592409,;KIRREL2,missense_variant,p.Leu9Phe,ENST00000347900,NM_199179.3;KIRREL2,missense_variant,p.Leu9Phe,ENST00000262625,NM_032123.6;KIRREL2,missense_variant,p.Leu9Phe,ENST00000586102,;NPHS1,intron_variant,,ENST00000591817,; T ENST00000360202 Transcript missense_variant 223/2942 25/2127 9/708 L/F Ctc/Ttc 1 1 KIRREL2 HGNC HGNC:18816 protein_coding YES CCDS12481.1 ENSP00000353331 Q6UWL6 UPI0000048F5B NM_199180.3 tolerated(0.06) 1/15 Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 35857144 35857144 C T 1 0 0 0 0 1 0 0 0 8189 681 24 3 3 KIRREL2 19 35857144 Missense_Mutation SNP C C3N-01489_T 54121 35857144 22760472 611 25541 ZNF585A 0 . GRCh38 19 37152764 37152764 + Nonsense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1135G>T p.Glu379Ter p.E379* ENST00000292841 5/5 113 96 17 172 172 0 strelka-varscan-mutect ZNF585A,stop_gained,p.Glu379Ter,ENST00000292841,NM_001288800.1;ZNF585A,stop_gained,p.Glu324Ter,ENST00000356958,NM_152655.3;ZNF585A,stop_gained,p.Glu324Ter,ENST00000392157,NM_199126.2;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585A,intron_variant,,ENST00000588723,;ZNF585A,intron_variant,,ENST00000587817,;CTC-454I21.3,downstream_gene_variant,,ENST00000590245,; A ENST00000292841 Transcript stop_gained 1394/8618 1135/2310 379/769 E/* Gag/Tag 1 -1 ZNF585A HGNC HGNC:26305 protein_coding YES CCDS74353.1 ENSP00000292841 Q6P3V2 UPI00002021E7 NM_001288800.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF105,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 81 37152764 37152764 C A 1 0 0 0 0 0 1 0 0 18591 922 32 2 2 ZNF585A 19 37152764 Nonsense_Mutation SNP C C3N-01489_T 1295620 37152764 21464852 612 25542 ZNF585B 0 . GRCh38 19 37186250 37186250 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.1287A>T p.Gln429His p.Q429H ENST00000532828 5/5 116 97 19 200 200 0 strelka-varscan-mutect ZNF585B,missense_variant,p.Gln429His,ENST00000532828,NM_152279.3;ZNF585B,missense_variant,p.Gln374His,ENST00000531805,;ZNF585B,3_prime_UTR_variant,,ENST00000527838,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF585B,downstream_gene_variant,,ENST00000591492,;ZNF585B,downstream_gene_variant,,ENST00000586320,;CTC-454I21.3,intron_variant,,ENST00000585860,;CTC-454I21.3,intron_variant,,ENST00000590245,;ZNF585B,downstream_gene_variant,,ENST00000392156,;ZNF585B,downstream_gene_variant,,ENST00000591273,;ZNF585B,downstream_gene_variant,,ENST00000526705,; A ENST00000532828 Transcript missense_variant 1539/6210 1287/2310 429/769 Q/H caA/caT 1 -1 ZNF585B HGNC HGNC:30948 protein_coding YES CCDS12500.1 ENSP00000433773 Q52M93 UPI00001AF01B NM_152279.3 deleterious(0.04) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF105,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 37186250 37186250 T A 1 0 0 0 0 1 0 0 0 18592 1838 64 4 4 ZNF585B 19 37186250 Missense_Mutation SNP T C3N-01489_T 33486 37186250 21431366 613 25543 ZNF573 0 . GRCh38 19 37738804 37738804 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1686C>A p.= p.T562T ENST00000536220 5/5 112 102 10 176 175 1 strelka-varscan-mutect ZNF573,synonymous_variant,p.=,ENST00000392138,;ZNF573,synonymous_variant,p.=,ENST00000536220,NM_001172691.1,NM_001172690.1;ZNF573,synonymous_variant,p.=,ENST00000590414,;ZNF573,synonymous_variant,p.=,ENST00000357309,NM_001172692.1,NM_001172689.1;ZNF573,synonymous_variant,p.=,ENST00000339503,NM_152360.3;ZNF573,downstream_gene_variant,,ENST00000378445,;ZNF573,downstream_gene_variant,,ENST00000585724,;ZNF573,intron_variant,,ENST00000590674,;ZNF573,3_prime_UTR_variant,,ENST00000589632,;ZNF573,3_prime_UTR_variant,,ENST00000586155,;ZNF573,downstream_gene_variant,,ENST00000489148,;ZNF573,downstream_gene_variant,,ENST00000591516,; T ENST00000536220 Transcript synonymous_variant 1755/2257 1686/1998 562/665 T acC/acA 1 -1 ZNF573 HGNC HGNC:26420 protein_coding YES CCDS59381.1 ENSP00000440464 Q86YE8 UPI000059D70C NM_001172691.1,NM_001172690.1 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF159,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 3 1 PASS rs1429501030 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 37738804 37738804 G T 1 0 0 0 0 0 0 0 1 18579 987 35 2 2 ZNF573 19 37738804 Silent SNP G C3N-01489_T 552554 37738804 20878812 614 25544 KCNK6 0 . GRCh38 19 38326630 38326630 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.360G>T p.Lys120Asn p.K120N ENST00000263372 2/3 101 85 16 158 158 0 strelka-varscan-mutect KCNK6,missense_variant,p.Lys120Asn,ENST00000263372,NM_004823.1;KCNK6,downstream_gene_variant,,ENST00000588137,; T ENST00000263372 Transcript missense_variant 467/5722 360/942 120/313 K/N aaG/aaT 1 1 KCNK6 HGNC HGNC:6281 protein_coding YES CCDS12513.1 ENSP00000263372 Q9Y257 B2RDS2 UPI0000030CB7 NM_004823.1 deleterious(0) 2/3 Gene3D:1.10.287.70,Pfam_domain:PF07885,PIRSF_domain:PIRSF038061,Prints_domain:PR01333,hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF28,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 38326630 38326630 G T 1 0 0 0 0 1 0 0 0 7987 991 35 2 2 KCNK6 19 38326630 Missense_Mutation SNP G C3N-01489_T 587826 38326630 20290986 615 25545 RYR1 0 . GRCh38 19 38448426 38448426 + Missense_Mutation SNP C C A rs200572262 C3N-01489_T C3N-01489_N C C c.872C>A p.Ala291Glu p.A291E ENST00000359596 10/106 355 305 50 491 491 0 strelka-varscan-mutect RYR1,missense_variant,p.Ala291Glu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Ala291Glu,ENST00000359596,NM_000540.2; A ENST00000359596 Transcript missense_variant 872/15117 872/15117 291/5038 A/E gCg/gAg rs200572262,COSM371085 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.01) 10/106 PROSITE_profiles:PS50919,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF02815,Gene3D:2.80.10.50,SMART_domains:SM00472,Superfamily_domains:SSF82109 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs200572262 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 38448426 38448426 C A 1 0 0 0 0 1 0 0 0 14028 768 27 1 1 RYR1 19 38448426 Missense_Mutation SNP C C3N-01489_T 121796 38448426 20169190 616 25546 RYR1 0 . GRCh38 19 38500655 38500655 + Missense_Mutation SNP G G T rs121918594 C3N-01489_T C3N-01489_N G G c.7373G>T p.Arg2458Leu p.R2458L ENST00000359596 46/106 408 354 54 490 490 0 strelka-varscan-mutect RYR1,missense_variant,p.Arg2458Leu,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Arg2458Leu,ENST00000359596,NM_000540.2;RYR1,missense_variant,p.Arg276Leu,ENST00000594335,; T ENST00000359596 Transcript missense_variant 7373/15117 7373/15117 2458/5038 R/L cGc/cTc rs121918594,CM118674,CM981783,RYR1:c.7373G>A,COSM5471002 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.01) 46/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 pathogenic 0,0,0,0,1 16917943 MODERATE 1 SNV 5 1,1,1,0,1 1 PASS rs121918594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 38500655 38500655 G T 1 0 0 0 0 1 0 0 0 14028 1087 38 1 1 RYR1 19 38500655 Missense_Mutation SNP G C3N-01489_T 52229 38500655 20116961 617 25547 ZNF780B 0 . GRCh38 19 40035450 40035450 + Missense_Mutation SNP C C T rs775945014 C3N-01489_T C3N-01489_N C C c.1409G>A p.Gly470Glu p.G470E ENST00000434248 5/5 244 211 33 307 306 1 strelka-varscan-mutect ZNF780B,missense_variant,p.Gly470Glu,ENST00000434248,;ZNF780B,missense_variant,p.Gly470Glu,ENST00000617676,NM_001005851.2;ZNF780B,missense_variant,p.Gly322Glu,ENST00000221355,;ZNF780B,downstream_gene_variant,,ENST00000598845,;ZNF780B,downstream_gene_variant,,ENST00000595995,; T ENST00000434248 Transcript missense_variant 1475/8665 1409/2502 470/833 G/E gGg/gAg rs775945014 1 -1 ZNF780B HGNC HGNC:33109 protein_coding YES CCDS46077.1 ENSP00000391641 Q9Y6R6 A0A024R0P7 UPI000007137F tolerated(1) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF203,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs775945014 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 40035450 40035450 C T 1 0 0 0 0 1 0 0 0 18736 623 22 3 3 ZNF780B 19 40035450 Missense_Mutation SNP C C3N-01489_T 1534795 40035450 18582166 618 25548 CYP2B6 0 . GRCh38 19 41010053 41010053 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.882G>T p.= p.S294S ENST00000324071 6/9 399 363 36 489 489 0 varscan-mutect CYP2B6,synonymous_variant,p.=,ENST00000324071,NM_000767.4;CYP2B6,intron_variant,,ENST00000593831,;CYP2B6,downstream_gene_variant,,ENST00000598834,;CYP2B6,non_coding_transcript_exon_variant,,ENST00000597612,;CYP2B6,downstream_gene_variant,,ENST00000594187,; T ENST00000324071 Transcript synonymous_variant 889/3054 882/1476 294/491 S tcG/tcT 1 1 CYP2B6 HGNC HGNC:2615 protein_coding YES CCDS12570.1 ENSP00000324648 P20813 UPI000012823F NM_000767.4 6/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,Prints_domain:PR00463,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF153,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs1239266674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 41010053 41010053 G T 1 0 0 0 0 0 0 0 1 3967 1074 38 1 1 CYP2B6 19 41010053 Silent SNP G C3N-01489_T 974603 41010053 17607563 619 25549 CYP2S1 0 . GRCh38 19 41198803 41198803 + Missense_Mutation SNP G G T rs778416663 C3N-01489_T C3N-01489_N G G c.749G>T p.Arg250Leu p.R250L ENST00000310054 5/9 176 147 29 224 224 0 strelka-varscan-mutect CYP2S1,missense_variant,p.Arg250Leu,ENST00000310054,NM_030622.7;CYP2S1,intron_variant,,ENST00000597754,;CYP2S1,intron_variant,,ENST00000600561,;CYP2S1,upstream_gene_variant,,ENST00000593890,;CYP2S1,intron_variant,,ENST00000593545,;CYP2S1,intron_variant,,ENST00000595590,; T ENST00000310054 Transcript missense_variant 965/2782 749/1515 250/504 R/L cGg/cTg rs778416663,COSM1249593 1 1 CYP2S1 HGNC HGNC:15654 protein_coding YES CCDS12573.1 ENSP00000308032 Q96SQ9 UPI00000467C9 NM_030622.7 deleterious(0.01) 5/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF23,Superfamily_domains:SSF48264 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs778416663 . 0 204 0 5 0 0 0 0 -20 0.9996103 1 1 1 0 T 3 4 81 41198803 41198803 G T 1 0 0 0 0 1 0 0 0 3977 1116 39 1 1 CYP2S1 19 41198803 Missense_Mutation SNP G C3N-01489_T 188750 41198803 17418813 620 25550 AXL 0 . GRCh38 19 41239235 41239235 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1206G>T p.= p.L402L ENST00000301178 9/20 89 82 7 140 140 0 strelka-varscan-mutect AXL,synonymous_variant,p.=,ENST00000301178,NM_021913.4;AXL,synonymous_variant,p.=,ENST00000359092,NM_001699.5;AXL,synonymous_variant,p.=,ENST00000593513,NM_001278599.1;AXL,non_coding_transcript_exon_variant,,ENST00000599659,; T ENST00000301178 Transcript synonymous_variant 1396/4737 1206/2685 402/894 L ctG/ctT 1 1 AXL HGNC HGNC:905 protein_coding YES CCDS12575.1 ENSP00000301178 P30530 UPI000014319B NM_021913.4 9/20 PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF323,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 41239235 41239235 G T 1 0 0 0 0 0 0 0 1 1395 1277 45 2 2 AXL 19 41239235 Silent SNP G C3N-01489_T 40432 41239235 17378381 621 25551 CEACAM7 0 . GRCh38 19 41683919 41683919 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.572G>T p.Arg191Met p.R191M ENST00000006724 3/5 304 277 27 452 452 0 strelka-varscan-mutect CEACAM7,missense_variant,p.Arg191Met,ENST00000006724,NM_006890.4,NM_001291485.1;CEACAM7,missense_variant,p.Arg191Met,ENST00000401731,;CEACAM7,intron_variant,,ENST00000602225,;CEACAM7,downstream_gene_variant,,ENST00000599715,; A ENST00000006724 Transcript missense_variant 774/2489 572/798 191/265 R/M aGg/aTg 1 -1 CEACAM7 HGNC HGNC:1819 protein_coding YES CCDS12583.1 ENSP00000006724 Q14002 UPI0000DBDD9E NM_006890.4,NM_001291485.1 deleterious(0) 3/5 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 41683919 41683919 C A 1 0 0 0 0 1 0 0 0 2903 681 24 2 2 CEACAM7 19 41683919 Missense_Mutation SNP C C3N-01489_T 444684 41683919 16933697 622 25552 ATP1A3 0 . GRCh38 19 41975659 41975659 + Missense_Mutation SNP A A T novel C3N-01489_T C3N-01489_N A A c.2272T>A p.Phe758Ile p.F758I ENST00000545399 16/23 289 255 34 382 382 0 strelka-varscan-mutect ATP1A3,missense_variant,p.Phe758Ile,ENST00000545399,NM_001256214.1;ATP1A3,missense_variant,p.Phe745Ile,ENST00000302102,NM_152296.4;ATP1A3,missense_variant,p.Phe715Ile,ENST00000602133,;ATP1A3,missense_variant,p.Phe756Ile,ENST00000543770,NM_001256213.1;ATP1A3,missense_variant,p.Phe745Ile,ENST00000441343,; T ENST00000545399 Transcript missense_variant 2456/3618 2272/3081 758/1026 F/I Ttt/Att 1 -1 ATP1A3 HGNC HGNC:801 protein_coding YES CCDS58664.1 ENSP00000444688 P13637 UPI0001914BDE NM_001256214.1 deleterious(0) 16/23 Gene3D:1.20.1110.10,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01106,TIGRFAM_domain:TIGR01494 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 41975659 41975659 A T 1 0 0 0 0 1 0 0 0 1282 72 3 4 4 ATP1A3 19 41975659 Missense_Mutation SNP A C3N-01489_T 291740 41975659 16641957 623 25553 PSG3 0 . GRCh38 19 42729863 42729863 + Silent SNP C C T rs764331640 C3N-01489_T C3N-01489_N C C c.903G>A p.= p.T301T ENST00000327495 4/7 215 189 26 305 305 0 varscan-mutect PSG3,synonymous_variant,p.=,ENST00000327495,NM_021016.3;PSG3,synonymous_variant,p.=,ENST00000595140,;PSG3,synonymous_variant,p.=,ENST00000614582,;PSG3,downstream_gene_variant,,ENST00000490592,;PSG3,3_prime_UTR_variant,,ENST00000594378,;PSG3,downstream_gene_variant,,ENST00000597009,; T ENST00000327495 Transcript synonymous_variant 1088/1961 903/1287 301/428 T acG/acA rs764331640,COSM3534867 1 -1 PSG3 HGNC HGNC:9520 protein_coding YES CCDS12611.1 ENSP00000332215 Q16557 UPI0000073DC1 NM_021016.3 4/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF669,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 0,1 LOW 1 SNV 1 0,1 1 PASS rs764331640 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 42729863 42729863 C T 1 0 0 0 0 0 0 0 1 12807 871 31 1 1 PSG3 19 42729863 Silent SNP C C3N-01489_T 754204 42729863 15887753 624 25554 PSG8 0 . GRCh38 19 42755263 42755263 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.713A>T p.Lys238Met p.K238M ENST00000306511 4/5 86 76 10 159 159 0 varscan-mutect PSG8,missense_variant,p.Lys238Met,ENST00000404209,NM_001130167.1;PSG8,missense_variant,p.Lys145Met,ENST00000401467,;PSG8,missense_variant,p.Lys116Met,ENST00000406636,NM_001130168.1;PSG8,missense_variant,p.Lys238Met,ENST00000306511,NM_182707.2;PSG8,non_coding_transcript_exon_variant,,ENST00000469260,;PSG8,intron_variant,,ENST00000600709,;PSG8,3_prime_UTR_variant,,ENST00000478387,;PSG8,non_coding_transcript_exon_variant,,ENST00000466163,; A ENST00000306511 Transcript missense_variant 811/1441 713/1281 238/426 K/M aAg/aTg 1 -1 PSG8 HGNC HGNC:9525 protein_coding YES CCDS33037.1 ENSP00000305005 Q9UQ74 UPI0000071471 NM_182707.2 deleterious(0.03) 4/5 hmmpanther:PTHR10489 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 42755263 42755263 T A 1 0 0 0 0 1 0 0 0 12812 1623 56 4 4 PSG8 19 42755263 Missense_Mutation SNP T C3N-01489_T 25400 42755263 15862353 625 25555 TEX101 0 . GRCh38 19 43418374 43418374 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.781C>A p.Pro261Thr p.P261T ENST00000602198 8/8 101 90 11 162 162 0 strelka-varscan-mutect TEX101,missense_variant,p.Pro261Thr,ENST00000602198,NM_031451.4;TEX101,missense_variant,p.Pro243Thr,ENST00000598265,NM_001130011.1;TEX101,non_coding_transcript_exon_variant,,ENST00000601707,; A ENST00000602198 Transcript missense_variant 1223/1446 781/804 261/267 P/T Cca/Aca COSM3371347 1 1 TEX101 HGNC HGNC:30722 protein_coding YES CCDS12619.1 ENSP00000472308 Q9BY14 A0A024R0T7 UPI000013CDD3 NM_031451.4 tolerated(0.59) 8/8 hmmpanther:PTHR16529,hmmpanther:PTHR16529:SF3,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99949 1 1 1 1 0 A 3 1 81 43418374 43418374 C A 1 0 0 0 0 1 0 0 0 16194 739 26 2 2 TEX101 19 43418374 Missense_Mutation SNP C C3N-01489_T 663111 43418374 15199242 626 25556 CEACAM20 0 . GRCh38 19 44525207 44525207 + Silent SNP G G C novel C3N-01489_T C3N-01489_N G G c.90C>G p.= p.A30A ENST00000614924 2/12 95 87 8 143 143 0 strelka-mutect CEACAM20,synonymous_variant,p.=,ENST00000621342,;CEACAM20,synonymous_variant,p.=,ENST00000617951,;CEACAM20,synonymous_variant,p.=,ENST00000614924,NM_001102597.2;CEACAM20,synonymous_variant,p.=,ENST00000611497,NM_001102600.2;CEACAM20,synonymous_variant,p.=,ENST00000614577,NM_001102599.2;CEACAM20,synonymous_variant,p.=,ENST00000620096,NM_001102598.2; C ENST00000614924 Transcript synonymous_variant 106/1809 90/1791 30/596 A gcC/gcG 1 -1 CEACAM20 HGNC HGNC:24879 protein_coding YES CCDS74393.1 ENSP00000481937 A0A087WYM6 UPI0003EC04B5 NM_001102597.2 2/12 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 81 44525207 44525207 G C 1 0 0 0 0 0 0 0 1 2897 1219 43 4 4 CEACAM20 19 44525207 Silent SNP G C3N-01489_T 1106833 44525207 14092409 627 25557 C5AR1 0 . GRCh38 19 47320626 47320626 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.849C>T p.= p.S283S ENST00000355085 2/2 117 101 16 191 191 0 strelka-varscan-mutect C5AR1,synonymous_variant,p.=,ENST00000355085,NM_001736.3;C5AR1,downstream_gene_variant,,ENST00000594787,; T ENST00000355085 Transcript synonymous_variant 871/2311 849/1053 283/350 S tcC/tcT 1 1 C5AR1 HGNC HGNC:1338 protein_coding YES CCDS33063.1 ENSP00000347197 P21730 UPI0000202756 NM_001736.3 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24225:SF29,hmmpanther:PTHR24225,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 47320626 47320626 C T 1 0 0 0 0 0 0 0 1 2092 610 22 3 3 C5AR1 19 47320626 Silent SNP C C3N-01489_T 2795419 47320626 11296990 628 25558 PRR12 0 . GRCh38 19 49596646 49596646 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.2311G>T p.Ala771Ser p.A771S ENST00000418929 4/14 112 96 16 154 154 0 strelka-varscan-mutect PRR12,missense_variant,p.Ala771Ser,ENST00000418929,NM_020719.1;PRR12,intron_variant,,ENST00000615927,; T ENST00000418929 Transcript missense_variant 2323/6955 2311/6111 771/2036 A/S Gcc/Tcc 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 tolerated(0.68) 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 49596646 49596646 G T 1 0 0 0 0 1 0 0 0 12719 1203 42 2 2 PRR12 19 49596646 Missense_Mutation SNP G C3N-01489_T 2276020 49596646 9020970 629 25559 MYBPC2 0 . GRCh38 19 50455619 50455619 + Nonsense_Mutation SNP C C G novel C3N-01489_T C3N-01489_N C C c.2313C>G p.Tyr771Ter p.Y771* ENST00000357701 20/28 99 91 8 120 120 0 strelka-varscan-mutect MYBPC2,stop_gained,p.Tyr771Ter,ENST00000357701,NM_004533.3; G ENST00000357701 Transcript stop_gained 2364/3593 2313/3426 771/1141 Y/* taC/taG 1 1 MYBPC2 HGNC HGNC:7550 protein_coding YES CCDS46152.1 ENSP00000350332 Q14324 A0A140VJQ0 UPI000013C628 NM_004533.3 20/28 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 200 8 0 0 0 0 0 -16.17537 0.9999922 1 1 1 0 G 4 3 81 50455619 50455619 C G 1 0 0 0 0 0 1 0 0 10012 518 18 4 4 MYBPC2 19 50455619 Nonsense_Mutation SNP C C3N-01489_T 858973 50455619 8161997 630 25560 SHANK1 0 . GRCh38 19 50716781 50716781 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.139G>T p.Ala47Ser p.A47S ENST00000293441 1/23 71 54 17 81 81 0 strelka-varscan-mutect SHANK1,missense_variant,p.Ala47Ser,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Ala47Ser,ENST00000391814,;SHANK1,missense_variant,p.Ala47Ser,ENST00000359082,;SHANK1,upstream_gene_variant,,ENST00000483128,; A ENST00000293441 Transcript missense_variant 158/6643 139/6486 47/2161 A/S Gca/Tca 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 tolerated(0.07) 1/23 MODERATE 1 SNV 1 1 PASS rs1162796795 . 0 199 10 0 0 0 0 0 -20 0.999993 1 1 1 0 A 3 1 81 50716781 50716781 C A 1 0 0 0 0 1 0 0 0 14523 739 26 2 2 SHANK1 19 50716781 Missense_Mutation SNP C C3N-01489_T 261162 50716781 7900835 631 25561 CD33 0 . GRCh38 19 51225352 51225352 + Missense_Mutation SNP G G T rs150461675 C3N-01489_T C3N-01489_N G G c.172G>T p.Gly58Cys p.G58C ENST00000262262 2/7 162 153 9 242 241 1 varscan-mutect CD33,missense_variant,p.Gly58Cys,ENST00000262262,NM_001772.3;CD33,missense_variant,p.Gly58Cys,ENST00000391796,NM_001177608.1;CD33,intron_variant,,ENST00000436584,;CD33,intron_variant,,ENST00000421133,NM_001082618.1;CD33,non_coding_transcript_exon_variant,,ENST00000601785,;CD33,upstream_gene_variant,,ENST00000598473,; T ENST00000262262 Transcript missense_variant 193/1444 172/1095 58/364 G/C Ggt/Tgt rs150461675 1 1 CD33 HGNC HGNC:1659 protein_coding YES CCDS33084.1 ENSP00000262262 P20138 Q546G0 UPI000013D285 NM_001772.3 deleterious(0.04) 2/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF52,hmmpanther:PTHR12035,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs150461675 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 51225352 51225352 G T 1 0 0 0 0 1 0 0 0 2709 1348 47 2 2 CD33 19 51225352 Missense_Mutation SNP G C3N-01489_T 508571 51225352 7392264 632 25562 ZNF649 0 . GRCh38 19 51890764 51890764 + Missense_Mutation SNP C C A rs557320893 C3N-01489_T C3N-01489_N C C c.1372G>T p.Gly458Trp p.G458W ENST00000354957 5/5 268 234 34 418 417 1 strelka-varscan-mutect ZNF649,missense_variant,p.Gly458Trp,ENST00000354957,NM_023074.3;ZNF649,missense_variant,p.Gly430Trp,ENST00000600738,;ZNF577,upstream_gene_variant,,ENST00000301399,NM_032679.2;ZNF649-AS1,intron_variant,,ENST00000600329,; A ENST00000354957 Transcript missense_variant 1657/3197 1372/1518 458/505 G/W Ggg/Tgg rs557320893 1 -1 ZNF649 HGNC HGNC:25741 protein_coding YES CCDS12843.1 ENSP00000347043 Q9BS31 UPI000006D442 NM_023074.3 tolerated(0.18) 5/5 MODERATE 1 SNV 1 1 PASS rs557320893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 51890764 51890764 C A 1 0 0 0 0 1 0 0 0 18637 623 22 2 2 ZNF649 19 51890764 Missense_Mutation SNP C C3N-01489_T 665412 51890764 6726852 633 25563 ZNF534 0 . GRCh38 19 52438622 52438622 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1201G>T p.Gly401Cys p.G401C ENST00000332323 4/4 72 66 6 122 121 1 strelka-varscan-mutect ZNF534,missense_variant,p.Gly401Cys,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Gly388Cys,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; T ENST00000332323 Transcript missense_variant 1262/2086 1201/2025 401/674 G/C Ggc/Tgc 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -13.83426 1 1 1 1 0 T 3 4 81 52438622 52438622 G T 1 0 0 0 0 1 0 0 0 18546 1348 47 2 2 ZNF534 19 52438622 Missense_Mutation SNP G C3N-01489_T 547858 52438622 6178994 634 25564 ZNF808 0 . GRCh38 19 52553106 52553106 + Splice_Site SNP G G T novel C3N-01489_T C3N-01489_N G G c.191-1G>T p.X64_splice ENST00000359798 40 35 5 54 54 0 strelka-varscan-mutect ZNF808,splice_acceptor_variant,,ENST00000359798,NM_001321424.1,NM_001039886.3;ZNF808,splice_acceptor_variant,,ENST00000465448,;ZNF808,splice_acceptor_variant,,ENST00000461321,;ZNF808,splice_acceptor_variant,,ENST00000461779,;ZNF808,splice_acceptor_variant,,ENST00000486474,;ZNF808,upstream_gene_variant,,ENST00000611267,;ZNF701,upstream_gene_variant,,ENST00000478039,;ZNF808,splice_acceptor_variant,,ENST00000487863,; T ENST00000359798 Transcript splice_acceptor_variant -/3600 191/2712 64/903 1 1 ZNF808 HGNC HGNC:33230 protein_coding YES CCDS46167.1 ENSP00000352846 Q8N4W9 UPI000041AA80 NM_001321424.1,NM_001039886.3 4/4 HIGH 1 SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -13.20526 1 1 1 1 0 T 5 4 81 52553106 52553106 G T 1 0 0 0 0 0 0 1 0 18758 956 33 2 2 ZNF808 19 52553106 Splice_Site SNP G C3N-01489_T 114484 52553106 6064510 635 25565 ERVV-1 0 . GRCh38 19 53014827 53014827 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.737G>T p.Arg246Leu p.R246L ENST00000602168 1/1 209 192 17 324 324 0 varscan-mutect ERVV-1,missense_variant,p.Arg246Leu,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; T ENST00000602168 Transcript missense_variant 907/2202 737/1434 246/477 R/L cGg/cTg 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 deleterious(0.02) 1/1 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424 MODERATE SNV 1 PASS rs903188416 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 53014827 53014827 G T 1 0 0 0 0 1 0 0 0 5106 1116 39 1 1 ERVV-1 19 53014827 Missense_Mutation SNP G C3N-01489_T 461721 53014827 5602789 636 25566 ZNF415 0 . GRCh38 19 53109465 53109465 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.580G>T p.Gly194Trp p.G194W ENST00000500065 4/4 136 119 17 241 241 0 strelka-varscan-mutect ZNF415,missense_variant,p.Gly194Trp,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Gly194Trp,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Gly194Trp,ENST00000243643,NM_018355.3;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,5_prime_UTR_variant,,ENST00000601493,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; A ENST00000500065 Transcript missense_variant 914/2496 580/1668 194/555 G/W Ggg/Tgg 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 deleterious(0.01) 4/4 hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 53109465 53109465 C A 1 0 0 0 0 1 0 0 0 18464 594 21 2 2 ZNF415 19 53109465 Missense_Mutation SNP C C3N-01489_T 94638 53109465 5508151 637 25567 ZNF677 0 . GRCh38 19 53238146 53238146 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.581G>T p.Ser194Ile p.S194I ENST00000598513 5/5 106 92 14 163 163 0 strelka-varscan-mutect ZNF677,missense_variant,p.Ser194Ile,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,missense_variant,p.Ser194Ile,ENST00000333952,;ZNF677,downstream_gene_variant,,ENST00000594681,;ZNF677,downstream_gene_variant,,ENST00000599012,;ZNF677,downstream_gene_variant,,ENST00000598806,;ZNF677,downstream_gene_variant,,ENST00000594517,;CTD-2245F17.6,upstream_gene_variant,,ENST00000596041,;ZNF677,downstream_gene_variant,,ENST00000599328,;ZNF677,downstream_gene_variant,,ENST00000593539,; A ENST00000598513 Transcript missense_variant 732/3497 581/1755 194/584 S/I aGc/aTc 1 -1 ZNF677 HGNC HGNC:28730 protein_coding YES CCDS12861.1 ENSP00000469391 Q86XU0 UPI000017DF85 NM_001317998.1,NM_182609.2 deleterious(0) 5/5 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF38 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 53238146 53238146 C A 1 0 0 0 0 1 0 0 0 18657 797 28 2 2 ZNF677 19 53238146 Missense_Mutation SNP C C3N-01489_T 128681 53238146 5379470 638 25568 MYADM 0 . GRCh38 19 53874047 53874047 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.518C>A p.Pro173His p.P173H ENST00000391769 3/3 246 214 32 381 381 0 strelka-varscan-mutect MYADM,missense_variant,p.Pro173His,ENST00000391769,NM_001290193.1,NM_001290190.1,NM_001020821.2,NM_001290189.1,NM_001020818.2;MYADM,missense_variant,p.Pro173His,ENST00000391771,NM_001020819.2;MYADM,missense_variant,p.Pro173His,ENST00000391770,NM_001290194.1,NM_001290192.1,NM_138373.4,NM_001290191.1;MYADM,missense_variant,p.Pro173His,ENST00000336967,NM_001020820.2,NM_001290188.1;MYADM,missense_variant,p.Pro173His,ENST00000391768,;MYADM,missense_variant,p.Pro173His,ENST00000421337,;MYADM,missense_variant,p.Pro173His,ENST00000439000,;MYADM,missense_variant,p.Pro173His,ENST00000448420,;MYADM,downstream_gene_variant,,ENST00000414489,;AC008753.6,upstream_gene_variant,,ENST00000455835,;AC008440.5,downstream_gene_variant,,ENST00000413496,; A ENST00000391769 Transcript missense_variant 798/3186 518/969 173/322 P/H cCc/cAc 1 1 MYADM HGNC HGNC:7544 protein_coding YES CCDS12866.1 ENSP00000375649 Q96S97 A0A024R4N0 UPI0000001BEF NM_001290193.1,NM_001290190.1,NM_001020821.2,NM_001290189.1,NM_001020818.2 tolerated(0.08) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS51225,hmmpanther:PTHR17068,hmmpanther:PTHR17068:SF3,Pfam_domain:PF01284 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 53874047 53874047 C A 1 0 0 0 0 1 0 0 0 10005 623 22 2 2 MYADM 19 53874047 Missense_Mutation SNP C C3N-01489_T 635901 53874047 4743569 639 25569 CACNG6 0 . GRCh38 19 53993193 53993193 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.316G>C p.Ala106Pro p.A106P ENST00000252729 1/4 185 157 28 208 208 0 strelka-varscan-mutect CACNG6,missense_variant,p.Ala106Pro,ENST00000252729,NM_145814.1;CACNG6,missense_variant,p.Ala106Pro,ENST00000352529,NM_031897.2;CACNG6,missense_variant,p.Ala106Pro,ENST00000346968,NM_145815.1;CACNG8,downstream_gene_variant,,ENST00000270458,NM_031895.5; C ENST00000252729 Transcript missense_variant 906/1853 316/783 106/260 A/P Gcg/Ccg 1 1 CACNG6 HGNC HGNC:13625 protein_coding YES CCDS12870.1 ENSP00000252729 Q9BXT2 UPI0000001276 NM_145814.1 deleterious(0.02) 1/4 Pfam_domain:PF13903,Prints_domain:PR01794,hmmpanther:PTHR15025,hmmpanther:PTHR15025:SF6 MODERATE 1 SNV 1 1 PASS rs1235805731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 53993193 53993193 G C 1 0 0 0 0 1 0 0 0 2249 1087 38 4 4 CACNG6 19 53993193 Missense_Mutation SNP G C3N-01489_T 119146 53993193 4624423 640 25570 MBOAT7 0 . GRCh38 19 54188326 54188326 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.97G>A p.Gly33Arg p.G33R ENST00000245615 3/8 132 120 12 172 172 0 strelka-varscan-mutect MBOAT7,missense_variant,p.Gly33Arg,ENST00000245615,NM_024298.4;MBOAT7,missense_variant,p.Gly2Glu,ENST00000431666,NM_001146083.2;MBOAT7,missense_variant,p.Gly2Glu,ENST00000338624,NM_001146056.2;MBOAT7,missense_variant,p.Gly33Arg,ENST00000391754,NM_001146082.2;MBOAT7,missense_variant,p.Gly33Arg,ENST00000414665,;MBOAT7,missense_variant,p.Gly33Arg,ENST00000453320,;TSEN34,upstream_gene_variant,,ENST00000302937,NM_024075.4;TSEN34,upstream_gene_variant,,ENST00000429671,NM_001282333.1;MBOAT7,upstream_gene_variant,,ENST00000495279,;TSEN34,upstream_gene_variant,,ENST00000396383,NM_001282332.1;TSEN34,upstream_gene_variant,,ENST00000396388,NM_001077446.3;TSEN34,upstream_gene_variant,,ENST00000455798,;TSEN34,upstream_gene_variant,,ENST00000456872,;MBOAT7,upstream_gene_variant,,ENST00000449249,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000474910,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000495968,;MBOAT7,missense_variant,p.Gly33Arg,ENST00000437868,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000491216,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000464098,;TSEN34,upstream_gene_variant,,ENST00000496583,; T ENST00000245615 Transcript missense_variant 578/2529 97/1419 33/472 G/R Gga/Aga 1 -1 MBOAT7 HGNC HGNC:15505 protein_coding YES CCDS12883.1 ENSP00000245615 Q96N66 UPI000013CBAC NM_024298.4 tolerated(0.05) 3/8 hmmpanther:PTHR13906:SF16,hmmpanther:PTHR13906 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 54188326 54188326 C T 1 0 0 0 0 1 0 0 0 9291 632 22 3 3 MBOAT7 19 54188326 Missense_Mutation SNP C C3N-01489_T 195133 54188326 4429290 641 25571 LILRB2 0 . GRCh38 19 54274713 54274713 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.1767C>A p.= p.P589P ENST00000391749 14/14 264 229 35 372 372 0 strelka-varscan-mutect LILRB2,synonymous_variant,p.=,ENST00000391748,NM_001278403.2;LILRB2,synonymous_variant,p.=,ENST00000434421,NM_001278404.2;LILRB2,synonymous_variant,p.=,ENST00000314446,NM_001080978.3;LILRB2,synonymous_variant,p.=,ENST00000391749,NM_005874.4;LILRB2,3_prime_UTR_variant,,ENST00000391746,NM_001278405.2;LILRB2,3_prime_UTR_variant,,ENST00000455108,;LILRB2,non_coding_transcript_exon_variant,,ENST00000493242,; T ENST00000391749 Transcript synonymous_variant 2039/2286 1767/1797 589/598 P ccC/ccA 1 -1 LILRB2 HGNC HGNC:6606 protein_coding YES CCDS12886.1 ENSP00000375629 Q8N423 UPI00034F23A2 NM_005874.4 14/14 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 54274713 54274713 G T 1 0 0 0 0 0 0 0 1 8699 1335 47 2 2 LILRB2 19 54274713 Silent SNP G C3N-01489_T 86387 54274713 4342903 642 25572 LILRA2 0 . GRCh38 19 54575460 54575460 + Missense_Mutation SNP C C A rs560494676 C3N-01489_T C3N-01489_N C C c.860C>A p.Pro287His p.P287H ENST00000251377 6/9 238 210 28 383 383 0 strelka-varscan-mutect LILRA2,missense_variant,p.Pro287His,ENST00000251376,NM_006866.3;LILRA2,missense_variant,p.Pro287His,ENST00000251377,;LILRA2,missense_variant,p.Pro287His,ENST00000391738,NM_001130917.2;LILRA2,missense_variant,p.Pro287His,ENST00000439534,;LILRA2,missense_variant,p.Pro275His,ENST00000391737,NM_001290270.1;LILRA1,intron_variant,,ENST00000618665,;LILRA2,intron_variant,,ENST00000629481,;LILRA2,upstream_gene_variant,,ENST00000472992,;LILRA2,downstream_gene_variant,,ENST00000495786,; A ENST00000251377 Transcript missense_variant 993/1799 860/1452 287/483 P/H cCc/cAc rs560494676,COSM4187744,COSM4187745,COSM5690440,COSM5690441 1 1 LILRA2 HGNC HGNC:6603 protein_coding YES CCDS46179.1 ENSP00000251377 Q8N149 UPI00034F238E tolerated(0.5) 6/9 PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,Gene3D:2.60.40.10,PIRSF_domain:PIRSF001979,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 0,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1 1 PASS rs560494676 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 54575460 54575460 C A 1 0 0 0 0 1 0 0 0 8694 623 22 2 2 LILRA2 19 54575460 Missense_Mutation SNP C C3N-01489_T 300747 54575460 4042156 643 25573 KIR3DL2 0 . GRCh38 19 54853878 54853878 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.487G>T p.Asp163Tyr p.D163Y ENST00000326321 4/9 582 512 70 866 866 0 strelka-varscan-mutect KIR3DL2,missense_variant,p.Asp163Tyr,ENST00000326321,NM_006737.3;KIR3DL2,missense_variant,p.Asp163Tyr,ENST00000270442,NM_001242867.1;KIR3DL1,intron_variant,,ENST00000402254,; T ENST00000326321 Transcript missense_variant 520/1877 487/1368 163/455 D/Y Gac/Tac 1 1 KIR3DL2 HGNC HGNC:6339 protein_coding YES CCDS12906.1 ENSP00000325525 P43630 A0A0U1WNF3 UPI000012DB25 NM_006737.3 tolerated(0.09) 4/9 Gene3D:2.60.40.10,Pfam_domain:PF00047,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF121,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 54853878 54853878 G T 1 0 0 0 0 1 0 0 0 8185 1174 41 2 2 KIR3DL2 19 54853878 Missense_Mutation SNP G C3N-01489_T 278418 54853878 3763738 644 25574 FCAR 0 . GRCh38 19 54889796 54889796 + Missense_Mutation SNP C C A rs61735070 C3N-01489_T C3N-01489_N C C c.797C>A p.Pro266Gln p.P266Q ENST00000355524 5/5 253 224 29 286 285 1 strelka-varscan-mutect FCAR,missense_variant,p.Pro266Gln,ENST00000355524,NM_002000.3;FCAR,missense_variant,p.Pro244Gln,ENST00000391725,NM_133269.3;FCAR,missense_variant,p.Pro254Gln,ENST00000359272,NM_133272.3;FCAR,missense_variant,p.Pro232Gln,ENST00000391724,NM_133278.3;FCAR,missense_variant,p.Pro158Gln,ENST00000391726,NM_133273.3;FCAR,missense_variant,p.Pro170Gln,ENST00000345937,NM_133271.3;FCAR,missense_variant,p.Pro157Gln,ENST00000353758,NM_133277.3;FCAR,3_prime_UTR_variant,,ENST00000391723,NM_133274.3;FCAR,downstream_gene_variant,,ENST00000469767,;CTB-61M7.2,upstream_gene_variant,,ENST00000594721,;FCAR,non_coding_transcript_exon_variant,,ENST00000482092,;FCAR,non_coding_transcript_exon_variant,,ENST00000471750,;FCAR,non_coding_transcript_exon_variant,,ENST00000472634,;FCAR,downstream_gene_variant,,ENST00000488066,; A ENST00000355524 Transcript missense_variant 807/1483 797/864 266/287 P/Q cCg/cAg rs61735070 1 1 FCAR HGNC HGNC:3608 protein_coding YES CCDS12907.1 ENSP00000347714 P24071 UPI000011B429 NM_002000.3 tolerated(0.68) 5/5 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF4 MODERATE 1 SNV 1 1 PASS rs61735070 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 54889796 54889796 C A 1 0 0 0 0 1 0 0 0 5636 652 23 1 1 FCAR 19 54889796 Missense_Mutation SNP C C3N-01489_T 35918 54889796 3727820 645 25575 NLRP7 0 . GRCh38 19 54940383 54940383 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.436T>C p.Phe146Leu p.F146L ENST00000588756 6/13 348 312 36 567 566 1 strelka-varscan-mutect NLRP7,missense_variant,p.Phe146Leu,ENST00000588756,;NLRP7,missense_variant,p.Phe146Leu,ENST00000328092,NM_139176.3;NLRP7,missense_variant,p.Phe146Leu,ENST00000592784,NM_001127255.1;NLRP7,missense_variant,p.Phe146Leu,ENST00000340844,NM_206828.3;NLRP7,missense_variant,p.Phe146Leu,ENST00000590030,;NLRP7,downstream_gene_variant,,ENST00000590659,;NLRP7,downstream_gene_variant,,ENST00000587103,;NLRP7,downstream_gene_variant,,ENST00000587844,;NLRP7,missense_variant,p.Phe146Leu,ENST00000586379,; G ENST00000588756 Transcript missense_variant 923/3826 436/3114 146/1037 F/L Ttc/Ctc 1 -1 NLRP7 HGNC HGNC:22947 protein_coding YES CCDS46183.1 ENSP00000467123 Q8WX94 UPI000174C6C4 tolerated(0.41) 6/13 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 54940383 54940383 A G 1 0 0 0 0 1 0 0 0 10520 14 1 5 5 NLRP7 19 54940383 Missense_Mutation SNP A C3N-01489_T 50587 54940383 3677233 646 25576 PTPRH 0 . GRCh38 19 55197344 55197344 + Frame_Shift_Del DEL G G - C3N-01489_T C3N-01489_N G G c.1763delC p.Pro588LeufsTer65 p.P588Lfs*65 ENST00000376350 9/20 156 137 19 249 248 1 sindel-varindel-pindel PTPRH,frameshift_variant,p.Pro588LeufsTer65,ENST00000376350,NM_002842.4;PTPRH,frameshift_variant,p.Pro410LeufsTer65,ENST00000263434,NM_001161440.2;PTPRH,non_coding_transcript_exon_variant,,ENST00000588559,; - ENST00000376350 Transcript frameshift_variant 1786/3877 1763/3348 588/1115 P/X cCt/ct COSM714656 1 -1 PTPRH HGNC HGNC:9672 protein_coding YES CCDS33110.1 ENSP00000365528 Q9HD43 UPI000052D443 NM_002842.4 9/20 PROSITE_profiles:PS50853,hmmpanther:PTHR19134:SF297,hmmpanther:PTHR19134,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 1 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 81 55197344 55197344 G - 1 0 1 0 1 0 0 0 0 12957 1000 35 0 0 PTPRH 19 55197344 Frame_Shift_Del DEL G C3N-01489_T 256961 55197344 3420272 647 25577 BRSK1 0 . GRCh38 19 55306390 55306390 + Missense_Mutation SNP C C A C3N-01489_T C3N-01489_N C C c.2029C>A p.Pro677Thr p.P677T ENST00000309383 17/19 388 351 37 438 438 0 strelka-varscan-mutect BRSK1,missense_variant,p.Pro677Thr,ENST00000309383,NM_032430.1;BRSK1,missense_variant,p.Pro693Thr,ENST00000590333,;BRSK1,missense_variant,p.Pro372Thr,ENST00000326848,;BRSK1,downstream_gene_variant,,ENST00000585418,;BRSK1,downstream_gene_variant,,ENST00000591774,;BRSK1,downstream_gene_variant,,ENST00000588584,;BRSK1,downstream_gene_variant,,ENST00000586626,; A ENST00000309383 Transcript missense_variant 2306/3079 2029/2337 677/778 P/T Ccg/Acg COSM5527426 1 1 BRSK1 HGNC HGNC:18994 protein_coding YES CCDS12921.1 ENSP00000310649 Q8TDC3 UPI0000070495 NM_032430.1 tolerated(0.57) 17/19 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 55306390 55306390 C A 1 0 0 0 0 1 0 0 0 1697 623 22 2 2 BRSK1 19 55306390 Missense_Mutation SNP C C3N-01489_T 109046 55306390 3311226 648 25578 TMEM150B 0 . GRCh38 19 55316851 55316851 + Missense_Mutation SNP C C A rs772056212 C3N-01489_T C3N-01489_N C C c.440G>T p.Gly147Val p.G147V ENST00000326652 7/8 76 69 7 141 141 0 strelka-varscan-mutect TMEM150B,missense_variant,p.Gly147Val,ENST00000326652,NM_001085488.2,NM_001282011.1;TMEM150B,missense_variant,p.Gly102Val,ENST00000585918,;BRSK1,downstream_gene_variant,,ENST00000309383,NM_032430.1;BRSK1,downstream_gene_variant,,ENST00000590333,;BRSK1,downstream_gene_variant,,ENST00000326848,;TMEM150B,downstream_gene_variant,,ENST00000591570,;CTD-2105E13.14,upstream_gene_variant,,ENST00000596786,;TMEM150B,3_prime_UTR_variant,,ENST00000586609,;TMEM150B,3_prime_UTR_variant,,ENST00000592603,;TMEM150B,3_prime_UTR_variant,,ENST00000592731,;TMEM150B,downstream_gene_variant,,ENST00000592891,; A ENST00000326652 Transcript missense_variant 623/943 440/702 147/233 G/V gGg/gTg rs772056212 1 -1 TMEM150B HGNC HGNC:34415 protein_coding YES CCDS42629.1 ENSP00000320757 A6NC51 UPI00001AF4D4 NM_001085488.2,NM_001282011.1 deleterious(0) 7/8 Pfam_domain:PF10277,hmmpanther:PTHR21324,hmmpanther:PTHR21324:SF3 MODERATE 1 SNV 1 1 PASS rs772056212 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 55316851 55316851 C A 1 0 0 0 0 1 0 0 0 16510 623 22 2 2 TMEM150B 19 55316851 Missense_Mutation SNP C C3N-01489_T 10461 55316851 3300765 649 25579 RFPL4A 0 . GRCh38 19 55761921 55761921 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.121G>C p.Glu41Gln p.E41Q ENST00000434937 2/3 103 87 16 180 180 0 varscan-mutect RFPL4A,missense_variant,p.Glu41Gln,ENST00000434937,NM_001145014.1; C ENST00000434937 Transcript missense_variant 292/1035 121/864 41/287 E/Q Gag/Cag 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 deleterious(0.02) 2/3 PROSITE_profiles:PS50089,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,Gene3D:3.30.40.10,Pfam_domain:PF15227,Superfamily_domains:SSF57850 MODERATE 1 SNV 5 1 PASS rs1344878786 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 55761921 55761921 G C 1 0 0 0 0 1 0 0 0 13428 1175 41 4 4 RFPL4A 19 55761921 Missense_Mutation SNP G C3N-01489_T 445070 55761921 2855695 650 25580 NLRP4 0 . GRCh38 19 55852353 55852353 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.273G>T p.Glu91Asp p.E91D ENST00000301295 2/10 157 137 20 250 250 0 strelka-varscan-mutect NLRP4,missense_variant,p.Glu91Asp,ENST00000301295,NM_134444.4;NLRP4,missense_variant,p.Glu91Asp,ENST00000587464,; T ENST00000301295 Transcript missense_variant 695/3670 273/2985 91/994 E/D gaG/gaT 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 deleterious(0.01) 2/10 PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Gene3D:1.10.533.10,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 55852353 55852353 G T 1 0 0 0 0 1 0 0 0 10517 933 33 2 2 NLRP4 19 55852353 Missense_Mutation SNP G C3N-01489_T 90432 55852353 2765263 651 25581 NLRP8 0 . GRCh38 19 55970686 55970686 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.2524G>C p.Glu842Gln p.E842Q ENST00000291971 6/10 88 79 9 144 144 0 strelka-mutect NLRP8,missense_variant,p.Glu842Gln,ENST00000291971,NM_176811.2;NLRP8,missense_variant,p.Glu842Gln,ENST00000590542,; C ENST00000291971 Transcript missense_variant 2595/3934 2524/3147 842/1048 E/Q Gag/Cag 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 tolerated(0.13) 6/10 hmmpanther:PTHR24106:SF54,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 2 1 PASS rs1417446557 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 55970686 55970686 G C 1 0 0 0 0 1 0 0 0 10521 1175 41 4 4 NLRP8 19 55970686 Missense_Mutation SNP G C3N-01489_T 118333 55970686 2646930 652 25582 AURKC 0 . GRCh38 19 57232586 57232586 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.341G>T p.Arg114Leu p.R114L ENST00000302804 4/7 479 422 57 696 695 1 strelka-varscan-mutect AURKC,missense_variant,p.Arg80Leu,ENST00000448930,;AURKC,missense_variant,p.Arg114Leu,ENST00000302804,NM_001015878.1;AURKC,missense_variant,p.Arg80Leu,ENST00000598785,NM_003160.2;AURKC,missense_variant,p.Arg95Leu,ENST00000415300,NM_001015879.1;AURKC,missense_variant,p.Arg111Leu,ENST00000599062,;AURKC,upstream_gene_variant,,ENST00000594599,;AURKC,missense_variant,p.Arg80Leu,ENST00000596375,;AURKC,3_prime_UTR_variant,,ENST00000601799,; T ENST00000302804 Transcript missense_variant 527/1247 341/930 114/309 R/L cGc/cTc 1 1 AURKC HGNC HGNC:11391 protein_coding YES CCDS33128.1 ENSP00000302898 Q9UQB9 UPI000013610A NM_001015878.1 deleterious(0.02) 4/7 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000654,PROSITE_profiles:PS50011,hmmpanther:PTHR24350,hmmpanther:PTHR24350:SF3,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1051922045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 57232586 57232586 G T 1 0 0 0 0 1 0 0 0 1380 1087 38 1 1 AURKC 19 57232586 Missense_Mutation SNP G C3N-01489_T 1261900 57232586 1385030 653 25583 ZSCAN4 0 . GRCh38 19 57676533 57676533 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.388C>A p.Pro130Thr p.P130T ENST00000318203 3/5 52 45 7 82 82 0 strelka-varscan-mutect ZSCAN4,missense_variant,p.Pro130Thr,ENST00000318203,NM_152677.2;ZSCAN4,missense_variant,p.Pro130Thr,ENST00000612521,; A ENST00000318203 Transcript missense_variant 1085/2246 388/1302 130/433 P/T Cct/Act 1 1 ZSCAN4 HGNC HGNC:23709 protein_coding YES CCDS12958.1 ENSP00000321963 Q8NAM6 UPI000006E923 NM_152677.2 deleterious(0) 3/5 hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF45,SMART_domains:SM00431 MODERATE 1 SNV 2 1 PASS . . 0 199 10 0 0 0 0 0 -16.3919 0.9999779 1 1 1 0 A 3 1 81 57676533 57676533 C A 1 0 0 0 0 1 0 0 0 18836 507 18 2 2 ZSCAN4 19 57676533 Missense_Mutation SNP C C3N-01489_T 443947 57676533 941083 654 25584 ZNF274 0 . GRCh38 19 58206803 58206803 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.340C>T p.Leu114Phe p.L114F ENST00000610905 5/8 209 179 30 328 327 1 strelka-mutect ZNF274,missense_variant,p.Leu82Phe,ENST00000345813,NM_016325.3;ZNF274,missense_variant,p.Leu114Phe,ENST00000610905,;ZNF274,missense_variant,p.Leu9Phe,ENST00000424679,NM_016324.3;ZNF274,missense_variant,p.Leu114Phe,ENST00000617501,NM_133502.2;ZNF274,missense_variant,p.Leu72Phe,ENST00000326804,NM_001278734.1;ZNF274,missense_variant,p.Leu9Phe,ENST00000594839,;ZNF274,downstream_gene_variant,,ENST00000601995,;ZNF274,non_coding_transcript_exon_variant,,ENST00000621145,;ZNF274,non_coding_transcript_exon_variant,,ENST00000619307,;ZNF274,non_coding_transcript_exon_variant,,ENST00000615675,;ZNF274,upstream_gene_variant,,ENST00000595146,; T ENST00000610905 Transcript missense_variant 528/2559 340/1962 114/653 L/F Ctc/Ttc 1 1 ZNF274 HGNC HGNC:13068 protein_coding YES CCDS74473.1 ENSP00000478533 Q96GC6 UPI0000161F3D deleterious(0) 5/8 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 58206803 58206803 C T 1 0 0 0 0 1 0 0 0 18385 681 24 3 3 ZNF274 19 58206803 Missense_Mutation SNP C C3N-01489_T 530270 58206803 410813 655 25585 SIRPA 0 . GRCh38 20 1924806 1924806 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1130G>T p.Gly377Val p.G377V ENST00000400068 6/9 270 243 27 391 391 0 strelka-varscan-mutect SIRPA,missense_variant,p.Gly377Val,ENST00000622179,;SIRPA,missense_variant,p.Gly377Val,ENST00000400068,NM_001040022.1;SIRPA,missense_variant,p.Gly377Val,ENST00000358771,NM_001040023.1;SIRPA,missense_variant,p.Gly377Val,ENST00000356025,NM_080792.2; T ENST00000400068 Transcript missense_variant 1490/4201 1130/1515 377/504 G/V gGt/gTt 1 1 SIRPA HGNC HGNC:9662 protein_coding YES CCDS13022.1 ENSP00000382941 P78324 UPI0000073ADE NM_001040022.1 deleterious(0.01) 6/9 Gene3D:2.60.40.10,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 1924806 1924806 G T 1 0 0 0 0 1 0 0 0 14595 1261 44 2 2 SIRPA 20 1924806 Missense_Mutation SNP G C3N-01489_T 1924806 62519361 656 25586 SIRPA 0 . GRCh38 20 1937554 1937554 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.1501G>T p.Val501Phe p.V501F ENST00000400068 9/9 107 100 7 139 139 0 strelka-varscan-mutect SIRPA,missense_variant,p.Val505Phe,ENST00000622179,;SIRPA,missense_variant,p.Val501Phe,ENST00000400068,NM_001040022.1;SIRPA,missense_variant,p.Val501Phe,ENST00000358771,NM_001040023.1;SIRPA,missense_variant,p.Val501Phe,ENST00000356025,NM_080792.2; T ENST00000400068 Transcript missense_variant 1861/4201 1501/1515 501/504 V/F Gtc/Ttc 1 1 SIRPA HGNC HGNC:9662 protein_coding YES CCDS13022.1 ENSP00000382941 P78324 UPI0000073ADE NM_001040022.1 deleterious(0) 9/9 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.51321 1 1 1 1 0 T 3 4 81 1937554 1937554 G T 1 0 0 0 0 1 0 0 0 14595 1261 44 2 2 SIRPA 20 1937554 Missense_Mutation SNP G C3N-01489_T 12748 1937554 62506613 657 25587 ADAM33 0 . GRCh38 20 3672186 3672186 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.1545G>T p.Trp515Cys p.W515C ENST00000356518 14/22 95 88 7 145 145 0 strelka-varscan-mutect ADAM33,missense_variant,p.Trp515Cys,ENST00000356518,NM_025220.3;ADAM33,missense_variant,p.Trp515Cys,ENST00000379861,NM_001282447.1;ADAM33,missense_variant,p.Trp515Cys,ENST00000350009,NM_153202.2;ADAM33,missense_variant,p.Trp395Cys,ENST00000619289,;ADAM33,intron_variant,,ENST00000617732,;ADAM33,non_coding_transcript_exon_variant,,ENST00000466620,;ADAM33,upstream_gene_variant,,ENST00000483362,; A ENST00000356518 Transcript missense_variant 1787/3677 1545/2442 515/813 W/C tgG/tgT 1 -1 ADAM33 HGNC HGNC:15478 protein_coding YES CCDS13058.1 ENSP00000348912 Q9BZ11 UPI0000048F2A NM_025220.3 deleterious(0.01) 14/22 hmmpanther:PTHR11905,hmmpanther:PTHR11905:SF38,Pfam_domain:PF08516,SMART_domains:SM00608 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.93261 1 1 1 1 0 A 3 1 81 3672186 3672186 C A 1 0 0 0 0 1 0 0 0 294 624 22 2 2 ADAM33 20 3672186 Missense_Mutation SNP C C3N-01489_T 1734632 3672186 60771981 658 25588 PLCB4 0 . GRCh38 20 9453397 9453397 + Silent SNP G G T C3N-01489_T C3N-01489_N G G c.2895G>T p.= p.V965V ENST00000378501 29/36 203 176 27 287 287 0 strelka-varscan-mutect PLCB4,synonymous_variant,p.=,ENST00000378501,NM_000933.3;PLCB4,synonymous_variant,p.=,ENST00000378493,;PLCB4,synonymous_variant,p.=,ENST00000378473,NM_001172646.1;PLCB4,synonymous_variant,p.=,ENST00000278655,NM_182797.2;PLCB4,synonymous_variant,p.=,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,; T ENST00000378501 Transcript synonymous_variant 2910/5833 2895/3585 965/1194 V gtG/gtT COSM383313 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 29/36 Superfamily_domains:0053448,Gene3D:1jadA00,Coiled-coils_(Ncoils):Coil,PIRSF_domain:PIRSF000956,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 9453397 9453397 G T 1 0 0 0 0 0 0 0 1 12124 1335 47 2 2 PLCB4 20 9453397 Silent SNP G C3N-01489_T 5781211 9453397 54990770 659 25589 CFAP61 0 . GRCh38 20 20263035 20263035 + Missense_Mutation SNP C C A rs780255308 C3N-01489_T C3N-01489_N C C c.2408C>A p.Thr803Lys p.T803K ENST00000245957 21/27 231 198 33 272 271 1 strelka-varscan-mutect CFAP61,missense_variant,p.Thr803Lys,ENST00000245957,NM_015585.3;CFAP61,missense_variant,p.Thr159Lys,ENST00000377293,;CFAP61,missense_variant,p.Thr159Lys,ENST00000389656,;RP5-1096J16.1,intron_variant,,ENST00000460400,;CFAP61,non_coding_transcript_exon_variant,,ENST00000488640,;CFAP61,missense_variant,p.Thr159Lys,ENST00000377308,; A ENST00000245957 Transcript missense_variant 2484/4082 2408/3714 803/1237 T/K aCg/aAg rs780255308,COSM3378986,COSM3378987,COSM4096997,COSM4096998 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 tolerated(0.08) 21/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs780255308 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 20263035 20263035 C A 1 0 0 0 0 1 0 0 0 3028 536 19 1 1 CFAP61 20 20263035 Missense_Mutation SNP C C3N-01489_T 10809638 20263035 44181132 660 25590 VSX1 0 . GRCh38 20 25076473 25076473 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.886C>A p.His296Asn p.H296N ENST00000376709 5/5 250 220 30 371 370 1 strelka-varscan-mutect VSX1,missense_variant,p.His296Asn,ENST00000376709,NM_014588.5;VSX1,intron_variant,,ENST00000429762,NM_001256272.1;VSX1,intron_variant,,ENST00000444511,NM_001256271.1;VSX1,downstream_gene_variant,,ENST00000376707,NM_199425.2;VSX1,non_coding_transcript_exon_variant,,ENST00000557285,;VSX1,intron_variant,,ENST00000409285,;VSX1,intron_variant,,ENST00000409958,; T ENST00000376709 Transcript missense_variant 1155/2192 886/1098 296/365 H/N Cac/Aac 1 -1 VSX1 HGNC HGNC:12723 protein_coding YES CCDS13168.1 ENSP00000365899 Q9NZR4 UPI0000138E43 NM_014588.5 tolerated(0.08) 5/5 hmmpanther:PTHR24323 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 25076473 25076473 G T 1 0 0 0 0 1 0 0 0 17785 1348 47 2 2 VSX1 20 25076473 Missense_Mutation SNP G C3N-01489_T 4813438 25076473 39367694 661 25591 REM1 0 . GRCh38 20 31484415 31484415 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.882T>A p.Asn294Lys p.N294K ENST00000201979 5/5 48 42 6 76 76 0 strelka-varscan-mutect REM1,missense_variant,p.Asn294Lys,ENST00000201979,NM_014012.5;LINC00028,upstream_gene_variant,,ENST00000435497,; A ENST00000201979 Transcript missense_variant 1175/1665 882/897 294/298 N/K aaT/aaA 1 1 REM1 HGNC HGNC:15922 protein_coding YES CCDS13181.1 ENSP00000201979 O75628 UPI0000073CEB NM_014012.5 deleterious(0) 5/5 PIRSF_domain:PIRSF038017,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF260 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.62603 0.9999999 1 1 1 0 A 3 1 81 31484415 31484415 T A 1 0 0 0 0 1 0 0 0 13392 1432 50 4 4 REM1 20 31484415 Missense_Mutation SNP T C3N-01489_T 6407942 31484415 32959752 662 25592 BPIFA3 0 . GRCh38 20 33217620 33217620 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.84C>A p.= p.G28G ENST00000375454 1/7 197 178 19 273 272 1 strelka-varscan-mutect BPIFA3,synonymous_variant,p.=,ENST00000375454,NM_178466.4;BPIFA3,synonymous_variant,p.=,ENST00000375452,NM_001042439.2;RP11-49G10.3,upstream_gene_variant,,ENST00000419613,;BPIFA3,non_coding_transcript_exon_variant,,ENST00000490499,;BPIFA3,non_coding_transcript_exon_variant,,ENST00000471233,; A ENST00000375454 Transcript synonymous_variant 294/1116 84/765 28/254 G ggC/ggA 1 1 BPIFA3 HGNC HGNC:16204 protein_coding YES CCDS13216.2 ENSP00000364603 Q9BQP9 UPI00003E72D6 NM_178466.4 1/7 hmmpanther:PTHR10504:SF85,hmmpanther:PTHR10504 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 33217620 33217620 C A 1 0 0 0 0 0 0 0 1 1656 726 26 2 2 BPIFA3 20 33217620 Silent SNP C C3N-01489_T 1733205 33217620 31226547 663 25593 BPIFA1 0 . GRCh38 20 33240237 33240237 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.433C>A p.Leu145Met p.L145M ENST00000354297 5/9 92 82 10 168 167 1 strelka-varscan-mutect BPIFA1,missense_variant,p.Leu145Met,ENST00000354297,NM_130852.2;BPIFA1,missense_variant,p.Leu145Met,ENST00000375422,NM_001243193.1;BPIFA1,missense_variant,p.Leu145Met,ENST00000375413,NM_016583.3;BPIFA1,missense_variant,p.Leu131Met,ENST00000618484,; A ENST00000354297 Transcript missense_variant 504/1079 433/771 145/256 L/M Ctg/Atg 1 1 BPIFA1 HGNC HGNC:15749 protein_coding YES CCDS13217.1 ENSP00000346251 Q9NP55 UPI0000048F11 NM_130852.2 tolerated(0.07) 5/9 hmmpanther:PTHR10504,hmmpanther:PTHR10504:SF70,Pfam_domain:PF01273,Superfamily_domains:SSF55394 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 33240237 33240237 C A 1 0 0 0 0 1 0 0 0 1654 695 24 2 2 BPIFA1 20 33240237 Missense_Mutation SNP C C3N-01489_T 22617 33240237 31203930 664 25594 C20orf144 0 . GRCh38 20 33663799 33663799 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.394C>T p.Pro132Ser p.P132S ENST00000375222 2/2 53 47 6 107 107 0 strelka-varscan-mutect C20orf144,missense_variant,p.Pro132Ser,ENST00000375222,NM_080825.3;NECAB3,intron_variant,,ENST00000246190,NM_031232.3;NECAB3,intron_variant,,ENST00000375238,NM_031231.3;NECAB3,intron_variant,,ENST00000439478,;NECAB3,intron_variant,,ENST00000606690,;NECAB3,intron_variant,,ENST00000480994,;ACTL10,upstream_gene_variant,,ENST00000330271,NM_001024675.1;NECAB3,intron_variant,,ENST00000494174,;NECAB3,intron_variant,,ENST00000606106,;NECAB3,upstream_gene_variant,,ENST00000606525,;NECAB3,upstream_gene_variant,,ENST00000483813,;NECAB3,upstream_gene_variant,,ENST00000485976,;NECAB3,upstream_gene_variant,,ENST00000478237,;NECAB3,upstream_gene_variant,,ENST00000463246,;NECAB3,upstream_gene_variant,,ENST00000498353,;NECAB3,upstream_gene_variant,,ENST00000477778,;C20orf144,non_coding_transcript_exon_variant,,ENST00000607738,;NECAB3,intron_variant,,ENST00000488489,;NECAB3,intron_variant,,ENST00000485399,;NECAB3,intron_variant,,ENST00000606699,;NECAB3,intron_variant,,ENST00000607805,;NECAB3,intron_variant,,ENST00000493590,; T ENST00000375222 Transcript missense_variant 456/571 394/462 132/153 P/S Ccc/Tcc 1 1 C20orf144 HGNC HGNC:16137 protein_coding YES CCDS13223.1 ENSP00000364370 Q9BQM9 UPI0000128613 NM_080825.3 tolerated_low_confidence(0.66) 2/2 hmmpanther:PTHR37335,hmmpanther:PTHR37335:SF1,Pfam_domain:PF15318 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.31371 0.9999999 1 1 1 0 T 3 4 81 33663799 33663799 C T 1 0 0 0 0 1 0 0 0 2003 855 30 3 3 C20orf144 20 33663799 Missense_Mutation SNP C C3N-01489_T 423562 33663799 30780368 665 25595 SLC32A1 0 . GRCh38 20 38727937 38727937 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.876G>T p.Trp292Cys p.W292C ENST00000217420 2/2 361 315 46 527 527 0 strelka-varscan-mutect SLC32A1,missense_variant,p.Trp292Cys,ENST00000217420,NM_080552.2; T ENST00000217420 Transcript missense_variant 1139/2574 876/1578 292/525 W/C tgG/tgT COSM3963556 1 1 SLC32A1 HGNC HGNC:11018 protein_coding YES CCDS13307.1 ENSP00000217420 Q9H598 UPI0000043423 NM_080552.2 deleterious(0) 2/2 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF221 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 38727937 38727937 G T 1 0 0 0 0 1 0 0 0 14835 1241 43 2 2 SLC32A1 20 38727937 Missense_Mutation SNP G C3N-01489_T 5064138 38727937 25716230 666 25596 PTPRT 0 . GRCh38 20 42106826 42106826 + Missense_Mutation SNP C C A rs182388300 C3N-01489_T C3N-01489_N C C c.3407G>T p.Arg1136Leu p.R1136L ENST00000373198 25/32 162 145 17 229 229 0 strelka-mutect PTPRT,missense_variant,p.Arg1136Leu,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Arg1139Leu,ENST00000373193,;PTPRT,missense_variant,p.Arg1107Leu,ENST00000373201,;PTPRT,missense_variant,p.Arg1116Leu,ENST00000373190,;PTPRT,missense_variant,p.Arg1127Leu,ENST00000373184,;PTPRT,missense_variant,p.Arg1126Leu,ENST00000356100,;PTPRT,missense_variant,p.Arg1117Leu,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Arg735Leu,ENST00000612229,;PTPRT,missense_variant,p.Arg752Leu,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 3643/12746 3407/4383 1136/1460 R/L cGt/cTt rs182388300 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 25/32 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 2 1 PASS rs182388300 . 0 206 0 3 0 0 0 0 -19.99994 0.9999862 1 1 1 0 A 3 1 81 42106826 42106826 C A 1 0 0 0 0 1 0 0 0 12967 536 19 1 1 PTPRT 20 42106826 Missense_Mutation SNP C C3N-01489_T 3378889 42106826 22337341 667 25597 PTPRT 0 . GRCh38 20 42472486 42472486 + Missense_Mutation SNP G G T rs778297716 C3N-01489_T C3N-01489_N G G c.1230C>A p.Phe410Leu p.F410L ENST00000373198 8/32 286 260 26 376 376 0 strelka-varscan-mutect PTPRT,missense_variant,p.Phe410Leu,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Phe410Leu,ENST00000373193,;PTPRT,missense_variant,p.Phe410Leu,ENST00000373201,;PTPRT,missense_variant,p.Phe410Leu,ENST00000373190,;PTPRT,missense_variant,p.Phe410Leu,ENST00000373184,;PTPRT,missense_variant,p.Phe410Leu,ENST00000356100,;PTPRT,missense_variant,p.Phe410Leu,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Phe28Leu,ENST00000612229,;PTPRT,missense_variant,p.Phe26Leu,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript missense_variant 1466/12746 1230/4383 410/1460 F/L ttC/ttA rs778297716 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 tolerated(1) 8/32 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00060,Superfamily_domains:SSF49265,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS rs778297716 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 42472486 42472486 G T 1 0 0 0 0 1 0 0 0 12967 1049 37 1 1 PTPRT 20 42472486 Missense_Mutation SNP G C3N-01489_T 365660 42472486 21971681 668 25598 SEMG2 0 . GRCh38 20 45222590 45222590 + Missense_Mutation SNP G G A rs572541768 C3N-01489_T C3N-01489_N G G c.958G>A p.Glu320Lys p.E320K ENST00000372769 2/3 277 248 29 401 400 1 strelka-varscan-mutect SEMG2,missense_variant,p.Glu320Lys,ENST00000372769,NM_003008.2; A ENST00000372769 Transcript missense_variant 1048/2051 958/1749 320/582 E/K Gag/Aag rs572541768 1 1 SEMG2 HGNC HGNC:10743 protein_coding YES CCDS13346.1 ENSP00000361855 Q02383 UPI0000135845 NM_003008.2 tolerated(0.37) 2/3 Pfam_domain:PF05474,hmmpanther:PTHR10547,hmmpanther:PTHR10547:SF6 MODERATE 1 SNV 1 1 PASS rs572541768 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 45222590 45222590 G A 1 0 0 0 0 1 0 0 0 14321 943 33 3 3 SEMG2 20 45222590 Missense_Mutation SNP G C3N-01489_T 2750104 45222590 19221577 669 25599 ZSWIM3 0 . GRCh38 20 45877739 45877739 + Missense_Mutation SNP G G T C3N-01489_T C3N-01489_N G G c.1181G>T p.Ser394Ile p.S394I ENST00000255152 2/2 103 94 9 208 208 0 strelka-varscan-mutect ZSWIM3,missense_variant,p.Ser394Ile,ENST00000255152,NM_080752.3;ZSWIM1,upstream_gene_variant,,ENST00000372523,NM_080603.4;ZSWIM1,upstream_gene_variant,,ENST00000372520,; T ENST00000255152 Transcript missense_variant 1390/2773 1181/2091 394/696 S/I aGc/aTc COSM3389782,COSM3389783 1 1 ZSWIM3 HGNC HGNC:16157 protein_coding YES CCDS13381.1 ENSP00000255152 Q96MP5 UPI00000736E4 NM_080752.3 deleterious(0) 2/2 hmmpanther:PTHR31569:SF3,hmmpanther:PTHR31569 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 2 0 0 0 0 -13.9447 0.9999998 1 1 1 0 T 3 4 81 45877739 45877739 G T 1 0 0 0 0 1 0 0 0 18843 971 34 2 2 ZSWIM3 20 45877739 Missense_Mutation SNP G C3N-01489_T 655149 45877739 18566428 670 25600 PREX1 0 . GRCh38 20 48651532 48651532 + Missense_Mutation SNP G G C rs138280268 C3N-01489_T C3N-01489_N G G c.2519C>G p.Pro840Arg p.P840R ENST00000371941 22/40 111 103 8 175 175 0 strelka-varscan-mutect PREX1,missense_variant,p.Pro840Arg,ENST00000371941,NM_020820.3;PREX1,missense_variant,p.Pro162Arg,ENST00000482556,; C ENST00000371941 Transcript missense_variant 2542/6636 2519/4980 840/1659 P/R cCc/cGc rs138280268 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 deleterious(0) 22/40 hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829 MODERATE 1 SNV 1 1 PASS rs138280268 . 0 207 0 2 0 0 0 0 -12.10796 0.9999997 1 1 1 0 C 3 2 81 48651532 48651532 G C 1 0 0 0 0 1 0 0 0 12610 1232 43 4 4 PREX1 20 48651532 Missense_Mutation SNP G C3N-01489_T 2773793 48651532 15792635 671 25601 ARFGEF2 0 . GRCh38 20 49033023 49033023 + Missense_Mutation SNP T T A novel C3N-01489_T C3N-01489_N T T c.5182T>A p.Phe1728Ile p.F1728I ENST00000371917 39/39 241 220 21 356 356 0 strelka-varscan-mutect ARFGEF2,missense_variant,p.Phe1728Ile,ENST00000371917,NM_006420.2; A ENST00000371917 Transcript missense_variant,splice_region_variant 5182/8852 5182/5358 1728/1785 F/I Ttc/Atc 1 1 ARFGEF2 HGNC HGNC:15853 protein_coding YES CCDS13411.1 ENSP00000360985 Q9Y6D5 UPI000013D378 NM_006420.2 deleterious(0.02) 39/39 hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF124,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1490090353 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 49033023 49033023 T A 1 0 0 0 0 1 0 0 0 976 1739 60 4 4 ARFGEF2 20 49033023 Missense_Mutation SNP T C3N-01489_T 381491 49033023 15411144 672 25602 ATP9A 0 . GRCh38 20 51713019 51713019 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.383A>G p.Tyr128Cys p.Y128C ENST00000338821 4/28 402 362 40 523 523 0 strelka-varscan-mutect ATP9A,missense_variant,p.Tyr128Cys,ENST00000338821,NM_006045.2;ATP9A,missense_variant,p.Tyr113Cys,ENST00000311637,; C ENST00000338821 Transcript missense_variant 648/8106 383/3144 128/1047 Y/C tAc/tGc 1 -1 ATP9A HGNC HGNC:13540 protein_coding YES CCDS33489.1 ENSP00000342481 O75110 UPI000004D334 NM_006045.2 tolerated(0.06) 4/28 Superfamily_domains:0049473,Gene3D:2.70.150.10,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF49,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 51713019 51713019 T C 1 0 0 0 0 1 0 0 0 1351 1638 57 5 5 ATP9A 20 51713019 Missense_Mutation SNP T C3N-01489_T 2679996 51713019 12731148 673 25603 ZFP64 0 . GRCh38 20 52104780 52104780 + Silent SNP C C A rs543049444 C3N-01489_T C3N-01489_N C C c.45G>T p.= p.S15S ENST00000395989 1/5 227 210 17 272 272 0 strelka-varscan-mutect ZFP64,synonymous_variant,p.=,ENST00000395989,;ZFP64,synonymous_variant,p.=,ENST00000395979,;ZFP64,intron_variant,,ENST00000361387,NM_199427.2;ZFP64,intron_variant,,ENST00000371523,NM_001319146.1;ZFP64,intron_variant,,ENST00000371518,;ZFP64,intron_variant,,ENST00000477786,; A ENST00000395989 Transcript synonymous_variant 144/762 45/663 15/221 S tcG/tcT rs543049444 1 -1 ZFP64 HGNC HGNC:15940 protein_coding ENSP00000379312 A2A2N5 UPI0000E5A345 1/5 LOW SNV 5 1 PASS rs543049444 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 52104780 52104780 C A 1 0 0 0 0 0 0 0 1 18228 639 23 1 1 ZFP64 20 52104780 Silent SNP C C3N-01489_T 391761 52104780 12339387 674 25604 CTSZ 0 . GRCh38 20 59006387 59006387 + Missense_Mutation SNP C C A rs773567578 C3N-01489_T C3N-01489_N C C c.242G>T p.Arg81Leu p.R81L ENST00000217131 2/6 192 175 17 239 239 0 strelka-varscan-mutect CTSZ,missense_variant,p.Arg81Leu,ENST00000217131,NM_001336.3;CTSZ,non_coding_transcript_exon_variant,,ENST00000503833,;CTSZ,non_coding_transcript_exon_variant,,ENST00000488395,;CTSZ,non_coding_transcript_exon_variant,,ENST00000472025,; A ENST00000217131 Transcript missense_variant 361/1495 242/912 81/303 R/L cGg/cTg rs773567578 1 -1 CTSZ HGNC HGNC:2547 protein_coding YES CCDS13474.1 ENSP00000217131 Q9UBR2 UPI000000D9CC NM_001336.3 deleterious(0.02) 2/6 hmmpanther:PTHR12411:SF377,hmmpanther:PTHR12411,Pfam_domain:PF00112,Gene3D:3.90.70.10,SMART_domains:SM00645,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs773567578 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 59006387 59006387 C A 1 0 0 0 0 1 0 0 0 3852 652 23 1 1 CTSZ 20 59006387 Missense_Mutation SNP C C3N-01489_T 6901607 59006387 5437780 675 25605 FAM217B 0 . GRCh38 20 59944676 59944676 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.733G>T p.Gly245Cys p.G245C ENST00000358293 5/5 295 268 27 432 431 1 strelka-varscan-mutect FAM217B,missense_variant,p.Gly245Cys,ENST00000358293,NM_001190826.1;FAM217B,missense_variant,p.Gly245Cys,ENST00000360816,NM_001190827.1,NM_022106.2;PPP1R3D,upstream_gene_variant,,ENST00000370996,NM_006242.3;FAM217B,downstream_gene_variant,,ENST00000421092,;FAM217B,non_coding_transcript_exon_variant,,ENST00000469084,; T ENST00000358293 Transcript missense_variant 1148/5152 733/1152 245/383 G/C Ggc/Tgc 1 1 FAM217B HGNC HGNC:16170 protein_coding YES CCDS13484.1 ENSP00000351040 Q9NTX9 UPI0000128624 NM_001190826.1 deleterious(0.01) 5/5 Pfam_domain:PF15344,hmmpanther:PTHR22145,hmmpanther:PTHR22145:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 59944676 59944676 G T 1 0 0 0 0 1 0 0 0 5407 1000 35 2 2 FAM217B 20 59944676 Missense_Mutation SNP G C3N-01489_T 938289 59944676 4499491 676 25606 HELZ2 0 . GRCh38 20 63563511 63563511 + Missense_Mutation SNP C C T rs369651267 C3N-01489_T C3N-01489_N C C c.5311G>A p.Val1771Ile p.V1771I ENST00000467148 8/19 46 39 7 54 54 0 strelka-varscan-mutect HELZ2,missense_variant,p.Val1771Ile,ENST00000467148,NM_001037335.2;HELZ2,missense_variant,p.Val1202Ile,ENST00000427522,NM_033405.3;HELZ2,upstream_gene_variant,,ENST00000478861,;HELZ2,downstream_gene_variant,,ENST00000454223,; T ENST00000467148 Transcript missense_variant 5381/8064 5311/7950 1771/2649 V/I Gtc/Atc rs369651267 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 tolerated(0.89) 8/19 MODERATE 1 SNV 1 1 PASS rs369651267 . 0 206 4 0 0 0 0 0 -17.23691 1 1 1 1 0 T 3 4 81 63563511 63563511 C T 1 0 0 0 0 1 0 0 0 6932 536 19 1 1 HELZ2 20 63563511 Missense_Mutation SNP C C3N-01489_T 3618835 63563511 880656 677 25607 CHODL 0 . GRCh38 21 18257059 18257059 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.479C>A p.Pro160His p.P160H ENST00000299295 3/6 102 93 9 169 169 0 strelka-varscan-mutect CHODL,missense_variant,p.Pro160His,ENST00000299295,NM_024944.2;CHODL,missense_variant,p.Pro119His,ENST00000400128,;CHODL,missense_variant,p.Pro119His,ENST00000400127,NM_001204176.1,NM_001204175.1;CHODL,missense_variant,p.Pro119His,ENST00000400135,NM_001204178.1;CHODL,missense_variant,p.Pro119His,ENST00000400131,NM_001204177.1;CHODL,missense_variant,p.Pro119His,ENST00000338326,;CHODL,missense_variant,p.Pro141His,ENST00000543733,NM_001204174.1; A ENST00000299295 Transcript missense_variant 870/2548 479/822 160/273 P/H cCc/cAc 1 1 CHODL HGNC HGNC:17807 protein_coding YES CCDS13570.1 ENSP00000299295 Q9H9P2 UPI0000037746 NM_024944.2 deleterious(0) 3/6 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR14789,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 18257059 18257059 C A 1 0 0 0 0 1 0 0 0 3124 623 22 2 2 CHODL 21 18257059 Missense_Mutation SNP C C3N-01489_T 18257059 28452924 678 25608 GABPA 0 . GRCh38 21 25764684 25764684 + Missense_Mutation SNP G G C rs2829900 C3N-01489_T C3N-01489_N G G c.1033G>C p.Glu345Gln p.E345Q ENST00000354828 9/10 204 188 16 306 306 0 varscan-mutect GABPA,missense_variant,p.Glu345Gln,ENST00000354828,NM_001197297.1;GABPA,missense_variant,p.Glu345Gln,ENST00000400075,NM_002040.3;LLPHP2,upstream_gene_variant,,ENST00000436405,; C ENST00000354828 Transcript missense_variant 1560/5120 1033/1365 345/454 E/Q Gaa/Caa rs2829900 1 1 GABPA HGNC HGNC:4071 protein_coding YES CCDS13575.1 ENSP00000346886 Q06546 A8IE48 UPI000012AFB2 NM_001197297.1 deleterious(0.01) 9/10 Gene3D:1.10.10.10,Pfam_domain:PF00178,PIRSF_domain:PIRSF001703,Prints_domain:PR00454,PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF195,SMART_domains:SM00413,Superfamily_domains:SSF46785 21595933 MODERATE 1 SNV 1 1 PASS rs2829900 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 25764684 25764684 G C 1 0 0 0 0 1 0 0 0 6028 1291 45 4 4 GABPA 21 25764684 Missense_Mutation SNP G C3N-01489_T 7507625 25764684 20945299 679 25609 LTN1 0 . GRCh38 21 28956790 28956790 + Silent SNP G G C novel C3N-01489_T C3N-01489_N G G c.3189C>G p.= p.V1063V ENST00000614971 16/30 77 68 9 99 99 0 strelka-varscan-mutect LTN1,synonymous_variant,p.=,ENST00000614971,NM_015565.2;LTN1,synonymous_variant,p.=,ENST00000389194,;LTN1,synonymous_variant,p.=,ENST00000361371,;LTN1,downstream_gene_variant,,ENST00000389195,;LTN1,downstream_gene_variant,,ENST00000475344,;LTN1,downstream_gene_variant,,ENST00000486427,; C ENST00000614971 Transcript synonymous_variant 3202/7756 3189/5439 1063/1812 V gtC/gtG 1 -1 LTN1 HGNC HGNC:13082 protein_coding YES CCDS33527.2 ENSP00000478783 O94822 UPI000049DF6C NM_015565.2 16/30 hmmpanther:PTHR12389 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.4877 1 1 1 1 0 C 2 2 81 28956790 28956790 G C 1 0 0 0 0 0 0 0 1 8987 929 33 4 4 LTN1 21 28956790 Silent SNP G C3N-01489_T 3192106 28956790 17753193 680 25610 ITSN1 0 . GRCh38 21 33867261 33867261 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.4103G>T p.Gly1368Val p.G1368V ENST00000381318 33/40 219 195 24 346 346 0 strelka-varscan-mutect ITSN1,missense_variant,p.Gly1368Val,ENST00000381318,NM_003024.2;ITSN1,missense_variant,p.Gly1363Val,ENST00000399367,;ITSN1,missense_variant,p.Gly104Val,ENST00000381284,;ITSN1,3_prime_UTR_variant,,ENST00000381285,;AP000304.12,intron_variant,,ENST00000429238,; T ENST00000381318 Transcript missense_variant 4391/17015 4103/5166 1368/1721 G/V gGg/gTg 1 1 ITSN1 HGNC HGNC:6183 protein_coding YES CCDS33545.1 ENSP00000370719 Q15811 UPI00001403C6 NM_003024.2 deleterious(0) 33/40 PROSITE_profiles:PS50010,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 33867261 33867261 G T 1 0 0 0 0 1 0 0 0 7832 1232 43 2 2 ITSN1 21 33867261 Missense_Mutation SNP G C3N-01489_T 4910471 33867261 12842722 681 25611 BACE2 0 . GRCh38 21 41168437 41168437 + Silent SNP C C T novel C3N-01489_T C3N-01489_N C C c.174C>T p.= p.D58D ENST00000330333 1/9 82 75 7 71 71 0 strelka-varscan-mutect BACE2,synonymous_variant,p.=,ENST00000347667,NM_138991.2;BACE2,synonymous_variant,p.=,ENST00000330333,NM_012105.4;BACE2,synonymous_variant,p.=,ENST00000328735,NM_138992.2;MIR3197,downstream_gene_variant,,ENST00000582241,; T ENST00000330333 Transcript synonymous_variant 637/2993 174/1557 58/518 D gaC/gaT 1 1 BACE2 HGNC HGNC:934 protein_coding YES CCDS13668.1 ENSP00000332979 Q9Y5Z0 UPI00000396BC NM_012105.4 1/9 hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF262,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.97705 0.9999998 1 1 1 0 T 2 4 81 41168437 41168437 C T 1 0 0 0 0 0 0 0 1 1440 535 19 1 1 BACE2 21 41168437 Silent SNP C C3N-01489_T 7301176 41168437 5541546 682 25612 PFKL 0 . GRCh38 21 44306727 44306727 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.132G>T p.= p.V44V ENST00000349048 2/22 205 186 19 291 291 0 strelka-varscan-mutect PFKL,synonymous_variant,p.=,ENST00000349048,NM_002626.5,NM_001002021.2;PFKL,downstream_gene_variant,,ENST00000628044,;PFKL,non_coding_transcript_exon_variant,,ENST00000496824,;PFKL,non_coding_transcript_exon_variant,,ENST00000491298,;PFKL,3_prime_UTR_variant,,ENST00000397961,;PFKL,non_coding_transcript_exon_variant,,ENST00000466134,; T ENST00000349048 Transcript synonymous_variant 187/2912 132/2343 44/780 V gtG/gtT 1 1 PFKL HGNC HGNC:8876 protein_coding YES CCDS33582.1 ENSP00000269848 P17858 UPI0000169D5F NM_002626.5,NM_001002021.2 2/22 Gene3D:3.40.50.450,HAMAP:MF_03184,Pfam_domain:PF00365,PIRSF_domain:PIRSF000533,hmmpanther:PTHR13697,hmmpanther:PTHR13697:SF14,Superfamily_domains:SSF53784,TIGRFAM_domain:TIGR02478 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 44306727 44306727 G T 1 0 0 0 0 0 0 0 1 11854 1335 47 2 2 PFKL 21 44306727 Silent SNP G C3N-01489_T 3138290 44306727 2403256 683 25613 COL6A2 0 . GRCh38 21 46112421 46112421 + Silent SNP G G T novel C3N-01489_T C3N-01489_N G G c.558G>T p.= p.R186R ENST00000300527 3/28 137 116 21 187 187 0 strelka-varscan-mutect COL6A2,synonymous_variant,p.=,ENST00000300527,NM_001849.3;COL6A2,synonymous_variant,p.=,ENST00000310645,NM_058175.2;COL6A2,synonymous_variant,p.=,ENST00000409416,;COL6A2,synonymous_variant,p.=,ENST00000397763,NM_058174.2;COL6A2,downstream_gene_variant,,ENST00000436769,;COL6A2,non_coding_transcript_exon_variant,,ENST00000460886,;COL6A2,upstream_gene_variant,,ENST00000485591,; T ENST00000300527 Transcript synonymous_variant 662/3461 558/3060 186/1019 R cgG/cgT 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 3/28 PROSITE_profiles:PS50234,hmmpanther:PTHR24023:SF119,hmmpanther:PTHR24023,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 81 46112421 46112421 G T 1 0 0 0 0 0 0 0 1 3489 1190 42 2 2 COL6A2 21 46112421 Silent SNP G C3N-01489_T 1805694 46112421 597562 684 25614 OR11H1 0 . GRCh38 22 15529105 15529105 + Missense_Mutation SNP T T A rs200268371 C3N-01489_T C3N-01489_N T T c.947T>A p.Leu316Gln p.L316Q ENST00000252835 1/1 135 121 14 242 242 0 varscan-mutect OR11H1,missense_variant,p.Leu316Gln,ENST00000252835,NM_001005239.1; A ENST00000252835 Transcript missense_variant 948/982 947/981 316/326 L/Q cTg/cAg rs200268371 1 1 OR11H1 HGNC HGNC:15404 protein_coding YES CCDS74807.1 ENSP00000252835 Q8NG94 UPI000004B1CF NM_001005239.1 deleterious(0) 1/1 hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs200268371 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 15529105 15529105 T A 1 0 0 0 0 1 0 0 0 11002 1580 55 4 4 OR11H1 22 15529105 Missense_Mutation SNP T C3N-01489_T 15529105 35289363 685 25615 CECR6 0 . GRCh38 22 17120288 17120288 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.840G>T p.= p.S280S ENST00000331437 1/1 49 28 21 75 74 1 strelka-varscan-mutect CECR6,synonymous_variant,p.=,ENST00000331437,NM_031890.3;CECR6,intron_variant,,ENST00000399875,NM_001163079.1;IL17RA,downstream_gene_variant,,ENST00000319363,NM_014339.6;IL17RA,downstream_gene_variant,,ENST00000612619,NM_001289905.1;AC006946.15,upstream_gene_variant,,ENST00000441544,;AC006946.15,upstream_gene_variant,,ENST00000428078,; A ENST00000331437 Transcript synonymous_variant 966/4954 840/1737 280/578 S tcG/tcT 1 -1 CECR6 HGNC HGNC:1844 protein_coding YES CCDS13740.1 ENSP00000329318 Q9BXQ6 UPI0000127513 NM_031890.3 1/1 Low_complexity_(Seg):seg LOW SNV 1 PASS rs1353898102 . 0 202 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 81 17120288 17120288 C A 1 0 0 0 0 0 0 0 1 2915 639 23 1 1 CECR6 22 17120288 Silent SNP C C3N-01489_T 1591183 17120288 33698180 686 25616 LRRC74B 0 . GRCh38 22 21046006 21046006 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.20G>A p.Arg7Lys p.R7K ENST00000442047 1/9 173 130 43 236 236 0 strelka-varscan-mutect LRRC74B,missense_variant,p.Arg7Lys,ENST00000442047,NM_001291006.1;AC002472.11,downstream_gene_variant,,ENST00000450652,;P2RX6P,upstream_gene_variant,,ENST00000439119,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000497328,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000473769,;P2RX6P,upstream_gene_variant,,ENST00000450626,; A ENST00000442047 Transcript missense_variant 20/1179 20/1179 7/392 R/K aGg/aAg 1 1 LRRC74B HGNC HGNC:34301 protein_coding YES CCDS77654.1 ENSP00000394078 Q6ZQY2 UPI000436DF24 NM_001291006.1 tolerated_low_confidence(0.77) 1/9 hmmpanther:PTHR24114,hmmpanther:PTHR24114:SF21 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 21046006 21046006 G A 1 0 0 0 0 1 0 0 0 8922 1000 35 3 3 LRRC74B 22 21046006 Missense_Mutation SNP G C3N-01489_T 3925718 21046006 29772462 687 25617 MYO18B 0 . GRCh38 22 26027105 26027105 + Silent SNP G G C rs374454209 C3N-01489_T C3N-01489_N G G c.7131G>C p.= p.S2377S ENST00000335473 43/44 147 134 13 281 281 0 strelka-varscan-mutect MYO18B,synonymous_variant,p.=,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,synonymous_variant,p.=,ENST00000407587,;MYO18B,synonymous_variant,p.=,ENST00000536101,;MYO18B,synonymous_variant,p.=,ENST00000543971,;MYO18B,synonymous_variant,p.=,ENST00000540454,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; C ENST00000335473 Transcript synonymous_variant 7381/8565 7131/7704 2377/2567 S tcG/tcC rs374454209,COSM3668590 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 43/44 0,1 LOW 1 SNV 1 0,1 1 PASS rs374454209 . 0 208 0 2 0 0 0 0 -18.32749 0.9999998 1 1 1 0 C 2 2 81 26027105 26027105 G C 1 0 0 0 0 0 0 0 1 10067 1074 38 4 4 MYO18B 22 26027105 Silent SNP G C3N-01489_T 4981099 26027105 24791363 688 25618 KREMEN1 0 . GRCh38 22 29137566 29137566 + Missense_Mutation SNP G G A rs751542642 C3N-01489_T C3N-01489_N G G c.856G>A p.Gly286Arg p.G286R ENST00000327813 6/10 115 107 8 163 163 0 strelka-varscan-mutect KREMEN1,missense_variant,p.Gly286Arg,ENST00000400335,NM_001039570.2;KREMEN1,missense_variant,p.Gly286Arg,ENST00000327813,NM_032045.4;KREMEN1,missense_variant,p.Gly284Arg,ENST00000407188,;RNU6-810P,downstream_gene_variant,,ENST00000364001,;KREMEN1,upstream_gene_variant,,ENST00000479755,;KREMEN1,3_prime_UTR_variant,,ENST00000453585,;KREMEN1,non_coding_transcript_exon_variant,,ENST00000474001,; A ENST00000327813 Transcript missense_variant 869/2719 856/1479 286/492 G/R Ggg/Agg rs751542642,COSM184518,COSM4696734 1 1 KREMEN1 HGNC HGNC:17550 protein_coding YES CCDS13849.1 ENSP00000331242 Q96MU8 UPI000002AD01 NM_032045.4 deleterious(0) 6/10 PROSITE_profiles:PS01180,hmmpanther:PTHR24269:SF13,hmmpanther:PTHR24269,PIRSF_domain:PIRSF036961,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs751542642 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 29137566 29137566 G A 1 0 0 0 0 1 0 0 0 8324 1116 39 1 1 KREMEN1 22 29137566 Missense_Mutation SNP G C3N-01489_T 3110461 29137566 21680902 689 25619 HMGXB4 0 . GRCh38 22 35264846 35264846 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.458G>T p.Ser153Ile p.S153I ENST00000216106 5/11 81 70 11 175 175 0 strelka-varscan-mutect HMGXB4,missense_variant,p.Ser153Ile,ENST00000216106,NM_001003681.2;HMGXB4,missense_variant,p.Ser44Ile,ENST00000455359,;HMGXB4,missense_variant,p.Ser44Ile,ENST00000420166,;HMGXB4,3_prime_UTR_variant,,ENST00000418170,;HMGXB4,downstream_gene_variant,,ENST00000498325,;HMGXB4,downstream_gene_variant,,ENST00000464480,; T ENST00000216106 Transcript missense_variant 586/4047 458/1806 153/601 S/I aGt/aTt 1 1 HMGXB4 HGNC HGNC:5003 protein_coding YES CCDS33641.1 ENSP00000216106 Q9UGU5 UPI00003765B4 NM_001003681.2 deleterious_low_confidence(0) 5/11 Low_complexity_(Seg):seg,Pfam_domain:PF13775 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 35264846 35264846 G T 1 0 0 0 0 1 0 0 0 7132 1029 36 2 2 HMGXB4 22 35264846 Missense_Mutation SNP G C3N-01489_T 6127280 35264846 15553622 690 25620 CSF2RB 0 . GRCh38 22 36926158 36926158 + Silent SNP C C A rs141354922 C3N-01489_T C3N-01489_N C C c.372C>A p.= p.T124T ENST00000403662 4/14 175 128 47 273 273 0 strelka-varscan-mutect CSF2RB,synonymous_variant,p.=,ENST00000403662,NM_000395.2;CSF2RB,synonymous_variant,p.=,ENST00000262825,;CSF2RB,synonymous_variant,p.=,ENST00000406230,;CSF2RB,synonymous_variant,p.=,ENST00000421539,; A ENST00000403662 Transcript synonymous_variant 594/4863 372/2694 124/897 T acC/acA rs141354922 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 4/14 hmmpanther:PTHR23037:SF22,hmmpanther:PTHR23037,PIRSF_domain:PIRSF001956,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs141354922 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 36926158 36926158 C A 1 0 0 0 0 0 0 0 1 3736 639 23 1 1 CSF2RB 22 36926158 Silent SNP C C3N-01489_T 1661312 36926158 13892310 691 25621 SCUBE1 0 . GRCh38 22 43223135 43223135 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1289G>A p.Cys430Tyr p.C430Y ENST00000360835 11/22 40 35 5 63 63 0 strelka-varscan-mutect SCUBE1,missense_variant,p.Cys430Tyr,ENST00000360835,NM_173050.3;SCUBE1,intron_variant,,ENST00000615096,; T ENST00000360835 Transcript missense_variant 1416/9808 1289/2967 430/988 C/Y tGc/tAc 1 -1 SCUBE1 HGNC HGNC:13441 protein_coding YES CCDS14048.1 ENSP00000354080 Q8IWY4 UPI000020790F NM_173050.3 deleterious(0) 11/22 hmmpanther:PTHR24046,hmmpanther:PTHR24046:SF4 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -12.90423 0.9999999 1 1 1 0 T 3 4 81 43223135 43223135 C T 1 0 0 0 0 1 0 0 0 14215 710 25 3 3 SCUBE1 22 43223135 Missense_Mutation SNP C C3N-01489_T 6296977 43223135 7595333 692 25622 CHKB 0 . GRCh38 22 50581857 50581857 + Silent SNP C C A novel C3N-01489_T C3N-01489_N C C c.339G>T p.= p.V113V ENST00000406938 3/11 414 384 30 719 718 1 strelka-varscan-mutect CHKB,synonymous_variant,p.=,ENST00000406938,NM_005198.4;CPT1B,upstream_gene_variant,,ENST00000395650,NM_004377.3;CPT1B,upstream_gene_variant,,ENST00000405237,NM_001145135.1,NM_001145137.1,NM_152245.2;CPT1B,upstream_gene_variant,,ENST00000312108,NM_152246.2;CPT1B,upstream_gene_variant,,ENST00000360719,;CPT1B,upstream_gene_variant,,ENST00000457250,NM_001145134.1;CPT1B,upstream_gene_variant,,ENST00000417176,;CHKB-AS1,upstream_gene_variant,,ENST00000380711,;CHKB,non_coding_transcript_exon_variant,,ENST00000463053,;CHKB,upstream_gene_variant,,ENST00000471515,;CHKB,upstream_gene_variant,,ENST00000464225,;CHKB-CPT1B,upstream_gene_variant,,ENST00000452668,;CHKB-CPT1B,non_coding_transcript_exon_variant,,ENST00000492556,;CHKB,non_coding_transcript_exon_variant,,ENST00000479003,;CHKB,non_coding_transcript_exon_variant,,ENST00000492582,;CHKB,non_coding_transcript_exon_variant,,ENST00000481673,;CHKB,non_coding_transcript_exon_variant,,ENST00000468532,;CHKB,non_coding_transcript_exon_variant,,ENST00000476289,;CHKB,non_coding_transcript_exon_variant,,ENST00000465842,;CHKB,intron_variant,,ENST00000484266,;CHKB-CPT1B,upstream_gene_variant,,ENST00000453634,;CPT1B,upstream_gene_variant,,ENST00000460853,;CHKB,upstream_gene_variant,,ENST00000489453,;CPT1B,upstream_gene_variant,,ENST00000476790,;CPT1B,upstream_gene_variant,,ENST00000461117,; A ENST00000406938 Transcript synonymous_variant 557/1638 339/1188 113/395 V gtG/gtT 1 -1 CHKB HGNC HGNC:1938 protein_coding YES CCDS14099.1 ENSP00000384400 Q9Y259 A0A024R4X4 UPI000012DE4D NM_005198.4 3/11 hmmpanther:PTHR22603:SF35,hmmpanther:PTHR22603,Gene3D:3.10.450.110,Pfam_domain:PF01633,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 50581857 50581857 C A 1 0 0 0 0 0 0 0 1 3107 608 21 2 2 CHKB 22 50581857 Silent SNP C C3N-01489_T 7358722 50581857 236611 693 25623 MID1 0 . GRCh38 X 10567191 10567191 + Silent SNP G G A novel C3N-01489_T C3N-01489_N G G c.357C>T p.= p.C119C ENST00000317552 2/10 77 62 15 141 141 0 strelka-varscan-mutect MID1,synonymous_variant,p.=,ENST00000317552,NM_000381.3,NM_033289.1;MID1,synonymous_variant,p.=,ENST00000453318,NM_001098624.2;MID1,synonymous_variant,p.=,ENST00000380780,;MID1,synonymous_variant,p.=,ENST00000380785,;MID1,synonymous_variant,p.=,ENST00000380779,NM_001193277.1;MID1,synonymous_variant,p.=,ENST00000380787,NM_033290.3;MID1,synonymous_variant,p.=,ENST00000380782,;MID1,synonymous_variant,p.=,ENST00000616003,NM_001193278.1,NM_001193279.1,NM_001193280.1;MID1,synonymous_variant,p.=,ENST00000610939,NM_001193281.1;MID1,synonymous_variant,p.=,ENST00000413894,;MID1,synonymous_variant,p.=,ENST00000423614,; A ENST00000317552 Transcript synonymous_variant 758/6463 357/2004 119/667 C tgC/tgT 1 -1 MID1 HGNC HGNC:7095 protein_coding YES CCDS14138.1 ENSP00000312678 O15344 A0A024RBV4 UPI000012F0E6 NM_000381.3,NM_033289.1 2/10 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF26,SMART_domains:SM00336 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 81 10567191 10567191 G A 1 0 0 0 0 0 0 0 1 9536 1195 42 3 3 MID1 23 10567191 Silent SNP G C3N-01489_T 10567191 145473704 694 25624 BEND2 0 . GRCh38 X 18171149 18171149 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.2037G>T p.Leu679Phe p.L679F ENST00000380033 13/14 129 110 19 185 185 0 strelka-varscan-mutect BEND2,missense_variant,p.Leu679Phe,ENST00000380033,NM_153346.4;BEND2,missense_variant,p.Leu588Phe,ENST00000380030,NM_001184767.1; A ENST00000380033 Transcript missense_variant 2170/4611 2037/2400 679/799 L/F ttG/ttT 1 -1 BEND2 HGNC HGNC:28509 protein_coding YES CCDS14184.1 ENSP00000369372 Q8NDZ0 UPI000013FE0F NM_153346.4 deleterious(0.02) 13/14 PROSITE_profiles:PS51457,hmmpanther:PTHR16213:SF35,hmmpanther:PTHR16213 MODERATE 1 SNV 1 1 PASS rs1026258780 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 18171149 18171149 C A 1 0 0 0 0 1 0 0 0 1546 593 21 2 2 BEND2 23 18171149 Missense_Mutation SNP C C3N-01489_T 7603958 18171149 137869746 695 25625 DMD 0 . GRCh38 X 32438297 32438297 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.4015C>A p.Leu1339Ile p.L1339I ENST00000357033 29/79 182 151 31 308 306 2 strelka-varscan-mutect DMD,missense_variant,p.Leu1339Ile,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Leu1335Ile,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Leu1339Ile,ENST00000620040,;DMD,missense_variant,p.Leu1335Ile,ENST00000619831,;DMD,intron_variant,,ENST00000420596,;DMD,intron_variant,,ENST00000448370,;DMD,intron_variant,,ENST00000488902,; T ENST00000357033 Transcript missense_variant 4222/13956 4015/11058 1339/3685 L/I Cta/Ata 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 tolerated(0.65) 29/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 32438297 32438297 G T 1 0 0 0 0 1 0 0 0 4387 962 34 2 2 DMD 23 32438297 Missense_Mutation SNP G C3N-01489_T 14267148 32438297 123602598 696 25626 FAM47B 0 . GRCh38 X 34942890 34942890 + Missense_Mutation SNP G G T novel C3N-01489_T C3N-01489_N G G c.59G>T p.Trp20Leu p.W20L ENST00000329357 1/1 54 43 11 88 88 0 strelka-varscan-mutect FAM47B,missense_variant,p.Trp20Leu,ENST00000329357,NM_152631.2; T ENST00000329357 Transcript missense_variant 95/2120 59/1938 20/645 W/L tGg/tTg 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 deleterious(0.01) 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 34942890 34942890 G T 1 0 0 0 0 1 0 0 0 5448 1357 47 2 2 FAM47B 23 34942890 Missense_Mutation SNP G C3N-01489_T 2504593 34942890 121098005 697 25627 CFAP47 0 . GRCh38 X 35956197 35956197 + Splice_Site SNP G G A C3N-01489_T C3N-01489_N G G c.1410+1G>A p.X470_splice ENST00000297866 49 30 19 79 79 0 strelka-varscan-mutect CFAP47,splice_donor_variant,,ENST00000378653,NM_001304548.1;CFAP47,splice_donor_variant,,ENST00000297866,NM_152632.3;CFAP47,splice_donor_variant,,ENST00000493930,; A ENST00000297866 Transcript splice_donor_variant -/3608 1410/2931 470/976 COSM1665905,COSM1665906 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 8/15 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 81 35956197 35956197 G A 1 0 0 0 0 0 0 1 0 3022 1275 44 3 3 CFAP47 23 35956197 Splice_Site SNP G C3N-01489_T 1013307 35956197 120084698 698 25628 BCOR 0 . GRCh38 X 40062799 40062799 + Missense_Mutation SNP T T A C3N-01489_T C3N-01489_N T T c.4120A>T p.Arg1374Trp p.R1374W ENST00000378444 9/15 115 83 32 187 187 0 strelka-varscan-mutect BCOR,missense_variant,p.Arg1340Trp,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Arg1374Trp,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Arg1322Trp,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Arg1340Trp,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Arg217Trp,ENST00000378463,;BCOR,missense_variant,p.Arg47Trp,ENST00000442018,;BCOR,missense_variant,p.Arg69Trp,ENST00000427012,;BCOR,missense_variant,p.Arg244Trp,ENST00000413905,;BCOR,downstream_gene_variant,,ENST00000406200,; A ENST00000378444 Transcript missense_variant 4349/6358 4120/5268 1374/1755 R/W Agg/Tgg COSM4665526,COSM4665527,COSM4665528 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 deleterious(0) 9/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117,Pfam_domain:PF15808 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1198189611 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 40062799 40062799 T A 1 0 0 0 0 1 0 0 0 1533 1579 55 4 4 BCOR 23 40062799 Missense_Mutation SNP T C3N-01489_T 4106602 40062799 115978096 699 25629 MED14 0 . GRCh38 X 40654469 40654469 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.4186A>G p.Thr1396Ala p.T1396A ENST00000324817 30/31 164 128 36 223 223 0 strelka-varscan-mutect MED14,missense_variant,p.Thr1396Ala,ENST00000324817,NM_004229.3;MED14,missense_variant,p.Thr295Ala,ENST00000433003,;MED14,missense_variant,p.Thr108Ala,ENST00000416199,;MED14,downstream_gene_variant,,ENST00000472736,; C ENST00000324817 Transcript missense_variant 4305/7984 4186/4365 1396/1454 T/A Acc/Gcc 1 -1 MED14 HGNC HGNC:2370 protein_coding YES CCDS14254.1 ENSP00000323720 O60244 UPI00001414B1 NM_004229.3 deleterious(0.02) 30/31 hmmpanther:PTHR12809 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 40654469 40654469 T C 1 0 0 0 0 1 0 0 0 9371 1725 60 5 5 MED14 23 40654469 Missense_Mutation SNP T C3N-01489_T 591670 40654469 115386426 700 25630 DDX3X 0 . GRCh38 X 41347352 41347352 + Nonsense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.1810C>T p.Gln604Ter p.Q604* ENST00000399959 16/17 76 57 19 105 105 0 strelka-varscan-mutect DDX3X,stop_gained,p.Gln604Ter,ENST00000399959,NM_001356.4,NM_001193416.2;DDX3X,stop_gained,p.Gln588Ter,ENST00000457138,NM_001193417.2;DDX3X,stop_gained,p.Gln604Ter,ENST00000629496,;DDX3X,stop_gained,p.Gln604Ter,ENST00000625837,;DDX3X,stop_gained,p.Gln604Ter,ENST00000626301,;DDX3X,stop_gained,p.Gln85Ter,ENST00000611968,;DDX3X,intron_variant,,ENST00000441189,;DDX3X,downstream_gene_variant,,ENST00000631641,;RN7SL15P,upstream_gene_variant,,ENST00000582825,;DDX3X,downstream_gene_variant,,ENST00000542215,;DDX3X,downstream_gene_variant,,ENST00000615313,;DDX3X,downstream_gene_variant,,ENST00000611546,;DDX3X,downstream_gene_variant,,ENST00000622198,;DDX3X,stop_gained,p.Gln604Ter,ENST00000629785,;DDX3X,stop_gained,p.Gln604Ter,ENST00000478993,;DDX3X,stop_gained,p.Gln604Ter,ENST00000630255,;DDX3X,stop_gained,p.Gln604Ter,ENST00000630858,;DDX3X,stop_gained,p.Gln604Ter,ENST00000630370,;DDX3X,stop_gained,p.Gln121Ter,ENST00000616050,;DDX3X,downstream_gene_variant,,ENST00000615742,; T ENST00000399959 Transcript stop_gained 2665/5399 1810/1989 604/662 Q/* Caa/Taa 1 1 DDX3X HGNC HGNC:2745 protein_coding YES CCDS43931.1 ENSP00000382840 O00571 UPI000013CB6D NM_001356.4,NM_001193416.2 16/17 Low_complexity_(Seg):seg,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF332 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 81 41347352 41347352 C T 1 0 0 0 0 0 1 0 0 4161 479 17 3 3 DDX3X 23 41347352 Nonsense_Mutation SNP C C3N-01489_T 692883 41347352 114693543 701 25631 RBM3 0 . GRCh38 X 48575658 48575658 + Missense_Mutation SNP G G A novel C3N-01489_T C3N-01489_N G G c.201G>A p.Met67Ile p.M67I ENST00000376759 3/7 86 63 23 126 126 0 strelka-varscan-mutect RBM3,missense_variant,p.Met67Ile,ENST00000376759,NM_006743.4;RBM3,missense_variant,p.Met67Ile,ENST00000376755,;RBM3,upstream_gene_variant,,ENST00000354480,;RP11-1148L6.9,upstream_gene_variant,,ENST00000376775,;RP11-1148L6.5,downstream_gene_variant,,ENST00000453810,;RBM3,non_coding_transcript_exon_variant,,ENST00000466764,;RBM3,non_coding_transcript_exon_variant,,ENST00000491240,;RBM3,non_coding_transcript_exon_variant,,ENST00000485213,;RBM3,non_coding_transcript_exon_variant,,ENST00000488216,;RBM3,non_coding_transcript_exon_variant,,ENST00000491236,;RBM3,non_coding_transcript_exon_variant,,ENST00000490127,;RBM3,intron_variant,,ENST00000489344,;RBM3,intron_variant,,ENST00000472897,; A ENST00000376759 Transcript missense_variant 264/2162 201/474 67/157 M/I atG/atA 1 1 RBM3 HGNC HGNC:9900 protein_coding YES CCDS14301.1 ENSP00000365950 P98179 A0A024QYX3 UPI000013337B NM_006743.4 deleterious(0.03) 3/7 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 48575658 48575658 G A 1 0 0 0 0 1 0 0 0 13295 1290 45 3 3 RBM3 23 48575658 Missense_Mutation SNP G C3N-01489_T 7228306 48575658 107465237 702 25632 CCNB3 0 . GRCh38 X 50310835 50310835 + Missense_Mutation SNP A A G novel C3N-01489_T C3N-01489_N A A c.2666A>G p.Glu889Gly p.E889G ENST00000376042 6/13 161 125 36 240 240 0 strelka-varscan-mutect CCNB3,missense_variant,p.Glu889Gly,ENST00000376042,;CCNB3,missense_variant,p.Glu889Gly,ENST00000276014,NM_033031.2;CCNB3,intron_variant,,ENST00000348603,NM_033670.2;CCNB3,intron_variant,,ENST00000376038,;CCNB3,intron_variant,,ENST00000476167,; G ENST00000376042 Transcript missense_variant 2964/4693 2666/4188 889/1395 E/G gAg/gGg 1 1 CCNB3 HGNC HGNC:18709 protein_coding YES CCDS14331.1 ENSP00000365210 Q8WWL7 UPI000022DC76 tolerated(0.21) 6/13 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 81 50310835 50310835 A G 1 0 0 0 0 1 0 0 0 2613 304 11 5 5 CCNB3 23 50310835 Missense_Mutation SNP A C3N-01489_T 1735177 50310835 105730060 703 25633 BMP15 0 . GRCh38 X 50916401 50916401 + Missense_Mutation SNP C C A novel C3N-01489_T C3N-01489_N C C c.973C>A p.Leu325Ile p.L325I ENST00000252677 2/2 23 19 4 21 21 0 strelka-mutect BMP15,missense_variant,p.Leu325Ile,ENST00000252677,NM_005448.2; A ENST00000252677 Transcript missense_variant 973/1179 973/1179 325/392 L/I Ctc/Atc 1 1 BMP15 HGNC HGNC:1068 protein_coding YES CCDS14334.1 ENSP00000252677 O95972 UPI000013CD7C NM_005448.2 deleterious(0) 2/2 Gene3D:2.10.90.10,Pfam_domain:PF00019,Prints_domain:PR00669,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF22,SMART_domains:SM00204,Superfamily_domains:SSF57501 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.09861 1 1 1 1 0 A 3 1 81 50916401 50916401 C A 1 0 0 0 0 1 0 0 0 1613 913 32 2 2 BMP15 23 50916401 Missense_Mutation SNP C C3N-01489_T 605566 50916401 105124494 704 25634 PCDH11X 0 . GRCh38 X 91835715 91835715 + Missense_Mutation SNP G G C C3N-01489_T C3N-01489_N G G c.211G>C p.Asp71His p.D71H ENST00000373094 1/7 213 170 43 342 342 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Asp71His,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Asp71His,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Asp71His,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Asp71His,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Asp71His,ENST00000373088,NM_001168362.1;PCDH11X,missense_variant,p.Asp71His,ENST00000504220,NM_001168361.1;PCDH11X,missense_variant,p.Asp71His,ENST00000395337,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000298274,;PCDH11X,non_coding_transcript_exon_variant,,ENST00000361724,; C ENST00000373094 Transcript missense_variant 1056/9179 211/4044 71/1347 D/H Gat/Cat COSM3564011,COSM3564012,COSM3564013,COSM384556,COSM384557 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 deleterious(0.01) 1/7 Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF25 1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 91835715 91835715 G C 1 0 0 0 0 1 0 0 0 11595 942 33 4 4 PCDH11X 23 91835715 Missense_Mutation SNP G C3N-01489_T 40919314 91835715 64205180 705 25635 TRMT2B 0 . GRCh38 X 101021270 101021270 + Silent SNP C C G novel C3N-01489_T C3N-01489_N C C c.897G>C p.= p.L299L ENST00000372936 10/14 46 34 12 80 80 0 strelka-varscan-mutect TRMT2B,synonymous_variant,p.=,ENST00000372936,NM_024917.5;TRMT2B,synonymous_variant,p.=,ENST00000545398,NM_001167972.1;TRMT2B,synonymous_variant,p.=,ENST00000372939,NM_001167971.1;TRMT2B,synonymous_variant,p.=,ENST00000372935,NM_001167970.1;TRMT2B,downstream_gene_variant,,ENST00000478422,; G ENST00000372936 Transcript synonymous_variant 1670/3327 897/1515 299/504 L ctG/ctC 1 -1 TRMT2B HGNC HGNC:25748 protein_coding YES CCDS14477.1 ENSP00000362027 Q96GJ1 A0A024RCF5 UPI0000070468 NM_024917.5 10/14 Gene3D:3.40.50.150,PROSITE_profiles:PS51621,PROSITE_profiles:PS51687,hmmpanther:PTHR11061,hmmpanther:PTHR11061:SF26,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 81 101021270 101021270 C G 1 0 0 0 0 0 0 0 1 17070 465 17 4 4 TRMT2B 23 101021270 Silent SNP C C3N-01489_T 9185555 101021270 55019625 706 25636 NXF3 0 . GRCh38 X 103084745 103084745 + Missense_Mutation SNP T T C novel C3N-01489_T C3N-01489_N T T c.167A>G p.His56Arg p.H56R ENST00000395065 2/20 64 47 17 84 84 0 strelka-varscan-mutect NXF3,missense_variant,p.His56Arg,ENST00000395065,NM_022052.1;NXF3,upstream_gene_variant,,ENST00000427570,;NXF3,upstream_gene_variant,,ENST00000497850,;NXF3,upstream_gene_variant,,ENST00000470724,;NXF3,upstream_gene_variant,,ENST00000460791,;NXF3,upstream_gene_variant,,ENST00000494300,;LL0XNC01-221F2.2,upstream_gene_variant,,ENST00000440243,; C ENST00000395065 Transcript missense_variant 269/1938 167/1596 56/531 H/R cAt/cGt 1 -1 NXF3 HGNC HGNC:8073 protein_coding YES CCDS14503.1 ENSP00000378504 Q9H4D5 UPI00000015F8 NM_022052.1 tolerated(1) 2/20 hmmpanther:PTHR10662,hmmpanther:PTHR10662:SF12 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 103084745 103084745 T C 1 0 0 0 0 1 0 0 0 10857 1464 51 5 5 NXF3 23 103084745 Missense_Mutation SNP T C3N-01489_T 2063475 103084745 52956150 707 25637 RGAG1 0 . GRCh38 X 110452805 110452805 + Missense_Mutation SNP G G C novel C3N-01489_T C3N-01489_N G G c.2188G>C p.Gly730Arg p.G730R ENST00000465301 3/4 109 98 11 160 160 0 strelka-varscan-mutect RGAG1,missense_variant,p.Gly730Arg,ENST00000465301,NM_020769.2;RGAG1,missense_variant,p.Gly730Arg,ENST00000540313,;RGAG1,downstream_gene_variant,,ENST00000520821,; C ENST00000465301 Transcript missense_variant 2434/5426 2188/4167 730/1388 G/R Ggg/Cgg 1 1 RGAG1 HGNC HGNC:29245 protein_coding YES CCDS14552.1 ENSP00000419786 Q8NET4 UPI000006F841 NM_020769.2 deleterious(0.01) 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF48 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 81 110452805 110452805 G C 1 0 0 0 0 1 0 0 0 13446 1000 35 4 4 RGAG1 23 110452805 Missense_Mutation SNP G C3N-01489_T 7368060 110452805 45588090 708 25638 IL13RA1 0 . GRCh38 X 118766538 118766538 + Missense_Mutation SNP G G T rs12837646 C3N-01489_T C3N-01489_N G G c.837G>T p.Glu279Asp p.E279D ENST00000371666 7/11 48 37 11 93 93 0 strelka-varscan-mutect IL13RA1,missense_variant,p.Glu279Asp,ENST00000371666,NM_001560.2;IL13RA1,non_coding_transcript_exon_variant,,ENST00000481868,;RP13-128O4.3,upstream_gene_variant,,ENST00000506969,; T ENST00000371666 Transcript missense_variant 904/4036 837/1284 279/427 E/D gaG/gaT rs12837646 1 1 IL13RA1 HGNC HGNC:5974 protein_coding YES CCDS14573.1 ENSP00000360730 P78552 UPI0000000CA3 NM_001560.2 tolerated(0.28) 7/11 PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF89,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs12837646 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 118766538 118766538 G T 1 0 0 0 0 1 0 0 0 7537 991 35 2 2 IL13RA1 23 118766538 Missense_Mutation SNP G C3N-01489_T 8313733 118766538 37274357 709 25639 ADGRG4 0 . GRCh38 X 136350117 136350117 + Missense_Mutation SNP C C A rs760205099 C3N-01489_T C3N-01489_N C C c.6411C>A p.Asp2137Glu p.D2137E ENST00000394143 6/26 89 66 23 161 161 0 strelka-varscan-mutect ADGRG4,missense_variant,p.Asp2137Glu,ENST00000394143,NM_153834.3;ADGRG4,missense_variant,p.Asp2137Glu,ENST00000370652,;ADGRG4,missense_variant,p.Asp1932Glu,ENST00000394141,; A ENST00000394143 Transcript missense_variant 6702/9931 6411/9243 2137/3080 D/E gaC/gaA rs760205099 1 1 ADGRG4 HGNC HGNC:18992 protein_coding YES CCDS35409.1 ENSP00000377699 Q8IZF6 UPI00004CEC5B NM_153834.3 deleterious(0) 6/26 MODERATE 1 SNV 1 1 PASS rs760205099 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 136350117 136350117 C A 1 0 0 0 0 1 0 0 0 371 506 18 2 2 ADGRG4 23 136350117 Missense_Mutation SNP C C3N-01489_T 17583579 136350117 19690778 710 25640 ZIC3 0 . GRCh38 X 137567697 137567697 + Missense_Mutation SNP G G A C3N-01489_T C3N-01489_N G G c.1006G>A p.Gly336Arg p.G336R ENST00000287538 1/3 121 107 14 203 202 1 strelka-varscan-mutect ZIC3,missense_variant,p.Gly336Arg,ENST00000287538,NM_003413.3;ZIC3,missense_variant,p.Gly336Arg,ENST00000370606,;RP1-137H15.2,upstream_gene_variant,,ENST00000442841,;RP1-137H15.2,upstream_gene_variant,,ENST00000456631,;ZIC3,upstream_gene_variant,,ENST00000478471,; A ENST00000287538 Transcript missense_variant 1556/3469 1006/1404 336/467 G/R Ggg/Agg COSM4106985,COSM4106986 1 1 ZIC3 HGNC HGNC:12874 protein_coding YES CCDS14663.1 ENSP00000287538 O60481 UPI000013C3DD NM_003413.3 deleterious(0.02) 1/3 PROSITE_profiles:PS50157,hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF25,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1474420006 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 81 137567697 137567697 G A 1 0 0 0 0 1 0 0 0 18259 1116 39 1 1 ZIC3 23 137567697 Missense_Mutation SNP G C3N-01489_T 1217580 137567697 18473198 711 25641 FGF13 0 . GRCh38 X 138708929 138708929 + Splice_Site SNP C C A novel C3N-01489_T C3N-01489_N C C c.218-1G>T p.X73_splice ENST00000436198 28 23 5 54 54 0 strelka-varscan-mutect FGF13,splice_acceptor_variant,,ENST00000315930,NM_004114.3;FGF13,splice_acceptor_variant,,ENST00000305414,NM_033642.2;FGF13,splice_acceptor_variant,,ENST00000436198,NM_001139500.1;FGF13,splice_acceptor_variant,,ENST00000626909,NM_001139498.1;FGF13,splice_acceptor_variant,,ENST00000455663,;Z83313.1,splice_acceptor_variant,,ENST00000441825,NM_001139501.1,NM_001139502.1;FGF13,splice_acceptor_variant,,ENST00000448673,;FGF13-AS1,upstream_gene_variant,,ENST00000438238,;FGF13-AS1,upstream_gene_variant,,ENST00000446383,; A ENST00000436198 Transcript splice_acceptor_variant -/1165 218/768 73/255 1 -1 FGF13 HGNC HGNC:3670 protein_coding YES CCDS55513.1 ENSP00000396198 Q92913 UPI00001484B4 NM_001139500.1 3/6 HIGH SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -14.17695 1 1 1 1 0 A 5 1 81 138708929 138708929 C A 1 0 0 0 0 0 0 1 0 5706 927 32 2 2 FGF13 23 138708929 Splice_Site SNP C C3N-01489_T 1141232 138708929 17331966 712 25642 ZNF185 0 . GRCh38 X 152918987 152918987 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.436C>T p.Pro146Ser p.P146S ENST00000535861 7/24 74 67 7 111 111 0 strelka-varscan-mutect ZNF185,missense_variant,p.Pro146Ser,ENST00000535861,NM_001178106.1;ZNF185,missense_variant,p.Pro146Ser,ENST00000539731,NM_001178107.1,NM_001178109.1;ZNF185,missense_variant,p.Pro146Ser,ENST00000449285,NM_001178108.1;ZNF185,missense_variant,p.Pro146Ser,ENST00000370268,NM_007150.3;ZNF185,missense_variant,p.Pro146Ser,ENST00000318504,NM_001178110.1;ZNF185,missense_variant,p.Pro11Ser,ENST00000318529,NM_001178113.1;ZNF185,missense_variant,p.Pro6Ser,ENST00000324823,;ZNF185,missense_variant,p.Pro146Ser,ENST00000370270,;ZNF185,upstream_gene_variant,,ENST00000426821,;ZNF185,upstream_gene_variant,,ENST00000447792,;ZNF185,missense_variant,p.Pro146Ser,ENST00000436731,; T ENST00000535861 Transcript missense_variant 484/4421 436/2166 146/721 P/S Ccc/Tcc 1 1 ZNF185 HGNC HGNC:12976 protein_coding YES CCDS55529.1 ENSP00000440847 O15231 UPI0001D27F7E NM_001178106.1 deleterious(0.02) 7/24 hmmpanther:PTHR15468,hmmpanther:PTHR15468:SF2 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -15.51887 1 1 1 1 0 T 3 4 81 152918987 152918987 C T 1 0 0 0 0 1 0 0 0 18332 521 18 3 3 ZNF185 23 152918987 Missense_Mutation SNP C C3N-01489_T 14210058 152918987 3121908 713 25643 HAUS7 0 . GRCh38 X 153470562 153470562 + Missense_Mutation SNP C C T novel C3N-01489_T C3N-01489_N C C c.26G>A p.Arg9Gln p.R9Q ENST00000370211 1/10 120 93 27 133 133 0 strelka-varscan-mutect HAUS7,missense_variant,p.Arg9Gln,ENST00000370211,NM_017518.7;TREX2,5_prime_UTR_variant,,ENST00000330912,;TREX2,5_prime_UTR_variant,,ENST00000338525,;TREX2,5_prime_UTR_variant,,ENST00000334497,;TREX2,5_prime_UTR_variant,,ENST00000370232,;HAUS7,5_prime_UTR_variant,,ENST00000370210,;HAUS7,5_prime_UTR_variant,,ENST00000626181,;HAUS7,non_coding_transcript_exon_variant,,ENST00000490453,;HAUS7,upstream_gene_variant,,ENST00000464993,;HAUS7,upstream_gene_variant,,ENST00000490165,; T ENST00000370211 Transcript missense_variant 70/1363 26/1107 9/368 R/Q cGa/cAa 1 -1 HAUS7 HGNC HGNC:32979 protein_coding YES CCDS35438.1 ENSP00000359230 Q99871 UPI00000731E0 NM_017518.7 tolerated_low_confidence(0.11) 1/10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 153470562 153470562 C T 1 0 0 0 0 1 0 0 0 6857 884 31 1 1 HAUS7 23 153470562 Missense_Mutation SNP C C3N-01489_T 551575 153470562 2570333 714 25644 IL9R 0 . GRCh38 X 156001454 156001454 + Missense_Mutation SNP G G T rs369236927 C3N-01489_T C3N-01489_N G G c.91G>T p.Gly31Cys p.G31C ENST00000369423 2/9 250 223 27 362 362 0 strelka-varscan-mutect IL9R,missense_variant,p.Gly31Cys,ENST00000369423,NM_176786.1;IL9R,intron_variant,,ENST00000244174,NM_002186.2;IL9R,non_coding_transcript_exon_variant,,ENST00000489233,;IL9R,upstream_gene_variant,,ENST00000494962,;AJ271736.10,upstream_gene_variant,,ENST00000483543,; T ENST00000369423 Transcript missense_variant 129/2032 91/1029 31/342 G/C Ggt/Tgt rs369236927,COSM5234022 1 1 IL9R HGNC HGNC:6030 protein_coding CCDS59180.1 ENSP00000358431 Q01113 UPI00001AF535 NM_176786.1 deleterious_low_confidence(0) 2/9 0,1 MODERATE SNV 1 0,1 1 PASS rs369236927 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 81 156001454 156001454 G T 1 0 0 0 0 1 0 0 0 7611 1116 39 1 1 IL9R 23 156001454 Missense_Mutation SNP G C3N-01489_T 2530892 156001454 39441 715 25645 HES3 0 . GRCh38 1 6245184 6245184 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.238C>T p.Leu80Phe p.L80F ENST00000377898 4/4 166 145 21 110 110 0 strelka-varscan-mutect HES3,missense_variant,p.Leu80Phe,ENST00000377898,NM_001024598.3;GPR153,downstream_gene_variant,,ENST00000377893,NM_207370.2; T ENST00000377898 Transcript missense_variant 303/697 238/561 80/186 L/F Ctt/Ttt 1 1 HES3 HGNC HGNC:26226 protein_coding YES CCDS41238.1 ENSP00000367130 Q5TGS1 UPI000047096C NM_001024598.3 deleterious(0) 4/4 hmmpanther:PTHR10985:SF5,hmmpanther:PTHR10985 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 82 6245184 6245184 C T 1 0 0 0 0 1 0 0 0 6951 681 24 3 3 HES3 1 6245184 Missense_Mutation SNP C C3N-01799_T 6245184 242711238 1 25646 UBR4 0 . GRCh38 1 19120257 19120257 + Missense_Mutation SNP G G C novel C3N-01799_T C3N-01799_N G G c.10233C>G p.Phe3411Leu p.F3411L ENST00000375254 69/106 274 255 19 229 228 1 strelka-varscan-mutect UBR4,missense_variant,p.Phe3411Leu,ENST00000375254,NM_020765.2;UBR4,downstream_gene_variant,,ENST00000417040,;UBR4,upstream_gene_variant,,ENST00000375218,;UBR4,downstream_gene_variant,,ENST00000425413,;UBR4,downstream_gene_variant,,ENST00000475973,; C ENST00000375254 Transcript missense_variant 10261/15906 10233/15552 3411/5183 F/L ttC/ttG 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 deleterious(0) 69/106 hmmpanther:PTHR21725,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 19120257 19120257 G C 1 0 0 0 0 1 0 0 0 17428 1165 41 4 4 UBR4 1 19120257 Missense_Mutation SNP G C3N-01799_T 12875073 19120257 229836165 2 25647 HSPG2 0 . GRCh38 1 21847779 21847779 + Missense_Mutation SNP C C G C3N-01799_T C3N-01799_N C C c.7935G>C p.Gln2645His p.Q2645H ENST00000374695 61/97 438 401 37 322 322 0 strelka-varscan-mutect HSPG2,missense_variant,p.Gln2645His,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,non_coding_transcript_exon_variant,,ENST00000453796,;HSPG2,downstream_gene_variant,,ENST00000493940,; G ENST00000374695 Transcript missense_variant 8015/14327 7935/13176 2645/4391 Q/H caG/caC COSM3803967,COSM3803968 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 deleterious(0.01) 61/97 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 21847779 21847779 C G 1 0 0 0 0 1 0 0 0 7326 912 32 4 4 HSPG2 1 21847779 Missense_Mutation SNP C C3N-01799_T 2727522 21847779 227108643 3 25648 LCE3D 0 . GRCh38 1 152579874 152579874 + Silent SNP A A G novel C3N-01799_T C3N-01799_N A A c.63T>C p.= p.C21C ENST00000368787 2/2 451 373 78 285 285 0 strelka-varscan-mutect LCE3D,synonymous_variant,p.=,ENST00000368787,NM_032563.1; G ENST00000368787 Transcript synonymous_variant 120/613 63/279 21/92 C tgT/tgC 1 -1 LCE3D HGNC HGNC:16615 protein_coding YES CCDS1014.1 ENSP00000357776 Q9BYE3 UPI000006EC48 NM_032563.1 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF27,hmmpanther:PTHR23263,Pfam_domain:PF14672 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 82 152579874 152579874 A G 1 0 0 0 0 0 0 0 1 8577 273 10 5 5 LCE3D 1 152579874 Silent SNP A C3N-01799_T 130732095 152579874 96376548 4 25649 SPRED2 0 . GRCh38 2 65344873 65344873 + Missense_Mutation SNP T T C novel C3N-01799_T C3N-01799_N T T c.50A>G p.Lys17Arg p.K17R ENST00000356388 2/6 166 128 38 122 122 0 strelka-varscan-mutect SPRED2,missense_variant,p.Lys17Arg,ENST00000356388,NM_181784.2;SPRED2,missense_variant,p.Lys14Arg,ENST00000443619,NM_001128210.1;SPRED2,missense_variant,p.Lys32Arg,ENST00000452315,;SPRED2,missense_variant,p.Lys17Arg,ENST00000440972,;SPRED2,upstream_gene_variant,,ENST00000427238,;SPRED2,non_coding_transcript_exon_variant,,ENST00000474228,;SPRED2,upstream_gene_variant,,ENST00000426832,; C ENST00000356388 Transcript missense_variant 240/4097 50/1257 17/418 K/R aAg/aGg 1 -1 SPRED2 HGNC HGNC:17722 protein_coding YES CCDS33211.1 ENSP00000348753 Q7Z698 UPI000013E7B4 NM_181784.2 tolerated(1) 2/6 PROSITE_profiles:PS50229,hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF11,Pfam_domain:PF00568,Gene3D:2.30.29.30,SMART_domains:SM00461,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 65344873 65344873 T C 1 0 0 0 0 1 0 0 0 15447 1609 56 5 5 SPRED2 2 65344873 Missense_Mutation SNP T C3N-01799_T 65344873 176848656 5 25650 IQSEC1 0 . GRCh38 3 12936107 12936107 + Silent SNP G G T novel C3N-01799_T C3N-01799_N G G c.909C>A p.= p.P303P ENST00000613206 3/14 215 197 18 134 134 0 strelka-varscan-mutect IQSEC1,synonymous_variant,p.=,ENST00000273221,NM_014869.6;IQSEC1,synonymous_variant,p.=,ENST00000618604,;IQSEC1,synonymous_variant,p.=,ENST00000613206,NM_001134382.2;IQSEC1,downstream_gene_variant,,ENST00000473088,; T ENST00000613206 Transcript synonymous_variant 1012/3582 909/3345 303/1114 P ccC/ccA 1 -1 IQSEC1 HGNC HGNC:29112 protein_coding YES CCDS74902.1 ENSP00000480301 A0A087WWK8 UPI00017E10F8 NM_001134382.2 3/14 hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 82 12936107 12936107 G T 1 0 0 0 0 0 0 0 1 7723 1219 43 2 2 IQSEC1 3 12936107 Silent SNP G C3N-01799_T 12936107 185359452 6 25651 IL17RD 0 . GRCh38 3 57110197 57110197 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.425G>C p.Arg142Thr p.R142T ENST00000296318 4/13 197 182 15 138 138 0 strelka-varscan IL17RD,missense_variant,p.Arg142Thr,ENST00000296318,NM_001318864.1,NM_017563.3;IL17RD,5_prime_UTR_variant,,ENST00000320057,;IL17RD,5_prime_UTR_variant,,ENST00000463523,;IL17RD,5_prime_UTR_variant,,ENST00000467210,;IL17RD,downstream_gene_variant,,ENST00000479825,;IL17RD,non_coding_transcript_exon_variant,,ENST00000469841,; G ENST00000296318 Transcript missense_variant 514/8720 425/2220 142/739 R/T aGa/aCa 1 -1 IL17RD HGNC HGNC:17616 protein_coding YES CCDS2880.2 ENSP00000296318 Q8NFM7 UPI0000047CC3 NM_001318864.1,NM_017563.3 tolerated(0.47) 4/13 hmmpanther:PTHR15583:SF14,hmmpanther:PTHR15583,Pfam_domain:PF16742 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 57110197 57110197 C G 1 0 0 0 0 1 0 0 0 7550 927 32 4 4 IL17RD 3 57110197 Missense_Mutation SNP C C3N-01799_T 44174090 57110197 141185362 7 25652 ALCAM 0 . GRCh38 3 105524410 105524410 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.296C>G p.Ser99Cys p.S99C ENST00000306107 3/16 336 288 48 271 271 0 strelka-varscan ALCAM,missense_variant,p.Ser99Cys,ENST00000306107,NM_001627.3,NM_001243281.1;ALCAM,missense_variant,p.Ser99Cys,ENST00000472644,NM_001243280.1;ALCAM,missense_variant,p.Ser48Cys,ENST00000486979,;ALCAM,non_coding_transcript_exon_variant,,ENST00000481337,;ALCAM,non_coding_transcript_exon_variant,,ENST00000470756,; G ENST00000306107 Transcript missense_variant 796/4701 296/1752 99/583 S/C tCt/tGt 1 1 ALCAM HGNC HGNC:400 protein_coding YES CCDS33810.1 ENSP00000305988 Q13740 UPI0000209ECA NM_001627.3,NM_001243281.1 tolerated(0.08) 3/16 Gene3D:2.60.40.10,hmmpanther:PTHR11973,hmmpanther:PTHR11973:SF2,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 105524410 105524410 C G 1 0 0 0 0 1 0 0 0 587 913 32 4 4 ALCAM 3 105524410 Missense_Mutation SNP C C3N-01799_T 48414213 105524410 92771149 8 25653 GAB1 0 . GRCh38 4 143337231 143337232 + Frame_Shift_Ins INS - - C rs755581817 C3N-01799_T C3N-01799_N - - c.50dupC p.Glu18GlyfsTer34 p.E18Gfs*34 ENST00000262995 1/11 163 135 28 121 120 1 sindel-varindel GAB1,frameshift_variant,p.Glu18GlyfsTer34,ENST00000262995,NM_207123.2;GAB1,frameshift_variant,p.Glu18GlyfsTer34,ENST00000262994,NM_002039.3;GAB1,frameshift_variant,p.Glu18GlyfsTer34,ENST00000514639,; C ENST00000262995 Transcript frameshift_variant 470-471/7981 43-44/2175 15/724 S/SX tcc/tCcc rs755581817 1 1 GAB1 HGNC HGNC:4066 protein_coding YES CCDS3760.1 ENSP00000262995 Q13480 UPI0000232A33 NM_207123.2 1/11 PROSITE_profiles:PS50003,hmmpanther:PTHR12156,hmmpanther:PTHR12156:SF18,Pfam_domain:PF00169,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 insertion 1 7 1 PASS . . 0 174 0 20 16 0 0 0 -14.86229 0.01344796 0 1 0 0 C 7 5 82 143337231 143337231 - C 1 0 1 1 0 0 0 0 0 6019 1667 58 0 0 GAB1 4 143337231 Frame_Shift_Ins INS - C3N-01799_T 143337231 46877324 9 25654 PCDHA13 0 . GRCh38 5 140882733 140882733 + Silent SNP T T C novel C3N-01799_T C3N-01799_N T T c.465T>C p.= p.D155D ENST00000289272 1/4 379 346 33 271 271 0 strelka-varscan-mutect PCDHA13,synonymous_variant,p.=,ENST00000289272,NM_018904.2;PCDHA13,synonymous_variant,p.=,ENST00000409494,;PCDHA13,synonymous_variant,p.=,ENST00000617769,NM_031865.1;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;PCDHA12,downstream_gene_variant,,ENST00000613593,NM_031864.2;AC005609.17,upstream_gene_variant,,ENST00000625195,; C ENST00000289272 Transcript synonymous_variant 465/5260 465/2853 155/950 D gaT/gaC 1 1 PCDHA13 HGNC HGNC:8667 protein_coding YES CCDS4240.1 ENSP00000289272 Q9Y5I0 UPI00001273D6 NM_018904.2 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF101,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 82 140882733 140882733 T C 1 0 0 0 0 0 0 0 1 11610 1461 51 5 5 PCDHA13 5 140882733 Silent SNP T C3N-01799_T 140882733 40655526 10 25655 DST 0 . GRCh38 6 56614401 56614401 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.4500G>C p.Leu1500Phe p.L1500F ENST00000312431 34/95 205 189 16 165 165 0 strelka-varscan-mutect DST,missense_variant,p.Leu1460Phe,ENST00000361203,;DST,missense_variant,p.Leu1460Phe,ENST00000421834,NM_183380.3;DST,missense_variant,p.Leu1500Phe,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Leu1460Phe,ENST00000370788,;DST,missense_variant,p.Leu1134Phe,ENST00000244364,NM_015548.4;DST,missense_variant,p.Leu1134Phe,ENST00000439203,;DST,downstream_gene_variant,,ENST00000370765,NM_001723.5;DST,downstream_gene_variant,,ENST00000520645,;DST,downstream_gene_variant,,ENST00000522360,; G ENST00000312431 Transcript missense_variant 4626/17756 4500/16614 1500/5537 L/F ttG/ttC 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 tolerated(0.08) 34/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 56614401 56614401 C G 1 0 0 0 0 1 0 0 0 4604 825 29 4 4 DST 6 56614401 Missense_Mutation SNP C C3N-01799_T 56614401 114191578 11 25656 SESN1 0 . GRCh38 6 108998527 108998527 + Missense_Mutation SNP C C A novel C3N-01799_T C3N-01799_N C C c.958G>T p.Ala320Ser p.A320S ENST00000436639 5/10 169 148 21 156 155 1 strelka-varscan-mutect SESN1,missense_variant,p.Ala320Ser,ENST00000436639,NM_014454.2;SESN1,missense_variant,p.Ala195Ser,ENST00000302071,NM_001199934.1;SESN1,missense_variant,p.Ala261Ser,ENST00000356644,NM_001199933.1;RP11-787I22.3,non_coding_transcript_exon_variant,,ENST00000605885,;SESN1,non_coding_transcript_exon_variant,,ENST00000368971,;SESN1,downstream_gene_variant,,ENST00000523632,; A ENST00000436639 Transcript missense_variant 1704/3509 958/1656 320/551 A/S Gca/Tca 1 -1 SESN1 HGNC HGNC:21595 protein_coding YES CCDS5070.1 ENSP00000393762 Q9Y6P5 UPI000002B36B NM_014454.2 tolerated(0.82) 5/10 hmmpanther:PTHR12474,hmmpanther:PTHR12474:SF3,Pfam_domain:PF04636 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 82 108998527 108998527 C A 1 0 0 0 0 1 0 0 0 14401 797 28 2 2 SESN1 6 108998527 Missense_Mutation SNP C C3N-01799_T 52384126 108998527 61807452 12 25657 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-01799_T C3N-01799_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 608 518 90 376 376 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-01799_T 55191822 104154151 13 25658 PCLO 0 . GRCh38 7 82951018 82951018 + Silent SNP C C A novel C3N-01799_T C3N-01799_N C C c.9570G>T p.= p.V3190V ENST00000333891 6/25 478 434 44 333 333 0 strelka-varscan-mutect PCLO,synonymous_variant,p.=,ENST00000333891,NM_033026.5;PCLO,synonymous_variant,p.=,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript synonymous_variant 9908/20329 9570/15429 3190/5142 V gtG/gtT 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 6/25 hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 82951018 82951018 C A 1 0 0 0 0 0 0 0 1 11671 465 17 2 2 PCLO 7 82951018 Silent SNP C C3N-01799_T 27759196 82951018 76394955 14 25659 PPP1R9A 0 . GRCh38 7 95120748 95120748 + Missense_Mutation SNP G G T novel C3N-01799_T C3N-01799_N G G c.1565G>T p.Gly522Val p.G522V ENST00000433360 4/20 217 183 34 182 182 0 strelka-varscan-mutect PPP1R9A,missense_variant,p.Gly522Val,ENST00000456331,NM_001166162.1;PPP1R9A,missense_variant,p.Gly522Val,ENST00000433881,;PPP1R9A,missense_variant,p.Gly522Val,ENST00000340694,NM_017650.2,NM_001166163.1;PPP1R9A,missense_variant,p.Gly522Val,ENST00000433360,NM_001166160.1;PPP1R9A,missense_variant,p.Gly522Val,ENST00000424654,;PPP1R9A,missense_variant,p.Gly522Val,ENST00000289495,NM_001166161.1;AC002429.5,intron_variant,,ENST00000637269,;AC002429.5,intron_variant,,ENST00000637876,; T ENST00000433360 Transcript missense_variant 1847/5369 1565/4125 522/1374 G/V gGt/gTt 1 1 PPP1R9A HGNC HGNC:14946 protein_coding YES CCDS55127.1 ENSP00000405514 Q9ULJ8 UPI000198CF27 NM_001166160.1 deleterious(0) 4/20 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR16154,hmmpanther:PTHR16154:SF22,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 82 95120748 95120748 G T 1 0 0 0 0 1 0 0 0 12501 1261 44 2 2 PPP1R9A 7 95120748 Missense_Mutation SNP G C3N-01799_T 12169730 95120748 64225225 15 25660 KRBA1 0 . GRCh38 7 149723826 149723826 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.967C>G p.Pro323Ala p.P323A ENST00000496259 8/17 280 248 32 163 163 0 strelka-varscan-mutect KRBA1,missense_variant,p.Pro289Ala,ENST00000319551,NM_032534.3;KRBA1,missense_variant,p.Pro323Ala,ENST00000496259,NM_001290187.1;KRBA1,missense_variant,p.Pro289Ala,ENST00000485033,;KRBA1,downstream_gene_variant,,ENST00000467333,;KRBA1,downstream_gene_variant,,ENST00000486744,;KRBA1,downstream_gene_variant,,ENST00000497895,;KRBA1,missense_variant,p.Pro246Ala,ENST00000621069,;KRBA1,non_coding_transcript_exon_variant,,ENST00000496080,; G ENST00000496259 Transcript missense_variant 1011/3763 967/3195 323/1064 P/A Ccc/Gcc 1 1 KRBA1 HGNC HGNC:22228 protein_coding YES CCDS78285.1 ENSP00000418647 A0A0C4DH65 UPI0003F48BD7 NM_001290187.1 tolerated(0.13) 8/17 hmmpanther:PTHR22740,SMART_domains:SM01258 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 149723826 149723826 C G 1 0 0 0 0 1 0 0 0 8319 855 30 4 4 KRBA1 7 149723826 Missense_Mutation SNP C C3N-01799_T 54603078 149723826 9622147 16 25661 WWP1 0 . GRCh38 8 86448253 86448253 + Missense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.2104G>A p.Glu702Lys p.E702K ENST00000517970 19/25 333 124 209 115 115 0 strelka-varscan-mutect WWP1,missense_variant,p.Glu702Lys,ENST00000517970,NM_007013.3;WWP1,missense_variant,p.Glu702Lys,ENST00000265428,;WWP1,missense_variant,p.Glu203Lys,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,; A ENST00000517970 Transcript missense_variant 2411/4686 2104/2769 702/922 E/K Gaa/Aaa 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 deleterious(0) 19/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 82 86448253 86448253 G A 1 0 0 0 0 1 0 0 0 17973 1291 45 3 3 WWP1 8 86448253 Missense_Mutation SNP G C3N-01799_T 86448253 58690383 17 25662 1 16 5 4 248 N G 1.052646e-11 WWP1 0 . GRCh38 8 86448275 86448275 + Nonsense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.2126G>A p.Trp709Ter p.W709* ENST00000517970 19/25 296 110 186 106 106 0 strelka-varscan-mutect WWP1,stop_gained,p.Trp709Ter,ENST00000517970,NM_007013.3;WWP1,stop_gained,p.Trp709Ter,ENST00000265428,;WWP1,stop_gained,p.Trp210Ter,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,; A ENST00000517970 Transcript stop_gained 2433/4686 2126/2769 709/922 W/* tGg/tAg 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 19/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 82 86448275 86448275 G A 1 0 0 0 0 0 1 0 0 17973 1357 47 3 3 WWP1 8 86448275 Nonsense_Mutation SNP G C3N-01799_T 22 86448275 58690361 18 25663 1 16 5 4 248 N G 1.052646e-11 WWP1 0 . GRCh38 8 86448424 86448424 + Missense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.2184G>A p.Met728Ile p.M728I ENST00000517970 20/25 463 196 267 188 188 0 strelka-varscan-mutect WWP1,missense_variant,p.Met728Ile,ENST00000517970,NM_007013.3;WWP1,missense_variant,p.Met728Ile,ENST00000265428,;WWP1,missense_variant,p.Met229Ile,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,; A ENST00000517970 Transcript missense_variant 2491/4686 2184/2769 728/922 M/I atG/atA 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 tolerated(0.11) 20/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999996 1 1 1 0 A 3 1 82 86448424 86448424 G A 1 0 0 0 0 1 0 0 0 17973 1348 47 3 3 WWP1 8 86448424 Missense_Mutation SNP G C3N-01799_T 149 86448424 58690212 19 25664 87 2 1 16 5 4 248 N G 1.052646e-11 WWP1 0 . GRCh38 8 86448427 86448427 + Silent SNP G G A novel C3N-01799_T C3N-01799_N G G c.2187G>A p.= p.E729E ENST00000517970 20/25 476 196 280 197 197 0 strelka-varscan-mutect WWP1,synonymous_variant,p.=,ENST00000517970,NM_007013.3;WWP1,synonymous_variant,p.=,ENST00000265428,;WWP1,synonymous_variant,p.=,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,; A ENST00000517970 Transcript synonymous_variant 2494/4686 2187/2769 729/922 E gaG/gaA 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 20/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 86448427 86448427 G A 1 0 0 0 0 0 0 0 1 17973 933 33 3 3 WWP1 8 86448427 Silent SNP G C3N-01799_T 3 86448427 58690209 20 25665 87 2 1 16 5 4 248 N G 1.052646e-11 WWP1 0 . GRCh38 8 86448500 86448500 + Missense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.2260G>A p.Asp754Asn p.D754N ENST00000517970 20/25 299 109 190 117 117 0 strelka-varscan-mutect WWP1,missense_variant,p.Asp754Asn,ENST00000517970,NM_007013.3;WWP1,missense_variant,p.Asp754Asn,ENST00000265428,;WWP1,downstream_gene_variant,,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000524036,;WWP1,non_coding_transcript_exon_variant,,ENST00000521997,;WWP1,downstream_gene_variant,,ENST00000518683,; A ENST00000517970 Transcript missense_variant 2567/4686 2260/2769 754/922 D/N Gat/Aat 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 deleterious(0) 20/25 PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,Pfam_domain:PF00632,Gene3D:1c4zA02,PIRSF_domain:PIRSF001569,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 82 86448500 86448500 G A 1 0 0 0 0 1 0 0 0 17973 942 33 3 3 WWP1 8 86448500 Missense_Mutation SNP G C3N-01799_T 73 86448500 58690136 21 25666 1 16 5 4 248 N G 1.052646e-11 PLEKHF2 0 . GRCh38 8 95154791 95154791 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.747C>G p.Asp249Glu p.D249E ENST00000315367 2/2 77 67 10 111 111 0 strelka-varscan-mutect PLEKHF2,missense_variant,p.Asp249Glu,ENST00000315367,NM_024613.3;PLEKHF2,missense_variant,p.Asp249Glu,ENST00000519516,; G ENST00000315367 Transcript missense_variant 988/2881 747/750 249/249 D/E gaC/gaG 1 1 PLEKHF2 HGNC HGNC:20757 protein_coding YES CCDS6267.1 ENSP00000322373 Q9H8W4 UPI0000035DB0 NM_024613.3 tolerated(0.17) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99399 1 1 1 1 0 G 3 3 82 95154791 95154791 C G 1 0 0 0 0 1 0 0 0 12160 564 20 4 4 PLEKHF2 8 95154791 Missense_Mutation SNP C C3N-01799_T 8706291 95154791 49983845 22 25667 MUSK 0 . GRCh38 9 110767883 110767883 + Silent SNP C C T novel C3N-01799_T C3N-01799_N C C c.984C>T p.= p.V328V ENST00000374448 9/15 398 357 41 274 274 0 strelka-varscan-mutect MUSK,synonymous_variant,p.=,ENST00000416899,;MUSK,synonymous_variant,p.=,ENST00000374448,NM_005592.3;MUSK,intron_variant,,ENST00000189978,NM_001166281.1,NM_001166280.1;MUSK,intron_variant,,ENST00000374440,;MUSK,non_coding_transcript_exon_variant,,ENST00000634612,; T ENST00000374448 Transcript synonymous_variant 1118/2754 984/2610 328/869 V gtC/gtT 1 1 MUSK HGNC HGNC:7525 protein_coding YES CCDS48005.1 ENSP00000363571 O15146 UPI000006D2F7 NM_005592.3 9/15 Gene3D:1ijyA00,Pfam_domain:PF01392,PROSITE_profiles:PS50038 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 82 110767883 110767883 C T 1 0 0 0 0 0 0 0 1 9987 842 30 3 3 MUSK 9 110767883 Silent SNP C C3N-01799_T 110767883 27626834 23 25668 2 17 3 3 186 C 4.460498e-08 MUSK 0 . GRCh38 9 110767910 110767910 + Silent SNP C C T novel C3N-01799_T C3N-01799_N C C c.1011C>T p.= p.L337L ENST00000374448 9/15 496 441 55 322 322 0 strelka-varscan-mutect MUSK,synonymous_variant,p.=,ENST00000416899,;MUSK,synonymous_variant,p.=,ENST00000374448,NM_005592.3;MUSK,intron_variant,,ENST00000189978,NM_001166281.1,NM_001166280.1;MUSK,intron_variant,,ENST00000374440,;MUSK,non_coding_transcript_exon_variant,,ENST00000634612,; T ENST00000374448 Transcript synonymous_variant 1145/2754 1011/2610 337/869 L ctC/ctT 1 1 MUSK HGNC HGNC:7525 protein_coding YES CCDS48005.1 ENSP00000363571 O15146 UPI000006D2F7 NM_005592.3 9/15 Gene3D:1ijyA00,Pfam_domain:PF01392,PROSITE_profiles:PS50038 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 82 110767910 110767910 C T 1 0 0 0 0 0 0 0 1 9987 813 29 3 3 MUSK 9 110767910 Silent SNP C C3N-01799_T 27 110767910 27626807 24 25669 2 17 3 3 186 C 4.460498e-08 MUSK 0 . GRCh38 9 110768068 110768068 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.1169C>T p.Pro390Leu p.P390L ENST00000374448 9/15 118 99 19 110 110 0 strelka-varscan-mutect MUSK,missense_variant,p.Pro390Leu,ENST00000416899,;MUSK,missense_variant,p.Pro390Leu,ENST00000374448,NM_005592.3;MUSK,intron_variant,,ENST00000189978,NM_001166281.1,NM_001166280.1;MUSK,intron_variant,,ENST00000374440,;MUSK,downstream_gene_variant,,ENST00000634612,; T ENST00000374448 Transcript missense_variant 1303/2754 1169/2610 390/869 P/L cCt/cTt 1 1 MUSK HGNC HGNC:7525 protein_coding YES CCDS48005.1 ENSP00000363571 O15146 UPI000006D2F7 NM_005592.3 deleterious(0.01) 9/15 Gene3D:1ijyA00,Pfam_domain:PF01392,PROSITE_profiles:PS50038,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF317 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 82 110768068 110768068 C T 1 0 0 0 0 1 0 0 0 9987 681 24 3 3 MUSK 9 110768068 Missense_Mutation SNP C C3N-01799_T 158 110768068 27626649 25 25670 2 17 3 3 186 C 4.460498e-08 DRD4 0 . GRCh38 11 640458 640458 + Missense_Mutation SNP G G C novel C3N-01799_T C3N-01799_N G G c.1115G>C p.Cys372Ser p.C372S ENST00000176183 4/4 289 258 31 209 209 0 strelka-varscan-mutect DRD4,missense_variant,p.Cys372Ser,ENST00000176183,NM_000797.3;DEAF1,downstream_gene_variant,,ENST00000382409,NM_021008.3;DEAF1,downstream_gene_variant,,ENST00000527658,;DRD4,downstream_gene_variant,,ENST00000528733,;DEAF1,downstream_gene_variant,,ENST00000527170,; C ENST00000176183 Transcript missense_variant 1127/1375 1115/1260 372/419 C/S tGt/tCt 1 1 DRD4 HGNC HGNC:3025 protein_coding YES CCDS7710.1 ENSP00000176183 P21917 UPI000011F17B NM_000797.3 deleterious(0) 4/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF37,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 640458 640458 G C 1 0 0 0 0 1 0 0 0 4578 1377 48 4 4 DRD4 11 640458 Missense_Mutation SNP G C3N-01799_T 640458 134446164 26 25671 SPON1 0 . GRCh38 11 14257895 14257895 + Missense_Mutation SNP G G A rs782473008 C3N-01799_T C3N-01799_N G G c.1489G>A p.Glu497Lys p.E497K ENST00000576479 11/16 59 55 4 49 49 0 strelka-mutect SPON1,missense_variant,p.Glu497Lys,ENST00000576479,NM_006108.3;RP11-21L19.1,downstream_gene_variant,,ENST00000534587,;SPON1,upstream_gene_variant,,ENST00000591785,; A ENST00000576479 Transcript missense_variant 1705/4837 1489/2424 497/807 E/K Gaa/Aaa rs782473008,COSM4831106 1 1 SPON1 HGNC HGNC:11252 protein_coding YES CCDS73262.1 ENSP00000460236 Q9HCB6 UPI000044404A NM_006108.3 tolerated(0.25) 11/16 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF18 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs782473008 . 0 207 3 0 0 0 0 0 -10.12769 1 1 1 1 0 A 3 1 82 14257895 14257895 G A 1 0 0 0 0 1 0 0 0 15435 1072 37 1 1 SPON1 11 14257895 Missense_Mutation SNP G C3N-01799_T 13617437 14257895 120828727 27 25672 NAV2 0 . GRCh38 11 19884346 19884346 + Missense_Mutation SNP C C G novel C3N-01799_T C3N-01799_N C C c.823C>G p.Gln275Glu p.Q275E ENST00000396087 6/41 272 253 19 153 153 0 strelka-varscan-mutect NAV2,missense_variant,p.Gln275Glu,ENST00000527559,;NAV2,missense_variant,p.Gln275Glu,ENST00000396087,NM_001244963.1;NAV2,intron_variant,,ENST00000540292,;NAV2,intron_variant,,ENST00000396085,NM_182964.5;NAV2,intron_variant,,ENST00000349880,NM_145117.4;NAV2,intron_variant,,ENST00000360655,NM_001111018.1;NAV2,downstream_gene_variant,,ENST00000534229,; G ENST00000396087 Transcript missense_variant 922/7882 823/7467 275/2488 Q/E Cag/Gag 1 1 NAV2 HGNC HGNC:15997 protein_coding YES CCDS58126.1 ENSP00000379396 Q8IVL1 UPI00001E0580 NM_001244963.1 deleterious(0.03) 6/41 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 19884346 19884346 C G 1 0 0 0 0 1 0 0 0 10193 827 29 4 4 NAV2 11 19884346 Missense_Mutation SNP C C3N-01799_T 5626451 19884346 115202276 28 25673 LRRC32 0 . GRCh38 11 76661164 76661164 + Silent SNP C C G novel C3N-01799_T C3N-01799_N C C c.429G>C p.= p.R143R ENST00000407242 3/3 73 67 6 79 79 0 varscan-mutect LRRC32,synonymous_variant,p.=,ENST00000407242,NM_005512.2;LRRC32,synonymous_variant,p.=,ENST00000260061,NM_001128922.1;LRRC32,synonymous_variant,p.=,ENST00000404995,;LRRC32,synonymous_variant,p.=,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,; G ENST00000407242 Transcript synonymous_variant 672/4311 429/1989 143/662 R cgG/cgC 1 -1 LRRC32 HGNC HGNC:4161 protein_coding YES CCDS8245.1 ENSP00000384126 Q14392 A0A024R5J7 UPI000012B0DF NM_005512.2 3/3 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF337,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 2 -4.368702 0 0 1 0 0 G 2 3 82 76661164 76661164 C G 1 0 0 0 0 0 0 0 1 8882 726 26 4 4 LRRC32 11 76661164 Silent SNP C C3N-01799_T 56776818 76661164 58425458 29 25674 88 2 LRRC32 0 . GRCh38 11 76661168 76661168 + Missense_Mutation SNP T T C novel C3N-01799_T C3N-01799_N T T c.425A>G p.Glu142Gly p.E142G ENST00000407242 3/3 70 65 5 69 69 0 varscan-mutect LRRC32,missense_variant,p.Glu142Gly,ENST00000407242,NM_005512.2;LRRC32,missense_variant,p.Glu142Gly,ENST00000260061,NM_001128922.1;LRRC32,missense_variant,p.Glu142Gly,ENST00000404995,;LRRC32,missense_variant,p.Glu142Gly,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,; C ENST00000407242 Transcript missense_variant 668/4311 425/1989 142/662 E/G gAg/gGg 1 -1 LRRC32 HGNC HGNC:4161 protein_coding YES CCDS8245.1 ENSP00000384126 Q14392 A0A024R5J7 UPI000012B0DF NM_005512.2 tolerated(0.07) 3/3 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF337,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 2 -4.656848 0 0 1 0 0 C 3 2 82 76661168 76661168 T C 1 0 0 0 0 1 0 0 0 8882 1551 54 5 5 LRRC32 11 76661168 Missense_Mutation SNP T C3N-01799_T 4 76661168 58425454 30 25675 88 2 CHD4 0 . GRCh38 12 6587559 6587559 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.3704G>A p.Gly1235Glu p.G1235E ENST00000357008 25/40 124 106 18 112 112 0 strelka-varscan-mutect CHD4,missense_variant,p.Gly1232Glu,ENST00000544484,;CHD4,missense_variant,p.Gly1228Glu,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Gly1235Glu,ENST00000357008,NM_001273.3;RP5-940J5.6,downstream_gene_variant,,ENST00000501075,;CHD4,splice_region_variant,,ENST00000540960,;CHD4,intron_variant,,ENST00000536301,;CHD4,downstream_gene_variant,,ENST00000537634,;CHD4,downstream_gene_variant,,ENST00000545083,; T ENST00000357008 Transcript missense_variant,splice_region_variant 3868/6496 3704/5739 1235/1912 G/E gGa/gAa 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 tolerated(0.54) 25/40 MODERATE 1 SNV 1 1 PASS . . 0 201 6 3 0 0 0 0 -20 0.9995206 1 1 1 0 T 3 4 82 6587559 6587559 C T 1 0 0 0 0 1 0 0 0 3086 869 30 3 3 CHD4 12 6587559 Missense_Mutation SNP C C3N-01799_T 6587559 126687750 31 25676 PA2G4 0 . GRCh38 12 56107048 56107048 + Silent SNP G G A novel C3N-01799_T C3N-01799_N G G c.276G>A p.= p.L92L ENST00000303305 3/13 293 262 31 173 173 0 strelka-varscan-mutect PA2G4,synonymous_variant,p.=,ENST00000303305,NM_006191.2;PA2G4,synonymous_variant,p.=,ENST00000552766,;PA2G4,synonymous_variant,p.=,ENST00000551061,;PA2G4,synonymous_variant,p.=,ENST00000553057,;RP11-603J24.9,synonymous_variant,p.=,ENST00000548861,;ERBB3,downstream_gene_variant,,ENST00000267101,NM_001982.3;ERBB3,downstream_gene_variant,,ENST00000415288,;ERBB3,downstream_gene_variant,,ENST00000549832,;ERBB3,downstream_gene_variant,,ENST00000553131,;ERBB3,downstream_gene_variant,,ENST00000550070,;RP11-603J24.17,intron_variant,,ENST00000548595,;PA2G4,non_coding_transcript_exon_variant,,ENST00000550166,;ERBB3,downstream_gene_variant,,ENST00000551085,;ERBB3,downstream_gene_variant,,ENST00000551242,;PA2G4,upstream_gene_variant,,ENST00000552266,;PA2G4,upstream_gene_variant,,ENST00000552528,; A ENST00000303305 Transcript synonymous_variant 695/2577 276/1185 92/394 L ttG/ttA 1 1 PA2G4 HGNC HGNC:8550 protein_coding YES CCDS8902.1 ENSP00000302886 Q9UQ80 A0A024RB85 UPI0000049B6B NM_006191.2 3/13 Gene3D:3.90.230.10,Pfam_domain:PF00557,hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF83,Superfamily_domains:SSF55920,TIGRFAM_domain:TIGR00495 LOW 1 SNV 1 1 PASS rs1219296678 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 56107048 56107048 G A 1 0 0 0 0 0 0 0 1 11438 1281 45 3 3 PA2G4 12 56107048 Silent SNP G C3N-01799_T 49519489 56107048 77168261 32 25677 SMARCC2 0 . GRCh38 12 56184856 56184856 + Silent SNP G G A novel C3N-01799_T C3N-01799_N G G c.480C>T p.= p.I160I ENST00000267064 5/28 221 191 30 176 176 0 strelka-varscan-mutect SMARCC2,synonymous_variant,p.=,ENST00000394023,NM_001130420.1;SMARCC2,synonymous_variant,p.=,ENST00000550164,;SMARCC2,synonymous_variant,p.=,ENST00000267064,NM_003075.3;SMARCC2,synonymous_variant,p.=,ENST00000347471,NM_139067.2;RP11-977G19.5,intron_variant,,ENST00000553176,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550859,;SMARCC2,3_prime_UTR_variant,,ENST00000552674,;SMARCC2,3_prime_UTR_variant,,ENST00000550519,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550150,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000552627,;SMARCC2,upstream_gene_variant,,ENST00000548130,;SMARCC2,upstream_gene_variant,,ENST00000549757,;SMARCC2,downstream_gene_variant,,ENST00000547356,; A ENST00000267064 Transcript synonymous_variant 567/4076 480/3645 160/1214 I atC/atT 1 -1 SMARCC2 HGNC HGNC:11105 protein_coding YES CCDS8907.1 ENSP00000267064 Q8TAQ2 A0A024RB22 UPI0000071C4E NM_003075.3 5/28 Pfam_domain:PF16496,Superfamily_domains:SSF52113 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 56184856 56184856 G A 1 0 0 0 0 0 0 0 1 15069 1280 45 3 3 SMARCC2 12 56184856 Silent SNP G C3N-01799_T 77808 56184856 77090453 33 25678 3 18 3 3 2370 N G_C 7.333595e-06 SMARCC2 0 . GRCh38 12 56184906 56184906 + Silent SNP G G A novel C3N-01799_T C3N-01799_N G G c.430C>T p.= p.L144L ENST00000267064 5/28 312 273 39 221 221 0 strelka-varscan-mutect SMARCC2,synonymous_variant,p.=,ENST00000394023,NM_001130420.1;SMARCC2,synonymous_variant,p.=,ENST00000550164,;SMARCC2,synonymous_variant,p.=,ENST00000267064,NM_003075.3;SMARCC2,synonymous_variant,p.=,ENST00000347471,NM_139067.2;RP11-977G19.5,intron_variant,,ENST00000553176,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550859,;SMARCC2,3_prime_UTR_variant,,ENST00000552674,;SMARCC2,3_prime_UTR_variant,,ENST00000550519,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550150,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000552627,;SMARCC2,upstream_gene_variant,,ENST00000548130,;SMARCC2,upstream_gene_variant,,ENST00000549757,;SMARCC2,downstream_gene_variant,,ENST00000547356,; A ENST00000267064 Transcript synonymous_variant 517/4076 430/3645 144/1214 L Ctg/Ttg 1 -1 SMARCC2 HGNC HGNC:11105 protein_coding YES CCDS8907.1 ENSP00000267064 Q8TAQ2 A0A024RB22 UPI0000071C4E NM_003075.3 5/28 Pfam_domain:PF16496,Superfamily_domains:SSF52113 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 56184906 56184906 G A 1 0 0 0 0 0 0 0 1 15069 933 33 3 3 SMARCC2 12 56184906 Silent SNP G C3N-01799_T 50 56184906 77090403 34 25679 3 18 3 3 2370 N G_C 7.333595e-06 SMARCC2 0 . GRCh38 12 56187225 56187225 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.193G>A p.Gly65Ser p.G65S ENST00000267064 2/28 243 176 67 128 128 0 strelka-varscan-mutect SMARCC2,missense_variant,p.Gly65Ser,ENST00000394023,NM_001130420.1;SMARCC2,missense_variant,p.Gly65Ser,ENST00000550164,;SMARCC2,missense_variant,p.Gly65Ser,ENST00000267064,NM_003075.3;SMARCC2,missense_variant,p.Gly65Ser,ENST00000347471,NM_139067.2;RP11-977G19.5,intron_variant,,ENST00000553176,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550859,;SMARCC2,missense_variant,p.Gly65Ser,ENST00000552674,;SMARCC2,missense_variant,p.Gly65Ser,ENST00000550519,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000550150,;SMARCC2,non_coding_transcript_exon_variant,,ENST00000547356,;SMARCC2,upstream_gene_variant,,ENST00000549757,;SMARCC2,upstream_gene_variant,,ENST00000552627,; T ENST00000267064 Transcript missense_variant 280/4076 193/3645 65/1214 G/S Ggc/Agc 1 -1 SMARCC2 HGNC HGNC:11105 protein_coding YES CCDS8907.1 ENSP00000267064 Q8TAQ2 A0A024RB22 UPI0000071C4E NM_003075.3 deleterious(0) 2/28 Pfam_domain:PF16496 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 82 56187225 56187225 C T 1 0 0 0 0 1 0 0 0 15069 594 21 3 3 SMARCC2 12 56187225 Missense_Mutation SNP C C3N-01799_T 2319 56187225 77088084 35 25680 3 18 3 3 2370 N G_C 7.333595e-06 LRP1 0 . GRCh38 12 57158496 57158496 + Missense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.1656G>A p.Met552Ile p.M552I ENST00000243077 11/89 417 292 125 184 183 1 strelka-varscan-mutect LRP1,missense_variant,p.Met552Ile,ENST00000243077,NM_002332.2;LRP1,downstream_gene_variant,,ENST00000554174,; A ENST00000243077 Transcript missense_variant 2122/14897 1656/13635 552/4544 M/I atG/atA 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 tolerated(0.12) 11/89 Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS rs1300376436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 82 57158496 57158496 G A 1 0 0 0 0 1 0 0 0 8846 1290 45 3 3 LRP1 12 57158496 Missense_Mutation SNP G C3N-01799_T 971271 57158496 76116813 36 25681 AVIL 0 . GRCh38 12 57811038 57811038 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.428G>A p.Arg143Lys p.R143K ENST00000257861 4/19 171 148 23 132 132 0 strelka-varscan-mutect AVIL,missense_variant,p.Arg143Lys,ENST00000257861,NM_006576.3;AVIL,missense_variant,p.Arg143Lys,ENST00000549994,;TSFM,downstream_gene_variant,,ENST00000548851,;RP11-571M6.18,upstream_gene_variant,,ENST00000602327,;RNU6-1083P,upstream_gene_variant,,ENST00000384022,;AVIL,upstream_gene_variant,,ENST00000550083,;AVIL,3_prime_UTR_variant,,ENST00000549851,;AVIL,non_coding_transcript_exon_variant,,ENST00000548843,;AVIL,upstream_gene_variant,,ENST00000549548,;AVIL,upstream_gene_variant,,ENST00000550537,;AVIL,upstream_gene_variant,,ENST00000549753,; T ENST00000257861 Transcript missense_variant 859/2891 428/2460 143/819 R/K aGa/aAa 1 -1 AVIL HGNC HGNC:14188 protein_coding YES CCDS8959.1 ENSP00000257861 O75366 UPI000013CF93 NM_006576.3 tolerated(1) 4/19 Gene3D:3.40.20.10,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF33,SMART_domains:SM00262,Superfamily_domains:SSF55753,Superfamily_domains:SSF82754 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 82 57811038 57811038 C T 1 0 0 0 0 1 0 0 0 1383 913 32 3 3 AVIL 12 57811038 Missense_Mutation SNP C C3N-01799_T 652542 57811038 75464271 37 25682 4 19 1623813 2 2 60 C 9.551826e-05 AVIL 0 . GRCh38 12 57811097 57811097 + Missense_Mutation SNP C C T novel C3N-01799_T C3N-01799_N C C c.369G>A p.Met123Ile p.M123I ENST00000257861 4/19 182 162 20 125 125 0 strelka-varscan-mutect AVIL,missense_variant,p.Met123Ile,ENST00000257861,NM_006576.3;AVIL,missense_variant,p.Met123Ile,ENST00000549994,;TSFM,downstream_gene_variant,,ENST00000548851,;RP11-571M6.18,upstream_gene_variant,,ENST00000602327,;RNU6-1083P,upstream_gene_variant,,ENST00000384022,;AVIL,upstream_gene_variant,,ENST00000550083,;AVIL,3_prime_UTR_variant,,ENST00000549851,;AVIL,non_coding_transcript_exon_variant,,ENST00000548843,;AVIL,upstream_gene_variant,,ENST00000549548,;AVIL,upstream_gene_variant,,ENST00000550537,;AVIL,upstream_gene_variant,,ENST00000549753,; T ENST00000257861 Transcript missense_variant 800/2891 369/2460 123/819 M/I atG/atA 1 -1 AVIL HGNC HGNC:14188 protein_coding YES CCDS8959.1 ENSP00000257861 O75366 UPI000013CF93 NM_006576.3 deleterious(0.01) 4/19 Gene3D:3.40.20.10,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF33,Superfamily_domains:SSF55753,Superfamily_domains:SSF82754 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 82 57811097 57811097 C T 1 0 0 0 0 1 0 0 0 1383 826 29 3 3 AVIL 12 57811097 Missense_Mutation SNP C C3N-01799_T 59 57811097 75464212 38 25683 4 19 1623813 2 2 60 C 9.551826e-05 MED13L 0 . GRCh38 12 116008970 116008970 + Missense_Mutation SNP C C G C3N-01799_T C3N-01799_N C C c.1443G>C p.Lys481Asn p.K481N ENST00000281928 10/31 473 401 72 420 420 0 strelka-varscan-mutect MED13L,missense_variant,p.Lys481Asn,ENST00000281928,NM_015335.4;MED13L,non_coding_transcript_exon_variant,,ENST00000549755,; G ENST00000281928 Transcript missense_variant 1650/14234 1443/6633 481/2210 K/N aaG/aaC COSM3811147 1 -1 MED13L HGNC HGNC:22962 protein_coding YES CCDS9177.1 ENSP00000281928 Q71F56 UPI0000241C1E NM_015335.4 deleterious(0.02) 10/31 hmmpanther:PTHR10791,hmmpanther:PTHR10791:SF64 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 116008970 116008970 C G 1 0 0 0 0 1 0 0 0 9370 912 32 4 4 MED13L 12 116008970 Missense_Mutation SNP C C3N-01799_T 58197873 116008970 17266339 39 25684 MYCBP2 0 . GRCh38 13 77093266 77093266 + Silent SNP T T C novel C3N-01799_T C3N-01799_N T T c.10152A>G p.= p.L3384L ENST00000544440 59/83 279 253 26 237 237 0 strelka-varscan-mutect MYCBP2,synonymous_variant,p.=,ENST00000357337,NM_015057.4;MYCBP2,synonymous_variant,p.=,ENST00000544440,;RP11-226E21.4,intron_variant,,ENST00000638101,;MYCBP2-AS1,intron_variant,,ENST00000593933,;MYCBP2-AS1,intron_variant,,ENST00000629771,;MYCBP2-AS1,intron_variant,,ENST00000627409,;MYCBP2-AS1,downstream_gene_variant,,ENST00000630676,;MYCBP2,downstream_gene_variant,,ENST00000482517,;MYCBP2,downstream_gene_variant,,ENST00000485061,;RP11-226E21.4,intron_variant,,ENST00000637192,; C ENST00000544440 Transcript synonymous_variant 10170/14664 10152/13923 3384/4640 L ctA/ctG 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 59/83 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 82 77093266 77093266 T C 1 0 0 0 0 0 0 0 1 10018 1625 57 5 5 MYCBP2 13 77093266 Silent SNP T C3N-01799_T 77093266 37271062 40 25685 SLC38A6 0 . GRCh38 14 61045351 61045351 + Silent SNP T T A novel C3N-01799_T C3N-01799_N T T c.750T>A p.= p.A250A ENST00000354886 11/17 242 208 34 186 186 0 strelka-varscan-mutect SLC38A6,synonymous_variant,p.=,ENST00000354886,NM_001172702.1;SLC38A6,synonymous_variant,p.=,ENST00000267488,NM_153811.2;SLC38A6,synonymous_variant,p.=,ENST00000451406,;SLC38A6,synonymous_variant,p.=,ENST00000529212,;SLC38A6,synonymous_variant,p.=,ENST00000533744,;SLC38A6,3_prime_UTR_variant,,ENST00000525723,;SLC38A6,3_prime_UTR_variant,,ENST00000491344,;SLC38A6,3_prime_UTR_variant,,ENST00000529345,;SLC38A6,3_prime_UTR_variant,,ENST00000527591,;SLC38A6,upstream_gene_variant,,ENST00000526539,;SLC38A6,downstream_gene_variant,,ENST00000528350,; A ENST00000354886 Transcript synonymous_variant 914/1730 750/1566 250/521 A gcT/gcA 1 1 SLC38A6 HGNC HGNC:19863 protein_coding YES CCDS53900.1 ENSP00000346959 Q8IZM9 UPI000049DDBA NM_001172702.1 11/17 hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF22,Pfam_domain:PF01490 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 82 61045351 61045351 T A 1 0 0 0 0 0 0 0 1 14886 1623 56 4 4 SLC38A6 14 61045351 Silent SNP T C3N-01799_T 61045351 45998367 41 25686 CLMN 0 . GRCh38 14 95319781 95319781 + Missense_Mutation SNP G G C rs367887539 C3N-01799_T C3N-01799_N G G c.12C>G p.His4Gln p.H4Q ENST00000298912 1/13 172 142 30 130 130 0 strelka-mutect CLMN,missense_variant,p.His4Gln,ENST00000298912,NM_024734.3;CLMN,missense_variant,p.His4Gln,ENST00000553733,; C ENST00000298912 Transcript missense_variant 126/12747 12/3009 4/1002 H/Q caC/caG rs367887539,COSM4770850 1 -1 CLMN HGNC HGNC:19972 protein_coding YES CCDS9933.1 ENSP00000298912 Q96JQ2 UPI000006DB99 NM_024734.3 tolerated(0.6) 1/13 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367887539 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 95319781 95319781 G C 1 0 0 0 0 1 0 0 0 3311 1136 40 4 4 CLMN 14 95319781 Missense_Mutation SNP G C3N-01799_T 34274430 95319781 11723937 42 25687 SPINT1 0 . GRCh38 15 40844614 40844614 + Silent SNP C C G rs760563007 C3N-01799_T C3N-01799_N C C c.60C>G p.= p.V20V ENST00000344051 2/11 281 247 34 189 189 0 strelka-varscan-mutect SPINT1,synonymous_variant,p.=,ENST00000344051,NM_181642.2;SPINT1,synonymous_variant,p.=,ENST00000562057,NM_003710.3,NM_001032367.1;SPINT1,synonymous_variant,p.=,ENST00000563656,;SPINT1,synonymous_variant,p.=,ENST00000568823,;SPINT1,upstream_gene_variant,,ENST00000568580,;RP11-532F12.5,upstream_gene_variant,,ENST00000564302,;RP11-532F12.5,upstream_gene_variant,,ENST00000565315,;RP11-532F12.5,upstream_gene_variant,,ENST00000568419,;RP11-532F12.5,upstream_gene_variant,,ENST00000568525,;RP11-532F12.5,upstream_gene_variant,,ENST00000563217,; G ENST00000344051 Transcript synonymous_variant 294/3056 60/1590 20/529 V gtC/gtG rs760563007 1 1 SPINT1 HGNC HGNC:11246 protein_coding YES CCDS10067.1 ENSP00000342098 O43278 UPI00001AE46F NM_181642.2 2/11 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR10083:SF231,hmmpanther:PTHR10083 LOW 1 SNV 1 1 PASS rs760563007 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 82 40844614 40844614 C G 1 0 0 0 0 0 0 0 1 15420 871 31 4 4 SPINT1 15 40844614 Silent SNP C C3N-01799_T 40844614 61146575 43 25688 ZSCAN2 0 . GRCh38 15 84620934 84620934 + Missense_Mutation SNP G G C novel C3N-01799_T C3N-01799_N G G c.739G>C p.Glu247Gln p.E247Q ENST00000448803 3/3 345 311 34 279 279 0 strelka-varscan-mutect ZSCAN2,missense_variant,p.Glu247Gln,ENST00000448803,NM_181877.3;ZSCAN2,missense_variant,p.Glu97Gln,ENST00000358472,;ZSCAN2,missense_variant,p.Glu246Gln,ENST00000327179,;ZSCAN2,missense_variant,p.Glu247Gln,ENST00000546148,;ZSCAN2,intron_variant,,ENST00000538076,;ZSCAN2,intron_variant,,ENST00000541040,;ZSCAN2,intron_variant,,ENST00000485222,;ZSCAN2,downstream_gene_variant,,ENST00000379358,NM_001007072.1;ZSCAN2,downstream_gene_variant,,ENST00000540936,;RP11-182J1.18,intron_variant,,ENST00000618330,;RP11-182J1.3,downstream_gene_variant,,ENST00000621980,;ZSCAN2,upstream_gene_variant,,ENST00000303310,;ZSCAN2,missense_variant,p.Glu247Gln,ENST00000540894,; C ENST00000448803 Transcript missense_variant 1031/3813 739/1845 247/614 E/Q Gag/Cag 1 1 ZSCAN2 HGNC HGNC:20994 protein_coding YES CCDS10329.2 ENSP00000410198 Q7Z7L9 UPI000021D4BC NM_181877.3 deleterious(0.03) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF9,hmmpanther:PTHR24387,Gene3D:3.30.160.60,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 84620934 84620934 G C 1 0 0 0 0 1 0 0 0 18825 943 33 4 4 ZSCAN2 15 84620934 Missense_Mutation SNP G C3N-01799_T 43776320 84620934 17370255 44 25689 ZNF843 0 . GRCh38 16 31435848 31435848 + Silent SNP C C T novel C3N-01799_T C3N-01799_N C C c.1002G>A p.= p.P334P ENST00000315678 2/2 39 35 4 25 25 0 strelka-mutect ZNF843,synonymous_variant,p.=,ENST00000315678,NM_001136509.1;ZNF843,synonymous_variant,p.=,ENST00000618063,;ZNF843,intron_variant,,ENST00000564218,; T ENST00000315678 Transcript synonymous_variant 1727/2137 1002/1047 334/348 P ccG/ccA 1 -1 ZNF843 HGNC HGNC:28710 protein_coding YES CCDS45471.1 ENSP00000322899 Q8N446 UPI000006D317 NM_001136509.1 2/2 LOW 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -10.81769 1 1 1 1 0 T 2 4 82 31435848 31435848 C T 1 0 0 0 0 0 0 0 1 18777 639 23 1 1 ZNF843 16 31435848 Silent SNP C C3N-01799_T 31435848 58902497 45 25690 FANCA 0 . GRCh38 16 89779885 89779885 + Frame_Shift_Del DEL T T - novel C3N-01799_T C3N-01799_N T T c.1699delA p.Thr567ProfsTer38 p.T567Pfs*38 ENST00000389301 18/43 497 439 58 366 366 0 sindel-varindel-pindel FANCA,frameshift_variant,p.Thr567ProfsTer38,ENST00000389301,NM_000135.2;FANCA,frameshift_variant,p.Thr567ProfsTer38,ENST00000568369,NM_001286167.1;FANCA,upstream_gene_variant,,ENST00000567284,;FANCA,frameshift_variant,p.Thr25ProfsTer38,ENST00000567510,; - ENST00000389301 Transcript frameshift_variant 1730/5451 1699/4368 567/1455 T/X Acc/cc 1 -1 FANCA HGNC HGNC:3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 UPI0000520A1A NM_000135.2 18/43 hmmpanther:PTHR12047,hmmpanther:PTHR12047:SF4 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 82 89779885 89779885 T - 1 0 1 0 1 0 0 0 0 5521 1696 59 0 0 FANCA 16 89779885 Frame_Shift_Del DEL T C3N-01799_T 58344037 89779885 558460 46 25691 ITGA2B 0 . GRCh38 17 44385299 44385299 + Missense_Mutation SNP G G A novel C3N-01799_T C3N-01799_N G G c.611C>T p.Ser204Phe p.S204F ENST00000262407 5/30 688 622 66 431 430 1 strelka-varscan-mutect ITGA2B,missense_variant,p.Ser204Phe,ENST00000262407,NM_000419.3;ITGA2B,non_coding_transcript_exon_variant,,ENST00000589645,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592944,;ITGA2B,non_coding_transcript_exon_variant,,ENST00000592253,;ITGA2B,upstream_gene_variant,,ENST00000592462,;ITGA2B,upstream_gene_variant,,ENST00000592226,;ITGA2B,upstream_gene_variant,,ENST00000591990,;ITGA2B,upstream_gene_variant,,ENST00000592075,; A ENST00000262407 Transcript missense_variant 643/3333 611/3120 204/1039 S/F tCc/tTc 1 -1 ITGA2B HGNC HGNC:6138 protein_coding YES CCDS32665.1 ENSP00000262407 P08514 UPI00001868B8 NM_000419.3 tolerated(0.08) 5/30 PROSITE_profiles:PS51470,hmmpanther:PTHR23220:SF73,hmmpanther:PTHR23220,Gene3D:3nigC00,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 82 44385299 44385299 G A 1 0 0 0 0 1 0 0 0 7783 1174 41 3 3 ITGA2B 17 44385299 Missense_Mutation SNP G C3N-01799_T 44385299 38872142 47 25692 TANC2 0 . GRCh38 17 63412030 63412030 + Frame_Shift_Del DEL C C - rs201127113 C3N-01799_T C3N-01799_N C C c.3576delC p.Ile1192MetfsTer28 p.I1192Mfs*28 ENST00000424789 21/25 201 175 26 149 149 0 sindel-varindel-pindel TANC2,frameshift_variant,p.Ile1192MetfsTer28,ENST00000424789,NM_025185.3;TANC2,frameshift_variant,p.Ile1121MetfsTer28,ENST00000583356,;TANC2,frameshift_variant,p.Ile1192MetfsTer28,ENST00000389520,;TANC2,frameshift_variant,p.Ile293MetfsTer28,ENST00000613171,;RP11-269G24.3,intron_variant,,ENST00000583552,;AC015923.1,intron_variant,,ENST00000431604,;TANC2,upstream_gene_variant,,ENST00000579541,; - ENST00000424789 Transcript frameshift_variant 3580/11721 3576/5973 1192/1990 I/X atC/at rs201127113 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 21/25 Gene3D:1.25.40.20,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH 1 deletion 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 82 63412030 63412030 C - 1 0 1 0 1 0 0 0 0 15942 874 31 0 0 TANC2 17 63412030 Frame_Shift_Del DEL C C3N-01799_T 19026731 63412030 19845411 48 25693 ADAMTS10 0 . GRCh38 19 8595790 8595790 + Missense_Mutation SNP C C G C3N-01799_T C3N-01799_N C C c.1451G>C p.Gly484Ala p.G484A ENST00000270328 11/25 644 591 53 443 443 0 strelka-varscan-mutect ADAMTS10,missense_variant,p.Gly484Ala,ENST00000270328,;ADAMTS10,missense_variant,p.Gly484Ala,ENST00000597188,NM_030957.3;ADAMTS10,upstream_gene_variant,,ENST00000595838,NM_001282352.1;ADAMTS10,downstream_gene_variant,,ENST00000596709,;ADAMTS10,downstream_gene_variant,,ENST00000596466,;ADAMTS10,3_prime_UTR_variant,,ENST00000596851,;ADAMTS10,3_prime_UTR_variant,,ENST00000593913,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000601163,;ADAMTS10,non_coding_transcript_exon_variant,,ENST00000601872,;ADAMTS10,upstream_gene_variant,,ENST00000603221,;ADAMTS10,upstream_gene_variant,,ENST00000593826,;ADAMTS10,upstream_gene_variant,,ENST00000596236,; G ENST00000270328 Transcript missense_variant 1682/4194 1451/3312 484/1103 G/A gGa/gCa COSM5391218 1 -1 ADAMTS10 HGNC HGNC:13201 protein_coding YES CCDS12206.1 ENSP00000270328 A0A0A0MQW6 UPI00025D3090 deleterious(0) 11/25 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF26 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 82 8595790 8595790 C G 1 0 0 0 0 1 0 0 0 300 855 30 4 4 ADAMTS10 19 8595790 Missense_Mutation SNP C C3N-01799_T 8595790 50021826 49 25694 PRR12 0 . GRCh38 19 49597094 49597094 + Missense_Mutation SNP G G C novel C3N-01799_T C3N-01799_N G G c.2759G>C p.Gly920Ala p.G920A ENST00000418929 4/14 378 337 41 257 257 0 strelka-varscan-mutect PRR12,missense_variant,p.Gly920Ala,ENST00000418929,NM_020719.1;PRR12,missense_variant,p.Gly99Ala,ENST00000615927,; C ENST00000418929 Transcript missense_variant 2771/6955 2759/6111 920/2036 G/A gGc/gCc 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 deleterious(0.04) 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 49597094 49597094 G C 1 0 0 0 0 1 0 0 0 12719 1203 42 4 4 PRR12 19 49597094 Missense_Mutation SNP G C3N-01799_T 41001304 49597094 9020522 50 25695 C20orf96 0 . GRCh38 20 277288 277288 + Missense_Mutation SNP T T C novel C3N-01799_T C3N-01799_N T T c.661A>G p.Ile221Val p.I221V ENST00000360321 7/11 307 287 20 248 248 0 strelka-varscan-mutect C20orf96,missense_variant,p.Ile220Val,ENST00000400269,NM_080571.1;C20orf96,missense_variant,p.Ile221Val,ENST00000360321,NM_153269.2;C20orf96,missense_variant,p.Ile186Val,ENST00000382369,; C ENST00000360321 Transcript missense_variant 800/1575 661/1092 221/363 I/V Atc/Gtc 1 -1 C20orf96 HGNC HGNC:16227 protein_coding YES CCDS12994.1 ENSP00000353470 Q9NUD7 UPI00001285F1 NM_153269.2 tolerated(1) 7/11 hmmpanther:PTHR28574:SF1,hmmpanther:PTHR28574,Pfam_domain:PF15397 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 82 277288 277288 T C 1 0 0 0 0 1 0 0 0 2011 1464 51 5 5 C20orf96 20 277288 Missense_Mutation SNP T C3N-01799_T 277288 64166879 51 25696 SYNJ1 0 . GRCh38 21 32643459 32643459 + Splice_Site SNP T T G novel C3N-01799_T C3N-01799_N T T c.3548-2A>C p.X1183_splice ENST00000433931 344 305 39 296 293 3 strelka-varscan-mutect SYNJ1,splice_acceptor_variant,,ENST00000382499,NM_203446.2;SYNJ1,splice_acceptor_variant,,ENST00000433931,NM_003895.3;SYNJ1,intron_variant,,ENST00000357345,NM_001160302.1;SYNJ1,intron_variant,,ENST00000382491,;SYNJ1,intron_variant,,ENST00000630077,NM_001160306.1;SYNJ1,intron_variant,,ENST00000438952,;SYNJ1,upstream_gene_variant,,ENST00000418301,; G ENST00000433931 Transcript splice_acceptor_variant -/4852 3548/4839 1183/1612 1 -1 SYNJ1 HGNC HGNC:11503 protein_coding YES CCDS33539.2 ENSP00000409667 J3KQV8 UPI0001A47572 NM_003895.3 26/31 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 82 32643459 32643459 T G 1 0 0 0 0 0 0 1 0 15846 1623 56 5 5 SYNJ1 21 32643459 Splice_Site SNP T C3N-01799_T 32643459 14066524 52 25697 CHD5 0 . GRCh38 1 6123995 6123995 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.4652T>A p.Val1551Glu p.V1551E ENST00000262450 31/42 195 178 17 123 123 0 strelka-varscan-mutect CHD5,missense_variant,p.Val1551Glu,ENST00000262450,NM_015557.2;CHD5,missense_variant,p.Val934Glu,ENST00000462991,;CHD5,3_prime_UTR_variant,,ENST00000377999,;CHD5,intron_variant,,ENST00000496404,;CHD5,downstream_gene_variant,,ENST00000491020,; T ENST00000262450 Transcript missense_variant 4752/9646 4652/5865 1551/1954 V/E gTg/gAg 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 tolerated(0.17) 31/42 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 6123995 6123995 A T 1 0 0 0 0 1 0 0 0 3087 159 6 4 4 CHD5 1 6123995 Missense_Mutation SNP A C3N-01823_T 6123995 242832427 1 25698 ESPN 0 . GRCh38 1 6445717 6445717 + Missense_Mutation SNP C C A rs576644460 C3N-01823_T C3N-01823_N C C c.1246C>A p.Pro416Thr p.P416T ENST00000377828 7/13 347 304 43 208 208 0 strelka-varscan-mutect ESPN,missense_variant,p.Pro416Thr,ENST00000636330,;ESPN,missense_variant,p.Pro416Thr,ENST00000377828,NM_031475.2;ESPN,missense_variant,p.Pro201Thr,ENST00000418286,;ESPN,upstream_gene_variant,,ENST00000461727,;ESPN,upstream_gene_variant,,ENST00000633239,;ESPN,upstream_gene_variant,,ENST00000416731,;ESPN,upstream_gene_variant,,ENST00000475228,;ESPN,upstream_gene_variant,,ENST00000632803,;ESPN,upstream_gene_variant,,ENST00000478323,;RP1-202O8.2,intron_variant,,ENST00000419034,;ESPN,downstream_gene_variant,,ENST00000633651,;ESPN,downstream_gene_variant,,ENST00000632142,;ESPN,upstream_gene_variant,,ENST00000475479,;ESPN,upstream_gene_variant,,ENST00000632593,; A ENST00000377828 Transcript missense_variant 1414/3531 1246/2565 416/854 P/T Ccg/Acg rs576644460 1 1 ESPN HGNC HGNC:13281 protein_coding YES CCDS70.1 ENSP00000367059 B1AK53 UPI000013D2B6 NM_031475.2 deleterious(0.01) 7/13 hmmpanther:PTHR24153:SF14,hmmpanther:PTHR24153 MODERATE 1 SNV 1 1 PASS rs576644460 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 6445717 6445717 C A 1 0 0 0 0 1 0 0 0 5116 623 22 2 2 ESPN 1 6445717 Missense_Mutation SNP C C3N-01823_T 321722 6445717 242510705 2 25699 KIAA2013 0 . GRCh38 1 11925687 11925687 + Missense_Mutation SNP T T C rs751115982 C3N-01823_T C3N-01823_N T T c.551A>G p.Asp184Gly p.D184G ENST00000376572 1/3 325 304 21 202 202 0 varscan-mutect KIAA2013,missense_variant,p.Asp184Gly,ENST00000376572,NM_138346.2;KIAA2013,missense_variant,p.Asp184Gly,ENST00000376576,;KIAA2013,missense_variant,p.Asp184Gly,ENST00000616327,; C ENST00000376572 Transcript missense_variant 737/2815 551/1905 184/634 D/G gAc/gGc rs751115982 1 -1 KIAA2013 HGNC HGNC:28513 protein_coding YES CCDS141.1 ENSP00000365756 Q8IYS2 UPI00000741FB NM_138346.2 deleterious(0.01) 1/3 hmmpanther:PTHR31386:SF2,hmmpanther:PTHR31386,Pfam_domain:PF10222 MODERATE 1 SNV 1 1 PASS rs751115982 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 11925687 11925687 T C 1 0 0 0 0 1 0 0 0 8132 1667 58 5 5 KIAA2013 1 11925687 Missense_Mutation SNP T C3N-01823_T 5479970 11925687 237030735 3 25700 GRIK3 0 . GRCh38 1 36841800 36841800 + Frame_Shift_Del DEL C C - novel C3N-01823_T C3N-01823_N C C c.1466delG p.Gly489AlafsTer31 p.G489Afs*31 ENST00000373091 10/16 447 408 39 364 364 0 sindel-varindel-pindel GRIK3,frameshift_variant,p.Gly489AlafsTer31,ENST00000373091,NM_000831.3;GRIK3,frameshift_variant,p.Gly489AlafsTer31,ENST00000373093,; - ENST00000373091 Transcript frameshift_variant 1483/9101 1466/2760 489/919 G/X gGc/gc 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 10/16 Gene3D:3.40.190.10,Pfam_domain:PF10613,Prints_domain:PR00177,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,SMART_domains:SM00079,SMART_domains:SM00918,Superfamily_domains:SSF53850 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 36841800 36841800 C - 1 0 1 0 1 0 0 0 0 6657 739 26 0 0 GRIK3 1 36841800 Frame_Shift_Del DEL C C3N-01823_T 24916113 36841800 212114622 4 25701 MTF1 0 . GRCh38 1 37815161 37815161 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.2237G>T p.Gly746Val p.G746V ENST00000373036 11/11 188 159 29 116 116 0 strelka-varscan-mutect MTF1,missense_variant,p.Gly746Val,ENST00000373036,NM_005955.2; A ENST00000373036 Transcript missense_variant 2378/7972 2237/2262 746/753 G/V gGc/gTc 1 -1 MTF1 HGNC HGNC:7428 protein_coding YES CCDS30676.1 ENSP00000362127 Q14872 UPI000006E9B3 NM_005955.2 deleterious_low_confidence(0.01) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 37815161 37815161 C A 1 0 0 0 0 1 0 0 0 9907 739 26 2 2 MTF1 1 37815161 Missense_Mutation SNP C C3N-01823_T 973361 37815161 211141261 5 25702 CDC20 0 . GRCh38 1 43359346 43359346 + Missense_Mutation SNP G G A C3N-01823_T C3N-01823_N G G c.131G>A p.Arg44Gln p.R44Q ENST00000372462 1/10 220 194 26 144 144 0 strelka-varscan-mutect CDC20,missense_variant,p.Arg44Gln,ENST00000372462,;CDC20,missense_variant,p.Arg44Gln,ENST00000310955,NM_001255.2;ELOVL1,downstream_gene_variant,,ENST00000621943,NM_001256399.1;ELOVL1,downstream_gene_variant,,ENST00000372458,NM_001256402.1,NM_022821.3;ELOVL1,downstream_gene_variant,,ENST00000413844,NM_001256401.1;RP1-92O14.3,upstream_gene_variant,,ENST00000424948,;ELOVL1,downstream_gene_variant,,ENST00000470769,;ELOVL1,downstream_gene_variant,,ENST00000464204,;ELOVL1,downstream_gene_variant,,ENST00000482302,;ELOVL1,downstream_gene_variant,,ENST00000497050,;ELOVL1,downstream_gene_variant,,ENST00000470968,;ELOVL1,downstream_gene_variant,,ENST00000497569,;ELOVL1,downstream_gene_variant,,ENST00000487209,;ELOVL1,downstream_gene_variant,,ENST00000468865,;CDC20,upstream_gene_variant,,ENST00000478882,;CDC20,upstream_gene_variant,,ENST00000482046,; A ENST00000372462 Transcript missense_variant 334/1777 131/1500 44/499 R/Q cGg/cAg COSM535136 1 1 CDC20 HGNC HGNC:1723 protein_coding YES CCDS484.1 ENSP00000361540 Q12834 UPI0000072C04 tolerated(0.16) 1/10 hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF3 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 43359346 43359346 G A 1 0 0 0 0 1 0 0 0 2762 1116 39 1 1 CDC20 1 43359346 Missense_Mutation SNP G C3N-01823_T 5544185 43359346 205597076 6 25703 SZT2 0 . GRCh38 1 43420214 43420214 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.1152C>T p.= p.A384A ENST00000562955 9/71 255 237 18 199 199 0 strelka-varscan-mutect SZT2,synonymous_variant,p.=,ENST00000562955,NM_015284.3;SZT2,synonymous_variant,p.=,ENST00000634258,;SZT2,upstream_gene_variant,,ENST00000470139,; T ENST00000562955 Transcript synonymous_variant 1152/12281 1152/10128 384/3375 A gcC/gcT 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 9/71 hmmpanther:PTHR14918 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 43420214 43420214 C T 1 0 0 0 0 0 0 0 1 15883 668 24 3 3 SZT2 1 43420214 Silent SNP C C3N-01823_T 60868 43420214 205536208 7 25704 LRRC7 0 . GRCh38 1 70039773 70039773 + Nonsense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.3835G>T p.Glu1279Ter p.E1279* ENST00000035383 19/25 94 85 9 78 78 0 strelka-varscan-mutect LRRC7,stop_gained,p.Glu1284Ter,ENST00000310961,;LRRC7,stop_gained,p.Glu1279Ter,ENST00000035383,NM_020794.2;LRRC7,stop_gained,p.Glu563Ter,ENST00000415775,; T ENST00000035383 Transcript stop_gained 3865/5000 3835/4614 1279/1537 E/* Gaa/Taa 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 19/25 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.00401 1 1 1 1 0 T 4 4 83 70039773 70039773 G T 1 0 0 0 0 0 1 0 0 8916 943 33 2 2 LRRC7 1 70039773 Nonsense_Mutation SNP G C3N-01823_T 26619559 70039773 178916649 8 25705 DNTTIP2 0 . GRCh38 1 93876389 93876389 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.1546A>T p.Ile516Phe p.I516F ENST00000436063 2/7 353 323 30 254 254 0 strelka-varscan-mutect DNTTIP2,missense_variant,p.Ile516Phe,ENST00000436063,NM_014597.4;DNTTIP2,downstream_gene_variant,,ENST00000528680,;DNTTIP2,non_coding_transcript_exon_variant,,ENST00000460191,;DNTTIP2,downstream_gene_variant,,ENST00000496672,;DNTTIP2,upstream_gene_variant,,ENST00000496535,;DNTTIP2,missense_variant,p.Ile516Phe,ENST00000359208,; A ENST00000436063 Transcript missense_variant 1604/5897 1546/2271 516/756 I/F Att/Ttt 1 -1 DNTTIP2 HGNC HGNC:24013 protein_coding YES CCDS44174.1 ENSP00000411010 Q5QJE6 UPI000006F063 NM_014597.4 deleterious(0.04) 2/7 hmmpanther:PTHR21686:SF12,hmmpanther:PTHR21686 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 93876389 93876389 T A 1 0 0 0 0 1 0 0 0 4496 1464 51 4 4 DNTTIP2 1 93876389 Missense_Mutation SNP T C3N-01823_T 23836616 93876389 155080033 9 25706 PLPPR5 0 . GRCh38 1 98953280 98953280 + Silent SNP T T C novel C3N-01823_T C3N-01823_N T T c.411A>G p.= p.V137V ENST00000263177 3/6 340 308 32 270 270 0 strelka-varscan-mutect PLPPR5,synonymous_variant,p.=,ENST00000370188,NM_001010861.2;PLPPR5,synonymous_variant,p.=,ENST00000263177,NM_001037317.1; C ENST00000263177 Transcript synonymous_variant 633/3288 411/966 137/321 V gtA/gtG 1 -1 PLPPR5 HGNC HGNC:31703 protein_coding YES CCDS30778.1 ENSP00000263177 Q32ZL2 UPI0000048D53 NM_001037317.1 3/6 Gene3D:1.20.144.10,Pfam_domain:PF01569,hmmpanther:PTHR10165,hmmpanther:PTHR10165:SF17,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 98953280 98953280 T C 1 0 0 0 0 0 0 0 1 12213 1741 61 5 5 PLPPR5 1 98953280 Silent SNP T C3N-01823_T 5076891 98953280 150003142 10 25707 COL11A1 0 . GRCh38 1 102889517 102889517 + Missense_Mutation SNP C C A C3N-01823_T C3N-01823_N C C c.4402G>T p.Gly1468Trp p.G1468W ENST00000370096 59/67 286 268 18 247 247 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gly1480Trp,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gly1468Trp,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gly1429Trp,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gly1352Trp,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; A ENST00000370096 Transcript missense_variant 4715/7286 4402/5421 1468/1806 G/W Ggg/Tgg COSM3975758,COSM3975759 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0) 59/67 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 102889517 102889517 C A 1 0 0 0 0 1 0 0 0 3455 681 24 2 2 COL11A1 1 102889517 Missense_Mutation SNP C C3N-01823_T 3936237 102889517 146066905 11 25708 GPR61 0 . GRCh38 1 109543161 109543161 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.139T>A p.Phe47Ile p.F47I ENST00000527748 2/2 98 86 12 67 67 0 varscan-mutect GPR61,missense_variant,p.Phe47Ile,ENST00000527748,;GPR61,missense_variant,p.Phe47Ile,ENST00000618721,NM_031936.4;GPR61,missense_variant,p.Phe47Ile,ENST00000616874,;RP5-1160K1.8,intron_variant,,ENST00000526411,;GPR61,upstream_gene_variant,,ENST00000526744,;GPR61,downstream_gene_variant,,ENST00000533959,;GPR61,missense_variant,p.Phe47Ile,ENST00000404129,;GPR61,missense_variant,p.Phe47Ile,ENST00000469383,; A ENST00000527748 Transcript missense_variant 822/4921 139/1356 47/451 F/I Ttc/Atc 1 1 GPR61 HGNC HGNC:13300 protein_coding YES CCDS801.1 ENSP00000432456 Q9BZJ8 G4XH66 UPI000003BCCB tolerated(0.13) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR22752,hmmpanther:PTHR22752:SF5,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 2 1 PASS rs1244295412 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 109543161 109543161 T A 1 0 0 0 0 1 0 0 0 6586 1609 56 4 4 GPR61 1 109543161 Missense_Mutation SNP T C3N-01823_T 6653644 109543161 139413261 12 25709 KCNA10 0 . GRCh38 1 110518614 110518614 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.174C>A p.Asn58Lys p.N58K ENST00000369771 1/1 158 140 18 107 107 0 strelka-varscan-mutect KCNA10,missense_variant,p.Asn58Lys,ENST00000369771,NM_005549.2; T ENST00000369771 Transcript missense_variant 562/1959 174/1536 58/511 N/K aaC/aaA 1 -1 KCNA10 HGNC HGNC:6219 protein_coding YES CCDS826.1 ENSP00000358786 Q16322 UPI0000071B2B NM_005549.2 tolerated_low_confidence(0.63) 1/1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 110518614 110518614 G T 1 0 0 0 0 1 0 0 0 7918 1252 44 2 2 KCNA10 1 110518614 Missense_Mutation SNP G C3N-01823_T 975453 110518614 138437808 13 25710 FAM19A3 0 . GRCh38 1 112724137 112724137 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.458G>A p.Arg153Lys p.R153K ENST00000369630 4/5 82 75 7 52 52 0 strelka-varscan-mutect FAM19A3,missense_variant,p.Arg153Lys,ENST00000369630,NM_001004440.1;FAM19A3,splice_region_variant,p.=,ENST00000361886,NM_182759.2; A ENST00000369630 Transcript missense_variant,splice_region_variant 675/1282 458/510 153/169 R/K aGg/aAg 1 1 FAM19A3 HGNC HGNC:21590 protein_coding YES CCDS30806.1 ENSP00000358644 Q7Z5A8 UPI0000160A38 NM_001004440.1 tolerated_low_confidence(0.07) 4/5 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -14.80096 0.9999797 1 1 1 0 A 3 1 83 112724137 112724137 G A 1 0 0 0 0 1 0 0 0 5380 1014 35 3 3 FAM19A3 1 112724137 Missense_Mutation SNP G C3N-01823_T 2205523 112724137 136232285 14 25711 FLG2 0 . GRCh38 1 152354964 152354964 + Missense_Mutation SNP C C G rs764546221 C3N-01823_T C3N-01823_N C C c.2822G>C p.Ser941Thr p.S941T ENST00000388718 3/3 525 478 47 325 324 1 varscan-mutect FLG2,missense_variant,p.Ser941Thr,ENST00000388718,NM_001014342.2;FLG-AS1,intron_variant,,ENST00000392688,;FLG-AS1,intron_variant,,ENST00000445097,;FLG-AS1,intron_variant,,ENST00000629331,; G ENST00000388718 Transcript missense_variant 2895/9124 2822/7176 941/2391 S/T aGt/aCt rs764546221,COSM1207209 1 -1 FLG2 HGNC HGNC:33276 protein_coding YES CCDS30861.1 ENSP00000373370 Q5D862 UPI00004E1DE5 NM_001014342.2 tolerated(0.47) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571:SF24,hmmpanther:PTHR22571 0,1 MODERATE SNV 5 0,1 1 PASS rs764546221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 152354964 152354964 C G 1 0 0 0 0 1 0 0 0 5785 565 20 4 4 FLG2 1 152354964 Missense_Mutation SNP C C3N-01823_T 39630827 152354964 96601458 15 25712 MUC1 0 . GRCh38 1 155187550 155187550 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.1135G>A p.Ala379Thr p.A379T ENST00000612778 6/8 305 280 25 198 198 0 strelka-varscan-mutect MUC1,missense_variant,p.Ala1157Thr,ENST00000611571,;MUC1,missense_variant,p.Ala379Thr,ENST00000612778,NM_001204286.1;MUC1,missense_variant,p.Ala370Thr,ENST00000620103,NM_001204285.1;MUC1,missense_variant,p.Ala177Thr,ENST00000457295,;MUC1,missense_variant,p.Ala137Thr,ENST00000462317,;MUC1,missense_variant,p.Ala136Thr,ENST00000338684,NM_001204289.1,NM_001204291.1;MUC1,missense_variant,p.Ala134Thr,ENST00000610359,NM_001204292.1;MUC1,missense_variant,p.Ala159Thr,ENST00000368392,NM_001018016.2,NM_001204288.1;MUC1,missense_variant,p.Ala124Thr,ENST00000438413,NM_001204290.1;MUC1,missense_variant,p.Ala168Thr,ENST00000337604,NM_001204287.1,NM_002456.5;MUC1,missense_variant,p.Ala150Thr,ENST00000368390,NM_001018017.2;MUC1,missense_variant,p.Ala125Thr,ENST00000368398,NM_001204294.1;MUC1,missense_variant,p.Ala98Thr,ENST00000343256,NM_001044390.2,NM_001204296.1;MUC1,splice_region_variant,,ENST00000615517,NM_001204295.1;MUC1,splice_region_variant,,ENST00000485118,;MUC1,splice_region_variant,,ENST00000471283,NM_001044393.2;MUC1,splice_region_variant,,ENST00000342482,;MUC1,3_prime_UTR_variant,,ENST00000462215,;MUC1,3_prime_UTR_variant,,ENST00000614519,;MUC1,intron_variant,,ENST00000611577,;MUC1,intron_variant,,ENST00000368393,NM_001204293.1;MUC1,intron_variant,,ENST00000368389,NM_001204297.1;MUC1,intron_variant,,ENST00000368396,NM_001044392.2,NM_001044391.2;TRIM46,downstream_gene_variant,,ENST00000392451,NM_001256600.1;TRIM46,downstream_gene_variant,,ENST00000368382,NM_001256599.1;TRIM46,downstream_gene_variant,,ENST00000611379,NM_001256601.1;TRIM46,downstream_gene_variant,,ENST00000334634,NM_025058.4;TRIM46,downstream_gene_variant,,ENST00000545012,NM_001282378.1;TRIM46,downstream_gene_variant,,ENST00000368383,;AC234582.2,upstream_gene_variant,,ENST00000623940,;AC234582.1,upstream_gene_variant,,ENST00000624572,;TRIM46,downstream_gene_variant,,ENST00000468878,;TRIM46,downstream_gene_variant,,ENST00000474430,;MUC1,downstream_gene_variant,,ENST00000466913,;MUC1,3_prime_UTR_variant,,ENST00000610468,;MUC1,3_prime_UTR_variant,,ENST00000498431,;MUC1,3_prime_UTR_variant,,ENST00000467134,;MUC1,non_coding_transcript_exon_variant,,ENST00000468978,;RP11-201K10.3,upstream_gene_variant,,ENST00000473363,;MUC1,downstream_gene_variant,,ENST00000620770,; T ENST00000612778 Transcript missense_variant 1207/1836 1135/1455 379/484 A/T Gcc/Acc 1 -1 MUC1 HGNC HGNC:7508 protein_coding YES CCDS72933.1 ENSP00000484824 A0A087X2A4 UPI000059C524 NM_001204286.1 tolerated(0.1) 6/8 hmmpanther:PTHR10006:SF8,hmmpanther:PTHR10006,SMART_domains:SM00200 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 155187550 155187550 C T 1 0 0 0 0 1 0 0 0 9968 724 25 3 3 MUC1 1 155187550 Missense_Mutation SNP C C3N-01823_T 2832586 155187550 93768872 16 25713 HAPLN2 0 . GRCh38 1 156625319 156625319 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.958C>G p.Arg320Gly p.R320G ENST00000255039 7/7 177 164 13 131 131 0 strelka-varscan-mutect HAPLN2,missense_variant,p.Arg320Gly,ENST00000255039,NM_021817.2;HAPLN2,downstream_gene_variant,,ENST00000456112,;HAPLN2,non_coding_transcript_exon_variant,,ENST00000494218,;HAPLN2,downstream_gene_variant,,ENST00000487988,;HAPLN2,downstream_gene_variant,,ENST00000482204,; G ENST00000255039 Transcript missense_variant 1365/1771 958/1023 320/340 R/G Cgc/Ggc 1 1 HAPLN2 HGNC HGNC:17410 protein_coding YES CCDS1148.1 ENSP00000255039 Q9GZV7 UPI00000012E0 NM_021817.2 deleterious(0) 7/7 Gene3D:3.10.100.10,Pfam_domain:PF00193,PROSITE_profiles:PS50963,hmmpanther:PTHR22804,SMART_domains:SM00445,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs1200781996 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 156625319 156625319 C G 1 0 0 0 0 1 0 0 0 6841 768 27 4 4 HAPLN2 1 156625319 Missense_Mutation SNP C C3N-01823_T 1437769 156625319 92331103 17 25714 FCRL2 0 . GRCh38 1 157748881 157748881 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.1387G>C p.Val463Leu p.V463L ENST00000361516 9/12 205 192 13 130 130 0 strelka-varscan-mutect FCRL2,missense_variant,p.Val463Leu,ENST00000361516,NM_030764.3;FCRL2,missense_variant,p.Val179Leu,ENST00000368181,;FCRL2,non_coding_transcript_exon_variant,,ENST00000368178,; G ENST00000361516 Transcript missense_variant 1436/2579 1387/1527 463/508 V/L Gtc/Ctc 1 -1 FCRL2 HGNC HGNC:14875 protein_coding YES CCDS1168.1 ENSP00000355157 Q96LA5 UPI000006E1F3 NM_030764.3 tolerated(0.26) 9/12 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF61,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 157748881 157748881 C G 1 0 0 0 0 1 0 0 0 5658 478 17 4 4 FCRL2 1 157748881 Missense_Mutation SNP C C3N-01823_T 1123562 157748881 91207541 18 25715 SPTA1 0 . GRCh38 1 158645537 158645537 + Silent SNP G G C rs369559397 C3N-01823_T C3N-01823_N G G c.3954C>G p.= p.A1318A ENST00000368147 28/52 693 641 52 490 490 0 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000465741,; C ENST00000368147 Transcript synonymous_variant 4135/7999 3954/7260 1318/2419 A gcC/gcG rs369559397 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 28/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS rs369559397 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 158645537 158645537 G C 1 0 0 0 0 0 0 0 1 15472 1103 39 4 4 SPTA1 1 158645537 Silent SNP G C3N-01823_T 896656 158645537 90310885 19 25716 OR10J3 0 . GRCh38 1 159314546 159314546 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.114G>T p.= p.L38L ENST00000332217 1/1 448 422 26 279 279 0 strelka-varscan-mutect OR10J3,synonymous_variant,p.=,ENST00000332217,NM_001004467.1; A ENST00000332217 Transcript synonymous_variant 114/990 114/990 38/329 L ctG/ctT 1 -1 OR10J3 HGNC HGNC:14992 protein_coding YES CCDS30909.1 ENSP00000331789 Q5JRS4 UPI0000441EEF NM_001004467.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF28,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 159314546 159314546 C A 1 0 0 0 0 0 0 0 1 10988 813 29 2 2 OR10J3 1 159314546 Silent SNP C C3N-01823_T 669009 159314546 89641876 20 25717 IGSF9 0 . GRCh38 1 159934258 159934258 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1036G>T p.Val346Phe p.V346F ENST00000368094 9/21 227 205 22 142 142 0 strelka-varscan-mutect IGSF9,missense_variant,p.Val346Phe,ENST00000368094,NM_001135050.1;IGSF9,missense_variant,p.Val330Phe,ENST00000361509,NM_020789.3;IGSF9,missense_variant,p.Val346Phe,ENST00000611023,;IGSF9,non_coding_transcript_exon_variant,,ENST00000476102,;IGSF9,upstream_gene_variant,,ENST00000493195,;IGSF9,upstream_gene_variant,,ENST00000496645,; A ENST00000368094 Transcript missense_variant 1234/4044 1036/3540 346/1179 V/F Gtt/Ttt 1 -1 IGSF9 HGNC HGNC:18132 protein_coding YES CCDS44254.1 ENSP00000357073 Q9P2J2 UPI000004A10B NM_001135050.1 deleterious(0.02) 9/21 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF708,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 83 159934258 159934258 C A 1 0 0 0 0 1 0 0 0 7513 507 18 2 2 IGSF9 1 159934258 Missense_Mutation SNP C C3N-01823_T 619712 159934258 89022164 21 25718 NOS1AP 0 . GRCh38 1 162355311 162355311 + Silent SNP A A T novel C3N-01823_T C3N-01823_N A A c.720A>T p.= p.L240L ENST00000361897 7/10 759 688 71 480 480 0 strelka-varscan-mutect NOS1AP,synonymous_variant,p.=,ENST00000361897,NM_014697.2;NOS1AP,synonymous_variant,p.=,ENST00000530878,NM_001164757.1;NOS1AP,synonymous_variant,p.=,ENST00000430120,; T ENST00000361897 Transcript synonymous_variant 1122/4931 720/1521 240/506 L ctA/ctT 1 1 NOS1AP HGNC HGNC:16859 protein_coding YES CCDS1237.1 ENSP00000355133 O75052 UPI000019C573 NM_014697.2 7/10 hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF39 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 162355311 162355311 A T 1 0 0 0 0 0 0 0 1 10587 407 15 4 4 NOS1AP 1 162355311 Silent SNP A C3N-01823_T 2421053 162355311 86601111 22 25719 MGST3 0 . GRCh38 1 165649894 165649894 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.47C>T p.Ala16Val p.A16V ENST00000367889 2/6 586 542 44 364 364 0 strelka-varscan-mutect MGST3,missense_variant,p.Ala30Val,ENST00000627653,;MGST3,missense_variant,p.Ala16Val,ENST00000367889,NM_004528.3;MGST3,missense_variant,p.Ala16Val,ENST00000367888,;MGST3,missense_variant,p.Ala16Val,ENST00000367884,;MGST3,missense_variant,p.Ala30Val,ENST00000367883,;MGST3,missense_variant,p.Ala30Val,ENST00000367885,;MGST3,non_coding_transcript_exon_variant,,ENST00000477450,;MGST3,downstream_gene_variant,,ENST00000461759,;MGST3,non_coding_transcript_exon_variant,,ENST00000609263,;MGST3,non_coding_transcript_exon_variant,,ENST00000461308,;MGST3,non_coding_transcript_exon_variant,,ENST00000488688,;MGST3,non_coding_transcript_exon_variant,,ENST00000495447,;MGST3,upstream_gene_variant,,ENST00000494074,; T ENST00000367889 Transcript missense_variant 487/1015 47/459 16/152 A/V gCt/gTt 1 1 MGST3 HGNC HGNC:7064 protein_coding YES CCDS1249.1 ENSP00000356864 O14880 A0A024R8Z1 UPI000012BC86 NM_004528.3 tolerated(1) 2/6 Gene3D:1.20.120.550,Pfam_domain:PF01124,hmmpanther:PTHR10250,hmmpanther:PTHR10250:SF17,Superfamily_domains:SSF161084,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 165649894 165649894 C T 1 0 0 0 0 1 0 0 0 9519 797 28 3 3 MGST3 1 165649894 Missense_Mutation SNP C C3N-01823_T 3294583 165649894 83306528 23 25720 PAPPA2 0 . GRCh38 1 176740188 176740188 + Silent SNP G G A C3N-01823_T C3N-01823_N G G c.4143G>A p.= p.Q1381Q ENST00000367662 14/23 375 279 96 236 236 0 strelka-varscan-mutect PAPPA2,synonymous_variant,p.=,ENST00000367662,NM_020318.2; A ENST00000367662 Transcript synonymous_variant 5307/9691 4143/5376 1381/1791 Q caG/caA COSM2094021,COSM5321695 1 1 PAPPA2 HGNC HGNC:14615 protein_coding YES CCDS41438.1 ENSP00000356634 Q9BXP8 UPI000004A835 NM_020318.2 14/23 hmmpanther:PTHR19325:SF1,hmmpanther:PTHR19325 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 176740188 176740188 G A 1 0 0 0 0 0 0 0 1 11513 991 35 3 3 PAPPA2 1 176740188 Silent SNP G C3N-01823_T 11090294 176740188 72216234 24 25721 AXDND1 0 . GRCh38 1 179370020 179370020 + Silent SNP C C A rs577148644 C3N-01823_T C3N-01823_N C C c.316C>A p.= p.R106R ENST00000367618 4/26 241 192 49 195 195 0 strelka-varscan-mutect AXDND1,synonymous_variant,p.=,ENST00000367618,NM_144696.5;AXDND1,synonymous_variant,p.=,ENST00000617277,;AXDND1,synonymous_variant,p.=,ENST00000434088,;AXDND1,synonymous_variant,p.=,ENST00000509175,;AXDND1,synonymous_variant,p.=,ENST00000511889,;AXDND1,downstream_gene_variant,,ENST00000508229,;AXDND1,non_coding_transcript_exon_variant,,ENST00000461179,;AXDND1,non_coding_transcript_exon_variant,,ENST00000510593,;AXDND1,synonymous_variant,p.=,ENST00000511157,;AXDND1,non_coding_transcript_exon_variant,,ENST00000507383,;AXDND1,non_coding_transcript_exon_variant,,ENST00000508285,; A ENST00000367618 Transcript synonymous_variant 703/3642 316/3039 106/1012 R Cga/Aga rs577148644,COSM2095301,COSM3984508,COSM5584522 1 1 AXDND1 HGNC HGNC:26564 protein_coding YES CCDS30948.1 ENSP00000356590 Q5T1B0 UPI000022AC91 NM_144696.5 4/26 hmmpanther:PTHR23052 0,1,1,1 LOW 1 SNV 1 0,1,1,1 1 PASS rs577148644 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 179370020 179370020 C A 1 0 0 0 0 0 0 0 1 1392 876 31 1 1 AXDND1 1 179370020 Silent SNP C C3N-01823_T 2629832 179370020 69586402 25 25722 TSEN15 0 . GRCh38 1 184054803 184054803 + Missense_Mutation SNP A A C novel C3N-01823_T C3N-01823_N A A c.293A>C p.Glu98Ala p.E98A ENST00000361641 3/5 194 182 12 133 133 0 varscan-mutect TSEN15,missense_variant,p.Glu98Ala,ENST00000361641,NM_001300764.1,NM_052965.3;TSEN15,missense_variant,p.Glu98Ala,ENST00000423085,NM_001127394.3;TSEN15,missense_variant,p.Glu98Ala,ENST00000533373,NM_001300766.1;TSEN15,missense_variant,p.Glu97Ala,ENST00000462677,;TSEN15,missense_variant,p.Glu98Ala,ENST00000485209,;TSEN15,non_coding_transcript_exon_variant,,ENST00000367518,;TSEN15,non_coding_transcript_exon_variant,,ENST00000457455,; C ENST00000361641 Transcript missense_variant 372/1960 293/516 98/171 E/A gAa/gCa 1 1 TSEN15 HGNC HGNC:16791 protein_coding YES CCDS1361.1 ENSP00000355299 Q8WW01 B1ALV0 UPI00000722DC NM_001300764.1,NM_052965.3 deleterious(0.05) 3/5 Pfam_domain:PF09631,hmmpanther:PTHR28582,hmmpanther:PTHR28582:SF1,Superfamily_domains:SSF53032 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 184054803 184054803 A C 1 0 0 0 0 1 0 0 0 17117 246 9 5 5 TSEN15 1 184054803 Missense_Mutation SNP A C3N-01823_T 4684783 184054803 64901619 26 25723 TPR 0 . GRCh38 1 186347339 186347339 + Missense_Mutation SNP G G C C3N-01823_T C3N-01823_N G G c.2896C>G p.Gln966Glu p.Q966E ENST00000367478 22/51 196 181 15 128 128 0 strelka-varscan-mutect TPR,missense_variant,p.Gln966Glu,ENST00000367478,NM_003292.2;TPR,downstream_gene_variant,,ENST00000474852,;TPR,upstream_gene_variant,,ENST00000481347,;TPR,downstream_gene_variant,,ENST00000491783,;TPR,downstream_gene_variant,,ENST00000469463,; C ENST00000367478 Transcript missense_variant 3193/9708 2896/7092 966/2363 Q/E Caa/Gaa COSM1500264 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 deleterious(0.02) 22/51 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18898 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 186347339 186347339 G C 1 0 0 0 0 1 0 0 0 16897 1299 45 4 4 TPR 1 186347339 Missense_Mutation SNP G C3N-01823_T 2292536 186347339 62609083 27 25724 F13B 0 . GRCh38 1 197057022 197057022 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.1162G>A p.Glu388Lys p.E388K ENST00000367412 7/12 362 268 94 273 273 0 strelka-varscan-mutect F13B,missense_variant,p.Glu388Lys,ENST00000367412,NM_001994.2; T ENST00000367412 Transcript missense_variant 1206/2217 1162/1986 388/661 E/K Gag/Aag 1 -1 F13B HGNC HGNC:3534 protein_coding YES CCDS1388.1 ENSP00000356382 P05160 UPI000013D8E0 NM_001994.2 tolerated(0.7) 7/12 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF314,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs1280513811 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 197057022 197057022 C T 1 0 0 0 0 1 0 0 0 5209 835 29 3 3 F13B 1 197057022 Missense_Mutation SNP C C3N-01823_T 10709683 197057022 51899400 28 25725 DSTYK 0 . GRCh38 1 205211521 205211521 + Silent SNP C C A rs759067934 C3N-01823_T C3N-01823_N C C c.15G>T p.= p.G5G ENST00000367162 1/13 94 65 29 57 57 0 strelka-varscan-mutect DSTYK,synonymous_variant,p.=,ENST00000367162,NM_015375.2;DSTYK,synonymous_variant,p.=,ENST00000367161,NM_199462.2; A ENST00000367162 Transcript synonymous_variant 46/7874 15/2790 5/929 G ggG/ggT rs759067934 1 -1 DSTYK HGNC HGNC:29043 protein_coding YES CCDS1451.1 ENSP00000356130 Q6XUX3 UPI00001D7D39 NM_015375.2 1/13 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs759067934 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 205211521 205211521 C A 1 0 0 0 0 0 0 0 1 4606 610 22 2 2 DSTYK 1 205211521 Silent SNP C C3N-01823_T 8154499 205211521 43744901 29 25726 USH2A 0 . GRCh38 1 215867076 215867076 + Missense_Mutation SNP C C G C3N-01823_T C3N-01823_N C C c.8776G>C p.Glu2926Gln p.E2926Q ENST00000307340 44/72 399 378 21 228 228 0 strelka-varscan-mutect USH2A,missense_variant,p.Glu2926Gln,ENST00000307340,NM_206933.2; G ENST00000307340 Transcript missense_variant 9163/18883 8776/15609 2926/5202 E/Q Gag/Cag COSM3483487,COSM3483488 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 tolerated(0.44) 44/72 Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 215867076 215867076 C G 1 0 0 0 0 1 0 0 0 17570 922 32 4 4 USH2A 1 215867076 Missense_Mutation SNP C C3N-01823_T 10655555 215867076 33089346 30 25727 COG2 0 . GRCh38 1 230687059 230687059 + Missense_Mutation SNP C C G C3N-01823_T C3N-01823_N C C c.1505C>G p.Thr502Arg p.T502R ENST00000366669 13/18 188 142 46 112 112 0 strelka-varscan-mutect COG2,missense_variant,p.Thr443Arg,ENST00000534989,;COG2,missense_variant,p.Thr502Arg,ENST00000366669,NM_007357.2;COG2,missense_variant,p.Thr502Arg,ENST00000366668,NM_001145036.1;COG2,non_coding_transcript_exon_variant,,ENST00000482012,;COG2,upstream_gene_variant,,ENST00000490900,;COG2,upstream_gene_variant,,ENST00000478710,;COG2,3_prime_UTR_variant,,ENST00000468893,;COG2,downstream_gene_variant,,ENST00000494371,; G ENST00000366669 Transcript missense_variant 1620/2921 1505/2217 502/738 T/R aCa/aGa COSM425561 1 1 COG2 HGNC HGNC:6546 protein_coding YES CCDS1584.1 ENSP00000355629 Q14746 B1ALW7 UPI0000127E38 NM_007357.2 tolerated(0.31) 13/18 hmmpanther:PTHR12961 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 230687059 230687059 C G 1 0 0 0 0 1 0 0 0 3446 478 17 4 4 COG2 1 230687059 Missense_Mutation SNP C C3N-01823_T 14819983 230687059 18269363 31 25728 RYR2 0 . GRCh38 1 237566764 237566764 + Frame_Shift_Del DEL G G - novel C3N-01823_T C3N-01823_N G G c.3412delG p.Asp1138MetfsTer31 p.D1138Mfs*31 ENST00000366574 28/105 201 145 56 149 149 0 sindel-varindel-pindel RYR2,frameshift_variant,p.Asp1138MetfsTer31,ENST00000366574,NM_001035.2;RYR2,frameshift_variant,p.Asp1122MetfsTer31,ENST00000360064,; - ENST00000366574 Transcript frameshift_variant 3729/16562 3412/14904 1138/4967 D/X Gat/at 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 28/105 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449,Superfamily_domains:SSF49899 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 237566764 237566764 G - 1 0 1 0 1 0 0 0 0 14029 1290 45 0 0 RYR2 1 237566764 Frame_Shift_Del DEL G C3N-01823_T 6879705 237566764 11389658 32 25729 FMN2 0 . GRCh38 1 240207352 240207352 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.2540C>T p.Ser847Phe p.S847F ENST00000319653 5/18 547 409 138 338 337 1 strelka-varscan-mutect FMN2,missense_variant,p.Ser847Phe,ENST00000319653,NM_001305424.1,NM_020066.4;FMN2,downstream_gene_variant,,ENST00000447095,; T ENST00000319653 Transcript missense_variant 2770/6434 2540/5169 847/1722 S/F tCt/tTt 1 1 FMN2 HGNC HGNC:14074 protein_coding YES CCDS31069.2 ENSP00000318884 Q9NZ56 UPI00015FA087 NM_001305424.1,NM_020066.4 deleterious_low_confidence(0.04) 5/18 SMART_domains:SM00498 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 240207352 240207352 C T 1 0 0 0 0 1 0 0 0 5806 913 32 3 3 FMN2 1 240207352 Missense_Mutation SNP C C3N-01823_T 2640588 240207352 8749070 33 25730 OR11L1 0 . GRCh38 1 247841144 247841144 + Nonsense_Mutation SNP G G C rs777726488 C3N-01823_T C3N-01823_N G G c.753C>G p.Tyr251Ter p.Y251* ENST00000355784 1/1 461 412 49 254 254 0 strelka-varscan-mutect OR11L1,stop_gained,p.Tyr251Ter,ENST00000355784,NM_001001959.1; C ENST00000355784 Transcript stop_gained 753/969 753/969 251/322 Y/* taC/taG rs777726488 1 -1 OR11L1 HGNC HGNC:14998 protein_coding YES CCDS31098.1 ENSP00000348033 Q8NGX0 UPI0000061EBC NM_001001959.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF295,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS rs777726488 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 83 247841144 247841144 G C 1 0 0 0 0 0 1 0 0 11007 1024 36 4 4 OR11L1 1 247841144 Nonsense_Mutation SNP G C3N-01823_T 7633792 247841144 1115278 34 25731 TRIM58 0 . GRCh38 1 247860665 247860665 + Missense_Mutation SNP G G T rs764514224 C3N-01823_T C3N-01823_N G G c.469G>T p.Ala157Ser p.A157S ENST00000366481 2/6 276 226 50 195 195 0 strelka-varscan-mutect TRIM58,missense_variant,p.Ala157Ser,ENST00000366481,NM_015431.3; T ENST00000366481 Transcript missense_variant 517/3225 469/1461 157/486 A/S Gcc/Tcc rs764514224 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 tolerated(0.06) 2/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393 MODERATE 1 SNV 1 1 PASS rs764514224 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 247860665 247860665 G T 1 0 0 0 0 1 0 0 0 17024 1087 38 1 1 TRIM58 1 247860665 Missense_Mutation SNP G C3N-01823_T 19521 247860665 1095757 35 25732 OR2M7 0 . GRCh38 1 248324204 248324204 + Missense_Mutation SNP C C T rs543782719 C3N-01823_T C3N-01823_N C C c.365G>A p.Arg122His p.R122H ENST00000317965 1/1 387 364 23 257 257 0 varscan-mutect OR2M7,missense_variant,p.Arg122His,ENST00000317965,NM_001004691.1; T ENST00000317965 Transcript missense_variant 365/939 365/939 122/312 R/H cGc/cAc rs543782719,COSM4837310 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 deleterious(0.03) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 0,1 MODERATE 1 SNV 0,1 1 PASS rs543782719 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 248324204 248324204 C T 1 0 0 0 0 1 0 0 0 11092 768 27 1 1 OR2M7 1 248324204 Missense_Mutation SNP C C3N-01823_T 463539 248324204 632218 36 25733 OR2T1 0 . GRCh38 1 248406541 248406541 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.547C>A p.Pro183Thr p.P183T ENST00000366474 1/1 280 254 26 153 153 0 strelka-varscan-mutect OR2T1,missense_variant,p.Pro183Thr,ENST00000366474,NM_030904.1; A ENST00000366474 Transcript missense_variant 547/1110 547/1110 183/369 P/T Cct/Act 1 1 OR2T1 HGNC HGNC:8277 protein_coding YES CCDS31115.1 ENSP00000355430 O43869 A0A126GVY3 UPI00003B2872 NM_030904.1 deleterious(0.03) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF125,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 248406541 248406541 C A 1 0 0 0 0 1 0 0 0 11094 623 22 2 2 OR2T1 1 248406541 Missense_Mutation SNP C C3N-01823_T 82337 248406541 549881 37 25734 OR14I1 0 . GRCh38 1 248681785 248681785 + Missense_Mutation SNP G G T rs758759072 C3N-01823_T C3N-01823_N G G c.520C>A p.Gln174Lys p.Q174K ENST00000342623 1/1 430 347 83 245 245 0 strelka-varscan-mutect OR14I1,missense_variant,p.Gln174Lys,ENST00000342623,NM_001004734.1; T ENST00000342623 Transcript missense_variant 520/936 520/936 174/311 Q/K Cag/Aag rs758759072 1 -1 OR14I1 HGNC HGNC:19575 protein_coding YES CCDS31125.1 ENSP00000339726 A6ND48 UPI0000199BC9 NM_001004734.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF316,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs758759072 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 248681785 248681785 G T 1 0 0 0 0 1 0 0 0 11024 1357 47 2 2 OR14I1 1 248681785 Missense_Mutation SNP G C3N-01823_T 275244 248681785 274637 38 25735 ATAD2B 0 . GRCh38 2 23926730 23926730 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.41C>G p.Ser14Cys p.S14C ENST00000238789 1/28 202 184 18 107 107 0 strelka-varscan-mutect ATAD2B,missense_variant,p.Ser14Cys,ENST00000238789,NM_017552.3,NM_001242338.2;ATAD2B,missense_variant,p.Ser14Cys,ENST00000439915,;UBXN2A,upstream_gene_variant,,ENST00000404924,;UBXN2A,upstream_gene_variant,,ENST00000446425,; C ENST00000238789 Transcript missense_variant 385/8103 41/4377 14/1458 S/C tCc/tGc 1 -1 ATAD2B HGNC HGNC:29230 protein_coding YES CCDS46227.1 ENSP00000238789 Q9ULI0 UPI00006C056C NM_017552.3,NM_001242338.2 deleterious_low_confidence(0.01) 1/28 Low_complexity_(Seg):seg,hmmpanther:PTHR23069:SF5,hmmpanther:PTHR23069 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.99993 0.9999998 1 1 1 0 C 3 2 83 23926730 23926730 G C 1 0 0 0 0 1 0 0 0 1220 1174 41 4 4 ATAD2B 2 23926730 Missense_Mutation SNP G C3N-01823_T 23926730 218266799 39 25736 KIF3C 0 . GRCh38 2 25981491 25981491 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.427G>T p.Ala143Ser p.A143S ENST00000264712 1/8 374 325 49 234 234 0 strelka-varscan-mutect KIF3C,missense_variant,p.Ala143Ser,ENST00000264712,NM_002254.6;KIF3C,missense_variant,p.Ala143Ser,ENST00000405914,;KIF3C,missense_variant,p.Ala143Ser,ENST00000455394,;KIF3C,missense_variant,p.Ala143Ser,ENST00000417737,;KIF3C,upstream_gene_variant,,ENST00000475453,; A ENST00000264712 Transcript missense_variant 1007/5344 427/2382 143/793 A/S Gcc/Tcc 1 -1 KIF3C HGNC HGNC:6321 protein_coding YES CCDS1719.1 ENSP00000264712 O14782 A2RU78 UPI000012DDB2 NM_002254.6 tolerated(0.12) 1/8 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF531,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 25981491 25981491 C A 1 0 0 0 0 1 0 0 0 8167 739 26 2 2 KIF3C 2 25981491 Missense_Mutation SNP C C3N-01823_T 2054761 25981491 216212038 40 25737 OTOF 0 . GRCh38 2 26516575 26516575 + Missense_Mutation SNP A A G novel C3N-01823_T C3N-01823_N A A c.352T>C p.Tyr118His p.Y118H ENST00000272371 5/47 521 474 47 302 301 1 strelka-varscan-mutect OTOF,missense_variant,p.Tyr118His,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Tyr118His,ENST00000403946,NM_001287489.1; G ENST00000272371 Transcript missense_variant 479/7156 352/5994 118/1997 Y/H Tat/Cat 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 deleterious(0) 5/47 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 26516575 26516575 A G 1 0 0 0 0 1 0 0 0 11369 391 14 5 5 OTOF 2 26516575 Missense_Mutation SNP A C3N-01823_T 535084 26516575 215676954 41 25738 ALK 0 . GRCh38 2 29225486 29225486 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.3147C>A p.= p.V1049V ENST00000389048 19/29 413 339 74 276 276 0 strelka-varscan-mutect ALK,synonymous_variant,p.=,ENST00000389048,NM_004304.4;ALK,synonymous_variant,p.=,ENST00000618119,;ALK,upstream_gene_variant,,ENST00000431873,;ALK,upstream_gene_variant,,ENST00000453137,; T ENST00000389048 Transcript synonymous_variant 4054/6220 3147/4863 1049/1620 V gtC/gtA 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 19/29 Low_complexity_(Seg):seg,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF276 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 29225486 29225486 G T 1 0 0 0 0 0 0 0 1 625 1161 41 2 2 ALK 2 29225486 Silent SNP G C3N-01823_T 2708911 29225486 212968043 42 25739 SPAST 0 . GRCh38 2 32136888 32136888 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.1333A>T p.Ser445Cys p.S445C ENST00000615843 11/17 344 279 65 249 248 1 strelka-varscan-mutect SPAST,missense_variant,p.Ser445Cys,ENST00000615843,NM_014946.3;SPAST,missense_variant,p.Ser445Cys,ENST00000315285,;SPAST,missense_variant,p.Ser413Cys,ENST00000345662,NM_199436.1;SPAST,missense_variant,p.Ser359Cys,ENST00000621856,; T ENST00000615843 Transcript missense_variant 1554/5212 1333/1851 445/616 S/C Agc/Tgc 1 1 SPAST HGNC HGNC:11233 protein_coding YES CCDS1778.1 ENSP00000480893 Q9UBP0 E5KRP5 UPI0000038A6B NM_014946.3 deleterious(0) 11/17 Gene3D:3.40.50.300,HAMAP:MF_03021,Pfam_domain:PF00004,PIRSF_domain:PIRSF037338,hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF86,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 32136888 32136888 A T 1 0 0 0 0 1 0 0 0 15328 420 15 4 4 SPAST 2 32136888 Missense_Mutation SNP A C3N-01823_T 2911402 32136888 210056641 43 25740 PRKD3 0 . GRCh38 2 37290926 37290926 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.501C>G p.Phe167Leu p.F167L ENST00000379066 4/19 217 204 13 175 175 0 strelka-varscan-mutect PRKD3,missense_variant,p.Phe167Leu,ENST00000379066,;PRKD3,missense_variant,p.Phe167Leu,ENST00000234179,NM_005813.4;PRKD3,missense_variant,p.Phe63Leu,ENST00000443187,;PRKD3,non_coding_transcript_exon_variant,,ENST00000494667,;PRKD3,non_coding_transcript_exon_variant,,ENST00000475912,;PRKD3,downstream_gene_variant,,ENST00000464552,; C ENST00000379066 Transcript missense_variant 1264/6111 501/2673 167/890 F/L ttC/ttG 1 -1 PRKD3 HGNC HGNC:9408 protein_coding YES CCDS1789.1 ENSP00000368356 O94806 UPI0000035B4D deleterious(0) 4/19 Gene3D:3.30.60.20,Pfam_domain:PF00130,PIRSF_domain:PIRSF000552,PROSITE_patterns:PS00479,PROSITE_profiles:PS50081,hmmpanther:PTHR22968,hmmpanther:PTHR22968:SF11,SMART_domains:SM00109,Superfamily_domains:SSF57889 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 37290926 37290926 G C 1 0 0 0 0 1 0 0 0 12653 933 33 4 4 PRKD3 2 37290926 Missense_Mutation SNP G C3N-01823_T 5154038 37290926 204902603 44 25741 LRPPRC 0 . GRCh38 2 43918329 43918329 + Missense_Mutation SNP C C A rs774857058 C3N-01823_T C3N-01823_N C C c.2966G>T p.Arg989Leu p.R989L ENST00000260665 28/38 363 318 45 268 268 0 strelka-varscan-mutect LRPPRC,missense_variant,p.Arg989Leu,ENST00000260665,NM_133259.3; A ENST00000260665 Transcript missense_variant 3024/6335 2966/4185 989/1394 R/L cGt/cTt rs774857058 1 -1 LRPPRC HGNC HGNC:15714 protein_coding YES CCDS33189.1 ENSP00000260665 P42704 E5KNY5 UPI000019B4D2 NM_133259.3 deleterious(0) 28/38 hmmpanther:PTHR24015,hmmpanther:PTHR24015:SF187 likely_pathogenic MODERATE 1 SNV 1 1 1 PASS rs774857058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 43918329 43918329 C A 1 0 0 0 0 1 0 0 0 8860 536 19 1 1 LRPPRC 2 43918329 Missense_Mutation SNP C C3N-01823_T 6627403 43918329 198275200 45 25742 SLC3A1 0 . GRCh38 2 44281462 44281462 + Missense_Mutation SNP G G A rs138395881 C3N-01823_T C3N-01823_N G G c.686G>A p.Arg229Gln p.R229Q ENST00000260649 3/10 443 368 75 316 315 1 strelka-varscan-mutect SLC3A1,missense_variant,p.Arg229Gln,ENST00000260649,NM_000341.3;SLC3A1,missense_variant,p.Arg229Gln,ENST00000409229,;SLC3A1,missense_variant,p.Arg229Gln,ENST00000409387,;SLC3A1,missense_variant,p.Arg229Gln,ENST00000611973,;SLC3A1,missense_variant,p.Arg229Gln,ENST00000409741,;SLC3A1,missense_variant,p.Arg229Gln,ENST00000410056,;SLC3A1,upstream_gene_variant,,ENST00000409380,;SLC3A1,upstream_gene_variant,,ENST00000427285,; A ENST00000260649 Transcript missense_variant 762/2989 686/2058 229/685 R/Q cGg/cAg rs138395881,COSM1161355,COSM373621 1 1 SLC3A1 HGNC HGNC:11025 protein_coding YES CCDS1819.1 ENSP00000260649 Q07837 A0A0S2Z4E1 UPI000013D0F2 NM_000341.3 tolerated(0.15) 3/10 Gene3D:3.90.400.10,Pfam_domain:PF00128,hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73,SMART_domains:SM00642,Superfamily_domains:SSF51445 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs138395881 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 44281462 44281462 G A 1 0 0 0 0 1 0 0 0 14904 1116 39 1 1 SLC3A1 2 44281462 Missense_Mutation SNP G C3N-01823_T 363133 44281462 197912067 46 25743 SRBD1 0 . GRCh38 2 45393107 45393110 + Frame_Shift_Del DEL TCCC TCCC - novel C3N-01823_T C3N-01823_N TCCC TCCC c.2533_2536delGGGA p.Gly845HisfsTer14 p.G845Hfs*14 ENST00000263736 20/21 77 64 13 61 61 0 sindel-varindel-pindel SRBD1,frameshift_variant,p.Gly845HisfsTer14,ENST00000263736,NM_018079.4;SRBD1,non_coding_transcript_exon_variant,,ENST00000490133,; - ENST00000263736 Transcript frameshift_variant 2596-2599/3681 2533-2536/2988 845-846/995 GT/X GGGAca/ca 1 -1 SRBD1 HGNC HGNC:25521 protein_coding YES CCDS1823.1 ENSP00000263736 Q8N5C6 UPI000004CC06 NM_018079.4 20/21 Gene3D:3bzcA04,hmmpanther:PTHR10724,hmmpanther:PTHR10724:SF1,Superfamily_domains:SSF47781 HIGH 1 deletion 2 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999865 1 1 1 0 - 7 5 83 45393107 45393107 TCCC - 1 0 1 0 1 0 0 0 0 15491 1667 58 0 0 SRBD1 2 45393107 Frame_Shift_Del DEL TCCC C3N-01823_T 1111645 45393107 196800422 47 25744 NRXN1 0 . GRCh38 2 50506606 50506606 + Nonsense_Mutation SNP C C A C3N-01823_T C3N-01823_N C C c.2506G>T p.Glu836Ter p.E836* ENST00000404971 14/24 204 188 16 136 136 0 strelka-varscan-mutect NRXN1,stop_gained,p.Glu796Ter,ENST00000406316,NM_004801.4;NRXN1,stop_gained,p.Glu788Ter,ENST00000625672,;NRXN1,stop_gained,p.Glu836Ter,ENST00000404971,NM_001135659.1;NRXN1,stop_gained,p.Glu796Ter,ENST00000401669,;NRXN1,stop_gained,p.Glu784Ter,ENST00000405472,;NRXN1,stop_gained,p.Glu788Ter,ENST00000630543,;NRXN1,stop_gained,p.Glu526Ter,ENST00000406859,;NRXN1,stop_gained,p.Glu511Ter,ENST00000402717,;NRXN1,intron_variant,,ENST00000495871,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636342,;NRXN1,stop_gained,p.Glu514Ter,ENST00000331040,;NRXN1,non_coding_transcript_exon_variant,,ENST00000474354,;NRXN1,non_coding_transcript_exon_variant,,ENST00000462791,; A ENST00000404971 Transcript stop_gained 3846/7578 2506/4644 836/1547 E/* Gag/Tag COSM1149135,COSM1306847,COSM1306848,COSM1306849,COSM4812491,COSM4859684,COSM721588,COSM721589 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 14/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs1285800435 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 50506606 50506606 C A 1 0 0 0 0 0 1 0 0 10724 893 31 1 1 NRXN1 2 50506606 Nonsense_Mutation SNP C C3N-01823_T 5113499 50506606 191686923 48 25745 XPO1 0 . GRCh38 2 61492037 61492042 + In_Frame_Del DEL GTTGAG GTTGAG - novel C3N-01823_T C3N-01823_N GTTGAG GTTGAG c.1880_1885delCTCAAC p.Pro627_Gln628del p.P627_Q628del ENST00000401558 16/25 163 154 9 124 124 0 sindel-varindel-pindel XPO1,inframe_deletion,p.Pro627_Gln628del,ENST00000401558,NM_003400.3;XPO1,inframe_deletion,p.Pro627_Gln628del,ENST00000404992,;XPO1,inframe_deletion,p.Pro627_Gln628del,ENST00000406957,;XPO1,upstream_gene_variant,,ENST00000494468,;XPO1,splice_region_variant,,ENST00000428210,;XPO1,splice_region_variant,,ENST00000481073,;XPO1,upstream_gene_variant,,ENST00000461407,;XPO1,downstream_gene_variant,,ENST00000460037,;XPO1,downstream_gene_variant,,ENST00000469337,;XPO1,downstream_gene_variant,,ENST00000437159,;XPO1,downstream_gene_variant,,ENST00000475744,; - ENST00000401558 Transcript inframe_deletion,splice_region_variant 2608-2613/4915 1880-1885/3216 627-629/1071 PQQ/Q cCTCAACag/cag 1 -1 XPO1 HGNC HGNC:12825 protein_coding YES CCDS33205.1 ENSP00000384863 O14980 UPI0000001C23 NM_003400.3 16/25 hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF4,Superfamily_domains:SSF48371 MODERATE 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.31372 1 1 1 1 0 - 7 5 83 61492037 61492037 GTTGAG - 1 0 1 0 1 0 0 0 0 18004 1391 48 0 0 XPO1 2 61492037 In_Frame_Del DEL GTTGAG C3N-01823_T 10985431 61492037 180701492 49 25746 EGR4 0 . GRCh38 2 73293523 73293523 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.104G>A p.Arg35Gln p.R35Q ENST00000545030 1/2 197 182 15 97 97 0 strelka-varscan-mutect EGR4,missense_variant,p.Arg35Gln,ENST00000545030,NM_001965.3;EGR4,5_prime_UTR_variant,,ENST00000436467,; T ENST00000545030 Transcript missense_variant 179/2372 104/1770 35/589 R/Q cGa/cAa 1 -1 EGR4 HGNC HGNC:3241 protein_coding YES CCDS1925.2 ENSP00000445626 Q05215 UPI0000EE25D4 NM_001965.3 tolerated_low_confidence(0.08) 1/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1269222518 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 73293523 73293523 C T 1 0 0 0 0 1 0 0 0 4810 884 31 1 1 EGR4 2 73293523 Missense_Mutation SNP C C3N-01823_T 11801486 73293523 168900006 50 25747 C2orf81 0 . GRCh38 2 74414607 74414607 + Missense_Mutation SNP C C A rs375005972 C3N-01823_T C3N-01823_N C C c.1489G>T p.Val497Leu p.V497L ENST00000290390 4/4 84 73 11 48 48 0 strelka-varscan-mutect C2orf81,missense_variant,p.Val497Leu,ENST00000290390,NM_001145054.1;C2orf81,missense_variant,p.Val491Leu,ENST00000612891,;C2orf81,missense_variant,p.Val429Leu,ENST00000517883,;AC005041.11,upstream_gene_variant,,ENST00000448783,;HMGA1P8,downstream_gene_variant,,ENST00000414130,; A ENST00000290390 Transcript missense_variant 1798/2227 1489/1767 497/588 V/L Gtg/Ttg rs375005972 1 -1 C2orf81 HGNC HGNC:34350 protein_coding YES ENSP00000290390 G3XAA6 UPI0000EE2496 NM_001145054.1 tolerated(0.13) 4/4 hmmpanther:PTHR34438,Pfam_domain:PF15479 MODERATE 1 SNV 5 1 PASS rs375005972 . 0 204 5 0 0 0 0 0 -19.99987 1 1 1 1 0 A 3 1 83 74414607 74414607 C A 1 0 0 0 0 1 0 0 0 2052 536 19 1 1 C2orf81 2 74414607 Missense_Mutation SNP C C3N-01823_T 1121084 74414607 167778922 51 25748 MARCO 0 . GRCh38 2 118992468 118992468 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1244G>T p.Gly415Val p.G415V ENST00000327097 15/17 217 172 45 126 126 0 strelka-varscan-mutect MARCO,missense_variant,p.Gly415Val,ENST00000327097,NM_006770.3;MARCO,upstream_gene_variant,,ENST00000494979,; T ENST00000327097 Transcript missense_variant 1379/1838 1244/1563 415/520 G/V gGt/gTt 1 1 MARCO HGNC HGNC:6895 protein_coding YES CCDS2124.1 ENSP00000318916 Q9UEW3 Q4ZG40 UPI0000000DF8 NM_006770.3 deleterious(0) 15/17 hmmpanther:PTHR24023:SF525,hmmpanther:PTHR24023,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -20 0.998228 1 1 1 0 T 3 4 83 118992468 118992468 G T 1 0 0 0 0 1 0 0 0 9236 1261 44 2 2 MARCO 2 118992468 Missense_Mutation SNP G C3N-01823_T 44577861 118992468 123201061 52 25749 MYO7B 0 . GRCh38 2 127584820 127584820 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1597G>T p.Ala533Ser p.A533S ENST00000428314 14/47 347 291 56 206 206 0 strelka-varscan-mutect MYO7B,missense_variant,p.Ala533Ser,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.Ala533Ser,ENST00000409816,; T ENST00000428314 Transcript missense_variant 1650/6715 1597/6351 533/2116 A/S Gcc/Tcc 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 tolerated(0.59) 14/47 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF505,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 127584820 127584820 G T 1 0 0 0 0 1 0 0 0 10084 1319 46 2 2 MYO7B 2 127584820 Missense_Mutation SNP G C3N-01823_T 8592352 127584820 114608709 53 25750 POTEJ 0 . GRCh38 2 130657706 130657706 + Silent SNP C C A rs748769597 C3N-01823_T C3N-01823_N C C c.2946C>A p.= p.A982A ENST00000409602 15/15 240 210 30 114 114 0 varscan-mutect POTEJ,synonymous_variant,p.=,ENST00000409602,NM_001277083.1; A ENST00000409602 Transcript synonymous_variant 2998/3383 2946/3117 982/1038 A gcC/gcA rs748769597 1 1 POTEJ HGNC HGNC:37094 protein_coding YES CCDS59432.1 ENSP00000387176 P0CG39 UPI0000DD7A4B NM_001277083.1 15/15 Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 5 1 PASS rs748769597 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 130657706 130657706 C A 1 0 0 0 0 0 0 0 1 12383 610 22 2 2 POTEJ 2 130657706 Silent SNP C C3N-01823_T 3072886 130657706 111535823 54 25751 POTEE 0 . GRCh38 2 131264359 131264359 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.2904C>A p.= p.G968G ENST00000356920 15/15 535 481 54 317 317 0 varscan-mutect POTEE,synonymous_variant,p.=,ENST00000356920,NM_001083538.1;PLEKHB2,intron_variant,,ENST00000404460,;POTEE,downstream_gene_variant,,ENST00000626191,;POTEE,downstream_gene_variant,,ENST00000613282,;POTEE,downstream_gene_variant,,ENST00000358087,;POTEE,downstream_gene_variant,,ENST00000514256,; A ENST00000356920 Transcript synonymous_variant 3240/4159 2904/3228 968/1075 G ggC/ggA 1 1 POTEE HGNC HGNC:33895 protein_coding YES CCDS46414.1 ENSP00000439189 Q6S8J3 UPI0000F58EC8 NM_001083538.1 15/15 Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS rs1243878586 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 131264359 131264359 C A 1 0 0 0 0 0 0 0 1 12378 697 25 2 2 POTEE 2 131264359 Silent SNP C C3N-01823_T 606653 131264359 110929170 55 25752 LRP1B 0 . GRCh38 2 141055226 141055226 + Missense_Mutation SNP C C A rs867777706 C3N-01823_T C3N-01823_N C C c.1442G>T p.Gly481Val p.G481V ENST00000389484 10/91 194 183 11 182 182 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gly481Val,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 2414/16535 1442/13800 481/4599 G/V gGa/gTa rs867777706 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 10/91 Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS rs867777706 . 0 208 0 2 0 0 0 0 -13.86568 0.9999995 1 1 1 0 A 3 1 83 141055226 141055226 C A 1 0 0 0 0 1 0 0 0 8850 855 30 2 2 LRP1B 2 141055226 Missense_Mutation SNP C C3N-01823_T 9790867 141055226 101138303 56 25753 ARHGAP15 0 . GRCh38 2 143624186 143624186 + Missense_Mutation SNP G G C C3N-01823_T C3N-01823_N G G c.1057G>C p.Gly353Arg p.G353R ENST00000295095 12/14 209 193 16 148 148 0 strelka-varscan-mutect ARHGAP15,missense_variant,p.Gly353Arg,ENST00000295095,NM_018460.3;ARHGAP15,3_prime_UTR_variant,,ENST00000419455,;ARHGAP15,non_coding_transcript_exon_variant,,ENST00000549436,; C ENST00000295095 Transcript missense_variant 1224/1775 1057/1428 353/475 G/R Gga/Cga COSM1235873,COSM3295712 1 1 ARHGAP15 HGNC HGNC:21030 protein_coding YES CCDS2184.1 ENSP00000295095 Q53QZ3 UPI0000035D98 NM_018460.3 deleterious(0) 12/14 PROSITE_profiles:PS50238,hmmpanther:PTHR23181,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1416890324 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 143624186 143624186 G C 1 0 0 0 0 1 0 0 0 990 1117 39 4 4 ARHGAP15 2 143624186 Missense_Mutation SNP G C3N-01823_T 2568960 143624186 98569343 57 25754 EPC2 0 . GRCh38 2 148784788 148784788 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2138G>T p.Cys713Phe p.C713F ENST00000258484 13/14 248 219 29 158 157 1 strelka-varscan-mutect EPC2,missense_variant,p.Cys713Phe,ENST00000258484,NM_015630.3; T ENST00000258484 Transcript missense_variant 2172/3649 2138/2424 713/807 C/F tGc/tTc 1 1 EPC2 HGNC HGNC:24543 protein_coding YES CCDS46422.1 ENSP00000258484 Q52LR7 UPI00005A7FE2 NM_015630.3 tolerated(0.45) 13/14 Pfam_domain:PF06752,hmmpanther:PTHR14898,hmmpanther:PTHR14898:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999894 1 1 1 0 T 3 4 83 148784788 148784788 G T 1 0 0 0 0 1 0 0 0 5007 1319 46 2 2 EPC2 2 148784788 Missense_Mutation SNP G C3N-01823_T 5160602 148784788 93408741 58 25755 PKP4 0 . GRCh38 2 158661402 158661402 + Silent SNP G G T rs757024469 C3N-01823_T C3N-01823_N G G c.2163G>T p.= p.L721L ENST00000389759 13/22 290 263 27 220 220 0 strelka-varscan-mutect PKP4,synonymous_variant,p.=,ENST00000389757,NM_001005476.2;PKP4,synonymous_variant,p.=,ENST00000389759,NM_001304970.1,NM_003628.4,NM_001304969.1;PKP4,synonymous_variant,p.=,ENST00000628904,;AC005042.4,non_coding_transcript_exon_variant,,ENST00000342892,;PKP4,upstream_gene_variant,,ENST00000495123,;PKP4,3_prime_UTR_variant,,ENST00000426248,;PKP4,3_prime_UTR_variant,,ENST00000421462,;PKP4,3_prime_UTR_variant,,ENST00000452162,;PKP4,non_coding_transcript_exon_variant,,ENST00000492496,;PKP4,upstream_gene_variant,,ENST00000480171,;PKP4,upstream_gene_variant,,ENST00000483881,; T ENST00000389759 Transcript synonymous_variant 2275/4443 2163/3579 721/1192 L ctG/ctT rs757024469 1 1 PKP4 HGNC HGNC:9026 protein_coding YES CCDS33305.1 ENSP00000374409 Q99569 UPI000044D379 NM_001304970.1,NM_003628.4,NM_001304969.1 13/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF8,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs757024469 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 158661402 158661402 G T 1 0 0 0 0 0 0 0 1 12083 1364 48 2 2 PKP4 2 158661402 Silent SNP G C3N-01823_T 9876614 158661402 83532127 59 25756 TANC1 0 . GRCh38 2 159178671 159178671 + Missense_Mutation SNP A A G rs867985244 C3N-01823_T C3N-01823_N A A c.2018A>G p.Asp673Gly p.D673G ENST00000263635 14/27 206 188 18 139 139 0 strelka-varscan-mutect TANC1,missense_variant,p.Asp673Gly,ENST00000263635,NM_033394.2,NM_001145909.1;TANC1,intron_variant,,ENST00000454300,; G ENST00000263635 Transcript missense_variant 2255/7470 2018/5586 673/1861 D/G gAc/gGc rs867985244 1 1 TANC1 HGNC HGNC:29364 protein_coding YES CCDS42766.1 ENSP00000263635 Q9C0D5 UPI0000421D80 NM_033394.2,NM_001145909.1 tolerated(0.06) 14/27 hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF23 MODERATE 1 SNV 5 1 PASS rs867985244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 159178671 159178671 A G 1 0 0 0 0 1 0 0 0 15941 275 10 5 5 TANC1 2 159178671 Missense_Mutation SNP A C3N-01823_T 517269 159178671 83014858 60 25757 TBR1 0 . GRCh38 2 161416533 161416533 + Silent SNP G G T C3N-01823_T C3N-01823_N G G c.123G>T p.= p.S41S ENST00000389554 1/6 258 231 27 160 160 0 strelka-varscan-mutect TBR1,synonymous_variant,p.=,ENST00000389554,NM_006593.2;PSMD14,downstream_gene_variant,,ENST00000409682,NM_005805.5;TBR1,upstream_gene_variant,,ENST00000410035,;TBR1,upstream_gene_variant,,ENST00000411412,;TBR1,upstream_gene_variant,,ENST00000489530,;TBR1,upstream_gene_variant,,ENST00000477804,;TBR1,non_coding_transcript_exon_variant,,ENST00000463544,;PSMD14,downstream_gene_variant,,ENST00000477232,;PSMD14,downstream_gene_variant,,ENST00000492908,; T ENST00000389554 Transcript synonymous_variant 440/4009 123/2049 41/682 S tcG/tcT COSM3568381 1 1 TBR1 HGNC HGNC:11590 protein_coding YES CCDS33310.1 ENSP00000374205 Q16650 UPI0000136A99 NM_006593.2 1/6 hmmpanther:PTHR11267:SF88,hmmpanther:PTHR11267 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 161416533 161416533 G T 1 0 0 0 0 0 0 0 1 16052 1045 37 1 1 TBR1 2 161416533 Silent SNP G C3N-01823_T 2237862 161416533 80776996 61 25758 FIGN 0 . GRCh38 2 163610797 163610797 + Missense_Mutation SNP C C G rs775365473 C3N-01823_T C3N-01823_N C C c.1035G>C p.Gln345His p.Q345H ENST00000333129 3/3 252 237 15 160 160 0 strelka-varscan-mutect FIGN,missense_variant,p.Gln345His,ENST00000333129,NM_018086.2;FIGN,intron_variant,,ENST00000409634,;FIGN,downstream_gene_variant,,ENST00000482917,; G ENST00000333129 Transcript missense_variant 1350/9536 1035/2280 345/759 Q/H caG/caC rs775365473,COSM4519935 1 -1 FIGN HGNC HGNC:13285 protein_coding YES CCDS2221.2 ENSP00000333836 Q5HY92 UPI000022BD13 NM_018086.2 tolerated(0.14) 3/3 hmmpanther:PTHR23074,hmmpanther:PTHR23074:SF14 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775365473 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 163610797 163610797 C G 1 0 0 0 0 1 0 0 0 5755 912 32 4 4 FIGN 2 163610797 Missense_Mutation SNP C C3N-01823_T 2194264 163610797 78582732 62 25759 LRP2 0 . GRCh38 2 169216275 169216275 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.5804G>T p.Trp1935Leu p.W1935L ENST00000263816 35/79 563 492 71 413 412 1 strelka-varscan-mutect LRP2,missense_variant,p.Trp1935Leu,ENST00000263816,NM_004525.2; A ENST00000263816 Transcript missense_variant 6090/15808 5804/13968 1935/4655 W/L tGg/tTg 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 deleterious(0) 35/79 Gene3D:2.120.10.30,PROSITE_profiles:PS51120,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 169216275 169216275 C A 1 0 0 0 0 1 0 0 0 8851 595 21 2 2 LRP2 2 169216275 Missense_Mutation SNP C C3N-01823_T 5605478 169216275 72977254 63 25760 SP9 0 . GRCh38 2 174336458 174336458 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.373C>A p.Gln125Lys p.Q125K ENST00000394967 2/2 117 104 13 71 71 0 strelka-varscan-mutect SP9,missense_variant,p.Gln125Lys,ENST00000394967,NM_001145250.1;RP11-572N21.1,non_coding_transcript_exon_variant,,ENST00000624790,; A ENST00000394967 Transcript missense_variant 520/2554 373/1455 125/484 Q/K Cag/Aag 1 1 SP9 HGNC HGNC:30690 protein_coding YES CCDS46453.1 ENSP00000378418 P0CG40 UPI0000EE2E67 NM_001145250.1 tolerated(0.11) 2/2 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 174336458 174336458 C A 1 0 0 0 0 1 0 0 0 15297 711 25 2 2 SP9 2 174336458 Missense_Mutation SNP C C3N-01823_T 5120183 174336458 67857071 64 25761 CHRNA1 0 . GRCh38 2 174754221 174754221 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.613C>T p.Pro205Ser p.P205S ENST00000261007 6/10 389 330 59 214 214 0 strelka-varscan-mutect CHRNA1,missense_variant,p.Pro180Ser,ENST00000348749,NM_000079.3;CHRNA1,missense_variant,p.Pro205Ser,ENST00000261007,NM_001039523.2;CHRNA1,missense_variant,p.Pro193Ser,ENST00000636168,;CHRNA1,missense_variant,p.Pro180Ser,ENST00000409323,;CHRNA1,missense_variant,p.Pro180Ser,ENST00000409219,;CHRNA1,missense_variant,p.Pro98Ser,ENST00000409542,;AC018890.6,intron_variant,,ENST00000442996,;CHRNA1,splice_region_variant,,ENST00000435083,; A ENST00000261007 Transcript missense_variant,splice_region_variant 680/1980 613/1449 205/482 P/S Ccg/Tcg 1 -1 CHRNA1 HGNC HGNC:1955 protein_coding YES CCDS33331.1 ENSP00000261007 P02708 UPI000012524E NM_001039523.2 tolerated(0.5) 6/10 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF74,Pfam_domain:PF02931,Gene3D:2.70.170.10,Superfamily_domains:0038932 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 174754221 174754221 G A 1 0 0 0 0 1 0 0 0 3141 1246 43 3 3 CHRNA1 2 174754221 Missense_Mutation SNP G C3N-01823_T 417763 174754221 67439308 65 25762 ZDBF2 0 . GRCh38 2 206305083 206305083 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.555T>A p.Asn185Lys p.N185K ENST00000374423 5/5 315 264 51 167 167 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Asn185Lys,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Asn183Lys,ENST00000611847,NM_001285549.1; A ENST00000374423 Transcript missense_variant 941/10286 555/7065 185/2354 N/K aaT/aaA 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 deleterious(0.01) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 206305083 206305083 T A 1 0 0 0 0 1 0 0 0 18174 1461 51 4 4 ZDBF2 2 206305083 Missense_Mutation SNP T C3N-01823_T 31550862 206305083 35888446 66 25763 PIKFYVE 0 . GRCh38 2 208330582 208330582 + Missense_Mutation SNP G G T rs746781460 C3N-01823_T C3N-01823_N G G c.3851G>T p.Arg1284Leu p.R1284L ENST00000264380 23/42 254 206 48 171 171 0 strelka-varscan-mutect PIKFYVE,missense_variant,p.Arg1284Leu,ENST00000264380,NM_015040.3;PIKFYVE,missense_variant,p.Arg1228Leu,ENST00000452564,;PIKFYVE,upstream_gene_variant,,ENST00000474721,;PIKFYVE,downstream_gene_variant,,ENST00000443896,; T ENST00000264380 Transcript missense_variant 4009/9901 3851/6297 1284/2098 R/L cGc/cTc rs746781460,COSM1220636 1 1 PIKFYVE HGNC HGNC:23785 protein_coding YES CCDS2382.1 ENSP00000264380 Q9Y2I7 UPI0000366FD6 NM_015040.3 deleterious(0) 23/42 hmmpanther:PTHR11353,hmmpanther:PTHR11353:SF57 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746781460 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 208330582 208330582 G T 1 0 0 0 0 1 0 0 0 12019 1087 38 1 1 PIKFYVE 2 208330582 Missense_Mutation SNP G C3N-01823_T 2025499 208330582 33862947 67 25764 UNC80 0 . GRCh38 2 209904791 209904791 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.4410G>C p.Gln1470His p.Q1470H ENST00000439458 28/64 344 283 61 183 183 0 strelka-varscan-mutect UNC80,missense_variant,p.Gln1470His,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.Gln1465His,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000489023,; C ENST00000439458 Transcript missense_variant 4490/13562 4410/9777 1470/3258 Q/H caG/caC 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 tolerated(0.54) 28/64 hmmpanther:PTHR31781,hmmpanther:PTHR31781:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 209904791 209904791 G C 1 0 0 0 0 1 0 0 0 17521 933 33 4 4 UNC80 2 209904791 Missense_Mutation SNP G C3N-01823_T 1574209 209904791 32288738 68 25765 TNS1 0 . GRCh38 2 217818717 217818717 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.3303G>T p.Gln1101His p.Q1101H ENST00000171887 24/33 147 132 15 96 96 0 strelka-varscan-mutect TNS1,missense_variant,p.Gln1101His,ENST00000171887,NM_022648.4;TNS1,missense_variant,p.Gln1088His,ENST00000611415,;TNS1,missense_variant,p.Gln731His,ENST00000615025,;TNS1,missense_variant,p.Gln1088His,ENST00000419504,;TNS1,missense_variant,p.Gln1080His,ENST00000430930,NM_001308023.1;TNS1,missense_variant,p.Gln212His,ENST00000446688,;TNS1,upstream_gene_variant,,ENST00000490566,;TNS1,upstream_gene_variant,,ENST00000495556,; A ENST00000171887 Transcript missense_variant 3756/10331 3303/5208 1101/1735 Q/H caG/caT 1 -1 TNS1 HGNC HGNC:11973 protein_coding YES CCDS2407.1 ENSP00000171887 Q9HBL0 UPI0000456EEB NM_022648.4 tolerated(0.67) 24/33 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 217818717 217818717 C A 1 0 0 0 0 1 0 0 0 16816 680 24 2 2 TNS1 2 217818717 Missense_Mutation SNP C C3N-01823_T 7913926 217818717 24374812 69 25766 PRKAG3 0 . GRCh38 2 218826947 218826947 + Silent SNP C C T C3N-01823_T C3N-01823_N C C c.1149G>A p.= p.L383L ENST00000439262 10/14 448 398 50 273 273 0 strelka-varscan-mutect PRKAG3,synonymous_variant,p.=,ENST00000439262,NM_017431.2;PRKAG3,synonymous_variant,p.=,ENST00000529249,;PRKAG3,downstream_gene_variant,,ENST00000430489,;MIR9500,downstream_gene_variant,,ENST00000635985,;PRKAG3,synonymous_variant,p.=,ENST00000233944,;PRKAG3,3_prime_UTR_variant,,ENST00000470307,;PRKAG3,non_coding_transcript_exon_variant,,ENST00000490971,; T ENST00000439262 Transcript synonymous_variant 1170/2301 1149/1470 383/489 L ctG/ctA COSM3719934 1 -1 PRKAG3 HGNC HGNC:9387 protein_coding YES CCDS2424.1 ENSP00000397133 Q9UGI9 A0A024R426 UPI0000043D98 NM_017431.2 10/14 PROSITE_profiles:PS51371,hmmpanther:PTHR13780:SF31,hmmpanther:PTHR13780,Gene3D:3.10.580.10,Pfam_domain:PF00571,SMART_domains:SM00116,Superfamily_domains:SSF54631 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 218826947 218826947 C T 1 0 0 0 0 0 0 0 1 12635 697 25 3 3 PRKAG3 2 218826947 Silent SNP C C3N-01823_T 1008230 218826947 23366582 70 25767 DOCK10 0 . GRCh38 2 224852939 224852939 + Missense_Mutation SNP T T C C3N-01823_T C3N-01823_N T T c.2072A>G p.Asn691Ser p.N691S ENST00000258390 17/56 62 53 9 41 41 0 strelka-varscan-mutect DOCK10,missense_variant,p.Asn685Ser,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Asn691Ser,ENST00000258390,NM_014689.2; C ENST00000258390 Transcript missense_variant 2140/7260 2072/6561 691/2186 N/S aAc/aGc COSM3046728,COSM4310343 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 tolerated(0.35) 17/56 Pfam_domain:PF14429,PROSITE_profiles:PS51650,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -19.93034 1 1 1 1 0 C 3 2 83 224852939 224852939 T C 1 0 0 0 0 1 0 0 0 4500 1739 60 5 5 DOCK10 2 224852939 Missense_Mutation SNP T C3N-01823_T 6025992 224852939 17340590 71 25768 DOCK10 0 . GRCh38 2 224865015 224865015 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1330G>T p.Val444Leu p.V444L ENST00000258390 12/56 407 345 62 290 290 0 strelka-varscan-mutect DOCK10,missense_variant,p.Val438Leu,ENST00000409592,NM_001290263.1;DOCK10,missense_variant,p.Val444Leu,ENST00000258390,NM_014689.2;DOCK10,non_coding_transcript_exon_variant,,ENST00000492369,; A ENST00000258390 Transcript missense_variant 1398/7260 1330/6561 444/2186 V/L Gtg/Ttg 1 -1 DOCK10 HGNC HGNC:23479 protein_coding YES CCDS46528.1 ENSP00000258390 Q96BY6 UPI000021D2A7 NM_014689.2 deleterious(0.02) 12/56 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF71 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 224865015 224865015 C A 1 0 0 0 0 1 0 0 0 4500 478 17 2 2 DOCK10 2 224865015 Missense_Mutation SNP C C3N-01823_T 12076 224865015 17328514 72 25769 ALPP 0 . GRCh38 2 232379822 232379822 + Silent SNP C C G novel C3N-01823_T C3N-01823_N C C c.543C>G p.= p.T181T ENST00000392027 5/11 400 359 41 266 266 0 strelka-varscan-mutect ALPP,synonymous_variant,p.=,ENST00000392027,NM_001632.4;AC068134.8,non_coding_transcript_exon_variant,,ENST00000439072,;AC068134.8,intron_variant,,ENST00000441266,;ALPP,upstream_gene_variant,,ENST00000485563,;ALPP,downstream_gene_variant,,ENST00000474529,; G ENST00000392027 Transcript synonymous_variant 812/2971 543/1608 181/535 T acC/acG 1 1 ALPP HGNC HGNC:439 protein_coding YES CCDS2490.1 ENSP00000375881 P05187 UPI0000131FF9 NM_001632.4 5/11 Gene3D:3.40.720.10,Pfam_domain:PF00245,hmmpanther:PTHR11596,hmmpanther:PTHR11596:SF31,SMART_domains:SM00098,Superfamily_domains:SSF53649 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 232379822 232379822 C G 1 0 0 0 0 0 0 0 1 648 668 24 4 4 ALPP 2 232379822 Silent SNP C C3N-01823_T 7514807 232379822 9813707 73 25770 KIF1A 0 . GRCh38 2 240721852 240721852 + Silent SNP T T C novel C3N-01823_T C3N-01823_N T T c.4698A>G p.= p.R1566R ENST00000498729 44/49 306 263 43 200 200 0 strelka-varscan-mutect KIF1A,synonymous_variant,p.=,ENST00000498729,NM_001244008.1;KIF1A,synonymous_variant,p.=,ENST00000320389,NM_004321.6;KIF1A,downstream_gene_variant,,ENST00000404283,;KIF1A,downstream_gene_variant,,ENST00000431776,;KIF1A,non_coding_transcript_exon_variant,,ENST00000460788,;KIF1A,non_coding_transcript_exon_variant,,ENST00000492812,;KIF1A,non_coding_transcript_exon_variant,,ENST00000465813,;KIF1A,downstream_gene_variant,,ENST00000494452,;KIF1A,upstream_gene_variant,,ENST00000488776,; C ENST00000498729 Transcript synonymous_variant 4945/9223 4698/5376 1566/1791 R agA/agG 1 -1 KIF1A HGNC HGNC:888 protein_coding YES CCDS58757.1 ENSP00000438388 Q12756 UPI0002065B81 NM_001244008.1 44/49 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 240721852 240721852 T C 1 0 0 0 0 0 0 0 1 8147 1548 54 5 5 KIF1A 2 240721852 Silent SNP T C3N-01823_T 8342030 240721852 1471677 74 25771 RPUSD3 0 . GRCh38 3 9840701 9840701 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.512A>G p.Tyr171Cys p.Y171C ENST00000383820 5/9 249 226 23 167 167 0 strelka-varscan-mutect RPUSD3,missense_variant,p.Tyr171Cys,ENST00000383820,NM_173659.3;RPUSD3,missense_variant,p.Tyr156Cys,ENST00000433535,NM_001142547.1;RPUSD3,missense_variant,p.Tyr139Cys,ENST00000424438,;RPUSD3,missense_variant,p.Tyr167Cys,ENST00000418713,;RPUSD3,missense_variant,p.Tyr162Cys,ENST00000427174,;TTLL3,intron_variant,,ENST00000455274,;TTLL3,downstream_gene_variant,,ENST00000383827,;RPUSD3,downstream_gene_variant,,ENST00000433972,;RPUSD3,downstream_gene_variant,,ENST00000433555,;RPUSD3,upstream_gene_variant,,ENST00000423108,;RPUSD3,downstream_gene_variant,,ENST00000485705,;RPUSD3,downstream_gene_variant,,ENST00000473522,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000484134,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000475470,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000464783,;RPUSD3,non_coding_transcript_exon_variant,,ENST00000472381,;TTLL3,downstream_gene_variant,,ENST00000483051,;RPUSD3,upstream_gene_variant,,ENST00000466141,;RPUSD3,downstream_gene_variant,,ENST00000451405,;RPUSD3,downstream_gene_variant,,ENST00000460909,; C ENST00000383820 Transcript missense_variant 514/1225 512/1056 171/351 Y/C tAc/tGc 1 -1 RPUSD3 HGNC HGNC:28437 protein_coding YES CCDS2586.2 ENSP00000373331 Q6P087 UPI000066D9E0 NM_173659.3 deleterious(0) 5/9 hmmpanther:PTHR11079,hmmpanther:PTHR11079:SF93,Pfam_domain:PF00849,Superfamily_domains:SSF55120 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 9840701 9840701 T C 1 0 0 0 0 1 0 0 0 13923 1652 57 5 5 RPUSD3 3 9840701 Missense_Mutation SNP T C3N-01823_T 9840701 188454858 75 25772 IQSEC1 0 . GRCh38 3 12936393 12936393 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.623C>G p.Thr208Ser p.T208S ENST00000613206 3/14 99 94 5 51 51 0 strelka-mutect IQSEC1,missense_variant,p.Thr222Ser,ENST00000273221,NM_014869.6;IQSEC1,missense_variant,p.Thr100Ser,ENST00000618604,;IQSEC1,missense_variant,p.Thr208Ser,ENST00000613206,NM_001134382.2;IQSEC1,downstream_gene_variant,,ENST00000473088,; C ENST00000613206 Transcript missense_variant 726/3582 623/3345 208/1114 T/S aCc/aGc 1 -1 IQSEC1 HGNC HGNC:29112 protein_coding YES CCDS74902.1 ENSP00000480301 A0A087WWK8 UPI00017E10F8 NM_001134382.2 tolerated(0.77) 3/14 hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663 MODERATE 1 SNV 2 1 PASS rs1457617498 . 0 202 8 0 0 0 0 0 -10.37781 0.9999804 1 1 1 0 C 3 2 83 12936393 12936393 G C 1 0 0 0 0 1 0 0 0 7723 1261 44 4 4 IQSEC1 3 12936393 Missense_Mutation SNP G C3N-01823_T 3095692 12936393 185359166 76 25773 HACL1 0 . GRCh38 3 15567939 15567939 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.1314G>T p.= p.V438V ENST00000321169 14/17 368 299 69 208 208 0 strelka-varscan-mutect HACL1,synonymous_variant,p.=,ENST00000321169,NM_012260.3;HACL1,synonymous_variant,p.=,ENST00000456194,NM_001284413.1;HACL1,synonymous_variant,p.=,ENST00000451445,NM_001284416.1;HACL1,synonymous_variant,p.=,ENST00000457447,NM_001284415.1;HACL1,synonymous_variant,p.=,ENST00000435217,;HACL1,3_prime_UTR_variant,,ENST00000628377,;HACL1,3_prime_UTR_variant,,ENST00000383779,;HACL1,3_prime_UTR_variant,,ENST00000422591,; A ENST00000321169 Transcript synonymous_variant 1682/2266 1314/1737 438/578 V gtG/gtT 1 -1 HACL1 HGNC HGNC:17856 protein_coding YES CCDS2627.1 ENSP00000323811 Q9UJ83 UPI000012CB25 NM_012260.3 14/17 Gene3D:3.40.50.970,Pfam_domain:PF02775,hmmpanther:PTHR18968,hmmpanther:PTHR18968:SF6,Superfamily_domains:SSF52518 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 15567939 15567939 C A 1 0 0 0 0 0 0 0 1 6827 581 21 2 2 HACL1 3 15567939 Silent SNP C C3N-01823_T 2631546 15567939 182727620 77 25774 XIRP1 0 . GRCh38 3 39184908 39184908 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.4538C>A p.Ala1513Asp p.A1513D ENST00000340369 2/2 61 54 7 49 49 0 strelka-mutect XIRP1,missense_variant,p.Ala1513Asp,ENST00000340369,NM_194293.2;XIRP1,missense_variant,p.Ala196Asp,ENST00000421646,;XIRP1,3_prime_UTR_variant,,ENST00000396251,NM_001198621.2; T ENST00000340369 Transcript missense_variant 4767/6460 4538/5532 1513/1843 A/D gCt/gAt 1 -1 XIRP1 HGNC HGNC:14301 protein_coding YES CCDS2683.1 ENSP00000343140 Q702N8 UPI00001BFB06 NM_194293.2 tolerated(0.08) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR22591 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -16.03581 0.9999999 1 1 1 0 T 3 4 83 39184908 39184908 G T 1 0 0 0 0 1 0 0 0 17988 971 34 2 2 XIRP1 3 39184908 Missense_Mutation SNP G C3N-01823_T 23616969 39184908 159110651 78 25775 MYRIP 0 . GRCh38 3 40182259 40182259 + Missense_Mutation SNP C C A rs200729271 C3N-01823_T C3N-01823_N C C c.913C>A p.Leu305Met p.L305M ENST00000302541 9/17 134 112 22 110 110 0 strelka-varscan-mutect MYRIP,missense_variant,p.Leu305Met,ENST00000302541,NM_015460.3;MYRIP,missense_variant,p.Leu216Met,ENST00000396217,NM_001284425.1;MYRIP,missense_variant,p.Leu118Met,ENST00000539167,NM_001284426.1;MYRIP,missense_variant,p.Leu305Met,ENST00000425621,NM_001284424.1;MYRIP,missense_variant,p.Leu305Met,ENST00000444716,NM_001284423.1;EIF1B-AS1,intron_variant,,ENST00000625390,;MYRIP,non_coding_transcript_exon_variant,,ENST00000459828,;MYRIP,missense_variant,p.Leu305Met,ENST00000458292,;MYRIP,3_prime_UTR_variant,,ENST00000458441,; A ENST00000302541 Transcript missense_variant 1255/5077 913/2580 305/859 L/M Ctg/Atg rs200729271 1 1 MYRIP HGNC HGNC:19156 protein_coding YES CCDS2689.1 ENSP00000301972 Q8NFW9 UPI0000074787 NM_015460.3 tolerated(0.24) 9/17 Pfam_domain:PF04698,hmmpanther:PTHR14555,hmmpanther:PTHR14555:SF6 MODERATE 1 SNV 1 1 PASS rs200729271 . 0 206 2 0 0 0 0 2 -2.799333 0 0 1 0 0 A 3 1 83 40182259 40182259 C A 1 0 0 0 0 1 0 0 0 10103 680 24 2 2 MYRIP 3 40182259 Missense_Mutation SNP C C3N-01823_T 997351 40182259 158113300 79 25776 TCAIM 0 . GRCh38 3 44367508 44367508 + Silent SNP G G T rs150831975 C3N-01823_T C3N-01823_N G G c.372G>T p.= p.V124V ENST00000342649 5/11 189 162 27 130 130 0 strelka-varscan-mutect TCAIM,synonymous_variant,p.=,ENST00000342649,NM_173826.3,NM_001282914.1;TCAIM,synonymous_variant,p.=,ENST00000417237,NM_001282915.1,NM_001282913.1;TCAIM,downstream_gene_variant,,ENST00000444602,;TCAIM,non_coding_transcript_exon_variant,,ENST00000494638,;TCAIM,intron_variant,,ENST00000431657,;TCAIM,intron_variant,,ENST00000412611,;TCAIM,intron_variant,,ENST00000417768,;TCAIM,intron_variant,,ENST00000462230,; T ENST00000342649 Transcript synonymous_variant 799/3687 372/1491 124/496 V gtG/gtT rs150831975,COSM109540 1 1 TCAIM HGNC HGNC:25241 protein_coding YES CCDS2712.1 ENSP00000341539 Q8N3R3 UPI0000140156 NM_173826.3,NM_001282914.1 5/11 hmmpanther:PTHR31596,Pfam_domain:PF14687 1,1 LOW 1 SNV 1 0,1 1 PASS rs150831975 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 44367508 44367508 G T 1 0 0 0 0 0 0 0 1 16072 1364 48 2 2 TCAIM 3 44367508 Silent SNP G C3N-01823_T 4185249 44367508 153928051 80 25777 EXOSC7 0 . GRCh38 3 44997127 44997127 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.295G>C p.Asp99His p.D99H ENST00000265564 4/8 246 220 26 155 155 0 strelka-varscan-mutect EXOSC7,missense_variant,p.Asp99His,ENST00000265564,NM_015004.3;EXOSC7,non_coding_transcript_exon_variant,,ENST00000461361,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000491476,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000468667,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000481405,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000482004,;CLEC3B,upstream_gene_variant,,ENST00000490386,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000467846,; C ENST00000265564 Transcript missense_variant 343/1055 295/876 99/291 D/H Gat/Cat 1 1 EXOSC7 HGNC HGNC:28112 protein_coding YES CCDS2725.1 ENSP00000265564 Q15024 A0A024R2P7 UPI000020A5E9 NM_015004.3 deleterious(0) 4/8 Pfam_domain:PF01138,hmmpanther:PTHR11097,hmmpanther:PTHR11097:SF8,Superfamily_domains:SSF54211 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 44997127 44997127 G C 1 0 0 0 0 1 0 0 0 5187 1290 45 4 4 EXOSC7 3 44997127 Missense_Mutation SNP G C3N-01823_T 629619 44997127 153298432 81 25778 SETD2 0 . GRCh38 3 47057034 47057034 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.6750A>T p.Gln2250His p.Q2250H ENST00000409792 15/21 256 213 43 183 183 0 strelka-varscan-mutect SETD2,missense_variant,p.Gln2250His,ENST00000409792,NM_014159.6;SETD2,3_prime_UTR_variant,,ENST00000330022,;SETD2,3_prime_UTR_variant,,ENST00000431180,;SETD2,3_prime_UTR_variant,,ENST00000445387,; A ENST00000409792 Transcript missense_variant 6793/8142 6750/7695 2250/2564 Q/H caA/caT 1 -1 SETD2 HGNC HGNC:18420 protein_coding YES CCDS2749.2 ENSP00000386759 Q9BYW2 UPI00017E10FB NM_014159.6 deleterious(0) 15/21 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 47057034 47057034 T A 1 0 0 0 0 1 0 0 0 14409 1606 56 4 4 SETD2 3 47057034 Missense_Mutation SNP T C3N-01823_T 2059907 47057034 151238525 82 25779 DHX30 0 . GRCh38 3 47840914 47840914 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.404A>T p.Asp135Val p.D135V ENST00000445061 7/22 436 395 41 372 372 0 strelka-varscan-mutect DHX30,missense_variant,p.Asp135Val,ENST00000445061,NM_138615.2;DHX30,missense_variant,p.Asp107Val,ENST00000348968,;DHX30,missense_variant,p.Asp163Val,ENST00000457607,;DHX30,missense_variant,p.Asp135Val,ENST00000446256,;DHX30,missense_variant,p.Asp96Val,ENST00000619982,NM_014966.3;DHX30,upstream_gene_variant,,ENST00000461905,;DHX30,3_prime_UTR_variant,,ENST00000395745,;DHX30,3_prime_UTR_variant,,ENST00000441384,; T ENST00000445061 Transcript missense_variant 811/4065 404/3585 135/1194 D/V gAc/gTc 1 1 DHX30 HGNC HGNC:16716 protein_coding YES CCDS2759.1 ENSP00000405620 Q7L2E3 A0A024R2T6 UPI000007112B NM_138615.2 deleterious_low_confidence(0.01) 7/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 47840914 47840914 A T 1 0 0 0 0 1 0 0 0 4308 275 10 4 4 DHX30 3 47840914 Missense_Mutation SNP A C3N-01823_T 783880 47840914 150454645 83 25780 CELSR3 0 . GRCh38 3 48653030 48653030 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.5606T>A p.Met1869Lys p.M1869K ENST00000164024 10/35 145 116 29 105 105 0 strelka-varscan-mutect CELSR3,missense_variant,p.Met1869Lys,ENST00000164024,NM_001407.2; T ENST00000164024 Transcript missense_variant 5887/11956 5606/9939 1869/3312 M/K aTg/aAg 1 -1 CELSR3 HGNC HGNC:3230 protein_coding YES CCDS2775.1 ENSP00000164024 Q9NYQ7 UPI00001AE5A6 NM_001407.2 tolerated(0.25) 10/35 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF38,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 48653030 48653030 A T 1 0 0 0 0 1 0 0 0 2930 217 8 4 4 CELSR3 3 48653030 Missense_Mutation SNP A C3N-01823_T 812116 48653030 149642529 84 25781 SLC25A20 0 . GRCh38 3 48859096 48859096 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.714G>T p.Gln238His p.Q238H ENST00000319017 7/9 302 261 41 226 226 0 strelka-varscan-mutect SLC25A20,missense_variant,p.Gln238His,ENST00000319017,NM_000387.5;SLC25A20,missense_variant,p.Gln165His,ENST00000430379,;SLC25A20,3_prime_UTR_variant,,ENST00000440964,;SLC25A20,upstream_gene_variant,,ENST00000479050,; A ENST00000319017 Transcript missense_variant 913/1879 714/906 238/301 Q/H caG/caT 1 -1 SLC25A20 HGNC HGNC:1421 protein_coding YES CCDS2779.1 ENSP00000326305 O43772 UPI000012ED5E NM_000387.5 deleterious(0) 7/9 PROSITE_profiles:PS50920,hmmpanther:PTHR24089:SF323,hmmpanther:PTHR24089,Gene3D:1okcA00,Pfam_domain:PF00153,Superfamily_domains:0048588 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 48859096 48859096 C A 1 0 0 0 0 1 0 0 0 14748 927 32 2 2 SLC25A20 3 48859096 Missense_Mutation SNP C C3N-01823_T 206066 48859096 149436463 85 25782 UBA7 0 . GRCh38 3 49810600 49810600 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1384G>T p.Gly462Trp p.G462W ENST00000333486 12/24 332 283 49 240 240 0 strelka-varscan-mutect UBA7,missense_variant,p.Gly462Trp,ENST00000333486,NM_003335.2;UBA7,upstream_gene_variant,,ENST00000584510,;UBA7,downstream_gene_variant,,ENST00000494212,;UBA7,non_coding_transcript_exon_variant,,ENST00000460703,;UBA7,non_coding_transcript_exon_variant,,ENST00000460516,;UBA7,upstream_gene_variant,,ENST00000483751,;UBA7,downstream_gene_variant,,ENST00000478688,;UBA7,upstream_gene_variant,,ENST00000488536,;UBA7,upstream_gene_variant,,ENST00000478875,;UBA7,upstream_gene_variant,,ENST00000497908,;UBA7,upstream_gene_variant,,ENST00000473992,;UBA7,upstream_gene_variant,,ENST00000489826,; A ENST00000333486 Transcript missense_variant 1543/3299 1384/3039 462/1012 G/W Ggg/Tgg 1 -1 UBA7 HGNC HGNC:12471 protein_coding YES CCDS2805.1 ENSP00000333266 P41226 UPI000006E3F8 NM_003335.2 deleterious(0) 12/24 Gene3D:3.40.50.720,Pfam_domain:PF00899,Prints_domain:PR01849,hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF143,Superfamily_domains:SSF69572,TIGRFAM_domain:TIGR01408 MODERATE 1 SNV 1 1 PASS rs1411809564 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 49810600 49810600 C A 1 0 0 0 0 1 0 0 0 17352 652 23 1 1 UBA7 3 49810600 Missense_Mutation SNP C C3N-01823_T 951504 49810600 148484959 86 25783 RBM6 0 . GRCh38 3 50077095 50077095 + Frame_Shift_Del DEL C C - C3N-01823_T C3N-01823_N C C c.3334delC p.Arg1112GlufsTer? p.R1112Efs*? ENST00000266022 21/21 201 180 21 223 223 0 sindel-varindel-pindel RBM6,frameshift_variant,p.Arg980GlufsTer?,ENST00000443081,;RBM6,frameshift_variant,p.Arg1112GlufsTer?,ENST00000266022,NM_005777.2;RBM6,frameshift_variant,p.Arg590GlufsTer?,ENST00000422955,;RBM6,frameshift_variant,p.Arg590GlufsTer?,ENST00000442092,NM_001167582.1;RBM6,frameshift_variant,p.Arg108GlufsTer?,ENST00000421682,;RBM6,3_prime_UTR_variant,,ENST00000454079,;RBM6,3_prime_UTR_variant,,ENST00000419610,;RBM6,intron_variant,,ENST00000434592,; - ENST00000266022 Transcript frameshift_variant 3593/3750 3334/3372 1112/1123 R/X Cga/ga COSM1046404 1 1 RBM6 HGNC HGNC:9903 protein_coding YES CCDS2809.1 ENSP00000266022 P78332 UPI000013D6C0 NM_005777.2 21/21 hmmpanther:PTHR13948,hmmpanther:PTHR13948:SF22 1 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 50077095 50077095 C - 1 0 1 0 1 0 0 0 0 13311 876 31 0 0 RBM6 3 50077095 Frame_Shift_Del DEL C C3N-01823_T 266495 50077095 148218464 87 25784 FHIT 0 . GRCh38 3 59752300 59752300 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.370G>T p.Asp124Tyr p.D124Y ENST00000468189 9/9 202 170 32 111 111 0 strelka-varscan-mutect FHIT,missense_variant,p.Asp124Tyr,ENST00000468189,;FHIT,missense_variant,p.Asp124Tyr,ENST00000492590,NM_002012.2,NM_001166243.1;FHIT,missense_variant,p.Asp124Tyr,ENST00000476844,;FHIT,non_coding_transcript_exon_variant,,ENST00000466788,; A ENST00000468189 Transcript missense_variant 741/1634 370/444 124/147 D/Y Gac/Tac 1 -1 FHIT HGNC HGNC:3701 protein_coding YES CCDS2894.1 ENSP00000417480 P49789 A0A024R366 UPI000000160B deleterious(0) 9/9 hmmpanther:PTHR23089:SF19,hmmpanther:PTHR23089,Gene3D:3.30.428.10,Superfamily_domains:SSF54197 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 59752300 59752300 C A 1 0 0 0 0 1 0 0 0 5742 855 30 2 2 FHIT 3 59752300 Missense_Mutation SNP C C3N-01823_T 9675205 59752300 138543259 88 25785 FRMD4B 0 . GRCh38 3 69249238 69249238 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.569G>T p.Gly190Val p.G190V ENST00000398540 7/23 165 154 11 135 135 0 strelka-varscan-mutect FRMD4B,missense_variant,p.Gly190Val,ENST00000398540,NM_015123.2;FRMD4B,missense_variant,p.Gly136Val,ENST00000460709,;FRMD4B,missense_variant,p.Gly136Val,ENST00000473029,;FRMD4B,missense_variant,p.Gly81Val,ENST00000493880,;FRMD4B,non_coding_transcript_exon_variant,,ENST00000470070,;FRMD4B,non_coding_transcript_exon_variant,,ENST00000483668,;FRMD4B,intron_variant,,ENST00000487751,; A ENST00000398540 Transcript missense_variant 653/5060 569/3105 190/1034 G/V gGa/gTa 1 -1 FRMD4B HGNC HGNC:24886 protein_coding YES CCDS46863.1 ENSP00000381549 Q9Y2L6 UPI00001C1DF1 NM_015123.2 deleterious(0.01) 7/23 PROSITE_profiles:PS50057,hmmpanther:PTHR23281:SF16,hmmpanther:PTHR23281,Pfam_domain:PF00373,Gene3D:1.20.80.10,SMART_domains:SM00295,Superfamily_domains:SSF47031,Prints_domain:PR00935 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 69249238 69249238 C A 1 0 0 0 0 1 0 0 0 5922 855 30 2 2 FRMD4B 3 69249238 Missense_Mutation SNP C C3N-01823_T 9496938 69249238 129046321 89 25786 OR5AC2 0 . GRCh38 3 98087764 98087764 + Missense_Mutation SNP G G A rs755877682 C3N-01823_T C3N-01823_N G G c.592G>A p.Ala198Thr p.A198T ENST00000358642 1/1 116 99 17 73 73 0 strelka-varscan-mutect OR5AC2,missense_variant,p.Ala198Thr,ENST00000358642,NM_054106.1; A ENST00000358642 Transcript missense_variant 592/930 592/930 198/309 A/T Gca/Aca rs755877682,COSM293479 1 1 OR5AC2 HGNC HGNC:15431 protein_coding YES CCDS33796.1 ENSP00000351466 Q9NZP5 UPI0000441EFD NM_054106.1 tolerated(0.39) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF96,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs755877682 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 83 98087764 98087764 G A 1 0 0 0 0 1 0 0 0 11213 1087 38 1 1 OR5AC2 3 98087764 Missense_Mutation SNP G C3N-01823_T 28838526 98087764 100207795 90 25787 OR5H14 0 . GRCh38 3 98150184 98150184 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.799G>T p.Ala267Ser p.A267S ENST00000437310 1/1 176 150 26 118 118 0 strelka-varscan-mutect OR5H14,missense_variant,p.Ala267Ser,ENST00000437310,NM_001005514.1;RP11-343D2.11,upstream_gene_variant,,ENST00000508964,; T ENST00000437310 Transcript missense_variant 859/1080 799/933 267/310 A/S Gct/Tct 1 1 OR5H14 HGNC HGNC:31286 protein_coding YES CCDS33798.1 ENSP00000401706 A6NHG9 UPI0000197F5D NM_001005514.1 tolerated(0.3) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF375,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999159 1 1 1 0 T 3 4 83 98150184 98150184 G T 1 0 0 0 0 1 0 0 0 11230 1203 42 2 2 OR5H14 3 98150184 Missense_Mutation SNP G C3N-01823_T 62420 98150184 100145375 91 25788 PARP14 0 . GRCh38 3 122700351 122700351 + Silent SNP G G A C3N-01823_T C3N-01823_N G G c.1797G>A p.= p.K599K ENST00000474629 6/17 249 225 24 189 189 0 strelka-varscan-mutect PARP14,synonymous_variant,p.=,ENST00000474629,NM_017554.2;PARP14,downstream_gene_variant,,ENST00000494811,;PARP14,synonymous_variant,p.=,ENST00000460683,;PARP14,upstream_gene_variant,,ENST00000474669,; A ENST00000474629 Transcript synonymous_variant 2063/7915 1797/5406 599/1801 K aaG/aaA COSM269816,COSM269817 1 1 PARP14 HGNC HGNC:29232 protein_coding YES CCDS46894.1 ENSP00000418194 Q460N5 UPI00015A20AB NM_017554.2 6/17 hmmpanther:PTHR14453,hmmpanther:PTHR14453:SF65 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 122700351 122700351 G A 1 0 0 0 0 0 0 0 1 11538 962 34 3 3 PARP14 3 122700351 Silent SNP G C3N-01823_T 24550167 122700351 75595208 92 25789 ACAD9 0 . GRCh38 3 128879766 128879766 + Silent SNP G G C rs564435799 C3N-01823_T C3N-01823_N G G c.75G>C p.= p.A25A ENST00000308982 1/18 417 396 21 230 229 1 strelka-varscan-mutect ACAD9,synonymous_variant,p.=,ENST00000308982,NM_014049.4;ACAD9,synonymous_variant,p.=,ENST00000514336,;ACAD9,non_coding_transcript_exon_variant,,ENST00000505602,;ACAD9,synonymous_variant,p.=,ENST00000511227,;ACAD9,synonymous_variant,p.=,ENST00000505867,;ACAD9,synonymous_variant,p.=,ENST00000505192,;ACAD9,synonymous_variant,p.=,ENST00000514643,;ACAD9,synonymous_variant,p.=,ENST00000512801,;ACAD9,synonymous_variant,p.=,ENST00000515429,; C ENST00000308982 Transcript synonymous_variant 156/2454 75/1866 25/621 A gcG/gcC rs564435799 1 1 ACAD9 HGNC HGNC:21497 protein_coding YES CCDS3053.1 ENSP00000312618 Q9H845 UPI00000498C3 NM_014049.4 1/18 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF121 LOW 1 SNV 1 1 PASS rs564435799 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 128879766 128879766 G C 1 0 0 0 0 0 0 0 1 154 1045 37 4 4 ACAD9 3 128879766 Silent SNP G C3N-01823_T 6179415 128879766 69415793 93 25790 U2SURP 0 . GRCh38 3 143037311 143037311 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2197G>T p.Asp733Tyr p.D733Y ENST00000473835 21/28 208 178 30 143 143 0 strelka-mutect U2SURP,missense_variant,p.Asp733Tyr,ENST00000473835,NM_001320219.1,NM_001080415.1;U2SURP,missense_variant,p.Asp732Tyr,ENST00000493598,;U2SURP,missense_variant,p.Asp53Tyr,ENST00000467348,;U2SURP,3_prime_UTR_variant,,ENST00000463563,;U2SURP,3_prime_UTR_variant,,ENST00000488497,;U2SURP,non_coding_transcript_exon_variant,,ENST00000480029,;U2SURP,non_coding_transcript_exon_variant,,ENST00000461844,;U2SURP,downstream_gene_variant,,ENST00000472373,;U2SURP,downstream_gene_variant,,ENST00000496100,; T ENST00000473835 Transcript missense_variant 2287/7276 2197/3090 733/1029 D/Y Gat/Tat 1 1 U2SURP HGNC HGNC:30855 protein_coding YES CCDS46928.1 ENSP00000418563 O15042 UPI0000160746 NM_001320219.1,NM_001080415.1 tolerated(0.13) 21/28 hmmpanther:PTHR23140:SF1,hmmpanther:PTHR23140 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 143037311 143037311 G T 1 0 0 0 0 1 0 0 0 17341 1290 45 2 2 U2SURP 3 143037311 Missense_Mutation SNP G C3N-01823_T 14157545 143037311 55258248 94 25791 HPS3 0 . GRCh38 3 149157440 149157440 + Missense_Mutation SNP A A T rs372479893 C3N-01823_T C3N-01823_N A A c.1600A>T p.Met534Leu p.M534L ENST00000296051 9/17 312 275 37 207 207 0 strelka-varscan-mutect HPS3,missense_variant,p.Met534Leu,ENST00000296051,NM_032383.3;HPS3,missense_variant,p.Met369Leu,ENST00000460120,NM_001308258.1;CP,downstream_gene_variant,,ENST00000479771,;CP,downstream_gene_variant,,ENST00000481169,;HPS3,downstream_gene_variant,,ENST00000462030,;HPS3,upstream_gene_variant,,ENST00000460822,;HPS3,downstream_gene_variant,,ENST00000486530,; T ENST00000296051 Transcript missense_variant 1740/4665 1600/3015 534/1004 M/L Atg/Ttg rs372479893 1 1 HPS3 HGNC HGNC:15597 protein_coding YES CCDS3140.1 ENSP00000296051 Q969F9 UPI000000D989 NM_032383.3 tolerated(0.46) 9/17 hmmpanther:PTHR28633,hmmpanther:PTHR28633:SF1,Pfam_domain:PF14762,PIRSF_domain:PIRSF037473 MODERATE 1 SNV 1 1 PASS rs372479893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 149157440 149157440 A T 1 0 0 0 0 1 0 0 0 7235 333 12 4 4 HPS3 3 149157440 Missense_Mutation SNP A C3N-01823_T 6120129 149157440 49138119 95 25792 POLN 0 . GRCh38 4 2208442 2208442 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.259C>T p.= p.L87L ENST00000511885 5/26 91 78 13 66 66 0 strelka-varscan-mutect POLN,synonymous_variant,p.=,ENST00000511885,NM_181808.3;POLN,synonymous_variant,p.=,ENST00000382865,;POLN,non_coding_transcript_exon_variant,,ENST00000515357,;POLN,non_coding_transcript_exon_variant,,ENST00000506518,;POLN,upstream_gene_variant,,ENST00000514858,; A ENST00000511885 Transcript synonymous_variant 613/3253 259/2703 87/900 L Ctg/Ttg 1 -1 POLN HGNC HGNC:18870 protein_coding YES CCDS3360.1 ENSP00000435506 Q7Z5Q5 UPI0000246FC3 NM_181808.3 5/26 LOW 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999979 1 1 1 0 A 2 1 83 2208442 2208442 G A 1 0 0 0 0 0 0 0 1 12317 962 34 3 3 POLN 4 2208442 Silent SNP G C3N-01823_T 2208442 188006113 96 25793 ADRA2C 0 . GRCh38 4 3767422 3767422 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.816G>T p.Glu272Asp p.E272D ENST00000330055 1/1 215 204 11 142 142 0 strelka-varscan-mutect ADRA2C,missense_variant,p.Glu272Asp,ENST00000330055,NM_000683.3;ADRA2C,missense_variant,p.Glu272Asp,ENST00000509482,;AC141928.1,upstream_gene_variant,,ENST00000511928,; T ENST00000330055 Transcript missense_variant 1025/2129 816/1389 272/462 E/D gaG/gaT 1 1 ADRA2C HGNC HGNC:283 protein_coding YES CCDS47004.1 ENSP00000386069 P18825 Q4W594 UPI000012500C NM_000683.3 tolerated(0.2) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF25,Pfam_domain:PF00001,SMART_domains:SM01381 MODERATE SNV 1 PASS rs1206174325 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 3767422 3767422 G T 1 0 0 0 0 1 0 0 0 415 933 33 2 2 ADRA2C 4 3767422 Missense_Mutation SNP G C3N-01823_T 1558980 3767422 186447133 97 25794 CPZ 0 . GRCh38 4 8614476 8614476 + Nonsense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.1481C>G p.Ser494Ter p.S494* ENST00000360986 9/11 138 128 10 93 93 0 strelka-varscan-mutect CPZ,stop_gained,p.Ser357Ter,ENST00000382480,NM_001014448.2;CPZ,stop_gained,p.Ser494Ter,ENST00000360986,NM_001014447.2;CPZ,stop_gained,p.Ser483Ter,ENST00000315782,NM_003652.3;GPR78,3_prime_UTR_variant,,ENST00000514302,;CPZ,3_prime_UTR_variant,,ENST00000515606,;GPR78,non_coding_transcript_exon_variant,,ENST00000513120,;CPZ,upstream_gene_variant,,ENST00000513486,; G ENST00000360986 Transcript stop_gained 1655/2267 1481/1959 494/652 S/* tCa/tGa 1 1 CPZ HGNC HGNC:2333 protein_coding YES CCDS33953.1 ENSP00000354255 Q66K79 UPI000020BCC5 NM_001014447.2 9/11 Gene3D:3.40.630.10,hmmpanther:PTHR11532,hmmpanther:PTHR11532:SF55,SMART_domains:SM00631,Superfamily_domains:SSF53187 HIGH 1 SNV 1 1 PASS rs1436870207 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 83 8614476 8614476 C G 1 0 0 0 0 0 1 0 0 3637 838 29 4 4 CPZ 4 8614476 Nonsense_Mutation SNP C C3N-01823_T 4847054 8614476 181600079 98 25795 PCDH7 0 . GRCh38 4 30724296 30724296 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2874G>T p.Lys958Asn p.K958N ENST00000543491 1/1 193 180 13 97 97 0 strelka-varscan-mutect PCDH7,missense_variant,p.Lys648Asn,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,missense_variant,p.Lys958Asn,ENST00000361762,NM_002589.2;PCDH7,missense_variant,p.Lys958Asn,ENST00000543491,NM_032456.2;PCDH7,missense_variant,p.Lys273Asn,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,intron_variant,,ENST00000507864,; T ENST00000543491 Transcript missense_variant 3444/4457 2874/3219 958/1072 K/N aaG/aaT 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 tolerated(0.1) 1/1 hmmpanther:PTHR24027:SF321,hmmpanther:PTHR24027,Pfam_domain:PF08374 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 30724296 30724296 G T 1 0 0 0 0 1 0 0 0 11603 962 34 2 2 PCDH7 4 30724296 Missense_Mutation SNP G C3N-01823_T 22109820 30724296 159490259 99 25796 SRP72 0 . GRCh38 4 56467659 56467659 + Silent SNP G G C rs552135994 C3N-01823_T C3N-01823_N G G c.24G>C p.= p.G8G ENST00000342756 1/19 71 65 6 42 42 0 strelka-mutect SRP72,synonymous_variant,p.=,ENST00000342756,NM_006947.3;SRP72,synonymous_variant,p.=,ENST00000510663,NM_001267722.1;SRP72,synonymous_variant,p.=,ENST00000504757,;PAICS,downstream_gene_variant,,ENST00000512576,NM_001079524.1; C ENST00000342756 Transcript synonymous_variant 745/3983 24/2016 8/671 G ggG/ggC rs552135994 1 1 SRP72 HGNC HGNC:11303 protein_coding YES CCDS3506.1 ENSP00000342181 O76094 V9HWK0 UPI000013EEB0 NM_006947.3 1/19 Low_complexity_(Seg):seg,hmmpanther:PTHR14094:SF9,hmmpanther:PTHR14094,PIRSF_domain:PIRSF038922 LOW 1 SNV 1 1 PASS rs552135994 . 0 204 5 0 0 0 0 0 -13.47971 1 1 1 1 0 C 2 2 83 56467659 56467659 G C 1 0 0 0 0 0 0 0 1 15518 1219 43 4 4 SRP72 4 56467659 Silent SNP G C3N-01823_T 25743363 56467659 133746896 100 25797 ARHGAP24 0 . GRCh38 4 85942129 85942129 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.455C>A p.Ala152Asp p.A152D ENST00000395184 5/10 326 297 29 244 244 0 strelka-varscan-mutect ARHGAP24,missense_variant,p.Ala152Asp,ENST00000395184,NM_001025616.2;ARHGAP24,missense_variant,p.Ala59Asp,ENST00000264343,NM_031305.2;ARHGAP24,missense_variant,p.Ala57Asp,ENST00000395183,NM_001042669.1;ARHGAP24,missense_variant,p.Ala67Asp,ENST00000514229,NM_001287805.1;ARHGAP24,missense_variant,p.Ala152Asp,ENST00000503995,;ARHGAP24,missense_variant,p.Ala26Asp,ENST00000509300,;ARHGAP24,missense_variant,p.Ala57Asp,ENST00000512201,;ARHGAP24,non_coding_transcript_exon_variant,,ENST00000502537,;ARHGAP24,non_coding_transcript_exon_variant,,ENST00000503917,; A ENST00000395184 Transcript missense_variant 921/4661 455/2247 152/748 A/D gCt/gAt 1 1 ARHGAP24 HGNC HGNC:25361 protein_coding YES CCDS34025.1 ENSP00000378611 Q8N264 UPI00001AF1D9 NM_001025616.2 deleterious(0) 5/10 PROSITE_profiles:PS50238,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF19,Gene3D:1.10.555.10,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 2 1 PASS rs1286516744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 85942129 85942129 C A 1 0 0 0 0 1 0 0 0 998 797 28 2 2 ARHGAP24 4 85942129 Missense_Mutation SNP C C3N-01823_T 29474470 85942129 104272426 101 25798 MTTP 0 . GRCh38 4 99583493 99583493 + Silent SNP G G T rs562221537 C3N-01823_T C3N-01823_N G G c.450G>T p.= p.T150T ENST00000511045 3/18 302 280 22 254 254 0 strelka-varscan-mutect MTTP,synonymous_variant,p.=,ENST00000457717,NM_000253.3;MTTP,synonymous_variant,p.=,ENST00000265517,;MTTP,synonymous_variant,p.=,ENST00000511045,NM_001300785.1;MTTP,synonymous_variant,p.=,ENST00000422897,;MTTP,synonymous_variant,p.=,ENST00000506883,;MTTP,downstream_gene_variant,,ENST00000515141,;MTTP,downstream_gene_variant,,ENST00000513404,;MTTP,downstream_gene_variant,,ENST00000505094,;MTTP,downstream_gene_variant,,ENST00000511610,;MTTP,downstream_gene_variant,,ENST00000505142,; T ENST00000511045 Transcript synonymous_variant 463/3154 450/2766 150/921 T acG/acT rs562221537 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 3/18 Gene3D:1lshA01,Pfam_domain:PF01347,PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1,SMART_domains:SM00638,Superfamily_domains:SSF56968 LOW 1 SNV 2 1 PASS rs562221537 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 99583493 99583493 G T 1 0 0 0 0 0 0 0 1 9961 1074 38 1 1 MTTP 4 99583493 Silent SNP G C3N-01823_T 13641364 99583493 90631062 102 25799 MTTP 0 . GRCh38 4 99606807 99606807 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.1485G>A p.= p.E495E ENST00000511045 11/18 586 537 49 408 407 1 strelka-varscan-mutect MTTP,synonymous_variant,p.=,ENST00000457717,NM_000253.3;MTTP,synonymous_variant,p.=,ENST00000265517,;MTTP,synonymous_variant,p.=,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; A ENST00000511045 Transcript synonymous_variant 1498/3154 1485/2766 495/921 E gaG/gaA 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 11/18 Superfamily_domains:0040642,Gene3D:1lshA02,Pfam_domain:PF01347,PROSITE_profiles:PS51211,hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1,SMART_domains:SM00638 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 99606807 99606807 G A 1 0 0 0 0 0 0 0 1 9961 991 35 3 3 MTTP 4 99606807 Silent SNP G C3N-01823_T 23314 99606807 90607748 103 25800 SLC9B2 0 . GRCh38 4 103044996 103044996 + Missense_Mutation SNP C C T rs780338146 C3N-01823_T C3N-01823_N C C c.890G>A p.Gly297Asp p.G297D ENST00000394785 8/12 164 149 15 149 149 0 strelka-varscan-mutect SLC9B2,missense_variant,p.Gly297Asp,ENST00000394785,NM_178833.5;SLC9B2,missense_variant,p.Gly297Asp,ENST00000362026,;SLC9B2,missense_variant,p.Gly240Asp,ENST00000503103,NM_001300756.1;SLC9B2,missense_variant,p.Gly240Asp,ENST00000503230,NM_001300754.1;SLC9B2,missense_variant,p.Gly197Asp,ENST00000506288,;SLC9B2,downstream_gene_variant,,ENST00000515424,;SLC9B2,upstream_gene_variant,,ENST00000510976,; T ENST00000394785 Transcript missense_variant,splice_region_variant 1522/3126 890/1614 297/537 G/D gGc/gAc rs780338146 1 -1 SLC9B2 HGNC HGNC:25143 protein_coding YES CCDS3662.1 ENSP00000378265 Q86UD5 A0A024RDJ7 UPI000020B27F NM_178833.5 deleterious(0.05) 8/12 Pfam_domain:PF00999,hmmpanther:PTHR31102,hmmpanther:PTHR31102:SF6 MODERATE 1 SNV 2 1 PASS rs780338146 . 0 207 0 2 0 0 0 0 -19.92696 0.9999998 1 1 1 0 T 3 4 83 103044996 103044996 C T 1 0 0 0 0 1 0 0 0 15005 753 26 3 3 SLC9B2 4 103044996 Missense_Mutation SNP C C3N-01823_T 3438189 103044996 87169559 104 25801 CFI 0 . GRCh38 4 109749507 109749507 + Missense_Mutation SNP C C A rs779679778 C3N-01823_T C3N-01823_N C C c.1036G>T p.Ala346Ser p.A346S ENST00000394634 9/13 506 447 59 336 335 1 strelka-varscan-mutect CFI,missense_variant,p.Ala346Ser,ENST00000394634,NM_000204.3;CFI,missense_variant,p.Ala354Ser,ENST00000394635,NM_001318057.1;CFI,missense_variant,p.Ala339Ser,ENST00000512148,;CFI,missense_variant,p.Ala346Ser,ENST00000618244,;CFI,non_coding_transcript_exon_variant,,ENST00000504853,;CFI,upstream_gene_variant,,ENST00000515512,; A ENST00000394634 Transcript missense_variant 1244/2159 1036/1752 346/583 A/S Gca/Tca rs779679778 1 -1 CFI HGNC HGNC:5394 protein_coding YES CCDS34049.1 ENSP00000378130 P05156 UPI0000D615A9 NM_000204.3 deleterious(0) 9/13 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF197,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs779679778 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 109749507 109749507 C A 1 0 0 0 0 1 0 0 0 3047 797 28 2 2 CFI 4 109749507 Missense_Mutation SNP C C3N-01823_T 6704511 109749507 80465048 105 25802 FAT4 0 . GRCh38 4 125451553 125451553 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.10537A>T p.Ser3513Cys p.S3513C ENST00000394329 9/17 396 361 35 240 240 0 strelka-varscan-mutect FAT4,missense_variant,p.Ser3513Cys,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Ser1811Cys,ENST00000335110,;FAT4,downstream_gene_variant,,ENST00000509444,; T ENST00000394329 Transcript missense_variant 10550/16123 10537/14946 3513/4981 S/C Agt/Tgt 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.05) 9/17 PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 125451553 125451553 A T 1 0 0 0 0 1 0 0 0 5552 188 7 4 4 FAT4 4 125451553 Missense_Mutation SNP A C3N-01823_T 15702046 125451553 64763002 106 25803 PCDH10 0 . GRCh38 4 133152635 133152635 + Frame_Shift_Del DEL C C - novel C3N-01823_T C3N-01823_N C C c.2496delC p.Asp833ThrfsTer2 p.D833Tfs*2 ENST00000264360 1/5 213 174 39 148 148 0 sindel-varindel-pindel PCDH10,frameshift_variant,p.Asp833ThrfsTer2,ENST00000264360,NM_032961.2;PCDH10,frameshift_variant,p.Asp833ThrfsTer2,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; - ENST00000264360 Transcript frameshift_variant 3321/8489 2495/3123 832/1040 T/X aCc/ac 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 1/5 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 133152635 133152635 C - 1 0 1 0 1 0 0 0 0 11594 507 18 0 0 PCDH10 4 133152635 Frame_Shift_Del DEL C C3N-01823_T 7701082 133152635 57061920 107 25804 SMARCA5 0 . GRCh38 4 143546872 143546872 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.2617G>C p.Glu873Gln p.E873Q ENST00000283131 20/24 172 154 18 180 180 0 strelka-varscan-mutect SMARCA5,missense_variant,p.Glu873Gln,ENST00000283131,NM_003601.3;SMARCA5,downstream_gene_variant,,ENST00000515531,;SMARCA5,upstream_gene_variant,,ENST00000508573,; C ENST00000283131 Transcript missense_variant 3079/7923 2617/3159 873/1052 E/Q Gaa/Caa 1 1 SMARCA5 HGNC HGNC:11101 protein_coding YES CCDS3761.1 ENSP00000283131 O60264 UPI000006E693 NM_003601.3 tolerated(0.16) 20/24 PROSITE_profiles:PS51293,Gene3D:1.10.10.60,SMART_domains:SM00717,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999867 1 1 1 0 C 3 2 83 143546872 143546872 G C 1 0 0 0 0 1 0 0 0 15064 943 33 4 4 SMARCA5 4 143546872 Missense_Mutation SNP G C3N-01823_T 10394237 143546872 46667683 108 25805 DCHS2 0 . GRCh38 4 154236918 154236918 + Missense_Mutation SNP C C A C3N-01823_T C3N-01823_N C C c.6369G>T p.Trp2123Cys p.W2123C ENST00000623607 25/25 360 338 22 196 196 0 strelka-varscan-mutect DCHS2,missense_variant,p.Trp2123Cys,ENST00000357232,;DCHS2,missense_variant,p.Trp2123Cys,ENST00000623607,NM_017639.3;RP11-9N12.2,non_coding_transcript_exon_variant,,ENST00000625026,;RP11-290O12.2,intron_variant,,ENST00000624941,;RP11-290O12.2,intron_variant,,ENST00000623325,; A ENST00000623607 Transcript missense_variant 6369/8912 6369/8751 2123/2916 W/C tgG/tgT COSM3775632,COSM4676463 1 -1 DCHS2 HGNC HGNC:23111 protein_coding YES CCDS3785.1 ENSP00000485514 Q6V1P9 UPI000035B018 NM_017639.3 deleterious(0) 25/25 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF305,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 154236918 154236918 C A 1 0 0 0 0 1 0 0 0 4091 856 30 2 2 DCHS2 4 154236918 Missense_Mutation SNP C C3N-01823_T 10690046 154236918 35977637 109 25806 DCHS2 0 . GRCh38 4 154490331 154490331 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.1025G>A p.Gly342Glu p.G342E ENST00000339452 1/8 378 344 34 266 266 0 strelka-varscan-mutect DCHS2,missense_variant,p.Gly342Glu,ENST00000339452,NM_001142552.1;DCHS2,non_coding_transcript_exon_variant,,ENST00000456341,; T ENST00000339452 Transcript missense_variant 1386/5064 1025/4110 342/1369 G/E gGg/gAg 1 -1 DCHS2 HGNC HGNC:23111 protein_coding CCDS47150.1 ENSP00000345062 A0A0A0MRC0 UPI00002372F1 NM_001142552.1 tolerated_low_confidence(0.08) 1/8 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,Low_complexity_(Seg):seg,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 154490331 154490331 C T 1 0 0 0 0 1 0 0 0 4091 623 22 3 3 DCHS2 4 154490331 Missense_Mutation SNP C C3N-01823_T 253413 154490331 35724224 110 25807 PLRG1 0 . GRCh38 4 154544482 154544482 + Frame_Shift_Del DEL G G - novel C3N-01823_T C3N-01823_N G G c.557delC p.Pro186GlnfsTer43 p.P186Qfs*43 ENST00000499023 7/15 296 270 26 233 233 0 sindel-varindel-pindel PLRG1,frameshift_variant,p.Pro186GlnfsTer43,ENST00000499023,NM_002669.3;PLRG1,frameshift_variant,p.Pro177GlnfsTer43,ENST00000302078,NM_001201564.1;PLRG1,frameshift_variant,p.Pro184GlnfsTer?,ENST00000504341,;RNU6-1285P,upstream_gene_variant,,ENST00000363480,;PLRG1,3_prime_UTR_variant,,ENST00000506192,;PLRG1,non_coding_transcript_exon_variant,,ENST00000506918,;PLRG1,upstream_gene_variant,,ENST00000506627,;PLRG1,downstream_gene_variant,,ENST00000503751,;PLRG1,downstream_gene_variant,,ENST00000512719,;PLRG1,downstream_gene_variant,,ENST00000515520,;PLRG1,downstream_gene_variant,,ENST00000509975,;PLRG1,upstream_gene_variant,,ENST00000507125,; - ENST00000499023 Transcript frameshift_variant 684/3351 557/1545 186/514 P/X cCa/ca 1 -1 PLRG1 HGNC HGNC:9089 protein_coding YES CCDS34083.1 ENSP00000424417 O43660 UPI0000070B39 NM_002669.3 7/15 hmmpanther:PTHR19923,hmmpanther:PTHR19923:SF0 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 154544482 154544482 G - 1 0 1 0 1 0 0 0 0 12214 1348 47 0 0 PLRG1 4 154544482 Frame_Shift_Del DEL G C3N-01823_T 54151 154544482 35670073 111 25808 RAPGEF2 0 . GRCh38 4 159346806 159346806 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.3037G>C p.Asp1013His p.D1013H ENST00000264431 19/24 193 158 35 147 147 0 strelka-varscan-mutect RAPGEF2,missense_variant,p.Asp1013His,ENST00000264431,NM_014247.2;RAPGEF2,missense_variant,p.Asp45His,ENST00000510253,;RAPGEF2,missense_variant,p.Asp119His,ENST00000502485,;RAPGEF2,upstream_gene_variant,,ENST00000505026,; C ENST00000264431 Transcript missense_variant 3456/6949 3037/4500 1013/1499 D/H Gac/Cac 1 1 RAPGEF2 HGNC HGNC:16854 protein_coding YES CCDS43277.1 ENSP00000264431 Q9Y4G8 UPI0000033783 NM_014247.2 tolerated(0.06) 19/24 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF217,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 159346806 159346806 G C 1 0 0 0 0 1 0 0 0 13203 1290 45 4 4 RAPGEF2 4 159346806 Missense_Mutation SNP G C3N-01823_T 4802324 159346806 30867749 112 25809 MARCH1 0 . GRCh38 4 163612309 163612309 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.972C>A p.= p.A324A ENST00000514618 7/10 105 95 10 76 76 0 strelka-varscan-mutect MARCH1,synonymous_variant,p.=,ENST00000514618,;MARCH1,intron_variant,,ENST00000503008,NM_001166373.1;MARCH1,intron_variant,,ENST00000274056,;MARCH1,intron_variant,,ENST00000339875,NM_017923.3;MARCH1,intron_variant,,ENST00000507270,;MARCH1,non_coding_transcript_exon_variant,,ENST00000512214,;MARCH1,intron_variant,,ENST00000510786,;MARCH1,intron_variant,,ENST00000505517,;MARCH1,downstream_gene_variant,,ENST00000511245,;MARCH1,downstream_gene_variant,,ENST00000510696,; T ENST00000514618 Transcript synonymous_variant 1460/3903 972/1638 324/545 A gcC/gcA 1 -1 MARCH1 HGNC HGNC:26077 protein_coding ENSP00000421322 D6RGC4 UPI0001D3B97D 7/10 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF53 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.86518 1 1 1 1 0 T 2 4 83 163612309 163612309 G T 1 0 0 0 0 0 0 0 1 9223 1335 47 2 2 MARCH1 4 163612309 Silent SNP G C3N-01823_T 4265503 163612309 26602246 113 25810 SPOCK3 0 . GRCh38 4 166912713 166912713 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.390G>T p.Gln130His p.Q130H ENST00000357154 6/12 227 189 38 201 200 1 strelka-varscan-mutect SPOCK3,missense_variant,p.Gln79His,ENST00000421836,NM_001204352.1;SPOCK3,missense_variant,p.Gln130His,ENST00000357154,NM_016950.2;SPOCK3,missense_variant,p.Gln130His,ENST00000506886,;SPOCK3,missense_variant,p.Gln127His,ENST00000357545,NM_001040159.1;SPOCK3,missense_variant,p.Gln130His,ENST00000511531,;SPOCK3,missense_variant,p.Gln127His,ENST00000504953,;SPOCK3,missense_variant,p.Gln10His,ENST00000541354,NM_001204355.1,NM_001204353.1;SPOCK3,missense_variant,p.Gln130His,ENST00000502330,;SPOCK3,missense_variant,p.Gln38His,ENST00000535728,NM_001204354.1;SPOCK3,missense_variant,p.Gln127His,ENST00000510741,NM_001204356.1;SPOCK3,missense_variant,p.Gln127His,ENST00000511269,;SPOCK3,missense_variant,p.Gln127His,ENST00000512648,NM_001204358.1;SPOCK3,missense_variant,p.Gln127His,ENST00000509854,;SPOCK3,intron_variant,,ENST00000512681,NM_001251967.1;SPOCK3,intron_variant,,ENST00000510403,;SPOCK3,3_prime_UTR_variant,,ENST00000502821,;SPOCK3,3_prime_UTR_variant,,ENST00000511905,;SPOCK3,3_prime_UTR_variant,,ENST00000505187,;SPOCK3,3_prime_UTR_variant,,ENST00000507370,;SPOCK3,3_prime_UTR_variant,,ENST00000511226,;SPOCK3,3_prime_UTR_variant,,ENST00000515316,;SPOCK3,intron_variant,,ENST00000502741,;SPOCK3,intron_variant,,ENST00000507086,;SPOCK3,intron_variant,,ENST00000515143,; A ENST00000357154 Transcript missense_variant 528/2986 390/1311 130/436 Q/H caG/caT 1 -1 SPOCK3 HGNC HGNC:13565 protein_coding YES CCDS54817.1 ENSP00000349677 Q9BQ16 UPI000004BA60 NM_016950.2 tolerated(0.47) 6/12 hmmpanther:PTHR22118,hmmpanther:PTHR22118:SF10,Superfamily_domains:SSF100895 MODERATE 1 SNV 5 1 PASS rs1355513406 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 166912713 166912713 C A 1 0 0 0 0 1 0 0 0 15434 564 20 2 2 SPOCK3 4 166912713 Missense_Mutation SNP C C3N-01823_T 3300404 166912713 23301842 114 25811 GALNTL6 0 . GRCh38 4 172311612 172311612 + Splice_Site SNP A A T novel C3N-01823_T C3N-01823_N A A c.248-2A>T p.X83_splice ENST00000506823 82 57 25 73 73 0 strelka-varscan-mutect GALNTL6,splice_acceptor_variant,,ENST00000506823,NM_001034845.2;GALNTL6,splice_acceptor_variant,,ENST00000508122,;GALNTL6,splice_acceptor_variant,,ENST00000457021,; T ENST00000506823 Transcript splice_acceptor_variant -/3922 248/1806 83/601 1 1 GALNTL6 HGNC HGNC:33844 protein_coding YES CCDS34104.1 ENSP00000423313 Q49A17 E5D8G0 UPI000058EB5C NM_001034845.2 3/12 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 83 172311612 172311612 A T 1 0 0 0 0 0 0 1 0 6093 434 15 4 4 GALNTL6 4 172311612 Splice_Site SNP A C3N-01823_T 5398899 172311612 17902943 115 25812 GPM6A 0 . GRCh38 4 175701737 175701737 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.68G>C p.Gly23Ala p.G23A ENST00000280187 3/8 221 161 60 171 171 0 strelka-varscan-mutect GPM6A,missense_variant,p.Gly23Ala,ENST00000280187,NM_005277.4;GPM6A,missense_variant,p.Gly23Ala,ENST00000393658,NM_201591.2;GPM6A,missense_variant,p.Gly12Ala,ENST00000506894,NM_201592.2;GPM6A,missense_variant,p.Gly16Ala,ENST00000515090,NM_001261448.1;GPM6A,missense_variant,p.Gly15Ala,ENST00000503397,;GPM6A,missense_variant,p.Gly23Ala,ENST00000513365,;GPM6A,missense_variant,p.Gly16Ala,ENST00000505304,;GPM6A,5_prime_UTR_variant,,ENST00000505561,;GPM6A,5_prime_UTR_variant,,ENST00000502754,;GPM6A,5_prime_UTR_variant,,ENST00000512897,;GPM6A,5_prime_UTR_variant,,ENST00000512610,;GPM6A,5_prime_UTR_variant,,ENST00000513667,;GPM6A,5_prime_UTR_variant,,ENST00000507540,;GPM6A,5_prime_UTR_variant,,ENST00000507520,;GPM6A,5_prime_UTR_variant,,ENST00000512509,;GPM6A,5_prime_UTR_variant,,ENST00000505375,;GPM6A,5_prime_UTR_variant,,ENST00000509865,; G ENST00000280187 Transcript missense_variant 114/2854 68/837 23/278 G/A gGg/gCg 1 -1 GPM6A HGNC HGNC:4460 protein_coding YES CCDS3824.1 ENSP00000280187 P51674 UPI000012EAE1 NM_005277.4 tolerated(0.25) 3/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR11683,hmmpanther:PTHR11683:SF4,Pfam_domain:PF01275,Prints_domain:PR00214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 175701737 175701737 C G 1 0 0 0 0 1 0 0 0 6517 623 22 4 4 GPM6A 4 175701737 Missense_Mutation SNP C C3N-01823_T 3390125 175701737 14512818 116 25813 GPM6A 0 . GRCh38 4 175787341 175787341 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.11T>A p.Leu4Gln p.L4Q ENST00000515090 1/7 295 215 80 209 209 0 strelka-varscan-mutect GPM6A,missense_variant,p.Leu4Gln,ENST00000515090,NM_001261448.1;GPM6A,missense_variant,p.Leu4Gln,ENST00000505304,;GPM6A,5_prime_UTR_variant,,ENST00000507520,;GPM6A,intron_variant,,ENST00000280187,NM_005277.4;GPM6A,intron_variant,,ENST00000393658,NM_201591.2;GPM6A,intron_variant,,ENST00000506894,NM_201592.2;GPM6A,intron_variant,,ENST00000503397,;GPM6A,intron_variant,,ENST00000513365,;GPM6A,intron_variant,,ENST00000505561,;GPM6A,intron_variant,,ENST00000502754,;GPM6A,intron_variant,,ENST00000512897,;GPM6A,intron_variant,,ENST00000512610,;GPM6A,intron_variant,,ENST00000513667,;GPM6A,intron_variant,,ENST00000507540,;GPM6A,intron_variant,,ENST00000512509,;GPM6A,intron_variant,,ENST00000505375,;GPM6A,intron_variant,,ENST00000509865,;RP11-806K15.1,upstream_gene_variant,,ENST00000514864,; T ENST00000515090 Transcript missense_variant 336/1500 11/816 4/271 L/Q cTg/cAg 1 -1 GPM6A HGNC HGNC:4460 protein_coding CCDS58936.1 ENSP00000423984 P51674 UPI0001915004 NM_001261448.1 tolerated_low_confidence(0.47) 1/7 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 175787341 175787341 A T 1 0 0 0 0 1 0 0 0 6517 202 7 4 4 GPM6A 4 175787341 Missense_Mutation SNP A C3N-01823_T 85604 175787341 14427214 117 25814 FAT1 0 . GRCh38 4 186709175 186709175 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.653A>G p.Tyr218Cys p.Y218C ENST00000441802 2/27 206 195 11 154 154 0 strelka-varscan-mutect FAT1,missense_variant,p.Tyr218Cys,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Tyr218Cys,ENST00000614102,;FAT1,missense_variant,p.Tyr218Cys,ENST00000509647,; C ENST00000441802 Transcript missense_variant 863/14786 653/13767 218/4588 Y/C tAt/tGt 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0) 2/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 186709175 186709175 T C 1 0 0 0 0 1 0 0 0 5549 1406 49 5 5 FAT1 4 186709175 Missense_Mutation SNP T C3N-01823_T 10921834 186709175 3505380 118 25815 ADAMTS16 0 . GRCh38 5 5232378 5232378 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1712G>T p.Gly571Val p.G571V ENST00000274181 12/23 302 281 21 180 180 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.Gly571Val,ENST00000274181,NM_139056.2;ADAMTS16,upstream_gene_variant,,ENST00000513709,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; T ENST00000274181 Transcript missense_variant 1850/4979 1712/3675 571/1224 G/V gGa/gTa 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 tolerated(0.07) 12/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 5232378 5232378 G T 1 0 0 0 0 1 0 0 0 305 1174 41 2 2 ADAMTS16 5 5232378 Missense_Mutation SNP G C3N-01823_T 5232378 176305881 119 25816 ICE1 0 . GRCh38 5 5462746 5462746 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.3412G>T p.Ala1138Ser p.A1138S ENST00000296564 13/19 328 299 29 208 207 1 strelka-varscan-mutect ICE1,missense_variant,p.Ala1138Ser,ENST00000296564,NM_015325.2; T ENST00000296564 Transcript missense_variant 3634/7927 3412/6801 1138/2266 A/S Gct/Tct 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0.02) 13/19 hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 5462746 5462746 G T 1 0 0 0 0 1 0 0 0 7384 1319 46 2 2 ICE1 5 5462746 Missense_Mutation SNP G C3N-01823_T 230368 5462746 176075513 120 25817 CTNND2 0 . GRCh38 5 11018016 11018016 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.3042C>A p.Asn1014Lys p.N1014K ENST00000304623 18/22 281 252 29 185 184 1 strelka-varscan-mutect CTNND2,missense_variant,p.Asn1014Lys,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Asn923Lys,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Asn677Lys,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Asn109Lys,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506324,;CTNND2,missense_variant,p.Asn793Lys,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 3232/5481 3042/3678 1014/1225 N/K aaC/aaA 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0.01) 18/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 11018016 11018016 G T 1 0 0 0 0 1 0 0 0 3829 1368 48 2 2 CTNND2 5 11018016 Missense_Mutation SNP G C3N-01823_T 5555270 11018016 170520243 121 25818 ADAMTS12 0 . GRCh38 5 33561066 33561066 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.4086C>A p.= p.L1362L ENST00000504830 20/24 233 188 45 173 173 0 strelka-varscan-mutect ADAMTS12,synonymous_variant,p.=,ENST00000504830,NM_030955.2;ADAMTS12,synonymous_variant,p.=,ENST00000352040,; T ENST00000504830 Transcript synonymous_variant 4422/8774 4086/4785 1362/1594 L ctC/ctA 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 20/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895,Superfamily_domains:SSF82895 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 33561066 33561066 G T 1 0 0 0 0 0 0 0 1 301 1161 41 2 2 ADAMTS12 5 33561066 Silent SNP G C3N-01823_T 22543050 33561066 147977193 122 25819 MROH2B 0 . GRCh38 5 41067164 41067164 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.145G>T p.Asp49Tyr p.D49Y ENST00000399564 3/42 337 305 32 295 295 0 strelka-varscan-mutect MROH2B,missense_variant,p.Asp49Tyr,ENST00000399564,NM_173489.4;MROH2B,non_coding_transcript_exon_variant,,ENST00000508575,; A ENST00000399564 Transcript missense_variant 596/5239 145/4758 49/1585 D/Y Gat/Tat 1 -1 MROH2B HGNC HGNC:26857 protein_coding YES CCDS47202.1 ENSP00000382476 Q7Z745 UPI000020CA04 NM_173489.4 deleterious(0.01) 3/42 Gene3D:1.25.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 41067164 41067164 C A 1 0 0 0 0 1 0 0 0 9745 826 29 2 2 MROH2B 5 41067164 Missense_Mutation SNP C C3N-01823_T 7506098 41067164 140471095 123 25820 CDC20B 0 . GRCh38 5 55119830 55119830 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.1430C>A p.Pro477His p.P477H ENST00000381375 11/12 357 243 114 189 188 1 strelka-varscan-mutect CDC20B,missense_variant,p.Pro477His,ENST00000296733,NM_152623.2;CDC20B,missense_variant,p.Pro477His,ENST00000381375,NM_001170402.1;CDC20B,missense_variant,p.Pro435His,ENST00000322374,NM_001145734.2;CDC20B,3_prime_UTR_variant,,ENST00000513180,; T ENST00000381375 Transcript missense_variant 1576/2591 1430/1560 477/519 P/H cCc/cAc COSM5081488,COSM5081489 1 -1 CDC20B HGNC HGNC:24222 protein_coding YES CCDS54852.1 ENSP00000370781 Q86Y33 UPI0000D61625 NM_001170402.1 deleterious(0) 11/12 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR19918,hmmpanther:PTHR19918:SF4,Superfamily_domains:SSF50978 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 55119830 55119830 G T 1 0 0 0 0 1 0 0 0 2763 1232 43 2 2 CDC20B 5 55119830 Missense_Mutation SNP G C3N-01823_T 14052666 55119830 126418429 124 25821 ZNF366 0 . GRCh38 5 72460340 72460340 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.1157C>A p.Thr386Lys p.T386K ENST00000318442 2/5 279 201 78 210 210 0 strelka-varscan-mutect ZNF366,missense_variant,p.Thr386Lys,ENST00000318442,NM_152625.2;ZNF366,downstream_gene_variant,,ENST00000414109,;ZNF366,downstream_gene_variant,,ENST00000514477,; T ENST00000318442 Transcript missense_variant 1648/3830 1157/2235 386/744 T/K aCg/aAg COSM4757239 1 -1 ZNF366 HGNC HGNC:18316 protein_coding YES CCDS4015.1 ENSP00000313158 Q8N895 UPI000013C368 NM_152625.2 deleterious(0.02) 2/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24390:SF38,hmmpanther:PTHR24390,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 72460340 72460340 G T 1 0 0 0 0 1 0 0 0 18442 1145 40 1 1 ZNF366 5 72460340 Missense_Mutation SNP G C3N-01823_T 17340510 72460340 109077919 125 25822 ZFYVE16 0 . GRCh38 5 80437441 80437441 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.756T>G p.Ser252Arg p.S252R ENST00000338008 3/18 123 111 12 65 65 0 strelka-varscan-mutect ZFYVE16,missense_variant,p.Ser252Arg,ENST00000338008,NM_014733.4;ZFYVE16,missense_variant,p.Ser252Arg,ENST00000510158,NM_001105251.2;ZFYVE16,missense_variant,p.Ser252Arg,ENST00000505560,NM_001284236.1;ZFYVE16,downstream_gene_variant,,ENST00000509562,;ZFYVE16,upstream_gene_variant,,ENST00000511050,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000512558,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000510995,; G ENST00000338008 Transcript missense_variant 936/6773 756/4620 252/1539 S/R agT/agG 1 1 ZFYVE16 HGNC HGNC:20756 protein_coding YES CCDS4050.1 ENSP00000337159 Q7Z3T8 UPI000013F4A0 NM_014733.4 deleterious(0.02) 3/18 hmmpanther:PTHR22835:SF43,hmmpanther:PTHR22835,PIRSF_domain:PIRSF037289 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99992 1 1 1 1 0 G 3 3 83 80437441 80437441 T G 1 0 0 0 0 1 0 0 0 18242 1722 60 5 5 ZFYVE16 5 80437441 Missense_Mutation SNP T C3N-01823_T 7977101 80437441 101100818 126 25823 ACOT12 0 . GRCh38 5 81330890 81330890 + Missense_Mutation SNP G G T rs151004328 C3N-01823_T C3N-01823_N G G c.1442C>A p.Pro481Gln p.P481Q ENST00000307624 14/15 115 83 32 89 89 0 strelka-varscan-mutect ACOT12,missense_variant,p.Pro481Gln,ENST00000307624,NM_130767.2;ACOT12,non_coding_transcript_exon_variant,,ENST00000508234,;ACOT12,non_coding_transcript_exon_variant,,ENST00000506440,; T ENST00000307624 Transcript missense_variant 1471/2086 1442/1668 481/555 P/Q cCg/cAg rs151004328 1 -1 ACOT12 HGNC HGNC:24436 protein_coding YES CCDS4055.1 ENSP00000303246 Q8WYK0 UPI0000126D7B NM_130767.2 deleterious(0.04) 14/15 Gene3D:3.30.530.20,Pfam_domain:PF01852,PROSITE_profiles:PS50848,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF3,Superfamily_domains:SSF55961 MODERATE 1 SNV 1 1 PASS rs151004328 . 0 191 15 3 0 0 0 0 -20 0.9968096 1 1 1 0 T 3 4 83 81330890 81330890 G T 1 0 0 0 0 1 0 0 0 192 1116 39 1 1 ACOT12 5 81330890 Missense_Mutation SNP G C3N-01823_T 893449 81330890 100207369 127 25824 XRCC4 0 . GRCh38 5 83204829 83204829 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.653G>C p.Cys218Ser p.C218S ENST00000511817 6/8 157 142 15 133 133 0 strelka-varscan-mutect XRCC4,missense_variant,p.Cys218Ser,ENST00000282268,NM_001318012.1,NM_022550.2,NM_003401.3;XRCC4,missense_variant,p.Cys218Ser,ENST00000511817,;XRCC4,missense_variant,p.Cys218Ser,ENST00000338635,NM_022406.2;XRCC4,missense_variant,p.Cys218Ser,ENST00000396027,;XRCC4,non_coding_transcript_exon_variant,,ENST00000509268,;XRCC4,non_coding_transcript_exon_variant,,ENST00000542685,;CTD-2110K23.1,downstream_gene_variant,,ENST00000468914,; C ENST00000511817 Transcript missense_variant 733/1636 653/1011 218/336 C/S tGt/tCt 1 1 XRCC4 HGNC HGNC:12831 protein_coding YES CCDS4059.1 ENSP00000421491 Q13426 A0A024RAQ8 UPI000006DF4E tolerated(0.83) 6/8 Pfam_domain:PF06632,hmmpanther:PTHR28559 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 83204829 83204829 G C 1 0 0 0 0 1 0 0 0 18014 1377 48 4 4 XRCC4 5 83204829 Missense_Mutation SNP G C3N-01823_T 1873939 83204829 98333430 128 25825 VCAN 0 . GRCh38 5 83512119 83512119 + Silent SNP C C A rs745476221 C3N-01823_T C3N-01823_N C C c.765C>A p.= p.L255L ENST00000265077 6/15 326 274 52 195 194 1 strelka-varscan-mutect VCAN,synonymous_variant,p.=,ENST00000265077,NM_004385.4;VCAN,synonymous_variant,p.=,ENST00000343200,NM_001164097.1;VCAN,synonymous_variant,p.=,ENST00000342785,NM_001164098.1;VCAN,synonymous_variant,p.=,ENST00000512590,;VCAN,synonymous_variant,p.=,ENST00000513960,;VCAN,synonymous_variant,p.=,ENST00000502527,NM_001126336.2;VCAN,synonymous_variant,p.=,ENST00000513984,;VCAN,non_coding_transcript_exon_variant,,ENST00000515397,; A ENST00000265077 Transcript synonymous_variant 1330/12625 765/10191 255/3396 L ctC/ctA rs745476221 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 6/15 PROSITE_profiles:PS50963,hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6,Pfam_domain:PF00193,Gene3D:3.10.100.10,SMART_domains:SM00445,Superfamily_domains:SSF56436,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs745476221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 83512119 83512119 C A 1 0 0 0 0 0 0 0 1 17683 813 29 2 2 VCAN 5 83512119 Silent SNP C C3N-01823_T 307290 83512119 98026140 129 25826 VCAN 0 . GRCh38 5 83539745 83539745 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.6742G>C p.Asp2248His p.D2248H ENST00000265077 8/15 490 404 86 333 333 0 strelka-varscan-mutect VCAN,missense_variant,p.Asp2248His,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Asp1261His,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; C ENST00000265077 Transcript missense_variant 7307/12625 6742/10191 2248/3396 D/H Gat/Cat 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.16) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 83539745 83539745 G C 1 0 0 0 0 1 0 0 0 17683 942 33 4 4 VCAN 5 83539745 Missense_Mutation SNP G C3N-01823_T 27626 83539745 97998514 130 25827 ACSL6 0 . GRCh38 5 131994087 131994087 + Missense_Mutation SNP G G C rs764258957 C3N-01823_T C3N-01823_N G G c.214C>G p.Arg72Gly p.R72G ENST00000379264 2/21 391 311 80 256 256 0 strelka-varscan-mutect ACSL6,missense_variant,p.Arg72Gly,ENST00000379264,NM_001009185.2;ACSL6,missense_variant,p.Arg47Gly,ENST00000379244,NM_001205248.1;ACSL6,missense_variant,p.Arg58Gly,ENST00000379246,NM_001205250.1;ACSL6,missense_variant,p.Arg72Gly,ENST00000296869,NM_015256.3,NM_001205247.1;ACSL6,missense_variant,p.Arg47Gly,ENST00000379240,;ACSL6,missense_variant,p.Arg47Gly,ENST00000543479,;ACSL6,missense_variant,p.Arg47Gly,ENST00000419502,;ACSL6,missense_variant,p.Arg47Gly,ENST00000430403,;ACSL6,missense_variant,p.Arg47Gly,ENST00000416557,;ACSL6,missense_variant,p.Arg47Gly,ENST00000414078,;ACSL6,intron_variant,,ENST00000357096,NM_001205251.1;ACSL6,intron_variant,,ENST00000379255,;ACSL6,intron_variant,,ENST00000431707,;ACSL6,intron_variant,,ENST00000434099,;ACSL6,intron_variant,,ENST00000441995,;ACSL6,non_coding_transcript_exon_variant,,ENST00000477640,;CTB-127M13.1,missense_variant,p.Arg47Gly,ENST00000413683,;ACSL6,non_coding_transcript_exon_variant,,ENST00000469164,; C ENST00000379264 Transcript missense_variant 323/6539 214/2169 72/722 R/G Cgg/Ggg rs764258957 1 -1 ACSL6 HGNC HGNC:16496 protein_coding YES CCDS34229.1 ENSP00000368566 Q9UKU0 UPI00004BA928 NM_001009185.2 tolerated(0.06) 2/21 hmmpanther:PTHR24096:SF239,hmmpanther:PTHR24096 MODERATE 1 SNV 1 1 PASS rs764258957 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 131994087 131994087 G C 1 0 0 0 0 1 0 0 0 223 1115 39 4 4 ACSL6 5 131994087 Missense_Mutation SNP G C3N-01823_T 48454342 131994087 49544172 131 25828 PCDHA1 0 . GRCh38 5 140788426 140788426 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.2136G>T p.= p.V712V ENST00000504120 1/4 435 329 106 276 276 0 strelka-varscan-mutect PCDHA1,synonymous_variant,p.=,ENST00000504120,NM_018900.3;PCDHA1,synonymous_variant,p.=,ENST00000378133,NM_031410.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,downstream_gene_variant,,ENST00000624712,;AC005609.16,downstream_gene_variant,,ENST00000624176,; T ENST00000504120 Transcript synonymous_variant 2136/5263 2136/2853 712/950 V gtG/gtT 1 1 PCDHA1 HGNC HGNC:8663 protein_coding YES CCDS54913.1 ENSP00000420840 Q9Y5I3 UPI00001273C7 NM_018900.3 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF92,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 140788426 140788426 G T 1 0 0 0 0 0 0 0 1 11606 1306 46 2 2 PCDHA1 5 140788426 Silent SNP G C3N-01823_T 8794339 140788426 40749833 132 25829 PCDHB6 0 . GRCh38 5 141151200 141151200 + Missense_Mutation SNP G G A C3N-01823_T C3N-01823_N G G c.943G>A p.Val315Met p.V315M ENST00000231136 1/1 454 414 40 331 330 1 strelka-varscan-mutect PCDHB6,missense_variant,p.Val315Met,ENST00000231136,NM_018939.3;PCDHB6,missense_variant,p.Val179Met,ENST00000622991,NM_001303145.1;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB17P,upstream_gene_variant,,ENST00000623466,;PCDHB17P,upstream_gene_variant,,ENST00000539533,; A ENST00000231136 Transcript missense_variant 1179/3266 943/2385 315/794 V/M Gtg/Atg COSM354458 1 1 PCDHB6 HGNC HGNC:8691 protein_coding YES CCDS4248.1 ENSP00000231136 Q9Y5E3 UPI0003CC25E7 NM_018939.3 tolerated_low_confidence(0.13) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF104,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 141151200 141151200 G A 1 0 0 0 0 1 0 0 0 11633 1145 40 1 1 PCDHB6 5 141151200 Missense_Mutation SNP G C3N-01823_T 362774 141151200 40387059 133 25830 PCDHB7 0 . GRCh38 5 141173475 141173475 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.640G>T p.Ala214Ser p.A214S ENST00000231137 1/1 175 139 36 110 110 0 strelka-varscan-mutect PCDHB7,missense_variant,p.Ala214Ser,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.3,downstream_gene_variant,,ENST00000623581,;AC005754.7,splice_region_variant,,ENST00000625128,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; T ENST00000231137 Transcript missense_variant 857/3765 640/2382 214/793 A/S Gct/Tct COSM4712354 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 141173475 141173475 G T 1 0 0 0 0 1 0 0 0 11634 1087 38 1 1 PCDHB7 5 141173475 Missense_Mutation SNP G C3N-01823_T 22275 141173475 40364784 134 25831 PCDHB8 0 . GRCh38 5 141178476 141178476 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.442C>A p.Pro148Thr p.P148T ENST00000239444 1/1 605 492 113 462 459 3 strelka-varscan-mutect PCDHB8,missense_variant,p.Pro148Thr,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; A ENST00000239444 Transcript missense_variant 687/2740 442/2406 148/801 P/T Cct/Act 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 tolerated_low_confidence(0.55) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 141178476 141178476 C A 1 0 0 0 0 1 0 0 0 11635 855 30 2 2 PCDHB8 5 141178476 Missense_Mutation SNP C C3N-01823_T 5001 141178476 40359783 135 25832 TIMD4 0 . GRCh38 5 156920478 156920478 + Silent SNP C C T rs145512953 C3N-01823_T C3N-01823_N C C c.1038G>A p.= p.S346S ENST00000274532 8/9 301 246 55 201 201 0 strelka-varscan-mutect TIMD4,synonymous_variant,p.=,ENST00000274532,NM_138379.2;TIMD4,synonymous_variant,p.=,ENST00000407087,NM_001146726.1;TIMD4,synonymous_variant,p.=,ENST00000406964,;APOOP1,upstream_gene_variant,,ENST00000604695,; T ENST00000274532 Transcript synonymous_variant 1095/1369 1038/1137 346/378 S tcG/tcA rs145512953 1 -1 TIMD4 HGNC HGNC:25132 protein_coding YES CCDS4332.1 ENSP00000274532 Q96H15 UPI000013DA13 NM_138379.2 8/9 hmmpanther:PTHR15498,hmmpanther:PTHR15498:SF29 LOW 1 SNV 1 1 PASS rs145512953 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 156920478 156920478 C T 1 0 0 0 0 0 0 0 1 16341 755 27 1 1 TIMD4 5 156920478 Silent SNP C C3N-01823_T 15742002 156920478 24617781 136 25833 TENM2 0 . GRCh38 5 168062224 168062224 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1474G>T p.Gly492Cys p.G492C ENST00000518659 7/29 405 342 63 170 170 0 strelka-varscan-mutect TENM2,missense_variant,p.Gly371Cys,ENST00000519204,;TENM2,missense_variant,p.Gly492Cys,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Gly260Cys,ENST00000520394,; T ENST00000518659 Transcript missense_variant 1513/8550 1474/8325 492/2774 G/C Ggt/Tgt 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 7/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 168062224 168062224 G T 1 0 0 0 0 1 0 0 0 16172 1348 47 2 2 TENM2 5 168062224 Missense_Mutation SNP G C3N-01823_T 11141746 168062224 13476035 137 25834 SLIT3 0 . GRCh38 5 168753907 168753907 + Missense_Mutation SNP C C A rs562240210 C3N-01823_T C3N-01823_N C C c.1786G>T p.Val596Leu p.V596L ENST00000332966 17/36 239 214 25 155 155 0 strelka-varscan-mutect SLIT3,missense_variant,p.Val596Leu,ENST00000519560,NM_003062.3;SLIT3,missense_variant,p.Val459Leu,ENST00000404867,;SLIT3,missense_variant,p.Val596Leu,ENST00000332966,NM_001271946.1;SLIT3,non_coding_transcript_exon_variant,,ENST00000519486,; A ENST00000332966 Transcript missense_variant 1859/4895 1786/4593 596/1530 V/L Gtg/Ttg rs562240210,COSM1065655,COSM3410126 1 -1 SLIT3 HGNC HGNC:11087 protein_coding YES CCDS64311.1 ENSP00000332164 O75094 UPI0001E8F75D NM_001271946.1 tolerated(0.29) 17/36 PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF15,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs562240210 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 168753907 168753907 C A 1 0 0 0 0 1 0 0 0 15032 536 19 1 1 SLIT3 5 168753907 Missense_Mutation SNP C C3N-01823_T 691683 168753907 12784352 138 25835 DOCK2 0 . GRCh38 5 169689272 169689272 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.782G>T p.Trp261Leu p.W261L ENST00000256935 9/52 300 226 74 144 144 0 strelka-varscan-mutect DOCK2,missense_variant,p.Trp261Leu,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Trp261Leu,ENST00000524185,; T ENST00000256935 Transcript missense_variant 862/6097 782/5493 261/1830 W/L tGg/tTg 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0) 9/52 hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF16172 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 169689272 169689272 G T 1 0 0 0 0 1 0 0 0 4502 1357 47 2 2 DOCK2 5 169689272 Missense_Mutation SNP G C3N-01823_T 935365 169689272 11848987 139 25836 DOCK2 0 . GRCh38 5 170067587 170067587 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.4545G>T p.Gln1515His p.Q1515H ENST00000256935 45/52 349 304 45 166 165 1 strelka-varscan-mutect DOCK2,missense_variant,p.Gln1515His,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Gln1007His,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520450,; T ENST00000256935 Transcript missense_variant 4625/6097 4545/5493 1515/1830 Q/H caG/caT 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 deleterious(0) 45/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 170067587 170067587 G T 1 0 0 0 0 1 0 0 0 4502 1020 36 2 2 DOCK2 5 170067587 Missense_Mutation SNP G C3N-01823_T 378315 170067587 11470672 140 25837 DOCK2 0 . GRCh38 5 170067675 170067675 + Missense_Mutation SNP A A G novel C3N-01823_T C3N-01823_N A A c.4633A>G p.Lys1545Glu p.K1545E ENST00000256935 45/52 143 121 22 77 77 0 strelka-varscan-mutect DOCK2,missense_variant,p.Lys1545Glu,ENST00000256935,NM_004946.2;DOCK2,missense_variant,p.Lys1037Glu,ENST00000520908,;DOCK2,non_coding_transcript_exon_variant,,ENST00000523351,;DOCK2,3_prime_UTR_variant,,ENST00000524185,;DOCK2,non_coding_transcript_exon_variant,,ENST00000520450,; G ENST00000256935 Transcript missense_variant 4713/6097 4633/5493 1545/1830 K/E Aag/Gag 1 1 DOCK2 HGNC HGNC:2988 protein_coding YES CCDS4371.1 ENSP00000256935 Q92608 UPI00001A38CC NM_004946.2 tolerated(0.07) 45/52 PROSITE_profiles:PS51651,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF73,Pfam_domain:PF06920 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 170067675 170067675 A G 1 0 0 0 0 1 0 0 0 4502 131 5 5 5 DOCK2 5 170067675 Missense_Mutation SNP A C3N-01823_T 88 170067675 11470584 141 25838 GABRP 0 . GRCh38 5 170789245 170789245 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.170G>A p.Gly57Asp p.G57D ENST00000518525 4/11 158 127 31 85 85 0 strelka-varscan-mutect GABRP,missense_variant,p.Gly57Asp,ENST00000518525,;GABRP,missense_variant,p.Gly57Asp,ENST00000265294,NM_014211.2;GABRP,missense_variant,p.Gly57Asp,ENST00000519385,NM_001291985.1;GABRP,missense_variant,p.Gly57Asp,ENST00000519598,;GABRP,missense_variant,p.Gly57Asp,ENST00000521481,;GABRP,missense_variant,p.Gly57Asp,ENST00000522868,;GABRP,missense_variant,p.Gly57Asp,ENST00000519196,;GABRP,missense_variant,p.Gly57Asp,ENST00000521009,;GABRP,downstream_gene_variant,,ENST00000518122,;CTC-455F18.1,upstream_gene_variant,,ENST00000518172,;GABRP,splice_region_variant,,ENST00000519137,; A ENST00000518525 Transcript missense_variant,splice_region_variant 634/3576 170/1323 57/440 G/D gGt/gAt 1 1 GABRP HGNC HGNC:4089 protein_coding YES CCDS4375.1 ENSP00000430100 O00591 UPI000003C534 tolerated(0.29) 4/11 hmmpanther:PTHR18945:SF33,hmmpanther:PTHR18945,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 170789245 170789245 G A 1 0 0 0 0 1 0 0 0 6045 1275 44 3 3 GABRP 5 170789245 Missense_Mutation SNP G C3N-01823_T 721570 170789245 10749014 142 25839 ZNF354B 0 . GRCh38 5 178883247 178883247 + Silent SNP A A T novel C3N-01823_T C3N-01823_N A A c.795A>T p.= p.T265T ENST00000322434 5/5 244 176 68 144 144 0 strelka-varscan-mutect ZNF354B,synonymous_variant,p.=,ENST00000322434,NM_058230.2;ZNF354B,downstream_gene_variant,,ENST00000520377,;RNU1-39P,upstream_gene_variant,,ENST00000383897,;ZNF354B,upstream_gene_variant,,ENST00000522714,;ZNF354B,upstream_gene_variant,,ENST00000522624,; T ENST00000322434 Transcript synonymous_variant 1021/2802 795/1839 265/612 T acA/acT 1 1 ZNF354B HGNC HGNC:17197 protein_coding YES CCDS4439.1 ENSP00000327143 Q96LW1 UPI0000071A24 NM_058230.2 5/5 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF87,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 178883247 178883247 A T 1 0 0 0 0 0 0 0 1 18437 175 7 4 4 ZNF354B 5 178883247 Silent SNP A C3N-01823_T 8094002 178883247 2655012 143 25840 SERPINB1 0 . GRCh38 6 2833727 2833727 + Missense_Mutation SNP C C T rs761685123 C3N-01823_T C3N-01823_N C C c.1021G>A p.Ala341Thr p.A341T ENST00000380739 7/7 386 328 58 232 232 0 strelka-varscan-mutect SERPINB1,missense_variant,p.Ala341Thr,ENST00000380739,NM_030666.3;SERPINB1,intron_variant,,ENST00000468511,;SERPINB1,downstream_gene_variant,,ENST00000476896,;SERPINB1,downstream_gene_variant,,ENST00000490094,;SERPINB1,downstream_gene_variant,,ENST00000460260,; T ENST00000380739 Transcript missense_variant 1224/2619 1021/1140 341/379 A/T Gca/Aca rs761685123,COSM451108 1 -1 SERPINB1 HGNC HGNC:3311 protein_coding YES CCDS4477.1 ENSP00000370115 P30740 V9HWH1 UPI000012D514 NM_030666.3 tolerated(0.59) 7/7 Gene3D:2.30.39.10,Pfam_domain:PF00079,hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF180,Low_complexity_(Seg):seg,SMART_domains:SM00093,Superfamily_domains:SSF56574 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs761685123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 2833727 2833727 C T 1 0 0 0 0 1 0 0 0 14372 768 27 1 1 SERPINB1 6 2833727 Missense_Mutation SNP C C3N-01823_T 2833727 167972252 144 25841 F13A1 0 . GRCh38 6 6197287 6197287 + Silent SNP A A T rs375255557 C3N-01823_T C3N-01823_N A A c.1152T>A p.= p.P384P ENST00000264870 9/15 716 595 121 389 389 0 strelka-varscan-mutect F13A1,synonymous_variant,p.=,ENST00000264870,NM_000129.3; T ENST00000264870 Transcript synonymous_variant 1418/3999 1152/2199 384/732 P ccT/ccA rs375255557 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 9/15 Gene3D:1ex0A02,Pfam_domain:PF01841,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF42,SMART_domains:SM00460,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS rs375255557 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 6197287 6197287 A T 1 0 0 0 0 0 0 0 1 5208 175 7 4 4 F13A1 6 6197287 Silent SNP A C3N-01823_T 3363560 6197287 164608692 145 25842 RREB1 0 . GRCh38 6 7226628 7226628 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.869C>T p.Ser290Phe p.S290F ENST00000379938 9/13 174 145 29 110 109 1 strelka-varscan-mutect RREB1,missense_variant,p.Ser290Phe,ENST00000379938,NM_001003699.3;RREB1,missense_variant,p.Ser290Phe,ENST00000349384,NM_001003698.3;RREB1,missense_variant,p.Ser290Phe,ENST00000379933,NM_001168344.1;RREB1,missense_variant,p.Ser290Phe,ENST00000334984,NM_001003700.1;RREB1,missense_variant,p.Ser290Phe,ENST00000483150,;RREB1,upstream_gene_variant,,ENST00000611109,; T ENST00000379938 Transcript missense_variant 1406/8778 869/5229 290/1742 S/F tCc/tTc 1 1 RREB1 HGNC HGNC:10449 protein_coding YES CCDS34335.1 ENSP00000369270 Q92766 UPI000020E496 NM_001003699.3 deleterious(0) 9/13 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF42 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 7226628 7226628 C T 1 0 0 0 0 1 0 0 0 13933 855 30 3 3 RREB1 6 7226628 Missense_Mutation SNP C C3N-01823_T 1029341 7226628 163579351 146 25843 JARID2 0 . GRCh38 6 15496861 15496861 + Missense_Mutation SNP G G T rs200762827 C3N-01823_T C3N-01823_N G G c.1636G>T p.Gly546Cys p.G546C ENST00000341776 7/18 111 91 20 61 61 0 strelka-varscan-mutect JARID2,missense_variant,p.Gly546Cys,ENST00000341776,NM_004973.3;JARID2,missense_variant,p.Gly374Cys,ENST00000397311,NM_001267040.1;JARID2,upstream_gene_variant,,ENST00000474854,; T ENST00000341776 Transcript missense_variant 1880/5755 1636/3741 546/1246 G/C Ggc/Tgc rs200762827 1 1 JARID2 HGNC HGNC:6196 protein_coding YES CCDS4533.1 ENSP00000341280 Q92833 UPI0000161C67 NM_004973.3 tolerated(0.05) 7/18 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF44,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs200762827 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 15496861 15496861 G T 1 0 0 0 0 1 0 0 0 7859 1116 39 1 1 JARID2 6 15496861 Missense_Mutation SNP G C3N-01823_T 8270233 15496861 155309118 147 25844 HIST1H3F 0 . GRCh38 6 26250395 26250395 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.211C>A p.Leu71Met p.L71M ENST00000618052 1/1 671 514 157 360 358 2 strelka-varscan-mutect HIST1H3F,missense_variant,p.Leu71Met,ENST00000618052,NM_021018.2;HIST1H2BH,upstream_gene_variant,,ENST00000619466,NM_003524.2;HIST1H4G,upstream_gene_variant,,ENST00000611444,NM_003547.2; T ENST00000618052 Transcript missense_variant 211/411 211/411 71/136 L/M Ctg/Atg 1 -1 HIST1H3F HGNC HGNC:4773 protein_coding YES CCDS4600.1 ENSP00000484095 P68431 UPI00000003C7 NM_021018.2 deleterious_low_confidence(0.01) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,PROSITE_patterns:PS00959,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 26250395 26250395 G T 1 0 0 0 0 1 0 0 0 7048 933 33 2 2 HIST1H3F 6 26250395 Missense_Mutation SNP G C3N-01823_T 10753534 26250395 144555584 148 25845 OR5V1 0 . GRCh38 6 29355782 29355782 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.414G>T p.Lys138Asn p.K138N ENST00000377154 4/4 347 251 96 187 185 2 strelka-varscan-mutect OR5V1,missense_variant,p.Lys138Asn,ENST00000377154,;OR5V1,missense_variant,p.Lys138Asn,ENST00000543825,NM_030876.5; A ENST00000377154 Transcript missense_variant 714/1266 414/966 138/321 K/N aaG/aaT 1 -1 OR5V1 HGNC HGNC:13972 protein_coding YES CCDS4657.1 ENSP00000366359 Q9UGF6 A0A126GV99 UPI000004186B tolerated(0.17) 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF295,hmmpanther:PTHR26453,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 29355782 29355782 C A 1 0 0 0 0 1 0 0 0 11252 680 24 2 2 OR5V1 6 29355782 Missense_Mutation SNP C C3N-01823_T 3105387 29355782 141450197 149 25846 TNF 0 . GRCh38 6 31577131 31577131 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.296A>T p.Glu99Val p.E99V ENST00000449264 4/4 160 133 27 77 77 0 strelka-varscan-mutect TNF,missense_variant,p.Glu99Val,ENST00000449264,NM_000594.3;LTA,downstream_gene_variant,,ENST00000454783,NM_001159740.2;LTA,downstream_gene_variant,,ENST00000418386,NM_000595.3;LTB,downstream_gene_variant,,ENST00000429299,NM_002341.1;LTB,downstream_gene_variant,,ENST00000446745,NM_009588.1;LTB,downstream_gene_variant,,ENST00000483972,;LTA,downstream_gene_variant,,ENST00000471842,;LTB,downstream_gene_variant,,ENST00000482429,;LTA,downstream_gene_variant,,ENST00000489638,; T ENST00000449264 Transcript missense_variant 471/1676 296/702 99/233 E/V gAg/gTg 1 1 TNF HGNC HGNC:11892 protein_coding YES CCDS4702.1 ENSP00000398698 P01375 Q5STB3 UPI000000D745 NM_000594.3 tolerated(0.08) 4/4 PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF23,Gene3D:2.60.120.40,SMART_domains:SM00207,Superfamily_domains:SSF49842,Prints_domain:PR01234 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999985 1 1 1 0 T 3 4 83 31577131 31577131 A T 1 0 0 0 0 1 0 0 0 16745 304 11 4 4 TNF 6 31577131 Missense_Mutation SNP A C3N-01823_T 2221349 31577131 139228848 150 25847 HLA-DQA2 0 . GRCh38 6 32741473 32741473 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.30G>T p.= p.G10G ENST00000374940 1/5 388 280 108 220 219 1 strelka-varscan-mutect HLA-DQA2,synonymous_variant,p.=,ENST00000374940,NM_020056.4; T ENST00000374940 Transcript synonymous_variant 132/1524 30/768 10/255 G ggG/ggT 1 1 HLA-DQA2 HGNC HGNC:4943 protein_coding YES CCDS4753.1 ENSP00000364076 P01906 Q76NI6 UPI0000001086 NM_020056.4 1/5 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR19944:SF54,hmmpanther:PTHR19944 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 32741473 32741473 G T 1 0 0 0 0 0 0 0 1 7094 1219 43 2 2 HLA-DQA2 6 32741473 Silent SNP G C3N-01823_T 1164342 32741473 138064506 151 25848 TULP1 0 . GRCh38 6 35512848 35512848 + Missense_Mutation SNP C C A rs373351673 C3N-01823_T C3N-01823_N C C c.11G>T p.Arg4Leu p.R4L ENST00000229771 1/15 665 615 50 288 288 0 strelka-varscan-mutect TULP1,missense_variant,p.Arg4Leu,ENST00000229771,NM_003322.4;TULP1,missense_variant,p.Arg4Leu,ENST00000614066,;TULP1,missense_variant,p.Arg4Leu,ENST00000322263,NM_001289395.1;TULP1,missense_variant,p.Arg4Leu,ENST00000428978,;TULP1,upstream_gene_variant,,ENST00000373892,;TULP1,upstream_gene_variant,,ENST00000448446,; A ENST00000229771 Transcript missense_variant 91/2162 11/1629 4/542 R/L cGg/cTg rs373351673,COSM1078383,COSM3674691 1 -1 TULP1 HGNC HGNC:12423 protein_coding YES CCDS4807.1 ENSP00000229771 O00294 UPI000045742A NM_003322.4 tolerated_low_confidence(0.11) 1/15 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs373351673 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 35512848 35512848 C A 1 0 0 0 0 1 0 0 0 17283 652 23 1 1 TULP1 6 35512848 Missense_Mutation SNP C C3N-01823_T 2771375 35512848 135293131 152 25849 TREML2 0 . GRCh38 6 41192458 41192458 + Missense_Mutation SNP G G T rs751699387 C3N-01823_T C3N-01823_N G G c.935C>A p.Pro312Gln p.P312Q ENST00000483722 5/5 350 303 47 223 223 0 strelka-varscan-mutect TREML2,missense_variant,p.Pro312Gln,ENST00000483722,NM_024807.3; T ENST00000483722 Transcript missense_variant 1121/3302 935/966 312/321 P/Q cCa/cAa rs751699387 1 -1 TREML2 HGNC HGNC:21092 protein_coding YES CCDS4853.2 ENSP00000418767 Q5T2D2 UPI0000074452 NM_024807.3 tolerated(0.07) 5/5 hmmpanther:PTHR16423:SF3,hmmpanther:PTHR16423 MODERATE 1 SNV 1 1 PASS rs751699387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 41192458 41192458 G T 1 0 0 0 0 1 0 0 0 16962 1348 47 2 2 TREML2 6 41192458 Missense_Mutation SNP G C3N-01823_T 5679610 41192458 129613521 153 25850 CUL9 0 . GRCh38 6 43186144 43186144 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.940G>T p.Val314Leu p.V314L ENST00000252050 4/41 239 195 44 138 138 0 strelka-varscan-mutect CUL9,missense_variant,p.Val314Leu,ENST00000252050,NM_015089.3;CUL9,missense_variant,p.Val314Leu,ENST00000372647,;SRF,downstream_gene_variant,,ENST00000265354,NM_003131.3;CUL9,non_coding_transcript_exon_variant,,ENST00000515773,;CUL9,non_coding_transcript_exon_variant,,ENST00000451399,;CUL9,upstream_gene_variant,,ENST00000510282,; T ENST00000252050 Transcript missense_variant 1024/7780 940/7554 314/2517 V/L Gtg/Ttg 1 1 CUL9 HGNC HGNC:15982 protein_coding YES CCDS4890.1 ENSP00000252050 Q8IWT3 UPI000006F22F NM_015089.3 deleterious(0.04) 4/41 hmmpanther:PTHR22771:SF2,hmmpanther:PTHR22771 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 43186144 43186144 G T 1 0 0 0 0 1 0 0 0 3871 1377 48 2 2 CUL9 6 43186144 Missense_Mutation SNP G C3N-01823_T 1993686 43186144 127619835 154 25851 PTCHD4 0 . GRCh38 6 48068414 48068414 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.242C>A p.Ala81Asp p.A81D ENST00000339488 1/3 348 298 50 202 202 0 strelka-varscan-mutect PTCHD4,missense_variant,p.Ala81Asp,ENST00000398738,NM_207499.2;PTCHD4,missense_variant,p.Ala81Asp,ENST00000339488,NM_001013732.3; T ENST00000339488 Transcript missense_variant 276/2850 242/2541 81/846 A/D gCc/gAc 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 deleterious(0) 1/3 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 48068414 48068414 G T 1 0 0 0 0 1 0 0 0 12887 1203 42 2 2 PTCHD4 6 48068414 Missense_Mutation SNP G C3N-01823_T 4882270 48068414 122737565 155 25852 PTCHD4 0 . GRCh38 6 48068439 48068439 + Silent SNP G G A rs546524803 C3N-01823_T C3N-01823_N G G c.217C>T p.= p.L73L ENST00000339488 1/3 303 266 37 185 185 0 strelka-varscan-mutect PTCHD4,synonymous_variant,p.=,ENST00000398738,NM_207499.2;PTCHD4,synonymous_variant,p.=,ENST00000339488,NM_001013732.3; A ENST00000339488 Transcript synonymous_variant 251/2850 217/2541 73/846 L Ctg/Ttg rs546524803 1 -1 PTCHD4 HGNC HGNC:21345 protein_coding YES CCDS34473.2 ENSP00000341914 Q6ZW05 UPI000179A8D3 NM_001013732.3 1/3 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF15 LOW 1 SNV 2 1 PASS rs546524803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 48068439 48068439 G A 1 0 0 0 0 0 0 0 1 12887 991 35 3 3 PTCHD4 6 48068439 Silent SNP G C3N-01823_T 25 48068439 122737540 156 25853 C6orf141 0 . GRCh38 6 49551007 49551007 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.215G>A p.Gly72Glu p.G72E ENST00000529246 1/1 320 293 27 195 195 0 strelka-varscan-mutect C6orf141,missense_variant,p.Gly72Glu,ENST00000529246,NM_001145652.1;C6orf141,upstream_gene_variant,,ENST00000424426,;C6orf141,missense_variant,p.Gly72Glu,ENST00000371194,;C6orf141,missense_variant,p.Gly72Glu,ENST00000414696,;C6orf141,upstream_gene_variant,,ENST00000526429,;C6orf141,upstream_gene_variant,,ENST00000530382,;C6orf141,upstream_gene_variant,,ENST00000415078,; A ENST00000529246 Transcript missense_variant 362/1450 215/735 72/244 G/E gGa/gAa 1 1 C6orf141 HGNC HGNC:21351 protein_coding YES CCDS55018.1 ENSP00000434602 Q5SZD1 UPI000013E9DC NM_001145652.1 deleterious(0.03) 1/1 hmmpanther:PTHR36880,hmmpanther:PTHR36880:SF1 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 49551007 49551007 G A 1 0 0 0 0 1 0 0 0 2119 1174 41 3 3 C6orf141 6 49551007 Missense_Mutation SNP G C3N-01823_T 1482568 49551007 121254972 157 25854 PKHD1 0 . GRCh38 6 51903644 51903644 + Silent SNP A A G C3N-01823_T C3N-01823_N A A c.6949T>C p.= p.L2317L ENST00000371117 43/67 576 473 103 386 386 0 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; G ENST00000371117 Transcript synonymous_variant 7225/16282 6949/12225 2317/4074 L Ttg/Ctg COSM1262280,COSM1262281 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 43/67 Gene3D:2.160.20.10,Pfam_domain:PF13229,SMART_domains:SM00710,Superfamily_domains:SSF51126 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 51903644 51903644 A G 1 0 0 0 0 0 0 0 1 12067 40 2 5 5 PKHD1 6 51903644 Silent SNP A C3N-01823_T 2352637 51903644 118902335 158 25855 BMP5 0 . GRCh38 6 55874554 55874554 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.312C>A p.= p.S104S ENST00000370830 1/7 425 339 86 259 259 0 strelka-varscan-mutect BMP5,synonymous_variant,p.=,ENST00000370830,NM_021073.2; T ENST00000370830 Transcript synonymous_variant 1011/3952 312/1365 104/454 S tcC/tcA 1 -1 BMP5 HGNC HGNC:1072 protein_coding YES CCDS4958.1 ENSP00000359866 P22003 M9VUD0 UPI0000126A2C NM_021073.2 1/7 Pfam_domain:PF00688 LOW 1 SNV 1 1 PASS rs1428483117 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 55874554 55874554 G T 1 0 0 0 0 0 0 0 1 1618 987 35 2 2 BMP5 6 55874554 Silent SNP G C3N-01823_T 3970910 55874554 114931425 159 25856 DST 0 . GRCh38 6 56509671 56509671 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.12212G>T p.Gly4071Val p.G4071V ENST00000312431 66/95 155 127 28 113 113 0 strelka-varscan-mutect DST,missense_variant,p.Gly6008Val,ENST00000361203,;DST,missense_variant,p.Gly4031Val,ENST00000421834,NM_183380.3;DST,missense_variant,p.Gly4071Val,ENST00000312431,NM_001144769.2,NM_001144770.1;DST,missense_variant,p.Gly3922Val,ENST00000370788,;DST,missense_variant,p.Gly3705Val,ENST00000244364,NM_015548.4;DST,missense_variant,p.Gly1223Val,ENST00000340834,; A ENST00000312431 Transcript missense_variant 12338/17756 12212/16614 4071/5537 G/V gGg/gTg 1 -1 DST HGNC HGNC:1090 protein_coding YES CCDS75474.1 ENSP00000307959 F6QMI7 UPI0001929509 NM_001144769.2,NM_001144770.1 deleterious(0.03) 66/95 hmmpanther:PTHR11915:SF38,hmmpanther:PTHR11915,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 56509671 56509671 C A 1 0 0 0 0 1 0 0 0 4604 623 22 2 2 DST 6 56509671 Missense_Mutation SNP C C3N-01823_T 635117 56509671 114296308 160 25857 MTO1 0 . GRCh38 6 73500578 73500578 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2042G>T p.Gly681Val p.G681V ENST00000415954 13/13 140 131 9 83 83 0 strelka-varscan-mutect MTO1,missense_variant,p.Gly641Val,ENST00000498286,NM_012123.3;MTO1,missense_variant,p.Gly666Val,ENST00000370300,NM_133645.2;MTO1,missense_variant,p.Gly681Val,ENST00000415954,NM_001123226.1;MTO1,missense_variant,p.Gly592Val,ENST00000370305,;MTO1,synonymous_variant,p.=,ENST00000521156,;MTO1,3_prime_UTR_variant,,ENST00000415228,;MTO1,3_prime_UTR_variant,,ENST00000523763,;MTO1,non_coding_transcript_exon_variant,,ENST00000370308,;MTO1,non_coding_transcript_exon_variant,,ENST00000462039,; T ENST00000415954 Transcript missense_variant 2319/2837 2042/2199 681/732 G/V gGg/gTg 1 1 MTO1 HGNC HGNC:19261 protein_coding YES CCDS47452.1 ENSP00000402038 Q9Y2Z2 UPI0001639C21 NM_001123226.1 deleterious(0) 13/13 hmmpanther:PTHR11806:SF0,hmmpanther:PTHR11806,Pfam_domain:PF13932,SMART_domains:SM01228 MODERATE 1 SNV 1 1 PASS . . 0 198 9 3 0 0 0 0 -12.4384 0.9920317 1 1 1 0 T 3 4 83 73500578 73500578 G T 1 0 0 0 0 1 0 0 0 9940 1246 43 2 2 MTO1 6 73500578 Missense_Mutation SNP G C3N-01823_T 16990907 73500578 97305401 161 25858 TMEM30A 0 . GRCh38 6 75256271 75256271 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.917G>T p.Gly306Val p.G306V ENST00000230461 7/7 132 109 23 79 79 0 strelka-varscan-mutect TMEM30A,missense_variant,p.Gly306Val,ENST00000230461,NM_018247.3;TMEM30A,missense_variant,p.Gly187Val,ENST00000370050,;TMEM30A,missense_variant,p.Gly270Val,ENST00000475111,NM_001143958.1;TMEM30A,downstream_gene_variant,,ENST00000518161,; A ENST00000230461 Transcript missense_variant 1247/4594 917/1086 306/361 G/V gGa/gTa 1 -1 TMEM30A HGNC HGNC:16667 protein_coding YES CCDS4983.1 ENSP00000230461 Q9NV96 UPI0000071AE1 NM_018247.3 deleterious(0) 7/7 hmmpanther:PTHR10926:SF17,hmmpanther:PTHR10926,Pfam_domain:PF03381,PIRSF_domain:PIRSF015840 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 75256271 75256271 C A 1 0 0 0 0 1 0 0 0 16629 855 30 2 2 TMEM30A 6 75256271 Missense_Mutation SNP C C3N-01823_T 1755693 75256271 95549708 162 25859 ASCC3 0 . GRCh38 6 100867962 100867962 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.36C>A p.= p.S12S ENST00000369162 2/42 364 343 21 337 337 0 strelka-varscan-mutect ASCC3,synonymous_variant,p.=,ENST00000369162,NM_006828.3;ASCC3,synonymous_variant,p.=,ENST00000369143,NM_022091.4;ASCC3,synonymous_variant,p.=,ENST00000522650,NM_001284271.1;ASCC3,synonymous_variant,p.=,ENST00000324723,;ASCC3,synonymous_variant,p.=,ENST00000324696,;ASCC3,non_coding_transcript_exon_variant,,ENST00000468245,; T ENST00000369162 Transcript synonymous_variant 381/8146 36/6609 12/2202 S tcC/tcA 1 -1 ASCC3 HGNC HGNC:18697 protein_coding YES CCDS5046.1 ENSP00000358159 Q8N3C0 UPI000014145A NM_006828.3 2/42 PIRSF_domain:PIRSF039073 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 100867962 100867962 G T 1 0 0 0 0 0 0 0 1 1175 987 35 2 2 ASCC3 6 100867962 Silent SNP G C3N-01823_T 25611691 100867962 69938017 163 25860 WASF1 0 . GRCh38 6 110100642 110100642 + Missense_Mutation SNP C C A rs764574206 C3N-01823_T C3N-01823_N C C c.1560G>T p.Gln520His p.Q520H ENST00000392589 11/11 183 155 28 137 137 0 strelka-varscan-mutect WASF1,missense_variant,p.Gln520His,ENST00000392589,NM_003931.2;WASF1,missense_variant,p.Gln520His,ENST00000392588,NM_001024934.1;WASF1,missense_variant,p.Gln520His,ENST00000359451,NM_001024935.1;WASF1,missense_variant,p.Gln520His,ENST00000392586,;WASF1,missense_variant,p.Gln520His,ENST00000392587,NM_001024936.1; A ENST00000392589 Transcript missense_variant 2397/3220 1560/1680 520/559 Q/H caG/caT rs764574206 1 -1 WASF1 HGNC HGNC:12732 protein_coding YES CCDS5080.1 ENSP00000376368 Q92558 UPI000003AC31 NM_003931.2 deleterious(0) 11/11 Pfam_domain:PF02205,hmmpanther:PTHR12902,hmmpanther:PTHR12902:SF8 MODERATE 1 SNV 5 1 PASS rs764574206 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 110100642 110100642 C A 1 0 0 0 0 1 0 0 0 17812 680 24 2 2 WASF1 6 110100642 Missense_Mutation SNP C C3N-01823_T 9232680 110100642 60705337 164 25861 REV3L 0 . GRCh38 6 111349293 111349293 + Silent SNP A A G novel C3N-01823_T C3N-01823_N A A c.7344T>C p.= p.Y2448Y ENST00000358835 21/33 134 125 9 122 122 0 strelka-varscan-mutect REV3L,synonymous_variant,p.=,ENST00000435970,NM_001286431.1,NM_001286432.1;REV3L,synonymous_variant,p.=,ENST00000358835,NM_002912.4;REV3L,synonymous_variant,p.=,ENST00000368802,;REV3L,synonymous_variant,p.=,ENST00000368805,;REV3L,3_prime_UTR_variant,,ENST00000422377,;REV3L,3_prime_UTR_variant,,ENST00000434009,;REV3L,3_prime_UTR_variant,,ENST00000413831,;REV3L,non_coding_transcript_exon_variant,,ENST00000492520,;FCF1P5,upstream_gene_variant,,ENST00000406490,; G ENST00000358835 Transcript synonymous_variant 7802/10815 7344/9393 2448/3130 Y taT/taC 1 -1 REV3L HGNC HGNC:9968 protein_coding YES CCDS5091.2 ENSP00000351697 O60673 UPI0000140023 NM_002912.4 21/33 hmmpanther:PTHR10322:SF5,hmmpanther:PTHR10322,Pfam_domain:PF03104,Gene3D:3.30.420.10,SMART_domains:SM00486,Superfamily_domains:SSF53098 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 111349293 111349293 A G 1 0 0 0 0 0 0 0 1 13411 224 8 5 5 REV3L 6 111349293 Silent SNP A C3N-01823_T 1248651 111349293 59456686 165 25862 NUS1 0 . GRCh38 6 117693042 117693042 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.416G>T p.Gly139Val p.G139V ENST00000368494 2/5 98 86 12 130 130 0 strelka-varscan-mutect NUS1,missense_variant,p.Gly139Val,ENST00000368494,NM_138459.3; T ENST00000368494 Transcript missense_variant,splice_region_variant 585/4676 416/882 139/293 G/V gGt/gTt 1 1 NUS1 HGNC HGNC:21042 protein_coding YES CCDS5118.1 ENSP00000357480 Q96E22 UPI000006FECA NM_138459.3 deleterious(0) 2/5 Gene3D:1uehA00,hmmpanther:PTHR21528,hmmpanther:PTHR21528:SF0,Superfamily_domains:SSF64005 MODERATE 1 SNV 1 1 PASS . . 0 202 5 2 0 0 0 0 -19.0762 0.9999383 1 1 1 0 T 3 4 83 117693042 117693042 G T 1 0 0 0 0 1 0 0 0 10843 1275 44 2 2 NUS1 6 117693042 Missense_Mutation SNP G C3N-01823_T 6343749 117693042 53112937 166 25863 MCM9 0 . GRCh38 6 118816011 118816011 + Missense_Mutation SNP C C T rs561450582 C3N-01823_T C3N-01823_N C C c.2245G>A p.Ala749Thr p.A749T ENST00000316316 13/13 168 152 16 139 139 0 strelka-varscan-mutect MCM9,missense_variant,p.Ala749Thr,ENST00000316316,;MCM9,missense_variant,p.Ala749Thr,ENST00000619706,NM_017696.2;MCM9,downstream_gene_variant,,ENST00000458674,; T ENST00000316316 Transcript missense_variant 2532/5101 2245/3432 749/1143 A/T Gca/Aca rs561450582 1 -1 MCM9 HGNC HGNC:21484 protein_coding YES CCDS56447.1 ENSP00000314505 Q9NXL9 UPI0001AE7302 tolerated_low_confidence(0.19) 13/13 MODERATE 1 SNV 5 1 PASS rs561450582 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 118816011 118816011 C T 1 0 0 0 0 1 0 0 0 9326 739 26 3 3 MCM9 6 118816011 Missense_Mutation SNP C C3N-01823_T 1122969 118816011 51989968 167 25864 MOXD1 0 . GRCh38 6 132320654 132320654 + Missense_Mutation SNP G G T rs372829567 C3N-01823_T C3N-01823_N G G c.1340C>A p.Thr447Lys p.T447K ENST00000367963 9/12 168 140 28 137 137 0 strelka-varscan-mutect MOXD1,missense_variant,p.Thr447Lys,ENST00000367963,NM_015529.3;MOXD1,missense_variant,p.Thr379Lys,ENST00000336749,;MOXD1,non_coding_transcript_exon_variant,,ENST00000489128,; T ENST00000367963 Transcript missense_variant 1459/3059 1340/1842 447/613 T/K aCg/aAg rs372829567 1 -1 MOXD1 HGNC HGNC:21063 protein_coding YES CCDS5152.2 ENSP00000356940 Q6UVY6 UPI000003F04F NM_015529.3 deleterious(0) 9/12 hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF28,Pfam_domain:PF03712,Gene3D:2.60.120.230,Superfamily_domains:SSF49742 MODERATE 1 SNV 1 1 PASS rs372829567 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 132320654 132320654 G T 1 0 0 0 0 1 0 0 0 9682 1145 40 1 1 MOXD1 6 132320654 Missense_Mutation SNP G C3N-01823_T 13504643 132320654 38485325 168 25865 SYNE1 0 . GRCh38 6 152472607 152472607 + Silent SNP A A G novel C3N-01823_T C3N-01823_N A A c.15T>C p.= p.H5H ENST00000495090 1/12 302 278 24 245 245 0 strelka-varscan-mutect SYNE1,synonymous_variant,p.=,ENST00000495090,;SYNE1,intron_variant,,ENST00000367255,NM_182961.3;SYNE1,intron_variant,,ENST00000423061,NM_033071.3;SYNE1,intron_variant,,ENST00000341594,;SYNE1,intron_variant,,ENST00000367248,;SYNE1,intron_variant,,ENST00000367253,;SYNE1,intron_variant,,ENST00000413186,;SYNE1,intron_variant,,ENST00000537750,;SYNE1,intron_variant,,ENST00000466159,;SYNE1,intron_variant,,ENST00000535896,;SYNE1,upstream_gene_variant,,ENST00000481502,;SYNE1,synonymous_variant,p.=,ENST00000474655,;SYNE1,intron_variant,,ENST00000461872,;SYNE1,upstream_gene_variant,,ENST00000468937,; G ENST00000495090 Transcript synonymous_variant 24/1907 15/1839 5/612 H caT/caC 1 -1 SYNE1 HGNC HGNC:17089 protein_coding ENSP00000438508 F5H422 UPI0001891C3D 1/12 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 152472607 152472607 A G 1 0 0 0 0 0 0 0 1 15837 446 16 5 5 SYNE1 6 152472607 Silent SNP A C3N-01823_T 20151953 152472607 18333372 169 25866 NOX3 0 . GRCh38 6 155436519 155436519 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.697A>T p.Ser233Cys p.S233C ENST00000159060 7/14 332 300 32 232 232 0 strelka-varscan-mutect NOX3,missense_variant,p.Ser233Cys,ENST00000159060,NM_015718.2; A ENST00000159060 Transcript missense_variant 800/2042 697/1707 233/568 S/C Agt/Tgt 1 -1 NOX3 HGNC HGNC:7890 protein_coding YES CCDS5250.1 ENSP00000159060 Q9HBY0 UPI000006EC80 NM_015718.2 deleterious(0) 7/14 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 155436519 155436519 T A 1 0 0 0 0 1 0 0 0 10603 1580 55 4 4 NOX3 6 155436519 Missense_Mutation SNP T C3N-01823_T 2963912 155436519 15369460 170 25867 ZDHHC14 0 . GRCh38 6 157542631 157542631 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.292G>C p.Ala98Pro p.A98P ENST00000359775 2/9 206 195 11 173 173 0 strelka-mutect ZDHHC14,missense_variant,p.Ala98Pro,ENST00000359775,NM_024630.2;ZDHHC14,missense_variant,p.Ala98Pro,ENST00000414563,NM_153746.1;ZDHHC14,missense_variant,p.Ala17Pro,ENST00000518214,;ZDHHC14,non_coding_transcript_exon_variant,,ENST00000523468,; C ENST00000359775 Transcript missense_variant 1181/7380 292/1467 98/488 A/P Gct/Cct 1 1 ZDHHC14 HGNC HGNC:20341 protein_coding YES CCDS5252.1 ENSP00000352821 Q8IZN3 UPI00000740DB NM_024630.2 deleterious(0.01) 2/9 hmmpanther:PTHR22883,hmmpanther:PTHR22883:SF28,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -13.3839 0.9999448 1 1 1 0 C 3 2 83 157542631 157542631 G C 1 0 0 0 0 1 0 0 0 18180 1087 38 4 4 ZDHHC14 6 157542631 Missense_Mutation SNP G C3N-01823_T 2106112 157542631 13263348 171 25868 C6orf118 0 . GRCh38 6 165298057 165298057 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.981G>T p.Lys327Asn p.K327N ENST00000230301 5/9 133 110 23 94 94 0 strelka-varscan-mutect C6orf118,missense_variant,p.Lys327Asn,ENST00000230301,NM_144980.3;C6orf118,upstream_gene_variant,,ENST00000494696,; A ENST00000230301 Transcript missense_variant 1002/1812 981/1410 327/469 K/N aaG/aaT 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 tolerated(0.06) 5/9 hmmpanther:PTHR34916,Pfam_domain:PF15739 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 165298057 165298057 C A 1 0 0 0 0 1 0 0 0 2115 912 32 2 2 C6orf118 6 165298057 Missense_Mutation SNP C C3N-01823_T 7755426 165298057 5507922 172 25869 MICALL2 0 . GRCh38 7 1438928 1438928 + Missense_Mutation SNP G G T rs773446328 C3N-01823_T C3N-01823_N G G c.2034C>A p.Asn678Lys p.N678K ENST00000297508 10/17 193 176 17 125 124 1 strelka-varscan-mutect MICALL2,missense_variant,p.Asn678Lys,ENST00000297508,NM_182924.3;MICALL2,non_coding_transcript_exon_variant,,ENST00000471899,;MICALL2,missense_variant,p.Thr635Asn,ENST00000413446,;MICALL2,non_coding_transcript_exon_variant,,ENST00000472100,;MICALL2,non_coding_transcript_exon_variant,,ENST00000496184,;MICALL2,non_coding_transcript_exon_variant,,ENST00000467394,;MICALL2,non_coding_transcript_exon_variant,,ENST00000479007,;MICALL2,non_coding_transcript_exon_variant,,ENST00000487156,;MICALL2,non_coding_transcript_exon_variant,,ENST00000487187,;MICALL2,intron_variant,,ENST00000467783,;MICALL2,upstream_gene_variant,,ENST00000470807,;MICALL2,upstream_gene_variant,,ENST00000460198,;MICALL2,upstream_gene_variant,,ENST00000493998,; T ENST00000297508 Transcript missense_variant 2210/3121 2034/2715 678/904 N/K aaC/aaA rs773446328 1 -1 MICALL2 HGNC HGNC:29672 protein_coding YES CCDS5324.1 ENSP00000297508 Q8IY33 UPI00000742E0 NM_182924.3 deleterious(0.03) 10/17 MODERATE 1 SNV 1 1 PASS rs773446328 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 1438928 1438928 G T 1 0 0 0 0 1 0 0 0 9531 1020 36 2 2 MICALL2 7 1438928 Missense_Mutation SNP G C3N-01823_T 1438928 157907045 173 25870 INTS1 0 . GRCh38 7 1487903 1487903 + Missense_Mutation SNP C C T rs764970654 C3N-01823_T C3N-01823_N C C c.2373G>A p.Met791Ile p.M791I ENST00000404767 19/48 512 413 99 274 273 1 strelka-varscan-mutect INTS1,missense_variant,p.Met791Ile,ENST00000404767,NM_001080453.2;INTS1,non_coding_transcript_exon_variant,,ENST00000468115,; T ENST00000404767 Transcript missense_variant 2459/6959 2373/6573 791/2190 M/I atG/atA rs764970654 1 -1 INTS1 HGNC HGNC:24555 protein_coding YES CCDS47526.1 ENSP00000385722 Q8N201 UPI0000D7211C NM_001080453.2 tolerated(0.46) 19/48 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21224:SF1,hmmpanther:PTHR21224 MODERATE 1 SNV 5 1 PASS rs764970654 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 1487903 1487903 C T 1 0 0 0 0 1 0 0 0 7677 710 25 3 3 INTS1 7 1487903 Missense_Mutation SNP C C3N-01823_T 48975 1487903 157858070 174 25871 WIPI2 0 . GRCh38 7 5228160 5228160 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.1070A>T p.Tyr357Phe p.Y357F ENST00000288828 11/13 298 256 42 157 156 1 varscan-mutect WIPI2,missense_variant,p.Tyr357Phe,ENST00000288828,NM_015610.3;WIPI2,missense_variant,p.Tyr339Phe,ENST00000401525,NM_016003.3;WIPI2,missense_variant,p.Tyr339Phe,ENST00000382384,NM_001033519.1;WIPI2,missense_variant,p.Tyr357Phe,ENST00000404704,NM_001033518.1;WIPI2,missense_variant,p.Tyr298Phe,ENST00000484262,NM_001278299.1,NM_001033520.1;WIPI2,downstream_gene_variant,,ENST00000488359,;WIPI2,downstream_gene_variant,,ENST00000480238,;WIPI2,non_coding_transcript_exon_variant,,ENST00000471851,;WIPI2,non_coding_transcript_exon_variant,,ENST00000466014,;WIPI2,upstream_gene_variant,,ENST00000479690,; T ENST00000288828 Transcript missense_variant 1302/4476 1070/1365 357/454 Y/F tAc/tTc 1 1 WIPI2 HGNC HGNC:32225 protein_coding YES CCDS5339.1 ENSP00000288828 Q9Y4P8 A0A024R823 UPI0000073E34 NM_015610.3 tolerated(0.07) 11/13 Gene3D:2.130.10.10,hmmpanther:PTHR11227,hmmpanther:PTHR11227:SF27,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 5228160 5228160 A T 1 0 0 0 0 1 0 0 0 17927 391 14 4 4 WIPI2 7 5228160 Missense_Mutation SNP A C3N-01823_T 3740257 5228160 154117813 175 25872 COL28A1 0 . GRCh38 7 7381603 7381603 + Missense_Mutation SNP C C T rs267601567 C3N-01823_T C3N-01823_N C C c.2146G>A p.Gly716Arg p.G716R ENST00000399429 28/35 355 288 67 234 234 0 strelka-varscan-mutect COL28A1,missense_variant,p.Gly716Arg,ENST00000399429,NM_001037763.2; T ENST00000399429 Transcript missense_variant 2287/4277 2146/3378 716/1125 G/R Gga/Aga rs267601567 1 -1 COL28A1 HGNC HGNC:22442 protein_coding YES CCDS43553.1 ENSP00000382356 Q2UY09 UPI000155D64E NM_001037763.2 deleterious(0) 28/35 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF578 MODERATE 1 SNV 1 1 PASS rs267601567 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 7381603 7381603 C T 1 0 0 0 0 1 0 0 0 3475 690 24 3 3 COL28A1 7 7381603 Missense_Mutation SNP C C3N-01823_T 2153443 7381603 151964370 176 25873 AGMO 0 . GRCh38 7 15544895 15544895 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.286A>G p.Ser96Gly p.S96G ENST00000342526 3/13 148 135 13 96 96 0 strelka-varscan-mutect AGMO,missense_variant,p.Ser96Gly,ENST00000342526,NM_001004320.1; C ENST00000342526 Transcript missense_variant 456/2475 286/1338 96/445 S/G Agt/Ggt 1 -1 AGMO HGNC HGNC:33784 protein_coding YES CCDS34604.1 ENSP00000341662 Q6ZNB7 X5D773 UPI0000050343 NM_001004320.1 tolerated(0.16) 3/13 hmmpanther:PTHR21624,hmmpanther:PTHR21624:SF1 MODERATE 1 SNV 1 1 PASS rs1483381569 . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 C 3 2 83 15544895 15544895 T C 1 0 0 0 0 1 0 0 0 463 1580 55 5 5 AGMO 7 15544895 Missense_Mutation SNP T C3N-01823_T 8163292 15544895 143801078 177 25874 NUPL2 0 . GRCh38 7 23200707 23200707 + Missense_Mutation SNP C C T rs267601462 C3N-01823_T C3N-01823_N C C c.1234C>T p.Pro412Ser p.P412S ENST00000258742 7/7 119 107 12 53 53 0 strelka-varscan-mutect NUPL2,missense_variant,p.Pro412Ser,ENST00000258742,NM_007342.2;NUPL2,downstream_gene_variant,,ENST00000413919,;NUPL2,downstream_gene_variant,,ENST00000548367,;NUPL2,downstream_gene_variant,,ENST00000487595,;NUPL2,3_prime_UTR_variant,,ENST00000438012,;NUPL2,3_prime_UTR_variant,,ENST00000437140,;NUPL2,non_coding_transcript_exon_variant,,ENST00000477844,;NUPL2,non_coding_transcript_exon_variant,,ENST00000485250,;NUPL2,non_coding_transcript_exon_variant,,ENST00000489145,;NUPL2,downstream_gene_variant,,ENST00000486136,; T ENST00000258742 Transcript missense_variant 1493/1795 1234/1272 412/423 P/S Cca/Tca rs267601462 1 1 NUPL2 HGNC HGNC:17010 protein_coding YES CCDS5379.1 ENSP00000258742 O15504 UPI0000072A3C NM_007342.2 deleterious(0) 7/7 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs267601462 . 0 206 4 0 0 0 0 0 -19.99993 1 1 1 1 0 T 3 4 83 23200707 23200707 C T 1 0 0 0 0 1 0 0 0 10840 855 30 3 3 NUPL2 7 23200707 Missense_Mutation SNP C C3N-01823_T 7655812 23200707 136145266 178 25875 SCRN1 0 . GRCh38 7 29926626 29926626 + Silent SNP T T A novel C3N-01823_T C3N-01823_N T T c.972A>T p.= p.I324I ENST00000434476 7/8 146 138 8 77 77 0 strelka-varscan-mutect SCRN1,synonymous_variant,p.=,ENST00000426154,NM_001145513.1;SCRN1,synonymous_variant,p.=,ENST00000242059,NM_014766.4;SCRN1,synonymous_variant,p.=,ENST00000409497,;SCRN1,synonymous_variant,p.=,ENST00000425819,NM_001145515.1;SCRN1,synonymous_variant,p.=,ENST00000434476,NM_001145514.1; A ENST00000434476 Transcript synonymous_variant 1021/1454 972/1305 324/434 I atA/atT 1 -1 SCRN1 HGNC HGNC:22192 protein_coding YES CCDS47567.1 ENSP00000388942 Q12765 UPI000194EC2F NM_001145514.1 7/8 hmmpanther:PTHR12994:SF7,hmmpanther:PTHR12994 LOW 1 SNV 2 1 PASS rs1396173846 . 0 204 6 0 0 0 0 0 -14.76037 0.9999994 1 1 1 0 A 2 1 83 29926626 29926626 T A 1 0 0 0 0 0 0 0 1 14208 1396 49 4 4 SCRN1 7 29926626 Silent SNP T C3N-01823_T 6725919 29926626 129419347 179 25876 AMPH 0 . GRCh38 7 38465510 38465510 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.706G>T p.Asp236Tyr p.D236Y ENST00000356264 9/21 313 260 53 228 228 0 strelka-varscan-mutect AMPH,missense_variant,p.Asp236Tyr,ENST00000356264,NM_001635.3;AMPH,missense_variant,p.Asp236Tyr,ENST00000325590,NM_139316.2;AMPH,upstream_gene_variant,,ENST00000441628,; A ENST00000356264 Transcript missense_variant 922/3418 706/2088 236/695 D/Y Gac/Tac 1 -1 AMPH HGNC HGNC:471 protein_coding YES CCDS5456.1 ENSP00000348602 P49418 UPI00001259EA NM_001635.3 deleterious(0) 9/21 Prints_domain:PR01252,PROSITE_profiles:PS51021,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF211 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 38465510 38465510 C A 1 0 0 0 0 1 0 0 0 686 826 29 2 2 AMPH 7 38465510 Missense_Mutation SNP C C3N-01823_T 8538884 38465510 120880463 180 25877 HECW1 0 . GRCh38 7 43442605 43442605 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.1021G>A p.Glu341Lys p.E341K ENST00000395891 10/30 351 327 24 187 187 0 strelka-varscan-mutect HECW1,missense_variant,p.Glu341Lys,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Glu341Lys,ENST00000453890,NM_001287059.1;HECW1,downstream_gene_variant,,ENST00000471043,;HECW1,downstream_gene_variant,,ENST00000492310,; A ENST00000395891 Transcript missense_variant 1626/9501 1021/4821 341/1606 E/K Gag/Aag 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious(0) 10/30 hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,Gene3D:2.60.40.150 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 43442605 43442605 G A 1 0 0 0 0 1 0 0 0 6924 1291 45 3 3 HECW1 7 43442605 Missense_Mutation SNP G C3N-01823_T 4977095 43442605 115903368 181 25878 TNS3 0 . GRCh38 7 47369277 47369277 + Missense_Mutation SNP C C A rs751534391 C3N-01823_T C3N-01823_N C C c.1369G>T p.Val457Leu p.V457L ENST00000311160 17/31 581 451 130 291 291 0 strelka-varscan-mutect TNS3,missense_variant,p.Val457Leu,ENST00000311160,NM_022748.11;TNS3,missense_variant,p.Val560Leu,ENST00000457718,;TNS3,downstream_gene_variant,,ENST00000450444,;TNS3,downstream_gene_variant,,ENST00000469470,; A ENST00000311160 Transcript missense_variant 1727/7618 1369/4338 457/1445 V/L Gtg/Ttg rs751534391,COSM241981 1 -1 TNS3 HGNC HGNC:21616 protein_coding YES CCDS5506.2 ENSP00000312143 Q68CZ2 UPI00001AE9DA NM_022748.11 tolerated(0.4) 17/31 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751534391 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 47369277 47369277 C A 1 0 0 0 0 1 0 0 0 16818 536 19 1 1 TNS3 7 47369277 Missense_Mutation SNP C C3N-01823_T 3926672 47369277 111976696 182 25879 PKD1L1 0 . GRCh38 7 47837052 47837052 + Missense_Mutation SNP C C G rs770135589 C3N-01823_T C3N-01823_N C C c.5812G>C p.Val1938Leu p.V1938L ENST00000289672 37/57 280 237 43 148 148 0 strelka-varscan-mutect PKD1L1,missense_variant,p.Val1938Leu,ENST00000289672,NM_138295.3;HUS1,intron_variant,,ENST00000436444,; G ENST00000289672 Transcript missense_variant 5863/9092 5812/8550 1938/2849 V/L Gtc/Ctc rs770135589 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.2) 37/57 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF145 MODERATE 1 SNV 1 1 PASS rs770135589 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 83 47837052 47837052 C G 1 0 0 0 0 1 0 0 0 12060 478 17 4 4 PKD1L1 7 47837052 Missense_Mutation SNP C C3N-01823_T 467775 47837052 111508921 183 25880 ABCA13 0 . GRCh38 7 48403729 48403729 + Missense_Mutation SNP C C G rs544438554 C3N-01823_T C3N-01823_N C C c.11920C>G p.Arg3974Gly p.R3974G ENST00000435803 39/62 282 245 37 167 167 0 strelka-varscan-mutect ABCA13,missense_variant,p.Arg3974Gly,ENST00000435803,NM_152701.4;ABCA13,missense_variant,p.Arg1281Gly,ENST00000544596,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,missense_variant,p.Arg240Gly,ENST00000453246,;ABCA13,non_coding_transcript_exon_variant,,ENST00000484268,; G ENST00000435803 Transcript missense_variant 11944/17184 11920/15177 3974/5058 R/G Cga/Gga rs544438554 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 tolerated(0.38) 39/62 PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs544438554 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 48403729 48403729 C G 1 0 0 0 0 1 0 0 0 35 644 23 4 4 ABCA13 7 48403729 Missense_Mutation SNP C C3N-01823_T 566677 48403729 110942244 184 25881 POM121L12 0 . GRCh38 7 53036434 53036434 + Missense_Mutation SNP G G C rs777106124 C3N-01823_T C3N-01823_N G G c.763G>C p.Val255Leu p.V255L ENST00000408890 1/1 289 248 41 178 178 0 strelka-varscan-mutect POM121L12,missense_variant,p.Val255Leu,ENST00000408890,NM_182595.3; C ENST00000408890 Transcript missense_variant 793/1283 763/891 255/296 V/L Gtg/Ctg rs777106124,COSM4969533 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.69) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 0,1 MODERATE 1 SNV 0,1 1 PASS rs777106124 . 0 207 0 3 0 0 0 0 -20 0.9999929 1 1 1 0 C 3 2 83 53036434 53036434 G C 1 0 0 0 0 1 0 0 0 12352 1145 40 4 4 POM121L12 7 53036434 Missense_Mutation SNP G C3N-01823_T 4632705 53036434 106309539 185 25882 BAZ1B 0 . GRCh38 7 73442754 73442754 + Missense_Mutation SNP G G C rs140665563 C3N-01823_T C3N-01823_N G G c.4065C>G p.Ile1355Met p.I1355M ENST00000339594 18/20 152 144 8 87 87 0 strelka-varscan-mutect BAZ1B,missense_variant,p.Ile1355Met,ENST00000339594,NM_032408.3;BAZ1B,missense_variant,p.Ile1355Met,ENST00000404251,; C ENST00000339594 Transcript missense_variant 4404/6102 4065/4452 1355/1483 I/M atC/atG rs140665563 1 -1 BAZ1B HGNC HGNC:961 protein_coding YES CCDS5549.1 ENSP00000342434 Q9UIG0 UPI0000126731 NM_032408.3 tolerated(0.18) 18/20 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF145,Pfam_domain:PF00439,Gene3D:1.20.920.10,SMART_domains:SM00297,Superfamily_domains:SSF47370 MODERATE 1 SNV 1 1 PASS rs140665563 . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 73442754 73442754 G C 1 0 0 0 0 1 0 0 0 1475 1048 37 4 4 BAZ1B 7 73442754 Missense_Mutation SNP G C3N-01823_T 20406320 73442754 85903219 186 25883 DYNC1I1 0 . GRCh38 7 95996046 95996046 + Silent SNP C C A rs778710835 C3N-01823_T C3N-01823_N C C c.993C>A p.= p.T331T ENST00000324972 10/17 263 204 59 209 208 1 strelka-varscan-mutect DYNC1I1,synonymous_variant,p.=,ENST00000324972,NM_004411.4;DYNC1I1,synonymous_variant,p.=,ENST00000447467,NM_001135556.1;DYNC1I1,synonymous_variant,p.=,ENST00000437599,NM_001278421.1;DYNC1I1,synonymous_variant,p.=,ENST00000359388,NM_001135557.1;DYNC1I1,synonymous_variant,p.=,ENST00000457059,;DYNC1I1,synonymous_variant,p.=,ENST00000630942,NM_001278422.1;DYNC1I1,synonymous_variant,p.=,ENST00000537881,;DYNC1I1,non_coding_transcript_exon_variant,,ENST00000519371,; A ENST00000324972 Transcript synonymous_variant 1186/2950 993/1938 331/645 T acC/acA rs778710835 1 1 DYNC1I1 HGNC HGNC:2963 protein_coding YES CCDS5644.1 ENSP00000320130 O14576 A4D1I7 UPI0000129A01 NM_004411.4 10/17 PROSITE_profiles:PS50294,hmmpanther:PTHR12442:SF34,hmmpanther:PTHR12442,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 1 1 PASS rs778710835 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 95996046 95996046 C A 1 0 0 0 0 0 0 0 1 4666 581 21 2 2 DYNC1I1 7 95996046 Silent SNP C C3N-01823_T 22553292 95996046 63349927 187 25884 RELN 0 . GRCh38 7 103917110 103917110 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.302C>T p.Ser101Leu p.S101L ENST00000428762 2/65 484 355 129 381 380 1 strelka-varscan-mutect RELN,missense_variant,p.Ser101Leu,ENST00000424685,;RELN,missense_variant,p.Ser101Leu,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Ser101Leu,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 462/11571 302/10383 101/3460 S/L tCa/tTa 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.07) 2/65 Low_complexity_(Seg):seg,PROSITE_profiles:PS51019,Pfam_domain:PF02014 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 103917110 103917110 G A 1 0 0 0 0 1 0 0 0 13390 1294 45 3 3 RELN 7 103917110 Missense_Mutation SNP G C3N-01823_T 7921064 103917110 55428863 188 25885 CPED1 0 . GRCh38 7 121266772 121266772 + Frame_Shift_Del DEL C C - rs148319751 C3N-01823_T C3N-01823_N C C c.2598delC p.Asn867IlefsTer10 p.N867Ifs*10 ENST00000310396 20/23 260 216 44 205 205 0 sindel-varindel-pindel CPED1,frameshift_variant,p.Asn867IlefsTer10,ENST00000310396,NM_024913.4;CPED1,downstream_gene_variant,,ENST00000450913,NM_001105533.1;CPED1,downstream_gene_variant,,ENST00000423795,;CPED1,downstream_gene_variant,,ENST00000466055,; - ENST00000310396 Transcript frameshift_variant 3064/5340 2597/3081 866/1026 S/X tCc/tc rs148319751 1 1 CPED1 HGNC HGNC:26159 protein_coding YES CCDS34739.1 ENSP00000309772 A4D0V7 UPI000013C813 NM_024913.4 20/23 hmmpanther:PTHR14776 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 121266772 121266772 C - 1 0 1 0 1 0 0 0 0 3598 855 30 0 0 CPED1 7 121266772 Frame_Shift_Del DEL C C3N-01823_T 17349662 121266772 38079201 189 25886 GRM8 0 . GRCh38 7 126446277 126446277 + Missense_Mutation SNP A A C rs185276581 C3N-01823_T C3N-01823_N A A c.2526T>G p.Ile842Met p.I842M ENST00000339582 10/11 312 253 59 209 209 0 strelka-varscan-mutect GRM8,missense_variant,p.Ile842Met,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Ile842Met,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Ile350Met,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000489939,;GRM8,non_coding_transcript_exon_variant,,ENST00000495315,;GRM8,missense_variant,p.Ile842Met,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; C ENST00000339582 Transcript missense_variant 3335/4057 2526/2727 842/908 I/M atT/atG rs185276581 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.06) 10/11 PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 MODERATE 1 SNV 5 1 PASS rs185276581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 126446277 126446277 A C 1 0 0 0 0 1 0 0 0 6685 10 1 5 5 GRM8 7 126446277 Missense_Mutation SNP A C3N-01823_T 5179505 126446277 32899696 190 25887 SMO 0 . GRCh38 7 129203577 129203577 + Silent SNP T T A novel C3N-01823_T C3N-01823_N T T c.525T>A p.= p.P175P ENST00000249373 2/12 142 93 49 83 83 0 strelka-varscan-mutect SMO,synonymous_variant,p.=,ENST00000249373,NM_005631.4;SMO,upstream_gene_variant,,ENST00000462420,;SMO,upstream_gene_variant,,ENST00000495998,; A ENST00000249373 Transcript synonymous_variant 805/3738 525/2364 175/787 P ccT/ccA 1 1 SMO HGNC HGNC:11119 protein_coding YES CCDS5811.1 ENSP00000249373 Q99835 UPI0000050447 NM_005631.4 2/12 PROSITE_profiles:PS50038,hmmpanther:PTHR11309:SF35,hmmpanther:PTHR11309,Gene3D:1ijyA00,Pfam_domain:PF01392,SMART_domains:SM00063,Superfamily_domains:SSF63501 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 129203577 129203577 T A 1 0 0 0 0 0 0 0 1 15121 1567 55 4 4 SMO 7 129203577 Silent SNP T C3N-01823_T 2757300 129203577 30142396 191 25888 KLRG2 0 . GRCh38 7 139453647 139453647 + Silent SNP C C G rs151265889 C3N-01823_T C3N-01823_N C C c.1170G>C p.= p.T390T ENST00000340940 5/5 526 469 57 316 315 1 strelka-varscan-mutect KLRG2,missense_variant,p.Arg273Pro,ENST00000393039,;KLRG2,synonymous_variant,p.=,ENST00000340940,NM_198508.2;RNU6-911P,downstream_gene_variant,,ENST00000516523,; G ENST00000340940 Transcript synonymous_variant 1240/2197 1170/1230 390/409 T acG/acC rs151265889 1 -1 KLRG2 HGNC HGNC:24778 protein_coding YES CCDS5854.1 ENSP00000339356 A4D1S0 UPI00001C0C37 NM_198508.2 5/5 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF133,SMART_domains:SM00034,Superfamily_domains:SSF56436 LOW 1 SNV 1 1 PASS rs151265889 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 139453647 139453647 C G 1 0 0 0 0 0 0 0 1 8292 768 27 4 4 KLRG2 7 139453647 Silent SNP C C3N-01823_T 10250070 139453647 19892326 192 25889 HIPK2 0 . GRCh38 7 139600527 139600527 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.2325G>A p.= p.V775V ENST00000406875 11/15 291 271 20 169 169 0 strelka-varscan-mutect HIPK2,synonymous_variant,p.=,ENST00000406875,NM_022740.4;HIPK2,synonymous_variant,p.=,ENST00000428878,NM_001113239.2;HIPK2,synonymous_variant,p.=,ENST00000342645,; T ENST00000406875 Transcript synonymous_variant 2420/15049 2325/3597 775/1198 V gtG/gtA 1 -1 HIPK2 HGNC HGNC:14402 protein_coding YES CCDS75667.1 ENSP00000385571 Q9H2X6 UPI000012C71E NM_022740.4 11/15 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 139600527 139600527 C T 1 0 0 0 0 0 0 0 1 7005 813 29 3 3 HIPK2 7 139600527 Silent SNP C C3N-01823_T 146880 139600527 19745446 193 25890 TAS2R3 0 . GRCh38 7 141764178 141764178 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.20G>T p.Gly7Val p.G7V ENST00000247879 1/1 117 99 18 79 79 0 strelka-varscan-mutect TAS2R3,missense_variant,p.Gly7Val,ENST00000247879,NM_016943.2;SSBP1,intron_variant,,ENST00000465582,; T ENST00000247879 Transcript missense_variant 82/1101 20/951 7/316 G/V gGg/gTg 1 1 TAS2R3 HGNC HGNC:14910 protein_coding YES CCDS5867.1 ENSP00000247879 Q9NYW6 UPI0000038B0B NM_016943.2 tolerated(0.59) 1/1 Pfam_domain:PF05296,hmmpanther:PTHR11394,hmmpanther:PTHR11394:SF49,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 141764178 141764178 G T 1 0 0 0 0 1 0 0 0 15971 1232 43 2 2 TAS2R3 7 141764178 Missense_Mutation SNP G C3N-01823_T 2163651 141764178 17581795 194 25891 OR2A1 0 . GRCh38 7 144318287 144318287 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.163C>T p.His55Tyr p.H55Y ENST00000408951 1/1 461 407 54 268 268 0 varscan-mutect OR2A1,missense_variant,p.His55Tyr,ENST00000408951,NM_001005287.1;OR2A1-AS1,intron_variant,,ENST00000463561,;OR2A1-AS1,intron_variant,,ENST00000486094,;OR2A1-AS1,intron_variant,,ENST00000476560,;OR2A1-AS1,intron_variant,,ENST00000487102,;OR2A1-AS1,intron_variant,,ENST00000475089,;OR2A1-AS1,intron_variant,,ENST00000478806,;OR2A1-AS1,intron_variant,,ENST00000488041,;OR2A1-AS1,intron_variant,,ENST00000496968,;OR2A1-AS1,intron_variant,,ENST00000489488,;OR2A1-AS1,intron_variant,,ENST00000467944,;OR2A1-AS1,intron_variant,,ENST00000461843,;OR2A1-AS1,intron_variant,,ENST00000493539,;OR2A1-AS1,downstream_gene_variant,,ENST00000478925,; T ENST00000408951 Transcript missense_variant 163/933 163/933 55/310 H/Y Cac/Tac 1 1 OR2A1 HGNC HGNC:8229 protein_coding YES CCDS43673.1 ENSP00000386175 Q8NGT9 UPI0000041DF3 NM_001005287.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF115,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 144318287 144318287 C T 1 0 0 0 0 1 0 0 0 11051 594 21 3 3 OR2A1 7 144318287 Missense_Mutation SNP C C3N-01823_T 2554109 144318287 15027686 195 25892 KCNH2 0 . GRCh38 7 150950977 150950977 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2089C>A p.Leu697Ile p.L697I ENST00000262186 8/15 363 321 42 259 259 0 strelka-varscan-mutect KCNH2,missense_variant,p.Leu697Ile,ENST00000262186,NM_000238.3;KCNH2,missense_variant,p.Leu357Ile,ENST00000330883,NM_172057.2;KCNH2,missense_variant,p.Leu581Ile,ENST00000430723,NM_172056.2;KCNH2,non_coding_transcript_exon_variant,,ENST00000532957,;KCNH2,non_coding_transcript_exon_variant,,ENST00000473610,;KCNH2,non_coding_transcript_exon_variant,,ENST00000461280,; T ENST00000262186 Transcript missense_variant 2491/4286 2089/3480 697/1159 L/I Ctc/Atc 1 -1 KCNH2 HGNC HGNC:6251 protein_coding YES CCDS5910.1 ENSP00000262186 Q12809 A0A090N8Q0 UPI0000062255 NM_000238.3 deleterious(0.02) 8/15 Gene3D:3bpzA01,Prints_domain:PR01470,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF506,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 150950977 150950977 G T 1 0 0 0 0 1 0 0 0 7948 1000 35 2 2 KCNH2 7 150950977 Missense_Mutation SNP G C3N-01823_T 6632690 150950977 8394996 196 25893 CSMD1 0 . GRCh38 8 2966587 2966587 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.9086C>G p.Thr3029Ser p.T3029S ENST00000520002 59/71 167 156 11 103 103 0 strelka-varscan-mutect CSMD1,missense_variant,p.Thr2890Ser,ENST00000537824,;CSMD1,missense_variant,p.Thr2446Ser,ENST00000335551,;CSMD1,missense_variant,p.Thr3029Ser,ENST00000520002,;CSMD1,missense_variant,p.Thr3029Ser,ENST00000602557,;CSMD1,missense_variant,p.Thr3028Ser,ENST00000635120,NM_033225.5;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,; C ENST00000520002 Transcript missense_variant 9642/11740 9086/10698 3029/3565 T/S aCt/aGt 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.58) 59/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs903799594 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 2966587 2966587 G C 1 0 0 0 0 1 0 0 0 3745 1029 36 4 4 CSMD1 8 2966587 Missense_Mutation SNP G C3N-01823_T 2966587 142172049 197 25894 CSMD1 0 . GRCh38 8 3018511 3018511 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.7998T>A p.Asn2666Lys p.N2666K ENST00000520002 53/71 166 154 12 129 129 0 strelka-varscan-mutect CSMD1,missense_variant,p.Asn2527Lys,ENST00000537824,;CSMD1,missense_variant,p.Asn2083Lys,ENST00000335551,;CSMD1,missense_variant,p.Asn2666Lys,ENST00000520002,;CSMD1,missense_variant,p.Asn2666Lys,ENST00000602557,;CSMD1,missense_variant,p.Asn2665Lys,ENST00000635120,NM_033225.5;CSMD1,intron_variant,,ENST00000400186,;CSMD1,intron_variant,,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000519623,; T ENST00000520002 Transcript missense_variant 8554/11740 7998/10698 2666/3565 N/K aaT/aaA 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 53/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs1336520131 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 3018511 3018511 A T 1 0 0 0 0 1 0 0 0 3745 214 8 4 4 CSMD1 8 3018511 Missense_Mutation SNP A C3N-01823_T 51924 3018511 142120125 198 25895 CSMD1 0 . GRCh38 8 3387504 3387504 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.2775C>A p.= p.P925P ENST00000520002 19/71 94 84 10 74 74 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; T ENST00000520002 Transcript synonymous_variant 3331/11740 2775/10698 925/3565 P ccC/ccA 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 19/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -19.91845 0.9999999 1 1 1 0 T 2 4 83 3387504 3387504 G T 1 0 0 0 0 0 0 0 1 3745 1335 47 2 2 CSMD1 8 3387504 Silent SNP G C3N-01823_T 368993 3387504 141751132 199 25896 CSMD1 0 . GRCh38 8 3997993 3997993 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.728G>T p.Gly243Val p.G243V ENST00000520002 5/71 338 319 19 210 210 0 strelka-varscan-mutect CSMD1,missense_variant,p.Gly105Val,ENST00000537824,;CSMD1,missense_variant,p.Gly243Val,ENST00000520002,;CSMD1,missense_variant,p.Gly243Val,ENST00000602557,;CSMD1,missense_variant,p.Gly243Val,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Gly243Val,ENST00000400186,;CSMD1,missense_variant,p.Gly243Val,ENST00000602723,; A ENST00000520002 Transcript missense_variant 1284/11740 728/10698 243/3565 G/V gGg/gTg 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 5/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 3997993 3997993 C A 1 0 0 0 0 1 0 0 0 3745 623 22 2 2 CSMD1 8 3997993 Missense_Mutation SNP C C3N-01823_T 610489 3997993 141140643 200 25897 TNKS 0 . GRCh38 8 9556017 9556017 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.78G>A p.= p.A26A ENST00000310430 1/27 218 201 17 137 136 1 strelka-varscan-mutect TNKS,synonymous_variant,p.=,ENST00000310430,NM_003747.2;TNKS,synonymous_variant,p.=,ENST00000522110,;TNKS,synonymous_variant,p.=,ENST00000520408,;RP11-375N15.2,non_coding_transcript_exon_variant,,ENST00000607598,; A ENST00000310430 Transcript synonymous_variant 104/9620 78/3984 26/1327 A gcG/gcA 1 1 TNKS HGNC HGNC:11941 protein_coding YES CCDS5974.1 ENSP00000311579 O95271 UPI000013F00D NM_003747.2 1/27 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs748879488 . 0 204 0 5 0 0 0 0 -19.97746 0.9983407 1 1 1 0 A 2 1 83 9556017 9556017 G A 1 0 0 0 0 0 0 0 1 16792 1074 38 1 1 TNKS 8 9556017 Silent SNP G C3N-01823_T 5558024 9556017 135582619 201 25898 PRSS55 0 . GRCh38 8 10538688 10538688 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.954A>T p.Lys318Asn p.K318N ENST00000328655 5/5 172 151 21 116 115 1 strelka-varscan-mutect PRSS55,missense_variant,p.Lys318Asn,ENST00000328655,NM_198464.3;PRSS51,intron_variant,,ENST00000637190,;PRSS55,intron_variant,,ENST00000522210,NM_001197020.1;PRSS55,intron_variant,,ENST00000518641,;PRSS51,intron_variant,,ENST00000523024,; T ENST00000328655 Transcript missense_variant 994/1124 954/1059 318/352 K/N aaA/aaT 1 1 PRSS55 HGNC HGNC:30824 protein_coding YES CCDS5976.1 ENSP00000333003 Q6UWB4 UPI0000160C84 NM_198464.3 deleterious(0.01) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 10538688 10538688 A T 1 0 0 0 0 1 0 0 0 12783 40 2 4 4 PRSS55 8 10538688 Missense_Mutation SNP A C3N-01823_T 982671 10538688 134599948 202 25899 GFRA2 0 . GRCh38 8 21750766 21750766 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.616C>A p.Gln206Lys p.Q206K ENST00000524240 4/9 489 446 43 353 353 0 strelka-varscan-mutect GFRA2,missense_variant,p.Gln206Lys,ENST00000524240,NM_001495.4;GFRA2,missense_variant,p.Gln206Lys,ENST00000517328,;GFRA2,missense_variant,p.Gln73Lys,ENST00000518077,NM_001165039.1;GFRA2,missense_variant,p.Gln101Lys,ENST00000517892,NM_001165038.1;GFRA2,missense_variant,p.Gln206Lys,ENST00000522071,;GFRA2,3_prime_UTR_variant,,ENST00000306793,; T ENST00000524240 Transcript missense_variant 1267/4921 616/1395 206/464 Q/K Cag/Aag 1 -1 GFRA2 HGNC HGNC:4244 protein_coding YES CCDS47816.1 ENSP00000428518 O00451 UPI000000D9B1 NM_001495.4 deleterious(0.02) 4/9 hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF4,PIRSF_domain:PIRSF038071,Pfam_domain:PF02351,SMART_domains:SM00907,Prints_domain:PR01316 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 21750766 21750766 G T 1 0 0 0 0 1 0 0 0 6222 1357 47 2 2 GFRA2 8 21750766 Missense_Mutation SNP G C3N-01823_T 11212078 21750766 123387870 203 25900 UNC5D 0 . GRCh38 8 35686710 35686710 + Splice_Site SNP G G T novel C3N-01823_T C3N-01823_N G G c.1084+1G>T p.X362_splice ENST00000404895 272 246 26 225 224 1 strelka-varscan-mutect UNC5D,splice_donor_variant,,ENST00000287272,;UNC5D,splice_donor_variant,,ENST00000453357,;UNC5D,splice_donor_variant,,ENST00000416672,;UNC5D,splice_donor_variant,,ENST00000404895,NM_080872.2;UNC5D,splice_donor_variant,,ENST00000420357,;UNC5D,splice_donor_variant,,ENST00000474634,; T ENST00000404895 Transcript splice_donor_variant -/3252 1084/2862 362/953 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 7/16 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 83 35686710 35686710 G T 1 0 0 0 0 0 0 1 0 17519 1275 44 2 2 UNC5D 8 35686710 Splice_Site SNP G C3N-01823_T 13935944 35686710 109451926 204 25901 UNC5D 0 . GRCh38 8 35774472 35774472 + Silent SNP C C T rs764330172 C3N-01823_T C3N-01823_N C C c.2652C>T p.= p.I884I ENST00000404895 16/17 176 147 29 110 110 0 strelka-varscan-mutect UNC5D,synonymous_variant,p.=,ENST00000287272,;UNC5D,synonymous_variant,p.=,ENST00000453357,;UNC5D,synonymous_variant,p.=,ENST00000416672,;UNC5D,synonymous_variant,p.=,ENST00000404895,NM_080872.2;UNC5D,synonymous_variant,p.=,ENST00000420357,;UNC5D,synonymous_variant,p.=,ENST00000449677,; T ENST00000404895 Transcript synonymous_variant 2980/3252 2652/2862 884/953 I atC/atT rs764330172 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 16/17 Gene3D:1.10.533.10,Pfam_domain:PF00531,hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5,SMART_domains:SM00005,Superfamily_domains:SSF47986 LOW 1 SNV 1 1 PASS rs764330172 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 35774472 35774472 C T 1 0 0 0 0 0 0 0 1 17519 840 29 3 3 UNC5D 8 35774472 Silent SNP C C3N-01823_T 87762 35774472 109364164 205 25902 KCNU1 0 . GRCh38 8 36845801 36845801 + Splice_Site SNP G G T rs373193777 C3N-01823_T C3N-01823_N G G c.1794-1G>T p.X598_splice ENST00000399881 152 126 26 113 112 1 strelka-varscan-mutect KCNU1,splice_acceptor_variant,,ENST00000399881,NM_001031836.2;KCNU1,splice_acceptor_variant,,ENST00000522372,; T ENST00000399881 Transcript splice_acceptor_variant -/3695 1794/3450 598/1149 rs373193777 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 17/26 HIGH 1 SNV 2 1 PASS rs373193777 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 83 36845801 36845801 G T 1 0 0 0 0 0 0 1 0 8009 956 33 2 2 KCNU1 8 36845801 Splice_Site SNP G C3N-01823_T 1071329 36845801 108292835 206 25903 CHRNB3 0 . GRCh38 8 42732033 42732033 + Silent SNP C C A rs201506201 C3N-01823_T C3N-01823_N C C c.726C>A p.= p.I242I ENST00000289957 5/6 259 215 44 175 175 0 strelka-varscan-mutect CHRNB3,synonymous_variant,p.=,ENST00000289957,NM_000749.3; A ENST00000289957 Transcript synonymous_variant 854/2294 726/1377 242/458 I atC/atA rs201506201,COSM336955 1 1 CHRNB3 HGNC HGNC:1963 protein_coding YES CCDS6134.1 ENSP00000289957 Q05901 UPI0000125272 NM_000749.3 5/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR18945:SF75,hmmpanther:PTHR18945,Gene3D:1.20.120.370,Pfam_domain:PF02932,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112 0,1 LOW 1 SNV 1 0,1 1 PASS rs201506201 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 42732033 42732033 C A 1 0 0 0 0 0 0 0 1 3152 845 30 2 2 CHRNB3 8 42732033 Silent SNP C C3N-01823_T 5886232 42732033 102406603 207 25904 THAP1 0 . GRCh38 8 42839283 42839283 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.170A>T p.His57Leu p.H57L ENST00000254250 2/3 291 243 48 192 192 0 strelka-varscan-mutect THAP1,missense_variant,p.His57Leu,ENST00000254250,NM_018105.2;THAP1,missense_variant,p.His57Leu,ENST00000529779,;THAP1,intron_variant,,ENST00000345117,NM_199003.1;THAP1,non_coding_transcript_exon_variant,,ENST00000532093,; A ENST00000254250 Transcript missense_variant 401/2161 170/642 57/213 H/L cAc/cTc 1 -1 THAP1 HGNC HGNC:20856 protein_coding YES CCDS6136.1 ENSP00000254250 Q9NVV9 UPI000007035E NM_018105.2 deleterious(0) 2/3 Pfam_domain:PF05485,PROSITE_profiles:PS50950,hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF85,SMART_domains:SM00692,SMART_domains:SM00980,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 42839283 42839283 T A 1 0 0 0 0 1 0 0 0 16273 1696 59 4 4 THAP1 8 42839283 Missense_Mutation SNP T C3N-01823_T 107250 42839283 102299353 208 25905 SNTG1 0 . GRCh38 8 50704724 50704724 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.1163C>G p.Ala388Gly p.A388G ENST00000522124 16/19 248 216 32 134 134 0 strelka-varscan-mutect SNTG1,missense_variant,p.Ala388Gly,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Ala388Gly,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Ala388Gly,ENST00000517473,NM_001287814.1;SNTG1,3_prime_UTR_variant,,ENST00000520825,;SNTG1,3_prime_UTR_variant,,ENST00000524004,; G ENST00000522124 Transcript missense_variant 1824/3504 1163/1554 388/517 A/G gCa/gGa 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 deleterious(0) 16/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 50704724 50704724 C G 1 0 0 0 0 1 0 0 0 15194 710 25 4 4 SNTG1 8 50704724 Missense_Mutation SNP C C3N-01823_T 7865441 50704724 94433912 209 25906 OPRK1 0 . GRCh38 8 53234943 53234943 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.426G>A p.Met142Ile p.M142I ENST00000265572 3/4 344 306 38 220 220 0 strelka-varscan-mutect OPRK1,missense_variant,p.Met53Ile,ENST00000612786,NM_001282904.1;OPRK1,missense_variant,p.Met142Ile,ENST00000265572,NM_001318497.1,NM_000912.3;OPRK1,missense_variant,p.Met128Ile,ENST00000613482,;OPRK1,missense_variant,p.Met142Ile,ENST00000520287,;OPRK1,missense_variant,p.Met53Ile,ENST00000524278,;RP11-162D9.3,intron_variant,,ENST00000524425,;OPRK1,3_prime_UTR_variant,,ENST00000522508,; T ENST00000265572 Transcript missense_variant 724/5014 426/1143 142/380 M/I atG/atA 1 -1 OPRK1 HGNC HGNC:8154 protein_coding YES CCDS6152.1 ENSP00000265572 P41145 UPI000011D794 NM_001318497.1,NM_000912.3 deleterious(0.01) 3/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00384,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF1,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 53234943 53234943 C T 1 0 0 0 0 1 0 0 0 10961 478 17 3 3 OPRK1 8 53234943 Missense_Mutation SNP C C3N-01823_T 2530219 53234943 91903693 210 25907 CHD7 0 . GRCh38 8 60822621 60822621 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.3076T>C p.Ser1026Pro p.S1026P ENST00000423902 12/38 340 311 29 242 242 0 strelka-varscan-mutect CHD7,missense_variant,p.Ser1026Pro,ENST00000423902,NM_017780.3;CHD7,missense_variant,p.Ser1026Pro,ENST00000525508,;CHD7,intron_variant,,ENST00000524602,; C ENST00000423902 Transcript missense_variant 3555/11568 3076/8994 1026/2997 S/P Tcc/Ccc 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 deleterious(0) 12/38 PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF658,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Pfam_domain:PF00176,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 60822621 60822621 T C 1 0 0 0 0 1 0 0 0 3089 1667 58 5 5 CHD7 8 60822621 Missense_Mutation SNP T C3N-01823_T 7587678 60822621 84316015 211 25908 KCNB2 0 . GRCh38 8 72937368 72937368 + Silent SNP A A T rs748409049 C3N-01823_T C3N-01823_N A A c.2013A>T p.= p.P671P ENST00000523207 3/3 372 331 41 190 190 0 strelka-varscan-mutect KCNB2,synonymous_variant,p.=,ENST00000523207,NM_004770.2; T ENST00000523207 Transcript synonymous_variant 2601/3582 2013/2736 671/911 P ccA/ccT rs748409049 1 1 KCNB2 HGNC HGNC:6232 protein_coding YES CCDS6209.1 ENSP00000430846 Q92953 UPI000012DC85 NM_004770.2 3/3 Pfam_domain:PF03521 LOW 1 SNV 1 1 PASS rs748409049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 72937368 72937368 A T 1 0 0 0 0 0 0 0 1 7929 175 7 4 4 KCNB2 8 72937368 Silent SNP A C3N-01823_T 12114747 72937368 72201268 212 25909 ZBTB10 0 . GRCh38 8 80499607 80499607 + Silent SNP T T C novel C3N-01823_T C3N-01823_N T T c.1086T>C p.= p.I362I ENST00000430430 3/7 312 279 33 256 256 0 strelka-varscan-mutect ZBTB10,synonymous_variant,p.=,ENST00000430430,;ZBTB10,synonymous_variant,p.=,ENST00000426744,NM_023929.4;ZBTB10,synonymous_variant,p.=,ENST00000455036,NM_001105539.2;ZBTB10,synonymous_variant,p.=,ENST00000610895,;ZBTB10,synonymous_variant,p.=,ENST00000379091,NM_001277145.1; C ENST00000430430 Transcript synonymous_variant 1865/10132 1086/2616 362/871 I atT/atC 1 1 ZBTB10 HGNC HGNC:30953 protein_coding YES CCDS47880.1 ENSP00000387462 Q96DT7 UPI0000E5AEF3 3/7 Gene3D:3.30.710.10,Pfam_domain:PF00651,hmmpanther:PTHR24414,hmmpanther:PTHR24414:SF27,Superfamily_domains:SSF54695 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 80499607 80499607 T C 1 0 0 0 0 0 0 0 1 18089 1771 62 5 5 ZBTB10 8 80499607 Silent SNP T C3N-01823_T 7562239 80499607 64639029 213 25910 CNGB3 0 . GRCh38 8 86670952 86670952 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.485C>A p.Pro162Gln p.P162Q ENST00000320005 4/18 457 411 46 302 302 0 strelka-varscan-mutect CNGB3,missense_variant,p.Pro162Gln,ENST00000320005,NM_019098.4; T ENST00000320005 Transcript missense_variant 533/4347 485/2430 162/809 P/Q cCa/cAa 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 deleterious(0) 4/18 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 86670952 86670952 G T 1 0 0 0 0 1 0 0 0 3381 1348 47 2 2 CNGB3 8 86670952 Missense_Mutation SNP G C3N-01823_T 6171345 86670952 58467684 214 25911 CSMD3 0 . GRCh38 8 112292692 112292692 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.8633C>T p.Pro2878Leu p.P2878L ENST00000297405 55/71 501 444 57 346 346 0 strelka-varscan-mutect CSMD3,missense_variant,p.Pro2878Leu,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro2838Leu,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro2709Leu,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Pro2148Leu,ENST00000339701,; A ENST00000297405 Transcript missense_variant 8878/13212 8633/11124 2878/3707 P/L cCt/cTt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 55/71 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF44,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 112292692 112292692 G A 1 0 0 0 0 1 0 0 0 3747 1000 35 3 3 CSMD3 8 112292692 Missense_Mutation SNP G C3N-01823_T 25621740 112292692 32845944 215 25912 CSMD3 0 . GRCh38 8 112656335 112656335 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.2823G>T p.Gln941His p.Q941H ENST00000297405 18/71 210 186 24 163 163 0 strelka-varscan-mutect CSMD3,missense_variant,p.Gln941His,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Gln901His,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Gln837His,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Gln281His,ENST00000339701,; A ENST00000297405 Transcript missense_variant 3068/13212 2823/11124 941/3707 Q/H caG/caT 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 18/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 112656335 112656335 C A 1 0 0 0 0 1 0 0 0 3747 912 32 2 2 CSMD3 8 112656335 Missense_Mutation SNP C C3N-01823_T 363643 112656335 32482301 216 25913 CSMD3 0 . GRCh38 8 112690013 112690013 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.2010C>A p.= p.P670P ENST00000297405 14/71 280 258 22 263 262 1 strelka-varscan-mutect CSMD3,synonymous_variant,p.=,ENST00000297405,NM_198123.1;CSMD3,synonymous_variant,p.=,ENST00000343508,NM_198124.1;CSMD3,synonymous_variant,p.=,ENST00000455883,NM_052900.2;CSMD3,synonymous_variant,p.=,ENST00000339701,; T ENST00000297405 Transcript synonymous_variant 2255/13212 2010/11124 670/3707 P ccC/ccA 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 14/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 112690013 112690013 G T 1 0 0 0 0 0 0 0 1 3747 987 35 2 2 CSMD3 8 112690013 Silent SNP G C3N-01823_T 33678 112690013 32448623 217 25914 CSMD3 0 . GRCh38 8 112921648 112921648 + Missense_Mutation SNP C C T C3N-01823_T C3N-01823_N C C c.1612G>A p.Asp538Asn p.D538N ENST00000297405 10/71 482 455 27 372 372 0 strelka-varscan-mutect CSMD3,missense_variant,p.Asp538Asn,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Asp498Asn,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Asp434Asn,ENST00000455883,NM_052900.2; T ENST00000297405 Transcript missense_variant 1857/13212 1612/11124 538/3707 D/N Gat/Aat COSM3644374,COSM3644375 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.01) 10/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 112921648 112921648 C T 1 0 0 0 0 1 0 0 0 3747 826 29 3 3 CSMD3 8 112921648 Missense_Mutation SNP C C3N-01823_T 231635 112921648 32216988 218 25915 ZHX2 0 . GRCh38 8 122952886 122952886 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.1376T>A p.Leu459His p.L459H ENST00000314393 3/4 495 428 67 367 367 0 strelka-varscan-mutect ZHX2,missense_variant,p.Leu459His,ENST00000314393,NM_014943.3;ZHX2,downstream_gene_variant,,ENST00000534247,; A ENST00000314393 Transcript missense_variant 2211/4624 1376/2514 459/837 L/H cTc/cAc 1 1 ZHX2 HGNC HGNC:18513 protein_coding YES CCDS6336.1 ENSP00000314709 Q9Y6X8 UPI0000073CCB NM_014943.3 deleterious(0.01) 3/4 PROSITE_profiles:PS50071,hmmpanther:PTHR15467,hmmpanther:PTHR15467:SF5,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 122952886 122952886 T A 1 0 0 0 0 1 0 0 0 18255 1551 54 4 4 ZHX2 8 122952886 Missense_Mutation SNP T C3N-01823_T 10031238 122952886 22185750 219 25916 ZHX2 0 . GRCh38 8 122952988 122952988 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1478G>T p.Arg493Leu p.R493L ENST00000314393 3/4 381 327 54 255 255 0 strelka-varscan-mutect ZHX2,missense_variant,p.Arg493Leu,ENST00000314393,NM_014943.3;ZHX2,downstream_gene_variant,,ENST00000534247,; T ENST00000314393 Transcript missense_variant 2313/4624 1478/2514 493/837 R/L cGg/cTg 1 1 ZHX2 HGNC HGNC:18513 protein_coding YES CCDS6336.1 ENSP00000314709 Q9Y6X8 UPI0000073CCB NM_014943.3 tolerated(0.16) 3/4 PROSITE_profiles:PS50071,hmmpanther:PTHR15467,hmmpanther:PTHR15467:SF5,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 122952988 122952988 G T 1 0 0 0 0 1 0 0 0 18255 1116 39 1 1 ZHX2 8 122952988 Missense_Mutation SNP G C3N-01823_T 102 122952988 22185648 220 25917 KCNQ3 0 . GRCh38 8 132129649 132129649 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.2232G>T p.Arg744Ser p.R744S ENST00000388996 15/15 396 351 45 232 232 0 strelka-varscan-mutect KCNQ3,missense_variant,p.Arg744Ser,ENST00000388996,NM_004519.3;KCNQ3,missense_variant,p.Arg623Ser,ENST00000621976,;KCNQ3,missense_variant,p.Arg732Ser,ENST00000519445,;KCNQ3,missense_variant,p.Arg624Ser,ENST00000521134,NM_001204824.1;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,; A ENST00000388996 Transcript missense_variant 2653/11441 2232/2619 744/872 R/S agG/agT 1 -1 KCNQ3 HGNC HGNC:6297 protein_coding YES CCDS34943.1 ENSP00000373648 O43525 UPI00001279F0 NM_004519.3 tolerated(0.12) 15/15 Prints_domain:PR01462 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 132129649 132129649 C A 1 0 0 0 0 1 0 0 0 8000 738 26 2 2 KCNQ3 8 132129649 Missense_Mutation SNP C C3N-01823_T 9176661 132129649 13008987 221 25918 TG 0 . GRCh38 8 132941414 132941414 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.5105C>G p.Ser1702Cys p.S1702C ENST00000220616 26/48 550 496 54 362 362 0 strelka-varscan-mutect TG,missense_variant,p.Ser1702Cys,ENST00000220616,NM_003235.4;TG,intron_variant,,ENST00000519178,;TG,3_prime_UTR_variant,,ENST00000523756,; G ENST00000220616 Transcript missense_variant 5145/8450 5105/8307 1702/2768 S/C tCt/tGt 1 1 TG HGNC HGNC:11764 protein_coding YES CCDS34944.1 ENSP00000220616 P01266 UPI000013C79F NM_003235.4 deleterious(0) 26/48 PIRSF_domain:PIRSF001831 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 132941414 132941414 C G 1 0 0 0 0 1 0 0 0 16246 913 32 4 4 TG 8 132941414 Missense_Mutation SNP C C3N-01823_T 811765 132941414 12197222 222 25919 FAM135B 0 . GRCh38 8 138152172 138152172 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2303C>A p.Thr768Asn p.T768N ENST00000395297 13/20 179 149 30 106 105 1 strelka-varscan-mutect FAM135B,missense_variant,p.Thr768Asn,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Thr768Asn,ENST00000276737,;FAM135B,missense_variant,p.Thr78Asn,ENST00000467365,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000395295,; T ENST00000395297 Transcript missense_variant 2474/6962 2303/4221 768/1406 T/N aCc/aAc 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 13/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS rs933172942 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 138152172 138152172 G T 1 0 0 0 0 1 0 0 0 5299 1261 44 2 2 FAM135B 8 138152172 Missense_Mutation SNP G C3N-01823_T 5210758 138152172 6986464 223 25920 COL22A1 0 . GRCh38 8 138679659 138679659 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.3030C>A p.= p.V1010V ENST00000303045 40/65 345 307 38 297 297 0 strelka-varscan-mutect COL22A1,synonymous_variant,p.=,ENST00000303045,NM_152888.2;COL22A1,intron_variant,,ENST00000435777,;COL22A1,intron_variant,,ENST00000341807,; T ENST00000303045 Transcript synonymous_variant 3477/6346 3030/4881 1010/1626 V gtC/gtA 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 40/65 hmmpanther:PTHR24023 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 138679659 138679659 G T 1 0 0 0 0 0 0 0 1 3469 1277 45 2 2 COL22A1 8 138679659 Silent SNP G C3N-01823_T 527487 138679659 6458977 224 25921 COL22A1 0 . GRCh38 8 138802889 138802889 + Missense_Mutation SNP C C T C3N-01823_T C3N-01823_N C C c.1540G>A p.Gly514Arg p.G514R ENST00000303045 11/65 365 329 36 228 228 0 strelka-varscan-mutect COL22A1,missense_variant,p.Gly514Arg,ENST00000303045,NM_152888.2;COL22A1,intron_variant,,ENST00000435777,; T ENST00000303045 Transcript missense_variant 1987/6346 1540/4881 514/1626 G/R Gga/Aga COSM4598793,COSM604278 1 -1 COL22A1 HGNC HGNC:22989 protein_coding YES CCDS6376.1 ENSP00000303153 Q8NFW1 UPI00001C1EA1 NM_152888.2 deleterious(0) 11/65 Low_complexity_(Seg):seg,hmmpanther:PTHR24023 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 138802889 138802889 C T 1 0 0 0 0 1 0 0 0 3469 632 22 3 3 COL22A1 8 138802889 Missense_Mutation SNP C C3N-01823_T 123230 138802889 6335747 225 25922 TRAPPC9 0 . GRCh38 8 140221540 140221540 + Frame_Shift_Del DEL C C - rs756688439 C3N-01823_T C3N-01823_N C C c.2769delG p.Gln924ArgfsTer12 p.Q924Rfs*12 ENST00000389328 17/23 596 545 51 396 396 0 varindel-pindel TRAPPC9,frameshift_variant,p.Gln924ArgfsTer12,ENST00000389328,NM_031466.6;TRAPPC9,frameshift_variant,p.Gln826ArgfsTer12,ENST00000438773,NM_001160372.2;TRAPPC9,frameshift_variant,p.Gln670ArgfsTer12,ENST00000520857,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000521667,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000520532,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000518839,;TRAPPC9,non_coding_transcript_exon_variant,,ENST00000517667,; - ENST00000389328 Transcript frameshift_variant 2784/4474 2769/3741 923/1246 R/X cgG/cg rs756688439 1 -1 TRAPPC9 HGNC HGNC:30832 protein_coding YES CCDS34946.1 ENSP00000373979 Q96Q05 UPI0000DBEF2B NM_031466.6 17/23 hmmpanther:PTHR21512,hmmpanther:PTHR21512:SF5 HIGH 1 deletion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 140221540 140221540 C - 1 0 1 0 1 0 0 0 0 16954 726 26 0 0 TRAPPC9 8 140221540 Frame_Shift_Del DEL C C3N-01823_T 1418651 140221540 4917096 226 25923 SMARCA2 0 . GRCh38 9 2159862 2159862 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.52T>G p.Ser18Ala p.S18A ENST00000302401 2/8 354 300 54 244 244 0 strelka-varscan-mutect SMARCA2,missense_variant,p.Ser18Ala,ENST00000302401,NM_001289400.1;SMARCA2,missense_variant,p.Ser16Ala,ENST00000382185,NM_001289399.1;SMARCA2,missense_variant,p.Ser16Ala,ENST00000417599,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000423555,;SMARCA2,missense_variant,p.Ser32Ala,ENST00000634343,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000635133,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000634435,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000634338,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000635530,;SMARCA2,intron_variant,,ENST00000382203,NM_001289396.1;SMARCA2,intron_variant,,ENST00000357248,NM_139045.3;SMARCA2,intron_variant,,ENST00000349721,NM_003070.4;SMARCA2,intron_variant,,ENST00000382194,;SMARCA2,intron_variant,,ENST00000450198,NM_001289397.1;SMARCA2,intron_variant,,ENST00000324954,NM_001289398.1;SMARCA2,intron_variant,,ENST00000382183,;SMARCA2,intron_variant,,ENST00000382186,;SMARCA2,intron_variant,,ENST00000634931,;SMARCA2,intron_variant,,ENST00000634772,;SMARCA2,intron_variant,,ENST00000452193,;SMARCA2,intron_variant,,ENST00000635388,;SMARCA2,intron_variant,,ENST00000634706,;SMARCA2,intron_variant,,ENST00000635688,;SMARCA2,upstream_gene_variant,,ENST00000634781,;SMARCA2,upstream_gene_variant,,ENST00000634688,;SMARCA2,upstream_gene_variant,,ENST00000416751,;RNU2-25P,downstream_gene_variant,,ENST00000411041,;SMARCA2,intron_variant,,ENST00000635739,;SMARCA2,intron_variant,,ENST00000636157,;SMARCA2,intron_variant,,ENST00000638139,;SMARCA2,intron_variant,,ENST00000634925,;SMARCA2,intron_variant,,ENST00000637856,;SMARCA2,upstream_gene_variant,,ENST00000635397,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000636367,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000635590,;SMARCA2,missense_variant,p.Ser16Ala,ENST00000634989,;SMARCA2,missense_variant,p.Ser29Ala,ENST00000635659,;SMARCA2,intron_variant,,ENST00000634760,; G ENST00000302401 Transcript missense_variant 572/2242 52/837 18/278 S/A Tcc/Gcc 1 1 SMARCA2 HGNC HGNC:11098 protein_coding CCDS75808.1 ENSP00000305411 B1ALF6 UPI0000211086 NM_001289400.1 tolerated_low_confidence(0.2) 2/8 Cleavage_site_(Signalp):SignalP-noTM MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 2159862 2159862 T G 1 0 0 0 0 1 0 0 0 15062 1435 50 5 5 SMARCA2 9 2159862 Missense_Mutation SNP T C3N-01823_T 2159862 136234855 227 25924 CDKN2A 0 . GRCh38 9 21971159 21971159 + Missense_Mutation SNP C C A rs863224605 C3N-01823_T C3N-01823_N C C c.200G>T p.Gly67Val p.G67V ENST00000498124 2/4 325 260 65 291 291 0 strelka-varscan-mutect CDKN2A,missense_variant,p.Gly67Val,ENST00000304494,NM_000077.4;CDKN2A,missense_variant,p.Gly16Val,ENST00000494262,;CDKN2A,missense_variant,p.Gly16Val,ENST00000498628,;CDKN2A,missense_variant,p.Gly67Val,ENST00000498124,NM_001195132.1;CDKN2A,missense_variant,p.Gly16Val,ENST00000578845,;CDKN2A,missense_variant,p.Gly67Val,ENST00000579122,;CDKN2A,missense_variant,p.Gly16Val,ENST00000497750,;CDKN2A,missense_variant,p.Gly16Val,ENST00000479692,;CDKN2A,synonymous_variant,p.=,ENST00000579755,NM_058195.3;CDKN2A,synonymous_variant,p.=,ENST00000530628,;CDKN2A-AS1,downstream_gene_variant,,ENST00000441769,;CDKN2A,non_coding_transcript_exon_variant,,ENST00000380150,;CDKN2A,upstream_gene_variant,,ENST00000577854,;CDKN2A,3_prime_UTR_variant,,ENST00000380151,;RP11-145E5.5,intron_variant,,ENST00000404796,; A ENST00000498124 Transcript missense_variant 239/880 200/504 67/167 G/V gGc/gTc rs863224605,COSM1107900,COSM1107901,COSM1107902,COSM13280,COSM3092318,COSM3092319,COSM3092320 1 -1 CDKN2A HGNC HGNC:1787 protein_coding YES CCDS56565.1 ENSP00000418915 P42771 UPI0001565711 NM_001195132.1 deleterious(0) 2/4 Gene3D:1.25.40.20,PROSITE_profiles:PS50297,hmmpanther:PTHR24148,hmmpanther:PTHR24148:SF38,Superfamily_domains:SSF48403 uncertain_significance 0,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs863224605 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 21971159 21971159 C A 1 0 0 0 0 1 0 0 0 2865 739 26 2 2 CDKN2A 9 21971159 Missense_Mutation SNP C C3N-01823_T 19811297 21971159 116423558 228 25925 SPINK4 0 . GRCh38 9 33221072 33221072 + Missense_Mutation SNP C C A rs755217720 C3N-01823_T C3N-01823_N C C c.94C>A p.Arg32Ser p.R32S ENST00000379725 2/5 310 270 40 161 161 0 strelka-varscan-mutect SPINK4,missense_variant,p.Arg32Ser,ENST00000379725,; A ENST00000379725 Transcript missense_variant 216/533 94/330 32/109 R/S Cgt/Agt rs755217720 1 1 SPINK4 HGNC HGNC:16646 protein_coding ENSP00000369048 Q5VZE7 UPI000021126F deleterious_low_confidence(0) 2/5 hmmpanther:PTHR21179 MODERATE 1 SNV 3 1 PASS rs755217720 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 33221072 33221072 C A 1 0 0 0 0 1 0 0 0 15414 652 23 1 1 SPINK4 9 33221072 Missense_Mutation SNP C C3N-01823_T 11249913 33221072 105173645 229 25926 PAX5 0 . GRCh38 9 36846856 36846857 + Frame_Shift_Ins INS - - T novel C3N-01823_T C3N-01823_N - - c.1085dupA p.Asn362LysfsTer12 p.N362Kfs*12 ENST00000358127 9/10 132 115 17 112 112 0 sindel-varindel-pindel PAX5,frameshift_variant,p.Asn362LysfsTer12,ENST00000358127,NM_016734.2;PAX5,frameshift_variant,p.Asn328LysfsTer12,ENST00000377852,NM_001280547.1;PAX5,frameshift_variant,p.Thr285AsnfsTer31,ENST00000523241,NM_001280549.1;PAX5,frameshift_variant,p.Asn319LysfsTer12,ENST00000414447,NM_001280554.1;PAX5,frameshift_variant,p.Asn254LysfsTer12,ENST00000522003,NM_001280556.1;PAX5,frameshift_variant,p.Asn262LysfsTer12,ENST00000446742,NM_001280555.1;PAX5,frameshift_variant,p.Asn189LysfsTer12,ENST00000524340,;PAX5,intron_variant,,ENST00000377853,NM_001280548.1;PAX5,intron_variant,,ENST00000520154,NM_001280550.1;PAX5,intron_variant,,ENST00000377847,NM_001280552.1;PAX5,intron_variant,,ENST00000520281,NM_001280553.1;PAX5,intron_variant,,ENST00000523145,NM_001280551.1;PAX5,intron_variant,,ENST00000522932,;PAX5,3_prime_UTR_variant,,ENST00000377840,;PAX5,3_prime_UTR_variant,,ENST00000523493,; T ENST00000358127 Transcript frameshift_variant 1239-1240/8615 1085-1086/1176 362/391 N/KX aac/aaAc 1 -1 PAX5 HGNC HGNC:8619 protein_coding YES CCDS6607.1 ENSP00000350844 Q02548 UPI000013136C NM_016734.2 9/10 Pfam_domain:PF12403 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 83 36846856 36846856 - T 1 0 1 1 0 0 0 0 0 11567 1261 44 0 0 PAX5 9 36846856 Frame_Shift_Ins INS - C3N-01823_T 3625784 36846856 101547861 230 25927 PGM5 0 . GRCh38 9 68392359 68392359 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.929G>T p.Ser310Ile p.S310I ENST00000396396 6/11 358 328 30 224 224 0 varscan-mutect PGM5,missense_variant,p.Ser310Ile,ENST00000396396,NM_021965.3;PGM5,missense_variant,p.Ser310Ile,ENST00000396392,;PGM5,downstream_gene_variant,,ENST00000431583,;RP11-88I18.2,downstream_gene_variant,,ENST00000590767,;RP11-88I18.2,downstream_gene_variant,,ENST00000629161,;RP11-88I18.2,downstream_gene_variant,,ENST00000629181,;PGM5,non_coding_transcript_exon_variant,,ENST00000604870,;PGM5,upstream_gene_variant,,ENST00000587852,; T ENST00000396396 Transcript missense_variant 1158/3338 929/1704 310/567 S/I aGc/aTc 1 1 PGM5 HGNC HGNC:8908 protein_coding YES CCDS6622.2 ENSP00000379678 Q15124 UPI0000210ABF NM_021965.3 deleterious(0) 6/11 Gene3D:3.40.120.10,hmmpanther:PTHR22573,hmmpanther:PTHR22573:SF27,Superfamily_domains:SSF53738 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 68392359 68392359 G T 1 0 0 0 0 1 0 0 0 11890 971 34 2 2 PGM5 9 68392359 Missense_Mutation SNP G C3N-01823_T 31545503 68392359 70002358 231 25928 TRPM6 0 . GRCh38 9 74762015 74762015 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.4656G>T p.Lys1552Asn p.K1552N ENST00000360774 26/39 335 317 18 237 237 0 strelka-varscan-mutect TRPM6,missense_variant,p.Lys1552Asn,ENST00000360774,NM_017662.4;TRPM6,missense_variant,p.Lys1547Asn,ENST00000361255,NM_001177311.1;TRPM6,missense_variant,p.Lys1547Asn,ENST00000449912,NM_001177310.1; A ENST00000360774 Transcript missense_variant 4894/8425 4656/6069 1552/2022 K/N aaG/aaT 1 -1 TRPM6 HGNC HGNC:17995 protein_coding YES CCDS6647.1 ENSP00000354006 Q9BX84 UPI000006E041 NM_017662.4 tolerated_low_confidence(0.05) 26/39 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 74762015 74762015 C A 1 0 0 0 0 1 0 0 0 17096 912 32 2 2 TRPM6 9 74762015 Missense_Mutation SNP C C3N-01823_T 6369656 74762015 63632702 232 25929 MFSD14B 0 . GRCh38 9 94441010 94441010 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.421T>C p.Ser141Pro p.S141P ENST00000375344 5/12 108 100 8 96 96 0 strelka-varscan-mutect MFSD14B,missense_variant,p.Ser141Pro,ENST00000375344,NM_032558.2; C ENST00000375344 Transcript missense_variant 690/3420 421/1521 141/506 S/P Tct/Cct 1 1 MFSD14B HGNC HGNC:23376 protein_coding YES CCDS6710.2 ENSP00000364493 Q5SR56 UPI000046FF5D NM_032558.2 deleterious(0) 5/12 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR23504:SF32,hmmpanther:PTHR23504,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473,Prints_domain:PR01035 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -12.21462 0.9999997 1 1 1 0 C 3 2 83 94441010 94441010 T C 1 0 0 0 0 1 0 0 0 9485 1667 58 5 5 MFSD14B 9 94441010 Missense_Mutation SNP T C3N-01823_T 19678995 94441010 43953707 233 25930 PALM2 0 . GRCh38 9 109942853 109942853 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.664G>A p.Glu222Lys p.E222K ENST00000314527 7/7 197 178 19 123 122 1 strelka-varscan-mutect PALM2,missense_variant,p.Glu190Lys,ENST00000374531,NM_001037293.2;PALM2,missense_variant,p.Glu188Lys,ENST00000483909,;PALM2-AKAP2,missense_variant,p.Glu222Lys,ENST00000413420,;PALM2,missense_variant,p.Glu222Lys,ENST00000314527,NM_053016.5;PALM2-AKAP2,intron_variant,,ENST00000374530,NM_007203.4;PALM2-AKAP2,intron_variant,,ENST00000302798,NM_147150.2;PALM2,downstream_gene_variant,,ENST00000497711,; A ENST00000314527 Transcript missense_variant 714/1332 664/1236 222/411 E/K Gaa/Aaa 1 1 PALM2 HGNC HGNC:15845 protein_coding YES CCDS48002.2 ENSP00000323805 Q8IXS6 UPI0000071924 NM_053016.5 deleterious(0) 7/7 Pfam_domain:PF03285,hmmpanther:PTHR10498 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 109942853 109942853 G A 1 0 0 0 0 1 0 0 0 11489 943 33 3 3 PALM2 9 109942853 Missense_Mutation SNP G C3N-01823_T 15501843 109942853 28451864 234 25931 COL27A1 0 . GRCh38 9 114301697 114301697 + Frame_Shift_Del DEL A A - novel C3N-01823_T C3N-01823_N A A c.4825delA p.Arg1609GlufsTer141 p.R1609Efs*141 ENST00000356083 55/61 78 64 14 57 57 0 sindel-varindel-pindel COL27A1,frameshift_variant,p.Arg1609GlufsTer141,ENST00000356083,NM_032888.3;COL27A1,upstream_gene_variant,,ENST00000490831,;COL27A1,downstream_gene_variant,,ENST00000494780,;COL27A1,3_prime_UTR_variant,,ENST00000494090,; - ENST00000356083 Transcript frameshift_variant 5216/7790 4825/5583 1609/1860 R/X Aga/ga 1 1 COL27A1 HGNC HGNC:22986 protein_coding YES CCDS6802.1 ENSP00000348385 Q8IZC6 UPI0000062271 NM_032888.3 55/61 Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF549,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 114301697 114301697 A - 1 0 1 0 1 0 0 0 0 3474 180 7 0 0 COL27A1 9 114301697 Frame_Shift_Del DEL A C3N-01823_T 4358844 114301697 24093020 235 25932 PHF19 0 . GRCh38 9 120862683 120862683 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.1092C>T p.= p.P364P ENST00000616568 11/15 364 300 64 256 256 0 strelka-varscan-mutect PHF19,synonymous_variant,p.=,ENST00000373896,NM_015651.2;PHF19,synonymous_variant,p.=,ENST00000616568,NM_001286840.1;PHF19,synonymous_variant,p.=,ENST00000419155,NM_001286842.1;PHF19,synonymous_variant,p.=,ENST00000453868,;PHF19,downstream_gene_variant,,ENST00000439674,;PHF19,non_coding_transcript_exon_variant,,ENST00000487555,;PHF19,non_coding_transcript_exon_variant,,ENST00000467266,;PHF19,upstream_gene_variant,,ENST00000462229,;PHF19,non_coding_transcript_exon_variant,,ENST00000464712,;PHF19,downstream_gene_variant,,ENST00000474402,;PHF19,downstream_gene_variant,,ENST00000478371,; A ENST00000616568 Transcript synonymous_variant 1159/4159 1092/1800 364/599 P ccC/ccT 1 -1 PHF19 HGNC HGNC:24566 protein_coding YES CCDS75889.1 ENSP00000483946 A0A087X169 UPI000387B942 NM_001286840.1 11/15 Low_complexity_(Seg):seg,hmmpanther:PTHR12628:SF6,hmmpanther:PTHR12628 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 120862683 120862683 G A 1 0 0 0 0 0 0 0 1 11915 1335 47 3 3 PHF19 9 120862683 Silent SNP G C3N-01823_T 6560986 120862683 17532034 236 25933 OR1L1 0 . GRCh38 9 122661814 122661814 + Silent SNP C C T rs377748271 C3N-01823_T C3N-01823_N C C c.99C>T p.= p.P33P ENST00000309623 1/1 311 279 32 188 188 0 strelka-varscan-mutect OR1L1,synonymous_variant,p.=,ENST00000373686,;OR1L1,synonymous_variant,p.=,ENST00000309623,NM_001005236.3; T ENST00000309623 Transcript synonymous_variant 99/933 99/933 33/310 P ccC/ccT rs377748271,COSM3654041 1 1 OR1L1 HGNC HGNC:8213 protein_coding YES CCDS35127.2 ENSP00000310773 A0A0B4J1S0 UPI0000041E03 NM_001005236.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF39,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 0,1 1 PASS rs377748271 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 122661814 122661814 C T 1 0 0 0 0 0 0 0 1 11041 581 21 3 3 OR1L1 9 122661814 Silent SNP C C3N-01823_T 1799131 122661814 15732903 237 25934 GAPVD1 0 . GRCh38 9 125350844 125350844 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.3622C>G p.Leu1208Val p.L1208V ENST00000394105 22/27 184 161 23 137 137 0 strelka-varscan-mutect GAPVD1,missense_variant,p.Leu1154Val,ENST00000470056,;GAPVD1,missense_variant,p.Leu1199Val,ENST00000394104,;GAPVD1,missense_variant,p.Leu1181Val,ENST00000297933,NM_001282680.1;GAPVD1,missense_variant,p.Leu1199Val,ENST00000495955,NM_001282679.1;GAPVD1,missense_variant,p.Leu1208Val,ENST00000394105,NM_015635.3;GAPVD1,missense_variant,p.Leu1133Val,ENST00000394083,;GAPVD1,missense_variant,p.Leu1160Val,ENST00000312123,NM_001282681.1;GAPVD1,non_coding_transcript_exon_variant,,ENST00000474637,;GAPVD1,upstream_gene_variant,,ENST00000467707,; G ENST00000394105 Transcript missense_variant 3782/5207 3622/4464 1208/1487 L/V Ctg/Gtg 1 1 GAPVD1 HGNC HGNC:23375 protein_coding YES CCDS35138.1 ENSP00000377665 Q14C86 A0A024R8A2 UPI00001D76F1 NM_015635.3 tolerated(0.1) 22/27 hmmpanther:PTHR23101:SF68,hmmpanther:PTHR23101 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 125350844 125350844 C G 1 0 0 0 0 1 0 0 0 6107 564 20 4 4 GAPVD1 9 125350844 Missense_Mutation SNP C C3N-01823_T 2689030 125350844 13043873 238 25935 PBX3 0 . GRCh38 9 125960847 125960847 + Missense_Mutation SNP C C G C3N-01823_T C3N-01823_N C C c.1007C>G p.Ser336Cys p.S336C ENST00000373489 6/9 107 89 18 70 70 0 strelka-varscan-mutect PBX3,missense_variant,p.Ser357Cys,ENST00000373487,;PBX3,missense_variant,p.Ser261Cys,ENST00000447726,NM_001134778.1;PBX3,missense_variant,p.Ser336Cys,ENST00000373489,NM_006195.5;PBX3,missense_variant,p.Ser336Cys,ENST00000342287,;PBX3,splice_region_variant,,ENST00000538998,;PBX3,splice_region_variant,,ENST00000373482,;PBX3,splice_region_variant,,ENST00000373492,; G ENST00000373489 Transcript missense_variant,splice_region_variant 1023/2775 1007/1305 336/434 S/C tCc/tGc COSM4456379 1 1 PBX3 HGNC HGNC:8634 protein_coding YES CCDS6865.1 ENSP00000362588 P40426 UPI00001313B3 NM_006195.5 deleterious(0) 6/9 Low_complexity_(Seg):seg,hmmpanther:PTHR11850:SF97,hmmpanther:PTHR11850 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 125960847 125960847 C G 1 0 0 0 0 1 0 0 0 11581 869 30 4 4 PBX3 9 125960847 Missense_Mutation SNP C C3N-01823_T 610003 125960847 12433870 239 25936 ZBTB34 0 . GRCh38 9 126880119 126880119 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.708G>T p.= p.V236V ENST00000373452 1/1 379 320 59 274 274 0 strelka-varscan-mutect ZBTB34,synonymous_variant,p.=,ENST00000319119,;ZBTB34,synonymous_variant,p.=,ENST00000373452,NM_001099270.1; T ENST00000373452 Transcript synonymous_variant 772/6528 708/1503 236/500 V gtG/gtT 1 1 ZBTB34 HGNC HGNC:31446 protein_coding YES CCDS48023.1 ENSP00000362551 Q8NCN2 UPI00004031FA NM_001099270.1 1/1 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 126880119 126880119 G T 1 0 0 0 0 0 0 0 1 18106 1277 45 2 2 ZBTB34 9 126880119 Silent SNP G C3N-01823_T 919272 126880119 11514598 240 25937 SETX 0 . GRCh38 9 132342744 132342744 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.444G>T p.Gln148His p.Q148H ENST00000224140 5/26 543 455 88 334 333 1 strelka-varscan-mutect SETX,missense_variant,p.Gln148His,ENST00000224140,NM_015046.5; A ENST00000224140 Transcript missense_variant 627/11100 444/8034 148/2677 Q/H caG/caT 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 tolerated(0.08) 5/26 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF377 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 132342744 132342744 C A 1 0 0 0 0 1 0 0 0 14420 680 24 2 2 SETX 9 132342744 Missense_Mutation SNP C C3N-01823_T 5462625 132342744 6051973 241 25938 TTF1 0 . GRCh38 9 132401644 132401644 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.1178A>C p.Lys393Thr p.K393T ENST00000334270 2/11 368 311 57 259 259 0 strelka-varscan-mutect TTF1,missense_variant,p.Lys393Thr,ENST00000334270,NM_007344.3;TTF1,intron_variant,,ENST00000612514,NM_001205296.1; G ENST00000334270 Transcript missense_variant 1218/3052 1178/2718 393/905 K/T aAg/aCg 1 -1 TTF1 HGNC HGNC:12397 protein_coding YES CCDS6948.1 ENSP00000333920 Q15361 A0A024R8C1 UPI00001B55A7 NM_007344.3 deleterious(0) 2/11 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 132401644 132401644 T G 1 0 0 0 0 1 0 0 0 17228 1609 56 5 5 TTF1 9 132401644 Missense_Mutation SNP T C3N-01823_T 58900 132401644 5993073 242 25939 STKLD1 0 . GRCh38 9 133385643 133385643 + Missense_Mutation SNP C C G rs369047700 C3N-01823_T C3N-01823_N C C c.246C>G p.His82Gln p.H82Q ENST00000371957 4/18 141 122 19 106 106 0 strelka-varscan-mutect STKLD1,missense_variant,p.His82Gln,ENST00000371957,NM_153710.4;STKLD1,downstream_gene_variant,,ENST00000468046,;STKLD1,downstream_gene_variant,,ENST00000475232,; G ENST00000371957 Transcript missense_variant 353/2825 246/2043 82/680 H/Q caC/caG rs369047700 1 1 STKLD1 HGNC HGNC:28669 protein_coding YES CCDS35169.1 ENSP00000361025 Q8NE28 UPI00001D768C NM_153710.4 deleterious(0) 4/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24363,hmmpanther:PTHR24363:SF5,Gene3D:3.30.200.20,Pfam_domain:PF00069,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs369047700 . 0 207 0 3 0 0 0 0 -20 0.9999921 1 1 1 0 G 3 3 83 133385643 133385643 C G 1 0 0 0 0 1 0 0 0 15685 535 19 4 4 STKLD1 9 133385643 Missense_Mutation SNP C C3N-01823_T 983999 133385643 5009074 243 25940 SARDH 0 . GRCh38 9 133708325 133708325 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1432C>A p.Leu478Met p.L478M ENST00000371872 11/21 160 140 20 100 100 0 strelka-varscan-mutect SARDH,missense_variant,p.Leu478Met,ENST00000371872,NM_007101.3;SARDH,missense_variant,p.Leu478Met,ENST00000439388,NM_001134707.1;SARDH,missense_variant,p.Leu198Met,ENST00000422262,;SARDH,missense_variant,p.Leu478Met,ENST00000427237,;SARDH,upstream_gene_variant,,ENST00000371868,; T ENST00000371872 Transcript missense_variant 1690/3344 1432/2757 478/918 L/M Ctg/Atg 1 -1 SARDH HGNC HGNC:10536 protein_coding YES CCDS6978.1 ENSP00000360938 Q9UL12 UPI000006F076 NM_007101.3 deleterious(0) 11/21 hmmpanther:PTHR13847:SF200,hmmpanther:PTHR13847,Pfam_domain:PF16350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 133708325 133708325 G T 1 0 0 0 0 1 0 0 0 14102 962 34 2 2 SARDH 9 133708325 Missense_Mutation SNP G C3N-01823_T 322682 133708325 4686392 244 25941 SNAPC4 0 . GRCh38 9 136387512 136387512 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1298G>T p.Gly433Val p.G433V ENST00000298532 12/23 406 336 70 263 263 0 strelka-varscan-mutect SNAPC4,missense_variant,p.Gly433Val,ENST00000298532,NM_003086.2;SNAPC4,missense_variant,p.Gly433Val,ENST00000637388,; A ENST00000298532 Transcript missense_variant 1667/5010 1298/4410 433/1469 G/V gGt/gTt 1 -1 SNAPC4 HGNC HGNC:11137 protein_coding YES CCDS6998.1 ENSP00000298532 Q5SXM2 A0A024R8F4 UPI000013E4EC NM_003086.2 deleterious(0) 12/23 Gene3D:1.10.10.60,Pfam_domain:PF00249,PROSITE_profiles:PS51294,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF486,SMART_domains:SM00717,Superfamily_domains:SSF46689,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 136387512 136387512 C A 1 0 0 0 0 1 0 0 0 15158 507 18 2 2 SNAPC4 9 136387512 Missense_Mutation SNP C C3N-01823_T 2679187 136387512 2007205 245 25942 NSMF 0 . GRCh38 9 137457595 137457595 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.440G>C p.Arg147Pro p.R147P ENST00000371475 3/16 180 156 24 91 91 0 strelka-varscan-mutect NSMF,missense_variant,p.Arg147Pro,ENST00000371475,NM_001130969.1;NSMF,missense_variant,p.Arg147Pro,ENST00000265663,NM_015537.4;NSMF,missense_variant,p.Arg147Pro,ENST00000437259,NM_001130970.1;NSMF,missense_variant,p.Arg147Pro,ENST00000371474,NM_001130971.1;NSMF,missense_variant,p.Arg147Pro,ENST00000371473,NM_001178064.1;NSMF,missense_variant,p.Arg147Pro,ENST00000371472,;PNPLA7,downstream_gene_variant,,ENST00000406427,NM_001098537.2;PNPLA7,downstream_gene_variant,,ENST00000277531,NM_152286.4;NSMF,upstream_gene_variant,,ENST00000339554,;NSMF,upstream_gene_variant,,ENST00000482448,;PNPLA7,downstream_gene_variant,,ENST00000492278,;PNPLA7,downstream_gene_variant,,ENST00000469998,;NSMF,upstream_gene_variant,,ENST00000371482,;NSMF,upstream_gene_variant,,ENST00000484316,;NSMF,upstream_gene_variant,,ENST00000371468,; G ENST00000371475 Transcript missense_variant 672/3646 440/1593 147/530 R/P cGg/cCg 1 -1 NSMF HGNC HGNC:29843 protein_coding YES CCDS48069.1 ENSP00000360530 Q6X4W1 UPI000035198D NM_001130969.1 tolerated_low_confidence(0.16) 3/16 hmmpanther:PTHR32061 MODERATE 1 SNV 1 1 PASS rs1332512759 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 137457595 137457595 C G 1 0 0 0 0 1 0 0 0 10739 652 23 4 4 NSMF 9 137457595 Missense_Mutation SNP C C3N-01823_T 1070083 137457595 937122 246 25943 CACNA1B 0 . GRCh38 9 138118717 138118717 + Silent SNP G G C novel C3N-01823_T C3N-01823_N G G c.5979G>C p.= p.L1993L ENST00000371372 44/47 208 171 37 112 112 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; C ENST00000371372 Transcript synonymous_variant 6124/9790 5979/7020 1993/2339 L ctG/ctC 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 44/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 138118717 138118717 G C 1 0 0 0 0 0 0 0 1 2227 1335 47 4 4 CACNA1B 9 138118717 Silent SNP G C3N-01823_T 661122 138118717 276000 247 25944 ADARB2 0 . GRCh38 10 1200195 1200195 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.162C>A p.= p.L54L ENST00000381310 1/3 221 173 48 138 138 0 strelka-varscan-mutect ADARB2,synonymous_variant,p.=,ENST00000381310,;ADARB2,intron_variant,,ENST00000381312,NM_018702.3;ADARB2,intron_variant,,ENST00000381305,;ADARB2,non_coding_transcript_exon_variant,,ENST00000477140,; T ENST00000381310 Transcript synonymous_variant 166/1810 162/747 54/248 L ctC/ctA 1 -1 ADARB2 HGNC HGNC:227 protein_coding ENSP00000370711 Q9NS39 UPI00001A81F9 1/3 Low_complexity_(Seg):seg,SMART_domains:SM00552 LOW SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 1200195 1200195 G T 1 0 0 0 0 0 0 0 1 327 1161 41 2 2 ADARB2 10 1200195 Silent SNP G C3N-01823_T 1200195 132597227 248 25945 ADARB2 0 . GRCh38 10 1363824 1363824 + Missense_Mutation SNP G G T rs777258791 C3N-01823_T C3N-01823_N G G c.281C>A p.Pro94His p.P94H ENST00000381312 3/10 291 256 35 216 215 1 strelka-varscan-mutect ADARB2,missense_variant,p.Pro94His,ENST00000381312,NM_018702.3;RP11-398B16.2,upstream_gene_variant,,ENST00000432987,; T ENST00000381312 Transcript missense_variant 607/8421 281/2220 94/739 P/H cCc/cAc rs777258791 1 -1 ADARB2 HGNC HGNC:227 protein_coding YES CCDS7058.1 ENSP00000370713 Q9NS39 UPI0000071776 NM_018702.3 deleterious(0.02) 3/10 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF17 MODERATE 1 SNV 1 1 PASS rs777258791 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 1363824 1363824 G T 1 0 0 0 0 1 0 0 0 327 1232 43 2 2 ADARB2 10 1363824 Missense_Mutation SNP G C3N-01823_T 163629 1363824 132433598 249 25946 ANKRD16 0 . GRCh38 10 5887899 5887899 + Silent SNP T T C novel C3N-01823_T C3N-01823_N T T c.483A>G p.= p.P161P ENST00000380094 2/8 377 313 64 274 274 0 strelka-varscan-mutect ANKRD16,synonymous_variant,p.=,ENST00000380094,NM_019046.2;ANKRD16,synonymous_variant,p.=,ENST00000380092,NM_001009941.2;ANKRD16,synonymous_variant,p.=,ENST00000191063,NM_001009943.2;FBXO18,upstream_gene_variant,,ENST00000397269,NM_001258452.1,NM_001258453.1;FBXO18,upstream_gene_variant,,ENST00000362091,NM_178150.2;FBXO18,upstream_gene_variant,,ENST00000470089,;FBXO18,upstream_gene_variant,,ENST00000462507,;ANKRD16,non_coding_transcript_exon_variant,,ENST00000492368,; C ENST00000380094 Transcript synonymous_variant 1027/2738 483/1086 161/361 P ccA/ccG 1 -1 ANKRD16 HGNC HGNC:23471 protein_coding YES CCDS31136.1 ENSP00000369436 Q6P6B7 UPI00001D809F NM_019046.2 2/8 PROSITE_profiles:PS50297,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF34,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 5887899 5887899 T C 1 0 0 0 0 0 0 0 1 746 1567 55 5 5 ANKRD16 10 5887899 Silent SNP T C3N-01823_T 4524075 5887899 127909523 250 25947 ITIH5 0 . GRCh38 10 7616014 7616014 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.907A>C p.Ser303Arg p.S303R ENST00000397146 7/14 177 154 23 104 104 0 strelka-varscan-mutect ITIH5,missense_variant,p.Ser303Arg,ENST00000397146,NM_030569.6;ITIH5,missense_variant,p.Ser303Arg,ENST00000397145,NM_001001851.2;ITIH5,missense_variant,p.Ser89Arg,ENST00000613909,NM_032817.5;ITIH5,non_coding_transcript_exon_variant,,ENST00000434980,;ITIH5,missense_variant,p.Ser81Arg,ENST00000461751,;ITIH5,non_coding_transcript_exon_variant,,ENST00000476417,; G ENST00000397146 Transcript missense_variant 986/6721 907/2829 303/942 S/R Agt/Cgt 1 -1 ITIH5 HGNC HGNC:21449 protein_coding YES ENSP00000380333 C9J2H1 UPI000014D02E NM_030569.6 deleterious(0.05) 7/14 PROSITE_profiles:PS50234,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF62,Pfam_domain:PF13768,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 7616014 7616014 T G 1 0 0 0 0 1 0 0 0 7813 1580 55 5 5 ITIH5 10 7616014 Missense_Mutation SNP T C3N-01823_T 1728115 7616014 126181408 251 25948 DCLRE1C 0 . GRCh38 10 14909184 14909184 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.1303T>A p.Cys435Ser p.C435S ENST00000378278 14/14 248 197 51 193 193 0 strelka-varscan-mutect DCLRE1C,missense_variant,p.Cys315Ser,ENST00000378255,NM_001289079.1;DCLRE1C,missense_variant,p.Cys315Ser,ENST00000396817,NM_001033858.2;DCLRE1C,missense_variant,p.Cys320Ser,ENST00000378246,NM_022487.3;DCLRE1C,missense_variant,p.Cys315Ser,ENST00000378254,NM_001289077.1;DCLRE1C,missense_variant,p.Cys315Ser,ENST00000378258,NM_001033857.2;DCLRE1C,missense_variant,p.Cys435Ser,ENST00000378278,NM_001033855.2;DCLRE1C,missense_variant,p.Cys320Ser,ENST00000378249,NM_001289078.1;DCLRE1C,missense_variant,p.Cys320Ser,ENST00000357717,NM_001289076.1;DCLRE1C,missense_variant,p.Cys88Ser,ENST00000378242,;DCLRE1C,intron_variant,,ENST00000378289,;SUV39H2,downstream_gene_variant,,ENST00000313519,NM_001193425.1,NM_024670.3;DCLRE1C,non_coding_transcript_exon_variant,,ENST00000492201,;DCLRE1C,non_coding_transcript_exon_variant,,ENST00000489845,;SUV39H2,downstream_gene_variant,,ENST00000378331,; T ENST00000378278 Transcript missense_variant 1341/2354 1303/2079 435/692 C/S Tgc/Agc 1 -1 DCLRE1C HGNC HGNC:17642 protein_coding YES CCDS31149.1 ENSP00000367527 Q96SD1 UPI000013EEDC NM_001033855.2 tolerated_low_confidence(0.69) 14/14 hmmpanther:PTHR23240,hmmpanther:PTHR23240:SF8 MODERATE 1 SNV 1 1 PASS rs921819288 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 14909184 14909184 A T 1 0 0 0 0 1 0 0 0 4098 217 8 4 4 DCLRE1C 10 14909184 Missense_Mutation SNP A C3N-01823_T 7293170 14909184 118888238 252 25949 VIM 0 . GRCh38 10 17234752 17234752 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.942G>C p.Gln314His p.Q314H ENST00000544301 6/10 564 495 69 389 389 0 strelka-varscan-mutect VIM,missense_variant,p.Gln314His,ENST00000544301,NM_003380.3;VIM,missense_variant,p.Gln314His,ENST00000224237,;VIM,missense_variant,p.Gln140His,ENST00000421459,;VIM,downstream_gene_variant,,ENST00000478317,;VIM,downstream_gene_variant,,ENST00000478746,;RP11-124N14.3,non_coding_transcript_exon_variant,,ENST00000456355,;VIM-AS1,upstream_gene_variant,,ENST00000605833,;VIM,non_coding_transcript_exon_variant,,ENST00000495528,;VIM,downstream_gene_variant,,ENST00000485947,;VIM,downstream_gene_variant,,ENST00000637053,;VIM,missense_variant,p.Gln132His,ENST00000469543,;VIM,missense_variant,p.Gln314His,ENST00000487938,; C ENST00000544301 Transcript missense_variant 1355/2128 942/1401 314/466 Q/H caG/caC 1 1 VIM HGNC HGNC:12692 protein_coding YES CCDS7120.1 ENSP00000446007 P08670 V9HWE1 UPI00000012EB NM_003380.3 tolerated(0.12) 6/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF27,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 17234752 17234752 G C 1 0 0 0 0 1 0 0 0 17712 991 35 4 4 VIM 10 17234752 Missense_Mutation SNP G C3N-01823_T 2325568 17234752 116562670 253 25950 MYO3A 0 . GRCh38 10 26157342 26157342 + Silent SNP G G C C3N-01823_T C3N-01823_N G G c.2826G>C p.= p.V942V ENST00000265944 26/35 602 516 86 413 413 0 strelka-varscan-mutect MYO3A,synonymous_variant,p.=,ENST00000265944,NM_017433.4;MYO3A,intron_variant,,ENST00000543632,; C ENST00000265944 Transcript synonymous_variant 2992/5581 2826/4851 942/1616 V gtG/gtC COSM1505239 1 1 MYO3A HGNC HGNC:7601 protein_coding YES CCDS7148.1 ENSP00000265944 Q8NEV4 UPI000014140A NM_017433.4 26/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF387,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 26157342 26157342 G C 1 0 0 0 0 0 0 0 1 10077 1335 47 4 4 MYO3A 10 26157342 Silent SNP G C3N-01823_T 8922590 26157342 107640080 254 25951 ARMC4 0 . GRCh38 10 27944922 27944922 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.1427T>A p.Met476Lys p.M476K ENST00000305242 11/20 260 197 63 183 181 2 strelka-varscan-mutect ARMC4,missense_variant,p.Met476Lys,ENST00000305242,NM_018076.3,NM_001290020.1;ARMC4,non_coding_transcript_exon_variant,,ENST00000480504,; T ENST00000305242 Transcript missense_variant 1520/3572 1427/3135 476/1044 M/K aTg/aAg 1 -1 ARMC4 HGNC HGNC:25583 protein_coding YES CCDS7157.1 ENSP00000306410 Q5T2S8 A0A140VKF7 UPI00001A95E1 NM_018076.3,NM_001290020.1 deleterious(0.03) 11/20 hmmpanther:PTHR23315:SF44,hmmpanther:PTHR23315,Superfamily_domains:SSF48371 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 27944922 27944922 A T 1 0 0 0 0 1 0 0 0 1094 217 8 4 4 ARMC4 10 27944922 Missense_Mutation SNP A C3N-01823_T 1787580 27944922 105852500 255 25952 ZNF37A 0 . GRCh38 10 38118708 38118708 + Silent SNP G G C novel C3N-01823_T C3N-01823_N G G c.1557G>C p.= p.G519G ENST00000361085 7/7 197 164 33 102 102 0 strelka-varscan-mutect ZNF37A,synonymous_variant,p.=,ENST00000361085,NM_001178101.1,NM_003421.2;ZNF37A,synonymous_variant,p.=,ENST00000351773,NM_001324248.1,NM_001324246.1,NM_001324249.1,NM_001007094.2;ZNF37A,intron_variant,,ENST00000638053,NM_001324256.1;ZNF37A,downstream_gene_variant,,ENST00000479469,;ZNF37A,downstream_gene_variant,,ENST00000477790,; C ENST00000361085 Transcript synonymous_variant 1902/8738 1557/1686 519/561 G ggG/ggC 1 1 ZNF37A HGNC HGNC:13102 protein_coding YES CCDS31183.1 ENSP00000354377 P17032 UPI000006E045 NM_001178101.1,NM_003421.2 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF188,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS rs1337850653 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 38118708 38118708 G C 1 0 0 0 0 0 0 0 1 18444 1219 43 4 4 ZNF37A 10 38118708 Silent SNP G C3N-01823_T 10173786 38118708 95678714 256 25953 WDFY4 0 . GRCh38 10 48774612 48774612 + Nonsense_Mutation SNP C C A C3N-01823_T C3N-01823_N C C c.2708C>A p.Ser903Ter p.S903* ENST00000325239 13/61 260 226 34 167 166 1 strelka-varscan-mutect WDFY4,stop_gained,p.Ser903Ter,ENST00000325239,NM_020945.1; A ENST00000325239 Transcript stop_gained 2708/9555 2708/9555 903/3184 S/* tCa/tAa COSM4923302,COSM4923303 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 13/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85,Superfamily_domains:SSF48371 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 48774612 48774612 C A 1 0 0 0 0 0 1 0 0 17831 838 29 2 2 WDFY4 10 48774612 Nonsense_Mutation SNP C C3N-01823_T 10655904 48774612 85022810 257 25954 WDFY4 0 . GRCh38 10 48778717 48778717 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.3282G>T p.= p.T1094T ENST00000325239 17/61 522 438 84 423 423 0 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1; T ENST00000325239 Transcript synonymous_variant 3282/9555 3282/9555 1094/3184 T acG/acT 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 17/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 LOW 1 SNV 5 1 PASS rs1025102712 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 48778717 48778717 G T 1 0 0 0 0 0 0 0 1 17831 1132 40 1 1 WDFY4 10 48778717 Silent SNP G C3N-01823_T 4105 48778717 85018705 258 25955 C10orf128 0 . GRCh38 10 49167936 49167936 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.70A>T p.Thr24Ser p.T24S ENST00000374153 2/7 408 370 38 295 293 2 strelka-varscan-mutect C10orf128,missense_variant,p.Thr18Ser,ENST00000374151,NM_001288743.1;C10orf128,missense_variant,p.Thr24Ser,ENST00000374148,;C10orf128,missense_variant,p.Thr24Ser,ENST00000374153,NM_001288740.1;C10orf128,missense_variant,p.Thr16Ser,ENST00000453436,NM_001288742.1;C10orf128,missense_variant,p.Thr24Ser,ENST00000474718,NM_001010863.2;C10orf128,non_coding_transcript_exon_variant,,ENST00000470884,;C10orf128,upstream_gene_variant,,ENST00000488276,;C10orf128,missense_variant,p.Thr45Ser,ENST00000374156,; A ENST00000374153 Transcript missense_variant 110/1569 70/390 24/129 T/S Aca/Tca 1 -1 C10orf128 HGNC HGNC:27274 protein_coding YES CCDS73128.1 ENSP00000363268 Q5T292 UPI0000470069 NM_001288740.1 tolerated(0.22) 2/7 Pfam_domain:PF14986,hmmpanther:PTHR37857,hmmpanther:PTHR37857:SF1 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 49167936 49167936 T A 1 0 0 0 0 1 0 0 0 1761 1725 60 4 4 C10orf128 10 49167936 Missense_Mutation SNP T C3N-01823_T 389219 49167936 84629486 259 25956 UBE2D1 0 . GRCh38 10 58361374 58361374 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.61T>A p.Cys21Ser p.C21S ENST00000373910 2/7 294 245 49 250 250 0 strelka-varscan-mutect UBE2D1,missense_variant,p.Cys21Ser,ENST00000373910,NM_003338.4;UBE2D1,5_prime_UTR_variant,,ENST00000615793,NM_001204880.1;UBE2D1,upstream_gene_variant,,ENST00000473824,; A ENST00000373910 Transcript missense_variant 288/2659 61/444 21/147 C/S Tgt/Agt 1 1 UBE2D1 HGNC HGNC:12474 protein_coding YES CCDS7252.1 ENSP00000363019 P51668 A0A024QZJ2 UPI0000001661 NM_003338.4 deleterious_low_confidence(0) 2/7 Gene3D:3.10.110.10,Pfam_domain:PF00179,PROSITE_profiles:PS50127,hmmpanther:PTHR24068,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 58361374 58361374 T A 1 0 0 0 0 1 0 0 0 17369 1580 55 4 4 UBE2D1 10 58361374 Missense_Mutation SNP T C3N-01823_T 9193438 58361374 75436048 260 25957 CDH23 0 . GRCh38 10 71798525 71798525 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.281C>A p.Thr94Asn p.T94N ENST00000398788 3/23 146 130 16 97 97 0 strelka-varscan-mutect CDH23,missense_variant,p.Thr2339Asn,ENST00000224721,NM_022124.5;CDH23,missense_variant,p.Thr2334Asn,ENST00000622827,;CDH23,missense_variant,p.Thr94Asn,ENST00000398788,NM_001171933.1;CDH23,missense_variant,p.Thr94Asn,ENST00000619887,NM_001171934.1;CDH23,non_coding_transcript_exon_variant,,ENST00000475158,; A ENST00000398788 Transcript missense_variant 598/4329 281/3345 94/1114 T/N aCc/aAc 1 1 CDH23 HGNC HGNC:13733 protein_coding YES CCDS53540.1 ENSP00000381768 Q9H251 UPI0000496839 NM_001171933.1 tolerated(0.23) 3/23 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF277,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 71798525 71798525 C A 1 0 0 0 0 1 0 0 0 2811 507 18 2 2 CDH23 10 71798525 Missense_Mutation SNP C C3N-01823_T 13437151 71798525 61998897 261 25958 PAX2 0 . GRCh38 10 100806491 100806491 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.678G>A p.= p.K226K ENST00000370296 6/11 579 518 61 373 373 0 strelka-varscan-mutect PAX2,synonymous_variant,p.=,ENST00000370296,NM_003988.3;PAX2,synonymous_variant,p.=,ENST00000428433,NM_003987.3,NM_003990.3;PAX2,synonymous_variant,p.=,ENST00000355243,NM_001304569.1,NM_000278.3,NM_003989.3;PAX2,synonymous_variant,p.=,ENST00000361791,;PAX2,synonymous_variant,p.=,ENST00000554172,;PAX2,non_coding_transcript_exon_variant,,ENST00000554363,;PAX2,non_coding_transcript_exon_variant,,ENST00000553492,; A ENST00000370296 Transcript synonymous_variant 1228/4140 678/1191 226/396 K aaG/aaA 1 1 PAX2 HGNC HGNC:8616 protein_coding YES CCDS7499.1 ENSP00000359319 Q02962 UPI000016AE71 NM_003988.3 6/11 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF172,Gene3D:1.10.10.60 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 100806491 100806491 G A 1 0 0 0 0 0 0 0 1 11564 962 34 3 3 PAX2 10 100806491 Silent SNP G C3N-01823_T 29007966 100806491 32990931 262 25959 TCERG1L 0 . GRCh38 10 131308248 131308248 + Silent SNP C C G rs144369307 C3N-01823_T C3N-01823_N C C c.633G>C p.= p.P211P ENST00000368642 3/12 205 181 24 188 188 0 strelka-varscan-mutect TCERG1L,synonymous_variant,p.=,ENST00000368642,NM_174937.3; G ENST00000368642 Transcript synonymous_variant 719/2618 633/1761 211/586 P ccG/ccC rs144369307,COSM427257 1 -1 TCERG1L HGNC HGNC:23533 protein_coding YES CCDS7662.2 ENSP00000357631 Q5VWI1 UPI00004589C8 NM_174937.3 3/12 hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF5 0,1 LOW 1 SNV 1 0,1 1 PASS rs144369307 . 0 197 0 10 3 0 0 0 -10.21052 0.4307957 1 1 0 0 G 2 3 83 131308248 131308248 C G 1 0 0 0 0 0 0 0 1 16093 755 27 4 4 TCERG1L 10 131308248 Silent SNP C C3N-01823_T 30501757 131308248 2489174 263 25960 TRPM5 0 . GRCh38 11 2415329 2415329 + Missense_Mutation SNP C C A rs80326119 C3N-01823_T C3N-01823_N C C c.1271G>T p.Arg424Leu p.R424L ENST00000155858 9/24 274 242 32 179 179 0 strelka-varscan-mutect TRPM5,missense_variant,p.Arg424Leu,ENST00000155858,NM_014555.3;TRPM5,missense_variant,p.Arg418Leu,ENST00000533881,;TRPM5,missense_variant,p.Arg424Leu,ENST00000533060,;TRPM5,missense_variant,p.Arg424Leu,ENST00000528453,; A ENST00000155858 Transcript missense_variant 1280/3929 1271/3498 424/1165 R/L cGc/cTc rs80326119 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 tolerated(0.05) 9/24 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5 MODERATE 1 SNV 1 1 PASS rs80326119 . 0 202 0 3 0 0 0 4 -5.505865 0 0 1 0 0 A 3 1 83 2415329 2415329 C A 1 0 0 0 0 1 0 0 0 17095 768 27 1 1 TRPM5 11 2415329 Missense_Mutation SNP C C3N-01823_T 2415329 132671293 264 25961 OR51B4 0 . GRCh38 11 5301558 5301558 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.389A>G p.Asn130Ser p.N130S ENST00000380224 1/1 370 301 69 232 232 0 strelka-varscan-mutect OR51B4,missense_variant,p.Asn130Ser,ENST00000380224,NM_033179.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,downstream_gene_variant,,ENST00000420465,; C ENST00000380224 Transcript missense_variant 439/983 389/933 130/310 N/S aAc/aGc 1 -1 OR51B4 HGNC HGNC:14708 protein_coding YES CCDS7757.1 ENSP00000369573 Q9Y5P0 UPI0000041B31 NM_033179.2 tolerated(0.61) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450:SF154,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 5301558 5301558 T C 1 0 0 0 0 1 0 0 0 11164 1725 60 5 5 OR51B4 11 5301558 Missense_Mutation SNP T C3N-01823_T 2886229 5301558 129785064 265 25962 OR56A3 0 . GRCh38 11 5948166 5948166 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.820C>A p.Pro274Thr p.P274T ENST00000329564 1/1 358 316 42 248 248 0 strelka-varscan-mutect OR56A3,missense_variant,p.Pro274Thr,ENST00000329564,NM_001003443.2;AC025016.1,downstream_gene_variant,,ENST00000528915,; A ENST00000329564 Transcript missense_variant 827/1022 820/948 274/315 P/T Cct/Act 1 1 OR56A3 HGNC HGNC:14786 protein_coding YES CCDS41614.1 ENSP00000331572 Q8NH54 A0A126GWL6 UPI0000041BF7 NM_001003443.2 deleterious(0.04) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF40,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 5948166 5948166 C A 1 0 0 0 0 1 0 0 0 11206 623 22 2 2 OR56A3 11 5948166 Missense_Mutation SNP C C3N-01823_T 646608 5948166 129138456 266 25963 DCHS1 0 . GRCh38 11 6622855 6622855 + Missense_Mutation SNP C C G rs576933170 C3N-01823_T C3N-01823_N C C c.8821G>C p.Val2941Leu p.V2941L ENST00000299441 21/21 488 428 60 399 399 0 strelka-varscan-mutect DCHS1,missense_variant,p.Val2941Leu,ENST00000299441,NM_003737.3;TPP1,upstream_gene_variant,,ENST00000299427,NM_000391.3;TPP1,upstream_gene_variant,,ENST00000533371,;TPP1,upstream_gene_variant,,ENST00000528657,;TPP1,upstream_gene_variant,,ENST00000436873,;RP11-732A19.5,downstream_gene_variant,,ENST00000526456,;RP11-732A19.9,downstream_gene_variant,,ENST00000545572,;TPP1,upstream_gene_variant,,ENST00000534644,;TPP1,upstream_gene_variant,,ENST00000524903,;TPP1,upstream_gene_variant,,ENST00000530040,;TPP1,upstream_gene_variant,,ENST00000428886,;TPP1,upstream_gene_variant,,ENST00000531754,;TPP1,upstream_gene_variant,,ENST00000528571,;TPP1,upstream_gene_variant,,ENST00000528917,; G ENST00000299441 Transcript missense_variant 9233/10765 8821/9897 2941/3298 V/L Gtg/Ctg rs576933170 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0.01) 21/21 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs576933170 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 6622855 6622855 C G 1 0 0 0 0 1 0 0 0 4090 536 19 4 4 DCHS1 11 6622855 Missense_Mutation SNP C C3N-01823_T 674689 6622855 128463767 267 25964 OR2AG2 0 . GRCh38 11 6768612 6768612 + Missense_Mutation SNP C C T rs201037101 C3N-01823_T C3N-01823_N C C c.346G>A p.Ala116Thr p.A116T ENST00000338569 1/1 372 353 19 233 233 0 varscan-mutect OR2AG2,missense_variant,p.Ala116Thr,ENST00000338569,NM_001004490.1; T ENST00000338569 Transcript missense_variant 444/1069 346/951 116/316 A/T Gcc/Acc rs201037101 1 -1 OR2AG2 HGNC HGNC:15143 protein_coding YES CCDS31413.1 ENSP00000342697 A6NM03 A0A126GWC6 UPI0000041C10 NM_001004490.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF183,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS rs201037101 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 6768612 6768612 C T 1 0 0 0 0 1 0 0 0 11062 739 26 3 3 OR2AG2 11 6768612 Missense_Mutation SNP C C3N-01823_T 145757 6768612 128318010 268 25965 OR2D2 0 . GRCh38 11 6892021 6892021 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.480C>A p.= p.T160T ENST00000299459 1/1 249 216 33 137 135 2 strelka-varscan-mutect OR2D2,synonymous_variant,p.=,ENST00000299459,NM_003700.1;RP11-413N10.3,intron_variant,,ENST00000637205,; T ENST00000299459 Transcript synonymous_variant 579/1110 480/927 160/308 T acC/acA 1 -1 OR2D2 HGNC HGNC:8244 protein_coding YES CCDS31416.1 ENSP00000299459 Q9H210 A0A126GVN9 UPI0000061F0B NM_003700.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF156,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 6892021 6892021 G T 1 0 0 0 0 0 0 0 1 11073 1335 47 2 2 OR2D2 11 6892021 Silent SNP G C3N-01823_T 123409 6892021 128194601 269 25966 NUCB2 0 . GRCh38 11 17331411 17331411 + Splice_Site SNP G G T novel C3N-01823_T C3N-01823_N G G c.1256-1G>T p.X419_splice ENST00000529010 43 35 8 43 43 0 strelka-varscan-mutect NUCB2,splice_acceptor_variant,,ENST00000529010,NM_005013.2;NUCB2,splice_acceptor_variant,,ENST00000622082,;NUCB2,splice_acceptor_variant,,ENST00000458064,;NUCB2,splice_acceptor_variant,,ENST00000527580,;NUCB2,splice_acceptor_variant,,ENST00000527735,;NUCB2,downstream_gene_variant,,ENST00000323688,;NUCB2,upstream_gene_variant,,ENST00000532240,;NUCB2,splice_acceptor_variant,,ENST00000533773,;NUCB2,splice_acceptor_variant,,ENST00000531242,; T ENST00000529010 Transcript splice_acceptor_variant -/2274 1256/1263 419/420 1 1 NUCB2 HGNC HGNC:8044 protein_coding YES CCDS41623.1 ENSP00000436455 V9HW75 UPI000012FE2C NM_005013.2 13/13 HIGH 1 SNV 1 1 PASS . . 1 198 11 0 0 0 0 0 -19.33741 0.9999731 1 1 1 0 T 5 4 83 17331411 17331411 G T 1 0 0 0 0 0 0 1 0 10785 956 33 2 2 NUCB2 11 17331411 Splice_Site SNP G C3N-01823_T 10439390 17331411 117755211 270 25967 UEVLD 0 . GRCh38 11 18534412 18534412 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.1166C>G p.Ser389Cys p.S389C ENST00000396197 11/12 267 244 23 195 195 0 strelka-varscan-mutect UEVLD,missense_variant,p.Ser389Cys,ENST00000396197,NM_001040697.2;UEVLD,missense_variant,p.Ser367Cys,ENST00000379387,NM_001261382.1;UEVLD,intron_variant,,ENST00000543987,NM_018314.4;UEVLD,intron_variant,,ENST00000535484,NM_001261385.1;UEVLD,intron_variant,,ENST00000320750,NM_001261383.1;UEVLD,intron_variant,,ENST00000541984,NM_001261386.1;Metazoa_SRP,upstream_gene_variant,,ENST00000616888,;UEVLD,non_coding_transcript_exon_variant,,ENST00000540666,;UEVLD,3_prime_UTR_variant,,ENST00000396196,;UEVLD,non_coding_transcript_exon_variant,,ENST00000539569,; C ENST00000396197 Transcript missense_variant 1195/4156 1166/1416 389/471 S/C tCt/tGt 1 -1 UEVLD HGNC HGNC:30866 protein_coding YES CCDS41624.1 ENSP00000379500 Q8IX04 UPI00001AF2D2 NM_001040697.2 deleterious(0.03) 11/12 hmmpanther:PTHR23306:SF18,hmmpanther:PTHR23306,Pfam_domain:PF02866,Gene3D:3.90.110.10,Superfamily_domains:SSF56327 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 18534412 18534412 G C 1 0 0 0 0 1 0 0 0 17457 942 33 4 4 UEVLD 11 18534412 Missense_Mutation SNP G C3N-01823_T 1203001 18534412 116552210 271 25968 SPTY2D1 0 . GRCh38 11 18616072 18616072 + Nonsense_Mutation SNP C C A rs746742966 C3N-01823_T C3N-01823_N C C c.202G>T p.Glu68Ter p.E68* ENST00000336349 3/6 117 95 22 83 83 0 strelka-varscan-mutect SPTY2D1,stop_gained,p.Glu68Ter,ENST00000336349,NM_194285.2;SPTY2D1,non_coding_transcript_exon_variant,,ENST00000543776,;SPTY2D1,non_coding_transcript_exon_variant,,ENST00000536336,; A ENST00000336349 Transcript stop_gained 438/5754 202/2058 68/685 E/* Gaa/Taa rs746742966 1 -1 SPTY2D1 HGNC HGNC:26818 protein_coding YES CCDS31441.1 ENSP00000337991 Q68D10 UPI00001607F0 NM_194285.2 3/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22691,hmmpanther:PTHR22691:SF8,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS rs746742966 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 18616072 18616072 C A 1 0 0 0 0 0 1 0 0 15484 864 30 2 2 SPTY2D1 11 18616072 Nonsense_Mutation SNP C C3N-01823_T 81660 18616072 116470550 272 25969 SLC6A5 0 . GRCh38 11 20604338 20604338 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.593T>C p.Leu198Pro p.L198P ENST00000525748 3/16 146 124 22 119 119 0 strelka-varscan-mutect SLC6A5,missense_variant,p.Leu198Pro,ENST00000525748,NM_004211.3;SLC6A5,intron_variant,,ENST00000298923,; C ENST00000525748 Transcript missense_variant 866/7084 593/2394 198/797 L/P cTg/cCg 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 tolerated(0.05) 3/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 20604338 20604338 T C 1 0 0 0 0 1 0 0 0 14970 1580 55 5 5 SLC6A5 11 20604338 Missense_Mutation SNP T C3N-01823_T 1988266 20604338 114482284 273 25970 NELL1 0 . GRCh38 11 21229421 21229421 + Missense_Mutation SNP C C A C3N-01823_T C3N-01823_N C C c.1600C>A p.Pro534Thr p.P534T ENST00000298925 15/21 296 266 30 210 210 0 strelka-varscan-mutect NELL1,missense_variant,p.Pro534Thr,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Pro449Thr,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Pro506Thr,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Pro506Thr,ENST00000532434,NM_201551.2;NELL1,downstream_gene_variant,,ENST00000530672,; A ENST00000298925 Transcript missense_variant 1753/3329 1600/2517 534/838 P/T Ccg/Acg COSM5613335 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 deleterious(0.01) 15/21 Gene3D:2.10.25.10,Pfam_domain:PF12947,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 21229421 21229421 C A 1 0 0 0 0 1 0 0 0 10364 507 18 2 2 NELL1 11 21229421 Missense_Mutation SNP C C3N-01823_T 625083 21229421 113857201 274 25971 WT1 0 . GRCh38 11 32435013 32435013 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.333G>A p.= p.P111P ENST00000332351 1/10 132 112 20 49 49 0 strelka-varscan-mutect WT1,synonymous_variant,p.=,ENST00000332351,NM_024426.4;WT1,synonymous_variant,p.=,ENST00000452863,NM_000378.4;WT1,synonymous_variant,p.=,ENST00000448076,NM_024424.3;WT1,upstream_gene_variant,,ENST00000379079,NM_001198551.1;WT1,upstream_gene_variant,,ENST00000530998,NM_001198552.1;WT1-AS,upstream_gene_variant,,ENST00000395900,;WT1-AS,upstream_gene_variant,,ENST00000494911,;WT1-AS,upstream_gene_variant,,ENST00000525436,;WT1-AS,upstream_gene_variant,,ENST00000478367,;WT1-AS,upstream_gene_variant,,ENST00000442957,;WT1-AS,upstream_gene_variant,,ENST00000459866,;WT1-AS_7,upstream_gene_variant,,ENST00000426618,;WT1-AS_3,upstream_gene_variant,,ENST00000613262,;WT1-AS_2,upstream_gene_variant,,ENST00000613208,;WT1-AS,upstream_gene_variant,,ENST00000612620,;WT1-AS_6,upstream_gene_variant,,ENST00000614919,;WT1-AS_1,upstream_gene_variant,,ENST00000619639,;WT1-AS,upstream_gene_variant,,ENST00000615677,;WT1,synonymous_variant,p.=,ENST00000379077,; T ENST00000332351 Transcript synonymous_variant 618/3122 333/1554 111/517 P ccG/ccA 1 -1 WT1 HGNC HGNC:12796 protein_coding YES CCDS7878.2 ENSP00000331327 J3KNN9 UPI0000D625D7 NM_024426.4 1/10 Low_complexity_(Seg):seg,Pfam_domain:PF02165,Prints_domain:PR00049 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999613 1 1 1 0 T 2 4 83 32435013 32435013 C T 1 0 0 0 0 0 0 0 1 17965 639 23 1 1 WT1 11 32435013 Silent SNP C C3N-01823_T 11205592 32435013 102651609 275 25972 HIPK3 0 . GRCh38 11 33351745 33351745 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.2945C>G p.Ser982Cys p.S982C ENST00000303296 15/17 479 440 39 337 337 0 strelka-varscan-mutect HIPK3,missense_variant,p.Ser982Cys,ENST00000303296,NM_005734.4;HIPK3,missense_variant,p.Ser961Cys,ENST00000456517,NM_001278162.1;HIPK3,missense_variant,p.Ser961Cys,ENST00000379016,NM_001048200.2;HIPK3,missense_variant,p.Ser961Cys,ENST00000525975,NM_001278163.1; G ENST00000303296 Transcript missense_variant 3250/7408 2945/3648 982/1215 S/C tCt/tGt 1 1 HIPK3 HGNC HGNC:4915 protein_coding YES CCDS7884.1 ENSP00000304226 Q9H422 UPI000006D7F8 NM_005734.4 tolerated(0.08) 15/17 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 33351745 33351745 C G 1 0 0 0 0 1 0 0 0 7006 913 32 4 4 HIPK3 11 33351745 Missense_Mutation SNP C C3N-01823_T 916732 33351745 101734877 276 25973 RAG1 0 . GRCh38 11 36574817 36574817 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1513G>T p.Ala505Ser p.A505S ENST00000299440 2/2 483 413 70 302 302 0 strelka-varscan-mutect RAG1,missense_variant,p.Ala505Ser,ENST00000299440,NM_000448.2;RAG2,downstream_gene_variant,,ENST00000524423,;RAG1,missense_variant,p.Ala505Ser,ENST00000534663,; T ENST00000299440 Transcript missense_variant 1625/6564 1513/3132 505/1043 A/S Gcc/Tcc 1 1 RAG1 HGNC HGNC:9831 protein_coding YES CCDS7902.1 ENSP00000299440 P15918 UPI000013E5A0 NM_000448.2 tolerated_low_confidence(0.19) 2/2 Pfam_domain:PF12940,hmmpanther:PTHR11539,hmmpanther:PTHR11539:SF0 MODERATE 1 SNV 1 1 PASS rs1255271221 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 36574817 36574817 G T 1 0 0 0 0 1 0 0 0 13164 1319 46 2 2 RAG1 11 36574817 Missense_Mutation SNP G C3N-01823_T 3223072 36574817 98511805 277 25974 SYT13 0 . GRCh38 11 45246456 45246456 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.903C>A p.= p.A301A ENST00000020926 5/6 353 302 51 265 265 0 strelka-varscan-mutect SYT13,synonymous_variant,p.=,ENST00000020926,NM_020826.2;SYT13,3_prime_UTR_variant,,ENST00000533332,; T ENST00000020926 Transcript synonymous_variant 1015/5144 903/1281 301/426 A gcC/gcA 1 -1 SYT13 HGNC HGNC:14962 protein_coding YES CCDS31470.1 ENSP00000020926 Q7L8C5 UPI000003AC01 NM_020826.2 5/6 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF250,Gene3D:2.60.40.150,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 45246456 45246456 G T 1 0 0 0 0 0 0 0 1 15863 1335 47 2 2 SYT13 11 45246456 Silent SNP G C3N-01823_T 8671639 45246456 89840166 278 25975 SLC35C1 0 . GRCh38 11 45810913 45810913 + Missense_Mutation SNP G G T rs757393960 C3N-01823_T C3N-01823_N G G c.673G>T p.Gly225Cys p.G225C ENST00000314134 2/2 553 501 52 372 372 0 strelka-varscan-mutect SLC35C1,missense_variant,p.Gly225Cys,ENST00000314134,NM_018389.4;SLC35C1,missense_variant,p.Gly212Cys,ENST00000442528,NM_001145265.1,NM_001145266.1;SLC35C1,downstream_gene_variant,,ENST00000530471,;SLC35C1,downstream_gene_variant,,ENST00000526817,;CTD-2210P24.6,upstream_gene_variant,,ENST00000534128,; T ENST00000314134 Transcript missense_variant 2069/4171 673/1095 225/364 G/C Ggc/Tgc rs757393960 1 1 SLC35C1 HGNC HGNC:20197 protein_coding YES CCDS7914.1 ENSP00000313318 Q96A29 B3KQH0 UPI000012A5BB NM_018389.4 deleterious(0.01) 2/2 hmmpanther:PTHR11132:SF96,hmmpanther:PTHR11132,Pfam_domain:PF03151 MODERATE 1 SNV 1 1 PASS rs757393960 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 45810913 45810913 G T 1 0 0 0 0 1 0 0 0 14849 1116 39 1 1 SLC35C1 11 45810913 Missense_Mutation SNP G C3N-01823_T 564457 45810913 89275709 279 25976 AGBL2 0 . GRCh38 11 47690231 47690231 + Silent SNP A A T novel C3N-01823_T C3N-01823_N A A c.1476T>A p.= p.I492I ENST00000525123 10/19 281 256 25 184 184 0 strelka-varscan-mutect AGBL2,synonymous_variant,p.=,ENST00000525123,NM_024783.3;AGBL2,synonymous_variant,p.=,ENST00000357610,;AGBL2,synonymous_variant,p.=,ENST00000528244,;AGBL2,downstream_gene_variant,,ENST00000532595,;AGBL2,non_coding_transcript_exon_variant,,ENST00000529712,;AGBL2,downstream_gene_variant,,ENST00000526331,;AGBL2,synonymous_variant,p.=,ENST00000528609,; T ENST00000525123 Transcript synonymous_variant 1762/3577 1476/2709 492/902 I atT/atA 1 -1 AGBL2 HGNC HGNC:26296 protein_coding YES CCDS7944.1 ENSP00000435582 Q5U5Z8 A0A140VKH9 UPI00001A95E3 NM_024783.3 10/19 Gene3D:3.40.630.10,Pfam_domain:PF00246,hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF19,Superfamily_domains:SSF53187 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 47690231 47690231 A T 1 0 0 0 0 0 0 0 1 452 10 1 4 4 AGBL2 11 47690231 Silent SNP A C3N-01823_T 1879318 47690231 87396391 280 25977 OR5D18 0 . GRCh38 11 55819803 55819803 + Silent SNP C C G rs745941878 C3N-01823_T C3N-01823_N C C c.174C>G p.= p.T58T ENST00000333976 1/1 169 131 38 98 98 0 strelka-varscan-mutect OR5D18,synonymous_variant,p.=,ENST00000333976,NM_001001952.1; G ENST00000333976 Transcript synonymous_variant 174/942 174/942 58/313 T acC/acG rs745941878 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs745941878 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 55819803 55819803 C G 1 0 0 0 0 0 0 0 1 11227 610 22 4 4 OR5D18 11 55819803 Silent SNP C C3N-01823_T 8129572 55819803 79266819 281 25978 OR5D16 0 . GRCh38 11 55838870 55838870 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.119G>T p.Ser40Ile p.S40I ENST00000378396 1/1 361 318 43 243 243 0 strelka-varscan-mutect OR5D16,missense_variant,p.Ser40Ile,ENST00000378396,NM_001005496.1; T ENST00000378396 Transcript missense_variant 119/987 119/987 40/328 S/I aGt/aTt 1 1 OR5D16 HGNC HGNC:15283 protein_coding YES CCDS31512.1 ENSP00000367649 Q8NGK9 UPI0000046198 NM_001005496.1 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1378718522 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 55838870 55838870 G T 1 0 0 0 0 1 0 0 0 11226 1029 36 2 2 OR5D16 11 55838870 Missense_Mutation SNP G C3N-01823_T 19067 55838870 79247752 282 25979 OR5T2 0 . GRCh38 11 56232216 56232216 + Silent SNP G G A rs567353421 C3N-01823_T C3N-01823_N G G c.970C>T p.= p.L324L ENST00000313264 1/1 156 125 31 100 100 0 strelka-mutect OR5T2,synonymous_variant,p.=,ENST00000313264,NM_001004746.1; A ENST00000313264 Transcript synonymous_variant 970/1080 970/1080 324/359 L Ctg/Ttg rs567353421,COSM928276 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 0,1 LOW 1 SNV 0,1 1 PASS rs567353421 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 56232216 56232216 G A 1 0 0 0 0 0 0 0 1 11250 962 34 3 3 OR5T2 11 56232216 Silent SNP G C3N-01823_T 393346 56232216 78854406 283 25980 OR5T2 0 . GRCh38 11 56232776 56232776 + Missense_Mutation SNP A A G novel C3N-01823_T C3N-01823_N A A c.410T>C p.Val137Ala p.V137A ENST00000313264 1/1 205 179 26 121 121 0 strelka-varscan-mutect OR5T2,missense_variant,p.Val137Ala,ENST00000313264,NM_001004746.1; G ENST00000313264 Transcript missense_variant 410/1080 410/1080 137/359 V/A gTa/gCa 1 -1 OR5T2 HGNC HGNC:15296 protein_coding YES CCDS31523.1 ENSP00000323688 Q8NGG2 UPI0000061E97 NM_001004746.1 tolerated(1) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF119,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 56232776 56232776 A G 1 0 0 0 0 1 0 0 0 11250 391 14 5 5 OR5T2 11 56232776 Missense_Mutation SNP A C3N-01823_T 560 56232776 78853846 284 25981 OR8H1 0 . GRCh38 11 56290640 56290640 + Nonsense_Mutation SNP G G T rs772055350 C3N-01823_T C3N-01823_N G G c.423C>A p.Cys141Ter p.C141* ENST00000313022 1/1 227 187 40 147 147 0 strelka-varscan-mutect OR8H1,stop_gained,p.Cys141Ter,ENST00000313022,NM_001005199.1;OR8H1,stop_gained,p.Cys137Ter,ENST00000610894,; T ENST00000313022 Transcript stop_gained 451/1038 423/936 141/311 C/* tgC/tgA rs772055350 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 SNV 1 PASS rs772055350 . 0 206 0 3 0 0 0 0 -20 0.9999952 1 1 1 0 T 4 4 83 56290640 56290640 G T 1 0 0 0 0 0 1 0 0 11305 1079 38 1 1 OR8H1 11 56290640 Nonsense_Mutation SNP G C3N-01823_T 57864 56290640 78795982 285 25982 TNKS1BP1 0 . GRCh38 11 57308990 57308990 + Missense_Mutation SNP C C A rs144018028 C3N-01823_T C3N-01823_N C C c.3721G>T p.Val1241Phe p.V1241F ENST00000532437 5/11 327 277 50 173 173 0 strelka-varscan-mutect TNKS1BP1,missense_variant,p.Val1241Phe,ENST00000532437,;TNKS1BP1,missense_variant,p.Val1241Phe,ENST00000358252,NM_033396.2;TNKS1BP1,downstream_gene_variant,,ENST00000530920,;TNKS1BP1,3_prime_UTR_variant,,ENST00000528882,; A ENST00000532437 Transcript missense_variant 4033/5952 3721/5190 1241/1729 V/F Gtc/Ttc rs144018028 1 -1 TNKS1BP1 HGNC HGNC:19081 protein_coding YES CCDS7951.1 ENSP00000437271 Q9C0C2 A0A024R542 UPI000013DB72 tolerated(0.06) 5/11 hmmpanther:PTHR22042,hmmpanther:PTHR22042:SF2 MODERATE 1 SNV 1 1 PASS rs144018028 . 0 207 0 3 0 0 0 0 -20 0.9999939 1 1 1 0 A 3 1 83 57308990 57308990 C A 1 0 0 0 0 1 0 0 0 16793 507 18 2 2 TNKS1BP1 11 57308990 Missense_Mutation SNP C C3N-01823_T 1018350 57308990 77777632 286 25983 MS4A12 0 . GRCh38 11 60497349 60497349 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.31G>A p.Glu11Lys p.E11K ENST00000016913 2/7 196 180 16 86 86 0 strelka-varscan-mutect MS4A12,missense_variant,p.Glu11Lys,ENST00000016913,NM_017716.2;MS4A12,missense_variant,p.Glu11Lys,ENST00000537076,NM_001164470.1;MS4A12,missense_variant,p.Glu11Lys,ENST00000530007,;MS4A12,missense_variant,p.Glu11Lys,ENST00000526784,;MS4A12,non_coding_transcript_exon_variant,,ENST00000525951,; A ENST00000016913 Transcript missense_variant 88/1167 31/804 11/267 E/K Gaa/Aaa 1 1 MS4A12 HGNC HGNC:13370 protein_coding YES CCDS7988.1 ENSP00000016913 Q9NXJ0 UPI000006D9F8 NM_017716.2 tolerated(1) 2/7 hmmpanther:PTHR23320,hmmpanther:PTHR23320:SF72 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 60497349 60497349 G A 1 0 0 0 0 1 0 0 0 9833 1291 45 3 3 MS4A12 11 60497349 Missense_Mutation SNP G C3N-01823_T 3188359 60497349 74589273 287 25984 TMEM132A 0 . GRCh38 11 60927364 60927364 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.261G>T p.Trp87Cys p.W87C ENST00000005286 2/11 265 236 29 169 169 0 strelka-varscan-mutect TMEM132A,missense_variant,p.Trp87Cys,ENST00000005286,NM_017870.3;TMEM132A,missense_variant,p.Trp87Cys,ENST00000453848,NM_178031.2;TMEM132A,5_prime_UTR_variant,,ENST00000544065,;TMEM109,downstream_gene_variant,,ENST00000227525,NM_024092.2;TMEM109,downstream_gene_variant,,ENST00000536171,;TMEM132A,upstream_gene_variant,,ENST00000536409,;RP11-881M11.4,upstream_gene_variant,,ENST00000543907,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000540276,;TMEM132A,downstream_gene_variant,,ENST00000543732,;TMEM109,downstream_gene_variant,,ENST00000540280,;TMEM132A,downstream_gene_variant,,ENST00000537110,;TMEM132A,downstream_gene_variant,,ENST00000537065,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000544098,;TMEM132A,non_coding_transcript_exon_variant,,ENST00000534983,; T ENST00000005286 Transcript missense_variant 414/3480 261/3075 87/1024 W/C tgG/tgT 1 1 TMEM132A HGNC HGNC:31092 protein_coding YES CCDS7997.1 ENSP00000005286 Q24JP5 UPI0000190977 NM_017870.3 deleterious(0.03) 2/11 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF9,Pfam_domain:PF15705 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 60927364 60927364 G T 1 0 0 0 0 1 0 0 0 16489 1212 42 2 2 TMEM132A 11 60927364 Missense_Mutation SNP G C3N-01823_T 430015 60927364 74159258 288 25985 CD5 0 . GRCh38 11 61121737 61121737 + Missense_Mutation SNP G G C rs369071318 C3N-01823_T C3N-01823_N G G c.932G>C p.Arg311Pro p.R311P ENST00000347785 6/11 96 90 6 57 57 0 strelka-mutect CD5,missense_variant,p.Arg311Pro,ENST00000347785,NM_014207.3;CD5,downstream_gene_variant,,ENST00000544014,; C ENST00000347785 Transcript missense_variant 1098/3221 932/1488 311/495 R/P cGg/cCg rs369071318 1 1 CD5 HGNC HGNC:1685 protein_coding YES CCDS8000.1 ENSP00000342681 P06127 UPI000013D472 NM_014207.3 deleterious(0.02) 6/11 Gene3D:3.10.250.10,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF306,SMART_domains:SM00202,Superfamily_domains:SSF56487 MODERATE 1 SNV 1 1 PASS rs369071318 . 0 202 7 0 0 0 0 0 -12.40254 0.999997 1 1 1 0 C 3 2 83 61121737 61121737 G C 1 0 0 0 0 1 0 0 0 2725 1116 39 4 4 CD5 11 61121737 Missense_Mutation SNP G C3N-01823_T 194373 61121737 73964885 289 25986 AHNAK 0 . GRCh38 11 62526689 62526689 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.7728C>A p.= p.A2576A ENST00000378024 5/5 439 362 77 230 230 0 strelka-varscan-mutect AHNAK,synonymous_variant,p.=,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; T ENST00000378024 Transcript synonymous_variant 8003/18787 7728/17673 2576/5890 A gcC/gcA 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 62526689 62526689 G T 1 0 0 0 0 0 0 0 1 491 1219 43 2 2 AHNAK 11 62526689 Silent SNP G C3N-01823_T 1404952 62526689 72559933 290 25987 SLC22A24 0 . GRCh38 11 63119076 63119076 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.666A>C p.Leu222Phe p.L222F ENST00000612278 4/10 158 147 11 82 82 0 strelka-varscan-mutect SLC22A24,missense_variant,p.Leu222Phe,ENST00000612278,NM_001136506.2;SLC22A24,missense_variant,p.Leu222Phe,ENST00000417740,;SLC22A24,missense_variant,p.Leu222Phe,ENST00000326192,NM_173586.2;RPL29P22,upstream_gene_variant,,ENST00000498718,; G ENST00000612278 Transcript missense_variant 1108/2101 666/1659 222/552 L/F ttA/ttC 1 -1 SLC22A24 HGNC HGNC:28542 protein_coding YES CCDS73308.1 ENSP00000480336 A0A087WWM3 UPI000004DAF7 NM_001136506.2 tolerated(0.12) 4/10 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50850,hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF208,Pfam_domain:PF00083,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.88734 1 1 1 1 0 G 3 3 83 63119076 63119076 T G 1 0 0 0 0 1 0 0 0 14718 1536 53 5 5 SLC22A24 11 63119076 Missense_Mutation SNP T C3N-01823_T 592387 63119076 71967546 291 25988 CDC42BPG 0 . GRCh38 11 64831704 64831704 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.3105G>A p.= p.L1035L ENST00000342711 28/37 167 155 12 83 83 0 strelka-varscan-mutect CDC42BPG,synonymous_variant,p.=,ENST00000342711,NM_017525.2;CDC42BPG,non_coding_transcript_exon_variant,,ENST00000491280,;CDC42BPG,downstream_gene_variant,,ENST00000468512,;CDC42BPG,downstream_gene_variant,,ENST00000480767,; T ENST00000342711 Transcript synonymous_variant 3105/5742 3105/4656 1035/1551 L ctG/ctA 1 -1 CDC42BPG HGNC HGNC:29829 protein_coding YES CCDS31601.1 ENSP00000345133 Q6DT37 UPI000047C9E2 NM_017525.2 28/37 PROSITE_profiles:PS50003,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF22,Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99397 1 1 1 1 0 T 2 4 83 64831704 64831704 C T 1 0 0 0 0 0 0 0 1 2777 581 21 3 3 CDC42BPG 11 64831704 Silent SNP C C3N-01823_T 1712628 64831704 70254918 292 25989 MRPL21 0 . GRCh38 11 68891343 68891343 + Silent SNP C C A rs753260565 C3N-01823_T C3N-01823_N C C c.606G>T p.= p.P202P ENST00000362034 7/7 298 259 39 235 235 0 strelka-varscan-mutect MRPL21,synonymous_variant,p.=,ENST00000362034,NM_181514.1;MRPL21,synonymous_variant,p.=,ENST00000450904,NM_181515.1;MRPL21,downstream_gene_variant,,ENST00000567045,;MRPL21,3_prime_UTR_variant,,ENST00000565125,;MRPL21,3_prime_UTR_variant,,ENST00000541279,;MRPL21,downstream_gene_variant,,ENST00000544567,;MRPL21,downstream_gene_variant,,ENST00000541265,; A ENST00000362034 Transcript synonymous_variant 616/683 606/618 202/205 P ccG/ccT rs753260565 1 -1 MRPL21 HGNC HGNC:14479 protein_coding YES CCDS8186.1 ENSP00000354580 Q7Z2W9 UPI00001A95D2 NM_181514.1 7/7 hmmpanther:PTHR21349,hmmpanther:PTHR21349:SF0 LOW 1 SNV 1 1 PASS rs753260565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 68891343 68891343 C A 1 0 0 0 0 0 0 0 1 9762 523 19 1 1 MRPL21 11 68891343 Silent SNP C C3N-01823_T 4059639 68891343 66195279 293 25990 GRM5 0 . GRCh38 11 88849907 88849907 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.910A>T p.Ser304Cys p.S304C ENST00000305447 2/9 260 222 38 141 141 0 strelka-varscan-mutect GRM5,missense_variant,p.Ser304Cys,ENST00000455756,NM_000842.4;GRM5,missense_variant,p.Ser304Cys,ENST00000305447,NM_001143831.2;GRM5,missense_variant,p.Ser304Cys,ENST00000305432,; A ENST00000305447 Transcript missense_variant,splice_region_variant 1060/4571 910/3639 304/1212 S/C Agt/Tgt 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 deleterious(0) 2/9 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 88849907 88849907 T A 1 0 0 0 0 1 0 0 0 6682 1594 55 4 4 GRM5 11 88849907 Missense_Mutation SNP T C3N-01823_T 19958564 88849907 46236715 294 25991 NOX4 0 . GRCh38 11 89373431 89373431 + Splice_Site SNP C C A rs201165492 C3N-01823_T C3N-01823_N C C c.1135+1G>T p.X379_splice ENST00000263317 104 87 17 127 126 1 strelka-varscan-mutect NOX4,splice_donor_variant,,ENST00000424319,NM_001291926.1;NOX4,splice_donor_variant,,ENST00000343727,NM_001291927.1;NOX4,splice_donor_variant,,ENST00000263317,NM_016931.4;NOX4,splice_donor_variant,,ENST00000527956,NM_001143837.1;NOX4,splice_donor_variant,,ENST00000534731,NM_001143836.2;NOX4,splice_donor_variant,,ENST00000532825,NM_001300995.1;NOX4,splice_donor_variant,,ENST00000528341,NM_001291929.1;NOX4,splice_donor_variant,,ENST00000527626,;NOX4,splice_donor_variant,,ENST00000375979,;NOX4,splice_donor_variant,,ENST00000531342,;NOX4,intron_variant,,ENST00000525196,;NOX4,splice_donor_variant,,ENST00000529343,; A ENST00000263317 Transcript splice_donor_variant -/2388 1135/1737 379/578 rs201165492 1 -1 NOX4 HGNC HGNC:7891 protein_coding YES CCDS8285.1 ENSP00000263317 Q9NPH5 UPI000045655B NM_016931.4 12/17 HIGH 1 SNV 1 1 PASS rs201165492 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 83 89373431 89373431 C A 1 0 0 0 0 0 0 1 0 10604 521 18 2 2 NOX4 11 89373431 Splice_Site SNP C C3N-01823_T 523524 89373431 45713191 295 25992 MED17 0 . GRCh38 11 93809746 93809746 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1614G>T p.Gln538His p.Q538H ENST00000251871 11/12 704 599 105 447 446 1 strelka-varscan-mutect MED17,missense_variant,p.Gln538His,ENST00000251871,NM_004268.4;MED17,non_coding_transcript_exon_variant,,ENST00000533367,;MED17,non_coding_transcript_exon_variant,,ENST00000525613,;MED17,non_coding_transcript_exon_variant,,ENST00000529626,;MED17,non_coding_transcript_exon_variant,,ENST00000531920,;MED17,intron_variant,,ENST00000533133,; T ENST00000251871 Transcript missense_variant 1901/4874 1614/1956 538/651 Q/H caG/caT 1 1 MED17 HGNC HGNC:2375 protein_coding YES CCDS8295.1 ENSP00000251871 Q9NVC6 UPI000013CD1D NM_004268.4 tolerated(0.13) 11/12 hmmpanther:PTHR13114 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 93809746 93809746 G T 1 0 0 0 0 1 0 0 0 9374 962 34 2 2 MED17 11 93809746 Missense_Mutation SNP G C3N-01823_T 4436315 93809746 41276876 296 25993 IZUMO1R 0 . GRCh38 11 94307484 94307484 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.545C>A p.Pro182Gln p.P182Q ENST00000328458 4/4 410 339 71 250 249 1 strelka-varscan-mutect IZUMO1R,missense_variant,p.Pro175Gln,ENST00000440961,;IZUMO1R,missense_variant,p.Pro182Gln,ENST00000328458,NM_001199206.1; A ENST00000328458 Transcript missense_variant 590/798 545/753 182/250 P/Q cCa/cAa 1 1 IZUMO1R HGNC HGNC:32565 protein_coding YES ENSP00000332963 J3KNP7 UPI00003D6FE9 NM_001199206.1 4/4 Pfam_domain:PF03024,hmmpanther:PTHR10517,hmmpanther:PTHR10517:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 94307484 94307484 C A 1 0 0 0 0 1 0 0 0 7840 594 21 2 2 IZUMO1R 11 94307484 Missense_Mutation SNP C C3N-01823_T 497738 94307484 40779138 297 25994 IZUMO1R 0 . GRCh38 11 94307609 94307609 + Missense_Mutation SNP C C A rs373997875 C3N-01823_T C3N-01823_N C C c.670C>A p.Arg224Ser p.R224S ENST00000328458 4/4 445 376 69 251 251 0 strelka-varscan-mutect IZUMO1R,missense_variant,p.Arg217Ser,ENST00000440961,;IZUMO1R,missense_variant,p.Arg224Ser,ENST00000328458,NM_001199206.1; A ENST00000328458 Transcript missense_variant 715/798 670/753 224/250 R/S Cgc/Agc rs373997875 1 1 IZUMO1R HGNC HGNC:32565 protein_coding YES ENSP00000332963 J3KNP7 UPI00003D6FE9 NM_001199206.1 4/4 hmmpanther:PTHR10517,hmmpanther:PTHR10517:SF10 MODERATE 1 SNV 5 1 PASS rs373997875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 94307609 94307609 C A 1 0 0 0 0 1 0 0 0 7840 652 23 1 1 IZUMO1R 11 94307609 Missense_Mutation SNP C C3N-01823_T 125 94307609 40779013 298 25995 CNTN5 0 . GRCh38 11 99845173 99845173 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.488G>T p.Ser163Ile p.S163I ENST00000524871 6/25 218 177 41 166 166 0 strelka-varscan-mutect CNTN5,missense_variant,p.Ser163Ile,ENST00000524871,NM_014361.3;CNTN5,missense_variant,p.Ser147Ile,ENST00000279463,;CNTN5,missense_variant,p.Ser85Ile,ENST00000619298,;CNTN5,missense_variant,p.Ser163Ile,ENST00000527185,NM_001243271.1;CNTN5,missense_variant,p.Ser163Ile,ENST00000528682,NM_001243270.1;CNTN5,missense_variant,p.Ser89Ile,ENST00000418526,NM_175566.2;CNTN5,non_coding_transcript_exon_variant,,ENST00000528727,; T ENST00000524871 Transcript missense_variant 778/6258 488/3303 163/1100 S/I aGt/aTt 1 1 CNTN5 HGNC HGNC:2175 protein_coding YES CCDS53696.1 ENSP00000435637 O94779 UPI000006DAB0 NM_014361.3 deleterious(0.03) 6/25 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF51,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 99845173 99845173 G T 1 0 0 0 0 1 0 0 0 3425 1029 36 2 2 CNTN5 11 99845173 Missense_Mutation SNP G C3N-01823_T 5537564 99845173 35241449 299 25996 PGR 0 . GRCh38 11 101128784 101128784 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.287C>G p.Ala96Gly p.A96G ENST00000325455 1/8 642 559 83 409 409 0 strelka-varscan-mutect PGR,missense_variant,p.Ala96Gly,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,missense_variant,p.Ala96Gly,ENST00000619228,;PGR,missense_variant,p.Ala96Gly,ENST00000617858,;PGR,missense_variant,p.Ala96Gly,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,NM_001271162.1;PGR,upstream_gene_variant,,ENST00000632634,;RP11-788M5.4,upstream_gene_variant,,ENST00000632820,;PGR,missense_variant,p.Ala96Gly,ENST00000534780,;PGR,missense_variant,p.Ala96Gly,ENST00000528960,;PGR,missense_variant,p.Ala96Gly,ENST00000526300,; C ENST00000325455 Transcript missense_variant 1741/13748 287/2802 96/933 A/G gCt/gGt 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 tolerated_low_confidence(0.14) 1/8 hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Pfam_domain:PF02161 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 101128784 101128784 G C 1 0 0 0 0 1 0 0 0 11894 971 34 4 4 PGR 11 101128784 Missense_Mutation SNP G C3N-01823_T 1283611 101128784 33957838 300 25997 OR6X1 0 . GRCh38 11 123754378 123754378 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.141G>A p.= p.V47V ENST00000327930 1/1 180 157 23 149 149 0 strelka-varscan-mutect OR6X1,synonymous_variant,p.=,ENST00000327930,NM_001005188.1; T ENST00000327930 Transcript synonymous_variant 168/1058 141/939 47/312 V gtG/gtA 1 -1 OR6X1 HGNC HGNC:14737 protein_coding YES CCDS31695.1 ENSP00000333724 Q8NH79 A0A126GVM0 UPI000004B1D5 NM_001005188.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF30,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 123754378 123754378 C T 1 0 0 0 0 0 0 0 1 11282 465 17 3 3 OR6X1 11 123754378 Silent SNP C C3N-01823_T 22625594 123754378 11332244 301 25998 OR8B4 0 . GRCh38 11 124424312 124424312 + Missense_Mutation SNP G G C C3N-01823_T C3N-01823_N G G c.560C>G p.Ser187Cys p.S187C ENST00000356130 1/1 342 321 21 253 253 0 strelka-varscan-mutect OR8B4,missense_variant,p.Ser187Cys,ENST00000356130,NM_001005196.1; C ENST00000356130 Transcript missense_variant 582/990 560/930 187/309 S/C tCc/tGc COSM231267 1 -1 OR8B4 HGNC HGNC:8473 protein_coding YES CCDS31710.1 ENSP00000348449 Q96RC9 UPI00000015B0 NM_001005196.1 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF208,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 124424312 124424312 G C 1 0 0 0 0 1 0 0 0 11299 1174 41 4 4 OR8B4 11 124424312 Missense_Mutation SNP G C3N-01823_T 669934 124424312 10662310 302 25999 WNK1 0 . GRCh38 12 896329 896329 + Missense_Mutation SNP G G T rs774379842 C3N-01823_T C3N-01823_N G G c.6598G>T p.Val2200Leu p.V2200L ENST00000340908 24/28 782 662 120 444 444 0 strelka-varscan-mutect WNK1,missense_variant,p.Val2361Leu,ENST00000530271,;WNK1,missense_variant,p.Val2208Leu,ENST00000537687,NM_001184985.1;WNK1,missense_variant,p.Val2200Leu,ENST00000340908,NM_213655.4;WNK1,missense_variant,p.Val1948Leu,ENST00000315939,NM_018979.3;WNK1,missense_variant,p.Val1700Leu,ENST00000535572,NM_014823.2;WNK1,upstream_gene_variant,,ENST00000544559,;WNK1,upstream_gene_variant,,ENST00000543065,;WNK1,upstream_gene_variant,,ENST00000542424,;WNK1,upstream_gene_variant,,ENST00000537603,; T ENST00000340908 Transcript missense_variant 7241/11208 6598/7905 2200/2634 V/L Gtg/Ttg rs774379842 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 deleterious(0) 24/28 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF46 MODERATE 1 SNV 5 1 PASS rs774379842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 896329 896329 G T 1 0 0 0 0 1 0 0 0 17933 1261 44 2 2 WNK1 12 896329 Missense_Mutation SNP G C3N-01823_T 896329 132378980 303 26000 KCNA5 0 . GRCh38 12 5044656 5044656 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.509C>A p.Pro170His p.P170H ENST00000252321 1/1 519 399 120 259 259 0 strelka-varscan-mutect KCNA5,missense_variant,p.Pro170His,ENST00000252321,NM_002234.3; A ENST00000252321 Transcript missense_variant 668/2800 509/1842 170/613 P/H cCc/cAc 1 1 KCNA5 HGNC HGNC:6224 protein_coding YES CCDS8536.1 ENSP00000252321 P22460 UPI000013CD56 NM_002234.3 deleterious(0) 1/1 Gene3D:3.30.710.10,Pfam_domain:PF02214,Prints_domain:PR00169,Prints_domain:PR01491,Prints_domain:PR01496,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF25,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 5044656 5044656 C A 1 0 0 0 0 1 0 0 0 7922 623 22 2 2 KCNA5 12 5044656 Missense_Mutation SNP C C3N-01823_T 4148327 5044656 128230653 304 26001 KLRG1 0 . GRCh38 12 9009053 9009053 + Nonsense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.436G>T p.Gly146Ter p.G146* ENST00000356986 4/5 281 242 39 176 175 1 strelka-varscan-mutect KLRG1,stop_gained,p.Gly146Ter,ENST00000266551,;KLRG1,stop_gained,p.Gly146Ter,ENST00000356986,NM_005810.3;KLRG1,stop_gained,p.Gly67Ter,ENST00000539240,;KLRG1,stop_gained,p.Gly67Ter,ENST00000543895,;KLRG1,non_coding_transcript_exon_variant,,ENST00000538029,;KLRG1,non_coding_transcript_exon_variant,,ENST00000544226,; T ENST00000356986 Transcript stop_gained 531/1206 436/570 146/189 G/* Gga/Tga COSM5470101,COSM5470102 1 1 KLRG1 HGNC HGNC:6380 protein_coding YES CCDS8599.1 ENSP00000349477 Q96E93 UPI000006D8A7 NM_005810.3 4/5 PROSITE_profiles:PS50041,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF166,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 83 9009053 9009053 G T 1 0 0 0 0 0 1 0 0 8291 1349 47 2 2 KLRG1 12 9009053 Nonsense_Mutation SNP G C3N-01823_T 3964397 9009053 124266256 305 26002 KLRC3 0 . GRCh38 12 10420464 10420464 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.87C>A p.Ser29Arg p.S29R ENST00000381903 1/6 184 158 26 129 129 0 strelka-varscan-mutect KLRC3,missense_variant,p.Ser29Arg,ENST00000396439,NM_002261.2;KLRC3,missense_variant,p.Ser29Arg,ENST00000381903,NM_007333.2;RP11-277P12.6,intron_variant,,ENST00000539033,; T ENST00000381903 Transcript missense_variant 87/798 87/774 29/257 S/R agC/agA 1 -1 KLRC3 HGNC HGNC:6376 protein_coding YES CCDS31744.1 ENSP00000371328 Q07444 UPI00001AF2AC NM_007333.2 tolerated(0.06) 1/6 hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF174 MODERATE SNV 2 1 PASS rs775775420 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 10420464 10420464 G T 1 0 0 0 0 1 0 0 0 8286 962 34 2 2 KLRC3 12 10420464 Missense_Mutation SNP G C3N-01823_T 1411411 10420464 122854845 306 26003 PIK3C2G 0 . GRCh38 12 18291003 18291003 + Missense_Mutation SNP A A G novel C3N-01823_T C3N-01823_N A A c.910A>G p.Met304Val p.M304V ENST00000538779 4/33 130 80 50 84 84 0 strelka-varscan-mutect PIK3C2G,missense_variant,p.Met304Val,ENST00000538779,NM_001288772.1,NM_001288774.1;PIK3C2G,missense_variant,p.Met304Val,ENST00000433979,NM_004570.5;PIK3C2G,missense_variant,p.Met304Val,ENST00000266497,;PIK3C2G,missense_variant,p.Met304Val,ENST00000535651,;PIK3C2G,missense_variant,p.Met96Val,ENST00000536967,;RERGL,intron_variant,,ENST00000541632,;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,; G ENST00000538779 Transcript missense_variant 1026/4963 910/4461 304/1486 M/V Atg/Gtg 1 1 PIK3C2G HGNC HGNC:8973 protein_coding YES CCDS73452.1 ENSP00000445381 F5H369 UPI00020655D2 NM_001288772.1,NM_001288774.1 deleterious(0.03) 4/33 PROSITE_profiles:PS51546,hmmpanther:PTHR10048:SF29,hmmpanther:PTHR10048,Pfam_domain:PF00794,Gene3D:3.10.20.90,Superfamily_domains:SSF54236 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 18291003 18291003 A G 1 0 0 0 0 1 0 0 0 12006 449 16 5 5 PIK3C2G 12 18291003 Missense_Mutation SNP A C3N-01823_T 7870539 18291003 114984306 307 26004 OVCH1 0 . GRCh38 12 29471909 29471909 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.1749C>A p.= p.P583P ENST00000318184 16/28 427 371 56 236 236 0 strelka-varscan-mutect OVCH1,synonymous_variant,p.=,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; T ENST00000318184 Transcript synonymous_variant 1749/3405 1749/3405 583/1134 P ccC/ccA 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 16/28 Gene3D:2.40.10.10,Pfam_domain:PF00089,PROSITE_profiles:PS50240,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 2 1 PASS rs929481308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 29471909 29471909 G T 1 0 0 0 0 0 0 0 1 11393 1219 43 2 2 OVCH1 12 29471909 Silent SNP G C3N-01823_T 11180906 29471909 103803400 308 26005 DENND5B 0 . GRCh38 12 31451992 31451992 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.1682A>C p.Gln561Pro p.Q561P ENST00000536562 7/23 387 341 46 158 158 0 strelka-varscan-mutect DENND5B,missense_variant,p.Gln526Pro,ENST00000389082,NM_144973.3;DENND5B,missense_variant,p.Gln561Pro,ENST00000536562,NM_001308339.1;DENND5B,missense_variant,p.Gln548Pro,ENST00000354285,;DENND5B,missense_variant,p.Gln478Pro,ENST00000546299,; G ENST00000536562 Transcript missense_variant 1833/4291 1682/3930 561/1309 Q/P cAg/cCg 1 -1 DENND5B HGNC HGNC:28338 protein_coding YES CCDS76542.1 ENSP00000444889 G3V1S3 UPI0000D621CB NM_001308339.1 tolerated(0.19) 7/23 PROSITE_profiles:PS50947,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF45,SMART_domains:SM00801 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 31451992 31451992 T G 1 0 0 0 0 1 0 0 0 4241 1580 55 5 5 DENND5B 12 31451992 Missense_Mutation SNP T C3N-01823_T 1980083 31451992 101823317 309 26006 PDZRN4 0 . GRCh38 12 41573658 41573658 + Missense_Mutation SNP G G T rs748727154 C3N-01823_T C3N-01823_N G G c.2879G>T p.Arg960Leu p.R960L ENST00000402685 10/10 416 210 206 117 117 0 strelka-varscan-mutect PDZRN4,missense_variant,p.Arg700Leu,ENST00000298919,;PDZRN4,missense_variant,p.Arg960Leu,ENST00000402685,NM_001164595.1;PDZRN4,missense_variant,p.Arg702Leu,ENST00000539469,NM_013377.3;PDZRN4,non_coding_transcript_exon_variant,,ENST00000548316,; T ENST00000402685 Transcript missense_variant 2887/3347 2879/3111 960/1036 R/L cGt/cTt rs748727154,COSM3398706,COSM3398707,COSM3398708 1 1 PDZRN4 HGNC HGNC:30552 protein_coding YES CCDS53777.1 ENSP00000384197 Q6ZMN7 UPI0000D621D0 NM_001164595.1 deleterious(0) 10/10 hmmpanther:PTHR15545,hmmpanther:PTHR15545:SF6,Low_complexity_(Seg):seg 0,1,1,1 MODERATE 1 SNV 2 0,1,1,1 1 PASS rs748727154 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 41573658 41573658 G T 1 0 0 0 0 1 0 0 0 11798 1145 40 1 1 PDZRN4 12 41573658 Missense_Mutation SNP G C3N-01823_T 10121666 41573658 91701651 310 26007 NELL2 0 . GRCh38 12 44508948 44508948 + Missense_Mutation SNP G G C rs770135751 C3N-01823_T C3N-01823_N G G c.2587C>G p.Leu863Val p.L863V ENST00000437801 21/21 402 348 54 183 183 0 strelka-varscan-mutect NELL2,missense_variant,p.Leu813Val,ENST00000429094,NM_001145108.1;NELL2,missense_variant,p.Leu863Val,ENST00000437801,NM_001145107.1;NELL2,missense_variant,p.Leu812Val,ENST00000395487,NM_001145109.1;NELL2,missense_variant,p.Leu813Val,ENST00000452445,NM_006159.2;NELL2,missense_variant,p.Leu765Val,ENST00000551601,;NELL2,missense_variant,p.Leu812Val,ENST00000549027,;NELL2,missense_variant,p.Leu836Val,ENST00000333837,NM_001145110.1; C ENST00000437801 Transcript missense_variant 2959/3279 2587/2601 863/866 L/V Ctt/Gtt rs770135751 1 -1 NELL2 HGNC HGNC:7751 protein_coding YES CCDS44863.1 ENSP00000416341 Q99435 UPI000191537D NM_001145107.1 deleterious(0.05) 21/21 hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF0,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 2 1 PASS rs770135751 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 44508948 44508948 G C 1 0 0 0 0 1 0 0 0 10365 1000 35 4 4 NELL2 12 44508948 Missense_Mutation SNP G C3N-01823_T 2935290 44508948 88766361 311 26008 KMT2D 0 . GRCh38 12 49037815 49037815 + Nonsense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.9541G>T p.Glu3181Ter p.E3181* ENST00000301067 34/54 385 333 52 182 182 0 strelka-varscan-mutect KMT2D,stop_gained,p.Glu3181Ter,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; A ENST00000301067 Transcript stop_gained 9541/19419 9541/16614 3181/5537 E/* Gag/Tag 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 34/54 HIGH 1 SNV 5 1 PASS rs797045672 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 49037815 49037815 C A 1 0 0 0 0 0 1 0 0 8298 835 29 2 2 KMT2D 12 49037815 Nonsense_Mutation SNP C C3N-01823_T 4528867 49037815 84237494 312 26009 SLC11A2 0 . GRCh38 12 50988397 50988397 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.1701G>T p.= p.L567L ENST00000394904 16/16 443 370 73 228 228 0 strelka-varscan-mutect SLC11A2,synonymous_variant,p.=,ENST00000394904,NM_001174125.1;SLC11A2,synonymous_variant,p.=,ENST00000262052,NM_000617.2,NM_001174128.1;SLC11A2,synonymous_variant,p.=,ENST00000262051,NM_001174126.1,NM_001174127.1;SLC11A2,synonymous_variant,p.=,ENST00000547198,;SLC11A2,synonymous_variant,p.=,ENST00000541174,NM_001174129.1;SLC11A2,synonymous_variant,p.=,ENST00000547688,;SLC11A2,synonymous_variant,p.=,ENST00000545993,NM_001174130.1;SLC11A2,synonymous_variant,p.=,ENST00000546743,;SLC11A2,synonymous_variant,p.=,ENST00000546636,;SLC11A2,synonymous_variant,p.=,ENST00000551215,;SLC11A2,non_coding_transcript_exon_variant,,ENST00000550782,;SLC11A2,downstream_gene_variant,,ENST00000551231,;SLC11A2,downstream_gene_variant,,ENST00000548554,; A ENST00000394904 Transcript synonymous_variant 1751/4156 1701/1773 567/590 L ctG/ctT 1 -1 SLC11A2 HGNC HGNC:10908 protein_coding YES CCDS53793.1 ENSP00000378364 P49281 UPI00001FC234 NM_001174125.1 16/16 hmmpanther:PTHR11706:SF40,hmmpanther:PTHR11706 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 50988397 50988397 C A 1 0 0 0 0 0 0 0 1 14646 581 21 2 2 SLC11A2 12 50988397 Silent SNP C C3N-01823_T 1950582 50988397 82286912 313 26010 KRT72 0 . GRCh38 12 52591491 52591491 + Silent SNP G G T rs778544219 C3N-01823_T C3N-01823_N G G c.936C>A p.= p.A312A ENST00000293745 5/9 123 105 18 43 43 0 strelka-varscan-mutect KRT72,synonymous_variant,p.=,ENST00000293745,NM_080747.2;KRT72,synonymous_variant,p.=,ENST00000537672,NM_001146225.1;KRT72,synonymous_variant,p.=,ENST00000354310,NM_001146226.1;KRT72,3_prime_UTR_variant,,ENST00000550829,; T ENST00000293745 Transcript synonymous_variant 1022/2015 936/1536 312/511 A gcC/gcA rs778544219 1 -1 KRT72 HGNC HGNC:28932 protein_coding YES CCDS8833.1 ENSP00000293745 Q14CN4 UPI0000055AC8 NM_080747.2 5/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF86,SMART_domains:SM01391 LOW 1 SNV 1 1 PASS rs778544219 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 52591491 52591491 G T 1 0 0 0 0 0 0 0 1 8367 1103 39 1 1 KRT72 12 52591491 Silent SNP G C3N-01823_T 1603094 52591491 80683818 314 26011 INHBE 0 . GRCh38 12 57456682 57456682 + Missense_Mutation SNP C C T C3N-01823_T C3N-01823_N C C c.887C>T p.Ser296Phe p.S296F ENST00000266646 2/2 366 335 31 154 154 0 strelka-varscan-mutect INHBE,missense_variant,p.Ser296Phe,ENST00000266646,NM_031479.3;INHBE,missense_variant,p.Ser241Phe,ENST00000547970,;GLI1,upstream_gene_variant,,ENST00000228682,NM_005269.2;GLI1,upstream_gene_variant,,ENST00000546141,NM_001167609.1;GLI1,upstream_gene_variant,,ENST00000543426,NM_001160045.1;GLI1,upstream_gene_variant,,ENST00000532291,;GLI1,upstream_gene_variant,,ENST00000528432,;INHBE,non_coding_transcript_exon_variant,,ENST00000551553,;INHBE,downstream_gene_variant,,ENST00000553033,;GLI1,upstream_gene_variant,,ENST00000530789,; T ENST00000266646 Transcript missense_variant 1103/2429 887/1053 296/350 S/F tCt/tTt COSM344196 1 1 INHBE HGNC HGNC:24029 protein_coding YES CCDS8939.1 ENSP00000266646 P58166 UPI000012D42C NM_031479.3 deleterious(0) 2/2 PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF6,hmmpanther:PTHR11848,Gene3D:2.10.90.10,Pfam_domain:PF00019,SMART_domains:SM00204,Superfamily_domains:SSF57501 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 57456682 57456682 C T 1 0 0 0 0 1 0 0 0 7646 913 32 3 3 INHBE 12 57456682 Missense_Mutation SNP C C3N-01823_T 4865191 57456682 75818627 315 26012 METTL21B 0 . GRCh38 12 57772895 57772895 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.171G>T p.Trp57Cys p.W57C ENST00000300209 1/3 163 135 28 72 72 0 strelka-varscan-mutect METTL21B,missense_variant,p.Trp57Cys,ENST00000333012,NM_206914.1;METTL21B,missense_variant,p.Trp57Cys,ENST00000300209,NM_015433.2;METTL21B,intron_variant,,ENST00000551420,;METTL21B,intron_variant,,ENST00000548256,;METTL1,upstream_gene_variant,,ENST00000324871,NM_005371.5;METTL1,upstream_gene_variant,,ENST00000257848,NM_023033.3;METTL1,upstream_gene_variant,,ENST00000547653,;CYP27B1,upstream_gene_variant,,ENST00000546609,;RP11-571M6.15,upstream_gene_variant,,ENST00000546504,;METTL1,upstream_gene_variant,,ENST00000548504,;METTL21B,non_coding_transcript_exon_variant,,ENST00000552307,;METTL1,upstream_gene_variant,,ENST00000548681,;RP11-571M6.15,upstream_gene_variant,,ENST00000553083,;METTL1,upstream_gene_variant,,ENST00000553125,;RP11-571M6.15,upstream_gene_variant,,ENST00000471530,;METTL1,upstream_gene_variant,,ENST00000549773,;METTL1,upstream_gene_variant,,ENST00000551117,; T ENST00000300209 Transcript missense_variant 296/2563 171/681 57/226 W/C tgG/tgT 1 1 METTL21B HGNC HGNC:24936 protein_coding YES CCDS8957.1 ENSP00000300209 Q96AZ1 UPI000006CEB5 NM_015433.2 deleterious(0) 1/3 Gene3D:3.40.50.150,Pfam_domain:PF10294,hmmpanther:PTHR14614,hmmpanther:PTHR14614:SF5,Superfamily_domains:SSF53335 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 57772895 57772895 G T 1 0 0 0 0 1 0 0 0 9446 1241 43 2 2 METTL21B 12 57772895 Missense_Mutation SNP G C3N-01823_T 316213 57772895 75502414 316 26013 SRGAP1 0 . GRCh38 12 64108996 64108996 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.1878G>T p.= p.S626S ENST00000355086 16/22 134 108 26 68 67 1 strelka-varscan-mutect SRGAP1,synonymous_variant,p.=,ENST00000355086,NM_020762.2;SRGAP1,synonymous_variant,p.=,ENST00000631006,;SRGAP1,synonymous_variant,p.=,ENST00000543397,;RP11-196H14.4,non_coding_transcript_exon_variant,,ENST00000535806,;SRGAP1,upstream_gene_variant,,ENST00000537585,; T ENST00000355086 Transcript synonymous_variant 2402/23331 1878/3258 626/1085 S tcG/tcT 1 1 SRGAP1 HGNC HGNC:17382 protein_coding YES CCDS8967.1 ENSP00000347198 Q7Z6B7 UPI00001A9CB9 NM_020762.2 16/22 PROSITE_profiles:PS50238,hmmpanther:PTHR14166:SF15,hmmpanther:PTHR14166,Gene3D:1.10.555.10,Pfam_domain:PF00620,SMART_domains:SM00324,Superfamily_domains:SSF48350 LOW 1 SNV 1 1 PASS rs1199429320 . 0 204 4 2 0 0 0 0 -20 0.9999898 1 1 1 0 T 2 4 83 64108996 64108996 G T 1 0 0 0 0 0 0 0 1 15504 1103 39 1 1 SRGAP1 12 64108996 Silent SNP G C3N-01823_T 6336101 64108996 69166313 317 26014 RAB3IP 0 . GRCh38 12 69755582 69755582 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.222A>T p.Leu74Phe p.L74F ENST00000550536 2/11 469 335 134 275 275 0 strelka-varscan-mutect RAB3IP,missense_variant,p.Leu74Phe,ENST00000550536,NM_175623.3;RAB3IP,missense_variant,p.Leu58Phe,ENST00000247833,NM_022456.4;RAB3IP,missense_variant,p.Leu58Phe,ENST00000378815,;RAB3IP,missense_variant,p.Leu74Phe,ENST00000362025,NM_175625.3;RAB3IP,missense_variant,p.Leu58Phe,ENST00000483530,NM_175624.3;RAB3IP,missense_variant,p.Leu58Phe,ENST00000549760,;RAB3IP,upstream_gene_variant,,ENST00000550647,;RAB3IP,upstream_gene_variant,,ENST00000547055,;RAB3IP,missense_variant,p.Leu74Phe,ENST00000378809,;RAB3IP,missense_variant,p.Leu74Phe,ENST00000552199,;RAB3IP,missense_variant,p.Leu58Phe,ENST00000417413,;RAB3IP,3_prime_UTR_variant,,ENST00000547591,; T ENST00000550536 Transcript missense_variant 679/9646 222/1431 74/476 L/F ttA/ttT 1 1 RAB3IP HGNC HGNC:16508 protein_coding YES CCDS8993.1 ENSP00000447300 Q96QF0 UPI000006EB02 NM_175623.3 deleterious_low_confidence(0) 2/11 hmmpanther:PTHR14430,hmmpanther:PTHR14430:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 69755582 69755582 A T 1 0 0 0 0 1 0 0 0 13097 417 15 4 4 RAB3IP 12 69755582 Missense_Mutation SNP A C3N-01823_T 5646586 69755582 63519727 318 26015 NAV3 0 . GRCh38 12 77831668 77831668 + Silent SNP C C A C3N-01823_T C3N-01823_N C C c.207C>A p.= p.P69P ENST00000397909 1/40 128 96 32 94 94 0 strelka-varscan-mutect NAV3,synonymous_variant,p.=,ENST00000397909,NM_001024383.1;NAV3,synonymous_variant,p.=,ENST00000536525,NM_014903.5;NAV3,synonymous_variant,p.=,ENST00000549464,;NAV3,intron_variant,,ENST00000550042,; A ENST00000397909 Transcript synonymous_variant 380/9821 207/7158 69/2385 P ccC/ccA COSM317664,COSM5657066 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 1/40 Superfamily_domains:SSF47576 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 77831668 77831668 C A 1 0 0 0 0 0 0 0 1 10194 610 22 2 2 NAV3 12 77831668 Silent SNP C C3N-01823_T 8076086 77831668 55443641 319 26016 OTOGL 0 . GRCh38 12 80222221 80222221 + Missense_Mutation SNP T T G rs778218262 C3N-01823_T C3N-01823_N T T c.438T>G p.Asp146Glu p.D146E ENST00000458043 6/58 176 163 13 131 131 0 strelka-varscan-mutect OTOGL,missense_variant,p.Asp146Glu,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Asp146Glu,ENST00000547103,; G ENST00000458043 Transcript missense_variant 444/8083 438/7035 146/2344 D/E gaT/gaG rs778218262 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 tolerated(1) 6/58 PROSITE_profiles:PS51233,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Pfam_domain:PF00094,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS rs778218262 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 80222221 80222221 T G 1 0 0 0 0 1 0 0 0 11371 1490 52 5 5 OTOGL 12 80222221 Missense_Mutation SNP T C3N-01823_T 2390553 80222221 53053088 320 26017 OTOGL 0 . GRCh38 12 80252180 80252180 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.1237G>A p.Asp413Asn p.D413N ENST00000458043 12/58 164 136 28 131 131 0 strelka-varscan-mutect OTOGL,missense_variant,p.Asp413Asn,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Asp413Asn,ENST00000547103,; A ENST00000458043 Transcript missense_variant 1243/8083 1237/7035 413/2344 D/N Gat/Aat 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 12/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999951 1 1 1 0 A 3 1 83 80252180 80252180 G A 1 0 0 0 0 1 0 0 0 11371 1290 45 3 3 OTOGL 12 80252180 Missense_Mutation SNP G C3N-01823_T 29959 80252180 53023129 321 26018 PWP1 0 . GRCh38 12 107692864 107692864 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.370A>T p.Asn124Tyr p.N124Y ENST00000412830 4/15 217 201 16 201 201 0 strelka-varscan-mutect PWP1,missense_variant,p.Asn124Tyr,ENST00000412830,NM_001317962.1,NM_007062.1;PWP1,missense_variant,p.Asn62Tyr,ENST00000541166,;PWP1,missense_variant,p.Asn62Tyr,ENST00000547995,;PWP1,missense_variant,p.Asn124Tyr,ENST00000552760,;PWP1,non_coding_transcript_exon_variant,,ENST00000547120,; T ENST00000412830 Transcript missense_variant 538/2621 370/1506 124/501 N/Y Aat/Tat 1 1 PWP1 HGNC HGNC:17015 protein_coding YES CCDS9114.1 ENSP00000387365 Q13610 A0A024RBH5 UPI0000132B9C NM_001317962.1,NM_007062.1 deleterious(0) 4/15 hmmpanther:PTHR14091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 107692864 107692864 A T 1 0 0 0 0 1 0 0 0 12997 362 13 4 4 PWP1 12 107692864 Missense_Mutation SNP A C3N-01823_T 27440684 107692864 25582445 322 26019 TBX5 0 . GRCh38 12 114403751 114403751 + Splice_Site SNP C C A novel C3N-01823_T C3N-01823_N C C c.147+1G>T p.X49_splice ENST00000310346 193 174 19 105 105 0 strelka-varscan-mutect TBX5,splice_donor_variant,,ENST00000310346,NM_000192.3;TBX5,splice_donor_variant,,ENST00000405440,NM_181486.2;TBX5,splice_donor_variant,,ENST00000526441,;TBX5,intron_variant,,ENST00000349716,NM_080717.2;TBX5-AS1,upstream_gene_variant,,ENST00000532697,;TBX5-AS1,upstream_gene_variant,,ENST00000531202,;TBX5-AS1,upstream_gene_variant,,ENST00000531024,;TBX5,splice_donor_variant,,ENST00000552726,; A ENST00000310346 Transcript splice_donor_variant -/3825 147/1557 49/518 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 2/8 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 83 114403751 114403751 C A 1 0 0 0 0 0 0 1 0 16065 521 18 2 2 TBX5 12 114403751 Splice_Site SNP C C3N-01823_T 6710887 114403751 18871558 323 26020 KSR2 0 . GRCh38 12 117761042 117761042 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.868G>T p.Gly290Trp p.G290W ENST00000425217 4/20 381 301 80 311 310 1 strelka-varscan-mutect KSR2,missense_variant,p.Gly319Trp,ENST00000339824,;KSR2,missense_variant,p.Gly290Trp,ENST00000425217,NM_173598.4; A ENST00000425217 Transcript missense_variant 923/17008 868/2766 290/921 G/W Ggg/Tgg 1 -1 KSR2 HGNC HGNC:18610 protein_coding YES CCDS61250.1 ENSP00000389715 E9PB13 UPI000164FA1C NM_173598.4 deleterious(0) 4/20 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 117761042 117761042 C A 1 0 0 0 0 1 0 0 0 8481 623 22 2 2 KSR2 12 117761042 Missense_Mutation SNP C C3N-01823_T 3357291 117761042 15514267 324 26021 DHX37 0 . GRCh38 12 124954178 124954178 + Silent SNP C C A C3N-01823_T C3N-01823_N C C c.2487G>T p.= p.L829L ENST00000308736 19/27 103 84 19 74 74 0 strelka-varscan-mutect DHX37,synonymous_variant,p.=,ENST00000308736,NM_032656.3;DHX37,synonymous_variant,p.=,ENST00000544745,;DHX37,non_coding_transcript_exon_variant,,ENST00000539298,;DHX37,upstream_gene_variant,,ENST00000542400,; A ENST00000308736 Transcript synonymous_variant 2586/4550 2487/3474 829/1157 L ctG/ctT COSM1511280 1 -1 DHX37 HGNC HGNC:17210 protein_coding YES CCDS9261.1 ENSP00000311135 Q8IY37 UPI00000742DC NM_032656.3 19/27 hmmpanther:PTHR18934:SF99,hmmpanther:PTHR18934,Pfam_domain:PF04408,SMART_domains:SM00847,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 124954178 124954178 C A 1 0 0 0 0 0 0 0 1 4314 813 29 2 2 DHX37 12 124954178 Silent SNP C C3N-01823_T 7193136 124954178 8321131 325 26022 BRCA2 0 . GRCh38 13 32332637 32332637 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.1159G>C p.Val387Leu p.V387L ENST00000380152 10/27 237 222 15 175 175 0 strelka-varscan-mutect BRCA2,missense_variant,p.Val387Leu,ENST00000380152,;BRCA2,missense_variant,p.Val387Leu,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,;BRCA2,non_coding_transcript_exon_variant,,ENST00000530893,; C ENST00000380152 Transcript missense_variant 1392/11986 1159/10257 387/3418 V/L Gtt/Ctt 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC tolerated(0.38) 10/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 MODERATE 1 SNV 5 1 PASS rs869320791 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 32332637 32332637 G C 1 0 0 0 0 1 0 0 0 1669 1029 36 4 4 BRCA2 13 32332637 Missense_Mutation SNP G C3N-01823_T 32332637 82031691 326 26023 PCDH17 0 . GRCh38 13 57634372 57634372 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1826C>A p.Thr609Asn p.T609N ENST00000377918 1/4 348 311 37 177 177 0 strelka-varscan-mutect PCDH17,missense_variant,p.Thr609Asn,ENST00000377918,NM_001040429.2;PCDH17,upstream_gene_variant,,ENST00000612954,;PCDH17,upstream_gene_variant,,ENST00000615375,;RP11-95F22.1,upstream_gene_variant,,ENST00000610846,;PCDH17,missense_variant,p.Thr609Asn,ENST00000484979,; A ENST00000377918 Transcript missense_variant 2561/8232 1826/3480 609/1159 T/N aCt/aAt 1 1 PCDH17 HGNC HGNC:14267 protein_coding YES CCDS31986.1 ENSP00000367151 O14917 UPI00001FCE5B NM_001040429.2 tolerated(0.11) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF41,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 57634372 57634372 C A 1 0 0 0 0 1 0 0 0 11599 565 20 2 2 PCDH17 13 57634372 Missense_Mutation SNP C C3N-01823_T 25301735 57634372 56729956 327 26024 KLHL1 0 . GRCh38 13 69701763 69701763 + Splice_Site SNP T T G novel C3N-01823_T C3N-01823_N T T c.2188-2A>C p.X730_splice ENST00000377844 160 130 30 136 136 0 strelka-varscan-mutect KLHL1,splice_acceptor_variant,,ENST00000377844,NM_020866.2;KLHL1,splice_acceptor_variant,,ENST00000545028,NM_001286725.1; G ENST00000377844 Transcript splice_acceptor_variant -/4115 2188/2247 730/748 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 10/10 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 5 3 83 69701763 69701763 T G 1 0 0 0 0 0 0 1 0 8229 1594 55 5 5 KLHL1 13 69701763 Splice_Site SNP T C3N-01823_T 12067391 69701763 44662565 328 26025 F7 0 . GRCh38 13 113110805 113110805 + Nonsense_Mutation SNP C C A rs771676411 C3N-01823_T C3N-01823_N C C c.246C>A p.Cys82Ter p.C82* ENST00000375581 3/9 317 284 33 192 192 0 strelka-varscan-mutect F7,stop_gained,p.Cys82Ter,ENST00000375581,NM_000131.4;F7,stop_gained,p.Cys60Ter,ENST00000346342,NM_019616.3;F7,intron_variant,,ENST00000541084,NM_001267554.1;F7,non_coding_transcript_exon_variant,,ENST00000473085,;F7,missense_variant,p.Leu56Ile,ENST00000444337,;F7,non_coding_transcript_exon_variant,,ENST00000479674,; A ENST00000375581 Transcript stop_gained 281/3109 246/1401 82/466 C/* tgC/tgA rs771676411 1 1 F7 HGNC HGNC:3544 protein_coding YES CCDS9528.1 ENSP00000364731 P08709 UPI000012A414 NM_000131.4 3/9 Gene3D:4.10.740.10,Pfam_domain:PF00594,PIRSF_domain:PIRSF001143,Prints_domain:PR00001,PROSITE_patterns:PS00011,PROSITE_profiles:PS50998,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF212,SMART_domains:SM00069,Superfamily_domains:SSF57630 HIGH 1 SNV 1 1 PASS rs771676411 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 113110805 113110805 C A 1 0 0 0 0 0 1 0 0 5217 805 28 2 2 F7 13 113110805 Nonsense_Mutation SNP C C3N-01823_T 43409042 113110805 1253523 329 26026 OR4Q3 0 . GRCh38 14 19747787 19747787 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.360C>A p.= p.A120A ENST00000331723 1/1 378 356 22 293 292 1 varscan-mutect OR4Q3,synonymous_variant,p.=,ENST00000331723,NM_172194.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000331723 Transcript synonymous_variant 360/942 360/942 120/313 A gcC/gcA 1 1 OR4Q3 HGNC HGNC:15426 protein_coding YES CCDS32020.1 ENSP00000330049 Q8NH05 A0A126GW32 UPI0000061EF0 NM_172194.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF208,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs986568323 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 19747787 19747787 C A 1 0 0 0 0 0 0 0 1 11157 668 24 2 2 OR4Q3 14 19747787 Silent SNP C C3N-01823_T 19747787 87295931 330 26027 OR11G2 0 . GRCh38 14 20197983 20197983 + Silent SNP A A T novel C3N-01823_T C3N-01823_N A A c.648A>T p.= p.L216L ENST00000357366 1/1 452 396 56 301 301 0 strelka-varscan-mutect OR11G2,synonymous_variant,p.=,ENST00000357366,NM_001005503.1; T ENST00000357366 Transcript synonymous_variant 648/1111 648/1038 216/345 L ctA/ctT 1 1 OR11G2 HGNC HGNC:15346 protein_coding YES CCDS32032.1 ENSP00000349930 Q8NGC1 UPI000015F241 NM_001005503.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF183,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS rs1340888666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 20197983 20197983 A T 1 0 0 0 0 0 0 0 1 11001 436 16 4 4 OR11G2 14 20197983 Silent SNP A C3N-01823_T 450196 20197983 86845735 331 26028 TEP1 0 . GRCh38 14 20403763 20403763 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.1154A>C p.His385Pro p.H385P ENST00000262715 6/55 332 313 19 262 262 0 strelka-varscan-mutect TEP1,missense_variant,p.His385Pro,ENST00000262715,NM_007110.4;TEP1,intron_variant,,ENST00000556935,;TEP1,downstream_gene_variant,,ENST00000556549,;TEP1,missense_variant,p.His385Pro,ENST00000555727,;TEP1,non_coding_transcript_exon_variant,,ENST00000557627,; G ENST00000262715 Transcript missense_variant 1195/10695 1154/7884 385/2627 H/P cAc/cCc 1 -1 TEP1 HGNC HGNC:11726 protein_coding YES CCDS9548.1 ENSP00000262715 Q99973 UPI000013D30B NM_007110.4 deleterious(0) 6/55 Low_complexity_(Seg):seg,PROSITE_profiles:PS50988,Pfam_domain:PF05731 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 20403763 20403763 T G 1 0 0 0 0 1 0 0 0 16175 1696 59 5 5 TEP1 14 20403763 Missense_Mutation SNP T C3N-01823_T 205780 20403763 86639955 332 26029 MYH7 0 . GRCh38 14 23423641 23423641 + Missense_Mutation SNP G G T rs569520562 C3N-01823_T C3N-01823_N G G c.3005C>A p.Ala1002Asp p.A1002D ENST00000355349 24/40 556 454 102 329 329 0 strelka-varscan-mutect MYH7,missense_variant,p.Ala1002Asp,ENST00000355349,NM_000257.3; T ENST00000355349 Transcript missense_variant 3168/6087 3005/5808 1002/1935 A/D gCc/gAc rs569520562 1 -1 MYH7 HGNC HGNC:7577 protein_coding YES CCDS9601.1 ENSP00000347507 P12883 UPI000014019B NM_000257.3 deleterious(0) 24/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF413,Superfamily_domains:SSF90257 MODERATE 1 SNV 1 1 PASS rs569520562 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 23423641 23423641 G T 1 0 0 0 0 1 0 0 0 10039 1203 42 2 2 MYH7 14 23423641 Missense_Mutation SNP G C3N-01823_T 3019878 23423641 83620077 333 26030 MBIP 0 . GRCh38 14 36320513 36320513 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.76T>A p.Ser26Thr p.S26T ENST00000416007 1/9 596 542 54 175 174 1 strelka-varscan-mutect MBIP,missense_variant,p.Ser26Thr,ENST00000621657,;MBIP,missense_variant,p.Ser26Thr,ENST00000416007,NM_016586.2;MBIP,missense_variant,p.Ser26Thr,ENST00000318473,NM_001144891.1;MBIP,missense_variant,p.Ser26Thr,ENST00000359527,NM_001308110.1;MBIP,missense_variant,p.Ser23Thr,ENST00000605579,;MBIP,missense_variant,p.Ser26Thr,ENST00000604336,;MBIP,missense_variant,p.Ser26Thr,ENST00000603139,;MBIP,upstream_gene_variant,,ENST00000604160,;RP11-964E11.3,upstream_gene_variant,,ENST00000634305,; T ENST00000416007 Transcript missense_variant 164/1648 76/1035 26/344 S/T Tcc/Acc 1 -1 MBIP HGNC HGNC:20427 protein_coding YES CCDS9658.1 ENSP00000399718 Q9NS73 UPI00001FD419 NM_016586.2 tolerated_low_confidence(0.43) 1/9 hmmpanther:PTHR23404,hmmpanther:PTHR23404:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 36320513 36320513 A T 1 0 0 0 0 1 0 0 0 9281 304 11 4 4 MBIP 14 36320513 Missense_Mutation SNP A C3N-01823_T 12896872 36320513 70723205 334 26031 RAD51B 0 . GRCh38 14 67885881 67885881 + Silent SNP A A T novel C3N-01823_T C3N-01823_N A A c.465A>T p.= p.I155I ENST00000487270 6/11 64 53 11 68 68 0 strelka-varscan-mutect RAD51B,synonymous_variant,p.=,ENST00000487270,NM_133509.3;RAD51B,synonymous_variant,p.=,ENST00000487861,NM_002877.5;RAD51B,synonymous_variant,p.=,ENST00000488612,;RAD51B,synonymous_variant,p.=,ENST00000471583,NM_133510.3;RAD51B,synonymous_variant,p.=,ENST00000390683,;RAD51B,non_coding_transcript_exon_variant,,ENST00000553595,;RAD51B,non_coding_transcript_exon_variant,,ENST00000555907,;RAD51B,non_coding_transcript_exon_variant,,ENST00000553734,;RAD51B,upstream_gene_variant,,ENST00000469165,;RAD51B,upstream_gene_variant,,ENST00000460526,;RAD51B,upstream_gene_variant,,ENST00000554244,;RAD51B,upstream_gene_variant,,ENST00000478014,;RAD51B,upstream_gene_variant,,ENST00000497460,;RAD51B,upstream_gene_variant,,ENST00000492236,;RAD51B,3_prime_UTR_variant,,ENST00000479335,NM_001321817.1;RAD51B,non_coding_transcript_exon_variant,,ENST00000474051,; T ENST00000487270 Transcript synonymous_variant 513/2596 465/1155 155/384 I atA/atT 1 1 RAD51B HGNC HGNC:9822 protein_coding YES CCDS9789.1 ENSP00000419471 O15315 UPI0000073AB0 NM_133509.3 6/11 PROSITE_profiles:PS50162,hmmpanther:PTHR22942:SF15,hmmpanther:PTHR22942,PIRSF_domain:PIRSF005856,Gene3D:3.40.50.300,Pfam_domain:PF08423,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 67885881 67885881 A T 1 0 0 0 0 0 0 0 1 13149 410 15 4 4 RAD51B 14 67885881 Silent SNP A C3N-01823_T 31565368 67885881 39157837 335 26032 ADCK1 0 . GRCh38 14 77933330 77933330 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.1511G>C p.Gly504Ala p.G504A ENST00000238561 11/11 232 194 38 195 195 0 strelka-varscan-mutect ADCK1,missense_variant,p.Gly504Ala,ENST00000238561,NM_020421.3;ADCK1,missense_variant,p.Gly436Ala,ENST00000341211,NM_001142545.1;ADCK1,non_coding_transcript_exon_variant,,ENST00000556560,;ADCK1,non_coding_transcript_exon_variant,,ENST00000555217,; C ENST00000238561 Transcript missense_variant 1610/2234 1511/1572 504/523 G/A gGg/gCg 1 1 ADCK1 HGNC HGNC:19038 protein_coding YES CCDS9869.1 ENSP00000238561 Q86TW2 UPI000014035F NM_020421.3 tolerated(0.15) 11/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 77933330 77933330 G C 1 0 0 0 0 1 0 0 0 331 1232 43 4 4 ADCK1 14 77933330 Missense_Mutation SNP G C3N-01823_T 10047449 77933330 29110388 336 26033 ASB2 0 . GRCh38 14 93956856 93956856 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.221C>G p.Pro74Arg p.P74R ENST00000555019 3/10 260 246 14 196 196 0 strelka-varscan-mutect ASB2,missense_variant,p.Pro74Arg,ENST00000555019,NM_001202429.1;ASB2,missense_variant,p.Pro26Arg,ENST00000315988,NM_016150.4;ASB2,5_prime_UTR_variant,,ENST00000555287,;ASB2,intron_variant,,ENST00000557613,;ASB2,upstream_gene_variant,,ENST00000555507,;ASB2,upstream_gene_variant,,ENST00000556062,;ASB2,intron_variant,,ENST00000556337,;ASB2,non_coding_transcript_exon_variant,,ENST00000556793,; C ENST00000555019 Transcript missense_variant 652/2842 221/1908 74/635 P/R cCt/cGt 1 -1 ASB2 HGNC HGNC:16012 protein_coding YES CCDS55940.1 ENSP00000451575 Q96Q27 A0A024R6E7 UPI000013D23C NM_001202429.1 tolerated(0.25) 3/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 93956856 93956856 G C 1 0 0 0 0 1 0 0 0 1165 1000 35 4 4 ASB2 14 93956856 Missense_Mutation SNP G C3N-01823_T 16023526 93956856 13086862 337 26034 SERPINA6 0 . GRCh38 14 94309906 94309906 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.714C>A p.Ser238Arg p.S238R ENST00000341584 3/5 492 467 25 355 354 1 strelka-varscan-mutect SERPINA6,missense_variant,p.Ser238Arg,ENST00000341584,NM_001756.3;SERPINA6,downstream_gene_variant,,ENST00000557225,;SERPINA6,3_prime_UTR_variant,,ENST00000555056,; T ENST00000341584 Transcript missense_variant 861/1534 714/1218 238/405 S/R agC/agA COSM1371784,COSM1371785 1 -1 SERPINA6 HGNC HGNC:1540 protein_coding YES CCDS9924.1 ENSP00000342850 P08185 UPI0000127182 NM_001756.3 tolerated(0.18) 3/5 hmmpanther:PTHR11461:SF34,hmmpanther:PTHR11461,Pfam_domain:PF00079,Gene3D:2.30.39.10,SMART_domains:SM00093,Superfamily_domains:SSF56574,Prints_domain:PR00780 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1212608733 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 94309906 94309906 G T 1 0 0 0 0 1 0 0 0 14369 1310 46 2 2 SERPINA6 14 94309906 Missense_Mutation SNP G C3N-01823_T 353050 94309906 12733812 338 26035 NPAP1 0 . GRCh38 15 24678814 24678814 + Nonsense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.2947A>T p.Arg983Ter p.R983* ENST00000329468 1/1 300 227 73 175 175 0 strelka-varscan-mutect NPAP1,stop_gained,p.Arg983Ter,ENST00000329468,NM_018958.2; T ENST00000329468 Transcript stop_gained 2947/7526 2947/3471 983/1156 R/* Aga/Tga 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 HIGH 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 83 24678814 24678814 A T 1 0 0 0 0 0 1 0 0 10609 412 15 4 4 NPAP1 15 24678814 Nonsense_Mutation SNP A C3N-01823_T 24678814 77312375 339 26036 ATP10A 0 . GRCh38 15 25679752 25679752 + Silent SNP G G A C3N-01823_T C3N-01823_N G G c.4089C>T p.= p.S1363S ENST00000356865 21/21 182 133 49 105 105 0 strelka-varscan-mutect ATP10A,synonymous_variant,p.=,ENST00000356865,NM_024490.3;ATP10A,downstream_gene_variant,,ENST00000555756,;ATP10A,3_prime_UTR_variant,,ENST00000555815,;ATP10A,downstream_gene_variant,,ENST00000555450,; A ENST00000356865 Transcript synonymous_variant 4201/6680 4089/4500 1363/1499 S tcC/tcT COSM3500176 1 -1 ATP10A HGNC HGNC:13542 protein_coding YES CCDS32178.1 ENSP00000349325 O60312 UPI0000124FAB NM_024490.3 21/21 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF81 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 25679752 25679752 G A 1 0 0 0 0 0 0 0 1 1268 1219 43 3 3 ATP10A 15 25679752 Silent SNP G C3N-01823_T 1000938 25679752 76311437 340 26037 OCA2 0 . GRCh38 15 27926159 27926159 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.2047C>T p.= p.L683L ENST00000354638 19/24 387 301 86 266 266 0 strelka-varscan-mutect OCA2,synonymous_variant,p.=,ENST00000354638,NM_000275.2;OCA2,synonymous_variant,p.=,ENST00000353809,NM_001300984.1; A ENST00000354638 Transcript synonymous_variant 2203/3186 2047/2517 683/838 L Ctg/Ttg 1 -1 OCA2 HGNC HGNC:8101 protein_coding YES CCDS10020.1 ENSP00000346659 Q04671 UPI000013D158 NM_000275.2 19/24 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF67,hmmpanther:PTHR10283,Pfam_domain:PF03600 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 27926159 27926159 G A 1 0 0 0 0 0 0 0 1 10892 933 33 3 3 OCA2 15 27926159 Silent SNP G C3N-01823_T 2246407 27926159 74065030 341 26038 OTUD7A 0 . GRCh38 15 31527223 31527223 + Silent SNP C C G novel C3N-01823_T C3N-01823_N C C c.738G>C p.= p.L246L ENST00000307050 5/11 267 206 61 157 157 0 strelka-varscan-mutect OTUD7A,synonymous_variant,p.=,ENST00000307050,NM_130901.1; G ENST00000307050 Transcript synonymous_variant 831/10770 738/2781 246/926 L ctG/ctC 1 -1 OTUD7A HGNC HGNC:20718 protein_coding YES CCDS10026.1 ENSP00000305926 Q8TE49 UPI0000073AA5 NM_130901.1 5/11 PROSITE_profiles:PS50802,hmmpanther:PTHR13367:SF9,hmmpanther:PTHR13367,Pfam_domain:PF02338 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 31527223 31527223 C G 1 0 0 0 0 0 0 0 1 11387 813 29 4 4 OTUD7A 15 31527223 Silent SNP C C3N-01823_T 3601064 31527223 70463966 342 26039 LPCAT4 0 . GRCh38 15 34363457 34363457 + Splice_Site SNP C C A novel C3N-01823_T C3N-01823_N C C c.712-1G>T p.X238_splice ENST00000314891 170 130 40 104 103 1 strelka-varscan-mutect LPCAT4,splice_acceptor_variant,,ENST00000314891,NM_153613.2;LPCAT4,splice_acceptor_variant,,ENST00000617710,;LPCAT4,downstream_gene_variant,,ENST00000623384,;LPCAT4,downstream_gene_variant,,ENST00000562431,;LPCAT4,non_coding_transcript_exon_variant,,ENST00000562404,;LPCAT4,upstream_gene_variant,,ENST00000563748,;LPCAT4,upstream_gene_variant,,ENST00000563240,;LPCAT4,downstream_gene_variant,,ENST00000566581,;LPCAT4,upstream_gene_variant,,ENST00000567507,;LPCAT4,downstream_gene_variant,,ENST00000569804,; A ENST00000314891 Transcript splice_acceptor_variant -/2262 712/1575 238/524 1 -1 LPCAT4 HGNC HGNC:30059 protein_coding YES CCDS32191.1 ENSP00000317300 Q643R3 UPI00003D0606 NM_153613.2 6/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 83 34363457 34363457 C A 1 0 0 0 0 0 0 1 0 8816 695 24 2 2 LPCAT4 15 34363457 Splice_Site SNP C C3N-01823_T 2836234 34363457 67627732 343 26040 GOLGA8A 0 . GRCh38 15 34381708 34381708 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.1602G>A p.= p.K534K ENST00000359187 15/16 72 61 11 57 57 0 varscan-mutect GOLGA8A,synonymous_variant,p.=,ENST00000432566,;GOLGA8A,synonymous_variant,p.=,ENST00000359187,NM_181077.3;MIR1233-1,downstream_gene_variant,,ENST00000408722,;GOLGA8A,non_coding_transcript_exon_variant,,ENST00000473125,; T ENST00000359187 Transcript synonymous_variant 1667/1877 1602/1812 534/603 K aaG/aaA 1 -1 GOLGA8A HGNC HGNC:31972 protein_coding YES CCDS10038.1 ENSP00000352111 A7E2F4 UPI000019C425 NM_181077.3 15/16 Pfam_domain:PF15070,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF7 LOW 1 SNV 1 1 PASS rs1324048532 . 0 207 2 0 0 0 0 0 -19.99999 1 1 1 1 0 T 2 4 83 34381708 34381708 C T 1 0 0 0 0 0 0 0 1 6447 796 28 3 3 GOLGA8A 15 34381708 Silent SNP C C3N-01823_T 18251 34381708 67609481 344 26041 UBR1 0 . GRCh38 15 42988950 42988950 + Missense_Mutation SNP C C A rs564247521 C3N-01823_T C3N-01823_N C C c.3866G>T p.Ser1289Ile p.S1289I ENST00000290650 35/47 317 251 66 244 244 0 strelka-mutect UBR1,missense_variant,p.Ser1289Ile,ENST00000290650,NM_174916.2;UBR1,non_coding_transcript_exon_variant,,ENST00000566493,; A ENST00000290650 Transcript missense_variant 3945/7761 3866/5250 1289/1749 S/I aGc/aTc rs564247521 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 deleterious(0.04) 35/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27 MODERATE 1 SNV 1 1 PASS rs564247521 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 42988950 42988950 C A 1 0 0 0 0 1 0 0 0 17425 797 28 2 2 UBR1 15 42988950 Missense_Mutation SNP C C3N-01823_T 8607242 42988950 59002239 345 26042 TGM5 0 . GRCh38 15 43239022 43239022 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.1140C>A p.= p.A380A ENST00000220420 9/13 667 499 168 441 439 2 strelka-varscan-mutect TGM5,synonymous_variant,p.=,ENST00000220420,NM_201631.3;TGM5,synonymous_variant,p.=,ENST00000610827,;TGM5,synonymous_variant,p.=,ENST00000611276,;TGM5,synonymous_variant,p.=,ENST00000622115,;TGM5,synonymous_variant,p.=,ENST00000349114,NM_004245.3;TGM5,non_coding_transcript_exon_variant,,ENST00000396996,;TGM5,downstream_gene_variant,,ENST00000635871,;TGM5,downstream_gene_variant,,ENST00000563838,; T ENST00000220420 Transcript synonymous_variant 1148/2767 1140/2163 380/720 A gcC/gcA 1 -1 TGM5 HGNC HGNC:11781 protein_coding YES CCDS32212.1 ENSP00000220420 O43548 UPI0000136CCF NM_201631.3 9/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF38,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 43239022 43239022 G T 1 0 0 0 0 0 0 0 1 16266 1335 47 2 2 TGM5 15 43239022 Silent SNP G C3N-01823_T 250072 43239022 58752167 346 26043 CYP19A1 0 . GRCh38 15 51210918 51210918 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.1402G>A p.Val468Ile p.V468I ENST00000396402 10/10 553 468 85 398 398 0 strelka-varscan-mutect CYP19A1,missense_variant,p.Val468Ile,ENST00000396402,NM_000103.3;CYP19A1,missense_variant,p.Val468Ile,ENST00000396404,NM_031226.2;CYP19A1,missense_variant,p.Val468Ile,ENST00000559878,;CYP19A1,downstream_gene_variant,,ENST00000558328,;CYP19A1,downstream_gene_variant,,ENST00000561075,;CYP19A1,downstream_gene_variant,,ENST00000559653,;CYP19A1,downstream_gene_variant,,ENST00000613097,;RP11-108K3.1,intron_variant,,ENST00000559909,;CYP19A1,downstream_gene_variant,,ENST00000478421,;CYP19A1,downstream_gene_variant,,ENST00000439712,;CYP19A1,downstream_gene_variant,,ENST00000557934,;CYP19A1,downstream_gene_variant,,ENST00000490076,;CYP19A1,downstream_gene_variant,,ENST00000558066,; T ENST00000396402 Transcript missense_variant 1556/4417 1402/1512 468/503 V/I Gtt/Att 1 -1 CYP19A1 HGNC HGNC:2594 protein_coding YES CCDS10139.1 ENSP00000379683 P11511 A0A024R5S8 UPI000013D0D7 NM_000103.3 tolerated(0.2) 10/10 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF43,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 51210918 51210918 C T 1 0 0 0 0 1 0 0 0 3951 478 17 3 3 CYP19A1 15 51210918 Missense_Mutation SNP C C3N-01823_T 7971896 51210918 50780271 347 26044 WDR72 0 . GRCh38 15 53597215 53597216 + Frame_Shift_Ins INS - - A novel C3N-01823_T C3N-01823_N - - c.3011dupT p.Leu1004PhefsTer8 p.L1004Ffs*8 ENST00000396328 18/20 178 150 28 180 180 0 sindel-varindel-pindel WDR72,frameshift_variant,p.Leu1004PhefsTer8,ENST00000396328,;WDR72,frameshift_variant,p.Leu1001PhefsTer8,ENST00000557913,;WDR72,frameshift_variant,p.Leu1004PhefsTer8,ENST00000360509,NM_182758.3;WDR72,frameshift_variant,p.Leu1014PhefsTer8,ENST00000559418,; A ENST00000396328 Transcript frameshift_variant 3251-3252/7507 3011-3012/3309 1004/1102 L/FX ttg/ttTg 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D 18/20 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 83 53597215 53597215 - A 1 0 1 1 0 0 0 0 0 17878 593 21 0 0 WDR72 15 53597215 Frame_Shift_Ins INS - C3N-01823_T 2386297 53597215 48393974 348 26045 MYO1E 0 . GRCh38 15 59218007 59218007 + Nonsense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.991A>T p.Lys331Ter p.K331* ENST00000288235 10/28 482 392 90 329 329 0 strelka-varscan-mutect MYO1E,stop_gained,p.Lys331Ter,ENST00000288235,NM_004998.3;MYO1E,stop_gained,p.Lys161Ter,ENST00000559269,;MYO1E,stop_gained,p.Lys51Ter,ENST00000559489,; A ENST00000288235 Transcript stop_gained 1391/8673 991/3327 331/1108 K/* Aag/Tag 1 -1 MYO1E HGNC HGNC:7599 protein_coding YES CCDS32254.1 ENSP00000288235 Q12965 Q4KMR3 UPI00001FE590 NM_004998.3 10/28 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF288,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 59218007 59218007 T A 1 0 0 0 0 0 1 0 0 10073 1821 63 4 4 MYO1E 15 59218007 Nonsense_Mutation SNP T C3N-01823_T 5620792 59218007 42773182 349 26046 TLN2 0 . GRCh38 15 62739397 62739397 + Missense_Mutation SNP A A G novel C3N-01823_T C3N-01823_N A A c.3737A>G p.Gln1246Arg p.Q1246R ENST00000561311 30/58 173 159 14 127 127 0 strelka-varscan-mutect TLN2,missense_variant,p.Gln1246Arg,ENST00000561311,NM_015059.2;TLN2,missense_variant,p.Gln244Arg,ENST00000306829,;TLN2,missense_variant,p.Gln271Arg,ENST00000636159,;TLN2,missense_variant,p.Gln160Arg,ENST00000494733,;TLN2,non_coding_transcript_exon_variant,,ENST00000559908,;TLN2,upstream_gene_variant,,ENST00000489129,; G ENST00000561311 Transcript missense_variant 3967/11880 3737/7629 1246/2542 Q/R cAg/cGg 1 1 TLN2 HGNC HGNC:15447 protein_coding YES CCDS32261.1 ENSP00000453508 Q9Y4G6 UPI00001FE5FC NM_015059.2 tolerated(0.34) 30/58 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15,Gene3D:1r0dB00,Superfamily_domains:SSF47220 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 62739397 62739397 A G 1 0 0 0 0 1 0 0 0 16394 188 7 5 5 TLN2 15 62739397 Missense_Mutation SNP A C3N-01823_T 3521390 62739397 39251792 350 26047 HCN4 0 . GRCh38 15 73343650 73343650 + Missense_Mutation SNP C C A rs759685985 C3N-01823_T C3N-01823_N C C c.944G>T p.Arg315Leu p.R315L ENST00000261917 2/8 266 212 54 194 193 1 strelka-varscan-mutect HCN4,missense_variant,p.Arg315Leu,ENST00000261917,NM_005477.2;RP11-272D12.1,downstream_gene_variant,,ENST00000558742,;RP11-272D12.1,downstream_gene_variant,,ENST00000557981,; A ENST00000261917 Transcript missense_variant 1938/7228 944/3612 315/1203 R/L cGc/cTc rs759685985,COSM5644073 1 -1 HCN4 HGNC HGNC:16882 protein_coding YES CCDS10248.1 ENSP00000261917 Q9Y3Q4 UPI000003FFB5 NM_005477.2 deleterious(0) 2/8 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR01463,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF375,Superfamily_domains:SSF81324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs759685985 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 73343650 73343650 C A 1 0 0 0 0 1 0 0 0 6886 768 27 1 1 HCN4 15 73343650 Missense_Mutation SNP C C3N-01823_T 10604253 73343650 28647539 351 26048 C15orf59 0 . GRCh38 15 73740613 73740613 + Silent SNP C C A rs144044826 C3N-01823_T C3N-01823_N C C c.186G>T p.= p.S62S ENST00000569673 3/3 110 85 25 83 83 0 strelka-varscan-mutect C15orf59,synonymous_variant,p.=,ENST00000569673,;C15orf59,synonymous_variant,p.=,ENST00000379822,NM_001039614.2;C15orf59,synonymous_variant,p.=,ENST00000559817,;C15orf59,non_coding_transcript_exon_variant,,ENST00000558834,; A ENST00000569673 Transcript synonymous_variant 1391/6573 186/882 62/293 S tcG/tcT rs144044826 1 -1 C15orf59 HGNC HGNC:33753 protein_coding YES CCDS32289.1 ENSP00000457205 Q2T9L4 UPI00001D778D 3/3 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15252,hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF3 LOW 1 SNV 5 1 PASS rs144044826 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 73740613 73740613 C A 1 0 0 0 0 0 0 0 1 1850 639 23 1 1 C15orf59 15 73740613 Silent SNP C C3N-01823_T 396963 73740613 28250576 352 26049 EDC3 0 . GRCh38 15 74655764 74655764 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.789G>A p.= p.V263V ENST00000315127 4/7 144 113 31 86 86 0 strelka-varscan-mutect EDC3,synonymous_variant,p.=,ENST00000315127,NM_001142444.1,NM_025083.3;EDC3,synonymous_variant,p.=,ENST00000426797,NM_001142443.1;EDC3,synonymous_variant,p.=,ENST00000568176,;EDC3,synonymous_variant,p.=,ENST00000562174,;EDC3,synonymous_variant,p.=,ENST00000566219,;EDC3,intron_variant,,ENST00000562974,;EDC3,downstream_gene_variant,,ENST00000563009,;EDC3,downstream_gene_variant,,ENST00000569561,;EDC3,3_prime_UTR_variant,,ENST00000565602,; T ENST00000315127 Transcript synonymous_variant 971/3763 789/1527 263/508 V gtG/gtA 1 -1 EDC3 HGNC HGNC:26114 protein_coding YES CCDS10267.1 ENSP00000320503 Q96F86 UPI000007309A NM_001142444.1,NM_025083.3 4/7 Pfam_domain:PF09532,hmmpanther:PTHR13612,hmmpanther:PTHR13612:SF0,SMART_domains:SM01199 LOW 1 SNV 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999806 1 1 1 0 T 2 4 83 74655764 74655764 C T 1 0 0 0 0 0 0 0 1 4735 697 25 3 3 EDC3 15 74655764 Silent SNP C C3N-01823_T 915151 74655764 27335425 353 26050 MAN2C1 0 . GRCh38 15 75361321 75361321 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1279G>T p.Gly427Cys p.G427C ENST00000565683 11/26 261 227 34 189 188 1 strelka-varscan-mutect MAN2C1,missense_variant,p.Gly427Cys,ENST00000565683,NM_001256494.1;MAN2C1,missense_variant,p.Gly427Cys,ENST00000267978,NM_006715.3;MAN2C1,missense_variant,p.Gly427Cys,ENST00000569482,NM_001256495.1;MAN2C1,missense_variant,p.Gly328Cys,ENST00000563622,NM_001256496.1;NEIL1,downstream_gene_variant,,ENST00000355059,NM_024608.3;MAN2C1,upstream_gene_variant,,ENST00000618257,;MAN2C1,downstream_gene_variant,,ENST00000566256,;MAN2C1,downstream_gene_variant,,ENST00000568374,;MAN2C1,downstream_gene_variant,,ENST00000561615,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000566253,;MAN2C1,downstream_gene_variant,,ENST00000563539,;MAN2C1,3_prime_UTR_variant,,ENST00000566634,;MAN2C1,3_prime_UTR_variant,,ENST00000421803,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000564785,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563441,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563013,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000562228,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000563058,;MAN2C1,non_coding_transcript_exon_variant,,ENST00000568944,;MAN2C1,upstream_gene_variant,,ENST00000567163,;MAN2C1,upstream_gene_variant,,ENST00000566099,;MAN2C1,upstream_gene_variant,,ENST00000561693,;MAN2C1,downstream_gene_variant,,ENST00000565534,;MAN2C1,downstream_gene_variant,,ENST00000570257,;MAN2C1,upstream_gene_variant,,ENST00000569176,;MAN2C1,downstream_gene_variant,,ENST00000569355,;MAN2C1,upstream_gene_variant,,ENST00000564929,;MAN2C1,upstream_gene_variant,,ENST00000566569,;MAN2C1,upstream_gene_variant,,ENST00000563794,;MAN2C1,upstream_gene_variant,,ENST00000564570,;MAN2C1,upstream_gene_variant,,ENST00000566013,;MAN2C1,upstream_gene_variant,,ENST00000563368,;MAN2C1,downstream_gene_variant,,ENST00000565801,;MAN2C1,upstream_gene_variant,,ENST00000562067,;MAN2C1,upstream_gene_variant,,ENST00000563596,;MAN2C1,downstream_gene_variant,,ENST00000562071,;MAN2C1,upstream_gene_variant,,ENST00000562461,;MAN2C1,downstream_gene_variant,,ENST00000565784,;MAN2C1,upstream_gene_variant,,ENST00000565953,;MAN2C1,downstream_gene_variant,,ENST00000565699,;MAN2C1,upstream_gene_variant,,ENST00000567360,;MAN2C1,upstream_gene_variant,,ENST00000563528,; A ENST00000565683 Transcript missense_variant 1291/3300 1279/3174 427/1057 G/C Ggc/Tgc 1 -1 MAN2C1 HGNC HGNC:6827 protein_coding YES CCDS58391.1 ENSP00000457788 Q9NTJ4 UPI0000229CBC NM_001256494.1 deleterious(0) 11/26 hmmpanther:PTHR11607,hmmpanther:PTHR11607:SF15,Pfam_domain:PF01074,Gene3D:3.20.110.10,Superfamily_domains:SSF88713 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 83 75361321 75361321 C A 1 0 0 0 0 1 0 0 0 9139 594 21 2 2 MAN2C1 15 75361321 Missense_Mutation SNP C C3N-01823_T 705557 75361321 26629868 354 26051 HMG20A 0 . GRCh38 15 77458439 77458439 + Missense_Mutation SNP C C A rs372649225 C3N-01823_T C3N-01823_N C C c.32C>A p.Pro11Gln p.P11Q ENST00000381714 3/11 250 203 47 231 230 1 strelka-varscan-mutect HMG20A,missense_variant,p.Pro11Gln,ENST00000381714,NM_018200.3;HMG20A,missense_variant,p.Pro11Gln,ENST00000336216,NM_001304504.1,NM_001304505.1;HMG20A,missense_variant,p.Pro11Gln,ENST00000560498,;HMG20A,missense_variant,p.Pro11Gln,ENST00000560867,;HMG20A,missense_variant,p.Pro11Gln,ENST00000559099,;HMG20A,5_prime_UTR_variant,,ENST00000558176,;HMG20A,intron_variant,,ENST00000558651,;HMG20A,missense_variant,p.Pro11Gln,ENST00000559035,;HMG20A,non_coding_transcript_exon_variant,,ENST00000560986,; A ENST00000381714 Transcript missense_variant 460/4112 32/1044 11/347 P/Q cCg/cAg rs372649225 1 1 HMG20A HGNC HGNC:5001 protein_coding YES CCDS10295.1 ENSP00000371133 Q9NP66 UPI00000737EF NM_018200.3 deleterious_low_confidence(0.01) 3/11 MODERATE 1 SNV 1 1 PASS rs372649225 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 77458439 77458439 C A 1 0 0 0 0 1 0 0 0 7113 652 23 1 1 HMG20A 15 77458439 Missense_Mutation SNP C C3N-01823_T 2097118 77458439 24532750 355 26052 ADAMTS7 0 . GRCh38 15 78765660 78765660 + Silent SNP C C G rs143941580 C3N-01823_T C3N-01823_N C C c.4251G>C p.= p.A1417A ENST00000388820 19/24 130 102 28 77 77 0 strelka-varscan-mutect ADAMTS7,synonymous_variant,p.=,ENST00000388820,NM_014272.3;ADAMTS7,downstream_gene_variant,,ENST00000566303,;ADAMTS7,downstream_gene_variant,,ENST00000565793,;ADAMTS7,upstream_gene_variant,,ENST00000569934,; G ENST00000388820 Transcript synonymous_variant 4462/5490 4251/5061 1417/1686 A gcG/gcC rs143941580,COSM3887558,COSM556033 1 -1 ADAMTS7 HGNC HGNC:223 protein_coding YES CCDS32303.1 ENSP00000373472 Q9UKP4 UPI00002263B3 NM_014272.3 19/24 PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF142,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs143941580 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 78765660 78765660 C G 1 0 0 0 0 0 0 0 1 315 639 23 4 4 ADAMTS7 15 78765660 Silent SNP C C3N-01823_T 1307221 78765660 23225529 356 26053 SAXO2 0 . GRCh38 15 82282120 82282120 + Missense_Mutation SNP C C G rs76375505 C3N-01823_T C3N-01823_N C C c.255C>G p.Asp85Glu p.D85E ENST00000339465 3/3 109 98 11 81 81 0 strelka-varscan-mutect SAXO2,missense_variant,p.Asp85Glu,ENST00000339465,NM_001008226.1;SAXO2,splice_region_variant,,ENST00000565501,; G ENST00000339465 Transcript missense_variant,splice_region_variant 324/3134 255/1197 85/398 D/E gaC/gaG rs76375505 1 1 SAXO2 HGNC HGNC:33727 protein_coding YES CCDS32310.1 ENSP00000340445 Q658L1 UPI00001D779A NM_001008226.1 tolerated(0.08) 3/3 hmmpanther:PTHR31516:SF6,hmmpanther:PTHR31516 MODERATE 1 SNV 1 1 PASS rs76375505 . 0 186 3 0 0 0 0 20 -3.443374 0 0 1 0 0 G 3 3 83 82282120 82282120 C G 1 0 0 0 0 1 0 0 0 14119 550 19 4 4 SAXO2 15 82282120 Missense_Mutation SNP C C3N-01823_T 3516460 82282120 19709069 357 26054 MRPL46 0 . GRCh38 15 88459763 88459763 + Missense_Mutation SNP C C A rs755201593 C3N-01823_T C3N-01823_N C C c.690G>T p.Lys230Asn p.K230N ENST00000312475 4/4 519 426 93 342 342 0 strelka-varscan-mutect MRPL46,missense_variant,p.Lys230Asn,ENST00000312475,NM_022163.3;RP11-97O12.7,non_coding_transcript_exon_variant,,ENST00000561140,;MRPL46,3_prime_UTR_variant,,ENST00000559538,;MRPL46,3_prime_UTR_variant,,ENST00000560703,;MRPL46,non_coding_transcript_exon_variant,,ENST00000558660,; A ENST00000312475 Transcript missense_variant 732/1019 690/840 230/279 K/N aaG/aaT rs755201593 1 -1 MRPL46 HGNC HGNC:1192 protein_coding YES CCDS10341.1 ENSP00000312311 Q9H2W6 UPI00000467E8 NM_022163.3 deleterious(0) 4/4 Gene3D:3.90.79.10,hmmpanther:PTHR13124,Superfamily_domains:SSF55811 MODERATE 1 SNV 1 1 PASS rs755201593 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 88459763 88459763 C A 1 0 0 0 0 1 0 0 0 9785 680 24 2 2 MRPL46 15 88459763 Missense_Mutation SNP C C3N-01823_T 6177643 88459763 13531426 358 26055 PDIA2 0 . GRCh38 16 284457 284457 + Silent SNP C C A rs369610324 C3N-01823_T C3N-01823_N C C c.270C>A p.= p.A90A ENST00000219406 2/11 584 552 32 480 479 1 strelka-varscan-mutect PDIA2,synonymous_variant,p.=,ENST00000219406,NM_006849.2;PDIA2,synonymous_variant,p.=,ENST00000404312,;PDIA2,synonymous_variant,p.=,ENST00000456379,;AXIN1,downstream_gene_variant,,ENST00000262320,NM_003502.3;AXIN1,downstream_gene_variant,,ENST00000354866,NM_181050.2;ARHGDIG,downstream_gene_variant,,ENST00000219409,NM_001176.3;ARHGDIG,downstream_gene_variant,,ENST00000447871,;ARHGDIG,downstream_gene_variant,,ENST00000414650,;PDIA2,upstream_gene_variant,,ENST00000435833,;ARHGDIG,downstream_gene_variant,,ENST00000435035,;ARHGDIG,downstream_gene_variant,,ENST00000412541,;AXIN1,downstream_gene_variant,,ENST00000457798,;PDIA2,upstream_gene_variant,,ENST00000462950,;PDIA2,non_coding_transcript_exon_variant,,ENST00000482665,;PDIA2,non_coding_transcript_exon_variant,,ENST00000467212,;AXIN1,downstream_gene_variant,,ENST00000461023,;ARHGDIG,downstream_gene_variant,,ENST00000477621,; A ENST00000219406 Transcript synonymous_variant 288/1698 270/1578 90/525 A gcC/gcA rs369610324,COSM4060578 1 1 PDIA2 HGNC HGNC:14180 protein_coding YES CCDS42089.1 ENSP00000219406 Q13087 UPI0000131481 NM_006849.2 2/11 PROSITE_profiles:PS51352,hmmpanther:PTHR18929,hmmpanther:PTHR18929:SF93,Gene3D:3.40.30.10,TIGRFAM_domain:TIGR01130,Pfam_domain:PF00085,Superfamily_domains:SSF52833 0,1 LOW 1 SNV 1 0,1 1 PASS rs369610324 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 284457 284457 C A 1 0 0 0 0 0 0 0 1 11756 639 23 1 1 PDIA2 16 284457 Silent SNP C C3N-01823_T 284457 90053888 359 26056 CAPN15 0 . GRCh38 16 552956 552956 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.2998G>T p.Val1000Leu p.V1000L ENST00000219611 13/14 162 131 31 101 100 1 strelka-varscan-mutect CAPN15,missense_variant,p.Val1000Leu,ENST00000219611,NM_005632.2;CAPN15,missense_variant,p.Val38Leu,ENST00000566977,;CAPN15,downstream_gene_variant,,ENST00000637507,;CAPN15,downstream_gene_variant,,ENST00000568988,;LA16c-366D1.3,intron_variant,,ENST00000565879,;CAPN15,non_coding_transcript_exon_variant,,ENST00000565010,; T ENST00000219611 Transcript missense_variant 3361/4744 2998/3261 1000/1086 V/L Gtg/Ttg COSM356801 1 1 CAPN15 HGNC HGNC:11182 protein_coding YES CCDS10410.1 ENSP00000219611 O75808 UPI0000071B68 NM_005632.2 deleterious(0) 13/14 1 MODERATE 1 SNV 1 1 1 PASS rs940163713 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 552956 552956 G T 1 0 0 0 0 1 0 0 0 2320 1145 40 1 1 CAPN15 16 552956 Missense_Mutation SNP G C3N-01823_T 268499 552956 89785389 360 26057 BAIAP3 0 . GRCh38 16 1341190 1341190 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.635C>A p.Pro212His p.P212H ENST00000324385 7/34 109 103 6 79 79 0 strelka-varscan-mutect BAIAP3,missense_variant,p.Pro194His,ENST00000628027,;BAIAP3,missense_variant,p.Pro212His,ENST00000324385,NM_003933.4;BAIAP3,missense_variant,p.Pro194His,ENST00000397488,NM_001286464.1;BAIAP3,missense_variant,p.Pro177His,ENST00000426824,NM_001199097.1;BAIAP3,missense_variant,p.Pro177His,ENST00000421665,NM_001199096.1;BAIAP3,missense_variant,p.Pro149His,ENST00000568887,NM_001199099.1;BAIAP3,missense_variant,p.Pro154His,ENST00000562208,NM_001199098.1;BAIAP3,upstream_gene_variant,,ENST00000566162,;BAIAP3,upstream_gene_variant,,ENST00000561793,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000567825,;BAIAP3,upstream_gene_variant,,ENST00000568198,;BAIAP3,upstream_gene_variant,,ENST00000561602,;BAIAP3,downstream_gene_variant,,ENST00000565665,; A ENST00000324385 Transcript missense_variant 793/4678 635/3564 212/1187 P/H cCc/cAc 1 1 BAIAP3 HGNC HGNC:948 protein_coding YES CCDS10434.1 ENSP00000324510 O94812 UPI0000071E58 NM_003933.4 deleterious(0.01) 7/34 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF65,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.3815 1 1 1 1 0 A 3 1 83 1341190 1341190 C A 1 0 0 0 0 1 0 0 0 1456 637 22 2 2 BAIAP3 16 1341190 Missense_Mutation SNP C C3N-01823_T 788234 1341190 88997155 361 26058 SHISA9 0 . GRCh38 16 13213268 13213268 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.863A>T p.Asp288Val p.D288V ENST00000558583 4/5 249 222 27 184 183 1 strelka-varscan-mutect SHISA9,missense_variant,p.Asp288Val,ENST00000558583,NM_001145204.2;SHISA9,intron_variant,,ENST00000566106,; T ENST00000558583 Transcript missense_variant 1308/6724 863/1275 288/424 D/V gAc/gTc 1 1 SHISA9 HGNC HGNC:37231 protein_coding YES CCDS45417.2 ENSP00000454014 B4DS77 UPI0001CE6F1C NM_001145204.2 tolerated(0.13) 4/5 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 13213268 13213268 A T 1 0 0 0 0 1 0 0 0 14546 275 10 4 4 SHISA9 16 13213268 Missense_Mutation SNP A C3N-01823_T 11872078 13213268 77125077 362 26059 GPR139 0 . GRCh38 16 20032167 20032167 + Silent SNP G G C novel C3N-01823_T C3N-01823_N G G c.630C>G p.= p.L210L ENST00000570682 2/2 259 224 35 206 206 0 strelka-varscan-mutect GPR139,synonymous_variant,p.=,ENST00000570682,NM_001002911.2;GPR139,3_prime_UTR_variant,,ENST00000326571,; C ENST00000570682 Transcript synonymous_variant 931/1613 630/1062 210/353 L ctC/ctG 1 -1 GPR139 HGNC HGNC:19995 protein_coding YES CCDS32398.1 ENSP00000458791 Q6DWJ6 A0A142CHG1 UPI000004C566 NM_001002911.2 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR22751,hmmpanther:PTHR22751:SF49,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 20032167 20032167 G C 1 0 0 0 0 0 0 0 1 6534 1277 45 4 4 GPR139 16 20032167 Silent SNP G C3N-01823_T 6818899 20032167 70306178 363 26060 UBFD1 0 . GRCh38 16 23558046 23558046 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.122G>T p.Gly41Val p.G41V ENST00000395878 2/7 49 38 11 19 19 0 strelka-mutect UBFD1,missense_variant,p.Gly41Val,ENST00000395878,NM_019116.2;UBFD1,missense_variant,p.Gly32Val,ENST00000567212,;UBFD1,missense_variant,p.Gly41Val,ENST00000567264,;EARS2,upstream_gene_variant,,ENST00000449606,NM_001083614.1;EARS2,upstream_gene_variant,,ENST00000563459,;EARS2,upstream_gene_variant,,ENST00000564501,;EARS2,upstream_gene_variant,,ENST00000563232,NM_001308211.1;UBFD1,non_coding_transcript_exon_variant,,ENST00000571064,;UBFD1,upstream_gene_variant,,ENST00000563366,;EARS2,upstream_gene_variant,,ENST00000564461,;EARS2,upstream_gene_variant,,ENST00000561859,;UBFD1,non_coding_transcript_exon_variant,,ENST00000566669,;UBFD1,upstream_gene_variant,,ENST00000569919,;UBFD1,upstream_gene_variant,,ENST00000565634,;EARS2,upstream_gene_variant,,ENST00000564668,;EARS2,upstream_gene_variant,,ENST00000564997,;EARS2,upstream_gene_variant,,ENST00000562799,;EARS2,upstream_gene_variant,,ENST00000563499,;EARS2,upstream_gene_variant,,ENST00000562581,; T ENST00000395878 Transcript missense_variant 503/5110 122/930 41/309 G/V gGg/gTg 1 1 UBFD1 HGNC HGNC:30565 protein_coding YES CCDS10613.2 ENSP00000379217 O14562 UPI00001FF0A3 NM_019116.2 tolerated_low_confidence(0.08) 2/7 hmmpanther:PTHR16470,Low_complexity_(Seg):seg MODERATE SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 23558046 23558046 G T 1 0 0 0 0 1 0 0 0 17408 1232 43 2 2 UBFD1 16 23558046 Missense_Mutation SNP G C3N-01823_T 3525879 23558046 66780299 364 26061 IL4R 0 . GRCh38 16 27363370 27363370 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2018G>T p.Ser673Ile p.S673I ENST00000395762 11/11 161 131 30 99 99 0 strelka-varscan-mutect IL4R,missense_variant,p.Ser673Ile,ENST00000395762,NM_000418.3;IL4R,missense_variant,p.Ser673Ile,ENST00000543915,NM_001257997.1,NM_001257406.1;IL4R,missense_variant,p.Ser658Ile,ENST00000170630,NM_001257407.1;IL4R,intron_variant,,ENST00000565352,;IL4R,downstream_gene_variant,,ENST00000565179,;IL4R,downstream_gene_variant,,ENST00000565915,;IL4R,3_prime_UTR_variant,,ENST00000568746,;IL4R,downstream_gene_variant,,ENST00000563886,; T ENST00000395762 Transcript missense_variant 2277/3685 2018/2478 673/825 S/I aGc/aTc 1 1 IL4R HGNC HGNC:6015 protein_coding YES CCDS10629.1 ENSP00000379111 P24394 UPI0000044371 NM_000418.3 deleterious(0.03) 11/11 hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF32,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999988 1 1 1 0 T 3 4 83 27363370 27363370 G T 1 0 0 0 0 1 0 0 0 7602 971 34 2 2 IL4R 16 27363370 Missense_Mutation SNP G C3N-01823_T 3805324 27363370 62974975 365 26062 GSG1L 0 . GRCh38 16 27807543 27807543 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.842G>C p.Arg281Thr p.R281T ENST00000447459 6/7 240 200 40 154 154 0 strelka-varscan-mutect GSG1L,missense_variant,p.Arg281Thr,ENST00000447459,NM_001109763.1;GSG1L,missense_variant,p.Arg230Thr,ENST00000395724,;GSG1L,missense_variant,p.Arg126Thr,ENST00000380897,NM_144675.2;GSG1L,missense_variant,p.Arg144Thr,ENST00000569166,; G ENST00000447459 Transcript missense_variant 927/4916 842/996 281/331 R/T aGg/aCg 1 -1 GSG1L HGNC HGNC:28283 protein_coding YES CCDS45450.1 ENSP00000394954 Q6UXU4 UPI0000EE765B NM_001109763.1 tolerated_low_confidence(0.57) 6/7 hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF35 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 27807543 27807543 C G 1 0 0 0 0 1 0 0 0 6704 681 24 4 4 GSG1L 16 27807543 Missense_Mutation SNP C C3N-01823_T 444173 27807543 62530802 366 26063 SH2B1 0 . GRCh38 16 28867412 28867412 + Nonsense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1021G>T p.Glu341Ter p.E341* ENST00000322610 5/11 309 293 16 193 193 0 strelka-mutect SH2B1,stop_gained,p.Glu341Ter,ENST00000337120,NM_001145796.1,NM_001145812.1,NM_015503.2;SH2B1,stop_gained,p.Glu341Ter,ENST00000322610,NM_001308293.1;SH2B1,stop_gained,p.Glu341Ter,ENST00000359285,NM_001145797.1;SH2B1,stop_gained,p.Glu341Ter,ENST00000618521,NM_001145795.1;SH2B1,stop_gained,p.Glu341Ter,ENST00000395532,;SH2B1,stop_gained,p.Glu5Ter,ENST00000538342,NM_001308294.1;SH2B1,stop_gained,p.Glu31Ter,ENST00000545570,;SH2B1,stop_gained,p.Glu5Ter,ENST00000561629,;SH2B1,stop_gained,p.Glu28Ter,ENST00000566176,;SH2B1,intron_variant,,ENST00000567536,;SH2B1,upstream_gene_variant,,ENST00000569651,;SH2B1,downstream_gene_variant,,ENST00000563591,;SH2B1,downstream_gene_variant,,ENST00000566209,;SH2B1,upstream_gene_variant,,ENST00000568868,;RP11-22P6.2,upstream_gene_variant,,ENST00000567731,;SH2B1,intron_variant,,ENST00000563674,;SH2B1,upstream_gene_variant,,ENST00000569471,; T ENST00000322610 Transcript stop_gained 1460/3095 1021/2271 341/756 E/* Gag/Tag 1 1 SH2B1 HGNC HGNC:30417 protein_coding YES CCDS53996.1 ENSP00000321221 Q9NRF2 A0A024QZD2 UPI00001AF36C NM_001308293.1 5/11 Gene3D:2.30.29.30,Pfam_domain:PF00169,hmmpanther:PTHR10872,hmmpanther:PTHR10872:SF3,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 83 28867412 28867412 G T 1 0 0 0 0 0 1 0 0 14485 1175 41 2 2 SH2B1 16 28867412 Nonsense_Mutation SNP G C3N-01823_T 1059869 28867412 61470933 367 26064 SPNS1 0 . GRCh38 16 28975325 28975325 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.174G>T p.= p.S58S ENST00000311008 1/12 56 51 5 43 43 0 strelka-mutect SPNS1,synonymous_variant,p.=,ENST00000311008,NM_001142448.1,NM_032038.2;SPNS1,synonymous_variant,p.=,ENST00000334536,NM_001142451.1;SPNS1,synonymous_variant,p.=,ENST00000565975,;SPNS1,synonymous_variant,p.=,ENST00000352260,NM_001142449.1;SPNS1,synonymous_variant,p.=,ENST00000566059,;SPNS1,synonymous_variant,p.=,ENST00000564476,;SPNS1,synonymous_variant,p.=,ENST00000567771,;SPNS1,5_prime_UTR_variant,,ENST00000323081,NM_001142450.1;SPNS1,5_prime_UTR_variant,,ENST00000568388,;SPNS1,upstream_gene_variant,,ENST00000568829,;RP11-264B17.4,intron_variant,,ENST00000567209,;SPNS1,upstream_gene_variant,,ENST00000561868,;RP11-264B17.3,non_coding_transcript_exon_variant,,ENST00000569969,;SPNS1,non_coding_transcript_exon_variant,,ENST00000568900,; T ENST00000311008 Transcript synonymous_variant 551/2208 174/1587 58/528 S tcG/tcT 1 1 SPNS1 HGNC HGNC:30621 protein_coding YES CCDS10646.1 ENSP00000309945 Q9H2V7 UPI000004DB99 NM_001142448.1,NM_032038.2 1/12 hmmpanther:PTHR23505,hmmpanther:PTHR23505:SF13,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.48041 1 1 1 1 0 T 2 4 83 28975325 28975325 G T 1 0 0 0 0 0 0 0 1 15427 1103 39 1 1 SPNS1 16 28975325 Silent SNP G C3N-01823_T 107913 28975325 61363020 368 26065 ZNF423 0 . GRCh38 16 49638063 49638063 + Missense_Mutation SNP G G T rs149688169 C3N-01823_T C3N-01823_N G G c.1089C>A p.Ser363Arg p.S363R ENST00000561648 5/9 469 442 27 284 284 0 strelka-varscan-mutect ZNF423,missense_variant,p.Ser363Arg,ENST00000561648,;ZNF423,missense_variant,p.Ser303Arg,ENST00000563137,;ZNF423,missense_variant,p.Ser363Arg,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Ser303Arg,ENST00000562871,;ZNF423,missense_variant,p.Ser246Arg,ENST00000535559,;ZNF423,missense_variant,p.Ser303Arg,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Ser246Arg,ENST00000567169,; T ENST00000561648 Transcript missense_variant 1390/7907 1089/3855 363/1284 S/R agC/agA rs149688169 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC tolerated(0.06) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 MODERATE 1 SNV 5 1 PASS rs149688169 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 49638063 49638063 G T 1 0 0 0 0 1 0 0 0 18470 1078 38 1 1 ZNF423 16 49638063 Missense_Mutation SNP G C3N-01823_T 20662738 49638063 40700282 369 26066 SNX20 0 . GRCh38 16 50673543 50673543 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.814G>T p.Ala272Ser p.A272S ENST00000330943 4/4 157 130 27 117 117 0 strelka-varscan-mutect SNX20,missense_variant,p.Ala272Ser,ENST00000330943,NM_182854.2;SNX20,intron_variant,,ENST00000300590,NM_153337.2;SNX20,intron_variant,,ENST00000423026,NM_001144972.1;SNX20,intron_variant,,ENST00000610485,;RP11-401P9.5,downstream_gene_variant,,ENST00000570167,;RP11-401P9.5,downstream_gene_variant,,ENST00000570241,;SNX20,intron_variant,,ENST00000568993,; A ENST00000330943 Transcript missense_variant 986/2904 814/951 272/316 A/S Gcc/Tcc 1 -1 SNX20 HGNC HGNC:30390 protein_coding YES CCDS10745.1 ENSP00000332062 Q7Z614 UPI000004348D NM_182854.2 tolerated(0.26) 4/4 Gene3D:1.25.40.10,hmmpanther:PTHR20939,hmmpanther:PTHR20939:SF1 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999952 1 1 1 0 A 3 1 83 50673543 50673543 C A 1 0 0 0 0 1 0 0 0 15213 768 27 1 1 SNX20 16 50673543 Missense_Mutation SNP C C3N-01823_T 1035480 50673543 39664802 370 26067 NOD2 0 . GRCh38 16 50722680 50722680 + Missense_Mutation SNP G G C C3N-01823_T C3N-01823_N G G c.2773G>C p.Asp925His p.D925H ENST00000300589 8/12 403 374 29 313 313 0 strelka-varscan-mutect NOD2,missense_variant,p.Asp925His,ENST00000300589,NM_022162.2,NM_001293557.1;NOD2,missense_variant,p.Asp137His,ENST00000534057,;RP11-327F22.1,downstream_gene_variant,,ENST00000563315,;NOD2,3_prime_UTR_variant,,ENST00000534067,;NOD2,3_prime_UTR_variant,,ENST00000529633,;NOD2,3_prime_UTR_variant,,ENST00000524712,;NOD2,3_prime_UTR_variant,,ENST00000527052,; C ENST00000300589 Transcript missense_variant 2878/4486 2773/3123 925/1040 D/H Gat/Cat COSM3510097 1 1 NOD2 HGNC HGNC:5331 protein_coding YES CCDS10746.1 ENSP00000300589 Q9HC29 UPI000005027A NM_022162.2,NM_001293557.1 deleterious(0.01) 8/12 hmmpanther:PTHR24106:SF64,hmmpanther:PTHR24106,Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 50722680 50722680 G C 1 0 0 0 0 1 0 0 0 10560 1290 45 4 4 NOD2 16 50722680 Missense_Mutation SNP G C3N-01823_T 49137 50722680 39615665 371 26068 CPNE2 0 . GRCh38 16 57123434 57123434 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.888C>T p.= p.F296F ENST00000290776 10/16 287 239 48 232 232 0 strelka-varscan-mutect CPNE2,synonymous_variant,p.=,ENST00000290776,NM_152727.5;CPNE2,synonymous_variant,p.=,ENST00000535318,;CPNE2,synonymous_variant,p.=,ENST00000565874,;CPNE2,synonymous_variant,p.=,ENST00000565766,;CPNE2,downstream_gene_variant,,ENST00000567487,;CPNE2,upstream_gene_variant,,ENST00000565951,;CPNE2,non_coding_transcript_exon_variant,,ENST00000566042,; T ENST00000290776 Transcript synonymous_variant 1177/2645 888/1647 296/548 F ttC/ttT 1 1 CPNE2 HGNC HGNC:2315 protein_coding YES CCDS10774.1 ENSP00000290776 Q96FN4 UPI000017DA4F NM_152727.5 10/16 hmmpanther:PTHR10857,hmmpanther:PTHR10857:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 57123434 57123434 C T 1 0 0 0 0 0 0 0 1 3607 854 30 3 3 CPNE2 16 57123434 Silent SNP C C3N-01823_T 6400754 57123434 33214911 372 26069 FAM192A 0 . GRCh38 16 57172824 57172824 + Nonsense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.178G>T p.Glu60Ter p.E60* ENST00000309137 3/7 292 273 19 227 227 0 varscan-mutect FAM192A,stop_gained,p.Glu60Ter,ENST00000309137,NM_024946.2;FAM192A,stop_gained,p.Glu60Ter,ENST00000567439,;FAM192A,stop_gained,p.Glu60Ter,ENST00000564108,;FAM192A,stop_gained,p.Glu60Ter,ENST00000565458,;FAM192A,stop_gained,p.Glu60Ter,ENST00000389447,;FAM192A,stop_gained,p.Glu60Ter,ENST00000569266,;FAM192A,stop_gained,p.Glu60Ter,ENST00000567044,;FAM192A,stop_gained,p.Glu60Ter,ENST00000566584,;FAM192A,stop_gained,p.Glu60Ter,ENST00000565760,;FAM192A,stop_gained,p.Glu60Ter,ENST00000568671,;FAM192A,stop_gained,p.Glu60Ter,ENST00000562324,;FAM192A,stop_gained,p.Glu60Ter,ENST00000570184,;FAM192A,stop_gained,p.Glu60Ter,ENST00000566481,;FAM192A,stop_gained,p.Glu60Ter,ENST00000562406,;FAM192A,5_prime_UTR_variant,,ENST00000566077,;FAM192A,intron_variant,,ENST00000565956,;FAM192A,downstream_gene_variant,,ENST00000566681,;FAM192A,downstream_gene_variant,,ENST00000564424,;FAM192A,stop_gained,p.Glu60Ter,ENST00000566403,; A ENST00000309137 Transcript stop_gained 437/2848 178/765 60/254 E/* Gaa/Taa 1 -1 FAM192A HGNC HGNC:29856 protein_coding YES CCDS42168.1 ENSP00000335808 Q9GZU8 A0A024R6T8 UPI000003620C NM_024946.2 3/7 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF10187,hmmpanther:PTHR13495,hmmpanther:PTHR13495:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 57172824 57172824 C A 1 0 0 0 0 0 1 0 0 5370 864 30 2 2 FAM192A 16 57172824 Nonsense_Mutation SNP C C3N-01823_T 49390 57172824 33165521 373 26070 TK2 0 . GRCh38 16 66512048 66512048 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.718C>T p.His240Tyr p.H240Y ENST00000299697 10/10 634 516 118 399 399 0 strelka-varscan-mutect TK2,missense_variant,p.His240Tyr,ENST00000299697,NM_004614.4,NM_001271934.1;TK2,missense_variant,p.His222Tyr,ENST00000620035,NM_001172645.1;TK2,missense_variant,p.His282Tyr,ENST00000451102,;TK2,missense_variant,p.His240Tyr,ENST00000544898,;TK2,missense_variant,p.His143Tyr,ENST00000527800,;TK2,missense_variant,p.His209Tyr,ENST00000527284,NM_001172643.1;TK2,missense_variant,p.His143Tyr,ENST00000525974,NM_001272050.1;TK2,missense_variant,p.His257Tyr,ENST00000564917,;TK2,missense_variant,p.His215Tyr,ENST00000545043,NM_001172644.1;TK2,missense_variant,p.His264Tyr,ENST00000417693,;TK2,missense_variant,p.His143Tyr,ENST00000563369,;TK2,3_prime_UTR_variant,,ENST00000569718,NM_001271935.1;TK2,intron_variant,,ENST00000561905,;TK2,downstream_gene_variant,,ENST00000563478,;RP11-403P17.3,downstream_gene_variant,,ENST00000568560,;TK2,non_coding_transcript_exon_variant,,ENST00000564792,;TK2,upstream_gene_variant,,ENST00000568170,;TK2,3_prime_UTR_variant,,ENST00000567357,;TK2,non_coding_transcript_exon_variant,,ENST00000562552,;TK2,non_coding_transcript_exon_variant,,ENST00000563099,;RP11-403P17.5,intron_variant,,ENST00000561728,;RP11-403P17.5,intron_variant,,ENST00000561527,; A ENST00000299697 Transcript missense_variant 1069/5114 718/798 240/265 H/Y Cac/Tac 1 -1 TK2 HGNC HGNC:11831 protein_coding YES CCDS10805.2 ENSP00000299697 O00142 UPI00001AECBD NM_004614.4,NM_001271934.1 deleterious(0) 10/10 hmmpanther:PTHR10513:SF24,hmmpanther:PTHR10513,Gene3D:3.40.50.300,PIRSF_domain:PIRSF000705,Pfam_domain:PF01712,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 66512048 66512048 G A 1 0 0 0 0 1 0 0 0 16375 1348 47 3 3 TK2 16 66512048 Missense_Mutation SNP G C3N-01823_T 9339224 66512048 23826297 374 26071 PHLPP2 0 . GRCh38 16 71679491 71679491 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.935G>T p.Gly312Val p.G312V ENST00000568954 7/19 240 226 14 199 197 2 strelka-varscan-mutect PHLPP2,missense_variant,p.Gly312Val,ENST00000393524,NM_001289003.1;PHLPP2,missense_variant,p.Gly312Val,ENST00000568954,NM_015020.3;PHLPP2,missense_variant,p.Gly347Val,ENST00000567016,;PHLPP2,missense_variant,p.Gly50Val,ENST00000568004,;PHLPP2,non_coding_transcript_exon_variant,,ENST00000538126,;PHLPP2,non_coding_transcript_exon_variant,,ENST00000574977,; A ENST00000568954 Transcript missense_variant 1314/8317 935/3972 312/1323 G/V gGg/gTg 1 -1 PHLPP2 HGNC HGNC:29149 protein_coding YES CCDS32479.1 ENSP00000457991 Q6ZVD8 UPI0000229F5A NM_015020.3 deleterious(0.04) 7/19 PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF252,Gene3D:3.80.10.10,SMART_domains:SM00364,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 71679491 71679491 C A 1 0 0 0 0 1 0 0 0 11943 623 22 2 2 PHLPP2 16 71679491 Missense_Mutation SNP C C3N-01823_T 5167443 71679491 18658854 375 26072 RFWD3 0 . GRCh38 16 74636555 74636555 + Missense_Mutation SNP T T G rs758670822 C3N-01823_T C3N-01823_N T T c.1217A>C p.His406Pro p.H406P ENST00000361070 8/13 319 260 59 217 217 0 strelka-varscan-mutect RFWD3,missense_variant,p.His406Pro,ENST00000361070,NM_018124.3;RFWD3,missense_variant,p.His406Pro,ENST00000571750,;RFWD3,upstream_gene_variant,,ENST00000575154,;RFWD3,downstream_gene_variant,,ENST00000575281,; G ENST00000361070 Transcript missense_variant 1315/4957 1217/2325 406/774 H/P cAt/cCt rs758670822 1 -1 RFWD3 HGNC HGNC:25539 protein_coding YES CCDS32486.1 ENSP00000354361 Q6PCD5 UPI0000366B66 NM_018124.3 deleterious(0.01) 8/13 hmmpanther:PTHR16047:SF7,hmmpanther:PTHR16047,Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS rs758670822 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 74636555 74636555 T G 1 0 0 0 0 1 0 0 0 13435 1464 51 5 5 RFWD3 16 74636555 Missense_Mutation SNP T C3N-01823_T 2957064 74636555 15701790 376 26073 SPIRE2 0 . GRCh38 16 89854332 89854332 + Missense_Mutation SNP G G T rs373339665 C3N-01823_T C3N-01823_N G G c.692G>T p.Arg231Leu p.R231L ENST00000378247 4/15 266 217 49 209 209 0 strelka-varscan-mutect SPIRE2,missense_variant,p.Arg231Leu,ENST00000378247,NM_032451.1;SPIRE2,missense_variant,p.Arg231Leu,ENST00000393062,;SPIRE2,downstream_gene_variant,,ENST00000564878,;SPIRE2,3_prime_UTR_variant,,ENST00000566337,;SPIRE2,non_coding_transcript_exon_variant,,ENST00000569108,;SPIRE2,non_coding_transcript_exon_variant,,ENST00000561883,; T ENST00000378247 Transcript missense_variant 735/3235 692/2145 231/714 R/L cGg/cTg rs373339665 1 1 SPIRE2 HGNC HGNC:30623 protein_coding YES CCDS32516.1 ENSP00000367494 Q8WWL2 UPI00001C1FA8 NM_032451.1 tolerated(0.48) 4/15 hmmpanther:PTHR21345,hmmpanther:PTHR21345:SF5 MODERATE 1 SNV 1 1 PASS rs373339665 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 89854332 89854332 G T 1 0 0 0 0 1 0 0 0 15425 1116 39 1 1 SPIRE2 16 89854332 Missense_Mutation SNP G C3N-01823_T 15217777 89854332 484013 377 26074 DOC2B 0 . GRCh38 17 172536 172536 + Splice_Site SNP C C A novel C3N-01823_T C3N-01823_N C C c.453+1G>T p.X151_splice ENST00000613549 97 66 31 58 58 0 strelka-varscan-mutect DOC2B,splice_donor_variant,,ENST00000613549,NM_003585.4;DOC2B,splice_donor_variant,,ENST00000609727,; A ENST00000613549 Transcript splice_donor_variant -/6048 453/1239 151/412 1 -1 DOC2B HGNC HGNC:2986 protein_coding YES CCDS73934.1 ENSP00000482950 A0A087WZX8 UPI000013ED38 NM_003585.4 2/8 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 83 172536 172536 C A 1 0 0 0 0 0 0 1 0 4498 521 18 2 2 DOC2B 17 172536 Splice_Site SNP C C3N-01823_T 172536 83084905 378 26075 SMG6 0 . GRCh38 17 2292916 2292916 + Missense_Mutation SNP T T G novel C3N-01823_T C3N-01823_N T T c.2213A>C p.Tyr738Ser p.Y738S ENST00000263073 5/19 349 286 63 243 243 0 strelka-varscan-mutect SMG6,missense_variant,p.Tyr738Ser,ENST00000263073,NM_017575.4; G ENST00000263073 Transcript missense_variant 2264/5960 2213/4260 738/1419 Y/S tAc/tCc 1 -1 SMG6 HGNC HGNC:17809 protein_coding YES CCDS11016.1 ENSP00000263073 Q86US8 UPI00002005C8 NM_017575.4 deleterious(0) 5/19 hmmpanther:PTHR15696:SF0,hmmpanther:PTHR15696,Pfam_domain:PF10374,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 2292916 2292916 T G 1 0 0 0 0 1 0 0 0 15091 1638 57 5 5 SMG6 17 2292916 Missense_Mutation SNP T C3N-01823_T 2120380 2292916 80964525 379 26076 USP6 0 . GRCh38 17 5136690 5136690 + Nonsense_Mutation SNP G G T rs756916065 C3N-01823_T C3N-01823_N G G c.715G>T p.Glu239Ter p.E239* ENST00000574788 18/38 389 321 68 264 264 0 strelka-varscan-mutect USP6,stop_gained,p.Glu239Ter,ENST00000574788,NM_001304284.1;USP6,stop_gained,p.Glu239Ter,ENST00000250066,NM_004505.3;USP6,downstream_gene_variant,,ENST00000572429,;USP6,stop_gained,p.Glu239Ter,ENST00000575709,;USP6,stop_gained,p.Glu239Ter,ENST00000572949,;USP6,downstream_gene_variant,,ENST00000357482,; T ENST00000574788 Transcript stop_gained 2945/8464 715/4221 239/1406 E/* Gag/Tag rs756916065 1 1 USP6 HGNC HGNC:12629 protein_coding YES CCDS11069.2 ENSP00000460380 P35125 UPI000006226F NM_001304284.1 18/38 Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF233,SMART_domains:SM00164,Superfamily_domains:SSF47923 HIGH 1 SNV 1 1 PASS rs756916065 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 83 5136690 5136690 G T 1 0 0 0 0 0 1 0 0 17629 1175 41 2 2 USP6 17 5136690 Nonsense_Mutation SNP G C3N-01823_T 2843774 5136690 78120751 380 26077 NLGN2 0 . GRCh38 17 7417172 7417172 + Silent SNP G G A rs747379386 C3N-01823_T C3N-01823_N G G c.1881G>A p.= p.T627T ENST00000302926 7/7 314 254 60 204 204 0 strelka-varscan-mutect NLGN2,synonymous_variant,p.=,ENST00000302926,NM_020795.3;NLGN2,synonymous_variant,p.=,ENST00000575301,;SPEM1,upstream_gene_variant,,ENST00000323675,NM_199339.2;NLGN2,downstream_gene_variant,,ENST00000570940,;RP11-104H15.7,upstream_gene_variant,,ENST00000575310,; A ENST00000302926 Transcript synonymous_variant 1954/4642 1881/2508 627/835 T acG/acA rs747379386 1 1 NLGN2 HGNC HGNC:14290 protein_coding YES CCDS11103.1 ENSP00000305288 Q8NFZ4 UPI0000049FD2 NM_020795.3 7/7 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF53,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs747379386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 7417172 7417172 G A 1 0 0 0 0 0 0 0 1 10499 1074 38 1 1 NLGN2 17 7417172 Silent SNP G C3N-01823_T 2280482 7417172 75840269 381 26078 TP53 0 . GRCh38 17 7675080 7675080 + Frame_Shift_Del DEL G G - rs863223300,rs869151209 C3N-01823_T C3N-01823_N G G c.532delC p.His178ThrfsTer69 p.H178Tfs*69 ENST00000269305 5/11 422 330 92 302 302 0 sindel-varindel-pindel TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000420246,;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000445888,;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000619485,;TP53,frameshift_variant,p.His46ThrfsTer69,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.His19ThrfsTer69,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.His46ThrfsTer69,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.His19ThrfsTer69,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.His46ThrfsTer69,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.His19ThrfsTer69,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000359597,;TP53,frameshift_variant,p.His167ThrfsTer69,ENST00000615910,;TP53,frameshift_variant,p.His178ThrfsTer69,ENST00000413465,;TP53,frameshift_variant,p.His46ThrfsTer69,ENST00000509690,;TP53,frameshift_variant,p.His85ThrfsTer69,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,frameshift_variant,p.His139ThrfsTer69,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; - ENST00000269305 Transcript frameshift_variant 722/2579 532/1182 178/393 H/X Cac/ac rs863223300,rs869151209,CD983489,CM111332,TP53_g.12520C>T,TP53_g.12520C>G,TP53_g.12520C>A,TP53_g.12520del,COSM111495,COSM111496,COSM111497,COSM111498,COSM44068,COSM44120,COSM44659,COSM44901,COSM4874415,COSM4874416,COSM5108058,COSM5108059,COSM5610919,COSM5610920,COSM5610921,COSM5610922,COSM5610923,COSM5610924,COSM984946,COSM984948,COSM984949,COSM984950 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 HIGH 1 deletion 1 1,0,1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 7675080 7675080 G - 1 0 1 0 1 0 0 0 0 16859 1348 47 0 0 TP53 17 7675080 Frame_Shift_Del DEL G C3N-01823_T 257908 7675080 75582361 382 26079 CCDC42 0 . GRCh38 17 8741530 8741530 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.436C>A p.Leu146Met p.L146M ENST00000293845 4/7 409 319 90 342 341 1 strelka-varscan-mutect CCDC42,missense_variant,p.Leu146Met,ENST00000293845,NM_144681.2;CCDC42,missense_variant,p.Leu146Met,ENST00000539522,NM_001158261.1;CCDC42,downstream_gene_variant,,ENST00000581598,; T ENST00000293845 Transcript missense_variant 663/1374 436/951 146/316 L/M Ctg/Atg 1 -1 CCDC42 HGNC HGNC:26528 protein_coding YES CCDS11145.1 ENSP00000293845 Q96M95 UPI000013E127 NM_144681.2 deleterious(0.03) 4/7 hmmpanther:PTHR21683:SF8,hmmpanther:PTHR21683,Pfam_domain:PF13863 MODERATE 1 SNV 2 1 PASS rs1358705392 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 8741530 8741530 G T 1 0 0 0 0 1 0 0 0 2522 962 34 2 2 CCDC42 17 8741530 Missense_Mutation SNP G C3N-01823_T 1066450 8741530 74515911 383 26080 MYOCD 0 . GRCh38 17 12753178 12753178 + Frame_Shift_Del DEL C C - novel C3N-01823_T C3N-01823_N C C c.1894delC p.Gln632SerfsTer12 p.Q632Sfs*12 ENST00000425538 10/14 242 192 50 166 166 0 sindel-varindel-pindel MYOCD,frameshift_variant,p.Gln632SerfsTer12,ENST00000425538,NM_001146312.2;MYOCD,frameshift_variant,p.Gln337SerfsTer12,ENST00000443061,;MYOCD,frameshift_variant,p.Gln632SerfsTer12,ENST00000343344,NM_153604.3;MYOCD,non_coding_transcript_exon_variant,,ENST00000395988,; - ENST00000425538 Transcript frameshift_variant 2090/8466 1890/2961 630/986 S/X agC/ag 1 1 MYOCD HGNC HGNC:16067 protein_coding YES CCDS54091.1 ENSP00000401678 Q8IZQ8 UPI000022A2E2 NM_001146312.2 10/14 hmmpanther:PTHR22793:SF11,hmmpanther:PTHR22793 HIGH 1 deletion 1 4 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999967 1 1 1 0 - 7 5 83 12753178 12753178 C - 1 0 1 0 1 0 0 0 0 10088 738 26 0 0 MYOCD 17 12753178 Frame_Shift_Del DEL C C3N-01823_T 4011648 12753178 70504263 384 26081 ELAC2 0 . GRCh38 17 12995745 12995745 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.1766A>T p.Gln589Leu p.Q589L ENST00000338034 19/24 576 477 99 415 414 1 strelka-varscan-mutect ELAC2,missense_variant,p.Gln589Leu,ENST00000338034,NM_018127.6,NM_173717.1;ELAC2,missense_variant,p.Gln570Leu,ENST00000395962,;ELAC2,missense_variant,p.Gln549Leu,ENST00000426905,NM_001165962.1;ELAC2,missense_variant,p.Gln389Leu,ENST00000584650,;ARHGAP44,downstream_gene_variant,,ENST00000379672,NM_014859.4;ARHGAP44,downstream_gene_variant,,ENST00000340825,NM_001321166.1;ELAC2,downstream_gene_variant,,ENST00000446899,;ELAC2,non_coding_transcript_exon_variant,,ENST00000484122,;ELAC2,non_coding_transcript_exon_variant,,ENST00000465825,;ELAC2,non_coding_transcript_exon_variant,,ENST00000480891,;ELAC2,non_coding_transcript_exon_variant,,ENST00000487229,;ELAC2,non_coding_transcript_exon_variant,,ENST00000491478,;ELAC2,non_coding_transcript_exon_variant,,ENST00000492559,;ARHGAP44,downstream_gene_variant,,ENST00000580768,NM_001321168.1;ELAC2,downstream_gene_variant,,ENST00000578104,;ELAC2,downstream_gene_variant,,ENST00000578991,;ELAC2,downstream_gene_variant,,ENST00000476042,; A ENST00000338034 Transcript missense_variant 2006/3148 1766/2481 589/826 Q/L cAg/cTg 1 -1 ELAC2 HGNC HGNC:14198 protein_coding YES CCDS11164.1 ENSP00000337445 Q9BQ52 A0A0S2Z5M8 UPI000004A07E NM_018127.6,NM_173717.1 tolerated(0.11) 19/24 hmmpanther:PTHR12553:SF49,hmmpanther:PTHR12553,Pfam_domain:PF12706,Gene3D:3.60.15.10,Superfamily_domains:SSF56281 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 12995745 12995745 T A 1 0 0 0 0 1 0 0 0 4880 1580 55 4 4 ELAC2 17 12995745 Missense_Mutation SNP T C3N-01823_T 242567 12995745 70261696 385 26082 NF1 0 . GRCh38 17 31337543 31337543 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.6603C>T p.= p.S2201S ENST00000358273 43/58 346 272 74 238 237 1 strelka-varscan-mutect NF1,synonymous_variant,p.=,ENST00000358273,NM_001042492.2;NF1,synonymous_variant,p.=,ENST00000356175,NM_000267.3;NF1,synonymous_variant,p.=,ENST00000456735,;NF1,downstream_gene_variant,,ENST00000581113,;NF1,3_prime_UTR_variant,,ENST00000579081,;NF1,upstream_gene_variant,,ENST00000471572,;NF1,upstream_gene_variant,,ENST00000581790,;NF1,downstream_gene_variant,,ENST00000479536,;NF1,upstream_gene_variant,,ENST00000584328,;NF1,upstream_gene_variant,,ENST00000582892,; T ENST00000358273 Transcript synonymous_variant 6986/12425 6603/8520 2201/2839 S tcC/tcT 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 43/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 31337543 31337543 C T 1 0 0 0 0 0 0 0 1 10393 668 24 3 3 NF1 17 31337543 Silent SNP C C3N-01823_T 18341798 31337543 51919898 386 26083 MED1 0 . GRCh38 17 39408077 39408077 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.4144A>G p.Lys1382Glu p.K1382E ENST00000300651 17/17 343 321 22 203 203 0 strelka-varscan-mutect MED1,missense_variant,p.Lys1382Glu,ENST00000300651,NM_004774.3;MED1,intron_variant,,ENST00000394287,;CTB-131K11.1,downstream_gene_variant,,ENST00000582842,;MED1,3_prime_UTR_variant,,ENST00000577831,; C ENST00000300651 Transcript missense_variant 4368/5844 4144/4746 1382/1581 K/E Aaa/Gaa 1 -1 MED1 HGNC HGNC:9234 protein_coding YES CCDS11336.1 ENSP00000300651 Q15648 UPI0000167F57 NM_004774.3 deleterious_low_confidence(0.03) 17/17 Low_complexity_(Seg):seg,hmmpanther:PTHR12881 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 39408077 39408077 T C 1 0 0 0 0 1 0 0 0 9364 1850 64 5 5 MED1 17 39408077 Missense_Mutation SNP T C3N-01823_T 8070534 39408077 43849364 387 26084 TCAP 0 . GRCh38 17 39665786 39665786 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.181G>T p.Val61Leu p.V61L ENST00000309889 2/2 125 106 19 58 57 1 strelka-varscan-mutect TCAP,missense_variant,p.Val61Leu,ENST00000309889,NM_003673.3;TCAP,splice_region_variant,,ENST00000578283,;STARD3,downstream_gene_variant,,ENST00000336308,NM_006804.3;STARD3,downstream_gene_variant,,ENST00000580611,;STARD3,downstream_gene_variant,,ENST00000394250,NM_001165938.1;STARD3,downstream_gene_variant,,ENST00000544210,NM_001165937.1;PNMT,upstream_gene_variant,,ENST00000269582,NM_002686.4;PNMT,upstream_gene_variant,,ENST00000394246,;PNMT,upstream_gene_variant,,ENST00000581428,;STARD3,downstream_gene_variant,,ENST00000583639,;STARD3,downstream_gene_variant,,ENST00000481171,;STARD3,downstream_gene_variant,,ENST00000584850,;STARD3,downstream_gene_variant,,ENST00000488876,;STARD3,downstream_gene_variant,,ENST00000471896,;STARD3,downstream_gene_variant,,ENST00000578577,;STARD3,downstream_gene_variant,,ENST00000585269,;STARD3,downstream_gene_variant,,ENST00000578384,;STARD3,downstream_gene_variant,,ENST00000578686,;STARD3,downstream_gene_variant,,ENST00000583884,; T ENST00000309889 Transcript missense_variant 1354/2123 181/504 61/167 V/L Gtg/Ttg 1 1 TCAP HGNC HGNC:11610 protein_coding YES CCDS11342.1 ENSP00000312624 O15273 A2TDC0 UPI0000136BAD NM_003673.3 tolerated(0.16) 2/2 hmmpanther:PTHR15143,hmmpanther:PTHR15143:SF0,Gene3D:1ya5T01,Pfam_domain:PF09470 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 39665786 39665786 G T 1 0 0 0 0 1 0 0 0 16073 1261 44 2 2 TCAP 17 39665786 Missense_Mutation SNP G C3N-01823_T 257709 39665786 43591655 388 26085 KRT24 0 . GRCh38 17 40703619 40703619 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.75C>A p.Ser25Arg p.S25R ENST00000264651 1/8 119 103 16 69 69 0 strelka-varscan-mutect KRT24,missense_variant,p.Ser25Arg,ENST00000264651,NM_019016.2; T ENST00000264651 Transcript missense_variant 132/1881 75/1578 25/525 S/R agC/agA 1 -1 KRT24 HGNC HGNC:18527 protein_coding YES CCDS11372.1 ENSP00000264651 Q2M2I5 UPI000013D54D NM_019016.2 tolerated_low_confidence(0.29) 1/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF207,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 83 40703619 40703619 G T 1 0 0 0 0 1 0 0 0 8343 1310 46 2 2 KRT24 17 40703619 Missense_Mutation SNP G C3N-01823_T 1037833 40703619 42553822 389 26086 EFTUD2 0 . GRCh38 17 44872503 44872503 + Nonsense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.937C>T p.Gln313Ter p.Q313* ENST00000426333 11/28 280 203 77 143 143 0 strelka-varscan-mutect EFTUD2,stop_gained,p.Gln313Ter,ENST00000426333,NM_004247.3;EFTUD2,stop_gained,p.Gln313Ter,ENST00000591382,NM_001258353.1;EFTUD2,stop_gained,p.Gln303Ter,ENST00000592576,NM_001258354.1;EFTUD2,stop_gained,p.Gln278Ter,ENST00000402521,NM_001142605.1;EFTUD2,synonymous_variant,p.=,ENST00000591856,;EFTUD2,non_coding_transcript_exon_variant,,ENST00000590367,;EFTUD2,upstream_gene_variant,,ENST00000586654,;EFTUD2,downstream_gene_variant,,ENST00000588374,;EFTUD2,downstream_gene_variant,,ENST00000587957,;EFTUD2,downstream_gene_variant,,ENST00000593200,; A ENST00000426333 Transcript stop_gained 1235/4548 937/2919 313/972 Q/* Cag/Tag 1 -1 EFTUD2 HGNC HGNC:30858 protein_coding YES CCDS11489.1 ENSP00000392094 Q15029 UPI0000137931 NM_004247.3 11/28 PROSITE_profiles:PS51722,hmmpanther:PTHR23115:SF5,hmmpanther:PTHR23115,Pfam_domain:PF00009,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 44872503 44872503 G A 1 0 0 0 0 0 1 0 0 4797 1357 47 3 3 EFTUD2 17 44872503 Nonsense_Mutation SNP G C3N-01823_T 4168884 44872503 38384938 390 26087 TOM1L1 0 . GRCh38 17 54938947 54938947 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.1057G>A p.Val353Ile p.V353I ENST00000575882 11/16 191 181 10 136 136 0 strelka-mutect TOM1L1,missense_variant,p.Val353Ile,ENST00000575882,NM_001321175.1,NM_001321176.1,NM_005486.2;TOM1L1,missense_variant,p.Val353Ile,ENST00000445275,;TOM1L1,missense_variant,p.Val276Ile,ENST00000348161,;TOM1L1,missense_variant,p.Val276Ile,ENST00000536554,;TOM1L1,missense_variant,p.Val346Ile,ENST00000572158,;TOM1L1,missense_variant,p.Val9Ile,ENST00000574318,;TOM1L1,downstream_gene_variant,,ENST00000570371,;TOM1L1,downstream_gene_variant,,ENST00000575333,NM_001321173.1;TOM1L1,downstream_gene_variant,,ENST00000572576,;TOM1L1,missense_variant,p.Val276Ile,ENST00000576932,;TOM1L1,3_prime_UTR_variant,,ENST00000571319,;TOM1L1,non_coding_transcript_exon_variant,,ENST00000574653,;TOM1L1,non_coding_transcript_exon_variant,,ENST00000572905,;TOM1L1,downstream_gene_variant,,ENST00000570623,; A ENST00000575882 Transcript missense_variant 1410/2507 1057/1431 353/476 V/I Gta/Ata 1 1 TOM1L1 HGNC HGNC:11983 protein_coding YES CCDS11582.1 ENSP00000460823 O75674 UPI000003E7E0 NM_001321175.1,NM_001321176.1,NM_005486.2 tolerated(0.25) 11/16 PIRSF_domain:PIRSF036948 MODERATE 1 SNV 1 1 PASS rs542984667 . 0 208 0 2 0 0 0 0 -12.60052 0.9999993 1 1 1 0 A 3 1 83 54938947 54938947 G A 1 0 0 0 0 1 0 0 0 16826 1377 48 3 3 TOM1L1 17 54938947 Missense_Mutation SNP G C3N-01823_T 10066444 54938947 28318494 391 26088 MARCH10 0 . GRCh38 17 62736822 62736822 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.1160C>T p.Pro387Leu p.P387L ENST00000583600 7/12 664 548 116 340 340 0 strelka-varscan-mutect MARCH10,missense_variant,p.Pro348Leu,ENST00000544856,NM_001288780.1;MARCH10,missense_variant,p.Pro387Leu,ENST00000583600,NM_001288779.1;MARCH10,missense_variant,p.Pro349Leu,ENST00000311269,NM_152598.3;MARCH10,missense_variant,p.Pro349Leu,ENST00000456609,NM_001100875.2;MARCH10,missense_variant,p.Pro217Leu,ENST00000580520,;RP11-156L14.1,non_coding_transcript_exon_variant,,ENST00000577270,;RP11-156L14.1,non_coding_transcript_exon_variant,,ENST00000582564,;RP11-156L14.1,downstream_gene_variant,,ENST00000579201,;RP11-156L14.1,downstream_gene_variant,,ENST00000584597,;MARCH10,upstream_gene_variant,,ENST00000579620,; A ENST00000583600 Transcript missense_variant 1445/3214 1160/2541 387/846 P/L cCc/cTc 1 -1 MARCH10 HGNC HGNC:26655 protein_coding YES CCDS74123.1 ENSP00000463080 J3KTN9 UPI0000EE65AE NM_001288779.1 tolerated(0.22) 7/12 hmmpanther:PTHR14471,hmmpanther:PTHR14471:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 62736822 62736822 G A 1 0 0 0 0 1 0 0 0 9224 1232 43 3 3 MARCH10 17 62736822 Missense_Mutation SNP G C3N-01823_T 7797875 62736822 20520619 392 26089 CYB561 0 . GRCh38 17 63434414 63434414 + Silent SNP G G T rs148303921 C3N-01823_T C3N-01823_N G G c.744C>A p.= p.P248P ENST00000392976 6/6 97 77 20 44 44 0 strelka-varscan-mutect CYB561,synonymous_variant,p.=,ENST00000392976,NM_001017916.1;CYB561,synonymous_variant,p.=,ENST00000392975,NM_001017917.1;CYB561,synonymous_variant,p.=,ENST00000360793,NM_001915.3;CYB561,synonymous_variant,p.=,ENST00000581573,;CYB561,synonymous_variant,p.=,ENST00000542042,;CYB561,synonymous_variant,p.=,ENST00000582034,;CYB561,synonymous_variant,p.=,ENST00000580691,;CYB561,synonymous_variant,p.=,ENST00000582997,;CYB561,synonymous_variant,p.=,ENST00000584291,;CYB561,3_prime_UTR_variant,,ENST00000584031,;CYB561,3_prime_UTR_variant,,ENST00000448884,;CYB561,3_prime_UTR_variant,,ENST00000585153,;CYB561,intron_variant,,ENST00000582297,;CYB561,downstream_gene_variant,,ENST00000578072,;CYB561,downstream_gene_variant,,ENST00000580592,;RP11-269G24.4,upstream_gene_variant,,ENST00000584608,;RP11-269G24.3,upstream_gene_variant,,ENST00000583552,;CYB561,non_coding_transcript_exon_variant,,ENST00000581163,;CYB561,downstream_gene_variant,,ENST00000577989,;CYB561,downstream_gene_variant,,ENST00000578016,;CYB561,non_coding_transcript_exon_variant,,ENST00000582143,;CYB561,downstream_gene_variant,,ENST00000577368,;CYB561,downstream_gene_variant,,ENST00000583478,; T ENST00000392976 Transcript synonymous_variant 1044/3151 744/756 248/251 P ccC/ccA rs148303921,COSM5561973 1 -1 CYB561 HGNC HGNC:2571 protein_coding YES CCDS11636.1 ENSP00000376702 P49447 UPI0000126C79 NM_001017916.1 6/6 hmmpanther:PTHR10106,hmmpanther:PTHR10106:SF14 0,1 LOW 1 SNV 3 0,1 1 PASS rs148303921 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 63434414 63434414 G T 1 0 0 0 0 0 0 0 1 3922 1103 39 1 1 CYB561 17 63434414 Silent SNP G C3N-01823_T 697592 63434414 19823027 393 26090 KIF19 0 . GRCh38 17 74343070 74343070 + Silent SNP C C A rs145969437 C3N-01823_T C3N-01823_N C C c.366C>A p.= p.G122G ENST00000389916 5/20 349 298 51 179 179 0 strelka-varscan-mutect KIF19,synonymous_variant,p.=,ENST00000389916,NM_153209.3;KIF19,synonymous_variant,p.=,ENST00000551294,;KIF19,non_coding_transcript_exon_variant,,ENST00000547389,;KIF19,non_coding_transcript_exon_variant,,ENST00000359939,; A ENST00000389916 Transcript synonymous_variant 504/3643 366/2997 122/998 G ggC/ggA rs145969437 1 1 KIF19 HGNC HGNC:26735 protein_coding YES CCDS32718.2 ENSP00000374566 Q2TAC6 UPI0000F0A553 NM_153209.3 5/20 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF434,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs145969437 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 74343070 74343070 C A 1 0 0 0 0 0 0 0 1 8146 697 25 2 2 KIF19 17 74343070 Silent SNP C C3N-01823_T 10908656 74343070 8914371 394 26091 TNRC6C 0 . GRCh38 17 78075162 78075162 + Missense_Mutation SNP G G A C3N-01823_T C3N-01823_N G G c.2935G>A p.Val979Met p.V979M ENST00000335749 8/21 329 277 52 177 177 0 strelka-varscan-mutect TNRC6C,missense_variant,p.Val979Met,ENST00000335749,NM_001142640.1;TNRC6C,missense_variant,p.Val982Met,ENST00000301624,NM_018996.3;TNRC6C,missense_variant,p.Val979Met,ENST00000588847,;TNRC6C,missense_variant,p.Val982Met,ENST00000588061,;TNRC6C,missense_variant,p.Val1189Met,ENST00000636222,;TNRC6C,non_coding_transcript_exon_variant,,ENST00000591851,;TNRC6C,non_coding_transcript_exon_variant,,ENST00000587990,; A ENST00000335749 Transcript missense_variant 3504/9740 2935/5181 979/1726 V/M Gtg/Atg COSM1153162,COSM985011 1 1 TNRC6C HGNC HGNC:29318 protein_coding YES CCDS45799.1 ENSP00000336783 Q9HCJ0 UPI0000EE5F80 NM_001142640.1 tolerated(0.94) 8/21 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF9,Superfamily_domains:SSF46934 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1212900362 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 78075162 78075162 G A 1 0 0 0 0 1 0 0 0 16815 1145 40 1 1 TNRC6C 17 78075162 Missense_Mutation SNP G C3N-01823_T 3732092 78075162 5182279 395 26092 TK1 0 . GRCh38 17 78185153 78185153 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.111G>A p.Met37Ile p.M37I ENST00000301634 3/7 204 188 16 100 100 0 strelka-varscan-mutect TK1,missense_variant,p.Met37Ile,ENST00000588734,;TK1,missense_variant,p.Met37Ile,ENST00000301634,NM_003258.4;TK1,missense_variant,p.Met37Ile,ENST00000590430,;TK1,missense_variant,p.Met37Ile,ENST00000590862,;TK1,missense_variant,p.Met37Ile,ENST00000586613,;AFMID,upstream_gene_variant,,ENST00000409257,NM_001010982.4;AFMID,upstream_gene_variant,,ENST00000327898,NM_001145526.2;AFMID,upstream_gene_variant,,ENST00000588800,;AFMID,upstream_gene_variant,,ENST00000591256,;AFMID,upstream_gene_variant,,ENST00000591952,;AFMID,upstream_gene_variant,,ENST00000589256,;AFMID,upstream_gene_variant,,ENST00000586542,;AFMID,upstream_gene_variant,,ENST00000586731,;TK1,non_coding_transcript_exon_variant,,ENST00000592126,;AFMID,upstream_gene_variant,,ENST00000592988,;AFMID,upstream_gene_variant,,ENST00000588199,;AFMID,upstream_gene_variant,,ENST00000589107,; T ENST00000301634 Transcript missense_variant 350/1628 111/705 37/234 M/I atG/atA 1 -1 TK1 HGNC HGNC:11830 protein_coding YES CCDS11754.1 ENSP00000301634 P04183 UPI000012DE94 NM_003258.4 tolerated(0.71) 3/7 hmmpanther:PTHR11441,hmmpanther:PTHR11441:SF0,Pfam_domain:PF00265,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.91915 0.9999997 1 1 1 0 T 3 4 83 78185153 78185153 C T 1 0 0 0 0 1 0 0 0 16374 826 29 3 3 TK1 17 78185153 Missense_Mutation SNP C C3N-01823_T 109991 78185153 5072288 396 26093 DNAH17 0 . GRCh38 17 78510481 78510481 + Missense_Mutation SNP G G T rs758994124 C3N-01823_T C3N-01823_N G G c.4139C>A p.Thr1380Lys p.T1380K ENST00000389840 27/81 233 176 57 93 93 0 strelka-varscan-mutect DNAH17,missense_variant,p.Thr1380Lys,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Thr1377Lys,ENST00000585328,;DNAH17,non_coding_transcript_exon_variant,,ENST00000587177,; T ENST00000389840 Transcript missense_variant 4264/13723 4139/13389 1380/4462 T/K aCg/aAg rs758994124 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 27/81 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE 1 SNV 5 1 PASS rs758994124 . 0 207 0 3 0 0 0 0 -20 0.9999976 1 1 1 0 T 3 4 83 78510481 78510481 G T 1 0 0 0 0 1 0 0 0 4416 1145 40 1 1 DNAH17 17 78510481 Missense_Mutation SNP G C3N-01823_T 325328 78510481 4746960 397 26094 SMCHD1 0 . GRCh38 18 2722649 2722649 + Silent SNP A A G novel C3N-01823_T C3N-01823_N A A c.2589A>G p.= p.P863P ENST00000320876 20/48 158 138 20 98 98 0 strelka-varscan-mutect SMCHD1,synonymous_variant,p.=,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,synonymous_variant,p.=,ENST00000577880,;SMCHD1,intron_variant,,ENST00000584897,;SMCHD1,upstream_gene_variant,,ENST00000581383,;SMCHD1,downstream_gene_variant,,ENST00000581711,; G ENST00000320876 Transcript synonymous_variant 2927/8821 2589/6018 863/2005 P ccA/ccG 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 20/48 hmmpanther:PTHR22640,hmmpanther:PTHR22640:SF2 LOW SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 2722649 2722649 A G 1 0 0 0 0 0 0 0 1 15081 175 7 5 5 SMCHD1 18 2722649 Silent SNP A C3N-01823_T 2722649 77650636 398 26095 ARHGAP28 0 . GRCh38 18 6859812 6859812 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.164A>T p.Asp55Val p.D55V ENST00000419673 4/17 209 169 40 151 151 0 strelka-varscan-mutect ARHGAP28,missense_variant,p.Asp55Val,ENST00000419673,NM_001010000.2;ARHGAP28,missense_variant,p.Asp55Val,ENST00000314319,;ARHGAP28,missense_variant,p.Asp162Val,ENST00000262227,;ARHGAP28,missense_variant,p.Asp214Val,ENST00000383472,;ARHGAP28,missense_variant,p.Asn50Ile,ENST00000531294,;ARHGAP28,missense_variant,p.Asp37Val,ENST00000532996,;ARHGAP28,missense_variant,p.Asp55Val,ENST00000581099,;ARHGAP28,intron_variant,,ENST00000577524,;ARHGAP28,intron_variant,,ENST00000584287,; T ENST00000419673 Transcript missense_variant 381/5492 164/1713 55/570 D/V gAt/gTt 1 1 ARHGAP28 HGNC HGNC:25509 protein_coding YES CCDS32785.1 ENSP00000392660 Q9P2N2 UPI00004CEC5C NM_001010000.2 tolerated(0.15) 4/17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 6859812 6859812 A T 1 0 0 0 0 1 0 0 0 1002 347 12 4 4 ARHGAP28 18 6859812 Missense_Mutation SNP A C3N-01823_T 4137163 6859812 73513473 399 26096 LAMA1 0 . GRCh38 18 6958545 6958545 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.7896G>T p.Glu2632Asp p.E2632D ENST00000389658 55/63 303 251 52 185 184 1 strelka-varscan-mutect LAMA1,missense_variant,p.Glu2632Asp,ENST00000389658,NM_005559.3;RP11-781P6.1,downstream_gene_variant,,ENST00000584722,;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488089,;LAMA1,non_coding_transcript_exon_variant,,ENST00000488064,;LAMA1,upstream_gene_variant,,ENST00000492048,; A ENST00000389658 Transcript missense_variant 7990/9657 7896/9228 2632/3075 E/D gaG/gaT 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 tolerated(0.48) 55/63 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 6958545 6958545 C A 1 0 0 0 0 1 0 0 0 8509 680 24 2 2 LAMA1 18 6958545 Missense_Mutation SNP C C3N-01823_T 98733 6958545 73414740 400 26097 PIEZO2 0 . GRCh38 18 10800389 10800389 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.1326C>A p.= p.A442A ENST00000503781 11/52 265 227 38 185 185 0 strelka-varscan-mutect PIEZO2,synonymous_variant,p.=,ENST00000383408,;PIEZO2,synonymous_variant,p.=,ENST00000302079,;PIEZO2,synonymous_variant,p.=,ENST00000580640,;PIEZO2,synonymous_variant,p.=,ENST00000503781,NM_022068.3;PIEZO2,synonymous_variant,p.=,ENST00000579112,;PIEZO2,synonymous_variant,p.=,ENST00000582913,; T ENST00000503781 Transcript synonymous_variant 1326/8259 1326/8259 442/2752 A gcC/gcA 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 11/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 LOW 1 SNV 1 1 PASS rs1259744368 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 10800389 10800389 G T 1 0 0 0 0 0 0 0 1 11975 1103 39 1 1 PIEZO2 18 10800389 Silent SNP G C3N-01823_T 3841844 10800389 69572896 401 26098 DSC2 0 . GRCh38 18 31074904 31074904 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1667G>T p.Gly556Val p.G556V ENST00000280904 12/16 504 434 70 403 402 1 strelka-varscan-mutect DSC2,missense_variant,p.Gly556Val,ENST00000280904,NM_024422.4;DSC2,missense_variant,p.Gly556Val,ENST00000251081,NM_004949.4; A ENST00000280904 Transcript missense_variant 2111/12325 1667/2706 556/901 G/V gGg/gTg 1 -1 DSC2 HGNC HGNC:3036 protein_coding YES CCDS11892.1 ENSP00000280904 Q02487 UPI00001298F9 NM_024422.4 deleterious(0) 12/16 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR01818,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF0,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs977269905 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 31074904 31074904 C A 1 0 0 0 0 1 0 0 0 4587 637 22 2 2 DSC2 18 31074904 Missense_Mutation SNP C C3N-01823_T 20274515 31074904 49298381 402 26099 CCDC178 0 . GRCh38 18 33224819 33224819 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1774G>T p.Asp592Tyr p.D592Y ENST00000583930 16/23 99 82 17 74 74 0 strelka-mutect CCDC178,missense_variant,p.Asp592Tyr,ENST00000383096,;CCDC178,missense_variant,p.Asp592Tyr,ENST00000403303,NM_001105528.1;CCDC178,missense_variant,p.Asp592Tyr,ENST00000583930,;CCDC178,missense_variant,p.Asp592Tyr,ENST00000300227,NM_198995.2;CCDC178,missense_variant,p.Asp592Tyr,ENST00000406524,;CCDC178,missense_variant,p.Asp592Tyr,ENST00000579947,;CCDC178,missense_variant,p.Asp139Tyr,ENST00000581524,;CCDC178,intron_variant,,ENST00000579916,; A ENST00000583930 Transcript missense_variant 1853/3094 1774/2676 592/891 D/Y Gat/Tat 1 -1 CCDC178 HGNC HGNC:29588 protein_coding YES CCDS77174.1 ENSP00000463254 F8W7A7 UPI00020655A5 deleterious(0.01) 16/23 Low_complexity_(Seg):seg,hmmpanther:PTHR35088:SF1,hmmpanther:PTHR35088 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 33224819 33224819 C A 1 0 0 0 0 1 0 0 0 2493 913 32 2 2 CCDC178 18 33224819 Missense_Mutation SNP C C3N-01823_T 2149915 33224819 47148466 403 26100 MOCOS 0 . GRCh38 18 36260143 36260143 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.2377G>C p.Asp793His p.D793H ENST00000261326 13/15 536 509 27 351 351 0 strelka-mutect MOCOS,missense_variant,p.Asp793His,ENST00000261326,NM_017947.2;MOCOS,non_coding_transcript_exon_variant,,ENST00000588132,; C ENST00000261326 Transcript missense_variant 2398/6160 2377/2667 793/888 D/H Gat/Cat 1 1 MOCOS HGNC HGNC:18234 protein_coding YES CCDS11919.1 ENSP00000261326 Q96EN8 UPI000013D165 NM_017947.2 tolerated(0.11) 13/15 HAMAP:MF_03050,Pfam_domain:PF03473,PROSITE_profiles:PS51340,hmmpanther:PTHR14237,hmmpanther:PTHR14237:SF19,Superfamily_domains:SSF50800 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 36260143 36260143 G C 1 0 0 0 0 1 0 0 0 9652 1174 41 4 4 MOCOS 18 36260143 Missense_Mutation SNP G C3N-01823_T 3035324 36260143 44113142 404 26101 MBD1 0 . GRCh38 18 50276851 50276851 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.373G>T p.Ala125Ser p.A125S ENST00000590208 4/16 656 551 105 442 440 2 strelka-varscan-mutect MBD1,missense_variant,p.Ala125Ser,ENST00000591416,;MBD1,missense_variant,p.Ala125Ser,ENST00000269468,NM_015846.3;MBD1,missense_variant,p.Ala125Ser,ENST00000347968,NM_015844.2;MBD1,missense_variant,p.Ala125Ser,ENST00000269471,NM_015845.3;MBD1,missense_variant,p.Ala125Ser,ENST00000339998,NM_001204142.1;MBD1,missense_variant,p.Ala125Ser,ENST00000590208,NM_001204136.1;MBD1,missense_variant,p.Ala125Ser,ENST00000353909,NM_015847.3;MBD1,missense_variant,p.Ala125Ser,ENST00000585672,NM_001204141.1;MBD1,missense_variant,p.Ala125Ser,ENST00000457839,NM_001204137.1,NM_001204138.1;MBD1,missense_variant,p.Ala125Ser,ENST00000382948,NM_001204139.1;MBD1,missense_variant,p.Ala125Ser,ENST00000585595,;MBD1,missense_variant,p.Ala125Ser,ENST00000398495,NM_001204140.1;MBD1,missense_variant,p.Ala50Ser,ENST00000592060,;MBD1,missense_variant,p.Ala125Ser,ENST00000587605,NM_001204143.1;MBD1,missense_variant,p.Ala125Ser,ENST00000398493,;MBD1,missense_variant,p.Ala125Ser,ENST00000588937,;MBD1,missense_variant,p.Ala125Ser,ENST00000591535,NM_001204151.1;MBD1,missense_variant,p.Ala125Ser,ENST00000398488,NM_002384.2;MBD1,upstream_gene_variant,,ENST00000589541,;MBD1,upstream_gene_variant,,ENST00000589733,;MBD1,3_prime_UTR_variant,,ENST00000590215,;MBD1,non_coding_transcript_exon_variant,,ENST00000586118,;MBD1,non_coding_transcript_exon_variant,,ENST00000589867,;MBD1,upstream_gene_variant,,ENST00000586679,;MBD1,upstream_gene_variant,,ENST00000586884,;MBD1,upstream_gene_variant,,ENST00000591661,;MBD1,downstream_gene_variant,,ENST00000589758,; A ENST00000590208 Transcript missense_variant 720/2913 373/1968 125/655 A/S Gct/Tct 1 -1 MBD1 HGNC HGNC:6916 protein_coding YES CCDS59320.1 ENSP00000468785 Q9UIS9 UPI0001F995B6 NM_001204136.1 tolerated(0.23) 4/16 hmmpanther:PTHR12396,hmmpanther:PTHR12396:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 50276851 50276851 C A 1 0 0 0 0 1 0 0 0 9271 797 28 2 2 MBD1 18 50276851 Missense_Mutation SNP C C3N-01823_T 14016708 50276851 30096434 405 26102 MALT1 0 . GRCh38 18 58715955 58715955 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.1006G>A p.Asp336Asn p.D336N ENST00000348428 9/17 173 162 11 160 160 0 strelka-varscan-mutect MALT1,missense_variant,p.Asp336Asn,ENST00000348428,NM_006785.3;MALT1,missense_variant,p.Asp325Asn,ENST00000345724,NM_173844.2;RP11-126O1.4,intron_variant,,ENST00000588835,; A ENST00000348428 Transcript missense_variant 1264/9368 1006/2475 336/824 D/N Gac/Aac 1 1 MALT1 HGNC HGNC:6819 protein_coding YES CCDS11967.1 ENSP00000319279 Q9UDY8 UPI000004D05E NM_006785.3 tolerated(0.41) 9/17 hmmpanther:PTHR22576,hmmpanther:PTHR22576:SF29,Superfamily_domains:SSF52129 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 58715955 58715955 G A 1 0 0 0 0 1 0 0 0 9123 1290 45 3 3 MALT1 18 58715955 Missense_Mutation SNP G C3N-01823_T 8439104 58715955 21657330 406 26103 ZNF407 0 . GRCh38 18 74632586 74632586 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1567G>T p.Gly523Cys p.G523C ENST00000299687 1/8 299 275 24 181 180 1 strelka-varscan-mutect ZNF407,missense_variant,p.Gly523Cys,ENST00000299687,NM_017757.2;ZNF407,missense_variant,p.Gly523Cys,ENST00000577538,NM_001146189.1;ZNF407,missense_variant,p.Gly523Cys,ENST00000582337,;ZNF407,missense_variant,p.Gly523Cys,ENST00000309902,NM_001146190.1; T ENST00000299687 Transcript missense_variant 1567/7948 1567/6747 523/2248 G/C Ggc/Tgc 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 deleterious(0) 1/8 MODERATE 1 SNV 1 1 PASS rs1252500651 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 74632586 74632586 G T 1 0 0 0 0 1 0 0 0 18459 1348 47 2 2 ZNF407 18 74632586 Missense_Mutation SNP G C3N-01823_T 15916631 74632586 5740699 407 26104 SALL3 0 . GRCh38 18 78992357 78992357 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.366C>A p.= p.G122G ENST00000537592 2/3 53 49 4 44 44 0 strelka-mutect SALL3,synonymous_variant,p.=,ENST00000537592,NM_171999.3;SALL3,synonymous_variant,p.=,ENST00000575389,;SALL3,5_prime_UTR_variant,,ENST00000536229,;SALL3,intron_variant,,ENST00000616649,;SALL3,upstream_gene_variant,,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; A ENST00000537592 Transcript synonymous_variant 366/6555 366/3903 122/1300 G ggC/ggA 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 LOW 1 SNV 5 1 PASS rs1466740497 . 0 204 5 0 0 0 0 0 -10.14095 1 1 1 1 0 A 2 1 83 78992357 78992357 C A 1 0 0 0 0 0 0 0 1 14071 755 27 1 1 SALL3 18 78992357 Silent SNP C C3N-01823_T 4359771 78992357 1380928 408 26105 ZNF556 0 . GRCh38 19 2877581 2877581 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.623G>A p.Cys208Tyr p.C208Y ENST00000307635 4/4 408 333 75 269 269 0 strelka-varscan-mutect ZNF556,missense_variant,p.Cys208Tyr,ENST00000307635,NM_024967.2;ZNF556,missense_variant,p.Cys207Tyr,ENST00000586426,NM_001300843.1;ZNF556,downstream_gene_variant,,ENST00000586470,;AC006130.4,upstream_gene_variant,,ENST00000586202,; A ENST00000307635 Transcript missense_variant 710/6574 623/1371 208/456 C/Y tGc/tAc 1 1 ZNF556 HGNC HGNC:25669 protein_coding YES CCDS12097.1 ENSP00000302603 Q9HAH1 UPI000006DA0F NM_024967.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF163,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 2877581 2877581 G A 1 0 0 0 0 1 0 0 0 18561 1319 46 3 3 ZNF556 19 2877581 Missense_Mutation SNP G C3N-01823_T 2877581 55740035 409 26106 MUC16 0 . GRCh38 19 8965816 8965816 + Missense_Mutation SNP C C A rs370110448 C3N-01823_T C3N-01823_N C C c.10954G>T p.Val3652Leu p.V3652L ENST00000397910 3/84 103 85 18 45 45 0 strelka-varscan-mutect MUC16,missense_variant,p.Val3652Leu,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 11158/43816 10954/43524 3652/14507 V/L Gta/Tta rs370110448 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS rs370110448 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 83 8965816 8965816 C A 1 0 0 0 0 1 0 0 0 9972 478 17 2 2 MUC16 19 8965816 Missense_Mutation SNP C C3N-01823_T 6088235 8965816 49651800 410 26107 KEAP1 0 . GRCh38 19 10489679 10489679 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.1500C>G p.Ile500Met p.I500M ENST00000171111 4/6 355 334 21 185 185 0 strelka-varscan-mutect KEAP1,missense_variant,p.Ile500Met,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Ile500Met,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Ile107Met,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,intron_variant,,ENST00000590593,;KEAP1,downstream_gene_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590237,; C ENST00000171111 Transcript missense_variant 2048/2955 1500/1875 500/624 I/M atC/atG 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 tolerated(0.22) 4/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 10489679 10489679 G C 1 0 0 0 0 1 0 0 0 8061 1280 45 4 4 KEAP1 19 10489679 Missense_Mutation SNP G C3N-01823_T 1523863 10489679 48127937 411 26108 KEAP1 0 . GRCh38 19 10492208 10492208 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.694A>T p.Ile232Phe p.I232F ENST00000171111 3/6 182 140 42 128 128 0 strelka-varscan-mutect KEAP1,missense_variant,p.Ile232Phe,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Ile232Phe,ENST00000393623,NM_012289.3;KEAP1,missense_variant,p.Ile232Phe,ENST00000592055,;KEAP1,upstream_gene_variant,,ENST00000592478,;CTC-429L19.3,upstream_gene_variant,,ENST00000592671,;KEAP1,non_coding_transcript_exon_variant,,ENST00000588024,;KEAP1,3_prime_UTR_variant,,ENST00000585845,;KEAP1,upstream_gene_variant,,ENST00000590593,;KEAP1,upstream_gene_variant,,ENST00000590237,; A ENST00000171111 Transcript missense_variant 1242/2955 694/1875 232/624 I/F Atc/Ttc 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0.02) 3/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Pfam_domain:PF07707,PIRSF_domain:PIRSF037037,SMART_domains:SM00875 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 10492208 10492208 T A 1 0 0 0 0 1 0 0 0 8061 1464 51 4 4 KEAP1 19 10492208 Missense_Mutation SNP T C3N-01823_T 2529 10492208 48125408 412 26109 SMARCA4 0 . GRCh38 19 11033518 11033518 + Splice_Site SNP G G T C3N-01823_T C3N-01823_N G G c.3774+1G>T p.X1258_splice ENST00000429416 501 392 109 350 350 0 strelka-varscan-mutect SMARCA4,splice_donor_variant,,ENST00000429416,NM_001128844.1;SMARCA4,splice_donor_variant,,ENST00000413806,;SMARCA4,splice_donor_variant,,ENST00000450717,NM_001128849.1;SMARCA4,splice_donor_variant,,ENST00000344626,NM_003072.3;SMARCA4,splice_donor_variant,,ENST00000590574,NM_001128847.1;SMARCA4,splice_donor_variant,,ENST00000589677,NM_001128846.1;SMARCA4,splice_donor_variant,,ENST00000541122,NM_001128845.1;SMARCA4,splice_donor_variant,,ENST00000444061,NM_001128848.1;SMARCA4,intron_variant,,ENST00000592158,;uc_338,upstream_gene_variant,,ENST00000620113,;SMARCA4,splice_donor_variant,,ENST00000538456,;SMARCA4,splice_donor_variant,,ENST00000585799,;SMARCA4,splice_donor_variant,,ENST00000591595,;SMARCA4,splice_donor_variant,,ENST00000592604,;SMARCA4,splice_donor_variant,,ENST00000586892,;SMARCA4,downstream_gene_variant,,ENST00000591545,; T ENST00000429416 Transcript splice_donor_variant -/5691 3774/4944 1258/1647 COSM3772494,COSM3772495 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 27/35 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 83 11033518 11033518 G T 1 0 0 0 0 0 0 1 0 15063 1275 44 2 2 SMARCA4 19 11033518 Splice_Site SNP G C3N-01823_T 541310 11033518 47584098 413 26110 GCDH 0 . GRCh38 19 12899508 12899508 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.1284C>G p.Ile428Met p.I428M ENST00000222214 12/12 562 527 35 412 412 0 strelka-varscan-mutect GCDH,missense_variant,p.Ile428Met,ENST00000222214,NM_000159.3,NM_013976.3;GCDH,missense_variant,p.Ile428Met,ENST00000591470,;SYCE2,intron_variant,,ENST00000293695,NM_001105578.1;SYCE2,intron_variant,,ENST00000592819,;GCDH,intron_variant,,ENST00000591050,;GCDH,downstream_gene_variant,,ENST00000588905,;GCDH,downstream_gene_variant,,ENST00000590472,;GCDH,downstream_gene_variant,,ENST00000589039,;GCDH,upstream_gene_variant,,ENST00000588242,;GCDH,3_prime_UTR_variant,,ENST00000590530,;GCDH,non_coding_transcript_exon_variant,,ENST00000591043,;GCDH,non_coding_transcript_exon_variant,,ENST00000585420,;GCDH,downstream_gene_variant,,ENST00000421816,;RPS6P25,downstream_gene_variant,,ENST00000464444,; G ENST00000222214 Transcript missense_variant 1495/1956 1284/1317 428/438 I/M atC/atG 1 1 GCDH HGNC HGNC:4189 protein_coding YES CCDS12286.1 ENSP00000222214 Q92947 A0A024R7F9 UPI000012B292 NM_000159.3,NM_013976.3 tolerated_low_confidence(0.17) 12/12 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF307,Pfam_domain:PF00441,Gene3D:1.20.140.10,Superfamily_domains:SSF47203 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 12899508 12899508 C G 1 0 0 0 0 1 0 0 0 6157 816 29 4 4 GCDH 19 12899508 Missense_Mutation SNP C C3N-01823_T 1865990 12899508 45718108 414 26111 CYP4F11 0 . GRCh38 19 15924799 15924799 + Silent SNP C C G rs757082382 C3N-01823_T C3N-01823_N C C c.609G>C p.= p.L203L ENST00000402119 5/12 306 244 62 208 208 0 strelka-varscan-mutect CYP4F11,synonymous_variant,p.=,ENST00000402119,NM_021187.3;CYP4F11,synonymous_variant,p.=,ENST00000248041,NM_001128932.1;CYP4F11,synonymous_variant,p.=,ENST00000620614,;CYP4F11,synonymous_variant,p.=,ENST00000326742,;CYP4F11,intron_variant,,ENST00000591841,; G ENST00000402119 Transcript synonymous_variant 1036/3161 609/1575 203/524 L ctG/ctC rs757082382 1 -1 CYP4F11 HGNC HGNC:13265 protein_coding YES CCDS12337.1 ENSP00000384588 Q9HBI6 UPI000013CC35 NM_021187.3 5/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF16,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs757082382 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 83 15924799 15924799 C G 1 0 0 0 0 0 0 0 1 3989 697 25 4 4 CYP4F11 19 15924799 Silent SNP C C3N-01823_T 3025291 15924799 42692817 415 26112 CYP4F11 0 . GRCh38 19 15927305 15927305 + Nonsense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.432G>A p.Trp144Ter p.W144* ENST00000402119 4/12 195 179 16 109 107 2 strelka-varscan-mutect CYP4F11,stop_gained,p.Trp144Ter,ENST00000402119,NM_021187.3;CYP4F11,stop_gained,p.Trp144Ter,ENST00000248041,NM_001128932.1;CYP4F11,stop_gained,p.Trp144Ter,ENST00000620614,;CYP4F11,stop_gained,p.Trp144Ter,ENST00000326742,;CYP4F11,5_prime_UTR_variant,,ENST00000591841,; T ENST00000402119 Transcript stop_gained 859/3161 432/1575 144/524 W/* tgG/tgA 1 -1 CYP4F11 HGNC HGNC:13265 protein_coding YES CCDS12337.1 ENSP00000384588 Q9HBI6 UPI000013CC35 NM_021187.3 4/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF16,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 83 15927305 15927305 C T 1 0 0 0 0 0 1 0 0 3989 856 30 3 3 CYP4F11 19 15927305 Nonsense_Mutation SNP C C3N-01823_T 2506 15927305 42690311 416 26113 CALR3 0 . GRCh38 19 16490378 16490378 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.386A>G p.Tyr129Cys p.Y129C ENST00000269881 3/9 379 346 33 234 233 1 strelka-varscan-mutect CALR3,missense_variant,p.Tyr129Cys,ENST00000269881,NM_145046.4;CALR3,intron_variant,,ENST00000600762,;CTD-3222D19.2,intron_variant,,ENST00000409035,; C ENST00000269881 Transcript missense_variant 449/1292 386/1155 129/384 Y/C tAt/tGt 1 -1 CALR3 HGNC HGNC:20407 protein_coding YES CCDS12344.1 ENSP00000269881 Q96L12 A0A140VJF7 UPI000013D85C NM_145046.4 tolerated(0.07) 3/9 hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF3,Pfam_domain:PF00262,PIRSF_domain:PIRSF002356,Gene3D:2.60.120.200,Superfamily_domains:SSF49899,Prints_domain:PR00626 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 16490378 16490378 T C 1 0 0 0 0 1 0 0 0 2284 1406 49 5 5 CALR3 19 16490378 Missense_Mutation SNP T C3N-01823_T 563073 16490378 42127238 417 26114 PLVAP 0 . GRCh38 19 17376971 17376971 + Silent SNP G G T C3N-01823_T C3N-01823_N G G c.318C>A p.= p.R106R ENST00000252590 1/6 270 216 54 150 150 0 strelka-varscan-mutect PLVAP,synonymous_variant,p.=,ENST00000252590,NM_031310.2;PLVAP,synonymous_variant,p.=,ENST00000599426,; T ENST00000252590 Transcript synonymous_variant 380/2305 318/1329 106/442 R cgC/cgA COSM5388999 1 -1 PLVAP HGNC HGNC:13635 protein_coding YES CCDS32952.1 ENSP00000252590 Q9BX97 UPI000003ED36 NM_031310.2 1/6 hmmpanther:PTHR21687:SF5,hmmpanther:PTHR21687,Pfam_domain:PF06637 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 17376971 17376971 G T 1 0 0 0 0 0 0 0 1 12222 1190 42 2 2 PLVAP 19 17376971 Silent SNP G C3N-01823_T 886593 17376971 41240645 418 26115 KLHL26 0 . GRCh38 19 18668358 18668358 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.961G>T p.Asp321Tyr p.D321Y ENST00000300976 3/3 251 223 28 108 107 1 strelka-varscan-mutect KLHL26,missense_variant,p.Asp321Tyr,ENST00000300976,NM_018316.1;KLHL26,intron_variant,,ENST00000599006,;KLHL26,downstream_gene_variant,,ENST00000595423,;KLHL26,downstream_gene_variant,,ENST00000595182,;KLHL26,downstream_gene_variant,,ENST00000596843,;KLHL26,downstream_gene_variant,,ENST00000600657,; T ENST00000300976 Transcript missense_variant 1051/4407 961/1848 321/615 D/Y Gac/Tac COSM4563166 1 1 KLHL26 HGNC HGNC:25623 protein_coding YES CCDS12384.1 ENSP00000300976 Q53HC5 A0A024R7N5 UPI0000071AC2 NM_018316.1 deleterious(0.02) 3/3 hmmpanther:PTHR24412:SF56,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037,Gene3D:1k3iA02,SMART_domains:SM00612,Superfamily_domains:0052715 1 MODERATE 1 SNV 1 1 1 PASS rs1422020469 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 18668358 18668358 G T 1 0 0 0 0 1 0 0 0 8245 1058 37 1 1 KLHL26 19 18668358 Missense_Mutation SNP G C3N-01823_T 1291387 18668358 39949258 419 26116 ZNF257 0 . GRCh38 19 22088182 22088182 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.432G>T p.Met144Ile p.M144I ENST00000594947 4/4 61 50 11 36 36 0 strelka-varscan-mutect ZNF257,missense_variant,p.Met144Ile,ENST00000594947,NM_033468.2;ZNF257,missense_variant,p.Met68Ile,ENST00000597927,;ZNF257,3_prime_UTR_variant,,ENST00000600162,;ZNF257,3_prime_UTR_variant,,ENST00000435820,NM_001316996.1; T ENST00000594947 Transcript missense_variant 576/3874 432/1692 144/563 M/I atG/atT COSM565872 1 1 ZNF257 HGNC HGNC:13498 protein_coding YES CCDS46030.1 ENSP00000470209 Q9Y2Q1 UPI0000E045CA NM_033468.2 tolerated(1) 4/4 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF127,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 4 1 1 PASS rs1400263933 . 1 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 83 22088182 22088182 G T 1 0 0 0 0 1 0 0 0 18376 1377 48 2 2 ZNF257 19 22088182 Missense_Mutation SNP G C3N-01823_T 3419824 22088182 36529434 420 26117 ZNF98 0 . GRCh38 19 22392330 22392330 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.905C>G p.Ala302Gly p.A302G ENST00000357774 4/4 95 74 21 46 46 0 strelka-varscan-mutect ZNF98,missense_variant,p.Ala302Gly,ENST00000357774,NM_001098626.1;ZNF98,downstream_gene_variant,,ENST00000593657,; C ENST00000357774 Transcript missense_variant 1027/2338 905/1719 302/572 A/G gCt/gGt 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 deleterious(0.02) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS rs776973686 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 22392330 22392330 G C 1 0 0 0 0 1 0 0 0 18796 971 34 4 4 ZNF98 19 22392330 Missense_Mutation SNP G C3N-01823_T 304148 22392330 36225286 421 26118 ZNF728 0 . GRCh38 19 22976488 22976488 + Silent SNP G G C rs754232352 C3N-01823_T C3N-01823_N G G c.849C>G p.= p.P283P ENST00000594710 4/4 365 298 67 196 196 0 strelka-varscan-mutect ZNF728,synonymous_variant,p.=,ENST00000594710,NM_001267716.1;ZNF728,downstream_gene_variant,,ENST00000599851,; C ENST00000594710 Transcript synonymous_variant 995/2015 849/1869 283/622 P ccC/ccG rs754232352 1 -1 ZNF728 HGNC HGNC:32463 protein_coding YES CCDS59370.1 ENSP00000471593 P0DKX0 UPI0002656E4B NM_001267716.1 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF239,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 LOW 1 SNV 3 1 PASS rs754232352 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 22976488 22976488 G C 1 0 0 0 0 0 0 0 1 18702 987 35 4 4 ZNF728 19 22976488 Silent SNP G C3N-01823_T 584158 22976488 35641128 422 26119 ZNF91 0 . GRCh38 19 23362326 23362327 + Frame_Shift_Ins INS - - T novel C3N-01823_T C3N-01823_N - - c.652dupA p.Thr218AsnfsTer10 p.T218Nfs*10 ENST00000300619 4/4 157 146 11 98 98 0 varindel-pindel ZNF91,frameshift_variant,p.Thr218AsnfsTer10,ENST00000300619,NM_003430.3;ZNF91,frameshift_variant,p.Thr186AsnfsTer10,ENST00000397082,NM_001300951.1;ZNF91,frameshift_variant,p.Thr119AsnfsTer10,ENST00000595533,;ZNF91,intron_variant,,ENST00000599743,;ZNF91,intron_variant,,ENST00000596989,;ZNF91,upstream_gene_variant,,ENST00000596528,;ZNF91,upstream_gene_variant,,ENST00000599281,;ZNF91,upstream_gene_variant,,ENST00000593341,; T ENST00000300619 Transcript frameshift_variant 858-859/5489 652-653/3576 218/1191 T/NX acc/aAcc 1 -1 ZNF91 HGNC HGNC:13166 protein_coding YES CCDS42541.1 ENSP00000300619 Q05481 UPI00002038F9 NM_003430.3 4/4 PROSITE_profiles:PS50157,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 HIGH 1 insertion 1 1 PASS . . 0 207 0 2 0 0 0 0 -14.95378 0.9999996 1 1 1 0 T 7 5 83 23362326 23362326 - T 1 0 1 1 0 0 0 0 0 18793 1261 44 0 0 ZNF91 19 23362326 Frame_Shift_Ins INS - C3N-01823_T 385838 23362326 35255290 423 26120 NUDT19 0 . GRCh38 19 32711868 32711868 + Missense_Mutation SNP C C G rs372447363 C3N-01823_T C3N-01823_N C C c.1039C>G p.Arg347Gly p.R347G ENST00000397061 3/3 576 522 54 420 420 0 strelka-varscan-mutect NUDT19,missense_variant,p.Arg347Gly,ENST00000397061,NM_001105570.1; G ENST00000397061 Transcript missense_variant 1039/2967 1039/1128 347/375 R/G Cgc/Ggc rs372447363 1 1 NUDT19 HGNC HGNC:32036 protein_coding YES CCDS42543.1 ENSP00000380251 A8MXV4 UPI00001D819F NM_001105570.1 tolerated(0.32) 3/3 hmmpanther:PTHR12318:SF0,hmmpanther:PTHR12318 MODERATE 1 SNV 2 1 PASS rs372447363 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 32711868 32711868 C G 1 0 0 0 0 1 0 0 0 10800 884 31 4 4 NUDT19 19 32711868 Missense_Mutation SNP C C3N-01823_T 9349542 32711868 25905748 424 26121 GPATCH1 0 . GRCh38 19 33126605 33126605 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2637G>T p.Lys879Asn p.K879N ENST00000170564 19/20 367 336 31 239 238 1 strelka-varscan-mutect GPATCH1,missense_variant,p.Lys879Asn,ENST00000170564,NM_018025.2;GPATCH1,non_coding_transcript_exon_variant,,ENST00000592262,; T ENST00000170564 Transcript missense_variant 2951/3492 2637/2796 879/931 K/N aaG/aaT 1 1 GPATCH1 HGNC HGNC:24658 protein_coding YES CCDS12428.1 ENSP00000170564 Q9BRR8 UPI000004EC71 NM_018025.2 deleterious_low_confidence(0.01) 19/20 Low_complexity_(Seg):seg,hmmpanther:PTHR13384:SF19,hmmpanther:PTHR13384 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 33126605 33126605 G T 1 0 0 0 0 1 0 0 0 6489 962 34 2 2 GPATCH1 19 33126605 Missense_Mutation SNP G C3N-01823_T 414737 33126605 25491011 425 26122 MAG 0 . GRCh38 19 35295708 35295708 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.142G>T p.Asp48Tyr p.D48Y ENST00000392213 4/11 271 224 47 167 166 1 strelka-varscan-mutect MAG,missense_variant,p.Asp48Tyr,ENST00000361922,NM_080600.2;MAG,missense_variant,p.Asp48Tyr,ENST00000392213,NM_002361.3;MAG,missense_variant,p.Asp23Tyr,ENST00000537831,NM_001199216.1;MAG,missense_variant,p.Asp48Tyr,ENST00000595791,;MAG,missense_variant,p.Asp23Tyr,ENST00000600291,;MAG,missense_variant,p.Asp48Tyr,ENST00000597035,; T ENST00000392213 Transcript missense_variant 301/2390 142/1881 48/626 D/Y Gat/Tat 1 1 MAG HGNC HGNC:6783 protein_coding YES CCDS12455.1 ENSP00000376048 P20916 UPI000012EB2F NM_002361.3 deleterious(0) 4/11 Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF54,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 35295708 35295708 G T 1 0 0 0 0 1 0 0 0 9078 1174 41 2 2 MAG 19 35295708 Missense_Mutation SNP G C3N-01823_T 2169103 35295708 23321908 426 26123 KRTDAP 0 . GRCh38 19 35490405 35490405 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.38C>A p.Ser13Tyr p.S13Y ENST00000338897 1/6 116 103 13 80 80 0 strelka-varscan-mutect KRTDAP,missense_variant,p.Ser13Tyr,ENST00000338897,NM_207392.2;KRTDAP,missense_variant,p.Ser13Tyr,ENST00000484218,NM_001244847.1;KRTDAP,intron_variant,,ENST00000479340,; T ENST00000338897 Transcript missense_variant 127/491 38/300 13/99 S/Y tCc/tAc 1 -1 KRTDAP HGNC HGNC:16313 protein_coding YES CCDS12462.1 ENSP00000339251 P60985 UPI0000035979 NM_207392.2 deleterious_low_confidence(0) 1/6 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR36463,hmmpanther:PTHR36463:SF1,PD940796 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 35490405 35490405 G T 1 0 0 0 0 1 0 0 0 8479 1174 41 2 2 KRTDAP 19 35490405 Missense_Mutation SNP G C3N-01823_T 194697 35490405 23127211 427 26124 NFKBID 0 . GRCh38 19 35890007 35890007 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.771G>T p.= p.G257G ENST00000396901 11/12 168 133 35 110 110 0 strelka-varscan-mutect NFKBID,synonymous_variant,p.=,ENST00000396901,NM_139239.1;NFKBID,synonymous_variant,p.=,ENST00000606253,;NFKBID,3_prime_UTR_variant,,ENST00000590828,;NFKBID,downstream_gene_variant,,ENST00000586361,; A ENST00000396901 Transcript synonymous_variant 1345/1834 771/942 257/313 G ggG/ggT 1 -1 NFKBID HGNC HGNC:15671 protein_coding YES CCDS42552.1 ENSP00000380109 Q8NI38 UPI000006EE99 NM_139239.1 11/12 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR24124,hmmpanther:PTHR24124:SF7,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 35890007 35890007 C A 1 0 0 0 0 0 0 0 1 10416 726 26 2 2 NFKBID 19 35890007 Silent SNP C C3N-01823_T 399602 35890007 22727609 428 26125 ZNF420 0 . GRCh38 19 37129047 37129047 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.2056G>A p.Val686Ile p.V686I ENST00000337995 5/5 108 100 8 49 49 0 strelka-varscan-mutect ZNF420,missense_variant,p.Val686Ile,ENST00000337995,NM_144689.3;ZNF420,intron_variant,,ENST00000304239,;ZNF420,intron_variant,,ENST00000585862,;CTC-454I21.3,intron_variant,,ENST00000588873,;ZNF420,downstream_gene_variant,,ENST00000589245,;ZNF420,downstream_gene_variant,,ENST00000587029,;ZNF420,downstream_gene_variant,,ENST00000590332,;CTC-454I21.4,intron_variant,,ENST00000587645,;ZNF585A,intron_variant,,ENST00000588723,;ZNF420,intron_variant,,ENST00000586540,;ZNF585A,intron_variant,,ENST00000587817,;ZNF420,downstream_gene_variant,,ENST00000589461,; A ENST00000337995 Transcript missense_variant 2271/3535 2056/2067 686/688 V/I Gtt/Att 1 1 ZNF420 HGNC HGNC:20649 protein_coding YES CCDS12498.1 ENSP00000338770 Q8TAQ5 UPI000007049F NM_144689.3 deleterious(0.02) 5/5 MODERATE 1 SNV 1 1 PASS rs1444427924 . 0 204 5 0 0 0 0 0 -16.03253 1 1 1 1 0 A 3 1 83 37129047 37129047 G A 1 0 0 0 0 1 0 0 0 18469 1029 36 3 3 ZNF420 19 37129047 Missense_Mutation SNP G C3N-01823_T 1239040 37129047 21488569 429 26126 ZNF383 0 . GRCh38 19 37243093 37243093 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.857T>A p.Val286Glu p.V286E ENST00000352998 5/5 209 193 16 113 113 0 strelka-varscan-mutect ZNF383,missense_variant,p.Val286Glu,ENST00000352998,NM_152604.1;ZNF383,missense_variant,p.Val286Glu,ENST00000589413,;ZNF383,missense_variant,p.Val286Glu,ENST00000590503,;ZNF383,downstream_gene_variant,,ENST00000588371,;ZNF383,non_coding_transcript_exon_variant,,ENST00000586068,;ZNF383,downstream_gene_variant,,ENST00000588250,; A ENST00000352998 Transcript missense_variant 1115/6760 857/1428 286/475 V/E gTa/gAa 1 1 ZNF383 HGNC HGNC:18609 protein_coding YES CCDS12501.1 ENSP00000340132 Q8NA42 UPI00000717CC NM_152604.1 tolerated(1) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 37243093 37243093 T A 1 0 0 0 0 1 0 0 0 18446 1638 57 4 4 ZNF383 19 37243093 Missense_Mutation SNP T C3N-01823_T 114046 37243093 21374523 430 26127 WDR87 0 . GRCh38 19 37886032 37886032 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.7639C>A p.Leu2547Ile p.L2547I ENST00000447313 6/6 227 181 46 153 153 0 strelka-varscan-mutect WDR87,missense_variant,p.Leu2547Ile,ENST00000447313,NM_001291088.1;WDR87,missense_variant,p.Leu2508Ile,ENST00000303868,NM_031951.4; T ENST00000447313 Transcript missense_variant 7800/9009 7639/8739 2547/2912 L/I Ctc/Atc 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 deleterious(0.04) 6/6 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 37886032 37886032 G T 1 0 0 0 0 1 0 0 0 17890 942 33 2 2 WDR87 19 37886032 Missense_Mutation SNP G C3N-01823_T 642939 37886032 20731584 431 26128 WDR87 0 . GRCh38 19 37886377 37886377 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.7294C>G p.Leu2432Val p.L2432V ENST00000447313 6/6 126 117 9 87 87 0 strelka-mutect WDR87,missense_variant,p.Leu2432Val,ENST00000447313,NM_001291088.1;WDR87,missense_variant,p.Leu2393Val,ENST00000303868,NM_031951.4; C ENST00000447313 Transcript missense_variant 7455/9009 7294/8739 2432/2912 L/V Ctg/Gtg 1 -1 WDR87 HGNC HGNC:29934 protein_coding YES CCDS74356.1 ENSP00000405012 E7ESW6 UPI0003EAEFEF NM_001291088.1 tolerated_low_confidence(0.48) 6/6 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -17.34807 1 1 1 1 0 C 3 2 83 37886377 37886377 G C 1 0 0 0 0 1 0 0 0 17890 1020 36 4 4 WDR87 19 37886377 Missense_Mutation SNP G C3N-01823_T 345 37886377 20731239 432 26129 RYR1 0 . GRCh38 19 38492546 38492546 + Missense_Mutation SNP C C A rs758631725 C3N-01823_T C3N-01823_N C C c.6184C>A p.Arg2062Ser p.R2062S ENST00000359596 38/106 568 517 51 392 392 0 strelka-varscan-mutect RYR1,missense_variant,p.Arg2062Ser,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Arg2062Ser,ENST00000359596,NM_000540.2;RYR1,upstream_gene_variant,,ENST00000594335,; A ENST00000359596 Transcript missense_variant 6184/15117 6184/15117 2062/5038 R/S Cgc/Agc rs758631725,COSM4077779 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0.03) 38/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs758631725 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 38492546 38492546 C A 1 0 0 0 0 1 0 0 0 14028 652 23 1 1 RYR1 19 38492546 Missense_Mutation SNP C C3N-01823_T 606169 38492546 20125070 433 26130 IFNL1 0 . GRCh38 19 39296853 39296853 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.220C>A p.Pro74Thr p.P74T ENST00000333625 2/5 196 176 20 112 112 0 strelka-varscan-mutect IFNL1,missense_variant,p.Pro74Thr,ENST00000333625,NM_172140.1; A ENST00000333625 Transcript missense_variant 317/857 220/603 74/200 P/T Ccc/Acc 1 1 IFNL1 HGNC HGNC:18363 protein_coding YES CCDS12531.1 ENSP00000329991 Q8IU54 UPI00000474AE NM_172140.1 deleterious(0.01) 2/5 PD856660,Pfam_domain:PF15177,hmmpanther:PTHR31943,hmmpanther:PTHR31943:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 83 39296853 39296853 C A 1 0 0 0 0 1 0 0 0 7452 623 22 2 2 IFNL1 19 39296853 Missense_Mutation SNP C C3N-01823_T 804307 39296853 19320763 434 26131 PRR19 0 . GRCh38 19 42310314 42310314 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.645G>C p.Trp215Cys p.W215C ENST00000499536 2/2 498 454 44 292 292 0 strelka-varscan-mutect PRR19,missense_variant,p.Trp215Cys,ENST00000499536,;PRR19,missense_variant,p.Trp215Cys,ENST00000341747,NM_199285.2;PRR19,3_prime_UTR_variant,,ENST00000598490,;TMEM145,upstream_gene_variant,,ENST00000598766,;TMEM145,upstream_gene_variant,,ENST00000301204,NM_173633.2;PRR19,downstream_gene_variant,,ENST00000595750,;TMEM145,upstream_gene_variant,,ENST00000601020,;TMEM145,upstream_gene_variant,,ENST00000595775,; C ENST00000499536 Transcript missense_variant 1456/1956 645/1071 215/356 W/C tgG/tgC 1 1 PRR19 HGNC HGNC:33728 protein_coding YES CCDS33036.1 ENSP00000445247 A6NJB7 UPI000016101F tolerated(0.1) 2/2 hmmpanther:PTHR37346,Pfam_domain:PF15455 MODERATE 1 SNV 2 1 PASS rs1216344387 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 42310314 42310314 G C 1 0 0 0 0 1 0 0 0 12727 1183 41 4 4 PRR19 19 42310314 Missense_Mutation SNP G C3N-01823_T 3013461 42310314 16307302 435 26132 ZNF226 0 . GRCh38 19 44176422 44176422 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1160G>T p.Gly387Val p.G387V ENST00000590089 7/7 235 164 71 149 149 0 strelka-varscan-mutect ZNF226,missense_variant,p.Gly387Val,ENST00000590089,NM_016444.2;ZNF226,missense_variant,p.Gly387Val,ENST00000454662,NM_001319090.1,NM_001319089.1,NM_001319088.1,NM_001032372.1;ZNF226,missense_variant,p.Gly387Val,ENST00000337433,NM_001032373.1;ZNF226,3_prime_UTR_variant,,ENST00000588883,;ZNF226,downstream_gene_variant,,ENST00000300823,NM_015919.3;ZNF226,downstream_gene_variant,,ENST00000413984,NM_001032374.1;ZNF226,downstream_gene_variant,,ENST00000589160,;ZNF226,downstream_gene_variant,,ENST00000588795,;ZNF226,downstream_gene_variant,,ENST00000590524,;ZNF226,downstream_gene_variant,,ENST00000585678,;ZNF226,downstream_gene_variant,,ENST00000586914,;ZNF226,downstream_gene_variant,,ENST00000588127,;ZNF226,downstream_gene_variant,,ENST00000586203,;ZNF226,downstream_gene_variant,,ENST00000590578,;ZNF226,downstream_gene_variant,,ENST00000590467,;ZNF226,downstream_gene_variant,,ENST00000586286,;ZNF226,downstream_gene_variant,,ENST00000585560,;ZNF226,downstream_gene_variant,,ENST00000588742,NM_001146220.2;ZNF226,downstream_gene_variant,,ENST00000590759,; T ENST00000590089 Transcript missense_variant 1527/2788 1160/2412 387/803 G/V gGg/gTg 1 1 ZNF226 HGNC HGNC:13019 protein_coding YES CCDS46102.1 ENSP00000465121 Q9NYT6 A0A024R0P4 UPI000013C32A NM_016444.2 deleterious(0.01) 7/7 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF177,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 44176422 44176422 G T 1 0 0 0 0 1 0 0 0 18357 1232 43 2 2 ZNF226 19 44176422 Missense_Mutation SNP G C3N-01823_T 1866108 44176422 14441194 436 26133 NANOS2 0 . GRCh38 19 45914597 45914597 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.97C>A p.Gln33Lys p.Q33K ENST00000341294 1/1 326 239 87 207 207 0 strelka-varscan-mutect NANOS2,missense_variant,p.Gln33Lys,ENST00000341294,NM_001029861.2; T ENST00000341294 Transcript missense_variant 274/1657 97/417 33/138 Q/K Caa/Aaa 1 -1 NANOS2 HGNC HGNC:23292 protein_coding YES CCDS33056.1 ENSP00000341021 P60321 UPI00001984F7 NM_001029861.2 tolerated(0.46) 1/1 hmmpanther:PTHR12887,hmmpanther:PTHR12887:SF7 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 45914597 45914597 G T 1 0 0 0 0 1 0 0 0 10161 1357 47 2 2 NANOS2 19 45914597 Missense_Mutation SNP G C3N-01823_T 1738175 45914597 12703019 437 26134 CRX 0 . GRCh38 19 47836276 47836276 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.134C>T p.Thr45Ile p.T45I ENST00000221996 3/4 480 433 47 330 330 0 strelka-varscan-mutect CRX,missense_variant,p.Thr45Ile,ENST00000221996,NM_000554.4;CRX,missense_variant,p.Thr45Ile,ENST00000539067,;CRX,missense_variant,p.Thr45Ile,ENST00000566686,;CRX,intron_variant,,ENST00000613299,;CRX,non_coding_transcript_exon_variant,,ENST00000556527,;CRX,upstream_gene_variant,,ENST00000602001,; T ENST00000221996 Transcript missense_variant 341/4470 134/900 45/299 T/I aCc/aTc 1 1 CRX HGNC HGNC:2383 protein_coding YES CCDS12706.1 ENSP00000221996 O43186 UPI00001284E0 NM_000554.4 deleterious(0.01) 3/4 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF331,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 47836276 47836276 C T 1 0 0 0 0 1 0 0 0 3704 507 18 3 3 CRX 19 47836276 Missense_Mutation SNP C C3N-01823_T 1921679 47836276 10781340 438 26135 NAPSA 0 . GRCh38 19 50361135 50361135 + Silent SNP A A C novel C3N-01823_T C3N-01823_N A A c.474T>G p.= p.G158G ENST00000253719 5/9 174 165 9 127 126 1 varscan-mutect NAPSA,synonymous_variant,p.=,ENST00000253719,NM_004851.1;NAPSA,synonymous_variant,p.=,ENST00000598915,;NR1H2,intron_variant,,ENST00000600355,;CTB-191K22.6,downstream_gene_variant,,ENST00000597049,;NR1H2,intron_variant,,ENST00000600978,;NAPSA,3_prime_UTR_variant,,ENST00000599233,;NAPSA,non_coding_transcript_exon_variant,,ENST00000599181,;NAPSA,non_coding_transcript_exon_variant,,ENST00000596653,;NR1H2,intron_variant,,ENST00000593532,;NAPSA,downstream_gene_variant,,ENST00000597378,;NAPSA,upstream_gene_variant,,ENST00000598044,; C ENST00000253719 Transcript synonymous_variant 683/1548 474/1263 158/420 G ggT/ggG 1 -1 NAPSA HGNC HGNC:13395 protein_coding YES CCDS12794.1 ENSP00000253719 O96009 UPI0000046F0E NM_004851.1 5/9 PROSITE_profiles:PS51767,hmmpanther:PTHR13683,hmmpanther:PTHR13683:SF237,Gene3D:2.40.70.10,Pfam_domain:PF00026,Superfamily_domains:SSF50630 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 83 50361135 50361135 A C 1 0 0 0 0 0 0 0 1 10176 173 6 5 5 NAPSA 19 50361135 Silent SNP A C3N-01823_T 2524859 50361135 8256481 439 26136 SHANK1 0 . GRCh38 19 50668297 50668297 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.3663C>A p.Ser1221Arg p.S1221R ENST00000293441 22/23 48 38 10 21 21 0 strelka-varscan-mutect SHANK1,missense_variant,p.Ser1221Arg,ENST00000293441,NM_016148.2;SHANK1,missense_variant,p.Ser1229Arg,ENST00000391814,;SHANK1,missense_variant,p.Ser1212Arg,ENST00000359082,;SHANK1,missense_variant,p.Ser608Arg,ENST00000391813,;SHANK1,upstream_gene_variant,,ENST00000468654,; T ENST00000293441 Transcript missense_variant 3682/6643 3663/6486 1221/2161 S/R agC/agA 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 tolerated(0.62) 22/23 Low_complexity_(Seg):seg,hmmpanther:PTHR24135:SF3,hmmpanther:PTHR24135 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -19.99994 0.9999911 1 1 1 0 T 3 4 83 50668297 50668297 G T 1 0 0 0 0 1 0 0 0 14523 1078 38 1 1 SHANK1 19 50668297 Missense_Mutation SNP G C3N-01823_T 307162 50668297 7949319 440 26137 SHANK1 0 . GRCh38 19 50702630 50702630 + Silent SNP G G T rs750041152 C3N-01823_T C3N-01823_N G G c.1584C>A p.= p.A528A ENST00000293441 11/23 115 107 8 95 94 1 strelka-varscan SHANK1,synonymous_variant,p.=,ENST00000293441,NM_016148.2;SHANK1,synonymous_variant,p.=,ENST00000391814,;SHANK1,synonymous_variant,p.=,ENST00000359082,;SHANK1,downstream_gene_variant,,ENST00000461154,; T ENST00000293441 Transcript synonymous_variant 1603/6643 1584/6486 528/2161 A gcC/gcA rs750041152,COSM4962202,COSM5660521 1 -1 SHANK1 HGNC HGNC:15474 protein_coding YES CCDS12799.1 ENSP00000293441 Q9Y566 UPI000013E109 NM_016148.2 11/23 Low_complexity_(Seg):seg,hmmpanther:PTHR24135,hmmpanther:PTHR24135:SF3 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 200 9 0 0 0 0 0 -15.52762 0.9999672 1 1 1 0 T 2 4 83 50702630 50702630 G T 1 0 0 0 0 0 0 0 1 14523 1103 39 1 1 SHANK1 19 50702630 Silent SNP G C3N-01823_T 34333 50702630 7914986 441 26138 AC018755.18 0 . GRCh38 19 51627709 51627709 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.1035G>C p.Glu345Asp p.E345D ENST00000534261 7/10 81 68 13 49 49 0 strelka-varscan-mutect SIGLEC5,missense_variant,p.Glu345Asp,ENST00000534261,NM_003830.3;AC018755.18,missense_variant,p.Glu345Asp,ENST00000429354,;AC018755.18,missense_variant,p.Glu345Asp,ENST00000599649,; G ENST00000534261 Transcript missense_variant 1435/2360 1035/1656 345/551 E/D gaG/gaC 1 -1 SIGLEC5 HGNC HGNC:10874 protein_coding YES CCDS33088.1 ENSP00000473238 O15389 UPI000011B40C NM_003830.3 deleterious(0.02) 7/10 hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF67,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 51627709 51627709 C G 1 0 0 0 0 1 0 0 0 125 680 24 4 4 AC018755.18 19 51627709 Missense_Mutation SNP C C3N-01823_T 925079 51627709 6989907 442 26139 FPR2 0 . GRCh38 19 51769212 51769212 + Missense_Mutation SNP G G A novel C3N-01823_T C3N-01823_N G G c.554G>A p.Gly185Asp p.G185D ENST00000598776 2/2 315 296 19 198 196 2 strelka-varscan-mutect FPR2,missense_variant,p.Gly185Asp,ENST00000598776,NM_001462.3;FPR2,missense_variant,p.Gly185Asp,ENST00000340023,NM_001005738.1;FPR2,missense_variant,p.Gly185Asp,ENST00000598953,;FPR1,intron_variant,,ENST00000594900,;FPR2,downstream_gene_variant,,ENST00000600258,;FPR2,downstream_gene_variant,,ENST00000599326,;FPR2,downstream_gene_variant,,ENST00000600722,; A ENST00000598776 Transcript missense_variant 1326/2621 554/1056 185/351 G/D gGc/gAc 1 1 FPR2 HGNC HGNC:3827 protein_coding YES CCDS12840.1 ENSP00000468897 P25090 A0A024R4P3 UPI00000012D0 NM_001462.3 tolerated(1) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00526,PROSITE_profiles:PS50262,hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF16,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 51769212 51769212 G A 1 0 0 0 0 1 0 0 0 5905 1203 42 3 3 FPR2 19 51769212 Missense_Mutation SNP G C3N-01823_T 141503 51769212 6848404 443 26140 ZNF432 0 . GRCh38 19 52034785 52034785 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.894C>T p.= p.F298F ENST00000594154 5/5 117 110 7 69 69 0 strelka-mutect ZNF432,synonymous_variant,p.=,ENST00000594154,NM_001322284.1,NM_001322285.1;ZNF432,synonymous_variant,p.=,ENST00000221315,NM_014650.2;ZNF432,downstream_gene_variant,,ENST00000600368,;ZNF614,upstream_gene_variant,,ENST00000597952,;ZNF432,downstream_gene_variant,,ENST00000598745,; A ENST00000594154 Transcript synonymous_variant 1107/4513 894/1959 298/652 F ttC/ttT 1 -1 ZNF432 HGNC HGNC:20810 protein_coding YES CCDS12848.1 ENSP00000470488 O94892 A0A024R4I3 UPI0000139CDC NM_001322284.1,NM_001322285.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF165,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 201 6 3 0 0 0 0 -10.29115 0.9972805 1 1 1 0 A 2 1 83 52034785 52034785 G A 1 0 0 0 0 0 0 0 1 18478 1165 41 3 3 ZNF432 19 52034785 Silent SNP G C3N-01823_T 265573 52034785 6582831 444 26141 ZNF578 0 . GRCh38 19 52511388 52511388 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1007G>T p.Cys336Phe p.C336F ENST00000421239 6/6 427 381 46 290 290 0 strelka-varscan-mutect ZNF578,missense_variant,p.Cys336Phe,ENST00000421239,NM_001099694.1;ZNF578,downstream_gene_variant,,ENST00000601120,;CTD-3099C6.5,non_coding_transcript_exon_variant,,ENST00000599143,; T ENST00000421239 Transcript missense_variant 1251/2017 1007/1773 336/590 C/F tGt/tTt 1 1 ZNF578 HGNC HGNC:26449 protein_coding YES CCDS54310.1 ENSP00000459216 Q96N58 UPI000048A457 NM_001099694.1 deleterious(0.01) 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 52511388 52511388 G T 1 0 0 0 0 1 0 0 0 18584 1377 48 2 2 ZNF578 19 52511388 Missense_Mutation SNP G C3N-01823_T 476603 52511388 6106228 445 26142 ZNF808 0 . GRCh38 19 52554898 52554898 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1982G>T p.Ser661Ile p.S661I ENST00000359798 5/5 253 224 29 169 169 0 strelka-varscan-mutect ZNF808,missense_variant,p.Ser661Ile,ENST00000359798,NM_001321424.1,NM_001039886.3;ZNF808,upstream_gene_variant,,ENST00000611267,;ZNF808,downstream_gene_variant,,ENST00000465448,;ZNF808,downstream_gene_variant,,ENST00000461321,;ZNF808,downstream_gene_variant,,ENST00000461779,;ZNF808,downstream_gene_variant,,ENST00000486474,;ZNF701,upstream_gene_variant,,ENST00000478039,;ZNF808,missense_variant,p.Ser592Ile,ENST00000487863,; T ENST00000359798 Transcript missense_variant 2162/3600 1982/2712 661/903 S/I aGt/aTt 1 1 ZNF808 HGNC HGNC:33230 protein_coding YES CCDS46167.1 ENSP00000352846 Q8N4W9 UPI000041AA80 NM_001321424.1,NM_001039886.3 tolerated(0.09) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF276,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 52554898 52554898 G T 1 0 0 0 0 1 0 0 0 18758 1029 36 2 2 ZNF808 19 52554898 Missense_Mutation SNP G C3N-01823_T 43510 52554898 6062718 446 26143 ERVV-1 0 . GRCh38 19 53015213 53015213 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.1123G>C p.Asp375His p.D375H ENST00000602168 1/1 172 154 18 100 100 0 varscan-mutect ERVV-1,missense_variant,p.Asp375His,ENST00000602168,NM_152473.2;CTD-2620I22.3,downstream_gene_variant,,ENST00000596769,;ZNF702P,intron_variant,,ENST00000600425,;ZNF702P,intron_variant,,ENST00000594516,; C ENST00000602168 Transcript missense_variant 1293/2202 1123/1434 375/477 D/H Gat/Cat 1 1 ERVV-1 HGNC HGNC:26501 protein_coding YES CCDS59419.1 ENSP00000473153 B6SEH8 M9QQA5 UPI00018258B8 NM_152473.2 deleterious(0.01) 1/1 hmmpanther:PTHR10424:SF8,hmmpanther:PTHR10424,Pfam_domain:PF00429,Gene3D:1.10.287.210,Superfamily_domains:SSF58069 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 53015213 53015213 G C 1 0 0 0 0 1 0 0 0 5106 942 33 4 4 ERVV-1 19 53015213 Missense_Mutation SNP G C3N-01823_T 460315 53015213 5602403 447 26144 LILRB3 0 . GRCh38 19 54221991 54221991 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.495G>T p.= p.R165R ENST00000245620 4/13 513 487 26 379 379 0 varscan-mutect LILRB3,synonymous_variant,p.=,ENST00000391750,NM_006864.3;LILRB3,synonymous_variant,p.=,ENST00000346401,;LILRB3,synonymous_variant,p.=,ENST00000245620,NM_001081450.2;LILRB3,downstream_gene_variant,,ENST00000445347,;CTB-83J4.1,upstream_gene_variant,,ENST00000601161,;LILRB3,upstream_gene_variant,,ENST00000469273,;LILRB3,synonymous_variant,p.=,ENST00000414379,;LILRB3,non_coding_transcript_exon_variant,,ENST00000468668,;RPS9,intron_variant,,ENST00000448962,;LILRB3,upstream_gene_variant,,ENST00000460208,;LILRB3,upstream_gene_variant,,ENST00000436504,; A ENST00000245620 Transcript synonymous_variant 497/2066 495/1899 165/632 R cgG/cgT 1 -1 LILRB3 HGNC HGNC:6607 protein_coding YES CCDS46175.1 ENSP00000245620 O75022 UPI00034F2393 NM_001081450.2 4/13 hmmpanther:PTHR11738:SF116,hmmpanther:PTHR11738,Gene3D:2.60.40.10,Pfam_domain:PF13895,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 54221991 54221991 C A 1 0 0 0 0 0 0 0 1 8700 842 30 2 2 LILRB3 19 54221991 Silent SNP C C3N-01823_T 1206778 54221991 4395625 448 26145 LILRB5 0 . GRCh38 19 54252497 54252497 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.1527C>A p.= p.G509G ENST00000449561 10/13 181 166 15 119 119 0 strelka-varscan-mutect LILRB5,synonymous_variant,p.=,ENST00000316219,NM_006840.4;LILRB5,synonymous_variant,p.=,ENST00000449561,NM_001081442.2,NM_001304457.1;LILRB5,synonymous_variant,p.=,ENST00000345866,NM_001081443.2;LILRB5,non_coding_transcript_exon_variant,,ENST00000621581,;LILRB5,non_coding_transcript_exon_variant,,ENST00000615654,;RPS9,downstream_gene_variant,,ENST00000448962,; T ENST00000449561 Transcript synonymous_variant 1598/2137 1527/1776 509/591 G ggC/ggA 1 -1 LILRB5 HGNC HGNC:6609 protein_coding YES CCDS46176.1 ENSP00000406478 O75023 UPI00034F239B NM_001081442.2,NM_001304457.1 10/13 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF108 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 54252497 54252497 G T 1 0 0 0 0 0 0 0 1 8702 1190 42 2 2 LILRB5 19 54252497 Silent SNP G C3N-01823_T 30506 54252497 4365119 449 26146 LAIR1 0 . GRCh38 19 54361047 54361047 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.233G>T p.Ser78Ile p.S78I ENST00000391742 3/10 360 326 34 258 257 1 strelka-varscan-mutect LAIR1,missense_variant,p.Ser78Ile,ENST00000391742,NM_002287.5;LAIR1,missense_variant,p.Ser60Ile,ENST00000391743,NM_001289026.2,NM_001289027.2;LAIR1,missense_variant,p.Ser77Ile,ENST00000434277,NM_001289025.2;LAIR1,missense_variant,p.Ser78Ile,ENST00000348231,NM_021706.4;LAIR1,missense_variant,p.Ser77Ile,ENST00000474878,NM_001289023.2;LAIR1,missense_variant,p.Ser72Ile,ENST00000438193,;LAIR1,upstream_gene_variant,,ENST00000622064,;LAIR1,non_coding_transcript_exon_variant,,ENST00000440716,;LAIR1,non_coding_transcript_exon_variant,,ENST00000423853,;LAIR1,non_coding_transcript_exon_variant,,ENST00000427131,;LAIR1,non_coding_transcript_exon_variant,,ENST00000463489,;LAIR1,non_coding_transcript_exon_variant,,ENST00000480122,;LAIR1,non_coding_transcript_exon_variant,,ENST00000484116,;LAIR1,non_coding_transcript_exon_variant,,ENST00000468656,;LAIR1,missense_variant,p.Ser78Ile,ENST00000418556,;LAIR1,missense_variant,p.Ser78Ile,ENST00000391741,;LAIR1,3_prime_UTR_variant,,ENST00000436513,;LAIR1,3_prime_UTR_variant,,ENST00000420483,;LAIR1,non_coding_transcript_exon_variant,,ENST00000467269,;LAIR1,non_coding_transcript_exon_variant,,ENST00000498511,;LAIR1,upstream_gene_variant,,ENST00000475389,;LAIR1,upstream_gene_variant,,ENST00000460312,; A ENST00000391742 Transcript missense_variant 386/4901 233/864 78/287 S/I aGt/aTt 1 -1 LAIR1 HGNC HGNC:6477 protein_coding YES CCDS12891.1 ENSP00000375622 Q6GTX8 UPI00034F23B9 NM_002287.5 tolerated(0.17) 3/10 Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF122,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 54361047 54361047 C A 1 0 0 0 0 1 0 0 0 8506 565 20 2 2 LAIR1 19 54361047 Missense_Mutation SNP C C3N-01823_T 108550 54361047 4256569 450 26147 LILRA1 0 . GRCh38 19 54595235 54595235 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.494C>T p.Pro165Leu p.P165L ENST00000251372 5/10 369 329 40 291 290 1 strelka-varscan-mutect LILRA1,missense_variant,p.Pro165Leu,ENST00000453777,NM_001278318.1;LILRA1,missense_variant,p.Pro165Leu,ENST00000251372,NM_006863.3;LILRA1,missense_variant,p.Pro165Leu,ENST00000618665,;LILRA2,downstream_gene_variant,,ENST00000251376,NM_006866.3;CTB-83J4.2,downstream_gene_variant,,ENST00000596330,;LILRA1,non_coding_transcript_exon_variant,,ENST00000473156,;LILRA1,non_coding_transcript_exon_variant,,ENST00000495417,;LILRA1,non_coding_transcript_exon_variant,,ENST00000477255,; T ENST00000251372 Transcript missense_variant 676/1910 494/1470 165/489 P/L cCa/cTa 1 1 LILRA1 HGNC HGNC:6602 protein_coding YES CCDS12901.1 ENSP00000251372 O75019 UPI0000034C00 NM_006863.3 tolerated(0.23) 5/10 Gene3D:2.60.40.10,PIRSF_domain:PIRSF001979,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 54595235 54595235 C T 1 0 0 0 0 1 0 0 0 8693 594 21 3 3 LILRA1 19 54595235 Missense_Mutation SNP C C3N-01823_T 234188 54595235 4022381 451 26148 KIR3DL2 0 . GRCh38 19 54850487 54850487 + Silent SNP G G T rs652188,rs652188 C3N-01823_T C3N-01823_N G G c.12G>T p.= p.T4T ENST00000326321 1/9 439 387 52 348 348 0 strelka-varscan-mutect KIR3DL2,synonymous_variant,p.=,ENST00000326321,NM_006737.3;KIR3DL2,synonymous_variant,p.=,ENST00000270442,NM_001242867.1;KIR3DL1,intron_variant,,ENST00000402254,;KIR2DS4,downstream_gene_variant,,ENST00000339924,;KIR2DS4,downstream_gene_variant,,ENST00000391729,; T ENST00000326321 Transcript synonymous_variant 45/1877 12/1368 4/455 T acG/acT rs652188,rs652188 1 1 KIR3DL2 HGNC HGNC:6339 protein_coding YES CCDS12906.1 ENSP00000325525 P43630 A0A0U1WNF3 UPI000012DB25 NM_006737.3 1/9 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF121,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS rs652188 . 0 20 0 0 0 0 0 190 -5.480077 0 0 1 0 0 T 2 4 83 54850487 54850487 G T 1 0 0 0 0 0 0 0 1 8185 1103 39 1 1 KIR3DL2 19 54850487 Silent SNP G C3N-01823_T 255252 54850487 3767129 452 26149 ZNF628 0 . GRCh38 19 55482565 55482565 + Nonsense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1372G>T p.Glu458Ter p.E458* ENST00000598519 3/3 111 103 8 63 63 0 strelka-varscan-mutect ZNF628,stop_gained,p.Glu458Ter,ENST00000598519,NM_033113.2;ZNF628,stop_gained,p.Glu457Ter,ENST00000391718,;NAT14,upstream_gene_variant,,ENST00000205194,NM_020378.3;NAT14,upstream_gene_variant,,ENST00000591590,;NAT14,upstream_gene_variant,,ENST00000588985,;ZNF628,downstream_gene_variant,,ENST00000591164,;NAT14,upstream_gene_variant,,ENST00000587400,;NAT14,upstream_gene_variant,,ENST00000592719,; T ENST00000598519 Transcript stop_gained 1925/3847 1372/3180 458/1059 E/* Gag/Tag 1 1 ZNF628 HGNC HGNC:28054 protein_coding YES CCDS33116.3 ENSP00000469591 Q5EBL2 UPI00026B9C6E NM_033113.2 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24376,hmmpanther:PTHR24376:SF19,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS rs1172822139 . 0 202 5 2 0 0 0 0 -12.10789 0.9998189 1 1 1 0 T 4 4 83 55482565 55482565 G T 1 0 0 0 0 0 1 0 0 18627 1059 37 1 1 ZNF628 19 55482565 Nonsense_Mutation SNP G C3N-01823_T 632078 55482565 3135051 453 26150 ZSCAN5A 0 . GRCh38 19 56222148 56222148 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.918C>T p.= p.S306S ENST00000391713 5/5 472 419 53 340 340 0 varscan-mutect ZSCAN5A,synonymous_variant,p.=,ENST00000391713,NM_024303.1;ZSCAN5A,synonymous_variant,p.=,ENST00000587340,NM_001322072.1;ZSCAN5A,synonymous_variant,p.=,ENST00000592355,;ZSCAN5A,synonymous_variant,p.=,ENST00000587492,;ZSCAN5A,synonymous_variant,p.=,ENST00000593106,;ZSCAN5A,downstream_gene_variant,,ENST00000592679,;ZSCAN5A,downstream_gene_variant,,ENST00000592509,;ZSCAN5A,downstream_gene_variant,,ENST00000588442,;ZSCAN5A,downstream_gene_variant,,ENST00000588955,;ZSCAN5A,downstream_gene_variant,,ENST00000592101,;CTD-2086L14.1,upstream_gene_variant,,ENST00000474329,; A ENST00000391713 Transcript synonymous_variant 1084/3562 918/1491 306/496 S tcC/tcT 1 -1 ZSCAN5A HGNC HGNC:23710 protein_coding YES CCDS12941.1 ENSP00000375593 Q9BUG6 A0A024R4S6 UPI0000072024 NM_024303.1 5/5 hmmpanther:PTHR10032:SF164,hmmpanther:PTHR10032 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 56222148 56222148 G A 1 0 0 0 0 0 0 0 1 18837 1335 47 3 3 ZSCAN5A 19 56222148 Silent SNP G C3N-01823_T 739583 56222148 2395468 454 26151 ZNF416 0 . GRCh38 19 57575890 57575890 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.116A>T p.Gln39Leu p.Q39L ENST00000196489 3/4 270 230 40 161 161 0 strelka-mutect ZNF416,missense_variant,p.Gln39Leu,ENST00000196489,NM_017879.1;ZIK1,upstream_gene_variant,,ENST00000598726,; A ENST00000196489 Transcript missense_variant 339/2561 116/1785 39/594 Q/L cAg/cTg 1 -1 ZNF416 HGNC HGNC:20645 protein_coding YES CCDS12954.1 ENSP00000196489 Q9BWM5 UPI000007314D NM_017879.1 tolerated(0.17) 3/4 PROSITE_profiles:PS50805,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF160,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 57575890 57575890 T A 1 0 0 0 0 1 0 0 0 18465 1580 55 4 4 ZNF416 19 57575890 Missense_Mutation SNP T C3N-01823_T 1353742 57575890 1041726 455 26152 TGM6 0 . GRCh38 20 2394557 2394557 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.113T>C p.Phe38Ser p.F38S ENST00000202625 2/13 739 583 156 440 440 0 strelka-varscan-mutect TGM6,missense_variant,p.Phe38Ser,ENST00000202625,NM_198994.2;TGM6,missense_variant,p.Phe38Ser,ENST00000381423,NM_001254734.1;TGM6,non_coding_transcript_exon_variant,,ENST00000477505,; C ENST00000202625 Transcript missense_variant 174/2292 113/2121 38/706 F/S tTc/tCc 1 1 TGM6 HGNC HGNC:16255 protein_coding YES CCDS13025.1 ENSP00000202625 O95932 UPI0000367011 NM_198994.2 deleterious(0) 2/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF50,PIRSF_domain:PIRSF000459,Gene3D:2.60.40.10,Pfam_domain:PF00868,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 2394557 2394557 T C 1 0 0 0 0 1 0 0 0 16267 1783 62 5 5 TGM6 20 2394557 Missense_Mutation SNP T C3N-01823_T 2394557 62049610 456 26153 C20orf141 0 . GRCh38 20 2815590 2815590 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.313C>A p.Gln105Lys p.Q105K ENST00000380589 2/2 265 205 60 120 120 0 strelka-varscan-mutect C20orf141,missense_variant,p.Gln105Lys,ENST00000380589,NM_080739.2;C20orf141,missense_variant,p.Gln105Lys,ENST00000603872,NM_001256538.1;RP5-860F19.8,intron_variant,,ENST00000380593,;TMEM239,upstream_gene_variant,,ENST00000361033,NM_001318207.1;TMEM239,upstream_gene_variant,,ENST00000380585,NM_001167670.1; A ENST00000380589 Transcript missense_variant 487/730 313/498 105/165 Q/K Cag/Aag 1 1 C20orf141 HGNC HGNC:16134 protein_coding YES CCDS13034.1 ENSP00000369963 Q9NUB4 UPI0000037B8A NM_080739.2 deleterious(0.02) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR39222:SF1,hmmpanther:PTHR39222 MODERATE 1 SNV 1 1 PASS rs770443043 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 2815590 2815590 C A 1 0 0 0 0 1 0 0 0 2002 827 29 2 2 C20orf141 20 2815590 Missense_Mutation SNP C C3N-01823_T 421033 2815590 61628577 457 26154 CST2 0 . GRCh38 20 23826609 23826609 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.52G>T p.Ala18Ser p.A18S ENST00000304725 1/3 279 221 58 139 139 0 strelka-mutect CST2,missense_variant,p.Ala18Ser,ENST00000304725,NM_001322.2; A ENST00000304725 Transcript missense_variant 123/748 52/426 18/141 A/S Gcc/Tcc 1 -1 CST2 HGNC HGNC:2474 protein_coding YES CCDS13161.1 ENSP00000307540 P09228 UPI0000128D74 NM_001322.2 tolerated(0.07) 1/3 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11413,hmmpanther:PTHR11413:SF48 MODERATE 1 SNV 1 1 PASS rs1427215914 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 23826609 23826609 C A 1 0 0 0 0 1 0 0 0 3772 739 26 2 2 CST2 20 23826609 Missense_Mutation SNP C C3N-01823_T 21011019 23826609 40617558 458 26155 PTPRT 0 . GRCh38 20 42448254 42448254 + Missense_Mutation SNP G G T C3N-01823_T C3N-01823_N G G c.1526C>A p.Pro509His p.P509H ENST00000373198 9/32 374 319 55 244 243 1 strelka-varscan-mutect PTPRT,missense_variant,p.Pro509His,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Pro509His,ENST00000373193,;PTPRT,missense_variant,p.Pro509His,ENST00000373201,;PTPRT,missense_variant,p.Pro509His,ENST00000373190,;PTPRT,missense_variant,p.Pro509His,ENST00000373184,;PTPRT,missense_variant,p.Pro509His,ENST00000356100,;PTPRT,missense_variant,p.Pro509His,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Pro127His,ENST00000612229,;PTPRT,missense_variant,p.Pro125His,ENST00000618610,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; T ENST00000373198 Transcript missense_variant 1762/12746 1526/4383 509/1460 P/H cCc/cAc COSM3546552,COSM3546553 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 9/32 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1162609724 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 42448254 42448254 G T 1 0 0 0 0 1 0 0 0 12967 1232 43 2 2 PTPRT 20 42448254 Missense_Mutation SNP G C3N-01823_T 18621645 42448254 21995913 459 26156 RBPJL 0 . GRCh38 20 45312260 45312260 + Missense_Mutation SNP G G C novel C3N-01823_T C3N-01823_N G G c.484G>C p.Asp162His p.D162H ENST00000343694 6/12 591 538 53 323 323 0 strelka-varscan-mutect RBPJL,missense_variant,p.Asp162His,ENST00000343694,NM_014276.3;RBPJL,missense_variant,p.Asp162His,ENST00000372741,NM_001281448.1;RBPJL,missense_variant,p.Asp162His,ENST00000372743,NM_001281449.1;MATN4,upstream_gene_variant,,ENST00000360607,NM_030590.3;MATN4,upstream_gene_variant,,ENST00000537548,;MATN4,upstream_gene_variant,,ENST00000353917,NM_030592.3;RBPJL,upstream_gene_variant,,ENST00000464504,;RBPJL,upstream_gene_variant,,ENST00000622729,; C ENST00000343694 Transcript missense_variant 556/2489 484/1554 162/517 D/H Gac/Cac 1 1 RBPJL HGNC HGNC:13761 protein_coding YES CCDS13349.1 ENSP00000341243 Q9UBG7 UPI0000047297 NM_014276.3 deleterious(0) 6/12 Gene3D:2.60.40.1450,Pfam_domain:PF09271,hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,SMART_domains:SM01267,Superfamily_domains:SSF49417 MODERATE 1 SNV 2 1 PASS rs1219416976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 45312260 45312260 G C 1 0 0 0 0 1 0 0 0 13330 942 33 4 4 RBPJL 20 45312260 Missense_Mutation SNP G C3N-01823_T 2864006 45312260 19131907 460 26157 ZNF335 0 . GRCh38 20 45950514 45950514 + Missense_Mutation SNP G G T rs146821427 C3N-01823_T C3N-01823_N G G c.3271C>A p.Arg1091Ser p.R1091S ENST00000322927 21/28 306 244 62 224 223 1 strelka-varscan-mutect ZNF335,missense_variant,p.Arg1091Ser,ENST00000322927,NM_022095.3;PCIF1,downstream_gene_variant,,ENST00000372409,NM_022104.3;PCIF1,downstream_gene_variant,,ENST00000479348,; T ENST00000322927 Transcript missense_variant 3372/4430 3271/4029 1091/1342 R/S Cgt/Agt rs146821427 1 -1 ZNF335 HGNC HGNC:15807 protein_coding YES CCDS13389.1 ENSP00000325326 Q9H4Z2 UPI0000001BC3 NM_022095.3 tolerated(0.18) 21/28 Gene3D:3.30.160.60,Pfam_domain:PF13909,PROSITE_profiles:PS50157,hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF36,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs146821427 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 45950514 45950514 G T 1 0 0 0 0 1 0 0 0 18424 1087 38 1 1 ZNF335 20 45950514 Missense_Mutation SNP G C3N-01823_T 638254 45950514 18493653 461 26158 MMP9 0 . GRCh38 20 46010019 46010019 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.292C>A p.= p.R98R ENST00000372330 2/13 491 409 82 242 242 0 strelka-varscan-mutect MMP9,synonymous_variant,p.=,ENST00000372330,NM_004994.2;RP11-465L10.10,downstream_gene_variant,,ENST00000535913,; A ENST00000372330 Transcript synonymous_variant 311/2336 292/2124 98/707 R Cgg/Agg 1 1 MMP9 HGNC HGNC:7176 protein_coding YES CCDS13390.1 ENSP00000361405 P14780 UPI000013C712 NM_004994.2 2/13 hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF30,PROSITE_patterns:PS00546,Gene3D:3.40.390.10,Superfamily_domains:SSF47090,Prints_domain:PR00138 LOW 1 SNV 1 1 PASS rs1371238110 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 46010019 46010019 C A 1 0 0 0 0 0 0 0 1 9632 527 19 1 1 MMP9 20 46010019 Silent SNP C C3N-01823_T 59505 46010019 18434148 462 26159 PREX1 0 . GRCh38 20 48627911 48627911 + Missense_Mutation SNP C C T rs771519895 C3N-01823_T C3N-01823_N C C c.4819G>A p.Gly1607Arg p.G1607R ENST00000371941 38/40 229 217 12 161 161 0 strelka-varscan-mutect PREX1,missense_variant,p.Gly1607Arg,ENST00000371941,NM_020820.3;PREX1,3_prime_UTR_variant,,ENST00000482556,; T ENST00000371941 Transcript missense_variant 4842/6636 4819/4980 1607/1659 G/R Ggg/Agg rs771519895,COSM3295199 1 -1 PREX1 HGNC HGNC:32594 protein_coding YES CCDS13410.1 ENSP00000361009 Q8TCU6 UPI000013D375 NM_020820.3 deleterious(0) 38/40 hmmpanther:PTHR22829:SF6,hmmpanther:PTHR22829 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771519895 . 0 207 0 3 0 0 0 0 -14.14685 0.9999425 1 1 1 0 T 3 4 83 48627911 48627911 C T 1 0 0 0 0 1 0 0 0 12610 652 23 1 1 PREX1 20 48627911 Missense_Mutation SNP C C3N-01823_T 2617892 48627911 15816256 463 26160 PTGIS 0 . GRCh38 20 49544345 49544345 + Nonsense_Mutation SNP C C A rs767832954 C3N-01823_T C3N-01823_N C C c.481G>T p.Glu161Ter p.E161* ENST00000244043 4/10 380 282 98 170 169 1 strelka-varscan-mutect PTGIS,stop_gained,p.Glu161Ter,ENST00000244043,NM_000961.3;PTGIS,non_coding_transcript_exon_variant,,ENST00000478971,; A ENST00000244043 Transcript stop_gained 511/5579 481/1503 161/500 E/* Gag/Tag rs767832954,COSM3911547 1 -1 PTGIS HGNC HGNC:9603 protein_coding YES CCDS13419.1 ENSP00000244043 Q16647 UPI00001328DF NM_000961.3 4/10 hmmpanther:PTHR24306,hmmpanther:PTHR24306:SF4,PIRSF_domain:PIRSF500628,PIRSF_domain:PIRSF000047,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 0,1 HIGH 1 SNV 1 0,1 1 PASS rs767832954 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 83 49544345 49544345 C A 1 0 0 0 0 0 1 0 0 12908 893 31 1 1 PTGIS 20 49544345 Nonsense_Mutation SNP C C3N-01823_T 916434 49544345 14899822 464 26161 MOCS3 0 . GRCh38 20 50958997 50958997 + Missense_Mutation SNP A A T novel C3N-01823_T C3N-01823_N A A c.155A>T p.Lys52Met p.K52M ENST00000244051 1/1 178 140 38 103 103 0 strelka-varscan-mutect MOCS3,missense_variant,p.Lys52Met,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; T ENST00000244051 Transcript missense_variant 172/5106 155/1383 52/460 K/M aAg/aTg 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 deleterious(0.03) 1/1 HAMAP:MF_03049,hmmpanther:PTHR10953,Superfamily_domains:SSF69572 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 50958997 50958997 A T 1 0 0 0 0 1 0 0 0 9655 72 3 4 4 MOCS3 20 50958997 Missense_Mutation SNP A C3N-01823_T 1414652 50958997 13485170 465 26162 PHACTR3 0 . GRCh38 20 59743128 59743128 + Missense_Mutation SNP C C A rs199841810 C3N-01823_T C3N-01823_N C C c.140C>A p.Pro47Gln p.P47Q ENST00000371015 2/13 209 156 53 101 101 0 strelka-varscan-mutect PHACTR3,missense_variant,p.Pro47Gln,ENST00000371015,NM_080672.4;PHACTR3,missense_variant,p.Pro6Gln,ENST00000395636,NM_183244.1;PHACTR3,missense_variant,p.Pro6Gln,ENST00000541461,NM_001281507.1;PHACTR3,missense_variant,p.Pro44Gln,ENST00000359926,NM_001199505.1;PHACTR3,missense_variant,p.Pro6Gln,ENST00000355648,NM_001199506.1;PHACTR3,missense_variant,p.Pro6Gln,ENST00000361300,NM_183246.1;PHACTR3,downstream_gene_variant,,ENST00000434923,; A ENST00000371015 Transcript missense_variant 607/2728 140/1680 47/559 P/Q cCg/cAg rs199841810,COSM3939422 1 1 PHACTR3 HGNC HGNC:15833 protein_coding YES CCDS13480.1 ENSP00000360054 Q96KR7 UPI000006D452 NM_080672.4 deleterious(0.01) 2/13 hmmpanther:PTHR12751:SF7,hmmpanther:PTHR12751 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199841810 . 0 203 3 4 0 0 0 0 -20 0.9998328 1 1 1 0 A 3 1 83 59743128 59743128 C A 1 0 0 0 0 1 0 0 0 11900 652 23 1 1 PHACTR3 20 59743128 Missense_Mutation SNP C C3N-01823_T 8784131 59743128 4701039 466 26163 LAMA5 0 . GRCh38 20 62318952 62318952 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.6933G>T p.Gln2311His p.Q2311H ENST00000252999 52/80 247 187 60 133 133 0 strelka-varscan-mutect LAMA5,missense_variant,p.Gln2311His,ENST00000252999,NM_005560.4;LAMA5,non_coding_transcript_exon_variant,,ENST00000481120,;LAMA5,upstream_gene_variant,,ENST00000370691,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000471042,; A ENST00000252999 Transcript missense_variant 7000/11426 6933/11088 2311/3695 Q/H caG/caT 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 tolerated(0.2) 52/80 Pfam_domain:PF06008 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 62318952 62318952 C A 1 0 0 0 0 1 0 0 0 8513 796 28 2 2 LAMA5 20 62318952 Missense_Mutation SNP C C3N-01823_T 2575824 62318952 2125215 467 26164 LAMA5 0 . GRCh38 20 62328426 62328426 + Silent SNP G G C rs369784534 C3N-01823_T C3N-01823_N G G c.4467C>G p.= p.R1489R ENST00000252999 35/80 40 36 4 17 17 0 strelka-mutect LAMA5,synonymous_variant,p.=,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000577688,;LAMA5,upstream_gene_variant,,ENST00000497363,;LAMA5,upstream_gene_variant,,ENST00000464134,; C ENST00000252999 Transcript synonymous_variant 4534/11426 4467/11088 1489/3695 R cgC/cgG rs369784534 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 35/80 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF261,hmmpanther:PTHR10574,PROSITE_patterns:PS01248,SMART_domains:SM00180 LOW 1 SNV 1 1 PASS rs369784534 . 1 206 3 0 0 0 0 0 -10.98341 1 1 1 1 0 C 2 2 83 62328426 62328426 G C 1 0 0 0 0 0 0 0 1 8513 1190 42 4 4 LAMA5 20 62328426 Silent SNP G C3N-01823_T 9474 62328426 2115741 468 26165 NCAM2 0 . GRCh38 21 21286340 21286340 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.409C>A p.= p.R137R ENST00000400546 4/18 252 239 13 206 205 1 strelka-varscan-mutect NCAM2,synonymous_variant,p.=,ENST00000400546,NM_004540.3;NCAM2,synonymous_variant,p.=,ENST00000284894,;NCAM2,non_coding_transcript_exon_variant,,ENST00000486367,;NCAM2,upstream_gene_variant,,ENST00000461281,; A ENST00000400546 Transcript synonymous_variant 658/8135 409/2514 137/837 R Cga/Aga 1 1 NCAM2 HGNC HGNC:7657 protein_coding YES CCDS42910.1 ENSP00000383392 O15394 UPI00001A3703 NM_004540.3 4/18 Gene3D:2.60.40.10,Pfam_domain:PF07679,Prints_domain:PR01838,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF35,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs1454498622 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 21286340 21286340 C A 1 0 0 0 0 0 0 0 1 10219 644 23 1 1 NCAM2 21 21286340 Silent SNP C C3N-01823_T 21286340 25423643 469 26166 GRIK1 0 . GRCh38 21 29561632 29561632 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.2348C>A p.Thr783Lys p.T783K ENST00000399907 15/17 186 168 18 134 134 0 strelka-varscan-mutect GRIK1,missense_variant,p.Thr768Lys,ENST00000399914,;GRIK1,missense_variant,p.Thr783Lys,ENST00000399907,NM_000830.3;GRIK1,missense_variant,p.Thr768Lys,ENST00000399909,;GRIK1,missense_variant,p.Thr783Lys,ENST00000399913,;GRIK1,missense_variant,p.Thr783Lys,ENST00000327783,;GRIK1,missense_variant,p.Thr768Lys,ENST00000389125,NM_175611.2;GRIK1,missense_variant,p.Thr783Lys,ENST00000389124,;BACH1,intron_variant,,ENST00000422809,;BACH1,intron_variant,,ENST00000468059,; T ENST00000399907 Transcript missense_variant 2760/3472 2348/2757 783/918 T/K aCa/aAa 1 -1 GRIK1 HGNC HGNC:4579 protein_coding YES CCDS42913.1 ENSP00000382791 P39086 UPI000012B612 NM_000830.3 deleterious(0) 15/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF36,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS rs1409612155 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 29561632 29561632 G T 1 0 0 0 0 1 0 0 0 6655 1377 48 2 2 GRIK1 21 29561632 Missense_Mutation SNP G C3N-01823_T 8275292 29561632 17148351 470 26167 CLDN8 0 . GRCh38 21 30215716 30215716 + Silent SNP C C A novel C3N-01823_T C3N-01823_N C C c.210G>T p.= p.L70L ENST00000399899 1/1 185 145 40 122 122 0 strelka-varscan-mutect CLDN8,synonymous_variant,p.=,ENST00000399899,NM_199328.2;LINC00307,upstream_gene_variant,,ENST00000451410,; A ENST00000399899 Transcript synonymous_variant 358/2068 210/678 70/225 L ctG/ctT 1 -1 CLDN8 HGNC HGNC:2050 protein_coding YES CCDS13587.1 ENSP00000382783 P56748 A0A0K0K1I9 UPI00000389FD NM_199328.2 1/1 Pfam_domain:PF00822,hmmpanther:PTHR12002,hmmpanther:PTHR12002:SF24 LOW SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 30215716 30215716 C A 1 0 0 0 0 0 0 0 1 3257 697 25 2 2 CLDN8 21 30215716 Silent SNP C C3N-01823_T 654084 30215716 16494267 471 26168 DYRK1A 0 . GRCh38 21 37512087 37512087 + Silent SNP C C T novel C3N-01823_T C3N-01823_N C C c.1848C>T p.= p.H616H ENST00000398960 11/11 307 248 59 224 224 0 strelka-varscan-mutect DYRK1A,synonymous_variant,p.=,ENST00000339659,NM_130436.2;DYRK1A,synonymous_variant,p.=,ENST00000398960,NM_001396.3;DYRK1A,3_prime_UTR_variant,,ENST00000338785,NM_101395.2;DYRK1A,downstream_gene_variant,,ENST00000398956,NM_130438.2; T ENST00000398960 Transcript synonymous_variant 1923/2422 1848/2292 616/763 H caC/caT 1 1 DYRK1A HGNC HGNC:3091 protein_coding YES CCDS42925.1 ENSP00000381932 Q13627 UPI0000129A31 NM_001396.3 11/11 Low_complexity_(Seg):seg,hmmpanther:PTHR24058:SF28,hmmpanther:PTHR24058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 37512087 37512087 C T 1 0 0 0 0 0 0 0 1 4678 506 18 3 3 DYRK1A 21 37512087 Silent SNP C C3N-01823_T 7296371 37512087 9197896 472 26169 TRAPPC10 0 . GRCh38 21 44083242 44083242 + Silent SNP G G T novel C3N-01823_T C3N-01823_N G G c.2178G>T p.= p.V726V ENST00000291574 14/23 255 240 15 142 141 1 strelka-varscan-mutect TRAPPC10,synonymous_variant,p.=,ENST00000291574,NM_003274.4;TRAPPC10,3_prime_UTR_variant,,ENST00000422875,;TRAPPC10,upstream_gene_variant,,ENST00000459741,;TRAPPC10,downstream_gene_variant,,ENST00000461889,;TRAPPC10,downstream_gene_variant,,ENST00000481460,; T ENST00000291574 Transcript synonymous_variant 2353/6976 2178/3780 726/1259 V gtG/gtT 1 1 TRAPPC10 HGNC HGNC:11868 protein_coding YES CCDS13704.1 ENSP00000291574 P48553 UPI0000129E26 NM_003274.4 14/23 hmmpanther:PTHR13251 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 83 44083242 44083242 G T 1 0 0 0 0 0 0 0 1 16940 1306 46 2 2 TRAPPC10 21 44083242 Silent SNP G C3N-01823_T 6571155 44083242 2626741 473 26170 SLC19A1 0 . GRCh38 21 45531788 45531788 + Missense_Mutation SNP T T C novel C3N-01823_T C3N-01823_N T T c.550A>G p.Thr184Ala p.T184A ENST00000311124 3/6 361 338 23 222 221 1 strelka-varscan-mutect SLC19A1,missense_variant,p.Thr184Ala,ENST00000311124,NM_194255.2;SLC19A1,missense_variant,p.Thr184Ala,ENST00000567670,;SLC19A1,missense_variant,p.Thr144Ala,ENST00000485649,NM_001205207.1;SLC19A1,missense_variant,p.Thr184Ala,ENST00000380010,NM_001205206.1;SLC19A1,upstream_gene_variant,,ENST00000417954,;SLC19A1,downstream_gene_variant,,ENST00000443742,;SLC19A1,downstream_gene_variant,,ENST00000427839,;SLC19A1,downstream_gene_variant,,ENST00000486303,; C ENST00000311124 Transcript missense_variant 703/3811 550/1776 184/591 T/A Acg/Gcg 1 -1 SLC19A1 HGNC HGNC:10937 protein_coding YES CCDS13725.1 ENSP00000308895 P41440 UPI000012AA0F NM_194255.2 tolerated(0.28) 3/6 Gene3D:1.20.1250.20,Pfam_domain:PF01770,PIRSF_domain:PIRSF028739,PIRSF_domain:PIRSF500793,hmmpanther:PTHR10686,hmmpanther:PTHR10686:SF12,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00806,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 45531788 45531788 T C 1 0 0 0 0 1 0 0 0 14694 1696 59 5 5 SLC19A1 21 45531788 Missense_Mutation SNP T C3N-01823_T 1448546 45531788 1178195 474 26171 CLTCL1 0 . GRCh38 22 19196326 19196326 + Silent SNP G G A novel C3N-01823_T C3N-01823_N G G c.4131C>T p.= p.T1377T ENST00000427926 26/33 270 256 14 215 215 0 strelka-varscan-mutect CLTCL1,synonymous_variant,p.=,ENST00000427926,NM_007098.3;CLTCL1,synonymous_variant,p.=,ENST00000621271,NM_001835.3;CLTCL1,synonymous_variant,p.=,ENST00000622493,;CLTCL1,synonymous_variant,p.=,ENST00000617926,;CLTCL1,3_prime_UTR_variant,,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,downstream_gene_variant,,ENST00000611723,; A ENST00000427926 Transcript synonymous_variant 4204/5513 4131/4923 1377/1640 T acC/acT 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 26/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Gene3D:1.25.40.10,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 19196326 19196326 G A 1 0 0 0 0 0 0 0 1 3339 1335 47 3 3 CLTCL1 22 19196326 Silent SNP G C3N-01823_T 19196326 31622142 475 26172 CLTCL1 0 . GRCh38 22 19210459 19210459 + Missense_Mutation SNP C C G rs781878409 C3N-01823_T C3N-01823_N C C c.3116G>C p.Arg1039Pro p.R1039P ENST00000427926 20/33 216 187 29 152 152 0 strelka-varscan-mutect CLTCL1,missense_variant,p.Arg1039Pro,ENST00000427926,NM_007098.3;CLTCL1,missense_variant,p.Arg1039Pro,ENST00000621271,NM_001835.3;CLTCL1,upstream_gene_variant,,ENST00000622493,;CLTCL1,upstream_gene_variant,,ENST00000617926,;CLTCL1,missense_variant,p.Arg1039Pro,ENST00000617103,;CLTCL1,non_coding_transcript_exon_variant,,ENST00000615606,;CLTCL1,upstream_gene_variant,,ENST00000611723,; G ENST00000427926 Transcript missense_variant 3189/5513 3116/4923 1039/1640 R/P cGg/cCg rs781878409 1 -1 CLTCL1 HGNC HGNC:2093 protein_coding YES CCDS46662.2 ENSP00000441158 P53675 UPI0000127ABE NM_007098.3 deleterious(0) 20/33 PROSITE_profiles:PS50236,hmmpanther:PTHR10292,hmmpanther:PTHR10292:SF6,Pfam_domain:PF00637,PIRSF_domain:PIRSF002290,SMART_domains:SM00299,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs781878409 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 19210459 19210459 C G 1 0 0 0 0 1 0 0 0 3339 652 23 4 4 CLTCL1 22 19210459 Missense_Mutation SNP C C3N-01823_T 14133 19210459 31608009 476 26173 SEZ6L 0 . GRCh38 22 26347799 26347799 + Missense_Mutation SNP C C G rs745800880 C3N-01823_T C3N-01823_N C C c.2293C>G p.Arg765Gly p.R765G ENST00000248933 11/17 293 266 27 167 167 0 strelka-varscan-mutect SEZ6L,missense_variant,p.Arg765Gly,ENST00000529632,NM_001184775.1;SEZ6L,missense_variant,p.Arg765Gly,ENST00000360929,NM_001184776.1;SEZ6L,missense_variant,p.Arg765Gly,ENST00000404234,NM_001184773.1;SEZ6L,missense_variant,p.Arg538Gly,ENST00000402979,;SEZ6L,missense_variant,p.Arg765Gly,ENST00000248933,NM_021115.4;SEZ6L,missense_variant,p.Arg765Gly,ENST00000629590,NM_001184774.1;SEZ6L,missense_variant,p.Arg538Gly,ENST00000403121,;SEZ6L,missense_variant,p.Arg765Gly,ENST00000343706,NM_001184777.1;SEZ6L,non_coding_transcript_exon_variant,,ENST00000483291,; G ENST00000248933 Transcript missense_variant 2388/3248 2293/3075 765/1024 R/G Cgg/Ggg rs745800880,COSM5057737 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 deleterious(0) 11/17 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF81,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs745800880 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 26347799 26347799 C G 1 0 0 0 0 1 0 0 0 14422 759 27 4 4 SEZ6L 22 26347799 Missense_Mutation SNP C C3N-01823_T 7137340 26347799 24470669 477 26174 GAL3ST1 0 . GRCh38 22 30556048 30556048 + Silent SNP T T A novel C3N-01823_T C3N-01823_N T T c.177A>T p.= p.P59P ENST00000402321 3/3 147 123 24 89 89 0 strelka-varscan-mutect GAL3ST1,synonymous_variant,p.=,ENST00000402321,;GAL3ST1,synonymous_variant,p.=,ENST00000406361,NM_001318104.1,NM_001318113.1;GAL3ST1,synonymous_variant,p.=,ENST00000401975,NM_001318110.1,NM_001318115.1,NM_004861.1;GAL3ST1,synonymous_variant,p.=,ENST00000338911,;GAL3ST1,synonymous_variant,p.=,ENST00000402369,NM_001318103.1,NM_001318109.1;GAL3ST1,synonymous_variant,p.=,ENST00000406955,NM_001318112.1,NM_001318114.1;GAL3ST1,synonymous_variant,p.=,ENST00000441967,;GAL3ST1,synonymous_variant,p.=,ENST00000452827,;GAL3ST1,synonymous_variant,p.=,ENST00000431313,;GAL3ST1,synonymous_variant,p.=,ENST00000437282,;GAL3ST1,synonymous_variant,p.=,ENST00000423299,;GAL3ST1,synonymous_variant,p.=,ENST00000423371,;GAL3ST1,synonymous_variant,p.=,ENST00000453479,;GAL3ST1,synonymous_variant,p.=,ENST00000443136,;GAL3ST1,synonymous_variant,p.=,ENST00000416358,;GAL3ST1,synonymous_variant,p.=,ENST00000448604,;GAL3ST1,synonymous_variant,p.=,ENST00000411821,;GAL3ST1,synonymous_variant,p.=,ENST00000445645,;GAL3ST1,synonymous_variant,p.=,ENST00000447224,;GAL3ST1,synonymous_variant,p.=,ENST00000426220,;GAL3ST1,synonymous_variant,p.=,ENST00000428682,;GAL3ST1,synonymous_variant,p.=,ENST00000427899,; A ENST00000402321 Transcript synonymous_variant 495/1908 177/1272 59/423 P ccA/ccT 1 -1 GAL3ST1 HGNC HGNC:24240 protein_coding YES CCDS13879.1 ENSP00000385735 Q99999 A0A024R1D7 UPI00001285C2 3/3 Pfam_domain:PF06990,hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF56 LOW 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 30556048 30556048 T A 1 0 0 0 0 0 0 0 1 6065 1567 55 4 4 GAL3ST1 22 30556048 Silent SNP T C3N-01823_T 4208249 30556048 20262420 478 26175 MORC2 0 . GRCh38 22 30946387 30946387 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.380G>T p.Cys127Phe p.C127F ENST00000397641 6/26 144 132 12 91 91 0 strelka-varscan-mutect MORC2,missense_variant,p.Cys127Phe,ENST00000397641,NM_001303257.1,NM_001303256.1;MORC2,missense_variant,p.Cys65Phe,ENST00000215862,NM_014941.2;MORC2,upstream_gene_variant,,ENST00000469915,;MORC2,non_coding_transcript_exon_variant,,ENST00000476152,; A ENST00000397641 Transcript missense_variant 789/5181 380/3099 127/1032 C/F tGc/tTc 1 -1 MORC2 HGNC HGNC:23573 protein_coding YES CCDS77668.1 ENSP00000380763 Q9Y6X9 UPI000041AB7E NM_001303257.1,NM_001303256.1 deleterious(0) 6/26 hmmpanther:PTHR23337:SF7,hmmpanther:PTHR23337,Pfam_domain:PF13589,Gene3D:3.30.565.10,Superfamily_domains:SSF55874 MODERATE 1 SNV 5 1 PASS . . 0 202 5 2 0 0 0 0 -16.91516 0.9998656 1 1 1 0 A 3 1 83 30946387 30946387 C A 1 0 0 0 0 1 0 0 0 9666 710 25 2 2 MORC2 22 30946387 Missense_Mutation SNP C C3N-01823_T 390339 30946387 19872081 479 26176 SFI1 0 . GRCh38 22 31611259 31611259 + Frame_Shift_Del DEL C C - novel C3N-01823_T C3N-01823_N C C c.2371delC p.Leu791TrpfsTer110 p.L791Wfs*110 ENST00000400288 23/33 155 144 11 99 99 0 varindel-pindel SFI1,frameshift_variant,p.Leu736TrpfsTer110,ENST00000540643,NM_001258325.1;SFI1,frameshift_variant,p.Leu760TrpfsTer110,ENST00000432498,NM_014775.3;SFI1,frameshift_variant,p.Leu791TrpfsTer110,ENST00000400288,NM_001007467.2;SFI1,frameshift_variant,p.Leu709TrpfsTer110,ENST00000400289,NM_001258326.1,NM_001258327.1;SFI1,frameshift_variant,p.Leu638TrpfsTer110,ENST00000443011,;SFI1,frameshift_variant,p.Leu374TrpfsTer110,ENST00000417682,;SFI1,non_coding_transcript_exon_variant,,ENST00000466991,;SFI1,upstream_gene_variant,,ENST00000474741,;SFI1,upstream_gene_variant,,ENST00000463436,;SFI1,frameshift_variant,p.Trp381GlyfsTer165,ENST00000452250,;SFI1,3_prime_UTR_variant,,ENST00000524296,;SFI1,non_coding_transcript_exon_variant,,ENST00000382162,;SFI1,non_coding_transcript_exon_variant,,ENST00000491973,;SFI1,upstream_gene_variant,,ENST00000464333,;SFI1,upstream_gene_variant,,ENST00000476577,;SFI1,upstream_gene_variant,,ENST00000357852,;SFI1,upstream_gene_variant,,ENST00000495107,;SFI1,downstream_gene_variant,,ENST00000488883,; - ENST00000400288 Transcript frameshift_variant 2476/4002 2371/3729 791/1242 L/X Ctg/tg 1 1 SFI1 HGNC HGNC:29064 protein_coding YES CCDS43004.1 ENSP00000383145 A8K8P3 UPI00004703B1 NM_001007467.2 23/33 hmmpanther:PTHR22028,hmmpanther:PTHR22028:SF4 HIGH 1 deletion 2 1 PASS . . 0 203 4 3 0 0 0 0 -14.84413 0.9993202 1 1 1 0 - 7 5 83 31611259 31611259 C - 1 0 1 0 1 0 0 0 0 14434 796 28 0 0 SFI1 22 31611259 Frame_Shift_Del DEL C C3N-01823_T 664872 31611259 19207209 480 26177 NLGN4X 0 . GRCh38 X 5903404 5903404 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.1274C>A p.Thr425Lys p.T425K ENST00000381095 5/6 217 156 61 95 95 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Thr425Lys,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Thr425Lys,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Thr425Lys,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Thr425Lys,ENST00000381092,;NLGN4X,missense_variant,p.Thr426Lys,ENST00000538097,;NLGN4X,upstream_gene_variant,,ENST00000477079,; T ENST00000381095 Transcript missense_variant 1902/5870 1274/2451 425/816 T/K aCa/aAa 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0) 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 5903404 5903404 G T 1 0 0 0 0 1 0 0 0 10501 1377 48 2 2 NLGN4X 23 5903404 Missense_Mutation SNP G C3N-01823_T 5903404 150137491 481 26178 SHROOM2 0 . GRCh38 X 9894706 9894706 + Missense_Mutation SNP T T A novel C3N-01823_T C3N-01823_N T T c.798T>A p.Ser266Arg p.S266R ENST00000380913 4/10 161 130 31 87 87 0 strelka-varscan-mutect SHROOM2,missense_variant,p.Ser266Arg,ENST00000380913,NM_001649.2;SHROOM2,upstream_gene_variant,,ENST00000493668,; A ENST00000380913 Transcript missense_variant 888/7447 798/4851 266/1616 S/R agT/agA 1 1 SHROOM2 HGNC HGNC:630 protein_coding YES CCDS14135.1 ENSP00000370299 Q13796 UPI0000125D05 NM_001649.2 tolerated(0.16) 4/10 hmmpanther:PTHR15012:SF8,hmmpanther:PTHR15012 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 83 9894706 9894706 T A 1 0 0 0 0 1 0 0 0 14557 1722 60 4 4 SHROOM2 23 9894706 Missense_Mutation SNP T C3N-01823_T 3991302 9894706 146146189 482 26179 PHKA2 0 . GRCh38 X 18894350 18894350 + Missense_Mutation SNP C C T C3N-01823_T C3N-01823_N C C c.3391G>A p.Val1131Met p.V1131M ENST00000379942 32/33 286 256 30 199 199 0 strelka-varscan-mutect PHKA2,missense_variant,p.Val1131Met,ENST00000379942,NM_000292.2;PHKA2-AS1,non_coding_transcript_exon_variant,,ENST00000439295,;PHKA2-AS1,downstream_gene_variant,,ENST00000452900,;PHKA2,non_coding_transcript_exon_variant,,ENST00000481718,;PHKA2,non_coding_transcript_exon_variant,,ENST00000469485,;PHKA2,non_coding_transcript_exon_variant,,ENST00000473739,;PHKA2,non_coding_transcript_exon_variant,,ENST00000473597,;PHKA2,downstream_gene_variant,,ENST00000469645,; T ENST00000379942 Transcript missense_variant 4057/5559 3391/3708 1131/1235 V/M Gtg/Atg COSM1741671 1 -1 PHKA2 HGNC HGNC:8926 protein_coding YES CCDS14190.1 ENSP00000369274 P46019 UPI000012DF4B NM_000292.2 deleterious(0) 32/33 hmmpanther:PTHR10749,hmmpanther:PTHR10749:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 18894350 18894350 C T 1 0 0 0 0 1 0 0 0 11932 536 19 1 1 PHKA2 23 18894350 Missense_Mutation SNP C C3N-01823_T 8999644 18894350 137146545 483 26180 FAM47B 0 . GRCh38 X 34943460 34943460 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.629G>T p.Ser210Ile p.S210I ENST00000329357 1/1 215 179 36 132 132 0 strelka-varscan-mutect FAM47B,missense_variant,p.Ser210Ile,ENST00000329357,NM_152631.2; T ENST00000329357 Transcript missense_variant 665/2120 629/1938 210/645 S/I aGt/aTt 1 1 FAM47B HGNC HGNC:26659 protein_coding YES CCDS14236.1 ENSP00000328307 Q8NA70 UPI000013F47B NM_152631.2 tolerated(0.2) 1/1 Pfam_domain:PF14642,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF192 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 34943460 34943460 G T 1 0 0 0 0 1 0 0 0 5448 1029 36 2 2 FAM47B 23 34943460 Missense_Mutation SNP G C3N-01823_T 16049110 34943460 121097435 484 26181 USP9X 0 . GRCh38 X 41143327 41143327 + Frame_Shift_Del DEL T T - novel C3N-01823_T C3N-01823_N T T c.1199delT p.Leu400CysfsTer11 p.L400Cfs*11 ENST00000324545 10/45 48 35 13 57 57 0 sindel-varindel-pindel USP9X,frameshift_variant,p.Leu400CysfsTer11,ENST00000324545,NM_001039590.2;USP9X,frameshift_variant,p.Leu400CysfsTer11,ENST00000378308,NM_001039591.2; - ENST00000324545 Transcript frameshift_variant 1831/12401 1198/7713 400/2570 L/X Ttg/tg 1 1 USP9X HGNC HGNC:12632 protein_coding YES CCDS43930.1 ENSP00000316357 Q93008 UPI00001AF419 NM_001039590.2 10/45 Gene3D:1.25.10.10 HIGH 1 deletion 5 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 83 41143327 41143327 T - 1 0 1 0 1 0 0 0 0 17633 1722 60 0 0 USP9X 23 41143327 Frame_Shift_Del DEL T C3N-01823_T 6199867 41143327 114897568 485 26182 AKAP4 0 . GRCh38 X 50193274 50193274 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.1439G>A p.Gly480Asp p.G480D ENST00000358526 5/6 180 141 39 162 162 0 strelka-varscan-mutect AKAP4,missense_variant,p.Gly480Asp,ENST00000358526,NM_003886.2;AKAP4,missense_variant,p.Gly471Asp,ENST00000376064,NM_139289.1;AKAP4,intron_variant,,ENST00000448865,;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,; T ENST00000358526 Transcript missense_variant 1563/2881 1439/2565 480/854 G/D gGc/gAc 1 -1 AKAP4 HGNC HGNC:374 protein_coding YES CCDS14329.1 ENSP00000351327 Q5JQC9 UPI000013DA96 NM_003886.2 tolerated(0.32) 5/6 hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 50193274 50193274 C T 1 0 0 0 0 1 0 0 0 537 739 26 3 3 AKAP4 23 50193274 Missense_Mutation SNP C C3N-01823_T 9049947 50193274 105847621 486 26183 SHROOM4 0 . GRCh38 X 50607471 50607471 + Missense_Mutation SNP C C G novel C3N-01823_T C3N-01823_N C C c.3671G>C p.Gly1224Ala p.G1224A ENST00000376020 6/9 149 120 29 99 99 0 strelka-varscan-mutect SHROOM4,missense_variant,p.Gly1224Ala,ENST00000376020,NM_020717.3;SHROOM4,missense_variant,p.Gly1108Ala,ENST00000460112,;SHROOM4,missense_variant,p.Gly1224Ala,ENST00000289292,; G ENST00000376020 Transcript missense_variant 3697/9556 3671/4482 1224/1493 G/A gGa/gCa 1 -1 SHROOM4 HGNC HGNC:29215 protein_coding YES CCDS35277.1 ENSP00000365188 Q9ULL8 UPI00001C2068 NM_020717.3 tolerated(0.09) 6/9 PROSITE_profiles:PS51307,hmmpanther:PTHR15012:SF35,hmmpanther:PTHR15012 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 83 50607471 50607471 C G 1 0 0 0 0 1 0 0 0 14559 855 30 4 4 SHROOM4 23 50607471 Missense_Mutation SNP C C3N-01823_T 414197 50607471 105433424 487 26184 XAGE5 0 . GRCh38 X 52815209 52815209 + Missense_Mutation SNP C C T novel C3N-01823_T C3N-01823_N C C c.296C>T p.Pro99Leu p.P99L ENST00000351072 4/5 72 62 10 89 89 0 strelka-varscan-mutect XAGE5,missense_variant,p.Pro99Leu,ENST00000351072,NM_130775.2;XAGE5,missense_variant,p.Pro99Leu,ENST00000375501,;XAGE5,3_prime_UTR_variant,,ENST00000375503,;XAGE5,non_coding_transcript_exon_variant,,ENST00000445860,; T ENST00000351072 Transcript missense_variant 362/478 296/327 99/108 P/L cCa/cTa 1 1 XAGE5 HGNC HGNC:30930 protein_coding YES CCDS14346.1 ENSP00000342240 Q8WWM1 UPI0000138FC9 NM_130775.2 tolerated(0.08) 4/5 hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF7,Pfam_domain:PF05831,SMART_domains:SM01379 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 52815209 52815209 C T 1 0 0 0 0 1 0 0 0 17980 594 21 3 3 XAGE5 23 52815209 Missense_Mutation SNP C C3N-01823_T 2207738 52815209 103225686 488 26185 P2RY10 0 . GRCh38 X 78961168 78961168 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.648G>T p.Trp216Cys p.W216C ENST00000171757 4/4 108 84 24 103 103 0 strelka-varscan-mutect P2RY10,missense_variant,p.Trp216Cys,ENST00000171757,NM_014499.2;P2RY10,missense_variant,p.Trp216Cys,ENST00000544091,NM_198333.1;P2RY10,downstream_gene_variant,,ENST00000475374,;P2RY10,downstream_gene_variant,,ENST00000461541,; T ENST00000171757 Transcript missense_variant 928/1714 648/1020 216/339 W/C tgG/tgT 1 1 P2RY10 HGNC HGNC:19906 protein_coding YES CCDS14442.1 ENSP00000171757 O00398 UPI0000050471 NM_014499.2 tolerated(0.16) 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF47,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 78961168 78961168 G T 1 0 0 0 0 1 0 0 0 11420 1270 44 2 2 P2RY10 23 78961168 Missense_Mutation SNP G C3N-01823_T 26145959 78961168 77079727 489 26186 BRWD3 0 . GRCh38 X 80724975 80724975 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1479G>T p.Trp493Cys p.W493C ENST00000373275 15/41 211 170 41 185 184 1 strelka-varscan-mutect BRWD3,missense_variant,p.Trp493Cys,ENST00000373275,NM_153252.4;BRWD3,upstream_gene_variant,,ENST00000473691,; A ENST00000373275 Transcript missense_variant 1696/11381 1479/5409 493/1802 W/C tgG/tgT 1 -1 BRWD3 HGNC HGNC:17342 protein_coding YES CCDS14447.1 ENSP00000362372 Q6RI45 UPI000045785B NM_153252.4 deleterious(0.02) 15/41 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR16266:SF25,hmmpanther:PTHR16266,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -19.99987 0.9980052 1 1 1 0 A 3 1 83 80724975 80724975 C A 1 0 0 0 0 1 0 0 0 1700 624 22 2 2 BRWD3 23 80724975 Missense_Mutation SNP C C3N-01823_T 1763807 80724975 75315920 490 26187 PCDH11X 0 . GRCh38 X 92618548 92618548 + Missense_Mutation SNP G G T novel C3N-01823_T C3N-01823_N G G c.3652G>T p.Ala1218Ser p.A1218S ENST00000373094 7/7 428 323 105 306 306 0 strelka-varscan-mutect PCDH11X,missense_variant,p.Ala1218Ser,ENST00000373094,NM_032968.4;PCDH11X,missense_variant,p.Ala1208Ser,ENST00000373097,NM_032969.4;PCDH11X,missense_variant,p.Ala1210Ser,ENST00000406881,NM_001168360.1;PCDH11X,missense_variant,p.Ala1200Ser,ENST00000361655,NM_001168363.1;PCDH11X,missense_variant,p.Ala1181Ser,ENST00000373088,NM_001168362.1;PCDH11X,3_prime_UTR_variant,,ENST00000504220,NM_001168361.1; T ENST00000373094 Transcript missense_variant 4497/9179 3652/4044 1218/1347 A/S Gct/Tct 1 1 PCDH11X HGNC HGNC:8656 protein_coding YES CCDS14461.1 ENSP00000362186 Q9BZA7 UPI0000070BD8 NM_032968.4 tolerated_low_confidence(0.45) 7/7 MODERATE 1 SNV 1 1 PASS rs1462233761 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 83 92618548 92618548 G T 1 0 0 0 0 1 0 0 0 11595 1319 46 2 2 PCDH11X 23 92618548 Missense_Mutation SNP G C3N-01823_T 11893573 92618548 63422347 491 26188 TEX13C 0 . GRCh38 X 125321230 125321230 + Missense_Mutation SNP C C A novel C3N-01823_T C3N-01823_N C C c.1111C>A p.Leu371Ile p.L371I ENST00000632600 1/1 295 242 53 182 182 0 strelka-varscan-mutect TEX13C,missense_variant,p.Leu371Ile,ENST00000632600,NM_001195272.1; A ENST00000632600 Transcript missense_variant 1111/5095 1111/2982 371/993 L/I Cta/Ata 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 tolerated(0.22) 1/1 MODERATE 1 SNV 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9977664 1 1 1 0 A 3 1 83 125321230 125321230 C A 1 0 0 0 0 1 0 0 0 16199 680 24 2 2 TEX13C 23 125321230 Missense_Mutation SNP C C3N-01823_T 32702682 125321230 30719665 492 26189 CCDC160 0 . GRCh38 X 134244998 134244998 + Silent SNP T T C rs367640741 C3N-01823_T C3N-01823_N T T c.198T>C p.= p.Y66Y ENST00000517294 3/3 91 75 16 72 72 0 strelka-varscan-mutect CCDC160,synonymous_variant,p.=,ENST00000517294,;CCDC160,synonymous_variant,p.=,ENST00000370809,NM_001101357.1; C ENST00000517294 Transcript synonymous_variant 581/1790 198/978 66/325 Y taT/taC rs367640741,COSM2726706 1 1 CCDC160 HGNC HGNC:37286 protein_coding YES CCDS48171.1 ENSP00000427951 A6NGH7 UPI00001993FD 3/3 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF71 0,1 LOW 1 SNV 5 0,1 1 PASS rs367640741 . 0 204 4 0 0 0 0 2 -2.519509 0 0 1 0 0 C 2 2 83 134244998 134244998 T C 1 0 0 0 0 0 0 0 1 2480 1413 49 5 5 CCDC160 23 134244998 Silent SNP T C3N-01823_T 8923768 134244998 21795897 493 26190 INTS6L 0 . GRCh38 X 135580000 135580000 + Missense_Mutation SNP G G C C3N-01823_T C3N-01823_N G G c.2221G>C p.Gly741Arg p.G741R ENST00000370752 15/17 89 72 17 78 78 0 strelka-varscan-mutect INTS6L,missense_variant,p.Gly741Arg,ENST00000370752,NM_182540.4;INTS6L,non_coding_transcript_exon_variant,,ENST00000481908,;INTS6L,non_coding_transcript_exon_variant,,ENST00000481429,;INTS6L,non_coding_transcript_exon_variant,,ENST00000494957,;INTS6L,non_coding_transcript_exon_variant,,ENST00000493637,;RP11-432N13.2,downstream_gene_variant,,ENST00000439300,; C ENST00000370752 Transcript missense_variant 2555/3793 2221/2586 741/861 G/R Gga/Cga COSM1465778 1 1 INTS6L HGNC HGNC:27334 protein_coding YES CCDS35401.1 ENSP00000359788 Q5JSJ4 UPI00004A3AAF NM_182540.4 tolerated(0.11) 15/17 hmmpanther:PTHR12957,hmmpanther:PTHR12957:SF22 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 83 135580000 135580000 G C 1 0 0 0 0 1 0 0 0 7685 1001 35 4 4 INTS6L 23 135580000 Missense_Mutation SNP G C3N-01823_T 1335002 135580000 20460895 494 26191 F9 0 . GRCh38 X 139551090 139551090 + Silent SNP T T A novel C3N-01823_T C3N-01823_N T T c.549T>A p.= p.V183V ENST00000218099 6/8 179 147 32 106 106 0 strelka-varscan-mutect F9,synonymous_variant,p.=,ENST00000218099,NM_000133.3;F9,synonymous_variant,p.=,ENST00000394090,;F9,downstream_gene_variant,,ENST00000479617,; A ENST00000218099 Transcript synonymous_variant 556/2780 549/1386 183/461 V gtT/gtA 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 6/8 Gene3D:2.10.25.10,PIRSF_domain:PIRSF001143,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF135 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 83 139551090 139551090 T A 1 0 0 0 0 0 0 0 1 5220 1828 64 4 4 F9 23 139551090 Silent SNP T C3N-01823_T 3971090 139551090 16489805 495 26192 AGRN 0 . GRCh38 1 1050300 1050300 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.4947A>T p.Arg1649Ser p.R1649S ENST00000379370 28/36 371 292 79 341 340 1 strelka-varscan-mutect AGRN,missense_variant,p.Arg1511Ser,ENST00000620552,NM_001305275.1;AGRN,missense_variant,p.Arg1649Ser,ENST00000379370,NM_198576.3;AGRN,upstream_gene_variant,,ENST00000419249,;RP11-54O7.14,upstream_gene_variant,,ENST00000418300,;AGRN,upstream_gene_variant,,ENST00000461111,;AGRN,downstream_gene_variant,,ENST00000492947,;AGRN,downstream_gene_variant,,ENST00000479707,;AGRN,downstream_gene_variant,,ENST00000466223,;AGRN,downstream_gene_variant,,ENST00000478677,; T ENST00000379370 Transcript missense_variant 4997/7323 4947/6138 1649/2045 R/S agA/agT 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 tolerated(0.14) 28/36 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF288,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 1050300 1050300 A T 1 0 0 0 0 1 0 0 0 476 301 11 4 4 AGRN 1 1050300 Missense_Mutation SNP A C3N-01842_T 1050300 247906122 1 26193 ESPN 0 . GRCh38 1 6445681 6445681 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1210G>T p.Ala404Ser p.A404S ENST00000377828 7/13 442 356 86 437 436 1 strelka-varscan-mutect ESPN,missense_variant,p.Ala404Ser,ENST00000636330,;ESPN,missense_variant,p.Ala404Ser,ENST00000377828,NM_031475.2;ESPN,missense_variant,p.Ala189Ser,ENST00000418286,;ESPN,upstream_gene_variant,,ENST00000461727,;ESPN,upstream_gene_variant,,ENST00000633239,;ESPN,upstream_gene_variant,,ENST00000416731,;ESPN,upstream_gene_variant,,ENST00000475228,;ESPN,upstream_gene_variant,,ENST00000632803,;ESPN,upstream_gene_variant,,ENST00000478323,;RP1-202O8.2,splice_region_variant,,ENST00000419034,;ESPN,downstream_gene_variant,,ENST00000633651,;ESPN,downstream_gene_variant,,ENST00000632142,;ESPN,upstream_gene_variant,,ENST00000475479,;ESPN,upstream_gene_variant,,ENST00000632593,; T ENST00000377828 Transcript missense_variant 1378/3531 1210/2565 404/854 A/S Gct/Tct 1 1 ESPN HGNC HGNC:13281 protein_coding YES CCDS70.1 ENSP00000367059 B1AK53 UPI000013D2B6 NM_031475.2 tolerated(0.1) 7/13 hmmpanther:PTHR24153:SF14,hmmpanther:PTHR24153 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 6445681 6445681 G T 1 0 0 0 0 1 0 0 0 5116 971 34 2 2 ESPN 1 6445681 Missense_Mutation SNP G C3N-01842_T 5395381 6445681 242510741 2 26194 FBXO44 0 . GRCh38 1 11658552 11658552 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.412G>T p.Val138Leu p.V138L ENST00000376770 5/7 173 133 40 204 204 0 strelka-varscan-mutect FBXO44,missense_variant,p.Val138Leu,ENST00000376770,NM_001014765.1;FBXO44,missense_variant,p.Val138Leu,ENST00000251547,NM_001304791.1,NM_033182.5;FBXO44,missense_variant,p.Gly128Val,ENST00000376768,;FBXO44,missense_variant,p.Gly4Val,ENST00000471895,;FBXO44,intron_variant,,ENST00000251546,NM_183412.2;FBXO44,intron_variant,,ENST00000376762,NM_183413.2;FBXO44,intron_variant,,ENST00000425796,;FBXO44,intron_variant,,ENST00000475435,;FBXO44,intron_variant,,ENST00000376760,NM_001304790.1;FBXO2,upstream_gene_variant,,ENST00000354287,NM_012168.5;FBXO2,upstream_gene_variant,,ENST00000465901,;FBXO2,upstream_gene_variant,,ENST00000466919,; T ENST00000376770 Transcript missense_variant 910/3320 412/768 138/255 V/L Gtg/Ttg 1 1 FBXO44 HGNC HGNC:24847 protein_coding YES CCDS132.1 ENSP00000365961 Q9H4M3 A0A024R4F9 UPI000013CD04 NM_001014765.1 tolerated(1) 5/7 PROSITE_profiles:PS51114,hmmpanther:PTHR12125:SF12,hmmpanther:PTHR12125,Gene3D:2.60.120.260,Pfam_domain:PF04300,SMART_domains:SM01198,Superfamily_domains:SSF49785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 11658552 11658552 G T 1 0 0 0 0 1 0 0 0 5616 1261 44 2 2 FBXO44 1 11658552 Missense_Mutation SNP G C3N-01842_T 5212871 11658552 237297870 3 26195 C1orf167 0 . GRCh38 1 11782242 11782242 + Missense_Mutation SNP G G A C3N-01842_T C3N-01842_N G G c.2986G>A p.Gly996Ser p.G996S ENST00000433342 14/21 117 94 23 135 135 0 strelka-varscan-mutect C1orf167,missense_variant,p.Gly996Ser,ENST00000433342,NM_001010881.1;C1orf167,missense_variant,p.Gly356Ser,ENST00000312793,;C1orf167,missense_variant,p.Gly139Ser,ENST00000444493,;C1orf167,missense_variant,p.Gly82Ser,ENST00000449278,;MTHFR,downstream_gene_variant,,ENST00000376592,;MTHFR,downstream_gene_variant,,ENST00000376583,;MTHFR,downstream_gene_variant,,ENST00000376590,NM_005957.4;RP11-56N19.5,upstream_gene_variant,,ENST00000376620,;C1orf167,downstream_gene_variant,,ENST00000484153,;C1orf167,upstream_gene_variant,,ENST00000475041,; A ENST00000433342 Transcript missense_variant 2986/4545 2986/4407 996/1468 G/S Ggc/Agc COSM5164971,COSM5164972 1 1 C1orf167 HGNC HGNC:25262 protein_coding YES ENSP00000414909 Q5SNV9 UPI0000DD7886 NM_001010881.1 deleterious(0.03) 14/21 hmmpanther:PTHR38493,hmmpanther:PTHR38493:SF1,Pfam_domain:PF15736 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999962 1 1 1 0 A 3 1 84 11782242 11782242 G A 1 0 0 0 0 1 0 0 0 1972 1232 43 3 3 C1orf167 1 11782242 Missense_Mutation SNP G C3N-01842_T 123690 11782242 237174180 4 26196 PRAMEF19 0 . GRCh38 1 13371641 13371641 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.53G>T p.Cys18Phe p.C18F ENST00000376101 1/3 193 163 30 257 257 0 varscan-mutect PRAMEF19,missense_variant,p.Cys18Phe,ENST00000376101,; A ENST00000376101 Transcript missense_variant 53/1233 53/1233 18/410 C/F tGc/tTc 1 -1 PRAMEF19 HGNC HGNC:24908 protein_coding YES ENSP00000365269 Q5SWL8 UPI0001661E5E deleterious(0.02) 1/3 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF5,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 13371641 13371641 C A 1 0 0 0 0 1 0 0 0 12561 710 25 2 2 PRAMEF19 1 13371641 Missense_Mutation SNP C C3N-01842_T 1589399 13371641 235584781 5 26197 PRDM2 0 . GRCh38 1 13781439 13781439 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.3644C>A p.Pro1215Gln p.P1215Q ENST00000235372 8/10 262 232 30 283 283 0 strelka-varscan-mutect PRDM2,missense_variant,p.Pro1215Gln,ENST00000235372,NM_012231.4;PRDM2,missense_variant,p.Pro1215Gln,ENST00000311066,NM_015866.4;PRDM2,missense_variant,p.Pro1014Gln,ENST00000413440,NM_001007257.2;PRDM2,missense_variant,p.Pro1014Gln,ENST00000343137,;PRDM2,intron_variant,,ENST00000376048,NM_001135610.1;PRDM2,intron_variant,,ENST00000503842,;PRDM2,intron_variant,,ENST00000505823,;PRDM2,downstream_gene_variant,,ENST00000487453,;PRDM2,downstream_gene_variant,,ENST00000407521,;PRDM2,intron_variant,,ENST00000491134,; A ENST00000235372 Transcript missense_variant 4500/7957 3644/5157 1215/1718 P/Q cCa/cAa 1 1 PRDM2 HGNC HGNC:9347 protein_coding YES CCDS150.1 ENSP00000235372 Q13029 UPI000013C9CD NM_012231.4 deleterious(0) 8/10 hmmpanther:PTHR24402:SF4,hmmpanther:PTHR24402,PIRSF_domain:PIRSF002395 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 13781439 13781439 C A 1 0 0 0 0 1 0 0 0 12589 594 21 2 2 PRDM2 1 13781439 Missense_Mutation SNP C C3N-01842_T 409798 13781439 235174983 6 26198 PADI2 0 . GRCh38 1 17093652 17093652 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.444G>T p.= p.G148G ENST00000375486 5/16 189 149 40 226 225 1 strelka-varscan-mutect PADI2,synonymous_variant,p.=,ENST00000375486,NM_007365.2;PADI2,synonymous_variant,p.=,ENST00000375481,; A ENST00000375486 Transcript synonymous_variant 508/4345 444/1998 148/665 G ggG/ggT 1 -1 PADI2 HGNC HGNC:18341 protein_coding YES CCDS177.1 ENSP00000364635 Q9Y2J8 A0A024RA98 UPI00001314AF NM_007365.2 5/16 Superfamily_domains:0044952,PD936484,Pfam_domain:PF08527,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF12 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 17093652 17093652 C A 1 0 0 0 0 0 0 0 1 11456 610 22 2 2 PADI2 1 17093652 Silent SNP C C3N-01842_T 3312213 17093652 231862770 7 26199 FGR 0 . GRCh38 1 27623885 27623885 + Missense_Mutation SNP G G T rs752716889 C3N-01842_T C3N-01842_N G G c.32C>A p.Pro11Gln p.P11Q ENST00000374005 3/13 133 99 34 144 142 2 strelka-varscan-mutect FGR,missense_variant,p.Pro11Gln,ENST00000374005,NM_005248.2;FGR,missense_variant,p.Pro11Gln,ENST00000399173,NM_001042747.1;FGR,missense_variant,p.Pro11Gln,ENST00000374004,;FGR,missense_variant,p.Pro11Gln,ENST00000374003,NM_001042729.1;FGR,missense_variant,p.Pro11Gln,ENST00000457296,;FGR,non_coding_transcript_exon_variant,,ENST00000468038,;FGR,non_coding_transcript_exon_variant,,ENST00000475472,; T ENST00000374005 Transcript missense_variant 321/2729 32/1590 11/529 P/Q cCg/cAg rs752716889 1 -1 FGR HGNC HGNC:3697 protein_coding YES CCDS305.1 ENSP00000363117 P09769 UPI000012A72F NM_005248.2 tolerated_low_confidence(0.07) 3/13 hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF224 MODERATE 1 SNV 1 1 PASS rs752716889 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 27623885 27623885 G T 1 0 0 0 0 1 0 0 0 5738 1116 39 1 1 FGR 1 27623885 Missense_Mutation SNP G C3N-01842_T 10530233 27623885 221332537 8 26200 LCK 0 . GRCh38 1 32285635 32285635 + Missense_Mutation SNP C C A rs542519367 C3N-01842_T C3N-01842_N C C c.1449C>A p.Asp483Glu p.D483E ENST00000336890 13/13 508 395 113 650 650 0 strelka-varscan-mutect LCK,missense_variant,p.Asp513Glu,ENST00000333070,;LCK,missense_variant,p.Asp490Glu,ENST00000373564,;LCK,missense_variant,p.Asp483Glu,ENST00000336890,NM_005356.4;LCK,missense_variant,p.Asp483Glu,ENST00000619559,NM_001042771.2;Y_RNA,downstream_gene_variant,,ENST00000516641,;LCK,non_coding_transcript_exon_variant,,ENST00000469765,; A ENST00000336890 Transcript missense_variant 1587/2117 1449/1530 483/509 D/E gaC/gaA rs542519367 1 1 LCK HGNC HGNC:6524 protein_coding YES CCDS359.1 ENSP00000337825 P06239 A0A0S2Z3Y8 UPI0000151F17 NM_005356.4 tolerated(1) 13/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF39,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS rs542519367 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 32285635 32285635 C A 1 0 0 0 0 1 0 0 0 8582 506 18 2 2 LCK 1 32285635 Missense_Mutation SNP C C3N-01842_T 4661750 32285635 216670787 9 26201 FOXJ3 0 . GRCh38 1 42278504 42278504 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.213C>A p.= p.V71V ENST00000372572 5/15 484 372 112 489 489 0 strelka-varscan-mutect FOXJ3,synonymous_variant,p.=,ENST00000372572,NM_001198851.1;FOXJ3,synonymous_variant,p.=,ENST00000372573,NM_001198850.1;FOXJ3,synonymous_variant,p.=,ENST00000361346,NM_014947.4;FOXJ3,synonymous_variant,p.=,ENST00000545068,;FOXJ3,synonymous_variant,p.=,ENST00000361776,NM_001198852.1;FOXJ3,synonymous_variant,p.=,ENST00000445886,;FOXJ3,synonymous_variant,p.=,ENST00000454417,; T ENST00000372572 Transcript synonymous_variant 525/5352 213/1869 71/622 V gtC/gtA 1 -1 FOXJ3 HGNC HGNC:29178 protein_coding YES CCDS30689.1 ENSP00000361653 Q9UPW0 UPI000013D359 NM_001198851.1 5/15 hmmpanther:PTHR11829:SF104,hmmpanther:PTHR11829,Gene3D:1.10.10.10 LOW 1 SNV 1 1 PASS rs1248255217 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 42278504 42278504 G T 1 0 0 0 0 0 0 0 1 5876 1161 41 2 2 FOXJ3 1 42278504 Silent SNP G C3N-01842_T 9992869 42278504 206677918 10 26202 PATJ 0 . GRCh38 1 62128851 62128851 + Missense_Mutation SNP G G T rs747934422 C3N-01842_T C3N-01842_N G G c.5177G>T p.Arg1726Leu p.R1726L ENST00000371158 41/43 184 151 33 180 180 0 strelka-varscan-mutect PATJ,missense_variant,p.Arg1726Leu,ENST00000371158,NM_176877.2;PATJ,missense_variant,p.Arg510Leu,ENST00000635137,;PATJ,intron_variant,,ENST00000613764,;PATJ,3_prime_UTR_variant,,ENST00000484937,;PATJ,downstream_gene_variant,,ENST00000472512,; T ENST00000371158 Transcript missense_variant 5291/8505 5177/5406 1726/1801 R/L cGg/cTg rs747934422 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 deleterious(0) 41/43 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 5 1 PASS rs747934422 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 62128851 62128851 G T 1 0 0 0 0 1 0 0 0 11558 1116 39 1 1 PATJ 1 62128851 Missense_Mutation SNP G C3N-01842_T 19850347 62128851 186827571 11 26203 LHX8 0 . GRCh38 1 75143169 75143169 + Missense_Mutation SNP C C A rs12084309 C3N-01842_T C3N-01842_N C C c.441C>A p.Asp147Glu p.D147E ENST00000294638 6/10 348 277 71 344 343 1 strelka-varscan-mutect LHX8,missense_variant,p.Asp147Glu,ENST00000294638,NM_001001933.1;LHX8,missense_variant,p.Asp137Glu,ENST00000356261,NM_001256114.1; A ENST00000294638 Transcript missense_variant 1105/2373 441/1071 147/356 D/E gaC/gaA rs12084309 1 1 LHX8 HGNC HGNC:28838 protein_coding YES CCDS30756.1 ENSP00000294638 Q68G74 UPI00001972E8 NM_001001933.1 deleterious(0) 6/10 Gene3D:2.10.110.10,Pfam_domain:PF00412,PROSITE_patterns:PS00478,PROSITE_profiles:PS50023,hmmpanther:PTHR24208,SMART_domains:SM00132,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS rs12084309 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 75143169 75143169 C A 1 0 0 0 0 1 0 0 0 8685 564 20 2 2 LHX8 1 75143169 Missense_Mutation SNP C C3N-01842_T 13014318 75143169 173813253 12 26204 ST6GALNAC3 0 . GRCh38 1 76412171 76412171 + Missense_Mutation SNP G G C rs746896290 C3N-01842_T C3N-01842_N G G c.377G>C p.Arg126Pro p.R126P ENST00000328299 3/5 364 287 77 416 416 0 strelka-varscan-mutect ST6GALNAC3,missense_variant,p.Arg126Pro,ENST00000328299,NM_152996.2;ST6GALNAC3,missense_variant,p.Arg55Pro,ENST00000621530,;ST6GALNAC3,non_coding_transcript_exon_variant,,ENST00000464140,; C ENST00000328299 Transcript missense_variant 525/6861 377/918 126/305 R/P cGa/cCa rs746896290 1 1 ST6GALNAC3 HGNC HGNC:19343 protein_coding YES CCDS672.1 ENSP00000329214 Q8NDV1 UPI000006F75A NM_152996.2 3/5 Pfam_domain:PF00777,hmmpanther:PTHR13713,hmmpanther:PTHR13713:SF49 MODERATE 1 SNV 1 1 PASS rs746896290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 76412171 76412171 G C 1 0 0 0 0 1 0 0 0 15603 1058 37 4 4 ST6GALNAC3 1 76412171 Missense_Mutation SNP G C3N-01842_T 1269002 76412171 172544251 13 26205 PIGK 0 . GRCh38 1 77219376 77219376 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.27G>T p.= p.R9R ENST00000370812 1/11 357 283 74 406 405 1 strelka-varscan-mutect PIGK,synonymous_variant,p.=,ENST00000370812,NM_005482.2;PIGK,synonymous_variant,p.=,ENST00000445065,;PIGK,synonymous_variant,p.=,ENST00000359130,;PIGK,non_coding_transcript_exon_variant,,ENST00000478391,; A ENST00000370812 Transcript synonymous_variant 51/4596 27/1188 9/395 R cgG/cgT 1 -1 PIGK HGNC HGNC:8965 protein_coding YES CCDS674.1 ENSP00000359848 Q92643 UPI000012B9D1 NM_005482.2 1/11 PIRSF_domain:PIRSF019663,PIRSF_domain:PIRSF500138,hmmpanther:PTHR12000,hmmpanther:PTHR12000:SF1,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 77219376 77219376 C A 1 0 0 0 0 0 0 0 1 11984 610 22 2 2 PIGK 1 77219376 Silent SNP C C3N-01842_T 807205 77219376 171737046 14 26206 ZZZ3 0 . GRCh38 1 77581808 77581808 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1876G>T p.Asp626Tyr p.D626Y ENST00000370801 8/15 226 168 58 226 226 0 strelka-varscan-mutect ZZZ3,missense_variant,p.Asp626Tyr,ENST00000370801,NM_015534.4;ZZZ3,missense_variant,p.Asp132Tyr,ENST00000370798,NM_001308237.1;ZZZ3,non_coding_transcript_exon_variant,,ENST00000476275,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000481346,;ZZZ3,non_coding_transcript_exon_variant,,ENST00000476195,;ZZZ3,downstream_gene_variant,,ENST00000474746,; A ENST00000370801 Transcript missense_variant 2352/4328 1876/2712 626/903 D/Y Gat/Tat 1 -1 ZZZ3 HGNC HGNC:24523 protein_coding YES CCDS677.1 ENSP00000359837 Q8IYH5 UPI0000074256 NM_015534.4 deleterious(0) 8/15 hmmpanther:PTHR22705 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 77581808 77581808 C A 1 0 0 0 0 1 0 0 0 18860 826 29 2 2 ZZZ3 1 77581808 Missense_Mutation SNP C C3N-01842_T 362432 77581808 171374614 15 26207 COL24A1 0 . GRCh38 1 85786439 85786439 + Frame_Shift_Del DEL C C - novel C3N-01842_T C3N-01842_N C C c.3974delG p.Arg1325LysfsTer13 p.R1325Kfs*13 ENST00000370571 48/60 131 102 29 215 215 0 sindel-varindel COL24A1,frameshift_variant,p.Arg1325LysfsTer13,ENST00000370571,NM_152890.5;COL24A1,3_prime_UTR_variant,,ENST00000426639,; - ENST00000370571 Transcript frameshift_variant 4341/6825 3974/5145 1325/1714 R/X aGa/aa 1 -1 COL24A1 HGNC HGNC:20821 protein_coding YES CCDS41353.1 ENSP00000359603 Q17RW2 UPI000013E81F NM_152890.5 48/60 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF590 HIGH 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 85786439 85786439 C - 1 0 1 0 1 0 0 0 0 3471 913 32 0 0 COL24A1 1 85786439 Frame_Shift_Del DEL C C3N-01842_T 8204631 85786439 163169983 16 26208 GBP1 0 . GRCh38 1 89055155 89055155 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1429C>A p.Gln477Lys p.Q477K ENST00000370473 9/11 170 124 46 143 142 1 strelka-varscan-mutect GBP1,missense_variant,p.Gln477Lys,ENST00000370473,NM_002053.2;GBP1,non_coding_transcript_exon_variant,,ENST00000484970,;GBP1,non_coding_transcript_exon_variant,,ENST00000468959,;GBP1,non_coding_transcript_exon_variant,,ENST00000479889,;GBP1,downstream_gene_variant,,ENST00000495131,;GBP1,downstream_gene_variant,,ENST00000459831,;GBP1,downstream_gene_variant,,ENST00000493139,; T ENST00000370473 Transcript missense_variant 1649/3035 1429/1779 477/592 Q/K Cag/Aag 1 -1 GBP1 HGNC HGNC:4182 protein_coding YES CCDS718.1 ENSP00000359504 P32455 UPI000013C9DF NM_002053.2 tolerated(0.1) 9/11 hmmpanther:PTHR10751,hmmpanther:PTHR10751:SF21,Pfam_domain:PF02841,Gene3D:1f5nA01,Superfamily_domains:0037397 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 89055155 89055155 G T 1 0 0 0 0 1 0 0 0 6144 1357 47 2 2 GBP1 1 89055155 Missense_Mutation SNP G C3N-01842_T 3268716 89055155 159901267 17 26209 BARHL2 0 . GRCh38 1 90717133 90717133 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.63T>A p.Ser21Arg p.S21R ENST00000370445 1/3 529 427 102 685 684 1 strelka-varscan-mutect BARHL2,missense_variant,p.Ser21Arg,ENST00000370445,NM_020063.1; T ENST00000370445 Transcript missense_variant 105/1979 63/1164 21/387 S/R agT/agA 1 -1 BARHL2 HGNC HGNC:954 protein_coding YES CCDS730.1 ENSP00000359474 Q9NY43 UPI00001B50ED NM_020063.1 tolerated_low_confidence(0.83) 1/3 hmmpanther:PTHR24330:SF4,hmmpanther:PTHR24330 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 90717133 90717133 A T 1 0 0 0 0 1 0 0 0 1466 40 2 4 4 BARHL2 1 90717133 Missense_Mutation SNP A C3N-01842_T 1661978 90717133 158239289 18 26210 ZNF644 0 . GRCh38 1 90940954 90940954 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.400G>A p.Gly134Ser p.G134S ENST00000337393 3/6 330 256 74 286 286 0 strelka-varscan-mutect ZNF644,missense_variant,p.Gly134Ser,ENST00000337393,NM_201269.2;ZNF644,missense_variant,p.Gly134Ser,ENST00000370440,;ZNF644,intron_variant,,ENST00000347275,NM_016620.3;ZNF644,intron_variant,,ENST00000361321,NM_032186.4;ZNF644,upstream_gene_variant,,ENST00000621077,;ZNF644,non_coding_transcript_exon_variant,,ENST00000498303,;ZNF644,intron_variant,,ENST00000467231,; T ENST00000337393 Transcript missense_variant 683/5763 400/3984 134/1327 G/S Ggc/Agc 1 -1 ZNF644 HGNC HGNC:29222 protein_coding YES CCDS731.1 ENSP00000337008 Q9H582 UPI000004A010 NM_201269.2 deleterious(0.05) 3/6 hmmpanther:PTHR24402:SF180,hmmpanther:PTHR24402 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 90940954 90940954 C T 1 0 0 0 0 1 0 0 0 18633 681 24 3 3 ZNF644 1 90940954 Missense_Mutation SNP C C3N-01842_T 223821 90940954 158015468 19 26211 SETSIP 0 . GRCh38 1 92074664 92074664 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.778G>T p.Asp260Tyr p.D260Y ENST00000596516 1/1 98 70 28 87 87 0 strelka-varscan-mutect SETSIP,missense_variant,p.Asp260Tyr,ENST00000596516,NM_001287737.1;SETSIP,missense_variant,p.Asp250Tyr,ENST00000485873,; A ENST00000596516 Transcript missense_variant 778/909 778/909 260/302 D/Y Gat/Tat 1 -1 SETSIP HGNC HGNC:42937 protein_coding YES CCDS72821.1 ENSP00000480946 P0DME0 UPI000016114F NM_001287737.1 deleterious(0.02) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11875:SF74,hmmpanther:PTHR11875 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 92074664 92074664 C A 1 0 0 0 0 1 0 0 0 14419 826 29 2 2 SETSIP 1 92074664 Missense_Mutation SNP C C3N-01842_T 1133710 92074664 156881758 20 26212 SNX7 0 . GRCh38 1 98684929 98684929 + Silent SNP A A T novel C3N-01842_T C3N-01842_N A A c.225A>T p.= p.P75P ENST00000306121 2/9 99 78 21 75 75 0 strelka-varscan-mutect SNX7,synonymous_variant,p.=,ENST00000306121,NM_015976.4;SNX7,synonymous_variant,p.=,ENST00000529992,NM_152238.3;SNX7,synonymous_variant,p.=,ENST00000454199,;SNX7,3_prime_UTR_variant,,ENST00000528824,; T ENST00000306121 Transcript synonymous_variant 234/1734 225/1356 75/451 P ccA/ccT 1 1 SNX7 HGNC HGNC:14971 protein_coding YES CCDS755.2 ENSP00000304429 Q9UNH6 UPI0000205396 NM_015976.4 2/9 hmmpanther:PTHR10555:SF21,hmmpanther:PTHR10555 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 98684929 98684929 A T 1 0 0 0 0 0 0 0 1 15228 117 5 4 4 SNX7 1 98684929 Silent SNP A C3N-01842_T 6610265 98684929 150271493 21 26213 RBM15 0 . GRCh38 1 110342023 110342023 + Missense_Mutation SNP C C G C3N-01842_T C3N-01842_N C C c.2618C>G p.Ser873Cys p.S873C ENST00000369784 1/3 275 199 76 338 338 0 strelka-varscan-mutect RBM15,missense_variant,p.Ser873Cys,ENST00000369784,;RBM15,missense_variant,p.Ser873Cys,ENST00000618772,NM_022768.4;RBM15,missense_variant,p.Ser873Cys,ENST00000602849,;RBM15,missense_variant,p.Ser873Cys,ENST00000487146,NM_001201545.1;RBM15,missense_variant,p.Ser829Cys,ENST00000617047,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,; G ENST00000369784 Transcript missense_variant 3518/4244 2618/2934 873/977 S/C tCt/tGt COSM3801227 1 1 RBM15 HGNC HGNC:14959 protein_coding YES CCDS822.1 ENSP00000358799 Q96T37 UPI000013E1C5 deleterious(0.03) 1/3 Low_complexity_(Seg):seg,PROSITE_profiles:PS50917,hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189,Gene3D:2.40.290.10,Pfam_domain:PF07744,Superfamily_domains:SSF100939 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 110342023 110342023 C G 1 0 0 0 0 1 0 0 0 13282 913 32 4 4 RBM15 1 110342023 Missense_Mutation SNP C C3N-01842_T 11657094 110342023 138614399 22 26214 KCNA2 0 . GRCh38 1 110603563 110603563 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.1220C>T p.Pro407Leu p.P407L ENST00000633222 3/3 483 390 93 548 548 0 strelka-varscan-mutect KCNA2,missense_variant,p.Pro407Leu,ENST00000633222,;KCNA2,missense_variant,p.Pro407Leu,ENST00000485317,;KCNA2,missense_variant,p.Pro407Leu,ENST00000316361,NM_004974.3;KCNA2,intron_variant,,ENST00000369770,NM_001204269.1;KCNA2,downstream_gene_variant,,ENST00000525120,; A ENST00000633222 Transcript missense_variant 1894/11877 1220/1500 407/499 P/L cCt/cTt 1 -1 KCNA2 HGNC HGNC:6220 protein_coding YES CCDS827.1 ENSP00000487785 P16389 UPI00001279A1 deleterious(0) 3/3 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,Prints_domain:PR01491,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF23,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 110603563 110603563 G A 1 0 0 0 0 1 0 0 0 7919 1000 35 3 3 KCNA2 1 110603563 Missense_Mutation SNP G C3N-01842_T 261540 110603563 138352859 23 26215 PTPN22 0 . GRCh38 1 113848602 113848602 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.853G>T p.Ala285Ser p.A285S ENST00000359785 11/21 223 184 39 198 198 0 strelka-varscan-mutect PTPN22,missense_variant,p.Ala285Ser,ENST00000359785,NM_001193431.1,NM_015967.5;PTPN22,missense_variant,p.Ala261Ser,ENST00000538253,NM_001308297.1;PTPN22,missense_variant,p.Ala285Ser,ENST00000420377,;PTPN22,missense_variant,p.Ala158Ser,ENST00000525799,;PTPN22,intron_variant,,ENST00000528414,NM_012411.4;PTPN22,intron_variant,,ENST00000460620,;PTPN22,3_prime_UTR_variant,,ENST00000532224,;PTPN22,non_coding_transcript_exon_variant,,ENST00000484147,; A ENST00000359785 Transcript missense_variant 989/3654 853/2424 285/807 A/S Gct/Tct 1 -1 PTPN22 HGNC HGNC:9652 protein_coding YES CCDS863.1 ENSP00000352833 A0A0B4J1S7 UPI000013CF18 NM_001193431.1,NM_015967.5 deleterious(0) 11/21 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF301,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000930,Gene3D:3.90.190.10,Pfam_domain:PF00102,SMART_domains:SM00404,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 113848602 113848602 C A 1 0 0 0 0 1 0 0 0 12941 710 25 2 2 PTPN22 1 113848602 Missense_Mutation SNP C C3N-01842_T 3245039 113848602 135107820 24 26216 RNF115 0 . GRCh38 1 145823834 145823834 + Missense_Mutation SNP C C A rs782120888 C3N-01842_T C3N-01842_N C C c.40G>T p.Ala14Ser p.A14S ENST00000582693 1/9 201 167 34 191 190 1 strelka-varscan-mutect RNF115,missense_variant,p.Ala14Ser,ENST00000582693,NM_014455.3;POLR3C,upstream_gene_variant,,ENST00000334163,NM_006468.7,NM_001303456.1;POLR3C,upstream_gene_variant,,ENST00000369294,;POLR3C,upstream_gene_variant,,ENST00000471254,;POLR3C,upstream_gene_variant,,ENST00000466003,; A ENST00000582693 Transcript missense_variant 244/9117 40/915 14/304 A/S Gct/Tct rs782120888 1 -1 RNF115 HGNC HGNC:18154 protein_coding YES CCDS72863.1 ENSP00000463650 Q9Y4L5 UPI00001B061B NM_014455.3 tolerated(0.17) 1/9 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs782120888 . 0 203 4 3 0 0 0 0 -20 0.9998778 1 1 1 0 A 3 1 84 145823834 145823834 C A 1 0 0 0 0 1 0 0 0 13608 768 27 1 1 RNF115 1 145823834 Missense_Mutation SNP C C3N-01842_T 31975232 145823834 103132588 25 26217 LCE3E 0 . GRCh38 1 152566036 152566036 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.173G>T p.Arg58Met p.R58M ENST00000368789 2/2 494 317 177 544 543 1 strelka-varscan-mutect LCE3E,missense_variant,p.Arg58Met,ENST00000368789,NM_178435.3; A ENST00000368789 Transcript missense_variant 229/611 173/279 58/92 R/M aGg/aTg 1 -1 LCE3E HGNC HGNC:29463 protein_coding YES CCDS1013.1 ENSP00000357778 Q5T5B0 UPI00001927D0 NM_178435.3 deleterious_low_confidence(0.01) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF43,hmmpanther:PTHR23263,Pfam_domain:PF14672 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 152566036 152566036 C A 1 0 0 0 0 1 0 0 0 8578 681 24 2 2 LCE3E 1 152566036 Missense_Mutation SNP C C3N-01842_T 6742202 152566036 96390386 26 26218 PYGO2 0 . GRCh38 1 154959050 154959050 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.950G>T p.Gly317Val p.G317V ENST00000368457 3/3 213 181 32 167 167 0 strelka-varscan-mutect PYGO2,missense_variant,p.Gly317Val,ENST00000368457,NM_138300.3;PYGO2,missense_variant,p.Gly280Val,ENST00000368456,;SHC1,downstream_gene_variant,,ENST00000448116,NM_001130040.1;SHC1,downstream_gene_variant,,ENST00000368445,NM_183001.4;PBXIP1,upstream_gene_variant,,ENST00000368463,NM_020524.2;PBXIP1,upstream_gene_variant,,ENST00000368465,NM_001317734.1;SHC1,downstream_gene_variant,,ENST00000368453,NM_003029.4;SHC1,downstream_gene_variant,,ENST00000368450,NM_001202859.1,NM_001130041.1;SHC1,downstream_gene_variant,,ENST00000368449,;SHC1,downstream_gene_variant,,ENST00000444664,;PBXIP1,upstream_gene_variant,,ENST00000368460,;RP11-307C12.12,upstream_gene_variant,,ENST00000605085,;SHC1,downstream_gene_variant,,ENST00000490667,;PYGO2,downstream_gene_variant,,ENST00000483463,;PBXIP1,upstream_gene_variant,,ENST00000490230,; A ENST00000368457 Transcript missense_variant 1122/3146 950/1221 317/406 G/V gGc/gTc 1 -1 PYGO2 HGNC HGNC:30257 protein_coding YES CCDS1075.1 ENSP00000357442 Q9BRQ0 Q5T170 UPI00000015CD NM_138300.3 tolerated(0.3) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23194,hmmpanther:PTHR23194:SF7 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 154959050 154959050 C A 1 0 0 0 0 1 0 0 0 13018 739 26 2 2 PYGO2 1 154959050 Missense_Mutation SNP C C3N-01842_T 2393014 154959050 93997372 27 26219 TNR 0 . GRCh38 1 175403191 175403191 + Nonsense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.925G>T p.Glu309Ter p.E309* ENST00000367674 4/23 239 193 46 226 226 0 strelka-varscan-mutect TNR,stop_gained,p.Glu309Ter,ENST00000367674,;TNR,stop_gained,p.Glu309Ter,ENST00000263525,NM_003285.2;TNR,intron_variant,,ENST00000422274,; A ENST00000367674 Transcript stop_gained 1634/12949 925/4077 309/1358 E/* Gag/Tag COSM676979 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 4/23 Gene3D:2.10.25.10,Pfam_domain:PF07974,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF254,SMART_domains:SM00181 1 HIGH 1 SNV 5 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 175403191 175403191 C A 1 0 0 0 0 0 1 0 0 16811 864 30 2 2 TNR 1 175403191 Nonsense_Mutation SNP C C3N-01842_T 20444141 175403191 73553231 28 26220 BRINP3 0 . GRCh38 1 190226286 190226286 + Nonsense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.757G>T p.Glu253Ter p.E253* ENST00000367462 6/8 277 190 87 190 188 2 strelka-varscan BRINP3,stop_gained,p.Glu253Ter,ENST00000367462,NM_199051.1;BRINP3,upstream_gene_variant,,ENST00000463404,; A ENST00000367462 Transcript stop_gained 1242/3142 757/2301 253/766 E/* Gaa/Taa 1 -1 BRINP3 HGNC HGNC:22393 protein_coding YES CCDS1373.1 ENSP00000356432 Q76B58 UPI00001C1D9A NM_199051.1 6/8 hmmpanther:PTHR15564,hmmpanther:PTHR15564:SF2,SMART_domains:SM00457 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 190226286 190226286 C A 1 0 0 0 0 0 1 0 0 1687 864 30 2 2 BRINP3 1 190226286 Nonsense_Mutation SNP C C3N-01842_T 14823095 190226286 58730136 29 26221 ASPM 0 . GRCh38 1 197117979 197117979 + Missense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.3875G>T p.Arg1292Ile p.R1292I ENST00000367409 17/28 523 357 166 331 331 0 strelka-varscan ASPM,missense_variant,p.Arg1292Ile,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Arg1292Ile,ENST00000294732,NM_001206846.1;ASPM,missense_variant,p.Arg542Ile,ENST00000367408,;ASPM,intron_variant,,ENST00000612785,; A ENST00000367409 Transcript missense_variant 4132/10887 3875/10434 1292/3477 R/I aGa/aTa COSM238862 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 deleterious(0) 17/28 Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 197117979 197117979 C A 1 0 0 0 0 1 0 0 0 1203 927 32 2 2 ASPM 1 197117979 Missense_Mutation SNP C C3N-01842_T 6891693 197117979 51838443 30 26222 CRB1 0 . GRCh38 1 197477715 197477715 + Missense_Mutation SNP G G T rs200670424 C3N-01842_T C3N-01842_N G G c.4057G>T p.Val1353Phe p.V1353F ENST00000367400 12/12 865 724 141 708 708 0 strelka-varscan CRB1,missense_variant,p.Val1329Phe,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Val1353Phe,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Val1241Phe,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Val817Phe,ENST00000538660,NM_001257966.1;CRB1,3_prime_UTR_variant,,ENST00000448952,;CRB1,3_prime_UTR_variant,,ENST00000484075,; T ENST00000367400 Transcript missense_variant 4192/4932 4057/4221 1353/1406 V/F Gtc/Ttc rs200670424 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0.03) 12/12 hmmpanther:PTHR24049,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 197477715 197477715 G T 1 0 0 0 0 1 0 0 0 3648 1377 48 2 2 CRB1 1 197477715 Missense_Mutation SNP G C3N-01842_T 359736 197477715 51478707 31 26223 DENND1B 0 . GRCh38 1 197672156 197672156 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.177G>C p.Arg59Ser p.R59S ENST00000620048 5/23 208 188 20 161 161 0 strelka-varscan DENND1B,missense_variant,p.Arg59Ser,ENST00000620048,NM_001195215.1;DENND1B,missense_variant,p.Arg49Ser,ENST00000235453,NM_001300858.1;DENND1B,missense_variant,p.Arg59Ser,ENST00000367396,NM_144977.4;DENND1B,missense_variant,p.Arg23Ser,ENST00000422998,;DENND1B,splice_region_variant,,ENST00000294738,;DENND1B,missense_variant,p.Arg59Ser,ENST00000294737,; G ENST00000620048 Transcript missense_variant,splice_region_variant 515/8375 177/2328 59/775 R/S agG/agC 1 -1 DENND1B HGNC HGNC:28404 protein_coding YES CCDS72997.1 ENSP00000479816 Q6P3S1 UPI000178DE4E NM_001195215.1 tolerated(0.65) 5/23 Pfam_domain:PF03456,PROSITE_profiles:PS50946,hmmpanther:PTHR13196,hmmpanther:PTHR13196:SF24,SMART_domains:SM00800 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 197672156 197672156 C G 1 0 0 0 0 1 0 0 0 4231 637 22 4 4 DENND1B 1 197672156 Missense_Mutation SNP C C3N-01842_T 194441 197672156 51284266 32 26224 PLXNA2 0 . GRCh38 1 208034574 208034574 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.4783G>C p.Val1595Leu p.V1595L ENST00000367033 27/32 273 235 38 293 293 0 strelka-varscan PLXNA2,missense_variant,p.Val1595Leu,ENST00000367033,NM_025179.3;PLXNA2,upstream_gene_variant,,ENST00000483048,;PLXNA2,downstream_gene_variant,,ENST00000463510,;PLXNA2,upstream_gene_variant,,ENST00000480053,; G ENST00000367033 Transcript missense_variant 5541/11444 4783/5685 1595/1894 V/L Gtg/Ctg 1 -1 PLXNA2 HGNC HGNC:9100 protein_coding YES CCDS31013.1 ENSP00000356000 O75051 UPI000022B239 NM_025179.3 tolerated(0.5) 27/32 hmmpanther:PTHR22625:SF37,hmmpanther:PTHR22625,Gene3D:3.10.20.90,Pfam_domain:PF08337 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 208034574 208034574 C G 1 0 0 0 0 1 0 0 0 12226 507 18 4 4 PLXNA2 1 208034574 Missense_Mutation SNP C C3N-01842_T 10362418 208034574 40921848 33 26225 MIXL1 0 . GRCh38 1 226223765 226223765 + Silent SNP G G C C3N-01842_T C3N-01842_N G G c.84G>C p.= p.A28A ENST00000542034 1/2 76 58 18 71 71 0 strelka-varscan MIXL1,synonymous_variant,p.=,ENST00000366810,NM_031944.2;MIXL1,synonymous_variant,p.=,ENST00000542034,NM_001282402.1;MIXL1,upstream_gene_variant,,ENST00000557734,; C ENST00000542034 Transcript synonymous_variant 148/839 84/723 28/240 A gcG/gcC COSM5663958 1 1 MIXL1 HGNC HGNC:13363 protein_coding YES CCDS60432.1 ENSP00000442439 Q9H2W2 UPI000189A780 NM_001282402.1 1/2 Low_complexity_(Seg):seg 1 LOW 1 SNV 1 1 1 PASS . . 0 196 12 2 0 0 0 0 -20 0.9993207 1 1 1 0 C 2 2 84 226223765 226223765 G C 1 0 0 0 0 0 0 0 1 9565 1074 38 4 4 MIXL1 1 226223765 Silent SNP G C3N-01842_T 18189191 226223765 22732657 34 26226 HEATR1 0 . GRCh38 1 236571664 236571664 + Nonsense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.3730G>T p.Glu1244Ter p.E1244* ENST00000366582 27/45 313 260 53 199 199 0 strelka-varscan HEATR1,stop_gained,p.Glu1244Ter,ENST00000366582,NM_018072.5;HEATR1,stop_gained,p.Glu1163Ter,ENST00000366581,;HEATR1,downstream_gene_variant,,ENST00000490339,; A ENST00000366582 Transcript stop_gained 3845/8447 3730/6435 1244/2144 E/* Gag/Tag 1 -1 HEATR1 HGNC HGNC:25517 protein_coding YES CCDS31066.1 ENSP00000355541 Q9H583 UPI000013D4D4 NM_018072.5 27/45 Gene3D:1.25.10.10,hmmpanther:PTHR13457,hmmpanther:PTHR13457:SF1,Superfamily_domains:SSF48371,Superfamily_domains:SSF48371 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 236571664 236571664 C A 1 0 0 0 0 0 1 0 0 6910 922 32 2 2 HEATR1 1 236571664 Nonsense_Mutation SNP C C3N-01842_T 10347899 236571664 12384758 35 26227 ACTN2 0 . GRCh38 1 236755073 236755073 + Missense_Mutation SNP C C G C3N-01842_T C3N-01842_N C C c.2029C>G p.Gln677Glu p.Q677E ENST00000542672 17/21 685 476 209 713 713 0 strelka-varscan ACTN2,missense_variant,p.Gln469Glu,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Gln677Glu,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Gln677Glu,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; G ENST00000542672 Transcript missense_variant 2249/4906 2029/2685 677/894 Q/E Cag/Gag COSM4432835,COSM4432836 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 tolerated(0.5) 17/21 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00150,Superfamily_domains:SSF46966 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 236755073 236755073 C G 1 0 0 0 0 1 0 0 0 249 595 21 4 4 ACTN2 1 236755073 Missense_Mutation SNP C C3N-01842_T 183409 236755073 12201349 36 26228 OR2T33 0 . GRCh38 1 248272974 248272974 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.841C>A p.Pro281Thr p.P281T ENST00000318021 1/1 518 433 85 448 448 0 strelka-varscan OR2T33,missense_variant,p.Pro281Thr,ENST00000318021,NM_001004695.1; T ENST00000318021 Transcript missense_variant 841/963 841/963 281/320 P/T Cct/Act 1 -1 OR2T33 HGNC HGNC:31255 protein_coding YES CCDS31109.1 ENSP00000324687 Q8NG76 UPI000004B237 NM_001004695.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF246,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 248272974 248272974 G T 1 0 0 0 0 1 0 0 0 11101 1232 43 2 2 OR2T33 1 248272974 Missense_Mutation SNP G C3N-01842_T 11517901 248272974 683448 37 26229 OR2T27 0 . GRCh38 1 248650301 248650301 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.584A>G p.Tyr195Cys p.Y195C ENST00000344889 1/1 152 128 24 129 129 0 strelka-varscan OR2T27,missense_variant,p.Tyr195Cys,ENST00000344889,NM_001001824.1; C ENST00000344889 Transcript missense_variant 584/954 584/954 195/317 Y/C tAc/tGc 1 -1 OR2T27 HGNC HGNC:31252 protein_coding YES CCDS31124.1 ENSP00000342008 Q8NH04 UPI000004F239 NM_001001824.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF78,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 2 205 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 248650301 248650301 T C 1 0 0 0 0 1 0 0 0 11098 1638 57 5 5 OR2T27 1 248650301 Missense_Mutation SNP T C3N-01842_T 377327 248650301 306121 38 26230 SOX11 0 . GRCh38 2 5692853 5692853 + Silent SNP G G A C3N-01842_T C3N-01842_N G G c.132G>A p.= p.T44T ENST00000322002 1/1 193 179 14 234 234 0 strelka-mutect SOX11,synonymous_variant,p.=,ENST00000322002,NM_003108.3;AC108025.2,upstream_gene_variant,,ENST00000453678,;AC010729.1,upstream_gene_variant,,ENST00000455579,;LINC01248,upstream_gene_variant,,ENST00000458264,;AC108025.2,upstream_gene_variant,,ENST00000420221,; A ENST00000322002 Transcript synonymous_variant 187/8719 132/1326 44/441 T acG/acA COSM4525423 1 1 SOX11 HGNC HGNC:11191 protein_coding YES CCDS1654.1 ENSP00000322568 P35716 UPI00001362AD NM_003108.3 1/1 PIRSF_domain:PIRSF038098,hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF113,Superfamily_domains:SSF47095 1 LOW SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 5692853 5692853 G A 1 0 0 0 0 0 0 0 1 15268 1103 39 1 1 SOX11 2 5692853 Silent SNP G C3N-01842_T 5692853 236500676 39 26231 GAREM2 0 . GRCh38 2 26184471 26184471 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.623C>A p.Pro208Gln p.P208Q ENST00000401533 4/6 227 184 43 324 324 0 strelka-varscan GAREM2,missense_variant,p.Pro131Gln,ENST00000407684,NM_001191033.1;GAREM2,missense_variant,p.Pro208Gln,ENST00000401533,NM_001168241.1;GAREM2,upstream_gene_variant,,ENST00000496070,; A ENST00000401533 Transcript missense_variant 753/4161 623/2625 208/874 P/Q cCg/cAg 1 1 GAREM2 HGNC HGNC:27172 protein_coding YES CCDS54336.1 ENSP00000384593 Q75VX8 UPI0000237273 NM_001168241.1 tolerated(0.42) 4/6 Pfam_domain:PF12736 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 26184471 26184471 C A 1 0 0 0 0 1 0 0 0 6110 652 23 1 1 GAREM2 2 26184471 Missense_Mutation SNP C C3N-01842_T 20491618 26184471 216009058 40 26232 LTBP1 0 . GRCh38 2 32947468 32947468 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.144C>A p.= p.P48P ENST00000404816 1/34 102 89 13 147 147 0 strelka-varscan LTBP1,synonymous_variant,p.=,ENST00000404816,NM_206943.2;Y_RNA,upstream_gene_variant,,ENST00000384224,; A ENST00000404816 Transcript synonymous_variant 497/6333 144/5166 48/1721 P ccC/ccA 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 1/34 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 32947468 32947468 C A 1 0 0 0 0 0 0 0 1 8979 610 22 2 2 LTBP1 2 32947468 Silent SNP C C3N-01842_T 6762997 32947468 209246061 41 26233 PRKD3 0 . GRCh38 2 37279827 37279827 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.1091C>T p.Ser364Leu p.S364L ENST00000379066 8/19 233 184 49 213 212 1 strelka-varscan PRKD3,missense_variant,p.Ser364Leu,ENST00000379066,;PRKD3,missense_variant,p.Ser364Leu,ENST00000234179,NM_005813.4;PRKD3,non_coding_transcript_exon_variant,,ENST00000494667,;PRKD3,upstream_gene_variant,,ENST00000469275,;PRKD3,downstream_gene_variant,,ENST00000475912,; A ENST00000379066 Transcript missense_variant 1854/6111 1091/2673 364/890 S/L tCa/tTa 1 -1 PRKD3 HGNC HGNC:9408 protein_coding YES CCDS1789.1 ENSP00000368356 O94806 UPI0000035B4D tolerated(0.15) 8/19 PIRSF_domain:PIRSF000552,hmmpanther:PTHR22968,hmmpanther:PTHR22968:SF11 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 37279827 37279827 G A 1 0 0 0 0 1 0 0 0 12653 1294 45 3 3 PRKD3 2 37279827 Missense_Mutation SNP G C3N-01842_T 4332359 37279827 204913702 42 26234 KCNG3 0 . GRCh38 2 42444320 42444320 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.925C>T p.Leu309Phe p.L309F ENST00000306078 2/2 423 322 101 421 421 0 strelka-varscan KCNG3,missense_variant,p.Leu309Phe,ENST00000306078,NM_133329.5;KCNG3,missense_variant,p.Leu298Phe,ENST00000394973,NM_172344.2;SNORD75,downstream_gene_variant,,ENST00000408373,; A ENST00000306078 Transcript missense_variant 1521/3824 925/1311 309/436 L/F Ctt/Ttt 1 -1 KCNG3 HGNC HGNC:18306 protein_coding YES CCDS1809.1 ENSP00000304127 Q8TAE7 UPI00000557D9 NM_133329.5 deleterious(0) 2/2 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF91,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 42444320 42444320 G A 1 0 0 0 0 1 0 0 0 7945 942 33 3 3 KCNG3 2 42444320 Missense_Mutation SNP G C3N-01842_T 5164493 42444320 199749209 43 26235 PAPOLG 0 . GRCh38 2 60783163 60783163 + Missense_Mutation SNP A A T rs374307901 C3N-01842_T C3N-01842_N A A c.1120A>T p.Ile374Leu p.I374L ENST00000238714 13/22 114 92 22 111 111 0 strelka-varscan PAPOLG,missense_variant,p.Ile42Leu,ENST00000412217,;PAPOLG,missense_variant,p.Ile374Leu,ENST00000238714,NM_022894.3;PAPOLG,non_coding_transcript_exon_variant,,ENST00000483370,;PAPOLG,3_prime_UTR_variant,,ENST00000414060,;PAPOLG,3_prime_UTR_variant,,ENST00000453839,;PAPOLG,non_coding_transcript_exon_variant,,ENST00000496283,; T ENST00000238714 Transcript missense_variant 1369/4263 1120/2211 374/736 I/L Ata/Tta rs374307901 1 1 PAPOLG HGNC HGNC:14982 protein_coding YES CCDS1863.1 ENSP00000238714 Q9BWT3 UPI00000704EB NM_022894.3 deleterious(0.03) 13/22 hmmpanther:PTHR10682,hmmpanther:PTHR10682:SF6,Gene3D:3.30.70.590,Pfam_domain:PF04926,Superfamily_domains:SSF55003 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 60783163 60783163 A T 1 0 0 0 0 1 0 0 0 11511 449 16 4 4 PAPOLG 2 60783163 Missense_Mutation SNP A C3N-01842_T 18338843 60783163 181410366 44 26236 ALMS1 0 . GRCh38 2 73448289 73448289 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1762G>T p.Gly588Cys p.G588C ENST00000613296 8/23 302 232 70 352 350 2 strelka-varscan-mutect ALMS1,missense_variant,p.Gly588Cys,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Gly546Cys,ENST00000484298,;ALMS1,missense_variant,p.Gly588Cys,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; T ENST00000613296 Transcript missense_variant 1873/12925 1762/12507 588/4168 G/C Ggc/Tgc 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 tolerated(0.06) 8/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS rs1367898096 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 73448289 73448289 G T 1 0 0 0 0 1 0 0 0 635 1232 43 2 2 ALMS1 2 73448289 Missense_Mutation SNP G C3N-01842_T 12665126 73448289 168745240 45 26237 CNNM4 0 . GRCh38 2 96761302 96761302 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.303C>T p.= p.T101T ENST00000377075 1/7 289 229 60 342 342 0 strelka-varscan-mutect CNNM4,synonymous_variant,p.=,ENST00000377075,NM_020184.3; T ENST00000377075 Transcript synonymous_variant 401/4800 303/2328 101/775 T acC/acT 1 1 CNNM4 HGNC HGNC:105 protein_coding YES CCDS2024.2 ENSP00000366275 Q6P4Q7 UPI0000207C95 NM_020184.3 1/7 hmmpanther:PTHR12064,hmmpanther:PTHR12064:SF26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 96761302 96761302 C T 1 0 0 0 0 0 0 0 1 3395 610 22 3 3 CNNM4 2 96761302 Silent SNP C C3N-01842_T 23313013 96761302 145432227 46 26238 TBC1D8 0 . GRCh38 2 101050643 101050643 + Splice_Site SNP T T G novel C3N-01842_T C3N-01842_N T T c.587-2A>C p.X196_splice ENST00000376840 136 106 30 143 143 0 strelka-varscan-mutect TBC1D8,splice_acceptor_variant,,ENST00000409318,;TBC1D8,splice_acceptor_variant,,ENST00000376840,NM_001102426.1; G ENST00000376840 Transcript splice_acceptor_variant -/3627 587/3423 196/1140 1 -1 TBC1D8 HGNC HGNC:17791 protein_coding YES CCDS46375.1 ENSP00000366036 O95759 UPI00015ADD19 NM_001102426.1 4/19 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 84 101050643 101050643 T G 1 0 0 0 0 0 0 1 0 16030 1594 55 5 5 TBC1D8 2 101050643 Splice_Site SNP T C3N-01842_T 4289341 101050643 141142886 47 26239 SLC9A2 0 . GRCh38 2 102704575 102704575 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1877C>A p.Ala626Asp p.A626D ENST00000233969 10/12 334 253 81 319 319 0 strelka-varscan-mutect SLC9A2,missense_variant,p.Ala626Asp,ENST00000233969,NM_003048.4;SLC9A2,downstream_gene_variant,,ENST00000469286,; A ENST00000233969 Transcript missense_variant 2019/5410 1877/2439 626/812 A/D gCc/gAc 1 1 SLC9A2 HGNC HGNC:11072 protein_coding YES CCDS2062.1 ENSP00000233969 Q9UBY0 UPI000012FD21 NM_003048.4 tolerated(0.5) 10/12 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF89,Pfam_domain:PF16644,TIGRFAM_domain:TIGR00840,Prints_domain:PR01086 MODERATE 1 SNV 1 1 PASS rs1393376411 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 102704575 102704575 C A 1 0 0 0 0 1 0 0 0 14994 739 26 2 2 SLC9A2 2 102704575 Missense_Mutation SNP C C3N-01842_T 1653932 102704575 139488954 48 26240 POU3F3 0 . GRCh38 2 104856767 104856767 + Silent SNP C C G C3N-01842_T C3N-01842_N C C c.1257C>G p.= p.G419G ENST00000361360 1/1 328 263 65 343 343 0 strelka-varscan-mutect POU3F3,synonymous_variant,p.=,ENST00000361360,NM_006236.1;RP11-13J10.1,intron_variant,,ENST00000598623,;LINC01158,upstream_gene_variant,,ENST00000447876,; G ENST00000361360 Transcript synonymous_variant 1257/3064 1257/1503 419/500 G ggC/ggG COSM4716744 1 1 POU3F3 HGNC HGNC:9216 protein_coding YES CCDS33265.1 ENSP00000355001 P20264 UPI0000131D87 NM_006236.1 1/1 Gene3D:1.10.10.60,Pfam_domain:PF00046,PIRSF_domain:PIRSF002629,Prints_domain:PR00028,PROSITE_profiles:PS50071,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF73,SMART_domains:SM00389,Superfamily_domains:SSF46689 1 LOW SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 104856767 104856767 C G 1 0 0 0 0 0 0 0 1 12392 755 27 4 4 POU3F3 2 104856767 Silent SNP C C3N-01842_T 2152192 104856767 137336762 49 26241 GPR45 0 . GRCh38 2 105242317 105242317 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.459G>T p.= p.A153A ENST00000258456 1/1 360 283 77 382 382 0 strelka-varscan-mutect GPR45,synonymous_variant,p.=,ENST00000258456,NM_007227.3; T ENST00000258456 Transcript synonymous_variant 575/1307 459/1119 153/372 A gcG/gcT 1 1 GPR45 HGNC HGNC:4503 protein_coding YES CCDS2066.1 ENSP00000258456 Q9Y5Y3 B5B0C1 UPI000013CFD3 NM_007227.3 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF4,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs1287925511 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 105242317 105242317 G T 1 0 0 0 0 0 0 0 1 6581 1103 39 1 1 GPR45 2 105242317 Silent SNP G C3N-01842_T 385550 105242317 136951212 50 26242 NT5DC4 0 . GRCh38 2 112721850 112721857 + Frame_Shift_Del DEL AGATTCGT AGATTCGT - novel C3N-01842_T C3N-01842_N AGATTCGT AGATTCGT c.44_51delAGATTCGT p.Lys15MetfsTer19 p.K15Mfs*19 ENST00000327581 2/17 406 362 44 588 588 0 sindel-varindel-pindel NT5DC4,frameshift_variant,p.Lys15MetfsTer19,ENST00000327581,;NT5DC4,upstream_gene_variant,,ENST00000497526,;NT5DC4,non_coding_transcript_exon_variant,,ENST00000484666,;NT5DC4,upstream_gene_variant,,ENST00000462854,;NT5DC4,upstream_gene_variant,,ENST00000470675,; - ENST00000327581 Transcript frameshift_variant 95-102/1767 44-51/1287 15-17/428 KIR/X aAGATTCGT/a 1 1 NT5DC4 HGNC HGNC:27678 protein_coding YES ENSP00000330247 Q86YG4 UPI0000197313 2/17 hmmpanther:PTHR12103,hmmpanther:PTHR12103:SF18,Gene3D:3.40.50.1000,Pfam_domain:PF05761,PIRSF_domain:PIRSF017434,TIGRFAM_domain:TIGR02244,Superfamily_domains:SSF56784 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 112721850 112721850 AGATTCGT - 1 0 1 0 1 0 0 0 0 10756 72 3 0 0 NT5DC4 2 112721850 Frame_Shift_Del DEL AGATTCGT C3N-01842_T 7479533 112721850 129471679 51 26243 DPP10 0 . GRCh38 2 115753238 115753238 + Missense_Mutation SNP C C G C3N-01842_T C3N-01842_N C C c.1027C>G p.Arg343Gly p.R343G ENST00000393147 11/26 251 214 37 209 209 0 strelka-varscan-mutect DPP10,missense_variant,p.Arg339Gly,ENST00000410059,NM_001321910.1,NM_001321911.1,NM_001321914.1,NM_001321905.1,NM_001321906.1,NM_020868.3;DPP10,missense_variant,p.Arg289Gly,ENST00000409163,NM_001178036.1,NM_001178037.1;DPP10,missense_variant,p.Arg332Gly,ENST00000310323,NM_001004360.3;DPP10,missense_variant,p.Arg343Gly,ENST00000393147,NM_001178034.1; G ENST00000393147 Transcript missense_variant 1382/2758 1027/2403 343/800 R/G Cga/Gga COSM1250643,COSM1250644,COSM5471268,COSM5471269 1 1 DPP10 HGNC HGNC:20823 protein_coding YES CCDS54388.1 ENSP00000376855 Q8N608 UPI00015E0A22 NM_001178034.1 deleterious(0) 11/26 hmmpanther:PTHR11731:SF21,hmmpanther:PTHR11731,Gene3D:2.140.10.30,Pfam_domain:PF00930,Superfamily_domains:SSF82171 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 84 115753238 115753238 C G 1 0 0 0 0 1 0 0 0 4542 644 23 4 4 DPP10 2 115753238 Missense_Mutation SNP C C3N-01842_T 3031388 115753238 126440291 52 26244 CNTNAP5 0 . GRCh38 2 124242303 124242303 + Nonsense_Mutation SNP C C A rs369801109 C3N-01842_T C3N-01842_N C C c.291C>A p.Tyr97Ter p.Y97* ENST00000431078 3/24 330 255 75 403 402 1 strelka-varscan-mutect CNTNAP5,stop_gained,p.Tyr97Ter,ENST00000431078,NM_130773.3;CNTNAP5,non_coding_transcript_exon_variant,,ENST00000470921,; A ENST00000431078 Transcript stop_gained 655/5284 291/3921 97/1306 Y/* taC/taA rs369801109,COSM3041875 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 3/24 PROSITE_profiles:PS50022,Gene3D:2.60.120.260,Pfam_domain:PF00754,SMART_domains:SM00231,Superfamily_domains:SSF49785 0,1 HIGH 1 SNV 1 0,1 1 PASS rs369801109 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 124242303 124242303 C A 1 0 0 0 0 0 1 0 0 3432 547 19 1 1 CNTNAP5 2 124242303 Nonsense_Mutation SNP C C3N-01842_T 8489065 124242303 117951226 53 26245 CNTNAP5 0 . GRCh38 2 124763798 124763798 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.2358C>A p.Asp786Glu p.D786E ENST00000431078 15/24 198 159 39 185 185 0 strelka-varscan-mutect CNTNAP5,missense_variant,p.Asp786Glu,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant,splice_region_variant 2722/5284 2358/3921 786/1306 D/E gaC/gaA 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0.01) 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 124763798 124763798 C A 1 0 0 0 0 1 0 0 0 3432 521 18 2 2 CNTNAP5 2 124763798 Missense_Mutation SNP C C3N-01842_T 521495 124763798 117429731 54 26246 LIMS2 0 . GRCh38 2 127639321 127639321 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1058G>T p.Arg353Leu p.R353L ENST00000324938 10/10 216 158 58 252 252 0 strelka-varscan-mutect LIMS2,missense_variant,p.Arg324Leu,ENST00000409455,;LIMS2,missense_variant,p.Arg324Leu,ENST00000410011,NM_001161404.1;LIMS2,missense_variant,p.Arg324Leu,ENST00000409808,;LIMS2,missense_variant,p.Arg353Leu,ENST00000324938,NM_017980.4;LIMS2,missense_variant,p.Arg329Leu,ENST00000355119,NM_001161403.1;LIMS2,missense_variant,p.Arg351Leu,ENST00000545738,NM_001136037.2;LIMS2,missense_variant,p.Arg177Leu,ENST00000410038,NM_001256542.1;LIMS2,missense_variant,p.Arg177Leu,ENST00000409286,;LIMS2,missense_variant,p.Arg177Leu,ENST00000409754,;LIMS2,missense_variant,p.Arg157Leu,ENST00000426981,;LIMS2,missense_variant,p.Arg177Leu,ENST00000409254,;MYO7B,downstream_gene_variant,,ENST00000428314,NM_001080527.1;MYO7B,downstream_gene_variant,,ENST00000409816,;MYO7B,downstream_gene_variant,,ENST00000409090,;LIMS2,non_coding_transcript_exon_variant,,ENST00000494613,;LIMS2,downstream_gene_variant,,ENST00000582671,;LIMS2,3_prime_UTR_variant,,ENST00000413578,;LIMS2,non_coding_transcript_exon_variant,,ENST00000469300,;LIMS2,non_coding_transcript_exon_variant,,ENST00000466410,;LIMS2,non_coding_transcript_exon_variant,,ENST00000476932,;LIMS2,non_coding_transcript_exon_variant,,ENST00000484252,;MYO7B,downstream_gene_variant,,ENST00000496841,;MYO7B,downstream_gene_variant,,ENST00000491278,;MYO7B,downstream_gene_variant,,ENST00000494959,; A ENST00000324938 Transcript missense_variant 1216/2111 1058/1098 353/365 R/L cGc/cTc 1 -1 LIMS2 HGNC HGNC:16084 protein_coding YES CCDS2147.1 ENSP00000326888 Q7Z4I7 UPI00001B5BF3 NM_017980.4 deleterious(0) 10/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24210:SF10,hmmpanther:PTHR24210,PIRSF_domain:PIRSF038003 MODERATE 1 SNV 1 1 PASS rs1178000923 . 0 203 0 5 2 0 0 0 -20 0.9742215 1 1 1 0 A 3 1 84 127639321 127639321 C A 1 0 0 0 0 1 0 0 0 8712 768 27 1 1 LIMS2 2 127639321 Missense_Mutation SNP C C3N-01842_T 2875523 127639321 114554208 55 26247 GPR148 0 . GRCh38 2 130730088 130730088 + Missense_Mutation SNP C C A rs147627830 C3N-01842_T C3N-01842_N C C c.937C>A p.Arg313Ser p.R313S ENST00000309926 1/1 127 93 34 94 94 0 strelka-varscan-mutect GPR148,missense_variant,p.Arg313Ser,ENST00000309926,NM_207364.2; A ENST00000309926 Transcript missense_variant 1019/1267 937/1044 313/347 R/S Cgt/Agt rs147627830,COSM715808 1 1 GPR148 HGNC HGNC:23623 protein_coding YES CCDS2163.1 ENSP00000308908 Q8TDV2 UPI0000048E0D NM_207364.2 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs147627830 . 0 200 10 0 0 0 0 0 -20 0.9999946 1 1 1 0 A 3 1 84 130730088 130730088 C A 1 0 0 0 0 1 0 0 0 6539 652 23 1 1 GPR148 2 130730088 Missense_Mutation SNP C C3N-01842_T 3090767 130730088 111463441 56 26248 LRP1B 0 . GRCh38 2 141049110 141049110 + Silent SNP C C A rs763729515 C3N-01842_T C3N-01842_N C C c.1665G>T p.= p.L555L ENST00000389484 11/91 423 330 93 411 411 0 strelka-varscan-mutect LRP1B,synonymous_variant,p.=,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript synonymous_variant 2637/16535 1665/13800 555/4599 L ctG/ctT rs763729515 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 11/91 Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS rs763729515 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 141049110 141049110 C A 1 0 0 0 0 0 0 0 1 8850 581 21 2 2 LRP1B 2 141049110 Silent SNP C C3N-01842_T 10319022 141049110 101144419 57 26249 KCNH7 0 . GRCh38 2 162400257 162400257 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.2339C>A p.Thr780Asn p.T780N ENST00000332142 10/16 379 308 71 412 412 0 strelka-varscan-mutect KCNH7,missense_variant,p.Thr780Asn,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Thr680Asn,ENST00000618399,; T ENST00000332142 Transcript missense_variant 2439/4113 2339/3591 780/1196 T/N aCt/aAt 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 tolerated(0.06) 10/16 PROSITE_profiles:PS50042,hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Pfam_domain:PF00027,Gene3D:2.60.120.10,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 162400257 162400257 G T 1 0 0 0 0 1 0 0 0 7953 1029 36 2 2 KCNH7 2 162400257 Missense_Mutation SNP G C3N-01842_T 21351147 162400257 79793272 58 26250 HOXD13 0 . GRCh38 2 176092940 176092940 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.50G>T p.Gly17Val p.G17V ENST00000392539 1/2 64 49 15 66 66 0 strelka-varscan-mutect HOXD13,missense_variant,p.Gly17Val,ENST00000392539,NM_000523.3; T ENST00000392539 Transcript missense_variant 50/2240 50/1032 17/343 G/V gGg/gTg 1 1 HOXD13 HGNC HGNC:5136 protein_coding YES CCDS2264.2 ENSP00000376322 P35453 UPI000020912A NM_000523.3 tolerated_low_confidence(0.28) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF182,hmmpanther:PTHR24326 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 176092940 176092940 G T 1 0 0 0 0 1 0 0 0 7216 1232 43 2 2 HOXD13 2 176092940 Missense_Mutation SNP G C3N-01842_T 13692683 176092940 66100589 59 26251 TTN 0 . GRCh38 2 178601751 178601751 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.55339C>A p.Pro18447Thr p.P18447T ENST00000589042 286/363 142 113 29 111 111 0 strelka-varscan-mutect TTN,missense_variant,p.Pro18447Thr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro16806Thr,ENST00000591111,;TTN,missense_variant,p.Pro16806Thr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro15879Thr,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Pro9382Thr,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Pro9574Thr,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Pro9507Thr,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000592689,;TTN-AS1,downstream_gene_variant,,ENST00000629117,;TTN-AS1,downstream_gene_variant,,ENST00000590932,;TTN-AS1,downstream_gene_variant,,ENST00000591332,;TTN-AS1,downstream_gene_variant,,ENST00000626517,; T ENST00000589042 Transcript missense_variant 55564/109224 55339/107976 18447/35991 P/T Ccg/Acg 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 286/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 178601751 178601751 G T 1 0 0 0 0 1 0 0 0 17245 1174 41 2 2 TTN 2 178601751 Missense_Mutation SNP G C3N-01842_T 2508811 178601751 63591778 60 26252 TTN 0 . GRCh38 2 178610097 178610097 + Silent SNP A A G novel C3N-01842_T C3N-01842_N A A c.51429T>C p.= p.D17143D ENST00000589042 271/363 546 416 130 431 431 0 strelka-varscan-mutect TTN,synonymous_variant,p.=,ENST00000589042,NM_001267550.2;TTN,synonymous_variant,p.=,ENST00000591111,;TTN,synonymous_variant,p.=,ENST00000615779,NM_001256850.1;TTN,synonymous_variant,p.=,ENST00000342992,NM_133378.4;TTN,synonymous_variant,p.=,ENST00000460472,NM_003319.4;TTN,synonymous_variant,p.=,ENST00000342175,NM_133437.4;TTN,synonymous_variant,p.=,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000627527,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000419746,; G ENST00000589042 Transcript synonymous_variant 51654/109224 51429/107976 17143/35991 D gaT/gaC 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 271/363 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 178610097 178610097 A G 1 0 0 0 0 0 0 0 1 17245 330 12 5 5 TTN 2 178610097 Silent SNP A C3N-01842_T 8346 178610097 63583432 61 26253 ZNF804A 0 . GRCh38 2 184937087 184937087 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.1691C>T p.Thr564Ile p.T564I ENST00000302277 4/4 170 141 29 102 102 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Thr564Ile,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Thr479Ile,ENST00000613975,; T ENST00000302277 Transcript missense_variant 2285/4690 1691/3630 564/1209 T/I aCt/aTt 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.14) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 84 184937087 184937087 C T 1 0 0 0 0 1 0 0 0 18755 565 20 3 3 ZNF804A 2 184937087 Missense_Mutation SNP C C3N-01842_T 6326990 184937087 57256442 62 26254 FSIP2 0 . GRCh38 2 185802023 185802023 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.12984C>A p.Ser4328Arg p.S4328R ENST00000343098 17/23 164 125 39 92 92 0 strelka-varscan-mutect FSIP2,missense_variant,p.Ser4328Arg,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Ser4239Arg,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 12984/21054 12984/20991 4328/6996 S/R agC/agA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0.02) 17/23 Pfam_domain:PF15783,hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 185802023 185802023 C A 1 0 0 0 0 1 0 0 0 5949 738 26 2 2 FSIP2 2 185802023 Missense_Mutation SNP C C3N-01842_T 864936 185802023 56391506 63 26255 FAM126B 0 . GRCh38 2 201022927 201022927 + Silent SNP T T C rs372235427 C3N-01842_T C3N-01842_N T T c.57A>G p.= p.L19L ENST00000418596 4/12 231 182 49 232 232 0 strelka-varscan-mutect FAM126B,synonymous_variant,p.=,ENST00000418596,NM_001321619.1,NM_001321629.1,NM_001321618.1,NM_001321622.1,NM_001321621.1,NM_173822.3;FAM126B,synonymous_variant,p.=,ENST00000452799,;FAM126B,synonymous_variant,p.=,ENST00000453765,;FAM126B,synonymous_variant,p.=,ENST00000446678,;FAM126B,upstream_gene_variant,,ENST00000485144,;FAM126B,synonymous_variant,p.=,ENST00000286181,;FAM126B,non_coding_transcript_exon_variant,,ENST00000498780,;FAM126B,non_coding_transcript_exon_variant,,ENST00000474118,;FAM126B,non_coding_transcript_exon_variant,,ENST00000485636,;FAM126B,downstream_gene_variant,,ENST00000494881,; C ENST00000418596 Transcript synonymous_variant 245/9333 57/1593 19/530 L ttA/ttG rs372235427,COSM237361 1 -1 FAM126B HGNC HGNC:28593 protein_coding YES CCDS2335.1 ENSP00000393667 Q8IXS8 UPI0000074347 NM_001321619.1,NM_001321629.1,NM_001321618.1,NM_001321622.1,NM_001321621.1,NM_173822.3 4/12 hmmpanther:PTHR31220,hmmpanther:PTHR31220:SF3 0,1 LOW 1 SNV 1 0,1 1 PASS rs372235427 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 201022927 201022927 T C 1 0 0 0 0 0 0 0 1 5282 1652 57 5 5 FAM126B 2 201022927 Silent SNP T C3N-01842_T 15220904 201022927 41170602 64 26256 NBEAL1 0 . GRCh38 2 203209190 203209190 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.7566G>T p.Gln2522His p.Q2522H ENST00000449802 52/55 131 98 33 155 155 0 strelka-varscan-mutect NBEAL1,missense_variant,p.Gln2522His,ENST00000449802,NM_001114132.1;NBEAL1,missense_variant,p.Gln537His,ENST00000414576,;NBEAL1,missense_variant,p.Gln50His,ENST00000434469,; T ENST00000449802 Transcript missense_variant 7899/10938 7566/8085 2522/2694 Q/H caG/caT 1 1 NBEAL1 HGNC HGNC:20681 protein_coding YES CCDS46495.1 ENSP00000399903 Q6ZS30 UPI000194EC27 NM_001114132.1 deleterious(0) 52/55 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR13743:SF59,hmmpanther:PTHR13743,Gene3D:2.130.10.10,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS rs1014402003 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 203209190 203209190 G T 1 0 0 0 0 1 0 0 0 10199 933 33 2 2 NBEAL1 2 203209190 Missense_Mutation SNP G C3N-01842_T 2186263 203209190 38984339 65 26257 ZDBF2 0 . GRCh38 2 206307640 206307640 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.3112G>T p.Gly1038Cys p.G1038C ENST00000374423 5/5 232 179 53 169 169 0 strelka-varscan-mutect ZDBF2,missense_variant,p.Gly1038Cys,ENST00000374423,NM_020923.2;ZDBF2,missense_variant,p.Gly1036Cys,ENST00000611847,NM_001285549.1; T ENST00000374423 Transcript missense_variant 3498/10286 3112/7065 1038/2354 G/C Ggt/Tgt 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 tolerated(0.07) 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 206307640 206307640 G T 1 0 0 0 0 1 0 0 0 18174 1348 47 2 2 ZDBF2 2 206307640 Missense_Mutation SNP G C3N-01842_T 3098450 206307640 35885889 66 26258 SMARCAL1 0 . GRCh38 2 216438462 216438462 + Nonsense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.1687C>T p.Arg563Ter p.R563* ENST00000357276 10/18 631 485 146 751 750 1 strelka-varscan-mutect SMARCAL1,stop_gained,p.Arg563Ter,ENST00000357276,NM_014140.3;SMARCAL1,stop_gained,p.Arg563Ter,ENST00000358207,NM_001127207.1;SMARCAL1,stop_gained,p.Arg121Ter,ENST00000445153,;SMARCAL1,intron_variant,,ENST00000392128,; T ENST00000357276 Transcript stop_gained 2017/3271 1687/2865 563/954 R/* Cga/Tga 1 1 SMARCAL1 HGNC HGNC:11102 protein_coding YES CCDS2403.1 ENSP00000349823 Q9NZC9 UPI000000DA30 NM_014140.3 10/18 PROSITE_profiles:PS51192,hmmpanther:PTHR10799:SF731,hmmpanther:PTHR10799,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540,Superfamily_domains:SSF52540 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 216438462 216438462 C T 1 0 0 0 0 0 1 0 0 15066 876 31 1 1 SMARCAL1 2 216438462 Nonsense_Mutation SNP C C3N-01842_T 10130822 216438462 25755067 67 26259 IGFBP2 0 . GRCh38 2 216660583 216660583 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.469G>T p.Gly157Cys p.G157C ENST00000233809 2/4 142 104 38 121 121 0 strelka-varscan-mutect IGFBP2,missense_variant,p.Gly157Cys,ENST00000233809,NM_000597.2;IGFBP2,missense_variant,p.Gly13Cys,ENST00000456764,;IGFBP2,5_prime_UTR_variant,,ENST00000434997,;IGFBP2,upstream_gene_variant,,ENST00000436812,;IGFBP2,non_coding_transcript_exon_variant,,ENST00000490362,; T ENST00000233809 Transcript missense_variant 598/1439 469/978 157/325 G/C Ggc/Tgc 1 1 IGFBP2 HGNC HGNC:5471 protein_coding YES CCDS42815.1 ENSP00000233809 P18065 UPI000013C98D NM_000597.2 tolerated(0.07) 2/4 hmmpanther:PTHR11551:SF5,hmmpanther:PTHR11551 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 216660583 216660583 G T 1 0 0 0 0 1 0 0 0 7485 1000 35 2 2 IGFBP2 2 216660583 Missense_Mutation SNP G C3N-01842_T 222121 216660583 25532946 68 26260 CFAP65 0 . GRCh38 2 219019549 219019549 + Missense_Mutation SNP G G T rs750313270 C3N-01842_T C3N-01842_N G G c.3430C>A p.Pro1144Thr p.P1144T ENST00000341552 20/35 223 175 48 254 254 0 strelka-varscan-mutect CFAP65,missense_variant,p.Pro1144Thr,ENST00000341552,NM_194302.3;CFAP65,missense_variant,p.Pro1144Thr,ENST00000453220,;CFAP65,missense_variant,p.Pro53Thr,ENST00000413871,;AC097468.4,downstream_gene_variant,,ENST00000441450,; T ENST00000341552 Transcript missense_variant 3514/5953 3430/5778 1144/1925 P/T Ccc/Acc rs750313270 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 deleterious(0) 20/35 hmmpanther:PTHR10270,hmmpanther:PTHR10270:SF223 MODERATE SNV 5 1 PASS rs750313270 . 0 206 0 4 0 0 0 0 -20 0.9999596 1 1 1 0 T 3 4 84 219019549 219019549 G T 1 0 0 0 0 1 0 0 0 3029 1232 43 2 2 CFAP65 2 219019549 Missense_Mutation SNP G C3N-01842_T 2358966 219019549 23173980 69 26261 PTPRN 0 . GRCh38 2 219302769 219302769 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.446C>A p.Ser149Tyr p.S149Y ENST00000295718 5/23 253 192 61 322 321 1 strelka-varscan-mutect PTPRN,missense_variant,p.Ser149Tyr,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Ser149Tyr,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Ser59Tyr,ENST00000423636,NM_001199764.1;PTPRN,missense_variant,p.Ser59Tyr,ENST00000446182,;PTPRN,missense_variant,p.Ser116Tyr,ENST00000440552,;PTPRN,missense_variant,p.Ser59Tyr,ENST00000412847,;PTPRN,missense_variant,p.Ser59Tyr,ENST00000442029,;PTPRN,missense_variant,p.Ser59Tyr,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,downstream_gene_variant,,ENST00000468454,;PTPRN,3_prime_UTR_variant,,ENST00000606213,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,non_coding_transcript_exon_variant,,ENST00000476930,;PTPRN,downstream_gene_variant,,ENST00000477819,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,;PTPRN,downstream_gene_variant,,ENST00000484986,; T ENST00000295718 Transcript missense_variant 687/3784 446/2940 149/979 S/Y tCc/tAc 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 tolerated(0.85) 5/23 Pfam_domain:PF14948,SMART_domains:SM01305 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 219302769 219302769 G T 1 0 0 0 0 1 0 0 0 12961 1174 41 2 2 PTPRN 2 219302769 Missense_Mutation SNP G C3N-01842_T 283220 219302769 22890760 70 26262 SLC4A3 0 . GRCh38 2 219629278 219629278 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.352C>A p.Pro118Thr p.P118T ENST00000273063 4/23 135 108 27 122 122 0 strelka-varscan-mutect SLC4A3,missense_variant,p.Pro118Thr,ENST00000358055,NM_005070.3;SLC4A3,missense_variant,p.Pro118Thr,ENST00000273063,NM_001326559.1,NM_201574.2;SLC4A3,missense_variant,p.Pro118Thr,ENST00000373760,;SLC4A3,missense_variant,p.Pro118Thr,ENST00000317151,;SLC4A3,upstream_gene_variant,,ENST00000413743,;AC009955.8,upstream_gene_variant,,ENST00000455896,;SLC4A3,non_coding_transcript_exon_variant,,ENST00000497589,;SLC4A3,missense_variant,p.Pro118Thr,ENST00000425141,;SLC4A3,upstream_gene_variant,,ENST00000416910,;SLC4A3,upstream_gene_variant,,ENST00000444906,; A ENST00000273063 Transcript missense_variant 566/4246 352/3780 118/1259 P/T Cct/Act 1 1 SLC4A3 HGNC HGNC:11029 protein_coding YES CCDS2446.1 ENSP00000273063 P48751 UPI000022BE50 NM_001326559.1,NM_201574.2 tolerated_low_confidence(0.07) 4/23 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 219629278 219629278 C A 1 0 0 0 0 1 0 0 0 14932 855 30 2 2 SLC4A3 2 219629278 Missense_Mutation SNP C C3N-01842_T 326509 219629278 22564251 71 26263 SLC19A3 0 . GRCh38 2 227702222 227702222 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.97C>A p.Pro33Thr p.P33T ENST00000258403 2/6 456 367 89 422 420 2 strelka-varscan-mutect SLC19A3,missense_variant,p.Pro33Thr,ENST00000258403,NM_025243.3;SLC19A3,missense_variant,p.Pro33Thr,ENST00000419059,;SLC19A3,missense_variant,p.Pro33Thr,ENST00000409287,;SLC19A3,missense_variant,p.Pro33Thr,ENST00000409456,;SLC19A3,missense_variant,p.Pro33Thr,ENST00000456524,;SLC19A3,missense_variant,p.Pro33Thr,ENST00000425817,;SLC19A3,missense_variant,p.Pro33Thr,ENST00000431622,;SLC19A3,non_coding_transcript_exon_variant,,ENST00000477697,; T ENST00000258403 Transcript missense_variant 169/3105 97/1491 33/496 P/T Cca/Aca 1 -1 SLC19A3 HGNC HGNC:16266 protein_coding YES CCDS2468.1 ENSP00000258403 Q9BZV2 UPI000004DAE9 NM_025243.3 deleterious(0) 2/6 hmmpanther:PTHR10686:SF17,hmmpanther:PTHR10686,PIRSF_domain:PIRSF028739,PIRSF_domain:PIRSF500795,Gene3D:1.20.1250.20,Pfam_domain:PF01770,TIGRFAM_domain:TIGR00806,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 227702222 227702222 G T 1 0 0 0 0 1 0 0 0 14696 1261 44 2 2 SLC19A3 2 227702222 Missense_Mutation SNP G C3N-01842_T 8072944 227702222 14491307 72 26264 NGEF 0 . GRCh38 2 232892965 232892965 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.1075C>T p.His359Tyr p.H359Y ENST00000264051 7/15 183 139 44 246 246 0 strelka-varscan-mutect NGEF,missense_variant,p.His359Tyr,ENST00000264051,NM_019850.2;NGEF,missense_variant,p.His267Tyr,ENST00000373552,NM_001114090.1;NGEF,missense_variant,p.His82Tyr,ENST00000416114,;NGEF,downstream_gene_variant,,ENST00000409079,;NGEF,upstream_gene_variant,,ENST00000424488,;NGEF,non_coding_transcript_exon_variant,,ENST00000420650,;NGEF,upstream_gene_variant,,ENST00000461944,; A ENST00000264051 Transcript missense_variant 1354/3215 1075/2133 359/710 H/Y Cac/Tac 1 -1 NGEF HGNC HGNC:7807 protein_coding YES CCDS2500.1 ENSP00000264051 Q8N5V2 UPI000013D4AE NM_019850.2 tolerated(0.63) 7/15 PROSITE_profiles:PS50010,hmmpanther:PTHR12845:SF8,hmmpanther:PTHR12845,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 232892965 232892965 G A 1 0 0 0 0 1 0 0 0 10430 1348 47 3 3 NGEF 2 232892965 Missense_Mutation SNP G C3N-01842_T 5190743 232892965 9300564 73 26265 IQSEC1 0 . GRCh38 3 12924601 12924601 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1710G>T p.Gln570His p.Q570H ENST00000613206 4/14 49 33 16 111 111 0 strelka-varscan-mutect IQSEC1,missense_variant,p.Gln584His,ENST00000273221,NM_014869.6;IQSEC1,missense_variant,p.Gln462His,ENST00000618604,;IQSEC1,missense_variant,p.Gln570His,ENST00000613206,NM_001134382.2; A ENST00000613206 Transcript missense_variant 1813/3582 1710/3345 570/1114 Q/H caG/caT 1 -1 IQSEC1 HGNC HGNC:29112 protein_coding YES CCDS74902.1 ENSP00000480301 A0A087WWK8 UPI00017E10F8 NM_001134382.2 deleterious(0) 4/14 PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF63,hmmpanther:PTHR10663,Gene3D:1.10.220.20,Pfam_domain:PF01369,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 12924601 12924601 C A 1 0 0 0 0 1 0 0 0 7723 564 20 2 2 IQSEC1 3 12924601 Missense_Mutation SNP C C3N-01842_T 12924601 185370958 74 26266 TOP2B 0 . GRCh38 3 25609584 25609584 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.3900G>T p.Arg1300Ser p.R1300S ENST00000435706 29/36 252 189 63 321 319 2 strelka-varscan TOP2B,missense_variant,p.Arg1300Ser,ENST00000435706,NM_001068.3;TOP2B,missense_variant,p.Arg1305Ser,ENST00000264331,;TOP2B,downstream_gene_variant,,ENST00000475717,;TOP2B,3_prime_UTR_variant,,ENST00000413971,; A ENST00000435706 Transcript missense_variant 4102/5389 3900/4866 1300/1621 R/S agG/agT 1 -1 TOP2B HGNC HGNC:11990 protein_coding YES CCDS46776.1 ENSP00000396704 Q02880 UPI000002B59A NM_001068.3 tolerated(0.05) 29/36 Low_complexity_(Seg):seg,hmmpanther:PTHR10169:SF36,hmmpanther:PTHR10169 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 25609584 25609584 C A 1 0 0 0 0 1 0 0 0 16842 622 22 2 2 TOP2B 3 25609584 Missense_Mutation SNP C C3N-01842_T 12684983 25609584 172685975 75 26267 SCN10A 0 . GRCh38 3 38698326 38698326 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.4894G>C p.Val1632Leu p.V1632L ENST00000449082 27/27 333 233 100 494 494 0 strelka-varscan SCN10A,missense_variant,p.Val1632Leu,ENST00000449082,NM_001293306.2,NM_006514.3,NM_001293307.2; G ENST00000449082 Transcript missense_variant 4894/6418 4894/5871 1632/1956 V/L Gtg/Ctg 1 -1 SCN10A HGNC HGNC:10582 protein_coding YES CCDS33736.1 ENSP00000390600 Q9Y5Y9 UPI0000209BDA NM_001293306.2,NM_006514.3,NM_001293307.2 deleterious(0.03) 27/27 hmmpanther:PTHR10037:SF208,hmmpanther:PTHR10037,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 38698326 38698326 C G 1 0 0 0 0 1 0 0 0 14181 478 17 4 4 SCN10A 3 38698326 Missense_Mutation SNP C C3N-01842_T 13088742 38698326 159597233 76 26268 EPHA6 0 . GRCh38 3 96987376 96987376 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.497C>A p.Thr166Lys p.T166K ENST00000389672 3/18 198 116 82 147 147 0 strelka-varscan EPHA6,missense_variant,p.Thr166Lys,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Thr166Lys,ENST00000470610,;EPHA6,missense_variant,p.Thr111Lys,ENST00000506569,NM_001278301.1; A ENST00000389672 Transcript missense_variant 535/3971 497/3393 166/1130 T/K aCa/aAa 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 MODERATE 1 SNV 2 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 96987376 96987376 C A 1 0 0 0 0 1 0 0 0 5018 478 17 2 2 EPHA6 3 96987376 Missense_Mutation SNP C C3N-01842_T 58289050 96987376 101308183 77 26269 FILIP1L 0 . GRCh38 3 99850274 99850274 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.1402A>G p.Arg468Gly p.R468G ENST00000354552 5/6 480 387 93 294 293 1 strelka-varscan FILIP1L,missense_variant,p.Arg468Gly,ENST00000331335,NM_001042459.2;FILIP1L,missense_variant,p.Arg468Gly,ENST00000354552,NM_182909.3;FILIP1L,missense_variant,p.Arg228Gly,ENST00000383694,NM_014890.3;FILIP1L,missense_variant,p.Arg228Gly,ENST00000495625,;FILIP1L,missense_variant,p.Arg228Gly,ENST00000471562,NM_001282794.1;FILIP1L,missense_variant,p.Arg44Gly,ENST00000487087,NM_001282793.1;CMSS1,intron_variant,,ENST00000421999,NM_032359.3;CMSS1,intron_variant,,ENST00000463526,;FILIP1L,upstream_gene_variant,,ENST00000477258,;CMSS1,intron_variant,,ENST00000496116,;FILIP1L,intron_variant,,ENST00000476723,;CMSS1,intron_variant,,ENST00000491299,; C ENST00000354552 Transcript missense_variant 1873/3970 1402/3408 468/1135 R/G Agg/Ggg 1 -1 FILIP1L HGNC HGNC:24589 protein_coding YES CCDS43117.1 ENSP00000346560 Q4L180 UPI00001B24B2 NM_182909.3 deleterious(0) 5/6 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23166,hmmpanther:PTHR23166:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 99850274 99850274 T C 1 0 0 0 0 1 0 0 0 5758 1608 56 5 5 FILIP1L 3 99850274 Missense_Mutation SNP T C3N-01842_T 2862898 99850274 98445285 78 26270 TOMM70 0 . GRCh38 3 100365612 100365612 + Silent SNP G G C novel C3N-01842_T C3N-01842_N G G c.1779C>G p.= p.A593A ENST00000284320 12/12 319 208 111 330 330 0 strelka-varscan TOMM70,synonymous_variant,p.=,ENST00000284320,NM_014820.4;NIT2,downstream_gene_variant,,ENST00000394140,NM_020202.4; C ENST00000284320 Transcript synonymous_variant 2228/4409 1779/1827 593/608 A gcC/gcG 1 -1 TOMM70 HGNC HGNC:11985 protein_coding YES CCDS33807.1 ENSP00000284320 O94826 UPI0000000C55 NM_014820.4 12/12 hmmpanther:PTHR22904:SF375,hmmpanther:PTHR22904,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 100365612 100365612 G C 1 0 0 0 0 0 0 0 1 16837 1219 43 4 4 TOMM70 3 100365612 Silent SNP G C3N-01842_T 515338 100365612 97929947 79 26271 AC026348.1 0 . GRCh38 3 113366135 113366135 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.2619G>T p.Leu873Phe p.L873F ENST00000393845 18/34 459 315 144 312 312 0 strelka-varscan AC026348.1,missense_variant,p.Leu873Phe,ENST00000393845,NM_001164496.1;CFAP44,missense_variant,p.Leu10Phe,ENST00000465636,;CFAP44,missense_variant,p.Leu873Phe,ENST00000295868,NM_018338.3;CFAP44,intron_variant,,ENST00000488854,;CFAP44,upstream_gene_variant,,ENST00000490481,;RP11-553D4.2,downstream_gene_variant,,ENST00000462549,; A ENST00000393845 Transcript missense_variant 2619/5565 2619/5565 873/1854 L/F ttG/ttT 1 -1 AC026348.1 Clone_based_ensembl_gene protein_coding YES CCDS54624.1 ENSP00000377428 Q96MT7 UPI0000367198 NM_001164496.1 deleterious(0.04) 18/34 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF18,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 113366135 113366135 C A 1 0 0 0 0 1 0 0 0 128 593 21 2 2 AC026348.1 3 113366135 Missense_Mutation SNP C C3N-01842_T 13000523 113366135 84929424 80 26272 POGLUT1 0 . GRCh38 3 119477416 119477416 + Nonsense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.424G>T p.Glu142Ter p.E142* ENST00000295588 4/11 268 181 87 257 257 0 strelka-varscan POGLUT1,stop_gained,p.Glu142Ter,ENST00000295588,NM_152305.2;POGLUT1,stop_gained,p.Glu129Ter,ENST00000476573,;POGLUT1,stop_gained,p.Glu142Ter,ENST00000486607,;POGLUT1,stop_gained,p.Glu142Ter,ENST00000497447,;POGLUT1,downstream_gene_variant,,ENST00000460339,;POGLUT1,upstream_gene_variant,,ENST00000481043,; T ENST00000295588 Transcript stop_gained 508/3533 424/1179 142/392 E/* Gag/Tag COSM4829026 1 1 POGLUT1 HGNC HGNC:22954 protein_coding YES CCDS2988.1 ENSP00000295588 Q8NBL1 UPI000003B0C3 NM_152305.2 4/11 Pfam_domain:PF05686,hmmpanther:PTHR12203,hmmpanther:PTHR12203:SF34,SMART_domains:SM00672 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 119477416 119477416 G T 1 0 0 0 0 0 1 0 0 12295 1175 41 2 2 POGLUT1 3 119477416 Nonsense_Mutation SNP G C3N-01842_T 6111281 119477416 78818143 81 26273 KALRN 0 . GRCh38 3 124398712 124398712 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.2181C>A p.= p.S727S ENST00000240874 13/34 439 372 67 435 435 0 strelka-varscan KALRN,synonymous_variant,p.=,ENST00000360013,NM_001024660.3;KALRN,synonymous_variant,p.=,ENST00000354186,;KALRN,synonymous_variant,p.=,ENST00000240874,NM_003947.4;KALRN,synonymous_variant,p.=,ENST00000460856,NM_001322989.1;KALRN,downstream_gene_variant,,ENST00000439170,;KALRN,non_coding_transcript_exon_variant,,ENST00000393501,;KALRN,non_coding_transcript_exon_variant,,ENST00000484224,;KALRN,non_coding_transcript_exon_variant,,ENST00000522553,; A ENST00000240874 Transcript synonymous_variant 2338/6537 2181/4992 727/1663 S tcC/tcA 1 1 KALRN HGNC HGNC:4814 protein_coding YES CCDS3027.1 ENSP00000240874 O60229 UPI000012C095 NM_003947.4 13/34 Gene3D:1.20.58.60,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 124398712 124398712 C A 1 0 0 0 0 0 0 0 1 7884 581 21 2 2 KALRN 3 124398712 Silent SNP C C3N-01842_T 4921296 124398712 73896847 82 26274 UMPS 0 . GRCh38 3 124737695 124737695 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.438C>T p.= p.V146V ENST00000232607 3/6 662 542 120 577 577 0 strelka-varscan UMPS,synonymous_variant,p.=,ENST00000232607,NM_000373.3;UMPS,non_coding_transcript_exon_variant,,ENST00000498715,;UMPS,upstream_gene_variant,,ENST00000495751,;UMPS,synonymous_variant,p.=,ENST00000479719,;UMPS,3_prime_UTR_variant,,ENST00000467167,;UMPS,3_prime_UTR_variant,,ENST00000460034,;UMPS,3_prime_UTR_variant,,ENST00000462091,;UMPS,3_prime_UTR_variant,,ENST00000497791,;UMPS,intron_variant,,ENST00000474588,;UMPS,upstream_gene_variant,,ENST00000487622,;RP11-71H17.1,upstream_gene_variant,,ENST00000475510,; T ENST00000232607 Transcript synonymous_variant 544/6738 438/1443 146/480 V gtC/gtT 1 1 UMPS HGNC HGNC:12563 protein_coding YES CCDS3029.1 ENSP00000232607 P11172 A8K5J1 UPI0000001223 NM_000373.3 3/6 HAMAP:MF_01208,hmmpanther:PTHR19278,hmmpanther:PTHR19278:SF9,Gene3D:3.40.50.2020,TIGRFAM_domain:TIGR00336,Pfam_domain:PF00156,Superfamily_domains:SSF53271 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 124737695 124737695 C T 1 0 0 0 0 0 0 0 1 17505 813 29 3 3 UMPS 3 124737695 Silent SNP C C3N-01842_T 338983 124737695 73557864 83 26275 UROC1 0 . GRCh38 3 126508040 126508040 + Missense_Mutation SNP A A T rs761278178 C3N-01842_T C3N-01842_N A A c.467T>A p.Met156Lys p.M156K ENST00000383579 5/21 488 377 111 487 486 1 strelka-varscan UROC1,missense_variant,p.Met156Lys,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.Met156Lys,ENST00000383579,NM_001165974.1; T ENST00000383579 Transcript missense_variant 501/2735 467/2211 156/736 M/K aTg/aAg rs761278178 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 deleterious(0) 5/21 Gene3D:1x87B01,HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 126508040 126508040 A T 1 0 0 0 0 1 0 0 0 17560 217 8 4 4 UROC1 3 126508040 Missense_Mutation SNP A C3N-01842_T 1770345 126508040 71787519 84 26276 COL6A5 0 . GRCh38 3 130440614 130440614 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.6264G>A p.= p.E2088E ENST00000265379 36/43 266 196 70 228 228 0 strelka-varscan COL6A5,synonymous_variant,p.=,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,synonymous_variant,p.=,ENST00000512836,;COL6A5,synonymous_variant,p.=,ENST00000373157,;COL6A5,upstream_gene_variant,,ENST00000512482,;COL6A5,synonymous_variant,p.=,ENST00000312481,; A ENST00000265379 Transcript synonymous_variant 6758/9214 6264/7836 2088/2611 E gaG/gaA 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 36/43 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF133,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 130440614 130440614 G A 1 0 0 0 0 0 0 0 1 3491 933 33 3 3 COL6A5 3 130440614 Silent SNP G C3N-01842_T 3932574 130440614 67854945 85 26277 STAG1 0 . GRCh38 3 136521216 136521216 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.673G>T p.Ala225Ser p.A225S ENST00000383202 7/34 368 310 58 282 280 2 strelka-varscan STAG1,missense_variant,p.Ala225Ser,ENST00000383202,NM_005862.2;STAG1,missense_variant,p.Ala225Ser,ENST00000236698,;STAG1,missense_variant,p.Ala225Ser,ENST00000480733,;STAG1,5_prime_UTR_variant,,ENST00000434713,;STAG1,3_prime_UTR_variant,,ENST00000629124,;STAG1,3_prime_UTR_variant,,ENST00000483235,;STAG1,3_prime_UTR_variant,,ENST00000487065,;STAG1,non_coding_transcript_exon_variant,,ENST00000462818,; A ENST00000383202 Transcript missense_variant 930/6055 673/3777 225/1258 A/S Gct/Tct 1 -1 STAG1 HGNC HGNC:11354 protein_coding YES CCDS3090.1 ENSP00000372689 Q8WVM7 UPI000020A2DE NM_005862.2 deleterious(0) 7/34 Pfam_domain:PF08514,hmmpanther:PTHR11199,hmmpanther:PTHR11199:SF6,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 136521216 136521216 C A 1 0 0 0 0 1 0 0 0 15620 753 26 2 2 STAG1 3 136521216 Missense_Mutation SNP C C3N-01842_T 6080602 136521216 61774343 86 26278 COPB2 0 . GRCh38 3 139383346 139383346 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.93G>T p.Leu31Phe p.L31F ENST00000333188 2/22 346 222 124 223 223 0 strelka-varscan COPB2,missense_variant,p.Leu31Phe,ENST00000333188,NM_004766.2;COPB2,missense_variant,p.Leu2Phe,ENST00000507777,;COPB2,missense_variant,p.Leu2Phe,ENST00000512242,;COPB2,missense_variant,p.Leu2Phe,ENST00000513274,;COPB2,missense_variant,p.Leu2Phe,ENST00000514508,;COPB2,missense_variant,p.Leu2Phe,ENST00000512153,;COPB2,missense_variant,p.Leu31Phe,ENST00000515006,;U6,upstream_gene_variant,,ENST00000637379,;COPB2,non_coding_transcript_exon_variant,,ENST00000510491,;COPB2,non_coding_transcript_exon_variant,,ENST00000504295,;COPB2,non_coding_transcript_exon_variant,,ENST00000510181,; A ENST00000333188 Transcript missense_variant 275/3360 93/2721 31/906 L/F ttG/ttT 1 -1 COPB2 HGNC HGNC:2232 protein_coding YES CCDS3108.1 ENSP00000329419 P35606 UPI0000161FB4 NM_004766.2 deleterious(0) 2/22 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR19876,PIRSF_domain:PIRSF005567,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 139383346 139383346 C A 1 0 0 0 0 1 0 0 0 3521 593 21 2 2 COPB2 3 139383346 Missense_Mutation SNP C C3N-01842_T 2862130 139383346 58912213 87 26279 HLTF 0 . GRCh38 3 149064833 149064834 + Frame_Shift_Ins INS - - A novel C3N-01842_T C3N-01842_N - - c.1023dupT p.Gly342TrpfsTer7 p.G342Wfs*7 ENST00000310053 9/25 302 212 90 235 235 0 sindel-varindel-pindel HLTF,frameshift_variant,p.Gly342TrpfsTer7,ENST00000310053,NM_001318934.1,NM_003071.3,NM_139048.2;HLTF,frameshift_variant,p.Gly342TrpfsTer7,ENST00000465259,;HLTF,frameshift_variant,p.Gly342TrpfsTer7,ENST00000392912,;HLTF,frameshift_variant,p.Gly342TrpfsTer7,ENST00000494055,;HLTF,upstream_gene_variant,,ENST00000493881,; A ENST00000310053 Transcript frameshift_variant 1217-1218/5317 1023-1024/3030 341-342/1009 -/X -/T 1 -1 HLTF HGNC HGNC:11099 protein_coding YES CCDS33875.1 ENSP00000308944 Q14527 UPI0000161FA7 NM_001318934.1,NM_003071.3,NM_139048.2 9/25 Pfam_domain:PF00176,SMART_domains:SM00487 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 84 149064833 149064833 - A 1 0 1 1 0 0 0 0 0 7105 603 21 0 0 HLTF 3 149064833 Frame_Shift_Ins INS - C3N-01842_T 9681487 149064833 49230726 88 26280 GFM1 0 . GRCh38 3 158646186 158646186 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.256G>T p.Gly86Cys p.G86C ENST00000264263 3/19 379 223 156 396 396 0 strelka-varscan GFM1,missense_variant,p.Gly86Cys,ENST00000486715,NM_024996.5;GFM1,missense_variant,p.Gly86Cys,ENST00000264263,NM_001308164.1;GFM1,missense_variant,p.Gly86Cys,ENST00000478576,NM_001308166.1;GFM1,missense_variant,p.Gly11Cys,ENST00000464732,;LXN,synonymous_variant,p.=,ENST00000482640,;GFM1,missense_variant,p.Gly86Cys,ENST00000478254,;GFM1,upstream_gene_variant,,ENST00000478251,; T ENST00000264263 Transcript missense_variant 294/3453 256/2313 86/770 G/C Ggt/Tgt 1 1 GFM1 HGNC HGNC:13780 protein_coding YES CCDS77851.1 ENSP00000264263 Q96RP9 UPI0001B78F61 NM_001308164.1 deleterious(0) 3/19 PROSITE_profiles:PS51722,HAMAP:MF_00054_B,hmmpanther:PTHR23115:SF162,hmmpanther:PTHR23115,TIGRFAM_domain:TIGR00231,TIGRFAM_domain:TIGR00484,Gene3D:3.40.50.300,Pfam_domain:PF00009,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 158646186 158646186 G T 1 0 0 0 0 1 0 0 0 6215 1348 47 2 2 GFM1 3 158646186 Missense_Mutation SNP G C3N-01842_T 9581353 158646186 39649373 89 26281 SI 0 . GRCh38 3 164982257 164982257 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.5401G>A p.Asp1801Asn p.D1801N ENST00000264382 47/48 300 252 48 222 222 0 strelka-varscan SI,missense_variant,p.Asp1801Asn,ENST00000264382,NM_001041.3; T ENST00000264382 Transcript missense_variant 5464/6011 5401/5484 1801/1827 D/N Gac/Aac 1 -1 SI HGNC HGNC:10856 protein_coding YES CCDS3196.1 ENSP00000264382 P14410 UPI000022C287 NM_001041.3 tolerated(0.56) 47/48 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 164982257 164982257 C T 1 0 0 0 0 1 0 0 0 14561 913 32 3 3 SI 3 164982257 Missense_Mutation SNP C C3N-01842_T 6336071 164982257 33313302 90 26282 PDCD10 0 . GRCh38 3 167704896 167704896 + Splice_Site SNP C C A novel C3N-01842_T C3N-01842_N C C c.97-1G>T p.X33_splice ENST00000392750 342 282 60 286 286 0 strelka-varscan PDCD10,splice_acceptor_variant,,ENST00000392750,NM_007217.3;PDCD10,splice_acceptor_variant,,ENST00000473645,NM_145859.1;PDCD10,splice_acceptor_variant,,ENST00000497056,NM_145860.1;PDCD10,splice_acceptor_variant,,ENST00000470131,;PDCD10,splice_acceptor_variant,,ENST00000461494,;PDCD10,splice_acceptor_variant,,ENST00000475915,;PDCD10,splice_acceptor_variant,,ENST00000492396,;PDCD10,splice_acceptor_variant,,ENST00000471885,;PDCD10,splice_acceptor_variant,,ENST00000487947,;PDCD10,splice_acceptor_variant,,ENST00000462725,;PDCD10,splice_acceptor_variant,,ENST00000492139,;PDCD10,splice_acceptor_variant,,ENST00000464360,;PDCD10,splice_acceptor_variant,,ENST00000479121,;PDCD10,splice_acceptor_variant,,ENST00000483451,;PDCD10,splice_acceptor_variant,,ENST00000494502,;PDCD10,splice_acceptor_variant,,ENST00000481136,; A ENST00000392750 Transcript splice_acceptor_variant -/2067 97/639 33/212 1 -1 PDCD10 HGNC HGNC:8761 protein_coding YES CCDS3202.1 ENSP00000376506 Q9BUL8 UPI0000071E33 NM_007217.3 3/8 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 84 167704896 167704896 C A 1 0 0 0 0 0 0 1 0 11704 811 28 2 2 PDCD10 3 167704896 Splice_Site SNP C C3N-01842_T 2722639 167704896 30590663 91 26283 SOX2 0 . GRCh38 3 181712903 181712904 + Frame_Shift_Ins INS - - C novel C3N-01842_T C3N-01842_N - - c.544dupC p.Gln182ProfsTer128 p.Q182Pfs*128 ENST00000325404 1/1 206 161 45 216 216 0 sindel-varindel-pindel SOX2,frameshift_variant,p.Gln182ProfsTer128,ENST00000325404,NM_003106.3;SOX2-OT,intron_variant,,ENST00000498731,;SOX2-OT,intron_variant,,ENST00000492337,;SOX2-OT,intron_variant,,ENST00000493521,;SOX2-OT,intron_variant,,ENST00000466034,;SOX2-OT,intron_variant,,ENST00000630553,;SOX2-OT,intron_variant,,ENST00000477928,;SOX2-OT,intron_variant,,ENST00000491282,;SOX2-OT,intron_variant,,ENST00000627530,;SOX2-OT,intron_variant,,ENST00000597828,;SOX2-OT,intron_variant,,ENST00000595084,;SOX2-OT,intron_variant,,ENST00000599082,;SOX2-OT,intron_variant,,ENST00000628496,;SOX2-OT,intron_variant,,ENST00000600386,;SOX2-OT,intron_variant,,ENST00000627501,;SOX2-OT,intron_variant,,ENST00000600778,;SOX2-OT,intron_variant,,ENST00000629112,;SOX2-OT,intron_variant,,ENST00000593549,;SOX2-OT,intron_variant,,ENST00000630887,;SOX2-OT,intron_variant,,ENST00000628343,;SOX2-OT,intron_variant,,ENST00000629781,;SOX2-OT,intron_variant,,ENST00000627738,;SOX2-OT,intron_variant,,ENST00000629830,;SOX2-OT,intron_variant,,ENST00000600801,;SOX2-OT,intron_variant,,ENST00000626619,;SOX2-OT,intron_variant,,ENST00000597651,;SOX2-OT,intron_variant,,ENST00000626299,;SOX2-OT,intron_variant,,ENST00000628810,;SOX2-OT,intron_variant,,ENST00000596250,;SOX2-OT,intron_variant,,ENST00000476964,;SOX2-OT,intron_variant,,ENST00000595287,;SOX2-OT,intron_variant,,ENST00000629552,;SOX2-OT,intron_variant,,ENST00000469278,;SOX2-OT,intron_variant,,ENST00000498226,;SOX2-OT,intron_variant,,ENST00000598474,;SOX2-OT,intron_variant,,ENST00000593330,;SOX2-OT,downstream_gene_variant,,ENST00000476125,;SOX2-OT,downstream_gene_variant,,ENST00000631025,;SOX2-OT,downstream_gene_variant,,ENST00000600962,;SOX2OT_exon4,upstream_gene_variant,,ENST00000610449,; C ENST00000325404 Transcript frameshift_variant 980-981/2513 543-544/954 181-182/317 -/X -/C 1 1 SOX2 HGNC HGNC:11195 protein_coding YES CCDS3239.1 ENSP00000323588 P48431 A0A0U3FYV6 UPI000003F545 NM_003106.3 1/1 hmmpanther:PTHR10270:SF231,hmmpanther:PTHR10270,Pfam_domain:PF12336 HIGH insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 84 181712903 181712903 - C 1 0 1 1 0 0 0 0 0 15275 1074 38 0 0 SOX2 3 181712903 Frame_Shift_Ins INS - C3N-01842_T 14008007 181712903 16582656 92 26284 ECE2 0 . GRCh38 3 184277977 184277977 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.885C>A p.Phe295Leu p.F295L ENST00000402825 5/19 244 206 38 305 305 0 strelka-varscan ECE2,missense_variant,p.Phe295Leu,ENST00000402825,NM_014693.3;ECE2,missense_variant,p.Phe177Leu,ENST00000404464,NM_001100121.1;ECE2,missense_variant,p.Phe148Leu,ENST00000359140,NM_001037324.2;ECE2,missense_variant,p.Phe223Leu,ENST00000357474,NM_001100120.1;ECE2,missense_variant,p.Phe169Leu,ENST00000430587,;ECE2,3_prime_UTR_variant,,ENST00000422932,;ECE2,non_coding_transcript_exon_variant,,ENST00000488401,;ECE2,non_coding_transcript_exon_variant,,ENST00000490579,;ECE2,downstream_gene_variant,,ENST00000474750,;ECE2,upstream_gene_variant,,ENST00000462596,; A ENST00000402825 Transcript missense_variant 885/3445 885/2652 295/883 F/L ttC/ttA 1 1 ECE2 HGNC HGNC:13275 protein_coding YES CCDS3256.2 ENSP00000384223 O60344 UPI0001596888 NM_014693.3 tolerated(0.75) 5/19 Pfam_domain:PF05649,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF127,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 184277977 184277977 C A 1 0 0 0 0 1 0 0 0 4716 912 32 2 2 ECE2 3 184277977 Missense_Mutation SNP C C3N-01842_T 2565074 184277977 14017582 93 26285 WHSC1 0 . GRCh38 4 1956181 1956181 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.2874C>G p.Phe958Leu p.F958L ENST00000382895 17/24 107 72 35 162 162 0 strelka-varscan-mutect WHSC1,missense_variant,p.Phe958Leu,ENST00000382895,NM_133330.2;WHSC1,missense_variant,p.Phe958Leu,ENST00000382892,NM_133331.2;WHSC1,missense_variant,p.Phe958Leu,ENST00000382891,NM_133335.3;WHSC1,missense_variant,p.Phe958Leu,ENST00000508803,NM_001042424.2;WHSC1,missense_variant,p.Phe306Leu,ENST00000382888,;WHSC1,missense_variant,p.Phe282Leu,ENST00000514329,;WHSC1,non_coding_transcript_exon_variant,,ENST00000482415,;WHSC1,non_coding_transcript_exon_variant,,ENST00000503207,;WHSC1,downstream_gene_variant,,ENST00000505643,;WHSC1,downstream_gene_variant,,ENST00000513726,;WHSC1,downstream_gene_variant,,ENST00000502425,;WHSC1,3_prime_UTR_variant,,ENST00000312087,;WHSC1,3_prime_UTR_variant,,ENST00000353275,;WHSC1,non_coding_transcript_exon_variant,,ENST00000507094,; G ENST00000382895 Transcript missense_variant 3305/7827 2874/4098 958/1365 F/L ttC/ttG 1 1 WHSC1 HGNC HGNC:12766 protein_coding YES CCDS33940.1 ENSP00000372351 O96028 UPI0000073F57 NM_133330.2 deleterious(0) 17/24 hmmpanther:PTHR22884:SF293,hmmpanther:PTHR22884,Gene3D:2.30.30.160,Pfam_domain:PF00855,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 1 PASS . . 0 187 18 5 0 0 0 0 -20 0.9862611 0 1 1 0 G 3 3 84 1956181 1956181 C G 1 0 0 0 0 1 0 0 0 17920 825 29 4 4 WHSC1 4 1956181 Missense_Mutation SNP C C3N-01842_T 1956181 188258374 94 26286 CWH43 0 . GRCh38 4 48994696 48994696 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.589C>A p.Leu197Met p.L197M ENST00000226432 5/16 288 209 79 435 434 1 strelka-varscan-mutect CWH43,missense_variant,p.Leu197Met,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Leu170Met,ENST00000513409,NM_001286791.1;CWH43,missense_variant,p.Leu197Met,ENST00000514053,; A ENST00000226432 Transcript missense_variant 772/2472 589/2100 197/699 L/M Ctg/Atg 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 deleterious(0.01) 5/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 48994696 48994696 C A 1 0 0 0 0 1 0 0 0 3883 796 28 2 2 CWH43 4 48994696 Missense_Mutation SNP C C3N-01842_T 47038515 48994696 141219859 95 26287 STAP1 0 . GRCh38 4 67593259 67593259 + Splice_Site SNP G G A novel C3N-01842_T C3N-01842_N G G c.730-1G>A p.X244_splice ENST00000265404 90 71 19 97 97 0 strelka-varscan-mutect STAP1,splice_acceptor_variant,,ENST00000265404,NM_012108.2;STAP1,splice_acceptor_variant,,ENST00000396225,NM_001317769.1; A ENST00000265404 Transcript splice_acceptor_variant -/1511 730/888 244/295 1 1 STAP1 HGNC HGNC:24133 protein_coding YES CCDS3515.1 ENSP00000265404 Q9ULZ2 A0A024RD91 UPI0000073E6C NM_012108.2 7/8 HIGH 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 A 5 1 84 67593259 67593259 G A 1 0 0 0 0 0 0 1 0 15627 1014 35 3 3 STAP1 4 67593259 Splice_Site SNP G C3N-01842_T 18598563 67593259 122621296 96 26288 TMPRSS11D 0 . GRCh38 4 67822459 67822459 + Silent SNP G G T rs758167149 C3N-01842_T C3N-01842_N G G c.1135C>A p.= p.R379R ENST00000283916 10/10 176 117 59 225 223 2 strelka-varscan-mutect TMPRSS11D,synonymous_variant,p.=,ENST00000283916,NM_004262.2;TMPRSS11D,downstream_gene_variant,,ENST00000514868,;UBA6-AS1,intron_variant,,ENST00000500538,;TMPRSS11D,non_coding_transcript_exon_variant,,ENST00000505533,; T ENST00000283916 Transcript synonymous_variant 1234/2817 1135/1257 379/418 R Cgg/Agg rs758167149,COSM3781181 1 -1 TMPRSS11D HGNC HGNC:24059 protein_coding YES CCDS3518.1 ENSP00000283916 O60235 UPI000003FE66 NM_004262.2 10/10 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF20,hmmpanther:PTHR24256,Gene3D:2.40.10.10,PIRSF_domain:PIRSF037941,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 0,1 LOW 1 SNV 1 0,1 1 PASS rs758167149 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 67822459 67822459 G T 1 0 0 0 0 0 0 0 1 16717 1086 38 1 1 TMPRSS11D 4 67822459 Silent SNP G C3N-01842_T 229200 67822459 122392096 97 26289 SEC24D 0 . GRCh38 4 118745044 118745044 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1724G>T p.Gly575Val p.G575V ENST00000280551 14/23 153 93 60 202 202 0 strelka-varscan-mutect SEC24D,missense_variant,p.Gly575Val,ENST00000280551,NM_001318066.1,NM_014822.2;SEC24D,missense_variant,p.Gly131Val,ENST00000419654,;SEC24D,missense_variant,p.Gly206Val,ENST00000511481,;SEC24D,non_coding_transcript_exon_variant,,ENST00000505134,;SEC24D,non_coding_transcript_exon_variant,,ENST00000511033,;SEC24D,3_prime_UTR_variant,,ENST00000514561,; A ENST00000280551 Transcript missense_variant 1963/4030 1724/3099 575/1032 G/V gGg/gTg 1 -1 SEC24D HGNC HGNC:10706 protein_coding YES CCDS3710.1 ENSP00000280551 O94855 UPI00001AEA4F NM_001318066.1,NM_014822.2 deleterious(0) 14/23 hmmpanther:PTHR13803:SF6,hmmpanther:PTHR13803,Gene3D:3.40.50.410,Pfam_domain:PF04811,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 118745044 118745044 C A 1 0 0 0 0 1 0 0 0 14274 623 22 2 2 SEC24D 4 118745044 Missense_Mutation SNP C C3N-01842_T 50922585 118745044 71469511 98 26290 FSTL5 0 . GRCh38 4 161500038 161500038 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.1436G>C p.Ser479Thr p.S479T ENST00000306100 12/16 279 199 80 266 266 0 strelka-varscan-mutect FSTL5,missense_variant,p.Ser479Thr,ENST00000306100,NM_020116.4;FSTL5,missense_variant,p.Ser478Thr,ENST00000379164,NM_001128427.2;FSTL5,missense_variant,p.Ser469Thr,ENST00000427802,NM_001128428.2;FSTL5,non_coding_transcript_exon_variant,,ENST00000511999,; G ENST00000306100 Transcript missense_variant 1873/4831 1436/2544 479/847 S/T aGt/aCt 1 -1 FSTL5 HGNC HGNC:21386 protein_coding YES CCDS3802.1 ENSP00000305334 Q8N475 UPI000020B66B NM_020116.4 tolerated(1) 12/16 hmmpanther:PTHR10913,hmmpanther:PTHR10913:SF44 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 161500038 161500038 C G 1 0 0 0 0 1 0 0 0 5954 565 20 4 4 FSTL5 4 161500038 Missense_Mutation SNP C C3N-01842_T 42754994 161500038 28714517 99 26291 MARCH1 0 . GRCh38 4 163612794 163612794 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.487T>A p.Ser163Thr p.S163T ENST00000514618 7/10 193 128 65 203 203 0 strelka-varscan-mutect MARCH1,missense_variant,p.Ser163Thr,ENST00000514618,;MARCH1,intron_variant,,ENST00000503008,NM_001166373.1;MARCH1,intron_variant,,ENST00000274056,;MARCH1,intron_variant,,ENST00000339875,NM_017923.3;MARCH1,intron_variant,,ENST00000507270,;MARCH1,non_coding_transcript_exon_variant,,ENST00000512214,;MARCH1,non_coding_transcript_exon_variant,,ENST00000511245,;MARCH1,intron_variant,,ENST00000510786,;MARCH1,intron_variant,,ENST00000505517,;MARCH1,downstream_gene_variant,,ENST00000510696,; T ENST00000514618 Transcript missense_variant 975/3903 487/1638 163/545 S/T Tct/Act 1 -1 MARCH1 HGNC HGNC:26077 protein_coding ENSP00000421322 D6RGC4 UPI0001D3B97D tolerated(0.07) 7/10 Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 163612794 163612794 A T 1 0 0 0 0 1 0 0 0 9223 333 12 4 4 MARCH1 4 163612794 Missense_Mutation SNP A C3N-01842_T 2112756 163612794 26601761 100 26292 TERT 0 . GRCh38 5 1294873 1294873 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.117G>T p.= p.V39V ENST00000310581 1/16 203 186 17 104 103 1 strelka-varscan-mutect TERT,synonymous_variant,p.=,ENST00000310581,NM_198253.2;TERT,synonymous_variant,p.=,ENST00000334602,NM_001193376.1;TERT,synonymous_variant,p.=,ENST00000508104,;TERT,non_coding_transcript_exon_variant,,ENST00000522877,;TERT,synonymous_variant,p.=,ENST00000460137,; A ENST00000310581 Transcript synonymous_variant 175/4018 117/3399 39/1132 V gtG/gtT 1 -1 TERT HGNC HGNC:11730 protein_coding YES CCDS3861.2 ENSP00000309572 O14746 UPI0000031309 NM_198253.2 1/16 hmmpanther:PTHR12066,hmmpanther:PTHR12066:SF0 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 1294873 1294873 C A 1 0 0 0 0 0 0 0 1 16183 697 25 2 2 TERT 5 1294873 Silent SNP C C3N-01842_T 1294873 180243386 101 26293 IRX1 0 . GRCh38 5 3600095 3600095 + Missense_Mutation SNP G G T rs368097265 C3N-01842_T C3N-01842_N G G c.1147G>T p.Gly383Cys p.G383C ENST00000302006 2/4 228 113 115 168 168 0 strelka-varscan-mutect IRX1,missense_variant,p.Gly383Cys,ENST00000302006,NM_024337.3;CTD-2012M11.3,non_coding_transcript_exon_variant,,ENST00000559410,; T ENST00000302006 Transcript missense_variant 1199/1858 1147/1443 383/480 G/C Ggc/Tgc rs368097265 1 1 IRX1 HGNC HGNC:14358 protein_coding YES CCDS34132.1 ENSP00000305244 P78414 UPI00001B6455 NM_024337.3 tolerated(0.07) 2/4 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF13 MODERATE 1 SNV 1 1 PASS rs368097265 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 3600095 3600095 G T 1 0 0 0 0 1 0 0 0 7751 1232 43 2 2 IRX1 5 3600095 Missense_Mutation SNP G C3N-01842_T 2305222 3600095 177938164 102 26294 ADAMTS16 0 . GRCh38 5 5237007 5237007 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.2062T>A p.Phe688Ile p.F688I ENST00000274181 14/23 342 170 172 177 177 0 strelka-varscan-mutect ADAMTS16,missense_variant,p.Phe688Ile,ENST00000274181,NM_139056.2;ADAMTS16,intron_variant,,ENST00000513709,;ADAMTS16,non_coding_transcript_exon_variant,,ENST00000433402,; A ENST00000274181 Transcript missense_variant 2200/4979 2062/3675 688/1224 F/I Ttt/Att 1 1 ADAMTS16 HGNC HGNC:17108 protein_coding YES CCDS43299.1 ENSP00000274181 Q8TE57 UPI00004572CA NM_139056.2 deleterious(0) 14/23 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF140 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 5237007 5237007 T A 1 0 0 0 0 1 0 0 0 305 1493 52 4 4 ADAMTS16 5 5237007 Missense_Mutation SNP T C3N-01842_T 1636912 5237007 176301252 103 26295 SEMA5A 0 . GRCh38 5 9197261 9197261 + Silent SNP G G A rs765586378 C3N-01842_T C3N-01842_N G G c.975C>T p.= p.S325S ENST00000382496 10/23 342 288 54 245 245 0 strelka-varscan SEMA5A,synonymous_variant,p.=,ENST00000382496,NM_003966.2;SEMA5A,downstream_gene_variant,,ENST00000513968,;SEMA5A,downstream_gene_variant,,ENST00000514923,; A ENST00000382496 Transcript synonymous_variant 1641/11762 975/3225 325/1074 S agC/agT rs765586378,COSM4854653 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 10/23 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF78,Pfam_domain:PF01403,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 84 9197261 9197261 G A 1 0 0 0 0 0 0 0 1 14313 1078 38 1 1 SEMA5A 5 9197261 Silent SNP G C3N-01842_T 3960254 9197261 172340998 104 26296 OTULIN 0 . GRCh38 5 14692977 14692977 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.988G>T p.Val330Leu p.V330L ENST00000284274 7/7 464 221 243 362 361 1 strelka-varscan OTULIN,missense_variant,p.Val330Leu,ENST00000284274,NM_138348.4;OTULIN,missense_variant,p.Val62Leu,ENST00000506417,;OTULIN,downstream_gene_variant,,ENST00000503023,;OTULIN,downstream_gene_variant,,ENST00000514913,; T ENST00000284274 Transcript missense_variant 1066/7800 988/1059 330/352 V/L Gta/Tta 1 1 OTULIN HGNC HGNC:25118 protein_coding YES CCDS43302.1 ENSP00000284274 Q96BN8 UPI0000374C00 NM_138348.4 tolerated(0.07) 7/7 hmmpanther:PTHR33662,hmmpanther:PTHR33662:SF2,Pfam_domain:PF16218,Prints_domain:PR02057,Prints_domain:PR02055 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 14692977 14692977 G T 1 0 0 0 0 1 0 0 0 11389 1261 44 2 2 OTULIN 5 14692977 Missense_Mutation SNP G C3N-01842_T 5495716 14692977 166845282 105 26297 PRDM9 0 . GRCh38 5 23526714 23526714 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1626C>A p.His542Gln p.H542Q ENST00000296682 11/11 889 421 468 541 539 2 strelka-varscan-mutect PRDM9,missense_variant,p.His542Gln,ENST00000296682,NM_020227.2;PRDM9,downstream_gene_variant,,ENST00000635252,; A ENST00000296682 Transcript missense_variant 1808/3691 1626/2685 542/894 H/Q caC/caA 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 deleterious(0.01) 11/11 PROSITE_profiles:PS50157,hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 23526714 23526714 C A 1 0 0 0 0 1 0 0 0 12595 506 18 2 2 PRDM9 5 23526714 Missense_Mutation SNP C C3N-01842_T 8833737 23526714 158011545 106 26298 C6 0 . GRCh38 5 41153913 41153913 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.2187G>C p.Glu729Asp p.E729D ENST00000263413 15/18 406 218 188 328 328 0 strelka-varscan C6,missense_variant,p.Glu729Asp,ENST00000263413,NM_001115131.2;C6,missense_variant,p.Glu729Asp,ENST00000337836,NM_000065.3;C6,non_coding_transcript_exon_variant,,ENST00000461473,;C6,downstream_gene_variant,,ENST00000511470,; G ENST00000263413 Transcript missense_variant 2452/3661 2187/2805 729/934 E/D gaG/gaC 1 -1 C6 HGNC HGNC:1339 protein_coding YES CCDS3936.1 ENSP00000263413 P13671 UPI000013D401 NM_001115131.2 tolerated(0.36) 15/18 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF23,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 41153913 41153913 C G 1 0 0 0 0 1 0 0 0 2111 796 28 4 4 C6 5 41153913 Missense_Mutation SNP C C3N-01842_T 17627199 41153913 140384346 107 26299 HMGCS1 0 . GRCh38 5 43298797 43298797 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.169G>T p.Gly57Cys p.G57C ENST00000325110 3/11 485 392 93 347 344 3 strelka-varscan HMGCS1,missense_variant,p.Gly57Cys,ENST00000325110,NM_001098272.2;HMGCS1,missense_variant,p.Gly57Cys,ENST00000433297,NM_002130.7;HMGCS1,missense_variant,p.Gly57Cys,ENST00000511774,;HMGCS1,non_coding_transcript_exon_variant,,ENST00000507004,;HMGCS1,non_coding_transcript_exon_variant,,ENST00000507293,;HMGCS1,upstream_gene_variant,,ENST00000508319,;HMGCS1,upstream_gene_variant,,ENST00000514610,; A ENST00000325110 Transcript missense_variant 376/3506 169/1563 57/520 G/C Ggc/Tgc 1 -1 HMGCS1 HGNC HGNC:5007 protein_coding YES CCDS34154.1 ENSP00000322706 Q01581 A0A024R059 UPI000012C9BC NM_001098272.2 deleterious(0) 3/11 Gene3D:3.40.47.10,Pfam_domain:PF01154,hmmpanther:PTHR11877,hmmpanther:PTHR11877:SF12,Superfamily_domains:SSF53901,TIGRFAM_domain:TIGR01833 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 43298797 43298797 C A 1 0 0 0 0 1 0 0 0 7124 623 22 2 2 HMGCS1 5 43298797 Missense_Mutation SNP C C3N-01842_T 2144884 43298797 138239462 108 26300 HCN1 0 . GRCh38 5 45396684 45396684 + Silent SNP T T A novel C3N-01842_T C3N-01842_N T T c.1038A>T p.= p.S346S ENST00000303230 4/8 885 423 462 566 566 0 strelka-varscan HCN1,synonymous_variant,p.=,ENST00000303230,NM_021072.3;HCN1,non_coding_transcript_exon_variant,,ENST00000637305,; A ENST00000303230 Transcript synonymous_variant 1279/9885 1038/2673 346/890 S tcA/tcT 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 4/8 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 45396684 45396684 T A 1 0 0 0 0 0 0 0 1 6883 1451 51 4 4 HCN1 5 45396684 Silent SNP T C3N-01842_T 2097887 45396684 136141575 109 26301 HCN1 0 . GRCh38 5 45695805 45695805 + Missense_Mutation SNP G G C C3N-01842_T C3N-01842_N G G c.289C>G p.Gln97Glu p.Q97E ENST00000303230 1/8 811 722 89 653 653 0 strelka-varscan HCN1,missense_variant,p.Gln97Glu,ENST00000303230,NM_021072.3;HCN1,missense_variant,p.Gln97Glu,ENST00000634658,;HCN1,upstream_gene_variant,,ENST00000638054,; C ENST00000303230 Transcript missense_variant 530/9885 289/2673 97/890 Q/E Cag/Gag COSM5696632 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 deleterious(0) 1/8 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 45695805 45695805 G C 1 0 0 0 0 1 0 0 0 6883 1328 46 4 4 HCN1 5 45695805 Missense_Mutation SNP G C3N-01842_T 299121 45695805 135842454 110 26302 ANKRD55 0 . GRCh38 5 56111473 56111473 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1275C>A p.= p.A425A ENST00000341048 10/12 269 235 34 470 469 1 strelka-varscan ANKRD55,synonymous_variant,p.=,ENST00000341048,NM_024669.2;ANKRD55,synonymous_variant,p.=,ENST00000504958,;ANKRD55,synonymous_variant,p.=,ENST00000434982,;ANKRD55,downstream_gene_variant,,ENST00000505970,; T ENST00000341048 Transcript synonymous_variant 1427/2502 1275/1845 425/614 A gcC/gcA 1 -1 ANKRD55 HGNC HGNC:25681 protein_coding YES CCDS34161.1 ENSP00000342295 Q3KP44 UPI00004572EF NM_024669.2 10/12 hmmpanther:PTHR24158,hmmpanther:PTHR24158:SF24 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 56111473 56111473 G T 1 0 0 0 0 0 0 0 1 785 1219 43 2 2 ANKRD55 5 56111473 Silent SNP G C3N-01842_T 10415668 56111473 125426786 111 26303 MAST4 0 . GRCh38 5 67160545 67160545 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.3738G>T p.= p.R1246R ENST00000403625 27/29 172 122 50 237 237 0 strelka-varscan MAST4,synonymous_variant,p.=,ENST00000403625,NM_001164664.1;MAST4,synonymous_variant,p.=,ENST00000405643,NM_001290226.1;MAST4,synonymous_variant,p.=,ENST00000261569,NM_001290227.1,NM_001297651.1;MAST4,synonymous_variant,p.=,ENST00000403666,NM_015183.2;MAST4,synonymous_variant,p.=,ENST00000443808,; T ENST00000403625 Transcript synonymous_variant 4033/10711 3738/7872 1246/2623 R cgG/cgT 1 1 MAST4 HGNC HGNC:19037 protein_coding YES CCDS54861.1 ENSP00000385727 J3QT34 UPI000173A2B0 NM_001164664.1 27/29 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 67160545 67160545 G T 1 0 0 0 0 0 0 0 1 9253 1161 41 2 2 MAST4 5 67160545 Silent SNP G C3N-01842_T 11049072 67160545 114377714 112 26304 CARTPT 0 . GRCh38 5 71719404 71719404 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.111C>T p.= p.A37A ENST00000296777 1/3 443 400 43 643 643 0 strelka-varscan CARTPT,synonymous_variant,p.=,ENST00000296777,NM_004291.3;CARTPT,upstream_gene_variant,,ENST00000513096,; T ENST00000296777 Transcript synonymous_variant 242/915 111/351 37/116 A gcC/gcT 1 1 CARTPT HGNC HGNC:24323 protein_coding YES CCDS4011.1 ENSP00000296777 Q16568 UPI00000015E9 NM_004291.3 1/3 hmmpanther:PTHR16655 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 71719404 71719404 C T 1 0 0 0 0 0 0 0 1 2358 610 22 3 3 CARTPT 5 71719404 Silent SNP C C3N-01842_T 4558859 71719404 109818855 113 26305 FBN2 0 . GRCh38 5 128335209 128335209 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.3934G>A p.Asp1312Asn p.D1312N ENST00000508053 36/71 525 371 154 692 691 1 strelka-varscan FBN2,missense_variant,p.Asp1312Asn,ENST00000508053,;FBN2,missense_variant,p.Asp1312Asn,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Asp1311Asn,ENST00000619499,;FBN2,missense_variant,p.Asp1279Asn,ENST00000508989,;FBN2,missense_variant,p.Asp162Asn,ENST00000507835,; T ENST00000508053 Transcript missense_variant 4909/11132 3934/8739 1312/2912 D/N Gat/Aat 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0.04) 36/71 Gene3D:2.10.25.10,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 128335209 128335209 C T 1 0 0 0 0 1 0 0 0 5566 826 29 3 3 FBN2 5 128335209 Missense_Mutation SNP C C3N-01842_T 56615805 128335209 53203050 114 26306 TGFBI 0 . GRCh38 5 136046403 136046403 + Missense_Mutation SNP G G T rs541270955 C3N-01842_T C3N-01842_N G G c.367G>T p.Asp123Tyr p.D123Y ENST00000442011 4/17 122 101 21 215 215 0 strelka-varscan TGFBI,missense_variant,p.Asp123Tyr,ENST00000442011,NM_000358.2;TGFBI,upstream_gene_variant,,ENST00000514554,;TGFBI,upstream_gene_variant,,ENST00000604555,;TGFBI,upstream_gene_variant,,ENST00000508767,;TGFBI,non_coding_transcript_exon_variant,,ENST00000504185,;TGFBI,missense_variant,p.Asp96Tyr,ENST00000507018,;TGFBI,non_coding_transcript_exon_variant,,ENST00000515433,;TGFBI,non_coding_transcript_exon_variant,,ENST00000506699,;TGFBI,upstream_gene_variant,,ENST00000509749,; T ENST00000442011 Transcript missense_variant 528/2804 367/2052 123/683 D/Y Gac/Tac rs541270955,CM033817 1 1 TGFBI HGNC HGNC:11771 protein_coding YES CCDS47266.1 ENSP00000416330 Q15582 A0A0S2Z4Q2 UPI0000000C6A NM_000358.2 deleterious(0) 4/17 Gene3D:2.30.180.10,Pfam_domain:PF02469,PIRSF_domain:PIRSF016553,PROSITE_profiles:PS50213,hmmpanther:PTHR10900,hmmpanther:PTHR10900:SF82,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 136046403 136046403 G T 1 0 0 0 0 1 0 0 0 16253 1174 41 2 2 TGFBI 5 136046403 Missense_Mutation SNP G C3N-01842_T 7711194 136046403 45491856 115 26307 TRPC7 0 . GRCh38 5 136274694 136274694 + Silent SNP A A G novel C3N-01842_T C3N-01842_N A A c.1107T>C p.= p.Y369Y ENST00000513104 4/12 169 121 48 249 249 0 strelka-varscan TRPC7,synonymous_variant,p.=,ENST00000513104,NM_020389.2;TRPC7,synonymous_variant,p.=,ENST00000378459,NM_001167577.1;TRPC7,intron_variant,,ENST00000502753,;TRPC7,intron_variant,,ENST00000352189,NM_001167576.1;TRPC7,synonymous_variant,p.=,ENST00000503275,;TRPC7,intron_variant,,ENST00000514963,; G ENST00000513104 Transcript synonymous_variant 1390/2987 1107/2589 369/862 Y taT/taC 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 4/12 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9,TIGRFAM_domain:TIGR00870,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 136274694 136274694 A G 1 0 0 0 0 0 0 0 1 17090 108 4 5 5 TRPC7 5 136274694 Silent SNP A C3N-01842_T 228291 136274694 45263565 116 26308 PCDHA6 0 . GRCh38 5 140829059 140829059 + Frame_Shift_Del DEL C C - novel C3N-01842_T C3N-01842_N C C c.968delC p.Thr323ArgfsTer15 p.T323Rfs*15 ENST00000529310 1/4 167 117 50 281 281 0 sindel-varindel PCDHA6,frameshift_variant,p.Thr323ArgfsTer15,ENST00000529310,NM_018909.3;PCDHA6,frameshift_variant,p.Thr323ArgfsTer15,ENST00000378126,NM_031848.2;PCDHA6,frameshift_variant,p.Thr323ArgfsTer15,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA5,downstream_gene_variant,,ENST00000614258,NM_031501.1; - ENST00000529310 Transcript frameshift_variant 1082/5374 968/2853 323/950 T/X aCg/ag 1 1 PCDHA6 HGNC HGNC:8672 protein_coding YES CCDS47281.1 ENSP00000433378 Q9UN73 UPI00001273CE NM_018909.3 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF131,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 140829059 140829059 C - 1 0 1 0 1 0 0 0 0 11615 536 19 0 0 PCDHA6 5 140829059 Frame_Shift_Del DEL C C3N-01842_T 4554365 140829059 40709200 117 26309 PCDHB12 0 . GRCh38 5 141211193 141211193 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.2286T>A p.Asn762Lys p.N762K ENST00000239450 1/1 149 104 45 234 234 0 strelka-varscan PCDHB12,missense_variant,p.Asn762Lys,ENST00000239450,NM_018932.3;PCDHB12,missense_variant,p.Asn425Lys,ENST00000624949,;PCDHB12,3_prime_UTR_variant,,ENST00000622978,;PCDHB13,upstream_gene_variant,,ENST00000341948,NM_018933.3;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239450 Transcript missense_variant 2475/3853 2286/2388 762/795 N/K aaT/aaA 1 1 PCDHB12 HGNC HGNC:8683 protein_coding YES CCDS4254.1 ENSP00000239450 Q9Y5F1 UPI000000DAFD NM_018932.3 deleterious_low_confidence(0.05) 1/1 hmmpanther:PTHR24028:SF59,hmmpanther:PTHR24028,Pfam_domain:PF16492 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 141211193 141211193 T A 1 0 0 0 0 1 0 0 0 11624 1403 49 4 4 PCDHB12 5 141211193 Missense_Mutation SNP T C3N-01842_T 382134 141211193 40327066 118 26310 JAKMIP2 0 . GRCh38 5 147648417 147648417 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.895G>C p.Glu299Gln p.E299Q ENST00000616793 5/22 207 152 55 253 253 0 strelka-varscan JAKMIP2,missense_variant,p.Glu299Gln,ENST00000616793,NM_001270941.1;JAKMIP2,missense_variant,p.Glu299Gln,ENST00000265272,NM_014790.4;JAKMIP2,missense_variant,p.Glu299Gln,ENST00000507386,NM_001270934.1;JAKMIP2,missense_variant,p.Glu257Gln,ENST00000333010,NM_001282282.1;JAKMIP2-AS1,intron_variant,,ENST00000626945,;JAKMIP2-AS1,intron_variant,,ENST00000627433,;JAKMIP2-AS1,intron_variant,,ENST00000630514,;JAKMIP2-AS1,intron_variant,,ENST00000630801,;JAKMIP2,non_coding_transcript_exon_variant,,ENST00000507343,;JAKMIP2,upstream_gene_variant,,ENST00000504845,; G ENST00000616793 Transcript missense_variant 1436/9272 895/2463 299/820 E/Q Gaa/Caa 1 -1 JAKMIP2 HGNC HGNC:29067 protein_coding YES CCDS75352.1 ENSP00000479248 Q96AA8 UPI0000E5AC9B NM_001270941.1 deleterious(0) 5/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 147648417 147648417 C G 1 0 0 0 0 1 0 0 0 7854 922 32 4 4 JAKMIP2 5 147648417 Missense_Mutation SNP C C3N-01842_T 6437224 147648417 33889842 119 26311 CDHR2 0 . GRCh38 5 176576145 176576145 + Missense_Mutation SNP C C A rs757549133 C3N-01842_T C3N-01842_N C C c.1154C>A p.Pro385His p.P385H ENST00000510636 12/32 195 127 68 240 240 0 strelka-varscan CDHR2,missense_variant,p.Pro385His,ENST00000510636,NM_001171976.1;CDHR2,missense_variant,p.Pro385His,ENST00000261944,NM_017675.4;CDHR2,missense_variant,p.Pro385His,ENST00000506348,; A ENST00000510636 Transcript missense_variant 1428/4509 1154/3933 385/1310 P/H cCc/cAc rs757549133 1 1 CDHR2 HGNC HGNC:18231 protein_coding YES CCDS34297.1 ENSP00000424565 Q9BYE9 UPI0000DBEE8C NM_001171976.1 deleterious(0) 12/32 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 176576145 176576145 C A 1 0 0 0 0 1 0 0 0 2822 623 22 2 2 CDHR2 5 176576145 Missense_Mutation SNP C C3N-01842_T 28927728 176576145 4962114 120 26312 F13A1 0 . GRCh38 6 6266637 6266637 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.492C>A p.= p.V164V ENST00000264870 4/15 893 776 117 635 633 2 strelka-varscan-mutect F13A1,synonymous_variant,p.=,ENST00000264870,NM_000129.3;F13A1,downstream_gene_variant,,ENST00000431222,;F13A1,downstream_gene_variant,,ENST00000414279,;F13A1,non_coding_transcript_exon_variant,,ENST00000479211,; T ENST00000264870 Transcript synonymous_variant 758/3999 492/2199 164/732 V gtC/gtA 1 -1 F13A1 HGNC HGNC:3531 protein_coding YES CCDS4496.1 ENSP00000264870 P00488 UPI000013D585 NM_000129.3 4/15 Gene3D:2.60.40.10,Pfam_domain:PF00868,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF42,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 6266637 6266637 G T 1 0 0 0 0 0 0 0 1 5208 929 33 2 2 F13A1 6 6266637 Silent SNP G C3N-01842_T 6266637 164539342 121 26313 WDR46 0 . GRCh38 6 33288814 33288814 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.269G>T p.Gly90Val p.G90V ENST00000374617 2/15 281 233 48 301 299 2 strelka-varscan-mutect WDR46,missense_variant,p.Gly90Val,ENST00000374617,NM_001164267.1,NM_005452.5;WDR46,missense_variant,p.Gly25Val,ENST00000444176,;RGL2,downstream_gene_variant,,ENST00000497454,NM_004761.4,NM_001243738.1;PFDN6,upstream_gene_variant,,ENST00000463584,;PFDN6,upstream_gene_variant,,ENST00000395131,;PFDN6,upstream_gene_variant,,ENST00000374606,NM_001185181.2;PFDN6,upstream_gene_variant,,ENST00000374607,NM_014260.3,NM_001265595.1,NM_001265596.1;PFDN6,upstream_gene_variant,,ENST00000374610,;PFDN6,upstream_gene_variant,,ENST00000622807,;WDR46,upstream_gene_variant,,ENST00000622788,;WDR46,non_coding_transcript_exon_variant,,ENST00000477718,;WDR46,non_coding_transcript_exon_variant,,ENST00000468157,;RGL2,downstream_gene_variant,,ENST00000437840,;RGL2,downstream_gene_variant,,ENST00000491168,;RGL2,downstream_gene_variant,,ENST00000471319,;B3GALT4,downstream_gene_variant,,ENST00000606990,;WDR46,non_coding_transcript_exon_variant,,ENST00000481025,;RGL2,downstream_gene_variant,,ENST00000483151,;RGL2,downstream_gene_variant,,ENST00000476616,;WDR46,upstream_gene_variant,,ENST00000489905,;PFDN6,upstream_gene_variant,,ENST00000491382,;PFDN6,upstream_gene_variant,,ENST00000395134,;WDR46,upstream_gene_variant,,ENST00000488944,; A ENST00000374617 Transcript missense_variant 626/2358 269/1833 90/610 G/V gGc/gTc 1 -1 WDR46 HGNC HGNC:13923 protein_coding YES CCDS4772.1 ENSP00000363746 O15213 UPI000045741F NM_001164267.1,NM_005452.5 tolerated(0.64) 2/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 33288814 33288814 C A 1 0 0 0 0 1 0 0 0 17859 739 26 2 2 WDR46 6 33288814 Missense_Mutation SNP C C3N-01842_T 27022177 33288814 137517165 122 26314 DNAH8 0 . GRCh38 6 38917264 38917264 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.10166C>T p.Thr3389Ile p.T3389I ENST00000327475 69/93 134 110 24 147 147 0 strelka-varscan-mutect DNAH8,missense_variant,p.Thr3389Ile,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Thr3172Ile,ENST00000359357,;DNAH8,missense_variant,p.Thr3389Ile,ENST00000449981,; T ENST00000327475 Transcript missense_variant 10275/14360 10166/14124 3389/4707 T/I aCa/aTa 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 69/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF12777 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 38917264 38917264 C T 1 0 0 0 0 1 0 0 0 4422 478 17 3 3 DNAH8 6 38917264 Missense_Mutation SNP C C3N-01842_T 5628450 38917264 131888715 123 26315 DNAH8 0 . GRCh38 6 38923083 38923083 + Missense_Mutation SNP G G C C3N-01842_T C3N-01842_N G G c.10688G>C p.Cys3563Ser p.C3563S ENST00000327475 72/93 275 227 48 293 292 1 strelka-varscan-mutect DNAH8,missense_variant,p.Cys3563Ser,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Cys3346Ser,ENST00000359357,;DNAH8,missense_variant,p.Cys3563Ser,ENST00000449981,;RP1-207H1.3,non_coding_transcript_exon_variant,,ENST00000416948,;RP1-207H1.3,non_coding_transcript_exon_variant,,ENST00000418399,;RP1-207H1.2,upstream_gene_variant,,ENST00000407768,; C ENST00000327475 Transcript missense_variant 10797/14360 10688/14124 3563/4707 C/S tGc/tCc COSM1444307,COSM1444308,COSM5136727 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 72/93 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF280,Pfam_domain:PF12777 1,1,1 MODERATE SNV 5 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 38923083 38923083 G C 1 0 0 0 0 1 0 0 0 4422 1319 46 4 4 DNAH8 6 38923083 Missense_Mutation SNP G C3N-01842_T 5819 38923083 131882896 124 26316 TRERF1 0 . GRCh38 6 42228512 42228512 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.3496C>T p.Pro1166Ser p.P1166S ENST00000541110 18/18 427 326 101 491 490 1 strelka-varscan-mutect TRERF1,missense_variant,p.Pro1166Ser,ENST00000541110,NM_001297573.1,NM_001297574.1;TRERF1,missense_variant,p.Pro1146Ser,ENST00000372922,NM_033502.3;TRERF1,missense_variant,p.Pro1075Ser,ENST00000340840,;TRERF1,missense_variant,p.Pro1063Ser,ENST00000354325,;TRERF1,missense_variant,p.Pro902Ser,ENST00000372917,; A ENST00000541110 Transcript missense_variant 4065/7646 3496/3663 1166/1220 P/S Ccc/Tcc 1 -1 TRERF1 HGNC HGNC:18273 protein_coding YES CCDS75455.1 ENSP00000439689 Q05GC8 UPI000022CBC8 NM_001297573.1,NM_001297574.1 deleterious_low_confidence(0) 18/18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 42228512 42228512 G A 1 0 0 0 0 1 0 0 0 16964 1203 42 3 3 TRERF1 6 42228512 Missense_Mutation SNP G C3N-01842_T 3305429 42228512 128577467 125 26317 XPO5 0 . GRCh38 6 43575836 43575836 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.29G>C p.Cys10Ser p.C10S ENST00000265351 1/32 169 131 38 168 168 0 strelka-varscan-mutect XPO5,missense_variant,p.Cys10Ser,ENST00000265351,NM_020750.2;POLH,upstream_gene_variant,,ENST00000372236,NM_006502.2;POLH,upstream_gene_variant,,ENST00000372226,NM_001291970.1;POLH,upstream_gene_variant,,ENST00000443535,;XPO5,missense_variant,p.Cys10Ser,ENST00000398799,; G ENST00000265351 Transcript missense_variant 240/5364 29/3615 10/1204 C/S tGc/tCc 1 -1 XPO5 HGNC HGNC:17675 protein_coding YES CCDS47430.1 ENSP00000265351 Q9HAV4 UPI000006CC97 NM_020750.2 deleterious(0.01) 1/32 hmmpanther:PTHR11223,hmmpanther:PTHR11223:SF3,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 43575836 43575836 C G 1 0 0 0 0 1 0 0 0 18006 710 25 4 4 XPO5 6 43575836 Missense_Mutation SNP C C3N-01842_T 1347324 43575836 127230143 126 26318 AARS2 0 . GRCh38 6 44300593 44300593 + Missense_Mutation SNP T T G novel C3N-01842_T C3N-01842_N T T c.2912A>C p.Glu971Ala p.E971A ENST00000244571 22/22 543 442 101 676 675 1 strelka-varscan-mutect AARS2,missense_variant,p.Glu971Ala,ENST00000244571,NM_020745.3;TMEM151B,intron_variant,,ENST00000438774,;TCTE1,upstream_gene_variant,,ENST00000371505,NM_182539.3;AARS2,non_coding_transcript_exon_variant,,ENST00000491573,;RP11-444E17.6,intron_variant,,ENST00000505802,; G ENST00000244571 Transcript missense_variant 2915/3854 2912/2958 971/985 E/A gAa/gCa 1 -1 AARS2 HGNC HGNC:21022 protein_coding YES CCDS34464.1 ENSP00000244571 Q5JTZ9 UPI00001C1E5A NM_020745.3 tolerated(0.19) 22/22 HAMAP:MF_00036_B,hmmpanther:PTHR11777:SF8,hmmpanther:PTHR11777 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 44300593 44300593 T G 1 0 0 0 0 1 0 0 0 24 1783 62 5 5 AARS2 6 44300593 Missense_Mutation SNP T C3N-01842_T 724757 44300593 126505386 127 26319 PGK2 0 . GRCh38 6 49786339 49786339 + Silent SNP A A T novel C3N-01842_T C3N-01842_N A A c.849T>A p.= p.P283P ENST00000304801 1/1 448 333 115 409 409 0 strelka-varscan-mutect PGK2,synonymous_variant,p.=,ENST00000304801,NM_138733.4; T ENST00000304801 Transcript synonymous_variant 969/1657 849/1254 283/417 P ccT/ccA 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 LOW 1 SNV 1 PASS rs35254270 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 49786339 49786339 A T 1 0 0 0 0 0 0 0 1 11880 175 7 4 4 PGK2 6 49786339 Silent SNP A C3N-01842_T 5485746 49786339 121019640 128 26320 PKHD1 0 . GRCh38 6 51746777 51746777 + Silent SNP G G T rs773916989 C3N-01842_T C3N-01842_N G G c.9942C>A p.= p.T3314T ENST00000371117 59/67 439 360 79 364 363 1 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; T ENST00000371117 Transcript synonymous_variant 10218/16282 9942/12225 3314/4074 T acC/acA rs773916989 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 59/67 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF299 LOW 1 SNV 1 1 PASS rs773916989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 51746777 51746777 G T 1 0 0 0 0 0 0 0 1 12067 1335 47 2 2 PKHD1 6 51746777 Silent SNP G C3N-01842_T 1960438 51746777 119059202 129 26321 GCM1 0 . GRCh38 6 53130876 53130876 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.497G>T p.Arg166Ile p.R166I ENST00000259803 5/6 299 246 53 330 330 0 strelka-varscan-mutect GCM1,missense_variant,p.Arg166Ile,ENST00000259803,NM_003643.3;RP11-506E9.3,upstream_gene_variant,,ENST00000566420,; A ENST00000259803 Transcript missense_variant 709/2765 497/1311 166/436 R/I aGa/aTa 1 -1 GCM1 HGNC HGNC:4197 protein_coding YES CCDS4950.1 ENSP00000259803 Q9NP62 UPI0000073F99 NM_003643.3 deleterious(0) 5/6 Superfamily_domains:0041800,PD014393,Pfam_domain:PF03615,PROSITE_profiles:PS50807,hmmpanther:PTHR12414,hmmpanther:PTHR12414:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 53130876 53130876 C A 1 0 0 0 0 1 0 0 0 6167 913 32 2 2 GCM1 6 53130876 Missense_Mutation SNP C C3N-01842_T 1384099 53130876 117675103 130 26322 EYS 0 . GRCh38 6 65405211 65405211 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.1019C>T p.Pro340Leu p.P340L ENST00000370621 6/44 323 259 64 244 242 2 strelka-varscan-mutect EYS,missense_variant,p.Pro340Leu,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Pro340Leu,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Pro340Leu,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Pro340Leu,ENST00000342421,NM_198283.1; A ENST00000370621 Transcript missense_variant 1546/10485 1019/9498 340/3165 P/L cCa/cTa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.1) 6/44 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 65405211 65405211 G A 1 0 0 0 0 1 0 0 0 5200 1348 47 3 3 EYS 6 65405211 Missense_Mutation SNP G C3N-01842_T 12274335 65405211 105400768 131 26323 EYS 0 . GRCh38 6 65494821 65494821 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.590C>A p.Thr197Lys p.T197K ENST00000370621 4/44 253 205 48 247 247 0 strelka-varscan-mutect EYS,missense_variant,p.Thr197Lys,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Thr197Lys,ENST00000370621,NM_001292009.1;EYS,missense_variant,p.Thr197Lys,ENST00000393380,NM_001142801.1;EYS,missense_variant,p.Thr197Lys,ENST00000342421,NM_198283.1;EYS,missense_variant,p.Thr94Lys,ENST00000471279,;EYS,non_coding_transcript_exon_variant,,ENST00000489873,; T ENST00000370621 Transcript missense_variant 1117/10485 590/9498 197/3165 T/K aCa/aAa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.24) 4/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 65494821 65494821 G T 1 0 0 0 0 1 0 0 0 5200 1377 48 2 2 EYS 6 65494821 Missense_Mutation SNP G C3N-01842_T 89610 65494821 105311158 132 26324 COL19A1 0 . GRCh38 6 69898978 69898978 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.122G>T p.Gly41Val p.G41V ENST00000620364 3/51 250 201 49 195 195 0 strelka-varscan-mutect COL19A1,missense_variant,p.Gly41Val,ENST00000620364,NM_001858.5; T ENST00000620364 Transcript missense_variant 224/6233 122/3429 41/1142 G/V gGa/gTa 1 1 COL19A1 HGNC HGNC:2196 protein_coding YES CCDS4970.1 ENSP00000480474 Q14993 UPI000004F1E3 NM_001858.5 tolerated(0.26) 3/51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 69898978 69898978 G T 1 0 0 0 0 1 0 0 0 3464 1174 41 2 2 COL19A1 6 69898978 Missense_Mutation SNP G C3N-01842_T 4404157 69898978 100907001 133 26325 MDN1 0 . GRCh38 6 89729026 89729026 + Nonsense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.5254G>T p.Glu1752Ter p.E1752* ENST00000369393 36/102 617 493 124 557 556 1 strelka-varscan-mutect MDN1,stop_gained,p.Glu1752Ter,ENST00000369393,NM_014611.2;MDN1,stop_gained,p.Glu1752Ter,ENST00000629399,; A ENST00000369393 Transcript stop_gained 5370/18413 5254/16791 1752/5596 E/* Gag/Tag 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 36/102 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64,SMART_domains:SM00382,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 89729026 89729026 C A 1 0 0 0 0 0 1 0 0 9353 864 30 2 2 MDN1 6 89729026 Nonsense_Mutation SNP C C3N-01842_T 19830048 89729026 81076953 134 26326 GPRC6A 0 . GRCh38 6 116792744 116792744 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.2179G>A p.Ala727Thr p.A727T ENST00000310357 6/6 186 157 29 185 185 0 strelka-varscan-mutect GPRC6A,missense_variant,p.Ala727Thr,ENST00000310357,NM_148963.3;GPRC6A,missense_variant,p.Ala656Thr,ENST00000368549,NM_001286355.1;GPRC6A,missense_variant,p.Ala552Thr,ENST00000530250,NM_001286354.1; T ENST00000310357 Transcript missense_variant 2201/2860 2179/2781 727/926 A/T Gca/Aca 1 -1 GPRC6A HGNC HGNC:18510 protein_coding YES CCDS5112.1 ENSP00000309493 Q5T6X5 UPI000013EFF9 NM_148963.3 tolerated(0.25) 6/6 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50259,hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF5,Pfam_domain:PF00003,Prints_domain:PR00248 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 116792744 116792744 C T 1 0 0 0 0 1 0 0 0 6607 797 28 3 3 GPRC6A 6 116792744 Missense_Mutation SNP C C3N-01842_T 27063718 116792744 54013235 135 26327 RFX6 0 . GRCh38 6 116931469 116931469 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.2750A>G p.Asn917Ser p.N917S ENST00000332958 19/19 342 256 86 312 312 0 strelka-varscan-mutect RFX6,missense_variant,p.Asn917Ser,ENST00000332958,NM_173560.3; G ENST00000332958 Transcript missense_variant 2766/3460 2750/2787 917/928 N/S aAc/aGc 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 deleterious_low_confidence(0) 19/19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 116931469 116931469 A G 1 0 0 0 0 1 0 0 0 13441 43 2 5 5 RFX6 6 116931469 Missense_Mutation SNP A C3N-01842_T 138725 116931469 53874510 136 26328 ARFGEF3 0 . GRCh38 6 138298693 138298693 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.3736G>C p.Glu1246Gln p.E1246Q ENST00000251691 22/34 180 134 46 301 301 0 strelka-varscan-mutect ARFGEF3,missense_variant,p.Glu1246Gln,ENST00000251691,NM_020340.4; C ENST00000251691 Transcript missense_variant 3902/14877 3736/6534 1246/2177 E/Q Gag/Cag 1 1 ARFGEF3 HGNC HGNC:21213 protein_coding YES CCDS5189.2 ENSP00000251691 Q5TH69 UPI000150AF4A NM_020340.4 deleterious(0) 22/34 Pfam_domain:PF09324 MODERATE 1 SNV 1 1 PASS rs1206143842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 138298693 138298693 G C 1 0 0 0 0 1 0 0 0 977 1291 45 4 4 ARFGEF3 6 138298693 Missense_Mutation SNP G C3N-01842_T 21367224 138298693 32507286 137 26329 TXLNB 0 . GRCh38 6 139288733 139288733 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.167C>T p.Ser56Phe p.S56F ENST00000358430 2/10 505 457 48 641 641 0 strelka-varscan-mutect TXLNB,missense_variant,p.Ser56Phe,ENST00000358430,NM_153235.3;RP11-445F6.2,downstream_gene_variant,,ENST00000441249,;RP11-445F6.2,downstream_gene_variant,,ENST00000440518,; A ENST00000358430 Transcript missense_variant 400/4753 167/2055 56/684 S/F tCt/tTt 1 -1 TXLNB HGNC HGNC:21617 protein_coding YES CCDS34545.1 ENSP00000351206 Q8N3L3 UPI0000072983 NM_153235.3 deleterious(0) 2/10 hmmpanther:PTHR16127,hmmpanther:PTHR16127:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 139288733 139288733 G A 1 0 0 0 0 1 0 0 0 17304 942 33 3 3 TXLNB 6 139288733 Missense_Mutation SNP G C3N-01842_T 990040 139288733 31517246 138 26330 NMBR 0 . GRCh38 6 142088484 142088484 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.175C>T p.= p.L59L ENST00000258042 1/3 470 425 45 625 625 0 strelka-varscan-mutect NMBR,synonymous_variant,p.=,ENST00000258042,NM_002511.2;RP11-137J7.2,intron_variant,,ENST00000454401,; A ENST00000258042 Transcript synonymous_variant 316/1354 175/1173 59/390 L Ctg/Ttg 1 -1 NMBR HGNC HGNC:7843 protein_coding YES CCDS5196.1 ENSP00000258042 P28336 UPI000013CFAB NM_002511.2 1/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF53,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 142088484 142088484 G A 1 0 0 0 0 0 0 0 1 10525 962 34 3 3 NMBR 6 142088484 Silent SNP G C3N-01842_T 2799751 142088484 28717495 139 26331 SHPRH 0 . GRCh38 6 145941688 145941688 + Missense_Mutation SNP C C G rs555121048 C3N-01842_T C3N-01842_N C C c.2425G>C p.Val809Leu p.V809L ENST00000367505 10/30 322 233 89 419 419 0 strelka-varscan-mutect SHPRH,missense_variant,p.Val809Leu,ENST00000629427,;SHPRH,missense_variant,p.Val809Leu,ENST00000367505,;SHPRH,missense_variant,p.Val809Leu,ENST00000438092,NM_173082.3;SHPRH,missense_variant,p.Val809Leu,ENST00000275233,NM_001042683.2;SHPRH,3_prime_UTR_variant,,ENST00000367503,;SHPRH,missense_variant,p.Val698Leu,ENST00000519632,;SHPRH,3_prime_UTR_variant,,ENST00000433355,;SHPRH,downstream_gene_variant,,ENST00000521977,; G ENST00000367505 Transcript missense_variant 2690/7201 2425/5052 809/1683 V/L Gta/Cta rs555121048 1 -1 SHPRH HGNC HGNC:19336 protein_coding YES CCDS43513.2 ENSP00000356475 Q149N8 UPI0000458A24 tolerated(0.14) 10/30 hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF552,Pfam_domain:PF00176,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs555121048 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 145941688 145941688 C G 1 0 0 0 0 1 0 0 0 14554 507 18 4 4 SHPRH 6 145941688 Missense_Mutation SNP C C3N-01842_T 3853204 145941688 24864291 140 26332 OPRM1 0 . GRCh38 6 154090082 154090082 + Missense_Mutation SNP C C A rs199564389 C3N-01842_T C3N-01842_N C C c.826C>A p.Pro276Thr p.P276T ENST00000434900 4/6 343 295 48 426 424 2 strelka-varscan-mutect OPRM1,missense_variant,p.Pro183Thr,ENST00000414028,NM_001145284.3;OPRM1,missense_variant,p.Pro83Thr,ENST00000522236,NM_001145287.2;OPRM1,missense_variant,p.Pro83Thr,ENST00000522555,NM_001285526.1;OPRM1,missense_variant,p.Pro183Thr,ENST00000435918,NM_001145283.2;OPRM1,missense_variant,p.Pro183Thr,ENST00000330432,NM_000914.4;OPRM1,missense_variant,p.Pro276Thr,ENST00000434900,NM_001145279.3,NM_001285524.1;OPRM1,missense_variant,p.Pro245Thr,ENST00000360422,NM_001285523.1;OPRM1,missense_variant,p.Pro83Thr,ENST00000520708,NM_001145280.3;OPRM1,missense_variant,p.Pro183Thr,ENST00000428397,NM_001008504.3;OPRM1,missense_variant,p.Pro183Thr,ENST00000229768,NM_001008505.2;OPRM1,missense_variant,p.Pro183Thr,ENST00000419506,NM_001145286.2;OPRM1,missense_variant,p.Pro183Thr,ENST00000337049,NM_001008503.2;OPRM1,missense_variant,p.Pro183Thr,ENST00000452687,NM_001145282.2;OPRM1,missense_variant,p.Pro183Thr,ENST00000524163,NM_001145285.2;OPRM1,missense_variant,p.Pro102Thr,ENST00000518759,NM_001145281.2;OPRM1,downstream_gene_variant,,ENST00000520282,;OPRM1,non_coding_transcript_exon_variant,,ENST00000522382,;OPRM1,non_coding_transcript_exon_variant,,ENST00000519613,;OPRM1,non_coding_transcript_exon_variant,,ENST00000521106,;OPRM1,missense_variant,p.Pro183Thr,ENST00000519083,;OPRM1,missense_variant,p.Pro183Thr,ENST00000522739,;OPRM1,intron_variant,,ENST00000524150,; A ENST00000434900 Transcript missense_variant 1344/2033 826/1482 276/493 P/T Ccc/Acc rs199564389,COSM341436,COSM341437,COSM341438,COSM4510080,COSM4510081,COSM4510082,COSM4510083,COSM4510084,COSM4510085 1 1 OPRM1 HGNC HGNC:8156 protein_coding YES CCDS47503.1 ENSP00000394624 P35372 UPI0001899627 NM_001145279.3,NM_001285524.1 deleterious(0.01) 4/6 PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF7,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00384 0,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1,1,1,1,1,1 1 PASS rs199564389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 154090082 154090082 C A 1 0 0 0 0 1 0 0 0 10962 855 30 2 2 OPRM1 6 154090082 Missense_Mutation SNP C C3N-01842_T 8148394 154090082 16715897 141 26333 T 0 . GRCh38 6 166158546 166158546 + Silent SNP G G T rs775111459 C3N-01842_T C3N-01842_N G G c.1077C>A p.= p.T359T ENST00000296946 9/9 89 79 10 109 109 0 strelka-varscan-mutect T,synonymous_variant,p.=,ENST00000296946,NM_003181.3;T,synonymous_variant,p.=,ENST00000366871,NM_001270484.1;T,synonymous_variant,p.=,ENST00000366876,; T ENST00000296946 Transcript synonymous_variant 1546/2436 1077/1308 359/435 T acC/acA rs775111459 1 -1 T HGNC HGNC:11515 protein_coding YES CCDS5290.1 ENSP00000296946 O15178 UPI0000126AB5 NM_003181.3 9/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF83 LOW 1 SNV 5 1 PASS rs775111459 . 0 201 7 0 0 0 0 2 -3.743282 0 0 1 0 0 T 2 4 84 166158546 166158546 G T 1 0 0 0 0 0 0 0 1 15884 1219 43 2 2 T 6 166158546 Silent SNP G C3N-01842_T 12068464 166158546 4647433 142 26334 CCR6 0 . GRCh38 6 167137302 167137302 + Silent SNP C C A rs188414355 C3N-01842_T C3N-01842_N C C c.1072C>A p.= p.R358R ENST00000341935 3/3 214 158 56 272 272 0 strelka-varscan-mutect CCR6,synonymous_variant,p.=,ENST00000341935,NM_031409.3;CCR6,synonymous_variant,p.=,ENST00000400926,NM_004367.5;CCR6,synonymous_variant,p.=,ENST00000349984,;RP11-517H2.6,non_coding_transcript_exon_variant,,ENST00000609590,; A ENST00000341935 Transcript synonymous_variant 1624/4018 1072/1125 358/374 R Cgg/Agg rs188414355,COSM3622816 1 1 CCR6 HGNC HGNC:1607 protein_coding YES CCDS5298.1 ENSP00000343952 P51684 UPI00000008CE NM_031409.3 3/3 hmmpanther:PTHR10489,Prints_domain:PR01529 0,1 LOW 1 SNV 1 0,1 1 PASS rs188414355 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 167137302 167137302 C A 1 0 0 0 0 0 0 0 1 2645 875 31 1 1 CCR6 6 167137302 Silent SNP C C3N-01842_T 978756 167137302 3668677 143 26335 KIF25 0 . GRCh38 6 168033902 168033902 + Missense_Mutation SNP C C A rs757300108 C3N-01842_T C3N-01842_N C C c.188C>A p.Ala63Glu p.A63E ENST00000443060 5/10 197 149 48 218 216 2 strelka-varscan-mutect KIF25,missense_variant,p.Ala63Glu,ENST00000443060,;KIF25,missense_variant,p.Ala63Glu,ENST00000354419,NM_030615.2;KIF25,missense_variant,p.Ala63Glu,ENST00000351261,NM_005355.3;KIF25,upstream_gene_variant,,ENST00000496008,;KIF25,downstream_gene_variant,,ENST00000515361,;KIF25,non_coding_transcript_exon_variant,,ENST00000504593,; A ENST00000443060 Transcript missense_variant 579/1613 188/1155 63/384 A/E gCg/gAg rs757300108 1 1 KIF25 HGNC HGNC:6390 protein_coding YES CCDS5305.1 ENSP00000388878 Q9UIL4 UPI000012DDAB deleterious(0) 5/10 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF421,Gene3D:3.40.850.10,Pfam_domain:PF00225,SMART_domains:SM00129,Superfamily_domains:SSF52540,Prints_domain:PR00380 MODERATE 1 SNV 5 1 PASS rs757300108 . 0 205 0 5 0 0 0 0 -20 0.9998198 1 1 1 0 A 3 1 84 168033902 168033902 C A 1 0 0 0 0 1 0 0 0 8158 768 27 1 1 KIF25 6 168033902 Missense_Mutation SNP C C3N-01842_T 896600 168033902 2772077 144 26336 KIF25 0 . GRCh38 6 168041981 168041981 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.659G>C p.Cys220Ser p.C220S ENST00000443060 8/10 126 92 34 194 194 0 strelka-varscan-mutect KIF25,missense_variant,p.Cys220Ser,ENST00000443060,;KIF25,missense_variant,p.Cys220Ser,ENST00000354419,NM_030615.2;KIF25,missense_variant,p.Cys220Ser,ENST00000351261,NM_005355.3; C ENST00000443060 Transcript missense_variant 1050/1613 659/1155 220/384 C/S tGc/tCc 1 1 KIF25 HGNC HGNC:6390 protein_coding YES CCDS5305.1 ENSP00000388878 Q9UIL4 UPI000012DDAB tolerated(0.45) 8/10 PROSITE_profiles:PS50067,Pfam_domain:PF00225,SMART_domains:SM00129 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 168041981 168041981 G C 1 0 0 0 0 1 0 0 0 8158 1319 46 4 4 KIF25 6 168041981 Missense_Mutation SNP G C3N-01842_T 8079 168041981 2763998 145 26337 SDK1 0 . GRCh38 7 4079506 4079506 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.3246C>A p.Ser1082Arg p.S1082R ENST00000404826 22/45 209 173 36 260 259 1 strelka-varscan-mutect SDK1,missense_variant,p.Ser1082Arg,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Ser1082Arg,ENST00000615806,;SDK1,missense_variant,p.Ser1082Arg,ENST00000389531,; A ENST00000404826 Transcript missense_variant 3385/10397 3246/6642 1082/2213 S/R agC/agA 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 deleterious(0.04) 22/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs1458568305 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 4079506 4079506 C A 1 0 0 0 0 1 0 0 0 14243 738 26 2 2 SDK1 7 4079506 Missense_Mutation SNP C C3N-01842_T 4079506 155266467 146 26338 SCIN 0 . GRCh38 7 12578189 12578189 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.325A>G p.Ser109Gly p.S109G ENST00000297029 2/16 156 125 31 152 152 0 strelka-varscan-mutect SCIN,missense_variant,p.Ser109Gly,ENST00000297029,NM_001112706.2;SCIN,missense_variant,p.Ser136Gly,ENST00000417018,;SCIN,missense_variant,p.Ser109Gly,ENST00000341757,;SCIN,downstream_gene_variant,,ENST00000436854,; G ENST00000297029 Transcript missense_variant 426/9713 325/2148 109/715 S/G Agc/Ggc 1 1 SCIN HGNC HGNC:21695 protein_coding YES CCDS47545.1 ENSP00000297029 Q9Y6U3 UPI000013C4DF NM_001112706.2 tolerated(1) 2/16 Gene3D:3.40.20.10,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF14,SMART_domains:SM00262,Superfamily_domains:SSF55753 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 12578189 12578189 A G 1 0 0 0 0 1 0 0 0 14174 420 15 5 5 SCIN 7 12578189 Missense_Mutation SNP A C3N-01842_T 8498683 12578189 146767784 147 26339 CHN2 0 . GRCh38 7 29398456 29398456 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.260G>T p.Arg87Leu p.R87L ENST00000222792 5/13 248 194 54 304 303 1 strelka-varscan-mutect CHN2,missense_variant,p.Arg87Leu,ENST00000222792,NM_004067.3,NM_001293071.1,NM_001293070.1,NM_001293072.1;CHN2,missense_variant,p.Arg87Leu,ENST00000495789,;CHN2,missense_variant,p.Arg162Leu,ENST00000439384,;CHN2,missense_variant,p.Arg87Leu,ENST00000539389,;CHN2,missense_variant,p.Arg87Leu,ENST00000539406,;CHN2,missense_variant,p.Arg100Leu,ENST00000409350,;CHN2,intron_variant,,ENST00000435288,;CHN2,upstream_gene_variant,,ENST00000446446,;CHN2,non_coding_transcript_exon_variant,,ENST00000409922,;CHN2,non_coding_transcript_exon_variant,,ENST00000412536,;CHN2,non_coding_transcript_exon_variant,,ENST00000409964,;CHN2,non_coding_transcript_exon_variant,,ENST00000482820,;CHN2,non_coding_transcript_exon_variant,,ENST00000478128,;CHN2,missense_variant,p.Gly121Cys,ENST00000474070,;CHN2,non_coding_transcript_exon_variant,,ENST00000491856,; T ENST00000222792 Transcript missense_variant 790/3530 260/1407 87/468 R/L cGg/cTg 1 1 CHN2 HGNC HGNC:1944 protein_coding YES CCDS5420.1 ENSP00000222792 P52757 UPI000012781F NM_004067.3,NM_001293071.1,NM_001293070.1,NM_001293072.1 deleterious(0.01) 5/13 PROSITE_profiles:PS50001,hmmpanther:PTHR23176,hmmpanther:PTHR23176:SF35,Pfam_domain:PF00017,PIRSF_domain:PIRSF038015,Gene3D:3.30.505.10,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS rs1454857779 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 29398456 29398456 G T 1 0 0 0 0 1 0 0 0 3123 1116 39 1 1 CHN2 7 29398456 Missense_Mutation SNP G C3N-01842_T 16820267 29398456 129947517 148 26340 POU6F2 0 . GRCh38 7 39085900 39085900 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.59C>T p.Ser20Leu p.S20L ENST00000403058 3/11 301 234 67 407 407 0 strelka-varscan-mutect POU6F2,missense_variant,p.Ser20Leu,ENST00000518318,NM_001166018.1;POU6F2,missense_variant,p.Ser12Leu,ENST00000559001,;POU6F2,missense_variant,p.Ser20Leu,ENST00000403058,NM_007252.3;POU6F2,missense_variant,p.Ser12Leu,ENST00000524147,;POU6F2,missense_variant,p.Ser12Leu,ENST00000520104,;POU6F2,missense_variant,p.Ser21Leu,ENST00000451021,;POU6F2,non_coding_transcript_exon_variant,,ENST00000517348,;POU6F2,non_coding_transcript_exon_variant,,ENST00000464276,; T ENST00000403058 Transcript missense_variant 213/2335 59/2076 20/691 S/L tCa/tTa 1 1 POU6F2 HGNC HGNC:21694 protein_coding YES CCDS34620.2 ENSP00000384004 P78424 UPI0000480E81 NM_007252.3 deleterious_low_confidence(0) 3/11 hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF68 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 39085900 39085900 C T 1 0 0 0 0 1 0 0 0 12401 838 29 3 3 POU6F2 7 39085900 Missense_Mutation SNP C C3N-01842_T 9687444 39085900 120260073 149 26341 HECW1 0 . GRCh38 7 43508999 43508999 + Missense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.3897C>A p.Phe1299Leu p.F1299L ENST00000395891 24/30 231 185 46 209 209 0 strelka-varscan-mutect HECW1,missense_variant,p.Phe1299Leu,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Phe1265Leu,ENST00000453890,NM_001287059.1;HECW1,intron_variant,,ENST00000429529,;AC011738.4,non_coding_transcript_exon_variant,,ENST00000436105,; A ENST00000395891 Transcript missense_variant 4502/9501 3897/4821 1299/1606 F/L ttC/ttA COSM261252,COSM4689935,COSM4689936 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 deleterious(0.03) 24/30 PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,SMART_domains:SM00119,Superfamily_domains:SSF56204 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 43508999 43508999 C A 1 0 0 0 0 1 0 0 0 6924 912 32 2 2 HECW1 7 43508999 Missense_Mutation SNP C C3N-01842_T 4423099 43508999 115836974 150 26342 POM121L12 0 . GRCh38 7 53036514 53036514 + Silent SNP C C A rs766989780 C3N-01842_T C3N-01842_N C C c.843C>A p.= p.V281V ENST00000408890 1/1 109 87 22 127 127 0 varscan-mutect POM121L12,synonymous_variant,p.=,ENST00000408890,NM_182595.3; A ENST00000408890 Transcript synonymous_variant 873/1283 843/891 281/296 V gtC/gtA rs766989780 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 LOW 1 SNV 1 PASS rs766989780 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 53036514 53036514 C A 1 0 0 0 0 0 0 0 1 12352 900 32 2 2 POM121L12 7 53036514 Silent SNP C C3N-01842_T 9527515 53036514 106309459 151 26343 WBSCR17 0 . GRCh38 7 71415961 71415961 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.662A>T p.Gln221Leu p.Q221L ENST00000333538 4/11 183 140 43 208 208 0 strelka-varscan-mutect WBSCR17,missense_variant,p.Gln221Leu,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Gln142Leu,ENST00000618959,;WBSCR17,downstream_gene_variant,,ENST00000447516,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; T ENST00000333538 Transcript missense_variant 1296/3884 662/1797 221/598 Q/L cAg/cTg 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 tolerated(0.06) 4/11 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 71415961 71415961 A T 1 0 0 0 0 1 0 0 0 17823 188 7 4 4 WBSCR17 7 71415961 Missense_Mutation SNP A C3N-01842_T 18379447 71415961 87930012 152 26344 SPDYE5 0 . GRCh38 7 75501540 75501540 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.934C>A p.Arg312Ser p.R312S ENST00000625065 6/8 256 190 66 312 311 1 strelka-varscan-mutect SPDYE5,missense_variant,p.Arg312Ser,ENST00000625065,;SPDYE5,missense_variant,p.Arg312Ser,ENST00000455862,;SPDYE5,intron_variant,,ENST00000624640,NM_001099435.2;PMS2P3,downstream_gene_variant,,ENST00000529061,; A ENST00000625065 Transcript missense_variant 1357/1700 934/1209 312/402 R/S Cgt/Agt 1 1 SPDYE5 HGNC HGNC:35464 protein_coding YES CCDS78241.1 ENSP00000485398 A0A096LPK5 UPI000387D8EA tolerated_low_confidence(0.48) 6/8 MODERATE 1 SNV 5 1 PASS rs1296859227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 75501540 75501540 C A 1 0 0 0 0 1 0 0 0 15381 768 27 1 1 SPDYE5 7 75501540 Missense_Mutation SNP C C3N-01842_T 4085579 75501540 83844433 153 26345 SPDYE5 0 . GRCh38 7 75501559 75501559 + Missense_Mutation SNP G G T rs782266846 C3N-01842_T C3N-01842_N G G c.953G>T p.Arg318Leu p.R318L ENST00000625065 6/8 431 359 72 545 543 2 strelka-varscan-mutect SPDYE5,missense_variant,p.Arg253Leu,ENST00000624640,NM_001099435.2;SPDYE5,missense_variant,p.Arg318Leu,ENST00000625065,;SPDYE5,missense_variant,p.Arg318Leu,ENST00000455862,;PMS2P3,downstream_gene_variant,,ENST00000529061,; T ENST00000625065 Transcript missense_variant 1376/1700 953/1209 318/402 R/L cGt/cTt rs782266846 1 1 SPDYE5 HGNC HGNC:35464 protein_coding YES CCDS78241.1 ENSP00000485398 A0A096LPK5 UPI000387D8EA tolerated_low_confidence(0.64) 6/8 MODERATE 1 SNV 5 1 PASS rs782266846 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 75501559 75501559 G T 1 0 0 0 0 1 0 0 0 15381 1145 40 1 1 SPDYE5 7 75501559 Missense_Mutation SNP G C3N-01842_T 19 75501559 83844414 154 26346 LMTK2 0 . GRCh38 7 98141398 98141398 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.233A>G p.Glu78Gly p.E78G ENST00000297293 3/14 176 142 34 161 160 1 varscan-mutect LMTK2,missense_variant,p.Glu78Gly,ENST00000297293,NM_014916.3;LMTK2,splice_region_variant,,ENST00000493372,; G ENST00000297293 Transcript missense_variant,splice_region_variant 526/8946 233/4512 78/1503 E/G gAa/gGa 1 1 LMTK2 HGNC HGNC:17880 protein_coding YES CCDS5654.1 ENSP00000297293 Q8IWU2 UPI000014F277 NM_014916.3 deleterious(0) 3/14 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF357,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 98141398 98141398 A G 1 0 0 0 0 1 0 0 0 8786 260 9 5 5 LMTK2 7 98141398 Missense_Mutation SNP A C3N-01842_T 22639839 98141398 61204575 155 26347 GPR85 0 . GRCh38 7 113083899 113083899 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.823G>C p.Asp275His p.D275H ENST00000297146 3/3 435 396 39 405 405 0 strelka-varscan-mutect GPR85,missense_variant,p.Asp275His,ENST00000297146,NM_001146265.1,NM_018970.6;GPR85,missense_variant,p.Asp275His,ENST00000424100,NM_001146267.1;GPR85,missense_variant,p.Asp275His,ENST00000449591,NM_001146266.1;GPR85,downstream_gene_variant,,ENST00000438062,;GPR85,downstream_gene_variant,,ENST00000449735,;GPR85,downstream_gene_variant,,ENST00000487573,;GPR85,missense_variant,p.Asp275His,ENST00000610164,; G ENST00000297146 Transcript missense_variant 1427/5079 823/1113 275/370 D/H Gac/Cac 1 -1 GPR85 HGNC HGNC:4536 protein_coding YES CCDS5758.1 ENSP00000297146 P60893 A4D0T8 UPI0000004048 NM_001146265.1,NM_018970.6 deleterious(0.01) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR19268,hmmpanther:PTHR19268:SF7,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 113083899 113083899 C G 1 0 0 0 0 1 0 0 0 6596 913 32 4 4 GPR85 7 113083899 Missense_Mutation SNP C C3N-01842_T 14942501 113083899 46262074 156 26348 SLC13A1 0 . GRCh38 7 123115532 123115532 + Missense_Mutation SNP C C G C3N-01842_T C3N-01842_N C C c.1774G>C p.Glu592Gln p.E592Q ENST00000194130 15/15 183 166 17 185 185 0 strelka-varscan-mutect SLC13A1,missense_variant,p.Glu592Gln,ENST00000194130,NM_022444.3;SLC13A1,3_prime_UTR_variant,,ENST00000539873,;SLC13A1,3_prime_UTR_variant,,ENST00000427975,;SLC13A1,3_prime_UTR_variant,,ENST00000439260,; G ENST00000194130 Transcript missense_variant 1814/3815 1774/1788 592/595 E/Q Gag/Cag COSM4842796 1 -1 SLC13A1 HGNC HGNC:10916 protein_coding YES CCDS5786.1 ENSP00000194130 Q9BZW2 A4D0X1 UPI0000049F9D NM_022444.3 tolerated(0.68) 15/15 hmmpanther:PTHR10283:SF65,hmmpanther:PTHR10283 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 123115532 123115532 C G 1 0 0 0 0 1 0 0 0 14656 835 29 4 4 SLC13A1 7 123115532 Missense_Mutation SNP C C3N-01842_T 10031633 123115532 36230441 157 26349 LEP 0 . GRCh38 7 128254614 128254614 + Silent SNP T T C novel C3N-01842_T C3N-01842_N T T c.355T>C p.= p.L119L ENST00000308868 3/3 388 293 95 448 447 1 strelka-varscan-mutect LEP,synonymous_variant,p.=,ENST00000308868,NM_000230.2; C ENST00000308868 Transcript synonymous_variant 406/3420 355/504 119/167 L Ttg/Ctg 1 1 LEP HGNC HGNC:6553 protein_coding YES CCDS5800.1 ENSP00000312652 P41159 A4D0Y8 UPI00000308D4 NM_000230.2 3/3 hmmpanther:PTHR11724:SF1,hmmpanther:PTHR11724,Gene3D:1.20.1250.10,PIRSF_domain:PIRSF001837,Pfam_domain:PF02024,Superfamily_domains:SSF47266,Prints_domain:PR00495,PD005698 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 128254614 128254614 T C 1 0 0 0 0 0 0 0 1 8635 1606 56 5 5 LEP 7 128254614 Silent SNP T C3N-01842_T 5139082 128254614 31091359 158 26350 FLNC 0 . GRCh38 7 128844728 128844728 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.3263A>G p.Lys1088Arg p.K1088R ENST00000325888 21/48 243 177 66 266 265 1 strelka-varscan-mutect FLNC,missense_variant,p.Lys1088Arg,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Lys1088Arg,ENST00000346177,NM_001127487.1;FLNC,downstream_gene_variant,,ENST00000388853,; G ENST00000325888 Transcript missense_variant 3524/9188 3263/8178 1088/2725 K/R aAg/aGg 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.21) 21/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 128844728 128844728 A G 1 0 0 0 0 1 0 0 0 5791 72 3 5 5 FLNC 7 128844728 Missense_Mutation SNP A C3N-01842_T 590114 128844728 30501245 159 26351 TMEM209 0 . GRCh38 7 130173867 130173867 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.1417A>G p.Thr473Ala p.T473A ENST00000397622 12/15 321 260 61 276 276 0 strelka-varscan-mutect TMEM209,missense_variant,p.Thr473Ala,ENST00000397622,NM_032842.3;TMEM209,missense_variant,p.Thr472Ala,ENST00000462753,;TMEM209,missense_variant,p.Thr431Ala,ENST00000473456,NM_001301163.1;RP11-775D22.3,non_coding_transcript_exon_variant,,ENST00000483283,;TMEM209,downstream_gene_variant,,ENST00000467599,;TMEM209,downstream_gene_variant,,ENST00000479804,; C ENST00000397622 Transcript missense_variant 1540/3545 1417/1686 473/561 T/A Act/Gct 1 -1 TMEM209 HGNC HGNC:21898 protein_coding YES CCDS47712.1 ENSP00000380747 Q96SK2 A0A140VJX5 UPI000020FAA2 NM_032842.3 deleterious(0.02) 12/15 Pfam_domain:PF09786,hmmpanther:PTHR21780,hmmpanther:PTHR21780:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 130173867 130173867 T C 1 0 0 0 0 1 0 0 0 16573 1725 60 5 5 TMEM209 7 130173867 Missense_Mutation SNP T C3N-01842_T 1329139 130173867 29172106 160 26352 PLXNA4 0 . GRCh38 7 132187554 132187554 + Silent SNP G G C novel C3N-01842_T C3N-01842_N G G c.2910C>G p.= p.T970T ENST00000359827 15/32 145 128 17 191 190 1 strelka-varscan-mutect PLXNA4,synonymous_variant,p.=,ENST00000359827,;PLXNA4,synonymous_variant,p.=,ENST00000321063,NM_020911.1; C ENST00000359827 Transcript synonymous_variant 3873/13786 2910/5685 970/1894 T acC/acG 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 15/32 Gene3D:2.60.40.10,Pfam_domain:PF01833,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,SMART_domains:SM00429,Superfamily_domains:SSF81296 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 132187554 132187554 G C 1 0 0 0 0 0 0 0 1 12228 1219 43 4 4 PLXNA4 7 132187554 Silent SNP G C3N-01842_T 2013687 132187554 27158419 161 26353 PLXNA4 0 . GRCh38 7 132210984 132210984 + Missense_Mutation SNP G G T rs544399380 C3N-01842_T C3N-01842_N G G c.2257C>A p.Leu753Met p.L753M ENST00000359827 10/32 237 189 48 256 256 0 strelka-varscan-mutect PLXNA4,missense_variant,p.Leu753Met,ENST00000359827,;PLXNA4,missense_variant,p.Leu753Met,ENST00000321063,NM_020911.1; T ENST00000359827 Transcript missense_variant 3220/13786 2257/5685 753/1894 L/M Ctg/Atg rs544399380 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B deleterious(0.02) 10/32 hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 MODERATE 1 SNV 5 1 PASS rs544399380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 132210984 132210984 G T 1 0 0 0 0 1 0 0 0 12228 991 35 2 2 PLXNA4 7 132210984 Missense_Mutation SNP G C3N-01842_T 23430 132210984 27134989 162 26354 NUP205 0 . GRCh38 7 135577872 135577872 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.725G>T p.Gly242Val p.G242V ENST00000285968 6/43 374 282 92 414 414 0 strelka-varscan-mutect NUP205,missense_variant,p.Gly242Val,ENST00000285968,NM_015135.2;NUP205,downstream_gene_variant,,ENST00000489493,; T ENST00000285968 Transcript missense_variant 751/6266 725/6039 242/2012 G/V gGc/gTc 1 1 NUP205 HGNC HGNC:18658 protein_coding YES CCDS34759.1 ENSP00000285968 Q92621 UPI00001D74D8 NM_015135.2 tolerated(0.06) 6/43 Pfam_domain:PF11894,hmmpanther:PTHR31344,hmmpanther:PTHR31344:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 135577872 135577872 G T 1 0 0 0 0 1 0 0 0 10824 1203 42 2 2 NUP205 7 135577872 Missense_Mutation SNP G C3N-01842_T 3366888 135577872 23768101 163 26355 DENND2A 0 . GRCh38 7 140601481 140601481 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.917C>A p.Pro306His p.P306H ENST00000275884 2/19 130 106 24 143 143 0 strelka-varscan-mutect DENND2A,missense_variant,p.Pro306His,ENST00000275884,NM_001318052.1;DENND2A,missense_variant,p.Pro306His,ENST00000492720,NM_001318053.1;DENND2A,missense_variant,p.Pro306His,ENST00000496613,;DENND2A,missense_variant,p.Pro306His,ENST00000537639,NM_015689.3;DENND2A,intron_variant,,ENST00000475837,;DENND2A,downstream_gene_variant,,ENST00000491728,;DENND2A,downstream_gene_variant,,ENST00000477488,;DENND2A,downstream_gene_variant,,ENST00000489552,;DENND2A,missense_variant,p.Pro306His,ENST00000461883,; T ENST00000275884 Transcript missense_variant 1335/3735 917/3030 306/1009 P/H cCt/cAt 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 deleterious(0.03) 2/19 Low_complexity_(Seg):seg,hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 140601481 140601481 G T 1 0 0 0 0 1 0 0 0 4233 1000 35 2 2 DENND2A 7 140601481 Missense_Mutation SNP G C3N-01842_T 5023609 140601481 18744492 164 26356 BRAF 0 . GRCh38 7 140753349 140753349 + Missense_Mutation SNP C C G rs121913361 C3N-01842_T C3N-01842_N C C c.1786G>C p.Gly596Arg p.G596R ENST00000288602 15/18 557 435 122 507 507 0 strelka-varscan-mutect BRAF,missense_variant,p.Gly204Arg,ENST00000496384,;BRAF,missense_variant,p.Gly596Arg,ENST00000288602,NM_004333.4;BRAF,missense_variant,p.Gly24Arg,ENST00000479537,;BRAF,3_prime_UTR_variant,,ENST00000497784,; G ENST00000288602 Transcript missense_variant 1847/2480 1786/2301 596/766 G/R Ggt/Cgt rs121913361,COSM36922,COSM469,COSM5329314 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 deleterious(0.01) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF43,SMART_domains:SM00220,Superfamily_domains:SSF56112 uncertain_significance 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913361 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 140753349 140753349 C G 1 0 0 0 0 1 0 0 0 1665 594 21 4 4 BRAF 7 140753349 Missense_Mutation SNP C C3N-01842_T 151868 140753349 18592624 165 26357 MGAM2 0 . GRCh38 7 142220771 142220771 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.6260C>A p.Thr2087Lys p.T2087K ENST00000477922 48/48 325 245 80 223 222 1 strelka-varscan-mutect MGAM2,missense_variant,p.Thr2087Lys,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; A ENST00000477922 Transcript missense_variant 6314/7867 6260/7548 2087/2515 T/K aCa/aAa 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 tolerated_low_confidence(0.07) 48/48 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 142220771 142220771 C A 1 0 0 0 0 1 0 0 0 9500 478 17 2 2 MGAM2 7 142220771 Missense_Mutation SNP C C3N-01842_T 1467422 142220771 17125202 166 26358 OR9A2 0 . GRCh38 7 143026477 143026477 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.656C>T p.Ser219Phe p.S219F ENST00000350513 1/1 453 350 103 423 423 0 strelka-varscan-mutect OR9A2,missense_variant,p.Ser219Phe,ENST00000350513,NM_001001658.1; A ENST00000350513 Transcript missense_variant 719/1038 656/933 219/310 S/F tCc/tTc 1 -1 OR9A2 HGNC HGNC:15093 protein_coding YES CCDS34767.1 ENSP00000316518 Q8NGT5 UPI0000041C18 NM_001001658.1 tolerated(0.08) 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF216,hmmpanther:PTHR24242,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 143026477 143026477 G A 1 0 0 0 0 1 0 0 0 11315 1174 41 3 3 OR9A2 7 143026477 Missense_Mutation SNP G C3N-01842_T 805706 143026477 16319496 167 26359 CNTNAP2 0 . GRCh38 7 147121106 147121106 + Missense_Mutation SNP G G T rs370716351 C3N-01842_T C3N-01842_N G G c.882G>T p.Arg294Ser p.R294S ENST00000361727 6/24 306 230 76 355 355 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Arg294Ser,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637555,; T ENST00000361727 Transcript missense_variant 1400/9896 882/3996 294/1331 R/S agG/agT rs370716351 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(0.19) 6/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs370716351 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 147121106 147121106 G T 1 0 0 0 0 1 0 0 0 3428 1165 41 2 2 CNTNAP2 7 147121106 Missense_Mutation SNP G C3N-01842_T 4094629 147121106 12224867 168 26360 ZNF212 0 . GRCh38 7 149253787 149253787 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.860G>T p.Cys287Phe p.C287F ENST00000335870 5/5 485 391 94 590 589 1 strelka-varscan-mutect ZNF212,missense_variant,p.Cys287Phe,ENST00000335870,NM_012256.3;ZNF212,downstream_gene_variant,,ENST00000481584,;ZNF212,3_prime_UTR_variant,,ENST00000488917,;ZNF212,downstream_gene_variant,,ENST00000462724,;ZNF212,downstream_gene_variant,,ENST00000486371,; T ENST00000335870 Transcript missense_variant 988/2810 860/1488 287/495 C/F tGc/tTc 1 1 ZNF212 HGNC HGNC:13004 protein_coding YES CCDS5896.1 ENSP00000338572 Q9UDV6 A0A090N8N3 UPI000013CEE2 NM_012256.3 tolerated(0.46) 5/5 hmmpanther:PTHR24390:SF49,hmmpanther:PTHR24390 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 149253787 149253787 G T 1 0 0 0 0 1 0 0 0 18345 1319 46 2 2 ZNF212 7 149253787 Missense_Mutation SNP G C3N-01842_T 2132681 149253787 10092186 169 26361 ZNF705G 0 . GRCh38 8 7360332 7360332 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.140G>T p.Gly47Val p.G47V ENST00000400156 5/7 624 490 134 533 532 1 strelka-varscan-mutect ZNF705G,missense_variant,p.Gly47Val,ENST00000400156,NM_001164457.1;FAM66B,upstream_gene_variant,,ENST00000606573,;FAM66B,upstream_gene_variant,,ENST00000529456,; A ENST00000400156 Transcript missense_variant,splice_region_variant 422/3644 140/903 47/300 G/V gGg/gTg 1 -1 ZNF705G HGNC HGNC:37134 protein_coding YES CCDS47773.1 ENSP00000383020 A8MUZ8 UPI0001761700 NM_001164457.1 deleterious(0) 5/7 PROSITE_profiles:PS50805,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF19,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 MODERATE 1 SNV 2 1 PASS rs1434974132 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 7360332 7360332 C A 1 0 0 0 0 1 0 0 0 18684 637 22 2 2 ZNF705G 8 7360332 Missense_Mutation SNP C C3N-01842_T 7360332 137778304 170 26362 SNTG1 0 . GRCh38 8 50536714 50536714 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.586G>T p.Gly196Cys p.G196C ENST00000522124 11/19 277 212 65 345 345 0 strelka-varscan-mutect SNTG1,missense_variant,p.Gly196Cys,ENST00000522124,NM_018967.3;SNTG1,missense_variant,p.Gly196Cys,ENST00000518864,NM_001287813.1;SNTG1,missense_variant,p.Gly196Cys,ENST00000517473,NM_001287814.1;SNTG1,missense_variant,p.Gly196Cys,ENST00000520825,; T ENST00000522124 Transcript missense_variant 1247/3504 586/1554 196/517 G/C Ggc/Tgc 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 tolerated(0.06) 11/19 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 50536714 50536714 G T 1 0 0 0 0 1 0 0 0 15194 1000 35 2 2 SNTG1 8 50536714 Missense_Mutation SNP G C3N-01842_T 43176382 50536714 94601922 171 26363 CHD7 0 . GRCh38 8 60836207 60836207 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.3913G>T p.Gly1305Cys p.G1305C ENST00000423902 16/38 306 219 87 386 386 0 strelka-varscan-mutect CHD7,missense_variant,p.Gly1305Cys,ENST00000423902,NM_017780.3;CHD7,intron_variant,,ENST00000524602,; T ENST00000423902 Transcript missense_variant 4392/11568 3913/8994 1305/2997 G/C Ggt/Tgt 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 deleterious(0) 16/38 PROSITE_profiles:PS51194,hmmpanther:PTHR10799:SF658,hmmpanther:PTHR10799,Pfam_domain:PF00271,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS rs1246333602 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 60836207 60836207 G T 1 0 0 0 0 1 0 0 0 3089 1348 47 2 2 CHD7 8 60836207 Missense_Mutation SNP G C3N-01842_T 10299493 60836207 84302429 172 26364 NCOA2 0 . GRCh38 8 70121371 70121371 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.4314G>T p.Arg1438Ser p.R1438S ENST00000452400 22/23 310 254 56 356 356 0 strelka-varscan-mutect NCOA2,missense_variant,p.Arg1438Ser,ENST00000452400,NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2;NCOA2,missense_variant,p.Arg564Ser,ENST00000518363,;NCOA2,intron_variant,,ENST00000518287,; A ENST00000452400 Transcript missense_variant 4496/8447 4314/4395 1438/1464 R/S agG/agT 1 -1 NCOA2 HGNC HGNC:7669 protein_coding YES CCDS47872.1 ENSP00000399968 Q15596 UPI000012FE42 NM_001321703.1,NM_001321707.1,NM_001321713.1,NM_006540.2 deleterious_low_confidence(0.01) 22/23 hmmpanther:PTHR10684:SF2,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 70121371 70121371 C A 1 0 0 0 0 1 0 0 0 10248 622 22 2 2 NCOA2 8 70121371 Missense_Mutation SNP C C3N-01842_T 9285164 70121371 75017265 173 26365 RDH10 0 . GRCh38 8 73319126 73319126 + Missense_Mutation SNP G G C C3N-01842_T C3N-01842_N G G c.556G>C p.Glu186Gln p.E186Q ENST00000240285 3/6 209 195 14 174 174 0 strelka-varscan-mutect RDH10,missense_variant,p.Glu186Gln,ENST00000240285,NM_172037.4;RDH10,missense_variant,p.Glu21Gln,ENST00000519380,;RDH10,missense_variant,p.Glu21Gln,ENST00000521928,;RDH10-AS1,intron_variant,,ENST00000514599,;RDH10-AS1,intron_variant,,ENST00000517475,;RDH10-AS1,upstream_gene_variant,,ENST00000520894,;RDH10,upstream_gene_variant,,ENST00000521013,; C ENST00000240285 Transcript missense_variant 1234/3949 556/1026 186/341 E/Q Gag/Cag COSM3779350 1 1 RDH10 HGNC HGNC:19975 protein_coding YES CCDS6213.1 ENSP00000240285 Q8IZV5 A0A024R7X6 UPI0000054C83 NM_172037.4 tolerated(0.13) 3/6 hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF466,Pfam_domain:PF00106,Gene3D:3.40.50.720,Superfamily_domains:SSF51735,Prints_domain:PR00081 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 73319126 73319126 G C 1 0 0 0 0 1 0 0 0 13358 1175 41 4 4 RDH10 8 73319126 Missense_Mutation SNP G C3N-01842_T 3197755 73319126 71819510 174 26366 ZFHX4 0 . GRCh38 8 76854772 76854772 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.7851G>T p.= p.L2617L ENST00000521891 10/11 126 91 35 137 137 0 strelka-varscan-mutect ZFHX4,synonymous_variant,p.=,ENST00000521891,NM_024721.4;ZFHX4,synonymous_variant,p.=,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000522409,; T ENST00000521891 Transcript synonymous_variant 8299/14019 7851/10851 2617/3616 L ctG/ctT 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 10/11 Gene3D:1.10.10.60,Pfam_domain:PF00046,PROSITE_profiles:PS50071,hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 5 1 PASS . . 0 199 10 0 0 0 0 0 -20 0.9999948 1 1 1 0 T 2 4 84 76854772 76854772 G T 1 0 0 0 0 0 0 0 1 18213 1335 47 2 2 ZFHX4 8 76854772 Silent SNP G C3N-01842_T 3535646 76854772 68283864 175 26367 LRRC69 0 . GRCh38 8 91124502 91124502 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.193C>A p.Leu65Ile p.L65I ENST00000448384 2/8 203 143 60 181 180 1 strelka-varscan-mutect LRRC69,missense_variant,p.Leu65Ile,ENST00000448384,NM_001129890.1;LRRC69,intron_variant,,ENST00000343709,;LRRC69,non_coding_transcript_exon_variant,,ENST00000522144,;LRRC69,intron_variant,,ENST00000520099,; A ENST00000448384 Transcript missense_variant 193/1044 193/1044 65/347 L/I Cta/Ata 1 1 LRRC69 HGNC HGNC:34303 protein_coding YES ENSP00000400803 Q6ZNQ3 UPI00006C0DD3 NM_001129890.1 deleterious(0.01) 2/8 Low_complexity_(Seg):seg,PROSITE_profiles:PS51450,hmmpanther:PTHR23155,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 91124502 91124502 C A 1 0 0 0 0 1 0 0 0 8915 564 20 2 2 LRRC69 8 91124502 Missense_Mutation SNP C C3N-01842_T 14269730 91124502 54014134 176 26368 POP1 0 . GRCh38 8 98140869 98140869 + Silent SNP C C T rs369502410 C3N-01842_T C3N-01842_N C C c.1575C>T p.= p.P525P ENST00000401707 11/16 462 360 102 426 426 0 strelka-varscan-mutect POP1,synonymous_variant,p.=,ENST00000401707,NM_001145860.1,NM_001145861.1;POP1,synonymous_variant,p.=,ENST00000349693,NM_015029.2; T ENST00000401707 Transcript synonymous_variant 1656/4719 1575/3075 525/1024 P ccC/ccT rs369502410 1 1 POP1 HGNC HGNC:30129 protein_coding YES CCDS6277.1 ENSP00000385787 Q99575 UPI0000131F33 NM_001145860.1,NM_001145861.1 11/16 hmmpanther:PTHR22731:SF3,hmmpanther:PTHR22731 LOW 1 SNV 2 1 PASS rs369502410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 98140869 98140869 C T 1 0 0 0 0 0 0 0 1 12365 581 21 3 3 POP1 8 98140869 Silent SNP C C3N-01842_T 7016367 98140869 46997767 177 26369 DPYS 0 . GRCh38 8 104381199 104381199 + Silent SNP C C T C3N-01842_T C3N-01842_N C C c.1559G>A p.= p.*520* ENST00000351513 9/10 360 291 69 427 427 0 strelka-varscan-mutect DPYS,stop_retained_variant,p.=,ENST00000351513,NM_001385.2;DPYS,intron_variant,,ENST00000533874,;DPYS,non_coding_transcript_exon_variant,,ENST00000521601,;DPYS,non_coding_transcript_exon_variant,,ENST00000521372,;DPYS,non_coding_transcript_exon_variant,,ENST00000520483,;DPYS,non_coding_transcript_exon_variant,,ENST00000520806,; T ENST00000351513 Transcript stop_retained_variant 1692/2127 1559/1560 520/519 * tGa/tAa COSM374647 1 -1 DPYS HGNC HGNC:3013 protein_coding YES CCDS6302.1 ENSP00000276651 Q14117 UPI000012986F NM_001385.2 9/10 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 104381199 104381199 C T 1 0 0 0 0 0 0 0 1 4561 837 29 3 3 DPYS 8 104381199 Silent SNP C C3N-01842_T 6240330 104381199 40757437 178 26370 CSMD3 0 . GRCh38 8 112682600 112682600 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.2519C>A p.Pro840Gln p.P840Q ENST00000297405 16/71 275 208 67 249 248 1 strelka-varscan-mutect CSMD3,missense_variant,p.Pro840Gln,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Pro800Gln,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Pro736Gln,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Pro180Gln,ENST00000339701,; T ENST00000297405 Transcript missense_variant 2764/13212 2519/11124 840/3707 P/Q cCa/cAa COSM4481534,COSM4481535 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0) 16/71 PROSITE_profiles:PS50923,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 112682600 112682600 G T 1 0 0 0 0 1 0 0 0 3747 1348 47 2 2 CSMD3 8 112682600 Missense_Mutation SNP G C3N-01842_T 8301401 112682600 32456036 179 26371 ADCY8 0 . GRCh38 8 130780500 130780500 + Missense_Mutation SNP T T G novel C3N-01842_T C3N-01842_N T T c.3646A>C p.Asn1216His p.N1216H ENST00000286355 18/18 222 159 63 403 403 0 strelka-varscan-mutect ADCY8,missense_variant,p.Asn1216His,ENST00000286355,NM_001115.2;ADCY8,missense_variant,p.Asn1085His,ENST00000377928,; G ENST00000286355 Transcript missense_variant 5739/5938 3646/3756 1216/1251 N/H Aac/Cac 1 -1 ADCY8 HGNC HGNC:239 protein_coding YES CCDS6363.1 ENSP00000286355 P40145 A0A0K0K1K3 UPI000012887C NM_001115.2 deleterious(0.01) 18/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 130780500 130780500 T G 1 0 0 0 0 1 0 0 0 344 1812 63 5 5 ADCY8 8 130780500 Missense_Mutation SNP T C3N-01842_T 18097900 130780500 14358136 180 26372 OC90 0 . GRCh38 8 132038794 132038794 + Frame_Shift_Del DEL G G - novel C3N-01842_T C3N-01842_N G G c.1212delC p.Arg405GlufsTer12 p.R405Efs*12 ENST00000262283 11/18 184 121 63 334 334 0 sindel-varindel-pindel RP11-240B13.2,frameshift_variant,p.Arg405GlufsTer12,ENST00000262283,;OC90,frameshift_variant,p.Arg209GlufsTer12,ENST00000254627,NM_001080399.2; - ENST00000262283 Transcript frameshift_variant 1312/2413 1212/2070 404/689 P/X ccC/cc 1 -1 RP11-240B13.2 Clone_based_vega_gene protein_coding YES ENSP00000262283 I6L893 UPI0000E5AF6B 11/18 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 132038794 132038794 G - 1 0 1 0 1 0 0 0 0 10891 1362 47 0 0 OC90 8 132038794 Frame_Shift_Del DEL G C3N-01842_T 1258294 132038794 13099842 181 26373 FAM135B 0 . GRCh38 8 138148654 138148654 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.3314A>G p.Glu1105Gly p.E1105G ENST00000395297 14/20 140 100 40 132 132 0 strelka-varscan-mutect FAM135B,missense_variant,p.Glu1105Gly,ENST00000395297,NM_015912.3;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,non_coding_transcript_exon_variant,,ENST00000395295,;FAM135B,intron_variant,,ENST00000276737,;FAM135B,intron_variant,,ENST00000467365,; C ENST00000395297 Transcript missense_variant 3485/6962 3314/4221 1105/1406 E/G gAa/gGa 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 14/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 138148654 138148654 T C 1 0 0 0 0 1 0 0 0 5299 1783 62 5 5 FAM135B 8 138148654 Missense_Mutation SNP T C3N-01842_T 6109860 138148654 6989982 182 26374 GLI4 0 . GRCh38 8 143276275 143276275 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.602A>T p.His201Leu p.H201L ENST00000340042 4/4 239 182 57 300 300 0 strelka-varscan-mutect GLI4,missense_variant,p.His201Leu,ENST00000340042,NM_138465.3;GLI4,missense_variant,p.His201Leu,ENST00000523522,;RP13-582O9.6,3_prime_UTR_variant,,ENST00000522452,;GLI4,3_prime_UTR_variant,,ENST00000517530,;GLI4,downstream_gene_variant,,ENST00000521682,;GLI4,downstream_gene_variant,,ENST00000344692,;GLI4,downstream_gene_variant,,ENST00000517468,;GLI4,downstream_gene_variant,,ENST00000520021,;MINCR,downstream_gene_variant,,ENST00000523031,;MINCR,downstream_gene_variant,,ENST00000517411,;MINCR,downstream_gene_variant,,ENST00000524335,;MINCR,downstream_gene_variant,,ENST00000521207,;MINCR,downstream_gene_variant,,ENST00000518073,;MINCR,downstream_gene_variant,,ENST00000519852,;GLI4,non_coding_transcript_exon_variant,,ENST00000523812,;GLI4,downstream_gene_variant,,ENST00000519876,;GLI4,downstream_gene_variant,,ENST00000522479,;GLI4,downstream_gene_variant,,ENST00000522033,; T ENST00000340042 Transcript missense_variant 687/1341 602/1131 201/376 H/L cAc/cTc 1 1 GLI4 HGNC HGNC:4320 protein_coding YES CCDS6398.1 ENSP00000345024 P10075 UPI0000070432 NM_138465.3 deleterious(0) 4/4 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF122,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 143276275 143276275 A T 1 0 0 0 0 1 0 0 0 6318 159 6 4 4 GLI4 8 143276275 Missense_Mutation SNP A C3N-01842_T 5127621 143276275 1862361 183 26375 RPL8 0 . GRCh38 8 144792092 144792092 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.38G>T p.Gly13Val p.G13V ENST00000262584 2/6 77 60 17 87 87 0 strelka-varscan-mutect RPL8,missense_variant,p.Gly13Val,ENST00000262584,NM_000973.3;RPL8,missense_variant,p.Gly13Val,ENST00000528957,NM_001317782.1;RPL8,missense_variant,p.Gly13Val,ENST00000394920,NM_001317771.1,NM_033301.1;RPL8,missense_variant,p.Gly13Val,ENST00000532702,;RPL8,missense_variant,p.Gly13Val,ENST00000533397,;RPL8,missense_variant,p.Gly13Val,ENST00000527914,;ZNF34,upstream_gene_variant,,ENST00000429371,NM_001286769.1;ZNF34,upstream_gene_variant,,ENST00000343459,NM_030580.4;ZNF34,upstream_gene_variant,,ENST00000534445,NM_001286770.1;RPL8,upstream_gene_variant,,ENST00000612162,;RPL8,non_coding_transcript_exon_variant,,ENST00000528296,;RPL8,intron_variant,,ENST00000529163,;RPL8,missense_variant,p.Gly13Val,ENST00000529920,;RPL8,non_coding_transcript_exon_variant,,ENST00000525232,;RPL8,non_coding_transcript_exon_variant,,ENST00000531767,;ZNF34,upstream_gene_variant,,ENST00000527740,;RPL8,upstream_gene_variant,,ENST00000526668,;RPL8,upstream_gene_variant,,ENST00000534781,;RPL8,upstream_gene_variant,,ENST00000531975,; A ENST00000262584 Transcript missense_variant 271/1041 38/774 13/257 G/V gGg/gTg 1 -1 RPL8 HGNC HGNC:10368 protein_coding YES CCDS6433.1 ENSP00000262584 P62917 UPI000000419E NM_000973.3 deleterious(0) 2/6 Gene3D:2.40.50.140,HAMAP:MF_01320_A,Pfam_domain:PF00181,PIRSF_domain:PIRSF002158,hmmpanther:PTHR13691,hmmpanther:PTHR13691:SF16,SMART_domains:SM01383,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 144792092 144792092 C A 1 0 0 0 0 1 0 0 0 13855 623 22 2 2 RPL8 8 144792092 Missense_Mutation SNP C C3N-01842_T 1515817 144792092 346544 184 26376 SPINK4 0 . GRCh38 9 33246685 33246685 + Missense_Mutation SNP G G A C3N-01842_T C3N-01842_N G G c.172G>A p.Gly58Arg p.G58R ENST00000379721 3/4 355 292 63 442 442 0 strelka-varscan-mutect SPINK4,missense_variant,p.Gly81Arg,ENST00000379725,;SPINK4,missense_variant,p.Gly58Arg,ENST00000379721,NM_014471.1;BAG1,downstream_gene_variant,,ENST00000493917,; A ENST00000379721 Transcript missense_variant 217/402 172/261 58/86 G/R Ggg/Agg COSM3926691,COSM3926692 1 1 SPINK4 HGNC HGNC:16646 protein_coding YES CCDS6536.1 ENSP00000369045 O60575 V9HWG8 UPI000012D8F5 NM_014471.1 deleterious(0.01) 3/4 PROSITE_profiles:PS51465,hmmpanther:PTHR21179,PROSITE_patterns:PS00282,Gene3D:3.30.60.30,Pfam_domain:PF00050,SMART_domains:SM00280,Superfamily_domains:SSF100895 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 33246685 33246685 G A 1 0 0 0 0 1 0 0 0 15414 1348 47 3 3 SPINK4 9 33246685 Missense_Mutation SNP G C3N-01842_T 33246685 105148032 185 26377 OR13J1 0 . GRCh38 9 35869721 35869721 + Missense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.681G>T p.Arg227Ser p.R227S ENST00000377981 1/1 355 288 67 410 405 5 strelka-varscan-mutect OR13J1,missense_variant,p.Arg227Ser,ENST00000377981,NM_001004487.1;LINC00950,downstream_gene_variant,,ENST00000629651,; A ENST00000377981 Transcript missense_variant 881/1339 681/939 227/312 R/S agG/agT COSM455936 1 -1 OR13J1 HGNC HGNC:15108 protein_coding YES CCDS35011.1 ENSP00000367219 Q8NGT2 UPI000003FF73 NM_001004487.1 deleterious(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF38,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs1442499587 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 35869721 35869721 C A 1 0 0 0 0 1 0 0 0 11020 622 22 2 2 OR13J1 9 35869721 Missense_Mutation SNP C C3N-01842_T 2623036 35869721 102524996 186 26378 AL135787.1 0 . GRCh38 9 111592940 111592940 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.195G>A p.= p.G65G ENST00000407693 4/10 192 154 38 230 230 0 strelka-varscan-mutect PTGR1,synonymous_variant,p.=,ENST00000407693,NM_001146108.1;PTGR1,synonymous_variant,p.=,ENST00000309195,NM_012212.3;AL135787.1,synonymous_variant,p.=,ENST00000538962,NM_001146109.1;PTGR1,intron_variant,,ENST00000422125,;PTGR1,synonymous_variant,p.=,ENST00000374324,;PTGR1,non_coding_transcript_exon_variant,,ENST00000374313,;PTGR1,non_coding_transcript_exon_variant,,ENST00000374308,;PTGR1,non_coding_transcript_exon_variant,,ENST00000485319,; T ENST00000407693 Transcript synonymous_variant 458/1407 195/990 65/329 G ggG/ggA 1 -1 PTGR1 HGNC HGNC:18429 protein_coding YES CCDS6779.1 ENSP00000385763 Q14914 UPI000012E24A NM_001146108.1 4/10 Gene3D:3.90.180.10,Pfam_domain:PF16884,hmmpanther:PTHR11695,hmmpanther:PTHR11695:SF528,SMART_domains:SM00829,Superfamily_domains:SSF50129,TIGRFAM_domain:TIGR02825 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 111592940 111592940 C T 1 0 0 0 0 0 0 0 1 573 726 26 3 3 AL135787.1 9 111592940 Silent SNP C C3N-01842_T 75723219 111592940 26801777 187 26379 TRIM32 0 . GRCh38 9 116699529 116699529 + Missense_Mutation SNP G G A rs750300057 C3N-01842_T C3N-01842_N G G c.1787G>A p.Arg596His p.R596H ENST00000450136 2/2 391 182 209 405 405 0 strelka-varscan-mutect TRIM32,missense_variant,p.Arg596His,ENST00000450136,NM_001099679.1,NM_012210.3;TRIM32,missense_variant,p.Arg596His,ENST00000373983,;ASTN2,intron_variant,,ENST00000313400,;ASTN2,intron_variant,,ENST00000361209,NM_014010.4;ASTN2,intron_variant,,ENST00000361477,NM_198187.3;ASTN2,intron_variant,,ENST00000373986,;TRIM32,downstream_gene_variant,,ENST00000411410,; A ENST00000450136 Transcript missense_variant 1948/3717 1787/1962 596/653 R/H cGc/cAc rs750300057,COSM1230316 1 1 TRIM32 HGNC HGNC:16380 protein_coding YES CCDS6817.1 ENSP00000408292 Q13049 A0A024R843 UPI000012CDB9 NM_001099679.1,NM_012210.3 deleterious(0.04) 2/2 Gene3D:2.120.10.30,PROSITE_profiles:PS51125,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF363,Superfamily_domains:SSF101898 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs750300057 . 0 208 0 0 2 0 0 0 -20 0.9996823 1 1 1 0 A 3 1 84 116699529 116699529 G A 1 0 0 0 0 1 0 0 0 16995 1087 38 1 1 TRIM32 9 116699529 Missense_Mutation SNP G C3N-01842_T 5106589 116699529 21695188 188 26380 SH2D3C 0 . GRCh38 9 127747154 127747154 + Frame_Shift_Del DEL G G - novel C3N-01842_T C3N-01842_N G G c.1257delC p.Tyr419Ter p.Y419* ENST00000314830 6/12 130 102 28 203 203 0 sindel-varindel-pindel SH2D3C,frameshift_variant,p.Tyr419Ter,ENST00000314830,NM_170600.2;SH2D3C,frameshift_variant,p.Tyr351Ter,ENST00000373276,NM_001252334.1;SH2D3C,frameshift_variant,p.Tyr65Ter,ENST00000429553,NM_001142531.1,NM_001142532.1;SH2D3C,frameshift_variant,p.Tyr262Ter,ENST00000373277,NM_005489.3;SH2D3C,frameshift_variant,p.Tyr261Ter,ENST00000420366,NM_001142533.1;SH2D3C,frameshift_variant,p.Tyr259Ter,ENST00000629203,NM_001142534.1;SH2D3C,frameshift_variant,p.Tyr65Ter,ENST00000440630,;SH2D3C,downstream_gene_variant,,ENST00000414380,;AL162426.1,downstream_gene_variant,,ENST00000625046,;SH2D3C,non_coding_transcript_exon_variant,,ENST00000488685,;SH2D3C,non_coding_transcript_exon_variant,,ENST00000464239,;SH2D3C,intron_variant,,ENST00000471939,;SH2D3C,intron_variant,,ENST00000468969,;SH2D3C,upstream_gene_variant,,ENST00000484160,; - ENST00000314830 Transcript frameshift_variant 1371/3124 1257/2583 419/860 Y/X taC/ta 1 -1 SH2D3C HGNC HGNC:16884 protein_coding YES CCDS6877.1 ENSP00000317817 Q8N5H7 UPI000006EC87 NM_170600.2 6/12 hmmpanther:PTHR14247,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999997 1 1 1 0 - 7 5 84 127747154 127747154 G - 1 0 1 0 1 0 0 0 0 14492 1372 48 0 0 SH2D3C 9 127747154 Frame_Shift_Del DEL G C3N-01842_T 11047625 127747154 10647563 189 26381 HMCN2 0 . GRCh38 9 130430556 130430556 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.14539C>A p.= p.R4847R ENST00000624552 95/98 247 193 54 245 244 1 strelka-varscan-mutect HMCN2,synonymous_variant,p.=,ENST00000624552,NM_001291815.1;HMCN2,synonymous_variant,p.=,ENST00000428715,;HMCN2,non_coding_transcript_exon_variant,,ENST00000623487,; A ENST00000624552 Transcript synonymous_variant 14539/15610 14539/15180 4847/5059 R Cgg/Agg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 95/98 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25 LOW 1 SNV 5 1 PASS rs1198681204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 130430556 130430556 C A 1 0 0 0 0 0 0 0 1 7112 643 23 1 1 HMCN2 9 130430556 Silent SNP C C3N-01842_T 2683402 130430556 7964161 190 26382 AIF1L 0 . GRCh38 9 131117838 131117838 + Silent SNP G G T rs750325550 C3N-01842_T C3N-01842_N G G c.363G>T p.= p.V121V ENST00000372309 6/7 190 145 45 209 208 1 strelka-varscan-mutect AIF1L,splice_region_variant,,ENST00000372298,;AIF1L,synonymous_variant,p.=,ENST00000372309,NM_001185095.1;AIF1L,synonymous_variant,p.=,ENST00000247291,NM_031426.3;AIF1L,synonymous_variant,p.=,ENST00000372302,;AIF1L,synonymous_variant,p.=,ENST00000372300,NM_001185096.1;AIF1L,synonymous_variant,p.=,ENST00000372301,;AIF1L,synonymous_variant,p.=,ENST00000372297,;AIF1L,downstream_gene_variant,,ENST00000472942,;AIF1L,3_prime_UTR_variant,,ENST00000372314,; T ENST00000372309 Transcript synonymous_variant 517/3515 363/531 121/176 V gtG/gtT rs750325550 1 1 AIF1L HGNC HGNC:28904 protein_coding YES CCDS55348.1 ENSP00000361383 Q9BQI0 UPI00001C1012 NM_001185095.1 6/7 Gene3D:1.10.238.10,hmmpanther:PTHR10356,hmmpanther:PTHR10356:SF5,Superfamily_domains:SSF47473 LOW 1 SNV 2 1 PASS rs750325550 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 131117838 131117838 G T 1 0 0 0 0 0 0 0 1 502 1304 45 2 2 AIF1L 9 131117838 Silent SNP G C3N-01842_T 687282 131117838 7276879 191 26383 CACNA1B 0 . GRCh38 9 138121523 138121523 + Missense_Mutation SNP C C T rs200435656 C3N-01842_T C3N-01842_N C C c.6544C>T p.Pro2182Ser p.P2182S ENST00000371372 47/47 52 36 16 56 56 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Pro2182Ser,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Pro2180Ser,ENST00000371363,;CACNA1B,missense_variant,p.Pro2183Ser,ENST00000371355,;CACNA1B,missense_variant,p.Pro2181Ser,ENST00000371357,;CACNA1B,intron_variant,,ENST00000277549,;CACNA1B,intron_variant,,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 6689/9790 6544/7020 2182/2339 P/S Ccc/Tcc rs200435656 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 deleterious(0.01) 47/47 MODERATE 1 SNV 5 1 PASS rs200435656 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 138121523 138121523 C T 1 0 0 0 0 1 0 0 0 2227 623 22 3 3 CACNA1B 9 138121523 Missense_Mutation SNP C C3N-01842_T 7003685 138121523 273194 192 26384 PFKP 0 . GRCh38 10 3105438 3105438 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.711G>T p.= p.V237V ENST00000381125 7/22 307 247 60 351 351 0 strelka-varscan-mutect PFKP,synonymous_variant,p.=,ENST00000381075,NM_001242339.1;PFKP,synonymous_variant,p.=,ENST00000381125,NM_001323069.1,NM_001323067.1,NM_002627.4;PFKP,synonymous_variant,p.=,ENST00000415005,;PFKP,synonymous_variant,p.=,ENST00000407806,;PFKP,synonymous_variant,p.=,ENST00000468050,;PFKP,downstream_gene_variant,,ENST00000607886,;PFKP,non_coding_transcript_exon_variant,,ENST00000460445,;PFKP,downstream_gene_variant,,ENST00000421751,; T ENST00000381125 Transcript synonymous_variant 787/2654 711/2355 237/784 V gtG/gtT 1 1 PFKP HGNC HGNC:8878 protein_coding YES CCDS7059.1 ENSP00000370517 Q01813 UPI00000012D2 NM_001323069.1,NM_001323067.1,NM_002627.4 7/22 Gene3D:3.40.50.450,HAMAP:MF_03184,Pfam_domain:PF00365,PIRSF_domain:PIRSF000533,Prints_domain:PR00476,hmmpanther:PTHR13697,hmmpanther:PTHR13697:SF5,Superfamily_domains:SSF53784,TIGRFAM_domain:TIGR02478 LOW 1 SNV 1 1 PASS rs971417114 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 3105438 3105438 G T 1 0 0 0 0 0 0 0 1 11856 1364 48 2 2 PFKP 10 3105438 Silent SNP G C3N-01842_T 3105438 130691984 193 26385 GATA3 0 . GRCh38 10 8069534 8069534 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.986G>C p.Trp329Ser p.W329S ENST00000379328 5/6 566 463 103 669 669 0 strelka-varscan-mutect GATA3,missense_variant,p.Trp329Ser,ENST00000379328,NM_001002295.1;GATA3,missense_variant,p.Trp328Ser,ENST00000346208,NM_002051.2;GATA3,non_coding_transcript_exon_variant,,ENST00000461472,; C ENST00000379328 Transcript missense_variant 1554/3078 986/1335 329/444 W/S tGg/tCg 1 1 GATA3 HGNC HGNC:4172 protein_coding YES CCDS31143.1 ENSP00000368632 P23771 UPI000002AA34 NM_001002295.1 deleterious(0.03) 5/6 PROSITE_profiles:PS50114,hmmpanther:PTHR10071:SF106,hmmpanther:PTHR10071,PROSITE_patterns:PS00344,Gene3D:3.30.50.10,Pfam_domain:PF00320,PIRSF_domain:PIRSF003027,SMART_domains:SM00401,Superfamily_domains:SSF57716 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 8069534 8069534 G C 1 0 0 0 0 1 0 0 0 6125 1357 47 4 4 GATA3 10 8069534 Missense_Mutation SNP G C3N-01842_T 4964096 8069534 125727888 194 26386 MPP7 0 . GRCh38 10 28120313 28120313 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.768C>G p.Phe256Leu p.F256L ENST00000337532 11/18 262 229 33 309 308 1 strelka-varscan-mutect MPP7,missense_variant,p.Phe256Leu,ENST00000337532,NM_001318170.1,NM_173496.3;MPP7,missense_variant,p.Phe256Leu,ENST00000375732,;MPP7,missense_variant,p.Phe256Leu,ENST00000375719,;MPP7,intron_variant,,ENST00000441595,;MPP7,downstream_gene_variant,,ENST00000481244,;MPP7,downstream_gene_variant,,ENST00000474731,;MPP7,missense_variant,p.Phe256Leu,ENST00000496637,; C ENST00000337532 Transcript missense_variant 1045/5080 768/1731 256/576 F/L ttC/ttG 1 -1 MPP7 HGNC HGNC:26542 protein_coding YES CCDS7158.1 ENSP00000337907 Q5T2T1 UPI00000558E1 NM_001318170.1,NM_173496.3 deleterious(0.03) 11/18 PROSITE_profiles:PS50002,hmmpanther:PTHR23122:SF39,hmmpanther:PTHR23122,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044,Prints_domain:PR00452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 28120313 28120313 G C 1 0 0 0 0 1 0 0 0 9705 1281 45 4 4 MPP7 10 28120313 Missense_Mutation SNP G C3N-01842_T 20050779 28120313 105677109 195 26387 EPC1 0 . GRCh38 10 32287117 32287117 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.1133A>T p.Asp378Val p.D378V ENST00000263062 7/15 186 148 38 255 253 2 strelka-varscan-mutect EPC1,missense_variant,p.Asp378Val,ENST00000319778,NM_001272019.2,NM_001272004.1;EPC1,missense_variant,p.Asp328Val,ENST00000375110,NM_001282391.1;EPC1,missense_variant,p.Asp378Val,ENST00000263062,NM_025209.3;RP11-166N17.3,downstream_gene_variant,,ENST00000419441,;EPC1,upstream_gene_variant,,ENST00000479380,;EPC1,non_coding_transcript_exon_variant,,ENST00000495790,; A ENST00000263062 Transcript missense_variant 1403/2913 1133/2511 378/836 D/V gAc/gTc 1 -1 EPC1 HGNC HGNC:19876 protein_coding YES CCDS7172.1 ENSP00000263062 Q9H2F5 UPI000006F77F NM_025209.3 deleterious(0) 7/15 hmmpanther:PTHR14898,hmmpanther:PTHR14898:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 32287117 32287117 T A 1 0 0 0 0 1 0 0 0 5006 1667 58 4 4 EPC1 10 32287117 Missense_Mutation SNP T C3N-01842_T 4166804 32287117 101510305 196 26388 ANKRD30A 0 . GRCh38 10 37197413 37197413 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.2481C>A p.= p.A827A ENST00000361713 29/36 321 226 95 252 252 0 strelka-varscan-mutect ANKRD30A,synonymous_variant,p.=,ENST00000374660,;ANKRD30A,synonymous_variant,p.=,ENST00000611781,;ANKRD30A,synonymous_variant,p.=,ENST00000602533,;ANKRD30A,synonymous_variant,p.=,ENST00000361713,NM_052997.2;ANKRD30A,downstream_gene_variant,,ENST00000475522,; A ENST00000361713 Transcript synonymous_variant 2580/4405 2481/4026 827/1341 A gcC/gcA 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 29/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 37197413 37197413 C A 1 0 0 0 0 0 0 0 1 761 608 21 2 2 ANKRD30A 10 37197413 Silent SNP C C3N-01842_T 4910296 37197413 96600009 197 26389 ZNF33A 0 . GRCh38 10 38055627 38055627 + Silent SNP A A G novel C3N-01842_T C3N-01842_N A A c.1557A>G p.= p.A519A ENST00000307441 6/6 342 305 37 315 315 0 strelka-varscan-mutect ZNF33A,synonymous_variant,p.=,ENST00000307441,NM_001324175.1,NM_001324177.1,NM_001324178.1,NM_001278173.1;ZNF33A,synonymous_variant,p.=,ENST00000374618,NM_001324175.1,NM_001324177.1,NM_001324176.1,NM_001278176.1,NM_001278179.1,NM_001278178.1,NM_001278171.1,NM_001278174.1,NM_001278175.1;ZNF33A,synonymous_variant,p.=,ENST00000458705,NM_006974.2;ZNF33A,synonymous_variant,p.=,ENST00000432900,NM_001278177.1,NM_006954.1;ZNF33A,synonymous_variant,p.=,ENST00000628825,NM_001278170.1;ZNF33A,intron_variant,,ENST00000469037,;ZNF33A,downstream_gene_variant,,ENST00000478556,; G ENST00000307441 Transcript synonymous_variant 1760/6196 1557/2490 519/829 A gcA/gcG 1 1 ZNF33A HGNC HGNC:13096 protein_coding YES CCDS73088.1 ENSP00000304268 A0A0A0MR11 UPI00032969BB NM_001324175.1,NM_001324177.1,NM_001324178.1,NM_001278173.1 6/6 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF204,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 38055627 38055627 A G 1 0 0 0 0 0 0 0 1 18426 204 8 5 5 ZNF33A 10 38055627 Silent SNP A C3N-01842_T 858214 38055627 95741795 198 26390 ZNF239 0 . GRCh38 10 43557280 43557280 + Missense_Mutation SNP T T A rs149602031 C3N-01842_T C3N-01842_N T T c.800A>T p.Lys267Met p.K267M ENST00000306006 2/2 330 242 88 438 438 0 strelka-varscan-mutect ZNF239,missense_variant,p.Lys267Met,ENST00000306006,NM_005674.2;ZNF239,missense_variant,p.Lys267Met,ENST00000374446,NM_001324351.1,NM_001324352.1,NM_001324349.1,NM_001099282.1;ZNF239,missense_variant,p.Lys267Met,ENST00000426961,NM_001099284.1;ZNF239,missense_variant,p.Lys267Met,ENST00000535642,NM_001099283.1;ZNF239,downstream_gene_variant,,ENST00000491188,; A ENST00000306006 Transcript missense_variant 1453/2389 800/1377 267/458 K/M aAg/aTg rs149602031 1 -1 ZNF239 HGNC HGNC:13031 protein_coding YES CCDS41502.1 ENSP00000307774 Q16600 UPI000006DD0E NM_005674.2 deleterious(0) 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF114,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs149602031 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 43557280 43557280 T A 1 0 0 0 0 1 0 0 0 18367 1609 56 4 4 ZNF239 10 43557280 Missense_Mutation SNP T C3N-01842_T 5501653 43557280 90240142 199 26391 GDF10 0 . GRCh38 10 47312733 47312733 + Silent SNP C C A rs150075852 C3N-01842_T C3N-01842_N C C c.1378C>A p.= p.R460R ENST00000580279 3/3 90 81 9 131 131 0 strelka-varscan-mutect GDF10,synonymous_variant,p.=,ENST00000580279,NM_004962.3; A ENST00000580279 Transcript synonymous_variant 1644/2458 1378/1437 460/478 R Cgg/Agg rs150075852 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 3/3 Gene3D:2.10.90.10,Pfam_domain:PF00019,PIRSF_domain:PIRSF037403,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF145,SMART_domains:SM00204,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS rs150075852 . 0 202 7 0 0 0 0 0 -18.67981 0.9999989 1 1 1 0 A 2 1 84 47312733 47312733 C A 1 0 0 0 0 0 0 0 1 6184 875 31 1 1 GDF10 10 47312733 Silent SNP C C3N-01842_T 3755453 47312733 86484689 200 26392 OGDHL 0 . GRCh38 10 49756943 49756943 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.208T>A p.Trp70Arg p.W70R ENST00000374103 3/23 70 49 21 98 98 0 strelka-varscan-mutect OGDHL,missense_variant,p.Trp70Arg,ENST00000374103,NM_018245.2;OGDHL,intron_variant,,ENST00000419399,NM_001143996.1;OGDHL,intron_variant,,ENST00000432695,NM_001143997.1;OGDHL,non_coding_transcript_exon_variant,,ENST00000471460,; T ENST00000374103 Transcript missense_variant 294/3704 208/3033 70/1010 W/R Tgg/Agg 1 -1 OGDHL HGNC HGNC:25590 protein_coding YES CCDS7234.1 ENSP00000363216 Q9ULD0 UPI000013D6A4 NM_018245.2 deleterious(0) 3/23 Pfam_domain:PF16078,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF5,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 84 49756943 49756943 A T 1 0 0 0 0 1 0 0 0 10914 202 7 4 4 OGDHL 10 49756943 Missense_Mutation SNP A C3N-01842_T 2444210 49756943 84040479 201 26393 PCDH15 0 . GRCh38 10 54153099 54153099 + Splice_Site SNP C C G rs761865629 C3N-01842_T C3N-01842_N C C c.1799+1G>C p.X600_splice ENST00000373957 425 347 78 567 567 0 strelka-varscan-mutect PCDH15,splice_donor_variant,,ENST00000614895,;PCDH15,splice_donor_variant,,ENST00000373965,NM_001142772.1;PCDH15,splice_donor_variant,,ENST00000414778,;PCDH15,splice_donor_variant,,ENST00000617051,;PCDH15,splice_donor_variant,,ENST00000373957,NM_001142763.1;PCDH15,splice_donor_variant,,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,splice_donor_variant,,ENST00000395430,NM_001142766.1;PCDH15,splice_donor_variant,,ENST00000395433,NM_001142773.1;PCDH15,splice_donor_variant,,ENST00000395432,NM_001142767.1;PCDH15,splice_donor_variant,,ENST00000320301,NM_033056.3;PCDH15,splice_donor_variant,,ENST00000622048,;PCDH15,splice_donor_variant,,ENST00000437009,NM_001142765.1;PCDH15,splice_donor_variant,,ENST00000617271,NM_001142770.1;PCDH15,splice_donor_variant,,ENST00000613657,NM_001142769.1;PCDH15,splice_donor_variant,,ENST00000395445,;PCDH15,splice_donor_variant,,ENST00000616114,;PCDH15,splice_donor_variant,,ENST00000395438,;PCDH15,splice_donor_variant,,ENST00000612394,;PCDH15,splice_donor_variant,,ENST00000621708,NM_001142771.1;PCDH15,splice_donor_variant,,ENST00000409834,;PCDH15,splice_donor_variant,,ENST00000373955,;PCDH15,splice_donor_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,splice_donor_variant,,ENST00000448885,;PCDH15,splice_donor_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; G ENST00000373957 Transcript splice_donor_variant -/7032 1799/5889 600/1962 rs761865629 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 15/34 HIGH 1 SNV 5 1 PASS rs761865629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 84 54153099 54153099 C G 1 0 0 0 0 0 0 1 0 11598 521 18 4 4 PCDH15 10 54153099 Splice_Site SNP C C3N-01842_T 4396156 54153099 79644323 202 26394 CHST3 0 . GRCh38 10 72005941 72005941 + Silent SNP A A T novel C3N-01842_T C3N-01842_N A A c.99A>T p.= p.I33I ENST00000373115 2/3 563 434 129 739 739 0 strelka-varscan-mutect CHST3,synonymous_variant,p.=,ENST00000373115,NM_004273.4; T ENST00000373115 Transcript synonymous_variant 536/6970 99/1440 33/479 I atA/atT 1 1 CHST3 HGNC HGNC:1971 protein_coding YES CCDS7312.1 ENSP00000362207 Q7LGC8 UPI000013CB04 NM_004273.4 2/3 PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF38,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs915527340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 72005941 72005941 A T 1 0 0 0 0 0 0 0 1 3165 410 15 4 4 CHST3 10 72005941 Silent SNP A C3N-01842_T 17852842 72005941 61791481 203 26395 ASCC1 0 . GRCh38 10 72204482 72204482 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.236A>G p.Asn79Ser p.N79S ENST00000342444 4/13 238 214 24 271 271 0 strelka-varscan-mutect ASCC1,missense_variant,p.Asn79Ser,ENST00000342444,NM_001198799.2;ASCC1,missense_variant,p.Asn79Ser,ENST00000394915,;ASCC1,intron_variant,,ENST00000394919,NM_001198798.2;ASCC1,intron_variant,,ENST00000317168,NM_001198800.2;ASCC1,intron_variant,,ENST00000486689,;ASCC1,intron_variant,,ENST00000317126,;ASCC1,intron_variant,,ENST00000524829,;ASCC1,intron_variant,,ENST00000527593,;ASCC1,intron_variant,,ENST00000530461,;ASCC1,intron_variant,,ENST00000526751,;ASCC1,intron_variant,,ENST00000531048,;ASCC1,intron_variant,,ENST00000492502,;ASCC1,missense_variant,p.Asn9Ser,ENST00000461369,;ASCC1,intron_variant,,ENST00000532011,; C ENST00000342444 Transcript missense_variant 338/2270 236/1203 79/400 N/S aAc/aGc 1 -1 ASCC1 HGNC HGNC:24268 protein_coding YES CCDS55713.1 ENSP00000339404 Q8N9N2 UPI000006F7E9 NM_001198799.2 tolerated_low_confidence(0.15) 4/13 PIRSF_domain:PIRSF027019 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 72204482 72204482 T C 1 0 0 0 0 1 0 0 0 1173 1725 60 5 5 ASCC1 10 72204482 Missense_Mutation SNP T C3N-01842_T 198541 72204482 61592940 204 26396 DNMBP 0 . GRCh38 10 99930364 99930364 + Missense_Mutation SNP C C G rs115073424 C3N-01842_T C3N-01842_N C C c.400G>C p.Gly134Arg p.G134R ENST00000636706 1/14 208 184 24 234 234 0 strelka-varscan-mutect DNMBP,missense_variant,p.Gly134Arg,ENST00000636706,NM_001318326.1;DNMBP,intron_variant,,ENST00000324109,NM_015221.2;DNMBP-AS1,intron_variant,,ENST00000434409,;DNMBP-AS1,downstream_gene_variant,,ENST00000427093,; G ENST00000636706 Transcript missense_variant 633/5437 400/3630 134/1209 G/R Ggg/Cgg rs115073424 1 -1 DNMBP HGNC HGNC:30373 protein_coding ENSP00000489875 UPI0005D010EE NM_001318326.1 deleterious_low_confidence(0) 1/14 MODERATE SNV 1 PASS rs115073424 . 0 206 0 3 0 0 0 0 -20 0.9999886 1 1 1 0 G 3 3 84 99930364 99930364 C G 1 0 0 0 0 1 0 0 0 4487 652 23 4 4 DNMBP 10 99930364 Missense_Mutation SNP C C3N-01842_T 27725882 99930364 33867058 205 26397 KAZALD1 0 . GRCh38 10 101062778 101062778 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.186C>T p.= p.A62A ENST00000370200 2/5 139 103 36 164 162 2 strelka-varscan-mutect KAZALD1,synonymous_variant,p.=,ENST00000370200,NM_030929.4;RP11-108L7.15,upstream_gene_variant,,ENST00000609242,;KAZALD1,intron_variant,,ENST00000477979,;KAZALD1,intron_variant,,ENST00000470106,;KAZALD1,upstream_gene_variant,,ENST00000465807,;KAZALD1,upstream_gene_variant,,ENST00000477267,;KAZALD1,upstream_gene_variant,,ENST00000608812,; T ENST00000370200 Transcript synonymous_variant 512/1913 186/915 62/304 A gcC/gcT 1 1 KAZALD1 HGNC HGNC:25460 protein_coding YES CCDS7509.1 ENSP00000359219 Q96I82 UPI000004283E NM_030929.4 2/5 Pfam_domain:PF00219,PIRSF_domain:PIRSF018239,PROSITE_profiles:PS51323,hmmpanther:PTHR14186,hmmpanther:PTHR14186:SF21,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 101062778 101062778 C T 1 0 0 0 0 0 0 0 1 7906 639 23 1 1 KAZALD1 10 101062778 Silent SNP C C3N-01842_T 1132414 101062778 32734644 206 26398 ACSL5 0 . GRCh38 10 112413208 112413208 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.1152C>T p.= p.F384F ENST00000356116 12/21 268 200 68 362 362 0 strelka-varscan-mutect ACSL5,synonymous_variant,p.=,ENST00000393081,NM_203380.1;ACSL5,synonymous_variant,p.=,ENST00000354273,;ACSL5,synonymous_variant,p.=,ENST00000356116,NM_016234.3;ACSL5,synonymous_variant,p.=,ENST00000354655,NM_203379.1;ACSL5,synonymous_variant,p.=,ENST00000433418,;RP11-324O2.3,intron_variant,,ENST00000424422,;RP11-324O2.3,intron_variant,,ENST00000631085,;RP11-324O2.3,upstream_gene_variant,,ENST00000449782,;RP11-324O2.3,upstream_gene_variant,,ENST00000598447,;RP11-324O2.3,upstream_gene_variant,,ENST00000627339,;RP11-324O2.3,upstream_gene_variant,,ENST00000594870,;ACSL5,non_coding_transcript_exon_variant,,ENST00000495539,;ACSL5,non_coding_transcript_exon_variant,,ENST00000467340,;ACSL5,downstream_gene_variant,,ENST00000479936,; T ENST00000356116 Transcript synonymous_variant 1264/3353 1152/2220 384/739 F ttC/ttT 1 1 ACSL5 HGNC HGNC:16526 protein_coding YES CCDS7572.1 ENSP00000348429 Q9ULC5 UPI000003ED0C NM_016234.3 12/21 hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF204,Gene3D:3.40.50.980,Pfam_domain:PF00501,Superfamily_domains:SSF56801 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 112413208 112413208 C T 1 0 0 0 0 0 0 0 1 222 912 32 3 3 ACSL5 10 112413208 Silent SNP C C3N-01842_T 11350430 112413208 21384214 207 26399 PRDX3 0 . GRCh38 10 119173809 119173809 + Silent SNP C C A C3N-01842_T C3N-01842_N C C c.375G>T p.= p.V125V ENST00000298510 4/7 188 167 21 196 196 0 strelka-varscan-mutect PRDX3,synonymous_variant,p.=,ENST00000298510,NM_006793.4,NM_001302272.1;PRDX3,non_coding_transcript_exon_variant,,ENST00000463322,;PRDX3,upstream_gene_variant,,ENST00000494433,; A ENST00000298510 Transcript synonymous_variant 418/1591 375/771 125/256 V gtG/gtT COSM5570648 1 -1 PRDX3 HGNC HGNC:9354 protein_coding YES CCDS7611.1 ENSP00000298510 P30048 UPI0000000C81 NM_006793.4,NM_001302272.1 4/7 PROSITE_profiles:PS51352,hmmpanther:PTHR10681:SF114,hmmpanther:PTHR10681,Pfam_domain:PF00578,Gene3D:3.40.30.10,Superfamily_domains:SSF52833 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 119173809 119173809 C A 1 0 0 0 0 0 0 0 1 12598 813 29 2 2 PRDX3 10 119173809 Silent SNP C C3N-01842_T 6760601 119173809 14623613 208 26400 GPR26 0 . GRCh38 10 123666959 123666959 + Silent SNP C C G novel C3N-01842_T C3N-01842_N C C c.552C>G p.= p.S184S ENST00000284674 1/3 314 285 29 415 415 0 strelka-varscan-mutect GPR26,synonymous_variant,p.=,ENST00000284674,NM_153442.3; G ENST00000284674 Transcript synonymous_variant 605/7514 552/1014 184/337 S tcC/tcG 1 1 GPR26 HGNC HGNC:4481 protein_coding YES CCDS7636.1 ENSP00000284674 Q8NDV2 UPI000006E821 NM_153442.3 1/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24245,hmmpanther:PTHR24245:SF6,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 123666959 123666959 C G 1 0 0 0 0 0 0 0 1 6568 668 24 4 4 GPR26 10 123666959 Silent SNP C C3N-01842_T 4493150 123666959 10130463 209 26401 C10orf90 0 . GRCh38 10 126429810 126429810 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1938G>T p.Lys646Asn p.K646N ENST00000284694 7/9 229 206 23 225 225 0 strelka-varscan-mutect C10orf90,missense_variant,p.Lys646Asn,ENST00000284694,NM_001004298.2;C10orf90,missense_variant,p.Lys599Asn,ENST00000356858,;C10orf90,missense_variant,p.Lys646Asn,ENST00000432642,;C10orf90,missense_variant,p.Lys189Asn,ENST00000424927,;C10orf90,missense_variant,p.Lys50Asn,ENST00000480379,; A ENST00000284694 Transcript missense_variant 2059/3076 1938/2100 646/699 K/N aaG/aaT 1 -1 C10orf90 HGNC HGNC:26563 protein_coding YES CCDS31310.1 ENSP00000284694 Q96M02 UPI00001D808F NM_001004298.2 deleterious(0) 7/9 Pfam_domain:PF15309,hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 126429810 126429810 C A 1 0 0 0 0 1 0 0 0 1773 680 24 2 2 C10orf90 10 126429810 Missense_Mutation SNP C C3N-01842_T 2762851 126429810 7367612 210 26402 MKI67 0 . GRCh38 10 128122996 128122996 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.172G>T p.Ala58Ser p.A58S ENST00000368654 4/15 111 77 34 79 79 0 strelka-varscan-mutect MKI67,missense_variant,p.Ala58Ser,ENST00000368654,NM_002417.4;MKI67,missense_variant,p.Ala58Ser,ENST00000368653,NM_001145966.1;MKI67,intron_variant,,ENST00000478293,; A ENST00000368654 Transcript missense_variant,splice_region_variant 548/12678 172/9771 58/3256 A/S Gca/Tca 1 -1 MKI67 HGNC HGNC:7107 protein_coding YES CCDS7659.1 ENSP00000357643 P46013 UPI000013DB54 NM_002417.4 deleterious(0) 4/15 Gene3D:2.60.200.20,Pfam_domain:PF00498,PROSITE_profiles:PS50006,hmmpanther:PTHR21603,hmmpanther:PTHR21603:SF17,SMART_domains:SM00240,Superfamily_domains:SSF49879 MODERATE 1 SNV 2 1 PASS rs1030439103 . 0 199 11 0 0 0 0 0 -20 0.9999902 1 1 1 0 A 3 1 84 128122996 128122996 C A 1 0 0 0 0 1 0 0 0 9566 753 26 2 2 MKI67 10 128122996 Missense_Mutation SNP C C3N-01842_T 1693186 128122996 5674426 211 26403 CDHR5 0 . GRCh38 11 624212 624212 + Splice_Site SNP C C A novel C3N-01842_T C3N-01842_N C C c.312+1G>T p.X104_splice ENST00000358353 234 185 49 266 265 1 strelka-varscan-mutect CDHR5,splice_donor_variant,,ENST00000358353,;CDHR5,splice_donor_variant,,ENST00000397542,NM_001171968.1,NM_021924.4;CDHR5,splice_donor_variant,,ENST00000349570,NM_031264.3;CDHR5,splice_donor_variant,,ENST00000526077,;CDHR5,splice_donor_variant,,ENST00000534311,;CDHR5,splice_donor_variant,,ENST00000531088,;SCT,downstream_gene_variant,,ENST00000176195,NM_021920.2;CDHR5,downstream_gene_variant,,ENST00000529337,;CDHR5,upstream_gene_variant,,ENST00000532949,;CDHR5,splice_donor_variant,,ENST00000531177,;CDHR5,splice_donor_variant,,ENST00000531899,; A ENST00000358353 Transcript splice_donor_variant -/3635 312/2538 104/845 1 -1 CDHR5 HGNC HGNC:7521 protein_coding YES CCDS7707.1 ENSP00000351118 Q9HBB8 UPI0000456444 4/15 HIGH SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 84 624212 624212 C A 1 0 0 0 0 0 0 1 0 2825 521 18 2 2 CDHR5 11 624212 Splice_Site SNP C C3N-01842_T 624212 134462410 212 26404 AP2A2 0 . GRCh38 11 1008018 1008018 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.2306A>G p.Asn769Ser p.N769S ENST00000332231 18/22 340 272 68 443 442 1 strelka-varscan-mutect AP2A2,missense_variant,p.Asn769Ser,ENST00000332231,NM_001242837.1;AP2A2,missense_variant,p.Asn768Ser,ENST00000448903,NM_012305.3;AP2A2,intron_variant,,ENST00000534328,;MUC6,downstream_gene_variant,,ENST00000421673,NM_005961.2;AP2A2,non_coding_transcript_exon_variant,,ENST00000525891,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529438,;AP2A2,3_prime_UTR_variant,,ENST00000528815,;AP2A2,non_coding_transcript_exon_variant,,ENST00000531497,;AP2A2,non_coding_transcript_exon_variant,,ENST00000526401,;AP2A2,non_coding_transcript_exon_variant,,ENST00000529427,;AP2A2,upstream_gene_variant,,ENST00000528816,;AP2A2,downstream_gene_variant,,ENST00000526376,; G ENST00000332231 Transcript missense_variant 2519/4656 2306/2823 769/940 N/S aAc/aGc 1 1 AP2A2 HGNC HGNC:562 protein_coding YES CCDS73234.1 ENSP00000327694 O94973 UPI000050AA18 NM_001242837.1 tolerated(1) 18/22 Gene3D:1kyfA01,PIRSF_domain:PIRSF037091,Pfam_domain:PF02883,SMART_domains:SM00809,Superfamily_domains:SSF49348 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 1008018 1008018 A G 1 0 0 0 0 1 0 0 0 856 43 2 5 5 AP2A2 11 1008018 Missense_Mutation SNP A C3N-01842_T 383806 1008018 134078604 213 26405 MUC6 0 . GRCh38 11 1024924 1024924 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.3145C>A p.Leu1049Ile p.L1049I ENST00000421673 24/33 377 296 81 434 434 0 strelka-varscan-mutect MUC6,missense_variant,p.Leu1049Ile,ENST00000421673,NM_005961.2;MUC6,upstream_gene_variant,,ENST00000527242,; T ENST00000421673 Transcript missense_variant 3196/8006 3145/7320 1049/2439 L/I Ctc/Atc COSM4487133,COSM4487134 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 tolerated(0.07) 24/33 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF264,hmmpanther:PTHR11339 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 1024924 1024924 G T 1 0 0 0 0 1 0 0 0 9980 942 33 2 2 MUC6 11 1024924 Missense_Mutation SNP G C3N-01842_T 16906 1024924 134061698 214 26406 MUC5AC 0 . GRCh38 11 1187982 1187982 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.9837G>A p.= p.V3279V ENST00000621226 31/49 174 144 30 160 160 0 strelka-varscan-mutect MUC5AC,synonymous_variant,p.=,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript synonymous_variant 9884/17448 9837/16965 3279/5654 V gtG/gtA 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 31/49 Pfam_domain:PF13330 LOW 1 SNV 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999986 1 1 1 0 A 2 1 84 1187982 1187982 G A 1 0 0 0 0 0 0 0 1 9978 1277 45 3 3 MUC5AC 11 1187982 Silent SNP G C3N-01842_T 163058 1187982 133898640 215 26407 MUC5AC 0 . GRCh38 11 1196452 1196452 + Nonsense_Mutation SNP C C A rs200151958 C3N-01842_T C3N-01842_N C C c.15702C>A p.Tyr5234Ter p.Y5234* ENST00000621226 38/49 318 264 54 340 340 0 strelka-varscan-mutect MUC5AC,stop_gained,p.Tyr5234Ter,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript stop_gained 15749/17448 15702/16965 5234/5654 Y/* taC/taA rs200151958 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 38/49 Gene3D:2.10.25.10,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,Superfamily_domains:SSF57567 HIGH 1 SNV 5 1 PASS rs200151958 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 1196452 1196452 C A 1 0 0 0 0 0 1 0 0 9978 547 19 1 1 MUC5AC 11 1196452 Nonsense_Mutation SNP C C3N-01842_T 8470 1196452 133890170 216 26408 OR51D1 0 . GRCh38 11 4640359 4640359 + Missense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.569C>A p.Ser190Tyr p.S190Y ENST00000357605 1/1 644 486 158 597 597 0 strelka-varscan-mutect OR51D1,missense_variant,p.Ser190Tyr,ENST00000357605,NM_001004751.2;OR51E1,upstream_gene_variant,,ENST00000396952,NM_152430.3; A ENST00000357605 Transcript missense_variant 645/1124 569/975 190/324 S/Y tCc/tAc COSM5372513 1 1 OR51D1 HGNC HGNC:15193 protein_coding YES CCDS31357.1 ENSP00000350222 Q8NGF3 A0A126GVM2 UPI000004B21E NM_001004751.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF166,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs772148760 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 4640359 4640359 C A 1 0 0 0 0 1 0 0 0 11167 855 30 2 2 OR51D1 11 4640359 Missense_Mutation SNP C C3N-01842_T 3443907 4640359 130446263 217 26409 OR51E2 0 . GRCh38 11 4682257 4682257 + Missense_Mutation SNP G G T rs767765213 C3N-01842_T C3N-01842_N G G c.455C>A p.Ser152Tyr p.S152Y ENST00000396950 2/2 536 415 121 605 605 0 strelka-varscan-mutect OR51E2,missense_variant,p.Ser152Tyr,ENST00000396950,NM_030774.3;OR51E2,downstream_gene_variant,,ENST00000532598,; T ENST00000396950 Transcript missense_variant 695/2781 455/963 152/320 S/Y tCc/tAc rs767765213,COSM3447737 1 -1 OR51E2 HGNC HGNC:15195 protein_coding YES CCDS7751.1 ENSP00000380153 Q9H255 A0A126GVK0 UPI000003B49B NM_030774.3 tolerated(0.36) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF92,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs767765213 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 4682257 4682257 G T 1 0 0 0 0 1 0 0 0 11169 1174 41 2 2 OR51E2 11 4682257 Missense_Mutation SNP G C3N-01842_T 41898 4682257 130404365 218 26410 OR51B5 0 . GRCh38 11 5343404 5343404 + Missense_Mutation SNP C C A rs748373536 C3N-01842_T C3N-01842_N C C c.121G>T p.Gly41Cys p.G41C ENST00000300773 1/1 206 168 38 245 242 3 strelka-varscan-mutect OR51B5,missense_variant,p.Gly41Cys,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; A ENST00000300773 Transcript missense_variant 121/939 121/939 41/312 G/C Ggc/Tgc rs748373536 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 tolerated(0.59) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs748373536 . 0 200 4 4 2 0 0 0 -19.97479 0.9450195 1 1 1 0 A 3 1 84 5343404 5343404 C A 1 0 0 0 0 1 0 0 0 11165 594 21 2 2 OR51B5 11 5343404 Missense_Mutation SNP C C3N-01842_T 661147 5343404 129743218 219 26411 OR52E8 0 . GRCh38 11 5857682 5857682 + Silent SNP C C A rs774887935 C3N-01842_T C3N-01842_N C C c.21G>T p.= p.T7T ENST00000537935 1/1 136 102 34 131 131 0 strelka-varscan-mutect OR52E8,synonymous_variant,p.=,ENST00000537935,NM_001005168.1;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; A ENST00000537935 Transcript synonymous_variant 53/1061 21/954 7/317 T acG/acT rs774887935,COSM4034245,COSM5286741 1 -1 OR52E8 HGNC HGNC:15217 protein_coding YES CCDS31400.1 ENSP00000444054 Q6IFG1 A0A126GVH0 UPI000004B211 NM_001005168.1 1/1 hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF170,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs774887935 . 0 199 11 0 0 0 0 0 -20 0.9999855 1 1 1 0 A 2 1 84 5857682 5857682 C A 1 0 0 0 0 0 0 0 1 11191 523 19 1 1 OR52E8 11 5857682 Silent SNP C C3N-01842_T 514278 5857682 129228940 220 26412 KCNC1 0 . GRCh38 11 17772537 17772537 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1443C>A p.His481Gln p.H481Q ENST00000265969 2/4 314 236 78 362 362 0 strelka-varscan-mutect KCNC1,missense_variant,p.His481Gln,ENST00000379472,NM_004976.4;KCNC1,missense_variant,p.His481Gln,ENST00000265969,NM_001112741.1;KCNC1,upstream_gene_variant,,ENST00000525802,; A ENST00000265969 Transcript missense_variant 2634/3887 1443/1758 481/585 H/Q caC/caA 1 1 KCNC1 HGNC HGNC:6233 protein_coding YES CCDS44547.1 ENSP00000265969 P48547 UPI0000E2291F NM_001112741.1 tolerated(0.24) 2/4 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF157,Prints_domain:PR01581 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 17772537 17772537 C A 1 0 0 0 0 1 0 0 0 7930 477 17 2 2 KCNC1 11 17772537 Missense_Mutation SNP C C3N-01842_T 11914855 17772537 117314085 221 26413 ELP4 0 . GRCh38 11 31520073 31520073 + Frame_Shift_Del DEL G G - novel C3N-01842_T C3N-01842_N G G c.242delG p.Gly81GlufsTer5 p.G81Efs*5 ENST00000395934 2/12 259 218 41 224 224 0 sindel-varindel-pindel ELP4,frameshift_variant,p.Gly81GlufsTer5,ENST00000395934,NM_001288726.1;ELP4,frameshift_variant,p.Gly81GlufsTer5,ENST00000350638,NM_019040.4;ELP4,frameshift_variant,p.Gly81GlufsTer5,ENST00000379163,NM_001288725.1;ELP4,frameshift_variant,p.Gly81GlufsTer5,ENST00000474374,; - ENST00000395934 Transcript frameshift_variant 248/1961 241/1608 81/535 G/X Gga/ga 1 1 ELP4 HGNC HGNC:1171 protein_coding YES CCDS73272.1 ENSP00000379267 G5E9D4 UPI000013FA14 NM_001288726.1 2/12 Low_complexity_(Seg):seg,hmmpanther:PTHR12896,Gene3D:3.40.50.300,Pfam_domain:PF05625 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 31520073 31520073 G - 1 0 1 0 1 0 0 0 0 4916 1349 47 0 0 ELP4 11 31520073 Frame_Shift_Del DEL G C3N-01842_T 13747536 31520073 103566549 222 26414 RAG2 0 . GRCh38 11 36593289 36593289 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.880G>T p.Asp294Tyr p.D294Y ENST00000618712 3/3 771 612 159 721 721 0 strelka-varscan-mutect RAG2,missense_variant,p.Asp294Tyr,ENST00000618712,NM_001243785.1,NM_001243786.1;RAG2,missense_variant,p.Asp294Tyr,ENST00000311485,NM_000536.3;C11orf74,upstream_gene_variant,,ENST00000446510,NM_001276723.1,NM_001276722.1;C11orf74,upstream_gene_variant,,ENST00000617650,NM_001276724.1;C11orf74,upstream_gene_variant,,ENST00000532470,;C11orf74,upstream_gene_variant,,ENST00000334307,NM_138787.3;C11orf74,upstream_gene_variant,,ENST00000534635,NM_001276725.1;C11orf74,upstream_gene_variant,,ENST00000531554,;C11orf74,upstream_gene_variant,,ENST00000347206,NM_001276727.1,NM_001276726.1;C11orf74,upstream_gene_variant,,ENST00000530697,;RAG2,downstream_gene_variant,,ENST00000529083,;RAG2,downstream_gene_variant,,ENST00000527033,;RAG2,downstream_gene_variant,,ENST00000532616,;C11orf74,upstream_gene_variant,,ENST00000527108,;RAG2,intron_variant,,ENST00000524423,;RAG2,downstream_gene_variant,,ENST00000528428,;RAG2,downstream_gene_variant,,ENST00000534379,;RAG2,downstream_gene_variant,,ENST00000530276,;RAG1,downstream_gene_variant,,ENST00000534663,;C11orf74,upstream_gene_variant,,ENST00000528092,;C11orf74,upstream_gene_variant,,ENST00000524539,; A ENST00000618712 Transcript missense_variant 1474/2818 880/1584 294/527 D/Y Gac/Tac 1 -1 RAG2 HGNC HGNC:9832 protein_coding YES CCDS7903.1 ENSP00000478672 P55895 UPI00001330E9 NM_001243785.1,NM_001243786.1 deleterious(0.01) 3/3 Superfamily_domains:0047741,Pfam_domain:PF03089,hmmpanther:PTHR10960,hmmpanther:PTHR10960:SF0 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 36593289 36593289 C A 1 0 0 0 0 1 0 0 0 13165 855 30 2 2 RAG2 11 36593289 Missense_Mutation SNP C C3N-01842_T 5073216 36593289 98493333 223 26415 TRIM48 0 . GRCh38 11 55269271 55269271 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.608A>G p.Gln203Arg p.Q203R ENST00000417545 5/6 565 440 125 646 646 0 strelka-varscan-mutect TRIM48,missense_variant,p.Gln203Arg,ENST00000417545,NM_024114.3;RP11-72M10.2,downstream_gene_variant,,ENST00000526762,; G ENST00000417545 Transcript missense_variant 694/1445 608/675 203/224 Q/R cAg/cGg 1 1 TRIM48 HGNC HGNC:19021 protein_coding YES CCDS7947.2 ENSP00000402414 Q8IWZ4 UPI0000374413 NM_024114.3 tolerated(0.15) 5/6 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF410 MODERATE 1 SNV 1 1 PASS . . 5 205 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 55269271 55269271 A G 1 0 0 0 0 1 0 0 0 17013 188 7 5 5 TRIM48 11 55269271 Missense_Mutation SNP A C3N-01842_T 18675982 55269271 79817351 224 26416 OR4C11 0 . GRCh38 11 55604214 55604214 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.160G>A p.Gly54Arg p.G54R ENST00000302231 1/1 291 211 80 263 262 1 strelka-varscan-mutect OR4C11,missense_variant,p.Gly54Arg,ENST00000302231,NM_001004700.2; T ENST00000302231 Transcript missense_variant 185/1045 160/933 54/310 G/R Gga/Aga 1 -1 OR4C11 HGNC HGNC:15167 protein_coding YES CCDS31503.1 ENSP00000306651 Q6IEV9 A0A126GVN6 UPI000013E7AD NM_001004700.2 tolerated(0.06) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF447,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 23 186 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 55604214 55604214 C T 1 0 0 0 0 1 0 0 0 11122 690 24 3 3 OR4C11 11 55604214 Missense_Mutation SNP C C3N-01842_T 334943 55604214 79482408 225 26417 OR5D18 0 . GRCh38 11 55819726 55819726 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.97C>G p.Leu33Val p.L33V ENST00000333976 1/1 204 163 41 174 174 0 strelka-varscan-mutect OR5D18,missense_variant,p.Leu33Val,ENST00000333976,NM_001001952.1; G ENST00000333976 Transcript missense_variant 97/942 97/942 33/313 L/V Ctg/Gtg 1 1 OR5D18 HGNC HGNC:15285 protein_coding YES CCDS31510.1 ENSP00000335025 Q8NGL1 UPI0000046197 NM_001001952.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF86,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 55819726 55819726 C G 1 0 0 0 0 1 0 0 0 11227 912 32 4 4 OR5D18 11 55819726 Missense_Mutation SNP C C3N-01842_T 215512 55819726 79266896 226 26418 OR5D16 0 . GRCh38 11 55839459 55839459 + Frame_Shift_Del DEL C C - rs372803354 C3N-01842_T C3N-01842_N C C c.709delC p.Arg237AlafsTer11 p.R237Afs*11 ENST00000378396 1/1 291 225 66 406 406 0 sindel-varindel-pindel OR5D16,frameshift_variant,p.Arg237AlafsTer11,ENST00000378396,NM_001005496.1; - ENST00000378396 Transcript frameshift_variant 708/987 708/987 236/328 H/X caC/ca rs372803354 1 1 OR5D16 HGNC HGNC:15283 protein_coding YES CCDS31512.1 ENSP00000367649 Q8NGK9 UPI0000046198 NM_001005496.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF243,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 55839459 55839459 C - 1 0 1 0 1 0 0 0 0 11226 506 18 0 0 OR5D16 11 55839459 Frame_Shift_Del DEL C C3N-01842_T 19733 55839459 79247163 227 26419 OR8H3 0 . GRCh38 11 56122811 56122811 + Missense_Mutation SNP G G A C3N-01842_T C3N-01842_N G G c.439G>A p.Gly147Arg p.G147R ENST00000313472 1/1 279 209 70 288 288 0 strelka-varscan-mutect OR8H3,missense_variant,p.Gly147Arg,ENST00000313472,NM_001005201.1; A ENST00000313472 Transcript missense_variant 439/939 439/939 147/312 G/R Ggg/Agg COSM1703962 1 1 OR8H3 HGNC HGNC:15309 protein_coding YES CCDS31519.1 ENSP00000323928 Q8N146 UPI0000041D25 NM_001005201.1 deleterious(0.02) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF280,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 56122811 56122811 G A 1 0 0 0 0 1 0 0 0 11307 1348 47 3 3 OR8H3 11 56122811 Missense_Mutation SNP G C3N-01842_T 283352 56122811 78963811 228 26420 OR5T3 0 . GRCh38 11 56252540 56252540 + Missense_Mutation SNP A A T C3N-01842_T C3N-01842_N A A c.341A>T p.Asn114Ile p.N114I ENST00000303059 1/1 413 311 102 338 338 0 strelka-varscan-mutect OR5T3,missense_variant,p.Asn114Ile,ENST00000303059,NM_001004747.1; T ENST00000303059 Transcript missense_variant 341/1023 341/1023 114/340 N/I aAt/aTt COSM3666400 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 56252540 56252540 A T 1 0 0 0 0 1 0 0 0 11251 101 4 4 4 OR5T3 11 56252540 Missense_Mutation SNP A C3N-01842_T 129729 56252540 78834082 229 26421 SLC43A3 0 . GRCh38 11 57414946 57414946 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.969G>T p.= p.G323G ENST00000533524 10/14 381 312 69 428 425 3 strelka-varscan-mutect SLC43A3,synonymous_variant,p.=,ENST00000395123,NM_014096.3;SLC43A3,synonymous_variant,p.=,ENST00000395124,NM_001278201.1,NM_199329.2;SLC43A3,synonymous_variant,p.=,ENST00000352187,NM_017611.2;SLC43A3,synonymous_variant,p.=,ENST00000529554,;SLC43A3,synonymous_variant,p.=,ENST00000533524,NM_001278206.1;SLC43A3,synonymous_variant,p.=,ENST00000530005,;RP11-872D17.8,upstream_gene_variant,,ENST00000529411,;SLC43A3,downstream_gene_variant,,ENST00000529113,;SLC43A3,downstream_gene_variant,,ENST00000528098,;SLC43A3,synonymous_variant,p.=,ENST00000525205,;RP11-872D17.8,non_coding_transcript_exon_variant,,ENST00000534081,; A ENST00000533524 Transcript synonymous_variant 1311/1879 969/1515 323/504 G ggG/ggT 1 -1 SLC43A3 HGNC HGNC:17466 protein_coding YES CCDS60784.1 ENSP00000434515 Q8NBI5 UPI0001AE6BEC NM_001278206.1 10/14 hmmpanther:PTHR20765:SF1,hmmpanther:PTHR20765,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 57414946 57414946 C A 1 0 0 0 0 0 0 0 1 14912 610 22 2 2 SLC43A3 11 57414946 Silent SNP C C3N-01842_T 1162406 57414946 77671676 230 26422 OSBP 0 . GRCh38 11 59600824 59600824 + Nonsense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.1174G>T p.Glu392Ter p.E392* ENST00000263847 6/14 278 223 55 274 274 0 strelka-varscan-mutect OSBP,stop_gained,p.Glu392Ter,ENST00000263847,NM_002556.2;OSBP,stop_gained,p.Glu12Ter,ENST00000525357,;OSBP,upstream_gene_variant,,ENST00000528903,; A ENST00000263847 Transcript stop_gained 1654/5083 1174/2424 392/807 E/* Gaa/Taa COSM276557 1 -1 OSBP HGNC HGNC:8503 protein_coding YES CCDS7974.1 ENSP00000263847 P22059 UPI0000130EAF NM_002556.2 6/14 hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF52 1 HIGH 1 SNV 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 59600824 59600824 C A 1 0 0 0 0 0 1 0 0 11339 840 29 2 2 OSBP 11 59600824 Nonsense_Mutation SNP C C3N-01842_T 2185878 59600824 75485798 231 26423 ZP1 0 . GRCh38 11 60869251 60869251 + Frame_Shift_Del DEL C C - novel C3N-01842_T C3N-01842_N C C c.304delC p.His102ThrfsTer11 p.H102Tfs*11 ENST00000278853 2/12 197 148 49 267 267 0 sindel-varindel-pindel ZP1,frameshift_variant,p.His102ThrfsTer11,ENST00000278853,NM_207341.3;ZP1,frameshift_variant,p.His33ThrfsTer40,ENST00000540908,;ZP1,upstream_gene_variant,,ENST00000537203,;ZP1,upstream_gene_variant,,ENST00000543020,;ZP1,upstream_gene_variant,,ENST00000542971,; - ENST00000278853 Transcript frameshift_variant 303/1954 303/1917 101/638 C/X tgC/tg 1 1 ZP1 HGNC HGNC:13187 protein_coding YES CCDS31572.1 ENSP00000278853 P60852 V9HWI9 UPI0000351AA0 NM_207341.3 2/12 hmmpanther:PTHR23343:SF41,hmmpanther:PTHR23343 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 60869251 60869251 C - 1 0 1 0 1 0 0 0 0 18807 747 26 0 0 ZP1 11 60869251 Frame_Shift_Del DEL C C3N-01842_T 1268427 60869251 74217371 232 26424 CD6 0 . GRCh38 11 61008637 61008637 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.573C>A p.Asp191Glu p.D191E ENST00000313421 4/13 172 144 28 263 262 1 strelka-varscan-mutect CD6,missense_variant,p.Asp191Glu,ENST00000313421,NM_006725.4;CD6,missense_variant,p.Asp191Glu,ENST00000352009,NM_001254750.1;CD6,missense_variant,p.Asp191Glu,ENST00000452451,NM_001254751.1;CD6,missense_variant,p.Asp191Glu,ENST00000433107,;CD6,missense_variant,p.Asp191Glu,ENST00000542157,;CD6,missense_variant,p.Asp35Glu,ENST00000538611,;CD6,intron_variant,,ENST00000545105,;CD6,downstream_gene_variant,,ENST00000538288,;CD6,missense_variant,p.Asp191Glu,ENST00000344931,;CD6,non_coding_transcript_exon_variant,,ENST00000541964,;CD6,downstream_gene_variant,,ENST00000542254,; A ENST00000313421 Transcript missense_variant 759/3252 573/2007 191/668 D/E gaC/gaA 1 1 CD6 HGNC HGNC:1691 protein_coding YES CCDS7999.1 ENSP00000323280 P30203 UPI000013F532 NM_006725.4 deleterious(0.02) 4/13 PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF331,PROSITE_patterns:PS00420,Pfam_domain:PF00530,Gene3D:3.10.250.10,SMART_domains:SM00202,Superfamily_domains:SSF56487,Prints_domain:PR00258 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 61008637 61008637 C A 1 0 0 0 0 1 0 0 0 2732 506 18 2 2 CD6 11 61008637 Missense_Mutation SNP C C3N-01842_T 139386 61008637 74077985 233 26425 MYRF 0 . GRCh38 11 61766217 61766217 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.394C>G p.Pro132Ala p.P132A ENST00000278836 3/27 78 59 19 84 84 0 strelka-varscan-mutect MYRF,missense_variant,p.Pro132Ala,ENST00000278836,NM_001127392.2;MYRF,missense_variant,p.Pro123Ala,ENST00000265460,NM_013279.3;TMEM258,downstream_gene_variant,,ENST00000535042,;MYRF,non_coding_transcript_exon_variant,,ENST00000537766,; G ENST00000278836 Transcript missense_variant 490/5927 394/3456 132/1151 P/A Cca/Gca 1 1 MYRF HGNC HGNC:1181 protein_coding YES CCDS44622.1 ENSP00000278836 Q9Y2G1 UPI0000D45F7B NM_001127392.2 tolerated(0.06) 3/27 hmmpanther:PTHR13029,hmmpanther:PTHR13029:SF16 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 G 3 3 84 61766217 61766217 C G 1 0 0 0 0 1 0 0 0 10101 637 22 4 4 MYRF 11 61766217 Missense_Mutation SNP C C3N-01842_T 757580 61766217 73320405 234 26426 AHNAK 0 . GRCh38 11 62524435 62524435 + Missense_Mutation SNP C C A rs754013307 C3N-01842_T C3N-01842_N C C c.9982G>T p.Asp3328Tyr p.D3328Y ENST00000378024 5/5 310 225 85 268 267 1 strelka-varscan-mutect AHNAK,missense_variant,p.Asp3328Tyr,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,; A ENST00000378024 Transcript missense_variant 10257/18787 9982/17673 3328/5890 D/Y Gat/Tat rs754013307,COSM3980497,COSM4909154 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0) 5/5 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs754013307 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 62524435 62524435 C A 1 0 0 0 0 1 0 0 0 491 855 30 2 2 AHNAK 11 62524435 Missense_Mutation SNP C C3N-01842_T 758218 62524435 72562187 235 26427 PPP1R14B 0 . GRCh38 11 64246445 64246445 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.229G>C p.Glu77Gln p.E77Q ENST00000309318 1/4 213 172 41 219 219 0 strelka-varscan-mutect PPP1R14B,missense_variant,p.Glu77Gln,ENST00000309318,NM_138689.2;FKBP2,downstream_gene_variant,,ENST00000394540,NM_057092.2;PPP1R14B,upstream_gene_variant,,ENST00000542235,;FKBP2,downstream_gene_variant,,ENST00000309366,NM_004470.3;FKBP2,downstream_gene_variant,,ENST00000535135,;FKBP2,downstream_gene_variant,,ENST00000449942,NM_001135208.1;PPP1R14B,upstream_gene_variant,,ENST00000392210,;RP11-783K16.13,downstream_gene_variant,,ENST00000545800,;RP11-783K16.5,intron_variant,,ENST00000544553,;RP11-783K16.5,upstream_gene_variant,,ENST00000538355,;FKBP2,downstream_gene_variant,,ENST00000541388,;FKBP2,downstream_gene_variant,,ENST00000536642,; G ENST00000309318 Transcript missense_variant 497/982 229/444 77/147 E/Q Gag/Cag 1 -1 PPP1R14B HGNC HGNC:9057 protein_coding YES CCDS31596.1 ENSP00000310117 Q96C90 UPI000006D596 NM_138689.2 tolerated(0.1) 1/4 Superfamily_domains:0039331,Gene3D:1j2mA00,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05361,hmmpanther:PTHR16188,hmmpanther:PTHR16188:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 64246445 64246445 C G 1 0 0 0 0 1 0 0 0 12470 864 30 4 4 PPP1R14B 11 64246445 Missense_Mutation SNP C C3N-01842_T 1722010 64246445 70840177 236 26428 NRXN2 0 . GRCh38 11 64622972 64622972 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.3954C>A p.= p.L1318L ENST00000265459 21/23 431 340 91 464 463 1 strelka-varscan-mutect NRXN2,synonymous_variant,p.=,ENST00000265459,NM_015080.3;NRXN2,synonymous_variant,p.=,ENST00000377559,NM_138732.2;NRXN2,synonymous_variant,p.=,ENST00000409571,;NRXN2,synonymous_variant,p.=,ENST00000377551,;NRXN2,synonymous_variant,p.=,ENST00000301894,NM_138734.2;NRXN2,synonymous_variant,p.=,ENST00000423049,;NRXN2,upstream_gene_variant,,ENST00000475737,;NRXN2,non_coding_transcript_exon_variant,,ENST00000464307,; T ENST00000265459 Transcript synonymous_variant 4416/6621 3954/5139 1318/1712 L ctC/ctA 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 21/23 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF593,SMART_domains:SM00282 LOW 1 SNV 5 1 PASS rs1249054849 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 64622972 64622972 G T 1 0 0 0 0 0 0 0 1 10725 1277 45 2 2 NRXN2 11 64622972 Silent SNP G C3N-01842_T 376527 64622972 70463650 237 26429 ATG2A 0 . GRCh38 11 64903660 64903660 + Frame_Shift_Del DEL C C - novel C3N-01842_T C3N-01842_N C C c.3465delG p.Arg1155SerfsTer38 p.R1155Sfs*38 ENST00000377264 25/41 81 68 13 94 94 0 sindel-varindel ATG2A,frameshift_variant,p.Arg1155SerfsTer38,ENST00000377264,NM_015104.2;ATG2A,frameshift_variant,p.Arg957SerfsTer38,ENST00000418259,;ATG2A,intron_variant,,ENST00000421419,;MIR6749,upstream_gene_variant,,ENST00000617008,; - ENST00000377264 Transcript frameshift_variant,splice_region_variant 3578/6357 3465/5817 1155/1938 R/X agG/ag 1 -1 ATG2A HGNC HGNC:29028 protein_coding YES CCDS31602.1 ENSP00000366475 Q2TAZ0 UPI00001C1F21 NM_015104.2 25/41 Pfam_domain:PF13329,hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF21 HIGH 1 deletion 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 64903660 64903660 C - 1 0 1 0 1 0 0 0 0 1245 521 18 0 0 ATG2A 11 64903660 Frame_Shift_Del DEL C C3N-01842_T 280688 64903660 70182962 238 26430 RBM14 0 . GRCh38 11 66625197 66625197 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.1321G>C p.Ala441Pro p.A441P ENST00000310137 2/3 208 182 26 188 188 0 strelka-varscan-mutect RBM14,missense_variant,p.Ala441Pro,ENST00000310137,NM_006328.3;RBM14-RBM4,intron_variant,,ENST00000412278,NM_001198845.1;RBM14,intron_variant,,ENST00000393979,NM_001198836.1;RBM14-RBM4,intron_variant,,ENST00000500635,NM_001198846.1;RBM14,intron_variant,,ENST00000409738,NM_001198837.1;RBM14,downstream_gene_variant,,ENST00000409372,;RBM14,downstream_gene_variant,,ENST00000443702,;RBM14-RBM4,intron_variant,,ENST00000511114,;RBM14,downstream_gene_variant,,ENST00000461478,;RBM14,downstream_gene_variant,,ENST00000496694,;RBM14-RBM4,intron_variant,,ENST00000421355,; C ENST00000310137 Transcript missense_variant 1460/2828 1321/2010 441/669 A/P Gcc/Ccc 1 1 RBM14 HGNC HGNC:14219 protein_coding YES CCDS8147.1 ENSP00000311747 Q96PK6 A0A0S2Z4Z0 UPI0000073D46 NM_006328.3 tolerated_low_confidence(0.26) 2/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 66625197 66625197 G C 1 0 0 0 0 1 0 0 0 13281 1319 46 4 4 RBM14 11 66625197 Missense_Mutation SNP G C3N-01842_T 1721537 66625197 68461425 239 26431 RCE1 0 . GRCh38 11 66843507 66843507 + Nonsense_Mutation SNP G G T rs111716594 C3N-01842_T C3N-01842_N G G c.52G>T p.Glu18Ter p.E18* ENST00000309657 1/8 161 129 32 238 238 0 strelka-varscan-mutect RCE1,stop_gained,p.Glu18Ter,ENST00000309657,NM_005133.2;RCE1,stop_gained,p.Glu18Ter,ENST00000524506,;C11orf80,downstream_gene_variant,,ENST00000525908,NM_024650.3;C11orf80,downstream_gene_variant,,ENST00000532565,;C11orf80,downstream_gene_variant,,ENST00000525449,;C11orf80,downstream_gene_variant,,ENST00000360962,;C11orf80,downstream_gene_variant,,ENST00000540737,NM_001302084.1;C11orf80,downstream_gene_variant,,ENST00000527634,;PC,downstream_gene_variant,,ENST00000529047,;RCE1,upstream_gene_variant,,ENST00000525356,NM_001032279.1;C11orf80,downstream_gene_variant,,ENST00000531415,;RCE1,upstream_gene_variant,,ENST00000534645,;RCE1,stop_gained,p.Glu18Ter,ENST00000524849,;RCE1,non_coding_transcript_exon_variant,,ENST00000533277,;C11orf80,downstream_gene_variant,,ENST00000532727,;RCE1,upstream_gene_variant,,ENST00000532775,;RCE1,upstream_gene_variant,,ENST00000530610,;RCE1,upstream_gene_variant,,ENST00000534822,; T ENST00000309657 Transcript stop_gained 96/1485 52/990 18/329 E/* Gag/Tag rs111716594 1 1 RCE1 HGNC HGNC:13721 protein_coding YES CCDS8151.1 ENSP00000309163 Q9Y256 UPI000012A4C6 NM_005133.2 1/8 hmmpanther:PTHR13046,hmmpanther:PTHR13046:SF1 HIGH 1 SNV 1 1 PASS rs111716594 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 66843507 66843507 G T 1 0 0 0 0 0 1 0 0 13346 1175 41 2 2 RCE1 11 66843507 Nonsense_Mutation SNP G C3N-01842_T 218310 66843507 68243115 240 26432 ARAP1 0 . GRCh38 11 72712484 72712484 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.832C>A p.Gln278Lys p.Q278K ENST00000393609 6/35 123 99 24 133 133 0 strelka-varscan-mutect ARAP1,missense_variant,p.Gln278Lys,ENST00000359373,;ARAP1,missense_variant,p.Gln278Lys,ENST00000393609,NM_001040118.2;ARAP1,missense_variant,p.Gln33Lys,ENST00000334211,NM_015242.4;ARAP1,missense_variant,p.Gln38Lys,ENST00000393605,;ARAP1,missense_variant,p.Gln33Lys,ENST00000426523,;ARAP1,missense_variant,p.Gln33Lys,ENST00000429686,NM_001135190.1;ARAP1,upstream_gene_variant,,ENST00000542264,;ARAP1,non_coding_transcript_exon_variant,,ENST00000465814,;RPS12P20,downstream_gene_variant,,ENST00000464109,; T ENST00000393609 Transcript missense_variant 1035/5145 832/4353 278/1450 Q/K Caa/Aaa 1 -1 ARAP1 HGNC HGNC:16925 protein_coding YES CCDS41687.1 ENSP00000377233 Q96P48 UPI000053F81B NM_001040118.2 tolerated(0.86) 6/35 Low_complexity_(Seg):seg,hmmpanther:PTHR23180:SF195,hmmpanther:PTHR23180 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 72712484 72712484 G T 1 0 0 0 0 1 0 0 0 960 1357 47 2 2 ARAP1 11 72712484 Missense_Mutation SNP G C3N-01842_T 5868977 72712484 62374138 241 26433 TRIM64B 0 . GRCh38 11 89875943 89875943 + Silent SNP C C A C3N-01842_T C3N-01842_N C C c.75G>T p.= p.P25P ENST00000329862 1/6 397 344 53 417 417 0 varscan-mutect TRIM64B,synonymous_variant,p.=,ENST00000329862,NM_001164397.1; A ENST00000329862 Transcript synonymous_variant 75/2689 75/1350 25/449 P ccG/ccT COSM2222689 1 -1 TRIM64B HGNC HGNC:37147 protein_coding YES CCDS53693.1 ENSP00000332969 A6NI03 UPI0001662600 NM_001164397.1 1/6 Gene3D:3.30.40.10,Pfam_domain:PF00097,PROSITE_profiles:PS50089,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF354,SMART_domains:SM00184,Superfamily_domains:SSF57850 1 LOW 1 SNV 1 1 1 PASS rs1192976298 . 3 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 89875943 89875943 C A 1 0 0 0 0 0 0 0 1 17032 639 23 1 1 TRIM64B 11 89875943 Silent SNP C C3N-01842_T 17163459 89875943 45210679 242 26434 TRIM49C 0 . GRCh38 11 90041097 90041097 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.906G>T p.= p.L302L ENST00000448984 8/8 278 219 59 260 259 1 strelka-varscan-mutect TRIM49C,synonymous_variant,p.=,ENST00000448984,NM_001195234.1; T ENST00000448984 Transcript synonymous_variant 1235/2163 906/1359 302/452 L ctG/ctT 1 1 TRIM49C HGNC HGNC:38877 protein_coding YES CCDS53694.1 ENSP00000388299 P0CI26 UPI000013EA2B NM_001195234.1 8/8 Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF310,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS rs1284704470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 90041097 90041097 G T 1 0 0 0 0 0 0 0 1 17016 1364 48 2 2 TRIM49C 11 90041097 Silent SNP G C3N-01842_T 165154 90041097 45045525 243 26435 HEPHL1 0 . GRCh38 11 94064423 94064423 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.721C>A p.Leu241Ile p.L241I ENST00000315765 4/20 213 170 43 214 213 1 strelka-varscan-mutect HEPHL1,missense_variant,p.Leu241Ile,ENST00000315765,NM_001098672.1; A ENST00000315765 Transcript missense_variant 729/5345 721/3480 241/1159 L/I Ctc/Atc 1 1 HEPHL1 HGNC HGNC:30477 protein_coding YES CCDS44710.1 ENSP00000313699 Q6MZM0 UPI0000237563 NM_001098672.1 tolerated(0.12) 4/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF655,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 94064423 94064423 C A 1 0 0 0 0 1 0 0 0 6939 681 24 2 2 HEPHL1 11 94064423 Missense_Mutation SNP C C3N-01842_T 4023326 94064423 41022199 244 26436 PGR 0 . GRCh38 11 101128606 101128606 + Silent SNP G G C C3N-01842_T C3N-01842_N G G c.465C>G p.= p.P155P ENST00000325455 1/8 235 196 39 287 287 0 strelka-varscan-mutect PGR,synonymous_variant,p.=,ENST00000325455,NM_000926.4,NM_001202474.3;PGR,synonymous_variant,p.=,ENST00000619228,;PGR,synonymous_variant,p.=,ENST00000617858,;PGR,synonymous_variant,p.=,ENST00000263463,NM_001271161.2;PGR,intron_variant,,ENST00000534013,NM_001271162.1;PGR,upstream_gene_variant,,ENST00000632634,;RP11-788M5.4,upstream_gene_variant,,ENST00000632820,;PGR,synonymous_variant,p.=,ENST00000534780,;PGR,synonymous_variant,p.=,ENST00000528960,;PGR,synonymous_variant,p.=,ENST00000526300,; C ENST00000325455 Transcript synonymous_variant 1919/13748 465/2802 155/933 P ccC/ccG COSM84108 1 -1 PGR HGNC HGNC:8910 protein_coding YES CCDS8310.1 ENSP00000325120 P06401 UPI0000046E22 NM_000926.4,NM_001202474.3 1/8 Low_complexity_(Seg):seg,hmmpanther:PTHR24084,hmmpanther:PTHR24084:SF7,Pfam_domain:PF02161 1 LOW 1 SNV 1 1 1 PASS rs1288681934 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 101128606 101128606 G C 1 0 0 0 0 0 0 0 1 11894 1103 39 4 4 PGR 11 101128606 Silent SNP G C3N-01842_T 7064183 101128606 33958016 245 26437 APOA1 0 . GRCh38 11 116836012 116836012 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.600G>A p.= p.A200A ENST00000236850 4/4 310 238 72 368 368 0 strelka-varscan-mutect APOA1,synonymous_variant,p.=,ENST00000236850,NM_000039.1;APOA1,synonymous_variant,p.=,ENST00000375323,;APOA1,synonymous_variant,p.=,ENST00000375320,NM_001318017.1;APOA1,synonymous_variant,p.=,ENST00000359492,NM_001318018.1;APOA1,synonymous_variant,p.=,ENST00000375329,;APOC3,downstream_gene_variant,,ENST00000375345,;APOC3,downstream_gene_variant,,ENST00000227667,NM_000040.1;APOC3,downstream_gene_variant,,ENST00000630701,;APOA1-AS,upstream_gene_variant,,ENST00000444200,;APOC3,downstream_gene_variant,,ENST00000470144,; T ENST00000236850 Transcript synonymous_variant 966/1227 600/804 200/267 A gcG/gcA 1 -1 APOA1 HGNC HGNC:600 protein_coding YES CCDS8378.1 ENSP00000236850 P02647 A0A024R3E3 UPI000002C911 NM_000039.1 4/4 Superfamily_domains:0053393,Gene3D:1gw3A00,Pfam_domain:PF01442,hmmpanther:PTHR18976,hmmpanther:PTHR18976:SF11,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 116836012 116836012 C T 1 0 0 0 0 0 0 0 1 903 755 27 1 1 APOA1 11 116836012 Silent SNP C C3N-01842_T 15707406 116836012 18250610 246 26438 C2CD2L 0 . GRCh38 11 119113860 119113860 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.1498A>G p.Ser500Gly p.S500G ENST00000336702 12/14 207 163 44 211 211 0 strelka-varscan-mutect C2CD2L,missense_variant,p.Ser500Gly,ENST00000336702,NM_014807.4,NM_001290474.1;C2CD2L,missense_variant,p.Ser247Gly,ENST00000528586,;C2CD2L,non_coding_transcript_exon_variant,,ENST00000525598,;C2CD2L,non_coding_transcript_exon_variant,,ENST00000529874,;C2CD2L,downstream_gene_variant,,ENST00000533458,; G ENST00000336702 Transcript missense_variant 1857/4771 1498/2124 500/707 S/G Agc/Ggc 1 1 C2CD2L HGNC HGNC:29000 protein_coding YES CCDS8413.1 ENSP00000338885 O14523 UPI0000192105 NM_014807.4,NM_001290474.1 tolerated(0.23) 12/14 hmmpanther:PTHR21119,hmmpanther:PTHR21119:SF8,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 119113860 119113860 A G 1 0 0 0 0 1 0 0 0 2025 202 7 5 5 C2CD2L 11 119113860 Missense_Mutation SNP A C3N-01842_T 2277848 119113860 15972762 247 26439 OR8D4 0 . GRCh38 11 123906602 123906602 + Silent SNP C C G rs79929702 C3N-01842_T C3N-01842_N C C c.171C>G p.= p.T57T ENST00000321355 1/1 243 185 58 241 241 0 strelka-varscan-mutect OR8D4,synonymous_variant,p.=,ENST00000321355,NM_001005197.1; G ENST00000321355 Transcript synonymous_variant 457/1331 171/945 57/314 T acC/acG rs79929702 1 1 OR8D4 HGNC HGNC:14840 protein_coding YES CCDS31698.1 ENSP00000325381 Q8NGM9 UPI0000040A83 NM_001005197.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF21,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs79929702 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 123906602 123906602 C G 1 0 0 0 0 0 0 0 1 11302 610 22 4 4 OR8D4 11 123906602 Silent SNP C C3N-01842_T 4792742 123906602 11180020 248 26440 FEZ1 0 . GRCh38 11 125455967 125455967 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.807C>T p.= p.S269S ENST00000278919 6/10 186 144 42 252 252 0 strelka-varscan-mutect FEZ1,synonymous_variant,p.=,ENST00000278919,NM_005103.4;FEZ1,synonymous_variant,p.=,ENST00000577924,;FEZ1,non_coding_transcript_exon_variant,,ENST00000527350,;FEZ1,upstream_gene_variant,,ENST00000526507,;FEZ1,upstream_gene_variant,,ENST00000532778,;FEZ1,non_coding_transcript_exon_variant,,ENST00000392709,;FEZ1,non_coding_transcript_exon_variant,,ENST00000524427,;FEZ1,upstream_gene_variant,,ENST00000530096,;FEZ1,downstream_gene_variant,,ENST00000533294,;FEZ1,downstream_gene_variant,,ENST00000534022,;FEZ1,upstream_gene_variant,,ENST00000528863,; A ENST00000278919 Transcript synonymous_variant 1042/1748 807/1179 269/392 S tcC/tcT 1 -1 FEZ1 HGNC HGNC:3659 protein_coding YES CCDS31716.1 ENSP00000278919 Q99689 UPI000012A6FE NM_005103.4 6/10 hmmpanther:PTHR12394:SF4,hmmpanther:PTHR12394,Pfam_domain:PF07763 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 125455967 125455967 G A 1 0 0 0 0 0 0 0 1 5686 987 35 3 3 FEZ1 11 125455967 Silent SNP G C3N-01842_T 1549365 125455967 9630655 249 26441 USP5 0 . GRCh38 12 6860222 6860222 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1202G>T p.Arg401Leu p.R401L ENST00000229268 10/20 140 100 40 180 179 1 strelka-varscan-mutect USP5,missense_variant,p.Arg401Leu,ENST00000229268,NM_001098536.1;USP5,missense_variant,p.Arg401Leu,ENST00000389231,NM_003481.2;USP5,intron_variant,,ENST00000542087,;USP5,upstream_gene_variant,,ENST00000541969,;USP5,non_coding_transcript_exon_variant,,ENST00000537267,;USP5,upstream_gene_variant,,ENST00000542371,;USP5,downstream_gene_variant,,ENST00000535080,; T ENST00000229268 Transcript missense_variant 1254/3181 1202/2577 401/858 R/L cGg/cTg 1 1 USP5 HGNC HGNC:12628 protein_coding YES CCDS41743.1 ENSP00000229268 P45974 A0A140VJZ1 UPI00001379E1 NM_001098536.1 tolerated(0.2) 10/20 PROSITE_profiles:PS50235,PIRSF_domain:PIRSF016308,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999765 1 1 1 0 T 3 4 84 6860222 6860222 G T 1 0 0 0 0 1 0 0 0 17624 1116 39 1 1 USP5 12 6860222 Missense_Mutation SNP G C3N-01842_T 6860222 126415087 250 26442 SLC2A14 0 . GRCh38 12 7821254 7821254 + Silent SNP C C A rs745710037 C3N-01842_T C3N-01842_N C C c.1050G>T p.= p.A350A ENST00000539924 7/10 266 201 65 300 300 0 strelka-varscan-mutect SLC2A14,synonymous_variant,p.=,ENST00000543909,NM_001286233.1;SLC2A14,synonymous_variant,p.=,ENST00000340749,NM_001286235.1;SLC2A14,synonymous_variant,p.=,ENST00000431042,NM_001286234.1;SLC2A14,synonymous_variant,p.=,ENST00000616981,;SLC2A14,synonymous_variant,p.=,ENST00000542546,;SLC2A14,synonymous_variant,p.=,ENST00000396589,NM_153449.3;SLC2A14,synonymous_variant,p.=,ENST00000539924,NM_001286237.1;SLC2A14,synonymous_variant,p.=,ENST00000535295,NM_001286236.1;SLC2A14,5_prime_UTR_variant,,ENST00000542505,; A ENST00000539924 Transcript synonymous_variant 1071/1873 1050/1608 350/535 A gcG/gcT rs745710037 1 -1 SLC2A14 HGNC HGNC:18301 protein_coding YES CCDS66302.1 ENSP00000445929 Q8TDB8 UPI0001915325 NM_001286237.1 7/10 Gene3D:1.20.1250.20,Pfam_domain:PF00083,PROSITE_profiles:PS50850,hmmpanther:PTHR23503,hmmpanther:PTHR23503:SF23,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00879,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS rs745710037 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 7821254 7821254 C A 1 0 0 0 0 0 0 0 1 14813 639 23 1 1 SLC2A14 12 7821254 Silent SNP C C3N-01842_T 961032 7821254 125454055 251 26443 CREBL2 0 . GRCh38 12 12635969 12635969 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.208G>C p.Glu70Gln p.E70Q ENST00000228865 2/4 252 198 54 295 295 0 strelka-varscan-mutect CREBL2,missense_variant,p.Glu70Gln,ENST00000228865,NM_001310.3;CREBL2,non_coding_transcript_exon_variant,,ENST00000540224,; C ENST00000228865 Transcript missense_variant 489/3754 208/363 70/120 E/Q Gaa/Caa 1 1 CREBL2 HGNC HGNC:2350 protein_coding YES CCDS8651.1 ENSP00000228865 O60519 UPI0000070749 NM_001310.3 deleterious(0.04) 2/4 Gene3D:1.20.5.170,Pfam_domain:PF07716,hmmpanther:PTHR21051,hmmpanther:PTHR21051:SF4,Superfamily_domains:SSF57959 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 12635969 12635969 G C 1 0 0 0 0 1 0 0 0 3662 1188 41 4 4 CREBL2 12 12635969 Missense_Mutation SNP G C3N-01842_T 4814715 12635969 120639340 252 26444 OVOS2 0 . GRCh38 12 31150207 31150207 + Silent SNP A A G novel C3N-01842_T C3N-01842_N A A c.900T>C p.= p.A300A ENST00000632817 8/34 302 244 58 318 318 0 strelka-varscan-mutect OVOS2,synonymous_variant,p.=,ENST00000398963,;OVOS2,synonymous_variant,p.=,ENST00000632817,; G ENST00000632817 Transcript synonymous_variant 900/4299 900/4299 300/1432 A gcT/gcC 1 -1 OVOS2 Clone_based_vega_gene protein_coding YES ENSP00000487815 A0A0J9YW53 UPI0001AE6AF7 8/34 hmmpanther:PTHR11412:SF77,hmmpanther:PTHR11412 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 31150207 31150207 A G 1 0 0 0 0 0 0 0 1 11399 175 7 5 5 OVOS2 12 31150207 Silent SNP A C3N-01842_T 18514238 31150207 102125102 253 26445 BICD1 0 . GRCh38 12 32327667 32327667 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.1212T>A p.His404Gln p.H404Q ENST00000281474 5/10 172 132 40 202 202 0 strelka-varscan-mutect BICD1,missense_variant,p.His404Gln,ENST00000548411,NM_001003398.1;BICD1,missense_variant,p.His404Gln,ENST00000281474,NM_001714.2;BICD1,upstream_gene_variant,,ENST00000547680,;BICD1,missense_variant,p.His404Gln,ENST00000395758,; A ENST00000281474 Transcript missense_variant 1315/3281 1212/2928 404/975 H/Q caT/caA 1 1 BICD1 HGNC HGNC:1049 protein_coding YES CCDS8726.1 ENSP00000281474 Q96G01 UPI00001AEA67 NM_001714.2 tolerated(0.4) 5/10 hmmpanther:PTHR31233,hmmpanther:PTHR31233:SF3,Pfam_domain:PF09730 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 32327667 32327667 T A 1 0 0 0 0 1 0 0 0 1577 1461 51 4 4 BICD1 12 32327667 Missense_Mutation SNP T C3N-01842_T 1177460 32327667 100947642 254 26446 ADAMTS20 0 . GRCh38 12 43551036 43551036 + Nonsense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.326T>A p.Leu109Ter p.L109* ENST00000389420 2/39 216 161 55 246 244 2 strelka-varscan-mutect ADAMTS20,stop_gained,p.Leu109Ter,ENST00000389420,NM_025003.3;ADAMTS20,stop_gained,p.Leu109Ter,ENST00000395541,;ADAMTS20,stop_gained,p.Leu109Ter,ENST00000553158,; T ENST00000389420 Transcript stop_gained 326/6076 326/5733 109/1910 L/* tTg/tAg 1 -1 ADAMTS20 HGNC HGNC:17178 protein_coding YES CCDS31778.2 ENSP00000374071 P59510 UPI00004565F4 NM_025003.3 2/39 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF165,Pfam_domain:PF01562 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 43551036 43551036 A T 1 0 0 0 0 0 1 0 0 310 131 5 4 4 ADAMTS20 12 43551036 Nonsense_Mutation SNP A C3N-01842_T 11223369 43551036 89724273 255 26447 BBS10 0 . GRCh38 12 76345965 76345965 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.2020A>T p.Ser674Cys p.S674C ENST00000393262 2/2 333 244 89 256 256 0 strelka-varscan-mutect BBS10,missense_variant,p.Ser674Cys,ENST00000393262,NM_024685.3; A ENST00000393262 Transcript missense_variant 2104/3595 2020/2172 674/723 S/C Agt/Tgt 1 -1 BBS10 HGNC HGNC:26291 protein_coding YES CCDS9014.2 ENSP00000376946 Q8TAM1 UPI0000D720FE NM_024685.3 tolerated(0.09) 2/2 hmmpanther:PTHR14667,Gene3D:1.10.560.10,Superfamily_domains:SSF48592 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 76345965 76345965 T A 1 0 0 0 0 1 0 0 0 1483 1580 55 4 4 BBS10 12 76345965 Missense_Mutation SNP T C3N-01842_T 32794929 76345965 56929344 256 26448 OTOGL 0 . GRCh38 12 80267297 80267297 + Missense_Mutation SNP G G T rs766524140 C3N-01842_T C3N-01842_N G G c.2408G>T p.Gly803Val p.G803V ENST00000458043 21/58 231 193 38 253 253 0 strelka-varscan-mutect OTOGL,missense_variant,p.Gly803Val,ENST00000458043,NM_173591.3;OTOGL,missense_variant,p.Gly803Val,ENST00000547103,; T ENST00000458043 Transcript missense_variant 2414/8083 2408/7035 803/2344 G/V gGa/gTa rs766524140 1 1 OTOGL HGNC HGNC:26901 protein_coding YES ENSP00000400895 A0A0A0MSS2 UPI0001D089C5 NM_173591.3 deleterious(0) 21/58 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF225,Gene3D:2.10.25.10,SMART_domains:SM00215 MODERATE 1 SNV 5 1 PASS rs766524140 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 80267297 80267297 G T 1 0 0 0 0 1 0 0 0 11371 1174 41 2 2 OTOGL 12 80267297 Missense_Mutation SNP G C3N-01842_T 3921332 80267297 53008012 257 26449 PTPRQ 0 . GRCh38 12 80546622 80546622 + Missense_Mutation SNP C C A rs774879303 C3N-01842_T C3N-01842_N C C c.3940C>A p.Arg1314Ser p.R1314S ENST00000614701 24/45 374 297 77 342 342 0 strelka-varscan-mutect PTPRQ,missense_variant,p.Arg1314Ser,ENST00000614701,NM_001145026.1;PTPRQ,missense_variant,p.Arg1356Ser,ENST00000616559,;PTPRQ,non_coding_transcript_exon_variant,,ENST00000551624,; A ENST00000614701 Transcript missense_variant 4118/8289 3940/6900 1314/2299 R/S Cgt/Agt rs774879303 1 1 PTPRQ HGNC HGNC:9679 protein_coding YES CCDS73501.1 ENSP00000482885 A0A087WZU1 UPI000192953C NM_001145026.1 tolerated(1) 24/45 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF414,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS rs774879303 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 80546622 80546622 C A 1 0 0 0 0 1 0 0 0 12964 652 23 1 1 PTPRQ 12 80546622 Missense_Mutation SNP C C3N-01842_T 279325 80546622 52728687 258 26450 LRRIQ1 0 . GRCh38 12 85047363 85047363 + Missense_Mutation SNP G G T rs774392243 C3N-01842_T C3N-01842_N G G c.571G>T p.Ala191Ser p.A191S ENST00000393217 6/27 471 405 66 286 284 2 strelka-varscan-mutect LRRIQ1,missense_variant,p.Ala191Ser,ENST00000393217,NM_001079910.1;LRRIQ1,missense_variant,p.Ala89Ser,ENST00000533414,;LRRIQ1,downstream_gene_variant,,ENST00000393212,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000529408,; T ENST00000393217 Transcript missense_variant 632/5394 571/5169 191/1722 A/S Gct/Tct rs774392243 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 deleterious(0) 6/27 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS rs774392243 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 85047363 85047363 G T 1 0 0 0 0 1 0 0 0 8935 971 34 2 2 LRRIQ1 12 85047363 Missense_Mutation SNP G C3N-01842_T 4500741 85047363 48227946 259 26451 SSH1 0 . GRCh38 12 108788192 108788192 + Silent SNP C C G novel C3N-01842_T C3N-01842_N C C c.2946G>C p.= p.L982L ENST00000326495 15/15 361 300 61 417 417 0 strelka-varscan-mutect SSH1,synonymous_variant,p.=,ENST00000326495,NM_018984.3;SSH1,downstream_gene_variant,,ENST00000326470,NM_001161331.1;SSH1,downstream_gene_variant,,ENST00000551165,NM_001161330.1;SSH1,3_prime_UTR_variant,,ENST00000546433,; G ENST00000326495 Transcript synonymous_variant 3040/13040 2946/3150 982/1049 L ctG/ctC 1 -1 SSH1 HGNC HGNC:30579 protein_coding YES CCDS9121.1 ENSP00000315713 Q8WYL5 UPI000003E894 NM_018984.3 15/15 LOW 1 SNV 1 1 PASS rs1297219380 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 108788192 108788192 C G 1 0 0 0 0 0 0 0 1 15560 581 21 4 4 SSH1 12 108788192 Silent SNP C C3N-01842_T 23740829 108788192 24487117 260 26452 ACACB 0 . GRCh38 12 109265127 109265127 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.6960G>C p.Lys2320Asn p.K2320N ENST00000338432 51/53 95 72 23 122 122 0 strelka-varscan-mutect ACACB,missense_variant,p.Lys2320Asn,ENST00000338432,;ACACB,missense_variant,p.Lys2320Asn,ENST00000377848,NM_001093.3;ACACB,downstream_gene_variant,,ENST00000377854,;ACACB,3_prime_UTR_variant,,ENST00000538526,;ACACB,non_coding_transcript_exon_variant,,ENST00000537279,; C ENST00000338432 Transcript missense_variant 7079/9360 6960/7377 2320/2458 K/N aaG/aaC 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB deleterious(0.02) 51/53 hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF01039,Gene3D:3.90.226.10,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 109265127 109265127 G C 1 0 0 0 0 1 0 0 0 150 933 33 4 4 ACACB 12 109265127 Missense_Mutation SNP G C3N-01842_T 476935 109265127 24010182 261 26453 MYO1H 0 . GRCh38 12 109401269 109401269 + Silent SNP A A T novel C3N-01842_T C3N-01842_N A A c.699A>T p.= p.S233S ENST00000431443 5/31 148 133 15 102 101 1 strelka-varscan-mutect MYO1H,synonymous_variant,p.=,ENST00000310903,;MYO1H,synonymous_variant,p.=,ENST00000431443,NM_001101421.3;MYO1H,upstream_gene_variant,,ENST00000542883,; T ENST00000431443 Transcript synonymous_variant 699/4258 699/3069 233/1022 S tcA/tcT 1 1 MYO1H HGNC HGNC:13879 protein_coding YES CCDS53826.1 ENSP00000444076 Q8N1T3 UPI0001AFF951 NM_001101421.3 5/31 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF353,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 109401269 109401269 A T 1 0 0 0 0 0 0 0 1 10076 173 6 4 4 MYO1H 12 109401269 Silent SNP A C3N-01842_T 136142 109401269 23874040 262 26454 LHX5 0 . GRCh38 12 113468305 113468305 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.497C>A p.Thr166Lys p.T166K ENST00000261731 3/5 247 193 54 317 315 2 strelka-varscan-mutect LHX5,missense_variant,p.Thr166Lys,ENST00000261731,NM_022363.2;LHX5-AS1,upstream_gene_variant,,ENST00000551357,;LHX5,downstream_gene_variant,,ENST00000557836,; T ENST00000261731 Transcript missense_variant 1071/2939 497/1209 166/402 T/K aCg/aAg 1 -1 LHX5 HGNC HGNC:14216 protein_coding YES CCDS9171.1 ENSP00000261731 Q9H2C1 UPI000012E662 NM_022363.2 tolerated(0.09) 3/5 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF115,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs1285111455 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 113468305 113468305 G T 1 0 0 0 0 1 0 0 0 8683 1145 40 1 1 LHX5 12 113468305 Missense_Mutation SNP G C3N-01842_T 4067036 113468305 19807004 263 26455 GCN1 0 . GRCh38 12 120142642 120142642 + Silent SNP C C A rs369342369 C3N-01842_T C3N-01842_N C C c.5694G>T p.= p.L1898L ENST00000300648 44/58 384 308 76 417 417 0 strelka-varscan-mutect GCN1,synonymous_variant,p.=,ENST00000300648,NM_006836.1;GCN1,upstream_gene_variant,,ENST00000547263,; A ENST00000300648 Transcript synonymous_variant 5707/8675 5694/8016 1898/2671 L ctG/ctT rs369342369 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 44/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS rs369342369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 120142642 120142642 C A 1 0 0 0 0 0 0 0 1 6169 581 21 2 2 GCN1 12 120142642 Silent SNP C C3N-01842_T 6674337 120142642 13132667 264 26456 GCN1 0 . GRCh38 12 120161976 120161976 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.2246C>T p.Ser749Phe p.S749F ENST00000300648 21/58 371 301 70 523 523 0 strelka-varscan-mutect GCN1,missense_variant,p.Ser749Phe,ENST00000300648,NM_006836.1;GCN1,non_coding_transcript_exon_variant,,ENST00000550471,;GCN1,upstream_gene_variant,,ENST00000547369,;GCN1,upstream_gene_variant,,ENST00000551920,;GCN1,downstream_gene_variant,,ENST00000551549,; A ENST00000300648 Transcript missense_variant 2259/8675 2246/8016 749/2671 S/F tCc/tTc 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 tolerated(0.7) 21/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 120161976 120161976 G A 1 0 0 0 0 1 0 0 0 6169 1174 41 3 3 GCN1 12 120161976 Missense_Mutation SNP G C3N-01842_T 19334 120161976 13113333 265 26457 FZD10 0 . GRCh38 12 130164551 130164551 + Missense_Mutation SNP C C G rs147350994 C3N-01842_T C3N-01842_N C C c.1609C>G p.Arg537Gly p.R537G ENST00000229030 1/1 207 165 42 285 285 0 strelka-varscan-mutect FZD10,missense_variant,p.Arg537Gly,ENST00000229030,NM_007197.3;FZD10,3_prime_UTR_variant,,ENST00000539839,;FZD10-AS1,upstream_gene_variant,,ENST00000505807,;FZD10-AS1,upstream_gene_variant,,ENST00000509760,;FZD10-AS1,upstream_gene_variant,,ENST00000537095,;FZD10-AS1,upstream_gene_variant,,ENST00000542000,; G ENST00000229030 Transcript missense_variant 2093/3281 1609/1746 537/581 R/G Cgt/Ggt rs147350994 1 1 FZD10 HGNC HGNC:4039 protein_coding YES CCDS9267.1 ENSP00000229030 Q9ULW2 UPI000004EC92 NM_007197.3 deleterious(0.01) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11309:SF86,hmmpanther:PTHR11309,Pfam_domain:PF01534,SMART_domains:SM01330 MODERATE SNV 1 PASS rs147350994 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 130164551 130164551 C G 1 0 0 0 0 1 0 0 0 6000 652 23 4 4 FZD10 12 130164551 Missense_Mutation SNP C C3N-01842_T 10002575 130164551 3110758 266 26458 RIMBP2 0 . GRCh38 12 130422538 130422538 + Silent SNP T T C novel C3N-01842_T C3N-01842_N T T c.2385A>G p.= p.A795A ENST00000261655 13/19 132 99 33 142 142 0 strelka-varscan-mutect RIMBP2,synonymous_variant,p.=,ENST00000261655,NM_015347.4;RP11-117L5.4,upstream_gene_variant,,ENST00000539532,;RP11-117L5.1,upstream_gene_variant,,ENST00000624734,; C ENST00000261655 Transcript synonymous_variant 2549/6321 2385/3159 795/1052 A gcA/gcG 1 -1 RIMBP2 HGNC HGNC:30339 protein_coding YES CCDS31925.1 ENSP00000261655 O15034 UPI00001C1F42 NM_015347.4 13/19 hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF18 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 130422538 130422538 T C 1 0 0 0 0 0 0 0 1 13538 1567 55 5 5 RIMBP2 12 130422538 Silent SNP T C3N-01842_T 257987 130422538 2852771 267 26459 TUBA3C 0 . GRCh38 13 19177224 19177224 + Silent SNP C C T rs527372781 C3N-01842_T C3N-01842_N C C c.759G>A p.= p.T253T ENST00000400113 4/5 264 185 79 427 425 2 strelka-varscan-mutect TUBA3C,synonymous_variant,p.=,ENST00000400113,NM_006001.2;TUBA3C,synonymous_variant,p.=,ENST00000618094,;RP11-408E5.8,downstream_gene_variant,,ENST00000612362,; T ENST00000400113 Transcript synonymous_variant 864/1551 759/1353 253/450 T acG/acA rs527372781,COSM81869 1 -1 TUBA3C HGNC HGNC:12408 protein_coding YES CCDS9284.1 ENSP00000382982 Q13748 Q1ZYQ1 UPI0000027DB1 NM_006001.2 4/5 hmmpanther:PTHR11588:SF94,hmmpanther:PTHR11588,Gene3D:3.40.50.1440,SMART_domains:SM00865,Superfamily_domains:SSF55307 0,1 LOW 1 SNV 5 0,1 1 PASS rs527372781 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 19177224 19177224 C T 1 0 0 0 0 0 0 0 1 17256 639 23 1 1 TUBA3C 13 19177224 Silent SNP C C3N-01842_T 19177224 95187104 268 26460 GJB6 0 . GRCh38 13 20222996 20222996 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.485A>G p.His162Arg p.H162R ENST00000356192 5/5 397 255 142 576 576 0 strelka-varscan-mutect GJB6,missense_variant,p.His162Arg,ENST00000356192,NM_001110219.2;GJB6,missense_variant,p.His162Arg,ENST00000400066,NM_001110220.2;GJB6,missense_variant,p.His162Arg,ENST00000636852,;GJB6,missense_variant,p.His162Arg,ENST00000241124,NM_006783.4;GJB6,missense_variant,p.His162Arg,ENST00000400065,NM_001110221.2; C ENST00000356192 Transcript missense_variant 1106/2131 485/786 162/261 H/R cAc/cGc 1 -1 GJB6 HGNC HGNC:4288 protein_coding YES CCDS9291.1 ENSP00000348521 O95452 A0A024RDS4 UPI0000074737 NM_001110219.2 tolerated(0.51) 5/5 Gene3D:2zw3A00,Pfam_domain:PF00029,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF23,SMART_domains:SM01089 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 20222996 20222996 T C 1 0 0 0 0 1 0 0 0 6289 1696 59 5 5 GJB6 13 20222996 Missense_Mutation SNP T C3N-01842_T 1045772 20222996 94141332 269 26461 CLN5 0 . GRCh38 13 76992240 76992240 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.289C>T p.Pro97Ser p.P97S ENST00000636183 1/4 393 305 88 440 439 1 strelka-varscan-mutect CLN5,missense_variant,p.Pro97Ser,ENST00000636183,NM_006493.2;CLN5,missense_variant,p.Pro52Ser,ENST00000637397,;CLN5,missense_variant,p.Pro67Ser,ENST00000636780,;CLN5,missense_variant,p.Pro48Ser,ENST00000377453,;CLN5,missense_variant,p.Pro51Ser,ENST00000616833,;CLN5,missense_variant,p.Pro55Ser,ENST00000637537,;CLN5,missense_variant,p.Pro49Ser,ENST00000636525,;CLN5,missense_variant,p.Pro49Ser,ENST00000636767,;CLN5,missense_variant,p.Pro62Ser,ENST00000485938,;RP11-226E21.4,missense_variant,p.Pro55Ser,ENST00000638147,;RP11-226E21.4,upstream_gene_variant,,ENST00000638101,;CLN5,upstream_gene_variant,,ENST00000636705,;RP11-226E21.4,upstream_gene_variant,,ENST00000635838,;CLN5,non_coding_transcript_exon_variant,,ENST00000635989,;CLN5,upstream_gene_variant,,ENST00000636405,;FBXL3,downstream_gene_variant,,ENST00000485797,;CLN5,missense_variant,p.Pro28Ser,ENST00000635915,;CLN5,non_coding_transcript_exon_variant,,ENST00000635905,;CLN5,upstream_gene_variant,,ENST00000636520,;CLN5,upstream_gene_variant,,ENST00000637278,;CLN5,upstream_gene_variant,,ENST00000636681,;RP11-226E21.4,upstream_gene_variant,,ENST00000637192,;CLN5,upstream_gene_variant,,ENST00000636602,;DHX9P1,downstream_gene_variant,,ENST00000436565,; T ENST00000636183 Transcript missense_variant 1581/6664 289/1224 97/407 P/S Ccc/Tcc 1 1 CLN5 HGNC HGNC:2076 protein_coding YES CCDS9456.1 ENSP00000490181 UPI0000127AD8 NM_006493.2 tolerated_low_confidence(0.76) 1/4 hmmpanther:PTHR15380 MODERATE 1 SNV 1 PASS rs1131691423 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 76992240 76992240 C T 1 0 0 0 0 1 0 0 0 3314 623 22 3 3 CLN5 13 76992240 Missense_Mutation SNP C C3N-01842_T 56769244 76992240 37372088 270 26462 SLITRK6 0 . GRCh38 13 85794764 85794764 + Missense_Mutation SNP A A T C3N-01842_T C3N-01842_N A A c.1745T>A p.Leu582His p.L582H ENST00000400286 2/2 347 275 72 254 254 0 strelka-varscan-mutect SLITRK6,missense_variant,p.Leu582His,ENST00000400286,NM_032229.2; T ENST00000400286 Transcript missense_variant 2344/4318 1745/2526 582/841 L/H cTt/cAt COSM3980081 1 -1 SLITRK6 HGNC HGNC:23503 protein_coding YES CCDS41903.1 ENSP00000383143 Q9H5Y7 UPI000004C9D6 NM_032229.2 tolerated(0.6) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 85794764 85794764 A T 1 0 0 0 0 1 0 0 0 15038 72 3 4 4 SLITRK6 13 85794764 Missense_Mutation SNP A C3N-01842_T 8802524 85794764 28569564 271 26463 SOX21 0 . GRCh38 13 94711283 94711283 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.767T>A p.Leu256Gln p.L256Q ENST00000376945 1/1 41 36 5 64 64 0 strelka-varscan-mutect SOX21,missense_variant,p.Leu256Gln,ENST00000376945,NM_007084.3;SOX21-AS1,upstream_gene_variant,,ENST00000438290,; T ENST00000376945 Transcript missense_variant 1117/2778 767/831 256/276 L/Q cTg/cAg 1 -1 SOX21 HGNC HGNC:11197 protein_coding YES CCDS9473.1 ENSP00000366144 Q9Y651 UPI000003F547 NM_007084.3 deleterious(0) 1/1 hmmpanther:PTHR10270 MODERATE SNV 1 PASS . . 0 205 5 0 0 0 0 0 -12.91684 1 1 1 1 0 T 3 4 84 94711283 94711283 A T 1 0 0 0 0 1 0 0 0 15276 188 7 4 4 SOX21 13 94711283 Missense_Mutation SNP A C3N-01842_T 8916519 94711283 19653045 272 26464 NALCN 0 . GRCh38 13 101229397 101229397 + Missense_Mutation SNP G G T rs749151544 C3N-01842_T C3N-01842_N G G c.1622C>A p.Pro541Gln p.P541Q ENST00000251127 13/44 127 92 35 94 94 0 strelka-varscan-mutect NALCN,missense_variant,p.Pro541Gln,ENST00000251127,NM_052867.2;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,;NALCN,non_coding_transcript_exon_variant,,ENST00000497170,; T ENST00000251127 Transcript missense_variant 1704/6818 1622/5217 541/1738 P/Q cCg/cAg rs749151544 1 -1 NALCN HGNC HGNC:19082 protein_coding YES CCDS9498.1 ENSP00000251127 Q8IZF0 A0A024RE05 UPI000004EBBD NM_052867.2 deleterious(0) 13/44 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF214,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs749151544 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 101229397 101229397 G T 1 0 0 0 0 1 0 0 0 10155 1130 39 1 1 NALCN 13 101229397 Missense_Mutation SNP G C3N-01842_T 6518114 101229397 13134931 273 26465 COL4A2 0 . GRCh38 13 110469293 110469293 + Silent SNP C C T rs375427719 C3N-01842_T C3N-01842_N C C c.2172C>T p.= p.D724D ENST00000360467 28/48 224 181 43 305 305 0 strelka-varscan-mutect COL4A2,synonymous_variant,p.=,ENST00000360467,NM_001846.2;COL4A2,non_coding_transcript_exon_variant,,ENST00000494852,; T ENST00000360467 Transcript synonymous_variant 2478/6281 2172/5139 724/1712 D gaC/gaT rs375427719,COSM3786138 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 28/48 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF588,Pfam_domain:PF01391,Pfam_domain:PF01391 0,1 LOW 1 SNV 5 0,1 1 PASS rs375427719 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 110469293 110469293 C T 1 0 0 0 0 0 0 0 1 3479 535 19 1 1 COL4A2 13 110469293 Silent SNP C C3N-01842_T 9239896 110469293 3895035 274 26466 SLC7A8 0 . GRCh38 14 23129655 23129655 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.1258A>T p.Ile420Phe p.I420F ENST00000316902 9/11 143 112 31 165 165 0 strelka-varscan-mutect SLC7A8,missense_variant,p.Ile420Phe,ENST00000316902,NM_012244.3;SLC7A8,missense_variant,p.Ile196Phe,ENST00000422941,NM_001267037.1;SLC7A8,missense_variant,p.Ile315Phe,ENST00000529705,NM_001267036.1;SLC7A8,missense_variant,p.Ile217Phe,ENST00000453702,NM_182728.2;SLC7A8,3_prime_UTR_variant,,ENST00000621729,;SLC7A8,intron_variant,,ENST00000469263,;SLC7A8,missense_variant,p.Ile223Phe,ENST00000339733,;SLC7A8,3_prime_UTR_variant,,ENST00000528860,;SLC7A8,non_coding_transcript_exon_variant,,ENST00000397310,;SLC7A8,non_coding_transcript_exon_variant,,ENST00000528806,;SLC7A8,non_coding_transcript_exon_variant,,ENST00000528186,; A ENST00000316902 Transcript missense_variant 1984/4216 1258/1608 420/535 I/F Atc/Ttc 1 -1 SLC7A8 HGNC HGNC:11066 protein_coding YES CCDS9590.1 ENSP00000320378 Q9UHI5 UPI000012E235 NM_012244.3 deleterious(0.01) 9/11 hmmpanther:PTHR11785:SF113,hmmpanther:PTHR11785,Pfam_domain:PF13520,TIGRFAM_domain:TIGR00911,PIRSF_domain:PIRSF006060 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 23129655 23129655 T A 1 0 0 0 0 1 0 0 0 14987 1478 51 4 4 SLC7A8 14 23129655 Missense_Mutation SNP T C3N-01842_T 23129655 83914063 275 26467 IPO4 0 . GRCh38 14 24184062 24184062 + Missense_Mutation SNP G G T rs559669192 C3N-01842_T C3N-01842_N G G c.1805C>A p.Ala602Glu p.A602E ENST00000354464 18/30 337 257 80 387 386 1 strelka-varscan-mutect IPO4,missense_variant,p.Ala602Glu,ENST00000354464,NM_024658.3;IPO4,missense_variant,p.Ala66Glu,ENST00000561462,;REC8,downstream_gene_variant,,ENST00000620473,;REC8,downstream_gene_variant,,ENST00000611366,NM_005132.2,NM_001048205.1;IPO4,upstream_gene_variant,,ENST00000558233,;RP11-468E2.2,downstream_gene_variant,,ENST00000625289,;REC8,downstream_gene_variant,,ENST00000559939,;IPO4,missense_variant,p.Ala602Glu,ENST00000560155,;RP11-468E2.2,3_prime_UTR_variant,,ENST00000561419,;IPO4,3_prime_UTR_variant,,ENST00000558780,;IPO4,3_prime_UTR_variant,,ENST00000558046,;IPO4,non_coding_transcript_exon_variant,,ENST00000561090,;IPO4,non_coding_transcript_exon_variant,,ENST00000560798,;IPO4,non_coding_transcript_exon_variant,,ENST00000559588,;IPO4,non_coding_transcript_exon_variant,,ENST00000561199,;REC8,downstream_gene_variant,,ENST00000619469,;REC8,downstream_gene_variant,,ENST00000559797,;IPO4,upstream_gene_variant,,ENST00000560935,;IPO4,upstream_gene_variant,,ENST00000561379,;IPO4,downstream_gene_variant,,ENST00000559253,;IPO4,downstream_gene_variant,,ENST00000560222,;REC8,downstream_gene_variant,,ENST00000558191,;IPO4,downstream_gene_variant,,ENST00000560315,;IPO4,downstream_gene_variant,,ENST00000558193,;IPO4,downstream_gene_variant,,ENST00000558718,;IPO4,downstream_gene_variant,,ENST00000561034,;IPO4,downstream_gene_variant,,ENST00000557996,;IPO4,downstream_gene_variant,,ENST00000559635,;REC8,downstream_gene_variant,,ENST00000558381,; T ENST00000354464 Transcript missense_variant 1982/3646 1805/3246 602/1081 A/E gCg/gAg rs559669192 1 -1 IPO4 HGNC HGNC:19426 protein_coding YES CCDS9616.1 ENSP00000346453 Q8TEX9 UPI000013CCB3 NM_024658.3 tolerated(0.07) 18/30 Gene3D:1.25.10.10,hmmpanther:PTHR10527,hmmpanther:PTHR10527:SF6,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs559669192 . 0 208 0 0 2 0 0 0 -20 0.9986546 1 1 1 0 T 3 4 84 24184062 24184062 G T 1 0 0 0 0 1 0 0 0 7698 1087 38 1 1 IPO4 14 24184062 Missense_Mutation SNP G C3N-01842_T 1054407 24184062 82859656 276 26468 G2E3 0 . GRCh38 14 30601876 30601876 + Missense_Mutation SNP G G T rs569030142 C3N-01842_T C3N-01842_N G G c.859G>T p.Gly287Cys p.G287C ENST00000206595 9/15 274 222 52 288 288 0 strelka-varscan-mutect G2E3,missense_variant,p.Gly287Cys,ENST00000206595,NM_017769.3;G2E3,missense_variant,p.Gly317Cys,ENST00000553504,;G2E3,missense_variant,p.Gly241Cys,ENST00000438909,NM_001308097.1;G2E3,missense_variant,p.Gly53Cys,ENST00000552515,;G2E3,non_coding_transcript_exon_variant,,ENST00000544007,;G2E3,downstream_gene_variant,,ENST00000549553,;G2E3,upstream_gene_variant,,ENST00000547638,;G2E3,missense_variant,p.Gly51Cys,ENST00000548934,; T ENST00000206595 Transcript missense_variant 1013/5804 859/2121 287/706 G/C Ggt/Tgt rs569030142 1 1 G2E3 HGNC HGNC:20338 protein_coding YES CCDS9638.1 ENSP00000206595 Q7L622 UPI000013F3A8 NM_017769.3 deleterious(0.02) 9/15 hmmpanther:PTHR12420,hmmpanther:PTHR12420:SF26,Gene3D:3.30.40.10,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS rs569030142 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 30601876 30601876 G T 1 0 0 0 0 1 0 0 0 6011 1232 43 2 2 G2E3 14 30601876 Missense_Mutation SNP G C3N-01842_T 6417814 30601876 76441842 277 26469 RALGAPA1 0 . GRCh38 14 35627832 35627832 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.4597G>A p.Val1533Met p.V1533M ENST00000307138 33/40 105 93 12 97 97 0 varscan-mutect RALGAPA1,missense_variant,p.Val1992Met,ENST00000637992,;RALGAPA1,missense_variant,p.Val1533Met,ENST00000307138,NM_194301.2;RALGAPA1,missense_variant,p.Val1533Met,ENST00000389698,NM_014990.1;RALGAPA1,missense_variant,p.Val1546Met,ENST00000382366,NM_001283043.1;RALGAPA1,missense_variant,p.Val1580Met,ENST00000553892,NM_001283044.1;RALGAPA1,missense_variant,p.Val171Met,ENST00000554259,;RALGAPA1,upstream_gene_variant,,ENST00000554573,; T ENST00000307138 Transcript missense_variant 5066/7911 4597/6252 1533/2083 V/M Gtg/Atg 1 -1 RALGAPA1 HGNC HGNC:17770 protein_coding YES CCDS32064.1 ENSP00000302647 Q6GYQ0 UPI00003B5C51 NM_194301.2 deleterious(0.02) 33/40 hmmpanther:PTHR10063:SF3,hmmpanther:PTHR10063 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -19.99998 0.9999992 1 1 1 0 T 3 4 84 35627832 35627832 C T 1 0 0 0 0 1 0 0 0 13172 507 18 3 3 RALGAPA1 14 35627832 Missense_Mutation SNP C C3N-01842_T 5025956 35627832 71415886 278 26470 LRFN5 0 . GRCh38 14 41887922 41887922 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1297C>A p.Leu433Ile p.L433I ENST00000298119 3/6 297 246 51 180 179 1 strelka-varscan-mutect LRFN5,missense_variant,p.Leu433Ile,ENST00000554171,;LRFN5,missense_variant,p.Leu433Ile,ENST00000298119,NM_152447.3;LRFN5,missense_variant,p.Leu433Ile,ENST00000554120,; A ENST00000298119 Transcript missense_variant 2486/3723 1297/2160 433/719 L/I Ctt/Att 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 tolerated(1) 3/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 41887922 41887922 C A 1 0 0 0 0 1 0 0 0 8835 565 20 2 2 LRFN5 14 41887922 Missense_Mutation SNP C C3N-01842_T 6260090 41887922 65155796 279 26471 TXNDC16 0 . GRCh38 14 52514887 52514887 + Missense_Mutation SNP T T A C3N-01842_T C3N-01842_N T T c.598A>T p.Ser200Cys p.S200C ENST00000281741 8/21 137 104 33 109 108 1 strelka-varscan-mutect TXNDC16,missense_variant,p.Ser200Cys,ENST00000281741,NM_001160047.1,NM_020784.2;TXNDC16,intron_variant,,ENST00000557374,;TXNDC16,intron_variant,,ENST00000554399,; A ENST00000281741 Transcript missense_variant 970/4564 598/2478 200/825 S/C Agt/Tgt COSM4913572 1 -1 TXNDC16 HGNC HGNC:19965 protein_coding YES CCDS32083.1 ENSP00000281741 Q9P2K2 UPI000059D245 NM_001160047.1,NM_020784.2 deleterious(0.03) 8/21 hmmpanther:PTHR22699,hmmpanther:PTHR22699:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 52514887 52514887 T A 1 0 0 0 0 1 0 0 0 17311 1609 56 4 4 TXNDC16 14 52514887 Missense_Mutation SNP T C3N-01842_T 10626965 52514887 54528831 280 26472 C14orf105 0 . GRCh38 14 57491049 57491049 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.246C>A p.Asp82Glu p.D82E ENST00000422976 2/7 527 444 83 307 307 0 strelka-varscan-mutect C14orf105,missense_variant,p.Asp82Glu,ENST00000216445,NM_018168.3,NM_001283059.1,NM_001283058.1;C14orf105,missense_variant,p.Asp82Glu,ENST00000422976,NM_001283056.1;C14orf105,missense_variant,p.Asp82Glu,ENST00000534126,NM_001283057.1;C14orf105,missense_variant,p.Asp82Glu,ENST00000526336,;C14orf105,missense_variant,p.Asp82Glu,ENST00000526745,;C14orf105,missense_variant,p.Asp82Glu,ENST00000530417,;C14orf105,3_prime_UTR_variant,,ENST00000534528,;C14orf105,3_prime_UTR_variant,,ENST00000529860,NM_001283060.1; T ENST00000422976 Transcript missense_variant 288/1153 246/1011 82/336 D/E gaC/gaA 1 -1 C14orf105 HGNC HGNC:20189 protein_coding YES CCDS61459.1 ENSP00000392368 F5GWJ3 UPI000204A979 NM_001283056.1 deleterious(0) 2/7 hmmpanther:PTHR16065,Pfam_domain:PF15398 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 57491049 57491049 G T 1 0 0 0 0 1 0 0 0 1827 1368 48 2 2 C14orf105 14 57491049 Missense_Mutation SNP G C3N-01842_T 4976162 57491049 49552669 281 26473 SYNE2 0 . GRCh38 14 63976676 63976676 + Missense_Mutation SNP G G T rs757157681 C3N-01842_T C3N-01842_N G G c.1242G>T p.Gln414His p.Q414H ENST00000358025 12/116 423 335 88 305 304 1 strelka-varscan-mutect SYNE2,missense_variant,p.Gln414His,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Gln414His,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Gln414His,ENST00000357395,;SYNE2,missense_variant,p.Gln414His,ENST00000554584,; T ENST00000358025 Transcript missense_variant 1454/21842 1242/20724 414/6907 Q/H caG/caT rs757157681 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(0.08) 12/116 hmmpanther:PTHR11915:SF317,hmmpanther:PTHR11915 MODERATE 1 SNV 5 1 PASS rs757157681 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 63976676 63976676 G T 1 0 0 0 0 1 0 0 0 15838 991 35 2 2 SYNE2 14 63976676 Missense_Mutation SNP G C3N-01842_T 6485627 63976676 43067042 282 26474 SPTB 0 . GRCh38 14 64750142 64750142 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.6615C>A p.Asn2205Lys p.N2205K ENST00000556626 34/36 220 180 40 172 172 0 strelka-varscan-mutect SPTB,missense_variant,p.Asn2205Lys,ENST00000556626,;SPTB,missense_variant,p.Asn2205Lys,ENST00000389722,NM_001024858.2;SPTB,missense_variant,p.Asn905Lys,ENST00000553938,;PLEKHG3,3_prime_UTR_variant,,ENST00000247226,NM_001308147.1;SPTB,non_coding_transcript_exon_variant,,ENST00000342835,;SPTB,non_coding_transcript_exon_variant,,ENST00000556227,; T ENST00000556626 Transcript missense_variant 6758/10153 6615/6987 2205/2328 N/K aaC/aaA 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D tolerated(0.52) 34/36 PROSITE_profiles:PS50003,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Pfam_domain:PF15410,Gene3D:2.30.29.30,SMART_domains:SM00233,SMART_domains:SM00150,Superfamily_domains:SSF50729,Prints_domain:PR00683 MODERATE 1 SNV 1 1 PASS rs1437599682 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 64750142 64750142 G T 1 0 0 0 0 1 0 0 0 15474 1252 44 2 2 SPTB 14 64750142 Missense_Mutation SNP G C3N-01842_T 773466 64750142 42293576 283 26475 ACTN1 0 . GRCh38 14 68885436 68885436 + Silent SNP T T A novel C3N-01842_T C3N-01842_N T T c.1374A>T p.= p.A458A ENST00000394419 12/22 94 87 7 93 92 1 strelka-varscan-mutect ACTN1,synonymous_variant,p.=,ENST00000193403,NM_001102.3;ACTN1,synonymous_variant,p.=,ENST00000394419,NM_001130004.1;ACTN1,synonymous_variant,p.=,ENST00000438964,NM_001130005.1;ACTN1,synonymous_variant,p.=,ENST00000376839,;ACTN1,synonymous_variant,p.=,ENST00000538545,;ACTN1,synonymous_variant,p.=,ENST00000544964,;ACTN1,upstream_gene_variant,,ENST00000555075,;ACTN1,upstream_gene_variant,,ENST00000553290,;ACTN1,upstream_gene_variant,,ENST00000556343,;ACTN1,non_coding_transcript_exon_variant,,ENST00000556083,;ACTN1,upstream_gene_variant,,ENST00000556432,;HMGN1P3,downstream_gene_variant,,ENST00000555136,; A ENST00000394419 Transcript synonymous_variant 1557/3464 1374/2745 458/914 A gcA/gcT 1 -1 ACTN1 HGNC HGNC:163 protein_coding YES CCDS45130.1 ENSP00000377941 P12814 UPI0000D79B2C NM_001130004.1 12/22 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF241,SMART_domains:SM00150,Superfamily_domains:SSF46966 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -14.57207 1 1 1 1 0 A 2 1 84 68885436 68885436 T A 1 0 0 0 0 0 0 0 1 248 1683 59 4 4 ACTN1 14 68885436 Silent SNP T C3N-01842_T 4135294 68885436 38158282 284 26476 SLC8A3 0 . GRCh38 14 70167199 70167199 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.1224G>T p.= p.L408L ENST00000381269 2/8 539 340 199 464 462 2 strelka-varscan-mutect SLC8A3,synonymous_variant,p.=,ENST00000381269,NM_183002.2;SLC8A3,synonymous_variant,p.=,ENST00000357887,NM_033262.4;SLC8A3,synonymous_variant,p.=,ENST00000356921,NM_182932.2;SLC8A3,synonymous_variant,p.=,ENST00000528359,;SLC8A3,synonymous_variant,p.=,ENST00000534137,NM_058240.3;SLC8A3,synonymous_variant,p.=,ENST00000494208,; A ENST00000381269 Transcript synonymous_variant 1978/5268 1224/2784 408/927 L ctG/ctT 1 -1 SLC8A3 HGNC HGNC:11070 protein_coding YES CCDS35498.1 ENSP00000370669 P57103 UPI0000073C9A NM_183002.2 2/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF7,Pfam_domain:PF03160,TIGRFAM_domain:TIGR00845,SMART_domains:SM00237,Superfamily_domains:SSF141072 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 70167199 70167199 C A 1 0 0 0 0 0 0 0 1 14991 581 21 2 2 SLC8A3 14 70167199 Silent SNP C C3N-01842_T 1281763 70167199 36876519 285 26477 SNW1 0 . GRCh38 14 77732539 77732539 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.837C>T p.= p.H279H ENST00000261531 9/14 270 221 49 214 214 0 strelka-varscan-mutect SNW1,synonymous_variant,p.=,ENST00000261531,NM_012245.2;SNW1,synonymous_variant,p.=,ENST00000555761,;SNW1,synonymous_variant,p.=,ENST00000554775,;SNW1,synonymous_variant,p.=,ENST00000554324,;SLIRP,intron_variant,,ENST00000557431,;SLIRP,intron_variant,,ENST00000556375,;SNW1,3_prime_UTR_variant,,ENST00000556428,;SNW1,non_coding_transcript_exon_variant,,ENST00000553565,;SLIRP,intron_variant,,ENST00000556310,; A ENST00000261531 Transcript synonymous_variant 900/2163 837/1611 279/536 H caC/caT 1 -1 SNW1 HGNC HGNC:16696 protein_coding YES CCDS9867.1 ENSP00000261531 Q13573 UPI000000DB2D NM_012245.2 9/14 hmmpanther:PTHR12096,Pfam_domain:PF02731 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 77732539 77732539 G A 1 0 0 0 0 0 0 0 1 15200 1368 48 3 3 SNW1 14 77732539 Silent SNP G C3N-01842_T 7565340 77732539 29311179 286 26478 CEP128 0 . GRCh38 14 80785278 80785278 + Missense_Mutation SNP C C T C3N-01842_T C3N-01842_N C C c.1828G>A p.Ala610Thr p.A610T ENST00000555265 15/25 458 365 93 339 339 0 strelka-varscan-mutect CEP128,missense_variant,p.Ala610Thr,ENST00000555265,;CEP128,missense_variant,p.Ala610Thr,ENST00000281129,NM_152446.3;CEP128,missense_variant,p.Ala302Thr,ENST00000554502,; T ENST00000555265 Transcript missense_variant 2204/4662 1828/3285 610/1094 A/T Gct/Act COSM958297 1 -1 CEP128 HGNC HGNC:20359 protein_coding YES CCDS32130.1 ENSP00000451162 Q6ZU80 UPI000022982E tolerated(0.58) 15/25 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF205 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 80785278 80785278 C T 1 0 0 0 0 1 0 0 0 2958 797 28 3 3 CEP128 14 80785278 Missense_Mutation SNP C C3N-01842_T 3052739 80785278 26258440 287 26479 FLRT2 0 . GRCh38 14 85623255 85623255 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.1741C>G p.Arg581Gly p.R581G ENST00000330753 2/2 39 33 6 32 32 0 strelka-mutect FLRT2,missense_variant,p.Arg581Gly,ENST00000330753,NM_013231.4;FLRT2,missense_variant,p.Arg581Gly,ENST00000554746,;FLRT2,upstream_gene_variant,,ENST00000553650,; G ENST00000330753 Transcript missense_variant 2508/33679 1741/1983 581/660 R/G Cgg/Ggg 1 1 FLRT2 HGNC HGNC:3761 protein_coding YES CCDS9877.1 ENSP00000332879 O43155 UPI0000049E10 NM_013231.4 deleterious(0) 2/2 hmmpanther:PTHR24369:SF23,hmmpanther:PTHR24369 MODERATE 1 SNV 1 1 PASS rs1157482367 . 1 205 3 0 0 0 0 0 -15.5871 1 1 1 1 0 G 3 3 84 85623255 85623255 C G 1 0 0 0 0 1 0 0 0 5795 643 23 4 4 FLRT2 14 85623255 Missense_Mutation SNP C C3N-01842_T 4837977 85623255 21420463 288 26480 GLRX5 0 . GRCh38 14 95535228 95535228 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.139G>T p.Ala47Ser p.A47S ENST00000331334 1/2 299 239 60 297 297 0 strelka-varscan-mutect GLRX5,missense_variant,p.Ala47Ser,ENST00000331334,NM_016417.2;GLRX5,upstream_gene_variant,,ENST00000557731,;SCARNA13,upstream_gene_variant,,ENST00000516672,;SNHG10,upstream_gene_variant,,ENST00000500370,;SNHG10,upstream_gene_variant,,ENST00000554169,;SNHG10,upstream_gene_variant,,ENST00000553559,;SNHG10,upstream_gene_variant,,ENST00000555866,;GLRX5,intron_variant,,ENST00000553672,; T ENST00000331334 Transcript missense_variant 636/1564 139/474 47/157 A/S Gcg/Tcg 1 1 GLRX5 HGNC HGNC:20134 protein_coding YES CCDS9936.1 ENSP00000328570 Q86SX6 UPI000000DC2E NM_016417.2 tolerated(0.38) 1/2 Gene3D:3.40.30.10,PROSITE_profiles:PS51354,hmmpanther:PTHR10293,Low_complexity_(Seg):seg,Superfamily_domains:SSF52833,TIGRFAM_domain:TIGR00365 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 95535228 95535228 G T 1 0 0 0 0 1 0 0 0 6341 1087 38 1 1 GLRX5 14 95535228 Missense_Mutation SNP G C3N-01842_T 9911973 95535228 11508490 289 26481 RTL1 0 . GRCh38 14 100883226 100883226 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1563C>A p.= p.G521G ENST00000534062 1/1 197 155 42 184 184 0 strelka-varscan-mutect RTL1,synonymous_variant,p.=,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,downstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; T ENST00000534062 Transcript synonymous_variant 1622/4193 1563/4077 521/1358 G ggC/ggA 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 1/1 LOW 1 SNV 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999802 1 1 1 0 T 2 4 84 100883226 100883226 G T 1 0 0 0 0 0 0 0 1 13984 1190 42 2 2 RTL1 14 100883226 Silent SNP G C3N-01842_T 5347998 100883226 6160492 290 26482 DYNC1H1 0 . GRCh38 14 102032468 102032468 + Splice_Site SNP G G T novel C3N-01842_T C3N-01842_N G G c.10079+1G>T p.X3360_splice ENST00000360184 554 445 109 518 518 0 strelka-varscan-mutect DYNC1H1,splice_donor_variant,,ENST00000360184,NM_001376.4;DYNC1H1,upstream_gene_variant,,ENST00000553423,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557551,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557242,;RP11-1017G21.4,downstream_gene_variant,,ENST00000553701,;DYNC1H1,upstream_gene_variant,,ENST00000556791,;DYNC1H1,downstream_gene_variant,,ENST00000554854,; T ENST00000360184 Transcript splice_donor_variant -/14333 10079/13941 3360/4646 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 52/77 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 84 102032468 102032468 G T 1 0 0 0 0 0 0 1 0 4665 1275 44 2 2 DYNC1H1 14 102032468 Splice_Site SNP G C3N-01842_T 1149242 102032468 5011250 291 26483 RCOR1 0 . GRCh38 14 102722286 102722286 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.1289G>T p.Arg430Leu p.R430L ENST00000262241 11/12 559 463 96 397 397 0 strelka-varscan-mutect RCOR1,missense_variant,p.Arg430Leu,ENST00000262241,NM_015156.3;RCOR1,3_prime_UTR_variant,,ENST00000560472,;RCOR1,downstream_gene_variant,,ENST00000559597,; T ENST00000262241 Transcript missense_variant 1515/5754 1289/1458 430/485 R/L cGc/cTc COSM3419640 1 1 RCOR1 HGNC HGNC:17441 protein_coding YES CCDS9974.2 ENSP00000262241 J3KN32 UPI0000D6A053 NM_015156.3 deleterious(0) 11/12 PROSITE_profiles:PS51293,hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF11,SMART_domains:SM00717,Superfamily_domains:SSF46689 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 102722286 102722286 G T 1 0 0 0 0 1 0 0 0 13352 1087 38 1 1 RCOR1 14 102722286 Missense_Mutation SNP G C3N-01842_T 689818 102722286 4321432 292 26484 GOLGA8J 0 . GRCh38 15 30087620 30087620 + Missense_Mutation SNP G G C novel C3N-01842_T C3N-01842_N G G c.527G>C p.Arg176Pro p.R176P ENST00000567927 8/19 41 29 12 75 75 0 strelka-varscan-mutect GOLGA8J,missense_variant,p.Arg176Pro,ENST00000567927,NM_001282472.1;RN7SL673P,upstream_gene_variant,,ENST00000616262,;GOLGA8J,non_coding_transcript_exon_variant,,ENST00000568123,; C ENST00000567927 Transcript missense_variant 527/1899 527/1899 176/632 R/P cGt/cCt 1 1 GOLGA8J HGNC HGNC:38650 protein_coding YES CCDS61574.1 ENSP00000456401 A6NMD2 UPI0001A5E7A2 NM_001282472.1 deleterious(0.01) 8/19 hmmpanther:PTHR10881:SF48,hmmpanther:PTHR10881 MODERATE 1 SNV 5 1 PASS rs1257778104 . 9 186 15 0 0 0 0 0 -20 0.9998238 1 1 1 0 C 3 2 84 30087620 30087620 G C 1 0 0 0 0 1 0 0 0 6452 1145 40 4 4 GOLGA8J 15 30087620 Missense_Mutation SNP G C3N-01842_T 30087620 71903569 293 26485 RYR3 0 . GRCh38 15 33816950 33816950 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.10591G>A p.Asp3531Asn p.D3531N ENST00000634891 75/104 119 89 30 159 159 0 strelka-varscan-mutect RYR3,missense_variant,p.Asp3531Asn,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Asp3534Asn,ENST00000622037,;RYR3,missense_variant,p.Asp3526Asn,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Asp3530Asn,ENST00000389232,;RYR3,intron_variant,,ENST00000634418,;RYR3,downstream_gene_variant,,ENST00000638085,;RYR3,downstream_gene_variant,,ENST00000638038,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,upstream_gene_variant,,ENST00000558060,;RYR3,upstream_gene_variant,,ENST00000557931,; A ENST00000634891 Transcript missense_variant 10692/15591 10591/14613 3531/4870 D/N Gat/Aat 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0.03) 75/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 33816950 33816950 G A 1 0 0 0 0 1 0 0 0 14030 1174 41 3 3 RYR3 15 33816950 Missense_Mutation SNP G C3N-01842_T 3729330 33816950 68174239 294 26486 RYR3 0 . GRCh38 15 33827204 33827204 + Nonsense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.11251C>T p.Gln3751Ter p.Q3751* ENST00000634891 85/104 161 91 70 236 236 0 strelka-varscan-mutect RYR3,stop_gained,p.Gln3751Ter,ENST00000634891,NM_001036.4;RYR3,stop_gained,p.Gln3754Ter,ENST00000622037,;RYR3,stop_gained,p.Gln3746Ter,ENST00000415757,NM_001243996.2;RYR3,stop_gained,p.Gln3750Ter,ENST00000389232,;RYR3,stop_gained,p.Gln3740Ter,ENST00000634418,;RYR3,upstream_gene_variant,,ENST00000638145,;RYR3,3_prime_UTR_variant,,ENST00000635790,;RYR3,downstream_gene_variant,,ENST00000558060,; T ENST00000634891 Transcript stop_gained 11352/15591 11251/14613 3751/4870 Q/* Cag/Tag 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 85/104 Pfam_domain:PF08454,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 33827204 33827204 C T 1 0 0 0 0 0 1 0 0 14030 840 29 3 3 RYR3 15 33827204 Nonsense_Mutation SNP C C3N-01842_T 10254 33827204 68163985 295 26487 CDAN1 0 . GRCh38 15 42730761 42730761 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.2011C>T p.Pro671Ser p.P671S ENST00000356231 14/28 275 212 63 270 270 0 strelka-varscan-mutect CDAN1,missense_variant,p.Pro671Ser,ENST00000356231,NM_138477.2;CTD-2036P10.6,downstream_gene_variant,,ENST00000617465,;CDAN1,missense_variant,p.Pro2Ser,ENST00000562465,; A ENST00000356231 Transcript missense_variant 2035/4637 2011/3684 671/1227 P/S Cct/Tct 1 -1 CDAN1 HGNC HGNC:1713 protein_coding YES CCDS32209.1 ENSP00000348564 Q8IWY9 UPI0000229BCB NM_138477.2 tolerated(0.4) 14/28 hmmpanther:PTHR28678 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 42730761 42730761 G A 1 0 0 0 0 1 0 0 0 2757 1246 43 3 3 CDAN1 15 42730761 Missense_Mutation SNP G C3N-01842_T 8903557 42730761 59260428 296 26488 WDR72 0 . GRCh38 15 53597223 53597223 + Nonsense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.3004A>T p.Lys1002Ter p.K1002* ENST00000396328 18/20 266 210 56 260 260 0 strelka-varscan-mutect WDR72,stop_gained,p.Lys1002Ter,ENST00000396328,;WDR72,stop_gained,p.Lys999Ter,ENST00000557913,;WDR72,stop_gained,p.Lys1002Ter,ENST00000360509,NM_182758.3;WDR72,stop_gained,p.Lys1012Ter,ENST00000559418,; A ENST00000396328 Transcript stop_gained 3244/7507 3004/3309 1002/1102 K/* Aag/Tag 1 -1 WDR72 HGNC HGNC:26790 protein_coding YES CCDS10151.1 ENSP00000379619 Q3MJ13 UPI00001D777D 18/20 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 53597223 53597223 T A 1 0 0 0 0 0 1 0 0 17878 1792 62 4 4 WDR72 15 53597223 Nonsense_Mutation SNP T C3N-01842_T 10866462 53597223 48393966 297 26489 UNC13C 0 . GRCh38 15 54015243 54015243 + Missense_Mutation SNP T T G novel C3N-01842_T C3N-01842_N T T c.2340T>G p.His780Gln p.H780Q ENST00000260323 1/32 382 302 80 372 371 1 strelka-varscan-mutect UNC13C,missense_variant,p.His780Gln,ENST00000260323,NM_001080534.1; G ENST00000260323 Transcript missense_variant 2340/12946 2340/6645 780/2214 H/Q caT/caG 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0.04) 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 54015243 54015243 T G 1 0 0 0 0 1 0 0 0 17510 1403 49 5 5 UNC13C 15 54015243 Missense_Mutation SNP T C3N-01842_T 418020 54015243 47975946 298 26490 LIPC 0 . GRCh38 15 58563558 58563558 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.1223T>C p.Val408Ala p.V408A ENST00000299022 8/9 546 415 131 534 534 0 strelka-varscan-mutect LIPC,missense_variant,p.Val408Ala,ENST00000414170,;LIPC,missense_variant,p.Val408Ala,ENST00000299022,NM_000236.2;LIPC,missense_variant,p.Val408Ala,ENST00000356113,;LIPC,missense_variant,p.Val347Ala,ENST00000433326,;LIPC,non_coding_transcript_exon_variant,,ENST00000559845,; C ENST00000299022 Transcript missense_variant 1458/2751 1223/1500 408/499 V/A gTg/gCg 1 1 LIPC HGNC HGNC:6619 protein_coding YES CCDS10166.1 ENSP00000299022 P11150 UPI000013E54D NM_000236.2 tolerated(0.94) 8/9 PROSITE_profiles:PS50095,hmmpanther:PTHR11610:SF2,hmmpanther:PTHR11610,PIRSF_domain:PIRSF000865,Pfam_domain:PF01477,Gene3D:2.60.60.20,SMART_domains:SM00308,Superfamily_domains:SSF49723,Prints_domain:PR00821 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 58563558 58563558 T C 1 0 0 0 0 1 0 0 0 8741 1696 59 5 5 LIPC 15 58563558 Missense_Mutation SNP T C3N-01842_T 4548315 58563558 43427631 299 26491 ZNF609 0 . GRCh38 15 64499732 64499732 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.313G>T p.Gly105Trp p.G105W ENST00000326648 1/9 544 419 125 580 576 4 strelka-varscan-mutect ZNF609,missense_variant,p.Gly105Trp,ENST00000326648,NM_015042.1;ZNF609,missense_variant,p.Gly105Trp,ENST00000416172,;ZNF609,upstream_gene_variant,,ENST00000558680,; T ENST00000326648 Transcript missense_variant 441/8746 313/4236 105/1411 G/W Ggg/Tgg 1 1 ZNF609 HGNC HGNC:29003 protein_coding YES CCDS32270.1 ENSP00000316527 O15014 UPI00001D7783 NM_015042.1 deleterious(0.02) 1/9 hmmpanther:PTHR21564:SF3,hmmpanther:PTHR21564 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 64499732 64499732 G T 1 0 0 0 0 1 0 0 0 18610 1000 35 2 2 ZNF609 15 64499732 Missense_Mutation SNP G C3N-01842_T 5936174 64499732 37491457 300 26492 ZNF609 0 . GRCh38 15 64675904 64675904 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.3050A>T p.Gln1017Leu p.Q1017L ENST00000326648 4/9 355 272 83 402 402 0 strelka-varscan-mutect ZNF609,missense_variant,p.Gln1017Leu,ENST00000326648,NM_015042.1;RNU6-549P,downstream_gene_variant,,ENST00000384433,;ZNF609,downstream_gene_variant,,ENST00000559364,; T ENST00000326648 Transcript missense_variant 3178/8746 3050/4236 1017/1411 Q/L cAg/cTg 1 1 ZNF609 HGNC HGNC:29003 protein_coding YES CCDS32270.1 ENSP00000316527 O15014 UPI00001D7783 NM_015042.1 tolerated(0.06) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR21564:SF3,hmmpanther:PTHR21564 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 64675904 64675904 A T 1 0 0 0 0 1 0 0 0 18610 188 7 4 4 ZNF609 15 64675904 Missense_Mutation SNP A C3N-01842_T 176172 64675904 37315285 301 26493 DPP8 0 . GRCh38 15 65456351 65456351 + Silent SNP C C A rs574744033 C3N-01842_T C3N-01842_N C C c.2040G>T p.= p.R680R ENST00000341861 16/20 258 207 51 199 199 0 strelka-varscan-mutect DPP8,synonymous_variant,p.=,ENST00000341861,NM_197960.2;DPP8,synonymous_variant,p.=,ENST00000300141,NM_130434.3;DPP8,synonymous_variant,p.=,ENST00000321147,NM_197961.2;DPP8,synonymous_variant,p.=,ENST00000559233,;DPP8,synonymous_variant,p.=,ENST00000558559,;DPP8,intron_variant,,ENST00000358939,NM_017743.4;DPP8,intron_variant,,ENST00000558786,;DPP8,non_coding_transcript_exon_variant,,ENST00000558363,;DPP8,upstream_gene_variant,,ENST00000560048,;DPP8,synonymous_variant,p.=,ENST00000395652,;DPP8,non_coding_transcript_exon_variant,,ENST00000560597,;RP11-349G13.3,upstream_gene_variant,,ENST00000605455,; A ENST00000341861 Transcript synonymous_variant 3621/8699 2040/2697 680/898 R cgG/cgT rs574744033 1 -1 DPP8 HGNC HGNC:16490 protein_coding YES CCDS10207.1 ENSP00000339208 Q6V1X1 A0A024R5Z6 UPI00001BFAFE NM_197960.2 16/20 hmmpanther:PTHR11731,hmmpanther:PTHR11731:SF98,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS rs574744033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 65456351 65456351 C A 1 0 0 0 0 0 0 0 1 4547 494 18 2 2 DPP8 15 65456351 Silent SNP C C3N-01842_T 780447 65456351 36534838 302 26494 HCN4 0 . GRCh38 15 73322651 73322651 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.3442C>A p.Gln1148Lys p.Q1148K ENST00000261917 8/8 347 266 81 423 423 0 strelka-varscan-mutect HCN4,missense_variant,p.Gln1148Lys,ENST00000261917,NM_005477.2; T ENST00000261917 Transcript missense_variant 4436/7228 3442/3612 1148/1203 Q/K Cag/Aag 1 -1 HCN4 HGNC HGNC:16882 protein_coding YES CCDS10248.1 ENSP00000261917 Q9Y3Q4 UPI000003FFB5 NM_005477.2 deleterious_low_confidence(0.04) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 73322651 73322651 G T 1 0 0 0 0 1 0 0 0 6886 1357 47 2 2 HCN4 15 73322651 Missense_Mutation SNP G C3N-01842_T 7866300 73322651 28668538 303 26495 CSK 0 . GRCh38 15 74801809 74801809 + Silent SNP T T A novel C3N-01842_T C3N-01842_N T T c.1002T>A p.= p.G334G ENST00000220003 11/13 232 197 35 233 232 1 strelka-varscan-mutect CSK,synonymous_variant,p.=,ENST00000220003,NM_004383.2;CSK,synonymous_variant,p.=,ENST00000567571,;CSK,synonymous_variant,p.=,ENST00000439220,NM_001127190.1;CSK,downstream_gene_variant,,ENST00000569915,;CSK,downstream_gene_variant,,ENST00000567123,;CSK,downstream_gene_variant,,ENST00000569462,;CSK,non_coding_transcript_exon_variant,,ENST00000568329,;CSK,non_coding_transcript_exon_variant,,ENST00000564216,;CSK,non_coding_transcript_exon_variant,,ENST00000567135,;CSK,non_coding_transcript_exon_variant,,ENST00000563010,;CSK,non_coding_transcript_exon_variant,,ENST00000569321,;CSK,downstream_gene_variant,,ENST00000563894,;CSK,downstream_gene_variant,,ENST00000562066,;CSK,downstream_gene_variant,,ENST00000566464,; A ENST00000220003 Transcript synonymous_variant 1731/2767 1002/1353 334/450 G ggT/ggA 1 1 CSK HGNC HGNC:2444 protein_coding YES CCDS10269.1 ENSP00000220003 P41240 B2R6Q4 UPI0000128541 NM_004383.2 11/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF52,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 74801809 74801809 T A 1 0 0 0 0 0 0 0 1 3744 1654 58 4 4 CSK 15 74801809 Silent SNP T C3N-01842_T 1479158 74801809 27189380 304 26496 ANPEP 0 . GRCh38 15 89806176 89806176 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.408G>T p.Arg136Ser p.R136S ENST00000300060 2/21 207 171 36 241 241 0 strelka-varscan-mutect ANPEP,missense_variant,p.Arg136Ser,ENST00000300060,NM_001150.2;ANPEP,downstream_gene_variant,,ENST00000559874,;ANPEP,downstream_gene_variant,,ENST00000560137,;ANPEP,upstream_gene_variant,,ENST00000558177,;ANPEP,upstream_gene_variant,,ENST00000560030,;ANPEP,upstream_gene_variant,,ENST00000560028,;ANPEP,upstream_gene_variant,,ENST00000559887,; A ENST00000300060 Transcript missense_variant 722/3678 408/2904 136/967 R/S agG/agT 1 -1 ANPEP HGNC HGNC:500 protein_coding YES CCDS10356.1 ENSP00000300060 P15144 A0A024RC61 UPI00001AECCF NM_001150.2 tolerated(0.44) 2/21 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF172,Pfam_domain:PF01433,Superfamily_domains:0038696 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 89806176 89806176 C A 1 0 0 0 0 1 0 0 0 817 622 22 2 2 ANPEP 15 89806176 Missense_Mutation SNP C C3N-01842_T 15004367 89806176 12185013 305 26497 IGF1R 0 . GRCh38 15 98707617 98707617 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.150G>A p.= p.E50E ENST00000268035 2/21 426 328 98 494 494 0 strelka-varscan-mutect IGF1R,synonymous_variant,p.=,ENST00000268035,NM_000875.4;IGF1R,synonymous_variant,p.=,ENST00000558762,NM_001291858.1;IGF1R,upstream_gene_variant,,ENST00000558355,;IGF1R,non_coding_transcript_exon_variant,,ENST00000559925,; A ENST00000268035 Transcript synonymous_variant 761/11803 150/4104 50/1367 E gaG/gaA 1 1 IGF1R HGNC HGNC:5465 protein_coding YES CCDS10378.1 ENSP00000268035 P08069 UPI000012D3EA NM_000875.4 2/21 hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF106,PIRSF_domain:PIRSF000620,Gene3D:3.80.20.20,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 98707617 98707617 G A 1 0 0 0 0 0 0 0 1 7477 933 33 3 3 IGF1R 15 98707617 Silent SNP G C3N-01842_T 8901441 98707617 3283572 306 26498 CERS3 0 . GRCh38 15 100455975 100455975 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.917T>A p.Leu306Gln p.L306Q ENST00000284382 12/13 299 241 58 235 235 0 strelka-varscan-mutect CERS3,missense_variant,p.Leu306Gln,ENST00000284382,NM_178842.3,NM_001290343.1;CERS3,missense_variant,p.Leu306Gln,ENST00000394113,NM_001290341.1;CERS3,missense_variant,p.Leu306Gln,ENST00000538112,NM_001290342.1;CERS3,intron_variant,,ENST00000560944,; T ENST00000284382 Transcript missense_variant 1341/3894 917/1152 306/383 L/Q cTa/cAa 1 -1 CERS3 HGNC HGNC:23752 protein_coding YES CCDS10384.1 ENSP00000284382 Q8IU89 UPI00001975AB NM_178842.3,NM_001290343.1 tolerated(0.11) 12/13 Pfam_domain:PF03798,PIRSF_domain:PIRSF005225,PROSITE_profiles:PS50922,hmmpanther:PTHR12560,hmmpanther:PTHR12560:SF18,SMART_domains:SM00724,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 100455975 100455975 A T 1 0 0 0 0 1 0 0 0 2997 420 15 4 4 CERS3 15 100455975 Missense_Mutation SNP A C3N-01842_T 1748358 100455975 1535214 307 26499 CERS3 0 . GRCh38 15 100484620 100484620 + Missense_Mutation SNP C C A rs764980198 C3N-01842_T C3N-01842_N C C c.337G>T p.Val113Leu p.V113L ENST00000284382 6/13 366 303 63 423 423 0 strelka-varscan-mutect CERS3,missense_variant,p.Val113Leu,ENST00000284382,NM_178842.3,NM_001290343.1;CERS3,missense_variant,p.Val113Leu,ENST00000394113,NM_001290341.1;CERS3,missense_variant,p.Val113Leu,ENST00000538112,NM_001290342.1;CERS3,missense_variant,p.Val113Leu,ENST00000558884,;CERS3,intron_variant,,ENST00000560944,; A ENST00000284382 Transcript missense_variant 761/3894 337/1152 113/383 V/L Gtg/Ttg rs764980198 1 -1 CERS3 HGNC HGNC:23752 protein_coding YES CCDS10384.1 ENSP00000284382 Q8IU89 UPI00001975AB NM_178842.3,NM_001290343.1 deleterious(0.01) 6/13 Gene3D:1.10.10.60,Pfam_domain:PF00046,PIRSF_domain:PIRSF005225,PROSITE_profiles:PS50071,hmmpanther:PTHR12560,hmmpanther:PTHR12560:SF18,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS rs764980198 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 100484620 100484620 C A 1 0 0 0 0 1 0 0 0 2997 507 18 2 2 CERS3 15 100484620 Missense_Mutation SNP C C3N-01842_T 28645 100484620 1506569 308 26500 IQCK 0 . GRCh38 16 19733755 19733755 + Missense_Mutation SNP G G T rs773201624 C3N-01842_T C3N-01842_N G G c.304G>T p.Val102Phe p.V102F ENST00000320394 4/10 348 278 70 351 351 0 strelka-varscan-mutect IQCK,missense_variant,p.Val102Phe,ENST00000320394,NM_153208.1;IQCK,missense_variant,p.Val102Phe,ENST00000564186,;IQCK,upstream_gene_variant,,ENST00000568387,;IQCK,missense_variant,p.Val102Phe,ENST00000308214,;IQCK,missense_variant,p.Gly80Val,ENST00000568126,;IQCK,missense_variant,p.Val100Phe,ENST00000561839,;IQCK,missense_variant,p.Gly80Val,ENST00000564955,;IQCK,missense_variant,p.Val96Phe,ENST00000561935,;IQCK,non_coding_transcript_exon_variant,,ENST00000568300,;IQCK,non_coding_transcript_exon_variant,,ENST00000564515,;IQCK,non_coding_transcript_exon_variant,,ENST00000566312,; T ENST00000320394 Transcript missense_variant 1003/3482 304/864 102/287 V/F Gtt/Ttt rs773201624 1 1 IQCK HGNC HGNC:28556 protein_coding YES CCDS10580.1 ENSP00000324901 Q8N0W5 UPI0000072C5C NM_153208.1 tolerated(0.22) 4/10 hmmpanther:PTHR34927 MODERATE 1 SNV 1 1 PASS rs773201624 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 19733755 19733755 G T 1 0 0 0 0 1 0 0 0 7719 1261 44 2 2 IQCK 16 19733755 Missense_Mutation SNP G C3N-01842_T 19733755 70604590 309 26501 ACSM2B 0 . GRCh38 16 20555477 20555477 + Splice_Site SNP C C A novel C3N-01842_T C3N-01842_N C C c.389-1G>T p.X130_splice ENST00000329697 178 149 29 154 154 0 strelka-varscan-mutect ACSM2B,splice_acceptor_variant,,ENST00000329697,NM_001105069.1;ACSM2B,splice_acceptor_variant,,ENST00000414188,;ACSM2B,splice_acceptor_variant,,ENST00000565232,;ACSM2B,splice_acceptor_variant,,ENST00000567001,NM_182617.3;ACSM2B,splice_acceptor_variant,,ENST00000565322,;ACSM2B,splice_acceptor_variant,,ENST00000568882,;ACSM2B,upstream_gene_variant,,ENST00000567288,;ACSM2B,upstream_gene_variant,,ENST00000569163,;ACSM2B,downstream_gene_variant,,ENST00000566384,;ACSM2B,downstream_gene_variant,,ENST00000569344,;ACSM2B,splice_acceptor_variant,,ENST00000569364,;ACSM2B,splice_acceptor_variant,,ENST00000563943,;ACSM2B,splice_acceptor_variant,,ENST00000569327,; A ENST00000329697 Transcript splice_acceptor_variant -/2935 389/1734 130/577 1 -1 ACSM2B HGNC HGNC:30931 protein_coding YES CCDS10586.1 ENSP00000327453 Q68CK6 UPI00001AFAA7 NM_001105069.1 3/13 HIGH 1 SNV 1 1 PASS rs1383375446 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 84 20555477 20555477 C A 1 0 0 0 0 0 0 1 0 226 695 24 2 2 ACSM2B 16 20555477 Splice_Site SNP C C3N-01842_T 821722 20555477 69782868 310 26502 THUMPD1 0 . GRCh38 16 20736976 20736976 + Silent SNP C C G rs369783164 C3N-01842_T C3N-01842_N C C c.966G>C p.= p.T322T ENST00000381337 4/5 338 270 68 363 363 0 strelka-varscan-mutect THUMPD1,synonymous_variant,p.=,ENST00000381337,NM_017736.4,NM_001304550.1;THUMPD1,synonymous_variant,p.=,ENST00000396083,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;THUMPD1,synonymous_variant,p.=,ENST00000636554,;THUMPD1,non_coding_transcript_exon_variant,,ENST00000570231,;THUMPD1,downstream_gene_variant,,ENST00000565248,;THUMPD1,downstream_gene_variant,,ENST00000569768,;AC004381.8,downstream_gene_variant,,ENST00000637768,; G ENST00000381337 Transcript synonymous_variant 1311/4122 966/1062 322/353 T acG/acC rs369783164 1 -1 THUMPD1 HGNC HGNC:23807 protein_coding YES CCDS10588.1 ENSP00000370741 Q9NXG2 A0A024R388 UPI000007226C NM_017736.4,NM_001304550.1 4/5 LOW 1 SNV 1 1 PASS rs369783164 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 20736976 20736976 C G 1 0 0 0 0 0 0 0 1 16316 523 19 4 4 THUMPD1 16 20736976 Silent SNP C C3N-01842_T 181499 20736976 69601369 311 26503 THUMPD1 0 . GRCh38 16 20737833 20737833 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.530A>T p.Lys177Ile p.K177I ENST00000381337 3/5 388 314 74 330 329 1 strelka-varscan-mutect THUMPD1,missense_variant,p.Lys177Ile,ENST00000381337,NM_017736.4,NM_001304550.1;THUMPD1,missense_variant,p.Lys177Ile,ENST00000396083,;ACSM3,intron_variant,,ENST00000561584,;ACSM3,intron_variant,,ENST00000568235,;ACSM3,intron_variant,,ENST00000501740,;THUMPD1,missense_variant,p.Lys177Ile,ENST00000636554,;THUMPD1,3_prime_UTR_variant,,ENST00000565248,;THUMPD1,non_coding_transcript_exon_variant,,ENST00000570231,;THUMPD1,downstream_gene_variant,,ENST00000569768,;AC004381.8,downstream_gene_variant,,ENST00000637768,; A ENST00000381337 Transcript missense_variant 875/4122 530/1062 177/353 K/I aAa/aTa 1 -1 THUMPD1 HGNC HGNC:23807 protein_coding YES CCDS10588.1 ENSP00000370741 Q9NXG2 A0A024R388 UPI000007226C NM_017736.4,NM_001304550.1 deleterious(0.01) 3/5 PROSITE_profiles:PS51165,hmmpanther:PTHR13452,hmmpanther:PTHR13452:SF10,Pfam_domain:PF02926,SMART_domains:SM00981,Superfamily_domains:SSF143437 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 20737833 20737833 T A 1 0 0 0 0 1 0 0 0 16316 1841 64 4 4 THUMPD1 16 20737833 Missense_Mutation SNP T C3N-01842_T 857 20737833 69600512 312 26504 VWA3A 0 . GRCh38 16 22132968 22132968 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.1941C>T p.= p.F647F ENST00000389398 20/34 290 235 55 349 349 0 strelka-varscan-mutect VWA3A,synonymous_variant,p.=,ENST00000389398,NM_173615.4;VWA3A,synonymous_variant,p.=,ENST00000568328,;VWA3A,synonymous_variant,p.=,ENST00000563389,;VWA3A,synonymous_variant,p.=,ENST00000299840,;VWA3A,non_coding_transcript_exon_variant,,ENST00000566668,; T ENST00000389398 Transcript synonymous_variant 2037/4600 1941/3555 647/1184 F ttC/ttT 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 20/34 hmmpanther:PTHR10338:SF95,hmmpanther:PTHR10338,Superfamily_domains:SSF53300 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 22132968 22132968 C T 1 0 0 0 0 0 0 0 1 17794 912 32 3 3 VWA3A 16 22132968 Silent SNP C C3N-01842_T 1395135 22132968 68205377 313 26505 IL21R 0 . GRCh38 16 27444706 27444706 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.672G>T p.Gln224His p.Q224H ENST00000337929 6/9 33 22 11 42 42 0 strelka-varscan-mutect IL21R,missense_variant,p.Gln224His,ENST00000337929,NM_181078.2;IL21R,missense_variant,p.Gln224His,ENST00000564089,NM_181079.4;IL21R,missense_variant,p.Gln224His,ENST00000395754,NM_021798.3;IL21R-AS1,downstream_gene_variant,,ENST00000563191,;IL21R,non_coding_transcript_exon_variant,,ENST00000564583,;IL21R,downstream_gene_variant,,ENST00000561953,; T ENST00000337929 Transcript missense_variant 1145/4849 672/1617 224/538 Q/H caG/caT 1 1 IL21R HGNC HGNC:6006 protein_coding YES CCDS10630.1 ENSP00000338010 Q9HBE5 UPI0000043CF0 NM_181078.2 tolerated(0.7) 6/9 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF7,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs1340404621 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 27444706 27444706 G T 1 0 0 0 0 1 0 0 0 7574 933 33 2 2 IL21R 16 27444706 Missense_Mutation SNP G C3N-01842_T 5311738 27444706 62893639 314 26506 ARMC5 0 . GRCh38 16 31460000 31460000 + Splice_Site SNP G G T novel C3N-01842_T C3N-01842_N G G c.760+1G>T p.X254_splice ENST00000408912 327 260 67 373 373 0 strelka-varscan-mutect ARMC5,splice_donor_variant,,ENST00000457010,NM_024742.2;ARMC5,splice_donor_variant,,ENST00000408912,NM_001288767.1;ARMC5,splice_donor_variant,,ENST00000268314,NM_001105247.1;ARMC5,splice_donor_variant,,ENST00000563544,NM_001301820.1;ARMC5,splice_donor_variant,,ENST00000538189,;ARMC5,splice_donor_variant,,ENST00000564900,;RP11-452L6.5,upstream_gene_variant,,ENST00000564629,;ARMC5,missense_variant,p.Gly3Val,ENST00000564514,; T ENST00000408912 Transcript splice_donor_variant -/3626 760/3093 254/1030 1 1 ARMC5 HGNC HGNC:25781 protein_coding YES CCDS73874.1 ENSP00000386125 J3KQ26 UPI0001AE681E NM_001288767.1 3/7 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 84 31460000 31460000 G T 1 0 0 0 0 0 0 1 0 1095 1275 44 2 2 ARMC5 16 31460000 Splice_Site SNP G C3N-01842_T 4015294 31460000 58878345 315 26507 SALL1 0 . GRCh38 16 51137517 51137517 + Silent SNP A A T novel C3N-01842_T C3N-01842_N A A c.3570T>A p.= p.P1190P ENST00000251020 3/3 181 160 21 209 208 1 varscan-mutect SALL1,synonymous_variant,p.=,ENST00000440970,NM_001127892.1;SALL1,synonymous_variant,p.=,ENST00000251020,NM_002968.2;SALL1,synonymous_variant,p.=,ENST00000570206,;SALL1,3_prime_UTR_variant,,ENST00000566102,; T ENST00000251020 Transcript synonymous_variant 3604/5146 3570/3975 1190/1324 P ccT/ccA 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 3/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 51137517 51137517 A T 1 0 0 0 0 0 0 0 1 14069 175 7 4 4 SALL1 16 51137517 Silent SNP A C3N-01842_T 19677517 51137517 39200828 316 26508 ADGRG1 0 . GRCh38 16 57656255 57656255 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1047G>T p.Trp349Cys p.W349C ENST00000568909 8/14 468 418 50 629 628 1 strelka-varscan-mutect ADGRG1,missense_variant,p.Trp349Cys,ENST00000568909,NM_001290143.1;ADGRG1,missense_variant,p.Trp349Cys,ENST00000562631,NM_201525.3;ADGRG1,missense_variant,p.Trp349Cys,ENST00000388813,NM_001145772.2;ADGRG1,missense_variant,p.Trp354Cys,ENST00000456916,NM_001145773.2;ADGRG1,missense_variant,p.Trp349Cys,ENST00000562558,NM_201524.3;ADGRG1,missense_variant,p.Trp349Cys,ENST00000568908,NM_001145770.2;ADGRG1,missense_variant,p.Trp349Cys,ENST00000540164,NM_001290144.1,NM_001145774.2;ADGRG1,missense_variant,p.Trp349Cys,ENST00000567835,NM_001290142.1,NM_005682.6,NM_001145771.2;ADGRG1,intron_variant,,ENST00000565391,;ADGRG1,downstream_gene_variant,,ENST00000561988,;ADGRG1,downstream_gene_variant,,ENST00000566271,;ADGRG1,downstream_gene_variant,,ENST00000561833,;ADGRG1,downstream_gene_variant,,ENST00000566169,;ADGRG1,downstream_gene_variant,,ENST00000569101,;ADGRG1,downstream_gene_variant,,ENST00000562467,;ADGRG1,downstream_gene_variant,,ENST00000567154,;ADGRG1,downstream_gene_variant,,ENST00000568234,;ADGRG1,downstream_gene_variant,,ENST00000561969,;ADGRG1,downstream_gene_variant,,ENST00000567915,;ADGRG1,downstream_gene_variant,,ENST00000565314,;ADGRG1,downstream_gene_variant,,ENST00000563862,;ADGRG1,downstream_gene_variant,,ENST00000561696,;ADGRG1,downstream_gene_variant,,ENST00000566164,;ADGRG1,downstream_gene_variant,,ENST00000567702,;ADGRG1,downstream_gene_variant,,ENST00000563445,;ADGRG1,downstream_gene_variant,,ENST00000565770,;ADGRG1,downstream_gene_variant,,ENST00000568791,;ADGRG1,downstream_gene_variant,,ENST00000563414,;ADGRG1,downstream_gene_variant,,ENST00000569494,;ADGRG1,downstream_gene_variant,,ENST00000561782,;ADGRG1,downstream_gene_variant,,ENST00000566123,;ADGRG1,downstream_gene_variant,,ENST00000569154,;ADGRG1,downstream_gene_variant,,ENST00000564729,;ADGRG1,downstream_gene_variant,,ENST00000565976,;ADGRG1,downstream_gene_variant,,ENST00000567553,;ADGRG1,downstream_gene_variant,,ENST00000566508,;ADGRG1,downstream_gene_variant,,ENST00000563548,;ADGRG1,downstream_gene_variant,,ENST00000563374,;ADGRG1,downstream_gene_variant,,ENST00000565013,;ADGRG1,downstream_gene_variant,,ENST00000567397,;ADGRG1,downstream_gene_variant,,ENST00000565587,;ADGRG1,downstream_gene_variant,,ENST00000568074,;ADGRG1,downstream_gene_variant,,ENST00000569372,;ADGRG1,downstream_gene_variant,,ENST00000565338,;ADGRG1,downstream_gene_variant,,ENST00000568531,;ADGRG1,downstream_gene_variant,,ENST00000564103,;ADGRG1,downstream_gene_variant,,ENST00000566778,;ADGRG1,downstream_gene_variant,,ENST00000568618,;ADGRG1,downstream_gene_variant,,ENST00000570044,;ADGRG1,downstream_gene_variant,,ENST00000568979,;ADGRG1,downstream_gene_variant,,ENST00000564338,;ADGRG1,downstream_gene_variant,,ENST00000566187,;ADGRG1,downstream_gene_variant,,ENST00000568157,;ADGRG1,downstream_gene_variant,,ENST00000564722,;ADGRG1,downstream_gene_variant,,ENST00000564360,;ADGRG1,downstream_gene_variant,,ENST00000569158,;ADGRG1,downstream_gene_variant,,ENST00000562003,;ADGRG1,downstream_gene_variant,,ENST00000562414,;ADGRG1,downstream_gene_variant,,ENST00000562682,;ADGRG1,downstream_gene_variant,,ENST00000569531,;ADGRG1,downstream_gene_variant,,ENST00000564912,;ADGRG1,downstream_gene_variant,,ENST00000566888,;ADGRG1,downstream_gene_variant,,ENST00000569132,;ADGRG1,downstream_gene_variant,,ENST00000569992,;ADGRG1,downstream_gene_variant,,ENST00000568700,;ADGRG1,downstream_gene_variant,,ENST00000562673,;ADGRG1,downstream_gene_variant,,ENST00000562608,;ADGRG1,downstream_gene_variant,,ENST00000561872,;ADGRG1,downstream_gene_variant,,ENST00000562101,;ADGRG1,3_prime_UTR_variant,,ENST00000564907,;ADGRG1,3_prime_UTR_variant,,ENST00000565539,;ADGRG1,downstream_gene_variant,,ENST00000568645,;ADGRG1,downstream_gene_variant,,ENST00000563007,;ADGRG1,downstream_gene_variant,,ENST00000565505,; T ENST00000568909 Transcript missense_variant 1221/4254 1047/2082 349/693 W/C tgG/tgT 1 1 ADGRG1 HGNC HGNC:4512 protein_coding YES CCDS32460.1 ENSP00000455215 Q9Y653 A0A024R6U7 UPI0000047817 NM_001290143.1 deleterious(0) 8/14 PROSITE_profiles:PS50221,hmmpanther:PTHR12011:SF318,hmmpanther:PTHR12011,Pfam_domain:PF01825,SMART_domains:SM00303,Prints_domain:PR01422 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 57656255 57656255 G T 1 0 0 0 0 1 0 0 0 368 1241 43 2 2 ADGRG1 16 57656255 Missense_Mutation SNP G C3N-01842_T 6518738 57656255 32682090 317 26509 CDH8 0 . GRCh38 16 61820955 61820955 + Missense_Mutation SNP C C A rs574584035 C3N-01842_T C3N-01842_N C C c.994G>T p.Ala332Ser p.A332S ENST00000577390 6/12 119 84 35 113 113 0 strelka-varscan-mutect CDH8,missense_variant,p.Ala332Ser,ENST00000577390,NM_001796.4;CDH8,missense_variant,p.Ala332Ser,ENST00000577730,;CDH8,missense_variant,p.Ala332Ser,ENST00000584337,;CDH8,missense_variant,p.Ala332Ser,ENST00000299345,;CDH8,missense_variant,p.Ala332Ser,ENST00000583382,;CDH8,missense_variant,p.Ala332Ser,ENST00000585315,;CDH8,upstream_gene_variant,,ENST00000582242,; A ENST00000577390 Transcript missense_variant 1949/9721 994/2400 332/799 A/S Gcc/Tcc rs574584035,COSM4671009 1 -1 CDH8 HGNC HGNC:1767 protein_coding YES CCDS10802.1 ENSP00000462701 P55286 UPI0000126D9F NM_001796.4 tolerated(0.1) 6/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF273,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs574584035 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 61820955 61820955 C A 1 0 0 0 0 1 0 0 0 2819 739 26 2 2 CDH8 16 61820955 Missense_Mutation SNP C C3N-01842_T 4164700 61820955 28517390 318 26510 CDH5 0 . GRCh38 16 66400913 66400914 + Frame_Shift_Ins INS - - A novel C3N-01842_T C3N-01842_N - - c.1736dupA p.Asn579LysfsTer176 p.N579Kfs*176 ENST00000341529 11/12 705 542 163 928 928 0 sindel-varindel-pindel CDH5,frameshift_variant,p.Asn579LysfsTer176,ENST00000341529,NM_001795.3;CDH5,frameshift_variant,p.Asn464LysfsTer176,ENST00000614547,;CDH5,frameshift_variant,p.Asn18LysfsTer176,ENST00000539168,;CDH5,3_prime_UTR_variant,,ENST00000565334,; A ENST00000341529 Transcript frameshift_variant 1882-1883/4120 1734-1735/2355 578-579/784 -/X -/A 1 1 CDH5 HGNC HGNC:1764 protein_coding YES CCDS10804.1 ENSP00000344115 P33151 UPI000016B272 NM_001795.3 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF89,hmmpanther:PTHR24027,Gene3D:2.60.40.60,SMART_domains:SM00112 HIGH 1 insertion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 84 66400913 66400913 - A 1 0 1 1 0 0 0 0 0 2816 718 25 0 0 CDH5 16 66400913 Frame_Shift_Ins INS - C3N-01842_T 4579958 66400913 23937432 319 26511 PMFBP1 0 . GRCh38 16 72124817 72124817 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.2539C>A p.Gln847Lys p.Q847K ENST00000237353 17/21 154 125 29 221 220 1 strelka-varscan-mutect PMFBP1,missense_variant,p.Gln852Lys,ENST00000537465,;PMFBP1,missense_variant,p.Gln847Lys,ENST00000237353,NM_031293.2;PMFBP1,missense_variant,p.Gln702Lys,ENST00000355636,NM_001160213.1;PMFBP1,missense_variant,p.Gln13Lys,ENST00000537792,;PMFBP1,3_prime_UTR_variant,,ENST00000379073,;PMFBP1,downstream_gene_variant,,ENST00000537392,; T ENST00000237353 Transcript missense_variant 2801/3527 2539/3024 847/1007 Q/K Cag/Aag COSM1287267 1 -1 PMFBP1 HGNC HGNC:17728 protein_coding YES CCDS32483.1 ENSP00000237353 Q8TBY8 UPI0000141554 NM_031293.2 tolerated(0.51) 17/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18881,hmmpanther:PTHR18881:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 72124817 72124817 G T 1 0 0 0 0 1 0 0 0 12241 1357 47 2 2 PMFBP1 16 72124817 Missense_Mutation SNP G C3N-01842_T 5723904 72124817 18213528 320 26512 KIAA0513 0 . GRCh38 16 85081375 85081375 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.963G>T p.Lys321Asn p.K321N ENST00000566428 9/13 367 322 45 473 473 0 strelka-varscan-mutect KIAA0513,missense_variant,p.Lys321Asn,ENST00000566428,NM_001286565.1;KIAA0513,missense_variant,p.Lys321Asn,ENST00000258180,NM_014732.3;KIAA0513,missense_variant,p.Lys321Asn,ENST00000538274,NM_001286566.1;KIAA0513,missense_variant,p.Lys118Asn,ENST00000562580,;KIAA0513,intron_variant,,ENST00000562564,;KIAA0513,downstream_gene_variant,,ENST00000567328,NM_001297766.1; T ENST00000566428 Transcript missense_variant 1594/7772 963/1236 321/411 K/N aaG/aaT 1 1 KIAA0513 HGNC HGNC:29058 protein_coding YES CCDS32499.1 ENSP00000457408 O60268 UPI0000139A26 NM_001286565.1 deleterious(0.03) 9/13 hmmpanther:PTHR13663,hmmpanther:PTHR13663:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 85081375 85081375 G T 1 0 0 0 0 1 0 0 0 8087 962 34 2 2 KIAA0513 16 85081375 Missense_Mutation SNP G C3N-01842_T 12956558 85081375 5256970 321 26513 FANCA 0 . GRCh38 16 89811040 89811040 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.315G>T p.= p.L105L ENST00000389301 4/43 646 469 177 877 873 4 strelka-varscan-mutect FANCA,synonymous_variant,p.=,ENST00000389301,NM_000135.2;FANCA,synonymous_variant,p.=,ENST00000568369,NM_001286167.1;FANCA,synonymous_variant,p.=,ENST00000563673,;FANCA,synonymous_variant,p.=,ENST00000389302,NM_001018112.1;FANCA,synonymous_variant,p.=,ENST00000534992,;FANCA,synonymous_variant,p.=,ENST00000543736,;FANCA,missense_variant,p.Gly101Trp,ENST00000563513,;FANCA,synonymous_variant,p.=,ENST00000565582,;FANCA,3_prime_UTR_variant,,ENST00000567943,;FANCA,non_coding_transcript_exon_variant,,ENST00000566889,;FANCA,non_coding_transcript_exon_variant,,ENST00000567883,;FANCA,upstream_gene_variant,,ENST00000567621,; A ENST00000389301 Transcript synonymous_variant 346/5451 315/4368 105/1455 L ctG/ctT 1 -1 FANCA HGNC HGNC:3582 protein_coding YES CCDS32515.1 ENSP00000373952 O15360 UPI0000520A1A NM_000135.2 4/43 hmmpanther:PTHR12047,hmmpanther:PTHR12047:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 89811040 89811040 C A 1 0 0 0 0 0 0 0 1 5521 581 21 2 2 FANCA 16 89811040 Silent SNP C C3N-01842_T 4729665 89811040 527305 322 26514 TP53 0 . GRCh38 17 7676096 7676096 + Nonsense_Mutation SNP C C T C3N-01842_T C3N-01842_N C C c.273G>A p.Trp91Ter p.W91* ENST00000269305 4/11 177 126 51 296 296 0 strelka-varscan-mutect TP53,stop_gained,p.Trp91Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Trp91Ter,ENST00000420246,;TP53,stop_gained,p.Trp52Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Trp52Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Trp91Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Trp52Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Trp91Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Trp52Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Trp91Ter,ENST00000445888,;TP53,stop_gained,p.Trp52Ter,ENST00000619485,;TP53,stop_gained,p.Trp91Ter,ENST00000359597,;TP53,stop_gained,p.Trp91Ter,ENST00000615910,;TP53,stop_gained,p.Trp91Ter,ENST00000413465,;TP53,stop_gained,p.Trp91Ter,ENST00000508793,;TP53,stop_gained,p.Trp91Ter,ENST00000604348,;TP53,stop_gained,p.Trp91Ter,ENST00000503591,;TP53,intron_variant,,ENST00000509690,;TP53,intron_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000510385,NM_001126116.1;TP53,upstream_gene_variant,,ENST00000618944,NM_001276698.1;TP53,upstream_gene_variant,,ENST00000504290,NM_001126117.1;TP53,upstream_gene_variant,,ENST00000610623,NM_001276699.1;TP53,upstream_gene_variant,,ENST00000504937,NM_001126115.1;TP53,upstream_gene_variant,,ENST00000619186,NM_001276697.1;TP53,upstream_gene_variant,,ENST00000576024,;TP53,upstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Trp52Ter,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; T ENST00000269305 Transcript stop_gained 463/2579 273/1182 91/393 W/* tgG/tgA CM065495,TP53_g.11504G>T,TP53_g.11504G>A,COSM1646881,COSM3958856,COSM44492,COSM4950188,COSM4950189,COSM4950190,COSM4950191,COSM4950192,COSM562611,COSM562612 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 4/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6 0,0,0,1,1,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 1,0,0,1,1,1,1,1,1,1,1,1,1 1 PASS rs876660548 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 7676096 7676096 C T 1 0 0 0 0 0 1 0 0 16859 740 26 3 3 TP53 17 7676096 Nonsense_Mutation SNP C C3N-01842_T 7676096 75581345 323 26515 MFSD6L 0 . GRCh38 17 8797365 8797365 + Missense_Mutation SNP C C A rs146978905 C3N-01842_T C3N-01842_N C C c.1756G>T p.Asp586Tyr p.D586Y ENST00000329805 1/1 49 40 9 41 41 0 strelka-varscan-mutect MFSD6L,missense_variant,p.Asp586Tyr,ENST00000329805,NM_152599.3; A ENST00000329805 Transcript missense_variant 1985/2188 1756/1761 586/586 D/Y Gac/Tac rs146978905 1 -1 MFSD6L HGNC HGNC:26656 protein_coding YES CCDS11146.1 ENSP00000330051 Q8IWD5 UPI0000141B5F NM_152599.3 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR16172:SF22,hmmpanther:PTHR16172 MODERATE 1 SNV 1 PASS rs146978905 . 0 208 2 0 0 0 0 0 -19.99592 1 1 1 1 0 A 3 1 84 8797365 8797365 C A 1 0 0 0 0 1 0 0 0 9494 913 32 2 2 MFSD6L 17 8797365 Missense_Mutation SNP C C3N-01842_T 1121269 8797365 74460076 324 26516 MYH1 0 . GRCh38 17 10501194 10501194 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.3654G>A p.= p.K1218K ENST00000226207 27/40 274 204 70 407 406 1 strelka-varscan-mutect MYH1,synonymous_variant,p.=,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript synonymous_variant 3749/6024 3654/5820 1218/1939 K aaG/aaA 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 27/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,Low_complexity_(Seg):seg LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 10501194 10501194 C T 1 0 0 0 0 0 0 0 1 10029 796 28 3 3 MYH1 17 10501194 Silent SNP C C3N-01842_T 1703829 10501194 72756247 325 26517 MAPK7 0 . GRCh38 17 19380860 19380860 + Silent SNP C C T C3N-01842_T C3N-01842_N C C c.651C>T p.= p.F217F ENST00000308406 4/7 162 102 60 249 249 0 strelka-varscan-mutect MAPK7,synonymous_variant,p.=,ENST00000308406,NM_139033.2;MAPK7,synonymous_variant,p.=,ENST00000395604,NM_002749.3;MAPK7,synonymous_variant,p.=,ENST00000395602,NM_139034.2;MAPK7,synonymous_variant,p.=,ENST00000299612,NM_139032.2;MAPK7,synonymous_variant,p.=,ENST00000443215,;MAPK7,synonymous_variant,p.=,ENST00000482850,;MFAP4,downstream_gene_variant,,ENST00000395592,NM_001198695.1;MFAP4,downstream_gene_variant,,ENST00000497081,;MFAP4,downstream_gene_variant,,ENST00000299610,NM_002404.2;B9D1,upstream_gene_variant,,ENST00000477478,;B9D1,upstream_gene_variant,,ENST00000575403,NM_001243475.1;MAPK7,downstream_gene_variant,,ENST00000579284,;MAPK7,downstream_gene_variant,,ENST00000603493,;B9D1,upstream_gene_variant,,ENST00000487415,;MAPK7,intron_variant,,ENST00000571657,;MAPK7,intron_variant,,ENST00000573417,;MFAP4,downstream_gene_variant,,ENST00000574313,;MAPK7,downstream_gene_variant,,ENST00000572968,;B9D1,upstream_gene_variant,,ENST00000468679,;MAPK7,3_prime_UTR_variant,,ENST00000581260,;MAPK7,non_coding_transcript_exon_variant,,ENST00000570306,;MAPK7,non_coding_transcript_exon_variant,,ENST00000490660,;MAPK7,non_coding_transcript_exon_variant,,ENST00000572716,;MFAP4,downstream_gene_variant,,ENST00000571210,;B9D1,upstream_gene_variant,,ENST00000476298,;MAPK7,downstream_gene_variant,,ENST00000573466,;MAPK7,downstream_gene_variant,,ENST00000486905,;MAPK7,downstream_gene_variant,,ENST00000572853,; T ENST00000308406 Transcript synonymous_variant 1037/3149 651/2451 217/816 F ttC/ttT COSM5385837 1 1 MAPK7 HGNC HGNC:6880 protein_coding YES CCDS11206.1 ENSP00000311005 Q13164 A0A024QZ20 UPI000006FED0 NM_139033.2 4/7 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF230,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 19380860 19380860 C T 1 0 0 0 0 0 0 0 1 9206 825 29 3 3 MAPK7 17 19380860 Silent SNP C C3N-01842_T 8879666 19380860 63876581 326 26518 CDRT15L2 0 . GRCh38 17 20580452 20580452 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.569G>A p.Gly190Asp p.G190D ENST00000399044 2/2 290 264 26 193 193 0 varscan-mutect CDRT15L2,missense_variant,p.Gly190Asp,ENST00000399044,NM_001190790.1;RP11-434D2.12,upstream_gene_variant,,ENST00000580931,;ZSWIM5P2,downstream_gene_variant,,ENST00000420212,; A ENST00000399044 Transcript missense_variant 589/1048 569/846 190/281 G/D gGc/gAc 1 1 CDRT15L2 HGNC HGNC:34075 protein_coding YES CCDS54096.1 ENSP00000382000 A8MXV6 UPI00001D7A81 NM_001190790.1 deleterious_low_confidence(0.01) 2/2 hmmpanther:PTHR16471,hmmpanther:PTHR16471:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 20580452 20580452 G A 1 0 0 0 0 1 0 0 0 2881 1203 42 3 3 CDRT15L2 17 20580452 Missense_Mutation SNP G C3N-01842_T 1199592 20580452 62676989 327 26519 MSL1 0 . GRCh38 17 40122995 40122995 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.383G>T p.Arg128Leu p.R128L ENST00000398532 1/9 226 178 48 279 279 0 strelka-varscan-mutect MSL1,missense_variant,p.Arg128Leu,ENST00000398532,;MSL1,missense_variant,p.Arg128Leu,ENST00000578648,;MSL1,missense_variant,p.Arg128Leu,ENST00000577454,;MSL1,intron_variant,,ENST00000579565,NM_001012241.1;MSL1,upstream_gene_variant,,ENST00000582920,;MSL1,upstream_gene_variant,,ENST00000578826,;MSL1,upstream_gene_variant,,ENST00000582884,; T ENST00000398532 Transcript missense_variant 698/4707 383/1845 128/614 R/L cGg/cTg 1 1 MSL1 HGNC HGNC:27905 protein_coding ENSP00000381543 Q68DK7 UPI00001D79E6 deleterious_low_confidence(0) 1/9 hmmpanther:PTHR21656 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 40122995 40122995 G T 1 0 0 0 0 1 0 0 0 9860 1116 39 1 1 MSL1 17 40122995 Missense_Mutation SNP G C3N-01842_T 19542543 40122995 43134446 328 26520 HEXIM2 0 . GRCh38 17 45169444 45169444 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.496C>A p.His166Asn p.H166N ENST00000307275 4/4 320 253 67 334 334 0 strelka-varscan-mutect HEXIM2,missense_variant,p.His166Asn,ENST00000307275,NM_001303438.1,NM_001303439.1,NM_001303437.1,NM_144608.2;HEXIM2,missense_variant,p.His166Asn,ENST00000592695,NM_001303440.1,NM_001303441.1;HEXIM2,missense_variant,p.His166Asn,ENST00000591576,NM_001303442.1,NM_001303444.1,NM_001303443.1;HEXIM2,missense_variant,p.His188Asn,ENST00000585340,NM_001303436.1;HEXIM2,downstream_gene_variant,,ENST00000589230,;HEXIM2,downstream_gene_variant,,ENST00000586681,;HEXIM2,downstream_gene_variant,,ENST00000593138,;HEXIM2,downstream_gene_variant,,ENST00000591070,;RP13-890H12.2,non_coding_transcript_exon_variant,,ENST00000589796,;RP13-890H12.2,downstream_gene_variant,,ENST00000589451,; A ENST00000307275 Transcript missense_variant 932/1528 496/861 166/286 H/N Cac/Aac 1 1 HEXIM2 HGNC HGNC:28591 protein_coding YES CCDS11496.1 ENSP00000302276 Q96MH2 UPI00000730EA NM_001303438.1,NM_001303439.1,NM_001303437.1,NM_144608.2 tolerated(0.18) 4/4 Pfam_domain:PF15313,hmmpanther:PTHR13469,hmmpanther:PTHR13469:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 45169444 45169444 C A 1 0 0 0 0 1 0 0 0 6961 594 21 2 2 HEXIM2 17 45169444 Missense_Mutation SNP C C3N-01842_T 5046449 45169444 38087997 329 26521 NSF 0 . GRCh38 17 46728916 46728916 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1890G>T p.= p.L630L ENST00000398238 17/21 291 233 58 213 213 0 strelka-varscan-mutect NSF,synonymous_variant,p.=,ENST00000398238,NM_006178.3;NSF,synonymous_variant,p.=,ENST00000575068,;NSF,synonymous_variant,p.=,ENST00000576346,;NSF,synonymous_variant,p.=,ENST00000465370,; T ENST00000398238 Transcript synonymous_variant 1997/3983 1890/2235 630/744 L ctG/ctT 1 1 NSF HGNC HGNC:8016 protein_coding YES CCDS42354.1 ENSP00000381293 P46459 UPI000006D238 NM_006178.3 17/21 Low_complexity_(Seg):seg,hmmpanther:PTHR23078,hmmpanther:PTHR23078:SF4,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 46728916 46728916 G T 1 0 0 0 0 0 0 0 1 10730 1277 45 2 2 NSF 17 46728916 Silent SNP G C3N-01842_T 1559472 46728916 36528525 330 26522 HOXB3 0 . GRCh38 17 48551118 48551118 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.512G>T p.Gly171Val p.G171V ENST00000470495 2/2 57 44 13 76 76 0 strelka-varscan-mutect HOXB3,missense_variant,p.Gly171Val,ENST00000470495,;HOXB3,missense_variant,p.Gly171Val,ENST00000311626,NM_002146.4;HOXB3,missense_variant,p.Gly171Val,ENST00000498678,;HOXB3,missense_variant,p.Gly98Val,ENST00000472863,;HOXB3,missense_variant,p.Gly98Val,ENST00000489475,;HOXB3,missense_variant,p.Gly39Val,ENST00000460160,;HOXB3,missense_variant,p.Gly171Val,ENST00000476342,;HOXB3,missense_variant,p.Gly37Val,ENST00000490677,;HOXB3,downstream_gene_variant,,ENST00000465120,;HOXB3,downstream_gene_variant,,ENST00000471459,;HOXB-AS1,non_coding_transcript_exon_variant,,ENST00000435312,;HOXB-AS1,non_coding_transcript_exon_variant,,ENST00000502764,;HOXB-AS3,intron_variant,,ENST00000465846,;HOXB-AS1,downstream_gene_variant,,ENST00000508688,;HOXB3,downstream_gene_variant,,ENST00000478644,; A ENST00000470495 Transcript missense_variant 1960/4208 512/1296 171/431 G/V gGt/gTt 1 -1 HOXB3 HGNC HGNC:5114 protein_coding YES CCDS11528.1 ENSP00000417207 P14651 UPI00001AEFBF tolerated(0.33) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24326:SF10,hmmpanther:PTHR24326,Gene3D:1.10.10.60 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 48551118 48551118 C A 1 0 0 0 0 1 0 0 0 7196 507 18 2 2 HOXB3 17 48551118 Missense_Mutation SNP C C3N-01842_T 1822202 48551118 34706323 331 26523 MYCBPAP 0 . GRCh38 17 50508565 50508565 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.20G>T p.Gly7Val p.G7V ENST00000323776 1/19 280 221 59 310 309 1 strelka-varscan-mutect MYCBPAP,missense_variant,p.Gly7Val,ENST00000323776,NM_032133.4;MYCBPAP,missense_variant,p.Gly7Val,ENST00000419930,;MYCBPAP,missense_variant,p.Gly7Val,ENST00000452039,;MYCBPAP,5_prime_UTR_variant,,ENST00000436259,;RP11-94C24.6,upstream_gene_variant,,ENST00000502300,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000576179,;MYCBPAP,non_coding_transcript_exon_variant,,ENST00000470609,;MYCBPAP,upstream_gene_variant,,ENST00000437498,;MYCBPAP,upstream_gene_variant,,ENST00000458692,; T ENST00000323776 Transcript missense_variant 182/3186 20/2955 7/984 G/V gGc/gTc 1 1 MYCBPAP HGNC HGNC:19677 protein_coding YES CCDS32680.2 ENSP00000323184 Q8TBZ2 A0A140VK87 UPI0000E5A00B NM_032133.4 tolerated_low_confidence(0.14) 1/19 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 50508565 50508565 G T 1 0 0 0 0 1 0 0 0 10019 1203 42 2 2 MYCBPAP 17 50508565 Missense_Mutation SNP G C3N-01842_T 1957447 50508565 32748876 332 26524 WFIKKN2 0 . GRCh38 17 50839554 50839554 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.266T>A p.Val89Glu p.V89E ENST00000311378 2/2 193 143 50 210 210 0 strelka-varscan-mutect WFIKKN2,missense_variant,p.Val89Glu,ENST00000311378,NM_175575.5;WFIKKN2,5_prime_UTR_variant,,ENST00000426127,;RP11-506D12.5,downstream_gene_variant,,ENST00000572491,; A ENST00000311378 Transcript missense_variant 794/3588 266/1731 89/576 V/E gTg/gAg 1 1 WFIKKN2 HGNC HGNC:30916 protein_coding YES CCDS11575.1 ENSP00000311184 Q8TEU8 UPI000004139B NM_175575.5 deleterious(0) 2/2 PROSITE_profiles:PS51390,hmmpanther:PTHR10083:SF87,hmmpanther:PTHR10083,Gene3D:4.10.75.10,Pfam_domain:PF00095,SMART_domains:SM00217 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 50839554 50839554 T A 1 0 0 0 0 1 0 0 0 17916 1696 59 4 4 WFIKKN2 17 50839554 Missense_Mutation SNP T C3N-01842_T 330989 50839554 32417887 333 26525 TSPOAP1 0 . GRCh38 17 58324932 58324932 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.821G>A p.Arg274Gln p.R274Q ENST00000343736 5/32 104 86 18 136 136 0 strelka-varscan-mutect TSPOAP1,missense_variant,p.Arg214Gln,ENST00000268893,NM_024418.2;TSPOAP1,missense_variant,p.Arg274Gln,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1-AS1,upstream_gene_variant,,ENST00000579527,;TSPOAP1-AS1,upstream_gene_variant,,ENST00000580515,;TSPOAP1-AS1,upstream_gene_variant,,ENST00000578334,;TSPOAP1-AS1,upstream_gene_variant,,ENST00000580633,;TSPOAP1,upstream_gene_variant,,ENST00000583624,; T ENST00000343736 Transcript missense_variant 985/5947 821/5574 274/1857 R/Q cGg/cAg 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 deleterious(0) 5/32 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 58324932 58324932 C T 1 0 0 0 0 1 0 0 0 17163 652 23 1 1 TSPOAP1 17 58324932 Missense_Mutation SNP C C3N-01842_T 7485378 58324932 24932509 334 26526 HEATR6 0 . GRCh38 17 60078838 60078838 + Missense_Mutation SNP C C T rs201049194 C3N-01842_T C3N-01842_N C C c.77G>A p.Arg26Gln p.R26Q ENST00000184956 1/20 279 210 69 329 327 2 strelka-varscan-mutect HEATR6,missense_variant,p.Arg26Gln,ENST00000184956,NM_022070.4;HEATR6,missense_variant,p.Arg26Gln,ENST00000585976,;HEATR6,missense_variant,p.Arg26Gln,ENST00000593097,;HEATR6,missense_variant,p.Arg26Gln,ENST00000593228,;HEATR6,5_prime_UTR_variant,,ENST00000613428,;CTD-2319I12.2,upstream_gene_variant,,ENST00000589740,;WFDC21P,downstream_gene_variant,,ENST00000590346,;WFDC21P,downstream_gene_variant,,ENST00000588180,;WFDC21P,downstream_gene_variant,,ENST00000587298,;WFDC21P,downstream_gene_variant,,ENST00000590012,;WFDC21P,downstream_gene_variant,,ENST00000589987,;WFDC21P,downstream_gene_variant,,ENST00000592556,;WFDC21P,downstream_gene_variant,,ENST00000566140,;HEATR6,non_coding_transcript_exon_variant,,ENST00000585712,;HEATR6,missense_variant,p.Arg26Gln,ENST00000587003,;HEATR6,missense_variant,p.Arg26Gln,ENST00000592664,;HEATR6,non_coding_transcript_exon_variant,,ENST00000591074,;HEATR6,upstream_gene_variant,,ENST00000590587,;WFDC21P,downstream_gene_variant,,ENST00000589777,; T ENST00000184956 Transcript missense_variant 94/3932 77/3546 26/1181 R/Q cGa/cAa rs201049194 1 -1 HEATR6 HGNC HGNC:24076 protein_coding YES CCDS11623.1 ENSP00000184956 Q6AI08 UPI0000366C37 NM_022070.4 tolerated_low_confidence(0.76) 1/20 hmmpanther:PTHR13366 MODERATE 1 SNV 1 1 PASS rs201049194 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 60078838 60078838 C T 1 0 0 0 0 1 0 0 0 6915 884 31 1 1 HEATR6 17 60078838 Missense_Mutation SNP C C3N-01842_T 1753906 60078838 23178603 335 26527 PPM1D 0 . GRCh38 17 60600463 60600463 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.49G>T p.Gly17Trp p.G17W ENST00000305921 1/6 375 292 83 533 533 0 strelka-varscan-mutect PPM1D,missense_variant,p.Gly17Trp,ENST00000305921,NM_003620.3;PPM1D,missense_variant,p.Gly17Trp,ENST00000629650,;PPM1D,upstream_gene_variant,,ENST00000590418,;PPM1D,missense_variant,p.Gly17Trp,ENST00000392995,; T ENST00000305921 Transcript missense_variant 281/4778 49/1818 17/605 G/W Ggg/Tgg 1 1 PPM1D HGNC HGNC:9277 protein_coding YES CCDS11625.1 ENSP00000306682 O15297 A0A0S2Z4M2 UPI0000130FE8 NM_003620.3 deleterious(0) 1/6 Gene3D:3.60.40.10,PROSITE_profiles:PS51746,hmmpanther:PTHR13832,hmmpanther:PTHR13832:SF359,SMART_domains:SM00332,Superfamily_domains:SSF81606 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 60600463 60600463 G T 1 0 0 0 0 1 0 0 0 12447 1116 39 1 1 PPM1D 17 60600463 Missense_Mutation SNP G C3N-01842_T 521625 60600463 22656978 336 26528 GH2 0 . GRCh38 17 63880778 63880778 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.450G>T p.= p.L150L ENST00000332800 4/4 344 282 62 428 428 0 strelka-varscan-mutect GH2,splice_region_variant,p.=,ENST00000456543,NM_022558.3;GH2,synonymous_variant,p.=,ENST00000332800,NM_022557.3;GH2,synonymous_variant,p.=,ENST00000423893,NM_002059.4;GH2,synonymous_variant,p.=,ENST00000449787,NM_022556.3;GH2,synonymous_variant,p.=,ENST00000622506,;CSH2,intron_variant,,ENST00000620751,; A ENST00000332800 Transcript synonymous_variant 584/1138 450/771 150/256 L ctG/ctT 1 -1 GH2 HGNC HGNC:4262 protein_coding YES CCDS11648.1 ENSP00000333157 P01242 UPI000002B3EF NM_022557.3 4/4 hmmpanther:PTHR11417:SF40,hmmpanther:PTHR11417,Gene3D:1.20.1250.10,Pfam_domain:PF00103,Superfamily_domains:SSF47266 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 63880778 63880778 C A 1 0 0 0 0 0 0 0 1 6246 840 29 2 2 GH2 17 63880778 Silent SNP C C3N-01842_T 3280315 63880778 19376663 337 26529 LRRC37A3 0 . GRCh38 17 64859937 64859937 + Missense_Mutation SNP C C G rs143533650 C3N-01842_T C3N-01842_N C C c.4209G>C p.Met1403Ile p.M1403I ENST00000584306 11/14 721 575 146 647 647 0 strelka-varscan-mutect LRRC37A3,missense_variant,p.Met1403Ile,ENST00000584306,NM_199340.3;LRRC37A3,missense_variant,p.Met1403Ile,ENST00000319651,;LRRC37A3,missense_variant,p.Met441Ile,ENST00000400877,;LRRC37A3,missense_variant,p.Met380Ile,ENST00000334962,;LRRC37A3,missense_variant,p.Met521Ile,ENST00000339474,NM_001303255.1;LRRC37A3,downstream_gene_variant,,ENST00000581368,;LRRC37A3,downstream_gene_variant,,ENST00000584788,;LRRC37A3,upstream_gene_variant,,ENST00000583510,;LRRC37A3,downstream_gene_variant,,ENST00000579305,; G ENST00000584306 Transcript missense_variant 4740/5665 4209/4905 1403/1634 M/I atG/atC rs143533650 1 -1 LRRC37A3 HGNC HGNC:32427 protein_coding YES CCDS32708.1 ENSP00000464535 O60309 UPI00005B2F0A NM_199340.3 tolerated(0.23) 11/14 hmmpanther:PTHR23045,hmmpanther:PTHR23045:SF7 MODERATE 1 SNV 1 1 PASS rs143533650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 64859937 64859937 C G 1 0 0 0 0 1 0 0 0 8887 594 21 4 4 LRRC37A3 17 64859937 Missense_Mutation SNP C C3N-01842_T 979159 64859937 18397504 338 26530 ABCA8 0 . GRCh38 17 68922279 68922279 + Frame_Shift_Del DEL T T - novel C3N-01842_T C3N-01842_N T T c.1464delA p.Glu488AspfsTer9 p.E488Dfs*9 ENST00000586539 12/40 118 93 25 91 91 0 sindel-varindel-pindel ABCA8,frameshift_variant,p.Glu488AspfsTer9,ENST00000430352,NM_001288986.1;ABCA8,frameshift_variant,p.Glu488AspfsTer9,ENST00000269080,NM_007168.3;ABCA8,frameshift_variant,p.Glu488AspfsTer9,ENST00000586539,NM_001288985.1;ABCA8,frameshift_variant,p.Glu119AspfsTer9,ENST00000615593,;ABCA8,frameshift_variant,p.Glu136AspfsTer9,ENST00000589533,;ABCA8,non_coding_transcript_exon_variant,,ENST00000541225,;ABCA8,upstream_gene_variant,,ENST00000587206,; - ENST00000586539 Transcript frameshift_variant 1653/5088 1464/4866 488/1621 E/X gaA/ga 1 -1 ABCA8 HGNC HGNC:38 protein_coding YES CCDS74139.1 ENSP00000467271 O94911 UPI0002065B1E NM_001288985.1 12/40 Gene3D:3.40.50.300,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF148,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 68922279 68922279 T - 1 0 1 0 1 0 0 0 0 42 1490 52 0 0 ABCA8 17 68922279 Frame_Shift_Del DEL T C3N-01842_T 4062342 68922279 14335162 339 26531 FBF1 0 . GRCh38 17 75925356 75925356 + Missense_Mutation SNP T T G rs369975590 C3N-01842_T C3N-01842_N T T c.917A>C p.Gln306Pro p.Q306P ENST00000627351 11/28 128 103 25 134 133 1 strelka-varscan-mutect FBF1,missense_variant,p.Gln306Pro,ENST00000586717,NM_001319193.1;FBF1,missense_variant,p.Gln265Pro,ENST00000319129,;FBF1,missense_variant,p.Gln320Pro,ENST00000636174,;FBF1,missense_variant,p.Gln319Pro,ENST00000592193,;FBF1,missense_variant,p.Gln306Pro,ENST00000627351,NM_001080542.1;FBF1,non_coding_transcript_exon_variant,,ENST00000585990,;RP11-552F3.12,non_coding_transcript_exon_variant,,ENST00000593156,;FBF1,upstream_gene_variant,,ENST00000586838,; G ENST00000627351 Transcript missense_variant 917/3402 917/3402 306/1133 Q/P cAg/cCg rs369975590 1 -1 FBF1 HGNC HGNC:24674 protein_coding YES CCDS45779.1 ENSP00000486708 Q8TES7 UPI0000DD841F NM_001080542.1 deleterious(0.04) 11/28 hmmpanther:PTHR33689,hmmpanther:PTHR33689:SF1 MODERATE 1 SNV 5 1 PASS rs369975590 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 75925356 75925356 T G 1 0 0 0 0 1 0 0 0 5557 1580 55 5 5 FBF1 17 75925356 Missense_Mutation SNP T C3N-01842_T 7003077 75925356 7332085 340 26532 RBFOX3 0 . GRCh38 17 79103187 79103187 + Missense_Mutation SNP G G A C3N-01842_T C3N-01842_N G G c.482C>T p.Thr161Met p.T161M ENST00000580155 8/15 290 227 63 353 351 2 strelka-varscan-mutect RBFOX3,missense_variant,p.Thr160Met,ENST00000583458,;RBFOX3,missense_variant,p.Thr161Met,ENST00000584778,;RBFOX3,missense_variant,p.Thr161Met,ENST00000580155,NM_001082575.2;RBFOX3,intron_variant,,ENST00000582043,;RBFOX3,upstream_gene_variant,,ENST00000578998,;RBFOX3,upstream_gene_variant,,ENST00000581393,; A ENST00000580155 Transcript missense_variant 995/1519 482/939 161/312 T/M aCg/aTg COSM4964845 1 -1 RBFOX3 HGNC HGNC:27097 protein_coding YES CCDS45805.1 ENSP00000463653 A6NFN3 UPI000020041C NM_001082575.2 deleterious(0.02) 8/15 PROSITE_profiles:PS50102,hmmpanther:PTHR15597,Gene3D:3.30.70.330,Pfam_domain:PF00076,PIRSF_domain:PIRSF037932,SMART_domains:SM00360,Superfamily_domains:SSF54928 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 79103187 79103187 G A 1 0 0 0 0 1 0 0 0 13273 1145 40 1 1 RBFOX3 17 79103187 Missense_Mutation SNP G C3N-01842_T 3177831 79103187 4154254 341 26533 BAHCC1 0 . GRCh38 17 81399801 81399801 + Missense_Mutation SNP A A T rs571740633 C3N-01842_T C3N-01842_N A A c.62A>T p.His21Leu p.H21L ENST00000584436 2/29 82 67 15 117 117 0 strelka-varscan-mutect BAHCC1,missense_variant,p.His21Leu,ENST00000584436,NM_001291324.1;BAHCC1,missense_variant,p.His21Leu,ENST00000307745,;MIR4740,downstream_gene_variant,,ENST00000584184,;BAHCC1,non_coding_transcript_exon_variant,,ENST00000583828,;BAHCC1,upstream_gene_variant,,ENST00000625166,;RP11-1055B8.1,upstream_gene_variant,,ENST00000624417,; T ENST00000584436 Transcript missense_variant 429/10801 62/7920 21/2639 H/L cAc/cTc rs571740633 1 1 BAHCC1 HGNC HGNC:29279 protein_coding YES CCDS74173.1 ENSP00000462154 A0A075B747 UPI0003EAE637 NM_001291324.1 deleterious(0) 2/29 MODERATE 1 SNV 5 1 PASS rs571740633 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 81399801 81399801 A T 1 0 0 0 0 1 0 0 0 1451 159 6 4 4 BAHCC1 17 81399801 Missense_Mutation SNP A C3N-01842_T 2296614 81399801 1857640 342 26534 NOTUM 0 . GRCh38 17 81960728 81960728 + Frame_Shift_Del DEL C C - rs773783101 C3N-01842_T C3N-01842_N C C c.182delG p.Gly61ValfsTer39 p.G61Vfs*39 ENST00000409678 1/11 140 110 30 199 198 1 sindel-varindel-pindel NOTUM,frameshift_variant,p.Gly61ValfsTer39,ENST00000409678,NM_178493.5;NOTUM,frameshift_variant,p.Gly61ValfsTer39,ENST00000425009,;NOTUM,upstream_gene_variant,,ENST00000477214,;RP11-498C9.17,downstream_gene_variant,,ENST00000580125,;NOTUM,non_coding_transcript_exon_variant,,ENST00000489218,; - ENST00000409678 Transcript frameshift_variant 566/2329 182/1491 61/496 G/X gGt/gt rs773783101 1 -1 NOTUM HGNC HGNC:27106 protein_coding YES CCDS32771.2 ENSP00000387310 Q6P988 UPI000004EE80 NM_178493.5 1/11 hmmpanther:PTHR21562,hmmpanther:PTHR21562:SF7 HIGH 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 81960728 81960728 C - 1 0 1 0 1 0 0 0 0 10598 507 18 0 0 NOTUM 17 81960728 Frame_Shift_Del DEL C C3N-01842_T 560927 81960728 1296713 343 26535 EPB41L3 0 . GRCh38 18 5395679 5395679 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.3002G>T p.Gly1001Val p.G1001V ENST00000341928 20/23 276 241 35 241 241 0 strelka-varscan-mutect EPB41L3,missense_variant,p.Gly1001Val,ENST00000341928,NM_012307.3;EPB41L3,missense_variant,p.Gly832Val,ENST00000342933,;EPB41L3,missense_variant,p.Gly960Val,ENST00000400111,;EPB41L3,missense_variant,p.Gly832Val,ENST00000544123,NM_001281533.1;EPB41L3,missense_variant,p.Gly779Val,ENST00000540638,NM_001281534.1;EPB41L3,missense_variant,p.Gly670Val,ENST00000545076,NM_001281535.1;EPB41L3,missense_variant,p.Gly54Val,ENST00000579951,;EPB41L3,downstream_gene_variant,,ENST00000578524,;EPB41L3,downstream_gene_variant,,ENST00000579271,;EPB41L3,downstream_gene_variant,,ENST00000581387,;EPB41L3,downstream_gene_variant,,ENST00000580647,;EPB41L3,downstream_gene_variant,,ENST00000580316,;EPB41L3,downstream_gene_variant,,ENST00000581292,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000542652,;EPB41L3,3_prime_UTR_variant,,ENST00000637651,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000578618,;EPB41L3,downstream_gene_variant,,ENST00000584055,; A ENST00000341928 Transcript missense_variant 3343/4706 3002/3264 1001/1087 G/V gGc/gTc 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 deleterious(0.04) 20/23 hmmpanther:PTHR23280:SF20,hmmpanther:PTHR23280,Pfam_domain:PF05902 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 2 -5.087721 0 0 1 0 0 A 3 1 84 5395679 5395679 C A 1 0 0 0 0 1 0 0 0 5001 739 26 2 2 EPB41L3 18 5395679 Missense_Mutation SNP C C3N-01842_T 5395679 74977606 344 26536 EPB41L3 0 . GRCh38 18 5415840 5415840 + Missense_Mutation SNP G G T rs758517478 C3N-01842_T C3N-01842_N G G c.2045C>A p.Pro682Gln p.P682Q ENST00000341928 13/23 191 165 26 185 185 0 strelka-varscan-mutect EPB41L3,missense_variant,p.Pro682Gln,ENST00000341928,NM_012307.3;EPB41L3,intron_variant,,ENST00000342933,;EPB41L3,intron_variant,,ENST00000400111,;EPB41L3,intron_variant,,ENST00000544123,NM_001281533.1;EPB41L3,intron_variant,,ENST00000540638,NM_001281534.1;EPB41L3,intron_variant,,ENST00000545076,NM_001281535.1;EPB41L3,intron_variant,,ENST00000578524,;EPB41L3,intron_variant,,ENST00000579271,;EPB41L3,intron_variant,,ENST00000581387,;EPB41L3,intron_variant,,ENST00000580647,;EPB41L3,intron_variant,,ENST00000580316,;EPB41L3,intron_variant,,ENST00000581292,;EPB41L3,downstream_gene_variant,,ENST00000584670,;EPB41L3,non_coding_transcript_exon_variant,,ENST00000582729,;EPB41L3,intron_variant,,ENST00000542652,;EPB41L3,intron_variant,,ENST00000578395,;EPB41L3,intron_variant,,ENST00000637651,;EPB41L3,intron_variant,,ENST00000578196,; T ENST00000341928 Transcript missense_variant 2386/4706 2045/3264 682/1087 P/Q cCg/cAg rs758517478 1 -1 EPB41L3 HGNC HGNC:3380 protein_coding YES CCDS11838.1 ENSP00000343158 Q9Y2J2 UPI0000129AFA NM_012307.3 tolerated(0.14) 13/23 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF20 MODERATE 1 SNV 1 1 PASS rs758517478 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 5415840 5415840 G T 1 0 0 0 0 1 0 0 0 5001 1116 39 1 1 EPB41L3 18 5415840 Missense_Mutation SNP G C3N-01842_T 20161 5415840 74957445 345 26537 MTCL1 0 . GRCh38 18 8824896 8824896 + Missense_Mutation SNP C C A rs115963216 C3N-01842_T C3N-01842_N C C c.3386C>A p.Pro1129Gln p.P1129Q ENST00000359865 15/17 296 183 113 287 287 0 strelka-varscan-mutect MTCL1,missense_variant,p.Pro1129Gln,ENST00000359865,NM_015210.3;MTCL1,missense_variant,p.Pro1129Gln,ENST00000400050,;MTCL1,missense_variant,p.Pro1088Gln,ENST00000517570,;MTCL1,missense_variant,p.Pro1448Gln,ENST00000306329,;MTCL1,missense_variant,p.Pro454Gln,ENST00000518815,; A ENST00000359865 Transcript missense_variant 3528/6093 3386/4761 1129/1586 P/Q cCg/cAg rs115963216,COSM4277089,COSM438416 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 tolerated(0.05) 15/17 hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs115963216 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 8824896 8824896 C A 1 0 0 0 0 1 0 0 0 9900 652 23 1 1 MTCL1 18 8824896 Missense_Mutation SNP C C3N-01842_T 3409056 8824896 71548389 346 26538 CEP192 0 . GRCh38 18 13100401 13100401 + Nonsense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.6760G>T p.Glu2254Ter p.E2254* ENST00000506447 38/45 432 337 95 368 367 1 strelka-varscan-mutect CEP192,stop_gained,p.Glu2254Ter,ENST00000506447,NM_032142.3;CEP192,stop_gained,p.Glu1779Ter,ENST00000325971,;CEP192,stop_gained,p.Glu1793Ter,ENST00000511820,;CEP192,3_prime_UTR_variant,,ENST00000430049,;CEP192,non_coding_transcript_exon_variant,,ENST00000540847,;CEP192,upstream_gene_variant,,ENST00000508539,;CEP192,stop_gained,p.Glu1854Ter,ENST00000510237,;CEP192,stop_gained,p.Glu802Ter,ENST00000589993,;CEP192,3_prime_UTR_variant,,ENST00000513432,;CEP192,downstream_gene_variant,,ENST00000508150,; T ENST00000506447 Transcript stop_gained 6840/7960 6760/7614 2254/2537 E/* Gag/Tag 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 38/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 13100401 13100401 G T 1 0 0 0 0 0 1 0 0 2967 1291 45 2 2 CEP192 18 13100401 Nonsense_Mutation SNP G C3N-01842_T 4275505 13100401 67272884 347 26539 DSG1 0 . GRCh38 18 31333634 31333634 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.730G>T p.Gly244Cys p.G244C ENST00000257192 7/15 568 433 135 671 670 1 strelka-varscan-mutect DSG1,missense_variant,p.Gly244Cys,ENST00000257192,NM_001942.3; T ENST00000257192 Transcript missense_variant 942/5045 730/3150 244/1049 G/C Ggc/Tgc COSM272618 1 1 DSG1 HGNC HGNC:3048 protein_coding YES CCDS11896.1 ENSP00000257192 Q02413 UPI000013CF4C NM_001942.3 deleterious(0) 7/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF9,SMART_domains:SM00112,Superfamily_domains:SSF49313 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 31333634 31333634 G T 1 0 0 0 0 1 0 0 0 4597 1348 47 2 2 DSG1 18 31333634 Missense_Mutation SNP G C3N-01842_T 18233233 31333634 49039651 348 26540 FHOD3 0 . GRCh38 18 36709283 36709283 + Missense_Mutation SNP G G A C3N-01842_T C3N-01842_N G G c.2425G>A p.Glu809Lys p.E809K ENST00000590592 18/29 369 281 88 457 456 1 strelka-varscan-mutect FHOD3,missense_variant,p.Glu634Lys,ENST00000257209,NM_025135.3;FHOD3,missense_variant,p.Glu809Lys,ENST00000590592,NM_001281740.1;FHOD3,missense_variant,p.Glu617Lys,ENST00000359247,NM_001281739.1;FHOD3,missense_variant,p.Glu395Lys,ENST00000592930,;FHOD3,intron_variant,,ENST00000591635,;FHOD3,non_coding_transcript_exon_variant,,ENST00000589114,;FHOD3,non_coding_transcript_exon_variant,,ENST00000587493,; A ENST00000590592 Transcript missense_variant 2425/4869 2425/4869 809/1622 E/K Gag/Aag COSM4440506 1 1 FHOD3 HGNC HGNC:26178 protein_coding YES CCDS62418.1 ENSP00000466937 Q2V2M9 UPI0002840E0A NM_001281740.1 deleterious_low_confidence(0) 18/29 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF213 1 MODERATE 1 SNV 1 1 1 PASS rs1044726015 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 36709283 36709283 G A 1 0 0 0 0 1 0 0 0 5748 1059 37 1 1 FHOD3 18 36709283 Missense_Mutation SNP G C3N-01842_T 5375649 36709283 43664002 349 26541 NARS 0 . GRCh38 18 57609356 57609356 + Splice_Site SNP C C A novel C3N-01842_T C3N-01842_N C C c.579+1G>T p.X193_splice ENST00000256854 197 159 38 177 177 0 strelka-varscan-mutect NARS,splice_donor_variant,,ENST00000256854,NM_004539.3;NARS,splice_donor_variant,,ENST00000587675,;NARS,splice_donor_variant,,ENST00000591599,;NARS,splice_donor_variant,,ENST00000588661,;NARS,downstream_gene_variant,,ENST00000587194,;NARS,splice_donor_variant,,ENST00000411676,;NARS,splice_donor_variant,,ENST00000540592,;NARS,intron_variant,,ENST00000586807,;NARS,upstream_gene_variant,,ENST00000589314,;NARS,upstream_gene_variant,,ENST00000589001,;NARS,downstream_gene_variant,,ENST00000587366,;NARS,downstream_gene_variant,,ENST00000590123,; A ENST00000256854 Transcript splice_donor_variant -/3099 579/1647 193/548 1 -1 NARS HGNC HGNC:7643 protein_coding YES CCDS32837.1 ENSP00000256854 O43776 UPI00001365E8 NM_004539.3 7/13 HIGH 1 SNV 1 1 PASS rs941650822 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 84 57609356 57609356 C A 1 0 0 0 0 0 0 1 0 10179 521 18 2 2 NARS 18 57609356 Splice_Site SNP C C3N-01842_T 20900073 57609356 22763929 350 26542 CTDP1 0 . GRCh38 18 79728978 79728978 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.2489G>T p.Gly830Val p.G830V ENST00000613122 11/13 519 434 85 648 648 0 strelka-varscan-mutect CTDP1,missense_variant,p.Gly830Val,ENST00000613122,NM_004715.4;CTDP1,missense_variant,p.Gly711Val,ENST00000299543,NM_001202504.1;CTDP1,missense_variant,p.Gly762Val,ENST00000591598,;CTDP1,intron_variant,,ENST00000075430,NM_048368.3; T ENST00000613122 Transcript missense_variant 2636/5866 2489/2886 830/961 G/V gGc/gTc 1 1 CTDP1 HGNC HGNC:2498 protein_coding YES CCDS12017.1 ENSP00000484525 Q9Y5B0 UPI000013C57B NM_004715.4 deleterious(0) 11/13 Pfam_domain:PF09309,hmmpanther:PTHR23081,hmmpanther:PTHR23081:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 79728978 79728978 G T 1 0 0 0 0 1 0 0 0 3810 1203 42 2 2 CTDP1 18 79728978 Missense_Mutation SNP G C3N-01842_T 22119622 79728978 644307 351 26543 BSG 0 . GRCh38 19 579579 579579 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.495G>A p.= p.E165E ENST00000333511 3/9 181 130 51 250 250 0 strelka-varscan-mutect BSG,splice_region_variant,p.=,ENST00000614867,;BSG,synonymous_variant,p.=,ENST00000333511,NM_001728.3;BSG,synonymous_variant,p.=,ENST00000353555,NM_001322243.1,NM_198589.2;BSG,synonymous_variant,p.=,ENST00000613627,;BSG,synonymous_variant,p.=,ENST00000573216,;BSG,5_prime_UTR_variant,,ENST00000545507,NM_198590.2;BSG,5_prime_UTR_variant,,ENST00000573784,;BSG,5_prime_UTR_variant,,ENST00000576984,;BSG,intron_variant,,ENST00000346916,NM_198591.2;BSG,intron_variant,,ENST00000618006,;BSG,non_coding_transcript_exon_variant,,ENST00000574970,;BSG,non_coding_transcript_exon_variant,,ENST00000571735,;BSG,non_coding_transcript_exon_variant,,ENST00000576925,;BSG,non_coding_transcript_exon_variant,,ENST00000572899,;BSG,upstream_gene_variant,,ENST00000618112,;BSG,downstream_gene_variant,,ENST00000590218,; A ENST00000333511 Transcript synonymous_variant 565/1974 495/1158 165/385 E gaG/gaA 1 1 BSG HGNC HGNC:1116 protein_coding YES CCDS12033.1 ENSP00000333769 P35613 UPI0000051E38 NM_001728.3 3/9 PROSITE_profiles:PS50835,hmmpanther:PTHR10075,hmmpanther:PTHR10075:SF12,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 579579 579579 G A 1 0 0 0 0 0 0 0 1 1703 1014 35 3 3 BSG 19 579579 Silent SNP G C3N-01842_T 579579 58038037 352 26544 STK11 0 . GRCh38 19 1219358 1219358 + Nonsense_Mutation SNP C C T rs730881970 C3N-01842_T C3N-01842_N C C c.409C>T p.Gln137Ter p.Q137* ENST00000326873 3/10 234 172 62 505 505 0 strelka-varscan-mutect STK11,stop_gained,p.Gln137Ter,ENST00000586243,;STK11,stop_gained,p.Gln137Ter,ENST00000326873,NM_000455.4;STK11,stop_gained,p.Gln13Ter,ENST00000585748,;STK11,intron_variant,,ENST00000585851,;STK11,upstream_gene_variant,,ENST00000585465,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,upstream_gene_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript stop_gained 859/2611 409/1302 137/433 Q/* Cag/Tag rs730881970,CM041079,COSM48901 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 3/10 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 uncertain_significance,pathogenic 0,0,1 HIGH 1 SNV 1 1,1,1 1 PASS rs730881970 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 1219358 1219358 C T 1 0 0 0 0 0 1 0 0 15664 711 25 3 3 STK11 19 1219358 Nonsense_Mutation SNP C C3N-01842_T 639779 1219358 57398258 353 26545 KDM4B 0 . GRCh38 19 5131294 5131294 + Nonsense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1534G>T p.Glu512Ter p.E512* ENST00000159111 12/23 135 95 40 213 213 0 strelka-varscan-mutect KDM4B,stop_gained,p.Glu546Ter,ENST00000611640,;KDM4B,stop_gained,p.Glu512Ter,ENST00000159111,NM_015015.2;KDM4B,stop_gained,p.Glu546Ter,ENST00000536461,;KDM4B,stop_gained,p.Glu258Ter,ENST00000588361,;KDM4B,upstream_gene_variant,,ENST00000588166,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,; T ENST00000159111 Transcript stop_gained 1752/5593 1534/3291 512/1096 E/* Gag/Tag 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 12/23 Low_complexity_(Seg):seg,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 5131294 5131294 G T 1 0 0 0 0 0 1 0 0 8047 1291 45 2 2 KDM4B 19 5131294 Nonsense_Mutation SNP G C3N-01842_T 3911936 5131294 53486322 354 26546 KDM4B 0 . GRCh38 19 5144044 5144044 + Silent SNP G G T rs139226669 C3N-01842_T C3N-01842_N G G c.2628G>T p.= p.T876T ENST00000159111 19/23 67 44 23 100 100 0 strelka-varscan-mutect KDM4B,synonymous_variant,p.=,ENST00000611640,;KDM4B,synonymous_variant,p.=,ENST00000159111,NM_015015.2;KDM4B,synonymous_variant,p.=,ENST00000536461,;KDM4B,downstream_gene_variant,,ENST00000588361,;KDM4B,non_coding_transcript_exon_variant,,ENST00000589104,; T ENST00000159111 Transcript synonymous_variant 2846/5593 2628/3291 876/1096 T acG/acT rs139226669 1 1 KDM4B HGNC HGNC:29136 protein_coding YES CCDS12138.1 ENSP00000159111 A0A0C4DFL8 UPI000023B7FC NM_015015.2 19/23 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF30,Pfam_domain:PF13832,SMART_domains:SM00249 LOW 1 SNV 1 1 PASS rs139226669 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 5144044 5144044 G T 1 0 0 0 0 0 0 0 1 8047 1132 40 1 1 KDM4B 19 5144044 Silent SNP G C3N-01842_T 12750 5144044 53473572 355 26547 PNPLA6 0 . GRCh38 19 7553920 7553920 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.2336C>T p.Ala779Val p.A779V ENST00000414982 21/34 386 268 118 538 538 0 strelka-varscan-mutect PNPLA6,missense_variant,p.Ala731Val,ENST00000221249,NM_006702.4;PNPLA6,missense_variant,p.Ala779Val,ENST00000414982,NM_001166111.1;PNPLA6,missense_variant,p.Ala704Val,ENST00000545201,NM_001166112.1;PNPLA6,missense_variant,p.Ala731Val,ENST00000450331,NM_001166113.1;PNPLA6,missense_variant,p.Ala769Val,ENST00000600737,NM_001166114.1;PNPLA6,downstream_gene_variant,,ENST00000594864,;PNPLA6,non_coding_transcript_exon_variant,,ENST00000599951,;PNPLA6,downstream_gene_variant,,ENST00000599311,;PNPLA6,downstream_gene_variant,,ENST00000595176,;PNPLA6,downstream_gene_variant,,ENST00000595889,;PNPLA6,upstream_gene_variant,,ENST00000595352,; T ENST00000414982 Transcript missense_variant 2531/4522 2336/4128 779/1375 A/V gCc/gTc 1 1 PNPLA6 HGNC HGNC:16268 protein_coding YES CCDS54206.1 ENSP00000407509 Q8IY17 UPI0001AE63FF NM_001166111.1 tolerated(0.23) 21/34 hmmpanther:PTHR14226,hmmpanther:PTHR14226:SF26 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 7553920 7553920 C T 1 0 0 0 0 1 0 0 0 12277 739 26 3 3 PNPLA6 19 7553920 Missense_Mutation SNP C C3N-01842_T 2409876 7553920 51063696 356 26548 MYO9B 0 . GRCh38 19 17184965 17184965 + Missense_Mutation SNP C C T rs748669405 C3N-01842_T C3N-01842_N C C c.2474C>T p.Pro825Leu p.P825L ENST00000595618 17/40 292 276 16 303 303 0 strelka-mutect MYO9B,missense_variant,p.Pro825Leu,ENST00000595618,NM_001130065.1;MYO9B,missense_variant,p.Pro825Leu,ENST00000594824,NM_004145.3;MYO9B,missense_variant,p.Pro825Leu,ENST00000397274,;MYO9B,missense_variant,p.Pro825Leu,ENST00000595641,;MYO9B,missense_variant,p.Pro117Leu,ENST00000602177,;MYO9B,downstream_gene_variant,,ENST00000594971,;MYO9B,non_coding_transcript_exon_variant,,ENST00000601749,;MYO9B,non_coding_transcript_exon_variant,,ENST00000601490,;MYO9B,downstream_gene_variant,,ENST00000598101,;MYO9B,downstream_gene_variant,,ENST00000598464,; T ENST00000595618 Transcript missense_variant 2626/7623 2474/6069 825/2022 P/L cCa/cTa rs748669405 1 1 MYO9B HGNC HGNC:7609 protein_coding YES CCDS46010.1 ENSP00000471457 Q13459 UPI000020367C NM_001130065.1 deleterious(0.01) 17/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF306,Low_complexity_(Seg):seg,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs748669405 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 17184965 17184965 C T 1 0 0 0 0 1 0 0 0 10086 594 21 3 3 MYO9B 19 17184965 Missense_Mutation SNP C C3N-01842_T 9631045 17184965 41432651 357 26549 UNC13A 0 . GRCh38 19 17641459 17641459 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.2570C>A p.Thr857Lys p.T857K ENST00000519716 21/44 342 233 109 327 327 0 strelka-varscan-mutect UNC13A,missense_variant,p.Thr857Lys,ENST00000519716,NM_001080421.2;UNC13A,missense_variant,p.Thr857Lys,ENST00000551649,;UNC13A,missense_variant,p.Thr857Lys,ENST00000552293,;UNC13A,missense_variant,p.Thr855Lys,ENST00000550896,; T ENST00000519716 Transcript missense_variant 2570/9838 2570/5112 857/1703 T/K aCa/aAa 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 tolerated(0.12) 21/44 hmmpanther:PTHR10480 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 17641459 17641459 G T 1 0 0 0 0 1 0 0 0 17508 1377 48 2 2 UNC13A 19 17641459 Missense_Mutation SNP G C3N-01842_T 456494 17641459 40976157 358 26550 UNC13A 0 . GRCh38 19 17645691 17645691 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.2339A>G p.Asp780Gly p.D780G ENST00000519716 19/44 230 191 39 221 221 0 strelka-varscan-mutect UNC13A,missense_variant,p.Asp780Gly,ENST00000519716,NM_001080421.2;UNC13A,missense_variant,p.Asp780Gly,ENST00000551649,;UNC13A,missense_variant,p.Asp780Gly,ENST00000552293,;UNC13A,missense_variant,p.Asp778Gly,ENST00000550896,; C ENST00000519716 Transcript missense_variant 2339/9838 2339/5112 780/1703 D/G gAc/gGc 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 deleterious(0) 19/44 Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR10480,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 5 1 PASS rs1330892660 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 17645691 17645691 T C 1 0 0 0 0 1 0 0 0 17508 1667 58 5 5 UNC13A 19 17645691 Missense_Mutation SNP T C3N-01842_T 4232 17645691 40971925 359 26551 ZNF729 0 . GRCh38 19 22316797 22316797 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.3380C>G p.Thr1127Ser p.T1127S ENST00000601693 4/4 505 421 84 341 341 0 strelka-varscan-mutect ZNF729,missense_variant,p.Thr1127Ser,ENST00000601693,NM_001242680.1; G ENST00000601693 Transcript missense_variant 3498/3877 3380/3759 1127/1252 T/S aCt/aGt 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 tolerated(0.11) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 22316797 22316797 C G 1 0 0 0 0 1 0 0 0 18703 565 20 4 4 ZNF729 19 22316797 Missense_Mutation SNP C C3N-01842_T 4671106 22316797 36300819 360 26552 ZNF99 0 . GRCh38 19 22758120 22758120 + Nonsense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1789G>T p.Glu597Ter p.E597* ENST00000596209 4/4 599 450 149 444 444 0 strelka-varscan-mutect ZNF99,stop_gained,p.Glu597Ter,ENST00000596209,NM_001080409.2;ZNF99,stop_gained,p.Glu506Ter,ENST00000397104,; A ENST00000596209 Transcript stop_gained 1880/7817 1789/2595 597/864 E/* Gaa/Taa 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 22758120 22758120 C A 1 0 0 0 0 0 1 0 0 18797 922 32 2 2 ZNF99 19 22758120 Nonsense_Mutation SNP C C3N-01842_T 441323 22758120 35859496 361 26553 ZNF99 0 . GRCh38 19 22758927 22758927 + Missense_Mutation SNP G G A rs545722379 C3N-01842_T C3N-01842_N G G c.982C>T p.Leu328Phe p.L328F ENST00000596209 4/4 484 382 102 364 364 0 strelka-varscan-mutect ZNF99,missense_variant,p.Leu328Phe,ENST00000596209,NM_001080409.2;ZNF99,missense_variant,p.Leu237Phe,ENST00000397104,; A ENST00000596209 Transcript missense_variant 1073/7817 982/2595 328/864 L/F Ctt/Ttt rs545722379 1 -1 ZNF99 HGNC HGNC:13175 protein_coding YES CCDS59369.1 ENSP00000472969 A8MXY4 UPI0000426011 NM_001080409.2 tolerated(0.05) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS rs545722379 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 22758927 22758927 G A 1 0 0 0 0 1 0 0 0 18797 1000 35 3 3 ZNF99 19 22758927 Missense_Mutation SNP G C3N-01842_T 807 22758927 35858689 362 26554 ZNF681 0 . GRCh38 19 23743725 23743725 + Nonsense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.1825A>T p.Lys609Ter p.K609* ENST00000402377 4/4 217 171 46 170 170 0 strelka-varscan-mutect ZNF681,stop_gained,p.Lys609Ter,ENST00000402377,NM_138286.2;ZNF681,downstream_gene_variant,,ENST00000528059,;ZNF681,downstream_gene_variant,,ENST00000531570,; A ENST00000402377 Transcript stop_gained 1967/6497 1825/1938 609/645 K/* Aag/Tag 1 -1 ZNF681 HGNC HGNC:26457 protein_coding YES CCDS12414.2 ENSP00000384000 Q96N22 UPI000022ABC8 NM_138286.2 4/4 Gene3D:3.30.160.60,Pfam_domain:PF13912,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF356,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 84 23743725 23743725 T A 1 0 0 0 0 0 1 0 0 18661 1763 61 4 4 ZNF681 19 23743725 Nonsense_Mutation SNP T C3N-01842_T 984798 23743725 34873891 363 26555 POP4 0 . GRCh38 19 29606324 29606324 + Missense_Mutation SNP G G T rs150671362 C3N-01842_T C3N-01842_N G G c.6G>T p.Lys2Asn p.K2N ENST00000585603 1/7 174 75 99 120 120 0 strelka-varscan-mutect POP4,missense_variant,p.Lys2Asn,ENST00000585603,NM_006627.2;POP4,missense_variant,p.Lys2Asn,ENST00000586420,;POP4,splice_region_variant,,ENST00000221770,;POP4,5_prime_UTR_variant,,ENST00000590688,;POP4,splice_region_variant,,ENST00000591824,;POP4,upstream_gene_variant,,ENST00000586136,;POP4,upstream_gene_variant,,ENST00000592759,;POP4,missense_variant,p.Lys2Asn,ENST00000586823,;POP4,missense_variant,p.Lys2Asn,ENST00000591061,;POP4,splice_region_variant,,ENST00000588551,;POP4,splice_region_variant,,ENST00000586173,; T ENST00000585603 Transcript missense_variant,splice_region_variant 2308/3385 6/663 2/220 K/N aaG/aaT rs150671362,COSM5505023 1 1 POP4 HGNC HGNC:30081 protein_coding YES CCDS12416.1 ENSP00000465213 O95707 UPI0000034DFA NM_006627.2 tolerated_low_confidence(0.2) 1/7 hmmpanther:PTHR13348,PIRSF_domain:PIRSF027081 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs150671362 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 29606324 29606324 G T 1 0 0 0 0 1 0 0 0 12366 956 33 2 2 POP4 19 29606324 Missense_Mutation SNP G C3N-01842_T 5862599 29606324 29011292 364 26556 GPATCH1 0 . GRCh38 19 33111722 33111722 + Splice_Site SNP A A T novel C3N-01842_T C3N-01842_N A A c.1586-2A>T p.X529_splice ENST00000170564 244 113 131 153 153 0 strelka-varscan-mutect GPATCH1,splice_acceptor_variant,,ENST00000170564,NM_018025.2;GPATCH1,splice_acceptor_variant,,ENST00000590062,;GPATCH1,upstream_gene_variant,,ENST00000592262,;GPATCH1,downstream_gene_variant,,ENST00000592165,; T ENST00000170564 Transcript splice_acceptor_variant -/3492 1586/2796 529/931 1 1 GPATCH1 HGNC HGNC:24658 protein_coding YES CCDS12428.1 ENSP00000170564 Q9BRR8 UPI000004EC71 NM_018025.2 11/19 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 84 33111722 33111722 A T 1 0 0 0 0 0 0 1 0 6489 202 7 4 4 GPATCH1 19 33111722 Splice_Site SNP A C3N-01842_T 3505398 33111722 25505894 365 26557 CYP2A13 0 . GRCh38 19 41090050 41090050 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.347T>A p.Val116Glu p.V116E ENST00000330436 3/9 317 136 181 173 173 0 strelka-varscan-mutect CYP2A13,missense_variant,p.Val116Glu,ENST00000330436,NM_000766.4; A ENST00000330436 Transcript missense_variant 347/1739 347/1485 116/494 V/E gTg/gAg 1 1 CYP2A13 HGNC HGNC:2608 protein_coding YES CCDS12571.1 ENSP00000332679 Q16696 UPI000013E07A NM_000766.4 tolerated(0.09) 3/9 hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF186,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 41090050 41090050 T A 1 0 0 0 0 1 0 0 0 3964 1710 59 4 4 CYP2A13 19 41090050 Missense_Mutation SNP T C3N-01842_T 7978328 41090050 17527566 366 26558 SYT3 0 . GRCh38 19 50630033 50630033 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.813G>A p.= p.K271K ENST00000338916 3/9 137 103 34 199 199 0 strelka-varscan-mutect SYT3,synonymous_variant,p.=,ENST00000338916,NM_032298.2;SYT3,synonymous_variant,p.=,ENST00000593901,NM_001160328.1;SYT3,synonymous_variant,p.=,ENST00000600079,NM_001160329.1;SYT3,downstream_gene_variant,,ENST00000598997,;SYT3,upstream_gene_variant,,ENST00000595117,;SYT3,upstream_gene_variant,,ENST00000595557,; T ENST00000338916 Transcript synonymous_variant 1447/2915 813/1773 271/590 K aaG/aaA 1 -1 SYT3 HGNC HGNC:11511 protein_coding YES CCDS12798.1 ENSP00000340914 Q9BQG1 A0A024R4I9 UPI0000047AEB NM_032298.2 3/9 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF176 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 50630033 50630033 C T 1 0 0 0 0 0 0 0 1 15869 796 28 3 3 SYT3 19 50630033 Silent SNP C C3N-01842_T 9539983 50630033 7987583 367 26559 KLK2 0 . GRCh38 19 50876871 50876871 + Splice_Site SNP G G C C3N-01842_T C3N-01842_N G G c.494-1G>C p.X165_splice ENST00000325321 124 107 17 160 160 0 strelka-varscan-mutect KLK2,splice_acceptor_variant,,ENST00000325321,NM_005551.4;KLK2,splice_acceptor_variant,,ENST00000358049,NM_001002231.2;KLK2,splice_acceptor_variant,,ENST00000391810,NM_001256080.1;KLK2,splice_acceptor_variant,,ENST00000600690,;KLK2,downstream_gene_variant,,ENST00000599568,;KLK2,downstream_gene_variant,,ENST00000593493,;KLK2,intron_variant,,ENST00000596950,;KLK2,downstream_gene_variant,,ENST00000597509,;KLK2,splice_acceptor_variant,,ENST00000595173,;KLK2,splice_acceptor_variant,,ENST00000594174,;KLK2,splice_acceptor_variant,,ENST00000599121,;KLK2,splice_acceptor_variant,,ENST00000597727,;KLK2,splice_acceptor_variant,,ENST00000595050,;KLK2,non_coding_transcript_exon_variant,,ENST00000600755,;KLK2,non_coding_transcript_exon_variant,,ENST00000600866,;KLK2,non_coding_transcript_exon_variant,,ENST00000599280,;KLK2,intron_variant,,ENST00000597439,;KLK2,intron_variant,,ENST00000601114,;KLK2,intron_variant,,ENST00000595316,;KLK2,downstream_gene_variant,,ENST00000601743,;KLK2,upstream_gene_variant,,ENST00000597461,;KLK2,downstream_gene_variant,,ENST00000595375,;KLK2,upstream_gene_variant,,ENST00000597911,; C ENST00000325321 Transcript splice_acceptor_variant -/3019 494/786 165/261 COSM1212703,COSM1212704 1 1 KLK2 HGNC HGNC:6363 protein_coding YES CCDS12808.1 ENSP00000313581 P20151 A0A024R4J4 UPI000004CA0C NM_005551.4 3/4 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 84 50876871 50876871 G C 1 0 0 0 0 0 0 1 0 8273 1043 36 4 4 KLK2 19 50876871 Splice_Site SNP G C3N-01842_T 246838 50876871 7740745 368 26560 SIGLEC12 0 . GRCh38 19 51497397 51497397 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1454C>A p.Ala485Asp p.A485D ENST00000291707 6/8 165 117 48 236 236 0 strelka-varscan-mutect SIGLEC12,missense_variant,p.Ala485Asp,ENST00000291707,NM_053003.3;SIGLEC12,missense_variant,p.Ala367Asp,ENST00000598614,NM_033329.2;SIGLEC12,3_prime_UTR_variant,,ENST00000596742,; T ENST00000291707 Transcript missense_variant 1510/2121 1454/1788 485/595 A/D gCt/gAt 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 deleterious(0) 6/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR12035:SF53,hmmpanther:PTHR12035 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 51497397 51497397 G T 1 0 0 0 0 1 0 0 0 14572 971 34 2 2 SIGLEC12 19 51497397 Missense_Mutation SNP G C3N-01842_T 620526 51497397 7120219 369 26561 ZNF615 0 . GRCh38 19 51993397 51993397 + Missense_Mutation SNP C C G rs147205148 C3N-01842_T C3N-01842_N C C c.1712G>C p.Arg571Pro p.R571P ENST00000594083 6/6 231 161 70 282 282 0 strelka-varscan-mutect ZNF615,missense_variant,p.Arg560Pro,ENST00000602063,NM_001321320.1,NM_001321317.1;ZNF615,missense_variant,p.Arg560Pro,ENST00000376716,NM_198480.3;ZNF615,missense_variant,p.Arg571Pro,ENST00000594083,NM_001321322.1,NM_001321321.1,NM_001321323.1,NM_001321319.1,NM_001321318.1;ZNF615,missense_variant,p.Arg565Pro,ENST00000391795,;ZNF615,missense_variant,p.Arg571Pro,ENST00000598071,NM_001199324.1;ZNF615,missense_variant,p.Arg569Pro,ENST00000618049,;ZNF615,missense_variant,p.Arg571Pro,ENST00000618487,;ZNF615,downstream_gene_variant,,ENST00000593650,;ZNF615,downstream_gene_variant,,ENST00000601178,;ZNF615,3_prime_UTR_variant,,ENST00000599177,;ZNF615,downstream_gene_variant,,ENST00000599115,; G ENST00000594083 Transcript missense_variant 1957/4020 1712/2229 571/742 R/P cGc/cCc rs147205148,COSM1395764,COSM1395765 1 -1 ZNF615 HGNC HGNC:24740 protein_coding YES CCDS59418.1 ENSP00000471549 Q8N8J6 UPI000022A99B NM_001321322.1,NM_001321321.1,NM_001321323.1,NM_001321319.1,NM_001321318.1 deleterious(0.02) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF167,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs147205148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 51993397 51993397 C G 1 0 0 0 0 1 0 0 0 18615 768 27 4 4 ZNF615 19 51993397 Missense_Mutation SNP C C3N-01842_T 496000 51993397 6624219 370 26562 ZNF534 0 . GRCh38 19 52438706 52438706 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1285G>T p.Gly429Cys p.G429C ENST00000332323 4/4 108 77 31 117 116 1 strelka-varscan-mutect ZNF534,missense_variant,p.Gly429Cys,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Gly416Cys,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; T ENST00000332323 Transcript missense_variant 1346/2086 1285/2025 429/674 G/C Ggc/Tgc 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 52438706 52438706 G T 1 0 0 0 0 1 0 0 0 18546 1348 47 2 2 ZNF534 19 52438706 Missense_Mutation SNP G C3N-01842_T 445309 52438706 6178910 371 26563 FAM71E2 0 . GRCh38 19 55358619 55358619 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.2249G>T p.Gly750Val p.G750V ENST00000424985 9/11 183 139 44 231 230 1 strelka-varscan-mutect FAM71E2,missense_variant,p.Gly750Val,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;COX6B2,upstream_gene_variant,,ENST00000586191,;CTD-2105E13.6,missense_variant,p.Gly300Val,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; A ENST00000424985 Transcript missense_variant 2443/3191 2249/2769 750/922 G/V gGg/gTg 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 tolerated(0.12) 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 55358619 55358619 C A 1 0 0 0 0 1 0 0 0 5476 623 22 2 2 FAM71E2 19 55358619 Missense_Mutation SNP C C3N-01842_T 2919913 55358619 3258997 372 26564 FAM71E2 0 . GRCh38 19 55358984 55358984 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1884C>A p.= p.T628T ENST00000424985 9/11 240 176 64 355 354 1 strelka-varscan-mutect FAM71E2,synonymous_variant,p.=,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;CTD-2105E13.6,synonymous_variant,p.=,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; T ENST00000424985 Transcript synonymous_variant 2078/3191 1884/2769 628/922 T acC/acA 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 LOW SNV 5 1 PASS rs892881819 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 55358984 55358984 G T 1 0 0 0 0 0 0 0 1 5476 1335 47 2 2 FAM71E2 19 55358984 Silent SNP G C3N-01842_T 365 55358984 3258632 373 26565 RFPL4A 0 . GRCh38 19 55762919 55762919 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.608C>G p.Pro203Arg p.P203R ENST00000434937 3/3 559 523 36 848 847 1 varscan-mutect RFPL4A,missense_variant,p.Pro203Arg,ENST00000434937,NM_001145014.1; G ENST00000434937 Transcript missense_variant 779/1035 608/864 203/287 P/R cCt/cGt 1 1 RFPL4A HGNC HGNC:16449 protein_coding YES CCDS46201.1 ENSP00000392936 A6NLU0 UPI0000D6181F NM_001145014.1 deleterious(0) 3/3 PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 55762919 55762919 C G 1 0 0 0 0 1 0 0 0 13428 681 24 4 4 RFPL4A 19 55762919 Missense_Mutation SNP C C3N-01842_T 403935 55762919 2854697 374 26566 RFPL4AL1 0 . GRCh38 19 55772923 55772923 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.608C>G p.Pro203Arg p.P203R ENST00000341750 3/3 317 233 84 441 441 0 strelka-varscan-mutect RFPL4AL1,missense_variant,p.Pro203Arg,ENST00000341750,NM_001277397.1;RFPL4AP1,upstream_gene_variant,,ENST00000530883,; G ENST00000341750 Transcript missense_variant 652/908 608/864 203/287 P/R cCt/cGt 1 1 RFPL4AL1 HGNC HGNC:45147 protein_coding YES CCDS59425.1 ENSP00000345151 F8VTS6 UPI000015FD78 NM_001277397.1 deleterious(0) 3/3 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR25462,hmmpanther:PTHR25462:SF228,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 55772923 55772923 C G 1 0 0 0 0 1 0 0 0 13429 681 24 4 4 RFPL4AL1 19 55772923 Missense_Mutation SNP C C3N-01842_T 10004 55772923 2844693 375 26567 NLRP4 0 . GRCh38 19 55858249 55858249 + Missense_Mutation SNP G G A rs267605697 C3N-01842_T C3N-01842_N G G c.856G>A p.Glu286Lys p.E286K ENST00000301295 3/10 261 180 81 491 491 0 strelka-varscan-mutect NLRP4,missense_variant,p.Glu286Lys,ENST00000301295,NM_134444.4;NLRP4,missense_variant,p.Glu211Lys,ENST00000587891,;NLRP4,upstream_gene_variant,,ENST00000589437,;NLRP4,downstream_gene_variant,,ENST00000587464,; A ENST00000301295 Transcript missense_variant 1278/3670 856/2985 286/994 E/K Gag/Aag rs267605697,COSM4560777,COSM4560778 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 tolerated(0.86) 3/10 hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs267605697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 55858249 55858249 G A 1 0 0 0 0 1 0 0 0 10517 1175 41 3 3 NLRP4 19 55858249 Missense_Mutation SNP G C3N-01842_T 85326 55858249 2759367 376 26568 C20orf141 0 . GRCh38 20 2815285 2815285 + Missense_Mutation SNP G G T rs374163831 C3N-01842_T C3N-01842_N G G c.101G>T p.Arg34Leu p.R34L ENST00000380593 2/3 91 56 35 116 116 0 strelka-varscan-mutect RP5-860F19.8,missense_variant,p.Arg34Leu,ENST00000380593,;C20orf141,missense_variant,p.Arg34Leu,ENST00000380589,NM_080739.2;C20orf141,missense_variant,p.Arg34Leu,ENST00000603872,NM_001256538.1;TMEM239,upstream_gene_variant,,ENST00000361033,NM_001318207.1;TMEM239,upstream_gene_variant,,ENST00000380585,NM_001167670.1; T ENST00000380593 Transcript missense_variant 184/1866 101/765 34/254 R/L cGt/cTt rs374163831,COSM1025481 1 1 RP5-860F19.8 Clone_based_vega_gene protein_coding YES ENSP00000369967 Q6ZPB1 UPI00001C10E8 tolerated_low_confidence(0.65) 2/3 hmmpanther:PTHR39222:SF1,hmmpanther:PTHR39222 0,1 MODERATE SNV 2 0,1 1 PASS rs374163831 . 0 203 5 2 0 0 0 0 -20 0.9999937 1 1 1 0 T 3 4 84 2815285 2815285 G T 1 0 0 0 0 1 0 0 0 2002 1145 40 1 1 C20orf141 20 2815285 Missense_Mutation SNP G C3N-01842_T 2815285 61628882 377 26569 C20orf196 0 . GRCh38 20 5863291 5863291 + Missense_Mutation SNP G G C rs566914252 C3N-01842_T C3N-01842_N G G c.446G>C p.Arg149Pro p.R149P ENST00000303142 3/3 314 219 95 310 310 0 strelka-varscan-mutect C20orf196,missense_variant,p.Arg149Pro,ENST00000303142,NM_001303477.1,NM_152504.3;C20orf196,missense_variant,p.Arg196Pro,ENST00000442185,;C20orf196,downstream_gene_variant,,ENST00000445603,; C ENST00000303142 Transcript missense_variant 533/1154 446/618 149/205 R/P cGg/cCg rs566914252 1 1 C20orf196 HGNC HGNC:26318 protein_coding YES CCDS13091.1 ENSP00000305875 Q8IYI0 UPI0000074251 NM_001303477.1,NM_152504.3 deleterious(0.01) 3/3 Pfam_domain:PF15021,hmmpanther:PTHR36863,hmmpanther:PTHR36863:SF1 MODERATE 1 SNV 1 1 PASS rs566914252 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 5863291 5863291 G C 1 0 0 0 0 1 0 0 0 2006 1116 39 4 4 C20orf196 20 5863291 Missense_Mutation SNP G C3N-01842_T 3048006 5863291 58580876 378 26570 BTBD3 0 . GRCh38 20 11919733 11919733 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.433G>T p.Gly145Trp p.G145W ENST00000405977 4/5 288 206 82 231 231 0 strelka-varscan-mutect BTBD3,missense_variant,p.Gly145Trp,ENST00000405977,;BTBD3,missense_variant,p.Gly145Trp,ENST00000378226,NM_014962.3;BTBD3,missense_variant,p.Gly84Trp,ENST00000399006,;BTBD3,missense_variant,p.Gly84Trp,ENST00000254977,NM_181443.3;BTBD3,missense_variant,p.Gly84Trp,ENST00000618296,NM_001282551.1;BTBD3,missense_variant,p.Gly84Trp,ENST00000618918,NM_001282550.1;BTBD3,missense_variant,p.Gly84Trp,ENST00000422390,;BTBD3,missense_variant,p.Gly34Trp,ENST00000430557,;BTBD3,missense_variant,p.Gly34Trp,ENST00000455911,;BTBD3,downstream_gene_variant,,ENST00000450368,;RP4-742J24.2,upstream_gene_variant,,ENST00000439529,;BTBD3,non_coding_transcript_exon_variant,,ENST00000488503,;BTBD3,non_coding_transcript_exon_variant,,ENST00000471120,;BTBD3,non_coding_transcript_exon_variant,,ENST00000473416,;BTBD3,upstream_gene_variant,,ENST00000473180,;BTBD3,3_prime_UTR_variant,,ENST00000449299,; T ENST00000405977 Transcript missense_variant 1058/5137 433/1569 145/522 G/W Ggg/Tgg COSM1532843 1 1 BTBD3 HGNC HGNC:15854 protein_coding YES CCDS13113.1 ENSP00000384545 Q9Y2F9 UPI0000126B03 deleterious(0) 4/5 PROSITE_profiles:PS50097,hmmpanther:PTHR24413,hmmpanther:PTHR24413:SF104,Pfam_domain:PF00651,Gene3D:3.30.710.10,SMART_domains:SM00225,Superfamily_domains:SSF54695 1 MODERATE SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 11919733 11919733 G T 1 0 0 0 0 1 0 0 0 1720 1348 47 2 2 BTBD3 20 11919733 Missense_Mutation SNP G C3N-01842_T 6056442 11919733 52524434 379 26571 CFAP61 0 . GRCh38 20 20251731 20251731 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.2296C>A p.His766Asn p.H766N ENST00000245957 20/27 245 187 58 242 242 0 strelka-varscan-mutect CFAP61,missense_variant,p.His766Asn,ENST00000245957,NM_015585.3;CFAP61,missense_variant,p.His122Asn,ENST00000377293,;CFAP61,missense_variant,p.His122Asn,ENST00000389656,;CFAP61,non_coding_transcript_exon_variant,,ENST00000476414,;CFAP61,non_coding_transcript_exon_variant,,ENST00000468719,;CFAP61,missense_variant,p.His122Asn,ENST00000377308,;RPL17P1,downstream_gene_variant,,ENST00000445304,; A ENST00000245957 Transcript missense_variant 2372/4082 2296/3714 766/1237 H/N Cac/Aac 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 deleterious(0) 20/27 Gene3D:3.50.50.60,hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 20251731 20251731 C A 1 0 0 0 0 1 0 0 0 3028 594 21 2 2 CFAP61 20 20251731 Missense_Mutation SNP C C3N-01842_T 8331998 20251731 44192436 380 26572 COMMD7 0 . GRCh38 20 32743389 32743390 + Frame_Shift_Ins INS - - A novel C3N-01842_T C3N-01842_N - - c.2dupT p.Met1? p.M1? ENST00000278980 1/9 82 55 27 122 122 0 sindel-varindel COMMD7,frameshift_variant,p.Met1?,ENST00000278980,NM_053041.2;COMMD7,frameshift_variant,p.Met1?,ENST00000446419,NM_001099339.1;COMMD7,frameshift_variant,p.Met1?,ENST00000474815,;COMMD7,frameshift_variant,p.Met1?,ENST00000610160,; A ENST00000278980 Transcript frameshift_variant,start_lost 608-609/1900 2-3/603 1/200 M/IX atg/atTg 1 -1 COMMD7 HGNC HGNC:16223 protein_coding YES CCDS42864.1 ENSP00000278980 Q86VX2 UPI000006D145 NM_053041.2 1/9 hmmpanther:PTHR16231,hmmpanther:PTHR16231:SF2 HIGH 1 insertion 1 1 PASS . . 0 203 5 2 0 0 0 0 -20 0.9999915 1 1 1 0 A 7 5 84 32743389 32743389 - A 1 0 1 1 0 0 0 0 0 3513 594 21 0 0 COMMD7 20 32743389 Frame_Shift_Ins INS - C3N-01842_T 12491658 32743389 31700778 381 26573 FAM83C 0 . GRCh38 20 35287196 35287196 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.1583C>A p.Thr528Asn p.T528N ENST00000374408 4/4 210 166 44 212 212 0 strelka-varscan-mutect FAM83C,missense_variant,p.Thr528Asn,ENST00000374408,NM_178468.5;EIF6,upstream_gene_variant,,ENST00000374450,NM_002212.3;EIF6,upstream_gene_variant,,ENST00000374436,NM_181468.2;EIF6,upstream_gene_variant,,ENST00000621148,NM_001267810.1;EIF6,upstream_gene_variant,,ENST00000374443,NM_181466.2;EIF6,upstream_gene_variant,,ENST00000456600,;FAM83C-AS1,downstream_gene_variant,,ENST00000429167,;EIF6,upstream_gene_variant,,ENST00000462894,;EIF6,upstream_gene_variant,,ENST00000447927,;EIF6,upstream_gene_variant,,ENST00000440766,;EIF6,upstream_gene_variant,,ENST00000415116,; T ENST00000374408 Transcript missense_variant 1680/3145 1583/2244 528/747 T/N aCc/aAc COSM723927 1 -1 FAM83C HGNC HGNC:16121 protein_coding YES CCDS13251.1 ENSP00000363529 Q9BQN1 UPI0000072DC0 NM_178468.5 tolerated_low_confidence(0.08) 4/4 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1449474417 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 35287196 35287196 G T 1 0 0 0 0 1 0 0 0 5493 1261 44 2 2 FAM83C 20 35287196 Missense_Mutation SNP G C3N-01842_T 2543807 35287196 29156971 382 26574 SPAG4 0 . GRCh38 20 35617805 35617805 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.503T>C p.Phe168Ser p.F168S ENST00000374273 4/12 272 200 72 272 272 0 strelka-varscan-mutect SPAG4,missense_variant,p.Phe168Ser,ENST00000374273,NM_001317931.1,NM_003116.1;SPAG4,missense_variant,p.Phe43Ser,ENST00000454819,;SPAG4,upstream_gene_variant,,ENST00000430878,;SPAG4,intron_variant,,ENST00000462896,;SPAG4,non_coding_transcript_exon_variant,,ENST00000468248,;SPAG4,non_coding_transcript_exon_variant,,ENST00000463973,;SPAG4,non_coding_transcript_exon_variant,,ENST00000498203,; C ENST00000374273 Transcript missense_variant 615/1453 503/1314 168/437 F/S tTc/tCc 1 1 SPAG4 HGNC HGNC:11214 protein_coding YES CCDS13259.1 ENSP00000363391 Q9NPE6 UPI0000135D8F NM_001317931.1,NM_003116.1 deleterious(0) 4/12 hmmpanther:PTHR12911,hmmpanther:PTHR12911:SF16,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 35617805 35617805 T C 1 0 0 0 0 1 0 0 0 15311 1783 62 5 5 SPAG4 20 35617805 Missense_Mutation SNP T C3N-01842_T 330609 35617805 28826362 383 26575 CDH22 0 . GRCh38 20 46178143 46178143 + Missense_Mutation SNP T T G novel C3N-01842_T C3N-01842_N T T c.1718A>C p.Asp573Ala p.D573A ENST00000537909 11/12 239 169 70 234 234 0 strelka-varscan-mutect CDH22,missense_variant,p.Asp573Ala,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Asp573Ala,ENST00000372262,; G ENST00000537909 Transcript missense_variant 2361/3902 1718/2487 573/828 D/A gAc/gCc 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 tolerated(0.14) 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 46178143 46178143 T G 1 0 0 0 0 1 0 0 0 2810 1667 58 5 5 CDH22 20 46178143 Missense_Mutation SNP T C3N-01842_T 10560338 46178143 18266024 384 26576 SULF2 0 . GRCh38 20 47678770 47678770 + Missense_Mutation SNP G G T C3N-01842_T C3N-01842_N G G c.1099C>A p.Pro367Thr p.P367T ENST00000359930 8/21 218 174 44 223 222 1 strelka-varscan-mutect SULF2,missense_variant,p.Pro367Thr,ENST00000359930,NM_018837.3;SULF2,missense_variant,p.Pro367Thr,ENST00000484875,NM_001161841.1;SULF2,missense_variant,p.Pro367Thr,ENST00000467815,NM_198596.2;CTD-2653D5.1,intron_variant,,ENST00000526566,;SULF2,upstream_gene_variant,,ENST00000465769,; T ENST00000359930 Transcript missense_variant 1951/4915 1099/2613 367/870 P/T Ccc/Acc COSM4927342 1 -1 SULF2 HGNC HGNC:20392 protein_coding YES CCDS13408.1 ENSP00000353007 Q8IWU5 UPI000003FFBA NM_018837.3 deleterious(0) 8/21 hmmpanther:PTHR10342:SF67,hmmpanther:PTHR10342,Pfam_domain:PF00884,Gene3D:3.40.720.10,PIRSF_domain:PIRSF036665,Superfamily_domains:SSF53649 1 MODERATE 1 SNV 1 1 1 PASS rs1288350734 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 47678770 47678770 G T 1 0 0 0 0 1 0 0 0 15759 1232 43 2 2 SULF2 20 47678770 Missense_Mutation SNP G C3N-01842_T 1500627 47678770 16765397 385 26577 MOCS3 0 . GRCh38 20 50959394 50959394 + Silent SNP C C T novel C3N-01842_T C3N-01842_N C C c.552C>T p.= p.P184P ENST00000244051 1/1 207 158 49 191 191 0 strelka-varscan-mutect MOCS3,synonymous_variant,p.=,ENST00000244051,NM_014484.4;DPM1,upstream_gene_variant,,ENST00000371582,NM_001317035.1;DPM1,upstream_gene_variant,,ENST00000371588,NM_003859.1;DPM1,upstream_gene_variant,,ENST00000371584,;DPM1,upstream_gene_variant,,ENST00000413082,;DPM1,upstream_gene_variant,,ENST00000466152,; T ENST00000244051 Transcript synonymous_variant 569/5106 552/1383 184/460 P ccC/ccT 1 1 MOCS3 HGNC HGNC:15765 protein_coding YES CCDS13435.1 ENSP00000244051 O95396 UPI000012F369 NM_014484.4 1/1 Gene3D:3.40.50.720,HAMAP:MF_03049,Pfam_domain:PF00899,hmmpanther:PTHR10953,Superfamily_domains:SSF69572 LOW SNV 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 50959394 50959394 C T 1 0 0 0 0 0 0 0 1 9655 581 21 3 3 MOCS3 20 50959394 Silent SNP C C3N-01842_T 3280624 50959394 13484773 386 26578 ZNF831 0 . GRCh38 20 59254539 59254539 + Silent SNP T T C novel C3N-01842_T C3N-01842_N T T c.4830T>C p.= p.S1610S ENST00000637017 8/8 359 277 82 304 304 0 strelka-varscan-mutect ZNF831,synonymous_variant,p.=,ENST00000637017,;ZNF831,synonymous_variant,p.=,ENST00000371030,NM_178457.2; C ENST00000637017 Transcript synonymous_variant 6379/10953 4830/5034 1610/1677 S agT/agC 1 1 ZNF831 HGNC HGNC:16167 protein_coding YES CCDS42894.1 ENSP00000490240 UPI00001D82E4 8/8 LOW 1 SNV 1 PASS rs1018224238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 84 59254539 59254539 T C 1 0 0 0 0 0 0 0 1 18770 1693 59 5 5 ZNF831 20 59254539 Silent SNP T C3N-01842_T 8295145 59254539 5189628 387 26579 CHRNA4 0 . GRCh38 20 63349716 63349716 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1695C>A p.= p.T565T ENST00000370263 5/6 232 161 71 189 189 0 strelka-varscan-mutect CHRNA4,synonymous_variant,p.=,ENST00000615287,;CHRNA4,synonymous_variant,p.=,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,non_coding_transcript_exon_variant,,ENST00000463705,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,downstream_gene_variant,,ENST00000628665,;CHRNA4,downstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000637243,;CHRNA4,3_prime_UTR_variant,,ENST00000627000,;CHRNA4,3_prime_UTR_variant,,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000630240,;CHRNA4,upstream_gene_variant,,ENST00000631289,; T ENST00000370263 Transcript synonymous_variant 1873/5577 1695/1884 565/627 T acC/acA 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 5/6 Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,Superfamily_domains:SSF90112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 63349716 63349716 G T 1 0 0 0 0 0 0 0 1 3145 1219 43 2 2 CHRNA4 20 63349716 Silent SNP G C3N-01842_T 4095177 63349716 1094451 388 26580 MYT1 0 . GRCh38 20 64219854 64219854 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.2113A>T p.Ser705Cys p.S705C ENST00000328439 13/23 298 195 103 218 218 0 strelka-varscan-mutect MYT1,missense_variant,p.Ser732Cys,ENST00000536311,;MYT1,missense_variant,p.Ser705Cys,ENST00000328439,NM_004535.2;MYT1,missense_variant,p.Ser407Cys,ENST00000622439,;MYT1,missense_variant,p.Ser407Cys,ENST00000360149,; T ENST00000328439 Transcript missense_variant 2477/5535 2113/3366 705/1121 S/C Agc/Tgc 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 deleterious(0) 13/23 Pfam_domain:PF08474,hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 64219854 64219854 A T 1 0 0 0 0 1 0 0 0 10105 188 7 4 4 MYT1 20 64219854 Missense_Mutation SNP A C3N-01842_T 870138 64219854 224313 389 26581 TPTE 0 . GRCh38 21 10569746 10569746 + Nonsense_Mutation SNP G G T rs755738282 C3N-01842_T C3N-01842_N G G c.730G>T p.Glu244Ter p.E244* ENST00000618007 13/24 955 859 96 692 691 1 strelka-varscan-mutect TPTE,stop_gained,p.Glu226Ter,ENST00000622113,NM_199259.3;TPTE,stop_gained,p.Glu244Ter,ENST00000618007,NM_199261.3;TPTE,stop_gained,p.Glu206Ter,ENST00000427445,NM_199260.3;TPTE,stop_gained,p.Glu106Ter,ENST00000612746,NM_001290224.1;TPTE,downstream_gene_variant,,ENST00000612957,;AL078471.5,splice_region_variant,,ENST00000612267,; T ENST00000618007 Transcript stop_gained,splice_region_variant 1060/2150 730/1656 244/551 E/* Gaa/Taa rs755738282 1 1 TPTE HGNC HGNC:12023 protein_coding YES CCDS74771.1 ENSP00000484403 P56180 UPI000016A18A NM_199261.3 13/24 PROSITE_profiles:PS51181,hmmpanther:PTHR12305:SF56,hmmpanther:PTHR12305,Gene3D:3.90.190.10,Superfamily_domains:SSF52799 HIGH 1 SNV 1 1 PASS rs755738282 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 10569746 10569746 G T 1 0 0 0 0 0 1 0 0 16911 1014 35 2 2 TPTE 21 10569746 Nonsense_Mutation SNP G C3N-01842_T 10569746 36140237 390 26582 TMPRSS15 0 . GRCh38 21 18326469 18326469 + Missense_Mutation SNP T T A novel C3N-01842_T C3N-01842_N T T c.1884A>T p.Lys628Asn p.K628N ENST00000284885 16/25 943 562 381 666 666 0 strelka-varscan-mutect TMPRSS15,missense_variant,p.Lys628Asn,ENST00000284885,NM_002772.2; A ENST00000284885 Transcript missense_variant 1918/3947 1884/3060 628/1019 K/N aaA/aaT 1 -1 TMPRSS15 HGNC HGNC:9490 protein_coding YES CCDS13571.1 ENSP00000284885 P98073 UPI000013DDBE NM_002772.2 tolerated(0.13) 16/25 PROSITE_profiles:PS01180,Pfam_domain:PF00431,PIRSF_domain:PIRSF001138,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 18326469 18326469 T A 1 0 0 0 0 1 0 0 0 16722 1606 56 4 4 TMPRSS15 21 18326469 Missense_Mutation SNP T C3N-01842_T 7756723 18326469 28383514 391 26583 ADAMTS1 0 . GRCh38 21 26844556 26844556 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.399C>A p.= p.P133P ENST00000284984 1/9 236 163 73 325 325 0 strelka-varscan-mutect ADAMTS1,synonymous_variant,p.=,ENST00000284984,NM_006988.4;ADAMTS1,upstream_gene_variant,,ENST00000451462,;ADAMTS1,upstream_gene_variant,,ENST00000517777,;ADAMTS1,upstream_gene_variant,,ENST00000517452,;ADAMTS1,upstream_gene_variant,,ENST00000464589,;ADAMTS1,upstream_gene_variant,,ENST00000492656,; T ENST00000284984 Transcript synonymous_variant 854/5191 399/2904 133/967 P ccC/ccA 1 -1 ADAMTS1 HGNC HGNC:217 protein_coding YES CCDS33524.1 ENSP00000284984 Q9UHI8 UPI000013DDC6 NM_006988.4 1/9 Pfam_domain:PF01562,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF40 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 26844556 26844556 G T 1 0 0 0 0 0 0 0 1 299 1335 47 2 2 ADAMTS1 21 26844556 Silent SNP G C3N-01842_T 8518087 26844556 19865427 392 26584 LSS 0 . GRCh38 21 46228553 46228553 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.61G>C p.Asp21His p.D21H ENST00000397728 2/22 288 226 62 396 396 0 strelka-varscan-mutect LSS,missense_variant,p.Asp21His,ENST00000397728,NM_002340.5;LSS,missense_variant,p.Asp21His,ENST00000356396,NM_001001438.2;LSS,missense_variant,p.Asp21His,ENST00000522411,NM_001145436.1;LSS,missense_variant,p.Asp22His,ENST00000450351,;LSS,5_prime_UTR_variant,,ENST00000457828,NM_001145437.1;MCM3AP-AS1,upstream_gene_variant,,ENST00000414659,;MCM3AP-AS1,upstream_gene_variant,,ENST00000455567,;MCM3AP-AS1,upstream_gene_variant,,ENST00000432735,;MCM3AP-AS1,upstream_gene_variant,,ENST00000421927,;MCM3AP-AS1,upstream_gene_variant,,ENST00000444998,;MCM3AP-AS1,upstream_gene_variant,,ENST00000420074,;MCM3AP-AS1,upstream_gene_variant,,ENST00000590829,;AP001469.5,downstream_gene_variant,,ENST00000626933,;MCM3AP-AS1,upstream_gene_variant,,ENST00000588753,;MCM3AP-AS1,upstream_gene_variant,,ENST00000591223,;LSS,non_coding_transcript_exon_variant,,ENST00000464357,;LSS,non_coding_transcript_exon_variant,,ENST00000472272,; G ENST00000397728 Transcript missense_variant 140/4936 61/2199 21/732 D/H Gac/Cac 1 -1 LSS HGNC HGNC:6708 protein_coding YES CCDS13733.1 ENSP00000380837 P48449 UPI000012A14D NM_002340.5 deleterious(0) 2/22 hmmpanther:PTHR11764,hmmpanther:PTHR11764:SF20 MODERATE 1 SNV 1 1 PASS rs1396507321 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 46228553 46228553 C G 1 0 0 0 0 1 0 0 0 8972 884 31 4 4 LSS 21 46228553 Missense_Mutation SNP C C3N-01842_T 19383997 46228553 481430 393 26585 LRRC74B 0 . GRCh38 22 21060512 21060512 + Missense_Mutation SNP C C A novel C3N-01842_T C3N-01842_N C C c.1163C>A p.Ala388Glu p.A388E ENST00000442047 9/9 126 66 60 95 95 0 strelka-varscan-mutect LRRC74B,missense_variant,p.Ala388Glu,ENST00000442047,NM_001291006.1;LRRC74B,non_coding_transcript_exon_variant,,ENST00000497328,;LRRC74B,non_coding_transcript_exon_variant,,ENST00000473769,;LRRC74B,downstream_gene_variant,,ENST00000469766,;TUBA3GP,upstream_gene_variant,,ENST00000410028,; A ENST00000442047 Transcript missense_variant 1163/1179 1163/1179 388/392 A/E gCg/gAg 1 1 LRRC74B HGNC HGNC:34301 protein_coding YES CCDS77654.1 ENSP00000394078 Q6ZQY2 UPI000436DF24 NM_001291006.1 deleterious_low_confidence(0.01) 9/9 MODERATE 1 SNV 5 1 PASS rs1197971673 . 0 200 9 0 0 0 0 0 -20 0.9999993 1 1 1 0 A 3 1 84 21060512 21060512 C A 1 0 0 0 0 1 0 0 0 8922 768 27 1 1 LRRC74B 22 21060512 Missense_Mutation SNP C C3N-01842_T 21060512 29757956 394 26586 MYO18B 0 . GRCh38 22 25868365 25868365 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.3931G>T p.Val1311Leu p.V1311L ENST00000335473 22/44 326 211 115 325 325 0 strelka-varscan-mutect MYO18B,missense_variant,p.Val1311Leu,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Val1312Leu,ENST00000407587,;MYO18B,missense_variant,p.Val1311Leu,ENST00000536101,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript missense_variant 4181/8565 3931/7704 1311/2567 V/L Gtg/Ttg 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0.02) 22/44 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 25868365 25868365 G T 1 0 0 0 0 1 0 0 0 10067 1261 44 2 2 MYO18B 22 25868365 Missense_Mutation SNP G C3N-01842_T 4807853 25868365 24950103 395 26587 ASPHD2 0 . GRCh38 22 26434192 26434192 + Silent SNP C C A rs770815305 C3N-01842_T C3N-01842_N C C c.577C>A p.= p.R193R ENST00000215906 2/4 267 237 30 227 227 0 strelka-varscan-mutect ASPHD2,synonymous_variant,p.=,ENST00000215906,NM_020437.4; A ENST00000215906 Transcript synonymous_variant 1015/3357 577/1110 193/369 R Cgg/Agg rs770815305 1 1 ASPHD2 HGNC HGNC:30437 protein_coding YES CCDS13834.2 ENSP00000215906 Q6ICH7 A0A024R1D0 UPI000037659F NM_020437.4 2/4 Pfam_domain:PF05118,hmmpanther:PTHR12366,hmmpanther:PTHR12366:SF21 LOW 1 SNV 1 1 PASS rs770815305 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 26434192 26434192 C A 1 0 0 0 0 0 0 0 1 1202 527 19 1 1 ASPHD2 22 26434192 Silent SNP C C3N-01842_T 565827 26434192 24384276 396 26588 SYN3 0 . GRCh38 22 32518282 32518282 + Silent SNP G G T novel C3N-01842_T C3N-01842_N G G c.1371C>A p.= p.S457S ENST00000358763 13/14 140 86 54 99 99 0 strelka-varscan-mutect SYN3,synonymous_variant,p.=,ENST00000358763,NM_001135774.1,NM_003490.3,NM_133633.2;SYN3,synonymous_variant,p.=,ENST00000332840,;SYN3,non_coding_transcript_exon_variant,,ENST00000467095,;SYN3,non_coding_transcript_exon_variant,,ENST00000459990,;SYN3,non_coding_transcript_exon_variant,,ENST00000468922,;SYN3,non_coding_transcript_exon_variant,,ENST00000483062,;SYN3,non_coding_transcript_exon_variant,,ENST00000461446,; T ENST00000358763 Transcript synonymous_variant 1614/3126 1371/1743 457/580 S tcC/tcA 1 -1 SYN3 HGNC HGNC:11496 protein_coding YES CCDS13908.1 ENSP00000351614 O14994 A0A024R1I8 UPI00001365D3 NM_001135774.1,NM_003490.3,NM_133633.2 13/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10841 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 32518282 32518282 G T 1 0 0 0 0 0 0 0 1 15832 1219 43 2 2 SYN3 22 32518282 Silent SNP G C3N-01842_T 6084090 32518282 18300186 397 26589 CSNK1E 0 . GRCh38 22 38294468 38294468 + Missense_Mutation SNP C C T novel C3N-01842_T C3N-01842_N C C c.952G>A p.Gly318Arg p.G318R ENST00000396832 8/11 203 164 39 304 304 0 strelka-varscan-mutect CSNK1E,missense_variant,p.Gly318Arg,ENST00000396832,NM_152221.2;CSNK1E,missense_variant,p.Gly318Arg,ENST00000359867,NM_001894.4;CSNK1E,missense_variant,p.Gly318Arg,ENST00000400206,NM_001289912.1;CSNK1E,missense_variant,p.Gly318Arg,ENST00000403904,;CSNK1E,missense_variant,p.Gly21Arg,ENST00000366216,;CSNK1E,missense_variant,p.Gly46Arg,ENST00000431632,;CSNK1E,downstream_gene_variant,,ENST00000405675,;CSNK1E,downstream_gene_variant,,ENST00000413574,;CSNK1E,downstream_gene_variant,,ENST00000451964,;CSNK1E,downstream_gene_variant,,ENST00000498529,;CSNK1E,3_prime_UTR_variant,,ENST00000431611,;CSNK1E,non_coding_transcript_exon_variant,,ENST00000494610,;CSNK1E,downstream_gene_variant,,ENST00000612795,;CSNK1E,downstream_gene_variant,,ENST00000442216,;CSNK1E,upstream_gene_variant,,ENST00000495232,; T ENST00000396832 Transcript missense_variant 1213/2791 952/1251 318/416 G/R Ggg/Agg 1 -1 CSNK1E HGNC HGNC:2453 protein_coding YES CCDS13970.1 ENSP00000380044 P49674 Q5U045 UPI000012DC67 NM_152221.2 tolerated_low_confidence(0.35) 8/11 hmmpanther:PTHR11909,hmmpanther:PTHR11909:SF161 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 38294468 38294468 C T 1 0 0 0 0 1 0 0 0 3753 623 22 3 3 CSNK1E 22 38294468 Missense_Mutation SNP C C3N-01842_T 5776186 38294468 12524000 398 26590 XPNPEP3 0 . GRCh38 22 40881900 40881900 + Silent SNP A A G novel C3N-01842_T C3N-01842_N A A c.312A>G p.= p.T104T ENST00000357137 3/10 332 291 41 401 401 0 strelka-varscan-mutect XPNPEP3,synonymous_variant,p.=,ENST00000357137,NM_022098.3;XPNPEP3,non_coding_transcript_exon_variant,,ENST00000465258,;XPNPEP3,3_prime_UTR_variant,,ENST00000428799,; G ENST00000357137 Transcript synonymous_variant 396/7988 312/1524 104/507 T acA/acG 1 1 XPNPEP3 HGNC HGNC:28052 protein_coding YES CCDS14007.1 ENSP00000349658 Q9NQH7 UPI00000401E0 NM_022098.3 3/10 Gene3D:3.40.350.10,Pfam_domain:PF05195,hmmpanther:PTHR10804,hmmpanther:PTHR10804:SF17,SMART_domains:SM01011,Superfamily_domains:SSF53092 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 84 40881900 40881900 A G 1 0 0 0 0 0 0 0 1 18003 204 8 5 5 XPNPEP3 22 40881900 Silent SNP A C3N-01842_T 2587432 40881900 9936568 399 26591 MXRA5 0 . GRCh38 X 3323235 3323235 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.2450T>A p.Val817Asp p.V817D ENST00000217939 5/7 198 124 74 236 236 0 strelka-varscan-mutect MXRA5,missense_variant,p.Val817Asp,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 2605/9793 2450/8487 817/2828 V/D gTc/gAc 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.12) 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 3323235 3323235 A T 1 0 0 0 0 1 0 0 0 10002 275 10 4 4 MXRA5 23 3323235 Missense_Mutation SNP A C3N-01842_T 3323235 152717660 400 26592 MAP7D2 0 . GRCh38 X 20016237 20016237 + Silent SNP G G T rs757262581 C3N-01842_T C3N-01842_N G G c.1501C>A p.= p.R501R ENST00000379643 11/17 279 148 131 361 361 0 strelka-varscan-mutect MAP7D2,synonymous_variant,p.=,ENST00000379651,NM_152780.3;MAP7D2,synonymous_variant,p.=,ENST00000379643,NM_001168465.1;MAP7D2,synonymous_variant,p.=,ENST00000443379,NM_001168466.1;MAP7D2,synonymous_variant,p.=,ENST00000452324,NM_001168467.1;MIR23C,downstream_gene_variant,,ENST00000579846,; T ENST00000379643 Transcript synonymous_variant 1539/3918 1501/2322 501/773 R Cgg/Agg rs757262581 1 -1 MAP7D2 HGNC HGNC:25899 protein_coding YES CCDS55386.1 ENSP00000368964 Q96T17 UPI00015E039B NM_001168465.1 11/17 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF05672,hmmpanther:PTHR15073,hmmpanther:PTHR15073:SF3,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs757262581 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 20016237 20016237 G T 1 0 0 0 0 0 0 0 1 9192 1086 38 1 1 MAP7D2 23 20016237 Silent SNP G C3N-01842_T 16693002 20016237 136024658 401 26593 IL1RAPL1 0 . GRCh38 X 29399266 29399266 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.661G>A p.Gly221Arg p.G221R ENST00000378993 5/11 151 84 67 93 93 0 strelka-varscan-mutect IL1RAPL1,missense_variant,p.Gly221Arg,ENST00000378993,NM_014271.3; A ENST00000378993 Transcript missense_variant 1334/3667 661/2091 221/696 G/R Gga/Aga 1 1 IL1RAPL1 HGNC HGNC:5996 protein_coding YES CCDS14218.1 ENSP00000368278 Q9NZN1 X5DNQ7 UPI000006D1BF NM_014271.3 tolerated(0.37) 5/11 PROSITE_profiles:PS50835,hmmpanther:PTHR11890:SF22,hmmpanther:PTHR11890,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 29399266 29399266 G A 1 0 0 0 0 1 0 0 0 7564 1349 47 3 3 IL1RAPL1 23 29399266 Missense_Mutation SNP G C3N-01842_T 9383029 29399266 126641629 402 26594 FAM47A 0 . GRCh38 X 34130679 34130679 + Missense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.1600C>A p.Pro534Thr p.P534T ENST00000346193 1/1 68 34 34 90 90 0 strelka-varscan-mutect FAM47A,missense_variant,p.Pro534Thr,ENST00000346193,NM_203408.3;FAM47A,missense_variant,p.Pro521Thr,ENST00000613251,; T ENST00000346193 Transcript missense_variant 1633/2556 1600/2376 534/791 P/T Cct/Act 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 deleterious(0.01) 1/1 Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 34130679 34130679 G T 1 0 0 0 0 1 0 0 0 5447 1203 42 2 2 FAM47A 23 34130679 Missense_Mutation SNP G C3N-01842_T 4731413 34130679 121910216 403 26595 CFAP47 0 . GRCh38 X 35975832 35975832 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.2632C>G p.Arg878Gly p.R878G ENST00000297866 15/16 176 132 44 176 176 0 strelka-varscan-mutect CFAP47,missense_variant,p.Arg878Gly,ENST00000378653,NM_001304548.1;CFAP47,missense_variant,p.Arg878Gly,ENST00000297866,NM_152632.3;CFAP47,3_prime_UTR_variant,,ENST00000493930,; G ENST00000297866 Transcript missense_variant 2698/3608 2632/2931 878/976 R/G Cgt/Ggt 1 1 CFAP47 HGNC HGNC:26708 protein_coding YES CCDS14237.2 ENSP00000297866 Q6ZTR5 UPI000022DD27 NM_152632.3 tolerated(0.18) 15/16 hmmpanther:PTHR23053,hmmpanther:PTHR23053:SF24 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 35975832 35975832 C G 1 0 0 0 0 1 0 0 0 3022 884 31 4 4 CFAP47 23 35975832 Missense_Mutation SNP C C3N-01842_T 1845153 35975832 120065063 404 26596 SRPX 0 . GRCh38 X 38160054 38160054 + Silent SNP G G T C3N-01842_T C3N-01842_N G G c.918C>A p.= p.S306S ENST00000378533 7/10 106 68 38 143 143 0 strelka-varscan-mutect SRPX,synonymous_variant,p.=,ENST00000378533,NM_006307.4;SRPX,synonymous_variant,p.=,ENST00000544439,NM_001170750.1;SRPX,synonymous_variant,p.=,ENST00000538295,NM_001170752.1;SRPX,synonymous_variant,p.=,ENST00000432886,NM_001170751.1;RP5-972B16.2,intron_variant,,ENST00000465127,;SRPX,non_coding_transcript_exon_variant,,ENST00000479015,; T ENST00000378533 Transcript synonymous_variant 1025/1874 918/1395 306/464 S tcC/tcA COSM4512840,COSM4512841 1 -1 SRPX HGNC HGNC:11309 protein_coding YES CCDS14245.1 ENSP00000367794 P78539 UPI0000135F5C NM_006307.4 7/10 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF375,hmmpanther:PTHR19325,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 84 38160054 38160054 G T 1 0 0 0 0 0 0 0 1 15525 1335 47 2 2 SRPX 23 38160054 Silent SNP G C3N-01842_T 2184222 38160054 117880841 405 26597 AKAP4 0 . GRCh38 X 50191001 50191001 + Frame_Shift_Del DEL C C - C3N-01842_T C3N-01842_N C C c.2524delG p.Ala842ProfsTer23 p.A842Pfs*23 ENST00000358526 6/6 110 66 44 188 188 0 sindel-varindel-pindel AKAP4,frameshift_variant,p.Ala842ProfsTer23,ENST00000358526,NM_003886.2;AKAP4,frameshift_variant,p.Ala833ProfsTer23,ENST00000376064,NM_139289.1;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,downstream_gene_variant,,ENST00000448865,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,; - ENST00000358526 Transcript frameshift_variant 2648/2881 2524/2565 842/854 A/X Gcc/cc COSM757052 1 -1 AKAP4 HGNC HGNC:374 protein_coding YES CCDS14329.1 ENSP00000351327 Q5JQC9 UPI000013DA96 NM_003886.2 6/6 hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807 1 HIGH 1 deletion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 84 50191001 50191001 C - 1 0 1 0 1 0 0 0 0 537 739 26 0 0 AKAP4 23 50191001 Frame_Shift_Del DEL C C3N-01842_T 12030947 50191001 105849894 406 26598 PHF8 0 . GRCh38 X 53985074 53985074 + Silent SNP C C A novel C3N-01842_T C3N-01842_N C C c.2391G>T p.= p.G797G ENST00000357988 18/22 182 97 85 228 228 0 strelka-varscan-mutect PHF8,synonymous_variant,p.=,ENST00000338154,NM_015107.2;PHF8,synonymous_variant,p.=,ENST00000357988,NM_001184896.1;PHF8,synonymous_variant,p.=,ENST00000338946,NM_001184897.1;PHF8,synonymous_variant,p.=,ENST00000396282,;PHF8,synonymous_variant,p.=,ENST00000322659,NM_001184898.1;PHF8,synonymous_variant,p.=,ENST00000443302,;PHF8,downstream_gene_variant,,ENST00000494928,; A ENST00000357988 Transcript synonymous_variant 2750/6024 2391/3183 797/1060 G ggG/ggT 1 -1 PHF8 HGNC HGNC:20672 protein_coding YES CCDS55420.1 ENSP00000350676 Q9UPP1 UPI00001C2071 NM_001184896.1 18/22 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF11,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 53985074 53985074 C A 1 0 0 0 0 0 0 0 1 11927 726 26 2 2 PHF8 23 53985074 Silent SNP C C3N-01842_T 3794073 53985074 102055821 407 26599 YIPF6 0 . GRCh38 X 68518777 68518777 + Silent SNP G G A novel C3N-01842_T C3N-01842_N G G c.273G>A p.= p.L91L ENST00000462683 4/7 120 68 52 117 117 0 strelka-varscan-mutect YIPF6,synonymous_variant,p.=,ENST00000462683,NM_173834.3;YIPF6,synonymous_variant,p.=,ENST00000374622,NM_001195214.1;YIPF6,synonymous_variant,p.=,ENST00000451537,;YIPF6,non_coding_transcript_exon_variant,,ENST00000374643,;YIPF6,downstream_gene_variant,,ENST00000470730,; A ENST00000462683 Transcript synonymous_variant 1017/6741 273/711 91/236 L ttG/ttA 1 1 YIPF6 HGNC HGNC:28304 protein_coding YES CCDS14389.1 ENSP00000417573 Q96EC8 UPI000003778F NM_173834.3 4/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR21236:SF1,hmmpanther:PTHR21236,Pfam_domain:PF04893 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 84 68518777 68518777 G A 1 0 0 0 0 0 0 0 1 18044 1368 48 3 3 YIPF6 23 68518777 Silent SNP G C3N-01842_T 14533703 68518777 87522118 408 26600 ZCCHC5 0 . GRCh38 X 78657437 78657437 + Nonsense_Mutation SNP G G T novel C3N-01842_T C3N-01842_N G G c.984C>A p.Cys328Ter p.C328* ENST00000321110 2/2 183 92 91 183 183 0 strelka-varscan-mutect ZCCHC5,stop_gained,p.Cys328Ter,ENST00000321110,NM_152694.2; T ENST00000321110 Transcript stop_gained 1280/2648 984/1428 328/475 C/* tgC/tgA 1 -1 ZCCHC5 HGNC HGNC:22997 protein_coding YES CCDS14440.1 ENSP00000316794 Q8N8U3 UPI00000710DD NM_152694.2 2/2 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF7 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 84 78657437 78657437 G T 1 0 0 0 0 0 1 0 0 18166 1311 46 2 2 ZCCHC5 23 78657437 Nonsense_Mutation SNP G C3N-01842_T 10138660 78657437 77383458 409 26601 IL1RAPL2 0 . GRCh38 X 104658975 104658975 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.62T>C p.Met21Thr p.M21T ENST00000372582 2/11 130 104 26 106 106 0 strelka-varscan-mutect IL1RAPL2,missense_variant,p.Met21Thr,ENST00000372582,NM_017416.1; C ENST00000372582 Transcript missense_variant 818/2985 62/2061 21/686 M/T aTg/aCg 1 1 IL1RAPL2 HGNC HGNC:5997 protein_coding YES CCDS14517.1 ENSP00000361663 Q9NP60 UPI0000073DF7 NM_017416.1 tolerated(0.43) 2/11 PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 104658975 104658975 T C 1 0 0 0 0 1 0 0 0 7565 1464 51 5 5 IL1RAPL2 23 104658975 Missense_Mutation SNP T C3N-01842_T 26001538 104658975 51381920 410 26602 PIH1D3 0 . GRCh38 X 107212948 107212948 + Missense_Mutation SNP A A T novel C3N-01842_T C3N-01842_N A A c.73A>T p.Ser25Cys p.S25C ENST00000535523 3/8 86 68 18 84 84 0 strelka-varscan-mutect PIH1D3,missense_variant,p.Ser25Cys,ENST00000535523,NM_001169154.1;PIH1D3,missense_variant,p.Ser25Cys,ENST00000372453,NM_173494.1;PIH1D3,missense_variant,p.Ser25Cys,ENST00000336387,; T ENST00000535523 Transcript missense_variant 410/1926 73/645 25/214 S/C Agt/Tgt 1 1 PIH1D3 HGNC HGNC:28570 protein_coding YES CCDS14528.1 ENSP00000441930 Q9NQM4 UPI0000073CF5 NM_001169154.1 deleterious(0.01) 3/8 hmmpanther:PTHR21083:SF0,hmmpanther:PTHR21083 MODERATE 1 SNV 5 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 84 107212948 107212948 A T 1 0 0 0 0 1 0 0 0 12002 304 11 4 4 PIH1D3 23 107212948 Missense_Mutation SNP A C3N-01842_T 2553973 107212948 48827947 411 26603 ACSL4 0 . GRCh38 X 109663267 109663267 + Missense_Mutation SNP C C G novel C3N-01842_T C3N-01842_N C C c.1649G>C p.Trp550Ser p.W550S ENST00000340800 14/17 92 44 48 89 89 0 strelka-varscan-mutect ACSL4,missense_variant,p.Trp550Ser,ENST00000340800,NM_001318509.1,NM_022977.2;ACSL4,missense_variant,p.Trp550Ser,ENST00000469796,;ACSL4,missense_variant,p.Trp509Ser,ENST00000348502,NM_001318510.1,NM_004458.2;ACSL4,upstream_gene_variant,,ENST00000505075,;ACSL4,splice_region_variant,,ENST00000514500,; G ENST00000340800 Transcript missense_variant 2154/5333 1649/2136 550/711 W/S tGg/tCg 1 -1 ACSL4 HGNC HGNC:3571 protein_coding YES CCDS14548.1 ENSP00000339787 O60488 UPI000012E293 NM_001318509.1,NM_022977.2 deleterious(0.03) 14/17 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF241,Superfamily_domains:SSF56801 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 109663267 109663267 C G 1 0 0 0 0 1 0 0 0 221 595 21 4 4 ACSL4 23 109663267 Missense_Mutation SNP C C3N-01842_T 2450319 109663267 46377628 412 26604 CAPN6 0 . GRCh38 X 111247385 111247385 + Missense_Mutation SNP T T C novel C3N-01842_T C3N-01842_N T T c.1726A>G p.Ile576Val p.I576V ENST00000324068 12/13 72 36 36 62 62 0 strelka-varscan-mutect CAPN6,missense_variant,p.Ile576Val,ENST00000324068,NM_014289.3; C ENST00000324068 Transcript missense_variant 1894/3568 1726/1926 576/641 I/V Att/Gtt 1 -1 CAPN6 HGNC HGNC:1483 protein_coding YES CCDS14555.1 ENSP00000317214 Q9Y6Q1 UPI0000126EA1 NM_014289.3 tolerated(0.15) 12/13 hmmpanther:PTHR10183:SF281,hmmpanther:PTHR10183,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 84 111247385 111247385 T C 1 0 0 0 0 1 0 0 0 2324 1464 51 5 5 CAPN6 23 111247385 Missense_Mutation SNP T C3N-01842_T 1584118 111247385 44793510 413 26605 KLHL13 0 . GRCh38 X 117909745 117909745 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.931T>C p.Cys311Arg p.C311R ENST00000539496 6/8 333 254 79 324 324 0 strelka-varscan-mutect KLHL13,missense_variant,p.Cys257Arg,ENST00000371876,;KLHL13,missense_variant,p.Cys308Arg,ENST00000262820,NM_033495.3;KLHL13,missense_variant,p.Cys257Arg,ENST00000447671,;KLHL13,missense_variant,p.Cys292Arg,ENST00000540167,NM_001168302.1;KLHL13,missense_variant,p.Cys266Arg,ENST00000545703,NM_001168303.1,NM_001168300.1;KLHL13,missense_variant,p.Cys257Arg,ENST00000371882,;KLHL13,missense_variant,p.Cys257Arg,ENST00000371878,;KLHL13,missense_variant,p.Cys292Arg,ENST00000541812,NM_001168301.1;KLHL13,missense_variant,p.Cys311Arg,ENST00000539496,NM_001168299.1;KLHL13,missense_variant,p.Cys257Arg,ENST00000469946,;Y_RNA,downstream_gene_variant,,ENST00000363421,; G ENST00000539496 Transcript missense_variant 931/3071 931/1977 311/658 C/R Tgt/Cgt 1 -1 KLHL13 HGNC HGNC:22931 protein_coding YES CCDS55480.1 ENSP00000443191 Q9P2N7 UPI0001914B0F NM_001168299.1 deleterious(0) 6/8 PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF68 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 117909745 117909745 A G 1 0 0 0 0 1 0 0 0 8233 130 5 5 5 KLHL13 23 117909745 Missense_Mutation SNP A C3N-01842_T 6662360 117909745 38131150 414 26606 KIAA1210 0 . GRCh38 X 119088721 119088721 + Missense_Mutation SNP G G A novel C3N-01842_T C3N-01842_N G G c.2509C>T p.Leu837Phe p.L837F ENST00000402510 11/14 147 76 71 126 126 0 strelka-varscan-mutect KIAA1210,missense_variant,p.Leu837Phe,ENST00000402510,NM_020721.1; A ENST00000402510 Transcript missense_variant 2509/7824 2509/5130 837/1709 L/F Ctc/Ttc 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 tolerated(0.07) 11/14 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 119088721 119088721 G A 1 0 0 0 0 1 0 0 0 8106 1000 35 3 3 KIAA1210 23 119088721 Missense_Mutation SNP G C3N-01842_T 1178976 119088721 36952174 415 26607 GLUD2 0 . GRCh38 X 121048861 121048861 + Missense_Mutation SNP G G T rs200024208 C3N-01842_T C3N-01842_N G G c.1177G>T p.Ala393Ser p.A393S ENST00000328078 1/1 329 196 133 443 443 0 strelka-varscan-mutect GLUD2,missense_variant,p.Ala393Ser,ENST00000328078,NM_012084.3; T ENST00000328078 Transcript missense_variant 1274/2493 1177/1677 393/558 A/S Gca/Tca rs200024208 1 1 GLUD2 HGNC HGNC:4336 protein_coding YES CCDS14603.1 ENSP00000327589 P49448 A0A140VK14 UPI0000129301 NM_012084.3 deleterious(0) 1/1 Gene3D:3.40.50.720,Pfam_domain:PF00208,hmmpanther:PTHR11606,hmmpanther:PTHR11606:SF15,SMART_domains:SM00839,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 PASS rs200024208 . 0 208 0 0 2 0 0 0 -20 0.9994806 1 1 1 0 T 3 4 84 121048861 121048861 G T 1 0 0 0 0 1 0 0 0 6354 1087 38 1 1 GLUD2 23 121048861 Missense_Mutation SNP G C3N-01842_T 1960140 121048861 34992034 416 26608 FGF13 0 . GRCh38 X 138632938 138632938 + Missense_Mutation SNP C C A rs762632439 C3N-01842_T C3N-01842_N C C c.680G>T p.Arg227Leu p.R227L ENST00000436198 7/7 92 50 42 128 128 0 strelka-varscan-mutect FGF13,missense_variant,p.Arg217Leu,ENST00000315930,NM_004114.3;FGF13,missense_variant,p.Arg164Leu,ENST00000305414,NM_033642.2;FGF13,missense_variant,p.Arg227Leu,ENST00000436198,NM_001139500.1;FGF13,missense_variant,p.Arg171Leu,ENST00000626909,NM_001139498.1;Z83313.1,missense_variant,p.Arg198Leu,ENST00000441825,NM_001139501.1,NM_001139502.1;FGF13,downstream_gene_variant,,ENST00000455663,; A ENST00000436198 Transcript missense_variant 930/1165 680/768 227/255 R/L cGa/cTa rs762632439,COSM1155279,COSM281153,COSM281154,COSM5697363,COSM5697364,COSM5697365 1 -1 FGF13 HGNC HGNC:3670 protein_coding YES CCDS55513.1 ENSP00000396198 Q92913 UPI00001484B4 NM_001139500.1 tolerated_low_confidence(0.24) 7/7 hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF77 0,1,1,1,1,1,1 MODERATE 1 SNV 2 0,1,1,1,1,1,1 1 PASS rs762632439 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 138632938 138632938 C A 1 0 0 0 0 1 0 0 0 5706 884 31 1 1 FGF13 23 138632938 Missense_Mutation SNP C C3N-01842_T 17584077 138632938 17407957 417 26609 ATP11C 0 . GRCh38 X 139804538 139804538 + Missense_Mutation SNP G G A rs770635734 C3N-01842_T C3N-01842_N G G c.497C>T p.Ser166Leu p.S166L ENST00000327569 6/30 123 70 53 114 114 0 strelka-varscan-mutect ATP11C,missense_variant,p.Ser163Leu,ENST00000370557,;ATP11C,missense_variant,p.Ser166Leu,ENST00000327569,NM_173694.4;ATP11C,missense_variant,p.Ser166Leu,ENST00000361648,NM_001010986.2;ATP11C,non_coding_transcript_exon_variant,,ENST00000485626,; A ENST00000327569 Transcript missense_variant 596/6115 497/3399 166/1132 S/L tCa/tTa rs770635734 1 -1 ATP11C HGNC HGNC:13554 protein_coding YES CCDS14668.1 ENSP00000332756 Q8NB49 UPI000036777E NM_173694.4 deleterious(0.03) 6/30 hmmpanther:PTHR24092:SF38,hmmpanther:PTHR24092,TIGRFAM_domain:TIGR01494,Gene3D:2.70.150.10,TIGRFAM_domain:TIGR01652,Pfam_domain:PF00122,Superfamily_domains:0049471 MODERATE 1 SNV 1 1 PASS rs770635734 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 139804538 139804538 G A 1 0 0 0 0 1 0 0 0 1273 1294 45 3 3 ATP11C 23 139804538 Missense_Mutation SNP G C3N-01842_T 1171600 139804538 16236357 418 26610 CXorf66 0 . GRCh38 X 139955924 139955924 + Missense_Mutation SNP A A G novel C3N-01842_T C3N-01842_N A A c.1058T>C p.Val353Ala p.V353A ENST00000370540 3/3 68 33 35 44 44 0 strelka-varscan-mutect CXorf66,missense_variant,p.Val353Ala,ENST00000370540,NM_001013403.2; G ENST00000370540 Transcript missense_variant 1082/1281 1058/1086 353/361 V/A gTc/gCc 1 -1 CXorf66 HGNC HGNC:33743 protein_coding YES CCDS35411.1 ENSP00000359571 Q5JRM2 UPI00001D7C1C NM_001013403.2 tolerated(0.2) 3/3 hmmpanther:PTHR37340,hmmpanther:PTHR37340:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 84 139955924 139955924 A G 1 0 0 0 0 1 0 0 0 3920 275 10 5 5 CXorf66 23 139955924 Missense_Mutation SNP A C3N-01842_T 151386 139955924 16084971 419 26611 SLITRK4 0 . GRCh38 X 143630519 143630519 + Missense_Mutation SNP C C A C3N-01842_T C3N-01842_N C C c.590G>T p.Gly197Val p.G197V ENST00000596188 2/2 188 102 86 167 167 0 strelka-varscan-mutect SLITRK4,missense_variant,p.Gly197Val,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.Gly197Val,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.Gly197Val,ENST00000356928,NM_001184749.2; A ENST00000596188 Transcript missense_variant 816/8545 590/2514 197/837 G/V gGg/gTg COSM3558807 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 deleterious(0) 2/2 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 84 143630519 143630519 C A 1 0 0 0 0 1 0 0 0 15036 623 22 2 2 SLITRK4 23 143630519 Missense_Mutation SNP C C3N-01842_T 3674595 143630519 12410376 420 26612 PLA2G5 0 . GRCh38 1 20089828 20089828 + Missense_Mutation SNP G G T rs200355236 C3N-02000_T C3N-02000_N G G c.225G>T p.Glu75Asp p.E75D ENST00000375108 4/5 163 125 38 231 231 0 strelka-varscan-mutect PLA2G5,missense_variant,p.Glu75Asp,ENST00000375108,NM_000929.2;PLA2G5,non_coding_transcript_exon_variant,,ENST00000486277,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000465698,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000489871,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000478803,;PLA2G5,non_coding_transcript_exon_variant,,ENST00000469069,;PLA2G5,downstream_gene_variant,,ENST00000460175,; T ENST00000375108 Transcript missense_variant 493/1161 225/417 75/138 E/D gaG/gaT rs200355236 1 1 PLA2G5 HGNC HGNC:9038 protein_coding YES CCDS202.1 ENSP00000364249 P39877 UPI00001310E7 NM_000929.2 tolerated(0.05) 4/5 hmmpanther:PTHR11716,hmmpanther:PTHR11716:SF10,Gene3D:1.20.90.10,Pfam_domain:PF00068,SMART_domains:SM00085,Superfamily_domains:SSF48619 MODERATE 1 SNV 1 1 PASS rs200355236 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 85 20089828 20089828 G T 1 0 0 0 0 1 0 0 0 12103 991 35 2 2 PLA2G5 1 20089828 Missense_Mutation SNP G C3N-02000_T 20089828 228866594 1 26613 THRAP3 0 . GRCh38 1 36286447 36286447 + Missense_Mutation SNP T T A novel C3N-02000_T C3N-02000_N T T c.217T>A p.Phe73Ile p.F73I ENST00000354618 4/12 165 127 38 168 168 0 strelka-varscan-mutect THRAP3,missense_variant,p.Phe73Ile,ENST00000354618,NM_001321471.1,NM_001321473.1,NM_005119.3;THRAP3,missense_variant,p.Phe73Ile,ENST00000469141,;THRAP3,downstream_gene_variant,,ENST00000478853,;THRAP3,upstream_gene_variant,,ENST00000466743,; A ENST00000354618 Transcript missense_variant 441/4432 217/2868 73/955 F/I Ttc/Atc 1 1 THRAP3 HGNC HGNC:22964 protein_coding YES CCDS405.1 ENSP00000346634 Q9Y2W1 UPI0000203F28 NM_001321471.1,NM_001321473.1,NM_005119.3 deleterious(0) 4/12 hmmpanther:PTHR15268 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 85 36286447 36286447 T A 1 0 0 0 0 1 0 0 0 16308 1841 64 4 4 THRAP3 1 36286447 Missense_Mutation SNP T C3N-02000_T 16196619 36286447 212669975 2 26614 ELF3 0 . GRCh38 1 202013241 202013241 + Missense_Mutation SNP C C T novel C3N-02000_T C3N-02000_N C C c.748C>T p.Pro250Ser p.P250S ENST00000359651 6/8 145 137 8 157 157 0 strelka-varscan ELF3,missense_variant,p.Pro250Ser,ENST00000359651,;ELF3,missense_variant,p.Pro250Ser,ENST00000367284,NM_001114309.1,NM_004433.4;ELF3,missense_variant,p.Pro250Ser,ENST00000367283,;ELF3,downstream_gene_variant,,ENST00000446188,;RP11-510N19.5,intron_variant,,ENST00000504773,;RP11-465N4.4,upstream_gene_variant,,ENST00000419190,;ELF3,non_coding_transcript_exon_variant,,ENST00000490203,;ELF3,non_coding_transcript_exon_variant,,ENST00000470384,;ELF3,downstream_gene_variant,,ENST00000495848,;ELF3,upstream_gene_variant,,ENST00000475698,;ELF3,downstream_gene_variant,,ENST00000498017,;ELF3,downstream_gene_variant,,ENST00000479874,; T ENST00000359651 Transcript missense_variant 3940/4994 748/1116 250/371 P/S Ccc/Tcc 1 1 ELF3 HGNC HGNC:3318 protein_coding YES CCDS1419.1 ENSP00000352673 P78545 A0A024R974 UPI0000034E32 deleterious(0) 6/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -10.90141 0.9999486 1 1 1 0 T 3 4 85 202013241 202013241 C T 1 0 0 0 0 1 0 0 0 4888 739 26 3 3 ELF3 1 202013241 Missense_Mutation SNP C C3N-02000_T 165726794 202013241 46943181 3 26615 PIK3C2B 0 . GRCh38 1 204438943 204438943 + Missense_Mutation SNP A A C novel C3N-02000_T C3N-02000_N A A c.3508T>G p.Tyr1170Asp p.Y1170D ENST00000367187 24/34 103 76 27 101 101 0 strelka-varscan-mutect PIK3C2B,missense_variant,p.Tyr1170Asp,ENST00000367187,NM_002646.3;PIK3C2B,missense_variant,p.Tyr1142Asp,ENST00000424712,;RP11-739N20.2,downstream_gene_variant,,ENST00000443515,; C ENST00000367187 Transcript missense_variant 4065/7686 3508/4905 1170/1634 Y/D Tat/Gat 1 -1 PIK3C2B HGNC HGNC:8972 protein_coding YES CCDS1446.1 ENSP00000356155 O00750 A2RUF7 UPI00002056D1 NM_002646.3 deleterious(0) 24/34 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF30,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 85 204438943 204438943 A C 1 0 0 0 0 1 0 0 0 12005 391 14 5 5 PIK3C2B 1 204438943 Missense_Mutation SNP A C3N-02000_T 2425702 204438943 44517479 4 26616 APOB 0 . GRCh38 2 21001838 21001838 + Silent SNP G G A C3N-02000_T C3N-02000_N G G c.13584C>T p.= p.Y4528Y ENST00000233242 29/29 234 206 28 176 176 0 strelka-varscan-mutect APOB,synonymous_variant,p.=,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; A ENST00000233242 Transcript synonymous_variant 13712/14121 13584/13692 4528/4563 Y taC/taT COSM1530638 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 29/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1,Pfam_domain:PF12491 1 LOW 1 SNV 1 1 1 PASS rs1490771906 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 85 21001838 21001838 G A 1 0 0 0 0 0 0 0 1 907 1256 44 3 3 APOB 2 21001838 Silent SNP G C3N-02000_T 21001838 221191691 5 26617 REV1 0 . GRCh38 2 99424174 99424174 + Frame_Shift_Del DEL T T - novel C3N-02000_T C3N-02000_N T T c.1654delA p.Thr552HisfsTer23 p.T552Hfs*23 ENST00000258428 10/23 176 102 74 76 76 0 sindel-varindel-pindel REV1,frameshift_variant,p.Thr552HisfsTer23,ENST00000258428,NM_016316.2;REV1,frameshift_variant,p.Thr551HisfsTer23,ENST00000393445,NM_001037872.1;REV1,downstream_gene_variant,,ENST00000450415,;REV1,non_coding_transcript_exon_variant,,ENST00000465835,;REV1,3_prime_UTR_variant,,ENST00000413697,;REV1,non_coding_transcript_exon_variant,,ENST00000481719,; - ENST00000258428 Transcript frameshift_variant 1883/4751 1654/3756 552/1251 T/X Aca/ca 1 -1 REV1 HGNC HGNC:14060 protein_coding YES CCDS2045.1 ENSP00000258428 Q9UBZ9 UPI0000073A14 NM_016316.2 10/23 PROSITE_profiles:PS50173,hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF12,Pfam_domain:PF00817,Gene3D:3.30.70.270,PIRSF_domain:PIRSF036573,Superfamily_domains:SSF56672 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 85 99424174 99424174 T - 1 0 1 0 1 0 0 0 0 13410 1725 60 0 0 REV1 2 99424174 Frame_Shift_Del DEL T C3N-02000_T 78422336 99424174 142769355 6 26618 SLC5A7 0 . GRCh38 2 108006062 108006062 + Missense_Mutation SNP T T C novel C3N-02000_T C3N-02000_N T T c.755T>C p.Ile252Thr p.I252T ENST00000264047 7/9 75 60 15 169 169 0 strelka-varscan SLC5A7,missense_variant,p.Ile252Thr,ENST00000264047,NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3;SLC5A7,missense_variant,p.Ile252Thr,ENST00000409059,; C ENST00000264047 Transcript missense_variant 1031/5152 755/1743 252/580 I/T aTc/aCc 1 1 SLC5A7 HGNC HGNC:14025 protein_coding YES CCDS2074.1 ENSP00000264047 Q9GZV3 UPI0000070792 NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3 deleterious(0) 7/9 Pfam_domain:PF00474,PROSITE_profiles:PS50283,hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF129,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 85 108006062 108006062 T C 1 0 0 0 0 1 0 0 0 14953 1435 50 5 5 SLC5A7 2 108006062 Missense_Mutation SNP T C3N-02000_T 8581888 108006062 134187467 7 26619 PRSS12 0 . GRCh38 4 118308451 118308451 + Missense_Mutation SNP C C T rs367921225 C3N-02000_T C3N-02000_N C C c.1616G>A p.Arg539His p.R539H ENST00000296498 8/13 219 188 31 274 274 0 strelka-varscan-mutect PRSS12,missense_variant,p.Arg539His,ENST00000296498,NM_003619.3;PRSS12,non_coding_transcript_exon_variant,,ENST00000515089,;PRSS12,downstream_gene_variant,,ENST00000503043,; T ENST00000296498 Transcript missense_variant 1899/4809 1616/2628 539/875 R/H cGt/cAt rs367921225,COSM1426528 1 -1 PRSS12 HGNC HGNC:9477 protein_coding YES CCDS3709.1 ENSP00000296498 P56730 UPI000013E34B NM_003619.3 deleterious(0) 8/13 Gene3D:3.10.250.10,Pfam_domain:PF00530,PROSITE_patterns:PS00420,PROSITE_profiles:PS50287,hmmpanther:PTHR19331,hmmpanther:PTHR19331:SF315,SMART_domains:SM00202,Superfamily_domains:SSF56487 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs367921225 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 85 118308451 118308451 C T 1 0 0 0 0 1 0 0 0 12762 536 19 1 1 PRSS12 4 118308451 Missense_Mutation SNP C C3N-02000_T 118308451 71906104 8 26620 MIER3 0 . GRCh38 5 56937586 56937586 + Missense_Mutation SNP G G T novel C3N-02000_T C3N-02000_N G G c.443C>A p.Pro148His p.P148H ENST00000381226 5/13 102 71 31 125 125 0 strelka-varscan-mutect MIER3,missense_variant,p.Pro148His,ENST00000381226,NM_001297598.1;MIER3,missense_variant,p.Pro143His,ENST00000381213,NM_152622.4;MIER3,missense_variant,p.Pro143His,ENST00000381199,NM_001297599.1;MIER3,missense_variant,p.Pro80His,ENST00000409421,;MIER3,missense_variant,p.Pro116His,ENST00000336942,;AC016644.1,upstream_gene_variant,,ENST00000438553,;MIER3,3_prime_UTR_variant,,ENST00000452157,;MIER3,3_prime_UTR_variant,,ENST00000451637,;MIER3,downstream_gene_variant,,ENST00000480115,; T ENST00000381226 Transcript missense_variant 459/5210 443/1668 148/555 P/H cCt/cAt 1 -1 MIER3 HGNC HGNC:26678 protein_coding YES CCDS78011.1 ENSP00000370624 Q7Z3K6 UPI000022C7A2 NM_001297598.1 tolerated(0.11) 5/13 hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 85 56937586 56937586 G T 1 0 0 0 0 1 0 0 0 9545 1000 35 2 2 MIER3 5 56937586 Missense_Mutation SNP G C3N-02000_T 56937586 124600673 9 26621 PCDHB8 0 . GRCh38 5 141180306 141180306 + Nonsense_Mutation SNP G G T novel C3N-02000_T C3N-02000_N G G c.2272G>T p.Gly758Ter p.G758* ENST00000239444 1/1 287 231 56 208 207 1 strelka-varscan-mutect PCDHB8,stop_gained,p.Gly758Ter,ENST00000239444,NM_019120.4;PCDHB16,upstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB7,downstream_gene_variant,,ENST00000231137,NM_018940.3;PCDHB16,upstream_gene_variant,,ENST00000625044,;CH17-140K24.5,upstream_gene_variant,,ENST00000623884,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;CH17-140K24.4,intron_variant,,ENST00000623995,;CH17-140K24.5,upstream_gene_variant,,ENST00000623407,; T ENST00000239444 Transcript stop_gained 2517/2740 2272/2406 758/801 G/* Gga/Tga 1 1 PCDHB8 HGNC HGNC:8693 protein_coding YES CCDS4250.1 ENSP00000239444 Q9UN66 UPI000192C41A NM_019120.4 1/1 hmmpanther:PTHR24028:SF61,hmmpanther:PTHR24028,Pfam_domain:PF16492 HIGH SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 85 141180306 141180306 G T 1 0 0 0 0 0 1 0 0 11635 1001 35 2 2 PCDHB8 5 141180306 Nonsense_Mutation SNP G C3N-02000_T 84242720 141180306 40357953 10 26622 LCP2 0 . GRCh38 5 170268480 170268480 + Missense_Mutation SNP G G A novel C3N-02000_T C3N-02000_N G G c.526C>T p.Arg176Trp p.R176W ENST00000046794 8/21 21 18 3 28 28 0 strelka-mutect LCP2,missense_variant,p.Arg176Trp,ENST00000046794,NM_005565.3;LCP2,missense_variant,p.Arg176Trp,ENST00000628092,;LCP2,upstream_gene_variant,,ENST00000521416,;LCP2,upstream_gene_variant,,ENST00000520344,;LCP2,downstream_gene_variant,,ENST00000519594,; A ENST00000046794 Transcript missense_variant,splice_region_variant 1142/4678 526/1602 176/533 R/W Cgg/Tgg 1 -1 LCP2 HGNC HGNC:6529 protein_coding YES CCDS47339.1 ENSP00000046794 Q13094 UPI000012E2AE NM_005565.3 deleterious(0) 8/21 hmmpanther:PTHR14098,hmmpanther:PTHR14098:SF1 MODERATE 1 SNV 1 1 PASS . . 7 200 3 0 0 0 0 0 -9.987138 1 1 1 1 0 A 3 1 85 170268480 170268480 G A 1 0 0 0 0 1 0 0 0 8598 1130 39 1 1 LCP2 5 170268480 Missense_Mutation SNP G C3N-02000_T 29088174 170268480 11269779 11 26623 THBS2 0 . GRCh38 6 169248910 169248910 + Missense_Mutation SNP G G A novel C3N-02000_T C3N-02000_N G G c.116C>T p.Thr39Ile p.T39I ENST00000366787 4/23 70 66 4 83 83 0 strelka-varscan-mutect THBS2,missense_variant,p.Thr39Ile,ENST00000366787,NM_003247.3;THBS2,missense_variant,p.Thr39Ile,ENST00000617924,;THBS2,missense_variant,p.Thr39Ile,ENST00000435791,;THBS2,upstream_gene_variant,,ENST00000472733,; A ENST00000366787 Transcript missense_variant 366/5811 116/3519 39/1172 T/I aCc/aTc 1 -1 THBS2 HGNC HGNC:11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 UPI0000231C7F NM_003247.3 deleterious(0.02) 4/23 hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF10,SMART_domains:SM00210,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 85 169248910 169248910 G A 1 0 0 0 0 1 0 0 0 16287 1261 44 3 3 THBS2 6 169248910 Missense_Mutation SNP G C3N-02000_T 169248910 1557069 12 26624 OR1N2 0 . GRCh38 9 122554083 122554083 + Missense_Mutation SNP T T G novel C3N-02000_T C3N-02000_N T T c.914T>G p.Phe305Cys p.F305C ENST00000373688 1/1 213 160 53 212 211 1 strelka-varscan-mutect OR1N2,missense_variant,p.Phe305Cys,ENST00000373688,NM_001004457.1;OR1N2,missense_variant,p.Phe287Cys,ENST00000616791,; G ENST00000373688 Transcript missense_variant 972/1103 914/993 305/330 F/C tTc/tGc 1 1 OR1N2 HGNC HGNC:15111 protein_coding YES CCDS35123.1 ENSP00000362792 Q8NGR9 UPI000004618C NM_001004457.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF156,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 85 122554083 122554083 T G 1 0 0 0 0 1 0 0 0 11048 1783 62 5 5 OR1N2 9 122554083 Missense_Mutation SNP T C3N-02000_T 122554083 15840634 13 26625 TAF3 0 . GRCh38 10 7965698 7965698 + Silent SNP C C A C3N-02000_T C3N-02000_N C C c.2188C>A p.= p.R730R ENST00000344293 3/7 48 43 5 53 53 0 strelka-mutect TAF3,synonymous_variant,p.=,ENST00000344293,NM_031923.3; A ENST00000344293 Transcript synonymous_variant 2394/4872 2188/2790 730/929 R Cga/Aga COSM5088697 1 1 TAF3 HGNC HGNC:17303 protein_coding YES CCDS41487.1 ENSP00000340271 Q5VWG9 UPI00004588FA NM_031923.3 3/7 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12321,hmmpanther:PTHR12321:SF34 1 LOW 1 SNV 2 1 1 PASS rs1038827422 . 0 185 21 3 0 0 0 0 -9.880942 0.9395449 0 1 1 0 A 2 1 85 7965698 7965698 C A 1 0 0 0 0 0 0 0 1 15921 760 27 1 1 TAF3 10 7965698 Silent SNP C C3N-02000_T 7965698 125831724 14 26626 MUC5B 0 . GRCh38 11 1245722 1245722 + Missense_Mutation SNP G G A novel C3N-02000_T C3N-02000_N G G c.8842G>A p.Glu2948Lys p.E2948K ENST00000529681 31/49 166 115 51 161 161 0 strelka-varscan-mutect MUC5B,missense_variant,p.Glu2948Lys,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,; A ENST00000529681 Transcript missense_variant 8900/17911 8842/17289 2948/5762 E/K Gag/Aag 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 deleterious(0.01) 31/49 Pfam_domain:PF13330 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 85 1245722 1245722 G A 1 0 0 0 0 1 0 0 0 9979 1291 45 3 3 MUC5B 11 1245722 Missense_Mutation SNP G C3N-02000_T 1245722 133840900 15 26627 CD4 0 . GRCh38 12 6816237 6816237 + Frame_Shift_Del DEL A A - novel C3N-02000_T C3N-02000_N A A c.792delA p.Lys264AsnfsTer49 p.K264Nfs*49 ENST00000011653 6/10 194 158 36 227 227 0 sindel-varindel-pindel CD4,frameshift_variant,p.Lys264AsnfsTer49,ENST00000011653,NM_000616.4;CD4,3_prime_UTR_variant,,ENST00000541982,;CD4,non_coding_transcript_exon_variant,,ENST00000538827,;CD4,downstream_gene_variant,,ENST00000536610,;CD4,downstream_gene_variant,,ENST00000536563,;CD4,downstream_gene_variant,,ENST00000536590,;CD4,non_coding_transcript_exon_variant,,ENST00000437800,;CD4,downstream_gene_variant,,ENST00000544344,;CD4,downstream_gene_variant,,ENST00000543755,; - ENST00000011653 Transcript frameshift_variant 1047/3114 789/1377 263/458 V/X gtA/gt 1 1 CD4 HGNC HGNC:1678 protein_coding YES CCDS8562.1 ENSP00000011653 P01730 UPI0000001294 NM_000616.4 6/10 hmmpanther:PTHR11422:SF0,hmmpanther:PTHR11422,Gene3D:2.60.40.10,Pfam_domain:PF09191,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 85 6816237 6816237 A - 1 0 1 0 1 0 0 0 0 2718 349 13 0 0 CD4 12 6816237 Frame_Shift_Del DEL A C3N-02000_T 6816237 126459072 16 26628 FAM90A1 0 . GRCh38 12 8222119 8222119 + Silent SNP G G A novel C3N-02000_T C3N-02000_N G G c.1098C>T p.= p.S366S ENST00000538603 7/7 645 606 39 638 638 0 varscan-mutect FAM90A1,synonymous_variant,p.=,ENST00000538603,NM_018088.3;FAM90A1,synonymous_variant,p.=,ENST00000307435,NM_001319982.1;FAM90A1,downstream_gene_variant,,ENST00000442295,;RP11-266K4.14,downstream_gene_variant,,ENST00000618256,;RP11-266K4.1,upstream_gene_variant,,ENST00000542600,; A ENST00000538603 Transcript synonymous_variant 1657/2513 1098/1395 366/464 S agC/agT 1 -1 FAM90A1 HGNC HGNC:25526 protein_coding YES CCDS31738.1 ENSP00000445418 Q86YD7 UPI000013EC10 NM_018088.3 7/7 hmmpanther:PTHR16035,hmmpanther:PTHR16035:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 85 8222119 8222119 G A 1 0 0 0 0 0 0 0 1 5507 1310 46 3 3 FAM90A1 12 8222119 Silent SNP G C3N-02000_T 1405882 8222119 125053190 17 26629 1 20 2 2 117 G 9.014354e-05 FAM90A1 0 . GRCh38 12 8222235 8222235 + Missense_Mutation SNP G G A novel C3N-02000_T C3N-02000_N G G c.982C>T p.Pro328Ser p.P328S ENST00000538603 7/7 605 572 33 594 594 0 varscan-mutect FAM90A1,missense_variant,p.Pro328Ser,ENST00000538603,NM_018088.3;FAM90A1,missense_variant,p.Pro328Ser,ENST00000307435,NM_001319982.1;FAM90A1,downstream_gene_variant,,ENST00000442295,;RP11-266K4.14,downstream_gene_variant,,ENST00000618256,;RP11-266K4.1,upstream_gene_variant,,ENST00000542600,; A ENST00000538603 Transcript missense_variant 1541/2513 982/1395 328/464 P/S Ccg/Tcg 1 -1 FAM90A1 HGNC HGNC:25526 protein_coding YES CCDS31738.1 ENSP00000445418 Q86YD7 UPI000013EC10 NM_018088.3 tolerated(0.66) 7/7 hmmpanther:PTHR16035,hmmpanther:PTHR16035:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 85 8222235 8222235 G A 1 0 0 0 0 1 0 0 0 5507 1232 43 3 3 FAM90A1 12 8222235 Missense_Mutation SNP G C3N-02000_T 116 8222235 125053074 18 26630 1 20 2 2 117 G 9.014354e-05 CDC16 0 . GRCh38 13 114259398 114259398 + Missense_Mutation SNP G G T novel C3N-02000_T C3N-02000_N G G c.1314G>T p.Glu438Asp p.E438D ENST00000360383 14/19 68 63 5 27 27 0 strelka-mutect CDC16,missense_variant,p.Glu438Asp,ENST00000360383,NM_001318517.1,NM_003903.3,NM_001078645.1;CDC16,missense_variant,p.Glu438Asp,ENST00000356221,;CDC16,missense_variant,p.Glu344Asp,ENST00000375310,;CDC16,missense_variant,p.Glu293Asp,ENST00000628084,;CDC16,missense_variant,p.Glu437Asp,ENST00000252457,;CDC16,missense_variant,p.Glu344Asp,ENST00000375308,;CDC16,missense_variant,p.Glu293Asp,ENST00000252458,;CDC16,upstream_gene_variant,,ENST00000461716,;CDC16,splice_region_variant,,ENST00000484907,; T ENST00000360383 Transcript missense_variant,splice_region_variant 1512/2211 1314/1863 438/620 E/D gaG/gaT 1 1 CDC16 HGNC HGNC:1720 protein_coding YES CCDS9542.2 ENSP00000353549 Q13042 A0A024RDZ2 UPI000006F728 NM_001318517.1,NM_003903.3,NM_001078645.1 tolerated(0.17) 14/19 PROSITE_profiles:PS50293,hmmpanther:PTHR12558:SF9,hmmpanther:PTHR12558,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -11.9659 1 1 1 1 0 T 3 4 85 114259398 114259398 G T 1 0 0 0 0 1 0 0 0 2761 1014 35 2 2 CDC16 13 114259398 Missense_Mutation SNP G C3N-02000_T 114259398 104930 19 26631 SLC12A4 0 . GRCh38 16 67954760 67954760 + Silent SNP A A G novel C3N-02000_T C3N-02000_N A A c.564T>C p.= p.Y188Y ENST00000422611 5/23 124 113 11 161 161 0 strelka-varscan-mutect SLC12A4,synonymous_variant,p.=,ENST00000316341,NM_001145961.1,NM_005072.4;SLC12A4,synonymous_variant,p.=,ENST00000422611,NM_001145962.1;SLC12A4,synonymous_variant,p.=,ENST00000576616,;SLC12A4,synonymous_variant,p.=,ENST00000541864,NM_001145964.1;SLC12A4,synonymous_variant,p.=,ENST00000572037,;SLC12A4,synonymous_variant,p.=,ENST00000537830,NM_001145963.1;SLC12A4,synonymous_variant,p.=,ENST00000571299,;SLC12A4,non_coding_transcript_exon_variant,,ENST00000572010,;SLC12A4,non_coding_transcript_exon_variant,,ENST00000570802,;SLC12A4,non_coding_transcript_exon_variant,,ENST00000573023,;SLC12A4,intron_variant,,ENST00000576377,;SLC12A4,upstream_gene_variant,,ENST00000574665,;SLC12A4,downstream_gene_variant,,ENST00000576462,;SLC12A4,upstream_gene_variant,,ENST00000573702,;SLC12A4,upstream_gene_variant,,ENST00000572476,;SLC12A4,upstream_gene_variant,,ENST00000572766,;SLC12A4,upstream_gene_variant,,ENST00000576513,; G ENST00000422611 Transcript synonymous_variant 604/4670 564/3264 188/1087 Y taT/taC 1 -1 SLC12A4 HGNC HGNC:10913 protein_coding YES CCDS54032.1 ENSP00000395983 Q9UP95 UPI00019863A8 NM_001145962.1 5/23 Transmembrane_helices:TMhelix,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF46,Pfam_domain:PF00324,TIGRFAM_domain:TIGR00930 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 85 67954760 67954760 A G 1 0 0 0 0 0 0 0 1 14650 108 4 5 5 SLC12A4 16 67954760 Silent SNP A C3N-02000_T 67954760 22383585 20 26632 TP53 0 . GRCh38 17 7675075 7675075 + Missense_Mutation SNP A A C C3N-02000_T C3N-02000_N A A c.537T>G p.His179Gln p.H179Q ENST00000269305 5/11 189 123 66 392 392 0 strelka-varscan-mutect TP53,missense_variant,p.His179Gln,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.His179Gln,ENST00000420246,;TP53,missense_variant,p.His140Gln,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.His140Gln,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.His179Gln,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.His140Gln,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.His179Gln,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.His140Gln,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.His179Gln,ENST00000445888,;TP53,missense_variant,p.His140Gln,ENST00000619485,;TP53,missense_variant,p.His47Gln,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.His20Gln,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.His47Gln,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.His20Gln,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.His47Gln,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.His20Gln,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.His179Gln,ENST00000359597,;TP53,missense_variant,p.His168Gln,ENST00000615910,;TP53,missense_variant,p.His179Gln,ENST00000413465,;TP53,missense_variant,p.His47Gln,ENST00000509690,;TP53,missense_variant,p.His86Gln,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.His140Gln,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 727/2579 537/1182 179/393 H/Q caT/caG CM0910925,TP53_g.12525T>G,TP53_g.12525T>C,TP53_g.12525T>A,COSM11249,COSM1158094,COSM1158095,COSM1158096,COSM1158097,COSM1649385,COSM2744837,COSM307263,COSM307264,COSM307265,COSM307266,COSM3388355,COSM3820720,COSM44214,COSM44793 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 5/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs876660821 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 85 7675075 7675075 A C 1 0 0 0 0 1 0 0 0 16859 214 8 5 5 TP53 17 7675075 Missense_Mutation SNP A C3N-02000_T 7675075 75582366 21 26633 PCSK4 0 . GRCh38 19 1487264 1487264 + Silent SNP C C T rs536873237 C3N-02000_T C3N-02000_N C C c.732G>A p.= p.S244S ENST00000300954 7/15 111 105 6 132 132 0 strelka-varscan-mutect PCSK4,missense_variant,p.Ala215Thr,ENST00000588671,;PCSK4,synonymous_variant,p.=,ENST00000300954,NM_017573.4;REEP6,upstream_gene_variant,,ENST00000233596,NM_138393.1;PCSK4,non_coding_transcript_exon_variant,,ENST00000587784,;PCSK4,downstream_gene_variant,,ENST00000590057,;PCSK4,downstream_gene_variant,,ENST00000591687,;PCSK4,missense_variant,p.Ala212Thr,ENST00000591201,;PCSK4,non_coding_transcript_exon_variant,,ENST00000586616,;PCSK4,non_coding_transcript_exon_variant,,ENST00000441747,;PCSK4,non_coding_transcript_exon_variant,,ENST00000588195,;REEP6,upstream_gene_variant,,ENST00000591735,;PCSK4,downstream_gene_variant,,ENST00000614078,;PCSK4,upstream_gene_variant,,ENST00000586002,;PCSK4,upstream_gene_variant,,ENST00000586074,;PCSK4,upstream_gene_variant,,ENST00000591303,; T ENST00000300954 Transcript synonymous_variant 794/2661 732/2268 244/755 S tcG/tcA rs536873237,COSM4074873 1 -1 PCSK4 HGNC HGNC:8746 protein_coding YES CCDS12069.2 ENSP00000300954 Q6UW60 A0A140VJQ9 UPI000014E136 NM_017573.4 7/15 hmmpanther:PTHR10795,hmmpanther:PTHR10795:SF386,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743 0,1 LOW 1 SNV 1 0,1 1 PASS rs536873237 . 0 204 5 0 0 0 0 0 -12.1041 1 1 1 1 0 T 2 4 85 1487264 1487264 C T 1 0 0 0 0 0 0 0 1 11690 755 27 1 1 PCSK4 19 1487264 Silent SNP C C3N-02000_T 1487264 57130352 22 26634 MYT1 0 . GRCh38 20 64213581 64213581 + Missense_Mutation SNP A A T novel C3N-02000_T C3N-02000_N A A c.1565A>T p.His522Leu p.H522L ENST00000328439 10/23 237 214 23 253 253 0 strelka-varscan-mutect MYT1,missense_variant,p.His522Leu,ENST00000536311,;MYT1,missense_variant,p.His522Leu,ENST00000328439,NM_004535.2;MYT1,missense_variant,p.His224Leu,ENST00000622439,;MYT1,missense_variant,p.His224Leu,ENST00000360149,; T ENST00000328439 Transcript missense_variant 1929/5535 1565/3366 522/1121 H/L cAt/cTt 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 deleterious(0.01) 10/23 hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 85 64213581 64213581 A T 1 0 0 0 0 1 0 0 0 10105 217 8 4 4 MYT1 20 64213581 Missense_Mutation SNP A C3N-02000_T 64213581 230586 23 26635 MAGEB6 0 . GRCh38 X 26195025 26195025 + Silent SNP C C T rs759811799 C3N-02000_T C3N-02000_N C C c.1179C>T p.= p.D393D ENST00000379034 2/2 110 95 15 147 147 0 strelka-varscan-mutect MAGEB6,synonymous_variant,p.=,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript synonymous_variant 1328/1949 1179/1224 393/407 D gaC/gaT rs759811799 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736 LOW 1 SNV 1 1 PASS rs759811799 . 0 203 7 0 0 0 0 0 -20 0.9999995 1 1 1 0 T 2 4 85 26195025 26195025 C T 1 0 0 0 0 0 0 0 1 9096 535 19 1 1 MAGEB6 23 26195025 Silent SNP C C3N-02000_T 26195025 129845870 24 26636 CSMD2 0 . GRCh38 1 33580818 33580818 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.7322C>T p.Ser2441Phe p.S2441F ENST00000373381 48/71 285 267 18 330 330 0 strelka-varscan-mutect CSMD2,missense_variant,p.Ser2441Phe,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Ser2401Phe,ENST00000619121,;CSMD2,missense_variant,p.Ser2443Phe,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Ser2443Phe,ENST00000241312,; A ENST00000373381 Transcript missense_variant 7499/13698 7322/10896 2441/3631 S/F tCt/tTt 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 tolerated(0.1) 48/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS rs1464400124 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 33580818 33580818 G A 1 0 0 0 0 1 0 0 0 3746 942 33 3 3 CSMD2 1 33580818 Missense_Mutation SNP G C3N-02002_T 33580818 215375604 1 26637 RGS4 0 . GRCh38 1 163073466 163073466 + Silent SNP A A G novel C3N-02002_T C3N-02002_N A A c.513A>G p.= p.A171A ENST00000421743 5/6 68 48 20 79 79 0 strelka-varscan-mutect RGS4,synonymous_variant,p.=,ENST00000421743,NM_001102445.2;RGS4,synonymous_variant,p.=,ENST00000367909,NM_005613.5;RGS4,synonymous_variant,p.=,ENST00000367906,NM_001113380.1;RGS4,synonymous_variant,p.=,ENST00000527809,;RGS4,synonymous_variant,p.=,ENST00000528938,;RGS4,synonymous_variant,p.=,ENST00000531057,;RGS4,intron_variant,,ENST00000367908,NM_001113381.1;RGS4,non_coding_transcript_exon_variant,,ENST00000491263,;RGS4,non_coding_transcript_exon_variant,,ENST00000527393,;RGS4,non_coding_transcript_exon_variant,,ENST00000533019,; G ENST00000421743 Transcript synonymous_variant 673/3311 513/909 171/302 A gcA/gcG 1 1 RGS4 HGNC HGNC:10000 protein_coding YES CCDS44270.1 ENSP00000397181 P49798 UPI0000E1EDBA NM_001102445.2 5/6 PROSITE_profiles:PS50132,hmmpanther:PTHR10845:SF184,hmmpanther:PTHR10845,Gene3D:1.10.196.10,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097,Prints_domain:PR01301 LOW 1 SNV 1 1 PASS rs1440969332 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 86 163073466 163073466 A G 1 0 0 0 0 0 0 0 1 13478 175 7 5 5 RGS4 1 163073466 Silent SNP A C3N-02002_T 129492648 163073466 85882956 2 26638 RNPEP 0 . GRCh38 1 201983038 201983038 + Silent SNP G G A novel C3N-02002_T C3N-02002_N G G c.372G>A p.= p.V124V ENST00000295640 1/11 162 152 10 171 171 0 strelka-varscan RNPEP,synonymous_variant,p.=,ENST00000295640,NM_020216.3;RNPEP,synonymous_variant,p.=,ENST00000367286,;RNPEP,upstream_gene_variant,,ENST00000447312,;SNORA70,downstream_gene_variant,,ENST00000383910,;RNPEP,non_coding_transcript_exon_variant,,ENST00000471105,;RNPEP,intron_variant,,ENST00000481780,;RNPEP,upstream_gene_variant,,ENST00000478617,;RNPEP,upstream_gene_variant,,ENST00000492849,;RNPEP,upstream_gene_variant,,ENST00000479726,;RNPEP,upstream_gene_variant,,ENST00000620670,;RNPEP,synonymous_variant,p.=,ENST00000487116,;RNPEP,synonymous_variant,p.=,ENST00000492587,;RP11-465N4.2,downstream_gene_variant,,ENST00000412093,; A ENST00000295640 Transcript synonymous_variant 415/2427 372/1953 124/650 V gtG/gtA 1 1 RNPEP HGNC HGNC:10078 protein_coding YES CCDS1418.1 ENSP00000295640 Q9H4A4 UPI00000463FA NM_020216.3 1/11 hmmpanther:PTHR11533:SF153,hmmpanther:PTHR11533,Pfam_domain:PF01433,Superfamily_domains:0038696 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.37126 0.9999996 1 1 1 0 A 2 1 86 201983038 201983038 G A 1 0 0 0 0 0 0 0 1 13688 1364 48 3 3 RNPEP 1 201983038 Silent SNP G C3N-02002_T 38909572 201983038 46973384 3 26639 GALNT5 0 . GRCh38 2 157258143 157258143 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.61G>A p.Ala21Thr p.A21T ENST00000259056 1/10 323 263 60 464 464 0 strelka-varscan GALNT5,missense_variant,p.Ala21Thr,ENST00000259056,NM_014568.1; A ENST00000259056 Transcript missense_variant 546/6171 61/2823 21/940 A/T Gct/Act 1 1 GALNT5 HGNC HGNC:4127 protein_coding YES CCDS2203.1 ENSP00000259056 Q7Z7M9 UPI000019AD19 NM_014568.1 deleterious(0.02) 1/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11675:SF16,hmmpanther:PTHR11675 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 157258143 157258143 G A 1 0 0 0 0 1 0 0 0 6087 971 34 3 3 GALNT5 2 157258143 Missense_Mutation SNP G C3N-02002_T 157258143 84935386 4 26640 1 21 2 2 31 G 4.371287e-05 GALNT5 0 . GRCh38 2 157258173 157258173 + Missense_Mutation SNP G G A rs761997163 C3N-02002_T C3N-02002_N G G c.91G>A p.Ala31Thr p.A31T ENST00000259056 1/10 234 188 46 344 344 0 strelka-varscan GALNT5,missense_variant,p.Ala31Thr,ENST00000259056,NM_014568.1; A ENST00000259056 Transcript missense_variant 576/6171 91/2823 31/940 A/T Gca/Aca rs761997163 1 1 GALNT5 HGNC HGNC:4127 protein_coding YES CCDS2203.1 ENSP00000259056 Q7Z7M9 UPI000019AD19 NM_014568.1 deleterious(0) 1/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR11675:SF16,hmmpanther:PTHR11675 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 157258173 157258173 G A 1 0 0 0 0 1 0 0 0 6087 1203 42 3 3 GALNT5 2 157258173 Missense_Mutation SNP G C3N-02002_T 30 157258173 84935356 5 26641 1 21 2 2 31 G 4.371287e-05 COPS8 0 . GRCh38 2 237089993 237089993 + Missense_Mutation SNP A A C novel C3N-02002_T C3N-02002_N A A c.330A>C p.Arg110Ser p.R110S ENST00000354371 4/8 101 89 12 176 176 0 strelka-varscan-mutect COPS8,missense_variant,p.Arg110Ser,ENST00000354371,NM_006710.4;COPS8,missense_variant,p.Arg61Ser,ENST00000392008,NM_198189.2;COPS8,missense_variant,p.Arg110Ser,ENST00000409334,;AC105760.2,upstream_gene_variant,,ENST00000418430,;COPS8,splice_region_variant,,ENST00000470452,;COPS8,splice_region_variant,,ENST00000419015,;COPS8,upstream_gene_variant,,ENST00000447464,; C ENST00000354371 Transcript missense_variant,splice_region_variant 983/4007 330/630 110/209 R/S agA/agC 1 1 COPS8 HGNC HGNC:24335 protein_coding YES CCDS2517.1 ENSP00000346340 Q99627 A0A024R4D1 UPI000006CD9B NM_006710.4 tolerated(0.19) 4/8 hmmpanther:PTHR13339,hmmpanther:PTHR13339:SF0,Pfam_domain:PF10075 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 86 237089993 237089993 A C 1 0 0 0 0 1 0 0 0 3533 318 11 5 5 COPS8 2 237089993 Missense_Mutation SNP A C3N-02002_T 79831820 237089993 5103536 6 26642 ALDH1L1 0 . GRCh38 3 126146833 126146833 + Splice_Site SNP A A C novel C3N-02002_T C3N-02002_N A A c.1106+2T>G p.X369_splice ENST00000273450 126 102 24 171 170 1 strelka-varscan-mutect ALDH1L1,splice_donor_variant,,ENST00000393434,NM_012190.3;ALDH1L1,splice_donor_variant,,ENST00000273450,NM_001270364.1;ALDH1L1,splice_donor_variant,,ENST00000472186,;ALDH1L1,splice_donor_variant,,ENST00000455064,;ALDH1L1,splice_donor_variant,,ENST00000393431,;ALDH1L1,splice_donor_variant,,ENST00000452905,NM_001270365.1;ALDH1L1,downstream_gene_variant,,ENST00000413612,;ALDH1L1,splice_donor_variant,,ENST00000476245,;ALDH1L1,splice_donor_variant,,ENST00000473607,;ALDH1L1,downstream_gene_variant,,ENST00000484724,; C ENST00000273450 Transcript splice_donor_variant -/3179 1106/2739 369/912 1 -1 ALDH1L1 HGNC HGNC:3978 protein_coding YES CCDS58851.1 ENSP00000273450 O75891 UPI0000425C57 NM_001270364.1 9/22 HIGH 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999988 1 1 1 0 C 5 2 86 126146833 126146833 A C 1 0 0 0 0 0 0 1 0 594 405 14 5 5 ALDH1L1 3 126146833 Splice_Site SNP A C3N-02002_T 126146833 72148726 7 26643 SAMD7 0 . GRCh38 3 169938493 169938493 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.1328G>A p.Ser443Asn p.S443N ENST00000428432 9/9 72 68 4 115 114 1 strelka-mutect SAMD7,missense_variant,p.Ser443Asn,ENST00000428432,NM_182610.3;SAMD7,missense_variant,p.Ser443Asn,ENST00000335556,NM_001304366.1;RP11-379K17.4,downstream_gene_variant,,ENST00000483289,;RP11-379K17.4,downstream_gene_variant,,ENST00000487580,;SAMD7,3_prime_UTR_variant,,ENST00000487910,; A ENST00000428432 Transcript missense_variant 1717/2399 1328/1341 443/446 S/N aGt/aAt 1 1 SAMD7 HGNC HGNC:25394 protein_coding YES CCDS3209.1 ENSP00000391299 Q7Z3H4 UPI00001A9D13 NM_182610.3 tolerated(0.39) 9/9 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -9.47117 1 1 1 1 0 A 3 1 86 169938493 169938493 G A 1 0 0 0 0 1 0 0 0 14084 1029 36 3 3 SAMD7 3 169938493 Missense_Mutation SNP G C3N-02002_T 43791660 169938493 28357066 8 26644 SCD5 0 . GRCh38 4 82636669 82636669 + Missense_Mutation SNP C C G rs762692893 C3N-02002_T C3N-02002_N C C c.724G>C p.Ala242Pro p.A242P ENST00000319540 4/5 271 224 47 338 338 0 strelka-varscan-mutect SCD5,missense_variant,p.Ala242Pro,ENST00000319540,NM_001037582.2; G ENST00000319540 Transcript missense_variant 1044/3101 724/993 242/330 A/P Gcc/Ccc rs762692893,COSM4644622 1 -1 SCD5 HGNC HGNC:21088 protein_coding YES CCDS34024.1 ENSP00000316329 Q86SK9 UPI000003F556 NM_001037582.2 deleterious(0) 4/5 Pfam_domain:PF00487,Prints_domain:PR00075,hmmpanther:PTHR11351,hmmpanther:PTHR11351:SF32 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762692893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 82636669 82636669 C G 1 0 0 0 0 1 0 0 0 14153 768 27 4 4 SCD5 4 82636669 Missense_Mutation SNP C C3N-02002_T 82636669 107577886 9 26645 PTPN13 0 . GRCh38 4 86750850 86750850 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.3031G>A p.Asp1011Asn p.D1011N ENST00000436978 18/48 127 84 43 130 130 0 strelka-varscan-mutect PTPN13,missense_variant,p.Asp1011Asn,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Asp1011Asn,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Asp1011Asn,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Asp1011Asn,ENST00000511467,;PTPN13,intron_variant,,ENST00000316707,NM_080684.2; A ENST00000436978 Transcript missense_variant 3511/8573 3031/7473 1011/2490 D/N Gat/Aat 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0.02) 18/48 PIRSF_domain:PIRSF000933 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 86750850 86750850 G A 1 0 0 0 0 1 0 0 0 12935 1290 45 3 3 PTPN13 4 86750850 Missense_Mutation SNP G C3N-02002_T 4114181 86750850 103463705 10 26646 CDH6 0 . GRCh38 5 31299568 31299568 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.748G>A p.Gly250Arg p.G250R ENST00000265071 5/12 228 191 37 240 239 1 strelka-varscan-mutect CDH6,missense_variant,p.Gly250Arg,ENST00000265071,NM_004932.3;CDH6,missense_variant,p.Gly195Arg,ENST00000514738,;CDH6,non_coding_transcript_exon_variant,,ENST00000508132,; A ENST00000265071 Transcript missense_variant 1013/8476 748/2373 250/790 G/R Ggg/Agg 1 1 CDH6 HGNC HGNC:1765 protein_coding YES CCDS3894.1 ENSP00000265071 P55285 UPI0000126D9B NM_004932.3 deleterious(0) 5/12 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF322,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 31299568 31299568 G A 1 0 0 0 0 1 0 0 0 2817 1348 47 3 3 CDH6 5 31299568 Missense_Mutation SNP G C3N-02002_T 31299568 150238691 11 26647 PAPD4 0 . GRCh38 5 79619704 79619704 + Missense_Mutation SNP A A C rs754089479 C3N-02002_T C3N-02002_N A A c.56A>C p.His19Pro p.H19P ENST00000453514 2/15 149 92 57 216 216 0 strelka-varscan-mutect PAPD4,missense_variant,p.His19Pro,ENST00000453514,NM_001114394.1,NM_001114393.1,NM_173797.3;PAPD4,missense_variant,p.His19Pro,ENST00000423041,NM_001297744.1;PAPD4,missense_variant,p.His19Pro,ENST00000296783,;PAPD4,missense_variant,p.His19Pro,ENST00000504233,NM_001297745.1;PAPD4,missense_variant,p.His19Pro,ENST00000428308,;PAPD4,non_coding_transcript_exon_variant,,ENST00000503620,;PAPD4,non_coding_transcript_exon_variant,,ENST00000515807,;PAPD4,non_coding_transcript_exon_variant,,ENST00000514095,;PAPD4,non_coding_transcript_exon_variant,,ENST00000508620,;PAPD4,non_coding_transcript_exon_variant,,ENST00000505571,; C ENST00000453514 Transcript missense_variant 749/3523 56/1455 19/484 H/P cAt/cCt rs754089479 1 1 PAPD4 HGNC HGNC:26776 protein_coding YES CCDS4048.1 ENSP00000397563 Q6PIY7 UPI000013E386 NM_001114394.1,NM_001114393.1,NM_173797.3 tolerated_low_confidence(0.23) 2/15 hmmpanther:PTHR12271 MODERATE 1 SNV 5 1 PASS rs754089479 . 0 207 0 3 0 0 0 0 -20 0.999999 1 1 1 0 C 3 2 86 79619704 79619704 A C 1 0 0 0 0 1 0 0 0 11505 217 8 5 5 PAPD4 5 79619704 Missense_Mutation SNP A C3N-02002_T 48320136 79619704 101918555 12 26648 SPZ1 0 . GRCh38 5 80321038 80321038 + Missense_Mutation SNP C C A novel C3N-02002_T C3N-02002_N C C c.823C>A p.Gln275Lys p.Q275K ENST00000296739 1/1 165 155 10 204 204 0 strelka-varscan-mutect SPZ1,missense_variant,p.Gln275Lys,ENST00000296739,NM_032567.3;SPZ1,downstream_gene_variant,,ENST00000511881,; A ENST00000296739 Transcript missense_variant 1064/1868 823/1293 275/430 Q/K Cag/Aag 1 1 SPZ1 HGNC HGNC:30721 protein_coding YES CCDS43336.1 ENSP00000369611 Q9BXG8 A0A140VKA5 UPI000020CBA6 NM_032567.3 deleterious(0.02) 1/1 hmmpanther:PTHR23158:SF40,hmmpanther:PTHR23158 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 80321038 80321038 C A 1 0 0 0 0 1 0 0 0 15486 827 29 2 2 SPZ1 5 80321038 Missense_Mutation SNP C C3N-02002_T 701334 80321038 101217221 13 26649 VCAN 0 . GRCh38 5 83540301 83540301 + Missense_Mutation SNP C C A rs764887873 C3N-02002_T C3N-02002_N C C c.7298C>A p.Ser2433Tyr p.S2433Y ENST00000265077 8/15 494 465 29 554 554 0 strelka-varscan-mutect VCAN,missense_variant,p.Ser2433Tyr,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Ser1446Tyr,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 7863/12625 7298/10191 2433/3396 S/Y tCt/tAt rs764887873 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 deleterious(0) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS rs764887873 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 83540301 83540301 C A 1 0 0 0 0 1 0 0 0 17683 913 32 2 2 VCAN 5 83540301 Missense_Mutation SNP C C3N-02002_T 3219263 83540301 97997958 14 26650 UQCRQ 0 . GRCh38 5 132867516 132867520 + Frame_Shift_Del DEL ATGGG ATGGG - novel C3N-02002_T C3N-02002_N ATGGG ATGGG c.183_187delATGGG p.Trp62AspfsTer2 p.W62Dfs*2 ENST00000378670 3/3 306 274 32 405 405 0 sindel-varindel UQCRQ,frameshift_variant,p.Trp62AspfsTer2,ENST00000378670,;UQCRQ,frameshift_variant,p.Trp62AspfsTer2,ENST00000378665,;UQCRQ,frameshift_variant,p.Trp62AspfsTer2,ENST00000378667,NM_014402.4;GDF9,upstream_gene_variant,,ENST00000378673,NM_005260.4;LEAP2,upstream_gene_variant,,ENST00000296877,NM_052971.2;GDF9,upstream_gene_variant,,ENST00000621295,NM_001288825.2;GDF9,upstream_gene_variant,,ENST00000624492,NM_001288824.2;GDF9,upstream_gene_variant,,ENST00000624495,NM_001288828.2,NM_001288826.2;GDF9,upstream_gene_variant,,ENST00000296875,NM_001288827.2;UQCRQ,non_coding_transcript_exon_variant,,ENST00000496429,;GDF9,upstream_gene_variant,,ENST00000464378,;GDF9,upstream_gene_variant,,ENST00000472320,;UQCRQ,non_coding_transcript_exon_variant,,ENST00000498309,;UQCRQ,downstream_gene_variant,,ENST00000480372,; - ENST00000378670 Transcript frameshift_variant 324-328/839 183-187/249 61-63/82 TWG/TX acATGGGgg/acgg 1 1 UQCRQ HGNC HGNC:29594 protein_coding YES CCDS34237.1 ENSP00000367939 O14949 UPI000015D476 3/3 hmmpanther:PTHR12119,hmmpanther:PTHR12119:SF3,Pfam_domain:PF02939,Gene3D:1.20.5.210,Superfamily_domains:SSF81508,PD331499 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 86 132867516 132867516 ATGGG - 1 0 1 0 1 0 0 0 0 17552 204 8 0 0 UQCRQ 5 132867516 Frame_Shift_Del DEL ATGGG C3N-02002_T 49327215 132867516 48670743 15 26651 PCDHA12 0 . GRCh38 5 140875559 140875559 + Silent SNP C C A novel C3N-02002_T C3N-02002_N C C c.87C>A p.= p.G29G ENST00000398631 1/4 266 168 98 377 376 1 strelka-varscan-mutect PCDHA12,synonymous_variant,p.=,ENST00000398631,NM_018903.3;PCDHA12,synonymous_variant,p.=,ENST00000613593,NM_031864.2;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,;PCDHA11,downstream_gene_variant,,ENST00000616325,NM_031861.2;AC005609.18,non_coding_transcript_exon_variant,,ENST00000624566,;AC005609.17,downstream_gene_variant,,ENST00000625195,; A ENST00000398631 Transcript synonymous_variant 87/5233 87/2826 29/941 G ggC/ggA 1 1 PCDHA12 HGNC HGNC:8666 protein_coding YES CCDS47285.1 ENSP00000381628 Q9UN75 UPI00001273D5 NM_018903.3 1/4 Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF76,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 86 140875559 140875559 C A 1 0 0 0 0 0 0 0 1 11609 726 26 2 2 PCDHA12 5 140875559 Silent SNP C C3N-02002_T 8008043 140875559 40662700 16 26652 ZNF300 0 . GRCh38 5 150895563 150895563 + Missense_Mutation SNP G G C novel C3N-02002_T C3N-02002_N G G c.1724C>G p.Ser575Cys p.S575C ENST00000446148 7/7 113 78 35 158 158 0 strelka-varscan-mutect ZNF300,missense_variant,p.Ser575Cys,ENST00000446148,NM_001172831.1;ZNF300,missense_variant,p.Ser559Cys,ENST00000274599,NM_052860.2;ZNF300,missense_variant,p.Ser559Cys,ENST00000394226,;ZNF300,missense_variant,p.Ser523Cys,ENST00000418587,NM_001172832.1;ZNF300,3_prime_UTR_variant,,ENST00000427179,;IRGM,intron_variant,,ENST00000520549,; C ENST00000446148 Transcript missense_variant 2152/3323 1724/1863 575/620 S/C tCt/tGt 1 -1 ZNF300 HGNC HGNC:13091 protein_coding YES CCDS54940.1 ENSP00000397178 Q96RE9 UPI0001AE74AD NM_001172831.1 tolerated(0.08) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF320,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF00096,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 86 150895563 150895563 G C 1 0 0 0 0 1 0 0 0 18406 942 33 4 4 ZNF300 5 150895563 Missense_Mutation SNP G C3N-02002_T 10020004 150895563 30642696 17 26653 LRRC16A 0 . GRCh38 6 25581348 25581349 + Frame_Shift_Ins INS - - T novel C3N-02002_T C3N-02002_N - - c.2916dupT p.Glu973Ter p.E973* ENST00000329474 31/37 179 168 11 250 249 1 varindel-pindel LRRC16A,frameshift_variant,p.Glu973Ter,ENST00000329474,NM_001173977.1,NM_017640.5;LRRC16A,frameshift_variant,p.Glu573Ter,ENST00000635618,; T ENST00000329474 Transcript frameshift_variant 3283-3284/5431 2915-2916/4116 972/1371 S/SX tct/tcTt 1 1 LRRC16A HGNC HGNC:21581 protein_coding YES CCDS54973.1 ENSP00000331983 Q5VZK9 UPI00004588AB NM_001173977.1,NM_017640.5 31/37 Pfam_domain:PF16000,hmmpanther:PTHR24112,hmmpanther:PTHR24112:SF39 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 86 25581348 25581348 - T 1 0 1 1 0 0 0 0 0 8867 913 32 0 0 LRRC16A 6 25581348 Frame_Shift_Ins INS - C3N-02002_T 25581348 145224631 18 26654 NOTCH4 0 . GRCh38 6 32196930 32196930 + Missense_Mutation SNP T T G novel C3N-02002_T C3N-02002_N T T c.5195A>C p.Lys1732Thr p.K1732T ENST00000375023 28/30 108 92 16 159 159 0 strelka-varscan NOTCH4,missense_variant,p.Lys1732Thr,ENST00000375023,NM_004557.3;GPSM3,upstream_gene_variant,,ENST00000375040,NM_001276501.1;GPSM3,upstream_gene_variant,,ENST00000487761,;GPSM3,upstream_gene_variant,,ENST00000375043,NM_022107.1;GPSM3,upstream_gene_variant,,ENST00000619085,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000474612,;NOTCH4,non_coding_transcript_exon_variant,,ENST00000491215,;GPSM3,upstream_gene_variant,,ENST00000472768,; G ENST00000375023 Transcript missense_variant 5334/6745 5195/6012 1732/2003 K/T aAa/aCa 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 deleterious(0.01) 28/30 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF64,Gene3D:1.25.40.20,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 32196930 32196930 T G 1 0 0 0 0 1 0 0 0 10596 1855 64 5 5 NOTCH4 6 32196930 Missense_Mutation SNP T C3N-02002_T 6615582 32196930 138609049 19 26655 TFAP2D 0 . GRCh38 6 50751296 50751296 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.1111G>A p.Asp371Asn p.D371N ENST00000008391 7/8 195 177 18 259 259 0 strelka-varscan-mutect TFAP2D,missense_variant,p.Asp371Asn,ENST00000008391,NM_172238.3;TFAP2D,downstream_gene_variant,,ENST00000492804,; A ENST00000008391 Transcript missense_variant 1339/1711 1111/1359 371/452 D/N Gac/Aac 1 1 TFAP2D HGNC HGNC:15581 protein_coding YES CCDS4933.1 ENSP00000008391 Q7Z6R9 UPI00001A3A89 NM_172238.3 tolerated(0.2) 7/8 hmmpanther:PTHR10812:SF5,hmmpanther:PTHR10812,Pfam_domain:PF03299 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 50751296 50751296 G A 1 0 0 0 0 1 0 0 0 16223 1290 45 3 3 TFAP2D 6 50751296 Missense_Mutation SNP G C3N-02002_T 18554366 50751296 120054683 20 26656 MAP3K7 0 . GRCh38 6 90516551 90516552 + Frame_Shift_Ins INS - - T novel C3N-02002_T C3N-02002_N - - c.1770dupA p.Gln591ThrfsTer41 p.Q591Tfs*41 ENST00000369329 17/17 228 168 60 340 339 1 sindel-varindel-pindel MAP3K7,frameshift_variant,p.Gln591ThrfsTer41,ENST00000369329,NM_145331.2;MAP3K7,frameshift_variant,p.Gln564ThrfsTer41,ENST00000369332,NM_003188.3;MAP3K7,frameshift_variant,p.Gln245ThrfsTer41,ENST00000369320,;MAP3K7,3_prime_UTR_variant,,ENST00000369325,NM_145332.2;MAP3K7,3_prime_UTR_variant,,ENST00000369327,NM_145333.2;MAP3K7,non_coding_transcript_exon_variant,,ENST00000479630,; T ENST00000369329 Transcript frameshift_variant 1932-1933/4911 1770-1771/1821 590-591/606 -/X -/A 1 -1 MAP3K7 HGNC HGNC:6859 protein_coding YES CCDS5028.1 ENSP00000358335 O43318 UPI000012EAD6 NM_145331.2 17/17 PIRSF_domain:PIRSF038168 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 86 90516551 90516551 - T 1 0 1 1 0 0 0 0 0 9178 1386 48 0 0 MAP3K7 6 90516551 Frame_Shift_Ins INS - C3N-02002_T 39765255 90516551 80289428 21 26657 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02002_T C3N-02002_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 463 312 151 545 545 0 strelka-varscan EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02002_T 55191822 104154151 22 26658 ZNF92 0 . GRCh38 7 65398599 65398600 + Frame_Shift_Ins INS - - A novel C3N-02002_T C3N-02002_N - - c.488dupA p.Asn163LysfsTer2 p.N163Kfs*2 ENST00000328747 4/4 38 23 15 118 118 0 sindel-varindel-pindel ZNF92,frameshift_variant,p.Asn163LysfsTer2,ENST00000328747,NM_152626.3;ZNF92,frameshift_variant,p.Asn131LysfsTer2,ENST00000357512,NM_001287532.1;ZNF92,frameshift_variant,p.Asn94LysfsTer2,ENST00000450302,NM_007139.3;ZNF92,frameshift_variant,p.Asn87LysfsTer2,ENST00000431504,NM_001287534.1,NM_001287533.1; A ENST00000328747 Transcript frameshift_variant 684-685/3210 485-486/1761 162/586 R/RX aga/agAa 1 1 ZNF92 HGNC HGNC:13168 protein_coding YES CCDS34646.1 ENSP00000332595 Q03936 V9HVY7 UPI0000073CE6 NM_152626.3 4/4 Gene3D:3.30.160.60,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF125,Superfamily_domains:SSF57667 HIGH 1 insertion 1 3 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 86 65398599 65398599 - A 1 0 1 1 0 0 0 0 0 18794 942 33 0 0 ZNF92 7 65398599 Frame_Shift_Ins INS - C3N-02002_T 10206777 65398599 93947374 23 26659 OPLAH 0 . GRCh38 8 144054885 144054885 + Frame_Shift_Del DEL G G - novel C3N-02002_T C3N-02002_N G G c.2438delC p.Pro813LeufsTer6 p.P813Lfs*6 ENST00000618853 18/27 91 60 31 120 120 0 sindel-varindel-pindel OPLAH,frameshift_variant,p.Pro813LeufsTer6,ENST00000618853,NM_017570.4;OPLAH,downstream_gene_variant,,ENST00000567871,;MIR6846,downstream_gene_variant,,ENST00000613469,;SMPD5,downstream_gene_variant,,ENST00000528912,;SMPD5,downstream_gene_variant,,ENST00000561181,;OPLAH,upstream_gene_variant,,ENST00000527993,;OPLAH,upstream_gene_variant,,ENST00000531027,; - ENST00000618853 Transcript frameshift_variant 2542/4031 2438/3867 813/1288 P/X cCt/ct 1 -1 OPLAH HGNC HGNC:8149 protein_coding YES CCDS75802.1 ENSP00000480476 O14841 UPI000035154E NM_017570.4 18/27 Pfam_domain:PF02538,hmmpanther:PTHR11365,hmmpanther:PTHR11365:SF2 HIGH 1 deletion 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999966 1 1 1 0 - 7 5 86 144054885 144054885 G - 1 0 1 0 1 0 0 0 0 10953 1000 35 0 0 OPLAH 8 144054885 Frame_Shift_Del DEL G C3N-02002_T 144054885 1083751 24 26660 KIAA1161 0 . GRCh38 9 34372393 34372393 + Missense_Mutation SNP T T G novel C3N-02002_T C3N-02002_N T T c.551A>C p.His184Pro p.H184P ENST00000297625 2/2 124 104 20 116 115 1 strelka-varscan-mutect KIAA1161,missense_variant,p.His184Pro,ENST00000297625,NM_020702.4;KIAA1161,intron_variant,,ENST00000379142,; G ENST00000297625 Transcript missense_variant 675/6398 551/2145 184/714 H/P cAc/cCc 1 -1 KIAA1161 HGNC HGNC:19918 protein_coding YES CCDS78391.1 ENSP00000297625 Q6NSJ0 UPI0001588862 NM_020702.4 deleterious(0) 2/2 hmmpanther:PTHR22762:SF70,hmmpanther:PTHR22762 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 34372393 34372393 T G 1 0 0 0 0 1 0 0 0 8104 1696 59 5 5 KIAA1161 9 34372393 Missense_Mutation SNP T C3N-02002_T 34372393 104022324 25 26661 GOLGA1 0 . GRCh38 9 124888389 124888389 + Missense_Mutation SNP G G C rs757022400 C3N-02002_T C3N-02002_N G G c.1769C>G p.Ser590Trp p.S590W ENST00000373555 19/23 120 113 7 176 176 0 strelka-varscan-mutect GOLGA1,missense_variant,p.Ser590Trp,ENST00000373555,NM_002077.3;RNU4-82P,upstream_gene_variant,,ENST00000362443,;GOLGA1,3_prime_UTR_variant,,ENST00000475407,;GOLGA1,downstream_gene_variant,,ENST00000485337,; C ENST00000373555 Transcript missense_variant 2103/4811 1769/2304 590/767 S/W tCg/tGg rs757022400 1 -1 GOLGA1 HGNC HGNC:4424 protein_coding YES CCDS6860.1 ENSP00000362656 Q92805 UPI000013D059 NM_002077.3 deleterious(0.02) 19/23 hmmpanther:PTHR23157:SF24,hmmpanther:PTHR23157 MODERATE 1 SNV 1 1 PASS rs757022400 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 86 124888389 124888389 G C 1 0 0 0 0 1 0 0 0 6430 1059 37 4 4 GOLGA1 9 124888389 Missense_Mutation SNP G C3N-02002_T 90515996 124888389 13506328 26 26662 SEC16A 0 . GRCh38 9 136443871 136443872 + Frame_Shift_Ins INS - - C novel C3N-02002_T C3N-02002_N - - c.6956dupG p.Pro2321SerfsTer75 p.P2321Sfs*75 ENST00000313050 29/30 177 150 27 180 180 0 sindel-varindel-pindel SEC16A,frameshift_variant,p.Pro2298SerfsTer75,ENST00000290037,NM_001276418.1;SEC16A,frameshift_variant,p.Pro2321SerfsTer75,ENST00000313050,NM_014866.1;SEC16A,frameshift_variant,p.Pro2098SerfsTer75,ENST00000371706,;SEC16A,frameshift_variant,p.Pro2118SerfsTer?,ENST00000431893,;SEC16A,frameshift_variant,p.Pro1023SerfsTer75,ENST00000453963,;SEC16A,frameshift_variant,p.Pro715SerfsTer75,ENST00000277537,;SEC16A,frameshift_variant,p.Pro349SerfsTer75,ENST00000313084,;INPP5E,upstream_gene_variant,,ENST00000371712,NM_001318502.1,NM_019892.4;SEC16A,non_coding_transcript_exon_variant,,ENST00000467838,;INPP5E,upstream_gene_variant,,ENST00000635815,; C ENST00000313050 Transcript frameshift_variant 7030-7031/8806 6956-6957/7074 2319/2357 G/GX ggc/ggGc 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 29/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13,Low_complexity_(Seg):seg HIGH 1 insertion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999939 1 1 1 0 C 7 5 86 136443871 136443871 - C 1 0 1 1 0 0 0 0 0 14263 1190 42 0 0 SEC16A 9 136443871 Frame_Shift_Ins INS - C3N-02002_T 11555482 136443871 1950846 27 26663 PRRG4 0 . GRCh38 11 32836768 32836768 + Missense_Mutation SNP G G A novel C3N-02002_T C3N-02002_N G G c.214G>A p.Glu72Lys p.E72K ENST00000257836 3/6 170 126 44 228 228 0 strelka-varscan-mutect PRRG4,missense_variant,p.Glu72Lys,ENST00000257836,NM_024081.5; A ENST00000257836 Transcript missense_variant 467/5530 214/681 72/226 E/K Gaa/Aaa 1 1 PRRG4 HGNC HGNC:30799 protein_coding YES CCDS7881.1 ENSP00000257836 Q9BZD6 A0A0S2Z5N9 UPI000013707A NM_024081.5 deleterious(0) 3/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50998,hmmpanther:PTHR24251:SF15,hmmpanther:PTHR24251,PROSITE_patterns:PS00011,Gene3D:4.10.740.10,Pfam_domain:PF00594,SMART_domains:SM00069,Superfamily_domains:SSF57630,Prints_domain:PR00001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 32836768 32836768 G A 1 0 0 0 0 1 0 0 0 12754 943 33 3 3 PRRG4 11 32836768 Missense_Mutation SNP G C3N-02002_T 32836768 102249854 28 26664 OR5AK2 0 . GRCh38 11 56989126 56989126 + Silent SNP C C A C3N-02002_T C3N-02002_N C C c.213C>A p.= p.I71I ENST00000326855 1/1 97 86 11 168 168 0 strelka-varscan-mutect OR5AK2,synonymous_variant,p.=,ENST00000326855,NM_001005323.1; A ENST00000326855 Transcript synonymous_variant 255/996 213/930 71/309 I atC/atA COSM3449593 1 1 OR5AK2 HGNC HGNC:15251 protein_coding YES CCDS31538.1 ENSP00000322784 Q8NH90 A0A126GW20 UPI0000041D03 NM_001005323.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF47,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 86 56989126 56989126 C A 1 0 0 0 0 0 0 0 1 11214 903 32 2 2 OR5AK2 11 56989126 Silent SNP C C3N-02002_T 24152358 56989126 78097496 29 26665 CD163L1 0 . GRCh38 12 7403685 7403685 + Missense_Mutation SNP G G A rs779416105 C3N-02002_T C3N-02002_N G G c.1288C>T p.Arg430Cys p.R430C ENST00000416109 6/20 247 219 28 452 452 0 strelka-varscan-mutect CD163L1,missense_variant,p.Arg420Cys,ENST00000313599,NM_174941.5;CD163L1,missense_variant,p.Arg430Cys,ENST00000416109,NM_001297650.1;CD163L1,missense_variant,p.Arg66Cys,ENST00000545926,; A ENST00000416109 Transcript missense_variant 1307/4603 1288/4392 430/1463 R/C Cgt/Tgt rs779416105,COSM4462727 1 -1 CD163L1 HGNC HGNC:30375 protein_coding YES CCDS73434.1 ENSP00000393474 Q9NR16 UPI0001AE6A76 NM_001297650.1 tolerated(0.06) 6/20 PROSITE_profiles:PS50287,Gene3D:3.10.250.10,Pfam_domain:PF00530,SMART_domains:SM00202,Superfamily_domains:SSF56487 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs779416105 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 7403685 7403685 G A 1 0 0 0 0 1 0 0 0 2671 1058 37 1 1 CD163L1 12 7403685 Missense_Mutation SNP G C3N-02002_T 7403685 125871624 30 26666 EFS 0 . GRCh38 14 23357550 23357550 + Silent SNP C C A novel C3N-02002_T C3N-02002_N C C c.1362G>T p.= p.V454V ENST00000216733 6/6 51 44 7 89 89 0 strelka-varscan-mutect EFS,synonymous_variant,p.=,ENST00000216733,NM_005864.3;EFS,synonymous_variant,p.=,ENST00000351354,NM_032459.2;EFS,synonymous_variant,p.=,ENST00000429593,NM_001277174.1;SLC22A17,upstream_gene_variant,,ENST00000397267,;SLC22A17,upstream_gene_variant,,ENST00000206544,NM_020372.3;SLC22A17,upstream_gene_variant,,ENST00000354772,;RP11-124D2.3,downstream_gene_variant,,ENST00000554010,;SLC22A17,upstream_gene_variant,,ENST00000397260,;SLC22A17,upstream_gene_variant,,ENST00000474057,;SLC22A17,upstream_gene_variant,,ENST00000557699,;SLC22A17,upstream_gene_variant,,ENST00000636431,; A ENST00000216733 Transcript synonymous_variant 1970/3118 1362/1686 454/561 V gtG/gtT 1 -1 EFS HGNC HGNC:16898 protein_coding YES CCDS9595.1 ENSP00000216733 O43281 UPI0000129D21 NM_005864.3 6/6 hmmpanther:PTHR10654,hmmpanther:PTHR10654:SF14,Pfam_domain:PF12026 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.86031 1 1 1 1 0 A 2 1 86 23357550 23357550 C A 1 0 0 0 0 0 0 0 1 4796 581 21 2 2 EFS 14 23357550 Silent SNP C C3N-02002_T 23357550 83686168 31 26667 BAHD1 0 . GRCh38 15 40458625 40458625 + Missense_Mutation SNP A A G novel C3N-02002_T C3N-02002_N A A c.161A>G p.Asn54Ser p.N54S ENST00000416165 2/7 75 64 11 143 143 0 strelka-varscan-mutect BAHD1,missense_variant,p.Asn54Ser,ENST00000561234,NM_001301132.1;BAHD1,missense_variant,p.Asn54Ser,ENST00000416165,NM_014952.4;BAHD1,missense_variant,p.Asn54Ser,ENST00000560846,;RP11-64K12.9,upstream_gene_variant,,ENST00000558601,; G ENST00000416165 Transcript missense_variant 232/4526 161/2343 54/780 N/S aAt/aGt 1 1 BAHD1 HGNC HGNC:29153 protein_coding YES CCDS10058.1 ENSP00000396976 Q8TBE0 A0A024R9K2 UPI000013D778 NM_014952.4 tolerated(0.64) 2/7 hmmpanther:PTHR12505 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 40458625 40458625 A G 1 0 0 0 0 1 0 0 0 1452 101 4 5 5 BAHD1 15 40458625 Missense_Mutation SNP A C3N-02002_T 40458625 61532564 32 26668 MYO9A 0 . GRCh38 15 71878142 71878142 + Missense_Mutation SNP A A C rs190268567 C3N-02002_T C3N-02002_N A A c.5829T>G p.Asp1943Glu p.D1943E ENST00000356056 31/42 100 88 12 143 143 0 strelka-mutect MYO9A,missense_variant,p.Asp1943Glu,ENST00000356056,NM_006901.3;MYO9A,missense_variant,p.Asp1943Glu,ENST00000564571,;MYO9A,missense_variant,p.Asp1943Glu,ENST00000444904,;MYO9A,missense_variant,p.Asp793Glu,ENST00000561618,; C ENST00000356056 Transcript missense_variant 6302/12411 5829/7647 1943/2548 D/E gaT/gaG rs190268567 1 -1 MYO9A HGNC HGNC:7608 protein_coding YES CCDS10239.1 ENSP00000348349 B2RTY4 UPI000013D213 NM_006901.3 tolerated(0.14) 31/42 MODERATE 1 SNV 1 1 PASS rs190268567 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 86 71878142 71878142 A C 1 0 0 0 0 1 0 0 0 10085 98 4 5 5 MYO9A 15 71878142 Missense_Mutation SNP A C3N-02002_T 31419517 71878142 30113047 33 26669 CREBBP 0 . GRCh38 16 3778035 3778035 + Missense_Mutation SNP G G C novel C3N-02002_T C3N-02002_N G G c.2089C>G p.Gln697Glu p.Q697E ENST00000262367 10/31 215 142 73 240 240 0 strelka-varscan-mutect CREBBP,missense_variant,p.Gln697Glu,ENST00000262367,NM_004380.2;CREBBP,missense_variant,p.Gln659Glu,ENST00000382070,NM_001079846.1;CREBBP,missense_variant,p.Gln232Glu,ENST00000570939,;CREBBP,missense_variant,p.Gln135Glu,ENST00000572134,;CREBBP,missense_variant,p.Gln47Glu,ENST00000571826,;CREBBP,downstream_gene_variant,,ENST00000635753,;CREBBP,downstream_gene_variant,,ENST00000636002,;CREBBP,non_coding_transcript_exon_variant,,ENST00000634839,;CREBBP,upstream_gene_variant,,ENST00000575237,; C ENST00000262367 Transcript missense_variant 2899/10803 2089/7329 697/2442 Q/E Cag/Gag 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 tolerated_low_confidence(0.09) 10/31 Low_complexity_(Seg):seg,hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 86 3778035 3778035 G C 1 0 0 0 0 1 0 0 0 3661 1386 48 4 4 CREBBP 16 3778035 Missense_Mutation SNP G C3N-02002_T 3778035 86560310 34 26670 UBFD1 0 . GRCh38 16 23562256 23562256 + Silent SNP T T C novel C3N-02002_T C3N-02002_N T T c.615T>C p.= p.S205S ENST00000395878 4/7 139 100 39 175 175 0 strelka-varscan-mutect UBFD1,synonymous_variant,p.=,ENST00000395878,NM_019116.2;UBFD1,synonymous_variant,p.=,ENST00000567212,;EARS2,upstream_gene_variant,,ENST00000449606,NM_001083614.1;EARS2,upstream_gene_variant,,ENST00000563459,;EARS2,upstream_gene_variant,,ENST00000564501,;EARS2,upstream_gene_variant,,ENST00000563232,NM_001308211.1;UBFD1,downstream_gene_variant,,ENST00000567264,;UBFD1,non_coding_transcript_exon_variant,,ENST00000571064,;UBFD1,non_coding_transcript_exon_variant,,ENST00000563366,;UBFD1,upstream_gene_variant,,ENST00000564106,;EARS2,upstream_gene_variant,,ENST00000561859,;UBFD1,non_coding_transcript_exon_variant,,ENST00000565634,;UBFD1,upstream_gene_variant,,ENST00000566136,;UBFD1,downstream_gene_variant,,ENST00000569919,;EARS2,upstream_gene_variant,,ENST00000564668,;UBFD1,downstream_gene_variant,,ENST00000566669,;EARS2,upstream_gene_variant,,ENST00000564997,;EARS2,upstream_gene_variant,,ENST00000562799,;EARS2,upstream_gene_variant,,ENST00000563499,;EARS2,upstream_gene_variant,,ENST00000562581,; C ENST00000395878 Transcript synonymous_variant 996/5110 615/930 205/309 S tcT/tcC 1 1 UBFD1 HGNC HGNC:30565 protein_coding YES CCDS10613.2 ENSP00000379217 O14562 UPI00001FF0A3 NM_019116.2 4/7 hmmpanther:PTHR16470 LOW SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 2 2 86 23562256 23562256 T C 1 0 0 0 0 0 0 0 1 17408 1567 55 5 5 UBFD1 16 23562256 Silent SNP T C3N-02002_T 19784221 23562256 66776089 35 26671 RUNDC1 0 . GRCh38 17 42981010 42981010 + Missense_Mutation SNP A A T novel C3N-02002_T C3N-02002_N A A c.434A>T p.Asp145Val p.D145V ENST00000361677 1/5 215 204 11 222 222 0 strelka-varscan RUNDC1,missense_variant,p.Asp145Val,ENST00000361677,NM_001321381.1,NM_173079.2;RUNDC1,missense_variant,p.Asp144Val,ENST00000589705,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000409399,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000360221,NM_025267.3;PTGES3L,upstream_gene_variant,,ENST00000409446,NM_001142654.1;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000409103,;PTGES3L,upstream_gene_variant,,ENST00000424284,;PTGES3L,upstream_gene_variant,,ENST00000591916,NM_001261430.1;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000454303,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000452752,;PTGES3L,upstream_gene_variant,,ENST00000451885,NM_001142653.1;RUNDC1,non_coding_transcript_exon_variant,,ENST00000590836,;PTGES3L,upstream_gene_variant,,ENST00000462157,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000423601,; T ENST00000361677 Transcript missense_variant 446/3828 434/1842 145/613 D/V gAc/gTc 1 1 RUNDC1 HGNC HGNC:25418 protein_coding YES CCDS11448.1 ENSP00000354622 Q96C34 UPI00001AED0E NM_001321381.1,NM_173079.2 tolerated(0.14) 1/5 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 86 42981010 42981010 A T 1 0 0 0 0 1 0 0 0 14004 275 10 4 4 RUNDC1 17 42981010 Missense_Mutation SNP A C3N-02002_T 42981010 40276431 36 26672 USP36 0 . GRCh38 17 78803908 78803908 + Missense_Mutation SNP A A C novel C3N-02002_T C3N-02002_N A A c.2287T>G p.Ser763Ala p.S763A ENST00000542802 16/21 73 57 16 99 98 1 strelka-varscan-mutect USP36,missense_variant,p.Ser763Ala,ENST00000542802,NM_001321291.1;USP36,missense_variant,p.Ser763Ala,ENST00000312010,NM_025090.3;USP36,upstream_gene_variant,,ENST00000592231,;USP36,downstream_gene_variant,,ENST00000449938,;USP36,upstream_gene_variant,,ENST00000588130,;USP36,downstream_gene_variant,,ENST00000588467,;USP36,missense_variant,p.Ser763Ala,ENST00000589225,;USP36,missense_variant,p.Ser763Ala,ENST00000588086,;USP36,upstream_gene_variant,,ENST00000587010,; C ENST00000542802 Transcript missense_variant 2731/6063 2287/3372 763/1123 S/A Tcc/Gcc 1 -1 USP36 HGNC HGNC:20062 protein_coding YES CCDS32755.1 ENSP00000441214 Q9P275 A0A024R8V6 UPI00000398BB NM_001321291.1 tolerated_low_confidence(0.13) 16/21 MODERATE 1 SNV 1 1 PASS . . 0 195 15 0 0 0 0 0 -20 0.9997804 1 1 1 0 C 3 2 86 78803908 78803908 A C 1 0 0 0 0 1 0 0 0 17609 275 10 5 5 USP36 17 78803908 Missense_Mutation SNP A C3N-02002_T 35822898 78803908 4453533 37 26673 U2AF1L4 0 . GRCh38 19 35744074 35744074 + Silent SNP C C A novel C3N-02002_T C3N-02002_N C C c.303G>T p.= p.V101V ENST00000292879 4/6 187 164 23 215 215 0 strelka-varscan-mutect U2AF1L4,synonymous_variant,p.=,ENST00000412391,;U2AF1L4,synonymous_variant,p.=,ENST00000378975,NM_001040425.2;U2AF1L4,synonymous_variant,p.=,ENST00000292879,NM_144987.3;PSENEN,upstream_gene_variant,,ENST00000587708,;IGFLR1,upstream_gene_variant,,ENST00000246532,;IGFLR1,upstream_gene_variant,,ENST00000592537,NM_024660.2;LIN37,upstream_gene_variant,,ENST00000301159,NM_019104.2;PSENEN,upstream_gene_variant,,ENST00000591949,;IGFLR1,upstream_gene_variant,,ENST00000592889,;IGFLR1,upstream_gene_variant,,ENST00000588992,;PSENEN,upstream_gene_variant,,ENST00000222266,NM_001281532.1,NM_172341.2;IGFLR1,upstream_gene_variant,,ENST00000591277,;IGFLR1,upstream_gene_variant,,ENST00000591748,;LIN37,upstream_gene_variant,,ENST00000587751,;U2AF1L4,downstream_gene_variant,,ENST00000587886,;IGFLR1,upstream_gene_variant,,ENST00000586140,;AC002398.11,downstream_gene_variant,,ENST00000591091,;AC002398.11,downstream_gene_variant,,ENST00000585365,;IGFLR1,upstream_gene_variant,,ENST00000587101,;U2AF1L4,downstream_gene_variant,,ENST00000588100,;LIN37,upstream_gene_variant,,ENST00000591076,;AD000671.6,3_prime_UTR_variant,,ENST00000589807,;U2AF1L4,3_prime_UTR_variant,,ENST00000587987,;U2AF1L4,3_prime_UTR_variant,,ENST00000591084,;U2AF1L4,3_prime_UTR_variant,,ENST00000594792,;U2AF1L4,3_prime_UTR_variant,,ENST00000591057,;U2AF1L4,3_prime_UTR_variant,,ENST00000589429,;U2AF1L4,3_prime_UTR_variant,,ENST00000600296,;U2AF1L4,3_prime_UTR_variant,,ENST00000601236,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000588892,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000588980,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000586476,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000590135,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000585554,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000592913,;U2AF1L4,non_coding_transcript_exon_variant,,ENST00000591855,;LIN37,upstream_gene_variant,,ENST00000595455,;LIN37,upstream_gene_variant,,ENST00000587108,;LIN37,upstream_gene_variant,,ENST00000590706,;IGFLR1,upstream_gene_variant,,ENST00000588018,;AC002398.9,upstream_gene_variant,,ENST00000591613,;IGFLR1,upstream_gene_variant,,ENST00000592693,;U2AF1L4,downstream_gene_variant,,ENST00000585771,;LIN37,upstream_gene_variant,,ENST00000592871,;IGFLR1,upstream_gene_variant,,ENST00000589175,;U2AF1L4,downstream_gene_variant,,ENST00000590650,; A ENST00000292879 Transcript synonymous_variant 357/729 303/609 101/202 V gtG/gtT 1 -1 U2AF1L4 HGNC HGNC:23020 protein_coding YES CCDS12473.1 ENSP00000292879 Q8WU68 UPI000013E0DB NM_144987.3 4/6 PROSITE_profiles:PS50102,hmmpanther:PTHR12620,hmmpanther:PTHR12620:SF3,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00361,Superfamily_domains:SSF54928,Prints_domain:PR01848 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 86 35744074 35744074 C A 1 0 0 0 0 0 0 0 1 17338 724 25 2 2 U2AF1L4 19 35744074 Silent SNP C C3N-02002_T 35744074 22873542 38 26674 ZNF146 0 . GRCh38 19 36236956 36236956 + Silent SNP A A T novel C3N-02002_T C3N-02002_N A A c.516A>T p.= p.I172I ENST00000456324 3/3 140 108 32 245 245 0 strelka-varscan-mutect ZNF146,synonymous_variant,p.=,ENST00000456324,NM_001099638.1,NM_001099639.1;ZNF146,synonymous_variant,p.=,ENST00000443387,NM_007145.2;ZNF565,intron_variant,,ENST00000355114,;ZNF146,downstream_gene_variant,,ENST00000586094,;ZNF146,downstream_gene_variant,,ENST00000591063,;ZNF146,downstream_gene_variant,,ENST00000587285,; T ENST00000456324 Transcript synonymous_variant 1965/3780 516/879 172/292 I atA/atT 1 1 ZNF146 HGNC HGNC:12931 protein_coding YES CCDS12492.1 ENSP00000400391 Q15072 UPI000013E6EC NM_001099638.1,NM_001099639.1 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 86 36236956 36236956 A T 1 0 0 0 0 0 0 0 1 18314 352 13 4 4 ZNF146 19 36236956 Silent SNP A C3N-02002_T 492882 36236956 22380660 39 26675 ADCK4 0 . GRCh38 19 40702667 40702667 + Missense_Mutation SNP C C A rs200480831 C3N-02002_T C3N-02002_N C C c.826G>T p.Ala276Ser p.A276S ENST00000324464 10/15 208 184 24 306 306 0 strelka-varscan-mutect ADCK4,missense_variant,p.Ala276Ser,ENST00000324464,NM_024876.3;ADCK4,missense_variant,p.Ala235Ser,ENST00000243583,NM_001142555.2;ADCK4,missense_variant,p.Ala167Ser,ENST00000595254,;ADCK4,downstream_gene_variant,,ENST00000601967,;ADCK4,downstream_gene_variant,,ENST00000594084,;ADCK4,downstream_gene_variant,,ENST00000594720,;ADCK4,downstream_gene_variant,,ENST00000600080,;ADCK4,downstream_gene_variant,,ENST00000594490,;ADCK4,3_prime_UTR_variant,,ENST00000599643,;ADCK4,non_coding_transcript_exon_variant,,ENST00000596455,;ADCK4,upstream_gene_variant,,ENST00000593724,;ADCK4,downstream_gene_variant,,ENST00000601451,;ADCK4,downstream_gene_variant,,ENST00000601304,;ADCK4,downstream_gene_variant,,ENST00000593544,; A ENST00000324464 Transcript missense_variant 1128/2443 826/1635 276/544 A/S Gcc/Tcc rs200480831 1 -1 ADCK4 HGNC HGNC:19041 protein_coding YES CCDS12562.1 ENSP00000315118 Q96D53 UPI0000071B0F NM_024876.3 deleterious(0.03) 10/15 Low_complexity_(Seg):seg,hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF22,Pfam_domain:PF03109 MODERATE 1 SNV 1 1 PASS rs200480831 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 86 40702667 40702667 C A 1 0 0 0 0 1 0 0 0 334 739 26 2 2 ADCK4 19 40702667 Missense_Mutation SNP C C3N-02002_T 4465711 40702667 17914949 40 26676 TRIM28 0 . GRCh38 19 58548884 58548884 + Silent SNP A A G novel C3N-02002_T C3N-02002_N A A c.1383A>G p.= p.A461A ENST00000253024 11/17 289 265 24 377 377 0 strelka-varscan-mutect TRIM28,splice_acceptor_variant,,ENST00000597136,;TRIM28,synonymous_variant,p.=,ENST00000253024,NM_005762.2;TRIM28,synonymous_variant,p.=,ENST00000341753,;CHMP2A,downstream_gene_variant,,ENST00000600118,;CHMP2A,downstream_gene_variant,,ENST00000312547,NM_014453.3;CHMP2A,downstream_gene_variant,,ENST00000601220,NM_198426.2;TRIM28,downstream_gene_variant,,ENST00000594806,;CHMP2A,downstream_gene_variant,,ENST00000600006,;CHMP2A,downstream_gene_variant,,ENST00000596708,;TRIM28,downstream_gene_variant,,ENST00000593582,;TRIM28,downstream_gene_variant,,ENST00000597968,;MIR6807,upstream_gene_variant,,ENST00000621968,;TRIM28,non_coding_transcript_exon_variant,,ENST00000601150,;TRIM28,non_coding_transcript_exon_variant,,ENST00000597995,;TRIM28,non_coding_transcript_exon_variant,,ENST00000595028,;TRIM28,downstream_gene_variant,,ENST00000597423,;TRIM28,upstream_gene_variant,,ENST00000598355,;TRIM28,upstream_gene_variant,,ENST00000595974,;CHMP2A,downstream_gene_variant,,ENST00000597209,;TRIM28,downstream_gene_variant,,ENST00000597618,;CHMP2A,downstream_gene_variant,,ENST00000600804,;TRIM28,downstream_gene_variant,,ENST00000597172,;TRIM28,upstream_gene_variant,,ENST00000600840,; G ENST00000253024 Transcript synonymous_variant 1672/2960 1383/2508 461/835 A gcA/gcG 1 1 TRIM28 HGNC HGNC:16384 protein_coding YES CCDS12985.1 ENSP00000253024 Q13263 UPI0000136C15 NM_005762.2 11/17 hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF346 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 86 58548884 58548884 A G 1 0 0 0 0 0 0 0 1 16991 175 7 5 5 TRIM28 19 58548884 Silent SNP A C3N-02002_T 17846217 58548884 68732 41 26677 TRPC4AP 0 . GRCh38 20 35054984 35054984 + Missense_Mutation SNP A A C novel C3N-02002_T C3N-02002_N A A c.520T>G p.Cys174Gly p.C174G ENST00000252015 5/19 188 173 15 279 279 0 strelka-mutect TRPC4AP,missense_variant,p.Cys174Gly,ENST00000252015,NM_015638.2;TRPC4AP,missense_variant,p.Cys174Gly,ENST00000451813,NM_199368.1; C ENST00000252015 Transcript missense_variant 610/3226 520/2394 174/797 C/G Tgt/Ggt 1 -1 TRPC4AP HGNC HGNC:16181 protein_coding YES CCDS13246.1 ENSP00000252015 Q8TEL6 UPI000004FADD NM_015638.2 tolerated(0.07) 5/19 hmmpanther:PTHR31743,hmmpanther:PTHR31743:SF1,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.5754 0.9999997 1 1 1 0 C 3 2 86 35054984 35054984 A C 1 0 0 0 0 1 0 0 0 17086 188 7 5 5 TRPC4AP 20 35054984 Missense_Mutation SNP A C3N-02002_T 35054984 29389183 42 26678 PARD6B 0 . GRCh38 20 50749951 50749951 + Missense_Mutation SNP A A G rs371618647 C3N-02002_T C3N-02002_N A A c.582A>G p.Ile194Met p.I194M ENST00000371610 3/3 307 291 16 408 408 0 strelka-varscan-mutect PARD6B,missense_variant,p.Ile194Met,ENST00000371610,NM_032521.2;PARD6B,intron_variant,,ENST00000396039,; G ENST00000371610 Transcript missense_variant 825/4615 582/1119 194/372 I/M atA/atG rs371618647 1 1 PARD6B HGNC HGNC:16245 protein_coding YES CCDS33485.1 ENSP00000360672 Q9BYG5 UPI000006FA7C NM_032521.2 deleterious(0) 3/3 PROSITE_profiles:PS50106,hmmpanther:PTHR14102,hmmpanther:PTHR14102:SF4,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs371618647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 86 50749951 50749951 A G 1 0 0 0 0 1 0 0 0 11526 439 16 5 5 PARD6B 20 50749951 Missense_Mutation SNP A C3N-02002_T 15694967 50749951 13694216 43 26679 CYP24A1 0 . GRCh38 20 54172944 54172944 + Silent SNP G G T novel C3N-02002_T C3N-02002_N G G c.414C>A p.= p.R138R ENST00000216862 2/12 284 216 68 373 373 0 strelka-varscan-mutect CYP24A1,synonymous_variant,p.=,ENST00000216862,NM_000782.4;CYP24A1,synonymous_variant,p.=,ENST00000395955,NM_001128915.1;CYP24A1,upstream_gene_variant,,ENST00000395954,;CYP24A1,non_coding_transcript_exon_variant,,ENST00000472970,; T ENST00000216862 Transcript synonymous_variant 808/3262 414/1545 138/514 R cgC/cgA 1 -1 CYP24A1 HGNC HGNC:2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 2/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF5,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 86 54172944 54172944 G T 1 0 0 0 0 0 0 0 1 3957 1074 38 1 1 CYP24A1 20 54172944 Silent SNP G C3N-02002_T 3422993 54172944 10271223 44 26680 RIPK4 0 . GRCh38 21 41756555 41756555 + Silent SNP G G A novel C3N-02002_T C3N-02002_N G G c.444C>T p.= p.N148N ENST00000332512 2/8 114 103 11 148 148 0 strelka-varscan-mutect RIPK4,synonymous_variant,p.=,ENST00000352483,;RIPK4,synonymous_variant,p.=,ENST00000332512,NM_020639.2; A ENST00000332512 Transcript synonymous_variant 509/3889 444/2355 148/784 N aaC/aaT 1 -1 RIPK4 HGNC HGNC:496 protein_coding YES CCDS13675.1 ENSP00000332454 P57078 UPI000002A3C9 NM_020639.2 2/8 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_patterns:PS00108,PROSITE_profiles:PS50011,hmmpanther:PTHR24198,hmmpanther:PTHR24198:SF65,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 86 41756555 41756555 G A 1 0 0 0 0 0 0 0 1 13557 1368 48 3 3 RIPK4 21 41756555 Silent SNP G C3N-02002_T 41756555 4953428 45 26681 MTOR 0 . GRCh38 1 11129790 11129790 + Missense_Mutation SNP A A C C3N-02003_T C3N-02003_N A A c.5662T>G p.Phe1888Val p.F1888V ENST00000361445 40/58 308 291 17 251 250 1 strelka-varscan-mutect MTOR,missense_variant,p.Phe1888Val,ENST00000361445,NM_004958.3;MTOR,missense_variant,p.Phe93Val,ENST00000376838,;MTOR,downstream_gene_variant,,ENST00000495435,; C ENST00000361445 Transcript missense_variant 5739/8677 5662/7650 1888/2549 F/V Ttc/Gtc COSM3358967,COSM3358968,COSM893814 1 -1 MTOR HGNC HGNC:3942 protein_coding YES CCDS127.1 ENSP00000354558 P42345 UPI000012ABD3 NM_004958.3 deleterious(0) 40/58 PROSITE_profiles:PS51189,hmmpanther:PTHR11139:SF9,hmmpanther:PTHR11139,Pfam_domain:PF02259 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 11129790 11129790 A C 1 0 0 0 0 1 0 0 0 9941 72 3 5 5 MTOR 1 11129790 Missense_Mutation SNP A C3N-02003_T 11129790 237826632 1 26682 NBPF1 0 . GRCh38 1 16591935 16591935 + Silent SNP T T C rs768058060 C3N-02003_T C3N-02003_N T T c.87A>G p.= p.A29A ENST00000430580 7/29 232 219 13 284 284 0 varscan-mutect NBPF1,synonymous_variant,p.=,ENST00000430580,NM_017940.4;NBPF1,synonymous_variant,p.=,ENST00000432949,;NBPF1,downstream_gene_variant,,ENST00000420513,;NBPF1,synonymous_variant,p.=,ENST00000392963,; C ENST00000430580 Transcript synonymous_variant 975/5932 87/3420 29/1139 A gcA/gcG rs768058060 1 -1 NBPF1 HGNC HGNC:26088 protein_coding YES ENSP00000474456 S4R3K2 UPI0000E04FDF NM_017940.4 7/29 LOW 1 SNV 5 1 PASS rs768058060 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 16591935 16591935 T C 1 0 0 0 0 0 0 0 1 10203 1567 55 5 5 NBPF1 1 16591935 Silent SNP T C3N-02003_T 5462145 16591935 232364487 2 26683 CROCC 0 . GRCh38 1 16924426 16924426 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.298A>G p.Ser100Gly p.S100G ENST00000375541 3/37 275 259 16 283 283 0 strelka-varscan-mutect CROCC,missense_variant,p.Ser100Gly,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Ser50Gly,ENST00000445545,;CROCC,intron_variant,,ENST00000467938,;CROCC,intron_variant,,ENST00000466256,; G ENST00000375541 Transcript missense_variant 367/6656 298/6054 100/2017 S/G Agc/Ggc 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 deleterious(0) 3/37 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 16924426 16924426 A G 1 0 0 0 0 1 0 0 0 3694 304 11 5 5 CROCC 1 16924426 Missense_Mutation SNP A C3N-02003_T 332491 16924426 232031996 3 26684 UBR4 0 . GRCh38 1 19088814 19088814 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.14375A>C p.Lys4792Thr p.K4792T ENST00000375254 98/106 390 337 53 350 350 0 strelka-varscan-mutect UBR4,missense_variant,p.Lys4792Thr,ENST00000375254,NM_020765.2;UBR4,missense_variant,p.Lys499Thr,ENST00000375224,;UBR4,downstream_gene_variant,,ENST00000467272,;UBR4,downstream_gene_variant,,ENST00000492606,; G ENST00000375254 Transcript missense_variant 14403/15906 14375/15552 4792/5183 K/T aAg/aCg 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 deleterious(0) 98/106 Low_complexity_(Seg):seg,hmmpanther:PTHR21725,Pfam_domain:PF13764 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 19088814 19088814 T G 1 0 0 0 0 1 0 0 0 17428 1609 56 5 5 UBR4 1 19088814 Missense_Mutation SNP T C3N-02003_T 2164388 19088814 229867608 4 26685 KDM1A 0 . GRCh38 1 23072163 23072163 + Nonsense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.1588G>T p.Glu530Ter p.E530* ENST00000400181 14/21 131 120 11 269 269 0 strelka-varscan-mutect KDM1A,stop_gained,p.Glu530Ter,ENST00000400181,NM_001009999.2;KDM1A,stop_gained,p.Glu506Ter,ENST00000356634,NM_015013.3;KDM1A,stop_gained,p.Glu14Ter,ENST00000465864,;RP1-184J9.2,intron_variant,,ENST00000427154,; T ENST00000400181 Transcript stop_gained 1692/3059 1588/2631 530/876 E/* Gaa/Taa 1 1 KDM1A HGNC HGNC:29079 protein_coding YES CCDS53278.1 ENSP00000383042 O60341 UPI0000403137 NM_001009999.2 14/21 Gene3D:1.10.287.80,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01593,PIRSF_domain:PIRSF038051,Low_complexity_(Seg):seg,Superfamily_domains:SSF51905 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 87 23072163 23072163 G T 1 0 0 0 0 0 1 0 0 8040 943 33 2 2 KDM1A 1 23072163 Nonsense_Mutation SNP G C3N-02003_T 3983349 23072163 225884259 5 26686 CSMD2 0 . GRCh38 1 33700635 33700635 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.3615A>G p.= p.G1205G ENST00000373381 23/71 216 202 14 246 246 0 strelka-varscan-mutect CSMD2,synonymous_variant,p.=,ENST00000373381,NM_001281956.1;CSMD2,synonymous_variant,p.=,ENST00000619121,;CSMD2,synonymous_variant,p.=,ENST00000373388,NM_052896.4;CSMD2,synonymous_variant,p.=,ENST00000373380,;CSMD2,synonymous_variant,p.=,ENST00000241312,; C ENST00000373381 Transcript synonymous_variant 3792/13698 3615/10896 1205/3631 G ggA/ggG 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 23/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 33700635 33700635 T C 1 0 0 0 0 0 0 0 1 3746 1538 54 5 5 CSMD2 1 33700635 Silent SNP T C3N-02003_T 10628472 33700635 215255787 6 26687 GJB5 0 . GRCh38 1 34757417 34757417 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.87C>T p.= p.F29F ENST00000338513 2/2 267 236 31 213 212 1 strelka-varscan-mutect GJB5,synonymous_variant,p.=,ENST00000338513,NM_005268.3;GJB4,upstream_gene_variant,,ENST00000339480,NM_153212.2;RP1-34M23.5,downstream_gene_variant,,ENST00000542839,;SMIM12,intron_variant,,ENST00000426886,; T ENST00000338513 Transcript synonymous_variant 260/1355 87/822 29/273 F ttC/ttT 1 1 GJB5 HGNC HGNC:4287 protein_coding YES CCDS382.1 ENSP00000340811 O95377 UPI0000051E62 NM_005268.3 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF29,Pfam_domain:PF00029,Gene3D:2zw3A00,Prints_domain:PR00206 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 34757417 34757417 C T 1 0 0 0 0 0 0 0 1 6288 825 29 3 3 GJB5 1 34757417 Silent SNP C C3N-02003_T 1056782 34757417 214199005 7 26688 INPP5B 0 . GRCh38 1 37886891 37886891 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1128G>A p.= p.R376R ENST00000373024 12/24 165 155 10 129 129 0 strelka-mutect INPP5B,synonymous_variant,p.=,ENST00000373023,;INPP5B,synonymous_variant,p.=,ENST00000458109,;INPP5B,synonymous_variant,p.=,ENST00000373027,NM_001297434.1;INPP5B,synonymous_variant,p.=,ENST00000373026,;INPP5B,synonymous_variant,p.=,ENST00000373024,NM_005540.2;RNU6-584P,downstream_gene_variant,,ENST00000410350,;SNORA63,downstream_gene_variant,,ENST00000516639,;INPP5B,non_coding_transcript_exon_variant,,ENST00000467066,; T ENST00000373024 Transcript synonymous_variant 1216/3060 1128/2742 376/913 R agG/agA 1 -1 INPP5B HGNC HGNC:6077 protein_coding YES CCDS41306.1 ENSP00000362115 P32019 UPI0000458AD7 NM_005540.2 12/24 hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF163,Pfam_domain:PF03372,Gene3D:3.60.10.10,SMART_domains:SM00128,Superfamily_domains:SSF56219 LOW 1 SNV 1 1 PASS . . 0 204 2 4 0 0 0 0 -12.98391 0.9983786 1 1 1 0 T 2 4 87 37886891 37886891 C T 1 0 0 0 0 0 0 0 1 7658 869 30 3 3 INPP5B 1 37886891 Silent SNP C C3N-02003_T 3129474 37886891 211069531 8 26689 FAF1 0 . GRCh38 1 50490618 50490618 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1623G>A p.= p.Q541Q ENST00000396153 17/19 226 204 22 272 272 0 strelka-varscan-mutect FAF1,synonymous_variant,p.=,ENST00000396153,NM_007051.2;FAF1,synonymous_variant,p.=,ENST00000371778,;FAF1,synonymous_variant,p.=,ENST00000494400,; T ENST00000396153 Transcript synonymous_variant 2075/6817 1623/1953 541/650 Q caG/caA 1 -1 FAF1 HGNC HGNC:3578 protein_coding YES CCDS554.1 ENSP00000379457 Q9UNN5 UPI0000032C67 NM_007051.2 17/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23322,hmmpanther:PTHR23322:SF29,Low_complexity_(Seg):seg,Superfamily_domains:SSF54236 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 50490618 50490618 C T 1 0 0 0 0 0 0 0 1 5241 912 32 3 3 FAF1 1 50490618 Silent SNP C C3N-02003_T 12603727 50490618 198465804 9 26690 CDCP2 0 . GRCh38 1 54139677 54139677 + Missense_Mutation SNP G G A C3N-02003_T C3N-02003_N G G c.1193C>T p.Ser398Phe p.S398F ENST00000371330 4/4 195 179 16 174 174 0 strelka-varscan-mutect CDCP2,missense_variant,p.Ser398Phe,ENST00000371330,NM_201546.3;CDCP2,intron_variant,,ENST00000530059,;RP11-446E24.3,non_coding_transcript_exon_variant,,ENST00000623663,;RP11-446E24.4,downstream_gene_variant,,ENST00000525949,;RP11-446E24.4,intron_variant,,ENST00000637610,;RP11-446E24.4,downstream_gene_variant,,ENST00000311841,; A ENST00000371330 Transcript missense_variant 2041/2723 1193/1350 398/449 S/F tCc/tTc COSM4461132 1 -1 CDCP2 HGNC HGNC:27297 protein_coding YES CCDS588.2 ENSP00000360381 Q5VXM1 UPI0000458963 NM_201546.3 deleterious_low_confidence(0.01) 4/4 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 54139677 54139677 G A 1 0 0 0 0 1 0 0 0 2797 1174 41 3 3 CDCP2 1 54139677 Missense_Mutation SNP G C3N-02003_T 3649059 54139677 194816745 10 26691 DNAJC6 0 . GRCh38 1 65386916 65386916 + Missense_Mutation SNP G G T rs756818465 C3N-02003_T C3N-02003_N G G c.1100G>T p.Arg367Leu p.R367L ENST00000371069 8/19 150 129 21 164 164 0 strelka-varscan-mutect DNAJC6,missense_variant,p.Arg297Leu,ENST00000263441,NM_001256865.1;DNAJC6,missense_variant,p.Arg310Leu,ENST00000395325,NM_014787.3;DNAJC6,missense_variant,p.Arg367Leu,ENST00000371069,NM_001256864.1;DNAJC6,missense_variant,p.Arg341Leu,ENST00000494710,;DNAJC6,non_coding_transcript_exon_variant,,ENST00000498720,; T ENST00000371069 Transcript missense_variant 1301/5365 1100/2913 367/970 R/L cGg/cTg rs756818465 1 1 DNAJC6 HGNC HGNC:15469 protein_coding YES CCDS58004.1 ENSP00000360108 O75061 UPI000022AE8A NM_001256864.1 deleterious(0) 8/19 PROSITE_profiles:PS51182,hmmpanther:PTHR23172:SF4,hmmpanther:PTHR23172,Pfam_domain:PF10409,Gene3D:1d5rA02,SMART_domains:SM01326,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS rs756818465 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 87 65386916 65386916 G T 1 0 0 0 0 1 0 0 0 4466 1116 39 1 1 DNAJC6 1 65386916 Missense_Mutation SNP G C3N-02003_T 11247239 65386916 183569506 11 26692 DPYD 0 . GRCh38 1 97573964 97573964 + Missense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.1135C>A p.Leu379Ile p.L379I ENST00000370192 11/23 220 207 13 380 380 0 strelka-varscan-mutect DPYD,missense_variant,p.Leu379Ile,ENST00000370192,NM_000110.3; T ENST00000370192 Transcript missense_variant 1236/4412 1135/3078 379/1025 L/I Ctt/Att 1 -1 DPYD HGNC HGNC:3012 protein_coding YES CCDS30777.1 ENSP00000359211 Q12882 UPI00000727C7 NM_000110.3 tolerated(0.2) 11/23 Low_complexity_(Seg):seg,hmmpanther:PTHR11938,hmmpanther:PTHR11938:SF5,Gene3D:3.50.50.60,Pfam_domain:PF07992,Superfamily_domains:SSF51971 MODERATE 1 SNV 1 1 PASS rs1463235938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 97573964 97573964 G T 1 0 0 0 0 1 0 0 0 4560 1029 36 2 2 DPYD 1 97573964 Missense_Mutation SNP G C3N-02003_T 32187048 97573964 151382458 12 26693 CHIA 0 . GRCh38 1 111318539 111318539 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.776A>G p.Lys259Arg p.K259R ENST00000369740 9/12 110 101 9 107 106 1 strelka-varscan-mutect CHIA,missense_variant,p.Lys259Arg,ENST00000369740,NM_201653.3;CHIA,missense_variant,p.Lys259Arg,ENST00000343320,;CHIA,missense_variant,p.Lys203Arg,ENST00000422815,;CHIA,missense_variant,p.Lys151Arg,ENST00000430615,NM_001258003.1,NM_021797.3,NM_001258001.1;CHIA,missense_variant,p.Lys98Arg,ENST00000451398,NM_001040623.2;CHIA,missense_variant,p.Lys98Arg,ENST00000353665,NM_001258004.1,NM_001258005.1;CHIA,missense_variant,p.Lys98Arg,ENST00000483391,NM_001258002.1;CHIA,missense_variant,p.Lys98Arg,ENST00000489524,;RP5-1125M8.2,intron_variant,,ENST00000426321,;CHIA,3_prime_UTR_variant,,ENST00000352594,;CHIA,non_coding_transcript_exon_variant,,ENST00000477918,; G ENST00000369740 Transcript missense_variant 879/1625 776/1431 259/476 K/R aAg/aGg 1 1 CHIA HGNC HGNC:17432 protein_coding YES CCDS41368.1 ENSP00000358755 Q9BZP6 UPI00000727DC NM_201653.3 deleterious(0.01) 9/12 Gene3D:3.20.20.80,Pfam_domain:PF00704,hmmpanther:PTHR11177,hmmpanther:PTHR11177:SF188,SMART_domains:SM00636,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 111318539 111318539 A G 1 0 0 0 0 1 0 0 0 3101 72 3 5 5 CHIA 1 111318539 Missense_Mutation SNP A C3N-02003_T 13744575 111318539 137637883 13 26694 VTCN1 0 . GRCh38 1 117153263 117153263 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.552A>C p.Gln184His p.Q184H ENST00000369458 4/6 191 178 13 198 198 0 strelka-varscan-mutect VTCN1,missense_variant,p.Gln89His,ENST00000539893,NM_001253849.1;VTCN1,missense_variant,p.Gln184His,ENST00000369458,NM_024626.3;VTCN1,missense_variant,p.Gln187His,ENST00000359008,;VTCN1,missense_variant,p.Gln68His,ENST00000328189,NM_001253850.1;VTCN1,downstream_gene_variant,,ENST00000430871,;VTCN1,non_coding_transcript_exon_variant,,ENST00000463461,;VTCN1,downstream_gene_variant,,ENST00000488493,; G ENST00000369458 Transcript missense_variant 631/2612 552/849 184/282 Q/H caA/caC 1 -1 VTCN1 HGNC HGNC:28873 protein_coding YES CCDS894.1 ENSP00000358470 Q7Z7D3 UPI00000389E3 NM_024626.3 tolerated(0.5) 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF0,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 117153263 117153263 T G 1 0 0 0 0 1 0 0 0 17788 1606 56 5 5 VTCN1 1 117153263 Missense_Mutation SNP T C3N-02003_T 5834724 117153263 131803159 14 26695 SPAG17 0 . GRCh38 1 117992613 117992613 + Missense_Mutation SNP A A C rs370423067 C3N-02003_T C3N-02003_N A A c.5214T>G p.Ile1738Met p.I1738M ENST00000336338 36/49 129 120 9 128 128 0 strelka-varscan-mutect SPAG17,missense_variant,p.Ile1738Met,ENST00000336338,NM_206996.2;SPAG17,missense_variant,p.Ile218Met,ENST00000437255,;SPAG17,upstream_gene_variant,,ENST00000483383,; C ENST00000336338 Transcript missense_variant 5280/6924 5214/6672 1738/2223 I/M atT/atG rs370423067 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 tolerated(0.06) 36/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS rs370423067 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 117992613 117992613 A C 1 0 0 0 0 1 0 0 0 15310 10 1 5 5 SPAG17 1 117992613 Missense_Mutation SNP A C3N-02003_T 839350 117992613 130963809 15 26696 SPAG17 0 . GRCh38 1 118005471 118005471 + Missense_Mutation SNP C C T rs749203278 C3N-02003_T C3N-02003_N C C c.4719G>A p.Met1573Ile p.M1573I ENST00000336338 32/49 148 133 15 139 139 0 strelka-mutect SPAG17,missense_variant,p.Met1573Ile,ENST00000336338,NM_206996.2;SPAG17,missense_variant,p.Met53Ile,ENST00000437255,; T ENST00000336338 Transcript missense_variant 4785/6924 4719/6672 1573/2223 M/I atG/atA rs749203278 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 deleterious(0) 32/49 hmmpanther:PTHR21963 MODERATE 1 SNV 1 1 PASS rs749203278 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 118005471 118005471 C T 1 0 0 0 0 1 0 0 0 15310 826 29 3 3 SPAG17 1 118005471 Missense_Mutation SNP C C3N-02003_T 12858 118005471 130950951 16 26697 HAO2 0 . GRCh38 1 119383042 119383042 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.298G>A p.Asp100Asn p.D100N ENST00000361035 4/9 160 143 17 117 117 0 strelka-varscan-mutect HAO2,missense_variant,p.Asp87Asn,ENST00000622548,;HAO2,missense_variant,p.Asp100Asn,ENST00000361035,NM_001005783.2;HAO2,missense_variant,p.Asp87Asn,ENST00000325945,NM_016527.3;HAO2,missense_variant,p.Asp87Asn,ENST00000457318,; A ENST00000361035 Transcript missense_variant 581/1668 298/1095 100/364 D/N Gat/Aat 1 1 HAO2 HGNC HGNC:4810 protein_coding YES CCDS76196.1 ENSP00000354314 Q9NYQ3 UPI0000470C15 NM_001005783.2 deleterious(0) 4/9 PROSITE_profiles:PS51349,hmmpanther:PTHR10578,hmmpanther:PTHR10578:SF68,Pfam_domain:PF01070,PIRSF_domain:PIRSF000138,Gene3D:3.20.20.70,Superfamily_domains:SSF51395 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 119383042 119383042 G A 1 0 0 0 0 1 0 0 0 6838 1290 45 3 3 HAO2 1 119383042 Missense_Mutation SNP G C3N-02003_T 1377571 119383042 129573380 17 26698 RPRD2 0 . GRCh38 1 150471721 150471721 + Missense_Mutation SNP T T A novel C3N-02003_T C3N-02003_N T T c.2773T>A p.Ser925Thr p.S925T ENST00000369068 11/11 289 269 20 256 256 0 strelka-varscan-mutect RPRD2,missense_variant,p.Ser899Thr,ENST00000401000,NM_001297674.1,NM_001297673.1;RPRD2,missense_variant,p.Ser925Thr,ENST00000369068,NM_015203.4;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,; A ENST00000369068 Transcript missense_variant 2777/4612 2773/4386 925/1461 S/T Tct/Act 1 1 RPRD2 HGNC HGNC:29039 protein_coding YES CCDS44216.1 ENSP00000358064 Q5VT52 UPI00001D7CA8 NM_015203.4 tolerated_low_confidence(0.07) 11/11 hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 150471721 150471721 T A 1 0 0 0 0 1 0 0 0 13871 1667 58 4 4 RPRD2 1 150471721 Missense_Mutation SNP T C3N-02003_T 31088679 150471721 98484701 18 26699 ARNT 0 . GRCh38 1 150816295 150816295 + Silent SNP A A C novel C3N-02003_T C3N-02003_N A A c.1914T>G p.= p.T638T ENST00000358595 19/22 200 183 17 202 202 0 strelka-varscan-mutect ARNT,synonymous_variant,p.=,ENST00000358595,NM_001668.3;ARNT,synonymous_variant,p.=,ENST00000354396,NM_001286036.1;ARNT,synonymous_variant,p.=,ENST00000515192,NM_001286035.1;ARNT,synonymous_variant,p.=,ENST00000505755,NM_178427.2,NM_001197325.1;RNU6-1309P,upstream_gene_variant,,ENST00000363305,;ARNT,intron_variant,,ENST00000471844,;ARNT,downstream_gene_variant,,ENST00000510273,; C ENST00000358595 Transcript synonymous_variant 2115/4887 1914/2370 638/789 T acT/acG 1 -1 ARNT HGNC HGNC:700 protein_coding YES CCDS970.1 ENSP00000351407 P27540 UPI0000030984 NM_001668.3 19/22 Low_complexity_(Seg):seg,hmmpanther:PTHR23042:SF50,hmmpanther:PTHR23042,Superfamily_domains:SSF88633 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 150816295 150816295 A C 1 0 0 0 0 0 0 0 1 1107 59 3 5 5 ARNT 1 150816295 Silent SNP A C3N-02003_T 344574 150816295 98140127 19 26700 PI4KB 0 . GRCh38 1 151292994 151292994 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.2345G>A p.Arg782Gln p.R782Q ENST00000368875 13/13 183 167 16 123 123 0 strelka-varscan-mutect PI4KB,missense_variant,p.Arg782Gln,ENST00000368875,NM_002651.2;PI4KB,missense_variant,p.Arg755Gln,ENST00000368874,NM_001198774.1;PI4KB,missense_variant,p.Arg770Gln,ENST00000368873,;PI4KB,missense_variant,p.Arg755Gln,ENST00000368872,NM_001198773.1;PI4KB,missense_variant,p.Arg438Gln,ENST00000529142,NM_001198775.1;PI4KB,missense_variant,p.Arg181Gln,ENST00000455060,;PI4KB,missense_variant,p.Glu66Lys,ENST00000446339,;ZNF687,downstream_gene_variant,,ENST00000324048,NM_001304763.1;ZNF687,downstream_gene_variant,,ENST00000336715,NM_001304764.1,NM_020832.2;ZNF687,downstream_gene_variant,,ENST00000426871,;PI4KB,downstream_gene_variant,,ENST00000489889,;ZNF687,downstream_gene_variant,,ENST00000436614,;ZNF687,downstream_gene_variant,,ENST00000449313,;ZNF687,downstream_gene_variant,,ENST00000459919,; T ENST00000368875 Transcript missense_variant 2926/3983 2345/2487 782/828 R/Q cGa/cAa 1 -1 PI4KB HGNC HGNC:8984 protein_coding YES CCDS993.1 ENSP00000357869 A0A0B4J1S8 UPI000007161F NM_002651.2 tolerated(0.3) 13/13 PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF22,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.98636 0.9999998 1 1 1 0 T 3 4 87 151292994 151292994 C T 1 0 0 0 0 1 0 0 0 11963 884 31 1 1 PI4KB 1 151292994 Missense_Mutation SNP C C3N-02003_T 476699 151292994 97663428 20 26701 FLG 0 . GRCh38 1 152304436 152304436 + Missense_Mutation SNP T T G C3N-02003_T C3N-02003_N T T c.10450A>C p.Ser3484Arg p.S3484R ENST00000368799 3/3 475 434 41 476 476 0 varscan-mutect FLG,missense_variant,p.Ser3484Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; G ENST00000368799 Transcript missense_variant 10486/12747 10450/12186 3484/4061 S/R Agt/Cgt COSM4127570 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 deleterious(0.02) 3/3 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS rs1205756804 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 152304436 152304436 T G 1 0 0 0 0 1 0 0 0 5784 1609 56 5 5 FLG 1 152304436 Missense_Mutation SNP T C3N-02003_T 1011442 152304436 96651986 21 26702 TMEM79 0 . GRCh38 1 156286432 156286432 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.930C>T p.= p.L310L ENST00000405535 3/4 338 305 33 338 338 0 strelka-varscan-mutect TMEM79,stop_gained,p.Gln72Ter,ENST00000357501,;TMEM79,stop_gained,p.Gln72Ter,ENST00000456810,;TMEM79,synonymous_variant,p.=,ENST00000405535,NM_032323.2;TMEM79,synonymous_variant,p.=,ENST00000295694,;SMG5,upstream_gene_variant,,ENST00000361813,NM_001323617.1,NM_001323616.1,NM_015327.2;TMEM79,non_coding_transcript_exon_variant,,ENST00000495881,;TMEM79,non_coding_transcript_exon_variant,,ENST00000463670,;TMEM79,non_coding_transcript_exon_variant,,ENST00000485135,;GLMP,downstream_gene_variant,,ENST00000497831,;GLMP,downstream_gene_variant,,ENST00000480968,;GLMP,downstream_gene_variant,,ENST00000472870,;GLMP,downstream_gene_variant,,ENST00000461597,; T ENST00000405535 Transcript synonymous_variant 1101/2201 930/1185 310/394 L ctC/ctT 1 1 TMEM79 HGNC HGNC:28196 protein_coding YES CCDS1138.1 ENSP00000384748 Q9BSE2 UPI000006F977 NM_032323.2 3/4 Gene3D:1.20.120.550,hmmpanther:PTHR31004,hmmpanther:PTHR31004:SF1,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 156286432 156286432 C T 1 0 0 0 0 0 0 0 1 16680 827 29 3 3 TMEM79 1 156286432 Silent SNP C C3N-02003_T 3981996 156286432 92669990 22 26703 NES 0 . GRCh38 1 156671932 156671932 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.2256A>C p.Gln752His p.Q752H ENST00000368223 4/4 192 182 10 305 305 0 strelka-varscan NES,missense_variant,p.Gln752His,ENST00000368223,NM_006617.1; G ENST00000368223 Transcript missense_variant 2389/5558 2256/4866 752/1621 Q/H caA/caC 1 -1 NES HGNC HGNC:7756 protein_coding YES CCDS1151.1 ENSP00000357206 P48681 UPI0000213DC0 NM_006617.1 deleterious(0) 4/4 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 156671932 156671932 T G 1 0 0 0 0 1 0 0 0 10372 1606 56 5 5 NES 1 156671932 Missense_Mutation SNP T C3N-02003_T 385500 156671932 92284490 23 26704 RRNAD1 0 . GRCh38 1 156736724 156736724 + Missense_Mutation SNP C C G rs374747953 C3N-02003_T C3N-02003_N C C c.1399C>G p.Leu467Val p.L467V ENST00000368216 8/8 226 211 15 136 136 0 strelka-varscan-mutect RRNAD1,missense_variant,p.Leu467Val,ENST00000368216,NM_015997.3;RRNAD1,3_prime_UTR_variant,,ENST00000368218,NM_001142560.1;RRNAD1,3_prime_UTR_variant,,ENST00000476229,;RRNAD1,downstream_gene_variant,,ENST00000519086,;MRPL24,downstream_gene_variant,,ENST00000434558,;MRPL24,downstream_gene_variant,,ENST00000361531,;MRPL24,downstream_gene_variant,,ENST00000368211,NM_145729.2,NM_024540.3;RRNAD1,downstream_gene_variant,,ENST00000484742,;MRPL24,downstream_gene_variant,,ENST00000412846,;RRNAD1,downstream_gene_variant,,ENST00000524343,;MRPL24,downstream_gene_variant,,ENST00000420938,;RRNAD1,downstream_gene_variant,,ENST00000522237,;RRNAD1,non_coding_transcript_exon_variant,,ENST00000481920,;RRNAD1,non_coding_transcript_exon_variant,,ENST00000497515,;MRPL24,downstream_gene_variant,,ENST00000478899,;RRNAD1,downstream_gene_variant,,ENST00000462397,;RRNAD1,downstream_gene_variant,,ENST00000517871,; G ENST00000368216 Transcript missense_variant 2029/2254 1399/1428 467/475 L/V Ctt/Gtt rs374747953 1 1 RRNAD1 HGNC HGNC:24273 protein_coding YES CCDS1154.1 ENSP00000357199 Q96FB5 UPI000013D8E3 NM_015997.3 tolerated_low_confidence(0.06) 8/8 hmmpanther:PTHR12496,hmmpanther:PTHR12496:SF2 MODERATE 1 SNV 1 1 PASS rs374747953 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 156736724 156736724 C G 1 0 0 0 0 1 0 0 0 13939 913 32 4 4 RRNAD1 1 156736724 Missense_Mutation SNP C C3N-02003_T 64792 156736724 92219698 24 26705 SPTA1 0 . GRCh38 1 158626895 158626895 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.5777A>G p.Asp1926Gly p.D1926G ENST00000368147 41/52 216 195 21 351 351 0 strelka-varscan-mutect SPTA1,missense_variant,p.Asp1926Gly,ENST00000368147,NM_003126.2;SPTA1,non_coding_transcript_exon_variant,,ENST00000461624,; C ENST00000368147 Transcript missense_variant 5958/7999 5777/7260 1926/2419 D/G gAc/gGc 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0) 41/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 158626895 158626895 T C 1 0 0 0 0 1 0 0 0 15472 1667 58 5 5 SPTA1 1 158626895 Missense_Mutation SNP T C3N-02003_T 1890171 158626895 90329527 25 26706 OR6N1 0 . GRCh38 1 158766333 158766333 + Missense_Mutation SNP G G A rs756922659 C3N-02003_T C3N-02003_N G G c.350C>T p.Ala117Val p.A117V ENST00000335094 1/1 185 169 16 132 132 0 strelka-varscan-mutect OR6N1,missense_variant,p.Ala117Val,ENST00000335094,NM_001005185.1; A ENST00000335094 Transcript missense_variant 350/939 350/939 117/312 A/V gCt/gTt rs756922659 1 -1 OR6N1 HGNC HGNC:15034 protein_coding YES CCDS30905.1 ENSP00000335535 Q8NGY5 UPI000003FE15 NM_001005185.1 tolerated(0.51) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF123,PROSITE_patterns:PS00237,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS rs1488715776 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 158766333 158766333 G A 1 0 0 0 0 1 0 0 0 11275 971 34 3 3 OR6N1 1 158766333 Missense_Mutation SNP G C3N-02003_T 139438 158766333 90190089 26 26707 ARHGAP30 0 . GRCh38 1 161048915 161048915 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.2106A>C p.Lys702Asn p.K702N ENST00000368013 12/12 286 266 20 269 268 1 strelka-varscan-mutect ARHGAP30,missense_variant,p.Lys702Asn,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,missense_variant,p.Lys525Asn,ENST00000368015,NM_001287602.1;ARHGAP30,intron_variant,,ENST00000368016,NM_181720.2;USF1,upstream_gene_variant,,ENST00000368021,NM_007122.4,NM_207005.2;USF1,upstream_gene_variant,,ENST00000368020,NM_001276373.1;USF1,upstream_gene_variant,,ENST00000534633,;ARHGAP30,3_prime_UTR_variant,,ENST00000490279,;ARHGAP30,non_coding_transcript_exon_variant,,ENST00000461003,;USF1,upstream_gene_variant,,ENST00000473969,;USF1,upstream_gene_variant,,ENST00000496363,;USF1,upstream_gene_variant,,ENST00000491629,;USF1,upstream_gene_variant,,ENST00000529476,;ARHGAP30,downstream_gene_variant,,ENST00000368018,; G ENST00000368013 Transcript missense_variant 2427/4394 2106/3306 702/1101 K/N aaA/aaC 1 -1 ARHGAP30 HGNC HGNC:27414 protein_coding YES CCDS30918.1 ENSP00000356992 Q7Z6I6 UPI0000160677 NM_001287600.1,NM_001025598.1 deleterious_low_confidence(0.01) 12/12 hmmpanther:PTHR15729:SF12,hmmpanther:PTHR15729 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 161048915 161048915 T G 1 0 0 0 0 1 0 0 0 1004 1606 56 5 5 ARHGAP30 1 161048915 Missense_Mutation SNP T C3N-02003_T 2282582 161048915 87907507 27 26708 RXRG 0 . GRCh38 1 165419889 165419889 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.423C>T p.= p.I141I ENST00000359842 3/10 93 84 9 103 103 0 strelka-varscan-mutect RXRG,synonymous_variant,p.=,ENST00000619224,NM_001256570.1,NM_001256571.1;RXRG,synonymous_variant,p.=,ENST00000359842,NM_006917.4;RXRG,non_coding_transcript_exon_variant,,ENST00000470566,; A ENST00000359842 Transcript synonymous_variant 726/2041 423/1392 141/463 I atC/atT 1 -1 RXRG HGNC HGNC:10479 protein_coding YES CCDS1248.1 ENSP00000352900 P48443 F1D8Q7 UPI000004989F NM_006917.4 3/10 PROSITE_profiles:PS51030,hmmpanther:PTHR24083:SF95,hmmpanther:PTHR24083,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -19.04684 1 1 1 1 0 A 2 1 87 165419889 165419889 G A 1 0 0 0 0 0 0 0 1 14026 932 33 3 3 RXRG 1 165419889 Silent SNP G C3N-02003_T 4370974 165419889 83536533 28 26709 CEP350 0 . GRCh38 1 180031482 180031482 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.3713G>A p.Gly1238Glu p.G1238E ENST00000367607 15/38 55 51 4 65 65 0 varscan-mutect CEP350,missense_variant,p.Gly1238Glu,ENST00000367607,NM_014810.4; A ENST00000367607 Transcript missense_variant 4131/13491 3713/9354 1238/3117 G/E gGa/gAa 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 deleterious(0.03) 15/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS . . 0 197 10 2 0 0 0 0 -8.101169 0.9970256 1 1 1 0 A 3 1 87 180031482 180031482 G A 1 0 0 0 0 1 0 0 0 2972 1174 41 3 3 CEP350 1 180031482 Missense_Mutation SNP G C3N-02003_T 14611593 180031482 68924940 29 26710 LAMC2 0 . GRCh38 1 183232690 183232690 + Missense_Mutation SNP A A T novel C3N-02003_T C3N-02003_N A A c.2053A>T p.Arg685Trp p.R685W ENST00000264144 14/23 337 273 64 276 275 1 strelka-varscan-mutect LAMC2,missense_variant,p.Arg685Trp,ENST00000264144,NM_005562.2;LAMC2,missense_variant,p.Arg685Trp,ENST00000493293,NM_018891.2; T ENST00000264144 Transcript missense_variant 2118/5147 2053/3582 685/1193 R/W Agg/Tgg 1 1 LAMC2 HGNC HGNC:6493 protein_coding YES CCDS1352.1 ENSP00000264144 Q13753 UPI000013D4CA NM_005562.2 deleterious(0.02) 14/23 hmmpanther:PTHR10574:SF270,hmmpanther:PTHR10574 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 183232690 183232690 A T 1 0 0 0 0 1 0 0 0 8519 295 11 4 4 LAMC2 1 183232690 Missense_Mutation SNP A C3N-02003_T 3201208 183232690 65723732 30 26711 PRG4 0 . GRCh38 1 186308169 186308169 + Missense_Mutation SNP A A G C3N-02003_T C3N-02003_N A A c.2450A>G p.Lys817Arg p.K817R ENST00000445192 7/13 412 382 30 413 413 0 varscan-mutect PRG4,missense_variant,p.Lys817Arg,ENST00000445192,NM_005807.4;PRG4,missense_variant,p.Lys776Arg,ENST00000367483,NM_001127708.2;PRG4,missense_variant,p.Lys774Arg,ENST00000635041,NM_001303232.1;PRG4,missense_variant,p.Lys724Arg,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,missense_variant,p.Lys683Arg,ENST00000367482,;TPR,downstream_gene_variant,,ENST00000367478,NM_003292.2;PRG4,downstream_gene_variant,,ENST00000533951,;RNU6-1240P,downstream_gene_variant,,ENST00000365155,; G ENST00000445192 Transcript missense_variant 2495/5044 2450/4215 817/1404 K/R aAg/aGg COSM901098 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 deleterious(0.01) 7/13 Low_complexity_(Seg):seg 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 186308169 186308169 A G 1 0 0 0 0 1 0 0 0 12615 72 3 5 5 PRG4 1 186308169 Missense_Mutation SNP A C3N-02003_T 3075479 186308169 62648253 31 26712 CRB1 0 . GRCh38 1 197328422 197328422 + Missense_Mutation SNP A A G C3N-02003_T C3N-02003_N A A c.71A>G p.Asn24Ser p.N24S ENST00000367400 2/12 100 90 10 145 145 0 strelka-mutect CRB1,missense_variant,p.Asn24Ser,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Asn24Ser,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Asn24Ser,ENST00000538660,NM_001257966.1;CRB1,splice_region_variant,,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Asn24Ser,ENST00000484075,;CRB1,splice_region_variant,,ENST00000475659,; G ENST00000367400 Transcript missense_variant,splice_region_variant 206/4932 71/4221 24/1406 N/S aAt/aGt COSM5314307 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 tolerated(0.82) 2/12 hmmpanther:PTHR24049,Cleavage_site_(Signalp):SignalP-noTM 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.91755 1 1 1 1 0 G 3 3 87 197328422 197328422 A G 1 0 0 0 0 1 0 0 0 3648 347 12 5 5 CRB1 1 197328422 Missense_Mutation SNP A C3N-02003_T 11020253 197328422 51628000 32 26713 TNNI1 0 . GRCh38 1 201410414 201410414 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.478G>A p.Asp160Asn p.D160N ENST00000361379 8/9 214 201 13 230 230 0 strelka-varscan-mutect TNNI1,missense_variant,p.Asp160Asn,ENST00000622580,;TNNI1,missense_variant,p.Asp160Asn,ENST00000361379,NM_003281.3;TNNI1,missense_variant,p.Asp160Asn,ENST00000336092,;TNNI1,missense_variant,p.Asp160Asn,ENST00000367312,;TNNI1,intron_variant,,ENST00000555948,;TNNI1,downstream_gene_variant,,ENST00000556362,;TNNI1,downstream_gene_variant,,ENST00000555340,; T ENST00000361379 Transcript missense_variant 571/5413 478/564 160/187 D/N Gac/Aac 1 -1 TNNI1 HGNC HGNC:11945 protein_coding YES CCDS1411.1 ENSP00000354488 P19237 UPI0000000CCA NM_003281.3 deleterious(0) 8/9 hmmpanther:PTHR13738:SF9,hmmpanther:PTHR13738,Gene3D:1.20.5.350,Superfamily_domains:SSF90250 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 201410414 201410414 C T 1 0 0 0 0 1 0 0 0 16799 826 29 3 3 TNNI1 1 201410414 Missense_Mutation SNP C C3N-02003_T 4081992 201410414 47546008 33 26714 PIGR 0 . GRCh38 1 206935691 206935691 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1173G>A p.= p.Q391Q ENST00000356495 5/11 249 220 29 254 254 0 strelka-varscan-mutect PIGR,synonymous_variant,p.=,ENST00000356495,NM_002644.3;PIGR,upstream_gene_variant,,ENST00000487208,;PIGR,downstream_gene_variant,,ENST00000491503,; T ENST00000356495 Transcript synonymous_variant 1357/4279 1173/2295 391/764 Q caG/caA 1 -1 PIGR HGNC HGNC:8968 protein_coding YES CCDS1474.1 ENSP00000348888 P01833 UPI000007407E NM_002644.3 5/11 hmmpanther:PTHR11860:SF55,hmmpanther:PTHR11860,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00406,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 206935691 206935691 C T 1 0 0 0 0 0 0 0 1 11991 912 32 3 3 PIGR 1 206935691 Silent SNP C C3N-02003_T 5525277 206935691 42020731 34 26715 USH2A 0 . GRCh38 1 216089072 216089072 + Missense_Mutation SNP T T C C3N-02003_T C3N-02003_N T T c.4826A>G p.Glu1609Gly p.E1609G ENST00000307340 23/72 117 106 11 198 198 0 strelka-varscan-mutect USH2A,missense_variant,p.Glu1609Gly,ENST00000307340,NM_206933.2;RP11-22M7.2,downstream_gene_variant,,ENST00000446411,;RP11-22M7.2,downstream_gene_variant,,ENST00000430890,;RP11-22M7.2,downstream_gene_variant,,ENST00000442606,;RP11-22M7.2,downstream_gene_variant,,ENST00000445619,;USH2A,non_coding_transcript_exon_variant,,ENST00000481786,;USH2A,upstream_gene_variant,,ENST00000463147,; C ENST00000307340 Transcript missense_variant 5213/18883 4826/15609 1609/5202 E/G gAa/gGa COSM5082283,COSM5082284,COSM5432748,COSM5432749 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0.03) 23/72 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 216089072 216089072 T C 1 0 0 0 0 1 0 0 0 17570 1783 62 5 5 USH2A 1 216089072 Missense_Mutation SNP T C3N-02003_T 9153381 216089072 32867350 35 26716 DISP1 0 . GRCh38 1 223005938 223005938 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.4541T>G p.Leu1514Arg p.L1514R ENST00000284476 8/8 150 141 9 195 195 0 strelka-varscan-mutect DISP1,missense_variant,p.Leu1514Arg,ENST00000284476,NM_032890.3; G ENST00000284476 Transcript missense_variant 4705/4762 4541/4575 1514/1524 L/R cTt/cGt 1 1 DISP1 HGNC HGNC:19711 protein_coding YES CCDS1536.1 ENSP00000284476 Q96F81 UPI000016069D NM_032890.3 deleterious_low_confidence(0.01) 8/8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 223005938 223005938 T G 1 0 0 0 0 1 0 0 0 4345 1609 56 5 5 DISP1 1 223005938 Missense_Mutation SNP T C3N-02003_T 6916866 223005938 25950484 36 26717 DNAH14 0 . GRCh38 1 225303315 225303315 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.8512T>G p.Leu2838Val p.L2838V ENST00000430092 55/84 126 112 14 115 115 0 strelka-varscan-mutect DNAH14,missense_variant,p.Leu2838Val,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Leu2838Val,ENST00000439375,;DNAH14,missense_variant,p.Leu2185Val,ENST00000445597,;DNAH14,missense_variant,p.Leu636Val,ENST00000327794,; G ENST00000430092 Transcript missense_variant 8727/13763 8512/13548 2838/4515 L/V Tta/Gta 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 deleterious(0.02) 55/84 hmmpanther:PTHR10676:SF254,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Pfam_domain:PF12780,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 225303315 225303315 T G 1 0 0 0 0 1 0 0 0 4415 1606 56 5 5 DNAH14 1 225303315 Missense_Mutation SNP T C3N-02003_T 2297377 225303315 23653107 37 26718 PGBD5 0 . GRCh38 1 230325322 230325322 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1367A>C p.Asp456Ala p.D456A ENST00000391860 6/7 109 100 9 108 107 1 strelka-varscan-mutect PGBD5,missense_variant,p.Asp456Ala,ENST00000391860,NM_001258311.1;PGBD5,missense_variant,p.Asp387Ala,ENST00000525115,;PGBD5,non_coding_transcript_exon_variant,,ENST00000530424,; G ENST00000391860 Transcript missense_variant 1810/10961 1367/1575 456/524 D/A gAc/gCc 1 -1 PGBD5 HGNC HGNC:19405 protein_coding YES ENSP00000375733 A0A0A0MS21 UPI000004EBDA NM_001258311.1 deleterious(0.02) 6/7 hmmpanther:PTHR28576,hmmpanther:PTHR28576:SF2,Pfam_domain:PF13843 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.379 1 1 1 1 0 G 3 3 87 230325322 230325322 T G 1 0 0 0 0 1 0 0 0 11874 1667 58 5 5 PGBD5 1 230325322 Missense_Mutation SNP T C3N-02003_T 5022007 230325322 18631100 38 26719 OR13G1 0 . GRCh38 1 247672444 247672444 + Missense_Mutation SNP C C T C3N-02003_T C3N-02003_N C C c.598G>A p.Asp200Asn p.D200N ENST00000359688 1/1 242 227 15 279 279 0 strelka-varscan-mutect OR13G1,missense_variant,p.Asp200Asn,ENST00000359688,NM_001005487.1;RP11-634B7.4,intron_variant,,ENST00000449298,;OR3D1P,downstream_gene_variant,,ENST00000438288,; T ENST00000359688 Transcript missense_variant 598/924 598/924 200/307 D/N Gat/Aat COSM3486753 1 -1 OR13G1 HGNC HGNC:14999 protein_coding YES CCDS31094.1 ENSP00000352717 Q8NGZ3 UPI0000061E5B NM_001005487.1 deleterious(0.03) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF237,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 247672444 247672444 C T 1 0 0 0 0 1 0 0 0 11018 826 29 3 3 OR13G1 1 247672444 Missense_Mutation SNP C C3N-02003_T 17347122 247672444 1283978 39 26720 SNTG2 0 . GRCh38 2 1267386 1267386 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1099T>C p.Trp367Arg p.W367R ENST00000308624 14/17 230 210 20 224 224 0 strelka-varscan-mutect SNTG2,missense_variant,p.Trp367Arg,ENST00000308624,NM_018968.3;SNTG2,missense_variant,p.Trp240Arg,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000471239,; C ENST00000308624 Transcript missense_variant 1228/1888 1099/1620 367/539 W/R Tgg/Cgg 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 deleterious(0.04) 14/17 hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 1267386 1267386 T C 1 0 0 0 0 1 0 0 0 15195 1580 55 5 5 SNTG2 2 1267386 Missense_Mutation SNP T C3N-02003_T 1267386 240926143 40 26721 TDRD15 0 . GRCh38 2 21139619 21139619 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.2152T>C p.= p.L718L ENST00000405799 4/4 98 87 11 159 159 0 strelka-varscan-mutect TDRD15,synonymous_variant,p.=,ENST00000405799,;TDRD15,synonymous_variant,p.=,ENST00000622654,; C ENST00000405799 Transcript synonymous_variant 2482/6135 2152/5805 718/1934 L Ttg/Ctg 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 21139619 21139619 T C 1 0 0 0 0 0 0 0 1 16141 1606 56 5 5 TDRD15 2 21139619 Silent SNP T C3N-02003_T 19872233 21139619 221053910 41 26722 PLB1 0 . GRCh38 2 28525931 28525931 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.311T>C p.Met104Thr p.M104T ENST00000327757 6/58 178 163 15 158 158 0 strelka-varscan-mutect PLB1,missense_variant,p.Met104Thr,ENST00000422425,NM_001170585.1;PLB1,missense_variant,p.Met104Thr,ENST00000327757,NM_153021.4;PLB1,missense_variant,p.Met103Thr,ENST00000404858,;PLB1,missense_variant,p.Met48Thr,ENST00000416713,; C ENST00000327757 Transcript missense_variant 355/5107 311/4377 104/1458 M/T aTg/aCg 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 tolerated(0.25) 6/58 hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 28525931 28525931 T C 1 0 0 0 0 1 0 0 0 12118 1464 51 5 5 PLB1 2 28525931 Missense_Mutation SNP T C3N-02003_T 7386312 28525931 213667598 42 26723 89 3 PLB1 0 . GRCh38 2 28525940 28525940 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.320T>C p.Met107Thr p.M107T ENST00000327757 6/58 179 165 14 151 151 0 strelka-varscan-mutect PLB1,missense_variant,p.Met107Thr,ENST00000422425,NM_001170585.1;PLB1,missense_variant,p.Met107Thr,ENST00000327757,NM_153021.4;PLB1,missense_variant,p.Met106Thr,ENST00000404858,;PLB1,missense_variant,p.Met51Thr,ENST00000416713,; C ENST00000327757 Transcript missense_variant 364/5107 320/4377 107/1458 M/T aTg/aCg 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 tolerated(0.07) 6/58 hmmpanther:PTHR21325,hmmpanther:PTHR21325:SF31 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -18.59636 0.9999997 1 1 1 0 C 3 2 87 28525940 28525940 T C 1 0 0 0 0 1 0 0 0 12118 1478 51 5 5 PLB1 2 28525940 Missense_Mutation SNP T C3N-02003_T 9 28525940 213667589 43 26724 89 3 PLB1 0 . GRCh38 2 28525947 28525947 + Splice_Site SNP T T C novel C3N-02003_T C3N-02003_N T T c.325+2T>C p.X109_splice ENST00000327757 179 167 12 149 149 0 strelka-varscan PLB1,splice_donor_variant,,ENST00000422425,NM_001170585.1;PLB1,splice_donor_variant,,ENST00000327757,NM_153021.4;PLB1,splice_donor_variant,,ENST00000404858,;PLB1,splice_donor_variant,,ENST00000416713,; C ENST00000327757 Transcript splice_donor_variant -/5107 325/4377 109/1458 1 1 PLB1 HGNC HGNC:30041 protein_coding YES CCDS33168.1 ENSP00000330442 Q6P1J6 UPI0000D6117C NM_153021.4 6/57 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 5 2 87 28525947 28525947 T C 1 0 0 0 0 0 0 1 0 12118 1710 59 5 5 PLB1 2 28525947 Splice_Site SNP T C3N-02003_T 7 28525947 213667582 44 26725 89 3 GALNT14 0 . GRCh38 2 31114807 31114807 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.250C>T p.His84Tyr p.H84Y ENST00000324589 3/16 132 121 11 209 209 0 strelka-varscan-mutect GALNT14,missense_variant,p.Ser2Leu,ENST00000406653,NM_001253827.1;GALNT14,missense_variant,p.His84Tyr,ENST00000324589,NM_001253826.1;GALNT14,intron_variant,,ENST00000349752,NM_024572.3;GALNT14,intron_variant,,ENST00000430167,;GALNT14,non_coding_transcript_exon_variant,,ENST00000498206,;GALNT14,intron_variant,,ENST00000464038,;GALNT14,intron_variant,,ENST00000496397,;GALNT14,intron_variant,,ENST00000485468,;GALNT14,intron_variant,,ENST00000490212,;GALNT14,intron_variant,,ENST00000461193,;GALNT14,intron_variant,,ENST00000455477,;GALNT14,intron_variant,,ENST00000424136,; A ENST00000324589 Transcript missense_variant 311/2169 250/1674 84/557 H/Y Cat/Tat 1 -1 GALNT14 HGNC HGNC:22946 protein_coding YES CCDS58706.1 ENSP00000314500 Q96FL9 UPI0000073A6F NM_001253826.1 tolerated_low_confidence(0.99) 3/16 MODERATE 1 SNV 2 1 PASS rs1475941089 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 31114807 31114807 G A 1 0 0 0 0 1 0 0 0 6080 1294 45 3 3 GALNT14 2 31114807 Missense_Mutation SNP G C3N-02003_T 2588860 31114807 211078722 45 26726 PLEKHH2 0 . GRCh38 2 43738371 43738371 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.2974G>A p.Asp992Asn p.D992N ENST00000282406 20/30 63 59 4 83 83 0 varscan-mutect PLEKHH2,missense_variant,p.Asp992Asn,ENST00000282406,NM_172069.3;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405000,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000405223,;PLEKHH2,non_coding_transcript_exon_variant,,ENST00000480103,;PLEKHH2,upstream_gene_variant,,ENST00000493408,; A ENST00000282406 Transcript missense_variant 3084/6981 2974/4482 992/1493 D/N Gac/Aac 1 1 PLEKHH2 HGNC HGNC:30506 protein_coding YES CCDS1812.1 ENSP00000282406 Q8IVE3 UPI000016021B NM_172069.3 tolerated(0.12) 20/30 PROSITE_profiles:PS51016,hmmpanther:PTHR22903,hmmpanther:PTHR22903:SF3,SMART_domains:SM00139 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -9.859294 1 1 1 1 0 A 3 1 87 43738371 43738371 G A 1 0 0 0 0 1 0 0 0 12170 1290 45 3 3 PLEKHH2 2 43738371 Missense_Mutation SNP G C3N-02003_T 12623564 43738371 198455158 46 26727 SLC3A1 0 . GRCh38 2 44320235 44320235 + Missense_Mutation SNP T T A rs766431278 C3N-02003_T C3N-02003_N T T c.1654T>A p.Tyr552Asn p.Y552N ENST00000260649 10/10 105 96 9 158 158 0 strelka-varscan-mutect SLC3A1,missense_variant,p.Tyr552Asn,ENST00000260649,NM_000341.3;SLC3A1,missense_variant,p.Tyr274Asn,ENST00000409380,;SLC3A1,missense_variant,p.Tyr183Asn,ENST00000409740,;PREPL,3_prime_UTR_variant,,ENST00000541738,NM_001171617.1;PREPL,3_prime_UTR_variant,,ENST00000409936,NM_001171606.1;PREPL,3_prime_UTR_variant,,ENST00000409411,NM_001171613.1;PREPL,3_prime_UTR_variant,,ENST00000409957,;PREPL,downstream_gene_variant,,ENST00000260648,NM_006036.4;PREPL,downstream_gene_variant,,ENST00000410081,;PREPL,downstream_gene_variant,,ENST00000409272,NM_001171603.1;SLC3A1,downstream_gene_variant,,ENST00000409229,;SLC3A1,downstream_gene_variant,,ENST00000409387,;PREPL,downstream_gene_variant,,ENST00000378511,NM_001042385.2;PREPL,downstream_gene_variant,,ENST00000378520,NM_001042386.2;SLC3A1,downstream_gene_variant,,ENST00000611973,;PREPL,downstream_gene_variant,,ENST00000420756,;PREPL,downstream_gene_variant,,ENST00000444696,;PREPL,3_prime_UTR_variant,,ENST00000426481,;PREPL,3_prime_UTR_variant,,ENST00000425263,; A ENST00000260649 Transcript missense_variant 1730/2989 1654/2058 552/685 Y/N Tat/Aat rs766431278,HM070021 1 1 SLC3A1 HGNC HGNC:11025 protein_coding YES CCDS1819.1 ENSP00000260649 Q07837 A0A0S2Z4E1 UPI000013D0F2 NM_000341.3 deleterious(0) 10/10 Gene3D:3.20.20.80,hmmpanther:PTHR10357,hmmpanther:PTHR10357:SF73,Superfamily_domains:SSF51445 MODERATE 1 SNV 1 0,1 1 PASS rs766431278 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 44320235 44320235 T A 1 0 0 0 0 1 0 0 0 14904 1406 49 4 4 SLC3A1 2 44320235 Missense_Mutation SNP T C3N-02003_T 581864 44320235 197873294 47 26728 LHCGR 0 . GRCh38 2 48688741 48688741 + Silent SNP G G C novel C3N-02003_T C3N-02003_N G G c.1056C>G p.= p.P352P ENST00000294954 11/11 198 185 13 299 299 0 strelka-varscan-mutect LHCGR,synonymous_variant,p.=,ENST00000294954,NM_000233.3;LHCGR,synonymous_variant,p.=,ENST00000405626,;STON1-GTF2A1L,intron_variant,,ENST00000402114,NM_001198593.1;LHCGR,intron_variant,,ENST00000403273,;LHCGR,intron_variant,,ENST00000401907,;GTF2A1L,intron_variant,,ENST00000508440,;RP11-310N16.1,intron_variant,,ENST00000602369,; C ENST00000294954 Transcript synonymous_variant 1078/3044 1056/2100 352/699 P ccC/ccG 1 -1 LHCGR HGNC HGNC:6585 protein_coding YES CCDS1842.1 ENSP00000294954 P22888 UPI000013E1E1 NM_000233.3 11/11 Gene3D:1.20.1070.10,Prints_domain:PR00373,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF1,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 48688741 48688741 G C 1 0 0 0 0 0 0 0 1 8671 987 35 4 4 LHCGR 2 48688741 Silent SNP G C3N-02003_T 4368506 48688741 193504788 48 26729 NRXN1 0 . GRCh38 2 50497387 50497387 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.2945T>C p.Ile982Thr p.I982T ENST00000404971 15/24 35 28 7 28 28 0 strelka-varscan-mutect NRXN1,missense_variant,p.Ile942Thr,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Ile934Thr,ENST00000625672,;NRXN1,missense_variant,p.Ile982Thr,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Ile942Thr,ENST00000401669,;NRXN1,missense_variant,p.Ile930Thr,ENST00000405472,;NRXN1,missense_variant,p.Ile934Thr,ENST00000630543,;NRXN1,missense_variant,p.Ile672Thr,ENST00000406859,;NRXN1,missense_variant,p.Ile657Thr,ENST00000402717,;NRXN1,upstream_gene_variant,,ENST00000625320,;NRXN1,downstream_gene_variant,,ENST00000495871,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,upstream_gene_variant,,ENST00000637889,;NRXN1,missense_variant,p.Ile660Thr,ENST00000331040,;NRXN1,downstream_gene_variant,,ENST00000474354,;NRXN1,downstream_gene_variant,,ENST00000462791,;NRXN1,upstream_gene_variant,,ENST00000626192,; G ENST00000404971 Transcript missense_variant 4285/7578 2945/4644 982/1547 I/T aTt/aCt 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 15/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -18.14705 1 1 1 1 0 G 3 3 87 50497387 50497387 A G 1 0 0 0 0 1 0 0 0 10724 101 4 5 5 NRXN1 2 50497387 Missense_Mutation SNP A C3N-02003_T 1808646 50497387 191696142 49 26730 MFSD9 0 . GRCh38 2 102718552 102718552 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1293G>A p.= p.G431G ENST00000258436 6/6 148 140 8 125 125 0 strelka-varscan-mutect MFSD9,synonymous_variant,p.=,ENST00000258436,NM_032718.3;MFSD9,upstream_gene_variant,,ENST00000496253,;MFSD9,3_prime_UTR_variant,,ENST00000438943,;MFSD9,3_prime_UTR_variant,,ENST00000437075,;MFSD9,downstream_gene_variant,,ENST00000411991,;MFSD9,downstream_gene_variant,,ENST00000428085,; T ENST00000258436 Transcript synonymous_variant 1337/4049 1293/1425 431/474 G ggG/ggA 1 -1 MFSD9 HGNC HGNC:28158 protein_coding YES CCDS2063.1 ENSP00000258436 Q8NBP5 UPI0000070215 NM_032718.3 6/6 PROSITE_profiles:PS50850,hmmpanther:PTHR23504,hmmpanther:PTHR23504:SF14,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -15.18396 1 1 1 1 0 T 2 4 87 102718552 102718552 C T 1 0 0 0 0 0 0 0 1 9497 610 22 3 3 MFSD9 2 102718552 Silent SNP C C3N-02003_T 52221165 102718552 139474977 50 26731 MGAT5 0 . GRCh38 2 134362324 134362324 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1296G>A p.= p.L432L ENST00000409645 11/17 102 90 12 165 165 0 strelka-varscan-mutect MGAT5,synonymous_variant,p.=,ENST00000409645,;MGAT5,synonymous_variant,p.=,ENST00000281923,NM_002410.4; A ENST00000409645 Transcript synonymous_variant 1548/8252 1296/2226 432/741 L ctG/ctA 1 1 MGAT5 HGNC HGNC:7049 protein_coding YES CCDS2171.1 ENSP00000386377 Q09328 UPI0000049D8F 11/17 hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF3,Pfam_domain:PF15024 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 134362324 134362324 G A 1 0 0 0 0 0 0 0 1 9509 1277 45 3 3 MGAT5 2 134362324 Silent SNP G C3N-02003_T 31643772 134362324 107831205 51 26732 NEB 0 . GRCh38 2 151677662 151677662 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.3677A>C p.Lys1226Thr p.K1226T ENST00000618972 34/183 214 200 14 240 240 0 strelka-varscan-mutect NEB,missense_variant,p.Lys1226Thr,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Lys1226Thr,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Lys1226Thr,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Lys1226Thr,ENST00000603639,;NEB,missense_variant,p.Lys1226Thr,ENST00000604864,;NEB,missense_variant,p.Lys1226Thr,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Lys1226Thr,ENST00000172853,; G ENST00000618972 Transcript missense_variant 3880/26307 3677/25683 1226/8560 K/T aAg/aCg 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.31) 34/183 PROSITE_profiles:PS51216,SMART_domains:SM00227 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 151677662 151677662 T G 1 0 0 0 0 1 0 0 0 10326 1609 56 5 5 NEB 2 151677662 Missense_Mutation SNP T C3N-02003_T 17315338 151677662 90515867 52 26733 SCN9A 0 . GRCh38 2 166277218 166277218 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.2606T>C p.Phe869Ser p.F869S ENST00000409672 16/27 220 198 22 232 232 0 varscan-mutect SCN9A,missense_variant,p.Phe880Ser,ENST00000303354,;SCN9A,missense_variant,p.Phe869Ser,ENST00000409672,NM_002977.3;SCN9A,missense_variant,p.Phe880Ser,ENST00000409435,;SCN9A,downstream_gene_variant,,ENST00000452182,;SCN9A,downstream_gene_variant,,ENST00000454569,;AC010127.3,non_coding_transcript_exon_variant,,ENST00000447809,; G ENST00000409672 Transcript missense_variant 2953/9768 2606/5934 869/1977 F/S tTt/tCt 1 -1 SCN9A HGNC HGNC:10597 protein_coding YES CCDS46441.1 ENSP00000386306 Q15858 UPI0000140AC7 NM_002977.3 deleterious(0.04) 16/27 Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF221,Low_complexity_(Seg):seg,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 166277218 166277218 A G 1 0 0 0 0 1 0 0 0 14194 14 1 5 5 SCN9A 2 166277218 Missense_Mutation SNP A C3N-02003_T 14599556 166277218 75916311 53 26734 OSBPL6 0 . GRCh38 2 178339753 178339753 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.976A>C p.Ile326Leu p.I326L ENST00000392505 11/26 65 61 4 91 91 0 varscan-mutect OSBPL6,missense_variant,p.Ile326Leu,ENST00000190611,NM_032523.3;OSBPL6,missense_variant,p.Ile326Leu,ENST00000359685,NM_001201482.1;OSBPL6,missense_variant,p.Ile326Leu,ENST00000392505,NM_001201480.1;OSBPL6,missense_variant,p.Ile326Leu,ENST00000409631,;OSBPL6,missense_variant,p.Ile305Leu,ENST00000315022,NM_145739.2;OSBPL6,intron_variant,,ENST00000409045,NM_001201481.1;OSBPL6,intron_variant,,ENST00000357080,; C ENST00000392505 Transcript missense_variant 1520/3637 976/2880 326/959 I/L Ata/Cta 1 1 OSBPL6 HGNC HGNC:16388 protein_coding YES CCDS56150.1 ENSP00000376293 Q9BZF3 UPI0000E5A29F NM_001201480.1 tolerated(0.62) 11/26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 178339753 178339753 A C 1 0 0 0 0 1 0 0 0 11347 101 4 5 5 OSBPL6 2 178339753 Missense_Mutation SNP A C3N-02003_T 12062535 178339753 63853776 54 26735 PRKRA 0 . GRCh38 2 178444472 178444472 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.346G>A p.Asp116Asn p.D116N ENST00000325748 4/8 202 188 14 403 403 0 strelka-varscan-mutect PRKRA,missense_variant,p.Asp116Asn,ENST00000325748,NM_003690.4;PRKRA,missense_variant,p.Asp105Asn,ENST00000432031,NM_001139517.1;PRKRA,missense_variant,p.Asp91Asn,ENST00000487082,NM_001139518.1;PRKRA,intron_variant,,ENST00000457633,;AC009948.5,downstream_gene_variant,,ENST00000453026,;PRKRA,downstream_gene_variant,,ENST00000470200,;PRKRA,downstream_gene_variant,,ENST00000460433,;PRKRA,3_prime_UTR_variant,,ENST00000424699,;PRKRA,3_prime_UTR_variant,,ENST00000448279,;PRKRA,non_coding_transcript_exon_variant,,ENST00000474793,;PRKRA,upstream_gene_variant,,ENST00000490501,;PRKRA,downstream_gene_variant,,ENST00000466165,; T ENST00000325748 Transcript missense_variant 547/1826 346/942 116/313 D/N Gac/Aac 1 -1 PRKRA HGNC HGNC:9438 protein_coding YES CCDS2279.1 ENSP00000318176 O75569 UPI0000073B07 NM_003690.4 tolerated(0.15) 4/8 hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 178444472 178444472 C T 1 0 0 0 0 1 0 0 0 12657 826 29 3 3 PRKRA 2 178444472 Missense_Mutation SNP C C3N-02003_T 104719 178444472 63749057 55 26736 TTN 0 . GRCh38 2 178552510 178552510 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.90390A>C p.Glu30130Asp p.E30130D ENST00000589042 335/363 73 68 5 84 84 0 varscan-mutect TTN,missense_variant,p.Glu30130Asp,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Glu28489Asp,ENST00000591111,;TTN,missense_variant,p.Glu28489Asp,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Glu27562Asp,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Glu21065Asp,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Glu21257Asp,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Glu21190Asp,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,;RP11-65L3.2,downstream_gene_variant,,ENST00000603415,;RP11-65L3.3,upstream_gene_variant,,ENST00000624360,; G ENST00000589042 Transcript missense_variant 90615/109224 90390/107976 30130/35991 E/D gaA/gaC 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 335/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -11.60265 1 1 1 1 0 G 3 3 87 178552510 178552510 T G 1 0 0 0 0 1 0 0 0 17245 1606 56 5 5 TTN 2 178552510 Missense_Mutation SNP T C3N-02003_T 108038 178552510 63641019 56 26737 ZC3H15 0 . GRCh38 2 186508674 186508674 + Missense_Mutation SNP A A G rs1043497 C3N-02003_T C3N-02003_N A A c.1222A>G p.Thr408Ala p.T408A ENST00000337859 10/10 162 144 18 230 230 0 strelka-varscan-mutect ZC3H15,missense_variant,p.Thr408Ala,ENST00000337859,NM_018471.2;ZC3H15,3_prime_UTR_variant,,ENST00000445547,;ZC3H15,downstream_gene_variant,,ENST00000468120,;ZC3H15,downstream_gene_variant,,ENST00000481101,;ZC3H15,downstream_gene_variant,,ENST00000496289,;ZC3H15,non_coding_transcript_exon_variant,,ENST00000498757,;ZC3H15,downstream_gene_variant,,ENST00000421536,; G ENST00000337859 Transcript missense_variant 1449/2138 1222/1281 408/426 T/A Act/Gct rs1043497 1 1 ZC3H15 HGNC HGNC:29528 protein_coding YES CCDS42791.1 ENSP00000338788 Q8WU90 UPI00000437CE NM_018471.2 tolerated(0.28) 10/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12681,hmmpanther:PTHR12681:SF5 MODERATE 1 SNV 1 1 PASS rs1043497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 186508674 186508674 A G 1 0 0 0 0 1 0 0 0 18142 159 6 5 5 ZC3H15 2 186508674 Missense_Mutation SNP A C3N-02003_T 7956164 186508674 55684855 57 26738 DYTN 0 . GRCh38 2 206663328 206663328 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.1208C>T p.Ser403Phe p.S403F ENST00000452335 11/12 141 126 15 160 160 0 strelka-varscan-mutect DYTN,missense_variant,p.Ser403Phe,ENST00000452335,NM_001093730.1; A ENST00000452335 Transcript missense_variant 1325/2051 1208/1737 403/578 S/F tCt/tTt 1 -1 DYTN HGNC HGNC:23279 protein_coding YES CCDS46502.1 ENSP00000396593 A2CJ06 UPI0000EE0AB9 NM_001093730.1 tolerated(0.19) 11/12 MODERATE 1 SNV 1 1 PASS rs1230202404 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 206663328 206663328 G A 1 0 0 0 0 1 0 0 0 4684 942 33 3 3 DYTN 2 206663328 Missense_Mutation SNP G C3N-02003_T 20154654 206663328 35530201 58 26739 UNC80 0 . GRCh38 2 209995587 209995587 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.9769C>G p.His3257Asp p.H3257D ENST00000439458 64/64 128 120 8 119 119 0 strelka-varscan-mutect UNC80,missense_variant,p.His3257Asp,ENST00000439458,NM_032504.1;UNC80,missense_variant,p.His3233Asp,ENST00000272845,NM_182587.3;UNC80,non_coding_transcript_exon_variant,,ENST00000477924,; G ENST00000439458 Transcript missense_variant 9849/13562 9769/9777 3257/3258 H/D Cat/Gat 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 deleterious_low_confidence(0.01) 64/64 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 209995587 209995587 C G 1 0 0 0 0 1 0 0 0 17521 826 29 4 4 UNC80 2 209995587 Missense_Mutation SNP C C3N-02003_T 3332259 209995587 32197942 59 26740 CFAP65 0 . GRCh38 2 219032558 219032558 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.557A>C p.Lys186Thr p.K186T ENST00000341552 6/35 136 120 16 144 144 0 strelka-varscan-mutect CFAP65,missense_variant,p.Lys186Thr,ENST00000341552,NM_194302.3;CFAP65,missense_variant,p.Lys186Thr,ENST00000453220,;CFAP65,missense_variant,p.Lys175Thr,ENST00000409865,NM_001278295.1;CFAP65,missense_variant,p.Lys121Thr,ENST00000410037,NM_001278296.1;CFAP65,missense_variant,p.Lys175Thr,ENST00000457968,;CFAP65,5_prime_UTR_variant,,ENST00000441968,;CFAP65,downstream_gene_variant,,ENST00000295729,NM_152389.3;CFAP65,downstream_gene_variant,,ENST00000458526,;CFAP65,downstream_gene_variant,,ENST00000436631,;CFAP65,non_coding_transcript_exon_variant,,ENST00000462848,;CFAP65,intron_variant,,ENST00000463683,;CFAP65,upstream_gene_variant,,ENST00000474601,; G ENST00000341552 Transcript missense_variant 641/5953 557/5778 186/1925 K/T aAg/aCg 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 deleterious(0.01) 6/35 MODERATE 1 SNV 5 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 87 219032558 219032558 T G 1 0 0 0 0 1 0 0 0 3029 1609 56 5 5 CFAP65 2 219032558 Missense_Mutation SNP T C3N-02003_T 9036971 219032558 23160971 60 26741 SPHKAP 0 . GRCh38 2 227991074 227991074 + Nonsense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.4885C>T p.Gln1629Ter p.Q1629* ENST00000392056 11/12 279 254 25 273 273 0 strelka-varscan-mutect SPHKAP,stop_gained,p.Gln1629Ter,ENST00000392056,NM_001142644.1;SPHKAP,stop_gained,p.Gln1600Ter,ENST00000344657,NM_030623.3;SPHKAP,non_coding_transcript_exon_variant,,ENST00000490603,; A ENST00000392056 Transcript stop_gained 4932/6917 4885/5103 1629/1700 Q/* Cag/Tag 1 -1 SPHKAP HGNC HGNC:30619 protein_coding YES CCDS46537.1 ENSP00000375909 Q2M3C7 UPI0000411D7E NM_001142644.1 11/12 hmmpanther:PTHR10226:SF7,hmmpanther:PTHR10226,Pfam_domain:PF05716 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 87 227991074 227991074 G A 1 0 0 0 0 0 1 0 0 15399 1328 46 3 3 SPHKAP 2 227991074 Nonsense_Mutation SNP G C3N-02003_T 8958516 227991074 14202455 61 26742 UGT1A4 0 . GRCh38 2 233719252 233719252 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.432T>G p.= p.T144T ENST00000373409 1/5 285 266 19 304 304 0 varscan-mutect UGT1A4,synonymous_variant,p.=,ENST00000373409,NM_007120.2;UGT1A6,intron_variant,,ENST00000305139,NM_001072.3;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A5,intron_variant,,ENST00000373414,NM_019078.1;UGT1A7,intron_variant,,ENST00000373426,NM_019077.2;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,NM_205862.1;UGT1A6,intron_variant,,ENST00000406651,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,intron_variant,,ENST00000478062,;UGT1A4,synonymous_variant,p.=,ENST00000450233,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,;RPL17P11,downstream_gene_variant,,ENST00000417593,; G ENST00000373409 Transcript synonymous_variant 475/2388 432/1605 144/534 T acT/acG 1 1 UGT1A4 HGNC HGNC:12536 protein_coding YES CCDS33405.1 ENSP00000362508 P22310 UPI0000001044 NM_007120.2 1/5 Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF173,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 233719252 233719252 T G 1 0 0 0 0 0 0 0 1 17472 1596 56 5 5 UGT1A4 2 233719252 Silent SNP T C3N-02003_T 5728178 233719252 8474277 62 26743 SEC13 0 . GRCh38 3 10304158 10304158 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.861C>T p.= p.F287F ENST00000383801 9/10 205 187 18 152 152 0 strelka-varscan-mutect SEC13,synonymous_variant,p.=,ENST00000397117,;SEC13,synonymous_variant,p.=,ENST00000383801,NM_001136026.2;SEC13,synonymous_variant,p.=,ENST00000397109,NM_001136232.2;SEC13,synonymous_variant,p.=,ENST00000350697,NM_183352.2;SEC13,synonymous_variant,p.=,ENST00000337354,NM_030673.3;SEC13,non_coding_transcript_exon_variant,,ENST00000492602,;SEC13,non_coding_transcript_exon_variant,,ENST00000479868,;SEC13,non_coding_transcript_exon_variant,,ENST00000477547,;SEC13,non_coding_transcript_exon_variant,,ENST00000490283,;SEC13,non_coding_transcript_exon_variant,,ENST00000476597,; A ENST00000383801 Transcript synonymous_variant 933/1479 861/1107 287/368 F ttC/ttT 1 -1 SEC13 HGNC HGNC:10697 protein_coding YES CCDS63540.1 ENSP00000373312 P55735 UPI0000D4C6C4 NM_001136026.2 9/10 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR11024,hmmpanther:PTHR11024:SF8,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 10304158 10304158 G A 1 0 0 0 0 0 0 0 1 14256 1281 45 3 3 SEC13 3 10304158 Silent SNP G C3N-02003_T 10304158 187991401 63 26744 SEC13 0 . GRCh38 3 10305658 10305658 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.623T>G p.Val208Gly p.V208G ENST00000383801 7/10 186 157 29 166 166 0 strelka-varscan-mutect SEC13,missense_variant,p.Val148Gly,ENST00000397117,;SEC13,missense_variant,p.Val208Gly,ENST00000383801,NM_001136026.2;SEC13,missense_variant,p.Val148Gly,ENST00000397109,NM_001136232.2;SEC13,missense_variant,p.Val162Gly,ENST00000350697,NM_183352.2;SEC13,missense_variant,p.Val165Gly,ENST00000337354,NM_030673.3;SEC13,upstream_gene_variant,,ENST00000492602,;SEC13,non_coding_transcript_exon_variant,,ENST00000479868,;SEC13,non_coding_transcript_exon_variant,,ENST00000477547,;SEC13,non_coding_transcript_exon_variant,,ENST00000490283,;SEC13,non_coding_transcript_exon_variant,,ENST00000476597,; C ENST00000383801 Transcript missense_variant 695/1479 623/1107 208/368 V/G gTt/gGt 1 -1 SEC13 HGNC HGNC:10697 protein_coding YES CCDS63540.1 ENSP00000373312 P55735 UPI0000D4C6C4 NM_001136026.2 tolerated(0.22) 7/10 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR11024,hmmpanther:PTHR11024:SF8,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 87 10305658 10305658 A C 1 0 0 0 0 1 0 0 0 14256 43 2 5 5 SEC13 3 10305658 Missense_Mutation SNP A C3N-02003_T 1500 10305658 187989901 64 26745 COL7A1 0 . GRCh38 3 48568530 48568530 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.7763A>G p.Gln2588Arg p.Q2588R ENST00000328333 104/118 62 56 6 42 42 0 strelka-varscan-mutect COL7A1,missense_variant,p.Gln2588Arg,ENST00000328333,NM_000094.3;UCN2,upstream_gene_variant,,ENST00000273610,NM_033199.3;COL7A1,downstream_gene_variant,,ENST00000422991,;COL7A1,upstream_gene_variant,,ENST00000470076,;COL7A1,non_coding_transcript_exon_variant,,ENST00000487017,;COL7A1,non_coding_transcript_exon_variant,,ENST00000459756,;COL7A1,non_coding_transcript_exon_variant,,ENST00000467985,;COL7A1,upstream_gene_variant,,ENST00000466591,;COL7A1,upstream_gene_variant,,ENST00000474432,;COL7A1,upstream_gene_variant,,ENST00000465238,;COL7A1,downstream_gene_variant,,ENST00000462475,; C ENST00000328333 Transcript missense_variant 7871/9276 7763/8835 2588/2944 Q/R cAa/cGa 1 -1 COL7A1 HGNC HGNC:2214 protein_coding YES CCDS2773.1 ENSP00000332371 Q02388 UPI0000126D20 NM_000094.3 deleterious(0.03) 104/118 Low_complexity_(Seg):seg,hmmpanther:PTHR24020,hmmpanther:PTHR24020:SF4,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs1233028552 . 0 205 5 0 0 0 0 0 -13.90159 1 1 1 1 0 C 3 2 87 48568530 48568530 T C 1 0 0 0 0 1 0 0 0 3493 1826 63 5 5 COL7A1 3 48568530 Missense_Mutation SNP T C3N-02003_T 38262872 48568530 149727029 65 26746 TLR9 0 . GRCh38 3 52223774 52223774 + Missense_Mutation SNP T T A novel C3N-02003_T C3N-02003_N T T c.542A>T p.Lys181Met p.K181M ENST00000360658 2/2 51 47 4 40 40 0 strelka-mutect TLR9,missense_variant,p.Lys181Met,ENST00000360658,NM_017442.3;RP11-330H6.5,missense_variant,p.Lys335Met,ENST00000494383,;TWF2,downstream_gene_variant,,ENST00000305533,NM_007284.3;TWF2,downstream_gene_variant,,ENST00000499914,;RP11-330H6.6,upstream_gene_variant,,ENST00000624096,;RP11-330H6.5,downstream_gene_variant,,ENST00000478201,; A ENST00000360658 Transcript missense_variant 1176/3870 542/3099 181/1032 K/M aAg/aTg 1 -1 TLR9 HGNC HGNC:15633 protein_coding YES CCDS2848.1 ENSP00000353874 Q9NR96 UPI0000001625 NM_017442.3 deleterious(0.03) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF37,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 52223774 52223774 T A 1 0 0 0 0 1 0 0 0 16404 1609 56 4 4 TLR9 3 52223774 Missense_Mutation SNP T C3N-02003_T 3655244 52223774 146071785 66 26747 SEMA3G 0 . GRCh38 3 52435820 52435820 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.2132T>C p.Leu711Pro p.L711P ENST00000231721 16/16 421 372 49 344 344 0 strelka-varscan-mutect SEMA3G,missense_variant,p.Leu711Pro,ENST00000231721,NM_020163.1;SEMA3G,downstream_gene_variant,,ENST00000465657,; G ENST00000231721 Transcript missense_variant 2132/4899 2132/2349 711/782 L/P cTg/cCg 1 -1 SEMA3G HGNC HGNC:30400 protein_coding YES CCDS2856.1 ENSP00000231721 Q9NS98 UPI000004250D NM_020163.1 deleterious(0) 16/16 hmmpanther:PTHR11036:SF20,hmmpanther:PTHR11036 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 52435820 52435820 A G 1 0 0 0 0 1 0 0 0 14306 188 7 5 5 SEMA3G 3 52435820 Missense_Mutation SNP A C3N-02003_T 212046 52435820 145859739 67 26748 FLNB 0 . GRCh38 3 58105107 58105107 + Silent SNP A A G novel C3N-02003_T C3N-02003_N A A c.1638A>G p.= p.E546E ENST00000490882 11/47 526 442 84 528 526 2 strelka-varscan-mutect FLNB,synonymous_variant,p.=,ENST00000295956,NM_001457.3;FLNB,synonymous_variant,p.=,ENST00000429972,NM_001164318.1;FLNB,synonymous_variant,p.=,ENST00000358537,NM_001164319.1;FLNB,synonymous_variant,p.=,ENST00000490882,NM_001164317.1;FLNB,synonymous_variant,p.=,ENST00000493452,; G ENST00000490882 Transcript synonymous_variant 1803/8079 1638/7902 546/2633 E gaA/gaG 1 1 FLNB HGNC HGNC:3755 protein_coding YES CCDS54599.1 ENSP00000420213 O75369 UPI0001765F91 NM_001164317.1 11/47 Gene3D:2.60.40.10,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF238,SMART_domains:SM00557,Superfamily_domains:SSF81296,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 58105107 58105107 A G 1 0 0 0 0 0 0 0 1 5790 69 3 5 5 FLNB 3 58105107 Silent SNP A C3N-02003_T 5669287 58105107 140190452 68 26749 USF3 0 . GRCh38 3 113657830 113657830 + Silent SNP A A G novel C3N-02003_T C3N-02003_N A A c.3852T>C p.= p.S1284S ENST00000316407 7/7 226 213 13 185 185 0 strelka-varscan-mutect USF3,synonymous_variant,p.=,ENST00000316407,NM_001009899.3;USF3,synonymous_variant,p.=,ENST00000478658,;USF3,intron_variant,,ENST00000491165,;USF3,non_coding_transcript_exon_variant,,ENST00000496826,; G ENST00000316407 Transcript synonymous_variant 4263/13708 3852/6738 1284/2245 S agT/agC 1 -1 USF3 HGNC HGNC:30494 protein_coding YES CCDS43133.1 ENSP00000320794 Q68DE3 UPI0004438052 NM_001009899.3 7/7 Low_complexity_(Seg):seg LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 113657830 113657830 A G 1 0 0 0 0 0 0 0 1 17567 272 10 5 5 USF3 3 113657830 Silent SNP A C3N-02003_T 55552723 113657830 84637729 69 26750 NME9 0 . GRCh38 3 138319545 138319545 + Missense_Mutation SNP T T A novel C3N-02003_T C3N-02003_N T T c.62A>T p.Lys21Ile p.K21I ENST00000383180 5/12 249 235 14 286 286 0 strelka-varscan-mutect NME9,missense_variant,p.Lys21Ile,ENST00000383180,NM_178130.2;NME9,missense_variant,p.Lys21Ile,ENST00000317876,;NME9,missense_variant,p.Lys43Ile,ENST00000333911,;NME9,missense_variant,p.Lys43Ile,ENST00000484930,;NME9,missense_variant,p.Lys13Ile,ENST00000474690,;NME9,missense_variant,p.Lys43Ile,ENST00000475751,;NME9,missense_variant,p.Lys21Ile,ENST00000492993,;NME9,3_prime_UTR_variant,,ENST00000488716,;NME9,non_coding_transcript_exon_variant,,ENST00000478220,; A ENST00000383180 Transcript missense_variant 300/2133 62/792 21/263 K/I aAa/aTa 1 -1 NME9 HGNC HGNC:21343 protein_coding YES CCDS3099.1 ENSP00000372667 Q86XW9 UPI0000073EC5 NM_178130.2 deleterious(0) 5/12 Gene3D:3.40.30.10,Pfam_domain:PF00085,PROSITE_patterns:PS00194,hmmpanther:PTHR11349,hmmpanther:PTHR11349:SF65,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 138319545 138319545 T A 1 0 0 0 0 1 0 0 0 10535 1841 64 4 4 NME9 3 138319545 Missense_Mutation SNP T C3N-02003_T 24661715 138319545 59976014 70 26751 CEP70 0 . GRCh38 3 138529236 138529236 + Missense_Mutation SNP T T A novel C3N-02003_T C3N-02003_N T T c.832A>T p.Ser278Cys p.S278C ENST00000264982 10/18 104 82 22 140 140 0 strelka-varscan-mutect CEP70,missense_variant,p.Ser278Cys,ENST00000264982,NM_001288965.1,NM_024491.3;CEP70,missense_variant,p.Ser278Cys,ENST00000481834,NM_001288966.1;CEP70,missense_variant,p.Ser260Cys,ENST00000474781,NM_001288964.1;CEP70,missense_variant,p.Ser278Cys,ENST00000484888,;CEP70,missense_variant,p.Ser126Cys,ENST00000489254,NM_001288967.1;CEP70,missense_variant,p.Ser258Cys,ENST00000462419,;CEP70,missense_variant,p.Ser257Cys,ENST00000468900,;CEP70,downstream_gene_variant,,ENST00000478673,; A ENST00000264982 Transcript missense_variant 1099/2732 832/1794 278/597 S/C Agt/Tgt 1 -1 CEP70 HGNC HGNC:29972 protein_coding YES CCDS3102.1 ENSP00000264982 Q8NHQ1 A0A140VJG2 UPI000013D5A3 NM_001288965.1,NM_024491.3 tolerated(0.09) 10/18 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14594,hmmpanther:PTHR14594:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 138529236 138529236 T A 1 0 0 0 0 1 0 0 0 2980 1609 56 4 4 CEP70 3 138529236 Missense_Mutation SNP T C3N-02003_T 209691 138529236 59766323 71 26752 DNAJB11 0 . GRCh38 3 186582026 186582026 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.631G>C p.Glu211Gln p.E211Q ENST00000439351 7/11 183 173 10 207 207 0 strelka-varscan-mutect DNAJB11,missense_variant,p.Glu211Gln,ENST00000439351,;DNAJB11,missense_variant,p.Glu211Gln,ENST00000265028,NM_016306.5;RP11-134F2.8,missense_variant,p.Glu12Gln,ENST00000418776,;RP11-573D15.8,intron_variant,,ENST00000630178,;RP11-573D15.8,intron_variant,,ENST00000625386,;DNAJB11,non_coding_transcript_exon_variant,,ENST00000495390,;DNAJB11,downstream_gene_variant,,ENST00000464877,; C ENST00000439351 Transcript missense_variant 1560/2398 631/1077 211/358 E/Q Gaa/Caa 1 1 DNAJB11 HGNC HGNC:14889 protein_coding YES CCDS3277.1 ENSP00000414398 Q9UBS4 UPI0000001BF7 deleterious(0) 7/11 hmmpanther:PTHR24078:SF206,hmmpanther:PTHR24078,Pfam_domain:PF01556,Gene3D:2.60.260.20,Superfamily_domains:SSF49493 MODERATE 1 SNV 1 1 PASS rs1205962470 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 186582026 186582026 G C 1 0 0 0 0 1 0 0 0 4431 943 33 4 4 DNAJB11 3 186582026 Missense_Mutation SNP G C3N-02003_T 48052790 186582026 11713533 72 26753 APOD 0 . GRCh38 3 195573909 195573909 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.186C>T p.= p.I62I ENST00000343267 3/5 241 221 20 246 246 0 strelka-varscan-mutect APOD,synonymous_variant,p.=,ENST00000343267,NM_001647.3;APOD,synonymous_variant,p.=,ENST00000421243,;APOD,synonymous_variant,p.=,ENST00000453131,;APOD,missense_variant,p.Ser103Phe,ENST00000458447,;APOD,non_coding_transcript_exon_variant,,ENST00000463719,; A ENST00000343267 Transcript synonymous_variant 548/1130 186/570 62/189 I atC/atT 1 -1 APOD HGNC HGNC:612 protein_coding YES CCDS33925.1 ENSP00000345179 P05090 UPI00000369E0 NM_001647.3 3/5 hmmpanther:PTHR10612,Pfam_domain:PF08212,Gene3D:2.40.128.20,PIRSF_domain:PIRSF036893,Superfamily_domains:SSF50814,Prints_domain:PR02058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 195573909 195573909 G A 1 0 0 0 0 0 0 0 1 923 1164 41 3 3 APOD 3 195573909 Silent SNP G C3N-02003_T 8991883 195573909 2721650 73 26754 FGFR3 0 . GRCh38 4 1805912 1805912 + Frame_Shift_Del DEL G G - C3N-02003_T C3N-02003_N G G c.1817delG p.Gly606AlafsTer22 p.G606Afs*22 ENST00000340107 13/18 75 65 10 61 61 0 sindel-varindel-pindel FGFR3,frameshift_variant,p.Gly606AlafsTer22,ENST00000340107,NM_001163213.1;FGFR3,frameshift_variant,p.Gly604AlafsTer22,ENST00000440486,NM_000142.4;FGFR3,frameshift_variant,p.Gly605AlafsTer22,ENST00000481110,;FGFR3,frameshift_variant,p.Gly604AlafsTer22,ENST00000260795,;FGFR3,frameshift_variant,p.Gly492AlafsTer22,ENST00000412135,NM_022965.3;FGFR3,frameshift_variant,p.Gly492AlafsTer22,ENST00000352904,;FGFR3,3_prime_UTR_variant,,ENST00000613647,;FGFR3,downstream_gene_variant,,ENST00000507588,;FGFR3,downstream_gene_variant,,ENST00000474521,;FGFR3,downstream_gene_variant,,ENST00000469068,; - ENST00000340107 Transcript frameshift_variant 2070/4293 1814/2427 605/808 R/X cGg/cg COSM2156094,COSM2156095 1 1 FGFR3 HGNC HGNC:3690 protein_coding YES CCDS54706.1 ENSP00000339824 P22607 UPI000002A9AC NM_001163213.1 13/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000628,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF353,SMART_domains:SM00219,Superfamily_domains:SSF56112 1,1 HIGH 1 deletion 5 3 1,1 1 PASS . . 0 198 11 0 0 0 0 0 -19.9879 0.999948 1 1 1 0 - 7 5 87 1805912 1805912 G - 1 0 1 0 1 0 0 0 0 5731 1116 39 0 0 FGFR3 4 1805912 Frame_Shift_Del DEL G C3N-02003_T 1805912 188408643 74 26755 HTT 0 . GRCh38 4 3074846 3074846 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.21G>A p.= p.L7L ENST00000355072 1/67 331 312 19 364 364 0 strelka-varscan-mutect HTT,synonymous_variant,p.=,ENST00000355072,NM_002111.7;HTT-AS,upstream_gene_variant,,ENST00000503893,;HTT-AS1_2,downstream_gene_variant,,ENST00000621529,; A ENST00000355072 Transcript synonymous_variant 166/13474 21/9429 7/3142 L ctG/ctA 1 1 HTT HGNC HGNC:4851 protein_coding YES CCDS43206.1 ENSP00000347184 P42858 UPI000013D567 NM_002111.7 1/67 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 3074846 3074846 G A 1 0 0 0 0 0 0 0 1 7353 1277 45 3 3 HTT 4 3074846 Silent SNP G C3N-02003_T 1268934 3074846 187139709 75 26756 DTHD1 0 . GRCh38 4 36308267 36308267 + Silent SNP T T G C3N-02003_T C3N-02003_N T T c.1494T>G p.= p.S498S ENST00000456874 6/9 170 155 15 211 211 0 strelka-varscan-mutect DTHD1,synonymous_variant,p.=,ENST00000456874,NM_001170700.2;DTHD1,synonymous_variant,p.=,ENST00000357504,NM_001136536.4;DTHD1,synonymous_variant,p.=,ENST00000507598,;RP11-431M7.2,downstream_gene_variant,,ENST00000504344,; G ENST00000456874 Transcript synonymous_variant 1552/3365 1494/2346 498/781 S tcT/tcG COSM1429503,COSM1429504 1 1 DTHD1 HGNC HGNC:37261 protein_coding YES CCDS54754.1 ENSP00000401597 Q6ZMT9 UPI00006C079E NM_001170700.2 6/9 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 36308267 36308267 T G 1 0 0 0 0 0 0 0 1 4609 1596 56 5 5 DTHD1 4 36308267 Silent SNP T C3N-02003_T 33233421 36308267 153906288 76 26757 POLR2B 0 . GRCh38 4 57024896 57024896 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2975A>C p.Asn992Thr p.N992T ENST00000381227 23/26 139 128 11 228 228 0 strelka-varscan-mutect POLR2B,missense_variant,p.Asn992Thr,ENST00000381227,;POLR2B,missense_variant,p.Asn985Thr,ENST00000441246,NM_001303269.1;POLR2B,missense_variant,p.Asn992Thr,ENST00000314595,NM_000938.2;POLR2B,missense_variant,p.Asn917Thr,ENST00000431623,NM_001303268.1;POLR2B,non_coding_transcript_exon_variant,,ENST00000478188,;POLR2B,non_coding_transcript_exon_variant,,ENST00000484821,;POLR2B,downstream_gene_variant,,ENST00000464918,; C ENST00000381227 Transcript missense_variant 3388/4108 2975/3525 992/1174 N/T aAc/aCc 1 1 POLR2B HGNC HGNC:9188 protein_coding YES CCDS3511.1 ENSP00000370625 P30876 UPI00001345D1 deleterious(0.03) 23/26 hmmpanther:PTHR20856:SF7,hmmpanther:PTHR20856,Pfam_domain:PF00562,Gene3D:2a6hC01,Superfamily_domains:SSF64484 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 57024896 57024896 A C 1 0 0 0 0 1 0 0 0 12325 43 2 5 5 POLR2B 4 57024896 Missense_Mutation SNP A C3N-02003_T 20716629 57024896 133189659 77 26758 CCDC158 0 . GRCh38 4 76369623 76369623 + Missense_Mutation SNP C C G C3N-02003_T C3N-02003_N C C c.1150G>C p.Ala384Pro p.A384P ENST00000388914 10/24 223 200 23 178 178 0 strelka-varscan-mutect CCDC158,missense_variant,p.Ala384Pro,ENST00000388914,NM_001042784.1;CCDC158,upstream_gene_variant,,ENST00000504667,; G ENST00000388914 Transcript missense_variant,splice_region_variant 1303/3663 1150/3342 384/1113 A/P Gct/Cct COSM734644 1 -1 CCDC158 HGNC HGNC:26374 protein_coding YES CCDS43242.1 ENSP00000373566 Q5M9N0 UPI00004DF23B NM_001042784.1 deleterious(0.02) 10/24 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15921,hmmpanther:PTHR13140,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 5 1 1 PASS . . 0 167 0 19 24 0 0 0 -7.956844 0 0 1 0 0 G 3 3 87 76369623 76369623 C G 1 0 0 0 0 1 0 0 0 2478 753 26 4 4 CCDC158 4 76369623 Missense_Mutation SNP C C3N-02003_T 19344727 76369623 113844932 78 26759 SHROOM3 0 . GRCh38 4 76754890 76754890 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.4407T>C p.= p.T1469T ENST00000296043 7/11 393 370 23 384 383 1 strelka-varscan-mutect SHROOM3,synonymous_variant,p.=,ENST00000296043,NM_020859.3;RP11-359D14.2,downstream_gene_variant,,ENST00000452412,;RP11-359D14.3,downstream_gene_variant,,ENST00000449007,;SHROOM3,downstream_gene_variant,,ENST00000469923,; C ENST00000296043 Transcript synonymous_variant 5360/11020 4407/5991 1469/1996 T acT/acC 1 1 SHROOM3 HGNC HGNC:30422 protein_coding YES CCDS3579.2 ENSP00000296043 Q8TF72 UPI0000E5AC1C NM_020859.3 7/11 hmmpanther:PTHR15012:SF33,hmmpanther:PTHR15012 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 76754890 76754890 T C 1 0 0 0 0 0 0 0 1 14558 1596 56 5 5 SHROOM3 4 76754890 Silent SNP T C3N-02003_T 385267 76754890 113459665 79 26760 HNRNPD 0 . GRCh38 4 82373569 82373570 + Frame_Shift_Ins INS - - C novel C3N-02003_T C3N-02003_N - - c.109dupG p.Ala37GlyfsTer33 p.A37Gfs*33 ENST00000313899 1/9 238 214 24 265 265 0 varindel-pindel HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000313899,NM_031370.2;HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000352301,NM_031369.2;HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000353341,NM_001003810.1,NM_002138.3;HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000507010,;HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000503822,;HNRNPD,intron_variant,,ENST00000509107,;HNRNPD,intron_variant,,ENST00000515432,;HNRNPD,upstream_gene_variant,,ENST00000509263,;RP11-127B20.3,upstream_gene_variant,,ENST00000609575,;RP11-127B20.3,upstream_gene_variant,,ENST00000609552,;HNRNPD,frameshift_variant,p.Ala37GlyfsTer33,ENST00000513584,; C ENST00000313899 Transcript frameshift_variant 387-388/3033 109-110/1068 37/355 A/GX gca/gGca 1 -1 HNRNPD HGNC HGNC:5036 protein_coding YES CCDS3592.1 ENSP00000313199 Q14103 A0A024RDF3 UPI0000000C3F NM_031370.2 1/9 Low_complexity_(Seg):seg,Pfam_domain:PF08143 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 87 82373569 82373569 - C 1 0 1 1 0 0 0 0 0 7157 1319 46 0 0 HNRNPD 4 82373569 Frame_Shift_Ins INS - C3N-02003_T 5618679 82373569 107840986 80 26761 HELQ 0 . GRCh38 4 83416792 83416792 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.3137T>C p.Leu1046Pro p.L1046P ENST00000295488 17/18 129 122 7 176 175 1 strelka-varscan-mutect HELQ,missense_variant,p.Leu1046Pro,ENST00000295488,NM_133636.3;HELQ,missense_variant,p.Leu979Pro,ENST00000510985,NM_001297756.1,NM_001297755.1,NM_001297757.1;HELQ,intron_variant,,ENST00000512539,;HELQ,3_prime_UTR_variant,,ENST00000508591,; G ENST00000295488 Transcript missense_variant 3300/3579 3137/3306 1046/1101 L/P cTc/cCc 1 -1 HELQ HGNC HGNC:18536 protein_coding YES CCDS3603.1 ENSP00000295488 Q8TDG4 UPI000013E25F NM_133636.3 deleterious(0) 17/18 Gene3D:1.10.150.20,Superfamily_domains:SSF158702 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 83416792 83416792 A G 1 0 0 0 0 1 0 0 0 6929 304 11 5 5 HELQ 4 83416792 Missense_Mutation SNP A C3N-02003_T 1043223 83416792 106797763 81 26762 TET2 0 . GRCh38 4 105235847 105235847 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1905A>C p.Gln635His p.Q635H ENST00000540549 3/11 279 254 25 287 287 0 strelka-varscan-mutect TET2,missense_variant,p.Gln656His,ENST00000513237,;TET2,missense_variant,p.Gln635His,ENST00000540549,;TET2,missense_variant,p.Gln635His,ENST00000380013,NM_001127208.2;TET2,missense_variant,p.Gln635His,ENST00000305737,NM_017628.4;TET2,missense_variant,p.Gln635His,ENST00000413648,;TET2,downstream_gene_variant,,ENST00000514870,;TET2,missense_variant,p.Gln635His,ENST00000265149,; C ENST00000540549 Transcript missense_variant 2765/10166 1905/6009 635/2002 Q/H caA/caC 1 1 TET2 HGNC HGNC:25941 protein_coding YES CCDS47120.1 ENSP00000442788 Q6N021 A0A158SIU0 UPI00001D75E4 tolerated(0.23) 3/11 hmmpanther:PTHR23358:SF3,hmmpanther:PTHR23358 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 105235847 105235847 A C 1 0 0 0 0 1 0 0 0 16191 69 3 5 5 TET2 4 105235847 Missense_Mutation SNP A C3N-02003_T 21819055 105235847 84978708 82 26763 KIAA1109 0 . GRCh38 4 122258836 122258836 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.6755A>C p.Lys2252Thr p.K2252T ENST00000264501 42/86 71 61 10 87 87 0 strelka-varscan-mutect KIAA1109,missense_variant,p.Lys2252Thr,ENST00000264501,;KIAA1109,missense_variant,p.Lys2252Thr,ENST00000388738,NM_015312.3;KIAA1109,missense_variant,p.Lys210Thr,ENST00000419325,;KIAA1109,missense_variant,p.Lys825Thr,ENST00000446180,; C ENST00000264501 Transcript missense_variant 7128/15896 6755/15018 2252/5005 K/T aAa/aCa 1 1 KIAA1109 HGNC HGNC:26953 protein_coding YES CCDS43267.1 ENSP00000264501 Q2LD37 UPI0000DD87B4 tolerated(0.1) 42/86 hmmpanther:PTHR31640:SF1,hmmpanther:PTHR31640 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 122258836 122258836 A C 1 0 0 0 0 1 0 0 0 8101 14 1 5 5 KIAA1109 4 122258836 Missense_Mutation SNP A C3N-02003_T 17022989 122258836 67955719 83 26764 FAT4 0 . GRCh38 4 125321388 125321388 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.4977T>C p.= p.S1659S ENST00000394329 1/17 109 99 10 129 129 0 strelka-varscan-mutect FAT4,synonymous_variant,p.=,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4; C ENST00000394329 Transcript synonymous_variant 4990/16123 4977/14946 1659/4981 S tcT/tcC 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 1/17 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 125321388 125321388 T C 1 0 0 0 0 0 0 0 1 5552 1567 55 5 5 FAT4 4 125321388 Silent SNP T C3N-02003_T 3062552 125321388 64893167 84 26765 PLK4 0 . GRCh38 4 127896804 127896804 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2707A>C p.Thr903Pro p.T903P ENST00000270861 15/16 126 114 12 176 176 0 strelka-mutect PLK4,missense_variant,p.Thr903Pro,ENST00000270861,NM_014264.4;PLK4,missense_variant,p.Thr825Pro,ENST00000515069,;PLK4,missense_variant,p.Thr842Pro,ENST00000507249,;PLK4,missense_variant,p.Thr871Pro,ENST00000513090,NM_001190799.1;PLK4,missense_variant,p.Thr862Pro,ENST00000514379,NM_001190801.1;PLK4,missense_variant,p.Thr149Pro,ENST00000508113,;RNU6-583P,downstream_gene_variant,,ENST00000516012,;PLK4,non_coding_transcript_exon_variant,,ENST00000510192,;PLK4,downstream_gene_variant,,ENST00000507454,; C ENST00000270861 Transcript missense_variant 2981/3841 2707/2913 903/970 T/P Act/Cct 1 1 PLK4 HGNC HGNC:11397 protein_coding YES CCDS3735.1 ENSP00000270861 O00444 UPI000007426E NM_014264.4 deleterious(0.03) 15/16 Pfam_domain:PF00659,PROSITE_profiles:PS50078,hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF50,Superfamily_domains:SSF82615 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -17.37532 0.9997988 1 1 1 0 C 3 2 87 127896804 127896804 A C 1 0 0 0 0 1 0 0 0 12193 57 2 5 5 PLK4 4 127896804 Missense_Mutation SNP A C3N-02003_T 2575416 127896804 62317751 85 26766 CLGN 0 . GRCh38 4 140396108 140396108 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.982G>A p.Glu328Lys p.E328K ENST00000325617 9/15 124 117 7 189 189 0 strelka-varscan-mutect CLGN,missense_variant,p.Glu328Lys,ENST00000325617,NM_004362.2;CLGN,missense_variant,p.Glu328Lys,ENST00000414773,NM_001130675.1;CLGN,downstream_gene_variant,,ENST00000509477,; T ENST00000325617 Transcript missense_variant 1423/3043 982/1833 328/610 E/K Gaa/Aaa 1 -1 CLGN HGNC HGNC:2060 protein_coding YES CCDS3751.1 ENSP00000326699 O14967 A0A140VKG2 UPI0000126E4A NM_004362.2 tolerated(0.39) 9/15 hmmpanther:PTHR11073,hmmpanther:PTHR11073:SF7,PROSITE_patterns:PS00805,Gene3D:2.60.120.200,Pfam_domain:PF00262,Superfamily_domains:SSF63887,Prints_domain:PR00626 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.26924 0.9999995 1 1 1 0 T 3 4 87 140396108 140396108 C T 1 0 0 0 0 1 0 0 0 3292 835 29 3 3 CLGN 4 140396108 Missense_Mutation SNP C C3N-02003_T 12499304 140396108 49818447 86 26767 TLR3 0 . GRCh38 4 186082851 186082851 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1165T>C p.Ser389Pro p.S389P ENST00000296795 4/5 71 65 6 112 111 1 strelka-varscan-mutect TLR3,missense_variant,p.Ser389Pro,ENST00000296795,NM_003265.2;TLR3,missense_variant,p.Ser112Pro,ENST00000504367,;TLR3,missense_variant,p.Ser325Pro,ENST00000513189,;TLR3,downstream_gene_variant,,ENST00000508051,;TLR3,non_coding_transcript_exon_variant,,ENST00000512264,; C ENST00000296795 Transcript missense_variant 1269/6015 1165/2715 389/904 S/P Tcc/Ccc 1 1 TLR3 HGNC HGNC:11849 protein_coding YES CCDS3846.1 ENSP00000296795 O15455 UPI0000049B3E NM_003265.2 deleterious(0.02) 4/5 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF5,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -10.41134 0.9999783 1 1 1 0 C 3 2 87 186082851 186082851 T C 1 0 0 0 0 1 0 0 0 16398 1551 54 5 5 TLR3 4 186082851 Missense_Mutation SNP T C3N-02003_T 45686743 186082851 4131704 87 26768 SDHA 0 . GRCh38 5 226006 226006 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.580G>C p.Asp194His p.D194H ENST00000264932 5/15 518 469 49 412 409 3 strelka-varscan-mutect SDHA,missense_variant,p.Asp194His,ENST00000264932,NM_004168.3;SDHA,missense_variant,p.Asp146His,ENST00000510361,NM_001294332.1;SDHA,missense_variant,p.Asp194His,ENST00000504309,;SDHA,intron_variant,,ENST00000617470,;SDHA,upstream_gene_variant,,ENST00000514233,;SDHA,non_coding_transcript_exon_variant,,ENST00000505555,;SDHA,non_coding_transcript_exon_variant,,ENST00000504824,;SDHA,non_coding_transcript_exon_variant,,ENST00000509420,;SDHA,upstream_gene_variant,,ENST00000514027,;SDHA,upstream_gene_variant,,ENST00000515752,;SDHA,upstream_gene_variant,,ENST00000512962,;SDHA,downstream_gene_variant,,ENST00000502379,;SDHA,downstream_gene_variant,,ENST00000509632,; C ENST00000264932 Transcript missense_variant 695/2390 580/1995 194/664 D/H Gat/Cat 1 1 SDHA HGNC HGNC:10680 protein_coding YES CCDS3853.1 ENSP00000264932 P31040 A0A024QZ30 UPI0000000C2C NM_004168.3 deleterious_low_confidence(0) 5/15 Gene3D:3.50.50.60,Pfam_domain:PF00890,PIRSF_domain:PIRSF000171,hmmpanther:PTHR11632,hmmpanther:PTHR11632:SF51,Superfamily_domains:SSF51905,TIGRFAM_domain:TIGR01812,TIGRFAM_domain:TIGR01816 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 226006 226006 G C 1 0 0 0 0 1 0 0 0 14235 1290 45 4 4 SDHA 5 226006 Missense_Mutation SNP G C3N-02003_T 226006 181312253 88 26769 CEP72 0 . GRCh38 5 639178 639178 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1296G>A p.= p.R432R ENST00000264935 8/12 89 83 6 86 86 0 strelka-varscan-mutect CEP72,synonymous_variant,p.=,ENST00000264935,NM_018140.3;CEP72,upstream_gene_variant,,ENST00000512038,; A ENST00000264935 Transcript synonymous_variant 1386/2434 1296/1944 432/647 R agG/agA 1 1 CEP72 HGNC HGNC:25547 protein_coding YES CCDS34126.1 ENSP00000264935 Q9P209 UPI0000072FB8 NM_018140.3 8/12 hmmpanther:PTHR23311,hmmpanther:PTHR23311:SF7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 639178 639178 G A 1 0 0 0 0 0 0 0 1 2981 1165 41 3 3 CEP72 5 639178 Silent SNP G C3N-02003_T 413172 639178 180899081 89 26770 PDZD2 0 . GRCh38 5 32090136 32090136 + Missense_Mutation SNP T T C rs762388229 C3N-02003_T C3N-02003_N T T c.6688T>C p.Ser2230Pro p.S2230P ENST00000438447 20/25 132 125 7 107 107 0 strelka-varscan-mutect PDZD2,missense_variant,p.Ser2230Pro,ENST00000438447,NM_178140.2; C ENST00000438447 Transcript missense_variant 7076/11704 6688/8520 2230/2839 S/P Tca/Cca rs762388229 1 1 PDZD2 HGNC HGNC:18486 protein_coding YES CCDS34137.1 ENSP00000402033 O15018 A0A024RE15 UPI000069648B NM_178140.2 tolerated(0.08) 20/25 hmmpanther:PTHR11324,hmmpanther:PTHR11324:SF16 MODERATE 1 SNV 1 1 PASS rs762388229 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 32090136 32090136 T C 1 0 0 0 0 1 0 0 0 11789 1551 54 5 5 PDZD2 5 32090136 Missense_Mutation SNP T C3N-02003_T 31450958 32090136 149448123 90 26771 TARS 0 . GRCh38 5 33460915 33460915 + Missense_Mutation SNP C C T rs756937101 C3N-02003_T C3N-02003_N C C c.1363C>T p.His455Tyr p.H455Y ENST00000455217 13/20 179 161 18 155 154 1 strelka-varscan-mutect TARS,missense_variant,p.His422Tyr,ENST00000265112,NM_152295.4;TARS,missense_variant,p.His422Tyr,ENST00000502553,NM_001258437.1;TARS,missense_variant,p.His455Tyr,ENST00000455217,NM_001258438.1;TARS,upstream_gene_variant,,ENST00000509410,;TARS,3_prime_UTR_variant,,ENST00000508361,;TARS,3_prime_UTR_variant,,ENST00000507716,;TARS,3_prime_UTR_variant,,ENST00000509731,;TARS,downstream_gene_variant,,ENST00000504698,; T ENST00000455217 Transcript missense_variant 1485/2523 1363/2271 455/756 H/Y Cat/Tat rs756937101,COSM4465025 1 1 TARS HGNC HGNC:11572 protein_coding YES CCDS58943.1 ENSP00000387710 P26639 UPI00017A6D60 NM_001258438.1 deleterious(0.02) 13/20 PROSITE_profiles:PS50862,HAMAP:MF_00184,hmmpanther:PTHR11451,hmmpanther:PTHR11451:SF36,TIGRFAM_domain:TIGR00418,Gene3D:3.30.930.10,Pfam_domain:PF00587,Superfamily_domains:SSF55681,Prints_domain:PR01047 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs756937101 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 33460915 33460915 C T 1 0 0 0 0 1 0 0 0 15958 826 29 3 3 TARS 5 33460915 Missense_Mutation SNP C C3N-02003_T 1370779 33460915 148077344 91 26772 LIFR 0 . GRCh38 5 38510633 38510633 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.822A>C p.Gln274His p.Q274H ENST00000263409 7/20 147 133 14 238 237 1 strelka-varscan-mutect LIFR,missense_variant,p.Gln274His,ENST00000263409,NM_002310.5;LIFR,missense_variant,p.Gln274His,ENST00000453190,NM_001127671.1;LIFR,non_coding_transcript_exon_variant,,ENST00000503088,; G ENST00000263409 Transcript missense_variant 985/10089 822/3294 274/1097 Q/H caA/caC 1 -1 LIFR HGNC HGNC:6597 protein_coding YES CCDS3927.1 ENSP00000263409 P42702 UPI000004CAC2 NM_002310.5 tolerated(0.09) 7/20 hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF105 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 38510633 38510633 T G 1 0 0 0 0 1 0 0 0 8689 1606 56 5 5 LIFR 5 38510633 Missense_Mutation SNP T C3N-02003_T 5049718 38510633 143027626 92 26773 ERCC8 0 . GRCh38 5 60898389 60898389 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.730C>T p.His244Tyr p.H244Y ENST00000265038 9/12 164 153 11 357 356 1 strelka-varscan-mutect ERCC8,missense_variant,p.His244Tyr,ENST00000265038,NM_000082.3,NM_001290285.1,NM_001007233.2;ERCC8,downstream_gene_variant,,ENST00000439176,;ERCC8,non_coding_transcript_exon_variant,,ENST00000462279,;ERCC8,non_coding_transcript_exon_variant,,ENST00000495985,;ERCC8,non_coding_transcript_exon_variant,,ENST00000484330,;ERCC8,3_prime_UTR_variant,,ENST00000381118,;ERCC8,downstream_gene_variant,,ENST00000497892,;GNL3LP1,upstream_gene_variant,,ENST00000399458,; A ENST00000265038 Transcript missense_variant 773/2017 730/1191 244/396 H/Y Cat/Tat 1 -1 ERCC8 HGNC HGNC:3439 protein_coding YES CCDS3978.1 ENSP00000265038 Q13216 UPI000000D8F8 NM_000082.3,NM_001290285.1,NM_001007233.2 deleterious(0) 9/12 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22850,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 60898389 60898389 G A 1 0 0 0 0 1 0 0 0 5069 1290 45 3 3 ERCC8 5 60898389 Missense_Mutation SNP G C3N-02003_T 22387756 60898389 120639870 93 26774 ARHGEF28 0 . GRCh38 5 73752958 73752958 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.231A>C p.Glu77Asp p.E77D ENST00000545377 4/37 408 387 21 339 338 1 strelka-varscan-mutect ARHGEF28,missense_variant,p.Glu77Asp,ENST00000545377,NM_001080479.2;ARHGEF28,missense_variant,p.Glu77Asp,ENST00000513042,NM_001177693.1;ARHGEF28,missense_variant,p.Glu77Asp,ENST00000426542,;ARHGEF28,missense_variant,p.Glu77Asp,ENST00000437974,;ARHGEF28,missense_variant,p.Glu77Asp,ENST00000296794,;ARHGEF28,missense_variant,p.Glu77Asp,ENST00000509848,; C ENST00000545377 Transcript missense_variant 407/6351 231/5196 77/1731 E/D gaA/gaC 1 1 ARHGEF28 HGNC HGNC:30322 protein_coding YES CCDS47231.2 ENSP00000441913 Q8N1W1 UPI00004DF58E NM_001080479.2 tolerated(0.12) 4/37 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF133 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 73752958 73752958 A C 1 0 0 0 0 1 0 0 0 1036 69 3 5 5 ARHGEF28 5 73752958 Missense_Mutation SNP A C3N-02003_T 12854569 73752958 107785301 94 26775 ACOT12 0 . GRCh38 5 81345957 81345957 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.701A>C p.Lys234Thr p.K234T ENST00000307624 7/15 311 292 19 352 352 0 strelka-varscan-mutect ACOT12,missense_variant,p.Lys234Thr,ENST00000307624,NM_130767.2;ACOT12,upstream_gene_variant,,ENST00000508234,; G ENST00000307624 Transcript missense_variant 730/2086 701/1668 234/555 K/T aAg/aCg 1 -1 ACOT12 HGNC HGNC:24436 protein_coding YES CCDS4055.1 ENSP00000303246 Q8WYK0 UPI0000126D7B NM_130767.2 tolerated(0.15) 7/15 Gene3D:3.10.129.10,Pfam_domain:PF03061,PROSITE_profiles:PS51770,hmmpanther:PTHR11049,hmmpanther:PTHR11049:SF3,Superfamily_domains:SSF54637 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 81345957 81345957 T G 1 0 0 0 0 1 0 0 0 192 1609 56 5 5 ACOT12 5 81345957 Missense_Mutation SNP T C3N-02003_T 7592999 81345957 100192302 95 26776 TTC37 0 . GRCh38 5 95503931 95503931 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.3100G>A p.Gly1034Ser p.G1034S ENST00000358746 31/43 221 209 12 288 288 0 strelka-varscan-mutect TTC37,missense_variant,p.Gly1034Ser,ENST00000358746,NM_014639.3;TTC37,downstream_gene_variant,,ENST00000515176,;TTC37,non_coding_transcript_exon_variant,,ENST00000508181,;TTC37,non_coding_transcript_exon_variant,,ENST00000512026,;TTC37,downstream_gene_variant,,ENST00000507805,; T ENST00000358746 Transcript missense_variant 3399/5706 3100/4695 1034/1564 G/S Ggt/Agt 1 -1 TTC37 HGNC HGNC:23639 protein_coding YES CCDS4072.1 ENSP00000351596 Q6PGP7 UPI00000709BD NM_014639.3 deleterious(0.01) 31/43 Gene3D:1.25.40.10,hmmpanther:PTHR15704,hmmpanther:PTHR15704:SF7,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 95503931 95503931 C T 1 0 0 0 0 1 0 0 0 17214 594 21 3 3 TTC37 5 95503931 Missense_Mutation SNP C C3N-02003_T 14157974 95503931 86034328 96 26777 PJA2 0 . GRCh38 5 109379075 109379075 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.412C>T p.Leu138Phe p.L138F ENST00000361189 4/10 144 133 11 171 171 0 strelka-varscan-mutect PJA2,missense_variant,p.Leu138Phe,ENST00000361189,NM_014819.4;PJA2,missense_variant,p.Leu138Phe,ENST00000361557,;PJA2,downstream_gene_variant,,ENST00000511624,;PJA2,downstream_gene_variant,,ENST00000512822,; A ENST00000361189 Transcript missense_variant 652/4889 412/2127 138/708 L/F Ctt/Ttt 1 -1 PJA2 HGNC HGNC:17481 protein_coding YES CCDS4099.1 ENSP00000354775 O43164 UPI000013D192 NM_014819.4 tolerated(0.71) 4/10 hmmpanther:PTHR15710,hmmpanther:PTHR15710:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 109379075 109379075 G A 1 0 0 0 0 1 0 0 0 12058 942 33 3 3 PJA2 5 109379075 Missense_Mutation SNP G C3N-02003_T 13875144 109379075 72159184 97 26778 JADE2 0 . GRCh38 5 134566272 134566272 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.1126G>C p.Glu376Gln p.E376Q ENST00000282605 9/12 375 344 31 327 326 1 strelka-varscan-mutect JADE2,missense_variant,p.Glu376Gln,ENST00000395003,NM_015288.5;JADE2,missense_variant,p.Glu376Gln,ENST00000361895,NM_001289984.1;JADE2,missense_variant,p.Glu376Gln,ENST00000402835,;JADE2,missense_variant,p.Glu376Gln,ENST00000282605,NM_001308143.1,NM_001289985.1;JADE2,downstream_gene_variant,,ENST00000431355,;JADE2,non_coding_transcript_exon_variant,,ENST00000470876,; C ENST00000282605 Transcript missense_variant 1212/2748 1126/2505 376/834 E/Q Gag/Cag 1 1 JADE2 HGNC HGNC:22984 protein_coding YES CCDS78061.1 ENSP00000282605 G3XAA4 UPI00000437CA NM_001308143.1,NM_001289985.1 tolerated(0.48) 9/12 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF84 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 134566272 134566272 G C 1 0 0 0 0 1 0 0 0 7845 1291 45 4 4 JADE2 5 134566272 Missense_Mutation SNP G C3N-02003_T 25187197 134566272 46971987 98 26779 SEC24A 0 . GRCh38 5 134697191 134697191 + Silent SNP A A G novel C3N-02003_T C3N-02003_N A A c.2052A>G p.= p.Q684Q ENST00000398844 14/23 64 57 7 81 81 0 strelka-varscan-mutect SEC24A,synonymous_variant,p.=,ENST00000398844,NM_021982.2;SEC24A,downstream_gene_variant,,ENST00000322887,NM_001252231.1;SEC24A,downstream_gene_variant,,ENST00000513123,;RNU6-1164P,downstream_gene_variant,,ENST00000364428,; G ENST00000398844 Transcript synonymous_variant 2340/6299 2052/3282 684/1093 Q caA/caG 1 1 SEC24A HGNC HGNC:10703 protein_coding YES CCDS43363.1 ENSP00000381823 O95486 UPI0000185FF9 NM_021982.2 14/23 Gene3D:3.40.50.410,Pfam_domain:PF04811,hmmpanther:PTHR13803,hmmpanther:PTHR13803:SF1,Superfamily_domains:SSF53300 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 134697191 134697191 A G 1 0 0 0 0 0 0 0 1 14271 69 3 5 5 SEC24A 5 134697191 Silent SNP A C3N-02003_T 130919 134697191 46841068 99 26780 PCDHA9 0 . GRCh38 5 140850249 140850249 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1754T>C p.Val585Ala p.V585A ENST00000532602 1/4 455 403 52 406 406 0 strelka-varscan-mutect PCDHA9,missense_variant,p.Val585Ala,ENST00000378122,NM_014005.4;PCDHA9,missense_variant,p.Val585Ala,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; C ENST00000532602 Transcript missense_variant 2787/6293 1754/2853 585/950 V/A gTg/gCg 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 tolerated_low_confidence(0.13) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 140850249 140850249 T C 1 0 0 0 0 1 0 0 0 11618 1696 59 5 5 PCDHA9 5 140850249 Missense_Mutation SNP T C3N-02003_T 6153058 140850249 40688010 100 26781 PCDHAC1 0 . GRCh38 5 140927896 140927896 + Missense_Mutation SNP A A C rs571131956 C3N-02003_T C3N-02003_N A A c.1004A>C p.Asp335Ala p.D335A ENST00000253807 1/4 402 343 59 293 293 0 strelka-varscan-mutect PCDHAC1,missense_variant,p.Asp335Ala,ENST00000253807,NM_018898.3;PCDHAC1,missense_variant,p.Asp335Ala,ENST00000409700,NM_031882.3;PCDHA9,intron_variant,,ENST00000532602,NM_031857.1;PCDHA11,intron_variant,,ENST00000398640,NM_018902.4;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA13,intron_variant,,ENST00000289272,NM_018904.2;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA10,intron_variant,,ENST00000307360,NM_018901.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA12,intron_variant,,ENST00000398631,NM_018903.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA13,intron_variant,,ENST00000409494,;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA10,intron_variant,,ENST00000506939,NM_031860.2;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA11,intron_variant,,ENST00000617408,; C ENST00000253807 Transcript missense_variant 1004/5299 1004/2892 335/963 D/A gAt/gCt rs571131956 1 1 PCDHAC1 HGNC HGNC:8676 protein_coding YES CCDS4241.1 ENSP00000253807 Q9H158 UPI000013CDF7 NM_018898.3 deleterious(0) 1/4 Gene3D:2.60.40.60,PROSITE_patterns:PS00232,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF132,SMART_domains:SM00112,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs571131956 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 140927896 140927896 A C 1 0 0 0 0 1 0 0 0 11619 333 12 5 5 PCDHAC1 5 140927896 Missense_Mutation SNP A C3N-02003_T 77647 140927896 40610363 101 26782 PCDHB3 0 . GRCh38 5 141101847 141101847 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1198T>C p.Phe400Leu p.F400L ENST00000231130 1/1 178 159 19 180 180 0 strelka-varscan-mutect PCDHB3,missense_variant,p.Phe400Leu,ENST00000231130,NM_018937.4;PCDHB2,downstream_gene_variant,,ENST00000194155,NM_018936.3;PCDHB2,downstream_gene_variant,,ENST00000622947,;PCDHB3,upstream_gene_variant,,ENST00000624513,;PCDHB2,downstream_gene_variant,,ENST00000624994,;AC005754.7,intron_variant,,ENST00000607216,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,; C ENST00000231130 Transcript missense_variant 1375/3355 1198/2391 400/796 F/L Ttt/Ctt 1 1 PCDHB3 HGNC HGNC:8688 protein_coding YES CCDS4245.1 ENSP00000231130 Q9Y5E6 UPI0003CC25DF NM_018937.4 deleterious_low_confidence(0.02) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF77,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 141101847 141101847 T C 1 0 0 0 0 1 0 0 0 11630 1841 64 5 5 PCDHB3 5 141101847 Missense_Mutation SNP T C3N-02003_T 173951 141101847 40436412 102 26783 PPARGC1B 0 . GRCh38 5 149835310 149835310 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.1752T>G p.= p.T584T ENST00000309241 7/12 216 198 18 182 181 1 strelka-varscan-mutect PPARGC1B,synonymous_variant,p.=,ENST00000309241,NM_133263.3;PPARGC1B,synonymous_variant,p.=,ENST00000394320,;PPARGC1B,synonymous_variant,p.=,ENST00000403750,NM_001172699.1;PPARGC1B,synonymous_variant,p.=,ENST00000360453,NM_001172698.1;PPARGC1B,synonymous_variant,p.=,ENST00000434684,; G ENST00000309241 Transcript synonymous_variant 1784/10568 1752/3072 584/1023 T acT/acG 1 1 PPARGC1B HGNC HGNC:30022 protein_coding YES CCDS4298.1 ENSP00000312649 Q86YN6 UPI000006F49D NM_133263.3 7/12 hmmpanther:PTHR15528:SF12,hmmpanther:PTHR15528 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 149835310 149835310 T G 1 0 0 0 0 0 0 0 1 12410 1596 56 5 5 PPARGC1B 5 149835310 Silent SNP T C3N-02003_T 8733463 149835310 31702949 103 26784 SLC36A1 0 . GRCh38 5 151463602 151463602 + Missense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.193C>A p.Leu65Ile p.L65I ENST00000243389 3/11 272 243 29 283 283 0 strelka-varscan-mutect SLC36A1,missense_variant,p.Leu65Ile,ENST00000243389,NM_078483.2;SLC36A1,missense_variant,p.Leu65Ile,ENST00000520701,;SLC36A1,missense_variant,p.Leu65Ile,ENST00000521925,;SLC36A1,missense_variant,p.Leu65Ile,ENST00000616007,;SLC36A1,missense_variant,p.Leu65Ile,ENST00000429484,NM_001308151.1;SLC36A1,missense_variant,p.Leu65Ile,ENST00000520111,;SLC36A1,missense_variant,p.Leu65Ile,ENST00000517945,;SLC36A1,missense_variant,p.Leu65Ile,ENST00000519829,;SLC36A1,non_coding_transcript_exon_variant,,ENST00000521351,; A ENST00000243389 Transcript missense_variant 416/5781 193/1431 65/476 L/I Ctc/Atc 1 1 SLC36A1 HGNC HGNC:18761 protein_coding YES CCDS4316.1 ENSP00000243389 Q7Z2H8 UPI00001A9D3C NM_078483.2 tolerated(0.42) 3/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF188,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 151463602 151463602 C A 1 0 0 0 0 1 0 0 0 14871 565 20 2 2 SLC36A1 5 151463602 Missense_Mutation SNP C C3N-02003_T 1628292 151463602 30074657 104 26785 CNOT8 0 . GRCh38 5 154870761 154870761 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.412G>C p.Glu138Gln p.E138Q ENST00000517876 5/8 126 115 11 166 166 0 strelka-varscan-mutect CNOT8,missense_variant,p.Glu138Gln,ENST00000517876,;CNOT8,missense_variant,p.Glu138Gln,ENST00000403027,NM_004779.5;CNOT8,missense_variant,p.Glu138Gln,ENST00000285896,NM_001301073.1;CNOT8,missense_variant,p.Glu32Gln,ENST00000521450,NM_001301082.1,NM_001301075.1;CNOT8,missense_variant,p.Glu32Gln,ENST00000521583,NM_001301077.1;CNOT8,missense_variant,p.Glu32Gln,ENST00000520671,NM_001301080.1;CNOT8,missense_variant,p.Glu32Gln,ENST00000523698,NM_001301083.1;CNOT8,missense_variant,p.Glu32Gln,ENST00000519903,;CNOT8,intron_variant,,ENST00000519404,NM_001301074.1;CNOT8,intron_variant,,ENST00000518775,;CNOT8,intron_variant,,ENST00000524105,NM_001301086.1;CNOT8,intron_variant,,ENST00000522458,;CNOT8,downstream_gene_variant,,ENST00000520472,;CNOT8,downstream_gene_variant,,ENST00000517568,;CNOT8,downstream_gene_variant,,ENST00000519211,;CNOT8,downstream_gene_variant,,ENST00000521402,;CNOT8,3_prime_UTR_variant,,ENST00000521729,;CNOT8,3_prime_UTR_variant,,ENST00000522644,;CNOT8,non_coding_transcript_exon_variant,,ENST00000522139,; C ENST00000517876 Transcript missense_variant 888/2708 412/879 138/292 E/Q Gag/Cag 1 1 CNOT8 HGNC HGNC:9207 protein_coding YES CCDS4329.1 ENSP00000430493 Q9UFF9 UPI0000000E08 deleterious(0.05) 5/8 hmmpanther:PTHR10797:SF1,hmmpanther:PTHR10797,Gene3D:3.30.420.10,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 154870761 154870761 G C 1 0 0 0 0 1 0 0 0 3405 943 33 4 4 CNOT8 5 154870761 Missense_Mutation SNP G C3N-02003_T 3407159 154870761 26667498 105 26786 UNC5A 0 . GRCh38 5 176868944 176868944 + Missense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.701C>A p.Ser234Tyr p.S234Y ENST00000329542 5/15 64 57 7 47 47 0 strelka-varscan-mutect UNC5A,missense_variant,p.Ser234Tyr,ENST00000329542,NM_133369.2;UNC5A,missense_variant,p.Ser200Tyr,ENST00000509580,;UNC5A,3_prime_UTR_variant,,ENST00000513890,; A ENST00000329542 Transcript missense_variant 975/3812 701/2529 234/842 S/Y tCc/tAc 1 1 UNC5A HGNC HGNC:12567 protein_coding YES CCDS34299.1 ENSP00000332737 Q6ZN44 UPI0000047F37 NM_133369.2 deleterious(0) 5/15 Low_complexity_(Seg):seg,PROSITE_profiles:PS50835,hmmpanther:PTHR12582:SF4,hmmpanther:PTHR12582,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -15.94215 1 1 1 1 0 A 3 1 87 176868944 176868944 C A 1 0 0 0 0 1 0 0 0 17515 855 30 2 2 UNC5A 5 176868944 Missense_Mutation SNP C C3N-02003_T 21998183 176868944 4669315 106 26787 HK3 0 . GRCh38 5 176881709 176881709 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.2376C>G p.Phe792Leu p.F792L ENST00000292432 17/19 216 205 11 136 136 0 strelka-varscan HK3,missense_variant,p.Phe792Leu,ENST00000292432,NM_002115.2;UNC5A,downstream_gene_variant,,ENST00000329542,NM_133369.2;HK3,downstream_gene_variant,,ENST00000514058,;HK3,non_coding_transcript_exon_variant,,ENST00000506834,;HK3,non_coding_transcript_exon_variant,,ENST00000514666,; C ENST00000292432 Transcript missense_variant 2468/3066 2376/2772 792/923 F/L ttC/ttG 1 -1 HK3 HGNC HGNC:4925 protein_coding YES CCDS4407.1 ENSP00000292432 P52790 A0A024R7R1 UPI000006E237 NM_002115.2 deleterious(0.02) 17/19 PROSITE_profiles:PS51748,hmmpanther:PTHR19443,hmmpanther:PTHR19443:SF1,Gene3D:3.40.367.20,Pfam_domain:PF03727,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 176881709 176881709 G C 1 0 0 0 0 1 0 0 0 7081 1165 41 4 4 HK3 5 176881709 Missense_Mutation SNP G C3N-02003_T 12765 176881709 4656550 107 26788 F12 0 . GRCh38 5 177404331 177404331 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.883T>C p.Cys295Arg p.C295R ENST00000253496 9/14 128 114 14 77 77 0 strelka-varscan-mutect F12,missense_variant,p.Cys295Arg,ENST00000253496,NM_000505.3;GRK6,intron_variant,,ENST00000502598,;GRK6,upstream_gene_variant,,ENST00000506296,;PFN3,upstream_gene_variant,,ENST00000358571,NM_001029886.2;F12,upstream_gene_variant,,ENST00000514943,;F12,non_coding_transcript_exon_variant,,ENST00000510358,;F12,non_coding_transcript_exon_variant,,ENST00000502854,;F12,non_coding_transcript_exon_variant,,ENST00000503736,;F12,upstream_gene_variant,,ENST00000504406,; G ENST00000253496 Transcript missense_variant 932/2049 883/1848 295/615 C/R Tgc/Cgc 1 -1 F12 HGNC HGNC:3530 protein_coding YES CCDS34302.1 ENSP00000253496 P00748 UPI000048055F NM_000505.3 deleterious(0) 9/14 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001146,Prints_domain:PR00018,PROSITE_profiles:PS50070,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF177,Low_complexity_(Seg):seg,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 87 177404331 177404331 A G 1 0 0 0 0 1 0 0 0 5207 159 6 5 5 F12 5 177404331 Missense_Mutation SNP A C3N-02003_T 522622 177404331 4133928 108 26789 ATXN1 0 . GRCh38 6 16327184 16327184 + Missense_Mutation SNP G G A rs144862299 C3N-02003_T C3N-02003_N G G c.1127C>T p.Ser376Leu p.S376L ENST00000244769 8/9 192 179 13 110 110 0 strelka-varscan-mutect ATXN1,missense_variant,p.Ser376Leu,ENST00000244769,NM_000332.3;ATXN1,missense_variant,p.Ser376Leu,ENST00000436367,NM_001128164.1; A ENST00000244769 Transcript missense_variant 2064/10602 1127/2448 376/815 S/L tCg/tTg rs144862299 1 -1 ATXN1 HGNC HGNC:10548 protein_coding YES CCDS34342.1 ENSP00000244769 P54253 UPI000013CB8B NM_000332.3 tolerated(0.3) 8/9 hmmpanther:PTHR13392,hmmpanther:PTHR13392:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs144862299 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 16327184 16327184 G A 1 0 0 0 0 1 0 0 0 1362 1059 37 1 1 ATXN1 6 16327184 Missense_Mutation SNP G C3N-02003_T 16327184 154478795 109 26790 BTN3A1 0 . GRCh38 6 26405912 26405912 + Missense_Mutation SNP A A G C3N-02003_T C3N-02003_N A A c.89A>G p.Gln30Arg p.Q30R ENST00000289361 3/10 178 167 11 125 125 0 varscan-mutect BTN3A1,missense_variant,p.Gln30Arg,ENST00000289361,NM_007048.5;BTN3A1,missense_variant,p.Gln30Arg,ENST00000414912,NM_001145008.1;BTN3A1,missense_variant,p.Gln30Arg,ENST00000425234,NM_001145009.1;BTN3A1,missense_variant,p.Gln30Arg,ENST00000476549,NM_194441.2;BTN3A1,missense_variant,p.Gln30Arg,ENST00000506698,;BTN3A1,missense_variant,p.Gln30Arg,ENST00000450085,;BTN3A1,missense_variant,p.Gln30Arg,ENST00000427334,;BTN3A1,non_coding_transcript_exon_variant,,ENST00000082468,;BTN3A1,upstream_gene_variant,,ENST00000502361,;BTN3A1,upstream_gene_variant,,ENST00000513047,;BTN3A1,downstream_gene_variant,,ENST00000465690,; G ENST00000289361 Transcript missense_variant 457/3434 89/1542 30/513 Q/R cAg/cGg COSM318962 1 1 BTN3A1 HGNC HGNC:1138 protein_coding YES CCDS4608.1 ENSP00000289361 O00481 UPI000013C904 NM_007048.5 tolerated(0.2) 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR24100,hmmpanther:PTHR24100:SF70 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 26405912 26405912 A G 1 0 0 0 0 1 0 0 0 1738 202 7 5 5 BTN3A1 6 26405912 Missense_Mutation SNP A C3N-02003_T 10078728 26405912 144400067 110 26791 MRPS18B 0 . GRCh38 6 30619508 30619508 + Missense_Mutation SNP C C T rs753507164 C3N-02003_T C3N-02003_N C C c.94C>T p.Leu32Phe p.L32F ENST00000259873 2/7 134 119 15 143 141 2 strelka-varscan-mutect MRPS18B,missense_variant,p.Leu32Phe,ENST00000259873,NM_014046.3;PPP1R10,upstream_gene_variant,,ENST00000376511,NM_002714.3;MRPS18B,non_coding_transcript_exon_variant,,ENST00000472229,;PPP1R10,upstream_gene_variant,,ENST00000484449,;PPP1R10,upstream_gene_variant,,ENST00000473954,;MRPS18B,non_coding_transcript_exon_variant,,ENST00000472267,;MRPS18B,non_coding_transcript_exon_variant,,ENST00000492316,; T ENST00000259873 Transcript missense_variant 251/1532 94/777 32/258 L/F Ctt/Ttt rs753507164 1 1 MRPS18B HGNC HGNC:14516 protein_coding YES CCDS4682.1 ENSP00000259873 Q9Y676 B0S7P4 UPI0000132F37 NM_014046.3 tolerated(0.26) 2/7 hmmpanther:PTHR13329:SF2,hmmpanther:PTHR13329 MODERATE 1 SNV 1 1 PASS rs753507164 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 30619508 30619508 C T 1 0 0 0 0 1 0 0 0 9806 913 32 3 3 MRPS18B 6 30619508 Missense_Mutation SNP C C3N-02003_T 4213596 30619508 140186471 111 26792 NRM 0 . GRCh38 6 30690939 30690939 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.36C>T p.= p.L12L ENST00000259953 2/5 271 246 25 267 267 0 strelka-varscan-mutect NRM,synonymous_variant,p.=,ENST00000259953,NM_007243.2;NRM,synonymous_variant,p.=,ENST00000376421,NM_001270707.1;NRM,synonymous_variant,p.=,ENST00000376420,NM_001270709.1;PPP1R18,upstream_gene_variant,,ENST00000274853,NM_133471.3;PPP1R18,upstream_gene_variant,,ENST00000615527,;PPP1R18,upstream_gene_variant,,ENST00000399199,NM_001134870.1;NRM,upstream_gene_variant,,ENST00000444096,;NRM,non_coding_transcript_exon_variant,,ENST00000470733,;NRM,non_coding_transcript_exon_variant,,ENST00000462857,;NRM,non_coding_transcript_exon_variant,,ENST00000482141,;NRM,non_coding_transcript_exon_variant,,ENST00000474864,;PPP1R18,upstream_gene_variant,,ENST00000488324,;NRM,upstream_gene_variant,,ENST00000495946,;PPP1R18,upstream_gene_variant,,ENST00000467662,; A ENST00000259953 Transcript synonymous_variant 388/1755 36/789 12/262 L ctC/ctT 1 -1 NRM HGNC HGNC:8003 protein_coding YES CCDS4686.1 ENSP00000259953 Q8IXM6 UPI0000049DF1 NM_007243.2 2/5 hmmpanther:PTHR31040,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 30690939 30690939 G A 1 0 0 0 0 0 0 0 1 10715 1045 37 1 1 NRM 6 30690939 Silent SNP G C3N-02003_T 71431 30690939 140115040 112 26793 MDC1 0 . GRCh38 6 30712210 30712210 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1732G>A p.Glu578Lys p.E578K ENST00000376406 5/15 122 113 9 114 114 0 strelka-varscan-mutect MDC1,missense_variant,p.Glu578Lys,ENST00000376406,NM_014641.2;MDC1,upstream_gene_variant,,ENST00000417033,;MDC1,downstream_gene_variant,,ENST00000613547,;MDC1,downstream_gene_variant,,ENST00000422266,;MDC1,downstream_gene_variant,,ENST00000416571,;MDC1,downstream_gene_variant,,ENST00000425072,;MDC1-AS1,intron_variant,,ENST00000442150,;MDC1,upstream_gene_variant,,ENST00000494654,;MDC1,upstream_gene_variant,,ENST00000492462,; T ENST00000376406 Transcript missense_variant 2380/7576 1732/6270 578/2089 E/K Gaa/Aaa 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 tolerated(0.09) 5/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 MODERATE SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -17.71133 1 1 1 1 0 T 3 4 87 30712210 30712210 C T 1 0 0 0 0 1 0 0 0 9341 835 29 3 3 MDC1 6 30712210 Missense_Mutation SNP C C3N-02003_T 21271 30712210 140093769 113 26794 GTF2H4 0 . GRCh38 6 30910036 30910036 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.347A>G p.Gln116Arg p.Q116R ENST00000259895 4/14 274 250 24 204 204 0 strelka-varscan-mutect GTF2H4,missense_variant,p.Gln116Arg,ENST00000259895,NM_001517.4;GTF2H4,missense_variant,p.Gln116Arg,ENST00000376316,;VARS2,upstream_gene_variant,,ENST00000321897,NM_020442.5;VARS2,upstream_gene_variant,,ENST00000542001,;VARS2,upstream_gene_variant,,ENST00000541562,NM_001167734.1;VARS2,upstream_gene_variant,,ENST00000625423,NM_001167733.2;VARS2,upstream_gene_variant,,ENST00000428017,;VARS2,upstream_gene_variant,,ENST00000421263,;GTF2H4,non_coding_transcript_exon_variant,,ENST00000453897,;VARS2,upstream_gene_variant,,ENST00000467717,;VARS2,non_coding_transcript_exon_variant,,ENST00000477288,;GTF2H4,non_coding_transcript_exon_variant,,ENST00000487746,;GTF2H4,upstream_gene_variant,,ENST00000483318,;GTF2H4,upstream_gene_variant,,ENST00000475845,; G ENST00000259895 Transcript missense_variant 570/1735 347/1389 116/462 Q/R cAg/cGg 1 1 GTF2H4 HGNC HGNC:4658 protein_coding YES CCDS34386.1 ENSP00000259895 Q92759 UPI000000D741 NM_001517.4 tolerated(0.29) 4/14 Pfam_domain:PF03849,hmmpanther:PTHR13152,TIGRFAM_domain:TIGR00625 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 30910036 30910036 A G 1 0 0 0 0 1 0 0 0 6746 188 7 5 5 GTF2H4 6 30910036 Missense_Mutation SNP A C3N-02003_T 197826 30910036 139895943 114 26795 NOTCH4 0 . GRCh38 6 32214183 32214183 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.2094A>G p.= p.A698A ENST00000375023 13/30 158 126 32 158 158 0 strelka-varscan-mutect NOTCH4,synonymous_variant,p.=,ENST00000375023,NM_004557.3;NOTCH4,non_coding_transcript_exon_variant,,ENST00000465528,;NOTCH4,downstream_gene_variant,,ENST00000473562,; C ENST00000375023 Transcript synonymous_variant 2233/6745 2094/6012 698/2003 A gcA/gcG 1 -1 NOTCH4 HGNC HGNC:7884 protein_coding YES CCDS34420.1 ENSP00000364163 Q99466 UPI0000130571 NM_004557.3 13/30 PROSITE_profiles:PS50026,hmmpanther:PTHR24033,hmmpanther:PTHR24033:SF64,Gene3D:2.10.25.10,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 32214183 32214183 T C 1 0 0 0 0 0 0 0 1 10596 1683 59 5 5 NOTCH4 6 32214183 Silent SNP T C3N-02003_T 1304147 32214183 138591796 115 26796 RGL2 0 . GRCh38 6 33295517 33295517 + Silent SNP G G T rs201012764 C3N-02003_T C3N-02003_N G G c.1011C>A p.= p.R337R ENST00000497454 7/18 118 111 7 60 60 0 strelka-mutect RGL2,synonymous_variant,p.=,ENST00000497454,NM_004761.4,NM_001243738.1;PFDN6,intron_variant,,ENST00000463584,;TAPBP,downstream_gene_variant,,ENST00000434618,NM_003190.4;PFDN6,downstream_gene_variant,,ENST00000395131,;PFDN6,downstream_gene_variant,,ENST00000374606,NM_001185181.2;RGL2,downstream_gene_variant,,ENST00000425946,;PFDN6,downstream_gene_variant,,ENST00000374607,NM_014260.3,NM_001265595.1,NM_001265596.1;PFDN6,downstream_gene_variant,,ENST00000374610,;RGL2,non_coding_transcript_exon_variant,,ENST00000437840,;RGL2,non_coding_transcript_exon_variant,,ENST00000491168,;RGL2,upstream_gene_variant,,ENST00000471319,;RGL2,downstream_gene_variant,,ENST00000485077,;RGL2,non_coding_transcript_exon_variant,,ENST00000483151,;RGL2,non_coding_transcript_exon_variant,,ENST00000476616,;RGL2,downstream_gene_variant,,ENST00000494550,;RGL2,downstream_gene_variant,,ENST00000478610,;PFDN6,downstream_gene_variant,,ENST00000491382,;PFDN6,downstream_gene_variant,,ENST00000395134,;RGL2,downstream_gene_variant,,ENST00000460988,; T ENST00000497454 Transcript synonymous_variant 1507/3278 1011/2334 337/777 R cgC/cgA rs201012764 1 -1 RGL2 HGNC HGNC:9769 protein_coding YES CCDS4774.1 ENSP00000420211 O15211 A0A024RCS9 UPI0000001621 NM_004761.4,NM_001243738.1 7/18 PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF213,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 LOW 1 SNV 1 1 PASS rs201012764 . 0 204 5 0 0 0 0 0 -13.77164 1 1 1 1 0 T 2 4 87 33295517 33295517 G T 1 0 0 0 0 0 0 0 1 13450 1074 38 1 1 RGL2 6 33295517 Silent SNP G C3N-02003_T 1081334 33295517 137510462 116 26797 RGL2 0 . GRCh38 6 33295732 33295732 + Nonsense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.796C>T p.Gln266Ter p.Q266* ENST00000497454 7/18 122 111 11 91 91 0 strelka-varscan-mutect RGL2,stop_gained,p.Gln266Ter,ENST00000497454,NM_004761.4,NM_001243738.1;PFDN6,intron_variant,,ENST00000463584,;TAPBP,downstream_gene_variant,,ENST00000434618,NM_003190.4;PFDN6,downstream_gene_variant,,ENST00000395131,;PFDN6,downstream_gene_variant,,ENST00000374606,NM_001185181.2;RGL2,downstream_gene_variant,,ENST00000425946,;PFDN6,downstream_gene_variant,,ENST00000374607,NM_014260.3,NM_001265595.1,NM_001265596.1;PFDN6,downstream_gene_variant,,ENST00000374610,;RGL2,non_coding_transcript_exon_variant,,ENST00000437840,;RGL2,non_coding_transcript_exon_variant,,ENST00000491168,;RGL2,upstream_gene_variant,,ENST00000471319,;RGL2,downstream_gene_variant,,ENST00000485077,;RGL2,non_coding_transcript_exon_variant,,ENST00000483151,;RGL2,non_coding_transcript_exon_variant,,ENST00000478610,;RGL2,upstream_gene_variant,,ENST00000476616,;RGL2,downstream_gene_variant,,ENST00000494550,;PFDN6,downstream_gene_variant,,ENST00000491382,;PFDN6,downstream_gene_variant,,ENST00000395134,;RGL2,downstream_gene_variant,,ENST00000460988,; A ENST00000497454 Transcript stop_gained 1292/3278 796/2334 266/777 Q/* Cag/Tag 1 -1 RGL2 HGNC HGNC:9769 protein_coding YES CCDS4774.1 ENSP00000420211 O15211 A0A024RCS9 UPI0000001621 NM_004761.4,NM_001243738.1 7/18 PROSITE_profiles:PS50009,hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF213,Gene3D:2ii0A02,Pfam_domain:PF00617,SMART_domains:SM00147,Superfamily_domains:0041591 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 87 33295732 33295732 G A 1 0 0 0 0 0 1 0 0 13450 1299 45 3 3 RGL2 6 33295732 Nonsense_Mutation SNP G C3N-02003_T 215 33295732 137510247 117 26798 NFKBIE 0 . GRCh38 6 44262637 44262637 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.808G>C p.Glu270Gln p.E270Q ENST00000275015 2/6 255 240 15 252 252 0 strelka-varscan-mutect NFKBIE,missense_variant,p.Glu270Gln,ENST00000275015,NM_004556.2;NFKBIE,missense_variant,p.Glu131Gln,ENST00000619360,;SLC35B2,upstream_gene_variant,,ENST00000615337,NM_001286511.1;NFKBIE,upstream_gene_variant,,ENST00000443607,;NFKBIE,intron_variant,,ENST00000477930,; G ENST00000275015 Transcript missense_variant 833/2581 808/1503 270/500 E/Q Gag/Cag 1 -1 NFKBIE HGNC HGNC:7799 protein_coding YES CCDS34463.1 ENSP00000275015 O00221 A0A024RD24 UPI000013DA3C NM_004556.2 tolerated(0.08) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50297,hmmpanther:PTHR24118:SF37,hmmpanther:PTHR24118,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 44262637 44262637 C G 1 0 0 0 0 1 0 0 0 10417 835 29 4 4 NFKBIE 6 44262637 Missense_Mutation SNP C C3N-02003_T 10966905 44262637 126543342 118 26799 ADGRF5 0 . GRCh38 6 46858259 46858259 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.3644T>G p.Phe1215Cys p.F1215C ENST00000283296 17/21 272 238 34 182 182 0 strelka-varscan-mutect ADGRF5,missense_variant,p.Phe1215Cys,ENST00000283296,NM_001098518.1;ADGRF5,missense_variant,p.Phe1215Cys,ENST00000265417,NM_015234.4;ADGRF5,downstream_gene_variant,,ENST00000498632,; C ENST00000283296 Transcript missense_variant 3933/5810 3644/4041 1215/1346 F/C tTt/tGt 1 -1 ADGRF5 HGNC HGNC:19030 protein_coding YES CCDS4919.1 ENSP00000283296 Q8IZF2 UPI000007075A NM_001098518.1 deleterious(0) 17/21 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF272,Pfam_domain:PF00002,Prints_domain:PR01695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 46858259 46858259 A C 1 0 0 0 0 1 0 0 0 367 14 1 5 5 ADGRF5 6 46858259 Missense_Mutation SNP A C3N-02003_T 2595622 46858259 123947720 119 26800 ADGRF5 0 . GRCh38 6 46860755 46860755 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.2339T>C p.Leu780Pro p.L780P ENST00000283296 16/21 89 70 19 116 116 0 strelka-varscan-mutect ADGRF5,missense_variant,p.Leu780Pro,ENST00000283296,NM_001098518.1;ADGRF5,missense_variant,p.Leu780Pro,ENST00000265417,NM_015234.4;ADGRF5,non_coding_transcript_exon_variant,,ENST00000498632,; G ENST00000283296 Transcript missense_variant 2628/5810 2339/4041 780/1346 L/P cTc/cCc 1 -1 ADGRF5 HGNC HGNC:19030 protein_coding YES CCDS4919.1 ENSP00000283296 Q8IZF2 UPI000007075A NM_001098518.1 deleterious(0) 16/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF272 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 46860755 46860755 A G 1 0 0 0 0 1 0 0 0 367 304 11 5 5 ADGRF5 6 46860755 Missense_Mutation SNP A C3N-02003_T 2496 46860755 123945224 120 26801 CENPQ 0 . GRCh38 6 49488424 49488424 + Nonsense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.550C>T p.Gln184Ter p.Q184* ENST00000335783 7/9 141 130 11 203 203 0 strelka-varscan-mutect CENPQ,stop_gained,p.Gln184Ter,ENST00000335783,NM_018132.3; T ENST00000335783 Transcript stop_gained 644/1733 550/807 184/268 Q/* Cag/Tag 1 1 CENPQ HGNC HGNC:21347 protein_coding YES CCDS4925.1 ENSP00000337289 Q7L2Z9 UPI000020DE7B NM_018132.3 7/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF13094,hmmpanther:PTHR31345,hmmpanther:PTHR31345:SF3 HIGH 1 SNV 1 1 PASS rs1396104443 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 87 49488424 49488424 C T 1 0 0 0 0 0 1 0 0 2949 827 29 3 3 CENPQ 6 49488424 Nonsense_Mutation SNP C C3N-02003_T 2627669 49488424 121317555 121 26802 IL17F 0 . GRCh38 6 52236949 52236949 + Silent SNP G G C novel C3N-02003_T C3N-02003_N G G c.474C>G p.= p.V158V ENST00000336123 3/3 446 412 34 337 337 0 strelka-varscan-mutect IL17F,synonymous_variant,p.=,ENST00000336123,NM_052872.3;IL17F,non_coding_transcript_exon_variant,,ENST00000478427,; C ENST00000336123 Transcript synonymous_variant 582/850 474/492 158/163 V gtC/gtG 1 -1 IL17F HGNC HGNC:16404 protein_coding YES CCDS4938.1 ENSP00000337432 Q96PD4 UPI0000038A0C NM_052872.3 3/3 hmmpanther:PTHR21295:SF8,hmmpanther:PTHR21295,Gene3D:2.10.90.10,Superfamily_domains:SSF57501 LOW 1 SNV 1 1 PASS rs1312601839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 52236949 52236949 G C 1 0 0 0 0 0 0 0 1 7546 1277 45 4 4 IL17F 6 52236949 Silent SNP G C3N-02003_T 2748525 52236949 118569030 122 26803 MCM3 0 . GRCh38 6 52284599 52284599 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.211G>A p.Glu71Lys p.E71K ENST00000616552 1/17 376 332 44 356 356 0 strelka-varscan-mutect MCM3,missense_variant,p.Glu71Lys,ENST00000616552,NM_002388.4;MCM3,missense_variant,p.Glu71Lys,ENST00000596288,;MCM3,missense_variant,p.Glu26Lys,ENST00000229854,;MCM3,splice_region_variant,p.=,ENST00000419835,NM_001270472.1;MCM3,missense_variant,p.Glu71Lys,ENST00000596983,; T ENST00000616552 Transcript missense_variant,splice_region_variant 283/3208 211/2562 71/853 E/K Gag/Aag 1 -1 MCM3 HGNC HGNC:6945 protein_coding YES CCDS4940.2 ENSP00000480987 P25205 UPI0000EE4F08 NM_002388.4 tolerated(0.23) 1/17 hmmpanther:PTHR11630,hmmpanther:PTHR11630:SF72,Gene3D:1ltlA01,Pfam_domain:PF14551,Superfamily_domains:SSF50249 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 52284599 52284599 C T 1 0 0 0 0 1 0 0 0 9319 898 31 1 1 MCM3 6 52284599 Missense_Mutation SNP C C3N-02003_T 47650 52284599 118521380 123 26804 ME1 0 . GRCh38 6 83211951 83211951 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1692G>A p.= p.Q564Q ENST00000369705 14/14 71 63 8 120 120 0 strelka-varscan-mutect ME1,synonymous_variant,p.=,ENST00000369705,NM_002395.5; T ENST00000369705 Transcript synonymous_variant 1809/3371 1692/1719 564/572 Q caG/caA 1 -1 ME1 HGNC HGNC:6983 protein_coding YES CCDS34492.1 ENSP00000358719 P48163 UPI000000127E NM_002395.5 14/14 Gene3D:3.40.50.720,hmmpanther:PTHR23406,hmmpanther:PTHR23406:SF17,Superfamily_domains:SSF51735 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 83211951 83211951 C T 1 0 0 0 0 0 0 0 1 9356 912 32 3 3 ME1 6 83211951 Silent SNP C C3N-02003_T 30927352 83211951 87594028 124 26805 RRAGD 0 . GRCh38 6 89387515 89387515 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.224A>G p.Lys75Arg p.K75R ENST00000369415 2/7 191 174 17 179 179 0 strelka-varscan-mutect RRAGD,missense_variant,p.Lys75Arg,ENST00000369415,NM_021244.4;RRAGD,intron_variant,,ENST00000359203,;RRAGD,non_coding_transcript_exon_variant,,ENST00000492783,; C ENST00000369415 Transcript missense_variant 501/4900 224/1203 75/400 K/R aAg/aGg 1 -1 RRAGD HGNC HGNC:19903 protein_coding YES CCDS5022.1 ENSP00000358423 Q9NQL2 UPI000006E549 NM_021244.4 deleterious(0) 2/7 Gene3D:3.40.50.300,Pfam_domain:PF04670,hmmpanther:PTHR11259,hmmpanther:PTHR11259:SF5,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 89387515 89387515 T C 1 0 0 0 0 1 0 0 0 13929 1609 56 5 5 RRAGD 6 89387515 Missense_Mutation SNP T C3N-02003_T 6175564 89387515 81418464 125 26806 SIM1 0 . GRCh38 6 100390753 100390753 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.1909G>C p.Glu637Gln p.E637Q ENST00000369208 12/12 376 339 37 343 343 0 strelka-varscan-mutect SIM1,missense_variant,p.Glu637Gln,ENST00000369208,;SIM1,missense_variant,p.Glu637Gln,ENST00000262901,NM_005068.2;SIM1,downstream_gene_variant,,ENST00000505753,; G ENST00000369208 Transcript missense_variant 2692/8430 1909/2301 637/766 E/Q Gag/Cag 1 -1 SIM1 HGNC HGNC:10882 protein_coding YES CCDS5045.1 ENSP00000358210 P81133 UPI000013D355 tolerated_low_confidence(0.2) 12/12 Pfam_domain:PF06621,PROSITE_profiles:PS51302,hmmpanther:PTHR23043,hmmpanther:PTHR23043:SF29 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 100390753 100390753 C G 1 0 0 0 0 1 0 0 0 14586 922 32 4 4 SIM1 6 100390753 Missense_Mutation SNP C C3N-02003_T 11003238 100390753 70415226 126 26807 MICAL1 0 . GRCh38 6 109447071 109447071 + Splice_Site SNP A A C novel C3N-02003_T C3N-02003_N A A c.2284+2T>G p.X762_splice ENST00000630715 99 74 25 74 74 0 strelka-varscan-mutect MICAL1,splice_donor_variant,,ENST00000630715,NM_001286613.1;MICAL1,splice_donor_variant,,ENST00000358807,NM_022765.3;MICAL1,splice_donor_variant,,ENST00000358577,NM_001159291.1;SMPD2,downstream_gene_variant,,ENST00000258052,NM_003080.2;MICAL1,downstream_gene_variant,,ENST00000433205,;SMPD2,downstream_gene_variant,,ENST00000458487,;MICAL1,downstream_gene_variant,,ENST00000483856,;MICAL1,splice_donor_variant,,ENST00000465904,;MICAL1,splice_donor_variant,,ENST00000456101,;SMPD2,downstream_gene_variant,,ENST00000439615,; C ENST00000630715 Transcript splice_donor_variant -/3678 2284/3261 762/1086 1 -1 MICAL1 HGNC HGNC:20619 protein_coding YES CCDS69170.1 ENSP00000486901 Q8TDZ2 UPI0002064DFD NM_001286613.1 17/24 HIGH SNV 2 1 PASS rs1363297935 . 0 201 8 0 0 0 0 0 -20 0.9999993 1 1 1 0 C 5 2 87 109447071 109447071 A C 1 0 0 0 0 0 0 1 0 9526 173 6 5 5 MICAL1 6 109447071 Splice_Site SNP A C3N-02003_T 9056318 109447071 61358908 127 26808 FBXO5 0 . GRCh38 6 152975594 152975594 + Missense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.131C>A p.Ser44Tyr p.S44Y ENST00000229758 2/5 52 47 5 86 86 0 strelka-varscan-mutect FBXO5,missense_variant,p.Ser44Tyr,ENST00000229758,NM_012177.3;FBXO5,5_prime_UTR_variant,,ENST00000367241,NM_001142522.1;FBXO5,upstream_gene_variant,,ENST00000477822,; T ENST00000229758 Transcript missense_variant 190/2037 131/1344 44/447 S/Y tCt/tAt 1 -1 FBXO5 HGNC HGNC:13584 protein_coding YES CCDS5242.1 ENSP00000229758 Q9UKT4 UPI000012A585 NM_012177.3 tolerated(0.07) 2/5 hmmpanther:PTHR15493,hmmpanther:PTHR15493:SF8 MODERATE 1 SNV 1 1 PASS rs1276603040 . 0 208 2 0 0 0 0 0 -12.67776 1 1 1 1 0 T 3 4 87 152975594 152975594 G T 1 0 0 0 0 1 0 0 0 5621 942 33 2 2 FBXO5 6 152975594 Missense_Mutation SNP G C3N-02003_T 43528523 152975594 17830385 128 26809 AHR 0 . GRCh38 7 17340021 17340021 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.2196T>G p.= p.T732T ENST00000242057 10/11 120 111 9 131 131 0 strelka-varscan-mutect AHR,synonymous_variant,p.=,ENST00000242057,NM_001621.4;RP11-507K12.1,synonymous_variant,p.=,ENST00000637807,;AHR,downstream_gene_variant,,ENST00000492120,;AHR,downstream_gene_variant,,ENST00000481944,;AHR,synonymous_variant,p.=,ENST00000463496,; G ENST00000242057 Transcript synonymous_variant 2839/6276 2196/2547 732/848 T acT/acG 1 1 AHR HGNC HGNC:348 protein_coding YES CCDS5366.1 ENSP00000242057 P35869 A0A024R9Z8 UPI0000125727 NM_001621.4 10/11 hmmpanther:PTHR10649:SF9,hmmpanther:PTHR10649 LOW 1 SNV 1 1 PASS rs1441798551 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 17340021 17340021 T G 1 0 0 0 0 0 0 0 1 493 1596 56 5 5 AHR 7 17340021 Silent SNP T C3N-02003_T 17340021 142005952 129 26810 ADCYAP1R1 0 . GRCh38 7 31064918 31064918 + Missense_Mutation SNP T T G C3N-02003_T C3N-02003_N T T c.139T>G p.Phe47Val p.F47V ENST00000614107 3/17 179 169 10 166 166 0 strelka-varscan-mutect ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000614107,NM_001199635.1,NM_001199636.1;ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000304166,NM_001118.4;ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000409363,NM_001199637.1;ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000409489,;ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000396211,;ADCYAP1R1,missense_variant,p.Phe47Val,ENST00000431811,; G ENST00000614107 Transcript missense_variant 428/6575 139/1491 47/496 F/V Ttc/Gtc COSM5544430 1 1 ADCYAP1R1 HGNC HGNC:242 protein_coding YES CCDS56480.1 ENSP00000483721 P41586 UPI0000DA58BA NM_001199635.1,NM_001199636.1 tolerated(0.56) 3/17 Prints_domain:PR01156,PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF228,Superfamily_domains:SSF111418 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 31064918 31064918 T G 1 0 0 0 0 1 0 0 0 347 1609 56 5 5 ADCYAP1R1 7 31064918 Missense_Mutation SNP T C3N-02003_T 13724897 31064918 128281055 130 26811 BMPER 0 . GRCh38 7 33905688 33905688 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.75C>T p.= p.V25V ENST00000297161 2/16 503 457 46 513 513 0 strelka-varscan-mutect BMPER,synonymous_variant,p.=,ENST00000297161,NM_133468.4;BMPER,synonymous_variant,p.=,ENST00000436222,;BMPER,synonymous_variant,p.=,ENST00000448280,;BMPER,synonymous_variant,p.=,ENST00000444773,;BMPER,non_coding_transcript_exon_variant,,ENST00000496609,; T ENST00000297161 Transcript synonymous_variant 449/5031 75/2058 25/685 V gtC/gtT 1 1 BMPER HGNC HGNC:24154 protein_coding YES CCDS5442.1 ENSP00000297161 Q8N8U9 A0A090N7U6 UPI000006D462 NM_133468.4 2/16 Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 33905688 33905688 C T 1 0 0 0 0 0 0 0 1 1623 900 32 3 3 BMPER 7 33905688 Silent SNP C C3N-02003_T 2840770 33905688 125440285 131 26812 DDC 0 . GRCh38 7 50539956 50539956 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.274G>C p.Asp92His p.D92H ENST00000444124 3/15 569 519 50 458 458 0 strelka-varscan-mutect DDC,missense_variant,p.Asp92His,ENST00000444124,NM_001082971.1;DDC,missense_variant,p.Asp92His,ENST00000357936,NM_000790.3;DDC,missense_variant,p.Asp92His,ENST00000617822,NM_001242887.1;DDC,missense_variant,p.Asp92His,ENST00000615193,NM_001242889.1;DDC,missense_variant,p.Asp92His,ENST00000431062,;DDC,missense_variant,p.Asp58His,ENST00000430300,;DDC,missense_variant,p.Asp92His,ENST00000380984,NM_001242890.1;FIGNL1,intron_variant,,ENST00000613602,;DDC,intron_variant,,ENST00000622873,NM_001242886.1;DDC,intron_variant,,ENST00000426377,NM_001242888.1;DDC,downstream_gene_variant,,ENST00000420203,;DDC-AS1,non_coding_transcript_exon_variant,,ENST00000454521,;DDC,non_coding_transcript_exon_variant,,ENST00000489162,;DDC,intron_variant,,ENST00000444733,; G ENST00000444124 Transcript missense_variant 475/2041 274/1443 92/480 D/H Gac/Cac 1 -1 DDC HGNC HGNC:2719 protein_coding YES CCDS5511.1 ENSP00000403644 P20711 A0A0S2Z3N4 UPI000013F150 NM_001082971.1 deleterious(0) 3/15 Gene3D:3.40.640.10,Pfam_domain:PF00282,Prints_domain:PR00800,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF70,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 50539956 50539956 C G 1 0 0 0 0 1 0 0 0 4128 855 30 4 4 DDC 7 50539956 Missense_Mutation SNP C C3N-02003_T 16634268 50539956 108806017 132 26813 ZNF479 0 . GRCh38 7 57120250 57120250 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1165G>A p.Asp389Asn p.D389N ENST00000331162 5/5 98 89 9 137 137 0 varscan-mutect ZNF479,missense_variant,p.Asp389Asn,ENST00000331162,NM_033273.2;ZNF479,missense_variant,p.Asp389Asn,ENST00000319636,;ZNF479,missense_variant,p.Asp277Asn,ENST00000620639,; T ENST00000331162 Transcript missense_variant 1436/2072 1165/1575 389/524 D/N Gac/Aac 1 -1 ZNF479 HGNC HGNC:23258 protein_coding YES CCDS43590.1 ENSP00000333776 Q96JC4 UPI000006E615 NM_033273.2 deleterious(0.01) 5/5 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 57120250 57120250 C T 1 0 0 0 0 1 0 0 0 18505 913 32 3 3 ZNF479 7 57120250 Missense_Mutation SNP C C3N-02003_T 6580294 57120250 102225723 133 26814 POMZP3 0 . GRCh38 7 76625684 76625684 + Splice_Site SNP C C T novel C3N-02003_T C3N-02003_N C C c.66-1G>A p.X22_splice ENST00000310842 157 147 10 162 162 0 varscan-mutect POMZP3,splice_acceptor_variant,,ENST00000310842,NM_012230.3;POMZP3,splice_acceptor_variant,,ENST00000275569,NM_152992.2;POMZP3,splice_acceptor_variant,,ENST00000454397,;AC004980.7,intron_variant,,ENST00000418663,;AC004980.7,intron_variant,,ENST00000450661,;AC004980.7,downstream_gene_variant,,ENST00000423084,;POMZP3,splice_acceptor_variant,,ENST00000424818,; T ENST00000310842 Transcript splice_acceptor_variant -/1490 66/564 22/187 1 -1 POMZP3 HGNC HGNC:9203 protein_coding YES CCDS43606.1 ENSP00000309233 Q6PJE2 UPI000059D9C5 NM_012230.3 2/6 HIGH 1 SNV 1 1 PASS rs1372152588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 87 76625684 76625684 C T 1 0 0 0 0 0 0 1 0 12361 927 32 3 3 POMZP3 7 76625684 Splice_Site SNP C C3N-02003_T 19505434 76625684 82720289 134 26815 VPS50 0 . GRCh38 7 93341429 93341429 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2061A>C p.Glu687Asp p.E687D ENST00000305866 23/28 79 74 5 70 70 0 strelka-varscan-mutect VPS50,missense_variant,p.Glu657Asp,ENST00000544910,NM_001257998.1;VPS50,missense_variant,p.Glu687Asp,ENST00000305866,NM_017667.3;VPS50,splice_region_variant,,ENST00000474412,;VPS50,splice_region_variant,,ENST00000467326,;VPS50,splice_region_variant,,ENST00000441602,;VPS50,splice_region_variant,,ENST00000471188,;VPS50,splice_region_variant,,ENST00000480943,; C ENST00000305866 Transcript missense_variant,splice_region_variant 2189/3613 2061/2895 687/964 E/D gaA/gaC 1 1 VPS50 HGNC HGNC:25956 protein_coding YES CCDS43617.1 ENSP00000307666 Q96JG6 UPI000015F998 NM_017667.3 tolerated(0.22) 23/28 hmmpanther:PTHR13258 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.26985 1 1 1 1 0 C 3 2 87 93341429 93341429 A C 1 0 0 0 0 1 0 0 0 17760 86 3 5 5 VPS50 7 93341429 Missense_Mutation SNP A C3N-02003_T 16715745 93341429 66004544 135 26816 TRRAP 0 . GRCh38 7 98890419 98890419 + Nonsense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.235C>T p.Gln79Ter p.Q79* ENST00000359863 4/72 53 46 7 98 98 0 strelka-varscan-mutect TRRAP,stop_gained,p.Gln79Ter,ENST00000359863,NM_001244580.1;TRRAP,stop_gained,p.Gln79Ter,ENST00000628380,;TRRAP,stop_gained,p.Gln79Ter,ENST00000355540,NM_003496.3;TRRAP,stop_gained,p.Gln79Ter,ENST00000446306,;TRRAP,downstream_gene_variant,,ENST00000417523,; T ENST00000359863 Transcript stop_gained 444/12677 235/11580 79/3859 Q/* Cag/Tag 1 1 TRRAP HGNC HGNC:12347 protein_coding YES CCDS59066.1 ENSP00000352925 Q9Y4A5 UPI00004575B4 NM_001244580.1 4/72 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF1,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -16.72046 1 1 1 1 0 T 4 4 87 98890419 98890419 C T 1 0 0 0 0 0 1 0 0 17107 827 29 3 3 TRRAP 7 98890419 Nonsense_Mutation SNP C C3N-02003_T 5548990 98890419 60455554 136 26817 CYP3A4 0 . GRCh38 7 99760982 99760982 + Splice_Site SNP C C A novel C3N-02003_T C3N-02003_N C C c.1254-1G>T p.X418_splice ENST00000336411 79 73 6 121 121 0 strelka-varscan-mutect CYP3A4,splice_acceptor_variant,,ENST00000354593,;CYP3A4,splice_acceptor_variant,,ENST00000336411,NM_017460.5,NM_001202855.2; A ENST00000336411 Transcript splice_acceptor_variant -/2153 1254/1512 418/503 1 -1 CYP3A4 HGNC HGNC:2637 protein_coding YES CCDS5674.1 ENSP00000337915 P08684 Q6GRK0 UPI000013E0B7 NM_017460.5,NM_001202855.2 11/12 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 87 99760982 99760982 C A 1 0 0 0 0 0 0 1 0 3981 927 32 2 2 CYP3A4 7 99760982 Splice_Site SNP C C3N-02003_T 870563 99760982 59584991 137 26818 NYAP1 0 . GRCh38 7 100489397 100489397 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1676A>C p.Lys559Thr p.K559T ENST00000300179 4/7 199 184 15 165 164 1 strelka-varscan-mutect NYAP1,missense_variant,p.Lys559Thr,ENST00000300179,NM_173564.3;NYAP1,missense_variant,p.Lys502Thr,ENST00000454988,;NYAP1,upstream_gene_variant,,ENST00000496985,;NYAP1,upstream_gene_variant,,ENST00000489641,; C ENST00000300179 Transcript missense_variant 1835/3581 1676/2526 559/841 K/T aAg/aCg 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 deleterious(0) 4/7 hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 100489397 100489397 A C 1 0 0 0 0 1 0 0 0 10872 72 3 5 5 NYAP1 7 100489397 Missense_Mutation SNP A C3N-02003_T 728415 100489397 58856576 138 26819 TFR2 0 . GRCh38 7 100629373 100629373 + Splice_Site SNP C C T novel C3N-02003_T C3N-02003_N C C c.1271-1G>A p.X424_splice ENST00000462107 352 332 20 280 280 0 strelka-mutect TFR2,splice_acceptor_variant,,ENST00000462107,;TFR2,splice_acceptor_variant,,ENST00000223051,NM_003227.3,NM_001206855.1;TFR2,splice_acceptor_variant,,ENST00000431692,;TFR2,splice_acceptor_variant,,ENST00000465294,;TFR2,splice_acceptor_variant,,ENST00000476304,;TFR2,splice_acceptor_variant,,ENST00000490084,;TFR2,intron_variant,,ENST00000462090,;TFR2,intron_variant,,ENST00000473374,;TFR2,intron_variant,,ENST00000473963,;TFR2,upstream_gene_variant,,ENST00000461176,;TFR2,downstream_gene_variant,,ENST00000473571,;TFR2,downstream_gene_variant,,ENST00000475011,; T ENST00000462107 Transcript splice_acceptor_variant -/3131 1271/2406 424/801 1 -1 TFR2 HGNC HGNC:11762 protein_coding YES CCDS34707.1 ENSP00000420525 Q9UP52 UPI0000136C99 10/18 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 87 100629373 100629373 C T 1 0 0 0 0 0 0 1 0 16244 927 32 3 3 TFR2 7 100629373 Splice_Site SNP C C3N-02003_T 139976 100629373 58716600 139 26820 HBP1 0 . GRCh38 7 107196144 107196144 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.1378G>A p.Asp460Asn p.D460N ENST00000222574 9/11 77 71 6 61 61 0 strelka-varscan-mutect HBP1,missense_variant,p.Asp460Asn,ENST00000222574,NM_012257.3;HBP1,missense_variant,p.Asp460Asn,ENST00000468410,NM_001244262.1;HBP1,missense_variant,p.Asp460Asn,ENST00000485846,;HBP1,missense_variant,p.Asp452Asn,ENST00000498408,;HBP1,missense_variant,p.Asp100Asn,ENST00000607681,;CTA-363E19.2,upstream_gene_variant,,ENST00000607036,;HBP1,non_coding_transcript_exon_variant,,ENST00000461963,;HBP1,missense_variant,p.Asp55Asn,ENST00000463790,;HBP1,non_coding_transcript_exon_variant,,ENST00000463202,;HBP1,downstream_gene_variant,,ENST00000483809,; A ENST00000222574 Transcript missense_variant 1564/2829 1378/1545 460/514 D/N Gat/Aat 1 1 HBP1 HGNC HGNC:23200 protein_coding YES CCDS5741.1 ENSP00000222574 O60381 A0A024R722 UPI000006DC04 NM_012257.3 deleterious(0.02) 9/11 Gene3D:1.10.30.10,Pfam_domain:PF00505,PROSITE_profiles:PS50118,hmmpanther:PTHR15499,SMART_domains:SM00398,Superfamily_domains:SSF47095 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.32522 1 1 1 1 0 A 3 1 87 107196144 107196144 G A 1 0 0 0 0 1 0 0 0 6871 942 33 3 3 HBP1 7 107196144 Missense_Mutation SNP G C3N-02003_T 6566771 107196144 52149829 140 26821 IMMP2L 0 . GRCh38 7 110963541 110963541 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.264G>A p.= p.K88K ENST00000405709 4/6 46 41 5 115 115 0 strelka-varscan-mutect IMMP2L,synonymous_variant,p.=,ENST00000405709,NM_032549.3;IMMP2L,synonymous_variant,p.=,ENST00000331762,NM_001244606.1;IMMP2L,synonymous_variant,p.=,ENST00000447215,;IMMP2L,synonymous_variant,p.=,ENST00000452895,;IMMP2L,synonymous_variant,p.=,ENST00000450877,;IMMP2L,non_coding_transcript_exon_variant,,ENST00000489381,;IMMP2L,non_coding_transcript_exon_variant,,ENST00000487733,; T ENST00000405709 Transcript synonymous_variant 707/1522 264/528 88/175 K aaG/aaA 1 -1 IMMP2L HGNC HGNC:14598 protein_coding YES CCDS5753.1 ENSP00000384966 Q96T52 A4D0S9 UPI000006D162 NM_032549.3 4/6 Gene3D:2.10.109.10,Pfam_domain:PF00717,hmmpanther:PTHR12383,hmmpanther:PTHR12383:SF3,Superfamily_domains:SSF51306,TIGRFAM_domain:TIGR02227 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 110963541 110963541 C T 1 0 0 0 0 0 0 0 1 7620 912 32 3 3 IMMP2L 7 110963541 Silent SNP C C3N-02003_T 3767397 110963541 48382432 141 26822 LINC00998 0 . GRCh38 7 113117415 113117415 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.164G>C p.Arg55Thr p.R55T ENST00000397764 3/3 246 231 15 237 237 0 strelka-varscan-mutect LINC00998,missense_variant,p.Arg55Thr,ENST00000397764,;LINC00998,missense_variant,p.Arg55Thr,ENST00000441359,;RP11-736E3.1,intron_variant,,ENST00000441928,;LINC00998,non_coding_transcript_exon_variant,,ENST00000413744,;LINC00998,downstream_gene_variant,,ENST00000439551,; G ENST00000397764 Transcript missense_variant 373/1070 164/180 55/59 R/T aGa/aCa 1 -1 LINC00998 HGNC HGNC:48953 protein_coding YES ENSP00000490095 A4D0T7 UPI0000037793 deleterious_low_confidence(0.01) 3/3 hmmpanther:PTHR36878:SF2,hmmpanther:PTHR36878 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 113117415 113117415 C G 1 0 0 0 0 1 0 0 0 8732 913 32 4 4 LINC00998 7 113117415 Missense_Mutation SNP C C3N-02003_T 2153874 113117415 46228558 142 26823 DENND2A 0 . GRCh38 7 140544657 140544657 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2288T>G p.Leu763Arg p.L763R ENST00000275884 13/19 501 463 38 428 428 0 strelka-varscan-mutect DENND2A,missense_variant,p.Leu763Arg,ENST00000275884,NM_001318052.1;DENND2A,missense_variant,p.Leu763Arg,ENST00000492720,NM_001318053.1;DENND2A,missense_variant,p.Leu763Arg,ENST00000496613,;DENND2A,missense_variant,p.Leu763Arg,ENST00000537639,NM_015689.3;DENND2A,missense_variant,p.Leu110Arg,ENST00000469373,;DENND2A,missense_variant,p.Leu763Arg,ENST00000461883,; C ENST00000275884 Transcript missense_variant 2706/3735 2288/3030 763/1009 L/R cTt/cGt 1 -1 DENND2A HGNC HGNC:22212 protein_coding YES CCDS43659.1 ENSP00000275884 Q9ULE3 UPI00001C1E63 NM_001318052.1 deleterious(0) 13/19 PROSITE_profiles:PS50211,hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF3,Pfam_domain:PF02141,SMART_domains:SM00799 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 140544657 140544657 A C 1 0 0 0 0 1 0 0 0 4233 72 3 5 5 DENND2A 7 140544657 Missense_Mutation SNP A C3N-02003_T 27427242 140544657 18801316 143 26824 TMEM178B 0 . GRCh38 7 141074662 141074662 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.352G>C p.Asp118His p.D118H ENST00000565468 1/4 57 51 6 42 42 0 strelka-mutect TMEM178B,missense_variant,p.Asp118His,ENST00000565468,NM_001195278.1;TMEM178B,missense_variant,p.Asp118His,ENST00000610315,;TMEM178B,non_coding_transcript_exon_variant,,ENST00000563442,; C ENST00000565468 Transcript missense_variant 431/10558 352/885 118/294 D/H Gac/Cac 1 1 TMEM178B HGNC HGNC:44112 protein_coding YES CCDS59086.1 ENSP00000456594 H3BS89 UPI0000E217DE NM_001195278.1 deleterious(0.01) 1/4 Pfam_domain:PF13903,hmmpanther:PTHR32005,hmmpanther:PTHR32005:SF1 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -14.16453 1 1 1 1 0 C 3 2 87 141074662 141074662 G C 1 0 0 0 0 1 0 0 0 16540 1058 37 4 4 TMEM178B 7 141074662 Missense_Mutation SNP G C3N-02003_T 530005 141074662 18271311 144 26825 ZNF786 0 . GRCh38 7 149071204 149071204 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1568A>C p.Lys523Thr p.K523T ENST00000491431 4/4 137 126 11 82 82 0 strelka-varscan-mutect ZNF786,missense_variant,p.Lys437Thr,ENST00000316286,;ZNF786,missense_variant,p.Lys523Thr,ENST00000491431,NM_152411.3; G ENST00000491431 Transcript missense_variant 1633/2874 1568/2349 523/782 K/T aAg/aCg 1 -1 ZNF786 HGNC HGNC:21806 protein_coding YES CCDS47738.1 ENSP00000417470 Q8N393 UPI000013FD40 NM_152411.3 deleterious(0.02) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF228,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 149071204 149071204 T G 1 0 0 0 0 1 0 0 0 18742 1609 56 5 5 ZNF786 7 149071204 Missense_Mutation SNP T C3N-02003_T 7996542 149071204 10274769 145 26826 AGAP3 0 . GRCh38 7 151142478 151142478 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2117A>C p.His706Pro p.H706P ENST00000397238 16/18 292 252 40 183 182 1 strelka-mutect AGAP3,missense_variant,p.His706Pro,ENST00000397238,NM_031946.5;AGAP3,missense_variant,p.His670Pro,ENST00000622464,;AGAP3,missense_variant,p.His375Pro,ENST00000463381,NM_001281300.1;AGAP3,missense_variant,p.His199Pro,ENST00000461065,;AGAP3,downstream_gene_variant,,ENST00000485904,;AGAP3,downstream_gene_variant,,ENST00000478320,;AGAP3,non_coding_transcript_exon_variant,,ENST00000473633,; C ENST00000397238 Transcript missense_variant 2117/3225 2117/2736 706/911 H/P cAc/cCc 1 1 AGAP3 HGNC HGNC:16923 protein_coding YES CCDS43681.1 ENSP00000380413 Q96P47 UPI0000DAC777 NM_031946.5 deleterious(0) 16/18 Pfam_domain:PF01412,Prints_domain:PR00405,PROSITE_profiles:PS50115,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF198,SMART_domains:SM00105,Superfamily_domains:SSF57863 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 151142478 151142478 A C 1 0 0 0 0 1 0 0 0 446 159 6 5 5 AGAP3 7 151142478 Missense_Mutation SNP A C3N-02003_T 2071274 151142478 8203495 146 26827 MFHAS1 0 . GRCh38 8 8892941 8892941 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.118T>G p.Cys40Gly p.C40G ENST00000276282 1/3 97 89 8 83 83 0 varscan-mutect MFHAS1,missense_variant,p.Cys40Gly,ENST00000276282,NM_004225.2;RNU6-682P,upstream_gene_variant,,ENST00000363843,; C ENST00000276282 Transcript missense_variant 705/6414 118/3159 40/1052 C/G Tgc/Ggc 1 -1 MFHAS1 HGNC HGNC:16982 protein_coding YES CCDS34844.1 ENSP00000276282 Q9Y4C4 UPI000013DAB6 NM_004225.2 tolerated_low_confidence(0.39) 1/3 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs771135733 . 0 206 2 0 0 0 0 2 -4.963794 0 0 1 0 0 C 3 2 87 8892941 8892941 A C 1 0 0 0 0 1 0 0 0 9474 188 7 5 5 MFHAS1 8 8892941 Missense_Mutation SNP A C3N-02003_T 8892941 136245695 147 26828 USP17L7 0 . GRCh38 8 12133023 12133023 + Missense_Mutation SNP A A C rs758871430 C3N-02003_T C3N-02003_N A A c.987T>G p.Ser329Arg p.S329R ENST00000530447 1/1 545 499 46 410 410 0 varscan-mutect USP17L7,missense_variant,p.Ser329Arg,ENST00000530447,NM_001256869.1;USP17L2,downstream_gene_variant,,ENST00000333796,NM_201402.2;FAM66D,intron_variant,,ENST00000434078,;RP11-1236K1.8,upstream_gene_variant,,ENST00000526505,; C ENST00000530447 Transcript missense_variant 1422/2028 987/1593 329/530 S/R agT/agG rs758871430 1 -1 USP17L7 HGNC HGNC:37180 protein_coding YES CCDS78305.1 ENSP00000485337 P0C7H9 UPI00001972BD NM_001256869.1 tolerated(0.13) 1/1 Pfam_domain:PF00443,PROSITE_patterns:PS00973,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 MODERATE SNV 1 PASS rs758871430 . 15 195 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 12133023 12133023 A C 1 0 0 0 0 1 0 0 0 17589 40 2 5 5 USP17L7 8 12133023 Missense_Mutation SNP A C3N-02003_T 3240082 12133023 133005613 148 26829 NAT2 0 . GRCh38 8 18400151 18400151 + Missense_Mutation SNP T T G rs111750824 C3N-02003_T C3N-02003_N T T c.148T>G p.Leu50Val p.L50V ENST00000286479 2/2 133 123 10 149 149 0 strelka-varscan-mutect NAT2,missense_variant,p.Leu50Val,ENST00000286479,NM_000015.2;NAT2,intron_variant,,ENST00000520116,; G ENST00000286479 Transcript missense_variant 255/1322 148/873 50/290 L/V Ttg/Gtg rs111750824 1 1 NAT2 HGNC HGNC:7646 protein_coding YES CCDS6008.1 ENSP00000286479 P11245 A4Z6T7 UPI000013DE51 NM_000015.2 deleterious(0) 2/2 Gene3D:1w5rA01,Pfam_domain:PF00797,Prints_domain:PR01543,hmmpanther:PTHR11786,hmmpanther:PTHR11786:SF6,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS rs111750824 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 18400151 18400151 T G 1 0 0 0 0 1 0 0 0 10186 1722 60 5 5 NAT2 8 18400151 Missense_Mutation SNP T C3N-02003_T 6267128 18400151 126738485 149 26830 FZD3 0 . GRCh38 8 28527517 28527517 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.757T>G p.Phe253Val p.F253V ENST00000537916 4/7 147 136 11 176 176 0 strelka-varscan-mutect FZD3,missense_variant,p.Phe253Val,ENST00000537916,NM_145866.1;FZD3,missense_variant,p.Phe253Val,ENST00000240093,NM_017412.3;RNA5SP259,upstream_gene_variant,,ENST00000365541,; G ENST00000537916 Transcript missense_variant 1240/13740 757/2001 253/666 F/V Ttc/Gtc 1 1 FZD3 HGNC HGNC:4041 protein_coding YES CCDS6069.1 ENSP00000437489 Q9NPG1 UPI000003156A NM_145866.1 tolerated(0.3) 4/7 Pfam_domain:PF01534,Prints_domain:PR00489,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF22,SMART_domains:SM01330,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 28527517 28527517 T G 1 0 0 0 0 1 0 0 0 6002 1609 56 5 5 FZD3 8 28527517 Missense_Mutation SNP T C3N-02003_T 10127366 28527517 116611119 150 26831 ADGRA2 0 . GRCh38 8 37830909 37830909 + Nonsense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.918C>A p.Cys306Ter p.C306* ENST00000412232 7/19 192 160 32 108 108 0 strelka-varscan-mutect ADGRA2,stop_gained,p.Cys306Ter,ENST00000315215,;ADGRA2,stop_gained,p.Cys306Ter,ENST00000412232,NM_032777.9;ADGRA2,downstream_gene_variant,,ENST00000428068,; A ENST00000412232 Transcript stop_gained 931/5651 918/4017 306/1338 C/* tgC/tgA 1 1 ADGRA2 HGNC HGNC:17849 protein_coding YES CCDS6097.2 ENSP00000406367 Q96PE1 UPI00004AE50D NM_032777.9 7/19 PROSITE_profiles:PS50835,hmmpanther:PTHR12011:SF33,hmmpanther:PTHR12011,Gene3D:2.60.40.10,SMART_domains:SM00409 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 87 37830909 37830909 C A 1 0 0 0 0 0 1 0 0 353 718 25 2 2 ADGRA2 8 37830909 Nonsense_Mutation SNP C C3N-02003_T 9303392 37830909 107307727 151 26832 KAT6A 0 . GRCh38 8 41977079 41977079 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.1292T>C p.Val431Ala p.V431A ENST00000396930 8/18 121 109 12 99 99 0 strelka-varscan-mutect KAT6A,missense_variant,p.Val431Ala,ENST00000396930,NM_001099412.1;KAT6A,missense_variant,p.Val431Ala,ENST00000406337,NM_001099413.1;KAT6A,missense_variant,p.Val431Ala,ENST00000265713,NM_006766.3;KAT6A,missense_variant,p.Val431Ala,ENST00000485568,NM_001305878.1;KAT6A,non_coding_transcript_exon_variant,,ENST00000470574,;KAT6A,non_coding_transcript_exon_variant,,ENST00000463961,; G ENST00000396930 Transcript missense_variant 1836/9285 1292/6015 431/2004 V/A gTg/gCg 1 -1 KAT6A HGNC HGNC:13013 protein_coding YES CCDS6124.1 ENSP00000380136 Q92794 UPI000013D666 NM_001099412.1 deleterious(0.04) 8/18 hmmpanther:PTHR10615:SF26,hmmpanther:PTHR10615 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.99994 1 1 1 1 0 G 3 3 87 41977079 41977079 A G 1 0 0 0 0 1 0 0 0 7898 159 6 5 5 KAT6A 8 41977079 Missense_Mutation SNP A C3N-02003_T 4146170 41977079 103161557 152 26833 PREX2 0 . GRCh38 8 68083390 68083390 + Splice_Site SNP T T A novel C3N-02003_T C3N-02003_N T T c.2027+2T>A p.X676_splice ENST00000288368 50 46 4 64 64 0 varscan-mutect PREX2,splice_donor_variant,,ENST00000288368,NM_024870.2;RP11-403D15.2,intron_variant,,ENST00000526901,;PREX2,splice_donor_variant,,ENST00000529398,;PREX2,splice_donor_variant,,ENST00000517617,; A ENST00000288368 Transcript splice_donor_variant -/10750 2027/4821 676/1606 1 1 PREX2 HGNC HGNC:22950 protein_coding YES CCDS6201.1 ENSP00000288368 Q70Z35 UPI0000375435 NM_024870.2 18/39 HIGH 1 SNV 1 1 PASS rs745454046 . 0 196 11 3 0 0 0 0 -8.133408 0.9899031 1 1 1 0 A 5 1 87 68083390 68083390 T A 1 0 0 0 0 0 0 1 0 12611 1652 57 4 4 PREX2 8 68083390 Splice_Site SNP T C3N-02003_T 26106311 68083390 77055246 153 26834 ZFHX4 0 . GRCh38 8 76704464 76704464 + Missense_Mutation SNP A A T novel C3N-02003_T C3N-02003_N A A c.376A>T p.Asn126Tyr p.N126Y ENST00000521891 2/11 269 255 14 218 218 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Asn126Tyr,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Asn126Tyr,ENST00000518282,;ZFHX4,missense_variant,p.Asn126Tyr,ENST00000520307,;ZFHX4,missense_variant,p.Asn126Tyr,ENST00000517585,;ZFHX4,missense_variant,p.Asn126Tyr,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; T ENST00000521891 Transcript missense_variant 824/14019 376/10851 126/3616 N/Y Aat/Tat 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 76704464 76704464 A T 1 0 0 0 0 1 0 0 0 18213 14 1 4 4 ZFHX4 8 76704464 Missense_Mutation SNP A C3N-02003_T 8621074 76704464 68434172 154 26835 MATN2 0 . GRCh38 8 97941899 97941899 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.835A>C p.Ile279Leu p.I279L ENST00000254898 4/19 181 167 14 157 157 0 strelka-varscan-mutect MATN2,missense_variant,p.Ile279Leu,ENST00000254898,NM_002380.3;MATN2,missense_variant,p.Ile279Leu,ENST00000521689,NM_030583.2;MATN2,missense_variant,p.Ile279Leu,ENST00000520016,;MATN2,missense_variant,p.Ile279Leu,ENST00000524308,;MATN2,missense_variant,p.Thr103Pro,ENST00000518154,;MATN2,splice_region_variant,,ENST00000522025,;MATN2,intron_variant,,ENST00000521041,;MATN2,splice_region_variant,,ENST00000523490,; C ENST00000254898 Transcript missense_variant,splice_region_variant 1066/4106 835/2871 279/956 I/L Atc/Ctc 1 1 MATN2 HGNC HGNC:6908 protein_coding YES CCDS55264.1 ENSP00000254898 O00339 A0A140VKH7 UPI000021037B NM_002380.3 tolerated(0.26) 4/19 Gene3D:2.10.25.10,hmmpanther:PTHR11132,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 97941899 97941899 A C 1 0 0 0 0 1 0 0 0 9260 86 3 5 5 MATN2 8 97941899 Missense_Mutation SNP A C3N-02003_T 21237435 97941899 47196737 155 26836 FER1L6 0 . GRCh38 8 123980593 123980593 + Missense_Mutation SNP T T G C3N-02003_T C3N-02003_N T T c.1192T>G p.Leu398Val p.L398V ENST00000522917 11/41 333 311 22 346 345 1 strelka-varscan-mutect FER1L6,missense_variant,p.Leu398Val,ENST00000522917,NM_001039112.2;FER1L6-AS1,downstream_gene_variant,,ENST00000518567,; G ENST00000522917 Transcript missense_variant 1398/6051 1192/5574 398/1857 L/V Ttg/Gtg COSM1095833 1 1 FER1L6 HGNC HGNC:28065 protein_coding YES CCDS43767.1 ENSP00000428280 Q2WGJ9 UPI0000E9B4AA NM_001039112.2 deleterious(0) 11/41 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF37 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 123980593 123980593 T G 1 0 0 0 0 1 0 0 0 5678 1606 56 5 5 FER1L6 8 123980593 Missense_Mutation SNP T C3N-02003_T 26038694 123980593 21158043 156 26837 PLEC 0 . GRCh38 8 143925192 143925192 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.5148G>A p.= p.Q1716Q ENST00000322810 31/32 381 355 26 282 282 0 strelka-varscan-mutect PLEC,synonymous_variant,p.=,ENST00000322810,NM_201380.3;PLEC,synonymous_variant,p.=,ENST00000345136,NM_201384.2;PLEC,synonymous_variant,p.=,ENST00000436759,NM_000445.4;PLEC,synonymous_variant,p.=,ENST00000354958,NM_201379.2;PLEC,synonymous_variant,p.=,ENST00000354589,NM_201382.3;PLEC,synonymous_variant,p.=,ENST00000357649,NM_201383.2;PLEC,synonymous_variant,p.=,ENST00000356346,NM_201378.3;PLEC,synonymous_variant,p.=,ENST00000398774,NM_201381.2;PLEC,synonymous_variant,p.=,ENST00000527096,;PLEC,intron_variant,,ENST00000527303,; T ENST00000322810 Transcript synonymous_variant 5318/15249 5148/14055 1716/4684 Q caG/caA 1 -1 PLEC HGNC HGNC:9069 protein_coding YES CCDS43772.1 ENSP00000323856 Q15149 UPI0000233FCD NM_201380.3 31/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF247 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 143925192 143925192 C T 1 0 0 0 0 0 0 0 1 12145 912 32 3 3 PLEC 8 143925192 Silent SNP C C3N-02003_T 19944599 143925192 1213444 157 26838 ROR2 0 . GRCh38 9 91726724 91726724 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.1203G>C p.Lys401Asn p.K401N ENST00000375708 8/9 446 405 41 456 456 0 strelka-varscan-mutect ROR2,missense_variant,p.Lys401Asn,ENST00000375708,NM_004560.3;ROR2,missense_variant,p.Lys261Asn,ENST00000375715,;ROR2,non_coding_transcript_exon_variant,,ENST00000550066,; G ENST00000375708 Transcript missense_variant 1402/4096 1203/2832 401/943 K/N aaG/aaC 1 -1 ROR2 HGNC HGNC:10257 protein_coding YES CCDS6691.1 ENSP00000364860 Q01974 UPI000013E8CA NM_004560.3 tolerated(0.2) 8/9 PIRSF_domain:PIRSF000624,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF132,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 91726724 91726724 C G 1 0 0 0 0 1 0 0 0 13704 912 32 4 4 ROR2 9 91726724 Missense_Mutation SNP C C3N-02003_T 91726724 46667993 158 26839 GALNT12 0 . GRCh38 9 98835358 98835358 + Missense_Mutation SNP T T C C3N-02003_T C3N-02003_N T T c.1027T>C p.Ser343Pro p.S343P ENST00000375011 5/10 215 181 34 345 345 0 strelka-varscan-mutect GALNT12,missense_variant,p.Ser343Pro,ENST00000375011,NM_024642.4;GALNT12,upstream_gene_variant,,ENST00000615204,;GALNT12,downstream_gene_variant,,ENST00000610463,; C ENST00000375011 Transcript missense_variant 1027/2735 1027/1746 343/581 S/P Tcc/Ccc COSM5410027 1 1 GALNT12 HGNC HGNC:19877 protein_coding YES CCDS6737.1 ENSP00000364150 Q8IXK2 UPI000004D295 NM_024642.4 deleterious(0.02) 5/10 Gene3D:3.90.550.10,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF18,Superfamily_domains:SSF53448 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 98835358 98835358 T C 1 0 0 0 0 1 0 0 0 6078 1783 62 5 5 GALNT12 9 98835358 Missense_Mutation SNP T C3N-02003_T 7108634 98835358 39559359 159 26840 EPB41L4B 0 . GRCh38 9 109267509 109267509 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.497C>G p.Ser166Cys p.S166C ENST00000374566 4/26 150 142 8 193 193 0 strelka-varscan-mutect EPB41L4B,missense_variant,p.Ser166Cys,ENST00000374566,NM_019114.4;EPB41L4B,missense_variant,p.Ser166Cys,ENST00000374557,NM_018424.3; C ENST00000374566 Transcript missense_variant 1015/5800 497/2703 166/900 S/C tCt/tGt 1 -1 EPB41L4B HGNC HGNC:19818 protein_coding YES CCDS43859.1 ENSP00000363694 Q9H329 UPI0000458994 NM_019114.4 deleterious(0) 4/26 Gene3D:1.20.80.10,Prints_domain:PR00661,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF18,SMART_domains:SM00295 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 109267509 109267509 G C 1 0 0 0 0 1 0 0 0 5003 942 33 4 4 EPB41L4B 9 109267509 Missense_Mutation SNP G C3N-02003_T 10432151 109267509 29127208 160 26841 ANAPC2 0 . GRCh38 9 137183755 137183755 + Missense_Mutation SNP T T G rs770005231 C3N-02003_T C3N-02003_N T T c.1085A>C p.Lys362Thr p.K362T ENST00000323927 5/13 146 130 16 119 119 0 strelka-varscan-mutect ANAPC2,missense_variant,p.Lys362Thr,ENST00000323927,NM_013366.3;SSNA1,upstream_gene_variant,,ENST00000322310,NM_003731.2;SSNA1,upstream_gene_variant,,ENST00000464553,;ANAPC2,upstream_gene_variant,,ENST00000483432,;ANAPC2,non_coding_transcript_exon_variant,,ENST00000495611,;ANAPC2,downstream_gene_variant,,ENST00000618649,;SSNA1,upstream_gene_variant,,ENST00000459860,;ANAPC2,upstream_gene_variant,,ENST00000471131,;SSNA1,upstream_gene_variant,,ENST00000463511,; G ENST00000323927 Transcript missense_variant 1090/2632 1085/2469 362/822 K/T aAg/aCg rs770005231 1 -1 ANAPC2 HGNC HGNC:19989 protein_coding YES CCDS7033.1 ENSP00000314004 Q9UJX6 UPI0000043E1B NM_013366.3 deleterious(0) 5/13 hmmpanther:PTHR11932:SF73,hmmpanther:PTHR11932 MODERATE 1 SNV 1 1 PASS rs770005231 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 137183755 137183755 T G 1 0 0 0 0 1 0 0 0 701 1609 56 5 5 ANAPC2 9 137183755 Missense_Mutation SNP T C3N-02003_T 27916246 137183755 1210962 161 26842 NOXA1 0 . GRCh38 9 137431292 137431292 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.755A>G p.Glu252Gly p.E252G ENST00000341349 8/14 233 196 37 198 198 0 strelka-varscan-mutect NOXA1,missense_variant,p.Glu252Gly,ENST00000341349,NM_001256067.1,NM_006647.1;NOXA1,missense_variant,p.Glu196Gly,ENST00000392815,NM_001256068.1;ENTPD8,downstream_gene_variant,,ENST00000371506,NM_001033113.1;ENTPD8,downstream_gene_variant,,ENST00000344119,NM_198585.2;ENTPD8,downstream_gene_variant,,ENST00000472938,;ENTPD8,downstream_gene_variant,,ENST00000461823,; G ENST00000341349 Transcript missense_variant 935/1678 755/1452 252/483 E/G gAg/gGg 1 1 NOXA1 HGNC HGNC:10668 protein_coding YES CCDS7042.1 ENSP00000342848 Q86UR1 UPI0000074717 NM_001256067.1,NM_006647.1 deleterious(0.05) 8/14 hmmpanther:PTHR15175:SF4,hmmpanther:PTHR15175 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 137431292 137431292 A G 1 0 0 0 0 1 0 0 0 10606 304 11 5 5 NOXA1 9 137431292 Missense_Mutation SNP A C3N-02003_T 247537 137431292 963425 162 26843 CACNA1B 0 . GRCh38 9 137917422 137917422 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.957C>T p.= p.I319I ENST00000371372 6/47 91 83 8 92 92 0 strelka-varscan-mutect CACNA1B,synonymous_variant,p.=,ENST00000371372,NM_000718.3;CACNA1B,synonymous_variant,p.=,ENST00000371363,;CACNA1B,synonymous_variant,p.=,ENST00000371355,;CACNA1B,synonymous_variant,p.=,ENST00000371357,;CACNA1B,synonymous_variant,p.=,ENST00000277549,;CACNA1B,synonymous_variant,p.=,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript synonymous_variant 1102/9790 957/7020 319/2339 I atC/atT 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 6/47 Pfam_domain:PF00520,Prints_domain:PR00167,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161,Superfamily_domains:SSF81324 LOW 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -16.93827 1 1 1 1 0 T 2 4 87 137917422 137917422 C T 1 0 0 0 0 0 0 0 1 2227 845 30 3 3 CACNA1B 9 137917422 Silent SNP C C3N-02003_T 486130 137917422 477295 163 26844 APBB1IP 0 . GRCh38 10 26536107 26536107 + Missense_Mutation SNP G G A C3N-02003_T C3N-02003_N G G c.934G>A p.Glu312Lys p.E312K ENST00000376236 10/15 83 76 7 167 167 0 strelka-varscan-mutect APBB1IP,missense_variant,p.Glu312Lys,ENST00000376236,NM_019043.3; A ENST00000376236 Transcript missense_variant 1389/2771 934/2001 312/666 E/K Gaa/Aaa COSM3806970,COSM5208041 1 1 APBB1IP HGNC HGNC:17379 protein_coding YES CCDS31167.1 ENSP00000365411 Q7Z5R6 UPI00001AF165 NM_019043.3 deleterious(0) 10/15 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR11243,hmmpanther:PTHR11243:SF14,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 26536107 26536107 G A 1 0 0 0 0 1 0 0 0 880 943 33 3 3 APBB1IP 10 26536107 Missense_Mutation SNP G C3N-02003_T 26536107 107261315 164 26845 BMS1 0 . GRCh38 10 42784427 42784427 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.33G>A p.= p.K11K ENST00000374518 2/23 127 118 9 111 111 0 varscan-mutect BMS1,synonymous_variant,p.=,ENST00000374518,NM_014753.3; A ENST00000374518 Transcript synonymous_variant 96/7753 33/3849 11/1282 K aaG/aaA 1 1 BMS1 HGNC HGNC:23505 protein_coding YES CCDS7199.1 ENSP00000363642 Q14692 UPI0000126A3E NM_014753.3 2/23 hmmpanther:PTHR12858:SF2,hmmpanther:PTHR12858 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 42784427 42784427 G A 1 0 0 0 0 0 0 0 1 1627 933 33 3 3 BMS1 10 42784427 Silent SNP G C3N-02003_T 16248320 42784427 91012995 165 26846 AGAP14P 0 . GRCh38 10 46358544 46358544 + Missense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.1888G>T p.Ala630Ser p.A630S ENST00000624701 9/9 592 554 38 605 605 0 varscan-mutect AGAP14P,missense_variant,p.Ala630Ser,ENST00000624701,; T ENST00000624701 Transcript missense_variant 1888/2058 1888/2058 630/685 A/S Gcc/Tcc 1 1 AGAP14P HGNC HGNC:23660 protein_coding YES ENSP00000485140 A0A096LNP0 UPI000514C5BF tolerated(0.15) 9/9 PROSITE_profiles:PS50297,PROSITE_profiles:PS50088,hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF213,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 46358544 46358544 G T 1 0 0 0 0 1 0 0 0 444 1203 42 2 2 AGAP14P 10 46358544 Missense_Mutation SNP G C3N-02003_T 3574117 46358544 87438878 166 26847 KAT6B 0 . GRCh38 10 74842971 74842971 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.114T>G p.= p.T38T ENST00000287239 3/18 420 384 36 463 463 0 strelka-varscan-mutect KAT6B,synonymous_variant,p.=,ENST00000287239,NM_012330.3;KAT6B,synonymous_variant,p.=,ENST00000372711,NM_001256468.1;KAT6B,synonymous_variant,p.=,ENST00000372724,NM_001256469.1;KAT6B,synonymous_variant,p.=,ENST00000372725,;KAT6B,synonymous_variant,p.=,ENST00000372714,;KAT6B,downstream_gene_variant,,ENST00000604130,; G ENST00000287239 Transcript synonymous_variant 603/8287 114/6222 38/2073 T acT/acG 1 1 KAT6B HGNC HGNC:17582 protein_coding YES CCDS7345.1 ENSP00000287239 Q8WYB5 UPI000013DEA0 NM_012330.3 3/18 hmmpanther:PTHR10615,hmmpanther:PTHR10615:SF73 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 74842971 74842971 T G 1 0 0 0 0 0 0 0 1 7899 1596 56 5 5 KAT6B 10 74842971 Silent SNP T C3N-02003_T 28484427 74842971 58954451 167 26848 DUSP13 0 . GRCh38 10 75097868 75097868 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.167A>G p.Lys56Arg p.K56R ENST00000372700 2/4 52 46 6 46 46 0 strelka-varscan-mutect DUSP13,missense_variant,p.Lys6Arg,ENST00000491677,;DUSP13,missense_variant,p.Lys142Arg,ENST00000478873,;DUSP13,missense_variant,p.Lys6Arg,ENST00000607131,;DUSP13,missense_variant,p.Lys28Arg,ENST00000605915,;DUSP13,missense_variant,p.Lys6Arg,ENST00000472493,NM_016364.3;DUSP13,missense_variant,p.Lys56Arg,ENST00000372700,NM_001007272.1;DUSP13,missense_variant,p.Lys184Arg,ENST00000607487,;DUSP13,missense_variant,p.Lys6Arg,ENST00000464872,;DUSP13,3_prime_UTR_variant,,ENST00000372702,NM_001007271.1;SAMD8,upstream_gene_variant,,ENST00000447533,;DUSP13,downstream_gene_variant,,ENST00000473072,;DUSP13,non_coding_transcript_exon_variant,,ENST00000607009,;DUSP13,3_prime_UTR_variant,,ENST00000479884,NM_001320842.1;DUSP13,3_prime_UTR_variant,,ENST00000494588,;DUSP13,3_prime_UTR_variant,,ENST00000394707,;DUSP13,3_prime_UTR_variant,,ENST00000308475,NM_001320843.1; C ENST00000372700 Transcript missense_variant 201/781 167/747 56/248 K/R aAg/aGg 1 -1 DUSP13 HGNC HGNC:19681 protein_coding YES CCDS31224.1 ENSP00000361785 Q9UII6 UPI0000481AED NM_001007272.1 tolerated(0.48) 2/4 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 75097868 75097868 T C 1 0 0 0 0 1 0 0 0 4635 1609 56 5 5 DUSP13 10 75097868 Missense_Mutation SNP T C3N-02003_T 254897 75097868 58699554 168 26849 KCNMA1 0 . GRCh38 10 77086489 77086489 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1439A>C p.Lys480Thr p.K480T ENST00000286628 11/28 389 354 35 425 424 1 strelka-varscan-mutect KCNMA1,missense_variant,p.Lys341Thr,ENST00000604624,NM_001322832.1,NM_001322829.1;KCNMA1,missense_variant,p.Lys480Thr,ENST00000286627,NM_002247.3;KCNMA1,missense_variant,p.Lys480Thr,ENST00000286628,NM_001161352.1;KCNMA1,missense_variant,p.Lys312Thr,ENST00000354353,;KCNMA1,missense_variant,p.Lys312Thr,ENST00000406533,NM_001322837.1,NM_001271519.1;KCNMA1,missense_variant,p.Lys480Thr,ENST00000372443,;KCNMA1,missense_variant,p.Lys480Thr,ENST00000372440,NM_001014797.2;KCNMA1,missense_variant,p.Lys480Thr,ENST00000404771,;KCNMA1,missense_variant,p.Lys454Thr,ENST00000457953,;KCNMA1,missense_variant,p.Lys480Thr,ENST00000626620,NM_001161353.1;KCNMA1,missense_variant,p.Lys415Thr,ENST00000372437,;KCNMA1,missense_variant,p.Lys454Thr,ENST00000372421,;KCNMA1,missense_variant,p.Lys417Thr,ENST00000372408,;KCNMA1,missense_variant,p.Lys431Thr,ENST00000372403,;KCNMA1,missense_variant,p.Lys312Thr,ENST00000404857,NM_001271518.1;KCNMA1,missense_variant,p.Lys159Thr,ENST00000434208,;KCNMA1,upstream_gene_variant,,ENST00000484507,; G ENST00000286628 Transcript missense_variant,splice_region_variant 1439/6100 1439/3711 480/1236 K/T aAg/aCg 1 -1 KCNMA1 HGNC HGNC:6284 protein_coding YES CCDS60569.1 ENSP00000286628 Q12791 UPI00003519E7 NM_001161352.1 tolerated(0.09) 11/28 Gene3D:3.40.50.720,hmmpanther:PTHR10027,hmmpanther:PTHR10027:SF28,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 77086489 77086489 T G 1 0 0 0 0 1 0 0 0 7990 1623 56 5 5 KCNMA1 10 77086489 Missense_Mutation SNP T C3N-02003_T 1988621 77086489 56710933 169 26850 MMRN2 0 . GRCh38 10 86943518 86943518 + Silent SNP A A C novel C3N-02003_T C3N-02003_N A A c.1266T>G p.= p.T422T ENST00000372027 6/7 384 353 31 348 346 2 strelka-varscan-mutect MMRN2,synonymous_variant,p.=,ENST00000372027,NM_024756.2;MMRN2,downstream_gene_variant,,ENST00000610081,;MMRN2,downstream_gene_variant,,ENST00000609457,;MMRN2,downstream_gene_variant,,ENST00000474994,;MMRN2,downstream_gene_variant,,ENST00000488950,;MMRN2,downstream_gene_variant,,ENST00000608090,;MMRN2,downstream_gene_variant,,ENST00000608753,; C ENST00000372027 Transcript synonymous_variant 1588/4375 1266/2850 422/949 T acT/acG 1 -1 MMRN2 HGNC HGNC:19888 protein_coding YES CCDS7379.1 ENSP00000361097 Q9H8L6 UPI000013F046 NM_024756.2 6/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 86943518 86943518 A C 1 0 0 0 0 0 0 0 1 9634 59 3 5 5 MMRN2 10 86943518 Silent SNP A C3N-02003_T 9857029 86943518 46853904 170 26851 LCOR 0 . GRCh38 10 96983655 96983655 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2265A>C p.Gln755His p.Q755H ENST00000286067 1/1 229 207 22 195 195 0 strelka-varscan-mutect LCOR,missense_variant,p.Gln1037His,ENST00000421806,;LCOR,missense_variant,p.Gln755His,ENST00000286067,NM_015652.2; C ENST00000286067 Transcript missense_variant 2372/4542 2265/3744 755/1247 Q/H caA/caC 1 1 LCOR HGNC HGNC:29503 protein_coding YES CCDS7452.1 ENSP00000286067 Q8N655 UPI000006F242 NM_015652.2 tolerated(0.11) 1/1 hmmpanther:PTHR14931,hmmpanther:PTHR14931:SF2 MODERATE 1 SNV 1 PASS rs1236204556 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 96983655 96983655 A C 1 0 0 0 0 1 0 0 0 8595 69 3 5 5 LCOR 10 96983655 Missense_Mutation SNP A C3N-02003_T 10040137 96983655 36813767 171 26852 CFAP43 0 . GRCh38 10 104131430 104131430 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.4732T>G p.Phe1578Val p.F1578V ENST00000357060 37/38 145 123 22 205 205 0 strelka-varscan-mutect CFAP43,missense_variant,p.Phe1578Val,ENST00000357060,NM_025145.5;CFAP43,missense_variant,p.Phe910Val,ENST00000434629,;CFAP43,missense_variant,p.Phe427Val,ENST00000457071,;CFAP43,downstream_gene_variant,,ENST00000479392,; C ENST00000357060 Transcript missense_variant 4848/5365 4732/4998 1578/1665 F/V Ttc/Gtc 1 -1 CFAP43 HGNC HGNC:26684 protein_coding YES CCDS31281.1 ENSP00000349568 Q8NDM7 UPI0000D60FC7 NM_025145.5 tolerated(0.5) 37/38 hmmpanther:PTHR14885,hmmpanther:PTHR14885:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 104131430 104131430 A C 1 0 0 0 0 1 0 0 0 3018 43 2 5 5 CFAP43 10 104131430 Missense_Mutation SNP A C3N-02003_T 7147775 104131430 29665992 172 26853 CTBP2 0 . GRCh38 10 125027261 125027261 + Missense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.499G>T p.Asp167Tyr p.D167Y ENST00000309035 1/9 183 170 13 148 148 0 strelka-mutect CTBP2,missense_variant,p.Asp167Tyr,ENST00000309035,NM_022802.2;CTBP2,intron_variant,,ENST00000337195,NM_001329.2;CTBP2,intron_variant,,ENST00000411419,NM_001083914.1;CTBP2,intron_variant,,ENST00000494626,NM_001290214.1;CTBP2,intron_variant,,ENST00000531469,NM_001290215.1;CTBP2,intron_variant,,ENST00000460976,;CTBP2,intron_variant,,ENST00000493552,; A ENST00000309035 Transcript missense_variant 630/3669 499/2958 167/985 D/Y Gat/Tat 1 -1 CTBP2 HGNC HGNC:2495 protein_coding YES CCDS7644.1 ENSP00000311825 P56545 UPI000013EE11 NM_022802.2 deleterious_low_confidence(0.03) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 125027261 125027261 C A 1 0 0 0 0 1 0 0 0 3804 855 30 2 2 CTBP2 10 125027261 Missense_Mutation SNP C C3N-02003_T 20895831 125027261 8770161 173 26854 CRACR2B 0 . GRCh38 11 830086 830086 + Nonsense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.559G>T p.Glu187Ter p.E187* ENST00000525077 4/9 198 186 12 187 187 0 strelka-varscan-mutect CRACR2B,stop_gained,p.Glu187Ter,ENST00000528542,;CRACR2B,stop_gained,p.Glu187Ter,ENST00000450448,NM_173584.4;CRACR2B,stop_gained,p.Glu187Ter,ENST00000525077,NM_001286606.1;PNPLA2,downstream_gene_variant,,ENST00000336615,NM_020376.3;CD151,upstream_gene_variant,,ENST00000397420,;CD151,upstream_gene_variant,,ENST00000322008,NM_139029.1,NM_004357.4;CD151,upstream_gene_variant,,ENST00000397421,NM_139030.3,NM_001039490.1;CRACR2B,downstream_gene_variant,,ENST00000527089,;CD151,upstream_gene_variant,,ENST00000527341,;CD151,upstream_gene_variant,,ENST00000524748,;CD151,upstream_gene_variant,,ENST00000526693,;CRACR2B,downstream_gene_variant,,ENST00000533803,;CD151,upstream_gene_variant,,ENST00000529810,;CRACR2B,downstream_gene_variant,,ENST00000528315,;CD151,upstream_gene_variant,,ENST00000525718,;CD151,upstream_gene_variant,,ENST00000525333,;CD151,upstream_gene_variant,,ENST00000528867,;CRACR2B,downstream_gene_variant,,ENST00000530183,;AP006621.8,intron_variant,,ENST00000532946,;CRACR2B,non_coding_transcript_exon_variant,,ENST00000528694,;CRACR2B,non_coding_transcript_exon_variant,,ENST00000527763,;CRACR2B,non_coding_transcript_exon_variant,,ENST00000530688,;PNPLA2,downstream_gene_variant,,ENST00000525250,;CD151,upstream_gene_variant,,ENST00000532045,;CD151,upstream_gene_variant,,ENST00000530726,;PNPLA2,downstream_gene_variant,,ENST00000529255,;CRACR2B,downstream_gene_variant,,ENST00000534191,;CD151,upstream_gene_variant,,ENST00000526661,;CRACR2B,downstream_gene_variant,,ENST00000530737,;CRACR2B,upstream_gene_variant,,ENST00000526531,;CRACR2B,downstream_gene_variant,,ENST00000534606,;CD151,upstream_gene_variant,,ENST00000531999,;CD151,upstream_gene_variant,,ENST00000525868,;CD151,upstream_gene_variant,,ENST00000530155,; T ENST00000525077 Transcript stop_gained 660/1578 559/1200 187/399 E/* Gag/Tag 1 1 CRACR2B HGNC HGNC:28703 protein_coding YES CCDS65995.1 ENSP00000435299 Q8N4Y2 UPI0001CF33F4 NM_001286606.1 4/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22621 HIGH 1 SNV 1 1 PASS rs1339082587 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 87 830086 830086 G T 1 0 0 0 0 0 1 0 0 3644 1175 41 2 2 CRACR2B 11 830086 Nonsense_Mutation SNP G C3N-02003_T 830086 134256536 174 26855 TRPM5 0 . GRCh38 11 2411686 2411686 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.2556C>T p.= p.I852I ENST00000155858 17/24 329 303 26 286 286 0 strelka-varscan-mutect TRPM5,synonymous_variant,p.=,ENST00000155858,NM_014555.3;TRPM5,synonymous_variant,p.=,ENST00000533881,;TRPM5,synonymous_variant,p.=,ENST00000533060,;TRPM5,synonymous_variant,p.=,ENST00000528453,;AC124057.5,downstream_gene_variant,,ENST00000433035,; A ENST00000155858 Transcript synonymous_variant 2565/3929 2556/3498 852/1165 I atC/atT 1 -1 TRPM5 HGNC HGNC:14323 protein_coding YES CCDS31340.1 ENSP00000155858 Q9NZQ8 UPI000003B069 NM_014555.3 17/24 Transmembrane_helices:TMhelix,hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF5,Pfam_domain:PF00520 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 2411686 2411686 G A 1 0 0 0 0 0 0 0 1 17095 932 33 3 3 TRPM5 11 2411686 Silent SNP G C3N-02003_T 1581600 2411686 132674936 175 26856 TRIM6 0 . GRCh38 11 5611048 5611048 + Silent SNP T T G C3N-02003_T C3N-02003_N T T c.1257T>G p.= p.A419A ENST00000380097 8/8 402 376 26 426 425 1 strelka-varscan-mutect TRIM6,synonymous_variant,p.=,ENST00000380097,NM_001003818.2;TRIM6,synonymous_variant,p.=,ENST00000278302,NM_058166.4;TRIM6,synonymous_variant,p.=,ENST00000621176,;TRIM6,synonymous_variant,p.=,ENST00000445329,;TRIM6,synonymous_variant,p.=,ENST00000380107,;TRIM6,synonymous_variant,p.=,ENST00000507320,;TRIM6,synonymous_variant,p.=,ENST00000506134,NM_001198644.1;TRIM6,synonymous_variant,p.=,ENST00000515022,NM_001198645.1;TRIM6-TRIM34,intron_variant,,ENST00000354852,NM_001003819.3;HBG2,intron_variant,,ENST00000380259,;TRIM6,downstream_gene_variant,,ENST00000424369,;AC015691.13,intron_variant,,ENST00000394793,;TRIM6,non_coding_transcript_exon_variant,,ENST00000481603,;TRIM6,non_coding_transcript_exon_variant,,ENST00000511284,;TRIM6,non_coding_transcript_exon_variant,,ENST00000469187,; G ENST00000380097 Transcript synonymous_variant 1499/3403 1257/1551 419/516 A gcT/gcG COSM4033943 1 1 TRIM6 HGNC HGNC:16277 protein_coding YES CCDS31389.1 ENSP00000369440 Q9C030 UPI000041A255 NM_001003818.2 8/8 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF51,SMART_domains:SM00449,Superfamily_domains:SSF49899 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 5611048 5611048 T G 1 0 0 0 0 0 0 0 1 17026 1596 56 5 5 TRIM6 11 5611048 Silent SNP T C3N-02003_T 3199362 5611048 129475574 176 26857 DCHS1 0 . GRCh38 11 6640615 6640615 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.999A>C p.Gln333His p.Q333H ENST00000299441 2/21 309 285 24 266 266 0 strelka-varscan-mutect DCHS1,missense_variant,p.Gln333His,ENST00000299441,NM_003737.3; G ENST00000299441 Transcript missense_variant 1411/10765 999/9897 333/3298 Q/H caA/caC 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 deleterious(0) 2/21 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 6640615 6640615 T G 1 0 0 0 0 1 0 0 0 4090 1606 56 5 5 DCHS1 11 6640615 Missense_Mutation SNP T C3N-02003_T 1029567 6640615 128446007 177 26858 ST5 0 . GRCh38 11 8714002 8714002 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1983C>T p.= p.F661F ENST00000534127 11/23 241 225 16 193 193 0 strelka-varscan-mutect ST5,synonymous_variant,p.=,ENST00000534127,NM_005418.3;ST5,synonymous_variant,p.=,ENST00000313726,NM_213618.1;ST5,synonymous_variant,p.=,ENST00000530991,;ST5,synonymous_variant,p.=,ENST00000526757,NM_139157.2;ST5,synonymous_variant,p.=,ENST00000530438,;ST5,synonymous_variant,p.=,ENST00000526099,;ST5,synonymous_variant,p.=,ENST00000533020,;ST5,synonymous_variant,p.=,ENST00000626808,;ST5,synonymous_variant,p.=,ENST00000528527,;ST5,intron_variant,,ENST00000530593,;ST5,downstream_gene_variant,,ENST00000526057,;ST5,downstream_gene_variant,,ENST00000528196,;ST5,downstream_gene_variant,,ENST00000530580,;ST5,downstream_gene_variant,,ENST00000533225,;ST5,downstream_gene_variant,,ENST00000527510,;ST5,downstream_gene_variant,,ENST00000531093,;ST5,downstream_gene_variant,,ENST00000531060,;RPL27A,intron_variant,,ENST00000531102,;ST5,downstream_gene_variant,,ENST00000533425,;ST5,downstream_gene_variant,,ENST00000532651,;ST5,upstream_gene_variant,,ENST00000526837,;ST5,synonymous_variant,p.=,ENST00000532734,;ST5,non_coding_transcript_exon_variant,,ENST00000530559,;ST5,upstream_gene_variant,,ENST00000526701,;ST5,upstream_gene_variant,,ENST00000530338,;ST5,downstream_gene_variant,,ENST00000527870,; A ENST00000534127 Transcript synonymous_variant 2369/4545 1983/3414 661/1137 F ttC/ttT 1 -1 ST5 HGNC HGNC:11350 protein_coding YES CCDS7791.1 ENSP00000433528 P78524 UPI00001AECB8 NM_005418.3 11/23 hmmpanther:PTHR15288,hmmpanther:PTHR15288:SF5 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 8714002 8714002 G A 1 0 0 0 0 0 0 0 1 15598 1304 45 3 3 ST5 11 8714002 Silent SNP G C3N-02003_T 2073387 8714002 126372620 178 26859 SWAP70 0 . GRCh38 11 9749924 9749924 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1712T>G p.Leu571Arg p.L571R ENST00000318950 12/12 233 221 12 263 263 0 strelka-varscan-mutect SWAP70,missense_variant,p.Leu571Arg,ENST00000318950,NM_015055.3;SWAP70,missense_variant,p.Leu513Arg,ENST00000447399,NM_001297714.1;RP11-540A21.2,downstream_gene_variant,,ENST00000500698,;SWAP70,intron_variant,,ENST00000534562,; G ENST00000318950 Transcript missense_variant 1815/4882 1712/1758 571/585 L/R cTt/cGt 1 1 SWAP70 HGNC HGNC:17070 protein_coding YES CCDS31426.1 ENSP00000315630 Q9UH65 UPI0000073652 NM_015055.3 deleterious(0) 12/12 hmmpanther:PTHR14383,hmmpanther:PTHR14383:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.22781 0.9999993 1 1 1 0 G 3 3 87 9749924 9749924 T G 1 0 0 0 0 1 0 0 0 15810 1609 56 5 5 SWAP70 11 9749924 Missense_Mutation SNP T C3N-02003_T 1035922 9749924 125336698 179 26860 PIK3C2A 0 . GRCh38 11 17097251 17097251 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.4132A>C p.Ser1378Arg p.S1378R ENST00000265970 26/32 117 107 10 166 166 0 strelka-varscan-mutect PIK3C2A,missense_variant,p.Ser1378Arg,ENST00000265970,NM_001321378.1,NM_002645.2;PIK3C2A,non_coding_transcript_exon_variant,,ENST00000531428,; G ENST00000265970 Transcript missense_variant 4132/8227 4132/5061 1378/1686 S/R Agt/Cgt 1 -1 PIK3C2A HGNC HGNC:8971 protein_coding YES CCDS7824.1 ENSP00000265970 O00443 L7RRS0 UPI000013D6B3 NM_001321378.1,NM_002645.2 deleterious(0) 26/32 Gene3D:1.10.1070.11,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF28,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 17097251 17097251 T G 1 0 0 0 0 1 0 0 0 12004 1609 56 5 5 PIK3C2A 11 17097251 Missense_Mutation SNP T C3N-02003_T 7347327 17097251 117989371 180 26861 KCNJ11 0 . GRCh38 11 17387674 17387674 + Missense_Mutation SNP C C T C3N-02003_T C3N-02003_N C C c.418G>A p.Glu140Lys p.E140K ENST00000339994 1/1 477 439 38 425 425 0 strelka-varscan-mutect KCNJ11,missense_variant,p.Glu140Lys,ENST00000339994,NM_000525.3;KCNJ11,missense_variant,p.Glu53Lys,ENST00000528731,NM_001166290.1;KCNJ11,missense_variant,p.Glu53Lys,ENST00000526912,;KCNJ11,missense_variant,p.Glu146Lys,ENST00000528992,;RP1-239B22.5,downstream_gene_variant,,ENST00000568280,;KCNJ11,upstream_gene_variant,,ENST00000526747,; T ENST00000339994 Transcript missense_variant 986/2801 418/1173 140/390 E/K Gag/Aag COSM687068 1 -1 KCNJ11 HGNC HGNC:6257 protein_coding YES CCDS31436.1 ENSP00000345708 Q14654 B2RC52 UPI0000161990 NM_000525.3 deleterious(0) 1/1 hmmpanther:PTHR11767:SF44,hmmpanther:PTHR11767,Pfam_domain:PF01007,Gene3D:1.10.287.70,PIRSF_domain:PIRSF005465,Superfamily_domains:SSF81324,Prints_domain:PR01320 1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 17387674 17387674 C T 1 0 0 0 0 1 0 0 0 7961 835 29 3 3 KCNJ11 11 17387674 Missense_Mutation SNP C C3N-02003_T 290423 17387674 117698948 181 26862 KCNA4 0 . GRCh38 11 30011449 30011449 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1230C>T p.= p.V410V ENST00000328224 2/2 152 129 23 127 127 0 strelka-varscan-mutect KCNA4,synonymous_variant,p.=,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript synonymous_variant 2464/4172 1230/1962 410/653 V gtC/gtT 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 2/2 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45,Superfamily_domains:SSF81324 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 30011449 30011449 G A 1 0 0 0 0 0 0 0 1 7921 929 33 3 3 KCNA4 11 30011449 Silent SNP G C3N-02003_T 12623775 30011449 105075173 182 26863 KIAA1549L 0 . GRCh38 11 33561691 33561691 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.3143A>C p.Asn1048Thr p.N1048T ENST00000321505 7/20 166 153 13 248 248 0 strelka-varscan-mutect KIAA1549L,missense_variant,p.Asn1048Thr,ENST00000321505,NM_012194.2;KIAA1549L,missense_variant,p.Asn1054Thr,ENST00000265654,;KIAA1549L,missense_variant,p.Asn446Thr,ENST00000526400,; C ENST00000321505 Transcript missense_variant 3323/11678 3143/5550 1048/1849 N/T aAc/aCc 1 1 KIAA1549L HGNC HGNC:24836 protein_coding YES CCDS44565.2 ENSP00000315295 Q6ZVL6 UPI0000E59322 NM_012194.2 deleterious(0) 7/20 hmmpanther:PTHR21590,hmmpanther:PTHR21590:SF3,Pfam_domain:PF12877 MODERATE 1 SNV 1 1 PASS rs1161754151 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 33561691 33561691 A C 1 0 0 0 0 1 0 0 0 8121 43 2 5 5 KIAA1549L 11 33561691 Missense_Mutation SNP A C3N-02003_T 3550242 33561691 101524931 183 26864 CKAP5 0 . GRCh38 11 46751221 46751221 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.5357A>C p.Asn1786Thr p.N1786T ENST00000529230 40/44 379 353 26 310 310 0 strelka-varscan-mutect CKAP5,missense_variant,p.Asn1786Thr,ENST00000529230,NM_001008938.3;CKAP5,missense_variant,p.Asn1726Thr,ENST00000312055,NM_014756.3;CKAP5,missense_variant,p.Asn1726Thr,ENST00000354558,;CKAP5,missense_variant,p.Asn25Thr,ENST00000525896,;CKAP5,downstream_gene_variant,,ENST00000526876,;CKAP5,downstream_gene_variant,,ENST00000527333,;MIR5582,downstream_gene_variant,,ENST00000579697,;CKAP5,non_coding_transcript_exon_variant,,ENST00000533413,; G ENST00000529230 Transcript missense_variant 5404/7121 5357/6099 1786/2032 N/T aAc/aCc 1 -1 CKAP5 HGNC HGNC:28959 protein_coding YES CCDS31477.1 ENSP00000432768 Q14008 UPI000013F21E NM_001008938.3 tolerated(0.18) 40/44 hmmpanther:PTHR12609:SF0,hmmpanther:PTHR12609,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 46751221 46751221 T G 1 0 0 0 0 1 0 0 0 3208 1725 60 5 5 CKAP5 11 46751221 Missense_Mutation SNP T C3N-02003_T 13189530 46751221 88335401 184 26865 MYBPC3 0 . GRCh38 11 47346295 47346295 + Silent SNP C C T C3N-02003_T C3N-02003_N C C c.1002G>A p.= p.E334E ENST00000545968 12/35 133 112 21 80 80 0 strelka-varscan-mutect MYBPC3,synonymous_variant,p.=,ENST00000545968,NM_000256.3;MYBPC3,synonymous_variant,p.=,ENST00000256993,;MYBPC3,synonymous_variant,p.=,ENST00000399249,;MYBPC3,synonymous_variant,p.=,ENST00000544791,; T ENST00000545968 Transcript synonymous_variant 1057/4226 1002/3825 334/1274 E gaG/gaA COSM5448178,COSM5448179 1 -1 MYBPC3 HGNC HGNC:7551 protein_coding YES CCDS53621.1 ENSP00000442795 Q14896 UPI000006EEAA NM_000256.3 12/35 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 47346295 47346295 C T 1 0 0 0 0 0 0 0 1 10013 796 28 3 3 MYBPC3 11 47346295 Silent SNP C C3N-02003_T 595074 47346295 87740327 185 26866 AHNAK 0 . GRCh38 11 62521947 62521947 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.12470A>C p.Asp4157Ala p.D4157A ENST00000378024 5/5 512 476 36 419 418 1 strelka-varscan-mutect AHNAK,missense_variant,p.Asp4157Ala,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; G ENST00000378024 Transcript missense_variant 12745/18787 12470/17673 4157/5890 D/A gAc/gCc 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 62521947 62521947 T G 1 0 0 0 0 1 0 0 0 491 1667 58 5 5 AHNAK 11 62521947 Missense_Mutation SNP T C3N-02003_T 15175652 62521947 72564675 186 26867 MAP3K11 0 . GRCh38 11 65598482 65598482 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.2353G>A p.Gly785Arg p.G785R ENST00000309100 10/10 127 114 13 107 107 0 strelka-varscan-mutect MAP3K11,missense_variant,p.Gly785Arg,ENST00000309100,NM_002419.3;MAP3K11,missense_variant,p.Gly528Arg,ENST00000530153,;MAP3K11,missense_variant,p.Gly201Arg,ENST00000532507,;KCNK7,upstream_gene_variant,,ENST00000394216,NM_005714.1;KCNK7,upstream_gene_variant,,ENST00000394217,NM_033348.1,NM_033455.1;KCNK7,upstream_gene_variant,,ENST00000340313,NM_033347.1;KCNK7,upstream_gene_variant,,ENST00000342202,;KCNK7,upstream_gene_variant,,ENST00000525254,;KCNK7,upstream_gene_variant,,ENST00000530380,;MAP3K11,downstream_gene_variant,,ENST00000534432,;MAP3K11,3_prime_UTR_variant,,ENST00000524848,; T ENST00000309100 Transcript missense_variant 2839/3566 2353/2544 785/847 G/R Ggg/Agg 1 -1 MAP3K11 HGNC HGNC:6850 protein_coding YES CCDS8107.1 ENSP00000309597 Q16584 A0A024R5E6 UPI0000049BF7 NM_002419.3 deleterious_low_confidence(0) 10/10 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 65598482 65598482 C T 1 0 0 0 0 1 0 0 0 9167 594 21 3 3 MAP3K11 11 65598482 Missense_Mutation SNP C C3N-02003_T 3076535 65598482 69488140 187 26868 KAT5 0 . GRCh38 11 65716771 65716771 + Missense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.1134C>A p.Asp378Glu p.D378E ENST00000341318 9/13 231 198 33 184 183 1 strelka-varscan-mutect KAT5,missense_variant,p.Asp378Glu,ENST00000341318,NM_182710.2;KAT5,missense_variant,p.Asp345Glu,ENST00000377046,NM_006388.3;KAT5,missense_variant,p.Asp293Glu,ENST00000352980,NM_182709.2;KAT5,missense_variant,p.Asp134Glu,ENST00000534650,;KAT5,missense_variant,p.Asp326Glu,ENST00000530446,NM_001206833.1;RNASEH2C,downstream_gene_variant,,ENST00000308418,NM_032193.3;RNASEH2C,downstream_gene_variant,,ENST00000528220,;KAT5,downstream_gene_variant,,ENST00000531880,;RNASEH2C,downstream_gene_variant,,ENST00000527610,;KAT5,upstream_gene_variant,,ENST00000533596,;KAT5,downstream_gene_variant,,ENST00000528198,;KAT5,downstream_gene_variant,,ENST00000534681,;KAT5,downstream_gene_variant,,ENST00000534104,;KAT5,downstream_gene_variant,,ENST00000530605,;KAT5,downstream_gene_variant,,ENST00000525204,;KAT5,downstream_gene_variant,,ENST00000534293,;KAT5,non_coding_transcript_exon_variant,,ENST00000533441,;RNASEH2C,intron_variant,,ENST00000534482,;RNASEH2C,downstream_gene_variant,,ENST00000531596,;KAT5,downstream_gene_variant,,ENST00000532042,;KAT5,downstream_gene_variant,,ENST00000527544,;RNASEH2C,downstream_gene_variant,,ENST00000533698,;RNASEH2C,downstream_gene_variant,,ENST00000530192,;KAT5,upstream_gene_variant,,ENST00000525600,; A ENST00000341318 Transcript missense_variant 1368/2296 1134/1641 378/546 D/E gaC/gaA 1 1 KAT5 HGNC HGNC:5275 protein_coding YES CCDS8110.1 ENSP00000340330 Q92993 UPI00001D3EFB NM_182710.2 deleterious(0) 9/13 PROSITE_profiles:PS51726,hmmpanther:PTHR10615,Gene3D:3.40.630.30,Pfam_domain:PF01853,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 65716771 65716771 C A 1 0 0 0 0 1 0 0 0 7897 564 20 2 2 KAT5 11 65716771 Missense_Mutation SNP C C3N-02003_T 118289 65716771 69369851 188 26869 RBM4B 0 . GRCh38 11 66668990 66668990 + Silent SNP A A C novel C3N-02003_T C3N-02003_N A A c.714T>G p.= p.A238A ENST00000525754 2/3 339 306 33 230 230 0 strelka-varscan-mutect RBM4B,synonymous_variant,p.=,ENST00000525754,;RBM4B,synonymous_variant,p.=,ENST00000310046,NM_031492.3;RBM4B,3_prime_UTR_variant,,ENST00000524637,;RBM4B,intron_variant,,ENST00000531969,NM_001286135.1;RBM4,downstream_gene_variant,,ENST00000396053,NM_001198844.1;RP11-658F2.8,downstream_gene_variant,,ENST00000550837,;RP11-658F2.8,downstream_gene_variant,,ENST00000548810,;RBM4B,upstream_gene_variant,,ENST00000529195,;RBM4B,upstream_gene_variant,,ENST00000534198,;RBM4B,upstream_gene_variant,,ENST00000528106,; C ENST00000525754 Transcript synonymous_variant 1383/2339 714/1080 238/359 A gcT/gcG 1 -1 RBM4B HGNC HGNC:28842 protein_coding YES CCDS8149.1 ENSP00000433071 Q9BQ04 UPI0000070053 2/3 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs1369084200 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 66668990 66668990 A C 1 0 0 0 0 0 0 0 1 13309 59 3 5 5 RBM4B 11 66668990 Silent SNP A C3N-02003_T 952219 66668990 68417632 189 26870 KDM2A 0 . GRCh38 11 67181354 67181354 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.216G>C p.Leu72Phe p.L72F ENST00000529006 4/21 113 99 14 115 115 0 strelka-mutect KDM2A,missense_variant,p.Leu72Phe,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Leu72Phe,ENST00000398645,;KDM2A,missense_variant,p.Leu55Phe,ENST00000308783,;KDM2A,downstream_gene_variant,,ENST00000527157,; C ENST00000529006 Transcript missense_variant 662/6967 216/3489 72/1162 L/F ttG/ttC 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 tolerated(0.16) 4/21 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 67181354 67181354 G C 1 0 0 0 0 1 0 0 0 8042 1281 45 4 4 KDM2A 11 67181354 Missense_Mutation SNP G C3N-02003_T 512364 67181354 67905268 190 26871 1 22 3 3 521 G 1.470778e-05 KDM2A 0 . GRCh38 11 67181375 67181375 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.237G>A p.= p.K79K ENST00000529006 4/21 100 86 14 106 106 0 strelka-mutect KDM2A,synonymous_variant,p.=,ENST00000529006,NM_012308.2;KDM2A,synonymous_variant,p.=,ENST00000398645,;KDM2A,synonymous_variant,p.=,ENST00000308783,;KDM2A,downstream_gene_variant,,ENST00000527157,; A ENST00000529006 Transcript synonymous_variant 683/6967 237/3489 79/1162 K aaG/aaA 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 4/21 Gene3D:1vrbA01,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,Superfamily_domains:SSF51197 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 67181375 67181375 G A 1 0 0 0 0 0 0 0 1 8042 933 33 3 3 KDM2A 11 67181375 Silent SNP G C3N-02003_T 21 67181375 67905247 191 26872 1 22 3 3 521 G 1.470778e-05 KDM2A 0 . GRCh38 11 67181874 67181874 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.289G>A p.Asp97Asn p.D97N ENST00000529006 5/21 298 199 99 265 265 0 strelka-varscan-mutect KDM2A,missense_variant,p.Asp97Asn,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Asp97Asn,ENST00000398645,;KDM2A,missense_variant,p.Asp80Asn,ENST00000308783,;KDM2A,downstream_gene_variant,,ENST00000527157,; A ENST00000529006 Transcript missense_variant 735/6967 289/3489 97/1162 D/N Gat/Aat 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 deleterious(0) 5/21 Gene3D:1vrbA01,hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3,Superfamily_domains:SSF51197 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 67181874 67181874 G A 1 0 0 0 0 1 0 0 0 8042 1290 45 3 3 KDM2A 11 67181874 Missense_Mutation SNP G C3N-02003_T 499 67181874 67904748 192 26873 1 22 3 3 521 G 1.470778e-05 KDM2A 0 . GRCh38 11 67231952 67231952 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.1471G>C p.Asp491His p.D491H ENST00000529006 12/21 171 161 10 65 65 0 strelka-varscan-mutect KDM2A,missense_variant,p.Asp491His,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Asp491His,ENST00000398645,;KDM2A,missense_variant,p.Asp474His,ENST00000308783,;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,non_coding_transcript_exon_variant,,ENST00000525041,; C ENST00000529006 Transcript missense_variant 1917/6967 1471/3489 491/1162 D/H Gat/Cat 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 tolerated(0.21) 12/21 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -17.69121 0.9999967 1 1 1 0 C 3 2 87 67231952 67231952 G C 1 0 0 0 0 1 0 0 0 8042 1290 45 4 4 KDM2A 11 67231952 Missense_Mutation SNP G C3N-02003_T 50078 67231952 67854670 193 26874 UNC93B1 0 . GRCh38 11 67991701 67991701 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1639T>G p.Ser547Ala p.S547A ENST00000227471 11/11 409 255 154 256 255 1 strelka-varscan-mutect UNC93B1,missense_variant,p.Ser547Ala,ENST00000227471,NM_030930.3;UNC93B1,intron_variant,,ENST00000610659,;UNC93B1,downstream_gene_variant,,ENST00000525368,; C ENST00000227471 Transcript missense_variant 1719/2316 1639/1794 547/597 S/A Tcg/Gcg 1 -1 UNC93B1 HGNC HGNC:13481 protein_coding YES CCDS73334.1 ENSP00000227471 Q9H1C4 UPI000034ECF5 NM_030930.3 deleterious(0) 11/11 hmmpanther:PTHR19444,hmmpanther:PTHR19444:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 67991701 67991701 A C 1 0 0 0 0 1 0 0 0 17523 304 11 5 5 UNC93B1 11 67991701 Missense_Mutation SNP A C3N-02003_T 759749 67991701 67094921 194 26875 PPFIA1 0 . GRCh38 11 70337382 70337382 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1446A>C p.Glu482Asp p.E482D ENST00000253925 12/28 111 69 42 90 90 0 strelka-varscan-mutect PPFIA1,missense_variant,p.Glu482Asp,ENST00000253925,NM_003626.3;PPFIA1,missense_variant,p.Glu482Asp,ENST00000389547,NM_177423.2;PPFIA1,missense_variant,p.Glu34Asp,ENST00000530798,;AP000487.6,intron_variant,,ENST00000528607,;PPFIA1,non_coding_transcript_exon_variant,,ENST00000532443,;PPFIA1,upstream_gene_variant,,ENST00000530294,;PPFIA1,upstream_gene_variant,,ENST00000526347,;PPFIA1,upstream_gene_variant,,ENST00000526074,;PPFIA1,upstream_gene_variant,,ENST00000528284,;PPFIA1,downstream_gene_variant,,ENST00000530932,;PPFIA1,missense_variant,p.Glu482Asp,ENST00000532504,;PPFIA1,missense_variant,p.Glu278Asp,ENST00000526262,;PPFIA1,upstream_gene_variant,,ENST00000526369,; C ENST00000253925 Transcript missense_variant 1661/5234 1446/3609 482/1202 E/D gaA/gaC 1 1 PPFIA1 HGNC HGNC:9245 protein_coding YES CCDS31627.1 ENSP00000253925 Q13136 UPI0000072426 NM_003626.3 tolerated(0.17) 12/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12587,hmmpanther:PTHR12587:SF15 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 70337382 70337382 A C 1 0 0 0 0 1 0 0 0 12418 69 3 5 5 PPFIA1 11 70337382 Missense_Mutation SNP A C3N-02003_T 2345681 70337382 64749240 195 26876 OR2AT4 0 . GRCh38 11 75089449 75089449 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.265T>G p.Leu89Val p.L89V ENST00000305159 1/1 496 469 27 261 261 0 strelka-varscan-mutect OR2AT4,missense_variant,p.Leu89Val,ENST00000305159,NM_001005285.1; C ENST00000305159 Transcript missense_variant 306/1042 265/963 89/320 L/V Tta/Gta 1 -1 OR2AT4 HGNC HGNC:19620 protein_coding YES CCDS31639.1 ENSP00000304846 A6NND4 A0A126GWB1 UPI0000061FA5 NM_001005285.1 tolerated(0.22) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF15,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 75089449 75089449 A C 1 0 0 0 0 1 0 0 0 11066 69 3 5 5 OR2AT4 11 75089449 Missense_Mutation SNP A C3N-02003_T 4752067 75089449 59997173 196 26877 RPS3 0 . GRCh38 11 75399557 75399557 + Nonsense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.10C>T p.Gln4Ter p.Q4* ENST00000278572 1/7 263 166 97 150 150 0 strelka-varscan-mutect RPS3,stop_gained,p.Gln4Ter,ENST00000531188,NM_001005.4;RPS3,stop_gained,p.Gln4Ter,ENST00000530164,;RPS3,stop_gained,p.Gln4Ter,ENST00000527446,NM_001256802.1;RPS3,stop_gained,p.Gln4Ter,ENST00000278572,NM_001260506.1;RPS3,stop_gained,p.Gln4Ter,ENST00000524851,;RPS3,stop_gained,p.Gln4Ter,ENST00000526608,;RPS3,stop_gained,p.Gln4Ter,ENST00000534440,;RPS3,stop_gained,p.Gln4Ter,ENST00000527273,;RPS3,5_prime_UTR_variant,,ENST00000422465,NM_001260507.1;RPS3,upstream_gene_variant,,ENST00000525933,;RPS3,upstream_gene_variant,,ENST00000528847,;SNORD15A,upstream_gene_variant,,ENST00000384214,;SNORD15B,upstream_gene_variant,,ENST00000384714,;RPS3,upstream_gene_variant,,ENST00000529285,;RPS3,upstream_gene_variant,,ENST00000534555,;RPS3,stop_gained,p.Gln4Ter,ENST00000530721,;RPS3,stop_gained,p.Gln1Ter,ENST00000526248,;RPS3,stop_gained,p.Gln4Ter,ENST00000532872,;RPS3,stop_gained,p.Gln4Ter,ENST00000528439,;RPS3,non_coding_transcript_exon_variant,,ENST00000529173,;RPS3,upstream_gene_variant,,ENST00000530170,;RPS3,upstream_gene_variant,,ENST00000525690,; T ENST00000278572 Transcript stop_gained 28/907 10/780 4/259 Q/* Caa/Taa 1 1 RPS3 HGNC HGNC:10420 protein_coding YES CCDS58161.1 ENSP00000278572 P23396 UPI0001EE4B77 NM_001260506.1 1/7 hmmpanther:PTHR11760,hmmpanther:PTHR11760:SF20 HIGH 1 SNV 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 87 75399557 75399557 C T 1 0 0 0 0 0 1 0 0 13898 711 25 3 3 RPS3 11 75399557 Nonsense_Mutation SNP C C3N-02003_T 310108 75399557 59687065 197 26878 PCF11 0 . GRCh38 11 83181165 83181165 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.4141C>G p.His1381Asp p.H1381D ENST00000298281 12/16 118 108 10 92 92 0 strelka-varscan-mutect PCF11,missense_variant,p.His1381Asp,ENST00000298281,NM_015885.3;PCF11,missense_variant,p.His166Asp,ENST00000530906,;PCF11-AS1,downstream_gene_variant,,ENST00000602322,;RP11-727A23.5,downstream_gene_variant,,ENST00000602381,;RP11-727A23.4,intron_variant,,ENST00000528133,;PCF11,non_coding_transcript_exon_variant,,ENST00000528336,; G ENST00000298281 Transcript missense_variant 4593/7677 4141/4668 1381/1555 H/D Cat/Gat 1 1 PCF11 HGNC HGNC:30097 protein_coding YES CCDS44689.1 ENSP00000298281 O94913 UPI00001BB2B7 NM_015885.3 deleterious(0) 12/16 hmmpanther:PTHR15921,hmmpanther:PTHR15921:SF3 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -19.48498 1 1 1 1 0 G 3 3 87 83181165 83181165 C G 1 0 0 0 0 1 0 0 0 11661 826 29 4 4 PCF11 11 83181165 Missense_Mutation SNP C C3N-02003_T 7781608 83181165 51905457 198 26879 PCSK7 0 . GRCh38 11 117225966 117225966 + Missense_Mutation SNP G G T novel C3N-02003_T C3N-02003_N G G c.825C>A p.Asn275Lys p.N275K ENST00000320934 6/17 487 305 182 299 299 0 strelka-varscan-mutect PCSK7,missense_variant,p.Asn275Lys,ENST00000320934,NM_004716.3;PCSK7,missense_variant,p.Asn275Lys,ENST00000540028,;PCSK7,missense_variant,p.Asn275Lys,ENST00000525027,;PCSK7,downstream_gene_variant,,ENST00000530269,;PCSK7,downstream_gene_variant,,ENST00000524507,;PCSK7,downstream_gene_variant,,ENST00000532301,;PCSK7,non_coding_transcript_exon_variant,,ENST00000534529,;PCSK7,upstream_gene_variant,,ENST00000528217,; T ENST00000320934 Transcript missense_variant 1456/4649 825/2358 275/785 N/K aaC/aaA 1 -1 PCSK7 HGNC HGNC:8748 protein_coding YES CCDS8382.1 ENSP00000325917 Q16549 UPI0000070E4E NM_004716.3 deleterious(0.01) 6/17 hmmpanther:PTHR10795:SF9,hmmpanther:PTHR10795,Gene3D:3.40.50.200,Pfam_domain:PF00082,Superfamily_domains:SSF52743 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 117225966 117225966 G T 1 0 0 0 0 1 0 0 0 11693 1368 48 2 2 PCSK7 11 117225966 Missense_Mutation SNP G C3N-02003_T 34044801 117225966 17860656 199 26880 CD3D 0 . GRCh38 11 118339488 118339488 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.413A>C p.Asp138Ala p.D138A ENST00000300692 4/5 904 805 99 533 532 1 strelka-varscan-mutect CD3D,missense_variant,p.Asp138Ala,ENST00000300692,NM_000732.4;CD3D,missense_variant,p.Asp99Ala,ENST00000534687,;CD3D,missense_variant,p.Asp94Ala,ENST00000392884,NM_001040651.1;CD3D,missense_variant,p.Asp65Ala,ENST00000529594,;CD3G,upstream_gene_variant,,ENST00000532917,NM_000073.2;CD3G,upstream_gene_variant,,ENST00000392883,;CD3G,upstream_gene_variant,,ENST00000532903,;CD3G,upstream_gene_variant,,ENST00000528540,;CD3D,non_coding_transcript_exon_variant,,ENST00000526561,;CD3G,upstream_gene_variant,,ENST00000292144,;CD3G,upstream_gene_variant,,ENST00000533462,;CD3G,upstream_gene_variant,,ENST00000527777,; G ENST00000300692 Transcript missense_variant 550/861 413/516 138/171 D/A gAc/gCc 1 -1 CD3D HGNC HGNC:1673 protein_coding YES CCDS8394.1 ENSP00000300692 P04234 B0YIY4 UPI0000127356 NM_000732.4 deleterious(0) 4/5 PROSITE_profiles:PS51055,hmmpanther:PTHR10570,hmmpanther:PTHR10570:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 118339488 118339488 T G 1 0 0 0 0 1 0 0 0 2714 1667 58 5 5 CD3D 11 118339488 Missense_Mutation SNP T C3N-02003_T 1113522 118339488 16747134 200 26881 UBE4A 0 . GRCh38 11 118389882 118389882 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.2766C>T p.= p.I922I ENST00000431736 17/20 100 95 5 72 72 0 strelka-mutect UBE4A,synonymous_variant,p.=,ENST00000252108,NM_001204077.1;UBE4A,synonymous_variant,p.=,ENST00000431736,NM_004788.3;UBE4A,synonymous_variant,p.=,ENST00000545354,; T ENST00000431736 Transcript synonymous_variant 2838/6061 2766/3222 922/1073 I atC/atT 1 1 UBE4A HGNC HGNC:12499 protein_coding YES CCDS8396.1 ENSP00000387362 Q14139 UPI000013CD3F NM_004788.3 17/20 hmmpanther:PTHR13931:SF2,hmmpanther:PTHR13931,Pfam_domain:PF10408 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -10.47652 0.9999993 1 1 1 0 T 2 4 87 118389882 118389882 C T 1 0 0 0 0 0 0 0 1 17406 903 32 3 3 UBE4A 11 118389882 Silent SNP C C3N-02003_T 50394 118389882 16696740 201 26882 CHD4 0 . GRCh38 12 6583207 6583207 + Missense_Mutation SNP C C T rs754606238 C3N-02003_T C3N-02003_N C C c.4051G>A p.Glu1351Lys p.E1351K ENST00000357008 26/40 147 139 8 140 140 0 strelka-varscan-mutect CHD4,missense_variant,p.Glu1348Lys,ENST00000544484,;CHD4,missense_variant,p.Glu1344Lys,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Glu1351Lys,ENST00000357008,NM_001273.3;SCARNA11,upstream_gene_variant,,ENST00000516089,;RP5-940J5.6,non_coding_transcript_exon_variant,,ENST00000501075,;CHD4,non_coding_transcript_exon_variant,,ENST00000540960,;CHD4,intron_variant,,ENST00000536301,;CHD4,upstream_gene_variant,,ENST00000542717,; T ENST00000357008 Transcript missense_variant 4215/6496 4051/5739 1351/1912 E/K Gag/Aag rs754606238 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 deleterious(0.01) 26/40 Low_complexity_(Seg):seg,Pfam_domain:PF06465,SMART_domains:SM01147 MODERATE 1 SNV 1 1 PASS rs754606238 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 6583207 6583207 C T 1 0 0 0 0 1 0 0 0 3086 864 30 3 3 CHD4 12 6583207 Missense_Mutation SNP C C3N-02003_T 6583207 126692102 202 26883 OLR1 0 . GRCh38 12 10166905 10166905 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.231G>C p.Gln77His p.Q77H ENST00000309539 3/6 231 217 14 273 273 0 strelka-varscan-mutect OLR1,missense_variant,p.Gln77His,ENST00000309539,NM_002543.3;OLR1,missense_variant,p.Gln77His,ENST00000545927,NM_001172633.1;OLR1,missense_variant,p.Gln77His,ENST00000432556,NM_001172632.1;OLR1,missense_variant,p.Gln77His,ENST00000544577,;OLR1,missense_variant,p.Gln24His,ENST00000539518,;OLR1,missense_variant,p.Gln24His,ENST00000543414,;OLR1,5_prime_UTR_variant,,ENST00000543993,;OLR1,5_prime_UTR_variant,,ENST00000339968,;OLR1,5_prime_UTR_variant,,ENST00000538745,;OLR1,5_prime_UTR_variant,,ENST00000538873,;TMEM52B,upstream_gene_variant,,ENST00000381923,NM_001079815.1;TMEM52B,upstream_gene_variant,,ENST00000545924,;TMEM52B,upstream_gene_variant,,ENST00000334148,; G ENST00000309539 Transcript missense_variant 292/2462 231/822 77/273 Q/H caG/caC 1 -1 OLR1 HGNC HGNC:8133 protein_coding YES CCDS8618.1 ENSP00000309124 P78380 A0A024RAU0 UPI000004A917 NM_002543.3 deleterious(0.02) 3/6 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF08391,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 10166905 10166905 C G 1 0 0 0 0 1 0 0 0 10938 912 32 4 4 OLR1 12 10166905 Missense_Mutation SNP C C3N-02003_T 3583698 10166905 123108404 203 26884 ABCC9 0 . GRCh38 12 21908181 21908181 + Missense_Mutation SNP A A C C3N-02003_T C3N-02003_N A A c.1351T>G p.Leu451Val p.L451V ENST00000261200 9/38 249 197 52 290 290 0 strelka-varscan-mutect ABCC9,missense_variant,p.Leu451Val,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Leu451Val,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Leu114Val,ENST00000544039,; C ENST00000261200 Transcript missense_variant 1351/8293 1351/4650 451/1549 L/V Tta/Gta COSM1243993,COSM1243994 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 tolerated(0.18) 9/38 PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 21908181 21908181 A C 1 0 0 0 0 1 0 0 0 63 11 1 5 5 ABCC9 12 21908181 Missense_Mutation SNP A C3N-02003_T 11741276 21908181 111367128 204 26885 SLC38A2 0 . GRCh38 12 46363081 46363081 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1119C>T p.= p.L373L ENST00000256689 13/16 134 127 7 238 238 0 strelka-varscan-mutect SLC38A2,synonymous_variant,p.=,ENST00000256689,NM_018976.4;SLC38A2,synonymous_variant,p.=,ENST00000551374,;SLC38A2,synonymous_variant,p.=,ENST00000612232,NM_001307936.1;SLC38A2,intron_variant,,ENST00000548111,;SLC38A2,downstream_gene_variant,,ENST00000547252,;SLC38A2,downstream_gene_variant,,ENST00000548870,;SLC38A2,3_prime_UTR_variant,,ENST00000549258,;SLC38A2,non_coding_transcript_exon_variant,,ENST00000548236,;SLC38A2,upstream_gene_variant,,ENST00000546520,;SLC38A2,upstream_gene_variant,,ENST00000548785,;SLC38A2,downstream_gene_variant,,ENST00000552414,;SLC38A2,upstream_gene_variant,,ENST00000552703,; A ENST00000256689 Transcript synonymous_variant 1564/4888 1119/1521 373/506 L ctC/ctT 1 -1 SLC38A2 HGNC HGNC:13448 protein_coding YES CCDS8749.1 ENSP00000256689 Q96QD8 A0A024R0W3 UPI000000121A NM_018976.4 13/16 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF207,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs758997542 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 46363081 46363081 G A 1 0 0 0 0 0 0 0 1 14882 1277 45 3 3 SLC38A2 12 46363081 Silent SNP G C3N-02003_T 24454900 46363081 86912228 205 26886 FAM186A 0 . GRCh38 12 50353011 50353011 + Missense_Mutation SNP G G A rs754227593 C3N-02003_T C3N-02003_N G G c.3821C>T p.Ala1274Val p.A1274V ENST00000327337 4/8 202 188 14 226 226 0 varscan-mutect FAM186A,missense_variant,p.Ala1274Val,ENST00000543111,;FAM186A,missense_variant,p.Ala1274Val,ENST00000327337,NM_001145475.1;FAM186A,upstream_gene_variant,,ENST00000543096,; A ENST00000327337 Transcript missense_variant 3821/7127 3821/7056 1274/2351 A/V gCc/gTc rs754227593 1 -1 FAM186A HGNC HGNC:26980 protein_coding YES CCDS44878.1 ENSP00000329995 A6NE01 UPI00001D7978 NM_001145475.1 deleterious(0.05) 4/8 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF2 MODERATE 1 SNV 5 1 PASS rs754227593 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 50353011 50353011 G A 1 0 0 0 0 1 0 0 0 5361 1203 42 3 3 FAM186A 12 50353011 Missense_Mutation SNP G C3N-02003_T 3989930 50353011 82922298 206 26887 OR6C76 0 . GRCh38 12 55426832 55426832 + Missense_Mutation SNP G G T rs545625846 C3N-02003_T C3N-02003_N G G c.579G>T p.Glu193Asp p.E193D ENST00000328314 1/1 105 76 29 90 90 0 strelka-varscan-mutect OR6C76,missense_variant,p.Glu193Asp,ENST00000328314,NM_001005183.1; T ENST00000328314 Transcript missense_variant 579/939 579/939 193/312 E/D gaG/gaT rs545625846 1 1 OR6C76 HGNC HGNC:31305 protein_coding YES CCDS31823.1 ENSP00000328402 A6NM76 A0A126GW16 UPI000023786F NM_001005183.1 deleterious_low_confidence(0.01) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26454,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs545625846 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 55426832 55426832 G T 1 0 0 0 0 1 0 0 0 11268 962 34 2 2 OR6C76 12 55426832 Missense_Mutation SNP G C3N-02003_T 5073821 55426832 77848477 207 26888 MYO1A 0 . GRCh38 12 57038949 57038949 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1393G>A p.Asp465Asn p.D465N ENST00000442789 17/29 605 566 39 448 448 0 strelka-varscan-mutect MYO1A,missense_variant,p.Asp465Asn,ENST00000442789,NM_001256041.1;MYO1A,missense_variant,p.Asp465Asn,ENST00000300119,NM_005379.3;MYO1A,downstream_gene_variant,,ENST00000492945,;MYO1A,non_coding_transcript_exon_variant,,ENST00000476795,;MYO1A,missense_variant,p.Asp303Asn,ENST00000554234,; T ENST00000442789 Transcript missense_variant 1681/3658 1393/3132 465/1043 D/N Gac/Aac 1 -1 MYO1A HGNC HGNC:7595 protein_coding YES CCDS8929.1 ENSP00000393392 Q9UBC5 UPI000012FAC2 NM_001256041.1 deleterious(0) 17/29 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF291,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 57038949 57038949 C T 1 0 0 0 0 1 0 0 0 10069 826 29 3 3 MYO1A 12 57038949 Missense_Mutation SNP C C3N-02003_T 1612117 57038949 76236360 208 26889 BEST3 0 . GRCh38 12 69654993 69654993 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.1921G>C p.Asp641His p.D641H ENST00000330891 10/10 164 149 15 158 158 0 strelka-varscan-mutect BEST3,missense_variant,p.Asp641His,ENST00000330891,NM_032735.2;BEST3,missense_variant,p.Asp535His,ENST00000553096,NM_001282613.1;BEST3,missense_variant,p.Asp428His,ENST00000488961,NM_152439.3;BEST3,intron_variant,,ENST00000331471,NM_001282614.1;BEST3,intron_variant,,ENST00000547208,; G ENST00000330891 Transcript missense_variant 2148/3532 1921/2007 641/668 D/H Gat/Cat 1 -1 BEST3 HGNC HGNC:17105 protein_coding YES CCDS8992.2 ENSP00000332413 Q8N1M1 UPI000006E397 NM_032735.2 deleterious_low_confidence(0) 10/10 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 69654993 69654993 C G 1 0 0 0 0 1 0 0 0 1554 826 29 4 4 BEST3 12 69654993 Missense_Mutation SNP C C3N-02003_T 12616044 69654993 63620316 209 26890 NAV3 0 . GRCh38 12 78006826 78006826 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.1288C>G p.Leu430Val p.L430V ENST00000397909 8/40 279 211 68 288 287 1 strelka-varscan-mutect NAV3,missense_variant,p.Leu430Val,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Leu430Val,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Leu430Val,ENST00000549464,;NAV3,missense_variant,p.Leu373Val,ENST00000550042,;NAV3,downstream_gene_variant,,ENST00000550503,;NAV3,downstream_gene_variant,,ENST00000547725,;NAV3,upstream_gene_variant,,ENST00000550673,; G ENST00000397909 Transcript missense_variant 1461/9821 1288/7158 430/2385 L/V Ctg/Gtg 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 tolerated(0.67) 8/40 Low_complexity_(Seg):seg,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 78006826 78006826 C G 1 0 0 0 0 1 0 0 0 10194 912 32 4 4 NAV3 12 78006826 Missense_Mutation SNP C C3N-02003_T 8351833 78006826 55268483 210 26891 GLT8D2 0 . GRCh38 12 103999473 103999473 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.326A>G p.Lys109Arg p.K109R ENST00000360814 6/11 168 158 10 210 210 0 strelka-varscan-mutect GLT8D2,missense_variant,p.Lys109Arg,ENST00000360814,NM_031302.3;GLT8D2,missense_variant,p.Lys109Arg,ENST00000548660,;GLT8D2,missense_variant,p.Lys109Arg,ENST00000546436,;GLT8D2,missense_variant,p.Lys48Arg,ENST00000546851,;GLT8D2,non_coding_transcript_exon_variant,,ENST00000550816,;GLT8D2,upstream_gene_variant,,ENST00000552572,; C ENST00000360814 Transcript missense_variant 732/1880 326/1050 109/349 K/R aAa/aGa 1 -1 GLT8D2 HGNC HGNC:24890 protein_coding YES CCDS9096.1 ENSP00000354053 Q9H1C3 UPI000004B633 NM_031302.3 tolerated(0.13) 6/11 Gene3D:3.90.550.10,Pfam_domain:PF01501,hmmpanther:PTHR13778,hmmpanther:PTHR13778:SF2,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -13.20029 0.9999995 1 1 1 0 C 3 2 87 103999473 103999473 T C 1 0 0 0 0 1 0 0 0 6347 1841 64 5 5 GLT8D2 12 103999473 Missense_Mutation SNP T C3N-02003_T 25992647 103999473 29275836 211 26892 UBE3B 0 . GRCh38 12 109521164 109521164 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.2093T>C p.Leu698Pro p.L698P ENST00000342494 20/28 110 103 7 120 120 0 strelka-varscan-mutect UBE3B,missense_variant,p.Leu698Pro,ENST00000342494,NM_130466.3;UBE3B,missense_variant,p.Leu698Pro,ENST00000434735,NM_183415.2;UBE3B,missense_variant,p.Leu698Pro,ENST00000539599,;UBE3B,3_prime_UTR_variant,,ENST00000449510,;UBE3B,non_coding_transcript_exon_variant,,ENST00000538070,;UBE3B,non_coding_transcript_exon_variant,,ENST00000539584,; C ENST00000342494 Transcript missense_variant 2688/5722 2093/3207 698/1068 L/P cTt/cCt 1 1 UBE3B HGNC HGNC:13478 protein_coding YES CCDS9129.1 ENSP00000340596 Q7Z3V4 A0A024RBI2 UPI000013DC3B NM_130466.3 deleterious(0) 20/28 hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF352,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -14.2399 1 1 1 1 0 C 3 2 87 109521164 109521164 T C 1 0 0 0 0 1 0 0 0 17403 1609 56 5 5 UBE3B 12 109521164 Missense_Mutation SNP T C3N-02003_T 5521691 109521164 23754145 212 26893 TBX5 0 . GRCh38 12 114355901 114355901 + Silent SNP G G A C3N-02003_T C3N-02003_N G G c.1188C>T p.= p.I396I ENST00000310346 9/9 523 479 44 519 519 0 strelka-varscan-mutect TBX5,synonymous_variant,p.=,ENST00000310346,NM_000192.3;TBX5,synonymous_variant,p.=,ENST00000349716,NM_080717.2;TBX5,synonymous_variant,p.=,ENST00000405440,NM_181486.2; A ENST00000310346 Transcript synonymous_variant 1855/3825 1188/1557 396/518 I atC/atT COSM3792220 1 -1 TBX5 HGNC HGNC:11604 protein_coding YES CCDS9173.1 ENSP00000309913 Q99593 UPI0000136AA2 NM_000192.3 9/9 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF28 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 114355901 114355901 G A 1 0 0 0 0 0 0 0 1 16065 1280 45 3 3 TBX5 12 114355901 Silent SNP G C3N-02003_T 4834737 114355901 18919408 213 26894 ACADS 0 . GRCh38 12 120737381 120737381 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.386A>C p.Lys129Thr p.K129T ENST00000242592 4/10 533 492 41 450 450 0 strelka-varscan-mutect ACADS,missense_variant,p.Lys129Thr,ENST00000242592,NM_000017.3;ACADS,missense_variant,p.Lys129Thr,ENST00000411593,NM_001302554.1;RP11-173P15.7,downstream_gene_variant,,ENST00000542620,;ACADS,non_coding_transcript_exon_variant,,ENST00000539690,; C ENST00000242592 Transcript missense_variant 537/1950 386/1239 129/412 K/T aAg/aCg 1 1 ACADS HGNC HGNC:90 protein_coding YES CCDS9207.1 ENSP00000242592 P16219 E5KSD5 UPI000004A863 NM_000017.3 tolerated(0.18) 4/10 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF303,Pfam_domain:PF02771,Gene3D:1.10.540.10,Superfamily_domains:SSF56645 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 120737381 120737381 A C 1 0 0 0 0 1 0 0 0 157 72 3 5 5 ACADS 12 120737381 Missense_Mutation SNP A C3N-02003_T 6381480 120737381 12537928 214 26895 CCDC62 0 . GRCh38 12 122788865 122788865 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.606G>A p.= p.V202V ENST00000253079 5/13 104 98 6 153 152 1 strelka-varscan-mutect CCDC62,synonymous_variant,p.=,ENST00000253079,NM_201435.4;CCDC62,synonymous_variant,p.=,ENST00000392441,;CCDC62,synonymous_variant,p.=,ENST00000392440,;CCDC62,intron_variant,,ENST00000537566,;CCDC62,downstream_gene_variant,,ENST00000539171,;CCDC62,synonymous_variant,p.=,ENST00000341952,; A ENST00000253079 Transcript synonymous_variant 950/3546 606/2055 202/684 V gtG/gtA 1 1 CCDC62 HGNC HGNC:30723 protein_coding YES CCDS9238.1 ENSP00000253079 Q6P9F0 UPI0000366924 NM_201435.4 5/13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 122788865 122788865 G A 1 0 0 0 0 0 0 0 1 2535 1277 45 3 3 CCDC62 12 122788865 Silent SNP G C3N-02003_T 2051484 122788865 10486444 215 26896 FRY 0 . GRCh38 13 32124665 32124665 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.619T>G p.Phe207Val p.F207V ENST00000542859 6/61 267 250 17 415 415 0 strelka-varscan-mutect FRY,missense_variant,p.Phe207Val,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Phe207Val,ENST00000380250,; G ENST00000542859 Transcript missense_variant 1115/13200 619/9042 207/3013 F/V Ttt/Gtt 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0) 6/61 Pfam_domain:PF14222,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 32124665 32124665 T G 1 0 0 0 0 1 0 0 0 5935 1609 56 5 5 FRY 13 32124665 Missense_Mutation SNP T C3N-02003_T 32124665 82239663 216 26897 MTRF1 0 . GRCh38 13 41240376 41240376 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.755A>C p.Lys252Thr p.K252T ENST00000379480 6/10 214 202 12 212 211 1 strelka-varscan-mutect MTRF1,missense_variant,p.Lys252Thr,ENST00000379480,NM_004294.2;MTRF1,missense_variant,p.Lys252Thr,ENST00000379477,;RP11-74J13.8,downstream_gene_variant,,ENST00000619407,; G ENST00000379480 Transcript missense_variant 856/2185 755/1338 252/445 K/T aAg/aCg 1 -1 MTRF1 HGNC HGNC:7469 protein_coding YES CCDS9378.1 ENSP00000368793 O75570 A0A024RDT1 UPI0000035FC6 NM_004294.2 deleterious(0) 6/10 Pfam_domain:PF03462,hmmpanther:PTHR11075,hmmpanther:PTHR11075:SF44,SMART_domains:SM00937,Superfamily_domains:SSF75620 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 41240376 41240376 T G 1 0 0 0 0 1 0 0 0 9945 1609 56 5 5 MTRF1 13 41240376 Missense_Mutation SNP T C3N-02003_T 9115711 41240376 73123952 217 26898 HTR2A 0 . GRCh38 13 46892582 46892582 + Missense_Mutation SNP A A T novel C3N-02003_T C3N-02003_N A A c.421T>A p.Trp141Arg p.W141R ENST00000542664 3/4 252 236 16 191 191 0 strelka-varscan-mutect HTR2A,missense_variant,p.Trp141Arg,ENST00000542664,NM_000621.4;HTR2A,missense_variant,p.Trp141Arg,ENST00000378688,;HTR2A,missense_variant,p.Trp57Arg,ENST00000543956,NM_001165947.2;HTR2A,downstream_gene_variant,,ENST00000612998,; T ENST00000542664 Transcript missense_variant 1152/5429 421/1416 141/471 W/R Tgg/Agg 1 -1 HTR2A HGNC HGNC:5293 protein_coding YES CCDS9405.1 ENSP00000437737 P28223 UPI000000126E NM_000621.4 deleterious(0) 3/4 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF30,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs1330614688 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 46892582 46892582 A T 1 0 0 0 0 1 0 0 0 7337 159 6 4 4 HTR2A 13 46892582 Missense_Mutation SNP A C3N-02003_T 5652206 46892582 67471746 218 26899 KPNA3 0 . GRCh38 13 49722551 49722551 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.482T>G p.Leu161Arg p.L161R ENST00000261667 8/17 94 86 8 131 131 0 strelka-varscan-mutect KPNA3,missense_variant,p.Leu161Arg,ENST00000261667,NM_002267.3; C ENST00000261667 Transcript missense_variant 897/4474 482/1566 161/521 L/R cTt/cGt 1 -1 KPNA3 HGNC HGNC:6396 protein_coding YES CCDS9421.1 ENSP00000261667 O00505 A0A024RDV7 UPI000012D5F9 NM_002267.3 tolerated(0.35) 8/17 PROSITE_profiles:PS50176,hmmpanther:PTHR23316,hmmpanther:PTHR23316:SF6,PIRSF_domain:PIRSF005673,Gene3D:1.25.10.10,Pfam_domain:PF00514,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 49722551 49722551 A C 1 0 0 0 0 1 0 0 0 8311 72 3 5 5 KPNA3 13 49722551 Missense_Mutation SNP A C3N-02003_T 2829969 49722551 64641777 219 26900 COL4A1 0 . GRCh38 13 110213955 110213955 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.205G>A p.Glu69Lys p.E69K ENST00000375820 3/52 494 455 39 376 376 0 strelka-varscan-mutect COL4A1,missense_variant,p.Glu69Lys,ENST00000375820,NM_001845.5;COL4A1,missense_variant,p.Glu69Lys,ENST00000543140,NM_001303110.1;COL4A1,missense_variant,p.Glu5Lys,ENST00000615732,; T ENST00000375820 Transcript missense_variant 327/6532 205/5010 69/1669 E/K Gag/Aag 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0.01) 3/52 Pfam_domain:PF01391,Pfam_domain:PF01391,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF543,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 110213955 110213955 C T 1 0 0 0 0 1 0 0 0 3478 835 29 3 3 COL4A1 13 110213955 Missense_Mutation SNP C C3N-02003_T 60491404 110213955 4150373 220 26901 TMCO3 0 . GRCh38 13 113500058 113500058 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.725T>C p.Leu242Pro p.L242P ENST00000434316 4/13 61 56 5 76 76 0 strelka-varscan-mutect TMCO3,missense_variant,p.Leu242Pro,ENST00000434316,NM_017905.4;TMCO3,missense_variant,p.Leu242Pro,ENST00000474393,;TMCO3,missense_variant,p.Leu12Pro,ENST00000622371,;TMCO3,missense_variant,p.Leu242Pro,ENST00000375391,;TMCO3,missense_variant,p.Leu13Pro,ENST00000462877,;TMCO3,downstream_gene_variant,,ENST00000473287,; C ENST00000434316 Transcript missense_variant 1084/3050 725/2034 242/677 L/P cTt/cCt 1 1 TMCO3 HGNC HGNC:20329 protein_coding YES CCDS9537.1 ENSP00000389399 Q6UWJ1 A0A024RE09 UPI000004C642 NM_017905.4 deleterious(0) 4/13 hmmpanther:PTHR16254:SF14,hmmpanther:PTHR16254 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 113500058 113500058 T C 1 0 0 0 0 1 0 0 0 16443 1609 56 5 5 TMCO3 13 113500058 Missense_Mutation SNP T C3N-02003_T 3286103 113500058 864270 221 26902 OR4M1 0 . GRCh38 14 19780764 19780764 + Missense_Mutation SNP T T A C3N-02003_T C3N-02003_N T T c.442T>A p.Ser148Thr p.S148T ENST00000315957 1/1 462 436 26 391 391 0 varscan-mutect OR4M1,missense_variant,p.Ser148Thr,ENST00000315957,NM_001005500.1;OR4N2,intron_variant,,ENST00000557414,; A ENST00000315957 Transcript missense_variant 523/1116 442/942 148/313 S/T Tcc/Acc COSM3494396 1 1 OR4M1 HGNC HGNC:14735 protein_coding YES CCDS32021.1 ENSP00000319654 Q8NGD0 A0A126GWC3 UPI0000061F0F NM_001005500.1 tolerated(0.16) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF53,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 19780764 19780764 T A 1 0 0 0 0 1 0 0 0 11152 1551 54 4 4 OR4M1 14 19780764 Missense_Mutation SNP T C3N-02003_T 19780764 87262954 222 26903 KLHL33 0 . GRCh38 14 20429270 20429270 + Missense_Mutation SNP A A C C3N-02003_T C3N-02003_N A A c.1181T>G p.Leu394Arg p.L394R ENST00000344581 4/4 424 393 31 350 347 3 strelka-varscan-mutect KLHL33,missense_variant,p.Leu658Arg,ENST00000636854,;KLHL33,missense_variant,p.Leu394Arg,ENST00000344581,NM_001109997.2;KLHL33,3_prime_UTR_variant,,ENST00000637228,; C ENST00000344581 Transcript missense_variant 1404/1863 1181/1602 394/533 L/R cTt/cGt COSM4750948,COSM4750949 1 -1 KLHL33 HGNC HGNC:31952 protein_coding YES CCDS53882.1 ENSP00000341549 A6NCF5 UPI00016630E8 NM_001109997.2 tolerated_low_confidence(0.11) 4/4 hmmpanther:PTHR24412:SF195,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037,Gene3D:1zgkA00,SMART_domains:SM00612,Superfamily_domains:0052715 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 20429270 20429270 A C 1 0 0 0 0 1 0 0 0 8252 72 3 5 5 KLHL33 14 20429270 Missense_Mutation SNP A C3N-02003_T 648506 20429270 86614448 223 26904 FAM179B 0 . GRCh38 14 45011980 45011980 + Missense_Mutation SNP A A G rs763560311 C3N-02003_T C3N-02003_N A A c.3143A>G p.Asp1048Gly p.D1048G ENST00000361462 7/20 87 64 23 113 113 0 strelka-varscan-mutect FAM179B,missense_variant,p.Asp1048Gly,ENST00000361462,NM_001308120.1;FAM179B,missense_variant,p.Asp1048Gly,ENST00000361577,NM_015091.2;KLHL28,intron_variant,,ENST00000556239,;KLHL28,intron_variant,,ENST00000553817,;FAM179B,synonymous_variant,p.=,ENST00000557423,;FAM179B,non_coding_transcript_exon_variant,,ENST00000556105,;FAM179B,downstream_gene_variant,,ENST00000555607,; G ENST00000361462 Transcript missense_variant 3326/6375 3143/5322 1048/1773 D/G gAc/gGc rs763560311,COSM1251821 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 tolerated(0.13) 7/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763560311 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 45011980 45011980 A G 1 0 0 0 0 1 0 0 0 5351 289 10 5 5 FAM179B 14 45011980 Missense_Mutation SNP A C3N-02003_T 24582710 45011980 62031738 224 26905 KIAA0586 0 . GRCh38 14 58488805 58488805 + Missense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.3871G>A p.Glu1291Lys p.E1291K ENST00000354386 26/34 272 257 15 238 238 0 strelka-mutect KIAA0586,missense_variant,p.Glu1223Lys,ENST00000619416,NM_001244190.1;KIAA0586,missense_variant,p.Glu1194Lys,ENST00000556134,;KIAA0586,missense_variant,p.Glu1153Lys,ENST00000619722,NM_001244191.1;KIAA0586,missense_variant,p.Glu1194Lys,ENST00000423743,NM_001244192.1;KIAA0586,missense_variant,p.Glu1291Lys,ENST00000354386,NM_001244189.1;KIAA0586,missense_variant,p.Glu1162Lys,ENST00000261244,NM_014749.3;KIAA0586,upstream_gene_variant,,ENST00000555397,;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571,; A ENST00000354386 Transcript missense_variant 4115/5226 3871/4935 1291/1644 E/K Gaa/Aaa 1 1 KIAA0586 HGNC HGNC:19960 protein_coding YES CCDS58320.1 ENSP00000346359 Q9BVV6 UPI0001AE6998 NM_001244189.1 deleterious(0) 26/34 Low_complexity_(Seg):seg,hmmpanther:PTHR15721:SF2,hmmpanther:PTHR15721,Pfam_domain:PF15324 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 58488805 58488805 G A 1 0 0 0 0 1 0 0 0 8089 1291 45 3 3 KIAA0586 14 58488805 Missense_Mutation SNP G C3N-02003_T 13476825 58488805 48554913 225 26906 SLC8A3 0 . GRCh38 14 70167618 70167618 + Nonsense_Mutation SNP T T A rs373562717 C3N-02003_T C3N-02003_N T T c.805A>T p.Lys269Ter p.K269* ENST00000381269 2/8 423 367 56 432 432 0 strelka-varscan-mutect SLC8A3,stop_gained,p.Lys269Ter,ENST00000381269,NM_183002.2;SLC8A3,stop_gained,p.Lys269Ter,ENST00000357887,NM_033262.4;SLC8A3,stop_gained,p.Lys269Ter,ENST00000356921,NM_182932.2;SLC8A3,stop_gained,p.Lys269Ter,ENST00000528359,;SLC8A3,stop_gained,p.Lys269Ter,ENST00000534137,NM_058240.3;SLC8A3,stop_gained,p.Lys269Ter,ENST00000494208,; A ENST00000381269 Transcript stop_gained 1559/5268 805/2784 269/927 K/* Aaa/Taa rs373562717 1 -1 SLC8A3 HGNC HGNC:11070 protein_coding YES CCDS35498.1 ENSP00000370669 P57103 UPI0000073C9A NM_183002.2 2/8 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF7,TIGRFAM_domain:TIGR00845,Pfam_domain:PF16494 HIGH 1 SNV 1 1 PASS rs373562717 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 87 70167618 70167618 T A 1 0 0 0 0 0 1 0 0 14991 1821 63 4 4 SLC8A3 14 70167618 Nonsense_Mutation SNP T C3N-02003_T 11678813 70167618 36876100 226 26907 FAM161B 0 . GRCh38 14 73946432 73946432 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.417G>A p.= p.Q139Q ENST00000286544 2/9 362 343 19 357 357 0 strelka-varscan-mutect FAM161B,synonymous_variant,p.=,ENST00000286544,NM_152445.2;COQ6,upstream_gene_variant,,ENST00000334571,NM_182476.2;COQ6,upstream_gene_variant,,ENST00000394026,NM_182480.2;COQ6,upstream_gene_variant,,ENST00000629426,;COQ6,upstream_gene_variant,,ENST00000554320,;COQ6,upstream_gene_variant,,ENST00000554920,;COQ6,upstream_gene_variant,,ENST00000555552,;COQ6,upstream_gene_variant,,ENST00000554341,;COQ6,upstream_gene_variant,,ENST00000553462,;COQ6,upstream_gene_variant,,ENST00000556300,;COQ6,upstream_gene_variant,,ENST00000557205,;COQ6,upstream_gene_variant,,ENST00000557584,;COQ6,upstream_gene_variant,,ENST00000553922,;COQ6,upstream_gene_variant,,ENST00000555196,;COQ6,upstream_gene_variant,,ENST00000554193,;COQ6,upstream_gene_variant,,ENST00000554217,; T ENST00000286544 Transcript synonymous_variant 616/4078 417/2133 139/710 Q caG/caA 1 -1 FAM161B HGNC HGNC:19854 protein_coding YES CCDS9822.2 ENSP00000286544 Q96MY7 UPI000206535E NM_152445.2 2/9 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF4 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 73946432 73946432 C T 1 0 0 0 0 0 0 0 1 5322 912 32 3 3 FAM161B 14 73946432 Silent SNP C C3N-02003_T 3778814 73946432 33097286 227 26908 FOS 0 . GRCh38 14 75280812 75280812 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.531T>C p.= p.S177S ENST00000303562 4/4 157 133 24 95 95 0 strelka-mutect FOS,synonymous_variant,p.=,ENST00000303562,NM_005252.3;FOS,synonymous_variant,p.=,ENST00000555686,;FOS,synonymous_variant,p.=,ENST00000535987,;FOS,synonymous_variant,p.=,ENST00000555347,;FOS,synonymous_variant,p.=,ENST00000555672,;FOS,downstream_gene_variant,,ENST00000554617,;FOS,downstream_gene_variant,,ENST00000555242,;FOS,downstream_gene_variant,,ENST00000554212,;FOS,downstream_gene_variant,,ENST00000557139,;FOS,downstream_gene_variant,,ENST00000556324,; C ENST00000303562 Transcript synonymous_variant 740/2158 531/1143 177/380 S tcT/tcC 1 1 FOS HGNC HGNC:3796 protein_coding YES CCDS9841.1 ENSP00000306245 P01100 Q6FG41 UPI000000D8F5 NM_005252.3 4/4 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00170,Prints_domain:PR00042,PROSITE_profiles:PS50217,hmmpanther:PTHR23351,hmmpanther:PTHR23351:SF4,SMART_domains:SM00338,Superfamily_domains:SSF57959 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 75280812 75280812 T C 1 0 0 0 0 0 0 0 1 5845 1567 55 5 5 FOS 14 75280812 Silent SNP T C3N-02003_T 1334380 75280812 31762906 228 26909 90 2 FOS 0 . GRCh38 14 75280816 75280816 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.535T>G p.Leu179Val p.L179V ENST00000303562 4/4 164 137 27 108 108 0 strelka-mutect FOS,missense_variant,p.Leu179Val,ENST00000303562,NM_005252.3;FOS,missense_variant,p.Leu65Val,ENST00000555686,;FOS,missense_variant,p.Leu143Val,ENST00000535987,;FOS,missense_variant,p.Leu31Val,ENST00000555347,;FOS,missense_variant,p.Leu29Val,ENST00000555672,;FOS,downstream_gene_variant,,ENST00000554617,;FOS,downstream_gene_variant,,ENST00000555242,;FOS,downstream_gene_variant,,ENST00000554212,;FOS,downstream_gene_variant,,ENST00000557139,;FOS,downstream_gene_variant,,ENST00000556324,; G ENST00000303562 Transcript missense_variant 744/2158 535/1143 179/380 L/V Ttg/Gtg 1 1 FOS HGNC HGNC:3796 protein_coding YES CCDS9841.1 ENSP00000306245 P01100 Q6FG41 UPI000000D8F5 NM_005252.3 deleterious(0) 4/4 Gene3D:1.20.5.170,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00170,Prints_domain:PR00042,PROSITE_profiles:PS50217,hmmpanther:PTHR23351,hmmpanther:PTHR23351:SF4,SMART_domains:SM00338,Superfamily_domains:SSF57959 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 75280816 75280816 T G 1 0 0 0 0 1 0 0 0 5845 1838 64 5 5 FOS 14 75280816 Missense_Mutation SNP T C3N-02003_T 4 75280816 31762902 229 26910 90 2 ANGEL1 0 . GRCh38 14 76791319 76791319 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1666G>A p.Glu556Lys p.E556K ENST00000251089 8/10 322 286 36 286 285 1 strelka-varscan-mutect ANGEL1,missense_variant,p.Glu556Lys,ENST00000251089,NM_015305.3;ANGEL1,missense_variant,p.Glu121Lys,ENST00000557179,;ANGEL1,missense_variant,p.Glu26Lys,ENST00000555079,;RP11-488C13.5,upstream_gene_variant,,ENST00000556072,; T ENST00000251089 Transcript missense_variant 1779/5176 1666/2013 556/670 E/K Gag/Aag 1 -1 ANGEL1 HGNC HGNC:19961 protein_coding YES CCDS9852.1 ENSP00000251089 Q9UNK9 A0A024R6B2 UPI0000139C7E NM_015305.3 tolerated(0.32) 8/10 Gene3D:3.60.10.10,Pfam_domain:PF03372,hmmpanther:PTHR12121,hmmpanther:PTHR12121:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 76791319 76791319 C T 1 0 0 0 0 1 0 0 0 706 864 30 3 3 ANGEL1 14 76791319 Missense_Mutation SNP C C3N-02003_T 1510503 76791319 30252399 230 26911 TSHR 0 . GRCh38 14 81144073 81144073 + Missense_Mutation SNP G G T rs121908875 C3N-02003_T C3N-02003_N G G c.2015G>T p.Cys672Phe p.C672F ENST00000541158 11/11 273 231 42 384 384 0 strelka-varscan-mutect TSHR,missense_variant,p.Cys672Phe,ENST00000541158,;TSHR,missense_variant,p.Cys672Phe,ENST00000298171,NM_000369.2;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,downstream_gene_variant,,ENST00000636454,;TSHR,missense_variant,p.Cys307Phe,ENST00000637447,; T ENST00000541158 Transcript missense_variant 2337/4566 2015/2295 672/764 C/F tGt/tTt rs121908875,CM941337 1 1 TSHR HGNC HGNC:12373 protein_coding YES CCDS9872.1 ENSP00000441235 A0A0A0MTJ0 UPI000013E4A2 deleterious(0.03) 11/11 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix pathogenic MODERATE SNV 5 1,1 1 PASS rs121908875 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 81144073 81144073 G T 1 0 0 0 0 1 0 0 0 17127 1377 48 2 2 TSHR 14 81144073 Missense_Mutation SNP G C3N-02003_T 4352754 81144073 25899645 231 26912 C14orf159 0 . GRCh38 14 91173319 91173319 + Missense_Mutation SNP T T C C3N-02003_T C3N-02003_N T T c.487T>C p.Phe163Leu p.F163L ENST00000518868 9/17 314 286 28 288 288 0 strelka-varscan-mutect C14orf159,missense_variant,p.Phe163Leu,ENST00000518868,NM_001286470.1;C14orf159,missense_variant,p.Phe158Leu,ENST00000523771,NM_001286471.1;C14orf159,missense_variant,p.Phe163Leu,ENST00000256324,NM_001102368.2;C14orf159,missense_variant,p.Phe158Leu,ENST00000522322,NM_001102367.2;C14orf159,missense_variant,p.Phe158Leu,ENST00000523816,NM_001102366.2;C14orf159,missense_variant,p.Phe163Leu,ENST00000521077,NM_001286472.1;C14orf159,missense_variant,p.Phe158Leu,ENST00000520328,NM_001102369.2;C14orf159,missense_variant,p.Phe163Leu,ENST00000412671,;C14orf159,missense_variant,p.Phe158Leu,ENST00000428926,NM_024952.7;C14orf159,missense_variant,p.Phe163Leu,ENST00000525393,;C14orf159,missense_variant,p.Phe163Leu,ENST00000517518,;C14orf159,missense_variant,p.Phe163Leu,ENST00000519950,;C14orf159,missense_variant,p.Phe163Leu,ENST00000522170,;C14orf159,downstream_gene_variant,,ENST00000521334,;C14orf159,downstream_gene_variant,,ENST00000523894,;C14orf159,downstream_gene_variant,,ENST00000521064,;C14orf159,downstream_gene_variant,,ENST00000518871,;C14orf159,intron_variant,,ENST00000518649,;C14orf159,missense_variant,p.Phe148Leu,ENST00000523461,;C14orf159,missense_variant,p.Phe65Leu,ENST00000517306,;C14orf159,synonymous_variant,p.=,ENST00000519994,;C14orf159,3_prime_UTR_variant,,ENST00000523837,;C14orf159,upstream_gene_variant,,ENST00000520130,; C ENST00000518868 Transcript missense_variant 1177/3075 487/1866 163/621 F/L Ttc/Ctc COSM1246480 1 1 C14orf159 HGNC HGNC:20498 protein_coding YES CCDS41979.1 ENSP00000428263 Q7Z3D6 UPI000000CC60 NM_001286470.1 tolerated(0.07) 9/17 hmmpanther:PTHR32022,PIRSF_domain:PIRSF037204,Pfam_domain:PF07286,Gene3D:2pifA01,Superfamily_domains:0054510 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 91173319 91173319 T C 1 0 0 0 0 1 0 0 0 1830 1609 56 5 5 C14orf159 14 91173319 Missense_Mutation SNP T C3N-02003_T 10029246 91173319 15870399 232 26913 91 2 C14orf159 0 . GRCh38 14 91173325 91173325 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.493T>G p.Cys165Gly p.C165G ENST00000518868 9/17 311 284 27 294 294 0 strelka-varscan-mutect C14orf159,missense_variant,p.Cys165Gly,ENST00000518868,NM_001286470.1;C14orf159,missense_variant,p.Cys160Gly,ENST00000523771,NM_001286471.1;C14orf159,missense_variant,p.Cys165Gly,ENST00000256324,NM_001102368.2;C14orf159,missense_variant,p.Cys160Gly,ENST00000522322,NM_001102367.2;C14orf159,missense_variant,p.Cys160Gly,ENST00000523816,NM_001102366.2;C14orf159,missense_variant,p.Cys165Gly,ENST00000521077,NM_001286472.1;C14orf159,missense_variant,p.Cys160Gly,ENST00000520328,NM_001102369.2;C14orf159,missense_variant,p.Cys165Gly,ENST00000412671,;C14orf159,missense_variant,p.Cys160Gly,ENST00000428926,NM_024952.7;C14orf159,missense_variant,p.Cys165Gly,ENST00000525393,;C14orf159,missense_variant,p.Cys165Gly,ENST00000517518,;C14orf159,missense_variant,p.Cys165Gly,ENST00000519950,;C14orf159,missense_variant,p.Cys165Gly,ENST00000522170,;C14orf159,downstream_gene_variant,,ENST00000521334,;C14orf159,downstream_gene_variant,,ENST00000523894,;C14orf159,downstream_gene_variant,,ENST00000521064,;C14orf159,downstream_gene_variant,,ENST00000518871,;C14orf159,intron_variant,,ENST00000518649,;C14orf159,missense_variant,p.Cys150Gly,ENST00000523461,;C14orf159,missense_variant,p.Cys67Gly,ENST00000517306,;C14orf159,synonymous_variant,p.=,ENST00000519994,;C14orf159,3_prime_UTR_variant,,ENST00000523837,;C14orf159,upstream_gene_variant,,ENST00000520130,; G ENST00000518868 Transcript missense_variant 1183/3075 493/1866 165/621 C/G Tgc/Ggc 1 1 C14orf159 HGNC HGNC:20498 protein_coding YES CCDS41979.1 ENSP00000428263 Q7Z3D6 UPI000000CC60 NM_001286470.1 deleterious(0.05) 9/17 hmmpanther:PTHR32022,PIRSF_domain:PIRSF037204,Pfam_domain:PF07286,Gene3D:2pifA01,Superfamily_domains:0054510 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 91173325 91173325 T G 1 0 0 0 0 1 0 0 0 1830 1580 55 5 5 C14orf159 14 91173325 Missense_Mutation SNP T C3N-02003_T 6 91173325 15870393 233 26914 91 2 DYNC1H1 0 . GRCh38 14 102036593 102036593 + Missense_Mutation SNP G G A C3N-02003_T C3N-02003_N G G c.10859G>A p.Arg3620Lys p.R3620K ENST00000360184 57/78 515 479 36 478 478 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Arg3620Lys,ENST00000360184,NM_001376.4;DYNC1H1,missense_variant,p.Arg96Lys,ENST00000553423,;RP11-1017G21.4,non_coding_transcript_exon_variant,,ENST00000557551,;RP11-1017G21.4,downstream_gene_variant,,ENST00000557242,;RP11-1017G21.4,downstream_gene_variant,,ENST00000553701,;DYNC1H1,non_coding_transcript_exon_variant,,ENST00000556791,;DYNC1H1,upstream_gene_variant,,ENST00000556139,;DYNC1H1,upstream_gene_variant,,ENST00000556499,;DYNC1H1,upstream_gene_variant,,ENST00000555800,; A ENST00000360184 Transcript missense_variant 11023/14333 10859/13941 3620/4646 R/K aGa/aAa COSM1300393 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 tolerated(0.09) 57/78 Pfam_domain:PF12781,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 102036593 102036593 G A 1 0 0 0 0 1 0 0 0 4665 942 33 3 3 DYNC1H1 14 102036593 Missense_Mutation SNP G C3N-02003_T 10863268 102036593 5007125 234 26915 NDN 0 . GRCh38 15 23686876 23686876 + Silent SNP C C T rs554311163 C3N-02003_T C3N-02003_N C C c.342G>A p.= p.Q114Q ENST00000331837 1/1 240 227 13 239 238 1 strelka-varscan-mutect NDN,synonymous_variant,p.=,ENST00000331837,NM_002487.2; T ENST00000331837 Transcript synonymous_variant 455/1931 342/966 114/321 Q caG/caA rs554311163 1 -1 NDN HGNC HGNC:7675 protein_coding YES CCDS10014.1 ENSP00000332643 Q99608 X5D982 UPI000012FEF1 NM_002487.2 1/1 Pfam_domain:PF01454,PROSITE_profiles:PS50838,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF10,SMART_domains:SM01373 LOW 1 SNV 1 PASS rs554311163 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 23686876 23686876 C T 1 0 0 0 0 0 0 0 1 10268 912 32 3 3 NDN 15 23686876 Silent SNP C C3N-02003_T 23686876 78304313 235 26916 CILP 0 . GRCh38 15 65198482 65198482 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1804G>A p.Glu602Lys p.E602K ENST00000261883 9/9 293 278 15 281 281 0 strelka-varscan-mutect CILP,missense_variant,p.Glu602Lys,ENST00000261883,NM_003613.3; T ENST00000261883 Transcript missense_variant 1971/5695 1804/3555 602/1184 E/K Gag/Aag 1 -1 CILP HGNC HGNC:1980 protein_coding YES CCDS10203.1 ENSP00000261883 O75339 UPI000013D21B NM_003613.3 tolerated(0.18) 9/9 hmmpanther:PTHR15031 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 65198482 65198482 C T 1 0 0 0 0 1 0 0 0 3191 864 30 3 3 CILP 15 65198482 Missense_Mutation SNP C C3N-02003_T 41511606 65198482 36792707 236 26917 WHAMM 0 . GRCh38 15 82818035 82818035 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.1050C>T p.= p.L350L ENST00000286760 4/10 134 125 9 141 141 0 varscan-mutect WHAMM,synonymous_variant,p.=,ENST00000286760,NM_001080435.2;WHAMM,non_coding_transcript_exon_variant,,ENST00000560964,; T ENST00000286760 Transcript synonymous_variant 1149/5101 1050/2430 350/809 L ctC/ctT 1 1 WHAMM HGNC HGNC:30493 protein_coding YES CCDS45333.1 ENSP00000286760 Q8TF30 UPI00001C1F94 NM_001080435.2 4/10 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15871,hmmpanther:PTHR23330,hmmpanther:PTHR23330:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 82818035 82818035 C T 1 0 0 0 0 0 0 0 1 17918 813 29 3 3 WHAMM 15 82818035 Silent SNP C C3N-02003_T 17619553 82818035 19173154 237 26918 TM6SF1 0 . GRCh38 15 83112877 83112877 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.173C>T p.Pro58Leu p.P58L ENST00000322019 2/10 301 283 18 234 234 0 strelka-varscan-mutect TM6SF1,missense_variant,p.Pro58Leu,ENST00000322019,NM_023003.3;TM6SF1,missense_variant,p.Pro58Leu,ENST00000379390,;TM6SF1,missense_variant,p.Pro58Leu,ENST00000565774,NM_001144903.1;RP11-382A20.3,3_prime_UTR_variant,,ENST00000568294,;TM6SF1,5_prime_UTR_variant,,ENST00000565982,;RP11-382A20.2,downstream_gene_variant,,ENST00000565513,;TM6SF1,non_coding_transcript_exon_variant,,ENST00000564988,;TM6SF1,missense_variant,p.Pro58Leu,ENST00000379384,;TM6SF1,missense_variant,p.Pro58Leu,ENST00000258909,; T ENST00000322019 Transcript missense_variant 447/2074 173/1113 58/370 P/L cCa/cTa 1 1 TM6SF1 HGNC HGNC:11860 protein_coding YES CCDS10323.1 ENSP00000317000 Q9BZW5 UPI0000039EA7 NM_023003.3 tolerated(0.17) 2/10 hmmpanther:PTHR14568,hmmpanther:PTHR14568:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 83112877 83112877 C T 1 0 0 0 0 1 0 0 0 16417 594 21 3 3 TM6SF1 15 83112877 Missense_Mutation SNP C C3N-02003_T 294842 83112877 18878312 238 26919 PDE8A 0 . GRCh38 15 85120999 85120999 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1937T>G p.Phe646Cys p.F646C ENST00000310298 19/23 125 116 9 68 68 0 strelka-varscan-mutect PDE8A,missense_variant,p.Phe646Cys,ENST00000310298,;PDE8A,missense_variant,p.Phe646Cys,ENST00000394553,NM_002605.2;PDE8A,missense_variant,p.Phe574Cys,ENST00000557957,NM_001243137.1;PDE8A,missense_variant,p.Phe600Cys,ENST00000339708,NM_173454.1;PDE8A,3_prime_UTR_variant,,ENST00000485596,;PDE8A,3_prime_UTR_variant,,ENST00000478717,;PDE8A,3_prime_UTR_variant,,ENST00000559742,;PDE8A,non_coding_transcript_exon_variant,,ENST00000560789,;PDE8A,non_coding_transcript_exon_variant,,ENST00000561024,;PDE8A,downstream_gene_variant,,ENST00000561374,;PDE8A,downstream_gene_variant,,ENST00000560333,; G ENST00000310298 Transcript missense_variant 2189/3984 1937/2490 646/829 F/C tTt/tGt 1 1 PDE8A HGNC HGNC:8793 protein_coding YES CCDS10336.1 ENSP00000311453 O60658 UPI0000127C00 deleterious(0) 19/23 Gene3D:1.10.1300.10,Pfam_domain:PF00233,hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF85,SMART_domains:SM00471,Superfamily_domains:SSF109604 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -17.17949 0.9999905 1 1 1 0 G 3 3 87 85120999 85120999 T G 1 0 0 0 0 1 0 0 0 11741 1841 64 5 5 PDE8A 15 85120999 Missense_Mutation SNP T C3N-02003_T 2008122 85120999 16870190 239 26920 KIF7 0 . GRCh38 15 89648556 89648556 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1142A>G p.Glu381Gly p.E381G ENST00000394412 5/19 135 126 9 109 109 0 strelka-varscan-mutect KIF7,missense_variant,p.Glu381Gly,ENST00000394412,NM_198525.2;KIF7,3_prime_UTR_variant,,ENST00000445906,; C ENST00000394412 Transcript missense_variant 1219/4551 1142/4032 381/1343 E/G gAg/gGg 1 -1 KIF7 HGNC HGNC:30497 protein_coding YES CCDS32325.2 ENSP00000377934 Q2M1P5 UPI00015F81C7 NM_198525.2 tolerated(0.07) 5/19 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 89648556 89648556 T C 1 0 0 0 0 1 0 0 0 8174 1551 54 5 5 KIF7 15 89648556 Missense_Mutation SNP T C3N-02003_T 4527557 89648556 12342633 240 26921 WDR93 0 . GRCh38 15 89733033 89733033 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1358C>T p.Pro453Leu p.P453L ENST00000268130 13/17 235 187 48 190 190 0 strelka-varscan-mutect WDR93,missense_variant,p.Pro453Leu,ENST00000268130,NM_020212.1;WDR93,intron_variant,,ENST00000560294,NM_001284395.1;WDR93,non_coding_transcript_exon_variant,,ENST00000444934,;WDR93,downstream_gene_variant,,ENST00000557825,; T ENST00000268130 Transcript missense_variant 1459/2409 1358/2061 453/686 P/L cCt/cTt 1 1 WDR93 HGNC HGNC:26924 protein_coding YES CCDS32326.1 ENSP00000268130 Q6P2C0 UPI00001D77A7 NM_020212.1 tolerated(1) 13/17 hmmpanther:PTHR12219:SF17,hmmpanther:PTHR12219,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 89733033 89733033 C T 1 0 0 0 0 1 0 0 0 17896 681 24 3 3 WDR93 15 89733033 Missense_Mutation SNP C C3N-02003_T 84477 89733033 12258156 241 26922 FURIN 0 . GRCh38 15 90880958 90880958 + Silent SNP C C G novel C3N-02003_T C3N-02003_N C C c.1710C>G p.= p.L570L ENST00000618099 15/16 253 236 17 180 180 0 strelka-varscan-mutect FURIN,synonymous_variant,p.=,ENST00000618099,NM_001289824.1;FURIN,synonymous_variant,p.=,ENST00000268171,NM_002569.3;FURIN,synonymous_variant,p.=,ENST00000610579,NM_001289823.1;FES,upstream_gene_variant,,ENST00000328850,NM_002005.3;FES,upstream_gene_variant,,ENST00000414248,NM_001143785.1;FES,upstream_gene_variant,,ENST00000394300,NM_001143783.1;FES,upstream_gene_variant,,ENST00000444422,NM_001143784.1;FES,upstream_gene_variant,,ENST00000394302,;FES,upstream_gene_variant,,ENST00000452243,;FURIN,downstream_gene_variant,,ENST00000559353,;FES,upstream_gene_variant,,ENST00000559355,;FURIN,downstream_gene_variant,,ENST00000560824,;FES,upstream_gene_variant,,ENST00000443697,;FES,upstream_gene_variant,,ENST00000416779,;FES,upstream_gene_variant,,ENST00000464684,;FES,upstream_gene_variant,,ENST00000470152,;FURIN,downstream_gene_variant,,ENST00000558794,;FES,upstream_gene_variant,,ENST00000481665,;FES,upstream_gene_variant,,ENST00000497945,;FURIN,downstream_gene_variant,,ENST00000560018,; G ENST00000618099 Transcript synonymous_variant 2090/4345 1710/2385 570/794 L ctC/ctG 1 1 FURIN HGNC HGNC:8568 protein_coding YES CCDS10364.1 ENSP00000483552 P09958 A0A024RC70 UPI0000000CC7 NM_001289824.1 15/16 hmmpanther:PTHR10795:SF379,hmmpanther:PTHR10795,Gene3D:2.60.120.260,Superfamily_domains:SSF49785 LOW SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 90880958 90880958 C G 1 0 0 0 0 0 0 0 1 5971 900 32 4 4 FURIN 15 90880958 Silent SNP C C3N-02003_T 1147925 90880958 11110231 242 26923 PIGQ 0 . GRCh38 16 574457 574457 + Missense_Mutation SNP T T A rs760925678 C3N-02003_T C3N-02003_N T T c.383T>A p.Leu128His p.L128H ENST00000026218 2/10 409 346 63 363 363 0 strelka-varscan-mutect PIGQ,missense_variant,p.Leu128His,ENST00000321878,NM_004204.3;PIGQ,missense_variant,p.Leu128His,ENST00000026218,NM_148920.2;PIGQ,missense_variant,p.Leu128His,ENST00000470411,;PIGQ,missense_variant,p.Leu128His,ENST00000422307,;PIGQ,missense_variant,p.Leu128His,ENST00000409527,;PIGQ,missense_variant,p.Leu128His,ENST00000293874,;NHLRC4,downstream_gene_variant,,ENST00000424439,NM_176677.2,NM_001301159.1;NHLRC4,downstream_gene_variant,,ENST00000540585,;PIGQ,upstream_gene_variant,,ENST00000540241,;PIGQ,downstream_gene_variant,,ENST00000439574,;LA16c-407A10.3,non_coding_transcript_exon_variant,,ENST00000635107,;LA16c-407A10.3,non_coding_transcript_exon_variant,,ENST00000409439,;PIGQ,upstream_gene_variant,,ENST00000635935,;PIGQ,upstream_gene_variant,,ENST00000544860,;PIGQ,downstream_gene_variant,,ENST00000637701,;PIGQ,missense_variant,p.Leu142His,ENST00000443147,;PIGQ,intron_variant,,ENST00000636657,;PIGQ,intron_variant,,ENST00000635909,;PIGQ,upstream_gene_variant,,ENST00000480424,;PIGQ,upstream_gene_variant,,ENST00000636005,;PIGQ,upstream_gene_variant,,ENST00000635205,;PIGQ,upstream_gene_variant,,ENST00000420990,;PIGQ,upstream_gene_variant,,ENST00000637468,;PIGQ,upstream_gene_variant,,ENST00000638143,;PIGQ,upstream_gene_variant,,ENST00000537901,; A ENST00000026218 Transcript missense_variant 471/2846 383/2283 128/760 L/H cTc/cAc rs760925678 1 1 PIGQ HGNC HGNC:14135 protein_coding YES CCDS10411.1 ENSP00000026218 Q9BRB3 UPI000006CC88 NM_148920.2 deleterious_low_confidence(0) 2/10 hmmpanther:PTHR21329,hmmpanther:PTHR21329:SF3 MODERATE 1 SNV 1 1 PASS rs760925678 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 574457 574457 T A 1 0 0 0 0 1 0 0 0 11990 1551 54 4 4 PIGQ 16 574457 Missense_Mutation SNP T C3N-02003_T 574457 89763888 243 26924 PRSS21 0 . GRCh38 16 2821575 2821575 + Silent SNP C C G rs201178045 C3N-02003_T C3N-02003_N C C c.915C>G p.= p.L305L ENST00000005995 6/6 153 143 10 131 131 0 strelka-varscan-mutect PRSS21,synonymous_variant,p.=,ENST00000450020,NM_144957.2;PRSS21,synonymous_variant,p.=,ENST00000005995,NM_144956.2,NM_006799.3;PRSS21,synonymous_variant,p.=,ENST00000574265,;PRSS21,3_prime_UTR_variant,,ENST00000574813,NM_001270452.1;PRSS21,intron_variant,,ENST00000575739,;PRSS21,downstream_gene_variant,,ENST00000577043,;PRSS21,downstream_gene_variant,,ENST00000570594,;PRSS21,downstream_gene_variant,,ENST00000575199,;PRSS21,downstream_gene_variant,,ENST00000570629,;PRSS21,downstream_gene_variant,,ENST00000571141,;EIF1P4,downstream_gene_variant,,ENST00000572664,; G ENST00000005995 Transcript synonymous_variant 957/1101 915/945 305/314 L ctC/ctG rs201178045 1 1 PRSS21 HGNC HGNC:9485 protein_coding YES CCDS10478.1 ENSP00000005995 Q9Y6M0 UPI000004813E NM_144956.2,NM_006799.3 6/6 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs201178045 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 2821575 2821575 C G 1 0 0 0 0 0 0 0 1 12765 900 32 4 4 PRSS21 16 2821575 Silent SNP C C3N-02003_T 2247118 2821575 87516770 244 26925 CREBBP 0 . GRCh38 16 3850337 3850337 + Missense_Mutation SNP T T C rs142268920 C3N-02003_T C3N-02003_N T T c.758A>G p.His253Arg p.H253R ENST00000262367 2/31 311 263 48 249 249 0 strelka-varscan-mutect CREBBP,missense_variant,p.His253Arg,ENST00000262367,NM_004380.2;CREBBP,missense_variant,p.His253Arg,ENST00000382070,NM_001079846.1;CREBBP,upstream_gene_variant,,ENST00000636895,; C ENST00000262367 Transcript missense_variant 1568/10803 758/7329 253/2442 H/R cAc/cGc rs142268920,COSM109403 1 -1 CREBBP HGNC HGNC:2348 protein_coding YES CCDS10509.1 ENSP00000262367 Q92793 UPI0000000620 NM_004380.2 tolerated(0.09) 2/31 hmmpanther:PTHR13808:SF5,hmmpanther:PTHR13808 1,1 MODERATE 1 SNV 1 0,1 1 PASS rs142268920 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 3850337 3850337 T C 1 0 0 0 0 1 0 0 0 3661 1696 59 5 5 CREBBP 16 3850337 Missense_Mutation SNP T C3N-02003_T 1028762 3850337 86488008 245 26926 KIAA0430 0 . GRCh38 16 15633711 15633711 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1139A>C p.Lys380Thr p.K380T ENST00000396368 5/27 260 243 17 290 290 0 strelka-varscan-mutect KIAA0430,missense_variant,p.Lys380Thr,ENST00000396368,NM_014647.3;KIAA0430,missense_variant,p.Lys380Thr,ENST00000540441,;KIAA0430,missense_variant,p.Lys380Thr,ENST00000551742,NM_001184998.1;KIAA0430,missense_variant,p.Lys377Thr,ENST00000548025,NM_001184999.1;KIAA0430,downstream_gene_variant,,ENST00000549219,;KIAA0430,missense_variant,p.Lys380Thr,ENST00000552553,;KIAA0430,non_coding_transcript_exon_variant,,ENST00000548216,; G ENST00000396368 Transcript missense_variant 1346/7743 1139/5229 380/1742 K/T aAg/aCg 1 -1 KIAA0430 HGNC HGNC:29562 protein_coding YES CCDS10562.2 ENSP00000379654 Q9Y4F3 UPI00006881BC NM_014647.3 tolerated(0.07) 5/27 Gene3D:3.40.50.1010,Pfam_domain:PF01936,hmmpanther:PTHR14379,hmmpanther:PTHR14379:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 15633711 15633711 T G 1 0 0 0 0 1 0 0 0 8086 1609 56 5 5 KIAA0430 16 15633711 Missense_Mutation SNP T C3N-02003_T 11783374 15633711 74704634 246 26927 VWA3A 0 . GRCh38 16 22142683 22142683 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.2510A>C p.Lys837Thr p.K837T ENST00000389398 25/34 184 163 21 211 210 1 strelka-varscan-mutect VWA3A,missense_variant,p.Lys837Thr,ENST00000389398,NM_173615.4;VWA3A,downstream_gene_variant,,ENST00000568328,;VWA3A,upstream_gene_variant,,ENST00000563755,;VWA3A,downstream_gene_variant,,ENST00000563389,;VWA3A,3_prime_UTR_variant,,ENST00000299840,;VWA3A,downstream_gene_variant,,ENST00000566668,; C ENST00000389398 Transcript missense_variant 2606/4600 2510/3555 837/1184 K/T aAg/aCg 1 1 VWA3A HGNC HGNC:27088 protein_coding YES CCDS45441.1 ENSP00000374049 A6NCI4 UPI0001663067 NM_173615.4 deleterious(0) 25/34 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 22142683 22142683 A C 1 0 0 0 0 1 0 0 0 17794 72 3 5 5 VWA3A 16 22142683 Missense_Mutation SNP A C3N-02003_T 6508972 22142683 68195662 247 26928 ERN2 0 . GRCh38 16 23695268 23695268 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1876T>G p.Phe626Val p.F626V ENST00000634482 15/22 335 310 25 229 229 0 strelka-varscan-mutect ERN2,missense_variant,p.Phe626Val,ENST00000634482,NM_033266.3;ERN2,missense_variant,p.Phe578Val,ENST00000256797,;ERN2,missense_variant,p.Phe526Val,ENST00000457008,NM_001308220.1;PLK1,downstream_gene_variant,,ENST00000300093,NM_005030.4;CTD-2196E14.8,downstream_gene_variant,,ENST00000624143,;ERN2,3_prime_UTR_variant,,ENST00000562562,;PLK1,downstream_gene_variant,,ENST00000562272,;ERN2,upstream_gene_variant,,ENST00000562458,; C ENST00000634482 Transcript missense_variant 2045/3616 1876/2925 626/974 F/V Ttc/Gtc 1 -1 ERN2 HGNC HGNC:16942 protein_coding YES CCDS32407.1 ENSP00000489461 A0A0U1RRC7 UPI000041A8F8 NM_033266.3 deleterious(0) 15/22 PROSITE_profiles:PS50011,hmmpanther:PTHR13954,hmmpanther:PTHR13954:SF15,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 23695268 23695268 A C 1 0 0 0 0 1 0 0 0 5096 72 3 5 5 ERN2 16 23695268 Missense_Mutation SNP A C3N-02003_T 1552585 23695268 66643077 248 26929 KIF22 0 . GRCh38 16 29798464 29798464 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.357G>C p.Gln119His p.Q119H ENST00000160827 3/14 267 240 27 229 229 0 strelka-varscan-mutect KIF22,missense_variant,p.Gln51His,ENST00000561482,NM_001256269.1,NM_001256270.1;KIF22,missense_variant,p.Gln51His,ENST00000400751,;KIF22,missense_variant,p.Gln119His,ENST00000160827,NM_007317.2;KIF22,missense_variant,p.Gln51His,ENST00000569382,;KIF22,missense_variant,p.Gln51His,ENST00000569636,;KIF22,upstream_gene_variant,,ENST00000563263,;KIF22,3_prime_UTR_variant,,ENST00000570173,;KIF22,non_coding_transcript_exon_variant,,ENST00000563666,;KIF22,upstream_gene_variant,,ENST00000565736,; C ENST00000160827 Transcript missense_variant 397/2113 357/1998 119/665 Q/H caG/caC 1 1 KIF22 HGNC HGNC:6391 protein_coding YES CCDS10653.1 ENSP00000160827 Q14807 UPI00000012C0 NM_007317.2 deleterious(0) 3/14 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF462,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1300084174 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 29798464 29798464 G C 1 0 0 0 0 1 0 0 0 8155 933 33 4 4 KIF22 16 29798464 Missense_Mutation SNP G C3N-02003_T 6103196 29798464 60539881 249 26930 TAOK2 0 . GRCh38 16 29979467 29979467 + Missense_Mutation SNP A A C C3N-02003_T C3N-02003_N A A c.614A>C p.Lys205Thr p.K205T ENST00000308893 8/16 43 36 7 40 40 0 strelka-varscan-mutect TAOK2,missense_variant,p.Lys205Thr,ENST00000308893,NM_016151.3;TAOK2,missense_variant,p.Lys205Thr,ENST00000279394,NM_004783.3;TAOK2,missense_variant,p.Lys205Thr,ENST00000543033,NM_001252043.1;TAOK2,upstream_gene_variant,,ENST00000416441,; C ENST00000308893 Transcript missense_variant 1657/5169 614/3708 205/1235 K/T aAa/aCa COSM4151305,COSM4151306 1 1 TAOK2 HGNC HGNC:16835 protein_coding YES CCDS10663.1 ENSP00000310094 Q9UL54 UPI000013EDDA NM_016151.3 deleterious(0) 8/16 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF188,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -17.38755 1 1 1 1 0 C 3 2 87 29979467 29979467 A C 1 0 0 0 0 1 0 0 0 15947 14 1 5 5 TAOK2 16 29979467 Missense_Mutation SNP A C3N-02003_T 181003 29979467 60358878 250 26931 KIFC3 0 . GRCh38 16 57795067 57795067 + Missense_Mutation SNP G G T C3N-02003_T C3N-02003_N G G c.247C>A p.Gln83Lys p.Q83K ENST00000379655 3/19 267 249 18 210 210 0 strelka-varscan-mutect KIFC3,missense_variant,p.Gln83Lys,ENST00000379655,NM_005550.3;KIFC3,missense_variant,p.Gln83Lys,ENST00000445690,NM_001318710.1,NM_001130100.1;KIFC3,missense_variant,p.Gln105Lys,ENST00000541240,;KIFC3,missense_variant,p.Gln132Lys,ENST00000563028,;KIFC3,missense_variant,p.Gln111Lys,ENST00000566648,;KIFC3,missense_variant,p.Gln83Lys,ENST00000565684,;KIFC3,missense_variant,p.Gln105Lys,ENST00000567059,;KIFC3,missense_variant,p.Gln83Lys,ENST00000564891,;KIFC3,5_prime_UTR_variant,,ENST00000465878,NM_001318715.1;KIFC3,5_prime_UTR_variant,,ENST00000421376,NM_001130099.1;KIFC3,5_prime_UTR_variant,,ENST00000565481,;KIFC3,5_prime_UTR_variant,,ENST00000562311,;KIFC3,5_prime_UTR_variant,,ENST00000562503,;KIFC3,5_prime_UTR_variant,,ENST00000561524,;KIFC3,5_prime_UTR_variant,,ENST00000569112,;KIFC3,5_prime_UTR_variant,,ENST00000562984,;CTD-2600O9.1,upstream_gene_variant,,ENST00000568697,;CTD-2600O9.1,upstream_gene_variant,,ENST00000620696,;KIFC3,non_coding_transcript_exon_variant,,ENST00000566975,;KIFC3,non_coding_transcript_exon_variant,,ENST00000565871,;KIFC3,intron_variant,,ENST00000567204,;KIFC3,non_coding_transcript_exon_variant,,ENST00000566914,; T ENST00000379655 Transcript missense_variant 505/3427 247/2502 83/833 Q/K Cag/Aag COSM3818166 1 -1 KIFC3 HGNC HGNC:6326 protein_coding YES CCDS10789.2 ENSP00000368976 Q9BVG8 UPI000059D399 NM_005550.3 tolerated_low_confidence(0.19) 3/19 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 57795067 57795067 G T 1 0 0 0 0 1 0 0 0 8179 1299 45 2 2 KIFC3 16 57795067 Missense_Mutation SNP G C3N-02003_T 27815600 57795067 32543278 251 26932 ZDHHC1 0 . GRCh38 16 67400961 67400961 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.424G>A p.Asp142Asn p.D142N ENST00000348579 4/11 128 120 8 118 118 0 strelka-varscan-mutect ZDHHC1,missense_variant,p.Asp142Asn,ENST00000348579,NM_013304.2;ZDHHC1,missense_variant,p.Asp11Asn,ENST00000565726,;ZDHHC1,non_coding_transcript_exon_variant,,ENST00000562122,;ZDHHC1,upstream_gene_variant,,ENST00000566075,;ZDHHC1,upstream_gene_variant,,ENST00000567311,;ZDHHC1,downstream_gene_variant,,ENST00000568650,; T ENST00000348579 Transcript missense_variant 766/2047 424/1458 142/485 D/N Gat/Aat 1 -1 ZDHHC1 HGNC HGNC:17916 protein_coding YES CCDS10836.1 ENSP00000340299 Q8WTX9 UPI000013C37E NM_013304.2 tolerated(0.14) 4/11 PROSITE_profiles:PS50216,hmmpanther:PTHR22883:SF8,hmmpanther:PTHR22883,Pfam_domain:PF01529 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -11.55616 0.9999606 1 1 1 0 T 3 4 87 67400961 67400961 C T 1 0 0 0 0 1 0 0 0 18175 869 30 3 3 ZDHHC1 16 67400961 Missense_Mutation SNP C C3N-02003_T 9605894 67400961 22937384 252 26933 COG8 0 . GRCh38 16 69339324 69339324 + Nonsense_Mutation SNP G G A novel C3N-02003_T C3N-02003_N G G c.229C>T p.Gln77Ter p.Q77* ENST00000306875 1/6 394 358 36 337 337 0 strelka-varscan-mutect COG8,stop_gained,p.Gln77Ter,ENST00000306875,NM_032382.4;COG8,stop_gained,p.Gln58Ter,ENST00000562595,;COG8,stop_gained,p.Gln77Ter,ENST00000562081,;COG8,stop_gained,p.Gln62Ter,ENST00000615447,;RP11-343C2.9,intron_variant,,ENST00000563634,;NIP7,upstream_gene_variant,,ENST00000254940,NM_016101.4;NIP7,upstream_gene_variant,,ENST00000254941,NM_001199434.1;NIP7,upstream_gene_variant,,ENST00000569637,;TMED6,downstream_gene_variant,,ENST00000288025,NM_144676.3;COG8,upstream_gene_variant,,ENST00000562949,;NIP7,upstream_gene_variant,,ENST00000562523,;COG8,upstream_gene_variant,,ENST00000567493,;NIP7,upstream_gene_variant,,ENST00000567202,;RP11-343C2.7,intron_variant,,ENST00000564737,;RP11-343C2.7,intron_variant,,ENST00000570293,;TMED6,downstream_gene_variant,,ENST00000568748,;NIP7,upstream_gene_variant,,ENST00000565034,;NIP7,upstream_gene_variant,,ENST00000562131,;NIP7,upstream_gene_variant,,ENST00000563364,; A ENST00000306875 Transcript stop_gained 344/4247 229/1839 77/612 Q/* Cag/Tag 1 -1 COG8 HGNC HGNC:18623 protein_coding YES CCDS10876.1 ENSP00000305459 Q96MW5 A0A024R6Z6 UPI000013EBA1 NM_032382.4 1/6 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21311:SF0,hmmpanther:PTHR21311,Pfam_domain:PF04124,PIRSF_domain:PIRSF015415 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 87 69339324 69339324 G A 1 0 0 0 0 0 1 0 0 3452 1328 46 3 3 COG8 16 69339324 Nonsense_Mutation SNP G C3N-02003_T 1938363 69339324 20999021 253 26934 MTSS1L 0 . GRCh38 16 70663750 70663750 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.2171T>C p.Leu724Pro p.L724P ENST00000338779 15/15 124 112 12 99 99 0 strelka-varscan-mutect MTSS1L,missense_variant,p.Leu724Pro,ENST00000338779,NM_138383.2;MTSS1L,missense_variant,p.Leu723Pro,ENST00000616026,;IL34,downstream_gene_variant,,ENST00000429149,NM_152456.2,NM_001172771.1;IL34,downstream_gene_variant,,ENST00000288098,NM_001172772.1;IL34,downstream_gene_variant,,ENST00000566361,;RP11-394B2.1,non_coding_transcript_exon_variant,,ENST00000623414,; G ENST00000338779 Transcript missense_variant 2446/4992 2171/2244 724/747 L/P cTg/cCg 1 -1 MTSS1L HGNC HGNC:25094 protein_coding YES CCDS32476.1 ENSP00000341171 Q765P7 UPI00001D627C NM_138383.2 deleterious(0) 15/15 hmmpanther:PTHR15708 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 70663750 70663750 A G 1 0 0 0 0 1 0 0 0 9960 188 7 5 5 MTSS1L 16 70663750 Missense_Mutation SNP A C3N-02003_T 1324426 70663750 19674595 254 26935 CNTNAP4 0 . GRCh38 16 76461992 76461992 + Missense_Mutation SNP C C T rs774408296 C3N-02003_T C3N-02003_N C C c.1370C>T p.Ser457Phe p.S457F ENST00000611870 9/24 178 162 16 167 167 0 strelka-varscan-mutect CNTNAP4,missense_variant,p.Ser457Phe,ENST00000307431,;CNTNAP4,missense_variant,p.Ser457Phe,ENST00000611870,NM_033401.3;CNTNAP4,missense_variant,p.Ser409Phe,ENST00000377504,;CNTNAP4,missense_variant,p.Ser460Phe,ENST00000476707,;CNTNAP4,missense_variant,p.Ser409Phe,ENST00000622250,;CNTNAP4,missense_variant,p.Ser384Phe,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; T ENST00000611870 Transcript missense_variant 1755/4867 1370/3927 457/1308 S/F tCt/tTt rs774408296 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 deleterious(0.02) 9/24 Gene3D:2.60.120.200,Pfam_domain:PF00054,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS rs774408296 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 76461992 76461992 C T 1 0 0 0 0 1 0 0 0 3431 913 32 3 3 CNTNAP4 16 76461992 Missense_Mutation SNP C C3N-02003_T 5798242 76461992 13876353 255 26936 CMC2 0 . GRCh38 16 80980812 80980812 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.278A>C p.Lys93Thr p.K93T ENST00000570195 5/6 189 175 14 175 175 0 strelka-varscan-mutect CMC2,missense_variant,p.Lys93Thr,ENST00000570195,;CMC2,missense_variant,p.Lys50Thr,ENST00000486645,;CMC2,missense_variant,p.Lys74Thr,ENST00000565925,;CMC2,missense_variant,p.Lys74Thr,ENST00000562713,;CMC2,missense_variant,p.Lys93Thr,ENST00000630396,;CMC2,intron_variant,,ENST00000219400,;CMC2,intron_variant,,ENST00000564249,;CMC2,intron_variant,,ENST00000565650,NM_020188.3;CMC2,intron_variant,,ENST00000565914,;CMC2,intron_variant,,ENST00000564174,;CMC2,intron_variant,,ENST00000565108,;CMC2,non_coding_transcript_exon_variant,,ENST00000562828,;CMC2,intron_variant,,ENST00000566231,;CMC2,intron_variant,,ENST00000569187,;CMC2,intron_variant,,ENST00000566918,;RP11-303E16.9,downstream_gene_variant,,ENST00000623577,;CMC2,downstream_gene_variant,,ENST00000565514,;CMC2,missense_variant,p.Lys74Thr,ENST00000565613,;CMC2,3_prime_UTR_variant,,ENST00000567593,;CMC2,non_coding_transcript_exon_variant,,ENST00000569666,;CMC2,intron_variant,,ENST00000563779,;CMC2,intron_variant,,ENST00000568228,;CMC2,intron_variant,,ENST00000570086,;CMC2,intron_variant,,ENST00000561614,;CMC2,intron_variant,,ENST00000566047,; G ENST00000570195 Transcript missense_variant 451/871 278/282 93/93 K/T aAg/aCg 1 -1 CMC2 HGNC HGNC:24447 protein_coding ENSP00000457106 H3BTB6 UPI0000409DDE deleterious_low_confidence(0.01) 5/6 MODERATE SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 80980812 80980812 T G 1 0 0 0 0 1 0 0 0 3351 1623 56 5 5 CMC2 16 80980812 Missense_Mutation SNP T C3N-02003_T 4518820 80980812 9357533 256 26937 OR1A2 0 . GRCh38 17 3198045 3198045 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.527A>C p.Asn176Thr p.N176T ENST00000381951 1/1 61 53 8 55 55 0 strelka-varscan-mutect OR1A2,missense_variant,p.Asn176Thr,ENST00000381951,NM_012352.2; C ENST00000381951 Transcript missense_variant 527/930 527/930 176/309 N/T aAt/aCt 1 1 OR1A2 HGNC HGNC:8180 protein_coding YES CCDS11021.1 ENSP00000371377 Q9Y585 A0A126GVH4 UPI0000041E56 NM_012352.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF319,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs1437387251 . 0 205 3 2 0 0 0 0 -14.48206 0.9999917 1 1 1 0 C 3 2 87 3198045 3198045 A C 1 0 0 0 0 1 0 0 0 11028 101 4 5 5 OR1A2 17 3198045 Missense_Mutation SNP A C3N-02003_T 3198045 80059396 257 26938 TP53 0 . GRCh38 17 7674263 7674263 + Missense_Mutation SNP A A G rs864622237 C3N-02003_T C3N-02003_N A A c.700T>C p.Tyr234His p.Y234H ENST00000269305 7/11 362 284 78 312 312 0 strelka-varscan-mutect TP53,missense_variant,p.Tyr234His,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Tyr234His,ENST00000420246,;TP53,missense_variant,p.Tyr195His,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Tyr195His,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Tyr234His,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Tyr195His,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Tyr234His,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Tyr195His,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Tyr234His,ENST00000445888,;TP53,missense_variant,p.Tyr195His,ENST00000619485,;TP53,missense_variant,p.Tyr102His,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Tyr75His,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Tyr102His,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Tyr75His,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Tyr102His,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Tyr75His,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Tyr234His,ENST00000359597,;TP53,missense_variant,p.Tyr223His,ENST00000615910,;TP53,missense_variant,p.Tyr234His,ENST00000413465,;TP53,missense_variant,p.Tyr102His,ENST00000509690,;TP53,missense_variant,p.Tyr141His,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.Tyr195His,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; G ENST00000269305 Transcript missense_variant 890/2579 700/1182 234/393 Y/H Tac/Cac rs864622237,TP53_g.13337T>G,TP53_g.13337T>C,TP53_g.13337T>A,COSM11152,COSM146342,COSM146343,COSM146344,COSM220767,COSM220768,COSM220769,COSM238604,COSM238605,COSM238606,COSM2744649,COSM3362381,COSM43768,COSM43956,COSM4782297,COSM4782298 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.01) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs864622237 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 7674263 7674263 A G 1 0 0 0 0 1 0 0 0 16859 420 15 5 5 TP53 17 7674263 Missense_Mutation SNP A C3N-02003_T 4476218 7674263 75583178 258 26939 PFAS 0 . GRCh38 17 8266348 8266348 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.2816T>C p.Val939Ala p.V939A ENST00000314666 22/28 168 153 15 163 163 0 strelka-mutect PFAS,missense_variant,p.Val939Ala,ENST00000314666,NM_012393.2;PFAS,missense_variant,p.Val43Ala,ENST00000546020,;PFAS,downstream_gene_variant,,ENST00000583059,;PFAS,downstream_gene_variant,,ENST00000585319,;PFAS,missense_variant,p.Val54Ala,ENST00000578979,;PFAS,3_prime_UTR_variant,,ENST00000580356,;PFAS,non_coding_transcript_exon_variant,,ENST00000580251,;PFAS,downstream_gene_variant,,ENST00000581288,; C ENST00000314666 Transcript missense_variant 2949/5371 2816/4017 939/1338 V/A gTt/gCt 1 1 PFAS HGNC HGNC:8863 protein_coding YES CCDS11136.1 ENSP00000313490 O15067 UPI00001A95E5 NM_012393.2 tolerated(1) 22/28 HAMAP:MF_00419,hmmpanther:PTHR10099,hmmpanther:PTHR10099:SF1,TIGRFAM_domain:TIGR01735,Pfam_domain:PF02769,Superfamily_domains:SSF56042 MODERATE 1 SNV 1 1 PASS rs1415158735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 8266348 8266348 T C 1 0 0 0 0 1 0 0 0 11844 1739 60 5 5 PFAS 17 8266348 Missense_Mutation SNP T C3N-02003_T 592085 8266348 74991093 259 26940 MYH1 0 . GRCh38 17 10501817 10501817 + Missense_Mutation SNP G G A C3N-02003_T C3N-02003_N G G c.3206C>T p.Ser1069Phe p.S1069F ENST00000226207 25/40 128 115 13 229 229 0 strelka-varscan-mutect MYH1,missense_variant,p.Ser1069Phe,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; A ENST00000226207 Transcript missense_variant 3301/6024 3206/5820 1069/1939 S/F tCc/tTc COSM227621 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 deleterious(0) 25/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454,Superfamily_domains:SSF90257 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 10501817 10501817 G A 1 0 0 0 0 1 0 0 0 10029 1174 41 3 3 MYH1 17 10501817 Missense_Mutation SNP G C3N-02003_T 2235469 10501817 72755624 260 26941 KSR1 0 . GRCh38 17 27605459 27605459 + Nonsense_Mutation SNP C C G rs774788692 C3N-02003_T C3N-02003_N C C c.1295C>G p.Ser432Ter p.S432* ENST00000398988 16/22 424 396 28 273 272 1 strelka-varscan-mutect KSR1,stop_gained,p.Ser432Ter,ENST00000398988,NM_014238.1;KSR1,stop_gained,p.Ser492Ter,ENST00000268763,;KSR1,stop_gained,p.Ser432Ter,ENST00000509603,;KSR1,stop_gained,p.Ser282Ter,ENST00000398982,;KSR1,upstream_gene_variant,,ENST00000582410,;KSR1,upstream_gene_variant,,ENST00000580430,;KSR1,downstream_gene_variant,,ENST00000581975,;KSR1,downstream_gene_variant,,ENST00000579961,;KSR1,non_coding_transcript_exon_variant,,ENST00000583525,; G ENST00000398988 Transcript stop_gained 1740/7237 1295/2289 432/762 S/* tCa/tGa rs774788692 1 1 KSR1 HGNC HGNC:6465 protein_coding YES CCDS58532.1 ENSP00000381958 Q8IVT5 UPI00005B2F0C NM_014238.1 16/22 Low_complexity_(Seg):seg,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF413 HIGH 1 SNV 5 1 PASS rs774788692 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 87 27605459 27605459 C G 1 0 0 0 0 0 1 0 0 8480 838 29 4 4 KSR1 17 27605459 Nonsense_Mutation SNP C C3N-02003_T 17103642 27605459 55651982 261 26942 EFCAB5 0 . GRCh38 17 30053398 30053398 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.1444A>G p.Ser482Gly p.S482G ENST00000394835 10/23 157 142 15 190 190 0 strelka-varscan-mutect EFCAB5,missense_variant,p.Ser482Gly,ENST00000394835,NM_198529.3;EFCAB5,missense_variant,p.Ser288Gly,ENST00000419434,;EFCAB5,missense_variant,p.Ser426Gly,ENST00000536908,NM_001145053.1;EFCAB5,missense_variant,p.Ser281Gly,ENST00000588978,;EFCAB5,downstream_gene_variant,,ENST00000584826,;EFCAB5,missense_variant,p.Ser482Gly,ENST00000440741,;EFCAB5,3_prime_UTR_variant,,ENST00000423598,;EFCAB5,upstream_gene_variant,,ENST00000581617,; G ENST00000394835 Transcript missense_variant 1636/5132 1444/4512 482/1503 S/G Agt/Ggt 1 1 EFCAB5 HGNC HGNC:24801 protein_coding YES CCDS11254.2 ENSP00000378312 A4FU69 UPI0000E59EF5 NM_198529.3 tolerated(0.27) 10/23 hmmpanther:PTHR31938,hmmpanther:PTHR31938:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 30053398 30053398 A G 1 0 0 0 0 1 0 0 0 4772 72 3 5 5 EFCAB5 17 30053398 Missense_Mutation SNP A C3N-02003_T 2447939 30053398 53204043 262 26943 CCL15 0 . GRCh38 17 35997825 35997825 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.284A>C p.Lys95Thr p.K95T ENST00000617897 4/4 357 303 54 259 258 1 strelka-varscan-mutect CCL15,missense_variant,p.Lys95Thr,ENST00000617897,NM_032965.5;CCL15,missense_variant,p.Lys43Thr,ENST00000614368,;RP11-104J23.1,upstream_gene_variant,,ENST00000619334,;CCL15-CCL14,missense_variant,p.Lys95Thr,ENST00000616694,;CCL15-CCL14,missense_variant,p.Lys95Thr,ENST00000610751,; G ENST00000617897 Transcript missense_variant 830/1073 284/342 95/113 K/T aAa/aCa 1 -1 CCL15 HGNC HGNC:10613 protein_coding YES CCDS11304.1 ENSP00000484078 Q16663 UPI0000030A51 NM_032965.5 deleterious(0.02) 4/4 hmmpanther:PTHR12015,hmmpanther:PTHR12015:SF76,Pfam_domain:PF00048,Gene3D:2.40.50.40,SMART_domains:SM00199,Superfamily_domains:SSF54117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 35997825 35997825 T G 1 0 0 0 0 1 0 0 0 2584 1841 64 5 5 CCL15 17 35997825 Missense_Mutation SNP T C3N-02003_T 5944427 35997825 47259616 263 26944 ACACA 0 . GRCh38 17 37330233 37330233 + Nonsense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.278C>G p.Ser93Ter p.S93* ENST00000616317 3/56 335 312 23 248 248 0 strelka-varscan-mutect ACACA,stop_gained,p.Ser93Ter,ENST00000616317,NM_198834.2;ACACA,stop_gained,p.Ser56Ter,ENST00000614428,NM_198836.2,NM_198839.2;ACACA,stop_gained,p.Ser56Ter,ENST00000616352,;ACACA,stop_gained,p.Ser56Ter,ENST00000614438,;ACACA,5_prime_UTR_variant,,ENST00000614789,;ACACA,5_prime_UTR_variant,,ENST00000621960,;ACACA,stop_gained,p.Ser93Ter,ENST00000615229,;ACACA,stop_gained,p.Ser93Ter,ENST00000617548,;ACACA,stop_gained,p.Ser56Ter,ENST00000612007,;ACACA,non_coding_transcript_exon_variant,,ENST00000613146,; C ENST00000616317 Transcript stop_gained 759/9961 278/7152 93/2383 S/* tCa/tGa 1 -1 ACACA HGNC HGNC:84 protein_coding YES CCDS42302.1 ENSP00000483300 Q13085 UPI00002263AC NM_198834.2 3/56 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 87 37330233 37330233 G C 1 0 0 0 0 0 1 0 0 149 1294 45 4 4 ACACA 17 37330233 Nonsense_Mutation SNP G C3N-02003_T 1332408 37330233 45927208 264 26945 STARD3 0 . GRCh38 17 39660472 39660472 + Silent SNP G G C novel C3N-02003_T C3N-02003_N G G c.900G>C p.= p.V300V ENST00000336308 11/15 364 343 21 256 254 2 strelka-varscan-mutect STARD3,synonymous_variant,p.=,ENST00000336308,NM_006804.3;STARD3,synonymous_variant,p.=,ENST00000580611,;STARD3,synonymous_variant,p.=,ENST00000394250,NM_001165938.1;STARD3,synonymous_variant,p.=,ENST00000544210,NM_001165937.1;TCAP,upstream_gene_variant,,ENST00000309889,NM_003673.3;STARD3,downstream_gene_variant,,ENST00000443521,;STARD3,downstream_gene_variant,,ENST00000581894,;TCAP,upstream_gene_variant,,ENST00000578283,;STARD3,downstream_gene_variant,,ENST00000583419,;STARD3,downstream_gene_variant,,ENST00000577248,;STARD3,downstream_gene_variant,,ENST00000579479,;STARD3,downstream_gene_variant,,ENST00000580331,;STARD3,downstream_gene_variant,,ENST00000583718,;STARD3,non_coding_transcript_exon_variant,,ENST00000583639,;STARD3,downstream_gene_variant,,ENST00000578232,;STARD3,downstream_gene_variant,,ENST00000582874,;STARD3,downstream_gene_variant,,ENST00000460894,;STARD3,downstream_gene_variant,,ENST00000585214,;STARD3,downstream_gene_variant,,ENST00000578254,;STARD3,3_prime_UTR_variant,,ENST00000578577,;STARD3,3_prime_UTR_variant,,ENST00000583884,;STARD3,non_coding_transcript_exon_variant,,ENST00000481171,;STARD3,non_coding_transcript_exon_variant,,ENST00000584850,;STARD3,non_coding_transcript_exon_variant,,ENST00000488876,;STARD3,non_coding_transcript_exon_variant,,ENST00000471896,;STARD3,non_coding_transcript_exon_variant,,ENST00000585269,;STARD3,non_coding_transcript_exon_variant,,ENST00000578384,;STARD3,non_coding_transcript_exon_variant,,ENST00000578686,;STARD3,downstream_gene_variant,,ENST00000583582,;STARD3,downstream_gene_variant,,ENST00000484773,;STARD3,downstream_gene_variant,,ENST00000580551,; C ENST00000336308 Transcript synonymous_variant 1118/2132 900/1338 300/445 V gtG/gtC 1 1 STARD3 HGNC HGNC:17579 protein_coding YES CCDS11341.1 ENSP00000337446 Q14849 UPI000013CE10 NM_006804.3 11/15 PROSITE_profiles:PS50848,hmmpanther:PTHR12136,hmmpanther:PTHR12136:SF51,Gene3D:3.30.530.20,Pfam_domain:PF01852,SMART_domains:SM00234,Superfamily_domains:SSF55961,Prints_domain:PR00978 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 87 39660472 39660472 G C 1 0 0 0 0 0 0 0 1 15632 1277 45 4 4 STARD3 17 39660472 Silent SNP G C3N-02003_T 2330239 39660472 43596969 265 26946 CNTD1 0 . GRCh38 17 42809477 42809477 + Missense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.935C>A p.Ser312Tyr p.S312Y ENST00000588408 7/7 304 286 18 233 233 0 strelka-mutect CNTD1,missense_variant,p.Ser312Tyr,ENST00000588408,NM_173478.2;CNTD1,missense_variant,p.Ser229Tyr,ENST00000588527,;CNTD1,3_prime_UTR_variant,,ENST00000586652,;BECN1,downstream_gene_variant,,ENST00000361523,NM_003766.3;BECN1,downstream_gene_variant,,ENST00000590099,NM_001313998.1;BECN1,downstream_gene_variant,,ENST00000438274,;BECN1,downstream_gene_variant,,ENST00000590764,;BECN1,downstream_gene_variant,,ENST00000588276,;BECN1,downstream_gene_variant,,ENST00000586589,;BECN1,downstream_gene_variant,,ENST00000590852,;CNTD1,downstream_gene_variant,,ENST00000585355,;BECN1,downstream_gene_variant,,ENST00000589663,;CNTD1,non_coding_transcript_exon_variant,,ENST00000315066,;BECN1,downstream_gene_variant,,ENST00000586754,;BECN1,downstream_gene_variant,,ENST00000617806,;BECN1,downstream_gene_variant,,ENST00000543382,;CNTD1,downstream_gene_variant,,ENST00000592166,;BECN1,downstream_gene_variant,,ENST00000589492,;BECN1,downstream_gene_variant,,ENST00000590185,;BECN1,downstream_gene_variant,,ENST00000587880,; A ENST00000588408 Transcript missense_variant 1211/2369 935/993 312/330 S/Y tCt/tAt 1 1 CNTD1 HGNC HGNC:26847 protein_coding YES CCDS11440.1 ENSP00000465204 Q8N815 UPI000006EFD8 NM_173478.2 deleterious_low_confidence(0) 7/7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 42809477 42809477 C A 1 0 0 0 0 1 0 0 0 3417 913 32 2 2 CNTD1 17 42809477 Missense_Mutation SNP C C3N-02003_T 3149005 42809477 40447964 266 26947 AOC3 0 . GRCh38 17 42852677 42852677 + Nonsense_Mutation SNP C C G C3N-02003_T C3N-02003_N C C c.1334C>G p.Ser445Ter p.S445* ENST00000308423 1/4 383 358 25 277 277 0 strelka-varscan-mutect AOC3,stop_gained,p.Ser445Ter,ENST00000308423,NM_003734.3;AOC3,stop_gained,p.Ser445Ter,ENST00000613571,NM_001277731.1;AOC2,downstream_gene_variant,,ENST00000253799,NM_009590.2;AOC2,downstream_gene_variant,,ENST00000452774,NM_001158.3;AOC3,upstream_gene_variant,,ENST00000591562,;AOC3,upstream_gene_variant,,ENST00000617500,NM_001277732.1;AOC3,upstream_gene_variant,,ENST00000592999,;AOC3,upstream_gene_variant,,ENST00000588033,;AOC3,upstream_gene_variant,,ENST00000587330,; G ENST00000308423 Transcript stop_gained 1494/4026 1334/2292 445/763 S/* tCa/tGa COSM1521492 1 1 AOC3 HGNC HGNC:550 protein_coding YES CCDS11444.1 ENSP00000312326 Q16853 UPI00000009FC NM_003734.3 1/4 hmmpanther:PTHR10638,hmmpanther:PTHR10638:SF23,Pfam_domain:PF01179,Gene3D:2.70.98.20,Superfamily_domains:SSF49998,Prints_domain:PR00766 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 87 42852677 42852677 C G 1 0 0 0 0 0 1 0 0 838 838 29 4 4 AOC3 17 42852677 Nonsense_Mutation SNP C C3N-02003_T 43200 42852677 40404764 267 26948 MEIOC 0 . GRCh38 17 44667100 44667100 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1189A>C p.Thr397Pro p.T397P ENST00000409122 5/8 107 99 8 120 120 0 strelka-varscan-mutect MEIOC,missense_variant,p.Thr397Pro,ENST00000409122,NM_001145080.2;MEIOC,missense_variant,p.Thr231Pro,ENST00000409464,;MEIOC,downstream_gene_variant,,ENST00000432494,;MEIOC,downstream_gene_variant,,ENST00000456912,;MEIOC,downstream_gene_variant,,ENST00000425535,;MEIOC,upstream_gene_variant,,ENST00000472403,; C ENST00000409122 Transcript missense_variant 1331/4604 1189/2859 397/952 T/P Act/Cct 1 1 MEIOC HGNC HGNC:26670 protein_coding YES CCDS45703.2 ENSP00000386452 A2RUB1 UPI0001881A86 NM_001145080.2 tolerated(0.09) 5/8 hmmpanther:PTHR33861,hmmpanther:PTHR33861:SF3 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -12.25088 0.9999997 1 1 1 0 C 3 2 87 44667100 44667100 A C 1 0 0 0 0 1 0 0 0 9410 43 2 5 5 MEIOC 17 44667100 Missense_Mutation SNP A C3N-02003_T 1814423 44667100 38590341 268 26949 ZNF652 0 . GRCh38 17 49298800 49298800 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1434C>T p.= p.F478F ENST00000362063 6/6 439 415 24 340 340 0 strelka-varscan-mutect ZNF652,synonymous_variant,p.=,ENST00000362063,NM_014897.2;ZNF652,synonymous_variant,p.=,ENST00000430262,NM_001145365.1;ZNF652,synonymous_variant,p.=,ENST00000508237,; A ENST00000362063 Transcript synonymous_variant 1753/5988 1434/1821 478/606 F ttC/ttT 1 -1 ZNF652 HGNC HGNC:29147 protein_coding YES CCDS32677.1 ENSP00000354686 Q9Y2D9 UPI000006D93D NM_014897.2 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF151,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 49298800 49298800 G A 1 0 0 0 0 0 0 0 1 18638 1165 41 3 3 ZNF652 17 49298800 Silent SNP G C3N-02003_T 4631700 49298800 33958641 269 26950 MRPS23 0 . GRCh38 17 57849380 57849380 + Silent SNP C C G novel C3N-02003_T C3N-02003_N C C c.75G>C p.= p.L25L ENST00000313608 2/5 161 147 14 104 104 0 strelka-varscan-mutect MRPS23,synonymous_variant,p.=,ENST00000313608,NM_016070.3;MRPS23,synonymous_variant,p.=,ENST00000578444,;MRPS23,5_prime_UTR_variant,,ENST00000579380,;MRPS23,non_coding_transcript_exon_variant,,ENST00000579768,; G ENST00000313608 Transcript synonymous_variant 121/5621 75/573 25/190 L ctG/ctC 1 -1 MRPS23 HGNC HGNC:14509 protein_coding YES CCDS11598.1 ENSP00000320184 Q9Y3D9 UPI0000073570 NM_016070.3 2/5 Pfam_domain:PF10484,hmmpanther:PTHR15925 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 57849380 57849380 C G 1 0 0 0 0 0 0 0 1 9811 813 29 4 4 MRPS23 17 57849380 Silent SNP C C3N-02003_T 8550580 57849380 25408061 270 26951 MTMR4 0 . GRCh38 17 58512414 58512414 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.186C>G p.Ile62Met p.I62M ENST00000323456 4/19 241 220 21 175 175 0 strelka-varscan-mutect MTMR4,missense_variant,p.Ile62Met,ENST00000323456,NM_004687.4;MTMR4,missense_variant,p.Ile62Met,ENST00000579925,;MTMR4,missense_variant,p.Ile76Met,ENST00000583656,;MTMR4,missense_variant,p.Ile66Met,ENST00000579921,;MTMR4,5_prime_UTR_variant,,ENST00000583243,;MTMR4,missense_variant,p.Ile76Met,ENST00000582390,;MTMR4,missense_variant,p.Ile62Met,ENST00000582663,;MTMR4,upstream_gene_variant,,ENST00000580983,;MTMR4,upstream_gene_variant,,ENST00000583966,; C ENST00000323456 Transcript missense_variant 311/5839 186/3588 62/1195 I/M atC/atG 1 -1 MTMR4 HGNC HGNC:7452 protein_coding YES CCDS11608.1 ENSP00000325285 Q9NYA4 UPI00002010DE NM_004687.4 deleterious(0) 4/19 Gene3D:2.30.29.30,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF64,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 58512414 58512414 G C 1 0 0 0 0 1 0 0 0 9933 1280 45 4 4 MTMR4 17 58512414 Missense_Mutation SNP G C3N-02003_T 663034 58512414 24745027 271 26952 KCNH6 0 . GRCh38 17 63543595 63543595 + Nonsense_Mutation SNP C C G rs188290086 C3N-02003_T C3N-02003_N C C c.2168C>G p.Ser723Ter p.S723* ENST00000583023 10/14 195 183 12 139 139 0 strelka-varscan-mutect KCNH6,stop_gained,p.Ser723Ter,ENST00000583023,NM_030779.3;KCNH6,stop_gained,p.Ser723Ter,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,stop_gained,p.Ser670Ter,ENST00000581784,NM_173092.2;KCNH6,stop_gained,p.Ser670Ter,ENST00000456941,;KCNH6,3_prime_UTR_variant,,ENST00000583465,; G ENST00000583023 Transcript stop_gained 2179/3821 2168/2985 723/994 S/* tCa/tGa rs188290086 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 10/14 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468 HIGH 1 SNV 1 1 PASS rs188290086 . 0 207 0 2 0 0 0 0 -15.2116 0.9999995 1 1 1 0 G 4 3 87 63543595 63543595 C G 1 0 0 0 0 0 1 0 0 7952 838 29 4 4 KCNH6 17 63543595 Nonsense_Mutation SNP C C3N-02003_T 5031181 63543595 19713846 272 26953 ICAM2 0 . GRCh38 17 64003949 64003949 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.344T>C p.Val115Ala p.V115A ENST00000412356 5/6 146 127 19 123 123 0 strelka-varscan-mutect ICAM2,missense_variant,p.Val115Ala,ENST00000412356,NM_001099786.1;ICAM2,missense_variant,p.Val115Ala,ENST00000418105,NM_001099787.1;ICAM2,missense_variant,p.Val115Ala,ENST00000449662,NM_000873.3;ICAM2,missense_variant,p.Val115Ala,ENST00000579687,NM_001099788.1;ICAM2,missense_variant,p.Val115Ala,ENST00000579788,NM_001099789.1;ICAM2,missense_variant,p.Val14Ala,ENST00000578379,;ICAM2,missense_variant,p.Val91Ala,ENST00000578892,;ICAM2,missense_variant,p.Val115Ala,ENST00000578313,;ICAM2,missense_variant,p.Val115Ala,ENST00000584084,;ICAM2,missense_variant,p.Val115Ala,ENST00000583366,;PRR29,3_prime_UTR_variant,,ENST00000412177,NM_001164257.1;PRR29,downstream_gene_variant,,ENST00000425164,NM_001191029.1;PRR29,downstream_gene_variant,,ENST00000579184,NM_001191030.1;PRR29,downstream_gene_variant,,ENST00000582540,;PRR29,downstream_gene_variant,,ENST00000577953,NM_001191031.1;PRR29,downstream_gene_variant,,ENST00000583891,;PRR29,downstream_gene_variant,,ENST00000580752,;PRR29-AS1,upstream_gene_variant,,ENST00000580942,;ICAM2,non_coding_transcript_exon_variant,,ENST00000581417,;ICAM2,non_coding_transcript_exon_variant,,ENST00000584403,;ICAM2,synonymous_variant,p.=,ENST00000583684,;PRR29,non_coding_transcript_exon_variant,,ENST00000225760,;PRR29,downstream_gene_variant,,ENST00000582530,;PRR29,downstream_gene_variant,,ENST00000579222,;ICAM2,downstream_gene_variant,,ENST00000580011,;ICAM2,downstream_gene_variant,,ENST00000583186,;ICAM2,downstream_gene_variant,,ENST00000580389,; G ENST00000412356 Transcript missense_variant 699/1334 344/828 115/275 V/A gTc/gCc 1 -1 ICAM2 HGNC HGNC:5345 protein_coding YES CCDS11657.1 ENSP00000415283 P13598 Q6FHE2 UPI000013C87E NM_001099786.1 deleterious(0) 5/6 Gene3D:2.60.40.10,Prints_domain:PR01472,hmmpanther:PTHR13771,hmmpanther:PTHR13771:SF3,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 64003949 64003949 A G 1 0 0 0 0 1 0 0 0 7380 275 10 5 5 ICAM2 17 64003949 Missense_Mutation SNP A C3N-02003_T 460354 64003949 19253492 273 26954 NT5C 0 . GRCh38 17 75130605 75130605 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.489C>T p.= p.F163F ENST00000245552 5/5 272 253 19 221 220 1 strelka-varscan-mutect NT5C,missense_variant,p.His162Tyr,ENST00000582170,;NT5C,missense_variant,p.Ser60Leu,ENST00000580423,;NT5C,synonymous_variant,p.=,ENST00000245552,NM_014595.2;NT5C,synonymous_variant,p.=,ENST00000582160,;NT5C,synonymous_variant,p.=,ENST00000578407,NM_001252377.1;NT5C,3_prime_UTR_variant,,ENST00000578337,;HN1,downstream_gene_variant,,ENST00000476258,NM_001002033.2,NM_001288609.1;ARMC7,downstream_gene_variant,,ENST00000245543,NM_024585.3;HN1,downstream_gene_variant,,ENST00000482348,NM_001288610.1;HN1,downstream_gene_variant,,ENST00000409753,NM_001288611.1,NM_016185.3;HN1,downstream_gene_variant,,ENST00000356033,NM_001002032.2;ARMC7,downstream_gene_variant,,ENST00000581078,NM_001304271.1;RP11-649A18.3,upstream_gene_variant,,ENST00000625094,;ARMC7,downstream_gene_variant,,ENST00000579096,;NT5C,downstream_gene_variant,,ENST00000579082,;NT5C,3_prime_UTR_variant,,ENST00000580758,;NT5C,3_prime_UTR_variant,,ENST00000582744,;NT5C,non_coding_transcript_exon_variant,,ENST00000583655,;NT5C,non_coding_transcript_exon_variant,,ENST00000577523,;NT5C,non_coding_transcript_exon_variant,,ENST00000579023,;NT5C,non_coding_transcript_exon_variant,,ENST00000578095,;NT5C,non_coding_transcript_exon_variant,,ENST00000584352,;HN1,downstream_gene_variant,,ENST00000304834,; A ENST00000245552 Transcript synonymous_variant 577/954 489/606 163/201 F ttC/ttT 1 -1 NT5C HGNC HGNC:17144 protein_coding YES CCDS11715.1 ENSP00000245552 Q8TCD5 V9HWF3 UPI000006D556 NM_014595.2 5/5 hmmpanther:PTHR16504,hmmpanther:PTHR16504:SF5,Gene3D:3.40.50.1000,Pfam_domain:PF06941,Superfamily_domains:SSF56784 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 75130605 75130605 G A 1 0 0 0 0 0 0 0 1 10747 1290 45 3 3 NT5C 17 75130605 Silent SNP G C3N-02003_T 11126656 75130605 8126836 274 26955 NUP85 0 . GRCh38 17 75235641 75235641 + Silent SNP C C A rs368572297 C3N-02003_T C3N-02003_N C C c.1933C>A p.= p.R645R ENST00000245544 19/19 147 139 8 168 168 0 strelka-varscan-mutect NUP85,synonymous_variant,p.=,ENST00000245544,NM_024844.4;NUP85,synonymous_variant,p.=,ENST00000579324,NM_001303276.1;NUP85,synonymous_variant,p.=,ENST00000540768,;NUP85,synonymous_variant,p.=,ENST00000579298,;NUP85,synonymous_variant,p.=,ENST00000579838,;NUP85,3_prime_UTR_variant,,ENST00000579900,;GGA3,downstream_gene_variant,,ENST00000537686,NM_138619.3;GGA3,downstream_gene_variant,,ENST00000538886,NM_014001.4;GGA3,downstream_gene_variant,,ENST00000582486,;GGA3,downstream_gene_variant,,ENST00000582717,NM_001172703.2,NM_001291641.1,NM_001291642.1;GGA3,downstream_gene_variant,,ENST00000578348,NM_001172704.2;NUP85,downstream_gene_variant,,ENST00000583070,;NUP85,downstream_gene_variant,,ENST00000579557,;GGA3,downstream_gene_variant,,ENST00000583282,;NUP85,3_prime_UTR_variant,,ENST00000581104,;NUP85,3_prime_UTR_variant,,ENST00000578987,;NUP85,3_prime_UTR_variant,,ENST00000584155,;GGA3,downstream_gene_variant,,ENST00000613421,;GGA3,downstream_gene_variant,,ENST00000621217,;GGA3,downstream_gene_variant,,ENST00000621870,;GGA3,downstream_gene_variant,,ENST00000614198,;NUP85,downstream_gene_variant,,ENST00000578830,;NUP85,downstream_gene_variant,,ENST00000577645,;GGA3,downstream_gene_variant,,ENST00000580646,;GGA3,downstream_gene_variant,,ENST00000584550,;NUP85,downstream_gene_variant,,ENST00000582681,;NUP85,downstream_gene_variant,,ENST00000580879,;GGA3,downstream_gene_variant,,ENST00000583667,;GGA3,downstream_gene_variant,,ENST00000578208,;GGA3,downstream_gene_variant,,ENST00000578773,;NUP85,downstream_gene_variant,,ENST00000578294,; A ENST00000245544 Transcript synonymous_variant 2004/2121 1933/1971 645/656 R Cgg/Agg rs368572297 1 1 NUP85 HGNC HGNC:8734 protein_coding YES CCDS32730.1 ENSP00000245544 Q9BW27 UPI00000735DC NM_024844.4 19/19 hmmpanther:PTHR13373,hmmpanther:PTHR13373:SF21,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs368572297 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 75235641 75235641 C A 1 0 0 0 0 0 0 0 1 10836 875 31 1 1 NUP85 17 75235641 Silent SNP C C3N-02003_T 105036 75235641 8021800 275 26956 LLGL2 0 . GRCh38 17 75563330 75563330 + Splice_Site SNP G G A C3N-02003_T C3N-02003_N G G c.694-1G>A p.X232_splice ENST00000392550 114 106 8 68 68 0 strelka-varscan-mutect LLGL2,splice_acceptor_variant,,ENST00000392550,NM_001031803.1;LLGL2,splice_acceptor_variant,,ENST00000167462,NM_004524.2;LLGL2,splice_acceptor_variant,,ENST00000577200,;LLGL2,splice_acceptor_variant,,ENST00000578363,;LLGL2,splice_acceptor_variant,,ENST00000375227,NM_001015002.1;LLGL2,downstream_gene_variant,,ENST00000578536,;LLGL2,downstream_gene_variant,,ENST00000581713,;LLGL2,downstream_gene_variant,,ENST00000580578,;LLGL2,downstream_gene_variant,,ENST00000583658,;LLGL2,downstream_gene_variant,,ENST00000579392,;LLGL2,splice_acceptor_variant,,ENST00000545227,;LLGL2,splice_acceptor_variant,,ENST00000582860,;LLGL2,non_coding_transcript_exon_variant,,ENST00000580027,;LLGL2,upstream_gene_variant,,ENST00000577500,;LLGL2,upstream_gene_variant,,ENST00000578638,; A ENST00000392550 Transcript splice_acceptor_variant -/3509 694/3063 232/1020 COSM1386002,COSM1386003,COSM5157998 1 1 LLGL2 HGNC HGNC:6629 protein_coding YES CCDS32733.1 ENSP00000376333 Q6P1M3 UPI00005905A8 NM_001031803.1 7/25 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -15.81757 1 1 1 1 0 A 5 1 87 75563330 75563330 G A 1 0 0 0 0 0 0 1 0 8758 985 34 3 3 LLGL2 17 75563330 Splice_Site SNP G C3N-02003_T 327689 75563330 7694111 276 26957 EXOC7 0 . GRCh38 17 76103418 76103418 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.69G>C p.Glu23Asp p.E23D ENST00000335146 2/20 116 108 8 81 81 0 strelka-varscan-mutect EXOC7,missense_variant,p.Glu23Asp,ENST00000589210,NM_001013839.3;EXOC7,missense_variant,p.Glu23Asp,ENST00000332065,NM_015219.4;EXOC7,missense_variant,p.Glu23Asp,ENST00000335146,NM_001145297.3;EXOC7,missense_variant,p.Glu23Asp,ENST00000405575,;EXOC7,missense_variant,p.Glu23Asp,ENST00000634349,NM_001145299.3;EXOC7,missense_variant,p.Glu23Asp,ENST00000411744,NM_001145298.3;EXOC7,missense_variant,p.Glu42Asp,ENST00000589507,;EXOC7,missense_variant,p.Glu23Asp,ENST00000406660,NM_001282314.1;EXOC7,5_prime_UTR_variant,,ENST00000607838,;EXOC7,5_prime_UTR_variant,,ENST00000467929,NM_001282313.1;EXOC7,upstream_gene_variant,,ENST00000357231,;EXOC7,upstream_gene_variant,,ENST00000442951,;EXOC7,upstream_gene_variant,,ENST00000420116,;EXOC7,non_coding_transcript_exon_variant,,ENST00000405068,; G ENST00000335146 Transcript missense_variant 123/3519 69/2208 23/735 E/D gaG/gaC 1 -1 EXOC7 HGNC HGNC:23214 protein_coding YES CCDS45782.1 ENSP00000334100 Q9UPT5 UPI00001AFC78 NM_001145297.3 tolerated(0.15) 2/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12542,hmmpanther:PTHR12542:SF7 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -15.60239 0.9999977 1 1 1 0 G 3 3 87 76103418 76103418 C G 1 0 0 0 0 1 0 0 0 5178 912 32 4 4 EXOC7 17 76103418 Missense_Mutation SNP C C3N-02003_T 540088 76103418 7154023 277 26958 DNAH17 0 . GRCh38 17 78485577 78485577 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.7456T>G p.Phe2486Val p.F2486V ENST00000389840 47/81 278 238 40 175 175 0 strelka-varscan-mutect DNAH17,missense_variant,p.Phe2486Val,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Phe2481Val,ENST00000585328,;DNAH17-AS1,intron_variant,,ENST00000591373,;DNAH17-AS1,intron_variant,,ENST00000588565,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586052,; C ENST00000389840 Transcript missense_variant 7581/13723 7456/13389 2486/4462 F/V Ttc/Gtc 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 47/81 Gene3D:3.40.50.300,Pfam_domain:PF12775,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 78485577 78485577 A C 1 0 0 0 0 1 0 0 0 4416 72 3 5 5 DNAH17 17 78485577 Missense_Mutation SNP A C3N-02003_T 2382159 78485577 4771864 278 26959 TIMP2 0 . GRCh38 17 78871001 78871001 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.237C>T p.= p.F79F ENST00000262768 3/5 90 83 7 50 50 0 strelka-mutect TIMP2,synonymous_variant,p.=,ENST00000262768,NM_003255.4;TIMP2,synonymous_variant,p.=,ENST00000536189,;TIMP2,synonymous_variant,p.=,ENST00000586057,;TIMP2,synonymous_variant,p.=,ENST00000585421,;CEP295NL,synonymous_variant,p.=,ENST00000586713,;TIMP2,synonymous_variant,p.=,ENST00000592761,; A ENST00000262768 Transcript synonymous_variant 536/3652 237/663 79/220 F ttC/ttT 1 -1 TIMP2 HGNC HGNC:11821 protein_coding YES CCDS11758.1 ENSP00000262768 P16035 A0A140VK57 UPI0000136F99 NM_003255.4 3/5 PROSITE_profiles:PS50189,hmmpanther:PTHR11844:SF24,hmmpanther:PTHR11844,Gene3D:2.40.50.120,Pfam_domain:PF00965,SMART_domains:SM00206,Superfamily_domains:SSF50242 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -14.64675 0.9999997 1 1 1 0 A 2 1 87 78871001 78871001 G A 1 0 0 0 0 0 0 0 1 16359 1304 45 3 3 TIMP2 17 78871001 Silent SNP G C3N-02003_T 385424 78871001 4386440 279 26960 SLC26A11 0 . GRCh38 17 80221740 80221740 + Silent SNP C C T novel C3N-02003_T C3N-02003_N C C c.180C>T p.= p.L60L ENST00000361193 3/18 277 262 15 197 197 0 strelka-varscan-mutect SLC26A11,synonymous_variant,p.=,ENST00000361193,NM_173626.3,NM_001166347.1;SLC26A11,synonymous_variant,p.=,ENST00000411502,;SLC26A11,synonymous_variant,p.=,ENST00000546047,NM_001166348.1,NM_001166349.1;SLC26A11,synonymous_variant,p.=,ENST00000572725,;SLC26A11,synonymous_variant,p.=,ENST00000571176,;SLC26A11,synonymous_variant,p.=,ENST00000577155,;SLC26A11,synonymous_variant,p.=,ENST00000574967,;SLC26A11,synonymous_variant,p.=,ENST00000576126,;SLC26A11,intron_variant,,ENST00000573809,;SGSH,upstream_gene_variant,,ENST00000326317,NM_000199.3;SGSH,upstream_gene_variant,,ENST00000570923,;SGSH,upstream_gene_variant,,ENST00000570427,;SGSH,upstream_gene_variant,,ENST00000576707,;SLC26A11,non_coding_transcript_exon_variant,,ENST00000571602,;SLC26A11,non_coding_transcript_exon_variant,,ENST00000571564,;SLC26A11,non_coding_transcript_exon_variant,,ENST00000572226,;SGSH,upstream_gene_variant,,ENST00000572208,;SLC26A11,non_coding_transcript_exon_variant,,ENST00000572652,;SLC26A11,intron_variant,,ENST00000571888,;SGSH,upstream_gene_variant,,ENST00000575282,;SGSH,upstream_gene_variant,,ENST00000573150,;SGSH,upstream_gene_variant,,ENST00000574505,;SGSH,upstream_gene_variant,,ENST00000571075,;SGSH,upstream_gene_variant,,ENST00000576941,;SGSH,upstream_gene_variant,,ENST00000571675,;SLC26A11,upstream_gene_variant,,ENST00000571072,;SGSH,upstream_gene_variant,,ENST00000575188,;SGSH,upstream_gene_variant,,ENST00000571051,; T ENST00000361193 Transcript synonymous_variant 460/2885 180/1821 60/606 L ctC/ctT 1 1 SLC26A11 HGNC HGNC:14471 protein_coding YES CCDS11771.2 ENSP00000355384 Q86WA9 UPI000003E7B7 NM_173626.3,NM_001166347.1 3/18 Pfam_domain:PF00916,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF89,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 80221740 80221740 C T 1 0 0 0 0 0 0 0 1 14786 813 29 3 3 SLC26A11 17 80221740 Silent SNP C C3N-02003_T 1350739 80221740 3035701 280 26961 ANAPC11 0 . GRCh38 17 81899433 81899433 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.301C>G p.Gln101Glu p.Q101E ENST00000357385 3/4 480 455 25 333 333 0 strelka-varscan-mutect ANAPC11,missense_variant,p.Gln101Glu,ENST00000357385,NM_001002244.2;ANAPC11,intron_variant,,ENST00000575195,;ANAPC11,intron_variant,,ENST00000612413,NM_001289418.1,NM_001289419.1;ANAPC11,intron_variant,,ENST00000344877,NM_016476.11,NM_001002248.2,NM_001002246.2;ANAPC11,intron_variant,,ENST00000574924,;ANAPC11,intron_variant,,ENST00000392376,NM_001002249.2;ANAPC11,intron_variant,,ENST00000572851,NM_001289415.1;ANAPC11,intron_variant,,ENST00000577747,;ANAPC11,intron_variant,,ENST00000571024,NM_001002247.2,NM_001002245.2;ANAPC11,intron_variant,,ENST00000571874,;ANAPC11,intron_variant,,ENST00000577425,;ANAPC11,intron_variant,,ENST00000578550,NM_001289417.1;ANAPC11,intron_variant,,ENST00000571570,NM_001289414.1;ANAPC11,intron_variant,,ENST00000572639,;ANAPC11,intron_variant,,ENST00000579978,;ANAPC11,intron_variant,,ENST00000579133,;ANAPC11,intron_variant,,ENST00000583839,NM_001289416.1;ANAPC11,intron_variant,,ENST00000578544,;ANAPC11,intron_variant,,ENST00000584197,;ANAPC11,intron_variant,,ENST00000585259,;PCYT2,downstream_gene_variant,,ENST00000538936,NM_002861.4;NPB,upstream_gene_variant,,ENST00000573081,;PCYT2,downstream_gene_variant,,ENST00000331285,NM_001282203.1;PCYT2,downstream_gene_variant,,ENST00000570391,NM_001282204.1;PCYT2,downstream_gene_variant,,ENST00000538721,NM_001184917.2,NM_001256434.2;PCYT2,downstream_gene_variant,,ENST00000571105,;NPB,upstream_gene_variant,,ENST00000333383,NM_148896.3;ANAPC11,downstream_gene_variant,,ENST00000584314,;ANAPC11,downstream_gene_variant,,ENST00000582222,;ANAPC11,non_coding_transcript_exon_variant,,ENST00000573956,; G ENST00000357385 Transcript missense_variant 437/881 301/591 101/196 Q/E Caa/Gaa 1 1 ANAPC11 HGNC HGNC:14452 protein_coding YES CCDS32769.1 ENSP00000349957 Q9NYG5 A0A024R8S1 UPI0000374311 NM_001002244.2 deleterious_low_confidence(0) 3/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 81899433 81899433 C G 1 0 0 0 0 1 0 0 0 697 827 29 4 4 ANAPC11 17 81899433 Missense_Mutation SNP C C3N-02003_T 1677693 81899433 1358008 281 26962 PIEZO2 0 . GRCh38 18 10702052 10702052 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.6039A>C p.Glu2013Asp p.E2013D ENST00000503781 39/52 111 100 11 173 173 0 strelka-mutect PIEZO2,missense_variant,p.Glu1964Asp,ENST00000383408,;PIEZO2,missense_variant,p.Glu2013Asp,ENST00000302079,;PIEZO2,missense_variant,p.Glu2038Asp,ENST00000580640,;PIEZO2,missense_variant,p.Glu2013Asp,ENST00000503781,NM_022068.3;PIEZO2,upstream_gene_variant,,ENST00000538948,;RP11-856M7.2,upstream_gene_variant,,ENST00000584167,;PIEZO2,3_prime_UTR_variant,,ENST00000582913,; G ENST00000503781 Transcript missense_variant 6039/8259 6039/8259 2013/2752 E/D gaA/gaC 1 -1 PIEZO2 HGNC HGNC:26270 protein_coding YES CCDS11850.2 ENSP00000421377 Q9H5I5 UPI0001B3CB29 NM_022068.3 tolerated(1) 39/52 hmmpanther:PTHR13167,hmmpanther:PTHR13167:SF24 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 10702052 10702052 T G 1 0 0 0 0 1 0 0 0 11975 1606 56 5 5 PIEZO2 18 10702052 Missense_Mutation SNP T C3N-02003_T 10702052 69671233 282 26963 CEP192 0 . GRCh38 18 13071178 13071178 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.5314C>G p.Leu1772Val p.L1772V ENST00000506447 28/45 92 87 5 116 116 0 strelka-mutect CEP192,missense_variant,p.Leu1772Val,ENST00000506447,NM_032142.3;CEP192,missense_variant,p.Leu1297Val,ENST00000325971,;CEP192,missense_variant,p.Leu1311Val,ENST00000511820,;CEP192,missense_variant,p.Leu195Val,ENST00000430049,;CEP192,intron_variant,,ENST00000507254,;CEP192,upstream_gene_variant,,ENST00000540847,;CEP192,missense_variant,p.Leu1372Val,ENST00000510237,;CEP192,missense_variant,p.Leu320Val,ENST00000589993,;CEP192,3_prime_UTR_variant,,ENST00000513432,; G ENST00000506447 Transcript missense_variant 5394/7960 5314/7614 1772/2537 L/V Ctg/Gtg 1 1 CEP192 HGNC HGNC:25515 protein_coding YES CCDS32792.2 ENSP00000427550 Q8TEP8 UPI0001B09235 NM_032142.3 tolerated(0.17) 28/45 hmmpanther:PTHR16029,hmmpanther:PTHR16029:SF10 MODERATE 1 SNV 5 1 PASS rs1251831457 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 13071178 13071178 C G 1 0 0 0 0 1 0 0 0 2967 912 32 4 4 CEP192 18 13071178 Missense_Mutation SNP C C3N-02003_T 2369126 13071178 67302107 283 26964 EPG5 0 . GRCh38 18 45952618 45952618 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.1034T>G p.Val345Gly p.V345G ENST00000282041 3/44 122 111 11 135 135 0 strelka-varscan-mutect EPG5,missense_variant,p.Val345Gly,ENST00000282041,NM_020964.2;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,; C ENST00000282041 Transcript missense_variant 1069/12633 1034/7740 345/2579 V/G gTt/gGt 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 deleterious(0) 3/44 hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 45952618 45952618 A C 1 0 0 0 0 1 0 0 0 5010 43 2 5 5 EPG5 18 45952618 Missense_Mutation SNP A C3N-02003_T 32881440 45952618 34420667 284 26965 AP3D1 0 . GRCh38 19 2109159 2109159 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.3399A>C p.= p.S1133S ENST00000355272 30/32 107 95 12 114 114 0 strelka-mutect AP3D1,synonymous_variant,p.=,ENST00000355272,NM_001261826.1;AP3D1,synonymous_variant,p.=,ENST00000345016,NM_003938.6;AP3D1,synonymous_variant,p.=,ENST00000589369,;AP3D1,intron_variant,,ENST00000586370,;AP3D1,non_coding_transcript_exon_variant,,ENST00000585652,;AP3D1,non_coding_transcript_exon_variant,,ENST00000589223,;AP3D1,non_coding_transcript_exon_variant,,ENST00000591650,;AP3D1,downstream_gene_variant,,ENST00000592488,; G ENST00000355272 Transcript synonymous_variant 3606/5034 3399/3648 1133/1215 S tcA/tcC 1 -1 AP3D1 HGNC HGNC:568 protein_coding YES CCDS58638.1 ENSP00000347416 O14617 UPI0000202F99 NM_001261826.1 30/32 hmmpanther:PTHR22781 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99998 0.9999999 1 1 1 0 G 2 3 87 2109159 2109159 T G 1 0 0 0 0 0 0 0 1 862 1799 63 5 5 AP3D1 19 2109159 Silent SNP T C3N-02003_T 2109159 56508457 285 26966 THOP1 0 . GRCh38 19 2810308 2810308 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.1460A>G p.Glu487Gly p.E487G ENST00000307741 10/13 134 125 9 94 93 1 strelka-mutect THOP1,missense_variant,p.Glu487Gly,ENST00000307741,NM_003249.3;THOP1,missense_variant,p.Glu366Gly,ENST00000586677,;THOP1,missense_variant,p.Glu70Gly,ENST00000590970,;THOP1,missense_variant,p.Glu31Gly,ENST00000587401,;THOP1,missense_variant,p.Glu111Gly,ENST00000591363,;THOP1,5_prime_UTR_variant,,ENST00000395212,;THOP1,5_prime_UTR_variant,,ENST00000587468,;THOP1,non_coding_transcript_exon_variant,,ENST00000591149,;THOP1,non_coding_transcript_exon_variant,,ENST00000592639,;THOP1,non_coding_transcript_exon_variant,,ENST00000589087,;THOP1,non_coding_transcript_exon_variant,,ENST00000590533,; G ENST00000307741 Transcript missense_variant 1663/4804 1460/2070 487/689 E/G gAg/gGg 1 1 THOP1 HGNC HGNC:11793 protein_coding YES CCDS12095.1 ENSP00000304467 P52888 UPI0000000C3E NM_003249.3 tolerated(0.07) 10/13 Gene3D:3.40.390.10,Pfam_domain:PF01432,hmmpanther:PTHR11804,hmmpanther:PTHR11804:SF50,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -16.87287 0.999989 1 1 1 0 G 3 3 87 2810308 2810308 A G 1 0 0 0 0 1 0 0 0 16305 318 11 5 5 THOP1 19 2810308 Missense_Mutation SNP A C3N-02003_T 701149 2810308 55807308 286 26967 TMIGD2 0 . GRCh38 19 4292652 4292652 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.796A>C p.Ser266Arg p.S266R ENST00000301272 5/5 149 130 19 111 111 0 strelka-varscan-mutect TMIGD2,missense_variant,p.Ser266Arg,ENST00000301272,NM_144615.2;TMIGD2,missense_variant,p.Ser262Arg,ENST00000595645,NM_001169126.1;TMIGD2,missense_variant,p.Ser146Arg,ENST00000600114,NM_001308232.1;TMIGD2,missense_variant,p.Ser94Arg,ENST00000600349,;SHD,downstream_gene_variant,,ENST00000543264,NM_020209.3;SHD,downstream_gene_variant,,ENST00000599689,;SHD,downstream_gene_variant,,ENST00000600475,;SHD,downstream_gene_variant,,ENST00000593383,;SHD,downstream_gene_variant,,ENST00000597466,; G ENST00000301272 Transcript missense_variant 842/1262 796/849 266/282 S/R Agc/Cgc 1 -1 TMIGD2 HGNC HGNC:28324 protein_coding YES CCDS12126.1 ENSP00000301272 Q96BF3 UPI000013E6F4 NM_144615.2 tolerated(0.14) 5/5 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 G 3 3 87 4292652 4292652 T G 1 0 0 0 0 1 0 0 0 16706 1609 56 5 5 TMIGD2 19 4292652 Missense_Mutation SNP T C3N-02003_T 1482344 4292652 54324964 287 26968 SEMA6B 0 . GRCh38 19 4548438 4548438 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.1279C>T p.= p.L427L ENST00000586582 13/17 77 70 7 68 68 0 strelka-varscan-mutect SEMA6B,synonymous_variant,p.=,ENST00000586582,NM_032108.3;SEMA6B,synonymous_variant,p.=,ENST00000586965,;SEMA6B,upstream_gene_variant,,ENST00000589889,; A ENST00000586582 Transcript synonymous_variant 1590/3986 1279/2667 427/888 L Ctg/Ttg 1 -1 SEMA6B HGNC HGNC:10739 protein_coding YES CCDS12131.1 ENSP00000467290 Q9H3T3 UPI000004BA6B NM_032108.3 13/17 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF10,SMART_domains:SM00630,Superfamily_domains:SSF101912 LOW 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -15.201 0.9999998 1 1 1 0 A 2 1 87 4548438 4548438 G A 1 0 0 0 0 0 0 0 1 14316 962 34 3 3 SEMA6B 19 4548438 Silent SNP G C3N-02003_T 255786 4548438 54069178 288 26969 MUC16 0 . GRCh38 19 8976725 8976725 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.4414A>C p.Thr1472Pro p.T1472P ENST00000397910 1/84 336 314 22 323 322 1 strelka-varscan-mutect MUC16,missense_variant,p.Thr1472Pro,ENST00000397910,NM_024690.2; G ENST00000397910 Transcript missense_variant 4618/43816 4414/43524 1472/14507 T/P Aca/Cca 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 1/84 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 8976725 8976725 T G 1 0 0 0 0 1 0 0 0 9972 1725 60 5 5 MUC16 19 8976725 Missense_Mutation SNP T C3N-02003_T 4428287 8976725 49640891 289 26970 RAB3D 0 . GRCh38 19 11325530 11325530 + Silent SNP G G A rs756183735 C3N-02003_T C3N-02003_N G G c.528C>T p.= p.F176F ENST00000222120 5/5 147 137 10 141 140 1 strelka-varscan-mutect RAB3D,synonymous_variant,p.=,ENST00000222120,NM_004283.3;RAB3D,synonymous_variant,p.=,ENST00000589655,;TSPAN16,intron_variant,,ENST00000316737,NM_012466.3;CTC-510F12.6,downstream_gene_variant,,ENST00000586051,;CTC-510F12.4,upstream_gene_variant,,ENST00000586356,;CTC-510F12.4,upstream_gene_variant,,ENST00000585801,; A ENST00000222120 Transcript synonymous_variant 789/4273 528/660 176/219 F ttC/ttT rs756183735,COSM3821928 1 -1 RAB3D HGNC HGNC:9779 protein_coding YES CCDS12257.1 ENSP00000222120 O95716 A0A024R7G2 UPI000000125B NM_004283.3 5/5 Gene3D:3.40.50.300,Pfam_domain:PF00071,Prints_domain:PR00449,PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF330,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,SMART_domains:SM00176,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 0,1 LOW 1 SNV 1 0,1 1 PASS rs756183735 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 11325530 11325530 G A 1 0 0 0 0 0 0 0 1 13093 1049 37 1 1 RAB3D 19 11325530 Silent SNP G C3N-02003_T 2348805 11325530 47292086 290 26971 B3GNT3 0 . GRCh38 19 17811579 17811579 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.576C>G p.Phe192Leu p.F192L ENST00000318683 3/3 79 73 6 57 57 0 strelka-varscan-mutect B3GNT3,missense_variant,p.Phe192Leu,ENST00000318683,NM_014256.3;B3GNT3,missense_variant,p.Phe192Leu,ENST00000595387,;B3GNT3,missense_variant,p.Phe192Leu,ENST00000599265,;INSL3,downstream_gene_variant,,ENST00000379695,NM_001265587.1;INSL3,downstream_gene_variant,,ENST00000598577,;INSL3,downstream_gene_variant,,ENST00000317306,NM_005543.3;B3GNT3,downstream_gene_variant,,ENST00000600777,; G ENST00000318683 Transcript missense_variant 723/2226 576/1119 192/372 F/L ttC/ttG 1 1 B3GNT3 HGNC HGNC:13528 protein_coding YES CCDS12364.1 ENSP00000321874 Q9Y2A9 UPI000007021E NM_014256.3 deleterious(0.02) 3/3 hmmpanther:PTHR11214:SF23,hmmpanther:PTHR11214,Pfam_domain:PF01762 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -12.94489 0.9999919 1 1 1 0 G 3 3 87 17811579 17811579 C G 1 0 0 0 0 1 0 0 0 1414 912 32 4 4 B3GNT3 19 17811579 Missense_Mutation SNP C C3N-02003_T 6486049 17811579 40806037 291 26972 ZNF536 0 . GRCh38 19 30444411 30444411 + Silent SNP C C T C3N-02003_T C3N-02003_N C C c.849C>T p.= p.F283F ENST00000355537 2/5 213 201 12 151 151 0 strelka-varscan-mutect ZNF536,synonymous_variant,p.=,ENST00000355537,NM_014717.1;ZNF536,synonymous_variant,p.=,ENST00000585628,;ZNF536,downstream_gene_variant,,ENST00000591488,; T ENST00000355537 Transcript synonymous_variant 996/4945 849/3903 283/1300 F ttC/ttT COSM5554118 1 1 ZNF536 HGNC HGNC:29025 protein_coding YES CCDS32984.1 ENSP00000347730 O15090 UPI000006ED3E NM_014717.1 2/5 PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 30444411 30444411 C T 1 0 0 0 0 0 0 0 1 18547 825 29 3 3 ZNF536 19 30444411 Silent SNP C C3N-02003_T 12632832 30444411 28173205 292 26973 ZNF781 0 . GRCh38 19 37669658 37669658 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.491G>A p.Arg164Lys p.R164K ENST00000358582 4/4 96 89 7 189 188 1 strelka-varscan-mutect ZNF781,missense_variant,p.Arg164Lys,ENST00000358582,NM_152605.3;ZNF781,missense_variant,p.Arg164Lys,ENST00000590008,;ZFP30,intron_variant,,ENST00000587199,;ZFP30,intron_variant,,ENST00000586732,;ZFP30,intron_variant,,ENST00000589676,;ZNF781,downstream_gene_variant,,ENST00000593040,; T ENST00000358582 Transcript missense_variant 1240/3147 491/984 164/327 R/K aGa/aAa 1 -1 ZNF781 HGNC HGNC:26745 protein_coding YES CCDS12507.1 ENSP00000351391 Q8N8C0 A0A024R0G3 UPI0000351D6C NM_152605.3 tolerated(0.52) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 37669658 37669658 C T 1 0 0 0 0 1 0 0 0 18737 913 32 3 3 ZNF781 19 37669658 Missense_Mutation SNP C C3N-02003_T 7225247 37669658 20947958 293 26974 RYR1 0 . GRCh38 19 38460411 38460411 + Silent SNP C C T rs780848817 C3N-02003_T C3N-02003_N C C c.2397C>T p.= p.F799F ENST00000359596 20/106 522 479 43 503 503 0 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2; T ENST00000359596 Transcript synonymous_variant 2397/15117 2397/15117 799/5038 F ttC/ttT rs780848817 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 20/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Prints_domain:PR00795 LOW 1 SNV 5 1 PASS rs780848817 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 87 38460411 38460411 C T 1 0 0 0 0 0 0 0 1 14028 825 29 3 3 RYR1 19 38460411 Silent SNP C C3N-02003_T 790753 38460411 20157205 294 26975 RYR1 0 . GRCh38 19 38511575 38511575 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.9137T>G p.Leu3046Arg p.L3046R ENST00000359596 61/106 594 548 46 574 572 2 strelka-varscan-mutect RYR1,missense_variant,p.Leu3046Arg,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Leu3046Arg,ENST00000359596,NM_000540.2;RYR1,synonymous_variant,p.=,ENST00000599547,;RYR1,intron_variant,,ENST00000594335,; G ENST00000359596 Transcript missense_variant 9137/15117 9137/15117 3046/5038 L/R cTt/cGt 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0) 61/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 38511575 38511575 T G 1 0 0 0 0 1 0 0 0 14028 1609 56 5 5 RYR1 19 38511575 Missense_Mutation SNP T C3N-02003_T 51164 38511575 20106041 295 26976 NTN5 0 . GRCh38 19 48664713 48664713 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.686G>A p.Arg229Lys p.R229K ENST00000270235 3/7 187 176 11 181 181 0 strelka-varscan-mutect NTN5,missense_variant,p.Arg229Lys,ENST00000270235,NM_145807.2;NTN5,5_prime_UTR_variant,,ENST00000596844,;SEC1P,intron_variant,,ENST00000430145,;SEC1P,intron_variant,,ENST00000474419,;SEC1P,intron_variant,,ENST00000483163,;NTN5,non_coding_transcript_exon_variant,,ENST00000600468,; T ENST00000270235 Transcript missense_variant 782/1836 686/1470 229/489 R/K aGa/aAa 1 -1 NTN5 HGNC HGNC:25208 protein_coding YES CCDS33068.1 ENSP00000270235 Q8WTR8 UPI000007032D NM_145807.2 tolerated(0.83) 3/7 PROSITE_profiles:PS50027,hmmpanther:PTHR10574,Gene3D:2.10.25.10,Pfam_domain:PF00053,SMART_domains:SM00180,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.0535 0.9999995 1 1 1 0 T 3 4 87 48664713 48664713 C T 1 0 0 0 0 1 0 0 0 10768 913 32 3 3 NTN5 19 48664713 Missense_Mutation SNP C C3N-02003_T 10153138 48664713 9952903 296 26977 RCN3 0 . GRCh38 19 49534257 49534257 + Missense_Mutation SNP C C T C3N-02003_T C3N-02003_N C C c.307C>T p.Arg103Cys p.R103C ENST00000270645 3/7 61 54 7 38 38 0 strelka-mutect RCN3,missense_variant,p.Arg103Cys,ENST00000270645,NM_020650.2;RCN3,missense_variant,p.Arg52Cys,ENST00000598833,;RCN3,missense_variant,p.Arg103Cys,ENST00000597801,;RCN3,intron_variant,,ENST00000593644,; T ENST00000270645 Transcript missense_variant 754/1859 307/987 103/328 R/C Cgc/Tgc COSM5564067 1 1 RCN3 HGNC HGNC:21145 protein_coding YES CCDS12771.1 ENSP00000270645 Q96D15 UPI000000D8C5 NM_020650.2 deleterious(0) 3/7 PROSITE_profiles:PS50222,hmmpanther:PTHR10827:SF47,hmmpanther:PTHR10827,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 1 MODERATE 1 SNV 1 1 1 PASS rs1451801927 . 0 206 4 0 0 0 0 0 -16.21188 1 1 1 1 0 T 3 4 87 49534257 49534257 C T 1 0 0 0 0 1 0 0 0 13351 884 31 1 1 RCN3 19 49534257 Missense_Mutation SNP C C3N-02003_T 869544 49534257 9083359 297 26978 KLK5 0 . GRCh38 19 50948969 50948969 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.482G>A p.Arg161Lys p.R161K ENST00000336334 4/6 385 361 24 399 399 0 strelka-varscan-mutect KLK5,missense_variant,p.Arg161Lys,ENST00000336334,NM_012427.4;KLK5,missense_variant,p.Arg161Lys,ENST00000391809,NM_001077491.1;KLK5,missense_variant,p.Arg161Lys,ENST00000593428,NM_001077492.1;KLK5,missense_variant,p.Arg161Lys,ENST00000594846,;CTB-147C22.8,upstream_gene_variant,,ENST00000601506,;CTB-147C22.8,upstream_gene_variant,,ENST00000594939,;KLK5,non_coding_transcript_exon_variant,,ENST00000595585,; T ENST00000336334 Transcript missense_variant 835/1563 482/882 161/293 R/K aGa/aAa 1 -1 KLK5 HGNC HGNC:6366 protein_coding YES CCDS12810.1 ENSP00000337733 Q9Y337 A0A024R4G4 UPI000003751F NM_012427.4 tolerated(0.72) 4/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF270,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 50948969 50948969 C T 1 0 0 0 0 1 0 0 0 8276 913 32 3 3 KLK5 19 50948969 Missense_Mutation SNP C C3N-02003_T 1414712 50948969 7668647 298 26979 IGLON5 0 . GRCh38 19 51325372 51325372 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.418T>C p.Ser140Pro p.S140P ENST00000270642 4/8 335 317 18 345 345 0 strelka-varscan-mutect IGLON5,missense_variant,p.Ser140Pro,ENST00000270642,NM_001101372.1; C ENST00000270642 Transcript missense_variant 418/2606 418/1011 140/336 S/P Tcg/Ccg 1 1 IGLON5 HGNC HGNC:34550 protein_coding YES CCDS46158.1 ENSP00000270642 A6NGN9 UPI000058F1A8 NM_001101372.1 tolerated(0.05) 4/8 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF148,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 51325372 51325372 T C 1 0 0 0 0 1 0 0 0 7502 1667 58 5 5 IGLON5 19 51325372 Missense_Mutation SNP T C3N-02003_T 376403 51325372 7292244 299 26980 ZNF534 0 . GRCh38 19 52438075 52438075 + Missense_Mutation SNP A A C rs753177019 C3N-02003_T C3N-02003_N A A c.654A>C p.Gln218His p.Q218H ENST00000332323 4/4 140 126 14 199 198 1 strelka-varscan-mutect ZNF534,missense_variant,p.Gln218His,ENST00000332323,NM_001143939.1;ZNF534,missense_variant,p.Gln205His,ENST00000433050,NM_001143938.1;ZNF534,intron_variant,,ENST00000301085,;ZNF534,intron_variant,,ENST00000617900,NM_001291368.1;ZNF534,intron_variant,,ENST00000432303,NM_001291369.1; C ENST00000332323 Transcript missense_variant 715/2086 654/2025 218/674 Q/H caA/caC rs753177019,COSM1395939 1 1 ZNF534 HGNC HGNC:26337 protein_coding YES CCDS46165.1 ENSP00000327538 Q76KX8 UPI0000351984 NM_001143939.1 deleterious(0.04) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF187,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs753177019 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 52438075 52438075 A C 1 0 0 0 0 1 0 0 0 18546 69 3 5 5 ZNF534 19 52438075 Missense_Mutation SNP A C3N-02003_T 1112703 52438075 6179541 300 26981 ZNF761 0 . GRCh38 19 53455607 53455607 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.1100C>T p.Ser367Leu p.S367L ENST00000432094 5/5 161 147 14 351 351 0 varscan-mutect ZNF761,missense_variant,p.Ser367Leu,ENST00000432094,NM_001289951.1,NM_001008401.3,NM_001289952.1;ZNF761,missense_variant,p.Ser367Leu,ENST00000454407,;ZNF761,3_prime_UTR_variant,,ENST00000334095,; T ENST00000432094 Transcript missense_variant 1407/4061 1100/2241 367/746 S/L tCa/tTa 1 1 ZNF761 HGNC HGNC:23179 protein_coding ENSP00000480218 A0A087WXT7 UPI0001825C19 NM_001289951.1,NM_001008401.3,NM_001289952.1 deleterious(0.04) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF350,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 53455607 53455607 C T 1 0 0 0 0 1 0 0 0 18719 838 29 3 3 ZNF761 19 53455607 Missense_Mutation SNP C C3N-02003_T 1017532 53455607 5162009 301 26982 SSC5D 0 . GRCh38 19 55518647 55518647 + Silent SNP C C G novel C3N-02003_T C3N-02003_N C C c.4371C>G p.= p.L1457L ENST00000389623 14/14 115 100 15 61 61 0 strelka-varscan-mutect SSC5D,synonymous_variant,p.=,ENST00000389623,NM_001144950.1; G ENST00000389623 Transcript synonymous_variant 4394/4845 4371/4722 1457/1573 L ctC/ctG 1 1 SSC5D HGNC HGNC:26641 protein_coding YES CCDS46196.1 ENSP00000374274 A1L4H1 UPI000192952A NM_001144950.1 14/14 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1381400435 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 55518647 55518647 C G 1 0 0 0 0 0 0 0 1 15558 813 29 4 4 SSC5D 19 55518647 Silent SNP C C3N-02003_T 2063040 55518647 3098969 302 26983 NLRP4 0 . GRCh38 19 55858230 55858230 + Missense_Mutation SNP C C G C3N-02003_T C3N-02003_N C C c.837C>G p.Ile279Met p.I279M ENST00000301295 3/10 286 264 22 205 205 0 strelka-varscan-mutect NLRP4,missense_variant,p.Ile279Met,ENST00000301295,NM_134444.4;NLRP4,missense_variant,p.Ile204Met,ENST00000587891,;NLRP4,upstream_gene_variant,,ENST00000589437,;NLRP4,downstream_gene_variant,,ENST00000587464,; G ENST00000301295 Transcript missense_variant 1259/3670 837/2985 279/994 I/M atC/atG COSM4896617,COSM4896618 1 1 NLRP4 HGNC HGNC:22943 protein_coding YES CCDS12936.1 ENSP00000301295 Q96MN2 UPI000013E6FD NM_134444.4 tolerated(0.11) 3/10 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF8,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 55858230 55858230 C G 1 0 0 0 0 1 0 0 0 10517 816 29 4 4 NLRP4 19 55858230 Missense_Mutation SNP C C3N-02003_T 339583 55858230 2759386 303 26984 MZF1 0 . GRCh38 19 58563115 58563115 + Missense_Mutation SNP C C T rs748787144 C3N-02003_T C3N-02003_N C C c.1162G>A p.Glu388Lys p.E388K ENST00000215057 6/6 189 170 19 130 130 0 strelka-varscan-mutect MZF1,missense_variant,p.Glu388Lys,ENST00000215057,NM_198055.1;MZF1,missense_variant,p.Glu388Lys,ENST00000599369,NM_003422.2;MZF1,3_prime_UTR_variant,,ENST00000594234,NM_001267033.1;UBE2M,upstream_gene_variant,,ENST00000253023,NM_003969.3;UBE2M,upstream_gene_variant,,ENST00000595957,;MZF1-AS1,intron_variant,,ENST00000600534,;MZF1-AS1,intron_variant,,ENST00000593642,;MZF1-AS1,intron_variant,,ENST00000600726,;MZF1,non_coding_transcript_exon_variant,,ENST00000600004,; T ENST00000215057 Transcript missense_variant 1723/2905 1162/2205 388/734 E/K Gag/Aag rs748787144,COSM5150477 1 -1 MZF1 HGNC HGNC:13108 protein_coding YES CCDS12988.1 ENSP00000215057 P28698 A0A024R4T5 UPI0000072863 NM_198055.1 deleterious(0.03) 6/6 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF2,SMART_domains:SM00355,Superfamily_domains:SSF57667 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs748787144 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 58563115 58563115 C T 1 0 0 0 0 1 0 0 0 10109 893 31 1 1 MZF1 19 58563115 Missense_Mutation SNP C C3N-02003_T 2704885 58563115 54501 304 26985 DEFB121 0 . GRCh38 20 31405017 31405017 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.127T>G p.Leu43Val p.L43V ENST00000376314 2/2 180 154 26 193 192 1 strelka-varscan-mutect DEFB121,missense_variant,p.Leu43Val,ENST00000376314,NM_001011878.2;DEFB121,non_coding_transcript_exon_variant,,ENST00000376312,; C ENST00000376314 Transcript missense_variant 241/389 127/231 43/76 L/V Tta/Gta 1 -1 DEFB121 HGNC HGNC:18101 protein_coding YES CCDS33456.1 ENSP00000417128 Q5J5C9 UPI00004A06B0 NM_001011878.2 deleterious(0.02) 2/2 hmmpanther:PTHR15001,hmmpanther:PTHR15001:SF30,Pfam_domain:PF13841,PD866254 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 31405017 31405017 A C 1 0 0 0 0 1 0 0 0 4211 98 4 5 5 DEFB121 20 31405017 Missense_Mutation SNP A C3N-02003_T 31405017 33039150 305 26986 RBM39 0 . GRCh38 20 35729517 35729517 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.307A>G p.Lys103Glu p.K103E ENST00000253363 5/17 156 147 9 188 188 0 strelka-varscan-mutect RBM39,missense_variant,p.Lys103Glu,ENST00000361162,NM_001323424.1,NM_004902.3;RBM39,missense_variant,p.Lys103Glu,ENST00000253363,NM_184234.2;RBM39,missense_variant,p.Lys103Glu,ENST00000374038,;RBM39,missense_variant,p.Lys103Glu,ENST00000434927,;RBM39,intron_variant,,ENST00000528062,NM_001242600.1,NM_001242599.1;RBM39,upstream_gene_variant,,ENST00000448303,;RBM39,downstream_gene_variant,,ENST00000426951,;RBM39,upstream_gene_variant,,ENST00000494274,;RBM39,downstream_gene_variant,,ENST00000442447,;RBM39,downstream_gene_variant,,ENST00000487604,;RBM39,missense_variant,p.Lys103Glu,ENST00000338163,;RBM39,3_prime_UTR_variant,,ENST00000403542,;RBM39,3_prime_UTR_variant,,ENST00000429968,;RBM39,3_prime_UTR_variant,,ENST00000444878,;RBM39,3_prime_UTR_variant,,ENST00000412738,;RBM39,3_prime_UTR_variant,,ENST00000416108,;RBM39,3_prime_UTR_variant,,ENST00000425184,;RBM39,non_coding_transcript_exon_variant,,ENST00000463004,;RBM39,non_coding_transcript_exon_variant,,ENST00000461283,;RBM39,non_coding_transcript_exon_variant,,ENST00000492779,;RBM39,non_coding_transcript_exon_variant,,ENST00000481037,;RBM39,intron_variant,,ENST00000455343,;RBM39,downstream_gene_variant,,ENST00000477334,;RBM39,upstream_gene_variant,,ENST00000490484,;RBM39,downstream_gene_variant,,ENST00000433027,;RBM39,downstream_gene_variant,,ENST00000449489,; C ENST00000253363 Transcript missense_variant 331/2488 307/1593 103/530 K/E Aaa/Gaa 1 -1 RBM39 HGNC HGNC:15923 protein_coding YES CCDS13266.1 ENSP00000253363 Q14498 UPI0000134418 NM_184234.2 tolerated(0.33) 5/17 Superfamily_domains:SSF54928,TIGRFAM_domain:TIGR01622 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 35729517 35729517 T C 1 0 0 0 0 1 0 0 0 13299 1850 64 5 5 RBM39 20 35729517 Missense_Mutation SNP T C3N-02003_T 4324500 35729517 28714650 306 26987 R3HDML 0 . GRCh38 20 44350776 44350776 + Missense_Mutation SNP A A C novel C3N-02003_T C3N-02003_N A A c.746A>C p.Lys249Thr p.K249T ENST00000217043 5/5 251 233 18 188 188 0 strelka-varscan-mutect R3HDML,missense_variant,p.Lys249Thr,ENST00000217043,NM_178491.3;HNF4A,upstream_gene_variant,,ENST00000316673,NM_175914.4;RP5-881L22.5,non_coding_transcript_exon_variant,,ENST00000438702,;RP5-881L22.5,non_coding_transcript_exon_variant,,ENST00000430481,; C ENST00000217043 Transcript missense_variant 918/1377 746/762 249/253 K/T aAg/aCg 1 1 R3HDML HGNC HGNC:16249 protein_coding YES CCDS13329.1 ENSP00000217043 Q9H3Y0 UPI00000422F8 NM_178491.3 tolerated(0.07) 5/5 hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 44350776 44350776 A C 1 0 0 0 0 1 0 0 0 13047 72 3 5 5 R3HDML 20 44350776 Missense_Mutation SNP A C3N-02003_T 8621259 44350776 20093391 307 26988 WFDC8 0 . GRCh38 20 45555799 45555799 + Missense_Mutation SNP T T A novel C3N-02003_T C3N-02003_N T T c.347A>T p.Lys116Ile p.K116I ENST00000357199 4/7 216 202 14 194 194 0 strelka-varscan-mutect WFDC8,missense_variant,p.Lys116Ile,ENST00000357199,NM_181510.2;WFDC8,missense_variant,p.Lys116Ile,ENST00000289953,NM_130896.2;RNA5SP485,downstream_gene_variant,,ENST00000365053,; A ENST00000357199 Transcript missense_variant 426/1268 347/726 116/241 K/I aAa/aTa 1 -1 WFDC8 HGNC HGNC:16163 protein_coding YES CCDS13361.1 ENSP00000361735 Q8IUA0 A0A140VK68 UPI000016059B NM_181510.2 deleterious(0.03) 4/7 Gene3D:4.10.410.10,Pfam_domain:PF00014,PROSITE_profiles:PS50279,hmmpanther:PTHR10083,SMART_domains:SM00131,Superfamily_domains:SSF57362 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 45555799 45555799 T A 1 0 0 0 0 1 0 0 0 17913 1841 64 4 4 WFDC8 20 45555799 Missense_Mutation SNP T C3N-02003_T 1205023 45555799 18888368 308 26989 ZSWIM3 0 . GRCh38 20 45878333 45878333 + Missense_Mutation SNP T T C novel C3N-02003_T C3N-02003_N T T c.1775T>C p.Leu592Pro p.L592P ENST00000255152 2/2 413 390 23 269 269 0 strelka-varscan-mutect ZSWIM3,missense_variant,p.Leu592Pro,ENST00000255152,NM_080752.3;ZSWIM1,upstream_gene_variant,,ENST00000372523,NM_080603.4;ZSWIM1,upstream_gene_variant,,ENST00000372520,; C ENST00000255152 Transcript missense_variant 1984/2773 1775/2091 592/696 L/P cTt/cCt 1 1 ZSWIM3 HGNC HGNC:16157 protein_coding YES CCDS13381.1 ENSP00000255152 Q96MP5 UPI00000736E4 NM_080752.3 tolerated(0.2) 2/2 hmmpanther:PTHR31569:SF3,hmmpanther:PTHR31569 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 45878333 45878333 T C 1 0 0 0 0 1 0 0 0 18843 1609 56 5 5 ZSWIM3 20 45878333 Missense_Mutation SNP T C3N-02003_T 322534 45878333 18565834 309 26990 ZSWIM1 0 . GRCh38 20 45883582 45883582 + Silent SNP C C G novel C3N-02003_T C3N-02003_N C C c.990C>G p.= p.L330L ENST00000372523 2/2 341 307 34 220 220 0 strelka-varscan-mutect ZSWIM1,synonymous_variant,p.=,ENST00000372523,NM_080603.4;ZSWIM1,synonymous_variant,p.=,ENST00000372520,;ZSWIM3,downstream_gene_variant,,ENST00000255152,NM_080752.3;SPATA25,downstream_gene_variant,,ENST00000372519,NM_080608.3; G ENST00000372523 Transcript synonymous_variant 1085/2769 990/1458 330/485 L ctC/ctG 1 1 ZSWIM1 HGNC HGNC:16155 protein_coding YES CCDS13382.2 ENSP00000361601 Q9BR11 UPI0000470896 NM_080603.4 2/2 hmmpanther:PTHR31569,hmmpanther:PTHR31569:SF0 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 45883582 45883582 C G 1 0 0 0 0 0 0 0 1 18841 813 29 4 4 ZSWIM1 20 45883582 Silent SNP C C3N-02003_T 5249 45883582 18560585 310 26991 NCOA3 0 . GRCh38 20 47627152 47627152 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.508C>T p.Leu170Phe p.L170F ENST00000371998 6/23 68 61 7 96 96 0 strelka-varscan-mutect NCOA3,missense_variant,p.Leu170Phe,ENST00000372004,NM_006534.3;NCOA3,missense_variant,p.Leu170Phe,ENST00000371997,NM_001174088.1;NCOA3,missense_variant,p.Leu170Phe,ENST00000371998,NM_001174087.1,NM_181659.2;NCOA3,non_coding_transcript_exon_variant,,ENST00000497292,;NCOA3,downstream_gene_variant,,ENST00000490248,;RP5-1049G16.4,downstream_gene_variant,,ENST00000448675,; T ENST00000371998 Transcript missense_variant 699/4668 508/4275 170/1424 L/F Ctt/Ttt 1 1 NCOA3 HGNC HGNC:7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 UPI000012FE45 NM_001174087.1,NM_181659.2 tolerated(0.23) 6/23 PROSITE_profiles:PS50112,hmmpanther:PTHR10684:SF3,hmmpanther:PTHR10684,PIRSF_domain:PIRSF038181,Gene3D:3.30.450.20,Pfam_domain:PF00989,SMART_domains:SM00091,Superfamily_domains:SSF55785 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.8214 1 1 1 1 0 T 3 4 87 47627152 47627152 C T 1 0 0 0 0 1 0 0 0 10249 913 32 3 3 NCOA3 20 47627152 Missense_Mutation SNP C C3N-02003_T 1743570 47627152 16817015 311 26992 MYT1 0 . GRCh38 20 64213555 64213555 + Silent SNP T T C novel C3N-02003_T C3N-02003_N T T c.1539T>C p.= p.A513A ENST00000328439 10/23 246 226 20 200 200 0 strelka-mutect MYT1,synonymous_variant,p.=,ENST00000536311,;MYT1,synonymous_variant,p.=,ENST00000328439,NM_004535.2;MYT1,synonymous_variant,p.=,ENST00000622439,;MYT1,synonymous_variant,p.=,ENST00000360149,; C ENST00000328439 Transcript synonymous_variant 1903/5535 1539/3366 513/1121 A gcT/gcC 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 10/23 Superfamily_domains:0042508,Pfam_domain:PF01530,hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999775 1 1 1 0 C 2 2 87 64213555 64213555 T C 1 0 0 0 0 0 0 0 1 10105 1567 55 5 5 MYT1 20 64213555 Silent SNP T C3N-02003_T 16586403 64213555 230612 312 26993 PCMTD2 0 . GRCh38 20 64260043 64260043 + Silent SNP T T G novel C3N-02003_T C3N-02003_N T T c.78T>G p.= p.T26T ENST00000308824 2/6 265 246 19 251 250 1 strelka-varscan-mutect PCMTD2,synonymous_variant,p.=,ENST00000308824,NM_018257.2;PCMTD2,synonymous_variant,p.=,ENST00000369758,NM_001104925.1;PCMTD2,synonymous_variant,p.=,ENST00000609372,;PCMTD2,synonymous_variant,p.=,ENST00000299468,;PCMTD2,synonymous_variant,p.=,ENST00000609764,;PCMTD2,synonymous_variant,p.=,ENST00000610074,;PCMTD2,synonymous_variant,p.=,ENST00000610196,;PCMTD2,non_coding_transcript_exon_variant,,ENST00000609297,;PCMTD2,upstream_gene_variant,,ENST00000608844,; G ENST00000308824 Transcript synonymous_variant 205/3843 78/1086 26/361 T acT/acG 1 1 PCMTD2 HGNC HGNC:15882 protein_coding YES CCDS13559.1 ENSP00000307854 Q9NV79 UPI0000049C88 NM_018257.2 2/6 Gene3D:3.40.50.150,Pfam_domain:PF01135,hmmpanther:PTHR11579,hmmpanther:PTHR11579:SF2,Superfamily_domains:SSF53335 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 87 64260043 64260043 T G 1 0 0 0 0 0 0 0 1 11675 1567 55 5 5 PCMTD2 20 64260043 Silent SNP T C3N-02003_T 46488 64260043 184124 313 26994 GRIK1 0 . GRCh38 21 29689774 29689774 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.498C>T p.= p.L166L ENST00000399907 3/17 217 198 19 209 209 0 strelka-varscan-mutect GRIK1,synonymous_variant,p.=,ENST00000399914,;GRIK1,synonymous_variant,p.=,ENST00000399907,NM_000830.3;GRIK1,synonymous_variant,p.=,ENST00000399909,;GRIK1,synonymous_variant,p.=,ENST00000399913,;GRIK1,synonymous_variant,p.=,ENST00000327783,;GRIK1,synonymous_variant,p.=,ENST00000389125,NM_175611.2;GRIK1,synonymous_variant,p.=,ENST00000389124,;GRIK1,non_coding_transcript_exon_variant,,ENST00000472429,; A ENST00000399907 Transcript synonymous_variant 910/3472 498/2757 166/918 L ctC/ctT 1 -1 GRIK1 HGNC HGNC:4579 protein_coding YES CCDS42913.1 ENSP00000382791 P39086 UPI000012B612 NM_000830.3 3/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF36,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 29689774 29689774 G A 1 0 0 0 0 0 0 0 1 6655 929 33 3 3 GRIK1 21 29689774 Silent SNP G C3N-02003_T 29689774 17020209 314 26995 PLA2G3 0 . GRCh38 22 31139982 31139982 + Missense_Mutation SNP G G C C3N-02003_T C3N-02003_N G G c.373C>G p.Pro125Ala p.P125A ENST00000215885 1/7 451 427 24 404 404 0 strelka-varscan-mutect PLA2G3,missense_variant,p.Pro125Ala,ENST00000215885,NM_015715.4; C ENST00000215885 Transcript missense_variant 626/2697 373/1530 125/509 P/A Cca/Gca COSM1616375,COSM1616376 1 -1 PLA2G3 HGNC HGNC:17934 protein_coding YES CCDS13889.1 ENSP00000215885 Q9NZ20 UPI00001AE5E4 NM_015715.4 tolerated(0.24) 1/7 hmmpanther:PTHR12253,hmmpanther:PTHR12253:SF19 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 31139982 31139982 G C 1 0 0 0 0 1 0 0 0 12096 1174 41 4 4 PLA2G3 22 31139982 Missense_Mutation SNP G C3N-02003_T 31139982 19678486 315 26996 SEPT3 0 . GRCh38 22 41986040 41986040 + Missense_Mutation SNP A A G novel C3N-02003_T C3N-02003_N A A c.259A>G p.Ser87Gly p.S87G ENST00000396426 3/11 267 238 29 220 220 0 strelka-varscan-mutect SEPT3,missense_variant,p.Ser87Gly,ENST00000396425,NM_019106.5;SEPT3,missense_variant,p.Ser87Gly,ENST00000396426,NM_145733.2;SEPT3,missense_variant,p.Ser23Gly,ENST00000406029,;SEPT3,missense_variant,p.Ser74Gly,ENST00000449288,;CTA-250D10.19,upstream_gene_variant,,ENST00000424613,;SEPT3,non_coding_transcript_exon_variant,,ENST00000460267,;SEPT3,intron_variant,,ENST00000396417,; G ENST00000396426 Transcript missense_variant 514/2586 259/1077 87/358 S/G Agc/Ggc 1 1 SEPT3 HGNC HGNC:10750 protein_coding YES CCDS14026.2 ENSP00000379704 Q9UH03 UPI000067DA91 NM_145733.2 tolerated(0.19) 3/11 Gene3D:3.40.50.300,Pfam_domain:PF00735,PIRSF_domain:PIRSF006698,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF62,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 41986040 41986040 A G 1 0 0 0 0 1 0 0 0 14341 304 11 5 5 SEPT3 22 41986040 Missense_Mutation SNP A C3N-02003_T 10846058 41986040 8832428 316 26997 PLCXD1 0 . GRCh38 X 291505 291505 + Missense_Mutation SNP C C G novel C3N-02003_T C3N-02003_N C C c.400C>G p.Leu134Val p.L134V ENST00000381657 5/7 162 140 22 189 189 0 strelka-varscan-mutect PLCXD1,missense_variant,p.Leu134Val,ENST00000381657,NM_018390.3;PLCXD1,missense_variant,p.Leu134Val,ENST00000399012,;PLCXD1,missense_variant,p.Leu134Val,ENST00000381663,;PLCXD1,missense_variant,p.Leu134Val,ENST00000430923,;PLCXD1,missense_variant,p.Leu134Val,ENST00000447472,;PLCXD1,missense_variant,p.Leu134Val,ENST00000415337,;PLCXD1,downstream_gene_variant,,ENST00000448477,;PLCXD1,downstream_gene_variant,,ENST00000445062,;PLCXD1,downstream_gene_variant,,ENST00000429181,;PLCXD1,downstream_gene_variant,,ENST00000443019,;PLCXD1,non_coding_transcript_exon_variant,,ENST00000484611,; G ENST00000381657 Transcript missense_variant 914/5507 400/972 134/323 L/V Ctc/Gtc 1 1 PLCXD1 HGNC HGNC:23148 protein_coding YES CCDS14103.1 ENSP00000371073 Q9NUJ7 UPI0000048190 NM_018390.3 deleterious(0) 5/7 Gene3D:3.20.20.190,Pfam_domain:PF00388,PROSITE_profiles:PS50007,hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF24,SMART_domains:SM00148,Superfamily_domains:SSF51695 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 291505 291505 C G 1 0 0 0 0 1 0 0 0 12135 565 20 4 4 PLCXD1 23 291505 Missense_Mutation SNP C C3N-02003_T 291505 155749390 317 26998 CSF2RA 0 . GRCh38 X 1285912 1285912 + Missense_Mutation SNP G G C novel C3N-02003_T C3N-02003_N G G c.211G>C p.Glu71Gln p.E71Q ENST00000417535 4/14 357 327 30 316 316 0 strelka-varscan-mutect CSF2RA,missense_variant,p.Glu71Gln,ENST00000381524,;CSF2RA,missense_variant,p.Glu71Gln,ENST00000417535,NM_001161530.1;CSF2RA,missense_variant,p.Glu71Gln,ENST00000432318,NM_001161529.1;CSF2RA,missense_variant,p.Glu71Gln,ENST00000381529,NM_006140.4,NM_172245.2;CSF2RA,missense_variant,p.Glu71Gln,ENST00000355432,NM_172246.2;CSF2RA,missense_variant,p.Glu71Gln,ENST00000381509,NM_001161531.1;CSF2RA,missense_variant,p.Glu71Gln,ENST00000355805,NM_172249.2;CSF2RA,missense_variant,p.Glu71Gln,ENST00000381500,NM_172247.2;CSF2RA,missense_variant,p.Glu71Gln,ENST00000412290,;CSF2RA,missense_variant,p.Glu71Gln,ENST00000494969,;CSF2RA,intron_variant,,ENST00000501036,NM_001161532.1;CSF2RA,non_coding_transcript_exon_variant,,ENST00000477940,;CSF2RA,intron_variant,,ENST00000493312,;CSF2RA,upstream_gene_variant,,ENST00000475259,;CSF2RA,downstream_gene_variant,,ENST00000481245,;CSF2RA,upstream_gene_variant,,ENST00000478256,;CSF2RA,missense_variant,p.Glu71Gln,ENST00000486791,; C ENST00000417535 Transcript missense_variant 405/1955 211/1305 71/434 E/Q Gaa/Caa 1 1 CSF2RA HGNC HGNC:2435 protein_coding YES CCDS55359.1 ENSP00000394227 P15509 UPI000159C3E4 NM_001161530.1 tolerated(0.39) 4/14 hmmpanther:PTHR23036:SF94,hmmpanther:PTHR23036 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 87 1285912 1285912 G C 1 0 0 0 0 1 0 0 0 3735 1175 41 4 4 CSF2RA 23 1285912 Missense_Mutation SNP G C3N-02003_T 994407 1285912 154754983 318 26999 MAGEB17 0 . GRCh38 X 16170609 16170609 + Nonsense_Mutation SNP C C G C3N-02003_T C3N-02003_N C C c.227C>G p.Ser76Ter p.S76* ENST00000400004 2/2 134 122 12 104 104 0 strelka-varscan-mutect MAGEB17,stop_gained,p.Ser76Ter,ENST00000400004,NM_001277307.1;MAGEB17,stop_gained,p.Ser76Ter,ENST00000400003,;RP11-431J24.2,splice_region_variant,,ENST00000435789,; G ENST00000400004 Transcript stop_gained 579/1434 227/1011 76/336 S/* tCa/tGa COSM4852663,COSM4852664 1 1 MAGEB17 HGNC HGNC:17418 protein_coding YES CCDS59524.1 ENSP00000382884 A8MXT2 UPI00001602F1 NM_001277307.1 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF67,Pfam_domain:PF12440,SMART_domains:SM01392 1,1 HIGH 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 87 16170609 16170609 C G 1 0 0 0 0 0 1 0 0 9090 838 29 4 4 MAGEB17 23 16170609 Nonsense_Mutation SNP C C3N-02003_T 14884697 16170609 139870286 319 27000 SCML2 0 . GRCh38 X 18256874 18256874 + Missense_Mutation SNP G G A C3N-02003_T C3N-02003_N G G c.1430C>T p.Ser477Phe p.S477F ENST00000251900 11/15 40 36 4 58 58 0 strelka-varscan-mutect SCML2,missense_variant,p.Ser477Phe,ENST00000251900,NM_006089.2; A ENST00000251900 Transcript missense_variant 1590/4200 1430/2103 477/700 S/F tCt/tTt COSM357787 1 -1 SCML2 HGNC HGNC:10581 protein_coding YES CCDS14185.1 ENSP00000251900 Q9UQR0 UPI0000071E54 NM_006089.2 deleterious(0.04) 11/15 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF84 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 87 18256874 18256874 G A 1 0 0 0 0 1 0 0 0 14179 942 33 3 3 SCML2 23 18256874 Missense_Mutation SNP G C3N-02003_T 2086265 18256874 137784021 320 27001 PPP4R3CP 0 . GRCh38 X 27462008 27462008 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1289A>C p.Glu430Ala p.E430A ENST00000412172 1/1 74 67 7 151 149 2 strelka-varscan-mutect PPP4R3CP,missense_variant,p.Glu430Ala,ENST00000412172,; G ENST00000412172 Transcript missense_variant 1334/3131 1289/2499 430/832 E/A gAg/gCg 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 87 27462008 27462008 T G 1 0 0 0 0 1 0 0 0 12529 1551 54 5 5 PPP4R3CP 23 27462008 Missense_Mutation SNP T C3N-02003_T 9205134 27462008 128578887 321 27002 FAM47C 0 . GRCh38 X 37010475 37010475 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.2065C>T p.His689Tyr p.H689Y ENST00000358047 1/1 148 127 21 192 192 0 strelka-varscan-mutect FAM47C,missense_variant,p.His689Tyr,ENST00000358047,NM_001013736.2; T ENST00000358047 Transcript missense_variant 2079/3270 2065/3108 689/1035 H/Y Cat/Tat 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0.04) 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642,Pfam_domain:PF14642 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 87 37010475 37010475 C T 1 0 0 0 0 1 0 0 0 5449 826 29 3 3 FAM47C 23 37010475 Missense_Mutation SNP C C3N-02003_T 9548467 37010475 119030420 322 27003 ZXDA 0 . GRCh38 X 57909757 57909757 + Nonsense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.664G>T p.Glu222Ter p.E222* ENST00000358697 1/1 78 69 9 41 41 0 strelka-varscan-mutect ZXDA,stop_gained,p.Glu222Ter,ENST00000358697,NM_007156.4; A ENST00000358697 Transcript stop_gained 1064/4113 664/2400 222/799 E/* Gag/Tag 1 -1 ZXDA HGNC HGNC:13198 protein_coding YES CCDS14376.1 ENSP00000351530 P98168 UPI000013C494 NM_007156.4 1/1 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF85 HIGH 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -19.64042 1 1 1 1 0 A 4 1 87 57909757 57909757 C A 1 0 0 0 0 0 1 0 0 18853 922 32 2 2 ZXDA 23 57909757 Nonsense_Mutation SNP C C3N-02003_T 20899282 57909757 98131138 323 27004 KIAA1210 0 . GRCh38 X 119088781 119088781 + Nonsense_Mutation SNP C C A novel C3N-02003_T C3N-02003_N C C c.2449G>T p.Glu817Ter p.E817* ENST00000402510 11/14 109 99 10 117 117 0 strelka-varscan-mutect KIAA1210,stop_gained,p.Glu817Ter,ENST00000402510,NM_020721.1; A ENST00000402510 Transcript stop_gained 2449/7824 2449/5130 817/1709 E/* Gaa/Taa 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 11/14 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -19.67522 0.9999998 1 1 1 0 A 4 1 87 119088781 119088781 C A 1 0 0 0 0 0 1 0 0 8106 922 32 2 2 KIAA1210 23 119088781 Nonsense_Mutation SNP C C3N-02003_T 61179024 119088781 36952114 324 27005 FGF13 0 . GRCh38 X 138635625 138635625 + Missense_Mutation SNP C C T novel C3N-02003_T C3N-02003_N C C c.463G>A p.Glu155Lys p.E155K ENST00000436198 6/7 109 91 18 93 93 0 strelka-varscan-mutect FGF13,missense_variant,p.Glu145Lys,ENST00000315930,NM_004114.3;FGF13,missense_variant,p.Glu92Lys,ENST00000305414,NM_033642.2;FGF13,missense_variant,p.Glu155Lys,ENST00000436198,NM_001139500.1;FGF13,missense_variant,p.Glu99Lys,ENST00000626909,NM_001139498.1;FGF13,missense_variant,p.Glu161Lys,ENST00000455663,;Z83313.1,missense_variant,p.Glu126Lys,ENST00000441825,NM_001139501.1,NM_001139502.1; T ENST00000436198 Transcript missense_variant 713/1165 463/768 155/255 E/K Gaa/Aaa 1 -1 FGF13 HGNC HGNC:3670 protein_coding YES CCDS55513.1 ENSP00000396198 Q92913 UPI00001484B4 NM_001139500.1 deleterious(0) 6/7 Gene3D:2.80.10.50,Pfam_domain:PF00167,Prints_domain:PR00262,Prints_domain:PR00263,PROSITE_patterns:PS00247,hmmpanther:PTHR11486,hmmpanther:PTHR11486:SF77,SMART_domains:SM00442,Superfamily_domains:SSF50353 MODERATE 1 SNV 2 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999984 1 1 1 0 T 3 4 87 138635625 138635625 C T 1 0 0 0 0 1 0 0 0 5706 922 32 3 3 FGF13 23 138635625 Missense_Mutation SNP C C3N-02003_T 19546844 138635625 17405270 325 27006 G6PD 0 . GRCh38 X 154535290 154535290 + Silent SNP G G A novel C3N-02003_T C3N-02003_N G G c.453C>T p.= p.L151L ENST00000393562 5/13 257 229 28 229 228 1 strelka-varscan-mutect G6PD,synonymous_variant,p.=,ENST00000393562,NM_000402.4;G6PD,synonymous_variant,p.=,ENST00000621232,;G6PD,synonymous_variant,p.=,ENST00000369620,;G6PD,synonymous_variant,p.=,ENST00000393564,NM_001042351.2;G6PD,synonymous_variant,p.=,ENST00000439227,;G6PD,synonymous_variant,p.=,ENST00000440967,;G6PD,synonymous_variant,p.=,ENST00000433845,;G6PD,non_coding_transcript_exon_variant,,ENST00000497281,;G6PD,upstream_gene_variant,,ENST00000490651,;G6PD,upstream_gene_variant,,ENST00000489497,;G6PD,downstream_gene_variant,,ENST00000488434,; A ENST00000393562 Transcript synonymous_variant 837/2631 453/1638 151/545 L ctC/ctT 1 -1 G6PD HGNC HGNC:4057 protein_coding YES CCDS14756.2 ENSP00000377192 P11413 UPI0000DA0861 NM_000402.4 5/13 Gene3D:3.40.50.720,HAMAP:MF_00966,Pfam_domain:PF00479,PIRSF_domain:PIRSF000110,hmmpanther:PTHR23429,hmmpanther:PTHR23429:SF0,Superfamily_domains:SSF51735,TIGRFAM_domain:TIGR00871 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 87 154535290 154535290 G A 1 0 0 0 0 0 0 0 1 6017 1277 45 3 3 G6PD 23 154535290 Silent SNP G C3N-02003_T 15899665 154535290 1505605 326 27007 GAB3 0 . GRCh38 X 154678277 154678277 + Missense_Mutation SNP T T G novel C3N-02003_T C3N-02003_N T T c.1665A>C p.Glu555Asp p.E555D ENST00000424127 10/10 62 53 9 65 65 0 strelka-mutect GAB3,missense_variant,p.Glu554Asp,ENST00000369575,NM_080612.3;GAB3,missense_variant,p.Glu516Asp,ENST00000369568,NM_001282283.1;GAB3,missense_variant,p.Glu555Asp,ENST00000424127,NM_001081573.2;GAB3,downstream_gene_variant,,ENST00000454973,;GAB3,non_coding_transcript_exon_variant,,ENST00000496390,;GAB3,downstream_gene_variant,,ENST00000475685,; G ENST00000424127 Transcript missense_variant 1717/2028 1665/1764 555/587 E/D gaA/gaC 1 -1 GAB3 HGNC HGNC:17515 protein_coding YES CCDS48198.1 ENSP00000399588 Q8WWW8 UPI0000F23D6F NM_001081573.2 tolerated(0.53) 10/10 hmmpanther:PTHR12156:SF2,hmmpanther:PTHR12156 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.83447 0.999998 1 1 1 0 G 3 3 87 154678277 154678277 T G 1 0 0 0 0 1 0 0 0 6021 1606 56 5 5 GAB3 23 154678277 Missense_Mutation SNP T C3N-02003_T 142987 154678277 1362618 327 27008 BLZF1 0 . GRCh38 1 169376943 169376943 + Missense_Mutation SNP A A C novel C3N-02067_T C3N-02067_N A A c.432A>C p.Lys144Asn p.K144N ENST00000367808 3/7 260 234 26 126 126 0 strelka-varscan-mutect BLZF1,missense_variant,p.Lys144Asn,ENST00000367808,NM_001320973.1;BLZF1,missense_variant,p.Lys144Asn,ENST00000329281,NM_003666.2;BLZF1,missense_variant,p.Lys144Asn,ENST00000367807,NM_001320972.1;BLZF1,missense_variant,p.Lys144Asn,ENST00000426663,;BLZF1,downstream_gene_variant,,ENST00000420531,; C ENST00000367808 Transcript missense_variant 855/2749 432/1203 144/400 K/N aaA/aaC 1 1 BLZF1 HGNC HGNC:1065 protein_coding YES CCDS1278.1 ENSP00000356782 Q9H2G9 A0A024R921 UPI000003B44E NM_001320973.1 deleterious(0) 3/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13066,hmmpanther:PTHR13066:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 88 169376943 169376943 A C 1 0 0 0 0 1 0 0 0 1608 69 3 5 5 BLZF1 1 169376943 Missense_Mutation SNP A C3N-02067_T 169376943 79579479 1 27009 PROM2 0 . GRCh38 2 95279001 95279009 + In_Frame_Del DEL GGCCCAGCA GGCCCAGCA - novel C3N-02067_T C3N-02067_N GGCCCAGCA GGCCCAGCA c.1132_1140delGCCCAGCAG p.Ala378_Gln380del p.A378_Q380del ENST00000317620 10/24 80 73 7 58 58 0 sindel-pindel PROM2,inframe_deletion,p.Ala378_Gln380del,ENST00000317620,NM_001165978.1;PROM2,inframe_deletion,p.Ala378_Gln380del,ENST00000317668,NM_144707.2;PROM2,inframe_deletion,p.Ala378_Gln380del,ENST00000403131,NM_001165977.1;PROM2,downstream_gene_variant,,ENST00000463580,;PROM2,upstream_gene_variant,,ENST00000497110,;PROM2,downstream_gene_variant,,ENST00000477767,;PROM2,3_prime_UTR_variant,,ENST00000431567,NM_001321070.1;PROM2,non_coding_transcript_exon_variant,,ENST00000487138,;PROM2,non_coding_transcript_exon_variant,,ENST00000478295,; - ENST00000317620 Transcript inframe_deletion 1264-1272/4728 1131-1139/2505 377-380/834 VAQQ/V gtGGCCCAGCAg/gtg 1 1 PROM2 HGNC HGNC:20685 protein_coding YES CCDS2012.1 ENSP00000318270 Q8N271 UPI0000071157 NM_001165978.1 10/24 hmmpanther:PTHR22730:SF6,hmmpanther:PTHR22730,Pfam_domain:PF05478 MODERATE 1 deletion 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -14.99793 0.9999986 1 1 1 0 - 7 5 88 95279001 95279001 GGCCCAGCA - 1 0 1 0 1 0 0 0 0 12688 1335 47 0 0 PROM2 2 95279001 In_Frame_Del DEL GGCCCAGCA C3N-02067_T 95279001 146914528 2 27010 PAX3 0 . GRCh38 2 222202111 222202111 + Missense_Mutation SNP C C A rs778236891 C3N-02067_T C3N-02067_N C C c.1253G>T p.Gly418Val p.G418V ENST00000392069 8/10 317 296 21 303 302 1 strelka-varscan-mutect PAX3,missense_variant,p.Gly418Val,ENST00000350526,NM_181457.3;PAX3,missense_variant,p.Gly418Val,ENST00000392069,NM_181459.3;PAX3,missense_variant,p.Gly418Val,ENST00000392070,NM_181458.3;PAX3,missense_variant,p.Gly417Val,ENST00000409551,NM_001127366.2;PAX3,intron_variant,,ENST00000344493,NM_181461.3;PAX3,intron_variant,,ENST00000336840,NM_181460.3;PAX3,non_coding_transcript_exon_variant,,ENST00000464706,;PAX3,downstream_gene_variant,,ENST00000555548,; A ENST00000392069 Transcript missense_variant 1619/3170 1253/1518 418/505 G/V gGt/gTt rs778236891,COSM5669647,COSM5669648 1 -1 PAX3 HGNC HGNC:8617 protein_coding YES CCDS2448.1 ENSP00000375921 P23760 UPI00001A8BF0 NM_181459.3 deleterious_low_confidence(0) 8/10 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF307 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 88 222202111 222202111 C A 1 0 0 0 0 1 0 0 0 11565 507 18 2 2 PAX3 2 222202111 Missense_Mutation SNP C C3N-02067_T 126923110 222202111 19991418 3 27011 DOCK3 0 . GRCh38 3 51312886 51312886 + Silent SNP C C T novel C3N-02067_T C3N-02067_N C C c.3237C>T p.= p.S1079S ENST00000266037 31/53 171 151 20 164 164 0 strelka-varscan-mutect DOCK3,synonymous_variant,p.=,ENST00000266037,NM_004947.4; T ENST00000266037 Transcript synonymous_variant 3260/8755 3237/6093 1079/2030 S agC/agT 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 31/53 hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 88 51312886 51312886 C T 1 0 0 0 0 0 0 0 1 4503 709 25 3 3 DOCK3 3 51312886 Silent SNP C C3N-02067_T 51312886 146982673 4 27012 ZNF639 0 . GRCh38 3 179329708 179329712 + Frame_Shift_Del DEL TAAAA TAAAA - novel C3N-02067_T C3N-02067_N TAAAA TAAAA c.151_155delAAATA p.Lys51PhefsTer2 p.K51Ffs*2 ENST00000326361 5/7 175 166 9 103 103 0 varindel-pindel ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000326361,NM_016331.2;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000496856,NM_001303426.1,NM_001303425.1;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000484866,;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000621687,;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000491818,;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000466264,;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000481587,;ZNF639,frameshift_variant,p.Lys51PhefsTer2,ENST00000494234,;ZNF639,non_coding_transcript_exon_variant,,ENST00000466663,;ZNF639,non_coding_transcript_exon_variant,,ENST00000483460,; - ENST00000326361 Transcript frameshift_variant 594-598/6064 149-153/1458 50-51/485 LK/X tTAAAA/t 1 1 ZNF639 HGNC HGNC:30950 protein_coding YES CCDS3227.1 ENSP00000325634 Q9UID6 UPI000003EA4C NM_016331.2 5/7 hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF35 HIGH 1 deletion 1 2 1 PASS . . 0 208 2 0 0 0 0 0 -16.30436 1 1 1 1 0 - 7 5 88 179329708 179329708 TAAAA - 1 0 1 0 1 0 0 0 0 18631 1764 61 0 0 ZNF639 3 179329708 Frame_Shift_Del DEL TAAAA C3N-02067_T 128016822 179329708 18965851 5 27013 FAM47E 0 . GRCh38 4 76256230 76256230 + Missense_Mutation SNP C C T rs371047529 C3N-02067_T C3N-02067_N C C c.127C>T p.Arg43Trp p.R43W ENST00000515604 2/7 179 165 14 154 154 0 strelka-varscan-mutect FAM47E-STBD1,missense_variant,p.Arg43Trp,ENST00000515604,NM_001242939.1;FAM47E,missense_variant,p.Arg43Trp,ENST00000424749,NM_001136570.2;FAM47E,intron_variant,,ENST00000502320,;FAM47E,intron_variant,,ENST00000510197,NM_001242936.1;FAM47E,intron_variant,,ENST00000510328,;FAM47E,intron_variant,,ENST00000512895,;FAM47E,upstream_gene_variant,,ENST00000606246,;FAM47E,non_coding_transcript_exon_variant,,ENST00000515589,;FAM47E-STBD1,intron_variant,,ENST00000509377,;FAM47E-STBD1,intron_variant,,ENST00000514365,; T ENST00000515604 Transcript missense_variant 153/3029 127/1056 43/351 R/W Cgg/Tgg rs371047529,COSM5645239,COSM5645240 1 1 FAM47E-STBD1 HGNC HGNC:44667 protein_coding YES CCDS58908.1 ENSP00000422067 UPI0000EE2C6D NM_001242939.1 deleterious(0) 2/7 Pfam_domain:PF14642,hmmpanther:PTHR11064,hmmpanther:PTHR11064:SF22 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS rs371047529 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 88 76256230 76256230 C T 1 0 0 0 0 1 0 0 0 5450 643 23 1 1 FAM47E 4 76256230 Missense_Mutation SNP C C3N-02067_T 76256230 113958325 6 27014 FCHO2 0 . GRCh38 5 73017228 73017228 + Missense_Mutation SNP T T G novel C3N-02067_T C3N-02067_N T T c.716T>G p.Ile239Arg p.I239R ENST00000430046 8/26 161 131 30 111 110 1 strelka-varscan-mutect FCHO2,missense_variant,p.Ile239Arg,ENST00000430046,NM_138782.2;FCHO2,missense_variant,p.Ile206Arg,ENST00000512348,NM_001146032.1;FCHO2,missense_variant,p.Ile239Arg,ENST00000287761,;FCHO2,missense_variant,p.Ile214Arg,ENST00000507345,;CTC-250P20.1,downstream_gene_variant,,ENST00000502452,; G ENST00000430046 Transcript missense_variant 832/4981 716/2433 239/810 I/R aTa/aGa 1 1 FCHO2 HGNC HGNC:25180 protein_coding YES CCDS47230.1 ENSP00000393776 Q0JRZ9 UPI000019971A NM_138782.2 tolerated(0.07) 8/26 PROSITE_profiles:PS51741,hmmpanther:PTHR23065:SF8,hmmpanther:PTHR23065,Superfamily_domains:SSF103657 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 88 73017228 73017228 T G 1 0 0 0 0 1 0 0 0 5650 1406 49 5 5 FCHO2 5 73017228 Missense_Mutation SNP T C3N-02067_T 73017228 108521031 7 27015 PCDHB16 0 . GRCh38 5 141182754 141182754 + Missense_Mutation SNP G G C rs782507416 C3N-02067_T C3N-02067_N G G c.195G>C p.Arg65Ser p.R65S ENST00000609684 1/1 98 86 12 56 56 0 strelka-varscan-mutect PCDHB16,missense_variant,p.Arg65Ser,ENST00000609684,NM_020957.3;PCDHB16,intron_variant,,ENST00000625044,;CH17-140K24.5,intron_variant,,ENST00000623884,;PCDHB9,upstream_gene_variant,,ENST00000316105,NM_019119.4;PCDHB8,downstream_gene_variant,,ENST00000239444,NM_019120.4;PCDHB9,upstream_gene_variant,,ENST00000624909,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,downstream_gene_variant,,ENST00000624549,;CH17-140K24.7,downstream_gene_variant,,ENST00000624089,;PCDHB9,upstream_gene_variant,,ENST00000623266,;CH17-140K24.4,downstream_gene_variant,,ENST00000623995,;CH17-140K24.5,intron_variant,,ENST00000623407,; C ENST00000609684 Transcript missense_variant 1356/5001 195/2331 65/776 R/S agG/agC rs782507416 1 1 PCDHB16 HGNC HGNC:14546 protein_coding YES CCDS4251.1 ENSP00000477314 Q9NRJ7 UPI00001273E9 NM_020957.3 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF71,Pfam_domain:PF08266,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS rs782507416 . 0 204 6 0 0 0 0 0 -19.99999 0.9999999 1 1 1 0 C 3 2 88 141182754 141182754 G C 1 0 0 0 0 1 0 0 0 11628 1165 41 4 4 PCDHB16 5 141182754 Missense_Mutation SNP G C3N-02067_T 68165526 141182754 40355505 8 27016 MAPK9 0 . GRCh38 5 180280543 180280543 + Missense_Mutation SNP C C T novel C3N-02067_T C3N-02067_N C C c.19G>A p.Asp7Asn p.D7N ENST00000452135 2/12 184 173 11 116 115 1 strelka-mutect MAPK9,missense_variant,p.Asp7Asn,ENST00000452135,NM_002752.4;MAPK9,missense_variant,p.Asp7Asn,ENST00000343111,NM_139069.2;MAPK9,missense_variant,p.Asp7Asn,ENST00000455781,NM_139070.2;MAPK9,missense_variant,p.Asp7Asn,ENST00000393360,NM_139068.2;MAPK9,missense_variant,p.Asp7Asn,ENST00000425491,NM_001135044.1;MAPK9,missense_variant,p.Asp7Asn,ENST00000539014,NM_001308244.1;MAPK9,missense_variant,p.Asp7Asn,ENST00000347470,;MAPK9,missense_variant,p.Asp7Asn,ENST00000397072,;MAPK9,missense_variant,p.Asp7Asn,ENST00000523583,;MAPK9,missense_variant,p.Asp7Asn,ENST00000393362,; T ENST00000452135 Transcript missense_variant 318/4815 19/1275 7/424 D/N Gac/Aac 1 -1 MAPK9 HGNC HGNC:6886 protein_coding YES CCDS4453.1 ENSP00000394560 P45984 UPI000006E3AD NM_002752.4 tolerated(0.24) 2/12 hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF172 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 88 180280543 180280543 C T 1 0 0 0 0 1 0 0 0 9211 826 29 3 3 MAPK9 5 180280543 Missense_Mutation SNP C C3N-02067_T 39097789 180280543 1257716 9 27017 CUL7 0 . GRCh38 6 43051710 43051710 + Missense_Mutation SNP G G A novel C3N-02067_T C3N-02067_N G G c.886C>T p.His296Tyr p.H296Y ENST00000535468 3/26 707 658 49 489 489 0 strelka-varscan-mutect CUL7,missense_variant,p.His296Tyr,ENST00000535468,NM_001168370.1;CUL7,missense_variant,p.His212Tyr,ENST00000265348,NM_014780.4;MRPL2,downstream_gene_variant,,ENST00000388752,NM_015950.4;MRPL2,downstream_gene_variant,,ENST00000230413,NM_001300848.1;MRPL2,downstream_gene_variant,,ENST00000489623,;CUL7,upstream_gene_variant,,ENST00000478630,;KLC4,intron_variant,,ENST00000467906,;MRPL2,downstream_gene_variant,,ENST00000491898,;MRPL2,downstream_gene_variant,,ENST00000470667,;MRPL2,downstream_gene_variant,,ENST00000480286,;MRPL2,downstream_gene_variant,,ENST00000485654,; A ENST00000535468 Transcript missense_variant 973/5504 886/5349 296/1782 H/Y Cac/Tac 1 -1 CUL7 HGNC HGNC:21024 protein_coding YES CCDS55003.1 ENSP00000438788 Q14999 UPI0001BE8116 NM_001168370.1 deleterious(0.01) 3/26 hmmpanther:PTHR22771,hmmpanther:PTHR22771:SF3 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 88 43051710 43051710 G A 1 0 0 0 0 1 0 0 0 3870 1377 48 3 3 CUL7 6 43051710 Missense_Mutation SNP G C3N-02067_T 43051710 127754269 10 27018 CD109 0 . GRCh38 6 73823498 73823498 + Silent SNP G G T novel C3N-02067_T C3N-02067_N G G c.4203G>T p.= p.L1401L ENST00000287097 33/33 148 139 9 119 119 0 strelka-varscan-mutect CD109,synonymous_variant,p.=,ENST00000437994,NM_001159587.2;CD109,synonymous_variant,p.=,ENST00000422508,NM_001159588.2;CD109,synonymous_variant,p.=,ENST00000287097,NM_133493.4; T ENST00000287097 Transcript synonymous_variant 4315/9130 4203/4338 1401/1445 L ctG/ctT 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 33/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80,Superfamily_domains:SSF49410 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 88 73823498 73823498 G T 1 0 0 0 0 0 0 0 1 2666 1364 48 2 2 CD109 6 73823498 Silent SNP G C3N-02067_T 30771788 73823498 96982481 11 27019 GET4 0 . GRCh38 7 887460 887460 + Missense_Mutation SNP G G A rs772387849 C3N-02067_T C3N-02067_N G G c.407G>A p.Gly136Asp p.G136D ENST00000265857 4/9 44 40 4 29 29 0 strelka-mutect GET4,missense_variant,p.Gly83Asp,ENST00000407192,;GET4,missense_variant,p.Gly136Asp,ENST00000265857,NM_015949.2;GET4,missense_variant,p.Gly83Asp,ENST00000412734,;GET4,missense_variant,p.Gly148Asp,ENST00000441491,;GET4,missense_variant,p.Gly97Asp,ENST00000426056,;RP11-449P15.2,upstream_gene_variant,,ENST00000609998,;SUN1,3_prime_UTR_variant,,ENST00000457861,;GET4,upstream_gene_variant,,ENST00000464468,;GET4,upstream_gene_variant,,ENST00000483469,; A ENST00000265857 Transcript missense_variant 501/2090 407/984 136/327 G/D gGc/gAc rs772387849 1 1 GET4 HGNC HGNC:21690 protein_coding YES CCDS5317.1 ENSP00000265857 Q7L5D6 UPI00001AE543 NM_015949.2 tolerated(0.61) 4/9 Low_complexity_(Seg):seg,hmmpanther:PTHR12875:SF0,hmmpanther:PTHR12875,Pfam_domain:PF04190 MODERATE 1 SNV 1 1 PASS rs772387849 . 0 202 7 0 0 0 0 0 -10.40461 0.9999987 1 1 1 0 A 3 1 88 887460 887460 G A 1 0 0 0 0 1 0 0 0 6210 1203 42 3 3 GET4 7 887460 Missense_Mutation SNP G C3N-02067_T 887460 158458513 12 27020 ABCB5 0 . GRCh38 7 20723035 20723035 + Missense_Mutation SNP G G A novel C3N-02067_T C3N-02067_N G G c.2441G>A p.Gly814Asp p.G814D ENST00000404938 21/28 320 304 16 205 205 0 strelka-varscan-mutect ABCB5,missense_variant,p.Gly814Asp,ENST00000404938,NM_001163941.1;ABCB5,missense_variant,p.Gly369Asp,ENST00000258738,NM_178559.5;ABCB5,upstream_gene_variant,,ENST00000441315,; A ENST00000404938 Transcript missense_variant 3093/5811 2441/3774 814/1257 G/D gGc/gAc 1 1 ABCB5 HGNC HGNC:46 protein_coding YES CCDS55090.1 ENSP00000384881 Q2M3G0 UPI000173A253 NM_001163941.1 deleterious(0) 21/28 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,hmmpanther:PTHR24221,hmmpanther:PTHR24221:SF217,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS rs1486643794 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 88 20723035 20723035 G A 1 0 0 0 0 1 0 0 0 48 1203 42 3 3 ABCB5 7 20723035 Missense_Mutation SNP G C3N-02067_T 19835575 20723035 138622938 13 27021 CCDC129 0 . GRCh38 7 31643366 31643366 + Missense_Mutation SNP C C T novel C3N-02067_T C3N-02067_N C C c.2074C>T p.His692Tyr p.H692Y ENST00000451887 11/15 489 414 75 358 358 0 strelka-varscan-mutect CCDC129,missense_variant,p.His518Tyr,ENST00000319386,;CCDC129,missense_variant,p.His676Tyr,ENST00000615280,NM_001257967.1;CCDC129,missense_variant,p.His574Tyr,ENST00000409210,;CCDC129,missense_variant,p.His692Tyr,ENST00000451887,NM_001257968.1;CCDC129,missense_variant,p.His666Tyr,ENST00000407970,NM_194300.3; T ENST00000451887 Transcript missense_variant 2168/3611 2074/3189 692/1062 H/Y Cac/Tac 1 1 CCDC129 HGNC HGNC:27363 protein_coding YES CCDS59050.1 ENSP00000395835 Q6ZRS4 UPI00020655D9 NM_001257968.1 tolerated(0.16) 11/15 hmmpanther:PTHR17469,hmmpanther:PTHR17469:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 88 31643366 31643366 C T 1 0 0 0 0 1 0 0 0 2456 594 21 3 3 CCDC129 7 31643366 Missense_Mutation SNP C C3N-02067_T 10920331 31643366 127702607 14 27022 EEPD1 0 . GRCh38 7 36287737 36287737 + Silent SNP G G A novel C3N-02067_T C3N-02067_N G G c.1275G>A p.= p.R425R ENST00000242108 6/8 256 182 74 159 159 0 strelka-varscan-mutect EEPD1,synonymous_variant,p.=,ENST00000242108,NM_030636.2;EEPD1,synonymous_variant,p.=,ENST00000534978,;EEPD1,non_coding_transcript_exon_variant,,ENST00000487069,;EEPD1,non_coding_transcript_exon_variant,,ENST00000468591,; A ENST00000242108 Transcript synonymous_variant 1993/4765 1275/1710 425/569 R cgG/cgA 1 1 EEPD1 HGNC HGNC:22223 protein_coding YES CCDS34619.1 ENSP00000242108 Q7L9B9 UPI000020ED9D NM_030636.2 6/8 hmmpanther:PTHR21180:SF32,hmmpanther:PTHR21180,Gene3D:3.60.10.10,Pfam_domain:PF03372,Superfamily_domains:SSF56219 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 88 36287737 36287737 G A 1 0 0 0 0 0 0 0 1 4763 1248 44 3 3 EEPD1 7 36287737 Silent SNP G C3N-02067_T 4644371 36287737 123058236 15 27023 EGFR 0 . GRCh38 7 55174775 55174786 + In_Frame_Del DEL ATTAAGAGAAGC ATTAAGAGAAGC - C3N-02067_T C3N-02067_N ATTAAGAGAAGC ATTAAGAGAAGC c.2239_2250delTTAAGAGAAGCA p.Leu747_Ala750del p.L747_A750del ENST00000275493 19/28 581 433 148 438 438 0 sindel-varindel EGFR,inframe_deletion,p.Leu747_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Leu702_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Leu702_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2415-2426/9821 2238-2249/3633 746-750/1210 ELREA/E gaATTAAGAGAAGCa/gaa COSM18428 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 1 MODERATE 1 deletion 1 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 88 55174775 55174775 ATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 98 4 0 0 EGFR 7 55174775 In_Frame_Del DEL ATTAAGAGAAGC C3N-02067_T 18887038 55174775 104171198 16 27024 OR2A42 0 . GRCh38 7 144232398 144232398 + Missense_Mutation SNP G G T novel C3N-02067_T C3N-02067_N G G c.446C>A p.Thr149Lys p.T149K ENST00000391496 1/1 98 86 12 71 71 0 varscan-mutect OR2A42,missense_variant,p.Thr149Lys,ENST00000391496,NM_001001802.2;RP4-545C24.1,intron_variant,,ENST00000498693,;RP4-545C24.1,intron_variant,,ENST00000464929,;RP4-545C24.1,intron_variant,,ENST00000460955,;RP4-545C24.1,intron_variant,,ENST00000493248,;RP4-545C24.1,intron_variant,,ENST00000489077,;RP4-545C24.1,intron_variant,,ENST00000477797,;RP4-545C24.1,downstream_gene_variant,,ENST00000480074,; T ENST00000391496 Transcript missense_variant 446/933 446/933 149/310 T/K aCg/aAg 1 -1 OR2A42 HGNC HGNC:31230 protein_coding YES CCDS56515.1 ENSP00000375334 Q8NGT9 UPI0000041DF3 NM_001001802.2 deleterious(0.01) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF115,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs1192475502 . 29 180 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 88 144232398 144232398 G T 1 0 0 0 0 1 0 0 0 11057 1145 40 1 1 OR2A42 7 144232398 Missense_Mutation SNP G C3N-02067_T 89057623 144232398 15113575 17 27025 FAM135B 0 . GRCh38 8 138153001 138153001 + Missense_Mutation SNP T T C rs759360519 C3N-02067_T C3N-02067_N T T c.1474A>G p.Met492Val p.M492V ENST00000395297 13/20 276 208 68 177 177 0 strelka-varscan-mutect FAM135B,missense_variant,p.Met492Val,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Met492Val,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,;FAM135B,upstream_gene_variant,,ENST00000467365,;FAM135B,upstream_gene_variant,,ENST00000395295,; C ENST00000395297 Transcript missense_variant 1645/6962 1474/4221 492/1406 M/V Atg/Gtg rs759360519 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 tolerated(0.87) 13/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 MODERATE 1 SNV 5 1 PASS rs759360519 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 88 138153001 138153001 T C 1 0 0 0 0 1 0 0 0 5299 1406 49 5 5 FAM135B 8 138153001 Missense_Mutation SNP T C3N-02067_T 138153001 6985635 18 27026 GRIN3A 0 . GRCh38 9 101737815 101737815 + Missense_Mutation SNP C C A novel C3N-02067_T C3N-02067_N C C c.165G>T p.Leu55Phe p.L55F ENST00000361820 1/9 141 133 8 165 165 0 strelka-varscan-mutect GRIN3A,missense_variant,p.Leu55Phe,ENST00000361820,NM_133445.2; A ENST00000361820 Transcript missense_variant 766/7770 165/3348 55/1115 L/F ttG/ttT 1 -1 GRIN3A HGNC HGNC:16767 protein_coding YES CCDS6758.1 ENSP00000355155 Q8TCU5 UPI0000367661 NM_133445.2 deleterious_low_confidence(0.01) 1/9 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF154 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -15.07367 1 1 1 1 0 A 3 1 88 101737815 101737815 C A 1 0 0 0 0 1 0 0 0 6665 709 25 2 2 GRIN3A 9 101737815 Missense_Mutation SNP C C3N-02067_T 101737815 36656902 19 27027 NUP160 0 . GRCh38 11 47798219 47798219 + Missense_Mutation SNP C C A novel C3N-02067_T C3N-02067_N C C c.3035G>T p.Gly1012Val p.G1012V ENST00000378460 25/36 175 160 15 122 122 0 strelka-varscan-mutect NUP160,missense_variant,p.Gly1012Val,ENST00000378460,NM_015231.1;NUP160,missense_variant,p.Gly977Val,ENST00000530326,;NUP160,missense_variant,p.Gly984Val,ENST00000528071,;RP11-692M12.5,downstream_gene_variant,,ENST00000604478,; A ENST00000378460 Transcript missense_variant 3082/5376 3035/4311 1012/1436 G/V gGt/gTt 1 -1 NUP160 HGNC HGNC:18017 protein_coding YES CCDS31484.1 ENSP00000367721 Q12769 UPI0000185FEB NM_015231.1 deleterious(0) 25/36 hmmpanther:PTHR21286 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 88 47798219 47798219 C A 1 0 0 0 0 1 0 0 0 10822 507 18 2 2 NUP160 11 47798219 Missense_Mutation SNP C C3N-02067_T 47798219 87288403 20 27028 CATSPER1 0 . GRCh38 11 66021817 66021817 + Missense_Mutation SNP T T G novel C3N-02067_T C3N-02067_N T T c.1492A>C p.Lys498Gln p.K498Q ENST00000312106 3/12 530 419 111 477 477 0 strelka-varscan-mutect CATSPER1,missense_variant,p.Lys498Gln,ENST00000312106,NM_053054.3;CATSPER1,upstream_gene_variant,,ENST00000529244,; G ENST00000312106 Transcript missense_variant 1630/2619 1492/2343 498/780 K/Q Aag/Cag 1 -1 CATSPER1 HGNC HGNC:17116 protein_coding YES CCDS8127.1 ENSP00000309052 Q8NEC5 UPI000045651C NM_053054.3 deleterious(0) 3/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037:SF216,hmmpanther:PTHR10037,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 88 66021817 66021817 T G 1 0 0 0 0 1 0 0 0 2387 1821 63 5 5 CATSPER1 11 66021817 Missense_Mutation SNP T C3N-02067_T 18223598 66021817 69064805 21 27029 DYNC2H1 0 . GRCh38 11 103253299 103253299 + Missense_Mutation SNP G G C novel C3N-02067_T C3N-02067_N G G c.10078G>C p.Val3360Leu p.V3360L ENST00000398093 67/90 105 99 6 72 72 0 strelka-varscan-mutect DYNC2H1,missense_variant,p.Val3353Leu,ENST00000375735,NM_001377.2;DYNC2H1,missense_variant,p.Val3360Leu,ENST00000398093,NM_001080463.1;DYNC2H1,intron_variant,,ENST00000334267,; C ENST00000398093 Transcript missense_variant 10078/12945 10078/12945 3360/4314 V/L Gta/Cta 1 1 DYNC2H1 HGNC HGNC:2962 protein_coding YES CCDS44717.1 ENSP00000381167 Q8NCM8 UPI0000481AC7 NM_001080463.1 deleterious(0.01) 67/90 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF282,Pfam_domain:PF12781 MODERATE 1 SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -12.01873 0.9999523 1 1 1 0 C 3 2 88 103253299 103253299 G C 1 0 0 0 0 1 0 0 0 4670 1261 44 4 4 DYNC2H1 11 103253299 Missense_Mutation SNP G C3N-02067_T 37231482 103253299 31833323 22 27030 PAX9 0 . GRCh38 14 36666467 36666467 + Missense_Mutation SNP G G A novel C3N-02067_T C3N-02067_N G G c.637G>A p.Asp213Asn p.D213N ENST00000361487 3/4 202 181 21 111 111 0 strelka-varscan-mutect PAX9,missense_variant,p.Asp213Asn,ENST00000361487,;PAX9,missense_variant,p.Asp213Asn,ENST00000402703,NM_006194.3;PAX9,missense_variant,p.Asp26Asn,ENST00000554201,;PAX9,non_coding_transcript_exon_variant,,ENST00000557107,;PAX9,downstream_gene_variant,,ENST00000553267,;PAX9,downstream_gene_variant,,ENST00000555639,; A ENST00000361487 Transcript missense_variant 862/4514 637/1026 213/341 D/N Gac/Aac 1 1 PAX9 HGNC HGNC:8623 protein_coding YES CCDS9662.1 ENSP00000355245 P55771 Q2L4T1 UPI0000131377 tolerated(0.18) 3/4 hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF297 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 88 36666467 36666467 G A 1 0 0 0 0 1 0 0 0 11571 1072 37 1 1 PAX9 14 36666467 Missense_Mutation SNP G C3N-02067_T 36666467 70377251 23 27031 TM6SF1 0 . GRCh38 15 83107724 83107724 + Missense_Mutation SNP C C T rs780558833 C3N-02067_T C3N-02067_N C C c.44C>T p.Ser15Leu p.S15L ENST00000322019 1/10 215 201 14 222 221 1 strelka-varscan-mutect TM6SF1,missense_variant,p.Ser15Leu,ENST00000322019,NM_023003.3;TM6SF1,missense_variant,p.Ser15Leu,ENST00000379390,;TM6SF1,missense_variant,p.Ser15Leu,ENST00000565774,NM_001144903.1;TM6SF1,5_prime_UTR_variant,,ENST00000565982,;RP11-382A20.5,downstream_gene_variant,,ENST00000566841,;TM6SF1,non_coding_transcript_exon_variant,,ENST00000564988,;TM6SF1,missense_variant,p.Ser15Leu,ENST00000379384,;TM6SF1,missense_variant,p.Ser15Leu,ENST00000258909,; T ENST00000322019 Transcript missense_variant 318/2074 44/1113 15/370 S/L tCg/tTg rs780558833,COSM3794466,COSM416787 1 1 TM6SF1 HGNC HGNC:11860 protein_coding YES CCDS10323.1 ENSP00000317000 Q9BZW5 UPI0000039EA7 NM_023003.3 tolerated(0.41) 1/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR14568,hmmpanther:PTHR14568:SF10 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs780558833 . 0 208 0 2 0 0 0 0 -17.42449 0.9999996 1 1 1 0 T 3 4 88 83107724 83107724 C T 1 0 0 0 0 1 0 0 0 16417 893 31 1 1 TM6SF1 15 83107724 Missense_Mutation SNP C C3N-02067_T 83107724 18883465 24 27032 TP53 0 . GRCh38 17 7674961 7674962 + Frame_Shift_Ins INS - - G C3N-02067_T C3N-02067_N - - c.569dupC p.Pro191SerfsTer18 p.P191Sfs*18 ENST00000269305 6/11 435 260 175 399 399 0 sindel-varindel-pindel TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000420246,;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000445888,;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000619485,;TP53,frameshift_variant,p.Pro59SerfsTer18,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.Pro32SerfsTer18,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.Pro59SerfsTer18,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.Pro32SerfsTer18,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.Pro59SerfsTer18,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.Pro32SerfsTer18,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000359597,;TP53,frameshift_variant,p.Pro180SerfsTer18,ENST00000615910,;TP53,frameshift_variant,p.Pro191SerfsTer18,ENST00000413465,;TP53,frameshift_variant,p.Pro59SerfsTer18,ENST00000509690,;TP53,frameshift_variant,p.Pro98SerfsTer18,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,frameshift_variant,p.Pro152SerfsTer18,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; G ENST00000269305 Transcript frameshift_variant 759-760/2579 569-570/1182 190/393 P/PX cct/ccCt TP53_g.12638_12639ins1 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 88 7674961 7674961 - G 1 0 1 1 0 0 0 0 0 16859 291 11 0 0 TP53 17 7674961 Frame_Shift_Ins INS - C3N-02067_T 7674961 75582480 25 27033 SMCR8 0 . GRCh38 17 18315915 18315915 + Silent SNP T T A novel C3N-02067_T C3N-02067_N T T c.126T>A p.= p.A42A ENST00000406438 1/2 251 197 54 182 182 0 strelka-varscan-mutect SMCR8,synonymous_variant,p.=,ENST00000406438,NM_144775.2;TOP3A,upstream_gene_variant,,ENST00000542570,NM_004618.3;TOP3A,upstream_gene_variant,,ENST00000321105,;TOP3A,upstream_gene_variant,,ENST00000580095,;TOP3A,upstream_gene_variant,,ENST00000582230,;TOP3A,upstream_gene_variant,,ENST00000584669,;TOP3A,upstream_gene_variant,,ENST00000584887,;TOP3A,upstream_gene_variant,,ENST00000584582,;TOP3A,upstream_gene_variant,,ENST00000582981,;TOP3A,upstream_gene_variant,,ENST00000472959,;TOP3A,upstream_gene_variant,,ENST00000461127,;TOP3A,upstream_gene_variant,,ENST00000583328,;TOP3A,upstream_gene_variant,,ENST00000585031,;TOP3A,upstream_gene_variant,,ENST00000580713,;RPL7AP65,downstream_gene_variant,,ENST00000418183,;RPL21P121,downstream_gene_variant,,ENST00000439258,; A ENST00000406438 Transcript synonymous_variant 606/8279 126/2814 42/937 A gcT/gcA 1 1 SMCR8 HGNC HGNC:17921 protein_coding YES CCDS11195.2 ENSP00000385025 Q8TEV9 UPI0000E0322D NM_144775.2 1/2 hmmpanther:PTHR31334:SF1,hmmpanther:PTHR31334 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 88 18315915 18315915 T A 1 0 0 0 0 0 0 0 1 15087 1509 53 4 4 SMCR8 17 18315915 Silent SNP T C3N-02067_T 10640954 18315915 64941526 26 27034 KRT10 0 . GRCh38 17 40819067 40819067 + Missense_Mutation SNP C C T rs753205769 C3N-02067_T C3N-02067_N C C c.1468G>A p.Gly490Ser p.G490S ENST00000269576 7/8 143 135 8 214 212 2 varscan-mutect KRT10,missense_variant,p.Gly490Ser,ENST00000269576,NM_000421.3;TMEM99,upstream_gene_variant,,ENST00000622451,NM_001195386.1;TMEM99,upstream_gene_variant,,ENST00000301665,NM_001195387.1,NM_145274.3;TMEM99,upstream_gene_variant,,ENST00000436612,;KRT10,upstream_gene_variant,,ENST00000635956,;TMEM99,upstream_gene_variant,,ENST00000496847,; T ENST00000269576 Transcript missense_variant 1478/2124 1468/1755 490/584 G/S Ggc/Agc rs753205769 1 -1 KRT10 HGNC HGNC:6413 protein_coding YES CCDS11377.1 ENSP00000269576 P13645 UPI000013D842 NM_000421.3 tolerated_low_confidence(0.69) 7/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF137,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs753205769 . 0 97 0 0 0 0 0 113 -6.354488 0 0 1 0 0 T 3 4 88 40819067 40819067 C T 1 0 0 0 0 1 0 0 0 8330 652 23 1 1 KRT10 17 40819067 Missense_Mutation SNP C C3N-02067_T 22503152 40819067 42438374 27 27035 SERPINB13 0 . GRCh38 18 63588683 63588683 + Missense_Mutation SNP G G A rs191405968 C3N-02067_T C3N-02067_N G G c.16G>A p.Ala6Thr p.A6T ENST00000269489 2/8 138 127 11 127 127 0 strelka-varscan-mutect SERPINB13,missense_variant,p.Ala6Thr,ENST00000269489,NM_001307923.1;SERPINB13,missense_variant,p.Ala6Thr,ENST00000344731,NM_012397.3;SERPINB13,missense_variant,p.Ala36Thr,ENST00000431153,;SERPINB13,upstream_gene_variant,,ENST00000415733,;SERPINB13,missense_variant,p.Ala6Thr,ENST00000438844,;SERPINB13,non_coding_transcript_exon_variant,,ENST00000479842,; A ENST00000269489 Transcript missense_variant 184/3206 16/1203 6/400 A/T Gcc/Acc rs191405968,COSM1737021 1 1 SERPINB13 HGNC HGNC:8944 protein_coding YES CCDS77195.1 ENSP00000269489 A0A0A0MQW3 UPI000004EE0A NM_001307923.1 tolerated(0.49) 2/8 hmmpanther:PTHR11461,hmmpanther:PTHR11461:SF161,Superfamily_domains:SSF56574 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs191405968 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 88 63588683 63588683 G A 1 0 0 0 0 1 0 0 0 14376 1087 38 1 1 SERPINB13 18 63588683 Missense_Mutation SNP G C3N-02067_T 63588683 16784602 28 27036 CBLN2 0 . GRCh38 18 72542051 72542051 + Missense_Mutation SNP G G A rs779844910 C3N-02067_T C3N-02067_N G G c.110C>T p.Ala37Val p.A37V ENST00000269503 3/5 83 76 7 88 88 0 strelka-varscan-mutect CBLN2,missense_variant,p.Ala37Val,ENST00000269503,NM_182511.3;CBLN2,missense_variant,p.Ala37Val,ENST00000585159,;CBLN2,intron_variant,,ENST00000584764,;CBLN2,intron_variant,,ENST00000581073,;CBLN2,intron_variant,,ENST00000583651,;CBLN2,downstream_gene_variant,,ENST00000580889,;CBLN2,upstream_gene_variant,,ENST00000581425,; A ENST00000269503 Transcript missense_variant 884/2945 110/675 37/224 A/V gCc/gTc rs779844910,COSM5056115 1 -1 CBLN2 HGNC HGNC:1544 protein_coding YES CCDS11999.1 ENSP00000269503 Q8IUK8 A0A024R380 UPI0000032E73 NM_182511.3 tolerated_low_confidence(0.24) 3/5 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-TM,hmmpanther:PTHR22923:SF50,hmmpanther:PTHR22923 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779844910 . 0 207 2 0 0 0 0 0 -15.41108 1 1 1 1 0 A 3 1 88 72542051 72542051 G A 1 0 0 0 0 1 0 0 0 2406 1203 42 3 3 CBLN2 18 72542051 Missense_Mutation SNP G C3N-02067_T 8953368 72542051 7831234 29 27037 ABCA7 0 . GRCh38 19 1058890 1058890 + Missense_Mutation SNP G G C novel C3N-02067_T C3N-02067_N G G c.5350G>C p.Val1784Leu p.V1784L ENST00000263094 39/47 60 39 21 40 40 0 strelka-varscan-mutect ABCA7,missense_variant,p.Val1784Leu,ENST00000263094,NM_019112.3;ABCA7,missense_variant,p.Val1784Leu,ENST00000433129,;ABCA7,missense_variant,p.Val1646Leu,ENST00000435683,;ABCA7,missense_variant,p.Val229Leu,ENST00000525073,;ABCA7,upstream_gene_variant,,ENST00000612569,;ABCA7,non_coding_transcript_exon_variant,,ENST00000532194,;ABCA7,downstream_gene_variant,,ENST00000530092,;ABCA7,downstream_gene_variant,,ENST00000529442,;ABCA7,upstream_gene_variant,,ENST00000525939,; C ENST00000263094 Transcript missense_variant 5581/6816 5350/6441 1784/2146 V/L Gtc/Ctc 1 1 ABCA7 HGNC HGNC:37 protein_coding YES CCDS12055.1 ENSP00000263094 Q8IZY2 UPI000013D3A4 NM_019112.3 tolerated(1) 39/47 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF49,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 88 1058890 1058890 G C 1 0 0 0 0 1 0 0 0 41 1261 44 4 4 ABCA7 19 1058890 Missense_Mutation SNP G C3N-02067_T 1058890 57558726 30 27038 CATSPERD 0 . GRCh38 19 5737193 5737193 + Silent SNP T T C C3N-02067_T C3N-02067_N T T c.447T>C p.= p.S149S ENST00000381624 6/22 198 142 56 172 172 0 strelka-varscan-mutect CATSPERD,synonymous_variant,p.=,ENST00000381624,NM_152784.3; C ENST00000381624 Transcript synonymous_variant 508/2516 447/2397 149/798 S agT/agC COSM4669487 1 1 CATSPERD HGNC HGNC:28598 protein_coding YES CCDS12149.2 ENSP00000371037 Q86XM0 UPI000059D641 NM_152784.3 6/22 Pfam_domain:PF15020,hmmpanther:PTHR33722,hmmpanther:PTHR33722:SF1 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 88 5737193 5737193 T C 1 0 0 0 0 0 0 0 1 2392 1722 60 5 5 CATSPERD 19 5737193 Silent SNP T C3N-02067_T 4678303 5737193 52880423 31 27039 TRMT1 0 . GRCh38 19 13116230 13116230 + Missense_Mutation SNP A A C rs748103642 C3N-02067_T C3N-02067_N A A c.170T>G p.Val57Gly p.V57G ENST00000592062 3/18 442 417 25 423 423 0 strelka-varscan-mutect TRMT1,missense_variant,p.Val57Gly,ENST00000592062,;TRMT1,missense_variant,p.Val57Gly,ENST00000437766,NM_017722.3;TRMT1,missense_variant,p.Val57Gly,ENST00000221504,NM_001142554.1;TRMT1,missense_variant,p.Val57Gly,ENST00000357720,NM_001136035.2;TRMT1,missense_variant,p.Val57Gly,ENST00000592814,;TRMT1,missense_variant,p.Val57Gly,ENST00000588229,;TRMT1,intron_variant,,ENST00000587487,;NACC1,upstream_gene_variant,,ENST00000292431,NM_052876.3;NACC1,upstream_gene_variant,,ENST00000586171,;TRMT1,non_coding_transcript_exon_variant,,ENST00000592892,;TRMT1,non_coding_transcript_exon_variant,,ENST00000592729,;TRMT1,non_coding_transcript_exon_variant,,ENST00000588813,;TRMT1,non_coding_transcript_exon_variant,,ENST00000591425,;TRMT1,upstream_gene_variant,,ENST00000593257,;TRMT1,missense_variant,p.Val57Gly,ENST00000591717,;TRMT1,missense_variant,p.Val57Gly,ENST00000588746,;TRMT1,missense_variant,p.Val57Gly,ENST00000586224,;TRMT1,non_coding_transcript_exon_variant,,ENST00000588511,;TRMT1,non_coding_transcript_exon_variant,,ENST00000593157,;TRMT1,non_coding_transcript_exon_variant,,ENST00000585622,;TRMT1,non_coding_transcript_exon_variant,,ENST00000590812,;TRMT1,non_coding_transcript_exon_variant,,ENST00000592606,;TRMT1,upstream_gene_variant,,ENST00000587633,; C ENST00000592062 Transcript missense_variant 741/2579 170/1980 57/659 V/G gTc/gGc rs748103642 1 -1 TRMT1 HGNC HGNC:25980 protein_coding YES CCDS12293.1 ENSP00000466967 Q9NXH9 A0A024R7I5 UPI0000000A02 deleterious(0) 3/18 PROSITE_profiles:PS51626,hmmpanther:PTHR10631:SF3,hmmpanther:PTHR10631,Pfam_domain:PF02005,TIGRFAM_domain:TIGR00308,Superfamily_domains:SSF53335 MODERATE SNV 5 1 PASS rs748103642 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 88 13116230 13116230 A C 1 0 0 0 0 1 0 0 0 17060 275 10 5 5 TRMT1 19 13116230 Missense_Mutation SNP A C3N-02067_T 7379037 13116230 45501386 32 27040 PDE4C 0 . GRCh38 19 18213433 18213433 + Missense_Mutation SNP C C T novel C3N-02067_T C3N-02067_N C C c.1543G>A p.Val515Met p.V515M ENST00000355502 17/19 223 202 21 177 177 0 strelka-varscan-mutect PDE4C,missense_variant,p.Val515Met,ENST00000355502,;PDE4C,missense_variant,p.Val515Met,ENST00000594617,NM_000923.4;PDE4C,missense_variant,p.Val515Met,ENST00000594465,;PDE4C,missense_variant,p.Val409Met,ENST00000447275,NM_001098819.2;PDE4C,missense_variant,p.Val483Met,ENST00000262805,NM_001098818.2;PDE4C,missense_variant,p.Val284Met,ENST00000539010,;PDE4C,missense_variant,p.Val285Met,ENST00000597297,;PDE4C,missense_variant,p.Val230Met,ENST00000598111,;AC068499.10,intron_variant,,ENST00000594805,;AC068499.10,downstream_gene_variant,,ENST00000599416,;PDE4C,3_prime_UTR_variant,,ENST00000599188,;PDE4C,non_coding_transcript_exon_variant,,ENST00000597360,; T ENST00000355502 Transcript missense_variant 2415/5979 1543/2139 515/712 V/M Gtg/Atg 1 -1 PDE4C HGNC HGNC:8782 protein_coding YES CCDS12373.1 ENSP00000347689 Q08493 UPI0000127BF8 deleterious(0) 17/19 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF106,Gene3D:1.10.1300.10,Pfam_domain:PF00233,SMART_domains:SM00471,Superfamily_domains:SSF109604 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 88 18213433 18213433 C T 1 0 0 0 0 1 0 0 0 11729 507 18 3 3 PDE4C 19 18213433 Missense_Mutation SNP C C3N-02067_T 5097203 18213433 40404183 33 27041 PEG3 0 . GRCh38 19 56816638 56816638 + Missense_Mutation SNP G G A rs199894739 C3N-02067_T C3N-02067_N G G c.1804C>T p.Arg602Cys p.R602C ENST00000326441 10/10 117 106 11 83 83 0 strelka-varscan-mutect PEG3,missense_variant,p.Arg602Cys,ENST00000326441,NM_001146186.1,NM_001146184.1,NM_006210.2;PEG3,missense_variant,p.Arg478Cys,ENST00000598410,NM_001146187.1;PEG3,missense_variant,p.Arg602Cys,ENST00000599534,;PEG3,missense_variant,p.Arg602Cys,ENST00000599577,;PEG3,missense_variant,p.Arg476Cys,ENST00000593695,NM_001146185.1;ZIM2,intron_variant,,ENST00000629319,NM_001146326.1,NM_001146327.1;ZIM2,intron_variant,,ENST00000599935,;ZIM2,intron_variant,,ENST00000593711,NM_015363.4;ZIM2,intron_variant,,ENST00000601070,;PEG3,downstream_gene_variant,,ENST00000600833,;ZIM2,intron_variant,,ENST00000595671,;ZIM2,intron_variant,,ENST00000597281,; A ENST00000326441 Transcript missense_variant 2168/8723 1804/4767 602/1588 R/C Cgt/Tgt rs199894739,COSM3960592,COSM3960593,COSM4081932,COSM4081933 1 -1 PEG3 HGNC HGNC:8826 protein_coding YES CCDS12948.1 ENSP00000326581 Q9GZU2 UPI000006D36D NM_001146186.1,NM_001146184.1,NM_006210.2 tolerated(0.05) 10/10 Low_complexity_(Seg):seg 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs199894739 . 0 201 9 0 0 0 0 0 -19.98583 0.9999834 1 1 1 0 A 3 1 88 56816638 56816638 G A 1 0 0 0 0 1 0 0 0 11808 1145 40 1 1 PEG3 19 56816638 Missense_Mutation SNP G C3N-02067_T 38603205 56816638 1800978 34 27042 SNX21 0 . GRCh38 20 45840710 45840710 + Silent SNP G G A rs752760310 C3N-02067_T C3N-02067_N G G c.519G>A p.= p.S173S ENST00000491381 4/4 318 301 17 253 253 0 strelka-varscan-mutect SNX21,synonymous_variant,p.=,ENST00000372542,;SNX21,synonymous_variant,p.=,ENST00000491381,NM_033421.3;SNX21,synonymous_variant,p.=,ENST00000342644,NM_001042632.2,NM_152897.2;SNX21,3_prime_UTR_variant,,ENST00000462307,NM_001042633.2;SNX21,3_prime_UTR_variant,,ENST00000372541,;ACOT8,downstream_gene_variant,,ENST00000217455,NM_005469.3;ACOT8,downstream_gene_variant,,ENST00000487205,;SNX21,downstream_gene_variant,,ENST00000614929,;SNX21,non_coding_transcript_exon_variant,,ENST00000344780,;SNX21,non_coding_transcript_exon_variant,,ENST00000472219,;SNX21,non_coding_transcript_exon_variant,,ENST00000478230,;SNX21,non_coding_transcript_exon_variant,,ENST00000465997,;SNX21,non_coding_transcript_exon_variant,,ENST00000372547,;SNX21,non_coding_transcript_exon_variant,,ENST00000486336,;ACOT8,downstream_gene_variant,,ENST00000484975,;ACOT8,downstream_gene_variant,,ENST00000493118,;ACOT8,downstream_gene_variant,,ENST00000484783,;ACOT8,downstream_gene_variant,,ENST00000461272,;ACOT8,downstream_gene_variant,,ENST00000483141,;ACOT8,downstream_gene_variant,,ENST00000488679,;ACOT8,downstream_gene_variant,,ENST00000486165,; A ENST00000491381 Transcript synonymous_variant 587/1607 519/1122 173/373 S tcG/tcA rs752760310 1 1 SNX21 HGNC HGNC:16154 protein_coding YES CCDS13377.1 ENSP00000418593 Q969T3 UPI0000135B51 NM_033421.3 4/4 PROSITE_profiles:PS50195,hmmpanther:PTHR20939:SF10,hmmpanther:PTHR20939,Pfam_domain:PF00787,Gene3D:3.30.1520.10,SMART_domains:SM00312,Superfamily_domains:SSF64268 LOW 1 SNV 1 1 PASS rs752760310 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 88 45840710 45840710 G A 1 0 0 0 0 0 0 0 1 15214 1103 39 1 1 SNX21 20 45840710 Silent SNP G C3N-02067_T 45840710 18603457 35 27043 VWA5B1 0 . GRCh38 1 20337827 20337827 + Missense_Mutation SNP T T G novel C3N-02087_T C3N-02087_N T T c.2124T>G p.Ile708Met p.I708M ENST00000375079 14/22 107 99 8 97 96 1 strelka-varscan-mutect VWA5B1,missense_variant,p.Ile708Met,ENST00000289815,NM_001039500.2;VWA5B1,missense_variant,p.Ile708Met,ENST00000375079,;VWA5B1,non_coding_transcript_exon_variant,,ENST00000525343,;VWA5B1,missense_variant,p.Ile135Met,ENST00000467486,;VWA5B1,3_prime_UTR_variant,,ENST00000485375,;VWA5B1,3_prime_UTR_variant,,ENST00000473325,; G ENST00000375079 Transcript missense_variant 2320/3859 2124/3663 708/1220 I/M atT/atG 1 1 VWA5B1 HGNC HGNC:26538 protein_coding YES ENSP00000364220 Q5TIE3 UPI000066D8B8 tolerated(0.23) 14/22 hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF109 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 20337827 20337827 T G 1 0 0 0 0 1 0 0 0 17797 1800 63 5 5 VWA5B1 1 20337827 Missense_Mutation SNP T C3N-02087_T 20337827 228618595 1 27044 PATJ 0 . GRCh38 1 61927829 61927829 + Nonsense_Mutation SNP C C T rs371868730 C3N-02087_T C3N-02087_N C C c.3670C>T p.Gln1224Ter p.Q1224* ENST00000371158 27/43 135 113 22 85 85 0 strelka-varscan-mutect PATJ,stop_gained,p.Gln1224Ter,ENST00000371158,NM_176877.2;PATJ,stop_gained,p.Gln70Ter,ENST00000494842,;PATJ,stop_gained,p.Gln40Ter,ENST00000490547,;PATJ,intron_variant,,ENST00000613764,;PATJ,stop_gained,p.Gln683Ter,ENST00000484937,;PATJ,splice_region_variant,,ENST00000484562,;PATJ,splice_region_variant,,ENST00000459752,;PATJ,splice_region_variant,,ENST00000635023,;PATJ,splice_region_variant,,ENST00000635214,; T ENST00000371158 Transcript stop_gained,splice_region_variant 3784/8505 3670/5406 1224/1801 Q/* Caa/Taa rs371868730,COSM1126970 1 1 PATJ HGNC HGNC:28881 protein_coding YES CCDS617.2 ENSP00000360200 Q8NI35 UPI0000204487 NM_176877.2 27/43 0,1 HIGH 1 SNV 5 0,1 1 PASS rs371868730 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 89 61927829 61927829 C T 1 0 0 0 0 0 1 0 0 11558 666 23 1 1 PATJ 1 61927829 Nonsense_Mutation SNP C C3N-02087_T 41590002 61927829 187028593 2 27045 RPRD2 0 . GRCh38 1 150473192 150473192 + Frame_Shift_Del DEL G G - rs758905047 C3N-02087_T C3N-02087_N G G c.4245delG p.Ser1416ValfsTer21 p.S1416Vfs*21 ENST00000369068 11/11 222 206 16 173 173 0 sindel-varindel-pindel RPRD2,frameshift_variant,p.Ser1390ValfsTer21,ENST00000401000,NM_001297674.1,NM_001297673.1;RPRD2,frameshift_variant,p.Ser1416ValfsTer21,ENST00000369068,NM_015203.4;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,; - ENST00000369068 Transcript frameshift_variant 4248/4612 4244/4386 1415/1461 R/X cGg/cg rs758905047 1 1 RPRD2 HGNC HGNC:29039 protein_coding YES CCDS44216.1 ENSP00000358064 Q5VT52 UPI00001D7CA8 NM_015203.4 11/11 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 89 150473192 150473192 G - 1 0 1 0 1 0 0 0 0 13871 1116 39 0 0 RPRD2 1 150473192 Frame_Shift_Del DEL G C3N-02087_T 88545363 150473192 98483230 3 27046 ISG20L2 0 . GRCh38 1 156727477 156727477 + Nonsense_Mutation SNP G G T novel C3N-02087_T C3N-02087_N G G c.176C>A p.Ser59Ter p.S59* ENST00000313146 1/3 229 198 31 168 168 0 strelka-varscan-mutect ISG20L2,stop_gained,p.Ser59Ter,ENST00000313146,NM_001303095.1;ISG20L2,stop_gained,p.Ser59Ter,ENST00000368219,;RRNAD1,upstream_gene_variant,,ENST00000368216,NM_015997.3;RRNAD1,upstream_gene_variant,,ENST00000368218,NM_001142560.1;RRNAD1,upstream_gene_variant,,ENST00000519086,;RRNAD1,upstream_gene_variant,,ENST00000476229,;RRNAD1,upstream_gene_variant,,ENST00000484742,;RRNAD1,upstream_gene_variant,,ENST00000524343,;RRNAD1,upstream_gene_variant,,ENST00000522237,;ISG20L2,non_coding_transcript_exon_variant,,ENST00000470713,;ISG20L2,non_coding_transcript_exon_variant,,ENST00000469074,;ISG20L2,upstream_gene_variant,,ENST00000472824,;ISG20L2,upstream_gene_variant,,ENST00000496538,;RRNAD1,upstream_gene_variant,,ENST00000517871,; T ENST00000313146 Transcript stop_gained 959/3303 176/1062 59/353 S/* tCa/tAa 1 -1 ISG20L2 HGNC HGNC:25745 protein_coding YES CCDS1153.1 ENSP00000323424 Q9H9L3 UPI000006D42B NM_001303095.1 1/3 hmmpanther:PTHR12801,hmmpanther:PTHR12801:SF78 HIGH 1 SNV 1 1 PASS rs1054598245 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 89 156727477 156727477 G T 1 0 0 0 0 0 1 0 0 7762 1294 45 2 2 ISG20L2 1 156727477 Nonsense_Mutation SNP G C3N-02087_T 6254285 156727477 92228945 4 27047 KDM5B 0 . GRCh38 1 202741600 202741600 + Silent SNP A A G novel C3N-02087_T C3N-02087_N A A c.2712T>C p.= p.L904L ENST00000367265 19/27 385 313 72 254 254 0 strelka-varscan-mutect KDM5B,synonymous_variant,p.=,ENST00000367265,NM_006618.3;KDM5B,synonymous_variant,p.=,ENST00000367264,;KDM5B,synonymous_variant,p.=,ENST00000235790,;KDM5B,downstream_gene_variant,,ENST00000498276,; G ENST00000367265 Transcript synonymous_variant 3877/10345 2712/4635 904/1544 L ctT/ctC 1 -1 KDM5B HGNC HGNC:18039 protein_coding YES CCDS30974.1 ENSP00000356234 Q9UGL1 UPI0000032AA2 NM_006618.3 19/27 Pfam_domain:PF08429,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 89 202741600 202741600 A G 1 0 0 0 0 0 0 0 1 8052 233 9 5 5 KDM5B 1 202741600 Silent SNP A C3N-02087_T 46014123 202741600 46214822 5 27048 DDX1 0 . GRCh38 2 15607303 15607303 + Missense_Mutation SNP C C T novel C3N-02087_T C3N-02087_N C C c.946C>T p.Pro316Ser p.P316S ENST00000381341 14/27 122 108 14 122 122 0 varscan-mutect DDX1,missense_variant,p.Pro316Ser,ENST00000381341,;DDX1,missense_variant,p.Pro316Ser,ENST00000233084,NM_004939.2;DDX1,missense_variant,p.Pro235Ser,ENST00000617198,;DDX1,missense_variant,p.Pro235Ser,ENST00000621973,; T ENST00000381341 Transcript missense_variant 1335/2817 946/2223 316/740 P/S Cct/Tct 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 deleterious(0) 14/27 PROSITE_profiles:PS51192,hmmpanther:PTHR24031:SF307,hmmpanther:PTHR24031,Pfam_domain:PF00270,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 15607303 15607303 C T 1 0 0 0 0 1 0 0 0 4145 855 30 3 3 DDX1 2 15607303 Missense_Mutation SNP C C3N-02087_T 15607303 226586226 6 27049 SLC8A1 0 . GRCh38 2 40429380 40429380 + Missense_Mutation SNP C C T novel C3N-02087_T C3N-02087_N C C c.901G>A p.Glu301Lys p.E301K ENST00000403092 2/11 159 149 10 183 183 0 strelka-varscan-mutect SLC8A1,missense_variant,p.Glu301Lys,ENST00000406785,;SLC8A1,missense_variant,p.Glu301Lys,ENST00000403092,;SLC8A1,missense_variant,p.Glu301Lys,ENST00000405901,NM_001112800.1;SLC8A1,missense_variant,p.Glu301Lys,ENST00000402441,NM_001112802.1;SLC8A1,missense_variant,p.Glu301Lys,ENST00000405269,;SLC8A1,missense_variant,p.Glu301Lys,ENST00000332839,NM_021097.2;SLC8A1,missense_variant,p.Glu301Lys,ENST00000408028,NM_001112801.1,NM_001252624.1;SLC8A1,missense_variant,p.Glu301Lys,ENST00000406391,;SLC8A1,downstream_gene_variant,,ENST00000417271,;SLC8A1,downstream_gene_variant,,ENST00000455476,;SLC8A1,downstream_gene_variant,,ENST00000448531,;SLC8A1,missense_variant,p.Glu298Lys,ENST00000407929,; T ENST00000403092 Transcript missense_variant 935/3178 901/2922 301/973 E/K Gaa/Aaa 1 -1 SLC8A1 HGNC HGNC:11068 protein_coding YES CCDS1806.1 ENSP00000384763 P32418 UPI000012FC46 tolerated(0.65) 2/11 Pfam_domain:PF16494,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF6,TIGRFAM_domain:TIGR00845 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 40429380 40429380 C T 1 0 0 0 0 1 0 0 0 14989 835 29 3 3 SLC8A1 2 40429380 Missense_Mutation SNP C C3N-02087_T 24822077 40429380 201764149 7 27050 TTN 0 . GRCh38 2 178568461 178568461 + Missense_Mutation SNP G G A novel C3N-02087_T C3N-02087_N G G c.77671C>T p.Pro25891Ser p.P25891S ENST00000589042 326/363 279 264 15 248 247 1 strelka-mutect TTN,missense_variant,p.Pro25891Ser,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Pro24250Ser,ENST00000591111,;TTN,missense_variant,p.Pro24250Ser,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Pro23323Ser,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Pro16826Ser,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Pro17018Ser,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Pro16951Ser,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,; A ENST00000589042 Transcript missense_variant 77896/109224 77671/107976 25891/35991 P/S Cct/Tct 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF48726,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS rs1214607347 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 89 178568461 178568461 G A 1 0 0 0 0 1 0 0 0 17245 1261 44 3 3 TTN 2 178568461 Missense_Mutation SNP G C3N-02087_T 138139081 178568461 63625068 8 27051 EPHA3 0 . GRCh38 3 89210003 89210003 + Silent SNP C C A novel C3N-02087_T C3N-02087_N C C c.297C>A p.= p.L99L ENST00000336596 3/17 198 186 12 199 199 0 strelka-varscan-mutect EPHA3,synonymous_variant,p.=,ENST00000336596,NM_005233.5;EPHA3,synonymous_variant,p.=,ENST00000494014,;EPHA3,synonymous_variant,p.=,ENST00000452448,NM_182644.2; A ENST00000336596 Transcript synonymous_variant 522/5809 297/2952 99/983 L ctC/ctA 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS rs1027305939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 89 89210003 89210003 C A 1 0 0 0 0 0 0 0 1 5015 813 29 2 2 EPHA3 3 89210003 Silent SNP C C3N-02087_T 89210003 109085556 9 27052 MASP1 0 . GRCh38 3 187253314 187253314 + Missense_Mutation SNP A A T novel C3N-02087_T C3N-02087_N A A c.746T>A p.Ile249Asn p.I249N ENST00000296280 6/11 383 357 26 294 292 2 strelka-varscan-mutect MASP1,missense_variant,p.Ile249Asn,ENST00000337774,NM_001879.5;MASP1,missense_variant,p.Ile249Asn,ENST00000296280,NM_139125.3;MASP1,missense_variant,p.Ile136Asn,ENST00000392472,;MASP1,missense_variant,p.Ile249Asn,ENST00000169293,NM_001031849.2;MASP1,missense_variant,p.Ile223Asn,ENST00000392470,;MASP1,downstream_gene_variant,,ENST00000392475,;MASP1,intron_variant,,ENST00000495249,;MASP1,downstream_gene_variant,,ENST00000490558,;MASP1,downstream_gene_variant,,ENST00000460839,;MASP1,upstream_gene_variant,,ENST00000483719,; T ENST00000296280 Transcript missense_variant,splice_region_variant 972/4015 746/2187 249/728 I/N aTc/aAc 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 deleterious(0.02) 6/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS01180,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 187253314 187253314 A T 1 0 0 0 0 1 0 0 0 9248 347 12 4 4 MASP1 3 187253314 Missense_Mutation SNP A C3N-02087_T 98043311 187253314 11042245 10 27053 MUC4 0 . GRCh38 3 195787436 195787436 + Missense_Mutation SNP G G A novel C3N-02087_T C3N-02087_N G G c.4144C>T p.Leu1382Phe p.L1382F ENST00000463781 2/25 14 10 4 15 15 0 varscan-mutect MUC4,missense_variant,p.Leu1382Phe,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Leu1382Phe,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Leu1382Phe,ENST00000478156,;MUC4,missense_variant,p.Leu1382Phe,ENST00000466475,;MUC4,missense_variant,p.Leu1382Phe,ENST00000477756,;MUC4,missense_variant,p.Leu1382Phe,ENST00000477086,;MUC4,missense_variant,p.Leu1382Phe,ENST00000480843,;MUC4,missense_variant,p.Leu1382Phe,ENST00000462323,;MUC4,missense_variant,p.Leu1382Phe,ENST00000470451,;MUC4,missense_variant,p.Leu1382Phe,ENST00000479406,; A ENST00000463781 Transcript missense_variant 4604/17110 4144/16239 1382/5412 L/F Ctt/Ttt 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 deleterious_low_confidence(0.04) 2/25 MODERATE 1 SNV 5 1 PASS rs1449285184 . 7 147 46 8 0 2 0 0 -2.805877 0.1284767 0 1 0 0 A 3 1 89 195787436 195787436 G A 1 0 0 0 0 1 0 0 0 9977 1000 35 3 3 MUC4 3 195787436 Missense_Mutation SNP G C3N-02087_T 8534122 195787436 2508123 11 27054 ZFYVE16 0 . GRCh38 5 80437641 80437641 + Nonsense_Mutation SNP C C A novel C3N-02087_T C3N-02087_N C C c.956C>A p.Ser319Ter p.S319* ENST00000338008 3/18 95 88 7 90 90 0 strelka-varscan-mutect ZFYVE16,stop_gained,p.Ser319Ter,ENST00000338008,NM_014733.4;ZFYVE16,stop_gained,p.Ser319Ter,ENST00000510158,NM_001105251.2;ZFYVE16,stop_gained,p.Ser319Ter,ENST00000505560,NM_001284236.1;ZFYVE16,downstream_gene_variant,,ENST00000509562,;ZFYVE16,upstream_gene_variant,,ENST00000511050,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000512558,;ZFYVE16,non_coding_transcript_exon_variant,,ENST00000510995,; A ENST00000338008 Transcript stop_gained 1136/6773 956/4620 319/1539 S/* tCa/tAa 1 1 ZFYVE16 HGNC HGNC:20756 protein_coding YES CCDS4050.1 ENSP00000337159 Q7Z3T8 UPI000013F4A0 NM_014733.4 3/18 hmmpanther:PTHR22835:SF43,hmmpanther:PTHR22835,PIRSF_domain:PIRSF037289 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.63158 1 1 1 1 0 A 4 1 89 80437641 80437641 C A 1 0 0 0 0 0 1 0 0 18242 838 29 2 2 ZFYVE16 5 80437641 Nonsense_Mutation SNP C C3N-02087_T 80437641 101100618 12 27055 VCAN 0 . GRCh38 5 83521689 83521689 + Missense_Mutation SNP C C T novel C3N-02087_T C3N-02087_N C C c.3383C>T p.Pro1128Leu p.P1128L ENST00000265077 7/15 146 129 17 147 147 0 strelka-varscan-mutect VCAN,missense_variant,p.Pro1128Leu,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Pro1128Leu,ENST00000342785,NM_001164098.1;VCAN,missense_variant,p.Pro1080Leu,ENST00000512590,;VCAN,intron_variant,,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000513960,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,intron_variant,,ENST00000515397,; T ENST00000265077 Transcript missense_variant 3948/12625 3383/10191 1128/3396 P/L cCa/cTa 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.09) 7/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 83521689 83521689 C T 1 0 0 0 0 1 0 0 0 17683 594 21 3 3 VCAN 5 83521689 Missense_Mutation SNP C C3N-02087_T 3084048 83521689 98016570 13 27056 JAKMIP2 0 . GRCh38 5 147612347 147612347 + Frame_Shift_Del DEL T T - novel C3N-02087_T C3N-02087_N T T c.2371delA p.Thr791GlnfsTer8 p.T791Qfs*8 ENST00000616793 20/22 129 115 14 121 121 0 sindel-varindel-pindel JAKMIP2,frameshift_variant,p.Thr791GlnfsTer8,ENST00000616793,NM_001270941.1;JAKMIP2,frameshift_variant,p.Thr791GlnfsTer8,ENST00000265272,NM_014790.4;JAKMIP2,frameshift_variant,p.Thr770GlnfsTer8,ENST00000507386,NM_001270934.1;JAKMIP2,frameshift_variant,p.Thr749GlnfsTer8,ENST00000333010,NM_001282282.1;JAKMIP2-AS1,intron_variant,,ENST00000626945,;JAKMIP2-AS1,intron_variant,,ENST00000627433,;JAKMIP2-AS1,intron_variant,,ENST00000630514,; - ENST00000616793 Transcript frameshift_variant 2912/9272 2371/2463 791/820 T/X Aca/ca 1 -1 JAKMIP2 HGNC HGNC:29067 protein_coding YES CCDS75352.1 ENSP00000479248 Q96AA8 UPI0000E5AC9B NM_001270941.1 20/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF7 HIGH deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 89 147612347 147612347 T - 1 0 1 0 1 0 0 0 0 7854 1725 60 0 0 JAKMIP2 5 147612347 Frame_Shift_Del DEL T C3N-02087_T 64090658 147612347 33925912 14 27057 EXOC2 0 . GRCh38 6 598883 598883 + Missense_Mutation SNP G G A C3N-02087_T C3N-02087_N G G c.947C>T p.Thr316Met p.T316M ENST00000230449 9/28 166 149 17 156 156 0 strelka-varscan-mutect EXOC2,missense_variant,p.Thr316Met,ENST00000230449,NM_018303.5; A ENST00000230449 Transcript missense_variant 1083/4449 947/2775 316/924 T/M aCg/aTg COSM5484859 1 -1 EXOC2 HGNC HGNC:24968 protein_coding YES CCDS34327.1 ENSP00000230449 Q96KP1 A0A024QZT2 UPI000003E7E3 NM_018303.5 deleterious(0) 9/28 hmmpanther:PTHR13043,Pfam_domain:PF15469 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 89 598883 598883 G A 1 0 0 0 0 1 0 0 0 5169 1145 40 1 1 EXOC2 6 598883 Missense_Mutation SNP G C3N-02087_T 598883 170207096 15 27058 C4B 0 . GRCh38 6 32028773 32028773 + Missense_Mutation SNP C C G novel C3N-02087_T C3N-02087_N C C c.3311C>G p.Ser1104Cys p.S1104C ENST00000435363 26/41 353 303 50 259 258 1 varscan-mutect C4B,missense_variant,p.Ser1104Cys,ENST00000435363,NM_001002029.3;C4B,missense_variant,p.Ser1104Cys,ENST00000425700,;C4B-AS1,downstream_gene_variant,,ENST00000415626,;C4B,upstream_gene_variant,,ENST00000468936,;C4B,upstream_gene_variant,,ENST00000463249,;C4B,downstream_gene_variant,,ENST00000461632,;C4B,upstream_gene_variant,,ENST00000468237,;C4B,upstream_gene_variant,,ENST00000485263,;C4B,upstream_gene_variant,,ENST00000478388,;C4B,downstream_gene_variant,,ENST00000474912,;C4B,upstream_gene_variant,,ENST00000486992,;C4B,downstream_gene_variant,,ENST00000478438,; G ENST00000435363 Transcript missense_variant 3395/5460 3311/5235 1104/1744 S/C tCt/tGt 1 1 C4B HGNC HGNC:1324 protein_coding YES CCDS47405.1 ENSP00000415941 P0C0L5 UPI000016A806 NM_001002029.3 deleterious(0.04) 26/41 hmmpanther:PTHR11412:SF96,hmmpanther:PTHR11412,Gene3D:1.50.10.20,Pfam_domain:PF07678,Superfamily_domains:SSF48239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 32028773 32028773 C G 1 0 0 0 0 1 0 0 0 2075 913 32 4 4 C4B 6 32028773 Missense_Mutation SNP C C3N-02087_T 31429890 32028773 138777206 16 27059 SP8 0 . GRCh38 7 20784295 20784295 + Missense_Mutation SNP C C G novel C3N-02087_T C3N-02087_N C C c.1522G>C p.Glu508Gln p.E508Q ENST00000418710 2/2 80 76 4 46 46 0 strelka-mutect SP8,missense_variant,p.Glu466Gln,ENST00000617581,;SP8,missense_variant,p.Glu490Gln,ENST00000361443,NM_198956.3;SP8,missense_variant,p.Glu508Gln,ENST00000418710,NM_182700.5; G ENST00000418710 Transcript missense_variant 1610/1618 1522/1527 508/508 E/Q Gag/Cag 1 -1 SP8 HGNC HGNC:19196 protein_coding YES CCDS43555.1 ENSP00000408792 Q8IXZ3 UPI00001AADF2 NM_182700.5 deleterious_low_confidence(0) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 20784295 20784295 C G 1 0 0 0 0 1 0 0 0 15296 922 32 4 4 SP8 7 20784295 Missense_Mutation SNP C C3N-02087_T 20784295 138561678 17 27060 VWC2 0 . GRCh38 7 49775630 49775630 + Frame_Shift_Del DEL G G - rs747210205 C3N-02087_T C3N-02087_N G G c.196delG p.Ala66ArgfsTer28 p.A66Rfs*28 ENST00000340652 2/4 117 100 17 88 88 0 sindel-varindel-pindel VWC2,frameshift_variant,p.Ala66ArgfsTer28,ENST00000340652,NM_198570.3; - ENST00000340652 Transcript frameshift_variant 751/11299 195/978 65/325 P/X ccG/cc rs747210205 1 1 VWC2 HGNC HGNC:30200 protein_coding YES CCDS5508.1 ENSP00000341819 Q2TAL6 UPI00002373A5 NM_198570.3 2/4 HIGH 1 deletion 1 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 89 49775630 49775630 G - 1 0 1 0 1 0 0 0 0 17802 1103 39 0 0 VWC2 7 49775630 Frame_Shift_Del DEL G C3N-02087_T 28991335 49775630 109570343 18 27061 EGFR 0 . GRCh38 7 55174774 55174791 + In_Frame_Del DEL AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT - rs121913422 C3N-02087_T C3N-02087_N AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT c.2237_2254delAATTAAGAGAAGCAACAT p.Glu746_Ser752delinsAla p.E746_S752delinsA ENST00000275493 19/28 535 451 84 411 411 0 sindel-varindel EGFR,inframe_deletion,p.Glu746_Ser752delinsAla,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2414-2431/9821 2237-2254/3633 746-752/1210 ELREATS/A gAATTAAGAGAAGCAACATct/gct rs121913422,COSM12367 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 89 55174774 55174774 AATTAAGAGAAGCAACAT - 1 0 1 0 1 0 0 0 0 4803 246 9 0 0 EGFR 7 55174774 In_Frame_Del DEL AATTAAGAGAAGCAACAT C3N-02087_T 5399144 55174774 104171199 19 27062 ADRA1A 0 . GRCh38 8 26770525 26770525 + Missense_Mutation SNP C C G novel C3N-02087_T C3N-02087_N C C c.1025G>C p.Arg342Thr p.R342T ENST00000380586 2/3 191 181 10 205 205 0 strelka-varscan-mutect ADRA1A,missense_variant,p.Arg342Thr,ENST00000380573,;ADRA1A,missense_variant,p.Arg342Thr,ENST00000380586,NM_033303.3;ADRA1A,missense_variant,p.Arg342Thr,ENST00000276393,NM_000680.2;ADRA1A,missense_variant,p.Arg342Thr,ENST00000380582,NM_033302.2;ADRA1A,missense_variant,p.Arg342Thr,ENST00000519229,;ADRA1A,missense_variant,p.Arg342Thr,ENST00000354550,NM_033304.2;ADRA1A,non_coding_transcript_exon_variant,,ENST00000518621,;ADRA1A,intron_variant,,ENST00000519096,;ADRA1A,intron_variant,,ENST00000521711,;RP11-384C12.1,upstream_gene_variant,,ENST00000486251,; G ENST00000380586 Transcript missense_variant 1461/2304 1025/1428 342/475 R/T aGa/aCa 1 -1 ADRA1A HGNC HGNC:277 protein_coding YES CCDS34869.1 ENSP00000369960 P35348 B0ZBD3 UPI000066DA42 NM_033303.3 tolerated(0.06) 2/3 Gene3D:1.20.1070.10,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF16,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 26770525 26770525 C G 1 0 0 0 0 1 0 0 0 410 913 32 4 4 ADRA1A 8 26770525 Missense_Mutation SNP C C3N-02087_T 26770525 118368111 20 27063 MAPKAP1 0 . GRCh38 9 125484523 125484523 + Missense_Mutation SNP T T C novel C3N-02087_T C3N-02087_N T T c.1127A>G p.Asp376Gly p.D376G ENST00000265960 9/12 189 167 22 167 167 0 strelka-varscan-mutect MAPKAP1,missense_variant,p.Asp376Gly,ENST00000265960,NM_001006617.1;MAPKAP1,missense_variant,p.Asp340Gly,ENST00000350766,NM_024117.3;MAPKAP1,missense_variant,p.Asp376Gly,ENST00000373498,;MAPKAP1,missense_variant,p.Asp184Gly,ENST00000373503,NM_001006620.1;MAPKAP1,missense_variant,p.Asp184Gly,ENST00000394063,NM_001006621.1;MAPKAP1,missense_variant,p.Asp148Gly,ENST00000420643,;MAPKAP1,intron_variant,,ENST00000373511,NM_001006619.1;MAPKAP1,upstream_gene_variant,,ENST00000444226,;MAPKAP1,non_coding_transcript_exon_variant,,ENST00000496063,;MAPKAP1,missense_variant,p.Asp148Gly,ENST00000497932,; C ENST00000265960 Transcript missense_variant 1460/3395 1127/1569 376/522 D/G gAt/gGt 1 -1 MAPKAP1 HGNC HGNC:18752 protein_coding YES CCDS35140.1 ENSP00000265960 Q9BPZ7 UPI00000372F6 NM_001006617.1 tolerated(0.29) 9/12 hmmpanther:PTHR13335 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 89 125484523 125484523 T C 1 0 0 0 0 1 0 0 0 9212 1435 50 5 5 MAPKAP1 9 125484523 Missense_Mutation SNP T C3N-02087_T 125484523 12910194 21 27064 MAPK8 0 . GRCh38 10 48434907 48434907 + Missense_Mutation SNP C C G C3N-02087_T C3N-02087_N C C c.1162C>G p.Gln388Glu p.Q388E ENST00000395611 12/12 110 100 10 70 70 0 strelka-varscan-mutect MAPK8,missense_variant,p.Gln388Glu,ENST00000395611,NM_001323330.1,NM_001323325.1,NM_001323323.1,NM_001323321.1,NM_001323322.1,NM_001278547.1;MAPK8,missense_variant,p.Gln388Glu,ENST00000374189,NM_001323329.1,NM_001323326.1,NM_001323324.1,NM_001323327.1,NM_001323331.1,NM_001323328.1,NM_001323302.1,NM_139049.2;MAPK8,missense_variant,p.Gln388Glu,ENST00000374176,;MAPK8,3_prime_UTR_variant,,ENST00000374182,NM_002750.3;MAPK8,3_prime_UTR_variant,,ENST00000374179,NM_139046.2;MAPK8,3_prime_UTR_variant,,ENST00000360332,NM_001323320.1,NM_001278548.1;MAPK8,non_coding_transcript_exon_variant,,ENST00000459755,;MAPK8,downstream_gene_variant,,ENST00000469879,;MAPK8,non_coding_transcript_exon_variant,,ENST00000469110,; G ENST00000395611 Transcript missense_variant 1394/5844 1162/1284 388/427 Q/E Cag/Gag COSM1745809 1 1 MAPK8 HGNC HGNC:6881 protein_coding YES CCDS7223.1 ENSP00000378974 P45983 A1L4K2 UPI000002AE0B NM_001323330.1,NM_001323325.1,NM_001323323.1,NM_001323321.1,NM_001323322.1,NM_001278547.1 tolerated_low_confidence(1) 12/12 hmmpanther:PTHR24055,hmmpanther:PTHR24055:SF222,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.8504 1 1 1 1 0 G 3 3 89 48434907 48434907 C G 1 0 0 0 0 1 0 0 0 9207 827 29 4 4 MAPK8 10 48434907 Missense_Mutation SNP C C3N-02087_T 48434907 85362515 22 27065 OIT3 0 . GRCh38 10 72900421 72900421 + Missense_Mutation SNP G G A novel C3N-02087_T C3N-02087_N G G c.481G>A p.Asp161Asn p.D161N ENST00000334011 3/9 194 175 19 132 132 0 strelka-varscan-mutect OIT3,missense_variant,p.Asp161Asn,ENST00000334011,NM_152635.2;OIT3,missense_variant,p.Asp161Asn,ENST00000622652,; A ENST00000334011 Transcript missense_variant 699/2365 481/1638 161/545 D/N Gat/Aat 1 1 OIT3 HGNC HGNC:29953 protein_coding YES CCDS7318.1 ENSP00000333900 Q8WWZ8 UPI00000389F9 NM_152635.2 tolerated(0.38) 3/9 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF326,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 89 72900421 72900421 G A 1 0 0 0 0 1 0 0 0 10924 942 33 3 3 OIT3 10 72900421 Missense_Mutation SNP G C3N-02087_T 24465514 72900421 60897001 23 27066 IDE 0 . GRCh38 10 92531860 92531860 + Silent SNP C C T novel C3N-02087_T C3N-02087_N C C c.549G>A p.= p.V183V ENST00000265986 4/25 130 120 10 172 172 0 strelka-varscan-mutect IDE,synonymous_variant,p.=,ENST00000265986,NM_001322795.1,NM_001322796.1,NM_004969.3;IDE,synonymous_variant,p.=,ENST00000436178,;IDE,3_prime_UTR_variant,,ENST00000478361,; T ENST00000265986 Transcript synonymous_variant 606/5877 549/3060 183/1019 V gtG/gtA 1 -1 IDE HGNC HGNC:5381 protein_coding YES CCDS7421.1 ENSP00000265986 P14735 UPI000013D6B6 NM_001322795.1,NM_001322796.1,NM_004969.3 4/25 hmmpanther:PTHR11851,hmmpanther:PTHR11851:SF155,Pfam_domain:PF00675,Gene3D:3.30.830.10,Superfamily_domains:SSF63411 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 89 92531860 92531860 C T 1 0 0 0 0 0 0 0 1 7393 813 29 3 3 IDE 10 92531860 Silent SNP C C3N-02087_T 19631439 92531860 41265562 24 27067 SLC35G1 0 . GRCh38 10 93900880 93900880 + Missense_Mutation SNP C C A C3N-02087_T C3N-02087_N C C c.488C>A p.Thr163Lys p.T163K ENST00000427197 3/3 294 271 23 281 281 0 strelka-varscan-mutect SLC35G1,missense_variant,p.Thr162Lys,ENST00000371408,NM_153226.2;SLC35G1,missense_variant,p.Thr163Lys,ENST00000427197,NM_001134658.1;SLC35G1,intron_variant,,ENST00000483386,;SLC35G1,intron_variant,,ENST00000603665,;SLC35G1,intron_variant,,ENST00000494992,;SLC35G1,intron_variant,,ENST00000605679,; A ENST00000427197 Transcript missense_variant 549/2402 488/1098 163/365 T/K aCg/aAg COSM198819 1 1 SLC35G1 HGNC HGNC:26607 protein_coding YES CCDS44459.1 ENSP00000400932 Q2M3R5 UPI000013FE98 NM_001134658.1 deleterious(0.03) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR22911,hmmpanther:PTHR22911:SF6,Pfam_domain:PF00892,Superfamily_domains:0043518 1 MODERATE 1 SNV 1 1 1 PASS rs1391420155 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 89 93900880 93900880 C A 1 0 0 0 0 1 0 0 0 14865 536 19 1 1 SLC35G1 10 93900880 Missense_Mutation SNP C C3N-02087_T 1369020 93900880 39896542 25 27068 KMT5B 0 . GRCh38 11 68158856 68158856 + Missense_Mutation SNP T T C rs763264500 C3N-02087_T C3N-02087_N T T c.1490A>G p.Glu497Gly p.E497G ENST00000304363 11/11 281 258 23 250 250 0 strelka-varscan-mutect KMT5B,missense_variant,p.Glu497Gly,ENST00000304363,NM_017635.4,NM_001300907.1;KMT5B,missense_variant,p.Glu497Gly,ENST00000615954,NM_001300908.1;KMT5B,3_prime_UTR_variant,,ENST00000441488,;KMT5B,3_prime_UTR_variant,,ENST00000427752,; C ENST00000304363 Transcript missense_variant 1844/5837 1490/2658 497/885 E/G gAg/gGg rs763264500 1 -1 KMT5B HGNC HGNC:24283 protein_coding YES CCDS31623.1 ENSP00000305899 Q4FZB7 UPI00003FF22C NM_017635.4,NM_001300907.1 tolerated(0.1) 11/11 hmmpanther:PTHR12977:SF12,hmmpanther:PTHR12977 MODERATE 1 SNV 5 1 PASS rs763264500 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 89 68158856 68158856 T C 1 0 0 0 0 1 0 0 0 8301 1551 54 5 5 KMT5B 11 68158856 Missense_Mutation SNP T C3N-02087_T 68158856 66927766 26 27069 NCAM1 0 . GRCh38 11 113275357 113275360 + Frame_Shift_Del DEL ACAG ACAG - novel C3N-02087_T C3N-02087_N ACAG ACAG c.2628_2631delGACA p.Thr877ArgfsTer? p.T877Rfs*? ENST00000619839 21/21 178 159 19 187 187 0 sindel-varindel-pindel NCAM1,frameshift_variant,p.Thr877ArgfsTer10,ENST00000615285,;NCAM1,frameshift_variant,p.Thr851ArgfsTer10,ENST00000615112,;NCAM1,frameshift_variant,p.Thr841ArgfsTer10,ENST00000618266,;NCAM1,frameshift_variant,p.Thr851ArgfsTer10,ENST00000316851,NM_181351.4;NCAM1,frameshift_variant,p.Thr877ArgfsTer?,ENST00000619839,NM_001242607.1;NCAM1,frameshift_variant,p.Thr841ArgfsTer10,ENST00000531044,NM_000615.6;NCAM1,frameshift_variant,p.Thr461ArgfsTer10,ENST00000528158,;NCAM1,frameshift_variant,p.Thr350ArgfsTer10,ENST00000533073,;NCAM1,frameshift_variant,p.Thr365ArgfsTer10,ENST00000528590,;NCAM1-AS1,upstream_gene_variant,,ENST00000526229,;RP11-839D17.3,downstream_gene_variant,,ENST00000529416,;NCAM1-AS1,upstream_gene_variant,,ENST00000533638,;RP11-839D17.3,downstream_gene_variant,,ENST00000526487,;RP11-839D17.3,downstream_gene_variant,,ENST00000533504,;NCAM1,non_coding_transcript_exon_variant,,ENST00000611284,;NCAM1,downstream_gene_variant,,ENST00000533226,; - ENST00000619839 Transcript frameshift_variant 2963-2966/2993 2625-2628/2655 875-876/884 TQ/X acACAG/ac 1 1 NCAM1 HGNC HGNC:7656 protein_coding YES CCDS73384.1 ENSP00000480132 A0A087WWD4 UPI00021269F1 NM_001242607.1 21/21 HIGH deletion 5 3 1 PASS . . 0 208 0 0 2 0 0 0 -8.275915 0.9941398 1 1 1 0 - 7 5 89 113275357 113275357 ACAG - 1 0 1 0 1 0 0 0 0 10218 146 6 0 0 NCAM1 11 113275357 Frame_Shift_Del DEL ACAG C3N-02087_T 45116501 113275357 21811265 27 27070 CKAP4 0 . GRCh38 12 106239846 106239846 + Silent SNP C C G rs781000102 C3N-02087_T C3N-02087_N C C c.987G>C p.= p.V329V ENST00000378026 2/2 215 203 12 198 198 0 strelka-varscan-mutect CKAP4,synonymous_variant,p.=,ENST00000378026,NM_006825.3;CKAP4,downstream_gene_variant,,ENST00000553039,;CKAP4,downstream_gene_variant,,ENST00000552828,; G ENST00000378026 Transcript synonymous_variant 1124/3093 987/1809 329/602 V gtG/gtC rs781000102 1 -1 CKAP4 HGNC HGNC:16991 protein_coding YES CCDS9103.1 ENSP00000367265 Q07065 A0A024RBH2 UPI00000723B9 NM_006825.3 2/2 hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF243 LOW 1 SNV 1 1 PASS rs781000102 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 89 106239846 106239846 C G 1 0 0 0 0 0 0 0 1 3207 813 29 4 4 CKAP4 12 106239846 Silent SNP C C3N-02087_T 106239846 27035463 28 27071 CUX2 0 . GRCh38 12 111320418 111320418 + Silent SNP G G A rs758742538 C3N-02087_T C3N-02087_N G G c.2409G>A p.= p.V803V ENST00000261726 17/22 316 298 18 218 218 0 strelka-varscan-mutect CUX2,synonymous_variant,p.=,ENST00000261726,NM_015267.3; A ENST00000261726 Transcript synonymous_variant 2563/6844 2409/4461 803/1486 V gtG/gtA rs758742538 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 17/22 Low_complexity_(Seg):seg,hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 LOW 1 SNV 1 1 PASS rs758742538 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 89 111320418 111320418 G A 1 0 0 0 0 0 0 0 1 3875 1364 48 3 3 CUX2 12 111320418 Silent SNP G C3N-02087_T 5080572 111320418 21954891 29 27072 GRK1 0 . GRCh38 13 113732938 113732938 + Missense_Mutation SNP G G A rs367690330 C3N-02087_T C3N-02087_N G G c.1249G>A p.Asp417Asn p.D417N ENST00000335678 6/7 272 252 20 244 244 0 strelka-varscan-mutect GRK1,missense_variant,p.Asp417Asn,ENST00000335678,;GRK1,non_coding_transcript_exon_variant,,ENST00000545304,;GRK1,upstream_gene_variant,,ENST00000606140,; A ENST00000335678 Transcript missense_variant 1481/4296 1249/1692 417/563 D/N Gat/Aat rs367690330 1 1 GRK1 HGNC HGNC:10013 protein_coding YES ENSP00000334876 Q15835 UPI0000133B08 tolerated(0.14) 6/7 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF11,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs367690330 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 89 113732938 113732938 G A 1 0 0 0 0 1 0 0 0 6671 1290 45 3 3 GRK1 13 113732938 Missense_Mutation SNP G C3N-02087_T 113732938 631390 30 27073 GSC 0 . GRCh38 14 94768635 94768635 + Missense_Mutation SNP G G T novel C3N-02087_T C3N-02087_N G G c.630C>A p.Asn210Lys p.N210K ENST00000238558 3/3 397 361 36 259 258 1 strelka-varscan-mutect GSC,missense_variant,p.Asn210Lys,ENST00000238558,NM_173849.2; T ENST00000238558 Transcript missense_variant 845/1264 630/774 210/257 N/K aaC/aaA 1 -1 GSC HGNC HGNC:4612 protein_coding YES CCDS9930.1 ENSP00000238558 P56915 UPI000000D86A NM_173849.2 deleterious(0.02) 3/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF275,hmmpanther:PTHR24329,PROSITE_patterns:PS00027,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 94768635 94768635 G T 1 0 0 0 0 1 0 0 0 6696 1252 44 2 2 GSC 14 94768635 Missense_Mutation SNP G C3N-02087_T 94768635 12275083 31 27074 VRK1 0 . GRCh38 14 96856208 96856208 + Missense_Mutation SNP A A C novel C3N-02087_T C3N-02087_N A A c.788A>C p.Asp263Ala p.D263A ENST00000216639 9/13 255 238 17 261 261 0 strelka-varscan-mutect VRK1,missense_variant,p.Asp263Ala,ENST00000216639,NM_003384.2;VRK1,missense_variant,p.Asp120Ala,ENST00000557222,;VRK1,missense_variant,p.Asp45Ala,ENST00000557352,;VRK1,upstream_gene_variant,,ENST00000555067,;VRK1,downstream_gene_variant,,ENST00000555351,; C ENST00000216639 Transcript missense_variant 937/1745 788/1191 263/396 D/A gAt/gCt 1 1 VRK1 HGNC HGNC:12718 protein_coding YES CCDS9947.1 ENSP00000216639 Q99986 UPI0000073867 NM_003384.2 deleterious(0.05) 9/13 PROSITE_profiles:PS50011,hmmpanther:PTHR11909:SF78,hmmpanther:PTHR11909,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1428656431 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 89 96856208 96856208 A C 1 0 0 0 0 1 0 0 0 17768 333 12 5 5 VRK1 14 96856208 Missense_Mutation SNP A C3N-02087_T 2087573 96856208 10187510 32 27075 ACSBG1 0 . GRCh38 15 78173592 78173592 + Splice_Site SNP C C T novel C3N-02087_T C3N-02087_N C C c.2089+1G>A p.X697_splice ENST00000258873 114 108 6 95 95 0 strelka-varscan-mutect ACSBG1,splice_donor_variant,,ENST00000258873,NM_001199377.1,NM_015162.4;ACSBG1,splice_donor_variant,,ENST00000560817,;IDH3A,downstream_gene_variant,,ENST00000299518,NM_005530.2;IDH3A,downstream_gene_variant,,ENST00000558554,;IDH3A,downstream_gene_variant,,ENST00000559205,;IDH3A,downstream_gene_variant,,ENST00000558535,;ACSBG1,splice_donor_variant,,ENST00000560124,;IDH3A,downstream_gene_variant,,ENST00000559889,;IDH3A,downstream_gene_variant,,ENST00000558602,;IDH3A,downstream_gene_variant,,ENST00000560667,;IDH3A,downstream_gene_variant,,ENST00000559803,;ACSBG1,downstream_gene_variant,,ENST00000560183,;IDH3A,downstream_gene_variant,,ENST00000558016,;IDH3A,downstream_gene_variant,,ENST00000557960,; T ENST00000258873 Transcript splice_donor_variant -/6357 2089/2175 697/724 1 -1 ACSBG1 HGNC HGNC:29567 protein_coding YES CCDS10298.1 ENSP00000258873 Q96GR2 UPI000006E955 NM_001199377.1,NM_015162.4 13/13 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 89 78173592 78173592 C T 1 0 0 0 0 0 0 1 0 215 521 18 3 3 ACSBG1 15 78173592 Splice_Site SNP C C3N-02087_T 78173592 23817597 33 27076 TP53 0 . GRCh38 17 7674233 7674233 + Missense_Mutation SNP C C T C3N-02087_T C3N-02087_N C C c.730G>A p.Gly244Ser p.G244S ENST00000269305 7/11 270 235 35 211 211 0 strelka-varscan-mutect TP53,missense_variant,p.Gly244Ser,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly244Ser,ENST00000420246,;TP53,missense_variant,p.Gly205Ser,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly205Ser,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly244Ser,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly205Ser,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly244Ser,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly205Ser,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly244Ser,ENST00000445888,;TP53,missense_variant,p.Gly205Ser,ENST00000619485,;TP53,missense_variant,p.Gly112Ser,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly85Ser,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly112Ser,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly85Ser,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly112Ser,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly85Ser,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly244Ser,ENST00000359597,;TP53,missense_variant,p.Gly233Ser,ENST00000615910,;TP53,missense_variant,p.Gly244Ser,ENST00000413465,;TP53,missense_variant,p.Gly112Ser,ENST00000509690,;TP53,missense_variant,p.Gly151Ser,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Gly205Ser,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; T ENST00000269305 Transcript missense_variant 920/2579 730/1182 244/393 G/S Ggc/Agc TP53_g.13367del,TP53_g.13367G>A,TP53_g.13367G>T,TP53_g.13367G>C,COSM10941,COSM11524,COSM1646853,COSM1716873,COSM3355992,COSM3733384,COSM3970348,COSM3970349,COSM44221,COSM44940,COSM673602,COSM673603,COSM673604,COSM984898,COSM984900,COSM984901,COSM99683,COSM99684,COSM99685 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs1057519989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 7674233 7674233 C T 1 0 0 0 0 1 0 0 0 16859 623 22 3 3 TP53 17 7674233 Missense_Mutation SNP C C3N-02087_T 7674233 75583208 34 27077 CCR7 0 . GRCh38 17 40555795 40555795 + Silent SNP G G A rs765607390 C3N-02087_T C3N-02087_N G G c.84C>T p.= p.V28V ENST00000246657 3/3 98 87 11 85 85 0 strelka-varscan-mutect CCR7,synonymous_variant,p.=,ENST00000246657,NM_001301714.1,NM_001838.3;CCR7,synonymous_variant,p.=,ENST00000579344,NM_001301718.1,NM_001301716.1,NM_001301717.1;CCR7,5_prime_UTR_variant,,ENST00000578085,; A ENST00000246657 Transcript synonymous_variant 147/2173 84/1137 28/378 V gtC/gtT rs765607390 1 -1 CCR7 HGNC HGNC:1608 protein_coding YES CCDS11369.1 ENSP00000246657 P32248 A0N0Q0 UPI0000001C2F NM_001301714.1,NM_001838.3 3/3 Prints_domain:PR00641,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF635 LOW 1 SNV 1 1 PASS rs765607390 . 0 208 2 0 0 0 0 0 -19.99965 1 1 1 1 0 A 2 1 89 40555795 40555795 G A 1 0 0 0 0 0 0 0 1 2646 1277 45 3 3 CCR7 17 40555795 Silent SNP G C3N-02087_T 32881562 40555795 42701646 35 27078 DNAJC7 0 . GRCh38 17 41977318 41977318 + Missense_Mutation SNP C C G rs781922631 C3N-02087_T C3N-02087_N C C c.1390G>C p.Asp464His p.D464H ENST00000457167 13/14 174 159 15 152 152 0 strelka-varscan-mutect DNAJC7,missense_variant,p.Asp464His,ENST00000457167,NM_003315.3;DNAJC7,missense_variant,p.Asp408His,ENST00000426588,NM_001144766.2;DNAJC7,missense_variant,p.Asp408His,ENST00000316603,;DNAJC7,missense_variant,p.Asp25His,ENST00000587727,;CNP,3_prime_UTR_variant,,ENST00000393892,NM_033133.4;CNP,downstream_gene_variant,,ENST00000393888,;CNP,downstream_gene_variant,,ENST00000472031,;CNP,downstream_gene_variant,,ENST00000592105,;DNAJC7,3_prime_UTR_variant,,ENST00000588814,;CNP,downstream_gene_variant,,ENST00000486438,;DNAJC7,downstream_gene_variant,,ENST00000586335,;DNAJC7,downstream_gene_variant,,ENST00000585693,; G ENST00000457167 Transcript missense_variant 1627/2022 1390/1485 464/494 D/H Gat/Cat rs781922631 1 -1 DNAJC7 HGNC HGNC:12392 protein_coding YES CCDS45677.1 ENSP00000406463 Q99615 UPI000013EC47 NM_003315.3 deleterious(0) 13/14 Gene3D:1.10.287.110,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF139,Superfamily_domains:SSF46565 MODERATE 1 SNV 1 1 PASS rs781922631 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 41977318 41977318 C G 1 0 0 0 0 1 0 0 0 4467 840 29 4 4 DNAJC7 17 41977318 Missense_Mutation SNP C C3N-02087_T 1421523 41977318 41280123 36 27079 MTCL1 0 . GRCh38 18 8784030 8784030 + Silent SNP C C T novel C3N-02087_T C3N-02087_N C C c.918C>T p.= p.L306L ENST00000359865 6/17 153 142 11 121 120 1 strelka-varscan-mutect MTCL1,synonymous_variant,p.=,ENST00000359865,NM_015210.3;MTCL1,synonymous_variant,p.=,ENST00000400050,;MTCL1,synonymous_variant,p.=,ENST00000517570,;MTCL1,synonymous_variant,p.=,ENST00000306329,;MTCL1,upstream_gene_variant,,ENST00000521018,;MTCL1,upstream_gene_variant,,ENST00000523811,;MTCL1,synonymous_variant,p.=,ENST00000520495,;MTCL1,upstream_gene_variant,,ENST00000517554,; T ENST00000359865 Transcript synonymous_variant 1060/6093 918/4761 306/1586 L ctC/ctT 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 6/17 Pfam_domain:PF11365,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 89 8784030 8784030 C T 1 0 0 0 0 0 0 0 1 9900 813 29 3 3 MTCL1 18 8784030 Silent SNP C C3N-02087_T 8784030 71589255 37 27080 SETBP1 0 . GRCh38 18 44949978 44949978 + Missense_Mutation SNP A A T novel C3N-02087_T C3N-02087_N A A c.638A>T p.Lys213Ile p.K213I ENST00000282030 4/6 303 282 21 307 307 0 strelka-varscan-mutect SETBP1,missense_variant,p.Lys213Ile,ENST00000282030,NM_015559.2; T ENST00000282030 Transcript missense_variant 934/9899 638/4791 213/1596 K/I aAa/aTa 1 1 SETBP1 HGNC HGNC:15573 protein_coding YES CCDS11923.2 ENSP00000282030 Q9Y6X0 UPI0000201C54 NM_015559.2 deleterious(0) 4/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 89 44949978 44949978 A T 1 0 0 0 0 1 0 0 0 14406 14 1 4 4 SETBP1 18 44949978 Missense_Mutation SNP A C3N-02087_T 36165948 44949978 35423307 38 27081 S1PR4 0 . GRCh38 19 3179798 3179798 + Missense_Mutation SNP G G C novel C3N-02087_T C3N-02087_N G G c.1006G>C p.Asp336His p.D336H ENST00000246115 1/1 66 61 5 56 56 0 strelka-mutect S1PR4,missense_variant,p.Asp336His,ENST00000246115,NM_003775.3;S1PR4,downstream_gene_variant,,ENST00000591346,; C ENST00000246115 Transcript missense_variant 1031/1565 1006/1155 336/384 D/H Gac/Cac 1 1 S1PR4 HGNC HGNC:3170 protein_coding YES CCDS12105.1 ENSP00000246115 O95977 UPI0000050462 NM_003775.3 deleterious(0.03) 1/1 hmmpanther:PTHR22750:SF13,hmmpanther:PTHR22750,Prints_domain:PR01526 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -11.74375 1 1 1 1 0 C 3 2 89 3179798 3179798 G C 1 0 0 0 0 1 0 0 0 14055 1174 41 4 4 S1PR4 19 3179798 Missense_Mutation SNP G C3N-02087_T 3179798 55437818 39 27082 TRMT1 0 . GRCh38 19 13109930 13109930 + Missense_Mutation SNP C C G novel C3N-02087_T C3N-02087_N C C c.1091G>C p.Gly364Ala p.G364A ENST00000592062 10/18 197 183 14 165 165 0 strelka-varscan-mutect TRMT1,missense_variant,p.Gly364Ala,ENST00000592062,;TRMT1,missense_variant,p.Gly364Ala,ENST00000437766,NM_017722.3;TRMT1,missense_variant,p.Gly364Ala,ENST00000357720,NM_001136035.2;TRMT1,missense_variant,p.Gly150Ala,ENST00000587487,;TRMT1,intron_variant,,ENST00000221504,NM_001142554.1;TRMT1,downstream_gene_variant,,ENST00000592814,;TRMT1,downstream_gene_variant,,ENST00000593257,;TRMT1,non_coding_transcript_exon_variant,,ENST00000588511,;TRMT1,non_coding_transcript_exon_variant,,ENST00000593157,;TRMT1,downstream_gene_variant,,ENST00000587633,;TRMT1,downstream_gene_variant,,ENST00000591717,;TRMT1,upstream_gene_variant,,ENST00000585435,;TRMT1,upstream_gene_variant,,ENST00000586830,; G ENST00000592062 Transcript missense_variant 1662/2579 1091/1980 364/659 G/A gGa/gCa 1 -1 TRMT1 HGNC HGNC:25980 protein_coding YES CCDS12293.1 ENSP00000466967 Q9NXH9 A0A024R7I5 UPI0000000A02 tolerated(0.73) 10/18 PROSITE_profiles:PS51626,hmmpanther:PTHR10631:SF3,hmmpanther:PTHR10631,Pfam_domain:PF02005,TIGRFAM_domain:TIGR00308 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 13109930 13109930 C G 1 0 0 0 0 1 0 0 0 17060 855 30 4 4 TRMT1 19 13109930 Missense_Mutation SNP C C3N-02087_T 9930132 13109930 45507686 40 27083 LZTR1 0 . GRCh38 22 20994672 20994672 + Missense_Mutation SNP A A G novel C3N-02087_T C3N-02087_N A A c.1730A>G p.Gln577Arg p.Q577R ENST00000215739 15/21 260 247 13 171 171 0 strelka-varscan-mutect LZTR1,missense_variant,p.Gln577Arg,ENST00000215739,NM_006767.3;LZTR1,upstream_gene_variant,,ENST00000415817,;LZTR1,non_coding_transcript_exon_variant,,ENST00000479606,;LZTR1,downstream_gene_variant,,ENST00000497716,;LZTR1,downstream_gene_variant,,ENST00000480895,;LZTR1,splice_acceptor_variant,,ENST00000415354,;LZTR1,missense_variant,p.Gln5Arg,ENST00000439171,;LZTR1,non_coding_transcript_exon_variant,,ENST00000495142,;LZTR1,non_coding_transcript_exon_variant,,ENST00000491432,;LZTR1,upstream_gene_variant,,ENST00000463909,;THAP7,downstream_gene_variant,,ENST00000498406,;LZTR1,upstream_gene_variant,,ENST00000498649,;LZTR1,upstream_gene_variant,,ENST00000452988,;LZTR1,downstream_gene_variant,,ENST00000414985,;LZTR1,downstream_gene_variant,,ENST00000443265,;LZTR1,downstream_gene_variant,,ENST00000492480,;LZTR1,upstream_gene_variant,,ENST00000464807,;LZTR1,downstream_gene_variant,,ENST00000461510,; G ENST00000215739 Transcript missense_variant 2089/4572 1730/2523 577/840 Q/R cAg/cGg 1 1 LZTR1 HGNC HGNC:6742 protein_coding YES CCDS33606.1 ENSP00000215739 Q8N653 UPI000013C695 NM_006767.3 tolerated(0.29) 15/21 hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF285,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 89 20994672 20994672 A G 1 0 0 0 0 1 0 0 0 9050 188 7 5 5 LZTR1 22 20994672 Missense_Mutation SNP A C3N-02087_T 20994672 29823796 41 27084 OR4F5 0 . GRCh38 1 69439 69439 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.349A>G p.Ile117Val p.I117V ENST00000335137 1/1 409 283 126 418 418 0 strelka-varscan-mutect OR4F5,missense_variant,p.Ile117Val,ENST00000335137,NM_001005484.1; G ENST00000335137 Transcript missense_variant 349/918 349/918 117/305 I/V Ata/Gta 1 1 OR4F5 HGNC HGNC:14825 protein_coding YES CCDS30547.1 ENSP00000334393 Q8NH21 UPI0000041BC1 NM_001005484.1 tolerated(1) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF179,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 36 174 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 69439 69439 A G 1 0 0 0 0 1 0 0 0 11142 449 16 5 5 OR4F5 1 69439 Missense_Mutation SNP A C3N-02089_T 69439 248886983 1 27085 PLEKHN1 0 . GRCh38 1 970400 970400 + Nonsense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.307C>T p.Gln103Ter p.Q103* ENST00000379410 3/16 177 155 22 168 168 0 strelka-varscan-mutect PLEKHN1,stop_gained,p.Gln103Ter,ENST00000379409,;PLEKHN1,stop_gained,p.Gln103Ter,ENST00000379410,NM_032129.2;PLEKHN1,stop_gained,p.Gln103Ter,ENST00000379407,NM_001160184.1;PERM1,downstream_gene_variant,,ENST00000433179,NM_001291366.1;PERM1,downstream_gene_variant,,ENST00000341290,NM_001291367.1;KLHL17,downstream_gene_variant,,ENST00000338591,NM_198317.2;KLHL17,downstream_gene_variant,,ENST00000622660,;PLEKHN1,upstream_gene_variant,,ENST00000491024,;PERM1,downstream_gene_variant,,ENST00000479361,;PLEKHN1,upstream_gene_variant,,ENST00000480267,; T ENST00000379410 Transcript stop_gained 342/2404 307/1836 103/611 Q/* Cag/Tag 1 1 PLEKHN1 HGNC HGNC:25284 protein_coding YES CCDS4.1 ENSP00000368720 Q494U1 UPI00001416D8 NM_032129.2 3/16 Gene3D:2.30.29.30,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 SNV 1 1 PASS rs1404948864 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 970400 970400 C T 1 0 0 0 0 0 1 0 0 12176 595 21 3 3 PLEKHN1 1 970400 Nonsense_Mutation SNP C C3N-02089_T 900961 970400 247986022 2 27086 AGRN 0 . GRCh38 1 1020188 1020188 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.16C>G p.His6Asp p.H6D ENST00000379370 1/36 120 92 28 43 43 0 strelka-varscan-mutect AGRN,missense_variant,p.His6Asp,ENST00000379370,NM_198576.3;AGRN,5_prime_UTR_variant,,ENST00000620552,NM_001305275.1; G ENST00000379370 Transcript missense_variant 66/7323 16/6138 6/2045 H/D Cac/Gac 1 1 AGRN HGNC HGNC:329 protein_coding YES CCDS30551.1 ENSP00000368678 O00468 UPI00001D7C8B NM_198576.3 tolerated_low_confidence(0.27) 1/36 PROSITE_profiles:PS51257,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 G 3 3 90 1020188 1020188 C G 1 0 0 0 0 1 0 0 0 476 594 21 4 4 AGRN 1 1020188 Missense_Mutation SNP C C3N-02089_T 49788 1020188 247936234 3 27087 LRRC47 0 . GRCh38 1 3781325 3781325 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1515A>C p.Glu505Asp p.E505D ENST00000378251 7/7 176 148 28 154 154 0 strelka-varscan-mutect LRRC47,missense_variant,p.Glu505Asp,ENST00000378251,NM_020710.2;RP1-286D6.5,upstream_gene_variant,,ENST00000607459,;RN7SL574P,upstream_gene_variant,,ENST00000581512,;LRRC47,3_prime_UTR_variant,,ENST00000479239,;LRRC47,non_coding_transcript_exon_variant,,ENST00000462356,; G ENST00000378251 Transcript missense_variant 1543/4310 1515/1752 505/583 E/D gaA/gaC 1 -1 LRRC47 HGNC HGNC:29207 protein_coding YES CCDS51.1 ENSP00000367498 Q8N1G4 A0A024R4G1 UPI000006DEDC NM_020710.2 deleterious(0.01) 7/7 hmmpanther:PTHR10947,hmmpanther:PTHR10947:SF3,SMART_domains:SM00873 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 3781325 3781325 T G 1 0 0 0 0 1 0 0 0 8900 1838 64 5 5 LRRC47 1 3781325 Missense_Mutation SNP T C3N-02089_T 2761137 3781325 245175097 4 27088 CEP104 0 . GRCh38 1 3852367 3852367 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.41G>T p.Gly14Val p.G14V ENST00000378230 2/22 202 172 30 178 178 0 strelka-varscan-mutect CEP104,missense_variant,p.Gly14Val,ENST00000378230,NM_014704.3;CEP104,missense_variant,p.Gly14Val,ENST00000378223,;CEP104,missense_variant,p.Gly14Val,ENST00000428079,;DFFB,upstream_gene_variant,,ENST00000338895,NM_001320136.1,NM_001282669.1;DFFB,upstream_gene_variant,,ENST00000378209,NM_004402.3;DFFB,upstream_gene_variant,,ENST00000625756,;CEP104,non_coding_transcript_exon_variant,,ENST00000494653,;DFFB,upstream_gene_variant,,ENST00000491998,;CEP104,upstream_gene_variant,,ENST00000494951,; A ENST00000378230 Transcript missense_variant 366/6424 41/2778 14/925 G/V gGa/gTa 1 -1 CEP104 HGNC HGNC:24866 protein_coding YES CCDS30571.1 ENSP00000367476 O60308 UPI0000139AA8 NM_014704.3 deleterious(0) 2/22 hmmpanther:PTHR13371:SF0,hmmpanther:PTHR13371,Superfamily_domains:SSF49785 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 3852367 3852367 C A 1 0 0 0 0 1 0 0 0 2954 855 30 2 2 CEP104 1 3852367 Missense_Mutation SNP C C3N-02089_T 71042 3852367 245104055 5 27089 KCNAB2 0 . GRCh38 1 6097320 6097320 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1121A>T p.Asn374Ile p.N374I ENST00000378083 15/16 142 125 17 109 109 0 strelka-varscan-mutect KCNAB2,missense_variant,p.Asn326Ile,ENST00000164247,NM_001199860.1;KCNAB2,missense_variant,p.Asn326Ile,ENST00000341524,NM_003636.3;KCNAB2,missense_variant,p.Asn326Ile,ENST00000378097,NM_001199861.1;KCNAB2,missense_variant,p.Asn312Ile,ENST00000352527,NM_172130.2;KCNAB2,missense_variant,p.Asn374Ile,ENST00000378083,NM_001199862.1;KCNAB2,missense_variant,p.Asn326Ile,ENST00000602612,;KCNAB2,missense_variant,p.Asn259Ile,ENST00000458166,NM_001199863.1;KCNAB2,missense_variant,p.Asn312Ile,ENST00000378092,;KCNAB2,intron_variant,,ENST00000378111,;CHD5,downstream_gene_variant,,ENST00000262450,NM_015557.2;KCNAB2,downstream_gene_variant,,ENST00000428161,;KCNAB2,downstream_gene_variant,,ENST00000389632,;KCNAB2,non_coding_transcript_exon_variant,,ENST00000481789,; T ENST00000378083 Transcript missense_variant 1410/4142 1121/1248 374/415 N/I aAt/aTt 1 1 KCNAB2 HGNC HGNC:6229 protein_coding YES CCDS55570.1 ENSP00000367323 Q13303 UPI000035E741 NM_001199862.1 deleterious(0.01) 15/16 hmmpanther:PTHR11732:SF196,hmmpanther:PTHR11732,Gene3D:3.20.20.100,Pfam_domain:PF00248,TIGRFAM_domain:TIGR01293,Superfamily_domains:SSF51430,Prints_domain:PR01578 MODERATE SNV 2 1 PASS rs1034508532 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 6097320 6097320 A T 1 0 0 0 0 1 0 0 0 7926 101 4 4 4 KCNAB2 1 6097320 Missense_Mutation SNP A C3N-02089_T 2244953 6097320 242859102 6 27090 CHD5 0 . GRCh38 1 6151033 6151033 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.993G>T p.Arg331Ser p.R331S ENST00000262450 7/42 31 27 4 28 28 0 strelka-mutect CHD5,missense_variant,p.Arg331Ser,ENST00000262450,NM_015557.2;CHD5,missense_variant,p.Arg331Ser,ENST00000496404,; A ENST00000262450 Transcript missense_variant,splice_region_variant 1093/9646 993/5865 331/1954 R/S agG/agT 1 -1 CHD5 HGNC HGNC:16816 protein_coding YES CCDS57.1 ENSP00000262450 Q8TDI0 UPI000006CD03 NM_015557.2 tolerated(0.09) 7/42 Gene3D:3.30.40.10,Low_complexity_(Seg):seg,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -11.42592 1 1 1 1 0 A 3 1 90 6151033 6151033 C A 1 0 0 0 0 1 0 0 0 3087 869 30 2 2 CHD5 1 6151033 Missense_Mutation SNP C C3N-02089_T 53713 6151033 242805389 7 27091 PHF13 0 . GRCh38 1 6616832 6616832 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.115G>T p.Ala39Ser p.A39S ENST00000377648 2/4 245 191 54 215 215 0 strelka-varscan-mutect PHF13,missense_variant,p.Ala39Ser,ENST00000377648,NM_153812.2;KLHL21,upstream_gene_variant,,ENST00000467612,;KLHL21,upstream_gene_variant,,ENST00000463043,;PHF13,intron_variant,,ENST00000495385,; T ENST00000377648 Transcript missense_variant 497/3681 115/903 39/300 A/S Gct/Tct 1 1 PHF13 HGNC HGNC:22983 protein_coding YES CCDS85.1 ENSP00000366876 Q86YI8 A0A158RFV6 UPI000013C9BF NM_153812.2 deleterious(0.05) 2/4 hmmpanther:PTHR14571 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 6616832 6616832 G T 1 0 0 0 0 1 0 0 0 11913 1319 46 2 2 PHF13 1 6616832 Missense_Mutation SNP G C3N-02089_T 465799 6616832 242339590 8 27092 CAMTA1 0 . GRCh38 1 7664768 7664768 + Missense_Mutation SNP G G T rs778144678 C3N-02089_T C3N-02089_N G G c.2221G>T p.Val741Leu p.V741L ENST00000303635 9/23 67 55 12 64 64 0 strelka-mutect CAMTA1,missense_variant,p.Val741Leu,ENST00000303635,NM_015215.3; T ENST00000303635 Transcript missense_variant 2428/8444 2221/5022 741/1673 V/L Gtg/Ttg rs778144678 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 deleterious_low_confidence(0.05) 9/23 hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 MODERATE 1 SNV 1 1 PASS rs778144678 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 7664768 7664768 G T 1 0 0 0 0 1 0 0 0 2306 1261 44 2 2 CAMTA1 1 7664768 Missense_Mutation SNP G C3N-02089_T 1047936 7664768 241291654 9 27093 CAMTA1 0 . GRCh38 1 7732504 7732504 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2971G>T p.Ala991Ser p.A991S ENST00000303635 12/23 230 182 48 188 187 1 strelka-varscan-mutect CAMTA1,missense_variant,p.Ala991Ser,ENST00000303635,NM_015215.3;CAMTA1,upstream_gene_variant,,ENST00000495233,; T ENST00000303635 Transcript missense_variant 3178/8444 2971/5022 991/1673 A/S Gcc/Tcc 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 deleterious(0.02) 12/23 hmmpanther:PTHR23335:SF11,hmmpanther:PTHR23335 MODERATE 1 SNV 1 1 PASS rs1315636304 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 7732504 7732504 G T 1 0 0 0 0 1 0 0 0 2306 1203 42 2 2 CAMTA1 1 7732504 Missense_Mutation SNP G C3N-02089_T 67736 7732504 241223918 10 27094 CAMTA1 0 . GRCh38 1 7745874 7745874 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.4400C>T p.Ser1467Phe p.S1467F ENST00000303635 18/23 208 180 28 210 210 0 strelka-varscan-mutect CAMTA1,missense_variant,p.Ser1467Phe,ENST00000303635,NM_015215.3;CAMTA1,missense_variant,p.Ser424Phe,ENST00000495233,;CAMTA1,missense_variant,p.Ser31Phe,ENST00000476864,;CAMTA1,intron_variant,,ENST00000490905,; T ENST00000303635 Transcript missense_variant 4607/8444 4400/5022 1467/1673 S/F tCt/tTt 1 1 CAMTA1 HGNC HGNC:18806 protein_coding YES CCDS30576.1 ENSP00000306522 Q9Y6Y1 UPI00001C1D72 NM_015215.3 deleterious(0.01) 18/23 Low_complexity_(Seg):seg,hmmpanther:PTHR23335,hmmpanther:PTHR23335:SF11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 7745874 7745874 C T 1 0 0 0 0 1 0 0 0 2306 913 32 3 3 CAMTA1 1 7745874 Missense_Mutation SNP C C3N-02089_T 13370 7745874 241210548 11 27095 DISP3 0 . GRCh38 1 11514490 11514490 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1417A>T p.Ile473Phe p.I473F ENST00000294484 4/21 152 121 31 139 139 0 strelka-varscan-mutect DISP3,missense_variant,p.Ile473Phe,ENST00000294484,NM_020780.1; T ENST00000294484 Transcript missense_variant 1555/5215 1417/4179 473/1392 I/F Att/Ttt 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 deleterious(0) 4/21 Transmembrane_helices:TMhelix,hmmpanther:PTHR10796:SF125,hmmpanther:PTHR10796,Gene3D:2j8sB01,Pfam_domain:PF02460,Superfamily_domains:SSF82866 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 11514490 11514490 A T 1 0 0 0 0 1 0 0 0 4347 217 8 4 4 DISP3 1 11514490 Missense_Mutation SNP A C3N-02089_T 3768616 11514490 237441932 12 27096 PRAMEF10 0 . GRCh38 1 12894981 12894981 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.471A>C p.Glu157Asp p.E157D ENST00000235347 3/4 168 150 18 170 170 0 varscan-mutect PRAMEF10,missense_variant,p.Glu157Asp,ENST00000235347,NM_001039361.4; G ENST00000235347 Transcript missense_variant 551/1525 471/1425 157/474 E/D gaA/gaC 1 -1 PRAMEF10 HGNC HGNC:27997 protein_coding YES CCDS41255.1 ENSP00000235347 O60809 UPI000442CF00 NM_001039361.4 tolerated(0.07) 3/4 hmmpanther:PTHR14224:SF28,hmmpanther:PTHR14224,PIRSF_domain:PIRSF038286 MODERATE 1 SNV 1 1 PASS rs1238869647 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 12894981 12894981 T G 1 0 0 0 0 1 0 0 0 12555 1838 64 5 5 PRAMEF10 1 12894981 Missense_Mutation SNP T C3N-02089_T 1380491 12894981 236061441 13 27097 PRAMEF7 0 . GRCh38 1 12920213 12920213 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1225G>T p.Glu409Ter p.E409* ENST00000616979 4/4 662 622 40 557 557 0 varscan-mutect PRAMEF7,stop_gained,p.Glu409Ter,ENST00000616979,NM_001012277.4;PRAMEF7,stop_gained,p.Glu409Ter,ENST00000330881,;RNU6-1072P,upstream_gene_variant,,ENST00000384703,; T ENST00000616979 Transcript stop_gained 1323/1592 1225/1425 409/474 E/* Gag/Tag 1 1 PRAMEF7 HGNC HGNC:28415 protein_coding YES CCDS30593.1 ENSP00000484237 Q5VXH5 UPI000058F1DF NM_001012277.4 4/4 PIRSF_domain:PIRSF038286,hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,Superfamily_domains:SSF52047 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 12920213 12920213 G T 1 0 0 0 0 0 1 0 0 12569 1175 41 2 2 PRAMEF7 1 12920213 Nonsense_Mutation SNP G C3N-02089_T 25232 12920213 236036209 14 27098 PRAMEF8 0 . GRCh38 1 13281571 13281571 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1225G>T p.Glu409Ter p.E409* ENST00000357367 4/4 119 112 7 91 91 0 varscan-mutect PRAMEF8,stop_gained,p.Glu409Ter,ENST00000357367,NM_001012276.3;PRAMEF8,stop_gained,p.Glu409Ter,ENST00000621519,;PRAMEF8,stop_gained,p.Glu409Ter,ENST00000614831,;RNU6-443P,upstream_gene_variant,,ENST00000384780,; A ENST00000357367 Transcript stop_gained 1308/1844 1225/1425 409/474 E/* Gag/Tag 1 -1 PRAMEF8 HGNC HGNC:24074 protein_coding YES CCDS72709.1 ENSP00000349931 Q5VWM4 UPI000191706C NM_001012276.3 4/4 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF30,PIRSF_domain:PIRSF038286,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 13281571 13281571 C A 1 0 0 0 0 0 1 0 0 12570 864 30 2 2 PRAMEF8 1 13281571 Nonsense_Mutation SNP C C3N-02089_T 361358 13281571 235674851 15 27099 FBXO42 0 . GRCh38 1 16251492 16251492 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1332G>C p.Leu444Phe p.L444F ENST00000375592 10/10 343 306 37 333 333 0 strelka-varscan-mutect FBXO42,missense_variant,p.Leu444Phe,ENST00000375592,NM_018994.2;FBXO42,missense_variant,p.Leu162Phe,ENST00000456164,;FBXO42,missense_variant,p.Leu162Phe,ENST00000444116,; G ENST00000375592 Transcript missense_variant 1549/6202 1332/2154 444/717 L/F ttG/ttC 1 -1 FBXO42 HGNC HGNC:29249 protein_coding YES CCDS30613.1 ENSP00000364742 Q6P3S6 A0A024QZB0 UPI0000161A51 NM_018994.2 tolerated(0.72) 10/10 hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF316 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 16251492 16251492 C G 1 0 0 0 0 1 0 0 0 5614 477 17 4 4 FBXO42 1 16251492 Missense_Mutation SNP C C3N-02089_T 2969921 16251492 232704930 16 27100 CROCC 0 . GRCh38 1 16939124 16939124 + Missense_Mutation SNP G G T rs749944892 C3N-02089_T C3N-02089_N G G c.1590G>T p.Lys530Asn p.K530N ENST00000375541 12/37 86 74 12 56 56 0 strelka-varscan-mutect CROCC,missense_variant,p.Lys530Asn,ENST00000375541,NM_014675.4;CROCC,missense_variant,p.Lys390Asn,ENST00000445545,;CROCC,missense_variant,p.Lys424Asn,ENST00000467938,;CROCC,missense_variant,p.Lys132Asn,ENST00000467715,;CROCC,non_coding_transcript_exon_variant,,ENST00000466256,;CROCC,non_coding_transcript_exon_variant,,ENST00000492631,;CROCC,non_coding_transcript_exon_variant,,ENST00000494191,; T ENST00000375541 Transcript missense_variant 1659/6656 1590/6054 530/2017 K/N aaG/aaT rs749944892 1 1 CROCC HGNC HGNC:21299 protein_coding YES CCDS30616.1 ENSP00000364691 Q5TZA2 UPI000042B0BB NM_014675.4 tolerated(0.26) 12/37 hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF17 MODERATE 1 SNV 5 1 PASS rs749944892 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 16939124 16939124 G T 1 0 0 0 0 1 0 0 0 3694 962 34 2 2 CROCC 1 16939124 Missense_Mutation SNP G C3N-02089_T 687632 16939124 232017298 17 27101 TAS1R2 0 . GRCh38 1 18857559 18857559 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.255C>A p.Asp85Glu p.D85E ENST00000375371 2/6 228 165 63 229 228 1 strelka-varscan-mutect TAS1R2,missense_variant,p.Asp85Glu,ENST00000375371,NM_152232.2;RP13-279N23.2,3_prime_UTR_variant,,ENST00000494072,; T ENST00000375371 Transcript missense_variant 277/2542 255/2520 85/839 D/E gaC/gaA 1 -1 TAS1R2 HGNC HGNC:14905 protein_coding YES CCDS187.1 ENSP00000364520 Q8TE23 UPI0000456168 NM_152232.2 tolerated(0.72) 2/6 hmmpanther:PTHR24061,hmmpanther:PTHR24061:SF441,Pfam_domain:PF01094,Gene3D:3.40.50.2300,Superfamily_domains:SSF53822,Prints_domain:PR00248 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 18857559 18857559 G T 1 0 0 0 0 1 0 0 0 15962 1368 48 2 2 TAS1R2 1 18857559 Missense_Mutation SNP G C3N-02089_T 1918435 18857559 230098863 18 27102 ALDH4A1 0 . GRCh38 1 18883374 18883374 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.508T>C p.Phe170Leu p.F170L ENST00000375341 6/15 344 307 37 280 280 0 strelka-varscan-mutect ALDH4A1,missense_variant,p.Phe170Leu,ENST00000375341,NM_003748.3;ALDH4A1,missense_variant,p.Phe170Leu,ENST00000538839,NM_001319218.1;ALDH4A1,missense_variant,p.Phe170Leu,ENST00000290597,NM_170726.2;ALDH4A1,missense_variant,p.Phe110Leu,ENST00000538309,NM_001161504.1;ALDH4A1,missense_variant,p.Phe154Leu,ENST00000432718,;MIR4695,upstream_gene_variant,,ENST00000577305,;ALDH4A1,non_coding_transcript_exon_variant,,ENST00000454547,;RP13-279N23.2,3_prime_UTR_variant,,ENST00000494072,; G ENST00000375341 Transcript missense_variant 766/3363 508/1692 170/563 F/L Ttc/Ctc 1 -1 ALDH4A1 HGNC HGNC:406 protein_coding YES CCDS188.1 ENSP00000364490 P30038 A0A024RAD8 UPI000007418C NM_003748.3 tolerated(0.63) 6/15 hmmpanther:PTHR14516,hmmpanther:PTHR14516:SF1,Gene3D:3.40.605.10,Pfam_domain:PF00171,TIGRFAM_domain:TIGR01236,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 18883374 18883374 A G 1 0 0 0 0 1 0 0 0 601 72 3 5 5 ALDH4A1 1 18883374 Missense_Mutation SNP A C3N-02089_T 25815 18883374 230073048 19 27103 UBR4 0 . GRCh38 1 19148074 19148074 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.7548A>T p.= p.P2516P ENST00000375254 51/106 160 120 40 161 161 0 strelka-varscan-mutect UBR4,synonymous_variant,p.=,ENST00000375254,NM_020765.2;UBR4,synonymous_variant,p.=,ENST00000417040,;UBR4,synonymous_variant,p.=,ENST00000425413,;UBR4,upstream_gene_variant,,ENST00000465036,;UBR4,downstream_gene_variant,,ENST00000419533,; A ENST00000375254 Transcript synonymous_variant 7576/15906 7548/15552 2516/5183 P ccA/ccT 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 51/106 Low_complexity_(Seg):seg,hmmpanther:PTHR21725 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 19148074 19148074 T A 1 0 0 0 0 0 0 0 1 17428 1567 55 4 4 UBR4 1 19148074 Silent SNP T C3N-02089_T 264700 19148074 229808348 20 27104 SH2D5 0 . GRCh38 1 20721956 20721956 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.1108delG p.Glu370ArgfsTer19 p.E370Rfs*19 ENST00000444387 10/10 129 114 15 133 133 0 sindel-varindel SH2D5,frameshift_variant,p.Glu286ArgfsTer19,ENST00000375031,NM_001103160.1;SH2D5,frameshift_variant,p.Glu370ArgfsTer19,ENST00000444387,NM_001103161.1;KIF17,upstream_gene_variant,,ENST00000247986,NM_020816.3;KIF17,upstream_gene_variant,,ENST00000400463,NM_001122819.2;KIF17,upstream_gene_variant,,ENST00000375044,NM_001287212.1;SH2D5,downstream_gene_variant,,ENST00000517430,;SH2D5,downstream_gene_variant,,ENST00000447746,;SH2D5,downstream_gene_variant,,ENST00000518294,;SH2D5,non_coding_transcript_exon_variant,,ENST00000460804,; - ENST00000444387 Transcript frameshift_variant 1506/1934 1108/1272 370/423 E/X Gag/ag 1 -1 SH2D5 HGNC HGNC:28819 protein_coding YES CCDS44080.1 ENSP00000406026 Q6ZV89 UPI0000EE70C3 NM_001103161.1 10/10 PROSITE_profiles:PS50001,Gene3D:3.30.505.10,Superfamily_domains:SSF55550 HIGH deletion 2 1 PASS . . 0 207 0 2 0 0 0 0 -19.99844 0.9999999 1 1 1 0 - 7 5 90 20721956 20721956 C - 1 0 1 0 1 0 0 0 0 14495 864 30 0 0 SH2D5 1 20721956 Frame_Shift_Del DEL C C3N-02089_T 1573882 20721956 228234466 21 27105 MYOM3 0 . GRCh38 1 24076231 24076231 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2629C>A p.Gln877Lys p.Q877K ENST00000374434 21/37 298 236 62 251 251 0 strelka-varscan-mutect MYOM3,missense_variant,p.Gln877Lys,ENST00000374434,NM_152372.3;RP11-293P20.4,intron_variant,,ENST00000429191,;RP11-293P20.2,intron_variant,,ENST00000439239,;MYOM3,intron_variant,,ENST00000448831,; T ENST00000374434 Transcript missense_variant 2792/5804 2629/4314 877/1437 Q/K Cag/Aag 1 -1 MYOM3 HGNC HGNC:26679 protein_coding YES CCDS41281.1 ENSP00000363557 Q5VTT5 UPI0000203A5D NM_152372.3 tolerated(0.09) 21/37 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 24076231 24076231 G T 1 0 0 0 0 1 0 0 0 10094 1386 48 2 2 MYOM3 1 24076231 Missense_Mutation SNP G C3N-02089_T 3354275 24076231 224880191 22 27106 OPRD1 0 . GRCh38 1 28863113 28863113 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.949C>T p.Leu317Phe p.L317F ENST00000234961 3/3 121 108 13 94 94 0 strelka-varscan-mutect OPRD1,missense_variant,p.Leu317Phe,ENST00000234961,NM_000911.3;OPRD1,missense_variant,p.Leu269Phe,ENST00000621425,; T ENST00000234961 Transcript missense_variant 1191/9345 949/1119 317/372 L/F Ctc/Ttc 1 1 OPRD1 HGNC HGNC:8153 protein_coding YES CCDS329.1 ENSP00000234961 P41143 UPI0000130D94 NM_000911.3 deleterious(0) 3/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24229:SF2,hmmpanther:PTHR24229,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 28863113 28863113 C T 1 0 0 0 0 1 0 0 0 10960 797 28 3 3 OPRD1 1 28863113 Missense_Mutation SNP C C3N-02089_T 4786882 28863113 220093309 23 27107 PUM1 0 . GRCh38 1 30945400 30945400 + Frame_Shift_Del DEL A A - novel C3N-02089_T C3N-02089_N A A c.2940delT p.Ile980MetfsTer32 p.I980Mfs*32 ENST00000426105 18/22 283 260 23 267 267 0 sindel-varindel-pindel PUM1,frameshift_variant,p.Ile981MetfsTer32,ENST00000373747,;PUM1,frameshift_variant,p.Ile978MetfsTer32,ENST00000257075,NM_014676.2;PUM1,frameshift_variant,p.Ile736MetfsTer32,ENST00000424085,;PUM1,frameshift_variant,p.Ile917MetfsTer32,ENST00000525843,;PUM1,frameshift_variant,p.Ile1016MetfsTer32,ENST00000373741,;PUM1,frameshift_variant,p.Ile980MetfsTer32,ENST00000426105,NM_001020658.1;PUM1,frameshift_variant,p.Ile954MetfsTer32,ENST00000440538,;PUM1,frameshift_variant,p.Ile919MetfsTer32,ENST00000373742,;PUM1,frameshift_variant,p.Ile692MetfsTer32,ENST00000498419,;PUM1,frameshift_variant,p.Ile131MetfsTer26,ENST00000529846,;PUM1,intron_variant,,ENST00000525997,;PUM1,downstream_gene_variant,,ENST00000527498,;PUM1,upstream_gene_variant,,ENST00000530669,; - ENST00000426105 Transcript frameshift_variant 3031/4043 2940/3567 980/1188 I/X atT/at 1 -1 PUM1 HGNC HGNC:14957 protein_coding YES CCDS44099.1 ENSP00000391723 Q14671 UPI0000203D8E NM_001020658.1 18/22 Gene3D:1.25.10.10,Pfam_domain:PF00806,PROSITE_profiles:PS50302,PROSITE_profiles:PS50303,hmmpanther:PTHR12537,hmmpanther:PTHR12537:SF1,SMART_domains:SM00025,Superfamily_domains:SSF48371 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 30945400 30945400 A - 1 0 1 0 1 0 0 0 0 12982 126 5 0 0 PUM1 1 30945400 Frame_Shift_Del DEL A C3N-02089_T 2082287 30945400 218011022 24 27108 ADGRB2 0 . GRCh38 1 31728270 31728270 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.4424A>T p.His1475Leu p.H1475L ENST00000373655 31/33 373 283 90 308 307 1 strelka-varscan-mutect ADGRB2,missense_variant,p.His1476Leu,ENST00000373658,;ADGRB2,missense_variant,p.His1475Leu,ENST00000373655,NM_001294335.1;ADGRB2,missense_variant,p.His1376Leu,ENST00000398542,;ADGRB2,missense_variant,p.His1442Leu,ENST00000527361,NM_001294336.1;ADGRB2,missense_variant,p.His1391Leu,ENST00000398556,;ADGRB2,missense_variant,p.His1409Leu,ENST00000398547,;ADGRB2,missense_variant,p.His1464Leu,ENST00000398538,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000465256,;ADGRB2,non_coding_transcript_exon_variant,,ENST00000530999,; A ENST00000373655 Transcript missense_variant 4766/5400 4424/4755 1475/1584 H/L cAc/cTc 1 -1 ADGRB2 HGNC HGNC:944 protein_coding YES CCDS72747.1 ENSP00000362759 O60241 UPI000046FEC7 NM_001294335.1 deleterious(0) 31/33 Prints_domain:PR01694 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 31728270 31728270 T A 1 0 0 0 0 1 0 0 0 356 1696 59 4 4 ADGRB2 1 31728270 Missense_Mutation SNP T C3N-02089_T 782870 31728270 217228152 25 27109 CSMD2 0 . GRCh38 1 33600966 33600966 + Missense_Mutation SNP C C G rs140769172 C3N-02089_T C3N-02089_N C C c.6755G>C p.Arg2252Pro p.R2252P ENST00000373381 44/71 231 200 31 182 182 0 strelka-varscan-mutect CSMD2,missense_variant,p.Arg2252Pro,ENST00000373381,NM_001281956.1;CSMD2,missense_variant,p.Arg2212Pro,ENST00000619121,;CSMD2,missense_variant,p.Arg2254Pro,ENST00000373388,NM_052896.4;CSMD2,missense_variant,p.Arg1125Pro,ENST00000373380,;CSMD2,missense_variant,p.Arg351Pro,ENST00000373377,;CSMD2,non_coding_transcript_exon_variant,,ENST00000489419,;CSMD2,missense_variant,p.Arg2254Pro,ENST00000241312,; G ENST00000373381 Transcript missense_variant 6932/13698 6755/10896 2252/3631 R/P cGg/cCg rs140769172,COSM3736700,COSM3736701,COSM3736702 1 -1 CSMD2 HGNC HGNC:19290 protein_coding YES CCDS60082.1 ENSP00000362479 Q7Z408 UPI0000578D0B NM_001281956.1 deleterious(0.02) 44/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs140769172 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 33600966 33600966 C G 1 0 0 0 0 1 0 0 0 3746 652 23 4 4 CSMD2 1 33600966 Missense_Mutation SNP C C3N-02089_T 1872696 33600966 215355456 26 27110 OSCP1 0 . GRCh38 1 36438895 36438895 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.128T>C p.Ile43Thr p.I43T ENST00000235532 2/10 89 83 6 88 88 0 strelka-mutect OSCP1,missense_variant,p.Ile53Thr,ENST00000356637,;OSCP1,missense_variant,p.Ile43Thr,ENST00000235532,NM_145047.4;OSCP1,missense_variant,p.Ile13Thr,ENST00000445843,;OSCP1,missense_variant,p.Ile43Thr,ENST00000354267,NM_206837.2;OSCP1,5_prime_UTR_variant,,ENST00000433045,;OSCP1,3_prime_UTR_variant,,ENST00000524789,;OSCP1,non_coding_transcript_exon_variant,,ENST00000528112,; G ENST00000235532 Transcript missense_variant 210/1455 128/1140 43/379 I/T aTc/aCc 1 -1 OSCP1 HGNC HGNC:29971 protein_coding YES CCDS409.2 ENSP00000235532 Q8WVF1 UPI000059CFA3 NM_145047.4 deleterious(0.04) 2/10 Pfam_domain:PF10188,hmmpanther:PTHR21439 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -13.00323 1 1 1 1 0 G 3 3 90 36438895 36438895 A G 1 0 0 0 0 1 0 0 0 11352 333 12 5 5 OSCP1 1 36438895 Missense_Mutation SNP A C3N-02089_T 2837929 36438895 212517527 27 27111 GNL2 0 . GRCh38 1 37574444 37574444 + Missense_Mutation SNP C C A rs373181030 C3N-02089_T C3N-02089_N C C c.1315G>T p.Asp439Tyr p.D439Y ENST00000373062 12/16 198 132 66 188 188 0 strelka-varscan-mutect GNL2,missense_variant,p.Asp439Tyr,ENST00000373062,NM_013285.2;GNL2,downstream_gene_variant,,ENST00000538069,;GNL2,upstream_gene_variant,,ENST00000462812,;GNL2,downstream_gene_variant,,ENST00000469191,; A ENST00000373062 Transcript missense_variant 1414/2334 1315/2196 439/731 D/Y Gac/Tac rs373181030,COSM1687476 1 -1 GNL2 HGNC HGNC:29925 protein_coding YES CCDS421.1 ENSP00000362153 Q13823 Q5T0F3 UPI0000000C9E NM_013285.2 deleterious(0) 12/16 Gene3D:1pujA02,hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF9 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs373181030 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 37574444 37574444 C A 1 0 0 0 0 1 0 0 0 6415 884 31 1 1 GNL2 1 37574444 Missense_Mutation SNP C C3N-02089_T 1135549 37574444 211381978 28 27112 PABPC4 0 . GRCh38 1 39565132 39565132 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1219G>T p.Gly407Cys p.G407C ENST00000372858 8/16 140 91 49 129 129 0 strelka-varscan-mutect PABPC4,missense_variant,p.Gly407Cys,ENST00000372857,NM_003819.3;PABPC4,missense_variant,p.Gly407Cys,ENST00000372856,NM_001135654.1;PABPC4,missense_variant,p.Gly407Cys,ENST00000372858,NM_001135653.1;PABPC4,missense_variant,p.Gly407Cys,ENST00000372862,;PABPC4,missense_variant,p.Gly309Cys,ENST00000421687,;PABPC4,missense_variant,p.Gly134Cys,ENST00000527718,;PABPC4,upstream_gene_variant,,ENST00000437136,;PABPC4,downstream_gene_variant,,ENST00000474378,;PABPC4,upstream_gene_variant,,ENST00000530186,;SNORA55,downstream_gene_variant,,ENST00000364587,;RP11-69E11.8,upstream_gene_variant,,ENST00000415255,;PABPC4,downstream_gene_variant,,ENST00000529216,;PABPC4,3_prime_UTR_variant,,ENST00000470443,;PABPC4,non_coding_transcript_exon_variant,,ENST00000525045,;PABPC4,non_coding_transcript_exon_variant,,ENST00000525669,;PABPC4,non_coding_transcript_exon_variant,,ENST00000483770,;PABPC4,upstream_gene_variant,,ENST00000468476,;PABPC4,upstream_gene_variant,,ENST00000492468,;PABPC4,downstream_gene_variant,,ENST00000513632,;PABPC4,upstream_gene_variant,,ENST00000482028,;PABPC4,downstream_gene_variant,,ENST00000525751,;PABPC4,upstream_gene_variant,,ENST00000484555,;PABPC4,upstream_gene_variant,,ENST00000477556,;PABPC4,downstream_gene_variant,,ENST00000492519,;PABPC4,upstream_gene_variant,,ENST00000461578,; A ENST00000372858 Transcript missense_variant 1669/2753 1219/1983 407/660 G/C Ggc/Tgc 1 -1 PABPC4 HGNC HGNC:8557 protein_coding YES CCDS44115.1 ENSP00000361949 Q13310 UPI00002057C5 NM_001135653.1 deleterious(0) 8/16 hmmpanther:PTHR24012:SF365,hmmpanther:PTHR24012,TIGRFAM_domain:TIGR01628 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 39565132 39565132 C A 1 0 0 0 0 1 0 0 0 11443 594 21 2 2 PABPC4 1 39565132 Missense_Mutation SNP C C3N-02089_T 1990688 39565132 209391290 29 27113 HIVEP3 0 . GRCh38 1 41584006 41584006 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.792G>T p.Glu264Asp p.E264D ENST00000372583 4/9 195 177 18 178 178 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Glu264Asp,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Glu264Asp,ENST00000372583,NM_024503.4;HIVEP3,upstream_gene_variant,,ENST00000460604,; A ENST00000372583 Transcript missense_variant 1678/12193 792/7221 264/2406 E/D gaG/gaT 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 tolerated(0.19) 4/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 41584006 41584006 C A 1 0 0 0 0 1 0 0 0 7077 912 32 2 2 HIVEP3 1 41584006 Missense_Mutation SNP C C3N-02089_T 2018874 41584006 207372416 30 27114 LURAP1 0 . GRCh38 1 46219974 46219974 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.474A>T p.Glu158Asp p.E158D ENST00000371980 2/2 265 217 48 217 217 0 strelka-varscan-mutect LURAP1,missense_variant,p.Glu158Asp,ENST00000371980,NM_001013615.2;POMGNT1,5_prime_UTR_variant,,ENST00000396420,;POMGNT1,5_prime_UTR_variant,,ENST00000371992,NM_001243766.1; T ENST00000371980 Transcript missense_variant 567/1854 474/720 158/239 E/D gaA/gaT 1 1 LURAP1 HGNC HGNC:32327 protein_coding YES CCDS30703.1 ENSP00000361048 Q96LR2 UPI0000072C34 NM_001013615.2 tolerated(0.15) 2/2 Pfam_domain:PF14854,hmmpanther:PTHR33767 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 46219974 46219974 A T 1 0 0 0 0 1 0 0 0 8993 40 2 4 4 LURAP1 1 46219974 Missense_Mutation SNP A C3N-02089_T 4635968 46219974 202736448 31 27115 FOXD2 0 . GRCh38 1 47439504 47439504 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1369G>T p.Ala457Ser p.A457S ENST00000334793 1/1 247 194 53 228 228 0 strelka-varscan-mutect FOXD2,missense_variant,p.Ala457Ser,ENST00000334793,NM_004474.3;FOXD2-AS1,upstream_gene_variant,,ENST00000445551,; T ENST00000334793 Transcript missense_variant 3488/4675 1369/1488 457/495 A/S Gct/Tct 1 1 FOXD2 HGNC HGNC:3803 protein_coding YES CCDS30708.1 ENSP00000335493 O60548 UPI000014153E NM_004474.3 tolerated_low_confidence(0.19) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF168 MODERATE 1 SNV 1 PASS rs1172082438 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 47439504 47439504 G T 1 0 0 0 0 1 0 0 0 5857 1319 46 2 2 FOXD2 1 47439504 Missense_Mutation SNP G C3N-02089_T 1219530 47439504 201516918 32 27116 OSBPL9 0 . GRCh38 1 51765935 51765935 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.922G>T p.Ala308Ser p.A308S ENST00000447887 12/24 150 108 42 171 171 0 strelka-varscan-mutect OSBPL9,missense_variant,p.Ala285Ser,ENST00000371714,NM_148908.3;OSBPL9,missense_variant,p.Ala308Ser,ENST00000447887,NM_148909.3;OSBPL9,missense_variant,p.Ala298Ser,ENST00000428468,NM_024586.5;OSBPL9,missense_variant,p.Ala281Ser,ENST00000453295,NM_148906.2;OSBPL9,missense_variant,p.Ala120Ser,ENST00000462759,NM_148904.3;OSBPL9,missense_variant,p.Ala188Ser,ENST00000361556,NM_148907.2;OSBPL9,missense_variant,p.Ala120Ser,ENST00000486942,NM_148905.3;OSBPL9,missense_variant,p.Ala133Ser,ENST00000531828,;OSBPL9,downstream_gene_variant,,ENST00000532975,;OSBPL9,downstream_gene_variant,,ENST00000527631,;OSBPL9,missense_variant,p.Ala99Ser,ENST00000531061,;OSBPL9,3_prime_UTR_variant,,ENST00000495776,;OSBPL9,3_prime_UTR_variant,,ENST00000435274,;OSBPL9,3_prime_UTR_variant,,ENST00000489990,;OSBPL9,3_prime_UTR_variant,,ENST00000528603,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000531819,;OSBPL9,non_coding_transcript_exon_variant,,ENST00000475697,;OSBPL9,downstream_gene_variant,,ENST00000526917,; T ENST00000447887 Transcript missense_variant 941/2940 922/2241 308/746 A/S Gct/Tct 1 1 OSBPL9 HGNC HGNC:16386 protein_coding YES CCDS44145.1 ENSP00000412733 Q96SU4 UPI0000167BAD NM_148909.3 deleterious(0.02) 12/24 Low_complexity_(Seg):seg,hmmpanther:PTHR10972:SF27,hmmpanther:PTHR10972 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 51765935 51765935 G T 1 0 0 0 0 1 0 0 0 11350 1319 46 2 2 OSBPL9 1 51765935 Missense_Mutation SNP G C3N-02089_T 4326431 51765935 197190487 33 27117 PRKAA2 0 . GRCh38 1 56707478 56707478 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.1424A>C p.Glu475Ala p.E475A ENST00000371244 9/9 122 104 18 142 142 0 strelka-varscan-mutect PRKAA2,missense_variant,p.Glu475Ala,ENST00000371244,NM_006252.3;PRKAA2,missense_variant,p.Glu475Ala,ENST00000610361,; C ENST00000371244 Transcript missense_variant 1490/9347 1424/1659 475/552 E/A gAa/gCa 1 1 PRKAA2 HGNC HGNC:9377 protein_coding YES CCDS605.1 ENSP00000360290 P54646 UPI00001250A9 NM_006252.3 tolerated(0.16) 9/9 Pfam_domain:PF16579,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF193,Superfamily_domains:SSF103243 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 56707478 56707478 A C 1 0 0 0 0 1 0 0 0 12627 260 9 5 5 PRKAA2 1 56707478 Missense_Mutation SNP A C3N-02089_T 4941543 56707478 192248944 34 27118 MYSM1 0 . GRCh38 1 58690401 58690401 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.235A>C p.Lys79Gln p.K79Q ENST00000472487 4/20 111 95 16 136 136 0 strelka-varscan-mutect MYSM1,missense_variant,p.Lys79Gln,ENST00000472487,NM_001085487.2;MYSM1,non_coding_transcript_exon_variant,,ENST00000466774,;MYSM1,non_coding_transcript_exon_variant,,ENST00000483003,;MYSM1,upstream_gene_variant,,ENST00000493821,;MYSM1,upstream_gene_variant,,ENST00000401044,;MYSM1,downstream_gene_variant,,ENST00000489282,; G ENST00000472487 Transcript missense_variant 275/7785 235/2487 79/828 K/Q Aaa/Caa 1 -1 MYSM1 HGNC HGNC:29401 protein_coding YES CCDS41343.1 ENSP00000418734 Q5VVJ2 UPI0000204444 NM_001085487.2 deleterious(0.02) 4/20 hmmpanther:PTHR12802:SF20,hmmpanther:PTHR12802 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 58690401 58690401 T G 1 0 0 0 0 1 0 0 0 10104 1850 64 5 5 MYSM1 1 58690401 Missense_Mutation SNP T C3N-02089_T 1982923 58690401 190266021 35 27119 ANKRD13C 0 . GRCh38 1 70324860 70324860 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.570delG p.Arg190SerfsTer3 p.R190Sfs*3 ENST00000370944 3/13 104 81 23 163 163 0 sindel-varindel-pindel ANKRD13C,frameshift_variant,p.Arg190SerfsTer3,ENST00000370944,NM_030816.4;ANKRD13C,intron_variant,,ENST00000262346,;ANKRD13C,non_coding_transcript_exon_variant,,ENST00000498735,; - ENST00000370944 Transcript frameshift_variant 884/4069 570/1626 190/541 R/X agG/ag 1 -1 ANKRD13C HGNC HGNC:25374 protein_coding YES CCDS648.2 ENSP00000359982 Q8N6S4 UPI0000140CE0 NM_030816.4 3/13 PROSITE_profiles:PS50297,hmmpanther:PTHR12447,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 HIGH 1 deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 70324860 70324860 C - 1 0 1 0 1 0 0 0 0 744 738 26 0 0 ANKRD13C 1 70324860 Frame_Shift_Del DEL C C3N-02089_T 11634459 70324860 178631562 36 27120 LHX8 0 . GRCh38 1 75143869 75143869 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.635C>A p.Ala212Asp p.A212D ENST00000294638 7/10 291 226 65 311 309 2 strelka-varscan-mutect LHX8,missense_variant,p.Ala212Asp,ENST00000294638,NM_001001933.1;LHX8,missense_variant,p.Ala202Asp,ENST00000356261,NM_001256114.1; A ENST00000294638 Transcript missense_variant 1299/2373 635/1071 212/356 A/D gCc/gAc 1 1 LHX8 HGNC HGNC:28838 protein_coding YES CCDS30756.1 ENSP00000294638 Q68G74 UPI00001972E8 NM_001001933.1 deleterious(0.05) 7/10 hmmpanther:PTHR24208 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 75143869 75143869 C A 1 0 0 0 0 1 0 0 0 8685 739 26 2 2 LHX8 1 75143869 Missense_Mutation SNP C C3N-02089_T 4819009 75143869 173812553 37 27121 MSH4 0 . GRCh38 1 75807087 75807087 + Frame_Shift_Del DEL A A - rs761636688 C3N-02089_T C3N-02089_N A A c.539delA p.Asn180ThrfsTer18 p.N180Tfs*18 ENST00000263187 3/20 84 57 27 153 153 0 sindel-varindel-pindel MSH4,frameshift_variant,p.Asn180ThrfsTer18,ENST00000263187,NM_002440.3; - ENST00000263187 Transcript frameshift_variant 638/3266 534/2811 178/936 L/X ttA/tt rs761636688 1 1 MSH4 HGNC HGNC:7327 protein_coding YES CCDS670.1 ENSP00000263187 O15457 UPI000006D934 NM_002440.3 3/20 Gene3D:3.30.420.110,Pfam_domain:PF05188,hmmpanther:PTHR11361,hmmpanther:PTHR11361:SF21 HIGH 1 deletion 1 5 1 PASS . . 0 204 2 3 0 0 0 0 -20 0.9999907 1 1 1 0 - 7 5 90 75807087 75807087 A - 1 0 1 0 1 0 0 0 0 9855 359 13 0 0 MSH4 1 75807087 Frame_Shift_Del DEL A C3N-02089_T 663218 75807087 173149335 38 27122 COL24A1 0 . GRCh38 1 86125017 86125017 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.1319C>T p.Ser440Phe p.S440F ENST00000370571 3/60 84 55 29 97 97 0 strelka-varscan-mutect COL24A1,missense_variant,p.Ser440Phe,ENST00000370571,NM_152890.5;COL24A1,downstream_gene_variant,,ENST00000496682,;COL24A1,missense_variant,p.Ser440Phe,ENST00000426639,; A ENST00000370571 Transcript missense_variant 1686/6825 1319/5145 440/1714 S/F tCt/tTt 1 -1 COL24A1 HGNC HGNC:20821 protein_coding YES CCDS41353.1 ENSP00000359603 Q17RW2 UPI000013E81F NM_152890.5 tolerated(0.08) 3/60 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 86125017 86125017 G A 1 0 0 0 0 1 0 0 0 3471 942 33 3 3 COL24A1 1 86125017 Missense_Mutation SNP G C3N-02089_T 10317930 86125017 162831405 39 27123 HFM1 0 . GRCh38 1 91314033 91314033 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.3168T>A p.Ser1056Arg p.S1056R ENST00000370425 29/39 111 83 28 159 158 1 strelka-varscan-mutect HFM1,missense_variant,p.Ser1056Arg,ENST00000370425,NM_001017975.4;HFM1,missense_variant,p.Ser268Arg,ENST00000430465,;HFM1,non_coding_transcript_exon_variant,,ENST00000462405,;HFM1,downstream_gene_variant,,ENST00000497520,; T ENST00000370425 Transcript missense_variant 3267/4931 3168/4308 1056/1435 S/R agT/agA 1 -1 HFM1 HGNC HGNC:20193 protein_coding YES CCDS30769.2 ENSP00000359454 A2PYH4 UPI0000F51F79 NM_001017975.4 deleterious(0.02) 29/39 Pfam_domain:PF02889,SMART_domains:SM00973 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 91314033 91314033 A T 1 0 0 0 0 1 0 0 0 6967 40 2 4 4 HFM1 1 91314033 Missense_Mutation SNP A C3N-02089_T 5189016 91314033 157642389 40 27124 FNDC7 0 . GRCh38 1 108718883 108718883 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.432G>T p.= p.V144V ENST00000370017 4/13 325 285 40 397 397 0 strelka-varscan-mutect FNDC7,synonymous_variant,p.=,ENST00000370017,NM_001144937.1;FNDC7,upstream_gene_variant,,ENST00000445274,; T ENST00000370017 Transcript synonymous_variant 709/3332 432/2202 144/733 V gtG/gtT 1 1 FNDC7 HGNC HGNC:26668 protein_coding YES CCDS44185.1 ENSP00000359034 Q5VTL7 UPI000187497A NM_001144937.1 4/13 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF204,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 108718883 108718883 G T 1 0 0 0 0 0 0 0 1 5830 1364 48 2 2 FNDC7 1 108718883 Silent SNP G C3N-02089_T 17404850 108718883 140237539 41 27125 AKNAD1 0 . GRCh38 1 108820622 108820622 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.2172T>A p.Phe724Leu p.F724L ENST00000370001 14/16 79 67 12 79 79 0 strelka-varscan-mutect AKNAD1,missense_variant,p.Phe724Leu,ENST00000370001,NM_152763.4;AKNAD1,downstream_gene_variant,,ENST00000369995,;AKNAD1,downstream_gene_variant,,ENST00000369994,;AKNAD1,upstream_gene_variant,,ENST00000477908,;AKNAD1,intron_variant,,ENST00000474186,;AKNAD1,downstream_gene_variant,,ENST00000461774,;AKNAD1,upstream_gene_variant,,ENST00000466413,;AKNAD1,downstream_gene_variant,,ENST00000603450,; T ENST00000370001 Transcript missense_variant 2441/3053 2172/2511 724/836 F/L ttT/ttA 1 -1 AKNAD1 HGNC HGNC:28398 protein_coding YES CCDS791.2 ENSP00000359018 Q5T1N1 UPI00004700A0 NM_152763.4 tolerated(0.59) 14/16 hmmpanther:PTHR21510,hmmpanther:PTHR21510:SF16 MODERATE 1 SNV 1 1 PASS rs1432028574 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 108820622 108820622 A T 1 0 0 0 0 1 0 0 0 548 28 1 4 4 AKNAD1 1 108820622 Missense_Mutation SNP A C3N-02089_T 101739 108820622 140135800 42 27126 SYT6 0 . GRCh38 1 114138055 114138055 + Splice_Site SNP T T A novel C3N-02089_T C3N-02089_N T T c.258-2A>T p.X86_splice ENST00000609117 77 53 24 79 79 0 strelka-varscan-mutect SYT6,splice_acceptor_variant,,ENST00000609117,;SYT6,splice_acceptor_variant,,ENST00000369547,NM_001270805.1;SYT6,splice_acceptor_variant,,ENST00000607941,NM_205848.3;SYT6,splice_acceptor_variant,,ENST00000610222,;SYT6,splice_acceptor_variant,,ENST00000608203,;SYT6,splice_acceptor_variant,,ENST00000609577,;SYT6,downstream_gene_variant,,ENST00000608879,;SYT6,splice_acceptor_variant,,ENST00000610121,;SYT6,splice_acceptor_variant,,ENST00000610096,; A ENST00000609117 Transcript splice_acceptor_variant -/4424 258/1278 86/425 1 -1 SYT6 HGNC HGNC:18638 protein_coding YES CCDS871.1 ENSP00000477344 Q5T7P8 I6L9C3 UPI000000DACA 2/7 HIGH 1 SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.999996 1 1 1 0 A 5 1 90 114138055 114138055 T A 1 0 0 0 0 0 0 1 0 15872 1594 55 4 4 SYT6 1 114138055 Splice_Site SNP T C3N-02089_T 5317433 114138055 134818367 43 27127 CD2 0 . GRCh38 1 116754824 116754824 + Missense_Mutation SNP G G T rs763125349 C3N-02089_T C3N-02089_N G G c.255G>T p.Lys85Asn p.K85N ENST00000369478 2/5 198 136 62 244 244 0 strelka-varscan-mutect CD2,missense_variant,p.Lys85Asn,ENST00000369478,NM_001767.3;CD2,missense_variant,p.Lys85Asn,ENST00000369477,; T ENST00000369478 Transcript missense_variant 363/1609 255/1056 85/351 K/N aaG/aaT rs763125349 1 1 CD2 HGNC HGNC:1639 protein_coding YES CCDS889.1 ENSP00000358490 P06729 Q53F96 UPI0000062209 NM_001767.3 tolerated(0.27) 2/5 hmmpanther:PTHR12080:SF54,hmmpanther:PTHR12080,Gene3D:2.60.40.10,Pfam_domain:PF07686,Superfamily_domains:SSF48726,Prints_domain:PR01870 MODERATE 1 SNV 1 1 PASS rs763125349 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 116754824 116754824 G T 1 0 0 0 0 1 0 0 0 2682 962 34 2 2 CD2 1 116754824 Missense_Mutation SNP G C3N-02089_T 2616769 116754824 132201598 44 27128 GJA5 0 . GRCh38 1 147758761 147758761 + Missense_Mutation SNP G G T rs368383054 C3N-02089_T C3N-02089_N G G c.478C>A p.Arg160Ser p.R160S ENST00000621517 2/2 520 421 99 303 303 0 strelka-varscan-mutect GJA5,missense_variant,p.Arg160Ser,ENST00000621517,NM_005266.6;GJA5,missense_variant,p.Arg160Ser,ENST00000579774,NM_181703.3;GJA5,missense_variant,p.Arg160Ser,ENST00000430508,;RP11-433J22.2,downstream_gene_variant,,ENST00000622634,;RP11-433J22.2,downstream_gene_variant,,ENST00000612401,; T ENST00000621517 Transcript missense_variant 622/3183 478/1077 160/358 R/S Cgc/Agc rs368383054 1 -1 GJA5 HGNC HGNC:4279 protein_coding YES CCDS929.1 ENSP00000484552 P36382 X5D2H9 UPI000013D8D2 NM_005266.6 deleterious(0) 2/2 Gene3D:2zw3A00,Pfam_domain:PF00029,Prints_domain:PR00206,Prints_domain:PR01135,hmmpanther:PTHR11984,hmmpanther:PTHR11984:SF13 MODERATE 1 SNV 2 1 PASS rs368383054 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 147758761 147758761 G T 1 0 0 0 0 1 0 0 0 6283 1116 39 1 1 GJA5 1 147758761 Missense_Mutation SNP G C3N-02089_T 31003937 147758761 101197661 45 27129 NBPF11 0 . GRCh38 1 148114441 148114441 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.1633C>T p.Pro545Ser p.P545S ENST00000615281 15/24 61 45 16 64 64 0 varscan-mutect NBPF11,missense_variant,p.Pro545Ser,ENST00000615281,NM_183372.5;NBPF11,missense_variant,p.Pro545Ser,ENST00000614015,NM_001101663.4;NBPF11,missense_variant,p.Pro510Ser,ENST00000614785,;NBPF11,missense_variant,p.Pro470Ser,ENST00000613531,;NBPF11,missense_variant,p.Pro470Ser,ENST00000614506,; A ENST00000615281 Transcript missense_variant 2784/5494 1633/2598 545/865 P/S Ccc/Tcc 1 -1 NBPF11 HGNC HGNC:31993 protein_coding YES CCDS41381.2 ENSP00000477509 Q86T75 UPI0000198783 NM_183372.5 tolerated(0.12) 15/24 Pfam_domain:PF06758,PROSITE_profiles:PS51316,hmmpanther:PTHR14199,hmmpanther:PTHR14199:SF20,SMART_domains:SM01148 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 148114441 148114441 G A 1 0 0 0 0 1 0 0 0 10205 1188 41 3 3 NBPF11 1 148114441 Missense_Mutation SNP G C3N-02089_T 355680 148114441 100841981 46 27130 RPRD2 0 . GRCh38 1 150472935 150472935 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.3987T>A p.Ser1329Arg p.S1329R ENST00000369068 11/11 168 158 10 126 126 0 strelka-varscan-mutect RPRD2,missense_variant,p.Ser1303Arg,ENST00000401000,NM_001297674.1,NM_001297673.1;RPRD2,missense_variant,p.Ser1329Arg,ENST00000369068,NM_015203.4;RPRD2,non_coding_transcript_exon_variant,,ENST00000492220,; A ENST00000369068 Transcript missense_variant 3991/4612 3987/4386 1329/1461 S/R agT/agA 1 1 RPRD2 HGNC HGNC:29039 protein_coding YES CCDS44216.1 ENSP00000358064 Q5VT52 UPI00001D7CA8 NM_015203.4 deleterious_low_confidence(0.01) 11/11 hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF0 MODERATE 1 SNV 1 1 PASS rs1460433223 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 150472935 150472935 T A 1 0 0 0 0 1 0 0 0 13871 1722 60 4 4 RPRD2 1 150472935 Missense_Mutation SNP T C3N-02089_T 2358494 150472935 98483487 47 27131 HRNR 0 . GRCh38 1 152220283 152220283 + Missense_Mutation SNP G G T rs760948919 C3N-02089_T C3N-02089_N G G c.1346C>A p.Ser449Tyr p.S449Y ENST00000368801 3/3 376 305 71 328 328 0 strelka-varscan-mutect HRNR,missense_variant,p.Ser449Tyr,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; T ENST00000368801 Transcript missense_variant 1422/9623 1346/8553 449/2850 S/Y tCt/tAt rs760948919 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS rs760948919 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 152220283 152220283 G T 1 0 0 0 0 1 0 0 0 7254 942 33 2 2 HRNR 1 152220283 Missense_Mutation SNP G C3N-02089_T 1747348 152220283 96736139 48 27132 CRNN 0 . GRCh38 1 152410509 152410509 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.573G>T p.Gln191His p.Q191H ENST00000271835 3/3 364 292 72 310 310 0 strelka-varscan-mutect CRNN,missense_variant,p.Gln191His,ENST00000271835,NM_016190.2;FLG-AS1,intron_variant,,ENST00000411804,;FLG-AS1,downstream_gene_variant,,ENST00000628475,; A ENST00000271835 Transcript missense_variant 636/1902 573/1488 191/495 Q/H caG/caT 1 -1 CRNN HGNC HGNC:1230 protein_coding YES CCDS1010.1 ENSP00000271835 Q9UBG3 UPI000006E106 NM_016190.2 deleterious(0.02) 3/3 hmmpanther:PTHR11639,hmmpanther:PTHR11639:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 152410509 152410509 C A 1 0 0 0 0 1 0 0 0 3693 912 32 2 2 CRNN 1 152410509 Missense_Mutation SNP C C3N-02089_T 190226 152410509 96545913 49 27133 LCE5A 0 . GRCh38 1 152511723 152511723 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.189G>C p.Glu63Asp p.E63D ENST00000334269 2/2 379 304 75 353 353 0 strelka-varscan-mutect LCE5A,missense_variant,p.Glu63Asp,ENST00000334269,NM_178438.4;CRCT1,upstream_gene_variant,,ENST00000368790,NM_019060.2;AL135842.1,downstream_gene_variant,,ENST00000624892,; C ENST00000334269 Transcript missense_variant 365/819 189/357 63/118 E/D gaG/gaC COSM340142 1 1 LCE5A HGNC HGNC:16614 protein_coding YES CCDS1011.1 ENSP00000333952 Q5TCM9 UPI00001615D7 NM_178438.4 tolerated_low_confidence(0.78) 2/2 Pfam_domain:PF14672,hmmpanther:PTHR23263,Low_complexity_(Seg):seg 1 MODERATE SNV 3 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 152511723 152511723 G C 1 0 0 0 0 1 0 0 0 8580 991 35 4 4 LCE5A 1 152511723 Missense_Mutation SNP G C3N-02089_T 101214 152511723 96444699 50 27134 KPRP 0 . GRCh38 1 152761298 152761298 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.1710G>A p.= p.V570V ENST00000606109 1/1 137 121 16 110 110 0 strelka-varscan-mutect KPRP,synonymous_variant,p.=,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript synonymous_variant 1738/2492 1710/1740 570/579 V gtG/gtA 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 1/1 LOW 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 152761298 152761298 G A 1 0 0 0 0 0 0 0 1 8316 1277 45 3 3 KPRP 1 152761298 Silent SNP G C3N-02089_T 249575 152761298 96195124 51 27135 LCE1A 0 . GRCh38 1 152827479 152827479 + Missense_Mutation SNP T T A rs776567406 C3N-02089_T C3N-02089_N T T c.7T>A p.Cys3Ser p.C3S ENST00000335123 1/1 173 141 32 185 185 0 strelka-varscan-mutect LCE1A,missense_variant,p.Cys3Ser,ENST00000335123,NM_178348.2; A ENST00000335123 Transcript missense_variant 7/422 7/333 3/110 C/S Tgc/Agc rs776567406 1 1 LCE1A HGNC HGNC:29459 protein_coding YES CCDS1028.1 ENSP00000334869 Q5T7P2 UPI0000192766 NM_178348.2 deleterious_low_confidence(0) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23263,Prints_domain:PR00021 MODERATE 1 SNV 1 PASS rs776567406 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 152827479 152827479 T A 1 0 0 0 0 1 0 0 0 8564 1580 55 4 4 LCE1A 1 152827479 Missense_Mutation SNP T C3N-02089_T 66181 152827479 96128943 52 27136 NUP210L 0 . GRCh38 1 154094967 154094967 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.2155T>A p.Tyr719Asn p.Y719N ENST00000368559 15/40 361 323 38 256 256 0 strelka-varscan-mutect NUP210L,missense_variant,p.Tyr719Asn,ENST00000368559,NM_207308.2;NUP210L,missense_variant,p.Tyr719Asn,ENST00000271854,NM_001159484.1; T ENST00000368559 Transcript missense_variant 2227/5889 2155/5667 719/1888 Y/N Tac/Aac 1 -1 NUP210L HGNC HGNC:29915 protein_coding YES CCDS41399.1 ENSP00000357547 Q5VU65 UPI000023724F NM_207308.2 deleterious(0.02) 15/40 hmmpanther:PTHR23019,hmmpanther:PTHR23019:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 154094967 154094967 A T 1 0 0 0 0 1 0 0 0 10826 420 15 4 4 NUP210L 1 154094967 Missense_Mutation SNP A C3N-02089_T 1267488 154094967 94861455 53 27137 ATP8B2 0 . GRCh38 1 154348496 154348496 + Missense_Mutation SNP C C A rs755752350 C3N-02089_T C3N-02089_N C C c.3351C>A p.Phe1117Leu p.F1117L ENST00000368489 27/28 155 141 14 99 99 0 strelka-varscan-mutect ATP8B2,missense_variant,p.Phe1117Leu,ENST00000368489,NM_020452.3;ATP8B2,non_coding_transcript_exon_variant,,ENST00000505882,; A ENST00000368489 Transcript missense_variant 3351/5861 3351/3672 1117/1223 F/L ttC/ttA rs755752350 1 1 ATP8B2 HGNC HGNC:13534 protein_coding YES CCDS1066.1 ENSP00000357475 P98198 UPI00001B92AB NM_020452.3 tolerated(0.39) 27/28 Superfamily_domains:0049473,Pfam_domain:PF16212,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF46,TIGRFAM_domain:TIGR01652,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs755752350 . 0 205 3 2 0 0 0 0 -19.42412 0.9999819 1 1 1 0 A 3 1 90 154348496 154348496 C A 1 0 0 0 0 1 0 0 0 1348 854 30 2 2 ATP8B2 1 154348496 Missense_Mutation SNP C C3N-02089_T 253529 154348496 94607926 54 27138 RUSC1 0 . GRCh38 1 155325407 155325407 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1625G>C p.Gly542Ala p.G542A ENST00000368352 5/10 179 169 10 79 79 0 strelka-varscan-mutect RUSC1,missense_variant,p.Gly542Ala,ENST00000368352,NM_001105203.1;RUSC1,missense_variant,p.Gly542Ala,ENST00000368354,NM_001105204.1;RUSC1,missense_variant,p.Gly132Ala,ENST00000368347,NM_001105205.1;RUSC1,missense_variant,p.Gly73Ala,ENST00000292254,NM_001278230.1;RUSC1,missense_variant,p.Gly73Ala,ENST00000368349,NM_001278229.1,NM_014328.4,NM_001278227.1,NM_001278228.1;RUSC1,missense_variant,p.Gly73Ala,ENST00000497930,;RUSC1,missense_variant,p.Gly73Ala,ENST00000489860,;RUSC1,missense_variant,p.Gly73Ala,ENST00000479924,;RUSC1,5_prime_UTR_variant,,ENST00000471876,;RUSC1,5_prime_UTR_variant,,ENST00000490373,;FDPS,downstream_gene_variant,,ENST00000356657,NM_001135821.1;FDPS,downstream_gene_variant,,ENST00000368356,NM_002004.3;FDPS,downstream_gene_variant,,ENST00000447866,NM_001135822.1,NM_001242824.1;FDPS,downstream_gene_variant,,ENST00000612683,;FDPS,downstream_gene_variant,,ENST00000611010,NM_001242825.1;FDPS,downstream_gene_variant,,ENST00000467076,;RUSC1,upstream_gene_variant,,ENST00000485924,;RUSC1-AS1,upstream_gene_variant,,ENST00000446880,;RUSC1-AS1,upstream_gene_variant,,ENST00000450199,;RUSC1-AS1,upstream_gene_variant,,ENST00000543656,;RUSC1-AS1,upstream_gene_variant,,ENST00000443642,;FDPS,downstream_gene_variant,,ENST00000492244,;RUSC1,missense_variant,p.Gly73Ala,ENST00000468764,;RUSC1,non_coding_transcript_exon_variant,,ENST00000462780,;RUSC1,non_coding_transcript_exon_variant,,ENST00000492536,;RUSC1,non_coding_transcript_exon_variant,,ENST00000467820,;RUSC1,non_coding_transcript_exon_variant,,ENST00000473331,;FDPS,downstream_gene_variant,,ENST00000490140,;FDPS,downstream_gene_variant,,ENST00000489324,; C ENST00000368352 Transcript missense_variant 1776/3403 1625/2709 542/902 G/A gGg/gCg 1 1 RUSC1 HGNC HGNC:17153 protein_coding YES CCDS41410.1 ENSP00000357336 Q9BVN2 UPI000046FDA5 NM_001105203.1 deleterious(0) 5/10 PROSITE_profiles:PS50826,hmmpanther:PTHR15591,Pfam_domain:PF02759,Superfamily_domains:0052343 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 155325407 155325407 G C 1 0 0 0 0 1 0 0 0 14011 1232 43 4 4 RUSC1 1 155325407 Missense_Mutation SNP G C3N-02089_T 976911 155325407 93631015 55 27139 IQGAP3 0 . GRCh38 1 156528601 156528601 + Silent SNP C C A rs754015306 C3N-02089_T C3N-02089_N C C c.4581G>T p.= p.G1527G ENST00000361170 36/38 222 153 69 161 161 0 strelka-varscan-mutect IQGAP3,synonymous_variant,p.=,ENST00000361170,NM_178229.4;IQGAP3,synonymous_variant,p.=,ENST00000491900,; A ENST00000361170 Transcript synonymous_variant 4592/5988 4581/4896 1527/1631 G ggG/ggT rs754015306 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 36/38 Low_complexity_(Seg):seg,hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149,Pfam_domain:PF03836 LOW 1 SNV 1 1 PASS rs754015306 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 156528601 156528601 C A 1 0 0 0 0 0 0 0 1 7722 842 30 2 2 IQGAP3 1 156528601 Silent SNP C C3N-02089_T 1203194 156528601 92427821 56 27140 BCAN 0 . GRCh38 1 156652833 156652833 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1883A>T p.Gln628Leu p.Q628L ENST00000329117 8/14 218 184 34 137 136 1 strelka-varscan-mutect BCAN,missense_variant,p.Gln628Leu,ENST00000329117,NM_021948.4;BCAN,missense_variant,p.Gln628Leu,ENST00000361588,NM_198427.1;BCAN,downstream_gene_variant,,ENST00000424639,;RP11-284F21.7,intron_variant,,ENST00000448869,;BCAN,upstream_gene_variant,,ENST00000496038,;BCAN,downstream_gene_variant,,ENST00000479949,;BCAN,downstream_gene_variant,,ENST00000491823,; T ENST00000329117 Transcript missense_variant 2219/3466 1883/2736 628/911 Q/L cAg/cTg 1 1 BCAN HGNC HGNC:23059 protein_coding YES CCDS1149.1 ENSP00000331210 Q96GW7 UPI000006F0E9 NM_021948.4 tolerated(0.4) 8/14 hmmpanther:PTHR22804 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 156652833 156652833 A T 1 0 0 0 0 1 0 0 0 1492 188 7 4 4 BCAN 1 156652833 Missense_Mutation SNP A C3N-02089_T 124232 156652833 92303589 57 27141 PEAR1 0 . GRCh38 1 156908753 156908753 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1214A>T p.Gln405Leu p.Q405L ENST00000338302 11/24 147 119 28 106 106 0 strelka-varscan-mutect PEAR1,missense_variant,p.Gln405Leu,ENST00000338302,;PEAR1,missense_variant,p.Gln405Leu,ENST00000292357,NM_001080471.1;PEAR1,downstream_gene_variant,,ENST00000455314,;PEAR1,non_coding_transcript_exon_variant,,ENST00000469390,;PEAR1,upstream_gene_variant,,ENST00000465101,;PEAR1,downstream_gene_variant,,ENST00000444016,;PEAR1,upstream_gene_variant,,ENST00000482505,; T ENST00000338302 Transcript missense_variant 1439/4970 1214/3114 405/1037 Q/L cAg/cTg 1 1 PEAR1 HGNC HGNC:33631 protein_coding YES CCDS30892.1 ENSP00000344465 Q5VY43 UPI000045889A tolerated(0.58) 11/24 PROSITE_profiles:PS50026,hmmpanther:PTHR24052,hmmpanther:PTHR24052:SF12,Gene3D:2gy5A03,SMART_domains:SM00181 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 156908753 156908753 A T 1 0 0 0 0 1 0 0 0 11801 188 7 4 4 PEAR1 1 156908753 Missense_Mutation SNP A C3N-02089_T 255920 156908753 92047669 58 27142 ETV3L 0 . GRCh38 1 157099271 157099271 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.166C>A p.His56Asn p.H56N ENST00000454449 2/5 308 282 26 273 273 0 varscan-mutect ETV3L,missense_variant,p.His56Asn,ENST00000454449,NM_001004341.2; T ENST00000454449 Transcript missense_variant 451/1976 166/1086 56/361 H/N Cat/Aat COSM1646006,COSM676315 1 -1 ETV3L HGNC HGNC:33834 protein_coding YES CCDS30893.1 ENSP00000430271 Q6ZN32 UPI000035E7AE NM_001004341.2 tolerated(0.22) 2/5 Gene3D:1.10.10.10,Pfam_domain:PF00178,PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF30,SMART_domains:SM00413,Superfamily_domains:SSF46785 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 157099271 157099271 G T 1 0 0 0 0 1 0 0 0 5144 1348 47 2 2 ETV3L 1 157099271 Missense_Mutation SNP G C3N-02089_T 190518 157099271 91857151 59 27143 CD1E 0 . GRCh38 1 158354502 158354502 + Missense_Mutation SNP C C A rs772321585 C3N-02089_T C3N-02089_N C C c.184C>A p.Leu62Met p.L62M ENST00000368167 2/6 232 161 71 199 198 1 strelka-varscan-mutect CD1E,missense_variant,p.Leu62Met,ENST00000368160,NM_001042583.2;CD1E,missense_variant,p.Leu62Met,ENST00000368161,NM_001042584.2;CD1E,missense_variant,p.Leu62Met,ENST00000368163,NM_001042585.2;CD1E,missense_variant,p.Leu62Met,ENST00000368167,NM_030893.3;CD1E,missense_variant,p.Leu62Met,ENST00000368165,NM_001185107.1;CD1E,missense_variant,p.Leu62Met,ENST00000368156,NM_001185115.1;CD1E,missense_variant,p.Leu62Met,ENST00000368155,NM_001185108.1;CD1E,intron_variant,,ENST00000444681,NM_001185114.1;CD1E,intron_variant,,ENST00000368166,NM_001042586.2;CD1E,intron_variant,,ENST00000368164,NM_001042587.2;CD1E,intron_variant,,ENST00000452291,NM_001185112.1;CD1E,intron_variant,,ENST00000368154,NM_001185113.1;CD1E,intron_variant,,ENST00000368157,NM_001185110.1;CD1E,upstream_gene_variant,,ENST00000368162,;CD1E,intron_variant,,ENST00000464822,; A ENST00000368167 Transcript missense_variant 423/1458 184/1167 62/388 L/M Ctg/Atg rs772321585 1 1 CD1E HGNC HGNC:1638 protein_coding YES CCDS41417.1 ENSP00000357149 P15812 UPI000046F8C2 NM_030893.3 tolerated(0.05) 2/6 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF146,Gene3D:3.30.500.10,Pfam_domain:PF16497,Superfamily_domains:SSF54452 MODERATE 1 SNV 1 1 PASS rs772321585 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 158354502 158354502 C A 1 0 0 0 0 1 0 0 0 2681 680 24 2 2 CD1E 1 158354502 Missense_Mutation SNP C C3N-02089_T 1255231 158354502 90601920 60 27144 OR10T2 0 . GRCh38 1 158398883 158398883 + Missense_Mutation SNP A A T rs141841653 C3N-02089_T C3N-02089_N A A c.584T>A p.Val195Glu p.V195E ENST00000334438 1/1 176 121 55 166 165 1 strelka-varscan-mutect OR10T2,missense_variant,p.Val195Glu,ENST00000334438,NM_001004475.1; T ENST00000334438 Transcript missense_variant 584/945 584/945 195/314 V/E gTg/gAg rs141841653 1 -1 OR10T2 HGNC HGNC:14816 protein_coding YES CCDS30895.1 ENSP00000334115 Q8NGX3 A0A126GV74 UPI000003F220 NM_001004475.1 deleterious(0.03) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF98,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs141841653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 158398883 158398883 A T 1 0 0 0 0 1 0 0 0 10996 159 6 4 4 OR10T2 1 158398883 Missense_Mutation SNP A C3N-02089_T 44381 158398883 90557539 61 27145 OR6P1 0 . GRCh38 1 158563150 158563150 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.455G>T p.Gly152Val p.G152V ENST00000334632 1/1 301 263 38 243 242 1 strelka-varscan-mutect OR6P1,missense_variant,p.Gly152Val,ENST00000334632,NM_001160325.1; A ENST00000334632 Transcript missense_variant 455/954 455/954 152/317 G/V gGc/gTc 1 -1 OR6P1 HGNC HGNC:15036 protein_coding YES CCDS53391.1 ENSP00000334721 Q8NGX9 A0A126GV72 UPI000004B1FF NM_001160325.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF73,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 90 158563150 158563150 C A 1 0 0 0 0 1 0 0 0 11277 739 26 2 2 OR6P1 1 158563150 Missense_Mutation SNP C C3N-02089_T 164267 158563150 90393272 62 27146 SPTA1 0 . GRCh38 1 158662855 158662855 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.2311T>A p.Leu771Met p.L771M ENST00000368147 17/52 588 532 56 442 441 1 strelka-varscan-mutect SPTA1,missense_variant,p.Leu771Met,ENST00000368147,NM_003126.2; T ENST00000368147 Transcript missense_variant 2492/7999 2311/7260 771/2419 L/M Ttg/Atg 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.01) 17/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 158662855 158662855 A T 1 0 0 0 0 1 0 0 0 15472 69 3 4 4 SPTA1 1 158662855 Missense_Mutation SNP A C3N-02089_T 99705 158662855 90293567 63 27147 CADM3 0 . GRCh38 1 159196443 159196443 + Silent SNP C C A rs373766355 C3N-02089_T C3N-02089_N C C c.873C>A p.= p.R291R ENST00000368124 7/10 210 179 31 168 168 0 strelka-varscan-mutect CADM3,synonymous_variant,p.=,ENST00000368125,NM_001127173.1;CADM3,synonymous_variant,p.=,ENST00000368124,NM_021189.3;CADM3,synonymous_variant,p.=,ENST00000416746,;CADM3-AS1,non_coding_transcript_exon_variant,,ENST00000415675,;CADM3-AS1,downstream_gene_variant,,ENST00000609696,; A ENST00000368124 Transcript synonymous_variant 1030/2546 873/1299 291/432 R cgC/cgA rs373766355,COSM1335327 1 1 CADM3 HGNC HGNC:17601 protein_coding YES CCDS1182.1 ENSP00000357106 Q8N126 UPI000006E8A2 NM_021189.3 7/10 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF57,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 LOW 1 SNV 1 0,1 1 PASS rs373766355 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 159196443 159196443 C A 1 0 0 0 0 0 0 0 1 2258 755 27 1 1 CADM3 1 159196443 Silent SNP C C3N-02089_T 533588 159196443 89759979 64 27148 CRP 0 . GRCh38 1 159713869 159713869 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.331C>A p.Pro111Thr p.P111T ENST00000255030 2/2 476 430 46 322 322 0 strelka-varscan-mutect CRP,missense_variant,p.Pro111Thr,ENST00000255030,NM_000567.2;CRP,5_prime_UTR_variant,,ENST00000437342,;CRP,intron_variant,,ENST00000368112,;CRP,intron_variant,,ENST00000368110,;CRP,intron_variant,,ENST00000368111,;CRP,intron_variant,,ENST00000489317,;CRP,upstream_gene_variant,,ENST00000473196,; T ENST00000255030 Transcript missense_variant 435/2015 331/675 111/224 P/T Cca/Aca COSM349823 1 -1 CRP HGNC HGNC:2367 protein_coding YES CCDS30911.1 ENSP00000255030 P02741 UPI0000128478 NM_000567.2 deleterious(0.02) 2/2 hmmpanther:PTHR19277:SF119,hmmpanther:PTHR19277,Pfam_domain:PF00354,Gene3D:2.60.120.200,SMART_domains:SM00159,Superfamily_domains:SSF49899 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 159713869 159713869 G T 1 0 0 0 0 1 0 0 0 3697 1174 41 2 2 CRP 1 159713869 Missense_Mutation SNP G C3N-02089_T 517426 159713869 89242553 65 27149 SLAMF8 0 . GRCh38 1 159832969 159832969 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.465delC p.Asn156ThrfsTer5 p.N156Tfs*5 ENST00000289707 3/5 457 327 130 261 261 0 sindel-varindel-pindel SLAMF8,frameshift_variant,p.Asn156ThrfsTer5,ENST00000289707,NM_020125.2;SLAMF8,frameshift_variant,p.Asn47ThrfsTer5,ENST00000368104,;C1orf204,downstream_gene_variant,,ENST00000368102,NM_001134233.1;C1orf204,downstream_gene_variant,,ENST00000621242,;SLAMF8,non_coding_transcript_exon_variant,,ENST00000471286,;C1orf204,downstream_gene_variant,,ENST00000491974,;SLAMF8,upstream_gene_variant,,ENST00000497141,; - ENST00000289707 Transcript frameshift_variant 610/2996 461/858 154/285 A/X gCc/gc 1 1 SLAMF8 HGNC HGNC:21391 protein_coding YES CCDS1188.1 ENSP00000289707 Q9P0V8 UPI000003E841 NM_020125.2 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF55,Superfamily_domains:SSF48726 HIGH 1 deletion 1 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 159832969 159832969 C - 1 0 1 0 1 0 0 0 0 14635 739 26 0 0 SLAMF8 1 159832969 Frame_Shift_Del DEL C C3N-02089_T 119100 159832969 89123453 66 27150 SLAMF9 0 . GRCh38 1 159953532 159953532 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.168C>T p.= p.S56S ENST00000368093 2/4 250 202 48 155 155 0 strelka-mutect SLAMF9,synonymous_variant,p.=,ENST00000368093,NM_033438.3;SLAMF9,synonymous_variant,p.=,ENST00000368092,NM_001146172.1;SLAMF9,non_coding_transcript_exon_variant,,ENST00000489098,;SLAMF9,upstream_gene_variant,,ENST00000466773,; A ENST00000368093 Transcript synonymous_variant 285/1156 168/870 56/289 S tcC/tcT COSM4024036 1 -1 SLAMF9 HGNC HGNC:18430 protein_coding YES CCDS1191.1 ENSP00000357072 Q96A28 UPI000013E1B2 NM_033438.3 2/4 Gene3D:2.60.40.10,hmmpanther:PTHR12080,hmmpanther:PTHR12080:SF18,Superfamily_domains:SSF48726 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 159953532 159953532 G A 1 0 0 0 0 0 0 0 1 14636 987 35 3 3 SLAMF9 1 159953532 Silent SNP G C3N-02089_T 120563 159953532 89002890 67 27151 NECTIN4 0 . GRCh38 1 161072819 161072819 + Nonsense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1375G>T p.Glu459Ter p.E459* ENST00000368012 9/9 671 452 219 409 409 0 strelka-varscan-mutect NECTIN4,stop_gained,p.Glu459Ter,ENST00000368012,NM_030916.2;ARHGAP30,upstream_gene_variant,,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,upstream_gene_variant,,ENST00000368015,NM_001287602.1;ARHGAP30,upstream_gene_variant,,ENST00000368016,NM_181720.2;NECTIN4,non_coding_transcript_exon_variant,,ENST00000486694,;ARHGAP30,upstream_gene_variant,,ENST00000461003,;ARHGAP30,upstream_gene_variant,,ENST00000490279,;ARHGAP30,upstream_gene_variant,,ENST00000368018,;ARHGAP30,upstream_gene_variant,,ENST00000471492,; A ENST00000368012 Transcript stop_gained 1678/3502 1375/1533 459/510 E/* Gaa/Taa COSM676682 1 -1 NECTIN4 HGNC HGNC:19688 protein_coding YES CCDS1216.1 ENSP00000356991 Q96NY8 K4PZ75 UPI000006F072 NM_030916.2 9/9 hmmpanther:PTHR23277:SF11,hmmpanther:PTHR23277 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 161072819 161072819 C A 1 0 0 0 0 0 1 0 0 10336 835 29 2 2 NECTIN4 1 161072819 Nonsense_Mutation SNP C C3N-02089_T 1119287 161072819 87883603 68 27152 SELE 0 . GRCh38 1 169728088 169728088 + Missense_Mutation SNP C C T C3N-02089_T C3N-02089_N C C c.1249G>A p.Glu417Lys p.E417K ENST00000333360 8/14 144 127 17 181 181 0 strelka-varscan-mutect SELE,missense_variant,p.Glu417Lys,ENST00000333360,NM_000450.2;SELE,missense_variant,p.Glu417Lys,ENST00000367777,;SELE,intron_variant,,ENST00000367776,;SELE,intron_variant,,ENST00000367775,;SELE,intron_variant,,ENST00000367774,;C1orf112,intron_variant,,ENST00000498289,;SELE,downstream_gene_variant,,ENST00000461085,; T ENST00000333360 Transcript missense_variant 1389/3857 1249/1833 417/610 E/K Gag/Aag COSM5598768 1 -1 SELE HGNC HGNC:10718 protein_coding YES CCDS1283.1 ENSP00000331736 P16581 UPI000012E44A NM_000450.2 tolerated(0.42) 8/14 PROSITE_profiles:PS50923,hmmpanther:PTHR19325:SF380,hmmpanther:PTHR19325,Pfam_domain:PF00084,Gene3D:2.10.70.10,SMART_domains:SM00032,Superfamily_domains:SSF57535 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 169728088 169728088 C T 1 0 0 0 0 1 0 0 0 14290 864 30 3 3 SELE 1 169728088 Missense_Mutation SNP C C3N-02089_T 8655269 169728088 79228334 69 27153 FMO4 0 . GRCh38 1 171341444 171341444 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1282T>G p.Phe428Val p.F428V ENST00000367749 10/10 114 94 20 123 123 0 strelka-varscan-mutect FMO4,missense_variant,p.Phe428Val,ENST00000367749,NM_002022.2;FMO4,non_coding_transcript_exon_variant,,ENST00000480136,;FMO4,downstream_gene_variant,,ENST00000475780,;RP4-798A17.5,upstream_gene_variant,,ENST00000450334,;TOP1P1,downstream_gene_variant,,ENST00000599419,; G ENST00000367749 Transcript missense_variant 1612/2252 1282/1677 428/558 F/V Ttt/Gtt 1 1 FMO4 HGNC HGNC:3772 protein_coding YES CCDS1295.1 ENSP00000356723 P31512 UPI000013C52B NM_002022.2 tolerated(1) 10/10 Gene3D:3.50.50.60,Pfam_domain:PF00743,PIRSF_domain:PIRSF000332,Prints_domain:PR01124,hmmpanther:PTHR23023,hmmpanther:PTHR23023:SF74,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 171341444 171341444 T G 1 0 0 0 0 1 0 0 0 5813 1493 52 5 5 FMO4 1 171341444 Missense_Mutation SNP T C3N-02089_T 1613356 171341444 77614978 70 27154 FASLG 0 . GRCh38 1 172665651 172665651 + Nonsense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.481G>T p.Glu161Ter p.E161* ENST00000367721 4/4 180 139 41 159 159 0 strelka-varscan-mutect FASLG,stop_gained,p.Glu161Ter,ENST00000367721,NM_000639.2;FASLG,3_prime_UTR_variant,,ENST00000340030,NM_001302746.1; T ENST00000367721 Transcript stop_gained 665/1888 481/846 161/281 E/* Gaa/Taa COSM677112 1 1 FASLG HGNC HGNC:11936 protein_coding YES CCDS1304.1 ENSP00000356694 P48023 Q53ZZ1 UPI000000D91A NM_000639.2 4/4 Gene3D:2.60.120.40,Pfam_domain:PF00229,Prints_domain:PR01681,PROSITE_profiles:PS50049,hmmpanther:PTHR11471,hmmpanther:PTHR11471:SF33,SMART_domains:SM00207,Superfamily_domains:SSF49842 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 172665651 172665651 G T 1 0 0 0 0 0 1 0 0 5542 1175 41 2 2 FASLG 1 172665651 Nonsense_Mutation SNP G C3N-02089_T 1324207 172665651 76290771 71 27155 TNR 0 . GRCh38 1 175386156 175386156 + Silent SNP C C A rs752380382 C3N-02089_T C3N-02089_N C C c.1653G>T p.= p.R551R ENST00000367674 8/23 123 79 44 101 101 0 strelka-varscan-mutect TNR,synonymous_variant,p.=,ENST00000367674,;TNR,synonymous_variant,p.=,ENST00000263525,NM_003285.2; A ENST00000367674 Transcript synonymous_variant 2362/12949 1653/4077 551/1358 R cgG/cgT rs752380382 1 -1 TNR HGNC HGNC:11953 protein_coding YES CCDS1318.1 ENSP00000356646 Q92752 UPI000013D41C 8/23 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs752380382 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 175386156 175386156 C A 1 0 0 0 0 0 0 0 1 16811 726 26 2 2 TNR 1 175386156 Silent SNP C C3N-02089_T 2720505 175386156 73570266 72 27156 HMCN1 0 . GRCh38 1 186019694 186019694 + Missense_Mutation SNP A A C rs751987871 C3N-02089_T C3N-02089_N A A c.5624A>C p.Lys1875Thr p.K1875T ENST00000271588 35/107 142 121 21 139 139 0 strelka-varscan-mutect HMCN1,missense_variant,p.Lys1875Thr,ENST00000271588,NM_031935.2; C ENST00000271588 Transcript missense_variant,splice_region_variant 5853/18208 5624/16908 1875/5635 K/T aAa/aCa rs751987871 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.08) 35/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs751987871 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 186019694 186019694 A C 1 0 0 0 0 1 0 0 0 7111 28 1 5 5 HMCN1 1 186019694 Missense_Mutation SNP A C3N-02089_T 10633538 186019694 62936728 73 27157 HMCN1 0 . GRCh38 1 186065390 186065390 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.7666G>T p.Ala2556Ser p.A2556S ENST00000271588 49/107 126 105 21 125 125 0 strelka-varscan-mutect HMCN1,missense_variant,p.Ala2556Ser,ENST00000271588,NM_031935.2; T ENST00000271588 Transcript missense_variant 7895/18208 7666/16908 2556/5635 A/S Gct/Tct 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 deleterious(0) 49/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 186065390 186065390 G T 1 0 0 0 0 1 0 0 0 7111 971 34 2 2 HMCN1 1 186065390 Missense_Mutation SNP G C3N-02089_T 45696 186065390 62891032 74 27158 HMCN1 0 . GRCh38 1 186172038 186172038 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.15721C>A p.Pro5241Thr p.P5241T ENST00000271588 102/107 187 150 37 209 209 0 strelka-varscan-mutect HMCN1,missense_variant,p.Pro5241Thr,ENST00000271588,NM_031935.2;HMCN1,missense_variant,p.Pro33Thr,ENST00000414277,;GS1-174L6.4,downstream_gene_variant,,ENST00000428391,;HMCN1,non_coding_transcript_exon_variant,,ENST00000475585,; A ENST00000271588 Transcript missense_variant 15950/18208 15721/16908 5241/5635 P/T Cca/Aca 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(0.23) 102/107 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 186172038 186172038 C A 1 0 0 0 0 1 0 0 0 7111 507 18 2 2 HMCN1 1 186172038 Missense_Mutation SNP C C3N-02089_T 106648 186172038 62784384 75 27159 TPR 0 . GRCh38 1 186344424 186344424 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.3368A>T p.Gln1123Leu p.Q1123L ENST00000367478 25/51 158 141 17 141 140 1 strelka-varscan-mutect TPR,missense_variant,p.Gln1123Leu,ENST00000367478,NM_003292.2;TPR,upstream_gene_variant,,ENST00000481347,; A ENST00000367478 Transcript missense_variant 3665/9708 3368/7092 1123/2363 Q/L cAg/cTg 1 -1 TPR HGNC HGNC:12017 protein_coding YES CCDS41446.1 ENSP00000356448 P12270 UPI000046FCF4 NM_003292.2 tolerated(0.4) 25/51 Pfam_domain:PF07926,hmmpanther:PTHR18898 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.99997 0.9999999 1 1 1 0 A 3 1 90 186344424 186344424 T A 1 0 0 0 0 1 0 0 0 16897 1580 55 4 4 TPR 1 186344424 Missense_Mutation SNP T C3N-02089_T 172386 186344424 62611998 76 27160 CFH 0 . GRCh38 1 196673114 196673114 + Silent SNP A A T rs771886580 C3N-02089_T C3N-02089_N A A c.195A>T p.= p.V65V ENST00000367429 2/22 310 208 102 354 354 0 strelka-varscan-mutect CFH,synonymous_variant,p.=,ENST00000367429,NM_000186.3;CFH,synonymous_variant,p.=,ENST00000630130,NM_001014975.2;CFH,synonymous_variant,p.=,ENST00000359637,;CFH,non_coding_transcript_exon_variant,,ENST00000496761,;CFH,upstream_gene_variant,,ENST00000466229,; T ENST00000367429 Transcript synonymous_variant 435/4127 195/3696 65/1231 V gtA/gtT rs771886580 1 1 CFH HGNC HGNC:4883 protein_coding YES CCDS1385.1 ENSP00000356399 P08603 A0A024R962 UPI000013C4D1 NM_000186.3 2/22 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF373,SMART_domains:SM00032,Superfamily_domains:SSF57535 LOW 1 SNV 1 1 PASS rs771886580 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 196673114 196673114 A T 1 0 0 0 0 0 0 0 1 3041 436 16 4 4 CFH 1 196673114 Silent SNP A C3N-02089_T 10328690 196673114 52283308 77 27161 CFH 0 . GRCh38 1 196726596 196726596 + Missense_Mutation SNP G G C rs758435912 C3N-02089_T C3N-02089_N G G c.2000G>C p.Gly667Ala p.G667A ENST00000367429 13/22 207 183 24 230 230 0 strelka-varscan-mutect CFH,missense_variant,p.Gly667Ala,ENST00000367429,NM_000186.3;CFH,non_coding_transcript_exon_variant,,ENST00000466229,; C ENST00000367429 Transcript missense_variant 2240/4127 2000/3696 667/1231 G/A gGa/gCa rs758435912 1 1 CFH HGNC HGNC:4883 protein_coding YES CCDS1385.1 ENSP00000356399 P08603 A0A024R962 UPI000013C4D1 NM_000186.3 deleterious(0) 13/22 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF373,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs758435912 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 196726596 196726596 G C 1 0 0 0 0 1 0 0 0 3041 1174 41 4 4 CFH 1 196726596 Missense_Mutation SNP G C3N-02089_T 53482 196726596 52229826 78 27162 ASPM 0 . GRCh38 1 197100643 197100643 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.8608T>G p.Phe2870Val p.F2870V ENST00000367409 18/28 292 259 33 312 311 1 strelka-varscan-mutect ASPM,missense_variant,p.Phe2870Val,ENST00000367409,NM_018136.4;ASPM,missense_variant,p.Phe856Val,ENST00000612785,;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000367408,; C ENST00000367409 Transcript missense_variant 8865/10887 8608/10434 2870/3477 F/V Ttt/Gtt 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 tolerated(0.11) 18/28 Pfam_domain:PF00612,PROSITE_profiles:PS50096,SMART_domains:SM00015 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 197100643 197100643 A C 1 0 0 0 0 1 0 0 0 1203 14 1 5 5 ASPM 1 197100643 Missense_Mutation SNP A C3N-02089_T 374047 197100643 51855779 79 27163 ZBTB41 0 . GRCh38 1 197200402 197200402 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.72A>T p.Glu24Asp p.E24D ENST00000367405 1/10 113 79 34 119 119 0 strelka-varscan-mutect ZBTB41,missense_variant,p.Glu24Asp,ENST00000367405,NM_194314.2;ZBTB41,non_coding_transcript_exon_variant,,ENST00000467322,; A ENST00000367405 Transcript missense_variant 141/8478 72/2730 24/909 E/D gaA/gaT 1 -1 ZBTB41 HGNC HGNC:24819 protein_coding YES CCDS30960.1 ENSP00000356375 Q5SVQ8 UPI00001D7DE7 NM_194314.2 tolerated_low_confidence(0.62) 1/10 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999984 1 1 1 0 A 3 1 90 197200402 197200402 T A 1 0 0 0 0 1 0 0 0 18112 1606 56 4 4 ZBTB41 1 197200402 Missense_Mutation SNP T C3N-02089_T 99759 197200402 51756020 80 27164 PIK3C2B 0 . GRCh38 1 204465316 204465316 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.937G>T p.Gly313Cys p.G313C ENST00000367187 4/34 168 130 38 152 152 0 strelka-varscan-mutect PIK3C2B,missense_variant,p.Gly313Cys,ENST00000367187,NM_002646.3;PIK3C2B,missense_variant,p.Gly313Cys,ENST00000424712,;PIK3C2B,missense_variant,p.Gly91Cys,ENST00000367184,;PIK3C2B,downstream_gene_variant,,ENST00000415899,;PIK3C2B,downstream_gene_variant,,ENST00000429009,; A ENST00000367187 Transcript missense_variant 1494/7686 937/4905 313/1634 G/C Ggc/Tgc 1 -1 PIK3C2B HGNC HGNC:8972 protein_coding YES CCDS1446.1 ENSP00000356155 O00750 A2RUF7 UPI00002056D1 NM_002646.3 tolerated(0.13) 4/34 hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 204465316 204465316 C A 1 0 0 0 0 1 0 0 0 12005 637 22 2 2 PIK3C2B 1 204465316 Missense_Mutation SNP C C3N-02089_T 7264914 204465316 44491106 81 27165 NFASC 0 . GRCh38 1 204954225 204954225 + Missense_Mutation SNP G G T rs769904507 C3N-02089_T C3N-02089_N G G c.253G>T p.Ala85Ser p.A85S ENST00000339876 6/30 324 235 89 298 298 0 strelka-varscan-mutect NFASC,missense_variant,p.Ala85Ser,ENST00000339876,NM_001005388.2;NFASC,missense_variant,p.Ala85Ser,ENST00000401399,;NFASC,missense_variant,p.Ala79Ser,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Ala79Ser,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Ala79Ser,ENST00000404076,;NFASC,missense_variant,p.Ala79Ser,ENST00000404907,;NFASC,missense_variant,p.Ala55Ser,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Ala55Ser,ENST00000367173,;NFASC,missense_variant,p.Ala79Ser,ENST00000513543,;NFASC,missense_variant,p.Ala85Ser,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,missense_variant,p.Ala85Ser,ENST00000505079,;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,upstream_gene_variant,,ENST00000504149,;NFASC,missense_variant,p.Ala85Ser,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000514644,;NFASC,upstream_gene_variant,,ENST00000512826,; T ENST00000339876 Transcript missense_variant 581/10333 253/3723 85/1240 A/S Gcc/Tcc rs769904507 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 tolerated(0.17) 6/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs769904507 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 204954225 204954225 G T 1 0 0 0 0 1 0 0 0 10396 1087 38 1 1 NFASC 1 204954225 Missense_Mutation SNP G C3N-02089_T 488909 204954225 44002197 82 27166 ELK4 0 . GRCh38 1 205620562 205620562 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.484C>G p.Leu162Val p.L162V ENST00000357992 3/5 297 271 26 338 338 0 strelka-varscan-mutect ELK4,missense_variant,p.Leu162Val,ENST00000357992,NM_001973.3;ELK4,missense_variant,p.Leu162Val,ENST00000289703,NM_021795.2;ELK4,downstream_gene_variant,,ENST00000468523,;ELK4,missense_variant,p.Leu162Val,ENST00000616704,;RP11-6B6.3,upstream_gene_variant,,ENST00000411645,; C ENST00000357992 Transcript missense_variant 824/10239 484/1296 162/431 L/V Ctt/Gtt 1 -1 ELK4 HGNC HGNC:3326 protein_coding YES CCDS1456.1 ENSP00000350681 P28324 A0A024R9C2 UPI0000129E67 NM_001973.3 deleterious(0.04) 3/5 hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF21 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 205620562 205620562 G C 1 0 0 0 0 1 0 0 0 4895 971 34 4 4 ELK4 1 205620562 Missense_Mutation SNP G C3N-02089_T 666337 205620562 43335860 83 27167 NUCKS1 0 . GRCh38 1 205718315 205718315 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.697G>T p.Gly233Trp p.G233W ENST00000367142 7/7 164 117 47 168 168 0 strelka-varscan-mutect NUCKS1,missense_variant,p.Gly233Trp,ENST00000367142,NM_022731.4;NUCKS1,downstream_gene_variant,,ENST00000464938,; A ENST00000367142 Transcript missense_variant 1000/6496 697/732 233/243 G/W Ggg/Tgg 1 -1 NUCKS1 HGNC HGNC:29923 protein_coding YES CCDS30987.1 ENSP00000356110 Q9H1E3 UPI000013096A NM_022731.4 deleterious(0) 7/7 hmmpanther:PTHR15361 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 205718315 205718315 C A 1 0 0 0 0 1 0 0 0 10786 681 24 2 2 NUCKS1 1 205718315 Missense_Mutation SNP C C3N-02089_T 97753 205718315 43238107 84 27168 CR1 0 . GRCh38 1 207614409 207614409 + Missense_Mutation SNP G G C rs55704352 C3N-02089_T C3N-02089_N G G c.6581G>C p.Arg2194Pro p.R2194P ENST00000367049 40/47 216 164 52 229 229 0 strelka-varscan-mutect CR1,missense_variant,p.Arg2194Pro,ENST00000367049,NM_000651.4;CR1,missense_variant,p.Arg1744Pro,ENST00000367051,;CR1,missense_variant,p.Arg1744Pro,ENST00000367052,;CR1,missense_variant,p.Arg1744Pro,ENST00000367053,;CR1,missense_variant,p.Arg1744Pro,ENST00000400960,NM_000573.3;CR1,intron_variant,,ENST00000529814,;CR1,downstream_gene_variant,,ENST00000534202,; C ENST00000367049 Transcript missense_variant 6581/7470 6581/7470 2194/2489 R/P cGa/cCa rs55704352,COSM5417191,COSM5417192 1 1 CR1 HGNC HGNC:2334 protein_coding YES CCDS44308.1 ENSP00000356016 E9PDY4 UPI000040E8CF NM_000651.4 deleterious(0.05) 40/47 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,SMART_domains:SM00032,Superfamily_domains:SSF57535 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs55704352 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 207614409 207614409 G C 1 0 0 0 0 1 0 0 0 3638 1072 37 4 4 CR1 1 207614409 Missense_Mutation SNP G C3N-02089_T 1896094 207614409 41342013 85 27169 C1orf74 0 . GRCh38 1 209783492 209783492 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.143G>A p.Arg48Gln p.R48Q ENST00000294811 2/2 157 130 27 135 135 0 strelka-varscan-mutect C1orf74,missense_variant,p.Arg48Gln,ENST00000294811,NM_152485.2;IRF6,downstream_gene_variant,,ENST00000367021,NM_006147.3;IRF6,downstream_gene_variant,,ENST00000542854,NM_001206696.1;TRAF3IP3,downstream_gene_variant,,ENST00000367024,NM_001320143.1;TRAF3IP3,downstream_gene_variant,,ENST00000367025,NM_025228.3;TRAF3IP3,downstream_gene_variant,,ENST00000367026,NM_001320144.1;TRAF3IP3,downstream_gene_variant,,ENST00000400959,;TRAF3IP3,downstream_gene_variant,,ENST00000367023,NM_001287754.1;TRAF3IP3,downstream_gene_variant,,ENST00000477431,;TRAF3IP3,downstream_gene_variant,,ENST00000467830,;TRAF3IP3,downstream_gene_variant,,ENST00000488702,;TRAF3IP3,downstream_gene_variant,,ENST00000476050,;TRAF3IP3,downstream_gene_variant,,ENST00000460314,;TRAF3IP3,downstream_gene_variant,,ENST00000478359,;TRAF3IP3,downstream_gene_variant,,ENST00000471368,; T ENST00000294811 Transcript missense_variant 400/4684 143/810 48/269 R/Q cGg/cAg 1 -1 C1orf74 HGNC HGNC:26319 protein_coding YES CCDS1491.1 ENSP00000294811 Q96LT6 A0A0A8K8E6 UPI0000073C4E NM_152485.2 tolerated(0.39) 2/2 Pfam_domain:PF14953,hmmpanther:PTHR31366 MODERATE 1 SNV 1 1 PASS rs1293294217 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 209783492 209783492 C T 1 0 0 0 0 1 0 0 0 1998 652 23 1 1 C1orf74 1 209783492 Missense_Mutation SNP C C3N-02089_T 2169083 209783492 39172930 86 27170 ITPKB 0 . GRCh38 1 226735863 226735863 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1596G>T p.Trp532Cys p.W532C ENST00000429204 2/8 78 45 33 62 62 0 strelka-varscan ITPKB,missense_variant,p.Trp532Cys,ENST00000429204,NM_002221.3;ITPKB,missense_variant,p.Trp532Cys,ENST00000272117,;ITPKB,missense_variant,p.Trp532Cys,ENST00000366784,; A ENST00000429204 Transcript missense_variant 1936/6162 1596/2841 532/946 W/C tgG/tgT 1 -1 ITPKB HGNC HGNC:6179 protein_coding YES CCDS1555.1 ENSP00000411152 P27987 UPI000013D92B NM_002221.3 deleterious_low_confidence(0.02) 2/8 hmmpanther:PTHR12400,hmmpanther:PTHR12400:SF4 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 226735863 226735863 C A 1 0 0 0 0 1 0 0 0 7824 624 22 2 2 ITPKB 1 226735863 Missense_Mutation SNP C C3N-02089_T 16952371 226735863 22220559 87 27171 OBSCN 0 . GRCh38 1 228372789 228372789 + Silent SNP C C A rs201953118 C3N-02089_T C3N-02089_N C C c.24882C>A p.= p.P8294P ENST00000570156 105/116 499 316 183 465 465 0 strelka-varscan OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000636476,; A ENST00000570156 Transcript synonymous_variant 24956/26925 24882/26772 8294/8923 P ccC/ccA rs201953118 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 105/116 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 228372789 228372789 C A 1 0 0 0 0 0 0 0 1 10889 668 24 2 2 OBSCN 1 228372789 Silent SNP C C3N-02089_T 1636926 228372789 20583633 88 27172 PCNX2 0 . GRCh38 1 233025357 233025357 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.4394G>T p.Gly1465Val p.G1465V ENST00000258229 26/34 171 126 45 186 186 0 strelka-varscan-mutect PCNX2,missense_variant,p.Gly1465Val,ENST00000258229,NM_014801.3;PCNX2,missense_variant,p.Gly117Val,ENST00000344698,;PCNX2,non_coding_transcript_exon_variant,,ENST00000522067,;PCNX2,non_coding_transcript_exon_variant,,ENST00000429988,;PCNX2,intron_variant,,ENST00000462233,; A ENST00000258229 Transcript missense_variant 4629/7518 4394/6414 1465/2137 G/V gGc/gTc 1 -1 PCNX2 HGNC HGNC:8736 protein_coding YES CCDS44335.1 ENSP00000258229 A6NKB5 UPI0000F58F23 NM_014801.3 deleterious(0) 26/34 hmmpanther:PTHR12372,hmmpanther:PTHR12372:SF5 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 233025357 233025357 C A 1 0 0 0 0 1 0 0 0 11680 739 26 2 2 PCNX2 1 233025357 Missense_Mutation SNP C C3N-02089_T 4652568 233025357 15931065 89 27173 NID1 0 . GRCh38 1 235990940 235990940 + Silent SNP G G T rs372553525 C3N-02089_T C3N-02089_N G G c.2874C>A p.= p.P958P ENST00000264187 14/20 190 127 63 206 206 0 strelka-varscan-mutect NID1,synonymous_variant,p.=,ENST00000264187,NM_002508.2;NID1,synonymous_variant,p.=,ENST00000366595,; T ENST00000264187 Transcript synonymous_variant 2957/5864 2874/3744 958/1247 P ccC/ccA rs372553525 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 14/20 Gene3D:2.120.10.30,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS rs372553525 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 235990940 235990940 G T 1 0 0 0 0 0 0 0 1 10447 1219 43 2 2 NID1 1 235990940 Silent SNP G C3N-02089_T 2965583 235990940 12965482 90 27174 ACTN2 0 . GRCh38 1 236755050 236755050 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2006G>T p.Gly669Val p.G669V ENST00000542672 17/21 405 263 142 377 375 2 strelka-varscan-mutect ACTN2,missense_variant,p.Gly461Val,ENST00000546208,NM_001278344.1;ACTN2,missense_variant,p.Gly669Val,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Gly669Val,ENST00000366578,NM_001103.3;ACTN2,non_coding_transcript_exon_variant,,ENST00000461367,; T ENST00000542672 Transcript missense_variant 2226/4906 2006/2685 669/894 G/V gGa/gTa 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0.02) 17/21 Gene3D:1.20.58.60,Pfam_domain:PF00435,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 236755050 236755050 G T 1 0 0 0 0 1 0 0 0 249 1174 41 2 2 ACTN2 1 236755050 Missense_Mutation SNP G C3N-02089_T 764110 236755050 12201372 91 27175 WDR64 0 . GRCh38 1 241757308 241757309 + Frame_Shift_Ins INS - - C novel C3N-02089_T C3N-02089_N - - c.1766_1767insC p.Met589IlefsTer8 p.M589Ifs*8 ENST00000366552 14/27 100 70 30 119 119 0 sindel-varindel-pindel WDR64,frameshift_variant,p.Met589IlefsTer8,ENST00000366552,NM_144625.4;WDR64,frameshift_variant,p.Met309IlefsTer8,ENST00000437684,;WDR64,frameshift_variant,p.Met360IlefsTer8,ENST00000414635,;WDR64,frameshift_variant,p.Met68IlefsTer8,ENST00000425826,;WDR64,frameshift_variant,p.Met148IlefsTer8,ENST00000472717,; C ENST00000366552 Transcript frameshift_variant 1973-1974/4371 1766-1767/3246 589/1081 M/IX atg/atCg 1 1 WDR64 HGNC HGNC:26570 protein_coding YES ENSP00000355510 B1ANS9 UPI0000519142 NM_144625.4 14/27 HIGH 1 insertion 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 7 5 90 241757308 241757308 - C 1 0 1 1 0 0 0 0 0 17874 1464 51 0 0 WDR64 1 241757308 Frame_Shift_Ins INS - C3N-02089_T 5002258 241757308 7199114 92 27176 OR14A2 0 . GRCh38 1 247723186 247723186 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.858A>T p.= p.V286V ENST00000366485 1/1 210 192 18 196 195 1 strelka-varscan-mutect OR14A2,synonymous_variant,p.=,ENST00000366485,;RP11-634B7.5,non_coding_transcript_exon_variant,,ENST00000426444,;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; A ENST00000366485 Transcript synonymous_variant 858/945 858/945 286/314 V gtA/gtT 1 -1 OR14A2 HGNC HGNC:15024 protein_coding YES ENSP00000355441 Q96R54 A0A126GWG8 UPI000004A5E7 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF346,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS rs1307361987 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 247723186 247723186 T A 1 0 0 0 0 0 0 0 1 11022 1741 61 4 4 OR14A2 1 247723186 Silent SNP T C3N-02089_T 5965878 247723186 1233236 93 27177 OR14A2 0 . GRCh38 1 247723411 247723411 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.633T>C p.= p.C211C ENST00000366485 1/1 114 75 39 143 143 0 strelka-varscan-mutect OR14A2,synonymous_variant,p.=,ENST00000366485,;RP11-634B7.5,non_coding_transcript_exon_variant,,ENST00000426444,;RP11-634B7.4,intron_variant,,ENST00000449298,;RP11-634B7.5,intron_variant,,ENST00000419891,; G ENST00000366485 Transcript synonymous_variant 633/945 633/945 211/314 C tgT/tgC 1 -1 OR14A2 HGNC HGNC:15024 protein_coding YES ENSP00000355441 Q96R54 A0A126GWG8 UPI000004A5E7 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF346,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 247723411 247723411 A G 1 0 0 0 0 0 0 0 1 11022 389 14 5 5 OR14A2 1 247723411 Silent SNP A C3N-02089_T 225 247723411 1233011 94 27178 OR2T2 0 . GRCh38 1 248453322 248453322 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.525C>A p.= p.I175I ENST00000342927 1/1 192 147 45 193 193 0 strelka-varscan-mutect OR2T2,synonymous_variant,p.=,ENST00000342927,NM_001004136.1; A ENST00000342927 Transcript synonymous_variant 525/975 525/975 175/324 I atC/atA 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1387292180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 248453322 248453322 C A 1 0 0 0 0 0 0 0 1 11097 816 29 2 2 OR2T2 1 248453322 Silent SNP C C3N-02089_T 729911 248453322 503100 95 27179 OR2T34 0 . GRCh38 1 248574325 248574325 + Missense_Mutation SNP C C A rs755310345 C3N-02089_T C3N-02089_N C C c.433G>T p.Val145Leu p.V145L ENST00000328782 1/1 69 49 20 106 106 0 strelka-varscan-mutect OR2T34,missense_variant,p.Val145Leu,ENST00000328782,NM_001001821.1; A ENST00000328782 Transcript missense_variant 433/957 433/957 145/318 V/L Gtg/Ttg rs755310345,COSM3487262 1 -1 OR2T34 HGNC HGNC:31256 protein_coding YES CCDS31120.1 ENSP00000330904 Q8NGX1 UPI0000061ED4 NM_001001821.1 tolerated(0.31) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF4,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 0,1 1 PASS rs755310345 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 248574325 248574325 C A 1 0 0 0 0 1 0 0 0 11102 507 18 2 2 OR2T34 1 248574325 Missense_Mutation SNP C C3N-02089_T 121003 248574325 382097 96 27180 SNTG2 0 . GRCh38 2 1165560 1165560 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.424A>T p.Arg142Ter p.R142* ENST00000308624 7/17 237 219 18 285 285 0 strelka-varscan-mutect SNTG2,stop_gained,p.Arg142Ter,ENST00000308624,NM_018968.3;SNTG2,intron_variant,,ENST00000407292,;SNTG2,non_coding_transcript_exon_variant,,ENST00000467759,;SNTG2,non_coding_transcript_exon_variant,,ENST00000463442,;SNTG2,non_coding_transcript_exon_variant,,ENST00000494178,;SNTG2,non_coding_transcript_exon_variant,,ENST00000475201,;SNTG2,3_prime_UTR_variant,,ENST00000450962,;SNTG2,downstream_gene_variant,,ENST00000452177,; T ENST00000308624 Transcript stop_gained 553/1888 424/1620 142/539 R/* Aga/Tga 1 1 SNTG2 HGNC HGNC:13741 protein_coding YES CCDS46220.1 ENSP00000311837 Q9NY99 UPI0000456D73 NM_018968.3 7/17 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF3,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 1165560 1165560 A T 1 0 0 0 0 0 1 0 0 15195 296 11 4 4 SNTG2 2 1165560 Nonsense_Mutation SNP A C3N-02089_T 1165560 241027969 97 27181 KLF11 0 . GRCh38 2 10046194 10046194 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.87G>C p.= p.R29R ENST00000305883 2/4 419 360 59 408 408 0 strelka-varscan-mutect KLF11,synonymous_variant,p.=,ENST00000535335,NM_001177718.1;KLF11,synonymous_variant,p.=,ENST00000305883,NM_003597.4;KLF11,synonymous_variant,p.=,ENST00000540845,NM_001177716.1;KLF11,synonymous_variant,p.=,ENST00000440320,;KLF11,synonymous_variant,p.=,ENST00000401510,;KLF11,synonymous_variant,p.=,ENST00000448523,; C ENST00000305883 Transcript synonymous_variant 249/4030 87/1539 29/512 R cgG/cgC 1 1 KLF11 HGNC HGNC:11811 protein_coding YES CCDS1668.1 ENSP00000307023 O14901 Q53QU8 UPI000012DEDA NM_003597.4 2/4 LOW 1 SNV 1 1 PASS rs1199072785 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 10046194 10046194 G C 1 0 0 0 0 0 0 0 1 8204 1190 42 4 4 KLF11 2 10046194 Silent SNP G C3N-02089_T 8880634 10046194 232147335 98 27182 NBAS 0 . GRCh38 2 15478240 15478240 + Missense_Mutation SNP C C A rs746801313 C3N-02089_T C3N-02089_N C C c.1133G>T p.Arg378Ile p.R378I ENST00000281513 13/52 238 183 55 278 278 0 strelka-varscan-mutect NBAS,missense_variant,p.Arg378Ile,ENST00000281513,NM_015909.3;NBAS,downstream_gene_variant,,ENST00000427792,; A ENST00000281513 Transcript missense_variant 1159/7281 1133/7116 378/2371 R/I aGa/aTa rs746801313,COSM1185839 1 -1 NBAS HGNC HGNC:15625 protein_coding YES CCDS1685.1 ENSP00000281513 A2RRP1 UPI00001AEA68 NM_015909.3 deleterious(0) 13/52 hmmpanther:PTHR15922,hmmpanther:PTHR15922:SF2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs746801313 . 0 113 2 5 88 2 0 0 -2.987874 0 0 1 0 0 A 3 1 90 15478240 15478240 C A 1 0 0 0 0 1 0 0 0 10197 913 32 2 2 NBAS 2 15478240 Missense_Mutation SNP C C3N-02089_T 5432046 15478240 226715289 99 27183 SMC6 0 . GRCh38 2 17720968 17720968 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.917G>T p.Arg306Ile p.R306I ENST00000448223 11/28 155 122 33 170 170 0 strelka-varscan-mutect SMC6,missense_variant,p.Arg306Ile,ENST00000448223,NM_001142286.1;SMC6,missense_variant,p.Arg306Ile,ENST00000351948,NM_024624.5;SMC6,missense_variant,p.Arg306Ile,ENST00000402989,;SMC6,missense_variant,p.Arg332Ile,ENST00000446852,;SMC6,missense_variant,p.Arg306Ile,ENST00000381272,; A ENST00000448223 Transcript missense_variant 1187/5233 917/3276 306/1091 R/I aGa/aTa 1 -1 SMC6 HGNC HGNC:20466 protein_coding YES CCDS1690.1 ENSP00000404092 Q96SB8 UPI0000073C3B NM_001142286.1 tolerated(0.22) 11/28 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR19306,hmmpanther:PTHR19306:SF5,Pfam_domain:PF02463,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 17720968 17720968 C A 1 0 0 0 0 1 0 0 0 15080 913 32 2 2 SMC6 2 17720968 Missense_Mutation SNP C C3N-02089_T 2242728 17720968 224472561 100 27184 NT5C1B 0 . GRCh38 2 18584522 18584522 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.895C>T p.Pro299Ser p.P299S ENST00000359846 5/10 224 178 46 216 216 0 strelka-varscan-mutect NT5C1B,missense_variant,p.Pro239Ser,ENST00000304081,NM_033253.3;NT5C1B,missense_variant,p.Pro299Ser,ENST00000359846,NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1;NT5C1B-RDH14,missense_variant,p.Pro299Ser,ENST00000532967,NM_001199104.1;NT5C1B-RDH14,missense_variant,p.Pro241Ser,ENST00000444297,NM_001199103.1;NT5C1B,upstream_gene_variant,,ENST00000418427,;NT5C1B,downstream_gene_variant,,ENST00000416783,;RNU6-1215P,upstream_gene_variant,,ENST00000384441,;NT5C1B,downstream_gene_variant,,ENST00000460052,;NT5C1B,3_prime_UTR_variant,,ENST00000406971,;NT5C1B,non_coding_transcript_exon_variant,,ENST00000490687,; A ENST00000359846 Transcript missense_variant 973/2475 895/1833 299/610 P/S Ccc/Tcc 1 -1 NT5C1B HGNC HGNC:17818 protein_coding YES CCDS33150.1 ENSP00000352904 Q96P26 A0A140VJC7 UPI000035B1B0 NM_001002006.2,NM_001199087.1,NM_001199088.1,NM_001199086.1 deleterious_low_confidence(0.01) 5/10 hmmpanther:PTHR31367,hmmpanther:PTHR31367:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 18584522 18584522 G A 1 0 0 0 0 1 0 0 0 10749 1232 43 3 3 NT5C1B 2 18584522 Missense_Mutation SNP G C3N-02089_T 863554 18584522 223609007 101 27185 WDCP 0 . GRCh38 2 24038110 24038110 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1385A>C p.Lys462Thr p.K462T ENST00000295148 2/4 160 109 51 225 225 0 strelka-varscan-mutect WDCP,missense_variant,p.Lys462Thr,ENST00000295148,NM_025203.2;WDCP,missense_variant,p.Lys462Thr,ENST00000406895,NM_001142319.1;WDCP,downstream_gene_variant,,ENST00000443232,;MFSD2B,intron_variant,,ENST00000453731,; G ENST00000295148 Transcript missense_variant 1443/3817 1385/2166 462/721 K/T aAg/aCg 1 -1 WDCP HGNC HGNC:26157 protein_coding YES CCDS1705.1 ENSP00000295148 Q9H6R7 UPI0000070788 NM_025203.2 deleterious(0.03) 2/4 Pfam_domain:PF15390,hmmpanther:PTHR14897,hmmpanther:PTHR14897:SF5 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 24038110 24038110 T G 1 0 0 0 0 1 0 0 0 17827 1609 56 5 5 WDCP 2 24038110 Missense_Mutation SNP T C3N-02089_T 5453588 24038110 218155419 102 27186 SLC4A1AP 0 . GRCh38 2 27669350 27669350 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1308G>T p.= p.R436R ENST00000613058 5/14 142 113 29 111 109 2 strelka-varscan SLC4A1AP,synonymous_variant,p.=,ENST00000613058,NM_018158.2;SLC4A1AP,synonymous_variant,p.=,ENST00000326019,;SLC4A1AP,synonymous_variant,p.=,ENST00000618046,;SLC4A1AP,synonymous_variant,p.=,ENST00000613517,;SLC4A1AP,3_prime_UTR_variant,,ENST00000427424,; T ENST00000613058 Transcript synonymous_variant 1590/2966 1308/2391 436/796 R cgG/cgT 1 1 SLC4A1AP HGNC HGNC:13813 protein_coding YES CCDS33166.1 ENSP00000479964 Q9BWU0 UPI000006F66B NM_018158.2 5/14 hmmpanther:PTHR23308:SF2,hmmpanther:PTHR23308,Pfam_domain:PF00035 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 27669350 27669350 G T 1 0 0 0 0 0 0 0 1 14930 1161 41 2 2 SLC4A1AP 2 27669350 Silent SNP G C3N-02089_T 3631240 27669350 214524179 103 27187 BRE 0 . GRCh38 2 28298392 28298392 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.989T>G p.Val330Gly p.V330G ENST00000344773 11/13 270 240 30 231 231 0 strelka-varscan BRE,missense_variant,p.Val330Gly,ENST00000344773,NM_004899.4;BRE,missense_variant,p.Val330Gly,ENST00000379632,NM_199193.2;BRE,missense_variant,p.Val330Gly,ENST00000361704,NM_199192.2;BRE,missense_variant,p.Val330Gly,ENST00000342045,NM_199194.2;BRE,missense_variant,p.Val330Gly,ENST00000379624,NM_001261840.1,NM_199191.2; G ENST00000344773 Transcript missense_variant 1127/1852 989/1248 330/415 V/G gTt/gGt 1 1 BRE HGNC HGNC:1106 protein_coding YES CCDS1764.1 ENSP00000343412 Q9NXR7 UPI0000072A9C NM_004899.4 deleterious(0) 11/13 hmmpanther:PTHR15189:SF7,hmmpanther:PTHR15189,Pfam_domain:PF06113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 28298392 28298392 T G 1 0 0 0 0 1 0 0 0 1679 1725 60 5 5 BRE 2 28298392 Missense_Mutation SNP T C3N-02089_T 629042 28298392 213895137 104 27188 WDR43 0 . GRCh38 2 28914140 28914140 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.678G>T p.Gln226His p.Q226H ENST00000407426 5/18 240 210 30 235 235 0 strelka-varscan WDR43,missense_variant,p.Gln226His,ENST00000407426,NM_015131.2;WDR43,missense_variant,p.Gln45His,ENST00000296126,;WDR43,missense_variant,p.Gln137His,ENST00000440983,;SNORD92,downstream_gene_variant,,ENST00000585078,; T ENST00000407426 Transcript missense_variant 734/3533 678/2034 226/677 Q/H caG/caT COSM1019951 1 1 WDR43 HGNC HGNC:28945 protein_coding YES CCDS46251.1 ENSP00000384302 Q15061 UPI00001C1DCD NM_015131.2 tolerated(0.22) 5/18 PROSITE_profiles:PS50294,hmmpanther:PTHR22847,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 28914140 28914140 G T 1 0 0 0 0 1 0 0 0 17855 962 34 2 2 WDR43 2 28914140 Missense_Mutation SNP G C3N-02089_T 615748 28914140 213279389 105 27189 FAM179A 0 . GRCh38 2 29052029 29052029 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2996C>A p.Thr999Asn p.T999N ENST00000379558 20/20 106 88 18 120 120 0 strelka-varscan FAM179A,missense_variant,p.Thr999Asn,ENST00000379558,NM_199280.2;FAM179A,non_coding_transcript_exon_variant,,ENST00000465300,;FAM179A,non_coding_transcript_exon_variant,,ENST00000475900,; A ENST00000379558 Transcript missense_variant 3347/12691 2996/3060 999/1019 T/N aCt/aAt 1 1 FAM179A HGNC HGNC:33715 protein_coding YES CCDS1769.2 ENSP00000368876 Q6ZUX3 UPI00014F7B81 NM_199280.2 deleterious_low_confidence(0.01) 20/20 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 29052029 29052029 C A 1 0 0 0 0 1 0 0 0 5350 565 20 2 2 FAM179A 2 29052029 Missense_Mutation SNP C C3N-02089_T 137889 29052029 213141500 106 27190 EHD3 0 . GRCh38 2 31266416 31266416 + Silent SNP G G C rs754356061 C3N-02089_T C3N-02089_N G G c.1320G>C p.= p.V440V ENST00000322054 6/6 133 118 15 139 139 0 strelka-varscan EHD3,synonymous_variant,p.=,ENST00000322054,NM_014600.2; C ENST00000322054 Transcript synonymous_variant 1605/4636 1320/1608 440/535 V gtG/gtC rs754356061 1 1 EHD3 HGNC HGNC:3244 protein_coding YES CCDS1774.1 ENSP00000327116 Q9NZN3 UPI0000140D07 NM_014600.2 6/6 Gene3D:1.10.238.10,hmmpanther:PTHR11216,hmmpanther:PTHR11216:SF67,SMART_domains:SM00027 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 31266416 31266416 G C 1 0 0 0 0 0 0 0 1 4815 1335 47 4 4 EHD3 2 31266416 Silent SNP G C3N-02089_T 2214387 31266416 210927113 107 27191 XDH 0 . GRCh38 2 31379934 31379934 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1175G>T p.Gly392Val p.G392V ENST00000379416 13/36 585 483 102 580 576 4 strelka-varscan XDH,missense_variant,p.Gly392Val,ENST00000379416,NM_000379.3;XDH,downstream_gene_variant,,ENST00000491727,;XDH,downstream_gene_variant,,ENST00000476043,; A ENST00000379416 Transcript missense_variant 1224/5688 1175/4002 392/1333 G/V gGc/gTc 1 -1 XDH HGNC HGNC:12805 protein_coding YES CCDS1775.1 ENSP00000368727 P47989 UPI0000036BC9 NM_000379.3 deleterious(0) 13/36 PROSITE_profiles:PS51387,hmmpanther:PTHR11908,hmmpanther:PTHR11908:SF78,Gene3D:3.30.465.10,TIGRFAM_domain:TIGR02963,Pfam_domain:PF00941,PIRSF_domain:PIRSF000127,Superfamily_domains:SSF56176 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 31379934 31379934 C A 1 0 0 0 0 1 0 0 0 17985 739 26 2 2 XDH 2 31379934 Missense_Mutation SNP C C3N-02089_T 113518 31379934 210813595 108 27192 LTBP1 0 . GRCh38 2 33188632 33188632 + Silent SNP C C A rs760753760 C3N-02089_T C3N-02089_N C C c.1482C>A p.= p.S494S ENST00000404816 7/34 190 152 38 212 210 2 strelka-varscan LTBP1,synonymous_variant,p.=,ENST00000404816,NM_206943.2;LTBP1,synonymous_variant,p.=,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,synonymous_variant,p.=,ENST00000404525,NM_001166265.1;LTBP1,synonymous_variant,p.=,ENST00000407925,NM_000627.3;LTBP1,synonymous_variant,p.=,ENST00000402934,;LTBP1,synonymous_variant,p.=,ENST00000432635,; A ENST00000404816 Transcript synonymous_variant 1835/6333 1482/5166 494/1721 S tcC/tcA rs760753760 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 7/34 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 LOW 1 SNV 5 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 33188632 33188632 C A 1 0 0 0 0 0 0 0 1 8979 639 23 1 1 LTBP1 2 33188632 Silent SNP C C3N-02089_T 1808698 33188632 209004897 109 27193 LTBP1 0 . GRCh38 2 33252688 33252688 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.2011G>A p.Val671Met p.V671M ENST00000404816 11/34 69 61 8 60 60 0 strelka-varscan LTBP1,missense_variant,p.Val671Met,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Val345Met,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Val345Met,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Val345Met,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Val345Met,ENST00000402934,;LTBP1,missense_variant,p.Val27Met,ENST00000413303,;LTBP1,upstream_gene_variant,,ENST00000468091,; A ENST00000404816 Transcript missense_variant 2364/6333 2011/5166 671/1721 V/M Gtg/Atg 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 tolerated(0.3) 11/34 Gene3D:3.90.290.10,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -17.83101 1 1 1 1 0 A 3 1 90 33252688 33252688 G A 1 0 0 0 0 1 0 0 0 8979 1377 48 3 3 LTBP1 2 33252688 Missense_Mutation SNP G C3N-02089_T 64056 33252688 208940841 110 27194 RASGRP3 0 . GRCh38 2 33558800 33558800 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1834C>A p.Gln612Lys p.Q612K ENST00000403687 17/18 292 255 37 232 232 0 strelka-varscan RASGRP3,missense_variant,p.Gln612Lys,ENST00000403687,NM_001139488.1;RASGRP3,missense_variant,p.Gln612Lys,ENST00000402538,NM_170672.2;RASGRP3,missense_variant,p.Gln611Lys,ENST00000407811,NM_015376.2;AC020594.5,intron_variant,,ENST00000437680,; A ENST00000403687 Transcript missense_variant 2574/4807 1834/2073 612/690 Q/K Cag/Aag 1 1 RASGRP3 HGNC HGNC:14545 protein_coding YES CCDS46256.1 ENSP00000384192 Q8IV61 UPI0000074694 NM_001139488.1 tolerated(0.72) 17/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 33558800 33558800 C A 1 0 0 0 0 1 0 0 0 13237 595 21 2 2 RASGRP3 2 33558800 Missense_Mutation SNP C C3N-02089_T 306112 33558800 208634729 111 27195 VIT 0 . GRCh38 2 36767263 36767263 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.657G>T p.= p.V219V ENST00000379242 7/16 51 45 6 48 48 0 strelka-varscan VIT,synonymous_variant,p.=,ENST00000379242,NM_053276.3;VIT,synonymous_variant,p.=,ENST00000389975,NM_001177969.1;VIT,synonymous_variant,p.=,ENST00000379241,NM_001177971.1;VIT,synonymous_variant,p.=,ENST00000404084,;VIT,synonymous_variant,p.=,ENST00000401530,NM_001177970.1;VIT,5_prime_UTR_variant,,ENST00000497382,; T ENST00000379242 Transcript synonymous_variant 959/2810 657/2082 219/693 V gtG/gtT COSM5547793 1 1 VIT HGNC HGNC:12697 protein_coding YES CCDS33180.1 ENSP00000368544 Q6UXI7 UPI000006E0F8 NM_053276.3 7/16 1 LOW 1 SNV 2 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.91188 1 1 1 1 0 T 2 4 90 36767263 36767263 G T 1 0 0 0 0 0 0 0 1 17718 1335 47 2 2 VIT 2 36767263 Silent SNP G C3N-02089_T 3208463 36767263 205426266 112 27196 GEMIN6 0 . GRCh38 2 38779105 38779105 + Missense_Mutation SNP C C A rs757128366 C3N-02089_T C3N-02089_N C C c.115C>A p.Pro39Thr p.P39T ENST00000281950 2/3 114 107 7 98 98 0 strelka-varscan GEMIN6,missense_variant,p.Pro39Thr,ENST00000281950,NM_024775.9;GEMIN6,missense_variant,p.Pro39Thr,ENST00000409011,;GEMIN6,missense_variant,p.Pro39Thr,ENST00000409566,; A ENST00000281950 Transcript missense_variant 231/3728 115/504 39/167 P/T Cca/Aca rs757128366 1 1 GEMIN6 HGNC HGNC:20044 protein_coding YES CCDS1799.1 ENSP00000281950 Q8WXD5 UPI000006E325 NM_024775.9 deleterious(0) 2/3 Pfam_domain:PF06372,hmmpanther:PTHR14710,hmmpanther:PTHR14710:SF2 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -13.98951 1 1 1 1 0 A 3 1 90 38779105 38779105 C A 1 0 0 0 0 1 0 0 0 6206 623 22 2 2 GEMIN6 2 38779105 Missense_Mutation SNP C C3N-02089_T 2011842 38779105 203414424 113 27197 MAP4K3 0 . GRCh38 2 39280352 39280352 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1634G>T p.Gly545Val p.G545V ENST00000263881 23/34 94 73 21 109 109 0 strelka-varscan MAP4K3,missense_variant,p.Gly545Val,ENST00000263881,NM_003618.3;MAP4K3,missense_variant,p.Gly524Val,ENST00000341681,NM_001270425.1;MAP4K3,missense_variant,p.Gly461Val,ENST00000437545,;SNORA67,downstream_gene_variant,,ENST00000516664,;MAP4K3,upstream_gene_variant,,ENST00000495648,; A ENST00000263881 Transcript missense_variant 1959/4362 1634/2685 545/894 G/V gGt/gTt 1 -1 MAP4K3 HGNC HGNC:6865 protein_coding YES CCDS1803.1 ENSP00000263881 Q8IVH8 UPI00000747E6 NM_003618.3 deleterious(0) 23/34 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF205,PIRSF_domain:PIRSF038172 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 39280352 39280352 C A 1 0 0 0 0 1 0 0 0 9185 521 18 2 2 MAP4K3 2 39280352 Missense_Mutation SNP C C3N-02089_T 501247 39280352 202913177 114 27198 HAAO 0 . GRCh38 2 42767503 42767503 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.795G>T p.Glu265Asp p.E265D ENST00000294973 10/10 327 302 25 280 279 1 strelka-varscan HAAO,missense_variant,p.Glu265Asp,ENST00000294973,NM_012205.2;OXER1,upstream_gene_variant,,ENST00000378661,NM_148962.4;HAAO,downstream_gene_variant,,ENST00000431905,;HAAO,non_coding_transcript_exon_variant,,ENST00000402698,;HAAO,non_coding_transcript_exon_variant,,ENST00000406007,;HAAO,downstream_gene_variant,,ENST00000406924,;HAAO,downstream_gene_variant,,ENST00000404451,; A ENST00000294973 Transcript missense_variant 851/1265 795/861 265/286 E/D gaG/gaT 1 -1 HAAO HGNC HGNC:4796 protein_coding YES CCDS33187.1 ENSP00000294973 P46952 UPI000007068E NM_012205.2 tolerated(0.42) 10/10 Gene3D:2.60.120.10,PIRSF_domain:PIRSF017681,hmmpanther:PTHR15497,Superfamily_domains:SSF51182 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 42767503 42767503 C A 1 0 0 0 0 1 0 0 0 6819 796 28 2 2 HAAO 2 42767503 Missense_Mutation SNP C C3N-02089_T 3487151 42767503 199426026 115 27199 GTF2A1L 0 . GRCh38 2 48646558 48646558 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.2606C>T p.Pro869Leu p.P869L ENST00000394754 8/11 197 176 21 219 219 0 strelka-varscan STON1-GTF2A1L,missense_variant,p.Pro869Leu,ENST00000394754,NM_172311.2;STON1-GTF2A1L,missense_variant,p.Pro869Leu,ENST00000405008,;STON1-GTF2A1L,missense_variant,p.Pro869Leu,ENST00000402114,NM_001198593.1;STON1-GTF2A1L,missense_variant,p.Pro822Leu,ENST00000394751,NM_001198594.1;GTF2A1L,missense_variant,p.Pro165Leu,ENST00000403751,NM_006872.4;GTF2A1L,missense_variant,p.Pro131Leu,ENST00000430487,NM_001193487.2;GTF2A1L,missense_variant,p.Pro174Leu,ENST00000437125,;GTF2A1L,missense_variant,p.Pro131Leu,ENST00000448460,;GTF2A1L,downstream_gene_variant,,ENST00000468326,;RP11-310N16.1,3_prime_UTR_variant,,ENST00000602369,;GTF2A1L,3_prime_UTR_variant,,ENST00000423675,; T ENST00000394754 Transcript missense_variant 2720/3824 2606/3549 869/1182 P/L cCt/cTt 1 1 STON1-GTF2A1L HGNC HGNC:30651 protein_coding YES CCDS1840.1 ENSP00000378236 Q53S48 UPI000013C976 NM_172311.2 deleterious(0) 8/11 hmmpanther:PTHR12694,hmmpanther:PTHR12694:SF9,Pfam_domain:PF03153,SMART_domains:SM01371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 48646558 48646558 C T 1 0 0 0 0 1 0 0 0 6735 681 24 3 3 GTF2A1L 2 48646558 Missense_Mutation SNP C C3N-02089_T 5879055 48646558 193546971 116 27200 GTF2A1L 0 . GRCh38 2 48669871 48669871 + Silent SNP T T C rs750466102 C3N-02089_T C3N-02089_N T T c.3240T>C p.= p.I1080I ENST00000394754 9/11 206 174 32 267 267 0 strelka-varscan STON1-GTF2A1L,synonymous_variant,p.=,ENST00000394754,NM_172311.2;STON1-GTF2A1L,synonymous_variant,p.=,ENST00000405008,;STON1-GTF2A1L,synonymous_variant,p.=,ENST00000402114,NM_001198593.1;STON1-GTF2A1L,synonymous_variant,p.=,ENST00000394751,NM_001198594.1;GTF2A1L,synonymous_variant,p.=,ENST00000403751,NM_006872.4;GTF2A1L,synonymous_variant,p.=,ENST00000430487,NM_001193487.2;GTF2A1L,synonymous_variant,p.=,ENST00000508440,;RP11-310N16.1,intron_variant,,ENST00000602369,; C ENST00000394754 Transcript synonymous_variant 3354/3824 3240/3549 1080/1182 I atT/atC rs750466102 1 1 STON1-GTF2A1L HGNC HGNC:30651 protein_coding YES CCDS1840.1 ENSP00000378236 Q53S48 UPI000013C976 NM_172311.2 9/11 hmmpanther:PTHR12694,hmmpanther:PTHR12694:SF9,Pfam_domain:PF03153,SMART_domains:SM01371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 48669871 48669871 T C 1 0 0 0 0 0 0 0 1 6735 1800 63 5 5 GTF2A1L 2 48669871 Silent SNP T C3N-02089_T 23313 48669871 193523658 117 27201 NRXN1 0 . GRCh38 2 50620086 50620086 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1376G>A p.Ser459Asn p.S459N ENST00000404971 9/24 76 66 10 94 94 0 strelka-varscan NRXN1,missense_variant,p.Ser419Asn,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Ser411Asn,ENST00000625672,;NRXN1,missense_variant,p.Ser459Asn,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Ser419Asn,ENST00000401669,;NRXN1,missense_variant,p.Ser407Asn,ENST00000405472,;NRXN1,missense_variant,p.Ser411Asn,ENST00000630543,;NRXN1,missense_variant,p.Ser391Asn,ENST00000628515,;NRXN1,missense_variant,p.Ser149Asn,ENST00000406859,;NRXN1,missense_variant,p.Ser134Asn,ENST00000402717,;NRXN1,missense_variant,p.Ser146Asn,ENST00000625891,;NRXN1,upstream_gene_variant,,ENST00000495871,;RP11-358H12.1,upstream_gene_variant,,ENST00000634985,;NRXN1,non_coding_transcript_exon_variant,,ENST00000636298,;NRXN1,non_coding_transcript_exon_variant,,ENST00000628761,;NRXN1,downstream_gene_variant,,ENST00000630431,;NRXN1,upstream_gene_variant,,ENST00000637605,;NRXN1,missense_variant,p.Ser146Asn,ENST00000331040,;NRXN1,3_prime_UTR_variant,,ENST00000626249,; T ENST00000404971 Transcript missense_variant 2716/7578 1376/4644 459/1547 S/N aGt/aAt 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 deleterious(0) 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF565,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99612 1 1 1 1 0 T 3 4 90 50620086 50620086 C T 1 0 0 0 0 1 0 0 0 10724 565 20 3 3 NRXN1 2 50620086 Missense_Mutation SNP C C3N-02089_T 1950215 50620086 191573443 118 27202 BCL11A 0 . GRCh38 2 60461064 60461064 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.1848C>A p.= p.G616G ENST00000335712 4/4 72 51 21 90 90 0 strelka-varscan BCL11A,synonymous_variant,p.=,ENST00000335712,NM_022893.3;BCL11A,synonymous_variant,p.=,ENST00000356842,NM_018014.3;BCL11A,synonymous_variant,p.=,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,3_prime_UTR_variant,,ENST00000631857,; T ENST00000335712 Transcript synonymous_variant 2076/5942 1848/2508 616/835 G ggC/ggA COSM3582394,COSM3582395 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 192 17 0 0 0 0 0 -20 0.9996747 1 1 1 0 T 2 4 90 60461064 60461064 G T 1 0 0 0 0 0 0 0 1 1510 1190 42 2 2 BCL11A 2 60461064 Silent SNP G C3N-02089_T 9840978 60461064 181732465 119 27203 BCL11A 0 . GRCh38 2 60461232 60461232 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1680G>A p.= p.E560E ENST00000335712 4/4 209 184 25 234 234 0 strelka-varscan BCL11A,synonymous_variant,p.=,ENST00000335712,NM_022893.3;BCL11A,synonymous_variant,p.=,ENST00000356842,NM_018014.3;BCL11A,synonymous_variant,p.=,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,3_prime_UTR_variant,,ENST00000631857,; T ENST00000335712 Transcript synonymous_variant 1908/5942 1680/2508 560/835 E gaG/gaA 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 60461232 60461232 C T 1 0 0 0 0 0 0 0 1 1510 680 24 3 3 BCL11A 2 60461232 Silent SNP C C3N-02089_T 168 60461232 181732297 120 27204 UGP2 0 . GRCh38 2 63887569 63887571 + In_Frame_Del DEL AGG AGG - novel C3N-02089_T C3N-02089_N AGG AGG c.1240_1242delGGA p.Gly414del p.G414del ENST00000337130 8/10 265 233 32 279 279 0 sindel-varindel-pindel UGP2,inframe_deletion,p.Gly414del,ENST00000337130,NM_006759.3;UGP2,inframe_deletion,p.Gly403del,ENST00000394417,NM_001001521.1;UGP2,inframe_deletion,p.Gly403del,ENST00000467648,;UGP2,inframe_deletion,p.Gly423del,ENST00000445915,;UGP2,inframe_deletion,p.Gly414del,ENST00000613823,;VPS54,downstream_gene_variant,,ENST00000409558,NM_001005739.1;UGP2,downstream_gene_variant,,ENST00000488245,;UGP2,downstream_gene_variant,,ENST00000491621,;UGP2,downstream_gene_variant,,ENST00000497883,;UGP2,downstream_gene_variant,,ENST00000475462,;UGP2,downstream_gene_variant,,ENST00000472047,;ACA59,upstream_gene_variant,,ENST00000515966,;UGP2,downstream_gene_variant,,ENST00000487469,;UGP2,downstream_gene_variant,,ENST00000495020,;UGP2,non_coding_transcript_exon_variant,,ENST00000475550,;UGP2,downstream_gene_variant,,ENST00000466642,;UGP2,downstream_gene_variant,,ENST00000487042,;UGP2,downstream_gene_variant,,ENST00000493222,;UGP2,downstream_gene_variant,,ENST00000467999,;UGP2,downstream_gene_variant,,ENST00000497510,;UGP2,downstream_gene_variant,,ENST00000467400,;UGP2,downstream_gene_variant,,ENST00000494536,;UGP2,downstream_gene_variant,,ENST00000496334,;UGP2,downstream_gene_variant,,ENST00000483461,; - ENST00000337130 Transcript inframe_deletion 1715-1717/2338 1239-1241/1527 413-414/508 AG/A gcAGGa/gca 1 1 UGP2 HGNC HGNC:12527 protein_coding YES CCDS1875.1 ENSP00000338703 Q16851 UPI000000DB95 NM_006759.3 8/10 hmmpanther:PTHR11952,Pfam_domain:PF01704,Gene3D:3.90.550.10,PIRSF_domain:PIRSF000806,Superfamily_domains:SSF53448 MODERATE 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 63887569 63887569 AGG - 1 0 1 0 1 0 0 0 0 17468 175 7 0 0 UGP2 2 63887569 In_Frame_Del DEL AGG C3N-02089_T 3426337 63887569 178305960 121 27205 BMP10 0 . GRCh38 2 68866313 68866313 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.593G>T p.Trp198Leu p.W198L ENST00000295379 2/2 286 226 60 255 255 0 strelka-varscan BMP10,missense_variant,p.Trp198Leu,ENST00000295379,NM_014482.1; A ENST00000295379 Transcript missense_variant 752/1584 593/1275 198/424 W/L tGg/tTg 1 -1 BMP10 HGNC HGNC:20869 protein_coding YES CCDS1890.1 ENSP00000295379 O95393 UPI0000126A11 NM_014482.1 deleterious(0) 2/2 hmmpanther:PTHR11848:SF39,hmmpanther:PTHR11848,Pfam_domain:PF00688 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 68866313 68866313 C A 1 0 0 0 0 1 0 0 0 1612 595 21 2 2 BMP10 2 68866313 Missense_Mutation SNP C C3N-02089_T 4978744 68866313 173327216 122 27206 ALMS1 0 . GRCh38 2 73448469 73448469 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.1942delG p.Val648PhefsTer25 p.V648Ffs*25 ENST00000613296 8/23 156 129 27 177 177 0 sindel-varindel-pindel ALMS1,frameshift_variant,p.Val648PhefsTer25,ENST00000613296,NM_015120.4;ALMS1,frameshift_variant,p.Val606PhefsTer25,ENST00000484298,;ALMS1,frameshift_variant,p.Val648PhefsTer25,ENST00000614410,;ALMS1,upstream_gene_variant,,ENST00000620466,;ALMS1,upstream_gene_variant,,ENST00000423048,; - ENST00000613296 Transcript frameshift_variant 2053/12925 1942/12507 648/4168 V/X Gtt/tt 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 8/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 73448469 73448469 G - 1 0 1 0 1 0 0 0 0 635 1029 36 0 0 ALMS1 2 73448469 Frame_Shift_Del DEL G C3N-02089_T 4582156 73448469 168745060 123 27207 C2orf78 0 . GRCh38 2 73816087 73816087 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1864C>G p.Pro622Ala p.P622A ENST00000409561 3/3 167 158 9 202 202 0 strelka-varscan C2orf78,missense_variant,p.Pro622Ala,ENST00000409561,NM_001080474.1; G ENST00000409561 Transcript missense_variant 1985/3045 1864/2769 622/922 P/A Ccc/Gcc 1 1 C2orf78 HGNC HGNC:34349 protein_coding YES CCDS46338.1 ENSP00000387124 A6NCI8 UPI000015FD87 NM_001080474.1 deleterious(0) 3/3 Pfam_domain:PF15442,hmmpanther:PTHR31466,hmmpanther:PTHR31466:SF1 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 73816087 73816087 C G 1 0 0 0 0 1 0 0 0 2050 739 26 4 4 C2orf78 2 73816087 Missense_Mutation SNP C C3N-02089_T 367618 73816087 168377442 124 27208 LRRTM4 0 . GRCh38 2 77519673 77519673 + Missense_Mutation SNP A A T rs775751336 C3N-02089_T C3N-02089_N A A c.196T>A p.Leu66Ile p.L66I ENST00000409093 3/4 347 253 94 279 279 0 strelka-varscan LRRTM4,missense_variant,p.Leu66Ile,ENST00000409088,NM_024993.4;LRRTM4,missense_variant,p.Leu67Ile,ENST00000409911,;LRRTM4,missense_variant,p.Leu67Ile,ENST00000409282,NM_001282928.1;LRRTM4,missense_variant,p.Leu66Ile,ENST00000409093,NM_001282924.1;LRRTM4,missense_variant,p.Leu66Ile,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; T ENST00000409093 Transcript missense_variant 533/2247 196/1773 66/590 L/I Tta/Ata rs775751336 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 deleterious(0) 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1,Gene3D:3.80.10.10,Pfam_domain:PF13855,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 77519673 77519673 A T 1 0 0 0 0 1 0 0 0 8948 69 3 4 4 LRRTM4 2 77519673 Missense_Mutation SNP A C3N-02089_T 3703586 77519673 164673856 125 27209 REG3A 0 . GRCh38 2 79158732 79158732 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.114C>A p.= p.I38I ENST00000393878 2/5 196 131 65 153 153 0 strelka-varscan REG3A,synonymous_variant,p.=,ENST00000393878,NM_138938.2;REG3A,synonymous_variant,p.=,ENST00000409839,NM_002580.2,NM_138937.2;REG3A,synonymous_variant,p.=,ENST00000305165,;AC011754.1,intron_variant,,ENST00000415201,;REG3A,non_coding_transcript_exon_variant,,ENST00000490901,;REG3A,downstream_gene_variant,,ENST00000464746,; T ENST00000393878 Transcript synonymous_variant 462/1095 114/528 38/175 I atC/atA COSM5514395 1 -1 REG3A HGNC HGNC:8601 protein_coding YES CCDS1965.1 ENSP00000377456 Q06141 Q53S56 UPI0000001C5B NM_138938.2 2/5 hmmpanther:PTHR22801:SF45,hmmpanther:PTHR22801,Gene3D:3.10.100.10,Superfamily_domains:SSF56436,Prints_domain:PR01504 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 79158732 79158732 G T 1 0 0 0 0 0 0 0 1 13382 1164 41 2 2 REG3A 2 79158732 Silent SNP G C3N-02089_T 1639059 79158732 163034797 126 27210 CTNNA2 0 . GRCh38 2 79744404 79744404 + Missense_Mutation SNP C C A rs751493653 C3N-02089_T C3N-02089_N C C c.120C>A p.Asn40Lys p.N40K ENST00000402739 2/18 125 107 18 87 87 0 strelka-varscan CTNNA2,missense_variant,p.Asn40Lys,ENST00000466387,;CTNNA2,missense_variant,p.Asn40Lys,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,missense_variant,p.Asn40Lys,ENST00000402739,NM_001282597.2;CTNNA2,missense_variant,p.Asn40Lys,ENST00000629316,NM_001164883.1;CTNNA2,missense_variant,p.Asn40Lys,ENST00000409971,;CTNNA2,missense_variant,p.Asn40Lys,ENST00000451966,;CTNNA2,non_coding_transcript_exon_variant,,ENST00000508970,; A ENST00000402739 Transcript missense_variant 125/3684 120/2862 40/953 N/K aaC/aaA rs751493653 1 1 CTNNA2 HGNC HGNC:2510 protein_coding YES CCDS62944.1 ENSP00000384638 P26232 UPI0000D9D4EC NM_001282597.2 deleterious(0.03) 2/18 Pfam_domain:PF01044,hmmpanther:PTHR18914,hmmpanther:PTHR18914:SF23 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 79744404 79744404 C A 1 0 0 0 0 1 0 0 0 3822 477 17 2 2 CTNNA2 2 79744404 Missense_Mutation SNP C C3N-02089_T 585672 79744404 162449125 127 27211 LRRTM1 0 . GRCh38 2 80302883 80302883 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.937G>T p.Gly313Trp p.G313W ENST00000295057 2/2 226 189 37 208 208 0 strelka-varscan LRRTM1,missense_variant,p.Gly313Trp,ENST00000295057,;LRRTM1,missense_variant,p.Gly313Trp,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Gly313Trp,ENST00000433224,;LRRTM1,missense_variant,p.Gly313Trp,ENST00000417012,; A ENST00000295057 Transcript missense_variant 1594/2599 937/1569 313/522 G/W Ggg/Tgg 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE deleterious(0) 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 80302883 80302883 C A 1 0 0 0 0 1 0 0 0 8945 652 23 1 1 LRRTM1 2 80302883 Missense_Mutation SNP C C3N-02089_T 558479 80302883 161890646 128 27212 DNAH6 0 . GRCh38 2 84605514 84605514 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.3096G>T p.Trp1032Cys p.W1032C ENST00000389394 20/77 147 121 26 141 141 0 strelka-varscan DNAH6,missense_variant,p.Trp1032Cys,ENST00000389394,NM_001370.1;DNAH6,missense_variant,p.Trp1032Cys,ENST00000237449,; T ENST00000389394 Transcript missense_variant 3233/12795 3096/12477 1032/4158 W/C tgG/tgT 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 deleterious(0) 20/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Pfam_domain:PF08393 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 84605514 84605514 G T 1 0 0 0 0 1 0 0 0 4420 1183 41 2 2 DNAH6 2 84605514 Missense_Mutation SNP G C3N-02089_T 4302631 84605514 157588015 129 27213 USP39 0 . GRCh38 2 85630865 85630865 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.868T>G p.Phe290Val p.F290V ENST00000323701 6/13 364 310 54 335 334 1 strelka-varscan USP39,missense_variant,p.Phe290Val,ENST00000323701,NM_006590.3;USP39,missense_variant,p.Phe212Val,ENST00000613444,NM_001256727.1;USP39,missense_variant,p.Phe187Val,ENST00000450066,NM_001256728.1;USP39,missense_variant,p.Phe290Val,ENST00000409470,NM_001256725.1;USP39,missense_variant,p.Phe290Val,ENST00000409766,NM_001256726.1;USP39,missense_variant,p.Phe290Val,ENST00000409025,;USP39,non_coding_transcript_exon_variant,,ENST00000459775,;USP39,non_coding_transcript_exon_variant,,ENST00000493829,;USP39,intron_variant,,ENST00000467885,; G ENST00000323701 Transcript missense_variant 878/2177 868/1698 290/565 F/V Ttc/Gtc 1 1 USP39 HGNC HGNC:20071 protein_coding YES CCDS33234.1 ENSP00000312981 Q53GS9 UPI000003771A NM_006590.3 deleterious(0) 6/13 PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF521,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 85630865 85630865 T G 1 0 0 0 0 1 0 0 0 17612 1841 64 5 5 USP39 2 85630865 Missense_Mutation SNP T C3N-02089_T 1025351 85630865 156562664 130 27214 POLR1A 0 . GRCh38 2 86100138 86100138 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.112T>A p.Tyr38Asn p.Y38N ENST00000263857 2/34 377 323 54 364 364 0 strelka-varscan POLR1A,missense_variant,p.Tyr38Asn,ENST00000263857,NM_015425.3;POLR1A,missense_variant,p.Tyr38Asn,ENST00000409681,;POLR1A,non_coding_transcript_exon_variant,,ENST00000486964,;POLR1A,intron_variant,,ENST00000424089,;POLR1A,intron_variant,,ENST00000409024,; T ENST00000263857 Transcript missense_variant 491/12749 112/5163 38/1720 Y/N Tac/Aac 1 -1 POLR1A HGNC HGNC:17264 protein_coding YES CCDS42706.1 ENSP00000263857 O95602 UPI0000D7DB86 NM_015425.3 deleterious(0.04) 2/34 hmmpanther:PTHR19376:SF11,hmmpanther:PTHR19376,Pfam_domain:PF04997,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 86100138 86100138 A T 1 0 0 0 0 1 0 0 0 12319 449 16 4 4 POLR1A 2 86100138 Missense_Mutation SNP A C3N-02089_T 469273 86100138 156093391 131 27215 FABP1 0 . GRCh38 2 88124466 88124466 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.361G>T p.Ala121Ser p.A121S ENST00000393750 3/3 78 69 9 52 51 1 strelka-varscan FABP1,missense_variant,p.Ala121Ser,ENST00000393750,;FABP1,intron_variant,,ENST00000295834,NM_001443.2;FABP1,non_coding_transcript_exon_variant,,ENST00000495375,;FABP1,downstream_gene_variant,,ENST00000472846,; A ENST00000393750 Transcript missense_variant 393/1839 361/375 121/124 A/S Gct/Tct 1 -1 FABP1 HGNC HGNC:3555 protein_coding ENSP00000377351 A8MW49 UPI0000D4DEDE tolerated_low_confidence(0.95) 3/3 MODERATE SNV 2 1 PASS . . 0 201 9 0 0 0 0 0 -19.16756 0.9999891 1 1 1 0 A 3 1 90 88124466 88124466 C A 1 0 0 0 0 1 0 0 0 5227 739 26 2 2 FABP1 2 88124466 Missense_Mutation SNP C C3N-02089_T 2024328 88124466 154069063 132 27216 KIAA1211L 0 . GRCh38 2 98822646 98822646 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1627G>T p.Glu543Ter p.E543* ENST00000397899 7/10 27 21 6 24 24 0 strelka-varscan KIAA1211L,stop_gained,p.Glu543Ter,ENST00000397899,NM_207362.2;KIAA1211L,downstream_gene_variant,,ENST00000423771,;KIAA1211L,downstream_gene_variant,,ENST00000462314,;KIAA1211L,upstream_gene_variant,,ENST00000464413,; A ENST00000397899 Transcript stop_gained 1959/3907 1627/2889 543/962 E/* Gag/Tag 1 -1 KIAA1211L HGNC HGNC:33454 protein_coding YES CCDS42720.1 ENSP00000380996 Q6NV74 UPI0000E59245 NM_207362.2 7/10 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 98822646 98822646 C A 1 0 0 0 0 0 1 0 0 8108 893 31 1 1 KIAA1211L 2 98822646 Nonsense_Mutation SNP C C3N-02089_T 10698180 98822646 143370883 133 27217 AFF3 0 . GRCh38 2 100007255 100007255 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.455G>T p.Ser152Ile p.S152I ENST00000409579 6/25 323 269 54 364 364 0 strelka-varscan AFF3,missense_variant,p.Ser127Ile,ENST00000409236,;AFF3,missense_variant,p.Ser127Ile,ENST00000317233,NM_002285.2;AFF3,missense_variant,p.Ser152Ile,ENST00000409579,NM_001025108.1;AFF3,missense_variant,p.Ser127Ile,ENST00000423966,;AFF3,missense_variant,p.Ser127Ile,ENST00000432037,;AFF3,missense_variant,p.Ser127Ile,ENST00000441400,;AFF3,downstream_gene_variant,,ENST00000440445,;AFF3,downstream_gene_variant,,ENST00000415384,;AFF3,downstream_gene_variant,,ENST00000424600,;AFF3,downstream_gene_variant,,ENST00000416492,;AFF3,non_coding_transcript_exon_variant,,ENST00000498090,;AFF3,upstream_gene_variant,,ENST00000430789,; A ENST00000409579 Transcript missense_variant 688/4342 455/3756 152/1251 S/I aGc/aTc 1 -1 AFF3 HGNC HGNC:6473 protein_coding YES CCDS33258.1 ENSP00000386834 P51826 UPI0000545269 NM_001025108.1 deleterious(0.02) 6/25 Low_complexity_(Seg):seg,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF16,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 100007255 100007255 C A 1 0 0 0 0 1 0 0 0 435 797 28 2 2 AFF3 2 100007255 Missense_Mutation SNP C C3N-02089_T 1184609 100007255 142186274 134 27218 FBLN7 0 . GRCh38 2 112187354 112187354 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1168G>C p.Asp390His p.D390H ENST00000331203 8/8 235 172 63 223 223 0 strelka-varscan FBLN7,missense_variant,p.Asp390His,ENST00000331203,NM_153214.2;FBLN7,missense_variant,p.Asp212His,ENST00000272559,;FBLN7,missense_variant,p.Asp344His,ENST00000409450,NM_001128165.1;FBLN7,missense_variant,p.Asp256His,ENST00000409667,;FBLN7,intron_variant,,ENST00000409903,;FBLN7,downstream_gene_variant,,ENST00000441565,;RP11-399B17.1,upstream_gene_variant,,ENST00000624058,; C ENST00000331203 Transcript missense_variant 1439/2301 1168/1320 390/439 D/H Gac/Cac 1 1 FBLN7 HGNC HGNC:26740 protein_coding YES CCDS2095.1 ENSP00000331411 Q53RD9 UPI000004E556 NM_153214.2 deleterious(0) 8/8 hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF287 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 112187354 112187354 G C 1 0 0 0 0 1 0 0 0 5564 942 33 4 4 FBLN7 2 112187354 Missense_Mutation SNP G C3N-02089_T 12180099 112187354 130006175 135 27219 ZC3H6 0 . GRCh38 2 112331809 112331809 + Missense_Mutation SNP G G T rs748326608 C3N-02089_T C3N-02089_N G G c.2891G>T p.Arg964Ile p.R964I ENST00000409871 12/12 195 164 31 199 198 1 strelka-varscan ZC3H6,missense_variant,p.Arg964Ile,ENST00000409871,NM_198581.2;ZC3H6,missense_variant,p.Arg964Ile,ENST00000343936,;ZC3H6,upstream_gene_variant,,ENST00000502881,; T ENST00000409871 Transcript missense_variant 3292/11542 2891/3570 964/1189 R/I aGa/aTa rs748326608 1 1 ZC3H6 HGNC HGNC:24762 protein_coding YES CCDS46393.1 ENSP00000386764 P61129 UPI00004215E8 NM_198581.2 deleterious(0) 12/12 hmmpanther:PTHR13119,hmmpanther:PTHR13119:SF22 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 90 112331809 112331809 G T 1 0 0 0 0 1 0 0 0 18146 942 33 2 2 ZC3H6 2 112331809 Missense_Mutation SNP G C3N-02089_T 144455 112331809 129861720 136 27220 IL37 0 . GRCh38 2 112913845 112913845 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.136G>A p.Val46Ile p.V46I ENST00000263326 2/5 195 173 22 166 165 1 strelka-varscan IL37,missense_variant,p.Val46Ile,ENST00000263326,NM_014439.3;IL37,missense_variant,p.Val46Ile,ENST00000353225,NM_173204.1;IL37,intron_variant,,ENST00000352179,NM_173202.1;IL37,intron_variant,,ENST00000349806,NM_173203.1;IL37,upstream_gene_variant,,ENST00000311328,NM_173205.1; A ENST00000263326 Transcript missense_variant 178/772 136/657 46/218 V/I Gtt/Att 1 1 IL37 HGNC HGNC:15563 protein_coding YES CCDS2103.1 ENSP00000263326 Q9NZH6 UPI000003C9C6 NM_014439.3 tolerated(0.22) 2/5 hmmpanther:PTHR10078:SF9,hmmpanther:PTHR10078 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 112913845 112913845 G A 1 0 0 0 0 1 0 0 0 7598 1377 48 3 3 IL37 2 112913845 Missense_Mutation SNP G C3N-02089_T 582036 112913845 129279684 137 27221 IL37 0 . GRCh38 2 112918666 112918666 + Missense_Mutation SNP C C A rs754171127 C3N-02089_T C3N-02089_N C C c.514C>A p.His172Asn p.H172N ENST00000263326 5/5 205 151 54 227 227 0 strelka-varscan IL37,missense_variant,p.His172Asn,ENST00000263326,NM_014439.3;IL37,missense_variant,p.His151Asn,ENST00000352179,NM_173202.1;IL37,missense_variant,p.His146Asn,ENST00000311328,NM_173205.1;IL37,missense_variant,p.His132Asn,ENST00000353225,NM_173204.1;IL37,missense_variant,p.His111Asn,ENST00000349806,NM_173203.1; A ENST00000263326 Transcript missense_variant 556/772 514/657 172/218 H/N Cac/Aac rs754171127 1 1 IL37 HGNC HGNC:15563 protein_coding YES CCDS2103.1 ENSP00000263326 Q9NZH6 UPI000003C9C6 NM_014439.3 tolerated(0.48) 5/5 hmmpanther:PTHR10078:SF9,hmmpanther:PTHR10078,Gene3D:2.80.10.50,Pfam_domain:PF00340,SMART_domains:SM00125,Superfamily_domains:SSF50353,Prints_domain:PR01360,Prints_domain:PR00264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 112918666 112918666 C A 1 0 0 0 0 1 0 0 0 7598 826 29 2 2 IL37 2 112918666 Missense_Mutation SNP C C3N-02089_T 4821 112918666 129274863 138 27222 STEAP3 0 . GRCh38 2 119257574 119257574 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.1303A>G p.Ser435Gly p.S435G ENST00000409811 5/6 150 127 23 108 108 0 strelka-varscan STEAP3,missense_variant,p.Ser435Gly,ENST00000409811,;STEAP3,intron_variant,,ENST00000393110,NM_182915.2;STEAP3,intron_variant,,ENST00000393106,NM_018234.2,NM_001008410.1;STEAP3,intron_variant,,ENST00000393107,; G ENST00000409811 Transcript missense_variant 1347/2103 1303/1374 435/457 S/G Agc/Ggc 1 1 STEAP3 HGNC HGNC:24592 protein_coding ENSP00000386510 B8ZZX6 UPI000013D445 deleterious_low_confidence(0.05) 5/6 MODERATE SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 119257574 119257574 A G 1 0 0 0 0 1 0 0 0 15656 304 11 5 5 STEAP3 2 119257574 Missense_Mutation SNP A C3N-02089_T 6338908 119257574 122935955 139 27223 EPB41L5 0 . GRCh38 2 120090483 120090483 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.1010G>T p.Gly337Val p.G337V ENST00000263713 12/25 158 126 32 141 141 0 strelka-varscan EPB41L5,missense_variant,p.Gly337Val,ENST00000263713,NM_020909.3;EPB41L5,missense_variant,p.Gly337Val,ENST00000452780,;EPB41L5,missense_variant,p.Gly337Val,ENST00000443902,NM_001184937.1;EPB41L5,missense_variant,p.Gly337Val,ENST00000443124,NM_001184938.1;EPB41L5,missense_variant,p.Gly337Val,ENST00000331393,NM_001184939.1;EPB41L5,non_coding_transcript_exon_variant,,ENST00000489017,;EPB41L5,upstream_gene_variant,,ENST00000461128,; T ENST00000263713 Transcript missense_variant 1224/6628 1010/2202 337/733 G/V gGa/gTa COSM3701924,COSM3701925 1 1 EPB41L5 HGNC HGNC:19819 protein_coding YES CCDS2130.1 ENSP00000263713 Q9HCM4 UPI00001B078A NM_020909.3 deleterious(0) 12/25 hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF15,Pfam_domain:PF08736,SMART_domains:SM01195,Superfamily_domains:SSF50729 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 120090483 120090483 G T 1 0 0 0 0 1 0 0 0 5004 1174 41 2 2 EPB41L5 2 120090483 Missense_Mutation SNP G C3N-02089_T 832909 120090483 122103046 140 27224 TFCP2L1 0 . GRCh38 2 121242410 121242410 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.717C>A p.= p.A239A ENST00000263707 7/15 247 192 55 298 297 1 strelka-varscan TFCP2L1,synonymous_variant,p.=,ENST00000263707,NM_014553.2; T ENST00000263707 Transcript synonymous_variant 815/9292 717/1440 239/479 A gcC/gcA 1 -1 TFCP2L1 HGNC HGNC:17925 protein_coding YES CCDS2134.1 ENSP00000263707 Q9NZI6 UPI0000072817 NM_014553.2 7/15 hmmpanther:PTHR11037,hmmpanther:PTHR11037:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 121242410 121242410 G T 1 0 0 0 0 0 0 0 1 16229 1219 43 2 2 TFCP2L1 2 121242410 Silent SNP G C3N-02089_T 1151927 121242410 120951119 141 27225 CNTNAP5 0 . GRCh38 2 124504482 124504482 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1250T>A p.Leu417Gln p.L417Q ENST00000431078 8/24 304 233 71 264 264 0 strelka-varscan CNTNAP5,missense_variant,p.Leu417Gln,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 1614/5284 1250/3921 417/1306 L/Q cTg/cAg 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 tolerated(0.15) 8/24 Low_complexity_(Seg):seg,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665,Pfam_domain:PF02210,Gene3D:2.60.120.200,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 124504482 124504482 T A 1 0 0 0 0 1 0 0 0 3432 1580 55 4 4 CNTNAP5 2 124504482 Missense_Mutation SNP T C3N-02089_T 3262072 124504482 117689047 142 27226 MAP3K19 0 . GRCh38 2 134964873 134964873 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.3964T>A p.Ser1322Thr p.S1322T ENST00000392915 13/13 153 134 19 141 141 0 strelka-varscan MAP3K19,missense_variant,p.Ser1322Thr,ENST00000392915,;MAP3K19,missense_variant,p.Ser1322Thr,ENST00000375845,NM_025052.4;MAP3K19,missense_variant,p.Ser1209Thr,ENST00000358371,NM_001018044.2;MAP3K19,missense_variant,p.Ser454Thr,ENST00000392917,NM_001282883.1;MAP3K19,missense_variant,p.Ser504Thr,ENST00000375844,NM_001018046.2;MAP3K19,missense_variant,p.Ser456Thr,ENST00000392918,NM_001018047.2; T ENST00000392915 Transcript missense_variant 4648/5030 3964/3987 1322/1328 S/T Tcc/Acc 1 -1 MAP3K19 HGNC HGNC:26249 protein_coding YES CCDS2176.2 ENSP00000376647 A8MWG7 UPI00004F77F2 tolerated(0.68) 13/13 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999907 1 1 1 0 T 3 4 90 134964873 134964873 A T 1 0 0 0 0 1 0 0 0 9172 304 11 4 4 MAP3K19 2 134964873 Missense_Mutation SNP A C3N-02089_T 10460391 134964873 107228656 143 27227 RAB3GAP1 0 . GRCh38 2 135115360 135115360 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.627G>T p.= p.L209L ENST00000442034 7/25 122 84 38 121 121 0 strelka-varscan RAB3GAP1,synonymous_variant,p.=,ENST00000264158,NM_012233.2;RAB3GAP1,synonymous_variant,p.=,ENST00000442034,NM_001172435.1;RAB3GAP1,synonymous_variant,p.=,ENST00000539493,;RAB3GAP1,non_coding_transcript_exon_variant,,ENST00000487003,; T ENST00000442034 Transcript synonymous_variant 637/4185 627/2967 209/988 L ctG/ctT COSM5266018,COSM5266019 1 1 RAB3GAP1 HGNC HGNC:17063 protein_coding YES CCDS54402.1 ENSP00000411418 Q15042 UPI0000D4C196 NM_001172435.1 7/25 hmmpanther:PTHR21422:SF9,hmmpanther:PTHR21422 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999985 1 1 1 0 T 2 4 90 135115360 135115360 G T 1 0 0 0 0 0 0 0 1 13094 1335 47 2 2 RAB3GAP1 2 135115360 Silent SNP G C3N-02089_T 150487 135115360 107078169 144 27228 LCT 0 . GRCh38 2 135817875 135817875 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.1173C>T p.= p.S391S ENST00000264162 6/17 357 309 48 337 337 0 strelka-varscan LCT,synonymous_variant,p.=,ENST00000264162,NM_002299.2;AC011893.3,upstream_gene_variant,,ENST00000437007,;LCT,upstream_gene_variant,,ENST00000452974,; A ENST00000264162 Transcript synonymous_variant 1184/6279 1173/5784 391/1927 S tcC/tcT COSM3566819 1 -1 LCT HGNC HGNC:6530 protein_coding YES CCDS2178.1 ENSP00000264162 P09848 UPI000013D4D2 NM_002299.2 6/17 PROSITE_patterns:PS00653,Pfam_domain:PF00232,Gene3D:3.20.20.80,Superfamily_domains:SSF51445 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 135817875 135817875 G A 1 0 0 0 0 0 0 0 1 8599 1335 47 3 3 LCT 2 135817875 Silent SNP G C3N-02089_T 702515 135817875 106375654 145 27229 THSD7B 0 . GRCh38 2 136882266 136882266 + Missense_Mutation SNP C C A rs748370242 C3N-02089_T C3N-02089_N C C c.88C>A p.His30Asn p.H30N ENST00000272643 1/27 138 120 18 145 145 0 strelka-varscan THSD7B,missense_variant,p.His30Asn,ENST00000409968,NM_001316349.1;THSD7B,missense_variant,p.His30Asn,ENST00000272643,;THSD7B,missense_variant,p.His30Asn,ENST00000472720,; A ENST00000272643 Transcript missense_variant 88/5939 88/4827 30/1608 H/N Cat/Aat rs748370242 1 1 THSD7B HGNC HGNC:29348 protein_coding YES ENSP00000272643 Q9C0I4 UPI0004E4C87A tolerated(0.2) 1/27 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF7,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 136882266 136882266 C A 1 0 0 0 0 1 0 0 0 16314 594 21 2 2 THSD7B 2 136882266 Missense_Mutation SNP C C3N-02089_T 1064391 136882266 105311263 146 27230 LRP1B 0 . GRCh38 2 140364709 140364709 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.11083G>T p.Gly3695Ter p.G3695* ENST00000389484 72/91 227 201 26 216 216 0 strelka-varscan LRP1B,stop_gained,p.Gly3695Ter,ENST00000389484,NM_018557.2; A ENST00000389484 Transcript stop_gained 12055/16535 11083/13800 3695/4599 G/* Gga/Tga 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 72/91 PROSITE_profiles:PS50068,Pfam_domain:PF00057,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 140364709 140364709 C A 1 0 0 0 0 0 1 0 0 8850 603 21 2 2 LRP1B 2 140364709 Nonsense_Mutation SNP C C3N-02089_T 3482443 140364709 101828820 147 27231 NEB 0 . GRCh38 2 151694400 151694400 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1819A>C p.Lys607Gln p.K607Q ENST00000618972 20/183 241 220 21 229 229 0 strelka-varscan NEB,missense_variant,p.Lys607Gln,ENST00000618972,NM_001271208.1;NEB,missense_variant,p.Lys607Gln,ENST00000397345,NM_001164508.1;NEB,missense_variant,p.Lys607Gln,ENST00000427231,NM_001164507.1;NEB,missense_variant,p.Lys607Gln,ENST00000603639,;NEB,missense_variant,p.Lys607Gln,ENST00000604864,;NEB,missense_variant,p.Lys607Gln,ENST00000409198,NM_004543.4;NEB,missense_variant,p.Lys607Gln,ENST00000172853,;NEB,non_coding_transcript_exon_variant,,ENST00000489048,; G ENST00000618972 Transcript missense_variant 2022/26307 1819/25683 607/8560 K/Q Aaa/Caa 1 -1 NEB HGNC HGNC:7720 protein_coding YES CCDS74588.1 ENSP00000484342 A0A087X1N7 UPI0004E4CCB0 NM_001271208.1 tolerated(0.06) 20/183 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 151694400 151694400 T G 1 0 0 0 0 1 0 0 0 10326 1792 62 5 5 NEB 2 151694400 Missense_Mutation SNP T C3N-02089_T 11329691 151694400 90499129 148 27232 ACVR1C 0 . GRCh38 2 157542786 157542786 + Silent SNP C C G rs114476591 C3N-02089_T C3N-02089_N C C c.1020G>C p.= p.A340A ENST00000243349 6/9 229 209 20 200 200 0 strelka-varscan ACVR1C,synonymous_variant,p.=,ENST00000243349,NM_145259.2;ACVR1C,synonymous_variant,p.=,ENST00000409680,NM_001111031.1;ACVR1C,synonymous_variant,p.=,ENST00000335450,NM_001111032.1;ACVR1C,synonymous_variant,p.=,ENST00000348328,NM_001111033.1; G ENST00000243349 Transcript synonymous_variant 1381/8994 1020/1482 340/493 A gcG/gcC rs114476591 1 -1 ACVR1C HGNC HGNC:18123 protein_coding YES CCDS2205.1 ENSP00000243349 Q8NER5 UPI000006CFAE NM_145259.2 6/9 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR23255,hmmpanther:PTHR23255:SF58,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 157542786 157542786 C G 1 0 0 0 0 0 0 0 1 266 639 23 4 4 ACVR1C 2 157542786 Silent SNP C C3N-02089_T 5848386 157542786 84650743 149 27233 PLA2R1 0 . GRCh38 2 159987222 159987222 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1971G>T p.Glu657Asp p.E657D ENST00000283243 12/30 334 295 39 292 292 0 strelka-varscan PLA2R1,missense_variant,p.Glu657Asp,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.Glu657Asp,ENST00000392771,NM_001007267.2; A ENST00000283243 Transcript missense_variant 2178/14371 1971/4392 657/1463 E/D gaG/gaT COSM3568340 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 tolerated(0.35) 12/30 hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 159987222 159987222 C A 1 0 0 0 0 1 0 0 0 12106 912 32 2 2 PLA2R1 2 159987222 Missense_Mutation SNP C C3N-02089_T 2444436 159987222 82206307 150 27234 PLA2R1 0 . GRCh38 2 160022856 160022856 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1103A>T p.Lys368Ile p.K368I ENST00000283243 7/30 61 43 18 72 72 0 strelka-varscan PLA2R1,missense_variant,p.Lys368Ile,ENST00000283243,NM_007366.4,NM_001195641.1;PLA2R1,missense_variant,p.Lys368Ile,ENST00000392771,NM_001007267.2; A ENST00000283243 Transcript missense_variant 1310/14371 1103/4392 368/1463 K/I aAa/aTa 1 -1 PLA2R1 HGNC HGNC:9042 protein_coding YES CCDS33309.1 ENSP00000283243 Q13018 UPI00001AEA9D NM_007366.4,NM_001195641.1 tolerated(0.38) 7/30 Gene3D:3.10.100.10,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF74 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 160022856 160022856 T A 1 0 0 0 0 1 0 0 0 12106 1855 64 4 4 PLA2R1 2 160022856 Missense_Mutation SNP T C3N-02089_T 35634 160022856 82170673 151 27235 IFIH1 0 . GRCh38 2 162282468 162282468 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1204G>T p.Glu402Ter p.E402* ENST00000263642 6/16 189 148 41 179 179 0 strelka-varscan IFIH1,stop_gained,p.Glu402Ter,ENST00000263642,NM_022168.3; A ENST00000263642 Transcript stop_gained 1600/3595 1204/3078 402/1025 E/* Gaa/Taa 1 -1 IFIH1 HGNC HGNC:18873 protein_coding YES CCDS2217.1 ENSP00000263642 Q9BYX4 UPI000013D436 NM_022168.3 6/16 Gene3D:3.40.50.300,Pfam_domain:PF04851,PROSITE_profiles:PS51192,hmmpanther:PTHR14074,hmmpanther:PTHR14074:SF14,SMART_domains:SM00487,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 162282468 162282468 C A 1 0 0 0 0 0 1 0 0 7420 922 32 2 2 IFIH1 2 162282468 Nonsense_Mutation SNP C C3N-02089_T 2259612 162282468 79911061 152 27236 SLC38A11 0 . GRCh38 2 164908703 164908703 + Silent SNP G G T rs138230187 C3N-02089_T C3N-02089_N G G c.864C>A p.= p.V288V ENST00000409149 10/11 109 93 16 107 107 0 strelka-varscan SLC38A11,synonymous_variant,p.=,ENST00000303735,NM_173512.2;SLC38A11,synonymous_variant,p.=,ENST00000409058,;SLC38A11,synonymous_variant,p.=,ENST00000409149,NM_001199148.1;SLC38A11,synonymous_variant,p.=,ENST00000409662,;SLC38A11,synonymous_variant,p.=,ENST00000424914,;AC013463.2,upstream_gene_variant,,ENST00000627211,;AC013463.2,upstream_gene_variant,,ENST00000629991,;AC013463.2,upstream_gene_variant,,ENST00000628960,;SLC38A11,downstream_gene_variant,,ENST00000493887,;SLC38A11,non_coding_transcript_exon_variant,,ENST00000483641,;SLC38A11,non_coding_transcript_exon_variant,,ENST00000470576,; T ENST00000409149 Transcript synonymous_variant 1156/1621 864/1221 288/406 V gtC/gtA rs138230187 1 -1 SLC38A11 HGNC HGNC:26836 protein_coding YES CCDS56142.1 ENSP00000386272 Q08AI6 UPI0000E44805 NM_001199148.1 10/11 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF54,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 90 164908703 164908703 G T 1 0 0 0 0 0 0 0 1 14881 1277 45 2 2 SLC38A11 2 164908703 Silent SNP G C3N-02089_T 2626235 164908703 77284826 153 27237 SCN3A 0 . GRCh38 2 165113881 165113881 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.3604A>G p.Ile1202Val p.I1202V ENST00000283254 20/28 335 313 22 303 303 0 strelka-varscan SCN3A,missense_variant,p.Ile1202Val,ENST00000360093,;SCN3A,missense_variant,p.Ile1202Val,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Ile1153Val,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Ile1153Val,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,; C ENST00000283254 Transcript missense_variant 4072/9091 3604/6003 1202/2000 I/V Att/Gtt 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 20/28 Gene3D:1.20.120.350,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 165113881 165113881 T C 1 0 0 0 0 1 0 0 0 14187 1406 49 5 5 SCN3A 2 165113881 Missense_Mutation SNP T C3N-02089_T 205178 165113881 77079648 154 27238 SCN3A 0 . GRCh38 2 165127873 165127873 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.3151A>G p.Asn1051Asp p.N1051D ENST00000283254 18/28 331 263 68 383 383 0 strelka-varscan SCN3A,missense_variant,p.Asn1051Asp,ENST00000360093,;SCN3A,missense_variant,p.Asn1051Asp,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Asn1002Asp,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Asn1002Asp,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000628085,;AC013463.2,intron_variant,,ENST00000625505,;SCN3A,upstream_gene_variant,,ENST00000484898,; C ENST00000283254 Transcript missense_variant 3619/9091 3151/6003 1051/2000 N/D Aat/Gat 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 tolerated(0.05) 18/28 Pfam_domain:PF06512,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 165127873 165127873 T C 1 0 0 0 0 1 0 0 0 14187 1812 63 5 5 SCN3A 2 165127873 Missense_Mutation SNP T C3N-02089_T 13992 165127873 77065656 155 27239 SCN3A 0 . GRCh38 2 165137971 165137971 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.2299A>T p.Thr767Ser p.T767S ENST00000283254 15/28 422 380 42 412 412 0 strelka-varscan SCN3A,missense_variant,p.Thr767Ser,ENST00000360093,;SCN3A,missense_variant,p.Thr767Ser,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Thr718Ser,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Thr718Ser,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,; A ENST00000283254 Transcript missense_variant 2767/9091 2299/6003 767/2000 T/S Act/Tct 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 15/28 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 165137971 165137971 T A 1 0 0 0 0 1 0 0 0 14187 1696 59 4 4 SCN3A 2 165137971 Missense_Mutation SNP T C3N-02089_T 10098 165137971 77055558 156 27240 SCN2A 0 . GRCh38 2 165326983 165326983 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.2148A>T p.Glu716Asp p.E716D ENST00000636071 14/28 356 315 41 352 352 0 strelka-varscan SCN2A,missense_variant,p.Glu716Asp,ENST00000636071,;SCN2A,missense_variant,p.Glu584Asp,ENST00000636985,;SCN2A,missense_variant,p.Glu716Asp,ENST00000637266,;SCN2A,missense_variant,p.Glu716Asp,ENST00000375437,NM_001040142.1;SCN2A,missense_variant,p.Glu716Asp,ENST00000283256,NM_021007.2;SCN2A,missense_variant,p.Glu716Asp,ENST00000375427,NM_001040143.1;SCN2A,missense_variant,p.Glu716Asp,ENST00000631182,;SCN2A,splice_region_variant,,ENST00000635945,;SCN2A,splice_region_variant,,ENST00000638151,;SCN2A,missense_variant,p.Glu716Asp,ENST00000636384,;SCN2A,missense_variant,p.Glu716Asp,ENST00000636769,;SCN2A,splice_region_variant,,ENST00000480032,;SCN2A,splice_region_variant,,ENST00000636662,;SCN2A,splice_region_variant,,ENST00000636135,;SCN2A,3_prime_UTR_variant,,ENST00000637367,; T ENST00000636071 Transcript missense_variant,splice_region_variant 2525/9303 2148/6018 716/2005 E/D gaA/gaT 1 1 SCN2A HGNC HGNC:10588 protein_coding YES CCDS33313.1 ENSP00000490107 UPI000002A663 tolerated(0.06) 14/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 165326983 165326983 A T 1 0 0 0 0 1 0 0 0 14185 86 3 4 4 SCN2A 2 165326983 Missense_Mutation SNP A C3N-02089_T 189012 165326983 76866546 157 27241 SCN1A 0 . GRCh38 2 165991689 165991689 + Missense_Mutation SNP G G C rs775593428 C3N-02089_T C3N-02089_N G G c.5586C>G p.Ile1862Met p.I1862M ENST00000303395 28/28 244 219 25 214 214 0 strelka-varscan SCN1A,missense_variant,p.Ile1851Met,ENST00000637988,;SCN1A,missense_variant,p.Ile1862Met,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,missense_variant,p.Ile1851Met,ENST00000635750,;SCN1A,missense_variant,p.Ile1862Met,ENST00000423058,;SCN1A,missense_variant,p.Ile1851Met,ENST00000375405,NM_006920.4;SCN1A,missense_variant,p.Ile1834Met,ENST00000409050,NM_001165964.1;SCN1A,3_prime_UTR_variant,,ENST00000635776,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000597623,;AC010127.3,intron_variant,,ENST00000630226,;SCN1A,3_prime_UTR_variant,,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000637038,;SCN1A,downstream_gene_variant,,ENST00000625916,;SCN1A,downstream_gene_variant,,ENST00000473295,; C ENST00000303395 Transcript missense_variant 6004/8533 5586/6030 1862/2009 I/M atC/atG rs775593428 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 deleterious(0) 28/28 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 165991689 165991689 G C 1 0 0 0 0 1 0 0 0 14183 1164 41 4 4 SCN1A 2 165991689 Missense_Mutation SNP G C3N-02089_T 664706 165991689 76201840 158 27242 SCN7A 0 . GRCh38 2 166406353 166406353 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.4276T>A p.Cys1426Ser p.C1426S ENST00000409855 25/25 310 275 35 355 354 1 strelka-varscan SCN7A,missense_variant,p.Cys1426Ser,ENST00000619410,;SCN7A,missense_variant,p.Cys1426Ser,ENST00000621965,;SCN7A,missense_variant,p.Cys1426Ser,ENST00000409855,NM_002976.3;SCN7A,3_prime_UTR_variant,,ENST00000424326,; T ENST00000409855 Transcript missense_variant 4403/7183 4276/5049 1426/1682 C/S Tgt/Agt 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 deleterious(0.02) 25/25 Transmembrane_helices:TMhelix,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF00520,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 166406353 166406353 A T 1 0 0 0 0 1 0 0 0 14192 188 7 4 4 SCN7A 2 166406353 Missense_Mutation SNP A C3N-02089_T 414664 166406353 75787176 159 27243 SCN7A 0 . GRCh38 2 166406632 166406632 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.3997A>C p.Met1333Leu p.M1333L ENST00000409855 25/25 64 47 17 76 76 0 strelka-varscan SCN7A,missense_variant,p.Met1333Leu,ENST00000619410,;SCN7A,missense_variant,p.Met1333Leu,ENST00000621965,;SCN7A,missense_variant,p.Met1333Leu,ENST00000409855,NM_002976.3;SCN7A,3_prime_UTR_variant,,ENST00000424326,; G ENST00000409855 Transcript missense_variant 4124/7183 3997/5049 1333/1682 M/L Atg/Ctg 1 -1 SCN7A HGNC HGNC:10594 protein_coding YES CCDS46442.1 ENSP00000386796 Q01118 UPI0000209019 NM_002976.3 tolerated(0.33) 25/25 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF14,Pfam_domain:PF00520,Gene3D:1.20.120.350,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.999998 1 1 1 0 G 3 3 90 166406632 166406632 T G 1 0 0 0 0 1 0 0 0 14192 1406 49 5 5 SCN7A 2 166406632 Missense_Mutation SNP T C3N-02089_T 279 166406632 75786897 160 27244 SPC25 0 . GRCh38 2 168877346 168877346 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.238G>C p.Asp80His p.D80H ENST00000282074 4/7 240 208 32 249 249 0 strelka-varscan SPC25,missense_variant,p.Asp80His,ENST00000282074,NM_020675.3;SPC25,missense_variant,p.Asp80His,ENST00000451987,;SPC25,non_coding_transcript_exon_variant,,ENST00000472216,;SPC25,non_coding_transcript_exon_variant,,ENST00000479309,; G ENST00000282074 Transcript missense_variant 380/1354 238/675 80/224 D/H Gat/Cat 1 -1 SPC25 HGNC HGNC:24031 protein_coding YES CCDS2229.1 ENSP00000282074 Q9HBM1 UPI000006D2C9 NM_020675.3 tolerated(0.09) 4/7 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14281:SF0,hmmpanther:PTHR14281 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 168877346 168877346 C G 1 0 0 0 0 1 0 0 0 15368 855 30 4 4 SPC25 2 168877346 Missense_Mutation SNP C C3N-02089_T 2470714 168877346 73316183 161 27245 LRP2 0 . GRCh38 2 169142686 169142686 + Missense_Mutation SNP C C T rs367958079 C3N-02089_T C3N-02089_N C C c.13096G>A p.Glu4366Lys p.E4366K ENST00000263816 71/79 486 393 93 421 421 0 strelka-varscan LRP2,missense_variant,p.Glu4366Lys,ENST00000263816,NM_004525.2;LRP2,upstream_gene_variant,,ENST00000491228,; T ENST00000263816 Transcript missense_variant 13382/15808 13096/13968 4366/4655 E/K Gag/Aag rs367958079 1 -1 LRP2 HGNC HGNC:6694 protein_coding YES CCDS2232.1 ENSP00000263816 P98164 UPI0000141BA5 NM_004525.2 tolerated(0.29) 71/79 Gene3D:2gy5A03,SMART_domains:SM00179,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 169142686 169142686 C T 1 0 0 0 0 1 0 0 0 8851 835 29 3 3 LRP2 2 169142686 Missense_Mutation SNP C C3N-02089_T 265340 169142686 73050843 162 27246 KLHL23 0 . GRCh38 2 169749506 169749506 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.1451A>C p.Glu484Ala p.E484A ENST00000392647 4/4 204 146 58 179 179 0 strelka-varscan KLHL23,missense_variant,p.Glu484Ala,ENST00000392647,NM_144711.5;KLHL23,missense_variant,p.Glu484Ala,ENST00000272797,NM_001199290.1;KLHL23,5_prime_UTR_variant,,ENST00000498202,;KLHL23,5_prime_UTR_variant,,ENST00000602521,;KLHL23,intron_variant,,ENST00000437875,;KLHL23,intron_variant,,ENST00000448589,;KLHL23,downstream_gene_variant,,ENST00000494387,; C ENST00000392647 Transcript missense_variant 1695/4077 1451/1677 484/558 E/A gAa/gCa 1 1 KLHL23 HGNC HGNC:27506 protein_coding YES CCDS2236.1 ENSP00000376419 Q8NBE8 UPI000006D999 NM_144711.5 tolerated(0.15) 4/4 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF244,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 169749506 169749506 A C 1 0 0 0 0 1 0 0 0 8242 246 9 5 5 KLHL23 2 169749506 Missense_Mutation SNP A C3N-02089_T 606820 169749506 72444023 163 27247 GAD1 0 . GRCh38 2 170858890 170858890 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1608C>A p.His536Gln p.H536Q ENST00000358196 16/17 426 373 53 441 440 1 strelka-varscan GAD1,missense_variant,p.His536Gln,ENST00000358196,NM_000817.2;GAD1,3_prime_UTR_variant,,ENST00000625689,;GAD1,3_prime_UTR_variant,,ENST00000493875,;GAD1,3_prime_UTR_variant,,ENST00000414527,;GAD1,non_coding_transcript_exon_variant,,ENST00000478562,;GAD1,non_coding_transcript_exon_variant,,ENST00000488724,; A ENST00000358196 Transcript missense_variant 2158/3604 1608/1785 536/594 H/Q caC/caA 1 1 GAD1 HGNC HGNC:4092 protein_coding YES CCDS2239.1 ENSP00000350928 Q99259 A0A0S2Z3V5 UPI000002D729 NM_000817.2 tolerated(0.33) 16/17 hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF57,Gene3D:3.90.1150.10,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 170858890 170858890 C A 1 0 0 0 0 1 0 0 0 6050 492 17 2 2 GAD1 2 170858890 Missense_Mutation SNP C C3N-02089_T 1109384 170858890 71334639 164 27248 OSBPL6 0 . GRCh38 2 178331581 178331581 + Missense_Mutation SNP A A C C3N-02089_T C3N-02089_N A A c.348A>C p.Leu116Phe p.L116F ENST00000392505 6/26 153 135 18 200 200 0 strelka-varscan OSBPL6,missense_variant,p.Leu116Phe,ENST00000190611,NM_032523.3;OSBPL6,missense_variant,p.Leu116Phe,ENST00000359685,NM_001201482.1;OSBPL6,missense_variant,p.Leu116Phe,ENST00000392505,NM_001201480.1;OSBPL6,missense_variant,p.Leu116Phe,ENST00000409045,NM_001201481.1;OSBPL6,missense_variant,p.Leu116Phe,ENST00000409631,;OSBPL6,missense_variant,p.Leu95Phe,ENST00000315022,NM_145739.2;OSBPL6,missense_variant,p.Leu116Phe,ENST00000357080,;OSBPL6,non_coding_transcript_exon_variant,,ENST00000477097,; C ENST00000392505 Transcript missense_variant 892/3637 348/2880 116/959 L/F ttA/ttC COSM3391147,COSM3391148,COSM84648 1 1 OSBPL6 HGNC HGNC:16388 protein_coding YES CCDS56150.1 ENSP00000376293 Q9BZF3 UPI0000E5A29F NM_001201480.1 deleterious(0) 6/26 PROSITE_profiles:PS50003,hmmpanther:PTHR10972:SF76,hmmpanther:PTHR10972,Gene3D:2.30.29.30,Pfam_domain:PF15409,SMART_domains:SM00233,Superfamily_domains:SSF50729 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 178331581 178331581 A C 1 0 0 0 0 1 0 0 0 11347 359 13 5 5 OSBPL6 2 178331581 Missense_Mutation SNP A C3N-02089_T 7472691 178331581 63861948 165 27249 TTN 0 . GRCh38 2 178564141 178564141 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.81991A>T p.Lys27331Ter p.K27331* ENST00000589042 326/363 309 272 37 290 290 0 strelka-varscan TTN,stop_gained,p.Lys27331Ter,ENST00000589042,NM_001267550.2;TTN,stop_gained,p.Lys25690Ter,ENST00000591111,;TTN,stop_gained,p.Lys25690Ter,ENST00000615779,NM_001256850.1;TTN,stop_gained,p.Lys24763Ter,ENST00000342992,NM_133378.4;TTN,stop_gained,p.Lys18266Ter,ENST00000460472,NM_003319.4;TTN,stop_gained,p.Lys18458Ter,ENST00000342175,NM_133437.4;TTN,stop_gained,p.Lys18391Ter,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000627564,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586707,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000592600,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000586831,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000438095,; A ENST00000589042 Transcript stop_gained 82216/109224 81991/107976 27331/35991 K/* Aaa/Taa 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 326/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 178564141 178564141 T A 1 0 0 0 0 0 1 0 0 17245 1792 62 4 4 TTN 2 178564141 Nonsense_Mutation SNP T C3N-02089_T 232560 178564141 63629388 166 27250 TTN 0 . GRCh38 2 178592584 178592584 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.59421T>A p.Ser19807Arg p.S19807R ENST00000589042 301/363 239 209 30 274 274 0 strelka-varscan TTN,missense_variant,p.Ser19807Arg,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser18166Arg,ENST00000591111,;TTN,missense_variant,p.Ser18166Arg,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser17239Arg,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ser10742Arg,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ser10934Arg,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ser10867Arg,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000419746,;TTN-AS1,intron_variant,,ENST00000456053,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000630096,;TTN-AS1,intron_variant,,ENST00000626954,;TTN-AS1,intron_variant,,ENST00000586452,;TTN-AS1,intron_variant,,ENST00000592689,;TTN-AS1,intron_variant,,ENST00000589234,;TTN-AS1,intron_variant,,ENST00000590807,;TTN-AS1,intron_variant,,ENST00000629117,;TTN-AS1,intron_variant,,ENST00000590932,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000626138,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000628826,;TTN-AS1,intron_variant,,ENST00000610290,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000592750,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589907,;TTN-AS1,intron_variant,,ENST00000591332,;TTN-AS1,intron_variant,,ENST00000628296,;TTN-AS1,intron_variant,,ENST00000626517,;TTN-AS1,downstream_gene_variant,,ENST00000590743,; T ENST00000589042 Transcript missense_variant 59646/109224 59421/107976 19807/35991 S/R agT/agA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 301/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 178592584 178592584 A T 1 0 0 0 0 1 0 0 0 17245 156 6 4 4 TTN 2 178592584 Missense_Mutation SNP A C3N-02089_T 28443 178592584 63600945 167 27251 TTN 0 . GRCh38 2 178711169 178711169 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.28067C>A p.Ala9356Asp p.A9356D ENST00000589042 97/363 178 157 21 157 155 2 strelka-varscan TTN,missense_variant,p.Ala9356Asp,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ala9039Asp,ENST00000591111,;TTN,missense_variant,p.Ala9039Asp,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ala8112Asp,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,; T ENST00000589042 Transcript missense_variant 28292/109224 28067/107976 9356/35991 A/D gCc/gAc COSM4088728,COSM4088729 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 97/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817:SF10,hmmpanther:PTHR13817,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 90 178711169 178711169 G T 1 0 0 0 0 1 0 0 0 17245 1203 42 2 2 TTN 2 178711169 Missense_Mutation SNP G C3N-02089_T 118585 178711169 63482360 168 27252 TTN 0 . GRCh38 2 178769864 178769864 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.8717C>A p.Ser2906Tyr p.S2906Y ENST00000589042 37/363 235 171 64 257 256 1 strelka-varscan TTN,missense_variant,p.Ser2906Tyr,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Ser2906Tyr,ENST00000591111,;TTN,missense_variant,p.Ser2906Tyr,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Ser2906Tyr,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Ser2860Tyr,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Ser2860Tyr,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Ser2860Tyr,ENST00000359218,NM_133432.3;TTN,missense_variant,p.Ser2906Tyr,ENST00000360870,NM_133379.4;TTN,upstream_gene_variant,,ENST00000634225,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000610005,;TTN-AS1,upstream_gene_variant,,ENST00000584485,;TTN-AS1,upstream_gene_variant,,ENST00000629094,; T ENST00000589042 Transcript missense_variant 8942/109224 8717/107976 2906/35991 S/Y tCc/tAc 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 37/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 178769864 178769864 G T 1 0 0 0 0 1 0 0 0 17245 1174 41 2 2 TTN 2 178769864 Missense_Mutation SNP G C3N-02089_T 58695 178769864 63423665 169 27253 DNAJC10 0 . GRCh38 2 182743627 182743627 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.1221A>T p.= p.P407P ENST00000264065 14/24 313 259 54 307 307 0 strelka-varscan DNAJC10,synonymous_variant,p.=,ENST00000264065,NM_018981.2;DNAJC10,synonymous_variant,p.=,ENST00000616986,NM_001271581.1;DNAJC10,intron_variant,,ENST00000613960,;DNAJC10,downstream_gene_variant,,ENST00000537515,;DNAJC10,3_prime_UTR_variant,,ENST00000418559,;DNAJC10,non_coding_transcript_exon_variant,,ENST00000491074,;DNAJC10,downstream_gene_variant,,ENST00000444005,; T ENST00000264065 Transcript synonymous_variant 1636/20129 1221/2382 407/793 P ccA/ccT 1 1 DNAJC10 HGNC HGNC:24637 protein_coding YES CCDS33345.1 ENSP00000264065 Q8IXB1 UPI000007376C NM_018981.2 14/24 hmmpanther:PTHR24078:SF235,hmmpanther:PTHR24078,Gene3D:3.40.30.10,PIRSF_domain:PIRSF037293,Superfamily_domains:SSF52833 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 182743627 182743627 A T 1 0 0 0 0 0 0 0 1 4443 175 7 4 4 DNAJC10 2 182743627 Silent SNP A C3N-02089_T 3973763 182743627 59449902 170 27254 FSIP2 0 . GRCh38 2 185800365 185800365 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.11326C>A p.Leu3776Ile p.L3776I ENST00000343098 17/23 111 78 33 97 97 0 strelka-varscan FSIP2,missense_variant,p.Leu3776Ile,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Leu3687Ile,ENST00000424728,;FSIP2-AS1,upstream_gene_variant,,ENST00000436557,;FSIP2-AS1,upstream_gene_variant,,ENST00000429929,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 11326/21054 11326/20991 3776/6996 L/I Cta/Ata 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0) 17/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 185800365 185800365 C A 1 0 0 0 0 1 0 0 0 5949 680 24 2 2 FSIP2 2 185800365 Missense_Mutation SNP C C3N-02089_T 3056738 185800365 56393164 171 27255 FSIP2 0 . GRCh38 2 185805529 185805529 + Nonsense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.16490C>A p.Ser5497Ter p.S5497* ENST00000343098 17/23 191 140 51 220 220 0 strelka-varscan FSIP2,stop_gained,p.Ser5497Ter,ENST00000343098,NM_173651.2;FSIP2,stop_gained,p.Ser5408Ter,ENST00000424728,;FSIP2,upstream_gene_variant,,ENST00000611759,;FSIP2,intron_variant,,ENST00000415915,; A ENST00000343098 Transcript stop_gained 16490/21054 16490/20991 5497/6996 S/* tCa/tAa COSM2711231,COSM2711232,COSM5687016,COSM5687017 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 17/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 1,1,1,1 HIGH 1 SNV 5 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 185805529 185805529 C A 1 0 0 0 0 0 1 0 0 5949 838 29 2 2 FSIP2 2 185805529 Nonsense_Mutation SNP C C3N-02089_T 5164 185805529 56388000 172 27256 CALCRL 0 . GRCh38 2 187380499 187380499 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.376C>A p.Gln126Lys p.Q126K ENST00000409998 8/16 156 140 16 154 153 1 strelka-varscan CALCRL,missense_variant,p.Gln126Lys,ENST00000409998,;CALCRL,missense_variant,p.Gln126Lys,ENST00000392370,NM_005795.5;CALCRL,missense_variant,p.Gln126Lys,ENST00000410068,NM_001271751.1;CALCRL,downstream_gene_variant,,ENST00000447403,;CALCRL,downstream_gene_variant,,ENST00000410102,;AC007319.1,intron_variant,,ENST00000412276,;AC007319.1,intron_variant,,ENST00000453517,; T ENST00000409998 Transcript missense_variant 1158/5223 376/1386 126/461 Q/K Cag/Aag 1 -1 CALCRL HGNC HGNC:16709 protein_coding YES CCDS2293.1 ENSP00000386972 Q16602 UPI00000503EF tolerated(0.76) 8/16 PROSITE_profiles:PS50227,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF67,Pfam_domain:PF02793,SMART_domains:SM00008,Superfamily_domains:SSF81321,Superfamily_domains:SSF111418 MODERATE 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -19.99868 0.9999861 1 1 1 0 T 3 4 90 187380499 187380499 G T 1 0 0 0 0 1 0 0 0 2270 1357 47 2 2 CALCRL 2 187380499 Missense_Mutation SNP G C3N-02089_T 1574970 187380499 54813030 173 27257 COL3A1 0 . GRCh38 2 188999542 188999542 + Nonsense_Mutation SNP G G T rs587779606 C3N-02089_T C3N-02089_N G G c.2194G>T p.Gly732Ter p.G732* ENST00000304636 31/51 359 326 33 424 423 1 strelka-varscan COL3A1,stop_gained,p.Gly732Ter,ENST00000304636,NM_000090.3;COL3A1,stop_gained,p.Gly732Ter,ENST00000317840,;COL3A1,downstream_gene_variant,,ENST00000637672,;COL3A1,upstream_gene_variant,,ENST00000467886,; T ENST00000304636 Transcript stop_gained 2364/5543 2194/4401 732/1466 G/* Gga/Tga rs587779606,CM119023 1 1 COL3A1 HGNC HGNC:2201 protein_coding YES CCDS2297.1 ENSP00000304408 P02461 UPI0000456EBA NM_000090.3 31/51 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF604 pathogenic HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 188999542 188999542 G T 1 0 0 0 0 0 1 0 0 3477 1001 35 2 2 COL3A1 2 188999542 Nonsense_Mutation SNP G C3N-02089_T 1619043 188999542 53193987 174 27258 DNAH7 0 . GRCh38 2 195960340 195960340 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2811G>T p.Gln937His p.Q937H ENST00000312428 18/65 162 148 14 187 187 0 strelka-varscan DNAH7,missense_variant,p.Gln937His,ENST00000312428,NM_018897.2; A ENST00000312428 Transcript missense_variant 2912/12394 2811/12075 937/4024 Q/H caG/caT 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.01) 18/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF08393 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 195960340 195960340 C A 1 0 0 0 0 1 0 0 0 4421 912 32 2 2 DNAH7 2 195960340 Missense_Mutation SNP C C3N-02089_T 6960798 195960340 46233189 175 27259 DNAH7 0 . GRCh38 2 196026790 196026790 + Missense_Mutation SNP C C A rs753885490 C3N-02089_T C3N-02089_N C C c.637G>T p.Asp213Tyr p.D213Y ENST00000312428 7/65 122 109 13 109 109 0 strelka-varscan DNAH7,missense_variant,p.Asp213Tyr,ENST00000312428,NM_018897.2;DNAH7,missense_variant,p.Asp213Tyr,ENST00000410072,;DNAH7,downstream_gene_variant,,ENST00000427816,; A ENST00000312428 Transcript missense_variant 738/12394 637/12075 213/4024 D/Y Gat/Tat rs753885490 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.03) 7/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 196026790 196026790 C A 1 0 0 0 0 1 0 0 0 4421 855 30 2 2 DNAH7 2 196026790 Missense_Mutation SNP C C3N-02089_T 66450 196026790 46166739 176 27260 FAM117B 0 . GRCh38 2 202755582 202755582 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1005C>T p.= p.T335T ENST00000392238 5/8 210 163 47 168 167 1 strelka-varscan FAM117B,synonymous_variant,p.=,ENST00000392238,NM_173511.3; T ENST00000392238 Transcript synonymous_variant 1005/5763 1005/1770 335/589 T acC/acT 1 1 FAM117B HGNC HGNC:14440 protein_coding YES CCDS33362.2 ENSP00000376071 Q6P1L5 UPI00015B3B88 NM_173511.3 5/8 Pfam_domain:PF15388,hmmpanther:PTHR14972,hmmpanther:PTHR14972:SF6 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 202755582 202755582 C T 1 0 0 0 0 0 0 0 1 5269 581 21 3 3 FAM117B 2 202755582 Silent SNP C C3N-02089_T 6728792 202755582 39437947 177 27261 IDH1 0 . GRCh38 2 208245337 208245337 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.502C>A p.Leu168Met p.L168M ENST00000415913 5/10 258 230 28 276 276 0 strelka-varscan IDH1,missense_variant,p.Leu168Met,ENST00000415913,NM_001282387.1;IDH1,missense_variant,p.Leu168Met,ENST00000345146,NM_005896.3;IDH1,missense_variant,p.Leu168Met,ENST00000446179,NM_001282386.1;IDH1,downstream_gene_variant,,ENST00000415282,;IDH1,downstream_gene_variant,,ENST00000417583,;IDH1,downstream_gene_variant,,ENST00000451391,;IDH1,downstream_gene_variant,,ENST00000462386,; T ENST00000415913 Transcript missense_variant 884/2441 502/1245 168/414 L/M Ctg/Atg 1 -1 IDH1 HGNC HGNC:5382 protein_coding YES CCDS2381.1 ENSP00000390265 O75874 V9HWJ2 UPI000012D1B4 NM_001282387.1 deleterious_low_confidence(0.03) 5/10 hmmpanther:PTHR11822,Gene3D:3.40.718.10,Pfam_domain:PF00180,TIGRFAM_domain:TIGR00127,PIRSF_domain:PIRSF000108,SMART_domains:SM01329,Superfamily_domains:SSF53659 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 208245337 208245337 G T 1 0 0 0 0 1 0 0 0 7394 991 35 2 2 IDH1 2 208245337 Missense_Mutation SNP G C3N-02089_T 5489755 208245337 33948192 178 27262 MAP2 0 . GRCh38 2 209697007 209697007 + Missense_Mutation SNP A A C rs781734507 C3N-02089_T C3N-02089_N A A c.4478A>C p.Tyr1493Ser p.Y1493S ENST00000360351 9/15 108 101 7 186 186 0 strelka-varscan MAP2,missense_variant,p.Tyr1493Ser,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Tyr1489Ser,ENST00000447185,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,downstream_gene_variant,,ENST00000445941,;MAP2,intron_variant,,ENST00000475600,;MAP2,intron_variant,,ENST00000471619,;MAP2,downstream_gene_variant,,ENST00000482864,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; C ENST00000360351 Transcript missense_variant 4984/9711 4478/5484 1493/1827 Y/S tAt/tCt rs781734507 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 deleterious(0.01) 9/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15,Pfam_domain:PF08377 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 209697007 209697007 A C 1 0 0 0 0 1 0 0 0 9157 449 16 5 5 MAP2 2 209697007 Missense_Mutation SNP A C3N-02089_T 1451670 209697007 32496522 179 27263 UNC80 0 . GRCh38 2 209840650 209840650 + Splice_Site SNP T T A novel C3N-02089_T C3N-02089_N T T c.3363+2T>A p.X1121_splice ENST00000439458 115 81 34 133 133 0 strelka-varscan UNC80,splice_donor_variant,,ENST00000439458,NM_032504.1;UNC80,splice_donor_variant,,ENST00000272845,NM_182587.3;UNC80,upstream_gene_variant,,ENST00000477301,;UNC80,splice_donor_variant,,ENST00000489023,; A ENST00000439458 Transcript splice_donor_variant -/13562 3363/9777 1121/3258 1 1 UNC80 HGNC HGNC:26582 protein_coding YES CCDS46504.1 ENSP00000391088 Q8N2C7 UPI00017E10C9 NM_032504.1 20/63 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 209840650 209840650 T A 1 0 0 0 0 0 0 1 0 17521 1652 57 4 4 UNC80 2 209840650 Splice_Site SNP T C3N-02089_T 143643 209840650 32352879 180 27264 SPAG16 0 . GRCh38 2 213310075 213310075 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.296T>A p.Leu99His p.L99H ENST00000331683 4/16 95 67 28 108 108 0 strelka-varscan SPAG16,missense_variant,p.Leu68His,ENST00000413312,;SPAG16,missense_variant,p.Leu99His,ENST00000331683,NM_024532.4;SPAG16,missense_variant,p.Leu99His,ENST00000447990,;SPAG16,missense_variant,p.Leu99His,ENST00000432529,NM_001025436.2;SPAG16,missense_variant,p.Leu99His,ENST00000272898,;SPAG16,non_coding_transcript_exon_variant,,ENST00000414961,;SPAG16,3_prime_UTR_variant,,ENST00000406979,;SPAG16,intron_variant,,ENST00000452556,;SPAG16,intron_variant,,ENST00000440779,; A ENST00000331683 Transcript missense_variant 391/2177 296/1896 99/631 L/H cTt/cAt 1 1 SPAG16 HGNC HGNC:23225 protein_coding YES CCDS2396.1 ENSP00000332592 Q8N0X2 UPI00001AFF12 NM_024532.4 tolerated(0.09) 4/16 hmmpanther:PTHR14604:SF3,hmmpanther:PTHR14604 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 213310075 213310075 T A 1 0 0 0 0 1 0 0 0 15309 1609 56 4 4 SPAG16 2 213310075 Missense_Mutation SNP T C3N-02089_T 3469425 213310075 28883454 181 27265 VWC2L 0 . GRCh38 2 214414377 214414377 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.184A>T p.Lys62Ter p.K62* ENST00000312504 2/4 304 283 21 313 313 0 strelka-varscan VWC2L,stop_gained,p.Lys62Ter,ENST00000312504,NM_001080500.2;VWC2L,stop_gained,p.Lys62Ter,ENST00000427124,;SPAG16,downstream_gene_variant,,ENST00000331683,NM_024532.4;SPAG16,downstream_gene_variant,,ENST00000451561,;AC107218.3,intron_variant,,ENST00000437883,;AC107218.3,intron_variant,,ENST00000412896,;SPAG16,downstream_gene_variant,,ENST00000480494,;VWC2L,non_coding_transcript_exon_variant,,ENST00000477752,;SPAG16,downstream_gene_variant,,ENST00000406979,; T ENST00000312504 Transcript stop_gained 986/4610 184/669 62/222 K/* Aag/Tag 1 1 VWC2L HGNC HGNC:37203 protein_coding YES CCDS46509.1 ENSP00000308976 B2RUY7 UPI00004912C1 NM_001080500.2 2/4 SMART_domains:SM00214 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 214414377 214414377 A T 1 0 0 0 0 0 1 0 0 17803 131 5 4 4 VWC2L 2 214414377 Nonsense_Mutation SNP A C3N-02089_T 1104302 214414377 27779152 182 27266 WNT10A 0 . GRCh38 2 218892841 218892841 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.824C>A p.Thr275Lys p.T275K ENST00000258411 4/4 114 82 32 69 69 0 strelka-varscan WNT10A,missense_variant,p.Thr275Lys,ENST00000258411,NM_025216.2;WNT10A,missense_variant,p.Asp111Glu,ENST00000458582,;WNT10A,downstream_gene_variant,,ENST00000483911,;WNT10A,upstream_gene_variant,,ENST00000489887,; A ENST00000258411 Transcript missense_variant 1457/2547 824/1254 275/417 T/K aCg/aAg 1 1 WNT10A HGNC HGNC:13829 protein_coding YES CCDS2426.1 ENSP00000258411 Q9GZT5 UPI0000032F2A NM_025216.2 deleterious(0) 4/4 Pfam_domain:PF00110,Prints_domain:PR01349,hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF89,SMART_domains:SM00097 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 218892841 218892841 C A 1 0 0 0 0 1 0 0 0 17938 536 19 1 1 WNT10A 2 218892841 Missense_Mutation SNP C C3N-02089_T 4478464 218892841 23300688 183 27267 PTPRN 0 . GRCh38 2 219302338 219302338 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.793C>G p.Pro265Ala p.P265A ENST00000295718 6/23 288 255 33 304 304 0 strelka-varscan PTPRN,missense_variant,p.Pro265Ala,ENST00000295718,NM_002846.3;PTPRN,missense_variant,p.Pro265Ala,ENST00000409251,NM_001199763.1;PTPRN,missense_variant,p.Pro175Ala,ENST00000423636,NM_001199764.1;PTPRN,downstream_gene_variant,,ENST00000446182,;PTPRN,downstream_gene_variant,,ENST00000440552,;PTPRN,downstream_gene_variant,,ENST00000412847,;PTPRN,downstream_gene_variant,,ENST00000442029,;PTPRN,downstream_gene_variant,,ENST00000451506,;AC114803.3,intron_variant,,ENST00000417355,;PTPRN,downstream_gene_variant,,ENST00000468454,;PTPRN,non_coding_transcript_exon_variant,,ENST00000462351,;PTPRN,downstream_gene_variant,,ENST00000606213,;PTPRN,downstream_gene_variant,,ENST00000476930,;PTPRN,upstream_gene_variant,,ENST00000489650,;PTPRN,upstream_gene_variant,,ENST00000486480,; C ENST00000295718 Transcript missense_variant 1034/3784 793/2940 265/979 P/A Cca/Gca COSM3577963 1 -1 PTPRN HGNC HGNC:9676 protein_coding YES CCDS2440.1 ENSP00000295718 Q16849 UPI0000132999 NM_002846.3 tolerated(0.1) 6/23 hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF2 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 219302338 219302338 G C 1 0 0 0 0 1 0 0 0 12961 1174 41 4 4 PTPRN 2 219302338 Missense_Mutation SNP G C3N-02089_T 409497 219302338 22891191 184 27268 SPEG 0 . GRCh38 2 219489126 219489126 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.8222G>T p.Gly2741Val p.G2741V ENST00000312358 35/41 286 218 68 330 330 0 strelka-varscan SPEG,missense_variant,p.Gly2741Val,ENST00000312358,NM_005876.4;SPEG,upstream_gene_variant,,ENST00000412982,;AC053503.11,intron_variant,,ENST00000429882,;SPEG,non_coding_transcript_exon_variant,,ENST00000485813,; T ENST00000312358 Transcript missense_variant 8354/10782 8222/9804 2741/3267 G/V gGc/gTc 1 1 SPEG HGNC HGNC:16901 protein_coding YES CCDS42824.1 ENSP00000311684 Q15772 UPI000066D99E NM_005876.4 deleterious(0) 35/41 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF728,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 219489126 219489126 G T 1 0 0 0 0 1 0 0 0 15387 1203 42 2 2 SPEG 2 219489126 Missense_Mutation SNP G C3N-02089_T 186788 219489126 22704403 185 27269 AGFG1 0 . GRCh38 2 227534855 227534855 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1107G>T p.Gln369His p.Q369H ENST00000409979 9/14 92 61 31 111 111 0 strelka-varscan-mutect AGFG1,missense_variant,p.Gln345His,ENST00000310078,NM_004504.4;AGFG1,missense_variant,p.Gln369His,ENST00000409979,NM_001135187.1;AGFG1,missense_variant,p.Gln345His,ENST00000409171,NM_001135188.1;AGFG1,missense_variant,p.Gln305His,ENST00000373671,NM_001135189.1;AGFG1,intron_variant,,ENST00000409315,;AGFG1,downstream_gene_variant,,ENST00000456594,;AGFG1,upstream_gene_variant,,ENST00000458212,; T ENST00000409979 Transcript missense_variant 1377/2089 1107/1755 369/584 Q/H caG/caT 1 1 AGFG1 HGNC HGNC:5175 protein_coding YES CCDS46533.1 ENSP00000387282 P52594 UPI0001814801 NM_001135187.1 deleterious_low_confidence(0.04) 9/14 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF259,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 227534855 227534855 G T 1 0 0 0 0 1 0 0 0 457 991 35 2 2 AGFG1 2 227534855 Missense_Mutation SNP G C3N-02089_T 8045729 227534855 14658674 186 27270 COL6A3 0 . GRCh38 2 237381429 237381429 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.1383C>A p.Phe461Leu p.F461L ENST00000295550 5/44 119 109 10 163 163 0 strelka-varscan-mutect COL6A3,missense_variant,p.Phe461Leu,ENST00000295550,NM_004369.3;COL6A3,missense_variant,p.Phe255Leu,ENST00000353578,NM_057167.3;COL6A3,missense_variant,p.Phe255Leu,ENST00000409809,;COL6A3,missense_variant,p.Phe54Leu,ENST00000472056,NM_057166.4;COL6A3,missense_variant,p.Phe54Leu,ENST00000347401,;COL6A3,missense_variant,p.Phe255Leu,ENST00000392004,NM_057165.4;COL6A3,missense_variant,p.Phe54Leu,ENST00000392003,NM_057164.4;COL6A3,missense_variant,p.Phe461Leu,ENST00000433762,; T ENST00000295550 Transcript missense_variant 1836/10749 1383/9534 461/3177 F/L ttC/ttA COSM3579677,COSM3579678,COSM5639491,COSM5639492 1 -1 COL6A3 HGNC HGNC:2213 protein_coding YES CCDS33412.1 ENSP00000295550 P12111 D9ZGF2 UPI0000456F39 NM_004369.3 deleterious(0.03) 5/44 PROSITE_profiles:PS50234,Gene3D:3.40.50.410,Pfam_domain:PF00092,SMART_domains:SM00327,Superfamily_domains:SSF53300 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 237381429 237381429 G T 1 0 0 0 0 1 0 0 0 3490 1281 45 2 2 COL6A3 2 237381429 Missense_Mutation SNP G C3N-02089_T 9846574 237381429 4812100 187 27271 FGD5 0 . GRCh38 3 14900431 14900431 + Silent SNP C C T rs546298225 C3N-02089_T C3N-02089_N C C c.3183C>T p.= p.S1061S ENST00000285046 8/20 260 164 96 288 287 1 strelka-varscan-mutect FGD5,synonymous_variant,p.=,ENST00000543601,NM_001320276.1;FGD5,synonymous_variant,p.=,ENST00000285046,NM_152536.3;FGD5,synonymous_variant,p.=,ENST00000457774,;FGD5,non_coding_transcript_exon_variant,,ENST00000476851,;FGD5,non_coding_transcript_exon_variant,,ENST00000468662,; T ENST00000285046 Transcript synonymous_variant 3293/5720 3183/4389 1061/1462 S tcC/tcT rs546298225,COSM728774,COSM728775 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 8/20 PROSITE_profiles:PS50010,hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF13,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs546298225 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 14900431 14900431 C T 1 0 0 0 0 0 0 0 1 5700 639 23 1 1 FGD5 3 14900431 Silent SNP C C3N-02089_T 14900431 183395128 188 27272 EOMES 0 . GRCh38 3 27717651 27717651 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1537A>G p.Arg513Gly p.R513G ENST00000449599 6/6 193 143 50 197 197 0 strelka-varscan-mutect EOMES,missense_variant,p.Arg494Gly,ENST00000295743,NM_005442.3;EOMES,missense_variant,p.Arg513Gly,ENST00000449599,NM_001278182.1;EOMES,missense_variant,p.Arg218Gly,ENST00000461503,NM_001278183.1;RP11-222K16.2,downstream_gene_variant,,ENST00000606069,; C ENST00000449599 Transcript missense_variant 1555/2829 1537/2118 513/705 R/G Aga/Gga 1 -1 EOMES HGNC HGNC:3372 protein_coding YES CCDS63585.1 ENSP00000388620 O95936 UPI00004DEF82 NM_001278182.1 deleterious(0.03) 6/6 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF13,Pfam_domain:PF16176 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 27717651 27717651 T C 1 0 0 0 0 1 0 0 0 4993 1559 54 5 5 EOMES 3 27717651 Missense_Mutation SNP T C3N-02089_T 12817220 27717651 170577908 189 27273 KLHL40 0 . GRCh38 3 42686752 42686752 + Missense_Mutation SNP G G T rs371753773 C3N-02089_T C3N-02089_N G G c.1134G>T p.Met378Ile p.M378I ENST00000287777 1/6 77 50 27 83 83 0 strelka-varscan-mutect KLHL40,missense_variant,p.Met378Ile,ENST00000287777,NM_152393.3; T ENST00000287777 Transcript missense_variant 1234/2517 1134/1866 378/621 M/I atG/atT rs371753773 1 1 KLHL40 HGNC HGNC:30372 protein_coding YES CCDS2703.1 ENSP00000287777 Q2TBA0 UPI000000D866 NM_152393.3 tolerated(0.06) 1/6 Superfamily_domains:0052715,Gene3D:1zgkA00,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF22,SMART_domains:SM00612 MODERATE 1 SNV 1 1 PASS rs371753773 . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 90 42686752 42686752 G T 1 0 0 0 0 1 0 0 0 8258 1290 45 2 2 KLHL40 3 42686752 Missense_Mutation SNP G C3N-02089_T 14969101 42686752 155608807 190 27274 EXOSC7 0 . GRCh38 3 45007530 45007530 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.726G>T p.= p.V242V ENST00000265564 7/8 132 82 50 115 114 1 strelka-varscan-mutect EXOSC7,synonymous_variant,p.=,ENST00000265564,NM_015004.3;EXOSC7,non_coding_transcript_exon_variant,,ENST00000461361,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000491476,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000468667,;EXOSC7,intron_variant,,ENST00000481405,;CLEC3B,intron_variant,,ENST00000490386,;EXOSC7,downstream_gene_variant,,ENST00000482004,;EXOSC7,upstream_gene_variant,,ENST00000459856,;EXOSC7,non_coding_transcript_exon_variant,,ENST00000486727,; T ENST00000265564 Transcript synonymous_variant 774/1055 726/876 242/291 V gtG/gtT 1 1 EXOSC7 HGNC HGNC:28112 protein_coding YES CCDS2725.1 ENSP00000265564 Q15024 A0A024R2P7 UPI000020A5E9 NM_015004.3 7/8 Pfam_domain:PF03725,hmmpanther:PTHR11097,hmmpanther:PTHR11097:SF8,Superfamily_domains:SSF55666 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 45007530 45007530 G T 1 0 0 0 0 0 0 0 1 5187 1335 47 2 2 EXOSC7 3 45007530 Silent SNP G C3N-02089_T 2320778 45007530 153288029 191 27275 MYL3 0 . GRCh38 3 46858462 46858462 + Splice_Site SNP C C A rs727503300 C3N-02089_T C3N-02089_N C C c.482-1G>T p.X161_splice ENST00000395869 252 194 58 307 306 1 strelka-varscan-mutect MYL3,splice_acceptor_variant,,ENST00000395869,;MYL3,splice_acceptor_variant,,ENST00000292327,NM_000258.2;MYL3,downstream_gene_variant,,ENST00000431168,; A ENST00000395869 Transcript splice_acceptor_variant -/1012 482/588 161/195 rs727503300 1 -1 MYL3 HGNC HGNC:7584 protein_coding YES CCDS2746.1 ENSP00000379210 P08590 A0A024R2Q5 UPI0000000CA2 4/5 uncertain_significance HIGH 1 SNV 1 1 1 PASS rs727503300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 46858462 46858462 C A 1 0 0 0 0 0 0 1 0 10048 695 24 2 2 MYL3 3 46858462 Splice_Site SNP C C3N-02089_T 1850932 46858462 151437097 192 27276 PLXNB1 0 . GRCh38 3 48423692 48423692 + Missense_Mutation SNP C C A rs201285818 C3N-02089_T C3N-02089_N C C c.920G>T p.Arg307Leu p.R307L ENST00000358536 3/38 217 156 61 204 204 0 strelka-varscan-mutect PLXNB1,missense_variant,p.Arg307Leu,ENST00000358536,NM_002673.5;PLXNB1,missense_variant,p.Arg307Leu,ENST00000296440,NM_001130082.2;PLXNB1,missense_variant,p.Arg307Leu,ENST00000456774,;PLXNB1,intron_variant,,ENST00000466353,;PLXNB1,upstream_gene_variant,,ENST00000484485,;PLXNB1,upstream_gene_variant,,ENST00000473683,;PLXNB1,missense_variant,p.Arg307Leu,ENST00000449094,;PLXNB1,upstream_gene_variant,,ENST00000462738,; A ENST00000358536 Transcript missense_variant 1190/7308 920/6408 307/2135 R/L cGg/cTg rs201285818,COSM5191086 1 -1 PLXNB1 HGNC HGNC:9103 protein_coding YES CCDS2765.1 ENSP00000351338 O43157 UPI0000038131 NM_002673.5 tolerated(0.29) 3/38 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF36,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201285818 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 48423692 48423692 C A 1 0 0 0 0 1 0 0 0 12229 652 23 1 1 PLXNB1 3 48423692 Missense_Mutation SNP C C3N-02089_T 1565230 48423692 149871867 193 27277 CELSR3 0 . GRCh38 3 48656341 48656341 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.4424A>T p.Glu1475Val p.E1475V ENST00000164024 3/35 83 74 9 115 115 0 strelka-varscan-mutect CELSR3,missense_variant,p.Glu1475Val,ENST00000164024,NM_001407.2; A ENST00000164024 Transcript missense_variant 4705/11956 4424/9939 1475/3312 E/V gAg/gTg 1 -1 CELSR3 HGNC HGNC:3230 protein_coding YES CCDS2775.1 ENSP00000164024 Q9NYQ7 UPI00001AE5A6 NM_001407.2 deleterious(0.01) 3/35 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF38,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1459005234 . 0 206 4 0 0 0 0 0 -19.22791 1 1 1 1 0 A 3 1 90 48656341 48656341 T A 1 0 0 0 0 1 0 0 0 2930 1551 54 4 4 CELSR3 3 48656341 Missense_Mutation SNP T C3N-02089_T 232649 48656341 149639218 194 27278 DOCK3 0 . GRCh38 3 50778683 50778683 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.46A>T p.Ser16Cys p.S16C ENST00000266037 2/53 110 79 31 128 128 0 strelka-varscan-mutect DOCK3,missense_variant,p.Ser16Cys,ENST00000266037,NM_004947.4; T ENST00000266037 Transcript missense_variant 69/8755 46/6093 16/2030 S/C Agc/Tgc 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 deleterious(0) 2/53 PROSITE_profiles:PS50002,hmmpanther:PTHR23317:SF66,hmmpanther:PTHR23317,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 50778683 50778683 A T 1 0 0 0 0 1 0 0 0 4503 188 7 4 4 DOCK3 3 50778683 Missense_Mutation SNP A C3N-02089_T 2122342 50778683 147516876 195 27279 DOCK3 0 . GRCh38 3 51375822 51375822 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.5487T>A p.= p.S1829S ENST00000266037 51/53 182 133 49 186 186 0 strelka-varscan-mutect DOCK3,synonymous_variant,p.=,ENST00000266037,NM_004947.4; A ENST00000266037 Transcript synonymous_variant 5510/8755 5487/6093 1829/2030 S tcT/tcA 1 1 DOCK3 HGNC HGNC:2989 protein_coding YES CCDS46835.1 ENSP00000266037 Q8IZD9 UPI000007412C NM_004947.4 51/53 LOW 1 SNV 1 1 PASS rs1336549935 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 51375822 51375822 T A 1 0 0 0 0 0 0 0 1 4503 1567 55 4 4 DOCK3 3 51375822 Silent SNP T C3N-02089_T 597139 51375822 146919737 196 27280 CACNA1D 0 . GRCh38 3 53800341 53800343 + In_Frame_Del DEL AGA AGA - rs778776240 C3N-02089_T C3N-02089_N AGA AGA c.5085_5087delAGA p.Glu1695del p.E1695del ENST00000288139 42/49 356 243 113 331 331 0 sindel-varindel CACNA1D,inframe_deletion,p.Glu1695del,ENST00000288139,NM_000720.3;CACNA1D,inframe_deletion,p.Glu1675del,ENST00000350061,NM_001128840.2;CACNA1D,inframe_deletion,p.Glu1684del,ENST00000637424,;CACNA1D,inframe_deletion,p.Glu1660del,ENST00000636570,;CACNA1D,inframe_deletion,p.Glu1660del,ENST00000422281,NM_001128839.2;CACNA1D,inframe_deletion,p.Glu1368del,ENST00000481478,;RP11-884K10.6,upstream_gene_variant,,ENST00000607740,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636629,;CACNA1D,inframe_deletion,p.Glu434del,ENST00000636448,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636633,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000636999,;CACNA1D,non_coding_transcript_exon_variant,,ENST00000637589,;CACNA1D,upstream_gene_variant,,ENST00000637844,; - ENST00000288139 Transcript inframe_deletion 5544-5546/9341 5076-5078/6546 1692-1693/2181 RE/R cgAGAa/cga rs778776240,COSM4584563,COSM4584564 1 1 CACNA1D HGNC HGNC:1391 protein_coding YES CCDS2872.1 ENSP00000288139 Q01668 UPI000005031A NM_000720.3 42/49 Pfam_domain:PF16885,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF139,Low_complexity_(Seg):seg 0,1,1 MODERATE 1 deletion 1 9 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 53800341 53800341 AGA - 1 0 1 0 1 0 0 0 0 2229 291 11 0 0 CACNA1D 3 53800341 In_Frame_Del DEL AGA C3N-02089_T 2424519 53800341 144495218 197 27281 DNAH12 0 . GRCh38 3 57404990 57404990 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.6734G>T p.Arg2245Ile p.R2245I ENST00000495027 42/74 79 65 14 96 96 0 strelka-varscan-mutect DNAH12,missense_variant,p.Arg2245Ile,ENST00000495027,NM_001291661.1;DNAH12,missense_variant,p.Arg2226Ile,ENST00000351747,; A ENST00000495027 Transcript missense_variant 6915/12146 6734/11883 2245/3960 R/I aGa/aTa COSM3427798 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 deleterious(0) 42/74 Gene3D:3.40.50.300,Pfam_domain:PF12780,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 57404990 57404990 C A 1 0 0 0 0 1 0 0 0 4414 913 32 2 2 DNAH12 3 57404990 Missense_Mutation SNP C C3N-02089_T 3604649 57404990 140890569 198 27282 DNAH12 0 . GRCh38 3 57458196 57458196 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.2956G>C p.Gly986Arg p.G986R ENST00000495027 21/74 96 78 18 120 120 0 strelka-varscan-mutect DNAH12,missense_variant,p.Gly986Arg,ENST00000495027,NM_001291661.1;DNAH12,missense_variant,p.Gly963Arg,ENST00000351747,; G ENST00000495027 Transcript missense_variant 3137/12146 2956/11883 986/3960 G/R Ggt/Cgt 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 tolerated(0.58) 21/74 Pfam_domain:PF08393,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 57458196 57458196 C G 1 0 0 0 0 1 0 0 0 4414 681 24 4 4 DNAH12 3 57458196 Missense_Mutation SNP C C3N-02089_T 53206 57458196 140837363 199 27283 PRICKLE2 0 . GRCh38 3 64099440 64099440 + Missense_Mutation SNP G G T rs748959217 C3N-02089_T C3N-02089_N G G c.2146C>A p.Pro716Thr p.P716T ENST00000295902 8/8 41 29 12 52 52 0 strelka-varscan-mutect PRICKLE2,missense_variant,p.Pro716Thr,ENST00000295902,NM_198859.3;PRICKLE2,missense_variant,p.Pro772Thr,ENST00000564377,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000482609,;PRICKLE2-AS1,non_coding_transcript_exon_variant,,ENST00000476308,;PRICKLE2-AS2,upstream_gene_variant,,ENST00000484703,;PRICKLE2-AS1,upstream_gene_variant,,ENST00000460946,; T ENST00000295902 Transcript missense_variant 2732/8305 2146/2535 716/844 P/T Cct/Act rs748959217 1 -1 PRICKLE2 HGNC HGNC:20340 protein_coding YES CCDS2902.1 ENSP00000295902 Q7Z3G6 A0A024R368 UPI0000160A8B NM_198859.3 tolerated(0.39) 8/8 hmmpanther:PTHR24211:SF18,hmmpanther:PTHR24211 MODERATE 1 SNV 1 1 PASS rs748959217 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 64099440 64099440 G T 1 0 0 0 0 1 0 0 0 12619 1232 43 2 2 PRICKLE2 3 64099440 Missense_Mutation SNP G C3N-02089_T 6641244 64099440 134196119 200 27284 FRMD4B 0 . GRCh38 3 69218327 69218327 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.784G>C p.Val262Leu p.V262L ENST00000398540 10/23 170 126 44 189 189 0 strelka-varscan-mutect FRMD4B,missense_variant,p.Val262Leu,ENST00000398540,NM_015123.2;FRMD4B,missense_variant,p.Val153Leu,ENST00000493880,;FRMD4B,non_coding_transcript_exon_variant,,ENST00000470070,;FRMD4B,non_coding_transcript_exon_variant,,ENST00000483668,;FRMD4B,non_coding_transcript_exon_variant,,ENST00000487751,; G ENST00000398540 Transcript missense_variant 868/5060 784/3105 262/1034 V/L Gta/Cta 1 -1 FRMD4B HGNC HGNC:24886 protein_coding YES CCDS46863.1 ENSP00000381549 Q9Y2L6 UPI00001C1DF1 NM_015123.2 deleterious(0.01) 10/23 PROSITE_profiles:PS50057,hmmpanther:PTHR23281:SF16,hmmpanther:PTHR23281,Gene3D:2.30.29.30,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 69218327 69218327 C G 1 0 0 0 0 1 0 0 0 5922 579 20 4 4 FRMD4B 3 69218327 Missense_Mutation SNP C C3N-02089_T 5118887 69218327 129077232 201 27285 EPHA6 0 . GRCh38 3 96987691 96987691 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.812G>A p.Gly271Glu p.G271E ENST00000389672 3/18 44 36 8 71 71 0 strelka-varscan-mutect EPHA6,missense_variant,p.Gly271Glu,ENST00000389672,NM_001080448.2;EPHA6,missense_variant,p.Gly271Glu,ENST00000470610,;EPHA6,missense_variant,p.Gly216Glu,ENST00000506569,NM_001278301.1; A ENST00000389672 Transcript missense_variant 850/3971 812/3393 271/1130 G/E gGg/gAg COSM5608437,COSM5608438,COSM5608439 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 deleterious(0.01) 3/18 Gene3D:2.60.120.260,Pfam_domain:PF01404,PROSITE_profiles:PS51550,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00615,Superfamily_domains:SSF49785 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -19.51675 1 1 1 1 0 A 3 1 90 96987691 96987691 G A 1 0 0 0 0 1 0 0 0 5018 1232 43 3 3 EPHA6 3 96987691 Missense_Mutation SNP G C3N-02089_T 27769364 96987691 101307868 202 27286 BOC 0 . GRCh38 3 113268446 113268446 + Splice_Site SNP G G T novel C3N-02089_T C3N-02089_N G G c.523+1G>T p.X175_splice ENST00000273395 127 117 10 120 120 0 strelka-varscan-mutect BOC,splice_donor_variant,,ENST00000495514,NM_033254.3;BOC,splice_donor_variant,,ENST00000355385,;BOC,splice_donor_variant,,ENST00000273395,NM_001301861.1;BOC,downstream_gene_variant,,ENST00000498710,;BOC,splice_donor_variant,,ENST00000477178,;BOC,splice_donor_variant,,ENST00000471963,;BOC,upstream_gene_variant,,ENST00000466059,;BOC,upstream_gene_variant,,ENST00000479182,; T ENST00000273395 Transcript splice_donor_variant -/4276 523/3348 175/1115 1 1 BOC HGNC HGNC:17173 protein_coding YES CCDS77788.1 ENSP00000273395 Q9BWV1 UPI0000D61B53 NM_001301861.1 5/19 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 113268446 113268446 G T 1 0 0 0 0 0 0 1 0 1637 1275 44 2 2 BOC 3 113268446 Splice_Site SNP G C3N-02089_T 16280755 113268446 85027113 203 27287 CD80 0 . GRCh38 3 119527829 119527829 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.809G>A p.Arg270Lys p.R270K ENST00000264246 6/7 208 165 43 191 191 0 strelka-varscan-mutect CD80,missense_variant,p.Arg270Lys,ENST00000264246,NM_005191.3;CD80,missense_variant,p.Arg270Lys,ENST00000478182,;CD80,missense_variant,p.Arg238Lys,ENST00000383669,;TIMMDC1,downstream_gene_variant,,ENST00000494664,NM_016589.3;TIMMDC1,downstream_gene_variant,,ENST00000493694,;TIMMDC1,downstream_gene_variant,,ENST00000264244,;TIMMDC1,downstream_gene_variant,,ENST00000492164,;TIMMDC1,downstream_gene_variant,,ENST00000498399,;TIMMDC1,downstream_gene_variant,,ENST00000463927,; T ENST00000264246 Transcript missense_variant 1172/2725 809/867 270/288 R/K aGa/aAa 1 -1 CD80 HGNC HGNC:1700 protein_coding YES CCDS2989.1 ENSP00000264246 P33681 A0N0P2 UPI000000D9F5 NM_005191.3 tolerated(0.57) 6/7 hmmpanther:PTHR25466,hmmpanther:PTHR25466:SF4,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 119527829 119527829 C T 1 0 0 0 0 1 0 0 0 2742 913 32 3 3 CD80 3 119527829 Missense_Mutation SNP C C3N-02089_T 6259383 119527829 78767730 204 27288 ADCY5 0 . GRCh38 3 123448368 123448368 + Frame_Shift_Del DEL C C - rs777800886 C3N-02089_T C3N-02089_N C C c.178delG p.Ala60ArgfsTer2 p.A60Rfs*2 ENST00000462833 1/21 78 73 5 65 65 0 varindel-pindel ADCY5,frameshift_variant,p.Ala60ArgfsTer2,ENST00000462833,NM_183357.2; - ENST00000462833 Transcript frameshift_variant 1391/7311 178/3786 60/1261 A/X Gcg/cg rs777800886,COSM3057110 1 -1 ADCY5 HGNC HGNC:236 protein_coding YES CCDS3022.1 ENSP00000419361 O95622 UPI000015E262 NM_183357.2 1/21 Pfam_domain:PF16214 0,1 HIGH 1 deletion 1 0,1 1 PASS . . 0 168 37 2 2 0 0 0 -3.521756 0.1760423 0 1 0 0 - 7 5 90 123448368 123448368 C - 1 0 1 0 1 0 0 0 0 341 739 26 0 0 ADCY5 3 123448368 Frame_Shift_Del DEL C C3N-02089_T 3920539 123448368 74847191 205 27289 KALRN 0 . GRCh38 3 124234918 124234918 + Missense_Mutation SNP G G T rs777198177 C3N-02089_T C3N-02089_N G G c.232G>T p.Val78Leu p.V78L ENST00000240874 3/34 202 163 39 207 207 0 strelka-varscan-mutect KALRN,missense_variant,p.Val78Leu,ENST00000360013,NM_001024660.3;KALRN,missense_variant,p.Val56Leu,ENST00000354186,;KALRN,missense_variant,p.Val78Leu,ENST00000240874,NM_003947.4;KALRN,missense_variant,p.Val78Leu,ENST00000460856,NM_001322989.1;KALRN,missense_variant,p.Val106Leu,ENST00000448253,; T ENST00000240874 Transcript missense_variant 389/6537 232/4992 78/1663 V/L Gtg/Ttg rs777198177 1 1 KALRN HGNC HGNC:4814 protein_coding YES CCDS3027.1 ENSP00000240874 O60229 UPI000012C095 NM_003947.4 tolerated(0.93) 3/34 Gene3D:3.40.525.10,Pfam_domain:PF00650,PROSITE_profiles:PS50191,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF49,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS rs777198177 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 124234918 124234918 G T 1 0 0 0 0 1 0 0 0 7884 1145 40 1 1 KALRN 3 124234918 Missense_Mutation SNP G C3N-02089_T 786550 124234918 74060641 206 27290 UROC1 0 . GRCh38 3 126504014 126504014 + Missense_Mutation SNP G G C rs372290750 C3N-02089_T C3N-02089_N G G c.883C>G p.Arg295Gly p.R295G ENST00000383579 9/21 483 439 44 409 409 0 strelka-varscan-mutect UROC1,missense_variant,p.Arg295Gly,ENST00000290868,NM_144639.2;UROC1,missense_variant,p.Arg295Gly,ENST00000383579,NM_001165974.1; C ENST00000383579 Transcript missense_variant 917/2735 883/2211 295/736 R/G Cgc/Ggc rs372290750,COSM1037768,COSM1593292 1 -1 UROC1 HGNC HGNC:26444 protein_coding YES CCDS54636.1 ENSP00000373073 Q96N76 UPI0000480109 NM_001165974.1 tolerated(0.23) 9/21 HAMAP:MF_00577,Pfam_domain:PF01175,hmmpanther:PTHR12216,hmmpanther:PTHR12216:SF3,Superfamily_domains:SSF111326 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs372290750 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 126504014 126504014 G C 1 0 0 0 0 1 0 0 0 17560 1116 39 4 4 UROC1 3 126504014 Missense_Mutation SNP G C3N-02089_T 2269096 126504014 71791545 207 27291 TXNRD3 0 . GRCh38 3 126630888 126630888 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1021G>T p.Gly341Cys p.G341C ENST00000524230 9/16 287 216 71 299 299 0 strelka-varscan-mutect TXNRD3,missense_variant,p.Gly341Cys,ENST00000524230,NM_052883.1;TXNRD3,missense_variant,p.Gly341Cys,ENST00000523403,NM_001173513.1;RP11-390G14.1,downstream_gene_variant,,ENST00000505008,; A ENST00000524230 Transcript missense_variant 1186/2950 1021/1932 341/643 G/C Ggt/Tgt 1 -1 TXNRD3 HGNC HGNC:20667 protein_coding YES CCDS77811.1 ENSP00000430031 H0YBQ0 UPI0004F236D1 NM_052883.1 deleterious(0) 9/16 hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF108,TIGRFAM_domain:TIGR01438,Gene3D:3.50.50.60,Pfam_domain:PF07992,Superfamily_domains:SSF51905,Prints_domain:PR00368,Prints_domain:PR00411 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 126630888 126630888 C A 1 0 0 0 0 1 0 0 0 17323 623 22 2 2 TXNRD3 3 126630888 Missense_Mutation SNP C C3N-02089_T 126874 126630888 71664671 208 27292 COL6A6 0 . GRCh38 3 130563119 130563119 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.116G>T p.Gly39Val p.G39V ENST00000358511 2/36 61 41 20 94 94 0 strelka-varscan-mutect COL6A6,missense_variant,p.Gly39Val,ENST00000358511,NM_001102608.1; T ENST00000358511 Transcript missense_variant 147/9581 116/6792 39/2263 G/V gGa/gTa 1 1 COL6A6 HGNC HGNC:27023 protein_coding YES CCDS46911.1 ENSP00000351310 A6NMZ7 UPI00015B6548 NM_001102608.1 deleterious(0) 2/36 Gene3D:3.40.50.410,Pfam_domain:PF00092,PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF61,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS rs1476025643 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 130563119 130563119 G T 1 0 0 0 0 1 0 0 0 3492 1174 41 2 2 COL6A6 3 130563119 Missense_Mutation SNP G C3N-02089_T 3932231 130563119 67732440 209 27293 TF 0 . GRCh38 3 133777100 133777100 + Silent SNP C C A rs778832620 C3N-02089_T C3N-02089_N C C c.1924C>A p.= p.R642R ENST00000402696 16/17 287 270 17 322 321 1 strelka-varscan-mutect TF,synonymous_variant,p.=,ENST00000402696,NM_001063.3;TF,3_prime_UTR_variant,,ENST00000461695,;TF,non_coding_transcript_exon_variant,,ENST00000467842,; A ENST00000402696 Transcript synonymous_variant 2409/2968 1924/2097 642/698 R Cgg/Agg rs778832620,COSM1616949 1 1 TF HGNC HGNC:11740 protein_coding YES CCDS3080.1 ENSP00000385834 P02787 UPI000013D5A6 NM_001063.3 16/17 Gene3D:3.40.190.10,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,PIRSF_domain:PIRSF500682,PROSITE_profiles:PS51408,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF31,SMART_domains:SM00094,Superfamily_domains:SSF53850 0,1 LOW 1 SNV 1 0,1 1 PASS rs778832620 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 133777100 133777100 C A 1 0 0 0 0 0 0 0 1 16218 643 23 1 1 TF 3 133777100 Silent SNP C C3N-02089_T 3213981 133777100 64518459 210 27294 EPHB1 0 . GRCh38 3 135154264 135154264 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1410G>T p.= p.R470R ENST00000398015 6/16 125 89 36 112 112 0 strelka-varscan-mutect EPHB1,synonymous_variant,p.=,ENST00000398015,NM_004441.4;EPHB1,synonymous_variant,p.=,ENST00000493838,;EPHB1,non_coding_transcript_exon_variant,,ENST00000488992,; T ENST00000398015 Transcript synonymous_variant 1780/4672 1410/2955 470/984 R cgG/cgT 1 1 EPHB1 HGNC HGNC:3392 protein_coding YES CCDS46921.1 ENSP00000381097 P54762 UPI000012A07E NM_004441.4 6/16 Gene3D:2.60.40.10,Pfam_domain:PF00041,PIRSF_domain:PIRSF000666,Prints_domain:PR00014,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF173,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS rs1357014273 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 135154264 135154264 G T 1 0 0 0 0 0 0 0 1 5021 1248 44 2 2 EPHB1 3 135154264 Silent SNP G C3N-02089_T 1377164 135154264 63141295 211 27295 PRR23A 0 . GRCh38 3 139006109 139006109 + Missense_Mutation SNP C C G C3N-02089_T C3N-02089_N C C c.160G>C p.Val54Leu p.V54L ENST00000383163 1/1 108 77 31 109 109 0 strelka-varscan-mutect PRR23A,missense_variant,p.Val54Leu,ENST00000383163,NM_001134659.1;MRPS22,intron_variant,,ENST00000495075,; G ENST00000383163 Transcript missense_variant 160/801 160/801 54/266 V/L Gtg/Ctg COSM5498865 1 -1 PRR23A HGNC HGNC:37172 protein_coding YES CCDS46923.1 ENSP00000372649 A6NEV1 UPI00003671C1 NM_001134659.1 deleterious(0.01) 1/1 hmmpanther:PTHR31813:SF7,hmmpanther:PTHR31813,Pfam_domain:PF10630 1 MODERATE SNV 1 1 PASS rs1207883412 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 139006109 139006109 C G 1 0 0 0 0 1 0 0 0 12729 536 19 4 4 PRR23A 3 139006109 Missense_Mutation SNP C C3N-02089_T 3851845 139006109 59289450 212 27296 CLSTN2 0 . GRCh38 3 140566217 140566217 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2832C>A p.= p.A944A ENST00000458420 17/17 267 231 36 221 221 0 strelka-varscan-mutect CLSTN2,synonymous_variant,p.=,ENST00000458420,NM_022131.2; A ENST00000458420 Transcript synonymous_variant 3022/14202 2832/2868 944/955 A gcC/gcA 1 1 CLSTN2 HGNC HGNC:17448 protein_coding YES CCDS3112.1 ENSP00000402460 Q9H4D0 UPI00001B0051 NM_022131.2 17/17 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF3 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 140566217 140566217 C A 1 0 0 0 0 0 0 0 1 3334 610 22 2 2 CLSTN2 3 140566217 Silent SNP C C3N-02089_T 1560108 140566217 57729342 213 27297 RASA2 0 . GRCh38 3 141529713 141529713 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.361G>T p.Val121Leu p.V121L ENST00000286364 4/24 120 103 17 129 129 0 strelka-varscan-mutect RASA2,missense_variant,p.Val121Leu,ENST00000286364,NM_001303246.1,NM_001303245.1,NM_006506.3;RASA2,missense_variant,p.Val121Leu,ENST00000452898,;RASA2-IT1,downstream_gene_variant,,ENST00000507770,;RASA2,3_prime_UTR_variant,,ENST00000515549,; T ENST00000286364 Transcript missense_variant 396/5614 361/2550 121/849 V/L Gta/Tta 1 1 RASA2 HGNC HGNC:9872 protein_coding YES CCDS3117.1 ENSP00000286364 Q15283 UPI00001351F5 NM_001303246.1,NM_001303245.1,NM_006506.3 deleterious(0) 4/24 PROSITE_profiles:PS50004,hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF21,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 90 141529713 141529713 G T 1 0 0 0 0 1 0 0 0 13220 1043 36 2 2 RASA2 3 141529713 Missense_Mutation SNP G C3N-02089_T 963496 141529713 56765846 214 27298 XRN1 0 . GRCh38 3 142403937 142403937 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1936A>G p.Ile646Val p.I646V ENST00000264951 17/42 229 203 26 274 274 0 strelka-varscan-mutect XRN1,missense_variant,p.Ile646Val,ENST00000264951,NM_019001.4;XRN1,missense_variant,p.Ile112Val,ENST00000498077,;XRN1,missense_variant,p.Ile646Val,ENST00000392981,NM_001282857.1;RNU6-1294P,downstream_gene_variant,,ENST00000515995,;XRN1,non_coding_transcript_exon_variant,,ENST00000472697,; C ENST00000264951 Transcript missense_variant 2054/10143 1936/5121 646/1706 I/V Ata/Gta 1 -1 XRN1 HGNC HGNC:30654 protein_coding YES CCDS3123.1 ENSP00000264951 Q8IZH2 UPI0000074113 NM_019001.4 tolerated(0.4) 17/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 142403937 142403937 T C 1 0 0 0 0 1 0 0 0 18017 1493 52 5 5 XRN1 3 142403937 Missense_Mutation SNP T C3N-02089_T 874224 142403937 55891622 215 27299 C3orf58 0 . GRCh38 3 143972692 143972692 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.360G>T p.Gln120His p.Q120H ENST00000315691 1/3 196 174 22 138 138 0 strelka-varscan-mutect C3orf58,missense_variant,p.Gln120His,ENST00000315691,NM_173552.3;C3orf58,upstream_gene_variant,,ENST00000441925,;C3orf58,upstream_gene_variant,,ENST00000495414,NM_001134470.1;C3orf58,upstream_gene_variant,,ENST00000492452,;C3orf58,non_coding_transcript_exon_variant,,ENST00000493396,;C3orf58,non_coding_transcript_exon_variant,,ENST00000491798,;C3orf58,upstream_gene_variant,,ENST00000483808,; T ENST00000315691 Transcript missense_variant 895/4346 360/1293 120/430 Q/H caG/caT 1 1 C3orf58 HGNC HGNC:28490 protein_coding YES CCDS3130.1 ENSP00000320081 Q8NDZ4 UPI000006EE5C NM_173552.3 deleterious(0.04) 1/3 PD307452,hmmpanther:PTHR32073,hmmpanther:PTHR32073:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 143972692 143972692 G T 1 0 0 0 0 1 0 0 0 2069 962 34 2 2 C3orf58 3 143972692 Missense_Mutation SNP G C3N-02089_T 1568755 143972692 54322867 216 27300 HLTF 0 . GRCh38 3 149063430 149063430 + Splice_Site SNP C C A novel C3N-02089_T C3N-02089_N C C c.1160+1G>T p.X387_splice ENST00000310053 145 124 21 145 145 0 strelka-varscan-mutect HLTF,splice_donor_variant,,ENST00000310053,NM_001318934.1,NM_003071.3,NM_139048.2;HLTF,splice_donor_variant,,ENST00000465259,;HLTF,splice_donor_variant,,ENST00000392912,;HLTF,splice_donor_variant,,ENST00000494055,;HLTF,upstream_gene_variant,,ENST00000493881,; A ENST00000310053 Transcript splice_donor_variant -/5317 1160/3030 387/1009 1 -1 HLTF HGNC HGNC:11099 protein_coding YES CCDS33875.1 ENSP00000308944 Q14527 UPI0000161FA7 NM_001318934.1,NM_003071.3,NM_139048.2 10/24 HIGH 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999125 1 1 1 0 A 5 1 90 149063430 149063430 C A 1 0 0 0 0 0 0 1 0 7105 521 18 2 2 HLTF 3 149063430 Splice_Site SNP C C3N-02089_T 5090738 149063430 49232129 217 27301 IGSF10 0 . GRCh38 3 151445035 151445035 + Missense_Mutation SNP C C A rs774688426 C3N-02089_T C3N-02089_N C C c.4946G>T p.Arg1649Met p.R1649M ENST00000282466 4/6 213 188 25 245 244 1 strelka-varscan-mutect IGSF10,missense_variant,p.Arg1649Met,ENST00000282466,NM_178822.4;IGSF10,upstream_gene_variant,,ENST00000489791,;IGSF10,upstream_gene_variant,,ENST00000495443,;IGSF10,upstream_gene_variant,,ENST00000493841,; A ENST00000282466 Transcript missense_variant 4946/11067 4946/7872 1649/2623 R/M aGg/aTg rs774688426 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 deleterious(0) 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs774688426 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 151445035 151445035 C A 1 0 0 0 0 1 0 0 0 7504 681 24 2 2 IGSF10 3 151445035 Missense_Mutation SNP C C3N-02089_T 2381605 151445035 46850524 218 27302 VEPH1 0 . GRCh38 3 157364363 157364363 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1277T>A p.Ile426Asn p.I426N ENST00000362010 8/14 337 295 42 296 296 0 strelka-mutect VEPH1,missense_variant,p.Ile426Asn,ENST00000362010,NM_001167912.1;VEPH1,missense_variant,p.Ile426Asn,ENST00000392833,NM_001167911.1;VEPH1,missense_variant,p.Ile426Asn,ENST00000392832,NM_024621.2;RP11-550I24.2,intron_variant,,ENST00000487238,;VEPH1,non_coding_transcript_exon_variant,,ENST00000488772,;VEPH1,non_coding_transcript_exon_variant,,ENST00000472419,; T ENST00000362010 Transcript missense_variant 1585/4202 1277/2502 426/833 I/N aTc/aAc 1 -1 VEPH1 HGNC HGNC:25735 protein_coding YES CCDS3179.1 ENSP00000354919 Q14D04 UPI000013F6EE NM_001167912.1 tolerated(0.11) 8/14 hmmpanther:PTHR21630 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 157364363 157364363 A T 1 0 0 0 0 1 0 0 0 17700 333 12 4 4 VEPH1 3 157364363 Missense_Mutation SNP A C3N-02089_T 5919328 157364363 40931196 219 27303 IQCJ 0 . GRCh38 3 159262565 159262565 + Missense_Mutation SNP G G T rs377145005 C3N-02089_T C3N-02089_N G G c.92G>T p.Arg31Leu p.R31L ENST00000476809 3/10 97 84 13 73 73 0 strelka-varscan-mutect IQCJ-SCHIP1,missense_variant,p.Arg58Leu,ENST00000485419,NM_001197113.1;IQCJ-SCHIP1,missense_variant,p.Arg31Leu,ENST00000476809,NM_001197114.1;IQCJ,missense_variant,p.Arg58Leu,ENST00000397832,NM_001042706.2;IQCJ,missense_variant,p.Arg31Leu,ENST00000482126,NM_001197100.1;IQCJ,missense_variant,p.Arg58Leu,ENST00000451172,NM_001042705.2;IQCJ,non_coding_transcript_exon_variant,,ENST00000481796,; T ENST00000476809 Transcript missense_variant 92/1611 92/1611 31/536 R/L cGa/cTa rs377145005,COSM1143196,COSM582480,COSM582481 1 1 IQCJ-SCHIP1 HGNC HGNC:38842 protein_coding YES CCDS56291.1 ENSP00000418692 UPI00016277EB NM_001197114.1 deleterious_low_confidence(0) 3/10 Pfam_domain:PF15157 0,1,1,1 MODERATE SNV 5 0,1,1,1 1 PASS rs377145005 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 159262565 159262565 G T 1 0 0 0 0 1 0 0 0 7718 1058 37 1 1 IQCJ 3 159262565 Missense_Mutation SNP G C3N-02089_T 1898202 159262565 39032994 220 27304 WDR49 0 . GRCh38 3 167505315 167505315 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1820A>G p.Lys607Arg p.K607R ENST00000308378 13/15 32 26 6 52 52 0 strelka-varscan-mutect WDR49,missense_variant,p.Lys607Arg,ENST00000308378,NM_178824.3;WDR49,missense_variant,p.Lys584Arg,ENST00000472600,;WDR49,intron_variant,,ENST00000479765,;WDR49,non_coding_transcript_exon_variant,,ENST00000476376,; C ENST00000308378 Transcript missense_variant 2126/2594 1820/2094 607/697 K/R aAa/aGa 1 -1 WDR49 HGNC HGNC:26587 protein_coding YES CCDS3201.1 ENSP00000311343 Q8IV35 UPI00000746AD NM_178824.3 tolerated(0.13) 13/15 hmmpanther:PTHR22844,hmmpanther:PTHR22844:SF219 MODERATE 1 SNV 1 1 PASS . . 4 203 3 0 0 0 0 0 -16.22427 1 1 1 1 0 C 3 2 90 167505315 167505315 T C 1 0 0 0 0 1 0 0 0 17862 1841 64 5 5 WDR49 3 167505315 Missense_Mutation SNP T C3N-02089_T 8242750 167505315 30790244 221 27305 SPATA16 0 . GRCh38 3 173117125 173117125 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.607C>A p.Leu203Ile p.L203I ENST00000351008 2/11 344 296 48 326 326 0 strelka-varscan-mutect SPATA16,missense_variant,p.Leu203Ile,ENST00000351008,NM_031955.5; T ENST00000351008 Transcript missense_variant 791/2106 607/1710 203/569 L/I Ctt/Att 1 -1 SPATA16 HGNC HGNC:29935 protein_coding YES CCDS3221.1 ENSP00000341765 Q9BXB7 A0A140VJV8 UPI000013D9BF NM_031955.5 deleterious(0.01) 2/11 Gene3D:1.25.40.10,Pfam_domain:PF15015,hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF336,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 173117125 173117125 G T 1 0 0 0 0 1 0 0 0 15331 1043 36 2 2 SPATA16 3 173117125 Missense_Mutation SNP G C3N-02089_T 5611810 173117125 25178434 222 27306 NLGN1 0 . GRCh38 3 174281072 174281072 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.2241T>C p.= p.I747I ENST00000457714 7/7 226 189 37 200 200 0 strelka-varscan-mutect NLGN1,synonymous_variant,p.=,ENST00000457714,NM_014932.3;NLGN1,synonymous_variant,p.=,ENST00000361589,;NLGN1,synonymous_variant,p.=,ENST00000401917,;NLGN1,downstream_gene_variant,,ENST00000415045,;NLGN1,downstream_gene_variant,,ENST00000466350,;NLGN1,downstream_gene_variant,,ENST00000469727,;NLGN1,downstream_gene_variant,,ENST00000469564,; C ENST00000457714 Transcript synonymous_variant 2670/8242 2241/2472 747/823 I atT/atC 1 1 NLGN1 HGNC HGNC:14291 protein_coding YES CCDS3222.1 ENSP00000392500 Q8N2Q7 UPI0000072F54 NM_014932.3 7/7 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 174281072 174281072 T C 1 0 0 0 0 0 0 0 1 10498 1771 62 5 5 NLGN1 3 174281072 Silent SNP T C3N-02089_T 1163947 174281072 24014487 223 27307 ABCC5 0 . GRCh38 3 183989297 183989297 + Silent SNP C C G novel C3N-02089_T C3N-02089_N C C c.216G>C p.= p.L72L ENST00000334444 3/30 210 185 25 174 174 0 strelka-varscan-mutect ABCC5,synonymous_variant,p.=,ENST00000334444,NM_005688.2;ABCC5,synonymous_variant,p.=,ENST00000265586,;ABCC5,synonymous_variant,p.=,ENST00000427120,;ABCC5,synonymous_variant,p.=,ENST00000382494,NM_001023587.1;ABCC5,synonymous_variant,p.=,ENST00000392579,;ABCC5,synonymous_variant,p.=,ENST00000437341,;ABCC5,synonymous_variant,p.=,ENST00000437205,NM_001320032.1;ABCC5,synonymous_variant,p.=,ENST00000443376,;ABCC5,3_prime_UTR_variant,,ENST00000438979,; G ENST00000334444 Transcript synonymous_variant 457/5921 216/4314 72/1437 L ctG/ctC 1 -1 ABCC5 HGNC HGNC:56 protein_coding YES CCDS43176.1 ENSP00000333926 O15440 UPI000004A33C NM_005688.2 3/30 hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF196 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 183989297 183989297 C G 1 0 0 0 0 0 0 0 1 60 581 21 4 4 ABCC5 3 183989297 Silent SNP C C3N-02089_T 9708225 183989297 14306262 224 27308 DVL3 0 . GRCh38 3 184170483 184170483 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1879C>T p.Pro627Ser p.P627S ENST00000313143 15/15 352 286 66 295 295 0 strelka-varscan-mutect DVL3,missense_variant,p.Pro627Ser,ENST00000313143,NM_004423.3;DVL3,missense_variant,p.Pro610Ser,ENST00000431765,;AP2M1,upstream_gene_variant,,ENST00000382456,NM_001025205.1;AP2M1,upstream_gene_variant,,ENST00000292807,NM_004068.3;AP2M1,upstream_gene_variant,,ENST00000411763,;DVL3,downstream_gene_variant,,ENST00000423300,;AP2M1,upstream_gene_variant,,ENST00000448139,;AP2M1,upstream_gene_variant,,ENST00000427072,;AP2M1,upstream_gene_variant,,ENST00000455925,;AP2M1,upstream_gene_variant,,ENST00000460862,;DVL3,non_coding_transcript_exon_variant,,ENST00000478247,;AP2M1,upstream_gene_variant,,ENST00000487958,;AP2M1,upstream_gene_variant,,ENST00000466598,;AP2M1,upstream_gene_variant,,ENST00000484469,;DVL3,downstream_gene_variant,,ENST00000478639,; T ENST00000313143 Transcript missense_variant 2127/5254 1879/2151 627/716 P/S Ccg/Tcg 1 1 DVL3 HGNC HGNC:3087 protein_coding YES CCDS3253.1 ENSP00000316054 Q92997 UPI00001299A9 NM_004423.3 tolerated(0.35) 15/15 Pfam_domain:PF12316,hmmpanther:PTHR10878,hmmpanther:PTHR10878:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 184170483 184170483 C T 1 0 0 0 0 1 0 0 0 4659 739 26 3 3 DVL3 3 184170483 Missense_Mutation SNP C C3N-02089_T 181186 184170483 14125076 225 27309 VWA5B2 0 . GRCh38 3 184236183 184236183 + Missense_Mutation SNP C C A rs771408820 C3N-02089_T C3N-02089_N C C c.1133C>A p.Pro378Gln p.P378Q ENST00000426955 8/19 275 202 73 206 206 0 strelka-varscan-mutect VWA5B2,missense_variant,p.Pro378Gln,ENST00000426955,NM_138345.1;VWA5B2,missense_variant,p.Pro159Gln,ENST00000273794,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000461141,;VWA5B2,non_coding_transcript_exon_variant,,ENST00000474580,;VWA5B2,downstream_gene_variant,,ENST00000497229,;VWA5B2,upstream_gene_variant,,ENST00000493493,; A ENST00000426955 Transcript missense_variant 1233/4120 1133/3729 378/1242 P/Q cCg/cAg rs771408820 1 1 VWA5B2 HGNC HGNC:25144 protein_coding YES CCDS54686.1 ENSP00000398688 Q8N398 UPI0000412DE9 NM_138345.1 deleterious(0) 8/19 Pfam_domain:PF13768,hmmpanther:PTHR10338,hmmpanther:PTHR10338:SF107,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs771408820 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 184236183 184236183 C A 1 0 0 0 0 1 0 0 0 17798 652 23 1 1 VWA5B2 3 184236183 Missense_Mutation SNP C C3N-02089_T 65700 184236183 14059376 226 27310 ADIPOQ 0 . GRCh38 3 186854350 186854350 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.381C>T p.= p.N127N ENST00000444204 4/4 295 274 21 306 306 0 strelka-varscan-mutect ADIPOQ,synonymous_variant,p.=,ENST00000444204,NM_001177800.1;ADIPOQ,synonymous_variant,p.=,ENST00000320741,NM_004797.3;ADIPOQ-AS1,non_coding_transcript_exon_variant,,ENST00000422718,; T ENST00000444204 Transcript synonymous_variant 486/4599 381/735 127/244 N aaC/aaT 1 1 ADIPOQ HGNC HGNC:13633 protein_coding YES CCDS3284.1 ENSP00000389814 Q15848 A8K660 UPI0000034252 NM_001177800.1 4/4 PROSITE_profiles:PS50871,hmmpanther:PTHR24023:SF557,hmmpanther:PTHR24023,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842,Prints_domain:PR00007 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 186854350 186854350 C T 1 0 0 0 0 0 0 0 1 390 477 17 3 3 ADIPOQ 3 186854350 Silent SNP C C3N-02089_T 2618167 186854350 11441209 227 27311 MASP1 0 . GRCh38 3 187241535 187241535 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1249C>A p.Gln417Lys p.Q417K ENST00000296280 10/11 303 251 52 289 288 1 strelka-varscan-mutect MASP1,missense_variant,p.Gln417Lys,ENST00000337774,NM_001879.5;MASP1,missense_variant,p.Gln417Lys,ENST00000296280,NM_139125.3;MASP1,missense_variant,p.Gln304Lys,ENST00000392472,;MASP1,downstream_gene_variant,,ENST00000169293,NM_001031849.2;MASP1,non_coding_transcript_exon_variant,,ENST00000468121,;MASP1,intron_variant,,ENST00000495249,;MASP1,non_coding_transcript_exon_variant,,ENST00000480349,; T ENST00000296280 Transcript missense_variant 1475/4015 1249/2187 417/728 Q/K Caa/Aaa 1 -1 MASP1 HGNC HGNC:6901 protein_coding YES CCDS33908.1 ENSP00000296280 P48740 UPI000007256E NM_139125.3 tolerated(0.62) 10/11 Gene3D:2.10.70.10,Pfam_domain:PF00084,PIRSF_domain:PIRSF001155,PROSITE_profiles:PS50923,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00032,Superfamily_domains:SSF50494,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS rs1335410378 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 187241535 187241535 G T 1 0 0 0 0 1 0 0 0 9248 1357 47 2 2 MASP1 3 187241535 Missense_Mutation SNP G C3N-02089_T 387185 187241535 11054024 228 27312 ATP13A4 0 . GRCh38 3 193514780 193514780 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.152A>T p.Tyr51Phe p.Y51F ENST00000342695 2/30 312 225 87 275 275 0 strelka-varscan-mutect ATP13A4,missense_variant,p.Tyr51Phe,ENST00000342695,NM_032279.3;ATP13A4,missense_variant,p.Tyr51Phe,ENST00000392443,;ATP13A4,missense_variant,p.Tyr51Phe,ENST00000295548,;ATP13A4,non_coding_transcript_exon_variant,,ENST00000489140,;ATP13A4,missense_variant,p.Tyr51Phe,ENST00000450950,;ATP13A4,non_coding_transcript_exon_variant,,ENST00000490925,; A ENST00000342695 Transcript missense_variant 475/4208 152/3591 51/1196 Y/F tAc/tTc 1 -1 ATP13A4 HGNC HGNC:25422 protein_coding YES CCDS3304.2 ENSP00000339182 Q4VNC1 UPI0000520D50 NM_032279.3 deleterious(0) 2/30 Pfam_domain:PF12409,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF279,TIGRFAM_domain:TIGR01657,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 193514780 193514780 T A 1 0 0 0 0 1 0 0 0 1278 1638 57 4 4 ATP13A4 3 193514780 Missense_Mutation SNP T C3N-02089_T 6273245 193514780 4780779 229 27313 LRCH3 0 . GRCh38 3 197817277 197817277 + Missense_Mutation SNP G G C rs757635482 C3N-02089_T C3N-02089_N G G c.509G>C p.Gly170Ala p.G170A ENST00000334859 3/19 90 63 27 119 119 0 strelka-mutect LRCH3,missense_variant,p.Gly170Ala,ENST00000438796,;LRCH3,missense_variant,p.Gly170Ala,ENST00000425562,;LRCH3,missense_variant,p.Gly170Ala,ENST00000414675,;LRCH3,missense_variant,p.Gly170Ala,ENST00000334859,NM_032773.3;LRCH3,intron_variant,,ENST00000441090,;LRCH3,upstream_gene_variant,,ENST00000493726,;LRCH3,intron_variant,,ENST00000443727,; C ENST00000334859 Transcript missense_variant 514/2258 509/2139 170/712 G/A gGa/gCa rs757635482 1 1 LRCH3 HGNC HGNC:28637 protein_coding YES CCDS3330.1 ENSP00000334375 Q96II8 UPI000006E903 NM_032773.3 deleterious(0.04) 3/19 hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF423,Gene3D:3.80.10.10,Pfam_domain:PF13855,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs757635482 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 197817277 197817277 G C 1 0 0 0 0 1 0 0 0 8828 1174 41 4 4 LRCH3 3 197817277 Missense_Mutation SNP G C3N-02089_T 4302497 197817277 478282 230 27314 DGKQ 0 . GRCh38 4 967129 967129 + Missense_Mutation SNP T T A rs772686752 C3N-02089_T C3N-02089_N T T c.1220A>T p.Lys407Met p.K407M ENST00000273814 9/23 67 57 10 67 67 0 strelka-mutect DGKQ,missense_variant,p.Lys407Met,ENST00000273814,NM_001347.3;DGKQ,missense_variant,p.Lys354Met,ENST00000509465,;DGKQ,upstream_gene_variant,,ENST00000515182,;DGKQ,downstream_gene_variant,,ENST00000510286,;DGKQ,splice_region_variant,,ENST00000502309,; A ENST00000273814 Transcript missense_variant,splice_region_variant 1294/4636 1220/2829 407/942 K/M aAg/aTg rs772686752 1 -1 DGKQ HGNC HGNC:2856 protein_coding YES CCDS3342.1 ENSP00000273814 P52824 A0A140VKC1 UPI00001AE9B4 NM_001347.3 deleterious(0) 9/23 PROSITE_profiles:PS50200,Pfam_domain:PF00788,SMART_domains:SM00314,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS rs772686752 . 0 207 3 0 0 0 0 0 -19.9991 1 1 1 1 0 A 3 1 90 967129 967129 T A 1 0 0 0 0 1 0 0 0 4279 1623 56 4 4 DGKQ 4 967129 Missense_Mutation SNP T C3N-02089_T 967129 189247426 231 27315 SLBP 0 . GRCh38 4 1693608 1693608 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.802G>T p.Ala268Ser p.A268S ENST00000489418 8/8 158 132 26 172 172 0 strelka-varscan-mutect SLBP,missense_variant,p.Ala268Ser,ENST00000489418,NM_006527.2;SLBP,missense_variant,p.Ala275Ser,ENST00000318386,;SLBP,missense_variant,p.Ala229Ser,ENST00000429429,;SLBP,missense_variant,p.Ala223Ser,ENST00000483348,;SLBP,missense_variant,p.Ala233Ser,ENST00000488267,NM_001306074.1;SLBP,downstream_gene_variant,,ENST00000480936,; A ENST00000489418 Transcript missense_variant 1169/1977 802/813 268/270 A/S Gcc/Tcc 1 -1 SLBP HGNC HGNC:10904 protein_coding YES CCDS3350.1 ENSP00000417686 Q14493 Q53XR2 UPI0000135A0D NM_006527.2 tolerated_low_confidence(0.27) 8/8 hmmpanther:PTHR17408,hmmpanther:PTHR17408:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 1693608 1693608 C A 1 0 0 0 0 1 0 0 0 14637 797 28 2 2 SLBP 4 1693608 Missense_Mutation SNP C C3N-02089_T 726479 1693608 188520947 232 27316 CFAP99 0 . GRCh38 4 2452150 2452150 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.965A>T p.Lys322Met p.K322M ENST00000616117 10/15 178 143 35 156 156 0 strelka-varscan-mutect CFAP99,missense_variant,p.Lys322Met,ENST00000635017,;CFAP99,missense_variant,p.Lys322Met,ENST00000616117,NM_001193282.2;CFAP99,missense_variant,p.Lys67Met,ENST00000506607,;CFAP99,downstream_gene_variant,,ENST00000511731,;CFAP99,downstream_gene_variant,,ENST00000514556,;CFAP99,downstream_gene_variant,,ENST00000515732,; T ENST00000616117 Transcript missense_variant 965/1941 965/1941 322/646 K/M aAg/aTg 1 1 CFAP99 HGNC HGNC:51180 protein_coding YES CCDS75092.1 ENSP00000480601 A0A087WWY8 UPI00043788D2 NM_001193282.2 tolerated(0.05) 10/15 hmmpanther:PTHR34649,hmmpanther:PTHR34649:SF1 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 2452150 2452150 A T 1 0 0 0 0 1 0 0 0 3036 72 3 4 4 CFAP99 4 2452150 Missense_Mutation SNP A C3N-02089_T 758542 2452150 187762405 233 27317 HGFAC 0 . GRCh38 4 3449238 3449239 + Frame_Shift_Ins INS - - T novel C3N-02089_T C3N-02089_N - - c.1808_1809insT p.Asp604GlyfsTer24 p.D604Gfs*24 ENST00000511533 15/15 89 70 19 93 92 1 sindel-varindel-pindel HGFAC,frameshift_variant,p.Asp597GlyfsTer24,ENST00000382774,NM_001528.3;HGFAC,frameshift_variant,p.Asp604GlyfsTer24,ENST00000511533,NM_001297439.1;HGFAC,splice_region_variant,,ENST00000509689,;HGFAC,downstream_gene_variant,,ENST00000506132,; T ENST00000511533 Transcript frameshift_variant,splice_region_variant 1835-1836/2016 1808-1809/1989 603/662 G/GX ggg/ggTg 1 1 HGFAC HGNC HGNC:4894 protein_coding YES CCDS75098.1 ENSP00000421801 D6RAR4 UPI0001D3B0DD NM_001297439.1 15/15 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF112,hmmpanther:PTHR24256,PROSITE_patterns:PS00135,Pfam_domain:PF00089,PIRSF_domain:PIRSF001146,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494,Prints_domain:PR00722 HIGH 1 insertion 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 90 3449238 3449238 - T 1 0 1 1 0 0 0 0 0 6970 1246 43 0 0 HGFAC 4 3449238 Frame_Shift_Ins INS - C3N-02089_T 997088 3449238 186765317 234 27318 OTOP1 0 . GRCh38 4 4197622 4197622 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.1212C>A p.= p.I404I ENST00000296358 5/6 179 153 26 194 194 0 strelka-varscan-mutect OTOP1,synonymous_variant,p.=,ENST00000296358,NM_177998.1; T ENST00000296358 Transcript synonymous_variant 1237/1864 1212/1839 404/612 I atC/atA COSM3603916 1 -1 OTOP1 HGNC HGNC:19656 protein_coding YES CCDS3372.1 ENSP00000296358 Q7RTM1 UPI0000186945 NM_177998.1 5/6 Pfam_domain:PF03189,hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF19 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 4197622 4197622 G T 1 0 0 0 0 0 0 0 1 11373 932 33 2 2 OTOP1 4 4197622 Silent SNP G C3N-02089_T 748384 4197622 186016933 235 27319 ZBTB49 0 . GRCh38 4 4320730 4320730 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1712G>T p.Cys571Phe p.C571F ENST00000337872 8/8 336 289 47 323 323 0 strelka-varscan-mutect ZBTB49,missense_variant,p.Cys571Phe,ENST00000337872,NM_145291.3;ZBTB49,downstream_gene_variant,,ENST00000504302,;RP11-265O12.1,upstream_gene_variant,,ENST00000509015,;ZBTB49,3_prime_UTR_variant,,ENST00000503703,;ZBTB49,3_prime_UTR_variant,,ENST00000515012,;ZBTB49,downstream_gene_variant,,ENST00000511458,; T ENST00000337872 Transcript missense_variant 1833/2889 1712/2298 571/765 C/F tGc/tTc 1 1 ZBTB49 HGNC HGNC:19883 protein_coding YES CCDS3375.1 ENSP00000338807 Q6ZSB9 UPI000022C559 NM_145291.3 deleterious(0) 8/8 Gene3D:3.30.160.60,Pfam_domain:PF12874,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF237,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 4320730 4320730 G T 1 0 0 0 0 1 0 0 0 18120 1319 46 2 2 ZBTB49 4 4320730 Missense_Mutation SNP G C3N-02089_T 123108 4320730 185893825 236 27320 EVC2 0 . GRCh38 4 5694340 5694340 + Missense_Mutation SNP G G A rs148388393 C3N-02089_T C3N-02089_N G G c.445C>T p.Arg149Cys p.R149C ENST00000344408 3/22 258 237 21 318 317 1 strelka-varscan-mutect EVC2,missense_variant,p.Arg69Cys,ENST00000310917,NM_001166136.1;EVC2,missense_variant,p.Arg149Cys,ENST00000344408,NM_147127.4;EVC2,missense_variant,p.Arg69Cys,ENST00000475313,;EVC2,missense_variant,p.Arg69Cys,ENST00000509670,; A ENST00000344408 Transcript missense_variant 499/4390 445/3927 149/1308 R/C Cgc/Tgc rs148388393,COSM4125251,COSM4125252,COSM5309198,COSM587555 1 -1 EVC2 HGNC HGNC:19747 protein_coding YES CCDS3382.2 ENSP00000342144 Q86UK5 UPI00001910B5 NM_147127.4 deleterious(0.02) 3/22 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF14 0,1,1,1,1 MODERATE 1 SNV 1 0,1,1,1,1 1 PASS rs148388393 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 5694340 5694340 G A 1 0 0 0 0 1 0 0 0 5153 1130 39 1 1 EVC2 4 5694340 Missense_Mutation SNP G C3N-02089_T 1373610 5694340 184520215 237 27321 EVC2 0 . GRCh38 4 5697597 5697597 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.279T>A p.= p.T93T ENST00000344408 2/22 275 254 21 277 276 1 strelka-varscan-mutect EVC2,synonymous_variant,p.=,ENST00000310917,NM_001166136.1;EVC2,synonymous_variant,p.=,ENST00000344408,NM_147127.4;EVC2,synonymous_variant,p.=,ENST00000475313,;EVC2,synonymous_variant,p.=,ENST00000509670,; T ENST00000344408 Transcript synonymous_variant 333/4390 279/3927 93/1308 T acT/acA 1 -1 EVC2 HGNC HGNC:19747 protein_coding YES CCDS3382.2 ENSP00000342144 Q86UK5 UPI00001910B5 NM_147127.4 2/22 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF14 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 5697597 5697597 A T 1 0 0 0 0 0 0 0 1 5153 202 7 4 4 EVC2 4 5697597 Silent SNP A C3N-02089_T 3257 5697597 184516958 238 27322 KIAA0232 0 . GRCh38 4 6862706 6862706 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2324G>T p.Gly775Val p.G775V ENST00000307659 7/10 99 84 15 131 131 0 strelka-varscan-mutect KIAA0232,missense_variant,p.Gly775Val,ENST00000307659,NM_014743.2;KIAA0232,missense_variant,p.Gly775Val,ENST00000425103,NM_001100590.1;KIAA0232,downstream_gene_variant,,ENST00000503069,; T ENST00000307659 Transcript missense_variant 2779/7841 2324/4188 775/1395 G/V gGt/gTt 1 1 KIAA0232 HGNC HGNC:28992 protein_coding YES CCDS43209.1 ENSP00000303928 Q92628 UPI000013EC3F NM_014743.2 deleterious_low_confidence(0.03) 7/10 Pfam_domain:PF15376,hmmpanther:PTHR17611,hmmpanther:PTHR17611:SF3 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 6862706 6862706 G T 1 0 0 0 0 1 0 0 0 8079 1261 44 2 2 KIAA0232 4 6862706 Missense_Mutation SNP G C3N-02089_T 1165109 6862706 183351849 239 27323 FAM200B 0 . GRCh38 4 15688413 15688413 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1436C>T p.Pro479Leu p.P479L ENST00000622362 2/2 100 80 20 158 158 0 strelka-varscan-mutect FAM200B,missense_variant,p.Pro479Leu,ENST00000622362,NM_001145191.1;FAM200B,missense_variant,p.Pro479Leu,ENST00000422728,;FAM200B,downstream_gene_variant,,ENST00000503617,;FAM200B,intron_variant,,ENST00000504137,;FAM200B,intron_variant,,ENST00000505260,;FAM200B,intron_variant,,ENST00000502856,;FAM200B,intron_variant,,ENST00000506610,;FAM200B,intron_variant,,ENST00000504823,;FAM200B,intron_variant,,ENST00000515697,;FAM200B,intron_variant,,ENST00000503600,;FAM200B,intron_variant,,ENST00000504598,;FAM200B,downstream_gene_variant,,ENST00000507305,;FAM200B,downstream_gene_variant,,ENST00000515430,;FAM200B,downstream_gene_variant,,ENST00000513053,;FAM200B,downstream_gene_variant,,ENST00000510920,;FAM200B,downstream_gene_variant,,ENST00000512855,;FAM200B,downstream_gene_variant,,ENST00000510032,;FAM200B,downstream_gene_variant,,ENST00000502502,;FAM200B,downstream_gene_variant,,ENST00000508567,;FAM200B,downstream_gene_variant,,ENST00000514803,;FAM200B,downstream_gene_variant,,ENST00000509022,;FAM200B,downstream_gene_variant,,ENST00000507992,;FAM200B,downstream_gene_variant,,ENST00000510186,; T ENST00000622362 Transcript missense_variant 2351/4377 1436/1974 479/657 P/L cCt/cTt 1 1 FAM200B HGNC HGNC:27740 protein_coding YES CCDS47028.1 ENSP00000483930 P0CF97 UPI0000160C4C NM_001145191.1 deleterious(0.01) 2/2 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF93,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 15688413 15688413 C T 1 0 0 0 0 1 0 0 0 5384 681 24 3 3 FAM200B 4 15688413 Missense_Mutation SNP C C3N-02089_T 8825707 15688413 174526142 240 27324 KCNIP4 0 . GRCh38 4 20732723 20732723 + Silent SNP G G T rs774475425 C3N-02089_T C3N-02089_N G G c.600C>A p.= p.L200L ENST00000382152 7/9 251 216 35 274 272 2 strelka-varscan-mutect KCNIP4,synonymous_variant,p.=,ENST00000382148,NM_001035003.1;KCNIP4,synonymous_variant,p.=,ENST00000359001,NM_147182.3;KCNIP4,synonymous_variant,p.=,ENST00000382152,NM_025221.5;KCNIP4,synonymous_variant,p.=,ENST00000382150,NM_147183.3;KCNIP4,synonymous_variant,p.=,ENST00000447367,NM_147181.3;KCNIP4,synonymous_variant,p.=,ENST00000509207,NM_001035004.1;PACRGL,intron_variant,,ENST00000507634,;PACRGL,downstream_gene_variant,,ENST00000360916,NM_145048.3;PACRGL,downstream_gene_variant,,ENST00000295290,;PACRGL,downstream_gene_variant,,ENST00000513459,NM_001317849.1;PACRGL,downstream_gene_variant,,ENST00000444671,NM_001130727.1;PACRGL,downstream_gene_variant,,ENST00000503585,NM_001258345.1;KCNIP4,non_coding_transcript_exon_variant,,ENST00000382149,;KCNIP4,3_prime_UTR_variant,,ENST00000515786,;PACRGL,intron_variant,,ENST00000471979,;PACRGL,intron_variant,,ENST00000467997,;PACRGL,intron_variant,,ENST00000506702,; T ENST00000382152 Transcript synonymous_variant 768/1767 600/753 200/250 L ctC/ctA rs774475425 1 -1 KCNIP4 HGNC HGNC:30083 protein_coding YES CCDS43216.1 ENSP00000371587 Q6PIL6 UPI000004A274 NM_025221.5 7/9 hmmpanther:PTHR23055:SF30,hmmpanther:PTHR23055,Pfam_domain:PF13499,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 LOW SNV 5 1 PASS rs774475425 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 20732723 20732723 G T 1 0 0 0 0 0 0 0 1 7958 1277 45 2 2 KCNIP4 4 20732723 Silent SNP G C3N-02089_T 5044310 20732723 169481832 241 27325 LGI2 0 . GRCh38 4 25024837 25024837 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.396C>T p.= p.L132L ENST00000382114 4/8 85 78 7 95 95 0 strelka-varscan-mutect LGI2,synonymous_variant,p.=,ENST00000382114,NM_018176.3;LGI2,synonymous_variant,p.=,ENST00000512108,; A ENST00000382114 Transcript synonymous_variant 582/6428 396/1638 132/545 L ctC/ctT 1 -1 LGI2 HGNC HGNC:18710 protein_coding YES CCDS3431.1 ENSP00000371548 Q8N0V4 UPI0000047256 NM_018176.3 4/8 hmmpanther:PTHR24367:SF21,hmmpanther:PTHR24367,Gene3D:3.80.10.10,Pfam_domain:PF13855,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS rs1422183165 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 25024837 25024837 G A 1 0 0 0 0 0 0 0 1 8662 1161 41 3 3 LGI2 4 25024837 Silent SNP G C3N-02089_T 4292114 25024837 165189718 242 27326 STIM2 0 . GRCh38 4 27017718 27017718 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1521G>T p.Met507Ile p.M507I ENST00000465503 12/13 119 103 16 171 171 0 strelka-varscan-mutect STIM2,missense_variant,p.Met499Ile,ENST00000467087,NM_020860.3;STIM2,missense_variant,p.Met499Ile,ENST00000467011,NM_001169117.1;STIM2,missense_variant,p.Met507Ile,ENST00000465503,NM_001169118.1;STIM2,missense_variant,p.Met207Ile,ENST00000473519,;STIM2,missense_variant,p.Met101Ile,ENST00000477474,;STIM2,upstream_gene_variant,,ENST00000504511,; T ENST00000465503 Transcript missense_variant 1899/3613 1521/2265 507/754 M/I atG/atT 1 1 STIM2 HGNC HGNC:19205 protein_coding YES CCDS54751.1 ENSP00000417569 H0Y860 UPI0001B79443 NM_001169118.1 tolerated(0.64) 12/13 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 27017718 27017718 G T 1 0 0 0 0 1 0 0 0 15661 1348 47 2 2 STIM2 4 27017718 Missense_Mutation SNP G C3N-02089_T 1992881 27017718 163196837 243 27327 TLR1 0 . GRCh38 4 38797108 38797108 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1724T>A p.Leu575Ter p.L575* ENST00000308979 4/4 314 286 28 316 316 0 varscan-mutect TLR1,stop_gained,p.Leu575Ter,ENST00000308979,NM_003263.3;TLR1,stop_gained,p.Leu575Ter,ENST00000502213,;TLR1,downstream_gene_variant,,ENST00000505940,;TLR1,downstream_gene_variant,,ENST00000508364,;TLR1,downstream_gene_variant,,ENST00000515861,;TLR1,downstream_gene_variant,,ENST00000506146,;TLR1,intron_variant,,ENST00000505744,;TLR1,upstream_gene_variant,,ENST00000510552,;TLR1,downstream_gene_variant,,ENST00000509754,;TLR1,downstream_gene_variant,,ENST00000508535,; T ENST00000308979 Transcript stop_gained 1998/2849 1724/2361 575/786 L/* tTa/tAa 1 -1 TLR1 HGNC HGNC:11847 protein_coding YES CCDS33973.1 ENSP00000354932 Q15399 UPI000013EDFA NM_003263.3 4/4 Pfam_domain:PF01463,PIRSF_domain:PIRSF037595,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF261,SMART_domains:SM00082 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 38797108 38797108 A T 1 0 0 0 0 0 1 0 0 16395 372 13 4 4 TLR1 4 38797108 Nonsense_Mutation SNP A C3N-02089_T 11779390 38797108 151417447 244 27328 LIMCH1 0 . GRCh38 4 41598924 41598924 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.242A>G p.Asn81Ser p.N81S ENST00000313860 4/27 118 83 35 106 106 0 strelka-varscan-mutect LIMCH1,missense_variant,p.Asn81Ser,ENST00000313860,NM_014988.3;LIMCH1,missense_variant,p.Asn81Ser,ENST00000512820,NM_001289122.1;LIMCH1,missense_variant,p.Asn81Ser,ENST00000512946,NM_001112717.2;LIMCH1,missense_variant,p.Asn81Ser,ENST00000508501,NM_001112718.2;LIMCH1,missense_variant,p.Asn81Ser,ENST00000512632,;LIMCH1,5_prime_UTR_variant,,ENST00000503057,;LIMCH1,5_prime_UTR_variant,,ENST00000513024,NM_001289124.1;LIMCH1,5_prime_UTR_variant,,ENST00000511496,;LIMCH1,5_prime_UTR_variant,,ENST00000509638,;LIMCH1,5_prime_UTR_variant,,ENST00000446625,;LIMCH1,5_prime_UTR_variant,,ENST00000511424,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000514190,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000515847,;LIMCH1,non_coding_transcript_exon_variant,,ENST00000512228,; G ENST00000313860 Transcript missense_variant 296/6165 242/3252 81/1083 N/S aAt/aGt 1 1 LIMCH1 HGNC HGNC:29191 protein_coding YES CCDS33977.1 ENSP00000316891 Q9UPQ0 UPI0000D61554 NM_014988.3 deleterious(0) 4/27 PROSITE_profiles:PS50021,hmmpanther:PTHR15551,hmmpanther:PTHR15551:SF3,Gene3D:1.10.418.10,Pfam_domain:PF00307,SMART_domains:SM00033,Superfamily_domains:SSF47576,Prints_domain:PR00888 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 41598924 41598924 A G 1 0 0 0 0 1 0 0 0 8705 115 4 5 5 LIMCH1 4 41598924 Missense_Mutation SNP A C3N-02089_T 2801816 41598924 148615631 245 27329 TXK 0 . GRCh38 4 48076431 48076431 + Silent SNP T T G novel C3N-02089_T C3N-02089_N T T c.1209A>C p.= p.I403I ENST00000264316 12/15 177 151 26 168 168 0 strelka-varscan-mutect TXK,synonymous_variant,p.=,ENST00000264316,NM_003328.2;TXK,synonymous_variant,p.=,ENST00000507351,;TXK,synonymous_variant,p.=,ENST00000514937,;TXK,intron_variant,,ENST00000509681,; G ENST00000264316 Transcript synonymous_variant 1295/2914 1209/1584 403/527 I atA/atC 1 -1 TXK HGNC HGNC:12434 protein_coding YES CCDS3480.1 ENSP00000264316 P42681 UPI000013D4F9 NM_003328.2 12/15 Gene3D:1.10.510.10,Pfam_domain:PF07714,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF247,SMART_domains:SM00219,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 48076431 48076431 T G 1 0 0 0 0 0 0 0 1 17302 1512 53 5 5 TXK 4 48076431 Silent SNP T C3N-02089_T 6477507 48076431 142138124 246 27330 CWH43 0 . GRCh38 4 49017326 49017326 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.1264G>A p.Val422Met p.V422M ENST00000226432 9/16 131 123 8 88 88 0 strelka-varscan-mutect CWH43,missense_variant,p.Val422Met,ENST00000226432,NM_025087.2;CWH43,missense_variant,p.Val395Met,ENST00000513409,NM_001286791.1;CWH43,splice_region_variant,,ENST00000514053,;CWH43,non_coding_transcript_exon_variant,,ENST00000506221,;TPI1P4,upstream_gene_variant,,ENST00000513630,; A ENST00000226432 Transcript missense_variant,splice_region_variant 1447/2472 1264/2100 422/699 V/M Gtg/Atg 1 1 CWH43 HGNC HGNC:26133 protein_coding YES CCDS3486.1 ENSP00000226432 Q9H720 UPI000020BC89 NM_025087.2 tolerated(0.27) 9/16 hmmpanther:PTHR14859,hmmpanther:PTHR14859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -15.66491 1 1 1 1 0 A 3 1 90 49017326 49017326 G A 1 0 0 0 0 1 0 0 0 3883 1043 36 3 3 CWH43 4 49017326 Missense_Mutation SNP G C3N-02089_T 940895 49017326 141197229 247 27331 PDGFRA 0 . GRCh38 4 54278459 54278459 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2100G>C p.Lys700Asn p.K700N ENST00000257290 15/23 183 134 49 176 176 0 strelka-varscan-mutect PDGFRA,missense_variant,p.Lys700Asn,ENST00000257290,NM_006206.4;RP11-231C18.3,missense_variant,p.Lys460Asn,ENST00000507166,;PDGFRA,missense_variant,p.Lys700Asn,ENST00000509490,;PDGFRA,non_coding_transcript_exon_variant,,ENST00000509092,;PDGFRA,non_coding_transcript_exon_variant,,ENST00000507536,;PDGFRA,downstream_gene_variant,,ENST00000461294,; C ENST00000257290 Transcript missense_variant 2431/6576 2100/3270 700/1089 K/N aaG/aaC 1 1 PDGFRA HGNC HGNC:8803 protein_coding YES CCDS3495.1 ENSP00000257290 P16234 UPI0000131793 NM_006206.4 deleterious(0) 15/23 PROSITE_profiles:PS50011,PIRSF_domain:PIRSF500950,PIRSF_domain:PIRSF000615,Pfam_domain:PF07714,SMART_domains:SM00220,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 54278459 54278459 G C 1 0 0 0 0 1 0 0 0 11749 962 34 4 4 PDGFRA 4 54278459 Missense_Mutation SNP G C3N-02089_T 5261133 54278459 135936096 248 27332 TECRL 0 . GRCh38 4 64322688 64322688 + Splice_Site SNP C C A novel C3N-02089_T C3N-02089_N C C c.435+1G>T p.X145_splice ENST00000381210 77 55 22 125 125 0 strelka-varscan-mutect TECRL,splice_donor_variant,,ENST00000381210,NM_001010874.4;TECRL,splice_donor_variant,,ENST00000507440,;TECRL,incomplete_terminal_codon_variant,p.=,ENST00000509536,;TECRL,splice_donor_variant,,ENST00000513125,;TECRL,splice_donor_variant,,ENST00000511356,; A ENST00000381210 Transcript splice_donor_variant -/3573 435/1092 145/363 1 -1 TECRL HGNC HGNC:27365 protein_coding YES CCDS33990.1 ENSP00000370607 Q5HYJ1 UPI0000141A54 NM_001010874.4 4/11 HIGH 1 SNV 1 1 PASS rs752358370 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 64322688 64322688 C A 1 0 0 0 0 0 0 1 0 16157 579 20 2 2 TECRL 4 64322688 Splice_Site SNP C C3N-02089_T 10044229 64322688 125891867 249 27333 EPHA5 0 . GRCh38 4 65348082 65348082 + Missense_Mutation SNP C C A rs745908821 C3N-02089_T C3N-02089_N C C c.2633G>T p.Arg878Ile p.R878I ENST00000622150 15/18 69 53 16 91 91 0 strelka-varscan-mutect EPHA5,missense_variant,p.Arg878Ile,ENST00000622150,NM_001281765.1;EPHA5,missense_variant,p.Arg856Ile,ENST00000613740,NM_001281766.1;EPHA5,missense_variant,p.Arg877Ile,ENST00000273854,NM_004439.6;EPHA5,missense_variant,p.Arg878Ile,ENST00000511294,NM_001281767.1;EPHA5,missense_variant,p.Arg714Ile,ENST00000432638,;EPHA5,missense_variant,p.Arg855Ile,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript missense_variant 3386/8421 2633/3117 878/1038 R/I aGa/aTa rs745908821 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 deleterious(0) 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs745908821 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 65348082 65348082 C A 1 0 0 0 0 1 0 0 0 5017 913 32 2 2 EPHA5 4 65348082 Missense_Mutation SNP C C3N-02089_T 1025394 65348082 124866473 250 27334 92 2 EPHA5 0 . GRCh38 4 65348083 65348083 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.2632A>T p.Arg878Ter p.R878* ENST00000622150 15/18 69 62 7 93 93 0 strelka-varscan-mutect EPHA5,stop_gained,p.Arg878Ter,ENST00000622150,NM_001281765.1;EPHA5,stop_gained,p.Arg856Ter,ENST00000613740,NM_001281766.1;EPHA5,stop_gained,p.Arg877Ter,ENST00000273854,NM_004439.6;EPHA5,stop_gained,p.Arg878Ter,ENST00000511294,NM_001281767.1;EPHA5,stop_gained,p.Arg714Ter,ENST00000432638,;EPHA5,stop_gained,p.Arg855Ter,ENST00000354839,NM_182472.3; A ENST00000622150 Transcript stop_gained 3385/8421 2632/3117 878/1038 R/* Aga/Tga 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 15/18 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000666,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00219,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 65348083 65348083 T A 1 0 0 0 0 0 1 0 0 5017 1559 54 4 4 EPHA5 4 65348083 Nonsense_Mutation SNP T C3N-02089_T 1 65348083 124866472 251 27335 92 2 UBA6 0 . GRCh38 4 67635480 67635480 + Silent SNP C C G rs139389373 C3N-02089_T C3N-02089_N C C c.1815G>C p.= p.P605P ENST00000322244 20/33 152 109 43 195 195 0 strelka-varscan-mutect UBA6,synonymous_variant,p.=,ENST00000322244,NM_018227.5;UBA6,synonymous_variant,p.=,ENST00000505673,;RP11-17P16.2,upstream_gene_variant,,ENST00000604441,; G ENST00000322244 Transcript synonymous_variant 1875/9564 1815/3159 605/1052 P ccG/ccC rs139389373 1 -1 UBA6 HGNC HGNC:25581 protein_coding YES CCDS3516.1 ENSP00000313454 A0AVT1 A0A024RDB0 UPI000004A4F7 NM_018227.5 20/33 hmmpanther:PTHR10953:SF141,hmmpanther:PTHR10953,Gene3D:3.40.50.720,TIGRFAM_domain:TIGR01408,Pfam_domain:PF00899,Superfamily_domains:SSF69572 LOW 1 SNV 1 1 PASS rs139389373 . 0 206 0 3 0 0 0 0 -20 0.9999981 1 1 1 0 G 2 3 90 67635480 67635480 C G 1 0 0 0 0 0 0 0 1 17351 755 27 4 4 UBA6 4 67635480 Silent SNP C C3N-02089_T 2287397 67635480 122579075 252 27336 GNRHR 0 . GRCh38 4 67740536 67740536 + Missense_Mutation SNP A A G C3N-02089_T C3N-02089_N A A c.931T>C p.Phe311Leu p.F311L ENST00000226413 3/3 153 100 53 215 215 0 strelka-varscan-mutect GNRHR,missense_variant,p.Phe311Leu,ENST00000226413,NM_000406.2;GNRHR,3_prime_UTR_variant,,ENST00000420975,NM_001012763.1;UBA6-AS1,intron_variant,,ENST00000500538,;UBA6-AS1,intron_variant,,ENST00000502758,; G ENST00000226413 Transcript missense_variant 956/2164 931/987 311/328 F/L Ttt/Ctt COSM5433779 1 -1 GNRHR HGNC HGNC:4421 protein_coding YES CCDS3517.1 ENSP00000226413 P30968 UPI000004EEC8 NM_000406.2 deleterious(0) 3/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24241,hmmpanther:PTHR24241:SF22,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 67740536 67740536 A G 1 0 0 0 0 1 0 0 0 6428 72 3 5 5 GNRHR 4 67740536 Missense_Mutation SNP A C3N-02089_T 105056 67740536 122474019 253 27337 TMPRSS11A 0 . GRCh38 4 67924148 67924148 + Missense_Mutation SNP C C T rs144009146 C3N-02089_T C3N-02089_N C C c.509G>A p.Gly170Glu p.G170E ENST00000334830 6/10 178 141 37 285 285 0 strelka-varscan-mutect TMPRSS11A,missense_variant,p.Gly167Glu,ENST00000508048,NM_001114387.1;TMPRSS11A,missense_variant,p.Gly170Glu,ENST00000334830,NM_182606.3;TMPRSS11A,intron_variant,,ENST00000513536,;UBA6-AS1,intron_variant,,ENST00000500538,; T ENST00000334830 Transcript missense_variant 1256/3054 509/1266 170/421 G/E gGg/gAg rs144009146 1 -1 TMPRSS11A HGNC HGNC:27954 protein_coding YES CCDS3519.1 ENSP00000334611 A0A0A0MR82 UPI0000457217 NM_182606.3 deleterious(0) 6/10 PIRSF_domain:PIRSF037941,Superfamily_domains:SSF50494 MODERATE SNV 2 1 PASS rs144009146 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 67924148 67924148 C T 1 0 0 0 0 1 0 0 0 16715 623 22 3 3 TMPRSS11A 4 67924148 Missense_Mutation SNP C C3N-02089_T 183612 67924148 122290407 254 27338 YTHDC1 0 . GRCh38 4 68337067 68337067 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.843A>G p.= p.T281T ENST00000344157 4/17 93 63 30 105 105 0 strelka-varscan-mutect YTHDC1,synonymous_variant,p.=,ENST00000344157,NM_001031732.2;YTHDC1,synonymous_variant,p.=,ENST00000355665,NM_133370.2;YTHDC1,synonymous_variant,p.=,ENST00000579690,;YTHDC1,downstream_gene_variant,,ENST00000510746,;YTHDC1,downstream_gene_variant,,ENST00000505251,; C ENST00000344157 Transcript synonymous_variant 1179/6232 843/2184 281/727 T acA/acG 1 -1 YTHDC1 HGNC HGNC:30626 protein_coding YES CCDS33992.1 ENSP00000339245 Q96MU7 UPI000020B86D NM_001031732.2 4/17 hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF33 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 68337067 68337067 T C 1 0 0 0 0 0 0 0 1 18057 1567 55 5 5 YTHDC1 4 68337067 Silent SNP T C3N-02089_T 412919 68337067 121877488 255 27339 ANKRD17 0 . GRCh38 4 73085441 73085441 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.6967G>T p.Val2323Phe p.V2323F ENST00000358602 30/34 129 109 20 149 149 0 strelka-varscan-mutect ANKRD17,missense_variant,p.Val2323Phe,ENST00000358602,NM_015574.1,NM_032217.3;ANKRD17,missense_variant,p.Val2207Phe,ENST00000558247,;ANKRD17,missense_variant,p.Val2210Phe,ENST00000509867,NM_001286771.1;ANKRD17,missense_variant,p.Val2072Phe,ENST00000330838,NM_198889.1;ANKRD17,upstream_gene_variant,,ENST00000510127,; A ENST00000358602 Transcript missense_variant 7084/10784 6967/7812 2323/2603 V/F Gtc/Ttc 1 -1 ANKRD17 HGNC HGNC:23575 protein_coding YES CCDS34004.1 ENSP00000351416 O75179 UPI00002263B0 NM_015574.1,NM_032217.3 deleterious_low_confidence(0.04) 30/34 hmmpanther:PTHR23206,hmmpanther:PTHR23206:SF1 MODERATE 1 SNV 5 1 PASS rs1243065828 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 73085441 73085441 C A 1 0 0 0 0 1 0 0 0 747 492 17 2 2 ANKRD17 4 73085441 Missense_Mutation SNP C C3N-02089_T 4748374 73085441 117129114 256 27340 MMRN1 0 . GRCh38 4 89909301 89909302 + Frame_Shift_Ins INS - - G novel C3N-02089_T C3N-02089_N - - c.651dupG p.Leu218ValfsTer41 p.L218Vfs*41 ENST00000394980 3/9 109 80 29 115 115 0 sindel-varindel-pindel MMRN1,frameshift_variant,p.Leu218ValfsTer41,ENST00000394980,;MMRN1,frameshift_variant,p.Leu218ValfsTer41,ENST00000264790,NM_007351.2;MMRN1,5_prime_UTR_variant,,ENST00000508372,; G ENST00000394980 Transcript frameshift_variant 968-969/5217 649-650/3687 217/1228 R/RX agg/aGgg 1 1 MMRN1 HGNC HGNC:7178 protein_coding YES CCDS3635.1 ENSP00000378431 Q13201 UPI000013D570 3/9 Pfam_domain:PF07546,PROSITE_profiles:PS51041,hmmpanther:PTHR15427,hmmpanther:PTHR15427:SF3 HIGH 1 insertion 5 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 90 89909301 89909301 - G 1 0 1 1 0 0 0 0 0 9633 179 7 0 0 MMRN1 4 89909301 Frame_Shift_Ins INS - C3N-02089_T 16823860 89909301 100305254 257 27341 EIF4E 0 . GRCh38 4 98885014 98885014 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.540A>G p.= p.V180V ENST00000505992 7/8 216 161 55 243 242 1 strelka-varscan-mutect EIF4E,synonymous_variant,p.=,ENST00000450253,NM_001968.3;EIF4E,synonymous_variant,p.=,ENST00000504432,;EIF4E,synonymous_variant,p.=,ENST00000280892,NM_001130678.1;EIF4E,synonymous_variant,p.=,ENST00000505992,NM_001130679.1;EIF4E,intron_variant,,ENST00000511644,;EIF4E,non_coding_transcript_exon_variant,,ENST00000505194,;EIF4E,3_prime_UTR_variant,,ENST00000515638,;EIF4E,downstream_gene_variant,,ENST00000507665,;EIF4E,downstream_gene_variant,,ENST00000505829,; C ENST00000505992 Transcript synonymous_variant 561/898 540/747 180/248 V gtA/gtG 1 -1 EIF4E HGNC HGNC:3287 protein_coding YES CCDS54779.1 ENSP00000425561 P06730 UPI00017BAF0A NM_001130679.1 7/8 hmmpanther:PTHR11960:SF14,hmmpanther:PTHR11960,Pfam_domain:PF01652,Gene3D:3.30.760.10,Superfamily_domains:SSF55418 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 98885014 98885014 T C 1 0 0 0 0 0 0 0 1 4862 1393 49 5 5 EIF4E 4 98885014 Silent SNP T C3N-02089_T 8975713 98885014 91329541 258 27342 MTTP 0 . GRCh38 4 99612978 99612978 + Missense_Mutation SNP C C G rs374643434 C3N-02089_T C3N-02089_N C C c.2136C>G p.Asn712Lys p.N712K ENST00000511045 15/18 346 254 92 404 404 0 strelka-varscan-mutect MTTP,missense_variant,p.Asn685Lys,ENST00000457717,NM_000253.3;MTTP,missense_variant,p.Asn685Lys,ENST00000265517,;MTTP,missense_variant,p.Asn712Lys,ENST00000511045,NM_001300785.1;RP11-766F14.1,intron_variant,,ENST00000508578,; G ENST00000511045 Transcript missense_variant 2149/3154 2136/2766 712/921 N/K aaC/aaG rs374643434 1 1 MTTP HGNC HGNC:7467 protein_coding YES CCDS75169.1 ENSP00000427679 E9PBP6 UPI0001D3B6EF NM_001300785.1 tolerated(0.08) 15/18 hmmpanther:PTHR13024,hmmpanther:PTHR13024:SF1 MODERATE 1 SNV 2 1 PASS rs374643434 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 99612978 99612978 C G 1 0 0 0 0 1 0 0 0 9961 506 18 4 4 MTTP 4 99612978 Missense_Mutation SNP C C3N-02089_T 727964 99612978 90601577 259 27343 EMCN 0 . GRCh38 4 100421316 100421316 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.630G>T p.= p.V210V ENST00000296420 8/12 299 232 67 314 314 0 strelka-varscan-mutect EMCN,synonymous_variant,p.=,ENST00000296420,NM_016242.3;EMCN,synonymous_variant,p.=,ENST00000511970,NM_001159694.1;EMCN,synonymous_variant,p.=,ENST00000502569,;EMCN,intron_variant,,ENST00000305864,;EMCN,intron_variant,,ENST00000506300,; A ENST00000296420 Transcript synonymous_variant 809/4037 630/786 210/261 V gtG/gtT 1 -1 EMCN HGNC HGNC:16041 protein_coding YES CCDS3655.1 ENSP00000296420 Q9ULC0 Q4W5J1 UPI000003777D NM_016242.3 8/12 Pfam_domain:PF07010,hmmpanther:PTHR15869,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 100421316 100421316 C A 1 0 0 0 0 0 0 0 1 4930 581 21 2 2 EMCN 4 100421316 Silent SNP C C3N-02089_T 808338 100421316 89793239 260 27344 ETNPPL 0 . GRCh38 4 108748090 108748090 + Nonsense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.997C>T p.Gln333Ter p.Q333* ENST00000296486 9/13 151 114 37 210 210 0 strelka-varscan-mutect ETNPPL,stop_gained,p.Gln333Ter,ENST00000296486,NM_031279.3;ETNPPL,stop_gained,p.Gln327Ter,ENST00000411864,NM_001146590.1;ETNPPL,stop_gained,p.Gln293Ter,ENST00000510706,;ETNPPL,stop_gained,p.Gln275Ter,ENST00000512646,NM_001146627.1;ETNPPL,non_coding_transcript_exon_variant,,ENST00000503912,;ETNPPL,downstream_gene_variant,,ENST00000505233,;ETNPPL,downstream_gene_variant,,ENST00000509402,;ETNPPL,downstream_gene_variant,,ENST00000511923,; A ENST00000296486 Transcript stop_gained 1152/2099 997/1500 333/499 Q/* Caa/Taa 1 -1 ETNPPL HGNC HGNC:14404 protein_coding YES CCDS3682.1 ENSP00000296486 Q8TBG4 UPI000004B638 NM_031279.3 9/13 hmmpanther:PTHR11986:SF63,hmmpanther:PTHR11986,Gene3D:3.90.1150.10,Pfam_domain:PF00202,Superfamily_domains:SSF53383 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 108748090 108748090 G A 1 0 0 0 0 0 1 0 0 5138 1299 45 3 3 ETNPPL 4 108748090 Nonsense_Mutation SNP G C3N-02089_T 8326774 108748090 81466465 261 27345 PCDH18 0 . GRCh38 4 137521223 137521223 + Missense_Mutation SNP G G C rs138873003 C3N-02089_T C3N-02089_N G G c.3214C>G p.Pro1072Ala p.P1072A ENST00000344876 4/4 87 63 24 102 102 0 strelka-varscan-mutect PCDH18,missense_variant,p.Pro1072Ala,ENST00000344876,NM_019035.4;PCDH18,missense_variant,p.Pro1071Ala,ENST00000412923,NM_001300828.1;PCDH18,missense_variant,p.Pro851Ala,ENST00000507846,;PCDH18,missense_variant,p.Pro283Ala,ENST00000510305,;PCDH18,missense_variant,p.Pro252Ala,ENST00000511115,;PCDH18,downstream_gene_variant,,ENST00000611581,;PCDH18,downstream_gene_variant,,ENST00000620262,; C ENST00000344876 Transcript missense_variant 3601/5906 3214/3408 1072/1135 P/A Cca/Gca rs138873003 1 -1 PCDH18 HGNC HGNC:14268 protein_coding YES CCDS34064.1 ENSP00000355082 Q9HCL0 UPI0000047A88 NM_019035.4 tolerated(0.45) 4/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF9 MODERATE 1 SNV 1 1 PASS rs138873003 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 137521223 137521223 G C 1 0 0 0 0 1 0 0 0 11600 1203 42 4 4 PCDH18 4 137521223 Missense_Mutation SNP G C3N-02089_T 28773133 137521223 52693332 262 27346 MAML3 0 . GRCh38 4 139890098 139890098 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.1338A>T p.= p.T446T ENST00000509479 2/5 246 182 64 227 227 0 strelka-varscan-mutect MAML3,synonymous_variant,p.=,ENST00000509479,NM_018717.4;MAML3,intron_variant,,ENST00000502696,;MAML3,upstream_gene_variant,,ENST00000398940,; A ENST00000509479 Transcript synonymous_variant 2195/6844 1338/3417 446/1138 T acA/acT 1 -1 MAML3 HGNC HGNC:16272 protein_coding YES CCDS54805.1 ENSP00000421180 Q96JK9 UPI00001C1E1E NM_018717.4 2/5 hmmpanther:PTHR15692,hmmpanther:PTHR15692:SF8 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 139890098 139890098 T A 1 0 0 0 0 0 0 0 1 9128 1567 55 4 4 MAML3 4 139890098 Silent SNP T C3N-02089_T 2368875 139890098 50324457 263 27347 C4orf51 0 . GRCh38 4 145726957 145726957 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.354C>A p.= p.V118V ENST00000438731 3/6 115 85 30 144 144 0 strelka-varscan C4orf51,synonymous_variant,p.=,ENST00000438731,NM_001080531.1; A ENST00000438731 Transcript synonymous_variant 443/932 354/609 118/202 V gtC/gtA 1 1 C4orf51 HGNC HGNC:37264 protein_coding YES CCDS47140.1 ENSP00000391404 C9J302 UPI0000DD7C19 NM_001080531.1 3/6 Pfam_domain:PF15849 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 145726957 145726957 C A 1 0 0 0 0 0 0 0 1 2090 813 29 2 2 C4orf51 4 145726957 Silent SNP C C3N-02089_T 5836859 145726957 44487598 264 27348 FAM160A1 0 . GRCh38 4 151577474 151577474 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.130G>C p.Asp44His p.D44H ENST00000435205 5/14 70 64 6 79 79 0 strelka-varscan FAM160A1,missense_variant,p.Asp44His,ENST00000435205,NM_001109977.1;FAM160A1,missense_variant,p.Asp44His,ENST00000505231,;FAM160A1,missense_variant,p.Asp44His,ENST00000512597,;FAM160A1,downstream_gene_variant,,ENST00000503146,;FAM160A1,downstream_gene_variant,,ENST00000513962,;RN7SKP35,downstream_gene_variant,,ENST00000517210,; C ENST00000435205 Transcript missense_variant 705/4576 130/3123 44/1040 D/H Gac/Cac COSM1052068,COSM1594374,COSM1594375 1 1 FAM160A1 HGNC HGNC:34237 protein_coding YES CCDS47146.1 ENSP00000413196 Q05DH4 UPI00015DE720 NM_001109977.1 deleterious(0) 5/14 hmmpanther:PTHR21705,hmmpanther:PTHR21705:SF6 1,1,1 MODERATE 1 SNV 5 1,1,1 1 PASS . . 0 205 5 0 0 0 0 0 -13.52375 1 1 1 1 0 C 3 2 90 151577474 151577474 G C 1 0 0 0 0 1 0 0 0 5317 1058 37 4 4 FAM160A1 4 151577474 Missense_Mutation SNP G C3N-02089_T 5850517 151577474 38637081 265 27349 RBM46 0 . GRCh38 4 154799055 154799055 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.893G>T p.Gly298Val p.G298V ENST00000281722 4/5 296 214 82 346 346 0 strelka-varscan RBM46,missense_variant,p.Gly298Val,ENST00000510397,NM_001277173.1;RBM46,missense_variant,p.Gly298Val,ENST00000281722,NM_144979.4;RBM46,missense_variant,p.Gly298Val,ENST00000514866,NM_001277171.1;RBM46,downstream_gene_variant,,ENST00000512640,; T ENST00000281722 Transcript missense_variant 1128/2583 893/1602 298/533 G/V gGa/gTa 1 1 RBM46 HGNC HGNC:28401 protein_coding YES CCDS3790.1 ENSP00000281722 Q8TBY0 UPI000007173F NM_144979.4 deleterious(0) 4/5 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF272,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01648,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 154799055 154799055 G T 1 0 0 0 0 1 0 0 0 13306 1174 41 2 2 RBM46 4 154799055 Missense_Mutation SNP G C3N-02089_T 3221581 154799055 35415500 266 27350 ADAM29 0 . GRCh38 4 174977485 174977485 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1960C>G p.Leu654Val p.L654V ENST00000615367 6/6 171 120 51 204 204 0 strelka-varscan ADAM29,missense_variant,p.Leu654Val,ENST00000615367,NM_001278125.1;ADAM29,missense_variant,p.Leu654Val,ENST00000359240,NM_014269.4,NM_001278126.1;ADAM29,missense_variant,p.Leu654Val,ENST00000445694,NM_001130703.1;ADAM29,missense_variant,p.Leu654Val,ENST00000404450,NM_001130704.1;ADAM29,missense_variant,p.Leu654Val,ENST00000514159,NM_001130705.1;ADAM29,missense_variant,p.Leu654Val,ENST00000618444,NM_001278127.1;ADAM29,downstream_gene_variant,,ENST00000502305,;ADAM29,downstream_gene_variant,,ENST00000505141,;ADAM29,downstream_gene_variant,,ENST00000502940,;RP13-577H12.2,downstream_gene_variant,,ENST00000507525,;ADAM29,downstream_gene_variant,,ENST00000515538,; G ENST00000615367 Transcript missense_variant 2691/3386 1960/2463 654/820 L/V Ctg/Gtg 1 1 ADAM29 HGNC HGNC:207 protein_coding YES CCDS3823.1 ENSP00000484862 Q9UKF5 A0A140VJD8 UPI000013E9DE NM_001278125.1 tolerated(0.27) 6/6 hmmpanther:PTHR11905:SF34,hmmpanther:PTHR11905 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 174977485 174977485 C G 1 0 0 0 0 1 0 0 0 291 680 24 4 4 ADAM29 4 174977485 Missense_Mutation SNP C C3N-02089_T 20178430 174977485 15237070 267 27351 TENM3 0 . GRCh38 4 182754807 182754807 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.4440T>A p.= p.S1480S ENST00000511685 22/28 237 165 72 248 248 0 strelka-varscan TENM3,synonymous_variant,p.=,ENST00000511685,NM_001080477.2;TENM3,non_coding_transcript_exon_variant,,ENST00000502950,; A ENST00000511685 Transcript synonymous_variant 4563/10896 4440/8100 1480/2699 S tcT/tcA 1 1 TENM3 HGNC HGNC:29944 protein_coding YES CCDS47165.1 ENSP00000424226 Q9P273 A0A140VJW8 UPI00006C0820 NM_001080477.2 22/28 Gene3D:2.120.10.30,hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF10,Low_complexity_(Seg):seg,Superfamily_domains:SSF101898,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 182754807 182754807 T A 1 0 0 0 0 0 0 0 1 16173 1538 54 4 4 TENM3 4 182754807 Silent SNP T C3N-02089_T 7777322 182754807 7459748 268 27352 FAT1 0 . GRCh38 4 186708199 186708199 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1629G>T p.Trp543Cys p.W543C ENST00000441802 2/27 164 119 45 206 206 0 strelka-varscan FAT1,missense_variant,p.Trp543Cys,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Trp543Cys,ENST00000614102,;FAT1,downstream_gene_variant,,ENST00000509647,; A ENST00000441802 Transcript missense_variant 1839/14786 1629/13767 543/4588 W/C tgG/tgT 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 deleterious(0) 2/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 186708199 186708199 C A 1 0 0 0 0 1 0 0 0 5549 624 22 2 2 FAT1 4 186708199 Missense_Mutation SNP C C3N-02089_T 3953392 186708199 3506356 269 27353 LRRC14B 0 . GRCh38 5 194933 194933 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1125C>T p.= p.S375S ENST00000328278 2/2 161 140 21 119 119 0 strelka-varscan-mutect LRRC14B,synonymous_variant,p.=,ENST00000328278,NM_001080478.1;PLEKHG4B,downstream_gene_variant,,ENST00000637938,;PLEKHG4B,downstream_gene_variant,,ENST00000283426,NM_052909.3;CCDC127,downstream_gene_variant,,ENST00000296824,NM_145265.2;CTD-2083E4.7,upstream_gene_variant,,ENST00000563761,; T ENST00000328278 Transcript synonymous_variant 1153/1573 1125/1545 375/514 S agC/agT 1 1 LRRC14B HGNC HGNC:37268 protein_coding YES CCDS47184.1 ENSP00000327675 A6NHZ5 UPI0000237324 NM_001080478.1 2/2 hmmpanther:PTHR14224,hmmpanther:PTHR14224:SF27,Gene3D:3.80.10.10,Superfamily_domains:SSF52047 LOW SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 90 194933 194933 C T 1 0 0 0 0 0 0 0 1 8865 738 26 3 3 LRRC14B 5 194933 Silent SNP C C3N-02089_T 194933 181343326 270 27354 AHRR 0 . GRCh38 5 422859 422859 + Splice_Site SNP G G T rs769366442 C3N-02089_T C3N-02089_N G G c.583+1G>T p.X195_splice ENST00000316418 91 76 15 83 83 0 strelka-varscan-mutect AHRR,splice_donor_variant,,ENST00000316418,NM_020731.4;AHRR,splice_donor_variant,,ENST00000506456,;AHRR,splice_donor_variant,,ENST00000505113,NM_001242412.1;AHRR,splice_donor_variant,,ENST00000512529,;AHRR,downstream_gene_variant,,ENST00000510400,;AHRR,downstream_gene_variant,,ENST00000514523,;AHRR,splice_donor_variant,,ENST00000510910,;CTD-2228K2.1,downstream_gene_variant,,ENST00000509301,; T ENST00000316418 Transcript splice_donor_variant -/5661 583/2160 195/719 rs769366442 1 1 AHRR HGNC HGNC:346 protein_coding YES CCDS43297.1 ENSP00000323816 A9YTQ3 UPI00004572BE NM_020731.4 6/11 HIGH 1 SNV 1 1 PASS rs769366442 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 5 4 90 422859 422859 G T 1 0 0 0 0 0 0 1 0 494 1275 44 2 2 AHRR 5 422859 Splice_Site SNP G C3N-02089_T 227926 422859 181115400 271 27355 PAPD7 0 . GRCh38 5 6743753 6743753 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.408G>T p.Gln136His p.Q136H ENST00000631941 6/13 155 141 14 145 145 0 strelka-varscan-mutect PAPD7,missense_variant,p.Gln386His,ENST00000230859,;PAPD7,missense_variant,p.Gln136His,ENST00000631941,NM_006999.4,NM_001171805.1;PAPD7,upstream_gene_variant,,ENST00000514697,;PAPD7,upstream_gene_variant,,ENST00000511764,; T ENST00000631941 Transcript missense_variant 596/1902 408/1629 136/542 Q/H caG/caT 1 1 PAPD7 HGNC HGNC:16705 protein_coding YES CCDS3871.1 ENSP00000488642 Q5XG87 UPI0000071E30 NM_006999.4,NM_001171805.1 deleterious(0.02) 6/13 Gene3D:3.30.460.10,hmmpanther:PTHR23092,hmmpanther:PTHR23092:SF24,Superfamily_domains:SSF81631 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -19.42412 0.9999998 1 1 1 0 T 3 4 90 6743753 6743753 G T 1 0 0 0 0 1 0 0 0 11507 1020 36 2 2 PAPD7 5 6743753 Missense_Mutation SNP G C3N-02089_T 6320894 6743753 174794506 272 27356 SEMA5A 0 . GRCh38 5 9044558 9044558 + Missense_Mutation SNP C C T rs529504980 C3N-02089_T C3N-02089_N C C c.2920G>A p.Val974Met p.V974M ENST00000382496 22/23 252 196 56 204 203 1 strelka-varscan-mutect SEMA5A,missense_variant,p.Val974Met,ENST00000382496,NM_003966.2;CTD-2215L10.1,intron_variant,,ENST00000506519,; T ENST00000382496 Transcript missense_variant 3586/11762 2920/3225 974/1074 V/M Gtg/Atg rs529504980,COSM402570 1 -1 SEMA5A HGNC HGNC:10736 protein_coding YES CCDS3875.1 ENSP00000371936 Q13591 X5DR95 UPI000004F25D NM_003966.2 deleterious(0.01) 22/23 Transmembrane_helices:TMhelix,hmmpanther:PTHR11036:SF78,hmmpanther:PTHR11036 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs529504980 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 9044558 9044558 C T 1 0 0 0 0 1 0 0 0 14313 536 19 1 1 SEMA5A 5 9044558 Missense_Mutation SNP C C3N-02089_T 2300805 9044558 172493701 273 27357 CCT5 0 . GRCh38 5 10250039 10250039 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.36A>T p.= p.L12L ENST00000503026 1/11 151 128 23 137 137 0 strelka-varscan-mutect CCT5,synonymous_variant,p.=,ENST00000503026,;CCT5,5_prime_UTR_variant,,ENST00000280326,NM_012073.3;CCT5,upstream_gene_variant,,ENST00000515676,NM_001306156.1;CCT5,upstream_gene_variant,,ENST00000506600,;FAM173B,upstream_gene_variant,,ENST00000280330,;CCT5,upstream_gene_variant,,ENST00000515390,;FAM173B,upstream_gene_variant,,ENST00000511437,NM_199133.3;FAM173B,upstream_gene_variant,,ENST00000510047,NM_001258388.1;CCT5,upstream_gene_variant,,ENST00000625723,;CTD-2256P15.1,downstream_gene_variant,,ENST00000509915,;FAM173B,upstream_gene_variant,,ENST00000510052,;CCT5,upstream_gene_variant,,ENST00000423695,;FAM173B,upstream_gene_variant,,ENST00000508553,;CCT5,upstream_gene_variant,,ENST00000503454,;FAM173B,upstream_gene_variant,,ENST00000506108,;CCT5,upstream_gene_variant,,ENST00000511700,;CCT5,upstream_gene_variant,,ENST00000512975,;FAM173B,upstream_gene_variant,,ENST00000504390,;CCT5,upstream_gene_variant,,ENST00000510326,;CCT5,upstream_gene_variant,,ENST00000508451,; T ENST00000503026 Transcript synonymous_variant 111/1933 36/1563 12/520 L ctA/ctT 1 1 CCT5 HGNC HGNC:1618 protein_coding ENSP00000423318 E9PCA1 UPI0001D3B13A 1/11 Superfamily_domains:SSF48592 LOW SNV 2 1 PASS rs994364333 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 10250039 10250039 A T 1 0 0 0 0 0 0 0 1 2657 436 16 4 4 CCT5 5 10250039 Silent SNP A C3N-02089_T 1205481 10250039 171288220 274 27358 CTNND2 0 . GRCh38 5 11098640 11098640 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.2572T>A p.Ser858Thr p.S858T ENST00000304623 15/22 282 222 60 240 240 0 strelka-varscan-mutect CTNND2,missense_variant,p.Ser858Thr,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Ser767Thr,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Ser521Thr,ENST00000503622,NM_001288716.1;CTNND2,5_prime_UTR_variant,,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,missense_variant,p.Ser612Thr,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript missense_variant 2762/5481 2572/3678 858/1225 S/T Tca/Aca 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 deleterious(0) 15/22 Gene3D:1.25.10.10,Pfam_domain:PF00514,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1465508768 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 11098640 11098640 A T 1 0 0 0 0 1 0 0 0 3829 304 11 4 4 CTNND2 5 11098640 Missense_Mutation SNP A C3N-02089_T 848601 11098640 170439619 275 27359 CTNND2 0 . GRCh38 5 11159614 11159614 + Missense_Mutation SNP A A C rs769382942 C3N-02089_T C3N-02089_N A A c.2121T>G p.His707Gln p.H707Q ENST00000304623 12/22 105 91 14 92 92 0 strelka-varscan-mutect CTNND2,missense_variant,p.His707Gln,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.His616Gln,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.His370Gln,ENST00000503622,NM_001288716.1;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,missense_variant,p.His461Gln,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; C ENST00000304623 Transcript missense_variant 2311/5481 2121/3678 707/1225 H/Q caT/caG rs769382942 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.57) 12/22 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs769382942 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 11159614 11159614 A C 1 0 0 0 0 1 0 0 0 3829 98 4 5 5 CTNND2 5 11159614 Missense_Mutation SNP A C3N-02089_T 60974 11159614 170378645 276 27360 DNAH5 0 . GRCh38 5 13721242 13721242 + Missense_Mutation SNP G G A rs148349630 C3N-02089_T C3N-02089_N G G c.12037C>T p.Arg4013Cys p.R4013C ENST00000265104 71/79 260 223 37 274 274 0 strelka-varscan-mutect DNAH5,missense_variant,p.Arg4013Cys,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript missense_variant 12142/15633 12037/13875 4013/4624 R/C Cgc/Tgc rs148349630 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 deleterious(0) 71/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS rs148349630 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 13721242 13721242 G A 1 0 0 0 0 1 0 0 0 4419 1130 39 1 1 DNAH5 5 13721242 Missense_Mutation SNP G C3N-02089_T 2561628 13721242 167817017 277 27361 DNAH5 0 . GRCh38 5 13770763 13770763 + Silent SNP C C A C3N-02089_T C3N-02089_N C C c.9591G>T p.= p.R3197R ENST00000265104 56/79 392 309 83 331 330 1 strelka-varscan-mutect DNAH5,synonymous_variant,p.=,ENST00000265104,NM_001369.2;DNAH5,non_coding_transcript_exon_variant,,ENST00000504001,; A ENST00000265104 Transcript synonymous_variant 9696/15633 9591/13875 3197/4624 R cgG/cgT COSM234626,COSM735553 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 56/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 13770763 13770763 C A 1 0 0 0 0 0 0 0 1 4419 842 30 2 2 DNAH5 5 13770763 Silent SNP C C3N-02089_T 49521 13770763 167767496 278 27362 DNAH5 0 . GRCh38 5 13922105 13922105 + Splice_Site SNP A A T novel C3N-02089_T C3N-02089_N A A c.660+2T>A p.X220_splice ENST00000265104 490 392 98 391 390 1 strelka-varscan-mutect DNAH5,splice_donor_variant,,ENST00000265104,NM_001369.2;DNAH5,splice_donor_variant,,ENST00000508040,; T ENST00000265104 Transcript splice_donor_variant -/15633 660/13875 220/4624 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 5/78 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 13922105 13922105 A T 1 0 0 0 0 0 0 1 0 4419 173 6 4 4 DNAH5 5 13922105 Splice_Site SNP A C3N-02089_T 151342 13922105 167616154 279 27363 TRIO 0 . GRCh38 5 14462866 14462866 + Frame_Shift_Del DEL C C - C3N-02089_T C3N-02089_N C C c.5609delC p.Pro1870ArgfsTer26 p.P1870Rfs*26 ENST00000344204 36/57 118 91 27 104 104 0 sindel-varindel-pindel TRIO,frameshift_variant,p.Pro1870ArgfsTer26,ENST00000344204,NM_007118.2;TRIO,frameshift_variant,p.Pro1603ArgfsTer26,ENST00000513206,;TRIO,upstream_gene_variant,,ENST00000620511,;TRIO,non_coding_transcript_exon_variant,,ENST00000515710,;TRIO,frameshift_variant,p.Pro1811ArgfsTer26,ENST00000512070,;TRIO,non_coding_transcript_exon_variant,,ENST00000515144,; - ENST00000344204 Transcript frameshift_variant 5632/11100 5608/9294 1870/3097 P/X Ccg/cg COSM2156630 1 1 TRIO HGNC HGNC:12303 protein_coding YES CCDS3883.1 ENSP00000339299 O75962 UPI000034ECE6 NM_007118.2 36/57 Pfam_domain:PF16609 1 HIGH 1 deletion 1 1 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999926 1 1 1 0 - 7 5 90 14462866 14462866 C - 1 0 1 0 1 0 0 0 0 17049 739 26 0 0 TRIO 5 14462866 Frame_Shift_Del DEL C C3N-02089_T 540761 14462866 167075393 280 27364 OTULIN 0 . GRCh38 5 14681595 14681595 + Silent SNP G G T rs771323670 C3N-02089_T C3N-02089_N G G c.456G>T p.= p.P152P ENST00000284274 4/7 167 135 32 109 109 0 strelka-varscan-mutect OTULIN,synonymous_variant,p.=,ENST00000284274,NM_138348.4;OTULIN,synonymous_variant,p.=,ENST00000506417,;OTULIN,synonymous_variant,p.=,ENST00000514913,;OTULIN,3_prime_UTR_variant,,ENST00000503023,;OTULIN,non_coding_transcript_exon_variant,,ENST00000508678,; T ENST00000284274 Transcript synonymous_variant 534/7800 456/1059 152/352 P ccG/ccT rs771323670 1 1 OTULIN HGNC HGNC:25118 protein_coding YES CCDS43302.1 ENSP00000284274 Q96BN8 UPI0000374C00 NM_138348.4 4/7 hmmpanther:PTHR33662,hmmpanther:PTHR33662:SF2,Pfam_domain:PF16218 LOW 1 SNV 1 1 PASS rs771323670 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 14681595 14681595 G T 1 0 0 0 0 0 0 0 1 11389 1103 39 1 1 OTULIN 5 14681595 Silent SNP G C3N-02089_T 218729 14681595 166856664 281 27365 CDH12 0 . GRCh38 5 21755829 21755829 + Silent SNP C C T rs764043124 C3N-02089_T C3N-02089_N C C c.1647G>A p.= p.G549G ENST00000382254 14/15 150 118 32 125 125 0 strelka-varscan-mutect CDH12,synonymous_variant,p.=,ENST00000382254,NM_004061.3;CDH12,synonymous_variant,p.=,ENST00000504376,;CDH12,synonymous_variant,p.=,ENST00000522262,;RP11-804N13.1,intron_variant,,ENST00000522350,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript synonymous_variant 2734/4164 1647/2385 549/794 G ggG/ggA rs764043124 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 14/15 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS rs764043124 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 21755829 21755829 C T 1 0 0 0 0 0 0 0 1 2801 842 30 3 3 CDH12 5 21755829 Silent SNP C C3N-02089_T 7074234 21755829 159782430 282 27366 PRDM9 0 . GRCh38 5 23522679 23522679 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.676A>T p.Lys226Ter p.K226* ENST00000296682 8/11 434 339 95 450 450 0 strelka-varscan-mutect PRDM9,stop_gained,p.Lys226Ter,ENST00000296682,NM_020227.2;PRDM9,stop_gained,p.Lys167Ter,ENST00000635252,; T ENST00000296682 Transcript stop_gained 858/3691 676/2685 226/894 K/* Aag/Tag 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 8/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10,Pfam_domain:PF00856 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 23522679 23522679 A T 1 0 0 0 0 0 1 0 0 12595 15 1 4 4 PRDM9 5 23522679 Nonsense_Mutation SNP A C3N-02089_T 1766850 23522679 158015580 283 27367 PRDM9 0 . GRCh38 5 23526486 23526486 + Missense_Mutation SNP G G T rs755834976 C3N-02089_T C3N-02089_N G G c.1398G>T p.Arg466Ser p.R466S ENST00000296682 11/11 426 331 95 369 369 0 strelka-varscan-mutect PRDM9,missense_variant,p.Arg466Ser,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Arg407Ser,ENST00000635252,; T ENST00000296682 Transcript missense_variant 1580/3691 1398/2685 466/894 R/S agG/agT rs755834976,COSM125569,COSM4526464 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 tolerated(0.25) 11/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs755834976 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 23526486 23526486 G T 1 0 0 0 0 1 0 0 0 12595 1165 41 2 2 PRDM9 5 23526486 Missense_Mutation SNP G C3N-02089_T 3807 23526486 158011773 284 27368 CDH10 0 . GRCh38 5 24491607 24491607 + Silent SNP G G T rs756815430 C3N-02089_T C3N-02089_N G G c.1845C>A p.= p.I615I ENST00000264463 11/12 193 154 39 169 169 0 strelka-varscan-mutect CDH10,synonymous_variant,p.=,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; T ENST00000264463 Transcript synonymous_variant 2353/3438 1845/2367 615/788 I atC/atA rs756815430,COSM3013940 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 11/12 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027 0,1 LOW 1 SNV 1 0,1 1 PASS rs756815430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 24491607 24491607 G T 1 0 0 0 0 0 0 0 1 2799 1048 37 1 1 CDH10 5 24491607 Silent SNP G C3N-02089_T 965121 24491607 157046652 285 27369 CDH6 0 . GRCh38 5 31316207 31316207 + Splice_Site SNP G G T novel C3N-02089_T C3N-02089_N G G c.1391-1G>T p.X464_splice ENST00000265071 98 87 11 88 88 0 strelka-varscan-mutect CDH6,splice_acceptor_variant,,ENST00000265071,NM_004932.3;CDH6,splice_acceptor_variant,,ENST00000514738,;CDH6,upstream_gene_variant,,ENST00000504835,; T ENST00000265071 Transcript splice_acceptor_variant -/8476 1391/2373 464/790 1 1 CDH6 HGNC HGNC:1765 protein_coding YES CCDS3894.1 ENSP00000265071 P55285 UPI0000126D9B NM_004932.3 8/11 HIGH 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.99965 1 1 1 1 0 T 5 4 90 31316207 31316207 G T 1 0 0 0 0 0 0 1 0 2817 956 33 2 2 CDH6 5 31316207 Splice_Site SNP G C3N-02089_T 6824600 31316207 150222052 286 27370 SUB1 0 . GRCh38 5 32588578 32588578 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.66C>G p.Asp22Glu p.D22E ENST00000265073 2/5 91 82 9 102 102 0 strelka-varscan-mutect SUB1,missense_variant,p.Asp22Glu,ENST00000265073,NM_006713.3;SUB1,missense_variant,p.Asp22Glu,ENST00000506237,;SUB1,missense_variant,p.Asp22Glu,ENST00000515355,;SUB1,missense_variant,p.Asp22Glu,ENST00000512913,;SUB1,missense_variant,p.Asp22Glu,ENST00000510442,;SUB1,missense_variant,p.Asp22Glu,ENST00000502897,;SUB1,non_coding_transcript_exon_variant,,ENST00000504016,;SUB1,intron_variant,,ENST00000504789,;SUB1,intron_variant,,ENST00000513013,;SUB1,missense_variant,p.Asp22Glu,ENST00000511615,;SUB1,non_coding_transcript_exon_variant,,ENST00000511988,;SUB1,upstream_gene_variant,,ENST00000511175,; G ENST00000265073 Transcript missense_variant 194/3507 66/384 22/127 D/E gaC/gaG 1 1 SUB1 HGNC HGNC:19985 protein_coding YES CCDS3897.1 ENSP00000265073 P53999 Q6IBA2 UPI0000044938 NM_006713.3 tolerated(0.71) 2/5 Low_complexity_(Seg):seg,hmmpanther:PTHR13215:SF7,hmmpanther:PTHR13215 MODERATE 1 SNV 1 1 PASS . . 0 189 17 4 0 0 0 0 -14.18811 0.9455165 1 1 1 0 G 3 3 90 32588578 32588578 C G 1 0 0 0 0 1 0 0 0 15746 477 17 4 4 SUB1 5 32588578 Missense_Mutation SNP C C3N-02089_T 1272371 32588578 148949681 287 27371 ADAMTS12 0 . GRCh38 5 33881227 33881227 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.381C>A p.= p.S127S ENST00000504830 2/24 336 251 85 333 333 0 strelka-varscan-mutect ADAMTS12,synonymous_variant,p.=,ENST00000504830,NM_030955.2;ADAMTS12,synonymous_variant,p.=,ENST00000352040,;ADAMTS12,synonymous_variant,p.=,ENST00000515401,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000509762,; T ENST00000504830 Transcript synonymous_variant 717/8774 381/4785 127/1594 S tcC/tcA 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 2/24 Pfam_domain:PF01562,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 33881227 33881227 G T 1 0 0 0 0 0 0 0 1 301 1219 43 2 2 ADAMTS12 5 33881227 Silent SNP G C3N-02089_T 1292649 33881227 147657032 288 27372 SPEF2 0 . GRCh38 5 35793212 35793212 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.4608G>A p.= p.R1536R ENST00000356031 32/37 219 176 43 218 217 1 strelka-varscan-mutect SPEF2,synonymous_variant,p.=,ENST00000440995,;SPEF2,synonymous_variant,p.=,ENST00000356031,NM_024867.3;SPEF2,downstream_gene_variant,,ENST00000637569,;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,downstream_gene_variant,,ENST00000635995,;SPEF2,3_prime_UTR_variant,,ENST00000506526,;SPEF2,3_prime_UTR_variant,,ENST00000513078,;SPEF2,3_prime_UTR_variant,,ENST00000637061,; A ENST00000356031 Transcript synonymous_variant 4762/5681 4608/5469 1536/1822 R cgG/cgA COSM3615698,COSM3615699 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 32/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0,Superfamily_domains:SSF47473 1,1 LOW 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 35793212 35793212 G A 1 0 0 0 0 0 0 0 1 15386 1161 41 3 3 SPEF2 5 35793212 Silent SNP G C3N-02089_T 1911985 35793212 145745047 289 27373 SPEF2 0 . GRCh38 5 35800000 35800000 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.4863G>T p.Lys1621Asn p.K1621N ENST00000356031 34/37 177 144 33 159 159 0 strelka-varscan-mutect SPEF2,missense_variant,p.Lys1616Asn,ENST00000440995,;SPEF2,missense_variant,p.Lys1621Asn,ENST00000356031,NM_024867.3;CTD-2113L7.1,intron_variant,,ENST00000510433,;SPEF2,3_prime_UTR_variant,,ENST00000506526,;SPEF2,3_prime_UTR_variant,,ENST00000513078,;SPEF2,3_prime_UTR_variant,,ENST00000637061,; T ENST00000356031 Transcript missense_variant 5017/5681 4863/5469 1621/1822 K/N aaG/aaT 1 1 SPEF2 HGNC HGNC:26293 protein_coding YES CCDS43309.1 ENSP00000348314 Q9C093 A0A140VKD0 UPI0001505B9F NM_024867.3 tolerated(0.1) 34/37 hmmpanther:PTHR14919,hmmpanther:PTHR14919:SF0 MODERATE 1 SNV 2 1 PASS rs1358707940 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 35800000 35800000 G T 1 0 0 0 0 1 0 0 0 15386 991 35 2 2 SPEF2 5 35800000 Missense_Mutation SNP G C3N-02089_T 6788 35800000 145738259 290 27374 EGFLAM 0 . GRCh38 5 38350592 38350592 + Missense_Mutation SNP C C A rs749431693 C3N-02089_T C3N-02089_N C C c.383C>A p.Pro128His p.P128H ENST00000354891 4/23 169 133 36 175 175 0 strelka-varscan-mutect EGFLAM,missense_variant,p.Pro128His,ENST00000322350,NM_152403.3;EGFLAM,missense_variant,p.Pro128His,ENST00000354891,NM_001205301.1;EGFLAM-AS3,upstream_gene_variant,,ENST00000505267,;EGFLAM,3_prime_UTR_variant,,ENST00000504709,; A ENST00000354891 Transcript missense_variant 729/3963 383/3054 128/1017 P/H cCt/cAt rs749431693,COSM221705 1 1 EGFLAM HGNC HGNC:26810 protein_coding YES CCDS56363.1 ENSP00000346964 Q63HQ2 UPI000022C806 NM_001205301.1 deleterious_low_confidence(0) 4/23 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs749431693 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 38350592 38350592 C A 1 0 0 0 0 1 0 0 0 4802 681 24 2 2 EGFLAM 5 38350592 Missense_Mutation SNP C C3N-02089_T 2550592 38350592 143187667 291 27375 C7 0 . GRCh38 5 40972540 40972540 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2020G>T p.Gly674Cys p.G674C ENST00000313164 15/18 81 57 24 73 73 0 strelka-varscan-mutect C7,missense_variant,p.Gly674Cys,ENST00000313164,NM_000587.2;C7,non_coding_transcript_exon_variant,,ENST00000494960,;C7,non_coding_transcript_exon_variant,,ENST00000486779,;C7,non_coding_transcript_exon_variant,,ENST00000513922,;C7,upstream_gene_variant,,ENST00000464864,;RP11-301A5.2,upstream_gene_variant,,ENST00000504890,; T ENST00000313164 Transcript missense_variant 2379/4257 2020/2532 674/843 G/C Ggc/Tgc 1 1 C7 HGNC HGNC:1346 protein_coding YES CCDS47201.1 ENSP00000322061 P10643 UPI000020CA08 NM_000587.2 deleterious(0.03) 15/18 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF389,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 40972540 40972540 G T 1 0 0 0 0 1 0 0 0 2134 1348 47 2 2 C7 5 40972540 Missense_Mutation SNP G C3N-02089_T 2621948 40972540 140565719 292 27376 PLCXD3 0 . GRCh38 5 41382213 41382213 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.425T>A p.Leu142Ter p.L142* ENST00000377801 2/3 322 238 84 236 236 0 strelka-varscan-mutect PLCXD3,stop_gained,p.Leu142Ter,ENST00000377801,;PLCXD3,stop_gained,p.Leu142Ter,ENST00000328457,NM_001005473.2; T ENST00000377801 Transcript stop_gained 500/7704 425/966 142/321 L/* tTg/tAg 1 -1 PLCXD3 HGNC HGNC:31822 protein_coding YES CCDS34150.1 ENSP00000367032 Q63HM9 UPI0000049DBB 2/3 Gene3D:3.20.20.190,PROSITE_profiles:PS50007,hmmpanther:PTHR13593,hmmpanther:PTHR13593:SF33,SMART_domains:SM00148,Superfamily_domains:SSF51695 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 41382213 41382213 A T 1 0 0 0 0 0 1 0 0 12137 131 5 4 4 PLCXD3 5 41382213 Nonsense_Mutation SNP A C3N-02089_T 409673 41382213 140156046 293 27377 OXCT1 0 . GRCh38 5 41739442 41739442 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1469G>T p.Trp490Leu p.W490L ENST00000196371 16/17 375 288 87 341 339 2 strelka-varscan-mutect OXCT1,missense_variant,p.Trp490Leu,ENST00000196371,NM_000436.3;OXCT1,missense_variant,p.Trp93Leu,ENST00000512084,;OXCT1,missense_variant,p.Trp304Leu,ENST00000509987,;OXCT1,missense_variant,p.Trp93Leu,ENST00000510634,;OXCT1,non_coding_transcript_exon_variant,,ENST00000508557,;OXCT1,non_coding_transcript_exon_variant,,ENST00000503374,; A ENST00000196371 Transcript missense_variant 1630/3388 1469/1563 490/520 W/L tGg/tTg 1 -1 OXCT1 HGNC HGNC:8527 protein_coding YES CCDS3937.1 ENSP00000196371 P55809 A0A024R040 UPI0000000C9A NM_000436.3 tolerated(0.52) 16/17 hmmpanther:PTHR13707:SF30,hmmpanther:PTHR13707,Pfam_domain:PF01144,Gene3D:3.40.810.20,PIRSF_domain:PIRSF000858,TIGRFAM_domain:TIGR02428,SMART_domains:SM00882,Superfamily_domains:SSF100950 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 41739442 41739442 C A 1 0 0 0 0 1 0 0 0 11401 595 21 2 2 OXCT1 5 41739442 Missense_Mutation SNP C C3N-02089_T 357229 41739442 139798817 294 27378 HCN1 0 . GRCh38 5 45645184 45645184 + Splice_Site SNP C C G novel C3N-02089_T C3N-02089_N C C c.849+1G>C p.X283_splice ENST00000303230 143 130 13 158 158 0 strelka-mutect HCN1,splice_donor_variant,,ENST00000303230,NM_021072.3;HCN1,missense_variant,p.Val284Leu,ENST00000634658,;HCN1,splice_donor_variant,,ENST00000637256,; G ENST00000303230 Transcript splice_donor_variant -/9885 849/2673 283/890 1 -1 HCN1 HGNC HGNC:4845 protein_coding YES CCDS3952.1 ENSP00000307342 O60741 UPI00001AED69 NM_021072.3 2/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 90 45645184 45645184 C G 1 0 0 0 0 0 0 1 0 6883 521 18 4 4 HCN1 5 45645184 Splice_Site SNP C C3N-02089_T 3905742 45645184 135893075 295 27379 EMB 0 . GRCh38 5 50441079 50441079 + Missense_Mutation SNP C C A rs536007220 C3N-02089_T C3N-02089_N C C c.73G>T p.Ala25Ser p.A25S ENST00000303221 1/9 110 85 25 65 65 0 strelka-varscan-mutect EMB,missense_variant,p.Ala25Ser,ENST00000303221,NM_198449.2;EMB,missense_variant,p.Ala25Ser,ENST00000508934,;EMB,intron_variant,,ENST00000506190,; A ENST00000303221 Transcript missense_variant 289/4281 73/984 25/327 A/S Gct/Tct rs536007220 1 -1 EMB HGNC HGNC:30465 protein_coding YES CCDS3953.1 ENSP00000302289 Q6PCB8 UPI0000160A6D NM_198449.2 tolerated_low_confidence(0.18) 1/9 hmmpanther:PTHR10075,hmmpanther:PTHR10075:SF4,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs536007220 . 0 198 12 0 0 0 0 0 -20 0.9999636 1 1 1 0 A 3 1 90 50441079 50441079 C A 1 0 0 0 0 1 0 0 0 4920 768 27 1 1 EMB 5 50441079 Missense_Mutation SNP C C3N-02089_T 4795895 50441079 131097180 296 27380 PARP8 0 . GRCh38 5 50815481 50815481 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1625G>T p.Gly542Val p.G542V ENST00000281631 15/26 257 198 59 214 214 0 strelka-varscan-mutect PARP8,missense_variant,p.Gly542Val,ENST00000281631,NM_024615.3;PARP8,missense_variant,p.Gly521Val,ENST00000505554,;PARP8,missense_variant,p.Gly542Val,ENST00000514067,NM_001178056.1;PARP8,missense_variant,p.Gly542Val,ENST00000505697,NM_001178055.1;PARP8,missense_variant,p.Gly295Val,ENST00000514342,;PARP8,non_coding_transcript_exon_variant,,ENST00000511363,;PARP8,non_coding_transcript_exon_variant,,ENST00000503561,;PARP8,3_prime_UTR_variant,,ENST00000515166,; T ENST00000281631 Transcript missense_variant 1783/7177 1625/2565 542/854 G/V gGa/gTa 1 1 PARP8 HGNC HGNC:26124 protein_coding YES CCDS3954.1 ENSP00000281631 Q8N3A8 UPI0000073D19 NM_024615.3 deleterious(0) 15/26 hmmpanther:PTHR21328,hmmpanther:PTHR21328:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 50815481 50815481 G T 1 0 0 0 0 1 0 0 0 11545 1174 41 2 2 PARP8 5 50815481 Missense_Mutation SNP G C3N-02089_T 374402 50815481 130722778 297 27381 MCIDAS 0 . GRCh38 5 55220416 55220416 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1108A>G p.Thr370Ala p.T370A ENST00000513312 7/7 136 95 41 157 157 0 strelka-varscan-mutect MCIDAS,missense_variant,p.Thr370Ala,ENST00000513312,NM_001190787.1;MCIDAS,downstream_gene_variant,,ENST00000515336,;MCIDAS,3_prime_UTR_variant,,ENST00000513468,; C ENST00000513312 Transcript missense_variant 1285/1736 1108/1158 370/385 T/A Acc/Gcc 1 -1 MCIDAS HGNC HGNC:40050 protein_coding YES CCDS54853.1 ENSP00000426359 D6RGH6 UPI000020C760 NM_001190787.1 deleterious(0) 7/7 hmmpanther:PTHR13372,hmmpanther:PTHR13372:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 55220416 55220416 T C 1 0 0 0 0 1 0 0 0 9315 1696 59 5 5 MCIDAS 5 55220416 Missense_Mutation SNP T C3N-02089_T 4404935 55220416 126317843 298 27382 ANKRD55 0 . GRCh38 5 56126995 56126995 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.724G>T p.Gly242Cys p.G242C ENST00000341048 8/12 127 103 24 158 158 0 strelka-varscan-mutect ANKRD55,missense_variant,p.Gly242Cys,ENST00000341048,NM_024669.2;ANKRD55,missense_variant,p.Gly199Cys,ENST00000504958,;RNU6-299P,downstream_gene_variant,,ENST00000517223,;ANKRD55,intron_variant,,ENST00000505970,; A ENST00000341048 Transcript missense_variant 876/2502 724/1845 242/614 G/C Ggc/Tgc 1 -1 ANKRD55 HGNC HGNC:25681 protein_coding YES CCDS34161.1 ENSP00000342295 Q3KP44 UPI00004572EF NM_024669.2 deleterious(0) 8/12 PROSITE_profiles:PS50297,hmmpanther:PTHR24158,hmmpanther:PTHR24158:SF24,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS rs1437793448 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 56126995 56126995 C A 1 0 0 0 0 1 0 0 0 785 623 22 2 2 ANKRD55 5 56126995 Missense_Mutation SNP C C3N-02089_T 906579 56126995 125411264 299 27383 RGS7BP 0 . GRCh38 5 64507800 64507800 + Silent SNP G G C rs762869588 C3N-02089_T C3N-02089_N G G c.255G>C p.= p.R85R ENST00000334025 2/6 135 105 30 145 145 0 strelka-varscan-mutect RGS7BP,synonymous_variant,p.=,ENST00000334025,NM_001029875.2;RGS7BP,intron_variant,,ENST00000508162,; C ENST00000334025 Transcript synonymous_variant 581/4160 255/774 85/257 R cgG/cgC rs762869588 1 1 RGS7BP HGNC HGNC:23271 protein_coding YES CCDS34170.1 ENSP00000334851 Q6MZT1 UPI00001D7F8B NM_001029875.2 2/6 hmmpanther:PTHR21029,hmmpanther:PTHR21029:SF14 LOW 1 SNV 1 1 PASS rs762869588 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 64507800 64507800 G C 1 0 0 0 0 0 0 0 1 13482 1219 43 4 4 RGS7BP 5 64507800 Silent SNP G C3N-02089_T 8380805 64507800 117030459 300 27384 BTF3 0 . GRCh38 5 73498723 73498723 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.56G>T p.Arg19Met p.R19M ENST00000380591 1/6 64 46 18 76 76 0 strelka-varscan-mutect BTF3,missense_variant,p.Arg19Met,ENST00000380591,NM_001037637.1;BTF3,intron_variant,,ENST00000335895,NM_001207.4;BTF3,intron_variant,,ENST00000507081,;BTF3,upstream_gene_variant,,ENST00000509708,;RP11-79P5.9,upstream_gene_variant,,ENST00000607001,;BTF3,intron_variant,,ENST00000514505,;BTF3,non_coding_transcript_exon_variant,,ENST00000512257,;BTF3,non_coding_transcript_exon_variant,,ENST00000510787,;BTF3,intron_variant,,ENST00000514360,;BTF3,intron_variant,,ENST00000508901,; T ENST00000380591 Transcript missense_variant 275/1237 56/621 19/206 R/M aGg/aTg 1 1 BTF3 HGNC HGNC:1125 protein_coding YES CCDS34185.1 ENSP00000369965 P20290 UPI0000049C1C NM_001037637.1 deleterious_low_confidence(0.05) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR10351 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 73498723 73498723 G T 1 0 0 0 0 1 0 0 0 1727 1000 35 2 2 BTF3 5 73498723 Missense_Mutation SNP G C3N-02089_T 8990923 73498723 108039536 301 27385 HAPLN1 0 . GRCh38 5 83652499 83652499 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.426T>A p.= p.I142I ENST00000274341 3/5 100 87 13 107 107 0 varscan-mutect HAPLN1,synonymous_variant,p.=,ENST00000274341,NM_001884.3;HAPLN1,synonymous_variant,p.=,ENST00000514416,;HAPLN1,synonymous_variant,p.=,ENST00000510978,;HAPLN1,synonymous_variant,p.=,ENST00000504713,;HAPLN1,synonymous_variant,p.=,ENST00000508307,;HAPLN1,synonymous_variant,p.=,ENST00000503117,;HAPLN1,synonymous_variant,p.=,ENST00000515590,; T ENST00000274341 Transcript synonymous_variant 1277/5607 426/1065 142/354 I atT/atA 1 -1 HAPLN1 HGNC HGNC:2380 protein_coding YES CCDS4061.1 ENSP00000274341 P10915 A0A024RAK9 UPI0000131BFF NM_001884.3 3/5 PROSITE_profiles:PS50835,hmmpanther:PTHR22804:SF10,hmmpanther:PTHR22804,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs897393192 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 83652499 83652499 A T 1 0 0 0 0 0 0 0 1 6840 126 5 4 4 HAPLN1 5 83652499 Silent SNP A C3N-02089_T 10153776 83652499 97885760 302 27386 LNPEP 0 . GRCh38 5 96996408 96996408 + Missense_Mutation SNP A A C rs779684633 C3N-02089_T C3N-02089_N A A c.1426A>C p.Thr476Pro p.T476P ENST00000231368 7/18 309 271 38 343 343 0 strelka-varscan-mutect LNPEP,missense_variant,p.Thr476Pro,ENST00000231368,NM_005575.2;LNPEP,missense_variant,p.Thr462Pro,ENST00000395770,NM_175920.3;LNPEP,non_coding_transcript_exon_variant,,ENST00000473914,;LNPEP,non_coding_transcript_exon_variant,,ENST00000474122,; C ENST00000231368 Transcript missense_variant 2118/12752 1426/3078 476/1025 T/P Aca/Cca rs779684633 1 1 LNPEP HGNC HGNC:6656 protein_coding YES CCDS4087.1 ENSP00000231368 Q9UIQ6 UPI000013C94B NM_005575.2 deleterious(0) 7/18 hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF42,Pfam_domain:PF01433,Gene3D:1.10.390.10,Superfamily_domains:SSF55486,Prints_domain:PR00756 MODERATE 1 SNV 1 1 PASS rs779684633 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 96996408 96996408 A C 1 0 0 0 0 1 0 0 0 8791 43 2 5 5 LNPEP 5 96996408 Missense_Mutation SNP A C3N-02089_T 13343909 96996408 84541851 303 27387 TSLP 0 . GRCh38 5 111071981 111071981 + Missense_Mutation SNP T T A rs753025356 C3N-02089_T C3N-02089_N T T c.91T>A p.Phe31Ile p.F31I ENST00000344895 1/4 137 123 14 179 179 0 strelka-varscan-mutect TSLP,missense_variant,p.Phe31Ile,ENST00000420978,;TSLP,missense_variant,p.Phe31Ile,ENST00000344895,NM_033035.4;TSLP,upstream_gene_variant,,ENST00000379706,NM_138551.4;CTC-551A13.2,downstream_gene_variant,,ENST00000507269,; A ENST00000344895 Transcript missense_variant 290/736 91/480 31/159 F/I Ttc/Atc rs753025356 1 1 TSLP HGNC HGNC:30743 protein_coding YES CCDS4101.1 ENSP00000339804 Q969D9 UPI000006DB21 NM_033035.4 deleterious(0) 1/4 Pfam_domain:PF15216,hmmpanther:PTHR38003 MODERATE 1 SNV 1 1 PASS rs753025356 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 111071981 111071981 T A 1 0 0 0 0 1 0 0 0 17133 1609 56 4 4 TSLP 5 111071981 Missense_Mutation SNP T C3N-02089_T 14075573 111071981 70466278 304 27388 APC 0 . GRCh38 5 112843535 112843535 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.7942delG p.Ala2648HisfsTer12 p.A2648Hfs*12 ENST00000257430 16/16 133 105 28 203 202 1 sindel-varindel-pindel APC,frameshift_variant,p.Ala2648HisfsTer12,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Ala2648HisfsTer12,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000508624,;APC,downstream_gene_variant,,ENST00000502371,; - ENST00000257430 Transcript frameshift_variant 7997/10701 7941/8532 2647/2843 M/X atG/at 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 16/16 hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 HIGH deletion 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 112843535 112843535 G - 1 0 1 0 1 0 0 0 0 883 1348 47 0 0 APC 5 112843535 Frame_Shift_Del DEL G C3N-02089_T 1771554 112843535 68694724 305 27389 SRP19 0 . GRCh38 5 112862509 112862509 + Missense_Mutation SNP T T A rs201250324 C3N-02089_T C3N-02089_N T T c.43T>A p.Phe15Ile p.F15I ENST00000505459 2/5 309 272 37 289 288 1 strelka-varscan-mutect SRP19,missense_variant,p.Phe15Ile,ENST00000505459,NM_003135.2;SRP19,missense_variant,p.Phe15Ile,ENST00000621420,NM_001204194.1;SRP19,missense_variant,p.Phe15Ile,ENST00000282999,NM_001204193.1;SRP19,missense_variant,p.Phe15Ile,ENST00000445150,;SRP19,intron_variant,,ENST00000515463,NM_001204196.1;CTC-487M23.8,splice_region_variant,,ENST00000512790,;CTC-487M23.8,splice_region_variant,,ENST00000503445,;CTC-487M23.8,missense_variant,p.Phe15Ile,ENST00000506997,;CTC-554D6.1,splice_region_variant,p.=,ENST00000520401,;SRP19,splice_region_variant,,ENST00000515755,;SRP19,non_coding_transcript_exon_variant,,ENST00000506987,;CTC-487M23.8,non_coding_transcript_exon_variant,,ENST00000509024,;SRP19,upstream_gene_variant,,ENST00000504696,; A ENST00000505459 Transcript missense_variant,splice_region_variant 198/2841 43/435 15/144 F/I Ttt/Att rs201250324 1 1 SRP19 HGNC HGNC:11300 protein_coding YES CCDS4108.1 ENSP00000424870 P09132 UPI000013DD11 NM_003135.2 deleterious(0) 2/5 hmmpanther:PTHR17453:SF0,hmmpanther:PTHR17453,Gene3D:3.30.56.30,Superfamily_domains:SSF69695 MODERATE 1 SNV 1 1 PASS rs201250324 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 112862509 112862509 T A 1 0 0 0 0 1 0 0 0 15515 1739 60 4 4 SRP19 5 112862509 Missense_Mutation SNP T C3N-02089_T 18974 112862509 68675750 306 27390 MEGF10 0 . GRCh38 5 127398729 127398729 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.713G>T p.Cys238Phe p.C238F ENST00000274473 8/26 183 143 40 280 280 0 strelka-varscan-mutect MEGF10,missense_variant,p.Cys238Phe,ENST00000274473,NM_032446.2;MEGF10,missense_variant,p.Cys238Phe,ENST00000503335,NM_001256545.1;MEGF10,missense_variant,p.Cys238Phe,ENST00000508365,NM_001308121.1;MEGF10,missense_variant,p.Cys238Phe,ENST00000418761,; T ENST00000274473 Transcript missense_variant 980/7594 713/3423 238/1140 C/F tGc/tTc 1 1 MEGF10 HGNC HGNC:29634 protein_coding YES CCDS4142.1 ENSP00000274473 Q96KG7 UPI000006F868 NM_032446.2 deleterious(0.01) 8/26 Gene3D:2gy5A03,PROSITE_profiles:PS50026,hmmpanther:PTHR24035,hmmpanther:PTHR24035:SF75,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 127398729 127398729 G T 1 0 0 0 0 1 0 0 0 9400 1319 46 2 2 MEGF10 5 127398729 Missense_Mutation SNP G C3N-02089_T 14536220 127398729 54139530 307 27391 FBN2 0 . GRCh38 5 128393264 128393264 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1336G>T p.Gly446Cys p.G446C ENST00000508053 16/71 311 214 97 305 305 0 strelka-varscan-mutect FBN2,missense_variant,p.Gly446Cys,ENST00000508053,;FBN2,missense_variant,p.Gly446Cys,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Gly445Cys,ENST00000619499,;FBN2,missense_variant,p.Gly413Cys,ENST00000508989,; A ENST00000508053 Transcript missense_variant 2311/11132 1336/8739 446/2912 G/C Ggc/Tgc 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 tolerated(0.11) 16/71 PIRSF_domain:PIRSF036312,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs1173562709 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 128393264 128393264 C A 1 0 0 0 0 1 0 0 0 5566 594 21 2 2 FBN2 5 128393264 Missense_Mutation SNP C C3N-02089_T 994535 128393264 53144995 308 27392 PCDHA2 0 . GRCh38 5 140795149 140795149 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.185G>T p.Arg62Leu p.R62L ENST00000526136 1/4 504 366 138 484 483 1 strelka-varscan-mutect PCDHA2,missense_variant,p.Arg62Leu,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Arg62Leu,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Arg62Leu,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; T ENST00000526136 Transcript missense_variant 185/5254 185/2847 62/948 R/L cGc/cTc COSM4711830,COSM4711831 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF08266,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 140795149 140795149 G T 1 0 0 0 0 1 0 0 0 11611 1087 38 1 1 PCDHA2 5 140795149 Missense_Mutation SNP G C3N-02089_T 12401885 140795149 40743110 309 27393 PCDHA2 0 . GRCh38 5 140796955 140796955 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1991C>A p.Thr664Asn p.T664N ENST00000526136 1/4 213 164 49 245 245 0 strelka-varscan-mutect PCDHA2,missense_variant,p.Thr664Asn,ENST00000526136,NM_018905.2;PCDHA2,missense_variant,p.Thr664Asn,ENST00000520672,NM_031496.1;PCDHA2,missense_variant,p.Thr664Asn,ENST00000378132,NM_031495.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA3,upstream_gene_variant,,ENST00000522353,NM_018906.2;PCDHA3,upstream_gene_variant,,ENST00000532566,NM_031497.1;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,intron_variant,,ENST00000624176,; A ENST00000526136 Transcript missense_variant 1991/5254 1991/2847 664/948 T/N aCc/aAc 1 1 PCDHA2 HGNC HGNC:8668 protein_coding YES CCDS54914.1 ENSP00000431748 Q9Y5H9 UPI00001273C9 NM_018905.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 140796955 140796955 C A 1 0 0 0 0 1 0 0 0 11611 507 18 2 2 PCDHA2 5 140796955 Missense_Mutation SNP C C3N-02089_T 1806 140796955 40741304 310 27394 PCDHA5 0 . GRCh38 5 140822796 140822796 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1021G>T p.Asp341Tyr p.D341Y ENST00000529859 1/4 132 81 51 178 176 2 strelka-varscan-mutect PCDHA5,missense_variant,p.Asp341Tyr,ENST00000529859,NM_018908.2;PCDHA5,missense_variant,p.Asp341Tyr,ENST00000614258,NM_031501.1;PCDHA5,missense_variant,p.Asp341Tyr,ENST00000529619,;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA4,intron_variant,,ENST00000512229,;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.16,upstream_gene_variant,,ENST00000624712,; T ENST00000529859 Transcript missense_variant 1021/5218 1021/2811 341/936 D/Y Gat/Tat 1 1 PCDHA5 HGNC HGNC:8671 protein_coding YES CCDS54917.1 ENSP00000436557 Q9Y5H7 UPI00001273CD NM_018908.2 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF111,PROSITE_patterns:PS00232,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 140822796 140822796 G T 1 0 0 0 0 1 0 0 0 11614 1174 41 2 2 PCDHA5 5 140822796 Missense_Mutation SNP G C3N-02089_T 25841 140822796 40715463 311 27395 PCDHA8 0 . GRCh38 5 140842938 140842938 + Missense_Mutation SNP C C A rs782409910 C3N-02089_T C3N-02089_N C C c.1617C>A p.Asp539Glu p.D539E ENST00000531613 1/4 727 509 218 672 672 0 strelka-varscan-mutect PCDHA8,missense_variant,p.Asp539Glu,ENST00000531613,NM_018911.2;PCDHA8,missense_variant,p.Asp539Glu,ENST00000378123,NM_031856.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA9,upstream_gene_variant,,ENST00000378122,NM_014005.4;PCDHA9,upstream_gene_variant,,ENST00000532602,NM_031857.1; A ENST00000531613 Transcript missense_variant 1617/5260 1617/2853 539/950 D/E gaC/gaA rs782409910 1 1 PCDHA8 HGNC HGNC:8674 protein_coding YES CCDS54919.1 ENSP00000434655 Q9Y5H6 UPI00001273D0 NM_018911.2 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF125,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs782409910 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 140842938 140842938 C A 1 0 0 0 0 1 0 0 0 11617 535 19 1 1 PCDHA8 5 140842938 Missense_Mutation SNP C C3N-02089_T 20142 140842938 40695321 312 27396 PCDHA9 0 . GRCh38 5 140850352 140850352 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1857C>A p.Ser619Arg p.S619R ENST00000532602 1/4 397 298 99 356 355 1 strelka-varscan-mutect PCDHA9,missense_variant,p.Ser619Arg,ENST00000378122,NM_014005.4;PCDHA9,missense_variant,p.Ser619Arg,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; A ENST00000532602 Transcript missense_variant 2890/6293 1857/2853 619/950 S/R agC/agA 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 tolerated_low_confidence(1) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 140850352 140850352 C A 1 0 0 0 0 1 0 0 0 11618 709 25 2 2 PCDHA9 5 140850352 Missense_Mutation SNP C C3N-02089_T 7414 140850352 40687907 313 27397 PCDHGA2 0 . GRCh38 5 141340854 141340854 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1883C>A p.Thr628Lys p.T628K ENST00000394576 1/4 272 194 78 350 350 0 strelka-varscan-mutect PCDHGA2,missense_variant,p.Thr628Lys,ENST00000394576,NM_018915.3;PCDHGA2,missense_variant,p.Thr628Lys,ENST00000528330,NM_032009.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA3,upstream_gene_variant,,ENST00000253812,NM_018916.3;PCDHGA3,upstream_gene_variant,,ENST00000619750,NM_032011.1;PCDHGA3,upstream_gene_variant,,ENST00000612467,; A ENST00000394576 Transcript missense_variant 1883/4605 1883/2799 628/932 T/K aCg/aAg COSM1165955,COSM1165956 1 1 PCDHGA2 HGNC HGNC:8700 protein_coding YES CCDS47289.1 ENSP00000378077 Q9Y5H1 UPI0000072E67 NM_018915.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF134,hmmpanther:PTHR24028,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 141340854 141340854 C A 1 0 0 0 0 1 0 0 0 11641 536 19 1 1 PCDHGA2 5 141340854 Missense_Mutation SNP C C3N-02089_T 490502 141340854 40197405 314 27398 PCDHGB7 0 . GRCh38 5 141418304 141418304 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.445G>T p.Gly149Trp p.G149W ENST00000398594 1/4 188 139 49 227 227 0 strelka-varscan-mutect PCDHGB7,missense_variant,p.Gly149Trp,ENST00000398594,NM_018927.3;PCDHGB7,missense_variant,p.Gly149Trp,ENST00000612073,NM_032101.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA10,intron_variant,,ENST00000398610,NM_018913.2;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGA11,upstream_gene_variant,,ENST00000398587,NM_018914.2;PCDHGA10,downstream_gene_variant,,ENST00000612503,NM_032090.1;PCDHGA11,upstream_gene_variant,,ENST00000622044,NM_032091.1;PCDHGA11,upstream_gene_variant,,ENST00000518882,NM_032092.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398594 Transcript missense_variant 614/4765 445/2790 149/929 G/W Ggg/Tgg 1 1 PCDHGB7 HGNC HGNC:8714 protein_coding YES CCDS47293.1 ENSP00000381594 Q9Y5F8 UPI000007141F NM_018927.3 deleterious(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF113,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 141418304 141418304 G T 1 0 0 0 0 1 0 0 0 11655 1232 43 2 2 PCDHGB7 5 141418304 Missense_Mutation SNP G C3N-02089_T 77450 141418304 40119955 315 27399 TCERG1 0 . GRCh38 5 146470713 146470713 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1477G>T p.Asp493Tyr p.D493Y ENST00000296702 8/22 175 128 47 186 186 0 strelka-varscan-mutect TCERG1,missense_variant,p.Asp493Tyr,ENST00000296702,NM_006706.3;TCERG1,missense_variant,p.Asp472Tyr,ENST00000394421,NM_001040006.1;TCERG1,non_coding_transcript_exon_variant,,ENST00000510724,;TCERG1,missense_variant,p.Asp493Tyr,ENST00000549332,;TCERG1,non_coding_transcript_exon_variant,,ENST00000507175,;TCERG1,downstream_gene_variant,,ENST00000513298,; T ENST00000296702 Transcript missense_variant 1515/4654 1477/3297 493/1098 D/Y Gat/Tat 1 1 TCERG1 HGNC HGNC:15630 protein_coding YES CCDS4282.1 ENSP00000296702 O14776 UPI000013E374 NM_006706.3 deleterious(0.01) 8/22 hmmpanther:PTHR15377,hmmpanther:PTHR15377:SF7,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 146470713 146470713 G T 1 0 0 0 0 1 0 0 0 16092 1174 41 2 2 TCERG1 5 146470713 Missense_Mutation SNP G C3N-02089_T 5052409 146470713 35067546 316 27400 SLC6A7 0 . GRCh38 5 150202413 150202413 + Missense_Mutation SNP T T A rs779330388 C3N-02089_T C3N-02089_N T T c.925T>A p.Phe309Ile p.F309I ENST00000230671 7/14 181 130 51 171 171 0 strelka-varscan-mutect SLC6A7,missense_variant,p.Phe309Ile,ENST00000230671,NM_014228.3;SLC6A7,missense_variant,p.Phe309Ile,ENST00000524041,; A ENST00000230671 Transcript missense_variant 1296/3739 925/1911 309/636 F/I Ttt/Att rs779330388 1 1 SLC6A7 HGNC HGNC:11054 protein_coding YES CCDS4305.1 ENSP00000230671 Q99884 UPI000013C93C NM_014228.3 deleterious(0.03) 7/14 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF35,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 MODERATE 1 SNV 1 1 PASS rs779330388 . 0 206 0 3 0 0 0 0 -20 0.9999981 1 1 1 0 A 3 1 90 150202413 150202413 T A 1 0 0 0 0 1 0 0 0 14972 1609 56 4 4 SLC6A7 5 150202413 Missense_Mutation SNP T C3N-02089_T 3731700 150202413 31335846 317 27401 ITK 0 . GRCh38 5 157245739 157245739 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1463G>T p.Cys488Phe p.C488F ENST00000422843 14/17 360 254 106 361 360 1 strelka-varscan-mutect ITK,missense_variant,p.Cys488Phe,ENST00000422843,NM_005546.3;ITK,intron_variant,,ENST00000519749,;ITK,non_coding_transcript_exon_variant,,ENST00000519402,;ITK,non_coding_transcript_exon_variant,,ENST00000523926,;ITK,downstream_gene_variant,,ENST00000520173,; T ENST00000422843 Transcript missense_variant 1615/4528 1463/1863 488/620 C/F tGt/tTt 1 1 ITK HGNC HGNC:6171 protein_coding YES CCDS4336.1 ENSP00000398655 Q08881 UPI000004CADA NM_005546.3 deleterious(0) 14/17 PROSITE_profiles:PS50011,hmmpanther:PTHR24418:SF61,hmmpanther:PTHR24418,PROSITE_patterns:PS00109,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112,Prints_domain:PR00109 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 157245739 157245739 G T 1 0 0 0 0 1 0 0 0 7815 1377 48 2 2 ITK 5 157245739 Missense_Mutation SNP G C3N-02089_T 7043326 157245739 24292520 318 27402 C1QTNF2 0 . GRCh38 5 160349254 160349254 + Missense_Mutation SNP C C A rs750083087 C3N-02089_T C3N-02089_N C C c.907G>T p.Gly303Trp p.G303W ENST00000393975 3/3 242 207 35 256 255 1 strelka-varscan-mutect C1QTNF2,missense_variant,p.Gly303Trp,ENST00000393975,NM_031908.4;CCNJL,upstream_gene_variant,,ENST00000521643,; A ENST00000393975 Transcript missense_variant 911/2414 907/993 303/330 G/W Ggg/Tgg rs750083087 1 -1 C1QTNF2 HGNC HGNC:14325 protein_coding YES CCDS4351.2 ENSP00000377545 Q9BXJ5 UPI0000D4B9D3 NM_031908.4 deleterious(0) 3/3 Gene3D:2.60.120.40,Pfam_domain:PF00386,PROSITE_profiles:PS50871,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF607,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS rs750083087 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 160349254 160349254 C A 1 0 0 0 0 1 0 0 0 1941 652 23 1 1 C1QTNF2 5 160349254 Missense_Mutation SNP C C3N-02089_T 3103515 160349254 21189005 319 27403 ZBED8 0 . GRCh38 5 160394470 160394470 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1021A>T p.Thr341Ser p.T341S ENST00000408953 2/2 218 147 71 325 325 0 strelka-varscan-mutect ZBED8,missense_variant,p.Thr341Ser,ENST00000408953,NM_022090.4;ZBED8,missense_variant,p.Thr341Ser,ENST00000523213,NM_001303251.1; A ENST00000408953 Transcript missense_variant 1529/2851 1021/1785 341/594 T/S Act/Tct 1 -1 ZBED8 HGNC HGNC:30804 protein_coding YES CCDS34283.1 ENSP00000386184 Q8IZ13 UPI00000741A3 NM_022090.4 tolerated(0.68) 2/2 hmmpanther:PTHR11697,hmmpanther:PTHR11697:SF102,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS rs1441526506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 160394470 160394470 T A 1 0 0 0 0 1 0 0 0 18085 1638 57 4 4 ZBED8 5 160394470 Missense_Mutation SNP T C3N-02089_T 45216 160394470 21143789 320 27404 ATP10B 0 . GRCh38 5 160620584 160620584 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.2179C>A p.Leu727Met p.L727M ENST00000327245 15/26 93 62 31 101 101 0 strelka-varscan-mutect ATP10B,missense_variant,p.Leu727Met,ENST00000327245,NM_025153.2;ATP10B,missense_variant,p.Leu335Met,ENST00000520108,;CTC-348L5.1,intron_variant,,ENST00000523598,; T ENST00000327245 Transcript missense_variant 3026/7566 2179/4386 727/1461 L/M Ctg/Atg COSM1283560 1 -1 ATP10B HGNC HGNC:13543 protein_coding YES CCDS43394.1 ENSP00000313600 O94823 UPI0000191DAE NM_025153.2 deleterious(0) 15/26 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF79,Pfam_domain:PF13246,TIGRFAM_domain:TIGR01652,Gene3D:3.40.1110.10,Superfamily_domains:SSF81660 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 160620584 160620584 G T 1 0 0 0 0 1 0 0 0 1269 991 35 2 2 ATP10B 5 160620584 Missense_Mutation SNP G C3N-02089_T 226114 160620584 20917675 321 27405 LCP2 0 . GRCh38 5 170262735 170262735 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.826G>C p.Gly276Arg p.G276R ENST00000046794 13/21 144 104 40 153 153 0 strelka-varscan-mutect LCP2,missense_variant,p.Gly276Arg,ENST00000046794,NM_005565.3;LCP2,missense_variant,p.Gly276Arg,ENST00000628092,;LCP2,missense_variant,p.Gly71Arg,ENST00000521416,;LCP2,missense_variant,p.Gly43Arg,ENST00000520344,;LCP2,upstream_gene_variant,,ENST00000523369,; G ENST00000046794 Transcript missense_variant 1442/4678 826/1602 276/533 G/R Ggg/Cgg 1 -1 LCP2 HGNC HGNC:6529 protein_coding YES CCDS47339.1 ENSP00000046794 Q13094 UPI000012E2AE NM_005565.3 deleterious(0) 13/21 hmmpanther:PTHR14098,hmmpanther:PTHR14098:SF1 MODERATE 1 SNV 1 1 PASS rs902403854 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 170262735 170262735 C G 1 0 0 0 0 1 0 0 0 8598 652 23 4 4 LCP2 5 170262735 Missense_Mutation SNP C C3N-02089_T 9642151 170262735 11275524 322 27406 CDHR2 0 . GRCh38 5 176591463 176591463 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.3713C>G p.Ser1238Cys p.S1238C ENST00000510636 30/32 248 188 60 251 251 0 strelka-varscan-mutect CDHR2,missense_variant,p.Ser1238Cys,ENST00000510636,NM_001171976.1;CDHR2,missense_variant,p.Ser1238Cys,ENST00000261944,NM_017675.4;CDHR2,missense_variant,p.Ser1238Cys,ENST00000506348,;GPRIN1,downstream_gene_variant,,ENST00000303991,NM_052899.2;CDHR2,non_coding_transcript_exon_variant,,ENST00000416365,;CDHR2,downstream_gene_variant,,ENST00000513031,;CDHR2,downstream_gene_variant,,ENST00000508085,; G ENST00000510636 Transcript missense_variant 3987/4509 3713/3933 1238/1310 S/C tCc/tGc 1 1 CDHR2 HGNC HGNC:18231 protein_coding YES CCDS34297.1 ENSP00000424565 Q9BYE9 UPI0000DBEE8C NM_001171976.1 deleterious(0) 30/32 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 176591463 176591463 C G 1 0 0 0 0 1 0 0 0 2822 855 30 4 4 CDHR2 5 176591463 Missense_Mutation SNP C C3N-02089_T 6328728 176591463 4946796 323 27407 MGAT1 0 . GRCh38 5 180792398 180792398 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.574G>T p.Ala192Ser p.A192S ENST00000333055 3/3 68 51 17 77 77 0 strelka-varscan-mutect MGAT1,missense_variant,p.Ala192Ser,ENST00000333055,;MGAT1,missense_variant,p.Ala192Ser,ENST00000446023,NM_001114618.1;MGAT1,missense_variant,p.Ala192Ser,ENST00000393340,NM_001114617.1;MGAT1,missense_variant,p.Ala192Ser,ENST00000307826,NM_002406.3;MGAT1,missense_variant,p.Ala192Ser,ENST00000427865,NM_001114620.1,NM_001114619.1;MGAT1,missense_variant,p.Ala192Ser,ENST00000504671,;MGAT1,downstream_gene_variant,,ENST00000506889,;MGAT1,downstream_gene_variant,,ENST00000502678,;MGAT1,downstream_gene_variant,,ENST00000514283,;MGAT1,downstream_gene_variant,,ENST00000514438,;MGAT1,downstream_gene_variant,,ENST00000507384,;MGAT1,downstream_gene_variant,,ENST00000506269,;MGAT1,downstream_gene_variant,,ENST00000513431,;MGAT1,downstream_gene_variant,,ENST00000512695,;MGAT1,downstream_gene_variant,,ENST00000514760,;MGAT1,downstream_gene_variant,,ENST00000504385,;MGAT1,downstream_gene_variant,,ENST00000505682,; A ENST00000333055 Transcript missense_variant 1247/8863 574/1338 192/445 A/S Gcg/Tcg 1 -1 MGAT1 HGNC HGNC:7044 protein_coding YES CCDS4458.1 ENSP00000332073 P26572 UPI000013CDF1 3/3 Gene3D:3.90.550.10,Pfam_domain:PF03071,hmmpanther:PTHR10468,hmmpanther:PTHR10468:SF0,Superfamily_domains:SSF53448 MODERATE 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 90 180792398 180792398 C A 1 0 0 0 0 1 0 0 0 9502 739 26 2 2 MGAT1 5 180792398 Missense_Mutation SNP C C3N-02089_T 4200935 180792398 745861 324 27408 FOXF2 0 . GRCh38 6 1390234 1390234 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.287G>C p.Arg96Pro p.R96P ENST00000259806 1/2 187 128 59 175 175 0 strelka-varscan-mutect FOXF2,missense_variant,p.Arg96Pro,ENST00000259806,NM_001452.1;MIR6720,downstream_gene_variant,,ENST00000611664,; C ENST00000259806 Transcript missense_variant 401/2187 287/1335 96/444 R/P cGg/cCg 1 1 FOXF2 HGNC HGNC:3810 protein_coding YES CCDS4472.1 ENSP00000259806 Q12947 UPI000012ADD6 NM_001452.1 deleterious(0.01) 1/2 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF224,Gene3D:1.10.10.10 MODERATE 1 SNV 1 1 PASS rs1227693674 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 1390234 1390234 G C 1 0 0 0 0 1 0 0 0 5868 1116 39 4 4 FOXF2 6 1390234 Missense_Mutation SNP G C3N-02089_T 1390234 169415745 325 27409 WRNIP1 0 . GRCh38 6 2766273 2766273 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.651G>C p.Glu217Asp p.E217D ENST00000380773 1/7 144 131 13 130 130 0 strelka-varscan-mutect WRNIP1,missense_variant,p.Glu217Asp,ENST00000380773,;WRNIP1,missense_variant,p.Glu217Asp,ENST00000618555,NM_020135.2;WRNIP1,missense_variant,p.Glu217Asp,ENST00000380771,NM_130395.2;WRNIP1,5_prime_UTR_variant,,ENST00000380769,;WRNIP1,upstream_gene_variant,,ENST00000380764,; C ENST00000380773 Transcript missense_variant 860/2670 651/1998 217/665 E/D gaG/gaC 1 1 WRNIP1 HGNC HGNC:20876 protein_coding YES CCDS4475.1 ENSP00000370150 Q96S55 UPI000004A506 tolerated(0.22) 1/7 Gene3D:3.40.50.300,hmmpanther:PTHR13779,hmmpanther:PTHR13779:SF7 MODERATE 1 SNV 1 1 PASS rs1290032226 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 2766273 2766273 G C 1 0 0 0 0 1 0 0 0 17960 933 33 4 4 WRNIP1 6 2766273 Missense_Mutation SNP G C3N-02089_T 1376039 2766273 168039706 326 27410 ECI2 0 . GRCh38 6 4126190 4126190 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.619G>A p.Asp207Asn p.D207N ENST00000380118 6/10 116 107 9 145 145 0 strelka-varscan-mutect ECI2,missense_variant,p.Asp177Asn,ENST00000465828,;ECI2,missense_variant,p.Asp207Asn,ENST00000380118,NM_206836.2;ECI2,missense_variant,p.Asp177Asn,ENST00000380125,NM_001166010.1;ECI2,missense_variant,p.Asp177Asn,ENST00000361538,NM_006117.2;C6orf201,intron_variant,,ENST00000380175,NM_001085401.2;ECI2,downstream_gene_variant,,ENST00000495548,;C6orf201,intron_variant,,ENST00000496987,;ECI2,3_prime_UTR_variant,,ENST00000380120,;ECI2,3_prime_UTR_variant,,ENST00000496241,;ECI2,non_coding_transcript_exon_variant,,ENST00000464583,;ECI2,non_coding_transcript_exon_variant,,ENST00000464057,;C6orf201,intron_variant,,ENST00000436110,;C6orf201,intron_variant,,ENST00000427996,;ECI2,intron_variant,,ENST00000478266,;C6orf201,intron_variant,,ENST00000451679,;ECI2,downstream_gene_variant,,ENST00000489086,; T ENST00000380118 Transcript missense_variant 656/1407 619/1185 207/394 D/N Gat/Aat 1 -1 ECI2 HGNC HGNC:14601 protein_coding YES CCDS43420.2 ENSP00000369461 O75521 UPI000004ECA9 NM_206836.2 tolerated(0.91) 6/10 hmmpanther:PTHR23310:SF72,hmmpanther:PTHR23310,Gene3D:3.90.226.10,Pfam_domain:PF00378,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 4126190 4126190 C T 1 0 0 0 0 1 0 0 0 4724 826 29 3 3 ECI2 6 4126190 Missense_Mutation SNP C C3N-02089_T 1359917 4126190 166679789 327 27411 ECI2 0 . GRCh38 6 4126207 4126207 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.602A>T p.Asp201Val p.D201V ENST00000380118 6/10 116 99 17 141 141 0 strelka-varscan-mutect ECI2,missense_variant,p.Asp171Val,ENST00000465828,;ECI2,missense_variant,p.Asp201Val,ENST00000380118,NM_206836.2;ECI2,missense_variant,p.Asp171Val,ENST00000380125,NM_001166010.1;ECI2,missense_variant,p.Asp171Val,ENST00000361538,NM_006117.2;C6orf201,intron_variant,,ENST00000380175,NM_001085401.2;ECI2,downstream_gene_variant,,ENST00000495548,;C6orf201,intron_variant,,ENST00000496987,;ECI2,3_prime_UTR_variant,,ENST00000380120,;ECI2,3_prime_UTR_variant,,ENST00000496241,;ECI2,non_coding_transcript_exon_variant,,ENST00000464583,;ECI2,non_coding_transcript_exon_variant,,ENST00000464057,;C6orf201,intron_variant,,ENST00000436110,;C6orf201,intron_variant,,ENST00000427996,;ECI2,intron_variant,,ENST00000478266,;C6orf201,intron_variant,,ENST00000451679,;ECI2,downstream_gene_variant,,ENST00000489086,; A ENST00000380118 Transcript missense_variant 639/1407 602/1185 201/394 D/V gAt/gTt 1 -1 ECI2 HGNC HGNC:14601 protein_coding YES CCDS43420.2 ENSP00000369461 O75521 UPI000004ECA9 NM_206836.2 deleterious(0) 6/10 hmmpanther:PTHR23310:SF72,hmmpanther:PTHR23310,Gene3D:3.90.226.10,Pfam_domain:PF00378,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 4126207 4126207 T A 1 0 0 0 0 1 0 0 0 4724 1435 50 4 4 ECI2 6 4126207 Missense_Mutation SNP T C3N-02089_T 17 4126207 166679772 328 27412 LYRM4 0 . GRCh38 6 5216654 5216654 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.171T>C p.= p.N57N ENST00000500576 2/3 314 287 27 369 369 0 strelka-varscan-mutect LYRM4,synonymous_variant,p.=,ENST00000330636,NM_020408.5;LYRM4,synonymous_variant,p.=,ENST00000464010,NM_001164841.2;LYRM4,synonymous_variant,p.=,ENST00000480566,;LYRM4,synonymous_variant,p.=,ENST00000500576,NM_001164840.2;LYRM4,intron_variant,,ENST00000468929,;LYRM4,synonymous_variant,p.=,ENST00000463032,; G ENST00000500576 Transcript synonymous_variant 175/592 171/393 57/130 N aaT/aaC 1 -1 LYRM4 HGNC HGNC:21365 protein_coding YES CCDS54962.1 ENSP00000443900 F5H189 UPI0001B71BCB NM_001164840.2 2/3 Pfam_domain:PF05347 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 5216654 5216654 A G 1 0 0 0 0 0 0 0 1 9033 446 16 5 5 LYRM4 6 5216654 Silent SNP A C3N-02089_T 1090447 5216654 165589325 329 27413 JARID2 0 . GRCh38 6 15501152 15501152 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2191G>T p.Glu731Ter p.E731* ENST00000341776 8/18 232 152 80 184 183 1 strelka-varscan-mutect JARID2,stop_gained,p.Glu731Ter,ENST00000341776,NM_004973.3;JARID2,stop_gained,p.Glu559Ter,ENST00000397311,NM_001267040.1;JARID2,upstream_gene_variant,,ENST00000474854,; T ENST00000341776 Transcript stop_gained 2435/5755 2191/3741 731/1246 E/* Gag/Tag 1 1 JARID2 HGNC HGNC:6196 protein_coding YES CCDS4533.1 ENSP00000341280 Q92833 UPI0000161C67 NM_004973.3 8/18 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF44 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 15501152 15501152 G T 1 0 0 0 0 0 1 0 0 7859 1175 41 2 2 JARID2 6 15501152 Nonsense_Mutation SNP G C3N-02089_T 10284498 15501152 155304827 330 27414 HDGFL1 0 . GRCh38 6 22569713 22569713 + Missense_Mutation SNP C C A rs534892452 C3N-02089_T C3N-02089_N C C c.138C>A p.His46Gln p.H46Q ENST00000510882 1/1 382 339 43 329 328 1 strelka-varscan-mutect HDGFL1,missense_variant,p.His46Gln,ENST00000510882,NM_138574.2; A ENST00000510882 Transcript missense_variant 221/2174 138/756 46/251 H/Q caC/caA rs534892452 1 1 HDGFL1 HGNC HGNC:21095 protein_coding YES CCDS34347.1 ENSP00000442129 Q5TGJ6 A0A140VJK8 UPI0000039B1A NM_138574.2 deleterious(0) 1/1 PROSITE_profiles:PS50812,hmmpanther:PTHR12550,hmmpanther:PTHR12550:SF48,Pfam_domain:PF00855,Gene3D:2.30.30.160,SMART_domains:SM00293,Superfamily_domains:SSF63748 MODERATE 1 SNV 1 PASS rs534892452 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 22569713 22569713 C A 1 0 0 0 0 1 0 0 0 6906 535 19 1 1 HDGFL1 6 22569713 Missense_Mutation SNP C C3N-02089_T 7068561 22569713 148236266 331 27415 HIST1H3C 0 . GRCh38 6 26045699 26045699 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.289T>A p.Cys97Ser p.C97S ENST00000612966 1/1 331 301 30 350 350 0 strelka-varscan-mutect HIST1H3C,missense_variant,p.Cys97Ser,ENST00000612966,NM_003531.2;HIST1H2BB,upstream_gene_variant,,ENST00000615966,NM_021062.2;U91328.2,downstream_gene_variant,,ENST00000454320,; A ENST00000612966 Transcript missense_variant 289/411 289/411 97/136 C/S Tgt/Agt 1 1 HIST1H3C HGNC HGNC:4768 protein_coding YES CCDS4576.1 ENSP00000484658 P68431 UPI00000003C7 NM_003531.2 tolerated_low_confidence(1) 1/1 hmmpanther:PTHR11426,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00428,Superfamily_domains:SSF47113,Prints_domain:PR00622 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 26045699 26045699 T A 1 0 0 0 0 1 0 0 0 7045 1812 63 4 4 HIST1H3C 6 26045699 Missense_Mutation SNP T C3N-02089_T 3475986 26045699 144760280 332 27416 HIST1H4G 0 . GRCh38 6 26246956 26246956 + Nonsense_Mutation SNP C C A rs201241505 C3N-02089_T C3N-02089_N C C c.22G>T p.Gly8Ter p.G8* ENST00000611444 1/1 66 49 17 58 58 0 strelka-varscan-mutect HIST1H4G,stop_gained,p.Gly8Ter,ENST00000611444,NM_003547.2;HIST1H2BH,upstream_gene_variant,,ENST00000619466,NM_003524.2;HIST1H3F,downstream_gene_variant,,ENST00000618052,NM_021018.2; A ENST00000611444 Transcript stop_gained 22/297 22/297 8/98 G/* Gga/Tga rs201241505 1 -1 HIST1H4G HGNC HGNC:4792 protein_coding YES CCDS4599.1 ENSP00000477870 Q99525 UPI000006D7D1 NM_003547.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR10484:SF20,hmmpanther:PTHR10484,Gene3D:1.10.20.10,Superfamily_domains:SSF47113,Prints_domain:PR00623 HIGH 1 SNV 1 PASS rs201241505 . 0 201 9 0 0 0 0 0 -20 0.9999979 1 1 1 0 A 4 1 90 26246956 26246956 C A 1 0 0 0 0 0 1 0 0 7059 661 23 1 1 HIST1H4G 6 26246956 Nonsense_Mutation SNP C C3N-02089_T 201257 26246956 144559023 333 27417 POM121L2 0 . GRCh38 6 27311313 27311313 + Missense_Mutation SNP T T C C3N-02089_T C3N-02089_N T T c.858A>G p.Ile286Met p.I286M ENST00000444565 1/1 273 233 40 303 303 0 strelka-varscan-mutect POM121L2,missense_variant,p.Ile286Met,ENST00000444565,NM_033482.3;POM121L2,upstream_gene_variant,,ENST00000429945,; C ENST00000444565 Transcript missense_variant 858/3108 858/3108 286/1035 I/M atA/atG COSM4625733 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 tolerated(0.09) 1/1 Pfam_domain:PF15229,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 27311313 27311313 T C 1 0 0 0 0 1 0 0 0 12353 1744 61 5 5 POM121L2 6 27311313 Missense_Mutation SNP T C3N-02089_T 1064357 27311313 143494666 334 27418 HIST1H2BM 0 . GRCh38 6 27815418 27815418 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.375C>T p.= p.S125S ENST00000621112 1/1 122 90 32 156 156 0 strelka-mutect HIST1H2BM,synonymous_variant,p.=,ENST00000621112,NM_003521.2;HIST1H3H,downstream_gene_variant,,ENST00000369163,NM_003536.2;HIST1H2AJ,upstream_gene_variant,,ENST00000333151,NM_021066.2; T ENST00000621112 Transcript synonymous_variant 375/381 375/381 125/126 S tcC/tcT 1 1 HIST1H2BM HGNC HGNC:4750 protein_coding YES CCDS4629.1 ENSP00000477907 Q99879 UPI0000001BD7 NM_003521.2 1/1 hmmpanther:PTHR23428,Gene3D:1.10.20.10,Superfamily_domains:SSF47113 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 27815418 27815418 C T 1 0 0 0 0 0 0 0 1 7040 581 21 3 3 HIST1H2BM 6 27815418 Silent SNP C C3N-02089_T 504105 27815418 142990561 335 27419 ZBED9 0 . GRCh38 6 28575319 28575319 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1386G>T p.= p.G462G ENST00000452236 3/4 200 175 25 198 198 0 strelka-varscan-mutect ZBED9,synonymous_variant,p.=,ENST00000452236,NM_052923.1;ZBED9,downstream_gene_variant,,ENST00000530247,; A ENST00000452236 Transcript synonymous_variant 2004/4877 1386/3978 462/1325 G ggG/ggT 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 3/4 PROSITE_profiles:PS50994,Gene3D:3.30.420.10,Superfamily_domains:SSF53098 LOW 1 SNV 1 1 PASS rs1190845655 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 28575319 28575319 C A 1 0 0 0 0 0 0 0 1 18086 842 30 2 2 ZBED9 6 28575319 Silent SNP C C3N-02089_T 759901 28575319 142230660 336 27420 TRIM10 0 . GRCh38 6 30154440 30154440 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.975G>T p.Leu325Phe p.L325F ENST00000449742 7/7 148 132 16 127 127 0 strelka-varscan-mutect TRIM10,missense_variant,p.Leu325Phe,ENST00000449742,NM_006778.3;TRIM10,missense_variant,p.Leu325Phe,ENST00000376704,NM_052828.2; A ENST00000449742 Transcript missense_variant 1051/3546 975/1446 325/481 L/F ttG/ttT 1 -1 TRIM10 HGNC HGNC:10072 protein_coding YES CCDS34375.1 ENSP00000397073 Q9UDY6 UPI000000D736 NM_006778.3 deleterious(0) 7/7 Pfam_domain:PF13765,Prints_domain:PR01407,Prints_domain:PR01407,PROSITE_profiles:PS50188,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF329,SMART_domains:SM00589,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.99947 0.9999876 1 1 1 0 A 3 1 90 30154440 30154440 C A 1 0 0 0 0 1 0 0 0 16975 477 17 2 2 TRIM10 6 30154440 Missense_Mutation SNP C C3N-02089_T 1579121 30154440 140651539 337 27421 MDC1 0 . GRCh38 6 30700498 30700498 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.6237T>C p.= p.F2079F ENST00000376406 15/15 130 90 40 113 113 0 strelka-varscan-mutect MDC1,synonymous_variant,p.=,ENST00000376406,NM_014641.2;MDC1,downstream_gene_variant,,ENST00000417033,;MDC1-AS1,upstream_gene_variant,,ENST00000442150,;MDC1,non_coding_transcript_exon_variant,,ENST00000489540,;RPL7P4,upstream_gene_variant,,ENST00000430239,; G ENST00000376406 Transcript synonymous_variant 6885/7576 6237/6270 2079/2089 F ttT/ttC 1 -1 MDC1 HGNC HGNC:21163 protein_coding YES CCDS34384.1 ENSP00000365588 Q14676 UPI00001AF453 NM_014641.2 15/15 hmmpanther:PTHR23196,hmmpanther:PTHR23196:SF1 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 30700498 30700498 A G 1 0 0 0 0 0 0 0 1 9341 127 5 5 5 MDC1 6 30700498 Silent SNP A C3N-02089_T 546058 30700498 140105481 338 27422 COL11A2 0 . GRCh38 6 33164869 33164869 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.4588A>G p.Arg1530Gly p.R1530G ENST00000374708 62/64 67 46 21 15 15 0 strelka-varscan-mutect COL11A2,missense_variant,p.Arg1616Gly,ENST00000341947,NM_080680.2;COL11A2,missense_variant,p.Arg1530Gly,ENST00000374708,NM_080681.2;COL11A2,missense_variant,p.Arg1509Gly,ENST00000361917,NM_080679.2;COL11A2,non_coding_transcript_exon_variant,,ENST00000477772,; C ENST00000374708 Transcript missense_variant 4847/6209 4588/4953 1530/1650 R/G Agg/Ggg 1 -1 COL11A2 HGNC HGNC:2187 protein_coding YES CCDS43452.1 ENSP00000363840 Q4VXY6 UPI000013E9A5 NM_080681.2 tolerated(0.05) 62/64 Pfam_domain:PF01410,PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF509,SMART_domains:SM00038 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 33164869 33164869 T C 1 0 0 0 0 1 0 0 0 3456 1521 53 5 5 COL11A2 6 33164869 Missense_Mutation SNP T C3N-02089_T 2464371 33164869 137641110 339 27423 TRERF1 0 . GRCh38 6 42259394 42259394 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2274G>T p.= p.P758P ENST00000541110 9/18 42 23 19 63 63 0 strelka-varscan-mutect TRERF1,synonymous_variant,p.=,ENST00000541110,NM_001297573.1,NM_001297574.1;TRERF1,synonymous_variant,p.=,ENST00000372922,NM_033502.3;TRERF1,synonymous_variant,p.=,ENST00000340840,;TRERF1,synonymous_variant,p.=,ENST00000354325,;TRERF1,synonymous_variant,p.=,ENST00000372917,; A ENST00000541110 Transcript synonymous_variant 2843/7646 2274/3663 758/1220 P ccG/ccT 1 -1 TRERF1 HGNC HGNC:18273 protein_coding YES CCDS75455.1 ENSP00000439689 Q05GC8 UPI000022CBC8 NM_001297573.1,NM_001297574.1 9/18 hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF19,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1249808642 . 0 199 11 0 0 0 0 0 -20 0.9999953 1 1 1 0 A 2 1 90 42259394 42259394 C A 1 0 0 0 0 0 0 0 1 16964 755 27 1 1 TRERF1 6 42259394 Silent SNP C C3N-02089_T 9094525 42259394 128546585 340 27424 ADGRF5 0 . GRCh38 6 46856779 46856779 + Splice_Site SNP T T C novel C3N-02089_T C3N-02089_N T T c.3817-2A>G p.X1273_splice ENST00000283296 149 136 13 167 167 0 varscan-mutect ADGRF5,splice_acceptor_variant,,ENST00000283296,NM_001098518.1;ADGRF5,splice_acceptor_variant,,ENST00000265417,NM_015234.4;ADGRF5,downstream_gene_variant,,ENST00000498632,; C ENST00000283296 Transcript splice_acceptor_variant -/5810 3817/4041 1273/1346 1 -1 ADGRF5 HGNC HGNC:19030 protein_coding YES CCDS4919.1 ENSP00000283296 Q8IZF2 UPI000007075A NM_001098518.1 18/20 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -18.07259 0.9999806 1 1 1 0 C 5 2 90 46856779 46856779 T C 1 0 0 0 0 0 0 1 0 367 1594 55 5 5 ADGRF5 6 46856779 Splice_Site SNP T C3N-02089_T 4597385 46856779 123949200 341 27425 OPN5 0 . GRCh38 6 47808352 47808352 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.955G>C p.Gly319Arg p.G319R ENST00000371211 5/7 215 187 28 158 158 0 strelka-varscan-mutect OPN5,missense_variant,p.Gly319Arg,ENST00000489301,;OPN5,missense_variant,p.Gly319Arg,ENST00000371211,NM_181744.3;OPN5,missense_variant,p.Gly319Arg,ENST00000393699,;OPN5,non_coding_transcript_exon_variant,,ENST00000244799,; C ENST00000371211 Transcript missense_variant 983/1801 955/1065 319/354 G/R Ggt/Cgt 1 1 OPN5 HGNC HGNC:19992 protein_coding YES CCDS4923.1 ENSP00000360255 Q6U736 UPI0000223E5B NM_181744.3 tolerated_low_confidence(0.46) 5/7 hmmpanther:PTHR24240:SF0,hmmpanther:PTHR24240 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 47808352 47808352 G C 1 0 0 0 0 1 0 0 0 10959 1348 47 4 4 OPN5 6 47808352 Missense_Mutation SNP G C3N-02089_T 951573 47808352 122997627 342 27426 MUT 0 . GRCh38 6 49453707 49453707 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.961A>T p.Lys321Ter p.K321* ENST00000274813 5/13 203 184 19 228 227 1 strelka-varscan-mutect MUT,stop_gained,p.Lys321Ter,ENST00000274813,NM_000255.3; A ENST00000274813 Transcript stop_gained 1089/3749 961/2253 321/750 K/* Aag/Tag 1 -1 MUT HGNC HGNC:7526 protein_coding YES CCDS4924.1 ENSP00000274813 P22033 A0A024RD82 UPI000013DA28 NM_000255.3 5/13 hmmpanther:PTHR23408,hmmpanther:PTHR23408:SF1,Gene3D:3.20.20.240,TIGRFAM_domain:TIGR00641,Pfam_domain:PF01642,Superfamily_domains:SSF51703 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 49453707 49453707 T A 1 0 0 0 0 0 1 0 0 9989 1850 64 4 4 MUT 6 49453707 Nonsense_Mutation SNP T C3N-02089_T 1645355 49453707 121352272 343 27427 CRISP1 0 . GRCh38 6 49846549 49846549 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.406G>C p.Asp136His p.D136H ENST00000335847 5/8 133 113 20 111 111 0 strelka-varscan-mutect CRISP1,missense_variant,p.Asp136His,ENST00000335847,NM_001131.2;CRISP1,missense_variant,p.Asp136His,ENST00000507853,NM_170609.1;CRISP1,missense_variant,p.Asp136His,ENST00000329411,;CRISP1,missense_variant,p.Asp136His,ENST00000505118,NM_001205220.1; G ENST00000335847 Transcript missense_variant 508/1911 406/750 136/249 D/H Gat/Cat 1 -1 CRISP1 HGNC HGNC:304 protein_coding YES CCDS4931.1 ENSP00000338276 P54107 A0A0K0K1I1 UPI0000128482 NM_001131.2 deleterious(0.03) 5/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10334:SF213,hmmpanther:PTHR10334,Gene3D:3.40.33.10,Pfam_domain:PF00188,SMART_domains:SM00198,Superfamily_domains:SSF55797 MODERATE 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999934 1 1 1 0 G 3 3 90 49846549 49846549 C G 1 0 0 0 0 1 0 0 0 3680 826 29 4 4 CRISP1 6 49846549 Missense_Mutation SNP C C3N-02089_T 392842 49846549 120959430 344 27428 PKHD1 0 . GRCh38 6 52025477 52025477 + Missense_Mutation SNP C C A rs751965771 C3N-02089_T C3N-02089_N C C c.4333G>T p.Val1445Phe p.V1445F ENST00000371117 32/67 78 50 28 97 97 0 strelka-mutect PKHD1,missense_variant,p.Val1445Phe,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Val1445Phe,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 4609/16282 4333/12225 1445/4074 V/F Gtt/Ttt rs751965771,COSM5654073,COSM5654074 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.03) 32/67 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs751965771 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 52025477 52025477 C A 1 0 0 0 0 1 0 0 0 12067 507 18 2 2 PKHD1 6 52025477 Missense_Mutation SNP C C3N-02089_T 2178928 52025477 118780502 345 27429 PKHD1 0 . GRCh38 6 52028305 52028305 + Silent SNP C C A rs138350291 C3N-02089_T C3N-02089_N C C c.3411G>T p.= p.T1137T ENST00000371117 30/67 396 269 127 377 376 1 strelka-varscan-mutect PKHD1,synonymous_variant,p.=,ENST00000371117,NM_138694.3;PKHD1,synonymous_variant,p.=,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript synonymous_variant 3687/16282 3411/12225 1137/4074 T acG/acT rs138350291,COSM1080197,COSM1596396 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 30/67 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs138350291 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 52028305 52028305 C A 1 0 0 0 0 0 0 0 1 12067 639 23 1 1 PKHD1 6 52028305 Silent SNP C C3N-02089_T 2828 52028305 118777674 346 27430 PKHD1 0 . GRCh38 6 52042892 52042892 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3064G>T p.Asp1022Tyr p.D1022Y ENST00000371117 27/67 184 124 60 234 234 0 strelka-varscan-mutect PKHD1,missense_variant,p.Asp1022Tyr,ENST00000371117,NM_138694.3;PKHD1,missense_variant,p.Asp1022Tyr,ENST00000340994,NM_170724.2; A ENST00000371117 Transcript missense_variant 3340/16282 3064/12225 1022/4074 D/Y Gat/Tat 1 -1 PKHD1 HGNC HGNC:9016 protein_coding YES CCDS4935.1 ENSP00000360158 P08F94 UPI000013C4C0 NM_138694.3 deleterious(0.04) 27/67 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs1257425837 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 52042892 52042892 C A 1 0 0 0 0 1 0 0 0 12067 855 30 2 2 PKHD1 6 52042892 Missense_Mutation SNP C C3N-02089_T 14587 52042892 118763087 347 27431 FAM83B 0 . GRCh38 6 54941068 54941068 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2097C>A p.= p.P699P ENST00000306858 5/5 126 111 15 121 120 1 strelka-varscan-mutect FAM83B,synonymous_variant,p.=,ENST00000306858,NM_001010872.2;RP3-523K23.2,upstream_gene_variant,,ENST00000562834,; A ENST00000306858 Transcript synonymous_variant 2213/3167 2097/3036 699/1011 P ccC/ccA 1 1 FAM83B HGNC HGNC:21357 protein_coding YES CCDS34479.1 ENSP00000304078 Q5T0W9 UPI00001D81EC NM_001010872.2 5/5 hmmpanther:PTHR16181:SF4,hmmpanther:PTHR16181 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -19.99894 0.9999999 1 1 1 0 A 2 1 90 54941068 54941068 C A 1 0 0 0 0 0 0 0 1 5492 581 21 2 2 FAM83B 6 54941068 Silent SNP C C3N-02089_T 2898176 54941068 115864911 348 27432 HMGCLL1 0 . GRCh38 6 55495523 55495523 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.781A>T p.Arg261Ter p.R261* ENST00000398661 8/10 154 130 24 164 164 0 strelka-varscan-mutect HMGCLL1,stop_gained,p.Arg261Ter,ENST00000398661,NM_019036.2;HMGCLL1,stop_gained,p.Arg231Ter,ENST00000274901,NM_001287746.1,NM_001042406.1;HMGCLL1,stop_gained,p.Arg199Ter,ENST00000308161,NM_001287741.1;HMGCLL1,stop_gained,p.Arg128Ter,ENST00000370850,NM_001287753.1;HMGCLL1,intron_variant,,ENST00000508459,;HMGCLL1,3_prime_UTR_variant,,ENST00000370852,; A ENST00000398661 Transcript stop_gained 913/2532 781/1113 261/370 R/* Aga/Tga 1 -1 HMGCLL1 HGNC HGNC:21359 protein_coding YES CCDS43475.1 ENSP00000381654 Q8TB92 UPI000023780E NM_019036.2 8/10 Gene3D:3.20.20.70,Pfam_domain:PF00682,PROSITE_profiles:PS50991,hmmpanther:PTHR10277,hmmpanther:PTHR10277:SF33,Superfamily_domains:SSF51569 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 55495523 55495523 T A 1 0 0 0 0 0 1 0 0 7122 1617 56 4 4 HMGCLL1 6 55495523 Nonsense_Mutation SNP T C3N-02089_T 554455 55495523 115310456 349 27433 LGSN 0 . GRCh38 6 63280110 63280110 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1441A>C p.Ile481Leu p.I481L ENST00000370657 4/4 190 167 23 201 201 0 strelka-varscan-mutect LGSN,missense_variant,p.Ile481Leu,ENST00000370657,NM_016571.2;LGSN,3_prime_UTR_variant,,ENST00000370658,NM_001143940.1;LGSN,3_prime_UTR_variant,,ENST00000622415,;LGSN,intron_variant,,ENST00000485906,; G ENST00000370657 Transcript missense_variant 1475/1949 1441/1530 481/509 I/L Att/Ctt 1 -1 LGSN HGNC HGNC:21016 protein_coding YES CCDS4964.1 ENSP00000359691 Q5TDP6 UPI000013DA35 NM_016571.2 deleterious(0.01) 4/4 hmmpanther:PTHR20852,hmmpanther:PTHR20852:SF7,Gene3D:3.30.590.10,Pfam_domain:PF00120,Superfamily_domains:SSF55931 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 63280110 63280110 T G 1 0 0 0 0 1 0 0 0 8669 1406 49 5 5 LGSN 6 63280110 Missense_Mutation SNP T C3N-02089_T 7784587 63280110 107525869 350 27434 ADGRB3 0 . GRCh38 6 69382911 69382911 + Silent SNP G G C C3N-02089_T C3N-02089_N G G c.4356G>C p.= p.R1452R ENST00000370598 31/32 120 108 12 118 118 0 strelka-mutect ADGRB3,synonymous_variant,p.=,ENST00000370598,NM_001704.2;ADGRB3,synonymous_variant,p.=,ENST00000546190,;ADGRB3,synonymous_variant,p.=,ENST00000238918,; C ENST00000370598 Transcript synonymous_variant 5177/6010 4356/4569 1452/1522 R cgG/cgC COSM3629266 1 1 ADGRB3 HGNC HGNC:945 protein_coding YES CCDS4968.1 ENSP00000359630 O60242 UPI00001AE6A9 NM_001704.2 31/32 1 LOW 1 SNV 1 1 1 PASS rs1478638766 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 69382911 69382911 G C 1 0 0 0 0 0 0 0 1 357 1219 43 4 4 ADGRB3 6 69382911 Silent SNP G C3N-02089_T 6102801 69382911 101423068 351 27435 B3GAT2 0 . GRCh38 6 70956046 70956046 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.384C>T p.= p.R128R ENST00000230053 1/4 124 95 29 110 110 0 strelka-varscan-mutect B3GAT2,synonymous_variant,p.=,ENST00000230053,NM_080742.2;B3GAT2,intron_variant,,ENST00000615536,; A ENST00000230053 Transcript synonymous_variant 993/6565 384/972 128/323 R cgC/cgT 1 -1 B3GAT2 HGNC HGNC:922 protein_coding YES CCDS4974.1 ENSP00000230053 Q9NPZ5 UPI000012670C NM_080742.2 1/4 hmmpanther:PTHR10896,hmmpanther:PTHR10896:SF8,Gene3D:3.90.550.10,Pfam_domain:PF03360,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 70956046 70956046 G A 1 0 0 0 0 0 0 0 1 1410 958 34 3 3 B3GAT2 6 70956046 Silent SNP G C3N-02089_T 1573135 70956046 99849933 352 27436 RIMS1 0 . GRCh38 6 72179846 72179846 + Missense_Mutation SNP C C T rs116476753 C3N-02089_T C3N-02089_N C C c.743C>T p.Ser248Leu p.S248L ENST00000521978 5/34 57 51 6 60 60 0 strelka-varscan-mutect RIMS1,missense_variant,p.Ser248Leu,ENST00000264839,;RIMS1,missense_variant,p.Ser248Leu,ENST00000521978,NM_014989.5;RIMS1,missense_variant,p.Ser248Leu,ENST00000491071,;RIMS1,missense_variant,p.Ser248Leu,ENST00000520567,;RIMS1,missense_variant,p.Ser248Leu,ENST00000517960,;RIMS1,missense_variant,p.Ser248Leu,ENST00000518273,;RIMS1,missense_variant,p.Ser248Leu,ENST00000522291,;RIMS1,upstream_gene_variant,,ENST00000517433,;RIMS1,non_coding_transcript_exon_variant,,ENST00000370419,; T ENST00000521978 Transcript missense_variant 743/5079 743/5079 248/1692 S/L tCg/tTg rs116476753 1 1 RIMS1 HGNC HGNC:17282 protein_coding YES CCDS47449.1 ENSP00000428417 Q86UR5 UPI00001908FB NM_014989.5 tolerated(0.13) 5/34 hmmpanther:PTHR12157:SF19,hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS rs116476753 . 0 192 5 0 0 0 0 13 -2.608566 0 0 1 0 0 T 3 4 90 72179846 72179846 C T 1 0 0 0 0 1 0 0 0 13542 893 31 1 1 RIMS1 6 72179846 Missense_Mutation SNP C C3N-02089_T 1223800 72179846 98626133 353 27437 CD109 0 . GRCh38 6 73782692 73782692 + Missense_Mutation SNP G G T rs750387262 C3N-02089_T C3N-02089_N G G c.2042G>T p.Gly681Val p.G681V ENST00000287097 18/33 136 90 46 189 189 0 strelka-varscan-mutect CD109,missense_variant,p.Gly681Val,ENST00000437994,NM_001159587.2;CD109,missense_variant,p.Gly604Val,ENST00000422508,NM_001159588.2;CD109,missense_variant,p.Gly681Val,ENST00000287097,NM_133493.4; T ENST00000287097 Transcript missense_variant 2154/9130 2042/4338 681/1445 G/V gGt/gTt rs750387262 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 tolerated(0.34) 18/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80 MODERATE 1 SNV 1 1 PASS rs750387262 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 73782692 73782692 G T 1 0 0 0 0 1 0 0 0 2666 1261 44 2 2 CD109 6 73782692 Missense_Mutation SNP G C3N-02089_T 1602846 73782692 97023287 354 27438 IMPG1 0 . GRCh38 6 76022180 76022180 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.602C>G p.Pro201Arg p.P201R ENST00000369950 6/17 244 175 69 285 285 0 strelka-varscan-mutect IMPG1,missense_variant,p.Pro201Arg,ENST00000369950,NM_001563.3;IMPG1,missense_variant,p.Pro123Arg,ENST00000611179,NM_001282368.1;IMPG1,downstream_gene_variant,,ENST00000369963,; C ENST00000369950 Transcript missense_variant 792/3558 602/2394 201/797 P/R cCt/cGt 1 -1 IMPG1 HGNC HGNC:6055 protein_coding YES CCDS4985.1 ENSP00000358966 Q17R60 UPI0000073F12 NM_001563.3 deleterious(0.03) 6/17 hmmpanther:PTHR12199 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 76022180 76022180 G C 1 0 0 0 0 1 0 0 0 7630 1000 35 4 4 IMPG1 6 76022180 Missense_Mutation SNP G C3N-02089_T 2239488 76022180 94783799 355 27439 IMPG1 0 . GRCh38 6 76034789 76034789 + Splice_Site SNP T T A novel C3N-02089_T C3N-02089_N T T c.302-2A>T p.X101_splice ENST00000369950 51 31 20 62 62 0 strelka-varscan-mutect IMPG1,splice_acceptor_variant,,ENST00000369950,NM_001563.3;IMPG1,splice_acceptor_variant,,ENST00000611179,NM_001282368.1;IMPG1,splice_acceptor_variant,,ENST00000369963,; A ENST00000369950 Transcript splice_acceptor_variant -/3558 302/2394 101/797 1 -1 IMPG1 HGNC HGNC:6055 protein_coding YES CCDS4985.1 ENSP00000358966 Q17R60 UPI0000073F12 NM_001563.3 2/16 HIGH 1 SNV 1 1 PASS rs1468714735 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 76034789 76034789 T A 1 0 0 0 0 0 0 1 0 7630 1594 55 4 4 IMPG1 6 76034789 Splice_Site SNP T C3N-02089_T 12609 76034789 94771190 356 27440 PRDM13 0 . GRCh38 6 99609220 99609220 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.310G>T p.Gly104Trp p.G104W ENST00000369215 3/4 221 150 71 201 201 0 strelka-varscan-mutect PRDM13,missense_variant,p.Gly104Trp,ENST00000369215,NM_021620.3;PRDM13,missense_variant,p.Arg113Met,ENST00000369214,; T ENST00000369215 Transcript missense_variant 615/2429 310/2124 104/707 G/W Ggg/Tgg 1 1 PRDM13 HGNC HGNC:13998 protein_coding YES CCDS43487.1 ENSP00000358217 Q9H4Q3 UPI000047099D NM_021620.3 deleterious(0) 3/4 PROSITE_profiles:PS50280,Gene3D:2.170.270.10,Superfamily_domains:SSF82199 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 99609220 99609220 G T 1 0 0 0 0 1 0 0 0 12585 1000 35 2 2 PRDM13 6 99609220 Missense_Mutation SNP G C3N-02089_T 23574431 99609220 71196759 357 27441 MCHR2 0 . GRCh38 6 99956006 99956006 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.142G>C p.Gly48Arg p.G48R ENST00000281806 2/6 88 62 26 80 80 0 strelka-varscan-mutect MCHR2,missense_variant,p.Gly48Arg,ENST00000281806,NM_001040179.1;MCHR2,missense_variant,p.Gly48Arg,ENST00000369212,NM_032503.2; G ENST00000281806 Transcript missense_variant 457/2368 142/1023 48/340 G/R Ggg/Cgg 1 -1 MCHR2 HGNC HGNC:20867 protein_coding YES CCDS5044.1 ENSP00000281806 Q969V1 UPI000003730F NM_001040179.1 deleterious(0) 2/6 Transmembrane_helices:TMhelix,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF7,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 99956006 99956006 C G 1 0 0 0 0 1 0 0 0 9314 681 24 4 4 MCHR2 6 99956006 Missense_Mutation SNP C C3N-02089_T 346786 99956006 70849973 358 27442 GRIK2 0 . GRCh38 6 101682564 101682564 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.735G>T p.Met245Ile p.M245I ENST00000421544 5/16 95 65 30 143 143 0 strelka-varscan-mutect GRIK2,missense_variant,p.Met245Ile,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Met245Ile,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Met245Ile,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Met207Ile,ENST00000318991,;GRIK2,missense_variant,p.Met207Ile,ENST00000369137,;GRIK2,missense_variant,p.Met207Ile,ENST00000369134,;GRIK2,missense_variant,p.Met245Ile,ENST00000358361,;GRIK2,missense_variant,p.Met16Ile,ENST00000455610,; T ENST00000421544 Transcript missense_variant 1225/4789 735/2727 245/908 M/I atG/atT 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 tolerated(0.38) 5/16 Gene3D:3.40.50.2300,Pfam_domain:PF01094,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38,Superfamily_domains:SSF53822 MODERATE 1 SNV 1 1 PASS . . 1 206 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 101682564 101682564 G T 1 0 0 0 0 1 0 0 0 6656 1348 47 2 2 GRIK2 6 101682564 Missense_Mutation SNP G C3N-02089_T 1726558 101682564 69123415 359 27443 GRIK2 0 . GRCh38 6 102055566 102055566 + Missense_Mutation SNP G G T rs778896944 C3N-02089_T C3N-02089_N G G c.2548G>T p.Ala850Ser p.A850S ENST00000421544 15/16 94 64 30 107 106 1 strelka-varscan-mutect GRIK2,missense_variant,p.Ala850Ser,ENST00000369138,NM_001166247.1;GRIK2,missense_variant,p.Ala850Ser,ENST00000413795,NM_175768.3;GRIK2,missense_variant,p.Ala850Ser,ENST00000421544,NM_021956.4;GRIK2,missense_variant,p.Ala812Ser,ENST00000318991,;GRIK2,missense_variant,p.Ala812Ser,ENST00000369137,;GRIK2,missense_variant,p.Ala812Ser,ENST00000369134,; T ENST00000421544 Transcript missense_variant 3038/4789 2548/2727 850/908 A/S Gct/Tct rs778896944,COSM393020,COSM393021 1 1 GRIK2 HGNC HGNC:4580 protein_coding YES CCDS5048.1 ENSP00000397026 Q13002 UPI000012B617 NM_021956.4 tolerated(0.2) 15/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF38 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs778896944 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 102055566 102055566 G T 1 0 0 0 0 1 0 0 0 6656 1087 38 1 1 GRIK2 6 102055566 Missense_Mutation SNP G C3N-02089_T 373002 102055566 68750413 360 27444 SESN1 0 . GRCh38 6 109009420 109009420 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.41C>T p.Pro14Leu p.P14L ENST00000356644 1/10 122 80 42 76 76 0 strelka-varscan-mutect SESN1,missense_variant,p.Pro14Leu,ENST00000356644,NM_001199933.1;SESN1,intron_variant,,ENST00000436639,NM_014454.2;SESN1,upstream_gene_variant,,ENST00000302071,NM_001199934.1; A ENST00000356644 Transcript missense_variant 136/2676 41/1479 14/492 P/L cCt/cTt 1 -1 SESN1 HGNC HGNC:21595 protein_coding CCDS56445.1 ENSP00000349061 Q9Y6P5 UPI000013588F NM_001199933.1 tolerated_low_confidence(0.06) 1/10 PROSITE_profiles:PS51257 MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 109009420 109009420 G A 1 0 0 0 0 1 0 0 0 14401 1000 35 3 3 SESN1 6 109009420 Missense_Mutation SNP G C3N-02089_T 6953854 109009420 61796559 361 27445 LAMA4 0 . GRCh38 6 112165217 112165217 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.1611T>A p.= p.S537S ENST00000230538 13/39 378 323 55 391 391 0 strelka-varscan-mutect LAMA4,synonymous_variant,p.=,ENST00000230538,NM_001105206.2;LAMA4,synonymous_variant,p.=,ENST00000522006,NM_001105207.2,NM_002290.4;LAMA4,synonymous_variant,p.=,ENST00000389463,;LAMA4,synonymous_variant,p.=,ENST00000424408,;RP1-142L7.5,intron_variant,,ENST00000626024,;RP1-142L7.5,intron_variant,,ENST00000585373,;RP1-142L7.5,intron_variant,,ENST00000629996,;RP1-142L7.5,downstream_gene_variant,,ENST00000625600,;LAMA4,upstream_gene_variant,,ENST00000523765,; T ENST00000230538 Transcript synonymous_variant 2009/6547 1611/5472 537/1823 S tcT/tcA 1 -1 LAMA4 HGNC HGNC:6484 protein_coding YES CCDS43491.1 ENSP00000230538 A0A0A0MQS9 UPI000153D541 NM_001105206.2 13/39 hmmpanther:PTHR10574:SF277,hmmpanther:PTHR10574,Pfam_domain:PF06008 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 112165217 112165217 A T 1 0 0 0 0 0 0 0 1 8512 175 7 4 4 LAMA4 6 112165217 Silent SNP A C3N-02089_T 3155797 112165217 58640762 362 27446 RFX6 0 . GRCh38 6 116928806 116928806 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.2446T>C p.Ser816Pro p.S816P ENST00000332958 18/19 317 196 121 291 291 0 strelka-varscan-mutect RFX6,missense_variant,p.Ser816Pro,ENST00000332958,NM_173560.3; C ENST00000332958 Transcript missense_variant 2462/3460 2446/2787 816/928 S/P Tca/Cca 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 tolerated_low_confidence(0.26) 18/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 116928806 116928806 T C 1 0 0 0 0 1 0 0 0 13441 1435 50 5 5 RFX6 6 116928806 Missense_Mutation SNP T C3N-02089_T 4763589 116928806 53877173 363 27447 SLC35F1 0 . GRCh38 6 118267115 118267116 + Frame_Shift_Ins INS - - T novel C3N-02089_T C3N-02089_N - - c.599dupT p.Ala202SerfsTer15 p.A202Sfs*15 ENST00000360388 4/8 130 84 46 142 142 0 sindel-varindel SLC35F1,frameshift_variant,p.Ala202SerfsTer15,ENST00000360388,NM_001029858.3;SLC35F1,frameshift_variant,p.Ala143SerfsTer15,ENST00000621341,; T ENST00000360388 Transcript frameshift_variant 799-800/4852 598-599/1227 200/408 V/VX gtg/gTtg 1 1 SLC35F1 HGNC HGNC:21483 protein_coding YES CCDS34524.1 ENSP00000353557 Q5T1Q4 UPI00001609C1 NM_001029858.3 4/8 Superfamily_domains:0043518,Pfam_domain:PF06027,hmmpanther:PTHR14233,hmmpanther:PTHR14233:SF10,Transmembrane_helices:TMhelix HIGH 1 insertion 1 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 90 118267115 118267115 - T 1 0 1 1 0 0 0 0 0 14859 1261 44 0 0 SLC35F1 6 118267115 Frame_Shift_Ins INS - C3N-02089_T 1338309 118267115 52538864 364 27448 TRDN 0 . GRCh38 6 123218623 123218623 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.2168G>A p.Gly723Glu p.G723E ENST00000334268 41/41 124 74 50 136 136 0 strelka-varscan-mutect TRDN,missense_variant,p.Gly723Glu,ENST00000334268,NM_006073.3; T ENST00000334268 Transcript missense_variant 2486/4770 2168/2190 723/729 G/E gGa/gAa 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 deleterious_low_confidence(0.03) 41/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 123218623 123218623 C T 1 0 0 0 0 1 0 0 0 16957 855 30 3 3 TRDN 6 123218623 Missense_Mutation SNP C C3N-02089_T 4951508 123218623 47587356 365 27449 TRDN 0 . GRCh38 6 123548612 123548612 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.233C>A p.Ala78Glu p.A78E ENST00000334268 3/41 47 32 15 60 60 0 strelka-varscan-mutect TRDN,missense_variant,p.Ala78Glu,ENST00000334268,NM_006073.3;TRDN,missense_variant,p.Ala78Glu,ENST00000628709,NM_001256020.1;TRDN,missense_variant,p.Ala78Glu,ENST00000542443,NM_001256022.1;TRDN,missense_variant,p.Ala78Glu,ENST00000546248,NM_001256021.1; T ENST00000334268 Transcript missense_variant,splice_region_variant 551/4770 233/2190 78/729 A/E gCa/gAa 1 -1 TRDN HGNC HGNC:12261 protein_coding YES CCDS55053.1 ENSP00000333984 Q13061 UPI0000D820CC NM_006073.3 deleterious_low_confidence(0) 3/41 hmmpanther:PTHR14106,hmmpanther:PTHR14106:SF0,Pfam_domain:PF05279 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 90 123548612 123548612 G T 1 0 0 0 0 1 0 0 0 16957 1333 46 2 2 TRDN 6 123548612 Missense_Mutation SNP G C3N-02089_T 329989 123548612 47257367 366 27450 L3MBTL3 0 . GRCh38 6 130133466 130133466 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1981C>A p.Pro661Thr p.P661T ENST00000529410 23/25 100 65 35 110 110 0 strelka-varscan-mutect L3MBTL3,missense_variant,p.Pro661Thr,ENST00000529410,;L3MBTL3,missense_variant,p.Pro661Thr,ENST00000368136,;L3MBTL3,missense_variant,p.Pro661Thr,ENST00000361794,NM_032438.2;L3MBTL3,missense_variant,p.Pro636Thr,ENST00000368139,;L3MBTL3,missense_variant,p.Pro636Thr,ENST00000526019,;L3MBTL3,missense_variant,p.Pro636Thr,ENST00000533560,NM_001007102.2;RP11-73O6.3,non_coding_transcript_exon_variant,,ENST00000415964,;RP11-73O6.3,downstream_gene_variant,,ENST00000614735,;RP11-73O6.3,downstream_gene_variant,,ENST00000609978,;RP11-73O6.3,downstream_gene_variant,,ENST00000622734,;RP11-73O6.3,downstream_gene_variant,,ENST00000591297,;RP11-73O6.3,downstream_gene_variant,,ENST00000617353,; A ENST00000529410 Transcript missense_variant 2460/4518 1981/2343 661/780 P/T Ccc/Acc 1 1 L3MBTL3 HGNC HGNC:23035 protein_coding YES CCDS34537.1 ENSP00000431962 Q96JM7 UPI00001C1E3E tolerated(0.39) 23/25 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF72 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 130133466 130133466 C A 1 0 0 0 0 1 0 0 0 8495 507 18 2 2 L3MBTL3 6 130133466 Missense_Mutation SNP C C3N-02089_T 6584854 130133466 40672513 367 27451 EPB41L2 0 . GRCh38 6 130885167 130885167 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1762C>A p.Gln588Lys p.Q588K ENST00000337057 12/20 263 224 39 234 234 0 strelka-varscan-mutect EPB41L2,missense_variant,p.Gln588Lys,ENST00000337057,NM_001431.3;EPB41L2,missense_variant,p.Gln588Lys,ENST00000368128,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000628542,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000527411,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000530481,NM_001199388.2;EPB41L2,missense_variant,p.Gln588Lys,ENST00000445890,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000528282,NM_001252660.1;EPB41L2,missense_variant,p.Gln588Lys,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,missense_variant,p.Gln588Lys,ENST00000529208,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000525271,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000527659,;EPB41L2,missense_variant,p.Gln588Lys,ENST00000525193,;EPB41L2,missense_variant,p.Gln79Lys,ENST00000456097,;EPB41L2,upstream_gene_variant,,ENST00000530757,;EPB41L2,upstream_gene_variant,,ENST00000524581,;EPB41L2,upstream_gene_variant,,ENST00000531410,;EPB41L2,upstream_gene_variant,,ENST00000525198,;EPB41L2,upstream_gene_variant,,ENST00000527423,;EPB41L2,upstream_gene_variant,,ENST00000527017,; T ENST00000337057 Transcript missense_variant 1944/4457 1762/3018 588/1005 Q/K Caa/Aaa 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 tolerated(0.55) 12/20 PIRSF_domain:PIRSF002304,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF17 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 130885167 130885167 G T 1 0 0 0 0 1 0 0 0 5000 1386 48 2 2 EPB41L2 6 130885167 Missense_Mutation SNP G C3N-02089_T 751701 130885167 39920812 368 27452 TAAR9 0 . GRCh38 6 132539138 132539138 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.849T>C p.= p.Y283Y ENST00000434551 1/1 59 36 23 83 83 0 strelka-varscan-mutect TAAR9,synonymous_variant,p.=,ENST00000434551,NM_175057.3; C ENST00000434551 Transcript synonymous_variant 849/1047 849/1047 283/348 Y taT/taC 1 1 TAAR9 HGNC HGNC:20977 protein_coding YES CCDS75520.1 ENSP00000424607 Q96RI9 UPI000000D880 NM_175057.3 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF79,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01830 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 132539138 132539138 T C 1 0 0 0 0 0 0 0 1 15890 1413 49 5 5 TAAR9 6 132539138 Silent SNP T C3N-02089_T 1653971 132539138 38266841 369 27453 TAAR6 0 . GRCh38 6 132570538 132570538 + Missense_Mutation SNP T T C C3N-02089_T C3N-02089_N T T c.217T>C p.Ser73Pro p.S73P ENST00000275198 1/1 240 213 27 237 237 0 strelka-varscan-mutect TAAR6,missense_variant,p.Ser73Pro,ENST00000275198,NM_175067.1; C ENST00000275198 Transcript missense_variant 217/1038 217/1038 73/345 S/P Tct/Cct COSM594293 1 1 TAAR6 HGNC HGNC:20978 protein_coding YES CCDS5155.1 ENSP00000275198 Q96RI8 UPI000000D881 NM_175067.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF271,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 132570538 132570538 T C 1 0 0 0 0 1 0 0 0 15888 1551 54 5 5 TAAR6 6 132570538 Missense_Mutation SNP T C3N-02089_T 31400 132570538 38235441 370 27454 NMBR 0 . GRCh38 6 142088397 142088397 + Missense_Mutation SNP C C G C3N-02089_T C3N-02089_N C C c.262G>C p.Gly88Arg p.G88R ENST00000258042 1/3 320 299 21 306 303 3 strelka-varscan-mutect NMBR,missense_variant,p.Gly88Arg,ENST00000258042,NM_002511.2;RP11-137J7.2,intron_variant,,ENST00000454401,; G ENST00000258042 Transcript missense_variant 403/1354 262/1173 88/390 G/R Ggg/Cgg COSM1440864 1 -1 NMBR HGNC HGNC:7843 protein_coding YES CCDS5196.1 ENSP00000258042 P28336 UPI000013CFAB NM_002511.2 deleterious(0) 1/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF53,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 0 2 0 0 0 -5.49152 0.9852734 1 1 1 0 G 3 3 90 142088397 142088397 C G 1 0 0 0 0 1 0 0 0 10525 652 23 4 4 NMBR 6 142088397 Missense_Mutation SNP C C3N-02089_T 9517859 142088397 28717582 371 27455 ADGRG6 0 . GRCh38 6 142419922 142419922 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.3137A>T p.Gln1046Leu p.Q1046L ENST00000367609 22/25 300 273 27 254 254 0 strelka-mutect ADGRG6,missense_variant,p.Gln1046Leu,ENST00000230173,NM_020455.5;ADGRG6,missense_variant,p.Gln1046Leu,ENST00000367609,NM_198569.2;ADGRG6,missense_variant,p.Gln1018Leu,ENST00000367608,NM_001032395.2;ADGRG6,missense_variant,p.Gln1018Leu,ENST00000296932,NM_001032394.2;ADGRG6,non_coding_transcript_exon_variant,,ENST00000472054,; T ENST00000367609 Transcript missense_variant 3538/6887 3137/3753 1046/1250 Q/L cAg/cTg 1 1 ADGRG6 HGNC HGNC:13841 protein_coding YES CCDS47489.1 ENSP00000356581 Q86SQ4 UPI000022CCE4 NM_198569.2 deleterious(0) 22/25 Gene3D:1.20.1070.10,Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF290,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 142419922 142419922 A T 1 0 0 0 0 1 0 0 0 373 188 7 4 4 ADGRG6 6 142419922 Missense_Mutation SNP A C3N-02089_T 331525 142419922 28386057 372 27456 AKAP12 0 . GRCh38 6 151349024 151349024 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.633G>T p.= p.G211G ENST00000402676 4/5 139 100 39 157 157 0 strelka-varscan-mutect AKAP12,synonymous_variant,p.=,ENST00000402676,NM_005100.3;AKAP12,synonymous_variant,p.=,ENST00000253332,;AKAP12,synonymous_variant,p.=,ENST00000354675,NM_144497.2;AKAP12,synonymous_variant,p.=,ENST00000359755,;AKAP12,non_coding_transcript_exon_variant,,ENST00000490177,; T ENST00000402676 Transcript synonymous_variant 873/8432 633/5349 211/1782 G ggG/ggT 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR23209 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 151349024 151349024 G T 1 0 0 0 0 0 0 0 1 531 1219 43 2 2 AKAP12 6 151349024 Silent SNP G C3N-02089_T 8929102 151349024 19456955 373 27457 SYNE1 0 . GRCh38 6 152148171 152148171 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.24850G>T p.Glu8284Ter p.E8284* ENST00000367255 137/146 167 117 50 142 142 0 strelka-varscan-mutect SYNE1,stop_gained,p.Glu8284Ter,ENST00000367255,NM_182961.3;SYNE1,stop_gained,p.Glu8213Ter,ENST00000423061,NM_033071.3;SYNE1,stop_gained,p.Glu7879Ter,ENST00000341594,;SYNE1,stop_gained,p.Glu1206Ter,ENST00000367251,;SYNE1,stop_gained,p.Glu930Ter,ENST00000367257,;SYNE1,stop_gained,p.Glu439Ter,ENST00000539504,;SYNE1,stop_gained,p.Glu439Ter,ENST00000354674,;SYNE1,non_coding_transcript_exon_variant,,ENST00000347037,;SYNE1,non_coding_transcript_exon_variant,,ENST00000460912,;SYNE1,non_coding_transcript_exon_variant,,ENST00000536990,;SYNE1,downstream_gene_variant,,ENST00000476519,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;SYNE1,non_coding_transcript_exon_variant,,ENST00000472563,;SYNE1,upstream_gene_variant,,ENST00000478916,;SYNE1,downstream_gene_variant,,ENST00000490866,; A ENST00000367255 Transcript stop_gained 25452/27748 24850/26394 8284/8797 E/* Gag/Tag 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 137/146 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 152148171 152148171 C A 1 0 0 0 0 0 1 0 0 15837 864 30 2 2 SYNE1 6 152148171 Nonsense_Mutation SNP C C3N-02089_T 799147 152148171 18657808 374 27458 SYNE1 0 . GRCh38 6 152284100 152284100 + Missense_Mutation SNP C C G rs757079165 C3N-02089_T C3N-02089_N C C c.18085G>C p.Val6029Leu p.V6029L ENST00000367255 96/146 306 276 30 333 333 0 strelka-varscan-mutect SYNE1,missense_variant,p.Val6029Leu,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Val5958Leu,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Val5624Leu,ENST00000341594,;SYNE1,missense_variant,p.Val204Leu,ENST00000540663,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,;SYNE1,non_coding_transcript_exon_variant,,ENST00000489156,;SYNE1,upstream_gene_variant,,ENST00000488376,; G ENST00000367255 Transcript missense_variant 18687/27748 18085/26394 6029/8797 V/L Gta/Cta rs757079165 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 96/146 SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS rs757079165 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 152284100 152284100 C G 1 0 0 0 0 1 0 0 0 15837 507 18 4 4 SYNE1 6 152284100 Missense_Mutation SNP C C3N-02089_T 135929 152284100 18521879 375 27459 SYNE1 0 . GRCh38 6 152347084 152347084 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.12053C>T p.Ser4018Leu p.S4018L ENST00000367255 73/146 172 131 41 145 145 0 strelka-varscan-mutect SYNE1,missense_variant,p.Ser4018Leu,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Ser3947Leu,ENST00000423061,NM_033071.3;SYNE1,intron_variant,,ENST00000341594,;SYNE1,non_coding_transcript_exon_variant,,ENST00000471834,; A ENST00000367255 Transcript missense_variant 12655/27748 12053/26394 4018/8797 S/L tCa/tTa 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 73/146 Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 152347084 152347084 G A 1 0 0 0 0 1 0 0 0 15837 1294 45 3 3 SYNE1 6 152347084 Missense_Mutation SNP G C3N-02089_T 62984 152347084 18458895 376 27460 SMOC2 0 . GRCh38 6 168510042 168510042 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.212G>A p.Cys71Tyr p.C71Y ENST00000354536 2/13 142 131 11 150 150 0 strelka-varscan-mutect SMOC2,missense_variant,p.Cys71Tyr,ENST00000354536,NM_022138.2;SMOC2,missense_variant,p.Cys71Tyr,ENST00000356284,NM_001166412.1; A ENST00000354536 Transcript missense_variant 432/3150 212/1374 71/457 C/Y tGc/tAc 1 1 SMOC2 HGNC HGNC:20323 protein_coding YES CCDS5307.1 ENSP00000346537 Q9H3U7 UPI0000072A56 NM_022138.2 deleterious(0) 2/13 PROSITE_profiles:PS51465,hmmpanther:PTHR12352,hmmpanther:PTHR12352:SF14,Gene3D:3.30.60.30,Pfam_domain:PF07648,SMART_domains:SM00280,Superfamily_domains:SSF100895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 168510042 168510042 G A 1 0 0 0 0 1 0 0 0 15123 1319 46 3 3 SMOC2 6 168510042 Missense_Mutation SNP G C3N-02089_T 16162958 168510042 2295937 377 27461 THBS2 0 . GRCh38 6 169241914 169241914 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.739G>T p.Gly247Cys p.G247C ENST00000366787 6/23 109 68 41 98 98 0 strelka-varscan-mutect THBS2,missense_variant,p.Gly247Cys,ENST00000366787,NM_003247.3;THBS2,missense_variant,p.Gly247Cys,ENST00000617924,;XXyac-YX65C7_A.2,downstream_gene_variant,,ENST00000444188,;THBS2,upstream_gene_variant,,ENST00000461848,;THBS2,downstream_gene_variant,,ENST00000472733,; A ENST00000366787 Transcript missense_variant 989/5811 739/3519 247/1172 G/C Ggt/Tgt 1 -1 THBS2 HGNC HGNC:11786 protein_coding YES CCDS34574.1 ENSP00000355751 P35442 UPI0000231C7F NM_003247.3 deleterious_low_confidence(0.01) 6/23 hmmpanther:PTHR10199,hmmpanther:PTHR10199:SF10 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 169241914 169241914 C A 1 0 0 0 0 1 0 0 0 16287 623 22 2 2 THBS2 6 169241914 Missense_Mutation SNP C C3N-02089_T 731872 169241914 1564065 378 27462 EIF3B 0 . GRCh38 7 2355343 2355343 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.424delG p.Ala142ArgfsTer22 p.A142Rfs*22 ENST00000360876 1/19 116 94 22 66 66 0 sindel-pindel EIF3B,frameshift_variant,p.Ala142ArgfsTer22,ENST00000360876,NM_001037283.1;EIF3B,frameshift_variant,p.Ala142ArgfsTer22,ENST00000397011,NM_003751.3;EIF3B,frameshift_variant,p.Ala103ArgfsTer22,ENST00000413917,;EIF3B,5_prime_UTR_variant,,ENST00000431643,;SNX8,upstream_gene_variant,,ENST00000435336,;SNX8,upstream_gene_variant,,ENST00000447136,; - ENST00000360876 Transcript frameshift_variant 478/3055 422/2445 141/814 R/X cGg/cg 1 1 EIF3B HGNC HGNC:3280 protein_coding YES CCDS5332.1 ENSP00000354125 P55884 A0A024R821 UPI000013F934 NM_001037283.1 1/19 Low_complexity_(Seg):seg,hmmpanther:PTHR14068:SF0,hmmpanther:PTHR14068,PIRSF_domain:PIRSF036424 HIGH 1 deletion 1 2 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 2355343 2355343 G - 1 0 1 0 1 0 0 0 0 4847 1116 39 0 0 EIF3B 7 2355343 Frame_Shift_Del DEL G C3N-02089_T 2355343 156990630 379 27463 SDK1 0 . GRCh38 7 3619221 3619221 + Missense_Mutation SNP C C T rs772186781 C3N-02089_T C3N-02089_N C C c.440C>T p.Thr147Ile p.T147I ENST00000404826 2/45 96 86 10 106 106 0 strelka-varscan-mutect SDK1,missense_variant,p.Thr147Ile,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Thr147Ile,ENST00000615806,;SDK1,missense_variant,p.Thr147Ile,ENST00000389531,; T ENST00000404826 Transcript missense_variant 579/10397 440/6642 147/2213 T/I aCc/aTc rs772186781 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 tolerated(0.07) 2/45 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs772186781 . 0 200 9 0 0 0 0 0 -19.85575 0.999986 1 1 1 0 T 3 4 90 3619221 3619221 C T 1 0 0 0 0 1 0 0 0 14243 507 18 3 3 SDK1 7 3619221 Missense_Mutation SNP C C3N-02089_T 1263878 3619221 155726752 380 27464 AP5Z1 0 . GRCh38 7 4781724 4781724 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.336G>T p.= p.L112L ENST00000348624 3/17 25 17 8 23 23 0 strelka-varscan-mutect AP5Z1,synonymous_variant,p.=,ENST00000348624,NM_014855.2;AP5Z1,non_coding_transcript_exon_variant,,ENST00000496303,;AP5Z1,intron_variant,,ENST00000477680,;AP5Z1,upstream_gene_variant,,ENST00000491375,;AP5Z1,upstream_gene_variant,,ENST00000477454,; T ENST00000348624 Transcript synonymous_variant 430/2901 336/2424 112/807 L ctG/ctT 1 1 AP5Z1 HGNC HGNC:22197 protein_coding YES CCDS47528.1 ENSP00000297562 O43299 UPI00003E5903 NM_014855.2 3/17 hmmpanther:PTHR12181:SF29,hmmpanther:PTHR12181 LOW 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.99873 1 1 1 1 0 T 2 4 90 4781724 4781724 G T 1 0 0 0 0 0 0 0 1 874 1277 45 2 2 AP5Z1 7 4781724 Silent SNP G C3N-02089_T 1162503 4781724 154564249 381 27465 WIPI2 0 . GRCh38 7 5199643 5199643 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.196C>A p.Gln66Lys p.Q66K ENST00000288828 3/13 218 186 32 207 206 1 strelka-varscan-mutect WIPI2,missense_variant,p.Gln66Lys,ENST00000288828,NM_015610.3;WIPI2,missense_variant,p.Gln48Lys,ENST00000401525,NM_016003.3;WIPI2,missense_variant,p.Gln48Lys,ENST00000382384,NM_001033519.1;WIPI2,missense_variant,p.Gln66Lys,ENST00000404704,NM_001033518.1;WIPI2,non_coding_transcript_exon_variant,,ENST00000485854,;WIPI2,non_coding_transcript_exon_variant,,ENST00000496867,;WIPI2,non_coding_transcript_exon_variant,,ENST00000466014,; A ENST00000288828 Transcript missense_variant 428/4476 196/1365 66/454 Q/K Cag/Aag 1 1 WIPI2 HGNC HGNC:32225 protein_coding YES CCDS5339.1 ENSP00000288828 Q9Y4P8 A0A024R823 UPI0000073E34 NM_015610.3 tolerated(0.79) 3/13 Gene3D:2.130.10.10,hmmpanther:PTHR11227,hmmpanther:PTHR11227:SF27,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 5199643 5199643 C A 1 0 0 0 0 1 0 0 0 17927 479 17 2 2 WIPI2 7 5199643 Missense_Mutation SNP C C3N-02089_T 417919 5199643 154146330 382 27466 TNRC18 0 . GRCh38 7 5332684 5332684 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.6085G>T p.Gly2029Cys p.G2029C ENST00000430969 19/30 212 168 44 166 166 0 strelka-varscan-mutect TNRC18,missense_variant,p.Gly2029Cys,ENST00000399537,;TNRC18,missense_variant,p.Gly2029Cys,ENST00000430969,NM_001080495.2;TNRC18,missense_variant,p.Gly66Cys,ENST00000455076,; A ENST00000430969 Transcript missense_variant 6434/10562 6085/8907 2029/2968 G/C Ggc/Tgc 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious(0) 19/30 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 5332684 5332684 C A 1 0 0 0 0 1 0 0 0 16812 623 22 2 2 TNRC18 7 5332684 Missense_Mutation SNP C C3N-02089_T 133041 5332684 154013289 383 27467 FBXL18 0 . GRCh38 7 5501447 5501447 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.822G>T p.= p.A274A ENST00000382368 3/5 311 218 93 219 218 1 strelka-varscan-mutect FBXL18,synonymous_variant,p.=,ENST00000382368,NM_024963.4;FBXL18,synonymous_variant,p.=,ENST00000458142,;FBXL18,synonymous_variant,p.=,ENST00000453700,;FBXL18,upstream_gene_variant,,ENST00000620087,;FBXL18,synonymous_variant,p.=,ENST00000415009,; A ENST00000382368 Transcript synonymous_variant 946/3498 822/2157 274/718 A gcG/gcT 1 -1 FBXL18 HGNC HGNC:21874 protein_coding YES CCDS43546.1 ENSP00000371805 Q96ME1 A0A024R857 UPI000020EA59 NM_024963.4 3/5 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF466 LOW 1 SNV 5 1 PASS rs1489828334 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 5501447 5501447 C A 1 0 0 0 0 0 0 0 1 5578 639 23 1 1 FBXL18 7 5501447 Silent SNP C C3N-02089_T 168763 5501447 153844526 384 27468 FBXL18 0 . GRCh38 7 5501536 5501536 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.733G>T p.Glu245Ter p.E245* ENST00000382368 3/5 239 200 39 181 181 0 strelka-varscan-mutect FBXL18,stop_gained,p.Glu245Ter,ENST00000382368,NM_024963.4;FBXL18,stop_gained,p.Glu129Ter,ENST00000458142,;FBXL18,stop_gained,p.Glu245Ter,ENST00000453700,;FBXL18,upstream_gene_variant,,ENST00000620087,;FBXL18,stop_gained,p.Glu245Ter,ENST00000415009,; A ENST00000382368 Transcript stop_gained 857/3498 733/2157 245/718 E/* Gag/Tag 1 -1 FBXL18 HGNC HGNC:21874 protein_coding YES CCDS43546.1 ENSP00000371805 Q96ME1 A0A024R857 UPI000020EA59 NM_024963.4 3/5 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF466 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 5501536 5501536 C A 1 0 0 0 0 0 1 0 0 5578 864 30 2 2 FBXL18 7 5501536 Nonsense_Mutation SNP C C3N-02089_T 89 5501536 153844437 385 27469 C1GALT1 0 . GRCh38 7 7234360 7234360 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.41G>T p.Cys14Phe p.C14F ENST00000436587 2/4 183 147 36 177 177 0 strelka-varscan-mutect C1GALT1,missense_variant,p.Cys14Phe,ENST00000436587,NM_020156.4;C1GALT1,missense_variant,p.Cys14Phe,ENST00000223122,;C1GALT1,missense_variant,p.Cys14Phe,ENST00000402468,;C1GALT1,missense_variant,p.Cys14Phe,ENST00000429911,;C1GALT1,missense_variant,p.Cys14Phe,ENST00000419721,;C1GALT1,non_coding_transcript_exon_variant,,ENST00000476068,; T ENST00000436587 Transcript missense_variant 264/6235 41/1092 14/363 C/F tGt/tTt 1 1 C1GALT1 HGNC HGNC:24337 protein_coding YES CCDS5355.1 ENSP00000389176 Q9NS00 A0A024RA32 UPI000003DC31 NM_020156.4 tolerated(0.73) 2/4 hmmpanther:PTHR23033,hmmpanther:PTHR23033:SF13,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS rs1404632180 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 7234360 7234360 G T 1 0 0 0 0 1 0 0 0 1929 1377 48 2 2 C1GALT1 7 7234360 Missense_Mutation SNP G C3N-02089_T 1732824 7234360 152111613 386 27470 THSD7A 0 . GRCh38 7 11406309 11406309 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.4228C>A p.Pro1410Thr p.P1410T ENST00000423059 22/28 91 76 15 73 73 0 strelka-varscan-mutect THSD7A,missense_variant,p.Pro1410Thr,ENST00000423059,NM_015204.2;THSD7A,missense_variant,p.Pro1410Thr,ENST00000617773,;AC004538.3,intron_variant,,ENST00000445839,;AC004160.4,upstream_gene_variant,,ENST00000425837,; T ENST00000423059 Transcript missense_variant 4480/10663 4228/4974 1410/1657 P/T Cct/Act 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 deleterious(0) 22/28 hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,SMART_domains:SM00209 MODERATE SNV 5 1 PASS rs980160026 . 0 203 7 0 0 0 0 0 -20 0.9999996 1 1 1 0 T 3 4 90 11406309 11406309 G T 1 0 0 0 0 1 0 0 0 16313 1203 42 2 2 THSD7A 7 11406309 Missense_Mutation SNP G C3N-02089_T 4171949 11406309 147939664 387 27471 TMEM196 0 . GRCh38 7 19772652 19772652 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.45C>A p.= p.S15S ENST00000405764 1/4 117 94 23 73 73 0 strelka-varscan TMEM196,synonymous_variant,p.=,ENST00000405844,;TMEM196,synonymous_variant,p.=,ENST00000405764,NM_152774.3;TMEM196,intron_variant,,ENST00000422233,;TMEM196,intron_variant,,ENST00000433641,;TMEM196,intron_variant,,ENST00000493519,; T ENST00000405764 Transcript synonymous_variant 742/3975 45/519 15/172 S tcC/tcA 1 -1 TMEM196 HGNC HGNC:22431 protein_coding YES CCDS34607.2 ENSP00000384234 Q5HYL7 UPI00005A9078 NM_152774.3 1/4 hmmpanther:PTHR28681,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 204 3 3 0 0 0 0 -20 0.9999518 1 1 1 0 T 2 4 90 19772652 19772652 G T 1 0 0 0 0 0 0 0 1 16558 1103 39 1 1 TMEM196 7 19772652 Silent SNP G C3N-02089_T 8366343 19772652 139573321 388 27472 HOXA1 0 . GRCh38 7 27094478 27094478 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.970G>C p.Gly324Arg p.G324R ENST00000343060 2/2 245 183 62 214 214 0 strelka-varscan-mutect HOXA1,missense_variant,p.Gly324Arg,ENST00000343060,NM_005522.4;HOXA1,3_prime_UTR_variant,,ENST00000355633,NM_153620.2;HOTAIRM1,upstream_gene_variant,,ENST00000428939,;HOTAIRM1,upstream_gene_variant,,ENST00000429611,;HOTAIRM1,upstream_gene_variant,,ENST00000434063,;HOTAIRM1,upstream_gene_variant,,ENST00000425358,;HOTAIRM1_2,upstream_gene_variant,,ENST00000616712,;HOTAIRM1,upstream_gene_variant,,ENST00000495032,;HOTAIRM1_1,upstream_gene_variant,,ENST00000622675,; G ENST00000343060 Transcript missense_variant 1032/2517 970/1008 324/335 G/R Ggg/Cgg 1 -1 HOXA1 HGNC HGNC:5099 protein_coding YES CCDS5401.1 ENSP00000343246 P49639 UPI000013C80E NM_005522.4 tolerated(0.43) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 27094478 27094478 C G 1 0 0 0 0 1 0 0 0 7182 623 22 4 4 HOXA1 7 27094478 Missense_Mutation SNP C C3N-02089_T 7321826 27094478 132251495 389 27473 HOXA4 0 . GRCh38 7 27130622 27130622 + Missense_Mutation SNP C C A rs746129531 C3N-02089_T C3N-02089_N C C c.112G>T p.Gly38Trp p.G38W ENST00000360046 1/2 134 101 33 94 94 0 strelka-varscan-mutect HOXA4,missense_variant,p.Gly38Trp,ENST00000360046,;HOXA4,missense_variant,p.Gly38Trp,ENST00000610970,NM_002141.4;HOXA4,missense_variant,p.Gly38Trp,ENST00000428284,;HOXA3,intron_variant,,ENST00000317201,;HOXA3,intron_variant,,ENST00000522788,;HOXA3,upstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA4,upstream_gene_variant,,ENST00000511914,;HOXA-AS2,intron_variant,,ENST00000521159,;HOXA-AS3,intron_variant,,ENST00000518848,;HOXA-AS2,downstream_gene_variant,,ENST00000517550,;HOXA-AS2,downstream_gene_variant,,ENST00000521687,;RP1-170O19.22,intron_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000521401,;HOXA3,intron_variant,,ENST00000518451,; A ENST00000360046 Transcript missense_variant 178/1747 112/963 38/320 G/W Ggg/Tgg rs746129531,COSM3880401 1 -1 HOXA4 HGNC HGNC:5105 protein_coding YES CCDS5405.1 ENSP00000353151 Q00056 UPI000013C810 deleterious(0.02) 1/2 hmmpanther:PTHR24326,hmmpanther:PTHR24326:SF211,Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs746129531 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 27130622 27130622 C A 1 0 0 0 0 1 0 0 0 7188 652 23 1 1 HOXA4 7 27130622 Missense_Mutation SNP C C3N-02089_T 36144 27130622 132215351 390 27474 ADCYAP1R1 0 . GRCh38 7 31092714 31092714 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.1025G>T p.Gly342Val p.G342V ENST00000614107 13/17 162 131 31 164 163 1 strelka-varscan-mutect ADCYAP1R1,missense_variant,p.Gly342Val,ENST00000614107,NM_001199635.1,NM_001199636.1;ADCYAP1R1,missense_variant,p.Gly342Val,ENST00000304166,NM_001118.4;ADCYAP1R1,missense_variant,p.Gly321Val,ENST00000409363,NM_001199637.1;ADCYAP1R1,missense_variant,p.Gly342Val,ENST00000409489,;ADCYAP1R1,missense_variant,p.Gly342Val,ENST00000396211,;ADCYAP1R1,missense_variant,p.Gly59Val,ENST00000436116,; T ENST00000614107 Transcript missense_variant 1314/6575 1025/1491 342/496 G/V gGc/gTc COSM3735292 1 1 ADCYAP1R1 HGNC HGNC:242 protein_coding YES CCDS56480.1 ENSP00000483721 P41586 UPI0000DA58BA NM_001199635.1,NM_001199636.1 deleterious(0.01) 13/17 Pfam_domain:PF00002,PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF228,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 5 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999961 1 1 1 0 T 3 4 90 31092714 31092714 G T 1 0 0 0 0 1 0 0 0 347 1203 42 2 2 ADCYAP1R1 7 31092714 Missense_Mutation SNP G C3N-02089_T 3962092 31092714 128253259 391 27475 CCDC129 0 . GRCh38 7 31643297 31643297 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.2005A>G p.Ile669Val p.I669V ENST00000451887 11/15 248 221 27 205 205 0 strelka-varscan-mutect CCDC129,missense_variant,p.Ile495Val,ENST00000319386,;CCDC129,missense_variant,p.Ile653Val,ENST00000615280,NM_001257967.1;CCDC129,missense_variant,p.Ile551Val,ENST00000409210,;CCDC129,missense_variant,p.Ile669Val,ENST00000451887,NM_001257968.1;CCDC129,missense_variant,p.Ile643Val,ENST00000407970,NM_194300.3; G ENST00000451887 Transcript missense_variant 2099/3611 2005/3189 669/1062 I/V Atc/Gtc 1 1 CCDC129 HGNC HGNC:27363 protein_coding YES CCDS59050.1 ENSP00000395835 Q6ZRS4 UPI00020655D9 NM_001257968.1 tolerated(1) 11/15 hmmpanther:PTHR17469,hmmpanther:PTHR17469:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 31643297 31643297 A G 1 0 0 0 0 1 0 0 0 2456 449 16 5 5 CCDC129 7 31643297 Missense_Mutation SNP A C3N-02089_T 550583 31643297 127702676 392 27476 DPY19L1 0 . GRCh38 7 34973594 34973594 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.615A>G p.= p.V205V ENST00000310974 8/22 80 57 23 59 59 0 strelka-varscan-mutect DPY19L1,synonymous_variant,p.=,ENST00000638088,;DPY19L1,synonymous_variant,p.=,ENST00000310974,NM_015283.1;DPY19L1,synonymous_variant,p.=,ENST00000446375,;DPY19L1,non_coding_transcript_exon_variant,,ENST00000462134,;DPY19L1,non_coding_transcript_exon_variant,,ENST00000463538,; C ENST00000310974 Transcript synonymous_variant 760/4870 615/2028 205/675 V gtA/gtG 1 -1 DPY19L1 HGNC HGNC:22205 protein_coding YES CCDS43567.1 ENSP00000308695 Q2PZI1 UPI000067CB92 NM_015283.1 8/22 Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF5,hmmpanther:PTHR31488,Pfam_domain:PF10034 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 34973594 34973594 T C 1 0 0 0 0 0 0 0 1 4555 1741 61 5 5 DPY19L1 7 34973594 Silent SNP T C3N-02089_T 3330297 34973594 124372379 393 27477 INHBA 0 . GRCh38 7 41690098 41690098 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.833G>T p.Gly278Val p.G278V ENST00000242208 3/3 254 174 80 205 204 1 strelka-varscan-mutect INHBA,missense_variant,p.Gly278Val,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Gly278Val,ENST00000638023,;INHBA,missense_variant,p.Gly278Val,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript missense_variant 1080/6064 833/1281 278/426 G/V gGg/gTg 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 deleterious(0.04) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00688 MODERATE 1 SNV 1 1 PASS rs1191953816 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 41690098 41690098 C A 1 0 0 0 0 1 0 0 0 7643 623 22 2 2 INHBA 7 41690098 Missense_Mutation SNP C C3N-02089_T 6716504 41690098 117655875 394 27478 ADCY1 0 . GRCh38 7 45622693 45622693 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.970C>A p.Leu324Met p.L324M ENST00000297323 4/20 226 187 39 185 185 0 strelka-varscan-mutect ADCY1,missense_variant,p.Leu324Met,ENST00000297323,NM_021116.2;ADCY1,missense_variant,p.Leu99Met,ENST00000432715,NM_001281768.1;ADCY1,missense_variant,p.Leu99Met,ENST00000621543,; A ENST00000297323 Transcript missense_variant 992/12503 970/3360 324/1119 L/M Ctg/Atg 1 1 ADCY1 HGNC HGNC:232 protein_coding YES CCDS34631.1 ENSP00000297323 Q08828 UPI0000199C4A NM_021116.2 deleterious(0.01) 4/20 PROSITE_profiles:PS50125,hmmpanther:PTHR11920:SF336,hmmpanther:PTHR11920,Pfam_domain:PF00211,PIRSF_domain:PIRSF039050,Gene3D:3.30.70.1230,SMART_domains:SM00044,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 45622693 45622693 C A 1 0 0 0 0 1 0 0 0 336 796 28 2 2 ADCY1 7 45622693 Missense_Mutation SNP C C3N-02089_T 3932595 45622693 113723280 395 27479 ABCA13 0 . GRCh38 7 48507884 48507884 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.13359C>A p.= p.I4453I ENST00000435803 50/62 88 68 20 75 74 1 strelka-varscan-mutect ABCA13,synonymous_variant,p.=,ENST00000435803,NM_152701.4;ABCA13,synonymous_variant,p.=,ENST00000544596,;ABCA13,synonymous_variant,p.=,ENST00000411975,;ABCA13,synonymous_variant,p.=,ENST00000435451,;ABCA13,non_coding_transcript_exon_variant,,ENST00000611776,;ABCA13,synonymous_variant,p.=,ENST00000453246,; A ENST00000435803 Transcript synonymous_variant 13383/17184 13359/15177 4453/5058 I atC/atA 1 1 ABCA13 HGNC HGNC:14638 protein_coding YES CCDS47584.1 ENSP00000411096 A0A0A0MT16 UPI00043788D8 NM_152701.4 50/62 hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF113,Pfam_domain:PF12698 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 48507884 48507884 C A 1 0 0 0 0 0 0 0 1 35 845 30 2 2 ABCA13 7 48507884 Silent SNP C C3N-02089_T 2885191 48507884 110838089 396 27480 POM121L12 0 . GRCh38 7 53035894 53035894 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.223A>T p.Thr75Ser p.T75S ENST00000408890 1/1 223 187 36 176 176 0 strelka-varscan-mutect POM121L12,missense_variant,p.Thr75Ser,ENST00000408890,NM_182595.3; T ENST00000408890 Transcript missense_variant 253/1283 223/891 75/296 T/S Acc/Tcc 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.42) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 53035894 53035894 A T 1 0 0 0 0 1 0 0 0 12352 159 6 4 4 POM121L12 7 53035894 Missense_Mutation SNP A C3N-02089_T 4528010 53035894 106310079 397 27481 WBSCR17 0 . GRCh38 7 71571364 71571364 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.1042G>A p.Asp348Asn p.D348N ENST00000333538 6/11 276 222 54 243 243 0 strelka-varscan WBSCR17,missense_variant,p.Asp348Asn,ENST00000333538,NM_022479.2;WBSCR17,missense_variant,p.Asp269Asn,ENST00000618959,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000498380,;WBSCR17,non_coding_transcript_exon_variant,,ENST00000467723,; A ENST00000333538 Transcript missense_variant 1676/3884 1042/1797 348/598 D/N Gat/Aat COSM3640212 1 1 WBSCR17 HGNC HGNC:16347 protein_coding YES CCDS5540.1 ENSP00000329654 Q6IS24 Q2L4S5 UPI00000502D5 NM_022479.2 tolerated(0.19) 6/11 Gene3D:3.90.550.10,hmmpanther:PTHR11675,hmmpanther:PTHR11675:SF38,Superfamily_domains:SSF53448 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 71571364 71571364 G A 1 0 0 0 0 1 0 0 0 17823 1174 41 3 3 WBSCR17 7 71571364 Missense_Mutation SNP G C3N-02089_T 18535470 71571364 87774609 398 27482 HGF 0 . GRCh38 7 81717236 81717236 + Silent SNP A A C novel C3N-02089_T C3N-02089_N A A c.1401T>G p.= p.S467S ENST00000222390 11/18 233 161 72 315 314 1 strelka-varscan HGF,synonymous_variant,p.=,ENST00000222390,NM_000601.4;HGF,synonymous_variant,p.=,ENST00000457544,NM_001010932.1; C ENST00000222390 Transcript synonymous_variant 1628/5989 1401/2187 467/728 S tcT/tcG 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 11/18 PROSITE_profiles:PS50070,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.20.10,Pfam_domain:PF00051,SMART_domains:SM00130,Superfamily_domains:SSF57440 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 81717236 81717236 A C 1 0 0 0 0 0 0 0 1 6969 318 11 5 5 HGF 7 81717236 Silent SNP A C3N-02089_T 10145872 81717236 77628737 399 27483 PCLO 0 . GRCh38 7 82847248 82847248 + Splice_Site SNP C C A novel C3N-02089_T C3N-02089_N C C c.13655-1G>T p.X4552_splice ENST00000333891 97 69 28 95 95 0 strelka-varscan PCLO,splice_acceptor_variant,,ENST00000333891,NM_033026.5;PCLO,splice_acceptor_variant,,ENST00000423517,NM_014510.2;PCLO,splice_acceptor_variant,,ENST00000618073,;PCLO,splice_acceptor_variant,,ENST00000426442,;PCLO,splice_acceptor_variant,,ENST00000413807,;PCLO,splice_acceptor_variant,,ENST00000456006,; A ENST00000333891 Transcript splice_acceptor_variant -/20329 13655/15429 4552/5142 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 10/24 HIGH 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 82847248 82847248 C A 1 0 0 0 0 0 0 1 0 11671 695 24 2 2 PCLO 7 82847248 Splice_Site SNP C C3N-02089_T 1130012 82847248 76498725 400 27484 PCLO 0 . GRCh38 7 82953281 82953281 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.7672A>T p.Thr2558Ser p.T2558S ENST00000333891 5/25 173 117 56 231 231 0 strelka-varscan PCLO,missense_variant,p.Thr2558Ser,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Thr2558Ser,ENST00000423517,NM_014510.2;PCLO,upstream_gene_variant,,ENST00000437081,; A ENST00000333891 Transcript missense_variant 8010/20329 7672/15429 2558/5142 T/S Acc/Tcc 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 tolerated(0.08) 5/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 82953281 82953281 T A 1 0 0 0 0 1 0 0 0 11671 1638 57 4 4 PCLO 7 82953281 Missense_Mutation SNP T C3N-02089_T 106033 82953281 76392692 401 27485 CDK14 0 . GRCh38 7 90917724 90917724 + Missense_Mutation SNP G G T rs756057096 C3N-02089_T C3N-02089_N G G c.826G>T p.Gly276Cys p.G276C ENST00000380050 8/15 91 69 22 109 109 0 strelka-varscan CDK14,missense_variant,p.Gly230Cys,ENST00000406263,NM_001287136.1;CDK14,missense_variant,p.Gly276Cys,ENST00000380050,NM_001287135.1;CDK14,missense_variant,p.Gly258Cys,ENST00000265741,NM_012395.3;CDK14,missense_variant,p.Gly147Cys,ENST00000436577,NM_001287137.1;CDK14,splice_region_variant,,ENST00000487145,;CDK14,splice_region_variant,,ENST00000431029,; T ENST00000380050 Transcript missense_variant,splice_region_variant 957/4995 826/1410 276/469 G/C Ggt/Tgt rs756057096,COSM3950943,COSM3950944 1 1 CDK14 HGNC HGNC:8883 protein_coding YES CCDS75626.1 ENSP00000369390 O94921 UPI000013EAF4 NM_001287135.1 deleterious(0) 8/15 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24056,hmmpanther:PTHR24056:SF154,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 90917724 90917724 G T 1 0 0 0 0 1 0 0 0 2834 1130 39 1 1 CDK14 7 90917724 Missense_Mutation SNP G C3N-02089_T 7964443 90917724 68428249 402 27486 FZD1 0 . GRCh38 7 91265677 91265677 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.797C>G p.Ala266Gly p.A266G ENST00000287934 1/1 65 53 12 61 61 0 strelka-varscan FZD1,missense_variant,p.Ala266Gly,ENST00000287934,NM_003505.1; G ENST00000287934 Transcript missense_variant 1314/6963 797/1944 266/647 A/G gCc/gGc 1 1 FZD1 HGNC HGNC:4038 protein_coding YES CCDS5620.1 ENSP00000287934 Q9UP38 UPI000005104D NM_003505.1 tolerated(0.46) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF81 MODERATE 1 SNV 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 91265677 91265677 C G 1 0 0 0 0 1 0 0 0 5999 739 26 4 4 FZD1 7 91265677 Missense_Mutation SNP C C3N-02089_T 347953 91265677 68080296 403 27487 LRRD1 0 . GRCh38 7 92146131 92146131 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2348G>T p.Cys783Phe p.C783F ENST00000458448 5/6 70 56 14 106 106 0 strelka-varscan LRRD1,missense_variant,p.Cys783Phe,ENST00000458448,;LRRD1,missense_variant,p.Cys783Phe,ENST00000430130,NM_001161528.1;LRRD1,intron_variant,,ENST00000343318,;CYP51A1,upstream_gene_variant,,ENST00000435873,;CYP51A1-AS1,intron_variant,,ENST00000453068,;LRRD1,intron_variant,,ENST00000422722,; A ENST00000458448 Transcript missense_variant 2549/2830 2348/2583 783/860 C/F tGt/tTt 1 -1 LRRD1 HGNC HGNC:34300 protein_coding YES CCDS55124.1 ENSP00000405987 A4D1F6 UPI0001662314 deleterious(0.01) 5/6 Gene3D:1.10.533.10,PROSITE_profiles:PS50017 MODERATE 1 SNV 5 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.9999965 1 1 1 0 A 3 1 90 92146131 92146131 C A 1 0 0 0 0 1 0 0 0 8932 478 17 2 2 LRRD1 7 92146131 Missense_Mutation SNP C C3N-02089_T 880454 92146131 67199842 404 27488 SAMD9L 0 . GRCh38 7 93134541 93134541 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.1431A>T p.= p.T477T ENST00000318238 5/5 202 152 50 233 233 0 strelka-varscan SAMD9L,synonymous_variant,p.=,ENST00000318238,NM_001303500.1,NM_152703.3;SAMD9L,synonymous_variant,p.=,ENST00000411955,NM_001303496.1,NM_001303498.1;SAMD9L,synonymous_variant,p.=,ENST00000437805,NM_001303497.1;SAMD9L,intron_variant,,ENST00000610760,;SAMD9L,downstream_gene_variant,,ENST00000446033,;SAMD9L,downstream_gene_variant,,ENST00000446959,;SAMD9L,downstream_gene_variant,,ENST00000439952,;SAMD9L,downstream_gene_variant,,ENST00000414791,; A ENST00000318238 Transcript synonymous_variant 2648/7134 1431/4755 477/1584 T acA/acT 1 -1 SAMD9L HGNC HGNC:1349 protein_coding YES CCDS34681.1 ENSP00000326247 Q8IVG5 UPI000020F567 NM_001303500.1,NM_152703.3 5/5 hmmpanther:PTHR16155,hmmpanther:PTHR16155:SF18 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 93134541 93134541 T A 1 0 0 0 0 0 0 0 1 14087 1799 63 4 4 SAMD9L 7 93134541 Silent SNP T C3N-02089_T 988410 93134541 66211432 405 27489 CALCR 0 . GRCh38 7 93479399 93479399 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.214A>T p.Lys72Ter p.K72* ENST00000359558 5/16 153 103 50 142 141 1 strelka-varscan CALCR,stop_gained,p.Lys72Ter,ENST00000359558,NM_001164737.1;CALCR,stop_gained,p.Lys54Ter,ENST00000421592,;CALCR,stop_gained,p.Lys54Ter,ENST00000394441,NM_001164738.1;CALCR,stop_gained,p.Lys54Ter,ENST00000426151,NM_001742.3;CALCR,stop_gained,p.Lys54Ter,ENST00000360249,;MIR653,downstream_gene_variant,,ENST00000385279,;MIR489,downstream_gene_variant,,ENST00000384923,;CALCR,stop_gained,p.Lys54Ter,ENST00000423724,;CALCR,stop_gained,p.Lys54Ter,ENST00000415529,; A ENST00000359558 Transcript stop_gained 514/3696 214/1527 72/508 K/* Aaa/Taa 1 -1 CALCR HGNC HGNC:1440 protein_coding YES CCDS55125.1 ENSP00000352561 A0A0A0MRG0 UPI0001B8380B NM_001164737.1 5/16 PROSITE_profiles:PS50227,hmmpanther:PTHR12011:SF84,hmmpanther:PTHR12011,Superfamily_domains:SSF111418,Prints_domain:PR01350,Prints_domain:PR00361 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 93479399 93479399 T A 1 0 0 0 0 0 1 0 0 2269 1821 63 4 4 CALCR 7 93479399 Nonsense_Mutation SNP T C3N-02089_T 344858 93479399 65866574 406 27490 PEG10 0 . GRCh38 7 94664395 94664395 + Missense_Mutation SNP G G T rs556674678 C3N-02089_T C3N-02089_N G G c.1067G>T p.Arg356Leu p.R356L ENST00000488574 2/2 114 85 29 125 125 0 strelka-varscan PEG10,missense_variant,p.Arg280Leu,ENST00000482108,NM_015068.3,NM_001184961.1,NM_001172437.2,NM_001040152.1;PEG10,missense_variant,p.Arg314Leu,ENST00000615790,NM_001184962.1;PEG10,missense_variant,p.Arg314Leu,ENST00000612941,;PEG10,missense_variant,p.Arg280Leu,ENST00000617526,;PEG10,missense_variant,p.Arg356Leu,ENST00000488574,NM_001172438.2;PEG10,missense_variant,p.Arg356Leu,ENST00000612748,;PEG10,downstream_gene_variant,,ENST00000613043,;PEG10,intron_variant,,ENST00000493935,;PEG10,upstream_gene_variant,,ENST00000465184,; T ENST00000488574 Transcript missense_variant 1284/2587 1067/1206 356/401 R/L cGc/cTc rs556674678,COSM5076254 1 1 PEG10 HGNC HGNC:14005 protein_coding YES CCDS75636.1 ENSP00000418944 B4DSP0 UPI0000037665 NM_001172438.2 deleterious(0) 2/2 hmmpanther:PTHR15503:SF10,hmmpanther:PTHR15503 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 94664395 94664395 G T 1 0 0 0 0 1 0 0 0 11807 1087 38 1 1 PEG10 7 94664395 Missense_Mutation SNP G C3N-02089_T 1184996 94664395 64681578 407 27491 TMEM130 0 . GRCh38 7 98851560 98851560 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.867C>A p.Cys289Ter p.C289* ENST00000416379 6/8 130 89 41 116 116 0 strelka-varscan TMEM130,stop_gained,p.Cys205Ter,ENST00000450876,;TMEM130,stop_gained,p.Cys289Ter,ENST00000339375,NM_152913.2;TMEM130,stop_gained,p.Cys289Ter,ENST00000416379,NM_001134450.1;TMEM130,stop_gained,p.Cys187Ter,ENST00000345589,NM_001134451.1;TMEM130,non_coding_transcript_exon_variant,,ENST00000461092,;TMEM130,upstream_gene_variant,,ENST00000474857,; T ENST00000416379 Transcript stop_gained 872/2881 867/1308 289/435 C/* tgC/tgA 1 -1 TMEM130 HGNC HGNC:25429 protein_coding YES CCDS47650.1 ENSP00000413163 Q8N3G9 UPI000006EF2E NM_001134450.1 6/8 hmmpanther:PTHR11861:SF10,hmmpanther:PTHR11861 HIGH 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 98851560 98851560 G T 1 0 0 0 0 0 1 0 0 16487 1195 42 2 2 TMEM130 7 98851560 Nonsense_Mutation SNP G C3N-02089_T 4187165 98851560 60494413 408 27492 GPC2 0 . GRCh38 7 100176280 100176280 + Silent SNP G G T rs373333632 C3N-02089_T C3N-02089_N G G c.252C>A p.= p.T84T ENST00000292377 2/10 278 192 86 257 256 1 strelka-varscan GPC2,synonymous_variant,p.=,ENST00000292377,NM_152742.2;STAG3,upstream_gene_variant,,ENST00000426455,NM_001282716.1;STAG3,upstream_gene_variant,,ENST00000615138,NM_001282717.1;STAG3,upstream_gene_variant,,ENST00000620100,;STAG3,upstream_gene_variant,,ENST00000317296,NM_012447.3;STAG3,upstream_gene_variant,,ENST00000394018,NM_001282718.1;STAG3,upstream_gene_variant,,ENST00000439782,;STAG3,upstream_gene_variant,,ENST00000416412,;STAG3,upstream_gene_variant,,ENST00000422690,;GPC2,upstream_gene_variant,,ENST00000490629,;GPC2,synonymous_variant,p.=,ENST00000480087,;GPC2,non_coding_transcript_exon_variant,,ENST00000471717,;STAG3,upstream_gene_variant,,ENST00000496157,;GPC2,upstream_gene_variant,,ENST00000486702,;STAG3,upstream_gene_variant,,ENST00000482546,; T ENST00000292377 Transcript synonymous_variant 420/2532 252/1740 84/579 T acC/acA rs373333632 1 -1 GPC2 HGNC HGNC:4450 protein_coding YES CCDS5689.1 ENSP00000292377 Q8N158 UPI000005340D NM_152742.2 2/10 hmmpanther:PTHR10822:SF24,hmmpanther:PTHR10822,Pfam_domain:PF01153 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 100176280 100176280 G T 1 0 0 0 0 0 0 0 1 6500 987 35 2 2 GPC2 7 100176280 Silent SNP G C3N-02089_T 1324720 100176280 59169693 409 27493 PILRB 0 . GRCh38 7 100358956 100358956 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.331A>T p.Arg111Trp p.R111W ENST00000452089 7/9 473 345 128 444 444 0 strelka-varscan PILRB,missense_variant,p.Gln163Leu,ENST00000448382,;PILRB,missense_variant,p.Arg111Trp,ENST00000452089,;PILRB,missense_variant,p.Arg111Trp,ENST00000457519,;PILRB,missense_variant,p.Arg30Trp,ENST00000438028,;PILRB,missense_variant,p.Arg111Trp,ENST00000422808,;PILRB,missense_variant,p.Arg111Trp,ENST00000419749,;PILRB,missense_variant,p.Arg111Trp,ENST00000443526,;PILRB,missense_variant,p.Arg111Trp,ENST00000609309,NM_178238.3;PILRB,missense_variant,p.Gln41Leu,ENST00000431140,;PILRB,missense_variant,p.Arg111Trp,ENST00000438231,;PILRB,missense_variant,p.Arg111Trp,ENST00000608825,;PILRB,downstream_gene_variant,,ENST00000455145,;PILRB,downstream_gene_variant,,ENST00000611937,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000310771,;STAG3L5P-PVRIG2P-PILRB,non_coding_transcript_exon_variant,,ENST00000444874,;STAG3L5P-PVRIG2P-PILRB,downstream_gene_variant,,ENST00000472646,;PILRB,downstream_gene_variant,,ENST00000493091,; T ENST00000452089 Transcript missense_variant 1390/2099 331/684 111/227 R/W Agg/Tgg 1 1 PILRB HGNC HGNC:18297 protein_coding YES CCDS43622.1 ENSP00000391748 Q9UKJ0 UPI000006EEBC deleterious(0.01) 7/9 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR15549,hmmpanther:PTHR15549:SF7,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 100358956 100358956 A T 1 0 0 0 0 1 0 0 0 12021 188 7 4 4 PILRB 7 100358956 Missense_Mutation SNP A C3N-02089_T 182676 100358956 58987017 410 27494 ZAN 0 . GRCh38 7 100773351 100773351 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.5492G>T p.Ser1831Ile p.S1831I ENST00000613979 30/48 262 188 74 292 292 0 strelka-varscan ZAN,missense_variant,p.Ser1831Ile,ENST00000613979,NM_003386.2;ZAN,missense_variant,p.Ser1831Ile,ENST00000618565,;ZAN,missense_variant,p.Ser1831Ile,ENST00000620596,NM_173059.2;ZAN,missense_variant,p.Ser1831Ile,ENST00000546292,;ZAN,missense_variant,p.Ser1831Ile,ENST00000542585,;ZAN,missense_variant,p.Ser1831Ile,ENST00000538115,;ZAN,missense_variant,p.Ser1831Ile,ENST00000546213,;ZAN,non_coding_transcript_exon_variant,,ENST00000620868,; T ENST00000613979 Transcript missense_variant 5657/8669 5492/8439 1831/2812 S/I aGc/aTc 1 1 ZAN HGNC HGNC:12857 protein_coding YES ENSP00000480750 A0A087WU49 UPI000441C79E NM_003386.2 deleterious(0) 30/48 Gene3D:2.10.25.10,Pfam_domain:PF01826,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF221,Low_complexity_(Seg):seg,SMART_domains:SM00181,Superfamily_domains:SSF57567 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 100773351 100773351 G T 1 0 0 0 0 1 0 0 0 18074 971 34 2 2 ZAN 7 100773351 Missense_Mutation SNP G C3N-02089_T 414395 100773351 58572622 411 27495 MUC17 0 . GRCh38 7 101043621 101043621 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.12205G>T p.Ala4069Ser p.A4069S ENST00000306151 3/13 135 90 45 144 144 0 strelka-varscan MUC17,missense_variant,p.Ala4069Ser,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Ala4069Ser,ENST00000379439,;MUC17,upstream_gene_variant,,ENST00000470303,; T ENST00000306151 Transcript missense_variant 12269/14247 12205/13482 4069/4493 A/S Gct/Tct 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 tolerated(0.28) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999:SF1,hmmpanther:PTHR37999 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 101043621 101043621 G T 1 0 0 0 0 1 0 0 0 9973 1319 46 2 2 MUC17 7 101043621 Missense_Mutation SNP G C3N-02089_T 270270 101043621 58302352 412 27496 CUX1 0 . GRCh38 7 102196963 102196963 + Missense_Mutation SNP T T G rs781975744 C3N-02089_T C3N-02089_N T T c.1585T>G p.Ser529Ala p.S529A ENST00000360264 15/24 204 164 40 243 243 0 strelka-varscan CUX1,missense_variant,p.Ser529Ala,ENST00000360264,NM_001202543.1;CUX1,missense_variant,p.Ser518Ala,ENST00000292535,NM_181552.3;CUX1,missense_variant,p.Ser518Ala,ENST00000549414,;CUX1,missense_variant,p.Ser518Ala,ENST00000550008,;CUX1,missense_variant,p.Ser416Ala,ENST00000546411,;CUX1,missense_variant,p.Ser416Ala,ENST00000556210,;CUX1,intron_variant,,ENST00000437600,NM_001913.4;CUX1,intron_variant,,ENST00000622516,NM_181500.3;CUX1,intron_variant,,ENST00000292538,;CUX1,intron_variant,,ENST00000547394,NM_001202544.2;CUX1,intron_variant,,ENST00000425244,NM_001202545.2;CUX1,intron_variant,,ENST00000393824,NM_001202546.2;SNORA48,upstream_gene_variant,,ENST00000517015,;CUX1,intron_variant,,ENST00000560541,;CUX1,intron_variant,,ENST00000558836,; G ENST00000360264 Transcript missense_variant 1605/13762 1585/4551 529/1516 S/A Tct/Gct rs781975744 1 1 CUX1 HGNC HGNC:2557 protein_coding YES CCDS56498.1 ENSP00000353401 P39880 UPI00001AEB98 NM_001202543.1 tolerated(0.41) 15/24 Low_complexity_(Seg):seg,hmmpanther:PTHR14043:SF4,hmmpanther:PTHR14043 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 102196963 102196963 T G 1 0 0 0 0 1 0 0 0 3874 1435 50 5 5 CUX1 7 102196963 Missense_Mutation SNP T C3N-02089_T 1153342 102196963 57149010 413 27497 CUX1 0 . GRCh38 7 102274301 102274301 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1441C>G p.Leu481Val p.L481V ENST00000437600 16/23 104 88 16 111 111 0 strelka-varscan CUX1,missense_variant,p.Leu481Val,ENST00000437600,NM_001913.4;CUX1,missense_variant,p.Leu479Val,ENST00000622516,NM_181500.3;CUX1,missense_variant,p.Leu481Val,ENST00000292538,;CUX1,missense_variant,p.Leu465Val,ENST00000547394,NM_001202544.2;CUX1,missense_variant,p.Leu435Val,ENST00000425244,NM_001202545.2;CUX1,missense_variant,p.Leu442Val,ENST00000393824,NM_001202546.2;CUX1,non_coding_transcript_exon_variant,,ENST00000560541,;CUX1,non_coding_transcript_exon_variant,,ENST00000558836,;CUX1,non_coding_transcript_exon_variant,,ENST00000487284,; G ENST00000437600 Transcript missense_variant 1568/3031 1441/2037 481/678 L/V Cta/Gta 1 1 CUX1 HGNC HGNC:2557 protein_coding CCDS5720.1 ENSP00000414091 Q13948 UPI00001A95D5 NM_001913.4 tolerated_low_confidence(0.15) 16/23 hmmpanther:PTHR14043:SF15,hmmpanther:PTHR14043,Pfam_domain:PF08172 MODERATE SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 102274301 102274301 C G 1 0 0 0 0 1 0 0 0 3874 680 24 4 4 CUX1 7 102274301 Missense_Mutation SNP C C3N-02089_T 77338 102274301 57071672 414 27498 RELN 0 . GRCh38 7 103589688 103589688 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.4053C>A p.= p.S1351S ENST00000428762 28/65 521 373 148 485 485 0 strelka-varscan RELN,synonymous_variant,p.=,ENST00000424685,;RELN,synonymous_variant,p.=,ENST00000428762,NM_005045.3;RELN,synonymous_variant,p.=,ENST00000343529,NM_173054.2; T ENST00000428762 Transcript synonymous_variant 4213/11571 4053/10383 1351/3460 S tcC/tcA 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 28/65 hmmpanther:PTHR11841 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 103589688 103589688 G T 1 0 0 0 0 0 0 0 1 13390 1335 47 2 2 RELN 7 103589688 Silent SNP G C3N-02089_T 1315387 103589688 55756285 415 27499 LAMB4 0 . GRCh38 7 108034328 108034328 + Silent SNP T T G novel C3N-02089_T C3N-02089_N T T c.4698A>C p.= p.L1566L ENST00000388781 31/34 138 118 20 180 180 0 strelka-varscan LAMB4,synonymous_variant,p.=,ENST00000388781,NM_007356.2;LAMB4,synonymous_variant,p.=,ENST00000205386,NM_001318046.1;LAMB4,synonymous_variant,p.=,ENST00000422975,;LAMB4,non_coding_transcript_exon_variant,,ENST00000483484,;LAMB4,non_coding_transcript_exon_variant,,ENST00000475572,; G ENST00000388781 Transcript synonymous_variant 4782/5858 4698/5286 1566/1761 L ctA/ctC 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 31/34 Coiled-coils_(Ncoils):Coil,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 108034328 108034328 T G 1 0 0 0 0 0 0 0 1 8517 1393 49 5 5 LAMB4 7 108034328 Silent SNP T C3N-02089_T 4444640 108034328 51311645 416 27500 LAMB4 0 . GRCh38 7 108116044 108116044 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.152T>A p.Leu51Gln p.L51Q ENST00000388781 3/34 146 94 52 132 132 0 strelka-varscan LAMB4,missense_variant,p.Leu51Gln,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Leu51Gln,ENST00000205386,NM_001318046.1;LAMB4,missense_variant,p.Leu51Gln,ENST00000418464,NM_001318048.1;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,; T ENST00000388781 Transcript missense_variant 236/5858 152/5286 51/1761 L/Q cTg/cAg 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0) 3/34 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF279,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 108116044 108116044 A T 1 0 0 0 0 1 0 0 0 8517 188 7 4 4 LAMB4 7 108116044 Missense_Mutation SNP A C3N-02089_T 81716 108116044 51229929 417 27501 DNAJB9 0 . GRCh38 7 108573194 108573194 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.513A>C p.Glu171Asp p.E171D ENST00000249356 3/3 171 160 11 198 198 0 strelka-varscan DNAJB9,missense_variant,p.Glu171Asp,ENST00000249356,NM_012328.2;THAP5,upstream_gene_variant,,ENST00000415914,NM_001130475.2;THAP5,upstream_gene_variant,,ENST00000313516,NM_182529.3;THAP5,upstream_gene_variant,,ENST00000438865,;DNAJB9,intron_variant,,ENST00000465725,;THAP5,upstream_gene_variant,,ENST00000493722,;THAP5,upstream_gene_variant,,ENST00000412935,;PNPLA8,upstream_gene_variant,,ENST00000489738,;THAP5,upstream_gene_variant,,ENST00000468884,;THAP5,upstream_gene_variant,,ENST00000446771,;THAP5,upstream_gene_variant,,ENST00000484452,;DNAJB9,downstream_gene_variant,,ENST00000491582,; C ENST00000249356 Transcript missense_variant 1059/2715 513/672 171/223 E/D gaA/gaC 1 1 DNAJB9 HGNC HGNC:6968 protein_coding YES CCDS5752.1 ENSP00000249356 Q9UBS3 Q6FIF1 UPI000000D769 NM_012328.2 tolerated(0.7) 3/3 hmmpanther:PTHR24078 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 108573194 108573194 A C 1 0 0 0 0 1 0 0 0 4441 69 3 5 5 DNAJB9 7 108573194 Missense_Mutation SNP A C3N-02089_T 457150 108573194 50772779 418 27502 PTPRZ1 0 . GRCh38 7 122061122 122061122 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.6850A>T p.Ser2284Cys p.S2284C ENST00000393386 30/30 71 52 19 65 65 0 strelka-varscan PTPRZ1,missense_variant,p.Ser2284Cys,ENST00000393386,NM_001206838.1,NM_002851.2;PTPRZ1,missense_variant,p.Ser1417Cys,ENST00000449182,NM_001206839.1;PTPRZ1,non_coding_transcript_exon_variant,,ENST00000474500,; T ENST00000393386 Transcript missense_variant 7261/8175 6850/6948 2284/2315 S/C Agc/Tgc 1 1 PTPRZ1 HGNC HGNC:9685 protein_coding YES CCDS34740.1 ENSP00000377047 P23471 UPI000020F9BB NM_001206838.1,NM_002851.2 deleterious(0) 30/30 Gene3D:3.90.190.10,SMART_domains:SM00194 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 122061122 122061122 A T 1 0 0 0 0 1 0 0 0 12969 304 11 4 4 PTPRZ1 7 122061122 Missense_Mutation SNP A C3N-02089_T 13487928 122061122 37284851 419 27503 GRM8 0 . GRCh38 7 126533230 126533230 + Missense_Mutation SNP G G T rs770527898 C3N-02089_T C3N-02089_N G G c.2152C>A p.Pro718Thr p.P718T ENST00000339582 9/11 76 67 9 112 112 0 strelka-varscan GRM8,missense_variant,p.Pro718Thr,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Pro718Thr,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Pro226Thr,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Pro718Thr,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; T ENST00000339582 Transcript missense_variant 2961/4057 2152/2727 718/908 P/T Ccc/Acc rs770527898,COSM5406411,COSM5406412 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.06) 9/11 Pfam_domain:PF00003,Prints_domain:PR00248,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS . . 0 207 3 0 0 0 0 0 -19.60651 1 1 1 1 0 T 3 4 90 126533230 126533230 G T 1 0 0 0 0 1 0 0 0 6685 1174 41 2 2 GRM8 7 126533230 Missense_Mutation SNP G C3N-02089_T 4472108 126533230 32812743 420 27504 PRRT4 0 . GRCh38 7 128352323 128352323 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1233C>A p.= p.T411T ENST00000446477 6/6 429 330 99 381 381 0 strelka-varscan PRRT4,synonymous_variant,p.=,ENST00000446477,NM_001174164.1;PRRT4,synonymous_variant,p.=,ENST00000535159,;PRRT4,synonymous_variant,p.=,ENST00000489517,;PRRT4,intron_variant,,ENST00000489835,NM_001114726.2;PRRT4,intron_variant,,ENST00000480290,; T ENST00000446477 Transcript synonymous_variant 1547/3544 1233/2700 411/899 T acC/acA 1 -1 PRRT4 HGNC HGNC:37280 protein_coding YES CCDS55160.1 ENSP00000415026 C9JH25 UPI0000DD7E1D NM_001174164.1 6/6 hmmpanther:PTHR35578,hmmpanther:PTHR35578:SF1,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 128352323 128352323 G T 1 0 0 0 0 0 0 0 1 12758 1335 47 2 2 PRRT4 7 128352323 Silent SNP G C3N-02089_T 1819093 128352323 30993650 421 27505 SLC13A4 0 . GRCh38 7 135691255 135691255 + Silent SNP G G T rs758216229 C3N-02089_T C3N-02089_N G G c.1389C>A p.= p.P463P ENST00000354042 13/16 180 121 59 177 177 0 strelka-varscan SLC13A4,synonymous_variant,p.=,ENST00000354042,NM_001318192.1,NM_012450.2;C7orf73,intron_variant,,ENST00000422968,;SLC13A4,non_coding_transcript_exon_variant,,ENST00000471405,;C7orf73,intron_variant,,ENST00000509448,; T ENST00000354042 Transcript synonymous_variant 2079/2897 1389/1881 463/626 P ccC/ccA rs758216229 1 -1 SLC13A4 HGNC HGNC:15827 protein_coding YES CCDS5840.1 ENSP00000297282 Q9UKG4 UPI00000343D9 NM_001318192.1,NM_012450.2 13/16 Pfam_domain:PF00939,hmmpanther:PTHR10283,hmmpanther:PTHR10283:SF63 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 135691255 135691255 G T 1 0 0 0 0 0 0 0 1 14659 987 35 2 2 SLC13A4 7 135691255 Silent SNP G C3N-02089_T 7338932 135691255 23654718 422 27506 HIPK2 0 . GRCh38 7 139620494 139620494 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1689G>T p.Gln563His p.Q563H ENST00000406875 7/15 253 177 76 291 291 0 strelka-varscan HIPK2,missense_variant,p.Gln563His,ENST00000406875,NM_022740.4;HIPK2,missense_variant,p.Gln563His,ENST00000428878,NM_001113239.2;HIPK2,missense_variant,p.Gln556His,ENST00000342645,; A ENST00000406875 Transcript missense_variant 1784/15049 1689/3597 563/1198 Q/H caG/caT 1 -1 HIPK2 HGNC HGNC:14402 protein_coding YES CCDS75667.1 ENSP00000385571 Q9H2X6 UPI000012C71E NM_022740.4 tolerated(0.27) 7/15 hmmpanther:PTHR24058:SF53,hmmpanther:PTHR24058 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 139620494 139620494 C A 1 0 0 0 0 1 0 0 0 7005 912 32 2 2 HIPK2 7 139620494 Missense_Mutation SNP C C3N-02089_T 3929239 139620494 19725479 423 27507 MGAM2 0 . GRCh38 7 142197494 142197494 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.4727T>C p.Leu1576Pro p.L1576P ENST00000477922 41/48 156 109 47 188 188 0 strelka-varscan MGAM2,missense_variant,p.Leu1576Pro,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; C ENST00000477922 Transcript missense_variant 4781/7867 4727/7548 1576/2515 L/P cTg/cCg 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 41/48 Pfam_domain:PF01055,hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55,Low_complexity_(Seg):seg,Superfamily_domains:SSF51445 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 142197494 142197494 T C 1 0 0 0 0 1 0 0 0 9500 1580 55 5 5 MGAM2 7 142197494 Missense_Mutation SNP T C3N-02089_T 2577000 142197494 17148479 424 27508 OR6V1 0 . GRCh38 7 143052726 143052726 + Missense_Mutation SNP G G T rs201116298 C3N-02089_T C3N-02089_N G G c.386G>T p.Arg129Leu p.R129L ENST00000418316 1/1 156 122 34 211 211 0 strelka-varscan OR6V1,missense_variant,p.Arg129Leu,ENST00000418316,NM_001001667.1; T ENST00000418316 Transcript missense_variant 407/1028 386/942 129/313 R/L cGc/cTc rs201116298 1 1 OR6V1 HGNC HGNC:15090 protein_coding YES CCDS47728.1 ENSP00000396085 Q8N148 A0A126GWQ4 UPI0000041C19 NM_001001667.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 143052726 143052726 G T 1 0 0 0 0 1 0 0 0 11281 1087 38 1 1 OR6V1 7 143052726 Missense_Mutation SNP G C3N-02089_T 855232 143052726 16293247 425 27509 ZNF746 0 . GRCh38 7 149474759 149474759 + Silent SNP C C A C3N-02089_T C3N-02089_N C C c.1563G>T p.= p.T521T ENST00000458143 7/7 101 68 33 95 95 0 strelka-varscan ZNF746,synonymous_variant,p.=,ENST00000340622,NM_152557.4;ZNF746,synonymous_variant,p.=,ENST00000458143,NM_001163474.1;ZNF746,downstream_gene_variant,,ENST00000471735,; A ENST00000458143 Transcript synonymous_variant 1834/3797 1563/1938 521/645 T acG/acT COSM3879192 1 -1 ZNF746 HGNC HGNC:21948 protein_coding YES CCDS55180.1 ENSP00000395007 Q6NUN9 UPI00015DA840 NM_001163474.1 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF13,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 LOW 1 SNV 2 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 149474759 149474759 C A 1 0 0 0 0 0 0 0 1 18712 755 27 1 1 ZNF746 7 149474759 Silent SNP C C3N-02089_T 6422033 149474759 9871214 426 27510 SSPO 0 . GRCh38 7 149791381 149791381 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.5004A>T p.= p.I1668I ENST00000378016 32/107 213 167 46 224 224 0 strelka-varscan SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,; T ENST00000378016 Transcript synonymous_variant 5004/15589 5004/15453 1668/5150 I atA/atT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 32/107 Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424,PROSITE_profiles:PS50068,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294,Prints_domain:PR00261 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 149791381 149791381 A T 1 0 0 0 0 0 0 0 1 15566 410 15 4 4 SSPO 7 149791381 Silent SNP A C3N-02089_T 316622 149791381 9554592 427 27511 SSPO 0 . GRCh38 7 149826546 149826546 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.14555G>T p.Cys4852Phe p.C4852F ENST00000378016 99/107 202 127 75 216 216 0 strelka-varscan SSPO,missense_variant,p.Cys4852Phe,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000492965,;SSPO,intron_variant,,ENST00000488835,;SSPO,intron_variant,,ENST00000461331,;SSPO,non_coding_transcript_exon_variant,,ENST00000465639,;SSPO,non_coding_transcript_exon_variant,,ENST00000472850,; T ENST00000378016 Transcript missense_variant 14555/15589 14555/15453 4852/5150 C/F tGc/tTc 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 deleterious(0) 99/107 Low_complexity_(Seg):seg,Pfam_domain:PF01826,Gene3D:2.10.25.10,Superfamily_domains:SSF57567,hmmpanther:PTHR11339:SF294,hmmpanther:PTHR11339 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 149826546 149826546 G T 1 0 0 0 0 1 0 0 0 15566 1319 46 2 2 SSPO 7 149826546 Missense_Mutation SNP G C3N-02089_T 35165 149826546 9519427 428 27512 ATG9B 0 . GRCh38 7 151021284 151021284 + Silent SNP G G C rs758260577,rs765626055 C3N-02089_T C3N-02089_N G G c.867C>G p.= p.A289A ENST00000605952 5/17 97 67 30 92 92 0 strelka-varscan ATG9B,synonymous_variant,p.=,ENST00000469530,NM_173681.5;ATG9B,non_coding_transcript_exon_variant,,ENST00000617967,;ATG9B,non_coding_transcript_exon_variant,,ENST00000473409,;ATG9B,non_coding_transcript_exon_variant,,ENST00000466157,;ATG9B,upstream_gene_variant,,ENST00000611177,;ATG9B,synonymous_variant,p.=,ENST00000605952,;ATG9B,non_coding_transcript_exon_variant,,ENST00000473134,; C ENST00000605952 Transcript synonymous_variant,NMD_transcript_variant 943/4572 867/2775 289/924 A gcC/gcG rs758260577,rs765626055 1 -1 ATG9B HGNC HGNC:21899 nonsense_mediated_decay YES ENSP00000475737 Q674R7 UPI00004286C0 5/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR13038:SF14,hmmpanther:PTHR13038 LOW 1 SNV 1 1 PASS . . 0 206 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 151021284 151021284 G C 1 0 0 0 0 0 0 0 1 1255 1103 39 4 4 ATG9B 7 151021284 Silent SNP G C3N-02089_T 1194738 151021284 8324689 429 27513 PRKAG2 0 . GRCh38 7 151568823 151568823 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.1126T>G p.Ser376Ala p.S376A ENST00000287878 11/16 385 332 53 402 402 0 strelka-varscan PRKAG2,missense_variant,p.Ser376Ala,ENST00000287878,NM_016203.3;PRKAG2,missense_variant,p.Ser252Ala,ENST00000492843,NM_001304527.1;PRKAG2,missense_variant,p.Ser135Ala,ENST00000418337,NM_024429.1,NM_001304531.1;PRKAG2,missense_variant,p.Ser332Ala,ENST00000392801,NM_001040633.1;PRKAG2,missense_variant,p.Ser135Ala,ENST00000476632,;PRKAG2,missense_variant,p.Ser60Ala,ENST00000478989,;PRKAG2,3_prime_UTR_variant,,ENST00000488258,;PRKAG2,downstream_gene_variant,,ENST00000491938,;PRKAG2,downstream_gene_variant,,ENST00000493872,;PRKAG2,upstream_gene_variant,,ENST00000479461,;PRKAG2,upstream_gene_variant,,ENST00000485183,; C ENST00000287878 Transcript missense_variant 1631/3305 1126/1710 376/569 S/A Tcc/Gcc 1 -1 PRKAG2 HGNC HGNC:9386 protein_coding YES CCDS5928.1 ENSP00000287878 Q9UGJ0 A0A090N8Q6 UPI00001250B5 NM_016203.3 tolerated(0.1) 11/16 Gene3D:3.10.580.10,Pfam_domain:PF00571,PROSITE_profiles:PS51371,hmmpanther:PTHR13780,hmmpanther:PTHR13780:SF26,SMART_domains:SM00116,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 151568823 151568823 A C 1 0 0 0 0 1 0 0 0 12634 304 11 5 5 PRKAG2 7 151568823 Missense_Mutation SNP A C3N-02089_T 547539 151568823 7777150 430 27514 HTR5A 0 . GRCh38 7 155071235 155071235 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.336G>T p.Arg112Ser p.R112S ENST00000287907 1/2 191 149 42 160 160 0 strelka-varscan HTR5A,missense_variant,p.Arg112Ser,ENST00000287907,NM_024012.3;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000395731,;HTR5A-AS1,non_coding_transcript_exon_variant,,ENST00000493904,;RP11-5C23.4,upstream_gene_variant,,ENST00000637588,; T ENST00000287907 Transcript missense_variant 912/2912 336/1074 112/357 R/S agG/agT 1 1 HTR5A HGNC HGNC:5300 protein_coding YES CCDS5936.1 ENSP00000287907 P47898 A4D2N2 UPI000004477E NM_024012.3 tolerated(0.78) 1/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF108,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 155071235 155071235 G T 1 0 0 0 0 1 0 0 0 7346 1194 42 2 2 HTR5A 7 155071235 Missense_Mutation SNP G C3N-02089_T 3502412 155071235 4274738 431 27515 ERICH1 0 . GRCh38 8 668702 668702 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1154A>T p.Asp385Val p.D385V ENST00000262109 5/6 257 232 25 234 234 0 strelka-varscan-mutect ERICH1,missense_variant,p.Asp154Val,ENST00000522893,;ERICH1,missense_variant,p.Asp385Val,ENST00000262109,NM_207332.2;ERICH1,missense_variant,p.Asp291Val,ENST00000522706,;ERICH1,downstream_gene_variant,,ENST00000518895,;ERICH1,missense_variant,p.Asp44Val,ENST00000523415,;ERICH1,non_coding_transcript_exon_variant,,ENST00000523053,; A ENST00000262109 Transcript missense_variant 1232/1813 1154/1332 385/443 D/V gAc/gTc 1 -1 ERICH1 HGNC HGNC:27234 protein_coding YES CCDS5955.1 ENSP00000262109 Q86X53 UPI000000DB6B NM_207332.2 deleterious(0) 5/6 hmmpanther:PTHR22444:SF1,hmmpanther:PTHR22444 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 668702 668702 T A 1 0 0 0 0 1 0 0 0 5081 1667 58 4 4 ERICH1 8 668702 Missense_Mutation SNP T C3N-02089_T 668702 144469934 432 27516 CSMD1 0 . GRCh38 8 3367183 3367183 + Missense_Mutation SNP C C A rs749444650 C3N-02089_T C3N-02089_N C C c.2967G>T p.Glu989Asp p.E989D ENST00000520002 21/71 355 289 66 371 371 0 strelka-varscan-mutect CSMD1,missense_variant,p.Glu850Asp,ENST00000537824,;CSMD1,missense_variant,p.Glu469Asp,ENST00000335551,;CSMD1,missense_variant,p.Glu989Asp,ENST00000520002,;CSMD1,missense_variant,p.Glu989Asp,ENST00000602557,;CSMD1,missense_variant,p.Glu988Asp,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Glu989Asp,ENST00000400186,;CSMD1,missense_variant,p.Glu989Asp,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; A ENST00000520002 Transcript missense_variant 3523/11740 2967/10698 989/3565 E/D gaG/gaT rs749444650,COSM4860975,COSM750624,COSM750625 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB tolerated(0.09) 21/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 0,1,1,1 MODERATE 1 SNV 5 0,1,1,1 1 PASS rs749444650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 3367183 3367183 C A 1 0 0 0 0 1 0 0 0 3745 680 24 2 2 CSMD1 8 3367183 Missense_Mutation SNP C C3N-02089_T 2698481 3367183 141771453 433 27517 CSMD1 0 . GRCh38 8 3708482 3708482 + Missense_Mutation SNP G G A rs752440260 C3N-02089_T C3N-02089_N G G c.941C>T p.Ala314Val p.A314V ENST00000520002 7/71 198 164 34 250 250 0 strelka-varscan-mutect CSMD1,missense_variant,p.Ala176Val,ENST00000537824,;CSMD1,missense_variant,p.Ala314Val,ENST00000520002,;CSMD1,missense_variant,p.Ala314Val,ENST00000602557,;CSMD1,missense_variant,p.Ala314Val,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Ala314Val,ENST00000400186,;CSMD1,missense_variant,p.Ala314Val,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000518151,; A ENST00000520002 Transcript missense_variant 1497/11740 941/10698 314/3565 A/V gCg/gTg rs752440260,COSM4675006,COSM4675007,COSM4675008,COSM4856945,COSM486409,COSM486410 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0.04) 7/71 0,1,1,1,1,1,1 MODERATE 1 SNV 5 0,1,1,1,1,1,1 1 PASS rs752440260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 3708482 3708482 G A 1 0 0 0 0 1 0 0 0 3745 1087 38 1 1 CSMD1 8 3708482 Missense_Mutation SNP G C3N-02089_T 341299 3708482 141430154 434 27518 XKR5 0 . GRCh38 8 6812010 6812010 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1249G>T p.Val417Leu p.V417L ENST00000618742 7/7 419 326 93 520 519 1 strelka-varscan-mutect XKR5,missense_variant,p.Val417Leu,ENST00000618742,NM_207411.4,NM_001289973.1;XKR5,3_prime_UTR_variant,,ENST00000618990,; A ENST00000618742 Transcript missense_variant 1400/4893 1249/2061 417/686 V/L Gtg/Ttg 1 -1 XKR5 HGNC HGNC:20782 protein_coding YES ENSP00000483879 A0A087X143 UPI0000EE786F NM_207411.4,NM_001289973.1 tolerated(0.1) 7/7 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF21 MODERATE 1 SNV 1 1 PASS rs1223247093 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 6812010 6812010 C A 1 0 0 0 0 1 0 0 0 17993 478 17 2 2 XKR5 8 6812010 Missense_Mutation SNP C C3N-02089_T 3103528 6812010 138326626 435 27519 USP17L7 0 . GRCh38 8 12133680 12133680 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.330C>A p.= p.S110S ENST00000530447 1/1 456 399 57 592 591 1 strelka-varscan-mutect USP17L7,synonymous_variant,p.=,ENST00000530447,NM_001256869.1;USP17L2,downstream_gene_variant,,ENST00000333796,NM_201402.2;FAM66D,intron_variant,,ENST00000434078,;RP11-1236K1.8,upstream_gene_variant,,ENST00000526505,; T ENST00000530447 Transcript synonymous_variant 765/2028 330/1593 110/530 S tcC/tcA 1 -1 USP17L7 HGNC HGNC:37180 protein_coding YES CCDS78305.1 ENSP00000485337 P0C7H9 UPI00001972BD NM_001256869.1 1/1 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 LOW SNV 1 PASS rs1445369381 . 24 186 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 12133680 12133680 G T 1 0 0 0 0 0 0 0 1 17589 1219 43 2 2 USP17L7 8 12133680 Silent SNP G C3N-02089_T 5321670 12133680 133004956 436 27520 USP17L2 0 . GRCh38 8 12137255 12137255 + Silent SNP A A T rs770432787 C3N-02089_T C3N-02089_N A A c.1506T>A p.= p.T502T ENST00000333796 1/1 738 663 75 785 785 0 strelka-varscan-mutect USP17L2,synonymous_variant,p.=,ENST00000333796,NM_201402.2;USP17L7,upstream_gene_variant,,ENST00000530447,NM_001256869.1;FAM66D,intron_variant,,ENST00000434078,; T ENST00000333796 Transcript synonymous_variant 1823/1910 1506/1593 502/530 T acT/acA rs770432787 1 -1 USP17L2 HGNC HGNC:34434 protein_coding YES CCDS43713.1 ENSP00000333329 Q6R6M4 UPI0000198137 NM_201402.2 1/1 LOW SNV 1 PASS rs770432787 . 30 180 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 12137255 12137255 A T 1 0 0 0 0 0 0 0 1 17586 175 7 4 4 USP17L2 8 12137255 Silent SNP A C3N-02089_T 3575 12137255 133001381 437 27521 RHOBTB2 0 . GRCh38 8 23010577 23010577 + Missense_Mutation SNP G G T rs747011587 C3N-02089_T C3N-02089_N G G c.1726G>T p.Val576Leu p.V576L ENST00000519685 9/12 123 104 19 102 102 0 strelka-varscan RHOBTB2,missense_variant,p.Val554Leu,ENST00000251822,NM_015178.2;RHOBTB2,missense_variant,p.Val561Leu,ENST00000522948,NM_001160037.1;RHOBTB2,missense_variant,p.Val576Leu,ENST00000519685,NM_001160036.1;RHOBTB2,downstream_gene_variant,,ENST00000524077,;RP11-875O11.1,intron_variant,,ENST00000502083,;RP11-875O11.1,upstream_gene_variant,,ENST00000523884,;RHOBTB2,downstream_gene_variant,,ENST00000523918,;RHOBTB2,non_coding_transcript_exon_variant,,ENST00000519210,; T ENST00000519685 Transcript missense_variant 2009/3505 1726/2250 576/749 V/L Gtg/Ttg rs747011587 1 1 RHOBTB2 HGNC HGNC:18756 protein_coding YES CCDS55210.1 ENSP00000427926 Q9BYZ6 UPI000020FD0D NM_001160036.1 tolerated(0.75) 9/12 PROSITE_profiles:PS50097,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.999994 1 1 1 0 T 3 4 90 23010577 23010577 G T 1 0 0 0 0 1 0 0 0 13507 1145 40 1 1 RHOBTB2 8 23010577 Missense_Mutation SNP G C3N-02089_T 10873322 23010577 122128059 438 27522 93 2 RHOBTB2 0 . GRCh38 8 23010580 23010580 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1729C>G p.Leu577Val p.L577V ENST00000519685 9/12 135 114 21 108 108 0 strelka-varscan RHOBTB2,missense_variant,p.Leu555Val,ENST00000251822,NM_015178.2;RHOBTB2,missense_variant,p.Leu562Val,ENST00000522948,NM_001160037.1;RHOBTB2,missense_variant,p.Leu577Val,ENST00000519685,NM_001160036.1;RHOBTB2,downstream_gene_variant,,ENST00000524077,;RP11-875O11.1,intron_variant,,ENST00000502083,;RP11-875O11.1,upstream_gene_variant,,ENST00000523884,;RHOBTB2,downstream_gene_variant,,ENST00000523918,;RHOBTB2,non_coding_transcript_exon_variant,,ENST00000519210,; G ENST00000519685 Transcript missense_variant 2012/3505 1729/2250 577/749 L/V Ctg/Gtg 1 1 RHOBTB2 HGNC HGNC:18756 protein_coding YES CCDS55210.1 ENSP00000427926 Q9BYZ6 UPI000020FD0D NM_001160036.1 deleterious(0.02) 9/12 PROSITE_profiles:PS50097,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 23010580 23010580 C G 1 0 0 0 0 1 0 0 0 13507 796 28 4 4 RHOBTB2 8 23010580 Missense_Mutation SNP C C3N-02089_T 3 23010580 122128056 439 27523 93 2 TNFRSF10A 0 . GRCh38 8 23191907 23191907 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.1194A>G p.= p.R398R ENST00000221132 10/10 428 396 32 385 382 3 strelka-varscan TNFRSF10A,synonymous_variant,p.=,ENST00000221132,NM_003844.3;TNFRSF10A,synonymous_variant,p.=,ENST00000613472,;RP11-1149O23.2,downstream_gene_variant,,ENST00000518308,;TNFRSF10A,non_coding_transcript_exon_variant,,ENST00000519862,; C ENST00000221132 Transcript synonymous_variant 1259/2714 1194/1407 398/468 R agA/agG 1 -1 TNFRSF10A HGNC HGNC:11904 protein_coding YES CCDS6039.1 ENSP00000221132 O00220 UPI000013C7A8 NM_003844.3 10/10 PROSITE_profiles:PS50017,hmmpanther:PTHR23097:SF113,hmmpanther:PTHR23097,Pfam_domain:PF00531,Gene3D:1.10.533.10,PIRSF_domain:PIRSF037867,SMART_domains:SM00005,Superfamily_domains:SSF47986 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 23191907 23191907 T C 1 0 0 0 0 0 0 0 1 16754 1548 54 5 5 TNFRSF10A 8 23191907 Silent SNP T C3N-02089_T 181327 23191907 121946729 440 27524 ADAM28 0 . GRCh38 8 24343585 24343585 + Splice_Site SNP G G T rs753075591 C3N-02089_T C3N-02089_N G G c.1990+1G>T p.X664_splice ENST00000265769 183 153 30 152 152 0 strelka-varscan ADAM28,splice_donor_variant,,ENST00000265769,NM_001304351.1,NM_014265.5;ADAM28,splice_donor_variant,,ENST00000521629,;ADAM28,splice_donor_variant,,ENST00000518326,;RP11-624C23.1,intron_variant,,ENST00000518988,;RP11-624C23.1,intron_variant,,ENST00000519689,;RP11-624C23.1,intron_variant,,ENST00000523700,;RP11-624C23.1,intron_variant,,ENST00000523578,;ADAM28,upstream_gene_variant,,ENST00000518737,;ADAM28,splice_donor_variant,,ENST00000523236,;ADAM28,splice_donor_variant,,ENST00000520665,;ADAM28,3_prime_UTR_variant,,ENST00000520448,; T ENST00000265769 Transcript splice_donor_variant -/7052 1990/2328 664/775 rs753075591 1 1 ADAM28 HGNC HGNC:206 protein_coding YES CCDS34865.1 ENSP00000265769 Q9UKQ2 UPI000049E0B9 NM_001304351.1,NM_014265.5 18/22 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 24343585 24343585 G T 1 0 0 0 0 0 0 1 0 290 1159 40 1 1 ADAM28 8 24343585 Splice_Site SNP G C3N-02089_T 1151678 24343585 120795051 441 27525 NUGGC 0 . GRCh38 8 28074376 28074376 + Missense_Mutation SNP G G C rs74881103 C3N-02089_T C3N-02089_N G G c.35C>G p.Pro12Arg p.P12R ENST00000413272 2/19 236 183 53 234 234 0 strelka-varscan NUGGC,missense_variant,p.Pro12Arg,ENST00000413272,NM_001010906.1;NUGGC,missense_variant,p.Pro12Arg,ENST00000418860,; C ENST00000413272 Transcript missense_variant 178/3887 35/2391 12/796 P/R cCg/cGg rs74881103 1 -1 NUGGC HGNC HGNC:33550 protein_coding YES CCDS47833.1 ENSP00000408697 Q68CJ6 UPI0000237454 NM_001010906.1 tolerated_low_confidence(0.18) 2/19 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9985124 1 1 1 0 C 3 2 90 28074376 28074376 G C 1 0 0 0 0 1 0 0 0 10814 1116 39 4 4 NUGGC 8 28074376 Missense_Mutation SNP G C3N-02089_T 3730791 28074376 117064260 442 27526 KIF13B 0 . GRCh38 8 29109945 29109945 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.4056C>T p.= p.N1352N ENST00000524189 33/40 138 121 17 169 169 0 strelka-varscan KIF13B,synonymous_variant,p.=,ENST00000524189,NM_015254.3;KIF13B,upstream_gene_variant,,ENST00000523130,;CTD-2647L4.1,upstream_gene_variant,,ENST00000523661,; A ENST00000524189 Transcript synonymous_variant 4095/8745 4056/5481 1352/1826 N aaC/aaT 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 33/40 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999905 1 1 1 0 A 2 1 90 29109945 29109945 G A 1 0 0 0 0 0 0 0 1 8139 1252 44 3 3 KIF13B 8 29109945 Silent SNP G C3N-02089_T 1035569 29109945 116028691 443 27527 KCNU1 0 . GRCh38 8 36918831 36918831 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.2531delC p.Pro844GlnfsTer22 p.P844Qfs*22 ENST00000399881 23/27 129 103 26 129 129 0 sindel-varindel-pindel KCNU1,frameshift_variant,p.Pro844GlnfsTer22,ENST00000399881,NM_001031836.2;KCNU1,frameshift_variant,p.Pro844GlnfsTer22,ENST00000522372,; - ENST00000399881 Transcript frameshift_variant 2567/3695 2530/3450 844/1149 P/X Cca/ca 1 1 KCNU1 HGNC HGNC:18867 protein_coding YES CCDS55220.1 ENSP00000382770 A8MYU2 UPI0000F079EF NM_001031836.2 23/27 Gene3D:3.40.50.720 HIGH 1 deletion 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 36918831 36918831 C - 1 0 1 0 1 0 0 0 0 8009 855 30 0 0 KCNU1 8 36918831 Frame_Shift_Del DEL C C3N-02089_T 7808886 36918831 108219805 444 27528 ZNF703 0 . GRCh38 8 37698088 37698088 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1187G>T p.Cys396Phe p.C396F ENST00000331569 2/2 233 176 57 193 193 0 strelka-varscan ZNF703,missense_variant,p.Cys396Phe,ENST00000331569,NM_025069.2; T ENST00000331569 Transcript missense_variant 1416/3349 1187/1773 396/590 C/F tGc/tTc 1 1 ZNF703 HGNC HGNC:25883 protein_coding YES CCDS6094.1 ENSP00000332325 Q9H7S9 UPI0000073D30 NM_025069.2 deleterious(0) 2/2 hmmpanther:PTHR12522,hmmpanther:PTHR12522:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 37698088 37698088 G T 1 0 0 0 0 1 0 0 0 18679 1319 46 2 2 ZNF703 8 37698088 Missense_Mutation SNP G C3N-02089_T 779257 37698088 107440548 445 27529 TM2D2 0 . GRCh38 8 38996222 38996222 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.218G>T p.Cys73Phe p.C73F ENST00000456397 1/4 97 88 9 87 87 0 strelka-varscan TM2D2,missense_variant,p.Cys73Phe,ENST00000456397,NM_078473.2;TM2D2,5_prime_UTR_variant,,ENST00000397070,NM_031940.3;TM2D2,intron_variant,,ENST00000456845,NM_001024380.1,NM_001024381.1;TM2D2,intron_variant,,ENST00000522142,;TM2D2,intron_variant,,ENST00000517872,;TM2D2,intron_variant,,ENST00000520152,;ADAM9,upstream_gene_variant,,ENST00000487273,NM_003816.2;ADAM9,upstream_gene_variant,,ENST00000481513,;ADAM9,upstream_gene_variant,,ENST00000466936,;TM2D2,intron_variant,,ENST00000522434,;TM2D2,upstream_gene_variant,,ENST00000521060,;TM2D2,non_coding_transcript_exon_variant,,ENST00000519186,;ADAM9,upstream_gene_variant,,ENST00000379917,;ADAM9,upstream_gene_variant,,ENST00000481873,;ADAM9,upstream_gene_variant,,ENST00000468065,;TM2D2,upstream_gene_variant,,ENST00000524331,; A ENST00000456397 Transcript missense_variant 312/3263 218/645 73/214 C/F tGc/tTc 1 -1 TM2D2 HGNC HGNC:24127 protein_coding YES CCDS6111.1 ENSP00000416050 Q9BX73 UPI000006FCA0 NM_078473.2 deleterious(0) 1/4 hmmpanther:PTHR21016,hmmpanther:PTHR21016:SF4 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -18.29885 0.9999947 1 1 1 0 A 3 1 90 38996222 38996222 C A 1 0 0 0 0 1 0 0 0 16409 710 25 2 2 TM2D2 8 38996222 Missense_Mutation SNP C C3N-02089_T 1298134 38996222 106142414 446 27530 SLC20A2 0 . GRCh38 8 42472107 42472107 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.284T>G p.Met95Arg p.M95R ENST00000342228 2/11 128 110 18 126 125 1 strelka-varscan SLC20A2,missense_variant,p.Met95Arg,ENST00000342228,NM_006749.4;SLC20A2,missense_variant,p.Met95Arg,ENST00000520262,NM_001257180.1;SLC20A2,missense_variant,p.Met95Arg,ENST00000520179,NM_001257181.1;SLC20A2,downstream_gene_variant,,ENST00000522707,;SLC20A2,downstream_gene_variant,,ENST00000518717,;SLC20A2,downstream_gene_variant,,ENST00000518384,;SLC20A2,downstream_gene_variant,,ENST00000517366,;SLC20A2,downstream_gene_variant,,ENST00000524237,;SLC20A2,missense_variant,p.Met95Arg,ENST00000524211,; C ENST00000342228 Transcript missense_variant 654/3657 284/1959 95/652 M/R aTg/aGg 1 -1 SLC20A2 HGNC HGNC:10947 protein_coding YES CCDS6132.1 ENSP00000340465 Q08357 UPI000006DC58 NM_006749.4 deleterious(0) 2/11 hmmpanther:PTHR11101,hmmpanther:PTHR11101:SF15,Pfam_domain:PF01384 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 42472107 42472107 A C 1 0 0 0 0 1 0 0 0 14705 231 8 5 5 SLC20A2 8 42472107 Missense_Mutation SNP A C3N-02089_T 3475885 42472107 102666529 447 27531 PRKDC 0 . GRCh38 8 47912484 47912484 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2860G>T p.Gly954Ter p.G954* ENST00000314191 25/86 126 81 45 97 97 0 strelka-varscan-mutect PRKDC,stop_gained,p.Gly954Ter,ENST00000314191,NM_006904.6;PRKDC,stop_gained,p.Gly954Ter,ENST00000338368,NM_001081640.1; A ENST00000314191 Transcript stop_gained 2917/13509 2860/12387 954/4128 G/* Gga/Tga 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 25/86 hmmpanther:PTHR11139:SF68,hmmpanther:PTHR11139,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 47912484 47912484 C A 1 0 0 0 0 0 1 0 0 12654 632 22 2 2 PRKDC 8 47912484 Nonsense_Mutation SNP C C3N-02089_T 5440377 47912484 97226152 448 27532 PXDNL 0 . GRCh38 8 51453677 51453677 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1091C>A p.Thr364Asn p.T364N ENST00000356297 10/23 555 481 74 404 404 0 strelka-varscan-mutect PXDNL,missense_variant,p.Thr364Asn,ENST00000356297,NM_144651.4; T ENST00000356297 Transcript missense_variant 1192/4805 1091/4392 364/1463 T/N aCc/aAc 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 tolerated(0.07) 10/23 PROSITE_profiles:PS50835,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs765536774 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 51453677 51453677 G T 1 0 0 0 0 1 0 0 0 13002 1261 44 2 2 PXDNL 8 51453677 Missense_Mutation SNP G C3N-02089_T 3541193 51453677 93684959 449 27533 ST18 0 . GRCh38 8 52161438 52161438 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1531G>C p.Val511Leu p.V511L ENST00000276480 14/26 226 205 21 185 185 0 strelka-mutect ST18,missense_variant,p.Val511Leu,ENST00000276480,NM_014682.2;ST18,missense_variant,p.Val511Leu,ENST00000517580,;ST18,3_prime_UTR_variant,,ENST00000522251,;ST18,3_prime_UTR_variant,,ENST00000521582,;ST18,3_prime_UTR_variant,,ENST00000521824,; G ENST00000276480 Transcript missense_variant 2215/6187 1531/3144 511/1047 V/L Gtt/Ctt 1 -1 ST18 HGNC HGNC:18695 protein_coding YES CCDS6149.1 ENSP00000276480 O60284 UPI0000046C30 NM_014682.2 deleterious(0.01) 14/26 hmmpanther:PTHR10816:SF9,hmmpanther:PTHR10816,Pfam_domain:PF08474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 52161438 52161438 C G 1 0 0 0 0 1 0 0 0 15590 565 20 4 4 ST18 8 52161438 Missense_Mutation SNP C C3N-02089_T 707761 52161438 92977198 450 27534 RB1CC1 0 . GRCh38 8 52656471 52656471 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3358G>T p.Val1120Leu p.V1120L ENST00000025008 15/24 144 106 38 141 141 0 strelka-varscan-mutect RB1CC1,missense_variant,p.Val1120Leu,ENST00000025008,NM_014781.4;RB1CC1,missense_variant,p.Val1120Leu,ENST00000435644,NM_001083617.1;RB1CC1,intron_variant,,ENST00000521611,;RB1CC1,downstream_gene_variant,,ENST00000523594,; A ENST00000025008 Transcript missense_variant 3882/6635 3358/4785 1120/1594 V/L Gtg/Ttg 1 -1 RB1CC1 HGNC HGNC:15574 protein_coding YES CCDS34892.1 ENSP00000025008 Q8TDY2 UPI0000DBEF23 NM_014781.4 tolerated_low_confidence(0.06) 15/24 hmmpanther:PTHR13222,hmmpanther:PTHR13222:SF1 MODERATE 1 SNV 1 1 PASS rs1390261760 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 52656471 52656471 C A 1 0 0 0 0 1 0 0 0 13260 507 18 2 2 RB1CC1 8 52656471 Missense_Mutation SNP C C3N-02089_T 495033 52656471 92482165 451 27535 RP1 0 . GRCh38 8 54627810 54627810 + Frame_Shift_Del DEL T T - novel C3N-02089_T C3N-02089_N T T c.3931delT p.Ser1311LeufsTer35 p.S1311Lfs*35 ENST00000220676 4/4 626 544 82 601 601 0 sindel-varindel-pindel RP1,frameshift_variant,p.Ser1311LeufsTer35,ENST00000220676,NM_006269.1;RP1,intron_variant,,ENST00000637698,;RP1,intron_variant,,ENST00000636932,; - ENST00000220676 Transcript frameshift_variant 4076/7100 3928/6471 1310/2156 F/X Ttt/tt 1 1 RP1 HGNC HGNC:10263 protein_coding YES CCDS6160.1 ENSP00000220676 P56715 UPI000013455B NM_006269.1 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF4 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 54627810 54627810 T - 1 0 1 0 1 0 0 0 0 13709 1725 60 0 0 RP1 8 54627810 Frame_Shift_Del DEL T C3N-02089_T 1971339 54627810 90510826 452 27536 XKR4 0 . GRCh38 8 55523425 55523425 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1151C>T p.Ala384Val p.A384V ENST00000327381 3/3 273 188 85 177 177 0 strelka-varscan-mutect XKR4,missense_variant,p.Ala384Val,ENST00000327381,NM_052898.1;XKR4,missense_variant,p.Ala384Val,ENST00000622811,;RP11-628E19.2,upstream_gene_variant,,ENST00000522918,;XKR4,upstream_gene_variant,,ENST00000518261,; T ENST00000327381 Transcript missense_variant 1251/19880 1151/1953 384/650 A/V gCc/gTc 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 tolerated(0.06) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14,Pfam_domain:PF09815 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 55523425 55523425 C T 1 0 0 0 0 1 0 0 0 17992 739 26 3 3 XKR4 8 55523425 Missense_Mutation SNP C C3N-02089_T 895615 55523425 89615211 453 27537 TOX 0 . GRCh38 8 58851541 58851541 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.676G>C p.Gly226Arg p.G226R ENST00000361421 4/9 165 109 56 129 129 0 strelka-varscan-mutect TOX,missense_variant,p.Gly226Arg,ENST00000361421,NM_014729.2; G ENST00000361421 Transcript missense_variant 897/4131 676/1581 226/526 G/R Ggc/Cgc 1 -1 TOX HGNC HGNC:18988 protein_coding YES CCDS34897.1 ENSP00000354842 O94900 UPI0000070A73 NM_014729.2 tolerated(0.2) 4/9 hmmpanther:PTHR13711,hmmpanther:PTHR13711:SF155 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 58851541 58851541 C G 1 0 0 0 0 1 0 0 0 16855 681 24 4 4 TOX 8 58851541 Missense_Mutation SNP C C3N-02089_T 3328116 58851541 86287095 454 27538 TTPA 0 . GRCh38 8 63066026 63066026 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.430G>T p.Val144Leu p.V144L ENST00000260116 3/5 360 331 29 271 270 1 strelka-varscan-mutect TTPA,missense_variant,p.Val144Leu,ENST00000260116,NM_000370.3;TTPA,intron_variant,,ENST00000521138,; A ENST00000260116 Transcript missense_variant 462/2338 430/837 144/278 V/L Gta/Tta 1 -1 TTPA HGNC HGNC:12404 protein_coding YES CCDS6178.1 ENSP00000260116 P49638 UPI00001377AC NM_000370.3 tolerated(0.18) 3/5 PROSITE_profiles:PS50191,hmmpanther:PTHR23324,hmmpanther:PTHR23324:SF52,Gene3D:3.40.525.10,Pfam_domain:PF00650,SMART_domains:SM00516,Superfamily_domains:SSF52087 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 63066026 63066026 C A 1 0 0 0 0 1 0 0 0 17246 478 17 2 2 TTPA 8 63066026 Missense_Mutation SNP C C3N-02089_T 4214485 63066026 82072610 455 27539 ADHFE1 0 . GRCh38 8 66454127 66454127 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.956T>G p.Ile319Ser p.I319S ENST00000396623 10/14 340 310 30 239 239 0 strelka-varscan-mutect ADHFE1,missense_variant,p.Ile319Ser,ENST00000396623,NM_144650.2;ADHFE1,missense_variant,p.Ile271Ser,ENST00000415254,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000496501,;ADHFE1,non_coding_transcript_exon_variant,,ENST00000480040,;ADHFE1,3_prime_UTR_variant,,ENST00000424777,;ADHFE1,3_prime_UTR_variant,,ENST00000426810,;ADHFE1,3_prime_UTR_variant,,ENST00000419955,;ADHFE1,3_prime_UTR_variant,,ENST00000276576,;ADHFE1,downstream_gene_variant,,ENST00000396621,;ADHFE1,downstream_gene_variant,,ENST00000422166,;ADHFE1,downstream_gene_variant,,ENST00000443372,; G ENST00000396623 Transcript missense_variant 987/1990 956/1404 319/467 I/S aTc/aGc 1 1 ADHFE1 HGNC HGNC:16354 protein_coding YES CCDS6190.2 ENSP00000379865 Q8IWW8 UPI000004966C NM_144650.2 deleterious(0.03) 10/14 Gene3D:1.20.1090.10,Pfam_domain:PF00465,hmmpanther:PTHR11496,hmmpanther:PTHR11496:SF62,Superfamily_domains:SSF56796 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 66454127 66454127 T G 1 0 0 0 0 1 0 0 0 387 1435 50 5 5 ADHFE1 8 66454127 Missense_Mutation SNP T C3N-02089_T 3388101 66454127 78684509 456 27540 EYA1 0 . GRCh38 8 71299215 71299215 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.658A>T p.Ser220Cys p.S220C ENST00000340726 9/18 551 483 68 421 421 0 strelka-varscan-mutect EYA1,missense_variant,p.Ser220Cys,ENST00000340726,NM_000503.5;EYA1,missense_variant,p.Ser214Cys,ENST00000303824,NM_001288575.1,NM_001288574.1;EYA1,missense_variant,p.Ser220Cys,ENST00000388742,NM_172058.3;EYA1,missense_variant,p.Ser187Cys,ENST00000388740,NM_172060.3;EYA1,missense_variant,p.Ser186Cys,ENST00000388741,;EYA1,missense_variant,p.Ser219Cys,ENST00000388743,;EYA1,missense_variant,p.Ser215Cys,ENST00000419131,NM_172059.3;EYA1,synonymous_variant,p.=,ENST00000465115,;EYA1,non_coding_transcript_exon_variant,,ENST00000496494,;EYA1,upstream_gene_variant,,ENST00000493349,; A ENST00000340726 Transcript missense_variant 1298/4326 658/1779 220/592 S/C Agt/Tgt 1 -1 EYA1 HGNC HGNC:3519 protein_coding YES CCDS34906.1 ENSP00000342626 Q99502 A0A024R813 UPI000012A3B3 NM_000503.5 tolerated(0.05) 9/18 hmmpanther:PTHR10190,hmmpanther:PTHR10190:SF11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 71299215 71299215 T A 1 0 0 0 0 1 0 0 0 5196 1580 55 4 4 EYA1 8 71299215 Missense_Mutation SNP T C3N-02089_T 4845088 71299215 73839421 457 27541 TRPA1 0 . GRCh38 8 72056987 72056987 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1124G>T p.Gly375Val p.G375V ENST00000262209 10/27 225 174 51 190 189 1 strelka-varscan-mutect TRPA1,missense_variant,p.Gly375Val,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Gly227Val,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,downstream_gene_variant,,ENST00000457356,;MSC-AS1,downstream_gene_variant,,ENST00000522519,;MSC-AS1,downstream_gene_variant,,ENST00000512290,;MSC-AS1,downstream_gene_variant,,ENST00000519751,;MSC-AS1,downstream_gene_variant,,ENST00000524152,;TRPA1,upstream_gene_variant,,ENST00000520788,; A ENST00000262209 Transcript missense_variant 1332/5223 1124/3360 375/1119 G/V gGa/gTa COSM5699970,COSM5699971 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 deleterious(0) 10/27 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6,Superfamily_domains:SSF48403 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 72056987 72056987 C A 1 0 0 0 0 1 0 0 0 17082 855 30 2 2 TRPA1 8 72056987 Missense_Mutation SNP C C3N-02089_T 757772 72056987 73081649 458 27542 TERF1 0 . GRCh38 8 73008907 73008907 + Silent SNP A A T rs768791939 C3N-02089_T C3N-02089_N A A c.21A>T p.= p.S7S ENST00000276603 1/10 205 181 24 126 126 0 strelka-varscan-mutect TERF1,synonymous_variant,p.=,ENST00000276602,NM_003218.3;TERF1,synonymous_variant,p.=,ENST00000276603,NM_017489.2;TERF1,synonymous_variant,p.=,ENST00000518874,;TERF1,upstream_gene_variant,,ENST00000517390,;TERF1,upstream_gene_variant,,ENST00000518695,; T ENST00000276603 Transcript synonymous_variant 44/1677 21/1320 7/439 S tcA/tcT rs768791939 1 1 TERF1 HGNC HGNC:11728 protein_coding YES CCDS6211.1 ENSP00000276603 P54274 UPI000013DAD5 NM_017489.2 1/10 PIRSF_domain:PIRSF038016 LOW 1 SNV 1 1 PASS rs768791939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 73008907 73008907 A T 1 0 0 0 0 0 0 0 1 16180 175 7 4 4 TERF1 8 73008907 Silent SNP A C3N-02089_T 951920 73008907 72129729 459 27543 ZFHX4 0 . GRCh38 8 76706431 76706431 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2343C>A p.Asn781Lys p.N781K ENST00000521891 2/11 261 179 82 202 202 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Asn781Lys,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Asn781Lys,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000520307,;ZFHX4,downstream_gene_variant,,ENST00000517585,;ZFHX4,downstream_gene_variant,,ENST00000523809,;ZFHX4,downstream_gene_variant,,ENST00000523885,;ZFHX4,intron_variant,,ENST00000517683,;ZFHX4,non_coding_transcript_exon_variant,,ENST00000458716,; A ENST00000521891 Transcript missense_variant 2791/14019 2343/10851 781/3616 N/K aaC/aaA 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0) 2/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 76706431 76706431 C A 1 0 0 0 0 1 0 0 0 18213 506 18 2 2 ZFHX4 8 76706431 Missense_Mutation SNP C C3N-02089_T 3697524 76706431 68432205 460 27544 PEX2 0 . GRCh38 8 76983845 76983845 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.334G>T p.Gly112Cys p.G112C ENST00000357039 4/4 432 399 33 394 394 0 strelka-varscan-mutect PEX2,missense_variant,p.Gly112Cys,ENST00000357039,NM_000318.2,NM_001172086.1;PEX2,missense_variant,p.Gly112Cys,ENST00000522527,NM_001079867.1;PEX2,missense_variant,p.Gly112Cys,ENST00000520103,NM_001172087.1;PEX2,missense_variant,p.Gly112Cys,ENST00000518986,;PEX2,downstream_gene_variant,,ENST00000519956,;PEX2,downstream_gene_variant,,ENST00000520203,; A ENST00000357039 Transcript missense_variant 730/4317 334/918 112/305 G/C Ggt/Tgt 1 -1 PEX2 HGNC HGNC:9717 protein_coding YES CCDS6221.1 ENSP00000349543 P28328 UPI000013E3FB NM_000318.2,NM_001172086.1 deleterious(0) 4/4 PD124462,Pfam_domain:PF04757 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 76983845 76983845 C A 1 0 0 0 0 1 0 0 0 11835 594 21 2 2 PEX2 8 76983845 Missense_Mutation SNP C C3N-02089_T 277414 76983845 68154791 461 27545 PSKH2 0 . GRCh38 8 86064476 86064476 + Missense_Mutation SNP C C A rs35915498 C3N-02089_T C3N-02089_N C C c.341G>T p.Arg114Leu p.R114L ENST00000276616 2/3 575 361 214 416 415 1 strelka-varscan-mutect PSKH2,missense_variant,p.Arg114Leu,ENST00000276616,NM_033126.1;ATP6V0D2,intron_variant,,ENST00000521564,;PSKH2,non_coding_transcript_exon_variant,,ENST00000517981,;PSKH2,non_coding_transcript_exon_variant,,ENST00000523010,; A ENST00000276616 Transcript missense_variant 416/1322 341/1158 114/385 R/L cGg/cTg rs35915498 1 -1 PSKH2 HGNC HGNC:18997 protein_coding YES CCDS6240.1 ENSP00000276616 Q96QS6 UPI000006F951 NM_033126.1 deleterious(0) 2/3 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF255,Pfam_domain:PF00069,Gene3D:3.30.200.20,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs35915498 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 86064476 86064476 C A 1 0 0 0 0 1 0 0 0 12816 652 23 1 1 PSKH2 8 86064476 Missense_Mutation SNP C C3N-02089_T 9080631 86064476 59074160 462 27546 CNGB3 0 . GRCh38 8 86628966 86628966 + Missense_Mutation SNP C C A rs772270787 C3N-02089_T C3N-02089_N C C c.1433G>T p.Arg478Leu p.R478L ENST00000320005 12/18 505 385 120 387 385 2 strelka-varscan-mutect CNGB3,missense_variant,p.Arg478Leu,ENST00000320005,NM_019098.4; A ENST00000320005 Transcript missense_variant 1481/4347 1433/2430 478/809 R/L cGa/cTa rs772270787,COSM3651524 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 deleterious(0) 12/18 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385,Gene3D:3bpzA01,Superfamily_domains:SSF51206 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772270787 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 86628966 86628966 C A 1 0 0 0 0 1 0 0 0 3381 884 31 1 1 CNGB3 8 86628966 Missense_Mutation SNP C C3N-02089_T 564490 86628966 58509670 463 27547 CNGB3 0 . GRCh38 8 86667085 86667085 + Missense_Mutation SNP C C A rs754946422 C3N-02089_T C3N-02089_N C C c.692G>T p.Trp231Leu p.W231L ENST00000320005 6/18 392 296 96 302 301 1 strelka-varscan-mutect CNGB3,missense_variant,p.Trp231Leu,ENST00000320005,NM_019098.4; A ENST00000320005 Transcript missense_variant 740/4347 692/2430 231/809 W/L tGg/tTg rs754946422,COSM343786 1 -1 CNGB3 HGNC HGNC:2153 protein_coding YES CCDS6244.1 ENSP00000316605 Q9NQW8 UPI000014076F NM_019098.4 deleterious(0) 6/18 Transmembrane_helices:TMhelix,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF385,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs754946422 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 86667085 86667085 C A 1 0 0 0 0 1 0 0 0 3381 595 21 2 2 CNGB3 8 86667085 Missense_Mutation SNP C C3N-02089_T 38119 86667085 58471551 464 27548 MMP16 0 . GRCh38 8 88041770 88041770 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1515G>T p.Lys505Asn p.K505N ENST00000286614 10/10 98 82 16 94 94 0 strelka-varscan-mutect MMP16,missense_variant,p.Lys505Asn,ENST00000286614,NM_005941.4; A ENST00000286614 Transcript missense_variant 1797/11558 1515/1824 505/607 K/N aaG/aaT 1 -1 MMP16 HGNC HGNC:7162 protein_coding YES CCDS6246.1 ENSP00000286614 P51512 UPI000003DC73 NM_005941.4 tolerated(0.89) 10/10 PROSITE_profiles:PS51642,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF26,Gene3D:2.110.10.10,PIRSF_domain:PIRSF001191,Pfam_domain:PF00045,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 88041770 88041770 C A 1 0 0 0 0 1 0 0 0 9618 680 24 2 2 MMP16 8 88041770 Missense_Mutation SNP C C3N-02089_T 1374685 88041770 57096866 465 27549 DPY19L4 0 . GRCh38 8 94739660 94739660 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.481G>C p.Val161Leu p.V161L ENST00000414645 6/19 144 97 47 107 107 0 strelka-varscan-mutect DPY19L4,missense_variant,p.Val161Leu,ENST00000414645,NM_181787.2;DPY19L4,missense_variant,p.Val132Leu,ENST00000519176,;DPY19L4,missense_variant,p.Val5Leu,ENST00000523020,;DPY19L4,missense_variant,p.Val11Leu,ENST00000521525,;DPY19L4,missense_variant,p.Val89Leu,ENST00000522422,;DPY19L4,missense_variant,p.Val93Leu,ENST00000519353,;DPY19L4,3_prime_UTR_variant,,ENST00000520774,; C ENST00000414645 Transcript missense_variant 580/6197 481/2172 161/723 V/L Gtg/Ctg 1 1 DPY19L4 HGNC HGNC:27829 protein_coding YES CCDS34924.1 ENSP00000389630 Q7Z388 A0A024R9F2 UPI00001A9D7A NM_181787.2 deleterious(0.01) 6/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 1 1 PASS rs1037399939 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 94739660 94739660 G C 1 0 0 0 0 1 0 0 0 4558 1029 36 4 4 DPY19L4 8 94739660 Missense_Mutation SNP G C3N-02089_T 6697890 94739660 50398976 466 27550 DPY19L4 0 . GRCh38 8 94765272 94765272 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.960A>C p.Leu320Phe p.L320F ENST00000414645 9/19 164 151 13 164 164 0 strelka-varscan-mutect DPY19L4,missense_variant,p.Leu320Phe,ENST00000414645,NM_181787.2;DPY19L4,intron_variant,,ENST00000523020,; C ENST00000414645 Transcript missense_variant 1059/6197 960/2172 320/723 L/F ttA/ttC 1 1 DPY19L4 HGNC HGNC:27829 protein_coding YES CCDS34924.1 ENSP00000389630 Q7Z388 A0A024R9F2 UPI00001A9D7A NM_181787.2 deleterious(0.02) 9/19 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF2,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 1 1 PASS rs1255253360 . 0 208 0 2 0 0 0 0 -17.66515 0.9999997 1 1 1 0 C 3 2 90 94765272 94765272 A C 1 0 0 0 0 1 0 0 0 4558 446 16 5 5 DPY19L4 8 94765272 Missense_Mutation SNP A C3N-02089_T 25612 94765272 50373364 467 27551 INTS8 0 . GRCh38 8 94856975 94856975 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1951C>T p.Pro651Ser p.P651S ENST00000523731 15/27 173 162 11 125 125 0 strelka-varscan-mutect INTS8,missense_variant,p.Pro651Ser,ENST00000523731,NM_017864.3;INTS8,missense_variant,p.Pro473Ser,ENST00000520526,;INTS8,non_coding_transcript_exon_variant,,ENST00000520845,;INTS8,missense_variant,p.Pro651Ser,ENST00000343161,;INTS8,missense_variant,p.Pro5Ser,ENST00000520315,;INTS8,3_prime_UTR_variant,,ENST00000523206,;INTS8,3_prime_UTR_variant,,ENST00000524333,;INTS8,non_coding_transcript_exon_variant,,ENST00000523321,; T ENST00000523731 Transcript missense_variant 2084/4633 1951/2988 651/995 P/S Cct/Tct 1 1 INTS8 HGNC HGNC:26048 protein_coding YES CCDS34925.1 ENSP00000430338 Q75QN2 UPI000023B7D0 NM_017864.3 tolerated(0.49) 15/27 hmmpanther:PTHR13350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 94856975 94856975 C T 1 0 0 0 0 1 0 0 0 7687 869 30 3 3 INTS8 8 94856975 Missense_Mutation SNP C C3N-02089_T 91703 94856975 50281661 468 27552 PTDSS1 0 . GRCh38 8 96299754 96299754 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.661G>C p.Asp221His p.D221H ENST00000517309 6/13 285 245 40 220 220 0 strelka-varscan-mutect PTDSS1,missense_variant,p.Asp221His,ENST00000517309,NM_014754.2;PTDSS1,missense_variant,p.Asp18His,ENST00000522072,;PTDSS1,non_coding_transcript_exon_variant,,ENST00000518776,;PTDSS1,3_prime_UTR_variant,,ENST00000337004,NM_001290225.1; C ENST00000517309 Transcript missense_variant 987/5177 661/1422 221/473 D/H Gac/Cac 1 1 PTDSS1 HGNC HGNC:9587 protein_coding YES CCDS6271.1 ENSP00000430548 P48651 UPI0000132810 NM_014754.2 deleterious(0) 6/13 Transmembrane_helices:TMhelix,hmmpanther:PTHR15362,hmmpanther:PTHR15362:SF8,Pfam_domain:PF03034 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 96299754 96299754 G C 1 0 0 0 0 1 0 0 0 12889 1174 41 4 4 PTDSS1 8 96299754 Missense_Mutation SNP G C3N-02089_T 1442779 96299754 48838882 469 27553 OSR2 0 . GRCh38 8 98948992 98948992 + Missense_Mutation SNP C C T rs756940497 C3N-02089_T C3N-02089_N C C c.403C>T p.Pro135Ser p.P135S ENST00000457907 3/5 362 301 61 227 226 1 strelka-varscan-mutect OSR2,missense_variant,p.Pro135Ser,ENST00000457907,NM_001286841.1;OSR2,missense_variant,p.Pro14Ser,ENST00000297565,NM_001142462.2;OSR2,missense_variant,p.Pro14Ser,ENST00000435298,NM_053001.3;OSR2,missense_variant,p.Pro14Ser,ENST00000522510,;OSR2,missense_variant,p.Pro14Ser,ENST00000523368,;OSR2,missense_variant,p.Pro14Ser,ENST00000518199,;OSR2,missense_variant,p.Pro67Ser,ENST00000520951,;RP11-44N12.5,downstream_gene_variant,,ENST00000606778,;OSR2,intron_variant,,ENST00000521044,;OSR2,intron_variant,,ENST00000520722,;OSR2,downstream_gene_variant,,ENST00000520791,; T ENST00000457907 Transcript missense_variant 824/2126 403/1302 135/433 P/S Ccg/Tcg rs756940497 1 1 OSR2 HGNC HGNC:15830 protein_coding YES CCDS69520.1 ENSP00000414657 Q8N2R0 UPI00017A85FA NM_001286841.1 deleterious_low_confidence(0) 3/5 hmmpanther:PTHR14196:SF4,hmmpanther:PTHR14196 MODERATE 1 SNV 2 1 PASS rs756940497 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 98948992 98948992 C T 1 0 0 0 0 1 0 0 0 11361 623 22 3 3 OSR2 8 98948992 Missense_Mutation SNP C C3N-02089_T 2649238 98948992 46189644 470 27554 ATP6V1C1 0 . GRCh38 8 103042376 103042376 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.169G>T p.Glu57Ter p.E57* ENST00000395862 3/13 281 253 28 219 219 0 strelka-varscan-mutect ATP6V1C1,stop_gained,p.Glu57Ter,ENST00000395862,NM_001695.4;ATP6V1C1,stop_gained,p.Glu57Ter,ENST00000518738,;ATP6V1C1,5_prime_UTR_variant,,ENST00000521514,;ATP6V1C1,intron_variant,,ENST00000518857,; T ENST00000395862 Transcript stop_gained 328/5612 169/1149 57/382 E/* Gaa/Taa 1 1 ATP6V1C1 HGNC HGNC:856 protein_coding YES CCDS6296.1 ENSP00000379203 P21283 A0A024R9I0 UPI0000049C2A NM_001695.4 3/13 hmmpanther:PTHR10137:SF5,hmmpanther:PTHR10137,Pfam_domain:PF03223,Gene3D:1u7lA02,Superfamily_domains:0049812 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 103042376 103042376 G T 1 0 0 0 0 0 1 0 0 1333 1291 45 2 2 ATP6V1C1 8 103042376 Nonsense_Mutation SNP G C3N-02089_T 4093384 103042376 42096260 471 27555 RIMS2 0 . GRCh38 8 103936633 103936633 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2458C>A p.His820Asn p.H820N ENST00000504942 13/24 153 139 14 141 140 1 strelka-varscan-mutect RIMS2,missense_variant,p.His612Asn,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.His598Asn,ENST00000436393,;RIMS2,missense_variant,p.His820Asn,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.His762Asn,ENST00000626043,;RIMS2,missense_variant,p.His612Asn,ENST00000408894,;RIMS2,missense_variant,p.His659Asn,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.His808Asn,ENST00000632716,;RIMS2,missense_variant,p.His214Asn,ENST00000507677,;RIMS2,missense_variant,p.His612Asn,ENST00000515551,; A ENST00000504942 Transcript missense_variant 2597/4228 2458/4050 820/1349 H/N Cac/Aac 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 13/24 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 103936633 103936633 C A 1 0 0 0 0 1 0 0 0 13543 594 21 2 2 RIMS2 8 103936633 Missense_Mutation SNP C C3N-02089_T 894257 103936633 41202003 472 27556 ZFPM2 0 . GRCh38 8 105803184 105803184 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.3102G>T p.Leu1034Phe p.L1034F ENST00000407775 8/8 139 117 22 119 118 1 strelka-varscan-mutect ZFPM2,missense_variant,p.Leu1034Phe,ENST00000407775,NM_012082.3;ZFPM2,missense_variant,p.Leu902Phe,ENST00000520492,;ZFPM2,missense_variant,p.Leu902Phe,ENST00000517361,;ZFPM2-AS1,intron_variant,,ENST00000524045,;ZFPM2-AS1,intron_variant,,ENST00000520433,;ZFPM2-AS1,intron_variant,,ENST00000518932,;ZFPM2-AS1,intron_variant,,ENST00000520594,;ZFPM2-AS1,intron_variant,,ENST00000509144,;ZFPM2-AS1,intron_variant,,ENST00000521622,;ZFPM2,non_coding_transcript_exon_variant,,ENST00000522296,;ZFPM2-AS1,intron_variant,,ENST00000520078,; T ENST00000407775 Transcript missense_variant 3352/4700 3102/3456 1034/1151 L/F ttG/ttT 1 1 ZFPM2 HGNC HGNC:16700 protein_coding YES CCDS47908.1 ENSP00000384179 Q8WW38 UPI000057A0B4 NM_012082.3 deleterious_low_confidence(0.03) 8/8 hmmpanther:PTHR12958,hmmpanther:PTHR12958:SF5 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 90 105803184 105803184 G T 1 0 0 0 0 1 0 0 0 18236 1368 48 2 2 ZFPM2 8 105803184 Missense_Mutation SNP G C3N-02089_T 1866551 105803184 39335452 473 27557 TRHR 0 . GRCh38 8 109087935 109087935 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.423A>G p.= p.R141R ENST00000518632 2/3 600 487 113 478 478 0 strelka-varscan-mutect TRHR,synonymous_variant,p.=,ENST00000518632,;TRHR,synonymous_variant,p.=,ENST00000311762,NM_003301.5; G ENST00000518632 Transcript synonymous_variant 774/1660 423/1197 141/398 R agA/agG 1 1 TRHR HGNC HGNC:12299 protein_coding YES CCDS6311.1 ENSP00000430711 P34981 UPI0000050437 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR00751,PROSITE_profiles:PS50262,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF115,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 109087935 109087935 A G 1 0 0 0 0 0 0 0 1 16969 301 11 5 5 TRHR 8 109087935 Silent SNP A C3N-02089_T 3284751 109087935 36050701 474 27558 CSMD3 0 . GRCh38 8 112337728 112337728 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.6656A>T p.Tyr2219Phe p.Y2219F ENST00000297405 43/71 115 84 31 100 100 0 varscan-mutect CSMD3,missense_variant,p.Tyr2219Phe,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Tyr2179Phe,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Tyr2115Phe,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Tyr1489Phe,ENST00000339701,;CSMD3,upstream_gene_variant,,ENST00000492692,; A ENST00000297405 Transcript missense_variant 6901/13212 6656/11124 2219/3707 Y/F tAt/tTt 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.02) 43/71 PROSITE_profiles:PS01180,SMART_domains:SM00042 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 112337728 112337728 T A 1 0 0 0 0 1 0 0 0 3747 1420 49 4 4 CSMD3 8 112337728 Missense_Mutation SNP T C3N-02089_T 3249793 112337728 32800908 475 27559 EIF3H 0 . GRCh38 8 116658839 116658839 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.431T>C p.Ile144Thr p.I144T ENST00000521861 3/8 235 185 50 170 169 1 strelka-varscan-mutect EIF3H,missense_variant,p.Ile144Thr,ENST00000521861,NM_003756.2;EIF3H,missense_variant,p.Ile158Thr,ENST00000276682,;EIF3H,missense_variant,p.Ile141Thr,ENST00000611080,;EIF3H,missense_variant,p.Ile112Thr,ENST00000518949,;EIF3H,missense_variant,p.Ile160Thr,ENST00000518995,;EIF3H,missense_variant,p.Ile168Thr,ENST00000522453,;EIF3H,3_prime_UTR_variant,,ENST00000522800,;EIF3H,non_coding_transcript_exon_variant,,ENST00000518034,;EIF3H,non_coding_transcript_exon_variant,,ENST00000517974,;EIF3H,upstream_gene_variant,,ENST00000520289,;EIF3H,downstream_gene_variant,,ENST00000519046,; G ENST00000521861 Transcript missense_variant 455/3959 431/1059 144/352 I/T aTt/aCt 1 -1 EIF3H HGNC HGNC:3273 protein_coding YES CCDS6319.1 ENSP00000429931 O15372 Q6IB98 UPI00000477E8 NM_003756.2 deleterious(0) 3/8 HAMAP:MF_03007,hmmpanther:PTHR10410:SF3,hmmpanther:PTHR10410,Pfam_domain:PF01398,SMART_domains:SM00232 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 116658839 116658839 A G 1 0 0 0 0 1 0 0 0 4852 101 4 5 5 EIF3H 8 116658839 Missense_Mutation SNP A C3N-02089_T 4321111 116658839 28479797 476 27560 DEPTOR 0 . GRCh38 8 120009038 120009038 + Missense_Mutation SNP G G A rs781608833 C3N-02089_T C3N-02089_N G G c.1006G>A p.Asp336Asn p.D336N ENST00000286234 8/9 314 279 35 169 169 0 strelka-varscan-mutect DEPTOR,missense_variant,p.Asp336Asn,ENST00000286234,NM_022783.3;DEPTOR,missense_variant,p.Asp235Asn,ENST00000523492,NM_001283012.1;DEPTOR,non_coding_transcript_exon_variant,,ENST00000518057,; A ENST00000286234 Transcript missense_variant 1136/2569 1006/1230 336/409 D/N Gac/Aac rs781608833 1 1 DEPTOR HGNC HGNC:22953 protein_coding YES CCDS6331.1 ENSP00000286234 Q8TB45 UPI000013DE38 NM_022783.3 deleterious(0.01) 8/9 Gene3D:2.30.42.10,PROSITE_profiles:PS50106,hmmpanther:PTHR22829,hmmpanther:PTHR22829:SF18,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs781608833 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 120009038 120009038 G A 1 0 0 0 0 1 0 0 0 4250 1290 45 3 3 DEPTOR 8 120009038 Missense_Mutation SNP G C3N-02089_T 3350199 120009038 25129598 477 27561 COL14A1 0 . GRCh38 8 120247696 120247696 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2563C>A p.Pro855Thr p.P855T ENST00000297848 21/48 239 184 55 185 185 0 strelka-varscan-mutect COL14A1,missense_variant,p.Pro855Thr,ENST00000297848,NM_021110.2;COL14A1,missense_variant,p.Pro855Thr,ENST00000309791,;COL14A1,missense_variant,p.Pro668Thr,ENST00000434620,;COL14A1,upstream_gene_variant,,ENST00000247781,;COL14A1,non_coding_transcript_exon_variant,,ENST00000432943,; A ENST00000297848 Transcript missense_variant 2833/6466 2563/5391 855/1796 P/T Ccg/Acg 1 1 COL14A1 HGNC HGNC:2191 protein_coding YES CCDS34938.1 ENSP00000297848 Q05707 UPI000046D377 NM_021110.2 tolerated(0.05) 21/48 PROSITE_profiles:PS50853,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 120247696 120247696 C A 1 0 0 0 0 1 0 0 0 3459 623 22 2 2 COL14A1 8 120247696 Missense_Mutation SNP C C3N-02089_T 238658 120247696 24890940 478 27562 MTBP 0 . GRCh38 8 120445548 120445548 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.78G>C p.= p.G26G ENST00000305949 1/22 161 150 11 86 86 0 strelka-varscan-mutect MTBP,synonymous_variant,p.=,ENST00000305949,NM_022045.4;MRPL13,upstream_gene_variant,,ENST00000306185,NM_014078.5;MRPL13,upstream_gene_variant,,ENST00000518918,;MTBP,synonymous_variant,p.=,ENST00000523373,;MTBP,non_coding_transcript_exon_variant,,ENST00000522308,;MTBP,non_coding_transcript_exon_variant,,ENST00000456899,;MRPL13,upstream_gene_variant,,ENST00000518696,;MRPL13,upstream_gene_variant,,ENST00000520677,; C ENST00000305949 Transcript synonymous_variant 123/3059 78/2715 26/904 G ggG/ggC 1 1 MTBP HGNC HGNC:7417 protein_coding YES CCDS6333.1 ENSP00000303398 Q96DY7 UPI00000703F0 NM_022045.4 1/22 Pfam_domain:PF14918,hmmpanther:PTHR14382,hmmpanther:PTHR14382:SF1 LOW 1 SNV 1 1 PASS rs1177853863 . 0 204 5 0 0 0 0 0 -19.71411 1 1 1 1 0 C 2 2 90 120445548 120445548 G C 1 0 0 0 0 0 0 0 1 9897 1190 42 4 4 MTBP 8 120445548 Silent SNP G C3N-02089_T 197852 120445548 24693088 479 27563 RNF139 0 . GRCh38 8 124486466 124486466 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.817T>A p.Phe273Ile p.F273I ENST00000303545 2/2 395 372 23 313 313 0 strelka-varscan-mutect RNF139,missense_variant,p.Phe273Ile,ENST00000303545,NM_007218.3;TATDN1,downstream_gene_variant,,ENST00000276692,NM_032026.3;TATDN1,downstream_gene_variant,,ENST00000522810,;TATDN1,downstream_gene_variant,,ENST00000630259,;TATDN1,downstream_gene_variant,,ENST00000519548,NM_001146160.1;RNF139,downstream_gene_variant,,ENST00000517684,;RP11-158K1.3,upstream_gene_variant,,ENST00000518639,;TATDN1,downstream_gene_variant,,ENST00000523631,;TATDN1,downstream_gene_variant,,ENST00000523214,NM_001317889.1;TATDN1,downstream_gene_variant,,ENST00000522927,NM_001317891.1; A ENST00000303545 Transcript missense_variant 1189/2637 817/1995 273/664 F/I Ttt/Att 1 1 RNF139 HGNC HGNC:17023 protein_coding YES CCDS6350.1 ENSP00000304051 Q8WU17 UPI0000071331 NM_007218.3 deleterious(0.05) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR22763:SF31,hmmpanther:PTHR22763,Pfam_domain:PF13705 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 124486466 124486466 T A 1 0 0 0 0 1 0 0 0 13620 1841 64 4 4 RNF139 8 124486466 Missense_Mutation SNP T C3N-02089_T 4040918 124486466 20652170 480 27564 TRIB1 0 . GRCh38 8 125436190 125436190 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.838G>C p.Gly280Arg p.G280R ENST00000311922 3/3 483 452 31 304 304 0 strelka-varscan-mutect TRIB1,missense_variant,p.Gly280Arg,ENST00000311922,NM_025195.3;TRIB1,missense_variant,p.Gly49Arg,ENST00000519576,;TRIB1,missense_variant,p.Gly114Arg,ENST00000520847,NM_001282985.1;TRIB1,downstream_gene_variant,,ENST00000521778,; C ENST00000311922 Transcript missense_variant 1420/3635 838/1119 280/372 G/R Gga/Cga COSM5612993 1 1 TRIB1 HGNC HGNC:16891 protein_coding YES CCDS6357.1 ENSP00000312150 Q96RU8 UPI00000717B2 NM_025195.3 deleterious(0) 3/3 PROSITE_profiles:PS50011,hmmpanther:PTHR22961,hmmpanther:PTHR22961:SF17,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 125436190 125436190 G C 1 0 0 0 0 1 0 0 0 16971 1349 47 4 4 TRIB1 8 125436190 Missense_Mutation SNP G C3N-02089_T 949724 125436190 19702446 481 27565 POU5F1B 0 . GRCh38 8 127416095 127416095 + Missense_Mutation SNP G G T rs780624994 C3N-02089_T C3N-02089_N G G c.229G>T p.Gly77Trp p.G77W ENST00000465342 2/2 333 210 123 201 201 0 strelka-varscan-mutect POU5F1B,missense_variant,p.Gly77Trp,ENST00000465342,NM_001159542.1;CASC8,intron_variant,,ENST00000502082,;CASC8,intron_variant,,ENST00000501396,;CASC8,intron_variant,,ENST00000523825,; T ENST00000465342 Transcript missense_variant 1386/5360 229/1080 77/359 G/W Ggg/Tgg rs780624994 1 1 POU5F1B HGNC HGNC:9223 protein_coding YES CCDS55274.1 ENSP00000419298 Q06416 UPI000013F18B NM_001159542.1 deleterious(0.01) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF86 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 127416095 127416095 G T 1 0 0 0 0 1 0 0 0 12398 1348 47 2 2 POU5F1B 8 127416095 Missense_Mutation SNP G C3N-02089_T 1979905 127416095 17722541 482 27566 POU5F1B 0 . GRCh38 8 127416570 127416570 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.704C>A p.Thr235Asn p.T235N ENST00000465342 2/2 795 481 314 538 536 2 strelka-varscan-mutect POU5F1B,missense_variant,p.Thr235Asn,ENST00000465342,NM_001159542.1;CASC8,intron_variant,,ENST00000502082,;CASC8,intron_variant,,ENST00000501396,;CASC8,intron_variant,,ENST00000523825,; A ENST00000465342 Transcript missense_variant 1861/5360 704/1080 235/359 T/N aCc/aAc 1 1 POU5F1B HGNC HGNC:9223 protein_coding YES CCDS55274.1 ENSP00000419298 Q06416 UPI000013F18B NM_001159542.1 deleterious(0.02) 2/2 PROSITE_profiles:PS50071,hmmpanther:PTHR11636,hmmpanther:PTHR11636:SF86,Pfam_domain:PF00046,Gene3D:1.10.10.60,SMART_domains:SM00389,Superfamily_domains:SSF46689,Prints_domain:PR00028 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 127416570 127416570 C A 1 0 0 0 0 1 0 0 0 12398 507 18 2 2 POU5F1B 8 127416570 Missense_Mutation SNP C C3N-02089_T 475 127416570 17722066 483 27567 KCNQ3 0 . GRCh38 8 132175596 132175596 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.790G>T p.Ala264Ser p.A264S ENST00000388996 5/15 583 336 247 402 400 2 strelka-varscan-mutect KCNQ3,missense_variant,p.Ala264Ser,ENST00000388996,NM_004519.3;KCNQ3,missense_variant,p.Ala143Ser,ENST00000621976,;KCNQ3,missense_variant,p.Ala264Ser,ENST00000519445,;KCNQ3,missense_variant,p.Ala144Ser,ENST00000521134,NM_001204824.1;KCNQ3,non_coding_transcript_exon_variant,,ENST00000519589,; A ENST00000388996 Transcript missense_variant 1211/11441 790/2619 264/872 A/S Gcc/Tcc COSM3395106 1 -1 KCNQ3 HGNC HGNC:6297 protein_coding YES CCDS34943.1 ENSP00000373648 O43525 UPI00001279F0 NM_004519.3 deleterious(0.01) 5/15 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,Prints_domain:PR01459,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF5,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 132175596 132175596 C A 1 0 0 0 0 1 0 0 0 8000 739 26 2 2 KCNQ3 8 132175596 Missense_Mutation SNP C C3N-02089_T 4759026 132175596 12963040 484 27568 PHF20L1 0 . GRCh38 8 132794478 132794478 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.152G>T p.Ser51Ile p.S51I ENST00000395386 3/21 310 288 22 204 204 0 strelka-varscan-mutect PHF20L1,missense_variant,p.Ser51Ile,ENST00000395386,NM_016018.4;PHF20L1,missense_variant,p.Ser51Ile,ENST00000395390,;PHF20L1,missense_variant,p.Ser51Ile,ENST00000622263,;PHF20L1,missense_variant,p.Ser51Ile,ENST00000220847,NM_001277196.1;PHF20L1,missense_variant,p.Ser51Ile,ENST00000337920,NM_198513.1;PHF20L1,missense_variant,p.Ser51Ile,ENST00000395376,;PHF20L1,missense_variant,p.Ser51Ile,ENST00000395379,;PHF20L1,missense_variant,p.Ser51Ile,ENST00000485595,;PHF20L1,missense_variant,p.Ser9Ile,ENST00000522580,;PHF20L1,missense_variant,p.Ser51Ile,ENST00000486199,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000361997,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000395383,;PHF20L1,non_coding_transcript_exon_variant,,ENST00000315808,;PHF20L1,upstream_gene_variant,,ENST00000521038,; T ENST00000395386 Transcript missense_variant 451/6237 152/3054 51/1017 S/I aGt/aTt 1 1 PHF20L1 HGNC HGNC:24280 protein_coding YES CCDS6367.2 ENSP00000378784 A8MW92 UPI0000DBD7AF NM_016018.4 deleterious(0) 3/21 hmmpanther:PTHR15856:SF26,hmmpanther:PTHR15856,Gene3D:2.30.30.160,SMART_domains:SM00743,SMART_domains:SM00333,Superfamily_domains:SSF63748 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 132794478 132794478 G T 1 0 0 0 0 1 0 0 0 11918 1029 36 2 2 PHF20L1 8 132794478 Missense_Mutation SNP G C3N-02089_T 618882 132794478 12344158 485 27569 FAM135B 0 . GRCh38 8 138178578 138178578 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.986C>A p.Ser329Tyr p.S329Y ENST00000395297 10/20 332 299 33 183 183 0 strelka-varscan-mutect FAM135B,missense_variant,p.Ser329Tyr,ENST00000395297,NM_015912.3;FAM135B,missense_variant,p.Ser329Tyr,ENST00000276737,;FAM135B,3_prime_UTR_variant,,ENST00000482951,; T ENST00000395297 Transcript missense_variant 1157/6962 986/4221 329/1406 S/Y tCc/tAc COSM3645573,COSM3645574 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 deleterious(0) 10/20 hmmpanther:PTHR12482:SF3,hmmpanther:PTHR12482 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 138178578 138178578 G T 1 0 0 0 0 1 0 0 0 5299 1174 41 2 2 FAM135B 8 138178578 Missense_Mutation SNP G C3N-02089_T 5384100 138178578 6960058 486 27570 CYP11B1 0 . GRCh38 8 142877077 142877077 + Silent SNP G G T rs373856010 C3N-02089_T C3N-02089_N G G c.541C>A p.= p.R181R ENST00000292427 3/9 383 334 49 257 257 0 varscan-mutect CYP11B1,synonymous_variant,p.=,ENST00000292427,NM_000497.3;CYP11B1,synonymous_variant,p.=,ENST00000377675,;CYP11B1,synonymous_variant,p.=,ENST00000517471,NM_001026213.1;GML,intron_variant,,ENST00000522728,;CYP11B1,upstream_gene_variant,,ENST00000519285,;CYP11B1,non_coding_transcript_exon_variant,,ENST00000314111,; T ENST00000292427 Transcript synonymous_variant 574/2664 541/1512 181/503 R Cgg/Agg rs373856010 1 -1 CYP11B1 HGNC HGNC:2591 protein_coding YES CCDS6392.1 ENSP00000292427 P15538 UPI000013E0BA NM_000497.3 3/9 hmmpanther:PTHR24279,hmmpanther:PTHR24279:SF46,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS rs373856010 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 142877077 142877077 G T 1 0 0 0 0 0 0 0 1 3948 1115 39 1 1 CYP11B1 8 142877077 Silent SNP G C3N-02089_T 4698499 142877077 2261559 487 27571 ZNF696 0 . GRCh38 8 143296665 143296665 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.990C>A p.Phe330Leu p.F330L ENST00000330143 3/3 126 114 12 93 93 0 strelka-varscan ZNF696,missense_variant,p.Phe330Leu,ENST00000330143,NM_030895.2;ZNF696,downstream_gene_variant,,ENST00000518575,;ZNF696,downstream_gene_variant,,ENST00000521537,;ZNF696,downstream_gene_variant,,ENST00000520333,;ZNF696,downstream_gene_variant,,ENST00000523891,;ZNF696,downstream_gene_variant,,ENST00000518432,; A ENST00000330143 Transcript missense_variant 1399/2795 990/1125 330/374 F/L ttC/ttA 1 1 ZNF696 HGNC HGNC:25872 protein_coding YES CCDS6399.1 ENSP00000328515 Q9H7X3 UPI000013E0BC NM_030895.2 deleterious(0) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF110,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.99989 1 1 1 1 0 A 3 1 90 143296665 143296665 C A 1 0 0 0 0 1 0 0 0 18672 854 30 2 2 ZNF696 8 143296665 Missense_Mutation SNP C C3N-02089_T 419588 143296665 1841971 488 27572 ZNF696 0 . GRCh38 8 143296688 143296688 + Missense_Mutation SNP G G T rs763590560 C3N-02089_T C3N-02089_N G G c.1013G>T p.Arg338Leu p.R338L ENST00000330143 3/3 101 90 11 101 101 0 strelka-varscan ZNF696,missense_variant,p.Arg338Leu,ENST00000330143,NM_030895.2;ZNF696,downstream_gene_variant,,ENST00000518575,;ZNF696,downstream_gene_variant,,ENST00000521537,;ZNF696,downstream_gene_variant,,ENST00000520333,;ZNF696,downstream_gene_variant,,ENST00000523891,;ZNF696,downstream_gene_variant,,ENST00000518432,; T ENST00000330143 Transcript missense_variant 1422/2795 1013/1125 338/374 R/L cGg/cTg rs763590560 1 1 ZNF696 HGNC HGNC:25872 protein_coding YES CCDS6399.1 ENSP00000328515 Q9H7X3 UPI000013E0BC NM_030895.2 tolerated(0.12) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF110,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 202 7 0 0 0 0 0 -19.9982 0.9999991 1 1 1 0 T 3 4 90 143296688 143296688 G T 1 0 0 0 0 1 0 0 0 18672 1116 39 1 1 ZNF696 8 143296688 Missense_Mutation SNP G C3N-02089_T 23 143296688 1841948 489 27573 ZNF623 0 . GRCh38 8 143650591 143650591 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.719G>C p.Cys240Ser p.C240S ENST00000501748 1/1 261 215 46 191 191 0 strelka-varscan-mutect ZNF623,missense_variant,p.Cys240Ser,ENST00000501748,NM_014789.3;ZNF623,missense_variant,p.Cys200Ser,ENST00000458270,NM_001082480.2;ZNF623,missense_variant,p.Cys200Ser,ENST00000526926,NM_001261843.1; C ENST00000501748 Transcript missense_variant 932/6759 719/1611 240/536 C/S tGt/tCt 1 1 ZNF623 HGNC HGNC:29084 protein_coding YES CCDS34957.1 ENSP00000445979 O75123 UPI0000139B4D NM_014789.3 deleterious(0) 1/1 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF244,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 143650591 143650591 G C 1 0 0 0 0 1 0 0 0 18622 1377 48 4 4 ZNF623 8 143650591 Missense_Mutation SNP G C3N-02089_T 353903 143650591 1488045 490 27574 CCDC166 0 . GRCh38 8 143706915 143706915 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1099G>T p.Gly367Cys p.G367C ENST00000542437 2/2 234 137 97 131 131 0 strelka-varscan-mutect CCDC166,missense_variant,p.Gly367Cys,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; A ENST00000542437 Transcript missense_variant 1099/1320 1099/1320 367/439 G/C Ggc/Tgc 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 deleterious(0.05) 2/2 hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 143706915 143706915 C A 1 0 0 0 0 1 0 0 0 2482 681 24 2 2 CCDC166 8 143706915 Missense_Mutation SNP C C3N-02089_T 56324 143706915 1431721 491 27575 CCDC166 0 . GRCh38 8 143707087 143707087 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.927G>A p.= p.Q309Q ENST00000542437 2/2 159 142 17 68 68 0 strelka-varscan-mutect CCDC166,synonymous_variant,p.=,ENST00000542437,NM_001162914.1;RP11-429J17.4,downstream_gene_variant,,ENST00000527579,;ZNF707,intron_variant,,ENST00000527561,;ZNF707,upstream_gene_variant,,ENST00000508587,; T ENST00000542437 Transcript synonymous_variant 927/1320 927/1320 309/439 Q caG/caA 1 -1 CCDC166 HGNC HGNC:41910 protein_coding YES CCDS55280.1 ENSP00000437468 P0CW27 UPI00016623E2 NM_001162914.1 2/2 hmmpanther:PTHR14845,hmmpanther:PTHR14845:SF4 LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 143707087 143707087 C T 1 0 0 0 0 0 0 0 1 2482 912 32 3 3 CCDC166 8 143707087 Silent SNP C C3N-02089_T 172 143707087 1431549 492 27576 MROH1 0 . GRCh38 8 144260937 144260937 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.4567C>A p.Pro1523Thr p.P1523T ENST00000528919 40/43 1112 1045 67 689 688 1 strelka-varscan-mutect MROH1,missense_variant,p.Pro1523Thr,ENST00000528919,NM_032450.2;MROH1,missense_variant,p.Pro1523Thr,ENST00000326134,;MROH1,missense_variant,p.Pro1514Thr,ENST00000534366,NM_001288814.1;MROH1,missense_variant,p.Pro485Thr,ENST00000544576,;BOP1,downstream_gene_variant,,ENST00000569669,NM_015201.4;BOP1,downstream_gene_variant,,ENST00000569403,;BOP1,downstream_gene_variant,,ENST00000616126,;BOP1,downstream_gene_variant,,ENST00000563210,;BOP1,downstream_gene_variant,,ENST00000568812,;BOP1,downstream_gene_variant,,ENST00000569160,; A ENST00000528919 Transcript missense_variant 4688/5234 4567/4926 1523/1641 P/T Ccc/Acc 1 1 MROH1 HGNC HGNC:26958 protein_coding YES CCDS47938.1 ENSP00000435565 Q8NDA8 UPI0001AE6FA6 NM_032450.2 deleterious(0.01) 40/43 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs930805641 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 144260937 144260937 C A 1 0 0 0 0 1 0 0 0 9743 623 22 2 2 MROH1 8 144260937 Missense_Mutation SNP C C3N-02089_T 553850 144260937 877699 493 27577 SLC39A4 0 . GRCh38 8 144414362 144414362 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1049G>A p.Cys350Tyr p.C350Y ENST00000301305 6/12 347 274 73 182 182 0 strelka-varscan-mutect SLC39A4,missense_variant,p.Cys325Tyr,ENST00000276833,NM_017767.2;SLC39A4,missense_variant,p.Cys350Tyr,ENST00000301305,NM_130849.3;SLC39A4,downstream_gene_variant,,ENST00000526658,;GS1-393G12.14,downstream_gene_variant,,ENST00000607491,;SLC39A4,upstream_gene_variant,,ENST00000531013,;SLC39A4,upstream_gene_variant,,ENST00000527148,;SLC39A4,upstream_gene_variant,,ENST00000532718,;SLC39A4,upstream_gene_variant,,ENST00000530807,;SLC39A4,upstream_gene_variant,,ENST00000531789,;SLC39A4,upstream_gene_variant,,ENST00000529462,; T ENST00000301305 Transcript missense_variant 1155/2174 1049/1944 350/647 C/Y tGc/tAc 1 -1 SLC39A4 HGNC HGNC:17129 protein_coding YES CCDS6424.1 ENSP00000301305 Q6P5W5 UPI0002064DC4 NM_130849.3 deleterious(0) 6/12 Pfam_domain:PF02535,hmmpanther:PTHR12191,hmmpanther:PTHR12191:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 144414362 144414362 C T 1 0 0 0 0 1 0 0 0 14898 710 25 3 3 SLC39A4 8 144414362 Missense_Mutation SNP C C3N-02089_T 153425 144414362 724274 494 27578 DMRT2 0 . GRCh38 9 1051966 1051966 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.353G>T p.Ser118Ile p.S118I ENST00000382251 3/5 96 74 22 52 52 0 strelka-varscan-mutect DMRT2,missense_variant,p.Ser118Ile,ENST00000259622,;DMRT2,missense_variant,p.Ser118Ile,ENST00000382255,NM_006557.6,NM_001130865.2;DMRT2,missense_variant,p.Ser118Ile,ENST00000382251,NM_181872.4;DMRT2,missense_variant,p.Ser118Ile,ENST00000635183,;DMRT2,missense_variant,p.Ser118Ile,ENST00000358146,;DMRT2,missense_variant,p.Ser118Ile,ENST00000412350,;DMRT2,intron_variant,,ENST00000302441,;LINC01230,downstream_gene_variant,,ENST00000625222,;DMRT2,upstream_gene_variant,,ENST00000634526,;DMRT2,upstream_gene_variant,,ENST00000634824,; T ENST00000382251 Transcript missense_variant 682/2292 353/1686 118/561 S/I aGc/aTc 1 1 DMRT2 HGNC HGNC:2935 protein_coding YES CCDS6444.1 ENSP00000371686 Q9Y5R5 UPI000013D066 NM_181872.4 deleterious(0.01) 3/5 hmmpanther:PTHR12322,hmmpanther:PTHR12322:SF72,Gene3D:1lpvA00,Superfamily_domains:0040609 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 1051966 1051966 G T 1 0 0 0 0 1 0 0 0 4393 971 34 2 2 DMRT2 9 1051966 Missense_Mutation SNP G C3N-02089_T 1051966 137342751 495 27579 GLDC 0 . GRCh38 9 6602146 6602146 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1118G>T p.Arg373Leu p.R373L ENST00000321612 8/25 371 349 22 347 347 0 strelka-varscan-mutect GLDC,missense_variant,p.Arg373Leu,ENST00000321612,NM_000170.2;GLDC,non_coding_transcript_exon_variant,,ENST00000463305,; A ENST00000321612 Transcript missense_variant 1269/3767 1118/3063 373/1020 R/L cGg/cTg COSM1109551 1 -1 GLDC HGNC HGNC:4313 protein_coding YES CCDS34987.1 ENSP00000370737 P23378 UPI0000684276 NM_000170.2 deleterious(0) 8/25 HAMAP:MF_00711,hmmpanther:PTHR11773,hmmpanther:PTHR11773:SF1,Pfam_domain:PF02347,TIGRFAM_domain:TIGR00461,Superfamily_domains:SSF53383 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 6602146 6602146 C A 1 0 0 0 0 1 0 0 0 6311 652 23 1 1 GLDC 9 6602146 Missense_Mutation SNP C C3N-02089_T 5550180 6602146 131792571 496 27580 NFIB 0 . GRCh38 9 14125656 14125657 + Frame_Shift_Ins INS - - GGGAT novel C3N-02089_T C3N-02089_N - - c.1031_1035dupATCCC p.Gly346IlefsTer50 p.G346Ifs*50 ENST00000380953 7/11 214 171 43 163 163 0 sindel-varindel NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000380959,NM_005596.3;NFIB,frameshift_variant,p.Gly94IlefsTer50,ENST00000543693,NM_001282787.1;NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000397581,;NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000397579,;NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000397575,;NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000380953,NM_001190737.1;NFIB,frameshift_variant,p.Gly342IlefsTer50,ENST00000606230,;NFIB,frameshift_variant,p.Gly346IlefsTer50,ENST00000637742,;NFIB,frameshift_variant,p.Gly372IlefsTer50,ENST00000380934,NM_001190738.1;NFIB,frameshift_variant,p.Gly337IlefsTer50,ENST00000636057,;NFIB,frameshift_variant,p.Gly339IlefsTer50,ENST00000635877,;NFIB,frameshift_variant,p.Gly337IlefsTer50,ENST00000637640,;NFIB,frameshift_variant,p.Gly267IlefsTer50,ENST00000636432,;NFIB,frameshift_variant,p.Gly167IlefsTer50,ENST00000636735,;NFIB,frameshift_variant,p.Gly94IlefsTer50,ENST00000380924,; GGGAT ENST00000380953 Transcript frameshift_variant 1191-1192/2381 1035-1036/1485 345-346/494 -/IX -/ATCCC 1 -1 NFIB HGNC HGNC:7785 protein_coding YES CCDS55291.1 ENSP00000370340 O00712 UPI0000211140 NM_001190737.1 7/11 Pfam_domain:PF00859,hmmpanther:PTHR11492,hmmpanther:PTHR11492:SF4 HIGH 1 insertion 1 1 PASS . . 0 205 0 4 0 0 0 0 -20 0.999952 1 1 1 0 GGGAT 7 5 90 14125656 14125656 - GGGAT 1 0 1 1 0 0 0 0 0 10408 661 23 0 0 NFIB 9 14125656 Frame_Shift_Ins INS - C3N-02089_T 7523510 14125656 124269061 497 27581 CCDC171 0 . GRCh38 9 15594046 15594046 + Silent SNP G G T rs149972101 C3N-02089_T C3N-02089_N G G c.549G>T p.= p.A183A ENST00000380701 6/26 159 115 44 204 203 1 strelka-varscan-mutect CCDC171,synonymous_variant,p.=,ENST00000380701,NM_173550.2;CCDC171,synonymous_variant,p.=,ENST00000535968,; T ENST00000380701 Transcript synonymous_variant 877/6512 549/3981 183/1326 A gcG/gcT rs149972101 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 6/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 LOW 1 SNV 1 1 PASS rs149972101 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 15594046 15594046 G T 1 0 0 0 0 0 0 0 1 2488 1159 40 1 1 CCDC171 9 15594046 Silent SNP G C3N-02089_T 1468390 15594046 122800671 498 27582 BNC2 0 . GRCh38 9 16419394 16419394 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.2895C>A p.= p.T965T ENST00000380672 7/7 50 38 12 74 74 0 strelka-varscan-mutect BNC2,synonymous_variant,p.=,ENST00000380672,NM_001317940.1,NM_017637.5;BNC2,synonymous_variant,p.=,ENST00000380667,;BNC2,3_prime_UTR_variant,,ENST00000545497,;BNC2,3_prime_UTR_variant,,ENST00000418777,;BNC2,3_prime_UTR_variant,,ENST00000411752,;BNC2,3_prime_UTR_variant,,ENST00000484726,; T ENST00000380672 Transcript synonymous_variant 2953/12844 2895/3300 965/1099 T acC/acA 1 -1 BNC2 HGNC HGNC:30988 protein_coding YES CCDS6482.2 ENSP00000370047 Q6ZN30 UPI000035E7B0 NM_001317940.1,NM_017637.5 7/7 Low_complexity_(Seg):seg,hmmpanther:PTHR15021:SF2,hmmpanther:PTHR15021 LOW 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 16419394 16419394 G T 1 0 0 0 0 0 0 0 1 1631 987 35 2 2 BNC2 9 16419394 Silent SNP G C3N-02089_T 825348 16419394 121975323 499 27583 DENND4C 0 . GRCh38 9 19346927 19346927 + Silent SNP G G T rs370975988 C3N-02089_T C3N-02089_N G G c.4011G>T p.= p.S1337S ENST00000602925 22/32 242 174 68 267 267 0 strelka-varscan-mutect DENND4C,synonymous_variant,p.=,ENST00000602925,NM_017925.6;DENND4C,synonymous_variant,p.=,ENST00000434457,;DENND4C,synonymous_variant,p.=,ENST00000380427,;DENND4C,synonymous_variant,p.=,ENST00000361024,;DENND4C,synonymous_variant,p.=,ENST00000380424,;DENND4C,3_prime_UTR_variant,,ENST00000494124,;DENND4C,non_coding_transcript_exon_variant,,ENST00000380437,; T ENST00000602925 Transcript synonymous_variant 4427/6831 4011/5730 1337/1909 S tcG/tcT rs370975988 1 1 DENND4C HGNC HGNC:26079 protein_coding YES CCDS6491.3 ENSP00000473565 R4GNB2 UPI0000EE421F NM_017925.6 22/32 Low_complexity_(Seg):seg,hmmpanther:PTHR12296,hmmpanther:PTHR12296:SF17 LOW 1 SNV 5 1 PASS rs370975988 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 19346927 19346927 G T 1 0 0 0 0 0 0 0 1 4239 1132 40 1 1 DENND4C 9 19346927 Silent SNP G C3N-02089_T 2927533 19346927 119047790 500 27584 SLC24A2 0 . GRCh38 9 19786168 19786168 + Silent SNP C C G novel C3N-02089_T C3N-02089_N C C c.699G>C p.= p.L233L ENST00000341998 1/10 341 258 83 448 448 0 strelka-varscan-mutect SLC24A2,synonymous_variant,p.=,ENST00000341998,NM_020344.3;SLC24A2,synonymous_variant,p.=,ENST00000286344,NM_001193288.2; G ENST00000341998 Transcript synonymous_variant 761/10749 699/1986 233/661 L ctG/ctC 1 -1 SLC24A2 HGNC HGNC:10976 protein_coding YES CCDS6493.1 ENSP00000344801 Q9UI40 UPI000004FA46 NM_020344.3 1/10 Transmembrane_helices:TMhelix,hmmpanther:PTHR10846,hmmpanther:PTHR10846:SF41,Pfam_domain:PF01699,TIGRFAM_domain:TIGR00367 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 19786168 19786168 C G 1 0 0 0 0 0 0 0 1 14732 813 29 4 4 SLC24A2 9 19786168 Silent SNP C C3N-02089_T 439241 19786168 118608549 501 27585 CDKN2A 0 . GRCh38 9 21974807 21974807 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.21C>T p.= p.S7S ENST00000498124 1/4 192 141 51 135 135 0 strelka-varscan-mutect CDKN2A,synonymous_variant,p.=,ENST00000304494,NM_000077.4;CDKN2A,synonymous_variant,p.=,ENST00000498124,NM_001195132.1;CDKN2A,synonymous_variant,p.=,ENST00000579122,;CDKN2A,intron_variant,,ENST00000579755,NM_058195.3;CDKN2A,intron_variant,,ENST00000494262,;CDKN2A,intron_variant,,ENST00000498628,;CDKN2A,intron_variant,,ENST00000530628,;CDKN2A,upstream_gene_variant,,ENST00000578845,;CDKN2A,upstream_gene_variant,,ENST00000497750,;CDKN2A,upstream_gene_variant,,ENST00000479692,;CDKN2A,upstream_gene_variant,,ENST00000380150,;CDKN2A,upstream_gene_variant,,ENST00000577854,;CDKN2A,synonymous_variant,p.=,ENST00000380151,;RP11-145E5.5,intron_variant,,ENST00000404796,; A ENST00000498124 Transcript synonymous_variant 60/880 21/504 7/167 S agC/agT 1 -1 CDKN2A HGNC HGNC:1787 protein_coding YES CCDS56565.1 ENSP00000418915 P42771 UPI0001565711 NM_001195132.1 1/4 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 21974807 21974807 G A 1 0 0 0 0 0 0 0 1 2865 1310 46 3 3 CDKN2A 9 21974807 Silent SNP G C3N-02089_T 2188639 21974807 116419910 502 27586 B4GALT1 0 . GRCh38 9 33113838 33113838 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1000G>C p.Val334Leu p.V334L ENST00000379731 5/6 438 336 102 387 387 0 strelka-varscan-mutect B4GALT1,missense_variant,p.Val334Leu,ENST00000379731,NM_001497.3;B4GALT1,intron_variant,,ENST00000535206,; G ENST00000379731 Transcript missense_variant 1187/4201 1000/1197 334/398 V/L Gtg/Ctg 1 -1 B4GALT1 HGNC HGNC:924 protein_coding YES CCDS6535.1 ENSP00000369055 P15291 UPI000002D22E NM_001497.3 tolerated(0.31) 5/6 hmmpanther:PTHR19300,hmmpanther:PTHR19300:SF5,Gene3D:3.90.550.10,Pfam_domain:PF02709,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs1379216670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 33113838 33113838 C G 1 0 0 0 0 1 0 0 0 1426 478 17 4 4 B4GALT1 9 33113838 Missense_Mutation SNP C C3N-02089_T 11139031 33113838 105280879 503 27587 NOL6 0 . GRCh38 9 33464119 33464119 + Missense_Mutation SNP C C T C3N-02089_T C3N-02089_N C C c.2822G>A p.Arg941Gln p.R941Q ENST00000297990 22/26 79 64 15 83 82 1 strelka-varscan-mutect NOL6,missense_variant,p.Arg941Gln,ENST00000297990,NM_022917.4;NOL6,missense_variant,p.Arg941Gln,ENST00000379471,;NOL6,5_prime_UTR_variant,,ENST00000379470,;NOL6,intron_variant,,ENST00000353159,NM_139235.3;MIR6851,downstream_gene_variant,,ENST00000617060,;NOL6,intron_variant,,ENST00000464829,; T ENST00000297990 Transcript missense_variant 2910/4741 2822/3441 941/1146 R/Q cGg/cAg COSM3952664,COSM3952665,COSM5475282,COSM5475283 1 -1 NOL6 HGNC HGNC:19910 protein_coding YES CCDS6543.1 ENSP00000297990 Q9H6R4 UPI0000050326 NM_022917.4 deleterious(0) 22/26 Pfam_domain:PF03813,hmmpanther:PTHR17972 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999959 1 1 1 0 T 3 4 90 33464119 33464119 C T 1 0 0 0 0 1 0 0 0 10569 652 23 1 1 NOL6 9 33464119 Missense_Mutation SNP C C3N-02089_T 350281 33464119 104930598 504 27588 PRSS3 0 . GRCh38 9 33750620 33750620 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.107delG p.Gly36AlafsTer63 p.G36Afs*63 ENST00000361005 1/5 61 48 13 58 58 0 sindel-varindel-pindel PRSS3,frameshift_variant,p.Gly36AlafsTer63,ENST00000361005,NM_007343.3;PRSS3,5_prime_UTR_variant,,ENST00000342836,NM_001197097.2;PRSS3,upstream_gene_variant,,ENST00000429677,NM_001197098.1;PRSS3,upstream_gene_variant,,ENST00000457896,;PRSS3,upstream_gene_variant,,ENST00000468152,; - ENST00000361005 Transcript frameshift_variant 104/966 104/915 35/304 R/X cGg/cg 1 1 PRSS3 HGNC HGNC:9486 protein_coding YES CCDS47958.1 ENSP00000354280 P35030 UPI000013C519 NM_007343.3 1/5 hmmpanther:PTHR24264,hmmpanther:PTHR24264:SF23 HIGH 1 deletion 1 3 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999588 1 1 1 0 - 7 5 90 33750620 33750620 G - 1 0 1 0 1 0 0 0 0 12769 1116 39 0 0 PRSS3 9 33750620 Frame_Shift_Del DEL G C3N-02089_T 286501 33750620 104644097 505 27589 ALDH1B1 0 . GRCh38 9 38396441 38396441 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.693C>T p.= p.P231P ENST00000377698 2/2 210 164 46 210 210 0 strelka-varscan-mutect ALDH1B1,synonymous_variant,p.=,ENST00000377698,NM_000692.4;ALDH1B1,downstream_gene_variant,,ENST00000635162,; T ENST00000377698 Transcript synonymous_variant 846/3066 693/1554 231/517 P ccC/ccT 1 1 ALDH1B1 HGNC HGNC:407 protein_coding YES CCDS6615.1 ENSP00000366927 P30837 UPI0000073000 NM_000692.4 2/2 hmmpanther:PTHR11699:SF211,hmmpanther:PTHR11699,Gene3D:3.40.605.10,Pfam_domain:PF00171,Superfamily_domains:SSF53720 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 38396441 38396441 C T 1 0 0 0 0 0 0 0 1 593 610 22 3 3 ALDH1B1 9 38396441 Silent SNP C C3N-02089_T 4645821 38396441 99998276 506 27590 SPATA31A3 0 . GRCh38 9 66987732 66987732 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2766G>T p.Trp922Cys p.W922C ENST00000428649 4/4 129 95 34 141 141 0 strelka-varscan-mutect SPATA31A3,missense_variant,p.Trp922Cys,ENST00000428649,NM_001083124.1;RP11-395E19.2,non_coding_transcript_exon_variant,,ENST00000616253,; A ENST00000428649 Transcript missense_variant 2828/4256 2766/4044 922/1347 W/C tgG/tgT 1 -1 SPATA31A3 HGNC HGNC:32003 protein_coding YES CCDS78400.1 ENSP00000485118 Q5VYP0 UPI00004588FC NM_001083124.1 tolerated(0.14) 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF18 MODERATE 1 SNV 1 1 PASS . . 0 206 0 0 3 0 0 0 -19.99999 0.9877161 1 1 1 0 A 3 1 90 66987732 66987732 C A 1 0 0 0 0 1 0 0 0 15344 740 26 2 2 SPATA31A3 9 66987732 Missense_Mutation SNP C C3N-02089_T 28591291 66987732 71406985 507 27591 TMC1 0 . GRCh38 9 72754793 72754793 + Nonsense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.650G>A p.Trp217Ter p.W217* ENST00000297784 12/24 404 286 118 453 453 0 strelka-varscan-mutect TMC1,stop_gained,p.Trp217Ter,ENST00000297784,NM_138691.2;TMC1,stop_gained,p.Trp217Ter,ENST00000340019,; A ENST00000297784 Transcript stop_gained 1190/3201 650/2283 217/760 W/* tGg/tAg 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 12/24 hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 72754793 72754793 G A 1 0 0 0 0 0 1 0 0 16430 1357 47 3 3 TMC1 9 72754793 Nonsense_Mutation SNP G C3N-02089_T 5767061 72754793 65639924 508 27592 TMC1 0 . GRCh38 9 72772512 72772512 + Missense_Mutation SNP G G A rs397517842 C3N-02089_T C3N-02089_N G G c.841G>A p.Gly281Arg p.G281R ENST00000297784 13/24 387 278 109 425 425 0 strelka-varscan-mutect TMC1,missense_variant,p.Gly281Arg,ENST00000297784,NM_138691.2;TMC1,missense_variant,p.Gly281Arg,ENST00000340019,; A ENST00000297784 Transcript missense_variant 1381/3201 841/2283 281/760 G/R Ggg/Agg rs397517842 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 deleterious(0) 13/24 hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302,Transmembrane_helices:TMhelix uncertain_significance MODERATE 1 SNV 1 1 1 PASS rs397517842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 72772512 72772512 G A 1 0 0 0 0 1 0 0 0 16430 1232 43 3 3 TMC1 9 72772512 Missense_Mutation SNP G C3N-02089_T 17719 72772512 65622205 509 27593 VPS13A 0 . GRCh38 9 77209440 77209440 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.403A>T p.Lys135Ter p.K135* ENST00000360280 6/72 198 172 26 261 261 0 strelka-varscan-mutect VPS13A,stop_gained,p.Lys135Ter,ENST00000360280,NM_033305.2;VPS13A,stop_gained,p.Lys135Ter,ENST00000376636,NM_001018037.1;VPS13A,stop_gained,p.Lys135Ter,ENST00000376634,NM_001018038.2;VPS13A,stop_gained,p.Lys135Ter,ENST00000357409,NM_015186.3;VPS13A,upstream_gene_variant,,ENST00000471439,; T ENST00000360280 Transcript stop_gained 663/15320 403/9525 135/3174 K/* Aaa/Taa 1 1 VPS13A HGNC HGNC:1908 protein_coding YES CCDS6655.1 ENSP00000353422 Q96RL7 UPI0000210B7A NM_033305.2 6/72 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR16166:SF22,hmmpanther:PTHR16166 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 77209440 77209440 A T 1 0 0 0 0 0 1 0 0 17736 15 1 4 4 VPS13A 9 77209440 Nonsense_Mutation SNP A C3N-02089_T 4436928 77209440 61185277 510 27594 KIF27 0 . GRCh38 9 83891487 83891487 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1617A>G p.Ile539Met p.I539M ENST00000297814 6/18 125 103 22 163 163 0 strelka-varscan-mutect KIF27,missense_variant,p.Ile539Met,ENST00000297814,NM_017576.2;KIF27,missense_variant,p.Ile539Met,ENST00000413982,NM_001271927.1;KIF27,missense_variant,p.Ile539Met,ENST00000334204,NM_001271928.1;KIF27,upstream_gene_variant,,ENST00000376347,; C ENST00000297814 Transcript missense_variant 1761/4653 1617/4206 539/1401 I/M atA/atG 1 -1 KIF27 HGNC HGNC:18632 protein_coding YES CCDS6665.1 ENSP00000297814 Q86VH2 UPI000018F32F NM_017576.2 tolerated(0.08) 6/18 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 83891487 83891487 T C 1 0 0 0 0 1 0 0 0 8161 1512 53 5 5 KIF27 9 83891487 Missense_Mutation SNP T C3N-02089_T 6682047 83891487 54503230 511 27595 WNK2 0 . GRCh38 9 93300059 93300059 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.6235G>T p.Val2079Phe p.V2079F ENST00000297954 26/30 108 97 11 134 134 0 strelka-varscan-mutect WNK2,missense_variant,p.Val2038Phe,ENST00000432730,;WNK2,missense_variant,p.Val2079Phe,ENST00000297954,NM_001282394.1;WNK2,missense_variant,p.Val2042Phe,ENST00000395477,NM_006648.3;WNK2,missense_variant,p.Val839Phe,ENST00000448251,;WNK2,intron_variant,,ENST00000411624,;WNK2,intron_variant,,ENST00000453718,;WNK2,downstream_gene_variant,,ENST00000427277,;WNK2,non_coding_transcript_exon_variant,,ENST00000479696,;WNK2,intron_variant,,ENST00000474009,; T ENST00000297954 Transcript missense_variant 6235/7138 6235/6894 2079/2297 V/F Gtt/Ttt 1 1 WNK2 HGNC HGNC:14542 protein_coding YES CCDS75858.1 ENSP00000297954 Q9Y3S1 UPI0000236D76 NM_001282394.1 deleterious(0) 26/30 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 93300059 93300059 G T 1 0 0 0 0 1 0 0 0 17934 1261 44 2 2 WNK2 9 93300059 Missense_Mutation SNP G C3N-02089_T 9408572 93300059 45094658 512 27596 FAM120AOS 0 . GRCh38 9 93452527 93452527 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.183C>A p.= p.A61A ENST00000375412 1/3 171 132 39 208 208 0 strelka-varscan-mutect FAM120AOS,synonymous_variant,p.=,ENST00000375412,NM_198841.2;FAM120A,intron_variant,,ENST00000277165,NM_014612.4,NM_001286722.1;FAM120A,intron_variant,,ENST00000375389,NM_001286724.1;FAM120A,intron_variant,,ENST00000446420,NM_001286723.1;FAM120AOS,upstream_gene_variant,,ENST00000423591,NM_001322224.1;FAM120AOS,upstream_gene_variant,,ENST00000428378,;FAM120AOS,intron_variant,,ENST00000520470,;FAM120AOS,intron_variant,,ENST00000483149,;FAM120AOS,upstream_gene_variant,,ENST00000479094,;FAM120AOS,upstream_gene_variant,,ENST00000520403,;FAM120AOS,upstream_gene_variant,,ENST00000523407,;FAM120AOS,upstream_gene_variant,,ENST00000483056,;FAM120AOS,upstream_gene_variant,,ENST00000428152,;FAM120AOS,upstream_gene_variant,,ENST00000476484,; T ENST00000375412 Transcript synonymous_variant 1066/2771 183/771 61/256 A gcC/gcA 1 -1 FAM120AOS HGNC HGNC:23389 protein_coding YES CCDS6705.1 ENSP00000364561 Q5T036 UPI000013F924 NM_198841.2 1/3 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 93452527 93452527 G T 1 0 0 0 0 0 0 0 1 5273 1335 47 2 2 FAM120AOS 9 93452527 Silent SNP G C3N-02089_T 152468 93452527 44942190 513 27597 ZNF169 0 . GRCh38 9 94300403 94300403 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.845G>C p.Arg282Thr p.R282T ENST00000395395 5/5 253 177 76 318 318 0 strelka-varscan-mutect ZNF169,missense_variant,p.Arg282Thr,ENST00000395395,NM_003448.2,NM_194320.3,NM_001301275.1;ZNF169,3_prime_UTR_variant,,ENST00000340911,;ZNF169,downstream_gene_variant,,ENST00000480716,; C ENST00000395395 Transcript missense_variant 935/1986 845/1812 282/603 R/T aGg/aCg COSM1111339 1 1 ZNF169 HGNC HGNC:12957 protein_coding YES CCDS6709.2 ENSP00000378792 Q14929 UPI00001C1EC1 NM_003448.2,NM_194320.3,NM_001301275.1 deleterious(0.02) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF13894,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF25,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 94300403 94300403 G C 1 0 0 0 0 1 0 0 0 18322 1000 35 4 4 ZNF169 9 94300403 Missense_Mutation SNP G C3N-02089_T 847876 94300403 44094314 514 27598 ZNF782 0 . GRCh38 9 96819699 96819699 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.324T>C p.= p.N108N ENST00000481138 6/6 89 79 10 108 108 0 strelka-varscan-mutect ZNF782,synonymous_variant,p.=,ENST00000481138,;ZNF782,synonymous_variant,p.=,ENST00000535338,NM_001001662.1;ZNF782,synonymous_variant,p.=,ENST00000289032,;ZNF782,synonymous_variant,p.=,ENST00000478850,;ZNF782,non_coding_transcript_exon_variant,,ENST00000466833,; G ENST00000481138 Transcript synonymous_variant 986/4213 324/2100 108/699 N aaT/aaC 1 -1 ZNF782 HGNC HGNC:33110 protein_coding YES CCDS35075.1 ENSP00000419397 Q6ZMW2 UPI00001D76E3 6/6 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF111 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 96819699 96819699 A G 1 0 0 0 0 0 0 0 1 18738 446 16 5 5 ZNF782 9 96819699 Silent SNP A C3N-02089_T 2519296 96819699 41575018 515 27599 AKAP2 0 . GRCh38 9 110156391 110156391 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.3068C>G p.Pro1023Arg p.P1023R ENST00000374530 9/11 127 96 31 123 123 0 strelka-varscan-mutect PALM2-AKAP2,missense_variant,p.Pro1023Arg,ENST00000374530,NM_007203.4;AKAP2,missense_variant,p.Pro881Arg,ENST00000374525,NM_001004065.4;PALM2-AKAP2,missense_variant,p.Pro1023Arg,ENST00000302798,NM_147150.2;AKAP2,missense_variant,p.Pro881Arg,ENST00000434623,NM_001198656.1;AKAP2,missense_variant,p.Pro792Arg,ENST00000259318,NM_001136562.2;AKAP2,non_coding_transcript_exon_variant,,ENST00000485762,;AKAP2,intron_variant,,ENST00000482335,;AKAP2,3_prime_UTR_variant,,ENST00000495980,; G ENST00000374530 Transcript missense_variant 3248/7507 3068/3312 1023/1103 P/R cCt/cGt 1 1 PALM2-AKAP2 HGNC HGNC:33529 protein_coding YES CCDS35100.1 ENSP00000363654 UPI0000125755 NM_007203.4 deleterious(0.01) 9/11 Pfam_domain:PF15304,hmmpanther:PTHR10498,hmmpanther:PTHR10498:SF10 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 110156391 110156391 C G 1 0 0 0 0 1 0 0 0 535 681 24 4 4 AKAP2 9 110156391 Missense_Mutation SNP C C3N-02089_T 13336692 110156391 28238326 516 27600 MUSK 0 . GRCh38 9 110668920 110668920 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.16A>T p.Asn6Tyr p.N6Y ENST00000374448 1/15 143 102 41 124 124 0 strelka-varscan-mutect MUSK,missense_variant,p.Asn6Tyr,ENST00000416899,;MUSK,missense_variant,p.Asn6Tyr,ENST00000374448,NM_005592.3;MUSK,missense_variant,p.Asn6Tyr,ENST00000189978,NM_001166281.1,NM_001166280.1;MUSK,missense_variant,p.Asn6Tyr,ENST00000374440,; T ENST00000374448 Transcript missense_variant 150/2754 16/2610 6/869 N/Y Aac/Tac 1 1 MUSK HGNC HGNC:7525 protein_coding YES CCDS48005.1 ENSP00000363571 O15146 UPI000006D2F7 NM_005592.3 tolerated_low_confidence(0.2) 1/15 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 110668920 110668920 A T 1 0 0 0 0 1 0 0 0 9987 130 5 4 4 MUSK 9 110668920 Missense_Mutation SNP A C3N-02089_T 512529 110668920 27725797 517 27601 RGS3 0 . GRCh38 9 113514653 113514653 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1673A>T p.Gln558Leu p.Q558L ENST00000374140 16/26 90 61 29 75 75 0 strelka-varscan-mutect RGS3,missense_variant,p.Gln558Leu,ENST00000374140,NM_144488.5;RGS3,missense_variant,p.Gln558Leu,ENST00000350696,NM_001282923.1;RGS3,missense_variant,p.Gln277Leu,ENST00000343817,NM_130795.3;RGS3,missense_variant,p.Gln277Leu,ENST00000394646,NM_001276261.1;RGS3,missense_variant,p.Gln446Leu,ENST00000317613,NM_017790.4;RGS3,missense_variant,p.Gln184Leu,ENST00000374136,NM_001322214.1;RGS3,upstream_gene_variant,,ENST00000496113,;RGS3,splice_region_variant,,ENST00000478599,;RGS3,upstream_gene_variant,,ENST00000460000,; T ENST00000374140 Transcript missense_variant,splice_region_variant 1882/4591 1673/3597 558/1198 Q/L cAg/cTg 1 1 RGS3 HGNC HGNC:9999 protein_coding YES CCDS43869.1 ENSP00000363255 P49796 UPI00001C0F58 NM_144488.5 deleterious(0) 16/26 Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 113514653 113514653 A T 1 0 0 0 0 1 0 0 0 13477 202 7 4 4 RGS3 9 113514653 Missense_Mutation SNP A C3N-02089_T 2845733 113514653 24880064 518 27602 ORM2 0 . GRCh38 9 114330794 114330794 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.260A>G p.Gln87Arg p.Q87R ENST00000431067 3/6 164 121 43 146 145 1 strelka-varscan-mutect ORM2,missense_variant,p.Gln87Arg,ENST00000431067,NM_000608.2;AKNA,downstream_gene_variant,,ENST00000307564,NM_030767.4;ORM1,downstream_gene_variant,,ENST00000259396,NM_000607.2; G ENST00000431067 Transcript missense_variant,splice_region_variant 296/760 260/606 87/201 Q/R cAg/cGg 1 1 ORM2 HGNC HGNC:8499 protein_coding YES CCDS6804.1 ENSP00000394936 P19652 UPI0000052DC9 NM_000608.2 tolerated(0.32) 3/6 hmmpanther:PTHR11967,hmmpanther:PTHR11967:SF2,Gene3D:2.40.128.20,PIRSF_domain:PIRSF036899,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR00708 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 114330794 114330794 A G 1 0 0 0 0 1 0 0 0 11334 202 7 5 5 ORM2 9 114330794 Missense_Mutation SNP A C3N-02089_T 816141 114330794 24063923 519 27603 TNC 0 . GRCh38 9 115085934 115085934 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.1797C>T p.= p.N599N ENST00000350763 3/28 130 103 27 145 145 0 strelka-varscan-mutect TNC,synonymous_variant,p.=,ENST00000350763,NM_002160.3;TNC,synonymous_variant,p.=,ENST00000535648,;TNC,synonymous_variant,p.=,ENST00000341037,;TNC,synonymous_variant,p.=,ENST00000423613,;TNC,synonymous_variant,p.=,ENST00000542877,;TNC,synonymous_variant,p.=,ENST00000537320,;TNC,downstream_gene_variant,,ENST00000534839,; A ENST00000350763 Transcript synonymous_variant 2209/7641 1797/6606 599/2201 N aaC/aaT 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 3/28 hmmpanther:PTHR19143:SF38,hmmpanther:PTHR19143,Gene3D:2gy5A03,SMART_domains:SM00181,PD936484 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 115085934 115085934 G A 1 0 0 0 0 0 0 0 1 16744 1368 48 3 3 TNC 9 115085934 Silent SNP G C3N-02089_T 755140 115085934 23308783 520 27604 TNC 0 . GRCh38 9 115090861 115090861 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.158T>A p.Val53Asp p.V53D ENST00000350763 2/28 464 332 132 454 453 1 strelka-varscan-mutect TNC,missense_variant,p.Val53Asp,ENST00000350763,NM_002160.3;TNC,missense_variant,p.Val53Asp,ENST00000535648,;TNC,missense_variant,p.Val53Asp,ENST00000341037,;TNC,missense_variant,p.Val53Asp,ENST00000423613,;TNC,missense_variant,p.Val53Asp,ENST00000542877,;TNC,missense_variant,p.Val53Asp,ENST00000537320,;TNC,missense_variant,p.Val53Asp,ENST00000534839,; T ENST00000350763 Transcript missense_variant 570/7641 158/6606 53/2201 V/D gTt/gAt 1 -1 TNC HGNC HGNC:5318 protein_coding YES CCDS6811.1 ENSP00000265131 P24821 UPI000013D5BD NM_002160.3 deleterious(0) 2/28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 115090861 115090861 A T 1 0 0 0 0 1 0 0 0 16744 43 2 4 4 TNC 9 115090861 Missense_Mutation SNP A C3N-02089_T 4927 115090861 23303856 521 27605 PAPPA 0 . GRCh38 9 116227517 116227517 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2198G>T p.Ser733Ile p.S733I ENST00000328252 6/22 247 201 46 218 218 0 strelka-varscan-mutect PAPPA,missense_variant,p.Ser733Ile,ENST00000328252,NM_002581.3; T ENST00000328252 Transcript missense_variant 2567/10959 2198/4884 733/1627 S/I aGc/aTc 1 1 PAPPA HGNC HGNC:8602 protein_coding YES CCDS6813.1 ENSP00000330658 Q13219 UPI00001E0589 NM_002581.3 deleterious(0) 6/22 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF347 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 116227517 116227517 G T 1 0 0 0 0 1 0 0 0 11512 971 34 2 2 PAPPA 9 116227517 Missense_Mutation SNP G C3N-02089_T 1136656 116227517 22167200 522 27606 OR1J1 0 . GRCh38 9 122477414 122477414 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.513C>G p.Asp171Glu p.D171E ENST00000259357 1/1 280 220 60 242 242 0 strelka-varscan-mutect OR1J1,missense_variant,p.Asp171Glu,ENST00000259357,NM_001004451.1;RP11-542K23.9,downstream_gene_variant,,ENST00000412262,; C ENST00000259357 Transcript missense_variant 513/969 513/969 171/322 D/E gaC/gaG 1 -1 OR1J1 HGNC HGNC:8208 protein_coding YES CCDS35120.1 ENSP00000259357 Q8NGS3 A0A126GWP9 UPI0000061E79 NM_001004451.1 tolerated_low_confidence(0.05) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF213,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 122477414 122477414 G C 1 0 0 0 0 1 0 0 0 11037 1252 44 4 4 OR1J1 9 122477414 Missense_Mutation SNP G C3N-02089_T 6249897 122477414 15917303 523 27607 OR1J1 0 . GRCh38 9 122477628 122477628 + Frame_Shift_Del DEL T T - novel C3N-02089_T C3N-02089_N T T c.299delA p.Gln100ArgfsTer11 p.Q100Rfs*11 ENST00000259357 1/1 222 176 46 222 222 0 sindel-varindel-pindel OR1J1,frameshift_variant,p.Gln100ArgfsTer11,ENST00000259357,NM_001004451.1;RP11-542K23.9,downstream_gene_variant,,ENST00000412262,; - ENST00000259357 Transcript frameshift_variant 299/969 299/969 100/322 Q/X cAg/cg 1 -1 OR1J1 HGNC HGNC:8208 protein_coding YES CCDS35120.1 ENSP00000259357 Q8NGS3 A0A126GWP9 UPI0000061E79 NM_001004451.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF213,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 HIGH deletion 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 122477628 122477628 T - 1 0 1 0 1 0 0 0 0 11037 1580 55 0 0 OR1J1 9 122477628 Frame_Shift_Del DEL T C3N-02089_T 214 122477628 15917089 524 27608 OR1J4 0 . GRCh38 9 122519481 122519481 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.341T>G p.Leu114Arg p.L114R ENST00000340750 1/1 193 154 39 182 181 1 strelka-varscan-mutect OR1J4,missense_variant,p.Leu114Arg,ENST00000340750,NM_001004452.1; G ENST00000340750 Transcript missense_variant 341/942 341/942 114/313 L/R cTt/cGt 1 1 OR1J4 HGNC HGNC:8211 protein_coding YES CCDS35122.1 ENSP00000343521 Q8NGS1 A0A126GW06 UPI0000041D07 NM_001004452.1 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF207,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1297884035 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 122519481 122519481 T G 1 0 0 0 0 1 0 0 0 11039 1609 56 5 5 OR1J4 9 122519481 Missense_Mutation SNP T C3N-02089_T 41853 122519481 15875236 525 27609 CERCAM 0 . GRCh38 9 128435835 128435835 + Missense_Mutation SNP G G A rs768275632 C3N-02089_T C3N-02089_N G G c.1718G>A p.Arg573His p.R573H ENST00000372838 12/13 292 214 78 195 195 0 strelka-varscan-mutect CERCAM,missense_variant,p.Arg495His,ENST00000372842,NM_001286760.1;CERCAM,missense_variant,p.Arg573His,ENST00000372838,NM_016174.4;CERCAM,missense_variant,p.Arg495His,ENST00000612334,;CERCAM,5_prime_UTR_variant,,ENST00000613052,;RP11-339B21.10,downstream_gene_variant,,ENST00000610052,;CERCAM,downstream_gene_variant,,ENST00000487001,;CERCAM,downstream_gene_variant,,ENST00000472858,;CERCAM,downstream_gene_variant,,ENST00000463535,; A ENST00000372838 Transcript missense_variant 2116/2685 1718/1788 573/595 R/H cGc/cAc rs768275632 1 1 CERCAM HGNC HGNC:23723 protein_coding YES CCDS6901.2 ENSP00000361929 Q5T4B2 UPI000046FF85 NM_016174.4 tolerated(0.07) 12/13 MODERATE 1 SNV 1 1 PASS rs768275632 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 128435835 128435835 G A 1 0 0 0 0 1 0 0 0 2992 1087 38 1 1 CERCAM 9 128435835 Missense_Mutation SNP G C3N-02089_T 5916354 128435835 9958882 526 27610 C9orf78 0 . GRCh38 9 129829254 129829254 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.729C>A p.= p.P243P ENST00000372447 8/9 122 89 33 108 108 0 strelka-varscan-mutect C9orf78,synonymous_variant,p.=,ENST00000372447,NM_016520.2;C9orf78,non_coding_transcript_exon_variant,,ENST00000461762,;C9orf78,non_coding_transcript_exon_variant,,ENST00000480023,;C9orf78,non_coding_transcript_exon_variant,,ENST00000461349,;C9orf78,downstream_gene_variant,,ENST00000461539,;C9orf78,downstream_gene_variant,,ENST00000492991,;C9orf78,downstream_gene_variant,,ENST00000495934,; T ENST00000372447 Transcript synonymous_variant 783/1795 729/870 243/289 P ccC/ccA 1 -1 C9orf78 HGNC HGNC:24932 protein_coding YES CCDS6931.1 ENSP00000361524 Q9NZ63 UPI000006F0CA NM_016520.2 8/9 hmmpanther:PTHR13486:SF2,hmmpanther:PTHR13486 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 129829254 129829254 G T 1 0 0 0 0 0 0 0 1 2191 1335 47 2 2 C9orf78 9 129829254 Silent SNP G C3N-02089_T 1393419 129829254 8565463 527 27611 HMCN2 0 . GRCh38 9 130393973 130393973 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.10463G>T p.Gly3488Val p.G3488V ENST00000624552 68/98 115 89 26 77 77 0 strelka-varscan-mutect HMCN2,missense_variant,p.Gly3488Val,ENST00000624552,NM_001291815.1;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,; T ENST00000624552 Transcript missense_variant 10463/15610 10463/15180 3488/5059 G/V gGg/gTg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 deleterious(0) 68/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 130393973 130393973 G T 1 0 0 0 0 1 0 0 0 7112 1232 43 2 2 HMCN2 9 130393973 Missense_Mutation SNP G C3N-02089_T 564719 130393973 8000744 528 27612 CEL 0 . GRCh38 9 133067172 133067172 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.871C>A p.Leu291Met p.L291M ENST00000372080 7/11 486 430 56 352 352 0 strelka-varscan-mutect CEL,missense_variant,p.Leu291Met,ENST00000372080,NM_001807.4;CEL,intron_variant,,ENST00000621209,; A ENST00000372080 Transcript missense_variant 887/2384 871/2271 291/756 L/M Ctg/Atg 1 1 CEL HGNC HGNC:1848 protein_coding YES CCDS43896.1 ENSP00000361151 X6R868 UPI000013E8C6 NM_001807.4 tolerated(0.16) 7/11 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 133067172 133067172 C A 1 0 0 0 0 1 0 0 0 2916 796 28 2 2 CEL 9 133067172 Missense_Mutation SNP C C3N-02089_T 2673199 133067172 5327545 529 27613 CEL 0 . GRCh38 9 133067183 133067183 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.882G>C p.Lys294Asn p.K294N ENST00000372080 7/11 429 387 42 339 339 0 strelka-varscan-mutect CEL,missense_variant,p.Lys294Asn,ENST00000372080,NM_001807.4;CEL,intron_variant,,ENST00000621209,; C ENST00000372080 Transcript missense_variant 898/2384 882/2271 294/756 K/N aaG/aaC 1 1 CEL HGNC HGNC:1848 protein_coding YES CCDS43896.1 ENSP00000361151 X6R868 UPI000013E8C6 NM_001807.4 tolerated(0.06) 7/11 hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF139,Pfam_domain:PF00135,Gene3D:3.40.50.1820,Superfamily_domains:SSF53474 MODERATE 1 SNV 5 1 PASS rs1189955377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 133067183 133067183 G C 1 0 0 0 0 1 0 0 0 2916 991 35 4 4 CEL 9 133067183 Missense_Mutation SNP G C3N-02089_T 11 133067183 5327534 530 27614 TMEM8C 0 . GRCh38 9 133520278 133520278 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.146C>T p.Ala49Val p.A49V ENST00000339996 2/5 173 133 40 123 123 0 strelka-varscan-mutect TMEM8C,missense_variant,p.Ala49Val,ENST00000339996,NM_001080483.2;TMEM8C,non_coding_transcript_exon_variant,,ENST00000413714,; A ENST00000339996 Transcript missense_variant 248/818 146/666 49/221 A/V gCc/gTc COSM285822 1 -1 TMEM8C HGNC HGNC:33778 protein_coding YES CCDS35170.1 ENSP00000419712 A6NI61 UPI00003676C5 NM_001080483.2 deleterious(0.02) 2/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR14319,hmmpanther:PTHR14319:SF5,Pfam_domain:PF12036 1 MODERATE 1 SNV 2 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999972 1 1 1 0 A 3 1 90 133520278 133520278 G A 1 0 0 0 0 1 0 0 0 16693 1203 42 3 3 TMEM8C 9 133520278 Missense_Mutation SNP G C3N-02089_T 453095 133520278 4874439 531 27615 COL5A1 0 . GRCh38 9 134806217 134806217 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.3287G>C p.Gly1096Ala p.G1096A ENST00000371817 42/66 262 221 41 216 216 0 strelka-varscan-mutect COL5A1,missense_variant,p.Gly1096Ala,ENST00000371817,NM_000093.4;COL5A1,missense_variant,p.Gly1096Ala,ENST00000618395,NM_001278074.1;COL5A1,upstream_gene_variant,,ENST00000463925,; C ENST00000371817 Transcript missense_variant 3701/8471 3287/5517 1096/1838 G/A gGa/gCa 1 1 COL5A1 HGNC HGNC:2209 protein_coding YES CCDS6982.1 ENSP00000360882 P20908 A0A024R8E5 UPI0000210EE3 NM_000093.4 deleterious(0) 42/66 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF387,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 134806217 134806217 G C 1 0 0 0 0 1 0 0 0 3485 1174 41 4 4 COL5A1 9 134806217 Missense_Mutation SNP G C3N-02089_T 1285939 134806217 3588500 532 27616 LCN9 0 . GRCh38 9 135663417 135663417 + Missense_Mutation SNP G G T rs757343312 C3N-02089_T C3N-02089_N G G c.96G>T p.Arg32Ser p.R32S ENST00000277526 1/7 223 180 43 164 163 1 strelka-varscan-mutect LCN9,missense_variant,p.Arg32Ser,ENST00000277526,NM_001001676.1;LCN9,missense_variant,p.Arg32Ser,ENST00000619315,;LCN9,splice_region_variant,,ENST00000430290,;LCN9,upstream_gene_variant,,ENST00000554343,; T ENST00000277526 Transcript missense_variant,splice_region_variant 96/531 96/531 32/176 R/S agG/agT rs757343312 1 1 LCN9 HGNC HGNC:17442 protein_coding YES CCDS56593.1 ENSP00000277526 Q8WX39 V9HWI8 UPI00003779EE NM_001001676.1 deleterious(0) 1/7 Gene3D:2.40.128.20,PROSITE_patterns:PS00213,hmmpanther:PTHR11430,hmmpanther:PTHR11430:SF28,Superfamily_domains:SSF50814 MODERATE 1 SNV 5 1 PASS rs757343312 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 135663417 135663417 G T 1 0 0 0 0 1 0 0 0 8593 1246 43 2 2 LCN9 9 135663417 Missense_Mutation SNP G C3N-02089_T 857200 135663417 2731300 533 27617 LHX3 0 . GRCh38 9 136205003 136205003 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.10delG p.Glu4LysfsTer169 p.E4Kfs*169 ENST00000371748 1/6 186 149 37 152 152 0 sindel-varindel-pindel LHX3,frameshift_variant,p.Glu4LysfsTer169,ENST00000371748,NM_178138.4;QSOX2,downstream_gene_variant,,ENST00000358701,NM_181701.3;LHX3,upstream_gene_variant,,ENST00000619587,;LHX3,upstream_gene_variant,,ENST00000371746,NM_014564.3; - ENST00000371748 Transcript frameshift_variant 107/2365 10/1194 4/397 E/X Gaa/aa 1 -1 LHX3 HGNC HGNC:6595 protein_coding CCDS6994.1 ENSP00000360813 Q9UBR4 F1T0D5 UPI000012E65D NM_178138.4 1/6 HIGH deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 136205003 136205003 C - 1 0 1 0 1 0 0 0 0 8681 864 30 0 0 LHX3 9 136205003 Frame_Shift_Del DEL C C3N-02089_T 541586 136205003 2189714 534 27618 QSOX2 0 . GRCh38 9 136219052 136219052 + Missense_Mutation SNP C C A rs781540198 C3N-02089_T C3N-02089_N C C c.934G>T p.Val312Leu p.V312L ENST00000358701 7/12 163 122 41 122 121 1 strelka-varscan-mutect QSOX2,missense_variant,p.Val312Leu,ENST00000358701,NM_181701.3;QSOX2,missense_variant,p.Val80Leu,ENST00000455222,; A ENST00000358701 Transcript missense_variant 972/4530 934/2097 312/698 V/L Gtg/Ttg rs781540198 1 -1 QSOX2 HGNC HGNC:30249 protein_coding YES CCDS35178.1 ENSP00000351536 Q6ZRP7 UPI00004A7AC1 NM_181701.3 tolerated(0.29) 7/12 hmmpanther:PTHR22897,hmmpanther:PTHR22897:SF7 MODERATE 1 SNV 2 1 PASS rs781540198 . 0 206 0 3 0 0 0 0 -20 0.9999977 1 1 1 0 A 3 1 90 136219052 136219052 C A 1 0 0 0 0 1 0 0 0 13039 536 19 1 1 QSOX2 9 136219052 Missense_Mutation SNP C C3N-02089_T 14049 136219052 2175665 535 27619 SEC16A 0 . GRCh38 9 136455788 136455788 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.5670G>A p.= p.G1890G ENST00000313050 18/30 105 85 20 76 76 0 strelka-varscan-mutect SEC16A,synonymous_variant,p.=,ENST00000290037,NM_001276418.1;SEC16A,synonymous_variant,p.=,ENST00000313050,NM_014866.1;SEC16A,synonymous_variant,p.=,ENST00000371706,;SEC16A,synonymous_variant,p.=,ENST00000431893,;SEC16A,synonymous_variant,p.=,ENST00000453963,;SEC16A,synonymous_variant,p.=,ENST00000277537,; T ENST00000313050 Transcript synonymous_variant 5744/8806 5670/7074 1890/2357 G ggG/ggA 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 18/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 136455788 136455788 C T 1 0 0 0 0 0 0 0 1 14263 637 22 3 3 SEC16A 9 136455788 Silent SNP C C3N-02089_T 236736 136455788 1938929 536 27620 ITGA8 0 . GRCh38 10 15672639 15672639 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.787G>T p.Asp263Tyr p.D263Y ENST00000378076 7/30 139 91 48 110 110 0 strelka-varscan-mutect ITGA8,missense_variant,p.Asp263Tyr,ENST00000378076,NM_003638.2,NM_001291494.1; A ENST00000378076 Transcript missense_variant 1141/6755 787/3192 263/1063 D/Y Gat/Tat 1 -1 ITGA8 HGNC HGNC:6144 protein_coding YES CCDS31155.1 ENSP00000367316 P53708 UPI00001D80A0 NM_003638.2,NM_001291494.1 deleterious(0) 7/30 Gene3D:3nigC00,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF5,SMART_domains:SM00191,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 15672639 15672639 C A 1 0 0 0 0 1 0 0 0 7789 826 29 2 2 ITGA8 10 15672639 Missense_Mutation SNP C C3N-02089_T 15672639 118124783 537 27621 CUBN 0 . GRCh38 10 16915997 16915997 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.7034G>T p.Gly2345Val p.G2345V ENST00000377833 46/67 333 225 108 261 261 0 strelka-varscan-mutect CUBN,missense_variant,p.Gly2345Val,ENST00000377833,NM_001081.3; A ENST00000377833 Transcript missense_variant 7100/11949 7034/10872 2345/3623 G/V gGt/gTt 1 -1 CUBN HGNC HGNC:2548 protein_coding YES CCDS7113.1 ENSP00000367064 O60494 UPI00001AE8F4 NM_001081.3 deleterious(0.01) 46/67 PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF645,Gene3D:2.60.120.290,Pfam_domain:PF00431,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 16915997 16915997 C A 1 0 0 0 0 1 0 0 0 3861 507 18 2 2 CUBN 10 16915997 Missense_Mutation SNP C C3N-02089_T 1243358 16915997 116881425 538 27622 MRC1 0 . GRCh38 10 17823426 17823426 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.414G>T p.Arg138Ser p.R138S ENST00000569591 2/30 598 509 89 444 444 0 strelka-varscan-mutect MRC1,missense_variant,p.Arg138Ser,ENST00000569591,NM_002438.3; T ENST00000569591 Transcript missense_variant 536/5198 414/4371 138/1456 R/S agG/agT 1 1 MRC1 HGNC HGNC:7228 protein_coding YES CCDS7123.2 ENSP00000455897 P22897 UPI000012EB9A NM_002438.3 deleterious(0) 2/30 PROSITE_profiles:PS50231,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF73,Gene3D:2.80.10.50,SMART_domains:SM00458,Superfamily_domains:SSF50370 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 17823426 17823426 G T 1 0 0 0 0 1 0 0 0 9722 1252 44 2 2 MRC1 10 17823426 Missense_Mutation SNP G C3N-02089_T 907429 17823426 115973996 539 27623 MALRD1 0 . GRCh38 10 19607834 19607834 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.6002C>T p.Pro2001Leu p.P2001L ENST00000454679 35/40 300 204 96 187 187 0 strelka-varscan-mutect MALRD1,missense_variant,p.Pro2001Leu,ENST00000454679,NM_001142308.2;MALRD1,missense_variant,p.Pro1380Leu,ENST00000377266,;MALRD1,missense_variant,p.Pro352Leu,ENST00000377265,; T ENST00000454679 Transcript missense_variant 6170/6880 6002/6471 2001/2156 P/L cCa/cTa 1 1 MALRD1 HGNC HGNC:24331 protein_coding YES CCDS73071.1 ENSP00000412763 Q5VYJ5 UPI000387C99A NM_001142308.2 deleterious(0) 35/40 PROSITE_profiles:PS50068,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF86,Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424,Prints_domain:PR00261 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 19607834 19607834 C T 1 0 0 0 0 1 0 0 0 9121 594 21 3 3 MALRD1 10 19607834 Missense_Mutation SNP C C3N-02089_T 1784408 19607834 114189588 540 27624 MLLT10 0 . GRCh38 10 21670518 21670518 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.865T>C p.Phe289Leu p.F289L ENST00000307729 10/23 286 256 30 243 242 1 strelka-varscan-mutect MLLT10,missense_variant,p.Phe289Leu,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Phe289Leu,ENST00000307729,;MLLT10,missense_variant,p.Phe289Leu,ENST00000631589,;MLLT10,missense_variant,p.Phe289Leu,ENST00000377059,NM_001195626.1;MLLT10,missense_variant,p.Phe29Leu,ENST00000438473,;MLLT10,upstream_gene_variant,,ENST00000420525,;MLLT10,non_coding_transcript_exon_variant,,ENST00000468309,; C ENST00000307729 Transcript missense_variant 1043/5032 865/3207 289/1068 F/L Ttt/Ctt 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 deleterious(0.01) 10/23 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 21670518 21670518 T C 1 0 0 0 0 1 0 0 0 9589 1493 52 5 5 MLLT10 10 21670518 Missense_Mutation SNP T C3N-02089_T 2062684 21670518 112126904 541 27625 EBLN1 0 . GRCh38 10 22209136 22209136 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.848delG p.Gly283ValfsTer19 p.G283Vfs*19 ENST00000422359 1/1 235 191 44 183 183 0 sindel-varindel-pindel EBLN1,frameshift_variant,p.Gly283ValfsTer19,ENST00000422359,NM_001199938.1; - ENST00000422359 Transcript frameshift_variant 886/1208 848/1101 283/366 G/X gGt/gt 1 -1 EBLN1 HGNC HGNC:39430 protein_coding YES CCDS60498.1 ENSP00000473842 P0CF75 UPI0000199CEF NM_001199938.1 1/1 Gene3D:1n93X02,Pfam_domain:PF06407,Superfamily_domains:0041272 HIGH 1 deletion 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 22209136 22209136 C - 1 0 1 0 1 0 0 0 0 4709 507 18 0 0 EBLN1 10 22209136 Frame_Shift_Del DEL C C3N-02089_T 538618 22209136 111588286 542 27626 OTUD1 0 . GRCh38 10 23440216 23440216 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.759G>A p.= p.R253R ENST00000376495 1/1 57 39 18 40 40 0 strelka-varscan-mutect OTUD1,synonymous_variant,p.=,ENST00000376495,NM_001145373.2; A ENST00000376495 Transcript synonymous_variant 759/2933 759/1446 253/481 R cgG/cgA 1 1 OTUD1 HGNC HGNC:27346 protein_coding YES CCDS44366.1 ENSP00000365678 Q5VV17 UPI0000458A32 NM_001145373.2 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR12419:SF15,hmmpanther:PTHR12419 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 23440216 23440216 G A 1 0 0 0 0 0 0 0 1 11381 1161 41 3 3 OTUD1 10 23440216 Silent SNP G C3N-02089_T 1231080 23440216 110357206 543 27627 GPR158 0 . GRCh38 10 25175769 25175769 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.349A>T p.Ser117Cys p.S117C ENST00000376351 1/11 261 205 56 195 195 0 strelka-varscan-mutect GPR158,missense_variant,p.Ser117Cys,ENST00000376351,NM_020752.2;GPR158-AS1,non_coding_transcript_exon_variant,,ENST00000449643,; T ENST00000376351 Transcript missense_variant 708/6959 349/3648 117/1215 S/C Agc/Tgc 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 deleterious(0.02) 1/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 MODERATE 1 SNV 1 1 PASS rs1376410629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 25175769 25175769 A T 1 0 0 0 0 1 0 0 0 6549 188 7 4 4 GPR158 10 25175769 Missense_Mutation SNP A C3N-02089_T 1735553 25175769 108621653 544 27628 GPR158 0 . GRCh38 10 25412320 25412320 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.1182T>C p.= p.P394P ENST00000376351 4/11 435 346 89 379 379 0 strelka-varscan-mutect GPR158,synonymous_variant,p.=,ENST00000376351,NM_020752.2; C ENST00000376351 Transcript synonymous_variant 1541/6959 1182/3648 394/1215 P ccT/ccC 1 1 GPR158 HGNC HGNC:23689 protein_coding YES CCDS31166.1 ENSP00000365529 Q5T848 UPI0000199875 NM_020752.2 4/11 hmmpanther:PTHR32546:SF11,hmmpanther:PTHR32546 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 25412320 25412320 T C 1 0 0 0 0 0 0 0 1 6549 1596 56 5 5 GPR158 10 25412320 Silent SNP T C3N-02089_T 236551 25412320 108385102 545 27629 KIF5B 0 . GRCh38 10 32048463 32048463 + Splice_Site SNP C C T novel C3N-02089_T C3N-02089_N C C c.214+1G>A p.X72_splice ENST00000302418 135 125 10 116 116 0 strelka-varscan-mutect KIF5B,splice_donor_variant,,ENST00000302418,NM_004521.2; T ENST00000302418 Transcript splice_donor_variant -/5877 214/2892 72/963 1 -1 KIF5B HGNC HGNC:6324 protein_coding YES CCDS7171.1 ENSP00000307078 P33176 V9HW29 UPI000012DE68 NM_004521.2 2/25 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 32048463 32048463 C T 1 0 0 0 0 0 0 1 0 8171 521 18 3 3 KIF5B 10 32048463 Splice_Site SNP C C3N-02089_T 6636143 32048463 101748959 546 27630 ANKRD30A 0 . GRCh38 10 37166624 37166624 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1916C>A p.Ser639Ter p.S639* ENST00000361713 19/36 101 81 20 83 83 0 varscan-mutect ANKRD30A,stop_gained,p.Ser639Ter,ENST00000374660,;ANKRD30A,stop_gained,p.Ser695Ter,ENST00000611781,;ANKRD30A,stop_gained,p.Ser639Ter,ENST00000361713,NM_052997.2;ANKRD30A,intron_variant,,ENST00000602533,; A ENST00000361713 Transcript stop_gained 2015/4405 1916/4026 639/1341 S/* tCa/tAa 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 19/36 HIGH 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 37166624 37166624 C A 1 0 0 0 0 0 1 0 0 761 838 29 2 2 ANKRD30A 10 37166624 Nonsense_Mutation SNP C C3N-02089_T 5118161 37166624 96630798 547 27631 ANKRD30A 0 . GRCh38 10 37219642 37219642 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3762C>A p.Asn1254Lys p.N1254K ENST00000361713 34/36 254 187 67 204 204 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Asn1373Lys,ENST00000374660,;ANKRD30A,missense_variant,p.Asn1310Lys,ENST00000611781,;ANKRD30A,missense_variant,p.Asn1254Lys,ENST00000602533,;ANKRD30A,missense_variant,p.Asn1254Lys,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript missense_variant 3861/4405 3762/4026 1254/1341 N/K aaC/aaA 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.13) 34/36 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF14915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 37219642 37219642 C A 1 0 0 0 0 1 0 0 0 761 477 17 2 2 ANKRD30A 10 37219642 Missense_Mutation SNP C C3N-02089_T 53018 37219642 96577780 548 27632 ALOX5 0 . GRCh38 10 45428690 45428690 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.907C>A p.Leu303Ile p.L303I ENST00000374391 7/14 295 251 44 231 230 1 strelka-varscan-mutect ALOX5,missense_variant,p.Leu303Ile,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,missense_variant,p.Leu303Ile,ENST00000542434,NM_001256154.1;ALOX5,3_prime_UTR_variant,,ENST00000612635,;ALOX5,downstream_gene_variant,,ENST00000483623,; A ENST00000374391 Transcript missense_variant 960/2506 907/2025 303/674 L/I Ctc/Atc 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 tolerated(0.42) 7/14 PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Gene3D:3.10.450.60,Pfam_domain:PF00305,Superfamily_domains:SSF48484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 45428690 45428690 C A 1 0 0 0 0 1 0 0 0 640 565 20 2 2 ALOX5 10 45428690 Missense_Mutation SNP C C3N-02089_T 8209048 45428690 88368732 549 27633 ALOX5 0 . GRCh38 10 45443204 45443204 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1439A>T p.Glu480Val p.E480V ENST00000374391 10/14 106 93 13 110 110 0 strelka-varscan-mutect ALOX5,missense_variant,p.Glu480Val,ENST00000374391,NM_001256153.1,NM_000698.3;ALOX5,missense_variant,p.Glu480Val,ENST00000542434,NM_001256154.1;ALOX5,3_prime_UTR_variant,,ENST00000612635,;RP11-67C2.2,downstream_gene_variant,,ENST00000435635,;ALOX5,non_coding_transcript_exon_variant,,ENST00000493336,;ALOX5,upstream_gene_variant,,ENST00000498461,;ALOX5,upstream_gene_variant,,ENST00000481117,;ALOX5,downstream_gene_variant,,ENST00000475300,; T ENST00000374391 Transcript missense_variant 1492/2506 1439/2025 480/674 E/V gAa/gTa 1 1 ALOX5 HGNC HGNC:435 protein_coding YES CCDS7212.1 ENSP00000363512 P09917 UPI0000043F84 NM_001256153.1,NM_000698.3 tolerated(0.06) 10/14 PROSITE_profiles:PS51393,hmmpanther:PTHR11771:SF5,hmmpanther:PTHR11771,Gene3D:1.20.245.10,Pfam_domain:PF00305,Superfamily_domains:SSF48484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 45443204 45443204 A T 1 0 0 0 0 1 0 0 0 640 246 9 4 4 ALOX5 10 45443204 Missense_Mutation SNP A C3N-02089_T 14514 45443204 88354218 550 27634 ZFAND4 0 . GRCh38 10 45626067 45626067 + Missense_Mutation SNP G G C rs35142284 C3N-02089_T C3N-02089_N G G c.1756C>G p.Arg586Gly p.R586G ENST00000344646 7/10 397 363 34 324 324 0 strelka-varscan-mutect ZFAND4,missense_variant,p.Arg512Gly,ENST00000374366,NM_001282906.1,NM_001282905.1;ZFAND4,missense_variant,p.Arg586Gly,ENST00000344646,NM_001128324.2,NM_174890.3;ZFAND4,intron_variant,,ENST00000374371,;ZFAND4,non_coding_transcript_exon_variant,,ENST00000374370,; C ENST00000344646 Transcript missense_variant 1972/3241 1756/2184 586/727 R/G Cgt/Ggt rs35142284,COSM918291 1 -1 ZFAND4 HGNC HGNC:23504 protein_coding YES CCDS7214.1 ENSP00000339484 Q86XD8 A0A024R7V9 UPI0000161363 NM_001128324.2,NM_174890.3 tolerated(0.33) 7/10 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs35142284 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 45626067 45626067 G C 1 0 0 0 0 1 0 0 0 18206 1145 40 4 4 ZFAND4 10 45626067 Missense_Mutation SNP G C3N-02089_T 182863 45626067 88171355 551 27635 RBP3 0 . GRCh38 10 47351224 47351224 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2740C>A p.Pro914Thr p.P914T ENST00000584701 1/4 280 235 45 272 270 2 strelka-varscan-mutect RBP3,missense_variant,p.Pro914Thr,ENST00000584701,NM_002900.2; A ENST00000584701 Transcript missense_variant 2854/4276 2740/3744 914/1247 P/T Ccc/Acc 1 1 RBP3 HGNC HGNC:9921 protein_coding YES CCDS73119.1 ENSP00000463151 P10745 UPI000012D87A NM_002900.2 deleterious(0) 1/4 Gene3D:3.90.226.10,Pfam_domain:PF03572,hmmpanther:PTHR11261,hmmpanther:PTHR11261:SF3,SMART_domains:SM00245,Superfamily_domains:SSF52096 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 47351224 47351224 C A 1 0 0 0 0 1 0 0 0 13325 739 26 2 2 RBP3 10 47351224 Missense_Mutation SNP C C3N-02089_T 1725157 47351224 86446198 552 27636 C10orf71 0 . GRCh38 10 49325241 49325241 + Nonsense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.2696G>A p.Trp899Ter p.W899* ENST00000374144 3/3 252 200 52 257 257 0 strelka-varscan-mutect C10orf71,stop_gained,p.Trp899Ter,ENST00000374144,NM_001135196.1; A ENST00000374144 Transcript stop_gained 2984/5230 2696/4308 899/1435 W/* tGg/tAg 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 3/3 hmmpanther:PTHR33775 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 49325241 49325241 G A 1 0 0 0 0 0 1 0 0 1769 1357 47 3 3 C10orf71 10 49325241 Nonsense_Mutation SNP G C3N-02089_T 1974017 49325241 84472181 553 27637 C10orf71 0 . GRCh38 10 49325336 49325336 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2791G>C p.Ala931Pro p.A931P ENST00000374144 3/3 240 215 25 199 198 1 strelka-varscan-mutect C10orf71,missense_variant,p.Ala931Pro,ENST00000374144,NM_001135196.1; C ENST00000374144 Transcript missense_variant 3079/5230 2791/4308 931/1435 A/P Gcc/Ccc 1 1 C10orf71 HGNC HGNC:26973 protein_coding YES CCDS44387.1 ENSP00000363259 Q711Q0 UPI0000161572 NM_001135196.1 tolerated(0.12) 3/3 hmmpanther:PTHR33775 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 49325336 49325336 G C 1 0 0 0 0 1 0 0 0 1769 1203 42 4 4 C10orf71 10 49325336 Missense_Mutation SNP G C3N-02089_T 95 49325336 84472086 554 27638 A1CF 0 . GRCh38 10 50844015 50844015 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.231G>T p.Glu77Asp p.E77D ENST00000395489 6/15 319 284 35 276 273 3 strelka-varscan-mutect A1CF,missense_variant,p.Glu77Asp,ENST00000395489,NM_001198819.1;A1CF,missense_variant,p.Glu77Asp,ENST00000395495,NM_001198820.1;A1CF,missense_variant,p.Glu69Asp,ENST00000282641,NM_001198818.1;A1CF,missense_variant,p.Glu69Asp,ENST00000374001,;A1CF,missense_variant,p.Glu77Asp,ENST00000373995,NM_138933.2;A1CF,missense_variant,p.Glu69Asp,ENST00000373997,NM_014576.3;A1CF,missense_variant,p.Glu69Asp,ENST00000373993,NM_138932.2;A1CF,missense_variant,p.Glu69Asp,ENST00000414883,;A1CF,non_coding_transcript_exon_variant,,ENST00000473480,; A ENST00000395489 Transcript missense_variant 631/9517 231/1809 77/602 E/D gaG/gaT 1 -1 A1CF HGNC HGNC:24086 protein_coding YES CCDS73133.1 ENSP00000378868 F8W9F8 UPI0001E92A39 NM_001198819.1 deleterious(0) 6/15 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF313,hmmpanther:PTHR24012,Gene3D:3.30.70.330,Pfam_domain:PF00076,TIGRFAM_domain:TIGR01648,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 2 1 PASS rs952822363 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 50844015 50844015 C A 1 0 0 0 0 1 0 0 0 2 680 24 2 2 A1CF 10 50844015 Missense_Mutation SNP C C3N-02089_T 1518679 50844015 82953407 555 27639 PRKG1 0 . GRCh38 10 52062555 52062555 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.859G>T p.Asp287Tyr p.D287Y ENST00000373980 7/18 99 69 30 97 97 0 strelka-varscan-mutect PRKG1,missense_variant,p.Asp287Tyr,ENST00000373980,NM_006258.3;PRKG1,missense_variant,p.Asp272Tyr,ENST00000373985,NM_001098512.2;PRKG1,missense_variant,p.Asp60Tyr,ENST00000401604,;PRKG1,missense_variant,p.Asp145Tyr,ENST00000373976,;PRKG1,non_coding_transcript_exon_variant,,ENST00000373975,; T ENST00000373980 Transcript missense_variant 1276/6928 859/2061 287/686 D/Y Gac/Tac 1 1 PRKG1 HGNC HGNC:9414 protein_coding YES CCDS7244.1 ENSP00000363092 Q13976 UPI000012DDCD NM_006258.3 tolerated(0.09) 7/18 Gene3D:2.60.120.10,Pfam_domain:PF00027,PIRSF_domain:PIRSF000559,PROSITE_profiles:PS50042,hmmpanther:PTHR24353,hmmpanther:PTHR24353:SF68,SMART_domains:SM00100,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 52062555 52062555 G T 1 0 0 0 0 1 0 0 0 12655 942 33 2 2 PRKG1 10 52062555 Missense_Mutation SNP G C3N-02089_T 1218540 52062555 81734867 556 27640 PCDH15 0 . GRCh38 10 54022911 54022911 + Missense_Mutation SNP G G T rs761375285 C3N-02089_T C3N-02089_N G G c.2522C>A p.Thr841Asn p.T841N ENST00000373957 20/35 259 236 23 285 285 0 strelka-varscan-mutect PCDH15,missense_variant,p.Thr841Asn,ENST00000614895,;PCDH15,missense_variant,p.Thr836Asn,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Thr836Asn,ENST00000414778,;PCDH15,missense_variant,p.Thr841Asn,ENST00000617051,;PCDH15,missense_variant,p.Thr841Asn,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Thr836Asn,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Thr836Asn,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Thr814Asn,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Thr799Asn,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Thr836Asn,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Thr765Asn,ENST00000622048,;PCDH15,missense_variant,p.Thr765Asn,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Thr836Asn,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Thr848Asn,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Thr843Asn,ENST00000395445,;PCDH15,missense_variant,p.Thr836Asn,ENST00000616114,;PCDH15,missense_variant,p.Thr836Asn,ENST00000395438,;PCDH15,missense_variant,p.Thr848Asn,ENST00000612394,;PCDH15,missense_variant,p.Thr841Asn,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Thr447Asn,ENST00000409834,;PCDH15,missense_variant,p.Thr836Asn,ENST00000373955,;PCDH15,intron_variant,,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,3_prime_UTR_variant,,ENST00000448885,;PCDH15,3_prime_UTR_variant,,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; T ENST00000373957 Transcript missense_variant 2917/7032 2522/5889 841/1962 T/N aCt/aAt rs761375285 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 tolerated(0.06) 20/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF11,Pfam_domain:PF00028,Gene3D:2.60.40.60,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs761375285 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 54022911 54022911 G T 1 0 0 0 0 1 0 0 0 11598 1029 36 2 2 PCDH15 10 54022911 Missense_Mutation SNP G C3N-02089_T 1960356 54022911 79774511 557 27641 MTRNR2L5 0 . GRCh38 10 55599956 55599956 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.57T>A p.= p.P19P ENST00000512524 1/1 50 41 9 55 55 0 strelka-varscan-mutect MTRNR2L5,synonymous_variant,p.=,ENST00000512524,NM_001190478.1;PCDH15,intron_variant,,ENST00000613346,;RP11-168O22.1,upstream_gene_variant,,ENST00000457975,; A ENST00000512524 Transcript synonymous_variant 654/739 57/75 19/24 P ccT/ccA 1 1 MTRNR2L5 HGNC HGNC:37162 protein_coding YES CCDS53537.1 ENSP00000437910 P0CJ72 UPI0001DA9316 NM_001190478.1 1/1 Pfam_domain:PF15040,hmmpanther:PTHR33895,hmmpanther:PTHR33895:SF4 LOW SNV 1 PASS . . 0 207 2 0 0 0 0 0 -19.99494 1 1 1 1 0 A 2 1 90 55599956 55599956 T A 1 0 0 0 0 0 0 0 1 9954 1509 53 4 4 MTRNR2L5 10 55599956 Silent SNP T C3N-02089_T 1577045 55599956 78197466 558 27642 IPMK 0 . GRCh38 10 58196387 58196387 + Silent SNP A A G novel C3N-02089_T C3N-02089_N A A c.940T>C p.= p.L314L ENST00000373935 6/6 264 245 19 326 326 0 strelka-varscan-mutect IPMK,synonymous_variant,p.=,ENST00000373935,NM_152230.4; G ENST00000373935 Transcript synonymous_variant 1263/6133 940/1251 314/416 L Ttg/Ctg 1 -1 IPMK HGNC HGNC:20739 protein_coding YES CCDS7250.1 ENSP00000363046 Q8NFU5 UPI000006FB8E NM_152230.4 6/6 Pfam_domain:PF03770 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 58196387 58196387 A G 1 0 0 0 0 0 0 0 1 7695 69 3 5 5 IPMK 10 58196387 Silent SNP A C3N-02089_T 2596431 58196387 75601035 559 27643 BICC1 0 . GRCh38 10 58817614 58817614 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.2586A>T p.= p.T862T ENST00000373886 19/21 219 198 21 196 196 0 strelka-varscan-mutect BICC1,synonymous_variant,p.=,ENST00000373886,NM_001080512.2;BICC1,downstream_gene_variant,,ENST00000263103,; T ENST00000373886 Transcript synonymous_variant 2590/5475 2586/2925 862/974 T acA/acT 1 1 BICC1 HGNC HGNC:19351 protein_coding YES CCDS31206.1 ENSP00000362993 Q9H694 UPI000059D156 NM_001080512.2 19/21 hmmpanther:PTHR10627,hmmpanther:PTHR10627:SF38 LOW 1 SNV 2 1 PASS rs1351703442 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 58817614 58817614 A T 1 0 0 0 0 0 0 0 1 1576 175 7 4 4 BICC1 10 58817614 Silent SNP A C3N-02089_T 621227 58817614 74979808 560 27644 JMJD1C 0 . GRCh38 10 63215591 63215591 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.784C>G p.Arg262Gly p.R262G ENST00000399262 6/26 64 59 5 59 59 0 strelka-varscan-mutect JMJD1C,missense_variant,p.Arg262Gly,ENST00000399262,NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2;JMJD1C,missense_variant,p.Arg80Gly,ENST00000542921,NM_001318153.1,NM_001282948.1;JMJD1C,non_coding_transcript_exon_variant,,ENST00000402544,;JMJD1C,non_coding_transcript_exon_variant,,ENST00000489372,;JMJD1C,non_coding_transcript_exon_variant,,ENST00000469152,;JMJD1C,downstream_gene_variant,,ENST00000633035,; C ENST00000399262 Transcript missense_variant 1003/8666 784/7623 262/2540 R/G Cgc/Ggc COSM1242396,COSM1242397 1 -1 JMJD1C HGNC HGNC:12313 protein_coding YES CCDS41532.1 ENSP00000382204 Q15652 UPI0000198BEF NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2 deleterious(0) 6/26 hmmpanther:PTHR12549,hmmpanther:PTHR12549:SF6 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1336559705 . 0 202 8 0 0 0 0 0 -11.52412 0.9999924 1 1 1 0 C 3 2 90 63215591 63215591 G C 1 0 0 0 0 1 0 0 0 7864 1145 40 4 4 JMJD1C 10 63215591 Missense_Mutation SNP G C3N-02089_T 4397977 63215591 70581831 561 27645 JMJD1C 0 . GRCh38 10 63380323 63380323 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.328G>T p.Ala110Ser p.A110S ENST00000399262 2/26 280 214 66 281 280 1 strelka-varscan-mutect JMJD1C,missense_variant,p.Ala110Ser,ENST00000399262,NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2;JMJD1C,non_coding_transcript_exon_variant,,ENST00000633035,; A ENST00000399262 Transcript missense_variant 547/8666 328/7623 110/2540 A/S Gca/Tca 1 -1 JMJD1C HGNC HGNC:12313 protein_coding YES CCDS41532.1 ENSP00000382204 Q15652 UPI0000198BEF NM_001318154.1,NM_001322252.1,NM_001322254.1,NM_001322258.1,NM_032776.2 deleterious(0.02) 2/26 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 63380323 63380323 C A 1 0 0 0 0 1 0 0 0 7864 724 25 2 2 JMJD1C 10 63380323 Missense_Mutation SNP C C3N-02089_T 164732 63380323 70417099 562 27646 STOX1 0 . GRCh38 10 68885361 68885361 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1565G>T p.Ser522Ile p.S522I ENST00000298596 3/4 133 96 37 209 209 0 strelka-varscan-mutect STOX1,missense_variant,p.Ser522Ile,ENST00000298596,NM_152709.4;STOX1,missense_variant,p.Ser522Ile,ENST00000399169,NM_001130161.2;STOX1,intron_variant,,ENST00000399165,NM_001130159.2;STOX1,intron_variant,,ENST00000399162,NM_001130160.2; T ENST00000298596 Transcript missense_variant 1648/3377 1565/2970 522/989 S/I aGc/aTc 1 1 STOX1 HGNC HGNC:23508 protein_coding YES CCDS41535.1 ENSP00000298596 Q6ZVD7 UPI00004B59B0 NM_152709.4 deleterious(0.01) 3/4 hmmpanther:PTHR22437,hmmpanther:PTHR22437:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 68885361 68885361 G T 1 0 0 0 0 1 0 0 0 15697 971 34 2 2 STOX1 10 68885361 Missense_Mutation SNP G C3N-02089_T 5505038 68885361 64912061 563 27647 UNC5B 0 . GRCh38 10 71293822 71293822 + Silent SNP C C A C3N-02089_T C3N-02089_N C C c.2064C>A p.= p.S688S ENST00000335350 13/17 242 179 63 269 269 0 strelka-varscan-mutect UNC5B,synonymous_variant,p.=,ENST00000335350,NM_170744.4;UNC5B,synonymous_variant,p.=,ENST00000373192,NM_001244889.1; A ENST00000335350 Transcript synonymous_variant 2480/6841 2064/2838 688/945 S tcC/tcA COSM235543 1 1 UNC5B HGNC HGNC:12568 protein_coding YES CCDS7309.1 ENSP00000334329 Q8IZJ1 UPI000000D753 NM_170744.4 13/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF6 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 71293822 71293822 C A 1 0 0 0 0 0 0 0 1 17516 610 22 2 2 UNC5B 10 71293822 Silent SNP C C3N-02089_T 2408461 71293822 62503600 564 27648 LRIT1 0 . GRCh38 10 84234331 84234331 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.637G>T p.Val213Phe p.V213F ENST00000372105 3/4 60 48 12 44 44 0 strelka-varscan-mutect LRIT1,missense_variant,p.Val213Phe,ENST00000372105,NM_015613.2; A ENST00000372105 Transcript missense_variant 659/2228 637/1872 213/623 V/F Gtt/Ttt 1 -1 LRIT1 HGNC HGNC:23404 protein_coding YES CCDS7373.1 ENSP00000361177 Q9P2V4 UPI000006F66C NM_015613.2 deleterious(0) 3/4 Gene3D:3.80.10.10,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF9,SMART_domains:SM00082,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS rs1315974055 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 84234331 84234331 C A 1 0 0 0 0 1 0 0 0 8842 507 18 2 2 LRIT1 10 84234331 Missense_Mutation SNP C C3N-02089_T 12940509 84234331 49563091 565 27649 LGI1 0 . GRCh38 10 93758224 93758224 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.80C>A p.Ser27Tyr p.S27Y ENST00000371418 1/8 516 383 133 473 472 1 strelka-varscan-mutect LGI1,missense_variant,p.Ser27Tyr,ENST00000630184,;LGI1,missense_variant,p.Ser27Tyr,ENST00000371418,NM_005097.2;LGI1,missense_variant,p.Ser27Tyr,ENST00000629035,;LGI1,missense_variant,p.Ser27Tyr,ENST00000630047,;LGI1,missense_variant,p.Ser27Tyr,ENST00000636155,;LGI1,missense_variant,p.Ser27Tyr,ENST00000371413,NM_001308275.1;LGI1,missense_variant,p.Ser27Tyr,ENST00000627699,;LGI1,missense_variant,p.Ser27Tyr,ENST00000478763,;LGI1,intron_variant,,ENST00000637689,;RP11-437J2.3,upstream_gene_variant,,ENST00000630034,;LGI1,upstream_gene_variant,,ENST00000637347,;LGI1,upstream_gene_variant,,ENST00000636683,;LGI1,upstream_gene_variant,,ENST00000636140,;LGI1,missense_variant,p.Ser27Tyr,ENST00000637037,;LGI1,missense_variant,p.Ser27Tyr,ENST00000635953,;LGI1,missense_variant,p.Ser27Tyr,ENST00000627420,;LGI1,missense_variant,p.Ser27Tyr,ENST00000637611,;LGI1,missense_variant,p.Ser27Tyr,ENST00000636754,;LGI1,missense_variant,p.Ser27Tyr,ENST00000636232,;LGI1,missense_variant,p.Ser27Tyr,ENST00000637925,;LGI1,missense_variant,p.Ser27Tyr,ENST00000638049,;LGI1,missense_variant,p.Ser27Tyr,ENST00000636946,;LGI1,missense_variant,p.Ser27Tyr,ENST00000630487,; A ENST00000371418 Transcript missense_variant 416/2381 80/1674 27/557 S/Y tCt/tAt 1 1 LGI1 HGNC HGNC:6572 protein_coding YES CCDS7431.1 ENSP00000360472 O95970 A0A0S2Z4S7 UPI0000048F03 NM_005097.2 tolerated(1) 1/8 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF17,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 93758224 93758224 C A 1 0 0 0 0 1 0 0 0 8661 913 32 2 2 LGI1 10 93758224 Missense_Mutation SNP C C3N-02089_T 9523893 93758224 40039198 566 27650 SLC35G1 0 . GRCh38 10 93901417 93901417 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1025T>A p.Val342Glu p.V342E ENST00000427197 3/3 87 69 18 108 108 0 strelka-varscan-mutect SLC35G1,missense_variant,p.Val341Glu,ENST00000371408,NM_153226.2;SLC35G1,missense_variant,p.Val342Glu,ENST00000427197,NM_001134658.1;SLC35G1,intron_variant,,ENST00000483386,;SLC35G1,intron_variant,,ENST00000603665,;SLC35G1,intron_variant,,ENST00000494992,;SLC35G1,intron_variant,,ENST00000605679,; A ENST00000427197 Transcript missense_variant 1086/2402 1025/1098 342/365 V/E gTg/gAg 1 1 SLC35G1 HGNC HGNC:26607 protein_coding YES CCDS44459.1 ENSP00000400932 Q2M3R5 UPI000013FE98 NM_001134658.1 deleterious(0) 3/3 Transmembrane_helices:TMhelix,hmmpanther:PTHR22911,hmmpanther:PTHR22911:SF6,Pfam_domain:PF00892,Superfamily_domains:0043518 MODERATE 1 SNV 1 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999564 1 1 1 0 A 3 1 90 93901417 93901417 T A 1 0 0 0 0 1 0 0 0 14865 1696 59 4 4 SLC35G1 10 93901417 Missense_Mutation SNP T C3N-02089_T 143193 93901417 39896005 567 27651 HELLS 0 . GRCh38 10 94593556 94593556 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2167G>C p.Gly723Arg p.G723R ENST00000394036 19/23 185 150 35 199 199 0 strelka-varscan-mutect HELLS,missense_variant,p.Gly114Arg,ENST00000371327,;HELLS,missense_variant,p.Gly723Arg,ENST00000394036,NM_001289067.1;HELLS,missense_variant,p.Gly677Arg,ENST00000348459,NM_001289069.1,NM_001289068.1,NM_001289074.1,NM_018063.4,NM_001289075.1;HELLS,missense_variant,p.Gly553Arg,ENST00000239026,NM_001289071.1;HELLS,missense_variant,p.Gly579Arg,ENST00000394045,NM_001289070.1,NM_001289072.1;HELLS,missense_variant,p.Gly539Arg,ENST00000371332,NM_001289073.1;RP11-119K6.6,intron_variant,,ENST00000432120,;HELLS,upstream_gene_variant,,ENST00000475263,;HELLS,downstream_gene_variant,,ENST00000464030,; C ENST00000394036 Transcript missense_variant 2167/3131 2167/2655 723/884 G/R Ggt/Cgt 1 1 HELLS HGNC HGNC:4861 protein_coding YES CCDS73162.1 ENSP00000377601 A0A0B4J1V9 UPI000023B7CF NM_001289067.1 deleterious(0) 19/23 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 94593556 94593556 G C 1 0 0 0 0 1 0 0 0 6928 1348 47 4 4 HELLS 10 94593556 Missense_Mutation SNP G C3N-02089_T 692139 94593556 39203866 568 27652 DNTT 0 . GRCh38 10 96304652 96304652 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.155T>A p.Leu52His p.L52H ENST00000371174 1/11 243 226 17 234 234 0 strelka-varscan-mutect DNTT,missense_variant,p.Leu52His,ENST00000371174,NM_004088.3;DNTT,missense_variant,p.Leu52His,ENST00000630152,NM_001017520.1;RP11-35J23.1,intron_variant,,ENST00000454484,; A ENST00000371174 Transcript missense_variant 257/1972 155/1530 52/509 L/H cTc/cAc 1 1 DNTT HGNC HGNC:2983 protein_coding YES CCDS7447.1 ENSP00000360216 P04053 UPI000013C84B NM_004088.3 deleterious(0) 1/11 Gene3D:3.40.50.10190,Pfam_domain:PF00533,PIRSF_domain:PIRSF000817,PIRSF_domain:PIRSF501175,Prints_domain:PR00871,PROSITE_profiles:PS50172,hmmpanther:PTHR11276,hmmpanther:PTHR11276:SF21,SMART_domains:SM00292,Superfamily_domains:SSF52113 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 96304652 96304652 T A 1 0 0 0 0 1 0 0 0 4494 1551 54 4 4 DNTT 10 96304652 Missense_Mutation SNP T C3N-02089_T 1711096 96304652 37492770 569 27653 CRTAC1 0 . GRCh38 10 98011163 98011163 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.199G>T p.Gly67Trp p.G67W ENST00000370597 2/15 237 171 66 235 234 1 strelka-varscan-mutect CRTAC1,missense_variant,p.Gly67Trp,ENST00000370597,NM_018058.6;CRTAC1,missense_variant,p.Gly67Trp,ENST00000370591,NM_001206528.2;CRTAC1,missense_variant,p.Gly59Trp,ENST00000309155,; A ENST00000370597 Transcript missense_variant 555/2890 199/1986 67/661 G/W Ggg/Tgg 1 -1 CRTAC1 HGNC HGNC:14882 protein_coding YES CCDS31266.1 ENSP00000359629 Q9NQ79 UPI000006D454 NM_018058.6 deleterious(0) 2/15 Pfam_domain:PF13517,hmmpanther:PTHR16026,hmmpanther:PTHR16026:SF4,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS rs1321493033 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 98011163 98011163 C A 1 0 0 0 0 1 0 0 0 3698 594 21 2 2 CRTAC1 10 98011163 Missense_Mutation SNP C C3N-02089_T 1706511 98011163 35786259 570 27654 PKD2L1 0 . GRCh38 10 100297508 100297508 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.830C>A p.Ser277Tyr p.S277Y ENST00000318222 5/16 343 253 90 284 282 2 strelka-varscan-mutect PKD2L1,missense_variant,p.Ser277Tyr,ENST00000318222,NM_001253837.1,NM_016112.2;PKD2L1,intron_variant,,ENST00000465680,;PKD2L1,3_prime_UTR_variant,,ENST00000528248,;PKD2L1,downstream_gene_variant,,ENST00000532547,; T ENST00000318222 Transcript missense_variant 1213/3043 830/2418 277/805 S/Y tCc/tAc 1 -1 PKD2L1 HGNC HGNC:9011 protein_coding YES CCDS7492.1 ENSP00000325296 Q9P0L9 UPI0000130FED NM_001253837.1,NM_016112.2 deleterious(0) 5/16 hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF105,Pfam_domain:PF08016 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 100297508 100297508 G T 1 0 0 0 0 1 0 0 0 12063 1174 41 2 2 PKD2L1 10 100297508 Missense_Mutation SNP G C3N-02089_T 2286345 100297508 33499914 571 27655 LDB1 0 . GRCh38 10 102108179 102108179 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.1150C>T p.= p.L384L ENST00000425280 11/11 463 329 134 379 379 0 strelka-varscan-mutect LDB1,synonymous_variant,p.=,ENST00000361198,NM_003893.4;LDB1,synonymous_variant,p.=,ENST00000425280,NM_001113407.1;LDB1,downstream_gene_variant,,ENST00000490751,;LDB1,downstream_gene_variant,,ENST00000461873,; A ENST00000425280 Transcript synonymous_variant 1493/2089 1150/1236 384/411 L Ctg/Ttg 1 -1 LDB1 HGNC HGNC:6532 protein_coding YES CCDS44472.1 ENSP00000392466 Q86U70 UPI00001F95EA NM_001113407.1 11/11 hmmpanther:PTHR10378,hmmpanther:PTHR10378:SF7 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 102108179 102108179 G A 1 0 0 0 0 0 0 0 1 8602 1020 36 3 3 LDB1 10 102108179 Silent SNP G C3N-02089_T 1810671 102108179 31689243 572 27656 GBF1 0 . GRCh38 10 102367480 102367480 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2559G>T p.Glu853Asp p.E853D ENST00000369983 21/40 181 155 26 207 207 0 strelka-varscan-mutect GBF1,missense_variant,p.Glu853Asp,ENST00000369983,NM_001199379.1,NM_001199378.1,NM_004193.2; T ENST00000369983 Transcript missense_variant,splice_region_variant 2819/6403 2559/5580 853/1859 E/D gaG/gaT 1 1 GBF1 HGNC HGNC:4181 protein_coding YES CCDS7533.1 ENSP00000359000 Q92538 UPI000012B228 NM_001199379.1,NM_001199378.1,NM_004193.2 tolerated(1) 21/40 PROSITE_profiles:PS50190,hmmpanther:PTHR10663:SF167,hmmpanther:PTHR10663,Pfam_domain:PF01369,Gene3D:1.10.1000.11,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 102367480 102367480 G T 1 0 0 0 0 1 0 0 0 6142 1043 36 2 2 GBF1 10 102367480 Missense_Mutation SNP G C3N-02089_T 259301 102367480 31429942 573 27657 ATRNL1 0 . GRCh38 10 115426288 115426288 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.3308G>A p.Arg1103Lys p.R1103K ENST00000355044 21/29 154 97 57 184 184 0 strelka-varscan-mutect ATRNL1,missense_variant,p.Arg1103Lys,ENST00000355044,NM_207303.4;ATRNL1,missense_variant,p.Arg187Lys,ENST00000526373,;ATRNL1,non_coding_transcript_exon_variant,,ENST00000534530,; A ENST00000355044 Transcript missense_variant 3434/8479 3308/4140 1103/1379 R/K aGa/aAa 1 1 ATRNL1 HGNC HGNC:29063 protein_coding YES CCDS7592.1 ENSP00000347152 Q5VV63 UPI000021CCF8 NM_207303.4 tolerated(1) 21/29 PROSITE_profiles:PS50027,hmmpanther:PTHR10574:SF224,hmmpanther:PTHR10574,SMART_domains:SM00180 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 115426288 115426288 G A 1 0 0 0 0 1 0 0 0 1360 942 33 3 3 ATRNL1 10 115426288 Missense_Mutation SNP G C3N-02089_T 13058808 115426288 18371134 574 27658 FGFR2 0 . GRCh38 10 121500865 121500865 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.1525C>G p.Pro509Ala p.P509A ENST00000457416 11/18 519 485 34 355 355 0 strelka-varscan-mutect FGFR2,missense_variant,p.Pro419Ala,ENST00000613048,NM_023029.2;FGFR2,missense_variant,p.Pro508Ala,ENST00000358487,NM_001320658.1,NM_000141.4;FGFR2,missense_variant,p.Pro280Ala,ENST00000478859,NM_001320654.1;FGFR2,missense_variant,p.Pro396Ala,ENST00000369061,NM_001144914.1;FGFR2,missense_variant,p.Pro419Ala,ENST00000357555,NM_001144915.1;FGFR2,missense_variant,p.Pro391Ala,ENST00000356226,NM_001144918.1,NM_001144916.1;FGFR2,missense_variant,p.Pro392Ala,ENST00000369060,NM_001144917.1;FGFR2,missense_variant,p.Pro509Ala,ENST00000457416,NM_022970.3;FGFR2,missense_variant,p.Pro394Ala,ENST00000369059,;FGFR2,missense_variant,p.Pro420Ala,ENST00000360144,NM_001144919.1;FGFR2,missense_variant,p.Pro509Ala,ENST00000369058,;FGFR2,missense_variant,p.Pro509Ala,ENST00000369056,NM_001144913.1;FGFR2,missense_variant,p.Pro417Ala,ENST00000336553,;FGFR2,missense_variant,p.Pro508Ala,ENST00000351936,;FGFR2,missense_variant,p.Pro506Ala,ENST00000346997,;FGFR2,missense_variant,p.Pro100Ala,ENST00000429361,;FGFR2,3_prime_UTR_variant,,ENST00000604236,; C ENST00000457416 Transcript missense_variant 2117/3061 1525/2469 509/822 P/A Ccc/Gcc COSM1716055,COSM1716056,COSM1716057,COSM1716058 1 -1 FGFR2 HGNC HGNC:3689 protein_coding YES CCDS7620.2 ENSP00000410294 P21802 UPI000002A99A NM_022970.3 tolerated(0.18) 11/18 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF130,PROSITE_patterns:PS00107,Pfam_domain:PF07714,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000628,SMART_domains:SM00219,Superfamily_domains:SSF56112 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 121500865 121500865 G C 1 0 0 0 0 1 0 0 0 5730 1203 42 4 4 FGFR2 10 121500865 Missense_Mutation SNP G C3N-02089_T 6074577 121500865 12296557 575 27659 CPXM2 0 . GRCh38 10 123713533 123713533 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.530C>A p.Ser177Tyr p.S177Y ENST00000615851 14/15 47 30 17 73 73 0 strelka-varscan-mutect CPXM2,missense_variant,p.Ser177Tyr,ENST00000615851,;CPXM2,non_coding_transcript_exon_variant,,ENST00000368854,; T ENST00000615851 Transcript missense_variant 2367/2512 530/675 177/224 S/Y tCt/tAt 1 -1 CPXM2 HGNC HGNC:26977 protein_coding ENSP00000483180 Q49AT5 UPI000056F13A tolerated(0.06) 14/15 SMART_domains:SM00631 MODERATE SNV 5 1 PASS rs1195981054 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 123713533 123713533 G T 1 0 0 0 0 1 0 0 0 3636 942 33 2 2 CPXM2 10 123713533 Missense_Mutation SNP G C3N-02089_T 2212668 123713533 10083889 576 27660 RIC8A 0 . GRCh38 11 208863 208863 + Silent SNP C C T C3N-02089_T C3N-02089_N C C c.9C>T p.= p.P3P ENST00000325207 1/10 267 190 77 211 211 0 strelka-varscan-mutect RIC8A,synonymous_variant,p.=,ENST00000526104,NM_001286134.1;RIC8A,synonymous_variant,p.=,ENST00000325207,NM_021932.5;RIC8A,synonymous_variant,p.=,ENST00000530889,;RIC8A,synonymous_variant,p.=,ENST00000528357,;RIC8A,synonymous_variant,p.=,ENST00000626818,;BET1L,upstream_gene_variant,,ENST00000325147,NM_016526.4;BET1L,upstream_gene_variant,,ENST00000382762,NM_001098787.1;RIC8A,upstream_gene_variant,,ENST00000527696,;RIC8A,upstream_gene_variant,,ENST00000527728,;BET1L,upstream_gene_variant,,ENST00000486280,;RIC8A,upstream_gene_variant,,ENST00000524854,;BET1L,upstream_gene_variant,,ENST00000410108,;RIC8A,upstream_gene_variant,,ENST00000527468,;BET1L,upstream_gene_variant,,ENST00000529614,;BET1L,upstream_gene_variant,,ENST00000332865,;RIC8A,upstream_gene_variant,,ENST00000529275,;RIC8A,upstream_gene_variant,,ENST00000611346,;RP11-304M2.5,downstream_gene_variant,,ENST00000526963,;RIC8A,upstream_gene_variant,,ENST00000531541,;RIC8A,synonymous_variant,p.=,ENST00000526982,;RIC8A,non_coding_transcript_exon_variant,,ENST00000532373,;RIC8A,upstream_gene_variant,,ENST00000530149,;BET1L,upstream_gene_variant,,ENST00000479463,;RIC8A,upstream_gene_variant,,ENST00000527039,;RIC8A,upstream_gene_variant,,ENST00000526557,;RIC8A,upstream_gene_variant,,ENST00000532241,; T ENST00000325207 Transcript synonymous_variant 334/2702 9/1614 3/537 P ccC/ccT COSM3666247 1 1 RIC8A HGNC HGNC:29550 protein_coding YES CCDS7690.1 ENSP00000325941 Q9NPQ8 UPI0000037C19 NM_021932.5 1/10 hmmpanther:PTHR12425:SF4,hmmpanther:PTHR12425 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 208863 208863 C T 1 0 0 0 0 0 0 0 1 13529 610 22 3 3 RIC8A 11 208863 Silent SNP C C3N-02089_T 208863 134877759 577 27661 MUC6 0 . GRCh38 11 1029106 1029106 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1320C>A p.Asp440Glu p.D440E ENST00000421673 11/33 346 308 38 336 336 0 strelka-varscan-mutect MUC6,missense_variant,p.Asp440Glu,ENST00000421673,NM_005961.2;MUC6,downstream_gene_variant,,ENST00000525923,; T ENST00000421673 Transcript missense_variant 1371/8006 1320/7320 440/2439 D/E gaC/gaA 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 tolerated(0.23) 11/33 PROSITE_profiles:PS51233,hmmpanther:PTHR11339:SF264,hmmpanther:PTHR11339,Pfam_domain:PF00094,SMART_domains:SM00216 MODERATE 1 SNV 5 1 PASS rs1201583132 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 1029106 1029106 G T 1 0 0 0 0 1 0 0 0 9980 1368 48 2 2 MUC6 11 1029106 Missense_Mutation SNP G C3N-02089_T 820243 1029106 134057516 578 27662 MUC5B 0 . GRCh38 11 1241626 1241626 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.4746G>A p.= p.E1582E ENST00000529681 31/49 125 88 37 116 115 1 strelka-varscan-mutect MUC5B,synonymous_variant,p.=,ENST00000529681,NM_002458.2;RP11-532E4.2,downstream_gene_variant,,ENST00000532061,;MUC5B,downstream_gene_variant,,ENST00000525715,; A ENST00000529681 Transcript synonymous_variant 4804/17911 4746/17289 1582/5762 E gaG/gaA COSM1976196,COSM1976197 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 31/49 Pfam_domain:PF13330 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 1241626 1241626 G A 1 0 0 0 0 0 0 0 1 9979 991 35 3 3 MUC5B 11 1241626 Silent SNP G C3N-02089_T 212520 1241626 133844996 579 27663 OR51T1 0 . GRCh38 11 4882615 4882615 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.797C>A p.Ala266Asp p.A266D ENST00000380378 1/1 152 99 53 142 140 2 strelka-varscan-mutect OR51T1,missense_variant,p.Ala266Asp,ENST00000380378,NM_001004759.1;OR51T1,missense_variant,p.Ala239Asp,ENST00000322049,;MMP26,intron_variant,,ENST00000380390,;MMP26,intron_variant,,ENST00000477339,; A ENST00000380378 Transcript missense_variant 797/1065 797/1065 266/354 A/D gCt/gAt COSM4192313,COSM4192314 1 1 OR51T1 HGNC HGNC:15205 protein_coding YES CCDS31363.1 ENSP00000369738 A0A0C4DFX5 UPI000015F1FF NM_001004759.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF6,Superfamily_domains:SSF81321 1,1 MODERATE SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 4882615 4882615 C A 1 0 0 0 0 1 0 0 0 11180 797 28 2 2 OR51T1 11 4882615 Missense_Mutation SNP C C3N-02089_T 3640989 4882615 130204007 580 27664 OR56A1 0 . GRCh38 11 6027681 6027681 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.24C>G p.= p.P8P ENST00000316650 1/1 44 32 12 63 63 0 strelka-varscan-mutect OR56A1,synonymous_variant,p.=,ENST00000316650,NM_001001917.2; C ENST00000316650 Transcript synonymous_variant 61/1071 24/957 8/318 P ccC/ccG 1 -1 OR56A1 HGNC HGNC:14781 protein_coding YES CCDS31405.1 ENSP00000321246 Q8NGH5 A0A126GVB5 UPI000013FE4B NM_001001917.2 1/1 hmmpanther:PTHR24248:SF62,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999948 1 1 1 0 C 2 2 90 6027681 6027681 G C 1 0 0 0 0 0 0 0 1 11205 1335 47 4 4 OR56A1 11 6027681 Silent SNP G C3N-02089_T 1145066 6027681 129058941 581 27665 USH1C 0 . GRCh38 11 17522896 17522896 + Missense_Mutation SNP G G C rs749821587 C3N-02089_T C3N-02089_N G G c.907C>G p.Arg303Gly p.R303G ENST00000005226 12/27 292 213 79 268 268 0 strelka-varscan-mutect USH1C,missense_variant,p.Arg303Gly,ENST00000005226,NM_153676.3;USH1C,missense_variant,p.Arg272Gly,ENST00000527720,;USH1C,missense_variant,p.Arg303Gly,ENST00000318024,NM_005709.3;USH1C,missense_variant,p.Arg284Gly,ENST00000527020,NM_001297764.1;USH1C,missense_variant,p.Arg314Gly,ENST00000526181,;USH1C,upstream_gene_variant,,ENST00000530700,;USH1C,missense_variant,p.Arg303Gly,ENST00000526313,; C ENST00000005226 Transcript missense_variant 907/2700 907/2700 303/899 R/G Cgg/Ggg rs749821587 1 -1 USH1C HGNC HGNC:12597 protein_coding YES CCDS7825.1 ENSP00000005226 Q9Y6N9 UPI00001D965A NM_153676.3 deleterious(0) 12/27 hmmpanther:PTHR23116,hmmpanther:PTHR23116:SF36,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs749821587 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 17522896 17522896 G C 1 0 0 0 0 1 0 0 0 17568 1086 38 4 4 USH1C 11 17522896 Missense_Mutation SNP G C3N-02089_T 11495215 17522896 117563726 582 27666 SLC6A5 0 . GRCh38 11 20630812 20630812 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1621C>A p.Gln541Lys p.Q541K ENST00000525748 10/16 420 313 107 486 485 1 strelka-varscan-mutect SLC6A5,missense_variant,p.Gln541Lys,ENST00000525748,NM_004211.3;SLC6A5,non_coding_transcript_exon_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; A ENST00000525748 Transcript missense_variant 1894/7084 1621/2394 541/797 Q/K Caa/Aaa 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 deleterious(0.03) 10/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158 MODERATE 1 SNV 1 1 PASS rs931802079 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 20630812 20630812 C A 1 0 0 0 0 1 0 0 0 14970 608 21 2 2 SLC6A5 11 20630812 Missense_Mutation SNP C C3N-02089_T 3107916 20630812 114455810 583 27667 NELL1 0 . GRCh38 11 20960546 20960546 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1370C>A p.Ser457Tyr p.S457Y ENST00000298925 13/21 142 89 53 142 142 0 strelka-varscan-mutect NELL1,missense_variant,p.Ser457Tyr,ENST00000298925,NM_001288713.1;NELL1,missense_variant,p.Ser372Tyr,ENST00000325319,NM_001288714.1;NELL1,missense_variant,p.Ser429Tyr,ENST00000357134,NM_006157.4;NELL1,missense_variant,p.Ser429Tyr,ENST00000532434,NM_201551.2;NELL1,non_coding_transcript_exon_variant,,ENST00000530672,; A ENST00000298925 Transcript missense_variant 1523/3329 1370/2517 457/838 S/Y tCt/tAt 1 1 NELL1 HGNC HGNC:7750 protein_coding YES CCDS73267.1 ENSP00000298925 J3KNC5 UPI0000228C6F NM_001288713.1 deleterious(0.02) 13/21 Gene3D:2.10.25.10,hmmpanther:PTHR24042,hmmpanther:PTHR24042:SF2,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 20960546 20960546 C A 1 0 0 0 0 1 0 0 0 10364 913 32 2 2 NELL1 11 20960546 Missense_Mutation SNP C C3N-02089_T 329734 20960546 114126076 584 27668 ANO5 0 . GRCh38 11 22255370 22255370 + Splice_Site SNP G G A novel C3N-02089_T C3N-02089_N G G c.1181-1G>A p.X394_splice ENST00000324559 152 137 15 190 189 1 strelka-varscan-mutect ANO5,splice_acceptor_variant,,ENST00000324559,NM_001142649.1,NM_213599.2; A ENST00000324559 Transcript splice_acceptor_variant -/6651 1181/2742 394/913 1 1 ANO5 HGNC HGNC:27337 protein_coding YES CCDS31444.1 ENSP00000315371 Q75V66 UPI000035B19B NM_001142649.1,NM_213599.2 12/21 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 22255370 22255370 G A 1 0 0 0 0 0 0 1 0 807 1043 36 3 3 ANO5 11 22255370 Splice_Site SNP G C3N-02089_T 1294824 22255370 112831252 585 27669 SLC17A6 0 . GRCh38 11 22341771 22341771 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.330C>A p.= p.V110V ENST00000263160 2/12 139 102 37 125 125 0 strelka-varscan-mutect SLC17A6,synonymous_variant,p.=,ENST00000263160,NM_020346.2;CTD-2140G10.2,upstream_gene_variant,,ENST00000528009,;CTD-2140G10.2,upstream_gene_variant,,ENST00000531304,;CTD-2140G10.2,upstream_gene_variant,,ENST00000530569,;SLC17A6,upstream_gene_variant,,ENST00000534115,; A ENST00000263160 Transcript synonymous_variant 767/3949 330/1749 110/582 V gtC/gtA 1 1 SLC17A6 HGNC HGNC:16703 protein_coding YES CCDS7856.1 ENSP00000263160 Q9P2U8 UPI0000073F14 NM_020346.2 2/12 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11662,hmmpanther:PTHR11662:SF201,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 22341771 22341771 C A 1 0 0 0 0 0 0 0 1 14686 813 29 2 2 SLC17A6 11 22341771 Silent SNP C C3N-02089_T 86401 22341771 112744851 586 27670 KCNA4 0 . GRCh38 11 30011179 30011179 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1500G>T p.Glu500Asp p.E500D ENST00000328224 2/2 225 162 63 298 298 0 strelka-varscan-mutect KCNA4,missense_variant,p.Glu500Asp,ENST00000328224,NM_002233.3;KCNA4,downstream_gene_variant,,ENST00000526518,; A ENST00000328224 Transcript missense_variant 2734/4172 1500/1962 500/653 E/D gaG/gaT 1 -1 KCNA4 HGNC HGNC:6222 protein_coding YES CCDS41629.1 ENSP00000328511 P22459 UPI00001649FF NM_002233.3 deleterious(0.01) 2/2 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF45,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 30011179 30011179 C A 1 0 0 0 0 1 0 0 0 7921 680 24 2 2 KCNA4 11 30011179 Missense_Mutation SNP C C3N-02089_T 7669408 30011179 105075443 587 27671 DCDC1 0 . GRCh38 11 30892999 30892999 + Splice_Site SNP T T A novel C3N-02089_T C3N-02089_N T T c.2215-2A>T p.X739_splice ENST00000406071 75 51 24 104 104 0 strelka-varscan-mutect DCDC1,splice_acceptor_variant,,ENST00000597505,;DCDC1,splice_acceptor_variant,,ENST00000406071,NM_020869.3;DCDC1,splice_acceptor_variant,,ENST00000483396,;DCDC1,splice_acceptor_variant,,ENST00000303697,;DCDC1,splice_acceptor_variant,,ENST00000444572,; A ENST00000406071 Transcript splice_acceptor_variant -/4758 2215/2673 739/890 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 16/19 HIGH 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 30892999 30892999 T A 1 0 0 0 0 0 0 1 0 4086 1594 55 4 4 DCDC1 11 30892999 Splice_Site SNP T C3N-02089_T 881820 30892999 104193623 588 27672 F2 0 . GRCh38 11 46725978 46725978 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.679G>T p.Val227Leu p.V227L ENST00000311907 7/14 342 249 93 202 201 1 strelka-varscan-mutect F2,missense_variant,p.Val227Leu,ENST00000311907,NM_001311257.1,NM_000506.3;F2,missense_variant,p.Val227Leu,ENST00000530231,;F2,missense_variant,p.Val217Leu,ENST00000442468,;F2,non_coding_transcript_exon_variant,,ENST00000490274,; T ENST00000311907 Transcript missense_variant 735/2023 679/1869 227/622 V/L Gtg/Ttg 1 1 F2 HGNC HGNC:3535 protein_coding YES CCDS31476.1 ENSP00000308541 P00734 UPI0000136ECD NM_001311257.1,NM_000506.3 deleterious(0.01) 7/14 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001149,PROSITE_profiles:PS50070,hmmpanther:PTHR24254,hmmpanther:PTHR24254:SF10,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 46725978 46725978 G T 1 0 0 0 0 1 0 0 0 5210 1261 44 2 2 F2 11 46725978 Missense_Mutation SNP G C3N-02089_T 15832979 46725978 88360644 589 27673 LRP4 0 . GRCh38 11 46875548 46875548 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.3833C>T p.Ala1278Val p.A1278V ENST00000378623 27/38 557 432 125 435 435 0 strelka-varscan-mutect LRP4,missense_variant,p.Ala1278Val,ENST00000378623,NM_002334.3;LRP4-AS1,downstream_gene_variant,,ENST00000502049,;LRP4-AS1,downstream_gene_variant,,ENST00000531719,;LRP4,upstream_gene_variant,,ENST00000527656,; A ENST00000378623 Transcript missense_variant 4076/8076 3833/5718 1278/1905 A/V gCt/gTt 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 tolerated(0.15) 27/38 PROSITE_profiles:PS51120,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF249,Gene3D:2.120.10.30,SMART_domains:SM00135,Superfamily_domains:SSF63825 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 46875548 46875548 G A 1 0 0 0 0 1 0 0 0 8854 971 34 3 3 LRP4 11 46875548 Missense_Mutation SNP G C3N-02089_T 149570 46875548 88211074 590 27674 LRP4 0 . GRCh38 11 46902808 46902808 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.174G>A p.= p.G58G ENST00000378623 2/38 330 248 82 230 230 0 strelka-varscan-mutect LRP4,synonymous_variant,p.=,ENST00000378623,NM_002334.3;LRP4,intron_variant,,ENST00000534404,; T ENST00000378623 Transcript synonymous_variant 417/8076 174/5718 58/1905 G ggG/ggA 1 -1 LRP4 HGNC HGNC:6696 protein_coding YES CCDS31478.1 ENSP00000367888 O75096 UPI0000D625E9 NM_002334.3 2/38 PROSITE_profiles:PS50068,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF249,PROSITE_patterns:PS01209,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 46902808 46902808 C T 1 0 0 0 0 0 0 0 1 8854 610 22 3 3 LRP4 11 46902808 Silent SNP C C3N-02089_T 27260 46902808 88183814 591 27675 FNBP4 0 . GRCh38 11 47744046 47744046 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1363A>C p.Lys455Gln p.K455Q ENST00000263773 8/17 467 423 44 351 351 0 strelka-varscan-mutect FNBP4,missense_variant,p.Lys455Gln,ENST00000263773,NM_001318339.1,NM_015308.2;FNBP4,non_coding_transcript_exon_variant,,ENST00000534003,;FNBP4,non_coding_transcript_exon_variant,,ENST00000527894,;FNBP4,upstream_gene_variant,,ENST00000528388,;FNBP4,non_coding_transcript_exon_variant,,ENST00000544590,; G ENST00000263773 Transcript missense_variant 1376/3972 1363/3054 455/1017 K/Q Aaa/Caa 1 -1 FNBP4 HGNC HGNC:19752 protein_coding YES CCDS41644.1 ENSP00000263773 Q8N3X1 UPI0000DBEF37 NM_001318339.1,NM_015308.2 deleterious(0) 8/17 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF175 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 47744046 47744046 T G 1 0 0 0 0 1 0 0 0 5823 1850 64 5 5 FNBP4 11 47744046 Missense_Mutation SNP T C3N-02089_T 841238 47744046 87342576 592 27676 OR4C3 0 . GRCh38 11 48325601 48325601 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.661G>T p.Gly221Cys p.G221C ENST00000319856 1/1 210 160 50 158 156 2 strelka-varscan-mutect OR4C3,missense_variant,p.Gly221Cys,ENST00000319856,NM_001004702.1;OR4C3,missense_variant,p.Gly84Cys,ENST00000611380,; T ENST00000319856 Transcript missense_variant 682/1036 661/990 221/329 G/C Ggt/Tgt 1 1 OR4C3 HGNC HGNC:14697 protein_coding YES CCDS31489.1 ENSP00000321419 Q8NH37 A0A126GVR6 UPI0000061EA2 NM_001004702.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF162,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 48325601 48325601 G T 1 0 0 0 0 1 0 0 0 11126 1348 47 2 2 OR4C3 11 48325601 Missense_Mutation SNP G C3N-02089_T 581555 48325601 86761021 593 27677 OR4A47 0 . GRCh38 11 48488856 48488856 + Missense_Mutation SNP C C G rs767746683 C3N-02089_T C3N-02089_N C C c.64C>G p.Gln22Glu p.Q22E ENST00000446524 1/1 71 46 25 87 87 0 strelka-varscan-mutect OR4A47,missense_variant,p.Gln22Glu,ENST00000446524,NM_001005512.2;OR4R1P,upstream_gene_variant,,ENST00000529879,;OR4A48P,upstream_gene_variant,,ENST00000531359,; G ENST00000446524 Transcript missense_variant 140/1064 64/930 22/309 Q/E Cag/Gag rs767746683 1 1 OR4A47 HGNC HGNC:31266 protein_coding YES CCDS31490.1 ENSP00000412752 Q6IF82 UPI00001971E5 NM_001005512.2 deleterious_low_confidence(0.03) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF87,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs767746683 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 48488856 48488856 C G 1 0 0 0 0 1 0 0 0 11119 711 25 4 4 OR4A47 11 48488856 Missense_Mutation SNP C C3N-02089_T 163255 48488856 86597766 594 27678 TRIM64C 0 . GRCh38 11 49056378 49056378 + Missense_Mutation SNP C C A rs748374237 C3N-02089_T C3N-02089_N C C c.742G>T p.Val248Leu p.V248L ENST00000617704 4/6 132 97 35 186 186 0 strelka-varscan-mutect TRIM64C,missense_variant,p.Val248Leu,ENST00000617704,NM_001206631.1;TRIM64C,missense_variant,p.Val245Leu,ENST00000530230,; A ENST00000617704 Transcript missense_variant 742/1353 742/1353 248/450 V/L Gtg/Ttg rs748374237 1 -1 TRIM64C HGNC HGNC:37148 protein_coding YES CCDS73287.1 ENSP00000481815 A0A087WYH8 UPI00006C1130 NM_001206631.1 tolerated(1) 4/6 hmmpanther:PTHR24103:SF354,hmmpanther:PTHR24103 MODERATE 1 SNV 5 1 PASS rs748374237 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 49056378 49056378 C A 1 0 0 0 0 1 0 0 0 17033 492 17 2 2 TRIM64C 11 49056378 Missense_Mutation SNP C C3N-02089_T 567522 49056378 86030244 595 27679 OR8J3 0 . GRCh38 11 56137411 56137411 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.308G>T p.Gly103Val p.G103V ENST00000301529 1/1 187 137 50 230 230 0 strelka-varscan-mutect OR8J3,missense_variant,p.Gly103Val,ENST00000301529,NM_001004064.1;OR5BN1P,upstream_gene_variant,,ENST00000532955,; A ENST00000301529 Transcript missense_variant 308/948 308/948 103/315 G/V gGg/gTg 1 -1 OR8J3 HGNC HGNC:15312 protein_coding YES CCDS31520.1 ENSP00000301529 Q8NGG0 A0A126GVE3 UPI0000061E99 NM_001004064.1 tolerated(0.35) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452:SF249,hmmpanther:PTHR26452,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 56137411 56137411 C A 1 0 0 0 0 1 0 0 0 11310 623 22 2 2 OR8J3 11 56137411 Missense_Mutation SNP C C3N-02089_T 7081033 56137411 78949211 596 27680 OR4D11 0 . GRCh38 11 59503725 59503725 + Silent SNP C C A rs544299419 C3N-02089_T C3N-02089_N C C c.150C>A p.= p.T50T ENST00000313253 1/1 105 80 25 143 143 0 strelka-varscan-mutect OR4D11,synonymous_variant,p.=,ENST00000313253,NM_001004706.1; A ENST00000313253 Transcript synonymous_variant 150/936 150/936 50/311 T acC/acA rs544299419 1 1 OR4D11 HGNC HGNC:15174 protein_coding YES CCDS31563.1 ENSP00000320077 Q8NGI4 A0A126GVQ9 UPI0000046486 NM_001004706.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF200,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs544299419 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 59503725 59503725 C A 1 0 0 0 0 0 0 0 1 11132 668 24 2 2 OR4D11 11 59503725 Silent SNP C C3N-02089_T 3366314 59503725 75582897 597 27681 RAB3IL1 0 . GRCh38 11 61907405 61907405 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.426G>T p.Glu142Asp p.E142D ENST00000394836 4/10 297 222 75 256 256 0 strelka-varscan-mutect RAB3IL1,missense_variant,p.Glu142Asp,ENST00000394836,NM_013401.3;RAB3IL1,missense_variant,p.Glu189Asp,ENST00000301773,NM_001271686.1;RAB3IL1,missense_variant,p.Glu189Asp,ENST00000531922,;RAB3IL1,upstream_gene_variant,,ENST00000530888,; A ENST00000394836 Transcript missense_variant 584/2284 426/1149 142/382 E/D gaG/gaT 1 -1 RAB3IL1 HGNC HGNC:9780 protein_coding YES CCDS8014.1 ENSP00000378313 Q8TBN0 UPI000007260E NM_013401.3 deleterious(0) 4/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14430:SF1,hmmpanther:PTHR14430,Pfam_domain:PF06428,Superfamily_domains:0053574 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 61907405 61907405 C A 1 0 0 0 0 1 0 0 0 13096 680 24 2 2 RAB3IL1 11 61907405 Missense_Mutation SNP C C3N-02089_T 2403680 61907405 73179217 598 27682 AHNAK 0 . GRCh38 11 62521950 62521950 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.12467G>T p.Gly4156Val p.G4156V ENST00000378024 5/5 332 252 80 359 359 0 strelka-varscan-mutect AHNAK,missense_variant,p.Gly4156Val,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,upstream_gene_variant,,ENST00000525875,; A ENST00000378024 Transcript missense_variant 12742/18787 12467/17673 4156/5890 G/V gGc/gTc 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0.02) 5/5 hmmpanther:PTHR23348,hmmpanther:PTHR23348:SF41 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 62521950 62521950 C A 1 0 0 0 0 1 0 0 0 491 739 26 2 2 AHNAK 11 62521950 Missense_Mutation SNP C C3N-02089_T 614545 62521950 72564672 599 27683 SLC22A9 0 . GRCh38 11 63370137 63370137 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.81T>G p.Phe27Leu p.F27L ENST00000279178 1/10 152 132 20 151 151 0 strelka-varscan-mutect SLC22A9,missense_variant,p.Phe27Leu,ENST00000279178,NM_080866.2;SLC22A10,downstream_gene_variant,,ENST00000525620,;SLC22A9,missense_variant,p.Phe27Leu,ENST00000536333,; G ENST00000279178 Transcript missense_variant 330/2343 81/1662 27/553 F/L ttT/ttG 1 1 SLC22A9 HGNC HGNC:16261 protein_coding YES CCDS8043.1 ENSP00000279178 Q8IVM8 UPI00000745FF NM_080866.2 tolerated(0.66) 1/10 hmmpanther:PTHR24064,hmmpanther:PTHR24064:SF288,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 63370137 63370137 T G 1 0 0 0 0 1 0 0 0 14727 1809 63 5 5 SLC22A9 11 63370137 Missense_Mutation SNP T C3N-02089_T 848187 63370137 71716485 600 27684 SNX32 0 . GRCh38 11 65852704 65852704 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.987C>A p.= p.T329T ENST00000308342 11/13 200 153 47 188 188 0 strelka-varscan-mutect SNX32,synonymous_variant,p.=,ENST00000308342,NM_152760.2;CFL1,downstream_gene_variant,,ENST00000525451,;CFL1,downstream_gene_variant,,ENST00000308162,NM_005507.2;CFL1,downstream_gene_variant,,ENST00000531407,;CFL1,downstream_gene_variant,,ENST00000527344,;MUS81,upstream_gene_variant,,ENST00000529857,;CFL1,downstream_gene_variant,,ENST00000524553,;CFL1,downstream_gene_variant,,ENST00000532134,;CFL1,downstream_gene_variant,,ENST00000534769,;CFL1,downstream_gene_variant,,ENST00000534784,;CFL1,downstream_gene_variant,,ENST00000530413,;CFL1,downstream_gene_variant,,ENST00000531413,;CFL1,downstream_gene_variant,,ENST00000526975,;CFL1,intron_variant,,ENST00000527752,;SNX32,downstream_gene_variant,,ENST00000531795,;SNX32,non_coding_transcript_exon_variant,,ENST00000530101,;CFL1,downstream_gene_variant,,ENST00000530945,;SNX32,downstream_gene_variant,,ENST00000526972,;SNX32,downstream_gene_variant,,ENST00000531503,;SNX32,downstream_gene_variant,,ENST00000533298,;SNX32,downstream_gene_variant,,ENST00000524729,;SNX32,downstream_gene_variant,,ENST00000533236,;SNX32,downstream_gene_variant,,ENST00000534387,; A ENST00000308342 Transcript synonymous_variant 1412/2003 987/1212 329/403 T acC/acA 1 1 SNX32 HGNC HGNC:26423 protein_coding YES CCDS8113.2 ENSP00000310620 Q86XE0 UPI000000DAEA NM_152760.2 11/13 hmmpanther:PTHR10555:SF137,hmmpanther:PTHR10555,Pfam_domain:PF09325,PIRSF_domain:PIRSF036924 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 65852704 65852704 C A 1 0 0 0 0 0 0 0 1 15223 581 21 2 2 SNX32 11 65852704 Silent SNP C C3N-02089_T 2482567 65852704 69233918 601 27685 TSGA10IP 0 . GRCh38 11 65959911 65959911 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1642C>A p.Pro548Thr p.P548T ENST00000532620 8/8 173 148 25 140 140 0 strelka-varscan-mutect TSGA10IP,missense_variant,p.Pro548Thr,ENST00000532620,NM_152762.2;SART1,upstream_gene_variant,,ENST00000312397,NM_005146.4;SART1,upstream_gene_variant,,ENST00000528573,;TSGA10IP,3_prime_UTR_variant,,ENST00000608857,;TSGA10IP,3_prime_UTR_variant,,ENST00000534740,;SART1,upstream_gene_variant,,ENST00000529532,;SART1,upstream_gene_variant,,ENST00000532333,;SART1,upstream_gene_variant,,ENST00000530251,; A ENST00000532620 Transcript missense_variant 1873/1925 1642/1671 548/556 P/T Ccc/Acc 1 1 TSGA10IP HGNC HGNC:26555 protein_coding YES CCDS66138.1 ENSP00000484252 Q3SY00 UPI0000EE47ED NM_152762.2 deleterious(0) 8/8 hmmpanther:PTHR21501,hmmpanther:PTHR21501:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 65959911 65959911 C A 1 0 0 0 0 1 0 0 0 17124 623 22 2 2 TSGA10IP 11 65959911 Missense_Mutation SNP C C3N-02089_T 107207 65959911 69126711 602 27686 ACY3 0 . GRCh38 11 67646875 67646875 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.169G>T p.Ala57Ser p.A57S ENST00000255082 3/8 189 153 36 132 132 0 strelka-varscan-mutect ACY3,missense_variant,p.Ala57Ser,ENST00000255082,NM_080658.1;ACY3,5_prime_UTR_variant,,ENST00000529256,;AP003385.2,downstream_gene_variant,,ENST00000426387,; A ENST00000255082 Transcript missense_variant 340/1300 169/960 57/319 A/S Gcc/Tcc COSM4659239 1 -1 ACY3 HGNC HGNC:24104 protein_coding YES CCDS8175.1 ENSP00000255082 Q96HD9 A0A024R5L2 UPI0000073C5C NM_080658.1 deleterious(0) 3/8 HAMAP:MF_00704,hmmpanther:PTHR15162:SF5,hmmpanther:PTHR15162,Pfam_domain:PF04952,PIRSF_domain:PIRSF018001,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 67646875 67646875 C A 1 0 0 0 0 1 0 0 0 271 797 28 2 2 ACY3 11 67646875 Missense_Mutation SNP C C3N-02089_T 1686964 67646875 67439747 603 27687 CPT1A 0 . GRCh38 11 68786036 68786036 + Splice_Site SNP C C A novel C3N-02089_T C3N-02089_N C C c.224-1G>T p.X75_splice ENST00000538994 221 208 13 170 169 1 strelka-varscan CPT1A,splice_acceptor_variant,,ENST00000538994,;CPT1A,intron_variant,,ENST00000265641,NM_001876.3;CPT1A,intron_variant,,ENST00000376618,NM_001031847.2;CPT1A,intron_variant,,ENST00000540367,;CPT1A,intron_variant,,ENST00000539743,; A ENST00000538994 Transcript splice_acceptor_variant -/617 224/237 75/78 1 -1 CPT1A HGNC HGNC:2328 protein_coding ENSP00000454332 H3BMD2 UPI00024674E8 4/4 HIGH SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 68786036 68786036 C A 1 0 0 0 0 0 0 1 0 3628 927 32 2 2 CPT1A 11 68786036 Splice_Site SNP C C3N-02089_T 1139161 68786036 66300586 604 27688 CPT1A 0 . GRCh38 11 68815465 68815465 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.10G>T p.Ala4Ser p.A4S ENST00000265641 2/19 388 331 57 311 310 1 strelka-varscan-mutect CPT1A,missense_variant,p.Ala4Ser,ENST00000265641,NM_001876.3;CPT1A,missense_variant,p.Ala4Ser,ENST00000376618,NM_001031847.2;CPT1A,missense_variant,p.Ala4Ser,ENST00000540367,;CPT1A,missense_variant,p.Ala4Ser,ENST00000539743,;CPT1A,missense_variant,p.Ala4Ser,ENST00000561996,;CPT1A,missense_variant,p.Ala4Ser,ENST00000565318,;CPT1A,missense_variant,p.Ala4Ser,ENST00000569129,; A ENST00000265641 Transcript missense_variant 165/5232 10/2322 4/773 A/S Gct/Tct 1 -1 CPT1A HGNC HGNC:2328 protein_coding YES CCDS8185.1 ENSP00000265641 P50416 A0A024R5F4 UPI000013D658 NM_001876.3 deleterious(0) 2/19 Pfam_domain:PF16484 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 68815465 68815465 C A 1 0 0 0 0 1 0 0 0 3628 797 28 2 2 CPT1A 11 68815465 Missense_Mutation SNP C C3N-02089_T 29429 68815465 66271157 605 27689 P4HA3 0 . GRCh38 11 74267161 74267161 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1715A>T p.Glu572Val p.E572V ENST00000427714 13/13 516 461 55 364 363 1 strelka-varscan-mutect P4HA3,missense_variant,p.Glu572Val,ENST00000427714,NM_001288748.1;P4HA3,3_prime_UTR_variant,,ENST00000331597,NM_182904.4;P4HA3,3_prime_UTR_variant,,ENST00000525968,;P4HA3,intron_variant,,ENST00000524388,;P4HA3,intron_variant,,ENST00000532689,; A ENST00000427714 Transcript missense_variant 1744/2248 1715/1815 572/604 E/V gAg/gTg 1 -1 P4HA3 HGNC HGNC:30135 protein_coding YES CCDS73347.1 ENSP00000401749 Q7Z4N8 UPI00017A7E1B NM_001288748.1 deleterious_low_confidence(0) 13/13 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 74267161 74267161 T A 1 0 0 0 0 1 0 0 0 11435 1551 54 4 4 P4HA3 11 74267161 Missense_Mutation SNP T C3N-02089_T 5451696 74267161 60819461 606 27690 SLCO2B1 0 . GRCh38 11 75165804 75165804 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.303G>T p.Leu101Phe p.L101F ENST00000289575 4/14 141 104 37 125 125 0 strelka-varscan-mutect SLCO2B1,missense_variant,p.Leu101Phe,ENST00000289575,NM_007256.4;SLCO2B1,missense_variant,p.Leu79Phe,ENST00000428359,NM_001145211.2;SLCO2B1,missense_variant,p.Leu79Phe,ENST00000531713,;SLCO2B1,missense_variant,p.Leu79Phe,ENST00000534186,;SLCO2B1,missense_variant,p.Leu79Phe,ENST00000527180,;SLCO2B1,5_prime_UTR_variant,,ENST00000454962,;SLCO2B1,5_prime_UTR_variant,,ENST00000532236,;SLCO2B1,intron_variant,,ENST00000525650,NM_001145212.2;SLCO2B1,upstream_gene_variant,,ENST00000526839,;SLCO2B1,downstream_gene_variant,,ENST00000534004,;SLCO2B1,downstream_gene_variant,,ENST00000525845,;SLCO2B1,downstream_gene_variant,,ENST00000530556,;SLCO2B1,intron_variant,,ENST00000526660,;SLCO2B1,intron_variant,,ENST00000531756,;SLCO2B1,downstream_gene_variant,,ENST00000531457,; T ENST00000289575 Transcript missense_variant 698/4494 303/2130 101/709 L/F ttG/ttT 1 1 SLCO2B1 HGNC HGNC:10962 protein_coding YES CCDS8235.1 ENSP00000289575 A0A024R5I4 UPI000000D99A NM_007256.4 deleterious(0.02) 4/14 Gene3D:1.20.1250.20,Pfam_domain:PF03137,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF87,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00805,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 75165804 75165804 G T 1 0 0 0 0 1 0 0 0 15014 1281 45 2 2 SLCO2B1 11 75165804 Missense_Mutation SNP G C3N-02089_T 898643 75165804 59920818 607 27691 MOGAT2 0 . GRCh38 11 75731173 75731173 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.892G>A p.Glu298Lys p.E298K ENST00000198801 6/6 214 187 27 165 165 0 strelka-varscan-mutect MOGAT2,missense_variant,p.Glu216Lys,ENST00000526712,;MOGAT2,missense_variant,p.Glu298Lys,ENST00000198801,NM_025098.2;MOGAT2,non_coding_transcript_exon_variant,,ENST00000624180,;MOGAT2,3_prime_UTR_variant,,ENST00000525093,; A ENST00000198801 Transcript missense_variant 962/1404 892/1005 298/334 E/K Gag/Aag COSM1298624 1 1 MOGAT2 HGNC HGNC:23248 protein_coding YES CCDS8240.1 ENSP00000198801 Q3SYC2 UPI000000D839 NM_025098.2 tolerated(0.33) 6/6 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF5 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 75731173 75731173 G A 1 0 0 0 0 1 0 0 0 9658 1175 41 3 3 MOGAT2 11 75731173 Missense_Mutation SNP G C3N-02089_T 565369 75731173 59355449 608 27692 MOGAT2 0 . GRCh38 11 75731184 75731184 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.903G>T p.= p.V301V ENST00000198801 6/6 242 208 34 189 189 0 strelka-varscan-mutect MOGAT2,synonymous_variant,p.=,ENST00000526712,;MOGAT2,synonymous_variant,p.=,ENST00000198801,NM_025098.2;MOGAT2,non_coding_transcript_exon_variant,,ENST00000624180,;MOGAT2,3_prime_UTR_variant,,ENST00000525093,; T ENST00000198801 Transcript synonymous_variant 973/1404 903/1005 301/334 V gtG/gtT 1 1 MOGAT2 HGNC HGNC:23248 protein_coding YES CCDS8240.1 ENSP00000198801 Q3SYC2 UPI000000D839 NM_025098.2 6/6 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF5 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 75731184 75731184 G T 1 0 0 0 0 0 0 0 1 9658 1277 45 2 2 MOGAT2 11 75731184 Silent SNP G C3N-02089_T 11 75731184 59355438 609 27693 LRRC32 0 . GRCh38 11 76660310 76660310 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.1283C>A p.Pro428Gln p.P428Q ENST00000407242 3/3 69 56 13 58 58 0 strelka-varscan-mutect LRRC32,missense_variant,p.Pro428Gln,ENST00000407242,NM_005512.2;LRRC32,missense_variant,p.Pro428Gln,ENST00000260061,NM_001128922.1;LRRC32,missense_variant,p.Pro428Gln,ENST00000404995,;LRRC32,downstream_gene_variant,,ENST00000421973,;RP11-672A2.4,upstream_gene_variant,,ENST00000531511,;AP001189.4,intron_variant,,ENST00000447519,;LRRC32,intron_variant,,ENST00000464145,; T ENST00000407242 Transcript missense_variant 1526/4311 1283/1989 428/662 P/Q cCa/cAa COSM1322154 1 -1 LRRC32 HGNC HGNC:4161 protein_coding YES CCDS8245.1 ENSP00000384126 Q14392 A0A024R5J7 UPI000012B0DF NM_005512.2 tolerated(0.37) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF337,SMART_domains:SM00368,Superfamily_domains:SSF52058 1 MODERATE 1 SNV 1 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 90 76660310 76660310 G T 1 0 0 0 0 1 0 0 0 8882 1348 47 2 2 LRRC32 11 76660310 Missense_Mutation SNP G C3N-02089_T 929126 76660310 58426312 610 27694 B3GNT6 0 . GRCh38 11 77039651 77039651 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.100C>T p.Pro34Ser p.P34S ENST00000622824 2/2 187 151 36 130 130 0 strelka-varscan-mutect B3GNT6,missense_variant,p.Pro34Ser,ENST00000622824,NM_138706.4;B3GNT6,missense_variant,p.Pro34Ser,ENST00000528622,; T ENST00000622824 Transcript missense_variant 181/2503 100/1155 34/384 P/S Cca/Tca 1 1 B3GNT6 HGNC HGNC:24141 protein_coding YES CCDS53681.1 ENSP00000484640 Q6ZMB0 A8K9Q8 UPI000006D55A NM_138706.4 tolerated(0.97) 2/2 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF24,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 77039651 77039651 C T 1 0 0 0 0 1 0 0 0 1417 739 26 3 3 B3GNT6 11 77039651 Missense_Mutation SNP C C3N-02089_T 379341 77039651 58046971 611 27695 MYO7A 0 . GRCh38 11 77192180 77192180 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.4054A>G p.Thr1352Ala p.T1352A ENST00000409709 31/49 450 386 64 367 367 0 strelka-varscan-mutect MYO7A,missense_variant,p.Thr1352Ala,ENST00000409709,NM_000260.3;MYO7A,missense_variant,p.Thr1352Ala,ENST00000458637,NM_001127180.1;MYO7A,missense_variant,p.Thr1341Ala,ENST00000409619,;MYO7A,missense_variant,p.Thr533Ala,ENST00000458169,;MYO7A,non_coding_transcript_exon_variant,,ENST00000481328,;MYO7A,downstream_gene_variant,,ENST00000467137,; G ENST00000409709 Transcript missense_variant 4326/7462 4054/6648 1352/2215 T/A Acg/Gcg 1 1 MYO7A HGNC HGNC:7606 protein_coding YES CCDS53683.1 ENSP00000386331 Q13402 UPI00001FAFE6 NM_000260.3 tolerated(0.23) 31/49 PROSITE_profiles:PS50057,Gene3D:1.20.80.10,SMART_domains:SM00295,Superfamily_domains:SSF47031,Superfamily_domains:SSF54236 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 77192180 77192180 A G 1 0 0 0 0 1 0 0 0 10083 159 6 5 5 MYO7A 11 77192180 Missense_Mutation SNP A C3N-02089_T 152529 77192180 57894442 612 27696 DLG2 0 . GRCh38 11 83930337 83930337 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1487A>G p.Glu496Gly p.E496G ENST00000376104 15/28 142 125 17 136 136 0 strelka-varscan-mutect DLG2,missense_variant,p.Glu391Gly,ENST00000398309,NM_001364.3;DLG2,missense_variant,p.Glu430Gly,ENST00000280241,NM_001206769.1;DLG2,missense_variant,p.Glu496Gly,ENST00000376104,NM_001142699.1;DLG2,missense_variant,p.Glu358Gly,ENST00000531015,;DLG2,missense_variant,p.Glu391Gly,ENST00000532653,NM_001300983.1;DLG2,missense_variant,p.Glu391Gly,ENST00000524982,;DLG2,missense_variant,p.Glu330Gly,ENST00000330014,;DLG2,missense_variant,p.Glu430Gly,ENST00000398301,;DLG2,intron_variant,,ENST00000418306,NM_001142700.1;DLG2,non_coding_transcript_exon_variant,,ENST00000529111,; C ENST00000376104 Transcript missense_variant 1799/5139 1487/2928 496/975 E/G gAg/gGg 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 tolerated(0.1) 15/28 PIRSF_domain:PIRSF001741 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 83930337 83930337 T C 1 0 0 0 0 1 0 0 0 4362 1551 54 5 5 DLG2 11 83930337 Missense_Mutation SNP T C3N-02089_T 6738157 83930337 51156285 613 27697 DLG2 0 . GRCh38 11 83980639 83980639 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.923T>A p.Leu308Ter p.L308* ENST00000376104 12/28 91 68 23 64 64 0 strelka-varscan-mutect DLG2,stop_gained,p.Leu203Ter,ENST00000398309,NM_001364.3;DLG2,stop_gained,p.Leu242Ter,ENST00000280241,NM_001206769.1;DLG2,stop_gained,p.Leu308Ter,ENST00000376104,NM_001142699.1;DLG2,stop_gained,p.Leu152Ter,ENST00000418306,NM_001142700.1;DLG2,stop_gained,p.Leu170Ter,ENST00000531015,;DLG2,stop_gained,p.Leu203Ter,ENST00000532653,NM_001300983.1;DLG2,stop_gained,p.Leu203Ter,ENST00000524982,;DLG2,stop_gained,p.Leu142Ter,ENST00000330014,;DLG2,stop_gained,p.Leu242Ter,ENST00000398301,;DLG2,stop_gained,p.Leu120Ter,ENST00000398299,;DLG2,non_coding_transcript_exon_variant,,ENST00000524941,;DLG2,non_coding_transcript_exon_variant,,ENST00000529111,; T ENST00000376104 Transcript stop_gained 1235/5139 923/2928 308/975 L/* tTa/tAa 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 12/28 PROSITE_profiles:PS50106,hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119,PIRSF_domain:PIRSF001741,Gene3D:2.30.42.10,Pfam_domain:PF00595,SMART_domains:SM00228,Superfamily_domains:SSF50156 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 83980639 83980639 A T 1 0 0 0 0 0 1 0 0 4362 376 13 4 4 DLG2 11 83980639 Nonsense_Mutation SNP A C3N-02089_T 50302 83980639 51105983 614 27698 TMEM135 0 . GRCh38 11 87091376 87091376 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.377C>A p.Thr126Lys p.T126K ENST00000305494 4/15 269 227 42 303 303 0 strelka-varscan-mutect TMEM135,missense_variant,p.Thr126Lys,ENST00000340353,NM_001168724.1;TMEM135,missense_variant,p.Thr126Lys,ENST00000305494,NM_022918.3;TMEM135,missense_variant,p.Thr126Lys,ENST00000525018,;TMEM135,missense_variant,p.Thr95Lys,ENST00000526733,;TMEM135,intron_variant,,ENST00000532959,;TMEM135,non_coding_transcript_exon_variant,,ENST00000529023,;TMEM135,non_coding_transcript_exon_variant,,ENST00000531800,;RP11-648O15.1,downstream_gene_variant,,ENST00000527404,; A ENST00000305494 Transcript missense_variant 416/2433 377/1377 126/458 T/K aCa/aAa 1 1 TMEM135 HGNC HGNC:26167 protein_coding YES CCDS8280.1 ENSP00000306344 Q86UB9 UPI00001FB0C7 NM_022918.3 deleterious(0.03) 4/15 hmmpanther:PTHR12459,hmmpanther:PTHR12459:SF3,Pfam_domain:PF15982 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 87091376 87091376 C A 1 0 0 0 0 1 0 0 0 16496 478 17 2 2 TMEM135 11 87091376 Missense_Mutation SNP C C3N-02089_T 3110737 87091376 47995246 615 27699 GRM5 0 . GRCh38 11 88567838 88567838 + Silent SNP C C T C3N-02089_T C3N-02089_N C C c.1845G>A p.= p.R615R ENST00000305447 7/9 323 272 51 233 232 1 strelka-varscan-mutect GRM5,synonymous_variant,p.=,ENST00000455756,NM_000842.4;GRM5,synonymous_variant,p.=,ENST00000305447,NM_001143831.2;GRM5,synonymous_variant,p.=,ENST00000305432,; T ENST00000305447 Transcript synonymous_variant 1995/4571 1845/3639 615/1212 R agG/agA COSM5613467,COSM5613468 1 -1 GRM5 HGNC HGNC:4597 protein_coding YES CCDS44694.1 ENSP00000306138 P41594 UPI000012F081 NM_001143831.2 7/9 Pfam_domain:PF00003,Prints_domain:PR00248,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF30 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 88567838 88567838 C T 1 0 0 0 0 0 0 0 1 6682 622 22 3 3 GRM5 11 88567838 Silent SNP C C3N-02089_T 1476462 88567838 46518784 616 27700 CEP295 0 . GRCh38 11 93697551 93697551 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.2639A>G p.Glu880Gly p.E880G ENST00000325212 15/30 170 148 22 163 163 0 strelka-varscan-mutect CEP295,missense_variant,p.Glu880Gly,ENST00000325212,NM_033395.1;CEP295,intron_variant,,ENST00000531700,;CEP295,upstream_gene_variant,,ENST00000530425,;CEP295,downstream_gene_variant,,ENST00000531877,;CEP295,downstream_gene_variant,,ENST00000531622,; G ENST00000325212 Transcript missense_variant 2801/8057 2639/7806 880/2601 E/G gAa/gGa 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 tolerated(0.11) 15/30 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF25 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 93697551 93697551 A G 1 0 0 0 0 1 0 0 0 2970 246 9 5 5 CEP295 11 93697551 Missense_Mutation SNP A C3N-02089_T 5129713 93697551 41389071 617 27701 HEPHL1 0 . GRCh38 11 94073077 94073077 + Missense_Mutation SNP T T A rs745921937 C3N-02089_T C3N-02089_N T T c.1285T>A p.Trp429Arg p.W429R ENST00000315765 7/20 208 165 43 175 175 0 strelka-varscan-mutect HEPHL1,missense_variant,p.Trp429Arg,ENST00000315765,NM_001098672.1; A ENST00000315765 Transcript missense_variant 1293/5345 1285/3480 429/1159 W/R Tgg/Agg rs745921937 1 1 HEPHL1 HGNC HGNC:30477 protein_coding YES CCDS44710.1 ENSP00000313699 Q6MZM0 UPI0000237563 NM_001098672.1 tolerated(0.36) 7/20 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF655,Gene3D:2.60.40.420,Superfamily_domains:SSF49503 MODERATE 1 SNV 5 1 PASS rs745921937 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 94073077 94073077 T A 1 0 0 0 0 1 0 0 0 6939 1580 55 4 4 HEPHL1 11 94073077 Missense_Mutation SNP T C3N-02089_T 375526 94073077 41013545 618 27702 C11orf88 0 . GRCh38 11 111514914 111514914 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.130G>T p.Ala44Ser p.A44S ENST00000332814 1/7 516 403 113 411 410 1 strelka-varscan-mutect C11orf88,missense_variant,p.Ala44Ser,ENST00000529167,;C11orf88,missense_variant,p.Ala44Ser,ENST00000332814,NM_207430.2;C11orf88,missense_variant,p.Ala44Ser,ENST00000375618,NM_001100388.1;BTG4,upstream_gene_variant,,ENST00000525791,;BTG4,upstream_gene_variant,,ENST00000356018,NM_017589.3;BTG4,upstream_gene_variant,,ENST00000456861,;MIR34B,downstream_gene_variant,,ENST00000385076,;MIR34C,downstream_gene_variant,,ENST00000384831,;RP11-794P6.6,non_coding_transcript_exon_variant,,ENST00000530283,;C11orf88,upstream_gene_variant,,ENST00000529661,; T ENST00000332814 Transcript missense_variant 130/795 130/591 44/196 A/S Gcg/Tcg 1 1 C11orf88 HGNC HGNC:25061 protein_coding YES CCDS41712.1 ENSP00000333845 Q6PI97 UPI00001D7746 NM_207430.2 deleterious(0) 1/7 hmmpanther:PTHR16213,hmmpanther:PTHR16213:SF61 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 111514914 111514914 G T 1 0 0 0 0 1 0 0 0 1800 1203 42 2 2 C11orf88 11 111514914 Missense_Mutation SNP G C3N-02089_T 17441837 111514914 23571708 619 27703 HTR3A 0 . GRCh38 11 113986541 113986541 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.747C>A p.= p.L249L ENST00000355556 7/8 286 220 66 251 251 0 strelka-varscan-mutect HTR3A,synonymous_variant,p.=,ENST00000504030,;HTR3A,synonymous_variant,p.=,ENST00000355556,NM_213621.3;HTR3A,synonymous_variant,p.=,ENST00000375498,NM_000869.5;HTR3A,synonymous_variant,p.=,ENST00000506841,;HTR3A,synonymous_variant,p.=,ENST00000299961,NM_001161772.2;HTR3A,missense_variant,p.Leu190Ile,ENST00000510849,;HTR3A,non_coding_transcript_exon_variant,,ENST00000502622,; A ENST00000355556 Transcript synonymous_variant 980/2331 747/1551 249/516 L ctC/ctA 1 1 HTR3A HGNC HGNC:5297 protein_coding YES CCDS8366.2 ENSP00000347754 P46098 UPI000013F7F1 NM_213621.3 7/8 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF52,Gene3D:1.20.120.370,TIGRFAM_domain:TIGR00860,Superfamily_domains:SSF90112,Prints_domain:PR00252 LOW 1 SNV 2 1 PASS rs1178120840 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 113986541 113986541 C A 1 0 0 0 0 0 0 0 1 7340 900 32 2 2 HTR3A 11 113986541 Silent SNP C C3N-02089_T 2471627 113986541 21100081 620 27704 DSCAML1 0 . GRCh38 11 117437396 117437396 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.4626C>A p.Ser1542Arg p.S1542R ENST00000321322 26/33 145 98 47 84 84 0 strelka-varscan-mutect DSCAML1,missense_variant,p.Ser1542Arg,ENST00000321322,NM_020693.3;DSCAML1,missense_variant,p.Ser1272Arg,ENST00000527706,; T ENST00000321322 Transcript missense_variant 4628/6899 4626/6342 1542/2113 S/R agC/agA 1 -1 DSCAML1 HGNC HGNC:14656 protein_coding YES CCDS8384.1 ENSP00000315465 Q8TD84 UPI00000726E2 NM_020693.3 deleterious(0.01) 26/33 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF171,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 117437396 117437396 G T 1 0 0 0 0 1 0 0 0 4590 1310 46 2 2 DSCAML1 11 117437396 Missense_Mutation SNP G C3N-02089_T 3450855 117437396 17649226 621 27705 FXYD2 0 . GRCh38 11 117822708 117822708 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.35C>A p.Pro12His p.P12H ENST00000292079 2/6 372 297 75 283 281 2 strelka-varscan-mutect FXYD2,missense_variant,p.Pro10His,ENST00000528014,;FXYD6-FXYD2,missense_variant,p.Pro90His,ENST00000614497,NM_001204268.1;FXYD2,missense_variant,p.Pro12His,ENST00000292079,NM_001680.4;FXYD2,missense_variant,p.Pro10His,ENST00000532119,;FXYD2,missense_variant,p.Pro10His,ENST00000260287,NM_021603.3;FXYD6-FXYD2,synonymous_variant,p.=,ENST00000532984,NM_001243598.2;RP11-728F11.3,downstream_gene_variant,,ENST00000531850,;FXYD2,upstream_gene_variant,,ENST00000514385,;FXYD2,non_coding_transcript_exon_variant,,ENST00000317594,;FXYD2,non_coding_transcript_exon_variant,,ENST00000534383,;FXYD2,non_coding_transcript_exon_variant,,ENST00000533281,; T ENST00000292079 Transcript missense_variant 101/571 35/201 12/66 P/H cCc/cAc 1 -1 FXYD2 HGNC HGNC:4026 protein_coding YES CCDS8386.1 ENSP00000292079 P54710 UPI00001262A8 NM_001680.4 deleterious(0) 2/6 Gene3D:1.20.5.780,hmmpanther:PTHR14132,hmmpanther:PTHR14132:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 117822708 117822708 G T 1 0 0 0 0 1 0 0 0 5989 1232 43 2 2 FXYD2 11 117822708 Missense_Mutation SNP G C3N-02089_T 385312 117822708 17263914 622 27706 FOXR1 0 . GRCh38 11 118978839 118978839 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.119C>A p.Pro40His p.P40H ENST00000317011 2/6 322 275 47 275 275 0 strelka-varscan-mutect FOXR1,missense_variant,p.Pro40His,ENST00000317011,NM_181721.2;FOXR1,missense_variant,p.Pro21His,ENST00000533282,;FOXR1,missense_variant,p.Pro40His,ENST00000531539,; A ENST00000317011 Transcript missense_variant 344/1159 119/879 40/292 P/H cCc/cAc COSM466425 1 1 FOXR1 HGNC HGNC:29980 protein_coding YES CCDS31688.1 ENSP00000314806 Q6PIV2 UPI0000192103 NM_181721.2 deleterious(0.01) 2/6 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF152,Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 118978839 118978839 C A 1 0 0 0 0 1 0 0 0 5896 623 22 2 2 FOXR1 11 118978839 Missense_Mutation SNP C C3N-02089_T 1156131 118978839 16107783 623 27707 GRIK4 0 . GRCh38 11 120956872 120956872 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1793G>T p.Trp598Leu p.W598L ENST00000527524 16/21 153 141 12 107 107 0 strelka-varscan-mutect GRIK4,missense_variant,p.Trp598Leu,ENST00000527524,NM_014619.4;GRIK4,missense_variant,p.Trp598Leu,ENST00000438375,NM_001282473.2,NM_001282470.2;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,; T ENST00000527524 Transcript missense_variant 2080/5802 1793/2871 598/956 W/L tGg/tTg 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 deleterious(0) 16/21 Transmembrane_helices:TMhelix,hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 120956872 120956872 G T 1 0 0 0 0 1 0 0 0 6658 1357 47 2 2 GRIK4 11 120956872 Missense_Mutation SNP G C3N-02089_T 1978033 120956872 14129750 624 27708 GRIK4 0 . GRCh38 11 120960972 120960972 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1938G>T p.= p.V646V ENST00000527524 17/21 295 232 63 184 183 1 strelka-varscan-mutect GRIK4,synonymous_variant,p.=,ENST00000527524,NM_014619.4;GRIK4,synonymous_variant,p.=,ENST00000438375,NM_001282473.2,NM_001282470.2;GRIK4,non_coding_transcript_exon_variant,,ENST00000533291,; T ENST00000527524 Transcript synonymous_variant 2225/5802 1938/2871 646/956 V gtG/gtT 1 1 GRIK4 HGNC HGNC:4582 protein_coding YES CCDS8433.1 ENSP00000435648 Q16099 UPI000013DB8D NM_014619.4 17/21 Transmembrane_helices:TMhelix,hmmpanther:PTHR18966:SF171,hmmpanther:PTHR18966,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Prints_domain:PR00177 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 120960972 120960972 G T 1 0 0 0 0 0 0 0 1 6658 1306 46 2 2 GRIK4 11 120960972 Silent SNP G C3N-02089_T 4100 120960972 14125650 625 27709 CRTAM 0 . GRCh38 11 122851756 122851756 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.257C>T p.Pro86Leu p.P86L ENST00000227348 3/10 359 290 69 300 300 0 strelka-varscan-mutect CRTAM,missense_variant,p.Pro86Leu,ENST00000227348,NM_019604.3; T ENST00000227348 Transcript missense_variant 304/2469 257/1182 86/393 P/L cCt/cTt 1 1 CRTAM HGNC HGNC:24313 protein_coding YES CCDS8437.1 ENSP00000227348 O95727 UPI000013C8B4 NM_019604.3 tolerated(0.24) 3/10 PROSITE_profiles:PS50835,hmmpanther:PTHR23277:SF48,hmmpanther:PTHR23277,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 122851756 122851756 C T 1 0 0 0 0 1 0 0 0 3699 681 24 3 3 CRTAM 11 122851756 Missense_Mutation SNP C C3N-02089_T 1890784 122851756 12234866 626 27710 GRAMD1B 0 . GRCh38 11 123613635 123613635 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1796G>T p.Gly599Val p.G599V ENST00000456860 16/21 145 108 37 106 105 1 strelka-varscan-mutect GRAMD1B,missense_variant,p.Gly592Val,ENST00000529750,NM_020716.2;GRAMD1B,missense_variant,p.Gly552Val,ENST00000529432,NM_001286564.1;GRAMD1B,missense_variant,p.Gly552Val,ENST00000638157,;GRAMD1B,missense_variant,p.Gly735Val,ENST00000635736,;GRAMD1B,missense_variant,p.Gly599Val,ENST00000456860,NM_001286563.1;GRAMD1B,missense_variant,p.Gly621Val,ENST00000638086,;GRAMD1B,missense_variant,p.Gly592Val,ENST00000322282,;GRAMD1B,missense_variant,p.Gly283Val,ENST00000450171,;GRAMD1B,downstream_gene_variant,,ENST00000534764,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000525945,; T ENST00000456860 Transcript missense_variant 2309/2805 1796/2238 599/745 G/V gGc/gTc 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 tolerated(0.53) 16/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319 MODERATE 1 SNV 2 1 PASS rs1280558584 . 0 204 4 2 0 0 0 0 -20 0.9999941 1 1 1 0 T 3 4 90 123613635 123613635 G T 1 0 0 0 0 1 0 0 0 6627 1203 42 2 2 GRAMD1B 11 123613635 Missense_Mutation SNP G C3N-02089_T 761879 123613635 11472987 627 27711 OR10G4 0 . GRCh38 11 124016411 124016411 + Silent SNP G G T rs150326783 C3N-02089_T C3N-02089_N G G c.837G>T p.= p.T279T ENST00000320891 1/1 166 130 36 148 148 0 strelka-varscan-mutect OR10G4,synonymous_variant,p.=,ENST00000320891,NM_001004462.1; T ENST00000320891 Transcript synonymous_variant 837/936 837/936 279/311 T acG/acT rs150326783,COSM273042 1 1 OR10G4 HGNC HGNC:14809 protein_coding YES CCDS31702.1 ENSP00000325076 Q8NGN3 A0A126GWS5 UPI0000041BAD NM_001004462.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF6,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 0,1 LOW 1 SNV 0,1 1 PASS rs150326783 . 0 206 0 4 0 0 0 0 -20 0.9999602 1 1 1 0 T 2 4 90 124016411 124016411 G T 1 0 0 0 0 0 0 0 1 10977 1074 38 1 1 OR10G4 11 124016411 Silent SNP G C3N-02089_T 402776 124016411 11070211 628 27712 FEZ1 0 . GRCh38 11 125456045 125456045 + Missense_Mutation SNP G G C rs773586831 C3N-02089_T C3N-02089_N G G c.729C>G p.Ile243Met p.I243M ENST00000278919 6/10 77 59 18 41 41 0 strelka-varscan-mutect FEZ1,missense_variant,p.Ile243Met,ENST00000278919,NM_005103.4;FEZ1,missense_variant,p.Ile176Met,ENST00000577924,;FEZ1,non_coding_transcript_exon_variant,,ENST00000527350,;FEZ1,upstream_gene_variant,,ENST00000526507,;FEZ1,upstream_gene_variant,,ENST00000532778,;FEZ1,non_coding_transcript_exon_variant,,ENST00000392709,;FEZ1,non_coding_transcript_exon_variant,,ENST00000524427,;FEZ1,non_coding_transcript_exon_variant,,ENST00000533294,;FEZ1,upstream_gene_variant,,ENST00000530096,;FEZ1,downstream_gene_variant,,ENST00000534022,;FEZ1,upstream_gene_variant,,ENST00000528863,; C ENST00000278919 Transcript missense_variant 964/1748 729/1179 243/392 I/M atC/atG rs773586831 1 -1 FEZ1 HGNC HGNC:3659 protein_coding YES CCDS31716.1 ENSP00000278919 Q99689 UPI000012A6FE NM_005103.4 deleterious(0) 6/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12394:SF4,hmmpanther:PTHR12394,Pfam_domain:PF07763 MODERATE 1 SNV 1 1 PASS rs773586831 . 0 201 8 0 0 0 0 0 -20 0.9999992 1 1 1 0 C 3 2 90 125456045 125456045 G C 1 0 0 0 0 1 0 0 0 5686 1164 41 4 4 FEZ1 11 125456045 Missense_Mutation SNP G C3N-02089_T 1439634 125456045 9630577 629 27713 EI24 0 . GRCh38 11 125578234 125578234 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.418G>C p.Val140Leu p.V140L ENST00000278903 6/11 224 195 29 203 203 0 strelka-varscan-mutect EI24,missense_variant,p.Val140Leu,ENST00000278903,NM_004879.4;EI24,missense_variant,p.Val140Leu,ENST00000620753,;EI24,missense_variant,p.Val140Leu,ENST00000527235,;EI24,missense_variant,p.Val126Leu,ENST00000534546,NM_001290135.1;EI24,missense_variant,p.Val183Leu,ENST00000524723,;EI24,missense_variant,p.Val140Leu,ENST00000527842,;EI24,5_prime_UTR_variant,,ENST00000618552,;EI24,5_prime_UTR_variant,,ENST00000615917,;EI24,downstream_gene_variant,,ENST00000527131,;EI24,downstream_gene_variant,,ENST00000527520,;RNU6-1156P,downstream_gene_variant,,ENST00000410365,;STT3A-AS1,intron_variant,,ENST00000530526,;EI24,3_prime_UTR_variant,,ENST00000531636,;EI24,downstream_gene_variant,,ENST00000529765,;EI24,upstream_gene_variant,,ENST00000530540,; C ENST00000278903 Transcript missense_variant 846/2455 418/1023 140/340 V/L Gtg/Ctg 1 1 EI24 HGNC HGNC:13276 protein_coding YES CCDS73410.1 ENSP00000278903 O14681 A0A024R3I8 UPI000006CFDB NM_004879.4 tolerated(0.11) 6/11 hmmpanther:PTHR21389:SF0,hmmpanther:PTHR21389,Pfam_domain:PF07264 MODERATE 1 SNV 1 1 PASS rs1289704430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 125578234 125578234 G C 1 0 0 0 0 1 0 0 0 4821 1029 36 4 4 EI24 11 125578234 Missense_Mutation SNP G C3N-02089_T 122189 125578234 9508388 630 27714 NCAPD3 0 . GRCh38 11 134192730 134192730 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2004G>T p.Trp668Cys p.W668C ENST00000534548 16/35 279 218 61 190 189 1 strelka-varscan-mutect NCAPD3,missense_variant,p.Trp668Cys,ENST00000534548,NM_015261.2;NCAPD3,missense_variant,p.Trp668Cys,ENST00000534532,;NCAPD3,missense_variant,p.Trp668Cys,ENST00000525964,; A ENST00000534548 Transcript missense_variant 2069/5061 2004/4497 668/1498 W/C tgG/tgT 1 -1 NCAPD3 HGNC HGNC:28952 protein_coding YES CCDS31723.1 ENSP00000433681 P42695 UPI00001C1EFE NM_015261.2 deleterious(0) 16/35 hmmpanther:PTHR14222:SF1,hmmpanther:PTHR14222,Gene3D:1.25.10.10,PIRSF_domain:PIRSF036508,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 134192730 134192730 C A 1 0 0 0 0 1 0 0 0 10222 624 22 2 2 NCAPD3 11 134192730 Missense_Mutation SNP C C3N-02089_T 8614496 134192730 893892 631 27715 CACNA2D4 0 . GRCh38 12 1846616 1846616 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2320G>T p.Gly774Cys p.G774C ENST00000382722 24/38 202 147 55 134 134 0 strelka-varscan-mutect CACNA2D4,missense_variant,p.Gly774Cys,ENST00000382722,NM_172364.4;CACNA2D4,missense_variant,p.Gly749Cys,ENST00000587995,;CACNA2D4,missense_variant,p.Gly774Cys,ENST00000586184,;CACNA2D4,missense_variant,p.Gly710Cys,ENST00000588077,;CACNA2D4,missense_variant,p.Gly710Cys,ENST00000585708,;CACNA2D4,missense_variant,p.Gly635Cys,ENST00000585732,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000539048,;CACNA2D4,missense_variant,p.Gly55Cys,ENST00000537784,;CACNA2D4,3_prime_UTR_variant,,ENST00000444595,;CACNA2D4,non_coding_transcript_exon_variant,,ENST00000280663,; A ENST00000382722 Transcript missense_variant 2683/5475 2320/3414 774/1137 G/C Ggc/Tgc 1 -1 CACNA2D4 HGNC HGNC:20202 protein_coding YES CCDS44785.1 ENSP00000372169 Q7Z3S7 UPI0000E593D9 NM_172364.4 deleterious(0.01) 24/38 hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF26,Pfam_domain:PF08473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 1846616 1846616 C A 1 0 0 0 0 1 0 0 0 2239 623 22 2 2 CACNA2D4 12 1846616 Missense_Mutation SNP C C3N-02089_T 1846616 131428693 632 27716 CACNA1C 0 . GRCh38 12 2679764 2679764 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.5556G>T p.= p.V1852V ENST00000347598 44/49 120 104 16 85 85 0 strelka-varscan-mutect CACNA1C,synonymous_variant,p.=,ENST00000399655,NM_000719.6;CACNA1C,synonymous_variant,p.=,ENST00000399634,NM_001167625.1;CACNA1C,synonymous_variant,p.=,ENST00000406454,;CACNA1C,synonymous_variant,p.=,ENST00000399617,NM_001167624.2;CACNA1C,synonymous_variant,p.=,ENST00000399603,NM_001167623.1;CACNA1C,synonymous_variant,p.=,ENST00000335762,;CACNA1C,synonymous_variant,p.=,ENST00000347598,NM_001129827.1,NM_199460.3;CACNA1C,synonymous_variant,p.=,ENST00000344100,NM_001129829.1;CACNA1C,synonymous_variant,p.=,ENST00000327702,NM_001129830.2;CACNA1C,synonymous_variant,p.=,ENST00000399638,NM_001129831.1;CACNA1C,synonymous_variant,p.=,ENST00000399606,NM_001129832.1;CACNA1C,synonymous_variant,p.=,ENST00000399621,NM_001129834.1;CACNA1C,synonymous_variant,p.=,ENST00000399637,NM_001129835.1;CACNA1C,synonymous_variant,p.=,ENST00000402845,NM_001129833.1;CACNA1C,synonymous_variant,p.=,ENST00000399629,NM_001129836.1;CACNA1C,synonymous_variant,p.=,ENST00000399591,NM_001129846.1,NM_001129838.1;CACNA1C,synonymous_variant,p.=,ENST00000399595,NM_001129837.1;CACNA1C,synonymous_variant,p.=,ENST00000399649,NM_001129839.1;CACNA1C,synonymous_variant,p.=,ENST00000399597,NM_001129842.1,NM_001129844.1;CACNA1C,synonymous_variant,p.=,ENST00000399601,NM_001129843.1;CACNA1C,synonymous_variant,p.=,ENST00000399641,NM_001129840.1;CACNA1C,synonymous_variant,p.=,ENST00000399644,NM_001129841.1;CACNA1C,synonymous_variant,p.=,ENST00000616390,;CACNA1C-AS1,intron_variant,,ENST00000501371,;CACNA1C,downstream_gene_variant,,ENST00000465934,; T ENST00000347598 Transcript synonymous_variant 5556/6655 5556/6561 1852/2186 V gtG/gtT 1 1 CACNA1C HGNC HGNC:1390 protein_coding YES CCDS44788.1 ENSP00000266376 Q13936 UPI0000E593E5 NM_001129827.1,NM_199460.3 44/49 Pfam_domain:PF16885,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF188 LOW 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.999948 1 1 1 0 T 2 4 90 2679764 2679764 G T 1 0 0 0 0 0 0 0 1 2228 1306 46 2 2 CACNA1C 12 2679764 Silent SNP G C3N-02089_T 833148 2679764 130595545 633 27717 PARP11 0 . GRCh38 12 3828941 3828941 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.237T>A p.= p.T79T ENST00000228820 3/8 227 196 31 193 193 0 strelka-varscan-mutect PARP11,synonymous_variant,p.=,ENST00000228820,NM_020367.5;PARP11,intron_variant,,ENST00000427057,NM_001286522.1;PARP11,intron_variant,,ENST00000447133,NM_001286521.1;PARP11,downstream_gene_variant,,ENST00000450737,;PARP11,synonymous_variant,p.=,ENST00000416739,;PARP11,synonymous_variant,p.=,ENST00000453942,;PARP11,intron_variant,,ENST00000458162,; T ENST00000228820 Transcript synonymous_variant 382/4424 237/1017 79/338 T acT/acA 1 -1 PARP11 HGNC HGNC:1186 protein_coding YES CCDS8523.2 ENSP00000228820 Q9NR21 UPI0000374D35 NM_020367.5 3/8 PROSITE_profiles:PS50918,hmmpanther:PTHR14453:SF10,hmmpanther:PTHR14453,Pfam_domain:PF02825,Superfamily_domains:SSF117839 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 3828941 3828941 A T 1 0 0 0 0 0 0 0 1 11536 59 3 4 4 PARP11 12 3828941 Silent SNP A C3N-02089_T 1149177 3828941 129446368 634 27718 LPAR5 0 . GRCh38 12 6620531 6620531 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.718C>T p.Leu240Phe p.L240F ENST00000329858 2/2 241 153 88 136 136 0 strelka-varscan-mutect LPAR5,missense_variant,p.Leu240Phe,ENST00000329858,NM_020400.5;LPAR5,missense_variant,p.Leu240Phe,ENST00000431922,NM_001142961.1;LPAR5,non_coding_transcript_exon_variant,,ENST00000540335,; A ENST00000329858 Transcript missense_variant 1475/3171 718/1119 240/372 L/F Ctc/Ttc 1 -1 LPAR5 HGNC HGNC:13307 protein_coding YES CCDS8553.1 ENSP00000327875 Q9H1C0 Q5KU18 UPI0000036A45 NM_020400.5 deleterious(0.03) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24234,hmmpanther:PTHR24234:SF6,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 6620531 6620531 G A 1 0 0 0 0 1 0 0 0 8811 1000 35 3 3 LPAR5 12 6620531 Missense_Mutation SNP G C3N-02089_T 2791590 6620531 126654778 635 27719 GPR162 0 . GRCh38 12 6824726 6824726 + Silent SNP C C T rs781809274 C3N-02089_T C3N-02089_N C C c.828C>T p.= p.I276I ENST00000311268 2/5 445 384 61 280 280 0 strelka-varscan-mutect GPR162,synonymous_variant,p.=,ENST00000311268,NM_019858.1;GPR162,intron_variant,,ENST00000428545,NM_014449.1;GPR162,intron_variant,,ENST00000382315,;GPR162,intron_variant,,ENST00000545321,;CD4,downstream_gene_variant,,ENST00000011653,NM_000616.4;P3H3,upstream_gene_variant,,ENST00000290510,NM_014262.4;GPR162,downstream_gene_variant,,ENST00000541431,;GPR162,upstream_gene_variant,,ENST00000542330,;P3H3,upstream_gene_variant,,ENST00000544813,;GPR162,non_coding_transcript_exon_variant,,ENST00000535220,;P3H3,upstream_gene_variant,,ENST00000536140,;CD4,downstream_gene_variant,,ENST00000437800,; T ENST00000311268 Transcript synonymous_variant 1615/2768 828/1767 276/588 I atC/atT rs781809274 1 1 GPR162 HGNC HGNC:16693 protein_coding YES CCDS8563.1 ENSP00000311528 Q16538 A0A0I9QPQ8 UPI000005046E NM_019858.1 2/5 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR16518:SF6,hmmpanther:PTHR16518,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR01991 LOW 1 SNV 1 1 PASS rs781809274 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 6824726 6824726 C T 1 0 0 0 0 0 0 0 1 6552 874 31 1 1 GPR162 12 6824726 Silent SNP C C3N-02089_T 204195 6824726 126450583 636 27720 GPR162 0 . GRCh38 12 6825613 6825613 + Missense_Mutation SNP G G T rs376678235 C3N-02089_T C3N-02089_N G G c.997G>T p.Asp333Tyr p.D333Y ENST00000311268 3/5 336 176 160 173 173 0 strelka-varscan-mutect GPR162,missense_variant,p.Asp333Tyr,ENST00000311268,NM_019858.1;GPR162,missense_variant,p.Asp49Tyr,ENST00000428545,NM_014449.1;GPR162,missense_variant,p.Asp29Tyr,ENST00000382315,;GPR162,missense_variant,p.Asp118Tyr,ENST00000545321,;CD4,downstream_gene_variant,,ENST00000011653,NM_000616.4;P3H3,upstream_gene_variant,,ENST00000290510,NM_014262.4;GPR162,downstream_gene_variant,,ENST00000541431,;P3H3,upstream_gene_variant,,ENST00000538102,;GPR162,upstream_gene_variant,,ENST00000542330,;P3H3,upstream_gene_variant,,ENST00000544813,;P3H3,upstream_gene_variant,,ENST00000536140,;P3H3,upstream_gene_variant,,ENST00000612048,;GPR162,downstream_gene_variant,,ENST00000535220,; T ENST00000311268 Transcript missense_variant 1784/2768 997/1767 333/588 D/Y Gac/Tac rs376678235 1 1 GPR162 HGNC HGNC:16693 protein_coding YES CCDS8563.1 ENSP00000311528 Q16538 A0A0I9QPQ8 UPI000005046E NM_019858.1 deleterious(0) 3/5 hmmpanther:PTHR16518:SF6,hmmpanther:PTHR16518,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs376678235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 6825613 6825613 G T 1 0 0 0 0 1 0 0 0 6552 1058 37 1 1 GPR162 12 6825613 Missense_Mutation SNP G C3N-02089_T 887 6825613 126449696 637 27721 C1RL 0 . GRCh38 12 7096546 7096546 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1309G>T p.Gly437Cys p.G437C ENST00000266542 6/6 402 226 176 269 269 0 strelka-varscan-mutect C1RL,missense_variant,p.Gly437Cys,ENST00000266542,NM_001297640.1,NM_016546.3;C1RL,3_prime_UTR_variant,,ENST00000544702,NM_001297642.1;C1RL,intron_variant,,ENST00000545280,;C1R,upstream_gene_variant,,ENST00000542285,NM_001733.4;C1R,upstream_gene_variant,,ENST00000536053,;C1R,upstream_gene_variant,,ENST00000535233,;C1RL,downstream_gene_variant,,ENST00000543933,;C1R,upstream_gene_variant,,ENST00000541042,;C1RL,downstream_gene_variant,,ENST00000534950,;C1R,upstream_gene_variant,,ENST00000540242,;C1R,upstream_gene_variant,,ENST00000538050,;C1R,upstream_gene_variant,,ENST00000543835,;C1R,upstream_gene_variant,,ENST00000540610,;C1RL,intron_variant,,ENST00000504702,;C1RL,intron_variant,,ENST00000539803,;C1R,upstream_gene_variant,,ENST00000540394,;C1R,upstream_gene_variant,,ENST00000543362,;C1R,upstream_gene_variant,,ENST00000536092,;C1R,upstream_gene_variant,,ENST00000545466,;C1RL,downstream_gene_variant,,ENST00000537833,;C1RL,downstream_gene_variant,,ENST00000534969,; A ENST00000266542 Transcript missense_variant 1402/3394 1309/1464 437/487 G/C Ggc/Tgc 1 -1 C1RL HGNC HGNC:21265 protein_coding YES CCDS8573.1 ENSP00000266542 Q9NZP8 UPI0000EE67FA NM_001297640.1,NM_016546.3 deleterious(0) 6/6 Gene3D:2.40.10.10,Pfam_domain:PF00089,Prints_domain:PR00722,PROSITE_patterns:PS00135,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF274,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 7096546 7096546 C A 1 0 0 0 0 1 0 0 0 1951 594 21 2 2 C1RL 12 7096546 Missense_Mutation SNP C C3N-02089_T 270933 7096546 126178763 638 27722 CD163 0 . GRCh38 12 7481197 7481197 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.3307C>T p.= p.L1103L ENST00000359156 15/17 199 165 34 183 183 0 strelka-varscan-mutect CD163,synonymous_variant,p.=,ENST00000359156,NM_004244.5;CD163,synonymous_variant,p.=,ENST00000396620,;CD163,synonymous_variant,p.=,ENST00000432237,NM_203416.3;CD163,synonymous_variant,p.=,ENST00000541972,;CD163,intron_variant,,ENST00000537626,;CD163,intron_variant,,ENST00000542280,;CD163L1,upstream_gene_variant,,ENST00000543276,;CD163,downstream_gene_variant,,ENST00000539632,;CD163,non_coding_transcript_exon_variant,,ENST00000537044,;CD163,downstream_gene_variant,,ENST00000538840,; A ENST00000359156 Transcript synonymous_variant 3510/4268 3307/3471 1103/1156 L Ctg/Ttg 1 -1 CD163 HGNC HGNC:1631 protein_coding YES CCDS8578.1 ENSP00000352071 Q86VB7 UPI00004565CC NM_004244.5 15/17 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 7481197 7481197 G A 1 0 0 0 0 0 0 0 1 2670 991 35 3 3 CD163 12 7481197 Silent SNP G C3N-02089_T 384651 7481197 125794112 639 27723 GDF3 0 . GRCh38 12 7695498 7695498 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.231C>T p.= p.G77G ENST00000329913 1/2 352 330 22 267 267 0 strelka-varscan-mutect GDF3,synonymous_variant,p.=,ENST00000329913,NM_020634.1; A ENST00000329913 Transcript synonymous_variant 279/1239 231/1095 77/364 G ggC/ggT COSM4044965 1 -1 GDF3 HGNC HGNC:4218 protein_coding YES CCDS8581.1 ENSP00000331745 Q9NR23 UPI0000049E0E NM_020634.1 1/2 hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF38 1 LOW 1 SNV 1 1 1 PASS rs1448664549 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 7695498 7695498 G A 1 0 0 0 0 0 0 0 1 6187 1074 38 1 1 GDF3 12 7695498 Silent SNP G C3N-02089_T 214301 7695498 125579811 640 27724 CLEC2D 0 . GRCh38 12 9694779 9694779 + Missense_Mutation SNP G G T rs376555412 C3N-02089_T C3N-02089_N G G c.563G>T p.Arg188Met p.R188M ENST00000261340 6/6 233 182 51 187 187 0 strelka-varscan-mutect CLEC2D,stop_gained,p.Gly161Ter,ENST00000290855,NM_013269.5;CLEC2D,stop_gained,p.Gly124Ter,ENST00000261339,NM_001197317.2;CLEC2D,missense_variant,p.Arg188Met,ENST00000261340,NM_001004419.4;CLEC2D,missense_variant,p.Arg167Met,ENST00000430909,;CLEC2D,missense_variant,p.Arg126Met,ENST00000543300,NM_001197318.2;CLEC2D,missense_variant,p.Arg100Met,ENST00000544322,;CLEC2D,missense_variant,p.Arg89Met,ENST00000545918,NM_001197319.2;CLEC2D,3_prime_UTR_variant,,ENST00000460309,;CLEC2D,downstream_gene_variant,,ENST00000466035,;CLEC2D,3_prime_UTR_variant,,ENST00000479877,;CLEC2D,3_prime_UTR_variant,,ENST00000325960,;CLEC2D,3_prime_UTR_variant,,ENST00000444971,;CLEC2D,downstream_gene_variant,,ENST00000476198,;CLEC2D,downstream_gene_variant,,ENST00000536355,;CLEC2D,downstream_gene_variant,,ENST00000492359,;RP11-75L1.2,upstream_gene_variant,,ENST00000396690,; T ENST00000261340 Transcript missense_variant 585/935 563/585 188/194 R/M aGg/aTg rs376555412 1 1 CLEC2D HGNC HGNC:14351 protein_coding YES CCDS31741.1 ENSP00000261340 Q9UHP7 UPI000003779D NM_001004419.4 deleterious_low_confidence(0.01) 6/6 SMART_domains:SM00034 MODERATE 1 SNV 1 1 PASS rs376555412 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 9694779 9694779 G T 1 0 0 0 0 1 0 0 0 3276 1001 35 2 2 CLEC2D 12 9694779 Missense_Mutation SNP G C3N-02089_T 1999281 9694779 123580530 641 27725 CDKN1B 0 . GRCh38 12 12718248 12718248 + Frame_Shift_Del DEL C C - rs752620765 C3N-02089_T C3N-02089_N C C c.410delC p.Pro137ArgfsTer8 p.P137Rfs*8 ENST00000228872 1/3 158 144 14 150 150 0 sindel-varindel-pindel CDKN1B,frameshift_variant,p.Pro137ArgfsTer8,ENST00000228872,NM_004064.4;CDKN1B,frameshift_variant,p.Pro137ArgfsTer8,ENST00000396340,;CDKN1B,intron_variant,,ENST00000442489,;RP11-180M15.7,upstream_gene_variant,,ENST00000614874,;CDKN1B,intron_variant,,ENST00000477087,; - ENST00000228872 Transcript frameshift_variant 1125/2657 409/597 137/198 P/X Ccg/cg rs752620765,COSM268297 1 1 CDKN1B HGNC HGNC:1785 protein_coding YES CCDS8653.1 ENSP00000228872 P46527 Q6I9V6 UPI0000035C92 NM_004064.4 1/3 hmmpanther:PTHR10265,hmmpanther:PTHR10265:SF9 0,1 HIGH 1 deletion 1 1 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 12718248 12718248 C - 1 0 1 0 1 0 0 0 0 2863 855 30 0 0 CDKN1B 12 12718248 Frame_Shift_Del DEL C C3N-02089_T 3023469 12718248 120557061 642 27726 PIK3C2G 0 . GRCh38 12 18290906 18290906 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.813C>G p.Ile271Met p.I271M ENST00000538779 4/33 249 231 18 219 219 0 strelka-varscan-mutect PIK3C2G,missense_variant,p.Ile271Met,ENST00000538779,NM_001288772.1,NM_001288774.1;PIK3C2G,missense_variant,p.Ile271Met,ENST00000433979,NM_004570.5;PIK3C2G,missense_variant,p.Ile271Met,ENST00000266497,;PIK3C2G,missense_variant,p.Ile271Met,ENST00000535651,;PIK3C2G,missense_variant,p.Ile63Met,ENST00000536967,;RERGL,intron_variant,,ENST00000541632,;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,; G ENST00000538779 Transcript missense_variant 929/4963 813/4461 271/1486 I/M atC/atG 1 1 PIK3C2G HGNC HGNC:8973 protein_coding YES CCDS73452.1 ENSP00000445381 F5H369 UPI00020655D2 NM_001288772.1,NM_001288774.1 deleterious(0) 4/33 hmmpanther:PTHR10048:SF29,hmmpanther:PTHR10048,Gene3D:3.10.20.90,Superfamily_domains:SSF54236 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 18290906 18290906 C G 1 0 0 0 0 1 0 0 0 12006 903 32 4 4 PIK3C2G 12 18290906 Missense_Mutation SNP C C3N-02089_T 5572658 18290906 114984403 643 27727 PIK3C2G 0 . GRCh38 12 18538221 18538221 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3389C>A p.Pro1130Gln p.P1130Q ENST00000538779 25/33 277 228 49 236 236 0 strelka-varscan-mutect PIK3C2G,missense_variant,p.Pro1130Gln,ENST00000538779,NM_001288772.1,NM_001288774.1;PIK3C2G,missense_variant,p.Pro1089Gln,ENST00000433979,NM_004570.5;PIK3C2G,missense_variant,p.Pro1089Gln,ENST00000266497,;PIK3C2G,3_prime_UTR_variant,,ENST00000546003,; A ENST00000538779 Transcript missense_variant 3505/4963 3389/4461 1130/1486 P/Q cCa/cAa 1 1 PIK3C2G HGNC HGNC:8973 protein_coding YES CCDS73452.1 ENSP00000445381 F5H369 UPI00020655D2 NM_001288772.1,NM_001288774.1 tolerated(0.09) 25/33 PROSITE_profiles:PS50290,hmmpanther:PTHR10048:SF29,hmmpanther:PTHR10048,Pfam_domain:PF00454,Gene3D:1.10.1070.11,SMART_domains:SM00146,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS rs1405941337 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 18538221 18538221 C A 1 0 0 0 0 1 0 0 0 12006 594 21 2 2 PIK3C2G 12 18538221 Missense_Mutation SNP C C3N-02089_T 247315 18538221 114737088 644 27728 ABCC9 0 . GRCh38 12 21894084 21894084 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1750C>G p.Pro584Ala p.P584A ENST00000261200 12/38 347 312 35 266 266 0 strelka-varscan-mutect ABCC9,missense_variant,p.Pro584Ala,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Pro584Ala,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Pro247Ala,ENST00000544039,; C ENST00000261200 Transcript missense_variant 1750/8293 1750/4650 584/1549 P/A Cca/Gca 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 deleterious(0) 12/38 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223:SF173,hmmpanther:PTHR24223,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 21894084 21894084 G C 1 0 0 0 0 1 0 0 0 63 1261 44 4 4 ABCC9 12 21894084 Missense_Mutation SNP G C3N-02089_T 3355863 21894084 111381225 645 27729 OVCH1 0 . GRCh38 12 29476276 29476276 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.1401C>G p.= p.V467V ENST00000318184 13/28 210 172 38 193 193 0 strelka-varscan-mutect OVCH1,synonymous_variant,p.=,ENST00000318184,NM_183378.2;OVCH1-AS1,intron_variant,,ENST00000551108,;OVCH1-AS1,intron_variant,,ENST00000549411,; C ENST00000318184 Transcript synonymous_variant 1401/3405 1401/3405 467/1134 V gtC/gtG 1 -1 OVCH1 HGNC HGNC:23080 protein_coding YES ENSP00000326708 Q7RTY7 UPI000040640A NM_183378.2 13/28 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR24251,hmmpanther:PTHR24251:SF17,SMART_domains:SM00042,Superfamily_domains:SSF49854 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 29476276 29476276 G C 1 0 0 0 0 0 0 0 1 11393 1277 45 4 4 OVCH1 12 29476276 Silent SNP G C3N-02089_T 7582192 29476276 103799033 646 27730 TMTC1 0 . GRCh38 12 29572185 29572185 + Missense_Mutation SNP C C A rs558596090 C3N-02089_T C3N-02089_N C C c.1452G>T p.Lys484Asn p.K484N ENST00000539277 9/18 258 217 41 230 230 0 strelka-varscan-mutect TMTC1,missense_variant,p.Lys376Asn,ENST00000256062,NM_175861.3;TMTC1,missense_variant,p.Lys546Asn,ENST00000551659,;TMTC1,missense_variant,p.Lys484Asn,ENST00000539277,NM_001193451.1;TMTC1,missense_variant,p.Lys83Asn,ENST00000550354,;TMTC1,intron_variant,,ENST00000552618,;TMTC1,non_coding_transcript_exon_variant,,ENST00000319685,;TMTC1,non_coding_transcript_exon_variant,,ENST00000546582,;TMTC1,non_coding_transcript_exon_variant,,ENST00000553189,; A ENST00000539277 Transcript missense_variant 1511/2758 1452/2649 484/882 K/N aaG/aaT rs558596090 1 -1 TMTC1 HGNC HGNC:24099 protein_coding YES CCDS53772.1 ENSP00000442046 Q8IUR5 UPI0001DD37FA NM_001193451.1 deleterious(0) 9/18 Gene3D:1.25.40.10,Pfam_domain:PF07719,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF401,SMART_domains:SM00028,SMART_domains:SM00386,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 1 PASS rs558596090 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 29572185 29572185 C A 1 0 0 0 0 1 0 0 0 16734 680 24 2 2 TMTC1 12 29572185 Missense_Mutation SNP C C3N-02089_T 95909 29572185 103703124 647 27731 TSPAN11 0 . GRCh38 12 30978610 30978610 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.326T>A p.Val109Asp p.V109D ENST00000261177 4/8 211 192 19 169 169 0 strelka-varscan-mutect TSPAN11,missense_variant,p.Val109Asp,ENST00000261177,NM_001080509.2;TSPAN11,missense_variant,p.Val109Asp,ENST00000546076,;TSPAN11,missense_variant,p.Val38Asp,ENST00000535215,;RP11-551L14.4,non_coding_transcript_exon_variant,,ENST00000613860,;RP11-551L14.4,non_coding_transcript_exon_variant,,ENST00000612219,; A ENST00000261177 Transcript missense_variant 385/5505 326/762 109/253 V/D gTc/gAc 1 1 TSPAN11 HGNC HGNC:30795 protein_coding YES CCDS31765.1 ENSP00000261177 A1L157 UPI00001AE7E4 NM_001080509.2 deleterious(0) 4/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR19282:SF198,hmmpanther:PTHR19282,Pfam_domain:PF00335,PIRSF_domain:PIRSF002419,Prints_domain:PR00259 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 A 3 1 90 30978610 30978610 T A 1 0 0 0 0 1 0 0 0 17140 1667 58 4 4 TSPAN11 12 30978610 Missense_Mutation SNP T C3N-02089_T 1406425 30978610 102296699 648 27732 SYT10 0 . GRCh38 12 33379902 33379902 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.1430G>T p.Gly477Val p.G477V ENST00000228567 6/7 263 218 45 235 234 1 strelka-varscan-mutect SYT10,missense_variant,p.Gly477Val,ENST00000228567,NM_198992.3;SYT10,3_prime_UTR_variant,,ENST00000539102,; A ENST00000228567 Transcript missense_variant 1727/4461 1430/1572 477/523 G/V gGg/gTg COSM4778925 1 -1 SYT10 HGNC HGNC:19266 protein_coding YES CCDS8732.1 ENSP00000228567 Q6XYQ8 UPI0000052B30 NM_198992.3 deleterious(0) 6/7 Gene3D:2.60.40.150,Pfam_domain:PF00168,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46,SMART_domains:SM00239,Superfamily_domains:SSF49562 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 33379902 33379902 C A 1 0 0 0 0 1 0 0 0 15860 623 22 2 2 SYT10 12 33379902 Missense_Mutation SNP C C3N-02089_T 2401292 33379902 99895407 649 27733 SYT10 0 . GRCh38 12 33382507 33382507 + Missense_Mutation SNP T T A rs752312991 C3N-02089_T C3N-02089_N T T c.1212A>T p.Lys404Asn p.K404N ENST00000228567 5/7 72 56 16 83 83 0 strelka-varscan-mutect SYT10,missense_variant,p.Lys404Asn,ENST00000228567,NM_198992.3;SYT10,3_prime_UTR_variant,,ENST00000539102,; A ENST00000228567 Transcript missense_variant 1509/4461 1212/1572 404/523 K/N aaA/aaT rs752312991 1 -1 SYT10 HGNC HGNC:19266 protein_coding YES CCDS8732.1 ENSP00000228567 Q6XYQ8 UPI0000052B30 NM_198992.3 deleterious(0) 5/7 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF46,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 33382507 33382507 T A 1 0 0 0 0 1 0 0 0 15860 1606 56 4 4 SYT10 12 33382507 Missense_Mutation SNP T C3N-02089_T 2605 33382507 99892802 650 27734 CNTN1 0 . GRCh38 12 40944017 40944017 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1530C>A p.= p.A510A ENST00000551295 14/24 139 119 20 158 157 1 strelka-varscan-mutect CNTN1,synonymous_variant,p.=,ENST00000551295,NM_001843.3;CNTN1,synonymous_variant,p.=,ENST00000347616,;CNTN1,synonymous_variant,p.=,ENST00000348761,NM_175038.2;CNTN1,synonymous_variant,p.=,ENST00000547849,NM_001256064.1;CNTN1,synonymous_variant,p.=,ENST00000547702,NM_001256063.1; A ENST00000551295 Transcript synonymous_variant 1647/5557 1530/3057 510/1018 A gcC/gcA 1 1 CNTN1 HGNC HGNC:2171 protein_coding YES CCDS8737.1 ENSP00000447006 Q12860 A0A024R104 UPI0000127EBA NM_001843.3 14/24 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF531,Gene3D:2.60.40.10,Pfam_domain:PF13927,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999928 1 1 1 0 A 2 1 90 40944017 40944017 C A 1 0 0 0 0 0 0 0 1 3421 610 22 2 2 CNTN1 12 40944017 Silent SNP C C3N-02089_T 7561510 40944017 92331292 651 27735 PPHLN1 0 . GRCh38 12 42446290 42446290 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1350G>T p.Lys450Asn p.K450N ENST00000395568 12/13 54 43 11 39 39 0 strelka-varscan-mutect PPHLN1,missense_variant,p.Lys426Asn,ENST00000432191,NM_001143787.1;PPHLN1,missense_variant,p.Lys450Asn,ENST00000395568,NM_016488.6;PPHLN1,missense_variant,p.Lys355Asn,ENST00000256678,;PPHLN1,missense_variant,p.Lys450Asn,ENST00000610488,;PPHLN1,missense_variant,p.Lys426Asn,ENST00000619544,;PPHLN1,intron_variant,,ENST00000317560,;PPHLN1,downstream_gene_variant,,ENST00000613154,;PPHLN1,downstream_gene_variant,,ENST00000549190,;PPHLN1,downstream_gene_variant,,ENST00000395580,NM_201515.1;PPHLN1,downstream_gene_variant,,ENST00000358314,NM_201439.1;PPHLN1,downstream_gene_variant,,ENST00000449194,NM_001143789.1,NM_001143788.1;PPHLN1,downstream_gene_variant,,ENST00000337898,;PPHLN1,downstream_gene_variant,,ENST00000552761,NM_201440.1,NM_201438.1;PPHLN1,non_coding_transcript_exon_variant,,ENST00000624028,; T ENST00000395568 Transcript missense_variant,splice_region_variant 1434/2170 1350/1377 450/458 K/N aaG/aaT 1 1 PPHLN1 HGNC HGNC:19369 protein_coding YES CCDS31777.1 ENSP00000378935 Q8NEY8 UPI0000351A1E NM_016488.6 deleterious_low_confidence(0) 12/13 MODERATE 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999907 1 1 1 0 T 3 4 90 42446290 42446290 G T 1 0 0 0 0 1 0 0 0 12424 1014 35 2 2 PPHLN1 12 42446290 Missense_Mutation SNP G C3N-02089_T 1502273 42446290 90829019 652 27736 DBX2 0 . GRCh38 12 45050574 45050574 + Silent SNP C C A rs773452523 C3N-02089_T C3N-02089_N C C c.354G>T p.= p.P118P ENST00000332700 1/4 367 289 78 267 267 0 strelka-varscan-mutect DBX2,synonymous_variant,p.=,ENST00000332700,NM_001004329.2;RP11-478B9.1,upstream_gene_variant,,ENST00000548424,; A ENST00000332700 Transcript synonymous_variant 526/2806 354/1020 118/339 P ccG/ccT rs773452523 1 -1 DBX2 HGNC HGNC:33186 protein_coding YES CCDS31781.1 ENSP00000331470 Q6ZNG2 UPI000041A784 NM_001004329.2 1/4 hmmpanther:PTHR24331,hmmpanther:PTHR24331:SF4 LOW 1 SNV 2 1 PASS rs773452523 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 45050574 45050574 C A 1 0 0 0 0 0 0 0 1 4060 639 23 1 1 DBX2 12 45050574 Silent SNP C C3N-02089_T 2604284 45050574 88224735 653 27737 PCED1B 0 . GRCh38 12 47235212 47235213 + Frame_Shift_Ins INS - - A novel C3N-02089_T C3N-02089_N - - c.151dupA p.Arg51LysfsTer10 p.R51Kfs*10 ENST00000546455 4/4 76 51 25 46 46 0 sindel-varindel-pindel PCED1B,frameshift_variant,p.Arg51LysfsTer10,ENST00000546455,NM_138371.2;PCED1B,frameshift_variant,p.Arg51LysfsTer10,ENST00000432328,NM_001281429.1;PCED1B,frameshift_variant,p.Arg51LysfsTer10,ENST00000549500,;PCED1B,frameshift_variant,p.Arg51LysfsTer10,ENST00000549630,;PCED1B,frameshift_variant,p.Arg51LysfsTer?,ENST00000551777,;PCED1B,intron_variant,,ENST00000548348,;RP11-493L12.3,downstream_gene_variant,,ENST00000547748,; A ENST00000546455 Transcript frameshift_variant 880-881/2328 149-150/1299 50/432 A/AX gca/gcAa 1 1 PCED1B HGNC HGNC:28255 protein_coding YES CCDS8752.1 ENSP00000446688 Q96HM7 A0A024R115 UPI000006E8D2 NM_138371.2 4/4 hmmpanther:PTHR14469,hmmpanther:PTHR14469:SF1 HIGH 1 insertion 1 2 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999987 1 1 1 0 A 7 5 90 47235212 47235212 - A 1 0 1 1 0 0 0 0 0 11660 710 25 0 0 PCED1B 12 47235212 Frame_Shift_Ins INS - C3N-02089_T 2184638 47235212 86040097 654 27738 ADCY6 0 . GRCh38 12 48776279 48776279 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1607G>T p.Gly536Val p.G536V ENST00000307885 7/21 359 295 64 324 324 0 strelka-varscan-mutect ADCY6,missense_variant,p.Gly536Val,ENST00000307885,NM_015270.3;ADCY6,missense_variant,p.Gly536Val,ENST00000550422,NM_020983.2;ADCY6,missense_variant,p.Gly536Val,ENST00000357869,;ADCY6,downstream_gene_variant,,ENST00000548820,;MIR4701,upstream_gene_variant,,ENST00000583094,;ADCY6,non_coding_transcript_exon_variant,,ENST00000552090,;ADCY6,upstream_gene_variant,,ENST00000548351,;ADCY6,upstream_gene_variant,,ENST00000547260,;ADCY6,upstream_gene_variant,,ENST00000552099,;ADCY6,downstream_gene_variant,,ENST00000551435,; A ENST00000307885 Transcript missense_variant 2302/6464 1607/3507 536/1168 G/V gGc/gTc 1 -1 ADCY6 HGNC HGNC:237 protein_coding YES CCDS8767.1 ENSP00000311405 O43306 UPI000003EC29 NM_015270.3 deleterious(0) 7/21 hmmpanther:PTHR11920:SF343,hmmpanther:PTHR11920,Gene3D:3.30.70.1230,PIRSF_domain:PIRSF039050,Superfamily_domains:SSF55073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 48776279 48776279 C A 1 0 0 0 0 1 0 0 0 342 739 26 2 2 ADCY6 12 48776279 Missense_Mutation SNP C C3N-02089_T 1541067 48776279 84499030 655 27739 94 2 ADCY6 0 . GRCh38 12 48776281 48776281 + Silent SNP A A C novel C3N-02089_T C3N-02089_N A A c.1605T>G p.= p.G535G ENST00000307885 7/21 361 298 63 321 321 0 strelka-varscan-mutect ADCY6,synonymous_variant,p.=,ENST00000307885,NM_015270.3;ADCY6,synonymous_variant,p.=,ENST00000550422,NM_020983.2;ADCY6,synonymous_variant,p.=,ENST00000357869,;ADCY6,downstream_gene_variant,,ENST00000548820,;MIR4701,upstream_gene_variant,,ENST00000583094,;ADCY6,non_coding_transcript_exon_variant,,ENST00000552090,;ADCY6,upstream_gene_variant,,ENST00000548351,;ADCY6,upstream_gene_variant,,ENST00000547260,;ADCY6,upstream_gene_variant,,ENST00000552099,;ADCY6,downstream_gene_variant,,ENST00000551435,; C ENST00000307885 Transcript synonymous_variant 2300/6464 1605/3507 535/1168 G ggT/ggG 1 -1 ADCY6 HGNC HGNC:237 protein_coding YES CCDS8767.1 ENSP00000311405 O43306 UPI000003EC29 NM_015270.3 7/21 hmmpanther:PTHR11920:SF343,hmmpanther:PTHR11920,Gene3D:3.30.70.1230,PIRSF_domain:PIRSF039050,Superfamily_domains:SSF55073 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 48776281 48776281 A C 1 0 0 0 0 0 0 0 1 342 146 6 5 5 ADCY6 12 48776281 Silent SNP A C3N-02089_T 2 48776281 84499028 656 27740 94 2 FAM186B 0 . GRCh38 12 49600159 49600159 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.1481T>A p.Leu494Gln p.L494Q ENST00000257894 4/7 101 81 20 90 90 0 strelka-varscan-mutect FAM186B,missense_variant,p.Leu494Gln,ENST00000257894,NM_032130.2;FAM186B,missense_variant,p.Leu107Gln,ENST00000532262,;FAM186B,intron_variant,,ENST00000551047,;PRPF40B,intron_variant,,ENST00000551063,;FAM186B,upstream_gene_variant,,ENST00000548841,;PRPF40B,non_coding_transcript_exon_variant,,ENST00000508736,;PRPF40B,intron_variant,,ENST00000527253,;PRPF40B,downstream_gene_variant,,ENST00000547764,;FAM186B,3_prime_UTR_variant,,ENST00000533372,;RP11-133N21.7,downstream_gene_variant,,ENST00000547655,; T ENST00000257894 Transcript missense_variant 1643/2944 1481/2682 494/893 L/Q cTg/cAg 1 -1 FAM186B HGNC HGNC:25296 protein_coding YES CCDS8788.1 ENSP00000257894 Q8IYM0 A0A024R129 UPI000007077C NM_032130.2 tolerated(0.13) 4/7 hmmpanther:PTHR33590,hmmpanther:PTHR33590:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 200 8 2 0 0 0 0 -20 0.9998405 1 1 1 0 T 3 4 90 49600159 49600159 A T 1 0 0 0 0 1 0 0 0 5362 188 7 4 4 FAM186B 12 49600159 Missense_Mutation SNP A C3N-02089_T 823878 49600159 83675150 657 27741 SLC11A2 0 . GRCh38 12 51005417 51005417 + Missense_Mutation SNP C C G rs773212190 C3N-02089_T C3N-02089_N C C c.290G>C p.Arg97Pro p.R97P ENST00000394904 4/16 368 299 69 340 340 0 strelka-varscan-mutect SLC11A2,missense_variant,p.Arg97Pro,ENST00000394904,NM_001174125.1;SLC11A2,missense_variant,p.Arg68Pro,ENST00000262052,NM_000617.2,NM_001174128.1;SLC11A2,missense_variant,p.Arg68Pro,ENST00000262051,NM_001174126.1,NM_001174127.1;SLC11A2,missense_variant,p.Arg68Pro,ENST00000547198,;SLC11A2,missense_variant,p.Arg68Pro,ENST00000541174,NM_001174129.1;SLC11A2,missense_variant,p.Arg97Pro,ENST00000547688,;SLC11A2,missense_variant,p.Arg64Pro,ENST00000545993,NM_001174130.1;SLC11A2,missense_variant,p.Arg21Pro,ENST00000550714,;SLC11A2,missense_variant,p.Arg68Pro,ENST00000548193,;SLC11A2,5_prime_UTR_variant,,ENST00000546743,;SLC11A2,5_prime_UTR_variant,,ENST00000547579,;SLC11A2,5_prime_UTR_variant,,ENST00000549110,;SLC11A2,5_prime_UTR_variant,,ENST00000547732,;SLC11A2,intron_variant,,ENST00000546488,;SLC11A2,non_coding_transcript_exon_variant,,ENST00000549193,;SLC11A2,non_coding_transcript_exon_variant,,ENST00000550995,;SLC11A2,missense_variant,p.Arg68Pro,ENST00000546636,;SLC11A2,3_prime_UTR_variant,,ENST00000547510,;SLC11A2,3_prime_UTR_variant,,ENST00000549625,;SLC11A2,downstream_gene_variant,,ENST00000550329,; G ENST00000394904 Transcript missense_variant 340/4156 290/1773 97/590 R/P cGt/cCt rs773212190 1 -1 SLC11A2 HGNC HGNC:10908 protein_coding YES CCDS53793.1 ENSP00000378364 P49281 UPI00001FC234 NM_001174125.1 deleterious(0) 4/16 HAMAP:MF_00221,hmmpanther:PTHR11706:SF40,hmmpanther:PTHR11706,TIGRFAM_domain:TIGR01197 MODERATE 1 SNV 1 1 PASS rs773212190 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 51005417 51005417 C G 1 0 0 0 0 1 0 0 0 14646 536 19 4 4 SLC11A2 12 51005417 Missense_Mutation SNP C C3N-02089_T 1405258 51005417 82269892 658 27742 KRT81 0 . GRCh38 12 52288135 52288135 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.749T>C p.Leu250Pro p.L250P ENST00000327741 5/9 439 407 32 362 362 0 varscan-mutect KRT81,missense_variant,p.Leu250Pro,ENST00000327741,NM_002281.3;KRT81,missense_variant,p.Leu250Pro,ENST00000615839,;KRT86,intron_variant,,ENST00000423955,NM_001320198.1;KRT86,intron_variant,,ENST00000553310,; G ENST00000327741 Transcript missense_variant 818/1929 749/1518 250/505 L/P cTc/cCc 1 -1 KRT81 HGNC HGNC:6458 protein_coding YES CCDS31805.1 ENSP00000369349 Q14533 UPI0000DBEEF8 NM_002281.3 deleterious(0) 5/9 Low_complexity_(Seg):seg,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF191,Pfam_domain:PF00038,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 52288135 52288135 A G 1 0 0 0 0 1 0 0 0 8377 304 11 5 5 KRT81 12 52288135 Missense_Mutation SNP A C3N-02089_T 1282718 52288135 80987174 659 27743 KRT85 0 . GRCh38 12 52367267 52367267 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.139G>T p.Gly47Trp p.G47W ENST00000257901 1/9 148 115 33 148 148 0 strelka-varscan-mutect KRT85,missense_variant,p.Gly47Trp,ENST00000257901,NM_002283.3;KRT85,upstream_gene_variant,,ENST00000544265,NM_001300810.1;KRT85,upstream_gene_variant,,ENST00000552537,; A ENST00000257901 Transcript missense_variant 215/2447 139/1524 47/507 G/W Ggg/Tgg 1 -1 KRT85 HGNC HGNC:6462 protein_coding YES CCDS8824.1 ENSP00000257901 P78386 UPI000006EB3B NM_002283.3 deleterious(0.02) 1/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF113 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 52367267 52367267 C A 1 0 0 0 0 1 0 0 0 8381 681 24 2 2 KRT85 12 52367267 Missense_Mutation SNP C C3N-02089_T 79132 52367267 80908042 660 27744 KRT82 0 . GRCh38 12 52406038 52406038 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.240C>A p.Tyr80Ter p.Y80* ENST00000257974 1/9 198 146 52 136 136 0 strelka-varscan-mutect KRT82,stop_gained,p.Tyr80Ter,ENST00000257974,NM_033033.3;RP11-1020M18.10,upstream_gene_variant,,ENST00000548135,;RP3-416H24.4,downstream_gene_variant,,ENST00000547174,; T ENST00000257974 Transcript stop_gained 318/2664 240/1542 80/513 Y/* taC/taA 1 -1 KRT82 HGNC HGNC:6459 protein_coding YES CCDS8826.1 ENSP00000257974 Q9NSB4 UPI000013CFA4 NM_033033.3 1/9 Pfam_domain:PF16208,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF129 HIGH 1 SNV 1 1 PASS rs1251795753 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 52406038 52406038 G T 1 0 0 0 0 0 1 0 0 8378 1256 44 2 2 KRT82 12 52406038 Nonsense_Mutation SNP G C3N-02089_T 38771 52406038 80869271 661 27745 SOAT2 0 . GRCh38 12 53118433 53118433 + Frame_Shift_Del DEL A A - novel C3N-02089_T C3N-02089_N A A c.862delA p.Arg288GlyfsTer39 p.R288Gfs*39 ENST00000301466 8/15 196 162 34 185 185 0 sindel-varindel SOAT2,frameshift_variant,p.Arg288GlyfsTer39,ENST00000301466,NM_003578.3;SOAT2,downstream_gene_variant,,ENST00000551896,;SOAT2,frameshift_variant,p.Arg288GlyfsTer97,ENST00000542365,; - ENST00000301466 Transcript frameshift_variant,splice_region_variant 922/2044 862/1569 288/522 R/X Agg/gg 1 1 SOAT2 HGNC HGNC:11178 protein_coding YES CCDS8847.1 ENSP00000301466 O75908 UPI0000135B61 NM_003578.3 8/15 Pfam_domain:PF03062,PIRSF_domain:PIRSF000439,PIRSF_domain:PIRSF500230,hmmpanther:PTHR10408,hmmpanther:PTHR10408:SF10 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 53118433 53118433 A - 1 0 1 0 1 0 0 0 0 15232 434 15 0 0 SOAT2 12 53118433 Frame_Shift_Del DEL A C3N-02089_T 712395 53118433 80156876 662 27746 OR10A7 0 . GRCh38 12 55221484 55221484 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.460C>A p.Pro154Thr p.P154T ENST00000326258 1/1 336 263 73 346 346 0 strelka-varscan-mutect OR10A7,missense_variant,p.Pro154Thr,ENST00000326258,NM_001005280.1; A ENST00000326258 Transcript missense_variant 460/951 460/951 154/316 P/T Cct/Act COSM694608 1 1 OR10A7 HGNC HGNC:15329 protein_coding YES CCDS31815.1 ENSP00000326718 Q8NGE5 A0A126GVR3 UPI0000041E35 NM_001005280.1 tolerated(0.1) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF22,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 55221484 55221484 C A 1 0 0 0 0 1 0 0 0 10970 855 30 2 2 OR10A7 12 55221484 Missense_Mutation SNP C C3N-02089_T 2103051 55221484 78053825 663 27747 LRP1 0 . GRCh38 12 57193217 57193217 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.7597G>T p.Ala2533Ser p.A2533S ENST00000243077 46/89 249 198 51 178 178 0 strelka-varscan-mutect LRP1,missense_variant,p.Ala2533Ser,ENST00000243077,NM_002332.2;LRP1,downstream_gene_variant,,ENST00000554118,;MIR1228,upstream_gene_variant,,ENST00000408438,; T ENST00000243077 Transcript missense_variant 8063/14897 7597/13635 2533/4544 A/S Gcc/Tcc 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 tolerated(0.26) 46/89 Gene3D:4.10.400.10,Pfam_domain:PF00057,PROSITE_profiles:PS50068,SMART_domains:SM00192,Superfamily_domains:SSF57424 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 57193217 57193217 G T 1 0 0 0 0 1 0 0 0 8846 1319 46 2 2 LRP1 12 57193217 Missense_Mutation SNP G C3N-02089_T 1971733 57193217 76082092 664 27748 OS9 0 . GRCh38 12 57715844 57715844 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.664A>G p.Ile222Val p.I222V ENST00000315970 6/15 123 83 40 85 85 0 strelka-varscan-mutect OS9,missense_variant,p.Ile222Val,ENST00000315970,NM_006812.3;OS9,missense_variant,p.Ile222Val,ENST00000257966,NM_001261420.1;OS9,missense_variant,p.Ile222Val,ENST00000389142,NM_001017957.2;OS9,missense_variant,p.Ile170Val,ENST00000435406,NM_001261422.1;OS9,missense_variant,p.Ile189Val,ENST00000551035,NM_001261421.1;OS9,missense_variant,p.Ile222Val,ENST00000552285,NM_001017956.2;OS9,missense_variant,p.Ile222Val,ENST00000389146,NM_001017958.2;OS9,missense_variant,p.Ile163Val,ENST00000439210,NM_001261423.1;OS9,missense_variant,p.Ile162Val,ENST00000550372,;OS9,intron_variant,,ENST00000413095,;OS9,intron_variant,,ENST00000547079,;RP11-571M6.7,intron_variant,,ENST00000549477,;OS9,3_prime_UTR_variant,,ENST00000552787,;OS9,non_coding_transcript_exon_variant,,ENST00000549307,;OS9,non_coding_transcript_exon_variant,,ENST00000553208,;OS9,non_coding_transcript_exon_variant,,ENST00000550438,;OS9,upstream_gene_variant,,ENST00000546916,;OS9,upstream_gene_variant,,ENST00000550202,;OS9,upstream_gene_variant,,ENST00000550699,; G ENST00000315970 Transcript missense_variant 705/2691 664/2004 222/667 I/V Att/Gtt 1 1 OS9 HGNC HGNC:16994 protein_coding YES CCDS31843.1 ENSP00000318165 Q13438 UPI0000130EAC NM_006812.3 tolerated(1) 6/15 Gene3D:2.70.130.10,hmmpanther:PTHR15414,hmmpanther:PTHR15414:SF0,Superfamily_domains:SSF50911 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 57715844 57715844 A G 1 0 0 0 0 1 0 0 0 11338 217 8 5 5 OS9 12 57715844 Missense_Mutation SNP A C3N-02089_T 522627 57715844 75559465 665 27749 CYP27B1 0 . GRCh38 12 57763170 57763170 + Missense_Mutation SNP C C A rs371735439 C3N-02089_T C3N-02089_N C C c.1499G>T p.Ser500Ile p.S500I ENST00000228606 9/9 473 427 46 416 416 0 strelka-varscan-mutect CYP27B1,missense_variant,p.Ser500Ile,ENST00000228606,NM_000785.3;MARCH9,downstream_gene_variant,,ENST00000266643,NM_138396.5;MARCH9,downstream_gene_variant,,ENST00000548358,;CYP27B1,downstream_gene_variant,,ENST00000546567,;CYP27B1,downstream_gene_variant,,ENST00000546609,;CYP27B1,downstream_gene_variant,,ENST00000546496,;CYP27B1,non_coding_transcript_exon_variant,,ENST00000547344,;CYP27B1,downstream_gene_variant,,ENST00000547451,;CYP27B1,downstream_gene_variant,,ENST00000552186,; A ENST00000228606 Transcript missense_variant 1709/2540 1499/1527 500/508 S/I aGc/aTc rs371735439 1 -1 CYP27B1 HGNC HGNC:2606 protein_coding YES CCDS8954.1 ENSP00000228606 O15528 UPI000000D77F NM_000785.3 deleterious(0.02) 9/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF3,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs371735439 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 57763170 57763170 C A 1 0 0 0 0 1 0 0 0 3962 797 28 2 2 CYP27B1 12 57763170 Missense_Mutation SNP C C3N-02089_T 47326 57763170 75512139 666 27750 95 2 CYP27B1 0 . GRCh38 12 57763175 57763175 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1494A>C p.Glu498Asp p.E498D ENST00000228606 9/9 476 429 47 425 424 1 strelka-varscan-mutect CYP27B1,missense_variant,p.Glu498Asp,ENST00000228606,NM_000785.3;MARCH9,downstream_gene_variant,,ENST00000266643,NM_138396.5;MARCH9,downstream_gene_variant,,ENST00000548358,;CYP27B1,downstream_gene_variant,,ENST00000546567,;CYP27B1,downstream_gene_variant,,ENST00000546609,;CYP27B1,downstream_gene_variant,,ENST00000546496,;CYP27B1,non_coding_transcript_exon_variant,,ENST00000547344,;CYP27B1,downstream_gene_variant,,ENST00000547451,;CYP27B1,downstream_gene_variant,,ENST00000552186,; G ENST00000228606 Transcript missense_variant 1704/2540 1494/1527 498/508 E/D gaA/gaC 1 -1 CYP27B1 HGNC HGNC:2606 protein_coding YES CCDS8954.1 ENSP00000228606 O15528 UPI000000D77F NM_000785.3 tolerated(0.45) 9/9 Gene3D:1.10.630.10,Pfam_domain:PF00067,hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF3,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 57763175 57763175 T G 1 0 0 0 0 1 0 0 0 3962 1838 64 5 5 CYP27B1 12 57763175 Missense_Mutation SNP T C3N-02089_T 5 57763175 75512134 667 27751 95 2 AVIL 0 . GRCh38 12 57807698 57807698 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.1224C>T p.= p.V408V ENST00000257861 11/19 281 230 51 258 258 0 strelka-varscan-mutect AVIL,synonymous_variant,p.=,ENST00000257861,NM_006576.3;TSFM,intron_variant,,ENST00000548851,;TSFM,downstream_gene_variant,,ENST00000550559,;AVIL,downstream_gene_variant,,ENST00000549994,;RP11-571M6.17,downstream_gene_variant,,ENST00000602802,;RNU6-1083P,upstream_gene_variant,,ENST00000384022,;AVIL,upstream_gene_variant,,ENST00000550083,;AVIL,3_prime_UTR_variant,,ENST00000549851,;AVIL,non_coding_transcript_exon_variant,,ENST00000548843,;AVIL,non_coding_transcript_exon_variant,,ENST00000550537,;AVIL,intron_variant,,ENST00000549548,;AVIL,upstream_gene_variant,,ENST00000549753,; A ENST00000257861 Transcript synonymous_variant 1655/2891 1224/2460 408/819 V gtC/gtT 1 -1 AVIL HGNC HGNC:14188 protein_coding YES CCDS8959.1 ENSP00000257861 O75366 UPI000013CF93 NM_006576.3 11/19 Gene3D:3.40.20.10,Pfam_domain:PF00626,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF33,SMART_domains:SM00262,Superfamily_domains:SSF55753,Superfamily_domains:SSF82754 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 57807698 57807698 G A 1 0 0 0 0 0 0 0 1 1383 1161 41 3 3 AVIL 12 57807698 Silent SNP G C3N-02089_T 44523 57807698 75467611 668 27752 PTPRB 0 . GRCh38 12 70539000 70539000 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.5793G>T p.= p.V1931V ENST00000334414 27/34 205 167 38 221 221 0 strelka-varscan-mutect PTPRB,synonymous_variant,p.=,ENST00000334414,NM_001109754.2;PTPRB,synonymous_variant,p.=,ENST00000550358,;PTPRB,synonymous_variant,p.=,ENST00000261266,NM_002837.4;PTPRB,synonymous_variant,p.=,ENST00000538708,NM_001206972.1;PTPRB,synonymous_variant,p.=,ENST00000550857,NM_001206971.1;RP11-588H23.3,non_coding_transcript_exon_variant,,ENST00000548687,;RP11-588H23.3,downstream_gene_variant,,ENST00000546836,;RP11-588H23.3,downstream_gene_variant,,ENST00000551438,;RP11-588H23.3,downstream_gene_variant,,ENST00000549460,;RP11-588H23.3,downstream_gene_variant,,ENST00000547656,;PTPRB,downstream_gene_variant,,ENST00000549400,; A ENST00000334414 Transcript synonymous_variant 5838/12316 5793/6648 1931/2215 V gtG/gtT 1 -1 PTPRB HGNC HGNC:9665 protein_coding YES CCDS44943.1 ENSP00000334928 P23467 UPI00002294FA NM_001109754.2 27/34 PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF288,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 70539000 70539000 C A 1 0 0 0 0 0 0 0 1 12950 581 21 2 2 PTPRB 12 70539000 Silent SNP C C3N-02089_T 12731302 70539000 62736309 669 27753 ZFC3H1 0 . GRCh38 12 71645016 71645016 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1140G>A p.= p.Q380Q ENST00000378743 4/35 260 234 26 246 245 1 strelka-varscan-mutect ZFC3H1,synonymous_variant,p.=,ENST00000378743,NM_144982.4;ZFC3H1,non_coding_transcript_exon_variant,,ENST00000550712,;ZFC3H1,synonymous_variant,p.=,ENST00000552994,; T ENST00000378743 Transcript synonymous_variant 1499/7285 1140/5970 380/1989 Q caG/caA 1 -1 ZFC3H1 HGNC HGNC:28328 protein_coding YES CCDS41813.1 ENSP00000368017 O60293 UPI00003668E9 NM_144982.4 4/35 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21563,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 71645016 71645016 C T 1 0 0 0 0 0 0 0 1 18210 564 20 3 3 ZFC3H1 12 71645016 Silent SNP C C3N-02089_T 1106016 71645016 61630293 670 27754 TRHDE 0 . GRCh38 12 72618890 72618890 + Splice_Site SNP G G A novel C3N-02089_T C3N-02089_N G G c.2187-1G>A p.X729_splice ENST00000261180 45 35 10 51 51 0 strelka-varscan-mutect TRHDE,splice_acceptor_variant,,ENST00000261180,NM_013381.2;TRHDE,splice_acceptor_variant,,ENST00000549138,;TRHDE,splice_acceptor_variant,,ENST00000549922,; A ENST00000261180 Transcript splice_acceptor_variant -/10733 2187/3075 729/1024 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 12/18 HIGH 1 SNV 1 1 PASS . . 0 197 13 0 0 0 0 0 -19.99997 0.9999276 1 1 1 0 A 5 1 90 72618890 72618890 G A 1 0 0 0 0 0 0 1 0 16968 1014 35 3 3 TRHDE 12 72618890 Splice_Site SNP G C3N-02089_T 973874 72618890 60656419 671 27755 TRHDE 0 . GRCh38 12 72621139 72621139 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.2366A>G p.Tyr789Cys p.Y789C ENST00000261180 14/19 189 157 32 138 138 0 strelka-varscan-mutect TRHDE,missense_variant,p.Tyr789Cys,ENST00000261180,NM_013381.2;TRHDE,downstream_gene_variant,,ENST00000549138,;TRHDE,non_coding_transcript_exon_variant,,ENST00000549922,; G ENST00000261180 Transcript missense_variant 2462/10733 2366/3075 789/1024 Y/C tAt/tGt 1 1 TRHDE HGNC HGNC:30748 protein_coding YES CCDS9004.1 ENSP00000261180 Q9UKU6 UPI0000136D52 NM_013381.2 deleterious(0) 14/19 Pfam_domain:PF11838,hmmpanther:PTHR11533,hmmpanther:PTHR11533:SF40 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 72621139 72621139 A G 1 0 0 0 0 1 0 0 0 16968 449 16 5 5 TRHDE 12 72621139 Missense_Mutation SNP A C3N-02089_T 2249 72621139 60654170 672 27756 NAV3 0 . GRCh38 12 78177182 78177183 + Frame_Shift_Ins INS - - A novel C3N-02089_T C3N-02089_N - - c.5167dupA p.Thr1723AsnfsTer9 p.T1723Nfs*9 ENST00000397909 27/40 320 264 56 308 308 0 sindel-varindel-pindel NAV3,frameshift_variant,p.Thr1723AsnfsTer9,ENST00000397909,NM_001024383.1;NAV3,frameshift_variant,p.Thr1723AsnfsTer9,ENST00000536525,NM_014903.5;NAV3,frameshift_variant,p.Thr618AsnfsTer9,ENST00000552895,;NAV3,frameshift_variant,p.Thr345AsnfsTer9,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000552300,;NAV3,upstream_gene_variant,,ENST00000548948,; A ENST00000397909 Transcript frameshift_variant 5339-5340/9821 5166-5167/7158 1722-1723/2385 -/X -/A 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 27/40 Low_complexity_(Seg):seg,hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 90 78177182 78177182 - A 1 0 1 1 0 0 0 0 0 10194 581 21 0 0 NAV3 12 78177182 Frame_Shift_Ins INS - C3N-02089_T 5556043 78177182 55098127 673 27757 SLC6A15 0 . GRCh38 12 84863588 84863588 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1669C>A p.Leu557Ile p.L557I ENST00000266682 11/12 46 35 11 68 68 0 strelka-varscan-mutect SLC6A15,missense_variant,p.Leu557Ile,ENST00000266682,NM_182767.5;SLC6A15,missense_variant,p.Leu265Ile,ENST00000309283,;SLC6A15,missense_variant,p.Leu450Ile,ENST00000552192,NM_001146335.2;SLC6A15,non_coding_transcript_exon_variant,,ENST00000548267,; T ENST00000266682 Transcript missense_variant 2211/4879 1669/2193 557/730 L/I Cta/Ata 1 -1 SLC6A15 HGNC HGNC:13621 protein_coding YES CCDS9026.1 ENSP00000266682 Q9H2J7 UPI0000038BF2 NM_182767.5 tolerated(1) 11/12 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF101 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999974 1 1 1 0 T 3 4 90 84863588 84863588 G T 1 0 0 0 0 1 0 0 0 14961 991 35 2 2 SLC6A15 12 84863588 Missense_Mutation SNP G C3N-02089_T 6686406 84863588 48411721 674 27758 LRRIQ1 0 . GRCh38 12 85056984 85056984 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2191G>T p.Glu731Ter p.E731* ENST00000393217 8/27 96 79 17 105 105 0 strelka-varscan-mutect LRRIQ1,stop_gained,p.Glu731Ter,ENST00000393217,NM_001079910.1;LRRIQ1,downstream_gene_variant,,ENST00000533414,;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,; T ENST00000393217 Transcript stop_gained 2252/5394 2191/5169 731/1722 E/* Gag/Tag 1 1 LRRIQ1 HGNC HGNC:25708 protein_coding YES CCDS41816.1 ENSP00000376910 Q96JM4 A0A140VJN5 UPI0000ED4E82 NM_001079910.1 8/27 HIGH 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 85056984 85056984 G T 1 0 0 0 0 0 1 0 0 8935 943 33 2 2 LRRIQ1 12 85056984 Nonsense_Mutation SNP G C3N-02089_T 193396 85056984 48218325 675 27759 CFAP54 0 . GRCh38 12 96626940 96626940 + Splice_Site SNP G G C novel C3N-02089_T C3N-02089_N G G c.4103+1G>C p.X1368_splice ENST00000524981 14 11 3 21 21 0 strelka-mutect CFAP54,splice_donor_variant,,ENST00000524981,NM_001306084.1;CFAP54,splice_donor_variant,,ENST00000637336,;CFAP54,splice_donor_variant,,ENST00000550977,;CFAP54,splice_donor_variant,,ENST00000554108,; C ENST00000524981 Transcript splice_donor_variant -/9766 4103/9291 1368/3096 1 1 CFAP54 HGNC HGNC:26456 protein_coding YES CCDS76588.1 ENSP00000431759 Q96N23 UPI0001F77A4D NM_001306084.1 30/67 HIGH 1 SNV 5 1 PASS rs1441860078 . 6 198 6 0 0 0 0 0 -10.41276 1 1 1 1 0 C 5 2 90 96626940 96626940 G C 1 0 0 0 0 0 0 1 0 3025 1275 44 4 4 CFAP54 12 96626940 Splice_Site SNP G C3N-02089_T 11569956 96626940 36648369 676 27760 ANKS1B 0 . GRCh38 12 98829272 98829272 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2968G>T p.Val990Phe p.V990F ENST00000547776 19/26 283 236 47 217 217 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Val990Phe,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Val216Phe,ENST00000549493,NM_181670.3;ANKS1B,missense_variant,p.Val262Phe,ENST00000550778,;ANKS1B,missense_variant,p.Val216Phe,ENST00000546960,NM_001204068.1;ANKS1B,5_prime_UTR_variant,,ENST00000341752,NM_001204081.1;ANKS1B,5_prime_UTR_variant,,ENST00000333732,NM_001204079.1,NM_001204080.1,NM_001204065.1;ANKS1B,5_prime_UTR_variant,,ENST00000546364,;ANKS1B,5_prime_UTR_variant,,ENST00000551560,;ANKS1B,5_prime_UTR_variant,,ENST00000552407,;ANKS1B,5_prime_UTR_variant,,ENST00000552748,;ANKS1B,5_prime_UTR_variant,,ENST00000548447,;ANKS1B,intron_variant,,ENST00000550693,NM_001204069.1;ANKS1B,intron_variant,,ENST00000549025,NM_001204066.1;ANKS1B,intron_variant,,ENST00000547010,;ANKS1B,intron_variant,,ENST00000549558,NM_020140.3;ANKS1B,intron_variant,,ENST00000547446,NM_001204067.1;ANKS1B,intron_variant,,ENST00000546568,NM_001204070.1;ANKS1B,intron_variant,,ENST00000549797,;ANKS1B,intron_variant,,ENST00000551613,;ANKS1B,intron_variant,,ENST00000551830,;ANKS1B,5_prime_UTR_variant,,ENST00000547362,;ANKS1B,downstream_gene_variant,,ENST00000552245,; A ENST00000547776 Transcript missense_variant 2968/3885 2968/3747 990/1248 V/F Gtt/Ttt 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 tolerated(0.08) 19/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 98829272 98829272 C A 1 0 0 0 0 1 0 0 0 795 536 19 1 1 ANKS1B 12 98829272 Missense_Mutation SNP C C3N-02089_T 2202332 98829272 34446037 677 27761 UHRF1BP1L 0 . GRCh38 12 100051154 100051154 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.3492A>G p.= p.L1164L ENST00000279907 16/21 216 175 41 230 230 0 strelka-varscan-mutect UHRF1BP1L,synonymous_variant,p.=,ENST00000279907,NM_015054.1;UHRF1BP1L,synonymous_variant,p.=,ENST00000545232,;UHRF1BP1L,upstream_gene_variant,,ENST00000548712,;UHRF1BP1L,non_coding_transcript_exon_variant,,ENST00000547504,; C ENST00000279907 Transcript synonymous_variant 3705/5168 3492/4395 1164/1464 L ctA/ctG 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 16/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 LOW 1 SNV 1 1 PASS rs1388113784 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 100051154 100051154 T C 1 0 0 0 0 0 0 0 1 17493 1625 57 5 5 UHRF1BP1L 12 100051154 Silent SNP T C3N-02089_T 1221882 100051154 33224155 678 27762 ACTR6 0 . GRCh38 12 100210152 100210152 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.459C>A p.= p.S153S ENST00000188312 5/11 141 129 12 147 147 0 strelka-varscan-mutect ACTR6,synonymous_variant,p.=,ENST00000188312,NM_022496.4;ACTR6,synonymous_variant,p.=,ENST00000546902,;ACTR6,synonymous_variant,p.=,ENST00000551617,;ACTR6,synonymous_variant,p.=,ENST00000552376,;ACTR6,synonymous_variant,p.=,ENST00000551652,;ACTR6,downstream_gene_variant,,ENST00000550813,;ACTR6,3_prime_UTR_variant,,ENST00000548180,;DEPDC4,intron_variant,,ENST00000378244,;ACTR6,intron_variant,,ENST00000553038,;ACTR6,intron_variant,,ENST00000552064,;ACTR6,downstream_gene_variant,,ENST00000551440,;ACTR6,downstream_gene_variant,,ENST00000547458,;ACTR6,downstream_gene_variant,,ENST00000551517,;ACTR6,downstream_gene_variant,,ENST00000549977,; A ENST00000188312 Transcript synonymous_variant 1224/2464 459/1191 153/396 S tcC/tcA 1 1 ACTR6 HGNC HGNC:24025 protein_coding YES CCDS9074.1 ENSP00000188312 Q9GZN1 UPI0000044716 NM_022496.4 5/11 hmmpanther:PTHR11937:SF47,hmmpanther:PTHR11937,Gene3D:3.30.420.40,Pfam_domain:PF00022,SMART_domains:SM00268,Superfamily_domains:SSF53067 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -17.03469 0.9999998 1 1 1 0 A 2 1 90 100210152 100210152 C A 1 0 0 0 0 0 0 0 1 259 668 24 2 2 ACTR6 12 100210152 Silent SNP C C3N-02089_T 158998 100210152 33065157 679 27763 NR1H4 0 . GRCh38 12 100561973 100561973 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.1197T>C p.= p.L399L ENST00000551379 8/9 253 221 32 280 279 1 strelka-varscan-mutect NR1H4,synonymous_variant,p.=,ENST00000548884,NM_005123.3;NR1H4,synonymous_variant,p.=,ENST00000392986,NM_001206979.1,NM_001206977.1;NR1H4,synonymous_variant,p.=,ENST00000549996,NM_001206978.1;NR1H4,synonymous_variant,p.=,ENST00000188403,NM_001206992.1;NR1H4,synonymous_variant,p.=,ENST00000551379,NM_001206993.1;NR1H4,3_prime_UTR_variant,,ENST00000321046,; C ENST00000551379 Transcript synonymous_variant 1225/1489 1197/1461 399/486 L ctT/ctC 1 1 NR1H4 HGNC HGNC:7967 protein_coding YES CCDS55876.1 ENSP00000447149 Q96RI1 UPI000006E701 NM_001206993.1 8/9 hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF155,Pfam_domain:PF00104,Gene3D:1.10.565.10,SMART_domains:SM00430,Superfamily_domains:SSF48508,Prints_domain:PR00398,Prints_domain:PR00546 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 100561973 100561973 T C 1 0 0 0 0 0 0 0 1 10675 1741 61 5 5 NR1H4 12 100561973 Silent SNP T C3N-02089_T 351821 100561973 32713336 680 27764 ANO4 0 . GRCh38 12 101042439 101042439 + Silent SNP C C A rs761457503 C3N-02089_T C3N-02089_N C C c.1125C>A p.= p.G375G ENST00000392977 12/28 167 133 34 162 162 0 strelka-varscan-mutect ANO4,synonymous_variant,p.=,ENST00000392979,NM_178826.3;ANO4,synonymous_variant,p.=,ENST00000392977,NM_001286615.1,NM_001286616.1;RP11-350G24.1,upstream_gene_variant,,ENST00000549036,;ANO4,non_coding_transcript_exon_variant,,ENST00000548940,;ANO4,downstream_gene_variant,,ENST00000549234,; A ENST00000392977 Transcript synonymous_variant 1335/3509 1125/2868 375/955 G ggC/ggA rs761457503 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 12/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547 LOW 1 SNV 2 1 PASS rs761457503 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 101042439 101042439 C A 1 0 0 0 0 0 0 0 1 806 755 27 1 1 ANO4 12 101042439 Silent SNP C C3N-02089_T 480466 101042439 32232870 681 27765 UTP20 0 . GRCh38 12 101338841 101338841 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.3897T>C p.= p.I1299I ENST00000261637 31/62 115 103 12 105 105 0 strelka-varscan-mutect UTP20,synonymous_variant,p.=,ENST00000261637,NM_014503.2; C ENST00000261637 Transcript synonymous_variant 4071/9025 3897/8358 1299/2785 I atT/atC 1 1 UTP20 HGNC HGNC:17897 protein_coding YES CCDS9081.1 ENSP00000261637 O75691 UPI00001FB38B NM_014503.2 31/62 Gene3D:1.25.10.10,Pfam_domain:PF07539,hmmpanther:PTHR17695,hmmpanther:PTHR17695:SF11,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 101338841 101338841 T C 1 0 0 0 0 0 0 0 1 17642 1771 62 5 5 UTP20 12 101338841 Silent SNP T C3N-02089_T 296402 101338841 31936468 682 27766 NUP37 0 . GRCh38 12 102101065 102101065 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.321T>G p.Phe107Leu p.F107L ENST00000552283 4/10 87 77 10 105 104 1 strelka-varscan-mutect NUP37,missense_variant,p.Phe107Leu,ENST00000552283,;NUP37,missense_variant,p.Phe107Leu,ENST00000251074,NM_024057.2;NUP37,missense_variant,p.Phe107Leu,ENST00000551744,;NUP37,non_coding_transcript_exon_variant,,ENST00000543021,;NUP37,non_coding_transcript_exon_variant,,ENST00000551200,; C ENST00000552283 Transcript missense_variant 461/2372 321/981 107/326 F/L ttT/ttG 1 -1 NUP37 HGNC HGNC:29929 protein_coding YES CCDS9089.1 ENSP00000448054 Q8NFH4 UPI00000372E7 tolerated(0.29) 4/10 hmmpanther:PTHR22806,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -19.98784 1 1 1 1 0 C 3 2 90 102101065 102101065 A C 1 0 0 0 0 1 0 0 0 10829 359 13 5 5 NUP37 12 102101065 Missense_Mutation SNP A C3N-02089_T 762224 102101065 31174244 683 27767 KIAA1033 0 . GRCh38 12 105164683 105164683 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.3400T>G p.Phe1134Val p.F1134V ENST00000620430 32/33 272 245 27 260 260 0 strelka-varscan-mutect KIAA1033,missense_variant,p.Phe1133Val,ENST00000332180,NM_015275.2;KIAA1033,missense_variant,p.Phe1134Val,ENST00000620430,NM_001293640.1;KIAA1033,downstream_gene_variant,,ENST00000551224,;KIAA1033,non_coding_transcript_exon_variant,,ENST00000547171,;KIAA1033,downstream_gene_variant,,ENST00000551290,;KIAA1033,3_prime_UTR_variant,,ENST00000550053,;KIAA1033,downstream_gene_variant,,ENST00000550786,;KIAA1033,downstream_gene_variant,,ENST00000550036,; G ENST00000620430 Transcript missense_variant 3487/5807 3400/3525 1134/1174 F/V Ttc/Gtc 1 1 KIAA1033 HGNC HGNC:29174 protein_coding YES CCDS73514.1 ENSP00000484713 A0A087X256 UPI000387C216 NM_001293640.1 deleterious(0) 32/33 Pfam_domain:PF14746,hmmpanther:PTHR31409,hmmpanther:PTHR31409:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 105164683 105164683 T G 1 0 0 0 0 1 0 0 0 8099 1841 64 5 5 KIAA1033 12 105164683 Missense_Mutation SNP T C3N-02089_T 3063618 105164683 28110626 684 27768 FICD 0 . GRCh38 12 108518820 108518820 + Nonsense_Mutation SNP C C A rs778735949 C3N-02089_T C3N-02089_N C C c.722C>A p.Ser241Ter p.S241* ENST00000552695 3/3 456 379 77 369 369 0 strelka-varscan-mutect FICD,stop_gained,p.Ser241Ter,ENST00000552695,NM_007076.2;FICD,3_prime_UTR_variant,,ENST00000361549,;FICD,intron_variant,,ENST00000549641,;SART3,downstream_gene_variant,,ENST00000228284,NM_014706.3;SART3,downstream_gene_variant,,ENST00000431469,;FICD,downstream_gene_variant,,ENST00000552758,;SART3,downstream_gene_variant,,ENST00000546728,; A ENST00000552695 Transcript stop_gained 957/3347 722/1377 241/458 S/* tCg/tAg rs778735949 1 1 FICD HGNC HGNC:18416 protein_coding YES CCDS9116.1 ENSP00000446479 Q9BVA6 A0A024RBM8 UPI0000048F49 NM_007076.2 3/3 Gene3D:1.10.3290.10,hmmpanther:PTHR13504,hmmpanther:PTHR13504:SF34 HIGH 1 SNV 1 1 PASS rs778735949 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 108518820 108518820 C A 1 0 0 0 0 0 1 0 0 5752 893 31 1 1 FICD 12 108518820 Nonsense_Mutation SNP C C3N-02089_T 3354137 108518820 24756489 685 27769 SSH1 0 . GRCh38 12 108789169 108789169 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1969G>T p.Ala657Ser p.A657S ENST00000326495 15/15 276 216 60 186 186 0 strelka-varscan-mutect SSH1,missense_variant,p.Ala657Ser,ENST00000326495,NM_018984.3;SSH1,downstream_gene_variant,,ENST00000326470,NM_001161331.1;SSH1,downstream_gene_variant,,ENST00000551165,NM_001161330.1;SSH1,3_prime_UTR_variant,,ENST00000546433,; A ENST00000326495 Transcript missense_variant 2063/13040 1969/3150 657/1049 A/S Gcc/Tcc 1 -1 SSH1 HGNC HGNC:30579 protein_coding YES CCDS9121.1 ENSP00000315713 Q8WYL5 UPI000003E894 NM_018984.3 deleterious_low_confidence(0.03) 15/15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 108789169 108789169 C A 1 0 0 0 0 1 0 0 0 15560 797 28 2 2 SSH1 12 108789169 Missense_Mutation SNP C C3N-02089_T 270349 108789169 24486140 686 27770 SSH1 0 . GRCh38 12 108800812 108800812 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1116G>T p.Trp372Cys p.W372C ENST00000326495 12/15 434 333 101 349 349 0 strelka-varscan-mutect SSH1,missense_variant,p.Trp372Cys,ENST00000326495,NM_018984.3;SSH1,missense_variant,p.Trp383Cys,ENST00000326470,NM_001161331.1;SSH1,missense_variant,p.Trp372Cys,ENST00000551165,NM_001161330.1;SSH1,3_prime_UTR_variant,,ENST00000546433,; A ENST00000326495 Transcript missense_variant 1210/13040 1116/3150 372/1049 W/C tgG/tgT 1 -1 SSH1 HGNC HGNC:30579 protein_coding YES CCDS9121.1 ENSP00000315713 Q8WYL5 UPI000003E894 NM_018984.3 deleterious(0) 12/15 PROSITE_profiles:PS50054,PROSITE_profiles:PS50056,hmmpanther:PTHR10159:SF138,hmmpanther:PTHR10159,Pfam_domain:PF00782,Gene3D:3.90.190.10,SMART_domains:SM00195,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 108800812 108800812 C A 1 0 0 0 0 1 0 0 0 15560 856 30 2 2 SSH1 12 108800812 Missense_Mutation SNP C C3N-02089_T 11643 108800812 24474497 687 27771 ACACB 0 . GRCh38 12 109167964 109167964 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.855G>T p.Glu285Asp p.E285D ENST00000338432 4/53 245 188 57 160 160 0 strelka-varscan-mutect ACACB,missense_variant,p.Glu285Asp,ENST00000338432,;ACACB,missense_variant,p.Glu285Asp,ENST00000377848,NM_001093.3;ACACB,missense_variant,p.Glu83Asp,ENST00000544726,;ACACB,5_prime_UTR_variant,,ENST00000377854,;ACACB,downstream_gene_variant,,ENST00000546328,; T ENST00000338432 Transcript missense_variant 974/9360 855/7377 285/2458 E/D gaG/gaT 1 1 ACACB HGNC HGNC:85 protein_coding YES CCDS31898.1 ENSP00000341044 O00763 UPI0000DBEEFB deleterious(0.01) 4/53 PROSITE_profiles:PS50979,hmmpanther:PTHR18866:SF94,hmmpanther:PTHR18866,Pfam_domain:PF00289,Gene3D:3.40.50.20,Superfamily_domains:SSF52440 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 109167964 109167964 G T 1 0 0 0 0 1 0 0 0 150 933 33 2 2 ACACB 12 109167964 Missense_Mutation SNP G C3N-02089_T 367152 109167964 24107345 688 27772 GIT2 0 . GRCh38 12 109967466 109967466 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.756G>T p.Met252Ile p.M252I ENST00000355312 8/20 238 194 44 215 214 1 strelka-varscan-mutect GIT2,missense_variant,p.Met252Ile,ENST00000355312,NM_057169.3;GIT2,missense_variant,p.Met252Ile,ENST00000361006,NM_001135214.1;GIT2,missense_variant,p.Met252Ile,ENST00000354574,NM_014776.3;GIT2,missense_variant,p.Met252Ile,ENST00000457474,NM_001135213.1;GIT2,missense_variant,p.Met252Ile,ENST00000547815,NM_139201.2;GIT2,missense_variant,p.Met252Ile,ENST00000553118,NM_057170.3;GIT2,missense_variant,p.Met252Ile,ENST00000551209,;GIT2,missense_variant,p.Met252Ile,ENST00000320063,;GIT2,missense_variant,p.Met190Ile,ENST00000550186,;TCHP,intron_variant,,ENST00000550780,;GIT2,non_coding_transcript_exon_variant,,ENST00000551721,;GIT2,non_coding_transcript_exon_variant,,ENST00000551455,; A ENST00000355312 Transcript missense_variant 756/5466 756/2280 252/759 M/I atG/atT 1 -1 GIT2 HGNC HGNC:4273 protein_coding YES CCDS9138.1 ENSP00000347464 Q14161 UPI000012B4C5 NM_057169.3 tolerated(0.1) 8/20 hmmpanther:PTHR23180,hmmpanther:PTHR23180:SF248 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 109967466 109967466 C A 1 0 0 0 0 1 0 0 0 6279 594 21 2 2 GIT2 12 109967466 Missense_Mutation SNP C C3N-02089_T 799502 109967466 23307843 689 27773 ATXN2 0 . GRCh38 12 111510561 111510561 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2060C>G p.Thr687Ser p.T687S ENST00000377617 12/25 111 87 24 114 114 0 strelka-varscan-mutect ATXN2,missense_variant,p.Thr687Ser,ENST00000377617,NM_002973.3;ATXN2,missense_variant,p.Thr687Ser,ENST00000550104,;ATXN2,missense_variant,p.Thr398Ser,ENST00000616825,;ATXN2,missense_variant,p.Thr527Ser,ENST00000608853,;ATXN2,missense_variant,p.Thr422Ser,ENST00000389153,;ATXN2,missense_variant,p.Thr422Ser,ENST00000542287,;ATXN2,missense_variant,p.Thr398Ser,ENST00000535949,;ATXN2,intron_variant,,ENST00000492467,;ATXN2,intron_variant,,ENST00000550236,;ATXN2,downstream_gene_variant,,ENST00000481331,;ATXN2,missense_variant,p.Thr608Ser,ENST00000483311,;ATXN2,non_coding_transcript_exon_variant,,ENST00000546483,;ATXN2,downstream_gene_variant,,ENST00000392645,; C ENST00000377617 Transcript missense_variant 2222/4702 2060/3942 687/1313 T/S aCt/aGt 1 -1 ATXN2 HGNC HGNC:10555 protein_coding YES CCDS31902.1 ENSP00000366843 Q99700 UPI0000DBEEFC NM_002973.3 tolerated_low_confidence(0.31) 12/25 hmmpanther:PTHR12854:SF11,hmmpanther:PTHR12854 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999918 1 1 1 0 C 3 2 90 111510561 111510561 G C 1 0 0 0 0 1 0 0 0 1365 1029 36 4 4 ATXN2 12 111510561 Missense_Mutation SNP G C3N-02089_T 1543095 111510561 21764748 690 27774 ALDH2 0 . GRCh38 12 111792775 111792775 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1076G>T p.Gly359Val p.G359V ENST00000261733 9/13 91 67 24 75 75 0 strelka-varscan-mutect ALDH2,missense_variant,p.Gly359Val,ENST00000261733,NM_000690.3;ALDH2,missense_variant,p.Gly312Val,ENST00000416293,NM_001204889.1;RP11-162P23.2,downstream_gene_variant,,ENST00000546840,;ALDH2,missense_variant,p.Gly56Val,ENST00000549106,;ALDH2,3_prime_UTR_variant,,ENST00000548536,; T ENST00000261733 Transcript missense_variant 1137/9569 1076/1554 359/517 G/V gGg/gTg 1 1 ALDH2 HGNC HGNC:404 protein_coding YES CCDS9155.1 ENSP00000261733 P05091 UPI0000129293 NM_000690.3 deleterious(0) 9/13 Gene3D:3.40.309.10,Pfam_domain:PF00171,hmmpanther:PTHR11699,hmmpanther:PTHR11699:SF211,Superfamily_domains:SSF53720 MODERATE 1 SNV 1 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.9999864 1 1 1 0 T 3 4 90 111792775 111792775 G T 1 0 0 0 0 1 0 0 0 596 1232 43 2 2 ALDH2 12 111792775 Missense_Mutation SNP G C3N-02089_T 282214 111792775 21482534 691 27775 PTPN11 0 . GRCh38 12 112488445 112488445 + Missense_Mutation SNP C C G rs397509344 C3N-02089_T C3N-02089_N C C c.1382C>G p.Ala461Gly p.A461G ENST00000351677 12/16 526 420 106 389 389 0 strelka-varscan-mutect PTPN11,missense_variant,p.Ala461Gly,ENST00000351677,NM_002834.3;PTPN11,missense_variant,p.Ala465Gly,ENST00000635625,;PTPN11,missense_variant,p.Ala132Gly,ENST00000635652,;PTPN11,downstream_gene_variant,,ENST00000392597,NM_080601.1; G ENST00000351677 Transcript missense_variant,splice_region_variant 1580/6101 1382/1782 461/593 A/G gCt/gGt rs397509344,COSM935282 1 1 PTPN11 HGNC HGNC:9644 protein_coding YES CCDS9163.1 ENSP00000340944 Q06124 UPI000013296E NM_002834.3 deleterious(0) 12/16 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF000929,Prints_domain:PR00700,PROSITE_patterns:PS00383,PROSITE_profiles:PS50055,PROSITE_profiles:PS50056,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF150,SMART_domains:SM00194,SMART_domains:SM00404,Superfamily_domains:SSF52799 pathogenic 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs397509344 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 112488445 112488445 C G 1 0 0 0 0 1 0 0 0 12933 811 28 4 4 PTPN11 12 112488445 Missense_Mutation SNP C C3N-02089_T 695670 112488445 20786864 692 27776 RPH3A 0 . GRCh38 12 112847831 112847831 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.219G>T p.Gln73His p.Q73H ENST00000389385 5/22 151 124 27 124 124 0 strelka-varscan-mutect RPH3A,missense_variant,p.Gln73His,ENST00000389385,NM_001143854.1;RPH3A,missense_variant,p.Gln73His,ENST00000415485,;RPH3A,missense_variant,p.Gln69His,ENST00000551052,NM_014954.3;RPH3A,missense_variant,p.Gln73His,ENST00000543106,;RPH3A,missense_variant,p.Gln73His,ENST00000551593,;RPH3A,missense_variant,p.Gln73His,ENST00000547728,;RPH3A,missense_variant,p.Gln6His,ENST00000550901,;RPH3A,missense_variant,p.Gln73His,ENST00000551198,;RPH3A,missense_variant,p.Gln73His,ENST00000552667,;RPH3A,missense_variant,p.Gln73His,ENST00000548197,;RPH3A,missense_variant,p.Gln73His,ENST00000553114,;RPH3A,missense_variant,p.Gln73His,ENST00000546703,;RPH3A,missense_variant,p.Gln73His,ENST00000547840,;RPH3A,missense_variant,p.Gln73His,ENST00000551748,;RPH3A,missense_variant,p.Gln73His,ENST00000549769,;RPH3A,missense_variant,p.Gln73His,ENST00000547686,;RPH3A,intron_variant,,ENST00000548866,;RPH3A,downstream_gene_variant,,ENST00000549736,;RPH3A,non_coding_transcript_exon_variant,,ENST00000552679,;RPH3A,upstream_gene_variant,,ENST00000547222,;RPH3A,3_prime_UTR_variant,,ENST00000547099,; T ENST00000389385 Transcript missense_variant 716/4679 219/2085 73/694 Q/H caG/caT 1 1 RPH3A HGNC HGNC:17056 protein_coding YES CCDS44979.1 ENSP00000374036 Q9Y2J0 UPI000013456D NM_001143854.1 deleterious(0.02) 5/22 PROSITE_profiles:PS50916,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118,Gene3D:3.30.40.10,Pfam_domain:PF02318,Superfamily_domains:SSF57903 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 112847831 112847831 G T 1 0 0 0 0 1 0 0 0 13803 991 35 2 2 RPH3A 12 112847831 Missense_Mutation SNP G C3N-02089_T 359386 112847831 20427478 693 27777 RPH3A 0 . GRCh38 12 112883342 112883342 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1376G>T p.Trp459Leu p.W459L ENST00000389385 16/22 352 274 78 308 308 0 strelka-varscan-mutect RPH3A,missense_variant,p.Trp459Leu,ENST00000389385,NM_001143854.1;RPH3A,missense_variant,p.Trp459Leu,ENST00000415485,;RPH3A,missense_variant,p.Trp455Leu,ENST00000551052,NM_014954.3;RPH3A,missense_variant,p.Trp459Leu,ENST00000543106,;RPH3A,missense_variant,p.Trp410Leu,ENST00000548866,;RPH3A,non_coding_transcript_exon_variant,,ENST00000549913,;RPH3A,non_coding_transcript_exon_variant,,ENST00000552755,;RPH3A,upstream_gene_variant,,ENST00000546687,; T ENST00000389385 Transcript missense_variant 1873/4679 1376/2085 459/694 W/L tGg/tTg 1 1 RPH3A HGNC HGNC:17056 protein_coding YES CCDS44979.1 ENSP00000374036 Q9Y2J0 UPI000013456D NM_001143854.1 deleterious(0) 16/22 PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF118,Pfam_domain:PF00168,Gene3D:2.60.40.150,SMART_domains:SM00239,Superfamily_domains:SSF49562 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 112883342 112883342 G T 1 0 0 0 0 1 0 0 0 13803 1357 47 2 2 RPH3A 12 112883342 Missense_Mutation SNP G C3N-02089_T 35511 112883342 20391967 694 27778 SLC8B1 0 . GRCh38 12 113310299 113310299 + Missense_Mutation SNP C C T C3N-02089_T C3N-02089_N C C c.1192G>A p.Gly398Ser p.G398S ENST00000552014 13/17 249 228 21 178 178 0 strelka-varscan-mutect SLC8B1,missense_variant,p.Gly398Ser,ENST00000552014,;SLC8B1,missense_variant,p.Gly398Ser,ENST00000202831,NM_024959.2;SLC8B1,missense_variant,p.Gly342Ser,ENST00000546737,;SLC8B1,upstream_gene_variant,,ENST00000550047,;SLC8B1,upstream_gene_variant,,ENST00000549069,;SLC8B1,non_coding_transcript_exon_variant,,ENST00000553238,;SLC8B1,missense_variant,p.Gly268Ser,ENST00000550672,;SLC8B1,non_coding_transcript_exon_variant,,ENST00000552565,; T ENST00000552014 Transcript missense_variant 1708/3289 1192/1755 398/584 G/S Ggc/Agc COSM4166057 1 -1 SLC8B1 HGNC HGNC:26175 protein_coding YES CCDS31909.1 ENSP00000447091 Q6J4K2 UPI000004FA44 tolerated(0.07) 13/17 Transmembrane_helices:TMhelix,hmmpanther:PTHR12266,hmmpanther:PTHR12266:SF0 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 113310299 113310299 C T 1 0 0 0 0 1 0 0 0 14992 681 24 3 3 SLC8B1 12 113310299 Missense_Mutation SNP C C3N-02089_T 426957 113310299 19965010 695 27779 SDSL 0 . GRCh38 12 113435408 113435408 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.523G>T p.Gly175Cys p.G175C ENST00000403593 6/8 103 76 27 91 91 0 strelka-varscan-mutect SDSL,missense_variant,p.Gly175Cys,ENST00000403593,NM_001304993.1;SDSL,missense_variant,p.Gly175Cys,ENST00000345635,NM_138432.3;SDSL,missense_variant,p.Gly71Cys,ENST00000546672,;SDSL,missense_variant,p.Gly117Cys,ENST00000553248,;SDSL,upstream_gene_variant,,ENST00000551760,; T ENST00000403593 Transcript missense_variant 785/1449 523/990 175/329 G/C Ggt/Tgt 1 1 SDSL HGNC HGNC:30404 protein_coding YES CCDS9170.1 ENSP00000385790 Q96GA7 A0A024RBL2 UPI0000072263 NM_001304993.1 deleterious(0) 6/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF99,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 113435408 113435408 G T 1 0 0 0 0 1 0 0 0 14252 1232 43 2 2 SDSL 12 113435408 Missense_Mutation SNP G C3N-02089_T 125109 113435408 19839901 696 27780 TBX3 0 . GRCh38 12 114676341 114676341 + Silent SNP G G T rs745496316 C3N-02089_T C3N-02089_N G G c.1071C>A p.= p.A357A ENST00000257566 6/8 440 349 91 328 327 1 strelka-varscan-mutect TBX3,synonymous_variant,p.=,ENST00000349155,NM_005996.3;TBX3,synonymous_variant,p.=,ENST00000257566,NM_016569.3;TBX3,downstream_gene_variant,,ENST00000552054,;TBX3,downstream_gene_variant,,ENST00000548503,; T ENST00000257566 Transcript synonymous_variant 1461/4208 1071/2232 357/743 A gcC/gcA rs745496316 1 -1 TBX3 HGNC HGNC:11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 A0A024RBL6 UPI0000136AA0 NM_016569.3 6/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91,Pfam_domain:PF12598 LOW 1 SNV 1 1 PASS rs745496316 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 114676341 114676341 G T 1 0 0 0 0 0 0 0 1 16064 987 35 2 2 TBX3 12 114676341 Silent SNP G C3N-02089_T 1240933 114676341 18598968 697 27781 NOS1 0 . GRCh38 12 117220129 117220129 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.4218C>A p.= p.T1406T ENST00000618760 28/30 168 126 42 151 151 0 strelka-varscan-mutect NOS1,synonymous_variant,p.=,ENST00000618760,NM_001204218.1;NOS1,synonymous_variant,p.=,ENST00000317775,NM_001204214.1,NM_000620.4,NM_001204213.1;NOS1,synonymous_variant,p.=,ENST00000338101,;NOS1,synonymous_variant,p.=,ENST00000344089,; T ENST00000618760 Transcript synonymous_variant 4929/12283 4218/4407 1406/1468 T acC/acA 1 -1 NOS1 HGNC HGNC:7872 protein_coding YES CCDS55890.1 ENSP00000477999 P29475 UPI00001FBC10 NM_001204218.1 28/30 hmmpanther:PTHR19384,hmmpanther:PTHR19384:SF63,Gene3D:3.40.50.80,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF52343 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 117220129 117220129 G T 1 0 0 0 0 0 0 0 1 10586 1219 43 2 2 NOS1 12 117220129 Silent SNP G C3N-02089_T 2543788 117220129 16055180 698 27782 HNF1A 0 . GRCh38 12 120988927 120988927 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.421C>A p.Gln141Lys p.Q141K ENST00000544413 2/10 702 557 145 501 500 1 strelka-varscan-mutect HNF1A,missense_variant,p.Gln141Lys,ENST00000257555,NM_000545.5;HNF1A,missense_variant,p.Gln141Lys,ENST00000541395,;HNF1A,missense_variant,p.Gln141Lys,ENST00000543427,;HNF1A,missense_variant,p.Gln141Lys,ENST00000617366,;HNF1A,missense_variant,p.Gln141Lys,ENST00000400024,;HNF1A,missense_variant,p.Gln141Lys,ENST00000544413,NM_001306179.1;HNF1A,intron_variant,,ENST00000615446,;HNF1A,intron_variant,,ENST00000538626,;HNF1A,intron_variant,,ENST00000535955,;HNF1A,missense_variant,p.Gln189Lys,ENST00000560968,;HNF1A,missense_variant,p.Gln141Lys,ENST00000538646,;HNF1A,missense_variant,p.Gln141Lys,ENST00000541924,;HNF1A,non_coding_transcript_exon_variant,,ENST00000402929,;HNF1A,intron_variant,,ENST00000540108,;HNF1A,intron_variant,,ENST00000544574,; A ENST00000544413 Transcript missense_variant 441/2014 421/1917 141/638 Q/K Cag/Aag 1 1 HNF1A HGNC HGNC:11621 protein_coding YES CCDS76611.1 ENSP00000438804 F5H0K0 UPI000204ABCC NM_001306179.1 deleterious(0) 2/10 Gene3D:1.10.260.40,Pfam_domain:PF04814,hmmpanther:PTHR11568,hmmpanther:PTHR11568:SF4,Superfamily_domains:SSF47413 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 120988927 120988927 C A 1 0 0 0 0 1 0 0 0 7142 595 21 2 2 HNF1A 12 120988927 Missense_Mutation SNP C C3N-02089_T 3768798 120988927 12286382 699 27783 KNTC1 0 . GRCh38 12 122549797 122549797 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1019C>A p.Thr340Lys p.T340K ENST00000333479 13/64 153 138 15 171 171 0 strelka-varscan-mutect KNTC1,missense_variant,p.Thr340Lys,ENST00000333479,NM_014708.4;KNTC1,missense_variant,p.Thr303Lys,ENST00000450485,; A ENST00000333479 Transcript missense_variant 1196/6975 1019/6630 340/2209 T/K aCa/aAa 1 1 KNTC1 HGNC HGNC:17255 protein_coding YES CCDS45002.1 ENSP00000328236 P50748 UPI0000047FD6 NM_014708.4 deleterious(0.01) 13/64 hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 122549797 122549797 C A 1 0 0 0 0 1 0 0 0 8308 478 17 2 2 KNTC1 12 122549797 Missense_Mutation SNP C C3N-02089_T 1560870 122549797 10725512 700 27784 KNTC1 0 . GRCh38 12 122597738 122597738 + Nonsense_Mutation SNP C C T rs73407858 C3N-02089_T C3N-02089_N C C c.4363C>T p.Gln1455Ter p.Q1455* ENST00000333479 44/64 245 224 21 230 230 0 strelka-varscan-mutect KNTC1,stop_gained,p.Gln1455Ter,ENST00000333479,NM_014708.4;KNTC1,stop_gained,p.Gln14Ter,ENST00000423927,;KNTC1,intron_variant,,ENST00000450485,;KNTC1,upstream_gene_variant,,ENST00000436959,;KNTC1,non_coding_transcript_exon_variant,,ENST00000545065,;KNTC1,intron_variant,,ENST00000535186,;KNTC1,non_coding_transcript_exon_variant,,ENST00000377192,; T ENST00000333479 Transcript stop_gained 4540/6975 4363/6630 1455/2209 Q/* Cag/Tag rs73407858 1 1 KNTC1 HGNC HGNC:17255 protein_coding YES CCDS45002.1 ENSP00000328236 P50748 UPI0000047FD6 NM_014708.4 44/64 hmmpanther:PTHR15688:SF1,hmmpanther:PTHR15688 HIGH 1 SNV 1 1 PASS rs73407858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 122597738 122597738 C T 1 0 0 0 0 0 1 0 0 8308 827 29 3 3 KNTC1 12 122597738 Nonsense_Mutation SNP C C3N-02089_T 47941 122597738 10677571 701 27785 ATP6V0A2 0 . GRCh38 12 123722375 123722375 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.221G>T p.Arg74Ile p.R74I ENST00000330342 3/20 342 266 76 278 278 0 strelka-varscan-mutect ATP6V0A2,missense_variant,p.Arg74Ile,ENST00000330342,NM_012463.3;ATP6V0A2,missense_variant,p.Arg74Ile,ENST00000613625,;ATP6V0A2,upstream_gene_variant,,ENST00000504192,;ATP6V0A2,non_coding_transcript_exon_variant,,ENST00000540368,;RPL27P12,upstream_gene_variant,,ENST00000472241,; T ENST00000330342 Transcript missense_variant 469/6542 221/2571 74/856 R/I aGa/aTa COSM1677456 1 1 ATP6V0A2 HGNC HGNC:18481 protein_coding YES CCDS9254.1 ENSP00000332247 Q9Y487 UPI00001AFC09 NM_012463.3 deleterious(0) 3/20 hmmpanther:PTHR11629:SF22,hmmpanther:PTHR11629,Pfam_domain:PF01496,PIRSF_domain:PIRSF001293 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 123722375 123722375 G T 1 0 0 0 0 1 0 0 0 1322 942 33 2 2 ATP6V0A2 12 123722375 Missense_Mutation SNP G C3N-02089_T 1124637 123722375 9552934 702 27786 DNAH10 0 . GRCh38 12 123808951 123808951 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.2788A>C p.Lys930Gln p.K930Q ENST00000638045 18/78 135 100 35 129 129 0 strelka-varscan-mutect DNAH10,missense_variant,p.Lys991Gln,ENST00000409039,;DNAH10,missense_variant,p.Lys930Gln,ENST00000638045,NM_207437.3;DNAH10,missense_variant,p.Lys805Gln,ENST00000614082,;DNAH10,splice_region_variant,,ENST00000467219,;DNAH10,splice_region_variant,,ENST00000447853,; C ENST00000638045 Transcript missense_variant,splice_region_variant 2813/13678 2788/13416 930/4471 K/Q Aag/Cag 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0.04) 18/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 123808951 123808951 A C 1 0 0 0 0 1 0 0 0 4411 144 5 5 5 DNAH10 12 123808951 Missense_Mutation SNP A C3N-02089_T 86576 123808951 9466358 703 27787 DNAH10 0 . GRCh38 12 123820706 123820706 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.3773A>G p.Gln1258Arg p.Q1258R ENST00000638045 23/78 267 204 63 212 212 0 strelka-varscan-mutect DNAH10,missense_variant,p.Gln1319Arg,ENST00000409039,;DNAH10,missense_variant,p.Gln1258Arg,ENST00000638045,NM_207437.3; G ENST00000638045 Transcript missense_variant 3798/13678 3773/13416 1258/4471 Q/R cAg/cGg 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 tolerated(0.08) 23/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF08393 MODERATE 1 SNV 1 PASS rs1468527398 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 123820706 123820706 A G 1 0 0 0 0 1 0 0 0 4411 188 7 5 5 DNAH10 12 123820706 Missense_Mutation SNP A C3N-02089_T 11755 123820706 9454603 704 27788 DNAH10 0 . GRCh38 12 123879281 123879281 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.8036A>T p.Gln2679Leu p.Q2679L ENST00000638045 48/78 185 162 23 176 176 0 strelka-varscan-mutect DNAH10,missense_variant,p.Gln2740Leu,ENST00000409039,;DNAH10,missense_variant,p.Gln2679Leu,ENST00000638045,NM_207437.3;DNAH10,3_prime_UTR_variant,,ENST00000497783,; T ENST00000638045 Transcript missense_variant 8061/13678 8036/13416 2679/4471 Q/L cAg/cTg 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0.01) 48/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF12775,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 123879281 123879281 A T 1 0 0 0 0 1 0 0 0 4411 188 7 4 4 DNAH10 12 123879281 Missense_Mutation SNP A C3N-02089_T 58575 123879281 9396028 705 27789 DNAH10 0 . GRCh38 12 123917694 123917694 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.10759A>T p.Asn3587Tyr p.N3587Y ENST00000638045 63/78 490 444 46 368 368 0 strelka-varscan-mutect DNAH10,missense_variant,p.Asn3648Tyr,ENST00000409039,;DNAH10,missense_variant,p.Asn3587Tyr,ENST00000638045,NM_207437.3;DNAH10,downstream_gene_variant,,ENST00000540041,;CCDC92,downstream_gene_variant,,ENST00000542348,; T ENST00000638045 Transcript missense_variant 10784/13678 10759/13416 3587/4471 N/Y Aac/Tac 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 deleterious(0.02) 63/78 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF12781 MODERATE 1 SNV 1 PASS rs1449477024 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 123917694 123917694 A T 1 0 0 0 0 1 0 0 0 4411 246 9 4 4 DNAH10 12 123917694 Missense_Mutation SNP A C3N-02089_T 38413 123917694 9357615 706 27790 AACS 0 . GRCh38 12 125136829 125136829 + Missense_Mutation SNP G G C rs546586609 C3N-02089_T C3N-02089_N G G c.1846G>C p.Val616Leu p.V616L ENST00000316519 17/18 306 288 18 219 219 0 strelka-varscan-mutect AACS,missense_variant,p.Val616Leu,ENST00000316519,NM_023928.3;AACS,non_coding_transcript_exon_variant,,ENST00000316543,;RP11-158L12.4,upstream_gene_variant,,ENST00000623804,;AACS,downstream_gene_variant,,ENST00000398953,;AACS,non_coding_transcript_exon_variant,,ENST00000539251,;AACS,intron_variant,,ENST00000545511,;AACS,intron_variant,,ENST00000543665,;AACS,downstream_gene_variant,,ENST00000536118,;AACS,downstream_gene_variant,,ENST00000538851,; C ENST00000316519 Transcript missense_variant 2052/3316 1846/2019 616/672 V/L Gtg/Ctg rs546586609 1 1 AACS HGNC HGNC:21298 protein_coding YES CCDS9263.1 ENSP00000324842 Q86V21 A0A024RBV2 UPI0000049787 NM_023928.3 deleterious(0.01) 17/18 hmmpanther:PTHR24095:SF183,hmmpanther:PTHR24095,TIGRFAM_domain:TIGR01217,Gene3D:3.30.300.30,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS rs546586609 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 125136829 125136829 G C 1 0 0 0 0 1 0 0 0 9 1145 40 4 4 AACS 12 125136829 Missense_Mutation SNP G C3N-02089_T 1219135 125136829 8138480 707 27791 TMEM132B 0 . GRCh38 12 125652520 125652520 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1979T>A p.Leu660Gln p.L660Q ENST00000299308 8/9 152 118 34 129 129 0 strelka-varscan-mutect TMEM132B,missense_variant,p.Leu660Gln,ENST00000299308,NM_052907.3;TMEM132B,missense_variant,p.Leu172Gln,ENST00000613307,NM_001286219.1;TMEM132B,non_coding_transcript_exon_variant,,ENST00000535886,; A ENST00000299308 Transcript missense_variant 1987/10906 1979/3237 660/1078 L/Q cTg/cAg 1 1 TMEM132B HGNC HGNC:29397 protein_coding YES CCDS41859.1 ENSP00000299308 Q14DG7 UPI00006BFF58 NM_052907.3 deleterious(0) 8/9 hmmpanther:PTHR13388:SF12,hmmpanther:PTHR13388,Pfam_domain:PF16070 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 125652520 125652520 T A 1 0 0 0 0 1 0 0 0 16490 1580 55 4 4 TMEM132B 12 125652520 Missense_Mutation SNP T C3N-02089_T 515691 125652520 7622789 708 27792 PUS1 0 . GRCh38 12 131932302 131932302 + Missense_Mutation SNP G G T rs762199189 C3N-02089_T C3N-02089_N G G c.431G>T p.Arg144Leu p.R144L ENST00000376649 3/6 294 214 80 294 294 0 strelka-varscan-mutect PUS1,missense_variant,p.Arg144Leu,ENST00000376649,NM_025215.5;PUS1,missense_variant,p.Arg91Leu,ENST00000542167,;PUS1,missense_variant,p.Arg116Leu,ENST00000443358,NM_001002020.2,NM_001002019.2;PUS1,missense_variant,p.Arg116Leu,ENST00000322060,;PUS1,missense_variant,p.Arg116Leu,ENST00000535067,;PUS1,missense_variant,p.Arg144Leu,ENST00000544213,;PUS1,missense_variant,p.Arg116Leu,ENST00000537484,;PUS1,missense_variant,p.Arg116Leu,ENST00000538037,;PUS1,missense_variant,p.Arg116Leu,ENST00000456665,;RP11-417L19.4,upstream_gene_variant,,ENST00000539078,;RP11-417L19.6,upstream_gene_variant,,ENST00000621809,;PUS1,non_coding_transcript_exon_variant,,ENST00000544662,; T ENST00000376649 Transcript missense_variant 931/4094 431/1284 144/427 R/L cGg/cTg rs762199189,COSM937127 1 1 PUS1 HGNC HGNC:15508 protein_coding YES CCDS9275.2 ENSP00000365837 Q9Y606 E5KMT5 UPI000006FC81 NM_025215.5 deleterious(0) 3/6 hmmpanther:PTHR11142:SF4,hmmpanther:PTHR11142,TIGRFAM_domain:TIGR00071,Gene3D:1dj0A02,Superfamily_domains:SSF55120 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762199189 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 131932302 131932302 G T 1 0 0 0 0 1 0 0 0 12988 1116 39 1 1 PUS1 12 131932302 Missense_Mutation SNP G C3N-02089_T 6279782 131932302 1343007 709 27793 LATS2 0 . GRCh38 13 20979797 20979797 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2666G>T p.Gly889Val p.G889V ENST00000382592 7/8 107 90 17 94 94 0 strelka-varscan-mutect LATS2,missense_variant,p.Gly889Val,ENST00000382592,NM_014572.2; A ENST00000382592 Transcript missense_variant,splice_region_variant 3072/5511 2666/3267 889/1088 G/V gGg/gTg 1 -1 LATS2 HGNC HGNC:6515 protein_coding YES CCDS9294.1 ENSP00000372035 Q9NRM7 A0A024RDM3 UPI000013DBF5 NM_014572.2 deleterious(0) 7/8 PROSITE_profiles:PS50011,hmmpanther:PTHR24356:SF149,hmmpanther:PTHR24356,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 20979797 20979797 C A 1 0 0 0 0 1 0 0 0 8552 637 22 2 2 LATS2 13 20979797 Missense_Mutation SNP C C3N-02089_T 20979797 93384531 710 27794 AMER2 0 . GRCh38 13 25171235 25171235 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.385A>T p.Ser129Cys p.S129C ENST00000515384 1/1 52 32 20 48 48 0 strelka-varscan-mutect AMER2,missense_variant,p.Ser129Cys,ENST00000357816,NM_199138.2;AMER2,missense_variant,p.Ser129Cys,ENST00000515384,NM_152704.3;LINC00463,downstream_gene_variant,,ENST00000413501,; A ENST00000515384 Transcript missense_variant 1053/3197 385/2016 129/671 S/C Agc/Tgc 1 -1 AMER2 HGNC HGNC:26360 protein_coding YES CCDS53859.1 ENSP00000426528 Q8N7J2 UPI0000231C76 NM_152704.3 tolerated(0.08) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR22237:SF1,hmmpanther:PTHR22237,Pfam_domain:PF09422 MODERATE SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 25171235 25171235 T A 1 0 0 0 0 1 0 0 0 668 1580 55 4 4 AMER2 13 25171235 Missense_Mutation SNP T C3N-02089_T 4191438 25171235 89193093 711 27795 HSPH1 0 . GRCh38 13 31137421 31137421 + Missense_Mutation SNP T T G rs763383146 C3N-02089_T C3N-02089_N T T c.2480A>C p.Glu827Ala p.E827A ENST00000630972 18/18 232 200 32 200 200 0 strelka-varscan-mutect HSPH1,missense_variant,p.Glu825Ala,ENST00000320027,NM_006644.3;HSPH1,missense_variant,p.Glu749Ala,ENST00000445273,NM_001286505.1;HSPH1,missense_variant,p.Glu827Ala,ENST00000630972,NM_001286504.1;HSPH1,missense_variant,p.Glu781Ala,ENST00000380405,NM_001286503.1;HSPH1,missense_variant,p.Glu89Ala,ENST00000435381,;HSPH1,3_prime_UTR_variant,,ENST00000602786,;HSPH1,non_coding_transcript_exon_variant,,ENST00000626866,;HSPH1,downstream_gene_variant,,ENST00000469538,; G ENST00000630972 Transcript missense_variant 2774/3570 2480/2583 827/860 E/A gAa/gCa rs763383146 1 -1 HSPH1 HGNC HGNC:16969 protein_coding YES CCDS66526.1 ENSP00000487365 Q92598 UPI00001FCBB0 NM_001286504.1 tolerated(0.44) 18/18 MODERATE 1 SNV 1 1 PASS rs763383146 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 31137421 31137421 T G 1 0 0 0 0 1 0 0 0 7327 1783 62 5 5 HSPH1 13 31137421 Missense_Mutation SNP T C3N-02089_T 5966186 31137421 83226907 712 27796 FRY 0 . GRCh38 13 32186285 32186285 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.3345C>A p.= p.P1115P ENST00000542859 27/61 291 254 37 326 326 0 strelka-varscan-mutect FRY,synonymous_variant,p.=,ENST00000542859,NM_023037.2;FRY,synonymous_variant,p.=,ENST00000380250,; A ENST00000542859 Transcript synonymous_variant 3841/13200 3345/9042 1115/3013 P ccC/ccA 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 27/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 32186285 32186285 C A 1 0 0 0 0 0 0 0 1 5935 610 22 2 2 FRY 13 32186285 Silent SNP C C3N-02089_T 1048864 32186285 82178043 713 27797 FREM2 0 . GRCh38 13 38690733 38690733 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.3389G>T p.Gly1130Val p.G1130V ENST00000280481 1/24 154 126 28 216 216 0 strelka-varscan-mutect FREM2,missense_variant,p.Gly1130Val,ENST00000280481,NM_207361.5; T ENST00000280481 Transcript missense_variant 3605/16070 3389/9510 1130/3169 G/V gGg/gTg 1 1 FREM2 HGNC HGNC:25396 protein_coding YES CCDS31960.1 ENSP00000280481 Q5SZK8 UPI000443805C NM_207361.5 deleterious(0) 1/24 hmmpanther:PTHR11878:SF32,hmmpanther:PTHR11878,Pfam_domain:PF16184 MODERATE 1 SNV 2 1 PASS rs1453406056 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 38690733 38690733 G T 1 0 0 0 0 1 0 0 0 5912 1232 43 2 2 FREM2 13 38690733 Missense_Mutation SNP G C3N-02089_T 6504448 38690733 75673595 714 27798 ENOX1 0 . GRCh38 13 43361426 43361426 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.235C>A p.Pro79Thr p.P79T ENST00000261488 6/17 171 146 25 261 260 1 strelka-varscan-mutect ENOX1,missense_variant,p.Pro79Thr,ENST00000261488,NM_001242863.1,NM_017993.3,NM_001127615.1;ENOX1,upstream_gene_variant,,ENST00000482207,; T ENST00000261488 Transcript missense_variant 813/2982 235/1932 79/643 P/T Cca/Aca 1 -1 ENOX1 HGNC HGNC:25474 protein_coding YES CCDS9389.1 ENSP00000261488 Q8TC92 A0A024RDT8 UPI0000071D6F NM_001242863.1,NM_017993.3,NM_001127615.1 deleterious(0) 6/17 hmmpanther:PTHR16001,hmmpanther:PTHR16001:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 43361426 43361426 G T 1 0 0 0 0 1 0 0 0 4971 1174 41 2 2 ENOX1 13 43361426 Missense_Mutation SNP G C3N-02089_T 4670693 43361426 71002902 715 27799 KCTD4 0 . GRCh38 13 45194078 45194078 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.490T>G p.Phe164Val p.F164V ENST00000379108 1/1 171 146 25 274 273 1 strelka-varscan-mutect KCTD4,missense_variant,p.Phe164Val,ENST00000379108,NM_198404.2;GTF2F2,intron_variant,,ENST00000340473,NM_004128.2; C ENST00000379108 Transcript missense_variant 640/1865 490/780 164/259 F/V Ttc/Gtc 1 -1 KCTD4 HGNC HGNC:23227 protein_coding YES CCDS9396.1 ENSP00000368402 Q8WVF5 UPI000013F484 NM_198404.2 tolerated(0.08) 1/1 hmmpanther:PTHR14499,hmmpanther:PTHR14499:SF9 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 45194078 45194078 A C 1 0 0 0 0 1 0 0 0 8028 14 1 5 5 KCTD4 13 45194078 Missense_Mutation SNP A C3N-02089_T 1832652 45194078 69170250 716 27800 SPERT 0 . GRCh38 13 45713969 45713969 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.944C>A p.Pro315Gln p.P315Q ENST00000310521 3/3 52 46 6 63 62 1 strelka-varscan-mutect SPERT,missense_variant,p.Pro279Gln,ENST00000378966,;SPERT,missense_variant,p.Pro315Gln,ENST00000310521,NM_152719.2;SPERT,missense_variant,p.Pro279Gln,ENST00000610924,NM_001286342.1;SPERT,downstream_gene_variant,,ENST00000533564,; A ENST00000310521 Transcript missense_variant 1024/1613 944/1347 315/448 P/Q cCg/cAg 1 1 SPERT HGNC HGNC:30720 protein_coding YES CCDS9399.1 ENSP00000309189 Q8NA61 A0A140VJV5 UPI0000070F5F NM_152719.2 tolerated(0.36) 3/3 hmmpanther:PTHR21533,hmmpanther:PTHR21533:SF13 MODERATE 1 SNV 2 1 PASS rs1181057262 . 0 204 6 0 0 0 0 0 -14.37363 0.9999999 1 1 1 0 A 3 1 90 45713969 45713969 C A 1 0 0 0 0 1 0 0 0 15390 652 23 1 1 SPERT 13 45713969 Missense_Mutation SNP C C3N-02089_T 519891 45713969 68650359 717 27801 LECT1 0 . GRCh38 13 52708616 52708616 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.709G>A p.Gly237Ser p.G237S ENST00000377962 6/7 121 99 22 168 168 0 strelka-varscan-mutect LECT1,missense_variant,p.Gly237Ser,ENST00000448904,NM_001011705.1;LECT1,missense_variant,p.Gly237Ser,ENST00000377962,NM_007015.2;LECT1,downstream_gene_variant,,ENST00000431550,; T ENST00000377962 Transcript missense_variant 788/1410 709/1005 237/334 G/S Ggc/Agc 1 -1 LECT1 HGNC HGNC:17005 protein_coding YES CCDS9437.1 ENSP00000367198 O75829 UPI000003F666 NM_007015.2 tolerated(0.68) 6/7 hmmpanther:PTHR14064:SF6,hmmpanther:PTHR14064 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 52708616 52708616 C T 1 0 0 0 0 1 0 0 0 8620 681 24 3 3 LECT1 13 52708616 Missense_Mutation SNP C C3N-02089_T 6994647 52708616 61655712 718 27802 KLHL1 0 . GRCh38 13 70107275 70107275 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.425G>T p.Gly142Val p.G142V ENST00000377844 1/11 108 66 42 155 155 0 strelka-varscan-mutect KLHL1,missense_variant,p.Gly142Val,ENST00000377844,NM_020866.2;KLHL1,missense_variant,p.Gly142Val,ENST00000545028,NM_001286725.1;ATXN8OS,non_coding_transcript_exon_variant,,ENST00000414504,;ATXN8OS,upstream_gene_variant,,ENST00000424524,; A ENST00000377844 Transcript missense_variant 1185/4115 425/2247 142/748 G/V gGg/gTg 1 -1 KLHL1 HGNC HGNC:6352 protein_coding YES CCDS9445.1 ENSP00000367075 Q9NR64 UPI000004B136 NM_020866.2 tolerated_low_confidence(0.22) 1/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 70107275 70107275 C A 1 0 0 0 0 1 0 0 0 8229 623 22 2 2 KLHL1 13 70107275 Missense_Mutation SNP C C3N-02089_T 17398659 70107275 44257053 719 27803 SPRY2 0 . GRCh38 13 80337380 80337380 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.326G>T p.Arg109Ile p.R109I ENST00000377102 2/2 306 225 81 221 221 0 strelka-varscan-mutect SPRY2,missense_variant,p.Arg109Ile,ENST00000377102,NM_001318537.1;SPRY2,missense_variant,p.Arg109Ile,ENST00000377104,NM_005842.2; A ENST00000377102 Transcript missense_variant 1304/2708 326/948 109/315 R/I aGa/aTa 1 -1 SPRY2 HGNC HGNC:11270 protein_coding YES CCDS9463.1 ENSP00000366306 O43597 UPI0000001301 NM_001318537.1 tolerated(0.09) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR12365,hmmpanther:PTHR12365:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 80337380 80337380 C A 1 0 0 0 0 1 0 0 0 15462 913 32 2 2 SPRY2 13 80337380 Missense_Mutation SNP C C3N-02089_T 10230105 80337380 34026948 720 27804 ABCC4 0 . GRCh38 13 95209574 95209574 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.645G>T p.= p.L215L ENST00000376887 6/31 84 71 13 85 85 0 strelka-varscan-mutect ABCC4,synonymous_variant,p.=,ENST00000376887,NM_005845.4,NM_001301829.1;ABCC4,synonymous_variant,p.=,ENST00000629385,NM_001105515.2;ABCC4,synonymous_variant,p.=,ENST00000536256,NM_001301830.1; A ENST00000376887 Transcript synonymous_variant 760/5839 645/3978 215/1325 L ctG/ctT 1 -1 ABCC4 HGNC HGNC:55 protein_coding YES CCDS9474.1 ENSP00000366084 O15439 UPI00001A36E6 NM_005845.4,NM_001301829.1 6/31 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF237,Pfam_domain:PF00664,Gene3D:2hydA01,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 95209574 95209574 C A 1 0 0 0 0 0 0 0 1 59 465 17 2 2 ABCC4 13 95209574 Silent SNP C C3N-02089_T 14872194 95209574 19154754 721 27805 DOCK9 0 . GRCh38 13 98883818 98883818 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.2464A>T p.Thr822Ser p.T822S ENST00000376460 22/57 68 63 5 113 113 0 strelka-varscan-mutect DOCK9,missense_variant,p.Thr834Ser,ENST00000448493,;DOCK9,missense_variant,p.Thr822Ser,ENST00000442173,;DOCK9,missense_variant,p.Thr822Ser,ENST00000376460,NM_001130048.1,NM_015296.2;DOCK9,missense_variant,p.Thr823Ser,ENST00000427887,NM_001130049.1;DOCK9,missense_variant,p.Thr822Ser,ENST00000627024,NM_001130050.1;DOCK9,missense_variant,p.Thr834Ser,ENST00000339416,;DOCK9,3_prime_UTR_variant,,ENST00000630992,;DOCK9,downstream_gene_variant,,ENST00000473165,; A ENST00000376460 Transcript missense_variant 2545/7549 2464/6207 822/2068 T/S Act/Tct 1 -1 DOCK9 HGNC HGNC:14132 protein_coding YES CCDS45062.1 ENSP00000365643 Q9BZ29 UPI000046FD7F NM_001130048.1,NM_015296.2 deleterious(0.02) 22/57 Pfam_domain:PF14429,hmmpanther:PTHR23317,hmmpanther:PTHR23317:SF77 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -11.78981 1 1 1 1 0 A 3 1 90 98883818 98883818 T A 1 0 0 0 0 1 0 0 0 4509 1652 57 4 4 DOCK9 13 98883818 Missense_Mutation SNP T C3N-02089_T 3674244 98883818 15480510 722 27806 CCDC168 0 . GRCh38 13 102745515 102745515 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.5182G>T p.Gly1728Cys p.G1728C ENST00000322527 4/4 108 89 19 133 133 0 strelka-varscan-mutect CCDC168,missense_variant,p.Gly1728Cys,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; A ENST00000322527 Transcript missense_variant 5320/21466 5182/21246 1728/7081 G/C Ggt/Tgt 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.03) 4/4 Pfam_domain:PF15804 MODERATE 1 SNV 3 1 PASS rs978110007 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 102745515 102745515 C A 1 0 0 0 0 1 0 0 0 2484 594 21 2 2 CCDC168 13 102745515 Missense_Mutation SNP C C3N-02089_T 3861697 102745515 11618813 723 27807 ERCC5 0 . GRCh38 13 102853811 102853811 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.319G>T p.Glu107Ter p.E107* ENST00000355739 3/15 179 163 16 193 192 1 strelka-varscan-mutect ERCC5,stop_gained,p.Glu107Ter,ENST00000355739,NM_000123.3;BIVM-ERCC5,stop_gained,p.Glu533Ter,ENST00000602836,NM_001204425.1;ERCC5,stop_gained,p.Glu107Ter,ENST00000535557,;ERCC5,3_prime_UTR_variant,,ENST00000472151,;ERCC5,non_coding_transcript_exon_variant,,ENST00000375958,; T ENST00000355739 Transcript stop_gained 1742/5082 319/3561 107/1186 E/* Gag/Tag 1 1 ERCC5 HGNC HGNC:3437 protein_coding YES CCDS32004.1 ENSP00000347978 P28715 UPI000006D0C3 NM_000123.3 3/15 Gene3D:3.40.50.1010,Prints_domain:PR00066,hmmpanther:PTHR16171,hmmpanther:PTHR16171:SF3,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00600 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 102853811 102853811 G T 1 0 0 0 0 0 1 0 0 5065 943 33 2 2 ERCC5 13 102853811 Nonsense_Mutation SNP G C3N-02089_T 108296 102853811 11510517 724 27808 MYO16 0 . GRCh38 13 109052334 109052334 + Silent SNP G G A novel C3N-02089_T C3N-02089_N G G c.2907G>A p.= p.Q969Q ENST00000457511 25/35 269 207 62 263 263 0 strelka-varscan-mutect MYO16,synonymous_variant,p.=,ENST00000457511,NM_001198950.1;MYO16,synonymous_variant,p.=,ENST00000356711,NM_015011.1;MYO16,synonymous_variant,p.=,ENST00000357550,;MYO16,downstream_gene_variant,,ENST00000251041,;MYO16,non_coding_transcript_exon_variant,,ENST00000375857,; A ENST00000457511 Transcript synonymous_variant 3529/7436 2907/5643 969/1880 Q caG/caA 1 1 MYO16 HGNC HGNC:29822 protein_coding YES CCDS73598.1 ENSP00000401633 F8W883 UPI00002375AE NM_001198950.1 25/35 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 109052334 109052334 G A 1 0 0 0 0 0 0 0 1 10065 1020 36 3 3 MYO16 13 109052334 Silent SNP G C3N-02089_T 6198523 109052334 5311994 725 27809 COL4A1 0 . GRCh38 13 110208859 110208859 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.683A>C p.Lys228Thr p.K228T ENST00000375820 12/52 335 285 50 386 384 2 strelka-varscan-mutect COL4A1,missense_variant,p.Lys228Thr,ENST00000375820,NM_001845.5;COL4A1,missense_variant,p.Lys228Thr,ENST00000543140,NM_001303110.1;COL4A1,missense_variant,p.Lys164Thr,ENST00000615732,; G ENST00000375820 Transcript missense_variant 805/6532 683/5010 228/1669 K/T aAa/aCa 1 -1 COL4A1 HGNC HGNC:2202 protein_coding YES CCDS9511.1 ENSP00000364979 P02462 UPI000004981D NM_001845.5 deleterious(0) 12/52 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 110208859 110208859 T G 1 0 0 0 0 1 0 0 0 3478 1841 64 5 5 COL4A1 13 110208859 Missense_Mutation SNP T C3N-02089_T 1156525 110208859 4155469 726 27810 ARHGEF7 0 . GRCh38 13 111303103 111303103 + Missense_Mutation SNP C C G C3N-02089_T C3N-02089_N C C c.2108C>G p.Thr703Ser p.T703S ENST00000218789 21/21 125 82 43 131 131 0 strelka-varscan-mutect ARHGEF7,missense_variant,p.Thr703Ser,ENST00000218789,;ARHGEF7,missense_variant,p.Thr644Ser,ENST00000375736,NM_003899.3;ARHGEF7,missense_variant,p.Thr644Ser,ENST00000426073,NM_001320851.1,NM_001320853.1,NM_001113513.1; G ENST00000218789 Transcript missense_variant 2605/5233 2108/2118 703/705 T/S aCc/aGc COSM3467279 1 1 ARHGEF7 HGNC HGNC:15607 protein_coding ENSP00000218789 B1ALK7 UPI000046FD82 tolerated(0.15) 21/21 Pfam_domain:PF16523,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF126 1 MODERATE SNV 5 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 111303103 111303103 C G 1 0 0 0 0 1 0 0 0 1047 507 18 4 4 ARHGEF7 13 111303103 Missense_Mutation SNP C C3N-02089_T 1094244 111303103 3061225 727 27811 OR4K1 0 . GRCh38 14 19935981 19935981 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.315C>A p.His105Gln p.H105Q ENST00000285600 1/1 159 118 41 187 187 0 strelka-varscan-mutect OR4K1,missense_variant,p.His105Gln,ENST00000285600,NM_001004063.2; A ENST00000285600 Transcript missense_variant 374/1076 315/936 105/311 H/Q caC/caA COSM1218664 1 1 OR4K1 HGNC HGNC:14726 protein_coding YES CCDS32025.1 ENSP00000285600 Q8NGD4 UPI0000041B4A NM_001004063.2 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF182,hmmpanther:PTHR26451,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 19935981 19935981 C A 1 0 0 0 0 1 0 0 0 11144 477 17 2 2 OR4K1 14 19935981 Missense_Mutation SNP C C3N-02089_T 19935981 87107737 728 27812 PRMT5 0 . GRCh38 14 22927562 22927562 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.414G>C p.Leu138Phe p.L138F ENST00000324366 4/17 188 138 50 221 221 0 strelka-varscan-mutect PRMT5,missense_variant,p.Leu138Phe,ENST00000324366,NM_006109.4;PRMT5,missense_variant,p.Leu121Phe,ENST00000397441,NM_001039619.2;PRMT5,missense_variant,p.Leu77Phe,ENST00000216350,NM_001282954.1,NM_001282953.1;PRMT5,missense_variant,p.Leu94Phe,ENST00000553897,NM_001282955.1;PRMT5,missense_variant,p.Leu39Phe,ENST00000555530,;PRMT5,missense_variant,p.Leu96Phe,ENST00000554910,;PRMT5,missense_variant,p.Leu100Phe,ENST00000556616,;PRMT5,missense_variant,p.Leu148Phe,ENST00000421938,;PRMT5,intron_variant,,ENST00000397440,NM_001282956.1;PRMT5,intron_variant,,ENST00000553550,;PRMT5,intron_variant,,ENST00000554867,;PRMT5,upstream_gene_variant,,ENST00000555454,;PRMT5,upstream_gene_variant,,ENST00000454731,;PRMT5,upstream_gene_variant,,ENST00000556043,;PRMT5,upstream_gene_variant,,ENST00000553502,;PRMT5,downstream_gene_variant,,ENST00000627278,;PRMT5-AS1,downstream_gene_variant,,ENST00000424245,;PRMT5-AS1,downstream_gene_variant,,ENST00000609885,;PRMT5-AS1,downstream_gene_variant,,ENST00000599580,;PRMT5-AS1,downstream_gene_variant,,ENST00000457443,;PRMT5-AS1,downstream_gene_variant,,ENST00000587245,;PRMT5-AS1,downstream_gene_variant,,ENST00000590290,;PRMT5-AS1,downstream_gene_variant,,ENST00000595662,;RP11-298I3.1,upstream_gene_variant,,ENST00000548322,;RP11-298I3.1,upstream_gene_variant,,ENST00000548819,;PRMT5,non_coding_transcript_exon_variant,,ENST00000553641,;PRMT5,intron_variant,,ENST00000554716,;PRMT5,upstream_gene_variant,,ENST00000476175,;PRMT5,downstream_gene_variant,,ENST00000556426,;PRMT5,3_prime_UTR_variant,,ENST00000553915,;PRMT5,3_prime_UTR_variant,,ENST00000557415,;PRMT5,3_prime_UTR_variant,,ENST00000553787,;PRMT5,non_coding_transcript_exon_variant,,ENST00000556032,;PRMT5,non_coding_transcript_exon_variant,,ENST00000553417,;PRMT5,downstream_gene_variant,,ENST00000557015,;PRMT5,upstream_gene_variant,,ENST00000557758,; G ENST00000324366 Transcript missense_variant 638/2531 414/1914 138/637 L/F ttG/ttC 1 -1 PRMT5 HGNC HGNC:10894 protein_coding YES CCDS9579.1 ENSP00000319169 O14744 UPI000006F09F NM_006109.4 deleterious(0.04) 4/17 hmmpanther:PTHR10738,PIRSF_domain:PIRSF015894 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 22927562 22927562 C G 1 0 0 0 0 1 0 0 0 12670 825 29 4 4 PRMT5 14 22927562 Missense_Mutation SNP C C3N-02089_T 2991581 22927562 84116156 729 27813 PSME2 0 . GRCh38 14 24143625 24143626 + Frame_Shift_Ins INS - - A novel C3N-02089_T C3N-02089_N - - c.598_599insT p.Gly200ValfsTer16 p.G200Vfs*16 ENST00000216802 10/11 185 148 37 215 215 0 sindel-varindel PSME2,frameshift_variant,p.Gly200ValfsTer16,ENST00000216802,NM_002818.2;PSME2,frameshift_variant,p.Gly215ValfsTer16,ENST00000615264,;PSME2,frameshift_variant,p.Gly189ValfsTer16,ENST00000560410,;RNF31,upstream_gene_variant,,ENST00000324103,NM_017999.4;RNF31,upstream_gene_variant,,ENST00000559275,NM_001310332.1;RNF31,upstream_gene_variant,,ENST00000560787,;PSME1,downstream_gene_variant,,ENST00000382708,NM_176783.2;PSME1,downstream_gene_variant,,ENST00000559123,;PSME1,downstream_gene_variant,,ENST00000206451,NM_001281529.1,NM_006263.3;EMC9,upstream_gene_variant,,ENST00000419198,;PSME1,downstream_gene_variant,,ENST00000561435,NM_001281528.1;RNF31,upstream_gene_variant,,ENST00000559533,;EMC9,upstream_gene_variant,,ENST00000560403,;EMC9,upstream_gene_variant,,ENST00000216799,NM_016049.3;RNF31,upstream_gene_variant,,ENST00000557991,;RNF31,upstream_gene_variant,,ENST00000560071,;RNF31,upstream_gene_variant,,ENST00000559308,;RNF31,upstream_gene_variant,,ENST00000559260,;RNF31,upstream_gene_variant,,ENST00000560875,;PSME2,downstream_gene_variant,,ENST00000559056,;PSME2,downstream_gene_variant,,ENST00000630027,;RP11-468E2.5,downstream_gene_variant,,ENST00000558478,;PSME2,upstream_gene_variant,,ENST00000620784,;PSME2,non_coding_transcript_exon_variant,,ENST00000471700,;EMC9,upstream_gene_variant,,ENST00000558200,;RNF31,upstream_gene_variant,,ENST00000557878,;RNF31,upstream_gene_variant,,ENST00000559438,;RNF31,upstream_gene_variant,,ENST00000559882,;RNF31,upstream_gene_variant,,ENST00000558634,;RNF31,upstream_gene_variant,,ENST00000559583,;PSME2,downstream_gene_variant,,ENST00000561103,;PSME2,downstream_gene_variant,,ENST00000559613,;PSME2,3_prime_UTR_variant,,ENST00000558273,;PSME2,3_prime_UTR_variant,,ENST00000560370,;PSME2,non_coding_transcript_exon_variant,,ENST00000558931,;PSME2,non_coding_transcript_exon_variant,,ENST00000559453,;PSME2,non_coding_transcript_exon_variant,,ENST00000559042,;PSME2,non_coding_transcript_exon_variant,,ENST00000559005,;RNF31,upstream_gene_variant,,ENST00000491351,;PSME1,downstream_gene_variant,,ENST00000560420,;RNF31,upstream_gene_variant,,ENST00000560342,;PSME1,downstream_gene_variant,,ENST00000561142,;PSME2,downstream_gene_variant,,ENST00000560788,;RNF31,upstream_gene_variant,,ENST00000558907,;EMC9,upstream_gene_variant,,ENST00000560600,;PSME1,downstream_gene_variant,,ENST00000559741,;PSME2,downstream_gene_variant,,ENST00000560592,;PSME2,downstream_gene_variant,,ENST00000559493,;PSME1,downstream_gene_variant,,ENST00000558112,;EMC9,upstream_gene_variant,,ENST00000558045,;EMC9,upstream_gene_variant,,ENST00000559101,;PSME2,downstream_gene_variant,,ENST00000559359,; A ENST00000216802 Transcript frameshift_variant 1238-1239/1404 598-599/720 200/239 G/VX ggg/gTgg 1 -1 PSME2 HGNC HGNC:9569 protein_coding YES CCDS9614.1 ENSP00000216802 Q9UL46 Q86SZ7 UPI000000CC17 NM_002818.2 10/11 Gene3D:1.20.120.180,Pfam_domain:PF02252,hmmpanther:PTHR10660,hmmpanther:PTHR10660:SF6,Superfamily_domains:SSF47216 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 90 24143625 24143625 - A 1 0 1 1 0 0 0 0 0 12858 623 22 0 0 PSME2 14 24143625 Frame_Shift_Ins INS - C3N-02089_T 1216063 24143625 82900093 730 27814 PRKD1 0 . GRCh38 14 29927380 29927380 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.133C>A p.Pro45Thr p.P45T ENST00000331968 1/18 163 128 35 167 166 1 strelka-varscan-mutect PRKD1,missense_variant,p.Pro45Thr,ENST00000331968,NM_002742.2;PRKD1,missense_variant,p.Pro45Thr,ENST00000616995,;PRKD1,missense_variant,p.Pro45Thr,ENST00000415220,;PRKD1,intron_variant,,ENST00000549503,; T ENST00000331968 Transcript missense_variant 363/3726 133/2739 45/912 P/T Ccg/Acg 1 -1 PRKD1 HGNC HGNC:9407 protein_coding YES CCDS9637.1 ENSP00000333568 Q15139 UPI0000456761 NM_002742.2 tolerated(0.08) 1/18 PIRSF_domain:PIRSF000552,hmmpanther:PTHR22968,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 29927380 29927380 G T 1 0 0 0 0 1 0 0 0 12651 1232 43 2 2 PRKD1 14 29927380 Missense_Mutation SNP G C3N-02089_T 5783755 29927380 77116338 731 27815 RALGAPA1 0 . GRCh38 14 35752054 35752054 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.772A>T p.Lys258Ter p.K258* ENST00000307138 8/40 103 73 30 167 167 0 strelka-varscan-mutect RALGAPA1,stop_gained,p.Lys258Ter,ENST00000637992,;RALGAPA1,stop_gained,p.Lys258Ter,ENST00000307138,NM_194301.2;RALGAPA1,stop_gained,p.Lys258Ter,ENST00000389698,NM_014990.1;RALGAPA1,stop_gained,p.Lys258Ter,ENST00000382366,NM_001283043.1;RALGAPA1,stop_gained,p.Lys258Ter,ENST00000553892,NM_001283044.1;SNORA31,upstream_gene_variant,,ENST00000517250,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554704,;RALGAPA1,intron_variant,,ENST00000555828,;RALGAPA1,non_coding_transcript_exon_variant,,ENST00000554652,;RALGAPA1,upstream_gene_variant,,ENST00000557104,; A ENST00000307138 Transcript stop_gained 1241/7911 772/6252 258/2083 K/* Aag/Tag 1 -1 RALGAPA1 HGNC HGNC:17770 protein_coding YES CCDS32064.1 ENSP00000302647 Q6GYQ0 UPI00003B5C51 NM_194301.2 8/40 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 35752054 35752054 T A 1 0 0 0 0 0 1 0 0 13172 1763 61 4 4 RALGAPA1 14 35752054 Nonsense_Mutation SNP T C3N-02089_T 5824674 35752054 71291664 732 27816 SLC25A21 0 . GRCh38 14 36711424 36711424 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.497A>T p.Gln166Leu p.Q166L ENST00000331299 7/10 188 172 16 196 196 0 strelka-varscan-mutect SLC25A21,missense_variant,p.Gln166Leu,ENST00000331299,NM_030631.3;SLC25A21,missense_variant,p.Gln166Leu,ENST00000555449,NM_001171170.1;SLC25A21,non_coding_transcript_exon_variant,,ENST00000556444,; A ENST00000331299 Transcript missense_variant 1013/2785 497/900 166/299 Q/L cAg/cTg 1 -1 SLC25A21 HGNC HGNC:14411 protein_coding YES CCDS9663.1 ENSP00000329452 Q9BQT8 UPI0000130BCE NM_030631.3 deleterious(0.04) 7/10 Superfamily_domains:0048588,Gene3D:1okcA00,Pfam_domain:PF00153,PROSITE_profiles:PS50920,hmmpanther:PTHR24089,hmmpanther:PTHR24089:SF390 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 36711424 36711424 T A 1 0 0 0 0 1 0 0 0 14749 1580 55 4 4 SLC25A21 14 36711424 Missense_Mutation SNP T C3N-02089_T 959370 36711424 70332294 733 27817 TRIM9 0 . GRCh38 14 51000803 51000803 + Silent SNP C C G novel C3N-02089_T C3N-02089_N C C c.1344G>C p.= p.L448L ENST00000298355 6/10 176 147 29 167 167 0 strelka-varscan-mutect TRIM9,synonymous_variant,p.=,ENST00000298355,NM_015163.5;TRIM9,synonymous_variant,p.=,ENST00000360392,NM_052978.4;TRIM9,synonymous_variant,p.=,ENST00000338969,; G ENST00000298355 Transcript synonymous_variant 2466/5284 1344/2133 448/710 L ctG/ctC 1 -1 TRIM9 HGNC HGNC:16288 protein_coding YES CCDS9703.1 ENSP00000298355 Q9C026 UPI000006D630 NM_015163.5 6/10 PROSITE_profiles:PS50853,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF400,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 51000803 51000803 C G 1 0 0 0 0 0 0 0 1 17046 581 21 4 4 TRIM9 14 51000803 Silent SNP C C3N-02089_T 14289379 51000803 56042915 734 27818 KIAA0586 0 . GRCh38 14 58465973 58465973 + Missense_Mutation SNP T T A rs752363556 C3N-02089_T C3N-02089_N T T c.2357T>A p.Met786Lys p.M786K ENST00000354386 17/34 163 154 9 150 150 0 strelka-varscan-mutect KIAA0586,missense_variant,p.Met718Lys,ENST00000619416,NM_001244190.1;KIAA0586,missense_variant,p.Met689Lys,ENST00000556134,;KIAA0586,missense_variant,p.Met648Lys,ENST00000619722,NM_001244191.1;KIAA0586,missense_variant,p.Met689Lys,ENST00000423743,NM_001244192.1;KIAA0586,missense_variant,p.Met786Lys,ENST00000354386,NM_001244189.1;KIAA0586,missense_variant,p.Met657Lys,ENST00000261244,NM_014749.3;KIAA0586,non_coding_transcript_exon_variant,,ENST00000538571,;HSBP1P1,downstream_gene_variant,,ENST00000555205,; A ENST00000354386 Transcript missense_variant 2601/5226 2357/4935 786/1644 M/K aTg/aAg rs752363556 1 1 KIAA0586 HGNC HGNC:19960 protein_coding YES CCDS58320.1 ENSP00000346359 Q9BVV6 UPI0001AE6998 NM_001244189.1 deleterious(0.01) 17/34 hmmpanther:PTHR15721:SF2,hmmpanther:PTHR15721,Pfam_domain:PF15324 MODERATE 1 SNV 2 1 PASS rs752363556 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 58465973 58465973 T A 1 0 0 0 0 1 0 0 0 8089 1464 51 4 4 KIAA0586 14 58465973 Missense_Mutation SNP T C3N-02089_T 7465170 58465973 48577745 735 27819 DPF3 0 . GRCh38 14 72892258 72892258 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.86T>C p.Leu29Pro p.L29P ENST00000610283 1/10 225 162 63 266 266 0 strelka-varscan-mutect DPF3,missense_variant,p.Leu29Pro,ENST00000610283,NM_001280544.1;DPF3,intron_variant,,ENST00000614862,NM_001280543.1;DPF3,intron_variant,,ENST00000541685,NM_012074.4;DPF3,intron_variant,,ENST00000546183,;DPF3,intron_variant,,ENST00000556509,NM_001280542.1;DPF3,missense_variant,p.Leu29Pro,ENST00000366353,;DPF3,intron_variant,,ENST00000381216,; G ENST00000610283 Transcript missense_variant 392/4520 86/1239 29/412 L/P cTa/cCa 1 -1 DPF3 HGNC HGNC:17427 protein_coding YES CCDS61496.1 ENSP00000479526 F8W7T1 UPI00020659D3 NM_001280544.1 deleterious_low_confidence(0.01) 1/10 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 72892258 72892258 A G 1 0 0 0 0 1 0 0 0 4532 420 15 5 5 DPF3 14 72892258 Missense_Mutation SNP A C3N-02089_T 14426285 72892258 34151460 736 27820 DNAL1 0 . GRCh38 14 73687323 73687323 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.329G>T p.Gly110Val p.G110V ENST00000553645 6/8 115 100 15 133 133 0 strelka-varscan-mutect DNAL1,missense_variant,p.Gly110Val,ENST00000553645,NM_031427.3;DNAL1,missense_variant,p.Gly71Val,ENST00000554871,NM_001201366.1;DNAL1,missense_variant,p.Gly71Val,ENST00000555631,;DNAL1,missense_variant,p.Gly23Val,ENST00000554339,;DNAL1,5_prime_UTR_variant,,ENST00000311089,;DNAL1,5_prime_UTR_variant,,ENST00000559993,;DNAL1,5_prime_UTR_variant,,ENST00000554113,;DNAL1,downstream_gene_variant,,ENST00000555919,;DNAL1,3_prime_UTR_variant,,ENST00000554159,; T ENST00000553645 Transcript missense_variant 370/8404 329/573 110/190 G/V gGg/gTg 1 1 DNAL1 HGNC HGNC:23247 protein_coding YES CCDS45134.1 ENSP00000452037 Q4LDG9 UPI000004470E NM_031427.3 deleterious(0) 6/8 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24365,SMART_domains:SM00365,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -19.99942 0.9994114 1 1 1 0 T 3 4 90 73687323 73687323 G T 1 0 0 0 0 1 0 0 0 4470 1232 43 2 2 DNAL1 14 73687323 Missense_Mutation SNP G C3N-02089_T 795065 73687323 33356395 737 27821 RPS6KL1 0 . GRCh38 14 74911813 74911813 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.512G>T p.Gly171Val p.G171V ENST00000354625 5/11 192 154 38 177 177 0 strelka-varscan-mutect RPS6KL1,missense_variant,p.Gly171Val,ENST00000354625,NM_031464.4;RPS6KL1,missense_variant,p.Gly171Val,ENST00000555647,;RPS6KL1,missense_variant,p.Gly171Val,ENST00000557413,;RPS6KL1,upstream_gene_variant,,ENST00000556848,;RPS6KL1,upstream_gene_variant,,ENST00000555910,;RPS6KL1,upstream_gene_variant,,ENST00000553315,;RPS6KL1,upstream_gene_variant,,ENST00000553789,;RPS6KL1,upstream_gene_variant,,ENST00000553971,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000554900,;RPS6KL1,missense_variant,p.Gly140Val,ENST00000555009,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000555834,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000553894,;RPS6KL1,non_coding_transcript_exon_variant,,ENST00000554834,;RPS6KL1,upstream_gene_variant,,ENST00000553646,; A ENST00000354625 Transcript missense_variant 997/5195 512/1650 171/549 G/V gGa/gTa 1 -1 RPS6KL1 HGNC HGNC:20222 protein_coding YES CCDS9834.2 ENSP00000346644 Q9Y6S9 UPI0000035B53 NM_031464.4 deleterious(0.01) 5/11 PROSITE_profiles:PS50011,hmmpanther:PTHR15508,Gene3D:3.30.200.20,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 74911813 74911813 C A 1 0 0 0 0 1 0 0 0 13914 855 30 2 2 RPS6KL1 14 74911813 Missense_Mutation SNP C C3N-02089_T 1224490 74911813 32131905 738 27822 NRXN3 0 . GRCh38 14 78645381 78645381 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.1013A>C p.Asn338Thr p.N338T ENST00000634499 5/20 62 50 12 74 73 1 strelka-varscan-mutect NRXN3,missense_variant,p.Asn338Thr,ENST00000634499,;NRXN3,missense_variant,p.Asn340Thr,ENST00000635466,;NRXN3,missense_variant,p.Asn101Thr,ENST00000335750,;NRXN3,missense_variant,p.Asn105Thr,ENST00000553363,;NRXN3,5_prime_UTR_variant,,ENST00000554719,NM_004796.5;NRXN3,intron_variant,,ENST00000553631,;NRXN3,non_coding_transcript_exon_variant,,ENST00000634266,;NRXN3,missense_variant,p.Asn338Thr,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556088,; C ENST00000634499 Transcript missense_variant 2018/6069 1013/4995 338/1664 N/T aAc/aCc 1 1 NRXN3 HGNC HGNC:8010 protein_coding ENSP00000488920 A0A0U1RQC5 UPI000719A152 5/20 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF405,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE SNV 5 1 PASS . . 0 201 9 0 0 0 0 0 -20 0.9999962 1 1 1 0 C 3 2 90 78645381 78645381 A C 1 0 0 0 0 1 0 0 0 10726 43 2 5 5 NRXN3 14 78645381 Missense_Mutation SNP A C3N-02089_T 3733568 78645381 28398337 739 27823 SEL1L 0 . GRCh38 14 81484303 81484303 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1968G>T p.= p.L656L ENST00000336735 19/21 145 120 25 160 160 0 strelka-varscan-mutect SEL1L,synonymous_variant,p.=,ENST00000336735,NM_005065.5;SEL1L,non_coding_transcript_exon_variant,,ENST00000554293,;SEL1L,downstream_gene_variant,,ENST00000555923,; A ENST00000336735 Transcript synonymous_variant 2085/7925 1968/2385 656/794 L ctG/ctT 1 -1 SEL1L HGNC HGNC:10717 protein_coding YES CCDS9876.1 ENSP00000337053 Q9UBV2 UPI0000135746 NM_005065.5 19/21 Gene3D:1.25.40.10,Pfam_domain:PF08238,hmmpanther:PTHR11102,hmmpanther:PTHR11102:SF70,SMART_domains:SM00671,Superfamily_domains:SSF81901 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 81484303 81484303 C A 1 0 0 0 0 0 0 0 1 14287 581 21 2 2 SEL1L 14 81484303 Silent SNP C C3N-02089_T 2838922 81484303 25559415 740 27824 UNC79 0 . GRCh38 14 93542568 93542568 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.1096G>A p.Asp366Asn p.D366N ENST00000256339 14/50 333 245 88 340 340 0 strelka-varscan-mutect UNC79,missense_variant,p.Asp543Asn,ENST00000553484,;UNC79,missense_variant,p.Asp543Asn,ENST00000555664,;UNC79,missense_variant,p.Asp366Asn,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Asp543Asn,ENST00000393151,;UNC79,missense_variant,p.Asp366Asn,ENST00000621021,; A ENST00000256339 Transcript missense_variant 1751/8400 1096/7377 366/2458 D/N Gat/Aat COSM4053132,COSM4053133 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious(0.03) 14/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696,Pfam_domain:PF14776 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 93542568 93542568 G A 1 0 0 0 0 1 0 0 0 17520 1290 45 3 3 UNC79 14 93542568 Missense_Mutation SNP G C3N-02089_T 12058265 93542568 13501150 741 27825 LINC00521 0 . GRCh38 14 94003352 94003352 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.496A>C p.Asn166His p.N166H ENST00000636493 5/7 116 106 10 95 95 0 strelka-varscan-mutect LINC00521,missense_variant,p.Asn166His,ENST00000636493,;LINC00521,downstream_gene_variant,,ENST00000449472,;LINC00521,downstream_gene_variant,,ENST00000455802,;LINC00521,splice_region_variant,,ENST00000444118,;LINC00521,splice_region_variant,,ENST00000359253,; C ENST00000636493 Transcript missense_variant,splice_region_variant 905/1279 496/819 166/272 N/H Aat/Cat 1 1 LINC00521 HGNC HGNC:19860 protein_coding YES ENSP00000490086 UPI0000EE335E tolerated(0.18) 5/7 hmmpanther:PTHR21683,hmmpanther:PTHR21683:SF10 MODERATE 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -19.60213 1 1 1 1 0 C 3 2 90 94003352 94003352 A C 1 0 0 0 0 1 0 0 0 8726 376 13 5 5 LINC00521 14 94003352 Missense_Mutation SNP A C3N-02089_T 460784 94003352 13040366 742 27826 DYNC1H1 0 . GRCh38 14 101997041 101997041 + Missense_Mutation SNP C C T rs774198261 C3N-02089_T C3N-02089_N C C c.3571C>T p.Arg1191Cys p.R1191C ENST00000360184 16/78 241 167 74 312 312 0 strelka-varscan-mutect DYNC1H1,missense_variant,p.Arg1191Cys,ENST00000360184,NM_001376.4; T ENST00000360184 Transcript missense_variant 3735/14333 3571/13941 1191/4646 R/C Cgc/Tgc rs774198261,COSM953452 1 1 DYNC1H1 HGNC HGNC:2961 protein_coding YES CCDS9966.1 ENSP00000348965 Q14204 UPI00001B515A NM_001376.4 deleterious(0) 16/78 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF28 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774198261 . 0 208 0 0 2 0 0 0 -20 0.999153 1 1 1 0 T 3 4 90 101997041 101997041 C T 1 0 0 0 0 1 0 0 0 4665 652 23 1 1 DYNC1H1 14 101997041 Missense_Mutation SNP C C3N-02089_T 7993689 101997041 5046677 743 27827 RP11-294C11.1 0 . GRCh38 15 21638766 21638766 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.762delG p.Pro255HisfsTer15 p.P255Hfs*15 ENST00000332663 1/1 43 30 13 56 56 0 sindel-varindel-pindel RP11-294C11.1,frameshift_variant,p.Pro255HisfsTer15,ENST00000332663,;RP11-983G14.1,intron_variant,,ENST00000628444,;RP11-983G14.1,intron_variant,,ENST00000625989,; - ENST00000332663 Transcript frameshift_variant 858/1084 760/942 254/313 G/X Ggg/gg 1 1 RP11-294C11.1 Clone_based_vega_gene protein_coding YES ENSP00000329467 A0A0X1KG70 UPI0004E4CC2D 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF53,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH deletion 2 1 PASS . . 30 179 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 21638766 21638766 G - 1 0 1 0 1 0 0 0 0 13726 1348 47 0 0 RP11-294C11.1 15 21638766 Frame_Shift_Del DEL G C3N-02089_T 21638766 80352423 744 27828 RP11-294C11.3 0 . GRCh38 15 21652590 21652590 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.656C>T p.Ala219Val p.A219V ENST00000623441 1/1 36 16 20 27 27 0 strelka-varscan-mutect RP11-294C11.3,missense_variant,p.Ala219Val,ENST00000623441,;RP11-294C11.3,missense_variant,p.Ala114Val,ENST00000629333,;RP11-983G14.1,non_coding_transcript_exon_variant,,ENST00000628444,; T ENST00000623441 Transcript missense_variant 747/1125 656/951 219/316 A/V gCa/gTa 1 1 RP11-294C11.3 Clone_based_vega_gene protein_coding YES ENSP00000485668 A0A096LPK9 UPI000514C5E0 tolerated(0.42) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF97,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS . . 48 159 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 21652590 21652590 C T 1 0 0 0 0 1 0 0 0 13727 710 25 3 3 RP11-294C11.3 15 21652590 Missense_Mutation SNP C C3N-02089_T 13824 21652590 80338599 745 27829 NPAP1 0 . GRCh38 15 24679086 24679086 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.3219T>A p.= p.A1073A ENST00000329468 1/1 204 137 67 235 235 0 strelka-varscan-mutect NPAP1,synonymous_variant,p.=,ENST00000329468,NM_018958.2; A ENST00000329468 Transcript synonymous_variant 3219/7526 3219/3471 1073/1156 A gcT/gcA 1 1 NPAP1 HGNC HGNC:1190 protein_coding YES CCDS10015.1 ENSP00000333735 Q9NZP6 UPI00001AFA1B NM_018958.2 1/1 hmmpanther:PTHR23193:SF15,hmmpanther:PTHR23193 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 24679086 24679086 T A 1 0 0 0 0 0 0 0 1 10609 1509 53 4 4 NPAP1 15 24679086 Silent SNP T C3N-02089_T 3026496 24679086 77312103 746 27830 AC124312.1 0 . GRCh38 15 25092308 25092308 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.70C>A p.His24Asn p.H24N ENST00000623624 1/1 193 144 49 209 207 2 strelka-varscan-mutect AC124312.1,missense_variant,p.His24Asn,ENST00000623624,;RP11-701H24.4,downstream_gene_variant,,ENST00000567527,;SNORD116-22,downstream_gene_variant,,ENST00000384430,;SNORD116-21,downstream_gene_variant,,ENST00000384507,;SNORD116-20,downstream_gene_variant,,ENST00000384529,;SNORD116-24,upstream_gene_variant,,ENST00000384549,;SNORD116-23,downstream_gene_variant,,ENST00000384645,;SNHG14,intron_variant,,ENST00000546682,;SNHG14,intron_variant,,ENST00000549804,;SNHG14,intron_variant,,ENST00000553108,; T ENST00000623624 Transcript missense_variant 70/418 70/417 24/138 H/N Cac/Aac 1 -1 AC124312.1 Clone_based_ensembl_gene protein_coding YES ENSP00000485422 A0A0B4J2H5 UPI000006F2CD 1/1 MODERATE SNV 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 25092308 25092308 G T 1 0 0 0 0 1 0 0 0 141 1348 47 2 2 AC124312.1 15 25092308 Missense_Mutation SNP G C3N-02089_T 413222 25092308 76898881 747 27831 HERC2 0 . GRCh38 15 28218639 28218639 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.5878A>T p.Thr1960Ser p.T1960S ENST00000261609 38/93 202 150 52 277 275 2 strelka-varscan-mutect HERC2,missense_variant,p.Thr1960Ser,ENST00000261609,NM_004667.5;HERC2,downstream_gene_variant,,ENST00000569335,; A ENST00000261609 Transcript missense_variant 5987/15337 5878/14505 1960/4834 T/S Act/Tct 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 tolerated(0.15) 38/93 MODERATE 1 SNV 1 1 PASS rs1300808716 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 28218639 28218639 T A 1 0 0 0 0 1 0 0 0 6942 1696 59 4 4 HERC2 15 28218639 Missense_Mutation SNP T C3N-02089_T 3126331 28218639 73772550 748 27832 FAM189A1 0 . GRCh38 15 29137156 29137156 + Frame_Shift_Del DEL G G - rs764555440 C3N-02089_T C3N-02089_N G G c.669delC p.Cys223TrpfsTer2 p.C223Wfs*2 ENST00000261275 6/11 154 121 33 182 182 0 sindel-varindel-pindel FAM189A1,frameshift_variant,p.Cys223TrpfsTer2,ENST00000261275,NM_015307.1;FAM189A1,non_coding_transcript_exon_variant,,ENST00000560021,; - ENST00000261275 Transcript frameshift_variant 669/4705 669/1620 223/539 C/X tgC/tg rs764555440 1 -1 FAM189A1 HGNC HGNC:29075 protein_coding YES CCDS45198.1 ENSP00000261275 O60320 UPI0001641C10 NM_015307.1 6/11 hmmpanther:PTHR17615,hmmpanther:PTHR17615:SF6 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 29137156 29137156 G - 1 0 1 0 1 0 0 0 0 5367 1079 38 0 0 FAM189A1 15 29137156 Frame_Shift_Del DEL G C3N-02089_T 918517 29137156 72854033 749 27833 FAN1 0 . GRCh38 15 30905419 30905419 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.756C>A p.= p.A252A ENST00000362065 2/15 224 201 23 260 258 2 strelka-varscan-mutect FAN1,synonymous_variant,p.=,ENST00000362065,NM_014967.4;FAN1,synonymous_variant,p.=,ENST00000561594,NM_001146095.1;FAN1,synonymous_variant,p.=,ENST00000561607,NM_001146094.1,NM_001146096.1;FAN1,synonymous_variant,p.=,ENST00000565466,;FAN1,intron_variant,,ENST00000562892,;FAN1,synonymous_variant,p.=,ENST00000565280,; A ENST00000362065 Transcript synonymous_variant 1047/4891 756/3054 252/1017 A gcC/gcA 1 1 FAN1 HGNC HGNC:29170 protein_coding YES CCDS32186.1 ENSP00000354497 Q9Y2M0 UPI000006D713 NM_014967.4 2/15 hmmpanther:PTHR15749:SF4,hmmpanther:PTHR15749 LOW 1 SNV 1 1 PASS rs1401385961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 30905419 30905419 C A 1 0 0 0 0 0 0 0 1 5520 610 22 2 2 FAN1 15 30905419 Silent SNP C C3N-02089_T 1768263 30905419 71085770 750 27834 RYR3 0 . GRCh38 15 33633064 33633064 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2983G>T p.Ala995Ser p.A995S ENST00000634891 24/104 147 120 27 154 154 0 strelka-varscan-mutect RYR3,missense_variant,p.Ala995Ser,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Ala995Ser,ENST00000622037,;RYR3,missense_variant,p.Ala995Ser,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Ala995Ser,ENST00000389232,;RYR3,missense_variant,p.Ala995Ser,ENST00000634418,;RYR3,downstream_gene_variant,,ENST00000636753,; T ENST00000634891 Transcript missense_variant 3084/15591 2983/14613 995/4870 A/S Gca/Tca 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0.01) 24/104 Pfam_domain:PF02026,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 33633064 33633064 G T 1 0 0 0 0 1 0 0 0 14030 1203 42 2 2 RYR3 15 33633064 Missense_Mutation SNP G C3N-02089_T 2727645 33633064 68358125 751 27835 RYR3 0 . GRCh38 15 33635747 33635747 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.3309G>T p.Trp1103Cys p.W1103C ENST00000634891 26/104 344 243 101 373 371 2 strelka-varscan-mutect RYR3,missense_variant,p.Trp1103Cys,ENST00000634891,NM_001036.4;RYR3,missense_variant,p.Trp1103Cys,ENST00000622037,;RYR3,missense_variant,p.Trp1103Cys,ENST00000415757,NM_001243996.2;RYR3,missense_variant,p.Trp1103Cys,ENST00000389232,;RYR3,missense_variant,p.Trp1103Cys,ENST00000634418,; T ENST00000634891 Transcript missense_variant 3410/15591 3309/14613 1103/4870 W/C tgG/tgT 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 deleterious(0) 26/104 Pfam_domain:PF00622,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 33635747 33635747 G T 1 0 0 0 0 1 0 0 0 14030 1241 43 2 2 RYR3 15 33635747 Missense_Mutation SNP G C3N-02089_T 2683 33635747 68355442 752 27836 PAK6 0 . GRCh38 15 40266486 40266486 + Silent SNP A A T novel C3N-02089_T C3N-02089_N A A c.849A>T p.= p.P283P ENST00000560346 5/11 41 36 5 41 41 0 strelka-varscan-mutect PAK6,synonymous_variant,p.=,ENST00000455577,NM_001276718.1;PAK6,synonymous_variant,p.=,ENST00000560346,;PAK6,synonymous_variant,p.=,ENST00000260404,NM_020168.5;BUB1B-PAK6,synonymous_variant,p.=,ENST00000441369,NM_001128628.2;PAK6,synonymous_variant,p.=,ENST00000542403,NM_001128629.2,NM_001276717.1;PAK6,synonymous_variant,p.=,ENST00000560669,;PAK6,downstream_gene_variant,,ENST00000561230,;PAK6,downstream_gene_variant,,ENST00000559617,;PAK6,downstream_gene_variant,,ENST00000559139,;PAK6,downstream_gene_variant,,ENST00000560684,;PAK6,downstream_gene_variant,,ENST00000558055,;PAK6,downstream_gene_variant,,ENST00000560806,;PAK6,downstream_gene_variant,,ENST00000558106,;PAK6,downstream_gene_variant,,ENST00000558878,;PAK6,downstream_gene_variant,,ENST00000558183,;PAK6,non_coding_transcript_exon_variant,,ENST00000559901,;PAK6,upstream_gene_variant,,ENST00000557926,;BUB1B-PAK6,3_prime_UTR_variant,,ENST00000558658,;BUB1B-PAK6,3_prime_UTR_variant,,ENST00000453867,;BUB1B-PAK6,downstream_gene_variant,,ENST00000559435,; T ENST00000560346 Transcript synonymous_variant 1432/4020 849/2046 283/681 P ccA/ccT 1 1 PAK6 HGNC HGNC:16061 protein_coding YES CCDS10054.1 ENSP00000453858 Q9NQU5 A0A024R9Q4 UPI0000001C3B 5/11 Low_complexity_(Seg):seg,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF182,Gene3D:3.30.200.20 LOW SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -12.91684 1 1 1 1 0 T 2 4 90 40266486 40266486 A T 1 0 0 0 0 0 0 0 1 11484 146 6 4 4 PAK6 15 40266486 Silent SNP A C3N-02089_T 6630739 40266486 61724703 753 27837 PAK6 0 . GRCh38 15 40273353 40273353 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1498G>T p.Glu500Ter p.E500* ENST00000560346 8/11 96 66 30 108 108 0 strelka-varscan-mutect PAK6,stop_gained,p.Glu500Ter,ENST00000455577,NM_001276718.1;PAK6,stop_gained,p.Glu500Ter,ENST00000560346,;PAK6,stop_gained,p.Glu500Ter,ENST00000260404,NM_020168.5;BUB1B-PAK6,stop_gained,p.Glu500Ter,ENST00000441369,NM_001128628.2;PAK6,stop_gained,p.Glu500Ter,ENST00000542403,NM_001128629.2,NM_001276717.1;PAK6,downstream_gene_variant,,ENST00000557926,;BUB1B-PAK6,3_prime_UTR_variant,,ENST00000558658,;BUB1B-PAK6,3_prime_UTR_variant,,ENST00000453867,;PAK6,upstream_gene_variant,,ENST00000557808,;PLCB2,downstream_gene_variant,,ENST00000560009,; T ENST00000560346 Transcript stop_gained 2081/4020 1498/2046 500/681 E/* Gag/Tag 1 1 PAK6 HGNC HGNC:16061 protein_coding YES CCDS10054.1 ENSP00000453858 Q9NQU5 A0A024R9Q4 UPI0000001C3B 8/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF182,Gene3D:3.30.200.20,Pfam_domain:PF00069,Superfamily_domains:SSF56112 HIGH SNV 5 1 PASS rs1293198742 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 40273353 40273353 G T 1 0 0 0 0 0 1 0 0 11484 1291 45 2 2 PAK6 15 40273353 Nonsense_Mutation SNP G C3N-02089_T 6867 40273353 61717836 754 27838 STARD9 0 . GRCh38 15 42689228 42689228 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.7650C>A p.= p.A2550A ENST00000290607 23/33 236 163 73 244 243 1 strelka-varscan-mutect STARD9,synonymous_variant,p.=,ENST00000290607,NM_020759.2;STARD9,upstream_gene_variant,,ENST00000562619,; A ENST00000290607 Transcript synonymous_variant 7707/15567 7650/14103 2550/4700 A gcC/gcA 1 1 STARD9 HGNC HGNC:19162 protein_coding YES CCDS53935.1 ENSP00000290607 Q9P2P6 UPI0001BE8155 NM_020759.2 23/33 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 42689228 42689228 C A 1 0 0 0 0 0 0 0 1 15639 581 21 2 2 STARD9 15 42689228 Silent SNP C C3N-02089_T 2415875 42689228 59301961 755 27839 TGM5 0 . GRCh38 15 43253557 43253557 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.633C>G p.Asp211Glu p.D211E ENST00000220420 5/13 418 303 115 409 409 0 strelka-varscan-mutect TGM5,missense_variant,p.Asp211Glu,ENST00000220420,NM_201631.3;TGM5,missense_variant,p.Asp210Glu,ENST00000610827,;TGM5,missense_variant,p.Asp128Glu,ENST00000611276,;TGM5,missense_variant,p.Asp212Glu,ENST00000622115,;TGM5,missense_variant,p.Asp129Glu,ENST00000349114,NM_004245.3;TGM5,non_coding_transcript_exon_variant,,ENST00000635871,; C ENST00000220420 Transcript missense_variant 641/2767 633/2163 211/720 D/E gaC/gaG 1 -1 TGM5 HGNC HGNC:11781 protein_coding YES CCDS32212.1 ENSP00000220420 O43548 UPI0000136CCF NM_201631.3 deleterious(0) 5/13 Gene3D:1ex0A02,PIRSF_domain:PIRSF000459,hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF38,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 43253557 43253557 G C 1 0 0 0 0 1 0 0 0 16266 1020 36 4 4 TGM5 15 43253557 Missense_Mutation SNP G C3N-02089_T 564329 43253557 58737632 756 27840 CKMT1B 0 . GRCh38 15 43599224 43599224 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1205G>C p.Arg402Thr p.R402T ENST00000300283 10/10 149 125 24 148 148 0 strelka-varscan-mutect CKMT1B,missense_variant,p.Arg402Thr,ENST00000300283,NM_020990.3;CKMT1B,missense_variant,p.Arg402Thr,ENST00000441322,;STRC,downstream_gene_variant,,ENST00000450892,NM_153700.2;STRC,downstream_gene_variant,,ENST00000541030,;CKMT1B,downstream_gene_variant,,ENST00000453782,;CKMT1B,downstream_gene_variant,,ENST00000627381,;CKMT1B,downstream_gene_variant,,ENST00000453733,;CKMT1B,downstream_gene_variant,,ENST00000437924,;CKMT1B,downstream_gene_variant,,ENST00000417289,;CKMT1B,downstream_gene_variant,,ENST00000449946,;RNU6-554P,upstream_gene_variant,,ENST00000410466,;CKMT1B,downstream_gene_variant,,ENST00000481666,;CKMT1B,downstream_gene_variant,,ENST00000498538,;CKMT1B,downstream_gene_variant,,ENST00000495545,;CKMT1B,upstream_gene_variant,,ENST00000411560,;CKMT1B,3_prime_UTR_variant,,ENST00000437534,;STRC,downstream_gene_variant,,ENST00000428650,;STRC,downstream_gene_variant,,ENST00000440125,;STRC,downstream_gene_variant,,ENST00000485556,;STRC,downstream_gene_variant,,ENST00000471703,;STRC,downstream_gene_variant,,ENST00000448437,;CKMT1B,downstream_gene_variant,,ENST00000475589,;CKMT1B,downstream_gene_variant,,ENST00000428981,;STRC,downstream_gene_variant,,ENST00000460952,;STRC,downstream_gene_variant,,ENST00000493750,; C ENST00000300283 Transcript missense_variant 1597/1779 1205/1254 402/417 R/T aGa/aCa 1 1 CKMT1B HGNC HGNC:1995 protein_coding YES CCDS10097.1 ENSP00000300283 P12532 UPI000012DCCE NM_020990.3 deleterious(0.03) 10/10 hmmpanther:PTHR11547,hmmpanther:PTHR11547:SF24,Superfamily_domains:SSF55931 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 43599224 43599224 G C 1 0 0 0 0 1 0 0 0 3213 942 33 4 4 CKMT1B 15 43599224 Missense_Mutation SNP G C3N-02089_T 345667 43599224 58391965 757 27841 EIF3J 0 . GRCh38 15 44551516 44551516 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.288A>C p.Lys96Asn p.K96N ENST00000261868 4/8 94 77 17 114 114 0 strelka-varscan-mutect EIF3J,missense_variant,p.Lys96Asn,ENST00000261868,NM_003758.3;EIF3J,missense_variant,p.Lys96Asn,ENST00000535391,NM_001284335.1;EIF3J,intron_variant,,ENST00000424492,NM_001284336.1;EIF3J,upstream_gene_variant,,ENST00000536248,;EIF3J,non_coding_transcript_exon_variant,,ENST00000558053,;EIF3J,non_coding_transcript_exon_variant,,ENST00000558227,; C ENST00000261868 Transcript missense_variant 426/2569 288/777 96/258 K/N aaA/aaC 1 1 EIF3J HGNC HGNC:3270 protein_coding YES CCDS10111.1 ENSP00000261868 O75822 A0A024R5S5 UPI000012D2F9 NM_003758.3 tolerated(0.06) 4/8 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,HAMAP:MF_03009,hmmpanther:PTHR21681,Pfam_domain:PF08597 MODERATE 1 SNV 1 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 44551516 44551516 A C 1 0 0 0 0 1 0 0 0 4854 11 1 5 5 EIF3J 15 44551516 Missense_Mutation SNP A C3N-02089_T 952292 44551516 57439673 758 27842 SLC12A1 0 . GRCh38 15 48269687 48269687 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2325C>A p.Asn775Lys p.N775K ENST00000396577 19/27 135 109 26 160 160 0 strelka-varscan-mutect SLC12A1,missense_variant,p.Asn775Lys,ENST00000396577,NM_001184832.1;SLC12A1,missense_variant,p.Asn775Lys,ENST00000380993,NM_000338.2;SLC12A1,missense_variant,p.Asn775Lys,ENST00000558405,;SLC12A1,missense_variant,p.Asn588Lys,ENST00000559641,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000560692,;SLC12A1,non_coding_transcript_exon_variant,,ENST00000558252,; A ENST00000396577 Transcript missense_variant 2540/4708 2325/3300 775/1099 N/K aaC/aaA 1 1 SLC12A1 HGNC HGNC:10910 protein_coding YES CCDS53940.1 ENSP00000379822 Q13621 UPI000013C794 NM_001184832.1 deleterious(0) 19/27 hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF45,TIGRFAM_domain:TIGR00930,Pfam_domain:PF03522 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 48269687 48269687 C A 1 0 0 0 0 1 0 0 0 14647 477 17 2 2 SLC12A1 15 48269687 Missense_Mutation SNP C C3N-02089_T 3718171 48269687 53721502 759 27843 TNFAIP8L3 0 . GRCh38 15 51058021 51058021 + Missense_Mutation SNP C C G rs200106121 C3N-02089_T C3N-02089_N C C c.739G>C p.Gly247Arg p.G247R ENST00000327536 3/3 156 134 22 172 172 0 strelka-varscan-mutect TNFAIP8L3,missense_variant,p.Gly247Arg,ENST00000327536,NM_207381.3;TNFAIP8L3,missense_variant,p.Gly159Arg,ENST00000637513,NM_001311175.1;RP11-108K3.1,intron_variant,,ENST00000559909,; G ENST00000327536 Transcript missense_variant 839/2262 739/879 247/292 G/R Ggg/Cgg rs200106121 1 -1 TNFAIP8L3 HGNC HGNC:20620 protein_coding YES CCDS32241.1 ENSP00000328016 Q5GJ75 UPI00004C7A8B NM_207381.3 deleterious(0.03) 3/3 Pfam_domain:PF05527,hmmpanther:PTHR12757,hmmpanther:PTHR12757:SF5 MODERATE 1 SNV 1 1 PASS rs200106121 . 0 205 0 2 0 0 0 2 -3.491492 0 0 1 0 0 G 3 3 90 51058021 51058021 C G 1 0 0 0 0 1 0 0 0 16753 652 23 4 4 TNFAIP8L3 15 51058021 Missense_Mutation SNP C C3N-02089_T 2788334 51058021 50933168 760 27844 LEO1 0 . GRCh38 15 51949814 51949815 + Frame_Shift_Ins INS - - A novel C3N-02089_T C3N-02089_N - - c.1791_1792insT p.Ile598TyrfsTer14 p.I598Yfs*14 ENST00000299601 10/12 86 75 11 102 102 0 sindel-varindel-pindel LEO1,frameshift_variant,p.Ile598TyrfsTer14,ENST00000299601,NM_001323904.1,NM_138792.3;LEO1,frameshift_variant,p.Ile538TyrfsTer14,ENST00000315141,NM_001286430.1;MAPK6,upstream_gene_variant,,ENST00000560802,;TMOD3,downstream_gene_variant,,ENST00000558714,;TMOD3,downstream_gene_variant,,ENST00000561408,;TMOD3,downstream_gene_variant,,ENST00000558300,;TMOD3,downstream_gene_variant,,ENST00000559202,;LEO1,downstream_gene_variant,,ENST00000558949,; A ENST00000299601 Transcript frameshift_variant 1852-1853/2193 1791-1792/2001 597-598/666 -/X -/T 1 -1 LEO1 HGNC HGNC:30401 protein_coding YES CCDS10146.1 ENSP00000299601 Q8WVC0 UPI0000071CA0 NM_001323904.1,NM_138792.3 10/12 hmmpanther:PTHR23146:SF0,hmmpanther:PTHR23146 HIGH 1 insertion 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.9999 1 1 1 1 0 A 7 5 90 51949814 51949814 - A 1 0 1 1 0 0 0 0 0 8634 1464 51 0 0 LEO1 15 51949814 Frame_Shift_Ins INS - C3N-02089_T 891793 51949814 50041375 761 27845 LEO1 0 . GRCh38 15 51958755 51958755 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1232G>A p.Arg411Lys p.R411K ENST00000299601 6/12 125 109 16 202 202 0 strelka-varscan-mutect LEO1,missense_variant,p.Arg411Lys,ENST00000299601,NM_001323904.1,NM_138792.3;LEO1,intron_variant,,ENST00000315141,NM_001286430.1;MAPK6,intron_variant,,ENST00000560802,;LEO1,upstream_gene_variant,,ENST00000558949,; T ENST00000299601 Transcript missense_variant 1293/2193 1232/2001 411/666 R/K aGg/aAg 1 -1 LEO1 HGNC HGNC:30401 protein_coding YES CCDS10146.1 ENSP00000299601 Q8WVC0 UPI0000071CA0 NM_001323904.1,NM_138792.3 tolerated(0.06) 6/12 hmmpanther:PTHR23146:SF0,hmmpanther:PTHR23146,Pfam_domain:PF04004 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 51958755 51958755 C T 1 0 0 0 0 1 0 0 0 8634 681 24 3 3 LEO1 15 51958755 Missense_Mutation SNP C C3N-02089_T 8941 51958755 50032434 762 27846 RFX7 0 . GRCh38 15 56094152 56094152 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.3285T>G p.Asn1095Lys p.N1095K ENST00000559447 9/9 204 175 29 235 235 0 strelka-varscan-mutect RFX7,missense_variant,p.Asn1095Lys,ENST00000559447,NM_022841.5;RFX7,missense_variant,p.Asn1095Lys,ENST00000559847,; C ENST00000559447 Transcript missense_variant 3557/10426 3285/4092 1095/1363 N/K aaT/aaG 1 -1 RFX7 HGNC HGNC:25777 protein_coding YES ENSP00000453281 Q2KHR2 UPI0000695D7E NM_022841.5 tolerated(0.1) 9/9 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 56094152 56094152 A C 1 0 0 0 0 1 0 0 0 13442 214 8 5 5 RFX7 15 56094152 Missense_Mutation SNP A C3N-02089_T 4135397 56094152 45897037 763 27847 IGDCC3 0 . GRCh38 15 65329544 65329544 + Missense_Mutation SNP C C T rs766501573 C3N-02089_T C3N-02089_N C C c.2051G>A p.Arg684Gln p.R684Q ENST00000327987 13/14 105 81 24 126 126 0 strelka-mutect IGDCC3,missense_variant,p.Arg684Gln,ENST00000327987,NM_004884.3;IGDCC3,downstream_gene_variant,,ENST00000558354,;IGDCC3,downstream_gene_variant,,ENST00000559231,; T ENST00000327987 Transcript missense_variant 2303/4479 2051/2445 684/814 R/Q cGg/cAg rs766501573 1 -1 IGDCC3 HGNC HGNC:9700 protein_coding YES CCDS10205.1 ENSP00000332773 Q8IVU1 UPI000019908F NM_004884.3 tolerated_low_confidence(0.14) 13/14 MODERATE 1 SNV 1 1 PASS rs766501573 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 65329544 65329544 C T 1 0 0 0 0 1 0 0 0 7474 652 23 1 1 IGDCC3 15 65329544 Missense_Mutation SNP C C3N-02089_T 9235392 65329544 36661645 764 27848 IGDCC4 0 . GRCh38 15 65384990 65384990 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.3306G>A p.= p.T1102T ENST00000352385 19/20 95 75 20 104 104 0 strelka-varscan-mutect IGDCC4,synonymous_variant,p.=,ENST00000352385,NM_020962.2;IGDCC4,non_coding_transcript_exon_variant,,ENST00000558048,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000559327,;IGDCC4,non_coding_transcript_exon_variant,,ENST00000561309,;IGDCC4,downstream_gene_variant,,ENST00000560319,; T ENST00000352385 Transcript synonymous_variant 3516/6508 3306/3753 1102/1250 T acG/acA 1 -1 IGDCC4 HGNC HGNC:13770 protein_coding YES CCDS10206.1 ENSP00000319623 Q8TDY8 UPI000006F31C NM_020962.2 19/20 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF40 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 65384990 65384990 C T 1 0 0 0 0 0 0 0 1 7475 755 27 1 1 IGDCC4 15 65384990 Silent SNP C C3N-02089_T 55446 65384990 36606199 765 27849 HCN4 0 . GRCh38 15 73323558 73323558 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2535C>G p.Ser845Arg p.S845R ENST00000261917 8/8 161 146 15 124 124 0 strelka-mutect HCN4,missense_variant,p.Ser845Arg,ENST00000261917,NM_005477.2; C ENST00000261917 Transcript missense_variant 3529/7228 2535/3612 845/1203 S/R agC/agG 1 -1 HCN4 HGNC HGNC:16882 protein_coding YES CCDS10248.1 ENSP00000261917 Q9Y3Q4 UPI000003FFB5 NM_005477.2 tolerated_low_confidence(0.05) 8/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 73323558 73323558 G C 1 0 0 0 0 1 0 0 0 6886 1194 42 4 4 HCN4 15 73323558 Missense_Mutation SNP G C3N-02089_T 7938568 73323558 28667631 766 27850 TBC1D21 0 . GRCh38 15 73884845 73884845 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.432G>T p.Arg144Ser p.R144S ENST00000300504 5/11 174 130 44 207 207 0 strelka-varscan-mutect TBC1D21,missense_variant,p.Arg144Ser,ENST00000300504,NM_153356.2;TBC1D21,missense_variant,p.Arg108Ser,ENST00000535547,NM_001286434.1;TBC1D21,intron_variant,,ENST00000562056,; T ENST00000300504 Transcript missense_variant 515/1207 432/1011 144/336 R/S agG/agT 1 1 TBC1D21 HGNC HGNC:28536 protein_coding YES CCDS10252.1 ENSP00000300504 Q8IYX1 UPI00000741CB NM_153356.2 tolerated(0.1) 5/11 PROSITE_profiles:PS50086,hmmpanther:PTHR22957:SF278,hmmpanther:PTHR22957,Gene3D:2qq8A02,Pfam_domain:PF00566,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 73884845 73884845 G T 1 0 0 0 0 1 0 0 0 16010 1194 42 2 2 TBC1D21 15 73884845 Missense_Mutation SNP G C3N-02089_T 561287 73884845 28106344 767 27851 HYKK 0 . GRCh38 15 78533248 78533248 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.700A>G p.Ile234Val p.I234V ENST00000569878 4/4 166 109 57 133 133 0 strelka-varscan-mutect HYKK,missense_variant,p.Ile234Val,ENST00000569878,;HYKK,missense_variant,p.Ile234Val,ENST00000388988,NM_001013619.2;HYKK,intron_variant,,ENST00000408962,NM_001083612.1;HYKK,intron_variant,,ENST00000563233,;HYKK,downstream_gene_variant,,ENST00000566332,;RP11-650L12.4,upstream_gene_variant,,ENST00000623556,;HYKK,downstream_gene_variant,,ENST00000566289,; G ENST00000569878 Transcript missense_variant 700/4097 700/1122 234/373 I/V Ata/Gta 1 1 HYKK HGNC HGNC:34403 protein_coding YES CCDS42063.1 ENSP00000455459 A2RU49 UPI0000366A7F tolerated(1) 4/4 Gene3D:3.90.1200.10,Pfam_domain:PF01636,hmmpanther:PTHR21064,hmmpanther:PTHR21064:SF1,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 78533248 78533248 A G 1 0 0 0 0 1 0 0 0 7365 101 4 5 5 HYKK 15 78533248 Missense_Mutation SNP A C3N-02089_T 4648403 78533248 23457941 768 27852 PSMA4 0 . GRCh38 15 78548903 78548903 + Missense_Mutation SNP C C T rs751350183 C3N-02089_T C3N-02089_N C C c.745C>T p.Arg249Cys p.R249C ENST00000044462 9/9 178 168 10 148 148 0 strelka-varscan-mutect PSMA4,missense_variant,p.Arg249Cys,ENST00000044462,;PSMA4,missense_variant,p.Arg249Cys,ENST00000559082,NM_001102667.1,NM_002789.4;PSMA4,missense_variant,p.Arg178Cys,ENST00000413382,NM_001102668.1;PSMA4,missense_variant,p.Arg218Cys,ENST00000560217,;PSMA4,3_prime_UTR_variant,,ENST00000558281,;PSMA4,3_prime_UTR_variant,,ENST00000558341,;PSMA4,3_prime_UTR_variant,,ENST00000558094,;PSMA4,downstream_gene_variant,,ENST00000560737,;PSMA4,downstream_gene_variant,,ENST00000559365,;PSMA4,downstream_gene_variant,,ENST00000559437,;PSMA4,downstream_gene_variant,,ENST00000559948,;PSMA4,downstream_gene_variant,,ENST00000559146,;PSMA4,downstream_gene_variant,,ENST00000559154,;PSMA4,downstream_gene_variant,,ENST00000557929,;PSMA4,downstream_gene_variant,,ENST00000559906,;PSMA4,non_coding_transcript_exon_variant,,ENST00000559934,;PSMA4,non_coding_transcript_exon_variant,,ENST00000560099,;PSMA4,downstream_gene_variant,,ENST00000558639,; T ENST00000044462 Transcript missense_variant 895/4411 745/786 249/261 R/C Cgt/Tgt rs751350183,COSM269960 1 1 PSMA4 HGNC HGNC:9533 protein_coding YES CCDS10303.1 ENSP00000044462 P25789 UPI000000DC2A deleterious(0.04) 9/9 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751350183 . 0 204 4 2 0 0 0 0 -12.92935 0.9998707 1 1 1 0 T 3 4 90 78548903 78548903 C T 1 0 0 0 0 1 0 0 0 12820 768 27 1 1 PSMA4 15 78548903 Missense_Mutation SNP C C3N-02089_T 15655 78548903 23442286 769 27853 CHRNA3 0 . GRCh38 15 78602030 78602030 + Missense_Mutation SNP G G C rs757145934 C3N-02089_T C3N-02089_N G G c.612C>G p.Ser204Arg p.S204R ENST00000326828 5/6 123 99 24 112 112 0 strelka-varscan-mutect CHRNA3,missense_variant,p.Ser204Arg,ENST00000326828,NM_000743.4;CHRNA3,missense_variant,p.Ser204Arg,ENST00000348639,NM_001166694.1;CHRNA3,non_coding_transcript_exon_variant,,ENST00000558903,;RP11-335K5.3,upstream_gene_variant,,ENST00000624172,;CHRNA3,missense_variant,p.Ser204Arg,ENST00000559658,; C ENST00000326828 Transcript missense_variant 997/3202 612/1518 204/505 S/R agC/agG rs757145934,COSM376466 1 -1 CHRNA3 HGNC HGNC:1957 protein_coding YES CCDS10305.1 ENSP00000315602 P32297 UPI000013D783 NM_000743.4 deleterious(0) 5/6 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF445,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs757145934 . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 C 3 2 90 78602030 78602030 G C 1 0 0 0 0 1 0 0 0 3144 1078 38 4 4 CHRNA3 15 78602030 Missense_Mutation SNP G C3N-02089_T 53127 78602030 23389159 770 27854 MORF4L1 0 . GRCh38 15 78840591 78840591 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.31G>T p.Asp11Tyr p.D11Y ENST00000379535 2/13 216 180 36 153 153 0 strelka-varscan-mutect MORF4L1,missense_variant,p.Asp11Tyr,ENST00000379535,; T ENST00000379535 Transcript missense_variant 595/2274 31/1047 11/348 D/Y Gat/Tat 1 1 MORF4L1 HGNC HGNC:16989 protein_coding ENSP00000368850 B3KTM8 UPI00001FE9BB deleterious_low_confidence(0) 2/13 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 78840591 78840591 G T 1 0 0 0 0 1 0 0 0 9669 1290 45 2 2 MORF4L1 15 78840591 Missense_Mutation SNP G C3N-02089_T 238561 78840591 23150598 771 27855 BCL2A1 0 . GRCh38 15 79970897 79970897 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.223A>C p.Met75Leu p.M75L ENST00000267953 1/2 369 297 72 263 261 2 strelka-varscan-mutect BCL2A1,missense_variant,p.Met75Leu,ENST00000267953,NM_004049.3;BCL2A1,missense_variant,p.Met75Leu,ENST00000335661,NM_001114735.1; G ENST00000267953 Transcript missense_variant 550/1033 223/528 75/175 M/L Atg/Ctg 1 -1 BCL2A1 HGNC HGNC:991 protein_coding YES CCDS10312.1 ENSP00000267953 Q16548 UPI00001268AE NM_004049.3 deleterious(0.02) 1/2 PROSITE_profiles:PS50062,hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF10,Pfam_domain:PF00452,Gene3D:1.10.437.10,SMART_domains:SM00337,Superfamily_domains:SSF56854,Prints_domain:PR01862,Prints_domain:PR01867 MODERATE 1 SNV 1 1 PASS rs1199987311 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 79970897 79970897 T G 1 0 0 0 0 1 0 0 0 1513 1435 50 5 5 BCL2A1 15 79970897 Missense_Mutation SNP T C3N-02089_T 1130306 79970897 22020292 772 27856 MESDC1 0 . GRCh38 15 81002532 81002532 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.261G>T p.Lys87Asn p.K87N ENST00000267984 1/1 27 20 7 24 24 0 strelka-mutect MESDC1,missense_variant,p.Lys87Asn,ENST00000267984,NM_022566.2;CFAP161,upstream_gene_variant,,ENST00000560091,;RP11-775C24.5,upstream_gene_variant,,ENST00000620635,; T ENST00000267984 Transcript missense_variant 1589/4845 261/1089 87/362 K/N aaG/aaT 1 1 MESDC1 HGNC HGNC:13519 protein_coding YES CCDS10316.1 ENSP00000267984 Q9H1K6 UPI000012EE04 NM_022566.2 deleterious(0) 1/1 hmmpanther:PTHR19981 MODERATE 1 SNV 1 PASS . . 1 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 81002532 81002532 G T 1 0 0 0 0 1 0 0 0 9425 991 35 2 2 MESDC1 15 81002532 Missense_Mutation SNP G C3N-02089_T 1031635 81002532 20988657 773 27857 IL16 0 . GRCh38 15 81300379 81300379 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3053C>A p.Pro1018His p.P1018H ENST00000302987 13/18 415 349 66 271 271 0 strelka-varscan-mutect IL16,missense_variant,p.Pro1018His,ENST00000394660,NM_001172128.1;IL16,missense_variant,p.Pro1018His,ENST00000302987,NM_172217.3;IL16,missense_variant,p.Pro317His,ENST00000394652,NM_004513.5;IL16,missense_variant,p.Pro322His,ENST00000558332,;RP11-761I4.4,downstream_gene_variant,,ENST00000607019,;IL16,downstream_gene_variant,,ENST00000560230,;IL16,upstream_gene_variant,,ENST00000559342,;IL16,3_prime_UTR_variant,,ENST00000360547,;IL16,3_prime_UTR_variant,,ENST00000560115,;IL16,3_prime_UTR_variant,,ENST00000558857,; A ENST00000302987 Transcript missense_variant 3053/3999 3053/3999 1018/1332 P/H cCc/cAc 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 deleterious(0) 13/18 hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 81300379 81300379 C A 1 0 0 0 0 1 0 0 0 7541 623 22 2 2 IL16 15 81300379 Missense_Mutation SNP C C3N-02089_T 297847 81300379 20690810 774 27858 GOLGA6L9 0 . GRCh38 15 82434057 82434057 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.457C>G p.Pro153Ala p.P153A ENST00000618348 6/9 297 247 50 222 222 0 strelka-varscan-mutect GOLGA6L9,missense_variant,p.Pro153Ala,ENST00000618348,NM_198181.3;RP11-152F13.8,non_coding_transcript_exon_variant,,ENST00000613086,;GOLGA6L9,non_coding_transcript_exon_variant,,ENST00000618706,;GOLGA6L9,downstream_gene_variant,,ENST00000558668,; G ENST00000618348 Transcript missense_variant 517/1710 457/1299 153/432 P/A Cca/Gca 1 1 GOLGA6L9 HGNC HGNC:37229 protein_coding YES CCDS45326.1 ENSP00000481078 A6NEM1 UPI000442D01A NM_198181.3 tolerated(0.1) 6/9 Pfam_domain:PF15070,hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF12 MODERATE 1 SNV 5 1 PASS rs1335888645 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 82434057 82434057 C G 1 0 0 0 0 1 0 0 0 6444 623 22 4 4 GOLGA6L9 15 82434057 Missense_Mutation SNP C C3N-02089_T 1133678 82434057 19557132 775 27859 RPS17 0 . GRCh38 15 82540099 82540099 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.37G>T p.Ala13Ser p.A13S ENST00000330244 2/5 790 540 250 454 454 0 strelka-varscan-mutect RPS17,missense_variant,p.Ala13Ser,ENST00000561157,;RP11-152F13.10,missense_variant,p.Ala272Ser,ENST00000562833,;RPS17,missense_variant,p.Ala13Ser,ENST00000330244,NM_001021.4;CPEB1,downstream_gene_variant,,ENST00000614918,;CPEB1,downstream_gene_variant,,ENST00000611031,;CPEB1,downstream_gene_variant,,ENST00000617958,;CPEB1,downstream_gene_variant,,ENST00000618449,NM_001079533.1;CPEB1,downstream_gene_variant,,ENST00000620182,NM_001288819.1;CPEB1,downstream_gene_variant,,ENST00000617522,;CPEB1,downstream_gene_variant,,ENST00000615198,NM_030594.4;CPEB1,downstream_gene_variant,,ENST00000617462,NM_001079535.1;CPEB1,downstream_gene_variant,,ENST00000616959,;CPEB1,downstream_gene_variant,,ENST00000611163,NM_001079534.1,NM_001288820.1;RP11-379H8.1,upstream_gene_variant,,ENST00000621893,;RPS17,missense_variant,p.Ala13Ser,ENST00000558397,;RPS17,missense_variant,p.Ala12Ser,ENST00000561068,;RPS17,non_coding_transcript_exon_variant,,ENST00000561440,;RPS17,non_coding_transcript_exon_variant,,ENST00000560612,;RPS17,non_coding_transcript_exon_variant,,ENST00000560639,;RPS17,non_coding_transcript_exon_variant,,ENST00000560229,;RPS17,non_coding_transcript_exon_variant,,ENST00000559776,;RPS17,non_coding_transcript_exon_variant,,ENST00000559273,;CPEB1,downstream_gene_variant,,ENST00000618698,;CPEB1,downstream_gene_variant,,ENST00000614977,; A ENST00000330244 Transcript missense_variant 173/592 37/408 13/135 A/S Gcc/Tcc 1 -1 RPS17 HGNC HGNC:10397 protein_coding YES CCDS10320.1 ENSP00000346046 P08708 UPI0000167B0C NM_001021.4 tolerated(0.55) 2/5 HAMAP:MF_00511,hmmpanther:PTHR10732,Gene3D:1rq6A00,Pfam_domain:PF00833,Superfamily_domains:0049231 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 82540099 82540099 C A 1 0 0 0 0 1 0 0 0 13882 739 26 2 2 RPS17 15 82540099 Missense_Mutation SNP C C3N-02089_T 106042 82540099 19451090 776 27860 AGBL1 0 . GRCh38 15 86224951 86224951 + Nonsense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.526A>T p.Lys176Ter p.K176* ENST00000441037 6/25 258 180 78 174 174 0 strelka-varscan-mutect AGBL1,stop_gained,p.Lys176Ter,ENST00000441037,;AGBL1,stop_gained,p.Lys130Ter,ENST00000635782,NM_152336.2;AGBL1,stop_gained,p.Lys130Ter,ENST00000421325,; T ENST00000441037 Transcript stop_gained,splice_region_variant 526/3551 526/3339 176/1112 K/* Aag/Tag 1 1 AGBL1 Clone_based_vega_gene HGNC:26504 protein_coding YES ENSP00000413001 Q96MI9 UPI000387C1D9 6/25 Gene3D:1.25.10.10,hmmpanther:PTHR12756,hmmpanther:PTHR12756:SF5,Superfamily_domains:SSF48371 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 86224951 86224951 A T 1 0 0 0 0 0 1 0 0 451 202 7 4 4 AGBL1 15 86224951 Nonsense_Mutation SNP A C3N-02089_T 3684852 86224951 15766238 777 27861 NR2F2 0 . GRCh38 15 96332379 96332379 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.274G>C p.Gly92Arg p.G92R ENST00000394166 1/3 530 443 87 303 303 0 strelka-varscan-mutect NR2F2,missense_variant,p.Gly92Arg,ENST00000394166,NM_021005.3;NR2F2,intron_variant,,ENST00000421109,NM_001145155.1;NR2F2,upstream_gene_variant,,ENST00000394171,NM_001145156.1;NR2F2,upstream_gene_variant,,ENST00000453270,NM_001145157.1;NR2F2,upstream_gene_variant,,ENST00000559679,;NR2F2,upstream_gene_variant,,ENST00000410719,; C ENST00000394166 Transcript missense_variant 1663/5275 274/1245 92/414 G/R Ggc/Cgc 1 1 NR2F2 HGNC HGNC:7976 protein_coding YES CCDS10375.1 ENSP00000377721 P24468 F1D8R0 UPI000000052E NM_021005.3 deleterious(0) 1/3 PROSITE_profiles:PS51030,hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF45,PROSITE_patterns:PS00031,Pfam_domain:PF00105,Gene3D:3.30.50.10,SMART_domains:SM00399,Superfamily_domains:SSF57716,Prints_domain:PR00047 MODERATE 1 SNV 1 1 PASS rs916901985 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 96332379 96332379 G C 1 0 0 0 0 1 0 0 0 10684 1116 39 4 4 NR2F2 15 96332379 Missense_Mutation SNP G C3N-02089_T 10107428 96332379 5658810 778 27862 SNRPA1 0 . GRCh38 15 101287673 101287673 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.339A>G p.= p.K113K ENST00000254193 4/9 369 345 24 207 207 0 strelka-varscan-mutect SNRPA1,synonymous_variant,p.=,ENST00000254193,NM_003090.2;SNRPA1,synonymous_variant,p.=,ENST00000559686,;SNRPA1,synonymous_variant,p.=,ENST00000626000,;SNRPA1,5_prime_UTR_variant,,ENST00000560496,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560856,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000394082,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560987,;SNRPA1,intron_variant,,ENST00000540017,;SNRPA1,downstream_gene_variant,,ENST00000558020,;SNRPA1,synonymous_variant,p.=,ENST00000559309,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560433,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000558036,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000558059,;SNRPA1,non_coding_transcript_exon_variant,,ENST00000560383,;SNRPA1,upstream_gene_variant,,ENST00000560307,; C ENST00000254193 Transcript synonymous_variant 412/1055 339/768 113/255 K aaA/aaG 1 -1 SNRPA1 HGNC HGNC:11152 protein_coding YES CCDS10391.1 ENSP00000254193 P09661 UPI000006DD72 NM_003090.2 4/9 hmmpanther:PTHR10552,Gene3D:3.80.10.10,Pfam_domain:PF14580,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 101287673 101287673 T C 1 0 0 0 0 0 0 0 1 15180 1490 52 5 5 SNRPA1 15 101287673 Silent SNP T C3N-02089_T 4955294 101287673 703516 779 27863 PKD1 0 . GRCh38 16 2103649 2103649 + Missense_Mutation SNP C C G C3N-02089_T C3N-02089_N C C c.8408G>C p.Gly2803Ala p.G2803A ENST00000262304 23/46 463 414 49 397 397 0 varscan-mutect PKD1,missense_variant,p.Gly2803Ala,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Gly2803Ala,ENST00000423118,NM_000296.3;PKD1,intron_variant,,ENST00000567946,;PKD1,downstream_gene_variant,,ENST00000488185,;PKD1,downstream_gene_variant,,ENST00000483024,;PKD1,downstream_gene_variant,,ENST00000612014,;PKD1,intron_variant,,ENST00000561991,;PKD1,downstream_gene_variant,,ENST00000473780,;PKD1,upstream_gene_variant,,ENST00000570193,;PKD1,downstream_gene_variant,,ENST00000483558,;PKD1,upstream_gene_variant,,ENST00000566905,;PKD1,upstream_gene_variant,,ENST00000475889,;PKD1,upstream_gene_variant,,ENST00000566784,;PKD1,downstream_gene_variant,,ENST00000564865,;PKD1,missense_variant,p.Gly1032Ala,ENST00000487932,;PKD1,non_coding_transcript_exon_variant,,ENST00000486339,;PKD1,non_coding_transcript_exon_variant,,ENST00000496574,;PKD1,non_coding_transcript_exon_variant,,ENST00000483731,;PKD1,non_coding_transcript_exon_variant,,ENST00000415938,;PKD1,non_coding_transcript_exon_variant,,ENST00000471603,;PKD1,non_coding_transcript_exon_variant,,ENST00000480227,;PKD1,non_coding_transcript_exon_variant,,ENST00000562297,;PKD1,downstream_gene_variant,,ENST00000568591,;PKD1,downstream_gene_variant,,ENST00000565639,;PKD1,upstream_gene_variant,,ENST00000474088,;PKD1,downstream_gene_variant,,ENST00000569983,;PKD1,upstream_gene_variant,,ENST00000469851,;PKD1,upstream_gene_variant,,ENST00000570253,;PKD1,downstream_gene_variant,,ENST00000564890,;PKD1,upstream_gene_variant,,ENST00000483814,; G ENST00000262304 Transcript missense_variant 8617/14138 8408/12912 2803/4303 G/A gGc/gCc COSM702335 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 tolerated(0.09) 23/46 PROSITE_profiles:PS51111,hmmpanther:PTHR10877,hmmpanther:PTHR10877:SF143 1 MODERATE 1 SNV 1 1 1 PASS rs1368840123 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 2103649 2103649 C G 1 0 0 0 0 1 0 0 0 12059 739 26 4 4 PKD1 16 2103649 Missense_Mutation SNP C C3N-02089_T 2103649 88234696 780 27864 GRIN2A 0 . GRCh38 16 9763164 9763164 + Missense_Mutation SNP G G C rs769629103 C3N-02089_T C3N-02089_N G G c.4380C>G p.Ile1460Met p.I1460M ENST00000396573 14/14 149 126 23 241 241 0 strelka-varscan-mutect GRIN2A,missense_variant,p.Ile1460Met,ENST00000396573,NM_000833.4;GRIN2A,missense_variant,p.Ile1323Met,ENST00000396575,;GRIN2A,missense_variant,p.Ile1460Met,ENST00000330684,NM_001134407.2;GRIN2A,3_prime_UTR_variant,,ENST00000562109,NM_001134408.2;GRIN2A,3_prime_UTR_variant,,ENST00000535259,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000461292,;GRIN2A,downstream_gene_variant,,ENST00000463531,; C ENST00000396573 Transcript missense_variant 4690/14450 4380/4395 1460/1464 I/M atC/atG rs769629103,COSM3513409 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 deleterious(0) 14/14 Pfam_domain:PF10565 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769629103 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 9763164 9763164 G C 1 0 0 0 0 1 0 0 0 6661 1048 37 4 4 GRIN2A 16 9763164 Missense_Mutation SNP G C3N-02089_T 7659515 9763164 80575181 781 27865 GRIN2A 0 . GRCh38 16 9763538 9763538 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.4006C>T p.Leu1336Phe p.L1336F ENST00000396573 14/14 198 147 51 233 233 0 strelka-varscan-mutect GRIN2A,missense_variant,p.Leu1336Phe,ENST00000396573,NM_000833.4;GRIN2A,missense_variant,p.Leu1199Phe,ENST00000396575,;GRIN2A,missense_variant,p.Leu1336Phe,ENST00000330684,NM_001134407.2;GRIN2A,intron_variant,,ENST00000562109,NM_001134408.2;GRIN2A,intron_variant,,ENST00000535259,;GRIN2A,non_coding_transcript_exon_variant,,ENST00000636273,;GRIN2A,intron_variant,,ENST00000461292,;GRIN2A,downstream_gene_variant,,ENST00000463531,; A ENST00000396573 Transcript missense_variant 4316/14450 4006/4395 1336/1464 L/F Ctc/Ttc 1 -1 GRIN2A HGNC HGNC:4585 protein_coding YES CCDS10539.1 ENSP00000379818 Q12879 Q547U9 UPI000000D7AB NM_000833.4 tolerated(0.71) 14/14 Low_complexity_(Seg):seg,Pfam_domain:PF10565 MODERATE 1 SNV 1 1 PASS . . 0 202 0 3 5 0 0 0 -20 0.7516799 1 1 1 0 A 3 1 90 9763538 9763538 G A 1 0 0 0 0 1 0 0 0 6661 1029 36 3 3 GRIN2A 16 9763538 Missense_Mutation SNP G C3N-02089_T 374 9763538 80574807 782 27866 SMG1 0 . GRCh38 16 18852072 18852072 + Missense_Mutation SNP T T G rs79443600 C3N-02089_T C3N-02089_N T T c.5047A>C p.Ile1683Leu p.I1683L ENST00000446231 33/63 57 47 10 78 78 0 strelka-varscan-mutect SMG1,missense_variant,p.Ile1683Leu,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Ile1573Leu,ENST00000565324,;SMG1,downstream_gene_variant,,ENST00000569764,;SMG1,upstream_gene_variant,,ENST00000563448,;SMG1,upstream_gene_variant,,ENST00000562668,; G ENST00000446231 Transcript missense_variant 5460/16115 5047/10986 1683/3661 I/L Att/Ctt rs79443600 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 tolerated(0.26) 33/63 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF71 MODERATE 1 SNV 1 1 PASS rs79443600 . 0 208 2 0 0 0 0 0 -19.99991 1 1 1 1 0 G 3 3 90 18852072 18852072 T G 1 0 0 0 0 1 0 0 0 15089 1449 50 5 5 SMG1 16 18852072 Missense_Mutation SNP T C3N-02089_T 9088534 18852072 71486273 783 27867 DNAH3 0 . GRCh38 16 21042203 21042203 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.4462G>T p.Val1488Leu p.V1488L ENST00000261383 32/62 42 34 8 59 59 0 strelka-varscan-mutect DNAH3,missense_variant,p.Val1488Leu,ENST00000261383,NM_017539.2;DNAH3,splice_region_variant,,ENST00000572640,;DNAH3,upstream_gene_variant,,ENST00000572931,; A ENST00000261383 Transcript missense_variant,splice_region_variant 4462/12394 4462/12351 1488/4116 V/L Gta/Tta 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 tolerated(1) 32/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF12774,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1379596389 . 0 202 8 0 0 0 0 0 -19.51095 0.9999988 1 1 1 0 A 3 1 90 21042203 21042203 C A 1 0 0 0 0 1 0 0 0 4418 521 18 2 2 DNAH3 16 21042203 Missense_Mutation SNP C C3N-02089_T 2190131 21042203 69296142 784 27868 XPO6 0 . GRCh38 16 28156247 28156247 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.924G>T p.= p.L308L ENST00000304658 7/24 146 96 50 181 181 0 strelka-varscan-mutect XPO6,synonymous_variant,p.=,ENST00000304658,NM_015171.3;XPO6,synonymous_variant,p.=,ENST00000565698,NM_001270940.1;XPO6,synonymous_variant,p.=,ENST00000574435,;XPO6,non_coding_transcript_exon_variant,,ENST00000561488,;XPO6,non_coding_transcript_exon_variant,,ENST00000569973,;XPO6,upstream_gene_variant,,ENST00000564337,;XPO6,downstream_gene_variant,,ENST00000573645,;XPO6,upstream_gene_variant,,ENST00000565284,;XPO6,upstream_gene_variant,,ENST00000570294,;XPO6,upstream_gene_variant,,ENST00000566175,; A ENST00000304658 Transcript synonymous_variant 1425/4422 924/3378 308/1125 L ctG/ctT 1 -1 XPO6 HGNC HGNC:19733 protein_coding YES CCDS42135.1 ENSP00000302790 Q96QU8 UPI000006F228 NM_015171.3 7/24 hmmpanther:PTHR21452,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 28156247 28156247 C A 1 0 0 0 0 0 0 0 1 18007 581 21 2 2 XPO6 16 28156247 Silent SNP C C3N-02089_T 7114044 28156247 62182098 785 27869 SEZ6L2 0 . GRCh38 16 29873338 29873338 + Missense_Mutation SNP A A T C3N-02089_T C3N-02089_N A A c.2390T>A p.Phe797Tyr p.F797Y ENST00000617533 14/18 368 316 52 322 322 0 strelka-varscan-mutect SEZ6L2,missense_variant,p.Phe797Tyr,ENST00000308713,NM_201575.3,NM_001114099.2;SEZ6L2,missense_variant,p.Phe797Tyr,ENST00000617533,NM_001243332.1;SEZ6L2,missense_variant,p.Phe753Tyr,ENST00000537485,NM_001243333.1;SEZ6L2,missense_variant,p.Phe727Tyr,ENST00000350527,NM_012410.3;SEZ6L2,missense_variant,p.Phe683Tyr,ENST00000346932,NM_001114100.2;SEZ6L2,downstream_gene_variant,,ENST00000563118,;SEZ6L2,downstream_gene_variant,,ENST00000568407,; T ENST00000617533 Transcript missense_variant 2635/3555 2390/2772 797/923 F/Y tTc/tAc COSM1563150,COSM1563151 1 -1 SEZ6L2 HGNC HGNC:30844 protein_coding YES CCDS73865.1 ENSP00000481917 A0A087WYL5 UPI00001FFE46 NM_001243332.1 tolerated(0.07) 14/18 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF92,SMART_domains:SM00032,Superfamily_domains:SSF57535 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 29873338 29873338 A T 1 0 0 0 0 1 0 0 0 14423 246 9 4 4 SEZ6L2 16 29873338 Missense_Mutation SNP A C3N-02089_T 1717091 29873338 60465007 786 27870 ZNF771 0 . GRCh38 16 30418183 30418183 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.770G>T p.Arg257Leu p.R257L ENST00000319296 3/3 73 52 21 86 86 0 strelka-varscan-mutect ZNF771,missense_variant,p.Arg257Leu,ENST00000319296,;ZNF771,missense_variant,p.Arg257Leu,ENST00000434417,NM_001142305.1,NM_016643.3;ZNF771,intron_variant,,ENST00000566625,;ZNF771,downstream_gene_variant,,ENST00000564550,;SNORA42,downstream_gene_variant,,ENST00000362917,; T ENST00000319296 Transcript missense_variant 1147/2371 770/954 257/317 R/L cGg/cTg 1 1 ZNF771 HGNC HGNC:29653 protein_coding YES CCDS45460.1 ENSP00000323945 Q7L3S4 UPI00001FFEDE deleterious(0) 3/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF199,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999953 1 1 1 0 T 3 4 90 30418183 30418183 G T 1 0 0 0 0 1 0 0 0 18727 1116 39 1 1 ZNF771 16 30418183 Missense_Mutation SNP G C3N-02089_T 544845 30418183 59920162 787 27871 ORAI3 0 . GRCh38 16 30949505 30949505 + Silent SNP G G T rs779214691 C3N-02089_T C3N-02089_N G G c.216G>T p.= p.S72S ENST00000318663 1/2 189 145 44 156 156 0 strelka-varscan-mutect ORAI3,synonymous_variant,p.=,ENST00000318663,NM_152288.2;ORAI3,synonymous_variant,p.=,ENST00000566237,;ORAI3,synonymous_variant,p.=,ENST00000562699,;FBXL19,downstream_gene_variant,,ENST00000338343,;FBXL19,downstream_gene_variant,,ENST00000380310,NM_001099784.2;FBXL19,downstream_gene_variant,,ENST00000471231,NM_001282351.1;FBXL19,downstream_gene_variant,,ENST00000427128,;FBXL19,downstream_gene_variant,,ENST00000565690,;FBXL19,downstream_gene_variant,,ENST00000562319,;FBXL19,downstream_gene_variant,,ENST00000565939,;FBXL19,downstream_gene_variant,,ENST00000566320,;AC135048.13,intron_variant,,ENST00000566056,;AC135048.13,intron_variant,,ENST00000562642,;ORAI3,synonymous_variant,p.=,ENST00000563161,; T ENST00000318663 Transcript synonymous_variant 440/2206 216/888 72/295 S tcG/tcT rs779214691 1 1 ORAI3 HGNC HGNC:28185 protein_coding YES CCDS10697.1 ENSP00000322249 Q9BRQ5 A0A024QZA7 UPI00000735E7 NM_152288.2 1/2 hmmpanther:PTHR31501:SF6,hmmpanther:PTHR31501,Pfam_domain:PF07856 LOW 1 SNV 1 1 PASS rs779214691 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 30949505 30949505 G T 1 0 0 0 0 0 0 0 1 11325 1103 39 1 1 ORAI3 16 30949505 Silent SNP G C3N-02089_T 531322 30949505 59388840 788 27872 ZNF423 0 . GRCh38 16 49637754 49637754 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.1398C>A p.Asn466Lys p.N466K ENST00000561648 5/9 343 295 48 394 394 0 strelka-varscan-mutect ZNF423,missense_variant,p.Asn466Lys,ENST00000561648,;ZNF423,missense_variant,p.Asn406Lys,ENST00000563137,;ZNF423,missense_variant,p.Asn466Lys,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Asn406Lys,ENST00000562871,;ZNF423,missense_variant,p.Asn349Lys,ENST00000535559,;ZNF423,missense_variant,p.Asn406Lys,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Asn349Lys,ENST00000567169,; T ENST00000561648 Transcript missense_variant 1699/7907 1398/3855 466/1284 N/K aaC/aaA COSM3927548,COSM3927549 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC tolerated(0.92) 5/9 hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs958714253 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 49637754 49637754 G T 1 0 0 0 0 1 0 0 0 18470 1252 44 2 2 ZNF423 16 49637754 Missense_Mutation SNP G C3N-02089_T 18688249 49637754 40700591 789 27873 SALL1 0 . GRCh38 16 51137158 51137158 + Missense_Mutation SNP C C A rs372873373 C3N-02089_T C3N-02089_N C C c.3929G>T p.Arg1310Leu p.R1310L ENST00000251020 3/3 201 141 60 224 223 1 strelka-varscan-mutect SALL1,missense_variant,p.Arg1213Leu,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Arg1310Leu,ENST00000251020,NM_002968.2;SALL1,3_prime_UTR_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000570206,; A ENST00000251020 Transcript missense_variant 3963/5146 3929/3975 1310/1324 R/L cGc/cTc rs372873373,COSM2834525 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.13) 3/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372873373 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 51137158 51137158 C A 1 0 0 0 0 1 0 0 0 14069 768 27 1 1 SALL1 16 51137158 Missense_Mutation SNP C C3N-02089_T 1499404 51137158 39201187 790 27874 AKTIP 0 . GRCh38 16 53494139 53494139 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.709A>G p.Ser237Gly p.S237G ENST00000300245 9/11 112 99 13 155 155 0 strelka-mutect AKTIP,missense_variant,p.Ser237Gly,ENST00000394657,NM_001012398.1,NM_022476.2;AKTIP,missense_variant,p.Ser237Gly,ENST00000300245,NM_001308325.1;AKTIP,missense_variant,p.Ser237Gly,ENST00000570004,;RBL2,downstream_gene_variant,,ENST00000262133,NM_001323611.1,NM_005611.3;AKTIP,downstream_gene_variant,,ENST00000568596,;AKTIP,downstream_gene_variant,,ENST00000568022,;AKTIP,downstream_gene_variant,,ENST00000570041,;AKTIP,downstream_gene_variant,,ENST00000563928,;AKTIP,downstream_gene_variant,,ENST00000565408,;RBL2,downstream_gene_variant,,ENST00000379935,;RP11-44F14.6,upstream_gene_variant,,ENST00000624610,;AKTIP,upstream_gene_variant,,ENST00000571523,;AKTIP,upstream_gene_variant,,ENST00000565431,;AKTIP,downstream_gene_variant,,ENST00000563108,;AKTIP,downstream_gene_variant,,ENST00000561799,;AKTIP,downstream_gene_variant,,ENST00000566045,; C ENST00000300245 Transcript missense_variant,splice_region_variant 927/2133 709/882 237/293 S/G Agc/Ggc 1 -1 AKTIP HGNC HGNC:16710 protein_coding YES CCDS76866.1 ENSP00000300245 Q9H8T0 A0A024R6S6 UPI00000433FA NM_001308325.1 tolerated(0.44) 9/11 hmmpanther:PTHR24067:SF41,hmmpanther:PTHR24067 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 53494139 53494139 T C 1 0 0 0 0 1 0 0 0 565 1536 53 5 5 AKTIP 16 53494139 Missense_Mutation SNP T C3N-02089_T 2356981 53494139 36844206 791 27875 CNTNAP4 0 . GRCh38 16 76489735 76489735 + Silent SNP C C A rs766597788 C3N-02089_T C3N-02089_N C C c.1932C>A p.= p.V644V ENST00000611870 13/24 53 36 17 71 71 0 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3;CNTNAP4,non_coding_transcript_exon_variant,,ENST00000471618,; A ENST00000611870 Transcript synonymous_variant 2317/4867 1932/3927 644/1308 V gtC/gtA rs766597788 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 13/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 LOW 1 SNV 1 1 PASS rs766597788 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 76489735 76489735 C A 1 0 0 0 0 0 0 0 1 3431 813 29 2 2 CNTNAP4 16 76489735 Silent SNP C C3N-02089_T 22995596 76489735 13848610 792 27876 CNTNAP4 0 . GRCh38 16 76498570 76498570 + Silent SNP C C A rs748587038 C3N-02089_T C3N-02089_N C C c.2241C>A p.= p.T747T ENST00000611870 15/24 80 53 27 105 105 0 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3;CNTNAP4,downstream_gene_variant,,ENST00000471618,; A ENST00000611870 Transcript synonymous_variant 2626/4867 2241/3927 747/1308 T acC/acA rs748587038,COSM1519973,COSM1519974 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 15/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659,Superfamily_domains:SSF49899 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs748587038 . 0 190 17 3 0 0 0 0 -20 0.9964668 1 1 1 0 A 2 1 90 76498570 76498570 C A 1 0 0 0 0 0 0 0 1 3431 608 21 2 2 CNTNAP4 16 76498570 Silent SNP C C3N-02089_T 8835 76498570 13839775 793 27877 HSD17B2 0 . GRCh38 16 82098237 82098237 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.965T>A p.Leu322Gln p.L322Q ENST00000199936 5/5 259 187 72 301 300 1 strelka-varscan-mutect HSD17B2,missense_variant,p.Leu322Gln,ENST00000199936,NM_002153.2;HSD17B2,missense_variant,p.Leu186Gln,ENST00000568090,;HSD17B2,3_prime_UTR_variant,,ENST00000566838,;RP11-510J16.5,intron_variant,,ENST00000567021,; A ENST00000199936 Transcript missense_variant 1158/1455 965/1164 322/387 L/Q cTg/cAg 1 1 HSD17B2 HGNC HGNC:5211 protein_coding YES CCDS10936.1 ENSP00000199936 P37059 UPI000004C78E NM_002153.2 deleterious(0) 5/5 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 82098237 82098237 T A 1 0 0 0 0 1 0 0 0 7279 1580 55 4 4 HSD17B2 16 82098237 Missense_Mutation SNP T C3N-02089_T 5599667 82098237 8240108 794 27878 ZNF469 0 . GRCh38 16 88434383 88434383 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.6829G>A p.Gly2277Arg p.G2277R ENST00000437464 2/2 276 193 83 290 290 0 strelka-varscan-mutect ZNF469,missense_variant,p.Gly2305Arg,ENST00000565624,;ZNF469,missense_variant,p.Gly2277Arg,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 6829/13203 6829/11778 2277/3925 G/R Ggg/Agg 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.36) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 88434383 88434383 G A 1 0 0 0 0 1 0 0 0 18500 1000 35 3 3 ZNF469 16 88434383 Missense_Mutation SNP G C3N-02089_T 6336146 88434383 1903962 795 27879 GSG2 0 . GRCh38 17 3724753 3724753 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.818G>T p.Arg273Met p.R273M ENST00000325418 1/1 371 261 110 391 389 2 strelka-varscan-mutect GSG2,missense_variant,p.Arg273Met,ENST00000325418,NM_031965.2;ITGAE,intron_variant,,ENST00000263087,NM_002208.4;ITGAE,downstream_gene_variant,,ENST00000574026,;CTD-3195I5.4,upstream_gene_variant,,ENST00000575043,;CTD-3195I5.3,downstream_gene_variant,,ENST00000571741,;ITGAE,intron_variant,,ENST00000571185,;ITGAE,upstream_gene_variant,,ENST00000570360,;ITGAE,upstream_gene_variant,,ENST00000572179,;ITGAE,intron_variant,,ENST00000570415,;ITGAE,upstream_gene_variant,,ENST00000572433,; T ENST00000325418 Transcript missense_variant 851/2797 818/2397 273/798 R/M aGg/aTg 1 1 GSG2 HGNC HGNC:19682 protein_coding YES CCDS11036.1 ENSP00000325290 Q8TF76 UPI0000141654 NM_031965.2 deleterious_low_confidence(0.03) 1/1 hmmpanther:PTHR24419,hmmpanther:PTHR24419:SF18 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 3724753 3724753 G T 1 0 0 0 0 1 0 0 0 6706 1000 35 2 2 GSG2 17 3724753 Missense_Mutation SNP G C3N-02089_T 3724753 79532688 796 27880 NCBP3 0 . GRCh38 17 3826154 3826154 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.543G>T p.= p.L181L ENST00000389005 5/13 140 118 22 96 96 0 strelka-varscan-mutect NCBP3,synonymous_variant,p.=,ENST00000389005,NM_001114118.2;NCBP3,upstream_gene_variant,,ENST00000577169,;NCBP3,non_coding_transcript_exon_variant,,ENST00000575815,;NCBP3,upstream_gene_variant,,ENST00000574911,;NCBP3,upstream_gene_variant,,ENST00000574379,; A ENST00000389005 Transcript synonymous_variant 571/12770 543/1863 181/620 L ctG/ctT 1 -1 NCBP3 HGNC HGNC:24612 protein_coding YES CCDS45578.1 ENSP00000373657 Q53F19 UPI00004DDA14 NM_001114118.2 5/13 hmmpanther:PTHR16291,hmmpanther:PTHR16291:SF0,Gene3D:3.30.70.330 LOW 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 90 3826154 3826154 C A 1 0 0 0 0 0 0 0 1 10230 697 25 2 2 NCBP3 17 3826154 Silent SNP C C3N-02089_T 101401 3826154 79431287 797 27881 ATP2A3 0 . GRCh38 17 3927983 3927983 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3137G>T p.Arg1046Met p.R1046M ENST00000359983 22/23 546 489 57 418 418 0 strelka-varscan-mutect ATP2A3,missense_variant,p.Arg1046Met,ENST00000359983,NM_174953.2,NM_174954.2;ATP2A3,missense_variant,p.Gly151Trp,ENST00000570845,;ATP2A3,missense_variant,p.Gln121His,ENST00000572116,;ATP2A3,intron_variant,,ENST00000309890,NM_174956.2;ATP2A3,intron_variant,,ENST00000397041,NM_005173.3;ATP2A3,intron_variant,,ENST00000397035,NM_174958.2;ATP2A3,intron_variant,,ENST00000352011,NM_174955.2;ATP2A3,intron_variant,,ENST00000397043,NM_174957.2;ATP2A3,intron_variant,,ENST00000570773,;ATP2A3,intron_variant,,ENST00000574999,;ATP2A3,downstream_gene_variant,,ENST00000576957,;ATP2A3,downstream_gene_variant,,ENST00000571245,; A ENST00000359983 Transcript missense_variant,splice_region_variant 3137/3290 3137/3159 1046/1052 R/M aGg/aTg 1 -1 ATP2A3 HGNC HGNC:813 protein_coding YES CCDS11042.1 ENSP00000353072 Q93084 UPI0000161584 NM_174953.2,NM_174954.2 22/23 MODERATE 1 SNV 5 1 PASS rs1304651049 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 3927983 3927983 C A 1 0 0 0 0 1 0 0 0 1291 695 24 2 2 ATP2A3 17 3927983 Missense_Mutation SNP C C3N-02089_T 101829 3927983 79329458 798 27882 ALOX15 0 . GRCh38 17 4637257 4637257 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.809G>C p.Gly270Ala p.G270A ENST00000570836 8/15 76 65 11 48 48 0 strelka-varscan-mutect ALOX15,missense_variant,p.Gly270Ala,ENST00000570836,;ALOX15,missense_variant,p.Gly270Ala,ENST00000293761,NM_001140.3;ALOX15,missense_variant,p.Gly231Ala,ENST00000574640,;ALOX15,downstream_gene_variant,,ENST00000572265,;ALOX15,downstream_gene_variant,,ENST00000576394,;ALOX15,splice_region_variant,,ENST00000576572,;ALOX15,downstream_gene_variant,,ENST00000573740,; G ENST00000570836 Transcript missense_variant,splice_region_variant 906/2784 809/1989 270/662 G/A gGa/gCa 1 -1 ALOX15 HGNC HGNC:433 protein_coding YES CCDS11049.1 ENSP00000458832 P16050 UPI000013E118 tolerated(1) 8/15 PROSITE_profiles:PS51393,hmmpanther:PTHR11771,hmmpanther:PTHR11771:SF33,Pfam_domain:PF00305,Gene3D:3.10.450.60,Superfamily_domains:SSF48484 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -19.99999 1 1 1 1 0 G 3 3 90 4637257 4637257 C G 1 0 0 0 0 1 0 0 0 638 869 30 4 4 ALOX15 17 4637257 Missense_Mutation SNP C C3N-02089_T 709274 4637257 78620184 799 27883 MINK1 0 . GRCh38 17 4885583 4885583 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.609T>G p.Asp203Glu p.D203E ENST00000355280 7/32 179 169 10 141 141 0 strelka-varscan MINK1,missense_variant,p.Asp203Glu,ENST00000355280,NM_153827.4,NM_015716.4;MINK1,missense_variant,p.Asp203Glu,ENST00000347992,NM_170663.4;MINK1,missense_variant,p.Asp203Glu,ENST00000453408,NM_001024937.3;RN7SL784P,downstream_gene_variant,,ENST00000577319,;MINK1,missense_variant,p.Asp66Glu,ENST00000571207,;MINK1,3_prime_UTR_variant,,ENST00000574453,NM_001321236.1;MINK1,3_prime_UTR_variant,,ENST00000577021,;MINK1,non_coding_transcript_exon_variant,,ENST00000572330,; G ENST00000355280 Transcript missense_variant 805/4961 609/3999 203/1332 D/E gaT/gaG 1 1 MINK1 HGNC HGNC:17565 protein_coding YES CCDS45588.1 ENSP00000347427 Q8N4C8 UPI00001678BB NM_153827.4,NM_015716.4 tolerated(0.07) 7/32 PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF196,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 4885583 4885583 T G 1 0 0 0 0 1 0 0 0 9551 1461 51 5 5 MINK1 17 4885583 Missense_Mutation SNP T C3N-02089_T 248326 4885583 78371858 800 27884 USP6 0 . GRCh38 17 5147094 5147094 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2331G>T p.Gln777His p.Q777H ENST00000574788 29/38 128 113 15 134 134 0 strelka-varscan-mutect USP6,missense_variant,p.Gln777His,ENST00000574788,NM_001304284.1;USP6,missense_variant,p.Gln777His,ENST00000250066,NM_004505.3;USP6,3_prime_UTR_variant,,ENST00000575709,;USP6,intron_variant,,ENST00000572949,; T ENST00000574788 Transcript missense_variant 4561/8464 2331/4221 777/1406 Q/H caG/caT 1 1 USP6 HGNC HGNC:12629 protein_coding YES CCDS11069.2 ENSP00000460380 P35125 UPI000006226F NM_001304284.1 tolerated_low_confidence(0.11) 29/38 Pfam_domain:PF00443,PROSITE_profiles:PS50235 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -19.99794 0.9999895 1 1 1 0 T 3 4 90 5147094 5147094 G T 1 0 0 0 0 1 0 0 0 17629 991 35 2 2 USP6 17 5147094 Missense_Mutation SNP G C3N-02089_T 261511 5147094 78110347 801 27885 CLEC10A 0 . GRCh38 17 7075618 7075618 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.707G>T p.Cys236Phe p.C236F ENST00000576617 7/7 120 83 37 97 97 0 strelka-varscan-mutect CLEC10A,missense_variant,p.Cys236Phe,ENST00000576617,;CLEC10A,intron_variant,,ENST00000254868,NM_182906.2;CLEC10A,intron_variant,,ENST00000416562,;CLEC10A,intron_variant,,ENST00000571664,NM_006344.2;CLEC10A,intron_variant,,ENST00000576549,;CLEC10A,downstream_gene_variant,,ENST00000571624,; A ENST00000576617 Transcript missense_variant 977/1800 707/771 236/256 C/F tGc/tTc 1 -1 CLEC10A HGNC HGNC:16916 protein_coding ENSP00000458728 Q8IUN9 UPI00004C7FF8 deleterious_low_confidence(0) 7/7 MODERATE SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999959 1 1 1 0 A 3 1 90 7075618 7075618 C A 1 0 0 0 0 1 0 0 0 3261 710 25 2 2 CLEC10A 17 7075618 Missense_Mutation SNP C C3N-02089_T 1928524 7075618 76181823 802 27886 C17orf74 0 . GRCh38 17 7426458 7426458 + Nonsense_Mutation SNP C C A rs768767420 C3N-02089_T C3N-02089_N C C c.467C>A p.Ser156Ter p.S156* ENST00000333870 3/3 369 327 42 335 335 0 strelka-varscan-mutect C17orf74,stop_gained,p.Ser156Ter,ENST00000333870,NM_175734.4;C17orf74,intron_variant,,ENST00000574034,;RP11-104H15.12,upstream_gene_variant,,ENST00000636696,;SPEM1,downstream_gene_variant,,ENST00000323675,NM_199339.2;RP11-104H15.7,intron_variant,,ENST00000575310,; A ENST00000333870 Transcript stop_gained 541/1651 467/1506 156/501 S/* tCa/tAa rs768767420 1 1 C17orf74 HGNC HGNC:27315 protein_coding YES CCDS42255.1 ENSP00000328061 Q0P670 UPI000015FC87 NM_175734.4 3/3 Pfam_domain:PF15670,hmmpanther:PTHR34834,hmmpanther:PTHR34834:SF2 HIGH 1 SNV 1 1 PASS rs768767420 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 7426458 7426458 C A 1 0 0 0 0 0 1 0 0 1888 838 29 2 2 C17orf74 17 7426458 Nonsense_Mutation SNP C C3N-02089_T 350840 7426458 75830983 803 27887 TP53 0 . GRCh38 17 7674893 7674893 + Missense_Mutation SNP C C A rs587778720 C3N-02089_T C3N-02089_N C C c.638G>T p.Arg213Leu p.R213L ENST00000269305 6/11 522 311 211 370 370 0 strelka-varscan-mutect TP53,missense_variant,p.Arg213Leu,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Arg213Leu,ENST00000420246,;TP53,missense_variant,p.Arg174Leu,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Arg174Leu,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Arg213Leu,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Arg174Leu,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Arg213Leu,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Arg174Leu,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Arg213Leu,ENST00000445888,;TP53,missense_variant,p.Arg174Leu,ENST00000619485,;TP53,missense_variant,p.Arg81Leu,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Arg54Leu,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Arg81Leu,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Arg54Leu,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Arg81Leu,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Arg54Leu,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Arg213Leu,ENST00000359597,;TP53,missense_variant,p.Arg202Leu,ENST00000615910,;TP53,missense_variant,p.Arg213Leu,ENST00000413465,;TP53,missense_variant,p.Arg81Leu,ENST00000509690,;TP53,missense_variant,p.Arg120Leu,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Arg174Leu,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 828/2579 638/1182 213/393 R/L cGa/cTa rs587778720,CM004906,CM022474,TP53_g.12707G>C,TP53_g.12707G>T,TP53_g.12707G>A,COSM10735,COSM11860,COSM131466,COSM131467,COSM131468,COSM131469,COSM1726594,COSM1741334,COSM241997,COSM241998,COSM241999,COSM242000,COSM3378349,COSM3403265,COSM3717650,COSM3717651,COSM3717652,COSM3717653,COSM3717654,COSM3717655,COSM43650 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 not_provided,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs587778720 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 7674893 7674893 C A 1 0 0 0 0 1 0 0 0 16859 884 31 1 1 TP53 17 7674893 Missense_Mutation SNP C C3N-02089_T 248435 7674893 75582548 804 27888 SPDYE4 0 . GRCh38 17 8757376 8757376 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.226G>T p.Glu76Ter p.E76* ENST00000328794 2/6 273 239 34 263 263 0 strelka-varscan-mutect SPDYE4,stop_gained,p.Glu76Ter,ENST00000328794,NM_001128076.1;SPDYE4,stop_gained,p.Glu5Ter,ENST00000580999,;SPDYE4,3_prime_UTR_variant,,ENST00000582989,; A ENST00000328794 Transcript stop_gained 403/923 226/714 76/237 E/* Gag/Tag 1 -1 SPDYE4 HGNC HGNC:35463 protein_coding YES CCDS45609.1 ENSP00000329522 A6NLX3 UPI0000DD83CC NM_001128076.1 2/6 hmmpanther:PTHR31156 HIGH 1 SNV 1 1 PASS rs992218890 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 8757376 8757376 C A 1 0 0 0 0 0 1 0 0 15380 835 29 2 2 SPDYE4 17 8757376 Nonsense_Mutation SNP C C3N-02089_T 1082483 8757376 74500065 805 27889 PIK3R6 0 . GRCh38 17 8803314 8803314 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.2224C>T p.Leu742Phe p.L742F ENST00000619866 20/20 223 197 26 215 215 0 strelka-varscan-mutect PIK3R6,missense_variant,p.Leu742Phe,ENST00000619866,NM_001010855.3,NM_001290211.1;PIK3R6,missense_variant,p.Leu742Phe,ENST00000614407,;MFSD6L,upstream_gene_variant,,ENST00000329805,NM_152599.3;PIK3R6,3_prime_UTR_variant,,ENST00000611951,;PIK3R6,3_prime_UTR_variant,,ENST00000613555,; A ENST00000619866 Transcript missense_variant 2464/3041 2224/2265 742/754 L/F Ctt/Ttt 1 -1 PIK3R6 HGNC HGNC:27101 protein_coding YES CCDS73985.1 ENSP00000480157 Q5UE93 UPI0000043463 NM_001010855.3,NM_001290211.1 deleterious(0) 20/20 hmmpanther:PTHR15593:SF1,hmmpanther:PTHR15593,Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 8803314 8803314 G A 1 0 0 0 0 1 0 0 0 12018 1000 35 3 3 PIK3R6 17 8803314 Missense_Mutation SNP G C3N-02089_T 45938 8803314 74454127 806 27890 PIK3R5 0 . GRCh38 17 8886247 8886247 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.2110C>T p.Arg704Cys p.R704C ENST00000447110 14/19 167 134 33 182 182 0 strelka-varscan-mutect PIK3R5,missense_variant,p.Arg704Cys,ENST00000447110,NM_001142633.2;PIK3R5,missense_variant,p.Arg318Cys,ENST00000616147,NM_001251852.1;PIK3R5,missense_variant,p.Arg318Cys,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,missense_variant,p.Arg318Cys,ENST00000623421,NM_001251855.1;PIK3R5,missense_variant,p.Arg704Cys,ENST00000581552,NM_014308.3;PIK3R5,missense_variant,p.Arg703Cys,ENST00000584803,;PIK3R5,upstream_gene_variant,,ENST00000585260,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000577214,;PIK3R5,upstream_gene_variant,,ENST00000583810,;PIK3R5,downstream_gene_variant,,ENST00000583039,; A ENST00000447110 Transcript missense_variant 2240/4495 2110/2643 704/880 R/C Cgt/Tgt 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 deleterious(0) 14/19 hmmpanther:PTHR15593,hmmpanther:PTHR15593:SF2,Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 8886247 8886247 G A 1 0 0 0 0 1 0 0 0 12017 1145 40 1 1 PIK3R5 17 8886247 Missense_Mutation SNP G C3N-02089_T 82933 8886247 74371194 807 27891 STX8 0 . GRCh38 17 9568444 9568444 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.44A>C p.Gln15Pro p.Q15P ENST00000306357 2/8 187 173 14 183 183 0 strelka-varscan-mutect STX8,missense_variant,p.Gln15Pro,ENST00000306357,NM_004853.2;STX8,missense_variant,p.Gln15Pro,ENST00000573016,;STX8,intron_variant,,ENST00000574431,;STX8,non_coding_transcript_exon_variant,,ENST00000573373,;STX8,non_coding_transcript_exon_variant,,ENST00000573077,;STX8,missense_variant,p.Gln15Pro,ENST00000575858,;STX8,missense_variant,p.Gln15Pro,ENST00000575294,;STX8,non_coding_transcript_exon_variant,,ENST00000574382,; G ENST00000306357 Transcript missense_variant 472/1246 44/711 15/236 Q/P cAa/cCa 1 -1 STX8 HGNC HGNC:11443 protein_coding YES CCDS32565.1 ENSP00000305255 Q9UNK0 UPI0000136169 NM_004853.2 deleterious(0.01) 2/8 hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF119,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 9568444 9568444 T G 1 0 0 0 0 1 0 0 0 15735 1812 63 5 5 STX8 17 9568444 Missense_Mutation SNP T C3N-02089_T 682197 9568444 73688997 808 27892 CFAP52 0 . GRCh38 17 9598302 9598302 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.605G>T p.Gly202Val p.G202V ENST00000352665 5/14 147 104 43 188 188 0 strelka-varscan-mutect CFAP52,missense_variant,p.Gly202Val,ENST00000352665,NM_145054.4;CFAP52,missense_variant,p.Gly134Val,ENST00000396219,NM_001080556.1;CFAP52,downstream_gene_variant,,ENST00000576499,;CFAP52,missense_variant,p.Asp47Tyr,ENST00000574937,;CFAP52,3_prime_UTR_variant,,ENST00000576630,;CFAP52,3_prime_UTR_variant,,ENST00000575247,;CFAP52,3_prime_UTR_variant,,ENST00000572333,;CFAP52,non_coding_transcript_exon_variant,,ENST00000576320,; T ENST00000352665 Transcript missense_variant 674/2193 605/1863 202/620 G/V gGa/gTa 1 1 CFAP52 HGNC HGNC:16053 protein_coding YES CCDS11149.2 ENSP00000339449 Q8N1V2 UPI00001AECC1 NM_145054.4 deleterious(0.01) 5/14 Gene3D:2.130.10.10,hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF14,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 9598302 9598302 G T 1 0 0 0 0 1 0 0 0 3023 1174 41 2 2 CFAP52 17 9598302 Missense_Mutation SNP G C3N-02089_T 29858 9598302 73659139 809 27893 MYH13 0 . GRCh38 17 10311927 10311927 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.4515G>T p.Glu1505Asp p.E1505D ENST00000418404 31/41 138 109 29 152 152 0 strelka-varscan-mutect MYH13,missense_variant,p.Glu1505Asp,ENST00000418404,;MYH13,missense_variant,p.Glu1505Asp,ENST00000252172,NM_003802.2;MYH13,missense_variant,p.Glu1505Asp,ENST00000621918,;RP11-401O9.4,intron_variant,,ENST00000609088,; A ENST00000418404 Transcript missense_variant 4679/6296 4515/5817 1505/1938 E/D gaG/gaT COSM975108,COSM975109 1 -1 MYH13 HGNC HGNC:7571 protein_coding YES CCDS45613.1 ENSP00000404570 Q9UKX3 UPI0000DB39EA deleterious(0.02) 31/41 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF504,Superfamily_domains:SSF90257 1,1 MODERATE SNV 5 1,1 1 PASS . . 0 194 0 13 3 0 0 0 -18.50953 0.5290714 1 1 1 0 A 3 1 90 10311927 10311927 C A 1 0 0 0 0 1 0 0 0 10032 912 32 2 2 MYH13 17 10311927 Missense_Mutation SNP C C3N-02089_T 713625 10311927 72945514 810 27894 MYH8 0 . GRCh38 17 10412699 10412699 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1177C>A p.Leu393Met p.L393M ENST00000403437 13/40 452 339 113 405 405 0 strelka-varscan-mutect MYH8,missense_variant,p.Leu393Met,ENST00000403437,NM_002472.2;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000403437 Transcript missense_variant 1272/6041 1177/5814 393/1937 L/M Ctg/Atg 1 -1 MYH8 HGNC HGNC:7578 protein_coding YES CCDS11153.1 ENSP00000384330 P13535 UPI000012FB7D NM_002472.2 deleterious(0.03) 13/40 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF368,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 10412699 10412699 G T 1 0 0 0 0 1 0 0 0 10041 933 33 2 2 MYH8 17 10412699 Missense_Mutation SNP G C3N-02089_T 100772 10412699 72844742 811 27895 MYH1 0 . GRCh38 17 10496117 10496117 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.5002C>A p.Gln1668Lys p.Q1668K ENST00000226207 35/40 213 193 20 251 250 1 strelka-varscan-mutect MYH1,missense_variant,p.Gln1668Lys,ENST00000226207,NM_005963.3;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; T ENST00000226207 Transcript missense_variant 5097/6024 5002/5820 1668/1939 Q/K Cag/Aag COSM368637 1 -1 MYH1 HGNC HGNC:7567 protein_coding YES CCDS11155.1 ENSP00000226207 P12882 UPI000013C891 NM_005963.3 tolerated(0.15) 35/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF454 1 MODERATE SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 10496117 10496117 G T 1 0 0 0 0 1 0 0 0 10029 1357 47 2 2 MYH1 17 10496117 Missense_Mutation SNP G C3N-02089_T 83418 10496117 72761324 812 27896 MYH2 0 . GRCh38 17 10525837 10525837 + Missense_Mutation SNP A A C rs372658014 C3N-02089_T C3N-02089_N A A c.4227T>G p.His1409Gln p.H1409Q ENST00000245503 31/40 159 119 40 187 187 0 strelka-varscan-mutect MYH2,missense_variant,p.His1409Gln,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.His1409Gln,ENST00000397183,NM_001100112.1;MYH2,intron_variant,,ENST00000532183,;MYH2,intron_variant,,ENST00000622564,;MYHAS,intron_variant,,ENST00000587182,;RP11-799N11.1,intron_variant,,ENST00000399342,;RP11-799N11.1,intron_variant,,ENST00000581304,; C ENST00000245503 Transcript missense_variant 4612/6339 4227/5826 1409/1941 H/Q caT/caG rs372658014 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 tolerated(0.69) 31/40 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF01576 MODERATE 1 SNV 1 1 PASS rs372658014 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 10525837 10525837 A C 1 0 0 0 0 1 0 0 0 10035 214 8 5 5 MYH2 17 10525837 Missense_Mutation SNP A C3N-02089_T 29720 10525837 72731604 813 27897 HS3ST3B1 0 . GRCh38 17 14301784 14301784 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.266C>A p.Pro89Gln p.P89Q ENST00000360954 1/2 154 137 17 128 128 0 strelka-varscan-mutect HS3ST3B1,missense_variant,p.Pro89Gln,ENST00000360954,NM_006041.2;RP11-214O1.1,upstream_gene_variant,,ENST00000571192,;RP11-214O1.2,upstream_gene_variant,,ENST00000583262,;HS3ST3B1,missense_variant,p.Pro89Gln,ENST00000466596,; A ENST00000360954 Transcript missense_variant 702/5367 266/1173 89/390 P/Q cCg/cAg 1 1 HS3ST3B1 HGNC HGNC:5198 protein_coding YES CCDS11167.1 ENSP00000354213 Q9Y662 UPI0000038167 NM_006041.2 tolerated_low_confidence(0.65) 1/2 hmmpanther:PTHR10605,hmmpanther:PTHR10605:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 14301784 14301784 C A 1 0 0 0 0 1 0 0 0 7260 652 23 1 1 HS3ST3B1 17 14301784 Missense_Mutation SNP C C3N-02089_T 3775947 14301784 68955657 814 27898 FBXW10 0 . GRCh38 17 18768668 18768668 + Missense_Mutation SNP G G T rs760267143 C3N-02089_T C3N-02089_N G G c.1839G>T p.Lys613Asn p.K613N ENST00000395665 10/14 168 155 13 156 156 0 varscan-mutect FBXW10,missense_variant,p.Lys642Asn,ENST00000308799,;FBXW10,missense_variant,p.Lys613Asn,ENST00000395665,NM_001267585.1;FBXW10,missense_variant,p.Lys613Asn,ENST00000301938,NM_001267586.1;FBXW10,upstream_gene_variant,,ENST00000573605,;FBXW10,3_prime_UTR_variant,,ENST00000574478,; T ENST00000395665 Transcript missense_variant 2060/3431 1839/3159 613/1052 K/N aaG/aaT rs760267143 1 1 FBXW10 HGNC HGNC:1211 protein_coding YES CCDS11199.3 ENSP00000379025 Q5XX13 UPI0000200B30 NM_001267585.1 deleterious(0) 10/14 PROSITE_profiles:PS50294,hmmpanther:PTHR19872,hmmpanther:PTHR19872:SF7,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS rs760267143 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 18768668 18768668 G T 1 0 0 0 0 1 0 0 0 5626 962 34 2 2 FBXW10 17 18768668 Missense_Mutation SNP G C3N-02089_T 4466884 18768668 64488773 815 27899 RNF112 0 . GRCh38 17 19415869 19415869 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1590C>A p.= p.A530A ENST00000461366 14/14 214 193 21 183 182 1 strelka-varscan-mutect RNF112,synonymous_variant,p.=,ENST00000461366,NM_007148.4;RNF112,downstream_gene_variant,,ENST00000575165,;AC004448.5,downstream_gene_variant,,ENST00000627753,;AC004448.2,upstream_gene_variant,,ENST00000437646,;snoMe28S-Am2634,upstream_gene_variant,,ENST00000636729,;CTB-187M2.2,upstream_gene_variant,,ENST00000579897,;RNF112,downstream_gene_variant,,ENST00000580109,;RNF112,non_coding_transcript_exon_variant,,ENST00000574782,;RNF112,downstream_gene_variant,,ENST00000574149,; A ENST00000461366 Transcript synonymous_variant 1805/3212 1590/1896 530/631 A gcC/gcA 1 1 RNF112 HGNC HGNC:12968 protein_coding YES CCDS58529.1 ENSP00000454919 Q9ULX5 UPI00001B0607 NM_007148.4 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10751:SF1,hmmpanther:PTHR10751 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 19415869 19415869 C A 1 0 0 0 0 0 0 0 1 13604 581 21 2 2 RNF112 17 19415869 Silent SNP C C3N-02089_T 647201 19415869 63841572 816 27900 MAP2K3 0 . GRCh38 17 21300566 21300566 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.187G>T p.Asp63Tyr p.D63Y ENST00000342679 4/12 361 307 54 331 331 0 strelka-varscan-mutect MAP2K3,missense_variant,p.Asp63Tyr,ENST00000342679,NM_145109.2;MAP2K3,missense_variant,p.Asp34Tyr,ENST00000361818,NM_002756.4;MAP2K3,missense_variant,p.Asp34Tyr,ENST00000613338,;MAP2K3,missense_variant,p.Asp34Tyr,ENST00000316920,;MAP2K3,missense_variant,p.Asp34Tyr,ENST00000526076,;MAP2K3,downstream_gene_variant,,ENST00000529517,;MAP2K3,downstream_gene_variant,,ENST00000627447,;MAP2K3,missense_variant,p.Asp63Tyr,ENST00000496046,;MAP2K3,3_prime_UTR_variant,,ENST00000395491,NM_001316332.1;MAP2K3,3_prime_UTR_variant,,ENST00000479129,;MAP2K3,non_coding_transcript_exon_variant,,ENST00000583508,;MAP2K3,downstream_gene_variant,,ENST00000483928,; T ENST00000342679 Transcript missense_variant 436/2303 187/1044 63/347 D/Y Gac/Tac 1 1 MAP2K3 HGNC HGNC:6843 protein_coding YES CCDS11217.1 ENSP00000345083 P46734 Q6FI23 UPI000012F48C NM_145109.2 deleterious(0) 4/12 Gene3D:3.30.200.20,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF191,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS rs1011375302 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 21300566 21300566 G T 1 0 0 0 0 1 0 0 0 9160 1290 45 2 2 MAP2K3 17 21300566 Missense_Mutation SNP G C3N-02089_T 1884697 21300566 61956875 817 27901 KCNJ12 0 . GRCh38 17 21416023 21416023 + Silent SNP T T C rs782231681 C3N-02089_T C3N-02089_N T T c.681T>C p.= p.H227H ENST00000583088 3/3 137 124 13 126 126 0 varscan-mutect KCNJ12,synonymous_variant,p.=,ENST00000583088,NM_021012.4;KCNJ12,synonymous_variant,p.=,ENST00000331718,; C ENST00000583088 Transcript synonymous_variant 1576/5425 681/1302 227/433 H caT/caC rs782231681 1 1 KCNJ12 HGNC HGNC:6258 protein_coding YES CCDS11219.1 ENSP00000463778 Q14500 UPI00000725C7 NM_021012.4 3/3 hmmpanther:PTHR11767,hmmpanther:PTHR11767:SF14,Gene3D:2.60.40.1400,Pfam_domain:PF01007,Superfamily_domains:SSF81296 LOW 1 SNV 1 1 PASS rs782231681 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 21416023 21416023 T C 1 0 0 0 0 0 0 0 1 7962 1461 51 5 5 KCNJ12 17 21416023 Silent SNP T C3N-02089_T 115457 21416023 61841418 818 27902 C17orf51 0 . GRCh38 17 21535507 21535507 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.459A>G p.= p.R153R ENST00000391411 2/2 99 79 20 103 103 0 strelka-varscan-mutect C17orf51,synonymous_variant,p.=,ENST00000391411,NM_001113434.4;C17orf51,3_prime_UTR_variant,,ENST00000412778,;RP11-822E23.2,intron_variant,,ENST00000579239,;RP11-822E23.8,non_coding_transcript_exon_variant,,ENST00000426261,;RP11-822E23.8,non_coding_transcript_exon_variant,,ENST00000468381,;C17orf51,non_coding_transcript_exon_variant,,ENST00000535846,;C17orf51,upstream_gene_variant,,ENST00000538604,; C ENST00000391411 Transcript synonymous_variant 717/7914 459/666 153/221 R agA/agG 1 -1 C17orf51 HGNC HGNC:27904 protein_coding YES CCDS45629.1 ENSP00000384286 A8MQB3 UPI00001A832D NM_001113434.4 2/2 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 21535507 21535507 T C 1 0 0 0 0 0 0 0 1 1882 1780 62 5 5 C17orf51 17 21535507 Silent SNP T C3N-02089_T 119484 21535507 61721934 819 27903 SARM1 0 . GRCh38 17 28381591 28381591 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.859G>T p.Val287Leu p.V287L ENST00000585482 2/9 145 105 40 93 93 0 strelka-varscan-mutect SARM1,missense_variant,p.Val287Leu,ENST00000585482,NM_015077.3;SARM1,upstream_gene_variant,,ENST00000578128,;SARM1,non_coding_transcript_exon_variant,,ENST00000379061,;CTB-96E2.3,non_coding_transcript_exon_variant,,ENST00000591482,;SARM1,upstream_gene_variant,,ENST00000585453,;SARM1,upstream_gene_variant,,ENST00000577870,;SARM1,upstream_gene_variant,,ENST00000582323,; T ENST00000585482 Transcript missense_variant 1230/10309 859/2175 287/724 V/L Gtg/Ttg 1 1 SARM1 HGNC HGNC:17074 protein_coding YES ENSP00000468032 Q6SZW1 UPI000021FB54 NM_015077.3 deleterious(0.03) 2/9 hmmpanther:PTHR22998,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1042000746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 28381591 28381591 G T 1 0 0 0 0 1 0 0 0 14103 1261 44 2 2 SARM1 17 28381591 Missense_Mutation SNP G C3N-02089_T 6846084 28381591 54875850 820 27904 FAM222B 0 . GRCh38 17 28759124 28759124 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.835A>T p.Arg279Trp p.R279W ENST00000581407 3/3 383 346 37 322 321 1 strelka-varscan-mutect FAM222B,missense_variant,p.Arg279Trp,ENST00000581407,NM_001288632.1,NM_018182.3,NM_001077498.2,NM_001288635.1,NM_001288633.1;FAM222B,missense_variant,p.Arg151Trp,ENST00000341217,NM_001288639.1,NM_001288636.1,NM_001288637.1,NM_001288638.1,NM_001288640.1;FAM222B,missense_variant,p.Arg279Trp,ENST00000452648,NM_001288634.1;FAM222B,3_prime_UTR_variant,,ENST00000582266,;FAM222B,downstream_gene_variant,,ENST00000583307,;FAM222B,downstream_gene_variant,,ENST00000577513,;FAM222B,downstream_gene_variant,,ENST00000577376,;FAM222B,downstream_gene_variant,,ENST00000581229,;FAM222B,downstream_gene_variant,,ENST00000584059,;FAM222B,downstream_gene_variant,,ENST00000583953,;FAM222B,downstream_gene_variant,,ENST00000582059,;FAM222B,downstream_gene_variant,,ENST00000581381,;FAM222B,downstream_gene_variant,,ENST00000583522,;FAM222B,downstream_gene_variant,,ENST00000577682,;FAM222B,downstream_gene_variant,,ENST00000579381,; A ENST00000581407 Transcript missense_variant 1017/4161 835/1689 279/562 R/W Agg/Tgg 1 -1 FAM222B HGNC HGNC:25563 protein_coding YES CCDS45637.1 ENSP00000462419 Q8WU58 A0A024QZ60 UPI000006F01C NM_001288632.1,NM_018182.3,NM_001077498.2,NM_001288635.1,NM_001288633.1 deleterious(0) 3/3 hmmpanther:PTHR16070,hmmpanther:PTHR16070:SF1,Pfam_domain:PF15258 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 28759124 28759124 T A 1 0 0 0 0 1 0 0 0 5417 1550 54 4 4 FAM222B 17 28759124 Missense_Mutation SNP T C3N-02089_T 377533 28759124 54498317 821 27905 ABHD15 0 . GRCh38 17 29566775 29566775 + Silent SNP C C T rs759500284 C3N-02089_T C3N-02089_N C C c.192G>A p.= p.E64E ENST00000307201 1/2 141 107 34 136 136 0 strelka-varscan-mutect ABHD15,synonymous_variant,p.=,ENST00000307201,NM_198147.2;TP53I13,upstream_gene_variant,,ENST00000301057,NM_138349.2;TP53I13,upstream_gene_variant,,ENST00000578749,;TP53I13,upstream_gene_variant,,ENST00000581411,;TP53I13,upstream_gene_variant,,ENST00000580183,;TP53I13,upstream_gene_variant,,ENST00000582829,;TP53I13,upstream_gene_variant,,ENST00000583940,;ABHD15-AS1,intron_variant,,ENST00000581474,;RP11-68I3.4,upstream_gene_variant,,ENST00000579050,;TP53I13,intron_variant,,ENST00000584522,;TP53I13,intron_variant,,ENST00000578073,;TP53I13,upstream_gene_variant,,ENST00000579674,;TP53I13,upstream_gene_variant,,ENST00000577934,;TP53I13,upstream_gene_variant,,ENST00000580132,; T ENST00000307201 Transcript synonymous_variant 363/3592 192/1407 64/468 E gaG/gaA rs759500284 1 -1 ABHD15 HGNC HGNC:26971 protein_coding YES CCDS32602.1 ENSP00000302657 Q6UXT9 UPI00001C1FC9 NM_198147.2 1/2 hmmpanther:PTHR10794:SF39,hmmpanther:PTHR10794 LOW 1 SNV 1 1 PASS rs759500284 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 29566775 29566775 C T 1 0 0 0 0 0 0 0 1 85 796 28 3 3 ABHD15 17 29566775 Silent SNP C C3N-02089_T 807651 29566775 53690666 822 27906 ATAD5 0 . GRCh38 17 30840655 30840655 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.2115A>C p.Gln705His p.Q705H ENST00000321990 4/23 166 144 22 157 157 0 strelka-varscan-mutect ATAD5,missense_variant,p.Gln705His,ENST00000321990,NM_024857.4;CTD-2349P21.11,intron_variant,,ENST00000580873,;ATAD5,missense_variant,p.Gln705His,ENST00000578295,;ATAD5,non_coding_transcript_exon_variant,,ENST00000585133,; C ENST00000321990 Transcript missense_variant 2493/6869 2115/5535 705/1844 Q/H caA/caC 1 1 ATAD5 HGNC HGNC:25752 protein_coding YES CCDS11260.1 ENSP00000313171 Q96QE3 UPI0000071E9E NM_024857.4 deleterious(0) 4/23 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 30840655 30840655 A C 1 0 0 0 0 1 0 0 0 1224 98 4 5 5 ATAD5 17 30840655 Missense_Mutation SNP A C3N-02089_T 1273880 30840655 52416786 823 27907 TMEM132E 0 . GRCh38 17 34637862 34637862 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2585C>A p.Pro862Gln p.P862Q ENST00000321639 10/10 122 103 19 98 98 0 strelka-varscan-mutect TMEM132E,missense_variant,p.Pro952Gln,ENST00000631683,NM_001304438.1;TMEM132E,missense_variant,p.Pro862Gln,ENST00000321639,;TMEM132E,downstream_gene_variant,,ENST00000577271,; A ENST00000321639 Transcript missense_variant 2913/4369 2585/2955 862/984 P/Q cCg/cAg 1 1 TMEM132E HGNC HGNC:26991 protein_coding YES ENSP00000316532 Q6IEE7 UPI000035960F tolerated(0.07) 10/10 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF7 MODERATE 1 SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 34637862 34637862 C A 1 0 0 0 0 1 0 0 0 16493 652 23 1 1 TMEM132E 17 34637862 Missense_Mutation SNP C C3N-02089_T 3797207 34637862 48619579 824 27908 TBC1D3B 0 . GRCh38 17 36169115 36169115 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.727G>C p.Val243Leu p.V243L ENST00000611257 10/14 1290 1207 83 1152 1152 0 varscan-mutect TBC1D3B,missense_variant,p.Val243Leu,ENST00000611257,NM_001001417.6;TBC1D3B,downstream_gene_variant,,ENST00000616006,;CTB-91J4.1,intron_variant,,ENST00000617914,;TBC1D3B,downstream_gene_variant,,ENST00000622280,;TBC1D3B,downstream_gene_variant,,ENST00000610580,; G ENST00000611257 Transcript missense_variant 844/2081 727/1650 243/549 V/L Gta/Cta 1 -1 TBC1D3B HGNC HGNC:27011 protein_coding YES CCDS42300.1 ENSP00000478473 A6NDS4 UPI000292EEF0 NM_001001417.6 tolerated(1) 10/14 Pfam_domain:PF00566,PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF233,SMART_domains:SM00164,Superfamily_domains:SSF47923 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 36169115 36169115 C G 1 0 0 0 0 1 0 0 0 16023 507 18 4 4 TBC1D3B 17 36169115 Missense_Mutation SNP C C3N-02089_T 1531253 36169115 47088326 825 27909 ACACA 0 . GRCh38 17 37192208 37192208 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.4298G>T p.Cys1433Phe p.C1433F ENST00000616317 37/56 382 271 111 425 424 1 strelka-varscan-mutect ACACA,missense_variant,p.Cys1433Phe,ENST00000616317,NM_198834.2;ACACA,missense_variant,p.Cys1338Phe,ENST00000612895,NM_198837.1;ACACA,missense_variant,p.Cys1396Phe,ENST00000614428,NM_198836.2,NM_198839.2;ACACA,missense_variant,p.Cys1318Phe,ENST00000617649,NM_198838.1;ACACA,missense_variant,p.Cys97Phe,ENST00000619546,;ACACA,non_coding_transcript_exon_variant,,ENST00000619245,;ACACA,upstream_gene_variant,,ENST00000618575,; A ENST00000616317 Transcript missense_variant 4779/9961 4298/7152 1433/2383 C/F tGt/tTt 1 -1 ACACA HGNC HGNC:84 protein_coding YES CCDS42302.1 ENSP00000483300 Q13085 UPI00002263AC NM_198834.2 deleterious(0.01) 37/56 hmmpanther:PTHR18866,hmmpanther:PTHR18866:SF97,Pfam_domain:PF08326 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 37192208 37192208 C A 1 0 0 0 0 1 0 0 0 149 478 17 2 2 ACACA 17 37192208 Missense_Mutation SNP C C3N-02089_T 1023093 37192208 46065233 826 27910 SRCIN1 0 . GRCh38 17 38558359 38558359 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.2069A>T p.Glu690Val p.E690V ENST00000617146 11/19 213 168 45 151 151 0 strelka-varscan-mutect SRCIN1,missense_variant,p.Glu690Val,ENST00000617146,NM_025248.2;SRCIN1,missense_variant,p.Glu724Val,ENST00000621492,;SRCIN1,missense_variant,p.Glu478Val,ENST00000622190,;SRCIN1,downstream_gene_variant,,ENST00000612431,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000621763,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000622519,;SRCIN1,non_coding_transcript_exon_variant,,ENST00000612208,; A ENST00000617146 Transcript missense_variant 2294/7058 2069/3552 690/1183 E/V gAg/gTg 1 -1 SRCIN1 HGNC HGNC:29506 protein_coding YES CCDS45660.1 ENSP00000484715 Q9C0H9 UPI0000E27F82 NM_025248.2 deleterious(0) 11/19 hmmpanther:PTHR22741,hmmpanther:PTHR22741:SF5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 38558359 38558359 T A 1 0 0 0 0 1 0 0 0 15494 1551 54 4 4 SRCIN1 17 38558359 Missense_Mutation SNP T C3N-02089_T 1366151 38558359 44699082 827 27911 KRT222 0 . GRCh38 17 40656548 40656548 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.742T>G p.Ser248Ala p.S248A ENST00000394052 6/6 280 247 33 271 271 0 strelka-varscan-mutect KRT222,missense_variant,p.Ser248Ala,ENST00000394052,NM_152349.2;RP5-1028K7.3,missense_variant,p.Ser248Ala,ENST00000476049,;KRT222,3_prime_UTR_variant,,ENST00000394049,;KRT222,downstream_gene_variant,,ENST00000581564,;KRT222,downstream_gene_variant,,ENST00000580719,; C ENST00000394052 Transcript missense_variant 784/1712 742/888 248/295 S/A Tct/Gct 1 -1 KRT222 HGNC HGNC:28695 protein_coding YES CCDS11371.1 ENSP00000377616 Q8N1A0 UPI0000072F8A NM_152349.2 deleterious(0) 6/6 MODERATE 1 SNV 1 1 PASS rs1184499878 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 40656548 40656548 A C 1 0 0 0 0 1 0 0 0 8341 246 9 5 5 KRT222 17 40656548 Missense_Mutation SNP A C3N-02089_T 2098189 40656548 42600893 828 27912 KRT28 0 . GRCh38 17 40797219 40797219 + Silent SNP C C A C3N-02089_T C3N-02089_N C C c.753G>T p.= p.P251P ENST00000306658 4/8 180 159 21 207 207 0 strelka-varscan-mutect KRT28,synonymous_variant,p.=,ENST00000306658,NM_181535.3; A ENST00000306658 Transcript synonymous_variant 819/1685 753/1395 251/464 P ccG/ccT COSM121114 1 -1 KRT28 HGNC HGNC:30842 protein_coding YES CCDS11376.1 ENSP00000305263 Q7Z3Y7 UPI0000246D70 NM_181535.3 4/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF215,Pfam_domain:PF00038,SMART_domains:SM01391,Prints_domain:PR01248 1 LOW 1 SNV 1 1 1 PASS rs1198821641 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 40797219 40797219 C A 1 0 0 0 0 0 0 0 1 8347 639 23 1 1 KRT28 17 40797219 Silent SNP C C3N-02089_T 140671 40797219 42460222 829 27913 ZNF385C 0 . GRCh38 17 42028926 42028926 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.587G>T p.Arg196Ile p.R196I ENST00000618554 5/8 374 314 60 322 321 1 strelka-varscan-mutect ZNF385C,missense_variant,p.Arg196Ile,ENST00000618554,NM_001242704.1;ZNF385C,missense_variant,p.Arg276Ile,ENST00000436535,;NKIRAS2,downstream_gene_variant,,ENST00000307641,NM_001001349.2;NKIRAS2,downstream_gene_variant,,ENST00000393885,NM_001144927.1,NM_017595.5;NKIRAS2,downstream_gene_variant,,ENST00000393880,;NKIRAS2,downstream_gene_variant,,ENST00000393881,;NKIRAS2,downstream_gene_variant,,ENST00000449471,NM_001144928.1;NKIRAS2,downstream_gene_variant,,ENST00000479407,NM_001144929.1;NKIRAS2,downstream_gene_variant,,ENST00000316082,;NKIRAS2,downstream_gene_variant,,ENST00000462043,;ZNF385C,upstream_gene_variant,,ENST00000461831,;NKIRAS2,downstream_gene_variant,,ENST00000393879,;ZNF385C,upstream_gene_variant,,ENST00000496039,;NKIRAS2,downstream_gene_variant,,ENST00000491638,;NKIRAS2,downstream_gene_variant,,ENST00000485789,; A ENST00000618554 Transcript missense_variant 587/2596 587/1275 196/424 R/I aGa/aTa 1 -1 ZNF385C HGNC HGNC:33722 protein_coding YES CCDS74065.1 ENSP00000480744 A0A087WX54 UPI0001E6F8A9 NM_001242704.1 tolerated(0.19) 5/8 hmmpanther:PTHR23067,hmmpanther:PTHR23067:SF6,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 42028926 42028926 C A 1 0 0 0 0 1 0 0 0 18450 913 32 2 2 ZNF385C 17 42028926 Missense_Mutation SNP C C3N-02089_T 1231707 42028926 41228515 830 27914 KAT2A 0 . GRCh38 17 42121000 42121000 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.305A>G p.Lys102Arg p.K102R ENST00000225916 1/18 249 219 30 213 210 3 strelka-varscan-mutect KAT2A,missense_variant,p.Lys102Arg,ENST00000225916,NM_021078.2;CTD-2132N18.3,intron_variant,,ENST00000592574,;HSPB9,upstream_gene_variant,,ENST00000565659,NM_033194.2;RAB5C,downstream_gene_variant,,ENST00000393860,;RAB5C,downstream_gene_variant,,ENST00000346213,NM_004583.3,NM_201434.2;RAB5C,downstream_gene_variant,,ENST00000547517,NM_001252039.1;KAT2A,missense_variant,p.Lys20Arg,ENST00000465682,;CTD-2132N18.3,intron_variant,,ENST00000592248,;CTD-2132N18.3,intron_variant,,ENST00000585562,;KAT2A,upstream_gene_variant,,ENST00000592310,; C ENST00000225916 Transcript missense_variant 359/3109 305/2514 102/837 K/R aAg/aGg 1 -1 KAT2A HGNC HGNC:4201 protein_coding YES CCDS11417.1 ENSP00000225916 Q92830 UPI000000D978 NM_021078.2 deleterious(0.04) 1/18 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF124,PIRSF_domain:PIRSF003048,Pfam_domain:PF06466 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 42121000 42121000 T C 1 0 0 0 0 1 0 0 0 7895 1609 56 5 5 KAT2A 17 42121000 Missense_Mutation SNP T C3N-02089_T 92074 42121000 41136441 831 27915 MEOX1 0 . GRCh38 17 43661506 43661506 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.29G>A p.Arg10Lys p.R10K ENST00000318579 1/3 71 52 19 67 67 0 strelka-varscan-mutect MEOX1,missense_variant,p.Arg10Lys,ENST00000318579,NM_004527.3;MEOX1,missense_variant,p.Arg10Lys,ENST00000329168,NM_013999.3;MEOX1,5_prime_UTR_variant,,ENST00000549132,;MEOX1,intron_variant,,ENST00000393661,NM_001040002.1; T ENST00000318579 Transcript missense_variant 449/2707 29/765 10/254 R/K aGg/aAg 1 -1 MEOX1 HGNC HGNC:7013 protein_coding YES CCDS11466.1 ENSP00000321684 P50221 UPI000012F410 NM_004527.3 deleterious(0.01) 1/3 hmmpanther:PTHR24328:SF8,hmmpanther:PTHR24328 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 43661506 43661506 C T 1 0 0 0 0 1 0 0 0 9418 681 24 3 3 MEOX1 17 43661506 Missense_Mutation SNP C C3N-02089_T 1540506 43661506 39595935 832 27916 FZD2 0 . GRCh38 17 44558772 44558772 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1084C>A p.His362Asn p.H362N ENST00000315323 1/1 223 161 62 177 177 0 strelka-varscan-mutect FZD2,missense_variant,p.His362Asn,ENST00000315323,NM_001466.3; A ENST00000315323 Transcript missense_variant 1314/2112 1084/1698 362/565 H/N Cac/Aac 1 1 FZD2 HGNC HGNC:4040 protein_coding YES CCDS11484.1 ENSP00000323901 Q14332 UPI0000050444 NM_001466.3 tolerated(0.51) 1/1 Pfam_domain:PF01534,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF34,SMART_domains:SM01330 MODERATE 1 SNV 1 PASS rs1220274619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 44558772 44558772 C A 1 0 0 0 0 1 0 0 0 6001 594 21 2 2 FZD2 17 44558772 Missense_Mutation SNP C C3N-02089_T 897266 44558772 38698669 833 27917 MRPL10 0 . GRCh38 17 47826697 47826697 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.502G>C p.Glu168Gln p.E168Q ENST00000290208 4/5 223 209 14 221 221 0 varscan-mutect MRPL10,missense_variant,p.Glu168Gln,ENST00000290208,;MRPL10,missense_variant,p.Glu158Gln,ENST00000351111,NM_145255.3;MRPL10,missense_variant,p.Glu168Gln,ENST00000414011,NM_148887.2;OSBPL7,upstream_gene_variant,,ENST00000007414,NM_145798.2;OSBPL7,upstream_gene_variant,,ENST00000392507,;OSBPL7,upstream_gene_variant,,ENST00000613735,;LRRC46,upstream_gene_variant,,ENST00000269025,NM_033413.3;MRPL10,3_prime_UTR_variant,,ENST00000421763,;OSBPL7,upstream_gene_variant,,ENST00000580140,;LRRC46,upstream_gene_variant,,ENST00000579971,;OSBPL7,upstream_gene_variant,,ENST00000580226,;LRRC46,upstream_gene_variant,,ENST00000579742,;OSBPL7,upstream_gene_variant,,ENST00000585051,;MRPL10,downstream_gene_variant,,ENST00000423147,;MRPL10,downstream_gene_variant,,ENST00000480901,;MRPL10,downstream_gene_variant,,ENST00000466016,; G ENST00000290208 Transcript missense_variant 955/2013 502/816 168/271 E/Q Gag/Cag 1 -1 MRPL10 HGNC HGNC:14055 protein_coding YES CCDS11517.1 ENSP00000290208 Q7Z7H8 UPI000013DFCA deleterious(0.04) 4/5 hmmpanther:PTHR11560:SF8,hmmpanther:PTHR11560,Pfam_domain:PF00466,Superfamily_domains:0053665 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 47826697 47826697 C G 1 0 0 0 0 1 0 0 0 9750 922 32 4 4 MRPL10 17 47826697 Missense_Mutation SNP C C3N-02089_T 3267925 47826697 35430744 834 27918 CA10 0 . GRCh38 17 52072334 52072334 + Nonsense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.121G>T p.Gly41Ter p.G41* ENST00000451037 2/9 204 170 34 228 227 1 strelka-varscan-mutect CA10,stop_gained,p.Gly41Ter,ENST00000451037,NM_020178.4;CA10,stop_gained,p.Gly41Ter,ENST00000442502,NM_001082534.1;CA10,stop_gained,p.Gly41Ter,ENST00000285273,NM_001082533.1;CA10,stop_gained,p.Gly41Ter,ENST00000575181,;CA10,5_prime_UTR_variant,,ENST00000570565,;CA10,non_coding_transcript_exon_variant,,ENST00000573294,;CA10,3_prime_UTR_variant,,ENST00000571371,; A ENST00000451037 Transcript stop_gained 1062/3189 121/987 41/328 G/* Gga/Tga COSM3519556,COSM3519557 1 -1 CA10 HGNC HGNC:1369 protein_coding YES CCDS32684.1 ENSP00000405388 Q9NS85 UPI000000167C NM_020178.4 2/9 PROSITE_profiles:PS51144,hmmpanther:PTHR18952,hmmpanther:PTHR18952:SF91,Pfam_domain:PF00194,Gene3D:3.10.200.10,SMART_domains:SM01057 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 52072334 52072334 C A 1 0 0 0 0 0 1 0 0 2197 632 22 2 2 CA10 17 52072334 Nonsense_Mutation SNP C C3N-02089_T 4245637 52072334 31185107 835 27919 LPO 0 . GRCh38 17 58244017 58244017 + Frame_Shift_Del DEL A A - rs756204121 C3N-02089_T C3N-02089_N A A c.100delA p.Ile34SerfsTer5 p.I34Sfs*5 ENST00000262290 3/13 178 159 19 174 174 0 varindel-pindel LPO,frameshift_variant,p.Ile34SerfsTer5,ENST00000262290,NM_006151.2;LPO,intron_variant,,ENST00000421678,NM_001160102.1;LPO,intron_variant,,ENST00000582328,;LPO,intron_variant,,ENST00000543544,;LPO,intron_variant,,ENST00000581008,;LPO,non_coding_transcript_exon_variant,,ENST00000578643,;LPO,non_coding_transcript_exon_variant,,ENST00000578403,;LPO,non_coding_transcript_exon_variant,,ENST00000582684,;LPO,intron_variant,,ENST00000580346,; - ENST00000262290 Transcript frameshift_variant 416/2979 100/2139 34/712 I/X Atc/tc rs756204121 1 1 LPO HGNC HGNC:6678 protein_coding YES CCDS32689.1 ENSP00000262290 P22079 UPI0000131631 NM_006151.2 3/13 hmmpanther:PTHR11475,hmmpanther:PTHR11475:SF67 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 58244017 58244017 A - 1 0 1 0 1 0 0 0 0 8821 217 8 0 0 LPO 17 58244017 Frame_Shift_Del DEL A C3N-02089_T 6171683 58244017 25013424 836 27920 TSPOAP1 0 . GRCh38 17 58312442 58312442 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2379C>A p.Tyr793Ter p.Y793* ENST00000343736 17/32 106 91 15 97 97 0 strelka-varscan-mutect TSPOAP1,stop_gained,p.Tyr733Ter,ENST00000268893,NM_024418.2;TSPOAP1,stop_gained,p.Tyr793Ter,ENST00000343736,NM_001261835.1,NM_004758.3;TSPOAP1,upstream_gene_variant,,ENST00000582679,;TSPOAP1,upstream_gene_variant,,ENST00000580669,;TSPOAP1,upstream_gene_variant,,ENST00000578486,;TSPOAP1,upstream_gene_variant,,ENST00000585149,; T ENST00000343736 Transcript stop_gained 2543/5947 2379/5574 793/1857 Y/* taC/taA 1 -1 TSPOAP1 HGNC HGNC:16831 protein_coding YES CCDS11605.1 ENSP00000345824 O95153 UPI000013D7E3 NM_001261835.1,NM_004758.3 17/32 PROSITE_profiles:PS50853,hmmpanther:PTHR14234,hmmpanther:PTHR14234:SF20,SMART_domains:SM00060 HIGH 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -19.99994 0.9999929 1 1 1 0 T 4 4 90 58312442 58312442 G T 1 0 0 0 0 0 1 0 0 17163 1256 44 2 2 TSPOAP1 17 58312442 Nonsense_Mutation SNP G C3N-02089_T 68425 58312442 24944999 837 27921 PRR11 0 . GRCh38 17 59185159 59185159 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.234T>A p.Asn78Lys p.N78K ENST00000262293 3/10 173 128 45 193 193 0 strelka-varscan-mutect PRR11,missense_variant,p.Asn78Lys,ENST00000262293,NM_018304.3;PRR11,missense_variant,p.Asn78Lys,ENST00000614081,;PRR11,missense_variant,p.Asn78Lys,ENST00000578777,;PRR11,missense_variant,p.Asn105Lys,ENST00000582995,;PRR11,missense_variant,p.Asn78Lys,ENST00000578542,;PRR11,missense_variant,p.Asn78Lys,ENST00000580177,;PRR11,non_coding_transcript_exon_variant,,ENST00000581182,;SPDYE22P,upstream_gene_variant,,ENST00000582158,; A ENST00000262293 Transcript missense_variant 546/2332 234/1083 78/360 N/K aaT/aaA 1 1 PRR11 HGNC HGNC:25619 protein_coding YES CCDS11614.1 ENSP00000262293 Q96HE9 D2SNZ4 UPI000006FA82 NM_018304.3 tolerated(0.36) 3/10 hmmpanther:PTHR23330 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 59185159 59185159 T A 1 0 0 0 0 1 0 0 0 12718 1403 49 4 4 PRR11 17 59185159 Missense_Mutation SNP T C3N-02089_T 872717 59185159 24072282 838 27922 KCNH6 0 . GRCh38 17 63544043 63544043 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.2265C>T p.= p.P755P ENST00000583023 11/14 56 40 16 42 42 0 strelka-varscan-mutect KCNH6,synonymous_variant,p.=,ENST00000583023,NM_030779.3;KCNH6,intron_variant,,ENST00000314672,NM_001278919.1,NM_001278920.1;KCNH6,intron_variant,,ENST00000581784,NM_173092.2;KCNH6,intron_variant,,ENST00000456941,;KCNH6,intron_variant,,ENST00000583465,; T ENST00000583023 Transcript synonymous_variant 2276/3821 2265/2985 755/994 P ccC/ccT 1 1 KCNH6 HGNC HGNC:18862 protein_coding YES CCDS11638.1 ENSP00000463533 Q9H252 UPI000012DCAB NM_030779.3 11/14 hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF468 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 63544043 63544043 C T 1 0 0 0 0 0 0 0 1 7952 668 24 3 3 KCNH6 17 63544043 Silent SNP C C3N-02089_T 4358884 63544043 19713398 839 27923 CSHL1 0 . GRCh38 17 63910247 63910247 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.386C>A p.Thr129Asn p.T129N ENST00000309894 4/5 339 267 72 388 388 0 strelka-varscan-mutect CSHL1,missense_variant,p.Thr35Asn,ENST00000450719,;CSHL1,missense_variant,p.Thr46Asn,ENST00000561003,;CSHL1,missense_variant,p.Thr124Asn,ENST00000392824,;CSHL1,missense_variant,p.Thr124Asn,ENST00000611417,;CSHL1,missense_variant,p.Thr67Asn,ENST00000259003,NM_001321068.1;CSHL1,missense_variant,p.Thr129Asn,ENST00000309894,NM_022581.1,NM_022579.1;CSHL1,missense_variant,p.Thr35Asn,ENST00000346606,NM_001318.2;CSHL1,missense_variant,p.Thr46Asn,ENST00000438387,NM_022580.1;CSHL1,non_coding_transcript_exon_variant,,ENST00000558099,;CSHL1,non_coding_transcript_exon_variant,,ENST00000560999,;CSHL1,non_coding_transcript_exon_variant,,ENST00000558609,; T ENST00000309894 Transcript missense_variant 386/669 386/669 129/222 T/N aCc/aAc 1 -1 CSHL1 HGNC HGNC:2442 protein_coding YES CCDS11652.1 ENSP00000309524 Q14406 UPI00001602B9 NM_022581.1,NM_022579.1 deleterious(0.04) 4/5 Gene3D:1.20.1250.10,Pfam_domain:PF00103,hmmpanther:PTHR11417,hmmpanther:PTHR11417:SF40,Superfamily_domains:SSF47266 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 63910247 63910247 G T 1 0 0 0 0 1 0 0 0 3743 1261 44 2 2 CSHL1 17 63910247 Missense_Mutation SNP G C3N-02089_T 366204 63910247 19347194 840 27924 CEP95 0 . GRCh38 17 64537085 64537085 + Silent SNP T T G novel C3N-02089_T C3N-02089_N T T c.2262T>G p.= p.L754L ENST00000556440 19/20 202 178 24 219 219 0 strelka-varscan-mutect CEP95,synonymous_variant,p.=,ENST00000556440,NM_138363.1;CEP95,synonymous_variant,p.=,ENST00000553412,;CEP95,synonymous_variant,p.=,ENST00000583676,;CEP95,3_prime_UTR_variant,,ENST00000553956,;CEP95,non_coding_transcript_exon_variant,,ENST00000581885,;CEP95,non_coding_transcript_exon_variant,,ENST00000580285,;CEP95,non_coding_transcript_exon_variant,,ENST00000581980,;CEP95,downstream_gene_variant,,ENST00000584857,;CEP95,downstream_gene_variant,,ENST00000579637,;CEP95,downstream_gene_variant,,ENST00000582698,; G ENST00000556440 Transcript synonymous_variant 2772/3139 2262/2466 754/821 L ctT/ctG 1 1 CEP95 HGNC HGNC:25141 protein_coding YES CCDS45763.1 ENSP00000450461 Q96GE4 UPI000006F4B3 NM_138363.1 19/20 hmmpanther:PTHR22545,hmmpanther:PTHR22545:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 64537085 64537085 T G 1 0 0 0 0 0 0 0 1 2988 1741 61 5 5 CEP95 17 64537085 Silent SNP T C3N-02089_T 626838 64537085 18720356 841 27925 LRRC37A3 0 . GRCh38 17 64895952 64895952 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1306C>A p.Gln436Lys p.Q436K ENST00000584306 3/14 113 100 13 125 125 0 varscan-mutect LRRC37A3,missense_variant,p.Gln436Lys,ENST00000584306,NM_199340.3;LRRC37A3,missense_variant,p.Gln436Lys,ENST00000319651,;LRRC37A3,intron_variant,,ENST00000400877,;LRRC37A3,intron_variant,,ENST00000339474,NM_001303255.1;LRRC37A3,intron_variant,,ENST00000581368,;LRRC37A3,upstream_gene_variant,,ENST00000584788,;LRRC37A3,upstream_gene_variant,,ENST00000580464,;RP11-927P21.1,intron_variant,,ENST00000584959,;RP11-927P21.1,intron_variant,,ENST00000577938,;RP11-927P21.1,intron_variant,,ENST00000584131,;RP11-927P21.2,upstream_gene_variant,,ENST00000581622,;LRRC37A3,downstream_gene_variant,,ENST00000577487,;LRRC37A3,downstream_gene_variant,,ENST00000580439,;RP11-927P21.9,downstream_gene_variant,,ENST00000607347,; T ENST00000584306 Transcript missense_variant 1837/5665 1306/4905 436/1634 Q/K Cag/Aag 1 -1 LRRC37A3 HGNC HGNC:32427 protein_coding YES CCDS32708.1 ENSP00000464535 O60309 UPI00005B2F0A NM_199340.3 tolerated(0.06) 3/14 hmmpanther:PTHR23045,hmmpanther:PTHR23045:SF7 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 64895952 64895952 G T 1 0 0 0 0 1 0 0 0 8887 1357 47 2 2 LRRC37A3 17 64895952 Missense_Mutation SNP G C3N-02089_T 358867 64895952 18361489 842 27926 BPTF 0 . GRCh38 17 67913097 67913097 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.5213G>T p.Arg1738Leu p.R1738L ENST00000306378 11/28 200 174 26 183 183 0 strelka-varscan-mutect BPTF,missense_variant,p.Arg1864Leu,ENST00000321892,NM_004459.6;BPTF,missense_variant,p.Arg1738Leu,ENST00000306378,NM_182641.3;BPTF,missense_variant,p.Arg1725Leu,ENST00000424123,;BPTF,missense_variant,p.Arg1801Leu,ENST00000544778,; T ENST00000306378 Transcript missense_variant 5273/9688 5213/8763 1738/2920 R/L cGa/cTa 1 1 BPTF HGNC HGNC:3581 protein_coding YES CCDS11673.1 ENSP00000307208 Q12830 UPI00002263BF NM_182641.3 tolerated(0.06) 11/28 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF5 MODERATE 1 SNV 1 1 PASS rs1264742600 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 67913097 67913097 G T 1 0 0 0 0 1 0 0 0 1664 1058 37 1 1 BPTF 17 67913097 Missense_Mutation SNP G C3N-02089_T 3017145 67913097 15344344 843 27927 ABCA5 0 . GRCh38 17 69313221 69313221 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.178G>T p.Glu60Ter p.E60* ENST00000392676 3/39 184 167 17 214 212 2 strelka-varscan-mutect ABCA5,stop_gained,p.Glu60Ter,ENST00000392676,NM_172232.3;ABCA5,stop_gained,p.Glu60Ter,ENST00000588877,NM_018672.4;ABCA5,stop_gained,p.Glu60Ter,ENST00000593153,;ABCA5,stop_gained,p.Glu60Ter,ENST00000592568,;ABCA5,upstream_gene_variant,,ENST00000589975,;ABCA5,downstream_gene_variant,,ENST00000588665,;ABCA5,downstream_gene_variant,,ENST00000589609,;ABCA5,stop_gained,p.Glu60Ter,ENST00000593253,;ABCA5,stop_gained,p.Glu60Ter,ENST00000587607,; A ENST00000392676 Transcript stop_gained 243/8220 178/4929 60/1642 E/* Gaa/Taa 1 -1 ABCA5 HGNC HGNC:35 protein_coding YES CCDS11685.1 ENSP00000376443 Q8WWZ7 UPI000013DD9E NM_172232.3 3/39 hmmpanther:PTHR19229:SF100,hmmpanther:PTHR19229,Pfam_domain:PF12698 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 69313221 69313221 C A 1 0 0 0 0 0 1 0 0 39 922 32 2 2 ABCA5 17 69313221 Nonsense_Mutation SNP C C3N-02089_T 1400124 69313221 13944220 844 27928 TMEM94 0 . GRCh38 17 75494745 75494745 + Silent SNP T T C novel C3N-02089_T C3N-02089_N T T c.2526T>C p.= p.D842D ENST00000314256 19/32 269 232 37 246 246 0 strelka-varscan-mutect TMEM94,synonymous_variant,p.=,ENST00000314256,NM_001321149.1,NM_014738.4;TMEM94,synonymous_variant,p.=,ENST00000375248,;TMEM94,synonymous_variant,p.=,ENST00000579208,;TMEM94,upstream_gene_variant,,ENST00000577247,;TMEM94,downstream_gene_variant,,ENST00000578853,;TMEM94,downstream_gene_variant,,ENST00000580918,;TMEM94,upstream_gene_variant,,ENST00000584694,;TMEM94,downstream_gene_variant,,ENST00000581252,;TMEM94,upstream_gene_variant,,ENST00000577245,;TMEM94,upstream_gene_variant,,ENST00000618984,;TMEM94,downstream_gene_variant,,ENST00000583795,;TMEM94,non_coding_transcript_exon_variant,,ENST00000585105,;TMEM94,non_coding_transcript_exon_variant,,ENST00000581085,;TMEM94,upstream_gene_variant,,ENST00000579898,;TMEM94,downstream_gene_variant,,ENST00000579241,;TMEM94,upstream_gene_variant,,ENST00000581453,;TMEM94,upstream_gene_variant,,ENST00000581867,;TMEM94,downstream_gene_variant,,ENST00000578624,;TMEM94,upstream_gene_variant,,ENST00000581723,;TMEM94,downstream_gene_variant,,ENST00000583071,;TMEM94,downstream_gene_variant,,ENST00000582843,;TMEM94,downstream_gene_variant,,ENST00000583296,;TMEM94,downstream_gene_variant,,ENST00000580441,;TMEM94,upstream_gene_variant,,ENST00000577194,;TMEM94,downstream_gene_variant,,ENST00000580849,; C ENST00000314256 Transcript synonymous_variant 2920/5213 2526/4071 842/1356 D gaT/gaC 1 1 TMEM94 HGNC HGNC:28983 protein_coding YES CCDS32732.1 ENSP00000313885 Q12767 A0A024R8S6 UPI0000139439 NM_001321149.1,NM_014738.4 19/32 hmmpanther:PTHR13219,hmmpanther:PTHR13219:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 75494745 75494745 T C 1 0 0 0 0 0 0 0 1 16697 1461 51 5 5 TMEM94 17 75494745 Silent SNP T C3N-02089_T 6181524 75494745 7762696 845 27929 FBF1 0 . GRCh38 17 75921470 75921470 + Splice_Site SNP A A T novel C3N-02089_T C3N-02089_N A A c.1570+2T>A p.X524_splice ENST00000627351 210 186 24 152 152 0 strelka-varscan-mutect FBF1,splice_donor_variant,,ENST00000586717,NM_001319193.1;FBF1,splice_donor_variant,,ENST00000319129,;FBF1,splice_donor_variant,,ENST00000636174,;FBF1,splice_donor_variant,,ENST00000592193,;FBF1,splice_donor_variant,,ENST00000627351,NM_001080542.1;FBF1,splice_donor_variant,,ENST00000585990,;RP11-552F3.12,splice_donor_variant,,ENST00000593156,;FBF1,splice_donor_variant,,ENST00000586838,;FBF1,upstream_gene_variant,,ENST00000588283,; T ENST00000627351 Transcript splice_donor_variant -/3402 1570/3402 524/1133 1 -1 FBF1 HGNC HGNC:24674 protein_coding YES CCDS45779.1 ENSP00000486708 Q8TES7 UPI0000DD841F NM_001080542.1 14/27 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 75921470 75921470 A T 1 0 0 0 0 0 0 1 0 5557 57 2 4 4 FBF1 17 75921470 Splice_Site SNP A C3N-02089_T 426725 75921470 7335971 846 27930 GALR2 0 . GRCh38 17 76077143 76077143 + Nonsense_Mutation SNP C C A rs113884061 C3N-02089_T C3N-02089_N C C c.876C>A p.Tyr292Ter p.Y292* ENST00000329003 2/2 633 565 68 468 468 0 strelka-varscan-mutect GALR2,stop_gained,p.Tyr292Ter,ENST00000329003,NM_003857.3;EXOC7,downstream_gene_variant,,ENST00000589210,NM_001013839.3;EXOC7,downstream_gene_variant,,ENST00000332065,NM_015219.4;SRP68,upstream_gene_variant,,ENST00000307877,NM_014230.3;SRP68,upstream_gene_variant,,ENST00000539137,NM_001260502.1;ZACN,upstream_gene_variant,,ENST00000334586,NM_180990.3;SRP68,upstream_gene_variant,,ENST00000629930,;EXOC7,downstream_gene_variant,,ENST00000591724,;ZACN,intron_variant,,ENST00000591500,;EXOC7,downstream_gene_variant,,ENST00000465252,;ZACN,upstream_gene_variant,,ENST00000590045,;ZACN,upstream_gene_variant,,ENST00000425015,;SRP68,upstream_gene_variant,,ENST00000592704,;ZACN,upstream_gene_variant,,ENST00000421794,;ZACN,upstream_gene_variant,,ENST00000524242,;SRP68,upstream_gene_variant,,ENST00000591272,; A ENST00000329003 Transcript stop_gained 966/1364 876/1164 292/387 Y/* taC/taA rs113884061 1 1 GALR2 HGNC HGNC:4133 protein_coding YES CCDS11739.1 ENSP00000329684 O43603 UPI000004B247 NM_003857.3 2/2 Transmembrane_helices:TMhelix,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,PROSITE_profiles:PS50262,hmmpanther:PTHR24230,hmmpanther:PTHR24230:SF13,Prints_domain:PR00237 HIGH 1 SNV 1 1 PASS rs113884061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 76077143 76077143 C A 1 0 0 0 0 0 1 0 0 6096 547 19 1 1 GALR2 17 76077143 Nonsense_Mutation SNP C C3N-02089_T 155673 76077143 7180298 847 27931 AANAT 0 . GRCh38 17 76469252 76469252 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.378C>A p.= p.S126S ENST00000250615 6/7 270 220 50 272 270 2 strelka-varscan-mutect AANAT,synonymous_variant,p.=,ENST00000250615,NM_001166579.1;AANAT,synonymous_variant,p.=,ENST00000392492,NM_001088.2;AANAT,synonymous_variant,p.=,ENST00000585649,;RHBDF2,downstream_gene_variant,,ENST00000591885,NM_001005498.3;RHBDF2,downstream_gene_variant,,ENST00000313080,NM_024599.5;RHBDF2,downstream_gene_variant,,ENST00000591860,;AANAT,3_prime_UTR_variant,,ENST00000587798,;RHBDF2,downstream_gene_variant,,ENST00000590168,;RHBDF2,downstream_gene_variant,,ENST00000589582,; A ENST00000250615 Transcript synonymous_variant 1385/1913 378/759 126/252 S tcC/tcA 1 1 AANAT HGNC HGNC:19 protein_coding YES CCDS54169.1 ENSP00000250615 Q16613 UPI000153D76E NM_001166579.1 6/7 PROSITE_profiles:PS51186,hmmpanther:PTHR10908,hmmpanther:PTHR10908:SF2,Gene3D:3.40.630.30,Superfamily_domains:SSF55729 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 76469252 76469252 C A 1 0 0 0 0 0 0 0 1 20 610 22 2 2 AANAT 17 76469252 Silent SNP C C3N-02089_T 392109 76469252 6788189 848 27932 MGAT5B 0 . GRCh38 17 76906117 76906117 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.988G>A p.Asp330Asn p.D330N ENST00000428789 7/16 177 151 26 142 142 0 strelka-varscan-mutect MGAT5B,missense_variant,p.Asp319Asn,ENST00000569840,NM_001199172.1;MGAT5B,missense_variant,p.Asp319Asn,ENST00000301618,NM_144677.2;MGAT5B,missense_variant,p.Asp330Asn,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,missense_variant,p.Asp330Asn,ENST00000565043,; A ENST00000428789 Transcript missense_variant 1091/4053 988/2406 330/801 D/N Gac/Aac 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 deleterious(0) 7/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 76906117 76906117 G A 1 0 0 0 0 1 0 0 0 9510 1174 41 3 3 MGAT5B 17 76906117 Missense_Mutation SNP G C3N-02089_T 436865 76906117 6351324 849 27933 MGAT5B 0 . GRCh38 17 76925013 76925013 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1106C>A p.Pro369His p.P369H ENST00000428789 8/16 210 182 28 167 166 1 strelka-varscan-mutect MGAT5B,missense_variant,p.Pro358His,ENST00000569840,NM_001199172.1;MGAT5B,missense_variant,p.Pro358His,ENST00000301618,NM_144677.2;MGAT5B,missense_variant,p.Pro369His,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000563627,;MGAT5B,missense_variant,p.Pro369His,ENST00000565043,; A ENST00000428789 Transcript missense_variant 1209/4053 1106/2406 369/801 P/H cCc/cAc 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 deleterious(0.02) 8/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 76925013 76925013 C A 1 0 0 0 0 1 0 0 0 9510 623 22 2 2 MGAT5B 17 76925013 Missense_Mutation SNP C C3N-02089_T 18896 76925013 6332428 850 27934 TBC1D16 0 . GRCh38 17 80010340 80010340 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.599G>T p.Arg200Leu p.R200L ENST00000310924 3/12 176 135 41 172 172 0 strelka-varscan-mutect TBC1D16,missense_variant,p.Arg200Leu,ENST00000310924,NM_019020.3; A ENST00000310924 Transcript missense_variant 715/10936 599/2304 200/767 R/L cGg/cTg 1 -1 TBC1D16 HGNC HGNC:28356 protein_coding YES CCDS11766.1 ENSP00000309794 Q8TBP0 UPI000006DDA6 NM_019020.3 tolerated(0.41) 3/12 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF285,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1239821391 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 80010340 80010340 C A 1 0 0 0 0 1 0 0 0 16005 652 23 1 1 TBC1D16 17 80010340 Missense_Mutation SNP C C3N-02089_T 3085327 80010340 3247101 851 27935 CCDC40 0 . GRCh38 17 80040182 80040182 + Frame_Shift_Del DEL G G - novel C3N-02089_T C3N-02089_N G G c.466delG p.Val156SerfsTer11 p.V156Sfs*11 ENST00000397545 3/20 120 103 17 128 128 0 sindel-varindel-pindel CCDC40,frameshift_variant,p.Val156SerfsTer11,ENST00000397545,NM_017950.3;CCDC40,frameshift_variant,p.Val156SerfsTer11,ENST00000374877,NM_001243342.1;CCDC40,frameshift_variant,p.Val156SerfsTer11,ENST00000374876,;CCDC40,frameshift_variant,p.Val156SerfsTer11,ENST00000269318,;CCDC40,frameshift_variant,p.Val126SerfsTer?,ENST00000574099,;TBC1D16,upstream_gene_variant,,ENST00000310924,NM_019020.3;CCDC40,downstream_gene_variant,,ENST00000576033,;CCDC40,downstream_gene_variant,,ENST00000572270,;CCDC40,non_coding_transcript_exon_variant,,ENST00000572083,;CCDC40,non_coding_transcript_exon_variant,,ENST00000576241,;CCDC40,intron_variant,,ENST00000573474,; - ENST00000397545 Transcript frameshift_variant 491/4294 464/3429 155/1142 R/X aGg/ag 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 3/20 HIGH deletion 5 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 80040182 80040182 G - 1 0 1 0 1 0 0 0 0 2521 1000 35 0 0 CCDC40 17 80040182 Frame_Shift_Del DEL G C3N-02089_T 29842 80040182 3217259 852 27936 CCDC40 0 . GRCh38 17 80081876 80081876 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1807G>T p.Glu603Ter p.E603* ENST00000397545 12/20 446 332 114 448 448 0 strelka-varscan-mutect CCDC40,stop_gained,p.Glu603Ter,ENST00000397545,NM_017950.3;CCDC40,stop_gained,p.Glu603Ter,ENST00000374877,NM_001243342.1;CCDC40,splice_region_variant,,ENST00000574799,;CCDC40,non_coding_transcript_exon_variant,,ENST00000572253,; T ENST00000397545 Transcript stop_gained,splice_region_variant 1834/4294 1807/3429 603/1142 E/* Gaa/Taa 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 12/20 hmmpanther:PTHR16275 HIGH 1 SNV 5 1 PASS rs948532763 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 80081876 80081876 G T 1 0 0 0 0 0 1 0 0 2521 1188 41 2 2 CCDC40 17 80081876 Nonsense_Mutation SNP G C3N-02089_T 41694 80081876 3175565 853 27937 RNF213 0 . GRCh38 17 80291636 80291636 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1280G>T p.Gly427Val p.G427V ENST00000582970 8/68 337 267 70 279 276 3 strelka-varscan-mutect RNF213,missense_variant,p.Gly427Val,ENST00000582970,NM_001256071.2;RNF213,missense_variant,p.Gly476Val,ENST00000508628,;RNF213,missense_variant,p.Gly427Val,ENST00000319921,NM_020954.3;RNF213,non_coding_transcript_exon_variant,,ENST00000559070,;RNF213,non_coding_transcript_exon_variant,,ENST00000573548,;RNF213,upstream_gene_variant,,ENST00000574060,; T ENST00000582970 Transcript missense_variant 1423/21055 1280/15624 427/5207 G/V gGt/gTt 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 tolerated(0.06) 8/68 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 80291636 80291636 G T 1 0 0 0 0 1 0 0 0 13656 1261 44 2 2 RNF213 17 80291636 Missense_Mutation SNP G C3N-02089_T 209760 80291636 2965805 854 27938 RFNG 0 . GRCh38 17 82051727 82051727 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.40G>T p.Ala14Ser p.A14S ENST00000310496 1/8 27 17 10 13 13 0 strelka-mutect RFNG,missense_variant,p.Ala14Ser,ENST00000310496,NM_002917.1;GPS1,intron_variant,,ENST00000585084,;GPS1,intron_variant,,ENST00000583961,;GPS1,intron_variant,,ENST00000580716,;GPS1,intron_variant,,ENST00000582327,;GPS1,upstream_gene_variant,,ENST00000392358,NM_212492.1;GPS1,upstream_gene_variant,,ENST00000320548,NM_001321093.1;GPS1,upstream_gene_variant,,ENST00000623761,;GPS1,upstream_gene_variant,,ENST00000578552,NM_001321092.1;GPS1,upstream_gene_variant,,ENST00000306823,NM_004127.4;GPS1,upstream_gene_variant,,ENST00000623691,;GPS1,upstream_gene_variant,,ENST00000624957,;RFNG,upstream_gene_variant,,ENST00000429557,;GPS1,upstream_gene_variant,,ENST00000583641,;RFNG,upstream_gene_variant,,ENST00000578356,;GPS1,upstream_gene_variant,,ENST00000583885,;GPS1,upstream_gene_variant,,ENST00000578168,;GPS1,upstream_gene_variant,,ENST00000581418,;GPS1,upstream_gene_variant,,ENST00000583009,;GPS1,upstream_gene_variant,,ENST00000581578,;GPS1,splice_region_variant,,ENST00000583983,;RFNG,upstream_gene_variant,,ENST00000584838,;GPS1,upstream_gene_variant,,ENST00000584229,;RFNG,upstream_gene_variant,,ENST00000580928,;RFNG,non_coding_transcript_exon_variant,,ENST00000582478,;GPS1,upstream_gene_variant,,ENST00000392357,;RFNG,upstream_gene_variant,,ENST00000583784,;RFNG,upstream_gene_variant,,ENST00000580953,;GPS1,upstream_gene_variant,,ENST00000584460,;RFNG,upstream_gene_variant,,ENST00000580793,;RFNG,upstream_gene_variant,,ENST00000578676,;RFNG,upstream_gene_variant,,ENST00000584515,;GPS1,upstream_gene_variant,,ENST00000580141,;GPS1,upstream_gene_variant,,ENST00000578279,;GPS1,upstream_gene_variant,,ENST00000583486,;GPS1,upstream_gene_variant,,ENST00000580723,;GPS1,upstream_gene_variant,,ENST00000578642,;GPS1,upstream_gene_variant,,ENST00000578392,;GPS1,upstream_gene_variant,,ENST00000580627,;RFNG,upstream_gene_variant,,ENST00000584463,; A ENST00000310496 Transcript missense_variant 48/1828 40/996 14/331 A/S Gcg/Tcg 1 -1 RFNG HGNC HGNC:9974 protein_coding YES CCDS32773.1 ENSP00000307971 Q9Y644 UPI00001A6F5D NM_002917.1 tolerated(0.53) 1/8 hmmpanther:PTHR10811,hmmpanther:PTHR10811:SF1,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix MODERATE SNV 2 1 PASS . . 14 195 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 82051727 82051727 C A 1 0 0 0 0 1 0 0 0 13423 768 27 1 1 RFNG 17 82051727 Missense_Mutation SNP C C3N-02089_T 1760091 82051727 1205714 855 27939 FOXK2 0 . GRCh38 17 82601389 82601389 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1873G>C p.Glu625Gln p.E625Q ENST00000335255 9/9 182 172 10 150 150 0 strelka-varscan-mutect FOXK2,missense_variant,p.Glu625Gln,ENST00000335255,NM_004514.3;RP13-638C3.4,downstream_gene_variant,,ENST00000576912,;FOXK2,non_coding_transcript_exon_variant,,ENST00000624186,;FOXK2,non_coding_transcript_exon_variant,,ENST00000529652,;FOXK2,non_coding_transcript_exon_variant,,ENST00000571989,;FOXK2,upstream_gene_variant,,ENST00000574694,;FOXK2,3_prime_UTR_variant,,ENST00000473637,; C ENST00000335255 Transcript missense_variant 2047/5265 1873/1983 625/660 E/Q Gag/Cag 1 1 FOXK2 HGNC HGNC:6036 protein_coding YES CCDS11813.1 ENSP00000335677 Q01167 UPI00001A8BEE NM_004514.3 deleterious(0.04) 9/9 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF106 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.82551 0.9999994 1 1 1 0 C 3 2 90 82601389 82601389 G C 1 0 0 0 0 1 0 0 0 5878 1175 41 4 4 FOXK2 17 82601389 Missense_Mutation SNP G C3N-02089_T 549662 82601389 656052 856 27940 SMCHD1 0 . GRCh38 18 2729410 2729410 + Splice_Site SNP G G T novel C3N-02089_T C3N-02089_N G G c.3048+1G>T p.X1016_splice ENST00000320876 82 65 17 74 74 0 strelka-varscan-mutect SMCHD1,splice_donor_variant,,ENST00000320876,NM_015295.2;RP11-703M24.5,intron_variant,,ENST00000583546,;SMCHD1,downstream_gene_variant,,ENST00000609587,;SMCHD1,splice_donor_variant,,ENST00000577880,;SMCHD1,splice_donor_variant,,ENST00000584897,;SMCHD1,splice_donor_variant,,ENST00000581631,;SMCHD1,downstream_gene_variant,,ENST00000581383,; T ENST00000320876 Transcript splice_donor_variant -/8821 3048/6018 1016/2005 1 1 SMCHD1 HGNC HGNC:29090 protein_coding YES CCDS45822.1 ENSP00000326603 A6NHR9 UPI00001D7AAD NM_015295.2 24/47 HIGH SNV 5 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 90 2729410 2729410 G T 1 0 0 0 0 0 0 1 0 15081 1391 48 2 2 SMCHD1 18 2729410 Splice_Site SNP G C3N-02089_T 2729410 77643875 857 27941 LPIN2 0 . GRCh38 18 2960808 2960808 + Silent SNP C C G C3N-02089_T C3N-02089_N C C c.33G>C p.= p.V11V ENST00000261596 2/20 562 412 150 483 483 0 strelka-varscan-mutect LPIN2,synonymous_variant,p.=,ENST00000261596,NM_014646.2;LPIN2,synonymous_variant,p.=,ENST00000584294,;LPIN2,synonymous_variant,p.=,ENST00000584915,;RP11-737O24.2,downstream_gene_variant,,ENST00000584431,; G ENST00000261596 Transcript synonymous_variant 272/6229 33/2691 11/896 V gtG/gtC COSM438053 1 -1 LPIN2 HGNC HGNC:14450 protein_coding YES CCDS11829.1 ENSP00000261596 Q92539 UPI000012E865 NM_014646.2 2/20 hmmpanther:PTHR12181,hmmpanther:PTHR12181:SF11,Pfam_domain:PF04571 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 90 2960808 2960808 C G 1 0 0 0 0 0 0 0 1 8819 813 29 4 4 LPIN2 18 2960808 Silent SNP C C3N-02089_T 231398 2960808 77412477 858 27942 MTCL1 0 . GRCh38 18 8783752 8783752 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.640G>A p.Val214Met p.V214M ENST00000359865 6/17 161 117 44 130 129 1 strelka-varscan-mutect MTCL1,missense_variant,p.Val214Met,ENST00000359865,NM_015210.3;MTCL1,missense_variant,p.Val214Met,ENST00000400050,;MTCL1,missense_variant,p.Val214Met,ENST00000517570,;MTCL1,missense_variant,p.Val574Met,ENST00000306329,;MTCL1,upstream_gene_variant,,ENST00000521018,;MTCL1,upstream_gene_variant,,ENST00000523811,;MTCL1,missense_variant,p.Val56Met,ENST00000520495,;MTCL1,upstream_gene_variant,,ENST00000517554,; A ENST00000359865 Transcript missense_variant 782/6093 640/4761 214/1586 V/M Gtg/Atg 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 deleterious(0) 6/17 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF11365,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 8783752 8783752 G A 1 0 0 0 0 1 0 0 0 9900 1261 44 3 3 MTCL1 18 8783752 Missense_Mutation SNP G C3N-02089_T 5822944 8783752 71589533 859 27943 ANKRD12 0 . GRCh38 18 9257955 9257955 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.4688T>G p.Val1563Gly p.V1563G ENST00000262126 9/13 196 183 13 140 140 0 strelka-varscan-mutect ANKRD12,missense_variant,p.Val1563Gly,ENST00000262126,NM_015208.4;ANKRD12,missense_variant,p.Val1540Gly,ENST00000400020,NM_001083625.2,NM_001204056.1;ANKRD12,downstream_gene_variant,,ENST00000546007,;RP11-888D10.4,upstream_gene_variant,,ENST00000609701,;RP11-21J18.1,downstream_gene_variant,,ENST00000578850,;ANKRD12,downstream_gene_variant,,ENST00000359158,; G ENST00000262126 Transcript missense_variant 4928/11288 4688/6189 1563/2062 V/G gTg/gGg 1 1 ANKRD12 HGNC HGNC:29135 protein_coding YES CCDS11843.1 ENSP00000262126 Q6UB98 UPI0000073327 NM_015208.4 deleterious_low_confidence(0) 9/13 hmmpanther:PTHR24149,hmmpanther:PTHR24149:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 9257955 9257955 T G 1 0 0 0 0 1 0 0 0 741 1696 59 5 5 ANKRD12 18 9257955 Missense_Mutation SNP T C3N-02089_T 474203 9257955 71115330 860 27944 PPP4R1 0 . GRCh38 18 9553366 9553366 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2247G>T p.= p.V749V ENST00000400556 16/20 275 243 32 273 273 0 strelka-varscan-mutect PPP4R1,synonymous_variant,p.=,ENST00000400556,NM_001042388.2;PPP4R1,synonymous_variant,p.=,ENST00000400555,NM_005134.3;PPP4R1,non_coding_transcript_exon_variant,,ENST00000579609,;PPP4R1,non_coding_transcript_exon_variant,,ENST00000584754,;PPP4R1,3_prime_UTR_variant,,ENST00000285124,;PPP4R1,upstream_gene_variant,,ENST00000582594,;PPP4R1,downstream_gene_variant,,ENST00000583438,;PPP4R1,downstream_gene_variant,,ENST00000577667,;PPP4R1,upstream_gene_variant,,ENST00000578010,;PPP4R1,upstream_gene_variant,,ENST00000578329,; A ENST00000400556 Transcript synonymous_variant 2321/3925 2247/2853 749/950 V gtG/gtT 1 -1 PPP4R1 HGNC HGNC:9320 protein_coding YES CCDS42412.1 ENSP00000383402 Q8TF05 UPI000006D6DE NM_001042388.2 16/20 hmmpanther:PTHR10648:SF8,hmmpanther:PTHR10648,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 9553366 9553366 C A 1 0 0 0 0 0 0 0 1 12525 813 29 2 2 PPP4R1 18 9553366 Silent SNP C C3N-02089_T 295411 9553366 70819919 861 27945 GNAL 0 . GRCh38 18 11689747 11689747 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.184G>T p.Ala62Ser p.A62S ENST00000334049 1/12 283 227 56 199 199 0 strelka-varscan-mutect GNAL,missense_variant,p.Ala62Ser,ENST00000334049,NM_182978.3;GNAL,non_coding_transcript_exon_variant,,ENST00000585590,; T ENST00000334049 Transcript missense_variant 792/6535 184/1377 62/458 A/S Gca/Tca 1 1 GNAL HGNC HGNC:4388 protein_coding YES CCDS11851.1 ENSP00000334051 P38405 UPI000017DF81 NM_182978.3 tolerated_low_confidence(0.43) 1/12 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9981277 1 1 1 0 T 3 4 90 11689747 11689747 G T 1 0 0 0 0 1 0 0 0 6387 1203 42 2 2 GNAL 18 11689747 Missense_Mutation SNP G C3N-02089_T 2136381 11689747 68683538 862 27946 ANKRD30B 0 . GRCh38 18 14851866 14851866 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3565C>A p.His1189Asn p.H1189N ENST00000358984 36/36 62 50 12 71 71 0 strelka-varscan-mutect ANKRD30B,missense_variant,p.His1189Asn,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; A ENST00000358984 Transcript missense_variant 3745/4359 3565/4179 1189/1392 H/N Cat/Aat 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 deleterious(0.01) 36/36 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS rs1238199613 . 0 203 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 A 3 1 90 14851866 14851866 C A 1 0 0 0 0 1 0 0 0 762 594 21 2 2 ANKRD30B 18 14851866 Missense_Mutation SNP C C3N-02089_T 3162119 14851866 65521419 863 27947 ROCK1 0 . GRCh38 18 20984464 20984464 + Silent SNP A A C novel C3N-02089_T C3N-02089_N A A c.2376T>G p.= p.T792T ENST00000399799 20/33 221 170 51 188 186 2 strelka-varscan-mutect ROCK1,synonymous_variant,p.=,ENST00000399799,NM_005406.2;ROCK1,synonymous_variant,p.=,ENST00000635540,;ROCK1,upstream_gene_variant,,ENST00000583556,; C ENST00000399799 Transcript synonymous_variant 3317/9484 2376/4065 792/1354 T acT/acG 1 -1 ROCK1 HGNC HGNC:10251 protein_coding YES CCDS11870.2 ENSP00000382697 Q13464 UPI000006F0A4 NM_005406.2 20/33 hmmpanther:PTHR22988:SF33,hmmpanther:PTHR22988,PIRSF_domain:PIRSF037568 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 20984464 20984464 A C 1 0 0 0 0 0 0 0 1 13695 291 11 5 5 ROCK1 18 20984464 Silent SNP A C3N-02089_T 6132598 20984464 59388821 864 27948 ESCO1 0 . GRCh38 18 21539956 21539956 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2007G>T p.Met669Ile p.M669I ENST00000269214 9/12 204 171 33 147 147 0 strelka-varscan-mutect ESCO1,start_lost,p.Met1?,ENST00000622333,;ESCO1,missense_variant,p.Met669Ile,ENST00000269214,NM_052911.2;ESCO1,3_prime_UTR_variant,,ENST00000383276,; A ENST00000269214 Transcript missense_variant 2945/4523 2007/2523 669/840 M/I atG/atT 1 -1 ESCO1 HGNC HGNC:24645 protein_coding YES CCDS32800.1 ENSP00000269214 Q5FWF5 A0A024RC19 UPI00001C1FF4 NM_052911.2 deleterious(0.05) 9/12 hmmpanther:PTHR11076,hmmpanther:PTHR11076:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 21539956 21539956 C A 1 0 0 0 0 1 0 0 0 5110 594 21 2 2 ESCO1 18 21539956 Missense_Mutation SNP C C3N-02089_T 555492 21539956 58833329 865 27949 CTAGE1 0 . GRCh38 18 22415687 22415687 + Missense_Mutation SNP C C T rs757466641 C3N-02089_T C3N-02089_N C C c.2125G>A p.Val709Ile p.V709I ENST00000391403 1/1 337 304 33 289 289 0 strelka-varscan-mutect CTAGE1,missense_variant,p.Val709Ile,ENST00000391403,NM_172241.2;CTAGE1,upstream_gene_variant,,ENST00000525417,;RP11-863N1.4,downstream_gene_variant,,ENST00000603437,; T ENST00000391403 Transcript missense_variant 2229/4313 2125/2238 709/745 V/I Gtc/Atc rs757466641 1 -1 CTAGE1 HGNC HGNC:24346 protein_coding YES CCDS45837.1 ENSP00000375220 Q96RT6 UPI00000721F4 NM_172241.2 deleterious(0.02) 1/1 hmmpanther:PTHR23158:SF39,hmmpanther:PTHR23158 MODERATE 1 SNV 1 PASS rs757466641 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 22415687 22415687 C T 1 0 0 0 0 1 0 0 0 3796 478 17 3 3 CTAGE1 18 22415687 Missense_Mutation SNP C C3N-02089_T 875731 22415687 57957598 866 27950 OSBPL1A 0 . GRCh38 18 24172424 24172424 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2153G>T p.Gly718Val p.G718V ENST00000319481 22/28 200 175 25 212 211 1 strelka-varscan-mutect OSBPL1A,missense_variant,p.Gly718Val,ENST00000319481,NM_080597.3;OSBPL1A,missense_variant,p.Gly205Val,ENST00000399443,NM_018030.4;OSBPL1A,missense_variant,p.Gly336Val,ENST00000357041,NM_001242508.1;OSBPL1A,missense_variant,p.Gly53Val,ENST00000578013,;RNA5SP452,upstream_gene_variant,,ENST00000363004,;OSBPL1A,3_prime_UTR_variant,,ENST00000578055,; A ENST00000319481 Transcript missense_variant 2360/4195 2153/2853 718/950 G/V gGt/gTt 1 -1 OSBPL1A HGNC HGNC:16398 protein_coding YES CCDS11884.1 ENSP00000320291 Q9BXW6 B0YJ56 UPI0000130E95 NM_080597.3 deleterious(0) 22/28 hmmpanther:PTHR10972:SF53,hmmpanther:PTHR10972,Pfam_domain:PF01237,Superfamily_domains:0051579 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 24172424 24172424 C A 1 0 0 0 0 1 0 0 0 11343 507 18 2 2 OSBPL1A 18 24172424 Missense_Mutation SNP C C3N-02089_T 1756737 24172424 56200861 867 27951 CDH2 0 . GRCh38 18 27985089 27985089 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2120G>T p.Gly707Val p.G707V ENST00000269141 13/16 302 230 72 290 290 0 strelka-varscan-mutect CDH2,missense_variant,p.Gly707Val,ENST00000269141,NM_001792.3;CDH2,missense_variant,p.Gly676Val,ENST00000399380,NM_001308176.1; A ENST00000269141 Transcript missense_variant 2544/4332 2120/2721 707/906 G/V gGg/gTg 1 -1 CDH2 HGNC HGNC:1759 protein_coding YES CCDS11891.1 ENSP00000269141 P19022 A0A024RC42 UPI000013D7FD NM_001792.3 tolerated(0.14) 13/16 Gene3D:2.60.40.60,Prints_domain:PR01820,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF79,SMART_domains:SM00112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 27985089 27985089 C A 1 0 0 0 0 1 0 0 0 2808 623 22 2 2 CDH2 18 27985089 Missense_Mutation SNP C C3N-02089_T 3812665 27985089 52388196 868 27952 DSG3 0 . GRCh38 18 31475733 31475733 + Missense_Mutation SNP G G T rs150853711 C3N-02089_T C3N-02089_N G G c.2473G>T p.Gly825Cys p.G825C ENST00000257189 16/16 325 240 85 287 287 0 strelka-varscan-mutect DSG3,missense_variant,p.Gly825Cys,ENST00000257189,NM_001944.2; T ENST00000257189 Transcript missense_variant 2556/5525 2473/3000 825/999 G/C Ggt/Tgt rs150853711 1 1 DSG3 HGNC HGNC:3050 protein_coding YES CCDS11898.1 ENSP00000257189 P32926 UPI000013CF4B NM_001944.2 deleterious(0) 16/16 Gene3D:4.10.900.10,Prints_domain:PR01818,Prints_domain:PR01819,hmmpanther:PTHR24025,hmmpanther:PTHR24025:SF3 MODERATE 1 SNV 1 1 PASS rs150853711 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 31475733 31475733 G T 1 0 0 0 0 1 0 0 0 4599 1348 47 2 2 DSG3 18 31475733 Missense_Mutation SNP G C3N-02089_T 3490644 31475733 48897552 869 27953 KLHL14 0 . GRCh38 18 32769772 32769772 + Missense_Mutation SNP G G T rs752039381 C3N-02089_T C3N-02089_N G G c.820C>A p.Leu274Met p.L274M ENST00000359358 2/9 54 47 7 63 63 0 strelka-mutect KLHL14,missense_variant,p.Leu274Met,ENST00000359358,NM_020805.1;KLHL14,missense_variant,p.Leu274Met,ENST00000358095,;KLHL14,downstream_gene_variant,,ENST00000583263,;AC012123.1,upstream_gene_variant,,ENST00000426194,; T ENST00000359358 Transcript missense_variant 1259/4312 820/1887 274/628 L/M Ctg/Atg rs752039381 1 -1 KLHL14 HGNC HGNC:29266 protein_coding YES CCDS32813.1 ENSP00000352314 Q9P2G3 UPI00001C1FF2 NM_020805.1 deleterious(0.01) 2/9 Pfam_domain:PF07707,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60,SMART_domains:SM00875 MODERATE 1 SNV 1 1 PASS rs752039381 . 0 206 4 0 0 0 0 0 -16.65262 1 1 1 1 0 T 3 4 90 32769772 32769772 G T 1 0 0 0 0 1 0 0 0 8234 962 34 2 2 KLHL14 18 32769772 Missense_Mutation SNP G C3N-02089_T 1294039 32769772 47603513 870 27954 DTNA 0 . GRCh38 18 34858315 34858315 + Silent SNP G G T C3N-02089_T C3N-02089_N G G c.1302G>T p.= p.R434R ENST00000598334 14/20 453 357 96 482 482 0 strelka-varscan-mutect DTNA,synonymous_variant,p.=,ENST00000283365,NM_032975.3;DTNA,synonymous_variant,p.=,ENST00000399121,NM_001198939.1;DTNA,synonymous_variant,p.=,ENST00000444659,NM_001390.4;DTNA,synonymous_variant,p.=,ENST00000595022,NM_001198940.1;DTNA,synonymous_variant,p.=,ENST00000348997,NM_032978.6,NM_001391.5;DTNA,synonymous_variant,p.=,ENST00000598334,NM_001198938.1;DTNA,synonymous_variant,p.=,ENST00000598142,;DTNA,synonymous_variant,p.=,ENST00000598774,NM_032979.4;DTNA,synonymous_variant,p.=,ENST00000399113,;DTNA,synonymous_variant,p.=,ENST00000269192,NM_001198942.1;DTNA,synonymous_variant,p.=,ENST00000601125,NM_001198943.1;DTNA,synonymous_variant,p.=,ENST00000597599,NM_001198941.1;DTNA,synonymous_variant,p.=,ENST00000591182,NM_032980.3;DTNA,synonymous_variant,p.=,ENST00000597674,NM_032981.4;DTNA,synonymous_variant,p.=,ENST00000556414,NM_001198944.1;DTNA,synonymous_variant,p.=,ENST00000596745,NM_001198945.1;DTNA,synonymous_variant,p.=,ENST00000599844,;DTNA,synonymous_variant,p.=,ENST00000587723,;DTNA,non_coding_transcript_exon_variant,,ENST00000601632,;DTNA,non_coding_transcript_exon_variant,,ENST00000601895,; T ENST00000598334 Transcript synonymous_variant 1628/3201 1302/2175 434/724 R cgG/cgT COSM4527688,COSM4527689,COSM4527690,COSM4527691,COSM4527692 1 1 DTNA HGNC HGNC:3057 protein_coding YES CCDS59312.1 ENSP00000470152 Q9Y4J8 UPI0001E92A2F NM_001198938.1 14/20 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915:SF209,hmmpanther:PTHR11915,PIRSF_domain:PIRSF038204 1,1,1,1,1 LOW 1 SNV 1 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 34858315 34858315 G T 1 0 0 0 0 0 0 0 1 4611 1190 42 2 2 DTNA 18 34858315 Silent SNP G C3N-02089_T 2088543 34858315 45514970 871 27955 PIK3C3 0 . GRCh38 18 42013507 42013507 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.1236G>A p.= p.K412K ENST00000262039 11/25 157 120 37 156 156 0 strelka-varscan-mutect PIK3C3,synonymous_variant,p.=,ENST00000262039,NM_002647.2;PIK3C3,synonymous_variant,p.=,ENST00000398870,NM_001308020.1; A ENST00000262039 Transcript synonymous_variant 1322/9443 1236/2664 412/887 K aaG/aaA COSM4855613 1 1 PIK3C3 HGNC HGNC:8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 UPI00000708CE NM_002647.2 11/25 Pfam_domain:PF00613,PIRSF_domain:PIRSF000587,PROSITE_profiles:PS51545,SMART_domains:SM00145 1 LOW 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 42013507 42013507 G A 1 0 0 0 0 0 0 0 1 12007 933 33 3 3 PIK3C3 18 42013507 Silent SNP G C3N-02089_T 7155192 42013507 38359778 872 27956 PIK3C3 0 . GRCh38 18 42049544 42049544 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.2202G>T p.= p.V734V ENST00000262039 21/25 180 138 42 206 205 1 strelka-varscan-mutect PIK3C3,synonymous_variant,p.=,ENST00000262039,NM_002647.2;PIK3C3,synonymous_variant,p.=,ENST00000398870,NM_001308020.1;PIK3C3,synonymous_variant,p.=,ENST00000589056,;PIK3C3,synonymous_variant,p.=,ENST00000597477,;PIK3C3,synonymous_variant,p.=,ENST00000587402,;RP11-687E1.2,upstream_gene_variant,,ENST00000611384,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000593098,;PIK3C3,non_coding_transcript_exon_variant,,ENST00000588631,; T ENST00000262039 Transcript synonymous_variant 2288/9443 2202/2664 734/887 V gtG/gtT 1 1 PIK3C3 HGNC HGNC:8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 UPI00000708CE NM_002647.2 21/25 Gene3D:1.10.1070.11,Pfam_domain:PF00454,PIRSF_domain:PIRSF000587,PROSITE_patterns:PS00916,PROSITE_profiles:PS50290,hmmpanther:PTHR10048,SMART_domains:SM00146,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS rs1409378681 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 42049544 42049544 G T 1 0 0 0 0 0 0 0 1 12007 1277 45 2 2 PIK3C3 18 42049544 Silent SNP G C3N-02089_T 36037 42049544 38323741 873 27957 DCC 0 . GRCh38 18 53526673 53526673 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.4168G>C p.Ala1390Pro p.A1390P ENST00000442544 28/29 395 327 68 372 372 0 strelka-varscan-mutect DCC,missense_variant,p.Ala1390Pro,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Ala1367Pro,ENST00000412726,;DCC,missense_variant,p.Ala1023Pro,ENST00000581580,;RP11-671P2.1,intron_variant,,ENST00000582064,;DCC,upstream_gene_variant,,ENST00000577224,;DCC,non_coding_transcript_exon_variant,,ENST00000579702,; C ENST00000442544 Transcript missense_variant 4784/10206 4168/4344 1390/1447 A/P Gca/Cca 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 tolerated(0.06) 28/29 Pfam_domain:PF06583,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 53526673 53526673 G C 1 0 0 0 0 1 0 0 0 4084 971 34 4 4 DCC 18 53526673 Missense_Mutation SNP G C3N-02089_T 11477129 53526673 26846612 874 27958 KIAA1468 0 . GRCh38 18 62264068 62264068 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.2430G>C p.= p.L810L ENST00000398130 17/29 189 162 27 201 201 0 strelka-varscan-mutect KIAA1468,synonymous_variant,p.=,ENST00000398130,NM_020854.3;KIAA1468,synonymous_variant,p.=,ENST00000256858,;KIAA1468,synonymous_variant,p.=,ENST00000587725,;KIAA1468,synonymous_variant,p.=,ENST00000588446,;KIAA1468,upstream_gene_variant,,ENST00000586920,; C ENST00000398130 Transcript synonymous_variant 2662/6178 2430/3651 810/1216 L ctG/ctC 1 1 KIAA1468 HGNC HGNC:29289 protein_coding YES CCDS11979.2 ENSP00000381198 Q9P260 UPI0000DA5AF7 NM_020854.3 17/29 Low_complexity_(Seg):seg,hmmpanther:PTHR32059,hmmpanther:PTHR32059:SF0 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 62264068 62264068 G C 1 0 0 0 0 0 0 0 1 8117 1306 46 4 4 KIAA1468 18 62264068 Silent SNP G C3N-02089_T 8737395 62264068 18109217 875 27959 BCL2 0 . GRCh38 18 63128632 63128632 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.713A>T p.His238Leu p.H238L ENST00000398117 2/2 145 127 18 133 133 0 strelka-varscan-mutect BCL2,missense_variant,p.His238Leu,ENST00000398117,NM_000633.2;BCL2,missense_variant,p.His238Leu,ENST00000333681,;BCL2,non_coding_transcript_exon_variant,,ENST00000590515,; A ENST00000398117 Transcript missense_variant 2175/7461 713/720 238/239 H/L cAc/cTc 1 -1 BCL2 HGNC HGNC:990 protein_coding YES CCDS11981.1 ENSP00000381185 P10415 A0A024R2B3 UPI000000D90E NM_000633.2 deleterious(0.03) 2/2 hmmpanther:PTHR11256,hmmpanther:PTHR11256:SF11,TIGRFAM_domain:TIGR00865 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 63128632 63128632 T A 1 0 0 0 0 1 0 0 0 1512 1696 59 4 4 BCL2 18 63128632 Missense_Mutation SNP T C3N-02089_T 864564 63128632 17244653 876 27960 DOK6 0 . GRCh38 18 69677853 69677853 + Nonsense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.409G>T p.Glu137Ter p.E137* ENST00000382713 4/8 153 96 57 125 124 1 strelka-varscan-mutect DOK6,stop_gained,p.Glu137Ter,ENST00000382713,NM_152721.5;DOK6,stop_gained,p.Glu41Ter,ENST00000582992,;DOK6,splice_region_variant,,ENST00000584435,;DOK6,splice_region_variant,,ENST00000582172,; T ENST00000382713 Transcript stop_gained,splice_region_variant 599/8890 409/996 137/331 E/* Gag/Tag COSM310693 1 1 DOK6 HGNC HGNC:28301 protein_coding YES CCDS32841.1 ENSP00000372160 Q6PKX4 UPI000035EC7C NM_152721.5 4/8 Gene3D:2.30.29.30,Pfam_domain:PF02174,PROSITE_profiles:PS51064,hmmpanther:PTHR21258,hmmpanther:PTHR21258:SF43,SMART_domains:SM00310,SMART_domains:SM01244,Superfamily_domains:SSF50729 1 HIGH 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 69677853 69677853 G T 1 0 0 0 0 0 1 0 0 4516 1362 47 2 2 DOK6 18 69677853 Nonsense_Mutation SNP G C3N-02089_T 6549221 69677853 10695432 877 27961 SOCS6 0 . GRCh38 18 70326017 70326017 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1349G>T p.Gly450Val p.G450V ENST00000397942 2/2 299 280 19 225 225 0 strelka-varscan-mutect SOCS6,missense_variant,p.Gly450Val,ENST00000397942,NM_004232.3;SOCS6,missense_variant,p.Gly450Val,ENST00000582322,;SOCS6,downstream_gene_variant,,ENST00000578377,; T ENST00000397942 Transcript missense_variant 1665/5848 1349/1608 450/535 G/V gGa/gTa 1 1 SOCS6 HGNC HGNC:16833 protein_coding YES CCDS11998.1 ENSP00000381034 O14544 A0A024R379 UPI0000072C28 NM_004232.3 deleterious(0) 2/2 PROSITE_profiles:PS50001,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF83,Gene3D:3.30.505.10,Pfam_domain:PF00017,SMART_domains:SM00252,Superfamily_domains:SSF55550 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 70326017 70326017 G T 1 0 0 0 0 1 0 0 0 15239 1174 41 2 2 SOCS6 18 70326017 Missense_Mutation SNP G C3N-02089_T 648164 70326017 10047268 878 27962 FBXO15 0 . GRCh38 18 74130415 74130415 + Splice_Site SNP C C A novel C3N-02089_T C3N-02089_N C C c.575+1G>T p.X192_splice ENST00000419743 152 142 10 139 139 0 strelka-varscan-mutect FBXO15,splice_donor_variant,,ENST00000419743,NM_152676.2,NM_001142958.1;FBXO15,upstream_gene_variant,,ENST00000579517,;FBXO15,downstream_gene_variant,,ENST00000582526,;FBXO15,splice_donor_variant,,ENST00000583443,;FBXO15,splice_donor_variant,,ENST00000581214,;FBXO15,splice_donor_variant,,ENST00000585174,;FBXO15,intron_variant,,ENST00000578399,;FBXO15,downstream_gene_variant,,ENST00000580552,; A ENST00000419743 Transcript splice_donor_variant -/1708 575/1533 192/510 1 -1 FBXO15 HGNC HGNC:13617 protein_coding YES CCDS45884.1 ENSP00000393154 Q8NCQ5 UPI00003CF23D NM_152676.2,NM_001142958.1 4/9 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 90 74130415 74130415 C A 1 0 0 0 0 0 0 1 0 5591 521 18 2 2 FBXO15 18 74130415 Splice_Site SNP C C3N-02089_T 3804398 74130415 6242870 879 27963 ZNF516 0 . GRCh38 18 76442431 76442431 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.624G>T p.= p.A208A ENST00000443185 3/7 241 203 38 168 166 2 strelka-varscan-mutect ZNF516,synonymous_variant,p.=,ENST00000443185,NM_014643.3;ZNF516,downstream_gene_variant,,ENST00000532857,; A ENST00000443185 Transcript synonymous_variant 942/8118 624/3492 208/1163 A gcG/gcT 1 -1 ZNF516 HGNC HGNC:28990 protein_coding YES CCDS74234.1 ENSP00000394757 Q92618 UPI00001394A1 NM_014643.3 3/7 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF3,SMART_domains:SM00355 LOW 1 SNV 1 1 PASS rs1192783535 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 76442431 76442431 C A 1 0 0 0 0 0 0 0 1 18532 871 31 1 1 ZNF516 18 76442431 Silent SNP C C3N-02089_T 2312016 76442431 3930854 880 27964 SALL3 0 . GRCh38 18 78995286 78995286 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.3295G>A p.Ala1099Thr p.A1099T ENST00000537592 2/3 178 133 45 187 187 0 strelka-varscan-mutect SALL3,missense_variant,p.Ala1099Thr,ENST00000537592,NM_171999.3;SALL3,missense_variant,p.Ala894Thr,ENST00000536229,;SALL3,missense_variant,p.Ala1027Thr,ENST00000575389,;SALL3,missense_variant,p.Ala759Thr,ENST00000616649,;SALL3,missense_variant,p.Ala92Thr,ENST00000573324,;SALL3,downstream_gene_variant,,ENST00000572928,; A ENST00000537592 Transcript missense_variant 3295/6555 3295/3903 1099/1300 A/T Gcg/Acg COSM4073436 1 1 SALL3 HGNC HGNC:10527 protein_coding YES CCDS12013.1 ENSP00000441823 Q9BXA9 UPI000013E5A7 NM_171999.3 tolerated(1) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF46 1 MODERATE 1 SNV 5 1 1 PASS rs1415842432 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 78995286 78995286 G A 1 0 0 0 0 1 0 0 0 14071 1203 42 3 3 SALL3 18 78995286 Missense_Mutation SNP G C3N-02089_T 2552855 78995286 1377999 881 27965 GZMM 0 . GRCh38 19 548571 548571 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.242T>C p.Leu81Pro p.L81P ENST00000264553 3/5 159 144 15 161 161 0 strelka-varscan-mutect GZMM,missense_variant,p.Leu42Pro,ENST00000592501,NM_001258351.1;GZMM,missense_variant,p.Leu81Pro,ENST00000264553,NM_005317.3; C ENST00000264553 Transcript missense_variant 279/940 242/774 81/257 L/P cTc/cCc 1 1 GZMM HGNC HGNC:4712 protein_coding YES CCDS12031.1 ENSP00000264553 P51124 UPI000013D531 NM_005317.3 deleterious(0.01) 3/5 PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF132,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.95436 0.9999998 1 1 1 0 C 3 2 90 548571 548571 T C 1 0 0 0 0 1 0 0 0 6801 1551 54 5 5 GZMM 19 548571 Missense_Mutation SNP T C3N-02089_T 548571 58069045 882 27966 MED16 0 . GRCh38 19 868891 868891 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2371C>A p.Pro791Thr p.P791T ENST00000325464 14/16 116 89 27 96 96 0 strelka-varscan-mutect MED16,missense_variant,p.Pro791Thr,ENST00000395808,;MED16,missense_variant,p.Pro810Thr,ENST00000312090,;MED16,missense_variant,p.Pro791Thr,ENST00000325464,NM_005481.2;MED16,missense_variant,p.Pro791Thr,ENST00000589119,;MED16,missense_variant,p.Pro168Thr,ENST00000269814,;MED16,missense_variant,p.Pro30Thr,ENST00000621073,;MED16,synonymous_variant,p.=,ENST00000607471,;MED16,intron_variant,,ENST00000616387,;MED16,intron_variant,,ENST00000617672,;MED16,downstream_gene_variant,,ENST00000592943,;MED16,downstream_gene_variant,,ENST00000586017,;MED16,downstream_gene_variant,,ENST00000606828,;MED16,3_prime_UTR_variant,,ENST00000606248,; T ENST00000325464 Transcript missense_variant 2522/2922 2371/2634 791/877 P/T Ccc/Acc 1 -1 MED16 HGNC HGNC:17556 protein_coding YES CCDS12047.1 ENSP00000325612 Q9Y2X0 UPI0000141671 NM_005481.2 deleterious(0.01) 14/16 Pfam_domain:PF11635,hmmpanther:PTHR13224,hmmpanther:PTHR13224:SF6 MODERATE 1 SNV 5 1 PASS rs1260046676 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 868891 868891 G T 1 0 0 0 0 1 0 0 0 9373 1246 43 2 2 MED16 19 868891 Missense_Mutation SNP G C3N-02089_T 320320 868891 57748725 883 27967 ABCA7 0 . GRCh38 19 1049383 1049383 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.2498A>C p.Gln833Pro p.Q833P ENST00000263094 18/47 100 76 24 98 98 0 strelka-varscan-mutect ABCA7,missense_variant,p.Gln833Pro,ENST00000263094,NM_019112.3;ABCA7,missense_variant,p.Gln833Pro,ENST00000433129,;ABCA7,missense_variant,p.Gln695Pro,ENST00000435683,;ABCA7,downstream_gene_variant,,ENST00000533574,;ABCA7,upstream_gene_variant,,ENST00000530092,; C ENST00000263094 Transcript missense_variant 2729/6816 2498/6441 833/2146 Q/P cAg/cCg 1 1 ABCA7 HGNC HGNC:37 protein_coding YES CCDS12055.1 ENSP00000263094 Q8IZY2 UPI000013D3A4 NM_019112.3 deleterious(0) 18/47 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF49,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 1049383 1049383 A C 1 0 0 0 0 1 0 0 0 41 188 7 5 5 ABCA7 19 1049383 Missense_Mutation SNP A C3N-02089_T 180492 1049383 57568233 884 27968 STK11 0 . GRCh38 19 1221271 1221271 + Nonsense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.793G>T p.Glu265Ter p.E265* ENST00000326873 6/10 158 114 44 138 138 0 strelka-varscan-mutect STK11,stop_gained,p.Glu265Ter,ENST00000586243,;STK11,stop_gained,p.Glu265Ter,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,non_coding_transcript_exon_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; T ENST00000326873 Transcript stop_gained 1243/2611 793/1302 265/433 E/* Gag/Tag CM102315,COSM371077 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 6/10 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,SMART_domains:SM00220,Superfamily_domains:SSF56112 0,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 1221271 1221271 G T 1 0 0 0 0 0 1 0 0 15664 1291 45 2 2 STK11 19 1221271 Nonsense_Mutation SNP G C3N-02089_T 171888 1221271 57396345 885 27969 APC2 0 . GRCh38 19 1469844 1469844 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.6543C>A p.= p.P2181P ENST00000535453 14/14 214 144 70 164 164 0 strelka-varscan-mutect APC2,synonymous_variant,p.=,ENST00000535453,;APC2,synonymous_variant,p.=,ENST00000233607,NM_005883.2;C19orf25,intron_variant,,ENST00000588427,;C19orf25,downstream_gene_variant,,ENST00000436106,;APC2,downstream_gene_variant,,ENST00000238483,;APC2,downstream_gene_variant,,ENST00000590469,;C19orf25,downstream_gene_variant,,ENST00000588871,;C19orf25,downstream_gene_variant,,ENST00000585675,NM_152482.2;C19orf25,downstream_gene_variant,,ENST00000588849,;C19orf25,downstream_gene_variant,,ENST00000427685,;C19orf25,downstream_gene_variant,,ENST00000592872,;C19orf25,downstream_gene_variant,,ENST00000586564,;C19orf25,downstream_gene_variant,,ENST00000590621,;APC2,downstream_gene_variant,,ENST00000593146,;C19orf25,downstream_gene_variant,,ENST00000592486,; A ENST00000535453 Transcript synonymous_variant 8256/11656 6543/6912 2181/2303 P ccC/ccA 1 1 APC2 HGNC HGNC:24036 protein_coding YES CCDS12068.1 ENSP00000442954 O95996 UPI0000073D85 14/14 hmmpanther:PTHR12607:SF3,hmmpanther:PTHR12607 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 1469844 1469844 C A 1 0 0 0 0 0 0 0 1 884 610 22 2 2 APC2 19 1469844 Silent SNP C C3N-02089_T 248573 1469844 57147772 886 27970 TCF3 0 . GRCh38 19 1615697 1615697 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1575G>T p.= p.R525R ENST00000262965 17/19 106 82 24 117 117 0 strelka-varscan-mutect TCF3,synonymous_variant,p.=,ENST00000262965,NM_003200.3;TCF3,synonymous_variant,p.=,ENST00000611869,;TCF3,synonymous_variant,p.=,ENST00000344749,;TCF3,synonymous_variant,p.=,ENST00000453954,;TCF3,synonymous_variant,p.=,ENST00000395423,;TCF3,synonymous_variant,p.=,ENST00000593064,;TCF3,synonymous_variant,p.=,ENST00000588136,NM_001136139.2;TCF3,synonymous_variant,p.=,ENST00000592628,;TCF3,synonymous_variant,p.=,ENST00000590684,;TCF3,synonymous_variant,p.=,ENST00000585731,;TCF3,synonymous_variant,p.=,ENST00000590436,;TCF3,synonymous_variant,p.=,ENST00000587425,;TCF3,downstream_gene_variant,,ENST00000586410,;RNU6-1223P,downstream_gene_variant,,ENST00000517124,;TCF3,synonymous_variant,p.=,ENST00000585855,;TCF3,synonymous_variant,p.=,ENST00000592395,;TCF3,synonymous_variant,p.=,ENST00000586164,;TCF3,non_coding_transcript_exon_variant,,ENST00000610756,;TCF3,downstream_gene_variant,,ENST00000590605,; A ENST00000262965 Transcript synonymous_variant 1644/4451 1575/1965 525/654 R cgG/cgT 1 -1 TCF3 HGNC HGNC:11633 protein_coding YES CCDS12074.1 ENSP00000262965 P15923 UPI0000136C80 NM_003200.3 17/19 hmmpanther:PTHR11793:SF7,hmmpanther:PTHR11793 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 1615697 1615697 C A 1 0 0 0 0 0 0 0 1 16101 610 22 2 2 TCF3 19 1615697 Silent SNP C C3N-02089_T 145853 1615697 57001919 887 27971 MKNK2 0 . GRCh38 19 2039852 2039852 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1159A>G p.Ser387Gly p.S387G ENST00000250896 14/14 90 60 30 67 67 0 strelka-mutect MKNK2,missense_variant,p.Ser387Gly,ENST00000250896,NM_199054.2;MKNK2,missense_variant,p.Ser387Gly,ENST00000591601,;MKNK2,3_prime_UTR_variant,,ENST00000588014,;MKNK2,intron_variant,,ENST00000309340,NM_017572.3;MKNK2,intron_variant,,ENST00000591142,;MKNK2,downstream_gene_variant,,ENST00000591588,;BTBD2,upstream_gene_variant,,ENST00000590646,;BTBD2,upstream_gene_variant,,ENST00000587742,;BTBD2,upstream_gene_variant,,ENST00000588395,;MKNK2,3_prime_UTR_variant,,ENST00000586828,;MKNK2,3_prime_UTR_variant,,ENST00000589441,;MKNK2,non_coding_transcript_exon_variant,,ENST00000587416,;MKNK2,downstream_gene_variant,,ENST00000586620,;MKNK2,downstream_gene_variant,,ENST00000585667,; C ENST00000250896 Transcript missense_variant 1404/3774 1159/1398 387/465 S/G Agc/Ggc 1 -1 MKNK2 HGNC HGNC:7111 protein_coding YES CCDS12080.1 ENSP00000250896 Q9HBH9 UPI000006E9B4 NM_199054.2 tolerated(0.1) 14/14 hmmpanther:PTHR24349:SF158,hmmpanther:PTHR24349,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 2039852 2039852 T C 1 0 0 0 0 1 0 0 0 9572 1594 55 5 5 MKNK2 19 2039852 Missense_Mutation SNP T C3N-02089_T 424155 2039852 56577764 888 27972 THOP1 0 . GRCh38 19 2811703 2811703 + Missense_Mutation SNP G G C rs372729243 C3N-02089_T C3N-02089_N G G c.1877G>C p.Arg626Pro p.R626P ENST00000307741 12/13 96 72 24 80 80 0 strelka-varscan-mutect THOP1,missense_variant,p.Arg626Pro,ENST00000307741,NM_003249.3;THOP1,missense_variant,p.Arg137Pro,ENST00000395212,;THOP1,missense_variant,p.Arg505Pro,ENST00000586677,;THOP1,missense_variant,p.Arg197Pro,ENST00000590970,;THOP1,missense_variant,p.Arg170Pro,ENST00000587401,;THOP1,missense_variant,p.Arg137Pro,ENST00000587468,;THOP1,intron_variant,,ENST00000591363,;THOP1,downstream_gene_variant,,ENST00000591149,;THOP1,downstream_gene_variant,,ENST00000592639,;THOP1,non_coding_transcript_exon_variant,,ENST00000589087,;THOP1,downstream_gene_variant,,ENST00000590533,; C ENST00000307741 Transcript missense_variant 2080/4804 1877/2070 626/689 R/P cGc/cCc rs372729243 1 1 THOP1 HGNC HGNC:11793 protein_coding YES CCDS12095.1 ENSP00000304467 P52888 UPI0000000C3E NM_003249.3 deleterious(0.02) 12/13 Gene3D:2o36A02,Pfam_domain:PF01432,hmmpanther:PTHR11804,hmmpanther:PTHR11804:SF50,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs372729243 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 2811703 2811703 G C 1 0 0 0 0 1 0 0 0 16305 1087 38 4 4 THOP1 19 2811703 Missense_Mutation SNP G C3N-02089_T 771851 2811703 55805913 889 27973 NMRK2 0 . GRCh38 19 3936610 3936610 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.62G>T p.Ser21Ile p.S21I ENST00000616156 3/8 133 116 17 114 114 0 strelka-varscan-mutect NMRK2,missense_variant,p.Ser21Ile,ENST00000616156,NM_001289117.1;NMRK2,missense_variant,p.Ser21Ile,ENST00000168977,NM_170678.2;NMRK2,missense_variant,p.Ser21Ile,ENST00000593949,;NMRK2,missense_variant,p.Ser12Ile,ENST00000599576,;NMRK2,upstream_gene_variant,,ENST00000597889,; T ENST00000616156 Transcript missense_variant 352/1139 62/708 21/235 S/I aGc/aTc COSM4619754 1 1 NMRK2 HGNC HGNC:17871 protein_coding YES CCDS74259.1 ENSP00000480091 Q9NPI5 UPI000189A7D7 NM_001289117.1 deleterious(0.01) 3/8 Gene3D:3.40.50.300,Pfam_domain:PF13238,hmmpanther:PTHR23404,hmmpanther:PTHR23404:SF7,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 3936610 3936610 G T 1 0 0 0 0 1 0 0 0 10542 971 34 2 2 NMRK2 19 3936610 Missense_Mutation SNP G C3N-02089_T 1124907 3936610 54681006 890 27974 PTPRS 0 . GRCh38 19 5223274 5223274 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2518G>T p.Val840Leu p.V840L ENST00000587303 17/37 16 12 4 27 27 0 strelka-mutect PTPRS,missense_variant,p.Val840Leu,ENST00000587303,NM_002850.3;PTPRS,missense_variant,p.Val818Leu,ENST00000588012,NM_130854.2;PTPRS,intron_variant,,ENST00000262963,;PTPRS,intron_variant,,ENST00000592099,NM_130853.2;PTPRS,intron_variant,,ENST00000353284,NM_130855.2;PTPRS,intron_variant,,ENST00000588552,;PTPRS,upstream_gene_variant,,ENST00000589851,; A ENST00000587303 Transcript missense_variant 2618/6353 2518/5847 840/1948 V/L Gtg/Ttg 1 -1 PTPRS HGNC HGNC:9681 protein_coding YES CCDS45930.1 ENSP00000467537 Q13332 UPI000059D63E NM_002850.3 tolerated(0.1) 17/37 PROSITE_profiles:PS50853,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 7 201 2 0 0 0 0 0 -13.23398 1 1 1 1 0 A 3 1 90 5223274 5223274 C A 1 0 0 0 0 1 0 0 0 12966 507 18 2 2 PTPRS 19 5223274 Missense_Mutation SNP C C3N-02089_T 1286664 5223274 53394342 891 27975 TUBB4A 0 . GRCh38 19 6495763 6495763 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.736C>A p.Leu246Met p.L246M ENST00000264071 4/4 595 430 165 619 618 1 strelka-varscan-mutect TUBB4A,missense_variant,p.Leu246Met,ENST00000264071,NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1;TUBB4A,missense_variant,p.Leu142Met,ENST00000594276,;TUBB4A,downstream_gene_variant,,ENST00000597686,NM_001289127.1;TUBB4A,downstream_gene_variant,,ENST00000601152,;TUBB4A,downstream_gene_variant,,ENST00000594075,;TUBB4A,downstream_gene_variant,,ENST00000598006,;TUBB4A,downstream_gene_variant,,ENST00000598635,NM_001289123.1;TUBB4A,downstream_gene_variant,,ENST00000596926,;TUBB4A,downstream_gene_variant,,ENST00000596291,;TUBB4A,downstream_gene_variant,,ENST00000601640,;TUBB4A,downstream_gene_variant,,ENST00000600216,;CTD-2396E7.10,downstream_gene_variant,,ENST00000596027,;CTD-2396E7.9,downstream_gene_variant,,ENST00000599292,;TUBB4A,downstream_gene_variant,,ENST00000595324,;TUBB4A,downstream_gene_variant,,ENST00000594290,; T ENST00000264071 Transcript missense_variant 1108/2552 736/1335 246/444 L/M Ctg/Atg 1 -1 TUBB4A HGNC HGNC:20774 protein_coding YES CCDS12168.1 ENSP00000264071 P04350 UPI000005FC27 NM_001289131.1,NM_006087.3,NM_001289129.1,NM_001289130.1 deleterious_low_confidence(0) 4/4 Gene3D:3.40.50.1440,Prints_domain:PR01163,hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF121,SMART_domains:SM00865,Superfamily_domains:SSF55307 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 6495763 6495763 G T 1 0 0 0 0 1 0 0 0 17268 962 34 2 2 TUBB4A 19 6495763 Missense_Mutation SNP G C3N-02089_T 1272489 6495763 52121853 892 27976 CLEC4G 0 . GRCh38 19 7730051 7730051 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.595C>G p.His199Asp p.H199D ENST00000328853 7/9 140 105 35 153 153 0 strelka-varscan-mutect CLEC4G,missense_variant,p.His199Asp,ENST00000328853,NM_198492.3,NM_001244856.1;CLEC4G,downstream_gene_variant,,ENST00000599020,;CLEC4G,downstream_gene_variant,,ENST00000598081,; C ENST00000328853 Transcript missense_variant 664/1360 595/882 199/293 H/D Cac/Gac 1 -1 CLEC4G HGNC HGNC:24591 protein_coding YES CCDS12185.1 ENSP00000327599 Q6UXB4 Q08G24 UPI000004C65D NM_198492.3,NM_001244856.1 deleterious(0) 7/9 Low_complexity_(Seg):seg,PROSITE_profiles:PS50041,hmmpanther:PTHR22802,hmmpanther:PTHR22802:SF245,Pfam_domain:PF00059,Gene3D:3.10.100.10,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs1162013324 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 7730051 7730051 G C 1 0 0 0 0 1 0 0 0 3285 1319 46 4 4 CLEC4G 19 7730051 Missense_Mutation SNP G C3N-02089_T 1234288 7730051 50887565 893 27977 MUC16 0 . GRCh38 19 8862903 8862903 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.42737C>A p.Thr14246Lys p.T14246K ENST00000397910 77/84 218 169 49 254 253 1 strelka-varscan-mutect MUC16,missense_variant,p.Thr14246Lys,ENST00000397910,NM_024690.2;MUC16,missense_variant,p.Thr1069Lys,ENST00000599436,;MUC16,downstream_gene_variant,,ENST00000596956,;MUC16,missense_variant,p.Thr1064Lys,ENST00000601404,;MUC16,3_prime_UTR_variant,,ENST00000596768,; T ENST00000397910 Transcript missense_variant 42941/43816 42737/43524 14246/14507 T/K aCa/aAa 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 77/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,Superfamily_domains:0047452 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 8862903 8862903 G T 1 0 0 0 0 1 0 0 0 9972 1377 48 2 2 MUC16 19 8862903 Missense_Mutation SNP G C3N-02089_T 1132852 8862903 49754713 894 27978 MUC16 0 . GRCh38 19 8951242 8951242 + Frame_Shift_Del DEL G G - C3N-02089_T C3N-02089_N G G c.25528delC p.Leu8510SerfsTer27 p.L8510Sfs*27 ENST00000397910 3/84 163 120 43 200 200 0 sindel-varindel-pindel MUC16,frameshift_variant,p.Leu8510SerfsTer27,ENST00000397910,NM_024690.2; - ENST00000397910 Transcript frameshift_variant 25732/43816 25528/43524 8510/14507 L/X Ctc/tc COSM229324,COSM229325,COSM229326 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg 1,1,1 HIGH 1 deletion 5 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 8951242 8951242 G - 1 0 1 0 1 0 0 0 0 9972 1000 35 0 0 MUC16 19 8951242 Frame_Shift_Del DEL G C3N-02089_T 88339 8951242 49666374 895 27979 MUC16 0 . GRCh38 19 8951987 8951987 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.24783A>T p.Glu8261Asp p.E8261D ENST00000397910 3/84 166 119 47 174 174 0 strelka-varscan-mutect MUC16,missense_variant,p.Glu8261Asp,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 24987/43816 24783/43524 8261/14507 E/D gaA/gaT 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 8951987 8951987 T A 1 0 0 0 0 1 0 0 0 9972 1606 56 4 4 MUC16 19 8951987 Missense_Mutation SNP T C3N-02089_T 745 8951987 49665629 896 27980 ZNF846 0 . GRCh38 19 9757604 9757604 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.1473A>T p.= p.T491T ENST00000397902 6/6 148 112 36 177 177 0 strelka-varscan-mutect ZNF846,synonymous_variant,p.=,ENST00000397902,NM_001077624.1;ZNF846,3_prime_UTR_variant,,ENST00000586293,;ZNF846,intron_variant,,ENST00000588267,;ZNF846,intron_variant,,ENST00000592859,;ZNF846,downstream_gene_variant,,ENST00000589412,;ZNF846,downstream_gene_variant,,ENST00000592587,;ZNF846,downstream_gene_variant,,ENST00000586814,;ZNF846,downstream_gene_variant,,ENST00000587650,;ZNF846,downstream_gene_variant,,ENST00000590471,;ZNF846,intron_variant,,ENST00000589453,;ZNF846,downstream_gene_variant,,ENST00000591377,;CTD-2623N2.3,upstream_gene_variant,,ENST00000588113,; A ENST00000397902 Transcript synonymous_variant 1887/2016 1473/1602 491/533 T acA/acT 1 -1 ZNF846 HGNC HGNC:27260 protein_coding YES CCDS42496.1 ENSP00000380999 Q147U1 UPI000041AAC3 NM_001077624.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24381:SF157,hmmpanther:PTHR24381,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00614,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs1277360127 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 9757604 9757604 T A 1 0 0 0 0 0 0 0 1 18780 1451 51 4 4 ZNF846 19 9757604 Silent SNP T C3N-02089_T 805617 9757604 48860012 897 27981 TYK2 0 . GRCh38 19 10357897 10357897 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2333G>T p.Trp778Leu p.W778L ENST00000525621 17/25 287 200 87 242 240 2 strelka-varscan-mutect TYK2,missense_variant,p.Trp778Leu,ENST00000525621,NM_003331.4;TYK2,missense_variant,p.Trp778Leu,ENST00000264818,;TYK2,missense_variant,p.Trp593Leu,ENST00000524462,;TYK2,missense_variant,p.Trp778Leu,ENST00000529370,;TYK2,downstream_gene_variant,,ENST00000525220,;TYK2,upstream_gene_variant,,ENST00000530560,;TYK2,upstream_gene_variant,,ENST00000529422,;TYK2,upstream_gene_variant,,ENST00000592137,;TYK2,3_prime_UTR_variant,,ENST00000533334,;TYK2,non_coding_transcript_exon_variant,,ENST00000529412,;TYK2,upstream_gene_variant,,ENST00000529739,;TYK2,upstream_gene_variant,,ENST00000530220,;TYK2,upstream_gene_variant,,ENST00000527481,;TYK2,upstream_gene_variant,,ENST00000534228,;TYK2,downstream_gene_variant,,ENST00000531620,; A ENST00000525621 Transcript missense_variant 2815/4347 2333/3564 778/1187 W/L tGg/tTg 1 -1 TYK2 HGNC HGNC:12440 protein_coding YES CCDS12236.1 ENSP00000431885 P29597 A0A024R7E4 UPI000013D573 NM_003331.4 deleterious(0) 17/25 Gene3D:1.10.510.10,Pfam_domain:PF07714,PIRSF_domain:PIRSF000636,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF244,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 10357897 10357897 C A 1 0 0 0 0 1 0 0 0 17325 595 21 2 2 TYK2 19 10357897 Missense_Mutation SNP C C3N-02089_T 600293 10357897 48259719 898 27982 KEAP1 0 . GRCh38 19 10489368 10489368 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1532G>T p.Gly511Val p.G511V ENST00000171111 5/6 48 31 17 41 41 0 strelka-varscan-mutect KEAP1,missense_variant,p.Gly511Val,ENST00000171111,NM_203500.1;KEAP1,missense_variant,p.Gly511Val,ENST00000393623,NM_012289.3;KEAP1,intron_variant,,ENST00000592478,;KEAP1,downstream_gene_variant,,ENST00000592055,;CTC-429L19.3,downstream_gene_variant,,ENST00000592671,;KEAP1,downstream_gene_variant,,ENST00000588024,;KEAP1,missense_variant,p.Arg102Ser,ENST00000590593,;KEAP1,non_coding_transcript_exon_variant,,ENST00000590237,;KEAP1,downstream_gene_variant,,ENST00000585845,; A ENST00000171111 Transcript missense_variant,splice_region_variant 2080/2955 1532/1875 511/624 G/V gGc/gTc 1 -1 KEAP1 HGNC HGNC:23177 protein_coding YES CCDS12239.1 ENSP00000171111 Q14145 A0A024R7C0 UPI000007139C NM_203500.1 deleterious(0) 5/6 hmmpanther:PTHR24412:SF162,hmmpanther:PTHR24412,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 10489368 10489368 C A 1 0 0 0 0 1 0 0 0 8061 753 26 2 2 KEAP1 19 10489368 Missense_Mutation SNP C C3N-02089_T 131471 10489368 48128248 899 27983 SMARCA4 0 . GRCh38 19 10994947 10994947 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1539G>T p.= p.R513R ENST00000429416 10/36 310 216 94 301 301 0 strelka-varscan-mutect SMARCA4,synonymous_variant,p.=,ENST00000429416,NM_001128844.1;SMARCA4,synonymous_variant,p.=,ENST00000413806,;SMARCA4,synonymous_variant,p.=,ENST00000450717,NM_001128849.1;SMARCA4,synonymous_variant,p.=,ENST00000344626,NM_003072.3;SMARCA4,synonymous_variant,p.=,ENST00000590574,NM_001128847.1;SMARCA4,synonymous_variant,p.=,ENST00000589677,NM_001128846.1;SMARCA4,synonymous_variant,p.=,ENST00000541122,NM_001128845.1;SMARCA4,synonymous_variant,p.=,ENST00000444061,NM_001128848.1;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,; T ENST00000429416 Transcript synonymous_variant 1820/5691 1539/4944 513/1647 R cgG/cgT 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 10/36 Coiled-coils_(Ncoils):Coil,PROSITE_profiles:PS51204,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Pfam_domain:PF07529,SMART_domains:SM00573 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 10994947 10994947 G T 1 0 0 0 0 0 0 0 1 15063 1219 43 2 2 SMARCA4 19 10994947 Silent SNP G C3N-02089_T 505579 10994947 47622669 900 27984 ZNF823 0 . GRCh38 19 11722315 11722315 + Nonsense_Mutation SNP C C A rs756194619 C3N-02089_T C3N-02089_N C C c.1219G>T p.Glu407Ter p.E407* ENST00000341191 4/4 180 159 21 205 205 0 strelka-varscan-mutect ZNF823,stop_gained,p.Glu407Ter,ENST00000341191,NM_001080493.3;ZNF823,stop_gained,p.Glu363Ter,ENST00000431998,NM_017507.1;ZNF823,downstream_gene_variant,,ENST00000586121,;ZNF823,downstream_gene_variant,,ENST00000440527,;CTC-499B15.6,downstream_gene_variant,,ENST00000586983,; A ENST00000341191 Transcript stop_gained 1373/2423 1219/1833 407/610 E/* Gaa/Taa rs756194619 1 -1 ZNF823 HGNC HGNC:30936 protein_coding YES CCDS45981.1 ENSP00000340683 P16415 UPI0000203407 NM_001080493.3 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF27,hmmpanther:PTHR24379,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS rs756194619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 11722315 11722315 C A 1 0 0 0 0 0 1 0 0 18765 835 29 2 2 ZNF823 19 11722315 Nonsense_Mutation SNP C C3N-02089_T 727368 11722315 46895301 901 27985 GCDH 0 . GRCh38 19 12891862 12891862 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.159G>T p.= p.P53P ENST00000222214 4/12 427 300 127 457 454 3 strelka-varscan-mutect GCDH,synonymous_variant,p.=,ENST00000222214,NM_000159.3,NM_013976.3;GCDH,synonymous_variant,p.=,ENST00000591470,;GCDH,synonymous_variant,p.=,ENST00000588905,;GCDH,synonymous_variant,p.=,ENST00000589039,;GCDH,synonymous_variant,p.=,ENST00000587072,;KLF1,upstream_gene_variant,,ENST00000264834,NM_006563.3;GCDH,synonymous_variant,p.=,ENST00000590530,;GCDH,3_prime_UTR_variant,,ENST00000590445,;GCDH,non_coding_transcript_exon_variant,,ENST00000591043,;GCDH,non_coding_transcript_exon_variant,,ENST00000585420,;GCDH,non_coding_transcript_exon_variant,,ENST00000421816,;GCDH,non_coding_transcript_exon_variant,,ENST00000590627,;GCDH,non_coding_transcript_exon_variant,,ENST00000587832,;GCDH,non_coding_transcript_exon_variant,,ENST00000585760,;RPS6P25,upstream_gene_variant,,ENST00000464444,; T ENST00000222214 Transcript synonymous_variant 370/1956 159/1317 53/438 P ccG/ccT 1 1 GCDH HGNC HGNC:4189 protein_coding YES CCDS12286.1 ENSP00000222214 Q92947 A0A024R7F9 UPI000012B292 NM_000159.3,NM_013976.3 4/12 hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF307,Gene3D:1.10.540.10,Superfamily_domains:SSF56645 LOW 1 SNV 1 1 PASS rs1315058754 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 12891862 12891862 G T 1 0 0 0 0 0 0 0 1 6157 1074 38 1 1 GCDH 19 12891862 Silent SNP G C3N-02089_T 1169547 12891862 45725754 902 27986 CACNA1A 0 . GRCh38 19 13234958 13234958 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.5212T>G p.Phe1738Val p.F1738V ENST00000360228 34/47 158 119 39 156 156 0 strelka-varscan-mutect CACNA1A,missense_variant,p.Phe1739Val,ENST00000638009,NM_001127221.1;CACNA1A,missense_variant,p.Phe1739Val,ENST00000635895,;CACNA1A,missense_variant,p.Phe1739Val,ENST00000637769,;CACNA1A,missense_variant,p.Phe1738Val,ENST00000360228,NM_001127222.1;CACNA1A,missense_variant,p.Phe1744Val,ENST00000614285,;CACNA1A,missense_variant,p.Phe1692Val,ENST00000637736,;CACNA1A,missense_variant,p.Phe1739Val,ENST00000636389,;CACNA1A,missense_variant,p.Phe1744Val,ENST00000638029,NM_023035.2;CACNA1A,missense_variant,p.Phe1744Val,ENST00000637432,NM_000068.3;CACNA1A,missense_variant,p.Phe1740Val,ENST00000573710,;CACNA1A,missense_variant,p.Phe1739Val,ENST00000635727,;CACNA1A,missense_variant,p.Phe1739Val,ENST00000636012,;CACNA1A,missense_variant,p.Phe1739Val,ENST00000637276,;CACNA1A,missense_variant,p.Phe1740Val,ENST00000637927,;CACNA1A,missense_variant,p.Phe1741Val,ENST00000636549,NM_001174080.1;CACNA1A,missense_variant,p.Phe225Val,ENST00000587525,;CACNA1A,missense_variant,p.Phe125Val,ENST00000585802,;CACNA1A,missense_variant,p.Phe103Val,ENST00000636473,;CACNA1A,missense_variant,p.Phe206Val,ENST00000637819,;CACNA1A,missense_variant,p.Phe170Val,ENST00000637297,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000574822,;CACNA1A,3_prime_UTR_variant,,ENST00000573891,;CACNA1A,3_prime_UTR_variant,,ENST00000637777,;CACNA1A,3_prime_UTR_variant,,ENST00000636058,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000635742,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637809,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000637832,;CACNA1A,non_coding_transcript_exon_variant,,ENST00000593267,;CACNA1A,upstream_gene_variant,,ENST00000636768,; C ENST00000360228 Transcript missense_variant 5447/8627 5212/7521 1738/2506 F/V Ttc/Gtc 1 -1 CACNA1A HGNC HGNC:1388 protein_coding YES CCDS45998.1 ENSP00000353362 O00555 UPI0000141565 NM_001127222.1 deleterious(0) 34/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF59,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Prints_domain:PR00167 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 13234958 13234958 A C 1 0 0 0 0 1 0 0 0 2226 72 3 5 5 CACNA1A 19 13234958 Missense_Mutation SNP A C3N-02089_T 343096 13234958 45382658 903 27987 NWD1 0 . GRCh38 19 16815148 16815148 + Nonsense_Mutation SNP C C A rs771041627 C3N-02089_T C3N-02089_N C C c.4514C>A p.Ser1505Ter p.S1505* ENST00000552788 18/18 401 295 106 378 378 0 strelka-varscan-mutect NWD1,stop_gained,p.Ser1505Ter,ENST00000552788,NM_001290355.1;NWD1,stop_gained,p.Ser1463Ter,ENST00000549814,;NWD1,3_prime_UTR_variant,,ENST00000524140,NM_001007525.3;NWD1,3_prime_UTR_variant,,ENST00000379808,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; A ENST00000552788 Transcript stop_gained 4514/6964 4514/4695 1505/1564 S/* tCa/tAa rs771041627 1 1 NWD1 HGNC HGNC:27619 protein_coding ENSP00000447224 Q149M9 UPI0001AE63B7 NM_001290355.1 18/18 HIGH SNV 5 1 PASS rs771041627 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 16815148 16815148 C A 1 0 0 0 0 0 1 0 0 10854 838 29 2 2 NWD1 19 16815148 Nonsense_Mutation SNP C C3N-02089_T 3580190 16815148 41802468 904 27988 ZNF208 0 . GRCh38 19 21973964 21973964 + Missense_Mutation SNP G G T rs780894918 C3N-02089_T C3N-02089_N G G c.1070C>A p.Thr357Asn p.T357N ENST00000397126 4/4 142 123 19 225 224 1 varscan-mutect ZNF208,missense_variant,p.Thr357Asn,ENST00000397126,NM_007153.3;ZNF208,missense_variant,p.Thr357Asn,ENST00000609966,;ZNF208,intron_variant,,ENST00000601773,;ZNF208,intron_variant,,ENST00000599916,; T ENST00000397126 Transcript missense_variant 1219/3992 1070/3843 357/1280 T/N aCt/aAt rs780894918 1 -1 ZNF208 HGNC HGNC:12999 protein_coding YES CCDS54240.1 ENSP00000380315 O43345 UPI0001B23C28 NM_007153.3 tolerated(0.35) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375:SF103,hmmpanther:PTHR24375,PROSITE_patterns:PS00028,Pfam_domain:PF13912,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS rs780894918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 21973964 21973964 G T 1 0 0 0 0 1 0 0 0 18343 1029 36 2 2 ZNF208 19 21973964 Missense_Mutation SNP G C3N-02089_T 5158816 21973964 36643652 905 27989 ZNF98 0 . GRCh38 19 22392793 22392793 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.442A>G p.Thr148Ala p.T148A ENST00000357774 4/4 75 54 21 109 109 0 strelka-varscan-mutect ZNF98,missense_variant,p.Thr148Ala,ENST00000357774,NM_001098626.1;ZNF98,missense_variant,p.Thr107Ala,ENST00000593657,; C ENST00000357774 Transcript missense_variant 564/2338 442/1719 148/572 T/A Act/Gct 1 -1 ZNF98 HGNC HGNC:13174 protein_coding YES CCDS46031.1 ENSP00000350418 A6NK75 UPI0000251DC5 NM_001098626.1 tolerated(0.21) 4/4 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 22392793 22392793 T C 1 0 0 0 0 1 0 0 0 18796 1725 60 5 5 ZNF98 19 22392793 Missense_Mutation SNP T C3N-02089_T 418829 22392793 36224823 906 27990 ZNF492 0 . GRCh38 19 22665095 22665095 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1426C>G p.Pro476Ala p.P476A ENST00000456783 4/4 150 135 15 190 189 1 varscan-mutect ZNF492,missense_variant,p.Pro476Ala,ENST00000456783,NM_020855.2;CTC-457E21.9,downstream_gene_variant,,ENST00000601860,; G ENST00000456783 Transcript missense_variant 1670/4245 1426/1596 476/531 P/A Ccc/Gcc 1 1 ZNF492 HGNC HGNC:23707 protein_coding YES CCDS46032.1 ENSP00000413660 Q9P255 UPI00001C200B NM_020855.2 deleterious(0.01) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF108,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1320712855 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 22665095 22665095 C G 1 0 0 0 0 1 0 0 0 18516 507 18 4 4 ZNF492 19 22665095 Missense_Mutation SNP C C3N-02089_T 272302 22665095 35952521 907 27991 ZNF728 0 . GRCh38 19 22975939 22975939 + Missense_Mutation SNP G G T rs752354751 C3N-02089_T C3N-02089_N G G c.1398C>A p.Ser466Arg p.S466R ENST00000594710 4/4 130 98 32 194 194 0 strelka-varscan-mutect ZNF728,missense_variant,p.Ser466Arg,ENST00000594710,NM_001267716.1;ZNF728,downstream_gene_variant,,ENST00000599851,; T ENST00000594710 Transcript missense_variant 1544/2015 1398/1869 466/622 S/R agC/agA rs752354751 1 -1 ZNF728 HGNC HGNC:32463 protein_coding YES CCDS59370.1 ENSP00000471593 P0DKX0 UPI0002656E4B NM_001267716.1 tolerated(0.39) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF239,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS rs752354751 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 22975939 22975939 G T 1 0 0 0 0 1 0 0 0 18702 1194 42 2 2 ZNF728 19 22975939 Missense_Mutation SNP G C3N-02089_T 310844 22975939 35641677 908 27992 UQCRFS1 0 . GRCh38 19 29207788 29207788 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.585G>T p.Leu195Phe p.L195F ENST00000304863 2/2 253 194 59 209 207 2 strelka-varscan-mutect UQCRFS1,missense_variant,p.Leu195Phe,ENST00000304863,NM_006003.2; A ENST00000304863 Transcript missense_variant 1008/3475 585/825 195/274 L/F ttG/ttT 1 -1 UQCRFS1 HGNC HGNC:12587 protein_coding YES CCDS12415.1 ENSP00000306397 P47985 UPI000013E9D6 NM_006003.2 deleterious(0) 2/2 PROSITE_profiles:PS51296,hmmpanther:PTHR10134,hmmpanther:PTHR10134:SF9,TIGRFAM_domain:TIGR01416,Gene3D:2.102.10.10,Pfam_domain:PF00355,Superfamily_domains:SSF50022 MODERATE 1 SNV 1 1 PASS rs1350969281 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 29207788 29207788 C A 1 0 0 0 0 1 0 0 0 17549 825 29 2 2 UQCRFS1 19 29207788 Missense_Mutation SNP C C3N-02089_T 6231849 29207788 29409828 909 27993 TSHZ3 0 . GRCh38 19 31277180 31277180 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2613G>T p.Lys871Asn p.K871N ENST00000240587 2/2 106 80 26 90 89 1 strelka-varscan-mutect TSHZ3,missense_variant,p.Lys871Asn,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; A ENST00000240587 Transcript missense_variant 2941/5176 2613/3246 871/1081 K/N aaG/aaT 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1465900081 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 31277180 31277180 C A 1 0 0 0 0 1 0 0 0 17130 564 20 2 2 TSHZ3 19 31277180 Missense_Mutation SNP C C3N-02089_T 2069392 31277180 27340436 910 27994 GRAMD1A 0 . GRCh38 19 35010379 35010379 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.525G>T p.Lys175Asn p.K175N ENST00000317991 6/20 300 220 80 227 227 0 strelka-varscan-mutect GRAMD1A,missense_variant,p.Lys262Asn,ENST00000599564,NM_001320036.1;GRAMD1A,missense_variant,p.Lys175Asn,ENST00000317991,NM_001320034.1,NM_020895.3;GRAMD1A,missense_variant,p.Lys168Asn,ENST00000411896,NM_001136199.1;GRAMD1A,missense_variant,p.Lys175Asn,ENST00000424536,;CTD-2527I21.14,downstream_gene_variant,,ENST00000605640,;GRAMD1A,non_coding_transcript_exon_variant,,ENST00000594597,;GRAMD1A,downstream_gene_variant,,ENST00000598073,;GRAMD1A,downstream_gene_variant,,ENST00000603669,;GRAMD1A,missense_variant,p.Lys175Asn,ENST00000600231,NM_001320035.1;GRAMD1A,non_coding_transcript_exon_variant,,ENST00000599476,;GRAMD1A,upstream_gene_variant,,ENST00000598118,;GRAMD1A,upstream_gene_variant,,ENST00000595596,;GRAMD1A,upstream_gene_variant,,ENST00000598362,;GRAMD1A,upstream_gene_variant,,ENST00000598580,; T ENST00000317991 Transcript missense_variant,splice_region_variant 717/2695 525/2175 175/724 K/N aaG/aaT 1 1 GRAMD1A HGNC HGNC:29305 protein_coding YES CCDS42546.1 ENSP00000441032 Q96CP6 UPI00000377B4 NM_001320034.1,NM_020895.3 deleterious(0) 6/20 hmmpanther:PTHR23319,hmmpanther:PTHR23319:SF8 MODERATE 1 SNV 1 1 PASS rs1171473459 . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 35010379 35010379 G T 1 0 0 0 0 1 0 0 0 6626 1014 35 2 2 GRAMD1A 19 35010379 Missense_Mutation SNP G C3N-02089_T 3733199 35010379 23607237 911 27995 MAG 0 . GRCh38 19 35295829 35295829 + Missense_Mutation SNP G G T rs764252583 C3N-02089_T C3N-02089_N G G c.263G>T p.Arg88Leu p.R88L ENST00000392213 4/11 255 190 65 129 129 0 strelka-varscan-mutect MAG,missense_variant,p.Arg88Leu,ENST00000361922,NM_080600.2;MAG,missense_variant,p.Arg88Leu,ENST00000392213,NM_002361.3;MAG,missense_variant,p.Arg63Leu,ENST00000537831,NM_001199216.1;MAG,missense_variant,p.Arg88Leu,ENST00000595791,;MAG,missense_variant,p.Arg63Leu,ENST00000600291,;MAG,intron_variant,,ENST00000597035,; T ENST00000392213 Transcript missense_variant 422/2390 263/1881 88/626 R/L cGc/cTc rs764252583,COSM386939,COSM386940 1 1 MAG HGNC HGNC:6783 protein_coding YES CCDS12455.1 ENSP00000376048 P20916 UPI000012EB2F NM_002361.3 deleterious(0) 4/11 Gene3D:2.60.40.10,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF54,Low_complexity_(Seg):seg,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs764252583 . 0 204 0 5 0 0 0 0 -20 0.9998285 1 1 1 0 T 3 4 90 35295829 35295829 G T 1 0 0 0 0 1 0 0 0 9078 1087 38 1 1 MAG 19 35295829 Missense_Mutation SNP G C3N-02089_T 285450 35295829 23321787 912 27996 ARHGAP33 0 . GRCh38 19 35780258 35780258 + Silent SNP C C A rs775899107 C3N-02089_T C3N-02089_N C C c.549C>A p.= p.L183L ENST00000314737 7/21 211 167 44 121 120 1 strelka-varscan-mutect ARHGAP33,synonymous_variant,p.=,ENST00000378944,NM_001172630.1;ARHGAP33,synonymous_variant,p.=,ENST00000314737,NM_052948.3;ARHGAP33,synonymous_variant,p.=,ENST00000007510,;ARHGAP33,upstream_gene_variant,,ENST00000587447,;ARHGAP33,upstream_gene_variant,,ENST00000588248,;ARHGAP33,downstream_gene_variant,,ENST00000221905,;ARHGAP33,downstream_gene_variant,,ENST00000589133,;ARHGAP33,upstream_gene_variant,,ENST00000591438,;ARHGAP33,upstream_gene_variant,,ENST00000593034,;ARHGAP33,upstream_gene_variant,,ENST00000601474,;ARHGAP33,upstream_gene_variant,,ENST00000587984,;ARHGAP33,downstream_gene_variant,,ENST00000590893,;ARHGAP33,upstream_gene_variant,,ENST00000586918,; A ENST00000314737 Transcript synonymous_variant 633/3858 549/3381 183/1126 L ctC/ctA rs775899107 1 1 ARHGAP33 HGNC HGNC:23085 protein_coding YES CCDS12477.1 ENSP00000320038 O14559 UPI000013F8F9 NM_052948.3 7/21 hmmpanther:PTHR15729:SF11,hmmpanther:PTHR15729 LOW 1 SNV 2 1 PASS rs775899107 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 35780258 35780258 C A 1 0 0 0 0 0 0 0 1 1007 813 29 2 2 ARHGAP33 19 35780258 Silent SNP C C3N-02089_T 484429 35780258 22837358 913 27997 KIRREL2 0 . GRCh38 19 35866422 35866422 + Missense_Mutation SNP C C A rs756538382 C3N-02089_T C3N-02089_N C C c.2057C>A p.Pro686His p.P686H ENST00000360202 15/15 320 223 97 218 217 1 strelka-varscan-mutect KIRREL2,missense_variant,p.Pro686His,ENST00000360202,NM_199180.3;KIRREL2,missense_variant,p.Pro651His,ENST00000592409,;KIRREL2,intron_variant,,ENST00000347900,NM_199179.3;KIRREL2,intron_variant,,ENST00000262625,NM_032123.6;APLP1,upstream_gene_variant,,ENST00000221891,NM_005166.3,NM_001024807.1;APLP1,upstream_gene_variant,,ENST00000537454,;APLP1,upstream_gene_variant,,ENST00000586861,;APLP1,upstream_gene_variant,,ENST00000592316,;APLP1,upstream_gene_variant,,ENST00000589743,;NPHS1,intron_variant,,ENST00000591817,;APLP1,upstream_gene_variant,,ENST00000590561,; A ENST00000360202 Transcript missense_variant 2255/2942 2057/2127 686/708 P/H cCc/cAc rs756538382 1 1 KIRREL2 HGNC HGNC:18816 protein_coding YES CCDS12481.1 ENSP00000353331 Q6UWL6 UPI0000048F5B NM_199180.3 deleterious(0) 15/15 Low_complexity_(Seg):seg,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF51 MODERATE 1 SNV 1 1 PASS rs756538382 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 35866422 35866422 C A 1 0 0 0 0 1 0 0 0 8189 623 22 2 2 KIRREL2 19 35866422 Missense_Mutation SNP C C3N-02089_T 86164 35866422 22751194 914 27998 WDR62 0 . GRCh38 19 36089105 36089105 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1836G>T p.Gln612His p.Q612H ENST00000401500 14/32 510 427 83 368 368 0 strelka-varscan-mutect WDR62,missense_variant,p.Gln612His,ENST00000401500,NM_001083961.1;WDR62,missense_variant,p.Gln612His,ENST00000270301,NM_173636.4;WDR62,splice_region_variant,,ENST00000587391,; T ENST00000401500 Transcript missense_variant,splice_region_variant 1871/4682 1836/4572 612/1523 Q/H caG/caT 1 1 WDR62 HGNC HGNC:24502 protein_coding YES CCDS46059.1 ENSP00000384792 O43379 UPI000022A7E9 NM_001083961.1 deleterious(0) 14/32 PROSITE_profiles:PS50294,hmmpanther:PTHR22847:SF434,hmmpanther:PTHR22847,Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS rs896840471 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 36089105 36089105 G T 1 0 0 0 0 1 0 0 0 17872 1014 35 2 2 WDR62 19 36089105 Missense_Mutation SNP G C3N-02089_T 222683 36089105 22528511 915 27999 ZNF567 0 . GRCh38 19 36719370 36719370 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.646G>T p.Glu216Ter p.E216* ENST00000536254 6/6 221 171 50 217 217 0 strelka-varscan-mutect ZNF567,stop_gained,p.Glu185Ter,ENST00000585696,;ZNF567,stop_gained,p.Glu216Ter,ENST00000536254,NM_001322917.1,NM_001322918.1,NM_001322915.1,NM_001322916.1,NM_001322913.1,NM_001300979.1;ZNF567,stop_gained,p.Glu185Ter,ENST00000360729,NM_001322912.1,NM_001322911.1,NM_152603.3;ZNF567,stop_gained,p.Glu185Ter,ENST00000588311,;ZNF850,intron_variant,,ENST00000589390,;ZNF567,intron_variant,,ENST00000589264,;ZNF567,intron_variant,,ENST00000591308,; T ENST00000536254 Transcript stop_gained 868/2825 646/1944 216/647 E/* Gag/Tag 1 1 ZNF567 HGNC HGNC:28696 protein_coding YES CCDS74349.1 ENSP00000441838 Q8N184 UPI000022A7F5 NM_001322917.1,NM_001322918.1,NM_001322915.1,NM_001322916.1,NM_001322913.1,NM_001300979.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF25,Superfamily_domains:SSF57667 HIGH 1 SNV 2 1 PASS rs912984115 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 36719370 36719370 G T 1 0 0 0 0 0 1 0 0 18572 1291 45 2 2 ZNF567 19 36719370 Nonsense_Mutation SNP G C3N-02089_T 630265 36719370 21898246 916 28000 ZNF568 0 . GRCh38 19 36991825 36991825 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.604G>T p.Glu202Ter p.E202* ENST00000617745 7/8 86 74 12 91 91 0 strelka-varscan-mutect ZNF568,stop_gained,p.Glu202Ter,ENST00000617745,NM_001204838.1;ZNF568,stop_gained,p.Glu138Ter,ENST00000455427,NM_001204839.1;ZNF568,stop_gained,p.Glu202Ter,ENST00000444991,;ZNF568,stop_gained,p.Glu70Ter,ENST00000433993,;ZNF568,stop_gained,p.Glu6Ter,ENST00000455817,;ZNF568,stop_gained,p.Glu6Ter,ENST00000588596,;ZNF568,downstream_gene_variant,,ENST00000592567,;ZNF568,non_coding_transcript_exon_variant,,ENST00000591887,; T ENST00000617745 Transcript stop_gained 804/2441 604/1908 202/635 E/* Gag/Tag 1 1 ZNF568 HGNC HGNC:25392 protein_coding CCDS74351.1 ENSP00000482444 A0A087WZ84 UPI0001FD28F8 NM_001204838.1 7/8 PROSITE_profiles:PS50805 HIGH SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 36991825 36991825 G T 1 0 0 0 0 0 1 0 0 18573 1175 41 2 2 ZNF568 19 36991825 Nonsense_Mutation SNP G C3N-02089_T 272455 36991825 21625791 917 28001 HKR1 0 . GRCh38 19 37362869 37362869 + Silent SNP G G T rs202210305 C3N-02089_T C3N-02089_N G G c.1074G>T p.= p.V358V ENST00000324411 6/6 276 218 58 259 259 0 strelka-varscan-mutect HKR1,synonymous_variant,p.=,ENST00000591471,;HKR1,synonymous_variant,p.=,ENST00000324411,NM_181786.2;HKR1,synonymous_variant,p.=,ENST00000544914,;HKR1,synonymous_variant,p.=,ENST00000392153,;HKR1,synonymous_variant,p.=,ENST00000541583,;HKR1,synonymous_variant,p.=,ENST00000589392,;HKR1,intron_variant,,ENST00000591134,;HKR1,downstream_gene_variant,,ENST00000591259,;HKR1,downstream_gene_variant,,ENST00000590582,;HKR1,downstream_gene_variant,,ENST00000592768,;HKR1,downstream_gene_variant,,ENST00000585623,;HKR1,downstream_gene_variant,,ENST00000592168,;HKR1,downstream_gene_variant,,ENST00000591391,;HKR1,downstream_gene_variant,,ENST00000591417,;HKR1,downstream_gene_variant,,ENST00000586897,;HKR1,non_coding_transcript_exon_variant,,ENST00000588820,;HKR1,downstream_gene_variant,,ENST00000590570,; T ENST00000324411 Transcript synonymous_variant 1343/2929 1074/1980 358/659 V gtG/gtT rs202210305 1 1 HKR1 HGNC HGNC:4928 protein_coding YES CCDS12502.1 ENSP00000315505 P10072 UPI00001AE470 NM_181786.2 6/6 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF129,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS rs202210305 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 37362869 37362869 G T 1 0 0 0 0 0 0 0 1 7083 1364 48 2 2 HKR1 19 37362869 Silent SNP G C3N-02089_T 371044 37362869 21254747 918 28002 RYR1 0 . GRCh38 19 38440795 38440795 + Silent SNP C C A rs768813714 C3N-02089_T C3N-02089_N C C c.96C>A p.= p.L32L ENST00000359596 2/106 155 124 31 107 107 0 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2; A ENST00000359596 Transcript synonymous_variant 96/15117 96/15117 32/5038 L ctC/ctA rs768813714 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 2/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF08709,Gene3D:2.80.10.50 LOW 1 SNV 5 1 PASS rs768813714 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 38440795 38440795 C A 1 0 0 0 0 0 0 0 1 14028 813 29 2 2 RYR1 19 38440795 Silent SNP C C3N-02089_T 1077926 38440795 20176821 919 28003 RYR1 0 . GRCh38 19 38446757 38446757 + Silent SNP A A C novel C3N-02089_T C3N-02089_N A A c.789A>C p.= p.P263P ENST00000359596 9/106 132 116 16 115 115 0 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2; C ENST00000359596 Transcript synonymous_variant 789/15117 789/15117 263/5038 P ccA/ccC 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 9/106 PROSITE_profiles:PS50919,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF02815,Gene3D:2.80.10.50,SMART_domains:SM00472,Superfamily_domains:SSF82109,Prints_domain:PR00795 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 90 38446757 38446757 A C 1 0 0 0 0 0 0 0 1 14028 146 6 5 5 RYR1 19 38446757 Silent SNP A C3N-02089_T 5962 38446757 20170859 920 28004 RYR1 0 . GRCh38 19 38455739 38455739 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1779G>T p.= p.G593G ENST00000359596 16/106 530 421 109 429 428 1 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2; T ENST00000359596 Transcript synonymous_variant 1779/15117 1779/15117 593/5038 G ggG/ggT 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 16/106 PROSITE_profiles:PS50188,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715,Pfam_domain:PF01365 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 38455739 38455739 G T 1 0 0 0 0 0 0 0 1 14028 1161 41 2 2 RYR1 19 38455739 Silent SNP G C3N-02089_T 8982 38455739 20161877 921 28005 RYR1 0 . GRCh38 19 38517541 38517541 + Nonsense_Mutation SNP G G T rs112151058 C3N-02089_T C3N-02089_N G G c.9868G>T p.Glu3290Ter p.E3290* ENST00000359596 66/106 407 324 83 349 348 1 strelka-varscan-mutect RYR1,stop_gained,p.Glu3290Ter,ENST00000355481,NM_001042723.1;RYR1,stop_gained,p.Glu3290Ter,ENST00000359596,NM_000540.2;RYR1,stop_gained,p.Glu226Ter,ENST00000599547,;RYR1,3_prime_UTR_variant,,ENST00000594335,; T ENST00000359596 Transcript stop_gained 9868/15117 9868/15117 3290/5038 E/* Gag/Tag rs112151058,CM091769 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 66/106 Low_complexity_(Seg):seg,hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 HIGH 1 SNV 5 0,1 1 PASS rs112151058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 38517541 38517541 G T 1 0 0 0 0 0 1 0 0 14028 1059 37 1 1 RYR1 19 38517541 Nonsense_Mutation SNP G C3N-02089_T 61802 38517541 20100075 922 28006 RYR1 0 . GRCh38 19 38567896 38567896 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.13638G>A p.= p.E4546E ENST00000359596 93/106 347 280 67 243 243 0 strelka-varscan-mutect RYR1,synonymous_variant,p.=,ENST00000355481,NM_001042723.1;RYR1,synonymous_variant,p.=,ENST00000359596,NM_000540.2;RYR1,synonymous_variant,p.=,ENST00000593677,;RYR1,downstream_gene_variant,,ENST00000594335,; A ENST00000359596 Transcript synonymous_variant 13638/15117 13638/15117 4546/5038 E gaG/gaA COSM5251931 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 93/106 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF15,Pfam_domain:PF06459 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 38567896 38567896 G A 1 0 0 0 0 0 0 0 1 14028 991 35 3 3 RYR1 19 38567896 Silent SNP G C3N-02089_T 50355 38567896 20049720 923 28007 IFNL1 0 . GRCh38 19 39296477 39296477 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.56C>T p.Ala19Val p.A19V ENST00000333625 1/5 211 170 41 186 186 0 strelka-varscan-mutect IFNL1,missense_variant,p.Ala19Val,ENST00000333625,NM_172140.1; T ENST00000333625 Transcript missense_variant 153/857 56/603 19/200 A/V gCa/gTa 1 1 IFNL1 HGNC HGNC:18363 protein_coding YES CCDS12531.1 ENSP00000329991 Q8IU54 UPI00000474AE NM_172140.1 deleterious(0.01) 1/5 hmmpanther:PTHR31943,hmmpanther:PTHR31943:SF6,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 39296477 39296477 C T 1 0 0 0 0 1 0 0 0 7452 710 25 3 3 IFNL1 19 39296477 Missense_Mutation SNP C C3N-02089_T 728581 39296477 19321139 924 28008 LTBP4 0 . GRCh38 19 40608517 40608517 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.1541C>T p.Pro514Leu p.P514L ENST00000308370 12/33 213 170 43 196 196 0 strelka-varscan-mutect LTBP4,missense_variant,p.Pro477Leu,ENST00000204005,NM_003573.2;LTBP4,missense_variant,p.Pro514Leu,ENST00000308370,NM_001042544.1;LTBP4,missense_variant,p.Pro447Leu,ENST00000396819,NM_001042545.1;LTBP4,upstream_gene_variant,,ENST00000243562,;LTBP4,upstream_gene_variant,,ENST00000601032,;LTBP4,upstream_gene_variant,,ENST00000599724,;LTBP4,upstream_gene_variant,,ENST00000612121,;LTBP4,upstream_gene_variant,,ENST00000597071,;LTBP4,upstream_gene_variant,,ENST00000598055,;LTBP4,non_coding_transcript_exon_variant,,ENST00000595529,;LTBP4,intron_variant,,ENST00000598717,;LTBP4,upstream_gene_variant,,ENST00000546155,;LTBP4,upstream_gene_variant,,ENST00000598256,;LTBP4,downstream_gene_variant,,ENST00000599016,;LTBP4,downstream_gene_variant,,ENST00000600026,;LTBP4,downstream_gene_variant,,ENST00000594537,;LTBP4,upstream_gene_variant,,ENST00000600499,;LTBP4,upstream_gene_variant,,ENST00000610893,;LTBP4,upstream_gene_variant,,ENST00000612845,;LTBP4,downstream_gene_variant,,ENST00000593738,; T ENST00000308370 Transcript missense_variant 1541/4948 1541/4875 514/1624 P/L cCt/cTt 1 1 LTBP4 HGNC HGNC:6717 protein_coding YES CCDS74369.1 ENSP00000311905 Q8N2S1 UPI0000DACAC4 NM_001042544.1 tolerated(0.08) 12/33 hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF43,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 40608517 40608517 C T 1 0 0 0 0 1 0 0 0 8982 681 24 3 3 LTBP4 19 40608517 Missense_Mutation SNP C C3N-02089_T 1312040 40608517 18009099 925 28009 B3GNT8 0 . GRCh38 19 41426386 41426386 + Silent SNP C C A rs145254457 C3N-02089_T C3N-02089_N C C c.393G>T p.= p.L131L ENST00000321702 3/3 165 128 37 142 142 0 strelka-varscan-mutect B3GNT8,synonymous_variant,p.=,ENST00000321702,NM_198540.2;BCKDHA,downstream_gene_variant,,ENST00000269980,NM_001164783.1,NM_000709.3;CTC-435M10.3,downstream_gene_variant,,ENST00000540732,;BCKDHA,downstream_gene_variant,,ENST00000457836,;ATP5SL,downstream_gene_variant,,ENST00000221943,NM_018035.2;ATP5SL,downstream_gene_variant,,ENST00000592922,NM_001320840.1,NM_001167871.1;ATP5SL,downstream_gene_variant,,ENST00000438807,NM_001320841.1,NM_001167870.1;BCKDHA,downstream_gene_variant,,ENST00000542943,;BCKDHA,downstream_gene_variant,,ENST00000541315,;BCKDHA,downstream_gene_variant,,ENST00000544905,;CTC-435M10.6,downstream_gene_variant,,ENST00000598887,;B3GNT8,non_coding_transcript_exon_variant,,ENST00000601379,;B3GNT8,intron_variant,,ENST00000601616,;BCKDHA,downstream_gene_variant,,ENST00000535632,;ATP5SL,downstream_gene_variant,,ENST00000589503,;BCKDHA,downstream_gene_variant,,ENST00000538423,;BCKDHA,downstream_gene_variant,,ENST00000545787,; A ENST00000321702 Transcript synonymous_variant 847/1874 393/1194 131/397 L ctG/ctT rs145254457 1 -1 B3GNT8 HGNC HGNC:24139 protein_coding YES CCDS12582.1 ENSP00000312700 Q7Z7M8 UPI0000140C01 NM_198540.2 3/3 hmmpanther:PTHR11214,hmmpanther:PTHR11214:SF87 LOW 1 SNV 1 1 PASS rs145254457 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 41426386 41426386 C A 1 0 0 0 0 0 0 0 1 1419 697 25 2 2 B3GNT8 19 41426386 Silent SNP C C3N-02089_T 817869 41426386 17191230 926 28010 ATP1A3 0 . GRCh38 19 41968884 41968884 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.2759C>A p.Thr920Asn p.T920N ENST00000545399 20/23 535 421 114 377 377 0 strelka-varscan-mutect ATP1A3,missense_variant,p.Thr920Asn,ENST00000545399,NM_001256214.1;ATP1A3,missense_variant,p.Thr907Asn,ENST00000302102,NM_152296.4;ATP1A3,missense_variant,p.Thr877Asn,ENST00000602133,;ATP1A3,missense_variant,p.Thr918Asn,ENST00000543770,NM_001256213.1;ATP1A3,missense_variant,p.Thr907Asn,ENST00000441343,; T ENST00000545399 Transcript missense_variant 2943/3618 2759/3081 920/1026 T/N aCc/aAc 1 -1 ATP1A3 HGNC HGNC:801 protein_coding YES CCDS58664.1 ENSP00000444688 P13637 UPI0001914BDE NM_001256214.1 deleterious(0.01) 20/23 Superfamily_domains:0049473,Gene3D:1.20.1110.10,Pfam_domain:PF00689,Prints_domain:PR00121,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF259,TIGRFAM_domain:TIGR01106,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 41968884 41968884 G T 1 0 0 0 0 1 0 0 0 1282 1261 44 2 2 ATP1A3 19 41968884 Missense_Mutation SNP G C3N-02089_T 542498 41968884 16648732 927 28011 ZNF574 0 . GRCh38 19 42080259 42080259 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.1654delC p.Arg552GlyfsTer15 p.R552Gfs*15 ENST00000600245 2/2 206 171 35 212 212 0 sindel-varindel-pindel ZNF574,frameshift_variant,p.Arg552GlyfsTer15,ENST00000600245,;ZNF574,frameshift_variant,p.Arg642GlyfsTer15,ENST00000222339,;ZNF574,frameshift_variant,p.Arg552GlyfsTer15,ENST00000359044,NM_022752.5;ZNF574,downstream_gene_variant,,ENST00000597391,; - ENST00000600245 Transcript frameshift_variant 2308/3598 1653/2691 551/896 Y/X taC/ta 1 1 ZNF574 HGNC HGNC:26166 protein_coding YES CCDS12596.1 ENSP00000469029 Q6ZN55 UPI00001AE536 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF38,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 HIGH 1 deletion 2 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 42080259 42080259 C - 1 0 1 0 1 0 0 0 0 18580 518 18 0 0 ZNF574 19 42080259 Frame_Shift_Del DEL C C3N-02089_T 111375 42080259 16537357 928 28012 PRR19 0 . GRCh38 19 42310677 42310677 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1008C>T p.= p.L336L ENST00000499536 2/2 58 45 13 61 60 1 strelka-varscan-mutect PRR19,synonymous_variant,p.=,ENST00000499536,;PRR19,synonymous_variant,p.=,ENST00000341747,NM_199285.2;PRR19,3_prime_UTR_variant,,ENST00000598490,;TMEM145,upstream_gene_variant,,ENST00000598766,;TMEM145,upstream_gene_variant,,ENST00000301204,NM_173633.2;PRR19,downstream_gene_variant,,ENST00000595750,;TMEM145,upstream_gene_variant,,ENST00000601020,;TMEM145,upstream_gene_variant,,ENST00000595775,; T ENST00000499536 Transcript synonymous_variant 1819/1956 1008/1071 336/356 L ctC/ctT 1 1 PRR19 HGNC HGNC:33728 protein_coding YES CCDS33036.1 ENSP00000445247 A6NJB7 UPI000016101F 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR37346,Pfam_domain:PF15455 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 42310677 42310677 C T 1 0 0 0 0 0 0 0 1 12727 900 32 3 3 PRR19 19 42310677 Silent SNP C C3N-02089_T 230418 42310677 16306939 929 28013 MEGF8 0 . GRCh38 19 42375986 42375986 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.7749G>T p.= p.P2583P ENST00000251268 42/42 110 92 18 91 91 0 strelka-varscan-mutect MEGF8,synonymous_variant,p.=,ENST00000378073,;MEGF8,synonymous_variant,p.=,ENST00000334370,NM_001410.2;MEGF8,synonymous_variant,p.=,ENST00000251268,NM_001271938.1;MEGF8,3_prime_UTR_variant,,ENST00000593647,;MEGF8,intron_variant,,ENST00000598762,;MEGF8,downstream_gene_variant,,ENST00000599787,; T ENST00000251268 Transcript synonymous_variant 7749/9549 7749/8538 2583/2845 P ccG/ccT 1 1 MEGF8 HGNC HGNC:3233 protein_coding YES CCDS62693.1 ENSP00000251268 Q7Z7M0 UPI00005788D1 NM_001271938.1 42/42 hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF287 LOW 1 SNV 5 1 PASS rs971026507 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 90 42375986 42375986 G T 1 0 0 0 0 0 0 0 1 9403 1132 40 1 1 MEGF8 19 42375986 Silent SNP G C3N-02089_T 65309 42375986 16241630 930 28014 PSG2 0 . GRCh38 19 43075438 43075438 + Missense_Mutation SNP T T G rs769965176 C3N-02089_T C3N-02089_N T T c.625A>C p.Lys209Gln p.K209Q ENST00000406487 3/6 280 234 46 246 245 1 strelka-varscan-mutect PSG2,missense_variant,p.Lys209Gln,ENST00000406487,NM_031246.3;PSG2,upstream_gene_variant,,ENST00000329509,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG2,intron_variant,,ENST00000593482,; G ENST00000406487 Transcript missense_variant 724/1538 625/1008 209/335 K/Q Aag/Cag rs769965176 1 -1 PSG2 HGNC HGNC:9519 protein_coding YES CCDS12616.1 ENSP00000385706 P11465 A0A024R0M4 UPI000013CCF5 NM_031246.3 deleterious(0) 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF615,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs769965176 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 43075438 43075438 T G 1 0 0 0 0 1 0 0 0 12806 1850 64 5 5 PSG2 19 43075438 Missense_Mutation SNP T C3N-02089_T 699452 43075438 15542178 931 28015 ZNF233 0 . GRCh38 19 44273173 44273173 + Missense_Mutation SNP T T A C3N-02089_T C3N-02089_N T T c.513T>A p.Asn171Lys p.N171K ENST00000391958 5/5 284 226 58 293 292 1 strelka-varscan-mutect ZNF233,missense_variant,p.Asn171Lys,ENST00000391958,NM_001207005.1,NM_181756.2;ZNF233,3_prime_UTR_variant,,ENST00000592581,;ZNF235,intron_variant,,ENST00000589799,;ZNF233,downstream_gene_variant,,ENST00000589522,;ZNF233,downstream_gene_variant,,ENST00000590668,;ZNF235,downstream_gene_variant,,ENST00000589248,;ZNF235,intron_variant,,ENST00000592844,; A ENST00000391958 Transcript missense_variant 640/2784 513/2013 171/670 N/K aaT/aaA COSM3535491 1 1 ZNF233 HGNC HGNC:30946 protein_coding YES CCDS33047.1 ENSP00000375820 A6NK53 UPI000049DEBE NM_001207005.1,NM_181756.2 deleterious(0.04) 5/5 1 MODERATE 1 SNV 2 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 44273173 44273173 T A 1 0 0 0 0 1 0 0 0 18363 1432 50 4 4 ZNF233 19 44273173 Missense_Mutation SNP T C3N-02089_T 1197735 44273173 14344443 932 28016 CLPTM1 0 . GRCh38 19 44987283 44987283 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.898A>T p.Ser300Cys p.S300C ENST00000337392 8/14 338 310 28 255 255 0 strelka-varscan-mutect CLPTM1,missense_variant,p.Ser286Cys,ENST00000541297,NM_001282175.1;CLPTM1,missense_variant,p.Ser300Cys,ENST00000337392,NM_001294.3;CLPTM1,missense_variant,p.Ser198Cys,ENST00000546079,NM_001282176.1;CLPTM1,upstream_gene_variant,,ENST00000586915,;CLPTM1,downstream_gene_variant,,ENST00000591304,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000589158,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000588855,;CLPTM1,non_coding_transcript_exon_variant,,ENST00000588274,;CLPTM1,downstream_gene_variant,,ENST00000587537,;CLPTM1,upstream_gene_variant,,ENST00000586975,;CLPTM1,upstream_gene_variant,,ENST00000589347,; T ENST00000337392 Transcript missense_variant 1048/2604 898/2010 300/669 S/C Agc/Tgc 1 1 CLPTM1 HGNC HGNC:2087 protein_coding YES CCDS12651.1 ENSP00000336994 O96005 A0A0S2Z3H2 UPI0000072CBA NM_001294.3 deleterious(0.04) 8/14 Pfam_domain:PF05602,hmmpanther:PTHR21347,hmmpanther:PTHR21347:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 44987283 44987283 A T 1 0 0 0 0 1 0 0 0 3326 188 7 4 4 CLPTM1 19 44987283 Missense_Mutation SNP A C3N-02089_T 714110 44987283 13630333 933 28017 SYMPK 0 . GRCh38 19 45816885 45816885 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.3171G>T p.= p.P1057P ENST00000245934 24/27 164 137 27 117 116 1 strelka-varscan-mutect SYMPK,synonymous_variant,p.=,ENST00000245934,NM_004819.2;SYMPK,downstream_gene_variant,,ENST00000599814,;SYMPK,downstream_gene_variant,,ENST00000599460,;RSPH6A,upstream_gene_variant,,ENST00000221538,NM_030785.3;RSPH6A,upstream_gene_variant,,ENST00000597055,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598155,;SYMPK,synonymous_variant,p.=,ENST00000596824,;SYMPK,3_prime_UTR_variant,,ENST00000600237,;SYMPK,non_coding_transcript_exon_variant,,ENST00000593504,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598329,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598364,; A ENST00000245934 Transcript synonymous_variant 3416/4195 3171/3825 1057/1274 P ccG/ccT 1 -1 SYMPK HGNC HGNC:22935 protein_coding YES CCDS12676.2 ENSP00000245934 Q92797 A0A024R0R6 UPI00002026C0 NM_004819.2 24/27 hmmpanther:PTHR15245:SF20,hmmpanther:PTHR15245,Pfam_domain:PF12295 LOW 1 SNV 1 1 PASS rs1285088024 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 45816885 45816885 C A 1 0 0 0 0 0 0 0 1 15829 755 27 1 1 SYMPK 19 45816885 Silent SNP C C3N-02089_T 829602 45816885 12800731 934 28018 SLC8A2 0 . GRCh38 19 47447854 47447854 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1718A>T p.Tyr573Phe p.Y573F ENST00000236877 4/10 240 195 45 196 196 0 strelka-varscan-mutect SLC8A2,missense_variant,p.Tyr573Phe,ENST00000236877,NM_015063.2;SLC8A2,missense_variant,p.Tyr329Phe,ENST00000542837,;SLC8A2,non_coding_transcript_exon_variant,,ENST00000539381,;SLC8A2,upstream_gene_variant,,ENST00000601757,; A ENST00000236877 Transcript missense_variant 2114/5234 1718/2766 573/921 Y/F tAc/tTc 1 -1 SLC8A2 HGNC HGNC:11069 protein_coding YES CCDS33065.1 ENSP00000236877 Q9UPR5 UPI000012FC49 NM_015063.2 tolerated(0.52) 4/10 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF8,Pfam_domain:PF03160,TIGRFAM_domain:TIGR00845,SMART_domains:SM00237,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 47447854 47447854 T A 1 0 0 0 0 1 0 0 0 14990 1638 57 4 4 SLC8A2 19 47447854 Missense_Mutation SNP T C3N-02089_T 1630969 47447854 11169762 935 28019 ZNF541 0 . GRCh38 19 47521959 47521959 + Nonsense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.3606T>G p.Tyr1202Ter p.Y1202* ENST00000391901 13/15 251 218 33 194 194 0 strelka-varscan-mutect ZNF541,stop_gained,p.Tyr1221Ter,ENST00000314121,;ZNF541,stop_gained,p.Tyr1202Ter,ENST00000391901,NM_001277075.1;ZNF541,stop_gained,p.Tyr722Ter,ENST00000595558,;ZNF541,stop_gained,p.Tyr535Ter,ENST00000263351,; C ENST00000391901 Transcript stop_gained 3606/4580 3606/4041 1202/1346 Y/* taT/taG 1 -1 ZNF541 HGNC HGNC:25294 protein_coding YES CCDS46133.2 ENSP00000375770 Q9H0D2 UPI0000E5A21D NM_001277075.1 13/15 PROSITE_profiles:PS51293,hmmpanther:PTHR16089,hmmpanther:PTHR16089:SF23,SMART_domains:SM00717,Superfamily_domains:SSF46689 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 4 2 90 47521959 47521959 A C 1 0 0 0 0 0 1 0 0 18549 108 4 5 5 ZNF541 19 47521959 Nonsense_Mutation SNP A C3N-02089_T 74105 47521959 11095657 936 28020 LIG1 0 . GRCh38 19 48137072 48137072 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.1267A>T p.Lys423Ter p.K423* ENST00000263274 14/28 284 253 31 271 271 0 strelka-mutect LIG1,stop_gained,p.Lys423Ter,ENST00000613670,;LIG1,stop_gained,p.Lys423Ter,ENST00000263274,NM_001320970.1,NM_000234.2;LIG1,stop_gained,p.Lys355Ter,ENST00000536218,NM_001289064.1;LIG1,stop_gained,p.Lys392Ter,ENST00000427526,NM_001320971.1,NM_001289063.1;LIG1,stop_gained,p.Lys422Ter,ENST00000594759,;LIG1,stop_gained,p.Lys423Ter,ENST00000601091,;LIG1,missense_variant,p.Arg414Ser,ENST00000542460,;LIG1,non_coding_transcript_exon_variant,,ENST00000594067,;LIG1,non_coding_transcript_exon_variant,,ENST00000597901,;LIG1,upstream_gene_variant,,ENST00000596457,;LIG1,upstream_gene_variant,,ENST00000596672,; A ENST00000263274 Transcript stop_gained 1687/3384 1267/2760 423/919 K/* Aag/Tag 1 -1 LIG1 HGNC HGNC:6598 protein_coding YES CCDS12711.1 ENSP00000263274 P18858 UPI0000129656 NM_001320970.1,NM_000234.2 14/28 hmmpanther:PTHR10459,Pfam_domain:PF04675,TIGRFAM_domain:TIGR00574,Gene3D:1x9nA01,Superfamily_domains:0050884 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 48137072 48137072 T A 1 0 0 0 0 0 1 0 0 8690 1792 62 4 4 LIG1 19 48137072 Nonsense_Mutation SNP T C3N-02089_T 615113 48137072 10480544 937 28021 PPP1R15A 0 . GRCh38 19 48874287 48874287 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1054G>T p.Glu352Ter p.E352* ENST00000200453 2/3 195 159 36 176 176 0 strelka-varscan-mutect PPP1R15A,stop_gained,p.Glu352Ter,ENST00000200453,NM_014330.3;PPP1R15A,upstream_gene_variant,,ENST00000600406,; T ENST00000200453 Transcript stop_gained 1323/2378 1054/2025 352/674 E/* Gaa/Taa 1 1 PPP1R15A HGNC HGNC:14375 protein_coding YES CCDS12738.1 ENSP00000200453 O75807 UPI000006F652 NM_014330.3 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR16489,hmmpanther:PTHR16489:SF14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 48874287 48874287 G T 1 0 0 0 0 0 1 0 0 12473 1175 41 2 2 PPP1R15A 19 48874287 Nonsense_Mutation SNP G C3N-02089_T 737215 48874287 9743329 938 28022 GYS1 0 . GRCh38 19 48982783 48982783 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.878T>C p.Phe293Ser p.F293S ENST00000323798 6/16 436 408 28 365 364 1 strelka-varscan-mutect GYS1,missense_variant,p.Phe293Ser,ENST00000323798,NM_002103.4;GYS1,missense_variant,p.Phe229Ser,ENST00000263276,NM_001161587.1;GYS1,downstream_gene_variant,,ENST00000457974,;GYS1,non_coding_transcript_exon_variant,,ENST00000484289,;GYS1,upstream_gene_variant,,ENST00000472004,;GYS1,upstream_gene_variant,,ENST00000496048,; G ENST00000323798 Transcript missense_variant 1075/3574 878/2214 293/737 F/S tTc/tCc 1 -1 GYS1 HGNC HGNC:4706 protein_coding YES CCDS12747.1 ENSP00000317904 P13807 UPI0000000C44 NM_002103.4 deleterious(0) 6/16 Pfam_domain:PF05693,hmmpanther:PTHR10176,hmmpanther:PTHR10176:SF2,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 48982783 48982783 A G 1 0 0 0 0 1 0 0 0 6794 246 9 5 5 GYS1 19 48982783 Missense_Mutation SNP A C3N-02089_T 108496 48982783 9634833 939 28023 PRR12 0 . GRCh38 19 49595242 49595242 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.907C>A p.Pro303Thr p.P303T ENST00000418929 4/14 274 253 21 233 233 0 strelka-varscan-mutect PRR12,missense_variant,p.Pro303Thr,ENST00000418929,NM_020719.1;PRR12,upstream_gene_variant,,ENST00000615927,;PRRG2,downstream_gene_variant,,ENST00000246794,NM_000951.2;NOSIP,upstream_gene_variant,,ENST00000599537,;PRRG2,downstream_gene_variant,,ENST00000596700,;PRRG2,downstream_gene_variant,,ENST00000543867,;PRRG2,downstream_gene_variant,,ENST00000597121,NM_001316335.1; A ENST00000418929 Transcript missense_variant 919/6955 907/6111 303/2036 P/T Ccc/Acc 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 tolerated(0.32) 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 49595242 49595242 C A 1 0 0 0 0 1 0 0 0 12719 507 18 2 2 PRR12 19 49595242 Missense_Mutation SNP C C3N-02089_T 612459 49595242 9022374 940 28024 PRR12 0 . GRCh38 19 49595384 49595384 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1049G>T p.Gly350Val p.G350V ENST00000418929 4/14 113 92 21 113 113 0 strelka-varscan-mutect PRR12,missense_variant,p.Gly350Val,ENST00000418929,NM_020719.1;PRR12,upstream_gene_variant,,ENST00000615927,;PRRG2,downstream_gene_variant,,ENST00000246794,NM_000951.2;PRRG2,downstream_gene_variant,,ENST00000596700,;PRRG2,downstream_gene_variant,,ENST00000543867,;PRRG2,downstream_gene_variant,,ENST00000597121,NM_001316335.1; T ENST00000418929 Transcript missense_variant 1061/6955 1049/6111 350/2036 G/V gGt/gTt 1 1 PRR12 HGNC HGNC:29217 protein_coding YES CCDS46143.1 ENSP00000394510 Q9ULL5 UPI0001596889 NM_020719.1 deleterious(0.01) 4/14 hmmpanther:PTHR14709,hmmpanther:PTHR14709:SF1,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 49595384 49595384 G T 1 0 0 0 0 1 0 0 0 12719 1261 44 2 2 PRR12 19 49595384 Missense_Mutation SNP G C3N-02089_T 142 49595384 9022232 941 28025 SYT3 0 . GRCh38 19 50630166 50630166 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.680C>A p.Pro227Gln p.P227Q ENST00000338916 3/9 31 27 4 30 30 0 strelka-varscan-mutect SYT3,missense_variant,p.Pro227Gln,ENST00000338916,NM_032298.2;SYT3,missense_variant,p.Pro227Gln,ENST00000593901,NM_001160328.1;SYT3,missense_variant,p.Pro227Gln,ENST00000600079,NM_001160329.1;SYT3,downstream_gene_variant,,ENST00000598997,;SYT3,upstream_gene_variant,,ENST00000595117,;SYT3,upstream_gene_variant,,ENST00000595557,; T ENST00000338916 Transcript missense_variant 1314/2915 680/1773 227/590 P/Q cCa/cAa 1 -1 SYT3 HGNC HGNC:11511 protein_coding YES CCDS12798.1 ENSP00000340914 Q9BQG1 A0A024R4I9 UPI0000047AEB NM_032298.2 tolerated(0.1) 3/9 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF176 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -11.72695 1 1 1 1 0 T 3 4 90 50630166 50630166 G T 1 0 0 0 0 1 0 0 0 15869 1362 47 2 2 SYT3 19 50630166 Missense_Mutation SNP G C3N-02089_T 1034782 50630166 7987450 942 28026 CTU1 0 . GRCh38 19 51104094 51104094 + Missense_Mutation SNP G G A C3N-02089_T C3N-02089_N G G c.476C>T p.Ala159Val p.A159V ENST00000421832 2/3 69 58 11 65 65 0 strelka-varscan-mutect CTU1,missense_variant,p.Ala159Val,ENST00000421832,NM_145232.3; A ENST00000421832 Transcript missense_variant 521/2087 476/1047 159/348 A/V gCg/gTg COSM2755761 1 -1 CTU1 HGNC HGNC:29590 protein_coding YES CCDS12824.1 ENSP00000390011 Q7Z7A3 UPI000013D897 NM_145232.3 deleterious(0) 2/3 Low_complexity_(Seg):seg,HAMAP:MF_03053,hmmpanther:PTHR11807,hmmpanther:PTHR11807:SF12,PIRSF_domain:PIRSF004976,Pfam_domain:PF01171,Gene3D:3.40.50.620,Superfamily_domains:SSF52402 1 MODERATE 1 SNV 2 1 1 PASS rs1169810550 . 0 204 6 0 0 0 0 0 -19.99999 0.9999999 1 1 1 0 A 3 1 90 51104094 51104094 G A 1 0 0 0 0 1 0 0 0 3856 1087 38 1 1 CTU1 19 51104094 Missense_Mutation SNP G C3N-02089_T 473928 51104094 7513522 943 28027 VSIG10L 0 . GRCh38 19 51341458 51341458 + Frame_Shift_Del DEL C C - novel C3N-02089_T C3N-02089_N C C c.590delG p.Gly197AlafsTer15 p.G197Afs*15 ENST00000335624 2/10 51 40 11 64 64 0 sindel-varindel-pindel VSIG10L,frameshift_variant,p.Gly197AlafsTer15,ENST00000335624,NM_001163922.1;ETFB,downstream_gene_variant,,ENST00000354232,NM_001014763.1;ETFB,downstream_gene_variant,,ENST00000309244,NM_001985.2;ETFB,downstream_gene_variant,,ENST00000596253,;CTD-2616J11.16,intron_variant,,ENST00000601148,;CTD-2616J11.16,intron_variant,,ENST00000594311,;CTD-2616J11.9,upstream_gene_variant,,ENST00000600974,;ETFB,downstream_gene_variant,,ENST00000594361,;VSIG10L,upstream_gene_variant,,ENST00000600663,; - ENST00000335624 Transcript frameshift_variant 590/3397 590/2604 197/867 G/X gGc/gc 1 -1 VSIG10L HGNC HGNC:27111 protein_coding YES CCDS54300.1 ENSP00000335623 Q86VR7 UPI00001D8188 NM_001163922.1 2/10 Gene3D:2.60.40.10,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF694,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH deletion 5 1 PASS . . 0 176 30 4 0 0 0 0 -19.92555 0.9134654 0 1 1 0 - 7 5 90 51341458 51341458 C - 1 0 1 0 1 0 0 0 0 17774 739 26 0 0 VSIG10L 19 51341458 Frame_Shift_Del DEL C C3N-02089_T 237364 51341458 7276158 944 28028 VSIG10L 0 . GRCh38 19 51341910 51341910 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.138G>T p.Gln46His p.Q46H ENST00000335624 2/10 220 173 47 222 222 0 strelka-varscan-mutect VSIG10L,missense_variant,p.Gln46His,ENST00000335624,NM_001163922.1;ETFB,downstream_gene_variant,,ENST00000354232,NM_001014763.1;ETFB,downstream_gene_variant,,ENST00000309244,NM_001985.2;ETFB,downstream_gene_variant,,ENST00000596253,;CTD-2616J11.16,non_coding_transcript_exon_variant,,ENST00000601148,;CTD-2616J11.16,non_coding_transcript_exon_variant,,ENST00000594311,;CTD-2616J11.9,upstream_gene_variant,,ENST00000600974,;ETFB,downstream_gene_variant,,ENST00000594361,;VSIG10L,upstream_gene_variant,,ENST00000600663,; A ENST00000335624 Transcript missense_variant 138/3397 138/2604 46/867 Q/H caG/caT 1 -1 VSIG10L HGNC HGNC:27111 protein_coding YES CCDS54300.1 ENSP00000335623 Q86VR7 UPI00001D8188 NM_001163922.1 deleterious_low_confidence(0.02) 2/10 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 51341910 51341910 C A 1 0 0 0 0 1 0 0 0 17774 680 24 2 2 VSIG10L 19 51341910 Missense_Mutation SNP C C3N-02089_T 452 51341910 7275706 945 28029 SIGLEC8 0 . GRCh38 19 51454689 51454689 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1143C>A p.Phe381Leu p.F381L ENST00000321424 5/7 160 134 26 136 136 0 strelka-varscan-mutect SIGLEC8,missense_variant,p.Phe381Leu,ENST00000321424,NM_014442.2;SIGLEC8,missense_variant,p.Phe272Leu,ENST00000430817,;SIGLEC8,missense_variant,p.Phe288Leu,ENST00000340550,;SIGLEC8,downstream_gene_variant,,ENST00000597352,; T ENST00000321424 Transcript missense_variant 1210/2949 1143/1500 381/499 F/L ttC/ttA 1 -1 SIGLEC8 HGNC HGNC:10877 protein_coding YES CCDS33086.1 ENSP00000321077 Q9NYZ4 UPI000013598B NM_014442.2 tolerated(0.45) 5/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF36 MODERATE 1 SNV 1 1 PASS rs1416773650 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 51454689 51454689 G T 1 0 0 0 0 1 0 0 0 14578 1304 45 2 2 SIGLEC8 19 51454689 Missense_Mutation SNP G C3N-02089_T 112779 51454689 7162927 946 28030 SIGLEC6 0 . GRCh38 19 51530785 51530785 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.602C>T p.Thr201Ile p.T201I ENST00000425629 3/8 277 211 66 218 218 0 strelka-varscan-mutect SIGLEC6,missense_variant,p.Thr201Ile,ENST00000346477,NM_198845.4;SIGLEC6,missense_variant,p.Thr201Ile,ENST00000425629,NM_001245.5;SIGLEC6,missense_variant,p.Thr201Ile,ENST00000359982,NM_001177548.1;SIGLEC6,missense_variant,p.Thr201Ile,ENST00000343300,NM_198846.4;SIGLEC6,missense_variant,p.Thr165Ile,ENST00000436458,NM_001177547.1;SIGLEC6,missense_variant,p.Thr190Ile,ENST00000391797,NM_001177549.1;SIGLEC6,upstream_gene_variant,,ENST00000474054,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000496422,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000489837,; A ENST00000425629 Transcript missense_variant 757/1852 602/1362 201/453 T/I aCa/aTa 1 -1 SIGLEC6 HGNC HGNC:10875 protein_coding YES CCDS12834.3 ENSP00000401502 O43699 A0A024R4K4 UPI0000223FFD NM_001245.5 deleterious(0.02) 3/8 Gene3D:2.60.40.10,Pfam_domain:PF00047,PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF52,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 51530785 51530785 G A 1 0 0 0 0 1 0 0 0 14576 1377 48 3 3 SIGLEC6 19 51530785 Missense_Mutation SNP G C3N-02089_T 76096 51530785 7086831 947 28031 ZNF841 0 . GRCh38 19 52066525 52066525 + Nonsense_Mutation SNP C C A rs752275004 C3N-02089_T C3N-02089_N C C c.1357G>T p.Gly453Ter p.G453* ENST00000594295 6/6 171 136 35 206 205 1 strelka-varscan-mutect ZNF841,stop_gained,p.Gly453Ter,ENST00000594295,NM_001136499.1;ZNF841,stop_gained,p.Gly337Ter,ENST00000426391,NM_001321349.1;ZNF841,stop_gained,p.Gly453Ter,ENST00000389534,;ZNF841,stop_gained,p.Gly349Ter,ENST00000601738,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,; A ENST00000594295 Transcript stop_gained 1760/3819 1357/2775 453/924 G/* Gga/Tga rs752275004 1 -1 ZNF841 HGNC HGNC:27611 protein_coding YES CCDS46161.1 ENSP00000470746 Q6ZN19 UPI00001D818B NM_001136499.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF75,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 HIGH SNV 3 1 PASS rs752275004 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 52066525 52066525 C A 1 0 0 0 0 0 1 0 0 18776 603 21 2 2 ZNF841 19 52066525 Nonsense_Mutation SNP C C3N-02089_T 535740 52066525 6551091 948 28032 ZNF841 0 . GRCh38 19 52066676 52066676 + Frame_Shift_Del DEL T T - novel C3N-02089_T C3N-02089_N T T c.1206delA p.Lys402AsnfsTer20 p.K402Nfs*20 ENST00000594295 6/6 169 134 35 215 215 0 sindel-varindel ZNF841,frameshift_variant,p.Lys402AsnfsTer20,ENST00000594295,NM_001136499.1;ZNF841,frameshift_variant,p.Lys286AsnfsTer20,ENST00000426391,NM_001321349.1;ZNF841,frameshift_variant,p.Lys402AsnfsTer20,ENST00000389534,;ZNF841,frameshift_variant,p.Lys298AsnfsTer20,ENST00000601738,;ZNF432,upstream_gene_variant,,ENST00000600368,;CTC-471J1.2,upstream_gene_variant,,ENST00000569091,;ZNF432,intron_variant,,ENST00000598446,;ZNF841,downstream_gene_variant,,ENST00000595599,; - ENST00000594295 Transcript frameshift_variant 1609/3819 1206/2775 402/924 K/X aaA/aa 1 -1 ZNF841 HGNC HGNC:27611 protein_coding YES CCDS46161.1 ENSP00000470746 Q6ZN19 UPI00001D818B NM_001136499.1 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF75,hmmpanther:PTHR24377,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH deletion 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 52066676 52066676 T - 1 0 1 0 1 0 0 0 0 18776 1490 52 0 0 ZNF841 19 52066676 Frame_Shift_Del DEL T C3N-02089_T 151 52066676 6550940 949 28033 ZNF528 0 . GRCh38 19 52405975 52405975 + Silent SNP G G T rs373691668 C3N-02089_T C3N-02089_N G G c.84G>T p.= p.A28A ENST00000360465 5/7 223 162 61 229 229 0 strelka-varscan-mutect ZNF528,synonymous_variant,p.=,ENST00000391788,;ZNF528,synonymous_variant,p.=,ENST00000360465,NM_032423.2;ZNF528,synonymous_variant,p.=,ENST00000598192,;ZNF528,synonymous_variant,p.=,ENST00000391787,;ZNF528,synonymous_variant,p.=,ENST00000594530,;ZNF528,downstream_gene_variant,,ENST00000493272,;ZNF528,downstream_gene_variant,,ENST00000494167,;ZNF528,upstream_gene_variant,,ENST00000448954,;ZNF528,downstream_gene_variant,,ENST00000436397,;ZNF528,downstream_gene_variant,,ENST00000531472,; T ENST00000360465 Transcript synonymous_variant 510/3978 84/1887 28/628 A gcG/gcT rs373691668 1 1 ZNF528 HGNC HGNC:29384 protein_coding YES CCDS33091.1 ENSP00000353652 Q3MIS6 UPI00001B6535 NM_032423.2 5/7 PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF143,hmmpanther:PTHR24377,Pfam_domain:PF01352,SMART_domains:SM00349,Superfamily_domains:0044637 LOW 1 SNV 1 1 PASS rs373691668 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 52405975 52405975 G T 1 0 0 0 0 0 0 0 1 18542 1074 38 1 1 ZNF528 19 52405975 Silent SNP G C3N-02089_T 339299 52405975 6211641 950 28034 VN1R4 0 . GRCh38 19 53267317 53267317 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.349G>T p.Ala117Ser p.A117S ENST00000311170 1/1 173 145 28 152 152 0 strelka-varscan-mutect VN1R4,missense_variant,p.Ala117Ser,ENST00000311170,NM_173857.2;CTD-2245F17.9,downstream_gene_variant,,ENST00000599803,; A ENST00000311170 Transcript missense_variant 407/1048 349/906 117/301 A/S Gca/Tca 1 -1 VN1R4 HGNC HGNC:19871 protein_coding YES CCDS33099.1 ENSP00000310856 Q7Z5H5 UPI000004B23A NM_173857.2 tolerated(0.05) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF03402,Prints_domain:PR01534,PROSITE_profiles:PS50262,hmmpanther:PTHR24062,hmmpanther:PTHR24062:SF80,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS . . 0 200 0 0 8 0 0 0 -14.47522 0.281059 1 1 0 0 A 3 1 90 53267317 53267317 C A 1 0 0 0 0 1 0 0 0 17728 739 26 2 2 VN1R4 19 53267317 Missense_Mutation SNP C C3N-02089_T 861342 53267317 5350299 951 28035 NLRP12 0 . GRCh38 19 53810479 53810479 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1180A>C p.Asn394His p.N394H ENST00000391773 3/10 790 640 150 701 701 0 strelka-varscan-mutect NLRP12,missense_variant,p.Asn394His,ENST00000324134,NM_144687.3;NLRP12,missense_variant,p.Asn394His,ENST00000391773,NM_001277126.1;NLRP12,missense_variant,p.Asn394His,ENST00000345770,;NLRP12,missense_variant,p.Asn394His,ENST00000391775,NM_001277129.1;NLRP12,missense_variant,p.Asn394His,ENST00000391772,;NLRP12,upstream_gene_variant,,ENST00000492915,; G ENST00000391773 Transcript missense_variant 1400/3715 1180/3189 394/1062 N/H Aac/Cac 1 -1 NLRP12 HGNC HGNC:22938 protein_coding YES CCDS62785.1 ENSP00000375653 P59046 UPI0000132BB3 NM_001277126.1 deleterious(0.01) 3/10 PROSITE_profiles:PS50837,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 53810479 53810479 T G 1 0 0 0 0 1 0 0 0 10511 1812 63 5 5 NLRP12 19 53810479 Missense_Mutation SNP T C3N-02089_T 543162 53810479 4807137 952 28036 LILRA6 0 . GRCh38 19 54240861 54240861 + Missense_Mutation SNP G G T rs199988938 C3N-02089_T C3N-02089_N G G c.925C>A p.Pro309Thr p.P309T ENST00000396365 5/8 472 417 55 379 379 0 strelka-varscan-mutect LILRA6,missense_variant,p.Pro309Thr,ENST00000396365,NM_024318.3;LILRA6,missense_variant,p.Pro309Thr,ENST00000245621,;LILRA6,3_prime_UTR_variant,,ENST00000430421,;RPS9,intron_variant,,ENST00000448962,;LILRA6,downstream_gene_variant,,ENST00000270464,; T ENST00000396365 Transcript missense_variant 965/1890 925/1446 309/481 P/T Ccc/Acc rs199988938 1 -1 LILRA6 HGNC HGNC:15495 protein_coding YES CCDS42610.1 ENSP00000379651 Q6PI73 U5XH19 UPI000292EF7A NM_024318.3 deleterious(0) 5/8 Gene3D:2.60.40.10,PIRSF_domain:PIRSF001979,PROSITE_profiles:PS50835,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF116,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs199988938 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 54240861 54240861 G T 1 0 0 0 0 1 0 0 0 8697 1232 43 2 2 LILRA6 19 54240861 Missense_Mutation SNP G C3N-02089_T 430382 54240861 4376755 953 28037 LILRB2 0 . GRCh38 19 54279619 54279619 + Silent SNP G G T rs762601346 C3N-02089_T C3N-02089_N G G c.384C>A p.= p.A128A ENST00000391749 5/14 160 124 36 161 161 0 varscan-mutect LILRB2,synonymous_variant,p.=,ENST00000391748,NM_001278403.2;LILRB2,synonymous_variant,p.=,ENST00000434421,NM_001278404.2;LILRB2,synonymous_variant,p.=,ENST00000314446,NM_001080978.3;LILRB2,synonymous_variant,p.=,ENST00000391749,NM_005874.4;LILRB2,synonymous_variant,p.=,ENST00000391746,NM_001278405.2;MIR4752,upstream_gene_variant,,ENST00000579672,;LILRB2,downstream_gene_variant,,ENST00000471216,;LILRB2,non_coding_transcript_exon_variant,,ENST00000493242,;LILRB2,upstream_gene_variant,,ENST00000455108,; T ENST00000391749 Transcript synonymous_variant 656/2286 384/1797 128/598 A gcC/gcA rs762601346 1 -1 LILRB2 HGNC HGNC:6606 protein_coding YES CCDS12886.1 ENSP00000375629 Q8N423 UPI00034F23A2 NM_005874.4 5/14 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS rs762601346 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 54279619 54279619 G T 1 0 0 0 0 0 0 0 1 8699 1219 43 2 2 LILRB2 19 54279619 Silent SNP G C3N-02089_T 38758 54279619 4337997 954 28038 KIR2DL1 0 . GRCh38 19 54775254 54775254 + Missense_Mutation SNP T T C rs754789231 C3N-02089_T C3N-02089_N T T c.460T>C p.Ser154Pro p.S154P ENST00000336077 4/8 175 163 12 160 160 0 varscan-mutect KIR2DL1,missense_variant,p.Ser154Pro,ENST00000336077,NM_014218.2;KIR2DL1,missense_variant,p.Ser154Pro,ENST00000291633,;CTB-61M7.1,intron_variant,,ENST00000400864,; C ENST00000336077 Transcript missense_variant 500/1596 460/1047 154/348 S/P Tcc/Ccc rs754789231 1 1 KIR2DL1 HGNC HGNC:6329 protein_coding YES CCDS12904.1 ENSP00000336769 Q6H2H3 UPI00001195F7 NM_014218.2 deleterious(0.03) 4/8 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF119,Gene3D:2.60.40.10,Pfam_domain:PF00047,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs754789231 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 54775254 54775254 T C 1 0 0 0 0 1 0 0 0 8181 1551 54 5 5 KIR2DL1 19 54775254 Missense_Mutation SNP T C3N-02089_T 495635 54775254 3842362 955 28039 KIR3DL2 0 . GRCh38 19 54855715 54855715 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.752A>T p.Asp251Val p.D251V ENST00000326321 5/9 306 250 56 247 247 0 strelka-varscan-mutect KIR3DL2,missense_variant,p.Asp251Val,ENST00000326321,NM_006737.3;KIR3DL2,missense_variant,p.Asp251Val,ENST00000270442,NM_001242867.1;KIR3DL1,intron_variant,,ENST00000402254,; T ENST00000326321 Transcript missense_variant 785/1877 752/1368 251/455 D/V gAc/gTc 1 1 KIR3DL2 HGNC HGNC:6339 protein_coding YES CCDS12906.1 ENSP00000325525 P43630 A0A0U1WNF3 UPI000012DB25 NM_006737.3 deleterious(0.01) 5/9 Gene3D:2.60.40.10,Pfam_domain:PF00047,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF121,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 54855715 54855715 A T 1 0 0 0 0 1 0 0 0 8185 275 10 4 4 KIR3DL2 19 54855715 Missense_Mutation SNP A C3N-02089_T 80461 54855715 3761901 956 28040 NLRP2 0 . GRCh38 19 55000881 55000881 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.3172C>T p.His1058Tyr p.H1058Y ENST00000543010 13/13 349 291 58 309 309 0 strelka-varscan-mutect NLRP2,missense_variant,p.His1058Tyr,ENST00000543010,NM_001174081.1;NLRP2,missense_variant,p.His1058Tyr,ENST00000448584,NM_017852.3;NLRP2,missense_variant,p.His1036Tyr,ENST00000537859,NM_001174082.1;NLRP2,missense_variant,p.His1055Tyr,ENST00000263437,;NLRP2,missense_variant,p.His1036Tyr,ENST00000339757,;NLRP2,missense_variant,p.His1034Tyr,ENST00000391721,;NLRP2,missense_variant,p.His1035Tyr,ENST00000427260,NM_001174083.1;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,non_coding_transcript_exon_variant,,ENST00000542755,; T ENST00000543010 Transcript missense_variant 3315/3576 3172/3189 1058/1062 H/Y Cat/Tat 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 tolerated(1) 13/13 hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106 MODERATE 1 SNV 1 1 PASS rs1220301290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 55000881 55000881 C T 1 0 0 0 0 1 0 0 0 10514 826 29 3 3 NLRP2 19 55000881 Missense_Mutation SNP C C3N-02089_T 145166 55000881 3616735 957 28041 PPP1R12C 0 . GRCh38 19 55093232 55093232 + Missense_Mutation SNP C C A rs770610718 C3N-02089_T C3N-02089_N C C c.1685G>T p.Gly562Val p.G562V ENST00000263433 14/22 259 205 54 194 194 0 strelka-varscan-mutect PPP1R12C,missense_variant,p.Gly562Val,ENST00000263433,NM_017607.3,NM_001271618.1;PPP1R12C,missense_variant,p.Gly488Val,ENST00000435544,;PPP1R12C,missense_variant,p.Gly518Val,ENST00000592993,;PPP1R12C,missense_variant,p.Gly77Val,ENST00000591938,;PPP1R12C,splice_region_variant,,ENST00000592754,;PPP1R12C,splice_region_variant,,ENST00000588277,;PPP1R12C,upstream_gene_variant,,ENST00000590268,;PPP1R12C,downstream_gene_variant,,ENST00000586197,; A ENST00000263433 Transcript missense_variant,splice_region_variant 1701/2924 1685/2349 562/782 G/V gGt/gTt rs770610718 1 -1 PPP1R12C HGNC HGNC:14947 protein_coding YES CCDS12916.1 ENSP00000263433 Q9BZL4 UPI000006FEE1 NM_017607.3,NM_001271618.1 deleterious(0.02) 14/22 hmmpanther:PTHR24179,hmmpanther:PTHR24179:SF27 MODERATE 1 SNV 1 1 PASS rs770610718 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 55093232 55093232 C A 1 0 0 0 0 1 0 0 0 12466 521 18 2 2 PPP1R12C 19 55093232 Missense_Mutation SNP C C3N-02089_T 92351 55093232 3524384 958 28042 PTPRH 0 . GRCh38 19 55197213 55197213 + Missense_Mutation SNP C C A rs142458859 C3N-02089_T C3N-02089_N C C c.1894G>T p.Val632Leu p.V632L ENST00000376350 9/20 479 446 33 379 379 0 strelka-varscan-mutect PTPRH,missense_variant,p.Val632Leu,ENST00000376350,NM_002842.4;PTPRH,missense_variant,p.Val454Leu,ENST00000263434,NM_001161440.2;PTPRH,non_coding_transcript_exon_variant,,ENST00000588559,; A ENST00000376350 Transcript missense_variant 1917/3877 1894/3348 632/1115 V/L Gtg/Ttg rs142458859 1 -1 PTPRH HGNC HGNC:9672 protein_coding YES CCDS33110.1 ENSP00000365528 Q9HD43 UPI000052D443 NM_002842.4 tolerated(0.07) 9/20 PROSITE_profiles:PS50853,hmmpanther:PTHR19134:SF297,hmmpanther:PTHR19134,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS rs142458859 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 55197213 55197213 C A 1 0 0 0 0 1 0 0 0 12957 565 20 2 2 PTPRH 19 55197213 Missense_Mutation SNP C C3N-02089_T 103981 55197213 3420403 959 28043 TMEM150B 0 . GRCh38 19 55320591 55320591 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.95C>A p.Thr32Asn p.T32N ENST00000326652 4/8 205 171 34 189 187 2 strelka-varscan-mutect TMEM150B,missense_variant,p.Thr32Asn,ENST00000326652,NM_001085488.2,NM_001282011.1;TMEM150B,missense_variant,p.Thr32Asn,ENST00000591570,;TMEM150B,upstream_gene_variant,,ENST00000585918,;TMEM150B,missense_variant,p.Thr32Asn,ENST00000586609,;TMEM150B,missense_variant,p.Thr32Asn,ENST00000592603,;TMEM150B,missense_variant,p.Thr32Asn,ENST00000592731,;TMEM150B,non_coding_transcript_exon_variant,,ENST00000592891,; T ENST00000326652 Transcript missense_variant 278/943 95/702 32/233 T/N aCt/aAt 1 -1 TMEM150B HGNC HGNC:34415 protein_coding YES CCDS42629.1 ENSP00000320757 A6NC51 UPI00001AF4D4 NM_001085488.2,NM_001282011.1 deleterious(0.02) 4/8 Pfam_domain:PF10277,hmmpanther:PTHR21324,hmmpanther:PTHR21324:SF3 MODERATE 1 SNV 1 1 PASS . . 0 206 0 4 0 0 0 0 -20 0.9999329 1 1 1 0 T 3 4 90 55320591 55320591 G T 1 0 0 0 0 1 0 0 0 16510 1029 36 2 2 TMEM150B 19 55320591 Missense_Mutation SNP G C3N-02089_T 123378 55320591 3297025 960 28044 FAM71E2 0 . GRCh38 19 55358606 55358606 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2262G>T p.= p.V754V ENST00000424985 9/11 200 164 36 177 176 1 strelka-varscan-mutect FAM71E2,synonymous_variant,p.=,ENST00000424985,NM_001145402.1;COX6B2,upstream_gene_variant,,ENST00000593184,;COX6B2,upstream_gene_variant,,ENST00000588572,;COX6B2,upstream_gene_variant,,ENST00000326529,NM_144613.4;COX6B2,upstream_gene_variant,,ENST00000590900,;COX6B2,upstream_gene_variant,,ENST00000589467,;COX6B2,upstream_gene_variant,,ENST00000586191,;CTD-2105E13.6,synonymous_variant,p.=,ENST00000591954,;FAM71E2,3_prime_UTR_variant,,ENST00000585734,;COX6B2,upstream_gene_variant,,ENST00000587854,;COX6B2,upstream_gene_variant,,ENST00000587357,; A ENST00000424985 Transcript synonymous_variant 2456/3191 2262/2769 754/922 V gtG/gtT 1 -1 FAM71E2 HGNC HGNC:25278 protein_coding YES ENSP00000398617 Q8N5Q1 UPI0001949ABA NM_001145402.1 9/11 hmmpanther:PTHR22574:SF12,hmmpanther:PTHR22574 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 55358606 55358606 C A 1 0 0 0 0 0 0 0 1 5476 581 21 2 2 FAM71E2 19 55358606 Silent SNP C C3N-02089_T 38015 55358606 3259010 961 28045 SBK2 0 . GRCh38 19 55530047 55530047 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.733G>T p.Asp245Tyr p.D245Y ENST00000413299 4/4 49 37 12 28 28 0 strelka-varscan-mutect SBK2,missense_variant,p.Asp245Tyr,ENST00000413299,NM_001101401.2;SBK2,missense_variant,p.Asp245Tyr,ENST00000344158,; A ENST00000413299 Transcript missense_variant 771/1085 733/1047 245/348 D/Y Gac/Tac 1 -1 SBK2 HGNC HGNC:34416 protein_coding YES CCDS42631.1 ENSP00000389015 P0C263 UPI00015DFA43 NM_001101401.2 deleterious(0) 4/4 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF167,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 55530047 55530047 C A 1 0 0 0 0 1 0 0 0 14125 855 30 2 2 SBK2 19 55530047 Missense_Mutation SNP C C3N-02089_T 171441 55530047 3087569 962 28046 NLRP8 0 . GRCh38 19 55955240 55955240 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.1182G>T p.= p.R394R ENST00000291971 3/10 196 150 46 209 209 0 strelka-varscan-mutect NLRP8,synonymous_variant,p.=,ENST00000291971,NM_176811.2;NLRP8,synonymous_variant,p.=,ENST00000590542,; T ENST00000291971 Transcript synonymous_variant 1253/3934 1182/3147 394/1048 R cgG/cgT 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 3/10 hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF54 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 55955240 55955240 G T 1 0 0 0 0 0 0 0 1 10521 1219 43 2 2 NLRP8 19 55955240 Silent SNP G C3N-02089_T 425193 55955240 2662376 963 28047 NLRP5 0 . GRCh38 19 56027135 56027135 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.902T>A p.Leu301Gln p.L301Q ENST00000390649 7/15 212 160 52 188 187 1 strelka-varscan-mutect NLRP5,missense_variant,p.Leu301Gln,ENST00000390649,NM_153447.4;NLRP5,missense_variant,p.Leu301Gln,ENST00000621651,; A ENST00000390649 Transcript missense_variant 902/3888 902/3603 301/1200 L/Q cTg/cAg 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 deleterious(0.03) 7/15 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF12,hmmpanther:PTHR24106,Pfam_domain:PF05729,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 56027135 56027135 T A 1 0 0 0 0 1 0 0 0 10518 1580 55 4 4 NLRP5 19 56027135 Missense_Mutation SNP T C3N-02089_T 71895 56027135 2590481 964 28048 NLRP5 0 . GRCh38 19 56032710 56032710 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.2376C>A p.= p.I792I ENST00000390649 8/15 175 144 31 170 170 0 strelka-varscan-mutect NLRP5,synonymous_variant,p.=,ENST00000390649,NM_153447.4;NLRP5,synonymous_variant,p.=,ENST00000621651,; A ENST00000390649 Transcript synonymous_variant 2376/3888 2376/3603 792/1200 I atC/atA 1 1 NLRP5 HGNC HGNC:21269 protein_coding YES CCDS12938.1 ENSP00000375063 P59047 UPI00001AEEBD NM_153447.4 8/15 Gene3D:3.80.10.10,SMART_domains:SM00368,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 56032710 56032710 C A 1 0 0 0 0 0 0 0 1 10518 845 30 2 2 NLRP5 19 56032710 Silent SNP C C3N-02089_T 5575 56032710 2584906 965 28049 DUXA 0 . GRCh38 19 57154446 57154446 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.581G>T p.Ser194Ile p.S194I ENST00000554048 6/6 243 226 17 198 198 0 strelka-varscan-mutect DUXA,missense_variant,p.Ser194Ile,ENST00000554048,NM_001012729.1;CTC-360J11.5,downstream_gene_variant,,ENST00000604851,;CTC-360J11.6,upstream_gene_variant,,ENST00000604182,; A ENST00000554048 Transcript missense_variant 581/1006 581/615 194/204 S/I aGt/aTt 1 -1 DUXA HGNC HGNC:32179 protein_coding YES CCDS33126.1 ENSP00000452398 A6NLW8 UPI0000198B7E NM_001012729.1 deleterious_low_confidence(0) 6/6 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 57154446 57154446 C A 1 0 0 0 0 1 0 0 0 4656 565 20 2 2 DUXA 19 57154446 Missense_Mutation SNP C C3N-02089_T 1121736 57154446 1463170 966 28050 ZNF304 0 . GRCh38 19 57357535 57357535 + Missense_Mutation SNP G G T rs781706276 C3N-02089_T C3N-02089_N G G c.1807G>T p.Ala603Ser p.A603S ENST00000443917 4/4 161 132 29 122 122 0 strelka-varscan-mutect ZNF304,missense_variant,p.Ala556Ser,ENST00000391705,NM_020657.3;ZNF304,missense_variant,p.Ala556Ser,ENST00000282286,;ZNF304,missense_variant,p.Ala603Ser,ENST00000443917,NM_001290318.1;ZNF304,missense_variant,p.Ala514Ser,ENST00000598744,NM_001290319.1; T ENST00000443917 Transcript missense_variant 2146/3391 1807/2121 603/706 A/S Gca/Tca rs781706276 1 1 ZNF304 HGNC HGNC:13505 protein_coding YES CCDS77365.1 ENSP00000401642 E7EQD3 UPI00015DFA73 NM_001290318.1 deleterious(0.05) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF205,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs781706276 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 57357535 57357535 G T 1 0 0 0 0 1 0 0 0 18408 971 34 2 2 ZNF304 19 57357535 Missense_Mutation SNP G C3N-02089_T 203089 57357535 1260081 967 28051 TRAPPC2B 0 . GRCh38 19 57365087 57365087 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.254T>A p.Met85Lys p.M85K ENST00000596755 1/1 494 455 39 477 477 0 varscan-mutect TRAPPC2B,missense_variant,p.Met85Lys,ENST00000596755,;TRAPPC2B,missense_variant,p.Met85Lys,ENST00000543226,;ZNF547,intron_variant,,ENST00000282282,NM_173631.3;AC003002.4,intron_variant,,ENST00000597658,;ZNF547,upstream_gene_variant,,ENST00000599604,;ZNF547,intron_variant,,ENST00000595335,; A ENST00000596755 Transcript missense_variant 1521/1743 254/423 85/140 M/K aTg/aAg 1 1 TRAPPC2B HGNC HGNC:10710 protein_coding YES ENSP00000469888 P0DI82 Q6IBE5 UPI000000162E deleterious(0) 1/1 hmmpanther:PTHR12403,hmmpanther:PTHR12403:SF15,Pfam_domain:PF04628,Gene3D:2j3wA00,Superfamily_domains:SSF64356 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 57365087 57365087 T A 1 0 0 0 0 1 0 0 0 16945 1464 51 4 4 TRAPPC2B 19 57365087 Missense_Mutation SNP T C3N-02089_T 7552 57365087 1252529 968 28052 ZNF17 0 . GRCh38 19 57421092 57421092 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1600T>G p.Phe534Val p.F534V ENST00000601808 3/3 133 122 11 134 133 1 strelka-varscan-mutect ZNF17,missense_variant,p.Phe536Val,ENST00000307658,;ZNF17,missense_variant,p.Phe534Val,ENST00000601808,NM_006959.2;AC004076.7,intron_variant,,ENST00000597410,;AC003002.6,downstream_gene_variant,,ENST00000596400,;AC003002.6,downstream_gene_variant,,ENST00000596617,;ZNF17,downstream_gene_variant,,ENST00000597350,;ZNF17,downstream_gene_variant,,ENST00000595206,;ZNF17,downstream_gene_variant,,ENST00000599867,;ZNF17,non_coding_transcript_exon_variant,,ENST00000602050,;ZNF17,downstream_gene_variant,,ENST00000595162,; G ENST00000601808 Transcript missense_variant 1813/2524 1600/1989 534/662 F/V Ttc/Gtc 1 1 ZNF17 HGNC HGNC:12958 protein_coding YES CCDS42636.1 ENSP00000471905 P17021 UPI00001D8198 NM_006959.2 tolerated(0.46) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF166,Low_complexity_(Seg):seg,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 57421092 57421092 T G 1 0 0 0 0 1 0 0 0 18323 1493 52 5 5 ZNF17 19 57421092 Missense_Mutation SNP T C3N-02089_T 56005 57421092 1196524 969 28053 ZNF814 0 . GRCh38 19 57873643 57873643 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1747A>G p.Lys583Glu p.K583E ENST00000435989 3/3 257 239 18 271 271 0 strelka-varscan-mutect ZNF814,missense_variant,p.Lys583Glu,ENST00000435989,NM_001144989.1;ZNF814,intron_variant,,ENST00000597832,;ZNF814,intron_variant,,ENST00000614383,;ZNF814,intron_variant,,ENST00000595295,;ZNF814,intron_variant,,ENST00000597342,;ZNF814,intron_variant,,ENST00000596604,;ZNF814,intron_variant,,ENST00000600634,;ZNF814,intron_variant,,ENST00000595048,;ZNF814,downstream_gene_variant,,ENST00000597807,;ZNF814,intron_variant,,ENST00000594629,;CTD-2583A14.11,downstream_gene_variant,,ENST00000604665,;ZNF814,intron_variant,,ENST00000597348,;ZNF814,intron_variant,,ENST00000595894,;ZNF814,upstream_gene_variant,,ENST00000594159,;CTD-2583A14.9,downstream_gene_variant,,ENST00000602124,;CTD-2583A14.11,downstream_gene_variant,,ENST00000603829,; C ENST00000435989 Transcript missense_variant 1982/3146 1747/2568 583/855 K/E Aaa/Gaa 1 -1 ZNF814 HGNC HGNC:33258 protein_coding YES CCDS46212.1 ENSP00000410545 B7Z6K7 UPI0001662BAD NM_001144989.1 deleterious(0) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 57873643 57873643 T C 1 0 0 0 0 1 0 0 0 18762 1792 62 5 5 ZNF814 19 57873643 Missense_Mutation SNP T C3N-02089_T 452551 57873643 743973 970 28054 ZNF256 0 . GRCh38 19 57942404 57942404 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.404A>T p.Gln135Leu p.Q135L ENST00000282308 3/3 377 320 57 359 359 0 strelka-varscan-mutect ZNF256,missense_variant,p.Gln135Leu,ENST00000282308,NM_005773.2;ZNF256,3_prime_UTR_variant,,ENST00000598928,; A ENST00000282308 Transcript missense_variant 601/2172 404/1884 135/627 Q/L cAg/cTg 1 -1 ZNF256 HGNC HGNC:13049 protein_coding YES CCDS12966.1 ENSP00000282308 Q9Y2P7 UPI00001D69EC NM_005773.2 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF214,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 57942404 57942404 T A 1 0 0 0 0 1 0 0 0 18375 1580 55 4 4 ZNF256 19 57942404 Missense_Mutation SNP T C3N-02089_T 68761 57942404 675212 971 28055 ZSCAN1 0 . GRCh38 19 58053628 58053628 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.804C>A p.= p.T268T ENST00000282326 6/6 492 418 74 398 397 1 strelka-varscan-mutect ZSCAN1,synonymous_variant,p.=,ENST00000282326,NM_182572.3;HNRNPDLP4,upstream_gene_variant,,ENST00000605144,; A ENST00000282326 Transcript synonymous_variant 1051/2054 804/1227 268/408 T acC/acA 1 1 ZSCAN1 HGNC HGNC:23712 protein_coding YES CCDS12969.1 ENSP00000282326 Q8NBB4 UPI000013DCD2 NM_182572.3 6/6 hmmpanther:PTHR10032:SF187,hmmpanther:PTHR10032 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 58053628 58053628 C A 1 0 0 0 0 0 0 0 1 18820 581 21 2 2 ZSCAN1 19 58053628 Silent SNP C C3N-02089_T 111224 58053628 563988 972 28056 SIRPG 0 . GRCh38 20 1636301 1636301 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.635G>T p.Arg212Met p.R212M ENST00000303415 3/6 286 207 79 331 331 0 strelka-varscan-mutect SIRPG,missense_variant,p.Arg179Met,ENST00000381580,;SIRPG,missense_variant,p.Arg212Met,ENST00000303415,NM_018556.3;SIRPG,missense_variant,p.Arg212Met,ENST00000381583,NM_001039508.1;SIRPG,missense_variant,p.Arg212Met,ENST00000216927,;SIRPG,intron_variant,,ENST00000344103,NM_080816.2;SIRPG-AS1,intron_variant,,ENST00000456177,;SIRPG-AS1,intron_variant,,ENST00000437384,; A ENST00000303415 Transcript missense_variant 700/1716 635/1164 212/387 R/M aGg/aTg 1 -1 SIRPG HGNC HGNC:15757 protein_coding YES CCDS13020.2 ENSP00000305529 Q9P1W8 UPI00001AE5FD NM_018556.3 deleterious(0.04) 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF6,Pfam_domain:PF07654,Gene3D:2.60.40.10,SMART_domains:SM00407,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 1636301 1636301 C A 1 0 0 0 0 1 0 0 0 14599 681 24 2 2 SIRPG 20 1636301 Missense_Mutation SNP C C3N-02089_T 1636301 62807866 973 28057 TMC2 0 . GRCh38 20 2602264 2602264 + Missense_Mutation SNP C C A rs751320695 C3N-02089_T C3N-02089_N C C c.1376C>A p.Ser459Tyr p.S459Y ENST00000358864 11/20 71 46 25 93 93 0 strelka-varscan-mutect TMC2,missense_variant,p.Ser459Tyr,ENST00000358864,NM_080751.2;TMC2,non_coding_transcript_exon_variant,,ENST00000496948,; A ENST00000358864 Transcript missense_variant 1391/3169 1376/2721 459/906 S/Y tCc/tAc rs751320695,COSM352955 1 1 TMC2 HGNC HGNC:16527 protein_coding YES CCDS13029.2 ENSP00000351732 Q8TDI7 UPI0000246C98 NM_080751.2 deleterious(0.02) 11/20 hmmpanther:PTHR23302,hmmpanther:PTHR23302:SF17 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751320695 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 2602264 2602264 C A 1 0 0 0 0 1 0 0 0 16431 855 30 2 2 TMC2 20 2602264 Missense_Mutation SNP C C3N-02089_T 965963 2602264 61841903 974 28058 GFRA4 0 . GRCh38 20 3661105 3661105 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.231C>A p.= p.P77P ENST00000319242 2/5 89 61 28 69 69 0 strelka-varscan-mutect GFRA4,synonymous_variant,p.=,ENST00000290417,NM_022139.3;GFRA4,synonymous_variant,p.=,ENST00000319242,NM_145762.2;GFRA4,synonymous_variant,p.=,ENST00000477160,; T ENST00000319242 Transcript synonymous_variant 231/900 231/900 77/299 P ccC/ccA 1 -1 GFRA4 HGNC HGNC:13821 protein_coding YES CCDS13056.1 ENSP00000313423 Q9GZZ7 UPI0000070328 NM_145762.2 2/5 Pfam_domain:PF02351,hmmpanther:PTHR10269,hmmpanther:PTHR10269:SF2,Low_complexity_(Seg):seg,SMART_domains:SM00907 LOW 1 SNV 2 1 PASS rs943616306 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 3661105 3661105 G T 1 0 0 0 0 0 0 0 1 6224 1103 39 1 1 GFRA4 20 3661105 Silent SNP G C3N-02089_T 1058841 3661105 60783062 975 28059 JAG1 0 . GRCh38 20 10642523 10642523 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2537G>T p.Cys846Phe p.C846F ENST00000254958 21/26 510 363 147 486 485 1 strelka-varscan-mutect JAG1,missense_variant,p.Cys846Phe,ENST00000254958,NM_000214.2;JAG1,downstream_gene_variant,,ENST00000613518,;JAG1,non_coding_transcript_exon_variant,,ENST00000423891,;JAG1,downstream_gene_variant,,ENST00000488480,;JAG1,downstream_gene_variant,,ENST00000612857,;JAG1,upstream_gene_variant,,ENST00000617357,;JAG1,downstream_gene_variant,,ENST00000622545,; A ENST00000254958 Transcript missense_variant 3114/6048 2537/3657 846/1218 C/F tGc/tTc 1 -1 JAG1 HGNC HGNC:6188 protein_coding YES CCDS13112.1 ENSP00000254958 P78504 UPI00000498B5 NM_000214.2 deleterious(0) 21/26 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00010,PROSITE_patterns:PS00022,PROSITE_profiles:PS50026,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF269,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 10642523 10642523 C A 1 0 0 0 0 1 0 0 0 7847 710 25 2 2 JAG1 20 10642523 Missense_Mutation SNP C C3N-02089_T 6981418 10642523 53801644 976 28060 AL031664.1 0 . GRCh38 20 17494545 17494545 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1527G>T p.Gln509His p.Q509H ENST00000377873 8/8 121 93 28 164 163 1 strelka-varscan-mutect BFSP1,missense_variant,p.Gln509His,ENST00000377873,NM_001195.4;BFSP1,missense_variant,p.Gln384His,ENST00000377868,NM_001161705.1,NM_001278607.1;AL031664.1,missense_variant,p.Gln370His,ENST00000536626,NM_001278606.1,NM_001278608.1; A ENST00000377873 Transcript missense_variant 1567/2207 1527/1998 509/665 Q/H caG/caT 1 -1 BFSP1 HGNC HGNC:1040 protein_coding YES CCDS13126.1 ENSP00000367104 Q12934 UPI00001268C7 NM_001195.4 tolerated(0.33) 8/8 hmmpanther:PTHR14069,hmmpanther:PTHR14069:SF0 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 17494545 17494545 C A 1 0 0 0 0 1 0 0 0 568 680 24 2 2 AL031664.1 20 17494545 Missense_Mutation SNP C C3N-02089_T 6852022 17494545 46949622 977 28061 DZANK1 0 . GRCh38 20 18393728 18393728 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1792A>C p.Lys598Gln p.K598Q ENST00000262547 17/21 125 114 11 130 130 0 strelka-varscan-mutect DZANK1,missense_variant,p.Lys405Gln,ENST00000357236,;DZANK1,missense_variant,p.Lys598Gln,ENST00000262547,NM_001099407.1;DZANK1,missense_variant,p.Lys598Gln,ENST00000358866,;DZANK1,missense_variant,p.Lys71Gln,ENST00000476058,;DZANK1,missense_variant,p.Lys308Gln,ENST00000329494,;DZANK1,missense_variant,p.Lys136Gln,ENST00000480488,;DZANK1,3_prime_UTR_variant,,ENST00000608192,;DZANK1,3_prime_UTR_variant,,ENST00000377630,;DZANK1,3_prime_UTR_variant,,ENST00000609267,;DZANK1,downstream_gene_variant,,ENST00000460891,; G ENST00000262547 Transcript missense_variant 2001/3498 1792/2259 598/752 K/Q Aag/Cag 1 -1 DZANK1 HGNC HGNC:15858 protein_coding YES CCDS46582.1 ENSP00000262547 Q9NVP4 UPI0000E064B4 NM_001099407.1 tolerated(0.13) 17/21 hmmpanther:PTHR16058,hmmpanther:PTHR16058:SF4 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 18393728 18393728 T G 1 0 0 0 0 1 0 0 0 4686 1850 64 5 5 DZANK1 20 18393728 Missense_Mutation SNP T C3N-02089_T 899183 18393728 46050439 978 28062 NINL 0 . GRCh38 20 25462454 25462454 + Nonsense_Mutation SNP C C A rs145654950 C3N-02089_T C3N-02089_N C C c.3511G>T p.Glu1171Ter p.E1171* ENST00000278886 20/24 413 355 58 184 184 0 strelka-varscan-mutect NINL,stop_gained,p.Glu1171Ter,ENST00000278886,NM_025176.4;NINL,stop_gained,p.Glu822Ter,ENST00000422516,NM_001318226.1;NINL,stop_gained,p.Glu124Ter,ENST00000336104,;NINL,non_coding_transcript_exon_variant,,ENST00000496509,;NINL,upstream_gene_variant,,ENST00000464285,; A ENST00000278886 Transcript stop_gained 3585/4969 3511/4149 1171/1382 E/* Gag/Tag rs145654950 1 -1 NINL HGNC HGNC:29163 protein_coding YES CCDS33452.1 ENSP00000278886 Q9Y2I6 UPI0000206B64 NM_025176.4 20/24 hmmpanther:PTHR18905:SF12,hmmpanther:PTHR18905 HIGH 1 SNV 1 1 PASS rs145654950 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 25462454 25462454 C A 1 0 0 0 0 0 1 0 0 10455 893 31 1 1 NINL 20 25462454 Nonsense_Mutation SNP C C3N-02089_T 7068726 25462454 38981713 979 28063 TPX2 0 . GRCh38 20 31793930 31793930 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1592G>T p.Arg531Ile p.R531I ENST00000300403 14/18 230 149 81 164 164 0 strelka-varscan-mutect TPX2,missense_variant,p.Arg567Ile,ENST00000340513,;TPX2,missense_variant,p.Arg531Ile,ENST00000300403,NM_012112.4; T ENST00000300403 Transcript missense_variant 2120/3497 1592/2244 531/747 R/I aGa/aTa 1 1 TPX2 HGNC HGNC:1249 protein_coding YES CCDS13190.1 ENSP00000300403 Q9ULW0 Q643R0 UPI00000015BB NM_012112.4 deleterious(0) 14/18 hmmpanther:PTHR14326,hmmpanther:PTHR14326:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 31793930 31793930 G T 1 0 0 0 0 1 0 0 0 16913 942 33 2 2 TPX2 20 31793930 Missense_Mutation SNP G C3N-02089_T 6331476 31793930 32650237 980 28064 XKR7 0 . GRCh38 20 31997388 31997388 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1671C>A p.= p.A557A ENST00000562532 3/3 195 161 34 96 95 1 strelka-varscan-mutect XKR7,synonymous_variant,p.=,ENST00000562532,NM_001011718.1; A ENST00000562532 Transcript synonymous_variant 1845/7844 1671/1740 557/579 A gcC/gcA 1 1 XKR7 HGNC HGNC:23062 protein_coding YES CCDS33459.1 ENSP00000477059 Q5GH72 UPI00004C7A9E NM_001011718.1 3/3 hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF9 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 31997388 31997388 C A 1 0 0 0 0 0 0 0 1 17995 581 21 2 2 XKR7 20 31997388 Silent SNP C C3N-02089_T 203458 31997388 32446779 981 28065 PLAGL2 0 . GRCh38 20 32197312 32197312 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.631G>T p.Val211Leu p.V211L ENST00000246229 3/3 311 166 145 213 212 1 strelka-varscan-mutect PLAGL2,missense_variant,p.Val211Leu,ENST00000246229,NM_002657.3; A ENST00000246229 Transcript missense_variant 896/5705 631/1491 211/496 V/L Gtg/Ttg 1 -1 PLAGL2 HGNC HGNC:9047 protein_coding YES CCDS13197.1 ENSP00000246229 Q9UPG8 UPI0000001C1D NM_002657.3 deleterious(0) 3/3 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR10032,hmmpanther:PTHR10032:SF124,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 32197312 32197312 C A 1 0 0 0 0 1 0 0 0 12114 565 20 2 2 PLAGL2 20 32197312 Missense_Mutation SNP C C3N-02089_T 199924 32197312 32246855 982 28066 BPIFB2 0 . GRCh38 20 33012884 33012884 + Silent SNP T T A novel C3N-02089_T C3N-02089_N T T c.285T>A p.= p.A95A ENST00000170150 4/16 290 177 113 187 187 0 strelka-varscan-mutect BPIFB2,synonymous_variant,p.=,ENST00000170150,NM_025227.2; A ENST00000170150 Transcript synonymous_variant 480/1898 285/1377 95/458 A gcT/gcA 1 1 BPIFB2 HGNC HGNC:16177 protein_coding YES CCDS13210.1 ENSP00000170150 Q8N4F0 UPI00000377B0 NM_025227.2 4/16 hmmpanther:PTHR10504:SF92,hmmpanther:PTHR10504,Pfam_domain:PF01273,PIRSF_domain:PIRSF002417,Superfamily_domains:SSF55394 LOW 1 SNV 1 1 PASS rs1197769063 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 33012884 33012884 T A 1 0 0 0 0 0 0 0 1 1658 1509 53 4 4 BPIFB2 20 33012884 Silent SNP T C3N-02089_T 815572 33012884 31431283 983 28067 BPIFB6 0 . GRCh38 20 33043363 33043363 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1325T>C p.Val442Ala p.V442A ENST00000349552 14/15 338 218 120 228 228 0 strelka-varscan-mutect BPIFB6,missense_variant,p.Val442Ala,ENST00000349552,NM_174897.2;BPIFB6,3_prime_UTR_variant,,ENST00000542375,;PUDPP3,downstream_gene_variant,,ENST00000445368,; C ENST00000349552 Transcript missense_variant 1325/1362 1325/1362 442/453 V/A gTa/gCa 1 1 BPIFB6 HGNC HGNC:16504 protein_coding YES CCDS13211.1 ENSP00000344929 Q8NFQ5 UPI000003C8F3 NM_174897.2 tolerated(0.25) 14/15 hmmpanther:PTHR10504:SF71,hmmpanther:PTHR10504,Gene3D:1ewfA02,Pfam_domain:PF02886,SMART_domains:SM00329,Superfamily_domains:SSF55394 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 33043363 33043363 T C 1 0 0 0 0 1 0 0 0 1661 1652 57 5 5 BPIFB6 20 33043363 Missense_Mutation SNP T C3N-02089_T 30479 33043363 31400804 984 28068 NECAB3 0 . GRCh38 20 33659885 33659885 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.643G>T p.Gly215Trp p.G215W ENST00000246190 7/12 219 122 97 103 103 0 strelka-varscan-mutect NECAB3,missense_variant,p.Gly215Trp,ENST00000246190,NM_031232.3;NECAB3,missense_variant,p.Gly215Trp,ENST00000375238,NM_031231.3;NECAB3,missense_variant,p.Gly215Trp,ENST00000439478,;NECAB3,missense_variant,p.Gly215Trp,ENST00000606690,;NECAB3,splice_region_variant,,ENST00000480994,;C20orf144,upstream_gene_variant,,ENST00000375222,NM_080825.3;RP1-63M2.7,upstream_gene_variant,,ENST00000621597,;NECAB3,splice_region_variant,,ENST00000606525,;NECAB3,splice_region_variant,,ENST00000483813,;NECAB3,splice_region_variant,,ENST00000485976,;NECAB3,splice_region_variant,,ENST00000494174,;NECAB3,splice_region_variant,,ENST00000478237,;NECAB3,splice_region_variant,,ENST00000463246,;NECAB3,splice_region_variant,,ENST00000498353,;NECAB3,downstream_gene_variant,,ENST00000606106,;NECAB3,upstream_gene_variant,,ENST00000477778,;NECAB3,splice_region_variant,,ENST00000488489,;NECAB3,splice_region_variant,,ENST00000485399,;NECAB3,splice_region_variant,,ENST00000607805,;NECAB3,3_prime_UTR_variant,,ENST00000493590,;C20orf144,upstream_gene_variant,,ENST00000607738,;NECAB3,downstream_gene_variant,,ENST00000606699,; A ENST00000246190 Transcript missense_variant,splice_region_variant 699/1989 643/1191 215/396 G/W Ggg/Tgg 1 -1 NECAB3 HGNC HGNC:15851 protein_coding YES CCDS42866.1 ENSP00000246190 Q96P71 UPI0000125101 NM_031232.3 deleterious(0) 7/12 hmmpanther:PTHR12178,hmmpanther:PTHR12178:SF3 MODERATE SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 33659885 33659885 C A 1 0 0 0 0 1 0 0 0 10330 695 24 2 2 NECAB3 20 33659885 Missense_Mutation SNP C C3N-02089_T 616522 33659885 30784282 985 28069 ACTL10 0 . GRCh38 20 33667994 33667994 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.497C>A p.Ala166Asp p.A166D ENST00000330271 1/1 110 101 9 48 48 0 strelka-varscan-mutect ACTL10,missense_variant,p.Ala166Asp,ENST00000330271,NM_001024675.1;NECAB3,intron_variant,,ENST00000246190,NM_031232.3;NECAB3,intron_variant,,ENST00000375238,NM_031231.3;NECAB3,intron_variant,,ENST00000439478,;NECAB3,intron_variant,,ENST00000606690,;NECAB3,upstream_gene_variant,,ENST00000480994,;C20orf144,downstream_gene_variant,,ENST00000375222,NM_080825.3;NECAB3,downstream_gene_variant,,ENST00000473892,;NECAB3,intron_variant,,ENST00000494174,;NECAB3,upstream_gene_variant,,ENST00000485976,;NECAB3,upstream_gene_variant,,ENST00000606106,;NECAB3,intron_variant,,ENST00000488489,;NECAB3,intron_variant,,ENST00000485399,;NECAB3,intron_variant,,ENST00000606699,;NECAB3,intron_variant,,ENST00000607805,;NECAB3,intron_variant,,ENST00000493590,;C20orf144,downstream_gene_variant,,ENST00000607738,;NECAB3,downstream_gene_variant,,ENST00000484824,;NECAB3,downstream_gene_variant,,ENST00000607055,; A ENST00000330271 Transcript missense_variant 1497/2028 497/738 166/245 A/D gCc/gAc 1 1 ACTL10 HGNC HGNC:16127 protein_coding YES CCDS33463.1 ENSP00000329647 Q5JWF8 UPI0000470AC1 NM_001024675.1 deleterious(0) 1/1 Gene3D:3.30.420.40,Pfam_domain:PF00022,hmmpanther:PTHR11937,hmmpanther:PTHR11937:SF183,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE SNV 1 PASS rs1189243529 . 0 206 2 2 0 0 0 0 -13.65748 0.9999931 1 1 1 0 A 3 1 90 33667994 33667994 C A 1 0 0 0 0 1 0 0 0 241 739 26 2 2 ACTL10 20 33667994 Missense_Mutation SNP C C3N-02089_T 8109 33667994 30776173 986 28070 PIGU 0 . GRCh38 20 34585515 34585537 + Frame_Shift_Del DEL TCAAACATCTCTGCAAAGAAGTA TCAAACATCTCTGCAAAGAAGTA - novel C3N-02089_T C3N-02089_N TCAAACATCTCTGCAAAGAAGTA TCAAACATCTCTGCAAAGAAGTA c.826_848delTACTTCTTTGCAGAGATGTTTGA p.Tyr276AlafsTer44 p.Y276Afs*44 ENST00000217446 9/12 284 258 26 252 252 0 sindel-pindel PIGU,frameshift_variant,p.Tyr276AlafsTer44,ENST00000217446,NM_080476.4;PIGU,frameshift_variant,p.Tyr256AlafsTer44,ENST00000374820,;PIGU,intron_variant,,ENST00000438215,;PIGU,intron_variant,,ENST00000480175,; - ENST00000217446 Transcript frameshift_variant 826-848/1632 826-848/1308 276-283/435 YFFAEMFE/X TACTTCTTTGCAGAGATGTTTGAg/g 1 -1 PIGU HGNC HGNC:15791 protein_coding YES CCDS13239.1 ENSP00000217446 Q9H490 UPI0000131ABC NM_080476.4 9/12 Pfam_domain:PF06728,hmmpanther:PTHR13121,Transmembrane_helices:TMhelix HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 34585515 34585515 TCAAACATCTCTGCAAAGAAGTA - 1 0 1 0 1 0 0 0 0 11994 1551 54 0 0 PIGU 20 34585515 Frame_Shift_Del DEL TCAAACATCTCTGCAAAGAAGTA C3N-02089_T 917521 34585515 29858652 987 28071 MMP24 0 . GRCh38 20 35254672 35254672 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.735C>A p.= p.A245A ENST00000246186 4/9 328 297 31 228 228 0 strelka-varscan-mutect MMP24,synonymous_variant,p.=,ENST00000246186,NM_006690.3;MMP24-AS1,intron_variant,,ENST00000635104,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000433764,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,downstream_gene_variant,,ENST00000453892,; A ENST00000246186 Transcript synonymous_variant 820/4414 735/1938 245/645 A gcC/gcA 1 1 MMP24 HGNC HGNC:7172 protein_coding YES CCDS46593.1 ENSP00000246186 Q9Y5R2 UPI000012F259 NM_006690.3 4/9 hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF00413,Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 LOW 1 SNV 1 1 PASS rs1234383513 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 35254672 35254672 C A 1 0 0 0 0 0 0 0 1 9624 668 24 2 2 MMP24 20 35254672 Silent SNP C C3N-02089_T 669157 35254672 29189495 988 28072 FAM83C 0 . GRCh38 20 35286823 35286823 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.1956T>G p.Asn652Lys p.N652K ENST00000374408 4/4 474 408 66 339 339 0 strelka-varscan-mutect FAM83C,missense_variant,p.Asn652Lys,ENST00000374408,NM_178468.5;EIF6,upstream_gene_variant,,ENST00000374450,NM_002212.3;EIF6,upstream_gene_variant,,ENST00000374436,NM_181468.2;EIF6,upstream_gene_variant,,ENST00000621148,NM_001267810.1;EIF6,upstream_gene_variant,,ENST00000374443,NM_181466.2;EIF6,upstream_gene_variant,,ENST00000456600,;FAM83C-AS1,downstream_gene_variant,,ENST00000429167,;EIF6,upstream_gene_variant,,ENST00000462894,;EIF6,upstream_gene_variant,,ENST00000447927,;EIF6,upstream_gene_variant,,ENST00000440766,;EIF6,upstream_gene_variant,,ENST00000415116,; C ENST00000374408 Transcript missense_variant 2053/3145 1956/2244 652/747 N/K aaT/aaG 1 -1 FAM83C HGNC HGNC:16121 protein_coding YES CCDS13251.1 ENSP00000363529 Q9BQN1 UPI0000072DC0 NM_178468.5 deleterious_low_confidence(0.01) 4/4 hmmpanther:PTHR16181,hmmpanther:PTHR16181:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 35286823 35286823 A C 1 0 0 0 0 1 0 0 0 5493 214 8 5 5 FAM83C 20 35286823 Missense_Mutation SNP A C3N-02089_T 32151 35286823 29157344 989 28073 CEP250 0 . GRCh38 20 35507849 35507849 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.6748G>T p.Glu2250Ter p.E2250* ENST00000397527 31/35 224 184 40 173 173 0 strelka-varscan-mutect CEP250,stop_gained,p.Glu2250Ter,ENST00000397527,NM_007186.4;CEP250,stop_gained,p.Glu738Ter,ENST00000422671,;CEP250,upstream_gene_variant,,ENST00000621352,; T ENST00000397527 Transcript stop_gained,splice_region_variant 7468/15703 6748/7329 2250/2442 E/* Gag/Tag 1 1 CEP250 HGNC HGNC:1859 protein_coding YES CCDS13255.1 ENSP00000380661 Q9BV73 UPI000006FE8F NM_007186.4 31/35 hmmpanther:PTHR23159:SF1,hmmpanther:PTHR23159 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 35507849 35507849 G T 1 0 0 0 0 0 1 0 0 2968 956 33 2 2 CEP250 20 35507849 Nonsense_Mutation SNP G C3N-02089_T 221026 35507849 28936318 990 28074 DLGAP4 0 . GRCh38 20 36431991 36431991 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.274G>T p.Ala92Ser p.A92S ENST00000373913 3/13 523 358 165 329 329 0 strelka-varscan-mutect DLGAP4,missense_variant,p.Ala92Ser,ENST00000373913,NM_014902.5;DLGAP4,missense_variant,p.Ala92Ser,ENST00000339266,;DLGAP4,missense_variant,p.Ala92Ser,ENST00000401952,;DLGAP4,missense_variant,p.Ala92Ser,ENST00000373907,; T ENST00000373913 Transcript missense_variant 754/5056 274/2970 92/989 A/S Gcc/Tcc 1 1 DLGAP4 HGNC HGNC:24476 protein_coding YES CCDS13274.1 ENSP00000363023 Q9Y2H0 UPI000013D34B NM_014902.5 tolerated(0.25) 3/13 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF19 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 36431991 36431991 G T 1 0 0 0 0 1 0 0 0 4369 1319 46 2 2 DLGAP4 20 36431991 Missense_Mutation SNP G C3N-02089_T 924142 36431991 28012176 991 28075 TGM2 0 . GRCh38 20 38138300 38138300 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.1428G>A p.= p.R476R ENST00000361475 10/13 403 331 72 355 355 0 strelka-varscan-mutect TGM2,synonymous_variant,p.=,ENST00000361475,NM_001323316.1,NM_001323318.1,NM_004613.2;TGM2,non_coding_transcript_exon_variant,,ENST00000468262,;TGM2,upstream_gene_variant,,ENST00000469269,; T ENST00000361475 Transcript synonymous_variant 1602/5070 1428/2064 476/687 R cgG/cgA 1 -1 TGM2 HGNC HGNC:11778 protein_coding YES CCDS13302.1 ENSP00000355330 P21980 V9HWG3 UPI0000136CCB NM_001323316.1,NM_001323318.1,NM_004613.2 10/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF6,Pfam_domain:PF00927,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000459,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 38138300 38138300 C T 1 0 0 0 0 0 0 0 1 16263 842 30 3 3 TGM2 20 38138300 Silent SNP C C3N-02089_T 1706309 38138300 26305867 992 28076 SLC32A1 0 . GRCh38 20 38724847 38724847 + Silent SNP G G A rs151110255 C3N-02089_T C3N-02089_N G G c.123G>A p.= p.A41A ENST00000217420 1/2 320 269 51 254 254 0 strelka-varscan-mutect SLC32A1,synonymous_variant,p.=,ENST00000217420,NM_080552.2; A ENST00000217420 Transcript synonymous_variant 386/2574 123/1578 41/525 A gcG/gcA rs151110255 1 1 SLC32A1 HGNC HGNC:11018 protein_coding YES CCDS13307.1 ENSP00000217420 Q9H598 UPI0000043423 NM_080552.2 1/2 LOW 1 SNV 1 1 PASS rs151110255 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 38724847 38724847 G A 1 0 0 0 0 0 0 0 1 14835 1103 39 1 1 SLC32A1 20 38724847 Silent SNP G C3N-02089_T 586547 38724847 25719320 993 28077 PPP1R16B 0 . GRCh38 20 38907034 38907034 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.878C>A p.Ser293Tyr p.S293Y ENST00000299824 8/11 204 166 38 181 181 0 strelka-varscan-mutect PPP1R16B,missense_variant,p.Ser293Tyr,ENST00000299824,NM_015568.2;PPP1R16B,missense_variant,p.Ser251Tyr,ENST00000373331,NM_001172735.1; A ENST00000299824 Transcript missense_variant 1067/6251 878/1704 293/567 S/Y tCc/tAc 1 1 PPP1R16B HGNC HGNC:15850 protein_coding YES CCDS13309.1 ENSP00000299824 Q96T49 UPI0000132059 NM_015568.2 tolerated(1) 8/11 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24186,hmmpanther:PTHR24186:SF6,Gene3D:1.25.40.20,PIRSF_domain:PIRSF038159,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 38907034 38907034 C A 1 0 0 0 0 1 0 0 0 12476 855 30 2 2 PPP1R16B 20 38907034 Missense_Mutation SNP C C3N-02089_T 182187 38907034 25537133 994 28078 PTPRT 0 . GRCh38 20 42791341 42791341 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.340A>T p.Arg114Trp p.R114W ENST00000373198 3/32 391 238 153 240 240 0 strelka-varscan-mutect PTPRT,missense_variant,p.Arg114Trp,ENST00000373198,NM_133170.3;PTPRT,missense_variant,p.Arg114Trp,ENST00000373193,;PTPRT,missense_variant,p.Arg114Trp,ENST00000373201,;PTPRT,missense_variant,p.Arg114Trp,ENST00000373190,;PTPRT,missense_variant,p.Arg114Trp,ENST00000373184,;PTPRT,missense_variant,p.Arg114Trp,ENST00000356100,;PTPRT,missense_variant,p.Arg114Trp,ENST00000373187,NM_007050.5;PTPRT,missense_variant,p.Arg43Trp,ENST00000620410,;PTPRT,3_prime_UTR_variant,,ENST00000617474,; A ENST00000373198 Transcript missense_variant 576/12746 340/4383 114/1460 R/W Agg/Tgg 1 -1 PTPRT HGNC HGNC:9682 protein_coding YES CCDS68127.1 ENSP00000362294 A0A075B6H0 UPI00001AF6FA NM_133170.3 deleterious(0) 3/32 Pfam_domain:PF00629,PROSITE_profiles:PS50060,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF208,SMART_domains:SM00137,Superfamily_domains:SSF49899 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 42791341 42791341 T A 1 0 0 0 0 1 0 0 0 12967 1579 55 4 4 PTPRT 20 42791341 Missense_Mutation SNP T C3N-02089_T 3884307 42791341 21652826 995 28079 JPH2 0 . GRCh38 20 44160068 44160068 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.719G>C p.Gly240Ala p.G240A ENST00000372980 2/6 264 226 38 142 142 0 strelka-varscan-mutect JPH2,missense_variant,p.Gly240Ala,ENST00000372980,NM_020433.4; G ENST00000372980 Transcript missense_variant 1592/4787 719/2091 240/696 G/A gGt/gCt 1 -1 JPH2 HGNC HGNC:14202 protein_coding YES CCDS13325.1 ENSP00000362071 Q9BR39 UPI000012DAC2 NM_020433.4 tolerated(0.59) 2/6 hmmpanther:PTHR23085:SF5,hmmpanther:PTHR23085,PIRSF_domain:PIRSF037387 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 44160068 44160068 C G 1 0 0 0 0 1 0 0 0 7873 507 18 4 4 JPH2 20 44160068 Missense_Mutation SNP C C3N-02089_T 1368727 44160068 20284099 996 28080 NCOA5 0 . GRCh38 20 46068638 46068638 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.366G>T p.Arg122Ser p.R122S ENST00000290231 4/8 172 92 80 135 135 0 strelka-varscan-mutect NCOA5,missense_variant,p.Arg122Ser,ENST00000290231,NM_020967.2;NCOA5,missense_variant,p.Arg17Ser,ENST00000372291,; A ENST00000290231 Transcript missense_variant,splice_region_variant 531/3220 366/1740 122/579 R/S agG/agT 1 -1 NCOA5 HGNC HGNC:15909 protein_coding YES CCDS13392.1 ENSP00000290231 Q9HCD5 UPI000000D7B2 NM_020967.2 tolerated(0.3) 4/8 hmmpanther:PTHR23295,hmmpanther:PTHR23295:SF3,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 46068638 46068638 C A 1 0 0 0 0 1 0 0 0 10251 869 30 2 2 NCOA5 20 46068638 Missense_Mutation SNP C C3N-02089_T 1908570 46068638 18375529 997 28081 SNAI1 0 . GRCh38 20 49987977 49987977 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.716A>T p.Gln239Leu p.Q239L ENST00000244050 3/3 156 128 28 139 139 0 strelka-varscan-mutect SNAI1,missense_variant,p.Gln239Leu,ENST00000244050,NM_005985.3; T ENST00000244050 Transcript missense_variant 777/1686 716/795 239/264 Q/L cAg/cTg 1 1 SNAI1 HGNC HGNC:11128 protein_coding YES CCDS13423.1 ENSP00000244050 O95863 UPI0000135B17 NM_005985.3 deleterious(0.01) 3/3 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF41,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs1232707935 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 49987977 49987977 A T 1 0 0 0 0 1 0 0 0 15147 188 7 4 4 SNAI1 20 49987977 Missense_Mutation SNP A C3N-02089_T 3919339 49987977 14456190 998 28082 ZFP64 0 . GRCh38 20 52084601 52084601 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1894G>C p.Val632Leu p.V632L ENST00000361387 9/9 150 116 34 139 139 0 strelka-varscan-mutect ZFP64,missense_variant,p.Val632Leu,ENST00000361387,NM_199427.2;ZFP64,missense_variant,p.Val413Leu,ENST00000371523,NM_001319146.1;ZFP64,intron_variant,,ENST00000371518,;ZFP64,downstream_gene_variant,,ENST00000395989,;ZFP64,downstream_gene_variant,,ENST00000456175,;ZFP64,downstream_gene_variant,,ENST00000477786,;ZFP64,downstream_gene_variant,,ENST00000467811,; G ENST00000361387 Transcript missense_variant 1955/2545 1894/1938 632/645 V/L Gtg/Ctg 1 -1 ZFP64 HGNC HGNC:15940 protein_coding CCDS13439.1 ENSP00000355179 Q9NTW7 UPI000013C56C NM_199427.2 tolerated_low_confidence(0.26) 9/9 hmmpanther:PTHR24403,hmmpanther:PTHR24403:SF34 MODERATE 1 SNV 1 1 PASS rs1309773863 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 52084601 52084601 C G 1 0 0 0 0 1 0 0 0 18228 536 19 4 4 ZFP64 20 52084601 Missense_Mutation SNP C C3N-02089_T 2096624 52084601 12359566 999 28083 PCK1 0 . GRCh38 20 57565111 57565111 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1390G>T p.Ala464Ser p.A464S ENST00000319441 9/10 191 177 14 164 164 0 strelka-varscan-mutect PCK1,missense_variant,p.Ala464Ser,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,non_coding_transcript_exon_variant,,ENST00000485958,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000470051,; T ENST00000319441 Transcript missense_variant 1554/4341 1390/1869 464/622 A/S Gcc/Tcc 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 tolerated(0.33) 9/10 Low_complexity_(Seg):seg,HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,Gene3D:3.90.228.20,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 57565111 57565111 G T 1 0 0 0 0 1 0 0 0 11669 1203 42 2 2 PCK1 20 57565111 Missense_Mutation SNP G C3N-02089_T 5480510 57565111 6879056 1000 28084 96 2 PCK1 0 . GRCh38 20 57565120 57565120 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1399G>C p.Ala467Pro p.A467P ENST00000319441 9/10 167 145 22 142 142 0 strelka-varscan-mutect PCK1,missense_variant,p.Ala467Pro,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,non_coding_transcript_exon_variant,,ENST00000485958,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000470051,; C ENST00000319441 Transcript missense_variant 1563/4341 1399/1869 467/622 A/P Gct/Cct 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 deleterious(0) 9/10 Low_complexity_(Seg):seg,HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,Gene3D:3.90.228.20,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795 MODERATE 1 SNV 1 1 PASS rs1358012223 . 0 207 0 3 0 0 0 0 -20 0.9999917 1 1 1 0 C 3 2 90 57565120 57565120 G C 1 0 0 0 0 1 0 0 0 11669 1203 42 4 4 PCK1 20 57565120 Missense_Mutation SNP G C3N-02089_T 9 57565120 6879047 1001 28085 96 2 EDN3 0 . GRCh38 20 59301644 59301644 + Missense_Mutation SNP G G T rs141776410 C3N-02089_T C3N-02089_N G G c.287G>T p.Arg96Leu p.R96L ENST00000337938 2/5 242 189 53 282 281 1 strelka-varscan-mutect EDN3,missense_variant,p.Arg96Leu,ENST00000311585,NM_207032.2;EDN3,missense_variant,p.Arg96Leu,ENST00000337938,NM_001302455.1,NM_207034.2;EDN3,missense_variant,p.Arg96Leu,ENST00000371028,;EDN3,missense_variant,p.Arg96Leu,ENST00000395654,NM_207033.2;EDN3,missense_variant,p.Arg96Leu,ENST00000371025,NM_001302456.1; T ENST00000337938 Transcript missense_variant 673/2636 287/717 96/238 R/L cGc/cTc rs141776410,COSM3740200,COSM3740201,COSM3740202 1 1 EDN3 HGNC HGNC:3178 protein_coding YES CCDS13477.1 ENSP00000337128 P14138 UPI000012A221 NM_001302455.1,NM_207034.2 deleterious(0) 2/5 hmmpanther:PTHR13874,hmmpanther:PTHR13874:SF11,Pfam_domain:PF00322,SMART_domains:SM00272,Prints_domain:PR00365 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs141776410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 59301644 59301644 G T 1 0 0 0 0 1 0 0 0 4746 1087 38 1 1 EDN3 20 59301644 Missense_Mutation SNP G C3N-02089_T 1736524 59301644 5142523 1002 28086 SYCP2 0 . GRCh38 20 59865417 59865417 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.4486G>T p.Val1496Leu p.V1496L ENST00000357552 44/45 180 161 19 242 242 0 strelka-varscan-mutect SYCP2,missense_variant,p.Val1496Leu,ENST00000357552,;SYCP2,missense_variant,p.Val1496Leu,ENST00000371001,NM_014258.2;SYCP2,missense_variant,p.Val182Leu,ENST00000412613,; A ENST00000357552 Transcript missense_variant 4712/5567 4486/4593 1496/1530 V/L Gtg/Ttg 1 -1 SYCP2 HGNC HGNC:11490 protein_coding YES CCDS13482.1 ENSP00000350162 Q9BX26 UPI0000135683 tolerated(0.6) 44/45 hmmpanther:PTHR15607,hmmpanther:PTHR15607:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 59865417 59865417 C A 1 0 0 0 0 1 0 0 0 15822 565 20 2 2 SYCP2 20 59865417 Missense_Mutation SNP C C3N-02089_T 563773 59865417 4578750 1003 28087 TCFL5 0 . GRCh38 20 62842050 62842050 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.1428G>T p.= p.L476L ENST00000335351 6/6 286 245 41 282 282 0 strelka-varscan-mutect TCFL5,synonymous_variant,p.=,ENST00000335351,NM_006602.3;COL9A3,downstream_gene_variant,,ENST00000343916,NM_001853.3;TCFL5,downstream_gene_variant,,ENST00000217162,;COL9A3,downstream_gene_variant,,ENST00000462700,;COL9A3,downstream_gene_variant,,ENST00000467819,;COL9A3,downstream_gene_variant,,ENST00000466532,;COL9A3,downstream_gene_variant,,ENST00000466192,;COL9A3,downstream_gene_variant,,ENST00000469802,;DPH3P1,upstream_gene_variant,,ENST00000486648,; A ENST00000335351 Transcript synonymous_variant 1521/2456 1428/1503 476/500 L ctG/ctT 1 -1 TCFL5 HGNC HGNC:11646 protein_coding YES CCDS13506.1 ENSP00000334294 Q9UL49 UPI0000206389 NM_006602.3 6/6 hmmpanther:PTHR15402:SF2,hmmpanther:PTHR15402 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 62842050 62842050 C A 1 0 0 0 0 0 0 0 1 16106 813 29 2 2 TCFL5 20 62842050 Silent SNP C C3N-02089_T 2976633 62842050 1602117 1004 28088 COL20A1 0 . GRCh38 20 63312827 63312827 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1969G>T p.Glu657Ter p.E657* ENST00000358894 16/36 82 69 13 59 59 0 strelka-varscan-mutect COL20A1,stop_gained,p.Glu664Ter,ENST00000422202,;COL20A1,stop_gained,p.Glu657Ter,ENST00000358894,NM_020882.2;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,; T ENST00000358894 Transcript stop_gained 2069/4172 1969/3855 657/1284 E/* Gag/Tag 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 16/36 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 63312827 63312827 G T 1 0 0 0 0 0 1 0 0 3467 1175 41 2 2 COL20A1 20 63312827 Nonsense_Mutation SNP G C3N-02089_T 470777 63312827 1131340 1005 28089 COL20A1 0 . GRCh38 20 63328423 63328423 + Missense_Mutation SNP G G T rs752115346 C3N-02089_T C3N-02089_N G G c.3706G>T p.Gly1236Trp p.G1236W ENST00000358894 34/36 311 196 115 178 177 1 strelka-varscan-mutect COL20A1,missense_variant,p.Gly1249Trp,ENST00000422202,;COL20A1,missense_variant,p.Gly1236Trp,ENST00000358894,NM_020882.2;COL20A1,missense_variant,p.Gly377Trp,ENST00000415763,;COL20A1,missense_variant,p.Gly232Trp,ENST00000455906,;COL20A1,upstream_gene_variant,,ENST00000496810,;COL20A1,non_coding_transcript_exon_variant,,ENST00000479501,;COL20A1,non_coding_transcript_exon_variant,,ENST00000471582,;COL20A1,non_coding_transcript_exon_variant,,ENST00000494913,; T ENST00000358894 Transcript missense_variant 3806/4172 3706/3855 1236/1284 G/W Ggg/Tgg rs752115346,COSM4581978,COSM4581979,COSM4581980 1 1 COL20A1 HGNC HGNC:14670 protein_coding YES CCDS46628.1 ENSP00000351767 Q9P218 UPI000051910D NM_020882.2 deleterious(0) 34/36 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF131 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs752115346 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 63328423 63328423 G T 1 0 0 0 0 1 0 0 0 3467 1232 43 2 2 COL20A1 20 63328423 Missense_Mutation SNP G C3N-02089_T 15596 63328423 1115744 1006 28090 CHRNA4 0 . GRCh38 20 63350607 63350607 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.804C>A p.= p.P268P ENST00000370263 5/6 666 549 117 436 436 0 strelka-varscan-mutect CHRNA4,synonymous_variant,p.=,ENST00000615287,;CHRNA4,synonymous_variant,p.=,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,non_coding_transcript_exon_variant,,ENST00000463705,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,downstream_gene_variant,,ENST00000628665,;CHRNA4,downstream_gene_variant,,ENST00000636652,;CHRNA4,downstream_gene_variant,,ENST00000637628,;CHRNA4,downstream_gene_variant,,ENST00000637243,;CHRNA4,3_prime_UTR_variant,,ENST00000627000,;CHRNA4,3_prime_UTR_variant,,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000630240,;CHRNA4,upstream_gene_variant,,ENST00000631289,; T ENST00000370263 Transcript synonymous_variant 982/5577 804/1884 268/627 P ccC/ccA 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 5/6 Gene3D:1.20.120.370,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 63350607 63350607 G T 1 0 0 0 0 0 0 0 1 3145 987 35 2 2 CHRNA4 20 63350607 Silent SNP G C3N-02089_T 22184 63350607 1093560 1007 28091 CHRNA4 0 . GRCh38 20 63359679 63359679 + Missense_Mutation SNP G G A rs370553755 C3N-02089_T C3N-02089_N G G c.97C>T p.Arg33Trp p.R33W ENST00000370263 2/6 382 310 72 222 221 1 strelka-varscan-mutect CHRNA4,missense_variant,p.Arg33Trp,ENST00000370263,NM_001256573.1,NM_000744.6;CHRNA4,5_prime_UTR_variant,,ENST00000615287,;RP11-261N11.8,upstream_gene_variant,,ENST00000370257,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000467563,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000628665,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000637443,;CHRNA4,intron_variant,,ENST00000463705,;CHRNA4,upstream_gene_variant,,ENST00000636652,;CHRNA4,upstream_gene_variant,,ENST00000636481,;CHRNA4,upstream_gene_variant,,ENST00000636726,;CHRNA4,upstream_gene_variant,,ENST00000637628,;CHRNA4,missense_variant,p.Arg33Trp,ENST00000627000,;CHRNA4,missense_variant,p.Arg8Trp,ENST00000498043,;CHRNA4,non_coding_transcript_exon_variant,,ENST00000626188,;CHRNA4,upstream_gene_variant,,ENST00000627869,;CHRNA4,downstream_gene_variant,,ENST00000628606,; A ENST00000370263 Transcript missense_variant 275/5577 97/1884 33/627 R/W Cgg/Tgg rs370553755 1 -1 CHRNA4 HGNC HGNC:1958 protein_coding YES CCDS13517.1 ENSP00000359285 P43681 UPI000012523B NM_001256573.1,NM_000744.6 tolerated(0.06) 2/6 hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF401,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS rs370553755 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 63359679 63359679 G A 1 0 0 0 0 1 0 0 0 3145 1115 39 1 1 CHRNA4 20 63359679 Missense_Mutation SNP G C3N-02089_T 9072 63359679 1084488 1008 28092 ABHD16B 0 . GRCh38 20 63861599 63861599 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.59C>T p.Ala20Val p.A20V ENST00000369916 1/1 450 370 80 254 253 1 strelka-varscan-mutect ABHD16B,missense_variant,p.Ala20Val,ENST00000369916,NM_080622.3;TPD52L2,upstream_gene_variant,,ENST00000217121,NM_199360.2;TPD52L2,upstream_gene_variant,,ENST00000352482,NM_199362.2;TPD52L2,upstream_gene_variant,,ENST00000615907,NM_001243895.1;TPD52L2,upstream_gene_variant,,ENST00000351424,NM_199361.2;TPD52L2,upstream_gene_variant,,ENST00000346249,NM_001243891.1,NM_003288.3;TPD52L2,upstream_gene_variant,,ENST00000358548,NM_199363.2;TPD52L2,upstream_gene_variant,,ENST00000348257,NM_199359.2;TPD52L2,upstream_gene_variant,,ENST00000611972,NM_001243894.1;TPD52L2,upstream_gene_variant,,ENST00000369927,NM_001243892.1;RP4-591C20.9,non_coding_transcript_exon_variant,,ENST00000601296,; T ENST00000369916 Transcript missense_variant 102/1491 59/1410 20/469 A/V gCc/gTc 1 1 ABHD16B HGNC HGNC:16128 protein_coding YES CCDS13539.1 ENSP00000358932 Q9H3Z7 UPI000012860E NM_080622.3 deleterious(0) 1/1 hmmpanther:PTHR12277:SF37,hmmpanther:PTHR12277 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 63861599 63861599 C T 1 0 0 0 0 1 0 0 0 87 739 26 3 3 ABHD16B 20 63861599 Missense_Mutation SNP C C3N-02089_T 501920 63861599 582568 1009 28093 CHODL 0 . GRCh38 21 18257053 18257053 + Missense_Mutation SNP G G T rs762990377 C3N-02089_T C3N-02089_N G G c.473G>T p.Gly158Val p.G158V ENST00000299295 3/6 113 82 31 126 126 0 strelka-varscan-mutect CHODL,missense_variant,p.Gly158Val,ENST00000299295,NM_024944.2;CHODL,missense_variant,p.Gly117Val,ENST00000400128,;CHODL,missense_variant,p.Gly117Val,ENST00000400127,NM_001204176.1,NM_001204175.1;CHODL,missense_variant,p.Gly117Val,ENST00000400135,NM_001204178.1;CHODL,missense_variant,p.Gly117Val,ENST00000400131,NM_001204177.1;CHODL,missense_variant,p.Gly117Val,ENST00000338326,;CHODL,missense_variant,p.Gly139Val,ENST00000543733,NM_001204174.1; T ENST00000299295 Transcript missense_variant 864/2548 473/822 158/273 G/V gGg/gTg rs762990377 1 1 CHODL HGNC HGNC:17807 protein_coding YES CCDS13570.1 ENSP00000299295 Q9H9P2 UPI0000037746 NM_024944.2 deleterious(0) 3/6 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR14789,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs762990377 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 18257053 18257053 G T 1 0 0 0 0 1 0 0 0 3124 1232 43 2 2 CHODL 21 18257053 Missense_Mutation SNP G C3N-02089_T 18257053 28452930 1010 28094 LTN1 0 . GRCh38 21 28969514 28969514 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1401G>T p.Gln467His p.Q467H ENST00000614971 9/30 123 99 24 179 179 0 strelka-varscan-mutect LTN1,missense_variant,p.Gln467His,ENST00000614971,NM_015565.2;LTN1,missense_variant,p.Gln467His,ENST00000389194,;LTN1,missense_variant,p.Gln421His,ENST00000361371,;LTN1,missense_variant,p.Gln467His,ENST00000389195,;LTN1,missense_variant,p.Gln350His,ENST00000483326,; A ENST00000614971 Transcript missense_variant 1414/7756 1401/5439 467/1812 Q/H caG/caT 1 -1 LTN1 HGNC HGNC:13082 protein_coding YES CCDS33527.2 ENSP00000478783 O94822 UPI000049DF6C NM_015565.2 tolerated(0.47) 9/30 hmmpanther:PTHR12389,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 28969514 28969514 C A 1 0 0 0 0 1 0 0 0 8987 796 28 2 2 LTN1 21 28969514 Missense_Mutation SNP C C3N-02089_T 10712461 28969514 17740469 1011 28095 TIAM1 0 . GRCh38 21 31266909 31266909 + Missense_Mutation SNP C C A C3N-02089_T C3N-02089_N C C c.64G>T p.Gly22Trp p.G22W ENST00000286827 5/29 101 71 30 89 89 0 strelka-mutect TIAM1,missense_variant,p.Gly22Trp,ENST00000286827,NM_003253.2;TIAM1,missense_variant,p.Gly22Trp,ENST00000541036,;TIAM1,missense_variant,p.Gly22Trp,ENST00000455508,;TIAM1,intron_variant,,ENST00000469412,; A ENST00000286827 Transcript missense_variant 536/7200 64/4776 22/1591 G/W Ggg/Tgg COSM1681930,COSM1681931 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 deleterious_low_confidence(0) 5/29 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 31266909 31266909 C A 1 0 0 0 0 1 0 0 0 16324 623 22 2 2 TIAM1 21 31266909 Missense_Mutation SNP C C3N-02089_T 2297395 31266909 15443074 1012 28096 PAXBP1 0 . GRCh38 21 32734960 32734960 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.2744A>C p.Glu915Ala p.E915A ENST00000331923 18/18 275 235 40 304 304 0 strelka-varscan-mutect PAXBP1,missense_variant,p.Glu915Ala,ENST00000331923,NM_016631.3;PAXBP1-AS1,intron_variant,,ENST00000440052,;PAXBP1-AS1,intron_variant,,ENST00000455170,;PAXBP1-AS1,downstream_gene_variant,,ENST00000458479,;PAXBP1,3_prime_UTR_variant,,ENST00000443785,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000466846,;PAXBP1,non_coding_transcript_exon_variant,,ENST00000497873,; G ENST00000331923 Transcript missense_variant 2934/3995 2744/2754 915/917 E/A gAa/gCa 1 -1 PAXBP1 HGNC HGNC:13579 protein_coding YES CCDS13619.1 ENSP00000328992 Q9Y5B6 UPI000012B294 NM_016631.3 deleterious(0.02) 18/18 hmmpanther:PTHR12214:SF2,hmmpanther:PTHR12214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 32734960 32734960 T G 1 0 0 0 0 1 0 0 0 11572 1783 62 5 5 PAXBP1 21 32734960 Missense_Mutation SNP T C3N-02089_T 1468051 32734960 13975023 1013 28097 OLIG1 0 . GRCh38 21 33070255 33070255 + Nonsense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.9T>A p.Tyr3Ter p.Y3* ENST00000382348 1/1 98 76 22 79 79 0 strelka-varscan-mutect OLIG1,stop_gained,p.Tyr3Ter,ENST00000382348,NM_138983.2;OLIG1,upstream_gene_variant,,ENST00000426947,;AP000282.2,intron_variant,,ENST00000454622,;OLIG1,upstream_gene_variant,,ENST00000498799,; A ENST00000382348 Transcript stop_gained 112/2277 9/816 3/271 Y/* taT/taA 1 1 OLIG1 HGNC HGNC:16983 protein_coding YES CCDS42920.2 ENSP00000371785 Q8TAK6 UPI0000130C80 NM_138983.2 1/1 HIGH SNV 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 33070255 33070255 T A 1 0 0 0 0 0 1 0 0 10935 1471 51 4 4 OLIG1 21 33070255 Nonsense_Mutation SNP T C3N-02089_T 335295 33070255 13639728 1014 28098 BRWD1 0 . GRCh38 21 39278752 39278752 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.994T>C p.Phe332Leu p.F332L ENST00000333229 10/42 78 60 18 100 100 0 strelka-varscan-mutect BRWD1,missense_variant,p.Phe332Leu,ENST00000342449,NM_033656.3;BRWD1,missense_variant,p.Phe332Leu,ENST00000333229,NM_018963.4;BRWD1,missense_variant,p.Phe332Leu,ENST00000380800,;BRWD1,missense_variant,p.Phe44Leu,ENST00000455867,;BRWD1,missense_variant,p.Phe44Leu,ENST00000412604,;BRWD1,missense_variant,p.Phe44Leu,ENST00000445245,;BRWD1,missense_variant,p.Phe44Leu,ENST00000430093,;BRWD1,missense_variant,p.Phe44Leu,ENST00000445668,;BRWD1,non_coding_transcript_exon_variant,,ENST00000496759,; G ENST00000333229 Transcript missense_variant 1322/10141 994/6963 332/2320 F/L Ttt/Ctt 1 -1 BRWD1 HGNC HGNC:12760 protein_coding YES CCDS13662.1 ENSP00000330753 Q9NSI6 UPI0000163C12 NM_018963.4 deleterious(0) 10/42 PROSITE_profiles:PS50294,hmmpanther:PTHR16266:SF26,hmmpanther:PTHR16266,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 39278752 39278752 A G 1 0 0 0 0 1 0 0 0 1699 14 1 5 5 BRWD1 21 39278752 Missense_Mutation SNP A C3N-02089_T 6208497 39278752 7431231 1015 28099 B3GALT5 0 . GRCh38 21 39661160 39661160 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.613A>G p.Ser205Gly p.S205G ENST00000398714 2/2 98 79 19 108 108 0 strelka-varscan-mutect B3GALT5,missense_variant,p.Ser201Gly,ENST00000380620,;B3GALT5,missense_variant,p.Ser201Gly,ENST00000380618,NM_006057.2,NM_033170.2,NM_033171.2;B3GALT5,missense_variant,p.Ser201Gly,ENST00000615480,NM_001278650.1;B3GALT5,missense_variant,p.Ser201Gly,ENST00000343118,;B3GALT5,missense_variant,p.Ser205Gly,ENST00000398714,NM_033172.2;AF064860.5,intron_variant,,ENST00000416555,; G ENST00000398714 Transcript missense_variant 613/2341 613/945 205/314 S/G Agt/Ggt 1 1 B3GALT5 HGNC HGNC:920 protein_coding YES CCDS74795.1 ENSP00000381699 A0A0A0MS93 UPI000354A018 NM_033172.2 deleterious(0.01) 2/2 hmmpanther:PTHR11214:SF18,hmmpanther:PTHR11214,Pfam_domain:PF01762 MODERATE SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 39661160 39661160 A G 1 0 0 0 0 1 0 0 0 1407 188 7 5 5 B3GALT5 21 39661160 Missense_Mutation SNP A C3N-02089_T 382408 39661160 7048823 1016 28100 DSCAM 0 . GRCh38 21 40013372 40013372 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.5701T>G p.Leu1901Val p.L1901V ENST00000400454 33/33 39 34 5 42 42 0 strelka-varscan-mutect DSCAM,missense_variant,p.Leu1901Val,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,missense_variant,p.Leu1736Val,ENST00000617870,;DSCAM,intron_variant,,ENST00000404019,; C ENST00000400454 Transcript missense_variant 6179/8552 5701/6039 1901/2012 L/V Ttg/Gtg 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 deleterious_low_confidence(0) 33/33 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -13.27361 1 1 1 1 0 C 3 2 90 40013372 40013372 A C 1 0 0 0 0 1 0 0 0 4589 11 1 5 5 DSCAM 21 40013372 Missense_Mutation SNP A C3N-02089_T 352212 40013372 6696611 1017 28101 POTEH 0 . GRCh38 22 15719721 15719721 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1582G>T p.Asp528Tyr p.D528Y ENST00000343518 10/11 33 25 8 37 37 0 varscan-mutect POTEH,missense_variant,p.Asp528Tyr,ENST00000343518,NM_001136213.1;POTEH,missense_variant,p.Asp491Tyr,ENST00000621704,;POTEH,3_prime_UTR_variant,,ENST00000452800,;LA16c-3G11.7,upstream_gene_variant,,ENST00000417657,; T ENST00000343518 Transcript missense_variant 1634/1928 1582/1638 528/545 D/Y Gat/Tat 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 deleterious_low_confidence(0) 10/11 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43 MODERATE 1 SNV 5 1 PASS . . 2 202 6 0 0 0 0 0 -19.94062 1 1 1 1 0 T 3 4 90 15719721 15719721 G T 1 0 0 0 0 1 0 0 0 12381 942 33 2 2 POTEH 22 15719721 Missense_Mutation SNP G C3N-02089_T 15719721 35098747 1018 28102 CECR1 0 . GRCh38 22 17191754 17191754 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.810G>A p.= p.Q270Q ENST00000399837 5/10 189 174 15 159 159 0 strelka-varscan-mutect CECR1,synonymous_variant,p.=,ENST00000399837,NM_001282226.1,NM_001282225.1;CECR1,synonymous_variant,p.=,ENST00000449907,NM_001282228.1,NM_001282227.1;CECR1,synonymous_variant,p.=,ENST00000610390,NM_001282229.1;CECR1,synonymous_variant,p.=,ENST00000399839,;CECR1,synonymous_variant,p.=,ENST00000262607,;CECR1,synonymous_variant,p.=,ENST00000330232,NM_177405.2;CECR1,non_coding_transcript_exon_variant,,ENST00000480276,;CECR1,upstream_gene_variant,,ENST00000469063,;AC005300.5,upstream_gene_variant,,ENST00000428401,; T ENST00000399837 Transcript synonymous_variant 1086/4505 810/1536 270/511 Q caG/caA 1 -1 CECR1 HGNC HGNC:1839 protein_coding YES CCDS13742.1 ENSP00000382731 Q9NZK5 UPI000013D2E8 NM_001282226.1,NM_001282225.1 5/10 hmmpanther:PTHR11409,hmmpanther:PTHR11409:SF39,Pfam_domain:PF00962,Gene3D:3.20.20.140,TIGRFAM_domain:TIGR01431,Superfamily_domains:SSF51556 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.55197 0.9999997 1 1 1 0 T 2 4 90 17191754 17191754 C T 1 0 0 0 0 0 0 0 1 2912 680 24 3 3 CECR1 22 17191754 Silent SNP C C3N-02089_T 1472033 17191754 33626714 1019 28103 MICAL3 0 . GRCh38 22 17818199 17818199 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.4462C>T p.Pro1488Ser p.P1488S ENST00000441493 26/32 127 99 28 107 106 1 strelka-varscan-mutect MICAL3,missense_variant,p.Pro1488Ser,ENST00000441493,NM_015241.2;MICAL3,upstream_gene_variant,,ENST00000577821,;MICAL3,downstream_gene_variant,,ENST00000498573,;MICAL3,downstream_gene_variant,,ENST00000578984,;MICAL3,upstream_gene_variant,,ENST00000579997,;MICAL3,upstream_gene_variant,,ENST00000580469,; A ENST00000441493 Transcript missense_variant 4815/9445 4462/6009 1488/2002 P/S Ccg/Tcg 1 -1 MICAL3 HGNC HGNC:24694 protein_coding YES CCDS46659.1 ENSP00000416015 Q7RTP6 UPI0001823FDE NM_015241.2 tolerated_low_confidence(0.08) 26/32 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF239 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 17818199 17818199 G A 1 0 0 0 0 1 0 0 0 9528 1203 42 3 3 MICAL3 22 17818199 Missense_Mutation SNP G C3N-02089_T 626445 17818199 33000269 1020 28104 CDC45 0 . GRCh38 22 19518882 19518882 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1771G>T p.Asp591Tyr p.D591Y ENST00000437685 19/20 358 285 73 262 261 1 strelka-varscan-mutect CDC45,missense_variant,p.Asp559Tyr,ENST00000407835,;CDC45,missense_variant,p.Asp591Tyr,ENST00000437685,NM_001178010.2;CDC45,missense_variant,p.Asp559Tyr,ENST00000263201,NM_003504.4;CDC45,missense_variant,p.Asp513Tyr,ENST00000404724,NM_001178011.2;CLDN5,downstream_gene_variant,,ENST00000406028,;CLDN5,downstream_gene_variant,,ENST00000403084,NM_001130861.1;CLDN5,downstream_gene_variant,,ENST00000413119,NM_003277.3;CLDN5,downstream_gene_variant,,ENST00000618236,;CDC45,non_coding_transcript_exon_variant,,ENST00000493724,;CDC45,downstream_gene_variant,,ENST00000471470,; T ENST00000437685 Transcript missense_variant 1914/2072 1771/1797 591/598 D/Y Gac/Tac 1 1 CDC45 HGNC HGNC:1739 protein_coding YES CCDS54499.1 ENSP00000405726 O75419 UPI000042153E NM_001178010.2 deleterious(0) 19/20 Pfam_domain:PF02724,hmmpanther:PTHR10507,hmmpanther:PTHR10507:SF0 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 19518882 19518882 G T 1 0 0 0 0 1 0 0 0 2784 1174 41 2 2 CDC45 22 19518882 Missense_Mutation SNP G C3N-02089_T 1700683 19518882 31299586 1021 28105 GGTLC2 0 . GRCh38 22 22647148 22647148 + Missense_Mutation SNP G G A novel C3N-02089_T C3N-02089_N G G c.368G>A p.Ser123Asn p.S123N ENST00000480559 4/5 525 412 113 452 452 0 strelka-varscan-mutect GGTLC2,missense_variant,p.Ser123Asn,ENST00000480559,NM_199127.2;GGTLC2,intron_variant,,ENST00000618722,NM_001282879.1;GGTLC2,intron_variant,,ENST00000613850,;GGTLC2,intron_variant,,ENST00000448514,;POM121L1P,upstream_gene_variant,,ENST00000402027,;GGTLC2,non_coding_transcript_exon_variant,,ENST00000417145,;POM121L1P,upstream_gene_variant,,ENST00000605258,; A ENST00000480559 Transcript missense_variant 368/657 368/657 123/218 S/N aGc/aAc 1 1 GGTLC2 HGNC HGNC:18596 protein_coding YES CCDS13802.2 ENSP00000419751 Q14390 UPI00004210AD NM_199127.2 tolerated(0.06) 4/5 hmmpanther:PTHR11686:SF28,hmmpanther:PTHR11686,Pfam_domain:PF01019,Superfamily_domains:SSF56235 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 22647148 22647148 G A 1 0 0 0 0 1 0 0 0 6243 971 34 3 3 GGTLC2 22 22647148 Missense_Mutation SNP G C3N-02089_T 3128266 22647148 28171320 1022 28106 IGLL1 0 . GRCh38 22 23575022 23575022 + Silent SNP G G C novel C3N-02089_T C3N-02089_N G G c.267C>G p.= p.S89S ENST00000330377 2/3 454 418 36 327 327 0 strelka-varscan-mutect IGLL1,synonymous_variant,p.=,ENST00000330377,NM_020070.3;IGLL1,synonymous_variant,p.=,ENST00000438703,;IGLL1,intron_variant,,ENST00000249053,NM_152855.2;AP000345.2,downstream_gene_variant,,ENST00000454863,;AP000345.2,downstream_gene_variant,,ENST00000458318,; C ENST00000330377 Transcript synonymous_variant 385/901 267/642 89/213 S tcC/tcG 1 -1 IGLL1 HGNC HGNC:5870 protein_coding YES CCDS13809.1 ENSP00000329312 P15814 UPI0000119C23 NM_020070.3 2/3 hmmpanther:PTHR23266,hmmpanther:PTHR23266:SF124 LOW 1 SNV 1 1 PASS rs1249165621 . 0 208 0 0 0 0 0 2 -14.1102 0 0 1 0 0 C 2 2 90 23575022 23575022 G C 1 0 0 0 0 0 0 0 1 7500 1335 47 4 4 IGLL1 22 23575022 Silent SNP G C3N-02089_T 927874 23575022 27243446 1023 28107 C22orf15 0 . GRCh38 22 23764139 23764139 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.78C>A p.= p.A26A ENST00000402217 2/6 276 223 53 261 261 0 strelka-varscan-mutect C22orf15,synonymous_variant,p.=,ENST00000402217,NM_182520.2;C22orf15,synonymous_variant,p.=,ENST00000305199,;C22orf15,synonymous_variant,p.=,ENST00000382821,;CHCHD10,downstream_gene_variant,,ENST00000484558,NM_213720.2;CHCHD10,downstream_gene_variant,,ENST00000401675,NM_001301339.1;CHCHD10,downstream_gene_variant,,ENST00000520222,;MMP11,upstream_gene_variant,,ENST00000477567,;MMP11,upstream_gene_variant,,ENST00000489582,;C22orf15,non_coding_transcript_exon_variant,,ENST00000477921,;C22orf15,non_coding_transcript_exon_variant,,ENST00000498542,;MMP11,upstream_gene_variant,,ENST00000465385,;CHCHD10,downstream_gene_variant,,ENST00000517886,;CHCHD10,downstream_gene_variant,,ENST00000523865,; A ENST00000402217 Transcript synonymous_variant 331/829 78/447 26/148 A gcC/gcA 1 1 C22orf15 HGNC HGNC:15558 protein_coding YES CCDS13814.2 ENSP00000384965 Q8WYQ4 UPI0000072091 NM_182520.2 2/6 Pfam_domain:PF15874,hmmpanther:PTHR33887,hmmpanther:PTHR33887:SF1 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 23764139 23764139 C A 1 0 0 0 0 0 0 0 1 2017 610 22 2 2 C22orf15 22 23764139 Silent SNP C C3N-02089_T 189117 23764139 27054329 1024 28108 PIWIL3 0 . GRCh38 22 24756517 24756517 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.544T>G p.Leu182Val p.L182V ENST00000332271 5/21 221 196 25 194 194 0 strelka-varscan-mutect PIWIL3,missense_variant,p.Leu182Val,ENST00000332271,NM_001255975.1,NM_001008496.3;PIWIL3,missense_variant,p.Leu73Val,ENST00000533313,;PIWIL3,missense_variant,p.Leu182Val,ENST00000616349,;PIWIL3,missense_variant,p.Leu73Val,ENST00000527701,;PIWIL3,non_coding_transcript_exon_variant,,ENST00000532537,; C ENST00000332271 Transcript missense_variant 961/3504 544/2649 182/882 L/V Tta/Gta 1 -1 PIWIL3 HGNC HGNC:18443 protein_coding YES CCDS33623.1 ENSP00000330031 Q7Z3Z3 UPI00002073D6 NM_001255975.1,NM_001008496.3 deleterious(0.01) 5/21 hmmpanther:PTHR22891,hmmpanther:PTHR22891:SF41,Superfamily_domains:SSF101690 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 24756517 24756517 A C 1 0 0 0 0 1 0 0 0 12055 98 4 5 5 PIWIL3 22 24756517 Missense_Mutation SNP A C3N-02089_T 992378 24756517 26061951 1025 28109 MYO18B 0 . GRCh38 22 25992395 25992395 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.6189G>T p.Arg2063Ser p.R2063S ENST00000335473 40/44 192 154 38 143 143 0 strelka-varscan-mutect MYO18B,missense_variant,p.Arg2063Ser,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Arg2064Ser,ENST00000407587,;MYO18B,missense_variant,p.Arg2063Ser,ENST00000536101,;MYO18B,missense_variant,p.Arg28Ser,ENST00000543971,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript missense_variant 6439/8565 6189/7704 2063/2567 R/S agG/agT 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0.01) 40/44 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 25992395 25992395 G T 1 0 0 0 0 1 0 0 0 10067 1194 42 2 2 MYO18B 22 25992395 Missense_Mutation SNP G C3N-02089_T 1235878 25992395 24826073 1026 28110 SEZ6L 0 . GRCh38 22 26292738 26292738 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.427C>A p.Gln143Lys p.Q143K ENST00000248933 2/17 340 262 78 249 249 0 strelka-varscan-mutect SEZ6L,missense_variant,p.Gln143Lys,ENST00000529632,NM_001184775.1;SEZ6L,missense_variant,p.Gln143Lys,ENST00000360929,NM_001184776.1;SEZ6L,missense_variant,p.Gln143Lys,ENST00000404234,NM_001184773.1;SEZ6L,missense_variant,p.Gln143Lys,ENST00000248933,NM_021115.4;SEZ6L,missense_variant,p.Gln143Lys,ENST00000629590,NM_001184774.1;SEZ6L,missense_variant,p.Gln143Lys,ENST00000343706,NM_001184777.1;SEZ6L,5_prime_UTR_variant,,ENST00000402979,;SEZ6L,5_prime_UTR_variant,,ENST00000403121,; A ENST00000248933 Transcript missense_variant 522/3248 427/3075 143/1024 Q/K Caa/Aaa 1 1 SEZ6L HGNC HGNC:10763 protein_coding YES CCDS13833.1 ENSP00000248933 Q9BYH1 UPI0000136779 NM_021115.4 tolerated_low_confidence(0.09) 2/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 26292738 26292738 C A 1 0 0 0 0 1 0 0 0 14422 595 21 2 2 SEZ6L 22 26292738 Missense_Mutation SNP C C3N-02089_T 300343 26292738 24525730 1027 28111 AP1B1 0 . GRCh38 22 29356599 29356599 + Silent SNP C C A novel C3N-02089_T C3N-02089_N C C c.543G>T p.= p.V181V ENST00000357586 6/23 82 66 16 66 66 0 strelka-varscan-mutect AP1B1,synonymous_variant,p.=,ENST00000357586,NM_001127.3;AP1B1,synonymous_variant,p.=,ENST00000432560,NM_145730.2;AP1B1,synonymous_variant,p.=,ENST00000317368,NM_001166019.1;AP1B1,synonymous_variant,p.=,ENST00000405198,;AP1B1,synonymous_variant,p.=,ENST00000402502,;AP1B1,synonymous_variant,p.=,ENST00000415447,;AP1B1,synonymous_variant,p.=,ENST00000421126,;AP1B1,upstream_gene_variant,,ENST00000415756,;AP1B1,downstream_gene_variant,,ENST00000473606,; A ENST00000357586 Transcript synonymous_variant 730/4176 543/2850 181/949 V gtG/gtT 1 -1 AP1B1 HGNC HGNC:554 protein_coding YES CCDS13855.1 ENSP00000350199 Q10567 UPI0000124FE1 NM_001127.3 6/23 Gene3D:1.25.10.10,Pfam_domain:PF01602,PIRSF_domain:PIRSF002291,hmmpanther:PTHR11134,hmmpanther:PTHR11134:SF12,SMART_domains:SM00185,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 29356599 29356599 C A 1 0 0 0 0 0 0 0 1 847 581 21 2 2 AP1B1 22 29356599 Silent SNP C C3N-02089_T 3063861 29356599 21461869 1028 28112 CSF2RB 0 . GRCh38 22 36937979 36937979 + Missense_Mutation SNP G G T rs369609939 C3N-02089_T C3N-02089_N G G c.2171G>T p.Gly724Val p.G724V ENST00000403662 14/14 572 424 148 505 502 3 strelka-varscan-mutect CSF2RB,missense_variant,p.Gly724Val,ENST00000403662,NM_000395.2;CSF2RB,missense_variant,p.Gly724Val,ENST00000262825,;CSF2RB,missense_variant,p.Gly730Val,ENST00000406230,; T ENST00000403662 Transcript missense_variant 2393/4863 2171/2694 724/897 G/V gGg/gTg rs369609939,COSM3554031 1 1 CSF2RB HGNC HGNC:2436 protein_coding YES CCDS13936.1 ENSP00000384053 P32927 UPI0000128C9F NM_000395.2 deleterious(0.04) 14/14 Low_complexity_(Seg):seg,hmmpanther:PTHR23037,hmmpanther:PTHR23037:SF22,PIRSF_domain:PIRSF001956 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs369609939 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 36937979 36937979 G T 1 0 0 0 0 1 0 0 0 3736 1232 43 2 2 CSF2RB 22 36937979 Missense_Mutation SNP G C3N-02089_T 7581380 36937979 13880489 1029 28113 C1QTNF6 0 . GRCh38 22 37182576 37182576 + Missense_Mutation SNP C C G rs755754179 C3N-02089_T C3N-02089_N C C c.449G>C p.Arg150Pro p.R150P ENST00000337843 3/3 236 158 78 236 236 0 strelka-varscan-mutect C1QTNF6,missense_variant,p.Arg150Pro,ENST00000337843,NM_031910.3;C1QTNF6,missense_variant,p.Arg150Pro,ENST00000397110,NM_182486.1;C1QTNF6,3_prime_UTR_variant,,ENST00000434784,;RP1-151B14.6,non_coding_transcript_exon_variant,,ENST00000419128,;C1QTNF6,non_coding_transcript_exon_variant,,ENST00000470655,;C1QTNF6,non_coding_transcript_exon_variant,,ENST00000493023,; G ENST00000337843 Transcript missense_variant 525/2934 449/837 150/278 R/P cGc/cCc rs755754179 1 -1 C1QTNF6 HGNC HGNC:14343 protein_coding YES CCDS13943.1 ENSP00000338812 Q9BXI9 A0A024R1J0 UPI0000035BB4 NM_031910.3 deleterious(0) 3/3 PROSITE_profiles:PS50871,hmmpanther:PTHR22923,hmmpanther:PTHR22923:SF54,Gene3D:2.60.120.40,Pfam_domain:PF00386,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS rs755754179 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 37182576 37182576 C G 1 0 0 0 0 1 0 0 0 1945 768 27 4 4 C1QTNF6 22 37182576 Missense_Mutation SNP C C3N-02089_T 244597 37182576 13635892 1030 28114 ELFN2 0 . GRCh38 22 37373782 37373782 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1753G>T p.Ala585Ser p.A585S ENST00000402918 3/3 80 59 21 107 105 2 strelka-varscan-mutect ELFN2,missense_variant,p.Ala585Ser,ENST00000402918,NM_052906.4;ELFN2,missense_variant,p.Ala585Ser,ENST00000613079,;ELFN2,intron_variant,,ENST00000430883,;ELFN2,intron_variant,,ENST00000452946,;RP1-63G5.8,downstream_gene_variant,,ENST00000609322,;ELFN2,downstream_gene_variant,,ENST00000435824,;ELFN2,downstream_gene_variant,,ENST00000415408,;ELFN2,downstream_gene_variant,,ENST00000414347,;ELFN2,downstream_gene_variant,,ENST00000451509,;ELFN2,downstream_gene_variant,,ENST00000424973,; A ENST00000402918 Transcript missense_variant 2539/8361 1753/2463 585/820 A/S Gct/Tct 1 -1 ELFN2 HGNC HGNC:29396 protein_coding YES CCDS33642.1 ENSP00000385277 Q5R3F8 UPI000004E87D NM_052906.4 tolerated(1) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR24367:SF248,hmmpanther:PTHR24367 MODERATE SNV 4 1 PASS . . 0 197 13 0 0 0 0 0 -20 0.9999473 1 1 1 0 A 3 1 90 37373782 37373782 C A 1 0 0 0 0 1 0 0 0 4892 710 25 2 2 ELFN2 22 37373782 Missense_Mutation SNP C C3N-02089_T 191206 37373782 13444686 1031 28115 GCAT 0 . GRCh38 22 37809972 37809972 + Missense_Mutation SNP G G T rs759363791 C3N-02089_T C3N-02089_N G G c.220G>T p.Gly74Cys p.G74C ENST00000323205 2/10 222 149 73 183 183 0 strelka-varscan-mutect GCAT,missense_variant,p.Gly74Cys,ENST00000323205,NM_001171690.1;GCAT,missense_variant,p.Gly74Cys,ENST00000445195,;GCAT,intron_variant,,ENST00000248924,NM_014291.3;GCAT,intron_variant,,ENST00000451984,;H1F0,downstream_gene_variant,,ENST00000340857,NM_005318.3;GCAT,intron_variant,,ENST00000415371,;GCAT,intron_variant,,ENST00000426858,;GCAT,intron_variant,,ENST00000478203,; T ENST00000323205 Transcript missense_variant 283/1656 220/1338 74/445 G/C Ggc/Tgc rs759363791 1 1 GCAT HGNC HGNC:4188 protein_coding YES CCDS54527.1 ENSP00000371110 O75600 UPI000020770F NM_001171690.1 tolerated_low_confidence(0.11) 2/10 HAMAP:MF_00985 MODERATE 1 SNV 2 1 PASS rs759363791 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 37809972 37809972 G T 1 0 0 0 0 1 0 0 0 6154 1000 35 2 2 GCAT 22 37809972 Missense_Mutation SNP G C3N-02089_T 436190 37809972 13008496 1032 28116 CHADL 0 . GRCh38 22 41238427 41238429 + In_Frame_Del DEL GTG GTG - novel C3N-02089_T C3N-02089_N GTG GTG c.643_645delCAC p.His215del p.H215del ENST00000216241 3/6 52 38 14 72 72 0 sindel-varindel-pindel CHADL,inframe_deletion,p.His215del,ENST00000216241,NM_138481.1;CHADL,inframe_deletion,p.His213del,ENST00000417999,;CHADL,intron_variant,,ENST00000455425,; - ENST00000216241 Transcript inframe_deletion 696-698/2533 643-645/2289 215/762 H/- CAC/- 1 -1 CHADL HGNC HGNC:25165 protein_coding YES CCDS46715.1 ENSP00000216241 Q6NUI6 UPI00001C2057 NM_138481.1 3/6 PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF24,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 MODERATE 1 deletion 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 90 41238427 41238427 GTG - 1 0 1 0 1 0 0 0 0 3069 1368 48 0 0 CHADL 22 41238427 In_Frame_Del DEL GTG C3N-02089_T 3428455 41238427 9580041 1033 28117 SMC1B 0 . GRCh38 22 45362961 45362961 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.2486A>G p.Lys829Arg p.K829R ENST00000357450 16/25 167 106 61 184 184 0 strelka-varscan-mutect SMC1B,missense_variant,p.Lys829Arg,ENST00000357450,NM_148674.4;SMC1B,missense_variant,p.Lys829Arg,ENST00000404354,NM_001291501.1; C ENST00000357450 Transcript missense_variant 2486/4201 2486/3708 829/1235 K/R aAg/aGg 1 -1 SMC1B HGNC HGNC:11112 protein_coding YES CCDS43027.1 ENSP00000350036 Q8NDV3 UPI0004438059 NM_148674.4 tolerated(0.21) 16/25 Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF147,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 45362961 45362961 T C 1 0 0 0 0 1 0 0 0 15075 1609 56 5 5 SMC1B 22 45362961 Missense_Mutation SNP T C3N-02089_T 4124534 45362961 5455507 1034 28118 FBLN1 0 . GRCh38 22 45563182 45563182 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.2082G>T p.= p.L694L ENST00000402984 16/16 98 92 6 152 152 0 strelka-varscan-mutect FBLN1,synonymous_variant,p.=,ENST00000402984,;FBLN1,synonymous_variant,p.=,ENST00000262722,NM_001996.3;FBLN1,intron_variant,,ENST00000327858,NM_006486.2;FBLN1,intron_variant,,ENST00000442170,NM_006485.3;FBLN1,downstream_gene_variant,,ENST00000340923,NM_006487.2; T ENST00000402984 Transcript synonymous_variant 2185/2355 2082/2166 694/721 L ctG/ctT 1 1 FBLN1 HGNC HGNC:3600 protein_coding ENSP00000385521 B1AHL2 UPI000165DBD3 16/16 PIRSF_domain:PIRSF036313,hmmpanther:PTHR24044,hmmpanther:PTHR24044:SF303 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 45563182 45563182 G T 1 0 0 0 0 0 0 0 1 5561 1277 45 2 2 FBLN1 22 45563182 Silent SNP G C3N-02089_T 200221 45563182 5255286 1035 28119 MLC1 0 . GRCh38 22 50076864 50076864 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.574G>T p.Ala192Ser p.A192S ENST00000311597 7/12 422 298 124 462 458 4 strelka-varscan-mutect MLC1,missense_variant,p.Ala192Ser,ENST00000311597,NM_015166.3;MLC1,missense_variant,p.Ala192Ser,ENST00000395876,NM_139202.2;MLC1,missense_variant,p.Ala162Ser,ENST00000442311,;MLC1,upstream_gene_variant,,ENST00000483836,;MLC1,upstream_gene_variant,,ENST00000470008,; A ENST00000311597 Transcript missense_variant 1181/3933 574/1134 192/377 A/S Gct/Tct 1 -1 MLC1 HGNC HGNC:17082 protein_coding YES CCDS14083.1 ENSP00000310375 Q15049 A0A024R4V4 UPI000004AD09 NM_015166.3 tolerated_low_confidence(0.18) 7/12 PD492528,hmmpanther:PTHR17597 MODERATE 1 SNV 1 1 PASS rs1320745505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 50076864 50076864 C A 1 0 0 0 0 1 0 0 0 9580 710 25 2 2 MLC1 22 50076864 Missense_Mutation SNP C C3N-02089_T 4513682 50076864 741604 1036 28120 SHANK3 0 . GRCh38 22 50720870 50720870 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.3034G>T p.Gly1012Cys p.G1012C ENST00000262795 24/25 42 29 13 28 28 0 strelka-varscan-mutect SHANK3,missense_variant,p.Gly1012Cys,ENST00000262795,;SHANK3,missense_variant,p.Gly1006Cys,ENST00000445220,NM_033517.1;SHANK3,non_coding_transcript_exon_variant,,ENST00000414786,; T ENST00000262795 Transcript missense_variant 3034/7091 3034/5193 1012/1730 G/C Ggc/Tgc 1 1 SHANK3 HGNC HGNC:14294 protein_coding YES ENSP00000489147 A0A0U1RQS4 UPI00071AFB18 tolerated(0.18) 24/25 Low_complexity_(Seg):seg,hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 50720870 50720870 G T 1 0 0 0 0 1 0 0 0 14525 1232 43 2 2 SHANK3 22 50720870 Missense_Mutation SNP G C3N-02089_T 644006 50720870 97598 1037 28121 PPP2R3B 0 . GRCh38 X 338613 338613 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.1568G>C p.Trp523Ser p.W523S ENST00000390665 12/13 254 178 76 199 199 0 strelka-varscan-mutect PPP2R3B,missense_variant,p.Trp523Ser,ENST00000390665,NM_013239.4;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000477110,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000479438,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000468169,;PPP2R3B,downstream_gene_variant,,ENST00000484364,;PPP2R3B,downstream_gene_variant,,ENST00000477636,; G ENST00000390665 Transcript missense_variant 1587/2151 1568/1728 523/575 W/S tGg/tCg 1 -1 PPP2R3B HGNC HGNC:13417 protein_coding YES CCDS14104.1 ENSP00000375080 Q9Y5P8 UPI00001BB8B8 NM_013239.4 tolerated(0.07) 12/13 hmmpanther:PTHR14095:SF1,hmmpanther:PTHR14095 MODERATE 1 SNV 1 1 PASS rs1409249215 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 338613 338613 C G 1 0 0 0 0 1 0 0 0 12512 595 21 4 4 PPP2R3B 23 338613 Missense_Mutation SNP C C3N-02089_T 338613 155702282 1038 28122 MXRA5 0 . GRCh38 X 3310703 3310703 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.7500C>A p.Asn2500Lys p.N2500K ENST00000217939 7/7 122 73 49 137 135 2 strelka-varscan-mutect MXRA5,missense_variant,p.Asn2500Lys,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript missense_variant 7655/9793 7500/8487 2500/2828 N/K aaC/aaA 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 deleterious(0) 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS rs1301527419 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 3310703 3310703 G T 1 0 0 0 0 1 0 0 0 10002 1136 40 1 1 MXRA5 23 3310703 Missense_Mutation SNP G C3N-02089_T 2972090 3310703 152730192 1039 28123 MXRA5 0 . GRCh38 X 3311192 3311192 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.7011C>A p.= p.V2337V ENST00000217939 7/7 172 133 39 185 185 0 strelka-varscan-mutect MXRA5,synonymous_variant,p.=,ENST00000217939,NM_015419.3; T ENST00000217939 Transcript synonymous_variant 7166/9793 7011/8487 2337/2828 V gtC/gtA 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 7/7 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 3311192 3311192 G T 1 0 0 0 0 0 0 0 1 10002 1277 45 2 2 MXRA5 23 3311192 Silent SNP G C3N-02089_T 489 3311192 152729703 1040 28124 MXRA5 0 . GRCh38 X 3323227 3323227 + Missense_Mutation SNP G G C C3N-02089_T C3N-02089_N G G c.2458C>G p.Pro820Ala p.P820A ENST00000217939 5/7 135 93 42 132 132 0 strelka-varscan-mutect MXRA5,missense_variant,p.Pro820Ala,ENST00000217939,NM_015419.3; C ENST00000217939 Transcript missense_variant 2613/9793 2458/8487 820/2828 P/A Cct/Gct COSM4947043,COSM75496 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 tolerated(0.45) 5/7 Low_complexity_(Seg):seg,hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 3323227 3323227 G C 1 0 0 0 0 1 0 0 0 10002 1261 44 4 4 MXRA5 23 3323227 Missense_Mutation SNP G C3N-02089_T 12035 3323227 152717668 1041 28125 MXRA5 0 . GRCh38 X 3324314 3324314 + Silent SNP G G A C3N-02089_T C3N-02089_N G G c.1371C>T p.= p.T457T ENST00000217939 5/7 114 84 30 132 132 0 strelka-varscan-mutect MXRA5,synonymous_variant,p.=,ENST00000217939,NM_015419.3; A ENST00000217939 Transcript synonymous_variant 1526/9793 1371/8487 457/2828 T acC/acT COSM2156773,COSM2156774 1 -1 MXRA5 HGNC HGNC:7539 protein_coding YES CCDS14124.1 ENSP00000217939 Q9NR99 UPI000013C73B NM_015419.3 5/7 hmmpanther:PTHR10489:SF680,hmmpanther:PTHR10489 1,1 LOW 1 SNV 5 1,1 1 PASS rs1201600302 . 0 206 0 4 0 0 0 0 -20 0.9999725 1 1 1 0 A 2 1 90 3324314 3324314 G A 1 0 0 0 0 0 0 0 1 10002 1219 43 3 3 MXRA5 23 3324314 Silent SNP G C3N-02089_T 1087 3324314 152716581 1042 28126 SHROOM2 0 . GRCh38 X 9895685 9895685 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.1777G>C p.Glu593Gln p.E593Q ENST00000380913 4/10 84 57 27 84 84 0 strelka-varscan-mutect SHROOM2,missense_variant,p.Glu593Gln,ENST00000380913,NM_001649.2;SHROOM2,upstream_gene_variant,,ENST00000493668,; C ENST00000380913 Transcript missense_variant 1867/7447 1777/4851 593/1616 E/Q Gag/Cag 1 1 SHROOM2 HGNC HGNC:630 protein_coding YES CCDS14135.1 ENSP00000370299 Q13796 UPI0000125D05 NM_001649.2 deleterious(0) 4/10 hmmpanther:PTHR15012:SF8,hmmpanther:PTHR15012 MODERATE 1 SNV 1 1 PASS rs1284409692 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 9895685 9895685 G C 1 0 0 0 0 1 0 0 0 14557 1175 41 4 4 SHROOM2 23 9895685 Missense_Mutation SNP G C3N-02089_T 6571371 9895685 146145210 1043 28127 FANCB 0 . GRCh38 X 14864633 14864633 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.878G>T p.Gly293Val p.G293V ENST00000398334 3/10 139 105 34 142 142 0 strelka-varscan-mutect FANCB,missense_variant,p.Gly293Val,ENST00000398334,NM_001324162.1,NM_001018113.1;FANCB,missense_variant,p.Gly293Val,ENST00000324138,NM_152633.2;FANCB,missense_variant,p.Gly293Val,ENST00000452869,;FANCB,downstream_gene_variant,,ENST00000489126,; A ENST00000398334 Transcript missense_variant 1146/3008 878/2580 293/859 G/V gGt/gTt 1 -1 FANCB HGNC HGNC:3583 protein_coding YES CCDS14161.1 ENSP00000381378 Q8NB91 A0A024RBW1 UPI000006E70A NM_001324162.1,NM_001018113.1 tolerated(0.06) 3/10 hmmpanther:PTHR28450 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 14864633 14864633 C A 1 0 0 0 0 1 0 0 0 5522 507 18 2 2 FANCB 23 14864633 Missense_Mutation SNP C C3N-02089_T 4968948 14864633 141176262 1044 28128 NHS 0 . GRCh38 X 17726495 17726495 + Missense_Mutation SNP A A C novel C3N-02089_T C3N-02089_N A A c.2326A>C p.Asn776His p.N776H ENST00000380060 6/8 103 72 31 120 120 0 strelka-varscan-mutect NHS,missense_variant,p.Asn617His,ENST00000615422,;NHS,missense_variant,p.Asn776His,ENST00000380060,NM_198270.3,NM_001291867.1;NHS,missense_variant,p.Asn620His,ENST00000398097,NM_001136024.3;NHS,missense_variant,p.Asn593His,ENST00000617601,NM_001291868.1;NHS,downstream_gene_variant,,ENST00000485305,; C ENST00000380060 Transcript missense_variant 2664/8761 2326/4893 776/1630 N/H Aat/Cat 1 1 NHS HGNC HGNC:7820 protein_coding YES CCDS14181.1 ENSP00000369400 Q6T4R5 UPI00001DFBF3 NM_198270.3,NM_001291867.1 tolerated(0.07) 6/8 Pfam_domain:PF15273,hmmpanther:PTHR23039,hmmpanther:PTHR23039:SF5 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 17726495 17726495 A C 1 0 0 0 0 1 0 0 0 10443 362 13 5 5 NHS 23 17726495 Missense_Mutation SNP A C3N-02089_T 2861862 17726495 138314400 1045 28129 MAGEB6 0 . GRCh38 X 26194464 26194464 + Silent SNP G G T rs774344871 C3N-02089_T C3N-02089_N G G c.618G>T p.= p.L206L ENST00000379034 2/2 71 58 13 104 104 0 strelka-varscan-mutect MAGEB6,synonymous_variant,p.=,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript synonymous_variant 767/1949 618/1224 206/407 L ctG/ctT rs774344871 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 2/2 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF80,hmmpanther:PTHR11736,SMART_domains:SM01373 LOW 1 SNV 1 1 PASS rs774344871 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 26194464 26194464 G T 1 0 0 0 0 0 0 0 1 9096 1306 46 2 2 MAGEB6 23 26194464 Silent SNP G C3N-02089_T 8467969 26194464 129846431 1046 28130 IL1RAPL1 0 . GRCh38 X 29283170 29283170 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.315C>A p.Phe105Leu p.F105L ENST00000378993 3/11 90 63 27 93 92 1 strelka-varscan-mutect IL1RAPL1,missense_variant,p.Phe105Leu,ENST00000378993,NM_014271.3; A ENST00000378993 Transcript missense_variant 988/3667 315/2091 105/696 F/L ttC/ttA 1 1 IL1RAPL1 HGNC HGNC:5996 protein_coding YES CCDS14218.1 ENSP00000368278 Q9NZN1 X5DNQ7 UPI000006D1BF NM_014271.3 deleterious(0) 3/11 PROSITE_profiles:PS50835,hmmpanther:PTHR11890:SF22,hmmpanther:PTHR11890,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1186311560 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 29283170 29283170 C A 1 0 0 0 0 1 0 0 0 7564 854 30 2 2 IL1RAPL1 23 29283170 Missense_Mutation SNP C C3N-02089_T 3088706 29283170 126757725 1047 28131 DDX3X 0 . GRCh38 X 41347415 41347415 + Nonsense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1873G>T p.Gly625Ter p.G625* ENST00000399959 16/17 54 38 16 62 61 1 strelka-varscan-mutect DDX3X,stop_gained,p.Gly625Ter,ENST00000399959,NM_001356.4,NM_001193416.2;DDX3X,stop_gained,p.Gly609Ter,ENST00000457138,NM_001193417.2;DDX3X,stop_gained,p.Gly625Ter,ENST00000629496,;DDX3X,stop_gained,p.Gly625Ter,ENST00000625837,;DDX3X,stop_gained,p.Gly625Ter,ENST00000626301,;DDX3X,stop_gained,p.Gly106Ter,ENST00000611968,;DDX3X,intron_variant,,ENST00000441189,;DDX3X,downstream_gene_variant,,ENST00000631641,;RN7SL15P,upstream_gene_variant,,ENST00000582825,;DDX3X,downstream_gene_variant,,ENST00000542215,;DDX3X,downstream_gene_variant,,ENST00000615313,;DDX3X,downstream_gene_variant,,ENST00000611546,;DDX3X,downstream_gene_variant,,ENST00000622198,;DDX3X,stop_gained,p.Gly625Ter,ENST00000629785,;DDX3X,stop_gained,p.Gly625Ter,ENST00000478993,;DDX3X,stop_gained,p.Gly625Ter,ENST00000630255,;DDX3X,stop_gained,p.Gly625Ter,ENST00000630858,;DDX3X,stop_gained,p.Gly625Ter,ENST00000630370,;DDX3X,stop_gained,p.Gly142Ter,ENST00000616050,;DDX3X,downstream_gene_variant,,ENST00000615742,; T ENST00000399959 Transcript stop_gained 2728/5399 1873/1989 625/662 G/* Gga/Tga 1 1 DDX3X HGNC HGNC:2745 protein_coding YES CCDS43931.1 ENSP00000382840 O00571 UPI000013CB6D NM_001356.4,NM_001193416.2 16/17 Low_complexity_(Seg):seg,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF332 HIGH 1 SNV 1 1 PASS rs1200557241 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 90 41347415 41347415 G T 1 0 0 0 0 0 1 0 0 4161 1117 39 1 1 DDX3X 23 41347415 Nonsense_Mutation SNP G C3N-02089_T 12064245 41347415 114693480 1048 28132 CXorf36 0 . GRCh38 X 45200818 45200818 + Silent SNP G G T novel C3N-02089_T C3N-02089_N G G c.9C>A p.= p.P3P ENST00000398000 1/5 66 45 21 88 88 0 strelka-varscan-mutect CXorf36,synonymous_variant,p.=,ENST00000398000,NM_176819.3;CXorf36,synonymous_variant,p.=,ENST00000377934,NM_024689.2;RP11-342D14.1,intron_variant,,ENST00000450527,;RP11-342D14.1,intron_variant,,ENST00000438181,; T ENST00000398000 Transcript synonymous_variant 84/4655 9/1302 3/433 P ccC/ccA 1 -1 CXorf36 HGNC HGNC:25866 protein_coding YES CCDS48096.1 ENSP00000381086 Q9H7Y0 UPI000059DAFE NM_176819.3 1/5 PD307452,hmmpanther:PTHR32073,hmmpanther:PTHR32073:SF8,Cleavage_site_(Signalp):SignalP-noTM LOW 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 45200818 45200818 G T 1 0 0 0 0 0 0 0 1 3912 1219 43 2 2 CXorf36 23 45200818 Silent SNP G C3N-02089_T 3853403 45200818 110840077 1049 28133 ELK1 0 . GRCh38 X 47641256 47641256 + Silent SNP C C T novel C3N-02089_T C3N-02089_N C C c.186G>A p.= p.R62R ENST00000247161 2/6 116 80 36 124 124 0 strelka-varscan-mutect ELK1,synonymous_variant,p.=,ENST00000247161,NM_005229.4;ELK1,synonymous_variant,p.=,ENST00000376983,NM_001114123.2;ELK1,synonymous_variant,p.=,ENST00000343894,NM_001257168.1; T ENST00000247161 Transcript synonymous_variant 286/2695 186/1287 62/428 R cgG/cgA 1 -1 ELK1 HGNC HGNC:3321 protein_coding YES CCDS14283.1 ENSP00000247161 P19419 A0A024R1A7 UPI0000129E66 NM_005229.4 2/6 PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF178,PROSITE_patterns:PS00346,Gene3D:1.10.10.10,Pfam_domain:PF00178,SMART_domains:SM00413,Superfamily_domains:SSF46785,Prints_domain:PR00454 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 90 47641256 47641256 C T 1 0 0 0 0 0 0 0 1 4893 610 22 3 3 ELK1 23 47641256 Silent SNP C C3N-02089_T 2440438 47641256 108399639 1050 28134 ZNF81 0 . GRCh38 X 47914926 47914926 + Missense_Mutation SNP G G T C3N-02089_T C3N-02089_N G G c.280G>T p.Gly94Trp p.G94W ENST00000376954 6/6 75 55 20 92 92 0 strelka-varscan-mutect ZNF81,missense_variant,p.Gly94Trp,ENST00000376954,;ZNF81,missense_variant,p.Gly94Trp,ENST00000338637,NM_007137.3;ZNF81,intron_variant,,ENST00000376950,; T ENST00000376954 Transcript missense_variant,splice_region_variant 648/7933 280/1986 94/661 G/W Ggg/Tgg COSM3561859,COSM3561860 1 1 ZNF81 HGNC HGNC:13156 protein_coding YES CCDS43933.1 ENSP00000366153 P51508 UPI000023FCDA deleterious(0.02) 6/6 hmmpanther:PTHR24377:SF5,hmmpanther:PTHR24377 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 47914926 47914926 G T 1 0 0 0 0 1 0 0 0 18759 1362 47 2 2 ZNF81 23 47914926 Missense_Mutation SNP G C3N-02089_T 273670 47914926 108125969 1051 28135 CACNA1F 0 . GRCh38 X 49218542 49218542 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.2874C>G p.His958Gln p.H958Q ENST00000376265 24/48 108 74 34 144 144 0 strelka-varscan-mutect CACNA1F,missense_variant,p.His958Gln,ENST00000376265,NM_005183.3;CACNA1F,missense_variant,p.His947Gln,ENST00000323022,NM_001256789.2;CACNA1F,missense_variant,p.His893Gln,ENST00000376251,NM_001256790.2;CACNA1F,downstream_gene_variant,,ENST00000480889,; C ENST00000376265 Transcript missense_variant,splice_region_variant 2936/6070 2874/5934 958/1977 H/Q caC/caG 1 -1 CACNA1F HGNC HGNC:1393 protein_coding YES CCDS35253.1 ENSP00000365441 O60840 UPI0000072854 NM_005183.3 tolerated(1) 24/48 hmmpanther:PTHR10037:SF184,hmmpanther:PTHR10037,Gene3D:1.20.120.350,Pfam_domain:PF00520,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 49218542 49218542 G C 1 0 0 0 0 1 0 0 0 2231 985 34 4 4 CACNA1F 23 49218542 Missense_Mutation SNP G C3N-02089_T 1303616 49218542 106822353 1052 28136 KDM5C 0 . GRCh38 X 53196852 53196852 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.2815G>T p.Ala939Ser p.A939S ENST00000375401 19/26 127 87 40 148 148 0 strelka-varscan-mutect KDM5C,missense_variant,p.Ala872Ser,ENST00000452825,NM_001146702.1;KDM5C,missense_variant,p.Ala939Ser,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Ala938Ser,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Ala939Ser,ENST00000375379,;KDM5C,missense_variant,p.Ala898Ser,ENST00000375383,;MIR6895,upstream_gene_variant,,ENST00000613497,;MIR6894,downstream_gene_variant,,ENST00000622662,;KDM5C,downstream_gene_variant,,ENST00000465402,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000481369,; A ENST00000375401 Transcript missense_variant 3348/6031 2815/4683 939/1560 A/S Gcc/Tcc 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 tolerated(0.44) 19/26 Pfam_domain:PF08429,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 53196852 53196852 C A 1 0 0 0 0 1 0 0 0 8053 739 26 2 2 KDM5C 23 53196852 Missense_Mutation SNP C C3N-02089_T 3978310 53196852 102844043 1053 28137 SPIN4 0 . GRCh38 X 63350246 63350246 + Nonsense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.574G>T p.Glu192Ter p.E192* ENST00000374884 1/1 83 61 22 104 104 0 strelka-varscan-mutect SPIN4,stop_gained,p.Glu192Ter,ENST00000374884,NM_001012968.2;LINC01278,intron_variant,,ENST00000610234,;LINC01278,intron_variant,,ENST00000610088,;SPIN4-AS1,intron_variant,,ENST00000451979,; A ENST00000374884 Transcript stop_gained 1099/4117 574/750 192/249 E/* Gag/Tag 1 -1 SPIN4 HGNC HGNC:27040 protein_coding YES CCDS43964.1 ENSP00000364018 Q56A73 X6R8Y7 UPI000013FD3C NM_001012968.2 1/1 hmmpanther:PTHR10405,hmmpanther:PTHR10405:SF9 HIGH SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 90 63350246 63350246 C A 1 0 0 0 0 0 1 0 0 15409 864 30 2 2 SPIN4 23 63350246 Nonsense_Mutation SNP C C3N-02089_T 10153394 63350246 92690649 1054 28138 MTMR8 0 . GRCh38 X 64331711 64331711 + Missense_Mutation SNP T T C novel C3N-02089_T C3N-02089_N T T c.1198A>G p.Thr400Ala p.T400A ENST00000374852 11/14 132 98 34 156 156 0 strelka-varscan-mutect MTMR8,missense_variant,p.Thr400Ala,ENST00000374852,NM_017677.3;MTMR8,non_coding_transcript_exon_variant,,ENST00000478487,;MTMR8,non_coding_transcript_exon_variant,,ENST00000462447,;MTMR8,downstream_gene_variant,,ENST00000461403,; C ENST00000374852 Transcript missense_variant 1266/2639 1198/2115 400/704 T/A Acc/Gcc 1 -1 MTMR8 HGNC HGNC:16825 protein_coding YES CCDS14379.1 ENSP00000363985 Q96EF0 UPI000006DFF7 NM_017677.3 tolerated(0.07) 11/14 Pfam_domain:PF06602,PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF36,SMART_domains:SM00404,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 64331711 64331711 T C 1 0 0 0 0 1 0 0 0 9936 1696 59 5 5 MTMR8 23 64331711 Missense_Mutation SNP T C3N-02089_T 981465 64331711 91709184 1055 28139 OTUD6A 0 . GRCh38 X 70062901 70062901 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.377G>T p.Arg126Leu p.R126L ENST00000338352 1/1 173 127 46 163 163 0 strelka-varscan-mutect OTUD6A,missense_variant,p.Arg126Leu,ENST00000338352,NM_207320.2; T ENST00000338352 Transcript missense_variant 411/1689 377/867 126/288 R/L cGc/cTc 1 1 OTUD6A HGNC HGNC:32312 protein_coding YES CCDS14395.1 ENSP00000339389 Q7L8S5 UPI00000712B7 NM_207320.2 tolerated(0.23) 1/1 hmmpanther:PTHR12419,hmmpanther:PTHR12419:SF13,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 70062901 70062901 G T 1 0 0 0 0 1 0 0 0 11385 1087 38 1 1 OTUD6A 23 70062901 Missense_Mutation SNP G C3N-02089_T 5731190 70062901 85977994 1056 28140 NAP1L2 0 . GRCh38 X 73213553 73213553 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.940T>C p.Tyr314His p.Y314H ENST00000373517 1/1 62 55 7 74 74 0 strelka-varscan-mutect NAP1L2,missense_variant,p.Tyr314His,ENST00000373517,NM_021963.3; G ENST00000373517 Transcript missense_variant 1296/2550 940/1383 314/460 Y/H Tat/Cat 1 -1 NAP1L2 HGNC HGNC:7638 protein_coding YES CCDS14423.1 ENSP00000362616 Q9ULW6 UPI00001303E8 NM_021963.3 tolerated(0.58) 1/1 hmmpanther:PTHR11875:SF36,hmmpanther:PTHR11875,Pfam_domain:PF00956,Superfamily_domains:SSF143113 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -16.45427 1 1 1 1 0 G 3 3 90 73213553 73213553 A G 1 0 0 0 0 1 0 0 0 10166 449 16 5 5 NAP1L2 23 73213553 Missense_Mutation SNP A C3N-02089_T 3150652 73213553 82827342 1057 28141 TGIF2LX 0 . GRCh38 X 89922166 89922166 + Silent SNP C C A rs775493588 C3N-02089_T C3N-02089_N C C c.81C>A p.= p.A27A ENST00000561129 1/1 110 81 29 145 145 0 strelka-varscan-mutect TGIF2LX,synonymous_variant,p.=,ENST00000561129,;TGIF2LX,synonymous_variant,p.=,ENST00000283891,NM_138960.3; A ENST00000561129 Transcript synonymous_variant 211/928 81/726 27/241 A gcC/gcA rs775493588 1 1 TGIF2LX HGNC HGNC:18570 protein_coding YES CCDS14459.1 ENSP00000453704 Q8IUE1 UPI0000074793 1/1 LOW 1 SNV 1 PASS rs775493588 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 90 89922166 89922166 C A 1 0 0 0 0 0 0 0 1 16260 610 22 2 2 TGIF2LX 23 89922166 Silent SNP C C3N-02089_T 16708613 89922166 66118729 1058 28142 ARL13A 0 . GRCh38 X 100973714 100973714 + Missense_Mutation SNP T T A novel C3N-02089_T C3N-02089_N T T c.25T>A p.Cys9Ser p.C9S ENST00000450049 2/8 70 52 18 92 92 0 strelka-varscan-mutect ARL13A,missense_variant,p.Cys9Ser,ENST00000450049,NM_001162491.1;ARL13A,missense_variant,p.Cys9Ser,ENST00000450457,; A ENST00000450049 Transcript missense_variant 138/1102 25/771 9/256 C/S Tgc/Agc 1 1 ARL13A HGNC HGNC:31709 protein_coding YES CCDS55463.1 ENSP00000398637 Q5H913 UPI0001747A4A NM_001162491.1 tolerated(0.08) 2/8 hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF111,SMART_domains:SM00177,SMART_domains:SM00178 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 100973714 100973714 T A 1 0 0 0 0 1 0 0 0 1065 1580 55 4 4 ARL13A 23 100973714 Missense_Mutation SNP T C3N-02089_T 11051548 100973714 55067181 1059 28143 HNRNPH2 0 . GRCh38 X 101412499 101412499 + Missense_Mutation SNP A A G novel C3N-02089_T C3N-02089_N A A c.511A>G p.Lys171Glu p.K171E ENST00000316594 2/2 86 64 22 87 87 0 strelka-varscan-mutect HNRNPH2,missense_variant,p.Lys171Glu,ENST00000316594,NM_001032393.2,NM_019597.4;GLA,upstream_gene_variant,,ENST00000218516,NM_000169.2;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409338,;RPL36A-HNRNPH2,downstream_gene_variant,,ENST00000409170,NM_001199973.1;GLA,upstream_gene_variant,,ENST00000479445,;GLA,upstream_gene_variant,,ENST00000486121,;GLA,upstream_gene_variant,,ENST00000480513,;GLA,upstream_gene_variant,,ENST00000493905,; G ENST00000316594 Transcript missense_variant 589/2223 511/1350 171/449 K/E Aaa/Gaa 1 1 HNRNPH2 HGNC HGNC:5042 protein_coding YES CCDS14485.1 ENSP00000361927 P55795 UPI0000134537 NM_001032393.2,NM_019597.4 deleterious(0) 2/2 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF33,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 101412499 101412499 A G 1 0 0 0 0 1 0 0 0 7161 247 9 5 5 HNRNPH2 23 101412499 Missense_Mutation SNP A C3N-02089_T 438785 101412499 54628396 1060 28144 DCX 0 . GRCh38 X 111333076 111333076 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.1026G>T p.Gln342His p.Q342H ENST00000338081 4/7 186 133 53 185 185 0 strelka-varscan-mutect DCX,missense_variant,p.Gln261His,ENST00000358070,;DCX,missense_variant,p.Gln342His,ENST00000338081,NM_000555.3;DCX,missense_variant,p.Gln261His,ENST00000636035,NM_001195553.1;DCX,missense_variant,p.Gln261His,ENST00000371993,NM_178153.2,NM_178151.2;DCX,missense_variant,p.Gln261His,ENST00000635795,NM_178152.2;DCX,missense_variant,p.Gln261His,ENST00000637570,;DCX,missense_variant,p.Gln261His,ENST00000356220,;DCX,missense_variant,p.Gln261His,ENST00000488120,;DCX,missense_variant,p.Gln261His,ENST00000637453,;DCX,missense_variant,p.Gln261His,ENST00000496551,; A ENST00000338081 Transcript missense_variant 1198/9402 1026/1326 342/441 Q/H caG/caT 1 -1 DCX HGNC HGNC:2714 protein_coding YES CCDS14556.1 ENSP00000337697 A0A140LJL1 UPI000013D33F NM_000555.3 tolerated(0.1) 4/7 PROSITE_profiles:PS50309,hmmpanther:PTHR24347:SF122,hmmpanther:PTHR24347,Gene3D:1mfwA00,PIRSF_domain:PIRSF037870,SMART_domains:SM00537,Superfamily_domains:SSF89837 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 111333076 111333076 C A 1 0 0 0 0 1 0 0 0 4121 680 24 2 2 DCX 23 111333076 Missense_Mutation SNP C C3N-02089_T 9920577 111333076 44707819 1061 28145 CT83 0 . GRCh38 X 116461892 116461892 + Missense_Mutation SNP C C A rs782064385 C3N-02089_T C3N-02089_N C C c.191G>T p.Arg64Leu p.R64L ENST00000371894 2/2 175 137 38 156 156 0 strelka-varscan-mutect CT83,missense_variant,p.Arg64Leu,ENST00000371894,NM_001017978.3;SLC6A14,downstream_gene_variant,,ENST00000598581,NM_007231.4;SLC6A14,downstream_gene_variant,,ENST00000463626,; A ENST00000371894 Transcript missense_variant 338/548 191/342 64/113 R/L cGg/cTg rs782064385 1 -1 CT83 HGNC HGNC:33494 protein_coding YES CCDS35372.1 ENSP00000360961 Q5H943 UPI0000036205 NM_001017978.3 tolerated(0.14) 2/2 Pfam_domain:PF15204,hmmpanther:PTHR38650 MODERATE 1 SNV 1 1 PASS rs782064385 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 116461892 116461892 C A 1 0 0 0 0 1 0 0 0 3794 652 23 1 1 CT83 23 116461892 Missense_Mutation SNP C C3N-02089_T 5128816 116461892 39579003 1062 28146 CT83 0 . GRCh38 X 116462000 116462000 + Missense_Mutation SNP G G C novel C3N-02089_T C3N-02089_N G G c.83C>G p.Thr28Ser p.T28S ENST00000371894 2/2 52 38 14 76 76 0 strelka-varscan-mutect CT83,missense_variant,p.Thr28Ser,ENST00000371894,NM_001017978.3;SLC6A14,downstream_gene_variant,,ENST00000598581,NM_007231.4;SLC6A14,downstream_gene_variant,,ENST00000463626,; C ENST00000371894 Transcript missense_variant 230/548 83/342 28/113 T/S aCt/aGt 1 -1 CT83 HGNC HGNC:33494 protein_coding YES CCDS35372.1 ENSP00000360961 Q5H943 UPI0000036205 NM_001017978.3 tolerated(0.23) 2/2 Pfam_domain:PF15204,hmmpanther:PTHR38650 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 90 116462000 116462000 G C 1 0 0 0 0 1 0 0 0 3794 1029 36 4 4 CT83 23 116462000 Missense_Mutation SNP G C3N-02089_T 108 116462000 39578895 1063 28147 TENM1 0 . GRCh38 X 124384692 124384692 + Missense_Mutation SNP C C T novel C3N-02089_T C3N-02089_N C C c.6239G>A p.Arg2080Lys p.R2080K ENST00000422452 30/32 76 61 15 83 83 0 strelka-varscan-mutect TENM1,missense_variant,p.Arg2080Lys,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Arg2073Lys,ENST00000371130,NM_014253.3;STAG2,intron_variant,,ENST00000469481,; T ENST00000422452 Transcript missense_variant 6303/12891 6239/8199 2080/2732 R/K aGa/aAa 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 tolerated(1) 30/32 hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 124384692 124384692 C T 1 0 0 0 0 1 0 0 0 16171 913 32 3 3 TENM1 23 124384692 Missense_Mutation SNP C C3N-02089_T 7922692 124384692 31656203 1064 28148 SMARCA1 0 . GRCh38 X 129497968 129497968 + Missense_Mutation SNP T T G novel C3N-02089_T C3N-02089_N T T c.1381A>C p.Asn461His p.N461H ENST00000371121 11/25 152 99 53 198 198 0 strelka-varscan-mutect SMARCA1,missense_variant,p.Asn461His,ENST00000371122,NM_003069.4;SMARCA1,missense_variant,p.Asn461His,ENST00000371123,NM_001282875.1;SMARCA1,missense_variant,p.Asn461His,ENST00000371121,NM_001282874.1;SMARCA1,non_coding_transcript_exon_variant,,ENST00000617310,; G ENST00000371121 Transcript missense_variant 1416/3564 1381/3213 461/1070 N/H Aat/Cat 1 -1 SMARCA1 HGNC HGNC:11097 protein_coding YES CCDS76019.1 ENSP00000360162 B7ZLQ5 UPI00004258DE NM_001282874.1 deleterious(0) 11/25 hmmpanther:PTHR10799:SF691,hmmpanther:PTHR10799,Pfam_domain:PF00176,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 129497968 129497968 T G 1 0 0 0 0 1 0 0 0 15061 1754 61 5 5 SMARCA1 23 129497968 Missense_Mutation SNP T C3N-02089_T 5113276 129497968 26542927 1065 28149 MAGEC3 0 . GRCh38 X 141896890 141896890 + Missense_Mutation SNP G G T novel C3N-02089_T C3N-02089_N G G c.1132G>T p.Asp378Tyr p.D378Y ENST00000298296 7/8 228 131 97 163 163 0 strelka-varscan-mutect MAGEC3,missense_variant,p.Asp378Tyr,ENST00000298296,NM_138702.1;MAGEC3,missense_variant,p.Asp80Tyr,ENST00000544766,NM_177456.2;MAGEC3,missense_variant,p.Asp80Tyr,ENST00000409007,;MAGEC3,5_prime_UTR_variant,,ENST00000443323,;MAGEC3,non_coding_transcript_exon_variant,,ENST00000483584,; T ENST00000298296 Transcript missense_variant 1132/1932 1132/1932 378/643 D/Y Gat/Tat 1 1 MAGEC3 HGNC HGNC:23798 protein_coding YES CCDS14676.1 ENSP00000298296 Q8TD91 UPI000006E09B NM_138702.1 deleterious(0) 7/8 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF86 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 141896890 141896890 G T 1 0 0 0 0 1 0 0 0 9100 1174 41 2 2 MAGEC3 23 141896890 Missense_Mutation SNP G C3N-02089_T 12398922 141896890 14144005 1066 28150 FMR1NB 0 . GRCh38 X 148024940 148024940 + Missense_Mutation SNP G G T rs782475138 C3N-02089_T C3N-02089_N G G c.708G>T p.Lys236Asn p.K236N ENST00000370467 5/6 145 72 73 107 107 0 strelka-varscan-mutect FMR1NB,missense_variant,p.Lys236Asn,ENST00000370467,NM_152578.2;FMR1NB,missense_variant,p.Lys66Asn,ENST00000489034,; T ENST00000370467 Transcript missense_variant 782/1021 708/768 236/255 K/N aaG/aaT rs782475138 1 1 FMR1NB HGNC HGNC:26372 protein_coding YES CCDS14683.1 ENSP00000359498 Q8N0W7 UPI0000062299 NM_152578.2 tolerated(0.09) 5/6 Low_complexity_(Seg):seg,hmmpanther:PTHR37360:SF1,hmmpanther:PTHR37360 MODERATE 1 SNV 1 1 PASS rs782475138 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 148024940 148024940 G T 1 0 0 0 0 1 0 0 0 5817 933 33 2 2 FMR1NB 23 148024940 Missense_Mutation SNP G C3N-02089_T 6128050 148024940 8015955 1067 28151 AFF2 0 . GRCh38 X 148978430 148978430 + Missense_Mutation SNP C C A novel C3N-02089_T C3N-02089_N C C c.3545C>A p.Ser1182Tyr p.S1182Y ENST00000370460 18/21 93 53 40 70 70 0 strelka-varscan-mutect AFF2,missense_variant,p.Ser1182Tyr,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,missense_variant,p.Ser823Tyr,ENST00000286437,NM_001170628.1;AFF2,missense_variant,p.Ser1147Tyr,ENST00000342251,NM_001169122.1;AFF2,missense_variant,p.Ser1147Tyr,ENST00000370457,NM_001169124.1,NM_001169125.1; A ENST00000370460 Transcript missense_variant 4024/13746 3545/3936 1182/1311 S/Y tCc/tAc 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 deleterious(0) 18/21 hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 90 148978430 148978430 C A 1 0 0 0 0 1 0 0 0 434 855 30 2 2 AFF2 23 148978430 Missense_Mutation SNP C C3N-02089_T 953490 148978430 7062465 1068 28152 NLGN4Y 0 . GRCh38 Y 14733478 14733478 + Missense_Mutation SNP A A T novel C3N-02089_T C3N-02089_N A A c.712A>T p.Ser238Cys p.S238C ENST00000297967 4/4 127 49 78 87 87 0 strelka-varscan-mutect NLGN4Y,missense_variant,p.Ser238Cys,ENST00000297967,NM_001164238.1;NLGN4Y,missense_variant,p.Ser218Cys,ENST00000413217,;NLGN4Y,intron_variant,,ENST00000382872,NM_001206850.1;NLGN4Y,intron_variant,,ENST00000382868,;NLGN4Y,intron_variant,,ENST00000339174,;NLGN4Y,intron_variant,,ENST00000355905,NM_014893.4;NLGN4Y,intron_variant,,ENST00000476359,; T ENST00000297967 Transcript missense_variant 811/882 712/771 238/256 S/C Agc/Tgc 1 1 NLGN4Y HGNC HGNC:15529 protein_coding CCDS55553.1 ENSP00000297967 Q8NFZ3 UPI00001D7C69 NM_001164238.1 deleterious_low_confidence(0.04) 4/4 MODERATE SNV 1 1 PASS . . 73 133 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 90 14733478 14733478 A T 1 0 0 0 0 1 0 0 0 10502 304 11 4 4 NLGN4Y 24 14733478 Missense_Mutation SNP A C3N-02089_T 14733478 42493937 1069 28153 RBMY1A1 0 . GRCh38 Y 21540640 21540640 + Missense_Mutation SNP C C G novel C3N-02089_T C3N-02089_N C C c.256C>G p.Pro86Ala p.P86A ENST00000382707 4/12 315 275 40 220 220 0 varscan-mutect RBMY1A1,missense_variant,p.Pro86Ala,ENST00000382707,NM_005058.2;RBMY1A1,missense_variant,p.Pro86Ala,ENST00000439108,;RBMY1A1,missense_variant,p.Pro86Ala,ENST00000303902,;RBMY1B,intron_variant,,ENST00000619219,;RBMY1A1,intron_variant,,ENST00000361046,NM_001320945.1; G ENST00000382707 Transcript missense_variant 408/1921 256/1491 86/496 P/A Cca/Gca 1 1 RBMY1A1 HGNC HGNC:9912 protein_coding YES CCDS14796.1 ENSP00000372154 P0DJD3 UPI000011D6E5 NM_005058.2 deleterious(0.03) 4/12 Gene3D:3.30.70.330,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 73 137 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 90 21540640 21540640 C G 1 0 0 0 0 1 0 0 0 13322 507 18 4 4 RBMY1A1 24 21540640 Missense_Mutation SNP C C3N-02089_T 6807162 21540640 35686775 1070 28154 ERRFI1 0 . GRCh38 1 8014130 8014130 + Missense_Mutation SNP G G T novel C3N-02145_T C3N-02145_N G G c.469C>A p.Pro157Thr p.P157T ENST00000377482 4/4 373 247 126 545 544 1 strelka-varscan-mutect ERRFI1,missense_variant,p.Pro157Thr,ENST00000377482,NM_018948.3;ERRFI1,3_prime_UTR_variant,,ENST00000467067,;ERRFI1,3_prime_UTR_variant,,ENST00000469499,;ERRFI1,intron_variant,,ENST00000474874,;ERRFI1,3_prime_UTR_variant,,ENST00000487559,; T ENST00000377482 Transcript missense_variant 693/3104 469/1389 157/462 P/T Cca/Aca 1 -1 ERRFI1 HGNC HGNC:18185 protein_coding YES CCDS94.1 ENSP00000366702 Q9UJM3 I6S2Y9 UPI000012F0FC NM_018948.3 deleterious(0) 4/4 hmmpanther:PTHR14254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 91 8014130 8014130 G T 1 0 0 0 0 1 0 0 0 5102 1203 42 2 2 ERRFI1 1 8014130 Missense_Mutation SNP G C3N-02145_T 8014130 240942292 1 28155 CLSTN1 0 . GRCh38 1 9731326 9731326 + Missense_Mutation SNP G G C novel C3N-02145_T C3N-02145_N G G c.2628C>G p.Ile876Met p.I876M ENST00000377298 18/19 333 237 96 311 311 0 strelka-varscan-mutect CLSTN1,missense_variant,p.Ile876Met,ENST00000377298,NM_001302883.1,NM_001009566.2;CLSTN1,missense_variant,p.Ile866Met,ENST00000361311,NM_014944.4;CLSTN1,missense_variant,p.Ile677Met,ENST00000435891,;PIK3CD,downstream_gene_variant,,ENST00000536656,;PIK3CD,downstream_gene_variant,,ENST00000628140,;PIK3CD,downstream_gene_variant,,ENST00000377346,NM_005026.3;PIK3CD,downstream_gene_variant,,ENST00000361110,;PIK3CD,downstream_gene_variant,,ENST00000543390,;CLSTN1,non_coding_transcript_exon_variant,,ENST00000477264,; C ENST00000377298 Transcript missense_variant 3421/5221 2628/2946 876/981 I/M atC/atG 1 -1 CLSTN1 HGNC HGNC:17447 protein_coding YES CCDS30580.1 ENSP00000366513 O94985 UPI0000127B95 NM_001302883.1,NM_001009566.2 deleterious(0.01) 18/19 Transmembrane_helices:TMhelix,hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 91 9731326 9731326 G C 1 0 0 0 0 1 0 0 0 3333 1164 41 4 4 CLSTN1 1 9731326 Missense_Mutation SNP G C3N-02145_T 1717196 9731326 239225096 2 28156 LEPR 0 . GRCh38 1 65617981 65617981 + Missense_Mutation SNP C C A novel C3N-02145_T C3N-02145_N C C c.2230C>A p.Leu744Ile p.L744I ENST00000349533 16/20 277 234 43 383 383 0 strelka-varscan-mutect LEPR,missense_variant,p.Leu744Ile,ENST00000349533,NM_002303.5;LEPR,missense_variant,p.Leu744Ile,ENST00000371060,NM_001003679.3;LEPR,missense_variant,p.Leu744Ile,ENST00000616738,NM_001198689.1;LEPR,missense_variant,p.Leu744Ile,ENST00000371059,NM_001003680.3,NM_001198687.1;LEPR,missense_variant,p.Leu744Ile,ENST00000344610,NM_001198688.1;LEPR,missense_variant,p.Leu744Ile,ENST00000371058,;LEPR,intron_variant,,ENST00000406510,;LEPR,upstream_gene_variant,,ENST00000471762,; A ENST00000349533 Transcript missense_variant 2415/8227 2230/3498 744/1165 L/I Ctc/Atc 1 1 LEPR HGNC HGNC:6554 protein_coding YES CCDS631.1 ENSP00000330393 P48357 UPI000014C37B NM_002303.5 deleterious(0) 16/20 PROSITE_profiles:PS50853,hmmpanther:PTHR23036:SF109,hmmpanther:PTHR23036,PROSITE_patterns:PS01353,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 91 65617981 65617981 C A 1 0 0 0 0 1 0 0 0 8636 565 20 2 2 LEPR 1 65617981 Missense_Mutation SNP C C3N-02145_T 55886655 65617981 183338441 3 28157 PTBP2 0 . GRCh38 1 96777871 96777871 + Silent SNP C C T novel C3N-02145_T C3N-02145_N C C c.633C>T p.= p.I211I ENST00000370197 7/14 141 117 24 191 191 0 strelka-varscan-mutect PTBP2,synonymous_variant,p.=,ENST00000609116,NM_001300989.1,NM_001300986.1,NM_001300990.1;PTBP2,synonymous_variant,p.=,ENST00000370197,NM_001300985.1,NM_001300987.1;PTBP2,synonymous_variant,p.=,ENST00000370198,NM_001300988.1;PTBP2,synonymous_variant,p.=,ENST00000426398,NM_021190.3;PTBP2,non_coding_transcript_exon_variant,,ENST00000482253,;PTBP2,non_coding_transcript_exon_variant,,ENST00000476419,; T ENST00000370197 Transcript synonymous_variant 688/3057 633/1614 211/537 I atC/atT 1 1 PTBP2 HGNC HGNC:17662 protein_coding YES CCDS72828.1 ENSP00000359216 Q9UKA9 UPI0000072708 NM_001300985.1,NM_001300987.1 7/14 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF400,TIGRFAM_domain:TIGR01649,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 200 7 3 0 0 0 0 -20 0.9994396 1 1 1 0 T 2 4 91 96777871 96777871 C T 1 0 0 0 0 0 0 0 1 12878 816 29 3 3 PTBP2 1 96777871 Silent SNP C C3N-02145_T 31159890 96777871 152178551 4 28158 1 23 2 2 62 C 5.925475e-05 PTBP2 0 . GRCh38 1 96777932 96777932 + Missense_Mutation SNP C C G novel C3N-02145_T C3N-02145_N C C c.694C>G p.Gln232Glu p.Q232E ENST00000370197 7/14 130 103 27 130 130 0 strelka-varscan-mutect PTBP2,missense_variant,p.Gln232Glu,ENST00000609116,NM_001300989.1,NM_001300986.1,NM_001300990.1;PTBP2,missense_variant,p.Gln232Glu,ENST00000370197,NM_001300985.1,NM_001300987.1;PTBP2,missense_variant,p.Gln232Glu,ENST00000370198,NM_001300988.1;PTBP2,missense_variant,p.Gln232Glu,ENST00000426398,NM_021190.3;PTBP2,non_coding_transcript_exon_variant,,ENST00000482253,;PTBP2,non_coding_transcript_exon_variant,,ENST00000476419,; G ENST00000370197 Transcript missense_variant 749/3057 694/1614 232/537 Q/E Caa/Gaa 1 1 PTBP2 HGNC HGNC:17662 protein_coding YES CCDS72828.1 ENSP00000359216 Q9UKA9 UPI0000072708 NM_001300985.1,NM_001300987.1 tolerated(0.1) 7/14 PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF400,TIGRFAM_domain:TIGR01649,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 G 3 3 91 96777932 96777932 C G 1 0 0 0 0 1 0 0 0 12878 827 29 4 4 PTBP2 1 96777932 Missense_Mutation SNP C C3N-02145_T 61 96777932 152178490 5 28159 1 23 2 2 62 C 5.925475e-05 LAMC1 0 . GRCh38 1 183103514 183103514 + Missense_Mutation SNP A A C novel C3N-02145_T C3N-02145_N A A c.605A>C p.Gln202Pro p.Q202P ENST00000258341 2/28 165 139 26 218 218 0 strelka-varscan-mutect LAMC1,missense_variant,p.Gln202Pro,ENST00000258341,NM_002293.3;LAMC1,5_prime_UTR_variant,,ENST00000484114,; C ENST00000258341 Transcript missense_variant 862/7889 605/4830 202/1609 Q/P cAg/cCg 1 1 LAMC1 HGNC HGNC:6492 protein_coding YES CCDS1351.1 ENSP00000258341 P11047 UPI000013CFC7 NM_002293.3 tolerated(0.12) 2/28 PROSITE_profiles:PS51117,hmmpanther:PTHR10574:SF270,hmmpanther:PTHR10574,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 91 183103514 183103514 A C 1 0 0 0 0 1 0 0 0 8518 188 7 5 5 LAMC1 1 183103514 Missense_Mutation SNP A C3N-02145_T 86325582 183103514 65852908 6 28160 BAP1 0 . GRCh38 3 52408576 52408576 + Silent SNP T T C novel C3N-02145_T C3N-02145_N T T c.153A>G p.= p.K51K ENST00000460680 4/17 183 124 59 291 291 0 strelka-varscan-mutect BAP1,synonymous_variant,p.=,ENST00000460680,NM_004656.3;BAP1,synonymous_variant,p.=,ENST00000296288,;BAP1,5_prime_UTR_variant,,ENST00000470173,;PHF7,upstream_gene_variant,,ENST00000327906,NM_016483.5;BAP1,upstream_gene_variant,,ENST00000469613,;PHF7,upstream_gene_variant,,ENST00000347025,;PHF7,upstream_gene_variant,,ENST00000614886,NM_001278221.1;PHF7,upstream_gene_variant,,ENST00000615126,;BAP1,upstream_gene_variant,,ENST00000478368,;PHF7,upstream_gene_variant,,ENST00000482327,;PHF7,upstream_gene_variant,,ENST00000472337,;BAP1,non_coding_transcript_exon_variant,,ENST00000483984,;BAP1,intron_variant,,ENST00000490917,;BAP1,upstream_gene_variant,,ENST00000471532,;PHF7,upstream_gene_variant,,ENST00000473145,;BAP1,upstream_gene_variant,,ENST00000490804,; C ENST00000460680 Transcript synonymous_variant 625/3937 153/2190 51/729 K aaA/aaG 1 -1 BAP1 HGNC HGNC:950 protein_coding YES CCDS2853.1 ENSP00000417132 Q92560 A0A024R305 UPI0000071B3D NM_004656.3 4/17 hmmpanther:PTHR10589:SF28,hmmpanther:PTHR10589,Pfam_domain:PF01088,Gene3D:3.40.532.10,Superfamily_domains:SSF54001 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 91 52408576 52408576 T C 1 0 0 0 0 0 0 0 1 1463 1490 52 5 5 BAP1 3 52408576 Silent SNP T C3N-02145_T 52408576 145886983 7 28161 MASP1 0 . GRCh38 3 187220248 187220248 + Silent SNP G G A novel C3N-02145_T C3N-02145_N G G c.1923C>T p.= p.A641A ENST00000337774 16/16 200 167 33 291 291 0 strelka-varscan MASP1,synonymous_variant,p.=,ENST00000337774,NM_001879.5; A ENST00000337774 Transcript synonymous_variant 2313/5276 1923/2100 641/699 A gcC/gcT 1 -1 MASP1 HGNC HGNC:6901 protein_coding CCDS33907.1 ENSP00000336792 P48740 UPI0000161FB8 NM_001879.5 16/16 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001155,Prints_domain:PR00722,PROSITE_patterns:PS00135,PROSITE_profiles:PS50240,hmmpanther:PTHR24255,hmmpanther:PTHR24255:SF13,SMART_domains:SM00020,Superfamily_domains:SSF50494 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 91 187220248 187220248 G A 1 0 0 0 0 0 0 0 1 9248 987 35 3 3 MASP1 3 187220248 Silent SNP G C3N-02145_T 134811672 187220248 11075311 8 28162 C5orf42 0 . GRCh38 5 37186366 37186366 + Missense_Mutation SNP G G A novel C3N-02145_T C3N-02145_N G G c.4109C>T p.Pro1370Leu p.P1370L ENST00000425232 24/52 172 135 37 297 297 0 strelka-varscan C5orf42,missense_variant,p.Pro1370Leu,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Pro1370Leu,ENST00000508244,;C5orf42,missense_variant,p.Pro418Leu,ENST00000514429,;C5orf42,missense_variant,p.Pro375Leu,ENST00000509849,; A ENST00000425232 Transcript missense_variant 4340/11199 4109/9594 1370/3197 P/L cCc/cTc 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0) 24/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 91 37186366 37186366 G A 1 0 0 0 0 1 0 0 0 2100 1232 43 3 3 C5orf42 5 37186366 Missense_Mutation SNP G C3N-02145_T 37186366 144351893 9 28163 APC 0 . GRCh38 5 112843749 112843758 + Frame_Shift_Del DEL GAAAATCGCC GAAAATCGCC - novel C3N-02145_T C3N-02145_N GAAAATCGCC GAAAATCGCC c.8155_8164delGAAAATCGCC p.Glu2719Ter p.E2719* ENST00000257430 16/16 189 125 64 378 378 0 sindel-varindel-pindel APC,frameshift_variant,p.Glu2719Ter,ENST00000257430,NM_000038.5;APC,frameshift_variant,p.Glu2719Ter,ENST00000508376,NM_001127510.2;APC,downstream_gene_variant,,ENST00000512211,;APC,downstream_gene_variant,,ENST00000507379,NM_001127511.2;CTC-554D6.1,intron_variant,,ENST00000520401,;APC,downstream_gene_variant,,ENST00000508624,;APC,downstream_gene_variant,,ENST00000502371,; - ENST00000257430 Transcript frameshift_variant 8211-8220/10701 8155-8164/8532 2719-2722/2843 ENRL/X GAAAATCGCCtg/tg 1 1 APC HGNC HGNC:583 protein_coding YES CCDS4107.1 ENSP00000257430 P25054 UPI000013CF60 NM_000038.5 16/16 Pfam_domain:PF05937,hmmpanther:PTHR12607,hmmpanther:PTHR12607:SF11 HIGH deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 91 112843749 112843749 GAAAATCGCC - 1 0 1 0 1 0 0 0 0 883 1175 41 0 0 APC 5 112843749 Frame_Shift_Del DEL GAAAATCGCC C3N-02145_T 75657383 112843749 68694510 10 28164 FAM71B 0 . GRCh38 5 157163188 157163188 + Silent SNP C C T rs369213663 C3N-02145_T C3N-02145_N C C c.1077G>A p.= p.S359S ENST00000302938 2/2 178 145 33 301 301 0 strelka-varscan FAM71B,synonymous_variant,p.=,ENST00000302938,NM_130899.2;ITK,intron_variant,,ENST00000521769,;MED7,upstream_gene_variant,,ENST00000524289,; T ENST00000302938 Transcript synonymous_variant 1173/2515 1077/1818 359/605 S tcG/tcA rs369213663,COSM260817 1 -1 FAM71B HGNC HGNC:28397 protein_coding YES CCDS4335.1 ENSP00000305596 Q8TC56 A0A140VJJ4 UPI000006F9DC NM_130899.2 2/2 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF2 0,1 LOW 1 SNV 1 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 91 157163188 157163188 C T 1 0 0 0 0 0 0 0 1 5472 871 31 1 1 FAM71B 5 157163188 Silent SNP C C3N-02145_T 44319439 157163188 24375071 11 28165 DEFB133 0 . GRCh38 6 49946121 49946121 + Missense_Mutation SNP T T G novel C3N-02145_T C3N-02145_N T T c.166A>C p.Asn56His p.N56H ENST00000398721 2/2 123 114 9 133 133 0 strelka-varscan DEFB133,missense_variant,p.Asn56His,ENST00000398721,NM_001166478.1;DEFB133,non_coding_transcript_exon_variant,,ENST00000620560,; G ENST00000398721 Transcript missense_variant 166/186 166/186 56/61 N/H Aat/Cat 1 -1 DEFB133 HGNC HGNC:31331 protein_coding YES ENSP00000485031 Q30KQ1 UPI00005E4A75 NM_001166478.1 deleterious_low_confidence(0.02) 2/2 hmmpanther:PTHR15001:SF26,hmmpanther:PTHR15001,Gene3D:3.10.360.10,Pfam_domain:PF13841,PD968187 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -17.67539 1 1 1 1 0 G 3 3 91 49946121 49946121 T G 1 0 0 0 0 1 0 0 0 4221 1841 64 5 5 DEFB133 6 49946121 Missense_Mutation SNP T C3N-02145_T 49946121 120859858 12 28166 PRDM1 0 . GRCh38 6 106095650 106095650 + Silent SNP G G A novel C3N-02145_T C3N-02145_N G G c.327G>A p.= p.K109K ENST00000369096 3/7 210 184 26 287 287 0 strelka-varscan-mutect PRDM1,synonymous_variant,p.=,ENST00000369096,NM_001198.3;PRDM1,synonymous_variant,p.=,ENST00000369091,;ATG5,intron_variant,,ENST00000636437,;PRDM1,upstream_gene_variant,,ENST00000369089,NM_182907.2;PRDM1,downstream_gene_variant,,ENST00000424894,;PRDM1,upstream_gene_variant,,ENST00000450060,;RP1-134E15.3,upstream_gene_variant,,ENST00000602426,;PRDM1,non_coding_transcript_exon_variant,,ENST00000489365,;ATG5,intron_variant,,ENST00000636335,;PRDM1,upstream_gene_variant,,ENST00000481163,; A ENST00000369096 Transcript synonymous_variant 561/5164 327/2478 109/825 K aaG/aaA 1 1 PRDM1 HGNC HGNC:9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 UPI0000D49069 NM_001198.3 3/7 Gene3D:2.170.270.10,PIRSF_domain:PIRSF013212,PROSITE_profiles:PS50280,SMART_domains:SM00317,Superfamily_domains:SSF82199 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 91 106095650 106095650 G A 1 0 0 0 0 0 0 0 1 12581 991 35 3 3 PRDM1 6 106095650 Silent SNP G C3N-02145_T 56149529 106095650 64710329 13 28167 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-02145_T C3N-02145_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 537 417 120 697 697 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 91 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-02145_T 55174772 104171201 14 28168 WEE2 0 . GRCh38 7 141725119 141725119 + Missense_Mutation SNP G G T novel C3N-02145_T C3N-02145_N G G c.1315G>T p.Ala439Ser p.A439S ENST00000397541 9/12 200 130 70 283 283 0 strelka-varscan-mutect WEE2,missense_variant,p.Ala439Ser,ENST00000397541,NM_001105558.1;WEE2,intron_variant,,ENST00000493845,;RNU1-82P,upstream_gene_variant,,ENST00000390851,;WEE2-AS1,intron_variant,,ENST00000488785,;WEE2-AS1,intron_variant,,ENST00000478332,;WEE2-AS1,intron_variant,,ENST00000462383,;WEE2-AS1,intron_variant,,ENST00000495800,;WEE2-AS1,intron_variant,,ENST00000465110,;WEE2-AS1,intron_variant,,ENST00000484172,;WEE2-AS1,intron_variant,,ENST00000486906,;WEE2-AS1,intron_variant,,ENST00000471512,;WEE2-AS1,intron_variant,,ENST00000459753,;WEE2-AS1,downstream_gene_variant,,ENST00000473776,; T ENST00000397541 Transcript missense_variant 1721/3061 1315/1704 439/567 A/S Gca/Tca 1 1 WEE2 HGNC HGNC:19684 protein_coding YES CCDS43660.1 ENSP00000380675 P0C1S8 UPI000004E9D3 NM_001105558.1 tolerated(0.7) 9/12 PROSITE_profiles:PS50011,hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF75,PIRSF_domain:PIRSF037281,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 91 141725119 141725119 G T 1 0 0 0 0 1 0 0 0 17902 1319 46 2 2 WEE2 7 141725119 Missense_Mutation SNP G C3N-02145_T 86550347 141725119 17620854 15 28169 SLC7A2 0 . GRCh38 8 17563626 17563626 + Silent SNP A A T novel C3N-02145_T C3N-02145_N A A c.1815A>T p.= p.P605P ENST00000004531 11/12 106 88 18 190 189 1 strelka-varscan-mutect SLC7A2,synonymous_variant,p.=,ENST00000470360,;SLC7A2,synonymous_variant,p.=,ENST00000494857,NM_001008539.3;SLC7A2,synonymous_variant,p.=,ENST00000004531,NM_001164771.1;SLC7A2,synonymous_variant,p.=,ENST00000398090,NM_003046.5;SLC7A2,synonymous_variant,p.=,ENST00000522656,; T ENST00000004531 Transcript synonymous_variant 1863/7560 1815/2097 605/698 P ccA/ccT 1 1 SLC7A2 HGNC HGNC:11060 protein_coding YES CCDS55203.1 ENSP00000004531 P52569 UPI0001A336A4 NM_001164771.1 11/12 Pfam_domain:PF13906,hmmpanther:PTHR11785,hmmpanther:PTHR11785:SF307,TIGRFAM_domain:TIGR00906,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 194 4 11 0 0 0 0 -20 0.9269232 1 1 1 0 T 2 4 91 17563626 17563626 A T 1 0 0 0 0 0 0 0 1 14980 175 7 4 4 SLC7A2 8 17563626 Silent SNP A C3N-02145_T 17563626 127575010 16 28170 STAU2 0 . GRCh38 8 73603745 73603745 + Missense_Mutation SNP C C A rs377142999 C3N-02145_T C3N-02145_N C C c.1010G>T p.Arg337Leu p.R337L ENST00000524300 10/15 161 137 24 190 190 0 strelka-varscan-mutect STAU2,missense_variant,p.Arg305Leu,ENST00000355780,NM_014393.2;STAU2,missense_variant,p.Arg317Leu,ENST00000521727,;STAU2,missense_variant,p.Arg337Leu,ENST00000519961,;STAU2,missense_variant,p.Arg337Leu,ENST00000524300,NM_001164380.1;STAU2,missense_variant,p.Arg117Leu,ENST00000521451,;STAU2,missense_variant,p.Arg305Leu,ENST00000522695,NM_001164381.1;STAU2,missense_variant,p.Arg305Leu,ENST00000522509,NM_001164384.1;STAU2,missense_variant,p.Arg233Leu,ENST00000521210,NM_001164382.1;STAU2,missense_variant,p.Arg299Leu,ENST00000517542,NM_001164385.1;STAU2,missense_variant,p.Arg165Leu,ENST00000523558,NM_001164383.1;STAU2,missense_variant,p.Arg165Leu,ENST00000518767,;STAU2,intron_variant,,ENST00000518502,;STAU2,missense_variant,p.Arg317Leu,ENST00000518981,; A ENST00000524300 Transcript missense_variant 1361/3065 1010/1713 337/570 R/L cGt/cTt rs377142999 1 -1 STAU2 HGNC HGNC:11371 protein_coding YES CCDS55247.1 ENSP00000428756 A0A0A0MTC5 UPI000013D271 NM_001164380.1 deleterious(0.01) 10/15 PROSITE_profiles:PS50137,hmmpanther:PTHR10910,hmmpanther:PTHR10910:SF60,Pfam_domain:PF00035,Gene3D:3.30.160.20,SMART_domains:SM00358,Superfamily_domains:SSF54768 MODERATE 1 SNV 2 1 PASS rs377142999 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 91 73603745 73603745 C A 1 0 0 0 0 1 0 0 0 15649 536 19 1 1 STAU2 8 73603745 Missense_Mutation SNP C C3N-02145_T 56040119 73603745 71534891 17 28171 TDRD7 0 . GRCh38 9 97460414 97460414 + Silent SNP A A C novel C3N-02145_T C3N-02145_N A A c.1092A>C p.= p.A364A ENST00000355295 7/17 442 309 133 688 688 0 strelka-varscan-mutect TDRD7,synonymous_variant,p.=,ENST00000355295,NM_001302884.1,NM_014290.2; C ENST00000355295 Transcript synonymous_variant 1387/3834 1092/3297 364/1098 A gcA/gcC 1 1 TDRD7 HGNC HGNC:30831 protein_coding YES CCDS6725.1 ENSP00000347444 Q8NHU6 UPI00002114B5 NM_001302884.1,NM_014290.2 7/17 PROSITE_profiles:PS51644 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 91 97460414 97460414 A C 1 0 0 0 0 0 0 0 1 16145 204 8 5 5 TDRD7 9 97460414 Silent SNP A C3N-02145_T 97460414 40934303 18 28172 VWCE 0 . GRCh38 11 61258937 61258937 + Missense_Mutation SNP G G A novel C3N-02145_T C3N-02145_N G G c.2606C>T p.Pro869Leu p.P869L ENST00000335613 20/20 53 34 19 70 70 0 strelka-varscan-mutect VWCE,missense_variant,p.Pro869Leu,ENST00000335613,NM_152718.2;VWCE,missense_variant,p.Pro334Leu,ENST00000535710,;VWCE,synonymous_variant,p.=,ENST00000613271,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,downstream_gene_variant,,ENST00000538438,; A ENST00000335613 Transcript missense_variant 2993/3640 2606/2868 869/955 P/L cCt/cTt 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 deleterious_low_confidence(0.03) 20/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 91 61258937 61258937 G A 1 0 0 0 0 1 0 0 0 17804 1000 35 3 3 VWCE 11 61258937 Missense_Mutation SNP G C3N-02145_T 61258937 73827685 19 28173 DRD2 0 . GRCh38 11 113418085 113418085 + Silent SNP G G A novel C3N-02145_T C3N-02145_N G G c.337C>T p.= p.L113L ENST00000362072 3/8 443 380 63 580 580 0 strelka-varscan-mutect DRD2,synonymous_variant,p.=,ENST00000362072,NM_000795.3;DRD2,synonymous_variant,p.=,ENST00000544518,;DRD2,synonymous_variant,p.=,ENST00000542968,;DRD2,synonymous_variant,p.=,ENST00000346454,NM_016574.3;DRD2,synonymous_variant,p.=,ENST00000538967,;DRD2,synonymous_variant,p.=,ENST00000543292,;DRD2,non_coding_transcript_exon_variant,,ENST00000535984,;DRD2,non_coding_transcript_exon_variant,,ENST00000540600,;DRD2,non_coding_transcript_exon_variant,,ENST00000539420,; A ENST00000362072 Transcript synonymous_variant 682/2789 337/1332 113/443 L Ctg/Ttg 1 -1 DRD2 HGNC HGNC:3023 protein_coding YES CCDS8361.1 ENSP00000354859 P14416 A0A024R3C5 UPI0000001315 NM_000795.3 3/8 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24248,hmmpanther:PTHR24248:SF68,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 91 113418085 113418085 G A 1 0 0 0 0 0 0 0 1 4576 933 33 3 3 DRD2 11 113418085 Silent SNP G C3N-02145_T 52159148 113418085 21668537 20 28174 OR10G7 0 . GRCh38 11 124038928 124038928 + Missense_Mutation SNP A A T novel C3N-02145_T C3N-02145_N A A c.74T>A p.Leu25His p.L25H ENST00000330487 1/1 314 289 25 522 522 0 varscan-mutect OR10G7,missense_variant,p.Leu25His,ENST00000330487,NM_001004463.1; T ENST00000330487 Transcript missense_variant 83/945 74/936 25/311 L/H cTc/cAc 1 -1 OR10G7 HGNC HGNC:14842 protein_coding YES CCDS31705.1 ENSP00000329689 Q8NGN6 A0A126GWF3 UPI0000040A84 NM_001004463.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF7,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 91 124038928 124038928 A T 1 0 0 0 0 1 0 0 0 10979 304 11 4 4 OR10G7 11 124038928 Missense_Mutation SNP A C3N-02145_T 10620843 124038928 11047694 21 28175 PACS2 0 . GRCh38 14 105352455 105352457 + In_Frame_Del DEL CTT CTT - C3N-02145_T C3N-02145_N CTT CTT c.287_289delTCT p.Phe96del p.F96del ENST00000447393 3/25 215 189 26 278 278 0 sindel-varindel-pindel PACS2,inframe_deletion,p.Phe96del,ENST00000447393,NM_001100913.2;PACS2,inframe_deletion,p.Phe96del,ENST00000325438,NM_015197.3;PACS2,inframe_deletion,p.Phe29del,ENST00000430725,NM_001243127.2;PACS2,inframe_deletion,p.Phe29del,ENST00000546915,;PACS2,intron_variant,,ENST00000547217,;PACS2,upstream_gene_variant,,ENST00000552138,;PACS2,downstream_gene_variant,,ENST00000548265,; - ENST00000447393 Transcript inframe_deletion 460-462/6365 285-287/2715 95-96/904 TF/T acCTTc/acc COSM1368694 1 1 PACS2 HGNC HGNC:23794 protein_coding YES CCDS45178.2 ENSP00000393559 Q86VP3 UPI0000E56F01 NM_001100913.2 3/25 hmmpanther:PTHR13280:SF15,hmmpanther:PTHR13280 1 MODERATE 1 deletion 1 2 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 91 105352455 105352455 CTT - 1 0 1 0 1 0 0 0 0 11451 668 24 0 0 PACS2 14 105352455 In_Frame_Del DEL CTT C3N-02145_T 105352455 1691263 22 28176 GLG1 0 . GRCh38 16 74469017 74469017 + Silent SNP G G A novel C3N-02145_T C3N-02145_N G G c.2365C>T p.= p.L789L ENST00000205061 17/27 189 130 59 305 305 0 strelka-varscan-mutect GLG1,synonymous_variant,p.=,ENST00000205061,NM_012201.5;GLG1,synonymous_variant,p.=,ENST00000422840,NM_001145667.1;GLG1,synonymous_variant,p.=,ENST00000447066,NM_001145666.1;GLG1,downstream_gene_variant,,ENST00000627032,;GLG1,3_prime_UTR_variant,,ENST00000562090,;GLG1,3_prime_UTR_variant,,ENST00000567951,;GLG1,non_coding_transcript_exon_variant,,ENST00000566601,;GLG1,non_coding_transcript_exon_variant,,ENST00000563432,;GLG1,upstream_gene_variant,,ENST00000561481,; A ENST00000205061 Transcript synonymous_variant 2385/8261 2365/3612 789/1203 L Ctg/Ttg 1 -1 GLG1 HGNC HGNC:4316 protein_coding YES CCDS32485.1 ENSP00000205061 Q92896 UPI00001FFBD9 NM_012201.5 17/27 hmmpanther:PTHR11884:SF1,hmmpanther:PTHR11884 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 91 74469017 74469017 G A 1 0 0 0 0 0 0 0 1 6314 933 33 3 3 GLG1 16 74469017 Silent SNP G C3N-02145_T 74469017 15869328 23 28177 WSB1 0 . GRCh38 17 27310119 27310119 + Nonsense_Mutation SNP C C T C3N-02145_T C3N-02145_N C C c.943C>T p.Arg315Ter p.R315* ENST00000262394 7/9 317 288 29 365 365 0 strelka-varscan-mutect WSB1,stop_gained,p.Arg315Ter,ENST00000262394,NM_015626.8;WSB1,stop_gained,p.Arg169Ter,ENST00000348811,NM_134265.2;WSB1,downstream_gene_variant,,ENST00000581185,;WSB1,downstream_gene_variant,,ENST00000579733,;WSB1,downstream_gene_variant,,ENST00000427287,;WSB1,downstream_gene_variant,,ENST00000583193,;WSB1,downstream_gene_variant,,ENST00000584114,;WSB1,non_coding_transcript_exon_variant,,ENST00000467843,;WSB1,non_coding_transcript_exon_variant,,ENST00000583096,;WSB1,downstream_gene_variant,,ENST00000487603,;WSB1,downstream_gene_variant,,ENST00000582208,; T ENST00000262394 Transcript stop_gained 1259/5139 943/1266 315/421 R/* Cga/Tga COSM4064808 1 1 WSB1 HGNC HGNC:19221 protein_coding YES CCDS11220.1 ENSP00000262394 Q9Y6I7 A0A024QZ51 UPI0000031568 NM_015626.8 7/9 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR15622:SF12,hmmpanther:PTHR15622,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:SSF50978 1 HIGH 1 SNV 1 1 1 PASS rs1243405786 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 91 27310119 27310119 C T 1 0 0 0 0 0 1 0 0 17961 528 19 1 1 WSB1 17 27310119 Nonsense_Mutation SNP C C3N-02145_T 27310119 55947322 24 28178 ERAL1 0 . GRCh38 17 28860514 28860514 + Silent SNP C C T rs541436173 C3N-02145_T C3N-02145_N C C c.1275C>T p.= p.C425C ENST00000254928 10/10 180 165 15 214 214 0 strelka-varscan-mutect ERAL1,synonymous_variant,p.=,ENST00000254928,NM_001317985.1,NM_005702.2;ERAL1,intron_variant,,ENST00000583487,;ERAL1,downstream_gene_variant,,ENST00000580917,;MIR4732,downstream_gene_variant,,ENST00000582320,;MIR4732,downstream_gene_variant,,ENST00000384886,;MIR4732,downstream_gene_variant,,ENST00000581873,;MIR4732,downstream_gene_variant,,ENST00000385059,;MIR451B,upstream_gene_variant,,ENST00000636285,;ERAL1,downstream_gene_variant,,ENST00000578001,;ERAL1,3_prime_UTR_variant,,ENST00000461894,;ERAL1,non_coding_transcript_exon_variant,,ENST00000471992,;ERAL1,downstream_gene_variant,,ENST00000412138,;ERAL1,downstream_gene_variant,,ENST00000577942,; T ENST00000254928 Transcript synonymous_variant 1372/1925 1275/1314 425/437 C tgC/tgT rs541436173,COSM3378114 1 1 ERAL1 HGNC HGNC:3424 protein_coding YES CCDS11244.1 ENSP00000254928 O75616 UPI000006DECC NM_001317985.1,NM_005702.2 10/10 HAMAP:MF_00367,hmmpanther:PTHR11649,hmmpanther:PTHR11649:SF3,Gene3D:3.30.300.20,Superfamily_domains:SSF54814 0,1 LOW 1 SNV 1 0,1 1 PASS rs541436173 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 91 28860514 28860514 C T 1 0 0 0 0 0 0 0 1 5051 776 27 1 1 ERAL1 17 28860514 Silent SNP C C3N-02145_T 1550395 28860514 54396927 25 28179 ANKRD30B 0 . GRCh38 18 14797838 14797838 + Silent SNP A A G rs529980396 C3N-02145_T C3N-02145_N A A c.2013A>G p.= p.R671R ENST00000358984 20/36 226 207 19 262 262 0 varscan-mutect ANKRD30B,synonymous_variant,p.=,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000579292,;ANKRD30B,3_prime_UTR_variant,,ENST00000580206,; G ENST00000358984 Transcript synonymous_variant 2193/4359 2013/4179 671/1392 R agA/agG rs529980396 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 20/36 LOW 1 SNV 1 1 PASS rs529980396 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 91 14797838 14797838 A G 1 0 0 0 0 0 0 0 1 762 301 11 5 5 ANKRD30B 18 14797838 Silent SNP A C3N-02145_T 14797838 65575447 26 28180 FFAR2 0 . GRCh38 19 35450155 35450155 + Silent SNP T T C novel C3N-02145_T C3N-02145_N T T c.441T>C p.= p.V147V ENST00000599180 2/2 223 206 17 330 330 0 strelka-varscan-mutect FFAR2,synonymous_variant,p.=,ENST00000599180,;FFAR2,synonymous_variant,p.=,ENST00000246549,NM_005306.2;FFAR2,intron_variant,,ENST00000601590,; C ENST00000599180 Transcript synonymous_variant 521/2133 441/993 147/330 V gtT/gtC 1 1 FFAR2 HGNC HGNC:4501 protein_coding YES CCDS12461.1 ENSP00000473159 O15552 C6KYL4 UPI0000050459 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF8,Superfamily_domains:SSF81321 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 91 35450155 35450155 T C 1 0 0 0 0 0 0 0 1 5691 1770 62 5 5 FFAR2 19 35450155 Silent SNP T C3N-02145_T 35450155 23167461 27 28181 SHISA7 0 . GRCh38 19 55442682 55442682 + Missense_Mutation SNP G G T novel C3N-02145_T C3N-02145_N G G c.182C>A p.Thr61Asn p.T61N ENST00000376325 1/4 33 19 14 52 52 0 strelka-varscan-mutect SHISA7,missense_variant,p.Thr61Asn,ENST00000376325,NM_001145176.1;SHISA7,upstream_gene_variant,,ENST00000416792,; T ENST00000376325 Transcript missense_variant 182/6033 182/1617 61/538 T/N aCc/aAc 1 -1 SHISA7 HGNC HGNC:35409 protein_coding YES CCDS46193.1 ENSP00000365503 A6NL88 UPI000193055E NM_001145176.1 deleterious_low_confidence(0.01) 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF2 MODERATE 1 SNV 2 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 91 55442682 55442682 G T 1 0 0 0 0 1 0 0 0 14545 1261 44 2 2 SHISA7 19 55442682 Missense_Mutation SNP G C3N-02145_T 19992527 55442682 3174934 28 28182 PORCN 0 . GRCh38 X 48516106 48516106 + Nonsense_Mutation SNP C C A novel C3N-02145_T C3N-02145_N C C c.1133C>A p.Ser378Ter p.S378* ENST00000326194 12/14 743 661 82 702 701 1 strelka-varscan-mutect PORCN,stop_gained,p.Ser372Ter,ENST00000359882,NM_203474.1;PORCN,stop_gained,p.Ser373Ter,ENST00000355961,NM_203473.2;PORCN,stop_gained,p.Ser378Ter,ENST00000326194,NM_203475.2;PORCN,stop_gained,p.Ser367Ter,ENST00000361988,NM_022825.3;PORCN,stop_gained,p.Ser322Ter,ENST00000355092,NM_001282167.1;PORCN,stop_gained,p.Ser373Ter,ENST00000537758,;PORCN,stop_gained,p.Ser372Ter,ENST00000367574,;PORCN,downstream_gene_variant,,ENST00000489940,;PORCN,downstream_gene_variant,,ENST00000486272,;PORCN,3_prime_UTR_variant,,ENST00000485288,;PORCN,3_prime_UTR_variant,,ENST00000472520,;PORCN,non_coding_transcript_exon_variant,,ENST00000491243,;PORCN,non_coding_transcript_exon_variant,,ENST00000459953,;PORCN,downstream_gene_variant,,ENST00000528612,;PORCN,downstream_gene_variant,,ENST00000470275,; A ENST00000326194 Transcript stop_gained 1176/1755 1133/1386 378/461 S/* tCa/tAa 1 1 PORCN HGNC HGNC:17652 protein_coding YES CCDS14299.1 ENSP00000322304 Q9H237 UPI000014187F NM_203475.2 12/14 hmmpanther:PTHR13906,hmmpanther:PTHR13906:SF13 HIGH 1 SNV 1 1 PASS rs1064795419 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 91 48516106 48516106 C A 1 0 0 0 0 0 1 0 0 12372 838 29 2 2 PORCN 23 48516106 Nonsense_Mutation SNP C C3N-02145_T 48516106 107524789 29 28183 TENM1 0 . GRCh38 X 124641808 124641808 + Missense_Mutation SNP C C T novel C3N-02145_T C3N-02145_N C C c.2060G>A p.Gly687Glu p.G687E ENST00000422452 11/32 394 288 106 411 411 0 strelka-varscan-mutect TENM1,missense_variant,p.Gly687Glu,ENST00000422452,NM_001163278.1,NM_001163279.1;TENM1,missense_variant,p.Gly687Glu,ENST00000371130,NM_014253.3; T ENST00000422452 Transcript missense_variant 2124/12891 2060/8199 687/2732 G/E gGa/gAa 1 -1 TENM1 HGNC HGNC:8117 protein_coding YES CCDS55488.1 ENSP00000403954 Q9UKZ4 UPI0000211B6A NM_001163278.1,NM_001163279.1 deleterious(0) 11/32 PROSITE_profiles:PS50026,hmmpanther:PTHR11219:SF7,hmmpanther:PTHR11219,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,SMART_domains:SM00181 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 91 124641808 124641808 C T 1 0 0 0 0 1 0 0 0 16171 855 30 3 3 TENM1 23 124641808 Missense_Mutation SNP C C3N-02145_T 76125702 124641808 31399087 30 28184 CFAP74 0 . GRCh38 1 1926734 1926734 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.3690G>A p.= p.L1230L ENST00000493964 30/38 308 270 38 344 344 0 strelka-varscan-mutect CFAP74,synonymous_variant,p.=,ENST00000493964,NM_001304360.1;CFAP74,non_coding_transcript_exon_variant,,ENST00000464311,;CFAP74,non_coding_transcript_exon_variant,,ENST00000412120,; T ENST00000493964 Transcript synonymous_variant 3846/5247 3690/4755 1230/1584 L ctG/ctA 1 -1 CFAP74 HGNC HGNC:29368 protein_coding YES ENSP00000417061 Q9C0B2 UPI0004620AE2 NM_001304360.1 30/38 hmmpanther:PTHR22538 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 1926734 1926734 C T 1 0 0 0 0 0 0 0 1 3033 465 17 3 3 CFAP74 1 1926734 Silent SNP C C3N-02149_T 1926734 247029688 1 28185 CCDC27 0 . GRCh38 1 3763184 3763184 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1031A>T p.Glu344Val p.E344V ENST00000294600 7/12 46 38 8 73 72 1 strelka-varscan-mutect CCDC27,missense_variant,p.Glu344Val,ENST00000294600,NM_152492.2;CCDC27,3_prime_UTR_variant,,ENST00000462521,; T ENST00000294600 Transcript missense_variant 1115/2176 1031/1971 344/656 E/V gAa/gTa 1 1 CCDC27 HGNC HGNC:26546 protein_coding YES CCDS50.1 ENSP00000294600 Q2M243 UPI000013E186 NM_152492.2 tolerated(0.21) 7/12 Low_complexity_(Seg):seg,hmmpanther:PTHR18853:SF8,hmmpanther:PTHR18853 MODERATE 1 SNV 1 1 PASS rs944169953 . 0 205 5 0 0 0 0 0 -19.38349 1 1 1 1 0 T 3 4 92 3763184 3763184 A T 1 0 0 0 0 1 0 0 0 2511 246 9 4 4 CCDC27 1 3763184 Missense_Mutation SNP A C3N-02149_T 1836450 3763184 245193238 2 28186 AJAP1 0 . GRCh38 1 4712045 4712045 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.175C>A p.= p.R59R ENST00000378191 2/6 126 99 27 181 181 0 strelka-varscan-mutect AJAP1,synonymous_variant,p.=,ENST00000378191,NM_018836.3;AJAP1,synonymous_variant,p.=,ENST00000378190,NM_001042478.1;AJAP1,non_coding_transcript_exon_variant,,ENST00000466761,; A ENST00000378191 Transcript synonymous_variant 556/11666 175/1236 59/411 R Cgg/Agg 1 1 AJAP1 HGNC HGNC:30801 protein_coding YES CCDS54.1 ENSP00000367433 Q9UKB5 UPI00000728B8 NM_018836.3 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR32422 LOW 1 SNV 1 1 PASS rs1342432950 . 0 206 2 2 0 0 0 0 -20 0.9999991 1 1 1 0 A 2 1 92 4712045 4712045 C A 1 0 0 0 0 0 0 0 1 516 643 23 1 1 AJAP1 1 4712045 Silent SNP C C3N-02149_T 948861 4712045 244244377 3 28187 PRDM2 0 . GRCh38 1 13779769 13779769 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.1974C>T p.= p.P658P ENST00000235372 8/10 182 145 37 281 281 0 strelka-varscan-mutect PRDM2,synonymous_variant,p.=,ENST00000235372,NM_012231.4;PRDM2,synonymous_variant,p.=,ENST00000311066,NM_015866.4;PRDM2,synonymous_variant,p.=,ENST00000413440,NM_001007257.2;PRDM2,synonymous_variant,p.=,ENST00000343137,;PRDM2,intron_variant,,ENST00000376048,NM_001135610.1;PRDM2,intron_variant,,ENST00000503842,;PRDM2,intron_variant,,ENST00000505823,;PRDM2,downstream_gene_variant,,ENST00000487453,;PRDM2,downstream_gene_variant,,ENST00000407521,;PRDM2,intron_variant,,ENST00000491134,; T ENST00000235372 Transcript synonymous_variant 2830/7957 1974/5157 658/1718 P ccC/ccT 1 1 PRDM2 HGNC HGNC:9347 protein_coding YES CCDS150.1 ENSP00000235372 Q13029 UPI000013C9CD NM_012231.4 8/10 Low_complexity_(Seg):seg,PIRSF_domain:PIRSF002395 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 13779769 13779769 C T 1 0 0 0 0 0 0 0 1 12589 581 21 3 3 PRDM2 1 13779769 Silent SNP C C3N-02149_T 9067724 13779769 235176653 4 28188 PRDM2 0 . GRCh38 1 13823184 13823184 + Nonstop_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.681A>G p.Ter227TrpextTer103 p.*227Wext*103 ENST00000376048 8/8 245 195 50 348 348 0 strelka-varscan-mutect PRDM2,stop_lost,p.Ter227TrpextTer103,ENST00000376048,NM_001135610.1;PRDM2,stop_lost,p.Ter63TrpextTer103,ENST00000503842,;PRDM2,stop_lost,p.Ter63TrpextTer?,ENST00000505823,;PRDM2,3_prime_UTR_variant,,ENST00000235372,NM_012231.4; G ENST00000376048 Transcript stop_lost 807/2688 681/681 227/226 */W tgA/tgG 1 1 PRDM2 HGNC HGNC:9347 protein_coding CCDS44061.1 ENSP00000365216 Q13029 UPI00001408AA NM_001135610.1 8/8 HIGH SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 92 13823184 13823184 A G 1 0 0 0 0 0 0 0 0 12589 259 9 5 5 PRDM2 1 13823184 Nonstop_Mutation SNP A C3N-02149_T 43415 13823184 235133238 5 28189 PADI3 0 . GRCh38 1 17249215 17249215 + Silent SNP C C A C3N-02149_T C3N-02149_N C C c.78C>A p.= p.L26L ENST00000375460 1/16 316 257 59 376 375 1 strelka-varscan-mutect PADI3,synonymous_variant,p.=,ENST00000375460,NM_016233.2;PADI1,downstream_gene_variant,,ENST00000375471,NM_013358.2;PADI1,downstream_gene_variant,,ENST00000460293,; A ENST00000375460 Transcript synonymous_variant 118/3189 78/1995 26/664 L ctC/ctA COSM414302,COSM5475583 1 1 PADI3 HGNC HGNC:18337 protein_coding YES CCDS179.1 ENSP00000364609 Q9ULW8 UPI000013D8A0 NM_016233.2 1/16 Pfam_domain:PF08526,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF10,Superfamily_domains:SSF49503 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 17249215 17249215 C A 1 0 0 0 0 0 0 0 1 11457 871 31 1 1 PADI3 1 17249215 Silent SNP C C3N-02149_T 3426031 17249215 231707207 6 28190 PADI3 0 . GRCh38 1 17259699 17259699 + Missense_Mutation SNP G G T rs201806996 C3N-02149_T C3N-02149_N G G c.214G>T p.Ala72Ser p.A72S ENST00000375460 2/16 93 81 12 111 111 0 strelka-varscan-mutect PADI3,missense_variant,p.Ala72Ser,ENST00000375460,NM_016233.2; T ENST00000375460 Transcript missense_variant 254/3189 214/1995 72/664 A/S Gcg/Tcg rs201806996 1 1 PADI3 HGNC HGNC:18337 protein_coding YES CCDS179.1 ENSP00000364609 Q9ULW8 UPI000013D8A0 NM_016233.2 tolerated(0.17) 2/16 Pfam_domain:PF08526,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF10,Superfamily_domains:SSF49503 MODERATE 1 SNV 1 1 PASS rs201806996 . 0 201 8 0 0 0 0 0 -20 0.9999972 1 1 1 0 T 3 4 92 17259699 17259699 G T 1 0 0 0 0 1 0 0 0 11457 1087 38 1 1 PADI3 1 17259699 Missense_Mutation SNP G C3N-02149_T 10484 17259699 231696723 7 28191 RHCE 0 . GRCh38 1 25408732 25408732 + Missense_Mutation SNP C C A rs144348222 C3N-02149_T C3N-02149_N C C c.286G>T p.Gly96Cys p.G96C ENST00000294413 2/10 299 215 84 285 285 0 strelka-varscan-mutect RHCE,missense_variant,p.Gly80Cys,ENST00000349320,;RHCE,missense_variant,p.Gly96Cys,ENST00000294413,NM_020485.4;RHCE,missense_variant,p.Gly96Cys,ENST00000349438,NM_138618.3;RHCE,missense_variant,p.Gly96Cys,ENST00000413854,;RHCE,missense_variant,p.Gly96Cys,ENST00000340849,NM_138617.3;RHCE,missense_variant,p.Gly96Cys,ENST00000346452,NM_138616.3;RHCE,non_coding_transcript_exon_variant,,ENST00000495048,;RHCE,non_coding_transcript_exon_variant,,ENST00000527187,;RHCE,intron_variant,,ENST00000533771,; A ENST00000294413 Transcript missense_variant 345/1591 286/1254 96/417 G/C Ggc/Tgc rs144348222,CM066600,BGMUT_678 1 -1 RHCE HGNC HGNC:10008 protein_coding YES CCDS30635.1 ENSP00000294413 P18577 UPI00001D9627 NM_020485.4 deleterious(0.01) 2/10 hmmpanther:PTHR11730:SF43,hmmpanther:PTHR11730,Gene3D:1.10.3430.10,Pfam_domain:PF00909,Superfamily_domains:0044218 MODERATE 1 SNV 1 0,1,0 1 PASS rs144348222 . 34 176 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 25408732 25408732 C A 1 0 0 0 0 1 0 0 0 13497 652 23 1 1 RHCE 1 25408732 Missense_Mutation SNP C C3N-02149_T 8149033 25408732 223547690 8 28192 PLK3 0 . GRCh38 1 44800672 44800672 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.209A>T p.Lys70Met p.K70M ENST00000372201 1/15 209 184 25 193 193 0 strelka-varscan-mutect PLK3,missense_variant,p.Lys70Met,ENST00000372201,NM_004073.2;PLK3,splice_region_variant,,ENST00000465443,;PLK3,upstream_gene_variant,,ENST00000492398,;PLK3,upstream_gene_variant,,ENST00000493100,;PLK3,upstream_gene_variant,,ENST00000461358,;PLK3,upstream_gene_variant,,ENST00000476731,;PLK3,upstream_gene_variant,,ENST00000461769,; T ENST00000372201 Transcript missense_variant,splice_region_variant 448/2492 209/1941 70/646 K/M aAg/aTg 1 1 PLK3 HGNC HGNC:2154 protein_coding YES CCDS515.1 ENSP00000361275 Q9H4B4 UPI000013ED1D NM_004073.2 deleterious(0) 1/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF42,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 44800672 44800672 A T 1 0 0 0 0 1 0 0 0 12192 86 3 4 4 PLK3 1 44800672 Missense_Mutation SNP A C3N-02149_T 19391940 44800672 204155750 9 28193 ZSWIM5 0 . GRCh38 1 45058738 45058738 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1123A>G p.Arg375Gly p.R375G ENST00000359600 4/14 329 168 161 229 228 1 strelka-varscan-mutect ZSWIM5,missense_variant,p.Arg375Gly,ENST00000359600,NM_020883.1; C ENST00000359600 Transcript missense_variant 1329/5819 1123/3558 375/1185 R/G Aga/Gga 1 -1 ZSWIM5 HGNC HGNC:29299 protein_coding YES CCDS41319.1 ENSP00000352614 Q9P217 UPI00001C1D76 NM_020883.1 deleterious(0.03) 4/14 hmmpanther:PTHR22619,hmmpanther:PTHR22619:SF2 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 45058738 45058738 T C 1 0 0 0 0 1 0 0 0 18845 1559 54 5 5 ZSWIM5 1 45058738 Missense_Mutation SNP T C3N-02149_T 258066 45058738 203897684 10 28194 MMACHC 0 . GRCh38 1 45500370 45500370 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.38A>T p.Glu13Val p.E13V ENST00000401061 1/4 840 457 383 627 627 0 strelka-varscan-mutect MMACHC,missense_variant,p.Glu13Val,ENST00000401061,NM_015506.2;MMACHC,5_prime_UTR_variant,,ENST00000616135,;CCDC163P,upstream_gene_variant,,ENST00000626657,;CCDC163P,upstream_gene_variant,,ENST00000629482,;CCDC163P,upstream_gene_variant,,ENST00000629009,;CCDC163P,upstream_gene_variant,,ENST00000628397,;CCDC163P,upstream_gene_variant,,ENST00000626177,;CCDC163P,upstream_gene_variant,,ENST00000625766,;CCDC163P,upstream_gene_variant,,ENST00000628293,;CCDC163P,upstream_gene_variant,,ENST00000629670,; T ENST00000401061 Transcript missense_variant 318/5296 38/849 13/282 E/V gAg/gTg 1 1 MMACHC HGNC HGNC:24525 protein_coding YES CCDS41324.1 ENSP00000383840 Q9Y4U1 UPI00001C1D6D NM_015506.2 deleterious(0.03) 1/4 hmmpanther:PTHR31457 MODERATE SNV 2 1 PASS rs1010232462 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 45500370 45500370 A T 1 0 0 0 0 1 0 0 0 9604 304 11 4 4 MMACHC 1 45500370 Missense_Mutation SNP A C3N-02149_T 441632 45500370 203456052 11 28195 ERICH3 0 . GRCh38 1 74572583 74572583 + Frame_Shift_Del DEL C C - rs767836444 C3N-02149_T C3N-02149_N C C c.3127delG p.Glu1043LysfsTer12 p.E1043Kfs*12 ENST00000326665 14/15 258 209 49 423 423 0 sindel-varindel-pindel ERICH3,frameshift_variant,p.Glu1043LysfsTer12,ENST00000326665,NM_001002912.4;ERICH3-AS1,upstream_gene_variant,,ENST00000612390,;ERICH3,non_coding_transcript_exon_variant,,ENST00000433746,;ERICH3,downstream_gene_variant,,ENST00000614534,; - ENST00000326665 Transcript frameshift_variant 3346/7159 3127/4593 1043/1530 E/X Gaa/aa rs767836444 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 14/15 hmmpanther:PTHR23034 HIGH deletion 5 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9979821 1 1 1 0 - 7 5 92 74572583 74572583 C - 1 0 1 0 1 0 0 0 0 5083 864 30 0 0 ERICH3 1 74572583 Frame_Shift_Del DEL C C3N-02149_T 29072213 74572583 174383839 12 28196 AK5 0 . GRCh38 1 77287049 77287049 + Missense_Mutation SNP G G C rs370854870 C3N-02149_T C3N-02149_N G G c.169G>C p.Asp57His p.D57H ENST00000354567 2/14 248 224 24 199 199 0 strelka-varscan-mutect AK5,missense_variant,p.Asp31His,ENST00000344720,NM_012093.3;AK5,missense_variant,p.Asp57His,ENST00000354567,NM_174858.2;AK5,missense_variant,p.Asp31His,ENST00000478407,;AK5,non_coding_transcript_exon_variant,,ENST00000317704,; C ENST00000354567 Transcript missense_variant 432/3251 169/1689 57/562 D/H Gat/Cat rs370854870 1 1 AK5 HGNC HGNC:365 protein_coding YES CCDS675.1 ENSP00000346577 Q9Y6K8 UPI0000167E20 NM_174858.2 deleterious(0) 2/14 hmmpanther:PTHR23359:SF79,hmmpanther:PTHR23359 MODERATE 1 SNV 1 1 PASS rs370854870 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 77287049 77287049 G C 1 0 0 0 0 1 0 0 0 522 1174 41 4 4 AK5 1 77287049 Missense_Mutation SNP G C3N-02149_T 2714466 77287049 171669373 13 28197 COL11A1 0 . GRCh38 1 102886979 102886979 + Missense_Mutation SNP T T G C3N-02149_T C3N-02149_N T T c.4686A>C p.Gln1562His p.Q1562H ENST00000370096 63/67 414 388 26 516 516 0 strelka-varscan-mutect COL11A1,missense_variant,p.Gln1574His,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Gln1562His,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Gln1523His,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Gln1446His,ENST00000512756,NM_080630.3;COL11A1,3_prime_UTR_variant,,ENST00000635193,; G ENST00000370096 Transcript missense_variant 4999/7286 4686/5421 1562/1806 Q/H caA/caC COSM893100,COSM893101 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 deleterious(0.02) 63/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 102886979 102886979 T G 1 0 0 0 0 1 0 0 0 3455 1606 56 5 5 COL11A1 1 102886979 Missense_Mutation SNP T C3N-02149_T 25599930 102886979 146069443 14 28198 COL11A1 0 . GRCh38 1 102913639 102913639 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.4030C>A p.Pro1344Thr p.P1344T ENST00000370096 53/67 246 203 43 401 401 0 strelka-varscan-mutect COL11A1,missense_variant,p.Pro1356Thr,ENST00000358392,NM_080629.2;COL11A1,missense_variant,p.Pro1344Thr,ENST00000370096,NM_001854.3;COL11A1,missense_variant,p.Pro1305Thr,ENST00000353414,NM_001190709.1;COL11A1,missense_variant,p.Pro1228Thr,ENST00000512756,NM_080630.3;COL11A1,splice_region_variant,,ENST00000635193,; T ENST00000370096 Transcript missense_variant,splice_region_variant 4343/7286 4030/5421 1344/1806 P/T Ccg/Acg 1 -1 COL11A1 HGNC HGNC:2186 protein_coding YES CCDS778.1 ENSP00000359114 P12107 UPI00002053EF NM_001854.3 tolerated(0.2) 53/67 hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF42,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 102913639 102913639 G T 1 0 0 0 0 1 0 0 0 3455 1275 44 2 2 COL11A1 1 102913639 Missense_Mutation SNP G C3N-02149_T 26660 102913639 146042783 15 28199 RBM15 0 . GRCh38 1 110341724 110341724 + Silent SNP G G T rs187367667 C3N-02149_T C3N-02149_N G G c.2319G>T p.= p.G773G ENST00000369784 1/3 217 202 15 328 327 1 strelka-varscan-mutect RBM15,synonymous_variant,p.=,ENST00000369784,;RBM15,synonymous_variant,p.=,ENST00000618772,NM_022768.4;RBM15,synonymous_variant,p.=,ENST00000602849,;RBM15,synonymous_variant,p.=,ENST00000487146,NM_001201545.1;RBM15,synonymous_variant,p.=,ENST00000617047,;RP5-1074L1.1,upstream_gene_variant,,ENST00000449169,; T ENST00000369784 Transcript synonymous_variant 3219/4244 2319/2934 773/977 G ggG/ggT rs187367667 1 1 RBM15 HGNC HGNC:14959 protein_coding YES CCDS822.1 ENSP00000358799 Q96T37 UPI000013E1C5 1/3 hmmpanther:PTHR23189:SF43,hmmpanther:PTHR23189 LOW 1 SNV 1 1 PASS rs187367667 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 110341724 110341724 G T 1 0 0 0 0 0 0 0 1 13282 1161 41 2 2 RBM15 1 110341724 Silent SNP G C3N-02149_T 7428085 110341724 138614698 16 28200 SLC16A1 0 . GRCh38 1 112917849 112917849 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.557T>C p.Leu186Pro p.L186P ENST00000538576 4/5 134 109 25 203 203 0 strelka-varscan SLC16A1,missense_variant,p.Leu186Pro,ENST00000538576,NM_001166496.1;SLC16A1,missense_variant,p.Leu186Pro,ENST00000369626,NM_003051.3;SLC16A1,missense_variant,p.Leu186Pro,ENST00000458229,;SLC16A1,missense_variant,p.Leu186Pro,ENST00000443580,;SLC16A1,missense_variant,p.Leu186Pro,ENST00000429288,;SLC16A1,downstream_gene_variant,,ENST00000481750,; G ENST00000538576 Transcript missense_variant 1389/4374 557/1503 186/500 L/P cTa/cCa 1 -1 SLC16A1 HGNC HGNC:10922 protein_coding YES CCDS858.1 ENSP00000441065 P53985 A0A024R0H1 UPI00000012F5 NM_001166496.1 deleterious(0) 4/5 Gene3D:1.20.1250.20,Pfam_domain:PF07690,PROSITE_profiles:PS50850,hmmpanther:PTHR11360,hmmpanther:PTHR11360:SF24,Superfamily_domains:SSF103473,TIGRFAM_domain:TIGR00892,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 112917849 112917849 A G 1 0 0 0 0 1 0 0 0 14668 420 15 5 5 SLC16A1 1 112917849 Missense_Mutation SNP A C3N-02149_T 2576125 112917849 136038573 17 28201 SETDB1 0 . GRCh38 1 150927957 150927957 + Silent SNP C C G C3N-02149_T C3N-02149_N C C c.243C>G p.= p.L81L ENST00000271640 2/22 193 163 30 207 207 0 strelka-varscan-mutect SETDB1,synonymous_variant,p.=,ENST00000271640,NM_001145415.1;SETDB1,synonymous_variant,p.=,ENST00000368969,NM_012432.3;SETDB1,synonymous_variant,p.=,ENST00000498193,;SETDB1,synonymous_variant,p.=,ENST00000534805,;SETDB1,synonymous_variant,p.=,ENST00000368962,NM_001243491.1;SETDB1,synonymous_variant,p.=,ENST00000368963,;SETDB1,synonymous_variant,p.=,ENST00000448029,;SETDB1,synonymous_variant,p.=,ENST00000423081,;SETDB1,synonymous_variant,p.=,ENST00000525956,;SETDB1,non_coding_transcript_exon_variant,,ENST00000459773,;SETDB1,non_coding_transcript_exon_variant,,ENST00000487584,;SETDB1,synonymous_variant,p.=,ENST00000368964,;SETDB1,non_coding_transcript_exon_variant,,ENST00000481219,;SETDB1,non_coding_transcript_exon_variant,,ENST00000463774,; G ENST00000271640 Transcript synonymous_variant 433/4437 243/3876 81/1291 L ctC/ctG COSM1583406,COSM895626 1 1 SETDB1 HGNC HGNC:10761 protein_coding YES CCDS44217.1 ENSP00000271640 Q15047 UPI0000135897 NM_001145415.1 2/22 PROSITE_profiles:PS51573 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 150927957 150927957 C G 1 0 0 0 0 0 0 0 1 14416 900 32 4 4 SETDB1 1 150927957 Silent SNP C C3N-02149_T 38010108 150927957 98028465 18 28202 FAM63A 0 . GRCh38 1 151002559 151002559 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.203T>A p.Val68Asp p.V68D ENST00000361738 3/11 360 305 55 361 361 0 strelka-varscan-mutect FAM63A,missense_variant,p.Val20Asp,ENST00000361936,NM_018379.4;FAM63A,missense_variant,p.Val20Asp,ENST00000622754,;FAM63A,missense_variant,p.Val68Asp,ENST00000361738,NM_001163258.1;FAM63A,intron_variant,,ENST00000312210,NM_001040217.2,NM_001163260.1;FAM63A,intron_variant,,ENST00000493834,NM_001163259.1;FAM63A,upstream_gene_variant,,ENST00000497067,;FAM63A,intron_variant,,ENST00000470877,; T ENST00000361738 Transcript missense_variant 423/1961 203/1554 68/517 V/D gTc/gAc 1 -1 FAM63A HGNC HGNC:25648 protein_coding YES CCDS53361.1 ENSP00000354669 Q8N5J2 UPI0001AE7915 NM_001163258.1 tolerated_low_confidence(0.07) 3/11 hmmpanther:PTHR18063,hmmpanther:PTHR18063:SF7 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 151002559 151002559 A T 1 0 0 0 0 1 0 0 0 5462 275 10 4 4 FAM63A 1 151002559 Missense_Mutation SNP A C3N-02149_T 74602 151002559 97953863 19 28203 SNX27 0 . GRCh38 1 151692565 151692565 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.1370C>G p.Thr457Ser p.T457S ENST00000368843 9/12 163 144 19 137 137 0 strelka-varscan-mutect SNX27,missense_variant,p.Thr457Ser,ENST00000368843,NM_030918.5;SNX27,missense_variant,p.Thr457Ser,ENST00000458013,;SNX27,missense_variant,p.Thr364Ser,ENST00000368838,;SNX27,3_prime_UTR_variant,,ENST00000368841,; G ENST00000368843 Transcript missense_variant 1490/7197 1370/1587 457/528 T/S aCt/aGt 1 1 SNX27 HGNC HGNC:20073 protein_coding YES CCDS1001.1 ENSP00000357836 Q96L92 UPI00001A962E NM_030918.5 tolerated(0.48) 9/12 hmmpanther:PTHR12431,hmmpanther:PTHR12431:SF17 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 151692565 151692565 C G 1 0 0 0 0 1 0 0 0 15218 565 20 4 4 SNX27 1 151692565 Missense_Mutation SNP C C3N-02149_T 690006 151692565 97263857 20 28204 HRNR 0 . GRCh38 1 152214686 152214686 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.6943T>G p.Tyr2315Asp p.Y2315D ENST00000368801 3/3 318 295 23 382 379 3 varscan-mutect HRNR,missense_variant,p.Tyr2315Asp,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENST00000368801 Transcript missense_variant 7019/9623 6943/8553 2315/2850 Y/D Tac/Gac 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 deleterious(0.04) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 152214686 152214686 A C 1 0 0 0 0 1 0 0 0 7254 420 15 5 5 HRNR 1 152214686 Missense_Mutation SNP A C3N-02149_T 522121 152214686 96741736 21 28205 LCE1B 0 . GRCh38 1 152812658 152812658 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.212G>T p.Gly71Val p.G71V ENST00000360090 1/1 309 254 55 395 394 1 strelka-varscan-mutect LCE1B,missense_variant,p.Gly71Val,ENST00000360090,NM_178349.1; T ENST00000360090 Transcript missense_variant 688/1139 212/357 71/118 G/V gGg/gTg 1 1 LCE1B HGNC HGNC:16611 protein_coding YES CCDS1027.1 ENSP00000353203 Q5T7P3 UPI000014099C NM_178349.1 deleterious_low_confidence(0) 1/1 Pfam_domain:PF14672,hmmpanther:PTHR23263,Low_complexity_(Seg):seg MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 152812658 152812658 G T 1 0 0 0 0 1 0 0 0 8565 1232 43 2 2 LCE1B 1 152812658 Missense_Mutation SNP G C3N-02149_T 597972 152812658 96143764 22 28206 SLC39A1 0 . GRCh38 1 153960582 153960582 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.491G>T p.Gly164Val p.G164V ENST00000368623 3/3 240 198 42 244 244 0 strelka-varscan-mutect SLC39A1,missense_variant,p.Gly164Val,ENST00000368623,;SLC39A1,missense_variant,p.Gly164Val,ENST00000310483,NM_014437.4;SLC39A1,missense_variant,p.Gly164Val,ENST00000368621,NM_001271957.1;SLC39A1,missense_variant,p.Gly164Val,ENST00000621013,NM_001271959.1;SLC39A1,missense_variant,p.Gly164Val,ENST00000617697,NM_001271960.1;SLC39A1,missense_variant,p.Gly164Val,ENST00000356205,NM_001271958.1;SLC39A1,missense_variant,p.Gly164Val,ENST00000429040,;SLC39A1,missense_variant,p.Gly164Val,ENST00000413622,;SLC39A1,missense_variant,p.Gly164Val,ENST00000417348,;SLC39A1,3_prime_UTR_variant,,ENST00000537590,NM_001271961.1;CRTC2,upstream_gene_variant,,ENST00000368633,NM_181715.2;CRTC2,upstream_gene_variant,,ENST00000368630,;MIR6737,downstream_gene_variant,,ENST00000617385,;RP11-422P24.12,upstream_gene_variant,,ENST00000633140,;SLC39A1,downstream_gene_variant,,ENST00000461071,;CRTC2,upstream_gene_variant,,ENST00000476883,;CRTC2,upstream_gene_variant,,ENST00000492073,;CRTC2,upstream_gene_variant,,ENST00000303569,;CRTC2,upstream_gene_variant,,ENST00000487235,; A ENST00000368623 Transcript missense_variant 1251/2723 491/975 164/324 G/V gGg/gTg 1 -1 SLC39A1 HGNC HGNC:12876 protein_coding YES CCDS1055.1 ENSP00000357612 Q9NY26 UPI000006DDFE deleterious(0.04) 3/3 Pfam_domain:PF02535,hmmpanther:PTHR11040,hmmpanther:PTHR11040:SF58 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 153960582 153960582 C A 1 0 0 0 0 1 0 0 0 14890 623 22 2 2 SLC39A1 1 153960582 Missense_Mutation SNP C C3N-02149_T 1147924 153960582 94995840 23 28207 CHRNB2 0 . GRCh38 1 154572061 154572061 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1238C>A p.Pro413His p.P413H ENST00000368476 5/6 89 74 15 58 58 0 strelka-varscan-mutect CHRNB2,missense_variant,p.Pro413His,ENST00000368476,NM_000748.2;CHRNB2,missense_variant,p.Pro415His,ENST00000637900,;CHRNB2,upstream_gene_variant,,ENST00000635876,;CHRNB2,missense_variant,p.Pro413His,ENST00000636034,;CHRNB2,downstream_gene_variant,,ENST00000636695,; A ENST00000368476 Transcript missense_variant 1502/5867 1238/1509 413/502 P/H cCc/cAc 1 1 CHRNB2 HGNC HGNC:1962 protein_coding YES CCDS1070.1 ENSP00000357461 P17787 Q5SXY3 UPI000012526E NM_000748.2 tolerated(0.4) 5/6 Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF80,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 154572061 154572061 C A 1 0 0 0 0 1 0 0 0 3151 623 22 2 2 CHRNB2 1 154572061 Missense_Mutation SNP C C3N-02149_T 611479 154572061 94384361 24 28208 KIAA0907 0 . GRCh38 1 155921507 155921507 + Nonsense_Mutation SNP G G C rs201266630 C3N-02149_T C3N-02149_N G G c.1134C>G p.Tyr378Ter p.Y378* ENST00000368321 10/14 347 322 25 501 501 0 strelka-varscan-mutect KIAA0907,stop_gained,p.Tyr378Ter,ENST00000368320,;KIAA0907,stop_gained,p.Tyr378Ter,ENST00000368321,NM_014949.3;KIAA0907,missense_variant,p.Arg345Gly,ENST00000368319,;SNORA80E,upstream_gene_variant,,ENST00000384744,;SCARNA4,downstream_gene_variant,,ENST00000625402,;SCARNA4,downstream_gene_variant,,ENST00000629045,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000482337,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000478002,;KIAA0907,non_coding_transcript_exon_variant,,ENST00000483237,;KIAA0907,downstream_gene_variant,,ENST00000466713,;KIAA0907,upstream_gene_variant,,ENST00000465953,;KIAA0907,upstream_gene_variant,,ENST00000466520,; C ENST00000368321 Transcript stop_gained 1158/2947 1134/1845 378/614 Y/* taC/taG rs201266630 1 -1 KIAA0907 HGNC HGNC:29145 protein_coding YES CCDS30885.1 ENSP00000357304 Q7Z7F0 UPI00001A36E0 NM_014949.3 10/14 Low_complexity_(Seg):seg,hmmpanther:PTHR15744:SF0,hmmpanther:PTHR15744 HIGH 1 SNV 1 1 PASS rs201266630 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 92 155921507 155921507 G C 1 0 0 0 0 0 1 0 0 8094 1149 40 4 4 KIAA0907 1 155921507 Nonsense_Mutation SNP G C3N-02149_T 1349446 155921507 93034915 25 28209 FCRL5 0 . GRCh38 1 157521280 157521280 + Missense_Mutation SNP C C A rs752277017 C3N-02149_T C3N-02149_N C C c.2252G>T p.Arg751Leu p.R751L ENST00000361835 11/17 134 113 21 169 169 0 strelka-varscan-mutect FCRL5,missense_variant,p.Arg751Leu,ENST00000361835,NM_001195388.1,NM_031281.2;FCRL5,downstream_gene_variant,,ENST00000368190,;FCRL5,non_coding_transcript_exon_variant,,ENST00000461387,;FCRL5,non_coding_transcript_exon_variant,,ENST00000497286,;FCRL5,upstream_gene_variant,,ENST00000483875,; A ENST00000361835 Transcript missense_variant 2410/5390 2252/2934 751/977 R/L cGc/cTc rs752277017 1 -1 FCRL5 HGNC HGNC:18508 protein_coding YES CCDS1165.1 ENSP00000354691 Q96RD9 UPI0000458907 NM_001195388.1,NM_031281.2 tolerated(0.25) 11/17 Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs752277017 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 157521280 157521280 C A 1 0 0 0 0 1 0 0 0 5660 768 27 1 1 FCRL5 1 157521280 Missense_Mutation SNP C C3N-02149_T 1599773 157521280 91435142 26 28210 SPTA1 0 . GRCh38 1 158636676 158636676 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.5275G>C p.Glu1759Gln p.E1759Q ENST00000368147 37/52 428 397 31 519 519 0 strelka-varscan-mutect SPTA1,missense_variant,p.Glu1759Gln,ENST00000368147,NM_003126.2;SPTA1,upstream_gene_variant,,ENST00000461624,;SPTA1,downstream_gene_variant,,ENST00000465741,; G ENST00000368147 Transcript missense_variant 5456/7999 5275/7260 1759/2419 E/Q Gag/Cag 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 deleterious(0.04) 37/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 158636676 158636676 C G 1 0 0 0 0 1 0 0 0 15472 922 32 4 4 SPTA1 1 158636676 Missense_Mutation SNP C C3N-02149_T 1115396 158636676 90319746 27 28211 OR6K6 0 . GRCh38 1 158755229 158755229 + Silent SNP A A G novel C3N-02149_T C3N-02149_N A A c.414A>G p.= p.T138T ENST00000368144 1/1 278 239 39 312 312 0 strelka-varscan-mutect OR6K6,synonymous_variant,p.=,ENST00000368144,NM_001005184.1; G ENST00000368144 Transcript synonymous_variant 510/1172 414/1032 138/343 T acA/acG 1 1 OR6K6 HGNC HGNC:15033 protein_coding YES CCDS30904.1 ENSP00000357126 Q8NGW6 UPI000015F229 NM_001005184.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 158755229 158755229 A G 1 0 0 0 0 0 0 0 1 11273 175 7 5 5 OR6K6 1 158755229 Silent SNP A C3N-02149_T 118553 158755229 90201193 28 28212 MNDA 0 . GRCh38 1 158847816 158847816 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.1076T>G p.Ile359Ser p.I359S ENST00000368141 6/7 264 241 23 330 328 2 strelka-varscan-mutect MNDA,missense_variant,p.Ile359Ser,ENST00000368141,NM_002432.1;MNDA,missense_variant,p.Ile65Ser,ENST00000438394,; G ENST00000368141 Transcript missense_variant 1337/1752 1076/1224 359/407 I/S aTc/aGc 1 1 MNDA HGNC HGNC:7183 protein_coding YES CCDS1177.1 ENSP00000357123 P41218 Q5VUU6 UPI0000001609 NM_002432.1 deleterious(0) 6/7 Gene3D:2.40.50.140,Pfam_domain:PF02760,PROSITE_profiles:PS50834,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF18,Superfamily_domains:SSF159141 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 158847816 158847816 T G 1 0 0 0 0 1 0 0 0 9640 1435 50 5 5 MNDA 1 158847816 Missense_Mutation SNP T C3N-02149_T 92587 158847816 90108606 29 28213 PYHIN1 0 . GRCh38 1 158942101 158942101 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.704A>T p.Gln235Leu p.Q235L ENST00000368140 5/9 284 244 40 328 327 1 strelka-varscan-mutect PYHIN1,missense_variant,p.Gln235Leu,ENST00000368140,NM_152501.4;PYHIN1,missense_variant,p.Gln226Leu,ENST00000368138,NM_198928.4;PYHIN1,missense_variant,p.Gln235Leu,ENST00000392254,NM_198929.4;PYHIN1,missense_variant,p.Gln226Leu,ENST00000392252,NM_198930.3;PYHIN1,downstream_gene_variant,,ENST00000368135,;PYHIN1,downstream_gene_variant,,ENST00000458222,;PYHIN1,non_coding_transcript_exon_variant,,ENST00000485134,; T ENST00000368140 Transcript missense_variant 949/2083 704/1479 235/492 Q/L cAa/cTa 1 1 PYHIN1 HGNC HGNC:28894 protein_coding YES CCDS1178.1 ENSP00000357122 Q6K0P9 UPI0000225618 NM_152501.4 tolerated(0.06) 5/9 Gene3D:2.40.50.140,Pfam_domain:PF02760,PROSITE_profiles:PS50834,hmmpanther:PTHR12200,hmmpanther:PTHR12200:SF14,Superfamily_domains:SSF159141 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 158942101 158942101 A T 1 0 0 0 0 1 0 0 0 13019 130 5 4 4 PYHIN1 1 158942101 Missense_Mutation SNP A C3N-02149_T 94285 158942101 90014321 30 28214 NCSTN 0 . GRCh38 1 160356659 160356659 + Frame_Shift_Del DEL G G - rs200141699 C3N-02149_T C3N-02149_N G G c.1699delG p.Val567TyrfsTer8 p.V567Yfs*8 ENST00000294785 15/17 277 232 45 377 377 0 sindel-varindel-pindel NCSTN,frameshift_variant,p.Val547TyrfsTer8,ENST00000368063,NM_001290184.1;NCSTN,frameshift_variant,p.Val567TyrfsTer8,ENST00000294785,NM_001290186.1,NM_015331.2;NCSTN,frameshift_variant,p.Val244TyrfsTer8,ENST00000435149,;NCSTN,downstream_gene_variant,,ENST00000424645,;NCSTN,downstream_gene_variant,,ENST00000421914,;NCSTN,downstream_gene_variant,,ENST00000424754,;NCSTN,non_coding_transcript_exon_variant,,ENST00000491390,;NCSTN,downstream_gene_variant,,ENST00000459963,;NCSTN,upstream_gene_variant,,ENST00000469159,; - ENST00000294785 Transcript frameshift_variant 1824/2936 1699/2130 567/709 V/X Gta/ta rs200141699 1 1 NCSTN HGNC HGNC:17091 protein_coding YES CCDS1203.1 ENSP00000294785 Q92542 UPI0000042050 NM_001290186.1,NM_015331.2 15/17 hmmpanther:PTHR21092:SF0,hmmpanther:PTHR21092 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 160356659 160356659 G - 1 0 1 0 1 0 0 0 0 10261 1377 48 0 0 NCSTN 1 160356659 Frame_Shift_Del DEL G C3N-02149_T 1414558 160356659 88599763 31 28215 NECTIN4 0 . GRCh38 1 161074251 161074251 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.1123C>T p.His375Tyr p.H375Y ENST00000368012 6/9 613 558 55 570 568 2 strelka-varscan-mutect NECTIN4,missense_variant,p.His375Tyr,ENST00000368012,NM_030916.2;ARHGAP30,upstream_gene_variant,,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,upstream_gene_variant,,ENST00000368015,NM_001287602.1;ARHGAP30,upstream_gene_variant,,ENST00000368016,NM_181720.2;NECTIN4,non_coding_transcript_exon_variant,,ENST00000486694,;ARHGAP30,upstream_gene_variant,,ENST00000461003,;ARHGAP30,upstream_gene_variant,,ENST00000490279,;ARHGAP30,upstream_gene_variant,,ENST00000368018,;ARHGAP30,upstream_gene_variant,,ENST00000471492,; A ENST00000368012 Transcript missense_variant 1426/3502 1123/1533 375/510 H/Y Cat/Tat 1 -1 NECTIN4 HGNC HGNC:19688 protein_coding YES CCDS1216.1 ENSP00000356991 Q96NY8 K4PZ75 UPI000006F072 NM_030916.2 tolerated(0.12) 6/9 hmmpanther:PTHR23277:SF11,hmmpanther:PTHR23277 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 161074251 161074251 G A 1 0 0 0 0 1 0 0 0 10336 1348 47 3 3 NECTIN4 1 161074251 Missense_Mutation SNP G C3N-02149_T 717592 161074251 87882171 32 28216 ADAMTS4 0 . GRCh38 1 161192079 161192079 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.2073C>A p.= p.S691S ENST00000367996 8/9 161 130 31 159 158 1 strelka-varscan-mutect ADAMTS4,synonymous_variant,p.=,ENST00000367996,NM_005099.4;ADAMTS4,downstream_gene_variant,,ENST00000367995,;ADAMTS4,downstream_gene_variant,,ENST00000478394,; T ENST00000367996 Transcript synonymous_variant 2502/9773 2073/2514 691/837 S tcC/tcA 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 8/9 hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF05986 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 161192079 161192079 G T 1 0 0 0 0 0 0 0 1 312 987 35 2 2 ADAMTS4 1 161192079 Silent SNP G C3N-02149_T 117828 161192079 87764343 33 28217 OLFML2B 0 . GRCh38 1 162000266 162000266 + Missense_Mutation SNP G G T rs146317042 C3N-02149_T C3N-02149_N G G c.799C>A p.Pro267Thr p.P267T ENST00000367940 5/8 273 239 34 288 287 1 strelka-varscan-mutect OLFML2B,missense_variant,p.Pro266Thr,ENST00000294794,NM_015441.2;OLFML2B,missense_variant,p.Pro267Thr,ENST00000367940,NM_001297713.1; T ENST00000367940 Transcript missense_variant 1009/2685 799/2256 267/751 P/T Ccc/Acc rs146317042 1 -1 OLFML2B HGNC HGNC:24558 protein_coding YES CCDS72966.1 ENSP00000356917 F2Z3N3 UPI0001AE79B2 NM_001297713.1 tolerated(0.38) 5/8 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF37 MODERATE 1 SNV 2 1 PASS rs146317042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 162000266 162000266 G T 1 0 0 0 0 1 0 0 0 10933 1261 44 2 2 OLFML2B 1 162000266 Missense_Mutation SNP G C3N-02149_T 808187 162000266 86956156 34 28218 CEP350 0 . GRCh38 1 180034046 180034046 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.3910A>T p.Ser1304Cys p.S1304C ENST00000367607 16/38 272 224 48 335 335 0 strelka-varscan CEP350,missense_variant,p.Ser1304Cys,ENST00000367607,NM_014810.4; T ENST00000367607 Transcript missense_variant 4328/13491 3910/9354 1304/3117 S/C Agc/Tgc 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 deleterious(0) 16/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 180034046 180034046 A T 1 0 0 0 0 1 0 0 0 2972 188 7 4 4 CEP350 1 180034046 Missense_Mutation SNP A C3N-02149_T 18033780 180034046 68922376 35 28219 PRG4 0 . GRCh38 1 186301648 186301648 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.256T>A p.Cys86Ser p.C86S ENST00000445192 4/13 619 516 103 754 754 0 strelka-varscan PRG4,missense_variant,p.Cys86Ser,ENST00000445192,NM_005807.4;PRG4,missense_variant,p.Cys45Ser,ENST00000367483,NM_001127708.2;PRG4,missense_variant,p.Cys86Ser,ENST00000635041,NM_001303232.1;PRG4,missense_variant,p.Cys86Ser,ENST00000367485,NM_001127709.2,NM_001127710.2;PRG4,missense_variant,p.Cys45Ser,ENST00000367482,;PRG4,missense_variant,p.Cys45Ser,ENST00000533951,; A ENST00000445192 Transcript missense_variant 301/5044 256/4215 86/1404 C/S Tgc/Agc 1 1 PRG4 HGNC HGNC:9364 protein_coding YES CCDS1369.1 ENSP00000399679 Q92954 UPI0004620CBB NM_005807.4 deleterious(0) 4/13 PROSITE_profiles:PS50958,hmmpanther:PTHR22917,hmmpanther:PTHR22917:SF1,PROSITE_patterns:PS00524,Pfam_domain:PF01033,SMART_domains:SM00201,Superfamily_domains:0049461,Prints_domain:PR00022 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 186301648 186301648 T A 1 0 0 0 0 1 0 0 0 12615 1580 55 4 4 PRG4 1 186301648 Missense_Mutation SNP T C3N-02149_T 6267602 186301648 62654774 36 28220 CRB1 0 . GRCh38 1 197421230 197421230 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1402A>T p.Ser468Cys p.S468C ENST00000367400 6/12 458 390 68 539 539 0 strelka-varscan CRB1,missense_variant,p.Ser399Cys,ENST00000535699,NM_001257965.1;CRB1,missense_variant,p.Ser468Cys,ENST00000367400,NM_201253.2;CRB1,missense_variant,p.Ser356Cys,ENST00000367399,NM_001193640.1;CRB1,missense_variant,p.Ser468Cys,ENST00000538660,NM_001257966.1;CRB1,5_prime_UTR_variant,,ENST00000367397,;CRB1,non_coding_transcript_exon_variant,,ENST00000476483,;CRB1,upstream_gene_variant,,ENST00000480086,;CRB1,missense_variant,p.Ser468Cys,ENST00000484075,; T ENST00000367400 Transcript missense_variant 1537/4932 1402/4221 468/1406 S/C Agc/Tgc 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 deleterious(0) 6/12 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_profiles:PS50026,hmmpanther:PTHR24049,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF49899,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 197421230 197421230 A T 1 0 0 0 0 1 0 0 0 3648 188 7 4 4 CRB1 1 197421230 Missense_Mutation SNP A C3N-02149_T 11119582 197421230 51535192 37 28221 LGR6 0 . GRCh38 1 202309145 202309145 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1375G>T p.Ala459Ser p.A459S ENST00000367278 15/18 229 197 32 230 229 1 strelka-varscan LGR6,missense_variant,p.Ala459Ser,ENST00000367278,NM_001017403.1;LGR6,missense_variant,p.Ala407Ser,ENST00000255432,NM_021636.2;LGR6,missense_variant,p.Ala320Ser,ENST00000439764,NM_001017404.1;LGR6,downstream_gene_variant,,ENST00000423542,;LGR6,downstream_gene_variant,,ENST00000308543,;LGR6,3_prime_UTR_variant,,ENST00000487787,; T ENST00000367278 Transcript missense_variant 1464/3567 1375/2904 459/967 A/S Gcc/Tcc 1 1 LGR6 HGNC HGNC:19719 protein_coding YES CCDS30971.1 ENSP00000356247 Q9HBX8 UPI0000161221 NM_001017403.1 tolerated(0.35) 15/18 hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF12,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 202309145 202309145 G T 1 0 0 0 0 1 0 0 0 8668 1203 42 2 2 LGR6 1 202309145 Missense_Mutation SNP G C3N-02149_T 4887915 202309145 46647277 38 28222 NFASC 0 . GRCh38 1 204979535 204979535 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.2152G>A p.Glu718Lys p.E718K ENST00000339876 19/30 314 280 34 305 305 0 strelka-varscan NFASC,missense_variant,p.Glu718Lys,ENST00000339876,NM_001005388.2;NFASC,missense_variant,p.Glu718Lys,ENST00000401399,;NFASC,missense_variant,p.Glu714Lys,ENST00000539706,NM_001160332.1;NFASC,missense_variant,p.Glu714Lys,ENST00000360049,NM_015090.3;NFASC,missense_variant,p.Glu697Lys,ENST00000404076,;NFASC,missense_variant,p.Glu714Lys,ENST00000404907,;NFASC,missense_variant,p.Glu705Lys,ENST00000430393,NM_001160331.1;NFASC,missense_variant,p.Glu688Lys,ENST00000367173,;NFASC,missense_variant,p.Glu714Lys,ENST00000513543,;NFASC,upstream_gene_variant,,ENST00000425360,;NFASC,downstream_gene_variant,,ENST00000403080,NM_001160333.1,NM_001005389.1;NFASC,non_coding_transcript_exon_variant,,ENST00000404977,;NFASC,non_coding_transcript_exon_variant,,ENST00000471392,;NFASC,upstream_gene_variant,,ENST00000468328,;NFASC,3_prime_UTR_variant,,ENST00000504476,;NFASC,non_coding_transcript_exon_variant,,ENST00000512826,;NFASC,downstream_gene_variant,,ENST00000514644,; A ENST00000339876 Transcript missense_variant 2480/10333 2152/3723 718/1240 E/K Gag/Aag 1 1 NFASC HGNC HGNC:29866 protein_coding YES CCDS53460.1 ENSP00000344786 O94856 UPI0000237208 NM_001005388.2 tolerated(0.11) 19/30 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF715,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 204979535 204979535 G A 1 0 0 0 0 1 0 0 0 10396 1059 37 1 1 NFASC 1 204979535 Missense_Mutation SNP G C3N-02149_T 2670390 204979535 43976887 39 28223 KLHDC8A 0 . GRCh38 1 205343579 205343579 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.26T>A p.Phe9Tyr p.F9Y ENST00000367156 5/9 94 88 6 93 93 0 strelka-varscan KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000367156,NM_001271863.1;KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000539253,NM_001271864.1,NM_001271865.1;KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000367155,NM_018203.2;KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000491471,;KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000606887,;KLHDC8A,missense_variant,p.Phe9Tyr,ENST00000607173,;KLHDC8A,5_prime_UTR_variant,,ENST00000607826,;KLHDC8A,intron_variant,,ENST00000460687,;KLHDC8A,upstream_gene_variant,,ENST00000606181,;KLHDC8A,downstream_gene_variant,,ENST00000606529,;KLHDC8A,downstream_gene_variant,,ENST00000607193,;KLHDC8A,downstream_gene_variant,,ENST00000606111,; T ENST00000367156 Transcript missense_variant 843/3177 26/1053 9/350 F/Y tTc/tAc 1 -1 KLHDC8A HGNC HGNC:25573 protein_coding YES CCDS30985.1 ENSP00000356124 Q8IYD2 A0A024R981 UPI00000728EF NM_001271863.1 tolerated(0.23) 5/9 hmmpanther:PTHR24412:SF123,hmmpanther:PTHR24412,Gene3D:1zgkA00,Superfamily_domains:0052715 MODERATE 1 SNV 2 1 PASS . . 0 204 5 0 0 0 0 0 -12.61332 1 1 1 1 0 T 3 4 92 205343579 205343579 A T 1 0 0 0 0 1 0 0 0 8226 246 9 4 4 KLHDC8A 1 205343579 Missense_Mutation SNP A C3N-02149_T 364044 205343579 43612843 40 28224 CR2 0 . GRCh38 1 207466684 207466684 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.217G>T p.Gly73Ter p.G73* ENST00000367057 2/20 407 323 84 524 522 2 strelka-varscan CR2,stop_gained,p.Gly73Ter,ENST00000367057,NM_001006658.2;CR2,stop_gained,p.Gly73Ter,ENST00000367058,NM_001877.4;CR2,stop_gained,p.Gly73Ter,ENST00000367059,;CR2,non_coding_transcript_exon_variant,,ENST00000479186,;CR2,upstream_gene_variant,,ENST00000485707,;CR2,upstream_gene_variant,,ENST00000475194,; T ENST00000367057 Transcript stop_gained 406/4240 217/3279 73/1092 G/* Gga/Tga 1 1 CR2 HGNC HGNC:2336 protein_coding YES CCDS31007.1 ENSP00000356024 P20023 UPI0000366600 NM_001006658.2 2/20 PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF391,Gene3D:2.10.70.10,Pfam_domain:PF00084,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 207466684 207466684 G T 1 0 0 0 0 0 1 0 0 3640 1349 47 2 2 CR2 1 207466684 Nonsense_Mutation SNP G C3N-02149_T 2123105 207466684 41489738 41 28225 USH2A 0 . GRCh38 1 215786688 215786688 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.10369A>T p.Asn3457Tyr p.N3457Y ENST00000307340 52/72 408 335 73 423 423 0 strelka-varscan USH2A,missense_variant,p.Asn3457Tyr,ENST00000307340,NM_206933.2; A ENST00000307340 Transcript missense_variant 10756/18883 10369/15609 3457/5202 N/Y Aac/Tac 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 deleterious(0) 52/72 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 215786688 215786688 T A 1 0 0 0 0 1 0 0 0 17570 1841 64 4 4 USH2A 1 215786688 Missense_Mutation SNP T C3N-02149_T 8320004 215786688 33169734 42 28226 GPATCH2 0 . GRCh38 1 217431359 217431359 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1373T>A p.Val458Glu p.V458E ENST00000366935 10/10 245 196 49 244 244 0 strelka-varscan GPATCH2,missense_variant,p.Val458Glu,ENST00000366935,NM_018040.3; T ENST00000366935 Transcript missense_variant 1484/5851 1373/1587 458/528 V/E gTa/gAa 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 deleterious(0) 10/10 hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 217431359 217431359 A T 1 0 0 0 0 1 0 0 0 6491 391 14 4 4 GPATCH2 1 217431359 Missense_Mutation SNP A C3N-02149_T 1644671 217431359 31525063 43 28227 BROX 0 . GRCh38 1 222725517 222725517 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.542A>C p.Glu181Ala p.E181A ENST00000340934 7/13 226 204 22 225 225 0 strelka-varscan BROX,missense_variant,p.Glu181Ala,ENST00000340934,NM_144695.3;BROX,missense_variant,p.Glu149Ala,ENST00000612948,NM_001288579.1;BROX,missense_variant,p.Glu149Ala,ENST00000539697,NM_001288580.1;BROX,missense_variant,p.Glu181Ala,ENST00000537020,NM_001288581.1;BROX,missense_variant,p.Glu181Ala,ENST00000426638,;BROX,non_coding_transcript_exon_variant,,ENST00000489191,;BROX,non_coding_transcript_exon_variant,,ENST00000473962,; C ENST00000340934 Transcript missense_variant 948/4124 542/1236 181/411 E/A gAa/gCa 1 1 BROX HGNC HGNC:26512 protein_coding YES CCDS1534.1 ENSP00000343742 Q5VW32 UPI000013E1D1 NM_144695.3 deleterious(0.03) 7/13 PROSITE_profiles:PS51180,hmmpanther:PTHR23032,hmmpanther:PTHR23032:SF1,Gene3D:2xs1A01,Pfam_domain:PF03097,SMART_domains:SM01041 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 222725517 222725517 A C 1 0 0 0 0 1 0 0 0 1693 246 9 5 5 BROX 1 222725517 Missense_Mutation SNP A C3N-02149_T 5294158 222725517 26230905 44 28228 CAPN8 0 . GRCh38 1 223544777 223544777 + Frame_Shift_Del DEL T T - novel C3N-02149_T C3N-02149_N T T c.1907delA p.Lys636ArgfsTer34 p.K636Rfs*34 ENST00000366872 18/21 256 211 45 298 298 0 sindel-varindel-pindel CAPN8,frameshift_variant,p.Lys636ArgfsTer34,ENST00000366872,;CAPN8,frameshift_variant,p.Lys89ArgfsTer34,ENST00000430824,;CAPN8,intron_variant,,ENST00000442247,;CAPN8,non_coding_transcript_exon_variant,,ENST00000482401,;CAPN8,upstream_gene_variant,,ENST00000482183,;CAPN8,upstream_gene_variant,,ENST00000484873,; - ENST00000366872 Transcript frameshift_variant 1995/2427 1907/2112 636/703 K/X aAg/ag 1 -1 CAPN8 HGNC HGNC:1485 protein_coding YES CCDS73038.1 ENSP00000355837 A6NHC0 UPI0000157E1A 18/21 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF52,Superfamily_domains:SSF47473 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 223544777 223544777 T - 1 0 1 0 1 0 0 0 0 2326 1623 56 0 0 CAPN8 1 223544777 Frame_Shift_Del DEL T C3N-02149_T 819260 223544777 25411645 45 28229 ACBD3 0 . GRCh38 1 226186468 226186468 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.208G>T p.Glu70Ter p.E70* ENST00000366812 1/8 182 135 47 269 269 0 strelka-varscan ACBD3,stop_gained,p.Glu70Ter,ENST00000366812,NM_022735.3;RP11-275I14.2,downstream_gene_variant,,ENST00000429867,; A ENST00000366812 Transcript stop_gained 263/3573 208/1587 70/528 E/* Gag/Tag 1 -1 ACBD3 HGNC HGNC:15453 protein_coding YES CCDS1551.1 ENSP00000355777 Q9H3P7 A0A024R3P9 UPI000006F1E1 NM_022735.3 1/8 hmmpanther:PTHR22973,hmmpanther:PTHR22973:SF11,Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 226186468 226186468 C A 1 0 0 0 0 0 1 0 0 166 864 30 2 2 ACBD3 1 226186468 Nonsense_Mutation SNP C C3N-02149_T 2641691 226186468 22769954 46 28230 OBSCN 0 . GRCh38 1 228371775 228371775 + Silent SNP G G C C3N-02149_T C3N-02149_N G G c.23868G>C p.= p.G7956G ENST00000570156 105/116 82 60 22 59 59 0 strelka-varscan OBSCN,synonymous_variant,p.=,ENST00000570156,NM_001271223.2;OBSCN,synonymous_variant,p.=,ENST00000366707,;OBSCN,synonymous_variant,p.=,ENST00000422127,NM_001098623.2;OBSCN,synonymous_variant,p.=,ENST00000636875,;OBSCN,synonymous_variant,p.=,ENST00000636476,; C ENST00000570156 Transcript synonymous_variant 23942/26925 23868/26772 7956/8923 G ggG/ggC COSM4794323,COSM4794324 1 1 OBSCN HGNC HGNC:15719 protein_coding YES CCDS59204.1 ENSP00000455507 H3BPX2 UPI00027FCDB5 NM_001271223.2 105/116 1,1 LOW 1 SNV 5 1,1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 C 2 2 92 228371775 228371775 G C 1 0 0 0 0 0 0 0 1 10889 1190 42 4 4 OBSCN 1 228371775 Silent SNP G C3N-02149_T 2185307 228371775 20584647 47 28231 NID1 0 . GRCh38 1 236032573 236032573 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1365C>A p.Asn455Lys p.N455K ENST00000264187 6/20 433 313 120 505 505 0 strelka-varscan NID1,missense_variant,p.Asn455Lys,ENST00000264187,NM_002508.2;NID1,missense_variant,p.Asn455Lys,ENST00000366595,; T ENST00000264187 Transcript missense_variant 1448/5864 1365/3744 455/1247 N/K aaC/aaA 1 -1 NID1 HGNC HGNC:7821 protein_coding YES CCDS1608.1 ENSP00000264187 P14543 UPI000013D4D9 NM_002508.2 deleterious(0) 6/20 Gene3D:2.40.155.10,Pfam_domain:PF07474,PROSITE_profiles:PS50993,hmmpanther:PTHR10529,hmmpanther:PTHR10529:SF107,SMART_domains:SM00682,Superfamily_domains:SSF54511 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 236032573 236032573 G T 1 0 0 0 0 1 0 0 0 10447 1368 48 2 2 NID1 1 236032573 Missense_Mutation SNP G C3N-02149_T 7660798 236032573 12923849 48 28232 ACTN2 0 . GRCh38 1 236717904 236717904 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.173A>T p.Gln58Leu p.Q58L ENST00000542672 2/21 643 591 52 675 673 2 strelka-varscan ACTN2,missense_variant,p.Gln58Leu,ENST00000542672,NM_001278343.1;ACTN2,missense_variant,p.Gln58Leu,ENST00000366578,NM_001103.3;ACTN2,5_prime_UTR_variant,,ENST00000546208,NM_001278344.1;ACTN2,non_coding_transcript_exon_variant,,ENST00000492634,; T ENST00000542672 Transcript missense_variant 393/4906 173/2685 58/894 Q/L cAg/cTg 1 1 ACTN2 HGNC HGNC:164 protein_coding YES CCDS60455.1 ENSP00000443495 P35609 UPI00002050CF NM_001278343.1 deleterious(0.01) 2/21 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF236,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 236717904 236717904 A T 1 0 0 0 0 1 0 0 0 249 188 7 4 4 ACTN2 1 236717904 Missense_Mutation SNP A C3N-02149_T 685331 236717904 12238518 49 28233 RYR2 0 . GRCh38 1 237709513 237709513 + Silent SNP A A T rs752142789 C3N-02149_T C3N-02149_N A A c.10176A>T p.= p.A3392A ENST00000366574 70/105 230 159 71 276 276 0 strelka-varscan RYR2,synonymous_variant,p.=,ENST00000366574,NM_001035.2;RYR2,synonymous_variant,p.=,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; T ENST00000366574 Transcript synonymous_variant 10493/16562 10176/14904 3392/4967 A gcA/gcT rs752142789 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 70/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 237709513 237709513 A T 1 0 0 0 0 0 0 0 1 14029 175 7 4 4 RYR2 1 237709513 Silent SNP A C3N-02149_T 991609 237709513 11246909 50 28234 ZP4 0 . GRCh38 1 237885886 237885886 + Missense_Mutation SNP C C G rs780199400 C3N-02149_T C3N-02149_N C C c.840G>C p.Arg280Ser p.R280S ENST00000611898 7/13 153 142 11 164 164 0 strelka-varscan ZP4,missense_variant,p.Arg280Ser,ENST00000611898,NM_021186.3;ZP4,missense_variant,p.Arg280Ser,ENST00000366570,;RP11-193H5.1,intron_variant,,ENST00000450451,; G ENST00000611898 Transcript missense_variant,splice_region_variant 1127/2474 840/1623 280/540 R/S agG/agC rs780199400 1 -1 ZP4 HGNC HGNC:15770 protein_coding YES CCDS1615.1 ENSP00000482304 Q12836 UPI000006F0E4 NM_021186.3 deleterious(0) 7/13 Pfam_domain:PF00100,PROSITE_profiles:PS51034,hmmpanther:PTHR23343,hmmpanther:PTHR23343:SF31,SMART_domains:SM00241 MODERATE SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -19.8861 1 1 1 1 0 G 3 3 92 237885886 237885886 C G 1 0 0 0 0 1 0 0 0 18810 753 26 4 4 ZP4 1 237885886 Missense_Mutation SNP C C3N-02149_T 176373 237885886 11070536 51 28235 TSSC1 0 . GRCh38 2 3194142 3194142 + Silent SNP G G C novel C3N-02149_T C3N-02149_N G G c.678C>G p.= p.A226A ENST00000382125 7/9 185 166 19 244 244 0 strelka-varscan-mutect TSSC1,synonymous_variant,p.=,ENST00000398659,;TSSC1,synonymous_variant,p.=,ENST00000382125,NM_003310.2;TSSC1,synonymous_variant,p.=,ENST00000441271,;TSSC1,non_coding_transcript_exon_variant,,ENST00000478754,;TSSC1,non_coding_transcript_exon_variant,,ENST00000463662,;TSSC1,3_prime_UTR_variant,,ENST00000455162,;TSSC1,3_prime_UTR_variant,,ENST00000435721,;TSSC1,non_coding_transcript_exon_variant,,ENST00000496433,;TSSC1,non_coding_transcript_exon_variant,,ENST00000482570,;TSSC1,downstream_gene_variant,,ENST00000470625,; C ENST00000382125 Transcript synonymous_variant 871/1766 678/1164 226/387 A gcC/gcG 1 -1 TSSC1 HGNC HGNC:12383 protein_coding YES CCDS1651.1 ENSP00000371559 Q53HC9 UPI000006DFE1 NM_003310.2 7/9 PROSITE_profiles:PS50294,PROSITE_profiles:PS50082,hmmpanther:PTHR14205:SF15,hmmpanther:PTHR14205,Gene3D:2.130.10.10,Pfam_domain:PF00400,SMART_domains:SM00320,Superfamily_domains:0049172 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 3194142 3194142 G C 1 0 0 0 0 0 0 0 1 17174 1219 43 4 4 TSSC1 2 3194142 Silent SNP G C3N-02149_T 3194142 238999387 52 28236 DCDC2C 0 . GRCh38 2 3752820 3752820 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.603C>A p.His201Gln p.H201Q ENST00000399143 5/11 267 240 27 375 374 1 strelka-varscan-mutect DCDC2C,missense_variant,p.His201Gln,ENST00000399143,NM_001287444.1;DCDC2C,missense_variant,p.His164Gln,ENST00000423741,;DCDC2C,intron_variant,,ENST00000537457,; A ENST00000399143 Transcript missense_variant 763/1480 603/1095 201/364 H/Q caC/caA 1 1 DCDC2C HGNC HGNC:32696 protein_coding YES CCDS74481.1 ENSP00000382097 A8MYV0 UPI0002742D44 NM_001287444.1 tolerated(0.44) 5/11 PROSITE_profiles:PS50309,hmmpanther:PTHR23004:SF9,hmmpanther:PTHR23004,Gene3D:1mfwA00,Pfam_domain:PF03607,SMART_domains:SM00537,Superfamily_domains:SSF89837 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 3752820 3752820 C A 1 0 0 0 0 1 0 0 0 4089 564 20 2 2 DCDC2C 2 3752820 Missense_Mutation SNP C C3N-02149_T 558678 3752820 238440709 53 28237 LPIN1 0 . GRCh38 2 11779646 11779646 + Splice_Site SNP G G T novel C3N-02149_T C3N-02149_N G G c.1104+1G>T p.X368_splice ENST00000449576 421 399 22 508 507 1 strelka-varscan-mutect LPIN1,splice_donor_variant,,ENST00000396097,;LPIN1,splice_donor_variant,,ENST00000425416,NM_001261427.1;LPIN1,splice_donor_variant,,ENST00000256720,NM_145693.2;LPIN1,splice_donor_variant,,ENST00000449576,NM_001261428.1;LPIN1,splice_donor_variant,,ENST00000396098,NM_001261429.1;LPIN1,splice_donor_variant,,ENST00000404113,;LPIN1,upstream_gene_variant,,ENST00000475286,;LPIN1,splice_donor_variant,,ENST00000396099,;LPIN1,upstream_gene_variant,,ENST00000460096,; T ENST00000449576 Transcript splice_donor_variant -/3077 1104/2928 368/975 1 1 LPIN1 HGNC HGNC:13345 protein_coding YES CCDS58699.1 ENSP00000397908 Q14693 UPI0002064F62 NM_001261428.1 8/21 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 92 11779646 11779646 G T 1 0 0 0 0 0 0 1 0 8818 1275 44 2 2 LPIN1 2 11779646 Splice_Site SNP G C3N-02149_T 8026826 11779646 230413883 54 28238 APOB 0 . GRCh38 2 21004644 21004644 + Frame_Shift_Del DEL C C - rs72654417 C3N-02149_T C3N-02149_N C C c.11820delG p.Leu3941Ter p.L3941* ENST00000233242 27/29 387 320 67 528 528 0 sindel-varindel-pindel APOB,frameshift_variant,p.Leu3941Ter,ENST00000233242,NM_000384.2;RP11-116D2.1,upstream_gene_variant,,ENST00000567376,; - ENST00000233242 Transcript frameshift_variant 11948/14121 11820/13692 3940/4563 T/X acG/ac rs72654417 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 27/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 21004644 21004644 C - 1 0 1 0 1 0 0 0 0 907 523 19 0 0 APOB 2 21004644 Frame_Shift_Del DEL C C3N-02149_T 9224998 21004644 221188885 55 28239 TDRD15 0 . GRCh38 2 21140303 21140303 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.2836C>T p.Pro946Ser p.P946S ENST00000405799 4/4 198 167 31 236 236 0 strelka-varscan TDRD15,missense_variant,p.Pro946Ser,ENST00000405799,;TDRD15,missense_variant,p.Pro946Ser,ENST00000622654,; T ENST00000405799 Transcript missense_variant 3166/6135 2836/5805 946/1934 P/S Cca/Tca 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 tolerated(0.17) 4/4 hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 MODERATE 1 SNV 2 1 PASS . . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 21140303 21140303 C T 1 0 0 0 0 1 0 0 0 16141 623 22 3 3 TDRD15 2 21140303 Missense_Mutation SNP C C3N-02149_T 135659 21140303 221053226 56 28240 OTOF 0 . GRCh38 2 26482505 26482505 + Missense_Mutation SNP G G C rs751973073 C3N-02149_T C3N-02149_N G G c.1480C>G p.Arg494Gly p.R494G ENST00000272371 14/47 170 155 15 234 234 0 strelka-varscan-mutect OTOF,missense_variant,p.Arg494Gly,ENST00000272371,NM_194248.2;OTOF,missense_variant,p.Arg494Gly,ENST00000403946,NM_001287489.1;OTOF,upstream_gene_variant,,ENST00000402415,NM_194322.2;OTOF,upstream_gene_variant,,ENST00000338581,NM_004802.3;OTOF,upstream_gene_variant,,ENST00000339598,NM_194323.2; C ENST00000272371 Transcript missense_variant 1607/7156 1480/5994 494/1997 R/G Cgc/Ggc rs751973073,COSM4133765 1 -1 OTOF HGNC HGNC:8515 protein_coding YES CCDS1725.1 ENSP00000272371 Q9HC10 UPI000013D94D NM_194248.2 deleterious(0) 14/47 PROSITE_profiles:PS50004,hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF32,Gene3D:2.60.40.150,Pfam_domain:PF00168,SMART_domains:SM00239,Superfamily_domains:SSF49562 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs751973073 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 26482505 26482505 G C 1 0 0 0 0 1 0 0 0 11369 1145 40 4 4 OTOF 2 26482505 Missense_Mutation SNP G C3N-02149_T 5342202 26482505 215711024 57 28241 DPYSL5 0 . GRCh38 2 26944783 26944783 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1568G>T p.Gly523Val p.G523V ENST00000288699 12/13 242 217 25 266 265 1 strelka-varscan-mutect DPYSL5,missense_variant,p.Gly523Val,ENST00000288699,NM_020134.3;DPYSL5,missense_variant,p.Gly523Val,ENST00000614712,NM_001253724.1;DPYSL5,missense_variant,p.Gly523Val,ENST00000401478,NM_001253723.1;DPYSL5,non_coding_transcript_exon_variant,,ENST00000484882,; T ENST00000288699 Transcript missense_variant 1726/5209 1568/1695 523/564 G/V gGg/gTg 1 1 DPYSL5 HGNC HGNC:20637 protein_coding YES CCDS1730.1 ENSP00000288699 Q9BPU6 UPI00000411CF NM_020134.3 tolerated(0.11) 12/13 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 26944783 26944783 G T 1 0 0 0 0 1 0 0 0 4565 1232 43 2 2 DPYSL5 2 26944783 Missense_Mutation SNP G C3N-02149_T 462278 26944783 215248746 58 28242 PRR30 0 . GRCh38 2 27138046 27138046 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.284C>A p.Pro95His p.P95H ENST00000335524 3/3 383 334 49 483 482 1 strelka-varscan-mutect PRR30,missense_variant,p.Pro95His,ENST00000335524,NM_178553.3;PRR30,intron_variant,,ENST00000432962,;PREB,upstream_gene_variant,,ENST00000260643,NM_013388.4;PREB,upstream_gene_variant,,ENST00000406567,;PREB,upstream_gene_variant,,ENST00000416802,;PREB,upstream_gene_variant,,ENST00000468045,;PREB,upstream_gene_variant,,ENST00000444452,;PREB,upstream_gene_variant,,ENST00000474802,; T ENST00000335524 Transcript missense_variant 810/2008 284/1239 95/412 P/H cCt/cAt 1 -1 PRR30 HGNC HGNC:28677 protein_coding YES CCDS1739.1 ENSP00000335017 Q53SZ7 UPI00001995FD NM_178553.3 deleterious(0) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22235:SF2,hmmpanther:PTHR22235,Pfam_domain:PF15728 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 27138046 27138046 G T 1 0 0 0 0 1 0 0 0 12737 1000 35 2 2 PRR30 2 27138046 Missense_Mutation SNP G C3N-02149_T 193263 27138046 215055483 59 28243 C2orf16 0 . GRCh38 2 27580900 27580900 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.4328G>A p.Arg1443Lys p.R1443K ENST00000408964 1/1 261 237 24 321 321 0 strelka-varscan-mutect C2orf16,missense_variant,p.Arg1443Lys,ENST00000408964,NM_032266.3;ZNF512,upstream_gene_variant,,ENST00000413371,NM_001271289.1,NM_001271318.1;ZNF512,upstream_gene_variant,,ENST00000556601,NM_001271287.1,NM_001271288.1;ZNF512,upstream_gene_variant,,ENST00000355467,NM_032434.3;ZNF512,upstream_gene_variant,,ENST00000416005,NM_001271286.1;ZNF512,upstream_gene_variant,,ENST00000379717,;RP11-158I13.2,upstream_gene_variant,,ENST00000505973,;ZNF512,upstream_gene_variant,,ENST00000494548,;ZNF512,upstream_gene_variant,,ENST00000461705,; A ENST00000408964 Transcript missense_variant 4379/6199 4328/5955 1443/1984 R/K aGa/aAa 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 tolerated(0.25) 1/1 hmmpanther:PTHR33888 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 27580900 27580900 G A 1 0 0 0 0 1 0 0 0 2032 942 33 3 3 C2orf16 2 27580900 Missense_Mutation SNP G C3N-02149_T 442854 27580900 214612629 60 28244 SULT6B1 0 . GRCh38 2 37171456 37171456 + Silent SNP G G T rs137864268 C3N-02149_T C3N-02149_N G G c.645C>A p.= p.V215V ENST00000407963 7/8 120 98 22 166 166 0 strelka-varscan-mutect SULT6B1,synonymous_variant,p.=,ENST00000535679,;SULT6B1,synonymous_variant,p.=,ENST00000407963,NM_001032377.1; T ENST00000407963 Transcript synonymous_variant 749/902 645/798 215/265 V gtC/gtA rs137864268,COSM3709630,COSM3709631 1 -1 SULT6B1 HGNC HGNC:33433 protein_coding YES CCDS33182.1 ENSP00000384950 A0A0C4DG03 UPI0000041280 NM_001032377.1 7/8 Gene3D:3.40.50.300,Pfam_domain:PF00685,hmmpanther:PTHR11783,hmmpanther:PTHR11783:SF55,Superfamily_domains:SSF52540 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs137864268 . 0 205 3 2 0 0 0 0 -20 0.9999958 1 1 1 0 T 2 4 92 37171456 37171456 G T 1 0 0 0 0 0 0 0 1 15770 1045 37 1 1 SULT6B1 2 37171456 Silent SNP G C3N-02149_T 9590556 37171456 205022073 61 28245 SRBD1 0 . GRCh38 2 45393108 45393108 + Silent SNP C C A rs752837606 C3N-02149_T C3N-02149_N C C c.2535G>T p.= p.G845G ENST00000263736 20/21 70 54 16 103 103 0 strelka-varscan-mutect SRBD1,synonymous_variant,p.=,ENST00000263736,NM_018079.4;SRBD1,non_coding_transcript_exon_variant,,ENST00000490133,; A ENST00000263736 Transcript synonymous_variant 2598/3681 2535/2988 845/995 G ggG/ggT rs752837606 1 -1 SRBD1 HGNC HGNC:25521 protein_coding YES CCDS1823.1 ENSP00000263736 Q8N5C6 UPI000004CC06 NM_018079.4 20/21 Gene3D:3bzcA04,hmmpanther:PTHR10724,hmmpanther:PTHR10724:SF1,Superfamily_domains:SSF47781 LOW 1 SNV 2 1 PASS rs752837606 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 45393108 45393108 C A 1 0 0 0 0 0 0 0 1 15491 842 30 2 2 SRBD1 2 45393108 Silent SNP C C3N-02149_T 8221652 45393108 196800421 62 28246 SERTAD2 0 . GRCh38 2 64636302 64636302 + Silent SNP C C A rs753265798 C3N-02149_T C3N-02149_N C C c.570G>T p.= p.T190T ENST00000313349 2/2 339 281 58 390 387 3 strelka-varscan-mutect SERTAD2,synonymous_variant,p.=,ENST00000313349,NM_014755.2;SERTAD2,downstream_gene_variant,,ENST00000476805,; A ENST00000313349 Transcript synonymous_variant 868/5549 570/945 190/314 T acG/acT rs753265798 1 -1 SERTAD2 HGNC HGNC:30784 protein_coding YES CCDS33210.1 ENSP00000326933 Q14140 UPI000004EC6D NM_014755.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR16277:SF10,hmmpanther:PTHR16277 LOW 1 SNV 1 1 PASS rs753265798 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 64636302 64636302 C A 1 0 0 0 0 0 0 0 1 14397 639 23 1 1 SERTAD2 2 64636302 Silent SNP C C3N-02149_T 19243194 64636302 177557227 63 28247 ETAA1 0 . GRCh38 2 67399598 67399598 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.401C>T p.Ser134Leu p.S134L ENST00000272342 3/6 208 188 20 301 301 0 strelka-varscan-mutect ETAA1,missense_variant,p.Ser134Leu,ENST00000272342,NM_019002.3;ETAA1,upstream_gene_variant,,ENST00000462772,; T ENST00000272342 Transcript missense_variant 531/3418 401/2781 134/926 S/L tCa/tTa 1 1 ETAA1 HGNC HGNC:24648 protein_coding YES CCDS1882.1 ENSP00000272342 Q9NY74 UPI00001414BC NM_019002.3 deleterious(0) 3/6 Pfam_domain:PF15350,hmmpanther:PTHR16434 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 67399598 67399598 C T 1 0 0 0 0 1 0 0 0 5129 838 29 3 3 ETAA1 2 67399598 Missense_Mutation SNP C C3N-02149_T 2763296 67399598 174793931 64 28248 RAB11FIP5 0 . GRCh38 2 73089195 73089195 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.552C>T p.= p.D184D ENST00000258098 2/5 584 480 104 700 700 0 strelka-varscan-mutect RAB11FIP5,synonymous_variant,p.=,ENST00000486777,;RAB11FIP5,synonymous_variant,p.=,ENST00000258098,NM_015470.2;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000493523,;RAB11FIP5,non_coding_transcript_exon_variant,,ENST00000475951,;RAB11FIP5,upstream_gene_variant,,ENST00000482554,;RAB11FIP5,upstream_gene_variant,,ENST00000479196,; A ENST00000258098 Transcript synonymous_variant 793/4342 552/1962 184/653 D gaC/gaT 1 -1 RAB11FIP5 HGNC HGNC:24845 protein_coding YES CCDS1923.1 ENSP00000258098 Q9BXF6 UPI000007079C NM_015470.2 2/5 hmmpanther:PTHR15746:SF14,hmmpanther:PTHR15746,Superfamily_domains:SSF49562 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 73089195 73089195 G A 1 0 0 0 0 0 0 0 1 13055 1368 48 3 3 RAB11FIP5 2 73089195 Silent SNP G C3N-02149_T 5689597 73089195 169104334 65 28249 ALMS1 0 . GRCh38 2 73600722 73600722 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.11713G>T p.Val3905Phe p.V3905F ENST00000613296 18/23 141 120 21 158 158 0 varscan-mutect ALMS1,missense_variant,p.Val3905Phe,ENST00000613296,NM_015120.4;ALMS1,missense_variant,p.Val3863Phe,ENST00000484298,;ALMS1,upstream_gene_variant,,ENST00000464408,;ALMS1,upstream_gene_variant,,ENST00000490821,;ALMS1,non_coding_transcript_exon_variant,,ENST00000620466,; T ENST00000613296 Transcript missense_variant 11824/12925 11713/12507 3905/4168 V/F Gtt/Ttt 1 1 ALMS1 HGNC HGNC:428 protein_coding YES CCDS42697.1 ENSP00000482968 A0A087WZY3 UPI00046209B2 NM_015120.4 deleterious(0.03) 18/23 hmmpanther:PTHR21553,hmmpanther:PTHR21553:SF22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 73600722 73600722 G T 1 0 0 0 0 1 0 0 0 635 1377 48 2 2 ALMS1 2 73600722 Missense_Mutation SNP G C3N-02149_T 511527 73600722 168592807 66 28250 LRRTM4 0 . GRCh38 2 77518810 77518810 + Silent SNP T T G rs529696389 C3N-02149_T C3N-02149_N T T c.1059A>C p.= p.A353A ENST00000409093 3/4 219 179 40 271 270 1 strelka-varscan-mutect LRRTM4,synonymous_variant,p.=,ENST00000409088,NM_024993.4;LRRTM4,synonymous_variant,p.=,ENST00000409911,;LRRTM4,synonymous_variant,p.=,ENST00000409282,NM_001282928.1;LRRTM4,synonymous_variant,p.=,ENST00000409093,NM_001282924.1;LRRTM4,synonymous_variant,p.=,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; G ENST00000409093 Transcript synonymous_variant 1396/2247 1059/1773 353/590 A gcA/gcC rs529696389 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1 LOW 1 SNV 2 1 PASS rs529696389 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 77518810 77518810 T G 1 0 0 0 0 0 0 0 1 8948 1567 55 5 5 LRRTM4 2 77518810 Silent SNP T C3N-02149_T 3918088 77518810 164674719 67 28251 REG3G 0 . GRCh38 2 79028222 79028222 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.474G>T p.Trp158Cys p.W158C ENST00000272324 6/6 136 119 17 165 165 0 strelka-varscan-mutect REG3G,missense_variant,p.Trp158Cys,ENST00000272324,NM_001008387.2;REG3G,missense_variant,p.Trp158Cys,ENST00000393897,NM_198448.3;REG3G,missense_variant,p.Trp112Cys,ENST00000409471,NM_001270040.1;REG3G,downstream_gene_variant,,ENST00000490944,;REG3G,downstream_gene_variant,,ENST00000498312,; T ENST00000272324 Transcript missense_variant 658/938 474/528 158/175 W/C tgG/tgT 1 1 REG3G HGNC HGNC:29595 protein_coding YES CCDS1962.1 ENSP00000272324 Q6UW15 UPI0000048F1E NM_001008387.2 deleterious(0) 6/6 PROSITE_profiles:PS50041,hmmpanther:PTHR22801,hmmpanther:PTHR22801:SF60,PROSITE_patterns:PS00615,Gene3D:3.10.100.10,Pfam_domain:PF00059,SMART_domains:SM00034,Superfamily_domains:SSF56436,Prints_domain:PR01504 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 79028222 79028222 G T 1 0 0 0 0 1 0 0 0 13383 1183 41 2 2 REG3G 2 79028222 Missense_Mutation SNP G C3N-02149_T 1509412 79028222 163165307 68 28252 LRRTM1 0 . GRCh38 2 80303352 80303352 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.468C>T p.= p.L156L ENST00000295057 2/2 331 312 19 361 361 0 strelka-varscan-mutect LRRTM1,synonymous_variant,p.=,ENST00000295057,;LRRTM1,synonymous_variant,p.=,ENST00000409148,NM_178839.4;LRRTM1,synonymous_variant,p.=,ENST00000416268,;LRRTM1,synonymous_variant,p.=,ENST00000452811,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,synonymous_variant,p.=,ENST00000433224,;LRRTM1,synonymous_variant,p.=,ENST00000417012,; A ENST00000295057 Transcript synonymous_variant 1125/2599 468/1569 156/522 L ctC/ctT 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE 2/2 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,SMART_domains:SM00369,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 80303352 80303352 G A 1 0 0 0 0 0 0 0 1 8945 929 33 3 3 LRRTM1 2 80303352 Silent SNP G C3N-02149_T 1275130 80303352 161890177 69 28253 DNAH6 0 . GRCh38 2 84653472 84653472 + Silent SNP A A T rs573582854 C3N-02149_T C3N-02149_N A A c.5232A>T p.= p.L1744L ENST00000389394 34/77 259 220 39 358 357 1 strelka-varscan-mutect DNAH6,synonymous_variant,p.=,ENST00000389394,NM_001370.1;DNAH6,synonymous_variant,p.=,ENST00000237449,;DNAH6,upstream_gene_variant,,ENST00000602588,; T ENST00000389394 Transcript synonymous_variant 5369/12795 5232/12477 1744/4158 L ctA/ctT rs573582854 1 1 DNAH6 HGNC HGNC:2951 protein_coding YES CCDS46348.1 ENSP00000374045 Q9C0G6 UPI000163AC9D NM_001370.1 34/77 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF136,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS rs573582854 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 84653472 84653472 A T 1 0 0 0 0 0 0 0 1 4420 407 15 4 4 DNAH6 2 84653472 Silent SNP A C3N-02149_T 4350120 84653472 157540057 70 28254 TEKT4 0 . GRCh38 2 94871678 94871678 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.99C>T p.= p.S33S ENST00000295201 1/6 275 237 38 296 296 0 strelka-varscan-mutect TEKT4,synonymous_variant,p.=,ENST00000295201,NM_144705.3,NM_001286559.1;AC097374.2,non_coding_transcript_exon_variant,,ENST00000568768,;AC097374.2,intron_variant,,ENST00000582835,;TEKT4,non_coding_transcript_exon_variant,,ENST00000468063,; T ENST00000295201 Transcript synonymous_variant 236/1505 99/1308 33/435 S agC/agT 1 1 TEKT4 HGNC HGNC:31012 protein_coding YES CCDS2005.1 ENSP00000295201 Q8WW24 UPI00000730A8 NM_144705.3,NM_001286559.1 1/6 hmmpanther:PTHR19960,hmmpanther:PTHR19960:SF26 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 94871678 94871678 C T 1 0 0 0 0 0 0 0 1 16167 796 28 3 3 TEKT4 2 94871678 Silent SNP C C3N-02149_T 10218206 94871678 147321851 71 28255 PROM2 0 . GRCh38 2 95287451 95287451 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2231G>T p.Trp744Leu p.W744L ENST00000317620 20/24 216 192 24 270 270 0 strelka-varscan-mutect PROM2,missense_variant,p.Trp744Leu,ENST00000317620,NM_001165978.1;PROM2,missense_variant,p.Trp744Leu,ENST00000317668,NM_144707.2;PROM2,missense_variant,p.Trp744Leu,ENST00000403131,NM_001165977.1;PROM2,upstream_gene_variant,,ENST00000462029,;PROM2,downstream_gene_variant,,ENST00000497110,;PROM2,upstream_gene_variant,,ENST00000495540,;PROM2,3_prime_UTR_variant,,ENST00000431567,NM_001321070.1;PROM2,non_coding_transcript_exon_variant,,ENST00000487138,; T ENST00000317620 Transcript missense_variant 2364/4728 2231/2505 744/834 W/L tGg/tTg 1 1 PROM2 HGNC HGNC:20685 protein_coding YES CCDS2012.1 ENSP00000318270 Q8N271 UPI0000071157 NM_001165978.1 deleterious(0) 20/24 hmmpanther:PTHR22730:SF6,hmmpanther:PTHR22730,Pfam_domain:PF05478 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 92 95287451 95287451 G T 1 0 0 0 0 1 0 0 0 12688 1357 47 2 2 PROM2 2 95287451 Missense_Mutation SNP G C3N-02149_T 415773 95287451 146906078 72 28256 CREG2 0 . GRCh38 2 101387182 101387182 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.276C>A p.= p.A92A ENST00000324768 1/4 32 27 5 59 59 0 strelka-varscan-mutect CREG2,synonymous_variant,p.=,ENST00000324768,NM_153836.3;CREG2,non_coding_transcript_exon_variant,,ENST00000486966,;CREG2,upstream_gene_variant,,ENST00000495455,; T ENST00000324768 Transcript synonymous_variant 414/6383 276/873 92/290 A gcC/gcA 1 -1 CREG2 HGNC HGNC:14272 protein_coding YES CCDS2052.1 ENSP00000315203 Q8IUH2 UPI0000074776 NM_153836.3 1/4 Low_complexity_(Seg):seg,hmmpanther:PTHR13343:SF15,hmmpanther:PTHR13343,PIRSF_domain:PIRSF036911 LOW 1 SNV 1 1 PASS rs1415355856 . 0 205 5 0 0 0 0 0 -13.58893 1 1 1 1 0 T 2 4 92 101387182 101387182 G T 1 0 0 0 0 0 0 0 1 3666 1219 43 2 2 CREG2 2 101387182 Silent SNP G C3N-02149_T 6099731 101387182 140806347 73 28257 SLC9A2 0 . GRCh38 2 102665151 102665175 + Frame_Shift_Del DEL ATTGATGTGTTTGCAGGAATCGCCA ATTGATGTGTTTGCAGGAATCGCCA - novel C3N-02149_T C3N-02149_N ATTGATGTGTTTGCAGGAATCGCCA ATTGATGTGTTTGCAGGAATCGCCA c.806_830delTTGATGTGTTTGCAGGAATCGCCAA p.Ile269ThrfsTer11 p.I269Tfs*11 ENST00000233969 3/12 297 268 29 394 394 0 sindel-varindel-pindel SLC9A2,frameshift_variant,p.Ile269ThrfsTer11,ENST00000233969,NM_003048.4; - ENST00000233969 Transcript frameshift_variant 947-971/5410 805-829/2439 269-277/812 IDVFAGIAN/X ATTGATGTGTTTGCAGGAATCGCCAac/ac 1 1 SLC9A2 HGNC HGNC:11072 protein_coding YES CCDS2062.1 ENSP00000233969 Q9UBY0 UPI000012FD21 NM_003048.4 3/12 hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF89,Pfam_domain:PF00999,TIGRFAM_domain:TIGR00840 HIGH 1 deletion 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999847 1 1 1 0 - 7 5 92 102665151 102665151 ATTGATGTGTTTGCAGGAATCGCCA - 1 0 1 0 1 0 0 0 0 14994 217 8 0 0 SLC9A2 2 102665151 Frame_Shift_Del DEL ATTGATGTGTTTGCAGGAATCGCCA C3N-02149_T 1277969 102665151 139528378 74 28258 UXS1 0 . GRCh38 2 106145227 106145227 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.435G>T p.Leu145Phe p.L145F ENST00000283148 6/15 169 144 25 231 231 0 strelka-varscan-mutect UXS1,missense_variant,p.Leu145Phe,ENST00000283148,NM_001253875.1;UXS1,missense_variant,p.Leu140Phe,ENST00000409501,NM_025076.4;UXS1,missense_variant,p.Leu83Phe,ENST00000457835,;UXS1,5_prime_UTR_variant,,ENST00000444193,;UXS1,intron_variant,,ENST00000416298,;UXS1,intron_variant,,ENST00000441952,;UXS1,non_coding_transcript_exon_variant,,ENST00000479621,;UXS1,non_coding_transcript_exon_variant,,ENST00000479774,;UXS1,downstream_gene_variant,,ENST00000483426,; A ENST00000283148 Transcript missense_variant 533/2099 435/1278 145/425 L/F ttG/ttT 1 -1 UXS1 HGNC HGNC:17729 protein_coding YES CCDS58721.1 ENSP00000283148 Q8NBZ7 UPI000003CA36 NM_001253875.1 tolerated(0.05) 6/15 hmmpanther:PTHR10366:SF399,hmmpanther:PTHR10366,Pfam_domain:PF16363,Gene3D:3.40.50.720,Superfamily_domains:SSF51735 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 92 106145227 106145227 C A 1 0 0 0 0 1 0 0 0 17654 825 29 2 2 UXS1 2 106145227 Missense_Mutation SNP C C3N-02149_T 3480076 106145227 136048302 75 28259 ST6GAL2 0 . GRCh38 2 106806710 106806710 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.1558C>A p.Pro520Thr p.P520T ENST00000409382 6/6 145 118 27 172 172 0 varscan-mutect ST6GAL2,missense_variant,p.Pro520Thr,ENST00000409382,NM_001142351.1;ST6GAL2,missense_variant,p.Pro520Thr,ENST00000361686,NM_001322362.1,NM_032528.2;ST6GAL2,missense_variant,p.Pro86Thr,ENST00000361803,; T ENST00000409382 Transcript missense_variant 2169/7275 1558/1590 520/529 P/T Cct/Act COSM1526976 1 -1 ST6GAL2 HGNC HGNC:10861 protein_coding YES CCDS2073.1 ENSP00000386942 Q96JF0 UPI000007477B NM_001142351.1 6/6 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 106806710 106806710 G T 1 0 0 0 0 1 0 0 0 15600 1232 43 2 2 ST6GAL2 2 106806710 Missense_Mutation SNP G C3N-02149_T 661483 106806710 135386819 76 28260 PSD4 0 . GRCh38 2 113182551 113182552 + Frame_Shift_Ins INS - - C novel C3N-02149_T C3N-02149_N - - c.98dupC p.Arg34LysfsTer7 p.R34Kfs*7 ENST00000245796 2/17 238 209 29 325 325 0 sindel-varindel PSD4,frameshift_variant,p.Arg34LysfsTer7,ENST00000441564,;PSD4,frameshift_variant,p.Arg34LysfsTer7,ENST00000245796,NM_012455.2;PSD4,non_coding_transcript_exon_variant,,ENST00000465917,;PSD4,intron_variant,,ENST00000485525,;PSD4,non_coding_transcript_exon_variant,,ENST00000418251,;PSD4,upstream_gene_variant,,ENST00000409656,; C ENST00000245796 Transcript frameshift_variant 290-291/5188 95-96/3171 32/1056 C/CX tgc/tgCc 1 1 PSD4 HGNC HGNC:19096 protein_coding YES CCDS33276.1 ENSP00000245796 Q8NDX1 UPI00004A0748 NM_012455.2 2/17 HIGH 1 insertion 1 3 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999898 1 1 1 0 C 7 5 92 113182551 113182551 - C 1 0 1 1 0 0 0 0 0 12800 1319 46 0 0 PSD4 2 113182551 Frame_Shift_Ins INS - C3N-02149_T 6375841 113182551 129010978 77 28261 CLASP1 0 . GRCh38 2 121367791 121367791 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.3683G>T p.Gly1228Val p.G1228V ENST00000263710 35/40 326 271 55 338 338 0 strelka-varscan-mutect CLASP1,missense_variant,p.Gly1228Val,ENST00000263710,NM_015282.2;CLASP1,missense_variant,p.Gly1161Val,ENST00000409078,NM_001142274.1;CLASP1,missense_variant,p.Gly1169Val,ENST00000397587,;CLASP1,missense_variant,p.Gly1167Val,ENST00000541377,NM_001207051.1;CLASP1,missense_variant,p.Gly1168Val,ENST00000455322,NM_001142273.1;CLASP1,missense_variant,p.Gly965Val,ENST00000452274,;CLASP1,non_coding_transcript_exon_variant,,ENST00000472776,; A ENST00000263710 Transcript missense_variant 4073/8092 3683/4617 1228/1538 G/V gGc/gTc 1 -1 CLASP1 HGNC HGNC:17088 protein_coding YES ENSP00000263710 Q7Z460 UPI00001A8BFF NM_015282.2 tolerated(0.55) 35/40 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 121367791 121367791 C A 1 0 0 0 0 1 0 0 0 3217 739 26 2 2 CLASP1 2 121367791 Missense_Mutation SNP C C3N-02149_T 8185240 121367791 120825738 78 28262 CNTNAP5 0 . GRCh38 2 124647874 124647874 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1990C>A p.Leu664Met p.L664M ENST00000431078 13/24 174 156 18 180 179 1 strelka-varscan-mutect CNTNAP5,missense_variant,p.Leu664Met,ENST00000431078,NM_130773.3; A ENST00000431078 Transcript missense_variant 2354/5284 1990/3921 664/1306 L/M Ctg/Atg 1 1 CNTNAP5 HGNC HGNC:18748 protein_coding YES CCDS46401.1 ENSP00000399013 Q8WYK1 UPI0000071988 NM_130773.3 deleterious(0.01) 13/24 hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF665 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 124647874 124647874 C A 1 0 0 0 0 1 0 0 0 3432 796 28 2 2 CNTNAP5 2 124647874 Missense_Mutation SNP C C3N-02149_T 3280083 124647874 117545655 79 28263 MYO7B 0 . GRCh38 2 127628466 127628466 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.4477G>T p.Ala1493Ser p.A1493S ENST00000428314 33/47 317 265 52 320 320 0 strelka-varscan-mutect MYO7B,missense_variant,p.Ala1493Ser,ENST00000428314,NM_001080527.1;MYO7B,missense_variant,p.Ala1493Ser,ENST00000409816,;MYO7B,missense_variant,p.Ala346Ser,ENST00000409090,;MYO7B,downstream_gene_variant,,ENST00000437387,;RP11-286H15.1,upstream_gene_variant,,ENST00000609697,;MYO7B,non_coding_transcript_exon_variant,,ENST00000496841,;MYO7B,non_coding_transcript_exon_variant,,ENST00000491278,; T ENST00000428314 Transcript missense_variant 4530/6715 4477/6351 1493/2116 A/S Gcc/Tcc 1 1 MYO7B HGNC HGNC:7607 protein_coding YES CCDS46405.1 ENSP00000415090 Q6PIF6 UPI00006C04F0 NM_001080527.1 tolerated(0.48) 33/47 PROSITE_profiles:PS50057 MODERATE 1 SNV 5 1 PASS rs1428392162 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 127628466 127628466 G T 1 0 0 0 0 1 0 0 0 10084 1203 42 2 2 MYO7B 2 127628466 Missense_Mutation SNP G C3N-02149_T 2980592 127628466 114565063 80 28264 POTEI 0 . GRCh38 2 130463684 130463684 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.2360A>T p.His787Leu p.H787L ENST00000451531 15/15 443 376 67 524 523 1 strelka-varscan-mutect POTEI,missense_variant,p.His787Leu,ENST00000451531,NM_001277406.1;POTEI,downstream_gene_variant,,ENST00000631234,;POTEI,downstream_gene_variant,,ENST00000615053,; A ENST00000451531 Transcript missense_variant 2791/7020 2360/3228 787/1075 H/L cAc/cTc 1 -1 POTEI HGNC HGNC:37093 protein_coding YES CCDS59431.1 ENSP00000392718 P0CG38 UPI00006C04CB NM_001277406.1 deleterious_low_confidence(0.01) 15/15 hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF50,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS rs1409024436 . 1 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 130463684 130463684 T A 1 0 0 0 0 1 0 0 0 12382 1696 59 4 4 POTEI 2 130463684 Missense_Mutation SNP T C3N-02149_T 2835218 130463684 111729845 81 28265 NCKAP5 0 . GRCh38 2 132784593 132784593 + Nonsense_Mutation SNP C C A rs76227896 C3N-02149_T C3N-02149_N C C c.2218G>T p.Glu740Ter p.E740* ENST00000409261 14/20 66 56 10 78 78 0 strelka-varscan-mutect NCKAP5,stop_gained,p.Glu740Ter,ENST00000409261,NM_207363.2;NCKAP5,stop_gained,p.Glu740Ter,ENST00000317721,;NCKAP5,intron_variant,,ENST00000405974,;NCKAP5,intron_variant,,ENST00000409213,NM_207481.3;NCKAP5,upstream_gene_variant,,ENST00000473859,; A ENST00000409261 Transcript stop_gained 2592/7594 2218/5730 740/1909 E/* Gag/Tag rs76227896 1 -1 NCKAP5 HGNC HGNC:29847 protein_coding YES CCDS46418.1 ENSP00000387128 O14513 UPI0000E07A3F NM_207363.2 14/20 hmmpanther:PTHR21740,hmmpanther:PTHR21740:SF0 HIGH 1 SNV 5 1 PASS rs76227896 . 0 195 13 2 0 0 0 0 -17.72852 0.9977941 1 1 1 0 A 4 1 92 132784593 132784593 C A 1 0 0 0 0 0 1 0 0 10241 835 29 2 2 NCKAP5 2 132784593 Nonsense_Mutation SNP C C3N-02149_T 2320909 132784593 109408936 82 28266 LRP1B 0 . GRCh38 2 141005395 141005395 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2443G>T p.Gly815Cys p.G815C ENST00000389484 15/91 256 218 38 300 300 0 strelka-varscan-mutect LRP1B,missense_variant,p.Gly815Cys,ENST00000389484,NM_018557.2;LRP1B,intron_variant,,ENST00000434794,; A ENST00000389484 Transcript missense_variant 3415/16535 2443/13800 815/4599 G/C Ggc/Tgc 1 -1 LRP1B HGNC HGNC:6693 protein_coding YES CCDS2182.1 ENSP00000374135 Q9NZR2 UPI00001B045B NM_018557.2 deleterious(0) 15/91 Pfam_domain:PF14670,Gene3D:2.10.25.10,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 141005395 141005395 C A 1 0 0 0 0 1 0 0 0 8850 681 24 2 2 LRP1B 2 141005395 Missense_Mutation SNP C C3N-02149_T 8220802 141005395 101188134 83 28267 SCN3A 0 . GRCh38 2 165131388 165131388 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.2421G>T p.Met807Ile p.M807I ENST00000283254 16/28 323 292 31 443 443 0 strelka-varscan-mutect SCN3A,missense_variant,p.Met807Ile,ENST00000360093,;SCN3A,missense_variant,p.Met807Ile,ENST00000283254,NM_006922.3,NM_001081676.1;SCN3A,missense_variant,p.Met758Ile,ENST00000409101,NM_001081677.1;SCN3A,missense_variant,p.Met758Ile,ENST00000440431,;AC013463.2,intron_variant,,ENST00000629817,;AC013463.2,intron_variant,,ENST00000625505,;AC013463.2,downstream_gene_variant,,ENST00000628085,;SCN3A,upstream_gene_variant,,ENST00000484898,; A ENST00000283254 Transcript missense_variant 2889/9091 2421/6003 807/2000 M/I atG/atT COSM4086152,COSM4086153 1 -1 SCN3A HGNC HGNC:10590 protein_coding YES CCDS33312.1 ENSP00000283254 Q9NY46 UPI000002A665 NM_006922.3,NM_001081676.1 deleterious(0) 16/28 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF219,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 165131388 165131388 C A 1 0 0 0 0 1 0 0 0 14187 594 21 2 2 SCN3A 2 165131388 Missense_Mutation SNP C C3N-02149_T 24125993 165131388 77062141 84 28268 CSRNP3 0 . GRCh38 2 165657932 165657932 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.320G>T p.Gly107Val p.G107V ENST00000314499 5/7 374 353 21 399 397 2 strelka-varscan-mutect CSRNP3,missense_variant,p.Gly107Val,ENST00000314499,NM_001172173.1;CSRNP3,missense_variant,p.Gly107Val,ENST00000342316,NM_024969.3;CSRNP3,missense_variant,p.Gly139Val,ENST00000409420,;CSRNP3,missense_variant,p.Gly107Val,ENST00000421875,;CSRNP3,missense_variant,p.Gly107Val,ENST00000409664,; T ENST00000314499 Transcript missense_variant 696/11788 320/1758 107/585 G/V gGc/gTc 1 1 CSRNP3 HGNC HGNC:30729 protein_coding YES CCDS2225.1 ENSP00000318258 Q8WYN3 UPI0000136882 NM_001172173.1 deleterious(0.02) 5/7 hmmpanther:PTHR13580,hmmpanther:PTHR13580:SF13,Pfam_domain:PF16019 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 165657932 165657932 G T 1 0 0 0 0 1 0 0 0 3766 1203 42 2 2 CSRNP3 2 165657932 Missense_Mutation SNP G C3N-02149_T 526544 165657932 76535597 85 28269 TTC21B 0 . GRCh38 2 165883800 165883800 + Silent SNP A A G novel C3N-02149_T C3N-02149_N A A c.3678T>C p.= p.H1226H ENST00000243344 26/29 354 311 43 486 486 0 strelka-varscan-mutect TTC21B,synonymous_variant,p.=,ENST00000243344,NM_024753.4;TTC21B,non_coding_transcript_exon_variant,,ENST00000497425,;TTC21B,synonymous_variant,p.=,ENST00000392695,; G ENST00000243344 Transcript synonymous_variant 3816/5482 3678/3951 1226/1316 H caT/caC 1 -1 TTC21B HGNC HGNC:25660 protein_coding YES CCDS33315.1 ENSP00000243344 Q7Z4L5 UPI000020900A NM_024753.4 26/29 PROSITE_profiles:PS50293,PROSITE_profiles:PS50005,hmmpanther:PTHR14699,hmmpanther:PTHR14699:SF1,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 165883800 165883800 A G 1 0 0 0 0 0 0 0 1 17196 446 16 5 5 TTC21B 2 165883800 Silent SNP A C3N-02149_T 225868 165883800 76309729 86 28270 SCN1A 0 . GRCh38 2 166052880 166052880 + Silent SNP T T A novel C3N-02149_T C3N-02149_N T T c.666A>T p.= p.R222R ENST00000303395 7/28 424 385 39 608 608 0 strelka-varscan-mutect SCN1A,synonymous_variant,p.=,ENST00000635776,;SCN1A,synonymous_variant,p.=,ENST00000637988,;SCN1A,synonymous_variant,p.=,ENST00000303395,NM_001202435.1,NM_001165963.1;SCN1A,synonymous_variant,p.=,ENST00000635750,;SCN1A,synonymous_variant,p.=,ENST00000423058,;SCN1A,synonymous_variant,p.=,ENST00000375405,NM_006920.4;SCN1A,synonymous_variant,p.=,ENST00000409050,NM_001165964.1;AC010127.3,intron_variant,,ENST00000629609,;AC010127.3,intron_variant,,ENST00000595647,;AC010127.3,intron_variant,,ENST00000599041,;AC010127.3,intron_variant,,ENST00000628933,;AC010127.3,intron_variant,,ENST00000627027,;AC010127.3,intron_variant,,ENST00000630226,;AC010127.3,intron_variant,,ENST00000595268,;SCN1A,synonymous_variant,p.=,ENST00000636194,;SCN1A,3_prime_UTR_variant,,ENST00000636759,;SCN1A,non_coding_transcript_exon_variant,,ENST00000637968,; A ENST00000303395 Transcript synonymous_variant 1084/8533 666/6030 222/2009 R cgA/cgT 1 -1 SCN1A HGNC HGNC:10585 protein_coding YES CCDS54413.1 ENSP00000303540 P35498 UPI000003C71D NM_001202435.1,NM_001165963.1 7/28 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF220,Superfamily_domains:SSF81324,Transmembrane_helices:TMhelix LOW 1 SNV 5 1 PASS rs1478277926 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 166052880 166052880 T A 1 0 0 0 0 0 0 0 1 14183 1538 54 4 4 SCN1A 2 166052880 Silent SNP T C3N-02149_T 169080 166052880 76140649 87 28271 XIRP2 0 . GRCh38 2 167247175 167247175 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.5783C>A p.Ser1928Tyr p.S1928Y ENST00000409195 9/11 318 279 39 354 353 1 strelka-varscan-mutect XIRP2,missense_variant,p.Ser1928Tyr,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Ser1706Tyr,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Ser1753Tyr,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; A ENST00000409195 Transcript missense_variant 5872/12675 5783/10650 1928/3549 S/Y tCt/tAt COSM363892 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.02) 9/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 1 MODERATE 1 SNV 5 1 1 PASS rs1026215891 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 167247175 167247175 C A 1 0 0 0 0 1 0 0 0 17989 913 32 2 2 XIRP2 2 167247175 Missense_Mutation SNP C C3N-02149_T 1194295 167247175 74946354 88 28272 FASTKD1 0 . GRCh38 2 169555188 169555188 + Missense_Mutation SNP C C T rs12618227 C3N-02149_T C3N-02149_N C C c.1150G>A p.Glu384Lys p.E384K ENST00000453153 7/15 162 150 12 323 323 0 strelka-varscan-mutect FASTKD1,missense_variant,p.Glu384Lys,ENST00000453153,NM_024622.4;FASTKD1,missense_variant,p.Glu384Lys,ENST00000453929,NM_001281476.1; T ENST00000453153 Transcript missense_variant 1497/2967 1150/2544 384/847 E/K Gaa/Aaa rs12618227,COSM207982 1 -1 FASTKD1 HGNC HGNC:26150 protein_coding YES CCDS33318.1 ENSP00000400513 Q53R41 UPI000050BC4D NM_024622.4 tolerated(0.06) 7/15 hmmpanther:PTHR21228:SF29,hmmpanther:PTHR21228 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs12618227 . 0 183 0 0 0 0 0 27 -6.068664 0 0 1 0 0 T 3 4 92 169555188 169555188 C T 1 0 0 0 0 1 0 0 0 5545 922 32 3 3 FASTKD1 2 169555188 Missense_Mutation SNP C C3N-02149_T 2308013 169555188 72638341 89 28273 WIPF1 0 . GRCh38 2 174581416 174581416 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.75G>T p.Leu25Phe p.L25F ENST00000392547 3/8 259 239 20 293 292 1 strelka-varscan-mutect WIPF1,missense_variant,p.Leu25Phe,ENST00000392547,NM_003387.4;WIPF1,missense_variant,p.Leu25Phe,ENST00000272746,;WIPF1,missense_variant,p.Leu25Phe,ENST00000409891,;WIPF1,missense_variant,p.Leu25Phe,ENST00000392546,;WIPF1,missense_variant,p.Leu25Phe,ENST00000359761,NM_001077269.1;WIPF1,missense_variant,p.Leu25Phe,ENST00000409415,;WIPF1,missense_variant,p.Leu25Phe,ENST00000410117,;WIPF1,missense_variant,p.Leu25Phe,ENST00000455428,;WIPF1,missense_variant,p.Leu25Phe,ENST00000436221,;AC018890.6,intron_variant,,ENST00000442996,;AC018890.6,intron_variant,,ENST00000412835,;AC010894.5,intron_variant,,ENST00000454203,;WIPF1,non_coding_transcript_exon_variant,,ENST00000480400,; A ENST00000392547 Transcript missense_variant 175/4587 75/1512 25/503 L/F ttG/ttT 1 -1 WIPF1 HGNC HGNC:12736 protein_coding YES CCDS2260.1 ENSP00000376330 O43516 A0A140VJZ9 UPI000013D4BD NM_003387.4 deleterious(0) 3/8 hmmpanther:PTHR23202,hmmpanther:PTHR23202:SF32 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 174581416 174581416 C A 1 0 0 0 0 1 0 0 0 17923 825 29 2 2 WIPF1 2 174581416 Missense_Mutation SNP C C3N-02149_T 5026228 174581416 67612113 90 28274 TTN 0 . GRCh38 2 178725976 178725976 + Nonsense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.20346T>A p.Cys6782Ter p.C6782* ENST00000589042 70/363 107 99 8 119 119 0 strelka-varscan-mutect TTN,stop_gained,p.Cys6782Ter,ENST00000589042,NM_001267550.2;TTN,stop_gained,p.Cys6465Ter,ENST00000591111,;TTN,stop_gained,p.Cys6465Ter,ENST00000615779,NM_001256850.1;TTN,stop_gained,p.Cys5538Ter,ENST00000342992,NM_133378.4;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;RP11-171I2.1,non_coding_transcript_exon_variant,,ENST00000590024,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625480,; T ENST00000589042 Transcript stop_gained 20571/109224 20346/107976 6782/35991 C/* tgT/tgA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 70/363 PROSITE_profiles:PS50835,hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10,Gene3D:2.60.40.10,Pfam_domain:PF07679,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS rs1471576272 . 0 206 4 0 0 0 0 0 -16.16646 1 1 1 1 0 T 4 4 92 178725976 178725976 A T 1 0 0 0 0 0 1 0 0 17245 157 6 4 4 TTN 2 178725976 Nonsense_Mutation SNP A C3N-02149_T 4144560 178725976 63467553 91 28275 ITGA4 0 . GRCh38 2 181511748 181511748 + Missense_Mutation SNP A A T rs748148308 C3N-02149_T C3N-02149_N A A c.1895A>T p.Gln632Leu p.Q632L ENST00000397033 17/28 266 234 32 373 373 0 strelka-varscan-mutect ITGA4,missense_variant,p.Gln632Leu,ENST00000397033,NM_000885.4;ITGA4,downstream_gene_variant,,ENST00000233573,;ITGA4,non_coding_transcript_exon_variant,,ENST00000476824,;ITGA4,non_coding_transcript_exon_variant,,ENST00000490435,; T ENST00000397033 Transcript missense_variant 2325/4189 1895/3099 632/1032 Q/L cAg/cTg rs748148308 1 1 ITGA4 HGNC HGNC:6140 protein_coding YES CCDS42788.1 ENSP00000380227 P13612 UPI000052D444 NM_000885.4 deleterious(0.04) 17/28 hmmpanther:PTHR23220:SF78,hmmpanther:PTHR23220,Pfam_domain:PF08441,Gene3D:2.60.40.1510,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs748148308 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 181511748 181511748 A T 1 0 0 0 0 1 0 0 0 7785 188 7 4 4 ITGA4 2 181511748 Missense_Mutation SNP A C3N-02149_T 2785772 181511748 60681781 92 28276 CERKL 0 . GRCh38 2 181656901 181656901 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.106C>G p.Pro36Ala p.P36A ENST00000339098 1/14 73 68 5 100 100 0 varscan-mutect CERKL,missense_variant,p.Pro36Ala,ENST00000410087,NM_201548.4;CERKL,missense_variant,p.Pro36Ala,ENST00000409440,NM_001160277.1;CERKL,missense_variant,p.Pro36Ala,ENST00000339098,NM_001030311.2;CERKL,missense_variant,p.Pro36Ala,ENST00000374970,NM_001030313.2;CERKL,missense_variant,p.Pro36Ala,ENST00000374969,NM_001030312.2;CERKL,intron_variant,,ENST00000479558,;CERKL,intron_variant,,ENST00000497337,;CERKL,intron_variant,,ENST00000476070,;CERKL,missense_variant,p.Pro36Ala,ENST00000374967,;CERKL,missense_variant,p.Pro36Ala,ENST00000452174,;CERKL,missense_variant,p.Pro36Ala,ENST00000421817,;CERKL,non_coding_transcript_exon_variant,,ENST00000494398,; C ENST00000339098 Transcript missense_variant 106/1677 106/1677 36/558 P/A Ccg/Gcg 1 -1 CERKL HGNC HGNC:21699 protein_coding YES CCDS42789.1 ENSP00000341159 Q49MI3 UPI000057259A NM_001030311.2 tolerated_low_confidence(0.52) 1/14 hmmpanther:PTHR12358:SF26,hmmpanther:PTHR12358 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 181656901 181656901 G C 1 0 0 0 0 1 0 0 0 2994 1232 43 4 4 CERKL 2 181656901 Missense_Mutation SNP G C3N-02149_T 145153 181656901 60536628 93 28277 ZNF804A 0 . GRCh38 2 184936298 184936298 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.902G>T p.Ser301Ile p.S301I ENST00000302277 4/4 164 148 16 218 218 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Ser301Ile,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Ser216Ile,ENST00000613975,; T ENST00000302277 Transcript missense_variant 1496/4690 902/3630 301/1209 S/I aGt/aTt COSM5614986 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 deleterious(0.04) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.99687 0.9999839 1 1 1 0 T 3 4 92 184936298 184936298 G T 1 0 0 0 0 1 0 0 0 18755 1029 36 2 2 ZNF804A 2 184936298 Missense_Mutation SNP G C3N-02149_T 3279397 184936298 57257231 94 28278 FSIP2 0 . GRCh38 2 185793022 185793022 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.6153C>A p.Ser2051Arg p.S2051R ENST00000343098 16/23 223 187 36 327 326 1 strelka-varscan-mutect FSIP2,missense_variant,p.Ser2051Arg,ENST00000343098,NM_173651.2;FSIP2,missense_variant,p.Ser1962Arg,ENST00000424728,;FSIP2-AS1,intron_variant,,ENST00000436557,;FSIP2-AS1,intron_variant,,ENST00000429929,;FSIP2,upstream_gene_variant,,ENST00000415915,; A ENST00000343098 Transcript missense_variant 6153/21054 6153/20991 2051/6996 S/R agC/agA 1 1 FSIP2 HGNC HGNC:21675 protein_coding YES CCDS54426.1 ENSP00000344403 J3QTJ6 UPI0001D420A1 NM_173651.2 deleterious(0.05) 16/23 hmmpanther:PTHR21856,hmmpanther:PTHR21856:SF6 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 185793022 185793022 C A 1 0 0 0 0 1 0 0 0 5949 709 25 2 2 FSIP2 2 185793022 Missense_Mutation SNP C C3N-02149_T 856724 185793022 56400507 95 28279 NABP1 0 . GRCh38 2 191683803 191683803 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.377G>T p.Gly126Val p.G126V ENST00000425611 4/6 182 166 16 307 306 1 strelka-varscan-mutect NABP1,missense_variant,p.Gly46Val,ENST00000410026,NM_001254736.1;NABP1,missense_variant,p.Gly126Val,ENST00000425611,NM_001031716.2;NABP1,missense_variant,p.Gly96Val,ENST00000435931,;NABP1,missense_variant,p.Gly46Val,ENST00000409510,;uc_338,downstream_gene_variant,,ENST00000617424,;NABP1,splice_region_variant,,ENST00000307849,;NABP1,splice_region_variant,,ENST00000451500,;NABP1,splice_region_variant,,ENST00000307834,;NABP1,splice_region_variant,,ENST00000462824,;NABP1,downstream_gene_variant,,ENST00000462712,;NABP1,downstream_gene_variant,,ENST00000491331,; T ENST00000425611 Transcript missense_variant,splice_region_variant 460/1878 377/615 126/204 G/V gGg/gTg COSM313436 1 1 NABP1 HGNC HGNC:26232 protein_coding YES CCDS33352.1 ENSP00000403683 Q96AH0 UPI000006F339 NM_001031716.2 tolerated(0.35) 4/6 hmmpanther:PTHR13356,hmmpanther:PTHR13356:SF1 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 191683803 191683803 G T 1 0 0 0 0 1 0 0 0 10137 1246 43 2 2 NABP1 2 191683803 Missense_Mutation SNP G C3N-02149_T 5890781 191683803 50509726 96 28280 CTLA4 0 . GRCh38 2 203870703 203870703 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.227A>T p.Gln76Leu p.Q76L ENST00000302823 2/4 398 354 44 531 531 0 strelka-varscan-mutect CTLA4,missense_variant,p.Gln76Leu,ENST00000302823,NM_005214.4;CTLA4,missense_variant,p.Gln39Leu,ENST00000427473,;CTLA4,missense_variant,p.Gln76Leu,ENST00000295854,NM_001037631.2;CTLA4,intron_variant,,ENST00000472206,;CTLA4,intron_variant,,ENST00000487393,; T ENST00000302823 Transcript missense_variant 384/1977 227/672 76/223 Q/L cAg/cTg 1 1 CTLA4 HGNC HGNC:2505 protein_coding YES CCDS2362.1 ENSP00000303939 P16410 UPI0000031FDF NM_005214.4 tolerated(0.06) 2/4 Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR11494,hmmpanther:PTHR11494:SF8,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 203870703 203870703 A T 1 0 0 0 0 1 0 0 0 3820 188 7 4 4 CTLA4 2 203870703 Missense_Mutation SNP A C3N-02149_T 12186900 203870703 38322826 97 28281 ZDBF2 0 . GRCh38 2 206308290 206308290 + Silent SNP T T A novel C3N-02149_T C3N-02149_N T T c.3762T>A p.= p.A1254A ENST00000374423 5/5 231 208 23 401 401 0 strelka-varscan-mutect ZDBF2,synonymous_variant,p.=,ENST00000374423,NM_020923.2;ZDBF2,synonymous_variant,p.=,ENST00000611847,NM_001285549.1; A ENST00000374423 Transcript synonymous_variant 4148/10286 3762/7065 1254/2354 A gcT/gcA 1 1 ZDBF2 HGNC HGNC:29313 protein_coding YES CCDS46501.1 ENSP00000363545 Q9HCK1 N0DVB2 UPI000022BDE3 NM_020923.2 5/5 hmmpanther:PTHR21639,hmmpanther:PTHR21639:SF5 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 206308290 206308290 T A 1 0 0 0 0 0 0 0 1 18174 1567 55 4 4 ZDBF2 2 206308290 Silent SNP T C3N-02149_T 2437587 206308290 35885239 98 28282 ERBB4 0 . GRCh38 2 211561925 211561925 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.2465A>T p.Asn822Ile p.N822I ENST00000342788 20/28 407 354 53 607 607 0 strelka-varscan-mutect ERBB4,missense_variant,p.Asn822Ile,ENST00000342788,NM_005235.2;ERBB4,missense_variant,p.Asn822Ile,ENST00000436443,NM_001042599.1;ERBB4,missense_variant,p.Asn796Ile,ENST00000402597,;ERBB4,non_coding_transcript_exon_variant,,ENST00000484594,; A ENST00000342788 Transcript missense_variant 2776/12136 2465/3927 822/1308 N/I aAc/aTc 1 -1 ERBB4 HGNC HGNC:3432 protein_coding YES CCDS2394.1 ENSP00000342235 Q15303 UPI00000499DF NM_005235.2 deleterious(0) 20/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF90,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000619,Gene3D:1.10.510.10,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 211561925 211561925 T A 1 0 0 0 0 1 0 0 0 5057 1725 60 4 4 ERBB4 2 211561925 Missense_Mutation SNP T C3N-02149_T 5253635 211561925 30631604 99 28283 PRKAG3 0 . GRCh38 2 218826969 218826969 + Missense_Mutation SNP A A T rs745901255 C3N-02149_T C3N-02149_N A A c.1127T>A p.Val376Glu p.V376E ENST00000439262 10/14 340 305 35 468 468 0 strelka-varscan-mutect PRKAG3,missense_variant,p.Val376Glu,ENST00000439262,NM_017431.2;PRKAG3,missense_variant,p.Val376Glu,ENST00000529249,;PRKAG3,downstream_gene_variant,,ENST00000430489,;MIR9500,downstream_gene_variant,,ENST00000635985,;PRKAG3,missense_variant,p.Val376Glu,ENST00000233944,;PRKAG3,3_prime_UTR_variant,,ENST00000470307,;PRKAG3,non_coding_transcript_exon_variant,,ENST00000490971,; T ENST00000439262 Transcript missense_variant 1148/2301 1127/1470 376/489 V/E gTg/gAg rs745901255 1 -1 PRKAG3 HGNC HGNC:9387 protein_coding YES CCDS2424.1 ENSP00000397133 Q9UGI9 A0A024R426 UPI0000043D98 NM_017431.2 deleterious(0) 10/14 PROSITE_profiles:PS51371,hmmpanther:PTHR13780:SF31,hmmpanther:PTHR13780,Gene3D:3.10.580.10,Pfam_domain:PF00571,SMART_domains:SM00116,Superfamily_domains:SSF54631 MODERATE 1 SNV 1 1 PASS rs745901255 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 218826969 218826969 A T 1 0 0 0 0 1 0 0 0 12635 159 6 4 4 PRKAG3 2 218826969 Missense_Mutation SNP A C3N-02149_T 7265044 218826969 23366560 100 28284 CFAP65 0 . GRCh38 2 219024112 219024112 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2498C>A p.Ala833Asp p.A833D ENST00000341552 15/35 297 272 25 437 437 0 strelka-varscan-mutect CFAP65,missense_variant,p.Ala833Asp,ENST00000341552,NM_194302.3;CFAP65,missense_variant,p.Ala833Asp,ENST00000453220,;CFAP65,downstream_gene_variant,,ENST00000441968,;CFAP65,downstream_gene_variant,,ENST00000409865,NM_001278295.1;CFAP65,downstream_gene_variant,,ENST00000410037,NM_001278296.1;CFAP65,upstream_gene_variant,,ENST00000413871,;CFAP65,downstream_gene_variant,,ENST00000462848,;CFAP65,downstream_gene_variant,,ENST00000463683,;CFAP65,downstream_gene_variant,,ENST00000474601,; T ENST00000341552 Transcript missense_variant 2582/5953 2498/5778 833/1925 A/D gCc/gAc 1 -1 CFAP65 HGNC HGNC:25325 protein_coding YES CCDS2430.2 ENSP00000340776 Q6ZU64 UPI0000609097 NM_194302.3 tolerated(0.06) 15/35 MODERATE 1 SNV 5 1 PASS rs750848836 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 219024112 219024112 G T 1 0 0 0 0 1 0 0 0 3029 1203 42 2 2 CFAP65 2 219024112 Missense_Mutation SNP G C3N-02149_T 197143 219024112 23169417 101 28285 FAM134A 0 . GRCh38 2 219182337 219182337 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.1340G>C p.Gly447Ala p.G447A ENST00000430297 9/9 275 250 25 348 348 0 strelka-varscan-mutect FAM134A,missense_variant,p.Gly447Ala,ENST00000430297,NM_024293.4;FAM134A,intron_variant,,ENST00000420189,;CNPPD1,upstream_gene_variant,,ENST00000409789,;FAM134A,downstream_gene_variant,,ENST00000458520,;FAM134A,downstream_gene_variant,,ENST00000452022,;FAM134A,downstream_gene_variant,,ENST00000430747,;FAM134A,downstream_gene_variant,,ENST00000443757,;FAM134A,3_prime_UTR_variant,,ENST00000273048,;FAM134A,downstream_gene_variant,,ENST00000452293,;FAM134A,downstream_gene_variant,,ENST00000465672,;FAM134A,downstream_gene_variant,,ENST00000481925,; C ENST00000430297 Transcript missense_variant 1476/4618 1340/1632 447/543 G/A gGc/gCc 1 1 FAM134A HGNC HGNC:28450 protein_coding YES CCDS2434.1 ENSP00000395249 Q8NC44 UPI000013D996 NM_024293.4 tolerated(0.19) 9/9 hmmpanther:PTHR20952,hmmpanther:PTHR20952:SF4 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -8.449062 0.9920734 1 1 1 0 C 3 2 92 219182337 219182337 G C 1 0 0 0 0 1 0 0 0 5295 1203 42 4 4 FAM134A 2 219182337 Missense_Mutation SNP G C3N-02149_T 158225 219182337 23011192 102 28286 SLC4A3 0 . GRCh38 2 219629396 219629396 + Frame_Shift_Del DEL A A - rs759883814,rs597306 C3N-02149_T C3N-02149_N A A c.470delA p.His157ProfsTer53 p.H157Pfs*53 ENST00000273063 4/23 68 64 4 82 82 0 varindel-pindel SLC4A3,frameshift_variant,p.His157ProfsTer113,ENST00000358055,NM_005070.3;SLC4A3,frameshift_variant,p.His157ProfsTer53,ENST00000273063,NM_001326559.1,NM_201574.2;SLC4A3,frameshift_variant,p.His157ProfsTer113,ENST00000373760,;SLC4A3,frameshift_variant,p.His157ProfsTer113,ENST00000317151,;SLC4A3,upstream_gene_variant,,ENST00000413743,;AC009955.8,upstream_gene_variant,,ENST00000455896,;SLC4A3,non_coding_transcript_exon_variant,,ENST00000497589,;SLC4A3,frameshift_variant,p.His157ProfsTer113,ENST00000425141,;SLC4A3,upstream_gene_variant,,ENST00000416910,;SLC4A3,upstream_gene_variant,,ENST00000444906,; - ENST00000273063 Transcript frameshift_variant 684/4246 470/3780 157/1259 H/X cAc/cc rs759883814,rs597306,COSM1405726 1 1 SLC4A3 HGNC HGNC:11029 protein_coding YES CCDS2446.1 ENSP00000273063 P48751 UPI000022BE50 NM_001326559.1,NM_201574.2 4/23 Prints_domain:PR01189 0,0,1 HIGH 1 deletion 1 0,0,1 1 PASS . . 0 0 0 0 0 0 0 210 -3.047256 0 0 1 0 0 - 7 5 92 219629396 219629396 A - 1 0 1 0 1 0 0 0 0 14932 159 6 0 0 SLC4A3 2 219629396 Frame_Shift_Del DEL A C3N-02149_T 447059 219629396 22564133 103 28287 SH3BP4 0 . GRCh38 2 235052594 235052594 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.2511G>T p.= p.V837V ENST00000409212 5/6 113 95 18 116 116 0 strelka-varscan SH3BP4,synonymous_variant,p.=,ENST00000409212,;SH3BP4,synonymous_variant,p.=,ENST00000392011,NM_014521.2;SH3BP4,synonymous_variant,p.=,ENST00000344528,; T ENST00000409212 Transcript synonymous_variant 3018/5231 2511/2892 837/963 V gtG/gtT 1 1 SH3BP4 HGNC HGNC:10826 protein_coding YES CCDS2513.1 ENSP00000386862 Q9P0V3 UPI000006DA47 5/6 hmmpanther:PTHR15603,hmmpanther:PTHR15603:SF3 LOW 1 SNV 5 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 235052594 235052594 G T 1 0 0 0 0 0 0 0 1 14504 1335 47 2 2 SH3BP4 2 235052594 Silent SNP G C3N-02149_T 15423198 235052594 7140935 104 28288 GPC1 0 . GRCh38 2 240466122 240466122 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1509C>A p.= p.V503V ENST00000264039 9/9 236 212 24 263 263 0 strelka-varscan GPC1,synonymous_variant,p.=,ENST00000264039,NM_002081.2;GPC1,synonymous_variant,p.=,ENST00000420138,;GPC1,synonymous_variant,p.=,ENST00000455111,;GPC1,downstream_gene_variant,,ENST00000425056,;GPC1,downstream_gene_variant,,ENST00000426280,;GPC1,downstream_gene_variant,,ENST00000427506,;GPC1,non_coding_transcript_exon_variant,,ENST00000466624,;GPC1,non_coding_transcript_exon_variant,,ENST00000495100,;GPC1,non_coding_transcript_exon_variant,,ENST00000469694,; A ENST00000264039 Transcript synonymous_variant 1757/3713 1509/1677 503/558 V gtC/gtA 1 1 GPC1 HGNC HGNC:4449 protein_coding YES CCDS2534.1 ENSP00000264039 P35052 UPI000013D4AA NM_002081.2 9/9 Low_complexity_(Seg):seg,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF8,Pfam_domain:PF01153 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 240466122 240466122 C A 1 0 0 0 0 0 0 0 1 6499 813 29 2 2 GPC1 2 240466122 Silent SNP C C3N-02149_T 5413528 240466122 1727407 105 28289 ATG7 0 . GRCh38 3 11315343 11315343 + Splice_Site SNP G G T novel C3N-02149_T C3N-02149_N G G c.529-1G>T p.X177_splice ENST00000354449 53 40 13 98 98 0 strelka-varscan-mutect ATG7,splice_acceptor_variant,,ENST00000354449,NM_006395.2;ATG7,splice_acceptor_variant,,ENST00000354956,NM_001136031.2;ATG7,splice_acceptor_variant,,ENST00000446450,NM_001144912.1;ATG7,splice_acceptor_variant,,ENST00000451830,;ATG7,downstream_gene_variant,,ENST00000451513,;ATG7,splice_acceptor_variant,,ENST00000488924,;ATG7,downstream_gene_variant,,ENST00000464282,;ATG7,splice_acceptor_variant,,ENST00000418682,;ATG7,splice_acceptor_variant,,ENST00000434066,;ATG7,intron_variant,,ENST00000424071,; T ENST00000354449 Transcript splice_acceptor_variant -/4959 529/2112 177/703 1 1 ATG7 HGNC HGNC:16935 protein_coding YES CCDS2605.1 ENSP00000346437 O95352 UPI00000705C7 NM_006395.2 6/18 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 92 11315343 11315343 G T 1 0 0 0 0 0 0 1 0 1253 956 33 2 2 ATG7 3 11315343 Splice_Site SNP G C3N-02149_T 11315343 186980216 106 28290 FGD5 0 . GRCh38 3 14819315 14819315 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.244G>T p.Gly82Cys p.G82C ENST00000285046 1/20 65 54 11 83 83 0 strelka-varscan-mutect FGD5,missense_variant,p.Gly82Cys,ENST00000285046,NM_152536.3;FGD5,5_prime_UTR_variant,,ENST00000543601,NM_001320276.1;FGD5,upstream_gene_variant,,ENST00000457774,; T ENST00000285046 Transcript missense_variant 354/5720 244/4389 82/1462 G/C Ggc/Tgc 1 1 FGD5 HGNC HGNC:19117 protein_coding YES CCDS46767.1 ENSP00000285046 Q6ZNL6 UPI00002372AE NM_152536.3 deleterious_low_confidence(0.01) 1/20 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.99999 0.9999985 1 1 1 0 T 3 4 92 14819315 14819315 G T 1 0 0 0 0 1 0 0 0 5700 1232 43 2 2 FGD5 3 14819315 Missense_Mutation SNP G C3N-02149_T 3503972 14819315 183476244 107 28291 RFTN1 0 . GRCh38 3 16370103 16370103 + Missense_Mutation SNP C C A rs138057177 C3N-02149_T C3N-02149_N C C c.1003G>T p.Ala335Ser p.A335S ENST00000334133 6/10 263 236 27 308 308 0 strelka-varscan-mutect RFTN1,missense_variant,p.Ala335Ser,ENST00000334133,NM_015150.1;RFTN1,missense_variant,p.Ala299Ser,ENST00000432519,;RFTN1,non_coding_transcript_exon_variant,,ENST00000483671,; A ENST00000334133 Transcript missense_variant 1276/2982 1003/1737 335/578 A/S Gca/Tca rs138057177 1 -1 RFTN1 HGNC HGNC:30278 protein_coding YES CCDS33712.1 ENSP00000334153 Q14699 UPI00001C1DE7 NM_015150.1 deleterious(0.04) 6/10 Pfam_domain:PF15250,hmmpanther:PTHR17601,hmmpanther:PTHR17601:SF3 MODERATE 1 SNV 1 1 PASS rs138057177 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 92 16370103 16370103 C A 1 0 0 0 0 1 0 0 0 13432 768 27 1 1 RFTN1 3 16370103 Missense_Mutation SNP C C3N-02149_T 1550788 16370103 181925456 108 28292 TBC1D5 0 . GRCh38 3 17161136 17161136 + Missense_Mutation SNP G G A rs781688564 C3N-02149_T C3N-02149_N G G c.2281C>T p.Arg761Cys p.R761C ENST00000446818 24/24 264 218 46 396 396 0 strelka-varscan-mutect TBC1D5,missense_variant,p.Arg739Cys,ENST00000253692,NM_014744.2;TBC1D5,missense_variant,p.Arg739Cys,ENST00000429383,;TBC1D5,missense_variant,p.Arg761Cys,ENST00000446818,NM_001134381.1;TBC1D5,non_coding_transcript_exon_variant,,ENST00000414318,; A ENST00000446818 Transcript missense_variant 2545/3124 2281/2454 761/817 R/C Cgc/Tgc rs781688564,COSM3590246 1 -1 TBC1D5 HGNC HGNC:19166 protein_coding YES CCDS46770.1 ENSP00000402935 Q92609 UPI00017E10F6 NM_001134381.1 tolerated_low_confidence(0.12) 24/24 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781688564 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 17161136 17161136 G A 1 0 0 0 0 1 0 0 0 16028 1058 37 1 1 TBC1D5 3 17161136 Missense_Mutation SNP G C3N-02149_T 791033 17161136 181134423 109 28293 CCDC13 0 . GRCh38 3 42752708 42752708 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.380G>T p.Gly127Val p.G127V ENST00000310232 4/16 144 102 42 191 191 0 strelka-varscan CCDC13,missense_variant,p.Gly127Val,ENST00000310232,NM_144719.3;CCDC13,non_coding_transcript_exon_variant,,ENST00000435327,;CCDC13,non_coding_transcript_exon_variant,,ENST00000492806,;CCDC13,non_coding_transcript_exon_variant,,ENST00000479576,;RP4-613B23.5,downstream_gene_variant,,ENST00000431549,; A ENST00000310232 Transcript missense_variant 464/2943 380/2148 127/715 G/V gGt/gTt 1 -1 CCDC13 HGNC HGNC:26358 protein_coding YES CCDS2705.1 ENSP00000309836 Q8IYE1 UPI00001AEF4E NM_144719.3 deleterious(0) 4/16 hmmpanther:PTHR31935,hmmpanther:PTHR31935:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 42752708 42752708 C A 1 0 0 0 0 1 0 0 0 2457 507 18 2 2 CCDC13 3 42752708 Missense_Mutation SNP C C3N-02149_T 25591572 42752708 155542851 110 28294 SMARCC1 0 . GRCh38 3 47662404 47662404 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2088G>T p.Met696Ile p.M696I ENST00000254480 20/28 313 253 60 453 453 0 strelka-varscan SMARCC1,missense_variant,p.Met696Ile,ENST00000254480,NM_003074.3;SMARCC1,non_coding_transcript_exon_variant,,ENST00000425518,;RP11-395P16.1,upstream_gene_variant,,ENST00000427885,; A ENST00000254480 Transcript missense_variant 2208/6375 2088/3318 696/1105 M/I atG/atT 1 -1 SMARCC1 HGNC HGNC:11104 protein_coding YES CCDS2758.1 ENSP00000254480 Q92922 UPI000013CE3B NM_003074.3 deleterious(0.01) 20/28 hmmpanther:PTHR12802,hmmpanther:PTHR12802:SF9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 47662404 47662404 C A 1 0 0 0 0 1 0 0 0 15068 826 29 2 2 SMARCC1 3 47662404 Missense_Mutation SNP C C3N-02149_T 4909696 47662404 150633155 111 28295 DCAF1 0 . GRCh38 3 51430072 51430072 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.1428C>A p.= p.L476L ENST00000423656 10/25 196 183 13 282 281 1 strelka-varscan DCAF1,synonymous_variant,p.=,ENST00000504652,NM_001171904.1;DCAF1,synonymous_variant,p.=,ENST00000423656,NM_014703.2;DCAF1,intron_variant,,ENST00000335891,; T ENST00000423656 Transcript synonymous_variant 1558/5946 1428/4524 476/1507 L ctC/ctA 1 -1 DCAF1 HGNC HGNC:30911 protein_coding YES CCDS74943.1 ENSP00000393183 Q9Y4B6 UPI00000716AC NM_014703.2 10/25 hmmpanther:PTHR13129,hmmpanther:PTHR13129:SF4,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 51430072 51430072 G T 1 0 0 0 0 0 0 0 1 4061 929 33 2 2 DCAF1 3 51430072 Silent SNP G C3N-02149_T 3767668 51430072 146865487 112 28296 FLNB 0 . GRCh38 3 58148795 58148795 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.6127C>A p.Leu2043Met p.L2043M ENST00000490882 37/47 295 243 52 419 417 2 strelka-varscan FLNB,missense_variant,p.Leu2012Met,ENST00000295956,NM_001457.3;FLNB,missense_variant,p.Leu2001Met,ENST00000429972,NM_001164318.1;FLNB,missense_variant,p.Leu1988Met,ENST00000358537,NM_001164319.1;FLNB,missense_variant,p.Leu2043Met,ENST00000490882,NM_001164317.1;FLNB,missense_variant,p.Leu1819Met,ENST00000493452,;FLNB,upstream_gene_variant,,ENST00000466455,;FLNB,non_coding_transcript_exon_variant,,ENST00000481470,;FLNB,upstream_gene_variant,,ENST00000477629,;FLNB,downstream_gene_variant,,ENST00000491408,;FLNB,upstream_gene_variant,,ENST00000470231,; A ENST00000490882 Transcript missense_variant 6292/8079 6127/7902 2043/2633 L/M Ctg/Atg COSM4502407,COSM4502408,COSM4502409 1 1 FLNB HGNC HGNC:3755 protein_coding YES CCDS54599.1 ENSP00000420213 O75369 UPI0001765F91 NM_001164317.1 deleterious(0) 37/47 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF238,SMART_domains:SM00557,Superfamily_domains:SSF81296 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 58148795 58148795 C A 1 0 0 0 0 1 0 0 0 5790 680 24 2 2 FLNB 3 58148795 Missense_Mutation SNP C C3N-02149_T 6718723 58148795 140146764 113 28297 PDZRN3 0 . GRCh38 3 73384864 73384864 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.1702G>A p.Asp568Asn p.D568N ENST00000263666 10/10 128 99 29 210 210 0 strelka-varscan PDZRN3,missense_variant,p.Asp568Asn,ENST00000263666,NM_015009.2;PDZRN3,missense_variant,p.Asp225Asn,ENST00000462146,NM_001303141.1;PDZRN3,missense_variant,p.Asp285Asn,ENST00000479530,NM_001303142.1;PDZRN3,missense_variant,p.Asp225Asn,ENST00000466780,NM_001303140.1;PDZRN3,missense_variant,p.Asp165Asn,ENST00000494559,;PDZRN3,missense_variant,p.Asp266Asn,ENST00000492909,NM_001303139.1;PDZRN3,downstream_gene_variant,,ENST00000466348,;PDZRN3,non_coding_transcript_exon_variant,,ENST00000478209,;PDZRN3,downstream_gene_variant,,ENST00000484487,; T ENST00000263666 Transcript missense_variant 1817/4248 1702/3201 568/1066 D/N Gac/Aac 1 -1 PDZRN3 HGNC HGNC:17704 protein_coding YES CCDS33789.1 ENSP00000263666 Q9UPQ7 UPI00001C1DE6 NM_015009.2 deleterious(0) 10/10 hmmpanther:PTHR15545:SF5,hmmpanther:PTHR15545 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 73384864 73384864 C T 1 0 0 0 0 1 0 0 0 11797 855 30 3 3 PDZRN3 3 73384864 Missense_Mutation SNP C C3N-02149_T 15236069 73384864 124910695 114 28298 SENP7 0 . GRCh38 3 101493969 101493969 + Splice_Site SNP C C A novel C3N-02149_T C3N-02149_N C C c.91-1G>T p.X31_splice ENST00000394095 121 103 18 217 217 0 strelka-varscan SENP7,splice_acceptor_variant,,ENST00000394095,NM_020654.4;SENP7,splice_acceptor_variant,,ENST00000314261,NM_001282801.1;SENP7,splice_acceptor_variant,,ENST00000394094,NM_001077203.2;SENP7,splice_acceptor_variant,,ENST00000394091,NM_001282803.1;SENP7,splice_acceptor_variant,,ENST00000348610,NM_001282802.1; A ENST00000394095 Transcript splice_acceptor_variant -/4945 91/3153 31/1050 1 -1 SENP7 HGNC HGNC:30402 protein_coding YES CCDS2941.2 ENSP00000377655 Q9BQF6 UPI0000E56ED1 NM_020654.4 2/23 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 92 101493969 101493969 C A 1 0 0 0 0 0 0 1 0 14327 927 32 2 2 SENP7 3 101493969 Splice_Site SNP C C3N-02149_T 28109105 101493969 96801590 115 28299 BOC 0 . GRCh38 3 113274438 113274438 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.1298C>A p.Ser433Tyr p.S433Y ENST00000273395 9/20 58 45 13 69 69 0 strelka-varscan BOC,missense_variant,p.Ser433Tyr,ENST00000495514,NM_033254.3;BOC,missense_variant,p.Ser433Tyr,ENST00000355385,;BOC,missense_variant,p.Ser433Tyr,ENST00000273395,NM_001301861.1;BOC,upstream_gene_variant,,ENST00000497495,;BOC,downstream_gene_variant,,ENST00000477178,;BOC,non_coding_transcript_exon_variant,,ENST00000466059,;BOC,non_coding_transcript_exon_variant,,ENST00000479182,;BOC,downstream_gene_variant,,ENST00000471963,; A ENST00000273395 Transcript missense_variant 1637/4276 1298/3348 433/1115 S/Y tCc/tAc COSM1616732 1 1 BOC HGNC HGNC:17173 protein_coding YES CCDS77788.1 ENSP00000273395 Q9BWV1 UPI0000D61B53 NM_001301861.1 tolerated(0.32) 9/20 Pfam_domain:PF16625,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF11 1 MODERATE 1 SNV 1 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999971 1 1 1 0 A 3 1 92 113274438 113274438 C A 1 0 0 0 0 1 0 0 0 1637 855 30 2 2 BOC 3 113274438 Missense_Mutation SNP C C3N-02149_T 11780469 113274438 85021121 116 28300 TF 0 . GRCh38 3 133754545 133754545 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.376T>C p.Phe126Leu p.F126L ENST00000402696 4/17 398 339 59 444 444 0 strelka-varscan TF,missense_variant,p.Phe126Leu,ENST00000402696,NM_001063.3;TF,5_prime_UTR_variant,,ENST00000482271,;TF,downstream_gene_variant,,ENST00000466911,;TF,non_coding_transcript_exon_variant,,ENST00000475382,;TFP1,non_coding_transcript_exon_variant,,ENST00000460564,;TF,3_prime_UTR_variant,,ENST00000494430,;TF,3_prime_UTR_variant,,ENST00000414694,;TF,non_coding_transcript_exon_variant,,ENST00000493011,;TF,non_coding_transcript_exon_variant,,ENST00000498622,;TF,intron_variant,,ENST00000485977,;TF,downstream_gene_variant,,ENST00000474287,;TF,downstream_gene_variant,,ENST00000460531,; C ENST00000402696 Transcript missense_variant 861/2968 376/2097 126/698 F/L Ttc/Ctc 1 1 TF HGNC HGNC:11740 protein_coding YES CCDS3080.1 ENSP00000385834 P02787 UPI000013D5A6 NM_001063.3 tolerated(0.05) 4/17 Gene3D:3.40.190.10,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,PIRSF_domain:PIRSF500682,PROSITE_profiles:PS51408,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF31,SMART_domains:SM00094,Superfamily_domains:SSF53850 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 133754545 133754545 T C 1 0 0 0 0 1 0 0 0 16218 1609 56 5 5 TF 3 133754545 Missense_Mutation SNP T C3N-02149_T 20480107 133754545 64541014 117 28301 GRK7 0 . GRCh38 3 141778459 141778459 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.175C>T p.= p.L59L ENST00000264952 1/4 402 344 58 401 401 0 strelka-varscan GRK7,synonymous_variant,p.=,ENST00000264952,NM_139209.2; T ENST00000264952 Transcript synonymous_variant 312/3239 175/1662 59/553 L Ctg/Ttg 1 1 GRK7 HGNC HGNC:17031 protein_coding YES CCDS3120.1 ENSP00000264952 Q8WTQ7 UPI000004244D NM_139209.2 1/4 hmmpanther:PTHR24355,hmmpanther:PTHR24355:SF12,Pfam_domain:PF00615,SMART_domains:SM00315,Superfamily_domains:SSF48097 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 141778459 141778459 C T 1 0 0 0 0 0 0 0 1 6677 680 24 3 3 GRK7 3 141778459 Silent SNP C C3N-02149_T 8023914 141778459 56517100 118 28302 ATR 0 . GRCh38 3 142553399 142553399 + Splice_Site SNP C C A rs372271245 C3N-02149_T C3N-02149_N C C c.2634-1G>T p.X878_splice ENST00000350721 313 266 47 427 426 1 strelka-varscan ATR,splice_acceptor_variant,,ENST00000350721,NM_001184.3;ATR,downstream_gene_variant,,ENST00000515149,;ATR,downstream_gene_variant,,ENST00000515863,; A ENST00000350721 Transcript splice_acceptor_variant -/8249 2634/7935 878/2644 rs372271245 1 -1 ATR HGNC HGNC:882 protein_coding YES CCDS3124.1 ENSP00000343741 Q13535 UPI0000031A31 NM_001184.3 12/46 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 92 142553399 142553399 C A 1 0 0 0 0 0 0 1 0 1356 695 24 2 2 ATR 3 142553399 Splice_Site SNP C C3N-02149_T 774940 142553399 55742160 119 28303 SLITRK3 0 . GRCh38 3 165188499 165188499 + Missense_Mutation SNP C C T C3N-02149_T C3N-02149_N C C c.2332G>A p.Gly778Arg p.G778R ENST00000475390 2/2 145 122 23 201 201 0 strelka-varscan SLITRK3,missense_variant,p.Gly778Arg,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,missense_variant,p.Gly778Arg,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; T ENST00000475390 Transcript missense_variant 2776/4555 2332/2934 778/977 G/R Ggg/Agg COSM347467 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 tolerated(0.19) 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 165188499 165188499 C T 1 0 0 0 0 1 0 0 0 15035 594 21 3 3 SLITRK3 3 165188499 Missense_Mutation SNP C C3N-02149_T 22635100 165188499 33107060 120 28304 CCDC39 0 . GRCh38 3 180616632 180616632 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2470C>A p.Gln824Lys p.Q824K ENST00000442201 18/20 189 157 32 252 252 0 strelka-varscan CCDC39,missense_variant,p.Gln824Lys,ENST00000442201,NM_181426.1;CCDC39,missense_variant,p.Gln8Lys,ENST00000473854,;TTC14,intron_variant,,ENST00000382584,NM_001288582.1;CCDC39,upstream_gene_variant,,ENST00000489868,;CCDC39,3_prime_UTR_variant,,ENST00000476379,; T ENST00000442201 Transcript missense_variant 2590/3279 2470/2826 824/941 Q/K Caa/Aaa 1 -1 CCDC39 HGNC HGNC:25244 protein_coding YES CCDS46964.1 ENSP00000405708 Q9UFE4 UPI00015D7298 NM_181426.1 tolerated(0.7) 18/20 hmmpanther:PTHR18962,hmmpanther:PTHR18962:SF0 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 180616632 180616632 G T 1 0 0 0 0 1 0 0 0 2520 1386 48 2 2 CCDC39 3 180616632 Missense_Mutation SNP G C3N-02149_T 15428133 180616632 17678927 121 28305 MCCC1 0 . GRCh38 3 183020200 183020200 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1907A>G p.Tyr636Cys p.Y636C ENST00000265594 17/19 508 425 83 567 567 0 strelka-varscan MCCC1,missense_variant,p.Tyr527Cys,ENST00000492597,;MCCC1,missense_variant,p.Tyr636Cys,ENST00000265594,NM_020166.4;MCCC1,missense_variant,p.Tyr486Cys,ENST00000610757,NM_001293273.1;MCCC1,missense_variant,p.Tyr589Cys,ENST00000476176,;MCCC1,3_prime_UTR_variant,,ENST00000629669,;MCCC1-AS1,downstream_gene_variant,,ENST00000471731,;MCCC1,downstream_gene_variant,,ENST00000489909,;MCCC1,3_prime_UTR_variant,,ENST00000497959,;MCCC1,3_prime_UTR_variant,,ENST00000497830,;MCCC1,3_prime_UTR_variant,,ENST00000495767,;MCCC1,non_coding_transcript_exon_variant,,ENST00000464601,; C ENST00000265594 Transcript missense_variant 2054/2545 1907/2178 636/725 Y/C tAc/tGc 1 -1 MCCC1 HGNC HGNC:6936 protein_coding YES CCDS3241.1 ENSP00000265594 Q96RQ3 A0A0S2Z693 UPI000013D646 NM_020166.4 deleterious(0.01) 17/19 hmmpanther:PTHR18866 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 183020200 183020200 T C 1 0 0 0 0 1 0 0 0 9304 1638 57 5 5 MCCC1 3 183020200 Missense_Mutation SNP T C3N-02149_T 2403568 183020200 15275359 122 28306 LAMP3 0 . GRCh38 3 183135830 183135830 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1004A>T p.His335Leu p.H335L ENST00000265598 5/6 226 189 37 259 259 0 strelka-varscan LAMP3,missense_variant,p.His335Leu,ENST00000265598,NM_014398.3;LAMP3,missense_variant,p.His311Leu,ENST00000466939,; A ENST00000265598 Transcript missense_variant 1260/3375 1004/1251 335/416 H/L cAt/cTt 1 -1 LAMP3 HGNC HGNC:14582 protein_coding YES CCDS3242.1 ENSP00000265598 Q9UQV4 UPI000006DB7A NM_014398.3 deleterious(0) 5/6 Pfam_domain:PF01299,Prints_domain:PR00336,PROSITE_profiles:PS51407,hmmpanther:PTHR11506,hmmpanther:PTHR11506:SF30 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 183135830 183135830 T A 1 0 0 0 0 1 0 0 0 8523 1464 51 4 4 LAMP3 3 183135830 Missense_Mutation SNP T C3N-02149_T 115630 183135830 15159729 123 28307 TBCCD1 0 . GRCh38 3 186556683 186556683 + Silent SNP T T C novel C3N-02149_T C3N-02149_N T T c.585A>G p.= p.S195S ENST00000424280 4/8 459 390 69 530 530 0 strelka-varscan TBCCD1,synonymous_variant,p.=,ENST00000424280,NM_001134415.1;TBCCD1,synonymous_variant,p.=,ENST00000338733,NM_018138.4;TBCCD1,synonymous_variant,p.=,ENST00000446782,NM_001286749.1;TBCCD1,synonymous_variant,p.=,ENST00000413695,;TBCCD1,downstream_gene_variant,,ENST00000430560,;TBCCD1,upstream_gene_variant,,ENST00000479590,; C ENST00000424280 Transcript synonymous_variant 1065/3058 585/1674 195/557 S tcA/tcG 1 -1 TBCCD1 HGNC HGNC:25546 protein_coding YES CCDS3276.1 ENSP00000411253 Q9NVR7 UPI0000073055 NM_001134415.1 4/8 hmmpanther:PTHR16052,hmmpanther:PTHR16052:SF0 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 186556683 186556683 T C 1 0 0 0 0 0 0 0 1 16037 1451 51 5 5 TBCCD1 3 186556683 Silent SNP T C3N-02149_T 3420853 186556683 11738876 124 28308 RTP2 0 . GRCh38 3 187698659 187698659 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.517G>T p.Glu173Ter p.E173* ENST00000358241 2/2 144 115 29 169 169 0 strelka-varscan RTP2,stop_gained,p.Glu173Ter,ENST00000358241,NM_001004312.2;RP11-211G3.3,upstream_gene_variant,,ENST00000449623,;RP11-211G3.3,upstream_gene_variant,,ENST00000437407,; A ENST00000358241 Transcript stop_gained 946/1346 517/678 173/225 E/* Gag/Tag 1 -1 RTP2 HGNC HGNC:32486 protein_coding YES CCDS33911.1 ENSP00000350976 Q5QGT7 UPI00001D801A NM_001004312.2 2/2 hmmpanther:PTHR14402:SF18,hmmpanther:PTHR14402 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 187698659 187698659 C A 1 0 0 0 0 0 1 0 0 13994 864 30 2 2 RTP2 3 187698659 Nonsense_Mutation SNP C C3N-02149_T 1141976 187698659 10596900 125 28309 NRROS 0 . GRCh38 3 196660227 196660227 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.584A>T p.Glu195Val p.E195V ENST00000328557 3/3 229 196 33 261 261 0 strelka-varscan NRROS,missense_variant,p.Glu195Val,ENST00000328557,NM_198565.2;PIGX,intron_variant,,ENST00000426755,; T ENST00000328557 Transcript missense_variant 787/2564 584/2079 195/692 E/V gAg/gTg 1 1 NRROS HGNC HGNC:24613 protein_coding YES CCDS3319.1 ENSP00000328625 Q86YC3 UPI000000DA7E NM_198565.2 deleterious(0) 3/3 PROSITE_profiles:PS51450,hmmpanther:PTHR24365:SF347,hmmpanther:PTHR24365,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52047 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 196660227 196660227 A T 1 0 0 0 0 1 0 0 0 10720 304 11 4 4 NRROS 3 196660227 Missense_Mutation SNP A C3N-02149_T 8961568 196660227 1635332 126 28310 C1QTNF7 0 . GRCh38 4 15442396 15442396 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.488C>A p.Thr163Asn p.T163N ENST00000295297 3/3 354 254 100 436 435 1 strelka-varscan C1QTNF7,missense_variant,p.Thr163Asn,ENST00000295297,NM_001135170.1;C1QTNF7,missense_variant,p.Thr156Asn,ENST00000429690,NM_001135171.1;C1QTNF7,missense_variant,p.Thr156Asn,ENST00000444304,NM_031911.4;C1QTNF7,downstream_gene_variant,,ENST00000397700,;C1QTNF7,downstream_gene_variant,,ENST00000382383,; A ENST00000295297 Transcript missense_variant 747/4516 488/891 163/296 T/N aCc/aAc 1 1 C1QTNF7 HGNC HGNC:14342 protein_coding YES CCDS47025.1 ENSP00000295297 Q9BXJ2 UPI000004E7F9 NM_001135170.1 deleterious(0.04) 3/3 PROSITE_profiles:PS50871,hmmpanther:PTHR24023:SF561,hmmpanther:PTHR24023,Pfam_domain:PF00386,Gene3D:2.60.120.40,SMART_domains:SM00110,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 15442396 15442396 C A 1 0 0 0 0 1 0 0 0 1946 507 18 2 2 C1QTNF7 4 15442396 Missense_Mutation SNP C C3N-02149_T 15442396 174772159 127 28311 GABRG1 0 . GRCh38 4 46065485 46065486 + Frame_Shift_Ins INS - - A novel C3N-02149_T C3N-02149_N - - c.420dupT p.Gly141TrpfsTer7 p.G141Wfs*7 ENST00000295452 4/9 284 228 56 390 390 0 sindel-varindel-pindel GABRG1,frameshift_variant,p.Gly141TrpfsTer7,ENST00000295452,NM_173536.3; A ENST00000295452 Transcript frameshift_variant 588-589/6785 420-421/1398 140-141/465 -/X -/T 1 -1 GABRG1 HGNC HGNC:4086 protein_coding YES CCDS3470.1 ENSP00000295452 Q8N1C3 UPI0000047AE2 NM_173536.3 4/9 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF93,TIGRFAM_domain:TIGR00860 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 92 46065485 46065485 - A 1 0 1 1 0 0 0 0 0 6042 603 21 0 0 GABRG1 4 46065485 Frame_Shift_Ins INS - C3N-02149_T 30623089 46065485 144149070 128 28312 FRYL 0 . GRCh38 4 48540476 48540476 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.6172G>T p.Gly2058Ter p.G2058* ENST00000358350 46/64 421 302 119 534 533 1 strelka-varscan-mutect FRYL,stop_gained,p.Gly2058Ter,ENST00000358350,NM_015030.1;FRYL,stop_gained,p.Gly2058Ter,ENST00000503238,;FRYL,stop_gained,p.Gly928Ter,ENST00000514617,;FRYL,5_prime_UTR_variant,,ENST00000507873,;FRYL,non_coding_transcript_exon_variant,,ENST00000512297,;FRYL,non_coding_transcript_exon_variant,,ENST00000513401,; A ENST00000358350 Transcript stop_gained 6777/11706 6172/9042 2058/3013 G/* Gga/Tga 1 -1 FRYL HGNC HGNC:29127 protein_coding YES CCDS43227.1 ENSP00000351113 O94915 UPI0000EBC149 NM_015030.1 46/64 Pfam_domain:PF14225,hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF9,Superfamily_domains:SSF48371 HIGH 1 SNV 5 1 PASS rs1225660262 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 48540476 48540476 C A 1 0 0 0 0 0 1 0 0 5936 690 24 2 2 FRYL 4 48540476 Nonsense_Mutation SNP C C3N-02149_T 2474991 48540476 141674079 129 28313 EPHA5 0 . GRCh38 4 65490705 65490705 + Silent SNP G G T rs554706022 C3N-02149_T C3N-02149_N G G c.1074C>A p.= p.P358P ENST00000622150 5/18 130 106 24 161 160 1 strelka-varscan EPHA5,synonymous_variant,p.=,ENST00000622150,NM_001281765.1;EPHA5,synonymous_variant,p.=,ENST00000613740,NM_001281766.1;EPHA5,synonymous_variant,p.=,ENST00000273854,NM_004439.6;EPHA5,synonymous_variant,p.=,ENST00000511294,NM_001281767.1;EPHA5,synonymous_variant,p.=,ENST00000354839,NM_182472.3;EPHA5,intron_variant,,ENST00000432638,; T ENST00000622150 Transcript synonymous_variant 1827/8421 1074/3117 358/1038 P ccC/ccA rs554706022 1 -1 EPHA5 HGNC HGNC:3389 protein_coding YES CCDS75133.1 ENSP00000480763 B7ZKJ3 UPI0000EE2CFD NM_001281765.1 5/18 Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF17,SMART_domains:SM00060,Superfamily_domains:SSF49265 LOW 1 SNV 1 1 PASS . . 0 201 7 2 0 0 0 0 -20 0.9998967 1 1 1 0 T 2 4 92 65490705 65490705 G T 1 0 0 0 0 0 0 0 1 5017 987 35 2 2 EPHA5 4 65490705 Silent SNP G C3N-02149_T 16950229 65490705 124723850 130 28314 SLC4A4 0 . GRCh38 4 71451255 71451255 + Nonsense_Mutation SNP G G T rs760529597 C3N-02149_T C3N-02149_N G G c.1276G>T p.Gly426Ter p.G426* ENST00000425175 11/25 439 348 91 553 552 1 strelka-varscan SLC4A4,stop_gained,p.Gly382Ter,ENST00000340595,NM_003759.3;SLC4A4,stop_gained,p.Gly426Ter,ENST00000425175,NM_001134742.1;SLC4A4,stop_gained,p.Gly426Ter,ENST00000264485,NM_001098484.2;SLC4A4,stop_gained,p.Gly426Ter,ENST00000351898,;SLC4A4,stop_gained,p.Gly382Ter,ENST00000512686,;SLC4A4,non_coding_transcript_exon_variant,,ENST00000514331,; T ENST00000425175 Transcript stop_gained 1393/7596 1276/3285 426/1094 G/* Gga/Tga rs760529597,COSM1430830,COSM1430831 1 1 SLC4A4 HGNC HGNC:11030 protein_coding YES CCDS47071.1 ENSP00000393557 Q9Y6R1 A5JJ20 UPI000152897D NM_001134742.1 11/25 hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF10,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00834 0,1,1 HIGH 1 SNV 5 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 71451255 71451255 G T 1 0 0 0 0 0 1 0 0 14933 1117 39 1 1 SLC4A4 4 71451255 Nonsense_Mutation SNP G C3N-02149_T 5960550 71451255 118763300 131 28315 SPARCL1 0 . GRCh38 4 87493687 87493687 + Silent SNP G G T rs746453849 C3N-02149_T C3N-02149_N G G c.1113C>A p.= p.A371A ENST00000418378 5/12 166 131 35 221 221 0 strelka-varscan-mutect SPARCL1,synonymous_variant,p.=,ENST00000418378,NM_001128310.2;SPARCL1,synonymous_variant,p.=,ENST00000282470,NM_004684.5;SPARCL1,synonymous_variant,p.=,ENST00000503414,NM_001291977.1,NM_001291976.1;SPARCL1,downstream_gene_variant,,ENST00000434434,;SPARCL1,downstream_gene_variant,,ENST00000541496,;SPARCL1,downstream_gene_variant,,ENST00000512317,;SPARCL1,downstream_gene_variant,,ENST00000509407,;SPARCL1,downstream_gene_variant,,ENST00000543631,;SPARCL1,downstream_gene_variant,,ENST00000458304,;SPARCL1,downstream_gene_variant,,ENST00000535835,; T ENST00000418378 Transcript synonymous_variant 1685/2994 1113/1995 371/664 A gcC/gcA rs746453849 1 -1 SPARCL1 HGNC HGNC:11220 protein_coding YES CCDS3622.1 ENSP00000414856 Q14515 A0A024RDE1 UPI000013DCE3 NM_001128310.2 5/12 hmmpanther:PTHR13866:SF16,hmmpanther:PTHR13866,PIRSF_domain:PIRSF002574 LOW 1 SNV 5 1 PASS rs746453849 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 87493687 87493687 G T 1 0 0 0 0 0 0 0 1 15327 1103 39 1 1 SPARCL1 4 87493687 Silent SNP G C3N-02149_T 16042432 87493687 102720868 132 28316 SPP1 0 . GRCh38 4 87981785 87981785 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.527G>A p.Arg176Lys p.R176K ENST00000395080 6/7 124 94 30 177 177 0 strelka-varscan-mutect SPP1,missense_variant,p.Arg162Lys,ENST00000237623,NM_000582.2;SPP1,missense_variant,p.Arg154Lys,ENST00000614857,NM_001251830.1;SPP1,missense_variant,p.Arg176Lys,ENST00000395080,NM_001040058.1;SPP1,missense_variant,p.Arg149Lys,ENST00000360804,NM_001040060.1;SPP1,missense_variant,p.Arg135Lys,ENST00000508233,NM_001251829.1;SPP1,non_coding_transcript_exon_variant,,ENST00000509659,;SPP1,downstream_gene_variant,,ENST00000509334,;SPP1,downstream_gene_variant,,ENST00000513981,;SPP1,downstream_gene_variant,,ENST00000508002,;SPP1,downstream_gene_variant,,ENST00000504310,;SPP1,downstream_gene_variant,,ENST00000505146,; A ENST00000395080 Transcript missense_variant 654/1473 527/945 176/314 R/K aGa/aAa 1 1 SPP1 HGNC HGNC:11255 protein_coding YES CCDS43250.1 ENSP00000378517 P10451 A0A024RDE2 UPI0000000E0B NM_001040058.1 tolerated(0.58) 6/7 hmmpanther:PTHR10607:SF1,hmmpanther:PTHR10607,Pfam_domain:PF00865,SMART_domains:SM00017 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 87981785 87981785 G A 1 0 0 0 0 1 0 0 0 15439 942 33 3 3 SPP1 4 87981785 Missense_Mutation SNP G C3N-02149_T 488098 87981785 102232770 133 28317 GRID2 0 . GRCh38 4 93490735 93490735 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1955T>C p.Leu652Pro p.L652P ENST00000282020 12/16 145 132 13 176 176 0 strelka-varscan-mutect GRID2,missense_variant,p.Leu652Pro,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Leu571Pro,ENST00000611049,;GRID2,missense_variant,p.Leu557Pro,ENST00000510992,NM_001286838.1; C ENST00000282020 Transcript missense_variant 2990/6117 1955/3024 652/1007 L/P cTc/cCc 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 deleterious(0) 12/16 Transmembrane_helices:TMhelix,hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079,Prints_domain:PR00177 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 93490735 93490735 T C 1 0 0 0 0 1 0 0 0 6652 1551 54 5 5 GRID2 4 93490735 Missense_Mutation SNP T C3N-02149_T 5508950 93490735 96723820 134 28318 SCLT1 0 . GRCh38 4 128948514 128948514 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1275G>T p.= p.V425V ENST00000281142 15/21 153 114 39 216 216 0 strelka-varscan-mutect SCLT1,synonymous_variant,p.=,ENST00000281142,NM_144643.3;SCLT1,intron_variant,,ENST00000503215,;SCLT1,intron_variant,,ENST00000439369,;SCLT1,non_coding_transcript_exon_variant,,ENST00000502495,;SCLT1,non_coding_transcript_exon_variant,,ENST00000506233,;RP11-209D20.2,downstream_gene_variant,,ENST00000612976,; A ENST00000281142 Transcript synonymous_variant 1779/3055 1275/2067 425/688 V gtG/gtT 1 -1 SCLT1 HGNC HGNC:26406 protein_coding YES CCDS3740.1 ENSP00000281142 Q96NL6 UPI000013DC5F NM_144643.3 15/21 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF478,Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 128948514 128948514 C A 1 0 0 0 0 0 0 0 1 14175 581 21 2 2 SCLT1 4 128948514 Silent SNP C C3N-02149_T 35457779 128948514 61266041 135 28319 TLL1 0 . GRCh38 4 166039438 166039438 + Missense_Mutation SNP C C A rs775648272 C3N-02149_T C3N-02149_N C C c.1258C>A p.Leu420Ile p.L420I ENST00000061240 10/21 292 253 39 449 447 2 strelka-varscan TLL1,missense_variant,p.Leu420Ile,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Leu420Ile,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,; A ENST00000061240 Transcript missense_variant 1905/6708 1258/3042 420/1013 L/I Ctt/Att rs775648272 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 tolerated(0.29) 10/21 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 166039438 166039438 C A 1 0 0 0 0 1 0 0 0 16391 695 24 2 2 TLL1 4 166039438 Missense_Mutation SNP C C3N-02149_T 37090924 166039438 24175117 136 28320 PLEKHG4B 0 . GRCh38 5 163495 163495 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.2355C>T p.= p.S785S ENST00000283426 11/18 231 153 78 186 186 0 strelka-varscan-mutect PLEKHG4B,synonymous_variant,p.=,ENST00000637938,;PLEKHG4B,synonymous_variant,p.=,ENST00000283426,NM_052909.3; T ENST00000283426 Transcript synonymous_variant 2405/11515 2355/3816 785/1271 S tcC/tcT 1 1 PLEKHG4B HGNC HGNC:29399 protein_coding YES CCDS34124.1 ENSP00000283426 Q96PX9 UPI0000D615EE NM_052909.3 11/18 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF119 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 163495 163495 C T 1 0 0 0 0 0 0 0 1 12165 668 24 3 3 PLEKHG4B 5 163495 Silent SNP C C3N-02149_T 163495 181374764 137 28321 SLC12A7 0 . GRCh38 5 1078715 1078715 + Silent SNP C C A rs750535834 C3N-02149_T C3N-02149_N C C c.1440G>T p.= p.V480V ENST00000264930 11/24 358 262 96 305 304 1 strelka-varscan-mutect SLC12A7,synonymous_variant,p.=,ENST00000264930,NM_006598.2;SLC12A7,synonymous_variant,p.=,ENST00000634447,;SLC12A7,upstream_gene_variant,,ENST00000513223,;SLC12A7,non_coding_transcript_exon_variant,,ENST00000510943,;SLC12A7,upstream_gene_variant,,ENST00000504576,; A ENST00000264930 Transcript synonymous_variant 1484/5280 1440/3252 480/1083 V gtG/gtT rs750535834 1 -1 SLC12A7 HGNC HGNC:10915 protein_coding YES CCDS34129.1 ENSP00000264930 Q9Y666 UPI0000141815 NM_006598.2 11/24 Pfam_domain:PF00324,hmmpanther:PTHR11827,hmmpanther:PTHR11827:SF47,TIGRFAM_domain:TIGR00930 LOW 1 SNV 1 1 PASS rs750535834 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 1078715 1078715 C A 1 0 0 0 0 0 0 0 1 14653 581 21 2 2 SLC12A7 5 1078715 Silent SNP C C3N-02149_T 915220 1078715 180459544 138 28322 SLC6A3 0 . GRCh38 5 1411267 1411267 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1245G>T p.= p.L415L ENST00000270349 9/15 665 594 71 568 567 1 strelka-varscan-mutect SLC6A3,synonymous_variant,p.=,ENST00000270349,NM_001044.4;SLC6A3,downstream_gene_variant,,ENST00000511750,; A ENST00000270349 Transcript synonymous_variant 1373/3936 1245/1863 415/620 L ctG/ctT 1 -1 SLC6A3 HGNC HGNC:11049 protein_coding YES CCDS3863.1 ENSP00000270349 Q01959 UPI000013548F NM_001044.4 9/15 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF38,Pfam_domain:PF00209,Superfamily_domains:0053687,Prints_domain:PR00176 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 1411267 1411267 C A 1 0 0 0 0 0 0 0 1 14968 697 25 2 2 SLC6A3 5 1411267 Silent SNP C C3N-02149_T 332552 1411267 180126992 139 28323 UBE2QL1 0 . GRCh38 5 6449114 6449114 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.221C>T p.Pro74Leu p.P74L ENST00000399816 1/2 128 89 39 126 126 0 strelka-varscan-mutect UBE2QL1,missense_variant,p.Pro74Leu,ENST00000399816,NM_001145161.2; T ENST00000399816 Transcript missense_variant 492/4317 221/486 74/161 P/L cCg/cTg 1 1 UBE2QL1 HGNC HGNC:37269 protein_coding YES CCDS47189.1 ENSP00000382713 A1L167 UPI000020BF29 NM_001145161.2 deleterious(0) 1/2 PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF72,hmmpanther:PTHR24068,Pfam_domain:PF00179,Gene3D:3.10.110.10,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 6449114 6449114 C T 1 0 0 0 0 1 0 0 0 17393 652 23 1 1 UBE2QL1 5 6449114 Missense_Mutation SNP C C3N-02149_T 5037847 6449114 175089145 140 28324 CTNND2 0 . GRCh38 5 11364718 11364718 + Silent SNP G G T rs138883759 C3N-02149_T C3N-02149_N G G c.1350C>A p.= p.T450T ENST00000304623 8/22 205 174 31 210 209 1 strelka-varscan-mutect CTNND2,synonymous_variant,p.=,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,synonymous_variant,p.=,ENST00000511377,NM_001288715.1;CTNND2,synonymous_variant,p.=,ENST00000503622,NM_001288716.1;CTNND2,synonymous_variant,p.=,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000504354,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506735,;CTNND2,downstream_gene_variant,,ENST00000511278,;CTNND2,synonymous_variant,p.=,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,;CTNND2,non_coding_transcript_exon_variant,,ENST00000507430,; T ENST00000304623 Transcript synonymous_variant 1540/5481 1350/3678 450/1225 T acC/acA rs138883759,COSM385245 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 8/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 0,1 LOW 1 SNV 1 0,1 1 PASS rs138883759 . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 92 11364718 11364718 G T 1 0 0 0 0 0 0 0 1 3829 1103 39 1 1 CTNND2 5 11364718 Silent SNP G C3N-02149_T 4915604 11364718 170173541 141 28325 CDH10 0 . GRCh38 5 24491805 24491805 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.1647C>A p.= p.T549T ENST00000264463 11/12 164 135 29 183 183 0 strelka-varscan-mutect CDH10,synonymous_variant,p.=,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; T ENST00000264463 Transcript synonymous_variant 2155/3438 1647/2367 549/788 T acC/acA 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 11/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 24491805 24491805 G T 1 0 0 0 0 0 0 0 1 2799 1335 47 2 2 CDH10 5 24491805 Silent SNP G C3N-02149_T 13127087 24491805 157046454 142 28326 MTMR12 0 . GRCh38 5 32230126 32230126 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1896G>T p.Glu632Asp p.E632D ENST00000382142 16/16 145 103 42 139 139 0 strelka-varscan-mutect MTMR12,missense_variant,p.Glu632Asp,ENST00000382142,NM_001040446.2;MTMR12,missense_variant,p.Glu578Asp,ENST00000280285,NM_001294343.1;MTMR12,missense_variant,p.Glu522Asp,ENST00000264934,NM_001294344.1;RNU6-1079P,downstream_gene_variant,,ENST00000362861,;MTMR12,non_coding_transcript_exon_variant,,ENST00000510216,; A ENST00000382142 Transcript missense_variant 2067/5187 1896/2244 632/747 E/D gaG/gaT 1 -1 MTMR12 HGNC HGNC:18191 protein_coding YES CCDS34138.1 ENSP00000371577 Q9C0I1 UPI00001678D2 NM_001040446.2 tolerated(0.51) 16/16 Pfam_domain:PF12578,PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF37,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 32230126 32230126 C A 1 0 0 0 0 1 0 0 0 9929 680 24 2 2 MTMR12 5 32230126 Missense_Mutation SNP C C3N-02149_T 7738321 32230126 149308133 143 28327 ADAMTS12 0 . GRCh38 5 33549282 33549282 + Silent SNP G G T rs61748195 C3N-02149_T C3N-02149_N G G c.4227C>A p.= p.A1409A ENST00000504830 21/24 241 211 30 229 228 1 strelka-varscan-mutect ADAMTS12,synonymous_variant,p.=,ENST00000504830,NM_030955.2;ADAMTS12,synonymous_variant,p.=,ENST00000352040,; T ENST00000504830 Transcript synonymous_variant 4563/8774 4227/4785 1409/1594 A gcC/gcA rs61748195,COSM4436224 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 21/24 Gene3D:2.20.100.10,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 0,1 LOW 1 SNV 1 0,1 1 PASS rs61748195 . 0 180 0 0 0 0 0 29 -3.759868 0 0 1 0 0 T 2 4 92 33549282 33549282 G T 1 0 0 0 0 0 0 0 1 301 1103 39 1 1 ADAMTS12 5 33549282 Silent SNP G C3N-02149_T 1319156 33549282 147988977 144 28328 ADAMTS12 0 . GRCh38 5 33577159 33577159 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.2867G>A p.Cys956Tyr p.C956Y ENST00000504830 19/24 552 483 69 498 498 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Cys956Tyr,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Cys871Tyr,ENST00000352040,;ADAMTS12,splice_region_variant,,ENST00000504582,; T ENST00000504830 Transcript missense_variant,splice_region_variant 3203/8774 2867/4785 956/1594 C/Y tGt/tAt 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0.03) 19/24 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 33577159 33577159 C T 1 0 0 0 0 1 0 0 0 301 492 17 3 3 ADAMTS12 5 33577159 Missense_Mutation SNP C C3N-02149_T 27877 33577159 147961100 145 28329 UGT3A1 0 . GRCh38 5 35955809 35955809 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1131G>T p.Glu377Asp p.E377D ENST00000274278 6/7 345 254 91 377 377 0 strelka-varscan-mutect UGT3A1,missense_variant,p.Glu377Asp,ENST00000274278,NM_152404.3;UGT3A1,missense_variant,p.Glu377Asp,ENST00000503189,;UGT3A1,missense_variant,p.Glu343Asp,ENST00000507113,;UGT3A1,downstream_gene_variant,,ENST00000625798,NM_001171873.1;UGT3A1,non_coding_transcript_exon_variant,,ENST00000513233,;UGT3A1,3_prime_UTR_variant,,ENST00000515801,; A ENST00000274278 Transcript missense_variant 1489/5122 1131/1572 377/523 E/D gaG/gaT 1 -1 UGT3A1 HGNC HGNC:26625 protein_coding YES CCDS3913.1 ENSP00000274278 Q6NUS8 A8K444 UPI000003C38B NM_152404.3 deleterious(0.02) 6/7 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF208,PROSITE_patterns:PS00375,Gene3D:3.40.50.2000,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 35955809 35955809 C A 1 0 0 0 0 1 0 0 0 17487 680 24 2 2 UGT3A1 5 35955809 Missense_Mutation SNP C C3N-02149_T 2378650 35955809 145582450 146 28330 SREK1 0 . GRCh38 5 66178817 66178817 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.1824G>A p.= p.G608G ENST00000334121 12/12 124 107 17 187 186 1 strelka-varscan-mutect SREK1,synonymous_variant,p.=,ENST00000334121,NM_001323527.1,NM_001323529.1,NM_001077199.2;SREK1,synonymous_variant,p.=,ENST00000380918,NM_001270492.1,NM_139168.3;SREK1,non_coding_transcript_exon_variant,,ENST00000284041,;SREK1,3_prime_UTR_variant,,ENST00000520953,;SREK1,3_prime_UTR_variant,,ENST00000522912,;SREK1,non_coding_transcript_exon_variant,,ENST00000519259,;SREK1,non_coding_transcript_exon_variant,,ENST00000522214,;SREK1,non_coding_transcript_exon_variant,,ENST00000519205,; A ENST00000334121 Transcript synonymous_variant 1983/6781 1824/1875 608/624 G ggG/ggA 1 1 SREK1 HGNC HGNC:17882 protein_coding YES CCDS43323.1 ENSP00000334538 Q8WXA9 UPI00000467F2 NM_001323527.1,NM_001323529.1,NM_001077199.2 12/12 hmmpanther:PTHR32343,hmmpanther:PTHR32343:SF7 LOW 1 SNV 2 1 PASS rs1224659869 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 66178817 66178817 G A 1 0 0 0 0 0 0 0 1 15500 1161 41 3 3 SREK1 5 66178817 Silent SNP G C3N-02149_T 30223008 66178817 115359442 147 28331 UTP15 0 . GRCh38 5 73578767 73578767 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1061A>T p.Asn354Ile p.N354I ENST00000296792 10/13 239 192 47 275 275 0 strelka-varscan-mutect UTP15,missense_variant,p.Asn164Ile,ENST00000543251,NM_001284431.1;UTP15,missense_variant,p.Asn354Ile,ENST00000296792,NM_032175.3;UTP15,missense_variant,p.Asn381Ile,ENST00000509005,;UTP15,missense_variant,p.Asn335Ile,ENST00000508491,NM_001284430.1;UTP15,downstream_gene_variant,,ENST00000512550,; T ENST00000296792 Transcript missense_variant 1316/3687 1061/1557 354/518 N/I aAc/aTc 1 1 UTP15 HGNC HGNC:25758 protein_coding YES CCDS34186.1 ENSP00000296792 Q8TED0 UPI000020CADC NM_032175.3 deleterious(0.03) 10/13 hmmpanther:PTHR19924:SF26,hmmpanther:PTHR19924,Pfam_domain:PF09384 MODERATE 1 SNV 1 1 PASS rs1223250851 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 73578767 73578767 A T 1 0 0 0 0 1 0 0 0 17640 43 2 4 4 UTP15 5 73578767 Missense_Mutation SNP A C3N-02149_T 7399950 73578767 107959492 148 28332 ADGRV1 0 . GRCh38 5 90829137 90829137 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.16562C>G p.Ala5521Gly p.A5521G ENST00000405460 77/90 68 50 18 84 84 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Ala5521Gly,ENST00000405460,NM_032119.3;ADGRV1,missense_variant,p.Ala1182Gly,ENST00000425867,; G ENST00000405460 Transcript missense_variant 16658/19338 16562/18921 5521/6306 A/G gCc/gGc 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 tolerated(0.33) 77/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS . . 0 200 9 0 0 0 0 0 -20 0.9999979 1 1 1 0 G 3 3 92 90829137 90829137 C G 1 0 0 0 0 1 0 0 0 379 739 26 4 4 ADGRV1 5 90829137 Missense_Mutation SNP C C3N-02149_T 17250370 90829137 90709122 149 28333 ST8SIA4 0 . GRCh38 5 100902928 100902928 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.28A>T p.Ile10Phe p.I10F ENST00000231461 1/5 217 181 36 338 338 0 strelka-varscan-mutect ST8SIA4,missense_variant,p.Ile10Phe,ENST00000231461,NM_005668.5;ST8SIA4,missense_variant,p.Ile10Phe,ENST00000451528,NM_175052.2;ST8SIA4,missense_variant,p.Ile10Phe,ENST00000523381,; A ENST00000231461 Transcript missense_variant 339/6303 28/1080 10/359 I/F Atc/Ttc 1 -1 ST8SIA4 HGNC HGNC:10871 protein_coding YES CCDS4091.1 ENSP00000231461 Q92187 UPI0000135973 NM_005668.5 1/5 PIRSF_domain:PIRSF005557,hmmpanther:PTHR11987,hmmpanther:PTHR11987:SF31,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS rs1374895196 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 100902928 100902928 T A 1 0 0 0 0 1 0 0 0 15612 1435 50 4 4 ST8SIA4 5 100902928 Missense_Mutation SNP T C3N-02149_T 10073791 100902928 80635331 150 28334 NUDT12 0 . GRCh38 5 103559156 103559156 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.519A>T p.Glu173Asp p.E173D ENST00000230792 3/7 58 41 17 78 78 0 strelka-varscan-mutect NUDT12,missense_variant,p.Glu173Asp,ENST00000230792,NM_031438.3;NUDT12,missense_variant,p.Glu155Asp,ENST00000507423,NM_001300741.1;NUDT12,upstream_gene_variant,,ENST00000515407,;NUDT12,downstream_gene_variant,,ENST00000508889,; A ENST00000230792 Transcript missense_variant 616/3492 519/1389 173/462 E/D gaA/gaT 1 -1 NUDT12 HGNC HGNC:18826 protein_coding YES CCDS4096.1 ENSP00000230792 Q9BQG2 UPI0000073C53 NM_031438.3 tolerated(0.14) 3/7 Pfam_domain:PF09296 MODERATE 1 SNV 1 1 PASS . . 1 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 103559156 103559156 T A 1 0 0 0 0 1 0 0 0 10792 1606 56 4 4 NUDT12 5 103559156 Missense_Mutation SNP T C3N-02149_T 2656228 103559156 77979103 151 28335 DMXL1 0 . GRCh38 5 119149701 119149701 + Nonsense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.3874A>T p.Lys1292Ter p.K1292* ENST00000539542 18/44 206 154 52 272 271 1 strelka-varscan-mutect DMXL1,stop_gained,p.Lys1292Ter,ENST00000539542,NM_001290321.2;DMXL1,stop_gained,p.Lys1292Ter,ENST00000311085,NM_001290322.2,NM_005509.5;MIR5706,upstream_gene_variant,,ENST00000579841,;DMXL1,downstream_gene_variant,,ENST00000512281,; T ENST00000539542 Transcript stop_gained 4055/11236 3874/9147 1292/3048 K/* Aaa/Taa 1 1 DMXL1 HGNC HGNC:2937 protein_coding YES CCDS75289.1 ENSP00000439479 F5H269 UPI000206568B NM_001290321.2 18/44 hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF12,Pfam_domain:PF12234 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 119149701 119149701 A T 1 0 0 0 0 0 1 0 0 4403 247 9 4 4 DMXL1 5 119149701 Nonsense_Mutation SNP A C3N-02149_T 15590545 119149701 62388558 152 28336 FBN2 0 . GRCh38 5 128395158 128395158 + Missense_Mutation SNP C C T rs142228933 C3N-02149_T C3N-02149_N C C c.1195G>A p.Gly399Arg p.G399R ENST00000508053 15/71 366 340 26 441 441 0 strelka-varscan-mutect FBN2,missense_variant,p.Gly399Arg,ENST00000508053,;FBN2,missense_variant,p.Gly399Arg,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Gly398Arg,ENST00000619499,;FBN2,missense_variant,p.Gly366Arg,ENST00000508989,; T ENST00000508053 Transcript missense_variant 2170/11132 1195/8739 399/2912 G/R Gga/Aga rs142228933 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0.02) 15/71 Gene3D:3.90.290.10,Pfam_domain:PF00683,PIRSF_domain:PIRSF036312,PROSITE_profiles:PS51364,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,Superfamily_domains:SSF57581 MODERATE 1 SNV 5 1 PASS rs142228933 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 128395158 128395158 C T 1 0 0 0 0 1 0 0 0 5566 661 23 1 1 FBN2 5 128395158 Missense_Mutation SNP C C3N-02149_T 9245457 128395158 53143101 153 28337 JADE2 0 . GRCh38 5 134579299 134579299 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2487G>T p.Met829Ile p.M829I ENST00000282605 12/12 71 47 24 98 98 0 strelka-varscan-mutect JADE2,missense_variant,p.Met785Ile,ENST00000395003,NM_015288.5;JADE2,missense_variant,p.Met786Ile,ENST00000361895,NM_001289984.1;JADE2,missense_variant,p.Met829Ile,ENST00000282605,NM_001308143.1,NM_001289985.1;JADE2,missense_variant,p.Met241Ile,ENST00000612830,;JADE2,3_prime_UTR_variant,,ENST00000402835,;JADE2,3_prime_UTR_variant,,ENST00000430087,;JADE2,downstream_gene_variant,,ENST00000470876,; T ENST00000282605 Transcript missense_variant 2573/2748 2487/2505 829/834 M/I atG/atT 1 1 JADE2 HGNC HGNC:22984 protein_coding YES CCDS78061.1 ENSP00000282605 G3XAA4 UPI00000437CA NM_001308143.1,NM_001289985.1 tolerated_low_confidence(0.14) 12/12 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 134579299 134579299 G T 1 0 0 0 0 1 0 0 0 7845 1348 47 2 2 JADE2 5 134579299 Missense_Mutation SNP G C3N-02149_T 6184141 134579299 46958960 154 28338 IL9 0 . GRCh38 5 135895786 135895786 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.31C>T p.= p.L11L ENST00000274520 1/5 284 227 57 393 393 0 strelka-varscan-mutect IL9,synonymous_variant,p.=,ENST00000274520,NM_000590.1;GS1-39E22.1,downstream_gene_variant,,ENST00000523722,;GS1-39E22.2,upstream_gene_variant,,ENST00000522973,; A ENST00000274520 Transcript synonymous_variant 42/591 31/435 11/144 L Ctg/Ttg 1 -1 IL9 HGNC HGNC:6029 protein_coding YES CCDS4189.1 ENSP00000274520 P15248 UPI000004F0F9 NM_000590.1 1/5 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR16926:SF1,hmmpanther:PTHR16926 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 135895786 135895786 G A 1 0 0 0 0 0 0 0 1 7610 991 35 3 3 IL9 5 135895786 Silent SNP G C3N-02149_T 1316487 135895786 45642473 155 28339 NRG2 0 . GRCh38 5 139887507 139887507 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.705C>A p.= p.T235T ENST00000361474 2/10 111 84 27 123 123 0 strelka-varscan-mutect NRG2,synonymous_variant,p.=,ENST00000541337,NM_001184935.1;NRG2,synonymous_variant,p.=,ENST00000361474,NM_004883.2;NRG2,synonymous_variant,p.=,ENST00000289422,NM_013982.2;NRG2,synonymous_variant,p.=,ENST00000358522,NM_013983.2;NRG2,synonymous_variant,p.=,ENST00000289409,NM_013981.3;NRG2,synonymous_variant,p.=,ENST00000340391,;NRG2,non_coding_transcript_exon_variant,,ENST00000518130,;NRG2,synonymous_variant,p.=,ENST00000378238,; T ENST00000361474 Transcript synonymous_variant 930/3020 705/2553 235/850 T acC/acA 1 -1 NRG2 HGNC HGNC:7998 protein_coding YES CCDS4217.1 ENSP00000354910 O14511 UPI0000130507 NM_004883.2 2/10 hmmpanther:PTHR11100,hmmpanther:PTHR11100:SF20 LOW 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 139887507 139887507 G T 1 0 0 0 0 0 0 0 1 10706 1246 43 2 2 NRG2 5 139887507 Silent SNP G C3N-02149_T 3991721 139887507 41650752 156 28340 PCDHB9 0 . GRCh38 5 141189185 141189185 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1867G>T p.Glu623Ter p.E623* ENST00000316105 1/1 316 266 50 425 425 0 strelka-varscan-mutect PCDHB9,stop_gained,p.Glu623Ter,ENST00000316105,NM_019119.4;PCDHB16,downstream_gene_variant,,ENST00000609684,NM_020957.3;PCDHB10,upstream_gene_variant,,ENST00000239446,NM_018930.3;PCDHB16,downstream_gene_variant,,ENST00000625044,;PCDHB9,downstream_gene_variant,,ENST00000624909,;CH17-140K24.5,downstream_gene_variant,,ENST00000623884,;CH17-140K24.7,intron_variant,,ENST00000624549,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624089,;CH17-140K24.6,downstream_gene_variant,,ENST00000625144,;PCDHB9,downstream_gene_variant,,ENST00000623266,;CH17-140K24.5,downstream_gene_variant,,ENST00000623407,; T ENST00000316105 Transcript stop_gained 2059/4415 1867/2394 623/797 E/* Gag/Tag 1 1 PCDHB9 HGNC HGNC:8694 protein_coding YES CCDS75328.1 ENSP00000478606 Q9Y5E1 UPI00005764A0 NM_019119.4 1/1 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF128,hmmpanther:PTHR24028,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 HIGH SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 141189185 141189185 G T 1 0 0 0 0 0 1 0 0 11636 1175 41 2 2 PCDHB9 5 141189185 Nonsense_Mutation SNP G C3N-02149_T 1301678 141189185 40349074 157 28341 PCDHGA1 0 . GRCh38 5 141332318 141332318 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1634A>T p.Asn545Ile p.N545I ENST00000517417 1/4 435 320 115 574 574 0 strelka-varscan-mutect PCDHGA1,missense_variant,p.Asn545Ile,ENST00000517417,NM_018912.2;PCDHGA1,missense_variant,p.Asn545Ile,ENST00000378105,NM_031993.1;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,; T ENST00000517417 Transcript missense_variant 1634/4604 1634/2796 545/931 N/I aAc/aTc 1 1 PCDHGA1 HGNC HGNC:8696 protein_coding YES CCDS54922.1 ENSP00000431083 Q9Y5H4 UPI0000070596 NM_018912.2 deleterious_low_confidence(0) 1/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF108,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 1 1 PASS rs1412029044 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 141332318 141332318 A T 1 0 0 0 0 1 0 0 0 11637 43 2 4 4 PCDHGA1 5 141332318 Missense_Mutation SNP A C3N-02149_T 143133 141332318 40205941 158 28342 PCDHGA3 0 . GRCh38 5 141346041 141346041 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2008G>T p.Asp670Tyr p.D670Y ENST00000253812 1/4 344 267 77 410 410 0 strelka-varscan-mutect PCDHGA3,missense_variant,p.Asp670Tyr,ENST00000253812,NM_018916.3;PCDHGA3,missense_variant,p.Asp670Tyr,ENST00000619750,NM_032011.1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,upstream_gene_variant,,ENST00000523390,NM_018922.2;PCDHGA2,downstream_gene_variant,,ENST00000528330,NM_032009.2;PCDHGB1,upstream_gene_variant,,ENST00000611598,NM_032095.1;AC005618.8,downstream_gene_variant,,ENST00000625053,;PCDHGA3,3_prime_UTR_variant,,ENST00000612467,; T ENST00000253812 Transcript missense_variant 2174/4771 2008/2799 670/932 D/Y Gac/Tac 1 1 PCDHGA3 HGNC HGNC:8701 protein_coding YES CCDS47290.1 ENSP00000253812 Q9Y5H0 UPI0000161C1A NM_018916.3 deleterious_low_confidence(0) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 141346041 141346041 G T 1 0 0 0 0 1 0 0 0 11642 1058 37 1 1 PCDHGA3 5 141346041 Missense_Mutation SNP G C3N-02149_T 13723 141346041 40192218 159 28343 PCDHGA4 0 . GRCh38 5 141356347 141356347 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1240A>T p.Thr414Ser p.T414S ENST00000571252 1/4 192 130 62 281 280 1 strelka-varscan-mutect PCDHGA4,missense_variant,p.Thr414Ser,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Thr414Ser,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 1323/4778 1240/2889 414/962 T/S Aca/Tca 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 tolerated_low_confidence(0.16) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1480466141 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 141356347 141356347 A T 1 0 0 0 0 1 0 0 0 11643 159 6 4 4 PCDHGA4 5 141356347 Missense_Mutation SNP A C3N-02149_T 10306 141356347 40181912 160 28344 PCDHGB3 0 . GRCh38 5 141372256 141372256 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1862T>A p.Leu621Gln p.L621Q ENST00000576222 1/4 251 199 52 283 283 0 strelka-varscan-mutect PCDHGB3,missense_variant,p.Leu621Gln,ENST00000576222,NM_018924.4;PCDHGB3,missense_variant,p.Leu621Gln,ENST00000618934,NM_032097.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,upstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGA6,upstream_gene_variant,,ENST00000517434,NM_018919.2;PCDHGA5,downstream_gene_variant,,ENST00000611914,NM_032054.1;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000576222 Transcript missense_variant 1993/4727 1862/2790 621/929 L/Q cTg/cAg 1 1 PCDHGB3 HGNC HGNC:8710 protein_coding YES CCDS58980.1 ENSP00000461862 Q9Y5G1 UPI0000EE35B5 NM_018924.4 deleterious(0.02) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF106,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 141372256 141372256 T A 1 0 0 0 0 1 0 0 0 11651 1580 55 4 4 PCDHGB3 5 141372256 Missense_Mutation SNP T C3N-02149_T 15909 141372256 40166003 161 28345 PCDHGA7 0 . GRCh38 5 141384258 141384258 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1359C>A p.= p.P453P ENST00000518325 1/4 192 145 47 242 241 1 strelka-varscan-mutect PCDHGA7,synonymous_variant,p.=,ENST00000518325,NM_018920.3;PCDHGA7,synonymous_variant,p.=,ENST00000617050,NM_032087.2;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGA6,downstream_gene_variant,,ENST00000610583,NM_032086.1;PCDHGB4,upstream_gene_variant,,ENST00000615384,NM_032098.1;PCDHGB4,upstream_gene_variant,,ENST00000519479,NM_003736.2;PCDHGA3,intron_variant,,ENST00000612467,; A ENST00000518325 Transcript synonymous_variant 1359/4605 1359/2799 453/932 P ccC/ccA 1 1 PCDHGA7 HGNC HGNC:8705 protein_coding YES CCDS54927.1 ENSP00000430024 Q9Y5G6 UPI000007146F NM_018920.3 1/4 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF56,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 141384258 141384258 C A 1 0 0 0 0 0 0 0 1 11646 610 22 2 2 PCDHGA7 5 141384258 Silent SNP C C3N-02149_T 12002 141384258 40154001 162 28346 TIGD6 0 . GRCh38 5 149995231 149995231 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1118A>G p.Gln373Arg p.Q373R ENST00000296736 2/2 278 221 57 387 387 0 strelka-varscan-mutect TIGD6,missense_variant,p.Gln373Arg,ENST00000296736,NM_030953.3;TIGD6,missense_variant,p.Gln373Arg,ENST00000515406,NM_001243253.1;HMGXB3,upstream_gene_variant,,ENST00000613459,;SLC26A2,downstream_gene_variant,,ENST00000503336,;TIGD6,downstream_gene_variant,,ENST00000532987,; C ENST00000296736 Transcript missense_variant 1893/4006 1118/1566 373/521 Q/R cAg/cGg 1 -1 TIGD6 HGNC HGNC:18332 protein_coding YES CCDS4301.1 ENSP00000296736 Q17RP2 UPI000006D946 NM_030953.3 tolerated(1) 2/2 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF179 MODERATE 1 SNV 1 1 PASS rs1261896517 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 149995231 149995231 T C 1 0 0 0 0 1 0 0 0 16338 1580 55 5 5 TIGD6 5 149995231 Missense_Mutation SNP T C3N-02149_T 8610973 149995231 31543028 163 28347 ADAM19 0 . GRCh38 5 157509410 157509410 + Missense_Mutation SNP C C A rs369469519 C3N-02149_T C3N-02149_N C C c.796G>T p.Gly266Trp p.G266W ENST00000257527 9/23 145 122 23 197 197 0 strelka-varscan-mutect ADAM19,missense_variant,p.Gly266Trp,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Gly266Trp,ENST00000517905,;ADAM19,missense_variant,p.Arg269Leu,ENST00000517951,; A ENST00000257527 Transcript missense_variant 875/6481 796/2757 266/918 G/W Ggg/Tgg rs369469519 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 tolerated(0.2) 9/23 PROSITE_profiles:PS50215,hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS rs369469519 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 157509410 157509410 C A 1 0 0 0 0 1 0 0 0 284 652 23 1 1 ADAM19 5 157509410 Missense_Mutation SNP C C3N-02149_T 7514179 157509410 24028849 164 28348 TENM2 0 . GRCh38 5 168203797 168203797 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.3539C>A p.Ser1180Tyr p.S1180Y ENST00000518659 18/29 106 75 31 159 159 0 strelka-varscan-mutect TENM2,missense_variant,p.Ser1059Tyr,ENST00000519204,;TENM2,missense_variant,p.Ser1180Tyr,ENST00000518659,NM_001122679.1;TENM2,missense_variant,p.Ser948Tyr,ENST00000520394,; A ENST00000518659 Transcript missense_variant 3578/8550 3539/8325 1180/2774 S/Y tCc/tAc 1 1 TENM2 HGNC HGNC:29943 protein_coding YES ENSP00000429430 Q9NT68 UPI0001C48FC2 NM_001122679.1 deleterious(0) 18/29 hmmpanther:PTHR11219,hmmpanther:PTHR11219:SF8 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 168203797 168203797 C A 1 0 0 0 0 1 0 0 0 16172 855 30 2 2 TENM2 5 168203797 Missense_Mutation SNP C C3N-02149_T 10694387 168203797 13334462 165 28349 GABRP 0 . GRCh38 5 170797472 170797472 + Silent SNP G G T rs148144716 C3N-02149_T C3N-02149_N G G c.465G>T p.= p.T155T ENST00000518525 7/11 143 117 26 185 184 1 strelka-varscan-mutect GABRP,synonymous_variant,p.=,ENST00000518525,;GABRP,synonymous_variant,p.=,ENST00000265294,NM_014211.2;GABRP,synonymous_variant,p.=,ENST00000519385,NM_001291985.1;GABRP,synonymous_variant,p.=,ENST00000519598,;GABRP,synonymous_variant,p.=,ENST00000521481,;GABRP,synonymous_variant,p.=,ENST00000522868,;GABRP,downstream_gene_variant,,ENST00000519196,;GABRP,downstream_gene_variant,,ENST00000521009,;GABRP,downstream_gene_variant,,ENST00000519137,; T ENST00000518525 Transcript synonymous_variant 929/3576 465/1323 155/440 T acG/acT rs148144716,COSM449314 1 1 GABRP HGNC HGNC:4089 protein_coding YES CCDS4375.1 ENSP00000430100 O00591 UPI000003C534 7/11 hmmpanther:PTHR18945:SF33,hmmpanther:PTHR18945,Pfam_domain:PF02931,Gene3D:2.70.170.10,TIGRFAM_domain:TIGR00860,Superfamily_domains:0038932 0,1 LOW 1 SNV 5 0,1 1 PASS rs148144716 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 170797472 170797472 G T 1 0 0 0 0 0 0 0 1 6045 1045 37 1 1 GABRP 5 170797472 Silent SNP G C3N-02149_T 2593675 170797472 10740787 166 28350 STK10 0 . GRCh38 5 172117503 172117503 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.498C>T p.= p.T166T ENST00000176763 4/19 229 181 48 299 298 1 strelka-varscan-mutect STK10,synonymous_variant,p.=,ENST00000176763,NM_005990.3;STK10,non_coding_transcript_exon_variant,,ENST00000519710,;STK10,upstream_gene_variant,,ENST00000522936,;STK10,upstream_gene_variant,,ENST00000517381,;STK10,upstream_gene_variant,,ENST00000518267,; A ENST00000176763 Transcript synonymous_variant 842/6060 498/2907 166/968 T acC/acT 1 -1 STK10 HGNC HGNC:11388 protein_coding YES CCDS34290.1 ENSP00000176763 O94804 UPI0000136104 NM_005990.3 4/19 PROSITE_profiles:PS50011,hmmpanther:PTHR24361:SF195,hmmpanther:PTHR24361,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 172117503 172117503 G A 1 0 0 0 0 0 0 0 1 15663 1219 43 3 3 STK10 5 172117503 Silent SNP G C3N-02149_T 1320031 172117503 9420756 167 28351 DRD1 0 . GRCh38 5 175441941 175441941 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1159C>A p.Leu387Met p.L387M ENST00000393752 2/2 143 116 27 181 181 0 strelka-varscan-mutect DRD1,missense_variant,p.Leu387Met,ENST00000393752,NM_000794.3; T ENST00000393752 Transcript missense_variant 2152/4054 1159/1341 387/446 L/M Ctg/Atg 1 -1 DRD1 HGNC HGNC:3020 protein_coding YES CCDS4393.1 ENSP00000377353 P21728 UPI00000503F5 NM_000794.3 tolerated_low_confidence(0.16) 2/2 Prints_domain:PR00565 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 175441941 175441941 G T 1 0 0 0 0 1 0 0 0 4575 933 33 2 2 DRD1 5 175441941 Missense_Mutation SNP G C3N-02149_T 3324438 175441941 6096318 168 28352 ADAMTS2 0 . GRCh38 5 179154901 179154901 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.1151G>A p.Gly384Asp p.G384D ENST00000251582 7/22 295 241 54 335 334 1 strelka-varscan-mutect ADAMTS2,missense_variant,p.Gly384Asp,ENST00000251582,NM_014244.4;ADAMTS2,missense_variant,p.Gly384Asp,ENST00000274609,NM_021599.2; T ENST00000251582 Transcript missense_variant 1253/6754 1151/3636 384/1211 G/D gGc/gAc 1 -1 ADAMTS2 HGNC HGNC:218 protein_coding YES CCDS4444.1 ENSP00000251582 O95450 UPI00001AE729 NM_014244.4 deleterious(0) 7/22 PROSITE_profiles:PS50215,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF141,Gene3D:3.40.390.10,Pfam_domain:PF01421,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 179154901 179154901 C T 1 0 0 0 0 1 0 0 0 309 739 26 3 3 ADAMTS2 5 179154901 Missense_Mutation SNP C C3N-02149_T 3712960 179154901 2383358 169 28353 FLT4 0 . GRCh38 5 180621718 180621718 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.1844T>C p.Leu615Pro p.L615P ENST00000261937 13/30 153 137 16 217 217 0 strelka-varscan-mutect FLT4,missense_variant,p.Leu615Pro,ENST00000261937,NM_182925.4;FLT4,missense_variant,p.Leu615Pro,ENST00000393347,NM_002020.4;FLT4,missense_variant,p.Leu615Pro,ENST00000502649,;FLT4,3_prime_UTR_variant,,ENST00000619105,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,non_coding_transcript_exon_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; G ENST00000261937 Transcript missense_variant 1923/5857 1844/4092 615/1363 L/P cTg/cCg 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 deleterious(0.05) 13/30 PROSITE_profiles:PS50835,Pfam_domain:PF13927,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 180621718 180621718 A G 1 0 0 0 0 1 0 0 0 5800 188 7 5 5 FLT4 5 180621718 Missense_Mutation SNP A C3N-02149_T 1466817 180621718 916541 170 28354 POM121L2 0 . GRCh38 6 27311264 27311264 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.907T>A p.Ser303Thr p.S303T ENST00000444565 1/1 250 194 56 346 346 0 strelka-varscan-mutect POM121L2,missense_variant,p.Ser303Thr,ENST00000444565,NM_033482.3;POM121L2,missense_variant,p.Ser17Thr,ENST00000429945,; T ENST00000444565 Transcript missense_variant 907/3108 907/3108 303/1035 S/T Tca/Aca 1 -1 POM121L2 HGNC HGNC:13973 protein_coding YES CCDS59497.1 ENSP00000392726 Q96KW2 UPI0000198C27 NM_033482.3 tolerated(0.92) 1/1 Pfam_domain:PF15229,hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF20 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 27311264 27311264 A T 1 0 0 0 0 1 0 0 0 12353 333 12 4 4 POM121L2 6 27311264 Missense_Mutation SNP A C3N-02149_T 27311264 143494715 171 28355 UHRF1BP1 0 . GRCh38 6 34870935 34870935 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.3800G>C p.Gly1267Ala p.G1267A ENST00000192788 18/21 341 308 33 485 485 0 strelka-varscan-mutect UHRF1BP1,missense_variant,p.Gly1267Ala,ENST00000192788,NM_017754.3;UHRF1BP1,missense_variant,p.Gly1267Ala,ENST00000452449,;RNY3P15,upstream_gene_variant,,ENST00000516297,; C ENST00000192788 Transcript missense_variant 3971/9570 3800/4323 1267/1440 G/A gGa/gCa 1 1 UHRF1BP1 HGNC HGNC:21216 protein_coding YES CCDS43455.1 ENSP00000192788 Q6BDS2 UPI00001B654C NM_017754.3 tolerated(0.27) 18/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 34870935 34870935 G C 1 0 0 0 0 1 0 0 0 17492 1174 41 4 4 UHRF1BP1 6 34870935 Missense_Mutation SNP G C3N-02149_T 7559671 34870935 135935044 172 28356 BRPF3 0 . GRCh38 6 36214234 36214234 + Missense_Mutation SNP G G T rs745818310 C3N-02149_T C3N-02149_N G G c.2837G>T p.Arg946Met p.R946M ENST00000357641 8/13 134 115 19 188 188 0 strelka-varscan-mutect BRPF3,missense_variant,p.Arg946Met,ENST00000357641,NM_015695.2;BRPF3,missense_variant,p.Arg946Met,ENST00000534400,;BRPF3,intron_variant,,ENST00000339717,;BRPF3,intron_variant,,ENST00000534694,;BRPF3,missense_variant,p.Arg157Met,ENST00000441730,;BRPF3,3_prime_UTR_variant,,ENST00000441123,;BRPF3,3_prime_UTR_variant,,ENST00000532330,;BRPF3,intron_variant,,ENST00000449261,;BRPF3,downstream_gene_variant,,ENST00000532538,; T ENST00000357641 Transcript missense_variant 3090/6052 2837/3618 946/1205 R/M aGg/aTg rs745818310 1 1 BRPF3 HGNC HGNC:14256 protein_coding YES CCDS34437.1 ENSP00000350267 Q9ULD4 UPI00001C1E4C NM_015695.2 tolerated(0.1) 8/13 hmmpanther:PTHR13793:SF19,hmmpanther:PTHR13793 MODERATE 1 SNV 1 1 PASS rs745818310 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 36214234 36214234 G T 1 0 0 0 0 1 0 0 0 1695 1000 35 2 2 BRPF3 6 36214234 Missense_Mutation SNP G C3N-02149_T 1343299 36214234 134591745 173 28357 SAYSD1 0 . GRCh38 6 39115026 39115026 + Missense_Mutation SNP G G A rs745828598 C3N-02149_T C3N-02149_N G G c.64C>T p.Pro22Ser p.P22S ENST00000229903 1/2 217 189 28 290 290 0 strelka-varscan-mutect SAYSD1,missense_variant,p.Pro22Ser,ENST00000229903,NM_018322.2;SAYSD1,non_coding_transcript_exon_variant,,ENST00000481599,;ANKRD18EP,downstream_gene_variant,,ENST00000405487,; A ENST00000229903 Transcript missense_variant 164/2020 64/552 22/183 P/S Cct/Tct rs745828598 1 -1 SAYSD1 HGNC HGNC:21025 protein_coding YES CCDS4840.1 ENSP00000229903 Q9NPB0 UPI0000039E7F NM_018322.2 tolerated(1) 1/2 Low_complexity_(Seg):seg,hmmpanther:PTHR13527,hmmpanther:PTHR13527:SF0 MODERATE 1 SNV 1 1 PASS rs745828598 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 39115026 39115026 G A 1 0 0 0 0 1 0 0 0 14120 1232 43 3 3 SAYSD1 6 39115026 Missense_Mutation SNP G C3N-02149_T 2900792 39115026 131690953 174 28358 KLHDC3 0 . GRCh38 6 43018536 43018536 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.713G>A p.Gly238Glu p.G238E ENST00000326974 6/11 426 348 78 500 500 0 strelka-varscan-mutect KLHDC3,missense_variant,p.Gly238Glu,ENST00000326974,NM_057161.3;KLHDC3,missense_variant,p.Gly104Glu,ENST00000244670,;KLHDC3,missense_variant,p.Gly238Glu,ENST00000332245,;RRP36,upstream_gene_variant,,ENST00000244496,NM_033112.2;MEA1,upstream_gene_variant,,ENST00000244711,NM_014623.2; A ENST00000326974 Transcript missense_variant 908/1909 713/1149 238/382 G/E gGg/gAg 1 1 KLHDC3 HGNC HGNC:20704 protein_coding YES CCDS4880.1 ENSP00000313995 Q9BQ90 UPI0000036176 NM_057161.3 deleterious(0) 6/11 Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 43018536 43018536 G A 1 0 0 0 0 1 0 0 0 8222 1232 43 3 3 KLHDC3 6 43018536 Missense_Mutation SNP G C3N-02149_T 3903510 43018536 127787443 175 28359 ZNF318 0 . GRCh38 6 43369293 43369293 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.73A>T p.Ser25Cys p.S25C ENST00000361428 1/10 49 43 6 54 54 0 strelka-varscan-mutect ZNF318,missense_variant,p.Ser25Cys,ENST00000361428,NM_014345.2;ZNF318,missense_variant,p.Ser25Cys,ENST00000605935,;RP11-213N20.1,downstream_gene_variant,,ENST00000428602,; A ENST00000361428 Transcript missense_variant 151/8006 73/6840 25/2279 S/C Agc/Tgc 1 -1 ZNF318 HGNC HGNC:13578 protein_coding YES CCDS4895.2 ENSP00000354964 Q5VUA4 UPI000049E044 NM_014345.2 tolerated_low_confidence(0.07) 1/10 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -14.64009 1 1 1 1 0 A 3 1 92 43369293 43369293 T A 1 0 0 0 0 1 0 0 0 18411 1580 55 4 4 ZNF318 6 43369293 Missense_Mutation SNP T C3N-02149_T 350757 43369293 127436686 176 28360 PGK2 0 . GRCh38 6 49786058 49786058 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1130C>A p.Ala377Asp p.A377D ENST00000304801 1/1 378 330 48 490 490 0 strelka-varscan-mutect PGK2,missense_variant,p.Ala377Asp,ENST00000304801,NM_138733.4; T ENST00000304801 Transcript missense_variant 1250/1657 1130/1254 377/417 A/D gCt/gAt 1 -1 PGK2 HGNC HGNC:8898 protein_coding YES CCDS4930.1 ENSP00000305995 P07205 A0A140VJR3 UPI0000001C72 NM_138733.4 deleterious(0) 1/1 Gene3D:3.40.50.1270,HAMAP:MF_00145,Pfam_domain:PF00162,PIRSF_domain:PIRSF000724,Prints_domain:PR00477,hmmpanther:PTHR11406,hmmpanther:PTHR11406:SF10,Superfamily_domains:SSF53748 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 49786058 49786058 G T 1 0 0 0 0 1 0 0 0 11880 971 34 2 2 PGK2 6 49786058 Missense_Mutation SNP G C3N-02149_T 6416765 49786058 121019921 177 28361 TINAG 0 . GRCh38 6 54308712 54308712 + Silent SNP G G C novel C3N-02149_T C3N-02149_N G G c.162G>C p.= p.G54G ENST00000259782 1/11 412 388 24 491 491 0 strelka-varscan-mutect TINAG,synonymous_variant,p.=,ENST00000259782,NM_014464.3;TINAG,synonymous_variant,p.=,ENST00000370869,;TINAG,synonymous_variant,p.=,ENST00000370864,;TINAG,non_coding_transcript_exon_variant,,ENST00000486436,; C ENST00000259782 Transcript synonymous_variant 258/1754 162/1431 54/476 G ggG/ggC 1 1 TINAG HGNC HGNC:14599 protein_coding YES CCDS4955.1 ENSP00000259782 Q9UJW2 UPI000013D078 NM_014464.3 1/11 hmmpanther:PTHR12411,hmmpanther:PTHR12411:SF274 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 54308712 54308712 G C 1 0 0 0 0 0 0 0 1 16362 1190 42 4 4 TINAG 6 54308712 Silent SNP G C3N-02149_T 4522654 54308712 116497267 178 28362 EYS 0 . GRCh38 6 64813378 64813378 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.3443G>T p.Arg1148Ile p.R1148I ENST00000370621 22/44 233 206 27 292 291 1 strelka-varscan-mutect EYS,missense_variant,p.Arg1148Ile,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Arg1148Ile,ENST00000370621,NM_001292009.1; A ENST00000370621 Transcript missense_variant,splice_region_variant 3970/10485 3443/9498 1148/3165 R/I aGa/aTa 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 tolerated(0.46) 22/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 MODERATE 1 SNV 1 1 PASS rs1334016191 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 64813378 64813378 C A 1 0 0 0 0 1 0 0 0 5200 695 24 2 2 EYS 6 64813378 Missense_Mutation SNP C C3N-02149_T 10504666 64813378 105992601 179 28363 EYS 0 . GRCh38 6 64886835 64886835 + Missense_Mutation SNP A A T rs779877426 C3N-02149_T C3N-02149_N A A c.2854T>A p.Cys952Ser p.C952S ENST00000370621 19/44 253 228 25 359 359 0 strelka-varscan-mutect EYS,missense_variant,p.Cys952Ser,ENST00000503581,NM_001142800.1;EYS,missense_variant,p.Cys952Ser,ENST00000370621,NM_001292009.1; T ENST00000370621 Transcript missense_variant 3381/10485 2854/9498 952/3165 C/S Tgt/Agt rs779877426,COSM3160491 1 -1 EYS HGNC HGNC:21555 protein_coding YES CCDS78156.1 ENSP00000359655 Q5T1H1 UPI0001AE72B3 NM_001292009.1 deleterious(0) 19/44 Gene3D:2.10.25.10,Pfam_domain:PF00008,PROSITE_patterns:PS00010,PROSITE_patterns:PS00022,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24033,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57196 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 205 0 0 3 0 0 0 -8.981802 0.9322892 1 1 1 0 T 3 4 92 64886835 64886835 A T 1 0 0 0 0 1 0 0 0 5200 130 5 4 4 EYS 6 64886835 Missense_Mutation SNP A C3N-02149_T 73457 64886835 105919144 180 28364 HTR1E 0 . GRCh38 6 87016051 87016051 + Silent SNP A A T novel C3N-02149_T C3N-02149_N A A c.717A>T p.= p.T239T ENST00000305344 2/2 207 175 32 373 373 0 strelka-varscan-mutect HTR1E,synonymous_variant,p.=,ENST00000305344,NM_000865.2; T ENST00000305344 Transcript synonymous_variant 1420/2052 717/1098 239/365 T acA/acT 1 1 HTR1E HGNC HGNC:5291 protein_coding YES CCDS5006.1 ENSP00000307766 P28566 UPI000000126D NM_000865.2 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF33,Pfam_domain:PF00001,SMART_domains:SM01381 LOW 1 SNV 1 1 PASS rs1385836989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 87016051 87016051 A T 1 0 0 0 0 0 0 0 1 7335 146 6 4 4 HTR1E 6 87016051 Silent SNP A C3N-02149_T 22129216 87016051 83789928 181 28365 HTR1E 0 . GRCh38 6 87016392 87016392 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.1058T>G p.Leu353Arg p.L353R ENST00000305344 2/2 71 63 8 100 100 0 strelka-varscan-mutect HTR1E,missense_variant,p.Leu353Arg,ENST00000305344,NM_000865.2; G ENST00000305344 Transcript missense_variant 1761/2052 1058/1098 353/365 L/R cTg/cGg 1 1 HTR1E HGNC HGNC:5291 protein_coding YES CCDS5006.1 ENSP00000307766 P28566 UPI000000126D NM_000865.2 tolerated(0.46) 2/2 hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF33,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -17.81197 1 1 1 1 0 G 3 3 92 87016392 87016392 T G 1 0 0 0 0 1 0 0 0 7335 1580 55 5 5 HTR1E 6 87016392 Missense_Mutation SNP T C3N-02149_T 341 87016392 83789587 182 28366 GABRR1 0 . GRCh38 6 89181996 89181996 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.858C>T p.= p.L286L ENST00000454853 8/10 205 194 11 306 306 0 strelka-varscan GABRR1,synonymous_variant,p.=,ENST00000611484,NM_001256704.1;GABRR1,synonymous_variant,p.=,ENST00000435811,NM_001256703.1;GABRR1,synonymous_variant,p.=,ENST00000621627,;GABRR1,synonymous_variant,p.=,ENST00000454853,NM_002042.4;GABRR1,synonymous_variant,p.=,ENST00000369451,NM_001267582.1;GABRR1,3_prime_UTR_variant,,ENST00000457434,; A ENST00000454853 Transcript synonymous_variant 969/2820 858/1440 286/479 L ctC/ctT 1 -1 GABRR1 HGNC HGNC:4090 protein_coding YES CCDS5019.2 ENSP00000412673 P24046 UPI0000D4AF7D NM_002042.4 8/10 Gene3D:1.20.58.390,Prints_domain:PR00252,Prints_domain:PR00253,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF30,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 89181996 89181996 G A 1 0 0 0 0 0 0 0 1 6047 1161 41 3 3 GABRR1 6 89181996 Silent SNP G C3N-02149_T 2165604 89181996 81623983 183 28367 GPR6 0 . GRCh38 6 109979238 109979238 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.171G>T p.= p.A57A ENST00000414000 3/3 250 195 55 351 351 0 strelka-varscan-mutect GPR6,synonymous_variant,p.=,ENST00000414000,NM_001286099.1;GPR6,synonymous_variant,p.=,ENST00000275169,NM_005284.4; T ENST00000414000 Transcript synonymous_variant 465/1945 171/1134 57/377 A gcG/gcT 1 1 GPR6 HGNC HGNC:4515 protein_coding YES CCDS69172.1 ENSP00000406986 P46095 UPI0001AE72E0 NM_001286099.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22750:SF19,hmmpanther:PTHR22750,Prints_domain:PR00649 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 109979238 109979238 G T 1 0 0 0 0 0 0 0 1 6585 1103 39 1 1 GPR6 6 109979238 Silent SNP G C3N-02149_T 20797242 109979238 60826741 184 28368 LAMA2 0 . GRCh38 6 129252196 129252196 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.1997A>G p.His666Arg p.H666R ENST00000421865 14/65 548 462 86 697 696 1 strelka-varscan-mutect LAMA2,missense_variant,p.His666Arg,ENST00000618192,;LAMA2,missense_variant,p.His666Arg,ENST00000617695,;LAMA2,missense_variant,p.His666Arg,ENST00000421865,NM_001079823.1,NM_000426.3; G ENST00000421865 Transcript missense_variant 2046/9640 1997/9369 666/3122 H/R cAt/cGt 1 1 LAMA2 HGNC HGNC:6482 protein_coding YES CCDS5138.1 ENSP00000400365 P24043 UPI00003673E0 NM_001079823.1,NM_000426.3 tolerated(0.36) 14/65 Pfam_domain:PF00052,PROSITE_profiles:PS51115,SMART_domains:SM00281 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 129252196 129252196 A G 1 0 0 0 0 1 0 0 0 8510 217 8 5 5 LAMA2 6 129252196 Missense_Mutation SNP A C3N-02149_T 19272958 129252196 41553783 185 28369 EPB41L2 0 . GRCh38 6 130901056 130901056 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1054G>T p.Glu352Ter p.E352* ENST00000337057 7/20 310 261 49 443 442 1 strelka-varscan-mutect EPB41L2,stop_gained,p.Glu352Ter,ENST00000337057,NM_001431.3;EPB41L2,stop_gained,p.Glu352Ter,ENST00000368128,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000628542,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000527411,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000530481,NM_001199388.2;EPB41L2,stop_gained,p.Glu352Ter,ENST00000445890,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000528282,NM_001252660.1;EPB41L2,stop_gained,p.Glu352Ter,ENST00000392427,NM_001135554.1,NM_001135555.3;EPB41L2,stop_gained,p.Glu352Ter,ENST00000529208,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000525271,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000527659,;EPB41L2,stop_gained,p.Glu352Ter,ENST00000525193,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000530148,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000528179,;EPB41L2,non_coding_transcript_exon_variant,,ENST00000526333,; A ENST00000337057 Transcript stop_gained 1236/4457 1054/3018 352/1005 E/* Gaa/Taa 1 -1 EPB41L2 HGNC HGNC:3379 protein_coding YES CCDS5141.1 ENSP00000338481 O43491 UPI0000129AF9 NM_001431.3 7/20 Gene3D:1.20.80.10,Pfam_domain:PF00373,PIRSF_domain:PIRSF002304,PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF17,SMART_domains:SM00295,Superfamily_domains:SSF47031 HIGH 1 SNV 1 1 PASS rs1467591047 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 130901056 130901056 C A 1 0 0 0 0 0 1 0 0 5000 922 32 2 2 EPB41L2 6 130901056 Nonsense_Mutation SNP C C3N-02149_T 1648860 130901056 39904923 186 28370 TAAR5 0 . GRCh38 6 132588963 132588963 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.724G>T p.Gly242Trp p.G242W ENST00000258034 1/1 203 185 18 250 250 0 strelka-varscan-mutect TAAR5,missense_variant,p.Gly242Trp,ENST00000258034,NM_003967.2; A ENST00000258034 Transcript missense_variant 724/1014 724/1014 242/337 G/W Ggg/Tgg 1 -1 TAAR5 HGNC HGNC:30236 protein_coding YES CCDS5156.1 ENSP00000258034 O14804 UPI000013CFAA NM_003967.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,PROSITE_profiles:PS50262,hmmpanther:PTHR24249,hmmpanther:PTHR24249:SF78,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 132588963 132588963 C A 1 0 0 0 0 1 0 0 0 15887 594 21 2 2 TAAR5 6 132588963 Missense_Mutation SNP C C3N-02149_T 1687907 132588963 38217016 187 28371 SLC35D3 0 . GRCh38 6 136924110 136924110 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.665A>T p.Asp222Val p.D222V ENST00000331858 2/2 198 184 14 263 261 2 strelka-varscan-mutect SLC35D3,missense_variant,p.Asp222Val,ENST00000331858,NM_001008783.2; T ENST00000331858 Transcript missense_variant 830/2359 665/1251 222/416 D/V gAc/gTc 1 1 SLC35D3 HGNC HGNC:15621 protein_coding YES CCDS34544.1 ENSP00000333591 Q5M8T2 UPI00003673E9 NM_001008783.2 deleterious(0) 2/2 hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF62 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 136924110 136924110 A T 1 0 0 0 0 1 0 0 0 14853 275 10 4 4 SLC35D3 6 136924110 Missense_Mutation SNP A C3N-02149_T 4335147 136924110 33881869 188 28372 CITED2 0 . GRCh38 6 139373434 139373434 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.526G>T p.Gly176Cys p.G176C ENST00000537332 2/2 24 16 8 142 141 1 strelka-varscan-mutect CITED2,missense_variant,p.Gly171Cys,ENST00000367651,NM_006079.4;CITED2,missense_variant,p.Gly171Cys,ENST00000536159,NM_001168388.2;CITED2,missense_variant,p.Gly176Cys,ENST00000537332,NM_001168389.2;CITED2,intron_variant,,ENST00000618718,; A ENST00000537332 Transcript missense_variant 601/1780 526/828 176/275 G/C Ggc/Tgc 1 -1 CITED2 HGNC HGNC:1987 protein_coding YES CCDS75530.1 ENSP00000444198 A0A0A0MTM3 UPI000264F4A0 NM_001168389.2 deleterious(0) 2/2 Low_complexity_(Seg):seg,Pfam_domain:PF04487 MODERATE 1 SNV 3 1 PASS . . 0 207 3 0 0 0 0 0 -19.99875 1 1 1 1 0 A 3 1 92 139373434 139373434 C A 1 0 0 0 0 1 0 0 0 3203 623 22 2 2 CITED2 6 139373434 Missense_Mutation SNP C C3N-02149_T 2449324 139373434 31432545 189 28373 HIVEP2 0 . GRCh38 6 142773388 142773388 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1351G>T p.Gly451Cys p.G451C ENST00000367603 5/10 390 364 26 534 533 1 strelka-varscan-mutect HIVEP2,missense_variant,p.Gly451Cys,ENST00000367603,NM_006734.3;HIVEP2,missense_variant,p.Gly451Cys,ENST00000367604,;HIVEP2,missense_variant,p.Gly451Cys,ENST00000012134,; A ENST00000367603 Transcript missense_variant 2094/9723 1351/7341 451/2446 G/C Ggt/Tgt 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 deleterious(0) 5/10 hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 142773388 142773388 C A 1 0 0 0 0 1 0 0 0 7076 623 22 2 2 HIVEP2 6 142773388 Missense_Mutation SNP C C3N-02149_T 3399954 142773388 28032591 190 28374 STXBP5 0 . GRCh38 6 147267089 147267089 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.636G>A p.= p.L212L ENST00000321680 7/28 239 219 20 372 372 0 strelka-varscan-mutect STXBP5,synonymous_variant,p.=,ENST00000367481,NM_139244.4;STXBP5,synonymous_variant,p.=,ENST00000321680,NM_001127715.2;STXBP5,synonymous_variant,p.=,ENST00000367480,;STXBP5,synonymous_variant,p.=,ENST00000546097,; A ENST00000321680 Transcript synonymous_variant 636/3456 636/3456 212/1151 L ttG/ttA 1 1 STXBP5 HGNC HGNC:19665 protein_coding YES CCDS47499.1 ENSP00000321826 Q5T5C0 UPI0000199FE0 NM_001127715.2 7/28 hmmpanther:PTHR10241:SF22,hmmpanther:PTHR10241,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 147267089 147267089 G A 1 0 0 0 0 0 0 0 1 15740 1304 45 3 3 STXBP5 6 147267089 Silent SNP G C3N-02149_T 4493701 147267089 23538890 191 28375 ARID1B 0 . GRCh38 6 157184365 157184365 + Frame_Shift_Del DEL G G - novel C3N-02149_T C3N-02149_N G G c.3481delG p.Glu1161SerfsTer50 p.E1161Sfs*50 ENST00000346085 13/20 396 355 41 543 543 0 sindel-varindel-pindel ARID1B,frameshift_variant,p.Glu1161SerfsTer50,ENST00000346085,NM_020732.3;ARID1B,frameshift_variant,p.Glu1201SerfsTer50,ENST00000636930,;ARID1B,frameshift_variant,p.Glu1148SerfsTer50,ENST00000350026,NM_017519.2;ARID1B,frameshift_variant,p.Glu670SerfsTer50,ENST00000414678,;ARID1B,frameshift_variant,p.Glu451SerfsTer50,ENST00000637904,;ARID1B,frameshift_variant,p.Glu391SerfsTer50,ENST00000635849,;ARID1B,frameshift_variant,p.Glu407SerfsTer50,ENST00000637015,;ARID1B,frameshift_variant,p.Glu398SerfsTer50,ENST00000637810,;ARID1B,frameshift_variant,p.Glu269SerfsTer50,ENST00000635957,;ARID1B,frameshift_variant,p.Glu215SerfsTer82,ENST00000400790,;ARID1B,frameshift_variant,p.Glu622SerfsTer24,ENST00000319584,;ARID1B,non_coding_transcript_exon_variant,,ENST00000637741,;ARID1B,3_prime_UTR_variant,,ENST00000637568,;ARID1B,non_coding_transcript_exon_variant,,ENST00000636940,;ARID1B,downstream_gene_variant,,ENST00000478761,; - ENST00000346085 Transcript frameshift_variant 4036/10194 3480/6750 1160/2249 E/X gaG/ga 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 13/20 hmmpanther:PTHR12656:SF11,hmmpanther:PTHR12656,Gene3D:1.10.150.60,Superfamily_domains:SSF46774 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 157184365 157184365 G - 1 0 1 0 1 0 0 0 0 1050 991 35 0 0 ARID1B 6 157184365 Frame_Shift_Del DEL G C3N-02149_T 9917276 157184365 13621614 192 28376 AGPAT4 0 . GRCh38 6 161154309 161154309 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.350G>T p.Gly117Val p.G117V ENST00000320285 4/9 202 152 50 240 240 0 strelka-varscan-mutect AGPAT4,missense_variant,p.Gly117Val,ENST00000320285,NM_020133.2;AGPAT4,splice_region_variant,p.=,ENST00000366911,;AGPAT4,splice_region_variant,,ENST00000436279,; A ENST00000320285 Transcript missense_variant,splice_region_variant 563/7865 350/1137 117/378 G/V gGc/gTc 1 -1 AGPAT4 HGNC HGNC:20885 protein_coding YES CCDS5280.1 ENSP00000314036 Q9NRZ5 UPI0000035BB6 NM_020133.2 deleterious(0.04) 4/9 hmmpanther:PTHR10983,hmmpanther:PTHR10983:SF8,Pfam_domain:PF01553,SMART_domains:SM00563,Superfamily_domains:0039877 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 161154309 161154309 C A 1 0 0 0 0 1 0 0 0 471 753 26 2 2 AGPAT4 6 161154309 Missense_Mutation SNP C C3N-02149_T 3969944 161154309 9651670 193 28377 C6orf118 0 . GRCh38 6 165302028 165302028 + Silent SNP G G C rs146166260 C3N-02149_T C3N-02149_N G G c.294C>G p.= p.P98P ENST00000230301 2/9 171 140 31 220 220 0 strelka-varscan-mutect C6orf118,synonymous_variant,p.=,ENST00000230301,NM_144980.3; C ENST00000230301 Transcript synonymous_variant 315/1812 294/1410 98/469 P ccC/ccG rs146166260,COSM5580456 1 -1 C6orf118 HGNC HGNC:21233 protein_coding YES CCDS5288.1 ENSP00000230301 Q5T5N4 UPI0000367401 NM_144980.3 2/9 hmmpanther:PTHR34916 0,1 LOW 1 SNV 1 0,1 1 PASS rs146166260 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 165302028 165302028 G C 1 0 0 0 0 0 0 0 1 2115 1103 39 4 4 C6orf118 6 165302028 Silent SNP G C3N-02149_T 4147719 165302028 5503951 194 28378 FAM20C 0 . GRCh38 7 256028 256028 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1252G>T p.Glu418Ter p.E418* ENST00000313766 6/10 190 162 28 149 149 0 strelka-varscan-mutect FAM20C,stop_gained,p.Glu418Ter,ENST00000313766,NM_020223.3;FAM20C,splice_region_variant,,ENST00000515795,;FAM20C,upstream_gene_variant,,ENST00000512382,; T ENST00000313766 Transcript stop_gained,splice_region_variant 1483/2751 1252/1755 418/584 E/* Gag/Tag 1 1 FAM20C HGNC HGNC:22140 protein_coding YES CCDS47522.1 ENSP00000322323 Q8IXL6 UPI00001B5C04 NM_020223.3 6/10 Pfam_domain:PF06702,hmmpanther:PTHR12450,hmmpanther:PTHR12450:SF11 HIGH 1 SNV 1 1 PASS rs1157345537 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 256028 256028 G T 1 0 0 0 0 0 1 0 0 5395 1072 37 1 1 FAM20C 7 256028 Nonsense_Mutation SNP G C3N-02149_T 256028 159089945 195 28379 DAGLB 0 . GRCh38 7 6426009 6426009 + Silent SNP G G A rs140347773 C3N-02149_T C3N-02149_N G G c.1035C>T p.= p.I345I ENST00000297056 7/15 306 258 48 302 302 0 strelka-varscan-mutect DAGLB,synonymous_variant,p.=,ENST00000297056,NM_139179.3;DAGLB,synonymous_variant,p.=,ENST00000436575,;DAGLB,synonymous_variant,p.=,ENST00000425398,NM_001142936.1;DAGLB,downstream_gene_variant,,ENST00000432248,;DAGLB,missense_variant,p.Ser159Phe,ENST00000454738,;DAGLB,upstream_gene_variant,,ENST00000462934,; A ENST00000297056 Transcript synonymous_variant 1205/2897 1035/2019 345/672 I atC/atT rs140347773 1 -1 DAGLB HGNC HGNC:28923 protein_coding YES CCDS5350.1 ENSP00000297056 Q8NCG7 UPI000006E01F NM_139179.3 7/15 hmmpanther:PTHR21493:SF87,hmmpanther:PTHR21493,Superfamily_domains:SSF53474 LOW 1 SNV 1 1 PASS rs140347773 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 6426009 6426009 G A 1 0 0 0 0 0 0 0 1 4029 1164 41 3 3 DAGLB 7 6426009 Silent SNP G C3N-02149_T 6169981 6426009 152919964 196 28380 C1GALT1 0 . GRCh38 7 7238402 7238402 + Nonsense_Mutation SNP C C G C3N-02149_T C3N-02149_N C C c.368C>G p.Ser123Ter p.S123* ENST00000436587 3/4 334 278 56 374 374 0 strelka-varscan-mutect C1GALT1,stop_gained,p.Ser123Ter,ENST00000436587,NM_020156.4;C1GALT1,stop_gained,p.Ser123Ter,ENST00000223122,;C1GALT1,stop_gained,p.Ser123Ter,ENST00000402468,;C1GALT1,stop_gained,p.Ser123Ter,ENST00000429911,;C1GALT1,downstream_gene_variant,,ENST00000419721,;C1GALT1,downstream_gene_variant,,ENST00000476068,; G ENST00000436587 Transcript stop_gained 591/6235 368/1092 123/363 S/* tCa/tGa COSM332140 1 1 C1GALT1 HGNC HGNC:24337 protein_coding YES CCDS5355.1 ENSP00000389176 Q9NS00 A0A024RA32 UPI000003DC31 NM_020156.4 3/4 Pfam_domain:PF02434,hmmpanther:PTHR23033,hmmpanther:PTHR23033:SF13 1 HIGH 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 92 7238402 7238402 C G 1 0 0 0 0 0 1 0 0 1929 838 29 4 4 C1GALT1 7 7238402 Nonsense_Mutation SNP C C3N-02149_T 812393 7238402 152107571 197 28381 THSD7A 0 . GRCh38 7 11593407 11593407 + Nonsense_Mutation SNP G G C C3N-02149_T C3N-02149_N G G c.1118C>G p.Ser373Ter p.S373* ENST00000423059 3/28 450 415 35 426 426 0 strelka-varscan-mutect THSD7A,stop_gained,p.Ser373Ter,ENST00000423059,NM_015204.2;THSD7A,stop_gained,p.Ser373Ter,ENST00000617773,; C ENST00000423059 Transcript stop_gained 1370/10663 1118/4974 373/1657 S/* tCa/tGa COSM5196365 1 -1 THSD7A HGNC HGNC:22207 protein_coding YES CCDS47543.1 ENSP00000406482 Q9UPZ6 UPI00006C0B74 NM_015204.2 3/28 PROSITE_profiles:PS50092,hmmpanther:PTHR11311,hmmpanther:PTHR11311:SF8,Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,Superfamily_domains:SSF82895 1 HIGH 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 92 11593407 11593407 G C 1 0 0 0 0 0 1 0 0 16313 1294 45 4 4 THSD7A 7 11593407 Nonsense_Mutation SNP G C3N-02149_T 4355005 11593407 147752566 198 28382 SP8 0 . GRCh38 7 20785084 20785084 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.733G>T p.Ala245Ser p.A245S ENST00000418710 2/2 164 129 35 183 183 0 strelka-varscan-mutect SP8,missense_variant,p.Ala203Ser,ENST00000617581,;SP8,missense_variant,p.Ala227Ser,ENST00000361443,NM_198956.3;SP8,missense_variant,p.Ala245Ser,ENST00000418710,NM_182700.5; A ENST00000418710 Transcript missense_variant 821/1618 733/1527 245/508 A/S Gct/Tct 1 -1 SP8 HGNC HGNC:19196 protein_coding YES CCDS43555.1 ENSP00000408792 Q8IXZ3 UPI00001AADF2 NM_182700.5 tolerated(0.18) 2/2 MODERATE 1 SNV 1 1 PASS rs1480117950 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 20785084 20785084 C A 1 0 0 0 0 1 0 0 0 15296 739 26 2 2 SP8 7 20785084 Missense_Mutation SNP C C3N-02149_T 9191677 20785084 138560889 199 28383 DNAH11 0 . GRCh38 7 21784435 21784435 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.9492C>A p.= p.A3164A ENST00000409508 58/82 209 173 36 289 289 0 strelka-varscan-mutect DNAH11,synonymous_variant,p.=,ENST00000409508,NM_001277115.1;DNAH11,synonymous_variant,p.=,ENST00000328843,;DNAH11,synonymous_variant,p.=,ENST00000620169,; A ENST00000409508 Transcript synonymous_variant 9523/14167 9492/13551 3164/4516 A gcC/gcA 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 58/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Pfam_domain:PF12777 LOW 1 SNV 5 1 PASS rs1209904480 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 21784435 21784435 C A 1 0 0 0 0 0 0 0 1 4413 581 21 2 2 DNAH11 7 21784435 Silent SNP C C3N-02149_T 999351 21784435 137561538 200 28384 OSBPL3 0 . GRCh38 7 24834655 24834655 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.1577T>G p.Ile526Ser p.I526S ENST00000313367 15/23 264 242 22 235 235 0 strelka-varscan-mutect OSBPL3,missense_variant,p.Ile526Ser,ENST00000313367,NM_015550.3;OSBPL3,missense_variant,p.Ile495Ser,ENST00000396431,NM_145320.2;OSBPL3,missense_variant,p.Ile490Ser,ENST00000396429,NM_145321.2;OSBPL3,missense_variant,p.Ile459Ser,ENST00000409069,NM_145322.2;OSBPL3,missense_variant,p.Ile495Ser,ENST00000409863,;OSBPL3,missense_variant,p.Ile526Ser,ENST00000409452,;OSBPL3,missense_variant,p.Ile490Ser,ENST00000409759,;OSBPL3,missense_variant,p.Ile459Ser,ENST00000409555,; C ENST00000313367 Transcript missense_variant 2029/6760 1577/2664 526/887 I/S aTc/aGc 1 -1 OSBPL3 HGNC HGNC:16370 protein_coding YES CCDS5390.1 ENSP00000315410 Q9H4L5 UPI0000001244 NM_015550.3 deleterious(0) 15/23 Superfamily_domains:0051579,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF15 MODERATE 1 SNV 1 1 PASS rs1351211994 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 24834655 24834655 A C 1 0 0 0 0 1 0 0 0 11345 333 12 5 5 OSBPL3 7 24834655 Missense_Mutation SNP A C3N-02149_T 3050220 24834655 134511318 201 28385 HOXA4 0 . GRCh38 7 27129234 27129234 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.954C>A p.= p.S318S ENST00000360046 2/2 265 213 52 269 269 0 strelka-varscan-mutect HOXA4,synonymous_variant,p.=,ENST00000360046,;HOXA4,synonymous_variant,p.=,ENST00000610970,NM_002141.4;HOXA4,synonymous_variant,p.=,ENST00000428284,;HOXA4,synonymous_variant,p.=,ENST00000511914,;HOXA3,intron_variant,,ENST00000317201,;HOXA3,intron_variant,,ENST00000522788,;HOXA3,upstream_gene_variant,,ENST00000612286,NM_153631.2;HOXA-AS2,intron_variant,,ENST00000521159,;HOXA-AS2,downstream_gene_variant,,ENST00000517550,;HOXA-AS2,downstream_gene_variant,,ENST00000521687,;HOXA-AS3,upstream_gene_variant,,ENST00000518848,;HOXA-AS2,downstream_gene_variant,,ENST00000524048,;RP1-170O19.22,non_coding_transcript_exon_variant,,ENST00000467897,;HOXA3,intron_variant,,ENST00000521401,;HOXA3,intron_variant,,ENST00000518451,; T ENST00000360046 Transcript synonymous_variant 1020/1747 954/963 318/320 S tcC/tcA 1 -1 HOXA4 HGNC HGNC:5105 protein_coding YES CCDS5405.1 ENSP00000353151 Q00056 UPI000013C810 2/2 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 27129234 27129234 G T 1 0 0 0 0 0 0 0 1 7188 987 35 2 2 HOXA4 7 27129234 Silent SNP G C3N-02149_T 2294579 27129234 132216739 202 28386 TRIL 0 . GRCh38 7 28957592 28957592 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.455A>T p.Glu152Val p.E152V ENST00000539664 1/1 368 318 50 345 344 1 strelka-varscan-mutect TRIL,missense_variant,p.Glu152Val,ENST00000539664,NM_014817.3;AC005013.5,upstream_gene_variant,,ENST00000436594,; A ENST00000539664 Transcript missense_variant 701/4935 455/2436 152/811 E/V gAg/gTg 1 -1 TRIL HGNC HGNC:22200 protein_coding YES CCDS75573.1 ENSP00000479256 Q7L0X0 UPI00005C3DAC NM_014817.3 tolerated(0.3) 1/1 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF263,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 28957592 28957592 T A 1 0 0 0 0 1 0 0 0 16974 1551 54 4 4 TRIL 7 28957592 Missense_Mutation SNP T C3N-02149_T 1828358 28957592 130388381 203 28387 NEUROD6 0 . GRCh38 7 31339042 31339042 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.227G>T p.Arg76Met p.R76M ENST00000297142 2/2 524 453 71 618 618 0 strelka-varscan-mutect NEUROD6,missense_variant,p.Arg76Met,ENST00000297142,NM_022728.3; A ENST00000297142 Transcript missense_variant 550/2131 227/1014 76/337 R/M aGg/aTg 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 deleterious(0) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,PIRSF_domain:PIRSF015618 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 31339042 31339042 C A 1 0 0 0 0 1 0 0 0 10388 681 24 2 2 NEUROD6 7 31339042 Missense_Mutation SNP C C3N-02149_T 2381450 31339042 128006931 204 28388 INHBA 0 . GRCh38 7 41689683 41689683 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.1248G>T p.Gln416His p.Q416H ENST00000242208 3/3 81 62 19 60 59 1 strelka-varscan-mutect INHBA,missense_variant,p.Gln416His,ENST00000242208,NM_002192.2;INHBA,missense_variant,p.Gln416His,ENST00000638023,;INHBA,missense_variant,p.Gln416His,ENST00000442711,;INHBA-AS1,upstream_gene_variant,,ENST00000415848,;INHBA-AS1,upstream_gene_variant,,ENST00000422822,;INHBA-AS1,upstream_gene_variant,,ENST00000420821,;INHBA,non_coding_transcript_exon_variant,,ENST00000464515,;INHBA,intron_variant,,ENST00000416150,; A ENST00000242208 Transcript missense_variant 1495/6064 1248/1281 416/426 Q/H caG/caT COSM3638669 1 -1 INHBA HGNC HGNC:6066 protein_coding YES CCDS5464.1 ENSP00000242208 P08476 A4D1W7 UPI000012D421 NM_002192.2 tolerated(0.08) 3/3 PROSITE_profiles:PS51362,hmmpanther:PTHR11848:SF133,hmmpanther:PTHR11848,Pfam_domain:PF00019,Gene3D:2.10.90.10,SMART_domains:SM00204,Superfamily_domains:SSF57501 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 41689683 41689683 C A 1 0 0 0 0 1 0 0 0 7643 912 32 2 2 INHBA 7 41689683 Missense_Mutation SNP C C3N-02149_T 10350641 41689683 117656290 205 28389 PURB 0 . GRCh38 7 44884800 44884800 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.549C>T p.= p.R183R ENST00000395699 1/1 236 175 61 228 228 0 strelka-varscan-mutect PURB,synonymous_variant,p.=,ENST00000395699,NM_033224.4;PURB,upstream_gene_variant,,ENST00000578157,;RP4-673M15.1,upstream_gene_variant,,ENST00000608450,; A ENST00000395699 Transcript synonymous_variant 562/9069 549/939 183/312 R cgC/cgT 1 -1 PURB HGNC HGNC:9702 protein_coding YES CCDS5499.1 ENSP00000379051 Q96QR8 UPI000006F6CE NM_033224.4 1/1 Pfam_domain:PF04845,hmmpanther:PTHR12611,hmmpanther:PTHR12611:SF4,SMART_domains:SM00712 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 44884800 44884800 G A 1 0 0 0 0 0 0 0 1 12986 1074 38 1 1 PURB 7 44884800 Silent SNP G C3N-02149_T 3195117 44884800 114461173 206 28390 RAMP3 0 . GRCh38 7 45183280 45183280 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.315C>A p.= p.T105T ENST00000242249 3/3 534 412 122 502 502 0 strelka-varscan-mutect RAMP3,synonymous_variant,p.=,ENST00000242249,NM_005856.2;RAMP3,synonymous_variant,p.=,ENST00000481345,;RAMP3,synonymous_variant,p.=,ENST00000496212,; A ENST00000242249 Transcript synonymous_variant 353/1323 315/447 105/148 T acC/acA 1 1 RAMP3 HGNC HGNC:9845 protein_coding YES CCDS5503.1 ENSP00000242249 O60896 A4D2L1 UPI0000134303 NM_005856.2 3/3 Pfam_domain:PF04901,hmmpanther:PTHR14076,hmmpanther:PTHR14076:SF2 LOW 1 SNV 1 1 PASS rs1043997154 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 45183280 45183280 C A 1 0 0 0 0 0 0 0 1 13182 639 23 1 1 RAMP3 7 45183280 Silent SNP C C3N-02149_T 298480 45183280 114162693 207 28391 IGFBP1 0 . GRCh38 7 45888724 45888724 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.72C>T p.= p.A24A ENST00000275525 1/4 435 404 31 405 404 1 strelka-varscan-mutect IGFBP1,synonymous_variant,p.=,ENST00000275525,NM_000596.2;IGFBP1,synonymous_variant,p.=,ENST00000457280,;IGFBP1,synonymous_variant,p.=,ENST00000468955,; T ENST00000275525 Transcript synonymous_variant 368/1653 72/780 24/259 A gcC/gcT 1 1 IGFBP1 HGNC HGNC:5469 protein_coding YES CCDS5504.1 ENSP00000275525 P08833 UPI000012D10E NM_000596.2 1/4 Cleavage_site_(Signalp):SignalP-noTM,PROSITE_profiles:PS51323,hmmpanther:PTHR11551,hmmpanther:PTHR11551:SF6 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 45888724 45888724 C T 1 0 0 0 0 0 0 0 1 7484 639 23 1 1 IGFBP1 7 45888724 Silent SNP C C3N-02149_T 705444 45888724 113457249 208 28392 UPP1 0 . GRCh38 7 48106943 48106943 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.507G>T p.Gln169His p.Q169H ENST00000331803 8/10 401 328 73 429 429 0 strelka-varscan-mutect UPP1,missense_variant,p.Gln169His,ENST00000331803,NM_001287426.1;UPP1,missense_variant,p.Gln169His,ENST00000395564,NM_003364.3;UPP1,downstream_gene_variant,,ENST00000436673,;UPP1,downstream_gene_variant,,ENST00000416681,;UPP1,non_coding_transcript_exon_variant,,ENST00000482015,;UPP1,3_prime_UTR_variant,,ENST00000457596,;UPP1,3_prime_UTR_variant,,ENST00000395560,;UPP1,3_prime_UTR_variant,,ENST00000444999,;UPP1,3_prime_UTR_variant,,ENST00000417464,;UPP1,non_coding_transcript_exon_variant,,ENST00000495446,;UPP1,downstream_gene_variant,,ENST00000421046,; T ENST00000331803 Transcript missense_variant 1130/1932 507/933 169/310 Q/H caG/caT 1 1 UPP1 HGNC HGNC:12576 protein_coding YES CCDS5507.1 ENSP00000330032 Q16831 UPI0000137AC5 NM_001287426.1 tolerated(0.38) 8/10 Gene3D:3.40.50.1580,Pfam_domain:PF01048,hmmpanther:PTHR21234,hmmpanther:PTHR21234:SF15,Superfamily_domains:SSF53167,TIGRFAM_domain:TIGR01719 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 48106943 48106943 G T 1 0 0 0 0 1 0 0 0 17538 933 33 2 2 UPP1 7 48106943 Missense_Mutation SNP G C3N-02149_T 2218219 48106943 111239030 209 28393 NUPR2 0 . GRCh38 7 56116097 56116097 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.218C>A p.Ala73Glu p.A73E ENST00000329309 1/2 146 105 41 148 147 1 strelka-varscan-mutect NUPR2,missense_variant,p.Ala73Glu,ENST00000329309,NM_001145712.1; T ENST00000329309 Transcript missense_variant 304/603 218/294 73/97 A/E gCg/gAg 1 -1 NUPR2 HGNC HGNC:44164 protein_coding YES CCDS59058.1 ENSP00000455442 A6NF83 UPI00001D751D NM_001145712.1 deleterious(0.03) 1/2 Pfam_domain:PF10195,hmmpanther:PTHR17149,hmmpanther:PTHR17149:SF3 MODERATE 1 SNV 1 1 PASS rs935923930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 56116097 56116097 G T 1 0 0 0 0 1 0 0 0 10842 1087 38 1 1 NUPR2 7 56116097 Missense_Mutation SNP G C3N-02149_T 8009154 56116097 103229876 210 28394 FZD9 0 . GRCh38 7 73435763 73435763 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1756G>T p.Glu586Ter p.E586* ENST00000344575 1/1 107 89 18 108 108 0 strelka-varscan-mutect FZD9,stop_gained,p.Glu586Ter,ENST00000344575,NM_003508.2;BAZ1B,downstream_gene_variant,,ENST00000339594,NM_032408.3; T ENST00000344575 Transcript stop_gained 1981/2338 1756/1776 586/591 E/* Gag/Tag 1 1 FZD9 HGNC HGNC:4047 protein_coding YES CCDS5548.1 ENSP00000345785 O00144 UPI000004EC98 NM_003508.2 1/1 hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF79 HIGH SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 73435763 73435763 G T 1 0 0 0 0 0 1 0 0 6008 1175 41 2 2 FZD9 7 73435763 Nonsense_Mutation SNP G C3N-02149_T 17319666 73435763 85910210 211 28395 CLIP2 0 . GRCh38 7 74338498 74338498 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.172G>T p.Ala58Ser p.A58S ENST00000223398 3/17 420 374 46 335 335 0 strelka-varscan-mutect CLIP2,missense_variant,p.Ala58Ser,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Ala58Ser,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Ala58Ser,ENST00000395060,; T ENST00000223398 Transcript missense_variant 499/5563 172/3141 58/1046 A/S Gct/Tct 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 tolerated(0.3) 3/17 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 74338498 74338498 G T 1 0 0 0 0 1 0 0 0 3302 971 34 2 2 CLIP2 7 74338498 Missense_Mutation SNP G C3N-02149_T 902735 74338498 85007475 212 28396 RCC1L 0 . GRCh38 7 75073575 75073575 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.163G>T p.Ala55Ser p.A55S ENST00000610322 1/11 95 70 25 165 165 0 strelka-varscan-mutect RCC1L,missense_variant,p.Ala55Ser,ENST00000614461,NM_148842.2;RCC1L,missense_variant,p.Ala55Ser,ENST00000610322,NM_030798.4;RCC1L,missense_variant,p.Ala55Ser,ENST00000618035,NM_001281441.1;RCC1L,intron_variant,,ENST00000615250,;RCC1L,non_coding_transcript_exon_variant,,ENST00000616051,; A ENST00000610322 Transcript missense_variant 219/2300 163/1395 55/464 A/S Gct/Tct 1 -1 RCC1L HGNC HGNC:14948 protein_coding YES CCDS5577.1 ENSP00000480364 Q96I51 UPI0000138F99 NM_030798.4 tolerated(0.46) 1/11 hmmpanther:PTHR22870 MODERATE 1 SNV 1 1 PASS . . 0 205 3 2 0 0 0 0 -20 0.999998 1 1 1 0 A 3 1 92 75073575 75073575 C A 1 0 0 0 0 1 0 0 0 13343 768 27 1 1 RCC1L 7 75073575 Missense_Mutation SNP C C3N-02149_T 735077 75073575 84272398 213 28397 HGF 0 . GRCh38 7 81702643 81702643 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2125G>T p.Val709Leu p.V709L ENST00000222390 18/18 225 174 51 248 248 0 strelka-varscan-mutect HGF,missense_variant,p.Val709Leu,ENST00000222390,NM_000601.4;HGF,missense_variant,p.Val704Leu,ENST00000457544,NM_001010932.1; A ENST00000222390 Transcript missense_variant 2352/5989 2125/2187 709/728 V/L Gta/Tta 1 -1 HGF HGNC HGNC:4893 protein_coding YES CCDS5597.1 ENSP00000222390 P14210 UPI000000D92B NM_000601.4 deleterious(0.01) 18/18 PROSITE_profiles:PS50240,hmmpanther:PTHR24256:SF190,hmmpanther:PTHR24256,PIRSF_domain:PIRSF500183,PIRSF_domain:PIRSF001152,Gene3D:2.40.10.10,Pfam_domain:PF00089,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 81702643 81702643 C A 1 0 0 0 0 1 0 0 0 6969 565 20 2 2 HGF 7 81702643 Missense_Mutation SNP C C3N-02149_T 6629068 81702643 77643330 214 28398 PCLO 0 . GRCh38 7 82915108 82915108 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.12878C>G p.Ser4293Cys p.S4293C ENST00000333891 7/25 403 329 74 406 406 0 strelka-varscan-mutect PCLO,missense_variant,p.Ser4293Cys,ENST00000333891,NM_033026.5;PCLO,missense_variant,p.Ser4293Cys,ENST00000423517,NM_014510.2;PCLO,missense_variant,p.Ser1013Cys,ENST00000437081,; C ENST00000333891 Transcript missense_variant 13216/20329 12878/15429 4293/5142 S/C tCc/tGc 1 -1 PCLO HGNC HGNC:13406 protein_coding YES CCDS47630.1 ENSP00000334319 Q9Y6V0 UPI0001573469 NM_033026.5 deleterious(0) 7/25 Low_complexity_(Seg):seg,hmmpanther:PTHR14113:SF6,hmmpanther:PTHR14113 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 82915108 82915108 G C 1 0 0 0 0 1 0 0 0 11671 1174 41 4 4 PCLO 7 82915108 Missense_Mutation SNP G C3N-02149_T 1212465 82915108 76430865 215 28399 ABCB4 0 . GRCh38 7 87447135 87447135 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.904G>T p.Gly302Cys p.G302C ENST00000265723 9/28 401 329 72 492 492 0 strelka-varscan-mutect ABCB4,missense_variant,p.Gly302Cys,ENST00000265723,NM_018849.2;ABCB4,missense_variant,p.Gly302Cys,ENST00000359206,NM_000443.3;ABCB4,missense_variant,p.Gly302Cys,ENST00000358400,NM_018850.2;ABCB4,missense_variant,p.Gly302Cys,ENST00000453593,; A ENST00000265723 Transcript missense_variant 1016/4020 904/3861 302/1286 G/C Ggt/Tgt 1 -1 ABCB4 HGNC HGNC:45 protein_coding YES CCDS5606.1 ENSP00000265723 P21439 UPI000013D66B NM_018849.2 deleterious(0) 9/28 Gene3D:2hydA01,Pfam_domain:PF00664,PROSITE_profiles:PS50929,Superfamily_domains:SSF90123,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 87447135 87447135 C A 1 0 0 0 0 1 0 0 0 47 623 22 2 2 ABCB4 7 87447135 Missense_Mutation SNP C C3N-02149_T 4532027 87447135 71898838 216 28400 STEAP1 0 . GRCh38 7 90160961 90160961 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.241A>T p.Ile81Leu p.I81L ENST00000297205 3/5 399 341 58 456 456 0 strelka-varscan-mutect STEAP1,missense_variant,p.Ile81Leu,ENST00000297205,NM_012449.2;STEAP2-AS1,intron_variant,,ENST00000478318,;STEAP1,non_coding_transcript_exon_variant,,ENST00000475789,;STEAP1,upstream_gene_variant,,ENST00000412573,; T ENST00000297205 Transcript missense_variant 441/1313 241/1020 81/339 I/L Ata/Tta 1 1 STEAP1 HGNC HGNC:11378 protein_coding YES CCDS5614.1 ENSP00000297205 Q9UHE8 UPI000003C398 NM_012449.2 tolerated(1) 3/5 Transmembrane_helices:TMhelix,hmmpanther:PTHR14239:SF3,hmmpanther:PTHR14239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 90160961 90160961 A T 1 0 0 0 0 1 0 0 0 15653 449 16 4 4 STEAP1 7 90160961 Missense_Mutation SNP A C3N-02149_T 2713826 90160961 69185012 217 28401 TECPR1 0 . GRCh38 7 98231059 98231059 + Silent SNP C C A rs775757627 C3N-02149_T C3N-02149_N C C c.2184G>T p.= p.P728P ENST00000447648 15/26 265 207 58 240 240 0 strelka-varscan-mutect TECPR1,synonymous_variant,p.=,ENST00000447648,NM_015395.2;TECPR1,non_coding_transcript_exon_variant,,ENST00000479911,;TECPR1,upstream_gene_variant,,ENST00000479975,;TECPR1,downstream_gene_variant,,ENST00000471397,;TECPR1,upstream_gene_variant,,ENST00000476659,;TECPR1,non_coding_transcript_exon_variant,,ENST00000490842,;TECPR1,non_coding_transcript_exon_variant,,ENST00000483740,; A ENST00000447648 Transcript synonymous_variant 2484/6564 2184/3498 728/1165 P ccG/ccT rs775757627,COSM3883664 1 -1 TECPR1 HGNC HGNC:22214 protein_coding YES CCDS47648.1 ENSP00000404923 Q7Z6L1 UPI0000161940 NM_015395.2 15/26 hmmpanther:PTHR23250,hmmpanther:PTHR23250:SF1,SMART_domains:SM00706 0,1 LOW 1 SNV 1 0,1 1 PASS rs775757627 . 0 205 0 5 0 0 0 0 -20 0.9997798 1 1 1 0 A 2 1 92 98231059 98231059 C A 1 0 0 0 0 0 0 0 1 16154 755 27 1 1 TECPR1 7 98231059 Silent SNP C C3N-02149_T 8070098 98231059 61114914 218 28402 CPSF4 0 . GRCh38 7 99448148 99448148 + Missense_Mutation SNP G G T rs563837153 C3N-02149_T C3N-02149_N G G c.182G>T p.Ser61Ile p.S61I ENST00000292476 3/8 238 194 44 229 229 0 strelka-varscan-mutect CPSF4,missense_variant,p.Ser61Ile,ENST00000436336,NM_001318160.1,NM_001081559.1;CPSF4,missense_variant,p.Ser61Ile,ENST00000292476,NM_006693.2;CPSF4,missense_variant,p.Ser61Ile,ENST00000451876,;CPSF4,missense_variant,p.Ser8Ile,ENST00000441580,;CPSF4,missense_variant,p.Ser8Ile,ENST00000412686,;CPSF4,missense_variant,p.Ser28Ile,ENST00000452047,;ATP5J2-PTCD1,intron_variant,,ENST00000413834,NM_001198879.1;PTCD1,intron_variant,,ENST00000430982,;CPSF4,upstream_gene_variant,,ENST00000440514,;CPSF4,non_coding_transcript_exon_variant,,ENST00000471455,;ATP5J2-PTCD1,non_coding_transcript_exon_variant,,ENST00000437572,;ATP5J2,downstream_gene_variant,,ENST00000466753,;CPSF4,3_prime_UTR_variant,,ENST00000430038,;CPSF4,non_coding_transcript_exon_variant,,ENST00000484112,;ATP5J2-PTCD1,intron_variant,,ENST00000451138,;CPSF4,upstream_gene_variant,,ENST00000465132,;CPSF4,upstream_gene_variant,,ENST00000482251,;ATP5J2,downstream_gene_variant,,ENST00000414062,;AC073063.10,upstream_gene_variant,,ENST00000434352,; T ENST00000292476 Transcript missense_variant 192/1691 182/810 61/269 S/I aGt/aTt rs563837153 1 1 CPSF4 HGNC HGNC:2327 protein_coding YES CCDS5664.1 ENSP00000292476 O95639 UPI0000072392 NM_006693.2 tolerated(0.14) 3/8 Pfam_domain:PF15663,hmmpanther:PTHR23102,hmmpanther:PTHR23102:SF18,SMART_domains:SM00356 MODERATE 1 SNV 1 1 PASS rs563837153 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 99448148 99448148 G T 1 0 0 0 0 1 0 0 0 3624 1029 36 2 2 CPSF4 7 99448148 Missense_Mutation SNP G C3N-02149_T 1217089 99448148 59897825 219 28403 AZGP1 0 . GRCh38 7 99968209 99968209 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.559C>A p.Pro187Thr p.P187T ENST00000292401 3/4 365 289 76 321 321 0 strelka-varscan-mutect AZGP1,missense_variant,p.Pro184Thr,ENST00000411734,;AZGP1,missense_variant,p.Pro187Thr,ENST00000292401,NM_001185.3;AZGP1,intron_variant,,ENST00000419575,;AZGP1,upstream_gene_variant,,ENST00000483612,;AZGP1,non_coding_transcript_exon_variant,,ENST00000477251,;AZGP1,downstream_gene_variant,,ENST00000495765,; T ENST00000292401 Transcript missense_variant 696/1307 559/897 187/298 P/T Cct/Act 1 -1 AZGP1 HGNC HGNC:910 protein_coding YES CCDS5680.1 ENSP00000292401 P25311 A0A140VK00 UPI00000720DE NM_001185.3 tolerated(0.26) 3/4 hmmpanther:PTHR16675,hmmpanther:PTHR16675:SF168,Gene3D:3.30.500.10,Pfam_domain:PF00129,Superfamily_domains:SSF54452,Prints_domain:PR01638 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 99968209 99968209 G T 1 0 0 0 0 1 0 0 0 1396 1232 43 2 2 AZGP1 7 99968209 Missense_Mutation SNP G C3N-02149_T 520061 99968209 59377764 220 28404 GAL3ST4 0 . GRCh38 7 100160191 100160191 + Silent SNP G G T rs769238120 C3N-02149_T C3N-02149_N G G c.1198C>A p.= p.R400R ENST00000360039 4/4 220 168 52 218 218 0 strelka-varscan-mutect GAL3ST4,synonymous_variant,p.=,ENST00000360039,NM_024637.4;GAL3ST4,synonymous_variant,p.=,ENST00000413800,;GAL3ST4,3_prime_UTR_variant,,ENST00000423751,;GAL3ST4,3_prime_UTR_variant,,ENST00000411994,;C7orf43,upstream_gene_variant,,ENST00000316937,NM_018275.4;C7orf43,upstream_gene_variant,,ENST00000456769,NM_001303470.1;C7orf43,upstream_gene_variant,,ENST00000457641,;GAL3ST4,downstream_gene_variant,,ENST00000498000,;LAMTOR4,downstream_gene_variant,,ENST00000490633,;C7orf43,upstream_gene_variant,,ENST00000584344,;GAL3ST4,non_coding_transcript_exon_variant,,ENST00000495882,;C7orf43,upstream_gene_variant,,ENST00000419037,;C7orf43,upstream_gene_variant,,ENST00000448720,;C7orf43,upstream_gene_variant,,ENST00000419841,;C7orf43,upstream_gene_variant,,ENST00000394035,;C7orf43,upstream_gene_variant,,ENST00000470260,;C7orf43,upstream_gene_variant,,ENST00000498638,;C7orf43,upstream_gene_variant,,ENST00000472061,; T ENST00000360039 Transcript synonymous_variant 1591/2537 1198/1461 400/486 R Cga/Aga rs769238120 1 -1 GAL3ST4 HGNC HGNC:24145 protein_coding YES CCDS5688.1 ENSP00000353142 Q96RP7 UPI0000070C68 NM_024637.4 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR14647,hmmpanther:PTHR14647:SF57,Pfam_domain:PF06990 LOW 1 SNV 1 1 PASS rs769238120 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 100160191 100160191 G T 1 0 0 0 0 0 0 0 1 6068 1124 39 1 1 GAL3ST4 7 100160191 Silent SNP G C3N-02149_T 191982 100160191 59185782 221 28405 GIGYF1 0 . GRCh38 7 100683845 100683845 + Missense_Mutation SNP C C T rs140997486 C3N-02149_T C3N-02149_N C C c.1942G>A p.Val648Ile p.V648I ENST00000275732 16/24 304 245 59 327 327 0 strelka-varscan-mutect GIGYF1,missense_variant,p.Val648Ile,ENST00000275732,NM_022574.4;GNB2,downstream_gene_variant,,ENST00000303210,NM_005273.3;GNB2,downstream_gene_variant,,ENST00000393926,;GNB2,downstream_gene_variant,,ENST00000393924,;GNB2,downstream_gene_variant,,ENST00000436220,;GNB2,downstream_gene_variant,,ENST00000424361,;GNB2,downstream_gene_variant,,ENST00000419828,;GNB2,downstream_gene_variant,,ENST00000427895,;GIGYF1,downstream_gene_variant,,ENST00000471340,;GNB2,downstream_gene_variant,,ENST00000469287,;GIGYF1,downstream_gene_variant,,ENST00000464111,;GIGYF1,downstream_gene_variant,,ENST00000472105,; T ENST00000275732 Transcript missense_variant 3152/6530 1942/3108 648/1035 V/I Gta/Ata rs140997486 1 -1 GIGYF1 HGNC HGNC:9126 protein_coding YES CCDS34708.1 ENSP00000275732 O75420 UPI00001BD8AD NM_022574.4 tolerated(0.16) 16/24 hmmpanther:PTHR14445,hmmpanther:PTHR14445:SF37 MODERATE 1 SNV 1 1 PASS rs140997486 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 100683845 100683845 C T 1 0 0 0 0 1 0 0 0 6257 536 19 1 1 GIGYF1 7 100683845 Missense_Mutation SNP C C3N-02149_T 523654 100683845 58662128 222 28406 MUC3A 0 . GRCh38 7 100960643 100960643 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.8864C>A p.Ala2955Glu p.A2955E ENST00000379458 2/12 146 124 22 166 166 0 strelka-varscan-mutect MUC3A,missense_variant,p.Ala2955Glu,ENST00000379458,NM_005960.1;MUC3A,missense_variant,p.Ala2955Glu,ENST00000483366,;RP11-395B7.2,downstream_gene_variant,,ENST00000618276,;RP11-395B7.2,downstream_gene_variant,,ENST00000610769,;MUC3A,missense_variant,p.Ala894Glu,ENST00000414964,; A ENST00000379458 Transcript missense_variant,splice_region_variant 8934/11226 8864/9972 2955/3323 A/E gCa/gAa 1 1 MUC3A HGNC HGNC:7513 protein_coding YES CCDS78262.1 ENSP00000368771 Q02505 UPI000455B941 NM_005960.1 deleterious_low_confidence(0.01) 2/12 hmmpanther:PTHR24041,hmmpanther:PTHR24041:SF22,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 100960643 100960643 C A 1 0 0 0 0 1 0 0 0 9976 724 25 2 2 MUC3A 7 100960643 Missense_Mutation SNP C C3N-02149_T 276798 100960643 58385330 223 28407 PUS7 0 . GRCh38 7 105481148 105481148 + Missense_Mutation SNP T T A C3N-02149_T C3N-02149_N T T c.1079A>T p.Gln360Leu p.Q360L ENST00000356362 9/16 211 181 30 274 274 0 strelka-varscan-mutect PUS7,missense_variant,p.Gln360Leu,ENST00000356362,NM_001318163.1,NM_001318164.1,NM_019042.3;PUS7,missense_variant,p.Gln360Leu,ENST00000469408,;PUS7,missense_variant,p.Gln360Leu,ENST00000481939,; A ENST00000356362 Transcript missense_variant 1294/3480 1079/1986 360/661 Q/L cAg/cTg COSM4186144 1 -1 PUS7 HGNC HGNC:26033 protein_coding YES CCDS34725.1 ENSP00000348722 Q96PZ0 UPI00001D483E NM_001318163.1,NM_001318164.1,NM_019042.3 deleterious(0.01) 9/16 Pfam_domain:PF01142,hmmpanther:PTHR13326,hmmpanther:PTHR13326:SF1,Superfamily_domains:SSF55120,TIGRFAM_domain:TIGR00094 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 105481148 105481148 T A 1 0 0 0 0 1 0 0 0 12991 1580 55 4 4 PUS7 7 105481148 Missense_Mutation SNP T C3N-02149_T 4520505 105481148 53864825 224 28408 CCDC71L 0 . GRCh38 7 106660583 106660583 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.314G>T p.Arg105Leu p.R105L ENST00000523505 1/1 263 212 51 265 265 0 strelka-varscan-mutect CCDC71L,missense_variant,p.Arg105Leu,ENST00000523505,NM_175884.4;CCDC71L,intron_variant,,ENST00000315965,;CTB-111H14.1,intron_variant,,ENST00000592441,;CTB-111H14.1,intron_variant,,ENST00000490856,; A ENST00000523505 Transcript missense_variant 414/4232 314/708 105/235 R/L cGg/cTg 1 -1 CCDC71L HGNC HGNC:26685 protein_coding YES CCDS55151.1 ENSP00000430897 Q8N9Z2 UPI00003CF1DF NM_175884.4 deleterious(0.01) 1/1 hmmpanther:PTHR14484:SF1,hmmpanther:PTHR14484,Pfam_domain:PF15374 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 106660583 106660583 C A 1 0 0 0 0 1 0 0 0 2545 652 23 1 1 CCDC71L 7 106660583 Missense_Mutation SNP C C3N-02149_T 1179435 106660583 52685390 225 28409 SLC26A4 0 . GRCh38 7 107710110 107710110 + Missense_Mutation SNP G G T rs761870156 C3N-02149_T C3N-02149_N G G c.2146G>T p.Asp716Tyr p.D716Y ENST00000265715 19/21 387 284 103 444 444 0 strelka-varscan-mutect SLC26A4,missense_variant,p.Asp716Tyr,ENST00000265715,NM_000441.1;SLC26A4,intron_variant,,ENST00000492030,; T ENST00000265715 Transcript missense_variant 2370/4930 2146/2343 716/780 D/Y Gac/Tac rs761870156 1 1 SLC26A4 HGNC HGNC:8818 protein_coding YES CCDS5746.1 ENSP00000265715 O43511 UPI00001315A4 NM_000441.1 deleterious(0.02) 19/21 Gene3D:3.30.750.24,Pfam_domain:PF01740,PROSITE_profiles:PS50801,hmmpanther:PTHR11814,hmmpanther:PTHR11814:SF33,Superfamily_domains:SSF52091,TIGRFAM_domain:TIGR00815 MODERATE 1 SNV 1 1 PASS rs761870156 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 107710110 107710110 G T 1 0 0 0 0 1 0 0 0 14789 1174 41 2 2 SLC26A4 7 107710110 Missense_Mutation SNP G C3N-02149_T 1049527 107710110 51635863 226 28410 LAMB4 0 . GRCh38 7 108063954 108063954 + Missense_Mutation SNP G G C rs767544532 C3N-02149_T C3N-02149_N G G c.2868C>G p.Phe956Leu p.F956L ENST00000388781 22/34 353 317 36 381 381 0 strelka-varscan-mutect LAMB4,missense_variant,p.Phe956Leu,ENST00000388781,NM_007356.2;LAMB4,missense_variant,p.Phe956Leu,ENST00000205386,NM_001318046.1;LAMB4,upstream_gene_variant,,ENST00000422975,;LAMB4,non_coding_transcript_exon_variant,,ENST00000475469,;LAMB4,non_coding_transcript_exon_variant,,ENST00000471677,; C ENST00000388781 Transcript missense_variant 2952/5858 2868/5286 956/1761 F/L ttC/ttG rs767544532,COSM1083977,COSM4863422 1 -1 LAMB4 HGNC HGNC:6491 protein_coding YES CCDS34732.1 ENSP00000373433 A4D0S4 UPI0000198CD5 NM_007356.2 deleterious(0.01) 22/34 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,SMART_domains:SM00180,Superfamily_domains:SSF57196 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs767544532 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 108063954 108063954 G C 1 0 0 0 0 1 0 0 0 8517 933 33 4 4 LAMB4 7 108063954 Missense_Mutation SNP G C3N-02149_T 353844 108063954 51282019 227 28411 CADPS2 0 . GRCh38 7 122387132 122387132 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.3206A>G p.Lys1069Arg p.K1069R ENST00000449022 24/30 307 262 45 265 265 0 strelka-varscan-mutect CADPS2,missense_variant,p.Lys1074Arg,ENST00000615869,;CADPS2,missense_variant,p.Lys967Arg,ENST00000313070,NM_001167940.1;CADPS2,missense_variant,p.Lys1067Arg,ENST00000334010,;CADPS2,missense_variant,p.Lys1023Arg,ENST00000412584,NM_001009571.3;CADPS2,missense_variant,p.Lys1069Arg,ENST00000449022,NM_017954.10;CADPS2,missense_variant,p.Lys672Arg,ENST00000397721,;CADPS2,missense_variant,p.Lys263Arg,ENST00000462699,;RP5-1101C3.1,intron_variant,,ENST00000591140,;RP5-1101C3.1,intron_variant,,ENST00000625850,;RP5-1101C3.1,intron_variant,,ENST00000628268,;RP5-1101C3.1,intron_variant,,ENST00000593910,;RP5-1101C3.1,intron_variant,,ENST00000626740,;RP5-1101C3.1,intron_variant,,ENST00000630777,;RP5-1101C3.1,intron_variant,,ENST00000631248,;RP5-1101C3.1,intron_variant,,ENST00000627005,;RP5-1101C3.1,downstream_gene_variant,,ENST00000626052,; C ENST00000449022 Transcript missense_variant 3226/4073 3206/3891 1069/1296 K/R aAa/aGa 1 -1 CADPS2 HGNC HGNC:16018 protein_coding YES CCDS55158.1 ENSP00000398481 Q86UW7 UPI0000668808 NM_017954.10 tolerated(0.54) 24/30 hmmpanther:PTHR12166,hmmpanther:PTHR12166:SF7 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 122387132 122387132 T C 1 0 0 0 0 1 0 0 0 2261 1841 64 5 5 CADPS2 7 122387132 Missense_Mutation SNP T C3N-02149_T 14323178 122387132 36958841 228 28412 RNF133 0 . GRCh38 7 122698074 122698074 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.845G>T p.Cys282Phe p.C282F ENST00000340112 1/1 315 267 48 380 379 1 strelka-varscan-mutect RNF133,missense_variant,p.Cys282Phe,ENST00000340112,NM_139175.1;CADPS2,intron_variant,,ENST00000615869,;CADPS2,intron_variant,,ENST00000313070,NM_001167940.1;CADPS2,intron_variant,,ENST00000334010,;CADPS2,intron_variant,,ENST00000412584,NM_001009571.3;CADPS2,intron_variant,,ENST00000449022,NM_017954.10;RNF148,downstream_gene_variant,,ENST00000434824,NM_198085.1;RNF148,downstream_gene_variant,,ENST00000447240,; A ENST00000340112 Transcript missense_variant 1083/1445 845/1131 282/376 C/F tGc/tTc 1 -1 RNF133 HGNC HGNC:21154 protein_coding YES CCDS5784.1 ENSP00000344489 Q8WVZ7 UPI0000070D9A NM_139175.1 deleterious(0) 1/1 PROSITE_profiles:PS50089,hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF38,Pfam_domain:PF13639,Gene3D:3.30.40.10,SMART_domains:SM00184,Superfamily_domains:SSF57850 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 122698074 122698074 C A 1 0 0 0 0 1 0 0 0 13617 710 25 2 2 RNF133 7 122698074 Missense_Mutation SNP C C3N-02149_T 310942 122698074 36647899 229 28413 LMOD2 0 . GRCh38 7 123656199 123656199 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.236A>T p.Lys79Ile p.K79I ENST00000458573 1/3 242 210 32 246 245 1 strelka-varscan-mutect LMOD2,missense_variant,p.Lys79Ile,ENST00000458573,NM_207163.1;LMOD2,missense_variant,p.Lys79Ile,ENST00000456238,; T ENST00000458573 Transcript missense_variant 393/2346 236/1644 79/547 K/I aAa/aTa 1 1 LMOD2 HGNC HGNC:6648 protein_coding YES CCDS47693.1 ENSP00000411932 Q6P5Q4 UPI0001572CCA NM_207163.1 deleterious(0) 1/3 Pfam_domain:PF03250,hmmpanther:PTHR10901,hmmpanther:PTHR10901:SF12 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 123656199 123656199 A T 1 0 0 0 0 1 0 0 0 8784 14 1 4 4 LMOD2 7 123656199 Missense_Mutation SNP A C3N-02149_T 958125 123656199 35689774 230 28414 IMPDH1 0 . GRCh38 7 128395001 128395001 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1438G>T p.Glu480Ter p.E480* ENST00000338791 14/17 488 375 113 511 509 2 strelka-varscan-mutect IMPDH1,stop_gained,p.Glu480Ter,ENST00000338791,NM_000883.3;IMPDH1,stop_gained,p.Glu394Ter,ENST00000626419,;IMPDH1,stop_gained,p.Glu470Ter,ENST00000354269,NM_001102605.1;IMPDH1,stop_gained,p.Glu444Ter,ENST00000348127,NM_183243.2,NM_001304521.1;IMPDH1,stop_gained,p.Glu447Ter,ENST00000419067,NM_001142576.1;IMPDH1,stop_gained,p.Glu370Ter,ENST00000496200,NM_001142575.1;IMPDH1,stop_gained,p.Glu394Ter,ENST00000470772,NM_001142573.1;IMPDH1,stop_gained,p.Glu390Ter,ENST00000480861,NM_001142574.1;IMPDH1,downstream_gene_variant,,ENST00000497868,;IMPDH1,splice_region_variant,,ENST00000460045,;IMPDH1,3_prime_UTR_variant,,ENST00000484496,;IMPDH1,3_prime_UTR_variant,,ENST00000469328,;IMPDH1,downstream_gene_variant,,ENST00000468842,; A ENST00000338791 Transcript stop_gained 1789/2881 1438/1800 480/599 E/* Gag/Tag 1 -1 IMPDH1 HGNC HGNC:6052 protein_coding YES CCDS34749.1 ENSP00000345096 P20839 UPI00001BDC74 NM_000883.3 14/17 HAMAP:MF_01964,hmmpanther:PTHR11911:SF74,hmmpanther:PTHR11911,Pfam_domain:PF00478,TIGRFAM_domain:TIGR01302,Gene3D:3.20.20.70,SMART_domains:SM01240,Superfamily_domains:SSF51412 HIGH 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 128395001 128395001 C A 1 0 0 0 0 0 1 0 0 7628 864 30 2 2 IMPDH1 7 128395001 Nonsense_Mutation SNP C C3N-02149_T 4738802 128395001 30950972 231 28415 FAM71F1 0 . GRCh38 7 128715584 128715584 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.143C>A p.Pro48His p.P48H ENST00000315184 1/7 415 319 96 400 400 0 strelka-varscan-mutect FAM71F1,missense_variant,p.Pro48His,ENST00000315184,NM_001282788.1,NM_032599.3;FAM71F1,intron_variant,,ENST00000621392,;FAM71F1,intron_variant,,ENST00000485070,NM_001282789.1;FAM71F1,upstream_gene_variant,,ENST00000466842,;FAM71F1,non_coding_transcript_exon_variant,,ENST00000483459,;FAM71F1,intron_variant,,ENST00000469348,;FAM71F1,missense_variant,p.Pro48His,ENST00000471558,;FAM71F1,intron_variant,,ENST00000484425,;FAM71F1,intron_variant,,ENST00000493738,; A ENST00000315184 Transcript missense_variant 196/1718 143/1035 48/344 P/H cCt/cAt 1 1 FAM71F1 HGNC HGNC:30704 protein_coding YES CCDS5804.1 ENSP00000326652 Q96KD3 A0A140VJJ3 UPI000006D961 NM_001282788.1,NM_032599.3 deleterious(0.01) 1/7 hmmpanther:PTHR22574,hmmpanther:PTHR22574:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 128715584 128715584 C A 1 0 0 0 0 1 0 0 0 5477 681 24 2 2 FAM71F1 7 128715584 Missense_Mutation SNP C C3N-02149_T 320583 128715584 30630389 232 28416 FLNC 0 . GRCh38 7 128848801 128848801 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.4746G>T p.Glu1582Asp p.E1582D ENST00000325888 28/48 633 563 70 672 669 3 strelka-varscan-mutect FLNC,missense_variant,p.Glu1582Asp,ENST00000325888,NM_001458.4;FLNC,missense_variant,p.Glu1582Asp,ENST00000346177,NM_001127487.1;RP11-309L24.2,downstream_gene_variant,,ENST00000469965,; T ENST00000325888 Transcript missense_variant 5007/9188 4746/8178 1582/2725 E/D gaG/gaT 1 1 FLNC HGNC HGNC:3756 protein_coding YES CCDS43644.1 ENSP00000327145 Q14315 UPI000006DE6D NM_001458.4 tolerated(0.25) 28/48 Gene3D:2.60.40.10,Pfam_domain:PF00630,PROSITE_profiles:PS50194,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF210,SMART_domains:SM00557,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS rs1417108770 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 128848801 128848801 G T 1 0 0 0 0 1 0 0 0 5791 991 35 2 2 FLNC 7 128848801 Missense_Mutation SNP G C3N-02149_T 133217 128848801 30497172 233 28417 KCP 0 . GRCh38 7 128892541 128892541 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.1594C>G p.Pro532Ala p.P532A ENST00000610776 16/40 81 70 11 72 72 0 strelka-varscan-mutect KCP,missense_variant,p.Pro532Ala,ENST00000610776,;KCP,missense_variant,p.Pro536Ala,ENST00000613019,;KCP,missense_variant,p.Pro475Ala,ENST00000620378,NM_001135914.1;KCP,non_coding_transcript_exon_variant,,ENST00000612224,;KCP,missense_variant,p.Pro536Ala,ENST00000611280,;KCP,non_coding_transcript_exon_variant,,ENST00000616669,; C ENST00000610776 Transcript missense_variant 1637/5108 1594/4887 532/1628 P/A Cca/Gca 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 tolerated(0.06) 16/40 PROSITE_profiles:PS50184,PROSITE_patterns:PS01208,Pfam_domain:PF00093,SMART_domains:SM00215,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -19.99987 0.9999976 1 1 1 0 C 3 2 92 128892541 128892541 G C 1 0 0 0 0 1 0 0 0 8012 1261 44 4 4 KCP 7 128892541 Missense_Mutation SNP G C3N-02149_T 43740 128892541 30453432 234 28418 PLXNA4 0 . GRCh38 7 132227590 132227590 + Silent SNP C C T rs369889571 C3N-02149_T C3N-02149_N C C c.1743G>A p.= p.T581T ENST00000359827 7/32 253 196 57 261 260 1 strelka-varscan-mutect PLXNA4,synonymous_variant,p.=,ENST00000359827,;PLXNA4,synonymous_variant,p.=,ENST00000321063,NM_020911.1; T ENST00000359827 Transcript synonymous_variant 2706/13786 1743/5685 581/1894 T acG/acA rs369889571,COSM5570176,COSM5570177 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 7/32 hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs369889571 . 0 207 0 3 0 0 0 0 -20 0.9999972 1 1 1 0 T 2 4 92 132227590 132227590 C T 1 0 0 0 0 0 0 0 1 12228 523 19 1 1 PLXNA4 7 132227590 Silent SNP C C3N-02149_T 3335049 132227590 27118383 235 28419 STRA8 0 . GRCh38 7 135246571 135246571 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.601G>T p.Ala201Ser p.A201S ENST00000275764 6/9 465 359 106 428 426 2 strelka-varscan-mutect STRA8,missense_variant,p.Ala201Ser,ENST00000275764,NM_182489.1;RP11-260N14.1,non_coding_transcript_exon_variant,,ENST00000637483,; T ENST00000275764 Transcript missense_variant 601/993 601/993 201/330 A/S Gcg/Tcg 1 1 STRA8 HGNC HGNC:30653 protein_coding YES CCDS5839.1 ENSP00000275764 Q7Z7C7 UPI00001A36D9 NM_182489.1 tolerated(1) 6/9 hmmpanther:PTHR35254 MODERATE 1 SNV 1 1 PASS rs1249509082 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 135246571 135246571 G T 1 0 0 0 0 1 0 0 0 15704 1203 42 2 2 STRA8 7 135246571 Missense_Mutation SNP G C3N-02149_T 3018981 135246571 24099402 236 28420 KLRG2 0 . GRCh38 7 139483346 139483346 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.297C>A p.= p.A99A ENST00000340940 1/5 206 172 34 250 250 0 strelka-varscan-mutect KLRG2,synonymous_variant,p.=,ENST00000340940,NM_198508.2;KLRG2,synonymous_variant,p.=,ENST00000393039,; T ENST00000340940 Transcript synonymous_variant 367/2197 297/1230 99/409 A gcC/gcA 1 -1 KLRG2 HGNC HGNC:24778 protein_coding YES CCDS5854.1 ENSP00000339356 A4D1S0 UPI00001C0C37 NM_198508.2 1/5 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 139483346 139483346 G T 1 0 0 0 0 0 0 0 1 8292 987 35 2 2 KLRG2 7 139483346 Silent SNP G C3N-02149_T 4236775 139483346 19862627 237 28421 EPHB6 0 . GRCh38 7 142864620 142864620 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.820G>T p.Val274Leu p.V274L ENST00000619012 7/20 93 77 16 66 66 0 strelka-varscan-mutect EPHB6,missense_variant,p.Val274Leu,ENST00000619012,;EPHB6,missense_variant,p.Val274Leu,ENST00000422643,NM_004445.5;EPHB6,5_prime_UTR_variant,,ENST00000411471,NM_001280794.2,NM_001280795.2;EPHB6,downstream_gene_variant,,ENST00000497095,;EPHB6,missense_variant,p.Glu183Asp,ENST00000611578,;EPHB6,3_prime_UTR_variant,,ENST00000614832,;EPHB6,non_coding_transcript_exon_variant,,ENST00000616380,;EPHB6,upstream_gene_variant,,ENST00000486511,; T ENST00000619012 Transcript missense_variant 1572/4011 820/3069 274/1022 V/L Gta/Tta 1 1 EPHB6 HGNC HGNC:3396 protein_coding YES CCDS5873.2 ENSP00000481994 F8WCM8 UPI0003EAF8C7 tolerated(1) 7/20 hmmpanther:PTHR24416:SF326,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666 MODERATE 1 SNV 1 1 PASS rs1263681604 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 142864620 142864620 G T 1 0 0 0 0 1 0 0 0 5025 1029 36 2 2 EPHB6 7 142864620 Missense_Mutation SNP G C3N-02149_T 3381274 142864620 16481353 238 28422 KEL 0 . GRCh38 7 142954264 142954264 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.844C>T p.= p.L282L ENST00000355265 8/19 402 372 30 446 446 0 strelka-varscan-mutect KEL,synonymous_variant,p.=,ENST00000355265,NM_000420.2;KEL,downstream_gene_variant,,ENST00000467543,;KEL,downstream_gene_variant,,ENST00000476829,;KEL,downstream_gene_variant,,ENST00000460479,;KEL,non_coding_transcript_exon_variant,,ENST00000479768,;KEL,downstream_gene_variant,,ENST00000494148,; A ENST00000355265 Transcript synonymous_variant 1319/2812 844/2199 282/732 L Ctg/Ttg 1 -1 KEL HGNC HGNC:6308 protein_coding YES CCDS34766.1 ENSP00000347409 P23276 A0A077QP03 UPI000000D923 NM_000420.2 8/19 hmmpanther:PTHR11733:SF128,hmmpanther:PTHR11733,Pfam_domain:PF05649,Gene3D:1r1hA02,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 142954264 142954264 G A 1 0 0 0 0 0 0 0 1 8062 962 34 3 3 KEL 7 142954264 Silent SNP G C3N-02149_T 89644 142954264 16391709 239 28423 TAS2R39 0 . GRCh38 7 143184084 143184084 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.666C>G p.Ile222Met p.I222M ENST00000446620 1/1 374 322 52 465 465 0 strelka-varscan-mutect TAS2R39,missense_variant,p.Ile222Met,ENST00000446620,NM_176881.2; G ENST00000446620 Transcript missense_variant 666/1017 666/1017 222/338 I/M atC/atG 1 1 TAS2R39 HGNC HGNC:18886 protein_coding YES CCDS47729.1 ENSP00000405095 P59534 UPI00000620BE NM_176881.2 deleterious(0.05) 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR11394:SF67,hmmpanther:PTHR11394,Pfam_domain:PF05296,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 143184084 143184084 C G 1 0 0 0 0 1 0 0 0 15975 816 29 4 4 TAS2R39 7 143184084 Missense_Mutation SNP C C3N-02149_T 229820 143184084 16161889 240 28424 CLCN1 0 . GRCh38 7 143341938 143341938 + Missense_Mutation SNP C C A rs80356704 C3N-02149_T C3N-02149_N C C c.1592C>A p.Ala531Glu p.A531E ENST00000343257 15/23 664 549 115 619 619 0 strelka-varscan-mutect CLCN1,missense_variant,p.Ala531Glu,ENST00000343257,NM_000083.2; A ENST00000343257 Transcript missense_variant 1679/3172 1592/2967 531/988 A/E gCg/gAg rs80356704,CM990364 1 1 CLCN1 HGNC HGNC:2019 protein_coding YES CCDS5881.1 ENSP00000339867 P35523 UPI000020F1EC NM_000083.2 deleterious(0) 15/23 Transmembrane_helices:TMhelix,hmmpanther:PTHR11689:SF29,hmmpanther:PTHR11689,Gene3D:1otsB00,Pfam_domain:PF00654,Superfamily_domains:SSF81340,Prints_domain:PR00762 pathogenic MODERATE 1 SNV 1 1,1 1 PASS rs80356704 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 143341938 143341938 C A 1 0 0 0 0 1 0 0 0 3226 768 27 1 1 CLCN1 7 143341938 Missense_Mutation SNP C C3N-02149_T 157854 143341938 16004035 241 28425 ARHGEF35 0 . GRCh38 7 144187727 144187727 + Silent SNP T T C novel C3N-02149_T C3N-02149_N T T c.657A>G p.= p.Q219Q ENST00000378115 2/2 248 232 16 268 268 0 varscan-mutect ARHGEF35,synonymous_variant,p.=,ENST00000378115,NM_001003702.2;CTAGE4,downstream_gene_variant,,ENST00000486333,NM_198495.2; C ENST00000378115 Transcript synonymous_variant 787/2431 657/1455 219/484 Q caA/caG 1 -1 ARHGEF35 HGNC HGNC:33846 protein_coding YES CCDS34770.1 ENSP00000367355 A5YM69 UPI00002373BE NM_001003702.2 2/2 Pfam_domain:PF15441,hmmpanther:PTHR12845,hmmpanther:PTHR12845:SF2,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 4 204 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 144187727 144187727 T C 1 0 0 0 0 0 0 0 1 1039 1606 56 5 5 ARHGEF35 7 144187727 Silent SNP T C3N-02149_T 845789 144187727 15158246 242 28426 OR2A1 0 . GRCh38 7 144318564 144318564 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.440C>A p.Ser147Tyr p.S147Y ENST00000408951 1/1 215 199 16 204 204 0 varscan-mutect OR2A1,missense_variant,p.Ser147Tyr,ENST00000408951,NM_001005287.1;OR2A1-AS1,intron_variant,,ENST00000463561,;OR2A1-AS1,intron_variant,,ENST00000486094,;OR2A1-AS1,intron_variant,,ENST00000476560,;OR2A1-AS1,intron_variant,,ENST00000487102,;OR2A1-AS1,intron_variant,,ENST00000475089,;OR2A1-AS1,intron_variant,,ENST00000478806,;OR2A1-AS1,intron_variant,,ENST00000488041,;OR2A1-AS1,intron_variant,,ENST00000496968,;OR2A1-AS1,intron_variant,,ENST00000489488,;OR2A1-AS1,intron_variant,,ENST00000467944,;OR2A1-AS1,intron_variant,,ENST00000461843,;OR2A1-AS1,intron_variant,,ENST00000493539,;OR2A1-AS1,downstream_gene_variant,,ENST00000478925,; A ENST00000408951 Transcript missense_variant 440/933 440/933 147/310 S/Y tCc/tAc 1 1 OR2A1 HGNC HGNC:8229 protein_coding YES CCDS43673.1 ENSP00000386175 Q8NGT9 UPI0000041DF3 NM_001005287.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF115,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS rs1433752498 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 144318564 144318564 C A 1 0 0 0 0 1 0 0 0 11051 855 30 2 2 OR2A1 7 144318564 Missense_Mutation SNP C C3N-02149_T 130837 144318564 15027409 243 28427 GIMAP8 0 . GRCh38 7 150477608 150477608 + Frame_Shift_Del DEL C C - C3N-02149_T C3N-02149_N C C c.1828delC p.Gln610ArgfsTer5 p.Q610Rfs*5 ENST00000307271 5/5 352 290 62 430 430 0 sindel-varindel-pindel GIMAP8,frameshift_variant,p.Gln610ArgfsTer5,ENST00000307271,NM_175571.3; - ENST00000307271 Transcript frameshift_variant 2400/4184 1826/1998 609/665 A/X gCc/gc COSM1208183,COSM3635964 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 5/5 PROSITE_profiles:PS51720,hmmpanther:PTHR10903:SF73,hmmpanther:PTHR10903,Gene3D:3.40.50.300,Pfam_domain:PF04548 1,1 HIGH 1 deletion 1 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 150477608 150477608 C - 1 0 1 0 1 0 0 0 0 6265 739 26 0 0 GIMAP8 7 150477608 Frame_Shift_Del DEL C C3N-02149_T 6159044 150477608 8868365 244 28428 NOS3 0 . GRCh38 7 150999017 150999017 + Silent SNP A A T rs780269670 C3N-02149_T C3N-02149_N A A c.888A>T p.= p.P296P ENST00000297494 8/27 254 208 46 252 252 0 strelka-varscan-mutect NOS3,synonymous_variant,p.=,ENST00000297494,NM_000603.4;NOS3,synonymous_variant,p.=,ENST00000461406,;NOS3,synonymous_variant,p.=,ENST00000484524,NM_001160111.1;NOS3,synonymous_variant,p.=,ENST00000467517,NM_001160109.1,NM_001160110.1;NOS3,upstream_gene_variant,,ENST00000460603,; T ENST00000297494 Transcript synonymous_variant 1245/4388 888/3612 296/1203 P ccA/ccT rs780269670 1 1 NOS3 HGNC HGNC:7876 protein_coding YES CCDS5912.1 ENSP00000297494 P29474 UPI000013E417 NM_000603.4 8/27 Low_complexity_(Seg):seg,Pfam_domain:PF02898,PIRSF_domain:PIRSF000333,Superfamily_domains:SSF56512 LOW 1 SNV 1 1 PASS rs780269670 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 150999017 150999017 A T 1 0 0 0 0 0 0 0 1 10589 175 7 4 4 NOS3 7 150999017 Silent SNP A C3N-02149_T 521409 150999017 8346956 245 28429 XRCC2 0 . GRCh38 7 152649279 152649279 + Missense_Mutation SNP T T A rs753457121 C3N-02149_T C3N-02149_N T T c.206A>T p.Lys69Ile p.K69I ENST00000359321 3/3 185 159 26 222 222 0 strelka-varscan-mutect XRCC2,missense_variant,p.Lys69Ile,ENST00000359321,NM_005431.1;XRCC2,non_coding_transcript_exon_variant,,ENST00000495707,; A ENST00000359321 Transcript missense_variant 292/3067 206/843 69/280 K/I aAa/aTa rs753457121 1 -1 XRCC2 HGNC HGNC:12829 protein_coding YES CCDS5933.1 ENSP00000352271 O43543 UPI000000D9C8 NM_005431.1 deleterious(0.03) 3/3 Gene3D:3.40.50.300,Pfam_domain:PF08423,PROSITE_profiles:PS50162,hmmpanther:PTHR22942,hmmpanther:PTHR22942:SF44,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs753457121 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 152649279 152649279 T A 1 0 0 0 0 1 0 0 0 18012 1841 64 4 4 XRCC2 7 152649279 Missense_Mutation SNP T C3N-02149_T 1650262 152649279 6696694 246 28430 PTPRN2 0 . GRCh38 7 157595264 157595264 + Missense_Mutation SNP G G T rs750506325 C3N-02149_T C3N-02149_N G G c.2470C>A p.Pro824Thr p.P824T ENST00000389418 17/23 317 249 68 333 333 0 strelka-varscan-mutect PTPRN2,missense_variant,p.Pro795Thr,ENST00000389413,NM_130843.2;PTPRN2,missense_variant,p.Pro786Thr,ENST00000409483,NM_001308267.1;PTPRN2,missense_variant,p.Pro824Thr,ENST00000389418,NM_001308268.1,NM_002847.3;PTPRN2,missense_variant,p.Pro807Thr,ENST00000389416,NM_130842.2; T ENST00000389418 Transcript missense_variant 2480/4706 2470/3048 824/1015 P/T Ccc/Acc rs750506325 1 -1 PTPRN2 HGNC HGNC:9677 protein_coding YES CCDS5947.1 ENSP00000374069 Q92932 UPI000002E7C7 NM_001308268.1,NM_002847.3 deleterious(0) 17/23 Gene3D:3.90.190.10,Pfam_domain:PF00102,Prints_domain:PR00700,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF266,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 1 1 PASS rs750506325 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 157595264 157595264 G T 1 0 0 0 0 1 0 0 0 12962 1203 42 2 2 PTPRN2 7 157595264 Missense_Mutation SNP G C3N-02149_T 4945985 157595264 1750709 247 28431 DLGAP2 0 . GRCh38 8 1697158 1697158 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.2526C>A p.= p.A842A ENST00000612087 10/11 44 29 15 54 54 0 strelka-varscan-mutect DLGAP2,synonymous_variant,p.=,ENST00000612087,NM_001277161.1;DLGAP2,synonymous_variant,p.=,ENST00000520901,;DLGAP2,synonymous_variant,p.=,ENST00000637795,;DLGAP2,synonymous_variant,p.=,ENST00000421627,;DLGAP2,synonymous_variant,p.=,ENST00000637152,NM_004745.4; A ENST00000612087 Transcript synonymous_variant 2660/10088 2526/2886 842/961 A gcC/gcA 1 1 DLGAP2 HGNC HGNC:2906 protein_coding YES CCDS75689.1 ENSP00000484215 H0YBY6 UPI0002B8CE71 NM_001277161.1 10/11 hmmpanther:PTHR12353,hmmpanther:PTHR12353:SF3,Pfam_domain:PF03359 LOW 1 SNV 5 1 PASS rs1208403661 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 1697158 1697158 C A 1 0 0 0 0 0 0 0 1 4367 581 21 2 2 DLGAP2 8 1697158 Silent SNP C C3N-02149_T 1697158 143441478 248 28432 RP1L1 0 . GRCh38 8 10612743 10612743 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.1355G>C p.Ser452Thr p.S452T ENST00000382483 4/4 118 96 22 109 109 0 strelka-varscan-mutect RP1L1,missense_variant,p.Ser452Thr,ENST00000382483,NM_178857.5; G ENST00000382483 Transcript missense_variant 1579/7973 1355/7203 452/2400 S/T aGt/aCt 1 -1 RP1L1 HGNC HGNC:15946 protein_coding YES CCDS43708.1 ENSP00000371923 A6NKC6 UPI00001AF9CC NM_178857.5 deleterious(0.04) 4/4 hmmpanther:PTHR23005,hmmpanther:PTHR23005:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 10612743 10612743 C G 1 0 0 0 0 1 0 0 0 13773 565 20 4 4 RP1L1 8 10612743 Missense_Mutation SNP C C3N-02149_T 8915585 10612743 134525893 249 28433 SGCZ 0 . GRCh38 8 14237672 14237672 + Missense_Mutation SNP G G T rs528398080 C3N-02149_T C3N-02149_N G G c.344C>A p.Pro115Gln p.P115Q ENST00000382080 4/8 145 118 27 202 202 0 strelka-varscan-mutect SGCZ,missense_variant,p.Pro115Gln,ENST00000382080,NM_139167.2;SGCZ,missense_variant,p.Pro68Gln,ENST00000421524,; T ENST00000382080 Transcript missense_variant 1060/2234 344/939 115/312 P/Q cCg/cAg rs528398080,COSM3319473,COSM5699440 1 -1 SGCZ HGNC HGNC:14075 protein_coding YES CCDS5992.2 ENSP00000371512 Q96LD1 UPI00002339F6 NM_139167.2 deleterious(0.01) 4/8 Pfam_domain:PF04790,hmmpanther:PTHR12939,hmmpanther:PTHR12939:SF5 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs528398080 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 14237672 14237672 G T 1 0 0 0 0 1 0 0 0 14464 1116 39 1 1 SGCZ 8 14237672 Missense_Mutation SNP G C3N-02149_T 3624929 14237672 130900964 250 28434 ANK1 0 . GRCh38 8 41668296 41668296 + Missense_Mutation SNP C C A rs753132695 C3N-02149_T C3N-02149_N C C c.5488G>T p.Ala1830Ser p.A1830S ENST00000265709 40/43 261 199 62 353 353 0 strelka-varscan-mutect ANK1,missense_variant,p.Ala1789Ser,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Ala1789Ser,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Ala1830Ser,ENST00000265709,NM_001142446.1;ANK1,missense_variant,p.Ala949Ser,ENST00000520299,;ANK1,upstream_gene_variant,,ENST00000314214,NM_020478.4;ANK1,upstream_gene_variant,,ENST00000522543,NM_001142445.1;ANK1,upstream_gene_variant,,ENST00000522231,;ANK1,upstream_gene_variant,,ENST00000348036,NM_020480.4;ANK1,upstream_gene_variant,,ENST00000335651,;RP11-930P14.1,downstream_gene_variant,,ENST00000522388,;RP11-930P14.1,downstream_gene_variant,,ENST00000520418,;RP11-930P14.1,downstream_gene_variant,,ENST00000585088,;ANK1,non_coding_transcript_exon_variant,,ENST00000524227,;ANK1,downstream_gene_variant,,ENST00000518061,;ANK1,upstream_gene_variant,,ENST00000518715,; A ENST00000265709 Transcript missense_variant 5770/6379 5488/5694 1830/1897 A/S Gcc/Tcc rs753132695 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 tolerated_low_confidence(0.38) 40/43 hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs753132695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 41668296 41668296 C A 1 0 0 0 0 1 0 0 0 720 739 26 2 2 ANK1 8 41668296 Missense_Mutation SNP C C3N-02149_T 27430624 41668296 103470340 251 28435 PRKDC 0 . GRCh38 8 47799288 47799288 + Missense_Mutation SNP C C T rs55753561 C3N-02149_T C3N-02149_N C C c.10219G>A p.Ala3407Thr p.A3407T ENST00000314191 72/86 159 145 14 196 196 0 strelka-varscan-mutect PRKDC,missense_variant,p.Ala3407Thr,ENST00000314191,NM_006904.6;PRKDC,missense_variant,p.Ala3407Thr,ENST00000338368,NM_001081640.1; T ENST00000314191 Transcript missense_variant 10276/13509 10219/12387 3407/4128 A/T Gct/Act rs55753561 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 tolerated(0.15) 72/86 PROSITE_profiles:PS51189,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF68,Pfam_domain:PF02259 MODERATE 1 SNV 1 1 PASS rs55753561 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 47799288 47799288 C T 1 0 0 0 0 1 0 0 0 12654 797 28 3 3 PRKDC 8 47799288 Missense_Mutation SNP C C3N-02149_T 6130992 47799288 97339348 252 28436 SNTG1 0 . GRCh38 8 50449727 50449727 + Splice_Site SNP T T A novel C3N-02149_T C3N-02149_N T T c.277+2T>A p.X93_splice ENST00000522124 77 62 15 93 93 0 strelka-varscan-mutect SNTG1,splice_donor_variant,,ENST00000522124,NM_018967.3;SNTG1,splice_donor_variant,,ENST00000518864,NM_001287813.1;SNTG1,splice_donor_variant,,ENST00000517473,NM_001287814.1;SNTG1,downstream_gene_variant,,ENST00000523085,;SNTG1,splice_donor_variant,,ENST00000520825,; A ENST00000522124 Transcript splice_donor_variant -/3504 277/1554 93/517 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 6/18 HIGH 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 92 50449727 50449727 T A 1 0 0 0 0 0 0 1 0 15194 1652 57 4 4 SNTG1 8 50449727 Splice_Site SNP T C3N-02149_T 2650439 50449727 94688909 253 28437 PXDNL 0 . GRCh38 8 51408578 51408578 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.3046C>T p.His1016Tyr p.H1016Y ENST00000356297 17/23 248 219 29 305 305 0 strelka-varscan-mutect PXDNL,missense_variant,p.His1016Tyr,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.His135Tyr,ENST00000522933,;PXDNL,missense_variant,p.His282Tyr,ENST00000522628,; A ENST00000356297 Transcript missense_variant 3147/4805 3046/4392 1016/1463 H/Y Cac/Tac 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 51408578 51408578 G A 1 0 0 0 0 1 0 0 0 13002 1348 47 3 3 PXDNL 8 51408578 Missense_Mutation SNP G C3N-02149_T 958851 51408578 93730058 254 28438 XKR4 0 . GRCh38 8 55102686 55102686 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.198C>A p.Cys66Ter p.C66* ENST00000327381 1/3 31 26 5 38 38 0 strelka-varscan-mutect XKR4,stop_gained,p.Cys66Ter,ENST00000327381,NM_052898.1;XKR4,stop_gained,p.Cys66Ter,ENST00000622811,; A ENST00000327381 Transcript stop_gained 298/19880 198/1953 66/650 C/* tgC/tgA 1 1 XKR4 HGNC HGNC:29394 protein_coding YES CCDS34893.1 ENSP00000328326 Q5GH76 UPI000016098C NM_052898.1 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF14 HIGH 1 SNV 1 1 PASS . . 2 207 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 55102686 55102686 C A 1 0 0 0 0 0 1 0 0 17992 805 28 2 2 XKR4 8 55102686 Nonsense_Mutation SNP C C3N-02149_T 3694108 55102686 90035950 255 28439 DNAJC5B 0 . GRCh38 8 66099998 66099998 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.567A>T p.Lys189Asn p.K189N ENST00000276570 6/6 157 140 17 232 232 0 strelka-varscan-mutect DNAJC5B,missense_variant,p.Lys189Asn,ENST00000276570,NM_033105.4;DNAJC5B,non_coding_transcript_exon_variant,,ENST00000519330,; T ENST00000276570 Transcript missense_variant 854/1382 567/600 189/199 K/N aaA/aaT 1 1 DNAJC5B HGNC HGNC:24138 protein_coding YES CCDS6183.1 ENSP00000276570 Q9UF47 A0A024R7Z1 UPI0000050F10 NM_033105.4 tolerated_low_confidence(0.23) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 66099998 66099998 A T 1 0 0 0 0 1 0 0 0 4464 69 3 4 4 DNAJC5B 8 66099998 Missense_Mutation SNP A C3N-02149_T 10997312 66099998 79038638 256 28440 SLCO5A1 0 . GRCh38 8 69832103 69832103 + Silent SNP G G T rs760891283 C3N-02149_T C3N-02149_N G G c.571C>A p.= p.R191R ENST00000260126 2/10 330 266 64 357 357 0 strelka-varscan-mutect SLCO5A1,synonymous_variant,p.=,ENST00000260126,NM_030958.2;SLCO5A1,synonymous_variant,p.=,ENST00000524945,NM_001146008.1;SLCO5A1,synonymous_variant,p.=,ENST00000530307,NM_001146009.1;RP11-159H10.3,upstream_gene_variant,,ENST00000528800,;RP11-159H10.3,upstream_gene_variant,,ENST00000501104,;RP11-159H10.3,upstream_gene_variant,,ENST00000533300,;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000528658,;SLCO5A1,downstream_gene_variant,,ENST00000531422,;SLCO5A1,downstream_gene_variant,,ENST00000524703,;SLCO5A1,synonymous_variant,p.=,ENST00000526750,;SLCO5A1,non_coding_transcript_exon_variant,,ENST00000532388,; T ENST00000260126 Transcript synonymous_variant 1278/9076 571/2547 191/848 R Cgg/Agg rs760891283 1 -1 SLCO5A1 HGNC HGNC:19046 protein_coding YES CCDS6205.1 ENSP00000260126 Q9H2Y9 UPI0000140F53 NM_030958.2 2/10 PROSITE_profiles:PS50850,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF91,Pfam_domain:PF03137,Gene3D:1.20.1250.20,TIGRFAM_domain:TIGR00805,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS rs760891283 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 69832103 69832103 G T 1 0 0 0 0 0 0 0 1 15018 1115 39 1 1 SLCO5A1 8 69832103 Silent SNP G C3N-02149_T 3732105 69832103 75306533 257 28441 TCEB1 0 . GRCh38 8 73946808 73946808 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.161A>T p.Glu54Val p.E54V ENST00000622804 5/5 92 81 11 119 119 0 strelka-varscan-mutect TCEB1,missense_variant,p.Glu54Val,ENST00000622804,NM_001204862.1;TCEB1,missense_variant,p.Glu54Val,ENST00000518127,NM_001204860.1,NM_001204857.1;TCEB1,missense_variant,p.Glu54Val,ENST00000520242,NM_001204858.1,NM_005648.3,NM_001204859.1;TCEB1,missense_variant,p.Glu38Val,ENST00000520210,NM_001204864.1,NM_001204863.1;TCEB1,missense_variant,p.Glu54Val,ENST00000522337,;TCEB1,missense_variant,p.Glu54Val,ENST00000519487,;TCEB1,missense_variant,p.Glu54Val,ENST00000523815,NM_001204861.1;TCEB1,missense_variant,p.Glu54Val,ENST00000284811,;TCEB1,missense_variant,p.Glu54Val,ENST00000519082,;TCEB1,intron_variant,,ENST00000602840,; A ENST00000622804 Transcript missense_variant 306/1976 161/339 54/112 E/V gAg/gTg 1 -1 TCEB1 HGNC HGNC:11617 protein_coding YES CCDS34910.1 ENSP00000478121 Q15369 A0A024R7Y5 UPI000002921A NM_001204862.1 deleterious(0.01) 5/5 hmmpanther:PTHR20648,Gene3D:3.30.710.10,Pfam_domain:PF03931,SMART_domains:SM00512,Superfamily_domains:SSF54695 MODERATE 1 SNV 5 1 PASS . . 0 203 7 0 0 0 0 0 -19.99944 0.9999993 1 1 1 0 A 3 1 92 73946808 73946808 T A 1 0 0 0 0 1 0 0 0 16086 1551 54 4 4 TCEB1 8 73946808 Missense_Mutation SNP T C3N-02149_T 4114705 73946808 71191828 258 28442 PMP2 0 . GRCh38 8 81444934 81444934 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.129C>A p.= p.I43I ENST00000256103 2/4 187 167 20 235 235 0 strelka-varscan-mutect PMP2,synonymous_variant,p.=,ENST00000256103,NM_002677.3;PMP2,intron_variant,,ENST00000519260,;RP11-157I4.4,intron_variant,,ENST00000524085,; T ENST00000256103 Transcript synonymous_variant 266/3608 129/399 43/132 I atC/atA 1 -1 PMP2 HGNC HGNC:9117 protein_coding YES CCDS6229.1 ENSP00000256103 P02689 UPI000013CEEB NM_002677.3 2/4 hmmpanther:PTHR11955:SF64,hmmpanther:PTHR11955,Gene3D:2.40.128.20,Pfam_domain:PF00061,Superfamily_domains:SSF50814 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 81444934 81444934 G T 1 0 0 0 0 0 0 0 1 12245 1280 45 2 2 PMP2 8 81444934 Silent SNP G C3N-02149_T 7498126 81444934 63693702 259 28443 SDC2 0 . GRCh38 8 96608361 96608361 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.333A>T p.Lys111Asn p.K111N ENST00000302190 4/5 188 170 18 209 209 0 strelka-varscan-mutect SDC2,missense_variant,p.Lys111Asn,ENST00000302190,NM_002998.3;SDC2,missense_variant,p.Lys75Asn,ENST00000518385,;SDC2,missense_variant,p.Lys82Asn,ENST00000519914,;SDC2,missense_variant,p.Lys82Asn,ENST00000522911,;SDC2,missense_variant,p.Lys82Asn,ENST00000523877,;SDC2,missense_variant,p.Lys82Asn,ENST00000521590,; T ENST00000302190 Transcript missense_variant 1254/3759 333/606 111/201 K/N aaA/aaT 1 1 SDC2 HGNC HGNC:10659 protein_coding YES CCDS6272.1 ENSP00000307046 P34741 A0A024R9D1 UPI000013E7A4 NM_002998.3 tolerated(0.38) 4/5 hmmpanther:PTHR10915,hmmpanther:PTHR10915:SF6 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 96608361 96608361 A T 1 0 0 0 0 1 0 0 0 14224 69 3 4 4 SDC2 8 96608361 Missense_Mutation SNP A C3N-02149_T 15163427 96608361 48530275 260 28444 RIMS2 0 . GRCh38 8 103989359 103989359 + Silent SNP T T C rs766062874 C3N-02149_T C3N-02149_N T T c.2982T>C p.= p.N994N ENST00000504942 17/24 287 260 27 348 348 0 strelka-varscan-mutect RIMS2,synonymous_variant,p.=,ENST00000507740,NM_014677.4;RIMS2,synonymous_variant,p.=,ENST00000436393,;RIMS2,synonymous_variant,p.=,ENST00000504942,NM_001100117.2;RIMS2,synonymous_variant,p.=,ENST00000626043,;RIMS2,synonymous_variant,p.=,ENST00000408894,;RIMS2,synonymous_variant,p.=,ENST00000262231,NM_001282881.1;RIMS2,synonymous_variant,p.=,ENST00000632716,; C ENST00000504942 Transcript synonymous_variant 3121/4228 2982/4050 994/1349 N aaT/aaC rs766062874,COSM4640823,COSM4640824,COSM4640825,COSM4640826,COSM4640827 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 17/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 0,1,1,1,1,1 LOW 1 SNV 2 0,1,1,1,1,1 1 PASS rs766062874 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 103989359 103989359 T C 1 0 0 0 0 0 0 0 1 13543 1403 49 5 5 RIMS2 8 103989359 Silent SNP T C3N-02149_T 7380998 103989359 41149277 261 28445 CSMD3 0 . GRCh38 8 112638759 112638759 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.3463G>A p.Ala1155Thr p.A1155T ENST00000297405 21/71 496 418 78 575 575 0 strelka-varscan-mutect CSMD3,missense_variant,p.Ala1155Thr,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Ala1115Thr,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Ala1051Thr,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Ala495Thr,ENST00000339701,;MIR2053,upstream_gene_variant,,ENST00000459295,; T ENST00000297405 Transcript missense_variant 3708/13212 3463/11124 1155/3707 A/T Gct/Act 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 deleterious(0.05) 21/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 112638759 112638759 C T 1 0 0 0 0 1 0 0 0 3747 739 26 3 3 CSMD3 8 112638759 Missense_Mutation SNP C C3N-02149_T 8649400 112638759 32499877 262 28446 NSMCE2 0 . GRCh38 8 125357814 125357814 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.622G>T p.Ala208Ser p.A208S ENST00000287437 7/8 264 218 46 260 260 0 strelka-varscan-mutect NSMCE2,missense_variant,p.Ala208Ser,ENST00000287437,NM_173685.2;NSMCE2,missense_variant,p.Ala208Ser,ENST00000522563,;NSMCE2,missense_variant,p.Ala148Ser,ENST00000517315,;NSMCE2,downstream_gene_variant,,ENST00000517532,; T ENST00000287437 Transcript missense_variant 838/1195 622/744 208/247 A/S Gcc/Tcc 1 1 NSMCE2 HGNC HGNC:26513 protein_coding YES CCDS6356.1 ENSP00000287437 Q96MF7 A0A024R9J6 UPI0000039EC8 NM_173685.2 tolerated(0.06) 7/8 PROSITE_profiles:PS51044,hmmpanther:PTHR21330,hmmpanther:PTHR21330:SF1,Pfam_domain:PF11789,Gene3D:3.30.40.10,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS rs1380066503 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 125357814 125357814 G T 1 0 0 0 0 1 0 0 0 10736 1217 42 2 2 NSMCE2 8 125357814 Missense_Mutation SNP G C3N-02149_T 12719055 125357814 19780822 263 28447 MYC 0 . GRCh38 8 127738759 127738759 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.542G>T p.Arg181Leu p.R181L ENST00000621592 2/3 114 98 16 95 95 0 strelka-varscan-mutect MYC,missense_variant,p.Arg181Leu,ENST00000621592,NM_002467.4;MYC,missense_variant,p.Arg181Leu,ENST00000613283,;MYC,missense_variant,p.Arg166Leu,ENST00000377970,;MYC,missense_variant,p.Arg180Leu,ENST00000524013,;MYC,missense_variant,p.Arg166Leu,ENST00000259523,;MYC,missense_variant,p.Arg180Leu,ENST00000517291,;MYC,downstream_gene_variant,,ENST00000520751,;CASC11,upstream_gene_variant,,ENST00000502463,;CASC11,upstream_gene_variant,,ENST00000518376,;CASC11,upstream_gene_variant,,ENST00000519071,; T ENST00000621592 Transcript missense_variant 1067/2366 542/1365 181/454 R/L cGc/cTc COSM4006841,COSM4006842 1 1 MYC HGNC HGNC:7553 protein_coding YES CCDS6359.2 ENSP00000478887 A0A087WUS5 UPI0000D624FF NM_002467.4 tolerated(0.31) 2/3 hmmpanther:PTHR11514,hmmpanther:PTHR11514:SF2,Pfam_domain:PF01056,PIRSF_domain:PIRSF001705 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1328542776 . 0 199 11 0 0 0 0 0 -20 0.9999549 1 1 1 0 T 3 4 92 127738759 127738759 G T 1 0 0 0 0 1 0 0 0 10016 1087 38 1 1 MYC 8 127738759 Missense_Mutation SNP G C3N-02149_T 2380945 127738759 17399877 264 28448 ZFAT 0 . GRCh38 8 134512483 134512483 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.3353C>T p.Ser1118Phe p.S1118F ENST00000377838 14/16 144 128 16 157 157 0 strelka-varscan-mutect ZFAT,missense_variant,p.Ser1106Phe,ENST00000520727,NM_001029939.3,NM_001289394.1;ZFAT,missense_variant,p.Ser1118Phe,ENST00000377838,NM_020863.3;ZFAT,missense_variant,p.Ser1106Phe,ENST00000429442,;ZFAT,missense_variant,p.Ser1106Phe,ENST00000520214,NM_001167583.2;ZFAT,missense_variant,p.Ser1056Phe,ENST00000523399,NM_001174157.1;ZFAT,intron_variant,,ENST00000520356,NM_001174158.1;ZFAT,upstream_gene_variant,,ENST00000521673,;ZFAT,downstream_gene_variant,,ENST00000517307,;ZFAT,upstream_gene_variant,,ENST00000522723,;ZFAT,3_prime_UTR_variant,,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000518408,; A ENST00000377838 Transcript missense_variant 3528/4597 3353/3732 1118/1243 S/F tCt/tTt 1 -1 ZFAT HGNC HGNC:19899 protein_coding YES CCDS47924.1 ENSP00000367069 Q9P243 UPI0000210061 NM_020863.3 deleterious(0.01) 14/16 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 134512483 134512483 G A 1 0 0 0 0 1 0 0 0 18209 942 33 3 3 ZFAT 8 134512483 Missense_Mutation SNP G C3N-02149_T 6773724 134512483 10626153 265 28449 GML 0 . GRCh38 8 142841206 142841206 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.162C>A p.= p.R54R ENST00000220940 3/4 180 161 19 205 205 0 strelka-varscan-mutect GML,synonymous_variant,p.=,ENST00000220940,NM_002066.2;GML,synonymous_variant,p.=,ENST00000522728,; A ENST00000220940 Transcript synonymous_variant 252/723 162/477 54/158 R cgC/cgA 1 1 GML HGNC HGNC:4375 protein_coding YES CCDS6391.1 ENSP00000220940 Q99445 UPI000012B8B1 NM_002066.2 3/4 hmmpanther:PTHR15049,hmmpanther:PTHR15049:SF2,PROSITE_patterns:PS00983,Gene3D:2.10.60.10,SMART_domains:SM00134,Superfamily_domains:SSF57302 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 142841206 142841206 C A 1 0 0 0 0 0 0 0 1 6371 784 28 2 2 GML 8 142841206 Silent SNP C C3N-02149_T 8328723 142841206 2297430 266 28450 WDR97 0 . GRCh38 8 144115547 144115547 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.4284G>T p.Trp1428Cys p.W1428C ENST00000323662 22/24 83 69 14 107 107 0 strelka-varscan-mutect WDR97,missense_variant,p.Trp1428Cys,ENST00000323662,;WDR97,downstream_gene_variant,,ENST00000533108,;WDR97,3_prime_UTR_variant,,ENST00000534167,;WDR97,non_coding_transcript_exon_variant,,ENST00000528691,;WDR97,non_coding_transcript_exon_variant,,ENST00000525150,;WDR97,non_coding_transcript_exon_variant,,ENST00000529209,; T ENST00000323662 Transcript missense_variant 4309/6916 4284/4869 1428/1622 W/C tgG/tgT 1 1 WDR97 HGNC HGNC:26959 protein_coding YES ENSP00000320648 A6NE52 UPI000173AA02 tolerated_low_confidence(0.2) 22/24 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 144115547 144115547 G T 1 0 0 0 0 1 0 0 0 17897 1241 43 2 2 WDR97 8 144115547 Missense_Mutation SNP G C3N-02149_T 1274341 144115547 1023089 267 28451 GLIS3 0 . GRCh38 9 4118232 4118232 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1246G>T p.Gly416Cys p.G416C ENST00000381971 4/11 112 68 44 145 145 0 strelka-varscan-mutect GLIS3,missense_variant,p.Gly261Cys,ENST00000324333,NM_152629.3;GLIS3,missense_variant,p.Gly416Cys,ENST00000381971,NM_001042413.1;GLIS3,downstream_gene_variant,,ENST00000477901,;GLIS3,downstream_gene_variant,,ENST00000481827,;GLIS3,downstream_gene_variant,,ENST00000462164,;GLIS3,downstream_gene_variant,,ENST00000478315,;GLIS3,downstream_gene_variant,,ENST00000478844,;GLIS3,downstream_gene_variant,,ENST00000490709,;GLIS3,downstream_gene_variant,,ENST00000473846,;GLIS3,upstream_gene_variant,,ENST00000467497,;GLIS3,downstream_gene_variant,,ENST00000491889,; A ENST00000381971 Transcript missense_variant 1840/3961 1246/2793 416/930 G/C Ggc/Tgc 1 -1 GLIS3 HGNC HGNC:28510 protein_coding YES CCDS43784.1 ENSP00000371398 Q8NEA6 UPI0000DA4C5E NM_001042413.1 tolerated(0.19) 4/11 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF83 MODERATE 1 SNV 5 1 PASS rs1161129948 . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 4118232 4118232 C A 1 0 0 0 0 1 0 0 0 6325 594 21 2 2 GLIS3 9 4118232 Missense_Mutation SNP C C3N-02149_T 4118232 134276485 268 28452 BAG1 0 . GRCh38 9 33258930 33258930 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.767G>T p.Gly256Val p.G256V ENST00000472232 4/7 206 192 14 196 195 1 strelka-mutect BAG1,missense_variant,p.Gly256Val,ENST00000472232,NM_004323.5;BAG1,missense_variant,p.Gly256Val,ENST00000634734,;BAG1,missense_variant,p.Gly141Val,ENST00000379704,NM_001172415.1;BAG1,missense_variant,p.Gly147Val,ENST00000473781,;BAG1,missense_variant,p.Gly46Val,ENST00000473464,;BAG1,downstream_gene_variant,,ENST00000635077,;BAG1,downstream_gene_variant,,ENST00000488499,;BAG1,non_coding_transcript_exon_variant,,ENST00000467389,;BAG1,upstream_gene_variant,,ENST00000493917,;BAG1,3_prime_UTR_variant,,ENST00000379707,;BAG1,non_coding_transcript_exon_variant,,ENST00000379701,;BAG1,upstream_gene_variant,,ENST00000468274,; A ENST00000472232 Transcript missense_variant 854/3867 767/1038 256/345 G/V gGa/gTa 1 -1 BAG1 HGNC HGNC:937 protein_coding YES CCDS35004.1 ENSP00000420514 J3QTA2 UPI000013C843 NM_004323.5 deleterious(0) 4/7 PROSITE_profiles:PS51035,hmmpanther:PTHR12329,hmmpanther:PTHR12329:SF16,Pfam_domain:PF02179,Gene3D:1.20.58.120,SMART_domains:SM00264,Superfamily_domains:SSF63491,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 33258930 33258930 C A 1 0 0 0 0 1 0 0 0 1444 855 30 2 2 BAG1 9 33258930 Missense_Mutation SNP C C3N-02149_T 29140698 33258930 105135787 269 28453 FAM205A 0 . GRCh38 9 34726978 34726978 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.262C>A p.Leu88Ile p.L88I ENST00000378788 4/4 129 85 44 121 121 0 strelka-varscan-mutect FAM205A,missense_variant,p.Leu88Ile,ENST00000378788,NM_001141917.1; T ENST00000378788 Transcript missense_variant 302/4225 262/4008 88/1335 L/I Ctt/Att 1 -1 FAM205A HGNC HGNC:41911 protein_coding YES CCDS55305.1 ENSP00000417711 Q6ZU69 UPI00017EE92B NM_001141917.1 tolerated(0.07) 4/4 hmmpanther:PTHR21859:SF15,hmmpanther:PTHR21859,Pfam_domain:PF15371 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 34726978 34726978 G T 1 0 0 0 0 1 0 0 0 5386 971 34 2 2 FAM205A 9 34726978 Missense_Mutation SNP G C3N-02149_T 1468048 34726978 103667739 270 28454 NTRK2 0 . GRCh38 9 84727734 84727734 + Nonsense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.934A>T p.Lys312Ter p.K312* ENST00000277120 9/19 305 244 61 463 463 0 strelka-varscan-mutect NTRK2,stop_gained,p.Lys312Ter,ENST00000277120,;NTRK2,stop_gained,p.Lys312Ter,ENST00000304053,NM_001018065.2;NTRK2,stop_gained,p.Lys312Ter,ENST00000376208,NM_001018066.2;NTRK2,stop_gained,p.Lys312Ter,ENST00000395882,NM_001291937.1,NM_001007097.2;NTRK2,stop_gained,p.Lys312Ter,ENST00000359847,;NTRK2,stop_gained,p.Lys312Ter,ENST00000376214,NM_006180.4;NTRK2,stop_gained,p.Lys312Ter,ENST00000376213,;NTRK2,stop_gained,p.Lys312Ter,ENST00000323115,NM_001018064.2; T ENST00000277120 Transcript stop_gained 1417/8633 934/2517 312/838 K/* Aaa/Taa 1 1 NTRK2 HGNC HGNC:8032 protein_coding YES CCDS6671.1 ENSP00000277120 Q16620 A0A024R230 UPI000006FA0D 9/19 Gene3D:2.60.40.10,Pfam_domain:PF07679,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF136,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 84727734 84727734 A T 1 0 0 0 0 0 1 0 0 10773 131 5 4 4 NTRK2 9 84727734 Nonsense_Mutation SNP A C3N-02149_T 50000756 84727734 53666983 271 28455 SPATA31E1 0 . GRCh38 9 87885039 87885039 + Silent SNP G G T rs754824104 C3N-02149_T C3N-02149_N G G c.552G>T p.= p.P184P ENST00000325643 4/4 274 225 49 317 317 0 strelka-varscan-mutect SPATA31E1,synonymous_variant,p.=,ENST00000325643,NM_178828.4; T ENST00000325643 Transcript synonymous_variant 618/4478 552/4338 184/1445 P ccG/ccT rs754824104,COSM5561783 1 1 SPATA31E1 HGNC HGNC:26672 protein_coding YES CCDS6676.1 ENSP00000322640 Q6ZUB1 UPI000036764A NM_178828.4 4/4 Pfam_domain:PF15371,hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF19,Low_complexity_(Seg):seg 0,1 LOW 1 SNV 1 0,1 1 PASS rs754824104 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 87885039 87885039 G T 1 0 0 0 0 0 0 0 1 15350 1132 40 1 1 SPATA31E1 9 87885039 Silent SNP G C3N-02149_T 3157305 87885039 50509678 272 28456 MFSD14C 0 . GRCh38 9 96949569 96949569 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.381G>T p.Met127Ile p.M127I ENST00000602917 4/5 127 103 24 171 171 0 strelka-varscan-mutect MFSD14C,missense_variant,p.Met127Ile,ENST00000637864,;MFSD14C,missense_variant,p.Met127Ile,ENST00000602917,;MFSD14C,missense_variant,p.Met127Ile,ENST00000375223,;MFSD14C,non_coding_transcript_exon_variant,,ENST00000506067,;MFSD14C,non_coding_transcript_exon_variant,,ENST00000637076,;MFSD14C,non_coding_transcript_exon_variant,,ENST00000637811,;MFSD14C,non_coding_transcript_exon_variant,,ENST00000637099,; A ENST00000602917 Transcript missense_variant 595/786 381/453 127/150 M/I atG/atT 1 -1 MFSD14C HGNC HGNC:23672 protein_coding YES ENSP00000473444 R4GN14 UPI00003745A2 deleterious(0.01) 4/5 PROSITE_profiles:PS50850,hmmpanther:PTHR23504,hmmpanther:PTHR23504:SF32,Pfam_domain:PF07690,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1170081413 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 96949569 96949569 C A 1 0 0 0 0 1 0 0 0 9486 826 29 2 2 MFSD14C 9 96949569 Missense_Mutation SNP C C3N-02149_T 9064530 96949569 41445148 273 28457 OR13C2 0 . GRCh38 9 104605226 104605226 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.402C>T p.= p.I134I ENST00000542196 1/1 194 172 22 290 290 0 varscan-mutect OR13C2,synonymous_variant,p.=,ENST00000542196,NM_001004481.1; A ENST00000542196 Transcript synonymous_variant 402/957 402/957 134/318 I atC/atT 1 -1 OR13C2 HGNC HGNC:14701 protein_coding YES CCDS35092.1 ENSP00000438815 Q8NGS9 A0A126GWR7 UPI0000041B29 NM_001004481.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF279,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 104605226 104605226 G A 1 0 0 0 0 0 0 0 1 11010 1280 45 3 3 OR13C2 9 104605226 Silent SNP G C3N-02149_T 7655657 104605226 33789491 274 28458 OR13C9 0 . GRCh38 9 104617803 104617803 + Silent SNP G G A C3N-02149_T C3N-02149_N G G c.402C>T p.= p.I134I ENST00000259362 1/1 184 148 36 211 211 0 strelka-varscan-mutect OR13C9,synonymous_variant,p.=,ENST00000259362,NM_001001956.1; A ENST00000259362 Transcript synonymous_variant 402/957 402/957 134/318 I atC/atT COSM3847248 1 -1 OR13C9 HGNC HGNC:15104 protein_coding YES CCDS35093.1 ENSP00000259362 Q8NGT0 UPI0000041D56 NM_001001956.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF23,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00245 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 104617803 104617803 G A 1 0 0 0 0 0 0 0 1 11015 1280 45 3 3 OR13C9 9 104617803 Silent SNP G C3N-02149_T 12577 104617803 33776914 275 28459 TRAF1 0 . GRCh38 9 120913609 120913609 + Missense_Mutation SNP C C T C3N-02149_T C3N-02149_N C C c.424G>A p.Glu142Lys p.E142K ENST00000373887 5/8 144 117 27 185 185 0 strelka-varscan-mutect TRAF1,missense_variant,p.Glu142Lys,ENST00000373887,NM_005658.4;TRAF1,missense_variant,p.Glu142Lys,ENST00000540010,NM_001190945.1;TRAF1,missense_variant,p.Glu20Lys,ENST00000546084,NM_001190947.1; T ENST00000373887 Transcript missense_variant 2870/6324 424/1251 142/416 E/K Gag/Aag COSM752830 1 -1 TRAF1 HGNC HGNC:12031 protein_coding YES CCDS6825.1 ENSP00000362994 Q13077 UPI0000001079 NM_005658.4 tolerated(0.39) 5/8 PIRSF_domain:PIRSF015614,hmmpanther:PTHR10131,hmmpanther:PTHR10131:SF29 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 120913609 120913609 C T 1 0 0 0 0 1 0 0 0 16920 864 30 3 3 TRAF1 9 120913609 Missense_Mutation SNP C C3N-02149_T 16295806 120913609 17481108 276 28460 CRB2 0 . GRCh38 9 123370676 123370676 + Silent SNP T T G novel C3N-02149_T C3N-02149_N T T c.1623T>G p.= p.P541P ENST00000373631 7/13 238 199 39 304 304 0 strelka-varscan-mutect CRB2,synonymous_variant,p.=,ENST00000373631,NM_173689.6;CRB2,synonymous_variant,p.=,ENST00000359999,;CRB2,synonymous_variant,p.=,ENST00000460253,; G ENST00000373631 Transcript synonymous_variant 1624/5550 1623/3858 541/1285 P ccT/ccG 1 1 CRB2 HGNC HGNC:18688 protein_coding YES CCDS6852.2 ENSP00000362734 Q5IJ48 UPI000022D9DE NM_173689.6 7/13 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR24043,hmmpanther:PTHR24043:SF1,SMART_domains:SM00282,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 123370676 123370676 T G 1 0 0 0 0 0 0 0 1 3649 1567 55 5 5 CRB2 9 123370676 Silent SNP T C3N-02149_T 2457067 123370676 15024041 277 28461 ANGPTL2 0 . GRCh38 9 127089068 127089068 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.1353C>A p.= p.V451V ENST00000373425 5/5 434 395 39 579 579 0 strelka-varscan-mutect ANGPTL2,synonymous_variant,p.=,ENST00000373425,NM_012098.2;ANGPTL2,synonymous_variant,p.=,ENST00000373417,;RALGPS1,intron_variant,,ENST00000259351,NM_014636.2;RALGPS1,intron_variant,,ENST00000373434,NM_001190728.1;RALGPS1,intron_variant,,ENST00000424082,NM_001322320.1,NM_001190729.1;RALGPS1,intron_variant,,ENST00000394022,;RALGPS1,intron_variant,,ENST00000373436,NM_001190730.1; T ENST00000373425 Transcript synonymous_variant 1971/3707 1353/1482 451/493 V gtC/gtA 1 -1 ANGPTL2 HGNC HGNC:490 protein_coding YES CCDS6868.1 ENSP00000362524 Q9UKU9 A0A024R868 UPI0000049E07 NM_012098.2 5/5 PROSITE_profiles:PS51406,hmmpanther:PTHR19143:SF24,hmmpanther:PTHR19143,Gene3D:4.10.530.10,Pfam_domain:PF00147,SMART_domains:SM00186,Superfamily_domains:SSF56496 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 127089068 127089068 G T 1 0 0 0 0 0 0 0 1 712 929 33 2 2 ANGPTL2 9 127089068 Silent SNP G C3N-02149_T 3718392 127089068 11305649 278 28462 SLC27A4 0 . GRCh38 9 128353416 128353416 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.1199T>G p.Val400Gly p.V400G ENST00000300456 9/13 321 259 62 364 364 0 strelka-varscan-mutect SLC27A4,missense_variant,p.Val400Gly,ENST00000300456,NM_005094.3;SLC27A4,intron_variant,,ENST00000372870,; G ENST00000300456 Transcript missense_variant,splice_region_variant 1316/3028 1199/1932 400/643 V/G gTg/gGg 1 1 SLC27A4 HGNC HGNC:10998 protein_coding YES CCDS6899.1 ENSP00000300456 Q6P1M0 A0A024R8D2 UPI0000038E80 NM_005094.3 deleterious(0) 9/13 Pfam_domain:PF00501,hmmpanther:PTHR24096,hmmpanther:PTHR24096:SF145,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 128353416 128353416 T G 1 0 0 0 0 1 0 0 0 14798 1710 59 5 5 SLC27A4 9 128353416 Missense_Mutation SNP T C3N-02149_T 1264348 128353416 10041301 279 28463 QSOX2 0 . GRCh38 9 136245629 136245629 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.175G>T p.Gly59Cys p.G59C ENST00000358701 1/12 95 77 18 196 196 0 strelka-varscan-mutect QSOX2,missense_variant,p.Gly59Cys,ENST00000358701,NM_181701.3;CR392000.1,upstream_gene_variant,,ENST00000624770,;WI2-1959D15.1,downstream_gene_variant,,ENST00000584807,; A ENST00000358701 Transcript missense_variant 213/4530 175/2097 59/698 G/C Ggc/Tgc COSM5698047 1 -1 QSOX2 HGNC HGNC:30249 protein_coding YES CCDS35178.1 ENSP00000351536 Q6ZRP7 UPI00004A7AC1 NM_181701.3 deleterious(0.03) 1/12 PROSITE_profiles:PS51352,hmmpanther:PTHR22897,hmmpanther:PTHR22897:SF7,Low_complexity_(Seg):seg,Superfamily_domains:SSF52833 1 MODERATE 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 136245629 136245629 C A 1 0 0 0 0 1 0 0 0 13039 623 22 2 2 QSOX2 9 136245629 Missense_Mutation SNP C C3N-02149_T 7892213 136245629 2149088 280 28464 FAM166A 0 . GRCh38 9 137245192 137245192 + Nonsense_Mutation SNP G G T rs760075142 C3N-02149_T C3N-02149_N G G c.549C>A p.Tyr183Ter p.Y183* ENST00000344774 4/7 45 41 4 53 53 0 varscan-mutect FAM166A,stop_gained,p.Tyr183Ter,ENST00000344774,NM_001001710.2;FAM166A,stop_gained,p.Tyr210Ter,ENST00000484720,;TUBB4B,downstream_gene_variant,,ENST00000340384,NM_006088.5;FAM166A,non_coding_transcript_exon_variant,,ENST00000471784,;TUBB4B,downstream_gene_variant,,ENST00000604929,; T ENST00000344774 Transcript stop_gained 604/1124 549/954 183/317 Y/* taC/taA rs760075142 1 -1 FAM166A HGNC HGNC:33818 protein_coding YES CCDS35186.1 ENSP00000344729 Q6J272 UPI00003775FA NM_001001710.2 4/7 hmmpanther:PTHR22146,hmmpanther:PTHR22146:SF5 HIGH 1 SNV 1 1 PASS rs760075142 . 0 161 41 7 0 0 0 0 -7.989866 0.2875683 0 1 0 0 T 4 4 92 137245192 137245192 G T 1 0 0 0 0 0 1 0 0 5327 1256 44 2 2 FAM166A 9 137245192 Nonsense_Mutation SNP G C3N-02149_T 999563 137245192 1149525 281 28465 EHMT1 0 . GRCh38 9 137775187 137775187 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.1726G>A p.Glu576Lys p.E576K ENST00000460843 11/27 301 278 23 309 309 0 strelka-varscan-mutect EHMT1,missense_variant,p.Glu576Lys,ENST00000460843,NM_024757.4;EHMT1,missense_variant,p.Glu545Lys,ENST00000637161,;EHMT1,missense_variant,p.Glu538Lys,ENST00000636027,;EHMT1,missense_variant,p.Glu576Lys,ENST00000462484,NM_001145527.1;EHMT1,intron_variant,,ENST00000465566,;RP11-188C12.2,downstream_gene_variant,,ENST00000626603,;EHMT1,missense_variant,p.Glu195Lys,ENST00000462942,;EHMT1,3_prime_UTR_variant,,ENST00000637261,;EHMT1,3_prime_UTR_variant,,ENST00000371394,;EHMT1,3_prime_UTR_variant,,ENST00000638071,;EHMT1,upstream_gene_variant,,ENST00000637891,; A ENST00000460843 Transcript missense_variant 1792/5137 1726/3897 576/1298 E/K Gaa/Aaa 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 deleterious(0.02) 11/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 137775187 137775187 G A 1 0 0 0 0 1 0 0 0 4819 1291 45 3 3 EHMT1 9 137775187 Missense_Mutation SNP G C3N-02149_T 529995 137775187 619530 282 28466 AKR1C4 0 . GRCh38 10 5196936 5196936 + Silent SNP C C G novel C3N-02149_T C3N-02149_N C C c.69C>G p.= p.T23T ENST00000380448 3/11 281 254 27 323 323 0 strelka-varscan-mutect AKR1C4,synonymous_variant,p.=,ENST00000380448,;AKR1C4,synonymous_variant,p.=,ENST00000263126,NM_001818.3;AKR1C4,downstream_gene_variant,,ENST00000469875,; G ENST00000380448 Transcript synonymous_variant 322/1414 69/972 23/323 T acC/acG 1 1 AKR1C4 HGNC HGNC:387 protein_coding YES CCDS7064.1 ENSP00000369814 P17516 UPI000013D3B2 3/11 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF134,Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 5196936 5196936 C G 1 0 0 0 0 0 0 0 1 556 668 24 4 4 AKR1C4 10 5196936 Silent SNP C C3N-02149_T 5196936 128600486 283 28467 97 2 AKR1C4 0 . GRCh38 10 5196941 5196941 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.74C>A p.Ala25Glu p.A25E ENST00000380448 3/11 271 243 28 298 298 0 strelka-varscan-mutect AKR1C4,missense_variant,p.Ala25Glu,ENST00000380448,;AKR1C4,missense_variant,p.Ala25Glu,ENST00000263126,NM_001818.3;AKR1C4,downstream_gene_variant,,ENST00000469875,; A ENST00000380448 Transcript missense_variant 327/1414 74/972 25/323 A/E gCa/gAa 1 1 AKR1C4 HGNC HGNC:387 protein_coding YES CCDS7064.1 ENSP00000369814 P17516 UPI000013D3B2 deleterious(0.02) 3/11 hmmpanther:PTHR11732,hmmpanther:PTHR11732:SF134,Gene3D:3.20.20.100,Pfam_domain:PF00248,PIRSF_domain:PIRSF000097,Superfamily_domains:SSF51430 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 92 5196941 5196941 C A 1 0 0 0 0 1 0 0 0 556 710 25 2 2 AKR1C4 10 5196941 Missense_Mutation SNP C C3N-02149_T 5 5196941 128600481 284 28468 97 2 GDI2 0 . GRCh38 10 5786050 5786050 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.389G>T p.Ser130Ile p.S130I ENST00000380191 5/11 184 137 47 187 187 0 strelka-varscan-mutect GDI2,missense_variant,p.Ser130Ile,ENST00000380191,NM_001494.3;GDI2,missense_variant,p.Gly85Val,ENST00000380181,NM_001115156.1;GDI2,missense_variant,p.Ser120Ile,ENST00000456041,;GDI2,missense_variant,p.Ser94Ile,ENST00000418688,;GDI2,missense_variant,p.Ser108Ile,ENST00000608581,;GDI2,missense_variant,p.Ser134Ile,ENST00000380127,;GDI2,upstream_gene_variant,,ENST00000447751,; A ENST00000380191 Transcript missense_variant,splice_region_variant 680/2412 389/1338 130/445 S/I aGc/aTc 1 -1 GDI2 HGNC HGNC:4227 protein_coding YES CCDS7071.1 ENSP00000369538 P50395 Q6IAT1 UPI000012B39E NM_001494.3 deleterious(0) 5/11 hmmpanther:PTHR11787:SF1,hmmpanther:PTHR11787,Pfam_domain:PF00996,Gene3D:1.10.405.10,Superfamily_domains:SSF51905,Prints_domain:PR00892 MODERATE 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 5786050 5786050 C A 1 0 0 0 0 1 0 0 0 6194 753 26 2 2 GDI2 10 5786050 Missense_Mutation SNP C C3N-02149_T 589109 5786050 128011372 285 28469 RPP38 0 . GRCh38 10 15103518 15103518 + Silent SNP A A G novel C3N-02149_T C3N-02149_N A A c.204A>G p.= p.K68K ENST00000616640 2/2 303 235 68 353 353 0 strelka-varscan-mutect RPP38,synonymous_variant,p.=,ENST00000616640,NM_006414.4,NM_001265601.1;RPP38,synonymous_variant,p.=,ENST00000378197,NM_183005.4;RPP38,synonymous_variant,p.=,ENST00000378203,NM_001097590.2;RPP38,synonymous_variant,p.=,ENST00000378202,;RPP38,synonymous_variant,p.=,ENST00000441850,;RPP38,synonymous_variant,p.=,ENST00000378201,;NMT2,downstream_gene_variant,,ENST00000378165,NM_004808.2;NMT2,downstream_gene_variant,,ENST00000378150,NM_001308295.1;NMT2,non_coding_transcript_exon_variant,,ENST00000466201,;RPP38,intron_variant,,ENST00000451677,;NMT2,downstream_gene_variant,,ENST00000486786,; G ENST00000616640 Transcript synonymous_variant 801/1537 204/852 68/283 K aaA/aaG 1 1 RPP38 HGNC HGNC:30329 protein_coding YES CCDS7108.1 ENSP00000478982 P78345 UPI000006F1AE NM_006414.4,NM_001265601.1 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR21596 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 15103518 15103518 A G 1 0 0 0 0 0 0 0 1 13867 11 1 5 5 RPP38 10 15103518 Silent SNP A C3N-02149_T 9317468 15103518 118693904 286 28470 TRDMT1 0 . GRCh38 10 17160360 17160360 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.404A>C p.Gln135Pro p.Q135P ENST00000377799 6/11 160 136 24 165 164 1 strelka-varscan-mutect TRDMT1,missense_variant,p.Gln135Pro,ENST00000377799,NM_004412.5;TRDMT1,missense_variant,p.Gln68Pro,ENST00000313936,;TRDMT1,missense_variant,p.Gln93Pro,ENST00000525762,;TRDMT1,synonymous_variant,p.=,ENST00000436968,;TRDMT1,intron_variant,,ENST00000488990,;TRDMT1,non_coding_transcript_exon_variant,,ENST00000452380,;TRDMT1,3_prime_UTR_variant,,ENST00000354631,;TRDMT1,3_prime_UTR_variant,,ENST00000495022,;TRDMT1,3_prime_UTR_variant,,ENST00000424636,; G ENST00000377799 Transcript missense_variant 452/3527 404/1176 135/391 Q/P cAa/cCa 1 -1 TRDMT1 HGNC HGNC:2977 protein_coding YES CCDS7114.1 ENSP00000367030 O14717 Q6ICS7 UPI0000129698 NM_004412.5 deleterious(0.02) 6/11 Gene3D:3.40.50.150,Pfam_domain:PF00145,PROSITE_profiles:PS51679,hmmpanther:PTHR10629,Superfamily_domains:SSF53335,TIGRFAM_domain:TIGR00675 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 17160360 17160360 T G 1 0 0 0 0 1 0 0 0 16956 1812 63 5 5 TRDMT1 10 17160360 Missense_Mutation SNP T C3N-02149_T 2056842 17160360 116637062 287 28471 ST8SIA6 0 . GRCh38 10 17321330 17321330 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.745G>T p.Glu249Ter p.E249* ENST00000377602 8/8 144 126 18 138 138 0 strelka-varscan-mutect ST8SIA6,stop_gained,p.Glu249Ter,ENST00000377602,NM_001004470.1;ST8SIA6,stop_gained,p.Glu70Ter,ENST00000440449,; A ENST00000377602 Transcript stop_gained 820/2276 745/1197 249/398 E/* Gaa/Taa 1 -1 ST8SIA6 HGNC HGNC:23317 protein_coding YES CCDS31158.1 ENSP00000366827 P61647 UPI0000359594 NM_001004470.1 8/8 hmmpanther:PTHR11987:SF29,hmmpanther:PTHR11987,Pfam_domain:PF00777,PIRSF_domain:PIRSF005557 HIGH 1 SNV 1 1 PASS rs1420671764 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 17321330 17321330 C A 1 0 0 0 0 0 1 0 0 15614 864 30 2 2 ST8SIA6 10 17321330 Nonsense_Mutation SNP C C3N-02149_T 160970 17321330 116476092 288 28472 SLC39A12 0 . GRCh38 10 17987575 17987575 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1193G>T p.Arg398Met p.R398M ENST00000377369 7/13 361 285 76 395 395 0 strelka-varscan-mutect SLC39A12,missense_variant,p.Arg398Met,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Arg398Met,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Arg398Met,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Arg264Met,ENST00000539911,NM_001282734.1; T ENST00000377369 Transcript missense_variant 1466/2808 1193/2076 398/691 R/M aGg/aTg 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 tolerated(0.09) 7/13 hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 17987575 17987575 G T 1 0 0 0 0 1 0 0 0 14893 1000 35 2 2 SLC39A12 10 17987575 Missense_Mutation SNP G C3N-02149_T 666245 17987575 115809847 289 28473 SLC39A12 0 . GRCh38 10 17995695 17995695 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.1573G>A p.Gly525Ser p.G525S ENST00000377369 10/13 239 181 58 257 256 1 strelka-varscan-mutect SLC39A12,missense_variant,p.Gly525Ser,ENST00000377369,NM_001145195.1;SLC39A12,missense_variant,p.Gly524Ser,ENST00000377371,NM_001282733.1;SLC39A12,missense_variant,p.Gly488Ser,ENST00000377374,NM_152725.3;SLC39A12,missense_variant,p.Gly391Ser,ENST00000539911,NM_001282734.1; A ENST00000377369 Transcript missense_variant 1846/2808 1573/2076 525/691 G/S Ggc/Agc 1 1 SLC39A12 HGNC HGNC:20860 protein_coding YES CCDS44362.1 ENSP00000366586 Q504Y0 UPI00004044FC NM_001145195.1 tolerated(0.59) 10/13 hmmpanther:PTHR12191:SF4,hmmpanther:PTHR12191,Pfam_domain:PF02535 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 17995695 17995695 G A 1 0 0 0 0 1 0 0 0 14893 1000 35 3 3 SLC39A12 10 17995695 Missense_Mutation SNP G C3N-02149_T 8120 17995695 115801727 290 28474 MALRD1 0 . GRCh38 10 19491566 19491566 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.5079G>T p.= p.R1693R ENST00000454679 30/40 311 267 44 373 373 0 strelka-varscan-mutect MALRD1,synonymous_variant,p.=,ENST00000454679,NM_001142308.2;MALRD1,synonymous_variant,p.=,ENST00000377266,;MALRD1,synonymous_variant,p.=,ENST00000377265,;MALRD1,non_coding_transcript_exon_variant,,ENST00000492202,;HMGN1P20,downstream_gene_variant,,ENST00000411849,;RP11-265G8.3,upstream_gene_variant,,ENST00000427935,; T ENST00000454679 Transcript synonymous_variant 5247/6880 5079/6471 1693/2156 R cgG/cgT 1 1 MALRD1 HGNC HGNC:24331 protein_coding YES CCDS73071.1 ENSP00000412763 Q5VYJ5 UPI000387C99A NM_001142308.2 30/40 PROSITE_profiles:PS50068,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF86,Gene3D:4.10.400.10,Pfam_domain:PF00057,SMART_domains:SM00192,Superfamily_domains:SSF57424 LOW 1 SNV 1 1 PASS . . 0 202 0 3 5 0 0 0 -18.85647 0.5282921 1 1 1 0 T 2 4 92 19491566 19491566 G T 1 0 0 0 0 0 0 0 1 9121 1219 43 2 2 MALRD1 10 19491566 Silent SNP G C3N-02149_T 1495871 19491566 114305856 291 28475 PLXDC2 0 . GRCh38 10 20001964 20001964 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.302A>T p.Gln101Leu p.Q101L ENST00000377252 2/14 356 300 56 367 366 1 strelka-varscan-mutect PLXDC2,missense_variant,p.Gln101Leu,ENST00000377252,NM_032812.8;PLXDC2,missense_variant,p.Gln101Leu,ENST00000377242,NM_001282736.1; T ENST00000377252 Transcript missense_variant 1143/12468 302/1590 101/529 Q/L cAg/cTg 1 1 PLXDC2 HGNC HGNC:21013 protein_coding YES CCDS7132.1 ENSP00000366460 Q6UX71 UPI0000048F2C NM_032812.8 tolerated(0.41) 2/14 hmmpanther:PTHR13055:SF11,hmmpanther:PTHR13055 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 20001964 20001964 A T 1 0 0 0 0 1 0 0 0 12224 188 7 4 4 PLXDC2 10 20001964 Missense_Mutation SNP A C3N-02149_T 510398 20001964 113795458 292 28476 ZNF438 0 . GRCh38 10 30849382 30849382 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1023G>T p.Lys341Asn p.K341N ENST00000442986 7/8 344 272 72 354 353 1 strelka-varscan-mutect ZNF438,missense_variant,p.Lys331Asn,ENST00000452305,NM_001143770.1,NM_001143771.1;ZNF438,missense_variant,p.Lys292Asn,ENST00000538351,NM_001143769.1;ZNF438,missense_variant,p.Lys341Asn,ENST00000442986,NM_182755.2;ZNF438,missense_variant,p.Lys331Asn,ENST00000331737,;ZNF438,missense_variant,p.Lys341Asn,ENST00000436087,NM_001143766.1,NM_001143768.1;ZNF438,missense_variant,p.Lys341Asn,ENST00000361310,;ZNF438,missense_variant,p.Lys341Asn,ENST00000413025,NM_001143767.1;ZNF438,5_prime_UTR_variant,,ENST00000375311,;ZNF438,intron_variant,,ENST00000609683,; A ENST00000442986 Transcript missense_variant 1458/3245 1023/2487 341/828 K/N aaG/aaT 1 -1 ZNF438 HGNC HGNC:21029 protein_coding YES CCDS7168.1 ENSP00000412363 Q7Z4V0 UPI00001B3D8F NM_182755.2 tolerated(0.11) 7/8 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 30849382 30849382 C A 1 0 0 0 0 1 0 0 0 18481 680 24 2 2 ZNF438 10 30849382 Missense_Mutation SNP C C3N-02149_T 10847418 30849382 102948040 293 28477 ANKRD30A 0 . GRCh38 10 37129951 37129951 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.112G>C p.Asp38His p.D38H ENST00000361713 2/36 110 97 13 192 192 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Asp38His,ENST00000374660,;ANKRD30A,missense_variant,p.Asp94His,ENST00000611781,;ANKRD30A,missense_variant,p.Asp38His,ENST00000602533,;ANKRD30A,missense_variant,p.Asp38His,ENST00000361713,NM_052997.2; C ENST00000361713 Transcript missense_variant 211/4405 112/4026 38/1341 D/H Gac/Cac 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 deleterious(0.01) 2/36 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 37129951 37129951 G C 1 0 0 0 0 1 0 0 0 761 942 33 4 4 ANKRD30A 10 37129951 Missense_Mutation SNP G C3N-02149_T 6280569 37129951 96667471 294 28478 ANKRD30A 0 . GRCh38 10 37153577 37153577 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1545C>A p.= p.L515L ENST00000361713 13/36 369 282 87 513 512 1 strelka-varscan-mutect ANKRD30A,synonymous_variant,p.=,ENST00000374660,;ANKRD30A,synonymous_variant,p.=,ENST00000611781,;ANKRD30A,synonymous_variant,p.=,ENST00000602533,;ANKRD30A,synonymous_variant,p.=,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript synonymous_variant 1644/4405 1545/4026 515/1341 L ctC/ctA 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 13/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147 LOW 1 SNV 5 1 PASS rs778359317 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 37153577 37153577 C A 1 0 0 0 0 0 0 0 1 761 927 32 2 2 ANKRD30A 10 37153577 Silent SNP C C3N-02149_T 23626 37153577 96643845 295 28479 ANXA8L1 0 . GRCh38 10 46390883 46390883 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.937G>T p.Gly313Cys p.G313C ENST00000619162 12/12 383 352 31 496 496 0 varscan-mutect ANXA8L1,missense_variant,p.Gly351Cys,ENST00000584982,;ANXA8L1,missense_variant,p.Gly251Cys,ENST00000613703,;ANXA8L1,missense_variant,p.Gly262Cys,ENST00000622769,NM_001278924.1;ANXA8L1,missense_variant,p.Gly256Cys,ENST00000611655,NM_001278923.1;ANXA8L1,missense_variant,p.Gly313Cys,ENST00000619162,NM_001098845.2;ANXA8L1,intron_variant,,ENST00000616785,; T ENST00000619162 Transcript missense_variant 1062/1109 937/984 313/327 G/C Ggc/Tgc 1 1 ANXA8L1 HGNC HGNC:23334 protein_coding YES CCDS73098.1 ENSP00000480221 Q5VT79 UPI000002BA02 NM_001098845.2 deleterious(0) 12/12 hmmpanther:PTHR10502,PROSITE_patterns:PS00223,Pfam_domain:PF00191,Gene3D:1.10.220.10,SMART_domains:SM00335,Superfamily_domains:SSF47874,Prints_domain:PR00196 MODERATE 1 SNV 1 1 PASS . . 10 197 0 2 0 0 0 0 -20 0.9999995 1 1 1 0 T 3 4 92 46390883 46390883 G T 1 0 0 0 0 1 0 0 0 833 1116 39 1 1 ANXA8L1 10 46390883 Missense_Mutation SNP G C3N-02149_T 9237306 46390883 87406539 296 28480 GDF10 0 . GRCh38 10 47310173 47310173 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.697G>T p.Gly233Trp p.G233W ENST00000580279 2/3 196 174 22 316 316 0 strelka-varscan-mutect GDF10,missense_variant,p.Gly233Trp,ENST00000580279,NM_004962.3; T ENST00000580279 Transcript missense_variant 963/2458 697/1437 233/478 G/W Ggg/Tgg 1 1 GDF10 HGNC HGNC:4215 protein_coding YES CCDS73117.1 ENSP00000464145 P55107 UPI0000126A13 NM_004962.3 tolerated(0.06) 2/3 PIRSF_domain:PIRSF037403,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF145 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 47310173 47310173 G T 1 0 0 0 0 1 0 0 0 6184 1232 43 2 2 GDF10 10 47310173 Missense_Mutation SNP G C3N-02149_T 919290 47310173 86487249 297 28481 WDFY4 0 . GRCh38 10 48828805 48828805 + Silent SNP C C A C3N-02149_T C3N-02149_N C C c.6249C>A p.= p.P2083P ENST00000325239 36/61 170 158 12 207 206 1 strelka-varscan-mutect WDFY4,synonymous_variant,p.=,ENST00000325239,NM_020945.1;WDFY4,synonymous_variant,p.=,ENST00000265453,;WDFY4,downstream_gene_variant,,ENST00000374161,; A ENST00000325239 Transcript synonymous_variant 6249/9555 6249/9555 2083/3184 P ccC/ccA COSM5180946 1 1 WDFY4 HGNC HGNC:29323 protein_coding YES CCDS44385.1 ENSP00000320563 Q6ZS81 UPI000176ADB8 NM_020945.1 36/61 hmmpanther:PTHR13743,hmmpanther:PTHR13743:SF85 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 48828805 48828805 C A 1 0 0 0 0 0 0 0 1 17831 581 21 2 2 WDFY4 10 48828805 Silent SNP C C3N-02149_T 1518632 48828805 84968617 298 28482 PCDH15 0 . GRCh38 10 54185201 54185201 + Missense_Mutation SNP C C A rs766969775 C3N-02149_T C3N-02149_N C C c.1388G>T p.Gly463Val p.G463V ENST00000373957 13/35 537 500 37 693 691 2 strelka-varscan-mutect PCDH15,missense_variant,p.Gly463Val,ENST00000614895,;PCDH15,missense_variant,p.Gly458Val,ENST00000373965,NM_001142772.1;PCDH15,missense_variant,p.Gly458Val,ENST00000414778,;PCDH15,missense_variant,p.Gly463Val,ENST00000617051,;PCDH15,missense_variant,p.Gly463Val,ENST00000373957,NM_001142763.1;PCDH15,missense_variant,p.Gly458Val,ENST00000361849,NM_001142768.1,NM_001142764.1;PCDH15,missense_variant,p.Gly458Val,ENST00000395430,NM_001142766.1;PCDH15,missense_variant,p.Gly436Val,ENST00000395433,NM_001142773.1;PCDH15,missense_variant,p.Gly421Val,ENST00000395432,NM_001142767.1;PCDH15,missense_variant,p.Gly458Val,ENST00000320301,NM_033056.3;PCDH15,missense_variant,p.Gly458Val,ENST00000622048,;PCDH15,missense_variant,p.Gly458Val,ENST00000437009,NM_001142765.1;PCDH15,missense_variant,p.Gly458Val,ENST00000617271,NM_001142770.1;PCDH15,missense_variant,p.Gly470Val,ENST00000613657,NM_001142769.1;PCDH15,missense_variant,p.Gly465Val,ENST00000395445,;PCDH15,missense_variant,p.Gly458Val,ENST00000616114,;PCDH15,missense_variant,p.Gly458Val,ENST00000395438,;PCDH15,missense_variant,p.Gly470Val,ENST00000612394,;PCDH15,missense_variant,p.Gly463Val,ENST00000621708,NM_001142771.1;PCDH15,missense_variant,p.Gly69Val,ENST00000409834,;PCDH15,missense_variant,p.Gly458Val,ENST00000373955,;PCDH15,missense_variant,p.Gly458Val,ENST00000395446,;PCDH15,intron_variant,,ENST00000395440,;PCDH15,intron_variant,,ENST00000395442,;PCDH15,intron_variant,,ENST00000495484,;PCDH15,missense_variant,p.Gly458Val,ENST00000448885,;PCDH15,missense_variant,p.Gly458Val,ENST00000373956,;PCDH15,intron_variant,,ENST00000414367,; A ENST00000373957 Transcript missense_variant 1783/7032 1388/5889 463/1962 G/V gGt/gTt rs766969775 1 -1 PCDH15 HGNC HGNC:14674 protein_coding YES CCDS73137.1 ENSP00000363068 A2A3D8 UPI0001884901 NM_001142763.1 deleterious(0) 13/35 PROSITE_profiles:PS50268,hmmpanther:PTHR24028:SF11,hmmpanther:PTHR24028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS rs766969775 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 54185201 54185201 C A 1 0 0 0 0 1 0 0 0 11598 507 18 2 2 PCDH15 10 54185201 Missense_Mutation SNP C C3N-02149_T 5356396 54185201 79612221 299 28483 NRG3 0 . GRCh38 10 81875750 81875750 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.410C>A p.Pro137His p.P137H ENST00000372141 1/9 379 275 104 375 375 0 strelka-varscan-mutect NRG3,missense_variant,p.Pro137His,ENST00000404547,;NRG3,missense_variant,p.Pro137His,ENST00000372141,NM_001165972.1,NM_001010848.3;NRG3,upstream_gene_variant,,ENST00000372142,NM_001165973.1;NRG3,upstream_gene_variant,,ENST00000556918,;NRG3,upstream_gene_variant,,ENST00000404576,;NRG3,upstream_gene_variant,,ENST00000602794,;NRG3,upstream_gene_variant,,ENST00000555784,; A ENST00000372141 Transcript missense_variant 437/2158 410/2091 137/696 P/H cCc/cAc 1 1 NRG3 HGNC HGNC:7999 protein_coding YES CCDS31233.1 ENSP00000361214 P56975 UPI00003D64C0 NM_001165972.1,NM_001010848.3 deleterious(0.01) 1/9 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1294798567 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 81875750 81875750 C A 1 0 0 0 0 1 0 0 0 10707 623 22 2 2 NRG3 10 81875750 Missense_Mutation SNP C C3N-02149_T 27690549 81875750 51921672 300 28484 CDHR1 0 . GRCh38 10 84214607 84214607 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.2566A>G p.Lys856Glu p.K856E ENST00000623527 17/17 246 229 17 328 328 0 strelka-varscan-mutect CDHR1,missense_variant,p.Lys856Glu,ENST00000623527,NM_033100.3;CDHR1,missense_variant,p.Lys595Glu,ENST00000372117,;CDHR1,intron_variant,,ENST00000332904,NM_001171971.2;CDHR1,intron_variant,,ENST00000623399,;CDHR1,non_coding_transcript_exon_variant,,ENST00000459673,;CDHR1,downstream_gene_variant,,ENST00000622973,; G ENST00000623527 Transcript missense_variant 2692/6781 2566/2580 856/859 K/E Aag/Gag 1 1 CDHR1 HGNC HGNC:14550 protein_coding YES CCDS7372.1 ENSP00000485478 Q96JP9 F1T0L2 UPI0000161C2F NM_033100.3 deleterious_low_confidence(0.01) 17/17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 84214607 84214607 A G 1 0 0 0 0 1 0 0 0 2821 131 5 5 5 CDHR1 10 84214607 Missense_Mutation SNP A C3N-02149_T 2338857 84214607 49582815 301 28485 LIPN 0 . GRCh38 10 88761420 88761420 + Silent SNP T T A novel C3N-02149_T C3N-02149_N T T c.15T>A p.= p.L5L ENST00000404459 1/9 244 190 54 306 306 0 strelka-varscan-mutect LIPN,synonymous_variant,p.=,ENST00000404459,NM_001102469.1; A ENST00000404459 Transcript synonymous_variant 15/1197 15/1197 5/398 L ctT/ctA 1 1 LIPN HGNC HGNC:23452 protein_coding YES CCDS44456.1 ENSP00000383923 Q5VXI9 UPI000150AF6A NM_001102469.1 1/9 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR11005,hmmpanther:PTHR11005:SF16,PIRSF_domain:PIRSF000862 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 88761420 88761420 T A 1 0 0 0 0 0 0 0 1 8750 1828 64 4 4 LIPN 10 88761420 Silent SNP T C3N-02149_T 4546813 88761420 45036002 302 28486 PPP1R3C 0 . GRCh38 10 91630800 91630800 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.81G>T p.Arg27Ser p.R27S ENST00000238994 2/2 391 357 34 239 239 0 strelka-varscan-mutect PPP1R3C,missense_variant,p.Arg27Ser,ENST00000238994,NM_005398.5; A ENST00000238994 Transcript missense_variant 166/2524 81/954 27/317 R/S agG/agT COSM5338803 1 -1 PPP1R3C HGNC HGNC:9293 protein_coding YES CCDS7416.1 ENSP00000238994 Q9UQK1 UPI000006EFF1 NM_005398.5 tolerated(0.12) 2/2 PIRSF_domain:PIRSF038207,PIRSF_domain:PIRSF500813,hmmpanther:PTHR12307,hmmpanther:PTHR12307:SF15 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 91630800 91630800 C A 1 0 0 0 0 1 0 0 0 12494 738 26 2 2 PPP1R3C 10 91630800 Missense_Mutation SNP C C3N-02149_T 2869380 91630800 42166622 303 28487 LCOR 0 . GRCh38 10 96982784 96982784 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1394G>T p.Gly465Val p.G465V ENST00000286067 1/1 208 151 57 251 250 1 strelka-varscan-mutect LCOR,missense_variant,p.Gly747Val,ENST00000421806,;LCOR,missense_variant,p.Gly465Val,ENST00000286067,NM_015652.2; T ENST00000286067 Transcript missense_variant 1501/4542 1394/3744 465/1247 G/V gGa/gTa 1 1 LCOR HGNC HGNC:29503 protein_coding YES CCDS7452.1 ENSP00000286067 Q8N655 UPI000006F242 NM_015652.2 tolerated(0.09) 1/1 hmmpanther:PTHR14931,hmmpanther:PTHR14931:SF2 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 96982784 96982784 G T 1 0 0 0 0 1 0 0 0 8595 1174 41 2 2 LCOR 10 96982784 Missense_Mutation SNP G C3N-02149_T 5351984 96982784 36814638 304 28488 PSD 0 . GRCh38 10 102412388 102412388 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1741G>T p.Gly581Cys p.G581C ENST00000020673 6/17 126 117 9 135 134 1 strelka-varscan-mutect PSD,missense_variant,p.Gly581Cys,ENST00000020673,NM_002779.4;PSD,missense_variant,p.Gly581Cys,ENST00000406432,NM_001270965.1;PSD,missense_variant,p.Gly202Cys,ENST00000611678,NM_001270966.1;PSD,upstream_gene_variant,,ENST00000461698,;PSD,downstream_gene_variant,,ENST00000492902,;PSD,downstream_gene_variant,,ENST00000472685,;PSD,upstream_gene_variant,,ENST00000488194,; A ENST00000020673 Transcript missense_variant 2268/4183 1741/3075 581/1024 G/C Ggc/Tgc 1 -1 PSD HGNC HGNC:9507 protein_coding YES CCDS31272.1 ENSP00000020673 A5PKW4 UPI0000404928 NM_002779.4 deleterious(0.02) 6/17 PROSITE_profiles:PS50190,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF115,Pfam_domain:PF01369,SMART_domains:SM00222,Superfamily_domains:SSF48425 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 102412388 102412388 C A 1 0 0 0 0 1 0 0 0 12797 623 22 2 2 PSD 10 102412388 Missense_Mutation SNP C C3N-02149_T 5429604 102412388 31385034 305 28489 CALHM1 0 . GRCh38 10 103458235 103458235 + Silent SNP G G T rs374478309 C3N-02149_T C3N-02149_N G G c.517C>A p.= p.R173R ENST00000329905 1/2 415 391 24 427 426 1 strelka-varscan-mutect CALHM1,synonymous_variant,p.=,ENST00000329905,NM_001001412.3;RP11-225H22.4,intron_variant,,ENST00000411906,; T ENST00000329905 Transcript synonymous_variant 654/3053 517/1041 173/346 R Cga/Aga rs374478309 1 -1 CALHM1 HGNC HGNC:23494 protein_coding YES CCDS7550.1 ENSP00000329926 Q8IU99 UPI000016144D NM_001001412.3 1/2 hmmpanther:PTHR32261,hmmpanther:PTHR32261:SF2,Pfam_domain:PF14798 LOW 1 SNV 1 1 PASS rs374478309 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 103458235 103458235 G T 1 0 0 0 0 0 0 0 1 2272 1124 39 1 1 CALHM1 10 103458235 Silent SNP G C3N-02149_T 1045847 103458235 30339187 306 28490 PNLIPRP1 0 . GRCh38 10 116592438 116592438 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.227C>T p.Ser76Leu p.S76L ENST00000528052 4/13 107 79 28 129 129 0 strelka-varscan-mutect PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000528052,NM_001303135.1;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000358834,NM_006229.3;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000534537,;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000531984,;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000530319,;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000527980,;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000471549,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000480870,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525157,;PNLIPRP1,upstream_gene_variant,,ENST00000510125,;PNLIPRP1,missense_variant,p.Ser76Leu,ENST00000497792,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000526223,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000531825,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000525820,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000482159,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000484402,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000529584,;PNLIPRP1,non_coding_transcript_exon_variant,,ENST00000470678,;PNLIPRP1,upstream_gene_variant,,ENST00000482833,;PNLIPRP1,downstream_gene_variant,,ENST00000530626,; T ENST00000528052 Transcript missense_variant 298/1533 227/1404 76/467 S/L tCa/tTa 1 1 PNLIPRP1 HGNC HGNC:9156 protein_coding YES CCDS7595.1 ENSP00000433933 P54315 UPI000012E6AA NM_001303135.1 tolerated(0.09) 4/13 Gene3D:3.40.50.1820,Pfam_domain:PF00151,PIRSF_domain:PIRSF000865,Prints_domain:PR00823,hmmpanther:PTHR11610,hmmpanther:PTHR11610:SF108,Superfamily_domains:SSF53474 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 116592438 116592438 C T 1 0 0 0 0 1 0 0 0 12258 838 29 3 3 PNLIPRP1 10 116592438 Missense_Mutation SNP C C3N-02149_T 13134203 116592438 17204984 307 28491 BTBD16 0 . GRCh38 10 122289911 122289911 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.388C>G p.Gln130Glu p.Q130E ENST00000260723 6/16 133 125 8 165 165 0 strelka-varscan-mutect BTBD16,missense_variant,p.Gln130Glu,ENST00000260723,NM_001318189.1,NM_144587.2;BTBD16,upstream_gene_variant,,ENST00000507495,; G ENST00000260723 Transcript missense_variant,splice_region_variant 639/1849 388/1521 130/506 Q/E Caa/Gaa 1 1 BTBD16 HGNC HGNC:26340 protein_coding YES CCDS31301.1 ENSP00000260723 Q32M84 UPI00003CEFB9 NM_001318189.1,NM_144587.2 tolerated(0.56) 6/16 Gene3D:3.30.710.10,hmmpanther:PTHR23231,hmmpanther:PTHR23231:SF4 MODERATE 1 SNV 2 1 PASS rs1031080773 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 122289911 122289911 C G 1 0 0 0 0 1 0 0 0 1715 840 29 4 4 BTBD16 10 122289911 Missense_Mutation SNP C C3N-02149_T 5697473 122289911 11507511 308 28492 TUBGCP2 0 . GRCh38 10 133298108 133298108 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.460C>G p.Leu154Val p.L154V ENST00000543663 5/19 114 107 7 123 123 0 strelka-varscan-mutect TUBGCP2,missense_variant,p.Leu154Val,ENST00000543663,NM_001256617.1;TUBGCP2,missense_variant,p.Leu154Val,ENST00000368563,NM_006659.3;TUBGCP2,missense_variant,p.Leu24Val,ENST00000417178,NM_001256618.1;TUBGCP2,missense_variant,p.Leu154Val,ENST00000252936,;RP11-122K13.12,upstream_gene_variant,,ENST00000424450,;TUBGCP2,downstream_gene_variant,,ENST00000470829,;TUBGCP2,missense_variant,p.Leu154Val,ENST00000482278,;TUBGCP2,3_prime_UTR_variant,,ENST00000487796,;TUBGCP2,downstream_gene_variant,,ENST00000480198,; C ENST00000543663 Transcript missense_variant 833/4302 460/2793 154/930 L/V Ctg/Gtg 1 -1 TUBGCP2 HGNC HGNC:18599 protein_coding YES CCDS58105.1 ENSP00000446093 Q9BSJ2 UPI00020651C0 NM_001256617.1 tolerated(0.49) 5/19 hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF13 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -14.29054 1 1 1 1 0 C 3 2 92 133298108 133298108 G C 1 0 0 0 0 1 0 0 0 17276 956 33 4 4 TUBGCP2 10 133298108 Missense_Mutation SNP G C3N-02149_T 11008197 133298108 499314 309 28493 MUC6 0 . GRCh38 11 1016021 1016021 + Silent SNP G G C rs772349712 C3N-02149_T C3N-02149_N G G c.6780C>G p.= p.T2260T ENST00000421673 31/33 77 59 18 83 83 0 strelka-varscan-mutect MUC6,synonymous_variant,p.=,ENST00000421673,NM_005961.2;MUC6,synonymous_variant,p.=,ENST00000532016,;AP2A2,downstream_gene_variant,,ENST00000332231,NM_001242837.1;AP2A2,downstream_gene_variant,,ENST00000448903,NM_012305.3;MUC6,downstream_gene_variant,,ENST00000527242,; C ENST00000421673 Transcript synonymous_variant 6831/8006 6780/7320 2260/2439 T acC/acG rs772349712 1 -1 MUC6 HGNC HGNC:7517 protein_coding YES CCDS44513.1 ENSP00000406861 Q6W4X9 UPI0000251DBE NM_005961.2 31/33 LOW SNV 5 1 PASS rs772349712 . 0 199 11 0 0 0 0 0 -20 0.9999835 1 1 1 0 C 2 2 92 1016021 1016021 G C 1 0 0 0 0 0 0 0 1 9980 1103 39 4 4 MUC6 11 1016021 Silent SNP G C3N-02149_T 1016021 134070601 310 28494 MUC5AC 0 . GRCh38 11 1158013 1158013 + Missense_Mutation SNP G G T rs752586982 C3N-02149_T C3N-02149_N G G c.14G>T p.Arg5Leu p.R5L ENST00000621226 1/49 213 176 37 181 180 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Arg5Leu,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript missense_variant 61/17448 14/16965 5/5654 R/L cGg/cTg rs752586982 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0.01) 1/49 PROSITE_profiles:PS51257,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 5 1 PASS rs752586982 . 0 206 0 3 0 0 0 0 -20 0.9999951 1 1 1 0 T 3 4 92 1158013 1158013 G T 1 0 0 0 0 1 0 0 0 9978 1116 39 1 1 MUC5AC 11 1158013 Missense_Mutation SNP G C3N-02149_T 141992 1158013 133928609 311 28495 MUC5AC 0 . GRCh38 11 1196400 1196400 + Missense_Mutation SNP C C A rs749148814 C3N-02149_T C3N-02149_N C C c.15650C>A p.Pro5217Gln p.P5217Q ENST00000621226 38/49 264 222 42 303 302 1 strelka-varscan-mutect MUC5AC,missense_variant,p.Pro5217Gln,ENST00000621226,NM_001304359.1; A ENST00000621226 Transcript missense_variant 15697/17448 15650/16965 5217/5654 P/Q cCa/cAa rs749148814 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 deleterious(0.01) 38/49 Gene3D:2.10.25.10,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS rs749148814 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 1196400 1196400 C A 1 0 0 0 0 1 0 0 0 9978 594 21 2 2 MUC5AC 11 1196400 Missense_Mutation SNP C C3N-02149_T 38387 1196400 133890222 312 28496 MUC5B 0 . GRCh38 11 1242657 1242657 + Missense_Mutation SNP C C A rs542594128 C3N-02149_T C3N-02149_N C C c.5777C>A p.Pro1926Gln p.P1926Q ENST00000529681 31/49 675 567 108 652 650 2 strelka-varscan-mutect MUC5B,missense_variant,p.Pro1926Gln,ENST00000529681,NM_002458.2;RP11-532E4.2,intron_variant,,ENST00000532061,;MUC5B,downstream_gene_variant,,ENST00000525715,; A ENST00000529681 Transcript missense_variant 5835/17911 5777/17289 1926/5762 P/Q cCg/cAg rs542594128 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated(0.11) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs542594128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 1242657 1242657 C A 1 0 0 0 0 1 0 0 0 9979 652 23 1 1 MUC5B 11 1242657 Missense_Mutation SNP C C3N-02149_T 46257 1242657 133843965 313 28497 BRSK2 0 . GRCh38 11 1451380 1451380 + Missense_Mutation SNP C C A rs765073528 C3N-02149_T C3N-02149_N C C c.1643C>A p.Pro548Gln p.P548Q ENST00000382179 15/20 336 275 61 321 321 0 strelka-varscan-mutect BRSK2,missense_variant,p.Pro502Gln,ENST00000308219,NM_003957.3;BRSK2,missense_variant,p.Pro502Gln,ENST00000528841,NM_001256627.1;BRSK2,missense_variant,p.Pro548Gln,ENST00000382179,NM_001256630.1;BRSK2,missense_variant,p.Pro442Gln,ENST00000528710,NM_001282218.1;BRSK2,missense_variant,p.Pro502Gln,ENST00000531197,NM_001256629.1;BRSK2,missense_variant,p.Pro41Gln,ENST00000533606,;BRSK2,missense_variant,p.Pro524Gln,ENST00000526678,;BRSK2,5_prime_UTR_variant,,ENST00000544817,;BRSK2,missense_variant,p.Pro502Gln,ENST00000529433,;BRSK2,3_prime_UTR_variant,,ENST00000529951,;BRSK2,upstream_gene_variant,,ENST00000526768,;BRSK2,upstream_gene_variant,,ENST00000531932,; A ENST00000382179 Transcript missense_variant 1896/3576 1643/2301 548/766 P/Q cCg/cAg rs765073528 1 1 BRSK2 HGNC HGNC:11405 protein_coding YES CCDS58108.1 ENSP00000371614 Q8IWQ3 UPI000035E827 NM_001256630.1 tolerated(0.13) 15/20 hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF84 MODERATE 1 SNV 2 1 PASS rs765073528 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 1451380 1451380 C A 1 0 0 0 0 1 0 0 0 1698 652 23 1 1 BRSK2 11 1451380 Missense_Mutation SNP C C3N-02149_T 208723 1451380 133635242 314 28498 OR51B5 0 . GRCh38 11 5343420 5343420 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.105C>A p.= p.S35S ENST00000300773 1/1 194 151 43 192 192 0 strelka-varscan-mutect OR51B5,synonymous_variant,p.=,ENST00000300773,NM_001005567.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,non_coding_transcript_exon_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300773 Transcript synonymous_variant 105/939 105/939 35/312 S tcC/tcA 1 -1 OR51B5 HGNC HGNC:19599 protein_coding YES CCDS31378.1 ENSP00000300773 Q9H339 UPI000013E697 NM_001005567.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF76,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 5343420 5343420 G T 1 0 0 0 0 0 0 0 1 11165 1335 47 2 2 OR51B5 11 5343420 Silent SNP G C3N-02149_T 3892040 5343420 129743202 315 28499 OR51Q1 0 . GRCh38 11 5422271 5422271 + Missense_Mutation SNP C C T rs760036060 C3N-02149_T C3N-02149_N C C c.71C>T p.Ala24Val p.A24V ENST00000300778 1/1 237 190 47 218 218 0 strelka-varscan-mutect OR51Q1,missense_variant,p.Ala24Val,ENST00000300778,NM_001004757.2;HBG2,intron_variant,,ENST00000380259,;HBE1,intron_variant,,ENST00000380237,;HBG2,intron_variant,,ENST00000380252,;HBE1,intron_variant,,ENST00000396895,;AC104389.28,intron_variant,,ENST00000415970,;AC104389.28,intron_variant,,ENST00000418729,;AC104389.28,intron_variant,,ENST00000420465,;AC104389.28,intron_variant,,ENST00000420726,; T ENST00000300778 Transcript missense_variant 161/1096 71/954 24/317 A/V gCc/gTc rs760036060 1 1 OR51Q1 HGNC HGNC:14851 protein_coding YES CCDS31381.1 ENSP00000300778 Q8NH59 UPI0000041BDB NM_001004757.2 tolerated(0.38) 1/1 Gene3D:1.20.1070.10,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF84,Superfamily_domains:SSF81321 MODERATE SNV 1 PASS rs760036060 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 5422271 5422271 C T 1 0 0 0 0 1 0 0 0 11178 739 26 3 3 OR51Q1 11 5422271 Missense_Mutation SNP C C3N-02149_T 78851 5422271 129664351 316 28500 OR56A1 0 . GRCh38 11 6026892 6026892 + Silent SNP G G T rs144053540 C3N-02149_T C3N-02149_N G G c.813C>A p.= p.A271A ENST00000316650 1/1 266 224 42 316 314 2 strelka-varscan-mutect OR56A1,synonymous_variant,p.=,ENST00000316650,NM_001001917.2; T ENST00000316650 Transcript synonymous_variant 850/1071 813/957 271/318 A gcC/gcA rs144053540 1 -1 OR56A1 HGNC HGNC:14781 protein_coding YES CCDS31405.1 ENSP00000321246 Q8NGH5 A0A126GVB5 UPI000013FE4B NM_001001917.2 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24248:SF62,hmmpanther:PTHR24248,Gene3D:1.20.1070.10,Pfam_domain:PF13853,SMART_domains:SM01381,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs144053540 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 92 6026892 6026892 G T 1 0 0 0 0 0 0 0 1 11205 1335 47 2 2 OR56A1 11 6026892 Silent SNP G C3N-02149_T 604621 6026892 129059730 317 28501 FAM160A2 0 . GRCh38 11 6217146 6217146 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.2440C>G p.Leu814Val p.L814V ENST00000524416 9/9 366 338 28 425 425 0 strelka-varscan-mutect FAM160A2,missense_variant,p.Leu814Val,ENST00000524416,;FAM160A2,intron_variant,,ENST00000265978,NM_032127.3;FAM160A2,intron_variant,,ENST00000449352,NM_001098794.1;FAM160A2,upstream_gene_variant,,ENST00000529360,;FAM160A2,downstream_gene_variant,,ENST00000532797,; C ENST00000524416 Transcript missense_variant 2751/3327 2440/2517 814/838 L/V Ctg/Gtg 1 -1 FAM160A2 HGNC HGNC:25378 protein_coding ENSP00000431773 E9PJK5 UPI0001F78748 9/9 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 6217146 6217146 G C 1 0 0 0 0 1 0 0 0 5318 933 33 4 4 FAM160A2 11 6217146 Missense_Mutation SNP G C3N-02149_T 190254 6217146 128869476 318 28502 CNGA4 0 . GRCh38 11 6240112 6240112 + Silent SNP G G T rs186291453 C3N-02149_T C3N-02149_N G G c.318G>T p.= p.S106S ENST00000379936 4/6 151 118 33 152 152 0 strelka-varscan-mutect CNGA4,synonymous_variant,p.=,ENST00000379936,NM_001037329.3;CNGA4,intron_variant,,ENST00000533426,; T ENST00000379936 Transcript synonymous_variant 433/1863 318/1728 106/575 S tcG/tcT rs186291453,COSM544220 1 1 CNGA4 HGNC HGNC:2152 protein_coding YES CCDS31408.1 ENSP00000369268 Q8IV77 UPI000004C7EC NM_001037329.3 4/6 Gene3D:1.10.287.70,Pfam_domain:PF00520,hmmpanther:PTHR10217,hmmpanther:PTHR10217:SF388,Superfamily_domains:SSF81324 0,1 LOW 1 SNV 2 0,1 1 PASS rs186291453 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 6240112 6240112 G T 1 0 0 0 0 0 0 0 1 3379 1045 37 1 1 CNGA4 11 6240112 Silent SNP G C3N-02149_T 22966 6240112 128846510 319 28503 DCHS1 0 . GRCh38 11 6631658 6631658 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.3633C>A p.Phe1211Leu p.F1211L ENST00000299441 7/21 56 47 9 54 54 0 strelka-varscan-mutect DCHS1,missense_variant,p.Phe1211Leu,ENST00000299441,NM_003737.3;RP11-732A19.6,intron_variant,,ENST00000526633,; T ENST00000299441 Transcript missense_variant 4045/10765 3633/9897 1211/3298 F/L ttC/ttA 1 -1 DCHS1 HGNC HGNC:13681 protein_coding YES CCDS7771.1 ENSP00000299441 Q96JQ0 UPI00001313B6 NM_003737.3 tolerated(0.09) 7/21 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF335,Superfamily_domains:SSF49313,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -19.93643 0.9999983 1 1 1 0 T 3 4 92 6631658 6631658 G T 1 0 0 0 0 1 0 0 0 4090 1165 41 2 2 DCHS1 11 6631658 Missense_Mutation SNP G C3N-02149_T 391546 6631658 128454964 320 28504 OR6A2 0 . GRCh38 11 6795200 6795200 + Frame_Shift_Del DEL C C - novel C3N-02149_T C3N-02149_N C C c.509delG p.Gly170AlafsTer44 p.G170Afs*44 ENST00000332601 1/1 353 290 63 409 409 0 sindel-varindel-pindel OR6A2,frameshift_variant,p.Gly170AlafsTer44,ENST00000332601,NM_003696.2; - ENST00000332601 Transcript frameshift_variant 584/1157 509/984 170/327 G/X gGc/gc 1 -1 OR6A2 HGNC HGNC:15301 protein_coding YES CCDS7772.1 ENSP00000330384 O95222 A0A126GW91 UPI0000061E92 NM_003696.2 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF234,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix HIGH 1 deletion 1 PASS . . 0 207 0 0 3 0 0 0 -20 0.9766154 1 1 1 0 - 7 5 92 6795200 6795200 C - 1 0 1 0 1 0 0 0 0 11254 739 26 0 0 OR6A2 11 6795200 Frame_Shift_Del DEL C C3N-02149_T 163542 6795200 128291422 321 28505 NLRP14 0 . GRCh38 11 7038713 7038713 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.127G>T p.Gly43Cys p.G43C ENST00000299481 2/12 279 229 50 301 301 0 strelka-varscan-mutect NLRP14,missense_variant,p.Gly43Cys,ENST00000299481,NM_176822.3; T ENST00000299481 Transcript missense_variant 473/3628 127/3282 43/1093 G/C Ggc/Tgc 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 tolerated(0.57) 2/12 PROSITE_profiles:PS50824,hmmpanther:PTHR24106:SF154,hmmpanther:PTHR24106,Pfam_domain:PF02758,Gene3D:1.10.533.10,SMART_domains:SM01289,Superfamily_domains:SSF47986 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 7038713 7038713 G T 1 0 0 0 0 1 0 0 0 10513 1348 47 2 2 NLRP14 11 7038713 Missense_Mutation SNP G C3N-02149_T 243513 7038713 128047909 322 28506 NLRP14 0 . GRCh38 11 7043105 7043105 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1079A>T p.Glu360Val p.E360V ENST00000299481 4/12 617 520 97 677 677 0 strelka-varscan-mutect NLRP14,missense_variant,p.Glu360Val,ENST00000299481,NM_176822.3; T ENST00000299481 Transcript missense_variant 1425/3628 1079/3282 360/1093 E/V gAg/gTg 1 1 NLRP14 HGNC HGNC:22939 protein_coding YES CCDS7776.1 ENSP00000299481 Q86W24 UPI0000167F6E NM_176822.3 deleterious(0.02) 4/12 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF154,hmmpanther:PTHR24106 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 7043105 7043105 A T 1 0 0 0 0 1 0 0 0 10513 304 11 4 4 NLRP14 11 7043105 Missense_Mutation SNP A C3N-02149_T 4392 7043105 128043517 323 28507 TRIM66 0 . GRCh38 11 8647975 8647975 + Silent SNP C C T C3N-02149_T C3N-02149_N C C c.396G>A p.= p.E132E ENST00000402157 7/22 220 177 43 235 235 0 strelka-varscan-mutect TRIM66,synonymous_variant,p.=,ENST00000402157,;TRIM66,synonymous_variant,p.=,ENST00000299550,NM_014818.1;TRIM66,non_coding_transcript_exon_variant,,ENST00000531498,;TRIM66,non_coding_transcript_exon_variant,,ENST00000529057,;TRIM66,non_coding_transcript_exon_variant,,ENST00000481014,; T ENST00000402157 Transcript synonymous_variant 837/10086 396/3738 132/1245 E gaG/gaA COSM5635027 1 -1 TRIM66 HGNC HGNC:29005 protein_coding YES ENSP00000384876 B5MCJ9 UPI00016113E8 7/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF121,SMART_domains:SM00502 1 LOW 1 SNV 5 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 8647975 8647975 C T 1 0 0 0 0 0 0 0 1 17035 695 24 3 3 TRIM66 11 8647975 Silent SNP C C3N-02149_T 1604870 8647975 126438647 324 28508 IPO7 0 . GRCh38 11 9438201 9438201 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2611G>T p.Gly871Ter p.G871* ENST00000379719 22/25 365 287 78 374 374 0 strelka-varscan-mutect IPO7,stop_gained,p.Gly871Ter,ENST00000379719,NM_006391.2;CTD-2371O3.2,upstream_gene_variant,,ENST00000531111,; T ENST00000379719 Transcript stop_gained 2753/6191 2611/3117 871/1038 G/* Gga/Tga 1 1 IPO7 HGNC HGNC:9852 protein_coding YES CCDS31425.1 ENSP00000369042 O95373 UPI0000072C06 NM_006391.2 22/25 hmmpanther:PTHR10997:SF27,hmmpanther:PTHR10997,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 9438201 9438201 G T 1 0 0 0 0 0 1 0 0 7700 1117 39 1 1 IPO7 11 9438201 Nonsense_Mutation SNP G C3N-02149_T 790226 9438201 125648421 325 28509 CYP2R1 0 . GRCh38 11 14879135 14879135 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1309G>T p.Ala437Ser p.A437S ENST00000334636 4/5 253 200 53 276 276 0 strelka-varscan-mutect CYP2R1,missense_variant,p.Ala437Ser,ENST00000334636,NM_024514.4;CYP2R1,missense_variant,p.Ala204Ser,ENST00000532378,;CYP2R1,downstream_gene_variant,,ENST00000526489,;CYP2R1,downstream_gene_variant,,ENST00000526276,;CYP2R1,downstream_gene_variant,,ENST00000532641,;CYP2R1,downstream_gene_variant,,ENST00000529043,;CYP2R1,3_prime_UTR_variant,,ENST00000532805,;CYP2R1,3_prime_UTR_variant,,ENST00000530609,;CYP2R1,3_prime_UTR_variant,,ENST00000534686,;CYP2R1,3_prime_UTR_variant,,ENST00000525015,; A ENST00000334636 Transcript missense_variant 1356/2235 1309/1506 437/501 A/S Gct/Tct 1 -1 CYP2R1 HGNC HGNC:20580 protein_coding YES CCDS7818.1 ENSP00000334592 Q6VVX0 UPI000003F04B NM_024514.4 tolerated(0.62) 4/5 hmmpanther:PTHR24300,hmmpanther:PTHR24300:SF48,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 14879135 14879135 C A 1 0 0 0 0 1 0 0 0 3976 797 28 2 2 CYP2R1 11 14879135 Missense_Mutation SNP C C3N-02149_T 5440934 14879135 120207487 326 28510 SLC6A5 0 . GRCh38 11 20626762 20626762 + Silent SNP C C A rs142573911 C3N-02149_T C3N-02149_N C C c.1315C>A p.= p.R439R ENST00000525748 8/16 547 467 80 532 531 1 strelka-varscan-mutect SLC6A5,synonymous_variant,p.=,ENST00000525748,NM_004211.3;SLC6A5,upstream_gene_variant,,ENST00000528440,;SLC6A5,3_prime_UTR_variant,,ENST00000298923,; A ENST00000525748 Transcript synonymous_variant 1588/7084 1315/2394 439/797 R Cga/Aga rs142573911,CM119605 1 1 SLC6A5 HGNC HGNC:11051 protein_coding YES CCDS7854.1 ENSP00000434364 Q9Y345 UPI00004564A5 NM_004211.3 8/16 Superfamily_domains:0053687,Pfam_domain:PF00209,PROSITE_profiles:PS50267,hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF158,Transmembrane_helices:TMhelix LOW 1 SNV 1 0,1 1 PASS rs142573911 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 20626762 20626762 C A 1 0 0 0 0 0 0 0 1 14970 644 23 1 1 SLC6A5 11 20626762 Silent SNP C C3N-02149_T 5747627 20626762 114459860 327 28511 ANO3 0 . GRCh38 11 26442096 26442096 + Silent SNP T T G rs761188253 C3N-02149_T C3N-02149_N T T c.225T>G p.= p.T75T ENST00000256737 2/27 162 133 29 188 188 0 strelka-varscan-mutect ANO3,synonymous_variant,p.=,ENST00000256737,NM_031418.2;ANO3,synonymous_variant,p.=,ENST00000525139,;ANO3,synonymous_variant,p.=,ENST00000531646,; G ENST00000256737 Transcript synonymous_variant 1077/6642 225/2946 75/981 T acT/acG rs761188253 1 1 ANO3 HGNC HGNC:14004 protein_coding YES CCDS31447.1 ENSP00000256737 Q9BYT9 UPI00001F9ED8 NM_031418.2 2/27 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF16 LOW 1 SNV 1 1 PASS rs761188253 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 26442096 26442096 T G 1 0 0 0 0 0 0 0 1 805 1567 55 5 5 ANO3 11 26442096 Silent SNP T C3N-02149_T 5815334 26442096 108644526 328 28512 HSD17B12 0 . GRCh38 11 43838326 43838326 + Silent SNP G G T rs775988662 C3N-02149_T C3N-02149_N G G c.546G>T p.= p.G182G ENST00000278353 8/11 222 165 57 306 305 1 strelka-varscan-mutect HSD17B12,synonymous_variant,p.=,ENST00000278353,NM_016142.2;HSD17B12,synonymous_variant,p.=,ENST00000637401,;HSD17B12,synonymous_variant,p.=,ENST00000531185,;HSD17B12,synonymous_variant,p.=,ENST00000638034,;RP11-613D13.5,intron_variant,,ENST00000530450,;RP11-613D13.5,upstream_gene_variant,,ENST00000499066,;RP11-613D13.5,upstream_gene_variant,,ENST00000524643,;RP11-472I20.4,non_coding_transcript_exon_variant,,ENST00000532864,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000527213,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000533802,;HSD17B12,missense_variant,p.Gly69Cys,ENST00000636007,;HSD17B12,3_prime_UTR_variant,,ENST00000527433,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000533090,;HSD17B12,non_coding_transcript_exon_variant,,ENST00000534053,; T ENST00000278353 Transcript synonymous_variant 816/2571 546/939 182/312 G ggG/ggT rs775988662 1 1 HSD17B12 HGNC HGNC:18646 protein_coding YES CCDS7905.1 ENSP00000278353 Q53GQ0 UPI000004C79B NM_016142.2 8/11 Gene3D:3.40.50.720,Pfam_domain:PF00106,PIRSF_domain:PIRSF000126,Prints_domain:PR00080,Prints_domain:PR00081,hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF573,Superfamily_domains:SSF51735,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs775988662 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 43838326 43838326 G T 1 0 0 0 0 0 0 0 1 7276 1219 43 2 2 HSD17B12 11 43838326 Silent SNP G C3N-02149_T 17396230 43838326 91248296 329 28513 OR8H1 0 . GRCh38 11 56290899 56290899 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.164T>G p.Leu55Arg p.L55R ENST00000313022 1/1 260 220 40 419 419 0 strelka-varscan-mutect OR8H1,missense_variant,p.Leu55Arg,ENST00000313022,NM_001005199.1;OR8H1,missense_variant,p.Leu51Arg,ENST00000610894,; C ENST00000313022 Transcript missense_variant 192/1038 164/936 55/311 L/R cTt/cGt 1 -1 OR8H1 HGNC HGNC:14824 protein_coding YES CCDS31526.1 ENSP00000323595 Q8NGG4 A0A126GVW6 UPI0000041BC0 NM_001005199.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF11,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 56290899 56290899 A C 1 0 0 0 0 1 0 0 0 11305 72 3 5 5 OR8H1 11 56290899 Missense_Mutation SNP A C3N-02149_T 12452573 56290899 78795723 330 28514 VWCE 0 . GRCh38 11 61281904 61281904 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.669G>A p.= p.E223E ENST00000335613 7/20 105 77 28 131 131 0 strelka-varscan-mutect VWCE,synonymous_variant,p.=,ENST00000335613,NM_152718.2;VWCE,5_prime_UTR_variant,,ENST00000613271,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,downstream_gene_variant,,ENST00000535599,;VWCE,downstream_gene_variant,,ENST00000538579,; T ENST00000335613 Transcript synonymous_variant 1056/3640 669/2868 223/955 E gaG/gaA 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 7/20 Gene3D:2.10.25.10,Pfam_domain:PF07645,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 61281904 61281904 C T 1 0 0 0 0 0 0 0 1 17804 564 20 3 3 VWCE 11 61281904 Silent SNP C C3N-02149_T 4991005 61281904 73804718 331 28515 NRXN2 0 . GRCh38 11 64651557 64651557 + Silent SNP G G T rs754628467 C3N-02149_T C3N-02149_N G G c.2616C>A p.= p.S872S ENST00000265459 14/23 295 218 77 335 334 1 strelka-varscan-mutect NRXN2,synonymous_variant,p.=,ENST00000265459,NM_015080.3;NRXN2,synonymous_variant,p.=,ENST00000377559,NM_138732.2;NRXN2,synonymous_variant,p.=,ENST00000409571,;NRXN2,synonymous_variant,p.=,ENST00000377551,;AP001092.4,intron_variant,,ENST00000433606,;NRXN2,non_coding_transcript_exon_variant,,ENST00000486057,; T ENST00000265459 Transcript synonymous_variant 3078/6621 2616/5139 872/1712 S tcC/tcA rs754628467,COSM4965816 1 -1 NRXN2 HGNC HGNC:8009 protein_coding YES CCDS8077.1 ENSP00000265459 Q9P2S2 UPI0000130AA2 NM_015080.3 14/23 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF593,SMART_domains:SM00282,Superfamily_domains:SSF49899 0,1 LOW SNV 5 0,1 1 PASS rs754628467 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 64651557 64651557 G T 1 0 0 0 0 0 0 0 1 10725 1103 39 1 1 NRXN2 11 64651557 Silent SNP G C3N-02149_T 3369653 64651557 70435065 332 28516 SSH3 0 . GRCh38 11 67307679 67307679 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.733G>C p.Glu245Gln p.E245Q ENST00000308127 7/14 234 218 16 247 247 0 strelka-varscan-mutect SSH3,missense_variant,p.Glu99Gln,ENST00000376757,;SSH3,missense_variant,p.Glu245Gln,ENST00000308127,NM_017857.3;SSH3,missense_variant,p.Glu245Gln,ENST00000308298,;SSH3,missense_variant,p.Glu9Gln,ENST00000527821,;SSH3,intron_variant,,ENST00000532181,;SSH3,non_coding_transcript_exon_variant,,ENST00000529224,;SSH3,upstream_gene_variant,,ENST00000531495,;SSH3,downstream_gene_variant,,ENST00000534112,;SSH3,upstream_gene_variant,,ENST00000525913,;SSH3,missense_variant,p.Glu245Gln,ENST00000532881,;SSH3,downstream_gene_variant,,ENST00000532600,; C ENST00000308127 Transcript missense_variant 911/2871 733/1980 245/659 E/Q Gag/Cag 1 1 SSH3 HGNC HGNC:30581 protein_coding YES CCDS8157.1 ENSP00000312081 Q8TE77 A0A024R5J4 UPI0000038D01 NM_017857.3 deleterious(0) 7/14 hmmpanther:PTHR10159:SF349,hmmpanther:PTHR10159 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 67307679 67307679 G C 1 0 0 0 0 1 0 0 0 15562 1291 45 4 4 SSH3 11 67307679 Missense_Mutation SNP G C3N-02149_T 2656122 67307679 67778943 333 28517 DLG2 0 . GRCh38 11 83459835 83459835 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.2911T>A p.Ser971Thr p.S971T ENST00000376104 28/28 177 145 32 194 194 0 strelka-varscan-mutect DLG2,missense_variant,p.Ser866Thr,ENST00000398309,NM_001364.3;DLG2,missense_variant,p.Ser905Thr,ENST00000280241,NM_001206769.1;DLG2,missense_variant,p.Ser330Thr,ENST00000426717,NM_001142702.1;DLG2,missense_variant,p.Ser971Thr,ENST00000376104,NM_001142699.1;DLG2,missense_variant,p.Ser745Thr,ENST00000418306,NM_001142700.1;DLG2,missense_variant,p.Ser848Thr,ENST00000532653,NM_001300983.1;DLG2,missense_variant,p.Ser862Thr,ENST00000524982,;DLG2,missense_variant,p.Ser787Thr,ENST00000330014,;DLG2,missense_variant,p.Ser344Thr,ENST00000404783,;DLG2,downstream_gene_variant,,ENST00000531015,;DLG2,downstream_gene_variant,,ENST00000457267,;DLG2,non_coding_transcript_exon_variant,,ENST00000529159,; T ENST00000376104 Transcript missense_variant 3223/5139 2911/2928 971/975 S/T Tca/Aca 1 -1 DLG2 HGNC HGNC:2901 protein_coding YES CCDS44690.1 ENSP00000365272 Q15700 UPI0000E59399 NM_001142699.1 tolerated(0.22) 28/28 hmmpanther:PTHR23119:SF6,hmmpanther:PTHR23119,PIRSF_domain:PIRSF001741,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 83459835 83459835 A T 1 0 0 0 0 1 0 0 0 4362 304 11 4 4 DLG2 11 83459835 Missense_Mutation SNP A C3N-02149_T 16152156 83459835 51626787 334 28518 FAT3 0 . GRCh38 11 92801602 92801602 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.8139G>C p.Met2713Ile p.M2713I ENST00000525166 9/27 177 125 52 197 197 0 strelka-varscan-mutect FAT3,missense_variant,p.Met2863Ile,ENST00000409404,NM_001008781.2;FAT3,missense_variant,p.Met2713Ile,ENST00000525166,; C ENST00000525166 Transcript missense_variant 8161/18699 8139/13320 2713/4439 M/I atG/atC 1 1 FAT3 HGNC HGNC:23112 protein_coding YES ENSP00000432586 E9PQ73 UPI0001F78895 tolerated(0.46) 9/27 PROSITE_profiles:PS50268,hmmpanther:PTHR24026:SF49,hmmpanther:PTHR24026,Gene3D:2.60.40.60,Pfam_domain:PF00028,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 92801602 92801602 G C 1 0 0 0 0 1 0 0 0 5551 1348 47 4 4 FAT3 11 92801602 Missense_Mutation SNP G C3N-02149_T 9341767 92801602 42285020 335 28519 CUL5 0 . GRCh38 11 108094908 108094908 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1664T>C p.Ile555Thr p.I555T ENST00000393094 15/19 170 127 43 269 269 0 strelka-varscan-mutect CUL5,missense_variant,p.Ile555Thr,ENST00000393094,NM_003478.3;CUL5,missense_variant,p.Ile555Thr,ENST00000531427,; C ENST00000393094 Transcript missense_variant 2280/6351 1664/2343 555/780 I/T aTa/aCa 1 1 CUL5 HGNC HGNC:2556 protein_coding YES CCDS31668.1 ENSP00000376808 Q93034 UPI00001380B0 NM_003478.3 deleterious(0) 15/19 Gene3D:1ldjA05,Pfam_domain:PF00888,PROSITE_profiles:PS50069,hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF76,SMART_domains:SM00182,Superfamily_domains:SSF75632 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 108094908 108094908 T C 1 0 0 0 0 1 0 0 0 3869 1406 49 5 5 CUL5 11 108094908 Missense_Mutation SNP T C3N-02149_T 15293306 108094908 26991714 336 28520 PPP2R1B 0 . GRCh38 11 111755309 111755309 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.829G>C p.Asp277His p.D277H ENST00000311129 6/16 125 115 10 136 136 0 strelka-varscan-mutect PPP2R1B,missense_variant,p.Asp277His,ENST00000527614,NM_002716.4;PPP2R1B,missense_variant,p.Asp277His,ENST00000311129,NM_181699.2;PPP2R1B,missense_variant,p.Asp277His,ENST00000341980,NM_001177562.1;PPP2R1B,missense_variant,p.Asp213His,ENST00000426998,NM_181700.1;PPP2R1B,missense_variant,p.Asp150His,ENST00000393055,NM_001177563.1;PPP2R1B,upstream_gene_variant,,ENST00000531890,;PPP2R1B,3_prime_UTR_variant,,ENST00000534521,;PPP2R1B,downstream_gene_variant,,ENST00000534500,; G ENST00000311129 Transcript missense_variant 850/2082 829/2004 277/667 D/H Gac/Cac 1 -1 PPP2R1B HGNC HGNC:9303 protein_coding YES CCDS8348.1 ENSP00000311344 P30154 UPI000006CEE0 NM_181699.2 deleterious(0.01) 6/16 Gene3D:1.25.10.10,Pfam_domain:PF13646,PROSITE_profiles:PS50077,hmmpanther:PTHR10648,hmmpanther:PTHR10648:SF9,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.44226 1 1 1 1 0 G 3 3 92 111755309 111755309 C G 1 0 0 0 0 1 0 0 0 12506 826 29 4 4 PPP2R1B 11 111755309 Missense_Mutation SNP C C3N-02149_T 3660401 111755309 23331313 337 28521 SIK3 0 . GRCh38 11 116862236 116862236 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.2051A>T p.Glu684Val p.E684V ENST00000375300 16/24 277 189 88 328 328 0 strelka-varscan-mutect SIK3,missense_variant,p.Glu726Val,ENST00000445177,;SIK3,missense_variant,p.Glu684Val,ENST00000375300,NM_025164.4,NM_001281748.1;SIK3,missense_variant,p.Glu684Val,ENST00000446921,NM_001281749.1;SIK3,non_coding_transcript_exon_variant,,ENST00000488337,;SIK3,3_prime_UTR_variant,,ENST00000415541,;SIK3,non_coding_transcript_exon_variant,,ENST00000465421,;SIK3,upstream_gene_variant,,ENST00000480468,; A ENST00000375300 Transcript missense_variant 2057/6213 2051/3966 684/1321 E/V gAg/gTg 1 -1 SIK3 HGNC HGNC:29165 protein_coding YES CCDS8379.2 ENSP00000364449 J3KPC8 UPI000066D90F NM_025164.4,NM_001281748.1 deleterious_low_confidence(0) 16/24 Low_complexity_(Seg):seg,hmmpanther:PTHR22971:SF3,hmmpanther:PTHR22971 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 116862236 116862236 T A 1 0 0 0 0 1 0 0 0 14583 1551 54 4 4 SIK3 11 116862236 Missense_Mutation SNP T C3N-02149_T 5106927 116862236 18224386 338 28522 CBL 0 . GRCh38 11 119278273 119278273 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.1203C>T p.= p.C401C ENST00000264033 8/16 510 484 26 592 592 0 strelka-varscan-mutect CBL,synonymous_variant,p.=,ENST00000264033,NM_005188.3;CBL,synonymous_variant,p.=,ENST00000634840,;CBL,synonymous_variant,p.=,ENST00000634586,;CBL,synonymous_variant,p.=,ENST00000637974,; T ENST00000264033 Transcript synonymous_variant 1345/11231 1203/2721 401/906 C tgC/tgT 1 1 CBL HGNC HGNC:1541 protein_coding YES CCDS8418.1 ENSP00000264033 P22681 UPI000013D4A7 NM_005188.3 8/16 Gene3D:3.30.40.10,Pfam_domain:PF14447,PROSITE_patterns:PS00518,PROSITE_profiles:PS50089,hmmpanther:PTHR23007,hmmpanther:PTHR23007:SF5,SMART_domains:SM00184,Superfamily_domains:SSF57850 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 119278273 119278273 C T 1 0 0 0 0 0 0 0 1 2401 718 25 3 3 CBL 11 119278273 Silent SNP C C3N-02149_T 2416037 119278273 15808349 339 28523 GRAMD1B 0 . GRCh38 11 123610255 123610255 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1428C>A p.= p.T476T ENST00000456860 14/21 337 259 78 396 396 0 strelka-varscan-mutect GRAMD1B,synonymous_variant,p.=,ENST00000529750,NM_020716.2;GRAMD1B,synonymous_variant,p.=,ENST00000529432,NM_001286564.1;GRAMD1B,synonymous_variant,p.=,ENST00000638157,;GRAMD1B,synonymous_variant,p.=,ENST00000635736,;GRAMD1B,synonymous_variant,p.=,ENST00000456860,NM_001286563.1;GRAMD1B,synonymous_variant,p.=,ENST00000638086,;GRAMD1B,synonymous_variant,p.=,ENST00000322282,;GRAMD1B,synonymous_variant,p.=,ENST00000450171,;GRAMD1B,downstream_gene_variant,,ENST00000534764,;GRAMD1B,non_coding_transcript_exon_variant,,ENST00000532581,;GRAMD1B,upstream_gene_variant,,ENST00000525945,; A ENST00000456860 Transcript synonymous_variant 1941/2805 1428/2238 476/745 T acC/acA 1 1 GRAMD1B HGNC HGNC:29214 protein_coding YES CCDS66253.1 ENSP00000402457 Q3KR37 UPI000023753E NM_001286563.1 14/21 hmmpanther:PTHR23319:SF3,hmmpanther:PTHR23319,Pfam_domain:PF16016 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 123610255 123610255 C A 1 0 0 0 0 0 0 0 1 6627 610 22 2 2 GRAMD1B 11 123610255 Silent SNP C C3N-02149_T 4331982 123610255 11476367 340 28524 OR8B12 0 . GRCh38 11 124542857 124542857 + Silent SNP G G A C3N-02149_T C3N-02149_N G G c.798C>T p.= p.P266P ENST00000306842 1/1 295 212 83 337 337 0 strelka-varscan-mutect OR8B12,synonymous_variant,p.=,ENST00000306842,NM_001005195.1;RP11-728D14.6,upstream_gene_variant,,ENST00000533869,; A ENST00000306842 Transcript synonymous_variant 823/998 798/933 266/310 P ccC/ccT COSM1506947 1 -1 OR8B12 HGNC HGNC:15307 protein_coding YES CCDS31711.1 ENSP00000307159 Q8NGG6 A0A126GWS7 UPI0000041E25 NM_001005195.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF267,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 124542857 124542857 G A 1 0 0 0 0 0 0 0 1 11296 1219 43 3 3 OR8B12 11 124542857 Silent SNP G C3N-02149_T 932602 124542857 10543765 341 28525 GALNT8 0 . GRCh38 12 4811318 4811318 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1277G>T p.Gly426Val p.G426V ENST00000280684 1/1 202 181 21 220 220 0 strelka-varscan-mutect GALNT8,missense_variant,p.Gly426Val,ENST00000433855,NM_002235.3;KCNA6,missense_variant,p.Gly426Val,ENST00000280684,;GALNT8,intron_variant,,ENST00000542998,;RP11-234B24.4,upstream_gene_variant,,ENST00000542988,;GALNT8,upstream_gene_variant,,ENST00000541339,; T ENST00000280684 Transcript missense_variant 2143/4237 1277/1590 426/529 G/V gGg/gTg 1 1 KCNA6 HGNC HGNC:6225 protein_coding YES CCDS8534.1 ENSP00000280684 P17658 UPI00001279AD deleterious(0) 1/1 Gene3D:1.10.287.70,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF104,Superfamily_domains:SSF81324 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 4811318 4811318 G T 1 0 0 0 0 1 0 0 0 6090 1232 43 2 2 GALNT8 12 4811318 Missense_Mutation SNP G C3N-02149_T 4811318 128463991 342 28526 CHD4 0 . GRCh38 12 6601469 6601469 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.619G>T p.Ala207Ser p.A207S ENST00000357008 6/40 406 376 30 369 369 0 strelka-varscan-mutect CHD4,missense_variant,p.Ala204Ser,ENST00000544484,;CHD4,missense_variant,p.Ala200Ser,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Ala207Ser,ENST00000357008,NM_001273.3;CHD4,missense_variant,p.Ala207Ser,ENST00000545942,;CHD4,downstream_gene_variant,,ENST00000545584,;CHD4,upstream_gene_variant,,ENST00000535810,;CHD4,upstream_gene_variant,,ENST00000536999,;CHD4,downstream_gene_variant,,ENST00000430771,; A ENST00000357008 Transcript missense_variant 783/6496 619/5739 207/1912 A/S Gca/Tca 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 deleterious(0) 6/40 Pfam_domain:PF08073 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 6601469 6601469 C A 1 0 0 0 0 1 0 0 0 3086 710 25 2 2 CHD4 12 6601469 Missense_Mutation SNP C C3N-02149_T 1790151 6601469 126673840 343 28527 NANOGNB 0 . GRCh38 12 7770025 7770025 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.145A>T p.Thr49Ser p.T49S ENST00000382119 2/4 178 169 9 207 207 0 strelka-varscan-mutect NANOGNB,missense_variant,p.Thr49Ser,ENST00000382119,NM_001145465.1; T ENST00000382119 Transcript missense_variant 215/907 145/567 49/188 T/S Act/Tct 1 1 NANOGNB HGNC HGNC:24958 protein_coding YES CCDS44826.1 ENSP00000371553 Q7Z5D8 UPI00001B3DAD NM_001145465.1 tolerated(0.21) 2/4 hmmpanther:PTHR12157 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 7770025 7770025 A T 1 0 0 0 0 1 0 0 0 10158 43 2 4 4 NANOGNB 12 7770025 Missense_Mutation SNP A C3N-02149_T 1168556 7770025 125505284 344 28528 KLRF2 0 . GRCh38 12 9895781 9895781 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.572G>A p.Gly191Asp p.G191D ENST00000535540 6/6 294 212 82 317 317 0 strelka-varscan-mutect KLRF2,missense_variant,p.Gly191Asp,ENST00000535540,NM_001190765.1;CLEC2A,downstream_gene_variant,,ENST00000339766,NM_207375.2; A ENST00000535540 Transcript missense_variant 679/731 572/624 191/207 G/D gGc/gAc 1 1 KLRF2 HGNC HGNC:37646 protein_coding YES CCDS53743.1 ENSP00000438244 D3W0D1 UPI0001CADE27 NM_001190765.1 tolerated(0.08) 6/6 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22800,hmmpanther:PTHR22800:SF147,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 9895781 9895781 G A 1 0 0 0 0 1 0 0 0 8290 1203 42 3 3 KLRF2 12 9895781 Missense_Mutation SNP G C3N-02149_T 2125756 9895781 123379528 345 28529 PRB2 0 . GRCh38 12 11393908 11393908 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.170C>T p.Pro57Leu p.P57L ENST00000389362 3/4 132 101 31 173 173 0 strelka-varscan-mutect PRB2,missense_variant,p.Pro57Leu,ENST00000389362,NM_006248.3;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,; A ENST00000389362 Transcript missense_variant 206/1429 170/1251 57/416 P/L cCa/cTa 1 -1 PRB2 HGNC HGNC:9338 protein_coding YES CCDS41757.2 ENSP00000374013 P02812 UPI0000EE5993 NM_006248.3 deleterious(0.01) 3/4 Low_complexity_(Seg):seg,Pfam_domain:PF15240,SMART_domains:SM01412 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 11393908 11393908 G A 1 0 0 0 0 1 0 0 0 12574 1348 47 3 3 PRB2 12 11393908 Missense_Mutation SNP G C3N-02149_T 1498127 11393908 121881401 346 28530 PRB2 0 . GRCh38 12 11393958 11393958 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.120C>A p.= p.P40P ENST00000389362 3/4 227 174 53 224 224 0 strelka-varscan-mutect PRB2,synonymous_variant,p.=,ENST00000389362,NM_006248.3;PRB1,intron_variant,,ENST00000546254,;PRB2,downstream_gene_variant,,ENST00000565533,;PRB2,downstream_gene_variant,,ENST00000545829,; T ENST00000389362 Transcript synonymous_variant 156/1429 120/1251 40/416 P ccC/ccA 1 -1 PRB2 HGNC HGNC:9338 protein_coding YES CCDS41757.2 ENSP00000374013 P02812 UPI0000EE5993 NM_006248.3 3/4 Low_complexity_(Seg):seg,hmmpanther:PTHR23203:SF2,hmmpanther:PTHR23203,Pfam_domain:PF15240,SMART_domains:SM01412 LOW 1 SNV 5 1 PASS rs1467532703 . 0 207 0 0 2 0 0 0 -20 0.9985708 1 1 1 0 T 2 4 92 11393958 11393958 G T 1 0 0 0 0 0 0 0 1 12574 1219 43 2 2 PRB2 12 11393958 Silent SNP G C3N-02149_T 50 11393958 121881351 347 28531 ABCC9 0 . GRCh38 12 21807466 21807466 + Silent SNP A A T novel C3N-02149_T C3N-02149_N A A c.4329T>A p.= p.T1443T ENST00000261200 36/38 565 387 178 674 674 0 strelka-varscan-mutect ABCC9,synonymous_variant,p.=,ENST00000261200,NM_020297.3;ABCC9,synonymous_variant,p.=,ENST00000261201,NM_005691.3;ABCC9,synonymous_variant,p.=,ENST00000544039,; T ENST00000261200 Transcript synonymous_variant 4329/8293 4329/4650 1443/1549 T acT/acA 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 36/38 PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF173,Pfam_domain:PF00005,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 21807466 21807466 A T 1 0 0 0 0 0 0 0 1 63 175 7 4 4 ABCC9 12 21807466 Silent SNP A C3N-02149_T 10413508 21807466 111467843 348 28532 PPFIBP1 0 . GRCh38 12 27671430 27671430 + Splice_Site SNP G G T novel C3N-02149_T C3N-02149_N G G c.1198-1G>T p.X400_splice ENST00000318304 60 40 20 91 91 0 strelka-varscan-mutect PPFIBP1,splice_acceptor_variant,,ENST00000318304,NM_177444.2;PPFIBP1,splice_acceptor_variant,,ENST00000228425,NM_003622.3;PPFIBP1,splice_acceptor_variant,,ENST00000537927,NM_001198915.1;PPFIBP1,splice_acceptor_variant,,ENST00000542629,NM_001198916.1;PPFIBP1,splice_acceptor_variant,,ENST00000540114,;PPFIBP1,splice_acceptor_variant,,ENST00000537261,;PPFIBP1,upstream_gene_variant,,ENST00000619325,; T ENST00000318304 Transcript splice_acceptor_variant -/6001 1198/3036 400/1011 1 1 PPFIBP1 HGNC HGNC:9249 protein_coding YES CCDS55812.1 ENSP00000314724 Q86W92 UPI00004565E6 NM_177444.2 13/28 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 92 27671430 27671430 G T 1 0 0 0 0 0 0 1 0 12422 1043 36 2 2 PPFIBP1 12 27671430 Splice_Site SNP G C3N-02149_T 5863964 27671430 105603879 349 28533 CAPRIN2 0 . GRCh38 12 30724398 30724398 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1959G>T p.= p.P653P ENST00000298892 10/17 229 164 65 305 305 0 strelka-varscan-mutect CAPRIN2,synonymous_variant,p.=,ENST00000298892,NM_023925.4,NM_001002259.2;CAPRIN2,synonymous_variant,p.=,ENST00000395805,NM_001206856.2;CAPRIN2,synonymous_variant,p.=,ENST00000417045,NM_032156.4;CAPRIN2,synonymous_variant,p.=,ENST00000433722,;CAPRIN2,synonymous_variant,p.=,ENST00000537108,;CAPRIN2,non_coding_transcript_exon_variant,,ENST00000620681,;CAPRIN2,downstream_gene_variant,,ENST00000538387,;CAPRIN2,3_prime_UTR_variant,,ENST00000537553,;CAPRIN2,3_prime_UTR_variant,,ENST00000454014,NM_001319842.1;CAPRIN2,3_prime_UTR_variant,,ENST00000548676,;CAPRIN2,downstream_gene_variant,,ENST00000553026,; A ENST00000298892 Transcript synonymous_variant 2710/4334 1959/3234 653/1077 P ccG/ccT 1 -1 CAPRIN2 HGNC HGNC:21259 protein_coding YES CCDS8720.1 ENSP00000298892 Q6IMN6 UPI000007080A NM_023925.4,NM_001002259.2 10/17 Pfam_domain:PF12287,hmmpanther:PTHR22922,hmmpanther:PTHR22922:SF5 LOW 1 SNV 1 1 PASS rs1036702394 . 0 206 0 3 0 0 0 0 -20 0.9999982 1 1 1 0 A 2 1 92 30724398 30724398 C A 1 0 0 0 0 0 0 0 1 2331 755 27 1 1 CAPRIN2 12 30724398 Silent SNP C C3N-02149_T 3052968 30724398 102550911 350 28534 ABCD2 0 . GRCh38 12 39619249 39619249 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.367T>A p.Tyr123Asn p.Y123N ENST00000308666 1/10 211 153 58 251 251 0 strelka-varscan-mutect ABCD2,missense_variant,p.Tyr123Asn,ENST00000308666,NM_005164.3; T ENST00000308666 Transcript missense_variant 503/6238 367/2223 123/740 Y/N Tat/Aat 1 -1 ABCD2 HGNC HGNC:66 protein_coding YES CCDS8734.1 ENSP00000310688 Q9UBJ2 UPI000004C4C6 NM_005164.3 deleterious(0) 1/10 PROSITE_profiles:PS50929,hmmpanther:PTHR11384,hmmpanther:PTHR11384:SF24,Pfam_domain:PF06472,Superfamily_domains:SSF90123 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 39619249 39619249 A T 1 0 0 0 0 1 0 0 0 65 420 15 4 4 ABCD2 12 39619249 Missense_Mutation SNP A C3N-02149_T 8894851 39619249 93656060 351 28535 ASIC1 0 . GRCh38 12 50077296 50077296 + Silent SNP G G T rs202004622 C3N-02149_T C3N-02149_N G G c.642G>T p.= p.T214T ENST00000228468 4/12 249 168 81 264 264 0 strelka-varscan-mutect ASIC1,synonymous_variant,p.=,ENST00000228468,NM_020039.3;ASIC1,synonymous_variant,p.=,ENST00000447966,NM_001095.3;ASIC1,synonymous_variant,p.=,ENST00000552438,NM_001256830.1;ASIC1,synonymous_variant,p.=,ENST00000453327,;ASIC1,upstream_gene_variant,,ENST00000552633,;ASIC1,missense_variant,p.Gly242Trp,ENST00000550558,;ASIC1,non_coding_transcript_exon_variant,,ENST00000551199,;ASIC1,upstream_gene_variant,,ENST00000548350,;ASIC1,downstream_gene_variant,,ENST00000549792,; T ENST00000228468 Transcript synonymous_variant 1027/4072 642/1725 214/574 T acG/acT rs202004622 1 1 ASIC1 HGNC HGNC:100 protein_coding YES CCDS8796.1 ENSP00000228468 P78348 UPI000013C8D6 NM_020039.3 4/12 hmmpanther:PTHR11690,hmmpanther:PTHR11690:SF170,Gene3D:2qtsA02,Pfam_domain:PF00858 LOW 1 SNV 1 1 PASS rs202004622 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 50077296 50077296 G T 1 0 0 0 0 0 0 0 1 1185 1103 39 1 1 ASIC1 12 50077296 Silent SNP G C3N-02149_T 10458047 50077296 83198013 352 28536 DIP2B 0 . GRCh38 12 50660258 50660258 + Silent SNP C C T C3N-02149_T C3N-02149_N C C c.366C>T p.= p.P122P ENST00000301180 4/38 202 183 19 227 227 0 strelka-varscan-mutect DIP2B,synonymous_variant,p.=,ENST00000301180,NM_173602.2;RNU6-238P,downstream_gene_variant,,ENST00000363313,;DIP2B,non_coding_transcript_exon_variant,,ENST00000549620,;DIP2B,non_coding_transcript_exon_variant,,ENST00000546719,; T ENST00000301180 Transcript synonymous_variant 400/8593 366/4731 122/1576 P ccC/ccT COSM3671095 1 1 DIP2B HGNC HGNC:29284 protein_coding YES CCDS31799.1 ENSP00000301180 Q9P265 UPI0000406CA1 NM_173602.2 4/38 Pfam_domain:PF06464,hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF22,SMART_domains:SM01137 1 LOW 1 SNV 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 50660258 50660258 C T 1 0 0 0 0 0 0 0 1 4333 581 21 3 3 DIP2B 12 50660258 Silent SNP C C3N-02149_T 582962 50660258 82615051 353 28537 SCN8A 0 . GRCh38 12 51806911 51806911 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.5425G>T p.Ala1809Ser p.A1809S ENST00000354534 27/27 217 180 37 215 215 0 strelka-varscan-mutect SCN8A,missense_variant,p.Ala1809Ser,ENST00000354534,NM_014191.3;SCN8A,missense_variant,p.Ala1768Ser,ENST00000545061,NM_001177984.2;SCN8A,missense_variant,p.Ala1820Ser,ENST00000599343,;SCN8A,missense_variant,p.Ala1809Ser,ENST00000627620,;SCN8A,missense_variant,p.Ala1768Ser,ENST00000355133,;RP11-923I11.3,downstream_gene_variant,,ENST00000565518,;SCN8A,3_prime_UTR_variant,,ENST00000637709,;SCN8A,3_prime_UTR_variant,,ENST00000636945,; T ENST00000354534 Transcript missense_variant 5603/11556 5425/5943 1809/1980 A/S Gca/Tca 1 1 SCN8A HGNC HGNC:10596 protein_coding YES CCDS44891.1 ENSP00000346534 Q9UQD0 UPI000006FD85 NM_014191.3 tolerated(1) 27/27 hmmpanther:PTHR10037:SF23,hmmpanther:PTHR10037 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 51806911 51806911 G T 1 0 0 0 0 1 0 0 0 14193 1203 42 2 2 SCN8A 12 51806911 Missense_Mutation SNP G C3N-02149_T 1146653 51806911 81468398 354 28538 ANKRD33 0 . GRCh38 12 51889135 51889135 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.465C>G p.Phe155Leu p.F155L ENST00000301190 3/5 326 248 78 333 333 0 strelka-varscan-mutect ANKRD33,missense_variant,p.Phe155Leu,ENST00000301190,NM_182608.3;ANKRD33,missense_variant,p.Phe20Leu,ENST00000340970,NM_001130015.1;ANKRD33,non_coding_transcript_exon_variant,,ENST00000547119,;ANKRD33,intron_variant,,ENST00000549316,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548526,;ANKRD33,non_coding_transcript_exon_variant,,ENST00000548383,;ANKRD33,intron_variant,,ENST00000549751,;ANKRD33,upstream_gene_variant,,ENST00000550652,; G ENST00000301190 Transcript missense_variant 692/1935 465/1359 155/452 F/L ttC/ttG 1 1 ANKRD33 HGNC HGNC:13788 protein_coding YES CCDS8815.1 ENSP00000301190 Q7Z3H0 UPI00003668C0 NM_182608.3 tolerated(0.17) 3/5 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50297,hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF29,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 51889135 51889135 C G 1 0 0 0 0 1 0 0 0 765 854 30 4 4 ANKRD33 12 51889135 Missense_Mutation SNP C C3N-02149_T 82224 51889135 81386174 355 28539 CBX5 0 . GRCh38 12 54252228 54252228 + Splice_Site SNP C C A novel C3N-02149_T C3N-02149_N C C c.138-1G>T p.X46_splice ENST00000209875 310 280 30 324 323 1 strelka-varscan-mutect CBX5,splice_acceptor_variant,,ENST00000209875,NM_012117.2;CBX5,splice_acceptor_variant,,ENST00000439541,NM_001127321.1;CBX5,splice_acceptor_variant,,ENST00000550411,NM_001127322.1;CBX5,splice_acceptor_variant,,ENST00000552562,;RN7SL390P,downstream_gene_variant,,ENST00000470634,;CBX5,non_coding_transcript_exon_variant,,ENST00000547872,; A ENST00000209875 Transcript splice_acceptor_variant -/11528 138/576 46/191 1 -1 CBX5 HGNC HGNC:1555 protein_coding YES CCDS8875.1 ENSP00000209875 P45973 V9HWG0 UPI00001271FC NM_012117.2 2/4 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 92 54252228 54252228 C A 1 0 0 0 0 0 0 1 0 2421 695 24 2 2 CBX5 12 54252228 Splice_Site SNP C C3N-02149_T 2363093 54252228 79023081 356 28540 APOF 0 . GRCh38 12 56361469 56361469 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.737A>C p.Lys246Thr p.K246T ENST00000398189 2/2 514 439 75 597 597 0 strelka-varscan-mutect APOF,missense_variant,p.Lys246Thr,ENST00000398189,NM_001638.2;STAT2,upstream_gene_variant,,ENST00000314128,NM_005419.3;STAT2,upstream_gene_variant,,ENST00000557235,NM_198332.1;STAT2,upstream_gene_variant,,ENST00000418572,;STAT2,upstream_gene_variant,,ENST00000556140,;STAT2,upstream_gene_variant,,ENST00000557417,;STAT2,upstream_gene_variant,,ENST00000555646,; G ENST00000398189 Transcript missense_variant 815/1715 737/981 246/326 K/T aAa/aCa 1 -1 APOF HGNC HGNC:615 protein_coding YES CCDS44923.1 ENSP00000381250 Q13790 UPI0000167B1E NM_001638.2 deleterious(0) 2/2 Pfam_domain:PF15148,hmmpanther:PTHR15011,hmmpanther:PTHR15011:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 56361469 56361469 T G 1 0 0 0 0 1 0 0 0 925 1841 64 5 5 APOF 12 56361469 Missense_Mutation SNP T C3N-02149_T 2109241 56361469 76913840 357 28541 AVPR1A 0 . GRCh38 12 63150135 63150135 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.702C>A p.= p.T234T ENST00000299178 1/2 501 439 62 598 598 0 strelka-varscan-mutect AVPR1A,synonymous_variant,p.=,ENST00000299178,NM_000706.4;AVPR1A,synonymous_variant,p.=,ENST00000550940,;RP11-715H19.2,upstream_gene_variant,,ENST00000624438,; T ENST00000299178 Transcript synonymous_variant 808/5963 702/1257 234/418 T acC/acA 1 -1 AVPR1A HGNC HGNC:895 protein_coding YES CCDS8965.1 ENSP00000299178 P37288 X5D2B0 UPI0000050439 NM_000706.4 1/2 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24241:SF17,hmmpanther:PTHR24241,Pfam_domain:PF00001,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 1 PASS rs1233023827 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 63150135 63150135 G T 1 0 0 0 0 0 0 0 1 1387 987 35 2 2 AVPR1A 12 63150135 Silent SNP G C3N-02149_T 6788666 63150135 70125174 358 28542 HELB 0 . GRCh38 12 66331463 66331463 + Missense_Mutation SNP A A T rs759121470 C3N-02149_T C3N-02149_N A A c.2980A>T p.Met994Leu p.M994L ENST00000247815 12/13 255 211 44 293 293 0 strelka-varscan-mutect HELB,missense_variant,p.Met994Leu,ENST00000247815,NM_033647.3;HELB,missense_variant,p.Met994Leu,ENST00000545134,;HELB,3_prime_UTR_variant,,ENST00000542394,;HELB,3_prime_UTR_variant,,ENST00000440906,; T ENST00000247815 Transcript missense_variant 3039/12866 2980/3264 994/1087 M/L Atg/Ttg rs759121470 1 1 HELB HGNC HGNC:17196 protein_coding YES CCDS8976.1 ENSP00000247815 Q8NG08 UPI000013CC2D NM_033647.3 tolerated(0.72) 12/13 MODERATE 1 SNV 1 1 PASS rs759121470 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 66331463 66331463 A T 1 0 0 0 0 1 0 0 0 6927 217 8 4 4 HELB 12 66331463 Missense_Mutation SNP A C3N-02149_T 3181328 66331463 66943846 359 28543 NAV3 0 . GRCh38 12 78119921 78119921 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.3725A>T p.Asp1242Val p.D1242V ENST00000397909 15/40 125 111 14 146 146 0 strelka-varscan-mutect NAV3,missense_variant,p.Asp1242Val,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Asp1242Val,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Asp314Val,ENST00000552895,;NAV3,upstream_gene_variant,,ENST00000550788,; T ENST00000397909 Transcript missense_variant 3898/9821 3725/7158 1242/2385 D/V gAt/gTt 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 15/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 78119921 78119921 A T 1 0 0 0 0 1 0 0 0 10194 333 12 4 4 NAV3 12 78119921 Missense_Mutation SNP A C3N-02149_T 11788458 78119921 55155388 360 28544 CRADD 0 . GRCh38 12 93678970 93678970 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.196C>T p.Pro66Ser p.P66S ENST00000542893 2/3 418 346 72 474 473 1 strelka-varscan-mutect CRADD,missense_variant,p.Pro66Ser,ENST00000542893,NM_001320099.1;CRADD,missense_variant,p.Pro66Ser,ENST00000332896,NM_003805.3;CRADD,missense_variant,p.Pro66Ser,ENST00000548483,;CRADD,missense_variant,p.Pro66Ser,ENST00000552983,;CRADD,missense_variant,p.Pro66Ser,ENST00000552033,NM_001320101.1;CRADD,non_coding_transcript_exon_variant,,ENST00000549615,;CRADD,missense_variant,p.Pro66Ser,ENST00000551065,; T ENST00000542893 Transcript missense_variant 514/1403 196/600 66/199 P/S Cct/Tct 1 1 CRADD HGNC HGNC:2340 protein_coding YES CCDS9048.1 ENSP00000439068 P78560 Q53XL1 UPI00001283AA NM_001320099.1 deleterious(0) 2/3 PROSITE_profiles:PS50209,hmmpanther:PTHR15034,Pfam_domain:PF00619,Gene3D:1.10.533.10,SMART_domains:SM00114,Superfamily_domains:SSF47986 MODERATE 1 SNV 1 1 PASS rs1407377581 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 93678970 93678970 C T 1 0 0 0 0 1 0 0 0 3645 623 22 3 3 CRADD 12 93678970 Missense_Mutation SNP C C3N-02149_T 15559049 93678970 39596339 361 28545 NTN4 0 . GRCh38 12 95786989 95786989 + Missense_Mutation SNP C C A rs142996736 C3N-02149_T C3N-02149_N C C c.535G>T p.Ala179Ser p.A179S ENST00000343702 2/10 213 187 26 255 251 4 strelka-varscan-mutect NTN4,missense_variant,p.Ala179Ser,ENST00000343702,NM_021229.3;NTN4,missense_variant,p.Ala142Ser,ENST00000344911,;NTN4,missense_variant,p.Ala142Ser,ENST00000538383,;NTN4,missense_variant,p.Ala179Ser,ENST00000553059,;NTN4,missense_variant,p.Ala142Ser,ENST00000547980,; A ENST00000343702 Transcript missense_variant 984/3615 535/1887 179/628 A/S Gct/Tct rs142996736,COSM1217983 1 -1 NTN4 HGNC HGNC:13658 protein_coding YES CCDS9054.1 ENSP00000340998 Q9HB63 UPI0000049824 NM_021229.3 tolerated(0.51) 2/10 PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF282,Pfam_domain:PF00055,SMART_domains:SM00136 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs142996736 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 95786989 95786989 C A 1 0 0 0 0 1 0 0 0 10767 768 27 1 1 NTN4 12 95786989 Missense_Mutation SNP C C3N-02149_T 2108019 95786989 37488320 362 28546 HAL 0 . GRCh38 12 95993802 95993802 + Missense_Mutation SNP G G A C3N-02149_T C3N-02149_N G G c.521C>T p.Ala174Val p.A174V ENST00000261208 7/21 496 429 67 662 662 0 strelka-varscan-mutect HAL,missense_variant,p.Ala174Val,ENST00000261208,NM_002108.3;HAL,missense_variant,p.Ala174Val,ENST00000538703,NM_001258334.1;HAL,missense_variant,p.Ala84Val,ENST00000546579,;HAL,intron_variant,,ENST00000541929,NM_001258333.1;HAL,intron_variant,,ENST00000552509,;RP11-256L6.3,upstream_gene_variant,,ENST00000551849,;HAL,upstream_gene_variant,,ENST00000551562,;HAL,intron_variant,,ENST00000544080,;HAL,intron_variant,,ENST00000546999,;HAL,upstream_gene_variant,,ENST00000549376,; A ENST00000261208 Transcript missense_variant 890/3913 521/1974 174/657 A/V gCc/gTc COSM944726 1 -1 HAL HGNC HGNC:4806 protein_coding YES CCDS9058.1 ENSP00000261208 P42357 UPI000012CE8E NM_002108.3 deleterious(0.02) 7/21 hmmpanther:PTHR10362,hmmpanther:PTHR10362:SF7,Gene3D:1.10.275.10,Pfam_domain:PF00221,TIGRFAM_domain:TIGR01225,Superfamily_domains:SSF48557 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 95993802 95993802 G A 1 0 0 0 0 1 0 0 0 6833 1203 42 3 3 HAL 12 95993802 Missense_Mutation SNP G C3N-02149_T 206813 95993802 37281507 363 28547 APAF1 0 . GRCh38 12 98662553 98662553 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.808A>G p.Thr270Ala p.T270A ENST00000551964 6/27 433 359 74 593 593 0 strelka-varscan-mutect APAF1,missense_variant,p.Thr270Ala,ENST00000357310,NM_181868.1;APAF1,missense_variant,p.Thr259Ala,ENST00000359972,NM_001160.2;APAF1,missense_variant,p.Thr259Ala,ENST00000550527,NM_013229.2;APAF1,missense_variant,p.Thr270Ala,ENST00000551964,NM_181861.1;APAF1,missense_variant,p.Thr270Ala,ENST00000333991,NM_181869.1;APAF1,missense_variant,p.Thr270Ala,ENST00000547045,;APAF1,missense_variant,p.Thr270Ala,ENST00000549007,;APAF1,missense_variant,p.Thr270Ala,ENST00000552268,; G ENST00000551964 Transcript missense_variant 1544/5444 808/3747 270/1248 T/A Aca/Gca 1 1 APAF1 HGNC HGNC:576 protein_coding YES CCDS9069.1 ENSP00000448165 O14727 UPI0000036328 NM_181861.1 tolerated(0.16) 6/27 Gene3D:3.40.50.300,Pfam_domain:PF00931,PIRSF_domain:PIRSF037646,hmmpanther:PTHR22845,hmmpanther:PTHR22845:SF5,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 98662553 98662553 A G 1 0 0 0 0 1 0 0 0 875 391 14 5 5 APAF1 12 98662553 Missense_Mutation SNP A C3N-02149_T 2668751 98662553 34612756 364 28548 RIC8B 0 . GRCh38 12 106851448 106851448 + Splice_Site SNP A A G novel C3N-02149_T C3N-02149_N A A c.1162-2A>G p.X388_splice ENST00000392839 95 78 17 156 156 0 strelka-varscan-mutect RIC8B,splice_acceptor_variant,,ENST00000392837,;RIC8B,splice_acceptor_variant,,ENST00000355478,;RIC8B,splice_acceptor_variant,,ENST00000392839,NM_018157.2;RIC8B,splice_acceptor_variant,,ENST00000548914,;RIC8B,intron_variant,,ENST00000549643,;RIC8B,splice_acceptor_variant,,ENST00000470960,;RIC8B,splice_acceptor_variant,,ENST00000462949,;RIC8B,splice_acceptor_variant,,ENST00000470628,; G ENST00000392839 Transcript splice_acceptor_variant -/2440 1162/1563 388/520 1 1 RIC8B HGNC HGNC:25555 protein_coding YES CCDS9109.2 ENSP00000376583 Q9NVN3 UPI00001FB46B NM_018157.2 6/8 HIGH 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 92 106851448 106851448 A G 1 0 0 0 0 0 0 1 0 13530 202 7 5 5 RIC8B 12 106851448 Splice_Site SNP A C3N-02149_T 8188895 106851448 26423861 365 28549 CIT 0 . GRCh38 12 119869129 119869129 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.169G>C p.Val57Leu p.V57L ENST00000392521 3/48 223 200 23 292 291 1 strelka-varscan-mutect CIT,missense_variant,p.Val57Leu,ENST00000392521,NM_001206999.1;CIT,missense_variant,p.Val57Leu,ENST00000261833,NM_007174.2;CIT,missense_variant,p.Val57Leu,ENST00000612548,; G ENST00000392521 Transcript missense_variant 225/8708 169/6210 57/2069 V/L Gtt/Ctt 1 -1 CIT HGNC HGNC:1985 protein_coding YES CCDS55891.1 ENSP00000376306 O14578 UPI0000683C41 NM_001206999.1 tolerated(0.63) 3/48 PIRSF_domain:PIRSF038145,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF26 MODERATE 1 SNV 1 1 PASS rs1225453765 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 119869129 119869129 C G 1 0 0 0 0 1 0 0 0 3201 478 17 4 4 CIT 12 119869129 Missense_Mutation SNP C C3N-02149_T 13017681 119869129 13406180 366 28550 RNF10 0 . GRCh38 12 120534894 120534894 + Missense_Mutation SNP C C T rs763897888 C3N-02149_T C3N-02149_N C C c.83C>T p.Ser28Leu p.S28L ENST00000325954 1/17 269 240 29 339 339 0 strelka-varscan-mutect RNF10,missense_variant,p.Ser28Leu,ENST00000325954,NM_014868.4;RNF10,missense_variant,p.Ser28Leu,ENST00000413266,;RNF10,missense_variant,p.Ser28Leu,ENST00000542438,;RNF10,upstream_gene_variant,,ENST00000537997,;COQ5,upstream_gene_variant,,ENST00000551769,;RNF10,downstream_gene_variant,,ENST00000539486,;RNF10,non_coding_transcript_exon_variant,,ENST00000551139,;RNF10,missense_variant,p.Ser28Leu,ENST00000538796,;RNF10,missense_variant,p.Ser8Leu,ENST00000536869,; T ENST00000325954 Transcript missense_variant 544/3825 83/2436 28/811 S/L tCg/tTg rs763897888 1 1 RNF10 HGNC HGNC:10055 protein_coding YES CCDS9201.1 ENSP00000322242 Q8N5U6 A0A024RBP0 UPI000006D77E NM_014868.4 deleterious_low_confidence(0.01) 1/17 Low_complexity_(Seg):seg,hmmpanther:PTHR12983 MODERATE 1 SNV 1 1 PASS rs763897888 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 120534894 120534894 C T 1 0 0 0 0 1 0 0 0 13600 893 31 1 1 RNF10 12 120534894 Missense_Mutation SNP C C3N-02149_T 665765 120534894 12740415 367 28551 OASL 0 . GRCh38 12 121031617 121031617 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.482G>T p.Gly161Val p.G161V ENST00000257570 3/6 104 91 13 107 107 0 strelka-varscan-mutect OASL,missense_variant,p.Gly161Val,ENST00000257570,NM_003733.3;OASL,missense_variant,p.Gly161Val,ENST00000620239,NM_001261825.1;OASL,missense_variant,p.Gly161Val,ENST00000339275,NM_198213.2;OASL,missense_variant,p.Gly59Val,ENST00000543677,; A ENST00000257570 Transcript missense_variant,splice_region_variant 753/3266 482/1545 161/514 G/V gGg/gTg 1 -1 OASL HGNC HGNC:8090 protein_coding YES CCDS9211.1 ENSP00000257570 Q15646 UPI000005339E NM_003733.3 deleterious(0) 3/6 Gene3D:3.30.460.10,hmmpanther:PTHR11258,hmmpanther:PTHR11258:SF16,Superfamily_domains:SSF81301 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 92 121031617 121031617 C A 1 0 0 0 0 1 0 0 0 10881 637 22 2 2 OASL 12 121031617 Missense_Mutation SNP C C3N-02149_T 496723 121031617 12243692 368 28552 KDM2B 0 . GRCh38 12 121453321 121453321 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1758G>T p.Lys586Asn p.K586N ENST00000377071 13/23 135 109 26 152 152 0 strelka-varscan-mutect KDM2B,missense_variant,p.Lys555Asn,ENST00000377069,NM_001005366.1;KDM2B,missense_variant,p.Lys586Asn,ENST00000377071,NM_032590.4;KDM2B,missense_variant,p.Lys469Asn,ENST00000611216,;KDM2B,missense_variant,p.Lys586Asn,ENST00000536437,;KDM2B,5_prime_UTR_variant,,ENST00000542973,;KDM2B,3_prime_UTR_variant,,ENST00000543025,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538503,;KDM2B,non_coding_transcript_exon_variant,,ENST00000538243,; A ENST00000377071 Transcript missense_variant 1831/4595 1758/4011 586/1336 K/N aaG/aaT 1 -1 KDM2B HGNC HGNC:13610 protein_coding YES CCDS41850.1 ENSP00000366271 Q8NHM5 UPI000006F36E NM_032590.4 deleterious(0.04) 13/23 hmmpanther:PTHR23123:SF10,hmmpanther:PTHR23123 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 121453321 121453321 C A 1 0 0 0 0 1 0 0 0 8043 680 24 2 2 KDM2B 12 121453321 Missense_Mutation SNP C C3N-02149_T 421704 121453321 11821988 369 28553 TMEM120B 0 . GRCh38 12 121743645 121743645 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.86A>G p.Tyr29Cys p.Y29C ENST00000449592 2/12 148 128 20 165 165 0 strelka-varscan-mutect TMEM120B,missense_variant,p.Tyr29Cys,ENST00000449592,NM_001080825.2;TMEM120B,missense_variant,p.Tyr8Cys,ENST00000541467,;TMEM120B,missense_variant,p.Tyr29Cys,ENST00000342607,; G ENST00000449592 Transcript missense_variant 187/7461 86/1020 29/339 Y/C tAc/tGc 1 1 TMEM120B HGNC HGNC:32008 protein_coding YES CCDS41852.1 ENSP00000404991 A0PK00 UPI0000160852 NM_001080825.2 deleterious(0.01) 2/12 hmmpanther:PTHR21433,hmmpanther:PTHR21433:SF2,Pfam_domain:PF07851,Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -20 0.9999514 1 1 1 0 G 3 3 92 121743645 121743645 A G 1 0 0 0 0 1 0 0 0 16478 391 14 5 5 TMEM120B 12 121743645 Missense_Mutation SNP A C3N-02149_T 290324 121743645 11531664 370 28554 TMEM132C 0 . GRCh38 12 128696077 128696077 + Silent SNP C C A C3N-02149_T C3N-02149_N C C c.1903C>A p.= p.R635R ENST00000435159 7/9 111 98 13 158 158 0 strelka-varscan-mutect TMEM132C,synonymous_variant,p.=,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript synonymous_variant 1903/4947 1903/3327 635/1108 R Cga/Aga COSM3359613,COSM3359614 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 7/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 1,1 LOW 1 SNV 5 1,1 1 PASS rs1376966220 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 128696077 128696077 C A 1 0 0 0 0 0 0 0 1 16491 760 27 1 1 TMEM132C 12 128696077 Silent SNP C C3N-02149_T 6952432 128696077 4579232 371 28555 SACS 0 . GRCh38 13 23340713 23340713 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.3163G>T p.Asp1055Tyr p.D1055Y ENST00000382292 9/9 77 67 10 96 96 0 strelka-varscan-mutect SACS,missense_variant,p.Asp1055Tyr,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Asp305Tyr,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; A ENST00000382292 Transcript missense_variant 3437/15324 3163/13740 1055/4579 D/Y Gac/Tac 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 deleterious(0) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.99549 1 1 1 1 0 A 3 1 92 23340713 23340713 C A 1 0 0 0 0 1 0 0 0 14063 826 29 2 2 SACS 13 23340713 Missense_Mutation SNP C C3N-02149_T 23340713 91023615 372 28556 ATP12A 0 . GRCh38 13 24698828 24698828 + Silent SNP C C A rs559369271 C3N-02149_T C3N-02149_N C C c.1701C>A p.= p.G567G ENST00000218548 12/23 130 115 15 169 169 0 strelka-varscan-mutect ATP12A,synonymous_variant,p.=,ENST00000381946,NM_001676.5;ATP12A,synonymous_variant,p.=,ENST00000218548,NM_001185085.1;RNY1P7,downstream_gene_variant,,ENST00000384743,; A ENST00000218548 Transcript synonymous_variant 2034/3732 1701/3138 567/1045 G ggC/ggA rs559369271 1 1 ATP12A HGNC HGNC:13816 protein_coding YES CCDS53858.1 ENSP00000218548 P54707 UPI000006D1DE NM_001185085.1 12/23 hmmpanther:PTHR24093:SF282,hmmpanther:PTHR24093,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01106,Superfamily_domains:SSF81660 LOW 1 SNV 1 1 PASS rs559369271 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 24698828 24698828 C A 1 0 0 0 0 0 0 0 1 1274 755 27 1 1 ATP12A 13 24698828 Silent SNP C C3N-02149_T 1358115 24698828 89665500 373 28557 98 2 ATP12A 0 . GRCh38 13 24698829 24698829 + Missense_Mutation SNP G G T rs757024432 C3N-02149_T C3N-02149_N G G c.1702G>T p.Gly568Trp p.G568W ENST00000218548 12/23 131 108 23 168 167 1 strelka-varscan-mutect ATP12A,missense_variant,p.Gly562Trp,ENST00000381946,NM_001676.5;ATP12A,missense_variant,p.Gly568Trp,ENST00000218548,NM_001185085.1;RNY1P7,downstream_gene_variant,,ENST00000384743,; T ENST00000218548 Transcript missense_variant 2035/3732 1702/3138 568/1045 G/W Ggg/Tgg rs757024432 1 1 ATP12A HGNC HGNC:13816 protein_coding YES CCDS53858.1 ENSP00000218548 P54707 UPI000006D1DE NM_001185085.1 deleterious(0) 12/23 hmmpanther:PTHR24093:SF282,hmmpanther:PTHR24093,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01106,Superfamily_domains:SSF81660 MODERATE 1 SNV 1 1 PASS rs757024432 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 24698829 24698829 G T 1 0 0 0 0 1 0 0 0 1274 1116 39 1 1 ATP12A 13 24698829 Missense_Mutation SNP G C3N-02149_T 1 24698829 89665499 374 28558 98 2 WASF3 0 . GRCh38 13 26682647 26682647 + Missense_Mutation SNP G G A rs201580275 C3N-02149_T C3N-02149_N G G c.1024G>A p.Gly342Arg p.G342R ENST00000335327 9/10 595 556 39 689 689 0 strelka-varscan-mutect WASF3,missense_variant,p.Gly339Arg,ENST00000361042,NM_001291965.1;WASF3,missense_variant,p.Gly342Arg,ENST00000335327,NM_006646.5; A ENST00000335327 Transcript missense_variant 1202/4790 1024/1509 342/502 G/R Gga/Aga rs201580275,COSM5012651,COSM5012652 1 1 WASF3 HGNC HGNC:12734 protein_coding YES CCDS9318.1 ENSP00000335055 Q9UPY6 Q5T8P4 UPI000013CEA7 NM_006646.5 tolerated(0.11) 9/10 hmmpanther:PTHR12902 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs201580275 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 26682647 26682647 G A 1 0 0 0 0 1 0 0 0 17814 1117 39 1 1 WASF3 13 26682647 Missense_Mutation SNP G C3N-02149_T 1983818 26682647 87681681 375 28559 TEX26 0 . GRCh38 13 30932737 30932737 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.22G>T p.Ala8Ser p.A8S ENST00000380473 1/7 154 130 24 219 219 0 strelka-varscan-mutect TEX26,missense_variant,p.Ala8Ser,ENST00000380473,NM_152325.1;TEX26-AS1,intron_variant,,ENST00000591131,;TEX26-AS1,intron_variant,,ENST00000591300,;TEX26-AS1,intron_variant,,ENST00000587596,;TEX26-AS1,upstream_gene_variant,,ENST00000585870,;TEX26-AS1,upstream_gene_variant,,ENST00000588425,;TEX26-AS1,upstream_gene_variant,,ENST00000411835,;TEX26-AS1,upstream_gene_variant,,ENST00000589840,;TEX26-AS1,upstream_gene_variant,,ENST00000585582,;TEX26-AS1,upstream_gene_variant,,ENST00000586464,;TEX26-AS1,upstream_gene_variant,,ENST00000588726,;TEX26-AS1,upstream_gene_variant,,ENST00000593246,;TEX26-AS1,upstream_gene_variant,,ENST00000590344,;TEX26-AS1,upstream_gene_variant,,ENST00000592950,;TEX26-AS1,upstream_gene_variant,,ENST00000586973,;TEX26-AS1,upstream_gene_variant,,ENST00000429200,;TEX26-AS1,upstream_gene_variant,,ENST00000451495,;TEX26-AS1,upstream_gene_variant,,ENST00000590721,;TEX26,non_coding_transcript_exon_variant,,ENST00000479195,;TEX26,missense_variant,p.Ala5Ser,ENST00000531960,; T ENST00000380473 Transcript missense_variant 35/1478 22/870 8/289 A/S Gct/Tct 1 1 TEX26 HGNC HGNC:28622 protein_coding YES CCDS9339.1 ENSP00000369840 Q8N6G2 UPI0000070D41 NM_152325.1 deleterious(0.02) 1/7 hmmpanther:PTHR33769:SF1,hmmpanther:PTHR33769 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 30932737 30932737 G T 1 0 0 0 0 1 0 0 0 16205 1203 42 2 2 TEX26 13 30932737 Missense_Mutation SNP G C3N-02149_T 4250090 30932737 83431591 376 28560 FRY 0 . GRCh38 13 32078966 32078966 + Missense_Mutation SNP A A T rs768798713 C3N-02149_T C3N-02149_N A A c.203A>T p.Lys68Ile p.K68I ENST00000542859 2/61 392 333 59 523 523 0 strelka-varscan-mutect FRY,missense_variant,p.Lys68Ile,ENST00000542859,NM_023037.2;FRY,missense_variant,p.Lys68Ile,ENST00000380250,;FRY,missense_variant,p.Lys65Ile,ENST00000436046,; T ENST00000542859 Transcript missense_variant 699/13200 203/9042 68/3013 K/I aAa/aTa rs768798713 1 1 FRY HGNC HGNC:20367 protein_coding YES CCDS41875.1 ENSP00000445043 Q5TBA9 UPI000046FD40 NM_023037.2 deleterious(0) 2/61 hmmpanther:PTHR12295,hmmpanther:PTHR12295:SF29 MODERATE 1 SNV 5 1 PASS rs768798713 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 32078966 32078966 A T 1 0 0 0 0 1 0 0 0 5935 14 1 4 4 FRY 13 32078966 Missense_Mutation SNP A C3N-02149_T 1146229 32078966 82285362 377 28561 CCNA1 0 . GRCh38 13 36437773 36437773 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.442G>T p.Asp148Tyr p.D148Y ENST00000255465 3/9 284 225 59 345 345 0 strelka-varscan-mutect CCNA1,missense_variant,p.Asp148Tyr,ENST00000255465,NM_003914.3;CCNA1,missense_variant,p.Asp104Tyr,ENST00000440264,NM_001111047.1,NM_001111046.1;CCNA1,missense_variant,p.Asp104Tyr,ENST00000630422,;CCNA1,missense_variant,p.Asp147Tyr,ENST00000625767,NM_001111045.1; T ENST00000255465 Transcript missense_variant 706/1879 442/1398 148/465 D/Y Gac/Tac 1 1 CCNA1 HGNC HGNC:1577 protein_coding YES CCDS9357.1 ENSP00000255465 P78396 UPI000012759F NM_003914.3 tolerated(0.21) 3/9 hmmpanther:PTHR10177,hmmpanther:PTHR10177:SF254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 36437773 36437773 G T 1 0 0 0 0 1 0 0 0 2608 942 33 2 2 CCNA1 13 36437773 Missense_Mutation SNP G C3N-02149_T 4358807 36437773 77926555 378 28562 PROSER1 0 . GRCh38 13 39017508 39017508 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.767A>T p.Gln256Leu p.Q256L ENST00000352251 10/13 323 290 33 423 423 0 strelka-varscan-mutect PROSER1,missense_variant,p.Gln256Leu,ENST00000352251,NM_025138.4;PROSER1,missense_variant,p.Gln234Leu,ENST00000625998,;PROSER1,intron_variant,,ENST00000484434,;PROSER1,upstream_gene_variant,,ENST00000468017,;PROSER1,non_coding_transcript_exon_variant,,ENST00000602899,;PROSER1,non_coding_transcript_exon_variant,,ENST00000602512,;PROSER1,downstream_gene_variant,,ENST00000496138,; A ENST00000352251 Transcript missense_variant 1601/5168 767/2835 256/944 Q/L cAg/cTg 1 -1 PROSER1 HGNC HGNC:20291 protein_coding YES CCDS9368.2 ENSP00000332034 Q86XN7 UPI00001FCC65 NM_025138.4 deleterious(0) 10/13 hmmpanther:PTHR14880,hmmpanther:PTHR14880:SF2 MODERATE 1 SNV 1 1 PASS rs1427926205 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 39017508 39017508 T A 1 0 0 0 0 1 0 0 0 12693 1580 55 4 4 PROSER1 13 39017508 Missense_Mutation SNP T C3N-02149_T 2579735 39017508 75346820 379 28563 ERICH6B 0 . GRCh38 13 45544887 45544887 + Missense_Mutation SNP G G T rs527763848 C3N-02149_T C3N-02149_N G G c.1745C>A p.Pro582His p.P582H ENST00000298738 14/15 352 281 71 477 476 1 strelka-varscan-mutect ERICH6B,missense_variant,p.Pro582His,ENST00000298738,NM_182542.2;ERICH6B,non_coding_transcript_exon_variant,,ENST00000482992,;ERICH6B,intron_variant,,ENST00000504261,; T ENST00000298738 Transcript missense_variant 1910/2421 1745/2091 582/696 P/H cCt/cAt rs527763848 1 -1 ERICH6B HGNC HGNC:26523 protein_coding YES CCDS45045.1 ENSP00000298738 Q5W0A0 UPI000013E513 NM_182542.2 deleterious(0) 14/15 Pfam_domain:PF14977,hmmpanther:PTHR23093,hmmpanther:PTHR23093:SF17 MODERATE 1 SNV 2 1 PASS rs527763848 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 45544887 45544887 G T 1 0 0 0 0 1 0 0 0 5087 1000 35 2 2 ERICH6B 13 45544887 Missense_Mutation SNP G C3N-02149_T 6527379 45544887 68819441 380 28564 LRCH1 0 . GRCh38 13 46728916 46728916 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.1939C>T p.Leu647Phe p.L647F ENST00000389797 18/20 127 118 9 199 199 0 strelka-varscan-mutect LRCH1,missense_variant,p.Leu612Phe,ENST00000311191,NM_001164213.1;LRCH1,missense_variant,p.Leu612Phe,ENST00000389798,NM_015116.2;LRCH1,missense_variant,p.Leu647Phe,ENST00000389797,NM_001164211.1; T ENST00000389797 Transcript missense_variant 2076/3314 1939/2292 647/763 L/F Ctc/Ttc 1 1 LRCH1 HGNC HGNC:20309 protein_coding YES CCDS53865.1 ENSP00000374447 Q9Y2L9 UPI00015DFE06 NM_001164211.1 deleterious(0) 18/20 Gene3D:1.10.418.10,Pfam_domain:PF00307,PROSITE_profiles:PS50021,SMART_domains:SM00033,Superfamily_domains:SSF47576 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -17.70981 1 1 1 1 0 T 3 4 92 46728916 46728916 C T 1 0 0 0 0 1 0 0 0 8826 681 24 3 3 LRCH1 13 46728916 Missense_Mutation SNP C C3N-02149_T 1184029 46728916 67635412 381 28565 RASA3 0 . GRCh38 13 113979384 113979384 + Missense_Mutation SNP A A T rs771630619 C3N-02149_T C3N-02149_N A A c.2468T>A p.Ile823Asn p.I823N ENST00000334062 24/24 268 245 23 307 306 1 strelka-varscan-mutect RASA3,missense_variant,p.Ile823Asn,ENST00000334062,NM_001320822.1,NM_007368.2; T ENST00000334062 Transcript missense_variant 2590/4191 2468/2505 823/834 I/N aTc/aAc rs771630619 1 -1 RASA3 HGNC HGNC:20331 protein_coding YES CCDS32016.1 ENSP00000335029 Q14644 UPI000000DBC1 NM_001320822.1,NM_007368.2 deleterious(0.01) 24/24 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF53 MODERATE 1 SNV 1 1 PASS rs771630619 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 113979384 113979384 A T 1 0 0 0 0 1 0 0 0 13221 333 12 4 4 RASA3 13 113979384 Missense_Mutation SNP A C3N-02149_T 67250468 113979384 384944 382 28566 PSMB11 0 . GRCh38 14 23042911 23042911 + Missense_Mutation SNP G G A rs774869639 C3N-02149_T C3N-02149_N G G c.686G>A p.Arg229Gln p.R229Q ENST00000408907 1/1 141 133 8 163 163 0 strelka-varscan-mutect PSMB11,missense_variant,p.Arg229Gln,ENST00000408907,NM_001099780.1;CDH24,downstream_gene_variant,,ENST00000397359,NM_022478.3;CDH24,downstream_gene_variant,,ENST00000487137,NM_144985.3;CDH24,downstream_gene_variant,,ENST00000267383,;CDH24,downstream_gene_variant,,ENST00000554034,;CDH24,downstream_gene_variant,,ENST00000610348,;CDH24,downstream_gene_variant,,ENST00000485922,; A ENST00000408907 Transcript missense_variant 745/2110 686/903 229/300 R/Q cGg/cAg rs774869639,COSM1587339,COSM1587340,COSM954607 1 1 PSMB11 HGNC HGNC:31963 protein_coding YES CCDS41923.1 ENSP00000386212 A5LHX3 UPI00001D7B85 NM_001099780.1 tolerated(0.27) 1/1 Gene3D:3.60.20.10,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF48,Superfamily_domains:SSF56235 0,1,1,1 MODERATE SNV 0,1,1,1 1 PASS rs774869639 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 23042911 23042911 G A 1 0 0 0 0 1 0 0 0 12827 1116 39 1 1 PSMB11 14 23042911 Missense_Mutation SNP G C3N-02149_T 23042911 84000807 383 28567 DHRS2 0 . GRCh38 14 23644458 23644458 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.590G>T p.Arg197Ile p.R197I ENST00000344777 7/9 283 240 43 404 404 0 strelka-varscan-mutect DHRS2,missense_variant,p.Arg197Ile,ENST00000250383,NM_005794.3;DHRS2,missense_variant,p.Arg197Ile,ENST00000344777,NM_182908.4;DHRS2,missense_variant,p.Arg197Ile,ENST00000611765,;DHRS2,missense_variant,p.Arg113Ile,ENST00000557535,;DHRS2,missense_variant,p.Arg97Ile,ENST00000553600,;DHRS2,missense_variant,p.Arg197Ile,ENST00000432832,;DHRS2,downstream_gene_variant,,ENST00000553896,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556729,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556701,;DHRS2,non_coding_transcript_exon_variant,,ENST00000556550,; T ENST00000344777 Transcript missense_variant 1028/1678 590/903 197/300 R/I aGa/aTa 1 1 DHRS2 HGNC HGNC:18349 protein_coding YES CCDS41927.1 ENSP00000344674 Q13268 UPI00001A3E34 NM_182908.4 deleterious(0) 7/9 Low_complexity_(Seg):seg,hmmpanther:PTHR24322,hmmpanther:PTHR24322:SF322,PROSITE_patterns:PS00061,Gene3D:3.40.50.720,Pfam_domain:PF00106,Superfamily_domains:SSF51735,Prints_domain:PR00081,Prints_domain:PR00080 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 23644458 23644458 G T 1 0 0 0 0 1 0 0 0 4295 942 33 2 2 DHRS2 14 23644458 Missense_Mutation SNP G C3N-02149_T 601547 23644458 83399260 384 28568 FOXG1 0 . GRCh38 14 28768684 28768684 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.1405G>T p.Gly469Trp p.G469W ENST00000313071 1/1 313 280 33 282 282 0 strelka-varscan-mutect FOXG1,missense_variant,p.Gly469Trp,ENST00000313071,NM_005249.4;LINC01551,upstream_gene_variant,,ENST00000399387,;LINC01551,upstream_gene_variant,,ENST00000552957,;LINC01551,upstream_gene_variant,,ENST00000548213,;FOXG1-AS1,upstream_gene_variant,,ENST00000551395,;FOXG1-AS1,upstream_gene_variant,,ENST00000546560,;FOXG1-AS1,upstream_gene_variant,,ENST00000549487,;FOXG1,downstream_gene_variant,,ENST00000637817,;FOXG1,downstream_gene_variant,,ENST00000636893,;FOXG1,downstream_gene_variant,,ENST00000636353,;FOXG1,downstream_gene_variant,,ENST00000637220,;FOXG1,downstream_gene_variant,,ENST00000636346,;FOXG1,downstream_gene_variant,,ENST00000636604,;FOXG1,downstream_gene_variant,,ENST00000637351,; T ENST00000313071 Transcript missense_variant 3297/4890 1405/1470 469/489 G/W Ggg/Tgg COSM698030 1 1 FOXG1 HGNC HGNC:3811 protein_coding YES CCDS9636.1 ENSP00000339004 P55316 UPI00001AE46C NM_005249.4 deleterious_low_confidence(0) 1/1 hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF165 1 MODERATE SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -11.76058 0.9940025 1 1 1 0 T 3 4 92 28768684 28768684 G T 1 0 0 0 0 1 0 0 0 5869 1348 47 2 2 FOXG1 14 28768684 Missense_Mutation SNP G C3N-02149_T 5124226 28768684 78275034 385 28569 FAM179B 0 . GRCh38 14 45032232 45032232 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.3668C>G p.Pro1223Arg p.P1223R ENST00000361462 11/20 170 134 36 201 201 0 varscan-mutect FAM179B,missense_variant,p.Pro1223Arg,ENST00000361462,NM_001308120.1;FAM179B,missense_variant,p.Pro1223Arg,ENST00000361577,NM_015091.2;KLHL28,intron_variant,,ENST00000556239,;KLHL28,intron_variant,,ENST00000553817,;FAM179B,3_prime_UTR_variant,,ENST00000557423,;FAM179B,downstream_gene_variant,,ENST00000556105,;FAM179B,downstream_gene_variant,,ENST00000555586,; G ENST00000361462 Transcript missense_variant 3851/6375 3668/5322 1223/1773 P/R cCt/cGt 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 tolerated(0.08) 11/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 45032232 45032232 C G 1 0 0 0 0 1 0 0 0 5351 681 24 4 4 FAM179B 14 45032232 Missense_Mutation SNP C C3N-02149_T 16263548 45032232 62011486 386 28570 SOS2 0 . GRCh38 14 50174485 50174485 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1037A>G p.Tyr346Cys p.Y346C ENST00000216373 8/23 96 81 15 140 140 0 strelka-varscan-mutect SOS2,missense_variant,p.Tyr346Cys,ENST00000216373,NM_006939.2;SOS2,missense_variant,p.Tyr51Cys,ENST00000555794,;SOS2,intron_variant,,ENST00000543680,; C ENST00000216373 Transcript missense_variant 1312/5498 1037/3999 346/1332 Y/C tAt/tGt 1 -1 SOS2 HGNC HGNC:11188 protein_coding YES CCDS9697.1 ENSP00000216373 Q07890 UPI000013C6E8 NM_006939.2 tolerated(0.1) 8/23 PROSITE_profiles:PS50010,hmmpanther:PTHR23113:SF150,hmmpanther:PTHR23113,Pfam_domain:PF00621,Gene3D:1.20.900.10,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS rs1486068977 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 50174485 50174485 T C 1 0 0 0 0 1 0 0 0 15259 1406 49 5 5 SOS2 14 50174485 Missense_Mutation SNP T C3N-02149_T 5142253 50174485 56869233 387 28571 EXOC5 0 . GRCh38 14 57268641 57268641 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.8C>T p.Thr3Ile p.T3I ENST00000621441 1/18 255 231 24 285 285 0 strelka-varscan-mutect EXOC5,missense_variant,p.Thr3Ile,ENST00000621441,NM_006544.3;EXOC5,missense_variant,p.Thr3Ile,ENST00000413566,;EXOC5,missense_variant,p.Thr3Ile,ENST00000340918,;AP5M1,upstream_gene_variant,,ENST00000261558,NM_018229.3;AP5M1,upstream_gene_variant,,ENST00000431972,;AP5M1,upstream_gene_variant,,ENST00000556995,;EXOC5,upstream_gene_variant,,ENST00000556318,;AP5M1,upstream_gene_variant,,ENST00000554213,;EXOC5,missense_variant,p.Thr3Ile,ENST00000555148,;EXOC5,non_coding_transcript_exon_variant,,ENST00000554598,;EXOC5,non_coding_transcript_exon_variant,,ENST00000555749,;AP5M1,upstream_gene_variant,,ENST00000554931,;AP5M1,upstream_gene_variant,,ENST00000555448,; A ENST00000621441 Transcript missense_variant 368/10589 8/2127 3/708 T/I aCc/aTc 1 -1 EXOC5 HGNC HGNC:10696 protein_coding YES CCDS45111.1 ENSP00000484855 O00471 UPI0000047E53 NM_006544.3 tolerated(0.09) 1/18 hmmpanther:PTHR12100:SF0,hmmpanther:PTHR12100 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 57268641 57268641 G A 1 0 0 0 0 1 0 0 0 5175 1261 44 3 3 EXOC5 14 57268641 Missense_Mutation SNP G C3N-02149_T 7094156 57268641 49775077 388 28572 DACT1 0 . GRCh38 14 58645788 58645788 + Missense_Mutation SNP A A T rs747687272 C3N-02149_T C3N-02149_N A A c.1165A>T p.Ser389Cys p.S389C ENST00000335867 4/4 398 292 106 512 511 1 strelka-varscan-mutect DACT1,missense_variant,p.Ser352Cys,ENST00000395153,NM_001079520.1;DACT1,missense_variant,p.Ser108Cys,ENST00000541264,;DACT1,missense_variant,p.Ser389Cys,ENST00000335867,NM_016651.5;DACT1,missense_variant,p.Ser108Cys,ENST00000556859,;DACT1,missense_variant,p.Ser108Cys,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,; T ENST00000335867 Transcript missense_variant 1189/2571 1165/2511 389/836 S/C Agt/Tgt rs747687272 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 deleterious(0.04) 4/4 hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268 MODERATE 1 SNV 2 1 PASS rs747687272 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 58645788 58645788 A T 1 0 0 0 0 1 0 0 0 4023 188 7 4 4 DACT1 14 58645788 Missense_Mutation SNP A C3N-02149_T 1377147 58645788 48397930 389 28573 DACT1 0 . GRCh38 14 58646706 58646706 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.2083C>T p.Arg695Trp p.R695W ENST00000335867 4/4 332 310 22 321 321 0 strelka-varscan-mutect DACT1,missense_variant,p.Arg658Trp,ENST00000395153,NM_001079520.1;DACT1,missense_variant,p.Arg414Trp,ENST00000541264,;DACT1,missense_variant,p.Arg695Trp,ENST00000335867,NM_016651.5;DACT1,missense_variant,p.Arg414Trp,ENST00000556859,;DACT1,downstream_gene_variant,,ENST00000421793,;DACT1,downstream_gene_variant,,ENST00000555845,; T ENST00000335867 Transcript missense_variant 2107/2571 2083/2511 695/836 R/W Cgg/Tgg 1 1 DACT1 HGNC HGNC:17748 protein_coding YES CCDS9736.1 ENSP00000337439 Q9NYF0 UPI000013E4D3 NM_016651.5 deleterious(0) 4/4 Low_complexity_(Seg):seg,hmmpanther:PTHR15919,hmmpanther:PTHR15919:SF12,Pfam_domain:PF15268 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 58646706 58646706 C T 1 0 0 0 0 1 0 0 0 4023 643 23 1 1 DACT1 14 58646706 Missense_Mutation SNP C C3N-02149_T 918 58646706 48397012 390 28574 SYNE2 0 . GRCh38 14 64051890 64051890 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.7977G>T p.= p.R2659R ENST00000358025 48/116 520 451 69 703 700 3 strelka-varscan-mutect SYNE2,synonymous_variant,p.=,ENST00000358025,NM_182914.2;SYNE2,synonymous_variant,p.=,ENST00000344113,NM_015180.4;SYNE2,synonymous_variant,p.=,ENST00000357395,;SYNE2,synonymous_variant,p.=,ENST00000554584,;SYNE2,downstream_gene_variant,,ENST00000557005,; T ENST00000358025 Transcript synonymous_variant 8189/21842 7977/20724 2659/6907 R cgG/cgT 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 48/116 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF317 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 64051890 64051890 G T 1 0 0 0 0 0 0 0 1 15838 1219 43 2 2 SYNE2 14 64051890 Silent SNP G C3N-02149_T 5405184 64051890 42991828 391 28575 SYNE2 0 . GRCh38 14 64087821 64087821 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.11635A>T p.Met3879Leu p.M3879L ENST00000358025 58/116 158 134 24 235 234 1 strelka-varscan-mutect SYNE2,missense_variant,p.Met3879Leu,ENST00000358025,NM_182914.2;SYNE2,missense_variant,p.Met3879Leu,ENST00000344113,NM_015180.4;SYNE2,missense_variant,p.Met3912Leu,ENST00000357395,;SYNE2,missense_variant,p.Met3912Leu,ENST00000554584,;SYNE2,missense_variant,p.Met513Leu,ENST00000555002,;SYNE2,missense_variant,p.Met264Leu,ENST00000394768,;ESR2,intron_variant,,ENST00000556275,;SYNE2,non_coding_transcript_exon_variant,,ENST00000557060,; T ENST00000358025 Transcript missense_variant 11847/21842 11635/20724 3879/6907 M/L Atg/Ttg 1 1 SYNE2 HGNC HGNC:17084 protein_coding YES CCDS9761.2 ENSP00000350719 Q8WXH0 UPI00003677E5 NM_182914.2 tolerated(0.15) 58/116 Superfamily_domains:SSF46966 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 64087821 64087821 A T 1 0 0 0 0 1 0 0 0 15838 101 4 4 4 SYNE2 14 64087821 Missense_Mutation SNP A C3N-02149_T 35931 64087821 42955897 392 28576 HSPA2 0 . GRCh38 14 64541498 64541498 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.649G>T p.Asp217Tyr p.D217Y ENST00000394709 2/2 419 364 55 546 546 0 strelka-varscan-mutect HSPA2,missense_variant,p.Asp217Tyr,ENST00000394709,;HSPA2,missense_variant,p.Asp217Tyr,ENST00000247207,NM_021979.3;RP11-973N13.4,upstream_gene_variant,,ENST00000554918,;HSPA2,non_coding_transcript_exon_variant,,ENST00000554883,; T ENST00000394709 Transcript missense_variant 725/5400 649/1920 217/639 D/Y Gat/Tat 1 1 HSPA2 HGNC HGNC:5235 protein_coding YES CCDS9766.1 ENSP00000378199 P54652 A0A024R6B5 UPI000012CC6A deleterious_low_confidence(0) 2/2 Gene3D:3.30.420.40,Pfam_domain:PF00012,hmmpanther:PTHR19375,hmmpanther:PTHR19375:SF216,Superfamily_domains:SSF53067 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 64541498 64541498 G T 1 0 0 0 0 1 0 0 0 7307 1174 41 2 2 HSPA2 14 64541498 Missense_Mutation SNP G C3N-02149_T 453677 64541498 42502220 393 28577 GPHN 0 . GRCh38 14 66776510 66776510 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.190G>T p.Glu64Ter p.E64* ENST00000478722 3/23 278 256 22 390 389 1 strelka-varscan-mutect GPHN,stop_gained,p.Glu64Ter,ENST00000478722,NM_020806.4;GPHN,stop_gained,p.Glu64Ter,ENST00000315266,NM_001024218.1;GPHN,stop_gained,p.Glu64Ter,ENST00000543237,;GPHN,stop_gained,p.Glu64Ter,ENST00000459628,;GPHN,non_coding_transcript_exon_variant,,ENST00000556020,;GPHN,3_prime_UTR_variant,,ENST00000553936,;GPHN,3_prime_UTR_variant,,ENST00000555668,;GPHN,3_prime_UTR_variant,,ENST00000557654,;GPHN,intron_variant,,ENST00000556633,; T ENST00000478722 Transcript stop_gained 1311/4297 190/2310 64/769 E/* Gaa/Taa 1 1 GPHN HGNC HGNC:15465 protein_coding YES CCDS9777.1 ENSP00000417901 Q9NQX3 UPI0000072592 NM_020806.4 3/23 Gene3D:3.40.980.10,Pfam_domain:PF00994,hmmpanther:PTHR10192,SMART_domains:SM00852,Superfamily_domains:SSF53218,TIGRFAM_domain:TIGR00177 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 66776510 66776510 G T 1 0 0 0 0 0 1 0 0 6512 943 33 2 2 GPHN 14 66776510 Nonsense_Mutation SNP G C3N-02149_T 2235012 66776510 40267208 394 28578 MED6 0 . GRCh38 14 70584920 70584920 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.634G>T p.Glu212Ter p.E212* ENST00000615788 8/9 240 214 26 294 294 0 strelka-varscan-mutect MED6,stop_gained,p.Glu212Ter,ENST00000256379,NM_005466.3;MED6,stop_gained,p.Glu212Ter,ENST00000615788,NM_001284211.1;MED6,stop_gained,p.Glu219Ter,ENST00000430055,NM_001284209.1;MED6,stop_gained,p.Glu212Ter,ENST00000554963,;MED6,missense_variant,p.Arg173Ile,ENST00000440435,NM_001284210.1;MED6,non_coding_transcript_exon_variant,,ENST00000555296,; A ENST00000615788 Transcript stop_gained 687/1700 634/774 212/257 E/* Gaa/Taa 1 -1 MED6 HGNC HGNC:19970 protein_coding YES CCDS73649.1 ENSP00000481920 A0A087WYL7 UPI0001EF1523 NM_001284211.1 8/9 Low_complexity_(Seg):seg,hmmpanther:PTHR13104,PIRSF_domain:PIRSF023869 HIGH 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 70584920 70584920 C A 1 0 0 0 0 0 1 0 0 9390 922 32 2 2 MED6 14 70584920 Nonsense_Mutation SNP C C3N-02149_T 3808410 70584920 36458798 395 28579 AREL1 0 . GRCh38 14 74674051 74674051 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.1141G>C p.Val381Leu p.V381L ENST00000356357 9/20 222 209 13 258 258 0 strelka-varscan-mutect AREL1,missense_variant,p.Val381Leu,ENST00000356357,NM_001039479.1;AREL1,missense_variant,p.Val220Leu,ENST00000556202,;AREL1,missense_variant,p.Val115Leu,ENST00000490805,;AREL1,non_coding_transcript_exon_variant,,ENST00000557401,;AREL1,missense_variant,p.Val381Leu,ENST00000555330,;AREL1,missense_variant,p.Val25Leu,ENST00000481010,;AREL1,non_coding_transcript_exon_variant,,ENST00000469797,;AREL1,non_coding_transcript_exon_variant,,ENST00000556327,;AREL1,downstream_gene_variant,,ENST00000553411,;AREL1,downstream_gene_variant,,ENST00000553279,; G ENST00000356357 Transcript missense_variant 1657/5456 1141/2472 381/823 V/L Gtg/Ctg 1 -1 AREL1 HGNC HGNC:20363 protein_coding YES CCDS41971.1 ENSP00000348714 O15033 UPI0000073D44 NM_001039479.1 tolerated(0.57) 9/20 hmmpanther:PTHR11254:SF340,hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 74674051 74674051 C G 1 0 0 0 0 1 0 0 0 966 565 20 4 4 AREL1 14 74674051 Missense_Mutation SNP C C3N-02149_T 4089131 74674051 32369667 396 28580 FLRT2 0 . GRCh38 14 85622387 85622387 + Silent SNP G G T C3N-02149_T C3N-02149_N G G c.873G>T p.= p.L291L ENST00000330753 2/2 174 158 16 255 255 0 strelka-varscan-mutect FLRT2,synonymous_variant,p.=,ENST00000330753,NM_013231.4;FLRT2,synonymous_variant,p.=,ENST00000554746,;FLRT2,upstream_gene_variant,,ENST00000553650,; T ENST00000330753 Transcript synonymous_variant 1640/33679 873/1983 291/660 L ctG/ctT COSM470301 1 1 FLRT2 HGNC HGNC:3761 protein_coding YES CCDS9877.1 ENSP00000332879 O43155 UPI0000049E10 NM_013231.4 2/2 hmmpanther:PTHR24369:SF23,hmmpanther:PTHR24369,Pfam_domain:PF13855,Gene3D:3.80.10.10,SMART_domains:SM00369,Superfamily_domains:SSF52058 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 85622387 85622387 G T 1 0 0 0 0 0 0 0 1 5795 1277 45 2 2 FLRT2 14 85622387 Silent SNP G C3N-02149_T 10948336 85622387 21421331 397 28581 GALC 0 . GRCh38 14 87934737 87934737 + Missense_Mutation SNP G G T rs756141815 C3N-02149_T C3N-02149_N G G c.2053C>A p.Arg685Ser p.R685S ENST00000261304 17/17 439 387 52 615 614 1 strelka-varscan-mutect GALC,missense_variant,p.Arg685Ser,ENST00000261304,NM_000153.3;GALC,missense_variant,p.Arg659Ser,ENST00000393569,NM_001201402.1;GALC,missense_variant,p.Arg662Ser,ENST00000393568,NM_001201401.1;GALC,intron_variant,,ENST00000544807,;GALC,intron_variant,,ENST00000555000,;GALC,downstream_gene_variant,,ENST00000555179,; T ENST00000261304 Transcript missense_variant 2160/3883 2053/2058 685/685 R/S Cgc/Agc rs756141815 1 -1 GALC HGNC HGNC:4115 protein_coding YES CCDS9878.2 ENSP00000261304 A0A0A0MQV0 UPI00001FD982 NM_000153.3 deleterious_low_confidence(0.03) 17/17 Pfam_domain:PF02057,hmmpanther:PTHR15172,hmmpanther:PTHR15172:SF1 MODERATE 1 SNV 1 1 PASS rs756141815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 87934737 87934737 G T 1 0 0 0 0 1 0 0 0 6069 1145 40 1 1 GALC 14 87934737 Missense_Mutation SNP G C3N-02149_T 2312350 87934737 19108981 398 28582 CPSF2 0 . GRCh38 14 92159028 92159028 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1867G>T p.Ala623Ser p.A623S ENST00000298875 14/16 142 129 13 215 215 0 strelka-varscan-mutect CPSF2,missense_variant,p.Ala623Ser,ENST00000298875,NM_017437.2;CPSF2,missense_variant,p.Ala140Ser,ENST00000555244,;CPSF2,downstream_gene_variant,,ENST00000556622,; T ENST00000298875 Transcript missense_variant 2152/13035 1867/2349 623/782 A/S Gca/Tca 1 1 CPSF2 HGNC HGNC:2325 protein_coding YES CCDS9902.1 ENSP00000298875 Q9P2I0 A0A024R6H0 UPI0000185F22 NM_017437.2 tolerated(0.17) 14/16 hmmpanther:PTHR11203,hmmpanther:PTHR11203:SF5,Pfam_domain:PF13299 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 92159028 92159028 G T 1 0 0 0 0 1 0 0 0 3621 1203 42 2 2 CPSF2 14 92159028 Missense_Mutation SNP G C3N-02149_T 4224291 92159028 14884690 399 28583 BTBD7 0 . GRCh38 14 93245914 93245914 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.2494G>C p.Gly832Arg p.G832R ENST00000334746 10/11 273 255 18 339 338 1 strelka-mutect BTBD7,missense_variant,p.Gly832Arg,ENST00000334746,NM_001002860.3;BTBD7,missense_variant,p.Gly481Arg,ENST00000554565,NM_001289133.1;BTBD7,missense_variant,p.Gly447Arg,ENST00000553975,;BTBD7,3_prime_UTR_variant,,ENST00000355125,;RP11-85G20.2,downstream_gene_variant,,ENST00000492041,; G ENST00000334746 Transcript missense_variant 2802/8430 2494/3399 832/1132 G/R Gga/Cga 1 -1 BTBD7 HGNC HGNC:18269 protein_coding YES CCDS32146.1 ENSP00000335615 Q9P203 UPI00001FDA78 NM_001002860.3 tolerated_low_confidence(0.08) 10/11 hmmpanther:PTHR16064 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 93245914 93245914 C G 1 0 0 0 0 1 0 0 0 1722 690 24 4 4 BTBD7 14 93245914 Missense_Mutation SNP C C3N-02149_T 1086886 93245914 13797804 400 28584 ATG2B 0 . GRCh38 14 96303210 96303210 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.4888G>T p.Asp1630Tyr p.D1630Y ENST00000359933 33/42 70 66 4 122 122 0 strelka-varscan-mutect ATG2B,missense_variant,p.Asp1630Tyr,ENST00000359933,NM_018036.5;ATG2B,non_coding_transcript_exon_variant,,ENST00000261834,; A ENST00000359933 Transcript missense_variant 5782/13684 4888/6237 1630/2078 D/Y Gat/Tat COSM265431 1 -1 ATG2B HGNC HGNC:20187 protein_coding YES CCDS9944.2 ENSP00000353010 Q96BY7 UPI000155D51F NM_018036.5 deleterious(0.02) 33/42 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF20 1 MODERATE 1 SNV 5 1 1 PASS . . 0 205 5 0 0 0 0 0 -9.532519 1 1 1 1 0 A 3 1 92 96303210 96303210 C A 1 0 0 0 0 1 0 0 0 1246 826 29 2 2 ATG2B 14 96303210 Missense_Mutation SNP C C3N-02149_T 3057296 96303210 10740508 401 28585 HHIPL1 0 . GRCh38 14 99662993 99662993 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1620C>A p.Tyr540Ter p.Y540* ENST00000330710 6/9 125 113 12 116 116 0 strelka-varscan-mutect HHIPL1,stop_gained,p.Tyr540Ter,ENST00000330710,NM_001127258.1;HHIPL1,stop_gained,p.Tyr540Ter,ENST00000357223,NM_032425.4; A ENST00000330710 Transcript stop_gained 1718/7390 1620/2349 540/782 Y/* taC/taA 1 1 HHIPL1 HGNC HGNC:19710 protein_coding YES CCDS45162.1 ENSP00000330601 Q96JK4 F1T0G3 UPI000022988D NM_001127258.1 6/9 Superfamily_domains:0046203,Gene3D:2.120.10.30,hmmpanther:PTHR19328,hmmpanther:PTHR19328:SF32 HIGH 1 SNV 1 1 PASS rs1401078911 . 0 204 6 0 0 0 0 0 -19.99981 0.9999998 1 1 1 0 A 4 1 92 99662993 99662993 C A 1 0 0 0 0 0 1 0 0 6978 489 17 2 2 HHIPL1 14 99662993 Nonsense_Mutation SNP C C3N-02149_T 3359783 99662993 7380725 402 28586 RTL1 0 . GRCh38 14 100882072 100882072 + Missense_Mutation SNP T T A C3N-02149_T C3N-02149_N T T c.2717A>T p.Tyr906Phe p.Y906F ENST00000534062 1/1 157 148 9 205 205 0 strelka-varscan-mutect RTL1,missense_variant,p.Tyr906Phe,ENST00000534062,NM_001134888.2;MEG8,intron_variant,,ENST00000637474,;MIR431,downstream_gene_variant,,ENST00000385266,;MIR127,upstream_gene_variant,,ENST00000384876,;MIR432,upstream_gene_variant,,ENST00000606207,;MIR433,downstream_gene_variant,,ENST00000384837,;MIR136,upstream_gene_variant,,ENST00000385207,; A ENST00000534062 Transcript missense_variant 2776/4193 2717/4077 906/1358 Y/F tAc/tTc COSM5667447 1 -1 RTL1 HGNC HGNC:14665 protein_coding YES CCDS53910.1 ENSP00000435342 A6NKG5 UPI00001D7B9E NM_001134888.2 tolerated(0.37) 1/1 hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF9,Superfamily_domains:SSF56672 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 100882072 100882072 T A 1 0 0 0 0 1 0 0 0 13984 1638 57 4 4 RTL1 14 100882072 Missense_Mutation SNP T C3N-02149_T 1219079 100882072 6161646 403 28587 KIF26A 0 . GRCh38 14 104172573 104172573 + Splice_Site SNP A A T novel C3N-02149_T C3N-02149_N A A c.1327-2A>T p.X443_splice ENST00000423312 77 70 7 86 85 1 strelka-mutect KIF26A,splice_acceptor_variant,,ENST00000315264,;KIF26A,splice_acceptor_variant,,ENST00000423312,NM_015656.1; T ENST00000423312 Transcript splice_acceptor_variant -/5649 1327/5649 443/1882 1 1 KIF26A HGNC HGNC:20226 protein_coding YES CCDS45171.1 ENSP00000388241 Q9ULI4 UPI00006C145D NM_015656.1 6/14 HIGH 1 SNV 5 1 PASS . . 0 202 8 0 0 0 0 0 -15.07606 0.9999945 1 1 1 0 T 5 4 92 104172573 104172573 A T 1 0 0 0 0 0 0 1 0 8159 434 15 4 4 KIF26A 14 104172573 Splice_Site SNP A C3N-02149_T 3290501 104172573 2871145 404 28588 SNRPN 0 . GRCh38 15 24976990 24976990 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.381G>T p.Leu127Phe p.L127F ENST00000400100 10/13 60 47 13 117 117 0 strelka-varscan-mutect SNRPN,missense_variant,p.Leu131Phe,ENST00000554227,;SNRPN,missense_variant,p.Leu127Phe,ENST00000400100,NM_022807.2,NM_022808.2,NM_022806.2;SNRPN,missense_variant,p.Leu127Phe,ENST00000400097,NM_022805.2;SNRPN,missense_variant,p.Leu127Phe,ENST00000390687,;SNRPN,missense_variant,p.Leu127Phe,ENST00000346403,;SNRPN,missense_variant,p.Leu127Phe,ENST00000577565,NM_003097.3;SNRPN,missense_variant,p.Leu127Phe,ENST00000579070,;SNRPN,downstream_gene_variant,,ENST00000584968,;SNHG14,upstream_gene_variant,,ENST00000551631,;SNRPN,downstream_gene_variant,,ENST00000553597,;SNURF,3_prime_UTR_variant,,ENST00000580062,;RP11-701H24.9,intron_variant,,ENST00000551312,;RP11-701H24.9,intron_variant,,ENST00000557230,;SNHG14,upstream_gene_variant,,ENST00000557108,; T ENST00000400100 Transcript missense_variant 1271/1751 381/723 127/240 L/F ttG/ttT 1 1 SNRPN HGNC HGNC:11164 protein_coding YES CCDS10017.1 ENSP00000382972 P63162 X5DP00 UPI000002948A NM_022807.2,NM_022808.2,NM_022806.2 deleterious(0) 10/13 PIRSF_domain:PIRSF037187,hmmpanther:PTHR10701,hmmpanther:PTHR10701:SF1,Superfamily_domains:SSF50182 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 24976990 24976990 G T 1 0 0 0 0 1 0 0 0 15190 1339 47 2 2 SNRPN 15 24976990 Missense_Mutation SNP G C3N-02149_T 24976990 77014199 405 28589 EPB42 0 . GRCh38 15 43220813 43220813 + Nonsense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.13G>T p.Glu5Ter p.E5* ENST00000300215 1/13 405 319 86 524 523 1 strelka-varscan-mutect EPB42,stop_gained,p.Glu5Ter,ENST00000300215,NM_000119.2;EPB42,splice_region_variant,,ENST00000441366,NM_001114134.1;EPB42,splice_region_variant,,ENST00000622454,;EPB42,splice_region_variant,,ENST00000540029,;EPB42,upstream_gene_variant,,ENST00000568508,; A ENST00000300215 Transcript stop_gained 471/4553 13/2166 5/721 E/* Gag/Tag COSM5271199 1 -1 EPB42 HGNC HGNC:3381 protein_coding YES CCDS10093.1 ENSP00000300215 P16452 UPI000013E639 NM_000119.2 1/13 1 HIGH 1 SNV 1 1 1 PASS rs1313275870 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 43220813 43220813 C A 1 0 0 0 0 0 1 0 0 5005 840 29 2 2 EPB42 15 43220813 Nonsense_Mutation SNP C C3N-02149_T 18243823 43220813 58770376 406 28590 DUOXA2 0 . GRCh38 15 45116663 45116663 + Missense_Mutation SNP C C A rs778830755 C3N-02149_T C3N-02149_N C C c.488C>A p.Pro163Gln p.P163Q ENST00000323030 4/6 313 252 61 331 329 2 strelka-varscan-mutect DUOXA2,missense_variant,p.Pro163Gln,ENST00000323030,NM_207581.3;DUOX2,upstream_gene_variant,,ENST00000389039,;DUOX2,upstream_gene_variant,,ENST00000603300,NM_014080.4;DUOXA1,downstream_gene_variant,,ENST00000558996,NM_001276268.1;DUOXA1,downstream_gene_variant,,ENST00000267803,NM_144565.3;DUOXA1,downstream_gene_variant,,ENST00000559014,NM_001276264.1;DUOXA1,downstream_gene_variant,,ENST00000613425,;DUOXA1,downstream_gene_variant,,ENST00000558422,NM_001276267.1;DUOXA1,downstream_gene_variant,,ENST00000430224,NM_001276265.1;DUOXA1,downstream_gene_variant,,ENST00000560572,NM_001276266.1;DUOXA1,downstream_gene_variant,,ENST00000558377,;DUOXA1,downstream_gene_variant,,ENST00000559226,;DUOXA1,downstream_gene_variant,,ENST00000558326,;DUOXA1,downstream_gene_variant,,ENST00000559988,;DUOXA2,3_prime_UTR_variant,,ENST00000491993,;DUOXA2,non_coding_transcript_exon_variant,,ENST00000350243,;DUOX2,upstream_gene_variant,,ENST00000558383,;DUOXA1,downstream_gene_variant,,ENST00000559013,; A ENST00000323030 Transcript missense_variant 773/1760 488/963 163/320 P/Q cCg/cAg rs778830755 1 1 DUOXA2 HGNC HGNC:32698 protein_coding YES CCDS10118.2 ENSP00000319705 Q1HG44 UPI000049DDDD NM_207581.3 tolerated(0.22) 4/6 hmmpanther:PTHR31158,hmmpanther:PTHR31158:SF2,Pfam_domain:PF10204 MODERATE 1 SNV 1 1 PASS rs778830755 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 45116663 45116663 C A 1 0 0 0 0 1 0 0 0 4625 652 23 1 1 DUOXA2 15 45116663 Missense_Mutation SNP C C3N-02149_T 1895850 45116663 56874526 407 28591 SEMA6D 0 . GRCh38 15 47762235 47762235 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.574T>G p.Leu192Val p.L192V ENST00000316364 8/19 231 216 15 339 339 0 strelka-varscan-mutect SEMA6D,missense_variant,p.Leu192Val,ENST00000316364,NM_153618.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000558014,NM_001198999.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000354744,NM_153617.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000358066,NM_020858.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000355997,NM_153619.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000389428,NM_153616.1;SEMA6D,missense_variant,p.Leu192Val,ENST00000558816,;SEMA6D,missense_variant,p.Leu192Val,ENST00000536845,;SEMA6D,missense_variant,p.Leu192Val,ENST00000389425,NM_024966.2;SEMA6D,missense_variant,p.Leu192Val,ENST00000559196,;SEMA6D,upstream_gene_variant,,ENST00000560006,;SEMA6D,downstream_gene_variant,,ENST00000561133,;SEMA6D,upstream_gene_variant,,ENST00000559064,;SEMA6D,downstream_gene_variant,,ENST00000559184,;SEMA6D,downstream_gene_variant,,ENST00000560636,;SEMA6D,upstream_gene_variant,,ENST00000558431,;SEMA6D,downstream_gene_variant,,ENST00000561106,; G ENST00000316364 Transcript missense_variant 1013/6099 574/3222 192/1073 L/V Ttg/Gtg 1 1 SEMA6D HGNC HGNC:16770 protein_coding YES CCDS32225.1 ENSP00000324857 Q8NFY4 UPI000006E201 NM_153618.1 deleterious(0.02) 8/19 PROSITE_profiles:PS51004,hmmpanther:PTHR11036:SF65,hmmpanther:PTHR11036,Gene3D:2.130.10.10,Pfam_domain:PF01403,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 47762235 47762235 T G 1 0 0 0 0 1 0 0 0 14318 1606 56 5 5 SEMA6D 15 47762235 Missense_Mutation SNP T C3N-02149_T 2645572 47762235 54228954 408 28592 HDC 0 . GRCh38 15 50252710 50252710 + Silent SNP G G A rs762914264 C3N-02149_T C3N-02149_N G G c.852C>T p.= p.P284P ENST00000267845 8/12 361 282 79 424 424 0 strelka-varscan-mutect HDC,synonymous_variant,p.=,ENST00000267845,NM_002112.3;HDC,synonymous_variant,p.=,ENST00000543581,NM_001306146.1;HDC,downstream_gene_variant,,ENST00000559683,;HDC,non_coding_transcript_exon_variant,,ENST00000559816,;HDC,downstream_gene_variant,,ENST00000558679,;HDC,downstream_gene_variant,,ENST00000558761,;HDC,downstream_gene_variant,,ENST00000559190,; A ENST00000267845 Transcript synonymous_variant 1255/2705 852/1989 284/662 P ccC/ccT rs762914264 1 -1 HDC HGNC HGNC:4855 protein_coding YES CCDS10134.1 ENSP00000267845 P19113 UPI0000128FB4 NM_002112.3 8/12 Gene3D:3.40.640.10,Pfam_domain:PF00282,hmmpanther:PTHR11999,hmmpanther:PTHR11999:SF68,Superfamily_domains:SSF53383 LOW 1 SNV 1 1 PASS rs762914264 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 50252710 50252710 G A 1 0 0 0 0 0 0 0 1 6902 1103 39 1 1 HDC 15 50252710 Silent SNP G C3N-02149_T 2490475 50252710 51738479 409 28593 UNC13C 0 . GRCh38 15 54014506 54014506 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1603T>A p.Trp535Arg p.W535R ENST00000260323 1/32 156 118 38 160 160 0 strelka-varscan-mutect UNC13C,missense_variant,p.Trp535Arg,ENST00000260323,NM_001080534.1; A ENST00000260323 Transcript missense_variant 1603/12946 1603/6645 535/2214 W/R Tgg/Agg 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 deleterious_low_confidence(0) 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 54014506 54014506 T A 1 0 0 0 0 1 0 0 0 17510 1580 55 4 4 UNC13C 15 54014506 Missense_Mutation SNP T C3N-02149_T 3761796 54014506 47976683 410 28594 RASGRF1 0 . GRCh38 15 79017797 79017797 + Silent SNP C C T C3N-02149_T C3N-02149_N C C c.1716G>A p.= p.K572K ENST00000419573 12/28 119 94 25 177 177 0 strelka-varscan-mutect RASGRF1,synonymous_variant,p.=,ENST00000419573,NM_002891.4;RASGRF1,synonymous_variant,p.=,ENST00000558480,NM_001145648.1;RASGRF1,non_coding_transcript_exon_variant,,ENST00000560334,; T ENST00000419573 Transcript synonymous_variant 1991/6294 1716/3822 572/1273 K aaG/aaA COSM5003293 1 -1 RASGRF1 HGNC HGNC:9875 protein_coding YES CCDS10309.1 ENSP00000405963 Q13972 UPI000013D1F1 NM_002891.4 12/28 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,SMART_domains:SM00233,Superfamily_domains:SSF50729 1 LOW 1 SNV 2 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 79017797 79017797 C T 1 0 0 0 0 0 0 0 1 13233 680 24 3 3 RASGRF1 15 79017797 Silent SNP C C3N-02149_T 25003291 79017797 22973392 411 28595 IL16 0 . GRCh38 15 81299991 81299991 + Nonsense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.2665C>T p.Arg889Ter p.R889* ENST00000302987 13/18 50 40 10 73 72 1 strelka-varscan-mutect IL16,stop_gained,p.Arg889Ter,ENST00000394660,NM_001172128.1;IL16,stop_gained,p.Arg889Ter,ENST00000302987,NM_172217.3;IL16,stop_gained,p.Arg188Ter,ENST00000394652,NM_004513.5;IL16,stop_gained,p.Arg193Ter,ENST00000558332,;RP11-761I4.4,downstream_gene_variant,,ENST00000607019,;IL16,non_coding_transcript_exon_variant,,ENST00000560230,;IL16,upstream_gene_variant,,ENST00000559342,;IL16,3_prime_UTR_variant,,ENST00000360547,;IL16,3_prime_UTR_variant,,ENST00000560115,;IL16,3_prime_UTR_variant,,ENST00000558857,; T ENST00000302987 Transcript stop_gained 2665/3999 2665/3999 889/1332 R/* Cga/Tga 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 13/18 hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324 HIGH 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -19.99991 0.9999965 1 1 1 0 T 4 4 92 81299991 81299991 C T 1 0 0 0 0 0 1 0 0 7541 760 27 1 1 IL16 15 81299991 Nonsense_Mutation SNP C C3N-02149_T 2282194 81299991 20691198 412 28596 BNC1 0 . GRCh38 15 83263218 83263218 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.2033T>C p.Leu678Pro p.L678P ENST00000345382 4/5 297 230 67 444 444 0 strelka-varscan-mutect BNC1,missense_variant,p.Leu678Pro,ENST00000345382,NM_001717.3;BNC1,missense_variant,p.Leu671Pro,ENST00000569704,NM_001301206.1;RP11-382A20.4,intron_variant,,ENST00000565495,; G ENST00000345382 Transcript missense_variant 2119/4610 2033/2985 678/994 L/P cTg/cCg 1 -1 BNC1 HGNC HGNC:1081 protein_coding YES CCDS10324.1 ENSP00000307041 Q01954 UPI0000126796 NM_001717.3 deleterious(0.01) 4/5 hmmpanther:PTHR15021,hmmpanther:PTHR15021:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 83263218 83263218 A G 1 0 0 0 0 1 0 0 0 1630 188 7 5 5 BNC1 15 83263218 Missense_Mutation SNP A C3N-02149_T 1963227 83263218 18727971 413 28597 PDE8A 0 . GRCh38 15 85113993 85113993 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.1306G>C p.Asp436His p.D436H ENST00000310298 15/23 221 186 35 297 297 0 strelka-varscan-mutect PDE8A,missense_variant,p.Asp436His,ENST00000310298,;PDE8A,missense_variant,p.Asp436His,ENST00000394553,NM_002605.2;PDE8A,missense_variant,p.Asp364His,ENST00000557957,NM_001243137.1;PDE8A,missense_variant,p.Asp390His,ENST00000339708,NM_173454.1;PDE8A,downstream_gene_variant,,ENST00000557819,;PDE8A,3_prime_UTR_variant,,ENST00000485596,;PDE8A,3_prime_UTR_variant,,ENST00000478717,;PDE8A,3_prime_UTR_variant,,ENST00000559742,;PDE8A,non_coding_transcript_exon_variant,,ENST00000560789,;PDE8A,non_coding_transcript_exon_variant,,ENST00000558543,;PDE8A,downstream_gene_variant,,ENST00000557954,;PDE8A,upstream_gene_variant,,ENST00000561374,;PDE8A,upstream_gene_variant,,ENST00000560333,;PDE8A,downstream_gene_variant,,ENST00000559086,; C ENST00000310298 Transcript missense_variant 1558/3984 1306/2490 436/829 D/H Gat/Cat 1 1 PDE8A HGNC HGNC:8793 protein_coding YES CCDS10336.1 ENSP00000311453 O60658 UPI0000127C00 deleterious(0.02) 15/23 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF85 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 85113993 85113993 G C 1 0 0 0 0 1 0 0 0 11741 942 33 4 4 PDE8A 15 85113993 Missense_Mutation SNP G C3N-02149_T 1850775 85113993 16877196 414 28598 ACAN 0 . GRCh38 15 88855369 88855369 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2784G>T p.Trp928Cys p.W928C ENST00000439576 12/18 145 112 33 206 206 0 strelka-varscan-mutect ACAN,missense_variant,p.Trp928Cys,ENST00000439576,NM_013227.3;ACAN,missense_variant,p.Trp928Cys,ENST00000617301,;ACAN,missense_variant,p.Trp928Cys,ENST00000559004,;ACAN,missense_variant,p.Trp928Cys,ENST00000561243,;ACAN,missense_variant,p.Trp928Cys,ENST00000352105,NM_001135.3;ACAN,downstream_gene_variant,,ENST00000558207,;ACAN,upstream_gene_variant,,ENST00000560601,; T ENST00000439576 Transcript missense_variant 3158/8840 2784/7593 928/2530 W/C tgG/tgT 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 deleterious(0.03) 12/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 88855369 88855369 G T 1 0 0 0 0 1 0 0 0 160 1212 42 2 2 ACAN 15 88855369 Missense_Mutation SNP G C3N-02149_T 3741376 88855369 13135820 415 28599 MCTP2 0 . GRCh38 15 94298495 94298495 + Missense_Mutation SNP C C G rs201364128 C3N-02149_T C3N-02149_N C C c.230C>G p.Ser77Trp p.S77W ENST00000357742 1/22 159 143 16 231 231 0 strelka-varscan-mutect MCTP2,missense_variant,p.Ser77Trp,ENST00000357742,NM_018349.3;MCTP2,missense_variant,p.Ser77Trp,ENST00000451018,NM_001159643.1;MCTP2,missense_variant,p.Ser77Trp,ENST00000543482,;MCTP2,non_coding_transcript_exon_variant,,ENST00000561608,;MCTP2,missense_variant,p.Ser77Trp,ENST00000456504,;MCTP2,non_coding_transcript_exon_variant,,ENST00000556363,; G ENST00000357742 Transcript missense_variant 230/7555 230/2637 77/878 S/W tCg/tGg rs201364128,COSM460615 1 1 MCTP2 HGNC HGNC:25636 protein_coding YES CCDS32338.1 ENSP00000350377 Q6DN12 UPI0000D613A2 NM_018349.3 deleterious(0.01) 1/22 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs201364128 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 94298495 94298495 C G 1 0 0 0 0 1 0 0 0 9337 893 31 4 4 MCTP2 15 94298495 Missense_Mutation SNP C C3N-02149_T 5443126 94298495 7692694 416 28600 MSLNL 0 . GRCh38 16 774860 774860 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.809T>G p.Leu270Arg p.L270R ENST00000543963 6/15 92 81 11 86 85 1 strelka-varscan-mutect MSLNL,missense_variant,p.Leu270Arg,ENST00000543963,;MSLNL,missense_variant,p.Leu220Arg,ENST00000442466,;MIR662,downstream_gene_variant,,ENST00000384847,;MSLNL,non_coding_transcript_exon_variant,,ENST00000537221,; C ENST00000543963 Transcript missense_variant 809/2259 809/2259 270/752 L/R cTg/cGg 1 -1 MSLNL HGNC HGNC:14170 protein_coding YES ENSP00000441381 H0YG18 UPI000204A8F3 deleterious(0) 6/15 Pfam_domain:PF06060,hmmpanther:PTHR23412,hmmpanther:PTHR23412:SF15 MODERATE 1 SNV 5 1 PASS . . 0 193 16 0 0 0 0 0 -19.99872 0.9988668 1 1 1 0 C 3 2 92 774860 774860 A C 1 0 0 0 0 1 0 0 0 9864 188 7 5 5 MSLNL 16 774860 Missense_Mutation SNP A C3N-02149_T 774860 89563485 417 28601 SSTR5 0 . GRCh38 16 1079624 1079624 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.756G>T p.= p.V252V ENST00000293897 1/1 132 114 18 186 186 0 strelka-varscan-mutect SSTR5,synonymous_variant,p.=,ENST00000293897,NM_001172560.1,NM_001053.3;SSTR5-AS1,upstream_gene_variant,,ENST00000569832,;SSTR5-AS1,upstream_gene_variant,,ENST00000566499,;SSTR5-AS1,upstream_gene_variant,,ENST00000624643,; T ENST00000293897 Transcript synonymous_variant 844/1362 756/1095 252/364 V gtG/gtT 1 1 SSTR5 HGNC HGNC:11334 protein_coding YES CCDS10429.1 ENSP00000293897 P35346 UPI00000015DC NM_001172560.1,NM_001053.3 1/1 Low_complexity_(Seg):seg,PROSITE_profiles:PS50262,hmmpanther:PTHR24229,hmmpanther:PTHR24229:SF20,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 1079624 1079624 G T 1 0 0 0 0 0 0 0 1 15578 1335 47 2 2 SSTR5 16 1079624 Silent SNP G C3N-02149_T 304764 1079624 89258721 418 28602 ANKS4B 0 . GRCh38 16 21250500 21250500 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.934G>T p.Asp312Tyr p.D312Y ENST00000311620 2/2 336 273 63 481 481 0 strelka-varscan-mutect ANKS4B,missense_variant,p.Asp312Tyr,ENST00000311620,NM_145865.2;CRYM,intron_variant,,ENST00000570401,;CRYM,intron_variant,,ENST00000574448,; T ENST00000311620 Transcript missense_variant 1007/4352 934/1254 312/417 D/Y Gat/Tat 1 1 ANKS4B HGNC HGNC:26795 protein_coding YES CCDS42130.1 ENSP00000308772 Q8N8V4 UPI000013F1C0 NM_145865.2 deleterious(0.01) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR24161,hmmpanther:PTHR24161:SF20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 21250500 21250500 G T 1 0 0 0 0 1 0 0 0 797 1290 45 2 2 ANKS4B 16 21250500 Missense_Mutation SNP G C3N-02149_T 20170876 21250500 69087845 419 28603 RBBP6 0 . GRCh38 16 24568957 24568957 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.2267C>G p.Ser756Cys p.S756C ENST00000319715 17/18 208 155 53 301 300 1 strelka-varscan-mutect RBBP6,missense_variant,p.Ser756Cys,ENST00000319715,NM_006910.4;RBBP6,missense_variant,p.Ser722Cys,ENST00000348022,NM_018703.3;RBBP6,missense_variant,p.Ser623Cys,ENST00000564314,;RBBP6,intron_variant,,ENST00000381039,;RBBP6,non_coding_transcript_exon_variant,,ENST00000562430,;RBBP6,downstream_gene_variant,,ENST00000570185,; G ENST00000319715 Transcript missense_variant 2699/6229 2267/5379 756/1792 S/C tCt/tGt 1 1 RBBP6 HGNC HGNC:9889 protein_coding YES CCDS10621.1 ENSP00000317872 Q7Z6E9 UPI00001A96B8 NM_006910.4 deleterious_low_confidence(0) 17/18 Low_complexity_(Seg):seg,hmmpanther:PTHR15439,hmmpanther:PTHR15439:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 24568957 24568957 C G 1 0 0 0 0 1 0 0 0 13264 913 32 4 4 RBBP6 16 24568957 Missense_Mutation SNP C C3N-02149_T 3318457 24568957 65769388 420 28604 APOBR 0 . GRCh38 16 28496428 28496428 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.1387G>A p.Val463Ile p.V463I ENST00000564831 2/4 50 45 5 97 97 0 strelka-varscan-mutect APOBR,missense_variant,p.Val463Ile,ENST00000564831,NM_018690.3;APOBR,missense_variant,p.Val454Ile,ENST00000431282,;CLN3,upstream_gene_variant,,ENST00000569430,;CLN3,upstream_gene_variant,,ENST00000636147,NM_001042432.1;CLN3,upstream_gene_variant,,ENST00000359984,NM_000086.2;CLN3,upstream_gene_variant,,ENST00000360019,NM_001286104.1;CLN3,upstream_gene_variant,,ENST00000357857,NM_001286110.1;CLN3,upstream_gene_variant,,ENST00000333496,;CLN3,upstream_gene_variant,,ENST00000631023,;CLN3,upstream_gene_variant,,ENST00000357806,;CLN3,upstream_gene_variant,,ENST00000567963,NM_001286109.1;CLN3,upstream_gene_variant,,ENST00000395653,;CLN3,upstream_gene_variant,,ENST00000565316,;CLN3,upstream_gene_variant,,ENST00000637100,;CLN3,upstream_gene_variant,,ENST00000636228,;CLN3,upstream_gene_variant,,ENST00000355477,;CLN3,upstream_gene_variant,,ENST00000635973,;IL27,downstream_gene_variant,,ENST00000356897,NM_145659.3;CLN3,upstream_gene_variant,,ENST00000568443,;CLN3,upstream_gene_variant,,ENST00000568497,;CLN3,upstream_gene_variant,,ENST00000565778,;CLN3,upstream_gene_variant,,ENST00000565688,;CLN3,upstream_gene_variant,,ENST00000568558,;CLN3,upstream_gene_variant,,ENST00000567804,;CLN3,upstream_gene_variant,,ENST00000636355,;CLN3,upstream_gene_variant,,ENST00000567160,;CLN3,upstream_gene_variant,,ENST00000565236,;CLN3,upstream_gene_variant,,ENST00000566816,;CLN3,upstream_gene_variant,,ENST00000637110,;CLN3,upstream_gene_variant,,ENST00000566472,;CLN3,upstream_gene_variant,,ENST00000566040,;CLN3,upstream_gene_variant,,ENST00000637686,;CLN3,upstream_gene_variant,,ENST00000565047,;CLN3,upstream_gene_variant,,ENST00000563874,;CLN3,upstream_gene_variant,,ENST00000636977,;RP11-435I10.4,upstream_gene_variant,,ENST00000635887,;RP11-435I10.4,upstream_gene_variant,,ENST00000636503,;RP11-435I10.4,upstream_gene_variant,,ENST00000637376,;RP11-435I10.4,upstream_gene_variant,,ENST00000636866,;RP11-435I10.4,upstream_gene_variant,,ENST00000636078,;CLN3,upstream_gene_variant,,ENST00000636853,;RP11-435I10.4,upstream_gene_variant,,ENST00000636017,;RP11-435I10.4,upstream_gene_variant,,ENST00000636766,;CLN3,upstream_gene_variant,,ENST00000636839,;CLN3,upstream_gene_variant,,ENST00000568076,;CLN3,upstream_gene_variant,,ENST00000561689,;RP11-435I10.4,upstream_gene_variant,,ENST00000637299,;CLN3,upstream_gene_variant,,ENST00000637107,;CLN3,upstream_gene_variant,,ENST00000635958,;CLN3,upstream_gene_variant,,ENST00000637184,;RP11-435I10.4,upstream_gene_variant,,ENST00000568224,;CLN3,upstream_gene_variant,,ENST00000568452,;CLN3,upstream_gene_variant,,ENST00000637871,;CLN3,upstream_gene_variant,,ENST00000637578,;CLN3,upstream_gene_variant,,ENST00000636172,;CLN3,upstream_gene_variant,,ENST00000566083,;CLN3,upstream_gene_variant,,ENST00000635861,;CLN3,upstream_gene_variant,,ENST00000566824,;CLN3,upstream_gene_variant,,ENST00000637699,;CLN3,upstream_gene_variant,,ENST00000565140,;CLN3,upstream_gene_variant,,ENST00000628023,;CLN3,upstream_gene_variant,,ENST00000568422,;CLN3,upstream_gene_variant,,ENST00000564574,;CLN3,upstream_gene_variant,,ENST00000569030,;CLN3,upstream_gene_variant,,ENST00000568472,;CLN3,upstream_gene_variant,,ENST00000566057,;CLN3,upstream_gene_variant,,ENST00000567495,;CLN3,upstream_gene_variant,,ENST00000637985,;CLN3,upstream_gene_variant,,ENST00000561505,; A ENST00000564831 Transcript missense_variant 1420/3792 1387/3294 463/1097 V/I Gta/Ata 1 1 APOBR HGNC HGNC:24087 protein_coding YES CCDS58442.1 ENSP00000457539 Q0VD83 UPI000013EFFC NM_018690.3 tolerated(0.22) 2/4 hmmpanther:PTHR15964:SF0,hmmpanther:PTHR15964 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -12.78244 1 1 1 1 0 A 3 1 92 28496428 28496428 G A 1 0 0 0 0 1 0 0 0 918 1261 44 3 3 APOBR 16 28496428 Missense_Mutation SNP G C3N-02149_T 3927471 28496428 61841917 421 28605 C16orf78 0 . GRCh38 16 49378518 49378518 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.319T>C p.Tyr107His p.Y107H ENST00000299191 3/5 261 211 50 356 356 0 strelka-mutect C16orf78,missense_variant,p.Tyr107His,ENST00000299191,NM_144602.3; C ENST00000299191 Transcript missense_variant 436/1068 319/798 107/265 Y/H Tat/Cat 1 1 C16orf78 HGNC HGNC:28479 protein_coding YES CCDS10738.1 ENSP00000299191 Q8WTQ4 UPI0000071013 NM_144602.3 tolerated(0.12) 3/5 Pfam_domain:PF15472,hmmpanther:PTHR35679 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 49378518 49378518 T C 1 0 0 0 0 1 0 0 0 1866 1522 53 5 5 C16orf78 16 49378518 Missense_Mutation SNP T C3N-02149_T 20882090 49378518 40959827 422 28606 ZNF423 0 . GRCh38 16 49637665 49637665 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1487A>T p.Gln496Leu p.Q496L ENST00000561648 5/9 231 183 48 321 320 1 strelka-varscan-mutect ZNF423,missense_variant,p.Gln496Leu,ENST00000561648,;ZNF423,missense_variant,p.Gln436Leu,ENST00000563137,;ZNF423,missense_variant,p.Gln496Leu,ENST00000262383,NM_015069.3;ZNF423,missense_variant,p.Gln436Leu,ENST00000562871,;ZNF423,missense_variant,p.Gln379Leu,ENST00000535559,;ZNF423,missense_variant,p.Gln436Leu,ENST00000562520,NM_001271620.1;ZNF423,missense_variant,p.Gln379Leu,ENST00000567169,; A ENST00000561648 Transcript missense_variant 1788/7907 1487/3855 496/1284 Q/L cAg/cTg 1 -1 ZNF423 HGNC HGNC:16762 protein_coding YES CCDS32445.1 ENSP00000455426 Q2M1K9 UPI0000353ABC deleterious(0.02) 5/9 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF210,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 49637665 49637665 T A 1 0 0 0 0 1 0 0 0 18470 1580 55 4 4 ZNF423 16 49637665 Missense_Mutation SNP T C3N-02149_T 259147 49637665 40700680 423 28607 NOD2 0 . GRCh38 16 50711943 50711943 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2032C>A p.Leu678Met p.L678M ENST00000300589 4/12 116 90 26 134 134 0 strelka-varscan-mutect NOD2,missense_variant,p.Leu678Met,ENST00000300589,NM_022162.2,NM_001293557.1;NOD2,upstream_gene_variant,,ENST00000534057,;RP11-327F22.6,upstream_gene_variant,,ENST00000602304,;NOD2,downstream_gene_variant,,ENST00000526417,;NOD2,downstream_gene_variant,,ENST00000532206,;NOD2,downstream_gene_variant,,ENST00000527070,;NOD2,upstream_gene_variant,,ENST00000534067,;NOD2,upstream_gene_variant,,ENST00000529633,;NOD2,upstream_gene_variant,,ENST00000524712,;NOD2,upstream_gene_variant,,ENST00000527052,; A ENST00000300589 Transcript missense_variant 2137/4486 2032/3123 678/1040 L/M Ctg/Atg 1 1 NOD2 HGNC HGNC:5331 protein_coding YES CCDS10746.1 ENSP00000300589 Q9HC29 UPI000005027A NM_022162.2,NM_001293557.1 deleterious(0.03) 4/12 hmmpanther:PTHR24106:SF64,hmmpanther:PTHR24106 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 50711943 50711943 C A 1 0 0 0 0 1 0 0 0 10560 680 24 2 2 NOD2 16 50711943 Missense_Mutation SNP C C3N-02149_T 1074278 50711943 39626402 424 28608 NUP93 0 . GRCh38 16 56842688 56842688 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.2460G>T p.= p.G820G ENST00000569842 22/23 59 43 16 69 69 0 strelka-varscan-mutect NUP93,synonymous_variant,p.=,ENST00000569842,;NUP93,intron_variant,,ENST00000542526,NM_001242796.1;NUP93,intron_variant,,ENST00000564887,NM_001242795.1;NUP93,intron_variant,,ENST00000308159,NM_014669.4;NUP93,intron_variant,,ENST00000569322,;NUP93,downstream_gene_variant,,ENST00000563486,;NUP93,downstream_gene_variant,,ENST00000563405,;NUP93,intron_variant,,ENST00000564278,;NUP93,intron_variant,,ENST00000563465,; T ENST00000569842 Transcript synonymous_variant 2556/2834 2460/2643 820/880 G ggG/ggT 1 1 NUP93 HGNC HGNC:28958 protein_coding ENSP00000458101 H3BVG0 UPI00024670A6 22/23 LOW SNV 5 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999947 1 1 1 0 T 2 4 92 56842688 56842688 G T 1 0 0 0 0 0 0 0 1 10838 1161 41 2 2 NUP93 16 56842688 Silent SNP G C3N-02149_T 6130745 56842688 33495657 425 28609 NLRC5 0 . GRCh38 16 57020833 57020833 + Silent SNP C C T rs776847858 C3N-02149_T C3N-02149_N C C c.121C>T p.= p.L41L ENST00000262510 3/49 432 396 36 500 500 0 strelka-varscan-mutect NLRC5,synonymous_variant,p.=,ENST00000262510,;NLRC5,synonymous_variant,p.=,ENST00000436936,NM_032206.4;NLRC5,synonymous_variant,p.=,ENST00000539144,;NLRC5,synonymous_variant,p.=,ENST00000544641,;NLRC5,upstream_gene_variant,,ENST00000538805,;NLRC5,downstream_gene_variant,,ENST00000538059,;NLRC5,synonymous_variant,p.=,ENST00000539881,;NLRC5,non_coding_transcript_exon_variant,,ENST00000538273,;NLRC5,upstream_gene_variant,,ENST00000545081,; T ENST00000262510 Transcript synonymous_variant 346/6822 121/5601 41/1866 L Ctg/Ttg rs776847858 1 1 NLRC5 HGNC HGNC:29933 protein_coding YES CCDS10773.1 ENSP00000262510 Q86WI3 UPI00001AEE94 3/49 LOW 1 SNV 5 1 PASS rs776847858 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 57020833 57020833 C T 1 0 0 0 0 0 0 0 1 10507 680 24 3 3 NLRC5 16 57020833 Silent SNP C C3N-02149_T 178145 57020833 33317512 426 28610 SLC7A6OS 0 . GRCh38 16 68304124 68304124 + Missense_Mutation SNP C C A rs139917756 C3N-02149_T C3N-02149_N C C c.580G>T p.Asp194Tyr p.D194Y ENST00000263997 3/5 357 283 74 506 506 0 strelka-varscan-mutect SLC7A6OS,missense_variant,p.Asp194Tyr,ENST00000263997,NM_032178.2;SLC7A6OS,missense_variant,p.Asp160Tyr,ENST00000568538,;SLC7A6OS,missense_variant,p.Asp36Tyr,ENST00000561590,;SLC7A6,downstream_gene_variant,,ENST00000566454,NM_001076785.2;SLC7A6,downstream_gene_variant,,ENST00000219343,NM_003983.5;SLC7A6,downstream_gene_variant,,ENST00000618043,;SLC7A6OS,missense_variant,p.Asp4Tyr,ENST00000568315,;SLC7A6OS,non_coding_transcript_exon_variant,,ENST00000561933,;SLC7A6,downstream_gene_variant,,ENST00000379152,; A ENST00000263997 Transcript missense_variant 599/4189 580/930 194/309 D/Y Gat/Tat rs139917756 1 -1 SLC7A6OS HGNC HGNC:25807 protein_coding YES CCDS10865.1 ENSP00000263997 Q96CW6 UPI000013D49E NM_032178.2 tolerated(0.06) 3/5 Pfam_domain:PF08574,hmmpanther:PTHR31196,hmmpanther:PTHR31196:SF2 MODERATE 1 SNV 1 1 PASS rs139917756 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 68304124 68304124 C A 1 0 0 0 0 1 0 0 0 14985 884 31 1 1 SLC7A6OS 16 68304124 Missense_Mutation SNP C C3N-02149_T 11283291 68304124 22034221 427 28611 CNTNAP4 0 . GRCh38 16 76535636 76535636 + Silent SNP G G A novel C3N-02149_T C3N-02149_N G G c.2847G>A p.= p.Q949Q ENST00000611870 18/24 335 264 71 415 414 1 strelka-varscan-mutect CNTNAP4,synonymous_variant,p.=,ENST00000307431,;CNTNAP4,synonymous_variant,p.=,ENST00000611870,NM_033401.3;CNTNAP4,synonymous_variant,p.=,ENST00000377504,;CNTNAP4,synonymous_variant,p.=,ENST00000476707,;CNTNAP4,synonymous_variant,p.=,ENST00000622250,;CNTNAP4,synonymous_variant,p.=,ENST00000478060,NM_138994.3; A ENST00000611870 Transcript synonymous_variant 3232/4867 2847/3927 949/1308 Q caG/caA 1 1 CNTNAP4 HGNC HGNC:18747 protein_coding YES CCDS73915.1 ENSP00000479811 Q9C0A0 UPI000013DCFF NM_033401.3 18/24 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF659 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 76535636 76535636 G A 1 0 0 0 0 0 0 0 1 3431 991 35 3 3 CNTNAP4 16 76535636 Silent SNP G C3N-02149_T 8231512 76535636 13802709 428 28612 FAM92B 0 . GRCh38 16 85110352 85110352 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.129G>T p.= p.R43R ENST00000539556 2/9 141 106 35 183 181 2 strelka-varscan-mutect FAM92B,synonymous_variant,p.=,ENST00000539556,NM_198491.2;FAM92B,synonymous_variant,p.=,ENST00000629253,;FAM92B,upstream_gene_variant,,ENST00000618669,; A ENST00000539556 Transcript synonymous_variant 285/1898 129/915 43/304 R cgG/cgT 1 -1 FAM92B HGNC HGNC:24781 protein_coding YES CCDS32500.1 ENSP00000443411 Q6ZTR7 UPI00001C0C61 NM_198491.2 2/9 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR21223,hmmpanther:PTHR21223:SF3,Pfam_domain:PF06730,Gene3D:1.20.1270.60,Superfamily_domains:SSF103657 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 85110352 85110352 C A 1 0 0 0 0 0 0 0 1 5511 610 22 2 2 FAM92B 16 85110352 Silent SNP C C3N-02149_T 8574716 85110352 5227993 429 28613 FOXL1 0 . GRCh38 16 86578917 86578917 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.194C>A p.Ala65Glu p.A65E ENST00000320241 1/1 495 401 94 618 618 0 strelka-varscan-mutect FOXL1,missense_variant,p.Ala65Glu,ENST00000320241,NM_005250.2;FOXL1,missense_variant,p.Ala65Glu,ENST00000593625,; A ENST00000320241 Transcript missense_variant 412/3655 194/1038 65/345 A/E gCg/gAg COSM5237864 1 1 FOXL1 HGNC HGNC:3817 protein_coding YES CCDS10959.1 ENSP00000326272 Q12952 UPI000012ADE2 NM_005250.2 deleterious(0) 1/1 PROSITE_profiles:PS50039,hmmpanther:PTHR11829,hmmpanther:PTHR11829:SF204,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 86578917 86578917 C A 1 0 0 0 0 1 0 0 0 5879 768 27 1 1 FOXL1 16 86578917 Missense_Mutation SNP C C3N-02149_T 1468565 86578917 3759428 430 28614 OR3A2 0 . GRCh38 17 3278928 3278928 + Nonsense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.8T>A p.Leu3Ter p.L3* ENST00000408891 1/1 26 17 9 44 44 0 strelka-varscan-mutect OR3A2,stop_gained,p.Leu3Ter,ENST00000408891,NM_002551.3;RP11-64J4.2,splice_region_variant,,ENST00000573491,;RP11-64J4.2,downstream_gene_variant,,ENST00000576166,; T ENST00000408891 Transcript stop_gained 47/1076 8/966 3/321 L/* tTa/tAa 1 -1 OR3A2 HGNC HGNC:8283 protein_coding YES CCDS42233.1 ENSP00000386180 P47893 A0A126GVQ3 UPI0000050B3C NM_002551.3 1/1 HIGH SNV 1 PASS . . 0 207 3 0 0 0 0 0 -19.99999 1 1 1 1 0 T 4 4 92 3278928 3278928 A T 1 0 0 0 0 0 1 0 0 11115 372 13 4 4 OR3A2 17 3278928 Nonsense_Mutation SNP A C3N-02149_T 3278928 79978513 431 28615 TP53 0 . GRCh38 17 7673728 7673728 + Nonsense_Mutation SNP C C A rs201744589 C3N-02149_T C3N-02149_N C C c.892G>T p.Glu298Ter p.E298* ENST00000269305 8/11 646 517 129 793 791 2 strelka-varscan-mutect TP53,stop_gained,p.Glu298Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Glu298Ter,ENST00000420246,;TP53,stop_gained,p.Glu259Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Glu259Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Glu298Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Glu259Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Glu298Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Glu259Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Glu298Ter,ENST00000445888,;TP53,stop_gained,p.Glu259Ter,ENST00000619485,;TP53,stop_gained,p.Glu166Ter,ENST00000510385,NM_001126116.1;TP53,stop_gained,p.Glu139Ter,ENST00000618944,NM_001276698.1;TP53,stop_gained,p.Glu166Ter,ENST00000504290,NM_001126117.1;TP53,stop_gained,p.Glu139Ter,ENST00000610623,NM_001276699.1;TP53,stop_gained,p.Glu166Ter,ENST00000504937,NM_001126115.1;TP53,stop_gained,p.Glu139Ter,ENST00000619186,NM_001276697.1;TP53,stop_gained,p.Glu298Ter,ENST00000359597,;TP53,stop_gained,p.Glu287Ter,ENST00000615910,;TP53,stop_gained,p.Glu166Ter,ENST00000509690,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Glu259Ter,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained 1082/2579 892/1182 298/393 E/* Gag/Tag rs201744589,CM031387,TP53_g.13872G>A,TP53_g.13872G>T,TP53_g.13872G>C,TP53_g.13872del,COSM10710,COSM121080,COSM1646820,COSM3723940,COSM44031,COSM45938 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 8/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6 uncertain_significance,likely_benign,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1 HIGH 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1 1 PASS rs201744589 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 7673728 7673728 C A 1 0 0 0 0 0 1 0 0 16859 893 31 1 1 TP53 17 7673728 Nonsense_Mutation SNP C C3N-02149_T 4394800 7673728 75583713 432 28616 PIK3R5 0 . GRCh38 17 8888253 8888253 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1534C>A p.Pro512Thr p.P512T ENST00000447110 10/19 364 293 71 500 500 0 strelka-varscan-mutect PIK3R5,missense_variant,p.Pro512Thr,ENST00000447110,NM_001142633.2;PIK3R5,missense_variant,p.Pro126Thr,ENST00000616147,NM_001251852.1;PIK3R5,missense_variant,p.Pro126Thr,ENST00000611902,NM_001251853.1,NM_001251851.1;PIK3R5,missense_variant,p.Pro126Thr,ENST00000623421,NM_001251855.1;PIK3R5,missense_variant,p.Pro512Thr,ENST00000581552,NM_014308.3;PIK3R5,missense_variant,p.Pro512Thr,ENST00000584803,;PIK3R5,downstream_gene_variant,,ENST00000578457,;PIK3R5,downstream_gene_variant,,ENST00000580959,;PIK3R5,downstream_gene_variant,,ENST00000584456,;PIK3R5,upstream_gene_variant,,ENST00000578743,;PIK3R5,downstream_gene_variant,,ENST00000577981,;PIK3R5,downstream_gene_variant,,ENST00000583812,;PIK3R5,3_prime_UTR_variant,,ENST00000269300,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000578515,;PIK3R5,non_coding_transcript_exon_variant,,ENST00000583039,;PIK3R5,upstream_gene_variant,,ENST00000577214,; T ENST00000447110 Transcript missense_variant 1664/4495 1534/2643 512/880 P/T Ccc/Acc 1 -1 PIK3R5 HGNC HGNC:30035 protein_coding YES CCDS11147.1 ENSP00000392812 Q8WYR1 L7RT34 UPI0000071DB4 NM_001142633.2 tolerated(0.53) 10/19 hmmpanther:PTHR15593,hmmpanther:PTHR15593:SF2,Pfam_domain:PF10486 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 8888253 8888253 G T 1 0 0 0 0 1 0 0 0 12017 1174 41 2 2 PIK3R5 17 8888253 Missense_Mutation SNP G C3N-02149_T 1214525 8888253 74369188 433 28617 DNAH9 0 . GRCh38 17 11902783 11902783 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.11471G>T p.Trp3824Leu p.W3824L ENST00000262442 60/69 190 158 32 273 270 3 strelka-varscan-mutect DNAH9,missense_variant,p.Trp3824Leu,ENST00000262442,NM_001372.3;DNAH9,missense_variant,p.Trp3824Leu,ENST00000454412,;DNAH9,missense_variant,p.Trp136Leu,ENST00000608377,NM_004662.2;DNAH9,non_coding_transcript_exon_variant,,ENST00000396001,;DNAH9,non_coding_transcript_exon_variant,,ENST00000581682,; T ENST00000262442 Transcript missense_variant 11539/13750 11471/13461 3824/4486 W/L tGg/tTg 1 1 DNAH9 HGNC HGNC:2953 protein_coding YES CCDS11160.1 ENSP00000262442 Q9NYC9 UPI0000141BA2 NM_001372.3 deleterious(0.01) 60/69 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF257 MODERATE 1 SNV 1 1 PASS rs1415835300 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 11902783 11902783 G T 1 0 0 0 0 1 0 0 0 4423 1357 47 2 2 DNAH9 17 11902783 Missense_Mutation SNP G C3N-02149_T 3014530 11902783 71354658 434 28618 SPECC1 0 . GRCh38 17 20110501 20110508 + Frame_Shift_Del DEL GAAGACCG GAAGACCG - novel C3N-02149_T C3N-02149_N GAAGACCG GAAGACCG c.222_229delGAAGACCG p.Lys74AsnfsTer25 p.K74Nfs*25 ENST00000261503 3/15 126 111 15 186 186 0 sindel-varindel-pindel SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000395529,NM_152904.4;SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000261503,NM_001033553.2;SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000395527,NM_001243439.1;SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000581973,;SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000583463,;SPECC1,frameshift_variant,p.Lys74AsnfsTer?,ENST00000583528,;SPECC1,frameshift_variant,p.Lys74AsnfsTer25,ENST00000583482,;SPECC1,downstream_gene_variant,,ENST00000580934,;SPECC1,non_coding_transcript_exon_variant,,ENST00000413167,;SPECC1,intron_variant,,ENST00000472876,;KCTD9P1,upstream_gene_variant,,ENST00000430462,; - ENST00000261503 Transcript frameshift_variant 273-280/3948 222-229/3207 74-77/1068 KKTA/NX aaGAAGACCGcc/aacc 1 1 SPECC1 HGNC HGNC:30615 protein_coding YES CCDS32590.1 ENSP00000261503 Q5M775 A0A024QYY9 UPI000020187D NM_001033553.2 3/15 hmmpanther:PTHR23167,hmmpanther:PTHR23167:SF3 HIGH 1 deletion 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 20110501 20110501 GAAGACCG - 1 0 1 0 1 0 0 0 0 15383 933 33 0 0 SPECC1 17 20110501 Frame_Shift_Del DEL GAAGACCG C3N-02149_T 8207718 20110501 63146940 435 28619 CCL1 0 . GRCh38 17 34360630 34360630 + Missense_Mutation SNP C C T rs780220490 C3N-02149_T C3N-02149_N C C c.220G>A p.Ala74Thr p.A74T ENST00000225842 3/3 333 316 17 390 390 0 strelka-varscan-mutect CCL1,missense_variant,p.Ala74Thr,ENST00000225842,NM_002981.2;CCL13,downstream_gene_variant,,ENST00000225844,NM_005408.2;CCL13,downstream_gene_variant,,ENST00000577681,; T ENST00000225842 Transcript missense_variant 290/592 220/291 74/96 A/T Gcc/Acc rs780220490,COSM3691481 1 -1 CCL1 HGNC HGNC:10609 protein_coding YES CCDS11282.1 ENSP00000225842 P22362 UPI00001362C4 NM_002981.2 deleterious(0.02) 3/3 hmmpanther:PTHR12015:SF5,hmmpanther:PTHR12015,PROSITE_patterns:PS00472,Gene3D:2.40.50.40,Pfam_domain:PF00048,SMART_domains:SM00199,Superfamily_domains:SSF54117 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs780220490 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 34360630 34360630 C T 1 0 0 0 0 1 0 0 0 2580 768 27 1 1 CCL1 17 34360630 Missense_Mutation SNP C C3N-02149_T 14250129 34360630 48896811 436 28620 KRT32 0 . GRCh38 17 41465925 41465925 + Nonsense_Mutation SNP C C A rs748226139 C3N-02149_T C3N-02149_N C C c.556G>T p.Glu186Ter p.E186* ENST00000225899 3/7 87 78 9 83 83 0 strelka-varscan-mutect KRT32,stop_gained,p.Glu186Ter,ENST00000225899,NM_002278.3;RNU2-32P,upstream_gene_variant,,ENST00000411193,; A ENST00000225899 Transcript stop_gained 660/1750 556/1347 186/448 E/* Gag/Tag rs748226139 1 -1 KRT32 HGNC HGNC:6449 protein_coding YES CCDS11393.1 ENSP00000225899 Q14532 UPI000013C883 NM_002278.3 3/7 Pfam_domain:PF00038,Prints_domain:PR01248,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF155,SMART_domains:SM01391 HIGH 1 SNV 1 1 PASS rs748226139 . 0 202 8 0 0 0 0 0 -18.7691 0.9999958 1 1 1 0 A 4 1 92 41465925 41465925 C A 1 0 0 0 0 0 1 0 0 8350 898 31 1 1 KRT32 17 41465925 Nonsense_Mutation SNP C C3N-02149_T 7105295 41465925 41791516 437 28621 KRT36 0 . GRCh38 17 41487606 41487606 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.831C>A p.= p.R277R ENST00000328119 4/7 99 68 31 133 133 0 strelka-varscan-mutect KRT36,synonymous_variant,p.=,ENST00000393986,;KRT36,synonymous_variant,p.=,ENST00000328119,NM_003771.4; T ENST00000328119 Transcript synonymous_variant 831/1644 831/1404 277/467 R cgC/cgA 1 -1 KRT36 HGNC HGNC:6454 protein_coding YES CCDS11395.1 ENSP00000329165 O76013 UPI000012DAFA NM_003771.4 4/7 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF193,SMART_domains:SM01391,Superfamily_domains:SSF46579 LOW 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 41487606 41487606 G T 1 0 0 0 0 0 0 0 1 8355 1306 46 2 2 KRT36 17 41487606 Silent SNP G C3N-02149_T 21681 41487606 41769835 438 28622 MEIOC 0 . GRCh38 17 44667951 44667951 + Silent SNP T T C novel C3N-02149_T C3N-02149_N T T c.2040T>C p.= p.F680F ENST00000409122 5/8 281 256 25 355 354 1 strelka-varscan-mutect MEIOC,synonymous_variant,p.=,ENST00000409122,NM_001145080.2;MEIOC,synonymous_variant,p.=,ENST00000409464,;MEIOC,downstream_gene_variant,,ENST00000432494,;MEIOC,downstream_gene_variant,,ENST00000456912,;MEIOC,upstream_gene_variant,,ENST00000472403,; C ENST00000409122 Transcript synonymous_variant 2182/4604 2040/2859 680/952 F ttT/ttC 1 1 MEIOC HGNC HGNC:26670 protein_coding YES CCDS45703.2 ENSP00000386452 A2RUB1 UPI0001881A86 NM_001145080.2 5/8 hmmpanther:PTHR33861,hmmpanther:PTHR33861:SF3 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 44667951 44667951 T C 1 0 0 0 0 0 0 0 1 9410 1780 62 5 5 MEIOC 17 44667951 Silent SNP T C3N-02149_T 3180345 44667951 38589490 439 28623 GJC1 0 . GRCh38 17 44805198 44805198 + Frame_Shift_Del DEL T T - novel C3N-02149_T C3N-02149_N T T c.620delA p.Tyr207LeufsTer12 p.Y207Lfs*12 ENST00000426548 3/3 346 324 22 415 415 0 varindel-pindel GJC1,frameshift_variant,p.Tyr207LeufsTer12,ENST00000426548,NM_001080383.1;GJC1,frameshift_variant,p.Tyr207LeufsTer12,ENST00000590758,;GJC1,frameshift_variant,p.Tyr207LeufsTer12,ENST00000330514,;GJC1,frameshift_variant,p.Tyr71LeufsTer12,ENST00000587113,;GJC1,frameshift_variant,p.Tyr207LeufsTer12,ENST00000592524,NM_005497.3;GJC1,downstream_gene_variant,,ENST00000591424,;GJC1,downstream_gene_variant,,ENST00000587239,;GJC1,upstream_gene_variant,,ENST00000586347,;GJC1,downstream_gene_variant,,ENST00000586267,; - ENST00000426548 Transcript frameshift_variant 890/7640 620/1191 207/396 Y/X tAt/tt 1 -1 GJC1 HGNC HGNC:4280 protein_coding YES CCDS11487.1 ENSP00000411528 P36383 UPI000013C62A NM_001080383.1 3/3 hmmpanther:PTHR11984:SF6,hmmpanther:PTHR11984,Pfam_domain:PF00029,Gene3D:2zw3A00,SMART_domains:SM01089 HIGH 1 deletion 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 44805198 44805198 T - 1 0 1 0 1 0 0 0 0 6291 1406 49 0 0 GJC1 17 44805198 Frame_Shift_Del DEL T C3N-02149_T 137247 44805198 38452243 440 28624 CCDC103 0 . GRCh38 17 44902575 44902575 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.487G>T p.Val163Leu p.V163L ENST00000417826 4/4 351 320 31 394 394 0 strelka-varscan-mutect CCDC103,missense_variant,p.Val163Leu,ENST00000417826,;FAM187A,missense_variant,p.Val163Leu,ENST00000412523,NM_001258399.1,NM_001258396.1,NM_213607.2,NM_001258395.1;CCDC103,missense_variant,p.Val163Leu,ENST00000410006,;CCDC103,missense_variant,p.Val163Leu,ENST00000357776,NM_001258398.1;FAM187A,5_prime_UTR_variant,,ENST00000331733,;EFTUD2,upstream_gene_variant,,ENST00000426333,NM_004247.3;EFTUD2,upstream_gene_variant,,ENST00000591382,NM_001258353.1;EFTUD2,upstream_gene_variant,,ENST00000592576,NM_001258354.1;GFAP,downstream_gene_variant,,ENST00000253408,NM_002055.4;EFTUD2,upstream_gene_variant,,ENST00000402521,NM_001142605.1;CCDC103,downstream_gene_variant,,ENST00000577339,;CCDC103,downstream_gene_variant,,ENST00000410027,NM_001258397.1;GFAP,downstream_gene_variant,,ENST00000588735,;EFTUD2,upstream_gene_variant,,ENST00000592701,;EFTUD2,upstream_gene_variant,,ENST00000593072,;AC015936.3,downstream_gene_variant,,ENST00000441312,;GFAP,downstream_gene_variant,,ENST00000592706,;GFAP,downstream_gene_variant,,ENST00000592065,;GFAP,downstream_gene_variant,,ENST00000589701,;EFTUD2,upstream_gene_variant,,ENST00000589825,;GFAP,downstream_gene_variant,,ENST00000585543,;EFTUD2,upstream_gene_variant,,ENST00000592408,;EFTUD2,upstream_gene_variant,,ENST00000590105,; T ENST00000417826 Transcript missense_variant 582/3397 487/729 163/242 V/L Gtg/Ttg 1 1 CCDC103 HGNC HGNC:32700 protein_coding YES CCDS11490.1 ENSP00000391692 Q8IW40 UPI0000074564 deleterious(0.01) 4/4 Pfam_domain:PF13877,hmmpanther:PTHR28572,hmmpanther:PTHR28572:SF1 MODERATE SNV 1 1 PASS rs1399679643 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 44902575 44902575 G T 1 0 0 0 0 1 0 0 0 2436 1261 44 2 2 CCDC103 17 44902575 Missense_Mutation SNP G C3N-02149_T 97377 44902575 38354866 441 28625 UBE2Z 0 . GRCh38 17 48927060 48927060 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.991G>C p.Glu331Gln p.E331Q ENST00000360943 7/7 253 237 16 344 344 0 strelka-varscan-mutect UBE2Z,missense_variant,p.Glu331Gln,ENST00000360943,NM_023079.4;SNF8,downstream_gene_variant,,ENST00000502492,NM_007241.2;SNF8,downstream_gene_variant,,ENST00000290330,;UBE2Z,downstream_gene_variant,,ENST00000514948,;AC091133.1,upstream_gene_variant,,ENST00000435491,;SNF8,downstream_gene_variant,,ENST00000514089,;UBE2Z,3_prime_UTR_variant,,ENST00000506498,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000513342,;UBE2Z,non_coding_transcript_exon_variant,,ENST00000506271,;SNF8,downstream_gene_variant,,ENST00000504000,;SNF8,downstream_gene_variant,,ENST00000510558,;SNF8,downstream_gene_variant,,ENST00000514929,;SNF8,downstream_gene_variant,,ENST00000507302,;SNF8,downstream_gene_variant,,ENST00000576353,;SNF8,downstream_gene_variant,,ENST00000515572,;SNF8,downstream_gene_variant,,ENST00000509989,;UBE2Z,downstream_gene_variant,,ENST00000504684,;SNF8,downstream_gene_variant,,ENST00000573795,;SNF8,downstream_gene_variant,,ENST00000509995,; C ENST00000360943 Transcript missense_variant 1126/3122 991/1065 331/354 E/Q Gag/Cag 1 1 UBE2Z HGNC HGNC:25847 protein_coding YES CCDS11540.2 ENSP00000354201 Q9H832 UPI00005A774B NM_023079.4 tolerated(0.13) 7/7 Gene3D:3.10.110.10 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 48927060 48927060 G C 1 0 0 0 0 1 0 0 0 17401 1291 45 4 4 UBE2Z 17 48927060 Missense_Mutation SNP G C3N-02149_T 4024485 48927060 34330381 442 28626 DGKE 0 . GRCh38 17 56861841 56861841 + Silent SNP A A T novel C3N-02149_T C3N-02149_N A A c.1335A>T p.= p.I445I ENST00000284061 10/12 169 137 32 226 225 1 strelka-varscan-mutect DGKE,synonymous_variant,p.=,ENST00000284061,NM_003647.2;DGKE,synonymous_variant,p.=,ENST00000572944,;DGKE,upstream_gene_variant,,ENST00000570738,; T ENST00000284061 Transcript synonymous_variant 1515/8660 1335/1704 445/567 I atA/atT 1 1 DGKE HGNC HGNC:2852 protein_coding YES CCDS11590.1 ENSP00000284061 P52429 A1L4Q0 UPI000012DD1F NM_003647.2 10/12 hmmpanther:PTHR11255,hmmpanther:PTHR11255:SF45,Pfam_domain:PF00609,SMART_domains:SM00045,Superfamily_domains:SSF111331 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 56861841 56861841 A T 1 0 0 0 0 0 0 0 1 4274 410 15 4 4 DGKE 17 56861841 Silent SNP A C3N-02149_T 7934781 56861841 26395600 443 28627 TANC2 0 . GRCh38 17 63200916 63200916 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.506G>T p.Ser169Ile p.S169I ENST00000424789 5/25 151 139 12 209 209 0 strelka-varscan-mutect TANC2,missense_variant,p.Ser169Ile,ENST00000424789,NM_025185.3;TANC2,missense_variant,p.Ser98Ile,ENST00000583356,;TANC2,missense_variant,p.Ser169Ile,ENST00000389520,;AC037445.1,intron_variant,,ENST00000581421,;AC037445.1,upstream_gene_variant,,ENST00000435892,; T ENST00000424789 Transcript missense_variant 510/11721 506/5973 169/1990 S/I aGt/aTt 1 1 TANC2 HGNC HGNC:30212 protein_coding YES CCDS45754.1 ENSP00000387593 Q9HCD6 UPI00015D57DF NM_025185.3 deleterious(0) 5/25 hmmpanther:PTHR24166,hmmpanther:PTHR24166:SF21 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 63200916 63200916 G T 1 0 0 0 0 1 0 0 0 15942 1029 36 2 2 TANC2 17 63200916 Missense_Mutation SNP G C3N-02149_T 6339075 63200916 20056525 444 28628 AXIN2 0 . GRCh38 17 65534037 65534037 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2280G>T p.Gln760His p.Q760H ENST00000307078 10/11 481 402 79 636 635 1 strelka-varscan-mutect AXIN2,missense_variant,p.Gln760His,ENST00000307078,NM_004655.3;AXIN2,missense_variant,p.Gln695His,ENST00000618960,;AXIN2,missense_variant,p.Gln695His,ENST00000375702,;AXIN2,intron_variant,,ENST00000611991,;AXIN2,non_coding_transcript_exon_variant,,ENST00000578251,;CTD-2535L24.2,downstream_gene_variant,,ENST00000577662,; A ENST00000307078 Transcript missense_variant 2594/4259 2280/2532 760/843 Q/H caG/caT 1 -1 AXIN2 HGNC HGNC:904 protein_coding YES CCDS11662.1 ENSP00000302625 Q9Y2T1 UPI00001AEE5A NM_004655.3 tolerated(0.09) 10/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 65534037 65534037 C A 1 0 0 0 0 1 0 0 0 1394 680 24 2 2 AXIN2 17 65534037 Missense_Mutation SNP C C3N-02149_T 2333121 65534037 17723404 445 28629 CACNG1 0 . GRCh38 17 67055117 67055117 + Missense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.319G>A p.Ala107Thr p.A107T ENST00000226021 3/4 113 104 9 129 129 0 strelka-varscan-mutect CACNG1,missense_variant,p.Ala107Thr,ENST00000226021,NM_000727.3; A ENST00000226021 Transcript missense_variant 390/1266 319/669 107/222 A/T Gca/Aca 1 1 CACNG1 HGNC HGNC:1405 protein_coding YES CCDS11668.1 ENSP00000226021 Q06432 UPI00001272A9 NM_000727.3 deleterious(0.04) 3/4 Pfam_domain:PF13903,hmmpanther:PTHR15025,hmmpanther:PTHR15025:SF1,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 202 6 2 0 0 0 0 -13.54028 0.9997113 1 1 1 0 A 3 1 92 67055117 67055117 G A 1 0 0 0 0 1 0 0 0 2244 1203 42 3 3 CACNG1 17 67055117 Missense_Mutation SNP G C3N-02149_T 1521080 67055117 16202324 446 28630 CD300E 0 . GRCh38 17 74617251 74617251 + Silent SNP G G A rs746024197 C3N-02149_T C3N-02149_N G G c.255C>T p.= p.L85L ENST00000392619 2/4 570 499 71 571 570 1 strelka-varscan-mutect CD300E,synonymous_variant,p.=,ENST00000392619,NM_181449.2;CD300E,synonymous_variant,p.=,ENST00000412268,; A ENST00000392619 Transcript synonymous_variant 372/3501 255/618 85/205 L ctC/ctT rs746024197,COSM1479964,COSM335451 1 -1 CD300E HGNC HGNC:28874 protein_coding YES CCDS11702.1 ENSP00000376395 Q496F6 UPI0000246EA0 NM_181449.2 2/4 PROSITE_profiles:PS50835,hmmpanther:PTHR11860,hmmpanther:PTHR11860:SF34,Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs746024197 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 74617251 74617251 G A 1 0 0 0 0 0 0 0 1 2702 1045 37 1 1 CD300E 17 74617251 Silent SNP G C3N-02149_T 7562134 74617251 8640190 447 28631 NAT9 0 . GRCh38 17 74772243 74772243 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.369G>T p.Glu123Asp p.E123D ENST00000357814 5/7 321 257 64 296 296 0 strelka-varscan-mutect NAT9,missense_variant,p.Glu123Asp,ENST00000357814,NM_001305083.1,NM_001305080.1,NM_001305078.1,NM_001305081.1,NM_015654.3;NAT9,missense_variant,p.Glu122Asp,ENST00000580301,NM_001305077.1;NAT9,missense_variant,p.Glu123Asp,ENST00000581136,;NAT9,missense_variant,p.Glu127Asp,ENST00000582870,;NAT9,missense_variant,p.Glu128Asp,ENST00000578822,;NAT9,missense_variant,p.Glu122Asp,ENST00000579218,;NAT9,missense_variant,p.Glu123Asp,ENST00000583476,NM_001305079.1;NAT9,missense_variant,p.Glu122Asp,ENST00000583757,NM_001305085.1;NAT9,missense_variant,p.Glu123Asp,ENST00000582524,NM_001305084.1;NAT9,intron_variant,,ENST00000580632,;TMEM104,upstream_gene_variant,,ENST00000335464,NM_017728.3;TMEM104,upstream_gene_variant,,ENST00000582330,;SLC9A3R1,downstream_gene_variant,,ENST00000262613,NM_004252.4;TMEM104,upstream_gene_variant,,ENST00000417024,;TMEM104,upstream_gene_variant,,ENST00000582773,NM_001321264.1;SLC9A3R1,downstream_gene_variant,,ENST00000413388,;SLC9A3R1,downstream_gene_variant,,ENST00000583369,;NAT9,downstream_gene_variant,,ENST00000581451,;TMEM104,upstream_gene_variant,,ENST00000578764,;NAT9,downstream_gene_variant,,ENST00000581466,;NAT9,downstream_gene_variant,,ENST00000578947,;NAT9,non_coding_transcript_exon_variant,,ENST00000580216,;NAT9,downstream_gene_variant,,ENST00000577428,;NAT9,downstream_gene_variant,,ENST00000585240,;NAT9,downstream_gene_variant,,ENST00000584409,;NAT9,downstream_gene_variant,,ENST00000583989,;NAT9,3_prime_UTR_variant,,ENST00000584022,;NAT9,non_coding_transcript_exon_variant,,ENST00000583834,;NAT9,non_coding_transcript_exon_variant,,ENST00000581762,;NAT9,non_coding_transcript_exon_variant,,ENST00000578798,;NAT9,non_coding_transcript_exon_variant,,ENST00000578862,;NAT9,downstream_gene_variant,,ENST00000582168,;SLC9A3R1,downstream_gene_variant,,ENST00000578958,;NAT9,downstream_gene_variant,,ENST00000582359,;NAT9,downstream_gene_variant,,ENST00000582993,;NAT9,downstream_gene_variant,,ENST00000583689,;NAT9,downstream_gene_variant,,ENST00000582118,;SLC9A3R1,downstream_gene_variant,,ENST00000581356,;NAT9,downstream_gene_variant,,ENST00000579837,;TMEM104,upstream_gene_variant,,ENST00000584246,; A ENST00000357814 Transcript missense_variant 443/1875 369/624 123/207 E/D gaG/gaT 1 -1 NAT9 HGNC HGNC:23133 protein_coding YES CCDS11706.1 ENSP00000350467 Q9BTE0 UPI000007106D NM_001305083.1,NM_001305080.1,NM_001305078.1,NM_001305081.1,NM_015654.3 deleterious(0) 5/7 Gene3D:3.40.630.30,Pfam_domain:PF13302,hmmpanther:PTHR13256,hmmpanther:PTHR13256:SF16,Superfamily_domains:SSF55729 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 74772243 74772243 C A 1 0 0 0 0 1 0 0 0 10190 680 24 2 2 NAT9 17 74772243 Missense_Mutation SNP C C3N-02149_T 154992 74772243 8485198 448 28632 EVPL 0 . GRCh38 17 76009170 76009170 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.4035G>A p.= p.R1345R ENST00000301607 22/22 206 171 35 262 262 0 strelka-varscan-mutect EVPL,synonymous_variant,p.=,ENST00000301607,NM_001988.2;EVPL,synonymous_variant,p.=,ENST00000586740,NM_001320747.1;TEN1-CDK3,downstream_gene_variant,,ENST00000569284,;CDK3,downstream_gene_variant,,ENST00000425876,;TEN1-CDK3,downstream_gene_variant,,ENST00000448471,NM_001258.2;EVPL,upstream_gene_variant,,ENST00000589231,;EVPL,non_coding_transcript_exon_variant,,ENST00000587569,;TEN1-CDK3,downstream_gene_variant,,ENST00000567351,;EVPL,downstream_gene_variant,,ENST00000593037,; T ENST00000301607 Transcript synonymous_variant 4289/6614 4035/6102 1345/2033 R cgG/cgA 1 -1 EVPL HGNC HGNC:3503 protein_coding YES CCDS11737.1 ENSP00000301607 Q92817 UPI000013E730 NM_001988.2 22/22 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23169,hmmpanther:PTHR23169:SF7 LOW 1 SNV 1 1 PASS rs1276121224 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 76009170 76009170 C T 1 0 0 0 0 0 0 0 1 5159 610 22 3 3 EVPL 17 76009170 Silent SNP C C3N-02149_T 1236927 76009170 7248271 449 28633 DNAH17 0 . GRCh38 17 78574938 78574938 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.120C>A p.Phe40Leu p.F40L ENST00000389840 2/81 412 326 86 490 489 1 strelka-varscan-mutect DNAH17,missense_variant,p.Phe40Leu,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Phe40Leu,ENST00000585328,;DNAH17,upstream_gene_variant,,ENST00000589793,; T ENST00000389840 Transcript missense_variant 245/13723 120/13389 40/4462 F/L ttC/ttA 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 tolerated(1) 2/81 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284 MODERATE 1 SNV 5 1 PASS rs1048073129 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 78574938 78574938 G T 1 0 0 0 0 1 0 0 0 4416 1281 45 2 2 DNAH17 17 78574938 Missense_Mutation SNP G C3N-02149_T 2565768 78574938 4682503 450 28634 CCDC40 0 . GRCh38 17 80086078 80086078 + Missense_Mutation SNP G G T rs371360520 C3N-02149_T C3N-02149_N G G c.2311G>T p.Val771Phe p.V771F ENST00000397545 14/20 580 467 113 607 607 0 strelka-varscan-mutect CCDC40,missense_variant,p.Val771Phe,ENST00000397545,NM_017950.3;CCDC40,missense_variant,p.Val771Phe,ENST00000374877,NM_001243342.1;CCDC40,upstream_gene_variant,,ENST00000573903,;CCDC40,non_coding_transcript_exon_variant,,ENST00000572253,;CCDC40,non_coding_transcript_exon_variant,,ENST00000574799,;CCDC40,upstream_gene_variant,,ENST00000575431,;CCDC40,upstream_gene_variant,,ENST00000574933,; T ENST00000397545 Transcript missense_variant 2338/4294 2311/3429 771/1142 V/F Gtc/Ttc rs371360520 1 1 CCDC40 HGNC HGNC:26090 protein_coding YES CCDS42395.1 ENSP00000380679 Q4G0X9 UPI0000201739 NM_017950.3 tolerated(0.07) 14/20 hmmpanther:PTHR16275 MODERATE 1 SNV 5 1 PASS rs371360520 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 80086078 80086078 G T 1 0 0 0 0 1 0 0 0 2521 1261 44 2 2 CCDC40 17 80086078 Missense_Mutation SNP G C3N-02149_T 1511140 80086078 3171363 451 28635 GAA 0 . GRCh38 17 80118295 80118295 + Nonsense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2584G>T p.Gly862Ter p.G862* ENST00000302262 18/20 43 37 6 34 34 0 strelka-mutect GAA,stop_gained,p.Gly862Ter,ENST00000302262,NM_000152.3;GAA,stop_gained,p.Gly862Ter,ENST00000390015,NM_001079803.1,NM_001079804.1;GAA,non_coding_transcript_exon_variant,,ENST00000573556,;GAA,downstream_gene_variant,,ENST00000572080,; T ENST00000302262 Transcript stop_gained 2803/3626 2584/2859 862/952 G/* Gga/Tga 1 1 GAA HGNC HGNC:4065 protein_coding YES CCDS32760.1 ENSP00000305692 P10253 UPI00000744FF NM_000152.3 18/20 hmmpanther:PTHR22762:SF92,hmmpanther:PTHR22762 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 80118295 80118295 G T 1 0 0 0 0 0 1 0 0 6018 1349 47 2 2 GAA 17 80118295 Nonsense_Mutation SNP G C3N-02149_T 32217 80118295 3139146 452 28636 ACTG1 0 . GRCh38 17 81510966 81510966 + Missense_Mutation SNP C C A rs727502881 C3N-02149_T C3N-02149_N C C c.945G>T p.Lys315Asn p.K315N ENST00000575842 4/5 530 478 52 665 665 0 strelka-varscan-mutect ACTG1,missense_variant,p.Lys315Asn,ENST00000575842,;ACTG1,missense_variant,p.Lys315Asn,ENST00000573283,NM_001199954.1;ACTG1,missense_variant,p.Lys315Asn,ENST00000575087,;ACTG1,missense_variant,p.Lys315Asn,ENST00000331925,NM_001614.3;ACTG1,missense_variant,p.Lys315Asn,ENST00000615544,;ACTG1,downstream_gene_variant,,ENST00000575994,;ACTG1,downstream_gene_variant,,ENST00000571721,;ACTG1,downstream_gene_variant,,ENST00000571691,;ACTG1,downstream_gene_variant,,ENST00000575659,;ACTG1,downstream_gene_variant,,ENST00000570382,;RP13-766D20.2,upstream_gene_variant,,ENST00000430912,;ACTG1,missense_variant,p.Lys315Asn,ENST00000576544,;ACTG1,3_prime_UTR_variant,,ENST00000572105,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576917,;ACTG1,non_coding_transcript_exon_variant,,ENST00000576209,;ACTG1,non_coding_transcript_exon_variant,,ENST00000574671,;ACTG1,downstream_gene_variant,,ENST00000576214,;RP13-766D20.1,upstream_gene_variant,,ENST00000448147,; A ENST00000575842 Transcript missense_variant 1372/2256 945/1128 315/375 K/N aaG/aaT rs727502881 1 -1 ACTG1 HGNC HGNC:144 protein_coding YES CCDS11782.1 ENSP00000458162 P63261 UPI0000000C38 deleterious_low_confidence(0.03) 4/5 hmmpanther:PTHR11937:SF244,hmmpanther:PTHR11937,Pfam_domain:PF00022,Gene3D:3.30.420.40,SMART_domains:SM00268,Superfamily_domains:SSF53067 likely_benign MODERATE 1 SNV 1 1 1 PASS rs727502881 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 81510966 81510966 C A 1 0 0 0 0 1 0 0 0 239 680 24 2 2 ACTG1 17 81510966 Missense_Mutation SNP C C3N-02149_T 1392671 81510966 1746475 453 28637 FSCN2 0 . GRCh38 17 81529089 81529089 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.558C>T p.= p.L186L ENST00000334850 1/5 594 553 41 619 619 0 strelka-varscan-mutect FSCN2,synonymous_variant,p.=,ENST00000417245,NM_012418.3;FSCN2,synonymous_variant,p.=,ENST00000334850,NM_001077182.2;RP13-766D20.2,downstream_gene_variant,,ENST00000442532,;RP13-766D20.2,downstream_gene_variant,,ENST00000430912,; T ENST00000334850 Transcript synonymous_variant 558/1551 558/1551 186/516 L ctC/ctT 1 1 FSCN2 HGNC HGNC:3960 protein_coding YES CCDS45810.1 ENSP00000334665 O14926 UPI0000E5925D NM_001077182.2 1/5 hmmpanther:PTHR10551:SF4,hmmpanther:PTHR10551,Pfam_domain:PF06268,Gene3D:2.80.10.50,Superfamily_domains:SSF50405 LOW SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 81529089 81529089 C T 1 0 0 0 0 0 0 0 1 5941 813 29 3 3 FSCN2 17 81529089 Silent SNP C C3N-02149_T 18123 81529089 1728352 454 28638 FASN 0 . GRCh38 17 82083610 82083610 + Missense_Mutation SNP C C T C3N-02149_T C3N-02149_N C C c.5248G>A p.Glu1750Lys p.E1750K ENST00000306749 31/43 676 611 65 718 717 1 strelka-varscan-mutect FASN,missense_variant,p.Glu1750Lys,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Glu1748Lys,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000636628,;FASN,upstream_gene_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,upstream_gene_variant,,ENST00000580382,;FASN,downstream_gene_variant,,ENST00000579410,; T ENST00000306749 Transcript missense_variant 5467/8565 5248/7536 1750/2511 E/K Gaa/Aaa COSM4854005 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 deleterious(0.01) 31/43 Gene3D:3.40.50.720,Pfam_domain:PF00107,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,SMART_domains:SM00829,Superfamily_domains:SSF51735 1 MODERATE 1 SNV 1 1 1 PASS rs1464240266 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 82083610 82083610 C T 1 0 0 0 0 1 0 0 0 5543 864 30 3 3 FASN 17 82083610 Missense_Mutation SNP C C3N-02149_T 554521 82083610 1173831 455 28639 FASN 0 . GRCh38 17 82084911 82084911 + Silent SNP C C A rs375434672 C3N-02149_T C3N-02149_N C C c.4452G>T p.= p.P1484P ENST00000306749 26/43 286 267 19 284 283 1 strelka-varscan-mutect FASN,synonymous_variant,p.=,ENST00000306749,NM_004104.4;FASN,synonymous_variant,p.=,ENST00000634990,;FASN,upstream_gene_variant,,ENST00000578424,;FASN,upstream_gene_variant,,ENST00000584610,;FASN,upstream_gene_variant,,ENST00000580382,;FASN,downstream_gene_variant,,ENST00000579410,; A ENST00000306749 Transcript synonymous_variant 4671/8565 4452/7536 1484/2511 P ccG/ccT rs375434672 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 26/43 hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280 LOW 1 SNV 1 1 PASS rs375434672 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 82084911 82084911 C A 1 0 0 0 0 0 0 0 1 5543 639 23 1 1 FASN 17 82084911 Silent SNP C C3N-02149_T 1301 82084911 1172530 456 28640 SECTM1 0 . GRCh38 17 82324580 82324580 + Splice_Site SNP A A C novel C3N-02149_T C3N-02149_N A A c.403+2T>G p.X135_splice ENST00000269389 74 70 4 83 83 0 varscan-mutect SECTM1,splice_donor_variant,,ENST00000269389,NM_003004.2;SECTM1,splice_donor_variant,,ENST00000580437,;SECTM1,splice_donor_variant,,ENST00000581691,;SECTM1,splice_donor_variant,,ENST00000582563,;SECTM1,splice_donor_variant,,ENST00000583093,;SECTM1,downstream_gene_variant,,ENST00000582290,;SECTM1,downstream_gene_variant,,ENST00000581954,;SECTM1,splice_donor_variant,,ENST00000581864,; C ENST00000269389 Transcript splice_donor_variant -/2235 403/747 135/248 1 -1 SECTM1 HGNC HGNC:10707 protein_coding YES CCDS11808.1 ENSP00000269389 Q8WVN6 UPI00000359A5 NM_003004.2 3/4 HIGH 1 SNV 1 1 PASS . . 0 154 45 9 0 0 0 0 -6.813293 0.08372163 0 1 0 0 C 5 2 92 82324580 82324580 A C 1 0 0 0 0 0 0 1 0 14285 173 6 5 5 SECTM1 17 82324580 Splice_Site SNP A C3N-02149_T 239669 82324580 932861 457 28641 NDC80 0 . GRCh38 18 2578085 2578085 + Silent SNP C C T rs751095916 C3N-02149_T C3N-02149_N C C c.420C>T p.= p.Y140Y ENST00000261597 5/17 230 215 15 338 338 0 strelka-varscan-mutect NDC80,synonymous_variant,p.=,ENST00000261597,NM_006101.2;NDC80,synonymous_variant,p.=,ENST00000576274,;NDC80,downstream_gene_variant,,ENST00000575515,;NDC80,upstream_gene_variant,,ENST00000574567,; T ENST00000261597 Transcript synonymous_variant 602/2172 420/1929 140/642 Y taC/taT rs751095916 1 1 NDC80 HGNC HGNC:16909 protein_coding YES CCDS11827.1 ENSP00000261597 O14777 A8K031 UPI0000073C92 NM_006101.2 5/17 Pfam_domain:PF03801,hmmpanther:PTHR10643,hmmpanther:PTHR10643:SF2 LOW 1 SNV 1 1 PASS rs751095916 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 2578085 2578085 C T 1 0 0 0 0 0 0 0 1 10263 547 19 1 1 NDC80 18 2578085 Silent SNP C C3N-02149_T 2578085 77795200 458 28642 MTCL1 0 . GRCh38 18 8720444 8720444 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.305A>T p.Glu102Val p.E102V ENST00000359865 4/17 330 202 128 325 325 0 strelka-varscan-mutect MTCL1,missense_variant,p.Glu102Val,ENST00000359865,NM_015210.3;MTCL1,missense_variant,p.Glu102Val,ENST00000400050,;MTCL1,missense_variant,p.Glu102Val,ENST00000517570,;MTCL1,missense_variant,p.Glu462Val,ENST00000306329,;MTCL1,downstream_gene_variant,,ENST00000523122,;Y_RNA,upstream_gene_variant,,ENST00000516510,;MTCL1,non_coding_transcript_exon_variant,,ENST00000522146,; T ENST00000359865 Transcript missense_variant 447/6093 305/4761 102/1586 E/V gAa/gTa 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 deleterious(0) 4/17 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3 MODERATE 1 SNV 2 1 PASS rs924193384 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 8720444 8720444 A T 1 0 0 0 0 1 0 0 0 9900 246 9 4 4 MTCL1 18 8720444 Missense_Mutation SNP A C3N-02149_T 6142359 8720444 71652841 459 28643 MTCL1 0 . GRCh38 18 8819200 8819200 + Nonsense_Mutation SNP G G T rs571648534 C3N-02149_T C3N-02149_N G G c.3097G>T p.Glu1033Ter p.E1033* ENST00000359865 13/17 390 357 33 345 342 3 strelka-varscan-mutect MTCL1,stop_gained,p.Glu1033Ter,ENST00000359865,NM_015210.3;MTCL1,stop_gained,p.Glu1033Ter,ENST00000400050,;MTCL1,stop_gained,p.Glu992Ter,ENST00000517570,;MTCL1,stop_gained,p.Glu1352Ter,ENST00000306329,;MTCL1,stop_gained,p.Glu358Ter,ENST00000518815,;MTCL1,non_coding_transcript_exon_variant,,ENST00000519823,;MTCL1,downstream_gene_variant,,ENST00000520926,; T ENST00000359865 Transcript stop_gained 3239/6093 3097/4761 1033/1586 E/* Gag/Tag rs571648534 1 1 MTCL1 HGNC HGNC:29121 protein_coding YES CCDS11841.1 ENSP00000352927 Q9Y4B5 UPI0000456B5B NM_015210.3 13/17 hmmpanther:PTHR15742,hmmpanther:PTHR15742:SF3,Low_complexity_(Seg):seg HIGH 1 SNV 2 1 PASS rs571648534 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 92 8819200 8819200 G T 1 0 0 0 0 0 1 0 0 9900 1059 37 1 1 MTCL1 18 8819200 Nonsense_Mutation SNP G C3N-02149_T 98756 8819200 71554085 460 28644 ZNF521 0 . GRCh38 18 25226897 25226897 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1021A>T p.Ser341Cys p.S341C ENST00000361524 4/8 400 309 91 472 470 2 strelka-varscan-mutect ZNF521,missense_variant,p.Ser341Cys,ENST00000361524,NM_015461.2;ZNF521,missense_variant,p.Ser121Cys,ENST00000584787,NM_001308225.1;ZNF521,missense_variant,p.Ser341Cys,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,missense_variant,p.Ser341Cys,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; A ENST00000361524 Transcript missense_variant 1170/4871 1021/3936 341/1311 S/C Agc/Tgc 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 deleterious(0.01) 4/8 hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 25226897 25226897 T A 1 0 0 0 0 1 0 0 0 18537 1580 55 4 4 ZNF521 18 25226897 Missense_Mutation SNP T C3N-02149_T 16407697 25226897 55146388 461 28645 GAREM1 0 . GRCh38 18 32310243 32310243 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.343G>T p.Ala115Ser p.A115S ENST00000269209 3/6 306 259 47 370 368 2 strelka-varscan-mutect GAREM1,missense_variant,p.Ala115Ser,ENST00000399218,NM_022751.2;GAREM1,missense_variant,p.Ala115Ser,ENST00000269209,NM_001242409.1;GAREM1,non_coding_transcript_exon_variant,,ENST00000578619,; A ENST00000269209 Transcript missense_variant 347/3006 343/2631 115/876 A/S Gca/Tca 1 -1 GAREM1 HGNC HGNC:26136 protein_coding YES CCDS56057.1 ENSP00000269209 Q9H706 UPI00005A72DA NM_001242409.1 tolerated(0.15) 3/6 Pfam_domain:PF12736,hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 32310243 32310243 C A 1 0 0 0 0 1 0 0 0 6109 739 26 2 2 GAREM1 18 32310243 Missense_Mutation SNP C C3N-02149_T 7083346 32310243 48063042 462 28646 PIK3C3 0 . GRCh38 18 41987877 41987877 + Silent SNP A A G novel C3N-02149_T C3N-02149_N A A c.597A>G p.= p.R199R ENST00000262039 5/25 226 213 13 237 237 0 strelka-varscan-mutect PIK3C3,synonymous_variant,p.=,ENST00000262039,NM_002647.2;PIK3C3,synonymous_variant,p.=,ENST00000398870,NM_001308020.1;PIK3C3,non_coding_transcript_exon_variant,,ENST00000589550,;PIK3C3,downstream_gene_variant,,ENST00000591011,; G ENST00000262039 Transcript synonymous_variant 683/9443 597/2664 199/887 R agA/agG 1 1 PIK3C3 HGNC HGNC:8974 protein_coding YES CCDS11920.1 ENSP00000262039 Q8NEB9 UPI00000708CE NM_002647.2 5/25 Gene3D:2.60.40.150,PIRSF_domain:PIRSF000587,hmmpanther:PTHR10048 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 41987877 41987877 A G 1 0 0 0 0 0 0 0 1 12007 301 11 5 5 PIK3C3 18 41987877 Silent SNP A C3N-02149_T 9677634 41987877 38385408 463 28647 NFATC1 0 . GRCh38 18 79410804 79410804 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.529C>T p.= p.L177L ENST00000427363 2/10 102 72 30 146 146 0 strelka-varscan-mutect NFATC1,synonymous_variant,p.=,ENST00000591814,NM_172390.2;NFATC1,synonymous_variant,p.=,ENST00000253506,NM_006162.4;NFATC1,synonymous_variant,p.=,ENST00000329101,NM_172387.2;NFATC1,synonymous_variant,p.=,ENST00000318065,NM_172389.2;NFATC1,synonymous_variant,p.=,ENST00000427363,NM_001278669.1;NFATC1,synonymous_variant,p.=,ENST00000592223,NM_001278675.1;NFATC1,synonymous_variant,p.=,ENST00000587635,;NFATC1,synonymous_variant,p.=,ENST00000542384,NM_001278670.1;NFATC1,synonymous_variant,p.=,ENST00000586434,NM_001278672.1;NFATC1,intron_variant,,ENST00000545796,NM_001278673.1;NFATC1,intron_variant,,ENST00000397790,NM_172388.2;NFATC1,intron_variant,,ENST00000590313,; T ENST00000427363 Transcript synonymous_variant 529/2832 529/2832 177/943 L Ctg/Ttg 1 1 NFATC1 HGNC HGNC:7775 protein_coding YES CCDS62467.1 ENSP00000389377 O95644 UPI000012FFB5 NM_001278669.1 2/10 Low_complexity_(Seg):seg,hmmpanther:PTHR12533:SF5,hmmpanther:PTHR12533 LOW 1 SNV 1 1 PASS rs1209927294 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 79410804 79410804 C T 1 0 0 0 0 0 0 0 1 10398 680 24 3 3 NFATC1 18 79410804 Silent SNP C C3N-02149_T 37422927 79410804 962481 464 28648 PARD6G 0 . GRCh38 18 80159830 80159830 + Missense_Mutation SNP G G A C3N-02149_T C3N-02149_N G G c.1072C>T p.His358Tyr p.H358Y ENST00000353265 3/3 82 62 20 167 167 0 strelka-varscan-mutect PARD6G,missense_variant,p.His358Tyr,ENST00000353265,NM_032510.3;PARD6G-AS1,intron_variant,,ENST00000586421,;PARD6G-AS1,intron_variant,,ENST00000589574,;PARD6G-AS1,intron_variant,,ENST00000587254,;PARD6G-AS1,intron_variant,,ENST00000585422,;AC139100.4,upstream_gene_variant,,ENST00000616901,; A ENST00000353265 Transcript missense_variant 1270/3868 1072/1131 358/376 H/Y Cac/Tac COSM4953167 1 -1 PARD6G HGNC HGNC:16076 protein_coding YES CCDS12022.1 ENSP00000343144 Q9BYG4 UPI000006DC0F NM_032510.3 deleterious_low_confidence(0.01) 3/3 hmmpanther:PTHR14102,hmmpanther:PTHR14102:SF3 1 MODERATE 1 SNV 1 1 1 PASS rs1036144243 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 80159830 80159830 G A 1 0 0 0 0 1 0 0 0 11527 1290 45 3 3 PARD6G 18 80159830 Missense_Mutation SNP G C3N-02149_T 749026 80159830 213455 465 28649 STK11 0 . GRCh38 19 1223059 1223059 + Nonsense_Mutation SNP G G A novel C3N-02149_T C3N-02149_N G G c.995G>A p.Trp332Ter p.W332* ENST00000326873 8/10 165 133 32 234 234 0 strelka-varscan-mutect STK11,stop_gained,p.Trp332Ter,ENST00000586243,;STK11,stop_gained,p.Trp332Ter,ENST00000326873,NM_000455.4;STK11,upstream_gene_variant,,ENST00000585465,;STK11,downstream_gene_variant,,ENST00000585748,;STK11,downstream_gene_variant,,ENST00000585851,;STK11,non_coding_transcript_exon_variant,,ENST00000589152,;STK11,non_coding_transcript_exon_variant,,ENST00000591133,;STK11,downstream_gene_variant,,ENST00000586358,;STK11,downstream_gene_variant,,ENST00000593219,; A ENST00000326873 Transcript stop_gained 1445/2611 995/1302 332/433 W/* tGg/tAg 1 1 STK11 HGNC HGNC:11389 protein_coding YES CCDS45896.1 ENSP00000324856 Q15831 A0A0S2Z4D1 UPI0000136105 NM_000455.4 8/10 Gene3D:1.10.510.10,hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF159,Superfamily_domains:SSF56112 HIGH 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999962 1 1 1 0 A 4 1 92 1223059 1223059 G A 1 0 0 0 0 0 1 0 0 15664 1357 47 3 3 STK11 19 1223059 Nonsense_Mutation SNP G C3N-02149_T 1223059 57394557 466 28650 S1PR4 0 . GRCh38 19 3178905 3178905 + Missense_Mutation SNP G G T rs776238408 C3N-02149_T C3N-02149_N G G c.113G>T p.Arg38Leu p.R38L ENST00000246115 1/1 140 117 23 151 151 0 strelka-varscan-mutect S1PR4,missense_variant,p.Arg38Leu,ENST00000246115,NM_003775.3;S1PR4,intron_variant,,ENST00000591346,; T ENST00000246115 Transcript missense_variant 138/1565 113/1155 38/384 R/L cGc/cTc rs776238408 1 1 S1PR4 HGNC HGNC:3170 protein_coding YES CCDS12105.1 ENSP00000246115 O95977 UPI0000050462 NM_003775.3 deleterious(0.03) 1/1 hmmpanther:PTHR22750:SF13,hmmpanther:PTHR22750,Prints_domain:PR01526 MODERATE 1 SNV 1 PASS rs776238408 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 3178905 3178905 G T 1 0 0 0 0 1 0 0 0 14055 1087 38 1 1 S1PR4 19 3178905 Missense_Mutation SNP G C3N-02149_T 1955846 3178905 55438711 467 28651 VAV1 0 . GRCh38 19 6828841 6828841 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.1206G>T p.= p.R402R ENST00000602142 13/27 270 222 48 345 345 0 strelka-varscan-mutect VAV1,synonymous_variant,p.=,ENST00000304076,NM_001258206.1;VAV1,synonymous_variant,p.=,ENST00000596764,NM_001258207.1;VAV1,synonymous_variant,p.=,ENST00000599806,;VAV1,synonymous_variant,p.=,ENST00000539284,;VAV1,synonymous_variant,p.=,ENST00000602142,NM_005428.3;VAV1,non_coding_transcript_exon_variant,,ENST00000601452,;VAV1,non_coding_transcript_exon_variant,,ENST00000600396,;VAV1,non_coding_transcript_exon_variant,,ENST00000597967,;VAV1,downstream_gene_variant,,ENST00000594082,; T ENST00000602142 Transcript synonymous_variant 1288/2620 1206/2538 402/845 R cgG/cgT 1 1 VAV1 HGNC HGNC:12657 protein_coding YES CCDS12174.1 ENSP00000472929 P15498 UPI0000138213 NM_005428.3 13/27 PROSITE_profiles:PS50003,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,Gene3D:2.30.29.30,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 6828841 6828841 G T 1 0 0 0 0 0 0 0 1 17676 1190 42 2 2 VAV1 19 6828841 Silent SNP G C3N-02149_T 3649936 6828841 51788775 468 28652 COL5A3 0 . GRCh38 19 9960875 9960875 + Missense_Mutation SNP C C A rs200584685 C3N-02149_T C3N-02149_N C C c.4867G>T p.Ala1623Ser p.A1623S ENST00000264828 66/67 171 159 12 212 212 0 strelka-varscan-mutect COL5A3,missense_variant,p.Ala1623Ser,ENST00000264828,NM_015719.3; A ENST00000264828 Transcript missense_variant 4953/6174 4867/5238 1623/1745 A/S Gcc/Tcc rs200584685 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 tolerated(0.64) 66/67 PROSITE_profiles:PS51461,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516,Pfam_domain:PF01410,SMART_domains:SM00038 MODERATE 1 SNV 1 1 PASS rs200584685 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 9960875 9960875 C A 1 0 0 0 0 1 0 0 0 3487 768 27 1 1 COL5A3 19 9960875 Missense_Mutation SNP C C3N-02149_T 3132034 9960875 48656741 469 28653 COL5A3 0 . GRCh38 19 9998015 9998015 + Missense_Mutation SNP A A C C3N-02149_T C3N-02149_N A A c.1169T>G p.Phe390Cys p.F390C ENST00000264828 10/67 187 158 29 289 288 1 strelka-varscan-mutect COL5A3,missense_variant,p.Phe390Cys,ENST00000264828,NM_015719.3;CTD-2553C6.1,downstream_gene_variant,,ENST00000592332,; C ENST00000264828 Transcript missense_variant 1255/6174 1169/5238 390/1745 F/C tTt/tGt COSM3528025 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 deleterious(0.01) 10/67 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 9998015 9998015 A C 1 0 0 0 0 1 0 0 0 3487 14 1 5 5 COL5A3 19 9998015 Missense_Mutation SNP A C3N-02149_T 37140 9998015 48619601 470 28654 ZNF844 0 . GRCh38 19 12076090 12076090 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.970C>G p.Leu324Val p.L324V ENST00000439326 4/4 314 284 30 427 427 0 strelka-varscan-mutect ZNF844,missense_variant,p.Leu324Val,ENST00000439326,NM_001136501.1;ZNF844,3_prime_UTR_variant,,ENST00000441304,;ZNF844,downstream_gene_variant,,ENST00000550826,; G ENST00000439326 Transcript missense_variant 1145/6620 970/2001 324/666 L/V Ctt/Gtt 1 1 ZNF844 HGNC HGNC:25932 protein_coding YES CCDS45985.1 ENSP00000392024 Q08AG5 UPI0000185F5D NM_001136501.1 tolerated(0.11) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24379:SF28,hmmpanther:PTHR24379,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 12076090 12076090 C G 1 0 0 0 0 1 0 0 0 18778 913 32 4 4 ZNF844 19 12076090 Missense_Mutation SNP C C3N-02149_T 2078075 12076090 46541526 471 28655 RLN3 0 . GRCh38 19 14030836 14030836 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.317G>T p.Ser106Ile p.S106I ENST00000431365 2/2 124 93 31 154 154 0 strelka-varscan-mutect RLN3,missense_variant,p.Ser106Ile,ENST00000431365,NM_080864.2;RLN3,3_prime_UTR_variant,,ENST00000585987,;IL27RA,upstream_gene_variant,,ENST00000263379,NM_004843.3;CTB-55O6.4,downstream_gene_variant,,ENST00000590528,; T ENST00000431365 Transcript missense_variant 374/580 317/429 106/142 S/I aGc/aTc 1 1 RLN3 HGNC HGNC:17135 protein_coding YES CCDS12302.1 ENSP00000397415 Q8WXF3 UPI0000042374 NM_080864.2 deleterious(0.03) 2/2 Pfam_domain:PF00049,hmmpanther:PTHR20968,hmmpanther:PTHR20968:SF0,SMART_domains:SM00078 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 14030836 14030836 G T 1 0 0 0 0 1 0 0 0 13569 971 34 2 2 RLN3 19 14030836 Missense_Mutation SNP G C3N-02149_T 1954746 14030836 44586780 472 28656 CCDC105 0 . GRCh38 19 15021500 15021500 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1022G>T p.Ser341Ile p.S341I ENST00000292574 4/7 155 143 12 179 179 0 strelka-varscan-mutect CCDC105,missense_variant,p.Ser341Ile,ENST00000292574,NM_173482.2;SLC1A6,intron_variant,,ENST00000595863,; T ENST00000292574 Transcript missense_variant 1104/1732 1022/1500 341/499 S/I aGc/aTc 1 1 CCDC105 HGNC HGNC:26866 protein_coding YES CCDS12322.1 ENSP00000292574 Q8IYK2 UPI0000073091 NM_173482.2 tolerated(0.1) 4/7 hmmpanther:PTHR35081,Pfam_domain:PF03148 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 15021500 15021500 G T 1 0 0 0 0 1 0 0 0 2437 971 34 2 2 CCDC105 19 15021500 Missense_Mutation SNP G C3N-02149_T 990664 15021500 43596116 473 28657 CYP4F2 0 . GRCh38 19 15885964 15885964 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1075C>A p.Gln359Lys p.Q359K ENST00000221700 9/13 130 108 22 207 206 1 strelka-varscan-mutect CYP4F2,missense_variant,p.Gln359Lys,ENST00000221700,NM_001082.4;CYP4F2,missense_variant,p.Gln359Lys,ENST00000011989,;CYP4F2,missense_variant,p.Gln22Lys,ENST00000589654,;CYP4F2,3_prime_UTR_variant,,ENST00000587671,;CYP4F2,non_coding_transcript_exon_variant,,ENST00000392846,;CYP4F2,non_coding_transcript_exon_variant,,ENST00000592710,; T ENST00000221700 Transcript missense_variant 1171/2407 1075/1563 359/520 Q/K Caa/Aaa 1 -1 CYP4F2 HGNC HGNC:2645 protein_coding YES CCDS12336.1 ENSP00000221700 P78329 UPI0000052BE6 NM_001082.4 tolerated(0.15) 9/13 hmmpanther:PTHR24291:SF45,hmmpanther:PTHR24291,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264,Prints_domain:PR00463 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 15885964 15885964 G T 1 0 0 0 0 1 0 0 0 3991 1328 46 2 2 CYP4F2 19 15885964 Missense_Mutation SNP G C3N-02149_T 864464 15885964 42731652 474 28658 SIN3B 0 . GRCh38 19 16870039 16870039 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.2482A>T p.Ser828Cys p.S828C ENST00000379803 14/20 92 68 24 121 121 0 strelka-varscan-mutect SIN3B,missense_variant,p.Ser828Cys,ENST00000379803,NM_015260.3;SIN3B,missense_variant,p.Ser796Cys,ENST00000248054,NM_001297595.1;SIN3B,missense_variant,p.Ser386Cys,ENST00000595541,NM_001297597.1;SIN3B,non_coding_transcript_exon_variant,,ENST00000595900,;SIN3B,downstream_gene_variant,,ENST00000599880,;SIN3B,non_coding_transcript_exon_variant,,ENST00000602204,;SIN3B,downstream_gene_variant,,ENST00000594372,; T ENST00000379803 Transcript missense_variant 2496/5129 2482/3489 828/1162 S/C Agc/Tgc 1 1 SIN3B HGNC HGNC:19354 protein_coding YES CCDS32946.1 ENSP00000369131 O75182 UPI0000425EFA NM_015260.3 tolerated(0.12) 14/20 hmmpanther:PTHR12346,hmmpanther:PTHR12346:SF1,Pfam_domain:PF16879 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 16870039 16870039 A T 1 0 0 0 0 1 0 0 0 14590 188 7 4 4 SIN3B 19 16870039 Missense_Mutation SNP A C3N-02149_T 984075 16870039 41747577 475 28659 USHBP1 0 . GRCh38 19 17259307 17259307 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.1028A>T p.His343Leu p.H343L ENST00000252597 7/13 108 85 23 124 124 0 varscan-mutect USHBP1,missense_variant,p.His343Leu,ENST00000252597,NM_031941.3;USHBP1,missense_variant,p.His279Leu,ENST00000431146,NM_001297703.1;USHBP1,downstream_gene_variant,,ENST00000594190,;USHBP1,downstream_gene_variant,,ENST00000598309,;AC010646.3,upstream_gene_variant,,ENST00000594059,;USHBP1,downstream_gene_variant,,ENST00000598570,;USHBP1,downstream_gene_variant,,ENST00000595993,;USHBP1,missense_variant,p.His343Leu,ENST00000324554,;USHBP1,3_prime_UTR_variant,,ENST00000597928,;USHBP1,downstream_gene_variant,,ENST00000600286,;USHBP1,downstream_gene_variant,,ENST00000596436,; A ENST00000252597 Transcript missense_variant 1202/3335 1028/2112 343/703 H/L cAt/cTt 1 -1 USHBP1 HGNC HGNC:24058 protein_coding YES CCDS12353.1 ENSP00000252597 Q8N6Y0 A0A024R7H3 UPI000006F7A8 NM_031941.3 deleterious(0.02) 7/13 hmmpanther:PTHR23347:SF5,hmmpanther:PTHR23347,Pfam_domain:PF10506 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 17259307 17259307 T A 1 0 0 0 0 1 0 0 0 17571 1464 51 4 4 USHBP1 19 17259307 Missense_Mutation SNP T C3N-02149_T 389268 17259307 41358309 476 28660 UNC13A 0 . GRCh38 19 17656314 17656314 + Missense_Mutation SNP C C A rs768640284 C3N-02149_T C3N-02149_N C C c.852G>T p.Glu284Asp p.E284D ENST00000519716 10/44 144 116 28 195 195 0 strelka-varscan-mutect UNC13A,missense_variant,p.Glu284Asp,ENST00000519716,NM_001080421.2;UNC13A,missense_variant,p.Glu284Asp,ENST00000551649,;UNC13A,missense_variant,p.Glu284Asp,ENST00000552293,;UNC13A,missense_variant,p.Glu284Asp,ENST00000550896,; A ENST00000519716 Transcript missense_variant 852/9838 852/5112 284/1703 E/D gaG/gaT rs768640284 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 tolerated_low_confidence(0.44) 10/44 hmmpanther:PTHR10480 MODERATE 1 SNV 5 1 PASS rs768640284 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 17656314 17656314 C A 1 0 0 0 0 1 0 0 0 17508 796 28 2 2 UNC13A 19 17656314 Missense_Mutation SNP C C3N-02149_T 397007 17656314 40961302 477 28661 NCAN 0 . GRCh38 19 19224431 19224431 + Missense_Mutation SNP G G C rs760694042 C3N-02149_T C3N-02149_N G G c.776G>C p.Gly259Ala p.G259A ENST00000252575 5/15 50 37 13 87 87 0 strelka-mutect NCAN,missense_variant,p.Gly259Ala,ENST00000252575,NM_004386.2;NCAN,upstream_gene_variant,,ENST00000590187,; C ENST00000252575 Transcript missense_variant,splice_region_variant 875/6387 776/3966 259/1321 G/A gGg/gCg rs760694042 1 1 NCAN HGNC HGNC:2465 protein_coding YES CCDS12397.1 ENSP00000252575 O14594 A0A024R7M3 UPI000013CD70 NM_004386.2 deleterious(0.04) 5/15 PROSITE_profiles:PS50963,hmmpanther:PTHR22804:SF24,hmmpanther:PTHR22804,SMART_domains:SM00445,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs760694042 . 0 202 8 0 0 0 0 0 -20 0.9999994 1 1 1 0 C 3 2 92 19224431 19224431 G C 1 0 0 0 0 1 0 0 0 10220 1246 43 4 4 NCAN 19 19224431 Missense_Mutation SNP G C3N-02149_T 1568117 19224431 39393185 478 28662 ZNF708 0 . GRCh38 19 21309246 21309246 + Missense_Mutation SNP C C G rs140295887 C3N-02149_T C3N-02149_N C C c.226G>C p.Ala76Pro p.A76P ENST00000356929 3/4 93 85 8 164 164 0 varscan-mutect ZNF708,missense_variant,p.Ala76Pro,ENST00000356929,NM_001297561.1,NM_021269.2;ZNF708,missense_variant,p.Ala12Pro,ENST00000601295,;ZNF708,splice_region_variant,,ENST00000602023,;ZNF708,splice_region_variant,,ENST00000598046,; G ENST00000356929 Transcript missense_variant,splice_region_variant 424/4004 226/1692 76/563 A/P Gct/Cct rs140295887 1 -1 ZNF708 HGNC HGNC:12945 protein_coding YES CCDS32980.1 ENSP00000349401 P17019 UPI000041F9DE NM_001297561.1,NM_021269.2 deleterious(0.01) 3/4 hmmpanther:PTHR24384:SF128,hmmpanther:PTHR24384 MODERATE 1 SNV 2 1 PASS rs140295887 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 21309246 21309246 C G 1 0 0 0 0 1 0 0 0 18687 695 24 4 4 ZNF708 19 21309246 Missense_Mutation SNP C C3N-02149_T 2084815 21309246 37308370 479 28663 CEP89 0 . GRCh38 19 32948286 32948286 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.575C>A p.Pro192Gln p.P192Q ENST00000305768 5/19 113 96 17 136 135 1 strelka-varscan-mutect CEP89,missense_variant,p.Pro192Gln,ENST00000305768,NM_032816.4;CEP89,missense_variant,p.Pro192Gln,ENST00000590597,;CEP89,missense_variant,p.Pro164Gln,ENST00000593276,;CEP89,missense_variant,p.Pro192Gln,ENST00000586984,;CEP89,missense_variant,p.Pro108Gln,ENST00000591698,; T ENST00000305768 Transcript missense_variant 664/5678 575/2352 192/783 P/Q cCa/cAa 1 -1 CEP89 HGNC HGNC:25907 protein_coding YES CCDS32987.1 ENSP00000306105 Q96ST8 UPI000020202C NM_032816.4 tolerated(0.09) 5/19 hmmpanther:PTHR36170 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 92 32948286 32948286 G T 1 0 0 0 0 1 0 0 0 2987 1348 47 2 2 CEP89 19 32948286 Missense_Mutation SNP G C3N-02149_T 11639040 32948286 25669330 480 28664 GPATCH1 0 . GRCh38 19 33081221 33081221 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.28G>C p.Glu10Gln p.E10Q ENST00000170564 1/20 335 307 28 396 396 0 strelka-varscan-mutect GPATCH1,missense_variant,p.Glu10Gln,ENST00000170564,NM_018025.2;GPATCH1,missense_variant,p.Glu10Gln,ENST00000592165,; C ENST00000170564 Transcript missense_variant 342/3492 28/2796 10/931 E/Q Gaa/Caa 1 1 GPATCH1 HGNC HGNC:24658 protein_coding YES CCDS12428.1 ENSP00000170564 Q9BRR8 UPI000004EC71 NM_018025.2 deleterious(0.01) 1/20 hmmpanther:PTHR13384:SF19,hmmpanther:PTHR13384 MODERATE 1 SNV 1 1 PASS rs1175557455 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 33081221 33081221 G C 1 0 0 0 0 1 0 0 0 6489 943 33 4 4 GPATCH1 19 33081221 Missense_Mutation SNP G C3N-02149_T 132935 33081221 25536395 481 28665 ZNF181 0 . GRCh38 19 34742056 34742056 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.1675C>T p.His559Tyr p.H559Y ENST00000492450 4/4 84 69 15 94 94 0 strelka-varscan-mutect ZNF181,missense_variant,p.His559Tyr,ENST00000492450,NM_001029997.3;ZNF181,missense_variant,p.His603Tyr,ENST00000392232,;ZNF181,missense_variant,p.His558Tyr,ENST00000459757,NM_001145665.1;ZNF181,downstream_gene_variant,,ENST00000595708,;ZNF181,downstream_gene_variant,,ENST00000599244,;ZNF181,downstream_gene_variant,,ENST00000593781,;ZNF181,non_coding_transcript_exon_variant,,ENST00000448715,; T ENST00000492450 Transcript missense_variant 1764/5086 1675/1716 559/571 H/Y Cac/Tac 1 1 ZNF181 HGNC HGNC:12971 protein_coding YES CCDS32990.2 ENSP00000420727 Q2M3W8 UPI000020207A NM_001029997.3 deleterious(0.04) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 34742056 34742056 C T 1 0 0 0 0 1 0 0 0 18329 826 29 3 3 ZNF181 19 34742056 Missense_Mutation SNP C C3N-02149_T 1660835 34742056 23875560 482 28666 WDR62 0 . GRCh38 19 36103185 36103185 + Silent SNP C C A rs201443416 C3N-02149_T C3N-02149_N C C c.3492C>A p.= p.T1164T ENST00000401500 29/32 629 589 40 713 712 1 strelka-varscan-mutect WDR62,synonymous_variant,p.=,ENST00000401500,NM_001083961.1;WDR62,synonymous_variant,p.=,ENST00000270301,NM_173636.4;WDR62,3_prime_UTR_variant,,ENST00000587391,; A ENST00000401500 Transcript synonymous_variant 3527/4682 3492/4572 1164/1523 T acC/acA rs201443416 1 1 WDR62 HGNC HGNC:24502 protein_coding YES CCDS46059.1 ENSP00000384792 O43379 UPI000022A7E9 NM_001083961.1 29/32 LOW 1 SNV 1 1 PASS rs201443416 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 36103185 36103185 C A 1 0 0 0 0 0 0 0 1 17872 610 22 2 2 WDR62 19 36103185 Silent SNP C C3N-02149_T 1361129 36103185 22514431 483 28667 ZNF567 0 . GRCh38 19 36712456 36712456 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.80A>T p.Gln27Leu p.Q27L ENST00000536254 4/6 246 222 24 341 341 0 strelka-varscan-mutect ZNF567,missense_variant,p.Gln27Leu,ENST00000536254,NM_001322917.1,NM_001322918.1,NM_001322915.1,NM_001322916.1,NM_001322913.1,NM_001300979.1;ZNF567,missense_variant,p.Gln6Leu,ENST00000589264,;ZNF567,5_prime_UTR_variant,,ENST00000585696,;ZNF567,5_prime_UTR_variant,,ENST00000360729,NM_001322912.1,NM_001322911.1,NM_152603.3;ZNF567,5_prime_UTR_variant,,ENST00000588311,;ZNF850,downstream_gene_variant,,ENST00000589390,;ZNF567,non_coding_transcript_exon_variant,,ENST00000590392,;ZNF567,upstream_gene_variant,,ENST00000591308,; T ENST00000536254 Transcript missense_variant 302/2825 80/1944 27/647 Q/L cAg/cTg 1 1 ZNF567 HGNC HGNC:28696 protein_coding YES CCDS74349.1 ENSP00000441838 Q8N184 UPI000022A7F5 NM_001322917.1,NM_001322918.1,NM_001322915.1,NM_001322916.1,NM_001322913.1,NM_001300979.1 deleterious(0) 4/6 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF25,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 36712456 36712456 A T 1 0 0 0 0 1 0 0 0 18572 188 7 4 4 ZNF567 19 36712456 Missense_Mutation SNP A C3N-02149_T 609271 36712456 21905160 484 28668 RYR1 0 . GRCh38 19 38504877 38504877 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.8197G>T p.Gly2733Cys p.G2733C ENST00000359596 51/106 635 577 58 773 772 1 strelka-varscan-mutect RYR1,missense_variant,p.Gly2733Cys,ENST00000355481,NM_001042723.1;RYR1,missense_variant,p.Gly2733Cys,ENST00000359596,NM_000540.2;RYR1,missense_variant,p.Gly551Cys,ENST00000594335,; T ENST00000359596 Transcript missense_variant 8197/15117 8197/15117 2733/5038 G/C Ggc/Tgc COSM4188727 1 1 RYR1 HGNC HGNC:10483 protein_coding YES CCDS33011.1 ENSP00000352608 P21817 UPI0000D7E62F NM_000540.2 deleterious(0) 51/106 hmmpanther:PTHR13715:SF15,hmmpanther:PTHR13715 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 38504877 38504877 G T 1 0 0 0 0 1 0 0 0 14028 1000 35 2 2 RYR1 19 38504877 Missense_Mutation SNP G C3N-02149_T 1792421 38504877 20112739 485 28669 ACP7 0 . GRCh38 19 39106990 39106990 + Missense_Mutation SNP C C A rs559239375 C3N-02149_T C3N-02149_N C C c.1157C>A p.Pro386His p.P386H ENST00000331256 12/13 246 221 25 321 320 1 strelka-varscan-mutect ACP7,missense_variant,p.Pro386His,ENST00000331256,NM_001004318.2;ACP7,intron_variant,,ENST00000594229,;ACP7,intron_variant,,ENST00000601531,;ACP7,3_prime_UTR_variant,,ENST00000601575,; A ENST00000331256 Transcript missense_variant 1431/2966 1157/1317 386/438 P/H cCc/cAc rs559239375 1 1 ACP7 HGNC HGNC:33781 protein_coding YES CCDS33018.1 ENSP00000327557 Q6ZNF0 UPI000041AA68 NM_001004318.2 deleterious(0.01) 12/13 Gene3D:3.60.21.10,Pfam_domain:PF14008,hmmpanther:PTHR22953,hmmpanther:PTHR22953:SF9,Superfamily_domains:SSF56300 MODERATE 1 SNV 2 1 PASS rs559239375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 39106990 39106990 C A 1 0 0 0 0 1 0 0 0 208 623 22 2 2 ACP7 19 39106990 Missense_Mutation SNP C C3N-02149_T 602113 39106990 19510626 486 28670 MAP3K10 0 . GRCh38 19 40206030 40206030 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.1308G>T p.= p.R436R ENST00000253055 5/10 187 169 18 183 183 0 strelka-mutect MAP3K10,synonymous_variant,p.=,ENST00000253055,NM_002446.3;MAP3K10,downstream_gene_variant,,ENST00000593906,;MAP3K10,3_prime_UTR_variant,,ENST00000594951,;MAP3K10,non_coding_transcript_exon_variant,,ENST00000594569,;MAP3K10,intron_variant,,ENST00000597986,;MAP3K10,intron_variant,,ENST00000593502,;MAP3K10,upstream_gene_variant,,ENST00000594791,;MAP3K10,downstream_gene_variant,,ENST00000601702,; T ENST00000253055 Transcript synonymous_variant 1596/3436 1308/2865 436/954 R cgG/cgT 1 1 MAP3K10 HGNC HGNC:6849 protein_coding YES CCDS12549.1 ENSP00000253055 Q02779 UPI000013CDAC NM_002446.3 5/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23257,hmmpanther:PTHR23257:SF515,PIRSF_domain:PIRSF000556 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 40206030 40206030 G T 1 0 0 0 0 0 0 0 1 9166 1219 43 2 2 MAP3K10 19 40206030 Silent SNP G C3N-02149_T 1099040 40206030 18411586 487 28671 PSG6 0 . GRCh38 19 42916413 42916413 + Missense_Mutation SNP C C T rs200758573 C3N-02149_T C3N-02149_N C C c.139G>A p.Glu47Lys p.E47K ENST00000292125 2/6 206 183 23 256 256 0 strelka-varscan-mutect PSG6,missense_variant,p.Glu47Lys,ENST00000187910,NM_001031850.3;PSG6,missense_variant,p.Glu47Lys,ENST00000402603,;PSG6,missense_variant,p.Glu47Lys,ENST00000292125,NM_002782.4;PSG6,5_prime_UTR_variant,,ENST00000601833,;PSG7,intron_variant,,ENST00000617049,;PSG6,intron_variant,,ENST00000594375,;PSG6,non_coding_transcript_exon_variant,,ENST00000402456,;PSG6,intron_variant,,ENST00000484292,;PSG6,upstream_gene_variant,,ENST00000595062,; T ENST00000292125 Transcript missense_variant 184/1391 139/1308 47/435 E/K Gag/Aag rs200758573,COSM3288481,COSM3288482,COSM349603 1 -1 PSG6 HGNC HGNC:9523 protein_coding YES CCDS12613.1 ENSP00000292125 Q00889 UPI00001327A1 NM_002782.4 deleterious(0.05) 2/6 Gene3D:2.60.40.10,Pfam_domain:PF07686,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1,1 MODERATE 1 SNV 1 0,1,1,1 1 PASS rs200758573 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 42916413 42916413 C T 1 0 0 0 0 1 0 0 0 12810 893 31 1 1 PSG6 19 42916413 Missense_Mutation SNP C C3N-02149_T 2710383 42916413 15701203 488 28672 PSG2 0 . GRCh38 19 43075585 43075585 + Nonsense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.478G>T p.Glu160Ter p.E160* ENST00000406487 3/6 153 119 34 209 209 0 strelka-varscan-mutect PSG2,stop_gained,p.Glu160Ter,ENST00000406487,NM_031246.3;PSG2,upstream_gene_variant,,ENST00000329509,;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG2,intron_variant,,ENST00000593482,; A ENST00000406487 Transcript stop_gained 577/1538 478/1008 160/335 E/* Gag/Tag COSM3288581 1 -1 PSG2 HGNC HGNC:9519 protein_coding YES CCDS12616.1 ENSP00000385706 P11465 A0A024R0M4 UPI000013CCF5 NM_031246.3 3/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF615,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,SMART_domains:SM00408,Superfamily_domains:SSF48726 1 HIGH 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 43075585 43075585 C A 1 0 0 0 0 0 1 0 0 12806 864 30 2 2 PSG2 19 43075585 Nonsense_Mutation SNP C C3N-02149_T 159172 43075585 15542031 489 28673 SULT2A1 0 . GRCh38 19 47883701 47883701 + Missense_Mutation SNP C C A rs763687131 C3N-02149_T C3N-02149_N C C c.221G>T p.Arg74Leu p.R74L ENST00000222002 2/6 313 294 19 362 361 1 strelka-varscan-mutect SULT2A1,missense_variant,p.Arg74Leu,ENST00000222002,NM_003167.3; A ENST00000222002 Transcript missense_variant 361/1987 221/858 74/285 R/L cGa/cTa rs763687131,COSM3536394 1 -1 SULT2A1 HGNC HGNC:11458 protein_coding YES CCDS12707.1 ENSP00000222002 Q06520 A8K015 UPI000013C7E8 NM_003167.3 deleterious(0.01) 2/6 hmmpanther:PTHR11783:SF8,hmmpanther:PTHR11783,Pfam_domain:PF00685,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs763687131 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 47883701 47883701 C A 1 0 0 0 0 1 0 0 0 15767 884 31 1 1 SULT2A1 19 47883701 Missense_Mutation SNP C C3N-02149_T 4808116 47883701 10733915 490 28674 SCAF1 0 . GRCh38 19 49651993 49651993 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.1604C>T p.Ser535Phe p.S535F ENST00000360565 7/11 41 36 5 107 107 0 strelka-mutect SCAF1,missense_variant,p.Ser535Phe,ENST00000360565,NM_021228.2;SCAF1,downstream_gene_variant,,ENST00000598359,; T ENST00000360565 Transcript missense_variant 1728/4306 1604/3939 535/1312 S/F tCc/tTc 1 1 SCAF1 HGNC HGNC:30403 protein_coding YES CCDS33074.1 ENSP00000353769 Q9H7N4 UPI0000071891 NM_021228.2 deleterious_low_confidence(0.03) 7/11 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -13.13869 1 1 1 1 0 T 3 4 92 49651993 49651993 C T 1 0 0 0 0 1 0 0 0 14132 855 30 3 3 SCAF1 19 49651993 Missense_Mutation SNP C C3N-02149_T 1768292 49651993 8965623 491 28675 ACPT 0 . GRCh38 19 50793909 50793909 + Missense_Mutation SNP T T C C3N-02149_T C3N-02149_N T T c.800T>C p.Leu267Pro p.L267P ENST00000270593 8/11 411 382 29 489 489 0 strelka-varscan-mutect ACPT,missense_variant,p.Leu267Pro,ENST00000270593,NM_033068.2;C19orf48,downstream_gene_variant,,ENST00000598463,NM_001290149.1;C19orf48,downstream_gene_variant,,ENST00000345523,NM_001290152.1,NM_001290155.1,NM_199250.2,NM_001290151.1,NM_001290150.1;C19orf48,downstream_gene_variant,,ENST00000391812,NM_199249.2,NM_001290154.1,NM_001290153.1;C19orf48,downstream_gene_variant,,ENST00000596655,NM_032712.2;C19orf48,downstream_gene_variant,,ENST00000597493,;C19orf48,downstream_gene_variant,,ENST00000597705,;C19orf48,downstream_gene_variant,,ENST00000596287,;C19orf48,downstream_gene_variant,,ENST00000601267,;C19orf48,downstream_gene_variant,,ENST00000600373,;C19orf48,downstream_gene_variant,,ENST00000593287,;CTD-2568A17.1,upstream_gene_variant,,ENST00000636757,;CTD-2568A17.8,upstream_gene_variant,,ENST00000594114,;C19orf48,downstream_gene_variant,,ENST00000595794,;C19orf48,downstream_gene_variant,,ENST00000599004,;C19orf48,downstream_gene_variant,,ENST00000596554,; C ENST00000270593 Transcript missense_variant 800/1347 800/1281 267/426 L/P cTt/cCt COSM221863 1 1 ACPT HGNC HGNC:14376 protein_coding YES CCDS12802.1 ENSP00000270593 Q9BZG2 UPI0000048D54 NM_033068.2 deleterious(0) 8/11 hmmpanther:PTHR11567,hmmpanther:PTHR11567:SF110,Gene3D:3.40.50.1240,Pfam_domain:PF00328,Superfamily_domains:SSF53254 1 MODERATE SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 50793909 50793909 T C 1 0 0 0 0 1 0 0 0 210 1609 56 5 5 ACPT 19 50793909 Missense_Mutation SNP T C3N-02149_T 1141916 50793909 7823707 492 28676 SIGLEC10 0 . GRCh38 19 51416890 51416890 + Missense_Mutation SNP G G T rs139983112 C3N-02149_T C3N-02149_N G G c.482C>A p.Thr161Lys p.T161K ENST00000339313 3/11 191 176 15 224 224 0 varscan-mutect SIGLEC10,missense_variant,p.Thr161Lys,ENST00000353836,NM_001171157.1;SIGLEC10,missense_variant,p.Thr161Lys,ENST00000339313,NM_033130.4;SIGLEC10,missense_variant,p.Thr161Lys,ENST00000525998,;SIGLEC10,missense_variant,p.Thr128Lys,ENST00000530476,;SIGLEC10,intron_variant,,ENST00000441969,NM_001171159.1;SIGLEC10,intron_variant,,ENST00000442846,NM_001171161.1;SIGLEC10,intron_variant,,ENST00000439889,NM_001171156.1;SIGLEC10,intron_variant,,ENST00000436984,NM_001171158.1;SIGLEC10,intron_variant,,ENST00000529627,;CTD-2616J11.2,intron_variant,,ENST00000532688,;CTD-2616J11.2,downstream_gene_variant,,ENST00000526996,;CTD-2616J11.3,downstream_gene_variant,,ENST00000532473,;SIGLEC10,non_coding_transcript_exon_variant,,ENST00000357375,;SIGLEC10,downstream_gene_variant,,ENST00000524527,; T ENST00000339313 Transcript missense_variant 599/2256 482/2094 161/697 T/K aCg/aAg rs139983112,COSM999998 1 -1 SIGLEC10 HGNC HGNC:15620 protein_coding YES CCDS12832.1 ENSP00000345243 Q96LC7 UPI0000047E1A NM_033130.4 tolerated(0.2) 3/11 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF68,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs139983112 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 51416890 51416890 G T 1 0 0 0 0 1 0 0 0 14570 1145 40 1 1 SIGLEC10 19 51416890 Missense_Mutation SNP G C3N-02149_T 622981 51416890 7200726 493 28677 SIGLEC12 0 . GRCh38 19 51500142 51500142 + Missense_Mutation SNP C C A rs746468203 C3N-02149_T C3N-02149_N C C c.586G>T p.Asp196Tyr p.D196Y ENST00000291707 2/8 529 484 45 556 555 1 strelka-varscan-mutect SIGLEC12,missense_variant,p.Asp196Tyr,ENST00000291707,NM_053003.3;SIGLEC12,missense_variant,p.Asp78Tyr,ENST00000598614,NM_033329.2;SIGLEC12,intron_variant,,ENST00000596742,;CTD-3073N11.7,downstream_gene_variant,,ENST00000594712,; A ENST00000291707 Transcript missense_variant 642/2121 586/1788 196/595 D/Y Gat/Tat rs746468203 1 -1 SIGLEC12 HGNC HGNC:15482 protein_coding YES CCDS12833.1 ENSP00000291707 Q96PQ1 UPI0000135992 NM_053003.3 tolerated(0.07) 2/8 hmmpanther:PTHR12035:SF53,hmmpanther:PTHR12035,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs746468203 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 51500142 51500142 C A 1 0 0 0 0 1 0 0 0 14572 884 31 1 1 SIGLEC12 19 51500142 Missense_Mutation SNP C C3N-02149_T 83252 51500142 7117474 494 28678 SIGLEC6 0 . GRCh38 19 51531316 51531316 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.271G>C p.Gly91Arg p.G91R ENST00000425629 2/8 177 165 12 205 205 0 strelka-varscan-mutect SIGLEC6,missense_variant,p.Gly91Arg,ENST00000346477,NM_198845.4;SIGLEC6,missense_variant,p.Gly91Arg,ENST00000425629,NM_001245.5;SIGLEC6,missense_variant,p.Gly91Arg,ENST00000359982,NM_001177548.1;SIGLEC6,missense_variant,p.Gly91Arg,ENST00000343300,NM_198846.4;SIGLEC6,missense_variant,p.Gly55Arg,ENST00000436458,NM_001177547.1;SIGLEC6,missense_variant,p.Gly91Arg,ENST00000391797,NM_001177549.1;SIGLEC6,upstream_gene_variant,,ENST00000474054,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000496422,;SIGLEC6,non_coding_transcript_exon_variant,,ENST00000489837,; G ENST00000425629 Transcript missense_variant 426/1852 271/1362 91/453 G/R Ggc/Cgc 1 -1 SIGLEC6 HGNC HGNC:10875 protein_coding YES CCDS12834.3 ENSP00000401502 O43699 A0A024R4K4 UPI0000223FFD NM_001245.5 deleterious(0) 2/8 Gene3D:2.60.40.10,Pfam_domain:PF07686,hmmpanther:PTHR12035,hmmpanther:PTHR12035:SF52,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 2 1 PASS rs1224957572 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 51531316 51531316 C G 1 0 0 0 0 1 0 0 0 14576 623 22 4 4 SIGLEC6 19 51531316 Missense_Mutation SNP C C3N-02149_T 31174 51531316 7086300 495 28679 ZNF528 0 . GRCh38 19 52415333 52415333 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.481A>T p.Asn161Tyr p.N161Y ENST00000360465 7/7 136 110 26 132 132 0 strelka-varscan-mutect ZNF528,missense_variant,p.Asn161Tyr,ENST00000360465,NM_032423.2;ZNF528,3_prime_UTR_variant,,ENST00000391788,;ZNF528,3_prime_UTR_variant,,ENST00000448954,;ZNF528,non_coding_transcript_exon_variant,,ENST00000598479,;ZNF528,non_coding_transcript_exon_variant,,ENST00000479718,; T ENST00000360465 Transcript missense_variant 907/3978 481/1887 161/628 N/Y Aat/Tat 1 1 ZNF528 HGNC HGNC:29384 protein_coding YES CCDS33091.1 ENSP00000353652 Q3MIS6 UPI00001B6535 NM_032423.2 deleterious(0.01) 7/7 MODERATE 1 SNV 1 1 PASS rs1165582978 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 52415333 52415333 A T 1 0 0 0 0 1 0 0 0 18542 14 1 4 4 ZNF528 19 52415333 Missense_Mutation SNP A C3N-02149_T 884017 52415333 6202283 496 28680 ZNF415 0 . GRCh38 19 53109566 53109566 + Missense_Mutation SNP T T C rs747957157 C3N-02149_T C3N-02149_N T T c.479A>G p.Tyr160Cys p.Y160C ENST00000500065 4/4 190 177 13 253 253 0 strelka-varscan-mutect ZNF415,missense_variant,p.Tyr160Cys,ENST00000500065,NM_001136038.2;ZNF415,missense_variant,p.Tyr160Cys,ENST00000421033,NM_001164309.1;ZNF415,missense_variant,p.Tyr160Cys,ENST00000243643,NM_018355.3;ZNF415,3_prime_UTR_variant,,ENST00000594011,;ZNF415,3_prime_UTR_variant,,ENST00000595193,;ZNF415,3_prime_UTR_variant,,ENST00000597503,;ZNF415,3_prime_UTR_variant,,ENST00000597748,;ZNF415,5_prime_UTR_variant,,ENST00000601493,;ZNF415,downstream_gene_variant,,ENST00000599261,;ZNF415,downstream_gene_variant,,ENST00000601110,;ZNF415,downstream_gene_variant,,ENST00000595813,;ZNF415,downstream_gene_variant,,ENST00000601215,;ZNF415,downstream_gene_variant,,ENST00000595174,;ZNF415,downstream_gene_variant,,ENST00000595359,;ZNF415,downstream_gene_variant,,ENST00000602024,;ZNF415,3_prime_UTR_variant,,ENST00000600120,;ZNF415,3_prime_UTR_variant,,ENST00000598578,; C ENST00000500065 Transcript missense_variant 813/2496 479/1668 160/555 Y/C tAt/tGt rs747957157,COSM192889,COSM5118648 1 -1 ZNF415 HGNC HGNC:20636 protein_coding YES CCDS54313.1 ENSP00000439435 Q09FC8 UPI0000E04BC1 NM_001136038.2 tolerated(0.16) 4/4 hmmpanther:PTHR24377:SF145,hmmpanther:PTHR24377 0,1,1 MODERATE 1 SNV 4 0,1,1 1 PASS rs747957157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 53109566 53109566 T C 1 0 0 0 0 1 0 0 0 18464 1406 49 5 5 ZNF415 19 53109566 Missense_Mutation SNP T C3N-02149_T 694233 53109566 5508050 497 28681 VN1R2 0 . GRCh38 19 53258443 53258443 + Nonsense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.68T>A p.Leu23Ter p.L23* ENST00000341702 1/1 90 75 15 148 148 0 strelka-varscan-mutect VN1R2,stop_gained,p.Leu23Ter,ENST00000341702,NM_173856.2;ZNF677,upstream_gene_variant,,ENST00000598513,NM_001317998.1,NM_182609.2;ZNF677,upstream_gene_variant,,ENST00000594681,;ZNF677,upstream_gene_variant,,ENST00000599012,;ZNF677,upstream_gene_variant,,ENST00000601828,;ZNF677,upstream_gene_variant,,ENST00000601413,;ZNF677,upstream_gene_variant,,ENST00000598806,;ZNF677,upstream_gene_variant,,ENST00000594517,;ZNF677,upstream_gene_variant,,ENST00000595293,;VN1R2,upstream_gene_variant,,ENST00000598458,; A ENST00000341702 Transcript stop_gained 152/1311 68/1188 23/395 L/* tTg/tAg 1 1 VN1R2 HGNC HGNC:19872 protein_coding YES CCDS12862.1 ENSP00000351244 Q8NFZ6 UPI0000062046 NM_173856.2 1/1 Transmembrane_helices:TMhelix HIGH SNV 1 PASS . . 0 202 0 7 0 0 0 0 -19.99999 0.9964237 1 1 1 0 A 4 1 92 53258443 53258443 T A 1 0 0 0 0 0 1 0 0 17727 1821 63 4 4 VN1R2 19 53258443 Nonsense_Mutation SNP T C3N-02149_T 148877 53258443 5359173 498 28682 BIRC8 0 . GRCh38 19 53290287 53290287 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.88G>T p.Ala30Ser p.A30S ENST00000426466 1/1 217 192 25 286 285 1 strelka-varscan-mutect BIRC8,missense_variant,p.Ala30Ser,ENST00000426466,NM_033341.4; A ENST00000426466 Transcript missense_variant 1340/2026 88/711 30/236 A/S Gct/Tct 1 -1 BIRC8 HGNC HGNC:14878 protein_coding YES CCDS12863.1 ENSP00000412957 Q96P09 UPI000003966A NM_033341.4 tolerated(1) 1/1 Gene3D:1.10.1170.10,Pfam_domain:PF00653,PROSITE_patterns:PS01282,PROSITE_profiles:PS50143,hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF102,SMART_domains:SM00238,Superfamily_domains:SSF57924 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 53290287 53290287 C A 1 0 0 0 0 1 0 0 0 1591 710 25 2 2 BIRC8 19 53290287 Missense_Mutation SNP C C3N-02149_T 31844 53290287 5327329 499 28683 KIR3DL3 0 . GRCh38 19 54726087 54726087 + Silent SNP C C A C3N-02149_T C3N-02149_N C C c.105C>A p.= p.P35P ENST00000291860 3/8 125 111 14 142 142 0 strelka-varscan-mutect KIR3DL3,synonymous_variant,p.=,ENST00000291860,NM_153443.4;CTB-61M7.1,intron_variant,,ENST00000400864,; A ENST00000291860 Transcript synonymous_variant 123/1691 105/1233 35/410 P ccC/ccA COSM287973 1 1 KIR3DL3 HGNC HGNC:16312 protein_coding YES CCDS12903.1 ENSP00000291860 A0A0B4J1R5 UPI00005056C3 NM_153443.4 3/8 hmmpanther:PTHR11738:SF91,hmmpanther:PTHR11738,Pfam_domain:PF00047,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 1 LOW 1 SNV 1 1 1 PASS rs1007367212 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 54726087 54726087 C A 1 0 0 0 0 0 0 0 1 8186 639 23 1 1 KIR3DL3 19 54726087 Silent SNP C C3N-02149_T 1435800 54726087 3891529 500 28684 GP6 0 . GRCh38 19 55027747 55027747 + Silent SNP C C T novel C3N-02149_T C3N-02149_N C C c.441G>A p.= p.K147K ENST00000310373 4/8 596 513 83 695 694 1 strelka-varscan-mutect GP6,synonymous_variant,p.=,ENST00000310373,NM_001083899.2;GP6,synonymous_variant,p.=,ENST00000417454,NM_016363.5;GP6,synonymous_variant,p.=,ENST00000333884,NM_001256017.2;GP6,synonymous_variant,p.=,ENST00000468239,;CTC-550B14.7,intron_variant,,ENST00000593060,;CTC-550B14.7,intron_variant,,ENST00000586845,;CTC-550B14.7,intron_variant,,ENST00000586961,;CTC-550B14.6,non_coding_transcript_exon_variant,,ENST00000585492,; T ENST00000310373 Transcript synonymous_variant 469/2268 441/1863 147/620 K aaG/aaA 1 -1 GP6 HGNC HGNC:14388 protein_coding YES CCDS42626.1 ENSP00000308782 Q9HCN6 UPI000013C631 NM_001083899.2 4/8 Gene3D:2.60.40.10,Pfam_domain:PF13895,hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF104,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 55027747 55027747 C T 1 0 0 0 0 0 0 0 1 6479 680 24 3 3 GP6 19 55027747 Silent SNP C C3N-02149_T 301660 55027747 3589869 501 28685 NLRP8 0 . GRCh38 19 55952604 55952604 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.434G>T p.Gly145Val p.G145V ENST00000291971 2/10 161 134 27 186 186 0 strelka-varscan-mutect NLRP8,missense_variant,p.Gly145Val,ENST00000291971,NM_176811.2;NLRP8,missense_variant,p.Gly145Val,ENST00000590542,; T ENST00000291971 Transcript missense_variant 505/3934 434/3147 145/1048 G/V gGa/gTa 1 1 NLRP8 HGNC HGNC:22940 protein_coding YES CCDS12937.1 ENSP00000291971 Q86W28 UPI00001BB3C9 NM_176811.2 tolerated(0.28) 2/10 MODERATE 1 SNV 2 1 PASS rs1286784227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 55952604 55952604 G T 1 0 0 0 0 1 0 0 0 10521 1174 41 2 2 NLRP8 19 55952604 Missense_Mutation SNP G C3N-02149_T 924857 55952604 2665012 502 28686 ZNF667 0 . GRCh38 19 56442180 56442180 + Missense_Mutation SNP T T G novel C3N-02149_T C3N-02149_N T T c.815A>C p.Lys272Thr p.K272T ENST00000504904 7/7 124 117 7 174 174 0 strelka-varscan-mutect ZNF667,missense_variant,p.Lys272Thr,ENST00000504904,NM_001321356.1;ZNF667,missense_variant,p.Lys272Thr,ENST00000292069,NM_022103.3;ZNF667,missense_variant,p.Lys54Thr,ENST00000629654,;ZNF667,3_prime_UTR_variant,,ENST00000591790,;ZNF667,downstream_gene_variant,,ENST00000587555,;ZNF667,3_prime_UTR_variant,,ENST00000592189,NM_001321355.1; G ENST00000504904 Transcript missense_variant 1535/4390 815/1833 272/610 K/T aAg/aCg 1 -1 ZNF667 HGNC HGNC:28854 protein_coding YES CCDS12944.1 ENSP00000439402 Q5HYK9 UPI0000202CEE NM_001321356.1 deleterious(0.02) 7/7 PROSITE_profiles:PS50157,hmmpanther:PTHR24390,hmmpanther:PTHR24390:SF46,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -13.69484 1 1 1 1 0 G 3 3 92 56442180 56442180 T G 1 0 0 0 0 1 0 0 0 18648 1609 56 5 5 ZNF667 19 56442180 Missense_Mutation SNP T C3N-02149_T 489576 56442180 2175436 503 28687 ZIM3 0 . GRCh38 19 57135065 57135065 + Silent SNP A A G C3N-02149_T C3N-02149_N A A c.1272T>C p.= p.C424C ENST00000269834 5/5 398 373 25 566 566 0 strelka-varscan-mutect ZIM3,synonymous_variant,p.=,ENST00000269834,NM_052882.1;USP29,downstream_gene_variant,,ENST00000254181,NM_020903.2;USP29,downstream_gene_variant,,ENST00000598197,; G ENST00000269834 Transcript synonymous_variant 1658/2627 1272/1419 424/472 C tgT/tgC COSM3960598 1 -1 ZIM3 HGNC HGNC:16366 protein_coding YES CCDS33125.1 ENSP00000269834 Q96PE6 UPI000013C3E0 NM_052882.1 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF30,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 92 57135065 57135065 A G 1 0 0 0 0 0 0 0 1 18263 157 6 5 5 ZIM3 19 57135065 Silent SNP A C3N-02149_T 692885 57135065 1482551 504 28688 ZNF264 0 . GRCh38 19 57193930 57193930 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.89A>T p.Gln30Leu p.Q30L ENST00000263095 2/4 122 102 20 183 183 0 strelka-varscan-mutect ZNF264,missense_variant,p.Gln30Leu,ENST00000263095,NM_003417.4;ZNF264,missense_variant,p.Gln30Leu,ENST00000536056,;ZNF264,missense_variant,p.Gln30Leu,ENST00000600531,;ZNF264,missense_variant,p.Gln30Leu,ENST00000599653,;ZNF264,missense_variant,p.Gln30Leu,ENST00000597447,;ZNF264,missense_variant,p.Gln30Leu,ENST00000594126,; T ENST00000263095 Transcript missense_variant 503/12163 89/1884 30/627 Q/L cAg/cTg 1 1 ZNF264 HGNC HGNC:13057 protein_coding YES CCDS33127.1 ENSP00000263095 O43296 UPI000013C33B NM_003417.4 deleterious(0.04) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF192,SMART_domains:SM00349 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 57193930 57193930 A T 1 0 0 0 0 1 0 0 0 18380 188 7 4 4 ZNF264 19 57193930 Missense_Mutation SNP A C3N-02149_T 58865 57193930 1423686 505 28689 ZNF324B 0 . GRCh38 19 58456293 58456293 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1349A>T p.Glu450Val p.E450V ENST00000336614 4/4 290 253 37 300 300 0 strelka-varscan-mutect ZNF324B,missense_variant,p.Glu450Val,ENST00000336614,NM_207395.2;ZNF324B,missense_variant,p.Glu450Val,ENST00000545523,;ZNF324B,downstream_gene_variant,,ENST00000598244,;ZNF324B,downstream_gene_variant,,ENST00000599193,;ZNF324B,downstream_gene_variant,,ENST00000594214,;ZNF324B,downstream_gene_variant,,ENST00000599194,; T ENST00000336614 Transcript missense_variant 1456/2996 1349/1635 450/544 E/V gAg/gTg 1 1 ZNF324B HGNC HGNC:33107 protein_coding YES CCDS33138.1 ENSP00000337473 Q6AW86 UPI000022AA2D NM_207395.2 deleterious(0) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF159,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 58456293 58456293 A T 1 0 0 0 0 1 0 0 0 18417 304 11 4 4 ZNF324B 19 58456293 Missense_Mutation SNP A C3N-02149_T 1262363 58456293 161323 506 28690 TCF15 0 . GRCh38 20 604594 604594 + Silent SNP T T C novel C3N-02149_T C3N-02149_N T T c.597A>G p.= p.R199R ENST00000246080 2/2 336 249 87 356 356 0 strelka-varscan-mutect TCF15,synonymous_variant,p.=,ENST00000246080,NM_004609.3; C ENST00000246080 Transcript synonymous_variant 758/1555 597/600 199/199 R agA/agG 1 -1 TCF15 HGNC HGNC:11627 protein_coding YES CCDS33432.1 ENSP00000246080 Q12870 UPI000013CBD4 NM_004609.3 2/2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 92 604594 604594 T C 1 0 0 0 0 0 0 0 1 16095 1432 50 5 5 TCF15 20 604594 Silent SNP T C3N-02149_T 604594 63839573 507 28691 SIRPA 0 . GRCh38 20 1921619 1921619 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.661G>T p.Asp221Tyr p.D221Y ENST00000400068 4/9 440 400 40 462 462 0 varscan-mutect SIRPA,missense_variant,p.Asp221Tyr,ENST00000622179,;SIRPA,missense_variant,p.Asp221Tyr,ENST00000400068,NM_001040022.1;SIRPA,missense_variant,p.Asp221Tyr,ENST00000358771,NM_001040023.1;SIRPA,missense_variant,p.Asp221Tyr,ENST00000356025,NM_080792.2; T ENST00000400068 Transcript missense_variant 1021/4201 661/1515 221/504 D/Y Gac/Tac 1 1 SIRPA HGNC HGNC:9662 protein_coding YES CCDS13022.1 ENSP00000382941 P78324 UPI0000073ADE NM_001040022.1 deleterious(0) 4/9 Gene3D:2.60.40.10,Pfam_domain:PF07654,PROSITE_profiles:PS50835,hmmpanther:PTHR19971,hmmpanther:PTHR19971:SF12,SMART_domains:SM00407,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 1921619 1921619 G T 1 0 0 0 0 1 0 0 0 14595 1174 41 2 2 SIRPA 20 1921619 Missense_Mutation SNP G C3N-02149_T 1317025 1921619 62522548 508 28692 TGM6 0 . GRCh38 20 2430540 2430540 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.1773C>A p.= p.T591T ENST00000202625 11/13 429 378 51 517 517 0 strelka-varscan-mutect TGM6,synonymous_variant,p.=,ENST00000202625,NM_198994.2;TGM6,synonymous_variant,p.=,ENST00000381423,NM_001254734.1; A ENST00000202625 Transcript synonymous_variant 1834/2292 1773/2121 591/706 T acC/acA 1 1 TGM6 HGNC HGNC:16255 protein_coding YES CCDS13025.1 ENSP00000202625 O95932 UPI0000367011 NM_198994.2 11/13 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF50,PIRSF_domain:PIRSF000459,Gene3D:2.60.40.10,Pfam_domain:PF00927,Superfamily_domains:SSF49309 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 2430540 2430540 C A 1 0 0 0 0 0 0 0 1 16267 581 21 2 2 TGM6 20 2430540 Silent SNP C C3N-02149_T 508921 2430540 62013627 509 28693 NOP56 0 . GRCh38 20 2656864 2656864 + Missense_Mutation SNP A A G novel C3N-02149_T C3N-02149_N A A c.1250A>G p.Asn417Ser p.N417S ENST00000329276 10/12 445 374 71 531 531 0 strelka-varscan-mutect NOP56,missense_variant,p.Asn417Ser,ENST00000329276,NM_006392.3;NOP56,missense_variant,p.Asn158Ser,ENST00000415272,;IDH3B,downstream_gene_variant,,ENST00000380843,NM_006899.3;IDH3B,downstream_gene_variant,,ENST00000613370,NM_001258384.1;IDH3B,downstream_gene_variant,,ENST00000474315,;IDH3B,downstream_gene_variant,,ENST00000380851,NM_174855.2;NOP56,downstream_gene_variant,,ENST00000445139,;SNORA51,downstream_gene_variant,,ENST00000606420,;SNORD86,downstream_gene_variant,,ENST00000391196,;SNORD110,downstream_gene_variant,,ENST00000408189,;SNORD57,upstream_gene_variant,,ENST00000448188,;SNORD56,downstream_gene_variant,,ENST00000413522,;NOP56,downstream_gene_variant,,ENST00000408135,;NOP56,non_coding_transcript_exon_variant,,ENST00000492135,;NOP56,non_coding_transcript_exon_variant,,ENST00000466447,;NOP56,non_coding_transcript_exon_variant,,ENST00000462630,;NOP56,non_coding_transcript_exon_variant,,ENST00000480447,;NOP56,non_coding_transcript_exon_variant,,ENST00000490753,;NOP56,non_coding_transcript_exon_variant,,ENST00000471023,;NOP56,downstream_gene_variant,,ENST00000484998,;NOP56,downstream_gene_variant,,ENST00000469588,;NOP56,downstream_gene_variant,,ENST00000480992,;NOP56,downstream_gene_variant,,ENST00000494697,;NOP56,downstream_gene_variant,,ENST00000460258,;NOP56,upstream_gene_variant,,ENST00000467857,;NOP56,downstream_gene_variant,,ENST00000496775,;NOP56,downstream_gene_variant,,ENST00000470143,;NOP56,missense_variant,p.Asn191Ser,ENST00000467196,;NOP56,non_coding_transcript_exon_variant,,ENST00000612233,;NOP56,non_coding_transcript_exon_variant,,ENST00000616692,;IDH3B,downstream_gene_variant,,ENST00000488299,;IDH3B,downstream_gene_variant,,ENST00000492240,;IDH3B,downstream_gene_variant,,ENST00000462967,;IDH3B,downstream_gene_variant,,ENST00000491065,;IDH3B,downstream_gene_variant,,ENST00000466494,;IDH3B,downstream_gene_variant,,ENST00000477689,;IDH3B,downstream_gene_variant,,ENST00000466999,;IDH3B,downstream_gene_variant,,ENST00000479376,; G ENST00000329276 Transcript missense_variant 1766/2400 1250/1785 417/594 N/S aAt/aGt 1 1 NOP56 HGNC HGNC:15911 protein_coding YES CCDS13030.1 ENSP00000370589 O00567 UPI000016A81D NM_006392.3 deleterious(0) 10/12 hmmpanther:PTHR10894,hmmpanther:PTHR10894:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 2656864 2656864 A G 1 0 0 0 0 1 0 0 0 10583 101 4 5 5 NOP56 20 2656864 Missense_Mutation SNP A C3N-02149_T 226324 2656864 61787303 510 28694 CDS2 0 . GRCh38 20 5173614 5173614 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.149A>T p.Asp50Val p.D50V ENST00000460006 2/13 224 201 23 269 269 0 strelka-varscan-mutect CDS2,missense_variant,p.Asp50Val,ENST00000460006,NM_003818.3;CDS2,intron_variant,,ENST00000450570,;CDS2,non_coding_transcript_exon_variant,,ENST00000468817,;CDS2,non_coding_transcript_exon_variant,,ENST00000486875,;CDS2,intron_variant,,ENST00000467923,;CDS2,upstream_gene_variant,,ENST00000379070,; T ENST00000460006 Transcript missense_variant 456/9298 149/1338 50/445 D/V gAt/gTt 1 1 CDS2 HGNC HGNC:1801 protein_coding YES CCDS13088.1 ENSP00000419879 O95674 UPI0000001293 NM_003818.3 tolerated(0.24) 2/13 hmmpanther:PTHR13773,hmmpanther:PTHR13773:SF4,PIRSF_domain:PIRSF018269 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 5173614 5173614 A T 1 0 0 0 0 1 0 0 0 2884 333 12 4 4 CDS2 20 5173614 Missense_Mutation SNP A C3N-02149_T 2516750 5173614 59270553 511 28695 KIF3B 0 . GRCh38 20 32310284 32310284 + Missense_Mutation SNP G G T rs746925417 C3N-02149_T C3N-02149_N G G c.507G>T p.Arg169Ser p.R169S ENST00000375712 2/9 182 153 29 192 191 1 strelka-varscan-mutect KIF3B,missense_variant,p.Arg169Ser,ENST00000375712,NM_004798.3; T ENST00000375712 Transcript missense_variant 674/6103 507/2244 169/747 R/S agG/agT rs746925417 1 1 KIF3B HGNC HGNC:6320 protein_coding YES CCDS13200.1 ENSP00000364864 O15066 UPI000012DDB1 NM_004798.3 tolerated(0.24) 2/9 PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF476,Pfam_domain:PF00225,Gene3D:3.40.850.10,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs746925417 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 92 32310284 32310284 G T 1 0 0 0 0 1 0 0 0 8166 1194 42 2 2 KIF3B 20 32310284 Missense_Mutation SNP G C3N-02149_T 27136670 32310284 32133883 512 28696 E2F1 0 . GRCh38 20 33679839 33679839 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.488A>G p.Gln163Arg p.Q163R ENST00000343380 3/7 521 413 108 586 585 1 strelka-varscan-mutect E2F1,missense_variant,p.Gln163Arg,ENST00000343380,NM_005225.2;RP1-63M2.5,downstream_gene_variant,,ENST00000606866,; C ENST00000343380 Transcript missense_variant 628/2503 488/1314 163/437 Q/R cAg/cGg 1 -1 E2F1 HGNC HGNC:3113 protein_coding YES CCDS13224.1 ENSP00000345571 Q01094 UPI000002EDEC NM_005225.2 deleterious(0) 3/7 Gene3D:1.10.10.10,Pfam_domain:PF02319,hmmpanther:PTHR12081,hmmpanther:PTHR12081:SF43,SMART_domains:SM01372,Superfamily_domains:SSF46785 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 33679839 33679839 T C 1 0 0 0 0 1 0 0 0 4690 1580 55 5 5 E2F1 20 33679839 Missense_Mutation SNP T C3N-02149_T 1369555 33679839 30764328 513 28697 MMP24 0 . GRCh38 20 35269803 35269803 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1238G>T p.Gly413Val p.G413V ENST00000246186 7/9 428 363 65 422 422 0 strelka-varscan-mutect MMP24,missense_variant,p.Gly413Val,ENST00000246186,NM_006690.3;MMP24-AS1,intron_variant,,ENST00000635104,;MMP24-AS1,intron_variant,,ENST00000566203,;MMP24-AS1,intron_variant,,ENST00000438751,;MMP24-AS1,intron_variant,,ENST00000456350,;MMP24-AS1,intron_variant,,ENST00000433764,;MMP24-AS1,intron_variant,,ENST00000454184,;MMP24-AS1,intron_variant,,ENST00000453892,;MMP24-AS1,downstream_gene_variant,,ENST00000455178,;RP4-614O4.11,intron_variant,,ENST00000444717,; T ENST00000246186 Transcript missense_variant 1323/4414 1238/1938 413/645 G/V gGc/gTc 1 1 MMP24 HGNC HGNC:7172 protein_coding YES CCDS46593.1 ENSP00000246186 Q9Y5R2 UPI000012F259 NM_006690.3 deleterious(0) 7/9 PROSITE_profiles:PS51642,hmmpanther:PTHR10201:SF138,hmmpanther:PTHR10201,Pfam_domain:PF00045,PIRSF_domain:PIRSF001191,Gene3D:2.110.10.10,SMART_domains:SM00120,Superfamily_domains:SSF50923 MODERATE 1 SNV 1 1 PASS rs1369380109 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 35269803 35269803 G T 1 0 0 0 0 1 0 0 0 9624 1203 42 2 2 MMP24 20 35269803 Missense_Mutation SNP G C3N-02149_T 1589964 35269803 29174364 514 28698 CEP250 0 . GRCh38 20 35494568 35494568 + Missense_Mutation SNP G G C novel C3N-02149_T C3N-02149_N G G c.3078G>C p.Gln1026His p.Q1026H ENST00000397527 24/35 312 296 16 278 278 0 strelka-varscan-mutect CEP250,missense_variant,p.Gln1026His,ENST00000397527,NM_007186.4;RP3-477O4.14,upstream_gene_variant,,ENST00000453914,;RP3-477O4.14,upstream_gene_variant,,ENST00000416260,;RP3-477O4.14,upstream_gene_variant,,ENST00000444933,;CEP250,non_coding_transcript_exon_variant,,ENST00000487467,;CEP250,upstream_gene_variant,,ENST00000425525,; C ENST00000397527 Transcript missense_variant 3798/15703 3078/7329 1026/2442 Q/H caG/caC 1 1 CEP250 HGNC HGNC:1859 protein_coding YES CCDS13255.1 ENSP00000380661 Q9BV73 UPI000006FE8F NM_007186.4 tolerated(0.51) 24/35 hmmpanther:PTHR23159:SF1,hmmpanther:PTHR23159 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 35494568 35494568 G C 1 0 0 0 0 1 0 0 0 2968 933 33 4 4 CEP250 20 35494568 Missense_Mutation SNP G C3N-02149_T 224765 35494568 28949599 515 28699 CHD6 0 . GRCh38 20 41413385 41413385 + Missense_Mutation SNP C C A rs202167043 C3N-02149_T C3N-02149_N C C c.7070G>T p.Ser2357Ile p.S2357I ENST00000373233 35/37 198 156 42 231 231 0 strelka-varscan-mutect CHD6,missense_variant,p.Ser2357Ile,ENST00000373233,NM_032221.4;CHD6,non_coding_transcript_exon_variant,,ENST00000480022,; A ENST00000373233 Transcript missense_variant 7248/10818 7070/8148 2357/2715 S/I aGt/aTt rs202167043 1 -1 CHD6 HGNC HGNC:19057 protein_coding YES CCDS13317.1 ENSP00000362330 Q8TD26 UPI0000168656 NM_032221.4 deleterious(0) 35/37 MODERATE 1 SNV 1 1 PASS rs202167043 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 41413385 41413385 C A 1 0 0 0 0 1 0 0 0 3088 565 20 2 2 CHD6 20 41413385 Missense_Mutation SNP C C3N-02149_T 5918817 41413385 23030782 516 28700 HNF4A 0 . GRCh38 20 44413749 44413749 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.441C>G p.Ser147Arg p.S147R ENST00000316099 4/10 674 560 114 638 638 0 strelka-varscan-mutect HNF4A,missense_variant,p.Ser147Arg,ENST00000316099,NM_001258355.1,NM_000457.4;HNF4A,missense_variant,p.Ser122Arg,ENST00000619550,NM_001287182.1,NM_001287183.1;HNF4A,missense_variant,p.Ser147Arg,ENST00000415691,NM_178849.2;HNF4A,missense_variant,p.Ser147Arg,ENST00000443598,NM_178850.2;HNF4A,missense_variant,p.Ser125Arg,ENST00000316673,NM_175914.4;HNF4A,missense_variant,p.Ser125Arg,ENST00000457232,NM_001030003.2;HNF4A,missense_variant,p.Ser125Arg,ENST00000609795,NM_001030004.2,NM_001287184.1;HNF4A,3_prime_UTR_variant,,ENST00000372920,; G ENST00000316099 Transcript missense_variant 530/6445 441/1425 147/474 S/R agC/agG 1 1 HNF4A HGNC HGNC:5024 protein_coding YES CCDS13330.1 ENSP00000312987 P41235 F1D8T1 UPI000016A0BA NM_001258355.1,NM_000457.4 tolerated(0.21) 4/10 hmmpanther:PTHR24083,hmmpanther:PTHR24083:SF41,Gene3D:1.10.565.10,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 44413749 44413749 C G 1 0 0 0 0 1 0 0 0 7144 709 25 4 4 HNF4A 20 44413749 Missense_Mutation SNP C C3N-02149_T 3000364 44413749 20030418 517 28701 NCOA3 0 . GRCh38 20 47635890 47635890 + Splice_Site SNP G G T novel C3N-02149_T C3N-02149_N G G c.1505-1G>T p.X502_splice ENST00000371998 88 72 16 133 132 1 strelka-varscan NCOA3,splice_acceptor_variant,,ENST00000372004,NM_006534.3;NCOA3,splice_acceptor_variant,,ENST00000371997,NM_001174088.1;NCOA3,splice_acceptor_variant,,ENST00000371998,NM_001174087.1,NM_181659.2;RP5-1049G16.4,upstream_gene_variant,,ENST00000448675,; T ENST00000371998 Transcript splice_acceptor_variant -/4668 1505/4275 502/1424 1 1 NCOA3 HGNC HGNC:7670 protein_coding YES CCDS13407.1 ENSP00000361066 Q9Y6Q9 UPI000012FE45 NM_001174087.1,NM_181659.2 11/22 HIGH 1 SNV 1 1 PASS . . 0 186 23 0 0 0 0 0 -20 0.9947143 0 1 1 0 T 5 4 92 47635890 47635890 G T 1 0 0 0 0 0 0 1 0 10249 1014 35 2 2 NCOA3 20 47635890 Splice_Site SNP G C3N-02149_T 3222141 47635890 16808277 518 28702 KCNB1 0 . GRCh38 20 49374382 49374382 + Missense_Mutation SNP A A C novel C3N-02149_T C3N-02149_N A A c.1178T>G p.Val393Gly p.V393G ENST00000371741 2/2 187 174 13 219 219 0 strelka-varscan-mutect KCNB1,missense_variant,p.Val393Gly,ENST00000371741,NM_004975.2;KCNB1,missense_variant,p.Val393Gly,ENST00000635465,;KCNB1,intron_variant,,ENST00000635878,;RP4-791K14.2,intron_variant,,ENST00000637341,;KCNB1,upstream_gene_variant,,ENST00000636838,;RP4-791K14.2,downstream_gene_variant,,ENST00000637091,;RP4-791K14.2,downstream_gene_variant,,ENST00000637575,;KCNB1,downstream_gene_variant,,ENST00000635210,;KCNB1,upstream_gene_variant,,ENST00000637131,; C ENST00000371741 Transcript missense_variant 1374/11879 1178/2577 393/858 V/G gTt/gGt 1 -1 KCNB1 HGNC HGNC:6231 protein_coding YES CCDS13418.1 ENSP00000360806 Q14721 UPI000012DC80 NM_004975.2 deleterious(0) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR11537:SF134,hmmpanther:PTHR11537,Pfam_domain:PF00520,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR00169 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 49374382 49374382 A C 1 0 0 0 0 1 0 0 0 7928 43 2 5 5 KCNB1 20 49374382 Missense_Mutation SNP A C3N-02149_T 1738492 49374382 15069785 519 28703 CEBPB 0 . GRCh38 20 50191067 50191067 + Missense_Mutation SNP C C G novel C3N-02149_T C3N-02149_N C C c.34C>G p.Leu12Val p.L12V ENST00000303004 1/1 252 238 14 272 272 0 strelka-mutect CEBPB,missense_variant,p.Leu12Val,ENST00000303004,NM_001285879.1,NM_005194.3,NM_001285878.1;CEBPB-AS1,intron_variant,,ENST00000613921,; G ENST00000303004 Transcript missense_variant 334/1956 34/1038 12/345 L/V Ctc/Gtc 1 1 CEBPB HGNC HGNC:1834 protein_coding YES CCDS13429.1 ENSP00000305422 P17676 UPI000000D8BA NM_001285879.1,NM_005194.3,NM_001285878.1 tolerated_low_confidence(0.44) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23334:SF21,hmmpanther:PTHR23334,PIRSF_domain:PIRSF005879,Prints_domain:PR01217 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 92 50191067 50191067 C G 1 0 0 0 0 1 0 0 0 2906 913 32 4 4 CEBPB 20 50191067 Missense_Mutation SNP C C3N-02149_T 816685 50191067 14253100 520 28704 PCK1 0 . GRCh38 20 57564208 57564208 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.1001G>T p.Gly334Val p.G334V ENST00000319441 7/10 212 162 50 205 205 0 strelka-varscan-mutect PCK1,missense_variant,p.Gly334Val,ENST00000319441,NM_002591.3;PCK1,non_coding_transcript_exon_variant,,ENST00000467047,;PCK1,non_coding_transcript_exon_variant,,ENST00000485958,;PCK1,downstream_gene_variant,,ENST00000475833,;PCK1,downstream_gene_variant,,ENST00000498194,;PCK1,downstream_gene_variant,,ENST00000470051,; T ENST00000319441 Transcript missense_variant 1165/4341 1001/1869 334/622 G/V gGt/gTt 1 1 PCK1 HGNC HGNC:8724 protein_coding YES CCDS13460.1 ENSP00000319814 P35558 UPI000013CB5A NM_002591.3 deleterious(0) 7/10 HAMAP:MF_00452,hmmpanther:PTHR11561:SF1,hmmpanther:PTHR11561,Pfam_domain:PF00821,PIRSF_domain:PIRSF001348,Superfamily_domains:SSF53795 MODERATE 1 SNV 1 1 PASS rs893585457 . 0 181 0 22 5 0 0 0 -20 0.1514322 0 1 0 0 T 3 4 92 57564208 57564208 G T 1 0 0 0 0 1 0 0 0 11669 1261 44 2 2 PCK1 20 57564208 Missense_Mutation SNP G C3N-02149_T 7373141 57564208 6879959 521 28705 GNAS 0 . GRCh38 20 58909542 58909542 + Missense_Mutation SNP G G T rs137854533 C3N-02149_T C3N-02149_N G G c.2610G>T p.Gln870His p.Q870H ENST00000371100 9/13 981 841 140 850 849 1 strelka-varscan-mutect GNAS,missense_variant,p.Gln870His,ENST00000371100,NM_080425.2;GNAS,missense_variant,p.Gln856His,ENST00000371102,;GNAS,missense_variant,p.Gln228His,ENST00000354359,NM_001077488.2;GNAS,missense_variant,p.Gln227His,ENST00000371085,NM_000516.4;GNAS,missense_variant,p.Gln213His,ENST00000371095,NM_080426.2;GNAS,missense_variant,p.Gln212His,ENST00000265620,NM_001077489.2;GNAS,3_prime_UTR_variant,,ENST00000313949,;GNAS,3_prime_UTR_variant,,ENST00000371075,NM_016592.2;GNAS,intron_variant,,ENST00000306090,;GNAS,downstream_gene_variant,,ENST00000419558,;GNAS,downstream_gene_variant,,ENST00000604005,;GNAS,downstream_gene_variant,,ENST00000450130,;GNAS,downstream_gene_variant,,ENST00000349036,;GNAS,downstream_gene_variant,,ENST00000603546,;GNAS,non_coding_transcript_exon_variant,,ENST00000464624,;GNAS,non_coding_transcript_exon_variant,,ENST00000477931,;GNAS,non_coding_transcript_exon_variant,,ENST00000480975,;GNAS,non_coding_transcript_exon_variant,,ENST00000488652,;GNAS,non_coding_transcript_exon_variant,,ENST00000470512,;GNAS,non_coding_transcript_exon_variant,,ENST00000488546,;GNAS,non_coding_transcript_exon_variant,,ENST00000480232,;GNAS,non_coding_transcript_exon_variant,,ENST00000476935,;GNAS,non_coding_transcript_exon_variant,,ENST00000492907,;GNAS,non_coding_transcript_exon_variant,,ENST00000481039,;GNAS,non_coding_transcript_exon_variant,,ENST00000467321,;GNAS,non_coding_transcript_exon_variant,,ENST00000468895,;GNAS,non_coding_transcript_exon_variant,,ENST00000493958,;GNAS,intron_variant,,ENST00000494081,;GNAS,downstream_gene_variant,,ENST00000472183,;GNAS,downstream_gene_variant,,ENST00000485673,;GNAS,downstream_gene_variant,,ENST00000482112,;GNAS,downstream_gene_variant,,ENST00000469431,;GNAS,downstream_gene_variant,,ENST00000490374,;GNAS,downstream_gene_variant,,ENST00000464788,;GNAS,downstream_gene_variant,,ENST00000467227,;GNAS,downstream_gene_variant,,ENST00000478585,;GNAS,non_coding_transcript_exon_variant,,ENST00000496934,;GNAS,non_coding_transcript_exon_variant,,ENST00000476196,;GNAS,non_coding_transcript_exon_variant,,ENST00000487862,;GNAS,non_coding_transcript_exon_variant,,ENST00000487981,;GNAS,non_coding_transcript_exon_variant,,ENST00000479025,;GNAS,upstream_gene_variant,,ENST00000475610,; T ENST00000371100 Transcript missense_variant 3162/4029 2610/3114 870/1037 Q/H caG/caT rs137854533,COSM27900,COSM3371733,COSM4168959,COSM4168960 1 1 GNAS HGNC HGNC:4392 protein_coding YES CCDS46622.1 ENSP00000360141 Q5JWF2 UPI0000E444AE NM_080425.2 deleterious(0.01) 9/13 Gene3D:3.40.50.300,Pfam_domain:PF00503,Prints_domain:PR00318,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF36,SMART_domains:SM00275,Superfamily_domains:SSF52540 pathogenic 0,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS rs137854533 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 58909542 58909542 G T 1 0 0 0 0 1 0 0 0 6390 962 34 2 2 GNAS 20 58909542 Missense_Mutation SNP G C3N-02149_T 1345334 58909542 5534625 522 28706 TCP10L 0 . GRCh38 21 32584231 32584231 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.74G>T p.Gly25Val p.G25V ENST00000300258 2/5 118 95 23 188 187 1 strelka-varscan-mutect TCP10L,missense_variant,p.Gly25Val,ENST00000300258,NM_144659.5;TCP10L,missense_variant,p.Gly25Val,ENST00000582575,;AP000275.65,intron_variant,,ENST00000553001,;AP000275.65,intron_variant,,ENST00000431216,;TCP10L,intron_variant,,ENST00000472557,;TCP10L,upstream_gene_variant,,ENST00000491828,; A ENST00000300258 Transcript missense_variant 188/2695 74/648 25/215 G/V gGg/gTg COSM4557987 1 -1 TCP10L HGNC HGNC:11657 protein_coding YES CCDS13616.1 ENSP00000300258 Q8TDR4 UPI0000136B0B NM_144659.5 deleterious(0.01) 2/5 hmmpanther:PTHR10331,hmmpanther:PTHR10331:SF24 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 32584231 32584231 C A 1 0 0 0 0 1 0 0 0 16118 623 22 2 2 TCP10L 21 32584231 Missense_Mutation SNP C C3N-02149_T 32584231 14125752 523 28707 IGSF5 0 . GRCh38 21 39746294 39746294 + Silent SNP G G T novel C3N-02149_T C3N-02149_N G G c.96G>T p.= p.V32V ENST00000380588 2/9 94 71 23 178 178 0 strelka-varscan-mutect IGSF5,synonymous_variant,p.=,ENST00000380588,NM_001080444.1;IGSF5,upstream_gene_variant,,ENST00000479378,; T ENST00000380588 Transcript synonymous_variant 199/2066 96/1224 32/407 V gtG/gtT 1 1 IGSF5 HGNC HGNC:5952 protein_coding YES CCDS33562.1 ENSP00000369962 Q9NSI5 UPI0000198970 NM_001080444.1 2/9 hmmpanther:PTHR12231,hmmpanther:PTHR12231:SF9 LOW 1 SNV 2 1 PASS . . 0 202 6 2 0 0 0 0 -20 0.9999684 1 1 1 0 T 2 4 92 39746294 39746294 G T 1 0 0 0 0 0 0 0 1 7510 1362 47 2 2 IGSF5 21 39746294 Silent SNP G C3N-02149_T 7162063 39746294 6963689 524 28708 ABCG1 0 . GRCh38 21 42260046 42260046 + Missense_Mutation SNP G G T rs535702283 C3N-02149_T C3N-02149_N G G c.631G>T p.Gly211Trp p.G211W ENST00000398437 3/16 128 107 21 183 183 0 strelka-varscan-mutect ABCG1,missense_variant,p.Gly211Trp,ENST00000398437,;ABCG1,intron_variant,,ENST00000398457,NM_207627.1,NM_207628.1;ABCG1,intron_variant,,ENST00000343687,NM_207174.1;ABCG1,intron_variant,,ENST00000361802,NM_004915.3;ABCG1,intron_variant,,ENST00000398449,NM_016818.2;ABCG1,intron_variant,,ENST00000347800,NM_207629.1;ABCG1,intron_variant,,ENST00000450121,;ABCG1,intron_variant,,ENST00000462050,; T ENST00000398437 Transcript missense_variant 779/3475 631/2475 211/824 G/W Ggg/Tgg rs535702283 1 1 ABCG1 HGNC HGNC:73 protein_coding ENSP00000381464 E9PGV9 UPI000035AC75 deleterious_low_confidence(0) 3/16 MODERATE SNV 1 1 PASS rs535702283 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 42260046 42260046 G T 1 0 0 0 0 1 0 0 0 72 1232 43 2 2 ABCG1 21 42260046 Missense_Mutation SNP G C3N-02149_T 2513752 42260046 4449937 525 28709 COL18A1 0 . GRCh38 21 45480138 45480138 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.2625C>A p.= p.S875S ENST00000359759 10/41 359 295 64 408 408 0 strelka-varscan-mutect COL18A1,synonymous_variant,p.=,ENST00000359759,NM_130444.2;COL18A1,synonymous_variant,p.=,ENST00000355480,NM_030582.3;COL18A1,synonymous_variant,p.=,ENST00000400337,NM_130445.3;MIR6815,downstream_gene_variant,,ENST00000611994,; A ENST00000359759 Transcript synonymous_variant 2625/6586 2625/5265 875/1754 S tcC/tcA 1 1 COL18A1 HGNC HGNC:2195 protein_coding YES CCDS77643.1 ENSP00000352798 P39060 UPI0001838820 NM_130444.2 10/41 hmmpanther:PTHR24023 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 45480138 45480138 C A 1 0 0 0 0 0 0 0 1 3463 668 24 2 2 COL18A1 21 45480138 Silent SNP C C3N-02149_T 3220092 45480138 1229845 526 28710 DIP2A 0 . GRCh38 21 46565761 46565761 + Missense_Mutation SNP G G T rs374347392 C3N-02149_T C3N-02149_N G G c.4213G>T p.Gly1405Trp p.G1405W ENST00000417564 36/38 191 148 43 291 291 0 strelka-varscan-mutect DIP2A,missense_variant,p.Gly1401Trp,ENST00000400274,NM_001146116.1;DIP2A,missense_variant,p.Gly1405Trp,ENST00000417564,NM_015151.3;DIP2A,non_coding_transcript_exon_variant,,ENST00000479654,;DIP2A,non_coding_transcript_exon_variant,,ENST00000478105,; T ENST00000417564 Transcript missense_variant 4234/6967 4213/4716 1405/1571 G/W Ggg/Tgg rs374347392 1 1 DIP2A HGNC HGNC:17217 protein_coding YES CCDS46655.1 ENSP00000392066 Q14689 UPI00001B2E47 NM_015151.3 deleterious(0) 36/38 Gene3D:2.30.38.10,Pfam_domain:PF00501,hmmpanther:PTHR22754,hmmpanther:PTHR22754:SF24,Superfamily_domains:SSF56801 MODERATE 1 SNV 1 1 PASS rs374347392 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 46565761 46565761 G T 1 0 0 0 0 1 0 0 0 4332 1116 39 1 1 DIP2A 21 46565761 Missense_Mutation SNP G C3N-02149_T 1085623 46565761 144222 527 28711 KIAA1671 0 . GRCh38 22 25038764 25038764 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.1634A>T p.Lys545Met p.K545M ENST00000358431 3/11 89 58 31 96 96 0 strelka-varscan-mutect KIAA1671,missense_variant,p.Lys545Met,ENST00000358431,NM_001145206.1;KIAA1671,missense_variant,p.Lys545Met,ENST00000406486,;KIAA1671,upstream_gene_variant,,ENST00000494730,;KIAA1671,upstream_gene_variant,,ENST00000461374,; T ENST00000358431 Transcript missense_variant 1660/10490 1634/5421 545/1806 K/M aAg/aTg 1 1 KIAA1671 HGNC HGNC:29345 protein_coding YES CCDS46676.1 ENSP00000351207 Q9BY89 UPI00002073DC NM_001145206.1 deleterious(0.02) 3/11 hmmpanther:PTHR22042,hmmpanther:PTHR22042:SF3 MODERATE 1 SNV 1 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 92 25038764 25038764 A T 1 0 0 0 0 1 0 0 0 8125 86 3 4 4 KIAA1671 22 25038764 Missense_Mutation SNP A C3N-02149_T 25038764 25779704 528 28712 DEPDC5 0 . GRCh38 22 31906401 31906401 + Silent SNP G G T C3N-02149_T C3N-02149_N G G c.4716G>T p.= p.L1572L ENST00000400246 43/43 404 376 28 459 459 0 strelka-varscan-mutect DEPDC5,missense_variant,p.Cys1552Phe,ENST00000382111,;DEPDC5,synonymous_variant,p.=,ENST00000400246,NM_001242896.1;DEPDC5,synonymous_variant,p.=,ENST00000400249,;DEPDC5,synonymous_variant,p.=,ENST00000382112,NM_001136029.2;DEPDC5,synonymous_variant,p.=,ENST00000400248,NM_014662.4;DEPDC5,synonymous_variant,p.=,ENST00000535622,NM_001242897.1;DEPDC5,synonymous_variant,p.=,ENST00000433147,;DEPDC5,intron_variant,,ENST00000497340,;DEPDC5,3_prime_UTR_variant,,ENST00000448753,; T ENST00000400246 Transcript synonymous_variant 4918/5551 4716/4812 1572/1603 L ctG/ctT COSM4883759,COSM4883760,COSM4883761 1 1 DEPDC5 HGNC HGNC:18423 protein_coding YES CCDS74849.1 ENSP00000383105 O75140 UPI000192C426 NM_001242896.1 43/43 hmmpanther:PTHR13179 1,1,1 LOW 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 31906401 31906401 G T 1 0 0 0 0 0 0 0 1 4248 1319 46 2 2 DEPDC5 22 31906401 Silent SNP G C3N-02149_T 6867637 31906401 18912067 529 28713 SLC5A1 0 . GRCh38 22 32104841 32104842 + Frame_Shift_Ins INS - - T novel C3N-02149_T C3N-02149_N - - c.1722dupT p.Ala575CysfsTer11 p.A575Cfs*11 ENST00000266088 14/15 441 414 27 524 524 0 varindel-pindel SLC5A1,frameshift_variant,p.Ala575CysfsTer11,ENST00000266088,NM_000343.3;SLC5A1,frameshift_variant,p.Ala448CysfsTer11,ENST00000543737,NM_001256314.1;SLC5A1,downstream_gene_variant,,ENST00000477969,; T ENST00000266088 Transcript frameshift_variant 1971-1972/5061 1721-1722/1995 574/664 D/DX gat/gaTt 1 1 SLC5A1 HGNC HGNC:11036 protein_coding YES CCDS13902.1 ENSP00000266088 P13866 UPI00001359EA NM_000343.3 14/15 hmmpanther:PTHR11819,hmmpanther:PTHR11819:SF151 HIGH 1 insertion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 7 5 92 32104841 32104841 - T 1 0 1 1 0 0 0 0 0 14944 333 12 0 0 SLC5A1 22 32104841 Frame_Shift_Ins INS - C3N-02149_T 198440 32104841 18713627 530 28714 TOM1 0 . GRCh38 22 35323137 35323137 + Missense_Mutation SNP C C T novel C3N-02149_T C3N-02149_N C C c.326C>T p.Pro109Leu p.P109L ENST00000411850 4/15 343 310 33 472 472 0 strelka-varscan-mutect TOM1,missense_variant,p.Pro109Leu,ENST00000411850,NM_001135732.1;TOM1,missense_variant,p.Pro109Leu,ENST00000449058,NM_005488.2;TOM1,missense_variant,p.Pro76Leu,ENST00000447733,NM_001135729.1;TOM1,missense_variant,p.Pro109Leu,ENST00000425375,NM_001135730.1;TOM1,missense_variant,p.Pro109Leu,ENST00000382034,;TOM1,missense_variant,p.Pro103Leu,ENST00000456128,;TOM1,missense_variant,p.Pro76Leu,ENST00000443206,;TOM1,missense_variant,p.Pro76Leu,ENST00000608749,;TOM1,missense_variant,p.Pro76Leu,ENST00000608674,;TOM1,missense_variant,p.Pro109Leu,ENST00000395736,;TOM1,synonymous_variant,p.=,ENST00000449508,;TOM1,3_prime_UTR_variant,,ENST00000404284,;TOM1,3_prime_UTR_variant,,ENST00000424387,;TOM1,3_prime_UTR_variant,,ENST00000439512,;TOM1,upstream_gene_variant,,ENST00000491987,;TOM1,downstream_gene_variant,,ENST00000487670,;TOM1,downstream_gene_variant,,ENST00000465529,;TOM1,upstream_gene_variant,,ENST00000497448,; T ENST00000411850 Transcript missense_variant 451/2390 326/1482 109/493 P/L cCa/cTa 1 1 TOM1 HGNC HGNC:11982 protein_coding YES CCDS46696.1 ENSP00000413697 O60784 UPI000000DB48 NM_001135732.1 deleterious(0) 4/15 PROSITE_profiles:PS50179,hmmpanther:PTHR13856,hmmpanther:PTHR13856:SF32,PIRSF_domain:PIRSF036948,Pfam_domain:PF00790,Gene3D:1.25.40.90,SMART_domains:SM00288,Superfamily_domains:SSF48464 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 35323137 35323137 C T 1 0 0 0 0 1 0 0 0 16825 594 21 3 3 TOM1 22 35323137 Missense_Mutation SNP C C3N-02149_T 3218296 35323137 15495331 531 28715 NFAM1 0 . GRCh38 22 42432320 42432320 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.38G>T p.Gly13Val p.G13V ENST00000329021 1/6 161 149 12 191 191 0 strelka-varscan-mutect NFAM1,missense_variant,p.Gly13Val,ENST00000329021,NM_145912.5;NFAM1,missense_variant,p.Gly13Val,ENST00000355469,; A ENST00000329021 Transcript missense_variant 76/5602 38/813 13/270 G/V gGc/gTc 1 -1 NFAM1 HGNC HGNC:29872 protein_coding YES CCDS14034.1 ENSP00000333680 Q8NET5 UPI00000701BF NM_145912.5 deleterious_low_confidence(0.02) 1/6 hmmpanther:PTHR35680,hmmpanther:PTHR35680:SF1,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 42432320 42432320 C A 1 0 0 0 0 1 0 0 0 10395 739 26 2 2 NFAM1 22 42432320 Missense_Mutation SNP C C3N-02149_T 7109183 42432320 8386148 532 28716 CSF2RA 0 . GRCh38 X 1303969 1303969 + Silent SNP A A T novel C3N-02149_T C3N-02149_N A A c.1095A>T p.= p.L365L ENST00000417535 12/14 490 456 34 642 641 1 strelka-varscan-mutect CSF2RA,synonymous_variant,p.=,ENST00000381524,;CSF2RA,synonymous_variant,p.=,ENST00000417535,NM_001161530.1;CSF2RA,synonymous_variant,p.=,ENST00000432318,NM_001161529.1;CSF2RA,synonymous_variant,p.=,ENST00000381529,NM_006140.4,NM_172245.2;CSF2RA,synonymous_variant,p.=,ENST00000501036,NM_001161532.1;CSF2RA,synonymous_variant,p.=,ENST00000381509,NM_001161531.1;CSF2RA,intron_variant,,ENST00000355432,NM_172246.2;CSF2RA,intron_variant,,ENST00000355805,NM_172249.2;CSF2RA,intron_variant,,ENST00000381500,NM_172247.2;CSF2RA,intron_variant,,ENST00000494969,;RNA5SP498,upstream_gene_variant,,ENST00000411342,;CSF2RA,non_coding_transcript_exon_variant,,ENST00000498153,;CSF2RA,intron_variant,,ENST00000475259,;CSF2RA,downstream_gene_variant,,ENST00000493312,;CSF2RA,stop_lost,p.Ter286LeuextTer35,ENST00000486791,; T ENST00000417535 Transcript synonymous_variant 1289/1955 1095/1305 365/434 L ctA/ctT 1 1 CSF2RA HGNC HGNC:2435 protein_coding YES CCDS55359.1 ENSP00000394227 P15509 UPI000159C3E4 NM_001161530.1 12/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR23036:SF94,hmmpanther:PTHR23036 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 1303969 1303969 A T 1 0 0 0 0 0 0 0 1 3735 349 13 4 4 CSF2RA 23 1303969 Silent SNP A C3N-02149_T 1303969 154736926 533 28717 NLGN4X 0 . GRCh38 X 5893485 5893485 + Missense_Mutation SNP G G T C3N-02149_T C3N-02149_N G G c.1783C>A p.Pro595Thr p.P595T ENST00000381095 6/6 67 53 14 78 78 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Pro595Thr,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Pro595Thr,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Pro595Thr,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Pro595Thr,ENST00000381092,;NLGN4X,missense_variant,p.Pro596Thr,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,; T ENST00000381095 Transcript missense_variant 2411/5870 1783/2451 595/816 P/T Cct/Act COSM4862863,COSM757939 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0) 6/6 Gene3D:3.40.50.1820,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 5893485 5893485 G T 1 0 0 0 0 1 0 0 0 10501 1174 41 2 2 NLGN4X 23 5893485 Missense_Mutation SNP G C3N-02149_T 4589516 5893485 150147410 534 28718 FRMPD4 0 . GRCh38 X 12710526 12710526 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1598C>A p.Thr533Asn p.T533N ENST00000380682 14/17 69 43 26 82 82 0 strelka-varscan-mutect FRMPD4,missense_variant,p.Thr533Asn,ENST00000380682,NM_014728.3;FRMPD4,missense_variant,p.Thr493Asn,ENST00000616992,; A ENST00000380682 Transcript missense_variant 2104/8465 1598/3969 533/1322 T/N aCc/aAc 1 1 FRMPD4 HGNC HGNC:29007 protein_coding YES CCDS35201.1 ENSP00000370057 Q14CM0 UPI00001C2066 NM_014728.3 tolerated(0.69) 14/17 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 12710526 12710526 C A 1 0 0 0 0 1 0 0 0 5930 507 18 2 2 FRMPD4 23 12710526 Missense_Mutation SNP C C3N-02149_T 6817041 12710526 143330369 535 28719 PIGA 0 . GRCh38 X 15325937 15325937 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.825G>T p.= p.R275R ENST00000333590 3/6 67 49 18 73 72 1 strelka-varscan-mutect PIGA,synonymous_variant,p.=,ENST00000333590,NM_002641.3;PIGA,synonymous_variant,p.=,ENST00000542278,;PIGA,synonymous_variant,p.=,ENST00000634582,NM_020473.3;PIGA,5_prime_UTR_variant,,ENST00000637296,;PIGA,5_prime_UTR_variant,,ENST00000634640,;PIGA,intron_variant,,ENST00000482148,;PIGA,upstream_gene_variant,,ENST00000475746,;PIGA,non_coding_transcript_exon_variant,,ENST00000635631,;PIGA,downstream_gene_variant,,ENST00000637799,;PIGA,3_prime_UTR_variant,,ENST00000637626,;PIGA,3_prime_UTR_variant,,ENST00000635598,;PIGA,3_prime_UTR_variant,,ENST00000638131,;PIGA,3_prime_UTR_variant,,ENST00000634286,;PIGA,non_coding_transcript_exon_variant,,ENST00000635045,;PIGA,non_coding_transcript_exon_variant,,ENST00000635480,;PIGA,non_coding_transcript_exon_variant,,ENST00000474662,;PIGA,downstream_gene_variant,,ENST00000634484,;PIGA,upstream_gene_variant,,ENST00000463173,; A ENST00000333590 Transcript synonymous_variant 967/3652 825/1455 275/484 R cgG/cgT 1 -1 PIGA HGNC HGNC:8957 protein_coding YES CCDS14165.1 ENSP00000369820 P37287 UPI0000131AAE NM_002641.3 3/6 hmmpanther:PTHR12526:SF232,hmmpanther:PTHR12526,Pfam_domain:PF00534,Gene3D:3.40.50.2000,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 1 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 15325937 15325937 C A 1 0 0 0 0 0 0 0 1 11978 610 22 2 2 PIGA 23 15325937 Silent SNP C C3N-02149_T 2615411 15325937 140714958 536 28720 CNKSR2 0 . GRCh38 X 21609177 21609177 + Missense_Mutation SNP G G T novel C3N-02149_T C3N-02149_N G G c.2252G>T p.Gly751Val p.G751V ENST00000379510 20/22 128 82 46 153 153 0 strelka-varscan-mutect CNKSR2,missense_variant,p.Gly721Val,ENST00000425654,NM_001168647.1;CNKSR2,missense_variant,p.Gly751Val,ENST00000379510,NM_014927.3;CNKSR2,missense_variant,p.Gly751Val,ENST00000279451,NM_001168648.1;CNKSR2,missense_variant,p.Gly702Val,ENST00000543067,NM_001168649.1; T ENST00000379510 Transcript missense_variant 2288/5315 2252/3105 751/1034 G/V gGg/gTg 1 1 CNKSR2 HGNC HGNC:19701 protein_coding YES CCDS14198.1 ENSP00000368824 Q8WXI2 UPI0000070D72 NM_014927.3 deleterious(0.03) 20/22 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 21609177 21609177 G T 1 0 0 0 0 1 0 0 0 3387 1232 43 2 2 CNKSR2 23 21609177 Missense_Mutation SNP G C3N-02149_T 6283240 21609177 134431718 537 28721 ZNF645 0 . GRCh38 X 22273348 22273348 + Missense_Mutation SNP G G T rs760755951 C3N-02149_T C3N-02149_N G G c.357G>T p.Gln119His p.Q119H ENST00000323684 1/1 168 119 49 224 224 0 strelka-varscan-mutect ZNF645,missense_variant,p.Gln119His,ENST00000323684,NM_152577.3;PTCHD1-AS,intron_variant,,ENST00000608254,; T ENST00000323684 Transcript missense_variant 406/1519 357/1278 119/425 Q/H caG/caT rs760755951 1 1 ZNF645 HGNC HGNC:26371 protein_coding YES CCDS14205.1 ENSP00000323348 Q8N7E2 UPI0000073BD5 NM_152577.3 deleterious(0.01) 1/1 PROSITE_profiles:PS50157,hmmpanther:PTHR13480,hmmpanther:PTHR13480:SF1 MODERATE 1 SNV 1 PASS rs760755951 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 22273348 22273348 G T 1 0 0 0 0 1 0 0 0 18634 1020 36 2 2 ZNF645 23 22273348 Missense_Mutation SNP G C3N-02149_T 664171 22273348 133767547 538 28722 POLA1 0 . GRCh38 X 24745498 24745498 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.2629A>T p.Thr877Ser p.T877S ENST00000379059 24/37 113 97 16 159 159 0 strelka-varscan-mutect POLA1,missense_variant,p.Thr883Ser,ENST00000379068,;POLA1,missense_variant,p.Thr877Ser,ENST00000379059,NM_016937.3;POLA1,missense_variant,p.Thr876Ser,ENST00000611764,;SCARNA23,downstream_gene_variant,,ENST00000516060,;POLA1,upstream_gene_variant,,ENST00000480125,; T ENST00000379059 Transcript missense_variant 2644/5440 2629/4389 877/1462 T/S Aca/Tca 1 1 POLA1 HGNC HGNC:9173 protein_coding YES CCDS14214.1 ENSP00000368349 P09884 UPI000014D383 NM_016937.3 deleterious(0) 24/37 hmmpanther:PTHR10322:SF21,hmmpanther:PTHR10322,TIGRFAM_domain:TIGR00592,Pfam_domain:PF00136,SMART_domains:SM00486,Superfamily_domains:SSF56672 MODERATE 1 SNV 1 1 PASS . . 1 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 24745498 24745498 A T 1 0 0 0 0 1 0 0 0 12297 391 14 4 4 POLA1 23 24745498 Missense_Mutation SNP A C3N-02149_T 2472150 24745498 131295397 539 28723 MAGEB18 0 . GRCh38 X 26139842 26139842 + Missense_Mutation SNP A A T C3N-02149_T C3N-02149_N A A c.857A>T p.Glu286Val p.E286V ENST00000325250 2/3 148 136 12 173 171 2 strelka-varscan-mutect MAGEB18,missense_variant,p.Glu286Val,ENST00000325250,NM_173699.3; T ENST00000325250 Transcript missense_variant 1044/1811 857/1032 286/343 E/V gAg/gTg COSM150773 1 1 MAGEB18 HGNC HGNC:28515 protein_coding YES CCDS14216.1 ENSP00000314543 Q96M61 UPI00001415E3 NM_173699.3 deleterious(0) 2/3 PROSITE_profiles:PS50838,hmmpanther:PTHR11736:SF23,hmmpanther:PTHR11736 1 MODERATE 1 SNV 1 1 1 PASS . . 0 208 0 2 0 0 0 0 -16.75981 0.9999998 1 1 1 0 T 3 4 92 26139842 26139842 A T 1 0 0 0 0 1 0 0 0 9091 304 11 4 4 MAGEB18 23 26139842 Missense_Mutation SNP A C3N-02149_T 1394344 26139842 129901053 540 28724 OTC 0 . GRCh38 X 38403721 38403721 + Missense_Mutation SNP T T A novel C3N-02149_T C3N-02149_N T T c.644T>A p.Leu215His p.L215H ENST00000039007 6/10 347 238 109 349 349 0 strelka-varscan-mutect OTC,missense_variant,p.Leu215His,ENST00000039007,NM_000531.5;RP5-972B16.2,intron_variant,,ENST00000465127,;OTC,downstream_gene_variant,,ENST00000488812,; A ENST00000039007 Transcript missense_variant 796/1585 644/1065 215/354 L/H cTt/cAt 1 1 OTC HGNC HGNC:8512 protein_coding YES CCDS14247.1 ENSP00000039007 P00480 UPI000013C550 NM_000531.5 deleterious(0) 6/10 Gene3D:3.40.50.1370,Pfam_domain:PF00185,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF1,Superfamily_domains:SSF53671,TIGRFAM_domain:TIGR00658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 38403721 38403721 T A 1 0 0 0 0 1 0 0 0 11367 1609 56 4 4 OTC 23 38403721 Missense_Mutation SNP T C3N-02149_T 12263879 38403721 117637174 541 28725 ELK1 0 . GRCh38 X 47641277 47641277 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.165G>T p.Met55Ile p.M55I ENST00000247161 2/6 164 100 64 208 208 0 strelka-varscan-mutect ELK1,missense_variant,p.Met55Ile,ENST00000247161,NM_005229.4;ELK1,missense_variant,p.Met55Ile,ENST00000376983,NM_001114123.2;ELK1,missense_variant,p.Met55Ile,ENST00000343894,NM_001257168.1; A ENST00000247161 Transcript missense_variant 265/2695 165/1287 55/428 M/I atG/atT 1 -1 ELK1 HGNC HGNC:3321 protein_coding YES CCDS14283.1 ENSP00000247161 P19419 A0A024R1A7 UPI0000129E66 NM_005229.4 deleterious(0.01) 2/6 PROSITE_profiles:PS50061,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF178,PROSITE_patterns:PS00346,Gene3D:1.10.10.10,Pfam_domain:PF00178,SMART_domains:SM00413,Superfamily_domains:SSF46785,Prints_domain:PR00454 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 47641277 47641277 C A 1 0 0 0 0 1 0 0 0 4893 826 29 2 2 ELK1 23 47641277 Missense_Mutation SNP C C3N-02149_T 9237556 47641277 108399618 542 28726 SSX3 0 . GRCh38 X 48347509 48347509 + Nonsense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.562G>T p.Glu188Ter p.E188* ENST00000298396 7/8 149 93 56 202 202 0 strelka-varscan-mutect SSX3,stop_gained,p.Glu188Ter,ENST00000298396,NM_021014.3;SSX3,downstream_gene_variant,,ENST00000612497,;SSX3,downstream_gene_variant,,ENST00000376893,;SSX3,non_coding_transcript_exon_variant,,ENST00000376895,; A ENST00000298396 Transcript stop_gained 615/1232 562/567 188/188 E/* Gag/Tag 1 -1 SSX3 HGNC HGNC:11337 protein_coding YES CCDS14291.1 ENSP00000298396 Q99909 UPI000013E4CD NM_021014.3 7/8 hmmpanther:PTHR14112:SF10,hmmpanther:PTHR14112 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 92 48347509 48347509 C A 1 0 0 0 0 0 1 0 0 15584 835 29 2 2 SSX3 23 48347509 Nonsense_Mutation SNP C C3N-02149_T 706232 48347509 107693386 543 28727 PIM2 0 . GRCh38 X 48915273 48915273 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.342G>T p.= p.L114L ENST00000376509 4/6 159 101 58 203 203 0 strelka-varscan-mutect PIM2,synonymous_variant,p.=,ENST00000376509,NM_006875.3;PIM2,synonymous_variant,p.=,ENST00000442430,;SLC35A2,upstream_gene_variant,,ENST00000376521,NM_001042498.2;SLC35A2,upstream_gene_variant,,ENST00000445167,NM_001032289.2;SLC35A2,upstream_gene_variant,,ENST00000247138,NM_005660.2;SLC35A2,upstream_gene_variant,,ENST00000616181,NM_001282650.1;SLC35A2,upstream_gene_variant,,ENST00000452555,NM_001282651.1;SLC35A2,upstream_gene_variant,,ENST00000635589,NM_001282649.1;SLC35A2,upstream_gene_variant,,ENST00000376515,NM_001282648.1;SLC35A2,upstream_gene_variant,,ENST00000635015,;SLC35A2,upstream_gene_variant,,ENST00000376512,;SLC35A2,upstream_gene_variant,,ENST00000446885,;SLC35A2,upstream_gene_variant,,ENST00000376529,NM_001282647.1;SLC35A2,upstream_gene_variant,,ENST00000635460,;SLC35A2,upstream_gene_variant,,ENST00000635238,;SLC35A2,upstream_gene_variant,,ENST00000634461,;SLC35A2,upstream_gene_variant,,ENST00000634665,;PIM2,upstream_gene_variant,,ENST00000485431,;SLC35A2,upstream_gene_variant,,ENST00000635628,;SLC35A2,upstream_gene_variant,,ENST00000635285,; A ENST00000376509 Transcript synonymous_variant 532/2075 342/936 114/311 L ctG/ctT 1 -1 PIM2 HGNC HGNC:8987 protein_coding YES CCDS14312.1 ENSP00000365692 Q9P1W9 A0A024QYW7 UPI0000049044 NM_006875.3 4/6 PROSITE_profiles:PS50011,hmmpanther:PTHR22984:SF10,hmmpanther:PTHR22984,PIRSF_domain:PIRSF037993,Gene3D:1.10.510.10,Pfam_domain:PF00069,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 48915273 48915273 C A 1 0 0 0 0 0 0 0 1 12023 581 21 2 2 PIM2 23 48915273 Silent SNP C C3N-02149_T 567764 48915273 107125622 544 28728 AKAP4 0 . GRCh38 X 50192328 50192328 + Silent SNP T T A novel C3N-02149_T C3N-02149_N T T c.2385A>T p.= p.G795G ENST00000358526 5/6 62 47 15 63 63 0 strelka-varscan-mutect AKAP4,synonymous_variant,p.=,ENST00000358526,NM_003886.2;AKAP4,synonymous_variant,p.=,ENST00000376064,NM_139289.1;AKAP4,downstream_gene_variant,,ENST00000437370,;AKAP4,downstream_gene_variant,,ENST00000448865,;AKAP4,non_coding_transcript_exon_variant,,ENST00000481402,;AKAP4,downstream_gene_variant,,ENST00000480926,; A ENST00000358526 Transcript synonymous_variant 2509/2881 2385/2565 795/854 G ggA/ggT 1 -1 AKAP4 HGNC HGNC:374 protein_coding YES CCDS14329.1 ENSP00000351327 Q5JQC9 UPI000013DA96 NM_003886.2 5/6 hmmpanther:PTHR10226:SF8,hmmpanther:PTHR10226,Pfam_domain:PF05716,SMART_domains:SM00807 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 50192328 50192328 T A 1 0 0 0 0 0 0 0 1 537 1538 54 4 4 AKAP4 23 50192328 Silent SNP T C3N-02149_T 1277055 50192328 105848567 545 28729 SMC1A 0 . GRCh38 X 53394870 53394870 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2881G>T p.Asp961Tyr p.D961Y ENST00000322213 19/25 243 167 76 300 298 2 strelka-varscan-mutect SMC1A,missense_variant,p.Asp939Tyr,ENST00000375340,NM_001281463.1;SMC1A,missense_variant,p.Asp961Tyr,ENST00000322213,NM_006306.3;SMC1A,missense_variant,p.Asp58Tyr,ENST00000470241,; A ENST00000322213 Transcript missense_variant 3009/9784 2881/3702 961/1233 D/Y Gac/Tac 1 -1 SMC1A HGNC HGNC:11111 protein_coding YES CCDS14352.1 ENSP00000323421 Q14683 UPI0000135A4D NM_006306.3 deleterious(0.04) 19/25 Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 53394870 53394870 C A 1 0 0 0 0 1 0 0 0 15074 855 30 2 2 SMC1A 23 53394870 Missense_Mutation SNP C C3N-02149_T 3202542 53394870 102646025 546 28730 HUWE1 0 . GRCh38 X 53565121 53565121 + Missense_Mutation SNP C C T C3N-02149_T C3N-02149_N C C c.6826G>A p.Glu2276Lys p.E2276K ENST00000342160 49/83 168 111 57 218 218 0 strelka-varscan-mutect HUWE1,missense_variant,p.Glu2276Lys,ENST00000342160,;HUWE1,missense_variant,p.Glu2276Lys,ENST00000262854,NM_031407.6;HUWE1,missense_variant,p.Glu2267Lys,ENST00000612484,; T ENST00000342160 Transcript missense_variant 7284/14796 6826/13125 2276/4374 E/K Gag/Aag COSM3965372,COSM3965373 1 -1 HUWE1 HGNC HGNC:30892 protein_coding YES CCDS35301.1 ENSP00000340648 Q7Z6Z7 A0A024R9W5 UPI00004A0DAC tolerated(0.13) 49/83 Low_complexity_(Seg):seg 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 53565121 53565121 C T 1 0 0 0 0 1 0 0 0 7357 835 29 3 3 HUWE1 23 53565121 Missense_Mutation SNP C C3N-02149_T 170251 53565121 102475774 547 28731 PGAM4 0 . GRCh38 X 77968898 77968898 + Silent SNP A A T novel C3N-02149_T C3N-02149_N A A c.741T>A p.= p.A247A ENST00000458128 1/1 188 133 55 149 149 0 strelka-varscan-mutect PGAM4,synonymous_variant,p.=,ENST00000458128,NM_001029891.2;ATP7A,intron_variant,,ENST00000341514,NM_000052.6;ATP7A,intron_variant,,ENST00000343533,NM_001282224.1;RP5-1000K24.2,downstream_gene_variant,,ENST00000602791,; T ENST00000458128 Transcript synonymous_variant 741/765 741/765 247/254 A gcT/gcA 1 -1 PGAM4 HGNC HGNC:21731 protein_coding YES CCDS35338.1 ENSP00000412189 Q8N0Y7 UPI0000131CD2 NM_001029891.2 1/1 hmmpanther:PTHR11931:SF14,hmmpanther:PTHR11931,Gene3D:3.40.50.1240,TIGRFAM_domain:TIGR01258 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 77968898 77968898 A T 1 0 0 0 0 0 0 0 1 11865 175 7 4 4 PGAM4 23 77968898 Silent SNP A C3N-02149_T 24403777 77968898 78071997 548 28732 TCEAL2 0 . GRCh38 X 102127004 102127004 + Frame_Shift_Del DEL A A - novel C3N-02149_T C3N-02149_N A A c.176delA p.Lys59ArgfsTer102 p.K59Rfs*102 ENST00000372780 3/3 202 142 60 270 270 0 sindel-varindel-pindel TCEAL2,frameshift_variant,p.Lys59ArgfsTer102,ENST00000372780,NM_080390.3;TCEAL2,frameshift_variant,p.Lys59ArgfsTer102,ENST00000329035,;TCEAL2,downstream_gene_variant,,ENST00000476749,; - ENST00000372780 Transcript frameshift_variant 393/1100 174/684 58/227 L/X ttA/tt 1 1 TCEAL2 HGNC HGNC:29818 protein_coding YES CCDS14496.1 ENSP00000361866 Q9H3H9 UPI00000709E1 NM_080390.3 3/3 hmmpanther:PTHR14754,hmmpanther:PTHR14754:SF15,Pfam_domain:PF04538 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 92 102127004 102127004 A - 1 0 1 0 1 0 0 0 0 16078 359 13 0 0 TCEAL2 23 102127004 Frame_Shift_Del DEL A C3N-02149_T 24158106 102127004 53913891 549 28733 ESX1 0 . GRCh38 X 104254538 104254538 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.122G>T p.Gly41Val p.G41V ENST00000372588 2/4 116 81 35 137 137 0 strelka-varscan-mutect ESX1,missense_variant,p.Gly41Val,ENST00000372588,NM_153448.3; A ENST00000372588 Transcript missense_variant 206/1495 122/1221 41/406 G/V gGa/gTa 1 -1 ESX1 HGNC HGNC:14865 protein_coding YES CCDS14516.1 ENSP00000361669 Q8N693 UPI0000073D09 NM_153448.3 tolerated_low_confidence(0.16) 2/4 hmmpanther:PTHR24329:SF374,hmmpanther:PTHR24329 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 104254538 104254538 C A 1 0 0 0 0 1 0 0 0 5125 855 30 2 2 ESX1 23 104254538 Missense_Mutation SNP C C3N-02149_T 2127534 104254538 51786357 550 28734 IL1RAPL2 0 . GRCh38 X 105749043 105749043 + Missense_Mutation SNP T T C novel C3N-02149_T C3N-02149_N T T c.1132T>C p.Tyr378His p.Y378H ENST00000372582 9/11 120 78 42 159 159 0 strelka-varscan-mutect IL1RAPL2,missense_variant,p.Tyr378His,ENST00000372582,NM_017416.1;IL1RAPL2,missense_variant,p.Tyr121His,ENST00000344799,;IL1RAPL2,non_coding_transcript_exon_variant,,ENST00000485671,; C ENST00000372582 Transcript missense_variant 1888/2985 1132/2061 378/686 Y/H Tac/Cac 1 1 IL1RAPL2 HGNC HGNC:5997 protein_coding YES CCDS14517.1 ENSP00000361663 Q9NP60 UPI0000073DF7 NM_017416.1 deleterious(0) 9/11 Prints_domain:PR01537,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF10,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 92 105749043 105749043 T C 1 0 0 0 0 1 0 0 0 7565 1522 53 5 5 IL1RAPL2 23 105749043 Missense_Mutation SNP T C3N-02149_T 1494505 105749043 50291852 551 28735 ZCCHC16 0 . GRCh38 X 112454953 112454953 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.225C>A p.= p.L75L ENST00000340433 1/1 73 49 24 75 75 0 strelka-varscan-mutect ZCCHC16,synonymous_variant,p.=,ENST00000340433,NM_001004308.2; A ENST00000340433 Transcript synonymous_variant 454/2613 225/933 75/310 L ctC/ctA 1 1 ZCCHC16 HGNC HGNC:25214 protein_coding YES CCDS35369.1 ENSP00000340590 Q6ZR62 UPI00001975B5 NM_001004308.2 1/1 hmmpanther:PTHR15503:SF8,hmmpanther:PTHR15503 LOW 1 SNV 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 112454953 112454953 C A 1 0 0 0 0 0 0 0 1 18159 813 29 2 2 ZCCHC16 23 112454953 Silent SNP C C3N-02149_T 6705910 112454953 43585942 552 28736 HTR2C 0 . GRCh38 X 114907332 114907332 + Missense_Mutation SNP C C A C3N-02149_T C3N-02149_N C C c.1294C>A p.Pro432Thr p.P432T ENST00000276198 6/6 148 98 50 185 185 0 strelka-varscan-mutect HTR2C,missense_variant,p.Pro432Thr,ENST00000276198,NM_000868.3;HTR2C,missense_variant,p.Pro432Thr,ENST00000371951,NM_001256760.2;HTR2C,3_prime_UTR_variant,,ENST00000371950,NM_001256761.2; A ENST00000276198 Transcript missense_variant 2022/4751 1294/1377 432/458 P/T Ccc/Acc COSM1113425 1 1 HTR2C HGNC HGNC:5295 protein_coding YES CCDS14564.1 ENSP00000276198 P28335 UPI000014653A NM_000868.3 tolerated_low_confidence(0.46) 6/6 Prints_domain:PR00517,PD015242 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 114907332 114907332 C A 1 0 0 0 0 1 0 0 0 7339 739 26 2 2 HTR2C 23 114907332 Missense_Mutation SNP C C3N-02149_T 2452379 114907332 41133563 553 28737 ENOX2 0 . GRCh38 X 130625414 130625414 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1733G>T p.Gly578Val p.G578V ENST00000338144 16/16 121 88 33 109 109 0 strelka-varscan-mutect ENOX2,missense_variant,p.Gly578Val,ENST00000338144,NM_182314.2;ENOX2,missense_variant,p.Gly549Val,ENST00000394363,NM_006375.3;ENOX2,missense_variant,p.Gly549Val,ENST00000370935,NM_001281736.1;ENOX2,missense_variant,p.Gly578Val,ENST00000370927,;ENOX2,missense_variant,p.Gly231Val,ENST00000610637,; A ENST00000338144 Transcript missense_variant 2234/4263 1733/1833 578/610 G/V gGt/gTt 1 -1 ENOX2 HGNC HGNC:2259 protein_coding YES CCDS14626.1 ENSP00000337146 Q16206 UPI00000729D5 NM_182314.2 tolerated(0.53) 16/16 hmmpanther:PTHR16001:SF7,hmmpanther:PTHR16001 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 130625414 130625414 C A 1 0 0 0 0 1 0 0 0 4972 507 18 2 2 ENOX2 23 130625414 Missense_Mutation SNP C C3N-02149_T 15718082 130625414 25415481 554 28738 ARHGAP36 0 . GRCh38 X 131084379 131084379 + Missense_Mutation SNP G G T rs763340310 C3N-02149_T C3N-02149_N G G c.720G>T p.Glu240Asp p.E240D ENST00000276211 5/12 83 64 19 87 87 0 strelka-varscan-mutect ARHGAP36,missense_variant,p.Glu240Asp,ENST00000276211,NM_144967.3;ARHGAP36,missense_variant,p.Glu228Asp,ENST00000370922,NM_001282607.1;ARHGAP36,missense_variant,p.Glu209Asp,ENST00000412432,;ARHGAP36,missense_variant,p.Glu104Asp,ENST00000370921,;ARHGAP36,missense_variant,p.Glu192Asp,ENST00000423277,; T ENST00000276211 Transcript missense_variant 1065/3083 720/1644 240/547 E/D gaG/gaT rs763340310 1 1 ARHGAP36 HGNC HGNC:26388 protein_coding YES CCDS14628.1 ENSP00000276211 Q6ZRI8 UPI0000041347 NM_144967.3 tolerated(0.99) 5/12 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR12635,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 2 1 PASS rs763340310 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 131084379 131084379 G T 1 0 0 0 0 1 0 0 0 1009 991 35 2 2 ARHGAP36 23 131084379 Missense_Mutation SNP G C3N-02149_T 458965 131084379 24956516 555 28739 SPANXD 0 . GRCh38 X 141697543 141697543 + Silent SNP G G T rs782085224 C3N-02149_T C3N-02149_N G G c.216C>A p.= p.A72A ENST00000370515 2/2 352 276 76 494 494 0 strelka-varscan-mutect SPANXD,synonymous_variant,p.=,ENST00000370515,NM_032417.3; T ENST00000370515 Transcript synonymous_variant 550/682 216/294 72/97 A gcC/gcA rs782085224,COSM4939356 1 -1 SPANXD HGNC HGNC:14332 protein_coding YES CCDS14675.1 ENSP00000359546 Q9BXN6 UPI0000070F37 NM_032417.3 2/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF1 0,1 LOW 1 SNV 1 0,1 1 PASS rs782085224 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 92 141697543 141697543 G T 1 0 0 0 0 0 0 0 1 15320 1219 43 2 2 SPANXD 23 141697543 Silent SNP G C3N-02149_T 10613164 141697543 14343352 556 28740 SLITRK2 0 . GRCh38 X 145824679 145824679 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.2254C>A p.Pro752Thr p.P752T ENST00000370490 1/1 191 149 42 234 233 1 strelka-varscan-mutect SLITRK2,missense_variant,p.Pro752Thr,ENST00000370490,NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2;SLITRK2,downstream_gene_variant,,ENST00000335565,;TMEM257,upstream_gene_variant,,ENST00000408967,NM_004709.2; A ENST00000370490 Transcript missense_variant 6509/7672 2254/2538 752/845 P/T Cct/Act 1 1 SLITRK2 HGNC HGNC:13449 protein_coding YES CCDS14680.1 ENSP00000359521 Q9H156 UPI000004E64B NM_001144005.2,NM_001144004.2,NM_001144003.2,NM_032539.4,NM_001144008.2,NM_001144010.2,NM_001144006.2,NM_001144009.2 tolerated(0.32) 1/1 MODERATE 1 SNV 1 PASS rs932637565 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 145824679 145824679 C A 1 0 0 0 0 1 0 0 0 15034 739 26 2 2 SLITRK2 23 145824679 Missense_Mutation SNP C C3N-02149_T 4127136 145824679 10216216 557 28741 AFF2 0 . GRCh38 X 148962727 148962727 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.2703C>A p.= p.S901S ENST00000370460 13/21 115 79 36 106 106 0 strelka-varscan-mutect AFF2,synonymous_variant,p.=,ENST00000370460,NM_001169123.1,NM_002025.3;AFF2,synonymous_variant,p.=,ENST00000286437,NM_001170628.1;AFF2,synonymous_variant,p.=,ENST00000342251,NM_001169122.1;AFF2,synonymous_variant,p.=,ENST00000370457,NM_001169124.1,NM_001169125.1; A ENST00000370460 Transcript synonymous_variant 3182/13746 2703/3936 901/1311 S tcC/tcA 1 1 AFF2 HGNC HGNC:3776 protein_coding YES CCDS14684.1 ENSP00000359489 P51816 UPI000049E130 NM_001169123.1,NM_002025.3 13/21 Low_complexity_(Seg):seg,hmmpanther:PTHR10528,hmmpanther:PTHR10528:SF18,Pfam_domain:PF05110 LOW 1 SNV 5 1 PASS . . 0 202 5 2 0 0 0 0 -20 0.9999902 1 1 1 0 A 2 1 92 148962727 148962727 C A 1 0 0 0 0 0 0 0 1 434 581 21 2 2 AFF2 23 148962727 Silent SNP C C3N-02149_T 3138048 148962727 7078168 558 28742 MAGEA4 0 . GRCh38 X 151923736 151923736 + Silent SNP C C A novel C3N-02149_T C3N-02149_N C C c.72C>A p.= p.G24G ENST00000360243 3/3 126 82 44 165 164 1 strelka-varscan-mutect MAGEA4,synonymous_variant,p.=,ENST00000360243,NM_001011550.1;MAGEA4,synonymous_variant,p.=,ENST00000370335,;MAGEA4,synonymous_variant,p.=,ENST00000370340,;MAGEA4,synonymous_variant,p.=,ENST00000393921,;MAGEA4,synonymous_variant,p.=,ENST00000276344,NM_001011548.1;MAGEA4,synonymous_variant,p.=,ENST00000393920,NM_002362.4,NM_001011549.1;MAGEA4,synonymous_variant,p.=,ENST00000416020,;MAGEA4,synonymous_variant,p.=,ENST00000431971,;MAGEA4,synonymous_variant,p.=,ENST00000441865,;MAGEA4,synonymous_variant,p.=,ENST00000457310,;MAGEA4,synonymous_variant,p.=,ENST00000430273,;MAGEA4,synonymous_variant,p.=,ENST00000425182,;MAGEA4,synonymous_variant,p.=,ENST00000448295,;MAGEA4,synonymous_variant,p.=,ENST00000431963,; A ENST00000360243 Transcript synonymous_variant 339/1773 72/954 24/317 G ggC/ggA 1 1 MAGEA4 HGNC HGNC:6802 protein_coding YES CCDS14702.1 ENSP00000353379 P43358 A0A024RC12 UPI000013EA1F NM_001011550.1 3/3 hmmpanther:PTHR11736:SF48,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS rs1478613516 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 92 151923736 151923736 C A 1 0 0 0 0 0 0 0 1 9084 726 26 2 2 MAGEA4 23 151923736 Silent SNP C C3N-02149_T 2961009 151923736 4117159 559 28743 DUSP9 0 . GRCh38 X 153649256 153649256 + Missense_Mutation SNP A A T novel C3N-02149_T C3N-02149_N A A c.398A>T p.Glu133Val p.E133V ENST00000342782 3/4 158 105 53 181 181 0 strelka-varscan-mutect DUSP9,missense_variant,p.Glu133Val,ENST00000342782,NM_001318503.1;DUSP9,missense_variant,p.Glu133Val,ENST00000370167,NM_001395.3;DUSP9,downstream_gene_variant,,ENST00000477033,; T ENST00000342782 Transcript missense_variant 663/2433 398/1155 133/384 E/V gAg/gTg 1 1 DUSP9 HGNC HGNC:3076 protein_coding YES CCDS14724.1 ENSP00000345853 Q99956 UPI0000049C1B NM_001318503.1 deleterious(0.03) 3/4 Gene3D:3.40.250.10,PIRSF_domain:PIRSF000939,PROSITE_profiles:PS50206,hmmpanther:PTHR10159,hmmpanther:PTHR10159:SF388,SMART_domains:SM00450,Superfamily_domains:SSF52821 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 92 153649256 153649256 A T 1 0 0 0 0 1 0 0 0 4654 304 11 4 4 DUSP9 23 153649256 Missense_Mutation SNP A C3N-02149_T 1725520 153649256 2391639 560 28744 NLGN4Y 0 . GRCh38 Y 14840594 14840594 + Missense_Mutation SNP C C A novel C3N-02149_T C3N-02149_N C C c.1783C>A p.Pro595Thr p.P595T ENST00000355905 6/6 602 557 45 847 847 0 varscan-mutect NLGN4Y,missense_variant,p.Pro427Thr,ENST00000382872,NM_001206850.1;NLGN4Y,missense_variant,p.Pro652Thr,ENST00000382868,;NLGN4Y,missense_variant,p.Pro595Thr,ENST00000339174,;NLGN4Y,missense_variant,p.Pro595Thr,ENST00000355905,NM_014893.4;NLGN4Y,non_coding_transcript_exon_variant,,ENST00000476359,; A ENST00000355905 Transcript missense_variant 2035/5167 1783/2451 595/816 P/T Cct/Act 1 1 NLGN4Y HGNC HGNC:15529 protein_coding YES CCDS14788.1 ENSP00000348169 Q8NFZ3 A0A024R9E7 UPI000004770C NM_014893.4 deleterious(0) 6/6 Gene3D:3.40.50.1820,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 64 146 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 92 14840594 14840594 C A 1 0 0 0 0 1 0 0 0 10502 855 30 2 2 NLGN4Y 24 14840594 Missense_Mutation SNP C C3N-02149_T 14840594 42386821 561 28745 ATAD3C 0 . GRCh38 1 1459181 1459181 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.762C>T p.= p.L254L ENST00000378785 9/12 216 176 40 156 156 0 strelka-varscan-mutect ATAD3C,synonymous_variant,p.=,ENST00000378785,NM_001039211.2;ATAD3C,downstream_gene_variant,,ENST00000475091,;ATAD3C,upstream_gene_variant,,ENST00000484537,; T ENST00000378785 Transcript synonymous_variant 1757/3859 762/1236 254/411 L ctC/ctT 1 1 ATAD3C HGNC HGNC:32151 protein_coding YES CCDS44039.1 ENSP00000368062 Q5T2N8 UPI00001619C0 NM_001039211.2 9/12 hmmpanther:PTHR23075:SF5,hmmpanther:PTHR23075,Gene3D:3.40.50.300,Pfam_domain:PF00004,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 1459181 1459181 C T 1 0 0 0 0 0 0 0 1 1223 813 29 3 3 ATAD3C 1 1459181 Silent SNP C C3N-02155_T 1459181 247497241 1 28746 HNRNPCL1 0 . GRCh38 1 12847765 12847765 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.525G>A p.= p.L175L ENST00000317869 2/2 1099 954 145 814 813 1 strelka-varscan-mutect HNRNPCL1,synonymous_variant,p.=,ENST00000317869,NM_001013631.2; T ENST00000317869 Transcript synonymous_variant 751/1108 525/882 175/293 L ttG/ttA 1 -1 HNRNPCL1 HGNC HGNC:29295 protein_coding YES CCDS30591.1 ENSP00000365370 O60812 UPI0000134525 NM_001013631.2 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR13968:SF17,hmmpanther:PTHR13968,PIRSF_domain:PIRSF037992 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 12847765 12847765 C T 1 0 0 0 0 0 0 0 1 7154 825 29 3 3 HNRNPCL1 1 12847765 Silent SNP C C3N-02155_T 11388584 12847765 236108657 2 28747 SZT2 0 . GRCh38 1 43428383 43428383 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.3892C>T p.His1298Tyr p.H1298Y ENST00000562955 27/71 435 361 74 382 382 0 strelka-varscan-mutect SZT2,missense_variant,p.His1298Tyr,ENST00000562955,NM_015284.3;SZT2,missense_variant,p.His1355Tyr,ENST00000634258,;SZT2,non_coding_transcript_exon_variant,,ENST00000470139,;SZT2,upstream_gene_variant,,ENST00000478140,; T ENST00000562955 Transcript missense_variant 3892/12281 3892/10128 1298/3375 H/Y Cat/Tat 1 1 SZT2 HGNC HGNC:29040 protein_coding YES CCDS30694.2 ENSP00000457168 Q5T011 UPI0001E24F46 NM_015284.3 deleterious_low_confidence(0.02) 27/71 hmmpanther:PTHR14918,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 43428383 43428383 C T 1 0 0 0 0 1 0 0 0 15883 826 29 3 3 SZT2 1 43428383 Missense_Mutation SNP C C3N-02155_T 30580618 43428383 205528039 3 28748 LRRC7 0 . GRCh38 1 70028369 70028369 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.1879G>C p.Glu627Gln p.E627Q ENST00000035383 16/25 266 222 44 159 159 0 strelka-varscan-mutect LRRC7,missense_variant,p.Glu632Gln,ENST00000310961,;LRRC7,missense_variant,p.Glu627Gln,ENST00000035383,NM_020794.2;LRRC7,intron_variant,,ENST00000415775,;RP11-181B18.1,intron_variant,,ENST00000414132,; C ENST00000035383 Transcript missense_variant,splice_region_variant 1909/5000 1879/4614 627/1537 E/Q Gag/Cag 1 1 LRRC7 HGNC HGNC:18531 protein_coding YES CCDS645.1 ENSP00000035383 Q96NW7 UPI000006F29B NM_020794.2 tolerated(0.24) 16/25 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 70028369 70028369 G C 1 0 0 0 0 1 0 0 0 8916 1188 41 4 4 LRRC7 1 70028369 Missense_Mutation SNP G C3N-02155_T 26599986 70028369 178928053 4 28749 TRIM33 0 . GRCh38 1 114511064 114511064 + Missense_Mutation SNP T T C novel C3N-02155_T C3N-02155_N T T c.13A>G p.Lys5Glu p.K5E ENST00000358465 1/20 247 216 31 69 69 0 strelka-varscan-mutect TRIM33,missense_variant,p.Lys5Glu,ENST00000358465,NM_015906.3;TRIM33,missense_variant,p.Lys5Glu,ENST00000369543,NM_033020.2; C ENST00000358465 Transcript missense_variant 97/8339 13/3384 5/1127 K/E Aaa/Gaa 1 -1 TRIM33 HGNC HGNC:16290 protein_coding YES CCDS872.1 ENSP00000351250 Q9UPN9 UPI000013D8CD NM_015906.3 deleterious_low_confidence(0) 1/20 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 114511064 114511064 T C 1 0 0 0 0 1 0 0 0 16996 1821 63 5 5 TRIM33 1 114511064 Missense_Mutation SNP T C3N-02155_T 44482695 114511064 134445358 5 28750 HIST2H3PS2 0 . GRCh38 1 143905727 143905727 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.240G>T p.Lys80Asn p.K80N ENST00000392948 1/1 894 702 192 458 458 0 strelka-varscan-mutect HIST2H3PS2,missense_variant,p.Lys80Asn,ENST00000392948,;RP5-998N21.7,intron_variant,,ENST00000444624,;RP5-998N21.10,non_coding_transcript_exon_variant,,ENST00000609879,;HIST2H2BB,upstream_gene_variant,,ENST00000609585,;HIST2H2BB,upstream_gene_variant,,ENST00000449108,; A ENST00000392948 Transcript missense_variant 240/411 240/411 80/136 K/N aaG/aaT 1 -1 HIST2H3PS2 HGNC HGNC:32060 protein_coding YES ENSP00000476960 Q5TEC6 UPI0000470A88 deleterious_low_confidence(0.04) 1/1 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,hmmpanther:PTHR11426,SMART_domains:SM00428,Superfamily_domains:SSF47113 MODERATE SNV 1 PASS . . 4 206 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 143905727 143905727 C A 1 0 0 0 0 1 0 0 0 7070 912 32 2 2 HIST2H3PS2 1 143905727 Missense_Mutation SNP C C3N-02155_T 29394663 143905727 105050695 6 28751 SEMA6C 0 . GRCh38 1 151132335 151132335 + Silent SNP C C G novel C3N-02155_T C3N-02155_N C C c.1476G>C p.= p.R492R ENST00000613223 14/14 240 195 45 108 108 0 strelka-varscan-mutect SEMA6C,synonymous_variant,p.=,ENST00000613223,;SEMA6C,synonymous_variant,p.=,ENST00000621728,;SEMA6C,3_prime_UTR_variant,,ENST00000341697,;SEMA6C,3_prime_UTR_variant,,ENST00000368914,NM_030913.4;SEMA6C,3_prime_UTR_variant,,ENST00000368913,NM_001178061.1;SEMA6C,3_prime_UTR_variant,,ENST00000368912,NM_001178062.1;RP11-68I18.10,upstream_gene_variant,,ENST00000563624,;SEMA6C,non_coding_transcript_exon_variant,,ENST00000479820,;SEMA6C,downstream_gene_variant,,ENST00000464018,;SEMA6C,downstream_gene_variant,,ENST00000489944,; G ENST00000613223 Transcript synonymous_variant 1812/1950 1476/1614 492/537 R cgG/cgC 1 -1 SEMA6C HGNC HGNC:10740 protein_coding ENSP00000482163 A0A087WYX3 UPI0001AE791C 14/14 LOW SNV 5 1 PASS rs1245567331 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 93 151132335 151132335 C G 1 0 0 0 0 0 0 0 1 14317 610 22 4 4 SEMA6C 1 151132335 Silent SNP C C3N-02155_T 7226608 151132335 97824087 7 28752 IQGAP3 0 . GRCh38 1 156550273 156550273 + Missense_Mutation SNP T T C novel C3N-02155_T C3N-02155_N T T c.1813A>G p.Thr605Ala p.T605A ENST00000361170 16/38 432 395 37 151 151 0 strelka-varscan-mutect IQGAP3,missense_variant,p.Thr605Ala,ENST00000361170,NM_178229.4;IQGAP3,missense_variant,p.Thr562Ala,ENST00000491900,; C ENST00000361170 Transcript missense_variant 1824/5988 1813/4896 605/1631 T/A Aca/Gca 1 -1 IQGAP3 HGNC HGNC:20669 protein_coding YES CCDS1144.1 ENSP00000354451 Q86VI3 UPI000046FFDD NM_178229.4 tolerated(0.65) 16/38 hmmpanther:PTHR14149:SF10,hmmpanther:PTHR14149 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 156550273 156550273 T C 1 0 0 0 0 1 0 0 0 7722 1638 57 5 5 IQGAP3 1 156550273 Missense_Mutation SNP T C3N-02155_T 5417938 156550273 92406149 8 28753 CAMSAP2 0 . GRCh38 1 200849683 200849683 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.2947G>A p.Val983Ile p.V983I ENST00000236925 12/18 604 529 75 292 292 0 strelka-varscan CAMSAP2,missense_variant,p.Val972Ile,ENST00000358823,NM_203459.2;CAMSAP2,missense_variant,p.Val983Ile,ENST00000236925,NM_001297707.1;CAMSAP2,missense_variant,p.Val956Ile,ENST00000413307,NM_001297708.1;CAMSAP2,intron_variant,,ENST00000447701,; A ENST00000236925 Transcript missense_variant 2996/7161 2947/4470 983/1489 V/I Gtt/Att 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 tolerated(0.3) 12/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 200849683 200849683 G A 1 0 0 0 0 1 0 0 0 2304 1377 48 3 3 CAMSAP2 1 200849683 Missense_Mutation SNP G C3N-02155_T 44299410 200849683 48106739 9 28754 KLHL12 0 . GRCh38 1 202894742 202894742 + Silent SNP G G T novel C3N-02155_T C3N-02155_N G G c.1143C>A p.= p.I381I ENST00000367261 9/12 352 299 53 212 211 1 strelka-varscan KLHL12,synonymous_variant,p.=,ENST00000367261,NM_001303051.1,NM_001303109.1,NM_021633.3;KLHL12,synonymous_variant,p.=,ENST00000367259,; T ENST00000367261 Transcript synonymous_variant 1362/3359 1143/1707 381/568 I atC/atA 1 -1 KLHL12 HGNC HGNC:19360 protein_coding YES CCDS1429.1 ENSP00000356230 Q53G59 UPI000006EE6A NM_001303051.1,NM_001303109.1,NM_021633.3 9/12 Superfamily_domains:0052715,Gene3D:1k3iA02,Pfam_domain:PF01344,PIRSF_domain:PIRSF037037,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF250,SMART_domains:SM00612 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 202894742 202894742 G T 1 0 0 0 0 0 0 0 1 8232 932 33 2 2 KLHL12 1 202894742 Silent SNP G C3N-02155_T 2045059 202894742 46061680 10 28755 TPO 0 . GRCh38 2 1477436 1477436 + Silent SNP C C T C3N-02155_T C3N-02155_N C C c.1170C>T p.= p.F390F ENST00000345913 8/17 324 278 46 141 141 0 strelka-varscan-mutect TPO,synonymous_variant,p.=,ENST00000422464,;TPO,synonymous_variant,p.=,ENST00000345913,NM_000547.5;TPO,synonymous_variant,p.=,ENST00000329066,NM_001206744.1;TPO,synonymous_variant,p.=,ENST00000382201,NM_001206745.1,NM_175719.3;TPO,synonymous_variant,p.=,ENST00000346956,NM_175721.3;TPO,intron_variant,,ENST00000382198,NM_175722.3;TPO,intron_variant,,ENST00000497517,; T ENST00000345913 Transcript synonymous_variant 1261/3145 1170/2802 390/933 F ttC/ttT COSM4646031,COSM4646032 1 1 TPO HGNC HGNC:12015 protein_coding YES CCDS1643.1 ENSP00000318820 P07202 UPI000013D480 NM_000547.5 8/17 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF60,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 1,1 LOW 1 SNV 1 1,1 1 PASS rs1362585989 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 1477436 1477436 C T 1 0 0 0 0 0 0 0 1 16891 854 30 3 3 TPO 2 1477436 Silent SNP C C3N-02155_T 1477436 240716093 11 28756 ATP6V1C2 0 . GRCh38 2 10768756 10768756 + Missense_Mutation SNP C C G rs201753402 C3N-02155_T C3N-02155_N C C c.416C>G p.Thr139Arg p.T139R ENST00000272238 6/14 469 368 101 256 256 0 strelka-varscan-mutect ATP6V1C2,missense_variant,p.Thr139Arg,ENST00000381661,NM_144583.3;ATP6V1C2,missense_variant,p.Thr149Arg,ENST00000635370,;ATP6V1C2,missense_variant,p.Thr139Arg,ENST00000272238,NM_001039362.1;RP11-791G15.2,intron_variant,,ENST00000606907,; G ENST00000272238 Transcript missense_variant 525/1565 416/1284 139/427 T/R aCg/aGg rs201753402 1 1 ATP6V1C2 HGNC HGNC:18264 protein_coding YES CCDS42653.1 ENSP00000272238 Q8NEY4 UPI0000208E71 NM_001039362.1 deleterious(0.03) 6/14 Superfamily_domains:0049812,Gene3D:1u7lA02,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF03223,hmmpanther:PTHR10137,hmmpanther:PTHR10137:SF4 MODERATE 1 SNV 5 1 PASS rs201753402 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 10768756 10768756 C G 1 0 0 0 0 1 0 0 0 1334 536 19 4 4 ATP6V1C2 2 10768756 Missense_Mutation SNP C C3N-02155_T 9291320 10768756 231424773 12 28757 ADCY3 0 . GRCh38 2 24824453 24824453 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.2661G>C p.Trp887Cys p.W887C ENST00000260600 16/21 405 302 103 242 242 0 strelka-varscan ADCY3,missense_variant,p.Trp887Cys,ENST00000260600,NM_004036.3;ADCY3,missense_variant,p.Trp888Cys,ENST00000405392,NM_001320613.1;ADCY3,missense_variant,p.Trp534Cys,ENST00000606682,;CENPO,downstream_gene_variant,,ENST00000380834,NM_001322101.1;CENPO,downstream_gene_variant,,ENST00000473706,NM_001199803.1;CENPO,downstream_gene_variant,,ENST00000260662,NM_024322.2;ADCY3,upstream_gene_variant,,ENST00000498288,;ADCY3,downstream_gene_variant,,ENST00000455323,;RP11-443B20.1,upstream_gene_variant,,ENST00000606114,;CENPO,downstream_gene_variant,,ENST00000395845,;CENPO,downstream_gene_variant,,ENST00000464156,;ADCY3,downstream_gene_variant,,ENST00000450524,;ADCY3,upstream_gene_variant,,ENST00000485887,; G ENST00000260600 Transcript missense_variant 3513/5050 2661/3435 887/1144 W/C tgG/tgC 1 -1 ADCY3 HGNC HGNC:234 protein_coding YES CCDS1715.1 ENSP00000260600 O60266 UPI000013D0ED NM_004036.3 deleterious(0.05) 16/21 hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF291,PIRSF_domain:PIRSF039050,SMART_domains:SM00044 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 24824453 24824453 C G 1 0 0 0 0 1 0 0 0 339 856 30 4 4 ADCY3 2 24824453 Missense_Mutation SNP C C3N-02155_T 14055697 24824453 217369076 13 28758 KHK 0 . GRCh38 2 27094576 27094576 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.309G>C p.Glu103Asp p.E103D ENST00000260599 3/8 800 692 108 463 463 0 strelka-varscan KHK,missense_variant,p.Glu103Asp,ENST00000260599,NM_000221.2;KHK,missense_variant,p.Glu103Asp,ENST00000429697,;KHK,intron_variant,,ENST00000260598,NM_006488.2;CGREF1,downstream_gene_variant,,ENST00000402550,NM_001166240.1;KHK,non_coding_transcript_exon_variant,,ENST00000490823,;KHK,non_coding_transcript_exon_variant,,ENST00000469936,;CGREF1,downstream_gene_variant,,ENST00000440612,;KHK,upstream_gene_variant,,ENST00000464371,; C ENST00000260599 Transcript missense_variant 822/2411 309/897 103/298 E/D gaG/gaC 1 1 KHK HGNC HGNC:6315 protein_coding YES CCDS1734.1 ENSP00000260599 P50053 A0A140VJM6 UPI000012DE02 NM_000221.2 tolerated(0.62) 3/8 Gene3D:3.40.1190.20,Pfam_domain:PF00294,hmmpanther:PTHR10584,hmmpanther:PTHR10584:SF177,Superfamily_domains:SSF53613 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 27094576 27094576 G C 1 0 0 0 0 1 0 0 0 8070 991 35 4 4 KHK 2 27094576 Missense_Mutation SNP G C3N-02155_T 2270123 27094576 215098953 14 28759 DYSF 0 . GRCh38 2 71568029 71568029 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.2644G>A p.Glu882Lys p.E882K ENST00000410020 25/56 512 449 63 321 320 1 strelka-varscan-mutect DYSF,missense_variant,p.Glu864Lys,ENST00000258104,NM_003494.3,NM_001130976.1;DYSF,missense_variant,p.Glu881Lys,ENST00000409582,NM_001130981.1,NM_001130977.1;DYSF,missense_variant,p.Glu895Lys,ENST00000413539,NM_001130979.1;DYSF,missense_variant,p.Glu864Lys,ENST00000429174,NM_001130978.1;DYSF,missense_variant,p.Glu881Lys,ENST00000409762,NM_001130980.1;DYSF,missense_variant,p.Glu882Lys,ENST00000410020,NM_001130987.1;DYSF,missense_variant,p.Glu896Lys,ENST00000409651,NM_001130982.1;DYSF,missense_variant,p.Glu865Lys,ENST00000409366,NM_001130983.1;DYSF,missense_variant,p.Glu882Lys,ENST00000410041,NM_001130985.1;DYSF,missense_variant,p.Glu851Lys,ENST00000409744,NM_001130984.1,NM_001130986.1;DYSF,missense_variant,p.Glu865Lys,ENST00000394120,NM_001130455.1;DYSF,upstream_gene_variant,,ENST00000461565,; A ENST00000410020 Transcript missense_variant 2785/6657 2644/6360 882/2119 E/K Gag/Aag 1 1 DYSF HGNC HGNC:3097 protein_coding YES CCDS46328.1 ENSP00000386881 O75923 UPI000171F710 NM_001130987.1 deleterious(0.03) 25/56 hmmpanther:PTHR12546,hmmpanther:PTHR12546:SF33 MODERATE 1 SNV 1 1 PASS rs1412382223 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 71568029 71568029 G A 1 0 0 0 0 1 0 0 0 4683 1291 45 3 3 DYSF 2 71568029 Missense_Mutation SNP G C3N-02155_T 44473453 71568029 170625500 15 28760 TLK1 0 . GRCh38 2 171061101 171061101 + Missense_Mutation SNP T T C rs34060370 C3N-02155_T C3N-02155_N T T c.386A>G p.Asn129Ser p.N129S ENST00000431350 4/21 431 370 61 336 335 1 strelka-varscan-mutect TLK1,missense_variant,p.Asn129Ser,ENST00000360843,;TLK1,missense_variant,p.Asn129Ser,ENST00000431350,NM_012290.4;TLK1,missense_variant,p.Asn81Ser,ENST00000521943,NM_001136554.1;TLK1,missense_variant,p.Asn33Ser,ENST00000434911,NM_001136555.1;TLK1,missense_variant,p.Asn33Ser,ENST00000453628,;TLK1,non_coding_transcript_exon_variant,,ENST00000486857,;TLK1,non_coding_transcript_exon_variant,,ENST00000413010,;TLK1,missense_variant,p.Asn129Ser,ENST00000409443,;TLK1,3_prime_UTR_variant,,ENST00000359766,; C ENST00000431350 Transcript missense_variant 791/5663 386/2301 129/766 N/S aAc/aGc rs34060370 1 -1 TLK1 HGNC HGNC:11841 protein_coding YES CCDS2241.1 ENSP00000411099 Q9UKI8 UPI0000073255 NM_012290.4 tolerated(0.85) 4/21 hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF22 MODERATE 1 SNV 1 1 PASS rs34060370 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 171061101 171061101 T C 1 0 0 0 0 1 0 0 0 16389 1725 60 5 5 TLK1 2 171061101 Missense_Mutation SNP T C3N-02155_T 99493072 171061101 71132428 16 28761 SSFA2 0 . GRCh38 2 181929601 181929601 + Nonsense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.3716C>A p.Ser1239Ter p.S1239* ENST00000320370 17/17 262 220 42 267 266 1 strelka-varscan-mutect SSFA2,stop_gained,p.Ser1239Ter,ENST00000320370,NM_006751.6;SSFA2,stop_gained,p.Ser184Ter,ENST00000451836,;SSFA2,3_prime_UTR_variant,,ENST00000431877,NM_001130445.2;SSFA2,3_prime_UTR_variant,,ENST00000409001,NM_001287503.1,NM_001287504.1;SSFA2,3_prime_UTR_variant,,ENST00000409136,;SSFA2,non_coding_transcript_exon_variant,,ENST00000467172,;SSFA2,3_prime_UTR_variant,,ENST00000440623,;SSFA2,3_prime_UTR_variant,,ENST00000416081,;SSFA2,3_prime_UTR_variant,,ENST00000454579,;SSFA2,non_coding_transcript_exon_variant,,ENST00000491720,; A ENST00000320370 Transcript stop_gained 3828/4965 3716/3771 1239/1256 S/* tCa/tAa 1 1 SSFA2 HGNC HGNC:11319 protein_coding CCDS2284.1 ENSP00000314669 P28290 UPI00000722F2 NM_006751.6 17/17 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 93 181929601 181929601 C A 1 0 0 0 0 0 1 0 0 15559 838 29 2 2 SSFA2 2 181929601 Nonsense_Mutation SNP C C3N-02155_T 10868500 181929601 60263928 17 28762 DNAH7 0 . GRCh38 2 195775866 195775866 + Missense_Mutation SNP C C G C3N-02155_T C3N-02155_N C C c.11182G>C p.Asp3728His p.D3728H ENST00000312428 60/65 228 193 35 174 174 0 strelka-varscan-mutect DNAH7,missense_variant,p.Asp3728His,ENST00000312428,NM_018897.2;DNAH7,missense_variant,p.Asp211His,ENST00000409063,; G ENST00000312428 Transcript missense_variant 11283/12394 11182/12075 3728/4024 D/H Gat/Cat COSM4521565 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0.04) 60/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF03028 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 195775866 195775866 C G 1 0 0 0 0 1 0 0 0 4421 826 29 4 4 DNAH7 2 195775866 Missense_Mutation SNP C C3N-02155_T 13846265 195775866 46417663 18 28763 CAPN10 0 . GRCh38 2 240587026 240587026 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.115G>A p.Glu39Lys p.E39K ENST00000391984 1/12 154 123 31 88 88 0 strelka-varscan-mutect CAPN10,missense_variant,p.Glu39Lys,ENST00000391984,NM_023083.3;CAPN10,missense_variant,p.Glu39Lys,ENST00000404753,;CAPN10,missense_variant,p.Glu39Lys,ENST00000354082,NM_023085.3;CAPN10,missense_variant,p.Glu39Lys,ENST00000270364,;CAPN10,missense_variant,p.Glu39Lys,ENST00000352879,;CAPN10,upstream_gene_variant,,ENST00000432084,;CAPN10-AS1,upstream_gene_variant,,ENST00000567819,;CAPN10,missense_variant,p.Glu39Lys,ENST00000416591,;CAPN10,missense_variant,p.Glu39Lys,ENST00000270361,;CAPN10,missense_variant,p.Glu39Lys,ENST00000391983,;CAPN10,missense_variant,p.Glu39Lys,ENST00000357048,;CAPN10,non_coding_transcript_exon_variant,,ENST00000463653,;CAPN10,upstream_gene_variant,,ENST00000494738,; A ENST00000391984 Transcript missense_variant 311/2644 115/2019 39/672 E/K Gag/Aag 1 1 CAPN10 HGNC HGNC:1477 protein_coding YES CCDS42838.1 ENSP00000375844 Q9HC96 UPI00001AE96D NM_023083.3 tolerated(0.13) 1/12 Pfam_domain:PF00648,PROSITE_profiles:PS50203,hmmpanther:PTHR10183,hmmpanther:PTHR10183:SF30,SMART_domains:SM00230,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 240587026 240587026 G A 1 0 0 0 0 1 0 0 0 2315 1059 37 1 1 CAPN10 2 240587026 Missense_Mutation SNP G C3N-02155_T 44811160 240587026 1606503 19 28764 SRGAP3 0 . GRCh38 3 8994470 8994470 + Missense_Mutation SNP G G A C3N-02155_T C3N-02155_N G G c.2281C>T p.Arg761Cys p.R761C ENST00000383836 19/22 433 348 85 389 389 0 strelka-varscan-mutect SRGAP3,missense_variant,p.Arg761Cys,ENST00000383836,NM_014850.3;SRGAP3,missense_variant,p.Arg737Cys,ENST00000360413,NM_001033117.2;SRGAP3,non_coding_transcript_exon_variant,,ENST00000520860,;SRGAP3,upstream_gene_variant,,ENST00000491467,; A ENST00000383836 Transcript missense_variant 2709/8656 2281/3300 761/1099 R/C Cgt/Tgt COSM1048896,COSM4120520 1 -1 SRGAP3 HGNC HGNC:19744 protein_coding YES CCDS2572.1 ENSP00000373347 O43295 UPI0000074099 NM_014850.3 deleterious(0) 19/22 PROSITE_profiles:PS50002,hmmpanther:PTHR14166,hmmpanther:PTHR14166:SF8,Gene3D:2.30.30.40,Pfam_domain:PF00018,SMART_domains:SM00326,Superfamily_domains:SSF50044 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1033693138 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 8994470 8994470 G A 1 0 0 0 0 1 0 0 0 15508 1087 38 1 1 SRGAP3 3 8994470 Missense_Mutation SNP G C3N-02155_T 8994470 189301089 20 28765 MYH15 0 . GRCh38 3 108437559 108437559 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.3276G>A p.= p.L1092L ENST00000273353 26/42 177 144 33 128 128 0 strelka-varscan-mutect MYH15,synonymous_variant,p.=,ENST00000273353,NM_014981.1;MYH15,non_coding_transcript_exon_variant,,ENST00000478998,; T ENST00000273353 Transcript synonymous_variant 3333/7074 3276/5841 1092/1946 L ctG/ctA 1 -1 MYH15 HGNC HGNC:31073 protein_coding YES CCDS43127.1 ENSP00000273353 Q9Y2K3 UPI0000253B6F NM_014981.1 26/42 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140:SF475,hmmpanther:PTHR13140,Pfam_domain:PF01576,Superfamily_domains:SSF90257 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 108437559 108437559 C T 1 0 0 0 0 0 0 0 1 10034 840 29 3 3 MYH15 3 108437559 Silent SNP C C3N-02155_T 99443089 108437559 89858000 21 28766 CCDC80 0 . GRCh38 3 112638807 112638807 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.1099C>T p.Arg367Trp p.R367W ENST00000206423 2/8 459 399 60 330 330 0 strelka-varscan-mutect CCDC80,missense_variant,p.Arg367Trp,ENST00000206423,NM_199511.2;CCDC80,missense_variant,p.Arg367Trp,ENST00000439685,NM_199512.2;CCDC80,upstream_gene_variant,,ENST00000461431,;CCDC80,downstream_gene_variant,,ENST00000475181,;CCDC80,downstream_gene_variant,,ENST00000480275,;CCDC80,downstream_gene_variant,,ENST00000469554,;CCDC80,downstream_gene_variant,,ENST00000473959,; A ENST00000206423 Transcript missense_variant 2053/12430 1099/2853 367/950 R/W Cgg/Tgg 1 -1 CCDC80 HGNC HGNC:30649 protein_coding YES CCDS2968.1 ENSP00000206423 Q76M96 UPI000004EE7F NM_199511.2 deleterious(0) 2/8 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1412000335 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 112638807 112638807 G A 1 0 0 0 0 1 0 0 0 2552 1115 39 1 1 CCDC80 3 112638807 Missense_Mutation SNP G C3N-02155_T 4201248 112638807 85656752 22 28767 HEG1 0 . GRCh38 3 125013040 125013040 + Silent SNP G G A C3N-02155_T C3N-02155_N G G c.2539C>T p.= p.L847L ENST00000311127 6/17 802 704 98 485 484 1 strelka-varscan-mutect HEG1,synonymous_variant,p.=,ENST00000311127,NM_020733.1;HEG1,downstream_gene_variant,,ENST00000477536,;HEG1,upstream_gene_variant,,ENST00000488654,; A ENST00000311127 Transcript synonymous_variant 2607/9156 2539/4146 847/1381 L Ctg/Ttg COSM4481737 1 -1 HEG1 HGNC HGNC:29227 protein_coding YES CCDS46898.1 ENSP00000311502 Q9ULI3 UPI00006C069B NM_020733.1 6/17 hmmpanther:PTHR24037:SF3,hmmpanther:PTHR24037 1 LOW 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 125013040 125013040 G A 1 0 0 0 0 0 0 0 1 6926 933 33 3 3 HEG1 3 125013040 Silent SNP G C3N-02155_T 12374233 125013040 73282519 23 28768 EEFSEC 0 . GRCh38 3 128341298 128341298 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.852C>G p.Asp284Glu p.D284E ENST00000254730 5/7 288 254 34 172 172 0 strelka-varscan-mutect EEFSEC,missense_variant,p.Asp284Glu,ENST00000254730,NM_021937.4;EEFSEC,missense_variant,p.Asp229Glu,ENST00000483457,;EEFSEC,non_coding_transcript_exon_variant,,ENST00000483569,;EEFSEC,non_coding_transcript_exon_variant,,ENST00000484438,; G ENST00000254730 Transcript missense_variant 906/2232 852/1791 284/596 D/E gaC/gaG 1 1 EEFSEC HGNC HGNC:24614 protein_coding YES CCDS33849.1 ENSP00000254730 P57772 UPI000013CE58 NM_021937.4 deleterious(0) 5/7 Gene3D:2.40.30.10,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF91,Superfamily_domains:SSF50447 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 128341298 128341298 C G 1 0 0 0 0 1 0 0 0 4762 506 18 4 4 EEFSEC 3 128341298 Missense_Mutation SNP C C3N-02155_T 3328258 128341298 69954261 24 28769 MED12L 0 . GRCh38 3 151355217 151355217 + Missense_Mutation SNP A A T novel C3N-02155_T C3N-02155_N A A c.2390A>T p.Asp797Val p.D797V ENST00000474524 16/43 256 215 41 212 212 0 strelka-varscan-mutect MED12L,missense_variant,p.Asp797Val,ENST00000474524,NM_053002.5;MED12L,missense_variant,p.Asp657Val,ENST00000273432,;P2RY12,intron_variant,,ENST00000302632,NM_176876.2,NM_022788.4;MED12L,non_coding_transcript_exon_variant,,ENST00000491549,;MED12L,downstream_gene_variant,,ENST00000468305,; T ENST00000474524 Transcript missense_variant 2428/10744 2390/6438 797/2145 D/V gAt/gTt 1 1 MED12L HGNC HGNC:16050 protein_coding YES CCDS33876.1 ENSP00000417235 Q86YW9 UPI000020A46B NM_053002.5 deleterious(0) 16/43 hmmpanther:PTHR13992:SF22,hmmpanther:PTHR13992 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 151355217 151355217 A T 1 0 0 0 0 1 0 0 0 9368 333 12 4 4 MED12L 3 151355217 Missense_Mutation SNP A C3N-02155_T 23013919 151355217 46940342 25 28770 PPM1L 0 . GRCh38 3 161065516 161065516 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.688G>T p.Asp230Tyr p.D230Y ENST00000498165 3/4 346 298 48 184 184 0 strelka-varscan-mutect PPM1L,missense_variant,p.Asp230Tyr,ENST00000498165,NM_001317911.1,NM_001317912.1,NM_139245.2;PPM1L,missense_variant,p.Asp51Tyr,ENST00000464260,;PPM1L,missense_variant,p.Asp103Tyr,ENST00000295839,;PPM1L,non_coding_transcript_exon_variant,,ENST00000480117,; T ENST00000498165 Transcript missense_variant 789/10934 688/1083 230/360 D/Y Gat/Tat 1 1 PPM1L HGNC HGNC:16381 protein_coding YES CCDS33886.1 ENSP00000417659 Q5SGD2 UPI000046F91B NM_001317911.1,NM_001317912.1,NM_139245.2 deleterious(0) 3/4 PROSITE_profiles:PS51746,hmmpanther:PTHR13832:SF290,hmmpanther:PTHR13832,Pfam_domain:PF00481,Gene3D:3.60.40.10,SMART_domains:SM00331,SMART_domains:SM00332,Superfamily_domains:SSF81606 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 161065516 161065516 G T 1 0 0 0 0 1 0 0 0 12454 1290 45 2 2 PPM1L 3 161065516 Missense_Mutation SNP G C3N-02155_T 9710299 161065516 37230043 26 28771 PHC3 0 . GRCh38 3 170117375 170117375 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.2044C>G p.Pro682Ala p.P682A ENST00000495893 10/15 490 410 80 356 356 0 strelka-varscan-mutect PHC3,missense_variant,p.Pro682Ala,ENST00000495893,NM_024947.3;PHC3,missense_variant,p.Pro670Ala,ENST00000494943,NM_001308116.1;PHC3,missense_variant,p.Pro629Ala,ENST00000467570,;PHC3,missense_variant,p.Pro144Ala,ENST00000486042,; C ENST00000495893 Transcript missense_variant 2076/12666 2044/2988 682/995 P/A Cca/Gca 1 -1 PHC3 HGNC HGNC:15682 protein_coding YES CCDS46952.1 ENSP00000420294 Q8NDX5 UPI00004DF1A6 NM_024947.3 deleterious(0.02) 10/15 hmmpanther:PTHR12247,hmmpanther:PTHR12247:SF88,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1470192058 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 170117375 170117375 G C 1 0 0 0 0 1 0 0 0 11907 1174 41 4 4 PHC3 3 170117375 Missense_Mutation SNP G C3N-02155_T 9051859 170117375 28178184 27 28772 KLHL24 0 . GRCh38 3 183650555 183650555 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.199G>A p.Asp67Asn p.D67N ENST00000454652 4/9 376 328 48 256 256 0 strelka-varscan-mutect KLHL24,missense_variant,p.Asp67Asn,ENST00000454652,NM_017644.3;KLHL24,missense_variant,p.Asp67Asn,ENST00000242810,;KLHL24,missense_variant,p.Asp67Asn,ENST00000476808,;KLHL24,missense_variant,p.Asp67Asn,ENST00000493074,;KLHL24,missense_variant,p.Asp67Asn,ENST00000468001,;KLHL24,missense_variant,p.Asp67Asn,ENST00000454495,;KLHL24,missense_variant,p.Asp67Asn,ENST00000482138,;KLHL24,missense_variant,p.Asp67Asn,ENST00000468101,;KLHL24,missense_variant,p.Asp67Asn,ENST00000427201,;KLHL24,missense_variant,p.Asp67Asn,ENST00000473045,;KLHL24,downstream_gene_variant,,ENST00000437402,;KLHL24,intron_variant,,ENST00000475827,; A ENST00000454652 Transcript missense_variant 585/7380 199/1803 67/600 D/N Gat/Aat 1 1 KLHL24 HGNC HGNC:25947 protein_coding YES CCDS3246.1 ENSP00000395012 Q6TFL4 UPI000020A86F NM_017644.3 deleterious(0) 4/9 Gene3D:3.30.710.10,Pfam_domain:PF00651,PIRSF_domain:PIRSF037037,PROSITE_profiles:PS50097,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF257,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 183650555 183650555 G A 1 0 0 0 0 1 0 0 0 8243 942 33 3 3 KLHL24 3 183650555 Missense_Mutation SNP G C3N-02155_T 13533180 183650555 14645004 28 28773 TBC1D1 0 . GRCh38 4 38115874 38115874 + Missense_Mutation SNP G G C C3N-02155_T C3N-02155_N G G c.2722G>C p.Glu908Gln p.E908Q ENST00000261439 16/20 524 461 63 407 407 0 strelka-varscan TBC1D1,missense_variant,p.Glu908Gln,ENST00000261439,NM_015173.3;TBC1D1,missense_variant,p.Glu1002Gln,ENST00000508802,NM_001253912.1;TBC1D1,missense_variant,p.Glu596Gln,ENST00000510573,;TBC1D1,missense_variant,p.Glu172Gln,ENST00000615497,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000407365,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000401554,;TBC1D1,upstream_gene_variant,,ENST00000406664,;TBC1D1,non_coding_transcript_exon_variant,,ENST00000511238,;TBC1D1,upstream_gene_variant,,ENST00000475531,; C ENST00000261439 Transcript missense_variant 3077/5700 2722/3507 908/1168 E/Q Gag/Cag COSM5344704 1 1 TBC1D1 HGNC HGNC:11578 protein_coding YES CCDS33972.1 ENSP00000261439 Q86TI0 B9A6J6 UPI0000367235 NM_015173.3 tolerated(1) 16/20 PROSITE_profiles:PS50086,hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF204,Pfam_domain:PF00566,Gene3D:2qq8A02,SMART_domains:SM00164,Superfamily_domains:SSF47923 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 38115874 38115874 G C 1 0 0 0 0 1 0 0 0 15997 943 33 4 4 TBC1D1 4 38115874 Missense_Mutation SNP G C3N-02155_T 38115874 152098681 29 28774 WDFY3 0 . GRCh38 4 84678189 84678190 + In_Frame_Ins INS - - CCT novel C3N-02155_T C3N-02155_N - - c.10235_10237dupAGG p.Glu3412dup p.E3412dup ENST00000295888 66/68 250 209 41 153 153 0 sindel-pindel WDFY3,inframe_insertion,p.Glu3412dup,ENST00000295888,NM_014991.4;WDFY3,non_coding_transcript_exon_variant,,ENST00000425179,; CCT ENST00000295888 Transcript inframe_insertion 10645-10646/14247 10237-10238/10581 3413/3526 V/EV gtc/gAGGtc 1 -1 WDFY3 HGNC HGNC:20751 protein_coding YES CCDS3609.1 ENSP00000295888 Q8IZQ1 A0A024RDI0 UPI000013E2C7 NM_014991.4 66/68 hmmpanther:PTHR13743:SF80,hmmpanther:PTHR13743,Gene3D:2.130.10.10,SMART_domains:SM00320,Superfamily_domains:SSF50978 MODERATE 1 insertion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 CCT 7 5 93 84678189 84678189 - CCT 1 0 1 1 0 0 0 0 0 17830 275 10 0 0 WDFY3 4 84678189 In_Frame_Ins INS - C3N-02155_T 46562315 84678189 105536366 30 28775 KIAA0922 0 . GRCh38 4 153602552 153602552 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.2464G>C p.Asp822His p.D822H ENST00000409959 23/35 225 194 31 167 167 0 strelka-varscan-mutect KIAA0922,missense_variant,p.Asp821His,ENST00000409663,NM_015196.3;KIAA0922,missense_variant,p.Asp822His,ENST00000409959,NM_001131007.1;KIAA0922,missense_variant,p.Asp599His,ENST00000240487,;KIAA0922,non_coding_transcript_exon_variant,,ENST00000497247,; C ENST00000409959 Transcript missense_variant 2513/5017 2464/4833 822/1610 D/H Gac/Cac 1 1 KIAA0922 HGNC HGNC:29146 protein_coding YES CCDS47148.1 ENSP00000386787 A2VDJ0 UPI00017BE9AB NM_001131007.1 deleterious(0) 23/35 hmmpanther:PTHR22050,hmmpanther:PTHR22050:SF2 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 153602552 153602552 G C 1 0 0 0 0 1 0 0 0 8095 942 33 4 4 KIAA0922 4 153602552 Missense_Mutation SNP G C3N-02155_T 68924363 153602552 36612003 31 28776 GUCY1B3 0 . GRCh38 4 155759798 155759798 + Silent SNP G G C novel C3N-02155_T C3N-02155_N G G c.15G>C p.= p.V5V ENST00000502959 2/15 243 216 27 145 145 0 strelka-mutect GUCY1B3,synonymous_variant,p.=,ENST00000264424,NM_000857.3;GUCY1B3,synonymous_variant,p.=,ENST00000502959,NM_001291951.1;GUCY1B3,synonymous_variant,p.=,ENST00000503520,NM_001291954.1;GUCY1B3,5_prime_UTR_variant,,ENST00000507146,NM_001291953.1;GUCY1B3,5_prime_UTR_variant,,ENST00000505764,NM_001291952.1;GUCY1B3,5_prime_UTR_variant,,ENST00000513437,;GUCY1B3,intron_variant,,ENST00000505154,NM_001291955.1; C ENST00000502959 Transcript synonymous_variant 135/2255 15/1926 5/641 V gtG/gtC 1 1 GUCY1B3 HGNC HGNC:4687 protein_coding YES CCDS77975.1 ENSP00000426786 E9PCN2 UPI0001D3B9A4 NM_001291951.1 2/15 hmmpanther:PTHR11920:SF318,hmmpanther:PTHR11920,Pfam_domain:PF07700,Gene3D:3sj5A00,Superfamily_domains:SSF111126 LOW 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 93 155759798 155759798 G C 1 0 0 0 0 0 0 0 1 6777 1277 45 4 4 GUCY1B3 4 155759798 Silent SNP G C3N-02155_T 2157246 155759798 34454757 32 28777 PPID 0 . GRCh38 4 158723232 158723232 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.57C>A p.Phe19Leu p.F19L ENST00000307720 1/10 547 444 103 339 339 0 strelka-varscan-mutect PPID,missense_variant,p.Phe19Leu,ENST00000307720,NM_005038.2; T ENST00000307720 Transcript missense_variant 165/1823 57/1113 19/370 F/L ttC/ttA 1 -1 PPID HGNC HGNC:9257 protein_coding YES CCDS3801.1 ENSP00000303754 Q08752 E5KN55 UPI0000128C6B NM_005038.2 deleterious(0) 1/10 Gene3D:2.40.100.10,PROSITE_profiles:PS50072,hmmpanther:PTHR11071,hmmpanther:PTHR11071:SF247,Superfamily_domains:SSF50891 MODERATE 1 SNV 1 1 PASS rs1450954192 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 158723232 158723232 G T 1 0 0 0 0 1 0 0 0 12432 933 33 2 2 PPID 4 158723232 Missense_Mutation SNP G C3N-02155_T 2963434 158723232 31491323 33 28778 MARCH1 0 . GRCh38 4 163854060 163854060 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.72C>G p.Ile24Met p.I24M ENST00000503008 3/8 273 228 45 237 237 0 strelka-varscan-mutect MARCH1,missense_variant,p.Ile24Met,ENST00000503008,NM_001166373.1;MARCH1,missense_variant,p.Ile24Met,ENST00000274056,;MARCH1,missense_variant,p.Ile24Met,ENST00000514618,;MARCH1,missense_variant,p.Ile24Met,ENST00000507270,;MARCH1,non_coding_transcript_exon_variant,,ENST00000503104,;MARCH1,intron_variant,,ENST00000510696,; C ENST00000503008 Transcript missense_variant 1049/5877 72/870 24/289 I/M atC/atG 1 -1 MARCH1 HGNC HGNC:26077 protein_coding YES CCDS54814.1 ENSP00000427223 Q8TCQ1 UPI0000037BB3 NM_001166373.1 tolerated_low_confidence(0.13) 3/8 hmmpanther:PTHR23012,hmmpanther:PTHR23012:SF53 MODERATE 1 SNV 1 1 PASS rs993664301 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 163854060 163854060 G C 1 0 0 0 0 1 0 0 0 9223 932 33 4 4 MARCH1 4 163854060 Missense_Mutation SNP G C3N-02155_T 5130828 163854060 26360495 34 28779 TLL1 0 . GRCh38 4 165989416 165989416 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.205G>A p.Asp69Asn p.D69N ENST00000061240 2/21 452 389 63 355 355 0 strelka-varscan-mutect TLL1,missense_variant,p.Asp69Asn,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Asp69Asn,ENST00000507499,;TLL1,missense_variant,p.Asp69Asn,ENST00000513213,NM_001204760.1;TLL1,5_prime_UTR_variant,,ENST00000506144,;TLL1,missense_variant,p.Asp69Asn,ENST00000509505,;TLL1,3_prime_UTR_variant,,ENST00000504560,; A ENST00000061240 Transcript missense_variant 852/6708 205/3042 69/1013 D/N Gac/Aac 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 deleterious_low_confidence(0) 2/21 PIRSF_domain:PIRSF001199,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 165989416 165989416 G A 1 0 0 0 0 1 0 0 0 16391 942 33 3 3 TLL1 4 165989416 Missense_Mutation SNP G C3N-02155_T 2135356 165989416 24225139 35 28780 DHX29 0 . GRCh38 5 55290229 55290229 + Missense_Mutation SNP T T G rs367664398 C3N-02155_T C3N-02155_N T T c.896A>C p.Lys299Thr p.K299T ENST00000251636 7/27 175 124 51 160 160 0 strelka-varscan DHX29,missense_variant,p.Lys299Thr,ENST00000251636,NM_019030.2;DHX29,missense_variant,p.Lys299Thr,ENST00000621106,;RP11-506H20.1,intron_variant,,ENST00000506435,;DHX29,non_coding_transcript_exon_variant,,ENST00000504778,; G ENST00000251636 Transcript missense_variant 1045/4502 896/4110 299/1369 K/T aAa/aCa rs367664398 1 -1 DHX29 HGNC HGNC:15815 protein_coding YES CCDS34158.1 ENSP00000251636 Q7Z478 UPI00001AE72C NM_019030.2 tolerated(0.55) 7/27 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 55290229 55290229 T G 1 0 0 0 0 1 0 0 0 4307 1841 64 5 5 DHX29 5 55290229 Missense_Mutation SNP T C3N-02155_T 55290229 126248030 36 28781 FBN2 0 . GRCh38 5 128301432 128301432 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.5996G>A p.Cys1999Tyr p.C1999Y ENST00000508053 53/71 513 358 155 444 444 0 strelka-varscan-mutect FBN2,missense_variant,p.Cys1999Tyr,ENST00000508053,;FBN2,missense_variant,p.Cys1999Tyr,ENST00000262464,NM_001999.3;FBN2,missense_variant,p.Cys1998Tyr,ENST00000619499,; T ENST00000508053 Transcript missense_variant 6971/11132 5996/8739 1999/2912 C/Y tGt/tAt 1 -1 FBN2 HGNC HGNC:3604 protein_coding YES CCDS34222.1 ENSP00000424571 P35556 UPI0000519468 deleterious(0) 53/71 Gene3D:2.10.25.10,Pfam_domain:PF07645,PIRSF_domain:PIRSF036312,PROSITE_patterns:PS00010,PROSITE_patterns:PS01186,PROSITE_patterns:PS01187,PROSITE_profiles:PS50026,hmmpanther:PTHR24039,hmmpanther:PTHR24039:SF26,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 128301432 128301432 C T 1 0 0 0 0 1 0 0 0 5566 478 17 3 3 FBN2 5 128301432 Missense_Mutation SNP C C3N-02155_T 73011203 128301432 53236827 37 28782 TRPC7 0 . GRCh38 5 136213497 136213497 + Missense_Mutation SNP C C T rs748677264 C3N-02155_T C3N-02155_N C C c.2527G>A p.Glu843Lys p.E843K ENST00000513104 12/12 426 301 125 352 352 0 strelka-varscan-mutect TRPC7,missense_variant,p.Glu843Lys,ENST00000513104,NM_020389.2;TRPC7,missense_variant,p.Glu788Lys,ENST00000502753,;TRPC7,missense_variant,p.Glu782Lys,ENST00000378459,NM_001167577.1;TRPC7,missense_variant,p.Glu727Lys,ENST00000352189,NM_001167576.1;TRPC7-AS1,upstream_gene_variant,,ENST00000514459,;TRPC7,3_prime_UTR_variant,,ENST00000503275,;TRPC7,3_prime_UTR_variant,,ENST00000514963,;TRPC7,non_coding_transcript_exon_variant,,ENST00000509288,; T ENST00000513104 Transcript missense_variant 2810/2987 2527/2589 843/862 E/K Gag/Aag rs748677264,COSM1061076,COSM1061078 1 -1 TRPC7 HGNC HGNC:20754 protein_coding YES CCDS47267.2 ENSP00000426070 Q9HCX4 UPI000004F27A NM_020389.2 tolerated(0.13) 12/12 hmmpanther:PTHR10117,hmmpanther:PTHR10117:SF9 0,1,1 MODERATE SNV 5 0,1,1 1 PASS rs748677264 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 136213497 136213497 C T 1 0 0 0 0 1 0 0 0 17090 893 31 1 1 TRPC7 5 136213497 Missense_Mutation SNP C C3N-02155_T 7912065 136213497 45324762 38 28783 PCDHA9 0 . GRCh38 5 140848652 140848652 + Missense_Mutation SNP G G C rs782279622 C3N-02155_T C3N-02155_N G G c.157G>C p.Gly53Arg p.G53R ENST00000532602 1/4 636 538 98 470 470 0 strelka-varscan-mutect PCDHA9,missense_variant,p.Gly53Arg,ENST00000378122,NM_014005.4;PCDHA9,missense_variant,p.Gly53Arg,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA8,downstream_gene_variant,,ENST00000378123,NM_031856.1;AC005609.19,downstream_gene_variant,,ENST00000623320,; C ENST00000532602 Transcript missense_variant 1190/6293 157/2853 53/950 G/R Ggg/Cgg rs782279622,COSM5688014,COSM5688015 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 deleterious_low_confidence(0.02) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Gene3D:2.60.40.60,Pfam_domain:PF08266,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs782279622 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 140848652 140848652 G C 1 0 0 0 0 1 0 0 0 11618 1232 43 4 4 PCDHA9 5 140848652 Missense_Mutation SNP G C3N-02155_T 4635155 140848652 40689607 39 28784 PCDHB7 0 . GRCh38 5 141175138 141175138 + Frame_Shift_Del DEL T T - rs782568457 C3N-02155_T C3N-02155_N T T c.2304delT p.Ile769SerfsTer36 p.I769Sfs*36 ENST00000231137 1/1 299 254 45 246 246 0 sindel-varindel-pindel PCDHB7,frameshift_variant,p.Ile769SerfsTer36,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,upstream_gene_variant,,ENST00000625128,;AC005754.7,upstream_gene_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; - ENST00000231137 Transcript frameshift_variant 2520/3765 2303/2382 768/793 I/X aTt/at rs782568457 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 1/1 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69 HIGH deletion 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 93 141175138 141175138 T - 1 0 1 0 1 0 0 0 0 11634 1493 52 0 0 PCDHB7 5 141175138 Frame_Shift_Del DEL T C3N-02155_T 326486 141175138 40363121 40 28785 PFN3 0 . GRCh38 5 177400277 177400277 + Silent SNP C C G novel C3N-02155_T C3N-02155_N C C c.300G>C p.= p.V100V ENST00000358571 1/1 382 326 56 196 196 0 strelka-varscan-mutect PFN3,synonymous_variant,p.=,ENST00000358571,NM_001029886.2;SLC34A1,downstream_gene_variant,,ENST00000324417,NM_003052.4;F12,downstream_gene_variant,,ENST00000253496,NM_000505.3;GRK6,upstream_gene_variant,,ENST00000506296,;GRK6,upstream_gene_variant,,ENST00000502598,;SLC34A1,downstream_gene_variant,,ENST00000513614,;F12,downstream_gene_variant,,ENST00000514943,;SLC34A1,downstream_gene_variant,,ENST00000507685,;F12,downstream_gene_variant,,ENST00000510358,;F12,downstream_gene_variant,,ENST00000502854,;F12,downstream_gene_variant,,ENST00000504406,;F12,downstream_gene_variant,,ENST00000503736,; G ENST00000358571 Transcript synonymous_variant 360/530 300/414 100/137 V gtG/gtC 1 -1 PFN3 HGNC HGNC:18627 protein_coding YES CCDS34301.1 ENSP00000351379 P60673 UPI000019788D NM_001029886.2 1/1 hmmpanther:PTHR13936,hmmpanther:PTHR13936:SF2,Gene3D:3.30.450.30,Pfam_domain:PF00235,SMART_domains:SM00392,Superfamily_domains:SSF55770 LOW SNV 1 PASS rs1463818621 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 93 177400277 177400277 C G 1 0 0 0 0 0 0 0 1 11859 581 21 4 4 PFN3 5 177400277 Silent SNP C C3N-02155_T 36225139 177400277 4137982 41 28786 FLT4 0 . GRCh38 5 180621866 180621866 + Missense_Mutation SNP C C T rs757667364 C3N-02155_T C3N-02155_N C C c.1696G>A p.Glu566Lys p.E566K ENST00000261937 13/30 269 236 33 136 135 1 strelka-varscan-mutect FLT4,missense_variant,p.Glu566Lys,ENST00000261937,NM_182925.4;FLT4,missense_variant,p.Glu566Lys,ENST00000393347,NM_002020.4;FLT4,missense_variant,p.Glu566Lys,ENST00000502649,;FLT4,3_prime_UTR_variant,,ENST00000619105,;FLT4,upstream_gene_variant,,ENST00000512795,;FLT4,non_coding_transcript_exon_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000507059,;FLT4,upstream_gene_variant,,ENST00000514810,; T ENST00000261937 Transcript missense_variant 1775/5857 1696/4092 566/1363 E/K Gag/Aag rs757667364 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 tolerated(0.18) 13/30 PROSITE_profiles:PS50835,hmmpanther:PTHR24416:SF49,hmmpanther:PTHR24416,Gene3D:2.60.40.10,Pfam_domain:PF13927,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs757667364 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 180621866 180621866 C T 1 0 0 0 0 1 0 0 0 5800 893 31 1 1 FLT4 5 180621866 Missense_Mutation SNP C C3N-02155_T 3221589 180621866 916393 42 28787 C6orf201 0 . GRCh38 6 4121959 4121959 + Nonsense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.295C>T p.Gln99Ter p.Q99* ENST00000380175 4/6 184 159 25 141 141 0 strelka-varscan-mutect C6orf201,stop_gained,p.Gln99Ter,ENST00000380175,NM_001085401.2;ECI2,intron_variant,,ENST00000465828,;ECI2,intron_variant,,ENST00000380118,NM_206836.2;ECI2,intron_variant,,ENST00000380125,NM_001166010.1;ECI2,intron_variant,,ENST00000361538,NM_006117.2;C6orf201,non_coding_transcript_exon_variant,,ENST00000496987,;C6orf201,stop_gained,p.Gln102Ter,ENST00000427996,;C6orf201,stop_gained,p.Gln99Ter,ENST00000451679,;C6orf201,3_prime_UTR_variant,,ENST00000436110,;ECI2,intron_variant,,ENST00000464583,;ECI2,intron_variant,,ENST00000464057,;ECI2,intron_variant,,ENST00000380120,;ECI2,intron_variant,,ENST00000496241,;ECI2,intron_variant,,ENST00000478266,; T ENST00000380175 Transcript stop_gained 1060/1834 295/423 99/140 Q/* Caa/Taa 1 1 C6orf201 HGNC HGNC:21620 protein_coding YES CCDS43419.1 ENSP00000420610 Q7Z4U5 UPI00004573AE NM_001085401.2 4/6 Pfam_domain:PF15023,hmmpanther:PTHR35968,hmmpanther:PTHR35968:SF1 HIGH 1 SNV 1 1 PASS rs1438775096 . 0 202 3 5 0 0 0 0 -20 0.9980968 1 1 1 0 T 4 4 93 4121959 4121959 C T 1 0 0 0 0 0 1 0 0 2122 827 29 3 3 C6orf201 6 4121959 Nonsense_Mutation SNP C C3N-02155_T 4121959 166684020 43 28788 DSP 0 . GRCh38 6 7585480 7585480 + Nonsense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.8218G>T p.Glu2740Ter p.E2740* ENST00000379802 24/24 472 408 64 314 314 0 strelka-varscan-mutect DSP,stop_gained,p.Glu2740Ter,ENST00000379802,NM_004415.2;DSP,stop_gained,p.Glu2141Ter,ENST00000418664,NM_001008844.1;SNRNP48,upstream_gene_variant,,ENST00000342415,NM_152551.3;SNRNP48,upstream_gene_variant,,ENST00000634363,; T ENST00000379802 Transcript stop_gained 8559/9796 8218/8616 2740/2871 E/* Gaa/Taa 1 1 DSP HGNC HGNC:3052 protein_coding YES CCDS4501.1 ENSP00000369129 P15924 UPI000013C67F NM_004415.2 24/24 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF234,Pfam_domain:PF00681,Gene3D:3.90.1290.10,SMART_domains:SM00250,Superfamily_domains:SSF75399 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 93 7585480 7585480 G T 1 0 0 0 0 0 1 0 0 4602 1175 41 2 2 DSP 6 7585480 Nonsense_Mutation SNP G C3N-02155_T 3463521 7585480 163220499 44 28789 OR14J1 0 . GRCh38 6 29307413 29307413 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.724C>A p.His242Asn p.H242N ENST00000377160 1/1 660 587 73 361 360 1 strelka-varscan-mutect OR14J1,missense_variant,p.His242Asn,ENST00000377160,NM_030946.1; A ENST00000377160 Transcript missense_variant 724/966 724/966 242/321 H/N Cac/Aac 1 1 OR14J1 HGNC HGNC:13971 protein_coding YES CCDS34362.1 ENSP00000366365 Q9UGF5 A0A126GW10 UPI0000041CEC NM_030946.1 deleterious(0) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF42,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 29307413 29307413 C A 1 0 0 0 0 1 0 0 0 11025 478 17 2 2 OR14J1 6 29307413 Missense_Mutation SNP C C3N-02155_T 21721933 29307413 141498566 45 28790 EHMT2 0 . GRCh38 6 31892528 31892528 + Missense_Mutation SNP T T C novel C3N-02155_T C3N-02155_N T T c.914A>G p.Glu305Gly p.E305G ENST00000375528 6/26 327 272 55 226 225 1 strelka-varscan-mutect EHMT2,missense_variant,p.Glu305Gly,ENST00000395728,;EHMT2,missense_variant,p.Glu305Gly,ENST00000375528,NM_001289413.1;EHMT2,missense_variant,p.Glu248Gly,ENST00000375537,NM_006709.4;EHMT2,missense_variant,p.Glu248Gly,ENST00000375530,NM_025256.6;EHMT2,non_coding_transcript_exon_variant,,ENST00000480912,;EHMT2,non_coding_transcript_exon_variant,,ENST00000463484,;EHMT2,downstream_gene_variant,,ENST00000465429,; C ENST00000375528 Transcript missense_variant 934/4047 914/3702 305/1233 E/G gAa/gGa 1 -1 EHMT2 HGNC HGNC:14129 protein_coding YES CCDS75425.1 ENSP00000364678 A2ABF8 UPI0000E5AD1F NM_001289413.1 deleterious_low_confidence(0.05) 6/26 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF361 MODERATE 1 SNV 2 1 PASS rs774225501 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 31892528 31892528 T C 1 0 0 0 0 1 0 0 0 4820 1783 62 5 5 EHMT2 6 31892528 Missense_Mutation SNP T C3N-02155_T 2585115 31892528 138913451 46 28791 TNXB 0 . GRCh38 6 32055855 32055855 + Silent SNP C C T rs566861372 C3N-02155_T C3N-02155_N C C c.8463G>A p.= p.V2821V ENST00000375244 24/44 100 88 12 52 52 0 strelka-varscan-mutect TNXB,synonymous_variant,p.=,ENST00000375244,NM_019105.6;TNXB,synonymous_variant,p.=,ENST00000611016,; T ENST00000375244 Transcript synonymous_variant 8665/13132 8463/12735 2821/4244 V gtG/gtA rs566861372 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 24/44 PROSITE_profiles:PS50853,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF244,Gene3D:2.60.40.10,Superfamily_domains:SSF49265 LOW 1 SNV 5 1 PASS rs566861372 . 0 199 6 0 0 0 0 4 -3.362644 0 0 1 0 0 T 2 4 93 32055855 32055855 C T 1 0 0 0 0 0 0 0 1 16820 840 29 3 3 TNXB 6 32055855 Silent SNP C C3N-02155_T 163327 32055855 138750124 47 28792 KHDRBS2 0 . GRCh38 6 62047915 62047915 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.299C>T p.Ser100Phe p.S100F ENST00000281156 3/9 435 389 46 294 294 0 strelka-varscan-mutect KHDRBS2,missense_variant,p.Ser100Phe,ENST00000281156,NM_152688.2; A ENST00000281156 Transcript missense_variant 578/2332 299/1050 100/349 S/F tCt/tTt 1 -1 KHDRBS2 HGNC HGNC:18114 protein_coding YES CCDS4963.1 ENSP00000281156 Q5VWX1 UPI000004D256 NM_152688.2 deleterious(0) 3/9 Gene3D:3.30.1370.10,Pfam_domain:PF00013,PROSITE_profiles:PS50084,hmmpanther:PTHR11208,hmmpanther:PTHR11208:SF34,SMART_domains:SM00322,Superfamily_domains:SSF54791 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 62047915 62047915 G A 1 0 0 0 0 1 0 0 0 8068 942 33 3 3 KHDRBS2 6 62047915 Missense_Mutation SNP G C3N-02155_T 29992060 62047915 108758064 48 28793 COL12A1 0 . GRCh38 6 75189685 75189685 + Missense_Mutation SNP C C G rs199736979 C3N-02155_T C3N-02155_N C C c.525G>C p.Glu175Asp p.E175D ENST00000322507 6/66 782 601 181 422 422 0 strelka-varscan-mutect COL12A1,missense_variant,p.Glu175Asp,ENST00000322507,NM_004370.5;COL12A1,missense_variant,p.Glu175Asp,ENST00000483888,;COL12A1,missense_variant,p.Glu175Asp,ENST00000416123,;COL12A1,5_prime_UTR_variant,,ENST00000615798,;COL12A1,intron_variant,,ENST00000345356,NM_080645.2;COL12A1,upstream_gene_variant,,ENST00000486533,; G ENST00000322507 Transcript missense_variant 835/11723 525/9192 175/3063 E/D gaG/gaC rs199736979 1 -1 COL12A1 HGNC HGNC:2188 protein_coding YES CCDS43482.1 ENSP00000325146 Q99715 UPI000045890B NM_004370.5 tolerated(1) 6/66 PROSITE_profiles:PS50234,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF106,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 1 1 PASS rs199736979 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 75189685 75189685 C G 1 0 0 0 0 1 0 0 0 3457 912 32 4 4 COL12A1 6 75189685 Missense_Mutation SNP C C3N-02155_T 13141770 75189685 95616294 49 28794 ZNF292 0 . GRCh38 6 87255140 87255140 + Missense_Mutation SNP A A C novel C3N-02155_T C3N-02155_N A A c.1511A>C p.Asn504Thr p.N504T ENST00000369577 8/8 839 731 108 544 543 1 strelka-varscan-mutect ZNF292,missense_variant,p.Asn504Thr,ENST00000369577,NM_015021.1;ZNF292,missense_variant,p.Asn499Thr,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,; C ENST00000369577 Transcript missense_variant 1554/10610 1511/8172 504/2723 N/T aAt/aCt 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 tolerated(0.86) 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 87255140 87255140 A C 1 0 0 0 0 1 0 0 0 18402 101 4 5 5 ZNF292 6 87255140 Missense_Mutation SNP A C3N-02155_T 12065455 87255140 83550839 50 28795 ZNF292 0 . GRCh38 6 87259774 87259774 + Missense_Mutation SNP A A T rs755899917 C3N-02155_T C3N-02155_N A A c.6145A>T p.Ser2049Cys p.S2049C ENST00000369577 8/8 347 299 48 225 225 0 strelka-varscan-mutect ZNF292,missense_variant,p.Ser2049Cys,ENST00000369577,NM_015021.1;ZNF292,missense_variant,p.Ser2044Cys,ENST00000339907,;ZNF292,intron_variant,,ENST00000496806,;ZNF292,downstream_gene_variant,,ENST00000466062,; T ENST00000369577 Transcript missense_variant 6188/10610 6145/8172 2049/2723 S/C Agt/Tgt rs755899917 1 1 ZNF292 HGNC HGNC:18410 protein_coding YES CCDS47457.1 ENSP00000358590 O60281 UPI000020D2CC NM_015021.1 tolerated(0.06) 8/8 hmmpanther:PTHR15507,hmmpanther:PTHR15507:SF14 MODERATE 1 SNV 2 1 PASS rs755899917 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 87259774 87259774 A T 1 0 0 0 0 1 0 0 0 18402 72 3 4 4 ZNF292 6 87259774 Missense_Mutation SNP A C3N-02155_T 4634 87259774 83546205 51 28796 FUT9 0 . GRCh38 6 96203810 96203810 + Missense_Mutation SNP G G T rs765166497 C3N-02155_T C3N-02155_N G G c.655G>T p.Gly219Trp p.G219W ENST00000302103 3/3 369 326 43 243 243 0 strelka-varscan-mutect FUT9,missense_variant,p.Gly219Trp,ENST00000302103,NM_006581.3; T ENST00000302103 Transcript missense_variant 981/12783 655/1080 219/359 G/W Ggg/Tgg rs765166497 1 1 FUT9 HGNC HGNC:4020 protein_coding YES CCDS5033.1 ENSP00000302599 Q9Y231 UPI000013E792 NM_006581.3 deleterious(0) 3/3 Pfam_domain:PF00852,hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF10,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS rs765166497 . 0 207 0 3 0 0 0 0 -20 0.9999894 1 1 1 0 T 3 4 93 96203810 96203810 G T 1 0 0 0 0 1 0 0 0 5983 1116 39 1 1 FUT9 6 96203810 Missense_Mutation SNP G C3N-02155_T 8944036 96203810 74602169 52 28797 FBXL4 0 . GRCh38 6 98875656 98875656 + Nonsense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.1461G>A p.Trp487Ter p.W487* ENST00000369244 9/10 952 851 101 554 554 0 strelka-varscan-mutect FBXL4,stop_gained,p.Trp487Ter,ENST00000369244,;FBXL4,stop_gained,p.Trp487Ter,ENST00000229971,NM_001278716.1,NM_012160.4; T ENST00000369244 Transcript stop_gained 1890/8035 1461/1866 487/621 W/* tgG/tgA 1 -1 FBXL4 HGNC HGNC:13601 protein_coding YES CCDS5041.1 ENSP00000358247 Q9UKA2 UPI000012ADE3 9/10 hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF474,Gene3D:3.80.10.10,SMART_domains:SM00367,Superfamily_domains:SSF52047 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 93 98875656 98875656 C T 1 0 0 0 0 0 1 0 0 5584 856 30 3 3 FBXL4 6 98875656 Nonsense_Mutation SNP C C3N-02155_T 2671846 98875656 71930323 53 28798 WASF1 0 . GRCh38 6 110103396 110103396 + Missense_Mutation SNP G G A rs141943257 C3N-02155_T C3N-02155_N G G c.875C>T p.Pro292Leu p.P292L ENST00000392589 9/11 240 211 29 141 141 0 strelka-varscan-mutect WASF1,missense_variant,p.Pro292Leu,ENST00000392589,NM_003931.2;WASF1,missense_variant,p.Pro292Leu,ENST00000392588,NM_001024934.1;WASF1,missense_variant,p.Pro292Leu,ENST00000359451,NM_001024935.1;WASF1,missense_variant,p.Pro292Leu,ENST00000392586,;WASF1,missense_variant,p.Pro292Leu,ENST00000392587,NM_001024936.1;WASF1,downstream_gene_variant,,ENST00000444391,; A ENST00000392589 Transcript missense_variant 1712/3220 875/1680 292/559 P/L cCg/cTg rs141943257 1 -1 WASF1 HGNC HGNC:12732 protein_coding YES CCDS5080.1 ENSP00000376368 Q92558 UPI000003AC31 NM_003931.2 deleterious(0.01) 9/11 hmmpanther:PTHR12902,hmmpanther:PTHR12902:SF8 MODERATE 1 SNV 5 1 PASS rs141943257 . 0 205 3 0 0 0 0 2 -5.144978 0 0 1 0 0 A 3 1 93 110103396 110103396 G A 1 0 0 0 0 1 0 0 0 17812 1116 39 1 1 WASF1 6 110103396 Missense_Mutation SNP G C3N-02155_T 11227740 110103396 60702583 54 28799 CNKSR3 0 . GRCh38 6 154450133 154450133 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.178G>A p.Glu60Lys p.E60K ENST00000607772 2/13 271 234 37 182 182 0 strelka-varscan-mutect CNKSR3,missense_variant,p.Glu60Lys,ENST00000607772,NM_173515.2;CNKSR3,5_prime_UTR_variant,,ENST00000479339,; T ENST00000607772 Transcript missense_variant 723/21063 178/1668 60/555 E/K Gag/Aag 1 -1 CNKSR3 HGNC HGNC:23034 protein_coding YES CCDS5246.1 ENSP00000475915 Q6P9H4 UPI000020D0EA NM_173515.2 deleterious(0) 2/13 Gene3D:1.10.150.50,Pfam_domain:PF00536,PROSITE_profiles:PS50105,hmmpanther:PTHR12844,hmmpanther:PTHR12844:SF17,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 154450133 154450133 C T 1 0 0 0 0 1 0 0 0 3388 864 30 3 3 CNKSR3 6 154450133 Missense_Mutation SNP C C3N-02155_T 44346737 154450133 16355846 55 28800 PLG 0 . GRCh38 6 160731870 160731870 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.1564C>G p.Pro522Ala p.P522A ENST00000308192 12/19 679 585 94 391 391 0 strelka-varscan-mutect PLG,missense_variant,p.Pro522Ala,ENST00000308192,NM_000301.3;PLG,downstream_gene_variant,,ENST00000297289,;PLG,downstream_gene_variant,,ENST00000493435,; G ENST00000308192 Transcript missense_variant 1627/2741 1564/2433 522/810 P/A Cca/Gca 1 1 PLG HGNC HGNC:9071 protein_coding YES CCDS5279.1 ENSP00000308938 P00747 UPI000000D8B8 NM_000301.3 deleterious(0.01) 12/19 Gene3D:2.40.20.10,Pfam_domain:PF00051,PIRSF_domain:PIRSF001150,PROSITE_profiles:PS50070,hmmpanther:PTHR24261,hmmpanther:PTHR24261:SF2,SMART_domains:SM00130,Superfamily_domains:SSF57440 MODERATE 1 SNV 1 1 PASS rs896552124 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 160731870 160731870 C G 1 0 0 0 0 1 0 0 0 12181 855 30 4 4 PLG 6 160731870 Missense_Mutation SNP C C3N-02155_T 6281737 160731870 10074109 56 28801 T 0 . GRCh38 6 166166813 166166813 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.250C>A p.Pro84Thr p.P84T ENST00000296946 3/9 627 543 84 434 432 2 strelka-varscan-mutect T,missense_variant,p.Pro84Thr,ENST00000296946,NM_003181.3;T,missense_variant,p.Pro84Thr,ENST00000366871,NM_001270484.1;T,missense_variant,p.Pro84Thr,ENST00000366876,;T,missense_variant,p.Pro84Thr,ENST00000461348,; T ENST00000296946 Transcript missense_variant 719/2436 250/1308 84/435 P/T Ccc/Acc 1 -1 T HGNC HGNC:11515 protein_coding YES CCDS5290.1 ENSP00000296946 O15178 UPI0000126AB5 NM_003181.3 deleterious(0) 3/9 Gene3D:1h6fA00,Pfam_domain:PF00907,PROSITE_profiles:PS50252,hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF83,SMART_domains:SM00425,Superfamily_domains:SSF49417 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 166166813 166166813 G T 1 0 0 0 0 1 0 0 0 15884 1232 43 2 2 T 6 166166813 Missense_Mutation SNP G C3N-02155_T 5434943 166166813 4639166 57 28802 SDK1 0 . GRCh38 7 4127461 4127461 + Missense_Mutation SNP G G A rs750145998 C3N-02155_T C3N-02155_N G G c.3904G>A p.Glu1302Lys p.E1302K ENST00000404826 26/45 636 579 57 245 245 0 strelka-varscan-mutect SDK1,missense_variant,p.Glu1302Lys,ENST00000404826,NM_152744.3;SDK1,missense_variant,p.Glu1302Lys,ENST00000615806,;SDK1,missense_variant,p.Glu1302Lys,ENST00000389531,;SDK1,upstream_gene_variant,,ENST00000476701,; A ENST00000404826 Transcript missense_variant 4043/10397 3904/6642 1302/2213 E/K Gaa/Aaa rs750145998,COSM1472066 1 1 SDK1 HGNC HGNC:19307 protein_coding YES CCDS34590.1 ENSP00000385899 Q7Z5N4 UPI0000DBEEC4 NM_152744.3 tolerated(0.19) 26/45 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF36,hmmpanther:PTHR10489,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs750145998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 4127461 4127461 G A 1 0 0 0 0 1 0 0 0 14243 1175 41 3 3 SDK1 7 4127461 Missense_Mutation SNP G C3N-02155_T 4127461 155218512 58 28803 TNRC18 0 . GRCh38 7 5312837 5312837 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.8054C>T p.Ala2685Val p.A2685V ENST00000430969 27/30 140 100 40 73 73 0 strelka-varscan-mutect TNRC18,missense_variant,p.Ala2685Val,ENST00000399537,;TNRC18,missense_variant,p.Ala2685Val,ENST00000430969,NM_001080495.2;TNRC18,downstream_gene_variant,,ENST00000328270,; A ENST00000430969 Transcript missense_variant 8403/10562 8054/8907 2685/2968 A/V gCa/gTa 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious_low_confidence(0) 27/30 hmmpanther:PTHR12505,hmmpanther:PTHR12505:SF21 MODERATE 1 SNV 5 1 PASS . . 0 197 13 0 0 0 0 0 -20 0.9999551 1 1 1 0 A 3 1 93 5312837 5312837 G A 1 0 0 0 0 1 0 0 0 16812 1319 46 3 3 TNRC18 7 5312837 Missense_Mutation SNP G C3N-02155_T 1185376 5312837 154033136 59 28804 USP42 0 . GRCh38 7 6153883 6153883 + Missense_Mutation SNP C C G rs779174997 C3N-02155_T C3N-02155_N C C c.2329C>G p.Pro777Ala p.P777A ENST00000306177 15/18 265 242 23 100 100 0 strelka-varscan-mutect USP42,missense_variant,p.Pro777Ala,ENST00000306177,NM_032172.2;USP42,missense_variant,p.Pro623Ala,ENST00000426246,;USP42,downstream_gene_variant,,ENST00000465073,;USP42,3_prime_UTR_variant,,ENST00000521713,;USP42,non_coding_transcript_exon_variant,,ENST00000479544,; G ENST00000306177 Transcript missense_variant 2487/5155 2329/3951 777/1316 P/A Ccg/Gcg rs779174997 1 1 USP42 HGNC HGNC:20068 protein_coding YES CCDS47535.1 ENSP00000301962 Q9H9J4 UPI0000416754 NM_032172.2 tolerated(0.64) 15/18 MODERATE 1 SNV 5 1 PASS rs779174997 . 0 203 4 3 0 0 0 0 -20 0.9995465 1 1 1 0 G 3 3 93 6153883 6153883 C G 1 0 0 0 0 1 0 0 0 17616 739 26 4 4 USP42 7 6153883 Missense_Mutation SNP C C3N-02155_T 841046 6153883 153192090 60 28805 HDAC9 0 . GRCh38 7 18629468 18629468 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.783G>A p.Met261Ile p.M261I ENST00000441542 6/25 519 434 85 217 217 0 strelka-varscan-mutect HDAC9,missense_variant,p.Met258Ile,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Met258Ile,ENST00000405010,NM_001321869.1,NM_001321870.1,NM_001321874.1,NM_001321875.1,NM_001321884.1,NM_001321886.1,NM_001321887.1,NM_001321890.1,NM_001321899.1,NM_001321900.1,NM_001321901.1,NM_001321902.1,NM_014707.1;HDAC9,missense_variant,p.Met261Ile,ENST00000441542,NM_178425.2;HDAC9,missense_variant,p.Met258Ile,ENST00000432645,NM_058176.2;HDAC9,missense_variant,p.Met230Ile,ENST00000456174,NM_001204148.1;HDAC9,intron_variant,,ENST00000622668,NM_001321879.1,NM_001321885.1,NM_001321893.1,NM_001321891.1,NM_001321894.1,NM_001204146.1;HDAC9,intron_variant,,ENST00000406072,NM_001321871.1,NM_001321872.1,NM_001321873.1,NM_001321888.1,NM_001321895.1,NM_001321898.1;HDAC9,intron_variant,,ENST00000401921,;HDAC9,intron_variant,,ENST00000417496,NM_001204144.1;HDAC9,intron_variant,,ENST00000428307,NM_001204145.1;HDAC9,intron_variant,,ENST00000524023,NM_001204147.1;HDAC9,non_coding_transcript_exon_variant,,ENST00000523867,;HDAC9,intron_variant,,ENST00000461159,; A ENST00000441542 Transcript missense_variant 783/3210 783/3210 261/1069 M/I atG/atA 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0.02) 6/25 PIRSF_domain:PIRSF037911 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 93 18629468 18629468 G A 1 0 0 0 0 1 0 0 0 6901 1377 48 3 3 HDAC9 7 18629468 Missense_Mutation SNP G C3N-02155_T 12475585 18629468 140716505 61 28806 HDAC9 0 . GRCh38 7 18975904 18975904 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.3121G>T p.Ala1041Ser p.A1041S ENST00000441542 24/25 530 485 45 227 227 0 strelka-varscan-mutect HDAC9,missense_variant,p.Ala1038Ser,ENST00000406451,NM_001321897.1,NM_178423.1;HDAC9,missense_variant,p.Ala997Ser,ENST00000401921,;HDAC9,missense_variant,p.Ala1041Ser,ENST00000441542,NM_178425.2;HDAC9,non_coding_transcript_exon_variant,,ENST00000496026,;HDAC9,non_coding_transcript_exon_variant,,ENST00000490851,; T ENST00000441542 Transcript missense_variant 3121/3210 3121/3210 1041/1069 A/S Gcc/Tcc 1 1 HDAC9 HGNC HGNC:14065 protein_coding YES CCDS47553.1 ENSP00000408617 Q9UKV0 UPI000019AB75 NM_178425.2 deleterious(0.01) 24/25 hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF136,PIRSF_domain:PIRSF037911 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 18975904 18975904 G T 1 0 0 0 0 1 0 0 0 6901 1203 42 2 2 HDAC9 7 18975904 Missense_Mutation SNP G C3N-02155_T 346436 18975904 140370069 62 28807 ZNRF2 0 . GRCh38 7 30285606 30285606 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.249C>T p.= p.L83L ENST00000323037 1/5 112 96 16 36 36 0 strelka-mutect ZNRF2,synonymous_variant,p.=,ENST00000323037,NM_147128.3;MIR550A1,upstream_gene_variant,,ENST00000385037,;hsa-mir-550a-1,downstream_gene_variant,,ENST00000637270,;ZNRF2,non_coding_transcript_exon_variant,,ENST00000459998,; T ENST00000323037 Transcript synonymous_variant 1300/3460 249/729 83/242 L ctC/ctT 1 1 ZNRF2 HGNC HGNC:22316 protein_coding YES CCDS5426.1 ENSP00000323879 Q8NHG8 A0A090N8Y8 UPI000006DDF0 NM_147128.3 1/5 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1403552142 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 30285606 30285606 C T 1 0 0 0 0 0 0 0 1 18805 871 31 1 1 ZNRF2 7 30285606 Silent SNP C C3N-02155_T 11309702 30285606 129060367 63 28808 NPSR1 0 . GRCh38 7 34658540 34658540 + Missense_Mutation SNP C C G rs267601496 C3N-02155_T C3N-02155_N C C c.128C>G p.Ser43Cys p.S43C ENST00000381539 1/10 391 354 37 166 166 0 strelka-varscan-mutect NPSR1,missense_variant,p.Ser43Cys,ENST00000360581,NM_207172.1;NPSR1,missense_variant,p.Ser43Cys,ENST00000359791,NM_207173.1;NPSR1,missense_variant,p.Ser43Cys,ENST00000531252,NM_001300933.1;NPSR1,missense_variant,p.Ser43Cys,ENST00000381542,NM_001300934.1;NPSR1,missense_variant,p.Ser43Cys,ENST00000381539,NM_001300935.1;NPSR1,missense_variant,p.Ser43Cys,ENST00000381553,;NPSR1,missense_variant,p.Ser43Cys,ENST00000465305,;NPSR1-AS1,intron_variant,,ENST00000419766,;NPSR1-AS1,intron_variant,,ENST00000539747,;NPSR1-AS1,intron_variant,,ENST00000439852,;NPSR1-AS1,intron_variant,,ENST00000358772,;NPSR1-AS1,intron_variant,,ENST00000431669,;NPSR1,missense_variant,p.Ser43Cys,ENST00000396095,;NPSR1,missense_variant,p.Ser43Cys,ENST00000381544,; G ENST00000381539 Transcript missense_variant 132/1233 128/1173 43/390 S/C tCc/tGc rs267601496 1 1 NPSR1 HGNC HGNC:23631 protein_coding YES CCDS75579.1 ENSP00000370950 Q6W5P4 UPI00004F9C01 NM_001300935.1 deleterious(0) 1/10 hmmpanther:PTHR24244,hmmpanther:PTHR24244:SF2 MODERATE 1 SNV 1 1 PASS rs267601496 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 34658540 34658540 C G 1 0 0 0 0 1 0 0 0 10656 855 30 4 4 NPSR1 7 34658540 Missense_Mutation SNP C C3N-02155_T 4372934 34658540 124687433 64 28809 DPY19L1 0 . GRCh38 7 35010491 35010491 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.522C>G p.Phe174Leu p.F174L ENST00000310974 6/22 380 337 43 187 187 0 varscan-mutect DPY19L1,missense_variant,p.Phe247Leu,ENST00000638088,;DPY19L1,missense_variant,p.Phe174Leu,ENST00000310974,NM_015283.1;DPY19L1,non_coding_transcript_exon_variant,,ENST00000481923,; C ENST00000310974 Transcript missense_variant 667/4870 522/2028 174/675 F/L ttC/ttG 1 -1 DPY19L1 HGNC HGNC:22205 protein_coding YES CCDS43567.1 ENSP00000308695 Q2PZI1 UPI000067CB92 NM_015283.1 tolerated(0.21) 6/22 Transmembrane_helices:TMhelix,hmmpanther:PTHR31488:SF5,hmmpanther:PTHR31488,Pfam_domain:PF10034 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 35010491 35010491 G C 1 0 0 0 0 1 0 0 0 4555 933 33 4 4 DPY19L1 7 35010491 Missense_Mutation SNP G C3N-02155_T 351951 35010491 124335482 65 28810 GPR141 0 . GRCh38 7 37740430 37740430 + Missense_Mutation SNP G G A rs141399721 C3N-02155_T C3N-02155_N G G c.37G>A p.Asp13Asn p.D13N ENST00000447769 4/4 224 205 19 97 96 1 strelka-varscan-mutect GPR141,missense_variant,p.Asp13Asn,ENST00000447769,;GPR141,missense_variant,p.Asp13Asn,ENST00000334425,NM_181791.1;GPR141,missense_variant,p.Asp13Asn,ENST00000450180,;EPDR1,intron_variant,,ENST00000476620,;GPR141,intron_variant,,ENST00000461610,; A ENST00000447769 Transcript missense_variant 326/1270 37/918 13/305 D/N Gat/Aat rs141399721,COSM601167 1 1 GPR141 HGNC HGNC:19997 protein_coding YES CCDS5451.1 ENSP00000390410 Q7Z602 UPI000004B92B tolerated(0.44) 4/4 hmmpanther:PTHR24237,hmmpanther:PTHR24237:SF0,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 3 0,1 1 PASS rs141399721 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 37740430 37740430 G A 1 0 0 0 0 1 0 0 0 6535 1058 37 1 1 GPR141 7 37740430 Missense_Mutation SNP G C3N-02155_T 2729939 37740430 121605543 66 28811 VPS41 0 . GRCh38 7 38754710 38754710 + Frame_Shift_Del DEL G G - rs765114320 C3N-02155_T C3N-02155_N G G c.1780delC p.Gln594SerfsTer60 p.Q594Sfs*60 ENST00000310301 21/29 580 517 63 278 278 0 sindel-varindel-pindel VPS41,frameshift_variant,p.Gln594SerfsTer60,ENST00000310301,NM_014396.3;VPS41,frameshift_variant,p.Gln569SerfsTer60,ENST00000395969,NM_080631.3;VPS41,downstream_gene_variant,,ENST00000462429,; - ENST00000310301 Transcript frameshift_variant 1835/5903 1780/2565 594/854 Q/X Cag/ag rs765114320 1 -1 VPS41 HGNC HGNC:12713 protein_coding YES CCDS5457.1 ENSP00000309457 P49754 UPI000000DAB7 NM_014396.3 21/29 PROSITE_profiles:PS50236,hmmpanther:PTHR12616,PIRSF_domain:PIRSF028921,Pfam_domain:PF00637,SMART_domains:SM00299 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 93 38754710 38754710 G - 1 0 1 0 1 0 0 0 0 17756 1386 48 0 0 VPS41 7 38754710 Frame_Shift_Del DEL G C3N-02155_T 1014280 38754710 120591263 67 28812 DBNL 0 . GRCh38 7 44059578 44059578 + Missense_Mutation SNP C C A rs537588038 C3N-02155_T C3N-02155_N C C c.994C>A p.Pro332Thr p.P332T ENST00000468694 11/13 468 395 73 218 218 0 strelka-varscan-mutect DBNL,missense_variant,p.Pro252Thr,ENST00000432854,;DBNL,missense_variant,p.Pro324Thr,ENST00000494774,NM_014063.6;DBNL,missense_variant,p.Pro332Thr,ENST00000468694,NM_001122956.1;DBNL,missense_variant,p.Pro229Thr,ENST00000490734,NM_001284315.1;DBNL,missense_variant,p.Pro323Thr,ENST00000448521,NM_001014436.2;DBNL,missense_variant,p.Pro299Thr,ENST00000452943,;DBNL,missense_variant,p.Pro220Thr,ENST00000440166,NM_001284313.1;DBNL,missense_variant,p.Pro275Thr,ENST00000456905,;DBNL,missense_variant,p.Pro31Thr,ENST00000452661,;PGAM2,downstream_gene_variant,,ENST00000297283,NM_000290.3;DBNL,non_coding_transcript_exon_variant,,ENST00000497184,;DBNL,3_prime_UTR_variant,,ENST00000441840,;DBNL,3_prime_UTR_variant,,ENST00000429716,;DBNL,3_prime_UTR_variant,,ENST00000411855,;DBNL,3_prime_UTR_variant,,ENST00000498733,;DBNL,non_coding_transcript_exon_variant,,ENST00000449997,;DBNL,downstream_gene_variant,,ENST00000441904,;DBNL,downstream_gene_variant,,ENST00000464762,;DBNL,downstream_gene_variant,,ENST00000458579,;DBNL,downstream_gene_variant,,ENST00000423561,;DBNL,downstream_gene_variant,,ENST00000439815,;DBNL,downstream_gene_variant,,ENST00000485932,; A ENST00000468694 Transcript missense_variant 1021/2068 994/1320 332/439 P/T Cca/Aca rs537588038 1 1 DBNL HGNC HGNC:2696 protein_coding YES CCDS47579.1 ENSP00000417653 Q9UJU6 UPI000007147D NM_001122956.1 tolerated(0.12) 11/13 hmmpanther:PTHR10829:SF12,hmmpanther:PTHR10829 MODERATE SNV 2 1 PASS rs537588038 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 93 44059578 44059578 C A 1 0 0 0 0 1 0 0 0 4055 855 30 2 2 DBNL 7 44059578 Missense_Mutation SNP C C3N-02155_T 5304868 44059578 115286395 68 28813 TNS3 0 . GRCh38 7 47283704 47283704 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.4090C>A p.Gln1364Lys p.Q1364K ENST00000311160 28/31 109 101 8 52 52 0 strelka-varscan-mutect TNS3,missense_variant,p.Gln1364Lys,ENST00000311160,NM_022748.11;TNS3,upstream_gene_variant,,ENST00000428457,; T ENST00000311160 Transcript missense_variant 4448/7618 4090/4338 1364/1445 Q/K Cag/Aag 1 -1 TNS3 HGNC HGNC:21616 protein_coding YES CCDS5506.2 ENSP00000312143 Q68CZ2 UPI00001AE9DA NM_022748.11 deleterious(0) 28/31 Gene3D:2.30.29.30,Pfam_domain:PF08416,hmmpanther:PTHR12305,hmmpanther:PTHR12305:SF42,SMART_domains:SM00462,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -16.39373 1 1 1 1 0 T 3 4 93 47283704 47283704 G T 1 0 0 0 0 1 0 0 0 16818 1299 45 2 2 TNS3 7 47283704 Missense_Mutation SNP G C3N-02155_T 3224126 47283704 112062269 69 28814 FIGNL1 0 . GRCh38 7 50447255 50447255 + Silent SNP C C G novel C3N-02155_T C3N-02155_N C C c.33G>C p.= p.L11L ENST00000419119 2/2 197 180 17 82 82 0 strelka-varscan-mutect FIGNL1,synonymous_variant,p.=,ENST00000419119,;FIGNL1,synonymous_variant,p.=,ENST00000433017,NM_001287492.1;FIGNL1,synonymous_variant,p.=,ENST00000611938,;FIGNL1,synonymous_variant,p.=,ENST00000395556,NM_001042762.2,NM_022116.4;FIGNL1,synonymous_variant,p.=,ENST00000356889,;FIGNL1,synonymous_variant,p.=,ENST00000615084,NM_001287496.1,NM_001287494.1,NM_001287493.1;FIGNL1,synonymous_variant,p.=,ENST00000617389,NM_001287495.1;FIGNL1,synonymous_variant,p.=,ENST00000613602,;FIGNL1,synonymous_variant,p.=,ENST00000440350,;FIGNL1,synonymous_variant,p.=,ENST00000435566,;FIGNL1,synonymous_variant,p.=,ENST00000420829,;FIGNL1,synonymous_variant,p.=,ENST00000422854,;FIGNL1,synonymous_variant,p.=,ENST00000448788,;FIGNL1,synonymous_variant,p.=,ENST00000436590,; G ENST00000419119 Transcript synonymous_variant 1587/3700 33/2025 11/674 L ctG/ctC 1 -1 FIGNL1 HGNC HGNC:13286 protein_coding YES CCDS5510.1 ENSP00000410811 Q6PIW4 UPI000013CE5D 2/2 hmmpanther:PTHR23074:SF75,hmmpanther:PTHR23074 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 93 50447255 50447255 C G 1 0 0 0 0 0 0 0 1 5756 813 29 4 4 FIGNL1 7 50447255 Silent SNP C C3N-02155_T 3163551 50447255 108898718 70 28815 POM121L12 0 . GRCh38 7 53035765 53035765 + Missense_Mutation SNP C C G C3N-02155_T C3N-02155_N C C c.94C>G p.Pro32Ala p.P32A ENST00000408890 1/1 624 580 44 233 233 0 strelka-varscan-mutect POM121L12,missense_variant,p.Pro32Ala,ENST00000408890,NM_182595.3; G ENST00000408890 Transcript missense_variant 124/1283 94/891 32/296 P/A Ccc/Gcc COSM4513777,COSM5274281 1 1 POM121L12 HGNC HGNC:25369 protein_coding YES CCDS43584.1 ENSP00000386133 Q8N7R1 UPI00001B6540 NM_182595.3 tolerated(0.27) 1/1 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF30 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 53035765 53035765 C G 1 0 0 0 0 1 0 0 0 12352 855 30 4 4 POM121L12 7 53035765 Missense_Mutation SNP C C3N-02155_T 2588510 53035765 106310208 71 28816 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02155_T C3N-02155_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 1233 596 637 562 560 2 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02155_T 2156057 55191822 104154151 72 28817 KMT2C 0 . GRCh38 7 152146674 152146674 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.13956G>C p.Gln4652His p.Q4652H ENST00000262189 53/59 426 314 112 403 403 0 strelka-varscan-mutect KMT2C,missense_variant,p.Gln4652His,ENST00000262189,NM_170606.2;KMT2C,missense_variant,p.Gln4652His,ENST00000355193,;KMT2C,missense_variant,p.Gln2213His,ENST00000360104,;KMT2C,missense_variant,p.Gln1269His,ENST00000424877,;KMT2C,3_prime_UTR_variant,,ENST00000558084,;KMT2C,non_coding_transcript_exon_variant,,ENST00000473186,; G ENST00000262189 Transcript missense_variant 14175/16862 13956/14736 4652/4911 Q/H caG/caC 1 -1 KMT2C HGNC HGNC:13726 protein_coding YES CCDS5931.1 ENSP00000262189 Q8NEZ4 UPI0000141B9F NM_170606.2 deleterious(0) 53/59 PROSITE_profiles:PS51543,hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF373,Pfam_domain:PF05965,SMART_domains:SM00542 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 152146674 152146674 C G 1 0 0 0 0 1 0 0 0 8297 796 28 4 4 KMT2C 7 152146674 Missense_Mutation SNP C C3N-02155_T 96954852 152146674 7199299 73 28818 MYOM2 0 . GRCh38 8 2085332 2085332 + Frame_Shift_Del DEL T T - novel C3N-02155_T C3N-02155_N T T c.1586delT p.Leu529ProfsTer37 p.L529Pfs*37 ENST00000262113 14/37 263 211 52 221 221 0 sindel-varindel-pindel MYOM2,frameshift_variant,p.Leu529ProfsTer37,ENST00000262113,NM_003970.3;MYOM2,intron_variant,,ENST00000523438,;MYOM2,non_coding_transcript_exon_variant,,ENST00000519518,;MYOM2,non_coding_transcript_exon_variant,,ENST00000518803,; - ENST00000262113 Transcript frameshift_variant 1727/5014 1586/4398 529/1465 L/X cTc/cc 1 1 MYOM2 HGNC HGNC:7614 protein_coding YES CCDS5957.1 ENSP00000262113 P54296 UPI000442D01B NM_003970.3 14/37 PROSITE_profiles:PS50853,hmmpanther:PTHR13817,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265,Prints_domain:PR00014 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 93 2085332 2085332 T - 1 0 1 0 1 0 0 0 0 10093 1551 54 0 0 MYOM2 8 2085332 Frame_Shift_Del DEL T C3N-02155_T 2085332 143053304 74 28819 PDLIM2 0 . GRCh38 8 22585154 22585154 + Missense_Mutation SNP C C G C3N-02155_T C3N-02155_N C C c.1203C>G p.Ile401Met p.I401M ENST00000308354 5/10 140 115 25 128 128 0 strelka-varscan-mutect PDLIM2,stop_gained,p.Ser151Ter,ENST00000622702,;PDLIM2,missense_variant,p.Ile151Met,ENST00000265810,NM_176871.3;PDLIM2,missense_variant,p.Ile401Met,ENST00000308354,NM_021630.5;PDLIM2,missense_variant,p.Ile401Met,ENST00000339162,;PDLIM2,missense_variant,p.Ile151Met,ENST00000397760,;PDLIM2,missense_variant,p.Ile151Met,ENST00000397761,;PDLIM2,missense_variant,p.Ile151Met,ENST00000409417,;PDLIM2,missense_variant,p.Ile151Met,ENST00000409141,NM_198042.3;PDLIM2,missense_variant,p.Ile151Met,ENST00000452226,;PDLIM2,missense_variant,p.Ile151Met,ENST00000456545,;PDLIM2,missense_variant,p.Ile151Met,ENST00000429812,;PDLIM2,missense_variant,p.Ile151Met,ENST00000426493,;PDLIM2,missense_variant,p.Ile151Met,ENST00000436754,;PDLIM2,upstream_gene_variant,,ENST00000464275,;AC037459.4,upstream_gene_variant,,ENST00000450780,;AC037459.4,upstream_gene_variant,,ENST00000447849,;PDLIM2,upstream_gene_variant,,ENST00000443561,;PDLIM2,upstream_gene_variant,,ENST00000614502,;AC037459.4,upstream_gene_variant,,ENST00000430850,;PDLIM2,downstream_gene_variant,,ENST00000616289,;PDLIM2,missense_variant,p.Ile63Met,ENST00000448520,;PDLIM2,3_prime_UTR_variant,,ENST00000416159,;PDLIM2,non_coding_transcript_exon_variant,,ENST00000491330,;PDLIM2,upstream_gene_variant,,ENST00000622226,; G ENST00000308354 Transcript missense_variant 1242/2236 1203/1809 401/602 I/M atC/atG COSM1133827,COSM1552139,COSM1552140,COSM421675 1 1 PDLIM2 HGNC HGNC:13992 protein_coding YES CCDS6032.2 ENSP00000312634 Q96JY6 UPI0000E5AE4E NM_021630.5 tolerated(0.08) 5/10 hmmpanther:PTHR24214,hmmpanther:PTHR24214:SF1 1,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999997 1 1 1 0 G 3 3 93 22585154 22585154 C G 1 0 0 0 0 1 0 0 0 11768 838 29 4 4 PDLIM2 8 22585154 Missense_Mutation SNP C C3N-02155_T 20499822 22585154 122553482 75 28820 KIF13B 0 . GRCh38 8 29123415 29123415 + Frame_Shift_Del DEL C C - novel C3N-02155_T C3N-02155_N C C c.3430delG p.Val1144Ter p.V1144* ENST00000524189 28/40 380 333 47 318 318 0 sindel-varindel-pindel KIF13B,frameshift_variant,p.Val1144Ter,ENST00000524189,NM_015254.3;CTD-2647L4.1,intron_variant,,ENST00000523661,; - ENST00000524189 Transcript frameshift_variant 3469/8745 3430/5481 1144/1826 V/X Gtg/tg 1 -1 KIF13B HGNC HGNC:14405 protein_coding YES CCDS55217.1 ENSP00000427900 Q9NQT8 UPI000035B257 NM_015254.3 28/40 Pfam_domain:PF12473 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 93 29123415 29123415 C - 1 0 1 0 1 0 0 0 0 8139 507 18 0 0 KIF13B 8 29123415 Frame_Shift_Del DEL C C3N-02155_T 6538261 29123415 116015221 76 28821 WRN 0 . GRCh38 8 31111748 31111749 + Frame_Shift_Ins INS - - A novel C3N-02155_T C3N-02155_N - - c.2227dupA p.Thr743AsnfsTer22 p.T743Nfs*22 ENST00000298139 19/35 373 309 64 296 294 2 sindel-varindel-pindel WRN,frameshift_variant,p.Thr743AsnfsTer22,ENST00000298139,NM_000553.4;WRN,non_coding_transcript_exon_variant,,ENST00000521620,; A ENST00000298139 Transcript frameshift_variant 2471-2472/5215 2222-2223/4299 741/1432 R/RX cga/cgAa 1 1 WRN HGNC HGNC:12791 protein_coding YES CCDS6082.1 ENSP00000298139 Q14191 UPI000013E49D NM_000553.4 19/35 hmmpanther:PTHR13710:SF87,hmmpanther:PTHR13710,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00614,Superfamily_domains:SSF52540 HIGH 1 insertion 1 5 1 PASS . . 0 204 0 0 5 0 0 0 -20 0.757673 1 1 1 0 A 7 5 93 31111748 31111748 - A 1 0 1 1 0 0 0 0 0 17959 1058 37 0 0 WRN 8 31111748 Frame_Shift_Ins INS - C3N-02155_T 1988333 31111748 114026888 77 28822 SHC3 0 . GRCh38 9 89046995 89046995 + Splice_Site SNP C C G novel C3N-02155_T C3N-02155_N C C c.963-1G>C p.X321_splice ENST00000375835 56 38 18 82 82 0 strelka-varscan-mutect SHC3,splice_acceptor_variant,,ENST00000375835,NM_016848.5;SHC3,upstream_gene_variant,,ENST00000375831,; G ENST00000375835 Transcript splice_acceptor_variant -/9768 963/1785 321/594 1 -1 SHC3 HGNC HGNC:18181 protein_coding YES CCDS6681.1 ENSP00000364995 Q92529 UPI0000073E1F NM_016848.5 7/11 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 93 89046995 89046995 C G 1 0 0 0 0 0 0 1 0 14531 927 32 4 4 SHC3 9 89046995 Splice_Site SNP C C3N-02155_T 89046995 49347722 78 28823 PHF2 0 . GRCh38 9 93676792 93676792 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.3031G>C p.Glu1011Gln p.E1011Q ENST00000359246 21/22 144 118 26 153 153 0 strelka-varscan-mutect PHF2,missense_variant,p.Glu1011Gln,ENST00000359246,NM_005392.3;PHF2,missense_variant,p.Glu224Gln,ENST00000375376,;PHF2,missense_variant,p.Glu243Gln,ENST00000610682,; C ENST00000359246 Transcript missense_variant 3398/5569 3031/3291 1011/1096 E/Q Gag/Cag 1 1 PHF2 HGNC HGNC:8920 protein_coding YES CCDS35069.1 ENSP00000352185 O75151 UPI0000211A97 NM_005392.3 tolerated(0.06) 21/22 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF14,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 93676792 93676792 G C 1 0 0 0 0 1 0 0 0 11916 943 33 4 4 PHF2 9 93676792 Missense_Mutation SNP G C3N-02155_T 4629797 93676792 44717925 79 28824 PLPP7 0 . GRCh38 9 131308114 131308114 + Missense_Mutation SNP C C A rs760054266 C3N-02155_T C3N-02155_N C C c.643C>A p.Arg215Ser p.R215S ENST00000372264 2/2 398 340 58 238 238 0 strelka-varscan-mutect PLPP7,missense_variant,p.Arg215Ser,ENST00000372264,NM_032728.3; A ENST00000372264 Transcript missense_variant 947/2095 643/816 215/271 R/S Cgt/Agt rs760054266,COSM204265 1 1 PLPP7 HGNC HGNC:28174 protein_coding YES CCDS6942.1 ENSP00000361338 Q8NBV4 UPI0000070B2A NM_032728.3 deleterious(0) 2/2 Gene3D:1.20.144.10,Pfam_domain:PF01569,hmmpanther:PTHR14969,hmmpanther:PTHR14969:SF17,Low_complexity_(Seg):seg,SMART_domains:SM00014,Superfamily_domains:SSF48317,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs760054266 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 131308114 131308114 C A 1 0 0 0 0 1 0 0 0 12208 768 27 1 1 PLPP7 9 131308114 Missense_Mutation SNP C C3N-02155_T 37631322 131308114 7086603 80 28825 FAM21C 0 . GRCh38 10 45784889 45784889 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.2676G>T p.Lys892Asn p.K892N ENST00000374362 25/30 85 67 18 76 76 0 strelka-varscan-mutect FAM21C,missense_variant,p.Lys892Asn,ENST00000336378,;FAM21C,missense_variant,p.Lys892Asn,ENST00000374362,NM_015262.2;FAM21C,missense_variant,p.Lys892Asn,ENST00000623400,;FAM21C,missense_variant,p.Lys892Asn,ENST00000540872,NM_001169106.1;FAM21C,missense_variant,p.Lys834Asn,ENST00000359860,;FAM21C,missense_variant,p.Lys817Asn,ENST00000537517,NM_001169107.1;FAM21C,non_coding_transcript_exon_variant,,ENST00000374359,;FAM21C,upstream_gene_variant,,ENST00000471102,; T ENST00000374362 Transcript missense_variant 2775/4623 2676/3963 892/1320 K/N aaG/aaT 1 1 FAM21C HGNC HGNC:23414 protein_coding YES CCDS44374.2 ENSP00000363482 Q9Y4E1 UPI0000551BE9 NM_015262.2 deleterious(0) 25/30 hmmpanther:PTHR21669:SF4,hmmpanther:PTHR21669 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 45784889 45784889 G T 1 0 0 0 0 1 0 0 0 5412 1020 36 2 2 FAM21C 10 45784889 Missense_Mutation SNP G C3N-02155_T 45784889 88012533 81 28826 CCAR1 0 . GRCh38 10 68749243 68749243 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.934C>T p.Pro312Ser p.P312S ENST00000265872 9/25 180 133 47 144 144 0 strelka-varscan-mutect CCAR1,missense_variant,p.Pro312Ser,ENST00000265872,NM_018237.3;CCAR1,missense_variant,p.Pro312Ser,ENST00000630771,;CCAR1,missense_variant,p.Pro297Ser,ENST00000543719,NM_001282960.1,NM_001282959.1;CCAR1,missense_variant,p.Pro297Ser,ENST00000539539,;CCAR1,missense_variant,p.Pro117Ser,ENST00000536012,;CCAR1,missense_variant,p.Pro286Ser,ENST00000543225,;CCAR1,missense_variant,p.Pro312Ser,ENST00000540210,;CCAR1,missense_variant,p.Pro312Ser,ENST00000541012,;CCAR1,3_prime_UTR_variant,,ENST00000543229,; T ENST00000265872 Transcript missense_variant 1053/4683 934/3453 312/1150 P/S Cct/Tct 1 1 CCAR1 HGNC HGNC:24236 protein_coding YES CCDS7282.1 ENSP00000265872 Q8IX12 UPI000004D30A NM_018237.3 tolerated(0.83) 9/25 hmmpanther:PTHR14304,hmmpanther:PTHR14304:SF14 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999979 1 1 1 0 T 3 4 93 68749243 68749243 C T 1 0 0 0 0 1 0 0 0 2431 739 26 3 3 CCAR1 10 68749243 Missense_Mutation SNP C C3N-02155_T 22964354 68749243 65048179 82 28827 P4HA1 0 . GRCh38 10 73051092 73051092 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.861G>C p.Gln287His p.Q287H ENST00000263556 7/15 173 135 38 186 186 0 strelka-varscan-mutect P4HA1,missense_variant,p.Gln287His,ENST00000263556,NM_000917.3;P4HA1,missense_variant,p.Gln287His,ENST00000394890,NM_001017962.2,NM_001142595.1;P4HA1,missense_variant,p.Gln287His,ENST00000440381,NM_001142596.1;P4HA1,missense_variant,p.Gln287His,ENST00000307116,;P4HA1,missense_variant,p.Gln287His,ENST00000373008,; G ENST00000263556 Transcript missense_variant 1102/2844 861/1605 287/534 Q/H caG/caC 1 -1 P4HA1 HGNC HGNC:8546 protein_coding YES CCDS7320.1 ENSP00000263556 P13674 Q5VSQ6 UPI000002B050 NM_000917.3 deleterious(0.01) 7/15 hmmpanther:PTHR10869,hmmpanther:PTHR10869:SF76 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 73051092 73051092 C G 1 0 0 0 0 1 0 0 0 11433 912 32 4 4 P4HA1 10 73051092 Missense_Mutation SNP C C3N-02155_T 4301849 73051092 60746330 83 28828 SH3PXD2A 0 . GRCh38 10 103602670 103602670 + Missense_Mutation SNP C C T rs764554398 C3N-02155_T C3N-02155_N C C c.2464G>A p.Ala822Thr p.A822T ENST00000355946 14/14 401 338 63 345 345 0 strelka-varscan-mutect SH3PXD2A,missense_variant,p.Ala850Thr,ENST00000369774,;SH3PXD2A,missense_variant,p.Ala822Thr,ENST00000355946,NM_014631.2;SH3PXD2A,missense_variant,p.Ala777Thr,ENST00000420222,;SH3PXD2A,non_coding_transcript_exon_variant,,ENST00000315994,; T ENST00000355946 Transcript missense_variant 2604/11245 2464/3318 822/1105 A/T Gcc/Acc rs764554398,COSM1321558 1 -1 SH3PXD2A HGNC HGNC:23664 protein_coding YES CCDS31278.1 ENSP00000348215 Q5TCZ1 UPI000041B175 NM_014631.2 tolerated(0.56) 14/14 Gene3D:2.30.30.40,Pfam_domain:PF00018,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF7,SMART_domains:SM00326,Superfamily_domains:SSF50044 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs764554398 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 103602670 103602670 C T 1 0 0 0 0 1 0 0 0 14515 768 27 1 1 SH3PXD2A 10 103602670 Missense_Mutation SNP C C3N-02155_T 30551578 103602670 30194752 84 28829 IKZF5 0 . GRCh38 10 122994179 122994179 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.861G>T p.Met287Ile p.M287I ENST00000368886 5/5 589 473 116 551 550 1 strelka-varscan-mutect IKZF5,missense_variant,p.Met287Ile,ENST00000368886,;IKZF5,missense_variant,p.Met287Ile,ENST00000617859,NM_001271840.1;PSTK,downstream_gene_variant,,ENST00000368887,NM_153336.2;PSTK,downstream_gene_variant,,ENST00000406217,;PSTK,intron_variant,,ENST00000497219,;PSTK,intron_variant,,ENST00000496079,;PSTK,downstream_gene_variant,,ENST00000465232,;IKZF5,downstream_gene_variant,,ENST00000479103,;PSTK,downstream_gene_variant,,ENST00000483455,;IKZF5,downstream_gene_variant,,ENST00000496605,;PSTK,downstream_gene_variant,,ENST00000483755,;IKZF5,downstream_gene_variant,,ENST00000469821,; A ENST00000368886 Transcript missense_variant 1182/4555 861/1260 287/419 M/I atG/atT 1 -1 IKZF5 HGNC HGNC:14283 protein_coding YES CCDS41574.1 ENSP00000357881 Q9H5V7 UPI000006DBBE tolerated(0.41) 5/5 hmmpanther:PTHR24387:SF7,hmmpanther:PTHR24387 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 122994179 122994179 C A 1 0 0 0 0 1 0 0 0 7526 826 29 2 2 IKZF5 10 122994179 Missense_Mutation SNP C C3N-02155_T 19391509 122994179 10803243 85 28830 BUB3 0 . GRCh38 10 123162806 123162806 + Missense_Mutation SNP A A G novel C3N-02155_T C3N-02155_N A A c.949A>G p.Thr317Ala p.T317A ENST00000368865 7/8 304 194 110 312 312 0 strelka-varscan-mutect BUB3,missense_variant,p.Thr317Ala,ENST00000368865,NM_004725.3;BUB3,missense_variant,p.Thr317Ala,ENST00000368858,NM_001007793.2;BUB3,intron_variant,,ENST00000368859,;BUB3,downstream_gene_variant,,ENST00000407911,;BUB3,non_coding_transcript_exon_variant,,ENST00000481952,; G ENST00000368865 Transcript missense_variant 1158/7828 949/987 317/328 T/A Aca/Gca 1 1 BUB3 HGNC HGNC:1151 protein_coding YES CCDS7635.1 ENSP00000357858 O43684 UPI0000126B30 NM_004725.3 tolerated(0.41) 7/8 hmmpanther:PTHR10971 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 123162806 123162806 A G 1 0 0 0 0 1 0 0 0 1748 275 10 5 5 BUB3 10 123162806 Missense_Mutation SNP A C3N-02155_T 168627 123162806 10634616 86 28831 OR52J3 0 . GRCh38 11 5047176 5047176 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.651C>G p.Ile217Met p.I217M ENST00000380370 1/1 306 240 66 186 186 0 strelka-varscan-mutect OR52J3,missense_variant,p.Ile217Met,ENST00000380370,NM_001001916.2; G ENST00000380370 Transcript missense_variant 651/936 651/936 217/311 I/M atC/atG 1 1 OR52J3 HGNC HGNC:14799 protein_coding YES CCDS31370.1 ENSP00000369728 Q8NH60 UPI0000046AE0 NM_001001916.2 deleterious(0.04) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26450,hmmpanther:PTHR26450:SF9,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 5047176 5047176 C G 1 0 0 0 0 1 0 0 0 11195 903 32 4 4 OR52J3 11 5047176 Missense_Mutation SNP C C3N-02155_T 5047176 130039446 87 28832 OR52E6 0 . GRCh38 11 5840983 5840983 + Silent SNP C C T rs540768482 C3N-02155_T C3N-02155_N C C c.915G>A p.= p.L305L ENST00000329322 1/1 52 42 10 39 39 0 strelka-varscan-mutect OR52E6,synonymous_variant,p.=,ENST00000329322,NM_001005167.1;OR52E6,synonymous_variant,p.=,ENST00000379946,;TRIM5,intron_variant,,ENST00000380027,NM_033093.2;TRIM5,intron_variant,,ENST00000412903,; T ENST00000329322 Transcript synonymous_variant 915/970 915/942 305/313 L ctG/ctA rs540768482,COSM4861479,COSM688227 1 -1 OR52E6 HGNC HGNC:15215 protein_coding YES CCDS53597.1 ENSP00000328878 Q96RD3 A0A126GVK5 UPI00000015AE NM_001005167.1 1/1 hmmpanther:PTHR26450:SF175,hmmpanther:PTHR26450,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 0,1,1 LOW 1 SNV 0,1,1 1 PASS rs540768482 . 0 204 6 0 0 0 0 0 -19.99991 1 1 1 1 0 T 2 4 93 5840983 5840983 C T 1 0 0 0 0 0 0 0 1 11190 813 29 3 3 OR52E6 11 5840983 Silent SNP C C3N-02155_T 793807 5840983 129245639 88 28833 LARGE2 0 . GRCh38 11 45922963 45922963 + Silent SNP C C T rs769760213 C3N-02155_T C3N-02155_N C C c.81C>T p.= p.F27F ENST00000531526 2/14 53 37 16 30 30 0 strelka-mutect LARGE2,splice_region_variant,p.=,ENST00000529052,NM_001300722.1;LARGE2,synonymous_variant,p.=,ENST00000531526,NM_152312.4;LARGE2,synonymous_variant,p.=,ENST00000325468,;LARGE2,synonymous_variant,p.=,ENST00000401752,NM_001300721.1;PEX16,upstream_gene_variant,,ENST00000532681,;PEX16,upstream_gene_variant,,ENST00000378750,NM_004813.2;PEX16,upstream_gene_variant,,ENST00000525192,;LARGE2,upstream_gene_variant,,ENST00000534410,;LARGE2,upstream_gene_variant,,ENST00000528236,;LARGE2,upstream_gene_variant,,ENST00000530437,;PEX16,upstream_gene_variant,,ENST00000528674,;PEX16,upstream_gene_variant,,ENST00000529030,;LARGE2,upstream_gene_variant,,ENST00000414027,;LARGE2,upstream_gene_variant,,ENST00000525609,; T ENST00000531526 Transcript synonymous_variant 192/2528 81/2166 27/721 F ttC/ttT rs769760213 1 1 LARGE2 HGNC HGNC:16522 protein_coding YES CCDS31473.1 ENSP00000432869 Q8N3Y3 UPI000004B639 NM_152312.4 2/14 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS rs769760213 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 45922963 45922963 C T 1 0 0 0 0 0 0 0 1 8538 883 31 1 1 LARGE2 11 45922963 Silent SNP C C3N-02155_T 40081980 45922963 89163659 89 28834 OR1S2 0 . GRCh38 11 58203945 58203945 + Silent SNP T T A novel C3N-02155_T C3N-02155_N T T c.237A>T p.= p.L79L ENST00000302592 1/1 538 454 84 357 357 0 strelka-varscan-mutect OR1S2,synonymous_variant,p.=,ENST00000302592,NM_001004459.1; A ENST00000302592 Transcript synonymous_variant 237/980 237/978 79/325 L ctA/ctT 1 -1 OR1S2 HGNC HGNC:15141 protein_coding YES CCDS31545.1 ENSP00000305469 Q8NGQ3 UPI0000041D68 NM_001004459.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF180,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 58203945 58203945 T A 1 0 0 0 0 0 0 0 1 11050 1393 49 4 4 OR1S2 11 58203945 Silent SNP T C3N-02155_T 12280982 58203945 76882677 90 28835 GLYATL1P3 0 . GRCh38 11 59094418 59094431 + Frame_Shift_Del DEL CTGGTAAATGACAA CTGGTAAATGACAA - novel C3N-02155_T C3N-02155_N CTGGTAAATGACAA CTGGTAAATGACAA c.545_558delTAAATGACAACTGG p.Val182GlufsTer6 p.V182Efs*6 ENST00000527482 5/5 56 46 10 49 49 0 sindel-varindel GLYATL1P3,frameshift_variant,p.Val182GlufsTer6,ENST00000527482,; - ENST00000527482 Transcript frameshift_variant 541-554/909 541-554/909 181-185/302 LVNDN/X CTGGTAAATGACAAc/c 1 1 GLYATL1P3 HGNC HGNC:37865 protein_coding YES ENSP00000488958 A0A0U1RQE8 UPI00000492E2 5/5 Gene3D:3.40.630.30,Pfam_domain:PF06021,hmmpanther:PTHR15298,hmmpanther:PTHR15298:SF7,Superfamily_domains:SSF55729 HIGH 1 deletion 5 4 1 PASS . . 0 205 5 0 0 0 0 0 -19.99982 1 1 1 1 0 - 7 5 93 59094418 59094418 CTGGTAAATGACAA - 1 0 1 0 1 0 0 0 0 6358 796 28 0 0 GLYATL1P3 11 59094418 Frame_Shift_Del DEL CTGGTAAATGACAA C3N-02155_T 890473 59094418 75992204 91 28836 FCHSD2 0 . GRCh38 11 72842707 72842707 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.1840G>A p.Gly614Arg p.G614R ENST00000409418 17/20 659 561 98 529 529 0 strelka-varscan-mutect FCHSD2,missense_variant,p.Gly638Arg,ENST00000409314,;FCHSD2,missense_variant,p.Gly558Arg,ENST00000311172,;FCHSD2,missense_variant,p.Gly614Arg,ENST00000409418,NM_014824.2;FCHSD2,missense_variant,p.Gly478Arg,ENST00000458644,;ATG16L2,3_prime_UTR_variant,,ENST00000534905,;FCHSD2,intron_variant,,ENST00000409263,;FCHSD2,downstream_gene_variant,,ENST00000409853,;FCHSD2,downstream_gene_variant,,ENST00000432043,; T ENST00000409418 Transcript missense_variant 2224/3154 1840/2223 614/740 G/R Ggg/Agg 1 -1 FCHSD2 HGNC HGNC:29114 protein_coding YES CCDS8218.2 ENSP00000386722 O94868 UPI0000251F08 NM_014824.2 deleterious(0.02) 17/20 PROSITE_profiles:PS50002,hmmpanther:PTHR15735:SF11,hmmpanther:PTHR15735,Gene3D:2.30.30.40,Pfam_domain:PF14604,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 72842707 72842707 C T 1 0 0 0 0 1 0 0 0 5652 594 21 3 3 FCHSD2 11 72842707 Missense_Mutation SNP C C3N-02155_T 13748289 72842707 62243915 92 28837 MRPL48 0 . GRCh38 11 73844852 73844852 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.247G>T p.Gly83Trp p.G83W ENST00000310614 5/8 354 300 54 262 262 0 strelka-varscan-mutect MRPL48,missense_variant,p.Gly83Trp,ENST00000310614,NM_016055.5;MRPL48,5_prime_UTR_variant,,ENST00000314282,;MRPL48,5_prime_UTR_variant,,ENST00000411840,;MRPL48,5_prime_UTR_variant,,ENST00000398483,;MRPL48,5_prime_UTR_variant,,ENST00000535277,;MRPL48,5_prime_UTR_variant,,ENST00000497094,;MRPL48,5_prime_UTR_variant,,ENST00000537007,;MRPL48,intron_variant,,ENST00000542303,NM_001318500.1;MRPL48,3_prime_UTR_variant,,ENST00000508278,;MRPL48,3_prime_UTR_variant,,ENST00000540162,;MRPL48,3_prime_UTR_variant,,ENST00000544140,;MRPL48,3_prime_UTR_variant,,ENST00000544819,;MRPL48,3_prime_UTR_variant,,ENST00000543058,;MRPL48,non_coding_transcript_exon_variant,,ENST00000543374,; T ENST00000310614 Transcript missense_variant 903/1536 247/639 83/212 G/W Ggg/Tgg 1 1 MRPL48 HGNC HGNC:16653 protein_coding YES CCDS44676.1 ENSP00000308717 Q96GC5 UPI0000073BDE NM_016055.5 deleterious(0) 5/8 hmmpanther:PTHR13473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 73844852 73844852 G T 1 0 0 0 0 1 0 0 0 9787 1232 43 2 2 MRPL48 11 73844852 Missense_Mutation SNP G C3N-02155_T 1002145 73844852 61241770 93 28838 MAP6 0 . GRCh38 11 75587812 75587812 + Silent SNP A A T novel C3N-02155_T C3N-02155_N A A c.1689T>A p.= p.G563G ENST00000304771 4/4 415 361 54 294 294 0 strelka-varscan-mutect MAP6,synonymous_variant,p.=,ENST00000304771,NM_033063.1;MAP6,synonymous_variant,p.=,ENST00000526740,;CTD-2530H12.4,intron_variant,,ENST00000527803,;MAP6,downstream_gene_variant,,ENST00000526689,; T ENST00000304771 Transcript synonymous_variant 2440/3334 1689/2442 563/813 G ggT/ggA 1 -1 MAP6 HGNC HGNC:6868 protein_coding YES CCDS31641.1 ENSP00000307093 Q96JE9 UPI0000251E6A NM_033063.1 4/4 hmmpanther:PTHR14759,hmmpanther:PTHR14759:SF2 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 75587812 75587812 A T 1 0 0 0 0 0 0 0 1 9188 262 10 4 4 MAP6 11 75587812 Silent SNP A C3N-02155_T 1742960 75587812 59498810 94 28839 C11orf54 0 . GRCh38 11 93755240 93755240 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.361C>T p.His121Tyr p.H121Y ENST00000331239 6/9 217 188 29 235 234 1 strelka-varscan-mutect C11orf54,missense_variant,p.His121Tyr,ENST00000528288,NM_014039.3;C11orf54,missense_variant,p.His121Tyr,ENST00000331239,NM_001286068.1,NM_001286069.1;C11orf54,missense_variant,p.His102Tyr,ENST00000540113,NM_001286070.1;C11orf54,missense_variant,p.His121Tyr,ENST00000528099,NM_001286067.1;C11orf54,missense_variant,p.His121Tyr,ENST00000354421,;C11orf54,missense_variant,p.His121Tyr,ENST00000526335,;C11orf54,missense_variant,p.His121Tyr,ENST00000527363,;C11orf54,missense_variant,p.His10Tyr,ENST00000533154,;C11orf54,missense_variant,p.His102Tyr,ENST00000530620,;C11orf54,intron_variant,,ENST00000617482,NM_001286071.1;C11orf54,intron_variant,,ENST00000531650,;TAF1D,intron_variant,,ENST00000527690,;C11orf54,downstream_gene_variant,,ENST00000533585,;C11orf54,downstream_gene_variant,,ENST00000527003,;C11orf54,downstream_gene_variant,,ENST00000530279,; T ENST00000331239 Transcript missense_variant 540/2522 361/948 121/315 H/Y Cac/Tac 1 1 C11orf54 HGNC HGNC:30204 protein_coding YES CCDS66204.1 ENSP00000331209 Q9H0W9 A0A024R396 UPI00000498C8 NM_001286068.1,NM_001286069.1 tolerated(0.09) 6/9 Pfam_domain:PF08925,hmmpanther:PTHR13204,SMART_domains:SM01168,Superfamily_domains:SSF117856 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 93755240 93755240 C T 1 0 0 0 0 1 0 0 0 1787 478 17 3 3 C11orf54 11 93755240 Missense_Mutation SNP C C3N-02155_T 18167428 93755240 41331382 95 28840 KRT80 0 . GRCh38 12 52191612 52191612 + Silent SNP T T A C3N-02155_T C3N-02155_N T T c.291A>T p.= p.L97L ENST00000394815 1/9 112 93 19 69 69 0 strelka-varscan-mutect KRT80,synonymous_variant,p.=,ENST00000313234,NM_001081492.1;KRT80,synonymous_variant,p.=,ENST00000394815,NM_182507.2; A ENST00000394815 Transcript synonymous_variant 389/3859 291/1359 97/452 L ctA/ctT COSM5470041,COSM5470042 1 -1 KRT80 HGNC HGNC:27056 protein_coding YES CCDS8821.2 ENSP00000378292 Q6KB66 UPI0000160118 NM_182507.2 1/9 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF185,SMART_domains:SM01391,Superfamily_domains:SSF64593 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 52191612 52191612 T A 1 0 0 0 0 0 0 0 1 8376 1741 61 4 4 KRT80 12 52191612 Silent SNP T C3N-02155_T 52191612 81083697 96 28841 LRP1 0 . GRCh38 12 57179876 57179876 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.5061C>T p.= p.A1687A ENST00000243077 30/89 286 252 34 253 253 0 strelka-varscan-mutect LRP1,synonymous_variant,p.=,ENST00000243077,NM_002332.2; T ENST00000243077 Transcript synonymous_variant 5527/14897 5061/13635 1687/4544 A gcC/gcT 1 1 LRP1 HGNC HGNC:6692 protein_coding YES CCDS8932.1 ENSP00000243077 Q07954 UPI00001B044F NM_002332.2 30/89 Gene3D:2.120.10.30,PROSITE_profiles:PS51120,SMART_domains:SM00135,Superfamily_domains:SSF63825 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 57179876 57179876 C T 1 0 0 0 0 0 0 0 1 8846 610 22 3 3 LRP1 12 57179876 Silent SNP C C3N-02155_T 4988264 57179876 76095433 97 28842 TSPAN19 0 . GRCh38 12 85017558 85017558 + Silent SNP C C T C3N-02155_T C3N-02155_N C C c.492G>A p.= p.K164K ENST00000532498 7/9 282 228 54 211 210 1 strelka-mutect TSPAN19,synonymous_variant,p.=,ENST00000532498,NM_001100917.1;TSPAN19,synonymous_variant,p.=,ENST00000525452,;TSPAN19,non_coding_transcript_exon_variant,,ENST00000547403,;TSPAN19,3_prime_UTR_variant,,ENST00000433494,;TSPAN19,non_coding_transcript_exon_variant,,ENST00000532628,;TSPAN19,downstream_gene_variant,,ENST00000552392,;TSPAN19,upstream_gene_variant,,ENST00000529820,; T ENST00000532498 Transcript synonymous_variant 573/998 492/747 164/248 K aaG/aaA COSM944011 1 -1 TSPAN19 HGNC HGNC:31886 protein_coding YES CCDS44949.1 ENSP00000433816 P0C672 UPI000003F7BD NM_001100917.1 7/9 hmmpanther:PTHR19282:SF211,hmmpanther:PTHR19282,PIRSF_domain:PIRSF002419,Pfam_domain:PF00335,Superfamily_domains:0037997 1 LOW 1 SNV 5 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 85017558 85017558 C T 1 0 0 0 0 0 0 0 1 17148 912 32 3 3 TSPAN19 12 85017558 Silent SNP C C3N-02155_T 27837682 85017558 48257751 98 28843 MED13L 0 . GRCh38 12 116008728 116008728 + Missense_Mutation SNP T T G novel C3N-02155_T C3N-02155_N T T c.1685A>C p.Gln562Pro p.Q562P ENST00000281928 10/31 380 318 62 250 250 0 strelka-varscan-mutect MED13L,missense_variant,p.Gln562Pro,ENST00000281928,NM_015335.4;MED13L,non_coding_transcript_exon_variant,,ENST00000549755,; G ENST00000281928 Transcript missense_variant 1892/14234 1685/6633 562/2210 Q/P cAg/cCg 1 -1 MED13L HGNC HGNC:22962 protein_coding YES CCDS9177.1 ENSP00000281928 Q71F56 UPI0000241C1E NM_015335.4 tolerated(0.19) 10/31 hmmpanther:PTHR10791,hmmpanther:PTHR10791:SF64,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 116008728 116008728 T G 1 0 0 0 0 1 0 0 0 9370 1580 55 5 5 MED13L 12 116008728 Missense_Mutation SNP T C3N-02155_T 30991170 116008728 17266581 99 28844 GCN1 0 . GRCh38 12 120157859 120157859 + Missense_Mutation SNP C C A rs372573006 C3N-02155_T C3N-02155_N C C c.3077G>T p.Arg1026Leu p.R1026L ENST00000300648 26/58 108 86 22 75 74 1 strelka-varscan-mutect GCN1,missense_variant,p.Arg1026Leu,ENST00000300648,NM_006836.1;MIR4498,upstream_gene_variant,,ENST00000577599,;GCN1,downstream_gene_variant,,ENST00000550471,;GCN1,downstream_gene_variant,,ENST00000547369,;GCN1,upstream_gene_variant,,ENST00000551920,;GCN1,upstream_gene_variant,,ENST00000548132,; A ENST00000300648 Transcript missense_variant 3090/8675 3077/8016 1026/2671 R/L cGg/cTg rs372573006,COSM3687992 1 -1 GCN1 HGNC HGNC:4199 protein_coding YES CCDS41847.1 ENSP00000300648 Q92616 UPI0000451CA7 NM_006836.1 tolerated(0.47) 26/58 Gene3D:1.25.10.10,hmmpanther:PTHR23346,hmmpanther:PTHR23346:SF7,Superfamily_domains:SSF48371 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs372573006 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 120157859 120157859 C A 1 0 0 0 0 1 0 0 0 6169 652 23 1 1 GCN1 12 120157859 Missense_Mutation SNP C C3N-02155_T 4149131 120157859 13117450 100 28845 HPD 0 . GRCh38 12 121857788 121857788 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.62C>G p.Ser21Cys p.S21C ENST00000289004 3/14 778 622 156 538 538 0 strelka-varscan-mutect HPD,missense_variant,p.Ser21Cys,ENST00000289004,NM_002150.2;HPD,5_prime_UTR_variant,,ENST00000543163,NM_001171993.1;RP11-7M8.2,downstream_gene_variant,,ENST00000543848,;HPD,non_coding_transcript_exon_variant,,ENST00000535114,;HPD,upstream_gene_variant,,ENST00000542159,; C ENST00000289004 Transcript missense_variant 98/1419 62/1182 21/393 S/C tCt/tGt 1 -1 HPD HGNC HGNC:5147 protein_coding YES CCDS9224.1 ENSP00000289004 A0A0B4J1R4 UPI0000366920 NM_002150.2 deleterious(0) 3/14 Gene3D:3.10.180.10,Pfam_domain:PF00903,PIRSF_domain:PIRSF009283,hmmpanther:PTHR11959,hmmpanther:PTHR11959:SF9,Superfamily_domains:SSF54593,TIGRFAM_domain:TIGR01263 MODERATE 1 SNV 1 1 PASS rs1390934610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 121857788 121857788 G C 1 0 0 0 0 1 0 0 0 7226 942 33 4 4 HPD 12 121857788 Missense_Mutation SNP G C3N-02155_T 1699929 121857788 11417521 101 28846 DNAH10 0 . GRCh38 12 123924364 123924364 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.11344G>A p.Glu3782Lys p.E3782K ENST00000638045 66/78 229 206 23 196 196 0 strelka-varscan-mutect DNAH10,missense_variant,p.Glu3843Lys,ENST00000409039,;DNAH10,missense_variant,p.Glu3782Lys,ENST00000638045,NM_207437.3;DNAH10OS,downstream_gene_variant,,ENST00000514254,;RP11-380L11.4,downstream_gene_variant,,ENST00000602952,;CCDC92,intron_variant,,ENST00000544798,;CCDC92,intron_variant,,ENST00000542348,;DNAH10,upstream_gene_variant,,ENST00000492261,;DNAH10,upstream_gene_variant,,ENST00000545078,; A ENST00000638045 Transcript missense_variant 11369/13678 11344/13416 3782/4471 E/K Gaa/Aaa 1 1 DNAH10 HGNC HGNC:2941 protein_coding YES CCDS9255.2 ENSP00000489675 UPI00014F7B89 NM_207437.3 tolerated(0.26) 66/78 hmmpanther:PTHR10676:SF135,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 123924364 123924364 G A 1 0 0 0 0 1 0 0 0 4411 943 33 3 3 DNAH10 12 123924364 Missense_Mutation SNP G C3N-02155_T 2066576 123924364 9350945 102 28847 BRCA2 0 . GRCh38 13 32341173 32341173 + Missense_Mutation SNP G G A rs587782174 C3N-02155_T C3N-02155_N G G c.6818G>A p.Arg2273Lys p.R2273K ENST00000380152 11/27 179 128 51 251 251 0 strelka-varscan-mutect BRCA2,missense_variant,p.Arg2273Lys,ENST00000380152,;BRCA2,missense_variant,p.Arg2273Lys,ENST00000544455,NM_000059.3;BRCA2,non_coding_transcript_exon_variant,,ENST00000614259,; A ENST00000380152 Transcript missense_variant 7051/11986 6818/10257 2273/3418 R/K aGa/aAa rs587782174 1 1 BRCA2 HGNC HGNC:1101 protein_coding YES CCDS9344.1 ENSP00000369497 P51587 UPI00001FCBCC tolerated(0.07) 11/27 hmmpanther:PTHR11289,hmmpanther:PTHR11289:SF0,PIRSF_domain:PIRSF002397 uncertain_significance MODERATE 1 SNV 5 1 1 PASS rs587782174 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 32341173 32341173 G A 1 0 0 0 0 1 0 0 0 1669 942 33 3 3 BRCA2 13 32341173 Missense_Mutation SNP G C3N-02155_T 32341173 82023155 103 28848 ARL11 0 . GRCh38 13 49630459 49630459 + Silent SNP G G A novel C3N-02155_T C3N-02155_N G G c.12G>A p.= p.V4V ENST00000282026 2/2 113 84 29 87 87 0 strelka-varscan-mutect ARL11,synonymous_variant,p.=,ENST00000282026,NM_138450.5;ARL11,intron_variant,,ENST00000490932,; A ENST00000282026 Transcript synonymous_variant 347/3760 12/591 4/196 V gtG/gtA 1 1 ARL11 HGNC HGNC:24046 protein_coding YES CCDS9419.1 ENSP00000282026 Q969Q4 UPI0000073EDE NM_138450.5 2/2 hmmpanther:PTHR11711,hmmpanther:PTHR11711:SF172,SMART_domains:SM00177,SMART_domains:SM00178 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 49630459 49630459 G A 1 0 0 0 0 0 0 0 1 1064 1277 45 3 3 ARL11 13 49630459 Silent SNP G C3N-02155_T 17289286 49630459 64733869 104 28849 KCNRG 0 . GRCh38 13 50020445 50020445 + Frame_Shift_Del DEL A A - novel C3N-02155_T C3N-02155_N A A c.812delA p.Lys271ArgfsTer27 p.K271Rfs*27 ENST00000312942 2/2 144 116 28 159 159 0 sindel-varindel-pindel KCNRG,frameshift_variant,p.Lys271ArgfsTer27,ENST00000312942,NM_173605.1;KCNRG,3_prime_UTR_variant,,ENST00000360473,NM_199464.2;TRIM13,downstream_gene_variant,,ENST00000378182,NM_213590.2,NM_052811.3;DLEU2,intron_variant,,ENST00000621282,;TRIM13,non_coding_transcript_exon_variant,,ENST00000478111,;TRIM13,non_coding_transcript_exon_variant,,ENST00000474805,; - ENST00000312942 Transcript frameshift_variant 1050/1527 810/819 270/272 I/X atA/at 1 1 KCNRG HGNC HGNC:18893 protein_coding YES CCDS9424.1 ENSP00000324191 Q8N5I3 UPI000000D8AF NM_173605.1 2/2 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 93 50020445 50020445 A - 1 0 1 0 1 0 0 0 0 8003 352 13 0 0 KCNRG 13 50020445 Frame_Shift_Del DEL A C3N-02155_T 389986 50020445 64343883 105 28850 OLFM4 0 . GRCh38 13 53043199 53043199 + Missense_Mutation SNP A A T novel C3N-02155_T C3N-02155_N A A c.665A>T p.Lys222Met p.K222M ENST00000219022 4/5 194 164 30 197 197 0 strelka-varscan-mutect OLFM4,missense_variant,p.Lys222Met,ENST00000219022,NM_006418.4; T ENST00000219022 Transcript missense_variant 743/2897 665/1533 222/510 K/M aAg/aTg 1 1 OLFM4 HGNC HGNC:17190 protein_coding YES CCDS9440.1 ENSP00000219022 Q6UX06 A0A024QZ95 UPI00000359F0 NM_006418.4 deleterious(0) 4/5 hmmpanther:PTHR23192,hmmpanther:PTHR23192:SF7 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 53043199 53043199 A T 1 0 0 0 0 1 0 0 0 10930 72 3 4 4 OLFM4 13 53043199 Missense_Mutation SNP A C3N-02155_T 3022754 53043199 61321129 106 28851 CCDC168 0 . GRCh38 13 102737692 102737692 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.13005G>T p.Met4335Ile p.M4335I ENST00000322527 4/4 243 197 46 275 275 0 strelka-varscan-mutect CCDC168,missense_variant,p.Met4335Ile,ENST00000322527,NM_001146197.1; A ENST00000322527 Transcript missense_variant 13143/21466 13005/21246 4335/7081 M/I atG/atT 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 tolerated(0.24) 4/4 Pfam_domain:PF15804 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 102737692 102737692 C A 1 0 0 0 0 1 0 0 0 2484 710 25 2 2 CCDC168 13 102737692 Missense_Mutation SNP C C3N-02155_T 49694493 102737692 11626636 107 28852 OSGEP 0 . GRCh38 14 20448755 20448755 + Missense_Mutation SNP G G A C3N-02155_T C3N-02155_N G G c.614C>T p.Ser205Leu p.S205L ENST00000206542 6/11 685 637 48 203 202 1 strelka-varscan-mutect OSGEP,missense_variant,p.Ser205Leu,ENST00000206542,NM_017807.3;OSGEP,downstream_gene_variant,,ENST00000553640,;RP11-203M5.7,upstream_gene_variant,,ENST00000555435,;OSGEP,downstream_gene_variant,,ENST00000556252,;OSGEP,downstream_gene_variant,,ENST00000554699,;OSGEP,3_prime_UTR_variant,,ENST00000555223,;OSGEP,non_coding_transcript_exon_variant,,ENST00000555656,;OSGEP,non_coding_transcript_exon_variant,,ENST00000556124,;OSGEP,non_coding_transcript_exon_variant,,ENST00000554249,;OSGEP,non_coding_transcript_exon_variant,,ENST00000554915,;OSGEP,non_coding_transcript_exon_variant,,ENST00000555785,;OSGEP,downstream_gene_variant,,ENST00000556439,;OSGEP,upstream_gene_variant,,ENST00000553292,; A ENST00000206542 Transcript missense_variant 1036/2002 614/1008 205/335 S/L tCa/tTa COSM1300475 1 -1 OSGEP HGNC HGNC:18028 protein_coding YES CCDS9549.1 ENSP00000206542 Q9NPF4 UPI0000033CBD NM_017807.3 deleterious(0) 6/11 HAMAP:MF_01446,Pfam_domain:PF00814,hmmpanther:PTHR11735,hmmpanther:PTHR11735:SF14,Superfamily_domains:SSF53067,TIGRFAM_domain:TIGR00329 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 20448755 20448755 G A 1 0 0 0 0 1 0 0 0 11354 1294 45 3 3 OSGEP 14 20448755 Missense_Mutation SNP G C3N-02155_T 20448755 86594963 108 28853 FAM179B 0 . GRCh38 14 45073496 45073496 + Nonsense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.5257C>T p.Gln1753Ter p.Q1753* ENST00000361462 20/20 654 512 142 312 311 1 strelka-varscan-mutect FAM179B,stop_gained,p.Gln1753Ter,ENST00000361462,NM_001308120.1;FAM179B,stop_gained,p.Gln1700Ter,ENST00000361577,NM_015091.2;FAM179B,stop_gained,p.Gln135Ter,ENST00000556823,;FAM179B,3_prime_UTR_variant,,ENST00000557423,; T ENST00000361462 Transcript stop_gained 5440/6375 5257/5322 1753/1773 Q/* Caa/Taa 1 1 FAM179B HGNC HGNC:19959 protein_coding YES CCDS76676.1 ENSP00000354917 G3XAE9 UPI000022974E NM_001308120.1 20/20 hmmpanther:PTHR21567,hmmpanther:PTHR21567:SF6,SMART_domains:SM01349 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 93 45073496 45073496 C T 1 0 0 0 0 0 1 0 0 5351 827 29 3 3 FAM179B 14 45073496 Nonsense_Mutation SNP C C3N-02155_T 24624741 45073496 61970222 109 28854 ATG2B 0 . GRCh38 14 96315560 96315560 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.3385C>G p.Pro1129Ala p.P1129A ENST00000359933 22/42 362 320 42 198 198 0 strelka-varscan-mutect ATG2B,missense_variant,p.Pro1129Ala,ENST00000359933,NM_018036.5;ATG2B,upstream_gene_variant,,ENST00000261834,;ATG2B,downstream_gene_variant,,ENST00000473234,;ATG2B,downstream_gene_variant,,ENST00000488421,; C ENST00000359933 Transcript missense_variant 4279/13684 3385/6237 1129/2078 P/A Ccg/Gcg 1 -1 ATG2B HGNC HGNC:20187 protein_coding YES CCDS9944.2 ENSP00000353010 Q96BY7 UPI000155D51F NM_018036.5 tolerated(0.14) 22/42 hmmpanther:PTHR13190,hmmpanther:PTHR13190:SF20 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 3 2 93 96315560 96315560 G C 1 0 0 0 0 1 0 0 0 1246 1232 43 4 4 ATG2B 14 96315560 Missense_Mutation SNP G C3N-02155_T 51242064 96315560 10728158 110 28855 ATP10A 0 . GRCh38 15 25862959 25862959 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.138G>A p.= p.K46K ENST00000356865 1/21 151 121 30 60 60 0 strelka-varscan-mutect ATP10A,synonymous_variant,p.=,ENST00000356865,NM_024490.3;ATP10A,synonymous_variant,p.=,ENST00000619904,;RP11-2C7.1,upstream_gene_variant,,ENST00000557558,;ATP10A,upstream_gene_variant,,ENST00000553577,;ATP10A,synonymous_variant,p.=,ENST00000555815,;ATP10A,synonymous_variant,p.=,ENST00000389967,; T ENST00000356865 Transcript synonymous_variant 250/6680 138/4500 46/1499 K aaG/aaA 1 -1 ATP10A HGNC HGNC:13542 protein_coding YES CCDS32178.1 ENSP00000349325 O60312 UPI0000124FAB NM_024490.3 1/21 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF81,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 201 8 0 0 0 0 0 -20 0.9999989 1 1 1 0 T 2 4 93 25862959 25862959 C T 1 0 0 0 0 0 0 0 1 1268 680 24 3 3 ATP10A 15 25862959 Silent SNP C C3N-02155_T 25862959 76128230 111 28856 MTMR10 0 . GRCh38 15 30941917 30941917 + Silent SNP C C T novel C3N-02155_T C3N-02155_N C C c.1887G>A p.= p.Q629Q ENST00000435680 16/16 544 437 107 415 415 0 strelka-varscan-mutect MTMR10,synonymous_variant,p.=,ENST00000435680,NM_017762.2;FAN1,3_prime_UTR_variant,,ENST00000362065,NM_014967.4;MTMR10,downstream_gene_variant,,ENST00000563714,;MTMR10,downstream_gene_variant,,ENST00000566981,;MTMR10,3_prime_UTR_variant,,ENST00000568604,;FAN1,3_prime_UTR_variant,,ENST00000565280,;MTMR10,3_prime_UTR_variant,,ENST00000567567,;MTMR10,non_coding_transcript_exon_variant,,ENST00000566338,;MTMR10,intron_variant,,ENST00000568547,; T ENST00000435680 Transcript synonymous_variant 1985/4961 1887/2334 629/777 Q caG/caA 1 -1 MTMR10 HGNC HGNC:25999 protein_coding YES CCDS45204.1 ENSP00000402537 Q9NXD2 X5D963 UPI00001FE130 NM_017762.2 16/16 PROSITE_profiles:PS51339,hmmpanther:PTHR10807,hmmpanther:PTHR10807:SF39,Pfam_domain:PF12578 LOW 1 SNV 1 1 PASS rs1400493880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 30941917 30941917 C T 1 0 0 0 0 0 0 0 1 9927 564 20 3 3 MTMR10 15 30941917 Silent SNP C C3N-02155_T 5078958 30941917 71049272 112 28857 RYR3 0 . GRCh38 15 33662266 33662266 + Frame_Shift_Del DEL C C - rs548311351 C3N-02155_T C3N-02155_N C C c.4738delC p.Leu1580CysfsTer44 p.L1580Cfs*44 ENST00000634891 35/104 306 267 39 220 220 0 sindel-varindel-pindel RYR3,frameshift_variant,p.Leu1580CysfsTer44,ENST00000634891,NM_001036.4;RYR3,frameshift_variant,p.Leu1580CysfsTer44,ENST00000622037,;RYR3,frameshift_variant,p.Leu1580CysfsTer44,ENST00000415757,NM_001243996.2;RYR3,frameshift_variant,p.Leu1580CysfsTer44,ENST00000389232,;RYR3,frameshift_variant,p.Leu1580CysfsTer44,ENST00000634418,; - ENST00000634891 Transcript frameshift_variant 4837/15591 4736/14613 1579/4870 A/X gCc/gc rs548311351,COSM5148421 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 35/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 0,1 HIGH 1 deletion 1 2 0,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 93 33662266 33662266 C - 1 0 1 0 1 0 0 0 0 14030 739 26 0 0 RYR3 15 33662266 Frame_Shift_Del DEL C C3N-02155_T 2720349 33662266 68328923 113 28858 ACTC1 0 . GRCh38 15 34790412 34790412 + Nonstop_Mutation SNP T T A novel C3N-02155_T C3N-02155_N T T c.1134A>T p.Ter378TyrextTer46 p.*378Yext*46 ENST00000290378 7/7 550 454 96 403 403 0 strelka-varscan-mutect ACTC1,stop_lost,p.Ter378TyrextTer46,ENST00000290378,NM_005159.4;RP11-814P5.1,intron_variant,,ENST00000503496,;RP11-814P5.1,downstream_gene_variant,,ENST00000558707,;ACTC1,downstream_gene_variant,,ENST00000557860,;ACTC1,downstream_gene_variant,,ENST00000560563,; A ENST00000290378 Transcript stop_lost 1790/4106 1134/1134 378/377 */Y taA/taT 1 -1 ACTC1 HGNC HGNC:143 protein_coding YES CCDS10041.1 ENSP00000290378 P68032 UPI0000003F15 NM_005159.4 7/7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 93 34790412 34790412 T A 1 0 0 0 0 0 0 0 0 238 1616 56 4 4 ACTC1 15 34790412 Nonstop_Mutation SNP T C3N-02155_T 1128146 34790412 67200777 114 28859 C15orf53 0 . GRCh38 15 38698397 38698397 + Missense_Mutation SNP G G T rs143270407 C3N-02155_T C3N-02155_N G G c.392G>T p.Arg131Leu p.R131L ENST00000318792 2/2 351 293 58 257 256 1 strelka-varscan-mutect C15orf53,missense_variant,p.Arg131Leu,ENST00000318792,NM_207444.2; T ENST00000318792 Transcript missense_variant 402/2043 392/540 131/179 R/L cGc/cTc rs143270407,COSM4054239 1 1 C15orf53 HGNC HGNC:33796 protein_coding YES CCDS10048.1 ENSP00000325144 Q8NAA6 UPI000007303A NM_207444.2 tolerated_low_confidence(0.46) 2/2 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs143270407 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 38698397 38698397 G T 1 0 0 0 0 1 0 0 0 1848 1087 38 1 1 C15orf53 15 38698397 Missense_Mutation SNP G C3N-02155_T 3907985 38698397 63292792 115 28860 DMXL2 0 . GRCh38 15 51491588 51491588 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.4943G>T p.Cys1648Phe p.C1648F ENST00000543779 20/43 442 374 68 331 331 0 strelka-varscan-mutect DMXL2,missense_variant,p.Cys1648Phe,ENST00000251076,NM_015263.3;DMXL2,missense_variant,p.Cys1648Phe,ENST00000543779,NM_001174116.1;DMXL2,missense_variant,p.Cys1012Phe,ENST00000449909,NM_001174117.1;RP11-707P17.1,intron_variant,,ENST00000561007,; A ENST00000543779 Transcript missense_variant 5033/10400 4943/9114 1648/3037 C/F tGc/tTc 1 -1 DMXL2 HGNC HGNC:2938 protein_coding YES CCDS53946.1 ENSP00000441858 Q8TDJ6 UPI00001FE4C2 NM_001174116.1 deleterious(0) 20/43 Pfam_domain:PF12234,hmmpanther:PTHR13950,hmmpanther:PTHR13950:SF11 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 51491588 51491588 C A 1 0 0 0 0 1 0 0 0 4404 710 25 2 2 DMXL2 15 51491588 Missense_Mutation SNP C C3N-02155_T 12793191 51491588 50499601 116 28861 FURIN 0 . GRCh38 15 90881347 90881347 + Silent SNP C C T rs767680799 C3N-02155_T C3N-02155_N C C c.1854C>T p.= p.F618F ENST00000618099 16/16 171 132 39 134 134 0 strelka-varscan-mutect FURIN,synonymous_variant,p.=,ENST00000618099,NM_001289824.1;FURIN,synonymous_variant,p.=,ENST00000268171,NM_002569.3;FURIN,synonymous_variant,p.=,ENST00000610579,NM_001289823.1;FES,upstream_gene_variant,,ENST00000328850,NM_002005.3;FES,upstream_gene_variant,,ENST00000414248,NM_001143785.1;FES,upstream_gene_variant,,ENST00000394300,NM_001143783.1;FES,upstream_gene_variant,,ENST00000444422,NM_001143784.1;FES,upstream_gene_variant,,ENST00000394302,;FES,upstream_gene_variant,,ENST00000452243,;FES,upstream_gene_variant,,ENST00000559355,;FURIN,downstream_gene_variant,,ENST00000560824,;FES,upstream_gene_variant,,ENST00000443697,;FES,upstream_gene_variant,,ENST00000416779,;FES,upstream_gene_variant,,ENST00000464684,;FES,upstream_gene_variant,,ENST00000470152,;FURIN,downstream_gene_variant,,ENST00000558794,;FES,upstream_gene_variant,,ENST00000481665,;FES,upstream_gene_variant,,ENST00000497945,;FURIN,downstream_gene_variant,,ENST00000560018,; T ENST00000618099 Transcript synonymous_variant 2234/4345 1854/2385 618/794 F ttC/ttT rs767680799,COSM3505432 1 1 FURIN HGNC HGNC:8568 protein_coding YES CCDS10364.1 ENSP00000483552 P09958 A0A024RC70 UPI0000000CC7 NM_001289824.1 16/16 hmmpanther:PTHR10795:SF379,hmmpanther:PTHR10795,Gene3D:2.10.220.10,SMART_domains:SM00261,Superfamily_domains:SSF57184 0,1 LOW SNV 5 0,1 1 PASS rs767680799 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 93 90881347 90881347 C T 1 0 0 0 0 0 0 0 1 5971 883 31 1 1 FURIN 15 90881347 Silent SNP C C3N-02155_T 39389759 90881347 11109842 117 28862 ATF7IP2 0 . GRCh38 16 10430957 10430957 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.337G>C p.Val113Leu p.V113L ENST00000396560 3/12 429 364 65 356 356 0 strelka-varscan-mutect ATF7IP2,missense_variant,p.Val113Leu,ENST00000396560,NM_024997.3;ATF7IP2,missense_variant,p.Val113Leu,ENST00000396559,NM_001256160.1;ATF7IP2,missense_variant,p.Val113Leu,ENST00000356427,;ATF7IP2,missense_variant,p.Val113Leu,ENST00000324570,;ATF7IP2,intron_variant,,ENST00000543967,;ATF7IP2,downstream_gene_variant,,ENST00000562527,;ATF7IP2,downstream_gene_variant,,ENST00000569939,;ATF7IP2,downstream_gene_variant,,ENST00000569900,;ATF7IP2,downstream_gene_variant,,ENST00000562102,;ATF7IP2,downstream_gene_variant,,ENST00000561932,;ATF7IP2,missense_variant,p.Val113Leu,ENST00000568027,;ATF7IP2,missense_variant,p.Val113Leu,ENST00000535850,; C ENST00000396560 Transcript missense_variant 564/3665 337/2049 113/682 V/L Gtt/Ctt 1 1 ATF7IP2 HGNC HGNC:20397 protein_coding YES CCDS10540.1 ENSP00000379808 Q5U623 UPI00001FEDD8 NM_024997.3 tolerated(0.06) 3/12 hmmpanther:PTHR23210,hmmpanther:PTHR23210:SF23 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 10430957 10430957 G C 1 0 0 0 0 1 0 0 0 1237 1377 48 4 4 ATF7IP2 16 10430957 Missense_Mutation SNP G C3N-02155_T 10430957 79907388 118 28863 ITGAD 0 . GRCh38 16 31416221 31416221 + Missense_Mutation SNP C C G C3N-02155_T C3N-02155_N C C c.2292C>G p.Phe764Leu p.F764L ENST00000389202 19/30 122 107 15 110 110 0 strelka-mutect ITGAD,missense_variant,p.Phe764Leu,ENST00000389202,NM_001318185.1,NM_005353.2; G ENST00000389202 Transcript missense_variant 2341/3912 2292/3486 764/1161 F/L ttC/ttG COSM3509227 1 1 ITGAD HGNC HGNC:6146 protein_coding YES CCDS32438.1 ENSP00000373854 Q13349 UPI000004B27A NM_001318185.1,NM_005353.2 deleterious(0) 19/30 Gene3D:1jv2A02,Pfam_domain:PF08441,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF19,Superfamily_domains:SSF69179 1 MODERATE 1 SNV 1 1 1 PASS rs1374291141 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 31416221 31416221 C G 1 0 0 0 0 1 0 0 0 7791 883 31 4 4 ITGAD 16 31416221 Missense_Mutation SNP C C3N-02155_T 20985264 31416221 58922124 119 28864 GPT2 0 . GRCh38 16 46884836 46884836 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.121C>T p.Arg41Cys p.R41C ENST00000340124 2/12 181 151 30 111 111 0 strelka-varscan-mutect GPT2,missense_variant,p.Arg41Cys,ENST00000340124,NM_133443.2;GPT2,5_prime_UTR_variant,,ENST00000440783,NM_001142466.1;GPT2,intron_variant,,ENST00000562132,; T ENST00000340124 Transcript missense_variant 233/3984 121/1572 41/523 R/C Cgc/Tgc 1 1 GPT2 HGNC HGNC:18062 protein_coding YES CCDS10725.1 ENSP00000345282 Q8TD30 A0A024R6R2 UPI000004DBE2 NM_133443.2 tolerated(0.05) 2/12 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999948 1 1 1 0 T 3 4 93 46884836 46884836 C T 1 0 0 0 0 1 0 0 0 6617 782 27 1 1 GPT2 16 46884836 Missense_Mutation SNP C C3N-02155_T 15468615 46884836 43453509 120 28865 MT1G 0 . GRCh38 16 56667233 56667233 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.173G>A p.Cys58Tyr p.C58Y ENST00000568675 2/2 384 321 63 301 301 0 strelka-varscan-mutect MT1G,missense_variant,p.Cys58Tyr,ENST00000568675,;MT1G,intron_variant,,ENST00000444837,NM_005950.2;MT1G,intron_variant,,ENST00000379811,NM_001301267.1;MT1G,intron_variant,,ENST00000569500,;MT1H,upstream_gene_variant,,ENST00000569155,;MT1H,upstream_gene_variant,,ENST00000332374,NM_005951.2; T ENST00000568675 Transcript missense_variant 201/628 173/207 58/68 C/Y tGc/tAc 1 -1 MT1G HGNC HGNC:7399 protein_coding ENSP00000456835 H3BSS0 UPI00024670A3 deleterious_low_confidence(0.04) 2/2 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 56667233 56667233 C T 1 0 0 0 0 1 0 0 0 9885 710 25 3 3 MT1G 16 56667233 Missense_Mutation SNP C C3N-02155_T 9782397 56667233 33671112 121 28866 SPG7 0 . GRCh38 16 89553023 89553023 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.1824G>T p.Gln608His p.Q608H ENST00000268704 14/17 571 476 95 412 412 0 strelka-varscan-mutect SPG7,missense_variant,p.Gln198His,ENST00000620811,;SPG7,missense_variant,p.Gln608His,ENST00000268704,NM_003119.3;SPG7,upstream_gene_variant,,ENST00000566682,;SPG7,upstream_gene_variant,,ENST00000565891,;SPG7,missense_variant,p.Gln123His,ENST00000561911,;SPG7,3_prime_UTR_variant,,ENST00000569820,;SPG7,3_prime_UTR_variant,,ENST00000566221,;SPG7,non_coding_transcript_exon_variant,,ENST00000561702,;SPG7,non_coding_transcript_exon_variant,,ENST00000565370,;SPG7,non_coding_transcript_exon_variant,,ENST00000568205,;SPG7,upstream_gene_variant,,ENST00000569720,;SPG7,downstream_gene_variant,,ENST00000563218,; T ENST00000268704 Transcript missense_variant 1839/3076 1824/2388 608/795 Q/H caG/caT 1 1 SPG7 HGNC HGNC:11237 protein_coding YES CCDS10977.1 ENSP00000268704 Q9UQ90 UPI0000031FAA NM_003119.3 deleterious(0.01) 14/17 HAMAP:MF_01458,hmmpanther:PTHR23076:SF68,hmmpanther:PTHR23076,Pfam_domain:PF01434,TIGRFAM_domain:TIGR01241,Superfamily_domains:SSF140990 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 89553023 89553023 G T 1 0 0 0 0 1 0 0 0 15395 956 33 2 2 SPG7 16 89553023 Missense_Mutation SNP G C3N-02155_T 32885790 89553023 785322 122 28867 KRT10 0 . GRCh38 17 40819067 40819067 + Missense_Mutation SNP C C T rs753205769 C3N-02155_T C3N-02155_N C C c.1468G>A p.Gly490Ser p.G490S ENST00000269576 7/8 343 321 22 220 218 2 varscan-mutect KRT10,missense_variant,p.Gly490Ser,ENST00000269576,NM_000421.3;TMEM99,upstream_gene_variant,,ENST00000622451,NM_001195386.1;TMEM99,upstream_gene_variant,,ENST00000301665,NM_001195387.1,NM_145274.3;TMEM99,upstream_gene_variant,,ENST00000436612,;KRT10,upstream_gene_variant,,ENST00000635956,;TMEM99,upstream_gene_variant,,ENST00000496847,; T ENST00000269576 Transcript missense_variant 1478/2124 1468/1755 490/584 G/S Ggc/Agc rs753205769 1 -1 KRT10 HGNC HGNC:6413 protein_coding YES CCDS11377.1 ENSP00000269576 P13645 UPI000013D842 NM_000421.3 tolerated_low_confidence(0.69) 7/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF137,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs753205769 . 0 97 0 0 0 0 0 113 -12.26056 0 0 1 0 0 T 3 4 93 40819067 40819067 C T 1 0 0 0 0 1 0 0 0 8330 652 23 1 1 KRT10 17 40819067 Missense_Mutation SNP C C3N-02155_T 40819067 42438374 123 28868 P3H4 0 . GRCh38 17 41809746 41809747 + Frame_Shift_Del DEL CA CA - novel C3N-02155_T C3N-02155_N CA CA c.875_876delTG p.Val292GlyfsTer13 p.V292Gfs*13 ENST00000355468 5/9 193 175 18 133 133 0 sindel-pindel P3H4,frameshift_variant,p.Val292GlyfsTer13,ENST00000355468,;P3H4,frameshift_variant,p.Val292GlyfsTer13,ENST00000393928,NM_006455.2;P3H4,intron_variant,,ENST00000592026,;FKBP10,upstream_gene_variant,,ENST00000321562,NM_021939.3;FKBP10,upstream_gene_variant,,ENST00000585664,;FKBP10,upstream_gene_variant,,ENST00000585922,;P3H4,downstream_gene_variant,,ENST00000590496,;FKBP10,upstream_gene_variant,,ENST00000429461,;P3H4,intron_variant,,ENST00000587455,;FKBP10,upstream_gene_variant,,ENST00000489591,;P3H4,upstream_gene_variant,,ENST00000484247,;P3H4,downstream_gene_variant,,ENST00000467164,;P3H4,upstream_gene_variant,,ENST00000465097,; - ENST00000355468 Transcript frameshift_variant 1342-1343/2791 875-876/1314 292/437 V/X gTG/g 1 -1 P3H4 HGNC HGNC:16946 protein_coding YES CCDS11408.1 ENSP00000347649 Q92791 UPI00001302A2 5/9 Gene3D:1.25.40.10,hmmpanther:PTHR13986,hmmpanther:PTHR13986:SF4 HIGH deletion 2 1 PASS . . 0 204 3 2 0 0 0 0 -19.99997 0.9999823 1 1 1 0 - 7 5 93 41809746 41809746 CA - 1 0 1 0 1 0 0 0 0 11432 581 21 0 0 P3H4 17 41809746 Frame_Shift_Del DEL CA C3N-02155_T 990679 41809746 41447695 124 28869 SLC4A1 0 . GRCh38 17 44259903 44259903 + Missense_Mutation SNP C C A C3N-02155_T C3N-02155_N C C c.515G>T p.Gly172Val p.G172V ENST00000262418 7/20 871 742 129 511 511 0 strelka-varscan-mutect SLC4A1,missense_variant,p.Gly172Val,ENST00000262418,NM_000342.3;SLC4A1,missense_variant,p.Gly172Val,ENST00000399246,;SLC4A1,downstream_gene_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; A ENST00000262418 Transcript missense_variant 671/4965 515/2736 172/911 G/V gGt/gTt COSM3190900,COSM706167 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 deleterious(0.03) 7/20 Gene3D:1hynR00,Pfam_domain:PF07565,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1222836115 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 44259903 44259903 C A 1 0 0 0 0 1 0 0 0 14927 507 18 2 2 SLC4A1 17 44259903 Missense_Mutation SNP C C3N-02155_T 2450157 44259903 38997538 125 28870 DBF4B 0 . GRCh38 17 44750642 44750642 + Missense_Mutation SNP G G C rs367600377 C3N-02155_T C3N-02155_N G G c.1237G>C p.Asp413His p.D413H ENST00000315005 14/14 207 183 24 124 124 0 strelka-varscan-mutect DBF4B,missense_variant,p.Asp413His,ENST00000315005,NM_145663.2;DBF4B,missense_variant,p.Asp413His,ENST00000393547,NM_025104.3;DBF4B,downstream_gene_variant,,ENST00000526924,;DBF4B,downstream_gene_variant,,ENST00000527862,; C ENST00000315005 Transcript missense_variant 1375/2997 1237/1848 413/615 D/H Gat/Cat rs367600377,COSM3795676,COSM3795677 1 1 DBF4B HGNC HGNC:17883 protein_coding YES CCDS11485.1 ENSP00000323663 Q8NFT6 UPI00000473C7 NM_145663.2 deleterious_low_confidence(0) 14/14 hmmpanther:PTHR15375:SF24,hmmpanther:PTHR15375 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs367600377 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 44750642 44750642 G C 1 0 0 0 0 1 0 0 0 4049 942 33 4 4 DBF4B 17 44750642 Missense_Mutation SNP G C3N-02155_T 490739 44750642 38506799 126 28871 ANKFN1 0 . GRCh38 17 56440386 56440386 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.979C>A p.Leu327Met p.L327M ENST00000318698 8/17 245 224 21 190 189 1 strelka-varscan-mutect ANKFN1,missense_variant,p.Leu327Met,ENST00000566473,;ANKFN1,missense_variant,p.Leu327Met,ENST00000318698,NM_153228.2;ANKFN1,missense_variant,p.Leu416Met,ENST00000635860,; A ENST00000318698 Transcript missense_variant 1014/2426 979/2292 327/763 L/M Ctg/Atg 1 1 ANKFN1 HGNC HGNC:26766 protein_coding YES CCDS32686.1 ENSP00000321627 Q8N957 UPI000049DE57 NM_153228.2 tolerated(0.23) 8/17 PROSITE_profiles:PS50853,hmmpanther:PTHR21437,hmmpanther:PTHR21437:SF3,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 56440386 56440386 C A 1 0 0 0 0 1 0 0 0 727 912 32 2 2 ANKFN1 17 56440386 Missense_Mutation SNP C C3N-02155_T 11689744 56440386 26817055 127 28872 RPS6KB1 0 . GRCh38 17 59934520 59934520 + Missense_Mutation SNP G G A C3N-02155_T C3N-02155_N G G c.866G>A p.Gly289Glu p.G289E ENST00000225577 9/15 307 266 41 165 165 0 strelka-varscan-mutect RPS6KB1,missense_variant,p.Gly236Glu,ENST00000393021,NM_001272044.1;RPS6KB1,missense_variant,p.Gly289Glu,ENST00000225577,NM_001272060.1,NM_003161.3;RPS6KB1,missense_variant,p.Gly289Glu,ENST00000406116,NM_001272043.1;RPS6KB1,missense_variant,p.Gly266Glu,ENST00000443572,NM_001272042.1;RPS6KB1,3_prime_UTR_variant,,ENST00000472940,;RPS6KB1,non_coding_transcript_exon_variant,,ENST00000590928,;RPS6KB1,non_coding_transcript_exon_variant,,ENST00000587622,;RPS6KB1,downstream_gene_variant,,ENST00000489824,; A ENST00000225577 Transcript missense_variant 887/5375 866/1578 289/525 G/E gGa/gAa COSM32843 1 1 RPS6KB1 HGNC HGNC:10436 protein_coding YES CCDS11621.1 ENSP00000225577 P23443 UPI000013C873 NM_001272060.1,NM_003161.3 deleterious(0) 9/15 PROSITE_profiles:PS50011,hmmpanther:PTHR24351:SF85,hmmpanther:PTHR24351,PIRSF_domain:PIRSF000605,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 1 MODERATE 1 SNV 1 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.999992 1 1 1 0 A 3 1 93 59934520 59934520 G A 1 0 0 0 0 1 0 0 0 13911 1188 41 3 3 RPS6KB1 17 59934520 Missense_Mutation SNP G C3N-02155_T 3494134 59934520 23322921 128 28873 DDX5 0 . GRCh38 17 64502049 64502049 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.1177C>A p.Pro393Thr p.P393T ENST00000225792 11/13 528 478 50 276 275 1 strelka-varscan-mutect DDX5,missense_variant,p.Pro393Thr,ENST00000225792,NM_004396.3;DDX5,missense_variant,p.Pro314Thr,ENST00000450599,;DDX5,missense_variant,p.Pro393Thr,ENST00000578804,;CEP95,upstream_gene_variant,,ENST00000556440,NM_138363.1;CEP95,upstream_gene_variant,,ENST00000553412,;DDX5,downstream_gene_variant,,ENST00000585111,;DDX5,downstream_gene_variant,,ENST00000577922,;CEP95,upstream_gene_variant,,ENST00000581056,;DDX5,downstream_gene_variant,,ENST00000577787,;DDX5,downstream_gene_variant,,ENST00000579996,;DDX5,downstream_gene_variant,,ENST00000584279,;DDX5,downstream_gene_variant,,ENST00000578190,;DDX5,downstream_gene_variant,,ENST00000581697,;DDX5,downstream_gene_variant,,ENST00000581806,;CEP95,upstream_gene_variant,,ENST00000580188,;DDX5,downstream_gene_variant,,ENST00000585060,;DDX5,downstream_gene_variant,,ENST00000583212,;DDX5,downstream_gene_variant,,ENST00000579091,;DDX5,downstream_gene_variant,,ENST00000583239,;DDX5,downstream_gene_variant,,ENST00000630471,;DDX5,upstream_gene_variant,,ENST00000579212,;DDX5,upstream_gene_variant,,ENST00000581130,;DDX5,non_coding_transcript_exon_variant,,ENST00000578491,;DDX5,upstream_gene_variant,,ENST00000580026,;DDX5,downstream_gene_variant,,ENST00000583699,;DDX5,upstream_gene_variant,,ENST00000581237,;DDX5,downstream_gene_variant,,ENST00000584500,;DDX5,3_prime_UTR_variant,,ENST00000540698,;DDX5,3_prime_UTR_variant,,ENST00000581693,;DDX5,non_coding_transcript_exon_variant,,ENST00000581230,;DDX5,non_coding_transcript_exon_variant,,ENST00000585317,;DDX5,non_coding_transcript_exon_variant,,ENST00000579461,;DDX5,non_coding_transcript_exon_variant,,ENST00000578758,;CEP95,upstream_gene_variant,,ENST00000579860,;DDX5,downstream_gene_variant,,ENST00000584549,;DDX5,downstream_gene_variant,,ENST00000583894,;DDX5,downstream_gene_variant,,ENST00000585223,;DDX5,downstream_gene_variant,,ENST00000582326,;DDX5,downstream_gene_variant,,ENST00000578400,;DDX5,downstream_gene_variant,,ENST00000581551,;DDX5,downstream_gene_variant,,ENST00000583201,;DDX5,downstream_gene_variant,,ENST00000583562,; T ENST00000225792 Transcript missense_variant 1579/2554 1177/1845 393/614 P/T Cct/Act 1 -1 DDX5 HGNC HGNC:2746 protein_coding YES CCDS11659.1 ENSP00000225792 P17844 UPI000003B456 NM_004396.3 deleterious(0.05) 11/13 PROSITE_profiles:PS51194,hmmpanther:PTHR24031:SF257,hmmpanther:PTHR24031,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 64502049 64502049 G T 1 0 0 0 0 1 0 0 0 4170 1174 41 2 2 DDX5 17 64502049 Missense_Mutation SNP G C3N-02155_T 4567529 64502049 18755392 129 28874 C17orf99 0 . GRCh38 17 78164143 78164143 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.419C>T p.Ala140Val p.A140V ENST00000340363 4/5 1162 1035 127 580 580 0 strelka-varscan-mutect C17orf99,missense_variant,p.Ala140Val,ENST00000340363,NM_001163075.1;C17orf99,missense_variant,p.Ala136Val,ENST00000591995,;C17orf99,synonymous_variant,p.=,ENST00000586029,;SYNGR2,upstream_gene_variant,,ENST00000225777,NM_004710.3;SYNGR2,upstream_gene_variant,,ENST00000589168,;SYNGR2,upstream_gene_variant,,ENST00000589711,;SYNGR2,upstream_gene_variant,,ENST00000588282,;SYNGR2,upstream_gene_variant,,ENST00000585591,;C17orf99,non_coding_transcript_exon_variant,,ENST00000451352,;C17orf99,downstream_gene_variant,,ENST00000586999,;C17orf99,upstream_gene_variant,,ENST00000586246,;SYNGR2,upstream_gene_variant,,ENST00000591770,;SYNGR2,upstream_gene_variant,,ENST00000589183,; T ENST00000340363 Transcript missense_variant 474/984 419/798 140/265 A/V gCa/gTa 1 1 C17orf99 HGNC HGNC:34490 protein_coding YES CCDS54171.1 ENSP00000343493 Q6UX52 UPI000049DE67 NM_001163075.1 tolerated(0.09) 4/5 hmmpanther:PTHR11481,hmmpanther:PTHR11481:SF67 MODERATE 1 SNV 1 1 PASS rs1310156119 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 78164143 78164143 C T 1 0 0 0 0 1 0 0 0 1896 710 25 3 3 C17orf99 17 78164143 Missense_Mutation SNP C C3N-02155_T 13662094 78164143 5093298 130 28875 DNAH17 0 . GRCh38 17 78426934 78426934 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.12763G>A p.Gly4255Arg p.G4255R ENST00000389840 78/81 553 488 65 243 242 1 strelka-varscan-mutect DNAH17,missense_variant,p.Gly4255Arg,ENST00000389840,NM_173628.3;DNAH17,missense_variant,p.Gly4250Arg,ENST00000585328,;PGS1,downstream_gene_variant,,ENST00000262764,NM_024419.4;DNAH17,non_coding_transcript_exon_variant,,ENST00000586052,;DNAH17,non_coding_transcript_exon_variant,,ENST00000586850,;DNAH17,non_coding_transcript_exon_variant,,ENST00000592192,;PGS1,downstream_gene_variant,,ENST00000588281,;PGS1,downstream_gene_variant,,ENST00000586880,;DNAH17,missense_variant,p.Gly1456Arg,ENST00000591369,;DNAH17,non_coding_transcript_exon_variant,,ENST00000590227,;PGS1,downstream_gene_variant,,ENST00000589426,;PGS1,downstream_gene_variant,,ENST00000589425,;PGS1,downstream_gene_variant,,ENST00000588169,;DNAH17,upstream_gene_variant,,ENST00000591647,; T ENST00000389840 Transcript missense_variant 12888/13723 12763/13389 4255/4462 G/R Ggg/Agg 1 -1 DNAH17 HGNC HGNC:2946 protein_coding YES ENSP00000374490 Q9UFH2 UPI0001B25601 NM_173628.3 deleterious(0) 78/81 Pfam_domain:PF03028,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF284,Low_complexity_(Seg):seg MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 78426934 78426934 C T 1 0 0 0 0 1 0 0 0 4416 623 22 3 3 DNAH17 17 78426934 Missense_Mutation SNP C C3N-02155_T 262791 78426934 4830507 131 28876 C1QTNF1 0 . GRCh38 17 79046594 79046594 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.195C>A p.Asp65Glu p.D65E ENST00000339142 4/5 541 485 56 273 272 1 strelka-varscan-mutect C1QTNF1,missense_variant,p.Asp65Glu,ENST00000339142,NM_198593.3;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000392445,;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000354124,NM_153372.1;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000579760,NM_030968.3;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000580474,;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000580454,;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000581774,;C1QTNF1,missense_variant,p.Asp65Glu,ENST00000583904,;C1QTNF1,5_prime_UTR_variant,,ENST00000311661,NM_198594.2;C1QTNF1,5_prime_UTR_variant,,ENST00000578229,;C1QTNF1,upstream_gene_variant,,ENST00000582625,; A ENST00000339142 Transcript missense_variant 750/3100 195/846 65/281 D/E gaC/gaA 1 1 C1QTNF1 HGNC HGNC:14324 protein_coding YES CCDS11761.1 ENSP00000340864 Q9BXJ1 UPI0000035539 NM_198593.3 tolerated(1) 4/5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 79046594 79046594 C A 1 0 0 0 0 1 0 0 0 1940 506 18 2 2 C1QTNF1 17 79046594 Missense_Mutation SNP C C3N-02155_T 619660 79046594 4210847 132 28877 TSPAN10 0 . GRCh38 17 81645038 81645038 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.197C>T p.Ser66Leu p.S66L ENST00000574882 3/4 353 311 42 162 162 0 strelka-varscan-mutect TSPAN10,missense_variant,p.Ser66Leu,ENST00000574882,NM_001290212.1;TSPAN10,missense_variant,p.Ser28Leu,ENST00000611590,NM_031945.4;NPLOC4,intron_variant,,ENST00000570300,;TSPAN10,missense_variant,p.Ser28Leu,ENST00000621293,;TSPAN10,non_coding_transcript_exon_variant,,ENST00000571707,; T ENST00000574882 Transcript missense_variant 398/1837 197/1182 66/393 S/L tCa/tTa 1 1 TSPAN10 HGNC HGNC:29942 protein_coding YES CCDS77130.1 ENSP00000480492 A0A087WWT4 UPI0003F48BD3 NM_001290212.1 tolerated(0.07) 3/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 81645038 81645038 C T 1 0 0 0 0 1 0 0 0 17139 838 29 3 3 TSPAN10 17 81645038 Missense_Mutation SNP C C3N-02155_T 2598444 81645038 1612403 133 28878 CDH20 0 . GRCh38 18 61499262 61499262 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.323C>A p.Thr108Asn p.T108N ENST00000262717 3/12 214 183 31 124 124 0 strelka-varscan-mutect CDH20,missense_variant,p.Thr108Asn,ENST00000262717,;CDH20,missense_variant,p.Thr108Asn,ENST00000536675,NM_031891.2;CDH20,missense_variant,p.Thr108Asn,ENST00000538374,; A ENST00000262717 Transcript missense_variant 721/3882 323/2406 108/801 T/N aCc/aAc 1 1 CDH20 HGNC HGNC:1760 protein_coding YES CCDS11977.1 ENSP00000262717 Q9HBT6 UPI000013D30D tolerated(0.13) 3/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF84,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 61499262 61499262 C A 1 0 0 0 0 1 0 0 0 2809 507 18 2 2 CDH20 18 61499262 Missense_Mutation SNP C C3N-02155_T 61499262 18874023 134 28879 NETO1 0 . GRCh38 18 72858999 72858999 + Missense_Mutation SNP T T C novel C3N-02155_T C3N-02155_N T T c.296A>G p.Asp99Gly p.D99G ENST00000327305 4/11 437 325 112 313 312 1 strelka-varscan-mutect NETO1,missense_variant,p.Asp99Gly,ENST00000327305,NM_138966.3;NETO1,missense_variant,p.Asp99Gly,ENST00000583169,NM_001201465.1;NETO1,missense_variant,p.Asp98Gly,ENST00000397929,NM_138999.1;NETO1,missense_variant,p.Asp95Gly,ENST00000579169,;NETO1,intron_variant,,ENST00000579730,; C ENST00000327305 Transcript missense_variant 954/3058 296/1602 99/533 D/G gAt/gGt 1 -1 NETO1 HGNC HGNC:13823 protein_coding YES CCDS12000.1 ENSP00000313088 Q8TDF5 A0A024R375 UPI000013E59E NM_138966.3 deleterious(0) 4/11 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF315,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 72858999 72858999 T C 1 0 0 0 0 1 0 0 0 10374 1435 50 5 5 NETO1 18 72858999 Missense_Mutation SNP T C3N-02155_T 11359737 72858999 7514286 135 28880 NWD1 0 . GRCh38 19 16762036 16762036 + Silent SNP G G A novel C3N-02155_T C3N-02155_N G G c.2031G>A p.= p.R677R ENST00000524140 8/19 240 150 90 211 211 0 strelka-varscan-mutect NWD1,synonymous_variant,p.=,ENST00000524140,NM_001007525.3;NWD1,synonymous_variant,p.=,ENST00000379808,;NWD1,synonymous_variant,p.=,ENST00000552788,NM_001290355.1;NWD1,synonymous_variant,p.=,ENST00000549814,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; A ENST00000524140 Transcript synonymous_variant 2449/7641 2031/4299 677/1432 R agG/agA 1 1 NWD1 HGNC HGNC:27619 protein_coding YES CCDS32945.2 ENSP00000428579 Q149M9 UPI0000D6173E NM_001007525.3 8/19 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF472 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 16762036 16762036 G A 1 0 0 0 0 0 0 0 1 10854 1194 42 3 3 NWD1 19 16762036 Silent SNP G C3N-02155_T 16762036 41855580 136 28881 NWD1 0 . GRCh38 19 16799909 16799909 + Silent SNP G G A C3N-02155_T C3N-02155_N G G c.3483G>A p.= p.G1161G ENST00000524140 17/19 90 71 19 77 77 0 strelka-varscan-mutect NWD1,synonymous_variant,p.=,ENST00000524140,NM_001007525.3;NWD1,synonymous_variant,p.=,ENST00000379808,;NWD1,synonymous_variant,p.=,ENST00000552788,NM_001290355.1;NWD1,intron_variant,,ENST00000549814,;CTD-2538G9.6,upstream_gene_variant,,ENST00000601661,;NWD1,3_prime_UTR_variant,,ENST00000518676,;NWD1,3_prime_UTR_variant,,ENST00000438489,; A ENST00000524140 Transcript synonymous_variant 3901/7641 3483/4299 1161/1432 G ggG/ggA COSM3530153,COSM3530154 1 1 NWD1 HGNC HGNC:27619 protein_coding YES CCDS32945.2 ENSP00000428579 Q149M9 UPI0000D6173E NM_001007525.3 17/19 Gene3D:2.130.10.10,PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF472,SMART_domains:SM00320,Superfamily_domains:SSF50978,Superfamily_domains:SSF50978 1,1 LOW 1 SNV 1 1,1 1 PASS rs1415100108 . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 16799909 16799909 G A 1 0 0 0 0 0 0 0 1 10854 1161 41 3 3 NWD1 19 16799909 Silent SNP G C3N-02155_T 37873 16799909 41817707 137 28882 RASGRP4 0 . GRCh38 19 38419949 38419949 + Missense_Mutation SNP T T C novel C3N-02155_T C3N-02155_N T T c.574A>G p.Lys192Glu p.K192E ENST00000615439 6/17 245 208 37 191 191 0 strelka-varscan-mutect RASGRP4,missense_variant,p.Lys192Glu,ENST00000618320,;RASGRP4,missense_variant,p.Lys192Glu,ENST00000615439,NM_170604.2;RASGRP4,missense_variant,p.Lys192Glu,ENST00000454404,NM_001146205.1;RASGRP4,missense_variant,p.Lys178Glu,ENST00000586305,NM_001146202.1;RASGRP4,missense_variant,p.Lys192Glu,ENST00000587753,NM_001146204.1;RASGRP4,missense_variant,p.Lys192Glu,ENST00000614135,;RASGRP4,missense_variant,p.Lys192Glu,ENST00000433821,NM_001146203.1;RASGRP4,missense_variant,p.Lys192Glu,ENST00000617966,;RASGRP4,missense_variant,p.Lys192Glu,ENST00000293062,NM_001146207.1;RASGRP4,missense_variant,p.Lys192Glu,ENST00000622174,;RASGRP4,missense_variant,p.Lys192Glu,ENST00000426920,NM_001146206.1;RASGRP4,missense_variant,p.Lys192Glu,ENST00000587738,;RASGRP4,missense_variant,p.Lys192Glu,ENST00000589358,;RASGRP4,missense_variant,p.Lys178Glu,ENST00000589474,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000615340,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000592322,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000588404,;RASGRP4,non_coding_transcript_exon_variant,,ENST00000589100,;RASGRP4,upstream_gene_variant,,ENST00000588708,; C ENST00000615439 Transcript missense_variant 788/3217 574/2022 192/673 K/E Aaa/Gaa 1 -1 RASGRP4 HGNC HGNC:18958 protein_coding YES CCDS46068.1 ENSP00000479844 Q8TDF6 UPI0000050F40 NM_170604.2 deleterious(0) 6/17 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF157,Gene3D:2ii0A01,Superfamily_domains:0041591 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 38419949 38419949 T C 1 0 0 0 0 1 0 0 0 13238 1821 63 5 5 RASGRP4 19 38419949 Missense_Mutation SNP T C3N-02155_T 21620040 38419949 20197667 138 28883 PPP1R37 0 . GRCh38 19 45145917 45145917 + Missense_Mutation SNP C C A novel C3N-02155_T C3N-02155_N C C c.1861C>A p.Gln621Lys p.Q621K ENST00000221462 11/13 247 207 40 170 170 0 strelka-varscan-mutect PPP1R37,missense_variant,p.Gln621Lys,ENST00000221462,NM_019121.1;MARK4,intron_variant,,ENST00000587566,;NKPD1,downstream_gene_variant,,ENST00000317951,NM_198478.3;PPP1R37,downstream_gene_variant,,ENST00000544069,;PPP1R37,downstream_gene_variant,,ENST00000544897,;PPP1R37,downstream_gene_variant,,ENST00000545910,;PPP1R37,non_coding_transcript_exon_variant,,ENST00000422370,;PPP1R37,non_coding_transcript_exon_variant,,ENST00000540059,; A ENST00000221462 Transcript missense_variant 2225/3163 1861/2076 621/691 Q/K Cag/Aag 1 1 PPP1R37 HGNC HGNC:27607 protein_coding YES CCDS56096.1 ENSP00000221462 O75864 UPI000041AA74 NM_019121.1 tolerated(0.41) 11/13 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 45145917 45145917 C A 1 0 0 0 0 1 0 0 0 12491 827 29 2 2 PPP1R37 19 45145917 Missense_Mutation SNP C C3N-02155_T 6725968 45145917 13471699 139 28884 PLA2G4C 0 . GRCh38 19 48077807 48077807 + Missense_Mutation SNP G G T novel C3N-02155_T C3N-02155_N G G c.892C>A p.Gln298Lys p.Q298K ENST00000599111 11/17 194 166 28 130 130 0 strelka-varscan-mutect PLA2G4C,missense_variant,p.Gln288Lys,ENST00000354276,NM_001159323.1;PLA2G4C,missense_variant,p.Gln298Lys,ENST00000599111,NM_001159322.1;PLA2G4C,missense_variant,p.Gln288Lys,ENST00000599921,NM_003706.2;PLA2G4C,missense_variant,p.Gln40Lys,ENST00000599300,;PLA2G4C,missense_variant,p.Gln104Lys,ENST00000601946,;PLA2G4C,upstream_gene_variant,,ENST00000595161,;PLA2G4C,intron_variant,,ENST00000599239,;PLA2G4C,upstream_gene_variant,,ENST00000596510,;PLA2G4C,non_coding_transcript_exon_variant,,ENST00000593765,;PLA2G4C,non_coding_transcript_exon_variant,,ENST00000598185,; T ENST00000599111 Transcript missense_variant 1194/2458 892/1656 298/551 Q/K Caa/Aaa 1 -1 PLA2G4C HGNC HGNC:9037 protein_coding YES CCDS59403.1 ENSP00000472546 Q9UP65 UPI00019A89DE NM_001159322.1 tolerated(0.6) 11/17 PROSITE_profiles:PS51210,SMART_domains:SM00022,Superfamily_domains:SSF52151 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 48077807 48077807 G T 1 0 0 0 0 1 0 0 0 12099 1328 46 2 2 PLA2G4C 19 48077807 Missense_Mutation SNP G C3N-02155_T 2931890 48077807 10539809 140 28885 ZNF766 0 . GRCh38 19 52290222 52290222 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.431C>G p.Ser144Cys p.S144C ENST00000439461 4/4 275 236 39 212 212 0 strelka-varscan-mutect ZNF766,missense_variant,p.Ser144Cys,ENST00000439461,NM_001010851.2;ZNF766,missense_variant,p.Ser159Cys,ENST00000593612,;ZNF766,missense_variant,p.Ser107Cys,ENST00000595000,;ZNF766,missense_variant,p.Ser85Cys,ENST00000593703,;ZNF766,3_prime_UTR_variant,,ENST00000599581,;ZNF766,downstream_gene_variant,,ENST00000600821,;ZNF766,downstream_gene_variant,,ENST00000595149,;CTD-2525I3.5,intron_variant,,ENST00000594865,; G ENST00000439461 Transcript missense_variant 474/6298 431/1407 144/468 S/C tCt/tGt 1 1 ZNF766 HGNC HGNC:28063 protein_coding YES CCDS46163.1 ENSP00000409652 Q5HY98 UPI0000202AF7 NM_001010851.2 deleterious(0.02) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 52290222 52290222 C G 1 0 0 0 0 1 0 0 0 18723 913 32 4 4 ZNF766 19 52290222 Missense_Mutation SNP C C3N-02155_T 4212415 52290222 6327394 141 28886 BRSK1 0 . GRCh38 19 55287283 55287283 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.301G>A p.Glu101Lys p.E101K ENST00000309383 3/19 327 269 58 292 291 1 strelka-varscan-mutect BRSK1,missense_variant,p.Glu101Lys,ENST00000309383,NM_032430.1;BRSK1,missense_variant,p.Glu117Lys,ENST00000590333,;BRSK1,missense_variant,p.Glu101Lys,ENST00000585418,;BRSK1,missense_variant,p.Glu58Lys,ENST00000592539,; A ENST00000309383 Transcript missense_variant 578/3079 301/2337 101/778 E/K Gag/Aag 1 1 BRSK1 HGNC HGNC:18994 protein_coding YES CCDS12921.1 ENSP00000310649 Q8TDC3 UPI0000070495 NM_032430.1 deleterious(0) 3/19 PROSITE_profiles:PS50011,hmmpanther:PTHR24343,hmmpanther:PTHR24343:SF130,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 55287283 55287283 G A 1 0 0 0 0 1 0 0 0 1697 1059 37 1 1 BRSK1 19 55287283 Missense_Mutation SNP G C3N-02155_T 2997061 55287283 3330333 142 28887 NOP56 0 . GRCh38 20 2654565 2654565 + Silent SNP G G A novel C3N-02155_T C3N-02155_N G G c.360G>A p.= p.E120E ENST00000329276 4/12 356 304 52 210 210 0 strelka-varscan-mutect NOP56,synonymous_variant,p.=,ENST00000329276,NM_006392.3;NOP56,synonymous_variant,p.=,ENST00000445139,;NOP56,upstream_gene_variant,,ENST00000415272,;IDH3B,downstream_gene_variant,,ENST00000380843,NM_006899.3;IDH3B,downstream_gene_variant,,ENST00000613370,NM_001258384.1;IDH3B,downstream_gene_variant,,ENST00000474315,;IDH3B,downstream_gene_variant,,ENST00000380851,NM_174855.2;SNORA51,upstream_gene_variant,,ENST00000606420,;SNORD86,upstream_gene_variant,,ENST00000391196,;SNORD110,downstream_gene_variant,,ENST00000408189,;SNORD57,upstream_gene_variant,,ENST00000448188,;SNORD56,upstream_gene_variant,,ENST00000413522,;NOP56,downstream_gene_variant,,ENST00000408135,;NOP56,non_coding_transcript_exon_variant,,ENST00000469588,;NOP56,non_coding_transcript_exon_variant,,ENST00000494697,;NOP56,non_coding_transcript_exon_variant,,ENST00000460258,;NOP56,non_coding_transcript_exon_variant,,ENST00000496775,;NOP56,upstream_gene_variant,,ENST00000492135,;NOP56,upstream_gene_variant,,ENST00000466447,;NOP56,upstream_gene_variant,,ENST00000484998,;NOP56,upstream_gene_variant,,ENST00000480992,;NOP56,upstream_gene_variant,,ENST00000462630,;NOP56,upstream_gene_variant,,ENST00000467857,;NOP56,downstream_gene_variant,,ENST00000470143,;NOP56,upstream_gene_variant,,ENST00000480447,;NOP56,upstream_gene_variant,,ENST00000490753,;NOP56,upstream_gene_variant,,ENST00000471023,;NOP56,upstream_gene_variant,,ENST00000612233,;NOP56,upstream_gene_variant,,ENST00000616692,;IDH3B,downstream_gene_variant,,ENST00000488299,;NOP56,upstream_gene_variant,,ENST00000467196,;IDH3B,downstream_gene_variant,,ENST00000492240,;IDH3B,downstream_gene_variant,,ENST00000466494,;IDH3B,downstream_gene_variant,,ENST00000477689,;IDH3B,downstream_gene_variant,,ENST00000466999,; A ENST00000329276 Transcript synonymous_variant 876/2400 360/1785 120/594 E gaG/gaA 1 1 NOP56 HGNC HGNC:15911 protein_coding YES CCDS13030.1 ENSP00000370589 O00567 UPI000016A81D NM_006392.3 4/12 hmmpanther:PTHR10894,hmmpanther:PTHR10894:SF0 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 2654565 2654565 G A 1 0 0 0 0 0 0 0 1 10583 933 33 3 3 NOP56 20 2654565 Silent SNP G C3N-02155_T 2654565 61789602 143 28888 NOP56 0 . GRCh38 20 2657087 2657087 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.1288G>A p.Glu430Lys p.E430K ENST00000329276 11/12 486 432 54 292 292 0 strelka-varscan-mutect NOP56,missense_variant,p.Glu430Lys,ENST00000329276,NM_006392.3;NOP56,missense_variant,p.Glu171Lys,ENST00000415272,;IDH3B,downstream_gene_variant,,ENST00000380843,NM_006899.3;IDH3B,downstream_gene_variant,,ENST00000613370,NM_001258384.1;IDH3B,downstream_gene_variant,,ENST00000474315,;IDH3B,downstream_gene_variant,,ENST00000380851,NM_174855.2;NOP56,downstream_gene_variant,,ENST00000445139,;SNORA51,downstream_gene_variant,,ENST00000606420,;SNORD86,downstream_gene_variant,,ENST00000391196,;SNORD110,downstream_gene_variant,,ENST00000408189,;SNORD57,downstream_gene_variant,,ENST00000448188,;SNORD56,downstream_gene_variant,,ENST00000413522,;NOP56,downstream_gene_variant,,ENST00000408135,;NOP56,non_coding_transcript_exon_variant,,ENST00000492135,;NOP56,non_coding_transcript_exon_variant,,ENST00000466447,;NOP56,non_coding_transcript_exon_variant,,ENST00000462630,;NOP56,non_coding_transcript_exon_variant,,ENST00000467857,;NOP56,non_coding_transcript_exon_variant,,ENST00000480447,;NOP56,non_coding_transcript_exon_variant,,ENST00000490753,;NOP56,non_coding_transcript_exon_variant,,ENST00000471023,;NOP56,downstream_gene_variant,,ENST00000484998,;NOP56,downstream_gene_variant,,ENST00000469588,;NOP56,downstream_gene_variant,,ENST00000480992,;NOP56,downstream_gene_variant,,ENST00000494697,;NOP56,downstream_gene_variant,,ENST00000460258,;NOP56,downstream_gene_variant,,ENST00000496775,;NOP56,downstream_gene_variant,,ENST00000470143,;NOP56,missense_variant,p.Glu204Lys,ENST00000467196,;NOP56,non_coding_transcript_exon_variant,,ENST00000612233,;NOP56,non_coding_transcript_exon_variant,,ENST00000616692,;IDH3B,downstream_gene_variant,,ENST00000488299,;IDH3B,downstream_gene_variant,,ENST00000492240,;IDH3B,downstream_gene_variant,,ENST00000462967,;IDH3B,downstream_gene_variant,,ENST00000491065,;IDH3B,downstream_gene_variant,,ENST00000466494,;IDH3B,downstream_gene_variant,,ENST00000477689,;IDH3B,downstream_gene_variant,,ENST00000466999,;IDH3B,downstream_gene_variant,,ENST00000479376,; A ENST00000329276 Transcript missense_variant 1804/2400 1288/1785 430/594 E/K Gaa/Aaa 1 1 NOP56 HGNC HGNC:15911 protein_coding YES CCDS13030.1 ENSP00000370589 O00567 UPI000016A81D NM_006392.3 tolerated(0.19) 11/12 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10894,hmmpanther:PTHR10894:SF0 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 2657087 2657087 G A 1 0 0 0 0 1 0 0 0 10583 1175 41 3 3 NOP56 20 2657087 Missense_Mutation SNP G C3N-02155_T 2522 2657087 61787080 144 28889 SNAP25 0 . GRCh38 20 10277721 10277721 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.109G>C p.Glu37Gln p.E37Q ENST00000254976 3/8 424 379 45 301 301 0 strelka-varscan-mutect SNAP25,missense_variant,p.Glu37Gln,ENST00000254976,NM_130811.2;SNAP25,missense_variant,p.Glu37Gln,ENST00000304886,NM_003081.3;SNAP25,missense_variant,p.Glu37Gln,ENST00000430336,;SNAP25-AS1,intron_variant,,ENST00000421143,;SNAP25-AS1,intron_variant,,ENST00000453544,;SNAP25,non_coding_transcript_exon_variant,,ENST00000492814,; C ENST00000254976 Transcript missense_variant 320/2053 109/621 37/206 E/Q Gaa/Caa 1 1 SNAP25 HGNC HGNC:11132 protein_coding YES CCDS13110.1 ENSP00000254976 P60880 UPI0000001103 NM_130811.2 tolerated(0.07) 3/8 PROSITE_profiles:PS50192,hmmpanther:PTHR19305,hmmpanther:PTHR19305:SF5,Gene3D:1.20.5.110,SMART_domains:SM00397,Superfamily_domains:SSF58038 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 10277721 10277721 G C 1 0 0 0 0 1 0 0 0 15151 1304 45 4 4 SNAP25 20 10277721 Missense_Mutation SNP G C3N-02155_T 7620634 10277721 54166446 145 28890 SLX4IP 0 . GRCh38 20 10623043 10623043 + Silent SNP G G A novel C3N-02155_T C3N-02155_N G G c.891G>A p.= p.R297R ENST00000334534 8/8 276 232 44 184 184 0 strelka-varscan-mutect SLX4IP,synonymous_variant,p.=,ENST00000334534,NM_001009608.1;SLX4IP,intron_variant,,ENST00000488816,; A ENST00000334534 Transcript synonymous_variant 1071/6062 891/1227 297/408 R agG/agA 1 1 SLX4IP HGNC HGNC:16225 protein_coding YES CCDS33439.1 ENSP00000335557 Q5VYV7 UPI00001D8318 NM_001009608.1 8/8 hmmpanther:PTHR28557,Pfam_domain:PF15744 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 93 10623043 10623043 G A 1 0 0 0 0 0 0 0 1 15049 1165 41 3 3 SLX4IP 20 10623043 Silent SNP G C3N-02155_T 345322 10623043 53821124 146 28891 FAM217B 0 . GRCh38 20 59944328 59944328 + Missense_Mutation SNP C C G novel C3N-02155_T C3N-02155_N C C c.385C>G p.Leu129Val p.L129V ENST00000358293 5/5 561 505 56 313 313 0 strelka-varscan-mutect FAM217B,missense_variant,p.Leu129Val,ENST00000358293,NM_001190826.1;FAM217B,missense_variant,p.Leu129Val,ENST00000360816,NM_001190827.1,NM_022106.2;PPP1R3D,upstream_gene_variant,,ENST00000370996,NM_006242.3;FAM217B,downstream_gene_variant,,ENST00000421092,;FAM217B,intron_variant,,ENST00000469084,; G ENST00000358293 Transcript missense_variant 800/5152 385/1152 129/383 L/V Ctt/Gtt 1 1 FAM217B HGNC HGNC:16170 protein_coding YES CCDS13484.1 ENSP00000351040 Q9NTX9 UPI0000128624 NM_001190826.1 tolerated(0.53) 5/5 Pfam_domain:PF15344,hmmpanther:PTHR22145,hmmpanther:PTHR22145:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 93 59944328 59944328 C G 1 0 0 0 0 1 0 0 0 5407 913 32 4 4 FAM217B 20 59944328 Missense_Mutation SNP C C3N-02155_T 49321285 59944328 4499839 147 28892 LAMA5 0 . GRCh38 20 62320576 62320576 + Missense_Mutation SNP G G A rs769500367 C3N-02155_T C3N-02155_N G G c.6742C>T p.Arg2248Trp p.R2248W ENST00000252999 50/80 381 336 45 169 169 0 strelka-varscan-mutect LAMA5,missense_variant,p.Arg2248Trp,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000497363,;LAMA5,downstream_gene_variant,,ENST00000464134,;LAMA5,upstream_gene_variant,,ENST00000471042,;LAMA5,upstream_gene_variant,,ENST00000481120,; A ENST00000252999 Transcript missense_variant 6809/11426 6742/11088 2248/3695 R/W Cgg/Tgg rs769500367,COSM4100100 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 deleterious(0) 50/80 Pfam_domain:PF06008 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769500367 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 62320576 62320576 G A 1 0 0 0 0 1 0 0 0 8513 1144 40 1 1 LAMA5 20 62320576 Missense_Mutation SNP G C3N-02155_T 2376248 62320576 2123591 148 28893 TIAM1 0 . GRCh38 21 31152751 31152751 + Missense_Mutation SNP A A C rs777903504 C3N-02155_T C3N-02155_N A A c.3251T>G p.Leu1084Arg p.L1084R ENST00000286827 20/29 239 204 35 145 145 0 strelka-varscan-mutect TIAM1,missense_variant,p.Leu1084Arg,ENST00000286827,NM_003253.2;TIAM1,missense_variant,p.Leu1024Arg,ENST00000541036,;TIAM1,missense_variant,p.Leu117Arg,ENST00000636887,; C ENST00000286827 Transcript missense_variant 3723/7200 3251/4776 1084/1591 L/R cTt/cGt rs777903504 1 -1 TIAM1 HGNC HGNC:11805 protein_coding YES CCDS13609.1 ENSP00000286827 Q13009 UPI000013DE6F NM_003253.2 deleterious(0) 20/29 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF88,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS rs777903504 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 31152751 31152751 A C 1 0 0 0 0 1 0 0 0 16324 72 3 5 5 TIAM1 21 31152751 Missense_Mutation SNP A C3N-02155_T 31152751 15557232 149 28894 PCNT 0 . GRCh38 21 46431955 46431955 + Missense_Mutation SNP G G A novel C3N-02155_T C3N-02155_N G G c.8491G>A p.Glu2831Lys p.E2831K ENST00000359568 38/47 771 672 99 397 397 0 strelka-varscan-mutect PCNT,missense_variant,p.Glu2831Lys,ENST00000359568,NM_006031.5;PCNT,non_coding_transcript_exon_variant,,ENST00000480896,;PCNT,non_coding_transcript_exon_variant,,ENST00000482575,; A ENST00000359568 Transcript missense_variant 8598/10560 8491/10011 2831/3336 E/K Gag/Aag 1 1 PCNT HGNC HGNC:16068 protein_coding YES CCDS33592.1 ENSP00000352572 O95613 UPI00001AEB88 NM_006031.5 tolerated(0.18) 38/47 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 93 46431955 46431955 G A 1 0 0 0 0 1 0 0 0 11678 1291 45 3 3 PCNT 21 46431955 Missense_Mutation SNP G C3N-02155_T 15279204 46431955 278028 150 28895 ANKRD54 0 . GRCh38 22 37844181 37844181 + Missense_Mutation SNP C C T novel C3N-02155_T C3N-02155_N C C c.58G>A p.Glu20Lys p.E20K ENST00000215941 1/8 330 267 63 202 202 0 strelka-varscan-mutect ANKRD54,missense_variant,p.Glu20Lys,ENST00000215941,NM_138797.2;ANKRD54,missense_variant,p.Glu20Lys,ENST00000411961,;ANKRD54,missense_variant,p.Glu20Lys,ENST00000434930,;ANKRD54,intron_variant,,ENST00000609454,;EIF3L,upstream_gene_variant,,ENST00000412331,;ANKRD54,upstream_gene_variant,,ENST00000406423,;ANKRD54,upstream_gene_variant,,ENST00000458278,;ANKRD54,upstream_gene_variant,,ENST00000424350,;ANKRD54,downstream_gene_variant,,ENST00000385210,;MIR659,downstream_gene_variant,,ENST00000384963,;ANKRD54,downstream_gene_variant,,ENST00000609706,;ANKRD54,upstream_gene_variant,,ENST00000464849,;ANKRD54,missense_variant,p.Glu33Lys,ENST00000413497,;ANKRD54,upstream_gene_variant,,ENST00000407117,; T ENST00000215941 Transcript missense_variant 251/2184 58/903 20/300 E/K Gag/Aag 1 -1 ANKRD54 HGNC HGNC:25185 protein_coding YES CCDS13959.1 ENSP00000215941 Q6NXT1 UPI0000073164 NM_138797.2 deleterious_low_confidence(0.02) 1/8 hmmpanther:PTHR24197 MODERATE 1 SNV 1 1 PASS rs1451394448 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 93 37844181 37844181 C T 1 0 0 0 0 1 0 0 0 784 864 30 3 3 ANKRD54 22 37844181 Missense_Mutation SNP C C3N-02155_T 37844181 12974287 151 28896 PTCHD1 0 . GRCh38 X 23335225 23335225 + Missense_Mutation SNP A A C novel C3N-02155_T C3N-02155_N A A c.350A>C p.Lys117Thr p.K117T ENST00000379361 1/3 172 62 110 113 113 0 strelka-varscan-mutect PTCHD1,missense_variant,p.Lys117Thr,ENST00000379361,NM_173495.2;PTCHD1,missense_variant,p.Lys12Thr,ENST00000616022,;PTCHD1,missense_variant,p.Lys53Thr,ENST00000456522,; C ENST00000379361 Transcript missense_variant,splice_region_variant 1210/13714 350/2667 117/888 K/T aAg/aCg 1 1 PTCHD1 HGNC HGNC:26392 protein_coding YES CCDS35215.2 ENSP00000368666 Q96NR3 X5DNX9 UPI000059DAD8 NM_173495.2 tolerated(0.37) 1/3 Pfam_domain:PF02460,hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF36 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 23335225 23335225 A C 1 0 0 0 0 1 0 0 0 12885 86 3 5 5 PTCHD1 23 23335225 Missense_Mutation SNP A C3N-02155_T 23335225 132705670 152 28897 PDK3 0 . GRCh38 X 24494820 24494820 + Missense_Mutation SNP G G C novel C3N-02155_T C3N-02155_N G G c.185G>C p.Arg62Thr p.R62T ENST00000441463 2/12 238 180 58 126 126 0 strelka-varscan-mutect PDK3,missense_variant,p.Arg62Thr,ENST00000441463,NM_001142386.2;PDK3,missense_variant,p.Arg62Thr,ENST00000379162,NM_005391.4;PDK3,non_coding_transcript_exon_variant,,ENST00000493226,; C ENST00000441463 Transcript missense_variant 185/1921 185/1248 62/415 R/T aGa/aCa 1 1 PDK3 HGNC HGNC:8811 protein_coding YES CCDS48088.1 ENSP00000387536 Q15120 UPI00002124D4 NM_001142386.2 deleterious(0) 2/12 hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF21,Gene3D:1.20.140.20,Pfam_domain:PF10436,Superfamily_domains:SSF69012 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 93 24494820 24494820 G C 1 0 0 0 0 1 0 0 0 11765 942 33 4 4 PDK3 23 24494820 Missense_Mutation SNP G C3N-02155_T 1159595 24494820 131546075 153 28898 KAZN 0 . GRCh38 1 15104095 15104095 + Missense_Mutation SNP G G A novel C3N-02158_T C3N-02158_N G G c.1954G>A p.Glu652Lys p.E652K ENST00000376030 13/15 283 222 61 143 143 0 strelka-varscan-mutect KAZN,missense_variant,p.Glu740Lys,ENST00000636203,;KAZN,missense_variant,p.Glu652Lys,ENST00000376030,NM_201628.2; A ENST00000376030 Transcript missense_variant 2248/6030 1954/2328 652/775 E/K Gag/Aag 1 1 KAZN HGNC HGNC:29173 protein_coding YES CCDS152.2 ENSP00000365198 Q674X7 UPI0000E1E68A NM_201628.2 deleterious(0) 13/15 Pfam_domain:PF07647,PROSITE_profiles:PS50105,hmmpanther:PTHR12776,hmmpanther:PTHR12776:SF1,SMART_domains:SM00454,Superfamily_domains:SSF47769 MODERATE 1 SNV 5 1 PASS rs1271683187 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 15104095 15104095 G A 1 0 0 0 0 1 0 0 0 7907 1059 37 1 1 KAZN 1 15104095 Missense_Mutation SNP G C3N-02158_T 15104095 233852327 1 28899 FBXO42 0 . GRCh38 1 16251771 16251771 + Silent SNP C C A novel C3N-02158_T C3N-02158_N C C c.1053G>T p.= p.V351V ENST00000375592 10/10 103 90 13 81 81 0 strelka-varscan-mutect FBXO42,synonymous_variant,p.=,ENST00000375592,NM_018994.2;FBXO42,synonymous_variant,p.=,ENST00000456164,;FBXO42,synonymous_variant,p.=,ENST00000444116,; A ENST00000375592 Transcript synonymous_variant 1270/6202 1053/2154 351/717 V gtG/gtT 1 -1 FBXO42 HGNC HGNC:29249 protein_coding YES CCDS30613.1 ENSP00000364742 Q6P3S6 A0A024QZB0 UPI0000161A51 NM_018994.2 10/10 Superfamily_domains:0052715,Gene3D:1zgkA00,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF316 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 94 16251771 16251771 C A 1 0 0 0 0 0 0 0 1 5614 581 21 2 2 FBXO42 1 16251771 Silent SNP C C3N-02158_T 1147676 16251771 232704651 2 28900 RPL5 0 . GRCh38 1 92833656 92833656 + Frame_Shift_Del DEL G G - novel C3N-02158_T C3N-02158_N G G c.185delG p.Cys62PhefsTer8 p.C62Ffs*8 ENST00000370321 3/8 353 287 66 281 281 0 sindel-varindel RPL5,frameshift_variant,p.Cys62PhefsTer8,ENST00000370321,NM_000969.3;RPL5,frameshift_variant,p.Cys12PhefsTer8,ENST00000315741,;FAM69A,intron_variant,,ENST00000615519,NM_001252273.1;SNORD21,upstream_gene_variant,,ENST00000383953,;RPL5,frameshift_variant,p.Cys62PhefsTer45,ENST00000470843,;RPL5,non_coding_transcript_exon_variant,,ENST00000461952,;RPL5,upstream_gene_variant,,ENST00000497519,; - ENST00000370321 Transcript frameshift_variant 275/1043 185/894 62/297 C/X tGt/tt 1 1 RPL5 HGNC HGNC:10360 protein_coding YES CCDS741.1 ENSP00000359345 P46777 A2RUM7 UPI00000702C9 NM_000969.3 3/8 Gene3D:3.30.420.100,HAMAP:MF_01337_A,Pfam_domain:PF17144,Prints_domain:PR00058,hmmpanther:PTHR23410,Superfamily_domains:SSF53137 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 94 92833656 92833656 G - 1 0 1 0 1 0 0 0 0 13850 1391 48 0 0 RPL5 1 92833656 Frame_Shift_Del DEL G C3N-02158_T 76581885 92833656 156122766 3 28901 KCNC4 0 . GRCh38 1 110223208 110223208 + Missense_Mutation SNP A A T rs557039649 C3N-02158_T C3N-02158_N A A c.923A>T p.Asp308Val p.D308V ENST00000369787 2/4 228 197 31 136 136 0 strelka-varscan-mutect KCNC4,missense_variant,p.Asp308Val,ENST00000369787,NM_004978.4;KCNC4,missense_variant,p.Asp308Val,ENST00000413138,;KCNC4,missense_variant,p.Asp308Val,ENST00000438661,NM_001039574.2;KCNC4,upstream_gene_variant,,ENST00000636402,;KCNC4,intron_variant,,ENST00000412512,;KCNC4,missense_variant,p.Asp308Val,ENST00000469655,;KCNC4,non_coding_transcript_exon_variant,,ENST00000459877,;KCNC4,non_coding_transcript_exon_variant,,ENST00000489935,; T ENST00000369787 Transcript missense_variant 950/18750 923/1908 308/635 D/V gAc/gTc rs557039649 1 1 KCNC4 HGNC HGNC:6236 protein_coding YES CCDS821.1 ENSP00000358802 Q03721 UPI000013CAC8 NM_004978.4 tolerated(0.28) 2/4 Gene3D:1.20.120.350,Pfam_domain:PF00520,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF48,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS rs557039649 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 110223208 110223208 A T 1 0 0 0 0 1 0 0 0 7933 275 10 4 4 KCNC4 1 110223208 Missense_Mutation SNP A C3N-02158_T 17389552 110223208 138733214 4 28902 PDZK1 0 . GRCh38 1 145682636 145682636 + Missense_Mutation SNP C C G novel C3N-02158_T C3N-02158_N C C c.461G>C p.Gly154Ala p.G154A ENST00000417171 4/9 318 299 19 256 256 0 varscan-mutect PDZK1,missense_variant,p.Gly154Ala,ENST00000417171,NM_002614.4,NM_001201325.1;PDZK1,missense_variant,p.Gly154Ala,ENST00000344770,;PDZK1,missense_variant,p.Gly154Ala,ENST00000443667,;PDZK1,intron_variant,,ENST00000451928,NM_001201326.1; G ENST00000417171 Transcript missense_variant,splice_region_variant 547/2230 461/1560 154/519 G/A gGt/gCt 1 -1 PDZK1 HGNC HGNC:8821 protein_coding YES CCDS72860.1 ENSP00000394485 Q5T2W1 UPI000006D202 NM_002614.4,NM_001201325.1 deleterious(0) 4/9 PROSITE_profiles:PS50106,hmmpanther:PTHR14191:SF6,hmmpanther:PTHR14191,Pfam_domain:PF00595,Gene3D:2.30.42.10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs1372253916 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 94 145682636 145682636 C G 1 0 0 0 0 1 0 0 0 11795 521 18 4 4 PDZK1 1 145682636 Missense_Mutation SNP C C3N-02158_T 35459428 145682636 103273786 5 28903 TRIM58 0 . GRCh38 1 247857496 247857496 + Missense_Mutation SNP C C T novel C3N-02158_T C3N-02158_N C C c.250C>T p.Arg84Trp p.R84W ENST00000366481 1/6 36 29 7 24 24 0 strelka-varscan-mutect TRIM58,missense_variant,p.Arg84Trp,ENST00000366481,NM_015431.3; T ENST00000366481 Transcript missense_variant 298/3225 250/1461 84/486 R/W Cgg/Tgg 1 1 TRIM58 HGNC HGNC:24150 protein_coding YES CCDS1636.1 ENSP00000355437 Q8NG06 UPI000020590E NM_015431.3 deleterious(0) 1/6 Low_complexity_(Seg):seg,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF393,Superfamily_domains:SSF57850 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -18.43376 1 1 1 1 0 T 3 4 94 247857496 247857496 C T 1 0 0 0 0 1 0 0 0 17024 759 27 1 1 TRIM58 1 247857496 Missense_Mutation SNP C C3N-02158_T 102174860 247857496 1098926 6 28904 GAREM2 0 . GRCh38 2 26184822 26184822 + Missense_Mutation SNP C C T novel C3N-02158_T C3N-02158_N C C c.974C>T p.Ala325Val p.A325V ENST00000401533 4/6 147 134 13 78 78 0 strelka-varscan GAREM2,missense_variant,p.Ala248Val,ENST00000407684,NM_001191033.1;GAREM2,missense_variant,p.Ala325Val,ENST00000401533,NM_001168241.1;GAREM2,upstream_gene_variant,,ENST00000496070,; T ENST00000401533 Transcript missense_variant 1104/4161 974/2625 325/874 A/V gCg/gTg 1 1 GAREM2 HGNC HGNC:27172 protein_coding YES CCDS54336.1 ENSP00000384593 Q75VX8 UPI0000237273 NM_001168241.1 tolerated(0.52) 4/6 hmmpanther:PTHR14454,hmmpanther:PTHR14454:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 26184822 26184822 C T 1 0 0 0 0 1 0 0 0 6110 768 27 1 1 GAREM2 2 26184822 Missense_Mutation SNP C C3N-02158_T 26184822 216008707 7 28905 LRRTM1 0 . GRCh38 2 80302577 80302577 + Missense_Mutation SNP C C G novel C3N-02158_T C3N-02158_N C C c.1243G>C p.Gly415Arg p.G415R ENST00000295057 2/2 157 134 23 125 125 0 strelka-varscan LRRTM1,missense_variant,p.Gly415Arg,ENST00000295057,;LRRTM1,missense_variant,p.Gly415Arg,ENST00000409148,NM_178839.4;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;LRRTM1,downstream_gene_variant,,ENST00000416268,;LRRTM1,downstream_gene_variant,,ENST00000452811,;LRRTM1,downstream_gene_variant,,ENST00000415098,;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Gly415Arg,ENST00000433224,;LRRTM1,missense_variant,p.Gly415Arg,ENST00000417012,; G ENST00000295057 Transcript missense_variant 1900/2599 1243/1569 415/522 G/R Ggc/Cgc 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE tolerated(0.5) 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 94 80302577 80302577 C G 1 0 0 0 0 1 0 0 0 8945 681 24 4 4 LRRTM1 2 80302577 Missense_Mutation SNP C C3N-02158_T 54117755 80302577 161890952 8 28906 TMEM131 0 . GRCh38 2 97758932 97758932 + Frame_Shift_Del DEL G G - novel C3N-02158_T C3N-02158_N G G c.5328delC p.Trp1777GlyfsTer133 p.W1777Gfs*133 ENST00000186436 40/41 199 168 31 180 180 0 sindel-varindel-pindel TMEM131,frameshift_variant,p.Trp1777GlyfsTer133,ENST00000186436,NM_015348.1;TMEM131,non_coding_transcript_exon_variant,,ENST00000485245,;TMEM131,non_coding_transcript_exon_variant,,ENST00000469447,;TMEM131,downstream_gene_variant,,ENST00000465767,; - ENST00000186436 Transcript frameshift_variant 5557/6640 5328/5652 1776/1883 S/X tcC/tc 1 -1 TMEM131 HGNC HGNC:30366 protein_coding YES CCDS46368.1 ENSP00000186436 Q92545 UPI00006C0498 NM_015348.1 40/41 Low_complexity_(Seg):seg,hmmpanther:PTHR22050:SF1,hmmpanther:PTHR22050 HIGH 1 deletion 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 94 97758932 97758932 G - 1 0 1 0 1 0 0 0 0 16488 987 35 0 0 TMEM131 2 97758932 Frame_Shift_Del DEL G C3N-02158_T 17456355 97758932 144434597 9 28907 CUL3 0 . GRCh38 2 224506964 224506964 + Frame_Shift_Del DEL T T - C3N-02158_T C3N-02158_N T T c.923delA p.Asn308MetfsTer3 p.N308Mfs*3 ENST00000264414 7/16 154 120 34 124 124 0 sindel-varindel-pindel CUL3,frameshift_variant,p.Asn308MetfsTer3,ENST00000264414,NM_003590.4;CUL3,frameshift_variant,p.Asn242MetfsTer3,ENST00000344951,NM_001257197.1;CUL3,frameshift_variant,p.Asn284MetfsTer3,ENST00000409777,;CUL3,frameshift_variant,p.Asn284MetfsTer3,ENST00000409096,NM_001257198.1;CUL3,upstream_gene_variant,,ENST00000617432,;CUL3,downstream_gene_variant,,ENST00000541548,;CUL3,non_coding_transcript_exon_variant,,ENST00000484081,;CUL3,upstream_gene_variant,,ENST00000481135,; - ENST00000264414 Transcript frameshift_variant 1262/6741 923/2307 308/768 N/X aAt/at COSM5640912 1 -1 CUL3 HGNC HGNC:2553 protein_coding YES CCDS2462.1 ENSP00000264414 Q13618 A0A024R475 UPI0000001C83 NM_003590.4 7/16 hmmpanther:PTHR11932,hmmpanther:PTHR11932:SF85,Pfam_domain:PF00888,Gene3D:1.20.1310.10,Superfamily_domains:SSF74788 1 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 94 224506964 224506964 T - 1 0 1 0 1 0 0 0 0 3866 1493 52 0 0 CUL3 2 224506964 Frame_Shift_Del DEL T C3N-02158_T 126748032 224506964 17686565 10 28908 EIF2A 0 . GRCh38 3 150572327 150572327 + Missense_Mutation SNP G G T C3N-02158_T C3N-02158_N G G c.1181G>T p.Gly394Val p.G394V ENST00000460851 10/14 170 141 29 165 165 0 strelka-varscan-mutect EIF2A,missense_variant,p.Gly394Val,ENST00000460851,NM_032025.3;EIF2A,missense_variant,p.Gly389Val,ENST00000273435,;EIF2A,missense_variant,p.Gly369Val,ENST00000487799,;EIF2A,missense_variant,p.Gly333Val,ENST00000406576,;EIF2A,missense_variant,p.Gly168Val,ENST00000465535,;SERP1,intron_variant,,ENST00000479209,;EIF2A,downstream_gene_variant,,ENST00000482093,;SERP1,intron_variant,,ENST00000490945,;SERP1,intron_variant,,ENST00000463647,;SERP1,intron_variant,,ENST00000491195,;SERP1,intron_variant,,ENST00000484608,;EIF2A,upstream_gene_variant,,ENST00000482471,;EIF2A,3_prime_UTR_variant,,ENST00000477551,;EIF2A,downstream_gene_variant,,ENST00000462221,;EIF2A,downstream_gene_variant,,ENST00000494558,;EIF2A,downstream_gene_variant,,ENST00000472926,; T ENST00000460851 Transcript missense_variant 1290/2198 1181/1758 394/585 G/V gGc/gTc COSM1039860,COSM1039861 1 1 EIF2A HGNC HGNC:3254 protein_coding YES CCDS46935.1 ENSP00000417229 Q9BY44 UPI00000473DB NM_032025.3 deleterious(0) 10/14 hmmpanther:PTHR13227,Pfam_domain:PF08662,PIRSF_domain:PIRSF017222 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 150572327 150572327 G T 1 0 0 0 0 1 0 0 0 4831 1203 42 2 2 EIF2A 3 150572327 Missense_Mutation SNP G C3N-02158_T 150572327 47723232 11 28909 KDR 0 . GRCh38 4 55110496 55110496 + Missense_Mutation SNP C C G novel C3N-02158_T C3N-02158_N C C c.1162G>C p.Val388Leu p.V388L ENST00000263923 9/30 370 331 39 301 300 1 strelka-varscan-mutect KDR,missense_variant,p.Val388Leu,ENST00000263923,NM_002253.2;KDR,non_coding_transcript_exon_variant,,ENST00000512566,; G ENST00000263923 Transcript missense_variant 1458/5831 1162/4071 388/1356 V/L Gtg/Ctg 1 -1 KDR HGNC HGNC:6307 protein_coding YES CCDS3497.1 ENSP00000263923 P35968 A0A024RD88 UPI000003AE04 NM_002253.2 deleterious(0.03) 9/30 Gene3D:2.60.40.10,Pfam_domain:PF07679,Prints_domain:PR01832,PROSITE_profiles:PS50835,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF45,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 94 55110496 55110496 C G 1 0 0 0 0 1 0 0 0 8059 565 20 4 4 KDR 4 55110496 Missense_Mutation SNP C C3N-02158_T 55110496 135104059 12 28910 ANKRD33B 0 . GRCh38 5 10649380 10649380 + Missense_Mutation SNP G G T C3N-02158_T C3N-02158_N G G c.752G>T p.Cys251Phe p.C251F ENST00000296657 4/4 281 204 77 199 199 0 strelka-varscan-mutect ANKRD33B,missense_variant,p.Cys251Phe,ENST00000296657,NM_001164440.1;ANKRD33B,3_prime_UTR_variant,,ENST00000504806,;RP11-54F2.1,downstream_gene_variant,,ENST00000508690,; T ENST00000296657 Transcript missense_variant 752/9188 752/1485 251/494 C/F tGc/tTc COSM4644625 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 deleterious(0.01) 4/4 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1,SMART_domains:SM00248 1 MODERATE 1 SNV 5 1 1 PASS rs1334539561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 10649380 10649380 G T 1 0 0 0 0 1 0 0 0 766 1319 46 2 2 ANKRD33B 5 10649380 Missense_Mutation SNP G C3N-02158_T 10649380 170888879 13 28911 DNAH5 0 . GRCh38 5 13718971 13718971 + Missense_Mutation SNP T T C novel C3N-02158_T C3N-02158_N T T c.12410A>G p.Gln4137Arg p.Q4137R ENST00000265104 72/79 566 497 69 394 394 0 strelka-varscan-mutect DNAH5,missense_variant,p.Gln4137Arg,ENST00000265104,NM_001369.2; C ENST00000265104 Transcript missense_variant 12515/15633 12410/13875 4137/4624 Q/R cAg/cGg 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 tolerated(0.34) 72/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF03028 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 94 13718971 13718971 T C 1 0 0 0 0 1 0 0 0 4419 1580 55 5 5 DNAH5 5 13718971 Missense_Mutation SNP T C3N-02158_T 3069591 13718971 167819288 14 28912 SLC45A2 0 . GRCh38 5 33984255 33984255 + Missense_Mutation SNP C C A novel C3N-02158_T C3N-02158_N C C c.329G>T p.Gly110Val p.G110V ENST00000296589 1/7 282 242 40 243 242 1 strelka-varscan-mutect SLC45A2,missense_variant,p.Gly110Val,ENST00000382102,NM_001012509.3;SLC45A2,missense_variant,p.Gly110Val,ENST00000296589,NM_016180.4;SLC45A2,missense_variant,p.Gly110Val,ENST00000509381,NM_001297417.2;AMACR,downstream_gene_variant,,ENST00000335606,NM_014324.5;AMACR,downstream_gene_variant,,ENST00000382072,NM_203382.2;AMACR,downstream_gene_variant,,ENST00000502637,;AMACR,downstream_gene_variant,,ENST00000382085,NM_001167595.1;SLC45A2,upstream_gene_variant,,ENST00000510600,;AMACR,downstream_gene_variant,,ENST00000514195,;SLC45A2,non_coding_transcript_exon_variant,,ENST00000505056,;C1QTNF3-AMACR,downstream_gene_variant,,ENST00000382079,;AMACR,downstream_gene_variant,,ENST00000506639,; A ENST00000296589 Transcript missense_variant 476/1772 329/1593 110/530 G/V gGa/gTa 1 -1 SLC45A2 HGNC HGNC:16472 protein_coding YES CCDS3901.1 ENSP00000296589 Q9UMX9 A0A076YIB8 UPI00001AEC19 NM_016180.4 tolerated(0.13) 1/7 Transmembrane_helices:TMhelix,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF34,Gene3D:1.20.1250.20,Pfam_domain:PF13347,Superfamily_domains:SSF103473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 33984255 33984255 C A 1 0 0 0 0 1 0 0 0 14918 855 30 2 2 SLC45A2 5 33984255 Missense_Mutation SNP C C3N-02158_T 20265284 33984255 147554004 15 28913 PXT1 0 . GRCh38 6 36400532 36400532 + Missense_Mutation SNP G G C rs373126614 C3N-02158_T C3N-02158_N G G c.222C>G p.His74Gln p.H74Q ENST00000454782 4/5 212 195 17 224 224 0 strelka-varscan PXT1,missense_variant,p.His74Gln,ENST00000454782,NM_152990.3;PXT1,upstream_gene_variant,,ENST00000619547,; C ENST00000454782 Transcript missense_variant 706/2108 222/405 74/134 H/Q caC/caG rs373126614 1 -1 PXT1 HGNC HGNC:18312 protein_coding YES CCDS4820.2 ENSP00000419944 Q8NFP0 UPI0000EE4DF4 NM_152990.3 tolerated_low_confidence(0.06) 4/5 Gene3D:1.10.437.10,hmmpanther:PTHR40381,hmmpanther:PTHR40381:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 94 36400532 36400532 G C 1 0 0 0 0 1 0 0 0 13007 1252 44 4 4 PXT1 6 36400532 Missense_Mutation SNP G C3N-02158_T 36400532 134405447 16 28914 CYP39A1 0 . GRCh38 6 46652559 46652559 + Silent SNP C C A novel C3N-02158_T C3N-02158_N C C c.24G>T p.= p.V8V ENST00000275016 1/12 70 60 10 67 67 0 strelka-varscan CYP39A1,synonymous_variant,p.=,ENST00000275016,NM_016593.4,NM_001278738.1;CYP39A1,5_prime_UTR_variant,,ENST00000619708,NM_001278739.1;SLC25A27,upstream_gene_variant,,ENST00000371347,NM_004277.4,NM_001204051.1;SLC25A27,upstream_gene_variant,,ENST00000411689,NM_001204052.1; A ENST00000275016 Transcript synonymous_variant 228/2176 24/1410 8/469 V gtG/gtT 1 -1 CYP39A1 HGNC HGNC:17449 protein_coding YES CCDS4916.1 ENSP00000275016 Q9NYL5 UPI000013DA3D NM_016593.4,NM_001278738.1 1/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR24304:SF2,hmmpanther:PTHR24304,PIRSF_domain:PIRSF000047 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.998 1 1 1 1 0 A 2 1 94 46652559 46652559 C A 1 0 0 0 0 0 0 0 1 3980 813 29 2 2 CYP39A1 6 46652559 Silent SNP C C3N-02158_T 10252027 46652559 124153420 17 28915 IKZF1 0 . GRCh38 7 50382699 50382699 + Missense_Mutation SNP C C T C3N-02158_T C3N-02158_N C C c.581C>T p.Thr194Met p.T194M ENST00000331340 5/8 75 59 16 65 65 0 strelka-varscan-mutect IKZF1,missense_variant,p.Thr194Met,ENST00000331340,NM_006060.5;IKZF1,missense_variant,p.Thr107Met,ENST00000343574,NM_001291839.1,NM_001220767.2,NM_001291841.1;IKZF1,missense_variant,p.Thr194Met,ENST00000357364,NM_001220768.2;IKZF1,missense_variant,p.Thr194Met,ENST00000439701,NM_001291837.1;IKZF1,missense_variant,p.Thr194Met,ENST00000359197,NM_001220765.2;IKZF1,missense_variant,p.Thr107Met,ENST00000438033,NM_001291838.1;IKZF1,intron_variant,,ENST00000349824,NM_001220771.2;IKZF1,intron_variant,,ENST00000615491,;IKZF1,intron_variant,,ENST00000440768,;IKZF1,intron_variant,,ENST00000346667,;IKZF1,intron_variant,,ENST00000612658,;IKZF1,intron_variant,,ENST00000426121,;IKZF1,non_coding_transcript_exon_variant,,ENST00000471793,; T ENST00000331340 Transcript missense_variant 736/6189 581/1560 194/519 T/M aCg/aTg COSM3265417 1 1 IKZF1 HGNC HGNC:13176 protein_coding YES CCDS75596.1 ENSP00000331614 Q13422 UPI000012D465 NM_006060.5 deleterious(0) 5/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24404,hmmpanther:PTHR24404:SF36,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 50382699 50382699 C T 1 0 0 0 0 1 0 0 0 7522 536 19 1 1 IKZF1 7 50382699 Missense_Mutation SNP C C3N-02158_T 50382699 108963274 18 28916 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-02158_T C3N-02158_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 425 276 149 364 364 0 sindel-varindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 94 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-02158_T 4792073 55174772 104171201 19 28917 CACNB2 0 . GRCh38 10 18401930 18401930 + Missense_Mutation SNP G G T novel C3N-02158_T C3N-02158_N G G c.220G>T p.Ala74Ser p.A74S ENST00000324631 3/14 358 297 61 317 317 0 strelka-varscan-mutect CACNB2,missense_variant,p.Ala19Ser,ENST00000396576,NM_000724.3;CACNB2,missense_variant,p.Ala19Ser,ENST00000617363,;CACNB2,missense_variant,p.Ala20Ser,ENST00000612134,;CACNB2,missense_variant,p.Ala19Ser,ENST00000615785,;CACNB2,missense_variant,p.Ala46Ser,ENST00000282343,NM_201571.3,NM_001167945.1;CACNB2,missense_variant,p.Ala26Ser,ENST00000377315,NM_201570.2;CACNB2,missense_variant,p.Ala74Ser,ENST00000324631,NM_201596.2,NM_201593.2;CACNB2,missense_variant,p.Ala20Ser,ENST00000377329,NM_201590.2;CACNB2,missense_variant,p.Ala19Ser,ENST00000377319,;CACNB2,missense_variant,p.Ala74Ser,ENST00000352115,NM_201597.2;CACNB2,missense_variant,p.Ala46Ser,ENST00000377331,NM_201572.3;CACNB2,missense_variant,p.Ala74Ser,ENST00000377328,;CACNB2,5_prime_UTR_variant,,ENST00000612743,;CACNB2,non_coding_transcript_exon_variant,,ENST00000498816,; T ENST00000324631 Transcript missense_variant 280/3446 220/1983 74/660 A/S Gca/Tca 1 1 CACNB2 HGNC HGNC:1402 protein_coding YES CCDS7125.1 ENSP00000320025 Q08289 UPI00001AEA80 NM_201596.2,NM_201593.2 deleterious(0.01) 3/14 hmmpanther:PTHR11824:SF9,hmmpanther:PTHR11824,Pfam_domain:PF12052 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 18401930 18401930 G T 1 0 0 0 0 1 0 0 0 2241 1203 42 2 2 CACNB2 10 18401930 Missense_Mutation SNP G C3N-02158_T 18401930 115395492 20 28918 FERMT3 0 . GRCh38 11 64220637 64220637 + Missense_Mutation SNP C C T novel C3N-02158_T C3N-02158_N C C c.1525C>T p.Pro509Ser p.P509S ENST00000279227 12/15 344 306 38 224 224 0 strelka-varscan-mutect FERMT3,missense_variant,p.Pro509Ser,ENST00000279227,NM_178443.2;FERMT3,missense_variant,p.Pro505Ser,ENST00000345728,NM_031471.5;FERMT3,synonymous_variant,p.=,ENST00000545896,;TRPT1,downstream_gene_variant,,ENST00000394546,NM_001160389.1;FERMT3,downstream_gene_variant,,ENST00000544997,;TRPT1,downstream_gene_variant,,ENST00000317459,NM_001033678.3,NM_001160390.1,NM_001160393.1;TRPT1,downstream_gene_variant,,ENST00000541278,NM_001160392.1;TRPT1,downstream_gene_variant,,ENST00000394547,NM_031472.3;TRPT1,downstream_gene_variant,,ENST00000546089,;TRPT1,downstream_gene_variant,,ENST00000545812,;TRPT1,downstream_gene_variant,,ENST00000544286,;TRPT1,downstream_gene_variant,,ENST00000546133,;TRPT1,downstream_gene_variant,,ENST00000540472,;TRPT1,downstream_gene_variant,,ENST00000539595,;TRPT1,downstream_gene_variant,,ENST00000536234,;TRPT1,downstream_gene_variant,,ENST00000539436,;TRPT1,downstream_gene_variant,,ENST00000542040,;FERMT3,downstream_gene_variant,,ENST00000541326,;TRPT1,downstream_gene_variant,,ENST00000537907,;FERMT3,downstream_gene_variant,,ENST00000540957,;FERMT3,downstream_gene_variant,,ENST00000546255,;TRPT1,downstream_gene_variant,,ENST00000536158,;TRPT1,downstream_gene_variant,,ENST00000541928,;FERMT3,upstream_gene_variant,,ENST00000540554,; T ENST00000279227 Transcript missense_variant 1620/2489 1525/2004 509/667 P/S Ccc/Tcc 1 1 FERMT3 HGNC HGNC:23151 protein_coding YES CCDS8060.1 ENSP00000279227 Q86UX7 UPI000019270B NM_178443.2 deleterious(0.04) 12/15 hmmpanther:PTHR16160,hmmpanther:PTHR16160:SF1,Pfam_domain:PF00373,Gene3D:1.20.80.10,SMART_domains:SM00295,Superfamily_domains:SSF47031 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 64220637 64220637 C T 1 0 0 0 0 1 0 0 0 5682 623 22 3 3 FERMT3 11 64220637 Missense_Mutation SNP C C3N-02158_T 64220637 70865985 21 28919 DPPA3 0 . GRCh38 12 7711647 7711647 + Missense_Mutation SNP A A G rs772947924 C3N-02158_T C3N-02158_N A A c.77A>G p.Asp26Gly p.D26G ENST00000345088 1/4 326 244 82 176 175 1 strelka-varscan-mutect DPPA3,missense_variant,p.Asp26Gly,ENST00000345088,NM_199286.3; G ENST00000345088 Transcript missense_variant 194/1079 77/480 26/159 D/G gAt/gGt rs772947924,COSM4211374 1 1 DPPA3 HGNC HGNC:19199 protein_coding YES CCDS8582.1 ENSP00000339250 Q6W0C5 UPI00001981F7 NM_199286.3 tolerated(0.63) 1/4 hmmpanther:PTHR31577,hmmpanther:PTHR31577:SF2,Pfam_domain:PF15549 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs772947924 . 0 129 0 5 37 39 0 0 -2.710216 0 0 1 0 0 G 3 3 94 7711647 7711647 A G 1 0 0 0 0 1 0 0 0 4550 347 12 5 5 DPPA3 12 7711647 Missense_Mutation SNP A C3N-02158_T 7711647 125563662 22 28920 PMCH 0 . GRCh38 12 102197633 102197633 + Missense_Mutation SNP T T G novel C3N-02158_T C3N-02158_N T T c.138A>C p.Lys46Asn p.K46N ENST00000329406 1/3 346 299 47 256 256 0 strelka-varscan-mutect PMCH,missense_variant,p.Lys46Asn,ENST00000329406,NM_002674.2;PARPBP,downstream_gene_variant,,ENST00000327680,NM_001319994.1,NM_017915.3;PARPBP,downstream_gene_variant,,ENST00000541394,;PARPBP,downstream_gene_variant,,ENST00000417507,;PARPBP,downstream_gene_variant,,ENST00000412715,;PARPBP,downstream_gene_variant,,ENST00000392911,;PARPBP,downstream_gene_variant,,ENST00000543784,;HELLPAR,non_coding_transcript_exon_variant,,ENST00000626826,;PARPBP,downstream_gene_variant,,ENST00000535811,;PARPBP,downstream_gene_variant,,ENST00000457614,; G ENST00000329406 Transcript missense_variant 213/766 138/498 46/165 K/N aaA/aaC 1 -1 PMCH HGNC HGNC:9109 protein_coding YES CCDS31885.1 ENSP00000332225 P20382 UPI000006D1DF NM_002674.2 deleterious(0.01) 1/3 hmmpanther:PTHR12091 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 94 102197633 102197633 T G 1 0 0 0 0 1 0 0 0 12237 1606 56 5 5 PMCH 12 102197633 Missense_Mutation SNP T C3N-02158_T 94485986 102197633 31077676 23 28921 MAP2K5 0 . GRCh38 15 67543417 67543417 + Missense_Mutation SNP G G A C3N-02158_T C3N-02158_N G G c.82G>A p.Ala28Thr p.A28T ENST00000178640 1/22 238 207 31 200 200 0 strelka-varscan-mutect MAP2K5,missense_variant,p.Ala28Thr,ENST00000178640,NM_145160.2;MAP2K5,missense_variant,p.Ala28Thr,ENST00000395476,NM_002757.3;RP11-502I4.3,upstream_gene_variant,,ENST00000604760,;MAP2K5,non_coding_transcript_exon_variant,,ENST00000560591,;MAP2K5,upstream_gene_variant,,ENST00000560086,; A ENST00000178640 Transcript missense_variant 709/2347 82/1347 28/448 A/T Gcg/Acg COSM194330 1 1 MAP2K5 HGNC HGNC:6845 protein_coding YES CCDS10224.1 ENSP00000178640 Q13163 A0A024R5Y2 UPI0000072D4A NM_145160.2 tolerated(0.24) 1/22 Gene3D:3.10.20.240,Pfam_domain:PF00564,PROSITE_profiles:PS51745,SMART_domains:SM00666,Superfamily_domains:SSF54277 1 MODERATE 1 SNV 1 1 1 PASS rs1376634815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 67543417 67543417 G A 1 0 0 0 0 1 0 0 0 9162 1087 38 1 1 MAP2K5 15 67543417 Missense_Mutation SNP G C3N-02158_T 67543417 34447772 24 28922 KDM6B 0 . GRCh38 17 7848714 7848714 + Missense_Mutation SNP C C T novel C3N-02158_T C3N-02158_N C C c.2426C>T p.Ser809Phe p.S809F ENST00000254846 11/22 242 209 33 112 112 0 strelka-varscan-mutect KDM6B,missense_variant,p.Ser809Phe,ENST00000254846,NM_001080424.1;KDM6B,missense_variant,p.Ser809Phe,ENST00000448097,;KDM6B,downstream_gene_variant,,ENST00000570632,;KDM6B,downstream_gene_variant,,ENST00000571047,;KDM6B,downstream_gene_variant,,ENST00000575521,; T ENST00000254846 Transcript missense_variant 2815/6713 2426/5049 809/1682 S/F tCc/tTc 1 1 KDM6B HGNC HGNC:29012 protein_coding YES CCDS32552.1 ENSP00000254846 O15054 UPI00006C175B NM_001080424.1 deleterious_low_confidence(0) 11/22 Low_complexity_(Seg):seg,hmmpanther:PTHR14017:SF5,hmmpanther:PTHR14017 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 7848714 7848714 C T 1 0 0 0 0 1 0 0 0 8056 855 30 3 3 KDM6B 17 7848714 Missense_Mutation SNP C C3N-02158_T 7848714 75408727 25 28923 NKIRAS2 0 . GRCh38 17 42022459 42022459 + Missense_Mutation SNP G G T novel C3N-02158_T C3N-02158_N G G c.155G>T p.Gly52Val p.G52V ENST00000307641 3/4 97 83 14 57 57 0 strelka-varscan-mutect NKIRAS2,missense_variant,p.Gly52Val,ENST00000307641,NM_001001349.2;NKIRAS2,missense_variant,p.Gly52Val,ENST00000393885,NM_001144927.1,NM_017595.5;NKIRAS2,missense_variant,p.Gly52Val,ENST00000393880,;NKIRAS2,missense_variant,p.Gly52Val,ENST00000393881,;NKIRAS2,missense_variant,p.Gly52Val,ENST00000449471,NM_001144928.1;NKIRAS2,missense_variant,p.Gly52Val,ENST00000479407,NM_001144929.1;NKIRAS2,missense_variant,p.Gly52Val,ENST00000316082,;NKIRAS2,missense_variant,p.Gly18Val,ENST00000587337,;NKIRAS2,intron_variant,,ENST00000462043,;ZNF385C,downstream_gene_variant,,ENST00000618554,NM_001242704.1;DNAJC7,upstream_gene_variant,,ENST00000457167,NM_003315.3;ZNF385C,downstream_gene_variant,,ENST00000436535,;DNAJC7,upstream_gene_variant,,ENST00000590348,;DNAJC7,upstream_gene_variant,,ENST00000589773,;DNAJC7,upstream_gene_variant,,ENST00000591787,;NKIRAS2,downstream_gene_variant,,ENST00000585955,;ZNF385C,downstream_gene_variant,,ENST00000461831,;NKIRAS2,missense_variant,p.Gly52Val,ENST00000485789,;NKIRAS2,3_prime_UTR_variant,,ENST00000491638,;NKIRAS2,non_coding_transcript_exon_variant,,ENST00000393879,;ZNF385C,downstream_gene_variant,,ENST00000496039,;NKIRAS2,downstream_gene_variant,,ENST00000587028,; T ENST00000307641 Transcript missense_variant 776/2948 155/576 52/191 G/V gGg/gTg 1 1 NKIRAS2 HGNC HGNC:17898 protein_coding YES CCDS11415.1 ENSP00000303580 Q9NYR9 A0A024R1Z4 UPI00000465E5 NM_001001349.2 deleterious(0) 3/4 Gene3D:3.40.50.300,Pfam_domain:PF00071,PROSITE_profiles:PS51419,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF236,SMART_domains:SM00173,SMART_domains:SM00175,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00231 MODERATE 1 SNV 1 1 PASS rs1390482677 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 42022459 42022459 G T 1 0 0 0 0 1 0 0 0 10480 1232 43 2 2 NKIRAS2 17 42022459 Missense_Mutation SNP G C3N-02158_T 34173745 42022459 41234982 26 28924 TMEM105 0 . GRCh38 17 81313796 81313796 + Missense_Mutation SNP C C T rs75774881 C3N-02158_T C3N-02158_N C C c.245G>A p.Arg82Gln p.R82Q ENST00000332900 3/3 329 287 42 186 186 0 strelka-varscan-mutect TMEM105,missense_variant,p.Arg82Gln,ENST00000332900,NM_178520.3;TMEM105,missense_variant,p.Arg60Gln,ENST00000574093,;LINC00482,upstream_gene_variant,,ENST00000332012,; T ENST00000332900 Transcript missense_variant 795/3321 245/390 82/129 R/Q cGa/cAa rs75774881 1 -1 TMEM105 HGNC HGNC:26794 protein_coding YES CCDS11781.1 ENSP00000329795 Q8N8V8 UPI0000071895 NM_178520.3 tolerated_low_confidence(0.37) 3/3 MODERATE SNV 2 1 PASS rs75774881 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 81313796 81313796 C T 1 0 0 0 0 1 0 0 0 16463 884 31 1 1 TMEM105 17 81313796 Missense_Mutation SNP C C3N-02158_T 39291337 81313796 1943645 27 28925 FASN 0 . GRCh38 17 82089381 82089381 + Missense_Mutation SNP G G A novel C3N-02158_T C3N-02158_N G G c.1969C>T p.Pro657Ser p.P657S ENST00000306749 13/43 349 308 41 240 239 1 strelka-varscan-mutect FASN,missense_variant,p.Pro657Ser,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Pro657Ser,ENST00000634990,;FASN,downstream_gene_variant,,ENST00000635197,;FASN,downstream_gene_variant,,ENST00000637525,;FASN,upstream_gene_variant,,ENST00000579410,; A ENST00000306749 Transcript missense_variant 2188/8565 1969/7536 657/2511 P/S Ccg/Tcg 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 tolerated(0.6) 13/43 Gene3D:3.30.70.250,Pfam_domain:PF00698,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,SMART_domains:SM00827,Superfamily_domains:SSF55048 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 82089381 82089381 G A 1 0 0 0 0 1 0 0 0 5543 1246 43 3 3 FASN 17 82089381 Missense_Mutation SNP G C3N-02158_T 775585 82089381 1168060 28 28926 SMARCA4 0 . GRCh38 19 11030751 11030751 + Missense_Mutation SNP G G A C3N-02158_T C3N-02158_N G G c.3404G>A p.Arg1135Gln p.R1135Q ENST00000429416 26/36 296 257 39 247 247 0 strelka-varscan-mutect SMARCA4,missense_variant,p.Arg1135Gln,ENST00000429416,NM_001128844.1;SMARCA4,missense_variant,p.Arg1199Gln,ENST00000413806,;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000450717,NM_001128849.1;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000344626,NM_003072.3;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000590574,NM_001128847.1;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000589677,NM_001128846.1;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000541122,NM_001128845.1;SMARCA4,missense_variant,p.Arg1135Gln,ENST00000444061,NM_001128848.1;SMARCA4,upstream_gene_variant,,ENST00000592158,;uc_338,upstream_gene_variant,,ENST00000620113,;SMARCA4,upstream_gene_variant,,ENST00000538456,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591545,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000585799,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000591595,;SMARCA4,non_coding_transcript_exon_variant,,ENST00000592604,;SMARCA4,upstream_gene_variant,,ENST00000586892,; A ENST00000429416 Transcript missense_variant 3685/5691 3404/4944 1135/1647 R/Q cGg/cAg COSM1740484,COSM1740485,COSM5131115,COSM5131116 1 1 SMARCA4 HGNC HGNC:11100 protein_coding YES CCDS12253.1 ENSP00000395654 P51532 A7E2E1 UPI000006F973 NM_001128844.1 deleterious(0) 26/36 PROSITE_profiles:PS51194,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF76,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 1,1,1,1 MODERATE 1 SNV 2 1,1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 11030751 11030751 G A 1 0 0 0 0 1 0 0 0 15063 1116 39 1 1 SMARCA4 19 11030751 Missense_Mutation SNP G C3N-02158_T 11030751 47586865 29 28927 ZNF792 0 . GRCh38 19 34959192 34959192 + Silent SNP G G C novel C3N-02158_T C3N-02158_N G G c.663C>G p.= p.A221A ENST00000404801 4/4 157 136 21 135 135 0 strelka-varscan-mutect ZNF792,synonymous_variant,p.=,ENST00000404801,NM_175872.4;ZNF792,synonymous_variant,p.=,ENST00000605484,; C ENST00000404801 Transcript synonymous_variant 1050/3888 663/1899 221/632 A gcC/gcG 1 -1 ZNF792 HGNC HGNC:24751 protein_coding YES CCDS12440.2 ENSP00000385099 Q3KQV3 UPI0000202090 NM_175872.4 4/4 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF187 LOW 1 SNV 2 1 PASS rs1386152188 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 94 34959192 34959192 G C 1 0 0 0 0 0 0 0 1 18749 1335 47 4 4 ZNF792 19 34959192 Silent SNP G C3N-02158_T 23928441 34959192 23658424 30 28928 CD33 0 . GRCh38 19 51225979 51225979 + Missense_Mutation SNP A A T C3N-02158_T C3N-02158_N A A c.595A>T p.Ile199Phe p.I199F ENST00000262262 3/7 184 161 23 175 175 0 strelka-varscan-mutect CD33,missense_variant,p.Ile72Phe,ENST00000436584,;CD33,missense_variant,p.Ile199Phe,ENST00000262262,NM_001772.3;CD33,missense_variant,p.Ile199Phe,ENST00000391796,NM_001177608.1;CD33,missense_variant,p.Ile72Phe,ENST00000421133,NM_001082618.1;CD33,non_coding_transcript_exon_variant,,ENST00000598473,;CD33,non_coding_transcript_exon_variant,,ENST00000601785,; T ENST00000262262 Transcript missense_variant 616/1444 595/1095 199/364 I/F Atc/Ttc COSM5603118,COSM5603119 1 1 CD33 HGNC HGNC:1659 protein_coding YES CCDS33084.1 ENSP00000262262 P20138 Q546G0 UPI000013D285 NM_001772.3 tolerated(0.06) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF52,hmmpanther:PTHR12035,Gene3D:2.60.40.10,Pfam_domain:PF00047,SMART_domains:SM00409,Superfamily_domains:SSF48726 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 51225979 51225979 A T 1 0 0 0 0 1 0 0 0 2709 101 4 4 4 CD33 19 51225979 Missense_Mutation SNP A C3N-02158_T 16266787 51225979 7391637 31 28929 IL11 0 . GRCh38 19 55368364 55368364 + Missense_Mutation SNP C C A rs764018519 C3N-02158_T C3N-02158_N C C c.275G>T p.Gly92Val p.G92V ENST00000264563 4/5 47 41 6 26 26 0 strelka-mutect IL11,missense_variant,p.Gly92Val,ENST00000264563,NM_000641.3;IL11,missense_variant,p.Gly92Val,ENST00000585513,;IL11,missense_variant,p.Gly13Val,ENST00000590625,NM_001267718.1;IL11,missense_variant,p.Gly13Val,ENST00000587093,; A ENST00000264563 Transcript missense_variant 338/2281 275/600 92/199 G/V gGt/gTt rs764018519 1 -1 IL11 HGNC HGNC:5966 protein_coding YES CCDS12923.1 ENSP00000264563 P20809 A8K3F7 UPI000000D8E5 NM_000641.3 deleterious(0.04) 4/5 Gene3D:1.20.1250.10,Pfam_domain:PF07400,hmmpanther:PTHR16922,hmmpanther:PTHR16922:SF0,Superfamily_domains:SSF47266 MODERATE 1 SNV 1 1 PASS rs764018519 . 0 207 3 0 0 0 0 0 -14.99363 1 1 1 1 0 A 3 1 94 55368364 55368364 C A 1 0 0 0 0 1 0 0 0 7530 507 18 2 2 IL11 19 55368364 Missense_Mutation SNP C C3N-02158_T 4142385 55368364 3249252 32 28930 KCNS1 0 . GRCh38 20 45097938 45097938 + Missense_Mutation SNP G G C novel C3N-02158_T C3N-02158_N G G c.834C>G p.Phe278Leu p.F278L ENST00000306117 4/5 238 212 26 183 183 0 strelka-varscan-mutect KCNS1,missense_variant,p.Phe278Leu,ENST00000306117,NM_002251.3;KCNS1,missense_variant,p.Phe278Leu,ENST00000537075,; C ENST00000306117 Transcript missense_variant 1231/4538 834/1581 278/526 F/L ttC/ttG 1 -1 KCNS1 HGNC HGNC:6300 protein_coding YES CCDS13342.1 ENSP00000307694 Q96KK3 A2RUL8 UPI000012DCD1 NM_002251.3 tolerated(0.17) 4/5 Gene3D:1.20.120.350,Pfam_domain:PF00520,Prints_domain:PR00169,hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF61,Superfamily_domains:SSF81324 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 94 45097938 45097938 G C 1 0 0 0 0 1 0 0 0 8004 933 33 4 4 KCNS1 20 45097938 Missense_Mutation SNP G C3N-02158_T 45097938 19346229 33 28931 CSE1L 0 . GRCh38 20 49085365 49085365 + Nonsense_Mutation SNP G G T novel C3N-02158_T C3N-02158_N G G c.1702G>T p.Glu568Ter p.E568* ENST00000262982 16/25 222 143 79 99 99 0 strelka-varscan-mutect CSE1L,stop_gained,p.Glu568Ter,ENST00000262982,NM_001316.3;CSE1L,stop_gained,p.Glu512Ter,ENST00000396192,NM_001256135.1; T ENST00000262982 Transcript stop_gained 1825/3553 1702/2916 568/971 E/* Gaa/Taa 1 1 CSE1L HGNC HGNC:2431 protein_coding YES CCDS13412.1 ENSP00000262982 P55060 UPI000013D377 NM_001316.3 16/25 hmmpanther:PTHR10997,hmmpanther:PTHR10997:SF8,Gene3D:1.25.10.10,Pfam_domain:PF03378,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 94 49085365 49085365 G T 1 0 0 0 0 0 1 0 0 3731 943 33 2 2 CSE1L 20 49085365 Nonsense_Mutation SNP G C3N-02158_T 3987427 49085365 15358802 34 28932 MAGEB6 0 . GRCh38 X 26194176 26194176 + Silent SNP A A T novel C3N-02158_T C3N-02158_N A A c.330A>T p.= p.S110S ENST00000379034 2/2 462 414 48 322 322 0 strelka-varscan-mutect MAGEB6,synonymous_variant,p.=,ENST00000379034,NM_173523.2; T ENST00000379034 Transcript synonymous_variant 479/1949 330/1224 110/407 S tcA/tcT 1 1 MAGEB6 HGNC HGNC:23796 protein_coding YES CCDS14217.1 ENSP00000368320 Q8N7X4 UPI00001413F4 NM_173523.2 2/2 Pfam_domain:PF12440,SMART_domains:SM01392 LOW 1 SNV 1 1 PASS . . 22 188 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 94 26194176 26194176 A T 1 0 0 0 0 0 0 0 1 9096 146 6 4 4 MAGEB6 23 26194176 Silent SNP A C3N-02158_T 26194176 129846719 35 28933 CFAP47 0 . GRCh38 X 36236700 36236700 + Silent SNP A A T novel C3N-02158_T C3N-02158_N A A c.7173A>T p.= p.L2391L ENST00000378653 48/64 289 244 45 166 166 0 strelka-varscan-mutect CFAP47,synonymous_variant,p.=,ENST00000378653,NM_001304548.1; T ENST00000378653 Transcript synonymous_variant 7239/9943 7173/9564 2391/3187 L ctA/ctT 1 1 CFAP47 HGNC HGNC:26708 protein_coding ENSP00000367922 A0A140T8X2 UPI000596DACD NM_001304548.1 48/64 hmmpanther:PTHR23053 LOW 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 94 36236700 36236700 A T 1 0 0 0 0 0 0 0 1 3022 378 14 4 4 CFAP47 23 36236700 Silent SNP A C3N-02158_T 10042524 36236700 119804195 36 28934 CHST7 0 . GRCh38 X 46575213 46575213 + Missense_Mutation SNP C C T novel C3N-02158_T C3N-02158_N C C c.1282C>T p.Arg428Trp p.R428W ENST00000276055 1/2 143 124 19 79 79 0 strelka-varscan-mutect CHST7,missense_variant,p.Arg428Trp,ENST00000276055,NM_019886.3; T ENST00000276055 Transcript missense_variant 1430/2289 1282/1461 428/486 R/W Cgg/Tgg 1 1 CHST7 HGNC HGNC:13817 protein_coding YES CCDS14268.1 ENSP00000276055 Q9NS84 UPI000000DADD NM_019886.3 deleterious(0.01) 1/2 Gene3D:3.40.50.300,Pfam_domain:PF00685,PIRSF_domain:PIRSF005883,hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF5,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS rs1456028098 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 94 46575213 46575213 C T 1 0 0 0 0 1 0 0 0 3169 643 23 1 1 CHST7 23 46575213 Missense_Mutation SNP C C3N-02158_T 10338513 46575213 109465682 37 28935 KDM5C 0 . GRCh38 X 53196698 53196698 + Missense_Mutation SNP C C A novel C3N-02158_T C3N-02158_N C C c.2969G>T p.Cys990Phe p.C990F ENST00000375401 19/26 167 150 17 97 97 0 strelka-varscan-mutect KDM5C,missense_variant,p.Cys923Phe,ENST00000452825,NM_001146702.1;KDM5C,missense_variant,p.Cys990Phe,ENST00000375401,NM_004187.3;KDM5C,missense_variant,p.Cys989Phe,ENST00000404049,NM_001282622.1;KDM5C,missense_variant,p.Cys990Phe,ENST00000375379,;KDM5C,missense_variant,p.Cys949Phe,ENST00000375383,;MIR6895,upstream_gene_variant,,ENST00000613497,;MIR6894,downstream_gene_variant,,ENST00000622662,;KDM5C,downstream_gene_variant,,ENST00000465402,;KDM5C,downstream_gene_variant,,ENST00000477109,;KDM5C,downstream_gene_variant,,ENST00000497100,;KDM5C,downstream_gene_variant,,ENST00000481369,; A ENST00000375401 Transcript missense_variant 3502/6031 2969/4683 990/1560 C/F tGc/tTc 1 -1 KDM5C HGNC HGNC:11114 protein_coding YES CCDS14351.1 ENSP00000364550 P41229 UPI000013CBE3 NM_004187.3 tolerated(0.08) 19/26 Pfam_domain:PF08429,hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF43 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.999999 1 1 1 0 A 3 1 94 53196698 53196698 C A 1 0 0 0 0 1 0 0 0 8053 710 25 2 2 KDM5C 23 53196698 Missense_Mutation SNP C C3N-02158_T 6621485 53196698 102844197 38 28936 EDA 0 . GRCh38 X 70035358 70035358 + Missense_Mutation SNP G G A novel C3N-02158_T C3N-02158_N G G c.925G>A p.Val309Ile p.V309I ENST00000374552 8/8 377 337 40 226 226 0 strelka-varscan-mutect EDA,missense_variant,p.Val309Ile,ENST00000374552,NM_001399.4;EDA,missense_variant,p.Val307Ile,ENST00000374553,NM_001005609.1;EDA,missense_variant,p.Val177Ile,ENST00000616899,;EDA,missense_variant,p.Val304Ile,ENST00000524573,NM_001005612.2;EDA,downstream_gene_variant,,ENST00000503592,; A ENST00000374552 Transcript missense_variant,splice_region_variant 1167/5278 925/1176 309/391 V/I Gta/Ata 1 1 EDA HGNC HGNC:3157 protein_coding YES CCDS14394.1 ENSP00000363680 Q92838 UPI0000052244 NM_001399.4 deleterious_low_confidence(0.03) 8/8 Gene3D:2.60.120.40,Pfam_domain:PF00229,PROSITE_profiles:PS50049,hmmpanther:PTHR15151,hmmpanther:PTHR15151:SF4,Superfamily_domains:SSF49842 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 70035358 70035358 G A 1 0 0 0 0 1 0 0 0 4731 1275 44 3 3 EDA 23 70035358 Missense_Mutation SNP G C3N-02158_T 16838660 70035358 86005537 39 28937 TEX11 0 . GRCh38 X 70682820 70682820 + Missense_Mutation SNP G G A C3N-02158_T C3N-02158_N G G c.1055C>T p.Ser352Phe p.S352F ENST00000395889 15/31 205 189 16 128 128 0 strelka-varscan-mutect TEX11,missense_variant,p.Ser352Phe,ENST00000395889,NM_001003811.1;TEX11,missense_variant,p.Ser337Phe,ENST00000374333,NM_031276.2;TEX11,missense_variant,p.Ser352Phe,ENST00000344304,;TEX11,missense_variant,p.Ser27Phe,ENST00000374320,; A ENST00000395889 Transcript missense_variant 1211/3133 1055/2823 352/940 S/F tCt/tTt COSM1124519,COSM4866011 1 -1 TEX11 HGNC HGNC:11733 protein_coding YES CCDS35323.1 ENSP00000379226 Q8IYF3 UPI000013CA89 NM_001003811.1 tolerated(0.26) 15/31 hmmpanther:PTHR22904,hmmpanther:PTHR22904:SF386,Pfam_domain:PF08631 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 94 70682820 70682820 G A 1 0 0 0 0 1 0 0 0 16195 956 33 3 3 TEX11 23 70682820 Missense_Mutation SNP G C3N-02158_T 647462 70682820 85358075 40 28938 F9 0 . GRCh38 X 139561619 139561619 + Missense_Mutation SNP T T C novel C3N-02158_T C3N-02158_N T T c.934T>C p.Tyr312His p.Y312H ENST00000218099 8/8 127 97 30 116 116 0 strelka-varscan-mutect F9,missense_variant,p.Tyr312His,ENST00000218099,NM_000133.3;F9,missense_variant,p.Tyr274His,ENST00000394090,; C ENST00000218099 Transcript missense_variant 941/2780 934/1386 312/461 Y/H Tac/Cac 1 1 F9 HGNC HGNC:3551 protein_coding YES CCDS14666.1 ENSP00000218099 P00740 UPI000002BA13 NM_000133.3 tolerated(0.17) 8/8 Gene3D:2.40.10.10,Pfam_domain:PF00089,PIRSF_domain:PIRSF001143,Prints_domain:PR00722,PROSITE_profiles:PS50240,hmmpanther:PTHR24256,hmmpanther:PTHR24256:SF135,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 94 139561619 139561619 T C 1 0 0 0 0 1 0 0 0 5220 1638 57 5 5 F9 23 139561619 Missense_Mutation SNP T C3N-02158_T 68878799 139561619 16479276 41 28939 WLS 0 . GRCh38 1 68126279 68126279 + Missense_Mutation SNP C C T novel C3N-02379_T C3N-02379_N C C c.1573G>A p.Val525Met p.V525M ENST00000262348 12/12 296 272 24 375 375 0 strelka-varscan-mutect WLS,missense_variant,p.Val525Met,ENST00000262348,NM_024911.6;WLS,missense_variant,p.Val434Met,ENST00000370976,NM_001193334.1;WLS,intron_variant,,ENST00000354777,NM_001002292.3;GNG12-AS1,intron_variant,,ENST00000420587,;GNG12-AS1,intron_variant,,ENST00000413628,;WLS,non_coding_transcript_exon_variant,,ENST00000498615,; T ENST00000262348 Transcript missense_variant 1827/2748 1573/1626 525/541 V/M Gtg/Atg 1 -1 WLS HGNC HGNC:30238 protein_coding CCDS642.1 ENSP00000262348 Q5T9L3 UPI0000049FDB NM_024911.6 tolerated(0.11) 12/12 hmmpanther:PTHR13449 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 68126279 68126279 C T 1 0 0 0 0 1 0 0 0 17932 478 17 3 3 WLS 1 68126279 Missense_Mutation SNP C C3N-02379_T 68126279 180830143 1 28940 PRRC2C 0 . GRCh38 1 171513033 171513033 + Missense_Mutation SNP G G A novel C3N-02379_T C3N-02379_N G G c.145G>A p.Gly49Ser p.G49S ENST00000338920 3/34 138 121 17 148 148 0 strelka-varscan-mutect PRRC2C,missense_variant,p.Gly51Ser,ENST00000367742,;PRRC2C,missense_variant,p.Gly49Ser,ENST00000338920,NM_015172.3;PRRC2C,missense_variant,p.Gly49Ser,ENST00000426496,;PRRC2C,5_prime_UTR_variant,,ENST00000392078,;PRRC2C,non_coding_transcript_exon_variant,,ENST00000476522,;PRRC2C,non_coding_transcript_exon_variant,,ENST00000467601,;PRRC2C,non_coding_transcript_exon_variant,,ENST00000463586,; A ENST00000338920 Transcript missense_variant 382/10355 145/8454 49/2817 G/S Ggt/Agt 1 1 PRRC2C HGNC HGNC:24903 protein_coding YES CCDS1296.2 ENSP00000343629 Q9Y520 UPI0000E265EC NM_015172.3 deleterious(0.01) 3/34 hmmpanther:PTHR14038,hmmpanther:PTHR14038:SF6,Pfam_domain:PF07001 MODERATE 1 SNV 5 1 PASS rs1408902539 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 171513033 171513033 G A 1 0 0 0 0 1 0 0 0 12750 1116 39 1 1 PRRC2C 1 171513033 Missense_Mutation SNP G C3N-02379_T 103386754 171513033 77443389 2 28941 RRP15 0 . GRCh38 1 218331041 218331041 + Missense_Mutation SNP G G T novel C3N-02379_T C3N-02379_N G G c.799G>T p.Asp267Tyr p.D267Y ENST00000366932 5/5 246 202 44 275 275 0 strelka-varscan-mutect RRP15,missense_variant,p.Asp267Tyr,ENST00000366932,NM_016052.3; T ENST00000366932 Transcript missense_variant 829/7771 799/849 267/282 D/Y Gat/Tat 1 1 RRP15 HGNC HGNC:24255 protein_coding YES CCDS1520.2 ENSP00000355899 Q9Y3B9 UPI0000205BC1 NM_016052.3 deleterious(0) 5/5 hmmpanther:PTHR13245 MODERATE 1 SNV 1 1 PASS rs1266530158 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 218331041 218331041 G T 1 0 0 0 0 1 0 0 0 13942 1290 45 2 2 RRP15 1 218331041 Missense_Mutation SNP G C3N-02379_T 46818008 218331041 30625381 3 28942 ZNF804A 0 . GRCh38 2 184938341 184938341 + Missense_Mutation SNP G G A C3N-02379_T C3N-02379_N G G c.2945G>A p.Gly982Glu p.G982E ENST00000302277 4/4 262 161 101 238 238 0 strelka-varscan-mutect ZNF804A,missense_variant,p.Gly982Glu,ENST00000302277,NM_194250.1;ZNF804A,missense_variant,p.Gly897Glu,ENST00000613975,; A ENST00000302277 Transcript missense_variant 3539/4690 2945/3630 982/1209 G/E gGa/gAa COSM1721105 1 1 ZNF804A HGNC HGNC:21711 protein_coding YES CCDS2291.1 ENSP00000303252 Q7Z570 UPI00001B4B18 NM_194250.1 tolerated(0.56) 4/4 hmmpanther:PTHR17614,hmmpanther:PTHR17614:SF13 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 184938341 184938341 G A 1 0 0 0 0 1 0 0 0 18755 1174 41 3 3 ZNF804A 2 184938341 Missense_Mutation SNP G C3N-02379_T 184938341 57255188 4 28943 ADAMTS9 0 . GRCh38 3 64631462 64631474 + Frame_Shift_Del DEL GTTGTCATCGTCT GTTGTCATCGTCT - novel C3N-02379_T C3N-02379_N GTTGTCATCGTCT GTTGTCATCGTCT c.2370_2382delAGACGATGACAAC p.Asp791ThrfsTer2 p.D791Tfs*2 ENST00000498707 16/40 223 185 38 243 243 0 sindel-varindel-pindel ADAMTS9,frameshift_variant,p.Asp791ThrfsTer2,ENST00000498707,NM_182920.1;ADAMTS9,frameshift_variant,p.Asp763ThrfsTer2,ENST00000295903,NM_001318781.1;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000482490,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000475557,; - ENST00000498707 Transcript frameshift_variant 2713-2725/7624 2370-2382/5808 790-794/1935 TDDDN/X acAGACGATGACAAC/ac 1 -1 ADAMTS9 HGNC HGNC:13202 protein_coding YES CCDS2903.1 ENSP00000418735 Q9P2N4 UPI00000463F0 NM_182920.1 16/40 hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF33,Pfam_domain:PF05986 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 95 64631462 64631462 GTTGTCATCGTCT - 1 0 1 0 1 0 0 0 0 317 1020 36 0 0 ADAMTS9 3 64631462 Frame_Shift_Del DEL GTTGTCATCGTCT C3N-02379_T 64631462 133664097 5 28944 PLD1 0 . GRCh38 3 171699816 171699816 + Nonsense_Mutation SNP C C A novel C3N-02379_T C3N-02379_N C C c.1156G>T p.Glu386Ter p.E386* ENST00000351298 12/27 183 137 46 174 174 0 strelka-varscan-mutect PLD1,stop_gained,p.Glu386Ter,ENST00000356327,NM_001130081.2;PLD1,stop_gained,p.Glu386Ter,ENST00000351298,NM_002662.4;PLD1,non_coding_transcript_exon_variant,,ENST00000481505,; A ENST00000351298 Transcript stop_gained 1283/5604 1156/3225 386/1074 E/* Gaa/Taa 1 -1 PLD1 HGNC HGNC:9067 protein_coding YES CCDS3216.1 ENSP00000342793 Q13393 UPI0000131BDC NM_002662.4 12/27 hmmpanther:PTHR18896,hmmpanther:PTHR18896:SF57,PIRSF_domain:PIRSF009376,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 95 171699816 171699816 C A 1 0 0 0 0 0 1 0 0 12139 922 32 2 2 PLD1 3 171699816 Nonsense_Mutation SNP C C3N-02379_T 107068354 171699816 26595743 6 28945 LSG1 0 . GRCh38 3 194651007 194651007 + Silent SNP A A G novel C3N-02379_T C3N-02379_N A A c.1293T>C p.= p.P431P ENST00000265245 10/14 157 145 12 129 129 0 strelka-varscan-mutect LSG1,synonymous_variant,p.=,ENST00000265245,NM_018385.2;LSG1,synonymous_variant,p.=,ENST00000437613,;LSG1,non_coding_transcript_exon_variant,,ENST00000466391,;LSG1,non_coding_transcript_exon_variant,,ENST00000461343,;LSG1,upstream_gene_variant,,ENST00000460584,;LSG1,upstream_gene_variant,,ENST00000475763,; G ENST00000265245 Transcript synonymous_variant 1608/3572 1293/1977 431/658 P ccT/ccC 1 -1 LSG1 HGNC HGNC:25652 protein_coding YES CCDS33922.1 ENSP00000265245 Q9H089 UPI0000DBEEC1 NM_018385.2 10/14 Gene3D:3.40.50.300,Pfam_domain:PF01926,PROSITE_profiles:PS51721,hmmpanther:PTHR11089,hmmpanther:PTHR11089:SF7,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 95 194651007 194651007 A G 1 0 0 0 0 0 0 0 1 8955 175 7 5 5 LSG1 3 194651007 Silent SNP A C3N-02379_T 22951191 194651007 3644552 7 28946 KIAA1211 0 . GRCh38 4 56327723 56327723 + Silent SNP C C T rs368775360 C3N-02379_T C3N-02379_N C C c.3621C>T p.= p.P1207P ENST00000504228 9/9 257 243 14 341 341 0 strelka-varscan-mutect KIAA1211,synonymous_variant,p.=,ENST00000504228,;KIAA1211,synonymous_variant,p.=,ENST00000541073,;KIAA1211,synonymous_variant,p.=,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000514330,; T ENST00000504228 Transcript synonymous_variant 3726/4628 3621/3702 1207/1233 P ccC/ccT rs368775360,COSM587539 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 9/9 0,1 LOW 1 SNV 5 0,1 1 PASS rs368775360 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 95 56327723 56327723 C T 1 0 0 0 0 0 0 0 1 8107 639 23 1 1 KIAA1211 4 56327723 Silent SNP C C3N-02379_T 56327723 133886832 8 28947 PTPN13 0 . GRCh38 4 86807769 86807769 + Missense_Mutation SNP T T C novel C3N-02379_T C3N-02379_N T T c.6970T>C p.Cys2324Arg p.C2324R ENST00000436978 45/48 293 248 45 324 323 1 strelka-varscan-mutect PTPN13,missense_variant,p.Cys2324Arg,ENST00000436978,NM_080685.2;PTPN13,missense_variant,p.Cys2300Arg,ENST00000427191,NM_006264.2;PTPN13,missense_variant,p.Cys2319Arg,ENST00000411767,NM_080683.2;PTPN13,missense_variant,p.Cys2324Arg,ENST00000511467,;PTPN13,missense_variant,p.Cys2128Arg,ENST00000316707,NM_080684.2; C ENST00000436978 Transcript missense_variant 7450/8573 6970/7473 2324/2490 C/R Tgc/Cgc 1 1 PTPN13 HGNC HGNC:9646 protein_coding YES CCDS47093.1 ENSP00000394794 Q12923 UPI000016075D NM_080685.2 deleterious(0) 45/48 PROSITE_profiles:PS50055,hmmpanther:PTHR19134:SF197,hmmpanther:PTHR19134,PIRSF_domain:PIRSF000933,Pfam_domain:PF00102,Gene3D:3.90.190.10,SMART_domains:SM00194,Superfamily_domains:SSF52799 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 86807769 86807769 T C 1 0 0 0 0 1 0 0 0 12935 1464 51 5 5 PTPN13 4 86807769 Missense_Mutation SNP T C3N-02379_T 30480046 86807769 103406786 9 28948 ETNPPL 0 . GRCh38 4 108748046 108748046 + Silent SNP C C T C3N-02379_T C3N-02379_N C C c.1041G>A p.= p.L347L ENST00000296486 9/13 254 233 21 236 236 0 strelka-varscan-mutect ETNPPL,synonymous_variant,p.=,ENST00000296486,NM_031279.3;ETNPPL,synonymous_variant,p.=,ENST00000411864,NM_001146590.1;ETNPPL,synonymous_variant,p.=,ENST00000510706,;ETNPPL,synonymous_variant,p.=,ENST00000512646,NM_001146627.1;ETNPPL,non_coding_transcript_exon_variant,,ENST00000503912,;ETNPPL,downstream_gene_variant,,ENST00000505233,;ETNPPL,downstream_gene_variant,,ENST00000509402,;ETNPPL,downstream_gene_variant,,ENST00000511923,; T ENST00000296486 Transcript synonymous_variant 1196/2099 1041/1500 347/499 L ctG/ctA COSM4436871 1 -1 ETNPPL HGNC HGNC:14404 protein_coding YES CCDS3682.1 ENSP00000296486 Q8TBG4 UPI000004B638 NM_031279.3 9/13 hmmpanther:PTHR11986:SF63,hmmpanther:PTHR11986,Gene3D:3.90.1150.10,Pfam_domain:PF00202,Superfamily_domains:SSF53383 1 LOW 1 SNV 1 1 1 PASS . . 0 206 0 0 2 0 0 0 -6.959101 0.9899439 1 1 1 0 T 2 4 95 108748046 108748046 C T 1 0 0 0 0 0 0 0 1 5138 813 29 3 3 ETNPPL 4 108748046 Silent SNP C C3N-02379_T 21940277 108748046 81466509 10 28949 HHIP 0 . GRCh38 4 144734750 144734751 + Frame_Shift_Ins INS - - C novel C3N-02379_T C3N-02379_N - - c.1772dupC p.Glu592Ter p.E592* ENST00000296575 12/13 37 27 10 51 51 0 sindel-varindel-pindel HHIP,frameshift_variant,p.Glu592Ter,ENST00000296575,NM_022475.2;HHIP,upstream_gene_variant,,ENST00000503090,; C ENST00000296575 Transcript frameshift_variant 2425-2426/10072 1770-1771/2103 590-591/700 -/X -/C 1 1 HHIP HGNC HGNC:14866 protein_coding YES CCDS3762.1 ENSP00000296575 Q96QV1 UPI0000071302 NM_022475.2 12/13 hmmpanther:PTHR19328,hmmpanther:PTHR19328:SF27,Gene3D:2.120.10.30 HIGH 1 insertion 1 2 1 PASS . . 0 198 11 0 0 0 0 0 -20 0.999987 1 1 1 0 C 7 5 95 144734750 144734750 - C 1 0 1 1 0 0 0 0 0 6977 1319 46 0 0 HHIP 4 144734750 Frame_Shift_Ins INS - C3N-02379_T 35986704 144734750 45479805 11 28950 TLL1 0 . GRCh38 4 166014512 166014512 + Silent SNP C C T rs750739998 C3N-02379_T C3N-02379_N C C c.994C>T p.= p.L332L ENST00000061240 8/21 357 293 64 465 464 1 strelka-varscan-mutect TLL1,synonymous_variant,p.=,ENST00000061240,NM_012464.4;TLL1,synonymous_variant,p.=,ENST00000507499,;TLL1,synonymous_variant,p.=,ENST00000513213,NM_001204760.1;TLL1,3_prime_UTR_variant,,ENST00000509505,; T ENST00000061240 Transcript synonymous_variant 1641/6708 994/3042 332/1013 L Cta/Tta rs750739998,COSM1309876 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 8/21 Gene3D:3.40.390.10,Pfam_domain:PF01400,PIRSF_domain:PIRSF001199,Prints_domain:PR00480,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,Superfamily_domains:SSF55486 0,1 LOW 1 SNV 1 0,1 1 PASS rs750739998 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 95 166014512 166014512 C T 1 0 0 0 0 0 0 0 1 16391 912 32 3 3 TLL1 4 166014512 Silent SNP C C3N-02379_T 21279762 166014512 24200043 12 28951 PCDHA9 0 . GRCh38 5 140849857 140849857 + Silent SNP G G A rs781928576 C3N-02379_T C3N-02379_N G G c.1362G>A p.= p.A454A ENST00000532602 1/4 541 448 93 570 570 0 strelka-varscan-mutect PCDHA9,synonymous_variant,p.=,ENST00000378122,NM_014005.4;PCDHA9,synonymous_variant,p.=,ENST00000532602,NM_031857.1;PCDHA6,intron_variant,,ENST00000529310,NM_018909.3;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA3,intron_variant,,ENST00000522353,NM_018906.2;PCDHA8,intron_variant,,ENST00000531613,NM_018911.2;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA4,intron_variant,,ENST00000530339,NM_018907.3;PCDHA7,intron_variant,,ENST00000525929,NM_018910.2;PCDHA5,intron_variant,,ENST00000529859,NM_018908.2;PCDHA4,intron_variant,,ENST00000512229,;PCDHA5,intron_variant,,ENST00000529619,;PCDHA6,intron_variant,,ENST00000527624,NM_031849.2;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;AC005609.19,upstream_gene_variant,,ENST00000623320,; A ENST00000532602 Transcript synonymous_variant 2395/6293 1362/2853 454/950 A gcG/gcA rs781928576,COSM1433949,COSM1433950 1 1 PCDHA9 HGNC HGNC:8675 protein_coding YES CCDS54920.1 ENSP00000436042 Q9Y5H5 UPI00001273D1 NM_031857.1 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF82,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs781928576 . 2 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 95 140849857 140849857 G A 1 0 0 0 0 0 0 0 1 11618 1132 40 1 1 PCDHA9 5 140849857 Silent SNP G C3N-02379_T 140849857 40688402 13 28952 PCDHB14 0 . GRCh38 5 141225295 141225295 + Missense_Mutation SNP G G A novel C3N-02379_T C3N-02379_N G G c.1790G>A p.Gly597Asp p.G597D ENST00000239449 1/1 196 157 39 149 149 0 strelka-varscan-mutect PCDHB14,missense_variant,p.Gly597Asp,ENST00000239449,NM_018934.3;PCDHB14,missense_variant,p.Gly444Asp,ENST00000624896,;CH17-140K24.8,intron_variant,,ENST00000624396,;CH17-140K24.2,intron_variant,,ENST00000624192,; A ENST00000239449 Transcript missense_variant 2364/4828 1790/2397 597/798 G/D gGc/gAc 1 1 PCDHB14 HGNC HGNC:8685 protein_coding YES CCDS4256.1 ENSP00000239449 Q9Y5E9 UPI00001273E7 NM_018934.3 deleterious_low_confidence(0) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF81,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 141225295 141225295 G A 1 0 0 0 0 1 0 0 0 11626 1203 42 3 3 PCDHB14 5 141225295 Missense_Mutation SNP G C3N-02379_T 375438 141225295 40312964 14 28953 PCDHGA3 0 . GRCh38 5 141345204 141345204 + Missense_Mutation SNP C C G novel C3N-02379_T C3N-02379_N C C c.1171C>G p.Pro391Ala p.P391A ENST00000253812 1/4 205 152 53 253 253 0 strelka-varscan-mutect PCDHGA3,missense_variant,p.Pro391Ala,ENST00000253812,NM_018916.3;PCDHGA3,missense_variant,p.Pro391Ala,ENST00000619750,NM_032011.1;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA2,downstream_gene_variant,,ENST00000528330,NM_032009.2;PCDHGB1,upstream_gene_variant,,ENST00000611598,NM_032095.1;AC005618.8,downstream_gene_variant,,ENST00000625053,;PCDHGA3,3_prime_UTR_variant,,ENST00000612467,; G ENST00000253812 Transcript missense_variant 1337/4771 1171/2799 391/932 P/A Cca/Gca 1 1 PCDHGA3 HGNC HGNC:8701 protein_coding YES CCDS47290.1 ENSP00000253812 Q9Y5H0 UPI0000161C1A NM_018916.3 deleterious_low_confidence(0) 1/4 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF75,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1490866629 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 141345204 141345204 C G 1 0 0 0 0 1 0 0 0 11642 739 26 4 4 PCDHGA3 5 141345204 Missense_Mutation SNP C C3N-02379_T 119909 141345204 40193055 15 28954 KIF4B 0 . GRCh38 5 155013923 155013923 + Missense_Mutation SNP A A G novel C3N-02379_T C3N-02379_N A A c.64A>G p.Lys22Glu p.K22E ENST00000435029 1/1 270 232 38 280 280 0 strelka-varscan-mutect KIF4B,missense_variant,p.Lys22Glu,ENST00000435029,NM_001099293.1; G ENST00000435029 Transcript missense_variant 169/4378 64/3705 22/1234 K/E Aaa/Gaa 1 1 KIF4B HGNC HGNC:6322 protein_coding YES CCDS47324.1 ENSP00000387875 Q2VIQ3 UPI000013D5DB NM_001099293.1 deleterious(0) 1/1 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF392,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 155013923 155013923 A G 1 0 0 0 0 1 0 0 0 8169 131 5 5 5 KIF4B 5 155013923 Missense_Mutation SNP A C3N-02379_T 13668719 155013923 26524336 16 28955 SQSTM1 0 . GRCh38 5 179836451 179836454 + Frame_Shift_Del DEL TGAT TGAT - novel C3N-02379_T C3N-02379_N TGAT TGAT c.1184_1187delTTGA p.Ile395SerfsTer67 p.I395Sfs*67 ENST00000389805 8/8 363 328 35 383 383 0 sindel-varindel-pindel SQSTM1,frameshift_variant,p.Ile395SerfsTer67,ENST00000389805,NM_003900.4;SQSTM1,frameshift_variant,p.Ile311SerfsTer67,ENST00000360718,NM_001142298.1,NM_001142299.1;SQSTM1,intron_variant,,ENST00000510187,;C5orf45,downstream_gene_variant,,ENST00000518219,;C5orf45,downstream_gene_variant,,ENST00000518235,;C5orf45,downstream_gene_variant,,ENST00000292586,NM_016175.3;C5orf45,downstream_gene_variant,,ENST00000523084,;C5orf45,downstream_gene_variant,,ENST00000376931,NM_001017987.2;C5orf45,downstream_gene_variant,,ENST00000520698,;C5orf45,downstream_gene_variant,,ENST00000610475,;C5orf45,downstream_gene_variant,,ENST00000521333,;C5orf45,downstream_gene_variant,,ENST00000523267,;C5orf45,3_prime_UTR_variant,,ENST00000522663,;C5orf45,downstream_gene_variant,,ENST00000520150,;C5orf45,downstream_gene_variant,,ENST00000521299,;SQSTM1,downstream_gene_variant,,ENST00000466342,;C5orf45,downstream_gene_variant,,ENST00000521675,;C5orf45,downstream_gene_variant,,ENST00000520900,;C5orf45,downstream_gene_variant,,ENST00000519208,;C5orf45,downstream_gene_variant,,ENST00000523737,;C5orf45,downstream_gene_variant,,ENST00000518950,;C5orf45,downstream_gene_variant,,ENST00000520995,; - ENST00000389805 Transcript frameshift_variant 1359-1362/2986 1181-1184/1323 394-395/440 LI/X cTGATt/ct 1 1 SQSTM1 HGNC HGNC:11280 protein_coding YES CCDS34317.1 ENSP00000374455 Q13501 UPI0000071099 NM_003900.4 8/8 PROSITE_profiles:PS50030,hmmpanther:PTHR15090,Pfam_domain:PF16577,Gene3D:1.10.8.10,SMART_domains:SM00165,Superfamily_domains:SSF46934 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 95 179836451 179836451 TGAT - 1 0 1 0 1 0 0 0 0 15489 1580 55 0 0 SQSTM1 5 179836451 Frame_Shift_Del DEL TGAT C3N-02379_T 24822528 179836451 1701808 17 28956 TTK 0 . GRCh38 6 80007958 80007958 + Missense_Mutation SNP G G C C3N-02379_T C3N-02379_N G G c.289G>C p.Ala97Pro p.A97P ENST00000369798 3/22 240 200 40 286 286 0 strelka-varscan-mutect TTK,missense_variant,p.Ala97Pro,ENST00000509894,;TTK,missense_variant,p.Ala97Pro,ENST00000230510,NM_001166691.1;TTK,missense_variant,p.Ala97Pro,ENST00000369798,NM_003318.4;TTK,missense_variant,p.Ala97Pro,ENST00000504040,;TTK,missense_variant,p.Ala97Pro,ENST00000511260,;TTK,missense_variant,p.Ala97Pro,ENST00000502580,;TTK,downstream_gene_variant,,ENST00000627129,;TTK,3_prime_UTR_variant,,ENST00000509313,;TTK,non_coding_transcript_exon_variant,,ENST00000430061,; C ENST00000369798 Transcript missense_variant 400/3010 289/2574 97/857 A/P Gcg/Ccg COSM4953596,COSM4953597 1 1 TTK HGNC HGNC:12401 protein_coding YES CCDS4993.1 ENSP00000358813 P33981 UPI0000073C7B NM_003318.4 deleterious(0.03) 3/22 hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF21,Gene3D:1.25.40.10,Superfamily_domains:SSF48452 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 80007958 80007958 G C 1 0 0 0 0 1 0 0 0 17232 971 34 4 4 TTK 6 80007958 Missense_Mutation SNP G C3N-02379_T 80007958 90798021 18 28957 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02379_T C3N-02379_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 1019 476 543 482 482 0 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02379_T 55191822 104154151 19 28958 MTUS1 0 . GRCh38 8 17754176 17754178 + In_Frame_Del DEL TGA TGA - novel C3N-02379_T C3N-02379_N TGA TGA c.1630_1632delTCA p.Ser544del p.S544del ENST00000262102 2/15 225 197 28 344 344 0 sindel-varindel-pindel MTUS1,inframe_deletion,p.Ser544del,ENST00000381869,NM_001001925.2;MTUS1,inframe_deletion,p.Ser544del,ENST00000262102,NM_001001924.2;MTUS1,inframe_deletion,p.Ser544del,ENST00000519263,;MTUS1,downstream_gene_variant,,ENST00000518755,;MTUS1,downstream_gene_variant,,ENST00000518891,;MTUS1,inframe_deletion,p.Ser279del,ENST00000520196,;MTUS1,non_coding_transcript_exon_variant,,ENST00000523718,; - ENST00000262102 Transcript inframe_deletion 1855-1857/6160 1630-1632/3813 544/1270 S/- TCA/- 1 -1 MTUS1 HGNC HGNC:29789 protein_coding YES CCDS43717.1 ENSP00000262102 Q9ULD2 UPI000003FF3C NM_001001924.2 2/15 hmmpanther:PTHR24200,hmmpanther:PTHR24200:SF7 MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 95 17754176 17754176 TGA - 1 0 1 0 1 0 0 0 0 9963 1567 55 0 0 MTUS1 8 17754176 In_Frame_Del DEL TGA C3N-02379_T 17754176 127384460 20 28959 TCEA1 0 . GRCh38 8 53999921 53999921 + Missense_Mutation SNP T T G rs779400625 C3N-02379_T C3N-02379_N T T c.256A>C p.Ile86Leu p.I86L ENST00000518784 3/3 106 69 37 103 103 0 strelka-varscan-mutect TCEA1,missense_variant,p.Ile86Leu,ENST00000518784,;TCEA1,intron_variant,,ENST00000521604,NM_006756.3;TCEA1,intron_variant,,ENST00000396401,NM_201437.2;TCEA1,intron_variant,,ENST00000522635,;TCEA1,intron_variant,,ENST00000520534,;TCEA1,intron_variant,,ENST00000521086,;TCEA1,intron_variant,,ENST00000522397,;TCEA1,intron_variant,,ENST00000521836,;TCEA1,intron_variant,,ENST00000517351,;TCEA1,intron_variant,,ENST00000518310,;TCEA1,downstream_gene_variant,,ENST00000519704,; G ENST00000518784 Transcript missense_variant 290/586 256/273 86/90 I/L Ata/Cta rs779400625 1 -1 TCEA1 HGNC HGNC:11612 protein_coding ENSP00000429182 E5RJ93 UPI0001E8F2CF tolerated_low_confidence(0.43) 3/3 MODERATE SNV 2 1 PASS rs779400625 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 53999921 53999921 T G 1 0 0 0 0 1 0 0 0 16074 1406 49 5 5 TCEA1 8 53999921 Missense_Mutation SNP T C3N-02379_T 36245745 53999921 91138715 21 28960 WWP1 0 . GRCh38 8 86431443 86431443 + Silent SNP G G C novel C3N-02379_T C3N-02379_N G G c.1425G>C p.= p.V475V ENST00000517970 13/25 140 128 12 137 137 0 strelka-varscan-mutect WWP1,synonymous_variant,p.=,ENST00000517970,NM_007013.3;WWP1,synonymous_variant,p.=,ENST00000265428,;WWP1,upstream_gene_variant,,ENST00000520453,;WWP1,non_coding_transcript_exon_variant,,ENST00000521079,;WWP1,downstream_gene_variant,,ENST00000520374,;WWP1,non_coding_transcript_exon_variant,,ENST00000518683,;WWP1,upstream_gene_variant,,ENST00000521997,; C ENST00000517970 Transcript synonymous_variant 1732/4686 1425/2769 475/922 V gtG/gtC 1 1 WWP1 HGNC HGNC:17004 protein_coding YES CCDS6242.1 ENSP00000427793 Q9H0M0 UPI0000035537 NM_007013.3 13/25 PROSITE_profiles:PS50020,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF299,PROSITE_patterns:PS01159,Pfam_domain:PF00397,PIRSF_domain:PIRSF001569,Gene3D:2.20.70.10,SMART_domains:SM00456,Superfamily_domains:SSF51045 LOW 1 SNV 1 1 PASS rs1247553548 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 95 86431443 86431443 G C 1 0 0 0 0 0 0 0 1 17973 1277 45 4 4 WWP1 8 86431443 Silent SNP G C3N-02379_T 32431522 86431443 58707193 22 28961 MROH1 0 . GRCh38 8 144260814 144260814 + Silent SNP T T C novel C3N-02379_T C3N-02379_N T T c.4518T>C p.= p.P1506P ENST00000528919 39/43 354 303 51 452 452 0 strelka-varscan-mutect MROH1,synonymous_variant,p.=,ENST00000528919,NM_032450.2;MROH1,synonymous_variant,p.=,ENST00000326134,;MROH1,synonymous_variant,p.=,ENST00000534366,NM_001288814.1;MROH1,synonymous_variant,p.=,ENST00000544576,;BOP1,downstream_gene_variant,,ENST00000569669,NM_015201.4;BOP1,downstream_gene_variant,,ENST00000569403,;BOP1,downstream_gene_variant,,ENST00000616126,;BOP1,downstream_gene_variant,,ENST00000563210,;BOP1,downstream_gene_variant,,ENST00000568812,;BOP1,downstream_gene_variant,,ENST00000569160,; C ENST00000528919 Transcript synonymous_variant 4639/5234 4518/4926 1506/1641 P ccT/ccC 1 1 MROH1 HGNC HGNC:26958 protein_coding YES CCDS47938.1 ENSP00000435565 Q8NDA8 UPI0001AE6FA6 NM_032450.2 39/43 hmmpanther:PTHR23120,hmmpanther:PTHR23120:SF13,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 95 144260814 144260814 T C 1 0 0 0 0 0 0 0 1 9743 1538 54 5 5 MROH1 8 144260814 Silent SNP T C3N-02379_T 57829371 144260814 877822 23 28962 MLLT10 0 . GRCh38 10 21713913 21713913 + Missense_Mutation SNP C C G novel C3N-02379_T C3N-02379_N C C c.1841C>G p.Ala614Gly p.A614G ENST00000307729 14/23 82 60 22 124 124 0 strelka-varscan-mutect MLLT10,missense_variant,p.Ala630Gly,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Ala614Gly,ENST00000307729,;MLLT10,missense_variant,p.Ala614Gly,ENST00000631589,;MLLT10,missense_variant,p.Ala614Gly,ENST00000377059,NM_001195626.1;MLLT10,missense_variant,p.Ala273Gly,ENST00000438473,;MLLT10,missense_variant,p.Ala177Gly,ENST00000420525,; G ENST00000307729 Transcript missense_variant 2019/5032 1841/3207 614/1068 A/G gCt/gGt 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 tolerated(0.16) 14/23 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 21713913 21713913 C G 1 0 0 0 0 1 0 0 0 9589 797 28 4 4 MLLT10 10 21713913 Missense_Mutation SNP C C3N-02379_T 21713913 112083509 24 28963 RHOBTB1 0 . GRCh38 10 60888417 60888417 + Missense_Mutation SNP A A C novel C3N-02379_T C3N-02379_N A A c.1251T>G p.Phe417Leu p.F417L ENST00000337910 6/11 178 142 36 164 164 0 strelka-varscan-mutect RHOBTB1,missense_variant,p.Phe417Leu,ENST00000337910,NM_001242359.1,NM_014836.4;RHOBTB1,missense_variant,p.Phe417Leu,ENST00000357917,;RHOBTB1,non_coding_transcript_exon_variant,,ENST00000483488,; C ENST00000337910 Transcript missense_variant 1589/4473 1251/2091 417/696 F/L ttT/ttG 1 -1 RHOBTB1 HGNC HGNC:18738 protein_coding YES CCDS7261.1 ENSP00000338671 O94844 A0A024QZL4 UPI000000D9B7 NM_001242359.1,NM_014836.4 deleterious(0.01) 6/11 PROSITE_profiles:PS50097,Gene3D:3.30.710.10,Pfam_domain:PF00651,SMART_domains:SM00225,Superfamily_domains:SSF54695 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 60888417 60888417 A C 1 0 0 0 0 1 0 0 0 13506 243 9 5 5 RHOBTB1 10 60888417 Missense_Mutation SNP A C3N-02379_T 39174504 60888417 72909005 25 28964 ADGRA1 0 . GRCh38 10 133102819 133102819 + Silent SNP G G A rs368145789 C3N-02379_T C3N-02379_N G G c.378G>A p.= p.P126P ENST00000392607 5/7 56 49 7 61 61 0 strelka-varscan-mutect ADGRA1,synonymous_variant,p.=,ENST00000607359,;ADGRA1,synonymous_variant,p.=,ENST00000392607,NM_001083909.2;ADGRA1,synonymous_variant,p.=,ENST00000392606,NM_001291085.1; A ENST00000392607 Transcript synonymous_variant 814/4283 378/1683 126/560 P ccG/ccA rs368145789 1 1 ADGRA1 HGNC HGNC:13838 protein_coding YES CCDS41580.1 ENSP00000376384 Q86SQ6 UPI00003D41AD NM_001083909.2 5/7 PROSITE_profiles:PS50261,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF261,Pfam_domain:PF00002 LOW 1 SNV 5 1 PASS rs368145789 . 0 200 9 0 0 0 0 0 -16.16871 0.9999904 1 1 1 0 A 2 1 95 133102819 133102819 G A 1 0 0 0 0 0 0 0 1 352 1132 40 1 1 ADGRA1 10 133102819 Silent SNP G C3N-02379_T 72214402 133102819 694603 26 28965 CDK2AP2 0 . GRCh38 11 67507640 67507640 + Missense_Mutation SNP G G C novel C3N-02379_T C3N-02379_N G G c.132C>G p.Phe44Leu p.F44L ENST00000301488 2/4 461 437 24 148 148 0 strelka-varscan-mutect CDK2AP2,missense_variant,p.Phe44Leu,ENST00000301488,NM_005851.4;CDK2AP2,missense_variant,p.Phe44Leu,ENST00000531506,;PITPNM1,upstream_gene_variant,,ENST00000356404,NM_004910.2;PITPNM1,upstream_gene_variant,,ENST00000436757,NM_001130848.1;PITPNM1,upstream_gene_variant,,ENST00000534749,;PITPNM1,upstream_gene_variant,,ENST00000528559,;PITPNM1,upstream_gene_variant,,ENST00000533391,;PITPNM1,upstream_gene_variant,,ENST00000524901,;PITPNM1,upstream_gene_variant,,ENST00000532703,;PITPNM1,upstream_gene_variant,,ENST00000527527,;PITPNM1,upstream_gene_variant,,ENST00000527103,;CDK2AP2,3_prime_UTR_variant,,ENST00000531178,;CDK2AP2,non_coding_transcript_exon_variant,,ENST00000525402,;CDK2AP2,non_coding_transcript_exon_variant,,ENST00000526447,; C ENST00000301488 Transcript missense_variant 681/1378 132/381 44/126 F/L ttC/ttG 1 -1 CDK2AP2 HGNC HGNC:30833 protein_coding YES CCDS8169.1 ENSP00000301488 O75956 Q6IAV4 UPI00001296A5 NM_005851.4 deleterious(0.01) 2/4 hmmpanther:PTHR22607,hmmpanther:PTHR22607:SF4,PIRSF_domain:PIRSF037709 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 67507640 67507640 G C 1 0 0 0 0 1 0 0 0 2843 1281 45 4 4 CDK2AP2 11 67507640 Missense_Mutation SNP G C3N-02379_T 67507640 67578982 27 28966 ANO6 0 . GRCh38 12 45388265 45388265 + Missense_Mutation SNP G G C C3N-02379_T C3N-02379_N G G c.1333G>C p.Ala445Pro p.A445P ENST00000423947 12/21 449 378 71 466 466 0 strelka-varscan-mutect ANO6,missense_variant,p.Ala424Pro,ENST00000320560,NM_001025356.2;ANO6,missense_variant,p.Ala406Pro,ENST00000441606,NM_001142678.1;ANO6,missense_variant,p.Ala445Pro,ENST00000423947,NM_001204803.1;ANO6,missense_variant,p.Ala424Pro,ENST00000425752,NM_001142679.1;ANO6,non_coding_transcript_exon_variant,,ENST00000426898,; C ENST00000423947 Transcript missense_variant 1570/5504 1333/2796 445/931 A/P Gca/Cca COSM1289763,COSM1289764 1 1 ANO6 HGNC HGNC:25240 protein_coding YES CCDS55819.1 ENSP00000409126 Q4KMQ2 UPI000022935A NM_001204803.1 deleterious(0) 12/21 hmmpanther:PTHR12308:SF21,hmmpanther:PTHR12308,Pfam_domain:PF04547 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 45388265 45388265 G C 1 0 0 0 0 1 0 0 0 808 971 34 4 4 ANO6 12 45388265 Missense_Mutation SNP G C3N-02379_T 45388265 87887044 28 28967 WNT10B 0 . GRCh38 12 48968255 48968255 + Silent SNP C C T rs763263982 C3N-02379_T C3N-02379_N C C c.402G>A p.= p.T134T ENST00000301061 4/5 495 454 41 503 503 0 strelka-varscan-mutect WNT10B,synonymous_variant,p.=,ENST00000301061,NM_003394.3;WNT10B,synonymous_variant,p.=,ENST00000403957,;WNT10B,synonymous_variant,p.=,ENST00000407467,;WNT10B,downstream_gene_variant,,ENST00000413630,;WNT10B,downstream_gene_variant,,ENST00000420388,;WNT10B,downstream_gene_variant,,ENST00000475740,; T ENST00000301061 Transcript synonymous_variant 751/2274 402/1170 134/389 T acG/acA rs763263982 1 -1 WNT10B HGNC HGNC:12775 protein_coding YES CCDS8775.1 ENSP00000301061 O00744 UPI0000138F21 NM_003394.3 4/5 hmmpanther:PTHR12027,hmmpanther:PTHR12027:SF76,Pfam_domain:PF00110,SMART_domains:SM00097,Prints_domain:PR01349 LOW 1 SNV 1 1 PASS rs763263982 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 95 48968255 48968255 C T 1 0 0 0 0 0 0 0 1 17939 639 23 1 1 WNT10B 12 48968255 Silent SNP C C3N-02379_T 3579990 48968255 84307054 29 28968 KMT2D 0 . GRCh38 12 49054123 49054123 + Silent SNP G G A novel C3N-02379_T C3N-02379_N G G c.528C>T p.= p.T176T ENST00000301067 5/54 55 39 16 78 78 0 strelka-varscan-mutect KMT2D,synonymous_variant,p.=,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000547610,; A ENST00000301067 Transcript synonymous_variant 528/19419 528/16614 176/5537 T acC/acT 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 5/54 Pfam_domain:PF13771,SMART_domains:SM00184,SMART_domains:SM00249 LOW 1 SNV 5 1 PASS . . 0 198 12 0 0 0 0 0 -20 0.9999773 1 1 1 0 A 2 1 95 49054123 49054123 G A 1 0 0 0 0 0 0 0 1 8298 1335 47 3 3 KMT2D 12 49054123 Silent SNP G C3N-02379_T 85868 49054123 84221186 30 28969 C12orf73 0 . GRCh38 12 103951591 103951592 + Frame_Shift_Del DEL TT TT - novel C3N-02379_T C3N-02379_N TT TT c.147_148delAA p.Lys49AsnfsTer22 p.K49Nfs*22 ENST00000378090 3/3 126 104 22 143 143 0 sindel-varindel-pindel C12orf73,frameshift_variant,p.Lys49AsnfsTer22,ENST00000378090,NM_001135570.1;C12orf73,frameshift_variant,p.Lys49AsnfsTer22,ENST00000549478,;C12orf73,frameshift_variant,p.Lys49AsnfsTer22,ENST00000553183,;C12orf73,frameshift_variant,p.Lys49AsnfsTer22,ENST00000547945,;C12orf73,3_prime_UTR_variant,,ENST00000547975,;C12orf73,3_prime_UTR_variant,,ENST00000552940,;HSP90B1,intron_variant,,ENST00000550595,;HSP90B1,downstream_gene_variant,,ENST00000299767,NM_003299.2;HSP90B1,downstream_gene_variant,,ENST00000614327,;C12orf73,downstream_gene_variant,,ENST00000546540,;C12orf73,downstream_gene_variant,,ENST00000546819,;C12orf73,non_coding_transcript_exon_variant,,ENST00000543740,;C12orf73,3_prime_UTR_variant,,ENST00000549960,;C12orf73,3_prime_UTR_variant,,ENST00000552460,;HSP90B1,downstream_gene_variant,,ENST00000548462,;HSP90B1,downstream_gene_variant,,ENST00000552051,; - ENST00000378090 Transcript frameshift_variant 353-354/1738 147-148/216 49-50/71 KT/NX aaAAcg/aacg 1 -1 C12orf73 HGNC HGNC:34450 protein_coding YES CCDS44964.1 ENSP00000367330 Q69YU5 UPI000015C160 NM_001135570.1 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR28492,hmmpanther:PTHR28492:SF1 HIGH 1 deletion 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.9999951 1 1 1 0 - 7 5 95 103951591 103951591 TT - 1 0 1 0 1 0 0 0 0 1822 1725 60 0 0 C12orf73 12 103951591 Frame_Shift_Del DEL TT C3N-02379_T 54897468 103951591 29323718 31 28970 PUS1 0 . GRCh38 12 131941823 131941823 + Missense_Mutation SNP C C T rs142072030 C3N-02379_T C3N-02379_N C C c.1076C>T p.Ala359Val p.A359V ENST00000376649 5/6 117 89 28 108 108 0 strelka-varscan-mutect PUS1,missense_variant,p.Ala359Val,ENST00000376649,NM_025215.5;PUS1,missense_variant,p.Ala306Val,ENST00000542167,;PUS1,missense_variant,p.Ala331Val,ENST00000443358,NM_001002020.2,NM_001002019.2;PUS1,missense_variant,p.Ala331Val,ENST00000322060,;PUS1,intron_variant,,ENST00000535067,;PUS1,downstream_gene_variant,,ENST00000537484,;PUS1,downstream_gene_variant,,ENST00000538037,;PUS1,non_coding_transcript_exon_variant,,ENST00000543754,; T ENST00000376649 Transcript missense_variant 1576/4094 1076/1284 359/427 A/V gCg/gTg rs142072030 1 1 PUS1 HGNC HGNC:15508 protein_coding YES CCDS9275.2 ENSP00000365837 Q9Y606 E5KMT5 UPI000006FC81 NM_025215.5 tolerated(0.34) 5/6 hmmpanther:PTHR11142:SF4,hmmpanther:PTHR11142 MODERATE 1 SNV 1 1 PASS rs142072030 . 0 202 6 2 0 0 0 0 -20 0.999967 1 1 1 0 T 3 4 95 131941823 131941823 C T 1 0 0 0 0 1 0 0 0 12988 768 27 1 1 PUS1 12 131941823 Missense_Mutation SNP C C3N-02379_T 27990232 131941823 1333486 32 28971 CT62 0 . GRCh38 15 71111234 71111234 + Missense_Mutation SNP G G T novel C3N-02379_T C3N-02379_N G G c.328C>A p.Gln110Lys p.Q110K ENST00000449977 4/4 344 261 83 414 414 0 strelka-varscan-mutect CT62,missense_variant,p.Gln110Lys,ENST00000449977,NM_001102658.1;CT62,missense_variant,p.Gln66Lys,ENST00000564862,;CT62,3_prime_UTR_variant,,ENST00000566432,;THSD4,intron_variant,,ENST00000355327,NM_024817.2;CT62,downstream_gene_variant,,ENST00000567117,;THSD4,upstream_gene_variant,,ENST00000620694,; T ENST00000449977 Transcript missense_variant 835/1825 328/411 110/136 Q/K Cag/Aag 1 -1 CT62 HGNC HGNC:27286 protein_coding YES CCDS45295.1 ENSP00000399356 P0C5K7 UPI000016137F NM_001102658.1 tolerated_low_confidence(0.26) 4/4 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 71111234 71111234 G T 1 0 0 0 0 1 0 0 0 3793 1299 45 2 2 CT62 15 71111234 Missense_Mutation SNP G C3N-02379_T 71111234 30879955 33 28972 SYT17 0 . GRCh38 16 19183542 19183542 + Missense_Mutation SNP C C A rs139600806 C3N-02379_T C3N-02379_N C C c.346C>A p.Arg116Ser p.R116S ENST00000355377 5/8 126 85 41 136 136 0 strelka-varscan-mutect SYT17,missense_variant,p.Arg55Ser,ENST00000562034,;SYT17,missense_variant,p.Arg116Ser,ENST00000355377,NM_016524.2;SYT17,missense_variant,p.Arg55Ser,ENST00000568115,;SYT17,missense_variant,p.Arg112Ser,ENST00000562711,NM_001308157.1;SYT17,missense_variant,p.Arg55Ser,ENST00000570264,;SYT17,missense_variant,p.Arg55Ser,ENST00000566261,;SYT17,non_coding_transcript_exon_variant,,ENST00000562274,;SYT17,upstream_gene_variant,,ENST00000565183,; A ENST00000355377 Transcript missense_variant 744/3081 346/1425 116/474 R/S Cgt/Agt rs139600806 1 1 SYT17 HGNC HGNC:24119 protein_coding YES CCDS10575.1 ENSP00000347538 Q9BSW7 UPI000007297F NM_016524.2 deleterious(0.04) 5/8 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF251,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs139600806 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 19183542 19183542 C A 1 0 0 0 0 1 0 0 0 15867 536 19 1 1 SYT17 16 19183542 Missense_Mutation SNP C C3N-02379_T 19183542 71154803 34 28973 N4BP1 0 . GRCh38 16 48561699 48561699 + Missense_Mutation SNP G G C novel C3N-02379_T C3N-02379_N G G c.944C>G p.Thr315Arg p.T315R ENST00000262384 2/7 348 328 20 383 383 0 strelka-varscan-mutect N4BP1,missense_variant,p.Thr315Arg,ENST00000262384,NM_153029.3;N4BP1,downstream_gene_variant,,ENST00000564710,;RP11-44I10.3,intron_variant,,ENST00000563994,;N4BP1,non_coding_transcript_exon_variant,,ENST00000564124,; C ENST00000262384 Transcript missense_variant 1181/7106 944/2691 315/896 T/R aCa/aGa 1 -1 N4BP1 HGNC HGNC:29850 protein_coding YES CCDS45479.1 ENSP00000262384 O75113 UPI000013D2A2 NM_153029.3 tolerated(0.38) 2/7 hmmpanther:PTHR12876:SF26,hmmpanther:PTHR12876 MODERATE 1 SNV 1 1 PASS rs1427249328 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 48561699 48561699 G C 1 0 0 0 0 1 0 0 0 10113 1377 48 4 4 N4BP1 16 48561699 Missense_Mutation SNP G C3N-02379_T 29378157 48561699 41776646 35 28974 RPGRIP1L 0 . GRCh38 16 53619195 53619195 + Missense_Mutation SNP A A T rs766943204 C3N-02379_T C3N-02379_N A A c.3446T>A p.Ile1149Asn p.I1149N ENST00000379925 24/27 255 202 53 324 323 1 strelka-varscan-mutect RPGRIP1L,missense_variant,p.Ile1069Asn,ENST00000262135,NM_001127897.1;RPGRIP1L,missense_variant,p.Ile1103Asn,ENST00000621565,NM_001308334.1;RPGRIP1L,missense_variant,p.Ile1149Asn,ENST00000379925,NM_015272.2;RPGRIP1L,missense_variant,p.Ile1115Asn,ENST00000563746,;RPGRIP1L,missense_variant,p.Ile1103Asn,ENST00000564374,; T ENST00000379925 Transcript missense_variant 3497/5297 3446/3948 1149/1315 I/N aTt/aAt rs766943204,COSM4722571 1 -1 RPGRIP1L HGNC HGNC:29168 protein_coding YES CCDS32447.1 ENSP00000369257 Q68CZ1 UPI000047DAF2 NM_015272.2 deleterious(0) 24/27 hmmpanther:PTHR14240:SF4,hmmpanther:PTHR14240 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs766943204 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 53619195 53619195 A T 1 0 0 0 0 1 0 0 0 13802 101 4 4 4 RPGRIP1L 16 53619195 Missense_Mutation SNP A C3N-02379_T 5057496 53619195 36719150 36 28975 DPEP2 0 . GRCh38 16 67990101 67990101 + Missense_Mutation SNP A A C novel C3N-02379_T C3N-02379_N A A c.940T>G p.Leu314Val p.L314V ENST00000572888 7/10 139 119 20 155 154 1 strelka-varscan-mutect DPEP2,missense_variant,p.Leu314Val,ENST00000572888,;DPEP2,missense_variant,p.Leu314Val,ENST00000393847,NM_022355.3;DPEP2,missense_variant,p.Leu106Val,ENST00000575510,;DUS2,intron_variant,,ENST00000571081,;DUS2,intron_variant,,ENST00000570709,;DPEP2,downstream_gene_variant,,ENST00000573808,;DPEP2,downstream_gene_variant,,ENST00000572624,;DUS2,upstream_gene_variant,,ENST00000575677,;DPEP2,downstream_gene_variant,,ENST00000574865,;DPEP2,3_prime_UTR_variant,,ENST00000575203,;DPEP2,downstream_gene_variant,,ENST00000268795,;DPEP2,downstream_gene_variant,,ENST00000574316,; C ENST00000572888 Transcript missense_variant 1591/2112 940/1461 314/486 L/V Ttg/Gtg 1 -1 DPEP2 HGNC HGNC:23028 protein_coding YES CCDS10857.1 ENSP00000458977 Q9H4A9 A0A024R6Y5 UPI000007277C deleterious(0.01) 7/10 Low_complexity_(Seg):seg,PROSITE_profiles:PS51365,hmmpanther:PTHR10443,hmmpanther:PTHR10443:SF9,Pfam_domain:PF01244,Gene3D:3.20.20.140,Superfamily_domains:SSF51556 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 67990101 67990101 A C 1 0 0 0 0 1 0 0 0 4528 11 1 5 5 DPEP2 16 67990101 Missense_Mutation SNP A C3N-02379_T 14370906 67990101 22348244 37 28976 MYBBP1A 0 . GRCh38 17 4548172 4548172 + Missense_Mutation SNP G G T rs752366577 C3N-02379_T C3N-02379_N G G c.1695C>A p.Phe565Leu p.F565L ENST00000381556 12/27 130 94 36 175 174 1 strelka-varscan-mutect MYBBP1A,missense_variant,p.Phe565Leu,ENST00000254718,NM_014520.3;MYBBP1A,missense_variant,p.Phe565Leu,ENST00000381556,NM_001105538.1;MYBBP1A,missense_variant,p.Phe485Leu,ENST00000573116,;MYBBP1A,missense_variant,p.Phe127Leu,ENST00000573723,;MYBBP1A,upstream_gene_variant,,ENST00000572759,;MYBBP1A,non_coding_transcript_exon_variant,,ENST00000573175,;MYBBP1A,upstream_gene_variant,,ENST00000571368,;MYBBP1A,upstream_gene_variant,,ENST00000574547,;MYBBP1A,downstream_gene_variant,,ENST00000570986,;MYBBP1A,upstream_gene_variant,,ENST00000571354,; T ENST00000381556 Transcript missense_variant 1757/4104 1695/3999 565/1332 F/L ttC/ttA rs752366577,COSM1302931,COSM4811984 1 -1 MYBBP1A HGNC HGNC:7546 protein_coding YES CCDS42238.1 ENSP00000370968 Q9BQG0 UPI0000551C8B NM_001105538.1 tolerated(0.21) 12/27 hmmpanther:PTHR13213,hmmpanther:PTHR13213:SF2,Pfam_domain:PF04931,Superfamily_domains:SSF48371 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs752366577 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 4548172 4548172 G T 1 0 0 0 0 1 0 0 0 10008 1281 45 2 2 MYBBP1A 17 4548172 Missense_Mutation SNP G C3N-02379_T 4548172 78709269 38 28977 TP53 0 . GRCh38 17 7674241 7674263 + Frame_Shift_Del DEL GAACTGTTACACATGTAGTTGTA GAACTGTTACACATGTAGTTGTA - novel C3N-02379_T C3N-02379_N GAACTGTTACACATGTAGTTGTA GAACTGTTACACATGTAGTTGTA c.700_722delTACAACTACATGTGTAACAGTTC p.Tyr234LeufsTer22 p.Y234Lfs*22 ENST00000269305 7/11 314 218 96 481 481 0 sindel-varindel-pindel TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000420246,;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000445888,;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000619485,;TP53,frameshift_variant,p.Tyr102LeufsTer22,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.Tyr75LeufsTer22,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.Tyr102LeufsTer22,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.Tyr75LeufsTer22,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.Tyr102LeufsTer22,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.Tyr75LeufsTer22,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.Tyr234LeufsTer22,ENST00000359597,;TP53,frameshift_variant,p.Tyr223LeufsTer22,ENST00000615910,;TP53,frameshift_variant,p.Tyr234LeufsTer95,ENST00000413465,;TP53,frameshift_variant,p.Tyr102LeufsTer22,ENST00000509690,;TP53,frameshift_variant,p.Tyr141LeufsTer?,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,frameshift_variant,p.Tyr195LeufsTer22,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; - ENST00000269305 Transcript frameshift_variant 890-912/2579 700-722/1182 234-241/393 YNYMCNSS/X TACAACTACATGTGTAACAGTTCc/c 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386,Prints_domain:PR00386 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 95 7674241 7674241 GAACTGTTACACATGTAGTTGTA - 1 0 1 0 1 0 0 0 0 16859 1174 41 0 0 TP53 17 7674241 Frame_Shift_Del DEL GAACTGTTACACATGTAGTTGTA C3N-02379_T 3126069 7674241 75583200 39 28978 KRT12 0 . GRCh38 17 40862600 40862600 + Missense_Mutation SNP G G C novel C3N-02379_T C3N-02379_N G G c.1352C>G p.Ser451Cys p.S451C ENST00000251643 7/8 436 406 30 436 436 0 strelka-varscan-mutect KRT12,missense_variant,p.Ser451Cys,ENST00000251643,NM_000223.3;RP5-1110E20.1,intron_variant,,ENST00000579136,; C ENST00000251643 Transcript missense_variant 1376/1867 1352/1485 451/494 S/C tCc/tGc 1 -1 KRT12 HGNC HGNC:6414 protein_coding YES CCDS11378.1 ENSP00000251643 Q99456 UPI000012DAE4 NM_000223.3 deleterious(0.04) 7/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF115 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 40862600 40862600 G C 1 0 0 0 0 1 0 0 0 8331 1174 41 4 4 KRT12 17 40862600 Missense_Mutation SNP G C3N-02379_T 33188359 40862600 42394841 40 28979 OTOP2 0 . GRCh38 17 74925609 74925609 + Missense_Mutation SNP G G A rs767255149 C3N-02379_T C3N-02379_N G G c.367G>A p.Gly123Ser p.G123S ENST00000331427 3/7 306 254 52 270 270 0 strelka-varscan-mutect OTOP2,missense_variant,p.Gly123Ser,ENST00000331427,NM_178160.2;OTOP2,missense_variant,p.Gly123Ser,ENST00000580223,;USH1G,upstream_gene_variant,,ENST00000614341,NM_001282489.2,NM_173477.4;OTOP2,non_coding_transcript_exon_variant,,ENST00000584711,;USH1G,upstream_gene_variant,,ENST00000579243,; A ENST00000331427 Transcript missense_variant 459/2147 367/1689 123/562 G/S Ggc/Agc rs767255149,COSM326048 1 1 OTOP2 HGNC HGNC:19657 protein_coding YES CCDS11708.1 ENSP00000332528 Q7RTS6 UPI000018F613 NM_178160.2 deleterious(0.02) 3/7 hmmpanther:PTHR21522,hmmpanther:PTHR21522:SF35,Pfam_domain:PF03189 0,1 MODERATE SNV 5 0,1 1 PASS rs767255149 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 74925609 74925609 G A 1 0 0 0 0 1 0 0 0 11374 1116 39 1 1 OTOP2 17 74925609 Missense_Mutation SNP G C3N-02379_T 34063009 74925609 8331832 41 28980 TBC1D16 0 . GRCh38 17 79940971 79940971 + Missense_Mutation SNP C C G novel C3N-02379_T C3N-02379_N C C c.2192G>C p.Gly731Ala p.G731A ENST00000310924 12/12 119 92 27 110 110 0 strelka-mutect TBC1D16,missense_variant,p.Gly731Ala,ENST00000310924,NM_019020.3;TBC1D16,missense_variant,p.Gly356Ala,ENST00000576768,NM_001271844.1;TBC1D16,missense_variant,p.Gly369Ala,ENST00000340848,NM_001271845.1;TBC1D16,downstream_gene_variant,,ENST00000572862,NM_001271846.1;TBC1D16,downstream_gene_variant,,ENST00000570373,; G ENST00000310924 Transcript missense_variant 2308/10936 2192/2304 731/767 G/A gGc/gCc 1 -1 TBC1D16 HGNC HGNC:28356 protein_coding YES CCDS11766.1 ENSP00000309794 Q8TBP0 UPI000006DDA6 NM_019020.3 tolerated(0.55) 12/12 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF285 MODERATE 1 SNV 1 1 PASS rs1011889144 . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 79940971 79940971 C G 1 0 0 0 0 1 0 0 0 16005 739 26 4 4 TBC1D16 17 79940971 Missense_Mutation SNP C C3N-02379_T 5015362 79940971 3316470 42 28981 LAMA3 0 . GRCh38 18 23842712 23842712 + Missense_Mutation SNP G G A rs771491240 C3N-02379_T C3N-02379_N G G c.3565G>A p.Ala1189Thr p.A1189T ENST00000313654 29/75 637 556 81 684 683 1 strelka-varscan-mutect LAMA3,missense_variant,p.Ala1189Thr,ENST00000313654,NM_198129.2;LAMA3,missense_variant,p.Ala1189Thr,ENST00000399516,NM_001127717.2; A ENST00000313654 Transcript missense_variant 3806/10661 3565/10002 1189/3333 A/T Gca/Aca rs771491240,COSM3787494 1 1 LAMA3 HGNC HGNC:6483 protein_coding YES CCDS42419.1 ENSP00000324532 Q16787 UPI000035154D NM_198129.2 deleterious(0) 29/75 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs771491240 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 23842712 23842712 G A 1 0 0 0 0 1 0 0 0 8511 1087 38 1 1 LAMA3 18 23842712 Missense_Mutation SNP G C3N-02379_T 23842712 56530573 43 28982 TRAPPC8 0 . GRCh38 18 31870431 31870431 + Missense_Mutation SNP G G T novel C3N-02379_T C3N-02379_N G G c.2329C>A p.Leu777Ile p.L777I ENST00000283351 16/29 181 170 11 143 143 0 strelka-varscan-mutect TRAPPC8,missense_variant,p.Leu777Ile,ENST00000283351,NM_014939.3;TRAPPC8,missense_variant,p.Leu723Ile,ENST00000582539,;TRAPPC8,downstream_gene_variant,,ENST00000582513,;TRAPPC8,missense_variant,p.Leu777Ile,ENST00000580104,;TRAPPC8,non_coding_transcript_exon_variant,,ENST00000578252,;TRAPPC8,downstream_gene_variant,,ENST00000577474,; T ENST00000283351 Transcript missense_variant 2665/6226 2329/4308 777/1435 L/I Ctt/Att 1 -1 TRAPPC8 HGNC HGNC:29169 protein_coding YES CCDS11901.1 ENSP00000283351 Q9Y2L5 UPI0000052E22 NM_014939.3 tolerated(0.09) 16/29 Low_complexity_(Seg):seg,hmmpanther:PTHR12975:SF6,hmmpanther:PTHR12975 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 31870431 31870431 G T 1 0 0 0 0 1 0 0 0 16953 971 34 2 2 TRAPPC8 18 31870431 Missense_Mutation SNP G C3N-02379_T 8027719 31870431 48502854 44 28983 DNAJB1 0 . GRCh38 19 14517015 14517029 + In_Frame_Del DEL GCTACCGCCACTGGG GCTACCGCCACTGGG - novel C3N-02379_T C3N-02379_N GCTACCGCCACTGGG GCTACCGCCACTGGG c.229_243delCCCAGTGGCGGTAGC p.Pro77_Ser81del p.P77_S81del ENST00000254322 2/3 67 58 9 102 102 0 sindel-varindel-pindel DNAJB1,inframe_deletion,p.Pro77_Ser81del,ENST00000254322,NM_006145.2;DNAJB1,inframe_deletion,p.Pro10_Ser14del,ENST00000595139,;DNAJB1,5_prime_UTR_variant,,ENST00000396969,NM_001300914.1;DNAJB1,5_prime_UTR_variant,,ENST00000594099,;DNAJB1,5_prime_UTR_variant,,ENST00000598235,;DNAJB1,5_prime_UTR_variant,,ENST00000595992,;DNAJB1,5_prime_UTR_variant,,ENST00000596853,;DNAJB1,5_prime_UTR_variant,,ENST00000596075,;DNAJB1,5_prime_UTR_variant,,ENST00000601533,;DNAJB1,5_prime_UTR_variant,,ENST00000598692,;TECR,upstream_gene_variant,,ENST00000600076,; - ENST00000254322 Transcript inframe_deletion 300-314/2264 229-243/1023 77-81/340 PSGGS/- CCCAGTGGCGGTAGC/- 1 -1 DNAJB1 HGNC HGNC:5270 protein_coding YES CCDS12312.1 ENSP00000254322 P25685 Q6FHS4 UPI0000000C3A NM_006145.2 2/3 Gene3D:1.10.287.110,Prints_domain:PR00625,hmmpanther:PTHR24078,hmmpanther:PTHR24078:SF306,Low_complexity_(Seg):seg,Superfamily_domains:SSF46565 MODERATE 1 deletion 1 1 PASS . . 0 196 13 0 0 0 0 0 -19.56744 0.9998015 1 1 1 0 - 7 5 95 14517015 14517015 GCTACCGCCACTGGG - 1 0 1 0 1 0 0 0 0 4430 1078 38 0 0 DNAJB1 19 14517015 In_Frame_Del DEL GCTACCGCCACTGGG C3N-02379_T 14517015 44100601 45 28984 CD22 0 . GRCh38 19 35338398 35338398 + Nonsense_Mutation SNP C C T novel C3N-02379_T C3N-02379_N C C c.1216C>T p.Gln406Ter p.Q406* ENST00000085219 6/14 91 67 24 113 112 1 strelka-varscan-mutect CD22,stop_gained,p.Gln406Ter,ENST00000085219,NM_001771.3;CD22,stop_gained,p.Gln406Ter,ENST00000544992,NM_001185100.1;CD22,stop_gained,p.Gln234Ter,ENST00000419549,NM_001278417.1;CD22,intron_variant,,ENST00000536635,NM_001185099.1;CD22,intron_variant,,ENST00000341773,NM_001185101.1;CD22,intron_variant,,ENST00000594250,;CD22,intron_variant,,ENST00000599811,;CD22,intron_variant,,ENST00000600424,;CD22,downstream_gene_variant,,ENST00000593867,;CD22,downstream_gene_variant,,ENST00000613136,;CD22,downstream_gene_variant,,ENST00000600131,;CD22,downstream_gene_variant,,ENST00000597916,;CD22,non_coding_transcript_exon_variant,,ENST00000601329,;CD22,intron_variant,,ENST00000598815,;CD22,intron_variant,,ENST00000597433,;CD22,downstream_gene_variant,,ENST00000598138,;CD22,downstream_gene_variant,,ENST00000598028,;CD22,downstream_gene_variant,,ENST00000601414,;CD22,downstream_gene_variant,,ENST00000601732,;CD22,downstream_gene_variant,,ENST00000600905,;CD22,stop_gained,p.Gln49Ter,ENST00000594125,;CD22,3_prime_UTR_variant,,ENST00000601769,;CD22,intron_variant,,ENST00000600655,;CD22,downstream_gene_variant,,ENST00000596492,;CD22,downstream_gene_variant,,ENST00000594349,;CD22,upstream_gene_variant,,ENST00000602123,;CD22,downstream_gene_variant,,ENST00000599717,; T ENST00000085219 Transcript stop_gained 1282/3268 1216/2544 406/847 Q/* Cag/Tag 1 1 CD22 HGNC HGNC:1643 protein_coding YES CCDS12457.1 ENSP00000085219 P20273 Q0EAF5 UPI000012733D NM_001771.3 6/14 PROSITE_profiles:PS50835,hmmpanther:PTHR12035:SF60,hmmpanther:PTHR12035,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -20 0.9999944 1 1 1 0 T 4 4 95 35338398 35338398 C T 1 0 0 0 0 0 1 0 0 2688 479 17 3 3 CD22 19 35338398 Nonsense_Mutation SNP C C3N-02379_T 20821383 35338398 23279218 46 28985 ZNF383 0 . GRCh38 19 37235658 37235658 + Missense_Mutation SNP G G A novel C3N-02379_T C3N-02379_N G G c.119G>A p.Gly40Asp p.G40D ENST00000352998 3/5 89 84 5 110 110 0 varscan-mutect ZNF383,missense_variant,p.Gly40Asp,ENST00000352998,NM_152604.1;ZNF383,missense_variant,p.Gly40Asp,ENST00000589413,;ZNF383,missense_variant,p.Gly40Asp,ENST00000590503,;ZNF383,missense_variant,p.Gly40Asp,ENST00000588371,;ZNF383,missense_variant,p.Gly40Asp,ENST00000588250,;ZNF383,non_coding_transcript_exon_variant,,ENST00000586068,; A ENST00000352998 Transcript missense_variant 377/6760 119/1428 40/475 G/D gGc/gAc 1 1 ZNF383 HGNC HGNC:18609 protein_coding YES CCDS12501.1 ENSP00000340132 Q8NA42 UPI00000717CC NM_152604.1 deleterious(0.03) 3/5 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24377,SMART_domains:SM00349 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -11.25823 1 1 1 1 0 A 3 1 95 37235658 37235658 G A 1 0 0 0 0 1 0 0 0 18446 1203 42 3 3 ZNF383 19 37235658 Missense_Mutation SNP G C3N-02379_T 1897260 37235658 21381958 47 28986 AKT2 0 . GRCh38 19 40235978 40235978 + Missense_Mutation SNP G G T novel C3N-02379_T C3N-02379_N G G c.1087C>A p.Leu363Ile p.L363I ENST00000392038 11/14 358 329 29 329 329 0 strelka-mutect AKT2,missense_variant,p.Leu363Ile,ENST00000392038,NM_001626.5;AKT2,missense_variant,p.Leu320Ile,ENST00000424901,;AKT2,missense_variant,p.Leu301Ile,ENST00000579047,NM_001243027.2,NM_001243028.2;AKT2,missense_variant,p.Leu320Ile,ENST00000311278,;AKT2,missense_variant,p.Leu219Ile,ENST00000578615,;AKT2,missense_variant,p.Leu32Ile,ENST00000476247,;AKT2,upstream_gene_variant,,ENST00000497948,;AKT2,downstream_gene_variant,,ENST00000578310,;AKT2,non_coding_transcript_exon_variant,,ENST00000391845,;AKT2,downstream_gene_variant,,ENST00000480878,;AKT2,downstream_gene_variant,,ENST00000486647,;AKT2,missense_variant,p.Leu19Ile,ENST00000489375,;AKT2,3_prime_UTR_variant,,ENST00000391844,;AKT2,3_prime_UTR_variant,,ENST00000584288,;AKT2,non_coding_transcript_exon_variant,,ENST00000483166,;AKT2,non_coding_transcript_exon_variant,,ENST00000476266,;AKT2,non_coding_transcript_exon_variant,,ENST00000496089,;AKT2,downstream_gene_variant,,ENST00000578975,;AKT2,downstream_gene_variant,,ENST00000537834,;AKT2,downstream_gene_variant,,ENST00000492463,;AKT2,downstream_gene_variant,,ENST00000580878,;AKT2,downstream_gene_variant,,ENST00000491778,;AKT2,downstream_gene_variant,,ENST00000579345,;AKT2,downstream_gene_variant,,ENST00000601166,;AKT2,downstream_gene_variant,,ENST00000578282,; T ENST00000392038 Transcript missense_variant 1386/5300 1087/1446 363/481 L/I Ctc/Atc 1 -1 AKT2 HGNC HGNC:392 protein_coding YES CCDS12552.1 ENSP00000375892 P31751 UPI0000049EDB NM_001626.5 deleterious(0.05) 11/14 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR24356,hmmpanther:PTHR24356:SF176,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 40235978 40235978 G T 1 0 0 0 0 1 0 0 0 563 1000 35 2 2 AKT2 19 40235978 Missense_Mutation SNP G C3N-02379_T 3000320 40235978 18381638 48 28987 CYP24A1 0 . GRCh38 20 54162811 54162811 + Missense_Mutation SNP G G A novel C3N-02379_T C3N-02379_N G G c.896C>T p.Ala299Val p.A299V ENST00000216862 7/12 418 280 138 500 500 0 strelka-varscan-mutect CYP24A1,missense_variant,p.Ala299Val,ENST00000216862,NM_000782.4;CYP24A1,missense_variant,p.Ala299Val,ENST00000395955,NM_001128915.1;CYP24A1,missense_variant,p.Ala157Val,ENST00000395954,;CYP24A1,non_coding_transcript_exon_variant,,ENST00000487593,; A ENST00000216862 Transcript missense_variant 1290/3262 896/1545 299/514 A/V gCa/gTa 1 -1 CYP24A1 HGNC HGNC:2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 tolerated(0.12) 7/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF5,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 54162811 54162811 G A 1 0 0 0 0 1 0 0 0 3957 1319 46 3 3 CYP24A1 20 54162811 Missense_Mutation SNP G C3N-02379_T 54162811 10281356 49 28988 NCAM2 0 . GRCh38 21 21410456 21410456 + Silent SNP T T C novel C3N-02379_T C3N-02379_N T T c.1378T>C p.= p.L460L ENST00000400546 10/18 58 52 6 51 50 1 strelka-varscan-mutect NCAM2,synonymous_variant,p.=,ENST00000400546,NM_004540.3;NCAM2,synonymous_variant,p.=,ENST00000284894,; C ENST00000400546 Transcript synonymous_variant 1627/8135 1378/2514 460/837 L Tta/Cta 1 1 NCAM2 HGNC HGNC:7657 protein_coding YES CCDS42910.1 ENSP00000383392 O15394 UPI00001A3703 NM_004540.3 10/18 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF35,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 95 21410456 21410456 T C 1 0 0 0 0 0 0 0 1 10219 1507 52 5 5 NCAM2 21 21410456 Silent SNP T C3N-02379_T 21410456 25299527 50 28989 RRP1B 0 . GRCh38 21 43672338 43672338 + Missense_Mutation SNP G G C novel C3N-02379_T C3N-02379_N G G c.244G>C p.Val82Leu p.V82L ENST00000340648 3/16 310 284 26 215 215 0 strelka-varscan-mutect RRP1B,missense_variant,p.Val82Leu,ENST00000340648,NM_015056.2; C ENST00000340648 Transcript missense_variant 361/5090 244/2277 82/758 V/L Gtc/Ctc 1 1 RRP1B HGNC HGNC:23818 protein_coding YES CCDS33577.1 ENSP00000339145 Q14684 UPI0000198EE6 NM_015056.2 deleterious(0.01) 3/16 Pfam_domain:PF05997,hmmpanther:PTHR13026,hmmpanther:PTHR13026:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 43672338 43672338 G C 1 0 0 0 0 1 0 0 0 13943 1029 36 4 4 RRP1B 21 43672338 Missense_Mutation SNP G C3N-02379_T 22261882 43672338 3037645 51 28990 ZDHHC8 0 . GRCh38 22 20139293 20139293 + Missense_Mutation SNP G G A novel C3N-02379_T C3N-02379_N G G c.204G>A p.Met68Ile p.M68I ENST00000405930 2/11 147 134 13 151 151 0 strelka-varscan-mutect ZDHHC8,missense_variant,p.Met68Ile,ENST00000334554,NM_013373.3;ZDHHC8,missense_variant,p.Met68Ile,ENST00000405930,NM_001185024.1;ZDHHC8,missense_variant,p.Met68Ile,ENST00000320602,;ZDHHC8,missense_variant,p.Met57Ile,ENST00000436518,;ZDHHC8,intron_variant,,ENST00000468112,;ZDHHC8,upstream_gene_variant,,ENST00000472497,;ZDHHC8,upstream_gene_variant,,ENST00000469212,; A ENST00000405930 Transcript missense_variant 204/3112 204/2337 68/778 M/I atG/atA 1 1 ZDHHC8 HGNC HGNC:18474 protein_coding YES CCDS54502.1 ENSP00000384716 Q9ULC8 UPI0000D62100 NM_001185024.1 deleterious(0.01) 2/11 hmmpanther:PTHR12349,hmmpanther:PTHR12349:SF1,Transmembrane_helices:TMhelix MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 20139293 20139293 G A 1 0 0 0 0 1 0 0 0 18197 1348 47 3 3 ZDHHC8 22 20139293 Missense_Mutation SNP G C3N-02379_T 20139293 30679175 52 28991 CRYBB2 0 . GRCh38 22 25224953 25224953 + Missense_Mutation SNP C C A novel C3N-02379_T C3N-02379_N C C c.90C>A p.His30Gln p.H30Q ENST00000398215 3/6 444 356 88 549 549 0 strelka-varscan-mutect CRYBB2,missense_variant,p.His30Gln,ENST00000398215,NM_000496.2; A ENST00000398215 Transcript missense_variant 261/886 90/618 30/205 H/Q caC/caA 1 1 CRYBB2 HGNC HGNC:2398 protein_coding YES CCDS13831.1 ENSP00000381273 P43320 R4UMM2 UPI000013C6A2 NM_000496.2 deleterious(0.02) 3/6 PROSITE_profiles:PS50915,hmmpanther:PTHR11818:SF11,hmmpanther:PTHR11818,Gene3D:2.60.20.10,Pfam_domain:PF00030,SMART_domains:SM00247,Superfamily_domains:SSF49695 MODERATE 1 SNV 1 1 PASS rs1446234610 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 95 25224953 25224953 C A 1 0 0 0 0 1 0 0 0 3713 564 20 2 2 CRYBB2 22 25224953 Missense_Mutation SNP C C3N-02379_T 5085660 25224953 25593515 53 28992 PPP2R3B 0 . GRCh38 X 361534 361534 + Silent SNP G G C rs746509401 C3N-02379_T C3N-02379_N G G c.381C>G p.= p.T127T ENST00000390665 2/13 410 383 27 241 241 0 strelka-varscan-mutect PPP2R3B,synonymous_variant,p.=,ENST00000390665,NM_013239.4;PPP2R3B,synonymous_variant,p.=,ENST00000381625,;PPP2R3B,non_coding_transcript_exon_variant,,ENST00000445792,;PPP2R3B,upstream_gene_variant,,ENST00000496630,; C ENST00000390665 Transcript synonymous_variant 400/2151 381/1728 127/575 T acC/acG rs746509401 1 -1 PPP2R3B HGNC HGNC:13417 protein_coding YES CCDS14104.1 ENSP00000375080 Q9Y5P8 UPI00001BB8B8 NM_013239.4 2/13 hmmpanther:PTHR14095:SF1,hmmpanther:PTHR14095 LOW 1 SNV 1 1 PASS rs746509401 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 95 361534 361534 G C 1 0 0 0 0 0 0 0 1 12512 987 35 4 4 PPP2R3B 23 361534 Silent SNP G C3N-02379_T 361534 155679361 54 28993 DMD 0 . GRCh38 X 31496922 31496922 + Missense_Mutation SNP C C T novel C3N-02379_T C3N-02379_N C C c.8413G>A p.Asp2805Asn p.D2805N ENST00000357033 57/79 505 415 90 537 537 0 strelka-varscan-mutect DMD,missense_variant,p.Asp2805Asn,ENST00000357033,NM_000109.3,NM_004006.2;DMD,missense_variant,p.Asp2801Asn,ENST00000378677,NM_004010.3,NM_004009.3;DMD,missense_variant,p.Asp2804Asn,ENST00000620040,;DMD,missense_variant,p.Asp2800Asn,ENST00000619831,;DMD,missense_variant,p.Asp345Asn,ENST00000378707,NM_004013.2;DMD,missense_variant,p.Asp345Asn,ENST00000359836,NM_004022.2;DMD,missense_variant,p.Asp345Asn,ENST00000541735,NM_004020.3,NM_004023.2;DMD,missense_variant,p.Asp501Asn,ENST00000358062,;DMD,missense_variant,p.Asp76Asn,ENST00000343523,NM_004014.2;DMD,missense_variant,p.Asp345Asn,ENST00000474231,NM_004021.2;DMD,non_coding_transcript_exon_variant,,ENST00000445312,; T ENST00000357033 Transcript missense_variant 8620/13956 8413/11058 2805/3685 D/N Gac/Aac 1 -1 DMD HGNC HGNC:2928 protein_coding YES CCDS14233.1 ENSP00000354923 A0A075B6G3 UPI000049E111 NM_000109.3,NM_004006.2 deleterious(0.01) 57/79 hmmpanther:PTHR11915:SF261,hmmpanther:PTHR11915,PIRSF_domain:PIRSF002341,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 95 31496922 31496922 C T 1 0 0 0 0 1 0 0 0 4387 826 29 3 3 DMD 23 31496922 Missense_Mutation SNP C C3N-02379_T 31135388 31496922 124543973 55 28994 USP27X 0 . GRCh38 X 49881333 49881333 + Missense_Mutation SNP T T G novel C3N-02379_T C3N-02379_N T T c.1026T>G p.Ser342Arg p.S342R ENST00000621775 1/1 423 335 88 391 390 1 strelka-varscan-mutect USP27X,missense_variant,p.Ser342Arg,ENST00000621775,NM_001145073.2;USP27X-AS1,upstream_gene_variant,,ENST00000437322,; G ENST00000621775 Transcript missense_variant 1386/2618 1026/1317 342/438 S/R agT/agG 1 1 USP27X HGNC HGNC:13486 protein_coding YES CCDS65260.1 ENSP00000483631 A6NNY8 UPI0000EE7A8D NM_001145073.2 tolerated(0.21) 1/1 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF368,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 95 49881333 49881333 T G 1 0 0 0 0 1 0 0 0 17599 1635 57 5 5 USP27X 23 49881333 Missense_Mutation SNP T C3N-02379_T 18384411 49881333 106159562 56 28995 PLS3 0 . GRCh38 X 115646524 115646524 + Silent SNP G G A novel C3N-02379_T C3N-02379_N G G c.1500G>A p.= p.Q500Q ENST00000355899 13/16 102 90 12 124 123 1 strelka-varscan-mutect PLS3,synonymous_variant,p.=,ENST00000355899,NM_005032.6;PLS3,synonymous_variant,p.=,ENST00000420625,;PLS3,synonymous_variant,p.=,ENST00000539310,NM_001172335.2,NM_001136025.4,NM_001282338.1;PLS3,synonymous_variant,p.=,ENST00000289290,NM_001282337.1;PLS3,downstream_gene_variant,,ENST00000497870,;PLS3,3_prime_UTR_variant,,ENST00000481823,;PLS3,downstream_gene_variant,,ENST00000466150,; A ENST00000355899 Transcript synonymous_variant 1587/3280 1500/1893 500/630 Q caG/caA 1 1 PLS3 HGNC HGNC:9091 protein_coding YES CCDS14568.1 ENSP00000348163 P13797 UPI000000D962 NM_005032.6 13/16 PROSITE_profiles:PS50021,hmmpanther:PTHR19961,hmmpanther:PTHR19961:SF32,PROSITE_patterns:PS00020,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.99999 1 1 1 1 0 A 2 1 95 115646524 115646524 G A 1 0 0 0 0 0 0 0 1 12216 962 34 3 3 PLS3 23 115646524 Silent SNP G C3N-02379_T 65765191 115646524 40394371 57 28996 SLITRK4 0 . GRCh38 X 143630564 143630564 + Missense_Mutation SNP T T C novel C3N-02379_T C3N-02379_N T T c.545A>G p.His182Arg p.H182R ENST00000596188 2/2 208 187 21 207 207 0 strelka-varscan-mutect SLITRK4,missense_variant,p.His182Arg,ENST00000596188,NM_001184750.2;SLITRK4,missense_variant,p.His182Arg,ENST00000338017,NM_173078.4;SLITRK4,missense_variant,p.His182Arg,ENST00000356928,NM_001184749.2; C ENST00000596188 Transcript missense_variant 771/8545 545/2514 182/837 H/R cAt/cGt 1 -1 SLITRK4 HGNC HGNC:23502 protein_coding YES CCDS14679.1 ENSP00000469205 Q8IW52 UPI000004E650 NM_001184750.2 deleterious(0.04) 2/2 Gene3D:3.80.10.10,PROSITE_profiles:PS51450,hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF11,SMART_domains:SM00365,SMART_domains:SM00369,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 95 143630564 143630564 T C 1 0 0 0 0 1 0 0 0 15036 1464 51 5 5 SLITRK4 23 143630564 Missense_Mutation SNP T C3N-02379_T 27984040 143630564 12410331 58 28997 EPHA8 0 . GRCh38 1 22593442 22593442 + Missense_Mutation SNP T T C novel C3N-02380_T C3N-02380_N T T c.1432T>C p.Tyr478His p.Y478H ENST00000166244 6/17 135 123 12 111 111 0 strelka-varscan-mutect EPHA8,missense_variant,p.Tyr478His,ENST00000166244,NM_020526.3;EPHA8,downstream_gene_variant,,ENST00000374644,NM_001006943.1; C ENST00000166244 Transcript missense_variant 1504/4943 1432/3018 478/1005 Y/H Tac/Cac 1 1 EPHA8 HGNC HGNC:3391 protein_coding YES CCDS225.1 ENSP00000166244 P29322 UPI000012A07B NM_020526.3 tolerated(0.1) 6/17 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,hmmpanther:PTHR24416:SF339,hmmpanther:PTHR24416,Pfam_domain:PF00041,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000666,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -19.99964 1 1 1 1 0 C 3 2 96 22593442 22593442 T C 1 0 0 0 0 1 0 0 0 5020 1522 53 5 5 EPHA8 1 22593442 Missense_Mutation SNP T C3N-02380_T 22593442 226362980 1 28998 MYCL 0 . GRCh38 1 39901203 39901203 + Frame_Shift_Del DEL G G - novel C3N-02380_T C3N-02380_N G G c.322delC p.His108ThrfsTer32 p.H108Tfs*32 ENST00000397332 2/3 154 142 12 131 131 0 sindel-varindel-pindel MYCL,frameshift_variant,p.His108ThrfsTer32,ENST00000397332,NM_001033082.2;MYCL,frameshift_variant,p.His108ThrfsTer32,ENST00000372815,NM_005376.4;MYCL,frameshift_variant,p.His78ThrfsTer32,ENST00000372816,NM_001033081.2;MYCL,frameshift_variant,p.His78ThrfsTer?,ENST00000450953,;RP1-118J21.5,downstream_gene_variant,,ENST00000418255,; - ENST00000397332 Transcript frameshift_variant 447/3256 322/1185 108/394 H/X Cac/ac 1 -1 MYCL HGNC HGNC:7555 protein_coding YES CCDS53300.1 ENSP00000380494 P12524 UPI000047097E NM_001033082.2 2/3 hmmpanther:PTHR11514,hmmpanther:PTHR11514:SF1,Pfam_domain:PF01056 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 96 39901203 39901203 G - 1 0 1 0 1 0 0 0 0 10020 1348 47 0 0 MYCL 1 39901203 Frame_Shift_Del DEL G C3N-02380_T 17307761 39901203 209055219 2 28999 SPAG17 0 . GRCh38 1 118039391 118039391 + Missense_Mutation SNP G G A C3N-02380_T C3N-02380_N G G c.3220C>T p.His1074Tyr p.H1074Y ENST00000336338 23/49 208 194 14 331 329 2 strelka-varscan-mutect SPAG17,missense_variant,p.His1074Tyr,ENST00000336338,NM_206996.2;SPAG17,non_coding_transcript_exon_variant,,ENST00000470550,;SPAG17,upstream_gene_variant,,ENST00000486589,; A ENST00000336338 Transcript missense_variant 3286/6924 3220/6672 1074/2223 H/Y Cat/Tat COSM4487724 1 -1 SPAG17 HGNC HGNC:26620 protein_coding YES CCDS899.1 ENSP00000337804 Q6Q759 UPI00001601FD NM_206996.2 deleterious(0.05) 23/49 hmmpanther:PTHR21963 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 118039391 118039391 G A 1 0 0 0 0 1 0 0 0 15310 1290 45 3 3 SPAG17 1 118039391 Missense_Mutation SNP G C3N-02380_T 78138188 118039391 130917031 3 29000 FAM89A 0 . GRCh38 1 231020094 231020094 + Silent SNP G G A novel C3N-02380_T C3N-02380_N G G c.324C>T p.= p.L108L ENST00000366654 2/2 161 152 9 133 133 0 strelka-varscan-mutect FAM89A,synonymous_variant,p.=,ENST00000366654,NM_198552.2;FAM89A,upstream_gene_variant,,ENST00000408363,;FAM89A,non_coding_transcript_exon_variant,,ENST00000494111,;FAM89A,non_coding_transcript_exon_variant,,ENST00000466258,;RP11-423F24.3,upstream_gene_variant,,ENST00000413346,; A ENST00000366654 Transcript synonymous_variant 359/1495 324/555 108/184 L ctC/ctT 1 -1 FAM89A HGNC HGNC:25057 protein_coding YES CCDS1590.1 ENSP00000355614 Q96GI7 UPI000006D6ED NM_198552.2 2/2 hmmpanther:PTHR21529 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -16.49265 1 1 1 1 0 A 2 1 96 231020094 231020094 G A 1 0 0 0 0 0 0 0 1 5504 929 33 3 3 FAM89A 1 231020094 Silent SNP G C3N-02380_T 112980703 231020094 17936328 4 29001 TSNAX 0 . GRCh38 1 231537287 231537287 + Nonsense_Mutation SNP G G T novel C3N-02380_T C3N-02380_N G G c.196G>T p.Glu66Ter p.E66* ENST00000366639 3/6 117 101 16 177 176 1 strelka-varscan-mutect TSNAX,stop_gained,p.Glu66Ter,ENST00000366639,NM_005999.2;TSNAX,stop_gained,p.Glu66Ter,ENST00000413309,;TSNAX,non_coding_transcript_exon_variant,,ENST00000602825,;TSNAX-DISC1,stop_gained,p.Glu66Ter,ENST00000602962,;TSNAX-DISC1,stop_gained,p.Glu66Ter,ENST00000602567,;TSNAX-DISC1,stop_gained,p.Glu66Ter,ENST00000602634,;TSNAX-DISC1,stop_gained,p.Glu66Ter,ENST00000602956,;TSNAX,non_coding_transcript_exon_variant,,ENST00000475168,;TSNAX,non_coding_transcript_exon_variant,,ENST00000476913,;TSNAX-DISC1,intron_variant,,ENST00000602885,; T ENST00000366639 Transcript stop_gained 354/2650 196/873 66/290 E/* Gaa/Taa 1 1 TSNAX HGNC HGNC:12380 protein_coding YES CCDS1596.1 ENSP00000355599 Q99598 A0A024R3V8 UPI0000137768 NM_005999.2 3/6 hmmpanther:PTHR10741,hmmpanther:PTHR10741:SF5,Pfam_domain:PF01997,Gene3D:1j1jA01,Superfamily_domains:0047790 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 96 231537287 231537287 G T 1 0 0 0 0 0 1 0 0 17136 1291 45 2 2 TSNAX 1 231537287 Nonsense_Mutation SNP G C3N-02380_T 517193 231537287 17419135 5 29002 GPAT2 0 . GRCh38 2 96026215 96026215 + Missense_Mutation SNP G G C novel C3N-02380_T C3N-02380_N G G c.1123C>G p.Arg375Gly p.R375G ENST00000434632 12/23 57 47 10 65 64 1 strelka-varscan-mutect GPAT2,missense_variant,p.Arg375Gly,ENST00000434632,NM_001321525.1;GPAT2,missense_variant,p.Arg375Gly,ENST00000359548,NM_207328.2;GPAT2,missense_variant,p.Arg304Gly,ENST00000453542,;GPAT2,downstream_gene_variant,,ENST00000439254,;FAHD2CP,downstream_gene_variant,,ENST00000607780,;FAHD2CP,downstream_gene_variant,,ENST00000467292,;FAHD2CP,downstream_gene_variant,,ENST00000443258,;GPAT2,downstream_gene_variant,,ENST00000468438,;FAHD2CP,downstream_gene_variant,,ENST00000483000,;GPAT2,non_coding_transcript_exon_variant,,ENST00000482704,;GPAT2,non_coding_transcript_exon_variant,,ENST00000471757,;GPAT2,non_coding_transcript_exon_variant,,ENST00000486463,;GPAT2,non_coding_transcript_exon_variant,,ENST00000484440,;FAHD2CP,downstream_gene_variant,,ENST00000427863,; C ENST00000434632 Transcript missense_variant 1583/3061 1123/2388 375/795 R/G Cgg/Ggg 1 -1 GPAT2 HGNC HGNC:27168 protein_coding YES CCDS42714.1 ENSP00000389395 Q6NUI2 UPI0000E5E123 NM_001321525.1 deleterious(0) 12/23 hmmpanther:PTHR12563,hmmpanther:PTHR12563:SF15 MODERATE 1 SNV 5 1 PASS rs1368619872 . 0 202 8 0 0 0 0 0 -19.99964 0.9999986 1 1 1 0 C 3 2 96 96026215 96026215 G C 1 0 0 0 0 1 0 0 0 6486 1115 39 4 4 GPAT2 2 96026215 Missense_Mutation SNP G C3N-02380_T 96026215 146167314 6 29003 UGT1A8 0 . GRCh38 2 233618097 233618097 + Silent SNP C C T novel C3N-02380_T C3N-02380_N C C c.390C>T p.= p.D130D ENST00000373450 1/5 126 109 17 210 210 0 strelka-varscan-mutect UGT1A8,synonymous_variant,p.=,ENST00000373450,NM_019076.4; T ENST00000373450 Transcript synonymous_variant 453/2407 390/1593 130/530 D gaC/gaT 1 1 UGT1A8 HGNC HGNC:12540 protein_coding YES CCDS33402.1 ENSP00000362549 Q9HAW9 Q5DSZ6 UPI0000072F75 NM_019076.4 1/5 hmmpanther:PTHR11926:SF405,hmmpanther:PTHR11926,Pfam_domain:PF00201,Superfamily_domains:SSF53756 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 96 233618097 233618097 C T 1 0 0 0 0 0 0 0 1 17476 506 18 3 3 UGT1A8 2 233618097 Silent SNP C C3N-02380_T 137591882 233618097 8575432 7 29004 THAP4 0 . GRCh38 2 241633645 241633645 + Missense_Mutation SNP A A C novel C3N-02380_T C3N-02380_N A A c.512T>G p.Leu171Arg p.L171R ENST00000407315 2/6 143 134 9 154 153 1 strelka-varscan-mutect THAP4,missense_variant,p.Leu171Arg,ENST00000407315,NM_015963.5;ATG4B,upstream_gene_variant,,ENST00000405546,NM_178326.2;ATG4B,upstream_gene_variant,,ENST00000404914,NM_013325.4;ATG4B,upstream_gene_variant,,ENST00000402096,;THAP4,upstream_gene_variant,,ENST00000612200,;ATG4B,upstream_gene_variant,,ENST00000425239,;ATG4B,upstream_gene_variant,,ENST00000400771,;ATG4B,upstream_gene_variant,,ENST00000430617,;ATG4B,upstream_gene_variant,,ENST00000419606,;ATG4B,upstream_gene_variant,,ENST00000625810,;ATG4B,upstream_gene_variant,,ENST00000491867,;ATG4B,upstream_gene_variant,,ENST00000482507,;ATG4B,upstream_gene_variant,,ENST00000494465,;ATG4B,upstream_gene_variant,,ENST00000483778,;ATG4B,upstream_gene_variant,,ENST00000493618,;ATG4B,upstream_gene_variant,,ENST00000475195,;ATG4B,upstream_gene_variant,,ENST00000468018,;ATG4B,upstream_gene_variant,,ENST00000400772,;ATG4B,upstream_gene_variant,,ENST00000465399,;ATG4B,upstream_gene_variant,,ENST00000479554,;ATG4B,upstream_gene_variant,,ENST00000415107,; C ENST00000407315 Transcript missense_variant 944/2367 512/1734 171/577 L/R cTg/cGg 1 -1 THAP4 HGNC HGNC:23187 protein_coding YES CCDS2551.1 ENSP00000385006 Q8WY91 UPI000018DBC4 NM_015963.5 tolerated_low_confidence(0.88) 2/6 hmmpanther:PTHR15854,hmmpanther:PTHR15854:SF4 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -12.52361 0.9999995 1 1 1 0 C 3 2 96 241633645 241633645 A C 1 0 0 0 0 1 0 0 0 16279 188 7 5 5 THAP4 2 241633645 Missense_Mutation SNP A C3N-02380_T 8015548 241633645 559884 8 29005 VCAN 0 . GRCh38 5 83541582 83541582 + Missense_Mutation SNP C C A novel C3N-02380_T C3N-02380_N C C c.8579C>A p.Ser2860Tyr p.S2860Y ENST00000265077 8/15 191 181 10 277 277 0 strelka-varscan-mutect VCAN,missense_variant,p.Ser2860Tyr,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Ser1873Tyr,ENST00000343200,NM_001164097.1;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN,downstream_gene_variant,,ENST00000513960,;VCAN-AS1,non_coding_transcript_exon_variant,,ENST00000513899,;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 9144/12625 8579/10191 2860/3396 S/Y tCc/tAc 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 deleterious(0.02) 8/15 hmmpanther:PTHR22804:SF6,hmmpanther:PTHR22804 MODERATE 1 SNV 1 1 PASS rs1397075309 . 0 208 0 2 0 0 0 0 -12.60052 0.9999993 1 1 1 0 A 3 1 96 83541582 83541582 C A 1 0 0 0 0 1 0 0 0 17683 855 30 2 2 VCAN 5 83541582 Missense_Mutation SNP C C3N-02380_T 83541582 97996677 9 29006 ADGRV1 0 . GRCh38 5 90627597 90627597 + Missense_Mutation SNP G G C novel C3N-02380_T C3N-02380_N G G c.1059G>C p.Glu353Asp p.E353D ENST00000405460 7/90 186 113 73 190 190 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Glu353Asp,ENST00000405460,NM_032119.3;ADGRV1,upstream_gene_variant,,ENST00000504142,;ADGRV1,downstream_gene_variant,,ENST00000508842,; C ENST00000405460 Transcript missense_variant 1155/19338 1059/18921 353/6306 E/D gaG/gaC 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 deleterious(0) 7/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,Superfamily_domains:SSF141072 MODERATE 1 SNV 1 1 PASS rs920194615 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 96 90627597 90627597 G C 1 0 0 0 0 1 0 0 0 379 933 33 4 4 ADGRV1 5 90627597 Missense_Mutation SNP G C3N-02380_T 7086015 90627597 90910662 10 29007 1 24 3 3 1147 G 1.099564e-06 ADGRV1 0 . GRCh38 5 90627757 90627757 + Missense_Mutation SNP G G A novel C3N-02380_T C3N-02380_N G G c.1219G>A p.Asp407Asn p.D407N ENST00000405460 7/90 51 35 16 52 52 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Asp407Asn,ENST00000405460,NM_032119.3;ADGRV1,upstream_gene_variant,,ENST00000504142,; A ENST00000405460 Transcript missense_variant 1315/19338 1219/18921 407/6306 D/N Gat/Aat 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 tolerated(0.34) 7/90 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20 MODERATE 1 SNV 1 1 PASS . . 1 200 9 0 0 0 0 0 -20 0.9999985 1 1 1 0 A 3 1 96 90627757 90627757 G A 1 0 0 0 0 1 0 0 0 379 1290 45 3 3 ADGRV1 5 90627757 Missense_Mutation SNP G C3N-02380_T 160 90627757 90910502 11 29008 1 24 3 3 1147 G 1.099564e-06 ADGRV1 0 . GRCh38 5 90628743 90628743 + Missense_Mutation SNP G G A C3N-02380_T C3N-02380_N G G c.1420G>A p.Asp474Asn p.D474N ENST00000405460 8/90 416 244 172 282 282 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Asp474Asn,ENST00000405460,NM_032119.3;ADGRV1,missense_variant,p.Asp63Asn,ENST00000504142,; A ENST00000405460 Transcript missense_variant 1516/19338 1420/18921 474/6306 D/N Gat/Aat COSM4006076 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 deleterious(0) 8/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,Superfamily_domains:SSF141072 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 90628743 90628743 G A 1 0 0 0 0 1 0 0 0 379 1290 45 3 3 ADGRV1 5 90628743 Missense_Mutation SNP G C3N-02380_T 986 90628743 90909516 12 29009 1 24 3 3 1147 G 1.099564e-06 THG1L 0 . GRCh38 5 157734622 157734622 + Missense_Mutation SNP T T C novel C3N-02380_T C3N-02380_N T T c.415T>C p.Phe139Leu p.F139L ENST00000231198 3/6 331 299 32 209 209 0 strelka-varscan-mutect THG1L,missense_variant,p.Phe139Leu,ENST00000231198,NM_001317825.1,NM_017872.3;THG1L,intron_variant,,ENST00000521655,;THG1L,upstream_gene_variant,,ENST00000523575,; C ENST00000231198 Transcript missense_variant 659/3107 415/897 139/298 F/L Ttt/Ctt 1 1 THG1L HGNC HGNC:26053 protein_coding YES CCDS4341.1 ENSP00000231198 Q9NWX6 UPI0000073782 NM_001317825.1,NM_017872.3 tolerated(0.06) 3/6 Pfam_domain:PF04446,PIRSF_domain:PIRSF028980,hmmpanther:PTHR12729,hmmpanther:PTHR12729:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 96 157734622 157734622 T C 1 0 0 0 0 1 0 0 0 16296 1725 60 5 5 THG1L 5 157734622 Missense_Mutation SNP T C3N-02380_T 67105879 157734622 23803637 13 29010 HACE1 0 . GRCh38 6 104785072 104785072 + Missense_Mutation SNP C C T novel C3N-02380_T C3N-02380_N C C c.1322G>A p.Cys441Tyr p.C441Y ENST00000262903 12/24 152 136 16 146 146 0 strelka-varscan-mutect HACE1,missense_variant,p.Cys441Tyr,ENST00000262903,NM_001321083.1,NM_020771.3;HACE1,missense_variant,p.Cys441Tyr,ENST00000369125,;HACE1,upstream_gene_variant,,ENST00000518503,;HACE1,upstream_gene_variant,,ENST00000517995,;HACE1,missense_variant,p.Cys43Tyr,ENST00000517424,;HACE1,3_prime_UTR_variant,,ENST00000416605,;HACE1,non_coding_transcript_exon_variant,,ENST00000369127,; T ENST00000262903 Transcript missense_variant 1599/4576 1322/2730 441/909 C/Y tGt/tAt 1 -1 HACE1 HGNC HGNC:21033 protein_coding YES CCDS5050.1 ENSP00000262903 Q8IYU2 UPI00001602DC NM_001321083.1,NM_020771.3 deleterious(0.03) 12/24 hmmpanther:PTHR11254 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 104785072 104785072 C T 1 0 0 0 0 1 0 0 0 6826 478 17 3 3 HACE1 6 104785072 Missense_Mutation SNP C C3N-02380_T 104785072 66020907 14 29011 TUBE1 0 . GRCh38 6 112071996 112071996 + Missense_Mutation SNP T T G novel C3N-02380_T C3N-02380_N T T c.1175A>C p.His392Pro p.H392P ENST00000368662 11/12 178 166 12 169 169 0 strelka-varscan-mutect TUBE1,missense_variant,p.His392Pro,ENST00000368662,NM_016262.4;WISP3,downstream_gene_variant,,ENST00000368666,NM_198239.1;WISP3,downstream_gene_variant,,ENST00000361714,;WISP3,downstream_gene_variant,,ENST00000604763,;WISP3,downstream_gene_variant,,ENST00000230529,NM_003880.3;WISP3,downstream_gene_variant,,ENST00000409166,;TUBE1,non_coding_transcript_exon_variant,,ENST00000604814,;WISP3,downstream_gene_variant,,ENST00000620524,;WISP3,downstream_gene_variant,,ENST00000613648,;TUBE1,downstream_gene_variant,,ENST00000441191,;TUBE1,3_prime_UTR_variant,,ENST00000605457,;TUBE1,downstream_gene_variant,,ENST00000604689,;WISP3,downstream_gene_variant,,ENST00000368664,;WISP3,downstream_gene_variant,,ENST00000454589,;TUBE1,downstream_gene_variant,,ENST00000604743,;TUBE1,downstream_gene_variant,,ENST00000604967,;TUBE1,downstream_gene_variant,,ENST00000603651,; G ENST00000368662 Transcript missense_variant 1254/2142 1175/1428 392/475 H/P cAt/cCt 1 -1 TUBE1 HGNC HGNC:20775 protein_coding YES CCDS5100.1 ENSP00000357651 Q9UJT0 UPI0000136A4E NM_016262.4 tolerated(0.15) 11/12 hmmpanther:PTHR11588,hmmpanther:PTHR11588:SF13,Pfam_domain:PF03953,Gene3D:3.30.1330.20,SMART_domains:SM00865,Superfamily_domains:SSF55307 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -15.54438 0.9999665 1 1 1 0 G 3 3 96 112071996 112071996 T G 1 0 0 0 0 1 0 0 0 17273 1464 51 5 5 TUBE1 6 112071996 Missense_Mutation SNP T C3N-02380_T 7286924 112071996 58733983 15 29012 EEPD1 0 . GRCh38 7 36155026 36155026 + Silent SNP G G A rs776101800 C3N-02380_T C3N-02380_N G G c.702G>A p.= p.P234P ENST00000242108 2/8 62 57 5 71 71 0 strelka-varscan-mutect EEPD1,synonymous_variant,p.=,ENST00000242108,NM_030636.2;EEPD1,synonymous_variant,p.=,ENST00000534978,; A ENST00000242108 Transcript synonymous_variant 1420/4765 702/1710 234/569 P ccG/ccA rs776101800,COSM118192 1 1 EEPD1 HGNC HGNC:22223 protein_coding YES CCDS34619.1 ENSP00000242108 Q7L9B9 UPI000020ED9D NM_030636.2 2/8 hmmpanther:PTHR21180:SF32,hmmpanther:PTHR21180 0,1 LOW 1 SNV 1 0,1 1 PASS rs776101800 . 0 195 14 0 0 0 0 0 -11.36515 0.9990534 1 1 1 0 A 2 1 96 36155026 36155026 G A 1 0 0 0 0 0 0 0 1 4763 1074 38 1 1 EEPD1 7 36155026 Silent SNP G C3N-02380_T 36155026 123190947 16 29013 EGFR 0 . GRCh38 7 55174772 55174786 + In_Frame_Del DEL GGAATTAAGAGAAGC GGAATTAAGAGAAGC - rs121913421 C3N-02380_T C3N-02380_N GGAATTAAGAGAAGC GGAATTAAGAGAAGC c.2235_2249delGGAATTAAGAGAAGC p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 429 332 97 450 450 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2412-2426/9821 2235-2249/3633 745-750/1210 KELREA/K aaGGAATTAAGAGAAGCa/aaa rs121913421,COSM6223 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PROSITE_patterns:PS00107,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 96 55174772 55174772 GGAATTAAGAGAAGC - 1 0 1 0 1 0 0 0 0 4803 991 35 0 0 EGFR 7 55174772 In_Frame_Del DEL GGAATTAAGAGAAGC C3N-02380_T 19019746 55174772 104171201 17 29014 ELP3 0 . GRCh38 8 28137770 28137770 + Missense_Mutation SNP G G T rs185393822 C3N-02380_T C3N-02380_N G G c.979G>T p.Gly327Trp p.G327W ENST00000256398 10/15 268 240 28 328 328 0 strelka-varscan-mutect ELP3,missense_variant,p.Gly327Trp,ENST00000256398,NM_018091.5;ELP3,missense_variant,p.Gly313Trp,ENST00000521015,NM_001284222.1;ELP3,missense_variant,p.Gly235Trp,ENST00000380353,NM_001284226.1;ELP3,missense_variant,p.Gly208Trp,ENST00000537665,NM_001284225.1,NM_001284224.1;ELP3,missense_variant,p.Gly255Trp,ENST00000524103,NM_001284220.1;ELP3,non_coding_transcript_exon_variant,,ENST00000520110,;ELP3,3_prime_UTR_variant,,ENST00000518112,;ELP3,3_prime_UTR_variant,,ENST00000519261,;ELP3,3_prime_UTR_variant,,ENST00000523687,; T ENST00000256398 Transcript missense_variant 1356/3452 979/1644 327/547 G/W Ggg/Tgg rs185393822 1 1 ELP3 HGNC HGNC:20696 protein_coding YES CCDS6065.1 ENSP00000256398 Q9H9T3 UPI000006F0B5 NM_018091.5 deleterious(0) 10/15 hmmpanther:PTHR11135,PIRSF_domain:PIRSF005669,Pfam_domain:PF16199,TIGRFAM_domain:TIGR01211,Gene3D:2qgqB01,SMART_domains:SM00729,Superfamily_domains:SSF102114 MODERATE 1 SNV 1 1 PASS rs185393822 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 28137770 28137770 G T 1 0 0 0 0 1 0 0 0 4915 1116 39 1 1 ELP3 8 28137770 Missense_Mutation SNP G C3N-02380_T 28137770 117000866 18 29015 UNC5D 0 . GRCh38 8 35726463 35726463 + Missense_Mutation SNP A A G rs780208018 C3N-02380_T C3N-02380_N A A c.1615A>G p.Arg539Gly p.R539G ENST00000404895 10/17 201 157 44 226 225 1 strelka-varscan-mutect UNC5D,missense_variant,p.Arg470Gly,ENST00000287272,;UNC5D,missense_variant,p.Arg534Gly,ENST00000453357,;UNC5D,missense_variant,p.Arg544Gly,ENST00000416672,;UNC5D,missense_variant,p.Arg539Gly,ENST00000404895,NM_080872.2;UNC5D,missense_variant,p.Arg472Gly,ENST00000420357,;UNC5D,missense_variant,p.Arg115Gly,ENST00000449677,;UNC5D,non_coding_transcript_exon_variant,,ENST00000474634,; G ENST00000404895 Transcript missense_variant 1943/3252 1615/2862 539/953 R/G Agg/Ggg rs780208018 1 1 UNC5D HGNC HGNC:18634 protein_coding YES CCDS6093.2 ENSP00000385143 Q6UXZ4 UPI00001D6915 NM_080872.2 tolerated(0.22) 10/17 hmmpanther:PTHR12582,hmmpanther:PTHR12582:SF5 MODERATE 1 SNV 1 1 PASS rs780208018 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 96 35726463 35726463 A G 1 0 0 0 0 1 0 0 0 17519 63 3 5 5 UNC5D 8 35726463 Missense_Mutation SNP A C3N-02380_T 7588693 35726463 109412173 19 29016 HPSE2 0 . GRCh38 10 98721796 98721796 + Missense_Mutation SNP C C A C3N-02380_T C3N-02380_N C C c.817G>T p.Ala273Ser p.A273S ENST00000370552 5/12 392 321 71 408 407 1 strelka-varscan-mutect HPSE2,missense_variant,p.Ala70Ser,ENST00000404542,;HPSE2,missense_variant,p.Ala273Ser,ENST00000370552,NM_021828.4;HPSE2,missense_variant,p.Ala215Ser,ENST00000370549,NM_001166244.1;HPSE2,missense_variant,p.Ala273Ser,ENST00000370546,NM_001166246.1;HPSE2,missense_variant,p.Ala161Ser,ENST00000628193,NM_001166245.1; A ENST00000370552 Transcript missense_variant 877/2295 817/1779 273/592 A/S Gca/Tca COSM5309453,COSM5309454 1 -1 HPSE2 HGNC HGNC:18374 protein_coding YES CCDS7477.1 ENSP00000359583 Q8WWQ2 UPI00001AEEC0 NM_021828.4 tolerated(0.44) 5/12 Gene3D:3.20.20.80,Pfam_domain:PF03662,hmmpanther:PTHR14363,hmmpanther:PTHR14363:SF15,Superfamily_domains:SSF51445 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1175821626 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 98721796 98721796 C A 1 0 0 0 0 1 0 0 0 7240 739 26 2 2 HPSE2 10 98721796 Missense_Mutation SNP C C3N-02380_T 98721796 35075626 20 29017 ABCC8 0 . GRCh38 11 17427128 17427128 + Missense_Mutation SNP C C G C3N-02380_T C3N-02380_N C C c.2143G>C p.Val715Leu p.V715L ENST00000302539 16/39 125 107 18 77 77 0 strelka-varscan-mutect ABCC8,missense_variant,p.Val715Leu,ENST00000302539,NM_001287174.1;ABCC8,missense_variant,p.Val715Leu,ENST00000389817,NM_000352.4;ABCC8,downstream_gene_variant,,ENST00000528202,;ABCC8,missense_variant,p.Val705Leu,ENST00000527905,;ABCC8,non_coding_transcript_exon_variant,,ENST00000531911,;ABCC8,downstream_gene_variant,,ENST00000532728,;ABCC8,downstream_gene_variant,,ENST00000635881,;ABCC8,downstream_gene_variant,,ENST00000526002,; G ENST00000302539 Transcript missense_variant 2212/4923 2143/4749 715/1582 V/L Gtg/Ctg CD061344 1 -1 ABCC8 HGNC HGNC:59 protein_coding YES CCDS73264.1 ENSP00000303960 Q09428 UPI00015DFF64 NM_001287174.1 tolerated(0.06) 16/39 Gene3D:3.40.50.300,Pfam_domain:PF00005,PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF187,SMART_domains:SM00382,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 96 17427128 17427128 C G 1 0 0 0 0 1 0 0 0 62 507 18 4 4 ABCC8 11 17427128 Missense_Mutation SNP C C3N-02380_T 17427128 117659494 21 29018 GUCY1A2 0 . GRCh38 11 106810176 106810176 + Silent SNP G G T novel C3N-02380_T C3N-02380_N G G c.1509C>A p.= p.A503A ENST00000282249 5/9 260 233 27 292 292 0 strelka-varscan-mutect GUCY1A2,synonymous_variant,p.=,ENST00000526355,NM_000855.2;GUCY1A2,synonymous_variant,p.=,ENST00000282249,NM_001256424.1;GUCY1A2,synonymous_variant,p.=,ENST00000347596,; T ENST00000282249 Transcript synonymous_variant 1899/3047 1509/2292 503/763 A gcC/gcA 1 -1 GUCY1A2 HGNC HGNC:4684 protein_coding YES CCDS58170.1 ENSP00000282249 P33402 UPI000002A79C NM_001256424.1 5/9 hmmpanther:PTHR11920,hmmpanther:PTHR11920:SF276,Pfam_domain:PF07701,SMART_domains:SM00044 LOW 1 SNV 1 1 PASS rs895547657 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 96 106810176 106810176 G T 1 0 0 0 0 0 0 0 1 6775 1219 43 2 2 GUCY1A2 11 106810176 Silent SNP G C3N-02380_T 89383048 106810176 28276446 22 29019 CAND1 0 . GRCh38 12 67297441 67297441 + Missense_Mutation SNP A A T novel C3N-02380_T C3N-02380_N A A c.526A>T p.Ile176Phe p.I176F ENST00000545606 5/15 161 122 39 178 178 0 strelka-varscan-mutect CAND1,missense_variant,p.Ile176Phe,ENST00000545606,NM_018448.4;CAND1,upstream_gene_variant,,ENST00000544619,;CAND1,downstream_gene_variant,,ENST00000540525,;CAND1,missense_variant,p.Ile58Phe,ENST00000540319,;CAND1,non_coding_transcript_exon_variant,,ENST00000535146,;CAND1,downstream_gene_variant,,ENST00000539434,; T ENST00000545606 Transcript missense_variant 963/11251 526/3693 176/1230 I/F Att/Ttt 1 1 CAND1 HGNC HGNC:30688 protein_coding YES CCDS8977.1 ENSP00000442318 Q86VP6 UPI0000037CC5 NM_018448.4 deleterious(0) 5/15 hmmpanther:PTHR12696,hmmpanther:PTHR12696:SF1,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS rs1450254942 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 67297441 67297441 A T 1 0 0 0 0 1 0 0 0 2308 101 4 4 4 CAND1 12 67297441 Missense_Mutation SNP A C3N-02380_T 67297441 65977868 23 29020 PIBF1 0 . GRCh38 13 72783536 72783536 + Missense_Mutation SNP A A G novel C3N-02380_T C3N-02380_N A A c.67A>G p.Ile23Val p.I23V ENST00000326291 2/18 150 133 17 275 275 0 strelka-varscan-mutect PIBF1,missense_variant,p.Ile23Val,ENST00000326291,NM_006346.2;PIBF1,missense_variant,p.Ile23Val,ENST00000617689,;PIBF1,intron_variant,,ENST00000615625,;DIS3,upstream_gene_variant,,ENST00000377767,NM_014953.4;DIS3,upstream_gene_variant,,ENST00000377780,NM_001128226.2;DIS3,upstream_gene_variant,,ENST00000545453,;PIBF1,intron_variant,,ENST00000489797,;DIS3,upstream_gene_variant,,ENST00000475871,;DIS3,upstream_gene_variant,,ENST00000490646,; G ENST00000326291 Transcript missense_variant 405/3154 67/2274 23/757 I/V Att/Gtt 1 1 PIBF1 HGNC HGNC:23352 protein_coding YES CCDS31991.1 ENSP00000317144 Q8WXW3 UPI00001418B9 NM_006346.2 tolerated(0.23) 2/18 Low_complexity_(Seg):seg,hmmpanther:PTHR18950:SF0,hmmpanther:PTHR18950 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 96 72783536 72783536 A G 1 0 0 0 0 1 0 0 0 11969 449 16 5 5 PIBF1 13 72783536 Missense_Mutation SNP A C3N-02380_T 72783536 41580792 24 29021 MTMR10 0 . GRCh38 15 30991474 30991474 + Silent SNP G G A novel C3N-02380_T C3N-02380_N G G c.33C>T p.= p.F11F ENST00000435680 1/16 80 72 8 74 73 1 varscan-mutect MTMR10,synonymous_variant,p.=,ENST00000435680,NM_017762.2;MTMR10,upstream_gene_variant,,ENST00000563714,;MTMR10,synonymous_variant,p.=,ENST00000568604,;MTMR10,synonymous_variant,p.=,ENST00000567567,;MTMR10,synonymous_variant,p.=,ENST00000564787,;MTMR10,non_coding_transcript_exon_variant,,ENST00000565728,; A ENST00000435680 Transcript synonymous_variant 131/4961 33/2334 11/777 F ttC/ttT 1 -1 MTMR10 HGNC HGNC:25999 protein_coding YES CCDS45204.1 ENSP00000402537 Q9NXD2 X5D963 UPI00001FE130 NM_017762.2 1/16 hmmpanther:PTHR10807:SF39,hmmpanther:PTHR10807 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -17.63102 1 1 1 1 0 A 2 1 96 30991474 30991474 G A 1 0 0 0 0 0 0 0 1 9927 1281 45 3 3 MTMR10 15 30991474 Silent SNP G C3N-02380_T 30991474 70999715 25 29022 CLPX 0 . GRCh38 15 65154978 65154978 + Missense_Mutation SNP A A G novel C3N-02380_T C3N-02380_N A A c.1415T>C p.Ile472Thr p.I472T ENST00000300107 11/14 360 325 35 414 414 0 strelka-varscan-mutect CLPX,missense_variant,p.Ile472Thr,ENST00000300107,NM_006660.3;CLPX,3_prime_UTR_variant,,ENST00000559152,;CLPX,non_coding_transcript_exon_variant,,ENST00000560166,;CLPX,downstream_gene_variant,,ENST00000558958,;CLPX,downstream_gene_variant,,ENST00000558103,; G ENST00000300107 Transcript missense_variant 1604/4695 1415/1902 472/633 I/T aTt/aCt 1 -1 CLPX HGNC HGNC:2088 protein_coding YES CCDS10202.1 ENSP00000300107 O76031 A0A024R5X7 UPI0000127B73 NM_006660.3 tolerated(0.71) 11/14 Pfam_domain:PF07724,hmmpanther:PTHR11262,hmmpanther:PTHR11262:SF14,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00382 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 96 65154978 65154978 A G 1 0 0 0 0 1 0 0 0 3328 101 4 5 5 CLPX 15 65154978 Missense_Mutation SNP A C3N-02380_T 34163504 65154978 36836211 26 29023 TMEM114 0 . GRCh38 16 8569816 8569816 + Missense_Mutation SNP G G A novel C3N-02380_T C3N-02380_N G G c.629C>T p.Ala210Val p.A210V ENST00000620492 4/4 149 141 8 158 158 0 strelka-varscan-mutect TMEM114,missense_variant,p.Ala210Val,ENST00000620492,NM_001146336.1;TMEM114,missense_variant,p.Ala129Val,ENST00000568335,NM_001290097.1;TMEM114,missense_variant,p.Ala164Val,ENST00000624696,NM_001290095.1;TMEM114,intron_variant,,ENST00000623677,;TMEM114,non_coding_transcript_exon_variant,,ENST00000444171,; A ENST00000620492 Transcript missense_variant 629/945 629/672 210/223 A/V gCc/gTc 1 -1 TMEM114 HGNC HGNC:33227 protein_coding YES CCDS73825.1 ENSP00000484263 B3SHH9 UPI0001813351 NM_001146336.1 deleterious(0) 4/4 hmmpanther:PTHR20516,hmmpanther:PTHR20516:SF2,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS rs1033272102 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 8569816 8569816 G A 1 0 0 0 0 1 0 0 0 16472 1203 42 3 3 TMEM114 16 8569816 Missense_Mutation SNP G C3N-02380_T 8569816 81768529 27 29024 LPCAT2 0 . GRCh38 16 55574708 55574708 + Missense_Mutation SNP G G T novel C3N-02380_T C3N-02380_N G G c.1293G>T p.Glu431Asp p.E431D ENST00000262134 12/14 261 241 20 227 227 0 strelka-varscan-mutect LPCAT2,missense_variant,p.Glu431Asp,ENST00000262134,NM_017839.4;LPCAT2,non_coding_transcript_exon_variant,,ENST00000565056,;LPCAT2,non_coding_transcript_exon_variant,,ENST00000566915,;LPCAT2,non_coding_transcript_exon_variant,,ENST00000563095,;LPCAT2,upstream_gene_variant,,ENST00000562299,; T ENST00000262134 Transcript missense_variant 1477/5391 1293/1635 431/544 E/D gaG/gaT 1 1 LPCAT2 HGNC HGNC:26032 protein_coding YES CCDS10753.1 ENSP00000262134 Q7L5N7 UPI00001BD900 NM_017839.4 tolerated(0.59) 12/14 PROSITE_profiles:PS50222,hmmpanther:PTHR23063,hmmpanther:PTHR23063:SF21,Pfam_domain:PF13499,Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 55574708 55574708 G T 1 0 0 0 0 1 0 0 0 8814 933 33 2 2 LPCAT2 16 55574708 Missense_Mutation SNP G C3N-02380_T 47004892 55574708 34763637 28 29025 TANGO6 0 . GRCh38 16 68875288 68875288 + Missense_Mutation SNP C C G novel C3N-02380_T C3N-02380_N C C c.1129C>G p.Gln377Glu p.Q377E ENST00000261778 5/18 93 88 5 101 101 0 strelka-varscan-mutect TANGO6,missense_variant,p.Gln377Glu,ENST00000261778,NM_024562.1;TANGO6,missense_variant,p.Gln23Glu,ENST00000565852,; G ENST00000261778 Transcript missense_variant,splice_region_variant 1141/4816 1129/3285 377/1094 Q/E Cag/Gag 1 1 TANGO6 HGNC HGNC:25749 protein_coding YES CCDS45516.1 ENSP00000261778 Q9C0B7 UPI00001FF4A8 NM_024562.1 deleterious(0) 5/18 hmmpanther:PTHR20959,hmmpanther:PTHR20959:SF1 MODERATE 1 SNV 1 1 PASS rs1163260258 . 0 205 4 0 0 0 0 0 -10.84217 1 1 1 1 0 G 3 3 96 68875288 68875288 C G 1 0 0 0 0 1 0 0 0 15944 608 21 4 4 TANGO6 16 68875288 Missense_Mutation SNP C C3N-02380_T 13300580 68875288 21463057 29 29026 TNRC6C 0 . GRCh38 17 78050009 78050009 + Missense_Mutation SNP G G T novel C3N-02380_T C3N-02380_N G G c.947G>T p.Gly316Val p.G316V ENST00000335749 3/21 113 100 13 84 84 0 strelka-varscan-mutect TNRC6C,missense_variant,p.Gly316Val,ENST00000335749,NM_001142640.1;TNRC6C,missense_variant,p.Gly316Val,ENST00000301624,NM_018996.3;TNRC6C,missense_variant,p.Gly316Val,ENST00000588847,;TNRC6C,missense_variant,p.Gly316Val,ENST00000588061,;TNRC6C,missense_variant,p.Gly526Val,ENST00000636222,;TNRC6C,intron_variant,,ENST00000585438,;TNRC6C,downstream_gene_variant,,ENST00000588549,;TNRC6C,upstream_gene_variant,,ENST00000591851,; T ENST00000335749 Transcript missense_variant 1516/9740 947/5181 316/1726 G/V gGc/gTc 1 1 TNRC6C HGNC HGNC:29318 protein_coding YES CCDS45799.1 ENSP00000336783 Q9HCJ0 UPI0000EE5F80 NM_001142640.1 deleterious(0) 3/21 hmmpanther:PTHR13020,hmmpanther:PTHR13020:SF9 MODERATE 1 SNV 5 1 PASS rs1354988685 . 0 202 7 0 0 0 0 0 -20 0.9999992 1 1 1 0 T 3 4 96 78050009 78050009 G T 1 0 0 0 0 1 0 0 0 16815 1203 42 2 2 TNRC6C 17 78050009 Missense_Mutation SNP G C3N-02380_T 78050009 5207432 30 29027 SMAD4 0 . GRCh38 18 51065576 51065576 + Missense_Mutation SNP T T A C3N-02380_T C3N-02380_N T T c.1109T>A p.Val370Asp p.V370D ENST00000342988 9/12 139 131 8 195 195 0 strelka-varscan-mutect SMAD4,missense_variant,p.Val370Asp,ENST00000342988,NM_005359.5;SMAD4,missense_variant,p.Val370Asp,ENST00000398417,;SMAD4,missense_variant,p.Val274Asp,ENST00000588745,;SMAD4,upstream_gene_variant,,ENST00000593223,;SMAD4,missense_variant,p.Val104Asp,ENST00000611848,;SMAD4,non_coding_transcript_exon_variant,,ENST00000591126,;SMAD4,intron_variant,,ENST00000592186,;SMAD4,upstream_gene_variant,,ENST00000590499,; A ENST00000342988 Transcript missense_variant 1647/8769 1109/1659 370/552 V/D gTc/gAc COSM5082878 1 1 SMAD4 HGNC HGNC:6770 protein_coding YES CCDS11950.1 ENSP00000341551 Q13485 A0A024R274 UPI0000053431 NM_005359.5 deleterious(0) 9/12 Gene3D:2.60.200.10,Pfam_domain:PF03166,PROSITE_profiles:PS51076,hmmpanther:PTHR13703,hmmpanther:PTHR13703:SF39,SMART_domains:SM00524,Superfamily_domains:SSF49879 1 MODERATE 1 SNV 5 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 51065576 51065576 T A 1 0 0 0 0 1 0 0 0 15053 1667 58 4 4 SMAD4 18 51065576 Missense_Mutation SNP T C3N-02380_T 51065576 29307709 31 29028 UNC13A 0 . GRCh38 19 17633116 17633116 + Missense_Mutation SNP G G A novel C3N-02380_T C3N-02380_N G G c.3293C>T p.Ala1098Val p.A1098V ENST00000519716 27/44 127 108 19 125 125 0 strelka-varscan-mutect UNC13A,missense_variant,p.Ala1098Val,ENST00000519716,NM_001080421.2;UNC13A,missense_variant,p.Ala1098Val,ENST00000551649,;UNC13A,missense_variant,p.Ala1098Val,ENST00000552293,;UNC13A,missense_variant,p.Ala1096Val,ENST00000550896,;UNC13A,upstream_gene_variant,,ENST00000601528,; A ENST00000519716 Transcript missense_variant 3293/9838 3293/5112 1098/1703 A/V gCc/gTc 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 deleterious(0) 27/44 Pfam_domain:PF06292,PROSITE_profiles:PS51258,hmmpanther:PTHR10480,SMART_domains:SM01145 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 17633116 17633116 G A 1 0 0 0 0 1 0 0 0 17508 1203 42 3 3 UNC13A 19 17633116 Missense_Mutation SNP G C3N-02380_T 17633116 40984500 32 29029 PSG2 0 . GRCh38 19 43081137 43081137 + Missense_Mutation SNP C C A rs148608529 C3N-02380_T C3N-02380_N C C c.174G>T p.Leu58Phe p.L58F ENST00000406487 2/6 226 207 19 257 257 0 varscan-mutect PSG2,missense_variant,p.Leu58Phe,ENST00000406487,NM_031246.3;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG2,intron_variant,,ENST00000593482,;PSG2,downstream_gene_variant,,ENST00000491995,; A ENST00000406487 Transcript missense_variant 273/1538 174/1008 58/335 L/F ttG/ttT rs148608529 1 -1 PSG2 HGNC HGNC:9519 protein_coding YES CCDS12616.1 ENSP00000385706 P11465 A0A024R0M4 UPI000013CCF5 NM_031246.3 deleterious(0) 2/6 Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs148608529 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 96 43081137 43081137 C A 1 0 0 0 0 1 0 0 0 12806 709 25 2 2 PSG2 19 43081137 Missense_Mutation SNP C C3N-02380_T 25448021 43081137 15536479 33 29030 PHF20 0 . GRCh38 20 35863161 35863161 + Missense_Mutation SNP G G T C3N-02380_T C3N-02380_N G G c.569G>T p.Arg190Leu p.R190L ENST00000374012 6/18 131 118 13 176 176 0 strelka-varscan-mutect PHF20,missense_variant,p.Arg190Leu,ENST00000374012,NM_016436.4;PHF20,missense_variant,p.Arg190Leu,ENST00000339089,;PHF20,missense_variant,p.Arg190Leu,ENST00000374000,;PHF20,missense_variant,p.Arg83Leu,ENST00000449988,;PHF20,non_coding_transcript_exon_variant,,ENST00000481202,;PHF20,non_coding_transcript_exon_variant,,ENST00000461122,;PHF20,non_coding_transcript_exon_variant,,ENST00000486408,;PHF20,non_coding_transcript_exon_variant,,ENST00000480940,;PHF20,non_coding_transcript_exon_variant,,ENST00000496305,;PHF20,intron_variant,,ENST00000495338,; T ENST00000374012 Transcript missense_variant 698/5922 569/3039 190/1012 R/L cGa/cTa COSM4713973 1 1 PHF20 HGNC HGNC:16098 protein_coding YES CCDS13268.1 ENSP00000363124 Q9BVI0 UPI000006E61B NM_016436.4 deleterious(0.01) 6/18 Pfam_domain:PF12618,hmmpanther:PTHR15856,hmmpanther:PTHR15856:SF27 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 35863161 35863161 G T 1 0 0 0 0 1 0 0 0 11917 1058 37 1 1 PHF20 20 35863161 Missense_Mutation SNP G C3N-02380_T 35863161 28581006 34 29031 EYA2 0 . GRCh38 20 47172863 47172863 + Silent SNP T T C novel C3N-02380_T C3N-02380_N T T c.1194T>C p.= p.V398V ENST00000327619 12/16 81 73 8 65 65 0 varscan-mutect EYA2,synonymous_variant,p.=,ENST00000327619,NM_005244.4;EYA2,synonymous_variant,p.=,ENST00000611592,;EYA2,synonymous_variant,p.=,ENST00000357410,NM_172110.3;EYA2,synonymous_variant,p.=,ENST00000497062,;EYA2,synonymous_variant,p.=,ENST00000317304,; C ENST00000327619 Transcript synonymous_variant 1568/2702 1194/1617 398/538 V gtT/gtC 1 1 EYA2 HGNC HGNC:3520 protein_coding YES CCDS13403.1 ENSP00000333640 O00167 UPI000012A3B4 NM_005244.4 12/16 hmmpanther:PTHR10190:SF7,hmmpanther:PTHR10190,Pfam_domain:PF00702,TIGRFAM_domain:TIGR01658 LOW 1 SNV 2 1 PASS . . 0 201 9 0 0 0 0 0 -16.9292 0.999985 1 1 1 0 C 2 2 96 47172863 47172863 T C 1 0 0 0 0 0 0 0 1 5197 1826 63 5 5 EYA2 20 47172863 Silent SNP T C3N-02380_T 11309702 47172863 17271304 35 29032 CYP24A1 0 . GRCh38 20 54171657 54171657 + Missense_Mutation SNP A A T rs748060893 C3N-02380_T C3N-02380_N A A c.463T>A p.Trp155Arg p.W155R ENST00000216862 3/12 715 655 60 552 552 0 strelka-varscan-mutect CYP24A1,missense_variant,p.Trp155Arg,ENST00000216862,NM_000782.4;CYP24A1,missense_variant,p.Trp155Arg,ENST00000395955,NM_001128915.1;CYP24A1,missense_variant,p.Trp13Arg,ENST00000395954,;CYP24A1,downstream_gene_variant,,ENST00000472970,; T ENST00000216862 Transcript missense_variant 857/3262 463/1545 155/514 W/R Tgg/Agg rs748060893 1 -1 CYP24A1 HGNC HGNC:2602 protein_coding YES CCDS33491.1 ENSP00000216862 Q07973 UPI00001281B8 NM_000782.4 deleterious(0) 3/12 hmmpanther:PTHR24291,hmmpanther:PTHR24291:SF5,Gene3D:1.10.630.10,Pfam_domain:PF00067,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS rs748060893 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 54171657 54171657 A T 1 0 0 0 0 1 0 0 0 3957 188 7 4 4 CYP24A1 20 54171657 Missense_Mutation SNP A C3N-02380_T 6998794 54171657 10272510 36 29033 SUSD2 0 . GRCh38 22 24187831 24187831 + Missense_Mutation SNP A A T novel C3N-02380_T C3N-02380_N A A c.2152A>T p.Ser718Cys p.S718C ENST00000358321 12/15 93 84 9 101 101 0 strelka-varscan-mutect SUSD2,missense_variant,p.Ser718Cys,ENST00000358321,NM_019601.3;SUSD2,non_coding_transcript_exon_variant,,ENST00000463101,; T ENST00000358321 Transcript missense_variant 2413/3404 2152/2469 718/822 S/C Agc/Tgc 1 1 SUSD2 HGNC HGNC:30667 protein_coding YES CCDS13824.1 ENSP00000351075 Q9UGT4 A0A140VJW3 UPI000006CC92 NM_019601.3 deleterious(0.03) 12/15 hmmpanther:PTHR13802,hmmpanther:PTHR13802:SF43 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -18.88718 1 1 1 1 0 T 3 4 96 24187831 24187831 A T 1 0 0 0 0 1 0 0 0 15793 304 11 4 4 SUSD2 22 24187831 Missense_Mutation SNP A C3N-02380_T 24187831 26630637 37 29034 NIPSNAP1 0 . GRCh38 22 29569274 29569274 + Missense_Mutation SNP G G C novel C3N-02380_T C3N-02380_N G G c.286C>G p.Pro96Ala p.P96A ENST00000216121 4/10 519 456 63 479 479 0 strelka-varscan-mutect NIPSNAP1,missense_variant,p.Pro96Ala,ENST00000216121,NM_003634.3,NM_001202502.1;NIPSNAP1,missense_variant,p.Pro113Ala,ENST00000415100,;NIPSNAP1,5_prime_UTR_variant,,ENST00000437094,;NIPSNAP1,missense_variant,p.Pro96Ala,ENST00000455496,;NIPSNAP1,downstream_gene_variant,,ENST00000496944,; C ENST00000216121 Transcript missense_variant 541/2237 286/855 96/284 P/A Ccc/Gcc 1 -1 NIPSNAP1 HGNC HGNC:7827 protein_coding YES CCDS13860.1 ENSP00000216121 Q9BPW8 UPI00001303FF NM_003634.3,NM_001202502.1 deleterious(0.05) 4/10 Gene3D:3.30.70.900,hmmpanther:PTHR21017,hmmpanther:PTHR21017:SF11,Superfamily_domains:SSF54909 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 96 29569274 29569274 G C 1 0 0 0 0 1 0 0 0 10464 1203 42 4 4 NIPSNAP1 22 29569274 Missense_Mutation SNP G C3N-02380_T 5381443 29569274 21249194 38 29035 OSBP2 0 . GRCh38 22 30695552 30695552 + Frame_Shift_Del DEL A A - novel C3N-02380_T C3N-02380_N A A c.643delA p.Arg215GlufsTer31 p.R215Efs*31 ENST00000332585 1/14 97 90 7 100 100 0 sindel-varindel-pindel OSBP2,frameshift_variant,p.Arg215GlufsTer31,ENST00000332585,NM_030758.3;OSBP2,frameshift_variant,p.Arg215GlufsTer31,ENST00000446658,NM_001282739.1;OSBP2,intron_variant,,ENST00000403222,;OSBP2,intron_variant,,ENST00000407373,;OSBP2,intron_variant,,ENST00000438716,NM_001282738.1; - ENST00000332585 Transcript frameshift_variant,splice_region_variant 747/4340 643/2751 215/916 R/X Aga/ga 1 1 OSBP2 HGNC HGNC:8504 protein_coding YES CCDS43002.1 ENSP00000332576 Q969R2 UPI0000161E15 NM_030758.3 1/14 Gene3D:2.30.29.30,Pfam_domain:PF00169,PROSITE_profiles:PS50003,hmmpanther:PTHR10972,hmmpanther:PTHR10972:SF51,SMART_domains:SM00233,Superfamily_domains:SSF50729 HIGH 1 deletion 1 1 PASS . . 0 206 4 0 0 0 0 0 -14.55799 1 1 1 1 0 - 7 5 96 30695552 30695552 A - 1 0 1 0 1 0 0 0 0 11340 202 7 0 0 OSBP2 22 30695552 Frame_Shift_Del DEL A C3N-02380_T 1126278 30695552 20122916 39 29036 CYB5R3 0 . GRCh38 22 42630944 42630944 + Missense_Mutation SNP C C T C3N-02380_T C3N-02380_N C C c.370G>A p.Val124Ile p.V124I ENST00000361740 4/9 356 315 41 324 324 0 strelka-varscan-mutect CYB5R3,missense_variant,p.Val124Ile,ENST00000361740,NM_001171660.1;CYB5R3,missense_variant,p.Val68Ile,ENST00000407623,NM_001129819.2,NM_007326.4;CYB5R3,missense_variant,p.Val91Ile,ENST00000352397,NM_000398.6;CYB5R3,missense_variant,p.Val68Ile,ENST00000407332,;CYB5R3,missense_variant,p.Val68Ile,ENST00000402438,NM_001171661.1;CYB5R3,missense_variant,p.Val68Ile,ENST00000438270,;CYB5R3,non_coding_transcript_exon_variant,,ENST00000470741,;CYB5R3,downstream_gene_variant,,ENST00000466276,; T ENST00000361740 Transcript missense_variant 370/2938 370/1005 124/334 V/I Gtc/Atc COSM5015737,COSM5015738 1 -1 CYB5R3 HGNC HGNC:2873 protein_coding YES CCDS54535.1 ENSP00000354468 P00387 UPI00019150F6 NM_001171660.1 tolerated(1) 4/9 Gene3D:2.40.30.10,Pfam_domain:PF00970,PROSITE_profiles:PS51384,hmmpanther:PTHR19370,hmmpanther:PTHR19370:SF121,Superfamily_domains:SSF63380 1,1 MODERATE 1 SNV 2 1,1 1 PASS rs1362518180 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 96 42630944 42630944 C T 1 0 0 0 0 1 0 0 0 3932 536 19 1 1 CYB5R3 22 42630944 Missense_Mutation SNP C C3N-02380_T 11935392 42630944 8187524 40 29037 OR6K2 0 . GRCh38 1 158700206 158700206 + Silent SNP A A G novel C3N-02421_T C3N-02421_N A A c.447T>C p.= p.V149V ENST00000359610 1/1 115 91 24 69 69 0 strelka-varscan-mutect OR6K2,synonymous_variant,p.=,ENST00000359610,NM_001005279.1;OR6K1P,upstream_gene_variant,,ENST00000456766,; G ENST00000359610 Transcript synonymous_variant 447/975 447/975 149/324 V gtT/gtC 1 -1 OR6K2 HGNC HGNC:15029 protein_coding YES CCDS30902.1 ENSP00000352626 Q8NGY2 A0A126GV58 UPI000004B208 NM_001005279.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF68,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 97 158700206 158700206 A G 1 0 0 0 0 0 0 0 1 11271 1 1 5 5 OR6K2 1 158700206 Silent SNP A C3N-02421_T 158700206 90256216 1 29038 OR6K6 0 . GRCh38 1 158755094 158755094 + Silent SNP C C T novel C3N-02421_T C3N-02421_N C C c.279C>T p.= p.V93V ENST00000368144 1/1 270 234 36 172 172 0 strelka-varscan-mutect OR6K6,synonymous_variant,p.=,ENST00000368144,NM_001005184.1; T ENST00000368144 Transcript synonymous_variant 375/1172 279/1032 93/343 V gtC/gtT 1 1 OR6K6 HGNC HGNC:15033 protein_coding YES CCDS30904.1 ENSP00000357126 Q8NGW6 UPI000015F229 NM_001005184.1 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF132,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 97 158755094 158755094 C T 1 0 0 0 0 0 0 0 1 11273 842 30 3 3 OR6K6 1 158755094 Silent SNP C C3N-02421_T 54888 158755094 90201328 2 29039 USH2A 0 . GRCh38 1 216325353 216325353 + Frame_Shift_Del DEL A A - novel C3N-02421_T C3N-02421_N A A c.1095delT p.Asn366IlefsTer4 p.N366Ifs*4 ENST00000307340 6/72 206 157 49 176 176 0 sindel-varindel-pindel USH2A,frameshift_variant,p.Asn366IlefsTer4,ENST00000307340,NM_206933.2;USH2A,frameshift_variant,p.Asn366IlefsTer4,ENST00000366942,NM_007123.5; - ENST00000307340 Transcript frameshift_variant 1482/18883 1095/15609 365/5202 L/X ctT/ct 1 -1 USH2A HGNC HGNC:12601 protein_coding YES CCDS31025.1 ENSP00000305941 O75445 UPI000034E5B6 NM_206933.2 6/72 Pfam_domain:PF00055,PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF274,SMART_domains:SM00136 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 216325353 216325353 A - 1 0 1 0 1 0 0 0 0 17570 349 13 0 0 USH2A 1 216325353 Frame_Shift_Del DEL A C3N-02421_T 57570259 216325353 32631069 3 29040 STAB1 0 . GRCh38 3 52512907 52512907 + Missense_Mutation SNP C C T novel C3N-02421_T C3N-02421_N C C c.3107C>T p.Pro1036Leu p.P1036L ENST00000321725 29/69 132 108 24 153 153 0 strelka-varscan-mutect STAB1,missense_variant,p.Pro1036Leu,ENST00000321725,NM_015136.2;STAB1,upstream_gene_variant,,ENST00000461325,;STAB1,downstream_gene_variant,,ENST00000481607,;STAB1,downstream_gene_variant,,ENST00000484850,; T ENST00000321725 Transcript missense_variant 3183/7928 3107/7713 1036/2570 P/L cCc/cTc 1 1 STAB1 HGNC HGNC:18628 protein_coding YES CCDS33768.1 ENSP00000312946 Q9NY15 UPI0000140C12 NM_015136.2 tolerated(0.31) 29/69 Gene3D:2.30.180.10,Pfam_domain:PF02469,PROSITE_profiles:PS50213,hmmpanther:PTHR24038,hmmpanther:PTHR24038:SF2,SMART_domains:SM00554,Superfamily_domains:SSF82153 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 52512907 52512907 C T 1 0 0 0 0 1 0 0 0 15615 623 22 3 3 STAB1 3 52512907 Missense_Mutation SNP C C3N-02421_T 52512907 145782652 4 29041 DNAH12 0 . GRCh38 3 57433418 57433418 + Silent SNP A A T novel C3N-02421_T C3N-02421_N A A c.4929T>A p.= p.I1643I ENST00000495027 32/74 204 171 33 183 183 0 strelka-varscan-mutect DNAH12,synonymous_variant,p.=,ENST00000495027,NM_001291661.1;DNAH12,synonymous_variant,p.=,ENST00000351747,; T ENST00000495027 Transcript synonymous_variant 5110/12146 4929/11883 1643/3960 I atT/atA 1 -1 DNAH12 HGNC HGNC:2943 protein_coding ENSP00000418137 E9PG32 UPI0004620994 NM_001291661.1 32/74 Gene3D:3.40.50.300,Pfam_domain:PF07728,hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF255,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 97 57433418 57433418 A T 1 0 0 0 0 0 0 0 1 4414 126 5 4 4 DNAH12 3 57433418 Silent SNP A C3N-02421_T 4920511 57433418 140862141 5 29042 FOXL2 0 . GRCh38 3 138946444 138946444 + Missense_Mutation SNP C C G novel C3N-02421_T C3N-02421_N C C c.279G>C p.Lys93Asn p.K93N ENST00000330315 1/1 329 261 68 338 338 0 strelka-varscan FOXL2,missense_variant,p.Lys93Asn,ENST00000330315,NM_023067.3;FOXL2NB,upstream_gene_variant,,ENST00000383165,NM_001040061.2;LINC01391,upstream_gene_variant,,ENST00000495287,;LINC01391,upstream_gene_variant,,ENST00000483650,;LINC01391,upstream_gene_variant,,ENST00000477059,;FOXL2NB,upstream_gene_variant,,ENST00000498709,;FOXL2NB,upstream_gene_variant,,ENST00000470680,; G ENST00000330315 Transcript missense_variant 697/2917 279/1131 93/376 K/N aaG/aaC 1 -1 FOXL2 HGNC HGNC:1092 protein_coding YES CCDS3105.1 ENSP00000333188 P58012 Q53ZD3 UPI0000050DB3 NM_023067.3 deleterious(0.01) 1/1 PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF177,hmmpanther:PTHR11829,Gene3D:1.10.10.10,Pfam_domain:PF00250,SMART_domains:SM00339,Superfamily_domains:SSF46785 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 97 138946444 138946444 C G 1 0 0 0 0 1 0 0 0 5880 912 32 4 4 FOXL2 3 138946444 Missense_Mutation SNP C C3N-02421_T 81513026 138946444 59349115 6 29043 ZNF330 0 . GRCh38 4 141226805 141226805 + Missense_Mutation SNP A A G novel C3N-02421_T C3N-02421_N A A c.250A>G p.Ile84Val p.I84V ENST00000262990 5/10 231 190 41 215 215 0 strelka-varscan-mutect ZNF330,missense_variant,p.Ile84Val,ENST00000262990,NM_014487.5,NM_001292002.1;ZNF330,missense_variant,p.Ile84Val,ENST00000512809,;ZNF330,missense_variant,p.Ile84Val,ENST00000503649,;ZNF330,missense_variant,p.Ile84Val,ENST00000512738,;ZNF330,missense_variant,p.His60Arg,ENST00000506302,;ZNF330,3_prime_UTR_variant,,ENST00000507532,;ZNF330,downstream_gene_variant,,ENST00000514826,;ZNF330,downstream_gene_variant,,ENST00000515453,; G ENST00000262990 Transcript missense_variant 478/1899 250/963 84/320 I/V Ata/Gta 1 1 ZNF330 HGNC HGNC:15462 protein_coding YES CCDS3754.1 ENSP00000262990 Q9Y3S2 UPI000006E4AB NM_014487.5,NM_001292002.1 tolerated(0.96) 5/10 Pfam_domain:PF06524,hmmpanther:PTHR13214,hmmpanther:PTHR13214:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 97 141226805 141226805 A G 1 0 0 0 0 1 0 0 0 18420 217 8 5 5 ZNF330 4 141226805 Missense_Mutation SNP A C3N-02421_T 141226805 48987750 7 29044 GABRG2 0 . GRCh38 5 162149174 162149174 + Missense_Mutation SNP C C T novel C3N-02421_T C3N-02421_N C C c.1109C>T p.Ser370Phe p.S370F ENST00000414552 9/11 606 438 168 402 402 0 strelka-varscan GABRG2,missense_variant,p.Ser330Phe,ENST00000356592,NM_198904.2;GABRG2,missense_variant,p.Ser370Phe,ENST00000414552,NM_198903.2;GABRG2,missense_variant,p.Ser330Phe,ENST00000361925,NM_000816.3;GABRG2,downstream_gene_variant,,ENST00000522053,;GABRG2,3_prime_UTR_variant,,ENST00000522990,;GABRG2,3_prime_UTR_variant,,ENST00000523372,; T ENST00000414552 Transcript missense_variant 1334/3927 1109/1548 370/515 S/F tCc/tTc 1 1 GABRG2 HGNC HGNC:4087 protein_coding YES CCDS47333.1 ENSP00000410732 P18507 UPI00017503BD NM_198903.2 deleterious(0) 9/11 hmmpanther:PTHR18945:SF498,hmmpanther:PTHR18945,Gene3D:1.20.58.390,Pfam_domain:PF02932,Superfamily_domains:SSF90112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 162149174 162149174 C T 1 0 0 0 0 1 0 0 0 6043 855 30 3 3 GABRG2 5 162149174 Missense_Mutation SNP C C3N-02421_T 162149174 19389085 8 29045 HIST1H2AG 0 . GRCh38 6 27133109 27133121 + Frame_Shift_Del DEL CTAAGGCCAAGAC CTAAGGCCAAGAC - novel C3N-02421_T C3N-02421_N CTAAGGCCAAGAC CTAAGGCCAAGAC c.38_50delCTAAGGCCAAGAC p.Ala13ValfsTer43 p.A13Vfs*43 ENST00000359193 1/1 91 76 15 136 136 0 sindel-varindel-pindel HIST1H2AG,frameshift_variant,p.Ala13ValfsTer43,ENST00000359193,NM_021064.4;HIST1H2BJ,upstream_gene_variant,,ENST00000607124,;HIST1H2BJ,upstream_gene_variant,,ENST00000606923,;HIST1H2BJ,upstream_gene_variant,,ENST00000339812,NM_021058.3; - ENST00000359193 Transcript frameshift_variant 68-80/2250 38-50/393 13-17/130 AKAKT/X gCTAAGGCCAAGACt/gt 1 1 HIST1H2AG HGNC HGNC:4737 protein_coding YES CCDS4619.1 ENSP00000352119 P0C0S8 A4FTV9 UPI0000000E01 NM_021064.4 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23430,Gene3D:1.10.20.10,Pfam_domain:PF00125,SMART_domains:SM00414,Superfamily_domains:SSF47113,Prints_domain:PR00620 HIGH deletion 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 - 7 5 97 27133109 27133109 CTAAGGCCAAGAC - 1 0 1 0 1 0 0 0 0 7021 797 28 0 0 HIST1H2AG 6 27133109 Frame_Shift_Del DEL CTAAGGCCAAGAC C3N-02421_T 27133109 143672870 9 29046 ZBED9 0 . GRCh38 6 28575227 28575227 + Missense_Mutation SNP G G A novel C3N-02421_T C3N-02421_N G G c.1478C>T p.Ser493Leu p.S493L ENST00000452236 3/4 296 226 70 276 276 0 strelka-varscan ZBED9,missense_variant,p.Ser493Leu,ENST00000452236,NM_052923.1;ZBED9,downstream_gene_variant,,ENST00000530247,; A ENST00000452236 Transcript missense_variant 2096/4877 1478/3978 493/1325 S/L tCa/tTa 1 -1 ZBED9 HGNC HGNC:13851 protein_coding YES CCDS34355.1 ENSP00000395259 Q6R2W3 UPI00001618B7 NM_052923.1 tolerated_low_confidence(0.24) 3/4 PROSITE_profiles:PS50994,Gene3D:3.30.420.10,Superfamily_domains:SSF53098 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 97 28575227 28575227 G A 1 0 0 0 0 1 0 0 0 18086 1294 45 3 3 ZBED9 6 28575227 Missense_Mutation SNP G C3N-02421_T 1442118 28575227 142230752 10 29047 TNXB 0 . GRCh38 6 32068655 32068655 + Frame_Shift_Del DEL G G - novel C3N-02421_T C3N-02421_N G G c.5955delC p.Ile1986SerfsTer8 p.I1986Sfs*8 ENST00000375244 17/44 91 75 16 102 102 0 sindel-varindel-pindel TNXB,frameshift_variant,p.Ile1986SerfsTer8,ENST00000375244,NM_019105.6;TNXB,3_prime_UTR_variant,,ENST00000613214,; - ENST00000375244 Transcript frameshift_variant 6157/13132 5955/12735 1985/4244 P/X ccC/cc 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 17/44 Low_complexity_(Seg):seg,Gene3D:2.60.40.10,SMART_domains:SM00060 HIGH 1 deletion 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 32068655 32068655 G - 1 0 1 0 1 0 0 0 0 16820 1335 47 0 0 TNXB 6 32068655 Frame_Shift_Del DEL G C3N-02421_T 3493428 32068655 138737324 11 29048 ADGRF5 0 . GRCh38 6 46859312 46859313 + Frame_Shift_Ins INS - - CTGGGTGG novel C3N-02421_T C3N-02421_N - - c.2583_2590dupCCACCCAG p.Glu864AlafsTer28 p.E864Afs*28 ENST00000283296 17/21 112 95 17 100 100 0 sindel-varindel ADGRF5,frameshift_variant,p.Glu864AlafsTer28,ENST00000283296,NM_001098518.1;ADGRF5,frameshift_variant,p.Glu864AlafsTer28,ENST00000265417,NM_015234.4;ADGRF5,downstream_gene_variant,,ENST00000498632,; CTGGGTGG ENST00000283296 Transcript frameshift_variant 2879-2880/5810 2590-2591/4041 864/1346 E/ATQX gaa/gCCACCCAGaa 1 -1 ADGRF5 HGNC HGNC:19030 protein_coding YES CCDS4919.1 ENSP00000283296 Q8IZF2 UPI000007075A NM_001098518.1 17/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF272 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 CTGGGTGG 7 5 97 46859312 46859312 - CTGGGTGG 1 0 1 1 0 0 0 0 0 367 1783 62 0 0 ADGRF5 6 46859312 Frame_Shift_Ins INS - C3N-02421_T 14790657 46859312 123946667 12 29049 PRDM1 0 . GRCh38 6 106104894 106104895 + Frame_Shift_Del DEL AG AG - C3N-02421_T C3N-02421_N AG AG c.740_741delAG p.Glu247ValfsTer23 p.E247Vfs*23 ENST00000369096 5/7 164 134 30 151 151 0 sindel-varindel-pindel PRDM1,frameshift_variant,p.Glu247ValfsTer23,ENST00000369096,NM_001198.3;PRDM1,frameshift_variant,p.Glu113ValfsTer23,ENST00000369089,NM_182907.2;PRDM1,frameshift_variant,p.Glu211ValfsTer23,ENST00000369091,;PRDM1,frameshift_variant,p.Glu126ValfsTer23,ENST00000450060,;ATG5,intron_variant,,ENST00000636437,;RP1-134E15.3,downstream_gene_variant,,ENST00000602426,;ATG5,intron_variant,,ENST00000636335,; - ENST00000369096 Transcript frameshift_variant 968-969/5164 734-735/2478 245/825 K/X aAG/a COSM3154290,COSM3154291 1 1 PRDM1 HGNC HGNC:9346 protein_coding YES CCDS5054.2 ENSP00000358092 O75626 UPI0000D49069 NM_001198.3 5/7 PIRSF_domain:PIRSF013212 1,1 HIGH 1 deletion 1 6 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 106104894 106104894 AG - 1 0 1 0 1 0 0 0 0 12581 72 3 0 0 PRDM1 6 106104894 Frame_Shift_Del DEL AG C3N-02421_T 59245582 106104894 64701085 13 29050 HIVEP2 0 . GRCh38 6 142753652 142753652 + Missense_Mutation SNP C C T novel C3N-02421_T C3N-02421_N C C c.6796G>A p.Ala2266Thr p.A2266T ENST00000367603 10/10 189 162 27 179 178 1 strelka-varscan-mutect HIVEP2,missense_variant,p.Ala2266Thr,ENST00000367603,NM_006734.3;HIVEP2,missense_variant,p.Ala2266Thr,ENST00000367604,;HIVEP2,missense_variant,p.Ala2266Thr,ENST00000012134,;RP1-67K17.3,non_coding_transcript_exon_variant,,ENST00000437067,; T ENST00000367603 Transcript missense_variant 7539/9723 6796/7341 2266/2446 A/T Gcg/Acg 1 -1 HIVEP2 HGNC HGNC:4921 protein_coding YES CCDS43510.1 ENSP00000356575 P31629 UPI00004708DD NM_006734.3 tolerated(0.34) 10/10 hmmpanther:PTHR23233:SF53,hmmpanther:PTHR23233 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 142753652 142753652 C T 1 0 0 0 0 1 0 0 0 7076 768 27 1 1 HIVEP2 6 142753652 Missense_Mutation SNP C C3N-02421_T 36648758 142753652 28052327 14 29051 TNRC18 0 . GRCh38 7 5351939 5351939 + Missense_Mutation SNP C C G novel C3N-02421_T C3N-02421_N C C c.5350G>C p.Ala1784Pro p.A1784P ENST00000430969 17/30 319 292 27 241 241 0 strelka-varscan-mutect TNRC18,missense_variant,p.Ala1784Pro,ENST00000399537,;TNRC18,missense_variant,p.Ala1784Pro,ENST00000430969,NM_001080495.2;TNRC18,downstream_gene_variant,,ENST00000440081,; G ENST00000430969 Transcript missense_variant 5699/10562 5350/8907 1784/2968 A/P Gcc/Ccc 1 -1 TNRC18 HGNC HGNC:11962 protein_coding YES CCDS47534.1 ENSP00000395538 O15417 UPI00016632FD NM_001080495.2 deleterious(0.01) 17/30 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 2 0 0 0 -8.233747 0.9909266 1 1 1 0 G 3 3 97 5351939 5351939 C G 1 0 0 0 0 1 0 0 0 16812 739 26 4 4 TNRC18 7 5351939 Missense_Mutation SNP C C3N-02421_T 5351939 153994034 15 29052 EGFR 0 . GRCh38 7 55174774 55174791 + In_Frame_Del DEL AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT - rs121913422 C3N-02421_T C3N-02421_N AATTAAGAGAAGCAACAT AATTAAGAGAAGCAACAT c.2237_2254delAATTAAGAGAAGCAACAT p.Glu746_Ser752delinsAla p.E746_S752delinsA ENST00000275493 19/28 474 377 97 430 430 0 sindel-varindel EGFR,inframe_deletion,p.Glu746_Ser752delinsAla,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ser707delinsAla,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2414-2431/9821 2237-2254/3633 746-752/1210 ELREATS/A gAATTAAGAGAAGCAACATct/gct rs121913422,COSM12367 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 55174774 55174774 AATTAAGAGAAGCAACAT - 1 0 1 0 1 0 0 0 0 4803 246 9 0 0 EGFR 7 55174774 In_Frame_Del DEL AATTAAGAGAAGCAACAT C3N-02421_T 49822835 55174774 104171199 16 29053 SNTG1 0 . GRCh38 8 50656970 50656970 + Frame_Shift_Del DEL C C - rs747482110 C3N-02421_T C3N-02421_N C C c.914delC p.Pro305ArgfsTer6 p.P305Rfs*6 ENST00000522124 14/19 76 63 13 99 99 0 sindel-varindel-pindel SNTG1,frameshift_variant,p.Pro305ArgfsTer6,ENST00000522124,NM_018967.3;SNTG1,frameshift_variant,p.Pro305ArgfsTer6,ENST00000518864,NM_001287813.1;SNTG1,frameshift_variant,p.Pro305ArgfsTer6,ENST00000517473,NM_001287814.1;SNTG1,frameshift_variant,p.Pro305ArgfsTer6,ENST00000520825,;SNTG1,frameshift_variant,p.Pro79ArgfsTer6,ENST00000524004,; - ENST00000522124 Transcript frameshift_variant 1572/3504 911/1554 304/517 S/X tCc/tc rs747482110,COSM351799,COSM351800 1 1 SNTG1 HGNC HGNC:13740 protein_coding YES CCDS6147.1 ENSP00000429842 Q9NSN8 A0A024R7Y0 UPI000004A0DD NM_018967.3 14/19 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR10554,hmmpanther:PTHR10554:SF2,SMART_domains:SM00233,Superfamily_domains:SSF50729 0,1,1 HIGH 1 deletion 1 3 0,1,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 50656970 50656970 C - 1 0 1 0 1 0 0 0 0 15194 855 30 0 0 SNTG1 8 50656970 Frame_Shift_Del DEL C C3N-02421_T 50656970 94481666 17 29054 TMEM67 0 . GRCh38 8 93754918 93754918 + Missense_Mutation SNP G G A novel C3N-02421_T C3N-02421_N G G c.4G>A p.Ala2Thr p.A2T ENST00000453321 1/28 166 121 45 100 100 0 strelka-varscan-mutect TMEM67,missense_variant,p.Ala2Thr,ENST00000453321,NM_153704.5;TMEM67,missense_variant,p.Ala2Thr,ENST00000453906,;TMEM67,intron_variant,,ENST00000409623,NM_001142301.1;TMEM67,intron_variant,,ENST00000452276,;TMEM67,intron_variant,,ENST00000518319,;TMEM67,intron_variant,,ENST00000498673,;TMEM67,upstream_gene_variant,,ENST00000521517,;TMEM67,missense_variant,p.Ala2Thr,ENST00000455946,;TMEM67,missense_variant,p.Ala2Thr,ENST00000521222,;TMEM67,non_coding_transcript_exon_variant,,ENST00000474944,;TMEM67,non_coding_transcript_exon_variant,,ENST00000481620,;TMEM67,non_coding_transcript_exon_variant,,ENST00000475305,;TMEM67,upstream_gene_variant,,ENST00000323130,;TMEM67,upstream_gene_variant,,ENST00000521065,; A ENST00000453321 Transcript missense_variant 62/4651 4/2988 2/995 A/T Gcg/Acg 1 1 TMEM67 HGNC HGNC:28396 protein_coding YES CCDS6258.2 ENSP00000389998 Q5HYA8 UPI0000D624E9 NM_153704.5 tolerated_low_confidence(0.31) 1/28 Cleavage_site_(Signalp):SignalP-TM MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 97 93754918 93754918 G A 1 0 0 0 0 1 0 0 0 16671 1203 42 3 3 TMEM67 8 93754918 Missense_Mutation SNP G C3N-02421_T 43097948 93754918 51383718 18 29055 DENND1A 0 . GRCh38 9 123381681 123381681 + Silent SNP G G A novel C3N-02421_T C3N-02421_N G G c.2781C>T p.= p.A927A ENST00000373624 22/22 82 60 22 53 53 0 strelka-varscan-mutect DENND1A,synonymous_variant,p.=,ENST00000373624,NM_020946.1;CRB2,downstream_gene_variant,,ENST00000373631,NM_173689.6;DENND1A,non_coding_transcript_exon_variant,,ENST00000473039,;CRB2,downstream_gene_variant,,ENST00000460253,; A ENST00000373624 Transcript synonymous_variant 2983/5010 2781/3030 927/1009 A gcC/gcT 1 -1 DENND1A HGNC HGNC:29324 protein_coding YES CCDS35133.1 ENSP00000362727 Q8TEH3 UPI00004589D2 NM_020946.1 22/22 LOW SNV 5 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 97 123381681 123381681 G A 1 0 0 0 0 0 0 0 1 4230 1219 43 3 3 DENND1A 9 123381681 Silent SNP G C3N-02421_T 123381681 15013036 19 29056 LRRC8A 0 . GRCh38 9 128907281 128907281 + Silent SNP C C T rs75533615 C3N-02421_T C3N-02421_N C C c.117C>T p.= p.A39A ENST00000259324 3/4 148 131 17 132 132 0 strelka-varscan-mutect LRRC8A,synonymous_variant,p.=,ENST00000259324,NM_001127244.1;LRRC8A,synonymous_variant,p.=,ENST00000372600,NM_019594.3;LRRC8A,synonymous_variant,p.=,ENST00000372599,NM_001127245.1; T ENST00000259324 Transcript synonymous_variant 640/4619 117/2433 39/810 A gcC/gcT rs75533615 1 1 LRRC8A HGNC HGNC:19027 protein_coding YES CCDS35155.1 ENSP00000259324 Q8IWT6 A0A024R892 UPI000004EF9E NM_001127244.1 3/4 Transmembrane_helices:TMhelix,Pfam_domain:PF12534 LOW 1 SNV 2 1 PASS rs75533615 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 97 128907281 128907281 C T 1 0 0 0 0 0 0 0 1 8925 639 23 1 1 LRRC8A 9 128907281 Silent SNP C C3N-02421_T 5525600 128907281 9487436 20 29057 SETX 0 . GRCh38 9 132326392 132326392 + Missense_Mutation SNP T T C novel C3N-02421_T C3N-02421_N T T c.5206A>G p.Arg1736Gly p.R1736G ENST00000224140 10/26 289 240 49 245 245 0 strelka-varscan-mutect SETX,missense_variant,p.Arg1736Gly,ENST00000224140,NM_015046.5; C ENST00000224140 Transcript missense_variant 5389/11100 5206/8034 1736/2677 R/G Aga/Gga 1 -1 SETX HGNC HGNC:445 protein_coding YES CCDS6947.1 ENSP00000224140 Q7Z333 UPI0000210D28 NM_015046.5 deleterious(0.01) 10/26 hmmpanther:PTHR10887,hmmpanther:PTHR10887:SF377 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 97 132326392 132326392 T C 1 0 0 0 0 1 0 0 0 14420 1588 55 5 5 SETX 9 132326392 Missense_Mutation SNP T C3N-02421_T 3419111 132326392 6068325 21 29058 PTPN6 0 . GRCh38 12 6955725 6955725 + Frame_Shift_Del DEL G G - novel C3N-02421_T C3N-02421_N G G c.815delG p.Gly272AlafsTer16 p.G272Afs*16 ENST00000456013 7/16 252 201 51 327 327 0 sindel-varindel-pindel PTPN6,frameshift_variant,p.Gly272AlafsTer16,ENST00000456013,NM_080549.3;PTPN6,frameshift_variant,p.Gly272AlafsTer16,ENST00000318974,NM_002831.5;PTPN6,frameshift_variant,p.Gly274AlafsTer16,ENST00000399448,NM_080548.4;PTPN6,downstream_gene_variant,,ENST00000543115,;PTPN6,downstream_gene_variant,,ENST00000541698,;PTPN6,downstream_gene_variant,,ENST00000538715,;PTPN6,downstream_gene_variant,,ENST00000542462,;PTPN6,upstream_gene_variant,,ENST00000539029,;PTPN6,upstream_gene_variant,,ENST00000537533,;PTPN6,downstream_gene_variant,,ENST00000542277,;PTPN6,downstream_gene_variant,,ENST00000540740,;PTPN6,downstream_gene_variant,,ENST00000543120,;PTPN6,downstream_gene_variant,,ENST00000534900,;PTPN6,non_coding_transcript_exon_variant,,ENST00000416215,;PTPN6,downstream_gene_variant,,ENST00000543744,;PTPN6,downstream_gene_variant,,ENST00000545153,;PTPN6,downstream_gene_variant,,ENST00000539365,;PTPN6,upstream_gene_variant,,ENST00000542761,;PTPN6,downstream_gene_variant,,ENST00000538318,;PTPN6,downstream_gene_variant,,ENST00000542848,;PTPN6,downstream_gene_variant,,ENST00000536013,;PTPN6,downstream_gene_variant,,ENST00000535462,;PTPN6,downstream_gene_variant,,ENST00000536521,; - ENST00000456013 Transcript frameshift_variant 1055/2389 813/1875 271/624 K/X aaG/aa 1 1 PTPN6 HGNC HGNC:9658 protein_coding YES CCDS44821.1 ENSP00000391592 P29350 UPI000014049A NM_080549.3 7/16 Gene3D:3.90.190.10,Pfam_domain:PF00102,PIRSF_domain:PIRSF000929,PROSITE_profiles:PS50055,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF65,SMART_domains:SM00194,Superfamily_domains:SSF52799 HIGH 1 deletion 1 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 97 6955725 6955725 G - 1 0 1 0 1 0 0 0 0 12946 991 35 0 0 PTPN6 12 6955725 Frame_Shift_Del DEL G C3N-02421_T 6955725 126319584 22 29059 FSCB 0 . GRCh38 14 44506822 44506822 + Nonsense_Mutation SNP G G A C3N-02421_T C3N-02421_N G G c.166C>T p.Gln56Ter p.Q56* ENST00000340446 1/1 100 90 10 93 93 0 strelka-varscan-mutect FSCB,stop_gained,p.Gln56Ter,ENST00000340446,NM_032135.3;RP11-163M18.1,upstream_gene_variant,,ENST00000557465,;RP11-163M18.1,upstream_gene_variant,,ENST00000556228,;RP11-163M18.1,upstream_gene_variant,,ENST00000555433,; A ENST00000340446 Transcript stop_gained 458/2938 166/2478 56/825 Q/* Cag/Tag COSM4990685 1 -1 FSCB HGNC HGNC:20494 protein_coding YES CCDS9679.1 ENSP00000344579 Q5H9T9 UPI00001FD466 NM_032135.3 1/1 hmmpanther:PTHR36135 1 HIGH SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 97 44506822 44506822 G A 1 0 0 0 0 0 1 0 0 5939 1299 45 3 3 FSCB 14 44506822 Nonsense_Mutation SNP G C3N-02421_T 44506822 62536896 23 29060 BRF1 0 . GRCh38 14 105217612 105217612 + Silent SNP C C T novel C3N-02421_T C3N-02421_N C C c.1704G>A p.= p.R568R ENST00000547530 15/18 245 192 53 219 219 0 strelka-varscan-mutect BRF1,synonymous_variant,p.=,ENST00000392557,NM_145685.2;BRF1,synonymous_variant,p.=,ENST00000547530,NM_001519.3;BRF1,synonymous_variant,p.=,ENST00000379937,NM_001242788.1;BRF1,synonymous_variant,p.=,ENST00000446501,NM_001242789.1;BRF1,synonymous_variant,p.=,ENST00000440513,NM_001242786.1;BRF1,synonymous_variant,p.=,ENST00000327359,NM_001242787.1;BRF1,intron_variant,,ENST00000619151,;BRF1,intron_variant,,ENST00000379932,;BRF1,intron_variant,,ENST00000551787,;BRF1,downstream_gene_variant,,ENST00000549655,;BRF1,downstream_gene_variant,,ENST00000552127,;BRF1,non_coding_transcript_exon_variant,,ENST00000549044,;BRF1,non_coding_transcript_exon_variant,,ENST00000547374,;BRF1,non_coding_transcript_exon_variant,,ENST00000635152,;BRF1,downstream_gene_variant,,ENST00000547562,;BRF1,upstream_gene_variant,,ENST00000546997,;BRF1,downstream_gene_variant,,ENST00000547052,; T ENST00000547530 Transcript synonymous_variant 1763/3358 1704/2034 568/677 R agG/agA 1 -1 BRF1 HGNC HGNC:11551 protein_coding YES CCDS10001.1 ENSP00000448387 Q92994 F8VS36 UPI0000136C55 NM_001519.3 15/18 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 97 105217612 105217612 C T 1 0 0 0 0 0 0 0 1 1680 854 30 3 3 BRF1 14 105217612 Silent SNP C C3N-02421_T 60710790 105217612 1826106 24 29061 ATP10A 0 . GRCh38 15 25694921 25694921 + Missense_Mutation SNP T T G rs139727745 C3N-02421_T C3N-02421_N T T c.2986A>C p.Lys996Gln p.K996Q ENST00000356865 14/21 222 188 34 284 283 1 strelka-varscan-mutect ATP10A,missense_variant,p.Lys996Gln,ENST00000356865,NM_024490.3;ATP10A,upstream_gene_variant,,ENST00000555756,;ATP10A,3_prime_UTR_variant,,ENST00000555815,; G ENST00000356865 Transcript missense_variant 3098/6680 2986/4500 996/1499 K/Q Aag/Cag rs139727745 1 -1 ATP10A HGNC HGNC:13542 protein_coding YES CCDS32178.1 ENSP00000349325 O60312 UPI0000124FAB NM_024490.3 tolerated(0.47) 14/21 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF81,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01652 MODERATE 1 SNV 1 1 PASS rs139727745 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 97 25694921 25694921 T G 1 0 0 0 0 1 0 0 0 1268 1821 63 5 5 ATP10A 15 25694921 Missense_Mutation SNP T C3N-02421_T 25694921 76296268 25 29062 AMFR 0 . GRCh38 16 56408097 56408097 + Missense_Mutation SNP G G A novel C3N-02421_T C3N-02421_N G G c.533C>T p.Thr178Met p.T178M ENST00000290649 4/14 185 156 29 135 135 0 strelka-varscan-mutect AMFR,missense_variant,p.Thr178Met,ENST00000290649,NM_001144.5;AMFR,missense_variant,p.Thr83Met,ENST00000565445,;AMFR,missense_variant,p.Thr83Met,ENST00000563664,;AMFR,upstream_gene_variant,,ENST00000492830,;AMFR,upstream_gene_variant,,ENST00000567738,;RP11-413H22.2,upstream_gene_variant,,ENST00000563090,;AMFR,non_coding_transcript_exon_variant,,ENST00000568657,; A ENST00000290649 Transcript missense_variant 744/3600 533/1932 178/643 T/M aCg/aTg 1 -1 AMFR HGNC HGNC:463 protein_coding YES CCDS10758.1 ENSP00000290649 Q9UKV5 UPI000013EDCA NM_001144.5 deleterious(0) 4/14 hmmpanther:PTHR22763,hmmpanther:PTHR22763:SF51 MODERATE 1 SNV 1 1 PASS rs1316980971 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 97 56408097 56408097 G A 1 0 0 0 0 1 0 0 0 670 1145 40 1 1 AMFR 16 56408097 Missense_Mutation SNP G C3N-02421_T 56408097 33930248 26 29063 C18orf8 0 . GRCh38 18 23518898 23518898 + Missense_Mutation SNP A A G novel C3N-02421_T C3N-02421_N A A c.662A>G p.Gln221Arg p.Q221R ENST00000269221 8/20 171 134 37 173 173 0 strelka-varscan-mutect C18orf8,missense_variant,p.Gln221Arg,ENST00000269221,NM_013326.4;C18orf8,missense_variant,p.Gln173Arg,ENST00000590868,NM_001318709.1;C18orf8,missense_variant,p.Gln173Arg,ENST00000615148,NM_001276342.1;NPC1,intron_variant,,ENST00000591107,;NPC1,downstream_gene_variant,,ENST00000590723,;C18orf8,missense_variant,p.Gln221Arg,ENST00000590870,;C18orf8,3_prime_UTR_variant,,ENST00000589215,NM_001318708.1;C18orf8,3_prime_UTR_variant,,ENST00000589860,;C18orf8,downstream_gene_variant,,ENST00000587690,; G ENST00000269221 Transcript missense_variant 772/2162 662/1974 221/657 Q/R cAg/cGg 1 1 C18orf8 HGNC HGNC:24326 protein_coding YES CCDS32803.1 ENSP00000269221 Q96DM3 UPI000013D80D NM_013326.4 tolerated(0.29) 8/20 hmmpanther:PTHR12897,Superfamily_domains:SSF50978 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 97 23518898 23518898 A G 1 0 0 0 0 1 0 0 0 1902 188 7 5 5 C18orf8 18 23518898 Missense_Mutation SNP A C3N-02421_T 23518898 56854387 27 29064 ZNF653 0 . GRCh38 19 11487133 11487133 + Silent SNP C C T novel C3N-02421_T C3N-02421_N C C c.1197G>A p.= p.K399K ENST00000293771 5/9 113 107 6 118 118 0 varscan-mutect ZNF653,synonymous_variant,p.=,ENST00000293771,NM_138783.3;ZNF653,synonymous_variant,p.=,ENST00000592756,;ZNF653,upstream_gene_variant,,ENST00000590296,;ZNF653,upstream_gene_variant,,ENST00000589051,;ZNF653,non_coding_transcript_exon_variant,,ENST00000590548,;CTC-398G3.6,intron_variant,,ENST00000585656,; T ENST00000293771 Transcript synonymous_variant 1334/2240 1197/1848 399/615 K aaG/aaA 1 -1 ZNF653 HGNC HGNC:25196 protein_coding YES CCDS12261.1 ENSP00000293771 Q96CK0 UPI000006FAFC NM_138783.3 5/9 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs1204133928 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 97 11487133 11487133 C T 1 0 0 0 0 0 0 0 1 18639 912 32 3 3 ZNF653 19 11487133 Silent SNP C C3N-02421_T 11487133 47130483 28 29065 NPHS1 0 . GRCh38 19 35845400 35845400 + Missense_Mutation SNP G G T novel C3N-02421_T C3N-02421_N G G c.1898C>A p.Thr633Asn p.T633N ENST00000378910 14/29 350 282 68 337 337 0 strelka-varscan-mutect NPHS1,missense_variant,p.Thr633Asn,ENST00000378910,NM_004646.3;NPHS1,missense_variant,p.Thr633Asn,ENST00000353632,;NPHS1,splice_region_variant,,ENST00000585400,;NPHS1,downstream_gene_variant,,ENST00000592132,; T ENST00000378910 Transcript missense_variant 1898/4276 1898/3726 633/1241 T/N aCc/aAc 1 -1 NPHS1 HGNC HGNC:7908 protein_coding YES CCDS32996.1 ENSP00000368190 O60500 UPI000004EF61 NM_004646.3 tolerated(0.11) 14/29 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR11640,hmmpanther:PTHR11640:SF31,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 35845400 35845400 G T 1 0 0 0 0 1 0 0 0 10630 1261 44 2 2 NPHS1 19 35845400 Missense_Mutation SNP G C3N-02421_T 24358267 35845400 22772216 29 29066 CEACAM21 0 . GRCh38 19 41579385 41579385 + Missense_Mutation SNP A A T novel C3N-02421_T C3N-02421_N A A c.457A>T p.Ser153Cys p.S153C ENST00000401445 3/7 249 234 15 231 231 0 strelka-varscan-mutect CEACAM21,missense_variant,p.Ser25Cys,ENST00000407170,NM_001288773.2,NM_001290113.1;CEACAM21,missense_variant,p.Ser153Cys,ENST00000187608,NM_033543.5;CEACAM21,missense_variant,p.Ser153Cys,ENST00000401445,NM_001098506.3;CEACAM21,upstream_gene_variant,,ENST00000632983,;CEACAM21,non_coding_transcript_exon_variant,,ENST00000482870,;CEACAM21,synonymous_variant,p.=,ENST00000457737,; T ENST00000401445 Transcript missense_variant 483/1008 457/882 153/293 S/C Agc/Tgc 1 1 CEACAM21 HGNC HGNC:28834 protein_coding YES CCDS46086.1 ENSP00000385739 Q3KPI0 UPI00005C40AA NM_001098506.3 deleterious(0) 3/7 PROSITE_profiles:PS50835,hmmpanther:PTHR12080,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 41579385 41579385 A T 1 0 0 0 0 1 0 0 0 2898 188 7 4 4 CEACAM21 19 41579385 Missense_Mutation SNP A C3N-02421_T 5733985 41579385 17038231 30 29067 CEACAM8 0 . GRCh38 19 42588883 42588883 + Missense_Mutation SNP G G A novel C3N-02421_T C3N-02421_N G G c.859C>T p.Pro287Ser p.P287S ENST00000244336 4/6 246 208 38 250 250 0 strelka-varscan-mutect CEACAM8,missense_variant,p.Pro287Ser,ENST00000244336,NM_001816.3;CEACAM8,intron_variant,,ENST00000599005,;LIPE-AS1,intron_variant,,ENST00000594688,;LIPE-AS1,intron_variant,,ENST00000594624,; A ENST00000244336 Transcript missense_variant 961/2305 859/1050 287/349 P/S Ccc/Tcc 1 -1 CEACAM8 HGNC HGNC:1820 protein_coding YES CCDS12610.1 ENSP00000244336 P31997 Q0Z7S6 UPI00000012A3 NM_001816.3 tolerated(0.08) 4/6 PROSITE_profiles:PS50835,hmmpanther:PTHR10489:SF615,hmmpanther:PTHR10489,Pfam_domain:PF13895,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 97 42588883 42588883 G A 1 0 0 0 0 1 0 0 0 2904 1232 43 3 3 CEACAM8 19 42588883 Missense_Mutation SNP G C3N-02421_T 1009498 42588883 16028733 31 29068 NLRP2 0 . GRCh38 19 54983032 54983033 + Frame_Shift_Del DEL GC GC - novel C3N-02421_T C3N-02421_N GC GC c.1338_1339delGC p.Leu447AlafsTer78 p.L447Afs*78 ENST00000543010 6/13 147 120 27 154 154 0 sindel-varindel NLRP2,frameshift_variant,p.Leu447AlafsTer78,ENST00000543010,NM_001174081.1;NLRP2,frameshift_variant,p.Leu447AlafsTer78,ENST00000448584,NM_017852.3;NLRP2,frameshift_variant,p.Leu425AlafsTer78,ENST00000537859,NM_001174082.1;NLRP2,frameshift_variant,p.Leu444AlafsTer78,ENST00000263437,;NLRP2,frameshift_variant,p.Leu425AlafsTer78,ENST00000339757,;NLRP2,frameshift_variant,p.Leu423AlafsTer78,ENST00000391721,;NLRP2,frameshift_variant,p.Leu424AlafsTer78,ENST00000427260,NM_001174083.1;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; - ENST00000543010 Transcript frameshift_variant 1477-1478/3576 1334-1335/3189 445/1062 G/X gGC/g 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 6/13 hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106 HIGH 1 deletion 1 4 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999958 1 1 1 0 - 7 5 97 54983032 54983032 GC - 1 0 1 0 1 0 0 0 0 10514 1203 42 0 0 NLRP2 19 54983032 Frame_Shift_Del DEL GC C3N-02421_T 12394149 54983032 3634584 32 29069 ANKRD60 0 . GRCh38 20 58218771 58218771 + Missense_Mutation SNP C C G novel C3N-02421_T C3N-02421_N C C c.762G>C p.Arg254Ser p.R254S ENST00000457363 4/4 88 73 15 68 68 0 strelka-varscan-mutect ANKRD60,missense_variant,p.Arg254Ser,ENST00000457363,NM_001304369.1; G ENST00000457363 Transcript missense_variant 762/1038 762/1038 254/345 R/S agG/agC 1 -1 ANKRD60 HGNC HGNC:16217 protein_coding YES CCDS77596.1 ENSP00000396747 Q9BZ19 UPI00015B3C70 NM_001304369.1 deleterious(0.02) 4/4 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR22677,Gene3D:1.25.40.20,Pfam_domain:PF12796,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 97 58218771 58218771 C G 1 0 0 0 0 1 0 0 0 787 854 30 4 4 ANKRD60 20 58218771 Missense_Mutation SNP C C3N-02421_T 58218771 6225396 33 29070 LAMA5 0 . GRCh38 20 62332429 62332429 + Missense_Mutation SNP G G T novel C3N-02421_T C3N-02421_N G G c.3495C>A p.Phe1165Leu p.F1165L ENST00000252999 28/80 156 148 8 160 160 0 strelka-varscan-mutect LAMA5,missense_variant,p.Phe1165Leu,ENST00000252999,NM_005560.4;LAMA5,downstream_gene_variant,,ENST00000577688,;LAMA5,downstream_gene_variant,,ENST00000474128,; T ENST00000252999 Transcript missense_variant 3562/11426 3495/11088 1165/3695 F/L ttC/ttA 1 -1 LAMA5 HGNC HGNC:6485 protein_coding YES CCDS33502.1 ENSP00000252999 O15230 UPI0000161FDC NM_005560.4 tolerated(0.06) 28/80 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 97 62332429 62332429 G T 1 0 0 0 0 1 0 0 0 8513 1165 41 2 2 LAMA5 20 62332429 Missense_Mutation SNP G C3N-02421_T 4113658 62332429 2111738 34 29071 DSCAM 0 . GRCh38 21 40124315 40124315 + Silent SNP G G A rs372164961 C3N-02421_T C3N-02421_N G G c.3576C>T p.= p.P1192P ENST00000400454 20/33 121 113 8 128 128 0 strelka-varscan-mutect DSCAM,synonymous_variant,p.=,ENST00000400454,NM_001389.3,NM_001271534.1;DSCAM,synonymous_variant,p.=,ENST00000617870,;DSCAM,synonymous_variant,p.=,ENST00000404019,; A ENST00000400454 Transcript synonymous_variant 4054/8552 3576/6039 1192/2012 P ccC/ccT rs372164961,COSM2818547 1 -1 DSCAM HGNC HGNC:3039 protein_coding YES CCDS42929.1 ENSP00000383303 O60469 UPI00000422DF NM_001389.3,NM_001271534.1 20/33 Low_complexity_(Seg):seg,PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF16,Pfam_domain:PF00041,Gene3D:2.60.40.10,SMART_domains:SM00060,Superfamily_domains:SSF49265 0,1 LOW 1 SNV 1 0,1 1 PASS rs372164961 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 97 40124315 40124315 G A 1 0 0 0 0 0 0 0 1 4589 1103 39 1 1 DSCAM 21 40124315 Silent SNP G C3N-02421_T 40124315 6585668 35 29072 DDX3X 0 . GRCh38 X 41345483 41345484 + Frame_Shift_Del DEL AG AG - novel C3N-02421_T C3N-02421_N AG AG c.1251_1252delGA p.Lys418SerfsTer15 p.K418Sfs*15 ENST00000399959 12/17 68 57 11 112 112 0 sindel-varindel-pindel DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000399959,NM_001356.4,NM_001193416.2;DDX3X,frameshift_variant,p.Lys402SerfsTer15,ENST00000457138,NM_001193417.2;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000629496,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000625837,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000626301,;DDX3X,intron_variant,,ENST00000441189,;DDX3X,upstream_gene_variant,,ENST00000611968,;DDX3X,downstream_gene_variant,,ENST00000631641,;RN7SL15P,downstream_gene_variant,,ENST00000582825,;DDX3X,non_coding_transcript_exon_variant,,ENST00000542215,;DDX3X,downstream_gene_variant,,ENST00000615313,;DDX3X,downstream_gene_variant,,ENST00000611546,;DDX3X,downstream_gene_variant,,ENST00000622198,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000629785,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000478993,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000630255,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000630858,;DDX3X,frameshift_variant,p.Lys418SerfsTer15,ENST00000630370,;DDX3X,upstream_gene_variant,,ENST00000616050,;DDX3X,downstream_gene_variant,,ENST00000615742,; - ENST00000399959 Transcript frameshift_variant 2105-2106/5399 1250-1251/1989 417/662 Q/X cAG/c 1 1 DDX3X HGNC HGNC:2745 protein_coding YES CCDS43931.1 ENSP00000382840 O00571 UPI000013CB6D NM_001356.4,NM_001193416.2 12/17 PROSITE_profiles:PS51194,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF332,Gene3D:3.40.50.300,SMART_domains:SM00487,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 1 PASS . . 0 206 3 0 0 0 0 0 -19.99999 1 1 1 1 0 - 7 5 97 41345483 41345483 AG - 1 0 1 0 1 0 0 0 0 4161 188 7 0 0 DDX3X 23 41345483 Frame_Shift_Del DEL AG C3N-02421_T 41345483 114695412 36 29073 PER3 0 . GRCh38 1 7827723 7827723 + Missense_Mutation SNP C C A novel C3N-02422_T C3N-02422_N C C c.2794C>A p.Pro932Thr p.P932T ENST00000613533 18/22 217 171 46 234 233 1 strelka-varscan-mutect PER3,missense_variant,p.Pro932Thr,ENST00000613533,NM_001289862.1;PER3,missense_variant,p.Pro932Thr,ENST00000377532,;PER3,missense_variant,p.Pro932Thr,ENST00000614998,NM_001289861.1,NM_001289863.1,NM_001289864.1;PER3,missense_variant,p.Pro924Thr,ENST00000361923,NM_016831.2;RP3-467L1.4,upstream_gene_variant,,ENST00000451646,; A ENST00000613533 Transcript missense_variant 3058/6318 2794/3633 932/1210 P/T Ccc/Acc 1 1 PER3 HGNC HGNC:8847 protein_coding YES CCDS72695.1 ENSP00000482093 P56645 UPI00003664CA NM_001289862.1 deleterious(0.01) 18/22 hmmpanther:PTHR11269,hmmpanther:PTHR11269:SF13 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 7827723 7827723 C A 1 0 0 0 0 1 0 0 0 11819 507 18 2 2 PER3 1 7827723 Missense_Mutation SNP C C3N-02422_T 7827723 241128699 1 29074 RERE 0 . GRCh38 1 8656283 8656283 + Silent SNP T T C C3N-02422_T C3N-02422_N T T c.15A>G p.= p.K5K ENST00000337907 3/24 113 106 7 94 94 0 varscan-mutect RERE,synonymous_variant,p.=,ENST00000337907,NM_012102.3;RERE,synonymous_variant,p.=,ENST00000400908,NM_001042681.1;RERE,synonymous_variant,p.=,ENST00000400907,;RERE,synonymous_variant,p.=,ENST00000468247,;RERE,non_coding_transcript_exon_variant,,ENST00000480342,; C ENST00000337907 Transcript synonymous_variant 650/8026 15/4701 5/1566 K aaA/aaG COSM4242522 1 -1 RERE HGNC HGNC:9965 protein_coding YES CCDS95.1 ENSP00000338629 Q9P2R6 A0A024R4E9 UPI00001419CC NM_012102.3 3/24 Low_complexity_(Seg):seg 1 LOW 1 SNV 1 1 1 PASS . . 0 202 2 4 0 0 0 0 -10.2853 0.9983375 1 1 1 0 C 2 2 98 8656283 8656283 T C 1 0 0 0 0 0 0 0 1 13401 1606 56 5 5 RERE 1 8656283 Silent SNP T C3N-02422_T 828560 8656283 240300139 2 29075 NBPF3 0 . GRCh38 1 21468693 21468693 + Missense_Mutation SNP G G T novel C3N-02422_T C3N-02422_N G G c.139G>T p.Gly47Cys p.G47C ENST00000318249 3/15 239 197 42 347 346 1 strelka-varscan-mutect NBPF3,missense_variant,p.Gly47Cys,ENST00000342104,NM_001256416.2;NBPF3,missense_variant,p.Gly47Cys,ENST00000318249,NM_032264.4;NBPF3,5_prime_UTR_variant,,ENST00000619554,;NBPF3,intron_variant,,ENST00000454000,NM_001256417.2;NBPF3,upstream_gene_variant,,ENST00000469876,;NBPF3,upstream_gene_variant,,ENST00000477050,;NBPF3,3_prime_UTR_variant,,ENST00000318220,;NBPF3,3_prime_UTR_variant,,ENST00000434838,;NBPF3,3_prime_UTR_variant,,ENST00000486229,; T ENST00000318249 Transcript missense_variant 314/3591 139/1902 47/633 G/C Ggc/Tgc 1 1 NBPF3 HGNC HGNC:25076 protein_coding YES CCDS216.1 ENSP00000316782 Q9H094 UPI0000037D6C NM_032264.4 deleterious(0) 3/15 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 21468693 21468693 G T 1 0 0 0 0 1 0 0 0 10212 1362 47 2 2 NBPF3 1 21468693 Missense_Mutation SNP G C3N-02422_T 12812410 21468693 227487729 3 29076 VAV3 0 . GRCh38 1 107760813 107760813 + Missense_Mutation SNP G G A rs764254114 C3N-02422_T C3N-02422_N G G c.988C>T p.Arg330Cys p.R330C ENST00000370056 10/27 107 98 9 154 154 0 strelka-varscan-mutect VAV3,missense_variant,p.Arg330Cys,ENST00000370056,NM_006113.4;VAV3,missense_variant,p.Arg330Cys,ENST00000527011,;VAV3,missense_variant,p.Arg325Cys,ENST00000490388,;VAV3,non_coding_transcript_exon_variant,,ENST00000343258,;VAV3,non_coding_transcript_exon_variant,,ENST00000469325,; A ENST00000370056 Transcript missense_variant 1263/4990 988/2544 330/847 R/C Cgt/Tgt rs764254114,COSM4020189 1 -1 VAV3 HGNC HGNC:12659 protein_coding YES CCDS785.1 ENSP00000359073 Q9UKW4 UPI0000138212 NM_006113.4 deleterious(0) 10/27 PROSITE_profiles:PS50010,hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF97,PROSITE_patterns:PS00741,Gene3D:1.20.900.10,Pfam_domain:PF00621,SMART_domains:SM00325,Superfamily_domains:SSF48065 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs764254114 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 107760813 107760813 G A 1 0 0 0 0 1 0 0 0 17678 1145 40 1 1 VAV3 1 107760813 Missense_Mutation SNP G C3N-02422_T 86292120 107760813 141195609 4 29077 CENPF 0 . GRCh38 1 214644570 214644570 + Missense_Mutation SNP G G A rs201574754 C3N-02422_T C3N-02422_N G G c.5000G>A p.Arg1667Gln p.R1667Q ENST00000366955 13/20 20 16 4 42 42 0 strelka-varscan-mutect CENPF,missense_variant,p.Arg1667Gln,ENST00000366955,NM_016343.3;CENPF,upstream_gene_variant,,ENST00000614578,;CENPF,upstream_gene_variant,,ENST00000467765,; A ENST00000366955 Transcript missense_variant 5168/10307 5000/9345 1667/3114 R/Q cGa/cAa rs201574754 1 1 CENPF HGNC HGNC:1857 protein_coding YES CCDS31023.1 ENSP00000355922 P49454 UPI00001AE985 NM_016343.3 tolerated(0.72) 13/20 hmmpanther:PTHR18874 MODERATE 1 SNV 1 1 PASS rs201574754 . 0 200 10 0 0 0 0 0 -12.01947 0.9999904 1 1 1 0 A 3 1 98 214644570 214644570 G A 1 0 0 0 0 1 0 0 0 2939 1058 37 1 1 CENPF 1 214644570 Missense_Mutation SNP G C3N-02422_T 106883757 214644570 34311852 5 29078 ITSN2 0 . GRCh38 2 24271871 24271871 + Nonsense_Mutation SNP G G A C3N-02422_T C3N-02422_N G G c.2152C>T p.Arg718Ter p.R718* ENST00000355123 19/40 133 124 9 215 215 0 strelka-varscan-mutect ITSN2,stop_gained,p.Arg718Ter,ENST00000355123,NM_006277.2;ITSN2,stop_gained,p.Arg691Ter,ENST00000361999,NM_019595.3;ITSN2,stop_gained,p.Arg701Ter,ENST00000622089,;ITSN2,stop_gained,p.Arg718Ter,ENST00000406921,NM_147152.2;SCARNA21,downstream_gene_variant,,ENST00000515996,; A ENST00000355123 Transcript stop_gained 2596/6300 2152/5094 718/1697 R/* Cga/Tga COSM1019093,COSM1592013 1 -1 ITSN2 HGNC HGNC:6184 protein_coding YES CCDS1710.2 ENSP00000347244 Q9NZM3 UPI000013D415 NM_006277.2 19/40 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil 1,1 HIGH 1 SNV 1 1,1 1 PASS rs1254470703 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 98 24271871 24271871 G A 1 0 0 0 0 0 1 0 0 7833 1095 38 1 1 ITSN2 2 24271871 Nonsense_Mutation SNP G C3N-02422_T 24271871 217921658 6 29079 LIMS2 0 . GRCh38 2 127664330 127664330 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.59G>A p.Arg20Gln p.R20Q ENST00000324938 1/10 43 38 5 29 29 0 strelka-mutect LIMS2,missense_variant,p.Arg20Gln,ENST00000324938,NM_017980.4;LIMS2,intron_variant,,ENST00000409455,;LIMS2,intron_variant,,ENST00000410011,NM_001161404.1;LIMS2,intron_variant,,ENST00000409808,;LIMS2,intron_variant,,ENST00000355119,NM_001161403.1;LIMS2,intron_variant,,ENST00000545738,NM_001136037.2;LIMS2,non_coding_transcript_exon_variant,,ENST00000466410,;LIMS2,non_coding_transcript_exon_variant,,ENST00000476932,; T ENST00000324938 Transcript missense_variant 217/2111 59/1098 20/365 R/Q cGg/cAg 1 -1 LIMS2 HGNC HGNC:16084 protein_coding YES CCDS2147.1 ENSP00000326888 Q7Z4I7 UPI00001B5BF3 NM_017980.4 tolerated_low_confidence(0.29) 1/10 hmmpanther:PTHR24210:SF10,hmmpanther:PTHR24210 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -12.78865 1 1 1 1 0 T 3 4 98 127664330 127664330 C T 1 0 0 0 0 1 0 0 0 8712 652 23 1 1 LIMS2 2 127664330 Missense_Mutation SNP C C3N-02422_T 103392459 127664330 114529199 7 29080 1 25 2 2 24 C 4.245009e-05 LIMS2 0 . GRCh38 2 127664353 127664353 + Silent SNP C C T novel C3N-02422_T C3N-02422_N C C c.36G>A p.= p.G12G ENST00000324938 1/10 38 33 5 16 16 0 strelka-mutect LIMS2,synonymous_variant,p.=,ENST00000324938,NM_017980.4;LIMS2,intron_variant,,ENST00000409455,;LIMS2,intron_variant,,ENST00000410011,NM_001161404.1;LIMS2,intron_variant,,ENST00000409808,;LIMS2,intron_variant,,ENST00000355119,NM_001161403.1;LIMS2,intron_variant,,ENST00000545738,NM_001136037.2;LIMS2,non_coding_transcript_exon_variant,,ENST00000466410,;LIMS2,non_coding_transcript_exon_variant,,ENST00000476932,; T ENST00000324938 Transcript synonymous_variant 194/2111 36/1098 12/365 G ggG/ggA 1 -1 LIMS2 HGNC HGNC:16084 protein_coding YES CCDS2147.1 ENSP00000326888 Q7Z4I7 UPI00001B5BF3 NM_017980.4 1/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24210:SF10,hmmpanther:PTHR24210 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 98 127664353 127664353 C T 1 0 0 0 0 0 0 0 1 8712 726 26 3 3 LIMS2 2 127664353 Silent SNP C C3N-02422_T 23 127664353 114529176 8 29081 1 25 2 2 24 C 4.245009e-05 IL17RE 0 . GRCh38 3 9907002 9907002 + Missense_Mutation SNP A A G novel C3N-02422_T C3N-02422_N A A c.568A>G p.Ile190Val p.I190V ENST00000383814 6/16 288 252 36 242 242 0 strelka-varscan-mutect IL17RE,missense_variant,p.Ile190Val,ENST00000454190,NM_001193380.1;IL17RE,missense_variant,p.Ile190Val,ENST00000383814,NM_153480.1,NM_153481.1;IL17RE,missense_variant,p.Ile223Val,ENST00000421412,NM_153483.2;IL17RE,missense_variant,p.Ile150Val,ENST00000454992,;IL17RE,missense_variant,p.Ile112Val,ENST00000444427,;IL17RE,synonymous_variant,p.=,ENST00000383815,;IL17RE,synonymous_variant,p.=,ENST00000434065,;IL17RE,non_coding_transcript_exon_variant,,ENST00000489181,;IL17RE,downstream_gene_variant,,ENST00000461534,;IL17RE,upstream_gene_variant,,ENST00000480244,;IL17RE,upstream_gene_variant,,ENST00000483258,; G ENST00000383814 Transcript missense_variant 673/2704 568/2004 190/667 I/V Att/Gtt 1 1 IL17RE HGNC HGNC:18439 protein_coding YES CCDS2589.1 ENSP00000373325 Q8NFR9 UPI000003E87E NM_153480.1,NM_153481.1 tolerated(0.19) 6/16 hmmpanther:PTHR15583:SF5,hmmpanther:PTHR15583,Pfam_domain:PF15037 MODERATE 1 SNV 1 1 PASS rs1486761584 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 9907002 9907002 A G 1 0 0 0 0 1 0 0 0 7551 449 16 5 5 IL17RE 3 9907002 Missense_Mutation SNP A C3N-02422_T 9907002 188388557 9 29082 TGM4 0 . GRCh38 3 44911322 44911322 + Missense_Mutation SNP A A G novel C3N-02422_T C3N-02422_N A A c.1829A>G p.Lys610Arg p.K610R ENST00000296125 13/14 183 157 26 227 226 1 strelka-varscan-mutect TGM4,missense_variant,p.Lys610Arg,ENST00000296125,NM_003241.3;ZDHHC3,downstream_gene_variant,,ENST00000339420,;TGM4,downstream_gene_variant,,ENST00000459830,; G ENST00000296125 Transcript missense_variant 1897/3388 1829/2055 610/684 K/R aAg/aGg 1 1 TGM4 HGNC HGNC:11780 protein_coding YES CCDS2723.1 ENSP00000296125 P49221 UPI0000136CCD NM_003241.3 tolerated(0.19) 13/14 hmmpanther:PTHR11590,hmmpanther:PTHR11590:SF45,Gene3D:2.60.40.10,PIRSF_domain:PIRSF000459,Pfam_domain:PF00927,Superfamily_domains:SSF49309 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 44911322 44911322 A G 1 0 0 0 0 1 0 0 0 16265 72 3 5 5 TGM4 3 44911322 Missense_Mutation SNP A C3N-02422_T 35004320 44911322 153384237 10 29083 EPHA3 0 . GRCh38 3 89210016 89210016 + Nonsense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.310C>T p.Arg104Ter p.R104* ENST00000336596 3/17 148 121 27 257 257 0 strelka-varscan-mutect EPHA3,stop_gained,p.Arg104Ter,ENST00000336596,NM_005233.5;EPHA3,stop_gained,p.Arg104Ter,ENST00000494014,;EPHA3,stop_gained,p.Arg104Ter,ENST00000452448,NM_182644.2; T ENST00000336596 Transcript stop_gained 535/5809 310/2952 104/983 R/* Cga/Tga 1 1 EPHA3 HGNC HGNC:3387 protein_coding YES CCDS2922.1 ENSP00000337451 P29320 A0A140VJJ0 UPI0000163BE4 NM_005233.5 3/17 PROSITE_profiles:PS51550,hmmpanther:PTHR24416:SF18,hmmpanther:PTHR24416,PIRSF_domain:PIRSF000666,Pfam_domain:PF01404,Gene3D:2.60.120.260,SMART_domains:SM00615,Superfamily_domains:SSF49785 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 98 89210016 89210016 C T 1 0 0 0 0 0 1 0 0 5015 528 19 1 1 EPHA3 3 89210016 Nonsense_Mutation SNP C C3N-02422_T 44298694 89210016 109085543 11 29084 NDUFB4 0 . GRCh38 3 120596370 120596370 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.11C>T p.Pro4Leu p.P4L ENST00000184266 1/3 342 271 71 223 223 0 strelka-varscan-mutect NDUFB4,missense_variant,p.Pro4Leu,ENST00000485064,NM_001168331.1;NDUFB4,missense_variant,p.Pro4Leu,ENST00000184266,NM_004547.5;NDUFB4,missense_variant,p.Pro4Leu,ENST00000492739,;NDUFB4,missense_variant,p.Pro4Leu,ENST00000461682,;NDUFB4,missense_variant,p.Pro4Leu,ENST00000491335,;NDUFB4,upstream_gene_variant,,ENST00000496588,; T ENST00000184266 Transcript missense_variant 62/671 11/390 4/129 P/L cCa/cTa 1 1 NDUFB4 HGNC HGNC:7699 protein_coding YES CCDS2999.1 ENSP00000184266 O95168 UPI000013C5EA NM_004547.5 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR15469,hmmpanther:PTHR15469:SF0 MODERATE 1 SNV 1 1 PASS rs1283578690 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 120596370 120596370 C T 1 0 0 0 0 1 0 0 0 10307 594 21 3 3 NDUFB4 3 120596370 Missense_Mutation SNP C C3N-02422_T 31386354 120596370 77699189 12 29085 TTC14 0 . GRCh38 3 180602952 180602952 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.223C>T p.Leu75Phe p.L75F ENST00000296015 2/12 58 51 7 132 132 0 strelka-varscan-mutect TTC14,missense_variant,p.Leu75Phe,ENST00000412756,NM_001042601.2;TTC14,missense_variant,p.Leu75Phe,ENST00000296015,NM_133462.3;TTC14,missense_variant,p.Leu75Phe,ENST00000382584,NM_001288582.1;TTC14,missense_variant,p.Leu75Phe,ENST00000491380,;TTC14,5_prime_UTR_variant,,ENST00000492617,;TTC14,5_prime_UTR_variant,,ENST00000495660,;CCDC39,3_prime_UTR_variant,,ENST00000473854,;RP11-496B10.3,upstream_gene_variant,,ENST00000472596,;TTC14,missense_variant,p.Leu75Phe,ENST00000465065,;TTC14,missense_variant,p.Leu75Phe,ENST00000470669,;TTC14,missense_variant,p.Leu75Phe,ENST00000462895,; T ENST00000296015 Transcript missense_variant 355/2881 223/2313 75/770 L/F Ctt/Ttt 1 1 TTC14 HGNC HGNC:24697 protein_coding YES CCDS3237.1 ENSP00000296015 Q96N46 UPI00000720AE NM_133462.3 deleterious(0) 2/12 hmmpanther:PTHR23184,hmmpanther:PTHR23184:SF9 MODERATE 1 SNV 1 1 PASS rs1020598792 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 180602952 180602952 C T 1 0 0 0 0 1 0 0 0 17191 797 28 3 3 TTC14 3 180602952 Missense_Mutation SNP C C3N-02422_T 60006582 180602952 17692607 13 29086 IGF2BP2 0 . GRCh38 3 185689606 185689606 + Silent SNP C C T rs748998986 C3N-02422_T C3N-02422_N C C c.444G>A p.= p.G148G ENST00000457616 6/16 381 341 40 378 378 0 strelka-varscan-mutect IGF2BP2,synonymous_variant,p.=,ENST00000382199,NM_006548.4;IGF2BP2,synonymous_variant,p.=,ENST00000457616,NM_001291869.1;IGF2BP2,synonymous_variant,p.=,ENST00000346192,NM_001007225.1;IGF2BP2,synonymous_variant,p.=,ENST00000421047,NM_001291875.1,NM_001291873.1,NM_001291874.1,NM_001291872.1;IGF2BP2,non_coding_transcript_exon_variant,,ENST00000461957,;IGF2BP2,non_coding_transcript_exon_variant,,ENST00000493302,;IGF2BP2,upstream_gene_variant,,ENST00000494906,; T ENST00000457616 Transcript synonymous_variant 496/3426 444/1818 148/605 G ggG/ggA rs748998986,COSM1647626,COSM730123 1 -1 IGF2BP2 HGNC HGNC:28867 protein_coding YES CCDS77870.1 ENSP00000410242 F8W930 UPI0001F77D7F NM_001291869.1 6/16 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,hmmpanther:PTHR10288,hmmpanther:PTHR10288:SF93,SMART_domains:SM00360,Superfamily_domains:SSF54928 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs748998986 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 98 185689606 185689606 C T 1 0 0 0 0 0 0 0 1 7480 726 26 3 3 IGF2BP2 3 185689606 Silent SNP C C3N-02422_T 5086654 185689606 12605953 14 29087 CDKL3 0 . GRCh38 5 134308430 134308430 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.1072G>A p.Val358Ile p.V358I ENST00000265334 9/13 66 59 7 98 98 0 strelka-varscan-mutect CDKL3,missense_variant,p.Val358Ile,ENST00000521118,;CDKL3,missense_variant,p.Val358Ile,ENST00000265334,NM_001113575.1;CDKL3,missense_variant,p.Val169Ile,ENST00000523054,NM_001300853.1;CDKL3,missense_variant,p.Val358Ile,ENST00000523832,NM_016508.3;CDKL3,missense_variant,p.Ser41Asn,ENST00000521755,;CDKL3,upstream_gene_variant,,ENST00000518990,;CTD-2410N18.4,non_coding_transcript_exon_variant,,ENST00000518409,;CDKL3,3_prime_UTR_variant,,ENST00000520693,;CDKL3,3_prime_UTR_variant,,ENST00000519312,;CDKL3,3_prime_UTR_variant,,ENST00000520592,;CTD-2410N18.4,non_coding_transcript_exon_variant,,ENST00000520515,; T ENST00000265334 Transcript missense_variant 1191/2130 1072/1779 358/592 V/I Gtc/Atc 1 -1 CDKL3 HGNC HGNC:15483 protein_coding YES CCDS47264.1 ENSP00000265334 Q8IVW4 UPI00000745AD NM_001113575.1 tolerated(0.14) 9/13 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1306125569 . 0 208 2 0 0 0 0 0 -16.22949 1 1 1 1 0 T 3 4 98 134308430 134308430 C T 1 0 0 0 0 1 0 0 0 2859 565 20 3 3 CDKL3 5 134308430 Missense_Mutation SNP C C3N-02422_T 134308430 47229829 15 29088 PCDHB7 0 . GRCh38 5 141173277 141173277 + Missense_Mutation SNP C C G novel C3N-02422_T C3N-02422_N C C c.442C>G p.Pro148Ala p.P148A ENST00000231137 1/1 105 94 11 118 118 0 strelka-varscan-mutect PCDHB7,missense_variant,p.Pro148Ala,ENST00000231137,NM_018940.3;PCDHB8,upstream_gene_variant,,ENST00000239444,NM_019120.4;CH17-140K24.3,downstream_gene_variant,,ENST00000623581,;CH17-140K24.2,intron_variant,,ENST00000624192,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000624802,;CH17-140K24.4,upstream_gene_variant,,ENST00000623995,; G ENST00000231137 Transcript missense_variant 659/3765 442/2382 148/793 P/A Cca/Gca 1 1 PCDHB7 HGNC HGNC:8692 protein_coding YES CCDS4249.1 ENSP00000231137 Q9Y5E2 UPI00001273E3 NM_018940.3 deleterious_low_confidence(0.05) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF69,Superfamily_domains:SSF49313 MODERATE SNV 1 PASS . . 0 208 2 0 0 0 0 0 -19.99917 1 1 1 1 0 G 3 3 98 141173277 141173277 C G 1 0 0 0 0 1 0 0 0 11634 855 30 4 4 PCDHB7 5 141173277 Missense_Mutation SNP C C3N-02422_T 6864847 141173277 40364982 16 29089 ROS1 0 . GRCh38 6 117326336 117326336 + Missense_Mutation SNP G G C novel C3N-02422_T C3N-02422_N G G c.5445C>G p.Cys1815Trp p.C1815W ENST00000368508 33/43 61 53 8 138 138 0 strelka-varscan-mutect ROS1,missense_variant,p.Cys1815Trp,ENST00000368508,NM_002944.2;ROS1,missense_variant,p.Cys1809Trp,ENST00000368507,;RP1-179P9.3,intron_variant,,ENST00000467125,;ROS1,downstream_gene_variant,,ENST00000403284,; C ENST00000368508 Transcript missense_variant 5644/7435 5445/7044 1815/2347 C/W tgC/tgG 1 -1 ROS1 HGNC HGNC:10261 protein_coding YES CCDS5116.1 ENSP00000357494 P08922 UPI000013D467 NM_002944.2 deleterious(0) 33/43 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF344,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 98 117326336 117326336 G C 1 0 0 0 0 1 0 0 0 13708 1311 46 4 4 ROS1 6 117326336 Missense_Mutation SNP G C3N-02422_T 117326336 53479643 17 29090 TULP4 0 . GRCh38 6 158503501 158503501 + Missense_Mutation SNP C C A novel C3N-02422_T C3N-02422_N C C c.3838C>A p.Pro1280Thr p.P1280T ENST00000367097 13/14 101 83 18 95 94 1 strelka-varscan-mutect TULP4,missense_variant,p.Pro1280Thr,ENST00000367097,NM_020245.4;TULP4,intron_variant,,ENST00000367094,NM_001007466.2;TULP4,downstream_gene_variant,,ENST00000613390,; A ENST00000367097 Transcript missense_variant 5367/11295 3838/4632 1280/1543 P/T Ccc/Acc 1 1 TULP4 HGNC HGNC:15530 protein_coding YES CCDS34561.1 ENSP00000356064 Q9NRJ4 UPI000013CD76 NM_020245.4 deleterious_low_confidence(0) 13/14 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 158503501 158503501 C A 1 0 0 0 0 1 0 0 0 17286 623 22 2 2 TULP4 6 158503501 Missense_Mutation SNP C C3N-02422_T 41177165 158503501 12302478 18 29091 NEUROD6 0 . GRCh38 7 31338860 31338860 + Nonsense_Mutation SNP G G A C3N-02422_T C3N-02422_N G G c.409C>T p.Arg137Ter p.R137* ENST00000297142 2/2 410 293 117 395 395 0 strelka-varscan-mutect NEUROD6,stop_gained,p.Arg137Ter,ENST00000297142,NM_022728.3; A ENST00000297142 Transcript stop_gained 732/2131 409/1014 137/337 R/* Cga/Tga COSM1089130 1 -1 NEUROD6 HGNC HGNC:13804 protein_coding YES CCDS5434.1 ENSP00000297142 Q96NK8 A0A090N7T3 UPI000000D77D NM_022728.3 2/2 PROSITE_profiles:PS50888,hmmpanther:PTHR19290:SF9,hmmpanther:PTHR19290,Gene3D:4.10.280.10,Pfam_domain:PF00010,PIRSF_domain:PIRSF015618,SMART_domains:SM00353,Superfamily_domains:SSF47459 1 HIGH 1 SNV 1 1 1 PASS rs1183382119 . 0 208 0 0 2 0 0 0 -20 0.9990342 1 1 1 0 A 4 1 98 31338860 31338860 G A 1 0 0 0 0 0 1 0 0 10388 1153 40 1 1 NEUROD6 7 31338860 Nonsense_Mutation SNP G C3N-02422_T 31338860 128007113 19 29092 GRM8 0 . GRCh38 7 126533593 126533593 + Missense_Mutation SNP C C T rs140162343 C3N-02422_T C3N-02422_N C C c.1789G>A p.Ala597Thr p.A597T ENST00000339582 9/11 398 359 39 434 434 0 strelka-varscan-mutect GRM8,missense_variant,p.Ala597Thr,ENST00000339582,NM_000845.2;GRM8,missense_variant,p.Ala597Thr,ENST00000358373,NM_001127323.1;GRM8,missense_variant,p.Ala105Thr,ENST00000444921,;GRM8,non_coding_transcript_exon_variant,,ENST00000480995,;GRM8,missense_variant,p.Ala597Thr,ENST00000472701,;GRM8,3_prime_UTR_variant,,ENST00000341617,; T ENST00000339582 Transcript missense_variant 2598/4057 1789/2727 597/908 A/T Gcc/Acc rs140162343,COSM269282 1 -1 GRM8 HGNC HGNC:4600 protein_coding YES CCDS5794.1 ENSP00000344173 O00222 UPI000012F085 NM_000845.2 tolerated(0.06) 9/11 Pfam_domain:PF00003,PROSITE_profiles:PS50259,hmmpanther:PTHR24060,hmmpanther:PTHR24060:SF26,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs140162343 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 126533593 126533593 C T 1 0 0 0 0 1 0 0 0 6685 768 27 1 1 GRM8 7 126533593 Missense_Mutation SNP C C3N-02422_T 95194733 126533593 32812380 20 29093 FBXO32 0 . GRCh38 8 123504656 123504656 + Missense_Mutation SNP T T A novel C3N-02422_T C3N-02422_N T T c.926A>T p.Gln309Leu p.Q309L ENST00000517956 8/9 161 136 25 209 209 0 strelka-varscan-mutect FBXO32,missense_variant,p.Gln309Leu,ENST00000517956,NM_148177.2,NM_058229.3;FBXO32,missense_variant,p.Gln216Leu,ENST00000443022,NM_001242463.1;FBXO32,non_coding_transcript_exon_variant,,ENST00000287396,;FBXO32,non_coding_transcript_exon_variant,,ENST00000524000,; A ENST00000517956 Transcript missense_variant 1118/6744 926/1068 309/355 Q/L cAg/cTg 1 -1 FBXO32 HGNC HGNC:16731 protein_coding YES CCDS6345.1 ENSP00000428205 Q969P5 A0A024R9F3 UPI0000034E28 NM_148177.2,NM_058229.3 deleterious(0) 8/9 hmmpanther:PTHR13123,hmmpanther:PTHR13123:SF6,Superfamily_domains:SSF81383 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 123504656 123504656 T A 1 0 0 0 0 1 0 0 0 5605 1580 55 4 4 FBXO32 8 123504656 Missense_Mutation SNP T C3N-02422_T 123504656 21633980 21 29094 OR1L6 0 . GRCh38 9 122750596 122750596 + Missense_Mutation SNP C C A novel C3N-02422_T C3N-02422_N C C c.749C>A p.Ala250Asp p.A250D ENST00000304720 1/1 115 101 14 191 191 0 strelka-varscan-mutect OR1L6,missense_variant,p.Ala286Asp,ENST00000373684,;OR1L6,missense_variant,p.Ala250Asp,ENST00000304720,NM_001004453.2; A ENST00000304720 Transcript missense_variant 749/936 749/936 250/311 A/D gCc/gAc 1 1 OR1L6 HGNC HGNC:8218 protein_coding YES CCDS35130.2 ENSP00000304235 A0A0C4DFP2 UPI000003CAAE NM_001004453.2 deleterious(0.04) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF342,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 122750596 122750596 C A 1 0 0 0 0 1 0 0 0 11044 739 26 2 2 OR1L6 9 122750596 Missense_Mutation SNP C C3N-02422_T 122750596 15644121 22 29095 URM1 0 . GRCh38 9 128389405 128389405 + Frame_Shift_Del DEL G G - novel C3N-02422_T C3N-02422_N G G c.335delG p.Gly112ValfsTer11 p.G112Vfs*11 ENST00000452446 4/4 195 173 22 188 187 1 sindel-varindel-pindel URM1,frameshift_variant,p.Gly112ValfsTer11,ENST00000452446,NM_001135947.2;URM1,3_prime_UTR_variant,,ENST00000372850,NM_001265582.1;URM1,intron_variant,,ENST00000372853,NM_030914.3;URM1,downstream_gene_variant,,ENST00000372847,;MIR219A2,downstream_gene_variant,,ENST00000608502,;RP11-339B21.11,upstream_gene_variant,,ENST00000609303,;MIR219A2,downstream_gene_variant,,ENST00000385220,;MIR219B,upstream_gene_variant,,ENST00000637023,;URM1,non_coding_transcript_exon_variant,,ENST00000483206,;URM1,intron_variant,,ENST00000470840,; - ENST00000452446 Transcript frameshift_variant 333/2944 333/441 111/146 L/X ctG/ct 1 1 URM1 HGNC HGNC:28378 protein_coding YES CCDS48035.1 ENSP00000412922 Q9BTM9 UPI00017A7D83 NM_001135947.2 4/4 HIGH 1 deletion 2 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 98 128389405 128389405 G - 1 0 1 0 1 0 0 0 0 17559 1335 47 0 0 URM1 9 128389405 Frame_Shift_Del DEL G C3N-02422_T 5638809 128389405 10005312 23 29096 SLC16A12 0 . GRCh38 10 89441136 89441136 + Missense_Mutation SNP A A T novel C3N-02422_T C3N-02422_N A A c.420T>A p.His140Gln p.H140Q ENST00000371790 5/8 356 310 46 488 488 0 strelka-varscan-mutect SLC16A12,missense_variant,p.His140Gln,ENST00000371790,NM_213606.3; T ENST00000371790 Transcript missense_variant 721/4617 420/1551 140/516 H/Q caT/caA 1 -1 SLC16A12 HGNC HGNC:23094 protein_coding YES CCDS7404.2 ENSP00000360855 E9PSF9 UPI0000049FA0 NM_213606.3 tolerated(0.42) 5/8 PROSITE_profiles:PS50850,hmmpanther:PTHR11360:SF28,hmmpanther:PTHR11360,Pfam_domain:PF07690,Gene3D:1.20.1250.20,Superfamily_domains:SSF103473 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 89441136 89441136 A T 1 0 0 0 0 1 0 0 0 14671 330 12 4 4 SLC16A12 10 89441136 Missense_Mutation SNP A C3N-02422_T 89441136 44356286 24 29097 R3HCC1L 0 . GRCh38 10 98209282 98209282 + Missense_Mutation SNP A A G novel C3N-02422_T C3N-02422_N A A c.1168A>G p.Thr390Ala p.T390A ENST00000612478 3/9 68 62 6 132 132 0 strelka-varscan-mutect R3HCC1L,missense_variant,p.Thr390Ala,ENST00000298999,NM_014472.4;R3HCC1L,missense_variant,p.Thr390Ala,ENST00000370584,NM_138469.2,NM_001256620.1;R3HCC1L,missense_variant,p.Thr390Ala,ENST00000612478,NM_001256619.1;R3HCC1L,missense_variant,p.Thr390Ala,ENST00000314594,;R3HCC1L,intron_variant,,ENST00000613938,;R3HCC1L,intron_variant,,ENST00000370586,NM_001256621.1; G ENST00000612478 Transcript missense_variant 1390/3337 1168/2379 390/792 T/A Act/Gct 1 1 R3HCC1L HGNC HGNC:23512 protein_coding YES CCDS73178.1 ENSP00000483494 A0A087X0M0 UPI00001F94F3 NM_001256619.1 tolerated(0.11) 3/9 hmmpanther:PTHR21678,hmmpanther:PTHR21678:SF7 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 98209282 98209282 A G 1 0 0 0 0 1 0 0 0 13043 43 2 5 5 R3HCC1L 10 98209282 Missense_Mutation SNP A C3N-02422_T 8768146 98209282 35588140 25 29098 NHLRC2 0 . GRCh38 10 113876722 113876722 + Missense_Mutation SNP T T C novel C3N-02422_T C3N-02422_N T T c.533T>C p.Leu178Ser p.L178S ENST00000369301 3/11 194 171 23 310 310 0 strelka-varscan-mutect NHLRC2,missense_variant,p.Leu178Ser,ENST00000369301,NM_198514.3; C ENST00000369301 Transcript missense_variant 745/11051 533/2181 178/726 L/S tTg/tCg 1 1 NHLRC2 HGNC HGNC:24731 protein_coding YES CCDS7585.1 ENSP00000358307 Q8NBF2 UPI0000071EAF NM_198514.3 deleterious(0) 3/11 Gene3D:3.40.30.10,PROSITE_profiles:PS51352,hmmpanther:PTHR13833,hmmpanther:PTHR13833:SF49,Superfamily_domains:SSF52833 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 98 113876722 113876722 T C 1 0 0 0 0 1 0 0 0 10439 1821 63 5 5 NHLRC2 10 113876722 Missense_Mutation SNP T C3N-02422_T 15667440 113876722 19920700 26 29099 SIK3 0 . GRCh38 11 117098352 117098352 + Missense_Mutation SNP G G T novel C3N-02422_T C3N-02422_N G G c.64C>A p.Pro22Thr p.P22T ENST00000375300 1/24 34 25 9 24 24 0 strelka-varscan-mutect SIK3,missense_variant,p.Pro16Thr,ENST00000445177,;SIK3,missense_variant,p.Pro22Thr,ENST00000375300,NM_025164.4,NM_001281748.1;SIK3,missense_variant,p.Pro22Thr,ENST00000446921,NM_001281749.1;AP000936.4,upstream_gene_variant,,ENST00000442124,;SIK3,upstream_gene_variant,,ENST00000485363,;SIK3,upstream_gene_variant,,ENST00000415541,; T ENST00000375300 Transcript missense_variant 70/6213 64/3966 22/1321 P/T Ccc/Acc 1 -1 SIK3 HGNC HGNC:29165 protein_coding YES CCDS8379.2 ENSP00000364449 J3KPC8 UPI000066D90F NM_025164.4,NM_001281748.1 tolerated_low_confidence(0.05) 1/24 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 16 191 2 0 0 0 0 0 -19.99993 1 1 1 1 0 T 3 4 98 117098352 117098352 G T 1 0 0 0 0 1 0 0 0 14583 1203 42 2 2 SIK3 11 117098352 Missense_Mutation SNP G C3N-02422_T 117098352 17988270 27 29100 NAV3 0 . GRCh38 12 78198618 78198618 + Missense_Mutation SNP G G A C3N-02422_T C3N-02422_N G G c.6460G>A p.Gly2154Arg p.G2154R ENST00000397909 36/40 63 54 9 154 154 0 strelka-varscan-mutect NAV3,missense_variant,p.Gly2154Arg,ENST00000397909,NM_001024383.1;NAV3,missense_variant,p.Gly2132Arg,ENST00000536525,NM_014903.5;NAV3,missense_variant,p.Gly1027Arg,ENST00000552895,;NAV3,missense_variant,p.Gly754Arg,ENST00000550788,;NAV3,upstream_gene_variant,,ENST00000551162,;NAV3,upstream_gene_variant,,ENST00000547884,; A ENST00000397909 Transcript missense_variant 6633/9821 6460/7158 2154/2385 G/R Gga/Aga COSM3465656,COSM3465657 1 1 NAV3 HGNC HGNC:15998 protein_coding YES CCDS66432.1 ENSP00000381007 Q8IVL0 UPI0000E59849 NM_001024383.1 deleterious(0) 36/40 hmmpanther:PTHR12784:SF18,hmmpanther:PTHR12784,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 78198618 78198618 G A 1 0 0 0 0 1 0 0 0 10194 1349 47 3 3 NAV3 12 78198618 Missense_Mutation SNP G C3N-02422_T 78198618 55076691 28 29101 PLEKHG7 0 . GRCh38 12 92756372 92756372 + Missense_Mutation SNP A A C novel C3N-02422_T C3N-02422_N A A c.681A>C p.Glu227Asp p.E227D ENST00000344636 8/12 98 86 12 218 218 0 strelka-varscan-mutect PLEKHG7,missense_variant,p.Glu227Asp,ENST00000344636,NM_001004330.2; C ENST00000344636 Transcript missense_variant 865/3584 681/1140 227/379 E/D gaA/gaC 1 1 PLEKHG7 HGNC HGNC:33829 protein_coding YES CCDS31873.1 ENSP00000344961 Q6ZR37 UPI00001C1015 NM_001004330.2 tolerated(0.11) 8/12 Gene3D:2.30.29.30,PROSITE_profiles:PS50003,hmmpanther:PTHR13217,SMART_domains:SM00233,Superfamily_domains:SSF50729 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 98 92756372 92756372 A C 1 0 0 0 0 1 0 0 0 12168 69 3 5 5 PLEKHG7 12 92756372 Missense_Mutation SNP A C3N-02422_T 14557754 92756372 40518937 29 29102 CUX2 0 . GRCh38 12 111320597 111320597 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.2588C>T p.Ala863Val p.A863V ENST00000261726 17/22 252 230 22 91 91 0 strelka-varscan-mutect CUX2,missense_variant,p.Ala863Val,ENST00000261726,NM_015267.3; T ENST00000261726 Transcript missense_variant 2742/6844 2588/4461 863/1486 A/V gCg/gTg 1 1 CUX2 HGNC HGNC:19347 protein_coding YES CCDS41837.1 ENSP00000261726 O14529 UPI00001FBB07 NM_015267.3 deleterious(0.02) 17/22 hmmpanther:PTHR14043,hmmpanther:PTHR14043:SF5 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 3 4 98 111320597 111320597 C T 1 0 0 0 0 1 0 0 0 3875 768 27 1 1 CUX2 12 111320597 Missense_Mutation SNP C C3N-02422_T 18564225 111320597 21954712 30 29103 RASL11A 0 . GRCh38 13 27273043 27273043 + Missense_Mutation SNP C C G novel C3N-02422_T C3N-02422_N C C c.278C>G p.Pro93Arg p.P93R ENST00000241463 4/4 80 64 16 106 106 0 strelka-varscan-mutect RASL11A,missense_variant,p.Pro93Arg,ENST00000241463,NM_206827.1;RASL11A,non_coding_transcript_exon_variant,,ENST00000480803,;RASL11A,non_coding_transcript_exon_variant,,ENST00000475647,; G ENST00000241463 Transcript missense_variant 896/1543 278/729 93/242 P/R cCc/cGc 1 1 RASL11A HGNC HGNC:23802 protein_coding YES CCDS9321.1 ENSP00000241463 Q6T310 UPI000013CAD1 NM_206827.1 tolerated(0.52) 4/4 PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF176,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,Pfam_domain:PF00071,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00174,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 27273043 27273043 C G 1 0 0 0 0 1 0 0 0 13242 623 22 4 4 RASL11A 13 27273043 Missense_Mutation SNP C C3N-02422_T 27273043 87091285 31 29104 METTL21C 0 . GRCh38 13 102694461 102694461 + Missense_Mutation SNP C C T rs753242037 C3N-02422_T C3N-02422_N C C c.38G>A p.Arg13His p.R13H ENST00000267273 1/4 65 57 8 79 79 0 strelka-varscan-mutect METTL21C,missense_variant,p.Arg13His,ENST00000267273,NM_001010977.2; T ENST00000267273 Transcript missense_variant 44/1088 38/795 13/264 R/H cGc/cAc rs753242037 1 -1 METTL21C HGNC HGNC:33717 protein_coding YES CCDS32003.1 ENSP00000267273 Q5VZV1 UPI000016196F NM_001010977.2 tolerated_low_confidence(0.59) 1/4 hmmpanther:PTHR14614,hmmpanther:PTHR14614:SF13 MODERATE 1 SNV 1 1 PASS rs753242037 . 0 204 5 0 0 0 0 0 -18.07201 1 1 1 1 0 T 3 4 98 102694461 102694461 C T 1 0 0 0 0 1 0 0 0 9447 768 27 1 1 METTL21C 13 102694461 Missense_Mutation SNP C C3N-02422_T 75421418 102694461 11669867 32 29105 ATP11A 0 . GRCh38 13 112862477 112862477 + Missense_Mutation SNP T T G novel C3N-02422_T C3N-02422_N T T c.2893T>G p.Phe965Val p.F965V ENST00000487903 25/30 288 235 53 343 343 0 strelka-varscan-mutect ATP11A,missense_variant,p.Phe965Val,ENST00000487903,;ATP11A,missense_variant,p.Phe965Val,ENST00000375645,NM_015205.2;ATP11A,missense_variant,p.Phe965Val,ENST00000375630,NM_032189.3;ATP11A,downstream_gene_variant,,ENST00000418678,;ATP11A,missense_variant,p.Val343Gly,ENST00000471555,;ATP11A,downstream_gene_variant,,ENST00000459908,; G ENST00000487903 Transcript missense_variant 2981/8858 2893/3405 965/1134 F/V Ttc/Gtc 1 1 ATP11A HGNC HGNC:13552 protein_coding YES CCDS32011.1 ENSP00000420387 P98196 UPI00001FCB27 deleterious(0) 25/30 Transmembrane_helices:TMhelix,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF33,Pfam_domain:PF16212,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 112862477 112862477 T G 1 0 0 0 0 1 0 0 0 1271 1725 60 5 5 ATP11A 13 112862477 Missense_Mutation SNP T C3N-02422_T 10168016 112862477 1501851 33 29106 EML1 0 . GRCh38 14 99939310 99939310 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.2362C>T p.Pro788Ser p.P788S ENST00000334192 22/23 182 155 27 187 187 0 strelka-varscan-mutect EML1,missense_variant,p.Pro769Ser,ENST00000262233,NM_004434.2;EML1,missense_variant,p.Pro788Ser,ENST00000334192,NM_001008707.1;EML1,missense_variant,p.Pro757Ser,ENST00000327921,;EML1,non_coding_transcript_exon_variant,,ENST00000553313,;EML1,downstream_gene_variant,,ENST00000557313,; T ENST00000334192 Transcript missense_variant 2496/4064 2362/2505 788/834 P/S Ccc/Tcc 1 1 EML1 HGNC HGNC:3330 protein_coding YES CCDS32154.1 ENSP00000334314 O00423 UPI00004A074E NM_001008707.1 deleterious(0) 22/23 hmmpanther:PTHR13720,hmmpanther:PTHR13720:SF22,Superfamily_domains:SSF50978 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 99939310 99939310 C T 1 0 0 0 0 1 0 0 0 4939 623 22 3 3 EML1 14 99939310 Missense_Mutation SNP C C3N-02422_T 99939310 7104408 34 29107 MGA 0 . GRCh38 15 41749735 41749735 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.6128C>T p.Ala2043Val p.A2043V ENST00000219905 17/24 139 120 19 207 207 0 strelka-varscan-mutect MGA,missense_variant,p.Ala1834Val,ENST00000566586,;MGA,missense_variant,p.Ala2043Val,ENST00000219905,NM_001164273.1;MGA,missense_variant,p.Ala2043Val,ENST00000570161,;MGA,missense_variant,p.Ala1834Val,ENST00000545763,NM_001080541.2;MGA,missense_variant,p.Ala691Val,ENST00000564190,;MGA,non_coding_transcript_exon_variant,,ENST00000566288,; T ENST00000219905 Transcript missense_variant 6309/12042 6128/9198 2043/3065 A/V gCa/gTa 1 1 MGA HGNC HGNC:14010 protein_coding YES CCDS55959.1 ENSP00000219905 Q8IWI9 UPI0001B2337E NM_001164273.1 deleterious_low_confidence(0.01) 17/24 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF32 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 41749735 41749735 C T 1 0 0 0 0 1 0 0 0 9498 710 25 3 3 MGA 15 41749735 Missense_Mutation SNP C C3N-02422_T 41749735 60241454 35 29108 SLC24A1 0 . GRCh38 15 65650605 65650605 + Missense_Mutation SNP G G C novel C3N-02422_T C3N-02422_N G G c.2456G>C p.Gly819Ala p.G819A ENST00000261892 7/10 128 103 25 119 119 0 strelka-varscan-mutect SLC24A1,missense_variant,p.Gly819Ala,ENST00000261892,NM_004727.2;SLC24A1,missense_variant,p.Gly819Ala,ENST00000339868,;SLC24A1,missense_variant,p.Gly801Ala,ENST00000537259,NM_001301033.1;SLC24A1,missense_variant,p.Gly819Ala,ENST00000399033,NM_001301031.1;SLC24A1,missense_variant,p.Gly801Ala,ENST00000546330,NM_001301032.1;SLC24A1,missense_variant,p.Gly705Ala,ENST00000544319,;SLC24A1,upstream_gene_variant,,ENST00000505666,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000449142,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000434116,;SLC24A1,non_coding_transcript_exon_variant,,ENST00000539516,; C ENST00000261892 Transcript missense_variant 2743/5768 2456/3300 819/1099 G/A gGt/gCt 1 1 SLC24A1 HGNC HGNC:10975 protein_coding YES CCDS45284.1 ENSP00000261892 O60721 UPI000013020C NM_004727.2 7/10 TIGRFAM_domain:TIGR00927,TIGRFAM_domain:TIGR00367 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 98 65650605 65650605 G C 1 0 0 0 0 1 0 0 0 14731 1261 44 4 4 SLC24A1 15 65650605 Missense_Mutation SNP G C3N-02422_T 23900870 65650605 36340584 36 29109 PKD1 0 . GRCh38 16 2118210 2118210 + Missense_Mutation SNP C C T novel C3N-02422_T C3N-02422_N C C c.782G>A p.Gly261Asp p.G261D ENST00000262304 5/46 349 321 28 194 194 0 varscan-mutect PKD1,missense_variant,p.Gly261Asp,ENST00000262304,NM_001009944.2;PKD1,missense_variant,p.Gly261Asp,ENST00000423118,NM_000296.3;PKD1,upstream_gene_variant,,ENST00000488185,;RP11-304L19.2,upstream_gene_variant,,ENST00000562027,;RP11-304L19.4,downstream_gene_variant,,ENST00000568795,;PKD1,upstream_gene_variant,,ENST00000570150,;PKD1,upstream_gene_variant,,ENST00000468674,;PKD1,upstream_gene_variant,,ENST00000483731,;PKD1,upstream_gene_variant,,ENST00000568591,;PKD1,upstream_gene_variant,,ENST00000565639,; T ENST00000262304 Transcript missense_variant 991/14138 782/12912 261/4303 G/D gGc/gAc 1 -1 PKD1 HGNC HGNC:9008 protein_coding YES CCDS32369.1 ENSP00000262304 P98161 UPI00001B0454 NM_001009944.2 tolerated(0.07) 5/46 PROSITE_profiles:PS51212,Low_complexity_(Seg):seg,SMART_domains:SM00321,TIGRFAM_domain:TIGR00864 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 2118210 2118210 C T 1 0 0 0 0 1 0 0 0 12059 739 26 3 3 PKD1 16 2118210 Missense_Mutation SNP C C3N-02422_T 2118210 88220135 37 29110 SRRM2 0 . GRCh38 16 2763775 2763775 + Missense_Mutation SNP T T G novel C3N-02422_T C3N-02422_N T T c.3247T>G p.Ser1083Ala p.S1083A ENST00000301740 11/15 299 249 50 296 295 1 strelka-varscan-mutect SRRM2,missense_variant,p.Ser1083Ala,ENST00000301740,NM_016333.3;SRRM2,intron_variant,,ENST00000630499,;SRRM2,downstream_gene_variant,,ENST00000576924,;SRRM2,downstream_gene_variant,,ENST00000571378,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,upstream_gene_variant,,ENST00000576878,;SRRM2,downstream_gene_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,upstream_gene_variant,,ENST00000573311,;SRRM2,upstream_gene_variant,,ENST00000570705,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,upstream_gene_variant,,ENST00000571041,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000573451,; G ENST00000301740 Transcript missense_variant 3796/9353 3247/8259 1083/2752 S/A Tca/Gca 1 1 SRRM2 HGNC HGNC:16639 protein_coding YES CCDS32373.1 ENSP00000301740 Q9UQ35 A0A140VK53 UPI000049DDFC NM_016333.3 deleterious_low_confidence(0.01) 11/15 hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 2763775 2763775 T G 1 0 0 0 0 1 0 0 0 15530 1435 50 5 5 SRRM2 16 2763775 Missense_Mutation SNP T C3N-02422_T 645565 2763775 87574570 38 29111 2 26 2 2 24 T 4.245009e-05 SRRM2 0 . GRCh38 16 2763798 2763798 + Silent SNP T T G novel C3N-02422_T C3N-02422_N T T c.3270T>G p.= p.S1090S ENST00000301740 11/15 302 250 52 318 318 0 strelka-varscan-mutect SRRM2,synonymous_variant,p.=,ENST00000301740,NM_016333.3;SRRM2,intron_variant,,ENST00000630499,;SRRM2,downstream_gene_variant,,ENST00000576924,;SRRM2,downstream_gene_variant,,ENST00000571378,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,upstream_gene_variant,,ENST00000574593,;SRRM2,upstream_gene_variant,,ENST00000572721,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,upstream_gene_variant,,ENST00000576878,;SRRM2,downstream_gene_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,upstream_gene_variant,,ENST00000572883,;SRRM2,upstream_gene_variant,,ENST00000573311,;SRRM2,upstream_gene_variant,,ENST00000570705,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,upstream_gene_variant,,ENST00000571041,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000573451,; G ENST00000301740 Transcript synonymous_variant 3819/9353 3270/8259 1090/2752 S tcT/tcG 1 1 SRRM2 HGNC HGNC:16639 protein_coding YES CCDS32373.1 ENSP00000301740 Q9UQ35 A0A140VK53 UPI000049DDFC NM_016333.3 11/15 hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 98 2763798 2763798 T G 1 0 0 0 0 0 0 0 1 15530 1538 54 5 5 SRRM2 16 2763798 Silent SNP T C3N-02422_T 23 2763798 87574547 39 29112 2 26 2 2 24 T 4.245009e-05 USP10 0 . GRCh38 16 84744694 84744694 + Silent SNP G G A C3N-02422_T C3N-02422_N G G c.225G>A p.= p.L75L ENST00000570191 5/15 85 67 18 114 114 0 strelka-varscan-mutect USP10,synonymous_variant,p.=,ENST00000219473,NM_005153.2;USP10,synonymous_variant,p.=,ENST00000570191,NM_001272075.1;USP10,synonymous_variant,p.=,ENST00000562283,;USP10,intron_variant,,ENST00000569038,;USP10,intron_variant,,ENST00000563892,;USP10,intron_variant,,ENST00000570053,;USP10,non_coding_transcript_exon_variant,,ENST00000562743,;USP10,downstream_gene_variant,,ENST00000562092,;USP10,missense_variant,p.Cys51Tyr,ENST00000540269,;USP10,3_prime_UTR_variant,,ENST00000563386,;USP10,non_coding_transcript_exon_variant,,ENST00000566512,;USP10,non_coding_transcript_exon_variant,,ENST00000563023,;USP10,intron_variant,,ENST00000563048,; A ENST00000570191 Transcript synonymous_variant 421/2717 225/2409 75/802 L ttG/ttA COSM1479144 1 1 USP10 HGNC HGNC:12608 protein_coding YES CCDS62004.1 ENSP00000457411 Q14694 UPI0001C67AA8 NM_001272075.1 5/15 1 LOW 1 SNV 2 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 98 84744694 84744694 G A 1 0 0 0 0 0 0 0 1 17575 1310 46 3 3 USP10 16 84744694 Silent SNP G C3N-02422_T 81980896 84744694 5593651 40 29113 SLC13A5 0 . GRCh38 17 6703023 6703023 + Silent SNP G G T rs373831482 C3N-02422_T C3N-02422_N G G c.663C>A p.= p.T221T ENST00000433363 5/12 243 212 31 174 174 0 strelka-varscan-mutect SLC13A5,synonymous_variant,p.=,ENST00000433363,NM_177550.4;SLC13A5,synonymous_variant,p.=,ENST00000293800,NM_001284509.1;SLC13A5,synonymous_variant,p.=,ENST00000381074,NM_001284510.1;SLC13A5,synonymous_variant,p.=,ENST00000573648,NM_001143838.2;SLC13A5,downstream_gene_variant,,ENST00000572352,;SLC13A5,downstream_gene_variant,,ENST00000576323,;SLC13A5,3_prime_UTR_variant,,ENST00000572094,;SLC13A5,non_coding_transcript_exon_variant,,ENST00000574824,;SLC13A5,downstream_gene_variant,,ENST00000575230,; T ENST00000433363 Transcript synonymous_variant 897/3435 663/1707 221/568 T acC/acA rs373831482 1 -1 SLC13A5 HGNC HGNC:23089 protein_coding YES CCDS11079.1 ENSP00000406220 Q86YT5 UPI000000D834 NM_177550.4 5/12 Transmembrane_helices:TMhelix,hmmpanther:PTHR10283:SF82,hmmpanther:PTHR10283,Pfam_domain:PF00939 LOW 1 SNV 1 1 PASS rs373831482 . 0 206 0 3 0 0 0 0 -20 0.9999908 1 1 1 0 T 2 4 98 6703023 6703023 G T 1 0 0 0 0 0 0 0 1 14660 1103 39 1 1 SLC13A5 17 6703023 Silent SNP G C3N-02422_T 6703023 76554418 41 29114 GAS2L2 0 . GRCh38 17 35752589 35752589 + Nonsense_Mutation SNP G G A novel C3N-02422_T C3N-02422_N G G c.262C>T p.Gln88Ter p.Q88* ENST00000604641 1/6 183 159 24 120 120 0 strelka-varscan-mutect GAS2L2,stop_gained,p.Gln88Ter,ENST00000604641,NM_139285.3;GAS2L2,stop_gained,p.Gln88Ter,ENST00000604063,;GAS2L2,stop_gained,p.Gln88Ter,ENST00000618498,;MMP28,downstream_gene_variant,,ENST00000615317,;RP1-161P9.5,downstream_gene_variant,,ENST00000603816,;TAF15,intron_variant,,ENST00000603067,;MMP28,downstream_gene_variant,,ENST00000619655,; A ENST00000604641 Transcript stop_gained 290/3014 262/2643 88/880 Q/* Cag/Tag 1 -1 GAS2L2 HGNC HGNC:24846 protein_coding YES CCDS11298.1 ENSP00000474529 Q8NHY3 UPI0000061E50 NM_139285.3 1/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS50021,hmmpanther:PTHR11915:SF308,hmmpanther:PTHR11915,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 98 35752589 35752589 G A 1 0 0 0 0 0 1 0 0 6117 1357 47 3 3 GAS2L2 17 35752589 Nonsense_Mutation SNP G C3N-02422_T 29049566 35752589 47504852 42 29115 CEP95 0 . GRCh38 17 64532950 64532950 + Frame_Shift_Del DEL A A - novel C3N-02422_T C3N-02422_N A A c.1785delA p.Glu595AspfsTer21 p.E595Dfs*21 ENST00000556440 15/20 110 86 24 216 216 0 sindel-varindel-pindel CEP95,frameshift_variant,p.Glu595AspfsTer21,ENST00000556440,NM_138363.1;CEP95,frameshift_variant,p.Glu530AspfsTer21,ENST00000553412,;CEP95,upstream_gene_variant,,ENST00000583676,;CEP95,downstream_gene_variant,,ENST00000583457,;CEP95,downstream_gene_variant,,ENST00000577476,;CEP95,3_prime_UTR_variant,,ENST00000553956,;CEP95,non_coding_transcript_exon_variant,,ENST00000582698,;CEP95,upstream_gene_variant,,ENST00000581885,;CEP95,upstream_gene_variant,,ENST00000580285,;CEP95,upstream_gene_variant,,ENST00000581980,;CEP95,downstream_gene_variant,,ENST00000579117,;CEP95,downstream_gene_variant,,ENST00000584857,;CEP95,downstream_gene_variant,,ENST00000579478,;CEP95,downstream_gene_variant,,ENST00000579637,; - ENST00000556440 Transcript frameshift_variant 2294/3139 1784/2466 595/821 E/X gAa/ga 1 1 CEP95 HGNC HGNC:25141 protein_coding YES CCDS45763.1 ENSP00000450461 Q96GE4 UPI000006F4B3 NM_138363.1 15/20 hmmpanther:PTHR22545,hmmpanther:PTHR22545:SF0 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 98 64532950 64532950 A - 1 0 1 0 1 0 0 0 0 2988 246 9 0 0 CEP95 17 64532950 Frame_Shift_Del DEL A C3N-02422_T 28780361 64532950 18724491 43 29116 RECQL5 0 . GRCh38 17 75662979 75662979 + Silent SNP G G A novel C3N-02422_T C3N-02422_N G G c.271C>T p.= p.L91L ENST00000317905 4/20 54 48 6 49 49 0 strelka-varscan-mutect RECQL5,synonymous_variant,p.=,ENST00000420326,NM_001003716.3;RECQL5,synonymous_variant,p.=,ENST00000317905,NM_004259.6;RECQL5,synonymous_variant,p.=,ENST00000423245,;RECQL5,synonymous_variant,p.=,ENST00000578201,;RECQL5,synonymous_variant,p.=,ENST00000584999,;RECQL5,synonymous_variant,p.=,ENST00000340830,NM_001003715.3;SAP30BP,upstream_gene_variant,,ENST00000584667,NM_013260.7;SAP30BP,upstream_gene_variant,,ENST00000355423,NM_001301839.1;SAP30BP,upstream_gene_variant,,ENST00000583536,NM_001301855.1;RECQL5,upstream_gene_variant,,ENST00000580078,;SAP30BP,upstream_gene_variant,,ENST00000579864,;SAP30BP,upstream_gene_variant,,ENST00000578354,;RECQL5,upstream_gene_variant,,ENST00000579274,;SAP30BP,upstream_gene_variant,,ENST00000582022,;SAP30BP,upstream_gene_variant,,ENST00000580322,;SAP30BP,upstream_gene_variant,,ENST00000293208,;SAP30BP,upstream_gene_variant,,ENST00000577292,;SAP30BP,upstream_gene_variant,,ENST00000542343,;SAP30BP,upstream_gene_variant,,ENST00000578288,;SAP30BP,upstream_gene_variant,,ENST00000580484,;RECQL5,upstream_gene_variant,,ENST00000582464,;SAP30BP,upstream_gene_variant,,ENST00000584861,;SAP30BP,upstream_gene_variant,,ENST00000579877,;SAP30BP,upstream_gene_variant,,ENST00000583170,;SAP30BP,upstream_gene_variant,,ENST00000583737,; A ENST00000317905 Transcript synonymous_variant 431/3704 271/2976 91/991 L Cta/Tta 1 -1 RECQL5 HGNC HGNC:9950 protein_coding YES CCDS42380.1 ENSP00000317636 O94762 A0A024R8M9 UPI0000133477 NM_004259.6 4/20 Gene3D:3.40.50.300,Pfam_domain:PF00270,PROSITE_profiles:PS51192,hmmpanther:PTHR13710,hmmpanther:PTHR13710:SF85,SMART_domains:SM00487,Superfamily_domains:SSF52540,TIGRFAM_domain:TIGR00614 LOW 1 SNV 1 1 PASS rs1452980294 . 0 203 7 0 0 0 0 0 -14.18802 0.9999992 1 1 1 0 A 2 1 98 75662979 75662979 G A 1 0 0 0 0 0 0 0 1 13373 962 34 3 3 RECQL5 17 75662979 Silent SNP G C3N-02422_T 11130029 75662979 7594462 44 29117 MBP 0 . GRCh38 18 77016995 77017008 + Frame_Shift_Del DEL TTCTGTGACGCCAT TTCTGTGACGCCAT - novel C3N-02422_T C3N-02422_N TTCTGTGACGCCAT TTCTGTGACGCCAT c.400_413delATGGCGTCACAGAA p.Met134GlufsTer35 p.M134Efs*35 ENST00000397860 4/4 250 216 34 225 224 1 sindel-pindel MBP,frameshift_variant,p.Met134GlufsTer35,ENST00000397860,NM_001025100.1;MBP,frameshift_variant,p.Met134GlufsTer35,ENST00000397863,;MBP,frameshift_variant,p.Met134GlufsTer35,ENST00000355994,NM_001025101.1;MBP,frameshift_variant,p.Met1_?5,ENST00000382582,NM_001025081.1;MBP,frameshift_variant,p.Met1_?5,ENST00000397875,;MBP,frameshift_variant,p.Met1_?5,ENST00000397866,NM_001025090.1;MBP,frameshift_variant,p.Met1_?5,ENST00000397865,NM_001025092.1;MBP,frameshift_variant,p.Met1_?5,ENST00000359645,NM_002385.2;MBP,frameshift_variant,p.Met134GlufsTer35,ENST00000579129,;MBP,frameshift_variant,p.Met134GlufsTer35,ENST00000580402,;MBP,frameshift_variant,p.Met1_?5,ENST00000397869,;MBP,frameshift_variant,p.Met1_?5,ENST00000498683,;MBP,frameshift_variant,p.Met1_?5,ENST00000528160,;MBP,frameshift_variant,p.Met1_?5,ENST00000527041,;MBP,frameshift_variant,p.Met1_?5,ENST00000526111,;MBP,frameshift_variant,p.Met1_?5,ENST00000578193,;MBP,frameshift_variant,p.Met1_?5,ENST00000354542,;MBP,frameshift_variant,p.Met134GlufsTer?,ENST00000581878,;MBP,frameshift_variant,p.Met1_?5,ENST00000578873,;MBP,non_coding_transcript_exon_variant,,ENST00000487778,;MBP,non_coding_transcript_exon_variant,,ENST00000581179,;MBP,non_coding_transcript_exon_variant,,ENST00000583266,;MBP,non_coding_transcript_exon_variant,,ENST00000585216,;MBP,non_coding_transcript_exon_variant,,ENST00000582282,;MBP,intron_variant,,ENST00000580473,;MBP,downstream_gene_variant,,ENST00000497479,;MBP,downstream_gene_variant,,ENST00000495162,;MBP,downstream_gene_variant,,ENST00000490754,;MBP,frameshift_variant,p.Met1_?5,ENST00000533278,;MBP,frameshift_variant,p.Met1_?5,ENST00000531144,;MBP,frameshift_variant,p.Met1_?5,ENST00000493623,;MBP,frameshift_variant,p.Met1_?5,ENST00000583474,;MBP,frameshift_variant,p.Met1_?5,ENST00000459948,;MBP,frameshift_variant,p.Met1_?5,ENST00000483025,;MBP,frameshift_variant,p.Met1_?5,ENST00000527975,;MBP,frameshift_variant,p.Met1_?5,ENST00000473302,;MBP,coding_sequence_variant,,ENST00000577755,;MBP,non_coding_transcript_exon_variant,,ENST00000484548,;MBP,non_coding_transcript_exon_variant,,ENST00000467108,;MBP,non_coding_transcript_exon_variant,,ENST00000397868,;MBP,non_coding_transcript_exon_variant,,ENST00000482445,; - ENST00000397860 Transcript frameshift_variant 615-628/4844 400-413/594 134-138/197 MASQK/X ATGGCGTCACAGAAg/g 1 -1 MBP HGNC HGNC:6925 protein_coding YES CCDS42450.1 ENSP00000380958 P02686 UPI000002ADA3 NM_001025100.1 4/4 hmmpanther:PTHR11429,hmmpanther:PTHR11429:SF0 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 98 77016995 77016995 TTCTGTGACGCCAT - 1 0 1 0 1 0 0 0 0 9292 1609 56 0 0 MBP 18 77016995 Frame_Shift_Del DEL TTCTGTGACGCCAT C3N-02422_T 77016995 3356290 45 29118 ZNF554 0 . GRCh38 19 2834517 2834517 + Missense_Mutation SNP A A T novel C3N-02422_T C3N-02422_N A A c.1282A>T p.Arg428Trp p.R428W ENST00000317243 5/5 327 257 70 356 356 0 strelka-varscan-mutect ZNF554,missense_variant,p.Arg428Trp,ENST00000317243,NM_001102651.1;ZNF554,downstream_gene_variant,,ENST00000591265,;ZNF554,3_prime_UTR_variant,,ENST00000590116,;ZNF554,non_coding_transcript_exon_variant,,ENST00000588534,; T ENST00000317243 Transcript missense_variant 1480/2736 1282/1617 428/538 R/W Agg/Tgg 1 1 ZNF554 HGNC HGNC:26629 protein_coding YES CCDS42462.1 ENSP00000321132 Q86TJ5 UPI000000DC5D NM_001102651.1 deleterious(0) 5/5 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF56,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 98 2834517 2834517 A T 1 0 0 0 0 1 0 0 0 18559 295 11 4 4 ZNF554 19 2834517 Missense_Mutation SNP A C3N-02422_T 2834517 55783099 46 29119 ATP4A 0 . GRCh38 19 35558664 35558664 + Silent SNP C C T rs763497915 C3N-02422_T C3N-02422_N C C c.1278G>A p.= p.S426S ENST00000262623 9/22 145 132 13 109 109 0 strelka-mutect ATP4A,synonymous_variant,p.=,ENST00000262623,NM_000704.2;ATP4A,upstream_gene_variant,,ENST00000592131,;ATP4A,upstream_gene_variant,,ENST00000592767,;ATP4A,downstream_gene_variant,,ENST00000590916,; T ENST00000262623 Transcript synonymous_variant 1307/3709 1278/3108 426/1035 S tcG/tcA rs763497915 1 -1 ATP4A HGNC HGNC:819 protein_coding YES CCDS12467.1 ENSP00000262623 P20648 UPI000016A49B NM_000704.2 9/22 hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF251,Gene3D:3.40.1110.10,TIGRFAM_domain:TIGR01106,Superfamily_domains:SSF81660 LOW 1 SNV 1 1 PASS rs763497915 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 98 35558664 35558664 C T 1 0 0 0 0 0 0 0 1 1298 639 23 1 1 ATP4A 19 35558664 Silent SNP C C3N-02422_T 32724147 35558664 23058952 47 29120 LILRB1 0 . GRCh38 19 54632171 54632171 + Missense_Mutation SNP G G A novel C3N-02422_T C3N-02422_N G G c.595G>A p.Ala199Thr p.A199T ENST00000324602 5/15 281 240 41 220 220 0 strelka-varscan-mutect LILRB1,missense_variant,p.Ala199Thr,ENST00000396331,NM_006669.6;LILRB1,missense_variant,p.Ala199Thr,ENST00000396327,NM_001081638.3;LILRB1,missense_variant,p.Ala199Thr,ENST00000396332,NM_001081639.3;LILRB1,missense_variant,p.Ala199Thr,ENST00000324602,NM_001081637.2;LILRB1,missense_variant,p.Ala235Thr,ENST00000427581,;LILRB1,missense_variant,p.Ala199Thr,ENST00000396315,;LILRB1,missense_variant,p.Ala199Thr,ENST00000396317,NM_001278398.2;AC009892.10,downstream_gene_variant,,ENST00000456337,;LILRB1,upstream_gene_variant,,ENST00000462628,;LILRB1,upstream_gene_variant,,ENST00000473412,;LILRB1,downstream_gene_variant,,ENST00000480257,;LILRB1,missense_variant,p.Ala199Thr,ENST00000421584,;LILRB1,upstream_gene_variant,,ENST00000480375,;LILRB1,upstream_gene_variant,,ENST00000487425,; A ENST00000324602 Transcript missense_variant 760/2774 595/1959 199/652 A/T Gct/Act 1 1 LILRB1 HGNC HGNC:6605 protein_coding YES CCDS42614.1 ENSP00000315997 A0A087WSV6 UPI00034F23AA NM_001081637.2 deleterious(0) 5/15 hmmpanther:PTHR11738,hmmpanther:PTHR11738:SF117,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE SNV 5 1 PASS rs1164583552 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 98 54632171 54632171 G A 1 0 0 0 0 1 0 0 0 8698 1319 46 3 3 LILRB1 19 54632171 Missense_Mutation SNP G C3N-02422_T 19073507 54632171 3985445 48 29121 PLCB4 0 . GRCh38 20 9478941 9478941 + Missense_Mutation SNP G G C novel C3N-02422_T C3N-02422_N G G c.3517G>C p.Gly1173Arg p.G1173R ENST00000378501 36/36 209 185 24 333 333 0 strelka-mutect PLCB4,missense_variant,p.Gly1173Arg,ENST00000378501,NM_000933.3;PLCB4,missense_variant,p.Met1160Ile,ENST00000378493,;PLCB4,missense_variant,p.Met1172Ile,ENST00000378473,NM_001172646.1;PLCB4,missense_variant,p.Met1160Ile,ENST00000278655,NM_182797.2;PLCB4,missense_variant,p.Met1172Ile,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,; C ENST00000378501 Transcript missense_variant 3532/5833 3517/3585 1173/1194 G/R Ggt/Cgt 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 deleterious_low_confidence(0.01) 36/36 hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 98 9478941 9478941 G C 1 0 0 0 0 1 0 0 0 12124 1348 47 4 4 PLCB4 20 9478941 Missense_Mutation SNP G C3N-02422_T 9478941 54965226 49 29122 RBPJL 0 . GRCh38 20 45311867 45311867 + Silent SNP G G A novel C3N-02422_T C3N-02422_N G G c.357G>A p.= p.T119T ENST00000343694 5/12 267 239 28 150 150 0 strelka-varscan-mutect RBPJL,synonymous_variant,p.=,ENST00000343694,NM_014276.3;RBPJL,synonymous_variant,p.=,ENST00000372741,NM_001281448.1;RBPJL,synonymous_variant,p.=,ENST00000372743,NM_001281449.1;MATN4,upstream_gene_variant,,ENST00000360607,NM_030590.3;MATN4,upstream_gene_variant,,ENST00000537548,;MATN4,upstream_gene_variant,,ENST00000353917,NM_030592.3;RBPJL,upstream_gene_variant,,ENST00000464504,;RBPJL,upstream_gene_variant,,ENST00000622729,; A ENST00000343694 Transcript synonymous_variant 429/2489 357/1554 119/517 T acG/acA 1 1 RBPJL HGNC HGNC:13761 protein_coding YES CCDS13349.1 ENSP00000341243 Q9UBG7 UPI0000047297 NM_014276.3 5/12 Gene3D:2.60.40.1450,Pfam_domain:PF09271,hmmpanther:PTHR10665,hmmpanther:PTHR10665:SF2,SMART_domains:SM01267,Superfamily_domains:SSF49417 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 98 45311867 45311867 G A 1 0 0 0 0 0 0 0 1 13330 1103 39 1 1 RBPJL 20 45311867 Silent SNP G C3N-02422_T 35832926 45311867 19132300 50 29123 FAM65C 0 . GRCh38 20 50602138 50602138 + Silent SNP C C T rs201413126 C3N-02422_T C3N-02422_N C C c.1581G>A p.= p.T527T ENST00000327979 13/22 109 91 18 71 71 0 strelka-varscan-mutect FAM65C,synonymous_variant,p.=,ENST00000327979,NM_001290268.1;FAM65C,synonymous_variant,p.=,ENST00000045083,NM_080829.3;FAM65C,upstream_gene_variant,,ENST00000488529,;FAM65C,non_coding_transcript_exon_variant,,ENST00000462493,; T ENST00000327979 Transcript synonymous_variant 1993/4377 1581/2841 527/946 T acG/acA rs201413126,COSM1027947 1 -1 FAM65C HGNC HGNC:16168 protein_coding YES CCDS13431.2 ENSP00000332663 Q96MK2 UPI0000DA5AF4 NM_001290268.1 13/22 hmmpanther:PTHR15829,hmmpanther:PTHR15829:SF15 0,1 LOW 1 SNV 2 0,1 1 PASS rs201413126 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 98 50602138 50602138 C T 1 0 0 0 0 0 0 0 1 5467 639 23 1 1 FAM65C 20 50602138 Silent SNP C C3N-02422_T 5290271 50602138 13842029 51 29124 USP25 0 . GRCh38 21 15831470 15831470 + Missense_Mutation SNP A A G novel C3N-02422_T C3N-02422_N A A c.1834A>G p.Ile612Val p.I612V ENST00000400183 16/26 267 220 47 432 431 1 strelka-varscan-mutect USP25,missense_variant,p.Ile612Val,ENST00000400183,NM_001283041.1;USP25,missense_variant,p.Ile612Val,ENST00000285681,NM_001283042.1;USP25,missense_variant,p.Ile612Val,ENST00000285679,NM_013396.4;USP25,missense_variant,p.Ile141Val,ENST00000453553,;USP25,intron_variant,,ENST00000351097,; G ENST00000400183 Transcript missense_variant 2203/5341 1834/3378 612/1125 I/V Att/Gtt 1 1 USP25 HGNC HGNC:12624 protein_coding YES CCDS63336.1 ENSP00000383044 Q9UHP3 UPI000040FA6E NM_001283041.1 tolerated(0.16) 16/26 PROSITE_profiles:PS50235,hmmpanther:PTHR24006:SF467,hmmpanther:PTHR24006,Pfam_domain:PF00443,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 98 15831470 15831470 A G 1 0 0 0 0 1 0 0 0 17597 449 16 5 5 USP25 21 15831470 Missense_Mutation SNP A C3N-02422_T 15831470 30878513 52 29125 CLDN5 0 . GRCh38 22 19524310 19524310 + Silent SNP C C T novel C3N-02422_T C3N-02422_N C C c.201G>A p.= p.A67A ENST00000406028 2/2 77 68 9 48 48 0 strelka-varscan-mutect CLDN5,synonymous_variant,p.=,ENST00000406028,;CLDN5,synonymous_variant,p.=,ENST00000403084,NM_001130861.1;CLDN5,synonymous_variant,p.=,ENST00000413119,NM_003277.3;CLDN5,5_prime_UTR_variant,,ENST00000618236,;CDC45,downstream_gene_variant,,ENST00000407835,;CDC45,downstream_gene_variant,,ENST00000437685,NM_001178010.2;CDC45,downstream_gene_variant,,ENST00000263201,NM_003504.4;CDC45,downstream_gene_variant,,ENST00000404724,NM_001178011.2;CDC45,downstream_gene_variant,,ENST00000493724,; T ENST00000406028 Transcript synonymous_variant 1262/2548 201/912 67/303 A gcG/gcA 1 -1 CLDN5 HGNC HGNC:2047 protein_coding YES CCDS13763.2 ENSP00000385477 D3DX19 UPI0000207B80 2/2 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS . . 0 203 7 0 0 0 0 0 -19.30602 0.9999993 1 1 1 0 T 2 4 98 19524310 19524310 C T 1 0 0 0 0 0 0 0 1 3254 755 27 1 1 CLDN5 22 19524310 Silent SNP C C3N-02422_T 19524310 31294158 53 29126 MYO18B 0 . GRCh38 22 25902701 25902701 + Missense_Mutation SNP C C T rs200771643 C3N-02422_T C3N-02422_N C C c.4912C>T p.Arg1638Trp p.R1638W ENST00000335473 30/44 227 202 25 223 223 0 strelka-varscan-mutect MYO18B,missense_variant,p.Arg1638Trp,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,missense_variant,p.Arg1639Trp,ENST00000407587,;MYO18B,missense_variant,p.Arg1638Trp,ENST00000536101,;CTA-125H2.2,intron_variant,,ENST00000609889,;CTA-125H2.2,intron_variant,,ENST00000608257,;CTA-125H2.2,upstream_gene_variant,,ENST00000453457,;CTA-125H2.2,upstream_gene_variant,,ENST00000600211,;CTA-125H2.2,upstream_gene_variant,,ENST00000609275,;CTA-125H2.2,upstream_gene_variant,,ENST00000597284,;CTA-125H2.2,upstream_gene_variant,,ENST00000609157,;CTA-125H2.2,upstream_gene_variant,,ENST00000608507,;CTA-125H2.2,upstream_gene_variant,,ENST00000595093,;CTA-125H2.2,upstream_gene_variant,,ENST00000608115,;CTA-125H2.2,upstream_gene_variant,,ENST00000597548,;CTA-125H2.2,upstream_gene_variant,,ENST00000594585,;CTA-125H2.2,upstream_gene_variant,,ENST00000595102,;CTA-125H2.2,upstream_gene_variant,,ENST00000594856,;CTA-125H2.2,upstream_gene_variant,,ENST00000599080,;CTA-125H2.2,upstream_gene_variant,,ENST00000594542,;CTA-125H2.2,upstream_gene_variant,,ENST00000600269,;CTA-125H2.2,upstream_gene_variant,,ENST00000609570,;CTA-125H2.2,upstream_gene_variant,,ENST00000600903,;CTA-125H2.2,upstream_gene_variant,,ENST00000599792,;CTA-125H2.2,upstream_gene_variant,,ENST00000609823,;CTA-125H2.2,upstream_gene_variant,,ENST00000607895,;MYO18B,non_coding_transcript_exon_variant,,ENST00000536204,;MYO18B,non_coding_transcript_exon_variant,,ENST00000534908,;MYO18B,3_prime_UTR_variant,,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; T ENST00000335473 Transcript missense_variant 5162/8565 4912/7704 1638/2567 R/W Cgg/Tgg rs200771643 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 deleterious(0.01) 30/44 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372 MODERATE 1 SNV 1 1 PASS rs200771643 . 0 207 0 3 0 0 0 0 -20 0.999988 1 1 1 0 T 3 4 98 25902701 25902701 C T 1 0 0 0 0 1 0 0 0 10067 643 23 1 1 MYO18B 22 25902701 Missense_Mutation SNP C C3N-02422_T 6378391 25902701 24915767 54 29127 GATA1 0 . GRCh38 X 48791905 48791905 + Silent SNP C C T rs782123071 C3N-02422_T C3N-02422_N C C c.282C>T p.= p.A94A ENST00000376670 3/6 196 169 27 189 188 1 strelka-varscan-mutect GATA1,synonymous_variant,p.=,ENST00000376670,NM_002049.3;GATA1,synonymous_variant,p.=,ENST00000376665,; T ENST00000376670 Transcript synonymous_variant 393/1497 282/1242 94/413 A gcC/gcT rs782123071,COSM291809 1 1 GATA1 HGNC HGNC:4170 protein_coding YES CCDS14305.1 ENSP00000365858 P15976 UPI000012B0FA NM_002049.3 3/6 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF190 0,1 LOW 1 SNV 1 0,1 1 PASS rs782123071 . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 98 48791905 48791905 C T 1 0 0 0 0 0 0 0 1 6123 639 23 1 1 GATA1 23 48791905 Silent SNP C C3N-02422_T 48791905 107248990 55 29128 TEX13C 0 . GRCh38 X 125320758 125320758 + Silent SNP G G A rs749280410 C3N-02422_T C3N-02422_N G G c.639G>A p.= p.Q213Q ENST00000632600 1/1 356 296 60 273 273 0 strelka-varscan-mutect TEX13C,synonymous_variant,p.=,ENST00000632600,NM_001195272.1; A ENST00000632600 Transcript synonymous_variant 639/5095 639/2982 213/993 Q caG/caA rs749280410 1 1 TEX13C HGNC HGNC:52277 protein_coding YES ENSP00000488022 A0A0J9YWL9 UPI000016014C NM_001195272.1 1/1 hmmpanther:PTHR23111,hmmpanther:PTHR23111:SF32 LOW 1 SNV 1 PASS rs749280410 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 98 125320758 125320758 G A 1 0 0 0 0 0 0 0 1 16199 933 33 3 3 TEX13C 23 125320758 Silent SNP G C3N-02422_T 76528853 125320758 30720137 56 29129 PLXNB3 0 . GRCh38 X 153768257 153768257 + Silent SNP C C T rs367873902 C3N-02422_T C3N-02422_N C C c.1164C>T p.= p.P388P ENST00000538966 5/37 53 43 10 29 29 0 strelka-varscan-mutect PLXNB3,synonymous_variant,p.=,ENST00000538966,NM_001163257.1;PLXNB3,synonymous_variant,p.=,ENST00000361971,NM_005393.2;U52111.14,upstream_gene_variant,,ENST00000434284,;U52111.14,upstream_gene_variant,,ENST00000416854,; T ENST00000538966 Transcript synonymous_variant 1435/6377 1164/5799 388/1932 P ccC/ccT rs367873902,COSM3406112,COSM3406113,COSM3406114 1 1 PLXNB3 HGNC HGNC:9105 protein_coding YES CCDS55536.1 ENSP00000442736 Q9ULL4 UPI0001AFF680 NM_001163257.1 5/37 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF33,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1,1,1 LOW SNV 5 0,1,1,1 1 PASS rs367873902 . 0 208 2 0 0 0 0 0 -19.99996 1 1 1 1 0 T 2 4 98 153768257 153768257 C T 1 0 0 0 0 0 0 0 1 12231 639 23 1 1 PLXNB3 23 153768257 Silent SNP C C3N-02422_T 28447499 153768257 2272638 57 29130 GABRD 0 . GRCh38 1 2029617 2029617 + Nonsense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.914C>G p.Ser305Ter p.S305* ENST00000378585 8/9 422 393 29 490 490 0 strelka-varscan-mutect GABRD,stop_gained,p.Ser305Ter,ENST00000378585,NM_000815.4; G ENST00000378585 Transcript stop_gained 1014/1928 914/1359 305/452 S/* tCa/tGa 1 1 GABRD HGNC HGNC:4084 protein_coding YES CCDS36.1 ENSP00000367848 O14764 UPI0000070D0A NM_000815.4 8/9 Gene3D:1.20.58.390,Pfam_domain:PF02932,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF34,Superfamily_domains:SSF90112,TIGRFAM_domain:TIGR00860 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 99 2029617 2029617 C G 1 0 0 0 0 0 1 0 0 6040 838 29 4 4 GABRD 1 2029617 Nonsense_Mutation SNP C C3N-02423_T 2029617 246926805 1 29131 MMEL1 0 . GRCh38 1 2606341 2606341 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.657G>T p.Gln219His p.Q219H ENST00000378412 8/24 134 125 9 146 146 0 strelka-varscan-mutect MMEL1,missense_variant,p.Gln219His,ENST00000378412,NM_033467.3;MMEL1,intron_variant,,ENST00000502556,;MMEL1,missense_variant,p.Gln219His,ENST00000504800,;MMEL1,non_coding_transcript_exon_variant,,ENST00000509374,; A ENST00000378412 Transcript missense_variant 819/2849 657/2340 219/779 Q/H caG/caT 1 -1 MMEL1 HGNC HGNC:14668 protein_coding YES CCDS30569.2 ENSP00000367668 Q495T6 UPI0000047596 NM_033467.3 tolerated(0.13) 8/24 Pfam_domain:PF05649,hmmpanther:PTHR11733,hmmpanther:PTHR11733:SF141,Superfamily_domains:SSF55486 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 2606341 2606341 C A 1 0 0 0 0 1 0 0 0 9609 796 28 2 2 MMEL1 1 2606341 Missense_Mutation SNP C C3N-02423_T 576724 2606341 246350081 2 29132 C1orf174 0 . GRCh38 1 3890015 3890015 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.677T>C p.Met226Thr p.M226T ENST00000361605 4/4 279 253 26 297 297 0 strelka-varscan-mutect C1orf174,missense_variant,p.Met226Thr,ENST00000361605,NM_207356.2;DFFB,downstream_gene_variant,,ENST00000338895,NM_001320136.1,NM_001282669.1;DFFB,downstream_gene_variant,,ENST00000378209,NM_004402.3;C1orf174,non_coding_transcript_exon_variant,,ENST00000486765,;C1orf174,non_coding_transcript_exon_variant,,ENST00000474140,;DFFB,downstream_gene_variant,,ENST00000491998,;DFFB,downstream_gene_variant,,ENST00000339350,NM_001320132.1;DFFB,downstream_gene_variant,,ENST00000468793,;DFFB,downstream_gene_variant,,ENST00000477548,;DFFB,downstream_gene_variant,,ENST00000378206,;DFFB,downstream_gene_variant,,ENST00000475969,;DFFB,downstream_gene_variant,,ENST00000461150,; G ENST00000361605 Transcript missense_variant 776/1666 677/732 226/243 M/T aTg/aCg 1 -1 C1orf174 HGNC HGNC:27915 protein_coding YES CCDS53.1 ENSP00000355306 Q8IYL3 UPI00001C1D98 NM_207356.2 deleterious(0) 4/4 Pfam_domain:PF15772,hmmpanther:PTHR28491,hmmpanther:PTHR28491:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 3890015 3890015 A G 1 0 0 0 0 1 0 0 0 1974 217 8 5 5 C1orf174 1 3890015 Missense_Mutation SNP A C3N-02423_T 1283674 3890015 245066407 3 29133 NOL9 0 . GRCh38 1 6545127 6545127 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.798C>G p.Ile266Met p.I266M ENST00000377705 4/12 200 187 13 233 233 0 strelka-varscan-mutect NOL9,missense_variant,p.Ile266Met,ENST00000377705,NM_024654.4;RNU6-731P,downstream_gene_variant,,ENST00000517213,;NOL9,upstream_gene_variant,,ENST00000464383,;NOL9,downstream_gene_variant,,ENST00000464665,;NOL9,downstream_gene_variant,,ENST00000460777,;RP11-58A11.2,upstream_gene_variant,,ENST00000456162,; C ENST00000377705 Transcript missense_variant 831/6649 798/2109 266/702 I/M atC/atG 1 -1 NOL9 HGNC HGNC:26265 protein_coding YES CCDS80.1 ENSP00000366934 Q5SY16 UPI00003664C8 NM_024654.4 deleterious(0) 4/12 hmmpanther:PTHR12755:SF3,hmmpanther:PTHR12755 MODERATE 1 SNV 1 1 PASS . . 0 205 0 4 0 0 0 0 -16.16468 0.9995461 1 1 1 0 C 3 2 99 6545127 6545127 G C 1 0 0 0 0 1 0 0 0 10572 1280 45 4 4 NOL9 1 6545127 Missense_Mutation SNP G C3N-02423_T 2655112 6545127 242411295 4 29134 SLC45A1 0 . GRCh38 1 8339552 8339552 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1936C>T p.Leu646Phe p.L646F ENST00000471889 8/9 399 377 22 442 442 0 strelka-varscan-mutect SLC45A1,missense_variant,p.Leu646Phe,ENST00000471889,NM_001080397.2;SLC45A1,missense_variant,p.Leu612Phe,ENST00000289877,;SLC45A1,downstream_gene_variant,,ENST00000481265,;SLC45A1,non_coding_transcript_exon_variant,,ENST00000497660,; T ENST00000471889 Transcript missense_variant 2219/2784 1936/2349 646/782 L/F Ctc/Ttc 1 1 SLC45A1 HGNC HGNC:17939 protein_coding YES CCDS30577.2 ENSP00000418096 A0A0A0MT80 UPI000045893A NM_001080397.2 tolerated(0.08) 8/9 Gene3D:1.20.1250.20,hmmpanther:PTHR19432,hmmpanther:PTHR19432:SF6,Low_complexity_(Seg):seg,Superfamily_domains:SSF103473,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 8339552 8339552 C T 1 0 0 0 0 1 0 0 0 14917 913 32 3 3 SLC45A1 1 8339552 Missense_Mutation SNP C C3N-02423_T 1794425 8339552 240616870 5 29135 MAD2L2 0 . GRCh38 1 11677610 11677610 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.164C>T p.Ser55Phe p.S55F ENST00000235310 6/11 238 222 16 264 264 0 strelka-varscan-mutect MAD2L2,missense_variant,p.Ser55Phe,ENST00000235310,;MAD2L2,missense_variant,p.Ser55Phe,ENST00000376692,NM_006341.3;MAD2L2,missense_variant,p.Ser55Phe,ENST00000456915,;MAD2L2,missense_variant,p.Ser55Phe,ENST00000376672,;MAD2L2,missense_variant,p.Ser55Phe,ENST00000376667,NM_001127325.1;MAD2L2,missense_variant,p.Ser55Phe,ENST00000376669,;MAD2L2,missense_variant,p.Ser85Phe,ENST00000445656,;FBXO6,downstream_gene_variant,,ENST00000376753,NM_018438.5;FBXO6,downstream_gene_variant,,ENST00000449067,;MAD2L2,non_coding_transcript_exon_variant,,ENST00000376655,;MAD2L2,non_coding_transcript_exon_variant,,ENST00000376664,; A ENST00000235310 Transcript missense_variant 1093/1860 164/636 55/211 S/F tCc/tTc 1 -1 MAD2L2 HGNC HGNC:6764 protein_coding YES CCDS134.1 ENSP00000235310 Q9UI95 A0A024R4I4 UPI0000000DF1 deleterious(0.01) 6/11 PROSITE_profiles:PS50815,hmmpanther:PTHR11842,hmmpanther:PTHR11842:SF10,Pfam_domain:PF02301,Gene3D:1go4B00,Superfamily_domains:0040144 MODERATE SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 11677610 11677610 G A 1 0 0 0 0 1 0 0 0 9066 1188 41 3 3 MAD2L2 1 11677610 Missense_Mutation SNP G C3N-02423_T 3338058 11677610 237278812 6 29136 PRDM2 0 . GRCh38 1 13781946 13781946 + Missense_Mutation SNP T T G rs756815524 C3N-02423_T C3N-02423_N T T c.4151T>G p.Val1384Gly p.V1384G ENST00000235372 8/10 327 309 18 359 358 1 strelka-varscan-mutect PRDM2,missense_variant,p.Val1384Gly,ENST00000235372,NM_012231.4;PRDM2,missense_variant,p.Val1384Gly,ENST00000311066,NM_015866.4;PRDM2,missense_variant,p.Val1183Gly,ENST00000413440,NM_001007257.2;PRDM2,missense_variant,p.Val1183Gly,ENST00000343137,;PRDM2,intron_variant,,ENST00000376048,NM_001135610.1;PRDM2,intron_variant,,ENST00000503842,;PRDM2,intron_variant,,ENST00000505823,;PRDM2,downstream_gene_variant,,ENST00000487453,;PRDM2,downstream_gene_variant,,ENST00000407521,;PRDM2,intron_variant,,ENST00000491134,; G ENST00000235372 Transcript missense_variant 5007/7957 4151/5157 1384/1718 V/G gTg/gGg rs756815524 1 1 PRDM2 HGNC HGNC:9347 protein_coding YES CCDS150.1 ENSP00000235372 Q13029 UPI000013C9CD NM_012231.4 deleterious(0) 8/10 PIRSF_domain:PIRSF002395 MODERATE 1 SNV 1 1 PASS rs756815524 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 13781946 13781946 T G 1 0 0 0 0 1 0 0 0 12589 1696 59 5 5 PRDM2 1 13781946 Missense_Mutation SNP T C3N-02423_T 2104336 13781946 235174476 7 29137 PADI4 0 . GRCh38 1 17331113 17331113 + Silent SNP G G T rs750711340 C3N-02423_T C3N-02423_N G G c.237G>T p.= p.T79T ENST00000375448 2/16 350 317 33 329 329 0 strelka-varscan-mutect PADI4,synonymous_variant,p.=,ENST00000375448,NM_012387.2;PADI4,synonymous_variant,p.=,ENST00000375453,;AC004824.1,intron_variant,,ENST00000624583,; T ENST00000375448 Transcript synonymous_variant 263/2267 237/1992 79/663 T acG/acT rs750711340,COSM3478837 1 1 PADI4 HGNC HGNC:18368 protein_coding YES CCDS180.1 ENSP00000364597 Q9UM07 UPI000013DFF1 NM_012387.2 2/16 Pfam_domain:PF08526,PIRSF_domain:PIRSF001247,hmmpanther:PTHR10837,hmmpanther:PTHR10837:SF3,Superfamily_domains:SSF49503 0,1 LOW 1 SNV 1 0,1 1 PASS rs750711340 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 17331113 17331113 G T 1 0 0 0 0 0 0 0 1 11458 1045 37 1 1 PADI4 1 17331113 Silent SNP G C3N-02423_T 3549167 17331113 231625309 8 29138 HSPG2 0 . GRCh38 1 21836830 21836830 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.10327G>T p.Gly3443Cys p.G3443C ENST00000374695 75/97 250 228 22 288 288 0 strelka-varscan-mutect HSPG2,missense_variant,p.Gly3443Cys,ENST00000374695,NM_005529.6,NM_001291860.1;HSPG2,intron_variant,,ENST00000374676,;HSPG2,upstream_gene_variant,,ENST00000635682,;HSPG2,non_coding_transcript_exon_variant,,ENST00000471322,; A ENST00000374695 Transcript missense_variant 10407/14327 10327/13176 3443/4391 G/C Ggt/Tgt 1 -1 HSPG2 HGNC HGNC:5273 protein_coding YES CCDS30625.1 ENSP00000363827 P98160 UPI0000212778 NM_005529.6,NM_001291860.1 deleterious(0) 75/97 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF273,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs1291417277 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 21836830 21836830 C A 1 0 0 0 0 1 0 0 0 7326 623 22 2 2 HSPG2 1 21836830 Missense_Mutation SNP C C3N-02423_T 4505717 21836830 227119592 9 29139 GRIK3 0 . GRCh38 1 37034061 37034061 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.48G>T p.Trp16Cys p.W16C ENST00000373091 1/16 175 155 20 166 166 0 strelka-varscan-mutect GRIK3,missense_variant,p.Trp16Cys,ENST00000373091,NM_000831.3;GRIK3,missense_variant,p.Trp16Cys,ENST00000373093,; A ENST00000373091 Transcript missense_variant 65/9101 48/2760 16/919 W/C tgG/tgT 1 -1 GRIK3 HGNC HGNC:4581 protein_coding YES CCDS416.1 ENSP00000362183 Q13003 UPI000013E311 NM_000831.3 tolerated_low_confidence(0.11) 1/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF174,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 37034061 37034061 C A 1 0 0 0 0 1 0 0 0 6657 624 22 2 2 GRIK3 1 37034061 Missense_Mutation SNP C C3N-02423_T 15197231 37034061 211922361 10 29140 HIVEP3 0 . GRCh38 1 41512965 41512965 + Missense_Mutation SNP G G T rs372441501 C3N-02423_T C3N-02423_N G G c.6256C>A p.Pro2086Thr p.P2086T ENST00000372583 8/9 143 123 20 142 142 0 strelka-varscan-mutect HIVEP3,missense_variant,p.Pro2086Thr,ENST00000372584,NM_001127714.2;HIVEP3,missense_variant,p.Pro2086Thr,ENST00000372583,NM_024503.4;HIVEP3,non_coding_transcript_exon_variant,,ENST00000460604,; T ENST00000372583 Transcript missense_variant 7142/12193 6256/7221 2086/2406 P/T Cca/Aca rs372441501 1 -1 HIVEP3 HGNC HGNC:13561 protein_coding YES CCDS463.1 ENSP00000361664 Q5T1R4 UPI000013CC24 NM_024503.4 deleterious(0.04) 8/9 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF50 MODERATE 1 SNV 1 1 PASS rs372441501 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 99 41512965 41512965 G T 1 0 0 0 0 1 0 0 0 7077 1203 42 2 2 HIVEP3 1 41512965 Missense_Mutation SNP G C3N-02423_T 4478904 41512965 207443457 11 29141 FAM159A 0 . GRCh38 1 52656909 52656909 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.442G>A p.Glu148Lys p.E148K ENST00000517870 3/3 151 140 11 203 203 0 strelka-varscan-mutect FAM159A,missense_variant,p.Glu148Lys,ENST00000517870,NM_001042693.1;FAM159A,intron_variant,,ENST00000401050,;FAM159A,intron_variant,,ENST00000440303,;FAM159A,intron_variant,,ENST00000424164,; A ENST00000517870 Transcript missense_variant 592/748 442/573 148/190 E/K Gag/Aag 1 1 FAM159A HGNC HGNC:28757 protein_coding YES CCDS41336.1 ENSP00000429726 Q6UWV7 UPI0000204364 NM_001042693.1 tolerated(0.1) 3/3 hmmpanther:PTHR31395,hmmpanther:PTHR31395:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 52656909 52656909 G A 1 0 0 0 0 1 0 0 0 5315 1291 45 3 3 FAM159A 1 52656909 Missense_Mutation SNP G C3N-02423_T 11143944 52656909 196299513 12 29142 ADGRL4 0 . GRCh38 1 78946311 78946311 + Frame_Shift_Del DEL T T - novel C3N-02423_T C3N-02423_N T T c.288delA p.Asp97ThrfsTer12 p.D97Tfs*12 ENST00000370742 3/15 109 96 13 143 143 0 sindel-varindel-pindel ADGRL4,frameshift_variant,p.Asp97ThrfsTer12,ENST00000370742,NM_022159.3; - ENST00000370742 Transcript frameshift_variant 352/3527 288/2073 96/690 Q/X caA/ca 1 -1 ADGRL4 HGNC HGNC:20822 protein_coding YES CCDS41352.1 ENSP00000359778 Q9HBW9 UPI00004561FF NM_022159.3 3/15 PROSITE_profiles:PS50026,hmmpanther:PTHR12011:SF59,hmmpanther:PTHR12011,Gene3D:2.40.155.10,SMART_domains:SM00181,SMART_domains:SM00179 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 99 78946311 78946311 T - 1 0 1 0 1 0 0 0 0 378 1606 56 0 0 ADGRL4 1 78946311 Frame_Shift_Del DEL T C3N-02423_T 26289402 78946311 170010111 13 29143 COL24A1 0 . GRCh38 1 85737507 85737507 + Splice_Site SNP T T A C3N-02423_T C3N-02423_N T T c.4673-2A>T p.X1558_splice ENST00000370571 133 118 15 123 123 0 strelka-varscan-mutect COL24A1,splice_acceptor_variant,,ENST00000370571,NM_152890.5;COL24A1,splice_acceptor_variant,,ENST00000426639,;COL24A1,splice_acceptor_variant,,ENST00000473734,; A ENST00000370571 Transcript splice_acceptor_variant -/6825 4673/5145 1558/1714 COSM682877 1 -1 COL24A1 HGNC HGNC:20821 protein_coding YES CCDS41353.1 ENSP00000359603 Q17RW2 UPI000013E81F NM_152890.5 57/59 1 HIGH 1 SNV 1 1 1 PASS rs1488737207 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 99 85737507 85737507 T A 1 0 0 0 0 0 0 1 0 3471 1536 53 4 4 COL24A1 1 85737507 Splice_Site SNP T C3N-02423_T 6791196 85737507 163218915 14 29144 CLCA2 0 . GRCh38 1 86439073 86439073 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.1170C>T p.= p.I390I ENST00000370565 7/14 212 188 24 270 270 0 strelka-mutect CLCA2,synonymous_variant,p.=,ENST00000370565,NM_006536.5;CLCA2,upstream_gene_variant,,ENST00000490884,; T ENST00000370565 Transcript synonymous_variant 1332/4025 1170/2832 390/943 I atC/atT 1 1 CLCA2 HGNC HGNC:2016 protein_coding YES CCDS708.1 ENSP00000359596 Q9UQC9 UPI0000035838 NM_006536.5 7/14 Gene3D:3.40.50.410,Pfam_domain:PF08434,PROSITE_profiles:PS50234,hmmpanther:PTHR10579,hmmpanther:PTHR10579:SF66,SMART_domains:SM00327,Superfamily_domains:SSF53300,TIGRFAM_domain:TIGR00868 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 86439073 86439073 C T 1 0 0 0 0 0 0 0 1 3222 816 29 3 3 CLCA2 1 86439073 Silent SNP C C3N-02423_T 701566 86439073 162517349 15 29145 SLC6A17 0 . GRCh38 1 110194749 110194749 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1470G>A p.= p.K490K ENST00000331565 9/12 440 398 42 481 481 0 strelka-mutect SLC6A17,synonymous_variant,p.=,ENST00000331565,NM_001010898.2;SLC6A17,non_coding_transcript_exon_variant,,ENST00000465159,; A ENST00000331565 Transcript synonymous_variant 1955/6427 1470/2184 490/727 K aaG/aaA 1 1 SLC6A17 HGNC HGNC:31399 protein_coding YES CCDS30799.1 ENSP00000330199 Q9H1V8 UPI0000470B3D NM_001010898.2 9/12 PROSITE_profiles:PS50267,hmmpanther:PTHR11616:SF102,hmmpanther:PTHR11616,Pfam_domain:PF00209,Superfamily_domains:0053687 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 110194749 110194749 G A 1 0 0 0 0 0 0 0 1 14963 991 35 3 3 SLC6A17 1 110194749 Silent SNP G C3N-02423_T 23755676 110194749 138761673 16 29146 CTTNBP2NL 0 . GRCh38 1 112456906 112456906 + Nonsense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1414C>T p.Gln472Ter p.Q472* ENST00000271277 6/6 296 279 17 291 291 0 strelka-varscan-mutect CTTNBP2NL,stop_gained,p.Gln472Ter,ENST00000271277,NM_018704.2;CTTNBP2NL,downstream_gene_variant,,ENST00000441739,;MIR4256,downstream_gene_variant,,ENST00000636356,;CTTNBP2NL,non_coding_transcript_exon_variant,,ENST00000607039,; T ENST00000271277 Transcript stop_gained 1639/5897 1414/1920 472/639 Q/* Cag/Tag 1 1 CTTNBP2NL HGNC HGNC:25330 protein_coding YES CCDS845.1 ENSP00000271277 Q9P2B4 A0A024R0C7 UPI000006ED23 NM_018704.2 6/6 Low_complexity_(Seg):seg,hmmpanther:PTHR23166 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 112456906 112456906 C T 1 0 0 0 0 0 1 0 0 3855 827 29 3 3 CTTNBP2NL 1 112456906 Nonsense_Mutation SNP C C3N-02423_T 2262157 112456906 136499516 17 29147 PTGFRN 0 . GRCh38 1 116986805 116986805 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.2478G>A p.= p.L826L ENST00000393203 9/9 166 147 19 168 168 0 strelka-varscan-mutect PTGFRN,synonymous_variant,p.=,ENST00000393203,NM_020440.3;PTGFRN,upstream_gene_variant,,ENST00000497385,; A ENST00000393203 Transcript synonymous_variant 2625/6178 2478/2640 826/879 L ctG/ctA 1 1 PTGFRN HGNC HGNC:9601 protein_coding YES CCDS890.1 ENSP00000376899 Q9P2B2 UPI000012ABC4 NM_020440.3 9/9 hmmpanther:PTHR12207,hmmpanther:PTHR12207:SF3 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 A 2 1 99 116986805 116986805 G A 1 0 0 0 0 0 0 0 1 12906 1304 45 3 3 PTGFRN 1 116986805 Silent SNP G C3N-02423_T 4529899 116986805 131969617 18 29148 FCGR1B 0 . GRCh38 1 121096145 121096145 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.836C>A p.Ala279Asp p.A279D ENST00000369384 5/5 196 180 16 192 192 0 varscan-mutect FCGR1B,missense_variant,p.Ala279Asp,ENST00000369384,NM_001017986.3;FCGR1B,missense_variant,p.Ala187Asp,ENST00000369383,NM_001004340.3;FCGR1B,downstream_gene_variant,,ENST00000616817,;FCGR1B,downstream_gene_variant,,ENST00000623603,NM_001244910.1;FCGR1B,downstream_gene_variant,,ENST00000369178,;RP11-439A17.9,intron_variant,,ENST00000457996,;RP11-439A17.10,intron_variant,,ENST00000426275,;FCGR1B,downstream_gene_variant,,ENST00000471609,;FCGR1B,downstream_gene_variant,,ENST00000466915,;FCGR1B,downstream_gene_variant,,ENST00000453173,;FCGR1B,downstream_gene_variant,,ENST00000615565,;FCGR1B,downstream_gene_variant,,ENST00000472543,; A ENST00000369384 Transcript missense_variant 879/1044 836/843 279/280 A/D gCc/gAc 1 1 FCGR1B HGNC HGNC:3614 protein_coding YES CCDS72845.1 ENSP00000358391 A0A0A0MRM3 UPI000274710C NM_001017986.3 deleterious_low_confidence(0) 5/5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 121096145 121096145 C A 1 0 0 0 0 1 0 0 0 5643 739 26 2 2 FCGR1B 1 121096145 Missense_Mutation SNP C C3N-02423_T 4109340 121096145 127860277 19 29149 TCHH 0 . GRCh38 1 152109877 152109877 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.3340G>A p.Glu1114Lys p.E1114K ENST00000614923 3/3 430 406 24 428 427 1 varscan-mutect TCHH,missense_variant,p.Glu1114Lys,ENST00000614923,NM_007113.3;TCHH,missense_variant,p.Glu1114Lys,ENST00000368804,; T ENST00000614923 Transcript missense_variant 3435/6995 3340/5832 1114/1943 E/K Gag/Aag 1 -1 TCHH HGNC HGNC:11791 protein_coding YES CCDS41396.1 ENSP00000480484 Q07283 UPI0000458A5E NM_007113.3 deleterious_low_confidence(0) 3/3 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR34855:SF1,hmmpanther:PTHR34855 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 152109877 152109877 C T 1 0 0 0 0 1 0 0 0 16107 922 32 3 3 TCHH 1 152109877 Missense_Mutation SNP C C3N-02423_T 31013732 152109877 96846545 20 29150 HRNR 0 . GRCh38 1 152220512 152220512 + Missense_Mutation SNP T T C novel C3N-02423_T C3N-02423_N T T c.1117A>G p.Ser373Gly p.S373G ENST00000368801 3/3 217 181 36 208 208 0 strelka-varscan-mutect HRNR,missense_variant,p.Ser373Gly,ENST00000368801,NM_001009931.2;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,; C ENST00000368801 Transcript missense_variant 1193/9623 1117/8553 373/2850 S/G Agc/Ggc 1 -1 HRNR HGNC HGNC:20846 protein_coding YES CCDS30859.1 ENSP00000357791 Q86YZ3 UPI00001D7CAD NM_001009931.2 tolerated(0.54) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR22571,hmmpanther:PTHR22571:SF25 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 152220512 152220512 T C 1 0 0 0 0 1 0 0 0 7254 1522 53 5 5 HRNR 1 152220512 Missense_Mutation SNP T C3N-02423_T 110635 152220512 96735910 21 29151 LCE2B 0 . GRCh38 1 152686914 152686914 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.71G>C p.Cys24Ser p.C24S ENST00000368780 2/2 268 200 68 252 252 0 strelka-varscan-mutect LCE2B,missense_variant,p.Cys24Ser,ENST00000368780,NM_014357.4; C ENST00000368780 Transcript missense_variant 125/612 71/333 24/110 C/S tGt/tCt 1 1 LCE2B HGNC HGNC:16610 protein_coding YES CCDS1020.1 ENSP00000357769 O14633 UPI000006D1D2 NM_014357.4 tolerated_low_confidence(0.5) 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR23263:SF50,hmmpanther:PTHR23263,Pfam_domain:PF14672,Prints_domain:PR00021 MODERATE 1 SNV 1 1 PASS rs1444083566 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 152686914 152686914 G C 1 0 0 0 0 1 0 0 0 8571 1377 48 4 4 LCE2B 1 152686914 Missense_Mutation SNP G C3N-02423_T 466402 152686914 96269508 22 29152 KPRP 0 . GRCh38 1 152760473 152760473 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.885C>A p.Cys295Ter p.C295* ENST00000606109 1/1 189 173 16 148 148 0 strelka-varscan-mutect KPRP,stop_gained,p.Cys295Ter,ENST00000606109,NM_001025231.1; A ENST00000606109 Transcript stop_gained 913/2492 885/1740 295/579 C/* tgC/tgA 1 1 KPRP HGNC HGNC:31823 protein_coding YES CCDS30862.1 ENSP00000475216 Q5T749 UPI0000199942 NM_001025231.1 1/1 hmmpanther:PTHR12241:SF98,hmmpanther:PTHR12241 HIGH 1 SNV 1 PASS rs893702052 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 152760473 152760473 C A 1 0 0 0 0 0 1 0 0 8316 718 25 2 2 KPRP 1 152760473 Nonsense_Mutation SNP C C3N-02423_T 73559 152760473 96195949 23 29153 PGLYRP4 0 . GRCh38 1 153337211 153337211 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.913C>G p.Leu305Val p.L305V ENST00000359650 8/9 280 262 18 246 246 0 strelka-varscan-mutect PGLYRP4,missense_variant,p.Leu301Val,ENST00000368739,;PGLYRP4,missense_variant,p.Leu305Val,ENST00000359650,NM_020393.3; C ENST00000359650 Transcript missense_variant 978/1834 913/1122 305/373 L/V Ctg/Gtg 1 -1 PGLYRP4 HGNC HGNC:30015 protein_coding YES CCDS30871.1 ENSP00000352672 Q96LB8 UPI000013F78A NM_020393.3 deleterious(0.03) 8/9 hmmpanther:PTHR11022:SF40,hmmpanther:PTHR11022,Gene3D:3.40.80.10,Pfam_domain:PF01510,SMART_domains:SM00701,SMART_domains:SM00644,Superfamily_domains:SSF55846 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 153337211 153337211 G C 1 0 0 0 0 1 0 0 0 11885 991 35 4 4 PGLYRP4 1 153337211 Missense_Mutation SNP G C3N-02423_T 576738 153337211 95619211 24 29154 SHC1 0 . GRCh38 1 154967706 154967706 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.948C>G p.= p.L316L ENST00000448116 7/12 219 191 28 143 143 0 strelka-varscan-mutect SHC1,synonymous_variant,p.=,ENST00000448116,NM_001130040.1;SHC1,synonymous_variant,p.=,ENST00000368445,NM_183001.4;SHC1,synonymous_variant,p.=,ENST00000368453,NM_003029.4;SHC1,synonymous_variant,p.=,ENST00000368450,NM_001202859.1,NM_001130041.1;SHC1,synonymous_variant,p.=,ENST00000368449,;SHC1,synonymous_variant,p.=,ENST00000414115,;SHC1,synonymous_variant,p.=,ENST00000412170,;SHC1,synonymous_variant,p.=,ENST00000444179,;SHC1,upstream_gene_variant,,ENST00000444664,;SHC1,downstream_gene_variant,,ENST00000366442,;SHC1,upstream_gene_variant,,ENST00000490667,;PYGO2,upstream_gene_variant,,ENST00000483463,; C ENST00000448116 Transcript synonymous_variant 1169/3481 948/1755 316/584 L ctC/ctG 1 -1 SHC1 HGNC HGNC:10840 protein_coding YES CCDS44233.1 ENSP00000401303 P29353 UPI00002048B4 NM_001130040.1 7/12 PROSITE_profiles:PS01179,hmmpanther:PTHR10337,hmmpanther:PTHR10337:SF2,Pfam_domain:PF00640,Gene3D:2.30.29.30,SMART_domains:SM00462,Superfamily_domains:SSF50729 LOW 1 SNV 1 1 PASS rs1166337293 . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 C 2 2 99 154967706 154967706 G C 1 0 0 0 0 0 0 0 1 14529 1277 45 4 4 SHC1 1 154967706 Silent SNP G C3N-02423_T 1630495 154967706 93988716 25 29155 SPTA1 0 . GRCh38 1 158678514 158678514 + Silent SNP G G T C3N-02423_T C3N-02423_N G G c.699C>A p.= p.P233P ENST00000368147 6/52 571 505 66 459 458 1 strelka-varscan-mutect SPTA1,synonymous_variant,p.=,ENST00000368147,NM_003126.2;SPTA1,synonymous_variant,p.=,ENST00000467387,; T ENST00000368147 Transcript synonymous_variant 880/7999 699/7260 233/2419 P ccC/ccA COSM529969 1 -1 SPTA1 HGNC HGNC:11272 protein_coding YES CCDS41423.1 ENSP00000357129 P02549 UPI0000458906 NM_003126.2 6/52 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF283,Pfam_domain:PF00435,Gene3D:1.20.58.60,SMART_domains:SM00150,Superfamily_domains:SSF46966,Superfamily_domains:SSF46966 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 158678514 158678514 G T 1 0 0 0 0 0 0 0 1 15472 987 35 2 2 SPTA1 1 158678514 Silent SNP G C3N-02423_T 3710808 158678514 90277908 26 29156 OR6K3 0 . GRCh38 1 158717281 158717281 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.835G>T p.Val279Leu p.V279L ENST00000368145 1/1 345 293 52 287 287 0 strelka-varscan-mutect OR6K3,missense_variant,p.Val295Leu,ENST00000368146,;OR6K3,missense_variant,p.Val279Leu,ENST00000368145,NM_001005327.2; A ENST00000368145 Transcript missense_variant 835/948 835/948 279/315 V/L Gta/Tta 1 -1 OR6K3 HGNC HGNC:15030 protein_coding YES CCDS30903.2 ENSP00000357127 A0A0C4DFU5 UPI0000061E5F NM_001005327.2 tolerated(0.06) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF35,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 158717281 158717281 C A 1 0 0 0 0 1 0 0 0 11272 478 17 2 2 OR6K3 1 158717281 Missense_Mutation SNP C C3N-02423_T 38767 158717281 90239141 27 29157 ITLN2 0 . GRCh38 1 160950665 160950665 + Missense_Mutation SNP T T G novel C3N-02423_T C3N-02423_N T T c.488A>C p.His163Pro p.H163P ENST00000368029 5/8 135 112 23 113 113 0 strelka-varscan-mutect ITLN2,missense_variant,p.His163Pro,ENST00000368029,NM_080878.2;RP11-544M22.1,downstream_gene_variant,,ENST00000356006,;ITLN2,non_coding_transcript_exon_variant,,ENST00000494442,;ITLN2,non_coding_transcript_exon_variant,,ENST00000490489,; G ENST00000368029 Transcript missense_variant 546/1151 488/978 163/325 H/P cAt/cCt 1 -1 ITLN2 HGNC HGNC:20599 protein_coding YES CCDS1212.1 ENSP00000357008 Q8WWU7 UPI0000048F3E NM_080878.2 deleterious(0) 5/8 hmmpanther:PTHR16146:SF21,hmmpanther:PTHR16146,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 160950665 160950665 T G 1 0 0 0 0 1 0 0 0 7817 1464 51 5 5 ITLN2 1 160950665 Missense_Mutation SNP T C3N-02423_T 2233384 160950665 88005757 28 29158 KLHDC9 0 . GRCh38 1 161098908 161098908 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.373G>A p.Gly125Ser p.G125S ENST00000368011 1/4 62 54 8 44 44 0 strelka-varscan-mutect KLHDC9,missense_variant,p.Gly125Ser,ENST00000392192,NM_001007255.2;KLHDC9,missense_variant,p.Gly125Ser,ENST00000368011,NM_152366.4;PFDN2,downstream_gene_variant,,ENST00000368010,NM_012394.3;KLHDC9,non_coding_transcript_exon_variant,,ENST00000490724,;KLHDC9,non_coding_transcript_exon_variant,,ENST00000469647,;KLHDC9,non_coding_transcript_exon_variant,,ENST00000392191,;KLHDC9,non_coding_transcript_exon_variant,,ENST00000494418,;PFDN2,downstream_gene_variant,,ENST00000468311,;KLHDC9,non_coding_transcript_exon_variant,,ENST00000471613,;KLHDC9,upstream_gene_variant,,ENST00000475934,; A ENST00000368011 Transcript missense_variant 515/1314 373/1050 125/349 G/S Ggt/Agt 1 1 KLHDC9 HGNC HGNC:28489 protein_coding YES CCDS30919.1 ENSP00000356990 Q8NEP7 UPI0000420905 NM_152366.4 tolerated(0.32) 1/4 Superfamily_domains:0047741,Gene3D:1zgkA00,hmmpanther:PTHR23244,hmmpanther:PTHR23244:SF299 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -18.18433 0.9999999 1 1 1 0 A 3 1 99 161098908 161098908 G A 1 0 0 0 0 1 0 0 0 8228 1348 47 3 3 KLHDC9 1 161098908 Missense_Mutation SNP G C3N-02423_T 148243 161098908 87857514 29 29159 METTL11B 0 . GRCh38 1 170167736 170167736 + Frame_Shift_Del DEL G G - novel C3N-02423_T C3N-02423_N G G c.831delG p.His278ThrfsTer? p.H278Tfs*? ENST00000439373 4/4 80 70 10 151 151 0 sindel-varindel-pindel METTL11B,frameshift_variant,p.His278ThrfsTer?,ENST00000439373,NM_001136107.1;METTL11B,downstream_gene_variant,,ENST00000367764,; - ENST00000439373 Transcript frameshift_variant 938/992 831/852 277/283 L/X ctG/ct 1 1 METTL11B HGNC HGNC:31932 protein_coding YES CCDS44275.1 ENSP00000408058 Q5VVY1 UPI0000418EF1 NM_001136107.1 4/4 hmmpanther:PTHR12753:SF2,hmmpanther:PTHR12753,Pfam_domain:PF05891,Superfamily_domains:SSF53335 HIGH 1 deletion 1 1 PASS . . 0 203 5 2 0 0 0 0 -16.7726 0.9999432 1 1 1 0 - 7 5 99 170167736 170167736 G - 1 0 1 0 1 0 0 0 0 9437 1306 46 0 0 METTL11B 1 170167736 Frame_Shift_Del DEL G C3N-02423_T 9068828 170167736 78788686 30 29160 CEP350 0 . GRCh38 1 180031482 180031482 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.3713G>A p.Gly1238Glu p.G1238E ENST00000367607 15/38 75 62 13 86 86 0 strelka-varscan-mutect CEP350,missense_variant,p.Gly1238Glu,ENST00000367607,NM_014810.4; A ENST00000367607 Transcript missense_variant 4131/13491 3713/9354 1238/3117 G/E gGa/gAa 1 1 CEP350 HGNC HGNC:24238 protein_coding YES CCDS1336.1 ENSP00000356579 Q5VT06 UPI000013CFC5 NM_014810.4 deleterious(0.03) 15/38 hmmpanther:PTHR13958:SF4,hmmpanther:PTHR13958 MODERATE 1 SNV 1 1 PASS . . 0 197 10 2 0 0 0 0 -19.99886 0.9994401 1 1 1 0 A 3 1 99 180031482 180031482 G A 1 0 0 0 0 1 0 0 0 2972 1174 41 3 3 CEP350 1 180031482 Missense_Mutation SNP G C3N-02423_T 9863746 180031482 68924940 31 29161 HMCN1 0 . GRCh38 1 186016025 186016025 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.4977G>A p.= p.L1659L ENST00000271588 32/107 203 191 12 210 210 0 strelka-varscan-mutect HMCN1,synonymous_variant,p.=,ENST00000271588,NM_031935.2; A ENST00000271588 Transcript synonymous_variant 5206/18208 4977/16908 1659/5635 L ctG/ctA 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 32/107 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.98833 0.9999995 1 1 1 0 A 2 1 99 186016025 186016025 G A 1 0 0 0 0 0 0 0 1 7111 1277 45 3 3 HMCN1 1 186016025 Silent SNP G C3N-02423_T 5984543 186016025 62940397 32 29162 RGS1 0 . GRCh38 1 192578418 192578418 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.477C>A p.= p.S159S ENST00000469578 4/4 163 124 39 183 183 0 strelka-varscan-mutect RGS1,synonymous_variant,p.=,ENST00000469578,;RGS1,intron_variant,,ENST00000367459,NM_002922.3;RGS1,intron_variant,,ENST00000498352,;RGS1,downstream_gene_variant,,ENST00000474373,;RGS1,downstream_gene_variant,,ENST00000583155,;RGS1,downstream_gene_variant,,ENST00000462589,; A ENST00000469578 Transcript synonymous_variant 497/1034 477/510 159/169 S tcC/tcA 1 1 RGS1 HGNC HGNC:9991 protein_coding ENSP00000464323 Q08116 UPI000020468A 4/4 Low_complexity_(Seg):seg,SMART_domains:SM00315 LOW SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 192578418 192578418 C A 1 0 0 0 0 0 0 0 1 13463 581 21 2 2 RGS1 1 192578418 Silent SNP C C3N-02423_T 6562393 192578418 56378004 33 29163 ASPM 0 . GRCh38 1 197102750 197102750 + Silent SNP C C T C3N-02423_T C3N-02423_N C C c.6501G>A p.= p.L2167L ENST00000367409 18/28 537 496 41 572 572 0 strelka-varscan-mutect ASPM,synonymous_variant,p.=,ENST00000367409,NM_018136.4;ASPM,intron_variant,,ENST00000294732,NM_001206846.1;ASPM,intron_variant,,ENST00000612785,;ASPM,intron_variant,,ENST00000367408,; T ENST00000367409 Transcript synonymous_variant 6758/10887 6501/10434 2167/3477 L ttG/ttA COSM4555322 1 -1 ASPM HGNC HGNC:19048 protein_coding YES CCDS1389.1 ENSP00000356379 Q8IZT6 UPI0000458904 NM_018136.4 18/28 SMART_domains:SM00015 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 197102750 197102750 C T 1 0 0 0 0 0 0 0 1 1203 825 29 3 3 ASPM 1 197102750 Silent SNP C C3N-02423_T 4524332 197102750 51853672 34 29164 PKP1 0 . GRCh38 1 201317620 201317620 + Missense_Mutation SNP C C A rs757337621 C3N-02423_T C3N-02423_N C C c.895C>A p.Pro299Thr p.P299T ENST00000263946 5/15 336 299 37 317 317 0 strelka-varscan-mutect PKP1,missense_variant,p.Pro299Thr,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Pro299Thr,ENST00000367324,NM_001005337.2;PKP1,missense_variant,p.Pro299Thr,ENST00000352845,;PKP1,non_coding_transcript_exon_variant,,ENST00000475988,; A ENST00000263946 Transcript missense_variant 1146/5447 895/2244 299/747 P/T Ccc/Acc rs757337621 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 tolerated(0.14) 5/15 Gene3D:1.25.10.10,Pfam_domain:PF00514,PROSITE_profiles:PS50176,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs757337621 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 201317620 201317620 C A 1 0 0 0 0 1 0 0 0 12080 623 22 2 2 PKP1 1 201317620 Missense_Mutation SNP C C3N-02423_T 4214870 201317620 47638802 35 29165 PKP1 0 . GRCh38 1 201325834 201325834 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.2165G>A p.Arg722Lys p.R722K ENST00000263946 13/15 486 442 44 418 417 1 strelka-varscan-mutect PKP1,missense_variant,p.Arg722Lys,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Arg701Lys,ENST00000367324,NM_001005337.2;PKP1,missense_variant,p.Arg722Lys,ENST00000352845,;PKP1,upstream_gene_variant,,ENST00000477817,; A ENST00000263946 Transcript missense_variant 2416/5447 2165/2244 722/747 R/K aGa/aAa 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 tolerated(1) 13/15 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 201325834 201325834 G A 1 0 0 0 0 1 0 0 0 12080 956 33 3 3 PKP1 1 201325834 Missense_Mutation SNP G C3N-02423_T 8214 201325834 47630588 36 29166 MDM4 0 . GRCh38 1 204549150 204549150 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.941C>G p.Ser314Cys p.S314C ENST00000367182 11/11 134 127 7 140 140 0 strelka-mutect MDM4,missense_variant,p.Ser314Cys,ENST00000367182,NM_002393.4;MDM4,missense_variant,p.Ser264Cys,ENST00000454264,NM_001204171.1;MDM4,missense_variant,p.Ser216Cys,ENST00000614459,NM_001278517.1;MDM4,missense_variant,p.Ser91Cys,ENST00000612738,NM_001278519.1;MDM4,missense_variant,p.Ser199Cys,ENST00000367179,;MDM4,missense_variant,p.Ser92Cys,ENST00000444261,;MDM4,3_prime_UTR_variant,,ENST00000391947,NM_001278516.1;MDM4,3_prime_UTR_variant,,ENST00000616250,NM_001278518.1;MDM4,3_prime_UTR_variant,,ENST00000621032,;MDM4,intron_variant,,ENST00000367183,NM_001204172.1;MDM4,downstream_gene_variant,,ENST00000507825,;MDM4,non_coding_transcript_exon_variant,,ENST00000463049,;MDM4,downstream_gene_variant,,ENST00000470908,;MDM4,downstream_gene_variant,,ENST00000471783,; G ENST00000367182 Transcript missense_variant 1103/10073 941/1473 314/490 S/C tCt/tGt 1 1 MDM4 HGNC HGNC:6974 protein_coding YES CCDS1447.1 ENSP00000356150 O15151 A0A024R990 UPI000007467F NM_002393.4 deleterious(0) 11/11 PROSITE_profiles:PS50199,hmmpanther:PTHR13844,hmmpanther:PTHR13844:SF20,PROSITE_patterns:PS01358,PIRSF_domain:PIRSF006748,Pfam_domain:PF00641,PIRSF_domain:PIRSF500699,Superfamily_domains:SSF90209 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 204549150 204549150 C G 1 0 0 0 0 1 0 0 0 9352 913 32 4 4 MDM4 1 204549150 Missense_Mutation SNP C C3N-02423_T 3223316 204549150 44407272 37 29167 HSD11B1 0 . GRCh38 1 209734371 209734371 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.729G>T p.= p.L243L ENST00000367028 7/7 254 231 23 255 255 0 strelka-varscan-mutect HSD11B1,synonymous_variant,p.=,ENST00000367028,NM_181755.2,NM_001206741.1;HSD11B1,synonymous_variant,p.=,ENST00000367027,NM_005525.3;HSD11B1,synonymous_variant,p.=,ENST00000261465,;HSD11B1,downstream_gene_variant,,ENST00000615289,; T ENST00000367028 Transcript synonymous_variant 883/1461 729/879 243/292 L ctG/ctT 1 1 HSD11B1 HGNC HGNC:5208 protein_coding YES CCDS1489.1 ENSP00000355995 P28845 X5D2L1 UPI000004C796 NM_181755.2,NM_001206741.1 7/7 Gene3D:3.40.50.720,Superfamily_domains:SSF51735 LOW 1 SNV 5 1 PASS rs1037600018 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 209734371 209734371 G T 1 0 0 0 0 0 0 0 1 7270 1335 47 2 2 HSD11B1 1 209734371 Silent SNP G C3N-02423_T 5185221 209734371 39222051 38 29168 GPATCH2 0 . GRCh38 1 217431272 217431272 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1460G>T p.Gly487Val p.G487V ENST00000366935 10/10 553 516 37 503 503 0 strelka-varscan-mutect GPATCH2,missense_variant,p.Gly487Val,ENST00000366935,NM_018040.3; A ENST00000366935 Transcript missense_variant 1571/5851 1460/1587 487/528 G/V gGa/gTa 1 -1 GPATCH2 HGNC HGNC:25499 protein_coding YES CCDS1518.1 ENSP00000355902 Q9NW75 UPI000004A012 NM_018040.3 deleterious(0) 10/10 Pfam_domain:PF01585,PROSITE_profiles:PS50174,hmmpanther:PTHR14195,hmmpanther:PTHR14195:SF4,SMART_domains:SM00443 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 217431272 217431272 C A 1 0 0 0 0 1 0 0 0 6491 855 30 2 2 GPATCH2 1 217431272 Missense_Mutation SNP C C3N-02423_T 7696901 217431272 31525150 39 29169 TARBP1 0 . GRCh38 1 234398394 234398394 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.4231C>G p.Gln1411Glu p.Q1411E ENST00000040877 26/30 117 110 7 95 95 0 strelka-varscan-mutect TARBP1,missense_variant,p.Gln1411Glu,ENST00000040877,NM_005646.3;TARBP1,non_coding_transcript_exon_variant,,ENST00000462259,;TARBP1,non_coding_transcript_exon_variant,,ENST00000496673,;TARBP1,non_coding_transcript_exon_variant,,ENST00000468077,;TARBP1,non_coding_transcript_exon_variant,,ENST00000484454,;TARBP1,intron_variant,,ENST00000483404,;TARBP1,downstream_gene_variant,,ENST00000481183,; C ENST00000040877 Transcript missense_variant 4231/5130 4231/4866 1411/1621 Q/E Cag/Gag 1 -1 TARBP1 HGNC HGNC:11568 protein_coding YES CCDS1601.1 ENSP00000040877 Q13395 UPI000006DB0F NM_005646.3 deleterious(0) 26/30 PROSITE_profiles:PS51624 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 234398394 234398394 G C 1 0 0 0 0 1 0 0 0 15954 1299 45 4 4 TARBP1 1 234398394 Missense_Mutation SNP G C3N-02423_T 16967122 234398394 14558028 40 29170 RYR2 0 . GRCh38 1 237456711 237456711 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1588C>G p.Leu530Val p.L530V ENST00000366574 16/105 110 103 7 115 115 0 strelka-varscan-mutect RYR2,missense_variant,p.Leu530Val,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Leu514Val,ENST00000360064,; G ENST00000366574 Transcript missense_variant 1905/16562 1588/14904 530/4967 L/V Ctg/Gtg 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.71) 16/105 Superfamily_domains:0048280,Pfam_domain:PF01365,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 237456711 237456711 C G 1 0 0 0 0 1 0 0 0 14029 912 32 4 4 RYR2 1 237456711 Missense_Mutation SNP C C3N-02423_T 3058317 237456711 11499711 41 29171 RYR2 0 . GRCh38 1 237496731 237496731 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2182G>C p.Asp728His p.D728H ENST00000366574 20/105 94 89 5 113 112 1 strelka-varscan-mutect RYR2,missense_variant,p.Asp728His,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Asp712His,ENST00000360064,; C ENST00000366574 Transcript missense_variant 2499/16562 2182/14904 728/4967 D/H Gat/Cat 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0) 20/105 Pfam_domain:PF00622,Prints_domain:PR00795,PROSITE_profiles:PS50188,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 237496731 237496731 G C 1 0 0 0 0 1 0 0 0 14029 1290 45 4 4 RYR2 1 237496731 Missense_Mutation SNP G C3N-02423_T 40020 237496731 11459691 42 29172 RYR2 0 . GRCh38 1 237625767 237625767 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.6129A>T p.Gln2043His p.Q2043H ENST00000366574 40/105 235 197 38 220 220 0 strelka-varscan-mutect RYR2,missense_variant,p.Gln2043His,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Gln2027His,ENST00000360064,; T ENST00000366574 Transcript missense_variant 6446/16562 6129/14904 2043/4967 Q/H caA/caT 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 deleterious(0.04) 40/105 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 237625767 237625767 A T 1 0 0 0 0 1 0 0 0 14029 69 3 4 4 RYR2 1 237625767 Missense_Mutation SNP A C3N-02423_T 129036 237625767 11330655 43 29173 OR6F1 0 . GRCh38 1 247711915 247711915 + Missense_Mutation SNP C C T rs374342386 C3N-02423_T C3N-02423_N C C c.841G>A p.Val281Met p.V281M ENST00000302084 1/1 279 250 29 303 303 0 strelka-varscan-mutect OR6F1,missense_variant,p.Val281Met,ENST00000302084,NM_001005286.1;RP11-634B7.5,non_coding_transcript_exon_variant,,ENST00000419891,;RP11-634B7.4,intron_variant,,ENST00000449298,; T ENST00000302084 Transcript missense_variant 841/927 841/927 281/308 V/M Gtg/Atg rs374342386 1 -1 OR6F1 HGNC HGNC:15027 protein_coding YES CCDS31095.1 ENSP00000305640 Q8NGZ6 A0A126GV68 UPI0000041CD7 NM_001005286.1 deleterious(0.01) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26454,hmmpanther:PTHR26454:SF12,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE SNV 1 PASS rs374342386 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 247711915 247711915 C T 1 0 0 0 0 1 0 0 0 11269 507 18 3 3 OR6F1 1 247711915 Missense_Mutation SNP C C3N-02423_T 10086148 247711915 1244507 44 29174 OR1C1 0 . GRCh38 1 247757780 247757780 + Silent SNP C C A rs113617040 C3N-02423_T C3N-02423_N C C c.627G>T p.= p.T209T ENST00000408896 1/1 270 255 15 299 299 0 strelka-varscan-mutect OR1C1,synonymous_variant,p.=,ENST00000408896,NM_012353.2; A ENST00000408896 Transcript synonymous_variant 627/945 627/945 209/314 T acG/acT rs113617040 1 -1 OR1C1 HGNC HGNC:8182 protein_coding YES CCDS41481.1 ENSP00000386138 Q15619 A0A126GV94 UPI000004B1DC NM_012353.2 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26451:SF388,hmmpanther:PTHR26451,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS rs113617040 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 247757780 247757780 C A 1 0 0 0 0 0 0 0 1 11029 755 27 1 1 OR1C1 1 247757780 Silent SNP C C3N-02423_T 45865 247757780 1198642 45 29175 PXDN 0 . GRCh38 2 1744377 1744377 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.79G>T p.Val27Leu p.V27L ENST00000252804 1/23 352 329 23 370 370 0 strelka-varscan-mutect PXDN,missense_variant,p.Val27Leu,ENST00000252804,NM_012293.2;PXDN,missense_variant,p.Val23Leu,ENST00000433670,;PXDN,missense_variant,p.Val27Leu,ENST00000425171,;PXDN,intron_variant,,ENST00000485177,; A ENST00000252804 Transcript missense_variant 130/6808 79/4440 27/1479 V/L Gtg/Ttg 1 -1 PXDN HGNC HGNC:14966 protein_coding YES CCDS46221.1 ENSP00000252804 Q92626 UPI00001C1DC2 NM_012293.2 tolerated(0.99) 1/23 Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 1744377 1744377 C A 1 0 0 0 0 1 0 0 0 13001 536 19 1 1 PXDN 2 1744377 Missense_Mutation SNP C C3N-02423_T 1744377 240449152 46 29176 RNASEH1 0 . GRCh38 2 3550377 3550377 + Missense_Mutation SNP G G C C3N-02423_T C3N-02423_N G G c.505C>G p.Pro169Ala p.P169A ENST00000315212 4/8 263 242 21 232 232 0 strelka-varscan-mutect RNASEH1,missense_variant,p.Pro169Ala,ENST00000315212,NM_002936.4,NM_001286834.1,NM_001286837.1;RP13-512J5.1,upstream_gene_variant,,ENST00000438485,;RNASEH1,3_prime_UTR_variant,,ENST00000436842,;RNASEH1,3_prime_UTR_variant,,ENST00000454734,;RNASEH1,non_coding_transcript_exon_variant,,ENST00000464986,; C ENST00000315212 Transcript missense_variant 861/1887 505/861 169/286 P/A Cct/Gct COSM3581345 1 -1 RNASEH1 HGNC HGNC:18466 protein_coding YES CCDS1647.1 ENSP00000313350 O60930 E5KN15 UPI00001343BC NM_002936.4,NM_001286834.1,NM_001286837.1 tolerated(0.05) 4/8 Gene3D:3.30.420.10,Pfam_domain:PF00075,PIRSF_domain:PIRSF036852,PROSITE_profiles:PS50879,hmmpanther:PTHR10642,hmmpanther:PTHR10642:SF0,Superfamily_domains:SSF53098 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 3550377 3550377 G C 1 0 0 0 0 1 0 0 0 13590 1188 41 4 4 RNASEH1 2 3550377 Missense_Mutation SNP G C3N-02423_T 1806000 3550377 238643152 47 29177 COLEC11 0 . GRCh38 2 3604355 3604355 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.57G>T p.= p.L19L ENST00000418971 3/8 306 275 31 263 263 0 strelka-varscan-mutect COLEC11,synonymous_variant,p.=,ENST00000382062,NM_001255984.1,NM_001255983.1;COLEC11,synonymous_variant,p.=,ENST00000418971,NM_001255985.1;COLEC11,synonymous_variant,p.=,ENST00000349077,NM_024027.4,NM_001255982.1;COLEC11,synonymous_variant,p.=,ENST00000438814,;COLEC11,5_prime_UTR_variant,,ENST00000236693,NM_199235.2;COLEC11,upstream_gene_variant,,ENST00000403096,NM_001255986.1;COLEC11,upstream_gene_variant,,ENST00000402794,NM_001255987.1;COLEC11,upstream_gene_variant,,ENST00000402922,NM_001255988.1;COLEC11,upstream_gene_variant,,ENST00000404205,NM_001255989.1;AC010907.2,upstream_gene_variant,,ENST00000456450,;COLEC11,non_coding_transcript_exon_variant,,ENST00000487365,;COLEC11,non_coding_transcript_exon_variant,,ENST00000460971,;COLEC11,non_coding_transcript_exon_variant,,ENST00000419002,;COLEC11,synonymous_variant,p.=,ENST00000416132,; T ENST00000418971 Transcript synonymous_variant 268/1595 57/858 19/285 L ctG/ctT 1 1 COLEC11 HGNC HGNC:17213 protein_coding YES CCDS58689.1 ENSP00000411770 Q9BWP8 UPI0001AE7699 NM_001255985.1 3/8 hmmpanther:PTHR24024,hmmpanther:PTHR24024:SF14,Cleavage_site_(Signalp):SignalP-noTM,Transmembrane_helices:TMhelix LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 3604355 3604355 G T 1 0 0 0 0 0 0 0 1 3501 1335 47 2 2 COLEC11 2 3604355 Silent SNP G C3N-02423_T 53978 3604355 238589174 48 29178 ALLC 0 . GRCh38 2 3671169 3671169 + Silent SNP A A C novel C3N-02423_T C3N-02423_N A A c.12A>C p.= p.A4A ENST00000252505 2/12 253 220 33 262 262 0 strelka-varscan-mutect ALLC,synonymous_variant,p.=,ENST00000252505,NM_018436.3; C ENST00000252505 Transcript synonymous_variant 174/1446 12/1176 4/391 A gcA/gcC 1 1 ALLC HGNC HGNC:17377 protein_coding YES CCDS46223.1 ENSP00000252505 B4DY77 UPI000050BBEF NM_018436.3 2/12 hmmpanther:PTHR12045,TIGRFAM_domain:TIGR02961,PIRSF_domain:PIRSF016516,Gene3D:2.60.120.260,Superfamily_domains:SSF49785 LOW 1 SNV 1 1 PASS rs975746309 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 3671169 3671169 A C 1 0 0 0 0 0 0 0 1 634 204 8 5 5 ALLC 2 3671169 Silent SNP A C3N-02423_T 66814 3671169 238522360 49 29179 KCNF1 0 . GRCh38 2 10912898 10912898 + Missense_Mutation SNP G G A rs773536391 C3N-02423_T C3N-02423_N G G c.472G>A p.Glu158Lys p.E158K ENST00000295082 1/1 237 225 12 206 206 0 strelka-varscan-mutect KCNF1,missense_variant,p.Glu158Lys,ENST00000295082,NM_002236.4; A ENST00000295082 Transcript missense_variant 962/2289 472/1485 158/494 E/K Gag/Aag rs773536391,COSM1751977,COSM381466 1 1 KCNF1 HGNC HGNC:6246 protein_coding YES CCDS1676.1 ENSP00000295082 Q9H3M0 UPI000012DC98 NM_002236.4 tolerated(0.6) 1/1 hmmpanther:PTHR11537,hmmpanther:PTHR11537:SF132 0,1,1 MODERATE 1 SNV 0,1,1 1 PASS rs773536391 . 0 208 0 2 0 0 0 0 -14.13442 0.9999993 1 1 1 0 A 3 1 99 10912898 10912898 G A 1 0 0 0 0 1 0 0 0 7943 1059 37 1 1 KCNF1 2 10912898 Missense_Mutation SNP G C3N-02423_T 7241729 10912898 231280631 50 29180 APOB 0 . GRCh38 2 21011677 21011677 + Frame_Shift_Del DEL C C - rs754640467 C3N-02423_T C3N-02423_N C C c.5191delG p.Val1731SerfsTer12 p.V1731Sfs*12 ENST00000233242 26/29 234 201 33 283 283 0 sindel-varindel-pindel APOB,frameshift_variant,p.Val1731SerfsTer12,ENST00000233242,NM_000384.2; - ENST00000233242 Transcript frameshift_variant 5319/14121 5191/13692 1731/4563 V/X Gtc/tc rs754640467 1 -1 APOB HGNC HGNC:603 protein_coding YES CCDS1703.1 ENSP00000233242 P04114 UPI0004620B75 NM_000384.2 26/29 hmmpanther:PTHR13769,hmmpanther:PTHR13769:SF1 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 99 21011677 21011677 C - 1 0 1 0 1 0 0 0 0 907 507 18 0 0 APOB 2 21011677 Frame_Shift_Del DEL C C3N-02423_T 10098779 21011677 221181852 51 29181 ABHD1 0 . GRCh38 2 27129553 27129553 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.544G>A p.Glu182Lys p.E182K ENST00000316470 5/9 333 315 18 330 330 0 strelka-varscan ABHD1,missense_variant,p.Glu182Lys,ENST00000316470,NM_032604.3;ABHD1,missense_variant,p.Glu182Lys,ENST00000621324,;ABHD1,missense_variant,p.Glu119Lys,ENST00000416071,;PREB,downstream_gene_variant,,ENST00000260643,NM_013388.4;PREB,downstream_gene_variant,,ENST00000406567,;PREB,downstream_gene_variant,,ENST00000456259,;PREB,downstream_gene_variant,,ENST00000430533,;PREB,downstream_gene_variant,,ENST00000416802,;ABHD1,missense_variant,p.Glu182Lys,ENST00000448950,;ABHD1,stop_retained_variant,p.=,ENST00000420647,;ABHD1,non_coding_transcript_exon_variant,,ENST00000489120,;ABHD1,downstream_gene_variant,,ENST00000622011,;PREB,downstream_gene_variant,,ENST00000468045,;PREB,downstream_gene_variant,,ENST00000444452,;PREB,downstream_gene_variant,,ENST00000474802,;ABHD1,upstream_gene_variant,,ENST00000496739,;PREB,downstream_gene_variant,,ENST00000441451,; A ENST00000316470 Transcript missense_variant 658/1400 544/1218 182/405 E/K Gag/Aag 1 1 ABHD1 HGNC HGNC:17553 protein_coding YES CCDS1736.1 ENSP00000326491 Q96SE0 A0A140VJD1 UPI000006D45E NM_032604.3 deleterious(0.01) 5/9 hmmpanther:PTHR10794,hmmpanther:PTHR10794:SF60,PIRSF_domain:PIRSF005211,Gene3D:3.40.50.1820,Pfam_domain:PF00561,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 27129553 27129553 G A 1 0 0 0 0 1 0 0 0 77 943 33 3 3 ABHD1 2 27129553 Missense_Mutation SNP G C3N-02423_T 6117876 27129553 215063976 52 29182 CAD 0 . GRCh38 2 27236755 27236755 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.4321G>A p.Gly1441Ser p.G1441S ENST00000264705 27/44 290 243 47 278 277 1 strelka-varscan CAD,missense_variant,p.Gly1441Ser,ENST00000264705,NM_004341.3;CAD,missense_variant,p.Gly1378Ser,ENST00000403525,NM_001306079.1;CAD,missense_variant,p.Gly93Ser,ENST00000458503,;CAD,upstream_gene_variant,,ENST00000456311,;CAD,downstream_gene_variant,,ENST00000464159,;CAD,upstream_gene_variant,,ENST00000491461,;CAD,upstream_gene_variant,,ENST00000487239,;CAD,downstream_gene_variant,,ENST00000475695,;CAD,downstream_gene_variant,,ENST00000479002,; A ENST00000264705 Transcript missense_variant 4483/7265 4321/6678 1441/2225 G/S Ggc/Agc 1 1 CAD HGNC HGNC:1424 protein_coding YES CCDS1742.1 ENSP00000264705 P27708 UPI000013D558 NM_004341.3 tolerated(0.6) 27/44 Gene3D:3.40.50.1380,hmmpanther:PTHR11405,hmmpanther:PTHR11405:SF5,Superfamily_domains:SSF52335 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 27236755 27236755 G A 1 0 0 0 0 1 0 0 0 2255 1000 35 3 3 CAD 2 27236755 Missense_Mutation SNP G C3N-02423_T 107202 27236755 214956774 53 29183 C2orf16 0 . GRCh38 2 27577563 27577563 + Missense_Mutation SNP G G A rs748621531 C3N-02423_T C3N-02423_N G G c.991G>A p.Glu331Lys p.E331K ENST00000408964 1/1 229 215 14 271 271 0 strelka-varscan C2orf16,missense_variant,p.Glu331Lys,ENST00000408964,NM_032266.3; A ENST00000408964 Transcript missense_variant 1042/6199 991/5955 331/1984 E/K Gaa/Aaa rs748621531,COSM1019754,COSM1019755,COSM279369 1 1 C2orf16 HGNC HGNC:25275 protein_coding YES CCDS42666.1 ENSP00000386190 Q68DN1 UPI0000D61179 NM_032266.3 tolerated(0.21) 1/1 hmmpanther:PTHR33888 0,1,1,1 MODERATE 1 SNV 0,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 27577563 27577563 G A 1 0 0 0 0 1 0 0 0 2032 943 33 3 3 C2orf16 2 27577563 Missense_Mutation SNP G C3N-02423_T 340808 27577563 214615966 54 29184 BIRC6 0 . GRCh38 2 32401294 32401294 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1166C>A p.Ser389Tyr p.S389Y ENST00000421745 7/74 371 339 32 370 370 0 strelka-varscan BIRC6,missense_variant,p.Ser389Tyr,ENST00000421745,NM_016252.3;BIRC6,non_coding_transcript_exon_variant,,ENST00000466527,; A ENST00000421745 Transcript missense_variant 1300/15703 1166/14574 389/4857 S/Y tCt/tAt 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 deleterious(0.01) 7/74 Gene3D:2.130.10.10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 32401294 32401294 C A 1 0 0 0 0 1 0 0 0 1589 913 32 2 2 BIRC6 2 32401294 Missense_Mutation SNP C C3N-02423_T 4823731 32401294 209792235 55 29185 BIRC6 0 . GRCh38 2 32401524 32401524 + Nonsense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1319C>G p.Ser440Ter p.S440* ENST00000421745 8/74 206 192 14 191 191 0 strelka-varscan BIRC6,stop_gained,p.Ser440Ter,ENST00000421745,NM_016252.3;BIRC6,downstream_gene_variant,,ENST00000466527,; G ENST00000421745 Transcript stop_gained 1453/15703 1319/14574 440/4857 S/* tCa/tGa 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 8/74 hmmpanther:PTHR10044,hmmpanther:PTHR10044:SF123 HIGH 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -17.69936 0.9999996 1 1 1 0 G 4 3 99 32401524 32401524 C G 1 0 0 0 0 0 1 0 0 1589 838 29 4 4 BIRC6 2 32401524 Nonsense_Mutation SNP C C3N-02423_T 230 32401524 209792005 56 29186 LTBP1 0 . GRCh38 2 33365416 33365416 + Missense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.4624G>T p.Gly1542Cys p.G1542C ENST00000404816 31/34 329 289 40 306 306 0 strelka-varscan LTBP1,missense_variant,p.Gly1542Cys,ENST00000404816,NM_206943.2;LTBP1,missense_variant,p.Gly1174Cys,ENST00000418533,NM_001166266.1,NM_001166264.1;LTBP1,missense_variant,p.Gly1163Cys,ENST00000404525,NM_001166265.1;LTBP1,missense_variant,p.Gly1216Cys,ENST00000407925,NM_000627.3;LTBP1,missense_variant,p.Gly1161Cys,ENST00000402934,;LTBP1,downstream_gene_variant,,ENST00000422669,; T ENST00000404816 Transcript missense_variant 4977/6333 4624/5166 1542/1721 G/C Ggc/Tgc COSM1649782,COSM40832,COSM4699459,COSM4699460,COSM574827 1 1 LTBP1 HGNC HGNC:6714 protein_coding YES CCDS33177.2 ENSP00000386043 Q14766 UPI000173A4A4 NM_206943.2 deleterious(0) 31/34 Gene3D:3.90.290.10,Pfam_domain:PF00683,PROSITE_profiles:PS51364,hmmpanther:PTHR24034,hmmpanther:PTHR24034:SF39,Superfamily_domains:SSF57581 1,1,1,1,1 MODERATE 1 SNV 5 1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 33365416 33365416 G T 1 0 0 0 0 1 0 0 0 8979 1232 43 2 2 LTBP1 2 33365416 Missense_Mutation SNP G C3N-02423_T 963892 33365416 208828113 57 29187 SOS1 0 . GRCh38 2 39022678 39022678 + Missense_Mutation SNP C C T rs771878514 C3N-02423_T C3N-02423_N C C c.1750G>A p.Glu584Lys p.E584K ENST00000426016 11/24 321 300 21 328 328 0 strelka-varscan SOS1,missense_variant,p.Glu584Lys,ENST00000426016,;SOS1,missense_variant,p.Glu584Lys,ENST00000402219,NM_005633.3;SOS1,missense_variant,p.Glu584Lys,ENST00000395038,;SOS1,downstream_gene_variant,,ENST00000472480,;SOS1,downstream_gene_variant,,ENST00000461545,; T ENST00000426016 Transcript missense_variant 1837/8517 1750/4002 584/1333 E/K Gag/Aag rs771878514,COSM1020874 1 -1 SOS1 HGNC HGNC:11187 protein_coding YES CCDS1802.1 ENSP00000387784 Q07889 UPI0000135CF0 deleterious(0.02) 11/24 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF168,Superfamily_domains:0041591 0,1 MODERATE 1 SNV 2 0,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 39022678 39022678 C T 1 0 0 0 0 1 0 0 0 15258 922 32 3 3 SOS1 2 39022678 Missense_Mutation SNP C C3N-02423_T 5657262 39022678 203170851 58 29188 NRXN1 0 . GRCh38 2 51027787 51027787 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.487C>G p.Arg163Gly p.R163G ENST00000404971 2/24 178 154 24 214 213 1 strelka-varscan NRXN1,missense_variant,p.Arg163Gly,ENST00000406316,NM_004801.4;NRXN1,missense_variant,p.Arg163Gly,ENST00000625672,;NRXN1,missense_variant,p.Arg163Gly,ENST00000404971,NM_001135659.1;NRXN1,missense_variant,p.Arg163Gly,ENST00000401669,;NRXN1,missense_variant,p.Arg163Gly,ENST00000405472,;NRXN1,missense_variant,p.Arg163Gly,ENST00000405581,;NRXN1,missense_variant,p.Arg163Gly,ENST00000630543,;NRXN1,missense_variant,p.Arg163Gly,ENST00000637511,;NRXN1,missense_variant,p.Arg163Gly,ENST00000628515,;NRXN1,missense_variant,p.Arg16Gly,ENST00000636066,;NRXN1,missense_variant,p.Arg163Gly,ENST00000626899,;NRXN1,missense_variant,p.Arg5Gly,ENST00000496792,;NRXN1,upstream_gene_variant,,ENST00000627198,;AC007682.1,upstream_gene_variant,,ENST00000440698,;NRXN1,downstream_gene_variant,,ENST00000635310,;NRXN1,downstream_gene_variant,,ENST00000635126,;NRXN1,downstream_gene_variant,,ENST00000636599,;NRXN1,upstream_gene_variant,,ENST00000637679,;NRXN1,downstream_gene_variant,,ENST00000638060,;NRXN1,downstream_gene_variant,,ENST00000637006,; C ENST00000404971 Transcript missense_variant 1827/7578 487/4644 163/1547 R/G Cgc/Ggc 1 -1 NRXN1 HGNC HGNC:8008 protein_coding YES CCDS46282.1 ENSP00000385142 Q9ULB1 UPI00015A218A NM_001135659.1 tolerated(0.07) 2/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,SMART_domains:SM00282,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 51027787 51027787 G C 1 0 0 0 0 1 0 0 0 10724 1087 38 4 4 NRXN1 2 51027787 Missense_Mutation SNP G C3N-02423_T 12005109 51027787 191165742 59 29189 AFTPH 0 . GRCh38 2 64551659 64551659 + Nonsense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.185C>G p.Ser62Ter p.S62* ENST00000238855 2/10 178 166 12 164 164 0 strelka-varscan AFTPH,stop_gained,p.Ser62Ter,ENST00000238855,NM_203437.3;AFTPH,stop_gained,p.Ser62Ter,ENST00000238856,NM_001002243.2,NM_017657.4;AFTPH,stop_gained,p.Ser62Ter,ENST00000409933,;AFTPH,upstream_gene_variant,,ENST00000409183,;AC008074.1,downstream_gene_variant,,ENST00000623932,;AFTPH,non_coding_transcript_exon_variant,,ENST00000498706,;AFTPH,upstream_gene_variant,,ENST00000487769,; G ENST00000238855 Transcript stop_gained 525/4113 185/2811 62/936 S/* tCa/tGa 1 1 AFTPH HGNC HGNC:25951 protein_coding YES CCDS46303.1 ENSP00000238855 Q6ULP2 UPI00003E1F8E NM_203437.3 2/10 hmmpanther:PTHR16156:SF9,hmmpanther:PTHR16156 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 99 64551659 64551659 C G 1 0 0 0 0 0 1 0 0 441 838 29 4 4 AFTPH 2 64551659 Nonsense_Mutation SNP C C3N-02423_T 13523872 64551659 177641870 60 29190 CLEC4F 0 . GRCh38 2 70816773 70816773 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.608G>T p.Ser203Ile p.S203I ENST00000272367 4/7 292 245 47 277 277 0 strelka-varscan CLEC4F,missense_variant,p.Ser203Ile,ENST00000272367,NM_001258027.1,NM_173535.2;CLEC4F,missense_variant,p.Ser203Ile,ENST00000426626,; A ENST00000272367 Transcript missense_variant 685/2475 608/1770 203/589 S/I aGc/aTc 1 -1 CLEC4F HGNC HGNC:25357 protein_coding YES CCDS1910.1 ENSP00000272367 Q8N1N0 UPI0000376BCC NM_001258027.1,NM_173535.2 deleterious(0.04) 4/7 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 70816773 70816773 C A 1 0 0 0 0 1 0 0 0 3284 797 28 2 2 CLEC4F 2 70816773 Missense_Mutation SNP C C3N-02423_T 6265114 70816773 171376756 61 29191 CD207 0 . GRCh38 2 70835755 70835755 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.22C>A p.Pro8Thr p.P8T ENST00000410009 1/6 393 326 67 403 402 1 strelka-varscan CD207,missense_variant,p.Pro8Thr,ENST00000410009,NM_015717.4; T ENST00000410009 Transcript missense_variant 68/1869 22/987 8/328 P/T Cct/Act 1 -1 CD207 HGNC HGNC:17935 protein_coding YES CCDS74520.1 ENSP00000386378 Q9UJ71 UPI0000410F0C NM_015717.4 deleterious(0.05) 1/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 70835755 70835755 G T 1 0 0 0 0 1 0 0 0 2686 1232 43 2 2 CD207 2 70835755 Missense_Mutation SNP G C3N-02423_T 18982 70835755 171357774 62 29192 DUSP11 0 . GRCh38 2 73779919 73779919 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.197G>T p.Gly66Val p.G66V ENST00000272444 1/9 363 300 63 318 318 0 strelka-varscan DUSP11,missense_variant,p.Gly66Val,ENST00000443070,;DUSP11,missense_variant,p.Gly66Val,ENST00000272444,NM_003584.2;DUSP11,missense_variant,p.Gly17Val,ENST00000452812,;C2orf78,upstream_gene_variant,,ENST00000409561,NM_001080474.1;DUSP11,upstream_gene_variant,,ENST00000480948,;DUSP11,upstream_gene_variant,,ENST00000477458,; A ENST00000272444 Transcript missense_variant 239/1653 197/1134 66/377 G/V gGa/gTa 1 -1 DUSP11 HGNC HGNC:3066 protein_coding YES CCDS1928.2 ENSP00000272444 O75319 UPI0000EE25F4 NM_003584.2 deleterious_low_confidence(0.02) 1/9 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 73779919 73779919 C A 1 0 0 0 0 1 0 0 0 4633 855 30 2 2 DUSP11 2 73779919 Missense_Mutation SNP C C3N-02423_T 2944164 73779919 168413610 63 29193 LRRTM4 0 . GRCh38 2 76748874 76748874 + Missense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.1594C>A p.Gln532Lys p.Q532K ENST00000409093 4/4 269 247 22 288 288 0 strelka-varscan LRRTM4,missense_variant,p.Gln533Lys,ENST00000409911,;LRRTM4,missense_variant,p.Gln532Lys,ENST00000409093,NM_001282924.1;LRRTM4,missense_variant,p.Gln532Lys,ENST00000409884,NM_001134745.1; T ENST00000409093 Transcript missense_variant 1931/2247 1594/1773 532/590 Q/K Cag/Aag COSM4699334,COSM4699335 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 tolerated_low_confidence(0.17) 4/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 76748874 76748874 G T 1 0 0 0 0 1 0 0 0 8948 1357 47 2 2 LRRTM4 2 76748874 Missense_Mutation SNP G C3N-02423_T 2968955 76748874 165444655 64 29194 LRRTM1 0 . GRCh38 2 80303675 80303675 + Missense_Mutation SNP G G T rs754652013 C3N-02423_T C3N-02423_N G G c.145C>A p.Leu49Met p.L49M ENST00000295057 2/2 101 93 8 82 82 0 strelka-varscan LRRTM1,missense_variant,p.Leu49Met,ENST00000295057,;LRRTM1,missense_variant,p.Leu49Met,ENST00000409148,NM_178839.4;LRRTM1,missense_variant,p.Leu49Met,ENST00000416268,;LRRTM1,missense_variant,p.Leu49Met,ENST00000452811,;LRRTM1,missense_variant,p.Leu49Met,ENST00000415098,;CTNNA2,intron_variant,,ENST00000466387,;CTNNA2,intron_variant,,ENST00000496558,NM_004389.3,NM_001282598.1;CTNNA2,intron_variant,,ENST00000402739,NM_001282597.2;CTNNA2,intron_variant,,ENST00000629316,NM_001164883.1;CTNNA2,upstream_gene_variant,,ENST00000541047,NM_001282600.1;CTNNA2,upstream_gene_variant,,ENST00000493024,;LRRTM1,missense_variant,p.Leu49Met,ENST00000433224,;LRRTM1,missense_variant,p.Leu49Met,ENST00000417012,; T ENST00000295057 Transcript missense_variant 802/2599 145/1569 49/522 L/M Ctg/Atg rs754652013 1 -1 LRRTM1 HGNC HGNC:19408 protein_coding YES CCDS1966.1 ENSP00000295057 Q86UE6 UPI000013E1FE tolerated(0.21) 2/2 Gene3D:3.80.10.10,hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF3,Superfamily_domains:SSF52058 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -16.69741 1 1 1 1 0 T 3 4 99 80303675 80303675 G T 1 0 0 0 0 1 0 0 0 8945 962 34 2 2 LRRTM1 2 80303675 Missense_Mutation SNP G C3N-02423_T 3554801 80303675 161889854 65 29195 IL1RL1 0 . GRCh38 2 102338882 102338882 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.107G>A p.Cys36Tyr p.C36Y ENST00000233954 3/11 224 181 43 215 215 0 strelka-varscan IL1RL1,missense_variant,p.Cys36Tyr,ENST00000311734,NM_003856.3;IL1RL1,missense_variant,p.Cys36Tyr,ENST00000409584,;IL1RL1,missense_variant,p.Cys36Tyr,ENST00000233954,NM_016232.4;IL1RL1,missense_variant,p.Cys36Tyr,ENST00000447231,;IL1RL1,intron_variant,,ENST00000404917,NM_001282408.1;IL18R1,intron_variant,,ENST00000410040,;IL1RL1,non_coding_transcript_exon_variant,,ENST00000473175,;IL1RL1,non_coding_transcript_exon_variant,,ENST00000482701,;IL1RL1,missense_variant,p.Cys36Tyr,ENST00000427077,;IL1RL1,non_coding_transcript_exon_variant,,ENST00000463990,; A ENST00000233954 Transcript missense_variant 378/2058 107/1671 36/556 C/Y tGt/tAt 1 1 IL1RL1 HGNC HGNC:5998 protein_coding YES CCDS2057.1 ENSP00000233954 Q01638 UPI000013C992 NM_016232.4 deleterious(0) 3/11 Gene3D:2.60.40.10,Pfam_domain:PF07679,Prints_domain:PR01536,PROSITE_profiles:PS50835,hmmpanther:PTHR11890,hmmpanther:PTHR11890:SF7,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 102338882 102338882 G A 1 0 0 0 0 1 0 0 0 7566 1377 48 3 3 IL1RL1 2 102338882 Missense_Mutation SNP G C3N-02423_T 22035207 102338882 139854647 66 29196 SLC5A7 0 . GRCh38 2 107997988 107997988 + Splice_Site SNP T T C novel C3N-02423_T C3N-02423_N T T c.597+2T>C p.X199_splice ENST00000264047 100 90 10 74 74 0 strelka-varscan SLC5A7,splice_donor_variant,,ENST00000264047,NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3;SLC5A7,splice_donor_variant,,ENST00000409059,; C ENST00000264047 Transcript splice_donor_variant -/5152 597/1743 199/580 1 1 SLC5A7 HGNC HGNC:14025 protein_coding YES CCDS2074.1 ENSP00000264047 Q9GZV3 UPI0000070792 NM_001305006.1,NM_001305007.1,NM_001305005.1,NM_021815.3 5/8 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.94333 1 1 1 1 0 C 5 2 99 107997988 107997988 T C 1 0 0 0 0 0 0 1 0 14953 1652 57 5 5 SLC5A7 2 107997988 Splice_Site SNP T C3N-02423_T 5659106 107997988 134195541 67 29197 AMER3 0 . GRCh38 2 130763048 130763048 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.976G>A p.Gly326Ser p.G326S ENST00000423981 2/2 216 204 12 225 225 0 strelka-varscan AMER3,missense_variant,p.Gly326Ser,ENST00000423981,NM_001105193.1,NM_001105195.1,NM_001105194.1;AMER3,missense_variant,p.Gly326Ser,ENST00000321420,NM_152698.2;AMER3,downstream_gene_variant,,ENST00000458606,;AMER3,downstream_gene_variant,,ENST00000431758,; A ENST00000423981 Transcript missense_variant 1086/6172 976/2586 326/861 G/S Ggc/Agc 1 1 AMER3 HGNC HGNC:26771 protein_coding YES CCDS2164.1 ENSP00000392700 Q8N944 UPI0000D61239 NM_001105193.1,NM_001105195.1,NM_001105194.1 tolerated(0.1) 2/2 hmmpanther:PTHR22237,hmmpanther:PTHR22237:SF2,Pfam_domain:PF09422 MODERATE 1 SNV 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 130763048 130763048 G A 1 0 0 0 0 1 0 0 0 669 1000 35 3 3 AMER3 2 130763048 Missense_Mutation SNP G C3N-02423_T 22765060 130763048 111430481 68 29198 XIRP2 0 . GRCh38 2 167245149 167245149 + Missense_Mutation SNP G G C rs751292919 C3N-02423_T C3N-02423_N G G c.3757G>C p.Glu1253Gln p.E1253Q ENST00000409195 9/11 191 176 15 219 219 0 strelka-varscan XIRP2,missense_variant,p.Glu1253Gln,ENST00000409195,NM_152381.5;XIRP2,missense_variant,p.Glu1031Gln,ENST00000409273,NM_001199144.1;XIRP2,missense_variant,p.Glu1078Gln,ENST00000628543,;XIRP2,intron_variant,,ENST00000409728,NM_001199143.1;XIRP2,intron_variant,,ENST00000409043,NM_001079810.3;XIRP2,intron_variant,,ENST00000409605,NM_001199145.1;XIRP2,upstream_gene_variant,,ENST00000295237,; C ENST00000409195 Transcript missense_variant 3846/12675 3757/10650 1253/3549 E/Q Gaa/Caa rs751292919 1 1 XIRP2 HGNC HGNC:14303 protein_coding YES CCDS42769.1 ENSP00000386840 A4UGR9 UPI0000E9BBED NM_152381.5 deleterious(0.01) 9/11 hmmpanther:PTHR22591,hmmpanther:PTHR22591:SF1 MODERATE 1 SNV 5 1 PASS . . 0 196 0 5 7 0 0 0 -5.075801 0.08496754 1 1 0 0 C 3 2 99 167245149 167245149 G C 1 0 0 0 0 1 0 0 0 17989 943 33 4 4 XIRP2 2 167245149 Missense_Mutation SNP G C3N-02423_T 36482101 167245149 74948380 69 29199 ABCB11 0 . GRCh38 2 168935363 168935363 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.2877C>T p.= p.F959F ENST00000263817 23/28 164 154 10 168 168 0 strelka-varscan ABCB11,synonymous_variant,p.=,ENST00000263817,NM_003742.2;ABCB11,3_prime_UTR_variant,,ENST00000439188,; A ENST00000263817 Transcript synonymous_variant 3002/4775 2877/3966 959/1321 F ttC/ttT 1 -1 ABCB11 HGNC HGNC:42 protein_coding YES CCDS46444.1 ENSP00000263817 O95342 UPI0000163BFA NM_003742.2 23/28 PROSITE_profiles:PS50929,hmmpanther:PTHR24221:SF165,hmmpanther:PTHR24221,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 168935363 168935363 G A 1 0 0 0 0 0 0 0 1 46 1281 45 3 3 ABCB11 2 168935363 Silent SNP G C3N-02423_T 1690214 168935363 73258166 70 29200 TLK1 0 . GRCh38 2 171006537 171006537 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1705G>A p.Val569Ile p.V569I ENST00000431350 17/21 155 147 8 166 166 0 strelka-varscan TLK1,missense_variant,p.Val590Ile,ENST00000360843,;TLK1,missense_variant,p.Val569Ile,ENST00000431350,NM_012290.4;TLK1,missense_variant,p.Val521Ile,ENST00000521943,NM_001136554.1;TLK1,missense_variant,p.Val473Ile,ENST00000434911,NM_001136555.1;TLK1,3_prime_UTR_variant,,ENST00000359766,;TLK1,3_prime_UTR_variant,,ENST00000409443,; T ENST00000431350 Transcript missense_variant 2110/5663 1705/2301 569/766 V/I Gta/Ata 1 -1 TLK1 HGNC HGNC:11841 protein_coding YES CCDS2241.1 ENSP00000411099 Q9UKI8 UPI0000073255 NM_012290.4 deleterious(0.03) 17/21 Gene3D:1.10.510.10,Pfam_domain:PF00069,PROSITE_profiles:PS50011,hmmpanther:PTHR22974,hmmpanther:PTHR22974:SF22,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 171006537 171006537 C T 1 0 0 0 0 1 0 0 0 16389 478 17 3 3 TLK1 2 171006537 Missense_Mutation SNP C C3N-02423_T 2071174 171006537 71186992 71 29201 TTN 0 . GRCh38 2 178645930 178645930 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.40398C>A p.Phe13466Leu p.F13466L ENST00000589042 217/363 121 101 20 115 115 0 strelka-varscan TTN,missense_variant,p.Phe13466Leu,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Phe11825Leu,ENST00000591111,;TTN,missense_variant,p.Phe11825Leu,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Phe10898Leu,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Phe305Leu,ENST00000446966,;TTN,missense_variant,p.Phe173Leu,ENST00000426232,;TTN,intron_variant,,ENST00000460472,NM_003319.4;TTN,intron_variant,,ENST00000342175,NM_133437.4;TTN,intron_variant,,ENST00000359218,NM_133432.3;TTN,intron_variant,,ENST00000414766,;RP11-171I2.3,downstream_gene_variant,,ENST00000605021,;TTN-AS1,intron_variant,,ENST00000589487,;TTN-AS1,intron_variant,,ENST00000585451,;TTN-AS1,intron_variant,,ENST00000625536,;TTN-AS1,intron_variant,,ENST00000592630,;TTN-AS1,intron_variant,,ENST00000625480,;TTN-AS1,intron_variant,,ENST00000431752,;TTN-AS1,intron_variant,,ENST00000626117,;TTN-AS1,intron_variant,,ENST00000589830,;TTN-AS1,downstream_gene_variant,,ENST00000590807,;TTN-AS1,downstream_gene_variant,,ENST00000628826,;TTN-AS1,downstream_gene_variant,,ENST00000418062,; T ENST00000589042 Transcript missense_variant 40623/109224 40398/107976 13466/35991 F/L ttC/ttA 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 217/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE 1 SNV 5 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 178645930 178645930 G T 1 0 0 0 0 1 0 0 0 17245 1165 41 2 2 TTN 2 178645930 Missense_Mutation SNP G C3N-02423_T 7639393 178645930 63547599 72 29202 TTN 0 . GRCh38 2 178775665 178775665 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.6199G>C p.Asp2067His p.D2067H ENST00000589042 28/363 457 419 38 469 468 1 strelka-varscan TTN,missense_variant,p.Asp2067His,ENST00000589042,NM_001267550.2;TTN,missense_variant,p.Asp2067His,ENST00000591111,;TTN,missense_variant,p.Asp2067His,ENST00000615779,NM_001256850.1;TTN,missense_variant,p.Asp2067His,ENST00000342992,NM_133378.4;TTN,missense_variant,p.Asp2021His,ENST00000460472,NM_003319.4;TTN,missense_variant,p.Asp2021His,ENST00000342175,NM_133437.4;TTN,missense_variant,p.Asp2021His,ENST00000359218,NM_133432.3;TTN,missense_variant,p.Asp2067His,ENST00000360870,NM_133379.4;TTN-AS1,intron_variant,,ENST00000629094,;TTN-AS1,upstream_gene_variant,,ENST00000582038,;TTN-AS1,downstream_gene_variant,,ENST00000585451,;TTN-AS1,downstream_gene_variant,,ENST00000584485,;TTN-AS1,downstream_gene_variant,,ENST00000610005,; G ENST00000589042 Transcript missense_variant 6424/109224 6199/107976 2067/35991 D/H Gac/Cac 1 -1 TTN HGNC HGNC:12403 protein_coding YES CCDS59435.1 ENSP00000467141 A0A0A0MTS7 UPI00046209C6 NM_001267550.2 28/363 hmmpanther:PTHR13817,hmmpanther:PTHR13817:SF10 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 178775665 178775665 C G 1 0 0 0 0 1 0 0 0 17245 826 29 4 4 TTN 2 178775665 Missense_Mutation SNP C C3N-02423_T 129735 178775665 63417864 73 29203 FAM171B 0 . GRCh38 2 186753961 186753961 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.924G>T p.Met308Ile p.M308I ENST00000304698 6/8 281 242 39 268 268 0 strelka-varscan FAM171B,missense_variant,p.Met308Ile,ENST00000304698,NM_177454.3;FAM171B,downstream_gene_variant,,ENST00000612606,; T ENST00000304698 Transcript missense_variant 1127/5826 924/2481 308/826 M/I atG/atT 1 1 FAM171B HGNC HGNC:29412 protein_coding YES CCDS33347.1 ENSP00000304108 Q6P995 UPI0000161631 NM_177454.3 tolerated(1) 6/8 hmmpanther:PTHR31626:SF2,hmmpanther:PTHR31626,Pfam_domain:PF10577 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 186753961 186753961 G T 1 0 0 0 0 1 0 0 0 5339 1348 47 2 2 FAM171B 2 186753961 Missense_Mutation SNP G C3N-02423_T 7978296 186753961 55439568 74 29204 DNAH7 0 . GRCh38 2 195960858 195960858 + Missense_Mutation SNP G G A rs759132556 C3N-02423_T C3N-02423_N G G c.2293C>T p.Pro765Ser p.P765S ENST00000312428 18/65 108 92 16 95 95 0 strelka-varscan-mutect DNAH7,missense_variant,p.Pro765Ser,ENST00000312428,NM_018897.2; A ENST00000312428 Transcript missense_variant 2394/12394 2293/12075 765/4024 P/S Cct/Tct rs759132556 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0) 18/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Pfam_domain:PF08393 MODERATE 1 SNV 1 1 PASS rs759132556 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 195960858 195960858 G A 1 0 0 0 0 1 0 0 0 4421 1232 43 3 3 DNAH7 2 195960858 Missense_Mutation SNP G C3N-02423_T 9206897 195960858 46232671 75 29205 TRAK2 0 . GRCh38 2 201380798 201380798 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.2490G>A p.= p.L830L ENST00000332624 16/16 470 446 24 449 448 1 strelka-varscan-mutect TRAK2,synonymous_variant,p.=,ENST00000332624,NM_015049.2; T ENST00000332624 Transcript synonymous_variant 2919/6510 2490/2745 830/914 L ttG/ttA 1 -1 TRAK2 HGNC HGNC:13206 protein_coding YES CCDS2347.1 ENSP00000328875 O60296 UPI0000125022 NM_015049.2 16/16 hmmpanther:PTHR15751,hmmpanther:PTHR15751:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 201380798 201380798 C T 1 0 0 0 0 0 0 0 1 16933 825 29 3 3 TRAK2 2 201380798 Silent SNP C C3N-02423_T 5419940 201380798 40812731 76 29206 PIKFYVE 0 . GRCh38 2 208326076 208326076 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.3265C>T p.Pro1089Ser p.P1089S ENST00000264380 20/42 263 245 18 253 253 0 strelka-varscan-mutect PIKFYVE,missense_variant,p.Pro1089Ser,ENST00000264380,NM_015040.3;PIKFYVE,missense_variant,p.Pro1033Ser,ENST00000452564,;PIKFYVE,3_prime_UTR_variant,,ENST00000443896,; T ENST00000264380 Transcript missense_variant 3423/9901 3265/6297 1089/2098 P/S Cct/Tct 1 1 PIKFYVE HGNC HGNC:23785 protein_coding YES CCDS2382.1 ENSP00000264380 Q9Y2I7 UPI0000366FD6 NM_015040.3 deleterious(0.01) 20/42 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 208326076 208326076 C T 1 0 0 0 0 1 0 0 0 12019 855 30 3 3 PIKFYVE 2 208326076 Missense_Mutation SNP C C3N-02423_T 6945278 208326076 33867453 77 29207 MAP2 0 . GRCh38 2 209693278 209693278 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1108G>A p.Glu370Lys p.E370K ENST00000360351 7/15 241 225 16 214 214 0 strelka-varscan-mutect MAP2,missense_variant,p.Glu370Lys,ENST00000360351,NM_002374.3;MAP2,missense_variant,p.Glu366Lys,ENST00000447185,;MAP2,missense_variant,p.Glu452Lys,ENST00000445941,;MAP2,intron_variant,,ENST00000392194,NM_031845.2;MAP2,intron_variant,,ENST00000199940,NM_001039538.1,NM_031847.2;MAP2,intron_variant,,ENST00000361559,;MAP2,intron_variant,,ENST00000452717,;MAP2,intron_variant,,ENST00000471619,;MAP2,intron_variant,,ENST00000482864,;MAP2,upstream_gene_variant,,ENST00000475600,;MAP2,downstream_gene_variant,,ENST00000461253,;MAP2,downstream_gene_variant,,ENST00000481649,; A ENST00000360351 Transcript missense_variant 1614/9711 1108/5484 370/1827 E/K Gag/Aag 1 1 MAP2 HGNC HGNC:6839 protein_coding YES CCDS2384.1 ENSP00000353508 P11137 A0A024R407 UPI000013D119 NM_002374.3 tolerated_low_confidence(0.14) 7/15 hmmpanther:PTHR11501,hmmpanther:PTHR11501:SF15 MODERATE 1 SNV 5 1 PASS rs1422571918 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 209693278 209693278 G A 1 0 0 0 0 1 0 0 0 9157 943 33 3 3 MAP2 2 209693278 Missense_Mutation SNP G C3N-02423_T 1367202 209693278 32500251 78 29208 PAX3 0 . GRCh38 2 222297173 222297173 + Silent SNP G G T rs369680052 C3N-02423_T C3N-02423_N G G c.126C>A p.= p.G42G ENST00000392069 2/10 482 403 79 383 383 0 strelka-varscan-mutect PAX3,synonymous_variant,p.=,ENST00000350526,NM_181457.3;PAX3,synonymous_variant,p.=,ENST00000392069,NM_181459.3;PAX3,synonymous_variant,p.=,ENST00000344493,NM_181461.3;PAX3,synonymous_variant,p.=,ENST00000392070,NM_181458.3;PAX3,synonymous_variant,p.=,ENST00000336840,NM_181460.3;PAX3,synonymous_variant,p.=,ENST00000409551,NM_001127366.2;PAX3,synonymous_variant,p.=,ENST00000409828,NM_000438.5;PAX3,synonymous_variant,p.=,ENST00000258387,NM_013942.4;CCDC140,upstream_gene_variant,,ENST00000295226,NM_153038.1; T ENST00000392069 Transcript synonymous_variant 492/3170 126/1518 42/505 G ggC/ggA rs369680052,COSM4711349,COSM4711350,COSM4711351,COSM4711352 1 -1 PAX3 HGNC HGNC:8617 protein_coding YES CCDS2448.1 ENSP00000375921 P23760 UPI00001A8BF0 NM_181459.3 2/10 Gene3D:1.10.10.10,Pfam_domain:PF00292,Prints_domain:PR00027,PROSITE_profiles:PS51057,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF307,SMART_domains:SM00351,Superfamily_domains:SSF46689 0,1,1,1,1 LOW SNV 5 0,1,1,1,1 1 PASS rs369680052 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 222297173 222297173 G T 1 0 0 0 0 0 0 0 1 11565 1074 38 1 1 PAX3 2 222297173 Silent SNP G C3N-02423_T 12603895 222297173 19896356 79 29209 DNER 0 . GRCh38 2 229447422 229447422 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1380C>T p.= p.F460F ENST00000341772 8/13 352 331 21 344 344 0 strelka-varscan-mutect DNER,synonymous_variant,p.=,ENST00000341772,NM_139072.3; A ENST00000341772 Transcript synonymous_variant 1515/3260 1380/2214 460/737 F ttC/ttT 1 -1 DNER HGNC HGNC:24456 protein_coding YES CCDS33390.1 ENSP00000345229 Q8NFT8 UPI0000048EB8 NM_139072.3 8/13 PROSITE_profiles:PS50026,hmmpanther:PTHR24044:SF275,hmmpanther:PTHR24044,PROSITE_patterns:PS01186,PROSITE_patterns:PS00022,Gene3D:2.10.25.10,Pfam_domain:PF00008,SMART_domains:SM00181,SMART_domains:SM00179,Superfamily_domains:SSF57184 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 229447422 229447422 G A 1 0 0 0 0 0 0 0 1 4480 1281 45 3 3 DNER 2 229447422 Silent SNP G C3N-02423_T 7150249 229447422 12746107 80 29210 TRIP12 0 . GRCh38 2 229771524 229771524 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.5722G>A p.Glu1908Lys p.E1908K ENST00000389044 39/42 158 150 8 151 151 0 strelka-mutect TRIP12,missense_variant,p.Glu1860Lys,ENST00000283943,NM_001284215.1,NM_004238.2;TRIP12,missense_variant,p.Glu1908Lys,ENST00000389044,NM_001284214.1;TRIP12,missense_variant,p.Glu1590Lys,ENST00000389045,NM_001284216.1;TRIP12,intron_variant,,ENST00000418123,;TRIP12,downstream_gene_variant,,ENST00000459841,; T ENST00000389044 Transcript missense_variant 5891/6405 5722/6123 1908/2040 E/K Gag/Aag 1 -1 TRIP12 HGNC HGNC:12306 protein_coding YES CCDS63146.1 ENSP00000373696 Q14669 UPI0000DA6BE7 NM_001284214.1 deleterious(0.01) 39/42 Pfam_domain:PF00632,PROSITE_profiles:PS50237,hmmpanther:PTHR11254,hmmpanther:PTHR11254:SF73,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -10.75021 0.9999993 1 1 1 0 T 3 4 99 229771524 229771524 C T 1 0 0 0 0 1 0 0 0 17053 869 30 3 3 TRIP12 2 229771524 Missense_Mutation SNP C C3N-02423_T 324102 229771524 12422005 81 29211 UGT1A3 0 . GRCh38 2 233729394 233729394 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.268G>A p.Asp90Asn p.D90N ENST00000482026 1/5 93 85 8 118 118 0 strelka-varscan-mutect UGT1A3,missense_variant,p.Asp90Asn,ENST00000482026,NM_019093.2;UGT1A6,intron_variant,,ENST00000305139,NM_001072.3;UGT1A9,intron_variant,,ENST00000354728,NM_021027.2;UGT1A10,intron_variant,,ENST00000344644,NM_019075.2;UGT1A8,intron_variant,,ENST00000373450,NM_019076.4;UGT1A4,intron_variant,,ENST00000373409,NM_007120.2;UGT1A5,intron_variant,,ENST00000373414,NM_019078.1;UGT1A7,intron_variant,,ENST00000373426,NM_019077.2;UGT1A10,intron_variant,,ENST00000373445,;UGT1A6,intron_variant,,ENST00000373424,NM_205862.1;UGT1A6,intron_variant,,ENST00000406651,;UGT1A6,intron_variant,,ENST00000480628,;UGT1A6,intron_variant,,ENST00000478062,;UGT1A4,intron_variant,,ENST00000450233,;UGT1A6,intron_variant,,ENST00000446481,;UGT1A6,intron_variant,,ENST00000484784,; A ENST00000482026 Transcript missense_variant 287/2364 268/1605 90/534 D/N Gat/Aat 1 1 UGT1A3 HGNC HGNC:12535 protein_coding YES CCDS2509.1 ENSP00000418532 P35503 Q5DT01 UPI0000001045 NM_019093.2 tolerated(0.26) 1/5 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF173,Pfam_domain:PF00201,Superfamily_domains:SSF53756 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -16.72634 1 1 1 1 0 A 3 1 99 233729394 233729394 G A 1 0 0 0 0 1 0 0 0 17471 1290 45 3 3 UGT1A3 2 233729394 Missense_Mutation SNP G C3N-02423_T 3957870 233729394 8464135 82 29212 CNTN4 0 . GRCh38 3 2819531 2819531 + Missense_Mutation SNP G G A rs377113483 C3N-02423_T C3N-02423_N G G c.404G>A p.Arg135His p.R135H ENST00000397461 6/24 376 346 30 421 421 0 strelka-varscan-mutect CNTN4,missense_variant,p.Arg135His,ENST00000397461,NM_001206955.1;CNTN4,missense_variant,p.Arg135His,ENST00000418658,NM_175607.2;CNTN4,missense_variant,p.Arg135His,ENST00000427331,;CNTN4,missense_variant,p.Arg135His,ENST00000427741,;CNTN4,non_coding_transcript_exon_variant,,ENST00000430505,;CNTN4,non_coding_transcript_exon_variant,,ENST00000438282,; A ENST00000397461 Transcript missense_variant 788/5198 404/3081 135/1026 R/H cGt/cAt rs377113483,COSM1537661,COSM3392328 1 1 CNTN4 HGNC HGNC:2174 protein_coding YES CCDS43041.1 ENSP00000380602 Q8IWV2 A0A024R2E5 UPI000007446C NM_001206955.1 deleterious(0.02) 6/24 Gene3D:2.60.40.10,Pfam_domain:PF13927,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF568,Low_complexity_(Seg):seg,SMART_domains:SM00409,Superfamily_domains:SSF48726 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs377113483 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 2819531 2819531 G A 1 0 0 0 0 1 0 0 0 3424 1145 40 1 1 CNTN4 3 2819531 Missense_Mutation SNP G C3N-02423_T 2819531 195476028 83 29213 PRRT3 0 . GRCh38 3 9946905 9946905 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.2268C>T p.= p.R756R ENST00000412055 4/4 303 248 55 261 261 0 strelka-varscan-mutect PRRT3,synonymous_variant,p.=,ENST00000412055,NM_207351.3;CRELD1,downstream_gene_variant,,ENST00000383811,NM_015513.4;CRELD1,downstream_gene_variant,,ENST00000326434,NM_001031717.3;CRELD1,downstream_gene_variant,,ENST00000452070,NM_001077415.2;CRELD1,downstream_gene_variant,,ENST00000397170,;PRRT3,downstream_gene_variant,,ENST00000411976,NM_001318871.1;CRELD1,downstream_gene_variant,,ENST00000435417,;PRRT3-AS1,upstream_gene_variant,,ENST00000431558,;CRELD1,downstream_gene_variant,,ENST00000489674,;PRRT3,synonymous_variant,p.=,ENST00000295984,;CRELD1,downstream_gene_variant,,ENST00000414117,;CRELD1,downstream_gene_variant,,ENST00000482691,;CRELD1,downstream_gene_variant,,ENST00000467713,; A ENST00000412055 Transcript synonymous_variant 2398/3761 2268/2946 756/981 R cgC/cgT 1 -1 PRRT3 HGNC HGNC:26591 protein_coding YES CCDS43049.1 ENSP00000392511 Q5FWE3 UPI000019962A NM_207351.3 4/4 hmmpanther:PTHR21712,hmmpanther:PTHR21712:SF27 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 9946905 9946905 G A 1 0 0 0 0 0 0 0 1 12757 1306 46 3 3 PRRT3 3 9946905 Silent SNP G C3N-02423_T 7127374 9946905 188348654 84 29214 ATG7 0 . GRCh38 3 11299364 11299364 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.163G>C p.Asp55His p.D55H ENST00000354449 3/19 246 226 20 200 200 0 strelka-varscan-mutect ATG7,missense_variant,p.Asp55His,ENST00000354449,NM_006395.2;ATG7,missense_variant,p.Asp55His,ENST00000354956,NM_001136031.2;ATG7,missense_variant,p.Asp55His,ENST00000446450,NM_001144912.1;ATG7,missense_variant,p.Asp55His,ENST00000451513,;ATG7,missense_variant,p.Asp55His,ENST00000435760,;ATG7,missense_variant,p.Asp55His,ENST00000423116,;ATG7,missense_variant,p.Asp55His,ENST00000419112,;ATG7,missense_variant,p.Asp55His,ENST00000444619,;ATG7,missense_variant,p.Asp55His,ENST00000451830,;ATG7,splice_region_variant,,ENST00000469654,;ATG7,splice_region_variant,,ENST00000460444,;ATG7,missense_variant,p.Asp55His,ENST00000418682,;ATG7,downstream_gene_variant,,ENST00000470474,; C ENST00000354449 Transcript missense_variant,splice_region_variant 188/4959 163/2112 55/703 D/H Gac/Cac 1 1 ATG7 HGNC HGNC:16935 protein_coding YES CCDS2605.1 ENSP00000346437 O95352 UPI00000705C7 NM_006395.2 tolerated(0.08) 3/19 hmmpanther:PTHR10953,hmmpanther:PTHR10953:SF3,Pfam_domain:PF16420,TIGRFAM_domain:TIGR01381 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 11299364 11299364 G C 1 0 0 0 0 1 0 0 0 1253 1304 45 4 4 ATG7 3 11299364 Missense_Mutation SNP G C3N-02423_T 1352459 11299364 186996195 85 29215 HDAC11 0 . GRCh38 3 13483561 13483561 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.249C>G p.= p.L83L ENST00000295757 3/10 154 146 8 101 101 0 strelka-varscan-mutect HDAC11,synonymous_variant,p.=,ENST00000295757,NM_024827.3;HDAC11,synonymous_variant,p.=,ENST00000446613,;HDAC11,synonymous_variant,p.=,ENST00000437379,;HDAC11,synonymous_variant,p.=,ENST00000433119,;HDAC11,synonymous_variant,p.=,ENST00000522202,NM_001136041.2;HDAC11,synonymous_variant,p.=,ENST00000402271,;HDAC11,synonymous_variant,p.=,ENST00000404040,;HDAC11,synonymous_variant,p.=,ENST00000405478,;HDAC11,synonymous_variant,p.=,ENST00000455904,;HDAC11,synonymous_variant,p.=,ENST00000416248,;HDAC11,synonymous_variant,p.=,ENST00000418189,;HDAC11,synonymous_variant,p.=,ENST00000404548,;HDAC11,synonymous_variant,p.=,ENST00000405025,;HDAC11,synonymous_variant,p.=,ENST00000434848,;HDAC11,intron_variant,,ENST00000402259,;HDAC11-AS1,upstream_gene_variant,,ENST00000424112,;HDAC11,non_coding_transcript_exon_variant,,ENST00000458642,;HDAC11,non_coding_transcript_exon_variant,,ENST00000475818,;HDAC11,non_coding_transcript_exon_variant,,ENST00000487585,;HDAC11,intron_variant,,ENST00000425430,; G ENST00000295757 Transcript synonymous_variant 432/2960 249/1044 83/347 L ctC/ctG 1 1 HDAC11 HGNC HGNC:19086 protein_coding YES CCDS2615.1 ENSP00000295757 Q96DB2 A0A024R2I1 UPI000012C3A7 NM_024827.3 3/10 Gene3D:3.40.800.20,Pfam_domain:PF00850,hmmpanther:PTHR10625,hmmpanther:PTHR10625:SF112,Superfamily_domains:SSF52768 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 13483561 13483561 C G 1 0 0 0 0 0 0 0 1 6893 840 29 4 4 HDAC11 3 13483561 Silent SNP C C3N-02423_T 2184197 13483561 184811998 86 29216 SGO1 0 . GRCh38 3 20161155 20161155 + Missense_Mutation SNP A A G rs755667806 C3N-02423_T C3N-02423_N A A c.1636T>C p.Phe546Leu p.F546L ENST00000263753 9/9 198 163 35 207 207 0 strelka-varscan-mutect SGO1,missense_variant,p.Phe546Leu,ENST00000263753,NM_001199252.1,NM_001012410.3;SGO1,missense_variant,p.Phe546Leu,ENST00000421451,;SGO1,missense_variant,p.Phe294Leu,ENST00000419233,NM_001012412.3,NM_001199254.1;SGO1,missense_variant,p.Phe277Leu,ENST00000306698,NM_001199256.1,NM_138484.3;SGO1,missense_variant,p.Phe294Leu,ENST00000425061,;SGO1,missense_variant,p.Phe277Leu,ENST00000452020,;SGO1,missense_variant,p.Phe200Leu,ENST00000443724,NM_001199257.1; G ENST00000263753 Transcript missense_variant 1776/2338 1636/1686 546/561 F/L Ttc/Ctc rs755667806 1 -1 SGO1 HGNC HGNC:25088 protein_coding YES CCDS33716.1 ENSP00000263753 Q5FBB7 UPI00004CE17A NM_001199252.1,NM_001012410.3 9/9 hmmpanther:PTHR21577,hmmpanther:PTHR21577:SF3 MODERATE 1 SNV 1 1 PASS rs755667806 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 20161155 20161155 A G 1 0 0 0 0 1 0 0 0 14474 101 4 5 5 SGO1 3 20161155 Missense_Mutation SNP A C3N-02423_T 6677594 20161155 178134404 87 29217 ZNF621 0 . GRCh38 3 40532339 40532339 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.569C>T p.Ser190Phe p.S190F ENST00000339296 5/5 331 311 20 346 346 0 strelka-varscan-mutect ZNF621,missense_variant,p.Ser190Phe,ENST00000339296,NM_198484.4;ZNF621,missense_variant,p.Ser79Phe,ENST00000431278,;ZNF621,missense_variant,p.Ser190Phe,ENST00000403205,NM_001098414.2;ZNF621,intron_variant,,ENST00000310898,NM_001287245.1;ZNF621,downstream_gene_variant,,ENST00000453351,;ZNF621,intron_variant,,ENST00000490457,;ZNF621,downstream_gene_variant,,ENST00000462161,;ZNF621,non_coding_transcript_exon_variant,,ENST00000492098,; T ENST00000339296 Transcript missense_variant 1021/6378 569/1320 190/439 S/F tCc/tTc 1 1 ZNF621 HGNC HGNC:24787 protein_coding YES CCDS2693.1 ENSP00000340841 Q6ZSS3 UPI00001C0DC3 NM_198484.4 tolerated(0.7) 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF209,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 40532339 40532339 C T 1 0 0 0 0 1 0 0 0 18620 855 30 3 3 ZNF621 3 40532339 Missense_Mutation SNP C C3N-02423_T 20371184 40532339 157763220 88 29218 LTF 0 . GRCh38 3 46437959 46437959 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.2079G>C p.= p.L693L ENST00000231751 16/17 337 316 21 343 343 0 strelka-varscan-mutect LTF,synonymous_variant,p.=,ENST00000231751,NM_002343.4;LTF,synonymous_variant,p.=,ENST00000443496,NM_001321122.1;LTF,synonymous_variant,p.=,ENST00000426532,NM_001199149.1;LTF,synonymous_variant,p.=,ENST00000417439,;LTF,downstream_gene_variant,,ENST00000493056,;LTF,downstream_gene_variant,,ENST00000478874,; G ENST00000231751 Transcript synonymous_variant 2375/2979 2079/2133 693/710 L ctG/ctC 1 -1 LTF HGNC HGNC:6720 protein_coding YES CCDS33747.1 ENSP00000231751 P02788 V9HWI4 UPI000016ABE3 NM_002343.4 16/17 PROSITE_profiles:PS51408,hmmpanther:PTHR11485:SF33,hmmpanther:PTHR11485,PIRSF_domain:PIRSF500683,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,Gene3D:3.40.190.10,SMART_domains:SM00094,Superfamily_domains:SSF53850 LOW 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -5.191398 0.9837394 1 1 1 0 G 2 3 99 46437959 46437959 C G 1 0 0 0 0 0 0 0 1 8985 813 29 4 4 LTF 3 46437959 Silent SNP C C3N-02423_T 5905620 46437959 151857600 89 29219 KIF9 0 . GRCh38 3 47271357 47271357 + Frame_Shift_Del DEL G G - novel C3N-02423_T C3N-02423_N G G c.471delC p.Tyr158MetfsTer9 p.Y158Mfs*9 ENST00000335044 5/21 382 351 31 393 393 0 varindel-pindel KIF9,frameshift_variant,p.Tyr158MetfsTer9,ENST00000335044,NM_001134878.1,NM_182902.3;KIF9,frameshift_variant,p.Tyr158MetfsTer9,ENST00000265529,;KIF9,frameshift_variant,p.Tyr158MetfsTer9,ENST00000444589,NM_022342.4;KIF9,frameshift_variant,p.Tyr158MetfsTer9,ENST00000452770,;KIF9,intron_variant,,ENST00000456548,;KIF9,downstream_gene_variant,,ENST00000425853,;KIF9,downstream_gene_variant,,ENST00000425452,;KIF9,downstream_gene_variant,,ENST00000432493,;KIF9,non_coding_transcript_exon_variant,,ENST00000487440,;KIF9,non_coding_transcript_exon_variant,,ENST00000484629,;KIF9,frameshift_variant,p.Tyr158MetfsTer9,ENST00000443784,; - ENST00000335044 Transcript frameshift_variant 829/3357 471/2373 157/790 P/X ccC/cc 1 -1 KIF9 HGNC HGNC:16666 protein_coding YES CCDS2752.1 ENSP00000333942 Q9HAQ2 UPI000012DE55 NM_001134878.1,NM_182902.3 5/21 Gene3D:3.40.850.10,Pfam_domain:PF00225,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF191,SMART_domains:SM00129,Superfamily_domains:SSF52540 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 99 47271357 47271357 G - 1 0 1 0 1 0 0 0 0 8175 987 35 0 0 KIF9 3 47271357 Frame_Shift_Del DEL G C3N-02423_T 833398 47271357 151024202 90 29220 C3orf14 0 . GRCh38 3 62321935 62321935 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.59C>T p.Ser20Leu p.S20L ENST00000494481 4/6 117 110 7 137 136 1 strelka-varscan-mutect C3orf14,missense_variant,p.Ser20Leu,ENST00000494481,NM_020685.4;C3orf14,missense_variant,p.Ser20Leu,ENST00000542214,;C3orf14,missense_variant,p.Ser20Leu,ENST00000232519,NM_001291942.1;C3orf14,missense_variant,p.Ser20Leu,ENST00000462069,NM_001291941.1;C3orf14,missense_variant,p.Ser20Leu,ENST00000465142,;PTPRG-AS1,intron_variant,,ENST00000490916,;PTPRG-AS1,intron_variant,,ENST00000495542,;PTPRG-AS1,upstream_gene_variant,,ENST00000474795,;PTPRG-AS1,upstream_gene_variant,,ENST00000462497,;PTPRG-AS1,upstream_gene_variant,,ENST00000466893,;PTPRG-AS1,upstream_gene_variant,,ENST00000475371,;PTPRG-AS1,upstream_gene_variant,,ENST00000479018,;PTPRG-AS1,upstream_gene_variant,,ENST00000498655,;C3orf14,non_coding_transcript_exon_variant,,ENST00000486169,;C3orf14,non_coding_transcript_exon_variant,,ENST00000491323,;PTPRG-AS1,upstream_gene_variant,,ENST00000479588,; T ENST00000494481 Transcript missense_variant 373/3525 59/387 20/128 S/L tCa/tTa 1 1 C3orf14 HGNC HGNC:25024 protein_coding YES CCDS2896.1 ENSP00000418086 Q9HBI5 A0A024R330 UPI00000729BA NM_020685.4 deleterious(0) 4/6 hmmpanther:PTHR14286,Pfam_domain:PF15134 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 62321935 62321935 C T 1 0 0 0 0 1 0 0 0 2059 840 29 3 3 C3orf14 3 62321935 Missense_Mutation SNP C C3N-02423_T 15050578 62321935 135973624 91 29221 CNTN3 0 . GRCh38 3 74301712 74301712 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1880C>A p.Pro627Gln p.P627Q ENST00000263665 14/22 156 135 21 195 194 1 strelka-varscan-mutect CNTN3,missense_variant,p.Pro627Gln,ENST00000263665,NM_020872.2; T ENST00000263665 Transcript missense_variant 1908/4948 1880/3087 627/1028 P/Q cCa/cAa 1 -1 CNTN3 HGNC HGNC:2173 protein_coding YES CCDS33790.1 ENSP00000263665 Q9P232 UPI00001A7974 NM_020872.2 deleterious(0) 14/22 PROSITE_profiles:PS50853,hmmpanther:PTHR10489:SF695,hmmpanther:PTHR10489,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 74301712 74301712 G T 1 0 0 0 0 1 0 0 0 3423 1348 47 2 2 CNTN3 3 74301712 Missense_Mutation SNP G C3N-02423_T 11979777 74301712 123993847 92 29222 TOMM70 0 . GRCh38 3 100400791 100400791 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.159G>T p.= p.A53A ENST00000284320 1/12 164 150 14 199 199 0 strelka-varscan-mutect TOMM70,synonymous_variant,p.=,ENST00000284320,NM_014820.4;LNP1,upstream_gene_variant,,ENST00000383693,NM_001085451.1;LNP1,upstream_gene_variant,,ENST00000489752,;LNP1,upstream_gene_variant,,ENST00000466996,; A ENST00000284320 Transcript synonymous_variant 608/4409 159/1827 53/608 A gcG/gcT 1 -1 TOMM70 HGNC HGNC:11985 protein_coding YES CCDS33807.1 ENSP00000284320 O94826 UPI0000000C55 NM_014820.4 1/12 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22904:SF375,hmmpanther:PTHR22904 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 100400791 100400791 C A 1 0 0 0 0 0 0 0 1 16837 639 23 1 1 TOMM70 3 100400791 Silent SNP C C3N-02423_T 26099079 100400791 97894768 93 29223 HHLA2 0 . GRCh38 3 108358070 108358070 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.912G>C p.Leu304Phe p.L304F ENST00000357759 6/10 175 158 17 189 189 0 strelka-varscan-mutect HHLA2,missense_variant,p.Leu304Phe,ENST00000357759,NM_007072.3;HHLA2,missense_variant,p.Leu207Phe,ENST00000482099,;HHLA2,missense_variant,p.Leu304Phe,ENST00000619531,NM_001282556.1;HHLA2,missense_variant,p.Leu304Phe,ENST00000489514,NM_001282557.1;HHLA2,missense_variant,p.Leu304Phe,ENST00000467761,;HHLA2,missense_variant,p.Leu240Phe,ENST00000467562,NM_001282559.1;HHLA2,missense_variant,p.Leu304Phe,ENST00000491820,NM_001282558.1;HHLA2,downstream_gene_variant,,ENST00000463019,;HHLA2,downstream_gene_variant,,ENST00000462629,;HHLA2,downstream_gene_variant,,ENST00000482430,;HHLA2,downstream_gene_variant,,ENST00000467282,; C ENST00000357759 Transcript missense_variant 1326/2666 912/1245 304/414 L/F ttG/ttC 1 1 HHLA2 HGNC HGNC:4905 protein_coding YES CCDS46883.1 ENSP00000350402 Q9UM44 UPI0000073CD9 NM_007072.3 deleterious(0.01) 6/10 PROSITE_profiles:PS50835,Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00406,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS rs952513353 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 108358070 108358070 G C 1 0 0 0 0 1 0 0 0 6981 1281 45 4 4 HHLA2 3 108358070 Missense_Mutation SNP G C3N-02423_T 7957279 108358070 89937489 94 29224 DTX3L 0 . GRCh38 3 122569254 122569254 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1165G>C p.Glu389Gln p.E389Q ENST00000296161 3/5 165 154 11 179 179 0 strelka-varscan-mutect DTX3L,missense_variant,p.Glu389Gln,ENST00000296161,NM_138287.3;DTX3L,intron_variant,,ENST00000383661,;PARP9,upstream_gene_variant,,ENST00000462315,NM_001146106.1;PARP9,upstream_gene_variant,,ENST00000360356,NM_001146102.1,NM_031458.2;PARP9,upstream_gene_variant,,ENST00000477522,NM_001146103.1,NM_001146105.1; C ENST00000296161 Transcript missense_variant 1354/5868 1165/2223 389/740 E/Q Gaa/Caa 1 1 DTX3L HGNC HGNC:30323 protein_coding YES CCDS3015.1 ENSP00000296161 Q8TDB6 UPI000000D9D0 NM_138287.3 tolerated(0.06) 3/5 hmmpanther:PTHR12622:SF23,hmmpanther:PTHR12622 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 122569254 122569254 G C 1 0 0 0 0 1 0 0 0 4619 943 33 4 4 DTX3L 3 122569254 Missense_Mutation SNP G C3N-02423_T 14211184 122569254 75726305 95 29225 MYLK 0 . GRCh38 3 123708819 123708819 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.2019G>C p.Gln673His p.Q673H ENST00000360304 14/33 161 148 13 175 175 0 varscan-mutect MYLK,missense_variant,p.Gln673His,ENST00000360772,;MYLK,missense_variant,p.Gln673His,ENST00000360304,NM_001321309.1,NM_053025.3;MYLK,missense_variant,p.Gln673His,ENST00000359169,NM_053027.3;MYLK,missense_variant,p.Gln604His,ENST00000354792,;MYLK,missense_variant,p.Gln604His,ENST00000346322,NM_053028.3,NM_053026.3;MYLK,missense_variant,p.Gln673His,ENST00000475616,;MYLK,3_prime_UTR_variant,,ENST00000464489,;MYLK,downstream_gene_variant,,ENST00000514623,; G ENST00000360304 Transcript missense_variant 2205/7738 2019/5745 673/1914 Q/H caG/caC 1 -1 MYLK HGNC HGNC:7590 protein_coding YES CCDS46896.1 ENSP00000353452 Q15746 UPI000020A0AE NM_001321309.1,NM_053025.3 deleterious(0.01) 14/33 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF700,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -17.77717 0.9999998 1 1 1 0 G 3 3 99 123708819 123708819 C G 1 0 0 0 0 1 0 0 0 10056 912 32 4 4 MYLK 3 123708819 Missense_Mutation SNP C C3N-02423_T 1139565 123708819 74586740 96 29226 KALRN 0 . GRCh38 3 124713018 124713018 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.3068A>G p.Lys1023Arg p.K1023R ENST00000291478 25/27 306 255 51 313 312 1 strelka-varscan-mutect KALRN,missense_variant,p.Lys1023Arg,ENST00000291478,NM_001322993.1,NM_007064.3;KALRN,missense_variant,p.Lys2720Arg,ENST00000360013,NM_001024660.3;KALRN,missense_variant,p.Lys2689Arg,ENST00000354186,; G ENST00000291478 Transcript missense_variant 3231/10888 3068/3870 1023/1289 K/R aAg/aGg 1 1 KALRN HGNC HGNC:4814 protein_coding CCDS3028.1 ENSP00000291478 O60229 UPI00001AEB7E NM_001322993.1,NM_007064.3 tolerated(0.44) 25/27 Gene3D:3.30.200.20,Pfam_domain:PF00069,PROSITE_profiles:PS50011,Low_complexity_(Seg):seg,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 124713018 124713018 A G 1 0 0 0 0 1 0 0 0 7884 72 3 5 5 KALRN 3 124713018 Missense_Mutation SNP A C3N-02423_T 1004199 124713018 73582541 97 29227 ZNF148 0 . GRCh38 3 125233299 125233299 + Missense_Mutation SNP T T C C3N-02423_T C3N-02423_N T T c.1427A>G p.Tyr476Cys p.Y476C ENST00000360647 9/9 192 180 12 224 224 0 strelka-varscan-mutect ZNF148,missense_variant,p.Tyr476Cys,ENST00000360647,NM_021964.2;ZNF148,missense_variant,p.Tyr476Cys,ENST00000485866,;ZNF148,missense_variant,p.Tyr476Cys,ENST00000484491,;ZNF148,missense_variant,p.Tyr476Cys,ENST00000492394,;ZNF148,intron_variant,,ENST00000468369,;ZNF148,non_coding_transcript_exon_variant,,ENST00000497929,;ZNF148,upstream_gene_variant,,ENST00000496732,; C ENST00000360647 Transcript missense_variant 1913/9651 1427/2385 476/794 Y/C tAt/tGt COSM1037649 1 -1 ZNF148 HGNC HGNC:12933 protein_coding YES CCDS3031.1 ENSP00000353863 Q9UQR1 UPI000013C2FF NM_021964.2 deleterious(0) 9/9 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 125233299 125233299 T C 1 0 0 0 0 1 0 0 0 18315 1406 49 5 5 ZNF148 3 125233299 Missense_Mutation SNP T C3N-02423_T 520281 125233299 73062260 98 29228 SLC41A3 0 . GRCh38 3 126033639 126033639 + Missense_Mutation SNP T T C novel C3N-02423_T C3N-02423_N T T c.421A>G p.Arg141Gly p.R141G ENST00000315891 4/12 234 212 22 271 271 0 strelka-varscan-mutect SLC41A3,missense_variant,p.Arg115Gly,ENST00000383598,NM_001008487.1;SLC41A3,missense_variant,p.Arg141Gly,ENST00000360370,NM_017836.3;SLC41A3,missense_variant,p.Arg141Gly,ENST00000315891,NM_001008485.1;SLC41A3,missense_variant,p.Arg105Gly,ENST00000346785,NM_001008486.1;SLC41A3,missense_variant,p.Arg24Gly,ENST00000508835,NM_001164475.1;SLC41A3,missense_variant,p.Arg156Gly,ENST00000514677,;SLC41A3,missense_variant,p.Arg193Gly,ENST00000513723,;SLC41A3,missense_variant,p.Arg141Gly,ENST00000512470,;SLC41A3,missense_variant,p.Arg105Gly,ENST00000514333,;SLC41A3,missense_variant,p.Arg141Gly,ENST00000507280,;SLC41A3,missense_variant,p.Arg141Gly,ENST00000514891,;SLC41A3,missense_variant,p.Arg141Gly,ENST00000504035,;SLC41A3,intron_variant,,ENST00000510651,;SLC41A3,downstream_gene_variant,,ENST00000509064,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000514023,;SLC41A3,missense_variant,p.Arg24Gly,ENST00000507008,;SLC41A3,non_coding_transcript_exon_variant,,ENST00000513464,; C ENST00000315891 Transcript missense_variant 660/1797 421/1524 141/507 R/G Aga/Gga 1 -1 SLC41A3 HGNC HGNC:31046 protein_coding YES CCDS33843.1 ENSP00000326070 Q96GZ6 UPI000013D523 NM_001008485.1 deleterious(0.04) 4/12 hmmpanther:PTHR16228:SF22,hmmpanther:PTHR16228,Gene3D:2zy9B03,Pfam_domain:PF01769,Superfamily_domains:0054748 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 126033639 126033639 T C 1 0 0 0 0 1 0 0 0 14909 1588 55 5 5 SLC41A3 3 126033639 Missense_Mutation SNP T C3N-02423_T 800340 126033639 72261920 99 29229 EEFSEC 0 . GRCh38 3 128153658 128153658 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.151C>G p.Leu51Val p.L51V ENST00000254730 1/7 383 347 36 393 393 0 strelka-varscan-mutect EEFSEC,missense_variant,p.Leu51Val,ENST00000254730,NM_021937.4;EEFSEC,missense_variant,p.Leu51Val,ENST00000483457,;RUVBL1,5_prime_UTR_variant,,ENST00000464873,NM_001319086.1;EEFSEC,upstream_gene_variant,,ENST00000484438,; G ENST00000254730 Transcript missense_variant 205/2232 151/1791 51/596 L/V Ctg/Gtg 1 1 EEFSEC HGNC HGNC:24614 protein_coding YES CCDS33849.1 ENSP00000254730 P57772 UPI000013CE58 NM_021937.4 deleterious(0) 1/7 Gene3D:3.40.50.300,Pfam_domain:PF00009,PROSITE_profiles:PS51722,hmmpanther:PTHR23115,hmmpanther:PTHR23115:SF91,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 128153658 128153658 C G 1 0 0 0 0 1 0 0 0 4762 912 32 4 4 EEFSEC 3 128153658 Missense_Mutation SNP C C3N-02423_T 2120019 128153658 70141901 100 29230 COL6A5 0 . GRCh38 3 130391213 130391213 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.2451T>A p.Phe817Leu p.F817L ENST00000265379 7/43 116 96 20 134 134 0 strelka-varscan-mutect COL6A5,missense_variant,p.Phe817Leu,ENST00000265379,NM_153264.6,NM_001278298.1;COL6A5,missense_variant,p.Phe817Leu,ENST00000312481,; A ENST00000265379 Transcript missense_variant 2945/9214 2451/7836 817/2611 F/L ttT/ttA 1 1 COL6A5 HGNC HGNC:26674 protein_coding YES ENSP00000265379 E9PAL5 UPI0004E4C944 NM_153264.6,NM_001278298.1 deleterious(0) 7/43 PROSITE_profiles:PS50234,Pfam_domain:PF00092,Gene3D:3.40.50.410,SMART_domains:SM00327,Superfamily_domains:SSF53300 MODERATE 1 SNV 5 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 130391213 130391213 T A 1 0 0 0 0 1 0 0 0 3491 1809 63 4 4 COL6A5 3 130391213 Missense_Mutation SNP T C3N-02423_T 2237555 130391213 67904346 101 29231 TF 0 . GRCh38 3 133777164 133777164 + Missense_Mutation SNP G G C C3N-02423_T C3N-02423_N G G c.1988G>C p.Arg663Thr p.R663T ENST00000402696 16/17 330 312 18 323 323 0 strelka-varscan-mutect TF,missense_variant,p.Arg663Thr,ENST00000402696,NM_001063.3;TF,3_prime_UTR_variant,,ENST00000461695,;TF,non_coding_transcript_exon_variant,,ENST00000467842,; C ENST00000402696 Transcript missense_variant 2473/2968 1988/2097 663/698 R/T aGa/aCa COSM728341 1 1 TF HGNC HGNC:11740 protein_coding YES CCDS3080.1 ENSP00000385834 P02787 UPI000013D5A6 NM_001063.3 tolerated(0.15) 16/17 Gene3D:3.40.190.10,Pfam_domain:PF00405,PIRSF_domain:PIRSF002549,PIRSF_domain:PIRSF500682,PROSITE_profiles:PS51408,hmmpanther:PTHR11485,hmmpanther:PTHR11485:SF31,SMART_domains:SM00094,Superfamily_domains:SSF53850 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 133777164 133777164 G C 1 0 0 0 0 1 0 0 0 16218 942 33 4 4 TF 3 133777164 Missense_Mutation SNP G C3N-02423_T 3385951 133777164 64518395 102 29232 HPS3 0 . GRCh38 3 149160259 149160259 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2086G>C p.Glu696Gln p.E696Q ENST00000296051 11/17 248 234 14 243 243 0 strelka-varscan-mutect HPS3,missense_variant,p.Glu696Gln,ENST00000296051,NM_032383.3;HPS3,missense_variant,p.Glu531Gln,ENST00000460120,NM_001308258.1;CP,downstream_gene_variant,,ENST00000479771,;HPS3,missense_variant,p.Glu72Gln,ENST00000460822,;CP,downstream_gene_variant,,ENST00000481169,; C ENST00000296051 Transcript missense_variant 2226/4665 2086/3015 696/1004 E/Q Gaa/Caa 1 1 HPS3 HGNC HGNC:15597 protein_coding YES CCDS3140.1 ENSP00000296051 Q969F9 UPI000000D989 NM_032383.3 tolerated(0.21) 11/17 hmmpanther:PTHR28633,hmmpanther:PTHR28633:SF1,PIRSF_domain:PIRSF037473,Pfam_domain:PF14763 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 149160259 149160259 G C 1 0 0 0 0 1 0 0 0 7235 1291 45 4 4 HPS3 3 149160259 Missense_Mutation SNP G C3N-02423_T 15383095 149160259 49135300 103 29233 CLRN1 0 . GRCh38 3 150941634 150941634 + Silent SNP A A T novel C3N-02423_T C3N-02423_N A A c.381T>A p.= p.P127P ENST00000328863 2/4 427 355 72 421 421 0 strelka-varscan-mutect CLRN1,synonymous_variant,p.=,ENST00000327047,NM_174878.2;CLRN1,synonymous_variant,p.=,ENST00000295911,NM_052995.2;CLRN1,synonymous_variant,p.=,ENST00000328863,NM_001195794.1;CLRN1,synonymous_variant,p.=,ENST00000468836,;CLRN1,synonymous_variant,p.=,ENST00000485607,;CLRN1-AS1,intron_variant,,ENST00000476886,;RP11-166N6.2,intron_variant,,ENST00000469268,;RP11-166N6.3,synonymous_variant,p.=,ENST00000569170,;RP11-166N6.3,synonymous_variant,p.=,ENST00000562308,;RP11-166N6.3,synonymous_variant,p.=,ENST00000565169,;CLRN1,non_coding_transcript_exon_variant,,ENST00000472224,; T ENST00000328863 Transcript synonymous_variant 381/738 381/738 127/245 P ccT/ccA 1 -1 CLRN1 HGNC HGNC:12605 protein_coding YES CCDS56285.1 ENSP00000329158 P58418 UPI0001E43709 NM_001195794.1 2/4 hmmpanther:PTHR31548:SF4,hmmpanther:PTHR31548,PD525711 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 150941634 150941634 A T 1 0 0 0 0 0 0 0 1 3329 59 3 4 4 CLRN1 3 150941634 Silent SNP A C3N-02423_T 1781375 150941634 47353925 104 29234 IGSF10 0 . GRCh38 3 151448488 151448488 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1493C>A p.Pro498Gln p.P498Q ENST00000282466 4/6 202 175 27 192 192 0 strelka-varscan-mutect IGSF10,missense_variant,p.Pro498Gln,ENST00000282466,NM_178822.4; T ENST00000282466 Transcript missense_variant 1493/11067 1493/7872 498/2623 P/Q cCa/cAa 1 -1 IGSF10 HGNC HGNC:26384 protein_coding YES CCDS3160.1 ENSP00000282466 Q6WRI0 UPI00001D629A NM_178822.4 tolerated(0.62) 4/6 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF29,SMART_domains:SM00406,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 151448488 151448488 G T 1 0 0 0 0 1 0 0 0 7504 1348 47 2 2 IGSF10 3 151448488 Missense_Mutation SNP G C3N-02423_T 506854 151448488 46847071 105 29235 DHX36 0 . GRCh38 3 154315281 154315281 + Splice_Site SNP C C A novel C3N-02423_T C3N-02423_N C C c.369-1G>T p.X123_splice ENST00000496811 87 74 13 106 106 0 strelka-varscan-mutect DHX36,splice_acceptor_variant,,ENST00000496811,NM_020865.2;DHX36,splice_acceptor_variant,,ENST00000308361,;DHX36,splice_acceptor_variant,,ENST00000329463,NM_001114397.1;DHX36,splice_acceptor_variant,,ENST00000481941,;DHX36,splice_acceptor_variant,,ENST00000491011,;DHX36,upstream_gene_variant,,ENST00000462464,; A ENST00000496811 Transcript splice_acceptor_variant -/6733 369/3027 123/1008 1 -1 DHX36 HGNC HGNC:14410 protein_coding YES CCDS3171.1 ENSP00000417078 Q9H2U1 UPI000013ED25 NM_020865.2 2/24 HIGH 1 SNV 1 1 PASS . . 1 203 5 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 99 154315281 154315281 C A 1 0 0 0 0 0 0 1 0 4313 927 32 2 2 DHX36 3 154315281 Splice_Site SNP C C3N-02423_T 2866793 154315281 43980278 106 29236 PLD1 0 . GRCh38 3 171674580 171674580 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2149C>G p.Pro717Ala p.P717A ENST00000351298 19/27 224 204 20 219 219 0 strelka-varscan-mutect PLD1,missense_variant,p.Pro679Ala,ENST00000356327,NM_001130081.2;PLD1,missense_variant,p.Pro717Ala,ENST00000351298,NM_002662.4;PLD1,upstream_gene_variant,,ENST00000446289,;PLD1,non_coding_transcript_exon_variant,,ENST00000471075,; C ENST00000351298 Transcript missense_variant 2276/5604 2149/3225 717/1074 P/A Cct/Gct 1 -1 PLD1 HGNC HGNC:9067 protein_coding YES CCDS3216.1 ENSP00000342793 Q13393 UPI0000131BDC NM_002662.4 deleterious(0.01) 19/27 hmmpanther:PTHR18896,hmmpanther:PTHR18896:SF57,PIRSF_domain:PIRSF009376,Gene3D:3.30.870.10,Superfamily_domains:SSF56024 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 171674580 171674580 G C 1 0 0 0 0 1 0 0 0 12139 1174 41 4 4 PLD1 3 171674580 Missense_Mutation SNP G C3N-02423_T 17359299 171674580 26620979 107 29237 PIK3CA 0 . GRCh38 3 179218303 179218303 + Missense_Mutation SNP G G A rs104886003 C3N-02423_T C3N-02423_N G G c.1633G>A p.Glu545Lys p.E545K ENST00000263967 10/21 136 129 7 149 149 0 varscan-mutect PIK3CA,missense_variant,p.Glu545Lys,ENST00000263967,NM_006218.2;PIK3CA,upstream_gene_variant,,ENST00000462255,; A ENST00000263967 Transcript missense_variant 1790/9093 1633/3207 545/1068 E/K Gag/Aag rs104886003,COSM125370,COSM27133,COSM295672,COSM763 1 1 PIK3CA HGNC HGNC:8975 protein_coding YES CCDS43171.1 ENSP00000263967 P42336 UPI000013D494 NM_006218.2 deleterious(0.02) 10/21 Gene3D:1.25.40.70,Pfam_domain:PF00613,PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF54,SMART_domains:SM00145,Superfamily_domains:SSF48371 not_provided,pathogenic 0,1,1,1,1 21264207 MODERATE 1 SNV 2 1,1,1,1,1 1 PASS rs104886003 . 0 208 0 2 0 0 0 0 -9.955755 0.9999993 1 1 1 0 A 3 1 99 179218303 179218303 G A 1 0 0 0 0 1 0 0 0 12008 1291 45 3 3 PIK3CA 3 179218303 Missense_Mutation SNP G C3N-02423_T 7543723 179218303 19077256 108 29238 MUC4 0 . GRCh38 3 195780901 195780901 + Missense_Mutation SNP G G A rs779385534 C3N-02423_T C3N-02423_N G G c.10679C>T p.Ser3560Leu p.S3560L ENST00000463781 2/25 598 567 31 735 734 1 varscan-mutect MUC4,missense_variant,p.Ser3560Leu,ENST00000463781,NM_018406.6;MUC4,missense_variant,p.Ser3560Leu,ENST00000475231,;MUC4,intron_variant,,ENST00000346145,NM_004532.5;MUC4,intron_variant,,ENST00000349607,NM_138297.4;MUC4,missense_variant,p.Ser3560Leu,ENST00000478156,;MUC4,missense_variant,p.Ser3560Leu,ENST00000466475,;MUC4,missense_variant,p.Ser3560Leu,ENST00000477756,;MUC4,missense_variant,p.Ser3560Leu,ENST00000477086,;MUC4,missense_variant,p.Ser3560Leu,ENST00000480843,;MUC4,missense_variant,p.Ser3560Leu,ENST00000462323,;MUC4,missense_variant,p.Ser3560Leu,ENST00000470451,;MUC4,missense_variant,p.Ser3560Leu,ENST00000479406,;MUC4,upstream_gene_variant,,ENST00000448861,;MUC4,upstream_gene_variant,,ENST00000308466,;MUC4,upstream_gene_variant,,ENST00000339251,;MUC4,upstream_gene_variant,,ENST00000415455,;MUC4,upstream_gene_variant,,ENST00000392407,; A ENST00000463781 Transcript missense_variant 11139/17110 10679/16239 3560/5412 S/L tCg/tTg rs779385534,COSM2944551 1 -1 MUC4 HGNC HGNC:7514 protein_coding YES CCDS54700.1 ENSP00000417498 E9PDY6 UPI0001B3CB30 NM_018406.6 deleterious_low_confidence(0) 2/25 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs779385534 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 195780901 195780901 G A 1 0 0 0 0 1 0 0 0 9977 1059 37 1 1 MUC4 3 195780901 Missense_Mutation SNP G C3N-02423_T 16562598 195780901 2514658 109 29239 IDUA 0 . GRCh38 4 1002005 1002005 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.816C>A p.= p.I272I ENST00000247933 7/14 162 152 10 150 150 0 strelka-varscan-mutect IDUA,synonymous_variant,p.=,ENST00000247933,NM_000203.4;IDUA,synonymous_variant,p.=,ENST00000514224,;IDUA,synonymous_variant,p.=,ENST00000514192,;IDUA,downstream_gene_variant,,ENST00000509948,;IDUA,downstream_gene_variant,,ENST00000502910,;IDUA,downstream_gene_variant,,ENST00000504568,;IDUA,non_coding_transcript_exon_variant,,ENST00000514698,;IDUA,downstream_gene_variant,,ENST00000506561,;IDUA,upstream_gene_variant,,ENST00000502829,;IDUA,downstream_gene_variant,,ENST00000508168,;IDUA,upstream_gene_variant,,ENST00000514417,; A ENST00000247933 Transcript synonymous_variant 904/2163 816/1962 272/653 I atC/atA 1 1 IDUA HGNC HGNC:5391 protein_coding YES CCDS3343.1 ENSP00000247933 P35475 UPI00004571D0 NM_000203.4 7/14 Gene3D:3.20.20.80,Pfam_domain:PF01229,hmmpanther:PTHR12631,hmmpanther:PTHR12631:SF8,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS rs1379813895 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 1002005 1002005 C A 1 0 0 0 0 0 0 0 1 7405 845 30 2 2 IDUA 4 1002005 Silent SNP C C3N-02423_T 1002005 189212550 110 29240 RNF4 0 . GRCh38 4 2497046 2497046 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.49C>G p.Gln17Glu p.Q17E ENST00000511600 3/8 247 233 14 177 177 0 strelka-varscan-mutect RNF4,missense_variant,p.Gln17Glu,ENST00000511600,;RNF4,missense_variant,p.Gln17Glu,ENST00000314289,NM_002938.4;RNF4,missense_variant,p.Gln17Glu,ENST00000541204,NM_001185010.2;RNF4,missense_variant,p.Gln17Glu,ENST00000506706,NM_001185009.2;RNF4,missense_variant,p.Gln17Glu,ENST00000511859,;RNF4,missense_variant,p.Gln17Glu,ENST00000509258,;RNF4,missense_variant,p.Gln17Glu,ENST00000502316,;RNF4,missense_variant,p.Gln17Glu,ENST00000507247,;RNF4,missense_variant,p.Gln17Glu,ENST00000504224,;RNF4,missense_variant,p.Gln17Glu,ENST00000513450,;RNF4,downstream_gene_variant,,ENST00000503659,;RNF4,non_coding_transcript_exon_variant,,ENST00000511843,;RNF4,non_coding_transcript_exon_variant,,ENST00000509388,;RNF4,non_coding_transcript_exon_variant,,ENST00000511892,;RNF4,non_coding_transcript_exon_variant,,ENST00000509206,;RNF4,non_coding_transcript_exon_variant,,ENST00000503123,;RNF4,intron_variant,,ENST00000513643,;RNF4,missense_variant,p.Gln17Glu,ENST00000513578,;RNF4,missense_variant,p.Gln17Glu,ENST00000513284,;RNF4,non_coding_transcript_exon_variant,,ENST00000507784,; G ENST00000511600 Transcript missense_variant 1564/4123 49/573 17/190 Q/E Cag/Gag 1 1 RNF4 HGNC HGNC:10067 protein_coding YES CCDS47001.1 ENSP00000426503 P78317 UPI0000134379 tolerated(0.15) 3/8 hmmpanther:PTHR23041:SF60,hmmpanther:PTHR23041 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -16.53614 0.9999995 1 1 1 0 G 3 3 99 2497046 2497046 C G 1 0 0 0 0 1 0 0 0 13672 827 29 4 4 RNF4 4 2497046 Missense_Mutation SNP C C3N-02423_T 1495041 2497046 187717509 111 29241 FAM193A 0 . GRCh38 4 2690734 2690734 + Missense_Mutation SNP G G A rs770167873 C3N-02423_T C3N-02423_N G G c.1694G>A p.Arg565Lys p.R565K ENST00000324666 13/20 174 165 9 135 135 0 strelka-varscan-mutect FAM193A,missense_variant,p.Arg856Lys,ENST00000637812,;FAM193A,missense_variant,p.Arg565Lys,ENST00000324666,NM_001256666.1;FAM193A,missense_variant,p.Arg565Lys,ENST00000382839,NM_003704.3;FAM193A,missense_variant,p.Arg565Lys,ENST00000505311,NM_001256668.1;FAM193A,missense_variant,p.Arg587Lys,ENST00000502458,NM_001256667.1;FAM193A,missense_variant,p.Arg565Lys,ENST00000545951,;FAM193A,missense_variant,p.Arg419Lys,ENST00000513350,;FAM193A,missense_variant,p.Arg565Lys,ENST00000512465,;FAM193A,missense_variant,p.Arg565Lys,ENST00000513898,; A ENST00000324666 Transcript missense_variant 2045/4846 1694/3798 565/1265 R/K aGa/aAa rs770167873 1 1 FAM193A HGNC HGNC:16822 protein_coding YES CCDS58875.1 ENSP00000324587 P78312 UPI0000551BCA NM_001256666.1 tolerated(0.13) 13/20 hmmpanther:PTHR15109:SF2,hmmpanther:PTHR15109 MODERATE 1 SNV 1 1 PASS rs770167873 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 2690734 2690734 G A 1 0 0 0 0 1 0 0 0 5371 942 33 3 3 FAM193A 4 2690734 Missense_Mutation SNP G C3N-02423_T 193688 2690734 187523821 112 29242 ZBTB49 0 . GRCh38 4 4320791 4320791 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1773G>C p.Glu591Asp p.E591D ENST00000337872 8/8 335 308 27 324 324 0 strelka-varscan-mutect ZBTB49,missense_variant,p.Glu591Asp,ENST00000337872,NM_145291.3;ZBTB49,downstream_gene_variant,,ENST00000504302,;RP11-265O12.1,upstream_gene_variant,,ENST00000509015,;ZBTB49,3_prime_UTR_variant,,ENST00000503703,;ZBTB49,3_prime_UTR_variant,,ENST00000515012,;ZBTB49,downstream_gene_variant,,ENST00000511458,; C ENST00000337872 Transcript missense_variant 1894/2889 1773/2298 591/765 E/D gaG/gaC 1 1 ZBTB49 HGNC HGNC:19883 protein_coding YES CCDS3375.1 ENSP00000338807 Q6ZSB9 UPI000022C559 NM_145291.3 tolerated(0.39) 8/8 hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 4320791 4320791 G C 1 0 0 0 0 1 0 0 0 18120 933 33 4 4 ZBTB49 4 4320791 Missense_Mutation SNP G C3N-02423_T 1630057 4320791 185893764 113 29243 ACOX3 0 . GRCh38 4 8394692 8394692 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1107C>T p.= p.F369F ENST00000356406 10/18 184 168 16 173 173 0 strelka-varscan-mutect ACOX3,synonymous_variant,p.=,ENST00000356406,NM_003501.2;ACOX3,synonymous_variant,p.=,ENST00000413009,NM_001101667.1;ACOX3,synonymous_variant,p.=,ENST00000503233,;RNA5SP152,downstream_gene_variant,,ENST00000365184,;ACOX3,non_coding_transcript_exon_variant,,ENST00000508302,;ACOX3,non_coding_transcript_exon_variant,,ENST00000510365,; A ENST00000356406 Transcript synonymous_variant 1185/2860 1107/2103 369/700 F ttC/ttT 1 -1 ACOX3 HGNC HGNC:121 protein_coding YES CCDS3401.1 ENSP00000348775 O15254 UPI000013EEE2 NM_003501.2 10/18 hmmpanther:PTHR10909:SF315,hmmpanther:PTHR10909,PIRSF_domain:PIRSF000168,Gene3D:1.20.140.10,Superfamily_domains:SSF47203 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 8394692 8394692 G A 1 0 0 0 0 0 0 0 1 202 933 33 3 3 ACOX3 4 8394692 Silent SNP G C3N-02423_T 4073901 8394692 181819863 114 29244 CPEB2 0 . GRCh38 4 15002685 15002685 + Silent SNP C C T C3N-02423_T C3N-02423_N C C c.12C>T p.= p.F4F ENST00000538197 1/12 67 61 6 69 69 0 strelka-varscan-mutect CPEB2,synonymous_variant,p.=,ENST00000538197,NM_001177382.1;CPEB2,synonymous_variant,p.=,ENST00000442003,NM_001177383.1,NM_001177381.1;CPEB2,upstream_gene_variant,,ENST00000259997,;CPEB2,upstream_gene_variant,,ENST00000382395,;CPEB2,upstream_gene_variant,,ENST00000382401,NM_001177384.1;CPEB2,upstream_gene_variant,,ENST00000507071,NM_182485.2;CPEB2,upstream_gene_variant,,ENST00000345451,NM_182646.2;CPEB2-AS1,upstream_gene_variant,,ENST00000500394,;RP11-665G4.1,downstream_gene_variant,,ENST00000502344,;RP11-665G4.1,downstream_gene_variant,,ENST00000513384,;CPEB2,upstream_gene_variant,,ENST00000503926,; T ENST00000538197 Transcript synonymous_variant 12/6878 12/3105 4/1034 F ttC/ttT COSM4437221 1 1 CPEB2 HGNC HGNC:21745 protein_coding YES CCDS56325.1 ENSP00000443985 Q7Z5Q1 UPI0001D0434B NM_001177382.1 1/12 1 LOW SNV 5 1 1 PASS . . 0 203 7 0 0 0 0 0 -13.51378 0.9999987 1 1 1 0 T 2 4 99 15002685 15002685 C T 1 0 0 0 0 0 0 0 1 3595 883 31 1 1 CPEB2 4 15002685 Silent SNP C C3N-02423_T 6607993 15002685 175211870 115 29245 PCDH7 0 . GRCh38 4 30721560 30721560 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.138C>A p.= p.V46V ENST00000543491 1/1 118 102 16 158 158 0 strelka-varscan PCDH7,synonymous_variant,p.=,ENST00000361762,NM_002589.2;PCDH7,synonymous_variant,p.=,ENST00000543491,NM_032456.2;PCDH7,upstream_gene_variant,,ENST00000511884,NM_032457.3,NM_001173523.1;PCDH7,upstream_gene_variant,,ENST00000621961,;PCDH7,upstream_gene_variant,,ENST00000509759,;PCDH7,upstream_gene_variant,,ENST00000507864,; A ENST00000543491 Transcript synonymous_variant 708/4457 138/3219 46/1072 V gtC/gtA 1 1 PCDH7 HGNC HGNC:8659 protein_coding YES CCDS75116.1 ENSP00000441802 O60245 UPI00001615DB NM_032456.2 1/1 hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF321,Gene3D:2.60.40.60,Pfam_domain:PF08266,Superfamily_domains:SSF49313 LOW 1 SNV 1 PASS . . 0 206 2 2 0 0 0 0 -19.99999 0.9999976 1 1 1 0 A 2 1 99 30721560 30721560 C A 1 0 0 0 0 0 0 0 1 11603 842 30 2 2 PCDH7 4 30721560 Silent SNP C C3N-02423_T 15718875 30721560 159492995 116 29246 TLR10 0 . GRCh38 4 38774319 38774319 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1272C>T p.= p.V424V ENST00000308973 4/4 127 118 9 134 134 0 strelka-varscan TLR10,synonymous_variant,p.=,ENST00000308973,NM_030956.3;TLR10,synonymous_variant,p.=,ENST00000613579,NM_001195108.1,NM_001195106.1;TLR10,synonymous_variant,p.=,ENST00000622002,NM_001195107.1;TLR10,synonymous_variant,p.=,ENST00000361424,NM_001017388.2;TLR10,synonymous_variant,p.=,ENST00000506111,;TLR10,synonymous_variant,p.=,ENST00000508334,;TLR10,downstream_gene_variant,,ENST00000502321,;TLR10,downstream_gene_variant,,ENST00000507953,; A ENST00000308973 Transcript synonymous_variant 1878/3958 1272/2436 424/811 V gtC/gtT 1 -1 TLR10 HGNC HGNC:15634 protein_coding YES CCDS3445.1 ENSP00000308925 Q9BXR5 A0A024R9W4 UPI0000048F1C NM_030956.3 4/4 hmmpanther:PTHR24365:SF131,hmmpanther:PTHR24365,PIRSF_domain:PIRSF037595,Gene3D:3.80.10.10,Superfamily_domains:SSF52058 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -17.4099 1 1 1 1 0 A 2 1 99 38774319 38774319 G A 1 0 0 0 0 0 0 0 1 16396 1277 45 3 3 TLR10 4 38774319 Silent SNP G C3N-02423_T 8052759 38774319 151440236 117 29247 PHOX2B 0 . GRCh38 4 41747358 41747358 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.420G>A p.= p.A140A ENST00000226382 2/3 336 311 25 307 307 0 strelka-varscan PHOX2B,synonymous_variant,p.=,ENST00000226382,NM_003924.3;RP11-227F19.2,upstream_gene_variant,,ENST00000510602,;RP11-227F19.1,upstream_gene_variant,,ENST00000508038,;PHOX2B,non_coding_transcript_exon_variant,,ENST00000510424,; T ENST00000226382 Transcript synonymous_variant 780/3030 420/945 140/314 A gcG/gcA 1 -1 PHOX2B HGNC HGNC:9143 protein_coding YES CCDS3463.1 ENSP00000226382 Q99453 UPI000000D936 NM_003924.3 2/3 PROSITE_profiles:PS50071,hmmpanther:PTHR24329,hmmpanther:PTHR24329:SF301,PROSITE_patterns:PS00027,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 41747358 41747358 C T 1 0 0 0 0 0 0 0 1 11947 755 27 1 1 PHOX2B 4 41747358 Silent SNP C C3N-02423_T 2973039 41747358 148467197 118 29248 ATP8A1 0 . GRCh38 4 42443569 42443569 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.3119G>T p.Gly1040Val p.G1040V ENST00000381668 33/37 160 132 28 154 154 0 strelka-varscan ATP8A1,missense_variant,p.Gly1040Val,ENST00000381668,NM_006095.2;ATP8A1,missense_variant,p.Gly1025Val,ENST00000264449,NM_001105529.1;ATP8A1,3_prime_UTR_variant,,ENST00000514372,;ATP8A1,3_prime_UTR_variant,,ENST00000506602,; A ENST00000381668 Transcript missense_variant 3351/8270 3119/3495 1040/1164 G/V gGa/gTa 1 -1 ATP8A1 HGNC HGNC:13531 protein_coding YES CCDS3466.1 ENSP00000371084 Q9Y2Q0 UPI0000125063 NM_006095.2 deleterious(0) 33/37 hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF56,Pfam_domain:PF16212,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 42443569 42443569 C A 1 0 0 0 0 1 0 0 0 1345 869 30 2 2 ATP8A1 4 42443569 Missense_Mutation SNP C C3N-02423_T 696211 42443569 147770986 119 29249 TXK 0 . GRCh38 4 48067693 48067693 + Missense_Mutation SNP G G A rs746410519 C3N-02423_T C3N-02423_N G G c.1528C>T p.Arg510Cys p.R510C ENST00000264316 15/15 331 284 47 281 281 0 strelka-varscan TXK,missense_variant,p.Arg510Cys,ENST00000264316,NM_003328.2;TXK,missense_variant,p.Arg165Cys,ENST00000507351,;TXK,3_prime_UTR_variant,,ENST00000514937,;TXK,3_prime_UTR_variant,,ENST00000509681,; A ENST00000264316 Transcript missense_variant 1614/2914 1528/1584 510/527 R/C Cgc/Tgc rs746410519 1 -1 TXK HGNC HGNC:12434 protein_coding YES CCDS3480.1 ENSP00000264316 P42681 UPI000013D4F9 NM_003328.2 deleterious(0) 15/15 Gene3D:1.10.510.10,Pfam_domain:PF07714,Prints_domain:PR00109,PROSITE_profiles:PS50011,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF247,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 48067693 48067693 G A 1 0 0 0 0 1 0 0 0 17302 1116 39 1 1 TXK 4 48067693 Missense_Mutation SNP G C3N-02423_T 5624124 48067693 142146862 120 29250 CEP135 0 . GRCh38 4 56011467 56011467 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.2561G>A p.Arg854Lys p.R854K ENST00000257287 20/26 298 242 56 318 317 1 strelka-varscan CEP135,missense_variant,p.Arg854Lys,ENST00000257287,NM_025009.4;CEP135,non_coding_transcript_exon_variant,,ENST00000506202,; A ENST00000257287 Transcript missense_variant 2685/5562 2561/3423 854/1140 R/K aGa/aAa COSM1671037 1 1 CEP135 HGNC HGNC:29086 protein_coding YES CCDS33986.1 ENSP00000257287 Q66GS9 UPI00003CE420 NM_025009.4 tolerated(0.75) 20/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR23159,hmmpanther:PTHR23159:SF18 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 56011467 56011467 G A 1 0 0 0 0 1 0 0 0 2960 942 33 3 3 CEP135 4 56011467 Missense_Mutation SNP G C3N-02423_T 7943774 56011467 134203088 121 29251 SMR3A 0 . GRCh38 4 70366752 70366752 + Missense_Mutation SNP C C G rs867137640 C3N-02423_T C3N-02423_N C C c.163C>G p.Pro55Ala p.P55A ENST00000226460 3/3 288 241 47 317 317 0 strelka-varscan SMR3A,missense_variant,p.Pro55Ala,ENST00000226460,NM_012390.3;SMR3B,upstream_gene_variant,,ENST00000504825,; G ENST00000226460 Transcript missense_variant 259/665 163/405 55/134 P/A Cct/Gct rs867137640 1 1 SMR3A HGNC HGNC:19216 protein_coding YES CCDS34000.1 ENSP00000226460 Q99954 UPI000013C8A0 NM_012390.3 tolerated_low_confidence(0.23) 3/3 Pfam_domain:PF15621,Prints_domain:PR01217,hmmpanther:PTHR14179,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 70366752 70366752 C G 1 0 0 0 0 1 0 0 0 15132 855 30 4 4 SMR3A 4 70366752 Missense_Mutation SNP C C3N-02423_T 14355285 70366752 119847803 122 29252 PRDM8 0 . GRCh38 4 80202279 80202279 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.817G>T p.Gly273Ter p.G273* ENST00000339711 10/10 362 306 56 369 369 0 strelka-varscan PRDM8,stop_gained,p.Gly273Ter,ENST00000339711,NM_020226.3;PRDM8,stop_gained,p.Gly273Ter,ENST00000504452,;PRDM8,stop_gained,p.Gly273Ter,ENST00000415738,NM_001099403.1;PRDM8,stop_gained,p.Gly273Ter,ENST00000515013,; T ENST00000339711 Transcript stop_gained 2048/4095 817/2070 273/689 G/* Gga/Tga 1 1 PRDM8 HGNC HGNC:13993 protein_coding YES CCDS43243.1 ENSP00000339764 Q9NQV8 A0A024RDC4 UPI0000422A1D NM_020226.3 10/10 Low_complexity_(Seg):seg HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 80202279 80202279 G T 1 0 0 0 0 0 1 0 0 12594 1233 43 2 2 PRDM8 4 80202279 Nonsense_Mutation SNP G C3N-02423_T 9835527 80202279 110012276 123 29253 GRID2 0 . GRCh38 4 93455803 93455803 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1687G>T p.Ala563Ser p.A563S ENST00000282020 11/16 479 414 65 529 529 0 strelka-varscan GRID2,missense_variant,p.Ala563Ser,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Ala482Ser,ENST00000611049,;GRID2,missense_variant,p.Ala468Ser,ENST00000510992,NM_001286838.1; T ENST00000282020 Transcript missense_variant 2722/6117 1687/3024 563/1007 A/S Gca/Tca 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 deleterious(0.01) 11/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:3.40.190.10,SMART_domains:SM00079 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 93455803 93455803 G T 1 0 0 0 0 1 0 0 0 6652 1319 46 2 2 GRID2 4 93455803 Missense_Mutation SNP G C3N-02423_T 13253524 93455803 96758752 124 29254 GRID2 0 . GRCh38 4 93455973 93455973 + Missense_Mutation SNP A A T C3N-02423_T C3N-02423_N A A c.1857A>T p.Gln619His p.Q619H ENST00000282020 11/16 124 109 15 144 143 1 strelka-varscan GRID2,missense_variant,p.Gln619His,ENST00000282020,NM_001510.3;GRID2,missense_variant,p.Gln538His,ENST00000611049,;GRID2,missense_variant,p.Gln524His,ENST00000510992,NM_001286838.1; T ENST00000282020 Transcript missense_variant,splice_region_variant 2892/6117 1857/3024 619/1007 Q/H caA/caT COSM1253697 1 1 GRID2 HGNC HGNC:4576 protein_coding YES CCDS3637.1 ENSP00000282020 O43424 UPI00001AEA78 NM_001510.3 deleterious(0) 11/16 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF109,Gene3D:1.10.287.70,Pfam_domain:PF00060,SMART_domains:SM00079 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 93455973 93455973 A T 1 0 0 0 0 1 0 0 0 6652 86 3 4 4 GRID2 4 93455973 Missense_Mutation SNP A C3N-02423_T 170 93455973 96758582 125 29255 BANK1 0 . GRCh38 4 101829994 101829994 + Nonsense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.257C>G p.Ser86Ter p.S86* ENST00000322953 2/17 142 129 13 152 152 0 strelka-varscan BANK1,stop_gained,p.Ser71Ter,ENST00000504592,;BANK1,stop_gained,p.Ser86Ter,ENST00000322953,NM_017935.4;BANK1,stop_gained,p.Ser56Ter,ENST00000444316,NM_001083907.2;BANK1,intron_variant,,ENST00000428908,NM_001127507.2;BANK1,intron_variant,,ENST00000508653,; G ENST00000322953 Transcript stop_gained 531/3372 257/2358 86/785 S/* tCa/tGa 1 1 BANK1 HGNC HGNC:18233 protein_coding YES CCDS34038.1 ENSP00000320509 Q8NDB2 UPI0000D6159D NM_017935.4 2/17 Low_complexity_(Seg):seg,hmmpanther:PTHR16267,hmmpanther:PTHR16267:SF13 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 99 101829994 101829994 C G 1 0 0 0 0 0 1 0 0 1461 838 29 4 4 BANK1 4 101829994 Nonsense_Mutation SNP C C3N-02423_T 8374021 101829994 88384561 126 29256 SPATA5 0 . GRCh38 4 122934126 122934126 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.535C>T p.= p.L179L ENST00000274008 5/16 70 60 10 90 90 0 strelka-varscan SPATA5,synonymous_variant,p.=,ENST00000274008,NM_145207.2;SPATA5,non_coding_transcript_exon_variant,,ENST00000422835,; T ENST00000274008 Transcript synonymous_variant 604/8137 535/2682 179/893 L Ctg/Ttg 1 1 SPATA5 HGNC HGNC:18119 protein_coding YES CCDS3730.1 ENSP00000274008 Q8NB90 UPI000013D9E6 NM_145207.2 5/16 hmmpanther:PTHR23077:SF27,hmmpanther:PTHR23077 LOW 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -19.998 1 1 1 1 0 T 2 4 99 122934126 122934126 C T 1 0 0 0 0 0 0 0 1 15355 912 32 3 3 SPATA5 4 122934126 Silent SNP C C3N-02423_T 21104132 122934126 67280429 127 29257 FAT4 0 . GRCh38 4 125477330 125477330 + Missense_Mutation SNP G G C rs141297199 C3N-02423_T C3N-02423_N G G c.12469G>C p.Asp4157His p.D4157H ENST00000394329 13/17 156 142 14 122 122 0 strelka-varscan FAT4,missense_variant,p.Asp4157His,ENST00000394329,NM_001291285.1,NM_001291303.1,NM_024582.4;FAT4,missense_variant,p.Asp2420His,ENST00000335110,; C ENST00000394329 Transcript missense_variant 12482/16123 12469/14946 4157/4981 D/H Gat/Cat rs141297199 1 1 FAT4 HGNC HGNC:23109 protein_coding YES CCDS3732.3 ENSP00000377862 Q6V0I7 UPI000155D6E3 NM_001291285.1,NM_001291303.1,NM_024582.4 deleterious(0.02) 13/17 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF43,SMART_domains:SM00179,Superfamily_domains:SSF49899 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 125477330 125477330 G C 1 0 0 0 0 1 0 0 0 5552 956 33 4 4 FAT4 4 125477330 Missense_Mutation SNP G C3N-02423_T 2543204 125477330 64737225 128 29258 IL15 0 . GRCh38 4 141729907 141729907 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.301G>T p.Glu101Ter p.E101* ENST00000296545 7/8 199 177 22 216 216 0 strelka-varscan IL15,stop_gained,p.Glu74Ter,ENST00000477265,;IL15,stop_gained,p.Glu101Ter,ENST00000296545,;IL15,stop_gained,p.Glu74Ter,ENST00000394159,;IL15,stop_gained,p.Glu101Ter,ENST00000320650,NM_000585.4;IL15,stop_gained,p.Glu74Ter,ENST00000514653,NM_172175.2;IL15,stop_gained,p.Glu101Ter,ENST00000529613,;IL15,downstream_gene_variant,,ENST00000509249,; T ENST00000296545 Transcript stop_gained 1145/2472 301/489 101/162 E/* Gag/Tag 1 1 IL15 HGNC HGNC:5977 protein_coding YES CCDS3755.1 ENSP00000296545 P40933 UPI0000031AC7 7/8 Pfam_domain:PF02372,Prints_domain:PR01930,hmmpanther:PTHR11323,hmmpanther:PTHR11323:SF0,Superfamily_domains:SSF47266 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 141729907 141729907 G T 1 0 0 0 0 0 1 0 0 7539 1291 45 2 2 IL15 4 141729907 Nonsense_Mutation SNP G C3N-02423_T 16252577 141729907 48484648 129 29259 PLRG1 0 . GRCh38 4 154537297 154537297 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1474G>C p.Asp492His p.D492H ENST00000499023 14/15 92 85 7 104 102 2 strelka-varscan PLRG1,missense_variant,p.Asp492His,ENST00000499023,NM_002669.3;PLRG1,missense_variant,p.Asp483His,ENST00000302078,NM_001201564.1;PLRG1,intron_variant,,ENST00000503251,;PLRG1,downstream_gene_variant,,ENST00000504341,;PLRG1,3_prime_UTR_variant,,ENST00000506627,;PLRG1,non_coding_transcript_exon_variant,,ENST00000512773,;PLRG1,downstream_gene_variant,,ENST00000506192,;PLRG1,downstream_gene_variant,,ENST00000506918,;PLRG1,downstream_gene_variant,,ENST00000507125,; G ENST00000499023 Transcript missense_variant 1601/3351 1474/1545 492/514 D/H Gat/Cat 1 -1 PLRG1 HGNC HGNC:9089 protein_coding YES CCDS34083.1 ENSP00000424417 O43660 UPI0000070B39 NM_002669.3 deleterious(0) 14/15 Gene3D:2.130.10.10,PROSITE_profiles:PS50294,hmmpanther:PTHR19923,hmmpanther:PTHR19923:SF0 MODERATE 1 SNV 1 1 PASS . . 0 198 12 0 0 0 0 0 -14.26793 0.9996832 1 1 1 0 G 3 3 99 154537297 154537297 C G 1 0 0 0 0 1 0 0 0 12214 855 30 4 4 PLRG1 4 154537297 Missense_Mutation SNP C C3N-02423_T 12807390 154537297 35677258 130 29260 FNIP2 0 . GRCh38 4 158769282 158769282 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.70G>T p.Ala24Ser p.A24S ENST00000264433 1/17 158 135 23 141 141 0 strelka-varscan FNIP2,missense_variant,p.Ala24Ser,ENST00000264433,NM_001323916.1,NM_020840.1;FNIP2,non_coding_transcript_exon_variant,,ENST00000504704,; T ENST00000264433 Transcript missense_variant 145/6925 70/3345 24/1114 A/S Gcc/Tcc 1 1 FNIP2 HGNC HGNC:29280 protein_coding YES CCDS47155.1 ENSP00000264433 Q9P278 UPI00001C1E0A NM_001323916.1,NM_020840.1 tolerated(0.73) 1/17 hmmpanther:PTHR21634,hmmpanther:PTHR21634:SF11,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 99 158769282 158769282 G T 1 0 0 0 0 1 0 0 0 5834 1319 46 2 2 FNIP2 4 158769282 Missense_Mutation SNP G C3N-02423_T 4231985 158769282 31445273 131 29261 TLL1 0 . GRCh38 4 166043359 166043359 + Missense_Mutation SNP T T G novel C3N-02423_T C3N-02423_N T T c.1464T>G p.Cys488Trp p.C488W ENST00000061240 12/21 442 396 46 468 468 0 strelka-varscan TLL1,missense_variant,p.Cys488Trp,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Cys488Trp,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,; G ENST00000061240 Transcript missense_variant 2111/6708 1464/3042 488/1013 C/W tgT/tgG 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 deleterious(0) 12/21 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 166043359 166043359 T G 1 0 0 0 0 1 0 0 0 16391 1702 59 5 5 TLL1 4 166043359 Missense_Mutation SNP T C3N-02423_T 7274077 166043359 24171196 132 29262 99 2 TLL1 0 . GRCh38 4 166043363 166043363 + Missense_Mutation SNP T T G novel C3N-02423_T C3N-02423_N T T c.1468T>G p.Trp490Gly p.W490G ENST00000061240 12/21 446 400 46 473 473 0 strelka-varscan TLL1,missense_variant,p.Trp490Gly,ENST00000061240,NM_012464.4;TLL1,missense_variant,p.Trp490Gly,ENST00000507499,;TLL1,3_prime_UTR_variant,,ENST00000509505,; G ENST00000061240 Transcript missense_variant 2115/6708 1468/3042 490/1013 W/G Tgg/Ggg 1 1 TLL1 HGNC HGNC:11843 protein_coding YES CCDS3811.1 ENSP00000061240 O43897 UPI0000072EED NM_012464.4 deleterious(0) 12/21 Gene3D:2.60.120.290,Pfam_domain:PF00431,PIRSF_domain:PIRSF001199,PROSITE_profiles:PS01180,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF304,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 166043363 166043363 T G 1 0 0 0 0 1 0 0 0 16391 1696 59 5 5 TLL1 4 166043363 Missense_Mutation SNP T C3N-02423_T 4 166043363 24171192 133 29263 99 2 DDX60L 0 . GRCh38 4 168391540 168391540 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.3915G>T p.Gln1305His p.Q1305H ENST00000260184 29/38 143 128 15 149 148 1 strelka-varscan DDX60L,missense_variant,p.Gln1305His,ENST00000511577,;DDX60L,missense_variant,p.Gln1305His,ENST00000260184,NM_001012967.2;DDX60L,missense_variant,p.Gln1306His,ENST00000505890,NM_001291510.1;DDX60L,missense_variant,p.Gln193His,ENST00000514580,;DDX60L,downstream_gene_variant,,ENST00000505863,;DDX60L,downstream_gene_variant,,ENST00000503190,; A ENST00000260184 Transcript missense_variant,splice_region_variant 4136/6754 3915/5121 1305/1706 Q/H caG/caT 1 -1 DDX60L HGNC HGNC:26429 protein_coding YES CCDS47161.1 ENSP00000260184 Q5H9U9 UPI0003EAE873 NM_001012967.2 deleterious(0) 29/38 PROSITE_profiles:PS51194,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 168391540 168391540 C A 1 0 0 0 0 1 0 0 0 4182 695 24 2 2 DDX60L 4 168391540 Missense_Mutation SNP C C3N-02423_T 2348177 168391540 21823015 134 29264 PALLD 0 . GRCh38 4 168926374 168926374 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.2008G>A p.Glu670Lys p.E670K ENST00000507735 12/12 187 174 13 167 167 0 strelka-varscan PALLD,missense_variant,p.Glu670Lys,ENST00000507735,NM_001166110.1;PALLD,missense_variant,p.Glu775Lys,ENST00000512127,NM_001166109.1;PALLD,3_prime_UTR_variant,,ENST00000261509,NM_016081.3;PALLD,downstream_gene_variant,,ENST00000505667,NM_001166108.1;PALLD,downstream_gene_variant,,ENST00000503290,;CBR4,intron_variant,,ENST00000509108,;PALLD,non_coding_transcript_exon_variant,,ENST00000507699,;CBR4,intron_variant,,ENST00000510042,; A ENST00000507735 Transcript missense_variant 2308/4379 2008/2019 670/672 E/K Gag/Aag 1 1 PALLD HGNC HGNC:17068 protein_coding CCDS54820.1 ENSP00000424016 Q8WX93 UPI00015B3BE3 NM_001166110.1 deleterious(0.01) 12/12 hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF741 MODERATE SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 168926374 168926374 G A 1 0 0 0 0 1 0 0 0 11487 1291 45 3 3 PALLD 4 168926374 Missense_Mutation SNP G C3N-02423_T 534834 168926374 21288181 135 29265 FAT1 0 . GRCh38 4 186619106 186619106 + Nonsense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.7480C>T p.Gln2494Ter p.Q2494* ENST00000441802 10/27 219 205 14 221 221 0 strelka-varscan FAT1,stop_gained,p.Gln2494Ter,ENST00000441802,NM_005245.3;FAT1,stop_gained,p.Gln2496Ter,ENST00000614102,; A ENST00000441802 Transcript stop_gained 7690/14786 7480/13767 2494/4588 Q/* Cag/Tag 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 10/27 Gene3D:2.60.40.60,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,Superfamily_domains:SSF49313 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 186619106 186619106 G A 1 0 0 0 0 0 1 0 0 5549 1299 45 3 3 FAT1 4 186619106 Nonsense_Mutation SNP G C3N-02423_T 17692732 186619106 3595449 136 29266 FAT1 0 . GRCh38 4 186619237 186619237 + Nonsense_Mutation SNP G G C C3N-02423_T C3N-02423_N G G c.7349C>G p.Ser2450Ter p.S2450* ENST00000441802 10/27 208 196 12 204 204 0 strelka-varscan FAT1,stop_gained,p.Ser2450Ter,ENST00000441802,NM_005245.3;FAT1,stop_gained,p.Ser2452Ter,ENST00000614102,; C ENST00000441802 Transcript stop_gained 7559/14786 7349/13767 2450/4588 S/* tCa/tGa COSM733828,COSM733829 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 10/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 HIGH 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 99 186619237 186619237 G C 1 0 0 0 0 0 1 0 0 5549 1294 45 4 4 FAT1 4 186619237 Nonsense_Mutation SNP G C3N-02423_T 131 186619237 3595318 137 29267 FAT1 0 . GRCh38 4 186620075 186620075 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.6511C>A p.Pro2171Thr p.P2171T ENST00000441802 10/27 233 219 14 235 234 1 strelka-varscan FAT1,missense_variant,p.Pro2171Thr,ENST00000441802,NM_005245.3;FAT1,missense_variant,p.Pro2173Thr,ENST00000614102,; T ENST00000441802 Transcript missense_variant 6721/14786 6511/13767 2171/4588 P/T Ccg/Acg 1 -1 FAT1 HGNC HGNC:3595 protein_coding YES CCDS47177.1 ENSP00000406229 Q14517 UPI000051946B NM_005245.3 tolerated(0.09) 10/27 Gene3D:2.60.40.60,Pfam_domain:PF00028,PROSITE_profiles:PS50268,hmmpanther:PTHR24026,hmmpanther:PTHR24026:SF42,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 186620075 186620075 G T 1 0 0 0 0 1 0 0 0 5549 1174 41 2 2 FAT1 4 186620075 Missense_Mutation SNP G C3N-02423_T 838 186620075 3594480 138 29268 ICE1 0 . GRCh38 5 5443172 5443172 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.314C>G p.Ser105Cys p.S105C ENST00000296564 6/19 153 145 8 144 144 0 strelka-varscan-mutect ICE1,missense_variant,p.Ser105Cys,ENST00000296564,NM_015325.2;ICE1,missense_variant,p.Ser28Cys,ENST00000512608,; G ENST00000296564 Transcript missense_variant 536/7927 314/6801 105/2266 S/C tCt/tGt 1 1 ICE1 HGNC HGNC:29154 protein_coding YES CCDS47187.1 ENSP00000296564 Q9Y2F5 UPI00015542F9 NM_015325.2 deleterious(0.05) 6/19 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11852:SF4,hmmpanther:PTHR11852 MODERATE 1 SNV 1 1 PASS rs1166787662 . 0 203 2 5 0 0 0 0 -10.47461 0.9917207 1 1 1 0 G 3 3 99 5443172 5443172 C G 1 0 0 0 0 1 0 0 0 7384 927 32 4 4 ICE1 5 5443172 Missense_Mutation SNP C C3N-02423_T 5443172 176095087 139 29269 ANKRD33B 0 . GRCh38 5 10564555 10564555 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.88G>T p.Val30Phe p.V30F ENST00000296657 1/4 159 138 21 142 142 0 strelka-varscan-mutect ANKRD33B,missense_variant,p.Val30Phe,ENST00000296657,NM_001164440.1;ANKRD33B,missense_variant,p.Val30Phe,ENST00000504806,; T ENST00000296657 Transcript missense_variant 88/9188 88/1485 30/494 V/F Gtc/Ttc 1 1 ANKRD33B HGNC HGNC:35240 protein_coding YES CCDS47191.1 ENSP00000296657 A6NCL7 UPI00001D7EE7 NM_001164440.1 deleterious(0.03) 1/4 hmmpanther:PTHR24173,hmmpanther:PTHR24173:SF1 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 10564555 10564555 G T 1 0 0 0 0 1 0 0 0 766 1261 44 2 2 ANKRD33B 5 10564555 Missense_Mutation SNP G C3N-02423_T 5121383 10564555 170973704 140 29270 CTNND2 0 . GRCh38 5 10973564 10973564 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.3567G>A p.= p.L1189L ENST00000304623 22/22 191 169 22 186 186 0 strelka-varscan-mutect CTNND2,synonymous_variant,p.=,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,synonymous_variant,p.=,ENST00000511377,NM_001288715.1;CTNND2,synonymous_variant,p.=,ENST00000503622,NM_001288716.1;CTNND2,synonymous_variant,p.=,ENST00000458100,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,downstream_gene_variant,,ENST00000506324,;CTNND2,3_prime_UTR_variant,,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,; T ENST00000304623 Transcript synonymous_variant 3757/5481 3567/3678 1189/1225 L ctG/ctA 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 22/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 LOW 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999891 1 1 1 0 T 2 4 99 10973564 10973564 C T 1 0 0 0 0 0 0 0 1 3829 581 21 3 3 CTNND2 5 10973564 Silent SNP C C3N-02423_T 409009 10973564 170564695 141 29271 CTNND2 0 . GRCh38 5 11364707 11364707 + Missense_Mutation SNP C C A rs750266236 C3N-02423_T C3N-02423_N C C c.1361G>T p.Arg454Leu p.R454L ENST00000304623 8/22 119 104 15 135 135 0 strelka-varscan-mutect CTNND2,missense_variant,p.Arg454Leu,ENST00000304623,NM_001332.3,NM_001288717.1;CTNND2,missense_variant,p.Arg363Leu,ENST00000511377,NM_001288715.1;CTNND2,missense_variant,p.Arg117Leu,ENST00000503622,NM_001288716.1;CTNND2,missense_variant,p.Arg194Leu,ENST00000502551,;CTNND2,non_coding_transcript_exon_variant,,ENST00000495388,;CTNND2,non_coding_transcript_exon_variant,,ENST00000504354,;CTNND2,non_coding_transcript_exon_variant,,ENST00000506735,;CTNND2,downstream_gene_variant,,ENST00000511278,;CTNND2,missense_variant,p.Arg208Leu,ENST00000513588,;CTNND2,3_prime_UTR_variant,,ENST00000504499,;CTNND2,non_coding_transcript_exon_variant,,ENST00000507430,; A ENST00000304623 Transcript missense_variant 1551/5481 1361/3678 454/1225 R/L cGc/cTc rs750266236 1 -1 CTNND2 HGNC HGNC:2516 protein_coding YES CCDS3881.1 ENSP00000307134 Q9UQB3 UPI000013E9AB NM_001332.3,NM_001288717.1 tolerated(0.14) 8/22 hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF9 MODERATE 1 SNV 1 1 PASS rs750266236 . 0 205 3 2 0 0 0 0 -19.99959 0.999991 1 1 1 0 A 3 1 99 11364707 11364707 C A 1 0 0 0 0 1 0 0 0 3829 768 27 1 1 CTNND2 5 11364707 Missense_Mutation SNP C C3N-02423_T 391143 11364707 170173552 142 29272 MARCH11 0 . GRCh38 5 16067483 16067483 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.1197G>T p.= p.V399V ENST00000332432 4/4 103 95 8 117 117 0 strelka-varscan-mutect MARCH11,synonymous_variant,p.=,ENST00000332432,NM_001102562.1;MARCH11,3_prime_UTR_variant,,ENST00000507111,; A ENST00000332432 Transcript synonymous_variant 1397/1741 1197/1209 399/402 V gtG/gtT 1 -1 MARCH11 HGNC HGNC:33609 protein_coding YES CCDS47192.1 ENSP00000333181 A6NNE9 UPI00015B3D4A NM_001102562.1 4/4 hmmpanther:PTHR23012:SF67,hmmpanther:PTHR23012 LOW 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -16.31827 1 1 1 1 0 A 2 1 99 16067483 16067483 C A 1 0 0 0 0 0 0 0 1 9225 813 29 2 2 MARCH11 5 16067483 Silent SNP C C3N-02423_T 4702776 16067483 165470776 143 29273 CDH12 0 . GRCh38 5 21842165 21842165 + Silent SNP G G T C3N-02423_T C3N-02423_N G G c.810C>A p.= p.P270P ENST00000382254 8/15 94 75 19 83 83 0 strelka-varscan-mutect CDH12,synonymous_variant,p.=,ENST00000382254,NM_004061.3;CDH12,synonymous_variant,p.=,ENST00000504376,;CDH12,synonymous_variant,p.=,ENST00000522262,;CDH12,non_coding_transcript_exon_variant,,ENST00000521384,;CDH12,non_coding_transcript_exon_variant,,ENST00000517378,; T ENST00000382254 Transcript synonymous_variant 1897/4164 810/2385 270/794 P ccC/ccA COSM5195062,COSM737307 1 -1 CDH12 HGNC HGNC:1751 protein_coding YES CCDS3890.1 ENSP00000371689 P55289 UPI00000622EB NM_004061.3 8/15 Gene3D:2.60.40.60,Prints_domain:PR00205,PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF96,Superfamily_domains:SSF49313 1,1 LOW 1 SNV 1 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 21842165 21842165 G T 1 0 0 0 0 0 0 0 1 2801 1362 47 2 2 CDH12 5 21842165 Silent SNP G C3N-02423_T 5774682 21842165 159696094 144 29274 PRDM9 0 . GRCh38 5 23526464 23526464 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1376G>T p.Arg459Met p.R459M ENST00000296682 11/11 454 394 60 545 545 0 varscan-mutect PRDM9,missense_variant,p.Arg459Met,ENST00000296682,NM_020227.2;PRDM9,missense_variant,p.Arg400Met,ENST00000635252,; T ENST00000296682 Transcript missense_variant 1558/3691 1376/2685 459/894 R/M aGg/aTg 1 1 PRDM9 HGNC HGNC:13994 protein_coding YES CCDS43307.1 ENSP00000296682 Q9NQV7 UPI00006C9E90 NM_020227.2 tolerated(0.13) 11/11 hmmpanther:PTHR16515,hmmpanther:PTHR16515:SF10 MODERATE 1 SNV 1 1 PASS rs1327487744 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 23526464 23526464 G T 1 0 0 0 0 1 0 0 0 12595 1000 35 2 2 PRDM9 5 23526464 Missense_Mutation SNP G C3N-02423_T 1684299 23526464 158011795 145 29275 CDH10 0 . GRCh38 5 24487819 24487819 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.2211C>A p.= p.A737A ENST00000264463 12/12 277 236 41 268 268 0 strelka-varscan-mutect CDH10,synonymous_variant,p.=,ENST00000264463,NM_006727.3;CDH10,non_coding_transcript_exon_variant,,ENST00000502921,;CDH10,3_prime_UTR_variant,,ENST00000510477,;CDH10,non_coding_transcript_exon_variant,,ENST00000503958,; T ENST00000264463 Transcript synonymous_variant 2719/3438 2211/2367 737/788 A gcC/gcA 1 -1 CDH10 HGNC HGNC:1749 protein_coding YES CCDS3892.1 ENSP00000264463 Q9Y6N8 X5D8X5 UPI0000167B7B NM_006727.3 12/12 hmmpanther:PTHR24027:SF290,hmmpanther:PTHR24027,Gene3D:4.10.900.10,Pfam_domain:PF01049 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 24487819 24487819 G T 1 0 0 0 0 0 0 0 1 2799 987 35 2 2 CDH10 5 24487819 Silent SNP G C3N-02423_T 961355 24487819 157050440 146 29276 ARHGEF28 0 . GRCh38 5 73867924 73867924 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.2201C>T p.Ser734Phe p.S734F ENST00000545377 19/37 215 202 13 250 250 0 strelka-mutect ARHGEF28,missense_variant,p.Ser734Phe,ENST00000545377,NM_001080479.2;ARHGEF28,missense_variant,p.Ser734Phe,ENST00000513042,NM_001177693.1;ARHGEF28,missense_variant,p.Ser734Phe,ENST00000426542,;ARHGEF28,missense_variant,p.Ser734Phe,ENST00000437974,;ARHGEF28,missense_variant,p.Ser734Phe,ENST00000296794,;ARHGEF28,missense_variant,p.Ser421Phe,ENST00000296799,NM_001244364.1;ARHGEF28,non_coding_transcript_exon_variant,,ENST00000506334,; T ENST00000545377 Transcript missense_variant 2377/6351 2201/5196 734/1731 S/F tCt/tTt 1 1 ARHGEF28 HGNC HGNC:30322 protein_coding YES CCDS47231.2 ENSP00000441913 Q8N1W1 UPI00004DF58E NM_001080479.2 deleterious(0) 19/37 hmmpanther:PTHR12673,hmmpanther:PTHR12673:SF133 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 73867924 73867924 C T 1 0 0 0 0 1 0 0 0 1036 913 32 3 3 ARHGEF28 5 73867924 Missense_Mutation SNP C C3N-02423_T 49380105 73867924 107670335 147 29277 VCAN 0 . GRCh38 5 83537805 83537805 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.4802T>A p.Val1601Asp p.V1601D ENST00000265077 8/15 399 351 48 472 472 0 strelka-varscan-mutect VCAN,missense_variant,p.Val1601Asp,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Val614Asp,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Val614Asp,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; A ENST00000265077 Transcript missense_variant 5367/12625 4802/10191 1601/3396 V/D gTt/gAt 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 tolerated(0.08) 8/15 Low_complexity_(Seg):seg,hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 83537805 83537805 T A 1 0 0 0 0 1 0 0 0 17683 1725 60 4 4 VCAN 5 83537805 Missense_Mutation SNP T C3N-02423_T 9669881 83537805 98000454 148 29278 VCAN 0 . GRCh38 5 83537852 83537852 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.4849G>C p.Glu1617Gln p.E1617Q ENST00000265077 8/15 234 194 40 319 319 0 strelka-varscan-mutect VCAN,missense_variant,p.Glu1617Gln,ENST00000265077,NM_004385.4;VCAN,missense_variant,p.Glu630Gln,ENST00000343200,NM_001164097.1;VCAN,missense_variant,p.Glu630Gln,ENST00000513960,;VCAN,intron_variant,,ENST00000342785,NM_001164098.1;VCAN,intron_variant,,ENST00000512590,;VCAN,intron_variant,,ENST00000502527,NM_001126336.2;VCAN-AS1,intron_variant,,ENST00000512090,;VCAN-AS1,downstream_gene_variant,,ENST00000513899,;VCAN,non_coding_transcript_exon_variant,,ENST00000513016,;VCAN,upstream_gene_variant,,ENST00000507162,;VCAN,downstream_gene_variant,,ENST00000515397,; C ENST00000265077 Transcript missense_variant 5414/12625 4849/10191 1617/3396 E/Q Gaa/Caa 1 1 VCAN HGNC HGNC:2464 protein_coding YES CCDS4060.1 ENSP00000265077 P13611 A0A024RAQ9 UPI000013178B NM_004385.4 deleterious(0) 8/15 hmmpanther:PTHR22804,hmmpanther:PTHR22804:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 83537852 83537852 G C 1 0 0 0 0 1 0 0 0 17683 943 33 4 4 VCAN 5 83537852 Missense_Mutation SNP G C3N-02423_T 47 83537852 98000407 149 29279 SEMA6A 0 . GRCh38 5 116502224 116502224 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.204C>T p.= p.L68L ENST00000257414 3/20 197 176 21 208 208 0 strelka-varscan-mutect SEMA6A,synonymous_variant,p.=,ENST00000343348,NM_020796.4;SEMA6A,synonymous_variant,p.=,ENST00000257414,NM_001300780.1;SEMA6A,synonymous_variant,p.=,ENST00000510263,;SEMA6A,synonymous_variant,p.=,ENST00000515009,;SEMA6A,synonymous_variant,p.=,ENST00000509665,;SEMA6A-AS1,intron_variant,,ENST00000510682,;SEMA6A-AS1,downstream_gene_variant,,ENST00000514214,;SEMA6A,non_coding_transcript_exon_variant,,ENST00000503962,; A ENST00000257414 Transcript synonymous_variant 453/4256 204/3144 68/1047 L ctC/ctT 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 3/20 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12,SMART_domains:SM00630,Superfamily_domains:SSF101912 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 116502224 116502224 G A 1 0 0 0 0 0 0 0 1 14315 929 33 3 3 SEMA6A 5 116502224 Silent SNP G C3N-02423_T 32964372 116502224 65036035 150 29280 PCDHGA1 0 . GRCh38 5 141331238 141331238 + Missense_Mutation SNP G G C C3N-02423_T C3N-02423_N G G c.554G>C p.Gly185Ala p.G185A ENST00000517417 1/4 164 154 10 214 214 0 strelka-varscan-mutect PCDHGA1,missense_variant,p.Gly185Ala,ENST00000517417,NM_018912.2;PCDHGA1,missense_variant,p.Gly185Ala,ENST00000378105,NM_031993.1;AC005618.6,downstream_gene_variant,,ENST00000606901,;AC005618.6,downstream_gene_variant,,ENST00000606674,; C ENST00000517417 Transcript missense_variant 554/4604 554/2796 185/931 G/A gGa/gCa COSM4552276,COSM4552277 1 1 PCDHGA1 HGNC HGNC:8696 protein_coding YES CCDS54922.1 ENSP00000431083 Q9Y5H4 UPI0000070596 NM_018912.2 deleterious_low_confidence(0.05) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF108,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs756137799 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 141331238 141331238 G C 1 0 0 0 0 1 0 0 0 11637 1174 41 4 4 PCDHGA1 5 141331238 Missense_Mutation SNP G C3N-02423_T 24829014 141331238 40207021 151 29281 PCDHGA4 0 . GRCh38 5 141357425 141357425 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.2318G>T p.Gly773Val p.G773V ENST00000571252 1/4 260 244 16 340 340 0 varscan-mutect PCDHGA4,missense_variant,p.Gly773Val,ENST00000571252,NM_018917.3;PCDHGA4,missense_variant,p.Gly773Val,ENST00000612927,NM_032053.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB2,upstream_gene_variant,,ENST00000522605,NM_018923.2;PCDHGB1,downstream_gene_variant,,ENST00000611598,NM_032095.1;PCDHGB2,upstream_gene_variant,,ENST00000622527,NM_032096.1;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000571252 Transcript missense_variant 2401/4778 2318/2889 773/962 G/V gGc/gTc 1 1 PCDHGA4 HGNC HGNC:8702 protein_coding YES CCDS58979.2 ENSP00000458570 A0A087WT05 UPI0003583741 NM_018917.3 deleterious_low_confidence(0) 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF94,Pfam_domain:PF16492 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 141357425 141357425 G T 1 0 0 0 0 1 0 0 0 11643 1203 42 2 2 PCDHGA4 5 141357425 Missense_Mutation SNP G C3N-02423_T 26187 141357425 40180834 152 29282 SH3PXD2B 0 . GRCh38 5 172394584 172394584 + Missense_Mutation SNP T T C C3N-02423_T C3N-02423_N T T c.288A>G p.Ile96Met p.I96M ENST00000311601 4/13 464 395 69 533 533 0 strelka-varscan-mutect SH3PXD2B,missense_variant,p.Ile96Met,ENST00000311601,NM_001017995.2;SH3PXD2B,missense_variant,p.Ile82Met,ENST00000636523,;SH3PXD2B,missense_variant,p.Ile96Met,ENST00000519643,NM_001308175.1; C ENST00000311601 Transcript missense_variant 459/7777 288/2736 96/911 I/M atA/atG COSM1132207 1 -1 SH3PXD2B HGNC HGNC:29242 protein_coding YES CCDS34291.1 ENSP00000309714 A1X283 UPI000020C12E NM_001017995.2 tolerated(0.11) 4/13 Gene3D:3.30.1520.10,Pfam_domain:PF00787,PROSITE_profiles:PS50195,hmmpanther:PTHR15706,hmmpanther:PTHR15706:SF8,SMART_domains:SM00312,Superfamily_domains:SSF64268 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 172394584 172394584 T C 1 0 0 0 0 1 0 0 0 14516 1628 57 5 5 SH3PXD2B 5 172394584 Missense_Mutation SNP T C3N-02423_T 31037159 172394584 9143675 153 29283 TBC1D9B 0 . GRCh38 5 179864083 179864083 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.3118G>A p.Glu1040Lys p.E1040K ENST00000356834 22/22 139 128 11 90 90 0 strelka-varscan-mutect TBC1D9B,missense_variant,p.Glu1040Lys,ENST00000356834,NM_198868.2;TBC1D9B,missense_variant,p.Glu1023Lys,ENST00000355235,NM_015043.3;TBC1D9B,missense_variant,p.Glu199Lys,ENST00000519746,;TBC1D9B,3_prime_UTR_variant,,ENST00000524222,;TBC1D9B,intron_variant,,ENST00000522472,;CTC-241N9.1,downstream_gene_variant,,ENST00000499601,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000518085,;TBC1D9B,downstream_gene_variant,,ENST00000522180,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000520794,;TBC1D9B,non_coding_transcript_exon_variant,,ENST00000521469,;TBC1D9B,downstream_gene_variant,,ENST00000520912,;TBC1D9B,downstream_gene_variant,,ENST00000519757,;C5orf45,upstream_gene_variant,,ENST00000519398,;TBC1D9B,downstream_gene_variant,,ENST00000522921,; T ENST00000356834 Transcript missense_variant 3156/5173 3118/3753 1040/1250 E/K Gaa/Aaa 1 -1 TBC1D9B HGNC HGNC:29097 protein_coding YES CCDS43408.1 ENSP00000349291 Q66K14 UPI000034ECFF NM_198868.2 deleterious(0.05) 22/22 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 179864083 179864083 C T 1 0 0 0 0 1 0 0 0 16033 835 29 3 3 TBC1D9B 5 179864083 Missense_Mutation SNP C C3N-02423_T 7469499 179864083 1674176 154 29284 RNF130 0 . GRCh38 5 180040481 180040481 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.414A>T p.Lys138Asn p.K138N ENST00000521389 2/9 170 135 35 113 113 0 strelka-varscan-mutect RNF130,missense_variant,p.Lys138Asn,ENST00000522208,;RNF130,missense_variant,p.Lys138Asn,ENST00000521389,NM_018434.5;RNF130,missense_variant,p.Lys138Asn,ENST00000261947,NM_001280801.1;RNF130,missense_variant,p.Lys138Asn,ENST00000520911,; A ENST00000521389 Transcript missense_variant 830/2263 414/1260 138/419 K/N aaA/aaT 1 -1 RNF130 HGNC HGNC:18280 protein_coding YES CCDS4451.1 ENSP00000430237 Q86XS8 UPI000003776B NM_018434.5 tolerated(0.5) 2/9 hmmpanther:PTHR22765,hmmpanther:PTHR22765:SF40,Pfam_domain:PF02225,Gene3D:3.50.30.30,Superfamily_domains:SSF52025 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 180040481 180040481 T A 1 0 0 0 0 1 0 0 0 13616 1606 56 4 4 RNF130 5 180040481 Missense_Mutation SNP T C3N-02423_T 176398 180040481 1497778 155 29285 NOL7 0 . GRCh38 6 13615446 13615446 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.88G>C p.Glu30Gln p.E30Q ENST00000451315 1/8 149 139 10 155 155 0 strelka-varscan-mutect NOL7,missense_variant,p.Glu30Gln,ENST00000451315,NM_016167.3;SIRT5,downstream_gene_variant,,ENST00000397350,NM_001242827.1;SIRT5,downstream_gene_variant,,ENST00000606117,NM_012241.4;SIRT5,downstream_gene_variant,,ENST00000359782,NM_001193267.2;NOL7,upstream_gene_variant,,ENST00000420088,;RP1-223E5.4,upstream_gene_variant,,ENST00000566170,;NOL7,upstream_gene_variant,,ENST00000474485,;SIRT5,downstream_gene_variant,,ENST00000379250,; C ENST00000451315 Transcript missense_variant 120/1184 88/774 30/257 E/Q Gag/Cag 1 1 NOL7 HGNC HGNC:21040 protein_coding YES CCDS4528.1 ENSP00000405674 Q9UMY1 A0A024QZW2 UPI000007196C NM_016167.3 tolerated_low_confidence(0.07) 1/8 hmmpanther:PTHR32337,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 13615446 13615446 G C 1 0 0 0 0 1 0 0 0 10570 1175 41 4 4 NOL7 6 13615446 Missense_Mutation SNP G C3N-02423_T 13615446 157190533 156 29286 PGBD1 0 . GRCh38 6 28301429 28301429 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.1575C>G p.= p.L525L ENST00000259883 7/7 280 262 18 272 272 0 strelka-varscan PGBD1,synonymous_variant,p.=,ENST00000259883,NM_032507.3,NM_001184743.1; G ENST00000259883 Transcript synonymous_variant 1980/3100 1575/2430 525/809 L ctC/ctG 1 1 PGBD1 HGNC HGNC:19398 protein_coding YES CCDS4648.1 ENSP00000259883 Q96JS3 UPI000006ED63 NM_032507.3,NM_001184743.1 7/7 Pfam_domain:PF13843,hmmpanther:PTHR23226,hmmpanther:PTHR23226:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 28301429 28301429 C G 1 0 0 0 0 0 0 0 1 11870 813 29 4 4 PGBD1 6 28301429 Silent SNP C C3N-02423_T 14685983 28301429 142504550 157 29287 OR2B3 0 . GRCh38 6 29087028 29087028 + Missense_Mutation SNP G G T rs199542279 C3N-02423_T C3N-02423_N G G c.221C>A p.Thr74Asn p.T74N ENST00000377173 1/1 381 348 33 439 438 1 strelka-varscan OR2B3,missense_variant,p.Thr74Asn,ENST00000377173,NM_001005226.2; T ENST00000377173 Transcript missense_variant 286/1007 221/942 74/313 T/N aCc/aAc rs199542279 1 -1 OR2B3 HGNC HGNC:8238 protein_coding YES CCDS34358.1 ENSP00000366378 O76000 A0A126GV76 UPI0000041DB9 NM_001005226.2 deleterious(0.02) 1/1 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR26453:SF103,hmmpanther:PTHR26453,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 29087028 29087028 G T 1 0 0 0 0 1 0 0 0 11069 1261 44 2 2 OR2B3 6 29087028 Missense_Mutation SNP G C3N-02423_T 785599 29087028 141718951 158 29288 DEF6 0 . GRCh38 6 35319641 35319641 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1333G>C p.Glu445Gln p.E445Q ENST00000316637 8/11 107 96 11 103 103 0 strelka-varscan DEF6,missense_variant,p.Glu445Gln,ENST00000316637,NM_022047.3;DEF6,downstream_gene_variant,,ENST00000468102,; C ENST00000316637 Transcript missense_variant 1338/2262 1333/1896 445/631 E/Q Gag/Cag 1 1 DEF6 HGNC HGNC:2760 protein_coding YES CCDS4802.1 ENSP00000319831 Q9H4E7 UPI000006E74E NM_022047.3 tolerated(0.08) 8/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR14383,hmmpanther:PTHR14383:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 35319641 35319641 G C 1 0 0 0 0 1 0 0 0 4189 943 33 4 4 DEF6 6 35319641 Missense_Mutation SNP G C3N-02423_T 6232613 35319641 135486338 159 29289 SRPK1 0 . GRCh38 6 35891003 35891003 + Nonsense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.85C>T p.Gln29Ter p.Q29* ENST00000373825 3/16 148 134 14 175 174 1 strelka-varscan SRPK1,stop_gained,p.Gln29Ter,ENST00000373825,NM_003137.4;SRPK1,stop_gained,p.Gln13Ter,ENST00000423325,;SRPK1,stop_gained,p.Gln45Ter,ENST00000361690,;SRPK1,stop_gained,p.Gln101Ter,ENST00000507909,;SRPK1,stop_gained,p.Gln45Ter,ENST00000512445,;SRPK1,intron_variant,,ENST00000510290,;SRPK1,non_coding_transcript_exon_variant,,ENST00000373821,;SRPK1,synonymous_variant,p.=,ENST00000508473,;SRPK1,non_coding_transcript_exon_variant,,ENST00000346162,;SRPK1,non_coding_transcript_exon_variant,,ENST00000513367,; A ENST00000373825 Transcript stop_gained 371/4592 85/1968 29/655 Q/* Cag/Tag 1 -1 SRPK1 HGNC HGNC:11305 protein_coding YES CCDS47415.1 ENSP00000362931 Q96SB4 UPI000020DBDD NM_003137.4 3/16 hmmpanther:PTHR24055:SF101,hmmpanther:PTHR24055 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 35891003 35891003 G A 1 0 0 0 0 0 1 0 0 15520 1299 45 3 3 SRPK1 6 35891003 Nonsense_Mutation SNP G C3N-02423_T 571362 35891003 134914976 160 29290 ADGRF5 0 . GRCh38 6 46884191 46884191 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.409C>G p.Leu137Val p.L137V ENST00000283296 5/21 175 160 15 196 196 0 strelka-varscan ADGRF5,missense_variant,p.Leu137Val,ENST00000283296,NM_001098518.1;ADGRF5,missense_variant,p.Leu137Val,ENST00000265417,NM_015234.4;ADGRF5,downstream_gene_variant,,ENST00000478711,; C ENST00000283296 Transcript missense_variant 698/5810 409/4041 137/1346 L/V Ctc/Gtc 1 -1 ADGRF5 HGNC HGNC:19030 protein_coding YES CCDS4919.1 ENSP00000283296 Q8IZF2 UPI000007075A NM_001098518.1 tolerated(0.83) 5/21 hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF272 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 46884191 46884191 G C 1 0 0 0 0 1 0 0 0 367 942 33 4 4 ADGRF5 6 46884191 Missense_Mutation SNP G C3N-02423_T 10993188 46884191 123921788 161 29291 HTR1B 0 . GRCh38 6 77462931 77462931 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.473C>T p.Ser158Leu p.S158L ENST00000369947 1/1 263 238 25 363 363 0 strelka-varscan HTR1B,missense_variant,p.Ser158Leu,ENST00000369947,NM_000863.1; A ENST00000369947 Transcript missense_variant 843/2021 473/1173 158/390 S/L tCa/tTa 1 -1 HTR1B HGNC HGNC:5287 protein_coding YES CCDS4986.1 ENSP00000358963 P28222 X5D7I5 UPI00000007CB NM_000863.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF16,Gene3D:1.20.1070.10,Pfam_domain:PF00001,SMART_domains:SM01381,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 77462931 77462931 G A 1 0 0 0 0 1 0 0 0 7333 1294 45 3 3 HTR1B 6 77462931 Missense_Mutation SNP G C3N-02423_T 30578740 77462931 93343048 162 29292 IBTK 0 . GRCh38 6 82202569 82202569 + Missense_Mutation SNP T T G novel C3N-02423_T C3N-02423_N T T c.2688A>C p.Leu896Phe p.L896F ENST00000306270 18/29 234 219 15 239 238 1 strelka-varscan IBTK,missense_variant,p.Leu896Phe,ENST00000306270,NM_015525.3;IBTK,missense_variant,p.Leu695Phe,ENST00000610980,;IBTK,missense_variant,p.Leu896Phe,ENST00000510291,NM_001300906.1;IBTK,missense_variant,p.Leu695Phe,ENST00000503631,;IBTK,3_prime_UTR_variant,,ENST00000503400,;IBTK,non_coding_transcript_exon_variant,,ENST00000505222,;IBTK,non_coding_transcript_exon_variant,,ENST00000369751,;IBTK,non_coding_transcript_exon_variant,,ENST00000445419,; G ENST00000306270 Transcript missense_variant 3238/6054 2688/4062 896/1353 L/F ttA/ttC 1 -1 IBTK HGNC HGNC:17853 protein_coding YES CCDS34490.1 ENSP00000305721 Q9P2D0 UPI000041929F NM_015525.3 tolerated(0.22) 18/29 hmmpanther:PTHR22872:SF2,hmmpanther:PTHR22872 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 82202569 82202569 T G 1 0 0 0 0 1 0 0 0 7376 1635 57 5 5 IBTK 6 82202569 Missense_Mutation SNP T C3N-02423_T 4739638 82202569 88603410 163 29293 HDAC2 0 . GRCh38 6 113959978 113959978 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.93G>A p.Met31Ile p.M31I ENST00000519065 2/14 185 170 15 209 209 0 strelka-varscan-mutect HDAC2,start_lost,p.Met1?,ENST00000368632,;HDAC2,start_lost,p.Met1?,ENST00000519108,;HDAC2,start_lost,p.Met1?,ENST00000521610,;HDAC2,start_lost,p.Met1?,ENST00000524334,;HDAC2,start_lost,p.Met1?,ENST00000518690,;HDAC2,start_lost,p.Met1?,ENST00000523240,;HDAC2,start_lost,p.Met1?,ENST00000520895,;HDAC2,start_lost,p.Met1?,ENST00000523628,;HDAC2,start_lost,p.Met1?,ENST00000522371,;HDAC2,missense_variant,p.Met31Ile,ENST00000519065,NM_001527.3;HDAC2,missense_variant,p.Met38Ile,ENST00000521163,;HDAC2,missense_variant,p.Met21Ile,ENST00000425835,;HDAC2,non_coding_transcript_exon_variant,,ENST00000521233,;HDAC2,non_coding_transcript_exon_variant,,ENST00000520170,;HDAC2,upstream_gene_variant,,ENST00000523334,;HDAC2,upstream_gene_variant,,ENST00000518756,; T ENST00000519065 Transcript missense_variant 470/9874 93/1467 31/488 M/I atG/atA 1 -1 HDAC2 HGNC HGNC:4853 protein_coding YES CCDS43493.2 ENSP00000430432 Q92769 UPI000020E11B NM_001527.3 deleterious(0) 2/14 hmmpanther:PTHR10625:SF109,hmmpanther:PTHR10625,Pfam_domain:PF00850,PIRSF_domain:PIRSF037913,Gene3D:3.40.800.20,Superfamily_domains:SSF52768,Prints_domain:PR01271 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 113959978 113959978 C T 1 0 0 0 0 1 0 0 0 6894 826 29 3 3 HDAC2 6 113959978 Missense_Mutation SNP C C3N-02423_T 31757409 113959978 56846001 164 29294 STX11 0 . GRCh38 6 144187078 144187078 + Missense_Mutation SNP A A C novel C3N-02423_T C3N-02423_N A A c.451A>C p.Met151Leu p.M151L ENST00000367568 2/2 464 363 101 552 551 1 strelka-varscan STX11,missense_variant,p.Met151Leu,ENST00000367568,NM_003764.3; C ENST00000367568 Transcript missense_variant 634/1926 451/864 151/287 M/L Atg/Ctg 1 1 STX11 HGNC HGNC:11429 protein_coding YES CCDS5205.1 ENSP00000356540 O75558 UPI0000001C25 NM_003764.3 tolerated(0.07) 2/2 Gene3D:1.20.58.70,Pfam_domain:PF00804,hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF30,SMART_domains:SM00503,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 144187078 144187078 A C 1 0 0 0 0 1 0 0 0 15721 333 12 5 5 STX11 6 144187078 Missense_Mutation SNP A C3N-02423_T 30227100 144187078 26618901 165 29295 TIAM2 0 . GRCh38 6 155130007 155130007 + Missense_Mutation SNP G G A rs182530977 C3N-02423_T C3N-02423_N G G c.784G>A p.Glu262Lys p.E262K ENST00000461783 6/29 254 238 16 264 264 0 strelka-varscan TIAM2,missense_variant,p.Glu262Lys,ENST00000461783,;TIAM2,missense_variant,p.Glu262Lys,ENST00000318981,NM_012454.3;TIAM2,missense_variant,p.Glu262Lys,ENST00000360366,;TIAM2,missense_variant,p.Glu262Lys,ENST00000529824,;TIAM2,missense_variant,p.Glu262Lys,ENST00000528535,;TIAM2,downstream_gene_variant,,ENST00000535583,;TIAM2,downstream_gene_variant,,ENST00000538270,;TIAM2,downstream_gene_variant,,ENST00000535231,;TIAM2,downstream_gene_variant,,ENST00000545347,; A ENST00000461783 Transcript missense_variant 2057/6981 784/5106 262/1701 E/K Gag/Aag rs182530977,COSM3622215,COSM3920967 1 1 TIAM2 HGNC HGNC:11806 protein_coding YES CCDS34558.1 ENSP00000437188 Q8IVF5 UPI00004DF8BE deleterious(0) 6/29 hmmpanther:PTHR22826:SF118,hmmpanther:PTHR22826 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 155130007 155130007 G A 1 0 0 0 0 1 0 0 0 16325 1059 37 1 1 TIAM2 6 155130007 Missense_Mutation SNP G C3N-02423_T 10942929 155130007 15675972 166 29296 LRRC72 0 . GRCh38 7 16532494 16532494 + Splice_Site SNP G G T rs778520591 C3N-02423_T C3N-02423_N G G c.91-1G>T p.X31_splice ENST00000401542 252 219 33 232 232 0 strelka-varscan-mutect LRRC72,splice_acceptor_variant,,ENST00000401542,NM_001195280.1;SOSTDC1,upstream_gene_variant,,ENST00000396652,;LRRC72,splice_acceptor_variant,,ENST00000482711,;LRRC72,splice_acceptor_variant,,ENST00000382124,; T ENST00000401542 Transcript splice_acceptor_variant -/1000 91/864 31/287 rs778520591 1 1 LRRC72 HGNC HGNC:42972 protein_coding YES CCDS56464.1 ENSP00000384971 A6NJI9 UPI000173A227 NM_001195280.1 1/8 HIGH 1 SNV 5 1 PASS rs778520591 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 99 16532494 16532494 G T 1 0 0 0 0 0 0 1 0 8919 1014 35 2 2 LRRC72 7 16532494 Splice_Site SNP G C3N-02423_T 16532494 142813479 167 29297 STK31 0 . GRCh38 7 23752830 23752830 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1131G>C p.Met377Ile p.M377I ENST00000355870 9/24 189 173 16 200 200 0 strelka-varscan STK31,missense_variant,p.Met354Ile,ENST00000354639,NM_032944.3,NM_001260504.1;STK31,missense_variant,p.Met377Ile,ENST00000355870,NM_031414.4;STK31,missense_variant,p.Met377Ile,ENST00000433467,NM_001260505.1;STK31,splice_region_variant,,ENST00000405627,;STK31,splice_region_variant,,ENST00000478321,;STK31,splice_region_variant,,ENST00000529549,;STK31,splice_region_variant,,ENST00000476399,; C ENST00000355870 Transcript missense_variant,splice_region_variant 1250/3326 1131/3060 377/1019 M/I atG/atC 1 1 STK31 HGNC HGNC:11407 protein_coding YES CCDS5386.1 ENSP00000348132 Q9BXU1 UPI0000167B73 NM_031414.4 tolerated(0.87) 9/24 hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 23752830 23752830 G C 1 0 0 0 0 1 0 0 0 15673 1304 45 4 4 STK31 7 23752830 Missense_Mutation SNP G C3N-02423_T 7220336 23752830 135593143 168 29298 STK31 0 . GRCh38 7 23832159 23832159 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.2853C>T p.= p.L951L ENST00000355870 24/24 174 162 12 176 176 0 strelka-varscan STK31,synonymous_variant,p.=,ENST00000354639,NM_032944.3,NM_001260504.1;STK31,synonymous_variant,p.=,ENST00000355870,NM_031414.4;STK31,synonymous_variant,p.=,ENST00000433467,NM_001260505.1;STK31,non_coding_transcript_exon_variant,,ENST00000405627,; T ENST00000355870 Transcript synonymous_variant 2972/3326 2853/3060 951/1019 L ctC/ctT 1 1 STK31 HGNC HGNC:11407 protein_coding YES CCDS5386.1 ENSP00000348132 Q9BXU1 UPI0000167B73 NM_031414.4 24/24 Gene3D:1.10.510.10,PROSITE_profiles:PS50011,hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF3,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 23832159 23832159 C T 1 0 0 0 0 0 0 0 1 15673 900 32 3 3 STK31 7 23832159 Silent SNP C C3N-02423_T 79329 23832159 135513814 169 29299 CPVL 0 . GRCh38 7 29095083 29095083 + Splice_Site SNP C C G novel C3N-02423_T C3N-02423_N C C c.462+1G>C p.X154_splice ENST00000409850 270 229 41 282 282 0 strelka-varscan CPVL,splice_donor_variant,,ENST00000409850,;CPVL,splice_donor_variant,,ENST00000265394,NM_031311.3;CPVL,splice_donor_variant,,ENST00000396276,NM_019029.2;CPVL,splice_donor_variant,,ENST00000448959,;CPVL,splice_donor_variant,,ENST00000447426,;CPVL,splice_donor_variant,,ENST00000458405,;CPVL,downstream_gene_variant,,ENST00000488891,; G ENST00000409850 Transcript splice_donor_variant -/2213 462/1431 154/476 1 -1 CPVL HGNC HGNC:14399 protein_coding YES CCDS5419.1 ENSP00000387164 Q9H3G5 A0A024RA40 UPI0000048F1B 9/16 HIGH 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 99 29095083 29095083 C G 1 0 0 0 0 0 0 1 0 3633 579 20 4 4 CPVL 7 29095083 Splice_Site SNP C C3N-02423_T 5262924 29095083 130250890 170 29300 ZNRF2 0 . GRCh38 7 30285633 30285633 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.276G>T p.= p.S92S ENST00000323037 1/5 63 56 7 70 70 0 strelka-varscan ZNRF2,synonymous_variant,p.=,ENST00000323037,NM_147128.3;MIR550A1,upstream_gene_variant,,ENST00000385037,;hsa-mir-550a-1,downstream_gene_variant,,ENST00000637270,;ZNRF2,non_coding_transcript_exon_variant,,ENST00000459998,; T ENST00000323037 Transcript synonymous_variant 1327/3460 276/729 92/242 S tcG/tcT 1 1 ZNRF2 HGNC HGNC:22316 protein_coding YES CCDS5426.1 ENSP00000323879 Q8NHG8 A0A090N8Y8 UPI000006DDF0 NM_147128.3 1/5 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -15.74355 0.9999883 1 1 1 0 T 2 4 99 30285633 30285633 G T 1 0 0 0 0 0 0 0 1 18805 1103 39 1 1 ZNRF2 7 30285633 Silent SNP G C3N-02423_T 1190550 30285633 129060340 171 29301 CRHR2 0 . GRCh38 7 30653490 30653490 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1287C>A p.Phe429Leu p.F429L ENST00000348438 13/13 206 167 39 209 209 0 strelka-varscan CRHR2,missense_variant,p.Phe388Leu,ENST00000341843,NM_001202481.1;CRHR2,missense_variant,p.Phe402Leu,ENST00000471646,NM_001883.4,NM_001202482.1;CRHR2,missense_variant,p.Phe429Leu,ENST00000348438,NM_001202475.1;CRHR2,3_prime_UTR_variant,,ENST00000506074,NM_001202483.1;CRHR2,3_prime_UTR_variant,,ENST00000452278,; T ENST00000348438 Transcript missense_variant 1357/1600 1287/1317 429/438 F/L ttC/ttA 1 -1 CRHR2 HGNC HGNC:2358 protein_coding YES CCDS56478.1 ENSP00000340943 Q13324 UPI000002A720 NM_001202475.1 tolerated(0.08) 13/13 Prints_domain:PR01279,hmmpanther:PTHR12011,hmmpanther:PTHR12011:SF274 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 30653490 30653490 G T 1 0 0 0 0 1 0 0 0 3673 1165 41 2 2 CRHR2 7 30653490 Missense_Mutation SNP G C3N-02423_T 367857 30653490 128692483 172 29302 HECW1 0 . GRCh38 7 43541210 43541210 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.4067A>G p.Tyr1356Cys p.Y1356C ENST00000395891 25/30 302 284 18 313 313 0 strelka-varscan-mutect HECW1,missense_variant,p.Tyr1356Cys,ENST00000395891,NM_015052.4;HECW1,missense_variant,p.Tyr1322Cys,ENST00000453890,NM_001287059.1;HECW1,missense_variant,p.Tyr80Cys,ENST00000429529,; G ENST00000395891 Transcript missense_variant 4672/9501 4067/4821 1356/1606 Y/C tAc/tGc 1 1 HECW1 HGNC HGNC:22195 protein_coding YES CCDS5469.2 ENSP00000379228 Q76N89 UPI0000D74C41 NM_015052.4 tolerated(0.06) 25/30 PROSITE_profiles:PS50237,hmmpanther:PTHR11254:SF79,hmmpanther:PTHR11254,Pfam_domain:PF00632,SMART_domains:SM00119,Superfamily_domains:SSF56204 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 43541210 43541210 A G 1 0 0 0 0 1 0 0 0 6924 391 14 5 5 HECW1 7 43541210 Missense_Mutation SNP A C3N-02423_T 12887720 43541210 115804763 173 29303 AEBP1 0 . GRCh38 7 44106819 44106819 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.527C>T p.Ser176Leu p.S176L ENST00000223357 2/21 244 221 23 247 247 0 strelka-varscan-mutect AEBP1,missense_variant,p.Ser176Leu,ENST00000223357,NM_001129.4;AEBP1,missense_variant,p.Ser134Leu,ENST00000455443,;AEBP1,missense_variant,p.Ser92Leu,ENST00000449162,;AEBP1,upstream_gene_variant,,ENST00000450684,;AEBP1,upstream_gene_variant,,ENST00000582839,;AEBP1,upstream_gene_variant,,ENST00000454218,;AEBP1,upstream_gene_variant,,ENST00000413907,;AEBP1,upstream_gene_variant,,ENST00000431035,;AEBP1,upstream_gene_variant,,ENST00000453052,;AEBP1,upstream_gene_variant,,ENST00000434445,; T ENST00000223357 Transcript missense_variant 832/4081 527/3477 176/1158 S/L tCa/tTa 1 1 AEBP1 HGNC HGNC:303 protein_coding YES CCDS5476.1 ENSP00000223357 Q8IUX7 UPI00000746E2 NM_001129.4 tolerated_low_confidence(0.38) 2/21 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 44106819 44106819 C T 1 0 0 0 0 1 0 0 0 424 838 29 3 3 AEBP1 7 44106819 Missense_Mutation SNP C C3N-02423_T 565609 44106819 115239154 174 29304 H2AFV 0 . GRCh38 7 44834534 44834534 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.354G>C p.= p.L118L ENST00000308153 5/5 199 184 15 177 177 0 strelka-varscan-mutect H2AFV,synonymous_variant,p.=,ENST00000308153,NM_012412.4;H2AFV,synonymous_variant,p.=,ENST00000350771,NM_201436.2;H2AFV,synonymous_variant,p.=,ENST00000349299,NM_201517.2;H2AFV,3_prime_UTR_variant,,ENST00000381124,NM_201516.2;H2AFV,3_prime_UTR_variant,,ENST00000521529,;H2AFV,intron_variant,,ENST00000222690,NM_138635.3;H2AFV,intron_variant,,ENST00000437072,;H2AFV,downstream_gene_variant,,ENST00000446531,; G ENST00000308153 Transcript synonymous_variant 446/752 354/387 118/128 L ctG/ctC 1 -1 H2AFV HGNC HGNC:20664 protein_coding YES CCDS5496.1 ENSP00000308405 Q71UI9 UPI00000001D4 NM_012412.4 5/5 hmmpanther:PTHR23430,Pfam_domain:PF16211,Gene3D:1.10.20.10,SMART_domains:SM00414,Prints_domain:PR00620 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 44834534 44834534 C G 1 0 0 0 0 0 0 0 1 6808 813 29 4 4 H2AFV 7 44834534 Silent SNP C C3N-02423_T 727715 44834534 114511439 175 29305 PKD1L1 0 . GRCh38 7 47813152 47813152 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.7315G>A p.Glu2439Lys p.E2439K ENST00000289672 49/57 150 133 17 142 142 0 strelka-varscan-mutect PKD1L1,missense_variant,p.Glu2439Lys,ENST00000289672,NM_138295.3;PKD1L1,missense_variant,p.Glu30Lys,ENST00000433506,;C7orf69,intron_variant,,ENST00000418326,;C7orf69,intron_variant,,ENST00000623971,;PKD1L1,upstream_gene_variant,,ENST00000462350,;PKD1L1,non_coding_transcript_exon_variant,,ENST00000483616,;HUS1,intron_variant,,ENST00000436444,; T ENST00000289672 Transcript missense_variant 7366/9092 7315/8550 2439/2849 E/K Gag/Aag 1 -1 PKD1L1 HGNC HGNC:18053 protein_coding YES CCDS34633.1 ENSP00000289672 Q8TDX9 UPI0000130FA9 NM_138295.3 tolerated(0.24) 49/57 hmmpanther:PTHR10877:SF145,hmmpanther:PTHR10877 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 47813152 47813152 C T 1 0 0 0 0 1 0 0 0 12060 864 30 3 3 PKD1L1 7 47813152 Missense_Mutation SNP C C3N-02423_T 2978618 47813152 111532821 176 29306 ZNF713 0 . GRCh38 7 55939035 55939035 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.361G>C p.Asp121His p.D121H ENST00000429591 7/7 91 85 6 93 93 0 strelka-mutect ZNF713,missense_variant,p.Asp121His,ENST00000429591,NM_182633.2;ZNF713,missense_variant,p.Asp108His,ENST00000633730,;RP11-15K19.2,intron_variant,,ENST00000426595,; C ENST00000429591 Transcript missense_variant 1149/4339 361/1332 121/443 D/H Gat/Cat 1 1 ZNF713 HGNC HGNC:22043 protein_coding YES ENSP00000416662 A0A0M3HEQ9 UPI0000140F17 NM_182633.2 deleterious(0.05) 7/7 hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF80 MODERATE 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -13.11095 1 1 1 1 0 C 3 2 99 55939035 55939035 G C 1 0 0 0 0 1 0 0 0 18692 1290 45 4 4 ZNF713 7 55939035 Missense_Mutation SNP G C3N-02423_T 8125883 55939035 103406938 177 29307 ZNF735 0 . GRCh38 7 64220020 64220020 + Silent SNP A A G novel C3N-02423_T C3N-02423_N A A c.969A>G p.= p.K323K ENST00000429565 4/4 255 241 14 373 373 0 varscan-mutect ZNF735,synonymous_variant,p.=,ENST00000429565,NM_001159524.1; G ENST00000429565 Transcript synonymous_variant 1082/1570 969/1239 323/412 K aaA/aaG 1 1 ZNF735 HGNC HGNC:32466 protein_coding YES CCDS78236.1 ENSP00000485547 P0CB33 UPI0001662441 NM_001159524.1 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF103,Superfamily_domains:SSF57667 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 64220020 64220020 A G 1 0 0 0 0 0 0 0 1 18706 40 2 5 5 ZNF735 7 64220020 Silent SNP A C3N-02423_T 8280985 64220020 95125953 178 29308 CCDC146 0 . GRCh38 7 77293138 77293138 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.2602G>T p.Glu868Ter p.E868* ENST00000285871 18/19 369 346 23 341 341 0 strelka-varscan CCDC146,stop_gained,p.Glu868Ter,ENST00000285871,NM_020879.2;CCDC146,non_coding_transcript_exon_variant,,ENST00000415740,;CCDC146,non_coding_transcript_exon_variant,,ENST00000488998,;CCDC146,non_coding_transcript_exon_variant,,ENST00000461259,;CCDC146,non_coding_transcript_exon_variant,,ENST00000478101,;CCDC146,non_coding_transcript_exon_variant,,ENST00000474733,; T ENST00000285871 Transcript stop_gained 2729/3333 2602/2868 868/955 E/* Gaa/Taa 1 1 CCDC146 HGNC HGNC:29296 protein_coding YES CCDS34671.1 ENSP00000285871 Q8IYE0 UPI000020F44F NM_020879.2 18/19 hmmpanther:PTHR32083,hmmpanther:PTHR32083:SF27 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 77293138 77293138 G T 1 0 0 0 0 0 1 0 0 2467 943 33 2 2 CCDC146 7 77293138 Nonsense_Mutation SNP G C3N-02423_T 13073118 77293138 82052835 179 29309 DMTF1 0 . GRCh38 7 87181328 87181328 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.697G>T p.Glu233Ter p.E233* ENST00000394703 11/20 57 53 4 89 89 0 strelka-varscan DMTF1,stop_gained,p.Glu233Ter,ENST00000394703,NM_021145.3;DMTF1,stop_gained,p.Glu233Ter,ENST00000331242,NM_001142327.1;DMTF1,stop_gained,p.Glu233Ter,ENST00000413276,;DMTF1,stop_gained,p.Glu145Ter,ENST00000432937,NM_001142326.1;DMTF1,downstream_gene_variant,,ENST00000425705,;DMTF1,downstream_gene_variant,,ENST00000430405,;uc_338,upstream_gene_variant,,ENST00000615087,;DMTF1,stop_gained,p.Glu233Ter,ENST00000412139,;DMTF1,stop_gained,p.Glu233Ter,ENST00000447863,;DMTF1,stop_gained,p.Glu233Ter,ENST00000579677,;DMTF1,stop_gained,p.Glu192Ter,ENST00000425406,;DMTF1,stop_gained,p.Glu233Ter,ENST00000547146,;DMTF1,stop_gained,p.Glu192Ter,ENST00000579850,;DMTF1,stop_gained,p.Glu233Ter,ENST00000584619,;DMTF1,non_coding_transcript_exon_variant,,ENST00000473521,;DMTF1,upstream_gene_variant,,ENST00000480982,;DMTF1,upstream_gene_variant,,ENST00000582887,;DMTF1,upstream_gene_variant,,ENST00000578926,; T ENST00000394703 Transcript stop_gained 1260/4038 697/2283 233/760 E/* Gag/Tag 1 1 DMTF1 HGNC HGNC:14603 protein_coding YES CCDS5601.1 ENSP00000378193 Q9Y222 UPI000006FB78 NM_021145.3 11/20 Gene3D:1.10.10.60,Pfam_domain:PF00249,PROSITE_profiles:PS50090,hmmpanther:PTHR10641,hmmpanther:PTHR10641:SF672,Low_complexity_(Seg):seg,SMART_domains:SM00717,Superfamily_domains:SSF46689 HIGH 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -10.07827 1 1 1 1 0 T 4 4 99 87181328 87181328 G T 1 0 0 0 0 0 1 0 0 4400 1291 45 2 2 DMTF1 7 87181328 Nonsense_Mutation SNP G C3N-02423_T 9888190 87181328 72164645 180 29310 ASNS 0 . GRCh38 7 97864320 97864320 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.426C>G p.= p.V142V ENST00000175506 5/14 308 280 28 350 350 0 strelka-varscan ASNS,synonymous_variant,p.=,ENST00000175506,NM_183356.3;ASNS,synonymous_variant,p.=,ENST00000394309,NM_133436.3;ASNS,synonymous_variant,p.=,ENST00000394308,NM_001673.4;ASNS,synonymous_variant,p.=,ENST00000422745,;ASNS,synonymous_variant,p.=,ENST00000444334,NM_001178075.1;ASNS,synonymous_variant,p.=,ENST00000437628,NM_001178077.1;ASNS,synonymous_variant,p.=,ENST00000455086,NM_001178076.1;ASNS,synonymous_variant,p.=,ENST00000442734,;ASNS,synonymous_variant,p.=,ENST00000437657,;ASNS,downstream_gene_variant,,ENST00000414884,;ASNS,downstream_gene_variant,,ENST00000448127,;ASNS,downstream_gene_variant,,ENST00000453600,;ASNS,downstream_gene_variant,,ENST00000451771,;ASNS,synonymous_variant,p.=,ENST00000454046,;ASNS,non_coding_transcript_exon_variant,,ENST00000495255,; C ENST00000175506 Transcript synonymous_variant 955/2356 426/1686 142/561 V gtC/gtG 1 -1 ASNS HGNC HGNC:753 protein_coding YES CCDS5652.1 ENSP00000175506 P08243 UPI0000169F55 NM_183356.3 5/14 PROSITE_profiles:PS51278,hmmpanther:PTHR11772:SF2,hmmpanther:PTHR11772,Pfam_domain:PF13537,TIGRFAM_domain:TIGR01536,Gene3D:3.60.20.10,Superfamily_domains:SSF56235 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 97864320 97864320 G C 1 0 0 0 0 0 0 0 1 1195 1277 45 4 4 ASNS 7 97864320 Silent SNP G C3N-02423_T 10682992 97864320 61481653 181 29311 NYAP1 0 . GRCh38 7 100493849 100493849 + Silent SNP C C A rs776885960 C3N-02423_T C3N-02423_N C C c.2472C>A p.= p.S824S ENST00000300179 7/7 103 91 12 98 98 0 strelka-varscan NYAP1,synonymous_variant,p.=,ENST00000300179,NM_173564.3;NYAP1,synonymous_variant,p.=,ENST00000454988,;NYAP1,non_coding_transcript_exon_variant,,ENST00000496985,;NYAP1,non_coding_transcript_exon_variant,,ENST00000489641,; A ENST00000300179 Transcript synonymous_variant 2631/3581 2472/2526 824/841 S tcC/tcA rs776885960 1 1 NYAP1 HGNC HGNC:22009 protein_coding YES CCDS5696.1 ENSP00000300179 Q6ZVC0 UPI00001C0A2E NM_173564.3 7/7 Pfam_domain:PF15452,hmmpanther:PTHR22633,hmmpanther:PTHR22633:SF2 LOW 1 SNV 2 1 PASS . . 0 206 3 0 0 0 0 0 -19.99999 1 1 1 1 0 A 2 1 99 100493849 100493849 C A 1 0 0 0 0 0 0 0 1 10872 639 23 1 1 NYAP1 7 100493849 Silent SNP C C3N-02423_T 2629529 100493849 58852124 182 29312 MUC17 0 . GRCh38 7 101032868 101032868 + Silent SNP C C A rs760837383 C3N-02423_T C3N-02423_N C C c.1452C>A p.= p.T484T ENST00000306151 3/13 252 214 38 293 293 0 strelka-varscan MUC17,synonymous_variant,p.=,ENST00000306151,NM_001040105.1;MUC17,synonymous_variant,p.=,ENST00000379439,; A ENST00000306151 Transcript synonymous_variant 1516/14247 1452/13482 484/4493 T acC/acA rs760837383 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999,hmmpanther:PTHR37999:SF1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 101032868 101032868 C A 1 0 0 0 0 0 0 0 1 9973 581 21 2 2 MUC17 7 101032868 Silent SNP C C3N-02423_T 539019 101032868 58313105 183 29313 MOGAT3 0 . GRCh38 7 101196015 101196015 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.957G>T p.= p.L319L ENST00000223114 7/7 270 229 41 185 185 0 strelka-varscan MOGAT3,stop_gained,p.Gly252Ter,ENST00000379423,NM_001287147.1;MOGAT3,synonymous_variant,p.=,ENST00000223114,NM_178176.3;MOGAT3,3_prime_UTR_variant,,ENST00000440203,; A ENST00000223114 Transcript synonymous_variant 1124/2132 957/1026 319/341 L ctG/ctT 1 -1 MOGAT3 HGNC HGNC:23249 protein_coding YES CCDS5714.1 ENSP00000223114 Q86VF5 UPI00000622D1 NM_178176.3 7/7 Pfam_domain:PF03982,hmmpanther:PTHR12317,hmmpanther:PTHR12317:SF23 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 101196015 101196015 C A 1 0 0 0 0 0 0 0 1 9659 603 21 2 2 MOGAT3 7 101196015 Silent SNP C C3N-02423_T 163147 101196015 58149958 184 29314 PAX4 0 . GRCh38 7 127613763 127613763 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.531G>T p.= p.L177L ENST00000341640 4/9 314 279 35 341 340 1 strelka-varscan-mutect PAX4,synonymous_variant,p.=,ENST00000341640,NM_006193.2;PAX4,synonymous_variant,p.=,ENST00000463946,;PAX4,synonymous_variant,p.=,ENST00000611453,;PAX4,synonymous_variant,p.=,ENST00000378740,;PAX4,synonymous_variant,p.=,ENST00000338516,;PAX4,synonymous_variant,p.=,ENST00000483494,;PAX4,non_coding_transcript_exon_variant,,ENST00000477423,; A ENST00000341640 Transcript synonymous_variant 737/2010 531/1032 177/343 L ctG/ctT 1 -1 PAX4 HGNC HGNC:8618 protein_coding YES CCDS5797.1 ENSP00000339906 O43316 UPI000013C824 NM_006193.2 4/9 PROSITE_profiles:PS50071,hmmpanther:PTHR24329:SF14,hmmpanther:PTHR24329,Gene3D:1.10.10.60,Pfam_domain:PF00046,SMART_domains:SM00389,Superfamily_domains:SSF46689 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 127613763 127613763 C A 1 0 0 0 0 0 0 0 1 11566 581 21 2 2 PAX4 7 127613763 Silent SNP C C3N-02423_T 26417748 127613763 31732210 185 29315 CALU 0 . GRCh38 7 128754643 128754643 + Silent SNP A A G novel C3N-02423_T C3N-02423_N A A c.360A>G p.= p.Q120Q ENST00000542996 4/8 258 220 38 184 184 0 strelka-varscan-mutect CALU,synonymous_variant,p.=,ENST00000542996,NM_001199672.1;CALU,synonymous_variant,p.=,ENST00000449187,NM_001130674.2;CALU,intron_variant,,ENST00000249364,NM_001219.4;CALU,intron_variant,,ENST00000535011,NM_001199673.1;CALU,intron_variant,,ENST00000479257,NM_001199671.1;CALU,upstream_gene_variant,,ENST00000493278,; G ENST00000542996 Transcript synonymous_variant 1303/4225 360/972 120/323 Q caA/caG 1 1 CALU HGNC HGNC:1458 protein_coding YES CCDS56507.1 ENSP00000438248 O43852 UPI0001D27CDB NM_001199672.1 4/8 Gene3D:1.10.238.10,PROSITE_profiles:PS50222,hmmpanther:PTHR10827,hmmpanther:PTHR10827:SF34,SMART_domains:SM00054,Superfamily_domains:SSF47473 LOW 1 SNV 1 1 PASS rs1469371528 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 128754643 128754643 A G 1 0 0 0 0 0 0 0 1 2285 98 4 5 5 CALU 7 128754643 Silent SNP A C3N-02423_T 1140880 128754643 30591330 186 29316 PLXNA4 0 . GRCh38 7 132168414 132168414 + Silent SNP G G C rs369419660 C3N-02423_T C3N-02423_N G G c.4176C>G p.= p.T1392T ENST00000359827 22/32 130 116 14 112 112 0 strelka-varscan-mutect PLXNA4,synonymous_variant,p.=,ENST00000359827,;PLXNA4,synonymous_variant,p.=,ENST00000321063,NM_020911.1; C ENST00000359827 Transcript synonymous_variant 5139/13786 4176/5685 1392/1894 T acC/acG rs369419660,COSM288842,COSM288843 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B 22/32 Pfam_domain:PF08337,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,Superfamily_domains:SSF48350 0,1,1 LOW 1 SNV 5 0,1,1 1 PASS rs369419660 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 132168414 132168414 G C 1 0 0 0 0 0 0 0 1 12228 1103 39 4 4 PLXNA4 7 132168414 Silent SNP G C3N-02423_T 3413771 132168414 27177559 187 29317 PLXNA4 0 . GRCh38 7 132194087 132194087 + Missense_Mutation SNP C C A C3N-02423_T C3N-02423_N C C c.2831G>T p.Arg944Leu p.R944L ENST00000359827 14/32 123 109 14 92 92 0 strelka-varscan-mutect PLXNA4,missense_variant,p.Arg944Leu,ENST00000359827,;PLXNA4,missense_variant,p.Arg944Leu,ENST00000321063,NM_020911.1; A ENST00000359827 Transcript missense_variant 3794/13786 2831/5685 944/1894 R/L cGg/cTg COSM5337167,COSM5337168 1 -1 PLXNA4 HGNC HGNC:9102 protein_coding YES CCDS43646.1 ENSP00000352882 Q9HCM2 A0A024R7A6 UPI000004E55B tolerated(0.45) 14/32 Gene3D:2.60.40.10,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF34,SMART_domains:SM00429,Superfamily_domains:SSF81296 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1057400085 . 0 204 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 132194087 132194087 C A 1 0 0 0 0 1 0 0 0 12228 652 23 1 1 PLXNA4 7 132194087 Missense_Mutation SNP C C3N-02423_T 25673 132194087 27151886 188 29318 STRA8 0 . GRCh38 7 135232026 135232026 + Silent SNP C C T rs781689842 C3N-02423_T C3N-02423_N C C c.48C>T p.= p.I16I ENST00000275764 1/9 260 240 20 270 270 0 strelka-varscan-mutect STRA8,synonymous_variant,p.=,ENST00000275764,NM_182489.1; T ENST00000275764 Transcript synonymous_variant 48/993 48/993 16/330 I atC/atT rs781689842 1 1 STRA8 HGNC HGNC:30653 protein_coding YES CCDS5839.1 ENSP00000275764 Q7Z7C7 UPI00001A36D9 NM_182489.1 1/9 hmmpanther:PTHR35254 LOW 1 SNV 1 1 PASS rs781689842 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 135232026 135232026 C T 1 0 0 0 0 0 0 0 1 15704 816 29 3 3 STRA8 7 135232026 Silent SNP C C3N-02423_T 3037939 135232026 24113947 189 29319 MGAM2 0 . GRCh38 7 142199954 142199954 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.5123A>G p.Asp1708Gly p.D1708G ENST00000477922 45/48 162 142 20 146 146 0 strelka-varscan-mutect MGAM2,missense_variant,p.Asp1708Gly,ENST00000477922,NM_001293626.1;MGAM2,non_coding_transcript_exon_variant,,ENST00000496337,; G ENST00000477922 Transcript missense_variant 5177/7867 5123/7548 1708/2515 D/G gAt/gGt 1 1 MGAM2 HGNC HGNC:28101 protein_coding YES CCDS78281.1 ENSP00000420449 Q2M2H8 A0A0A6YYI8 UPI0002B8321D NM_001293626.1 deleterious(0) 45/48 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF55 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 142199954 142199954 A G 1 0 0 0 0 1 0 0 0 9500 333 12 5 5 MGAM2 7 142199954 Missense_Mutation SNP A C3N-02423_T 6967928 142199954 17146019 190 29320 CNTNAP2 0 . GRCh38 7 147300240 147300240 + Missense_Mutation SNP G G A rs777884519 C3N-02423_T C3N-02423_N G G c.1448G>A p.Arg483Gln p.R483Q ENST00000361727 9/24 404 375 29 380 380 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Arg483Gln,ENST00000361727,NM_014141.5;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636870,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637825,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,; A ENST00000361727 Transcript missense_variant 1966/9896 1448/3996 483/1331 R/Q cGa/cAa rs777884519,COSM1086966 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 tolerated(0.68) 9/24 Gene3D:2.60.120.200,Pfam_domain:PF02210,PROSITE_profiles:PS50025,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF644,SMART_domains:SM00282,Superfamily_domains:SSF49899 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs777884519 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 147300240 147300240 G A 1 0 0 0 0 1 0 0 0 3428 1058 37 1 1 CNTNAP2 7 147300240 Missense_Mutation SNP G C3N-02423_T 5100286 147300240 12045733 191 29321 NOS3 0 . GRCh38 7 150995230 150995230 + Silent SNP C C T C3N-02423_T C3N-02423_N C C c.186C>T p.= p.P62P ENST00000297494 3/27 99 84 15 109 109 0 strelka-varscan-mutect NOS3,synonymous_variant,p.=,ENST00000297494,NM_000603.4;NOS3,synonymous_variant,p.=,ENST00000484524,NM_001160111.1;NOS3,synonymous_variant,p.=,ENST00000467517,NM_001160109.1,NM_001160110.1;NOS3,5_prime_UTR_variant,,ENST00000461406,; T ENST00000297494 Transcript synonymous_variant 543/4388 186/3612 62/1203 P ccC/ccT COSM4904828 1 1 NOS3 HGNC HGNC:7876 protein_coding YES CCDS5912.1 ENSP00000297494 P29474 UPI000013E417 NM_000603.4 3/27 PIRSF_domain:PIRSF000333 1 LOW 1 SNV 1 1 1 PASS rs1048775049 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 99 150995230 150995230 C T 1 0 0 0 0 0 0 0 1 10589 610 22 3 3 NOS3 7 150995230 Silent SNP C C3N-02423_T 3694990 150995230 8350743 192 29322 ABCF2 0 . GRCh38 7 151224098 151224098 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.384C>G p.= p.L128L ENST00000222388 4/16 410 387 23 378 378 0 strelka-varscan-mutect ABCF2,synonymous_variant,p.=,ENST00000287844,NM_007189.2;ABCF2,synonymous_variant,p.=,ENST00000222388,NM_005692.4;ABCF2,synonymous_variant,p.=,ENST00000468073,;ABCF2,synonymous_variant,p.=,ENST00000441774,;ABCF2,upstream_gene_variant,,ENST00000473874,;ABCF2,downstream_gene_variant,,ENST00000477252,; C ENST00000222388 Transcript synonymous_variant 430/2185 384/1905 128/634 L ctC/ctG 1 -1 ABCF2 HGNC HGNC:71 protein_coding YES CCDS5922.1 ENSP00000222388 Q9UG63 A0A090N7Y2 UPI000004C4C9 NM_005692.4 4/16 PROSITE_profiles:PS50893,hmmpanther:PTHR19211,hmmpanther:PTHR19211:SF15,Gene3D:3.40.50.300,Pfam_domain:PF00005,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 151224098 151224098 G C 1 0 0 0 0 0 0 0 1 70 929 33 4 4 ABCF2 7 151224098 Silent SNP G C3N-02423_T 228868 151224098 8121875 193 29323 CSMD1 0 . GRCh38 8 3188895 3188895 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.5518G>T p.Gly1840Ter p.G1840* ENST00000520002 36/71 112 93 19 83 83 0 strelka-mutect CSMD1,stop_gained,p.Gly1701Ter,ENST00000537824,;CSMD1,stop_gained,p.Gly1320Ter,ENST00000335551,;CSMD1,stop_gained,p.Gly1840Ter,ENST00000520002,;CSMD1,stop_gained,p.Gly1840Ter,ENST00000602557,;CSMD1,stop_gained,p.Gly1839Ter,ENST00000635120,NM_033225.5;CSMD1,stop_gained,p.Gly1840Ter,ENST00000400186,;CSMD1,stop_gained,p.Gly1840Ter,ENST00000602723,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523387,;CSMD1,non_coding_transcript_exon_variant,,ENST00000523488,; A ENST00000520002 Transcript stop_gained 6074/11740 5518/10698 1840/3565 G/* Gga/Tga 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 36/71 Gene3D:2.60.120.290,Pfam_domain:PF00431,PROSITE_profiles:PS01180,SMART_domains:SM00042,Superfamily_domains:SSF49854 HIGH 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 3188895 3188895 C A 1 0 0 0 0 0 1 0 0 3745 632 22 2 2 CSMD1 8 3188895 Nonsense_Mutation SNP C C3N-02423_T 3188895 141949741 194 29324 USP17L4 0 . GRCh38 8 7338044 7338044 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.930G>C p.Gln310His p.Q310H ENST00000526929 1/1 202 190 12 218 218 0 varscan-mutect USP17L4,missense_variant,p.Gln310His,ENST00000526929,NM_001256874.1;USP17L1,downstream_gene_variant,,ENST00000529559,NM_001256873.1;FAM66B,intron_variant,,ENST00000606573,;FAM66B,intron_variant,,ENST00000529456,;AC130360.8,upstream_gene_variant,,ENST00000425489,; C ENST00000526929 Transcript missense_variant 930/1593 930/1593 310/530 Q/H caG/caC 1 1 USP17L4 HGNC HGNC:37176 protein_coding YES CCDS78299.1 ENSP00000485243 A6NCW7 UPI0000251F84 NM_001256874.1 tolerated(0.05) 1/1 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,hmmpanther:PTHR24006:SF511,Superfamily_domains:SSF54001 MODERATE SNV 1 PASS rs1477246501 . 10 200 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 7338044 7338044 G C 1 0 0 0 0 1 0 0 0 17588 933 33 4 4 USP17L4 8 7338044 Missense_Mutation SNP G C3N-02423_T 4149149 7338044 137800592 195 29325 XKR6 0 . GRCh38 8 11200616 11200616 + Nonsense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.724C>T p.Gln242Ter p.Q242* ENST00000416569 1/3 72 59 13 94 94 0 strelka-varscan-mutect XKR6,stop_gained,p.Gln242Ter,ENST00000416569,NM_173683.3;XKR6,stop_gained,p.Gln242Ter,ENST00000297303,;AF131215.8,upstream_gene_variant,,ENST00000602443,;XKR6,stop_gained,p.Gln74Ter,ENST00000529336,; A ENST00000416569 Transcript stop_gained 751/3382 724/1926 242/641 Q/* Cag/Tag 1 -1 XKR6 HGNC HGNC:27806 protein_coding YES CCDS5978.2 ENSP00000416707 Q5GH73 UPI00004C7A9D NM_173683.3 1/3 Pfam_domain:PF09815,hmmpanther:PTHR32129,hmmpanther:PTHR32129:SF7 HIGH 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 11200616 11200616 G A 1 0 0 0 0 0 1 0 0 17994 1328 46 3 3 XKR6 8 11200616 Nonsense_Mutation SNP G C3N-02423_T 3862572 11200616 133938020 196 29326 DLC1 0 . GRCh38 8 13499885 13499885 + Missense_Mutation SNP C C T C3N-02423_T C3N-02423_N C C c.187G>A p.Asp63Asn p.D63N ENST00000276297 2/18 219 207 12 278 278 0 strelka-varscan-mutect DLC1,missense_variant,p.Asp63Asn,ENST00000276297,NM_182643.2;DLC1,missense_variant,p.Asp63Asn,ENST00000511869,NM_024767.3;DLC1,missense_variant,p.Asp63Asn,ENST00000316609,;DLC1,missense_variant,p.Asp63Asn,ENST00000631382,;DLC1,upstream_gene_variant,,ENST00000517868,;DLC1,non_coding_transcript_exon_variant,,ENST00000517333,; T ENST00000276297 Transcript missense_variant 597/7447 187/4587 63/1528 D/N Gac/Aac COSM4849445,COSM4849446,COSM4849447 1 -1 DLC1 HGNC HGNC:2897 protein_coding YES CCDS5989.1 ENSP00000276297 Q96QB1 UPI0000210275 NM_182643.2 deleterious_low_confidence(0) 2/18 hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF2 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS rs1217234965 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 13499885 13499885 C T 1 0 0 0 0 1 0 0 0 4356 826 29 3 3 DLC1 8 13499885 Missense_Mutation SNP C C3N-02423_T 2299269 13499885 131638751 197 29327 FZD3 0 . GRCh38 8 28527718 28527718 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.958G>A p.Gly320Ser p.G320S ENST00000537916 4/7 312 271 41 287 287 0 strelka-varscan-mutect FZD3,missense_variant,p.Gly320Ser,ENST00000537916,NM_145866.1;FZD3,missense_variant,p.Gly320Ser,ENST00000240093,NM_017412.3;RNA5SP259,upstream_gene_variant,,ENST00000365541,; A ENST00000537916 Transcript missense_variant 1441/13740 958/2001 320/666 G/S Ggt/Agt COSM1252900 1 1 FZD3 HGNC HGNC:4041 protein_coding YES CCDS6069.1 ENSP00000437489 Q9NPG1 UPI000003156A NM_145866.1 tolerated(0.57) 4/7 Pfam_domain:PF01534,PROSITE_profiles:PS50261,hmmpanther:PTHR11309,hmmpanther:PTHR11309:SF22,SMART_domains:SM01330 1 MODERATE 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 28527718 28527718 G A 1 0 0 0 0 1 0 0 0 6002 1232 43 3 3 FZD3 8 28527718 Missense_Mutation SNP G C3N-02423_T 15027833 28527718 116610918 198 29328 CHRNA6 0 . GRCh38 8 42765113 42765113 + Silent SNP G G A C3N-02423_T C3N-02423_N G G c.171C>T p.= p.D57D ENST00000276410 2/6 150 120 30 188 188 0 strelka-varscan-mutect CHRNA6,synonymous_variant,p.=,ENST00000276410,NM_004198.3;CHRNA6,synonymous_variant,p.=,ENST00000534622,NM_001199279.1;CHRNA6,5_prime_UTR_variant,,ENST00000533810,;CHRNA6,non_coding_transcript_exon_variant,,ENST00000530869,;CHRNA6,non_coding_transcript_exon_variant,,ENST00000529467,; A ENST00000276410 Transcript synonymous_variant 527/2400 171/1485 57/494 D gaC/gaT COSM5452633 1 -1 CHRNA6 HGNC HGNC:15963 protein_coding YES CCDS6135.1 ENSP00000276410 Q15825 UPI0000061DF6 NM_004198.3 2/6 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF82,TIGRFAM_domain:TIGR00860 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 42765113 42765113 G A 1 0 0 0 0 0 0 0 1 3147 1252 44 3 3 CHRNA6 8 42765113 Silent SNP G C3N-02423_T 14237395 42765113 102373523 199 29329 PXDNL 0 . GRCh38 8 51408447 51408447 + Missense_Mutation SNP T T A rs558871648 C3N-02423_T C3N-02423_N T T c.3177A>T p.Leu1059Phe p.L1059F ENST00000356297 17/23 430 376 54 515 515 0 strelka-varscan-mutect PXDNL,missense_variant,p.Leu1059Phe,ENST00000356297,NM_144651.4;PXDNL,missense_variant,p.Leu178Phe,ENST00000522933,;PXDNL,missense_variant,p.Leu325Phe,ENST00000522628,; A ENST00000356297 Transcript missense_variant 3278/4805 3177/4392 1059/1463 L/F ttA/ttT rs558871648 1 -1 PXDNL HGNC HGNC:26359 protein_coding YES CCDS47855.1 ENSP00000348645 A1KZ92 UPI0001AE6ED6 NM_144651.4 deleterious(0.01) 17/23 PROSITE_profiles:PS50292,hmmpanther:PTHR11475:SF38,hmmpanther:PTHR11475,Gene3D:1.10.640.10,Pfam_domain:PF03098,Superfamily_domains:SSF48113,Prints_domain:PR00457 MODERATE 1 SNV 1 1 PASS rs558871648 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 51408447 51408447 T A 1 0 0 0 0 1 0 0 0 13002 1751 61 4 4 PXDNL 8 51408447 Missense_Mutation SNP T C3N-02423_T 8643334 51408447 93730189 200 29330 CHD7 0 . GRCh38 8 60820083 60820083 + Missense_Mutation SNP G G T rs773685788 C3N-02423_T C3N-02423_N G G c.2690G>T p.Arg897Leu p.R897L ENST00000423902 9/38 148 128 20 137 137 0 strelka-varscan-mutect CHD7,missense_variant,p.Arg897Leu,ENST00000423902,NM_017780.3;CHD7,missense_variant,p.Arg897Leu,ENST00000525508,;CHD7,intron_variant,,ENST00000524602,; T ENST00000423902 Transcript missense_variant 3169/11568 2690/8994 897/2997 R/L cGg/cTg rs773685788 1 1 CHD7 HGNC HGNC:20626 protein_coding YES CCDS47865.1 ENSP00000392028 Q9P2D1 UPI0000251DA6 NM_017780.3 deleterious(0.03) 9/38 PROSITE_profiles:PS50013,hmmpanther:PTHR10799:SF658,hmmpanther:PTHR10799,Gene3D:2.40.50.40,Pfam_domain:PF00385,SMART_domains:SM00298,Superfamily_domains:SSF54160 MODERATE 1 SNV 5 1 PASS rs773685788 . 0 204 2 3 0 0 0 0 -20 0.9999493 1 1 1 0 T 3 4 99 60820083 60820083 G T 1 0 0 0 0 1 0 0 0 3089 1116 39 1 1 CHD7 8 60820083 Missense_Mutation SNP G C3N-02423_T 9411636 60820083 84318553 201 29331 TRPA1 0 . GRCh38 8 72023877 72023877 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.3086T>A p.Ile1029Lys p.I1029K ENST00000262209 26/27 251 225 26 315 315 0 strelka-varscan-mutect TRPA1,missense_variant,p.Ile1029Lys,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Ile881Lys,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;TRPA1,upstream_gene_variant,,ENST00000520596,; T ENST00000262209 Transcript missense_variant 3294/5223 3086/3360 1029/1119 I/K aTa/aAa 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 tolerated(0.78) 26/27 hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 72023877 72023877 A T 1 0 0 0 0 1 0 0 0 17082 449 16 4 4 TRPA1 8 72023877 Missense_Mutation SNP A C3N-02423_T 11203794 72023877 73114759 202 29332 TRPA1 0 . GRCh38 8 72025976 72025976 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.3035C>A p.Ser1012Tyr p.S1012Y ENST00000262209 25/27 424 366 58 369 369 0 strelka-varscan-mutect TRPA1,missense_variant,p.Ser1012Tyr,ENST00000262209,NM_007332.2;TRPA1,missense_variant,p.Ser864Tyr,ENST00000523582,;MSC-AS1,intron_variant,,ENST00000457356,;MSC-AS1,intron_variant,,ENST00000522519,;MSC-AS1,intron_variant,,ENST00000518916,;MSC-AS1,intron_variant,,ENST00000519751,;MSC-AS1,intron_variant,,ENST00000524152,;MSC-AS1,intron_variant,,ENST00000519068,;MSC-AS1,upstream_gene_variant,,ENST00000512290,;TRPA1,upstream_gene_variant,,ENST00000520596,; T ENST00000262209 Transcript missense_variant 3243/5223 3035/3360 1012/1119 S/Y tCt/tAt 1 -1 TRPA1 HGNC HGNC:497 protein_coding YES CCDS34908.1 ENSP00000262209 O75762 UPI000021081A NM_007332.2 tolerated(1) 25/27 hmmpanther:PTHR24190,hmmpanther:PTHR24190:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 72025976 72025976 G T 1 0 0 0 0 1 0 0 0 17082 942 33 2 2 TRPA1 8 72025976 Missense_Mutation SNP G C3N-02423_T 2099 72025976 73112660 203 29333 PSKH2 0 . GRCh38 8 86069616 86069616 + Missense_Mutation SNP A A G rs777827063 C3N-02423_T C3N-02423_N A A c.7T>C p.Cys3Arg p.C3R ENST00000276616 1/3 79 70 9 84 84 0 strelka-mutect PSKH2,missense_variant,p.Cys3Arg,ENST00000276616,NM_033126.1;ATP6V0D2,intron_variant,,ENST00000521564,;ATP6V0D2,upstream_gene_variant,,ENST00000523635,;PSKH2,intron_variant,,ENST00000517981,;PSKH2,intron_variant,,ENST00000523010,; G ENST00000276616 Transcript missense_variant 82/1322 7/1158 3/385 C/R Tgc/Cgc rs777827063 1 -1 PSKH2 HGNC HGNC:18997 protein_coding YES CCDS6240.1 ENSP00000276616 Q96QS6 UPI000006F951 NM_033126.1 deleterious_low_confidence(0) 1/3 hmmpanther:PTHR24347,hmmpanther:PTHR24347:SF255 MODERATE 1 SNV 1 1 PASS rs777827063 . 0 201 9 0 0 0 0 0 -19.11797 0.9999889 1 1 1 0 G 3 3 99 86069616 86069616 A G 1 0 0 0 0 1 0 0 0 12816 159 6 5 5 PSKH2 8 86069616 Missense_Mutation SNP A C3N-02423_T 14043640 86069616 59069020 204 29334 FAM92A1 0 . GRCh38 8 93701342 93701342 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.145G>C p.Asp49His p.D49H ENST00000518322 2/9 387 355 32 390 390 0 varscan-mutect FAM92A1,missense_variant,p.Asp49His,ENST00000518322,NM_145269.4;FAM92A1,missense_variant,p.Asp49His,ENST00000522324,;FAM92A1,missense_variant,p.Asp49His,ENST00000620645,;FAM92A1,missense_variant,p.Asp49His,ENST00000423990,NM_001283034.1;FAM92A1,missense_variant,p.Asp49His,ENST00000522803,;FAM92A1,missense_variant,p.Asp60His,ENST00000523453,;FAM92A1,5_prime_UTR_variant,,ENST00000520955,;FAM92A1,5_prime_UTR_variant,,ENST00000523475,;FAM92A1,5_prime_UTR_variant,,ENST00000518829,;FAM92A1,upstream_gene_variant,,ENST00000517718,;FAM92A1,upstream_gene_variant,,ENST00000521641,;FAM92A1,upstream_gene_variant,,ENST00000519135,;LINC00535,upstream_gene_variant,,ENST00000501400,;FAM92A1,missense_variant,p.Asp49His,ENST00000518116,;FAM92A1,missense_variant,p.Asp49His,ENST00000452913,;FAM92A1,missense_variant,p.Asp49His,ENST00000359421,;FAM92A1,missense_variant,p.Asp49His,ENST00000520937,;FAM92A1,non_coding_transcript_exon_variant,,ENST00000523577,; C ENST00000518322 Transcript missense_variant 286/4241 145/870 49/289 D/H Gac/Cac 1 1 FAM92A1 HGNC HGNC:30452 protein_coding YES CCDS47892.1 ENSP00000429367 A1XBS5 UPI000156FA8B NM_145269.4 deleterious(0) 2/9 hmmpanther:PTHR21223:SF4,hmmpanther:PTHR21223,Pfam_domain:PF06730,Superfamily_domains:SSF103657 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 93701342 93701342 G C 1 0 0 0 0 1 0 0 0 5510 942 33 4 4 FAM92A1 8 93701342 Missense_Mutation SNP G C3N-02423_T 7631726 93701342 51437294 205 29335 CSMD3 0 . GRCh38 8 112383612 112383612 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.5986T>C p.Tyr1996His p.Y1996H ENST00000297405 37/71 421 362 59 380 379 1 strelka-varscan-mutect CSMD3,missense_variant,p.Tyr1996His,ENST00000297405,NM_198123.1;CSMD3,missense_variant,p.Tyr1956His,ENST00000343508,NM_198124.1;CSMD3,missense_variant,p.Tyr1892His,ENST00000455883,NM_052900.2;CSMD3,missense_variant,p.Tyr1266His,ENST00000339701,; G ENST00000297405 Transcript missense_variant 6231/13212 5986/11124 1996/3707 Y/H Tat/Cat 1 -1 CSMD3 HGNC HGNC:19291 protein_coding YES CCDS6315.1 ENSP00000297405 Q7Z407 UPI00001E0584 NM_198123.1 tolerated(0.16) 37/71 PROSITE_profiles:PS01180,Pfam_domain:PF00431,Gene3D:2.60.120.290,SMART_domains:SM00042,Superfamily_domains:SSF49854 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 112383612 112383612 A G 1 0 0 0 0 1 0 0 0 3747 362 13 5 5 CSMD3 8 112383612 Missense_Mutation SNP A C3N-02423_T 18682270 112383612 32755024 206 29336 EXT1 0 . GRCh38 8 118110340 118110340 + Missense_Mutation SNP A A C novel C3N-02423_T C3N-02423_N A A c.707T>G p.Leu236Arg p.L236R ENST00000378204 1/11 407 338 69 412 412 0 strelka-varscan-mutect EXT1,missense_variant,p.Leu236Arg,ENST00000378204,NM_000127.2;EXT1,missense_variant,p.Leu26Arg,ENST00000436216,;EXT1,intron_variant,,ENST00000437196,; C ENST00000378204 Transcript missense_variant 1514/8270 707/2241 236/746 L/R cTc/cGc 1 -1 EXT1 HGNC HGNC:3512 protein_coding YES CCDS6324.1 ENSP00000367446 Q16394 UPI000012A3A1 NM_000127.2 deleterious(0.01) 1/11 Pfam_domain:PF03016,hmmpanther:PTHR11062,hmmpanther:PTHR11062:SF97 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 118110340 118110340 A C 1 0 0 0 0 1 0 0 0 5191 304 11 5 5 EXT1 8 118110340 Missense_Mutation SNP A C3N-02423_T 5726728 118110340 27028296 207 29337 HAS2 0 . GRCh38 8 121628831 121628831 + Silent SNP G G A rs373683528 C3N-02423_T C3N-02423_N G G c.510C>T p.= p.H170H ENST00000303924 2/4 433 405 28 462 462 0 strelka-varscan-mutect HAS2,synonymous_variant,p.=,ENST00000303924,NM_005328.2; A ENST00000303924 Transcript synonymous_variant 1048/4190 510/1659 170/552 H caC/caT rs373683528 1 -1 HAS2 HGNC HGNC:4819 protein_coding YES CCDS6335.1 ENSP00000306991 Q92819 UPI000012C0A9 NM_005328.2 2/4 Gene3D:3.90.550.10,hmmpanther:PTHR22913,hmmpanther:PTHR22913:SF7 LOW 1 SNV 1 1 PASS rs373683528 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 121628831 121628831 G A 1 0 0 0 0 0 0 0 1 6848 1136 40 1 1 HAS2 8 121628831 Silent SNP G C3N-02423_T 3518491 121628831 23509805 208 29338 KLHL38 0 . GRCh38 8 123651899 123651899 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1028G>C p.Ser343Thr p.S343T ENST00000325995 1/3 238 201 37 273 273 0 strelka-varscan-mutect KLHL38,missense_variant,p.Ser343Thr,ENST00000325995,NM_001081675.2;CTD-2552K11.2,intron_variant,,ENST00000524355,; G ENST00000325995 Transcript missense_variant 1052/1982 1028/1746 343/581 S/T aGc/aCc 1 -1 KLHL38 HGNC HGNC:34435 protein_coding YES CCDS43766.1 ENSP00000321475 Q2WGJ6 UPI00001D82D1 NM_001081675.2 tolerated(0.38) 1/3 hmmpanther:PTHR24412:SF8,hmmpanther:PTHR24412,PIRSF_domain:PIRSF037037,Gene3D:1zgkA00,SMART_domains:SM00612,Superfamily_domains:0052715 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 123651899 123651899 C G 1 0 0 0 0 1 0 0 0 8256 797 28 4 4 KLHL38 8 123651899 Missense_Mutation SNP C C3N-02423_T 2023068 123651899 21486737 209 29339 ZFAT 0 . GRCh38 8 134532844 134532844 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.3105C>T p.= p.L1035L ENST00000377838 12/16 160 152 8 169 169 0 strelka-varscan-mutect ZFAT,synonymous_variant,p.=,ENST00000520727,NM_001029939.3,NM_001289394.1;ZFAT,synonymous_variant,p.=,ENST00000377838,NM_020863.3;ZFAT,synonymous_variant,p.=,ENST00000429442,;ZFAT,synonymous_variant,p.=,ENST00000520214,NM_001167583.2;ZFAT,synonymous_variant,p.=,ENST00000520356,NM_001174158.1;ZFAT,synonymous_variant,p.=,ENST00000523399,NM_001174157.1;ZFAT,non_coding_transcript_exon_variant,,ENST00000517307,;ZFAT,3_prime_UTR_variant,,ENST00000523243,;ZFAT,3_prime_UTR_variant,,ENST00000523924,;ZFAT,non_coding_transcript_exon_variant,,ENST00000518408,; A ENST00000377838 Transcript synonymous_variant 3280/4597 3105/3732 1035/1243 L ctC/ctT 1 -1 ZFAT HGNC HGNC:19899 protein_coding YES CCDS47924.1 ENSP00000367069 Q9P243 UPI0000210061 NM_020863.3 12/16 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF218 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 134532844 134532844 G A 1 0 0 0 0 0 0 0 1 18209 1277 45 3 3 ZFAT 8 134532844 Silent SNP G C3N-02423_T 10880945 134532844 10605792 210 29340 FAM135B 0 . GRCh38 8 138139097 138139097 + Splice_Site SNP C C A novel C3N-02423_T C3N-02423_N C C c.3791-1G>T p.X1264_splice ENST00000395297 194 181 13 150 149 1 strelka-mutect FAM135B,splice_acceptor_variant,,ENST00000395297,NM_015912.3;FAM135B,splice_acceptor_variant,,ENST00000482951,;FAM135B,splice_acceptor_variant,,ENST00000276737,;FAM135B,downstream_gene_variant,,ENST00000467365,;FAM135B,downstream_gene_variant,,ENST00000395295,; A ENST00000395297 Transcript splice_acceptor_variant -/6962 3791/4221 1264/1406 1 -1 FAM135B HGNC HGNC:28029 protein_coding YES CCDS6375.2 ENSP00000378710 Q49AJ0 UPI000057A0DB NM_015912.3 17/19 HIGH 1 SNV 5 1 PASS . . 0 207 0 3 0 0 0 0 -16.47287 0.9999661 1 1 1 0 A 5 1 99 138139097 138139097 C A 1 0 0 0 0 0 0 1 0 5299 695 24 2 2 FAM135B 8 138139097 Splice_Site SNP C C3N-02423_T 3606253 138139097 6999539 211 29341 TAF1L 0 . GRCh38 9 32631682 32631682 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.3898C>T p.Leu1300Phe p.L1300F ENST00000242310 1/1 611 424 187 577 577 0 strelka-varscan-mutect TAF1L,missense_variant,p.Leu1300Phe,ENST00000242310,NM_153809.2;RP11-555J4.4,upstream_gene_variant,,ENST00000430787,; A ENST00000242310 Transcript missense_variant 3988/6216 3898/5481 1300/1826 L/F Ctc/Ttc 1 -1 TAF1L HGNC HGNC:18056 protein_coding YES CCDS35003.1 ENSP00000418379 Q8IZX4 UPI000007408A NM_153809.2 deleterious(0.01) 1/1 Pfam_domain:PF15288,PIRSF_domain:PIRSF003047,hmmpanther:PTHR13900,hmmpanther:PTHR13900:SF0 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 32631682 32631682 G A 1 0 0 0 0 1 0 0 0 15919 1000 35 3 3 TAF1L 9 32631682 Missense_Mutation SNP G C3N-02423_T 32631682 105763035 212 29342 TMEM8B 0 . GRCh38 9 35853525 35853525 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.1104C>T p.= p.R368R ENST00000377988 13/13 148 139 9 89 89 0 strelka-varscan-mutect TMEM8B,synonymous_variant,p.=,ENST00000377988,NM_001042590.2;TMEM8B,synonymous_variant,p.=,ENST00000377991,NM_001042589.2; T ENST00000377988 Transcript synonymous_variant 2410/3731 1104/1419 368/472 R cgC/cgT 1 1 TMEM8B HGNC HGNC:21427 protein_coding YES CCDS43800.1 ENSP00000367227 A6NDV4 UPI00002113B9 NM_001042590.2 13/13 Pfam_domain:PF12036,hmmpanther:PTHR14319,hmmpanther:PTHR14319:SF6 LOW 1 SNV 1 1 PASS . . 0 200 10 0 0 0 0 0 -16.33894 0.9998906 1 1 1 0 T 2 4 99 35853525 35853525 C T 1 0 0 0 0 0 0 0 1 16692 726 26 3 3 TMEM8B 9 35853525 Silent SNP C C3N-02423_T 3221843 35853525 102541192 213 29343 TMC1 0 . GRCh38 9 72754876 72754876 + Missense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.733G>T p.Asp245Tyr p.D245Y ENST00000297784 12/24 536 495 41 479 477 2 strelka-varscan-mutect TMC1,missense_variant,p.Asp245Tyr,ENST00000297784,NM_138691.2;TMC1,missense_variant,p.Asp245Tyr,ENST00000340019,; T ENST00000297784 Transcript missense_variant 1273/3201 733/2283 245/760 D/Y Gac/Tac COSM4557557 1 1 TMC1 HGNC HGNC:16513 protein_coding YES CCDS6643.1 ENSP00000297784 Q8TDI8 UPI0000161FA9 NM_138691.2 deleterious(0.02) 12/24 hmmpanther:PTHR23302:SF18,hmmpanther:PTHR23302 1 MODERATE 1 SNV 1 1 1 PASS rs1469818234 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 72754876 72754876 G T 1 0 0 0 0 1 0 0 0 16430 1058 37 1 1 TMC1 9 72754876 Missense_Mutation SNP G C3N-02423_T 36901351 72754876 65639841 214 29344 PRUNE2 0 . GRCh38 9 76710226 76710226 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.2048C>A p.Pro683His p.P683H ENST00000376718 8/19 275 251 24 283 283 0 strelka-varscan-mutect PRUNE2,missense_variant,p.Pro683His,ENST00000376718,NM_015225.2;PRUNE2,missense_variant,p.Pro324His,ENST00000428286,;PRUNE2,missense_variant,p.Pro683His,ENST00000443509,NM_001308047.1,NM_001308048.1;PRUNE2,missense_variant,p.Pro5His,ENST00000426088,; T ENST00000376718 Transcript missense_variant 2172/12584 2048/9267 683/3088 P/H cCt/cAt 1 -1 PRUNE2 HGNC HGNC:25209 protein_coding YES CCDS47982.1 ENSP00000365908 Q8WUY3 UPI0001612CC0 NM_015225.2 deleterious(0) 8/19 MODERATE 1 SNV 5 1 PASS rs1351656815 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 76710226 76710226 G T 1 0 0 0 0 1 0 0 0 12791 1000 35 2 2 PRUNE2 9 76710226 Missense_Mutation SNP G C3N-02423_T 3955350 76710226 61684491 215 29345 FOXB2 0 . GRCh38 9 77019721 77019721 + Missense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.67G>T p.Ala23Ser p.A23S ENST00000376708 1/1 463 431 32 439 439 0 strelka-varscan-mutect FOXB2,missense_variant,p.Ala23Ser,ENST00000376708,NM_001013735.1; T ENST00000376708 Transcript missense_variant 67/1299 67/1299 23/432 A/S Gcc/Tcc COSM1463029,COSM1463030,COSM1463031 1 1 FOXB2 HGNC HGNC:23315 protein_coding YES CCDS35045.1 ENSP00000365898 Q5VYV0 UPI00004588EE NM_001013735.1 deleterious(0) 1/1 PROSITE_profiles:PS50039,hmmpanther:PTHR11829:SF215,hmmpanther:PTHR11829,PROSITE_patterns:PS00657,Pfam_domain:PF00250,Gene3D:1.10.10.10,SMART_domains:SM00339,Superfamily_domains:SSF46785,Prints_domain:PR00053 1,1,1 MODERATE 1 SNV 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 77019721 77019721 G T 1 0 0 0 0 1 0 0 0 5853 1087 38 1 1 FOXB2 9 77019721 Missense_Mutation SNP G C3N-02423_T 309495 77019721 61374996 216 29346 S1PR3 0 . GRCh38 9 89002112 89002112 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.912G>C p.Glu304Asp p.E304D ENST00000375846 1/1 174 165 9 171 171 0 strelka-varscan-mutect S1PR3,missense_variant,p.Glu304Asp,ENST00000375846,;S1PR3,missense_variant,p.Glu304Asp,ENST00000358157,NM_005226.3;SHC3,downstream_gene_variant,,ENST00000375835,NM_016848.5; C ENST00000375846 Transcript missense_variant 5607/8505 912/1137 304/378 E/D gaG/gaC 1 1 S1PR3 HGNC HGNC:3167 protein_coding YES CCDS6680.1 ENSP00000365006 Q99500 UPI0000140B93 tolerated(0.89) 1/1 hmmpanther:PTHR22750,hmmpanther:PTHR22750:SF24,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR01523,Prints_domain:PR00237 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 89002112 89002112 G C 1 0 0 0 0 1 0 0 0 14054 933 33 4 4 S1PR3 9 89002112 Missense_Mutation SNP G C3N-02423_T 11982391 89002112 49392605 217 29347 CORO2A 0 . GRCh38 9 98126821 98126821 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1174C>G p.Pro392Ala p.P392A ENST00000343933 11/12 110 96 14 151 151 0 strelka-varscan-mutect CORO2A,missense_variant,p.Pro392Ala,ENST00000343933,NM_003389.3;CORO2A,missense_variant,p.Pro392Ala,ENST00000375077,NM_052820.3; C ENST00000343933 Transcript missense_variant,splice_region_variant 1432/5635 1174/1578 392/525 P/A Cca/Gca 1 -1 CORO2A HGNC HGNC:2255 protein_coding YES CCDS6735.1 ENSP00000343746 Q92828 A0A024R150 UPI0000127C45 NM_003389.3 deleterious(0.01) 11/12 Pfam_domain:PF16300,hmmpanther:PTHR10856,hmmpanther:PTHR10856:SF2,SMART_domains:SM01167 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 98126821 98126821 G C 1 0 0 0 0 1 0 0 0 3550 1246 43 4 4 CORO2A 9 98126821 Missense_Mutation SNP G C3N-02423_T 9124709 98126821 40267896 218 29348 SMC2 0 . GRCh38 9 104098487 104098487 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.360C>T p.= p.V120V ENST00000286398 4/25 137 126 11 137 137 0 strelka-varscan-mutect SMC2,synonymous_variant,p.=,ENST00000286398,NM_001042551.1,NM_006444.2,NM_001265602.1;SMC2,synonymous_variant,p.=,ENST00000374793,;SMC2,synonymous_variant,p.=,ENST00000374787,NM_001042550.1;SMC2,5_prime_UTR_variant,,ENST00000440179,; T ENST00000286398 Transcript synonymous_variant 664/5992 360/3594 120/1197 V gtC/gtT 1 1 SMC2 HGNC HGNC:14011 protein_coding YES CCDS35086.1 ENSP00000286398 O95347 A0A024R158 UPI000013DE44 NM_001042551.1,NM_006444.2,NM_001265602.1 4/25 Gene3D:3.40.50.300,Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF9,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.96761 1 1 1 1 0 T 2 4 99 104098487 104098487 C T 1 0 0 0 0 0 0 0 1 15076 813 29 3 3 SMC2 9 104098487 Silent SNP C C3N-02423_T 5971666 104098487 34296230 219 29349 OR13C5 0 . GRCh38 9 104598732 104598732 + Missense_Mutation SNP T T A C3N-02423_T C3N-02423_N T T c.682A>T p.Ile228Phe p.I228F ENST00000374779 1/1 289 240 49 397 397 0 strelka-varscan-mutect OR13C5,missense_variant,p.Ile228Phe,ENST00000374779,NM_001004482.1; A ENST00000374779 Transcript missense_variant 682/957 682/957 228/318 I/F Att/Ttt COSM4709656 1 -1 OR13C5 HGNC HGNC:15100 protein_coding YES CCDS35091.1 ENSP00000363911 Q8NGS8 UPI0000041D12 NM_001004482.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF121,Low_complexity_(Seg):seg,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 104598732 104598732 T A 1 0 0 0 0 1 0 0 0 11013 1493 52 4 4 OR13C5 9 104598732 Missense_Mutation SNP T C3N-02423_T 500245 104598732 33795985 220 29350 FRRS1L 0 . GRCh38 9 109141472 109141472 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.733G>C p.Glu245Gln p.E245Q ENST00000561981 4/5 411 385 26 404 404 0 strelka-varscan-mutect FRRS1L,missense_variant,p.Glu245Gln,ENST00000561981,NM_014334.2; G ENST00000561981 Transcript missense_variant 733/8197 733/1035 245/344 E/Q Gaa/Caa 1 -1 FRRS1L HGNC HGNC:1362 protein_coding YES CCDS35098.1 ENSP00000477141 Q9P0K9 UPI000013D040 NM_014334.2 tolerated(0.07) 4/5 PROSITE_profiles:PS50836,hmmpanther:PTHR23130,hmmpanther:PTHR23130:SF65,Pfam_domain:PF03351,SMART_domains:SM00664 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 109141472 109141472 C G 1 0 0 0 0 1 0 0 0 5932 922 32 4 4 FRRS1L 9 109141472 Missense_Mutation SNP C C3N-02423_T 4542740 109141472 29253245 221 29351 PTPN3 0 . GRCh38 9 109463358 109463358 + Missense_Mutation SNP C C G rs539799147 C3N-02423_T C3N-02423_N C C c.77G>C p.Arg26Pro p.R26P ENST00000374541 2/26 263 246 17 237 237 0 strelka-varscan-mutect PTPN3,missense_variant,p.Arg26Pro,ENST00000262539,;PTPN3,missense_variant,p.Arg26Pro,ENST00000374541,NM_001145368.1,NM_002829.3; G ENST00000374541 Transcript missense_variant 182/6703 77/2742 26/913 R/P cGa/cCa rs539799147,COSM1103770 1 -1 PTPN3 HGNC HGNC:9655 protein_coding YES CCDS6776.1 ENSP00000363667 P26045 UPI000013D2D2 NM_001145368.1,NM_002829.3 deleterious(0.02) 2/26 PIRSF_domain:PIRSF000927,hmmpanther:PTHR19134,hmmpanther:PTHR19134:SF309,SMART_domains:SM00295 0,1 MODERATE 1 SNV 5 0,1 1 PASS rs539799147 . 0 207 0 2 0 0 0 0 -19.79204 0.9999996 1 1 1 0 G 3 3 99 109463358 109463358 C G 1 0 0 0 0 1 0 0 0 12943 884 31 4 4 PTPN3 9 109463358 Missense_Mutation SNP C C3N-02423_T 321886 109463358 28931359 222 29352 PSMB7 0 . GRCh38 9 124356865 124356865 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.621C>T p.= p.F207F ENST00000259457 7/8 236 223 13 194 194 0 strelka-varscan-mutect PSMB7,synonymous_variant,p.=,ENST00000259457,NM_002799.3;NEK6,downstream_gene_variant,,ENST00000373600,NM_001145001.2;NEK6,downstream_gene_variant,,ENST00000320246,NM_014397.5;NEK6,downstream_gene_variant,,ENST00000373603,;NEK6,downstream_gene_variant,,ENST00000539416,NM_001166169.1;NEK6,downstream_gene_variant,,ENST00000546191,NM_001166170.1;NEK6,downstream_gene_variant,,ENST00000540326,NM_001166167.1;NEK6,downstream_gene_variant,,ENST00000545174,NM_001166168.1;NEK6,downstream_gene_variant,,ENST00000394199,NM_001166171.1;PSMB7,non_coding_transcript_exon_variant,,ENST00000498485,; A ENST00000259457 Transcript synonymous_variant 635/980 621/834 207/277 F ttC/ttT 1 -1 PSMB7 HGNC HGNC:9544 protein_coding YES CCDS6855.1 ENSP00000259457 Q99436 E9KL30 UPI00001325C7 NM_002799.3 7/8 Gene3D:3.60.20.10,Pfam_domain:PF00227,Prints_domain:PR00141,PROSITE_profiles:PS51476,hmmpanther:PTHR11599,hmmpanther:PTHR11599:SF42,Superfamily_domains:SSF56235 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 124356865 124356865 G A 1 0 0 0 0 0 0 0 1 12833 1281 45 3 3 PSMB7 9 124356865 Silent SNP G C3N-02423_T 14893507 124356865 14037852 223 29353 CERCAM 0 . GRCh38 9 128424423 128424423 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.575G>T p.Arg192Leu p.R192L ENST00000372838 5/13 231 209 22 265 265 0 strelka-varscan-mutect CERCAM,missense_variant,p.Arg114Leu,ENST00000372842,NM_001286760.1;CERCAM,missense_variant,p.Arg192Leu,ENST00000372838,NM_016174.4;CERCAM,missense_variant,p.Arg114Leu,ENST00000612334,;CERCAM,missense_variant,p.Arg114Leu,ENST00000420512,;CERCAM,upstream_gene_variant,,ENST00000613052,;CERCAM,downstream_gene_variant,,ENST00000411852,;CERCAM,downstream_gene_variant,,ENST00000420034,;CERCAM,downstream_gene_variant,,ENST00000447915,;CERCAM,non_coding_transcript_exon_variant,,ENST00000483893,;CERCAM,downstream_gene_variant,,ENST00000493788,;CERCAM,upstream_gene_variant,,ENST00000487001,;CERCAM,non_coding_transcript_exon_variant,,ENST00000463535,;CERCAM,downstream_gene_variant,,ENST00000483737,; T ENST00000372838 Transcript missense_variant 973/2685 575/1788 192/595 R/L cGc/cTc 1 1 CERCAM HGNC HGNC:23723 protein_coding YES CCDS6901.2 ENSP00000361929 Q5T4B2 UPI000046FF85 NM_016174.4 deleterious(0.01) 5/13 hmmpanther:PTHR10730,hmmpanther:PTHR10730:SF9,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS rs1453902081 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 128424423 128424423 G T 1 0 0 0 0 1 0 0 0 2992 1087 38 1 1 CERCAM 9 128424423 Missense_Mutation SNP G C3N-02423_T 4067558 128424423 9970294 224 29354 ODF2 0 . GRCh38 9 128469311 128469311 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.378G>C p.Lys126Asn p.K126N ENST00000434106 5/21 344 318 26 320 320 0 strelka-varscan-mutect ODF2,missense_variant,p.Lys121Asn,ENST00000351030,NM_001242352.1;ODF2,missense_variant,p.Lys126Asn,ENST00000434106,NM_153433.1;ODF2,missense_variant,p.Lys102Asn,ENST00000393527,NM_002540.4,NM_153435.1;ODF2,missense_variant,p.Lys126Asn,ENST00000604420,NM_001242353.1;ODF2,missense_variant,p.Lys121Asn,ENST00000372807,;ODF2,missense_variant,p.Lys102Asn,ENST00000444119,;ODF2,missense_variant,p.Lys107Asn,ENST00000372791,NM_153437.2;ODF2,missense_variant,p.Lys170Asn,ENST00000372814,NM_153432.1,NM_153439.1;ODF2,missense_variant,p.Lys107Asn,ENST00000546203,NM_153440.1;ODF2,missense_variant,p.Lys126Asn,ENST00000393533,NM_153436.1;ODF2,missense_variant,p.Lys107Asn,ENST00000446274,;ODF2,missense_variant,p.Lys117Asn,ENST00000497812,;ODF2,intron_variant,,ENST00000448249,NM_001242354.1;ODF2,intron_variant,,ENST00000421776,;ODF2,intron_variant,,ENST00000432065,;ODF2,downstream_gene_variant,,ENST00000470061,;ODF2-AS1,intron_variant,,ENST00000420801,;ODF2,non_coding_transcript_exon_variant,,ENST00000469582,; C ENST00000434106 Transcript missense_variant 741/3890 378/2490 126/829 K/N aaG/aaC 1 1 ODF2 HGNC HGNC:8114 protein_coding YES CCDS56588.1 ENSP00000403453 Q5BJF6 UPI0000211922 NM_153433.1 deleterious(0) 5/21 hmmpanther:PTHR23162,hmmpanther:PTHR23162:SF8 MODERATE 1 SNV 1 1 PASS rs1234955789 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 128469311 128469311 G C 1 0 0 0 0 1 0 0 0 10905 933 33 4 4 ODF2 9 128469311 Missense_Mutation SNP G C3N-02423_T 44888 128469311 9925406 225 29355 HMCN2 0 . GRCh38 9 130305000 130305000 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1811G>A p.Arg604Gln p.R604Q ENST00000624552 11/98 80 74 6 75 75 0 strelka-varscan-mutect HMCN2,missense_variant,p.Arg604Gln,ENST00000624552,NM_001291815.1;HMCN2,upstream_gene_variant,,ENST00000611173,; A ENST00000624552 Transcript missense_variant,splice_region_variant 1811/15610 1811/15180 604/5059 R/Q cGa/cAa 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 tolerated(1) 11/98 SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 205 5 0 0 0 0 0 -13.11014 1 1 1 1 0 A 3 1 99 130305000 130305000 G A 1 0 0 0 0 1 0 0 0 7112 1072 37 1 1 HMCN2 9 130305000 Missense_Mutation SNP G C3N-02423_T 1835689 130305000 8089717 226 29356 DBH 0 . GRCh38 9 133647861 133647861 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1040C>T p.Ser347Leu p.S347L ENST00000393056 6/12 511 472 39 548 548 0 strelka-varscan-mutect DBH,missense_variant,p.Ser347Leu,ENST00000393056,NM_000787.3;DBH,downstream_gene_variant,,ENST00000263611,; T ENST00000393056 Transcript missense_variant 1052/2763 1040/1854 347/617 S/L tCa/tTa 1 1 DBH HGNC HGNC:2689 protein_coding YES CCDS6977.2 ENSP00000376776 P09172 UPI0000E5D219 NM_000787.3 deleterious(0) 6/12 Gene3D:1yi9A01,hmmpanther:PTHR10157,hmmpanther:PTHR10157:SF29,Superfamily_domains:SSF49742 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 133647861 133647861 C T 1 0 0 0 0 1 0 0 0 4050 838 29 3 3 DBH 9 133647861 Missense_Mutation SNP C C3N-02423_T 3342861 133647861 4746856 227 29357 SARDH 0 . GRCh38 9 133718950 133718950 + Missense_Mutation SNP G G C C3N-02423_T C3N-02423_N G G c.1008C>G p.Ile336Met p.I336M ENST00000371872 7/21 94 87 7 129 129 0 strelka-varscan-mutect SARDH,missense_variant,p.Ile336Met,ENST00000371872,NM_007101.3;SARDH,missense_variant,p.Ile336Met,ENST00000439388,NM_001134707.1;SARDH,missense_variant,p.Ile56Met,ENST00000422262,;SARDH,missense_variant,p.Ile336Met,ENST00000427237,;SARDH,missense_variant,p.Ile247Met,ENST00000371867,; C ENST00000371872 Transcript missense_variant 1266/3344 1008/2757 336/918 I/M atC/atG COSM238140 1 -1 SARDH HGNC HGNC:10536 protein_coding YES CCDS6978.1 ENSP00000360938 Q9UL12 UPI000006F076 NM_007101.3 deleterious(0.02) 7/21 hmmpanther:PTHR13847:SF200,hmmpanther:PTHR13847,Pfam_domain:PF01266,Gene3D:3.30.9.10,Superfamily_domains:SSF54373 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 133718950 133718950 G C 1 0 0 0 0 1 0 0 0 14102 932 33 4 4 SARDH 9 133718950 Missense_Mutation SNP G C3N-02423_T 71089 133718950 4675767 228 29358 EHMT1 0 . GRCh38 9 137762816 137762816 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.1643A>T p.His548Leu p.H548L ENST00000460843 10/27 503 473 30 532 532 0 strelka-varscan-mutect EHMT1,missense_variant,p.His548Leu,ENST00000460843,NM_024757.4;EHMT1,missense_variant,p.His517Leu,ENST00000637161,;EHMT1,missense_variant,p.His548Leu,ENST00000629335,;EHMT1,missense_variant,p.His510Leu,ENST00000636027,;EHMT1,missense_variant,p.His548Leu,ENST00000462484,NM_001145527.1;EHMT1,missense_variant,p.His530Leu,ENST00000637977,;EHMT1,missense_variant,p.His112Leu,ENST00000465566,;EHMT1,downstream_gene_variant,,ENST00000626066,;EHMT1,downstream_gene_variant,,ENST00000629808,;EHMT1,missense_variant,p.His167Leu,ENST00000462942,;EHMT1,3_prime_UTR_variant,,ENST00000637261,;EHMT1,3_prime_UTR_variant,,ENST00000371394,;EHMT1,3_prime_UTR_variant,,ENST00000638071,; T ENST00000460843 Transcript missense_variant 1709/5137 1643/3897 548/1298 H/L cAt/cTt 1 1 EHMT1 HGNC HGNC:24650 protein_coding YES CCDS7050.2 ENSP00000417980 Q9H9B1 UPI000194EC2D NM_024757.4 deleterious(0.04) 10/27 hmmpanther:PTHR22884,hmmpanther:PTHR22884:SF364 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 137762816 137762816 A T 1 0 0 0 0 1 0 0 0 4819 231 8 4 4 EHMT1 9 137762816 Missense_Mutation SNP A C3N-02423_T 4043866 137762816 631901 229 29359 TUBB8 0 . GRCh38 10 48614 48614 + Splice_Site SNP C C A novel C3N-02423_T C3N-02423_N C C c.277+1G>T p.X93_splice ENST00000568584 276 225 51 329 329 0 strelka-varscan-mutect TUBB8,splice_donor_variant,,ENST00000568584,NM_177987.2;TUBB8,splice_donor_variant,,ENST00000561967,;TUBB8,splice_donor_variant,,ENST00000562809,;TUBB8,intron_variant,,ENST00000564130,;TUBB8,intron_variant,,ENST00000568866,;TUBB8,splice_donor_variant,,ENST00000563456,;TUBB8,missense_variant,p.Val68Leu,ENST00000567466,;FAM166AP7,downstream_gene_variant,,ENST00000416477,; A ENST00000568584 Transcript splice_donor_variant -/1790 277/1335 93/444 1 -1 TUBB8 HGNC HGNC:20773 protein_coding YES CCDS7051.1 ENSP00000456206 Q3ZCM7 UPI000007238E NM_177987.2 3/3 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 99 48614 48614 C A 1 0 0 0 0 0 0 1 0 17271 521 18 2 2 TUBB8 10 48614 Splice_Site SNP C C3N-02423_T 48614 133748808 230 29360 FAM171A1 0 . GRCh38 10 15213089 15213089 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.2499G>A p.= p.E833E ENST00000378116 8/8 107 94 13 139 139 0 strelka-varscan-mutect FAM171A1,synonymous_variant,p.=,ENST00000378116,NM_001010924.1;FAM171A1,downstream_gene_variant,,ENST00000477161,; T ENST00000378116 Transcript synonymous_variant 2506/3952 2499/2673 833/890 E gaG/gaA 1 -1 FAM171A1 HGNC HGNC:23522 protein_coding YES CCDS31154.1 ENSP00000367356 Q5VUB5 UPI00001414CA NM_001010924.1 8/8 hmmpanther:PTHR31626,hmmpanther:PTHR31626:SF1,Pfam_domain:PF10577 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 15213089 15213089 C T 1 0 0 0 0 0 0 0 1 5337 680 24 3 3 FAM171A1 10 15213089 Silent SNP C C3N-02423_T 15164475 15213089 118584333 231 29361 SKIDA1 0 . GRCh38 10 21515290 21515290 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.2533C>T p.His845Tyr p.H845Y ENST00000449193 4/4 227 199 28 217 217 0 strelka-varscan-mutect SKIDA1,missense_variant,p.His845Tyr,ENST00000449193,NM_207371.3;SKIDA1,missense_variant,p.His766Tyr,ENST00000444772,;SKIDA1,downstream_gene_variant,,ENST00000633225,;SKIDA1,downstream_gene_variant,,ENST00000487107,; A ENST00000449193 Transcript missense_variant 4786/6598 2533/2727 845/908 H/Y Cat/Tat 1 -1 SKIDA1 HGNC HGNC:32697 protein_coding YES CCDS44363.1 ENSP00000410041 E9PAX1 UPI00015386B3 NM_207371.3 deleterious(0) 4/4 hmmpanther:PTHR23187:SF2,hmmpanther:PTHR23187,Pfam_domain:PF15223 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 21515290 21515290 G A 1 0 0 0 0 1 0 0 0 14620 1290 45 3 3 SKIDA1 10 21515290 Missense_Mutation SNP G C3N-02423_T 6302201 21515290 112282132 232 29362 ZEB1 0 . GRCh38 10 31510793 31510793 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.605G>T p.Ser202Ile p.S202I ENST00000361642 5/9 457 373 84 517 515 2 strelka-varscan-mutect ZEB1,missense_variant,p.Ser185Ile,ENST00000446923,NM_001323656.1,NM_001323664.1,NM_001323657.1,NM_001323650.1,NM_001128128.2,NM_001174094.1;ZEB1,missense_variant,p.Ser202Ile,ENST00000361642,NM_001174096.1;ZEB1,missense_variant,p.Ser201Ile,ENST00000320985,NM_030751.5;ZEB1,missense_variant,p.Ser181Ile,ENST00000560721,NM_001174093.1;ZEB1,missense_variant,p.Ser134Ile,ENST00000542815,NM_001174095.1;ZEB1,missense_variant,p.Ser185Ile,ENST00000559476,;ZEB1,missense_variant,p.Ser202Ile,ENST00000424869,;ZEB1,missense_variant,p.Ser127Ile,ENST00000558440,;ZEB1,5_prime_UTR_variant,,ENST00000561212,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559858,;ZEB1,non_coding_transcript_exon_variant,,ENST00000561061,;ZEB1,3_prime_UTR_variant,,ENST00000437844,NM_001323663.1,NM_001323661.1,NM_001323644.1,NM_001323649.1,NM_001323659.1,NM_001323652.1,NM_001323673.1,NM_001323662.1,NM_001323676.1,NM_001323653.1,NM_001323655.1,NM_001323645.1,NM_001323647.1,NM_001323660.1,NM_001323671.1,NM_001323638.1,NM_001323665.1,NM_001323643.1,NM_001323677.1,NM_001323641.1,NM_001323642.1,NM_001323658.1,NM_001323651.1,NM_001323672.1,NM_001323654.1;ZEB1,non_coding_transcript_exon_variant,,ENST00000488625,;ZEB1,non_coding_transcript_exon_variant,,ENST00000542879,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558655,;ZEB1,non_coding_transcript_exon_variant,,ENST00000561304,;ZEB1,non_coding_transcript_exon_variant,,ENST00000559496,;ZEB1,non_coding_transcript_exon_variant,,ENST00000558863,;ZEB1,non_coding_transcript_exon_variant,,ENST00000557827,; T ENST00000361642 Transcript missense_variant 668/5990 605/3378 202/1125 S/I aGt/aTt 1 1 ZEB1 HGNC HGNC:11642 protein_coding YES CCDS53505.1 ENSP00000354487 P37275 UPI000068F51D NM_001174096.1 deleterious(0) 5/9 Pfam_domain:PF05605,PROSITE_profiles:PS50157,hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF17,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 31510793 31510793 G T 1 0 0 0 0 1 0 0 0 18199 1029 36 2 2 ZEB1 10 31510793 Missense_Mutation SNP G C3N-02423_T 9995503 31510793 102286629 233 29363 BMS1 0 . GRCh38 10 42792513 42792513 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.800C>A p.Pro267Gln p.P267Q ENST00000374518 7/23 145 127 18 163 161 2 strelka-varscan-mutect BMS1,missense_variant,p.Pro267Gln,ENST00000374518,NM_014753.3; A ENST00000374518 Transcript missense_variant 863/7753 800/3849 267/1282 P/Q cCa/cAa 1 1 BMS1 HGNC HGNC:23505 protein_coding YES CCDS7199.1 ENSP00000363642 Q14692 UPI0000126A3E NM_014753.3 tolerated(0.06) 7/23 hmmpanther:PTHR12858:SF2,hmmpanther:PTHR12858,Pfam_domain:PF08142,SMART_domains:SM00785 MODERATE 1 SNV 1 1 PASS . . 0 205 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 42792513 42792513 C A 1 0 0 0 0 1 0 0 0 1627 594 21 2 2 BMS1 10 42792513 Missense_Mutation SNP C C3N-02423_T 11281720 42792513 91004909 234 29364 HPSE2 0 . GRCh38 10 99232487 99232487 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.309C>A p.= p.T103T ENST00000370552 2/12 308 285 23 362 362 0 strelka-varscan-mutect HPSE2,synonymous_variant,p.=,ENST00000370552,NM_021828.4;HPSE2,synonymous_variant,p.=,ENST00000370549,NM_001166244.1;HPSE2,synonymous_variant,p.=,ENST00000370546,NM_001166246.1;HPSE2,synonymous_variant,p.=,ENST00000628193,NM_001166245.1;HPSE2,synonymous_variant,p.=,ENST00000614306,; T ENST00000370552 Transcript synonymous_variant 369/2295 309/1779 103/592 T acC/acA 1 -1 HPSE2 HGNC HGNC:18374 protein_coding YES CCDS7477.1 ENSP00000359583 Q8WWQ2 UPI00001AEEC0 NM_021828.4 2/12 hmmpanther:PTHR14363,hmmpanther:PTHR14363:SF15,Superfamily_domains:SSF51445 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 99232487 99232487 G T 1 0 0 0 0 0 0 0 1 7240 1219 43 2 2 HPSE2 10 99232487 Silent SNP G C3N-02423_T 56439974 99232487 34564935 235 29365 DNMBP 0 . GRCh38 10 99956398 99956398 + Missense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.1076C>A p.Ser359Tyr p.S359Y ENST00000324109 4/17 290 273 17 353 353 0 strelka-varscan-mutect DNMBP,missense_variant,p.Ser359Tyr,ENST00000324109,NM_015221.2;DNMBP-AS1,intron_variant,,ENST00000434409,; T ENST00000324109 Transcript missense_variant 1168/6400 1076/4734 359/1577 S/Y tCt/tAt COSM4010991,COSM4010992 1 -1 DNMBP HGNC HGNC:30373 protein_coding YES CCDS7485.1 ENSP00000315659 Q6XZF7 UPI000013D6C9 NM_015221.2 tolerated_low_confidence(0.76) 4/17 hmmpanther:PTHR22834:SF19,hmmpanther:PTHR22834 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 99956398 99956398 G T 1 0 0 0 0 1 0 0 0 4487 942 33 2 2 DNMBP 10 99956398 Missense_Mutation SNP G C3N-02423_T 723911 99956398 33841024 236 29366 KAZALD1 0 . GRCh38 10 101064268 101064268 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.519G>C p.Gln173His p.Q173H ENST00000370200 3/5 136 128 8 155 155 0 strelka-varscan-mutect KAZALD1,missense_variant,p.Gln173His,ENST00000370200,NM_030929.4;RP11-108L7.15,upstream_gene_variant,,ENST00000609242,;KAZALD1,non_coding_transcript_exon_variant,,ENST00000477267,;KAZALD1,non_coding_transcript_exon_variant,,ENST00000477979,;KAZALD1,non_coding_transcript_exon_variant,,ENST00000470106,;KAZALD1,upstream_gene_variant,,ENST00000465807,;KAZALD1,upstream_gene_variant,,ENST00000608812,; C ENST00000370200 Transcript missense_variant 845/1913 519/915 173/304 Q/H caG/caC 1 1 KAZALD1 HGNC HGNC:25460 protein_coding YES CCDS7509.1 ENSP00000359219 Q96I82 UPI000004283E NM_030929.4 tolerated(0.55) 3/5 Gene3D:2.60.40.10,Pfam_domain:PF07679,PIRSF_domain:PIRSF018239,PROSITE_profiles:PS50835,hmmpanther:PTHR14186,hmmpanther:PTHR14186:SF21,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 101064268 101064268 G C 1 0 0 0 0 1 0 0 0 7906 933 33 4 4 KAZALD1 10 101064268 Missense_Mutation SNP G C3N-02423_T 1107870 101064268 32733154 237 29367 ENO4 0 . GRCh38 10 116879333 116879333 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1580C>T p.Ser527Leu p.S527L ENST00000341276 12/14 138 129 9 210 210 0 strelka-varscan-mutect ENO4,missense_variant,p.Ser530Leu,ENST00000622726,;ENO4,missense_variant,p.Ser527Leu,ENST00000341276,NM_001242699.1;ENO4,missense_variant,p.Ser210Leu,ENST00000409522,;ENO4,missense_variant,p.Ser292Leu,ENST00000369207,;SHTN1,downstream_gene_variant,,ENST00000615301,NM_018330.6;SHTN1,downstream_gene_variant,,ENST00000355371,NM_001127211.2;SHTN1,downstream_gene_variant,,ENST00000260777,NM_001258298.1; T ENST00000341276 Transcript missense_variant 1635/2865 1580/1878 527/625 S/L tCa/tTa 1 1 ENO4 HGNC HGNC:31670 protein_coding YES CCDS73206.1 ENSP00000345555 J3KNX1 UPI00016624E4 NM_001242699.1 deleterious(0) 12/14 Gene3D:3.20.20.120,Pfam_domain:PF00113,hmmpanther:PTHR11902,hmmpanther:PTHR11902:SF1,SMART_domains:SM01192,Superfamily_domains:SSF51604 MODERATE SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -12.67629 0.9999996 1 1 1 0 T 3 4 99 116879333 116879333 C T 1 0 0 0 0 1 0 0 0 4968 838 29 3 3 ENO4 10 116879333 Missense_Mutation SNP C C3N-02423_T 15815065 116879333 16918089 238 29368 NSMCE4A 0 . GRCh38 10 121959596 121959596 + Splice_Site SNP C C G C3N-02423_T C3N-02423_N C C c.989-1G>C p.X330_splice ENST00000369023 114 106 8 165 165 0 strelka-mutect NSMCE4A,splice_acceptor_variant,,ENST00000369023,NM_001167865.1,NM_017615.2;NSMCE4A,downstream_gene_variant,,ENST00000369017,;RP11-500G22.4,downstream_gene_variant,,ENST00000618971,;NSMCE4A,splice_acceptor_variant,,ENST00000489266,;NSMCE4A,splice_acceptor_variant,,ENST00000468209,;NSMCE4A,non_coding_transcript_exon_variant,,ENST00000459911,;NSMCE4A,non_coding_transcript_exon_variant,,ENST00000477289,;NSMCE4A,downstream_gene_variant,,ENST00000483541,; G ENST00000369023 Transcript splice_acceptor_variant -/1394 989/1158 330/385 COSM4835448 1 -1 NSMCE4A HGNC HGNC:25935 protein_coding YES CCDS7624.1 ENSP00000358019 Q9NXX6 UPI000013D40C NM_001167865.1,NM_017615.2 8/10 1 HIGH 1 SNV 1 1 1 PASS rs1215260075 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 5 3 99 121959596 121959596 C G 1 0 0 0 0 0 0 1 0 10738 927 32 4 4 NSMCE4A 10 121959596 Splice_Site SNP C C3N-02423_T 5080263 121959596 11837826 239 29369 ACADSB 0 . GRCh38 10 123040500 123040500 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.338G>T p.Gly113Val p.G113V ENST00000358776 4/11 314 252 62 347 346 1 strelka-varscan-mutect ACADSB,missense_variant,p.Gly113Val,ENST00000358776,NM_001609.3;ACADSB,missense_variant,p.Gly11Val,ENST00000368869,;ACADSB,non_coding_transcript_exon_variant,,ENST00000411816,; T ENST00000358776 Transcript missense_variant 352/5859 338/1299 113/432 G/V gGc/gTc 1 1 ACADSB HGNC HGNC:91 protein_coding YES CCDS7634.1 ENSP00000357873 P45954 A0A0S2Z3P9 UPI00001251DF NM_001609.3 deleterious(0) 4/11 Gene3D:1.10.540.10,Pfam_domain:PF02771,hmmpanther:PTHR10909,hmmpanther:PTHR10909:SF10,Superfamily_domains:SSF56645 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 123040500 123040500 G T 1 0 0 0 0 1 0 0 0 158 1203 42 2 2 ACADSB 10 123040500 Missense_Mutation SNP G C3N-02423_T 1080904 123040500 10756922 240 29370 TUB 0 . GRCh38 11 8039693 8039693 + Splice_Site SNP G G T novel C3N-02423_T C3N-02423_N G G c.203+1G>T p.X68_splice ENST00000305253 40 29 11 43 43 0 strelka-varscan-mutect TUB,splice_donor_variant,,ENST00000305253,NM_003320.4;TUB,intron_variant,,ENST00000534099,;RP11-236J17.6,non_coding_transcript_exon_variant,,ENST00000526646,;RP11-236J17.6,non_coding_transcript_exon_variant,,ENST00000528151,; T ENST00000305253 Transcript splice_donor_variant -/6420 203/1686 68/561 1 1 TUB HGNC HGNC:12406 protein_coding YES CCDS7786.1 ENSP00000305426 P50607 UPI000013EA27 NM_003320.4 2/12 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 99 8039693 8039693 G T 1 0 0 0 0 0 0 1 0 17252 1275 44 2 2 TUB 11 8039693 Splice_Site SNP G C3N-02423_T 8039693 127046929 241 29371 C11orf16 0 . GRCh38 11 8921390 8921390 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1330C>A p.Pro444Thr p.P444T ENST00000326053 6/7 319 268 51 402 402 0 strelka-varscan-mutect C11orf16,missense_variant,p.Pro444Thr,ENST00000326053,NM_020643.2;C11orf16,intron_variant,,ENST00000525780,;AKIP1,downstream_gene_variant,,ENST00000529876,;AKIP1,downstream_gene_variant,,ENST00000309377,NM_020642.3;AKIP1,downstream_gene_variant,,ENST00000299576,NM_001206646.1;AKIP1,downstream_gene_variant,,ENST00000309357,NM_001206647.1;AKIP1,downstream_gene_variant,,ENST00000525005,;AKIP1,downstream_gene_variant,,ENST00000396648,;AKIP1,downstream_gene_variant,,ENST00000534147,;AKIP1,downstream_gene_variant,,ENST00000534506,;AKIP1,downstream_gene_variant,,ENST00000524577,;AKIP1,downstream_gene_variant,,ENST00000529942,NM_001206648.1;AKIP1,downstream_gene_variant,,ENST00000530281,; T ENST00000326053 Transcript missense_variant 1437/1908 1330/1404 444/467 P/T Ccg/Acg 1 -1 C11orf16 HGNC HGNC:1169 protein_coding YES CCDS7794.1 ENSP00000318999 Q9NQ32 UPI0000456489 NM_020643.2 tolerated(0.11) 6/7 hmmpanther:PTHR14343,hmmpanther:PTHR14343:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 8921390 8921390 G T 1 0 0 0 0 1 0 0 0 1777 1232 43 2 2 C11orf16 11 8921390 Missense_Mutation SNP G C3N-02423_T 881697 8921390 126165232 242 29372 OTOG 0 . GRCh38 11 17578505 17578505 + Missense_Mutation SNP C C T rs749040674 C3N-02423_T C3N-02423_N C C c.2774C>T p.Ser925Leu p.S925L ENST00000399391 22/55 74 65 9 88 88 0 strelka-varscan-mutect OTOG,missense_variant,p.Ser913Leu,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Ser925Leu,ENST00000399391,NM_001277269.1;OTOG,5_prime_UTR_variant,,ENST00000342528,; T ENST00000399391 Transcript missense_variant 2774/8778 2774/8778 925/2925 S/L tCg/tTg rs749040674 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 deleterious(0) 22/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228,Gene3D:2.10.25.10,Superfamily_domains:SSF57567 MODERATE 1 SNV 5 1 PASS rs749040674 . 0 204 5 0 0 0 0 0 -19.54358 1 1 1 1 0 T 3 4 99 17578505 17578505 C T 1 0 0 0 0 1 0 0 0 11370 893 31 1 1 OTOG 11 17578505 Missense_Mutation SNP C C3N-02423_T 8657115 17578505 117508117 243 29373 LMO2 0 . GRCh38 11 33869539 33869539 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.55G>A p.Glu19Lys p.E19K ENST00000257818 4/6 97 92 5 161 161 0 strelka-varscan-mutect LMO2,missense_variant,p.Glu19Lys,ENST00000257818,NM_005574.3;LMO2,5_prime_UTR_variant,,ENST00000395833,NM_001142315.1,NM_001142316.1;LMO2,downstream_gene_variant,,ENST00000493667,;LMO2,non_coding_transcript_exon_variant,,ENST00000465614,;LMO2,upstream_gene_variant,,ENST00000464025,;LMO2,upstream_gene_variant,,ENST00000411482,; T ENST00000257818 Transcript missense_variant 885/2294 55/684 19/227 E/K Gag/Aag 1 -1 LMO2 HGNC HGNC:6642 protein_coding YES CCDS7888.2 ENSP00000257818 P25791 UPI00001F9F84 NM_005574.3 tolerated_low_confidence(0.16) 4/6 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1288824626 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 33869539 33869539 C T 1 0 0 0 0 1 0 0 0 8778 864 30 3 3 LMO2 11 33869539 Missense_Mutation SNP C C3N-02423_T 16291034 33869539 101217083 244 29374 CD44 0 . GRCh38 11 35229203 35229203 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.2099A>G p.Asn700Ser p.N700S ENST00000428726 18/18 216 171 45 253 252 1 strelka-varscan-mutect CD44,missense_variant,p.Asn319Ser,ENST00000263398,NM_001001391.1;CD44,missense_variant,p.Asn700Ser,ENST00000428726,NM_000610.3;CD44,missense_variant,p.Asn657Ser,ENST00000415148,NM_001001389.1;CD44,missense_variant,p.Asn451Ser,ENST00000433892,NM_001001390.1;CD44,missense_variant,p.Asn387Ser,ENST00000434472,NM_001202555.1;CD44,missense_variant,p.Asn298Ser,ENST00000352818,NM_001202556.1;CD44,missense_variant,p.Asn164Ser,ENST00000526669,;CD44,missense_variant,p.Asn248Ser,ENST00000279452,;CD44,missense_variant,p.Asn40Ser,ENST00000525469,;CD44,missense_variant,p.Asn219Ser,ENST00000278385,;CD44,synonymous_variant,p.=,ENST00000278386,NM_001001392.1;CD44,downstream_gene_variant,,ENST00000525688,;CD44,3_prime_UTR_variant,,ENST00000425428,;CD44,non_coding_transcript_exon_variant,,ENST00000527326,; G ENST00000428726 Transcript missense_variant 2222/3046 2099/2229 700/742 N/S aAc/aGc 1 1 CD44 HGNC HGNC:1681 protein_coding YES CCDS7897.1 ENSP00000398632 P16070 UPI000013D3FE NM_000610.3 deleterious(0) 18/18 hmmpanther:PTHR10225,hmmpanther:PTHR10225:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 35229203 35229203 A G 1 0 0 0 0 1 0 0 0 2721 43 2 5 5 CD44 11 35229203 Missense_Mutation SNP A C3N-02423_T 1359664 35229203 99857419 245 29375 CHST1 0 . GRCh38 11 45650732 45650732 + Silent SNP G G A rs200379237 C3N-02423_T C3N-02423_N G G c.192C>T p.= p.L64L ENST00000308064 4/4 155 143 12 223 223 0 strelka-varscan-mutect CHST1,synonymous_variant,p.=,ENST00000308064,NM_003654.5;RP11-495O11.1,upstream_gene_variant,,ENST00000525563,;CHST1,upstream_gene_variant,,ENST00000533673,;CHST1,downstream_gene_variant,,ENST00000531322,; A ENST00000308064 Transcript synonymous_variant 863/2718 192/1236 64/411 L ctC/ctT rs200379237 1 -1 CHST1 HGNC HGNC:1969 protein_coding YES CCDS7913.1 ENSP00000309270 O43916 UPI0000073EA0 NM_003654.5 4/4 hmmpanther:PTHR10704,hmmpanther:PTHR10704:SF36,Pfam_domain:PF00685,Gene3D:3.40.50.300,PIRSF_domain:PIRSF005883,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs200379237 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 45650732 45650732 G A 1 0 0 0 0 0 0 0 1 3157 1277 45 3 3 CHST1 11 45650732 Silent SNP G C3N-02423_T 10421529 45650732 89435890 246 29376 MYBPC3 0 . GRCh38 11 47343538 47343538 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1177G>T p.Glu393Ter p.E393* ENST00000545968 13/35 134 124 10 114 114 0 strelka-varscan-mutect MYBPC3,stop_gained,p.Glu393Ter,ENST00000545968,NM_000256.3;MYBPC3,stop_gained,p.Glu393Ter,ENST00000256993,;MYBPC3,stop_gained,p.Glu393Ter,ENST00000399249,;MYBPC3,stop_gained,p.Glu393Ter,ENST00000544791,; A ENST00000545968 Transcript stop_gained 1232/4226 1177/3825 393/1274 E/* Gag/Tag 1 -1 MYBPC3 HGNC HGNC:7551 protein_coding YES CCDS53621.1 ENSP00000442795 Q14896 UPI000006EEAA NM_000256.3 13/35 PROSITE_profiles:PS50835,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 47343538 47343538 C A 1 0 0 0 0 0 1 0 0 10013 835 29 2 2 MYBPC3 11 47343538 Nonsense_Mutation SNP C C3N-02423_T 1692806 47343538 87743084 247 29377 FOLH1 0 . GRCh38 11 49154375 49154375 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1741G>A p.Gly581Arg p.G581R ENST00000256999 16/19 271 251 20 304 304 0 varscan-mutect FOLH1,missense_variant,p.Gly566Arg,ENST00000340334,NM_001193471.1;FOLH1,missense_variant,p.Gly581Arg,ENST00000256999,NM_004476.1;FOLH1,missense_variant,p.Gly581Arg,ENST00000356696,NM_001014986.1;FOLH1,missense_variant,p.Gly273Arg,ENST00000343844,NM_001193473.1;FOLH1,missense_variant,p.Gly566Arg,ENST00000533034,NM_001193472.1;FOLH1,3_prime_UTR_variant,,ENST00000525826,;FOLH1,non_coding_transcript_exon_variant,,ENST00000458311,;FOLH1,non_coding_transcript_exon_variant,,ENST00000532018,; T ENST00000256999 Transcript missense_variant 2002/2635 1741/2253 581/750 G/R Gga/Aga 1 -1 FOLH1 HGNC HGNC:3788 protein_coding YES CCDS7946.1 ENSP00000256999 Q04609 UPI0000000A01 NM_004476.1 deleterious(0) 16/19 Gene3D:3.40.630.10,hmmpanther:PTHR10404,hmmpanther:PTHR10404:SF36,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 49154375 49154375 C T 1 0 0 0 0 1 0 0 0 5840 690 24 3 3 FOLH1 11 49154375 Missense_Mutation SNP C C3N-02423_T 1810837 49154375 85932247 248 29378 OR4A5 0 . GRCh38 11 54707254 54707254 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.370A>T p.Ile124Phe p.I124F ENST00000319760 1/1 212 192 20 228 228 0 varscan-mutect OR4A5,missense_variant,p.Ile124Phe,ENST00000319760,NM_001005272.3; T ENST00000319760 Transcript missense_variant 370/948 370/948 124/315 I/F Atc/Ttc 1 1 OR4A5 HGNC HGNC:15162 protein_coding YES CCDS73289.1 ENSP00000367664 Q8NH83 A0A126GWJ2 UPI0000041D58 NM_001005272.3 deleterious_low_confidence(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF306,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 54707254 54707254 A T 1 0 0 0 0 1 0 0 0 11120 217 8 4 4 OR4A5 11 54707254 Missense_Mutation SNP A C3N-02423_T 5552879 54707254 80379368 249 29379 OR4C15 0 . GRCh38 11 55554739 55554739 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.433A>T p.Ile145Phe p.I145F ENST00000314644 1/1 321 291 30 341 341 0 strelka-varscan-mutect OR4C15,missense_variant,p.Ile145Phe,ENST00000314644,NM_001001920.1; T ENST00000314644 Transcript missense_variant 433/1113 433/1113 145/370 I/F Atc/Ttc 1 1 OR4C15 HGNC HGNC:15171 protein_coding YES CCDS31501.1 ENSP00000324958 Q8NGM1 UPI00003B288E NM_001001920.1 deleterious_low_confidence(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF14,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00245 MODERATE 1 SNV 1 PASS rs1293802668 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 55554739 55554739 A T 1 0 0 0 0 1 0 0 0 11125 217 8 4 4 OR4C15 11 55554739 Missense_Mutation SNP A C3N-02423_T 847485 55554739 79531883 250 29380 OR8K5 0 . GRCh38 11 56160000 56160000 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.318G>T p.Met106Ile p.M106I ENST00000313447 1/1 208 174 34 231 231 0 strelka-varscan-mutect OR8K5,missense_variant,p.Met106Ile,ENST00000313447,NM_001004058.2; A ENST00000313447 Transcript missense_variant 318/924 318/924 106/307 M/I atG/atT 1 -1 OR8K5 HGNC HGNC:15315 protein_coding YES CCDS31521.1 ENSP00000323853 Q8NH50 UPI000004B231 NM_001004058.2 tolerated_low_confidence(0.51) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF60,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 56160000 56160000 C A 1 0 0 0 0 1 0 0 0 11312 478 17 2 2 OR8K5 11 56160000 Missense_Mutation SNP C C3N-02423_T 605261 56160000 78926622 251 29381 GLYAT 0 . GRCh38 11 58709973 58709973 + Missense_Mutation SNP C C G rs373776314 C3N-02423_T C3N-02423_N C C c.684G>C p.Met228Ile p.M228I ENST00000611865 5/5 168 159 9 156 156 0 strelka-varscan-mutect GLYAT,missense_variant,p.Met228Ile,ENST00000611865,;GLYAT,missense_variant,p.Met228Ile,ENST00000344743,NM_201648.2;GLYAT,missense_variant,p.Met228Ile,ENST00000529732,;GLYAT,intron_variant,,ENST00000586098,;GLYAT,downstream_gene_variant,,ENST00000278400,NM_005838.3; G ENST00000611865 Transcript missense_variant 684/1899 684/891 228/296 M/I atG/atC rs373776314,COSM3450042 1 -1 GLYAT HGNC HGNC:13734 protein_coding YES CCDS7970.1 ENSP00000484592 Q6IB77 UPI00003667C7 tolerated(0.49) 5/5 hmmpanther:PTHR15298:SF9,hmmpanther:PTHR15298,Gene3D:3.40.630.30,Pfam_domain:PF08444,Superfamily_domains:SSF55729 0,1 MODERATE 1 SNV 3 0,1 1 PASS rs373776314 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 58709973 58709973 C G 1 0 0 0 0 1 0 0 0 6356 826 29 4 4 GLYAT 11 58709973 Missense_Mutation SNP C C3N-02423_T 2549973 58709973 76376649 252 29382 VWCE 0 . GRCh38 11 61259075 61259076 + Frame_Shift_Ins INS - - TT novel C3N-02423_T C3N-02423_N - - c.2467_2468insAA p.Pro823GlnfsTer9 p.P823Qfs*9 ENST00000335613 20/20 225 180 45 226 226 0 sindel-varindel-pindel VWCE,frameshift_variant,p.Pro823GlnfsTer9,ENST00000335613,NM_152718.2;VWCE,frameshift_variant,p.Pro539GlnfsTer9,ENST00000613271,;VWCE,frameshift_variant,p.Pro288GlnfsTer9,ENST00000535710,;VWCE,3_prime_UTR_variant,,ENST00000301770,;VWCE,downstream_gene_variant,,ENST00000538438,; TT ENST00000335613 Transcript frameshift_variant 2854-2855/3640 2467-2468/2868 823/955 P/QX cca/cAAca 1 -1 VWCE HGNC HGNC:26487 protein_coding YES CCDS8002.1 ENSP00000334186 Q96DN2 UPI000013E751 NM_152718.2 20/20 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF250 HIGH 1 insertion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 TT 7 5 99 61259075 61259075 - TT 1 0 1 1 0 0 0 0 0 17804 1348 47 0 0 VWCE 11 61259075 Frame_Shift_Ins INS - C3N-02423_T 2549102 61259075 73827547 253 29383 TMEM216 0 . GRCh38 11 61392639 61392639 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.8C>T p.Pro3Leu p.P3L ENST00000515837 1/5 217 188 29 217 217 0 strelka-varscan-mutect TMEM216,missense_variant,p.Pro3Leu,ENST00000515837,NM_001173990.2;TMEM216,missense_variant,p.Pro3Leu,ENST00000334888,NM_001173991.2;TMEM216,5_prime_UTR_variant,,ENST00000398979,NM_016499.5;TMEM216,non_coding_transcript_exon_variant,,ENST00000541473,;TMEM216,non_coding_transcript_exon_variant,,ENST00000544795,; T ENST00000515837 Transcript missense_variant 953/1958 8/438 3/145 P/L cCa/cTa 1 1 TMEM216 HGNC HGNC:25018 protein_coding YES CCDS53640.1 ENSP00000440638 Q9P0N5 UPI0001915109 NM_001173990.2 deleterious_low_confidence(0) 1/5 MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 3 4 99 61392639 61392639 C T 1 0 0 0 0 1 0 0 0 16580 594 21 3 3 TMEM216 11 61392639 Missense_Mutation SNP C C3N-02423_T 133564 61392639 73693983 254 29384 FTH1 0 . GRCh38 11 61965033 61965033 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.341C>A p.Ser114Ter p.S114* ENST00000273550 3/4 593 562 31 547 546 1 varscan-mutect FTH1,stop_gained,p.Ser114Ter,ENST00000273550,NM_002032.2;FTH1,stop_gained,p.Ser114Ter,ENST00000620041,;FTH1,stop_gained,p.Ser84Ter,ENST00000526640,;FTH1,stop_gained,p.Ser44Ter,ENST00000532601,;FTH1,stop_gained,p.Ser44Ter,ENST00000529548,;BEST1,3_prime_UTR_variant,,ENST00000449131,NM_001139443.1;FTH1,intron_variant,,ENST00000530019,;FTH1,intron_variant,,ENST00000529191,;FTH1,intron_variant,,ENST00000529631,;BEST1,downstream_gene_variant,,ENST00000378043,NM_004183.3,NM_001300787.1;BEST1,downstream_gene_variant,,ENST00000534553,;BEST1,downstream_gene_variant,,ENST00000526988,;RP11-810P12.7,upstream_gene_variant,,ENST00000623785,;FTH1,3_prime_UTR_variant,,ENST00000534180,;FTH1,3_prime_UTR_variant,,ENST00000532829,;FTH1,non_coding_transcript_exon_variant,,ENST00000533138,;FTH1,non_coding_transcript_exon_variant,,ENST00000534719,;BEST1,downstream_gene_variant,,ENST00000524877,;BEST1,downstream_gene_variant,,ENST00000524926,; T ENST00000273550 Transcript stop_gained 576/1229 341/552 114/183 S/* tCa/tAa 1 -1 FTH1 HGNC HGNC:3976 protein_coding YES CCDS41655.1 ENSP00000273550 P02794 A0A024R525 UPI000000122C NM_002032.2 3/4 Gene3D:1.20.1260.10,Pfam_domain:PF00210,PROSITE_profiles:PS50905,hmmpanther:PTHR11431,hmmpanther:PTHR11431:SF37,Superfamily_domains:SSF47240 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 61965033 61965033 G T 1 0 0 0 0 0 1 0 0 5956 1294 45 2 2 FTH1 11 61965033 Nonsense_Mutation SNP G C3N-02423_T 572394 61965033 73121589 255 29385 GANAB 0 . GRCh38 11 62625915 62625915 + Missense_Mutation SNP T T G novel C3N-02423_T C3N-02423_N T T c.2801A>C p.Glu934Ala p.E934A ENST00000346178 25/25 239 210 29 216 216 0 strelka-varscan-mutect GANAB,missense_variant,p.Glu934Ala,ENST00000346178,NM_198335.3;GANAB,missense_variant,p.Glu815Ala,ENST00000540933,NM_001278194.1;GANAB,missense_variant,p.Glu912Ala,ENST00000356638,NM_198334.2;GANAB,missense_variant,p.Glu820Ala,ENST00000534779,NM_001278192.1,NM_001278193.1;B3GAT3,upstream_gene_variant,,ENST00000531383,NM_001288722.1;B3GAT3,upstream_gene_variant,,ENST00000265471,NM_001288721.1,NM_012200.3;B3GAT3,upstream_gene_variant,,ENST00000534026,NM_001288723.1;B3GAT3,upstream_gene_variant,,ENST00000534715,;GANAB,3_prime_UTR_variant,,ENST00000532402,;GANAB,non_coding_transcript_exon_variant,,ENST00000528503,;B3GAT3,upstream_gene_variant,,ENST00000532585,;GANAB,downstream_gene_variant,,ENST00000531563,; G ENST00000346178 Transcript missense_variant 2817/3906 2801/2901 934/966 E/A gAa/gCa 1 -1 GANAB HGNC HGNC:4138 protein_coding YES CCDS41656.1 ENSP00000340466 Q14697 UPI0000052BE8 NM_198335.3 tolerated(0.15) 25/25 hmmpanther:PTHR22762,hmmpanther:PTHR22762:SF51 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 62625915 62625915 T G 1 0 0 0 0 1 0 0 0 6101 1783 62 5 5 GANAB 11 62625915 Missense_Mutation SNP T C3N-02423_T 660882 62625915 72460707 256 29386 PLCB3 0 . GRCh38 11 64255254 64255254 + Missense_Mutation SNP C C G rs775042914 C3N-02423_T C3N-02423_N C C c.408C>G p.Phe136Leu p.F136L ENST00000540288 5/32 359 335 24 324 324 0 strelka-varscan-mutect PLCB3,missense_variant,p.Phe136Leu,ENST00000540288,NM_001316314.1,NM_000932.2;PLCB3,missense_variant,p.Phe136Leu,ENST00000279230,;PLCB3,missense_variant,p.Phe69Leu,ENST00000325234,NM_001184883.1; G ENST00000540288 Transcript missense_variant 511/4469 408/3705 136/1234 F/L ttC/ttG rs775042914 1 1 PLCB3 HGNC HGNC:9056 protein_coding YES CCDS8064.1 ENSP00000443631 Q01970 UPI0000131AFF NM_001316314.1,NM_000932.2 tolerated(0.46) 5/32 hmmpanther:PTHR10336:SF11,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000956,Gene3D:2.30.29.30,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS rs775042914 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 64255254 64255254 C G 1 0 0 0 0 1 0 0 0 12123 825 29 4 4 PLCB3 11 64255254 Missense_Mutation SNP C C3N-02423_T 1629339 64255254 70831368 257 29387 TRMT112 0 . GRCh38 11 64317105 64317105 + Missense_Mutation SNP C C T C3N-02423_T C3N-02423_N C C c.223G>A p.Glu75Lys p.E75K ENST00000544844 3/4 295 280 15 326 326 0 strelka-varscan-mutect TRMT112,missense_variant,p.Glu75Lys,ENST00000544844,NM_016404.2;TRMT112,missense_variant,p.Glu31Lys,ENST00000535750,;TRMT112,missense_variant,p.Glu75Lys,ENST00000539854,NM_001286084.1;TRMT112,missense_variant,p.Glu70Lys,ENST00000308774,NM_001286082.1;TRMT112,3_prime_UTR_variant,,ENST00000535126,;ESRRA,downstream_gene_variant,,ENST00000405666,NM_001282450.1;ESRRA,downstream_gene_variant,,ENST00000406310,NM_001282451.1;ESRRA,downstream_gene_variant,,ENST00000000442,NM_004451.4;PRDX5,upstream_gene_variant,,ENST00000265462,NM_012094.4;ESRRA,downstream_gene_variant,,ENST00000539594,;ESRRA,downstream_gene_variant,,ENST00000545035,;PRDX5,upstream_gene_variant,,ENST00000352435,NM_181651.2;PRDX5,upstream_gene_variant,,ENST00000347941,NM_181652.2;TRMT112,non_coding_transcript_exon_variant,,ENST00000537918,;ESRRA,downstream_gene_variant,,ENST00000467987,; T ENST00000544844 Transcript missense_variant 781/1106 223/378 75/125 E/K Gag/Aag COSM1298370 1 -1 TRMT112 HGNC HGNC:26940 protein_coding YES CCDS8068.1 ENSP00000438349 Q9UI30 A0A024R565 UPI00000473D9 NM_016404.2 tolerated(0.17) 3/4 Pfam_domain:PF03966,hmmpanther:PTHR12773,hmmpanther:PTHR12773:SF1 1 MODERATE 1 SNV 1 1 1 PASS rs1481135577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 64317105 64317105 C T 1 0 0 0 0 1 0 0 0 17065 835 29 3 3 TRMT112 11 64317105 Missense_Mutation SNP C C3N-02423_T 61851 64317105 70769517 258 29388 SLCO2B1 0 . GRCh38 11 75196637 75196637 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.1557C>T p.= p.G519G ENST00000289575 10/14 186 162 24 180 180 0 strelka-varscan-mutect SLCO2B1,synonymous_variant,p.=,ENST00000289575,NM_007256.4;SLCO2B1,synonymous_variant,p.=,ENST00000454962,;SLCO2B1,synonymous_variant,p.=,ENST00000532236,;SLCO2B1,synonymous_variant,p.=,ENST00000428359,NM_001145211.2;SLCO2B1,synonymous_variant,p.=,ENST00000525650,NM_001145212.2;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000531756,;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000530012,;SLCO2B1,non_coding_transcript_exon_variant,,ENST00000528108,;SLCO2B1,upstream_gene_variant,,ENST00000530015,; T ENST00000289575 Transcript synonymous_variant 1952/4494 1557/2130 519/709 G ggC/ggT 1 1 SLCO2B1 HGNC HGNC:10962 protein_coding YES CCDS8235.1 ENSP00000289575 A0A024R5I4 UPI000000D99A NM_007256.4 10/14 Pfam_domain:PF03137,PROSITE_profiles:PS51465,hmmpanther:PTHR11388,hmmpanther:PTHR11388:SF87,TIGRFAM_domain:TIGR00805 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 2 4 99 75196637 75196637 C T 1 0 0 0 0 0 0 0 1 15014 784 28 3 3 SLCO2B1 11 75196637 Silent SNP C C3N-02423_T 10879532 75196637 59889985 259 29389 UBTFL1 0 . GRCh38 11 90086896 90086896 + Missense_Mutation SNP C C A rs748845279 C3N-02423_T C3N-02423_N C C c.947C>A p.Pro316Gln p.P316Q ENST00000530464 1/1 153 142 11 156 156 0 varscan-mutect UBTFL1,missense_variant,p.Pro316Gln,ENST00000530464,NM_001143975.1; A ENST00000530464 Transcript missense_variant 947/1182 947/1182 316/393 P/Q cCg/cAg rs748845279 1 1 UBTFL1 HGNC HGNC:14533 protein_coding YES ENSP00000485108 P0CB47 UPI0000185F50 NM_001143975.1 tolerated(0.08) 1/1 hmmpanther:PTHR13711:SF221,hmmpanther:PTHR13711 MODERATE 1 SNV 1 PASS rs748845279 . 8 198 4 0 0 0 0 0 -19.85392 1 1 1 1 0 A 3 1 99 90086896 90086896 C A 1 0 0 0 0 1 0 0 0 17434 652 23 1 1 UBTFL1 11 90086896 Missense_Mutation SNP C C3N-02423_T 14890259 90086896 44999726 260 29390 CEP295 0 . GRCh38 11 93699947 93699947 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.5035G>T p.Ala1679Ser p.A1679S ENST00000325212 15/30 281 225 56 250 250 0 strelka-varscan-mutect CEP295,missense_variant,p.Ala1679Ser,ENST00000325212,NM_033395.1;CEP295,5_prime_UTR_variant,,ENST00000530425,;CEP295,intron_variant,,ENST00000531700,;CEP295,downstream_gene_variant,,ENST00000531877,;CEP295,downstream_gene_variant,,ENST00000531622,; T ENST00000325212 Transcript missense_variant 5197/8057 5035/7806 1679/2601 A/S Gca/Tca 1 1 CEP295 HGNC HGNC:29366 protein_coding YES CCDS44708.1 ENSP00000316681 Q9C0D2 UPI0000251F0E NM_033395.1 tolerated(0.18) 15/30 MODERATE 1 SNV 2 1 PASS rs1373811900 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 93699947 93699947 G T 1 0 0 0 0 1 0 0 0 2970 1319 46 2 2 CEP295 11 93699947 Missense_Mutation SNP G C3N-02423_T 3613051 93699947 41386675 261 29391 ATM 0 . GRCh38 11 108227685 108227685 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.61A>G p.Thr21Ala p.T21A ENST00000278616 2/63 471 429 42 380 380 0 strelka-varscan-mutect ATM,missense_variant,p.Thr21Ala,ENST00000278616,NM_000051.3;ATM,missense_variant,p.Thr21Ala,ENST00000452508,;ATM,missense_variant,p.Thr21Ala,ENST00000530958,;ATM,missense_variant,p.Thr21Ala,ENST00000527805,;ATM,missense_variant,p.Thr21Ala,ENST00000527891,;ATM,missense_variant,p.Thr21Ala,ENST00000601453,;ATM,missense_variant,p.Thr21Ala,ENST00000526567,;ATM,missense_variant,p.Thr21Ala,ENST00000532931,;Y_RNA,downstream_gene_variant,,ENST00000384240,; G ENST00000278616 Transcript missense_variant 446/13147 61/9171 21/3056 T/A Aca/Gca 1 1 ATM HGNC HGNC:795 protein_coding YES CCDS31669.1 ENSP00000278616 Q13315 A0A024R3C7 UPI000016B511 NM_000051.3 deleterious(0.01) 2/63 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF72,Pfam_domain:PF11640,SMART_domains:SM01342 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 108227685 108227685 A G 1 0 0 0 0 1 0 0 0 1261 391 14 5 5 ATM 11 108227685 Missense_Mutation SNP A C3N-02423_T 14527738 108227685 26858937 262 29392 DIXDC1 0 . GRCh38 11 111929909 111929909 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.56C>T p.Ser19Phe p.S19F ENST00000529225 2/6 318 297 21 285 285 0 strelka-varscan-mutect DIXDC1,missense_variant,p.Ser19Phe,ENST00000529225,NM_001278542.1;C11orf52,downstream_gene_variant,,ENST00000278601,NM_080659.2;C11orf52,downstream_gene_variant,,ENST00000529342,;RNA5SP351,downstream_gene_variant,,ENST00000459480,;C11orf52,downstream_gene_variant,,ENST00000527286,;HSPB2-C11orf52,downstream_gene_variant,,ENST00000534100,;C11orf52,downstream_gene_variant,,ENST00000529012,; T ENST00000529225 Transcript missense_variant,splice_region_variant 336/1945 56/657 19/218 S/F tCt/tTt 1 1 DIXDC1 HGNC HGNC:23695 protein_coding CCDS60957.1 ENSP00000434130 Q155Q3 UPI0001F78119 NM_001278542.1 tolerated(0.07) 2/6 PROSITE_profiles:PS50021,Gene3D:1.10.418.10 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 111929909 111929909 C T 1 0 0 0 0 1 0 0 0 4348 927 32 3 3 DIXDC1 11 111929909 Missense_Mutation SNP C C3N-02423_T 3702224 111929909 23156713 263 29393 CADM1 0 . GRCh38 11 115238533 115238533 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.391C>T p.Pro131Ser p.P131S ENST00000331581 3/12 475 433 42 485 484 1 strelka-varscan-mutect CADM1,missense_variant,p.Pro131Ser,ENST00000452722,NM_014333.3;CADM1,missense_variant,p.Pro131Ser,ENST00000542447,NM_001098517.1;CADM1,missense_variant,p.Pro90Ser,ENST00000621709,;CADM1,missense_variant,p.Pro90Ser,ENST00000612471,;CADM1,missense_variant,p.Pro131Ser,ENST00000537058,NM_001301044.1;CADM1,missense_variant,p.Pro131Ser,ENST00000536727,NM_001301045.1;CADM1,missense_variant,p.Pro130Ser,ENST00000545380,;CADM1,missense_variant,p.Pro131Ser,ENST00000331581,NM_001301043.1;CADM1,missense_variant,p.Pro90Ser,ENST00000621043,;CADM1,missense_variant,p.Pro90Ser,ENST00000616271,;CADM1,missense_variant,p.Pro90Ser,ENST00000612235,;CADM1,missense_variant,p.Pro98Ser,ENST00000545094,;CADM1,missense_variant,p.Pro115Ser,ENST00000543249,;CADM1,5_prime_UTR_variant,,ENST00000542450,;CADM1,5_prime_UTR_variant,,ENST00000543540,;CADM1,non_coding_transcript_exon_variant,,ENST00000537140,;CADM1,3_prime_UTR_variant,,ENST00000540951,;CADM1,non_coding_transcript_exon_variant,,ENST00000541434,; A ENST00000331581 Transcript missense_variant 562/1766 391/1416 131/471 P/S Cca/Tca 1 -1 CADM1 HGNC HGNC:5951 protein_coding YES CCDS73399.1 ENSP00000329797 Q9BY67 X5D7A8 UPI000204AF0D NM_001301043.1 tolerated(0.07) 3/12 Gene3D:2.60.40.10,Pfam_domain:PF07686,PROSITE_profiles:PS50835,hmmpanther:PTHR23277,hmmpanther:PTHR23277:SF53,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 115238533 115238533 G A 1 0 0 0 0 1 0 0 0 2256 1232 43 3 3 CADM1 11 115238533 Missense_Mutation SNP G C3N-02423_T 3308624 115238533 19848089 264 29394 VPS11 0 . GRCh38 11 119077583 119077583 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.1508T>A p.Leu503Gln p.L503Q ENST00000621676 9/16 232 206 26 187 187 0 strelka-varscan-mutect VPS11,missense_variant,p.Leu493Gln,ENST00000614944,NM_001290185.1;VPS11,missense_variant,p.Leu503Gln,ENST00000621676,NM_021729.5;VPS11,missense_variant,p.Leu160Gln,ENST00000530809,;VPS11,5_prime_UTR_variant,,ENST00000620429,;VPS11,non_coding_transcript_exon_variant,,ENST00000534551,;VPS11,upstream_gene_variant,,ENST00000524454,;VPS11,non_coding_transcript_exon_variant,,ENST00000622309,;VPS11,downstream_gene_variant,,ENST00000526829,; A ENST00000621676 Transcript missense_variant 1640/3313 1508/2826 503/941 L/Q cTg/cAg 1 1 VPS11 HGNC HGNC:14583 protein_coding YES CCDS73404.1 ENSP00000481126 A0A087WXL6 UPI0000161C99 NM_021729.5 deleterious(0) 9/16 PROSITE_profiles:PS50236,hmmpanther:PTHR23323:SF24,hmmpanther:PTHR23323,Pfam_domain:PF00637,Gene3D:1.25.40.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 119077583 119077583 T A 1 0 0 0 0 1 0 0 0 17735 1580 55 4 4 VPS11 11 119077583 Missense_Mutation SNP T C3N-02423_T 3839050 119077583 16009039 265 29395 HINFP 0 . GRCh38 11 119130746 119130746 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.203G>T p.Trp68Leu p.W68L ENST00000350777 3/10 221 179 42 205 205 0 strelka-varscan-mutect HINFP,missense_variant,p.Trp68Leu,ENST00000350777,NM_198971.2,NM_015517.4;HINFP,missense_variant,p.Trp68Leu,ENST00000527410,NM_001243259.1;HINFP,missense_variant,p.Trp68Leu,ENST00000529988,;HINFP,downstream_gene_variant,,ENST00000530678,;HINFP,non_coding_transcript_exon_variant,,ENST00000532312,;HINFP,non_coding_transcript_exon_variant,,ENST00000527354,;HINFP,non_coding_transcript_exon_variant,,ENST00000531022,;HINFP,non_coding_transcript_exon_variant,,ENST00000529354,;HINFP,non_coding_transcript_exon_variant,,ENST00000531360,;HINFP,upstream_gene_variant,,ENST00000527755,;HINFP,upstream_gene_variant,,ENST00000532860,;HINFP,upstream_gene_variant,,ENST00000529808,;HINFP,downstream_gene_variant,,ENST00000527206,;HINFP,upstream_gene_variant,,ENST00000529610,; T ENST00000350777 Transcript missense_variant 266/3163 203/1554 68/517 W/L tGg/tTg 1 1 HINFP HGNC HGNC:17850 protein_coding YES CCDS8414.1 ENSP00000318085 Q9BQA5 A0A024R3F5 UPI000013EB5D NM_198971.2,NM_015517.4 deleterious(0) 3/10 hmmpanther:PTHR24391,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 119130746 119130746 G T 1 0 0 0 0 1 0 0 0 6998 1357 47 2 2 HINFP 11 119130746 Missense_Mutation SNP G C3N-02423_T 53163 119130746 15955876 266 29396 ARHGAP32 0 . GRCh38 11 128970679 128970679 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.4492C>T p.Pro1498Ser p.P1498S ENST00000310343 22/22 272 233 39 225 225 0 strelka-varscan-mutect ARHGAP32,missense_variant,p.Pro1498Ser,ENST00000310343,NM_001142685.1;ARHGAP32,missense_variant,p.Pro1149Ser,ENST00000392657,NM_014715.3;ARHGAP32,missense_variant,p.Pro1149Ser,ENST00000527272,;ARHGAP32,3_prime_UTR_variant,,ENST00000524655,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000526162,; A ENST00000310343 Transcript missense_variant 4492/10111 4492/6264 1498/2087 P/S Cca/Tca 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 tolerated_low_confidence(0.49) 22/22 hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 128970679 128970679 G A 1 0 0 0 0 1 0 0 0 1006 1174 41 3 3 ARHGAP32 11 128970679 Missense_Mutation SNP G C3N-02423_T 9839933 128970679 6115943 267 29397 ARHGAP32 0 . GRCh38 11 129041001 129041001 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.930C>G p.= p.L310L ENST00000310343 10/22 229 214 15 210 210 0 strelka-varscan-mutect ARHGAP32,synonymous_variant,p.=,ENST00000310343,NM_001142685.1;ARHGAP32,synonymous_variant,p.=,ENST00000524655,;ARHGAP32,non_coding_transcript_exon_variant,,ENST00000533509,; C ENST00000310343 Transcript synonymous_variant 930/10111 930/6264 310/2087 L ctC/ctG 1 -1 ARHGAP32 HGNC HGNC:17399 protein_coding YES CCDS44769.1 ENSP00000310561 A7KAX9 UPI000159C61F NM_001142685.1 10/22 PROSITE_profiles:PS50002,hmmpanther:PTHR15729:SF9,hmmpanther:PTHR15729,Pfam_domain:PF14604,Gene3D:2.30.30.40,SMART_domains:SM00326,Superfamily_domains:SSF50044 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 129041001 129041001 G C 1 0 0 0 0 0 0 0 1 1006 929 33 4 4 ARHGAP32 11 129041001 Silent SNP G C3N-02423_T 70322 129041001 6045621 268 29398 NFRKB 0 . GRCh38 11 129865949 129865949 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.3641C>G p.Ser1214Cys p.S1214C ENST00000524794 23/25 139 131 8 121 121 0 strelka-varscan-mutect NFRKB,missense_variant,p.Ser1189Cys,ENST00000446488,NM_001143835.1;NFRKB,missense_variant,p.Ser1214Cys,ENST00000524794,NM_006165.3;NFRKB,missense_variant,p.Ser1189Cys,ENST00000524746,;NFRKB,downstream_gene_variant,,ENST00000531755,; C ENST00000524794 Transcript missense_variant 3762/4351 3641/3975 1214/1324 S/C tCt/tGt 1 -1 NFRKB HGNC HGNC:7802 protein_coding YES CCDS8483.1 ENSP00000436926 Q6P4R8 UPI000006E542 NM_006165.3 deleterious_low_confidence(0) 23/25 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -15.2549 1 1 1 1 0 C 3 2 99 129865949 129865949 G C 1 0 0 0 0 1 0 0 0 10420 942 33 4 4 NFRKB 11 129865949 Missense_Mutation SNP G C3N-02423_T 824948 129865949 5220673 269 29399 KRAS 0 . GRCh38 12 25245351 25245351 + Missense_Mutation SNP C C A rs121913530 C3N-02423_T C3N-02423_N C C c.34G>T p.Gly12Cys p.G12C ENST00000256078 2/6 292 236 56 338 337 1 strelka-varscan-mutect KRAS,missense_variant,p.Gly12Cys,ENST00000311936,NM_004985.4;KRAS,missense_variant,p.Gly12Cys,ENST00000556131,;KRAS,missense_variant,p.Gly12Cys,ENST00000256078,NM_033360.3;KRAS,missense_variant,p.Gly12Cys,ENST00000557334,; A ENST00000256078 Transcript missense_variant 98/1119 34/570 12/189 G/C Ggt/Tgt rs121913530,CM076251,COSM1140136,COSM1152506,COSM1157797,COSM516,COSM517,COSM518 1 -1 KRAS HGNC HGNC:6407 protein_coding YES CCDS8703.1 ENSP00000256078 P01116 L7RSL8 UPI0000133132 NM_033360.3 deleterious(0.04) 2/6 Low_complexity_(Seg):seg,PROSITE_profiles:PS51421,hmmpanther:PTHR24070:SF186,hmmpanther:PTHR24070,Pfam_domain:PF00071,Gene3D:3.40.50.300,TIGRFAM_domain:TIGR00231,SMART_domains:SM00175,SMART_domains:SM00173,SMART_domains:SM00176,SMART_domains:SM00174,Superfamily_domains:SSF52540,Prints_domain:PR00449 not_provided,pathogenic 0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS rs121913530 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 25245351 25245351 C A 1 0 0 0 0 1 0 0 0 8318 594 21 2 2 KRAS 12 25245351 Missense_Mutation SNP C C3N-02423_T 25245351 108029958 270 29400 KIAA1551 0 . GRCh38 12 31984301 31984301 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.3346G>C p.Glu1116Gln p.E1116Q ENST00000312561 4/6 92 85 7 118 118 0 strelka-varscan-mutect KIAA1551,missense_variant,p.Glu1116Gln,ENST00000312561,NM_018169.3;KIAA1551,downstream_gene_variant,,ENST00000381054,;KIAA1551,downstream_gene_variant,,ENST00000540924,;KIAA1551,intron_variant,,ENST00000535596,;KIAA1551,intron_variant,,ENST00000397578,;KIAA1551,intron_variant,,ENST00000541981,;KIAA1551,upstream_gene_variant,,ENST00000543763,; C ENST00000312561 Transcript missense_variant 3760/6230 3346/5244 1116/1747 E/Q Gaa/Caa 1 1 KIAA1551 HGNC HGNC:25559 protein_coding YES CCDS8725.2 ENSP00000310338 Q9HCM1 UPI0000577B2F NM_018169.3 deleterious(0.02) 4/6 Pfam_domain:PF15395,hmmpanther:PTHR21604 MODERATE 1 SNV 1 1 PASS rs1242195681 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 31984301 31984301 G C 1 0 0 0 0 1 0 0 0 8122 943 33 4 4 KIAA1551 12 31984301 Missense_Mutation SNP G C3N-02423_T 6738950 31984301 101291008 271 29401 KMT2D 0 . GRCh38 12 49054375 49054375 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.442G>A p.Gly148Ser p.G148S ENST00000301067 4/54 241 219 22 213 213 0 strelka-varscan-mutect KMT2D,missense_variant,p.Gly148Ser,ENST00000301067,NM_003482.3;KMT2D,downstream_gene_variant,,ENST00000547610,; T ENST00000301067 Transcript missense_variant 442/19419 442/16614 148/5537 G/S Ggc/Agc 1 -1 KMT2D HGNC HGNC:7133 protein_coding YES CCDS44873.1 ENSP00000301067 O14686 UPI0000EE84D6 NM_003482.3 deleterious(0.02) 4/54 Low_complexity_(Seg):seg,Pfam_domain:PF13771 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 49054375 49054375 C T 1 0 0 0 0 1 0 0 0 8298 681 24 3 3 KMT2D 12 49054375 Missense_Mutation SNP C C3N-02423_T 17070074 49054375 84220934 272 29402 LMBR1L 0 . GRCh38 12 49100580 49100580 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.1149A>T p.Arg383Ser p.R383S ENST00000267102 14/17 178 146 32 187 187 0 strelka-varscan-mutect LMBR1L,missense_variant,p.Arg383Ser,ENST00000267102,NM_001300750.1,NM_018113.3;LMBR1L,missense_variant,p.Arg363Ser,ENST00000547382,NM_001300751.1;LMBR1L,missense_variant,p.Arg73Ser,ENST00000547698,;LMBR1L,downstream_gene_variant,,ENST00000547675,;LMBR1L,downstream_gene_variant,,ENST00000551782,;LMBR1L,downstream_gene_variant,,ENST00000551854,;LMBR1L,downstream_gene_variant,,ENST00000550137,;LMBR1L,downstream_gene_variant,,ENST00000552449,;LMBR1L,downstream_gene_variant,,ENST00000553204,;LMBR1L,downstream_gene_variant,,ENST00000552153,;LMBR1L,downstream_gene_variant,,ENST00000549429,;LMBR1L,missense_variant,p.Arg79Ser,ENST00000553040,;LMBR1L,3_prime_UTR_variant,,ENST00000417750,;LMBR1L,3_prime_UTR_variant,,ENST00000547670,;LMBR1L,non_coding_transcript_exon_variant,,ENST00000550867,;LMBR1L,non_coding_transcript_exon_variant,,ENST00000552577,;LMBR1L,non_coding_transcript_exon_variant,,ENST00000551143,;LMBR1L,non_coding_transcript_exon_variant,,ENST00000551272,;LMBR1L,intron_variant,,ENST00000547813,;LMBR1L,downstream_gene_variant,,ENST00000457164,;LMBR1L,downstream_gene_variant,,ENST00000551169,;LMBR1L,downstream_gene_variant,,ENST00000552141,;LMBR1L,downstream_gene_variant,,ENST00000549730,;LMBR1L,downstream_gene_variant,,ENST00000552879,;LMBR1L,downstream_gene_variant,,ENST00000549296,;LMBR1L,downstream_gene_variant,,ENST00000549587,;LMBR1L,downstream_gene_variant,,ENST00000550815,; A ENST00000267102 Transcript missense_variant 1492/2934 1149/1470 383/489 R/S agA/agT 1 -1 LMBR1L HGNC HGNC:18268 protein_coding YES CCDS8780.2 ENSP00000267102 Q6UX01 A0A024R0Y9 UPI0000071212 NM_001300750.1,NM_018113.3 deleterious(0.02) 14/17 Pfam_domain:PF04791,hmmpanther:PTHR12625,hmmpanther:PTHR12625:SF2 MODERATE 1 SNV 1 1 PASS rs1447857566 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 49100580 49100580 T A 1 0 0 0 0 1 0 0 0 8765 1432 50 4 4 LMBR1L 12 49100580 Missense_Mutation SNP T C3N-02423_T 46205 49100580 84174729 273 29403 SUOX 0 . GRCh38 12 56002703 56002703 + Nonsense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.211C>T p.Gln71Ter p.Q71* ENST00000394109 2/3 151 143 8 161 161 0 strelka-varscan-mutect SUOX,stop_gained,p.Gln71Ter,ENST00000394109,;SUOX,stop_gained,p.Gln71Ter,ENST00000394115,NM_000456.2;SUOX,stop_gained,p.Gln71Ter,ENST00000266971,NM_001032386.1;SUOX,stop_gained,p.Gln71Ter,ENST00000548274,;SUOX,stop_gained,p.Gln71Ter,ENST00000356124,NM_001032387.1;SUOX,stop_gained,p.Gln71Ter,ENST00000546833,;SUOX,stop_gained,p.Gln71Ter,ENST00000551841,;SUOX,stop_gained,p.Gln71Ter,ENST00000552258,;IKZF4,upstream_gene_variant,,ENST00000262032,;SUOX,downstream_gene_variant,,ENST00000547586,;SUOX,non_coding_transcript_exon_variant,,ENST00000550478,;SUOX,intron_variant,,ENST00000551698,;SUOX,intron_variant,,ENST00000550340,;SUOX,intron_variant,,ENST00000552363,;IKZF4,upstream_gene_variant,,ENST00000548601,;SUOX,downstream_gene_variant,,ENST00000550121,;SUOX,stop_gained,p.Gln71Ter,ENST00000550065,;SUOX,non_coding_transcript_exon_variant,,ENST00000546712,;SUOX,non_coding_transcript_exon_variant,,ENST00000552813,; T ENST00000394109 Transcript stop_gained 935/2860 211/1638 71/545 Q/* Cag/Tag 1 1 SUOX HGNC HGNC:11460 protein_coding YES CCDS8901.2 ENSP00000377668 P51687 A0A024RB79 UPI00001FC4A1 2/3 hmmpanther:PTHR19372,hmmpanther:PTHR19372:SF7 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 56002703 56002703 C T 1 0 0 0 0 0 1 0 0 15781 827 29 3 3 SUOX 12 56002703 Nonsense_Mutation SNP C C3N-02423_T 6902123 56002703 77272606 274 29404 NACA 0 . GRCh38 12 56720985 56720985 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.545C>T p.Ser182Leu p.S182L ENST00000550952 3/11 222 208 14 286 286 0 strelka-varscan-mutect NACA,missense_variant,p.Ser182Leu,ENST00000454682,;NACA,missense_variant,p.Ser182Leu,ENST00000550952,NM_001113203.2;NACA,intron_variant,,ENST00000356769,NM_001113202.1;NACA,intron_variant,,ENST00000552540,NM_001113201.2;NACA,intron_variant,,ENST00000393891,NM_005594.5;NACA,intron_variant,,ENST00000548563,;NACA,intron_variant,,ENST00000546392,;NACA,intron_variant,,ENST00000549855,;NACA,intron_variant,,ENST00000549259,;NACA,intron_variant,,ENST00000552055,;NACA,intron_variant,,ENST00000546862,;NACA,upstream_gene_variant,,ENST00000550920,;NACA,downstream_gene_variant,,ENST00000546917,;NACA,intron_variant,,ENST00000551793,;NACA,intron_variant,,ENST00000551775,;NACA,intron_variant,,ENST00000551520,;NACA,intron_variant,,ENST00000547914,;NACA,intron_variant,,ENST00000548084,; A ENST00000550952 Transcript missense_variant 584/2922 545/2778 182/925 S/L tCa/tTa 1 -1 NACA HGNC HGNC:7629 protein_coding YES CCDS44925.2 ENSP00000448035 E9PAV3 UPI000014145D NM_001113203.2 tolerated_low_confidence(0.26) 3/11 hmmpanther:PTHR21713:SF3,hmmpanther:PTHR21713 MODERATE 1 SNV 2 1 PASS rs1458983567 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 56720985 56720985 G A 1 0 0 0 0 1 0 0 0 10139 1294 45 3 3 NACA 12 56720985 Missense_Mutation SNP G C3N-02423_T 718282 56720985 76554324 275 29405 NEDD1 0 . GRCh38 12 96940523 96940523 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1253C>T p.Ser418Leu p.S418L ENST00000557644 9/15 104 97 7 128 128 0 strelka-varscan-mutect NEDD1,missense_variant,p.Ser411Leu,ENST00000266742,NM_152905.3;NEDD1,missense_variant,p.Ser411Leu,ENST00000429527,NM_001135176.1;NEDD1,missense_variant,p.Ser322Leu,ENST00000457368,;NEDD1,missense_variant,p.Ser322Leu,ENST00000411739,NM_001135177.1;NEDD1,missense_variant,p.Ser418Leu,ENST00000557644,NM_001135175.1;NEDD1,downstream_gene_variant,,ENST00000553609,;NEDD1,downstream_gene_variant,,ENST00000555114,;NEDD1,downstream_gene_variant,,ENST00000557454,;NEDD1,downstream_gene_variant,,ENST00000555806,; T ENST00000557644 Transcript missense_variant 1399/2367 1253/2004 418/667 S/L tCa/tTa 1 1 NEDD1 HGNC HGNC:7723 protein_coding YES CCDS44955.1 ENSP00000451211 Q8NHV4 UPI000004D249 NM_001135175.1 deleterious(0) 9/15 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 96940523 96940523 C T 1 0 0 0 0 1 0 0 0 10337 838 29 3 3 NEDD1 12 96940523 Missense_Mutation SNP C C3N-02423_T 40219538 96940523 36334786 276 29406 UHRF1BP1L 0 . GRCh38 12 100058764 100058764 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.2513C>T p.Ser838Leu p.S838L ENST00000279907 14/21 181 164 17 187 186 1 strelka-varscan-mutect UHRF1BP1L,missense_variant,p.Ser838Leu,ENST00000279907,NM_015054.1;UHRF1BP1L,missense_variant,p.Ser488Leu,ENST00000545232,; A ENST00000279907 Transcript missense_variant 2726/5168 2513/4395 838/1464 S/L tCa/tTa 1 -1 UHRF1BP1L HGNC HGNC:29102 protein_coding YES CCDS31882.1 ENSP00000279907 A0JNW5 UPI0000160563 NM_015054.1 tolerated(0.47) 14/21 hmmpanther:PTHR22774,hmmpanther:PTHR22774:SF17 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 100058764 100058764 G A 1 0 0 0 0 1 0 0 0 17493 1294 45 3 3 UHRF1BP1L 12 100058764 Missense_Mutation SNP G C3N-02423_T 3118241 100058764 33216545 277 29407 MYBPC1 0 . GRCh38 12 101667803 101667803 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2407G>C p.Asp803His p.D803H ENST00000452455 22/30 288 263 25 364 364 0 strelka-varscan-mutect MYBPC1,missense_variant,p.Asp816His,ENST00000549145,;MYBPC1,missense_variant,p.Asp686His,ENST00000551300,;MYBPC1,missense_variant,p.Asp810His,ENST00000361466,NM_002465.3;MYBPC1,missense_variant,p.Asp810His,ENST00000361685,NM_206819.2;MYBPC1,missense_variant,p.Asp803His,ENST00000452455,NM_001254718.1;MYBPC1,missense_variant,p.Asp759His,ENST00000547405,NM_001254722.1;MYBPC1,missense_variant,p.Asp785His,ENST00000553190,NM_206821.2;MYBPC1,missense_variant,p.Asp771His,ENST00000547509,;MYBPC1,missense_variant,p.Asp772His,ENST00000392934,NM_001254723.1;MYBPC1,missense_variant,p.Asp785His,ENST00000545503,NM_001254719.1;MYBPC1,missense_variant,p.Asp773His,ENST00000541119,NM_001254720.1;MYBPC1,missense_variant,p.Asp766His,ENST00000536007,NM_001254721.1;MYBPC1,missense_variant,p.Asp803His,ENST00000550270,NM_206820.2;MYBPC1,non_coding_transcript_exon_variant,,ENST00000548298,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000548532,;MYBPC1,intron_variant,,ENST00000550501,;MYBPC1,non_coding_transcript_exon_variant,,ENST00000549608,; C ENST00000452455 Transcript missense_variant 2509/3861 2407/3522 803/1173 D/H Gat/Cat 1 1 MYBPC1 HGNC HGNC:7549 protein_coding YES CCDS58268.1 ENSP00000400908 Q00872 UPI0001AE6B26 NM_001254718.1 deleterious(0) 22/30 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR13817,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 101667803 101667803 G C 1 0 0 0 0 1 0 0 0 10011 942 33 4 4 MYBPC1 12 101667803 Missense_Mutation SNP G C3N-02423_T 1609039 101667803 31607506 278 29408 C12orf42 0 . GRCh38 12 103302531 103302531 + Silent SNP G G A rs763470684 C3N-02423_T C3N-02423_N G G c.660C>T p.= p.I220I ENST00000378113 6/6 89 84 5 113 113 0 strelka-varscan-mutect C12orf42,synonymous_variant,p.=,ENST00000548048,;C12orf42,synonymous_variant,p.=,ENST00000378113,NM_001099336.2,NM_001278419.1;C12orf42,synonymous_variant,p.=,ENST00000548883,NM_198521.3;C12orf42,downstream_gene_variant,,ENST00000552578,;C12orf42,intron_variant,,ENST00000546526,;C12orf42,intron_variant,,ENST00000552977,;C12orf42,intron_variant,,ENST00000550650,;C12orf42,downstream_gene_variant,,ENST00000548789,;C12orf42,3_prime_UTR_variant,,ENST00000551134,;C12orf42,intron_variant,,ENST00000547347,; A ENST00000378113 Transcript synonymous_variant 925/1513 660/1083 220/360 I atC/atT rs763470684 1 -1 C12orf42 HGNC HGNC:24729 protein_coding YES CCDS44963.1 ENSP00000367353 Q96LP6 UPI00001D7906 NM_001099336.2,NM_001278419.1 6/6 Pfam_domain:PF15380,hmmpanther:PTHR40708,hmmpanther:PTHR40708:SF1 LOW 1 SNV 5 1 PASS rs763470684 . 0 205 4 0 0 0 0 0 -10.9572 1 1 1 1 0 A 2 1 99 103302531 103302531 G A 1 0 0 0 0 0 0 0 1 1810 1048 37 1 1 C12orf42 12 103302531 Silent SNP G C3N-02423_T 1634728 103302531 29972778 279 29409 ANAPC5 0 . GRCh38 12 121308666 121308666 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.2082C>G p.= p.L694L ENST00000261819 17/17 230 214 16 235 235 0 strelka-varscan-mutect ANAPC5,synonymous_variant,p.=,ENST00000261819,NM_016237.4;ANAPC5,synonymous_variant,p.=,ENST00000541887,;ANAPC5,synonymous_variant,p.=,ENST00000441917,NM_001137559.1;ANAPC5,synonymous_variant,p.=,ENST00000535482,;ANAPC5,non_coding_transcript_exon_variant,,ENST00000544314,;ANAPC5,3_prime_UTR_variant,,ENST00000539079,;ANAPC5,non_coding_transcript_exon_variant,,ENST00000534976,;ANAPC5,non_coding_transcript_exon_variant,,ENST00000535641,;ANAPC5,non_coding_transcript_exon_variant,,ENST00000422342,; C ENST00000261819 Transcript synonymous_variant 2204/2513 2082/2268 694/755 L ctC/ctG 1 -1 ANAPC5 HGNC HGNC:15713 protein_coding YES CCDS9220.1 ENSP00000261819 Q9UJX4 UPI000006DF80 NM_016237.4 17/17 Gene3D:1.25.40.10,hmmpanther:PTHR12830,Low_complexity_(Seg):seg,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 121308666 121308666 G C 1 0 0 0 0 0 0 0 1 703 1277 45 4 4 ANAPC5 12 121308666 Silent SNP G C3N-02423_T 18006135 121308666 11966643 280 29410 TMEM132C 0 . GRCh38 12 128706209 128706209 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.3241G>A p.Asp1081Asn p.D1081N ENST00000435159 9/9 153 121 32 138 138 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Asp1081Asn,ENST00000435159,NM_001136103.2; A ENST00000435159 Transcript missense_variant 3241/4947 3241/3327 1081/1108 D/N Gac/Aac 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 tolerated(0.31) 9/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4 MODERATE 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 128706209 128706209 G A 1 0 0 0 0 1 0 0 0 16491 1174 41 3 3 TMEM132C 12 128706209 Missense_Mutation SNP G C3N-02423_T 7397543 128706209 4569100 281 29411 SFSWAP 0 . GRCh38 12 131714860 131714860 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.427G>T p.Asp143Tyr p.D143Y ENST00000541286 3/19 244 201 43 237 237 0 strelka-varscan-mutect SFSWAP,missense_variant,p.Asp143Tyr,ENST00000261674,NM_004592.3;SFSWAP,missense_variant,p.Asp143Tyr,ENST00000541286,NM_001261411.1;SFSWAP,3_prime_UTR_variant,,ENST00000538548,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000535236,;SFSWAP,non_coding_transcript_exon_variant,,ENST00000540469,;SFSWAP,downstream_gene_variant,,ENST00000535399,; T ENST00000541286 Transcript missense_variant 520/3219 427/3012 143/1003 D/Y Gat/Tat 1 1 SFSWAP HGNC HGNC:10790 protein_coding YES CCDS58290.1 ENSP00000437738 Q12872 UPI000204AB4C NM_001261411.1 deleterious(0) 3/19 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF09750,hmmpanther:PTHR13161,hmmpanther:PTHR13161:SF15,SMART_domains:SM01141 MODERATE 1 SNV 1 1 PASS rs1318996778 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 131714860 131714860 G T 1 0 0 0 0 1 0 0 0 14444 1174 41 2 2 SFSWAP 12 131714860 Missense_Mutation SNP G C3N-02423_T 3008651 131714860 1560449 282 29412 EP400NL 0 . GRCh38 12 132104557 132104557 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.330T>A p.Phe110Leu p.F110L ENST00000389560 5/6 164 138 26 185 185 0 strelka-varscan-mutect EP400NL,missense_variant,p.Phe110Leu,ENST00000389560,;EP400NL,missense_variant,p.Phe110Leu,ENST00000454179,;EP400NL,missense_variant,p.Phe110Leu,ENST00000539205,;EP400NL,intron_variant,,ENST00000392352,;EP400NL,intron_variant,,ENST00000443539,;EP400NL,intron_variant,,ENST00000407361,;EP400NL,intron_variant,,ENST00000488030,;RP13-977J11.6,upstream_gene_variant,,ENST00000624002,;EP400NL,missense_variant,p.Phe179Leu,ENST00000446190,;EP400NL,missense_variant,p.Phe111Leu,ENST00000332441,; A ENST00000389560 Transcript missense_variant 651/1726 330/1260 110/419 F/L ttT/ttA 1 1 EP400NL HGNC HGNC:26602 protein_coding YES ENSP00000374211 H9KV84 UPI000024323A tolerated_low_confidence(0.05) 5/6 Pfam_domain:PF15790 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 132104557 132104557 T A 1 0 0 0 0 1 0 0 0 4996 1809 63 4 4 EP400NL 12 132104557 Missense_Mutation SNP T C3N-02423_T 389697 132104557 1170752 283 29413 SACS 0 . GRCh38 13 23331760 23331760 + Missense_Mutation SNP T T C novel C3N-02423_T C3N-02423_N T T c.12116A>G p.Lys4039Arg p.K4039R ENST00000382292 9/9 334 306 28 364 363 1 strelka-varscan-mutect SACS,missense_variant,p.Lys4039Arg,ENST00000382292,NM_014363.5;SACS,missense_variant,p.Lys3289Arg,ENST00000402364,NM_001278055.1;SACS,intron_variant,,ENST00000455470,;SACS,intron_variant,,ENST00000423156,; C ENST00000382292 Transcript missense_variant 12390/15324 12116/13740 4039/4579 K/R aAa/aGa 1 -1 SACS HGNC HGNC:10519 protein_coding YES CCDS9300.2 ENSP00000371729 Q9NZJ4 UPI000047039D NM_014363.5 deleterious(0.03) 9/9 hmmpanther:PTHR15600,hmmpanther:PTHR15600:SF28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 23331760 23331760 T C 1 0 0 0 0 1 0 0 0 14063 1841 64 5 5 SACS 13 23331760 Missense_Mutation SNP T C3N-02423_T 23331760 91032568 284 29414 ATP8A2 0 . GRCh38 13 25968581 25968581 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.3279G>T p.Lys1093Asn p.K1093N ENST00000381655 35/37 146 135 11 178 177 1 strelka-mutect ATP8A2,missense_variant,p.Lys1093Asn,ENST00000381655,NM_016529.4;ATP8A2,missense_variant,p.Lys899Asn,ENST00000255283,;ATP8A2,3_prime_UTR_variant,,ENST00000281620,; T ENST00000381655 Transcript missense_variant 3421/9575 3279/3567 1093/1188 K/N aaG/aaT 1 1 ATP8A2 HGNC HGNC:13533 protein_coding YES CCDS41873.1 ENSP00000371070 Q9NTI2 UPI0000229592 NM_016529.4 deleterious(0.01) 35/37 hmmpanther:PTHR24092:SF66,hmmpanther:PTHR24092,Pfam_domain:PF16212,TIGRFAM_domain:TIGR01652,Superfamily_domains:0049473 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 25968581 25968581 G T 1 0 0 0 0 1 0 0 0 1346 962 34 2 2 ATP8A2 13 25968581 Missense_Mutation SNP G C3N-02423_T 2636821 25968581 88395747 285 29415 STARD13 0 . GRCh38 13 33110853 33110853 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.2662C>T p.His888Tyr p.H888Y ENST00000336934 11/14 318 292 26 334 334 0 strelka-varscan-mutect STARD13,missense_variant,p.His888Tyr,ENST00000336934,NM_178006.3;STARD13,missense_variant,p.His880Tyr,ENST00000255486,NM_178007.2;STARD13,missense_variant,p.His770Tyr,ENST00000399365,NM_052851.2;STARD13,downstream_gene_variant,,ENST00000491333,; A ENST00000336934 Transcript missense_variant 2779/5917 2662/3342 888/1113 H/Y Cac/Tac 1 -1 STARD13 HGNC HGNC:19164 protein_coding YES CCDS9348.1 ENSP00000338785 Q9Y3M8 A0A024RDV4 UPI000006226E NM_178006.3 tolerated(0.72) 11/14 hmmpanther:PTHR12659,hmmpanther:PTHR12659:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 33110853 33110853 G A 1 0 0 0 0 1 0 0 0 15631 1348 47 3 3 STARD13 13 33110853 Missense_Mutation SNP G C3N-02423_T 7142272 33110853 81253475 286 29416 NEK3 0 . GRCh38 13 52141040 52141040 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.907G>T p.Gly303Ter p.G303* ENST00000618534 11/16 136 125 11 169 169 0 strelka-varscan-mutect NEK3,stop_gained,p.Gly303Ter,ENST00000618534,NM_152720.2;NEK3,stop_gained,p.Gly303Ter,ENST00000610828,NM_002498.2;NEK3,stop_gained,p.Gly303Ter,ENST00000620675,;NEK3,stop_gained,p.Gly33Ter,ENST00000618856,;NEK3,intron_variant,,ENST00000611833,NM_001146099.1;NEK3,intron_variant,,ENST00000617054,;NEK3,downstream_gene_variant,,ENST00000551355,; A ENST00000618534 Transcript stop_gained 1302/2414 907/1521 303/506 G/* Gga/Tga 1 -1 NEK3 HGNC HGNC:7746 protein_coding YES CCDS73576.1 ENSP00000484443 P51956 UPI000012FF28 NM_152720.2 11/16 hmmpanther:PTHR24362:SF7,hmmpanther:PTHR24362 HIGH 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 52141040 52141040 C A 1 0 0 0 0 0 1 0 0 10353 632 22 2 2 NEK3 13 52141040 Nonsense_Mutation SNP C C3N-02423_T 19030187 52141040 62223288 287 29417 KLF5 0 . GRCh38 13 73075764 73075764 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.1252G>A p.Asp418Asn p.D418N ENST00000377687 4/4 109 102 7 109 109 0 strelka-mutect KLF5,missense_variant,p.Asp418Asn,ENST00000377687,NM_001730.4;KLF5,missense_variant,p.Asp327Asn,ENST00000539231,NM_001286818.1;KLF5,non_coding_transcript_exon_variant,,ENST00000464404,; A ENST00000377687 Transcript missense_variant 1788/3566 1252/1374 418/457 D/N Gat/Aat COSM353847 1 1 KLF5 HGNC HGNC:6349 protein_coding YES CCDS9448.1 ENSP00000366915 Q13887 Q5T6X2 UPI0000000C89 NM_001730.4 deleterious(0) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF60,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 204 5 0 0 0 0 0 -14.05015 1 1 1 1 0 A 3 1 99 73075764 73075764 G A 1 0 0 0 0 1 0 0 0 8214 1174 41 3 3 KLF5 13 73075764 Missense_Mutation SNP G C3N-02423_T 20934724 73075764 41288564 288 29418 GPC6 0 . GRCh38 13 94306115 94306115 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1144G>T p.Asp382Tyr p.D382Y ENST00000377047 6/9 255 225 30 299 298 1 strelka-varscan-mutect GPC6,missense_variant,p.Asp382Tyr,ENST00000377047,NM_005708.3;GPC6,missense_variant,p.Asp90Tyr,ENST00000617456,; T ENST00000377047 Transcript missense_variant 1759/6467 1144/1668 382/555 D/Y Gac/Tac 1 1 GPC6 HGNC HGNC:4454 protein_coding YES CCDS9469.1 ENSP00000366246 Q9Y625 UPI0000032F5B NM_005708.3 deleterious(0) 6/9 Pfam_domain:PF01153,hmmpanther:PTHR10822,hmmpanther:PTHR10822:SF31 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 94306115 94306115 G T 1 0 0 0 0 1 0 0 0 6504 1174 41 2 2 GPC6 13 94306115 Missense_Mutation SNP G C3N-02423_T 21230351 94306115 20058213 289 29419 RNF113B 0 . GRCh38 13 98176893 98176893 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.344A>T p.Glu115Val p.E115V ENST00000267291 1/2 369 335 34 335 335 0 strelka-varscan-mutect RNF113B,missense_variant,p.Glu115Val,ENST00000267291,NM_178861.4;FARP1,intron_variant,,ENST00000596580,;FARP1,intron_variant,,ENST00000319562,NM_005766.3;FARP1,intron_variant,,ENST00000627049,;FARP1,intron_variant,,ENST00000595437,NM_001286839.1;FARP1,intron_variant,,ENST00000376581,NM_001001715.3;FARP1,upstream_gene_variant,,ENST00000598389,;FARP1,intron_variant,,ENST00000600648,; A ENST00000267291 Transcript missense_variant 373/1376 344/969 115/322 E/V gAg/gTg 1 -1 RNF113B HGNC HGNC:17267 protein_coding YES CCDS9486.1 ENSP00000267291 Q8IZP6 UPI000006F203 NM_178861.4 deleterious(0) 1/2 hmmpanther:PTHR12930,hmmpanther:PTHR12930:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 98176893 98176893 T A 1 0 0 0 0 1 0 0 0 13606 1551 54 4 4 RNF113B 13 98176893 Missense_Mutation SNP T C3N-02423_T 3870778 98176893 16187435 290 29420 TMTC4 0 . GRCh38 13 100606375 100606375 + Missense_Mutation SNP C C A rs757442715 C3N-02423_T C3N-02423_N C C c.2117G>T p.Ser706Ile p.S706I ENST00000342624 18/19 237 199 38 242 241 1 strelka-varscan-mutect TMTC4,missense_variant,p.Ser706Ile,ENST00000342624,NM_032813.3;TMTC4,missense_variant,p.Ser687Ile,ENST00000376234,NM_001079669.2;TMTC4,missense_variant,p.Ser576Ile,ENST00000328767,NM_001286453.1; A ENST00000342624 Transcript missense_variant 2376/3602 2117/2283 706/760 S/I aGt/aTt rs757442715 1 -1 TMTC4 HGNC HGNC:25904 protein_coding YES CCDS9497.2 ENSP00000343871 Q5T4D3 UPI000004B63E NM_032813.3 tolerated(0.17) 18/19 Gene3D:1.25.40.10,Pfam_domain:PF13432,PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF440,SMART_domains:SM00028,Superfamily_domains:SSF48452 MODERATE 1 SNV 2 1 PASS rs757442715 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 100606375 100606375 C A 1 0 0 0 0 1 0 0 0 16737 565 20 2 2 TMTC4 13 100606375 Missense_Mutation SNP C C3N-02423_T 2429482 100606375 13757953 291 29421 OR4N2 0 . GRCh38 14 19827632 19827632 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.184T>A p.Phe62Ile p.F62I ENST00000315947 1/1 157 140 17 223 223 0 varscan-mutect OR4N2,missense_variant,p.Phe62Ile,ENST00000315947,NM_001004723.2;OR4N2,missense_variant,p.Phe62Ile,ENST00000557677,;OR4N2,downstream_gene_variant,,ENST00000557414,; A ENST00000315947 Transcript missense_variant 184/924 184/924 62/307 F/I Ttt/Att 1 1 OR4N2 HGNC HGNC:14742 protein_coding YES CCDS32022.1 ENSP00000319601 Q8NGD1 A0A126GVT2 UPI000004A5DF NM_001004723.2 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF439,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 19827632 19827632 T A 1 0 0 0 0 1 0 0 0 11153 1609 56 4 4 OR4N2 14 19827632 Missense_Mutation SNP T C3N-02423_T 19827632 87216086 292 29422 OR11H6 0 . GRCh38 14 20224082 20224082 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.373C>A p.Leu125Met p.L125M ENST00000315519 1/1 215 180 35 220 220 0 strelka-varscan-mutect OR11H6,missense_variant,p.Leu125Met,ENST00000315519,NM_001004480.1; A ENST00000315519 Transcript missense_variant 451/1174 373/993 125/330 L/M Ctg/Atg 1 1 OR11H6 HGNC HGNC:15349 protein_coding YES CCDS32033.1 ENSP00000319071 Q8NGC7 A0A126GVP4 UPI000004B1F1 NM_001004480.1 tolerated(0.36) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF90,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999946 1 1 1 0 A 3 1 99 20224082 20224082 C A 1 0 0 0 0 1 0 0 0 11006 564 20 2 2 OR11H6 14 20224082 Missense_Mutation SNP C C3N-02423_T 396450 20224082 86819636 293 29423 DCAF11 0 . GRCh38 14 24123183 24123183 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1515G>A p.= p.G505G ENST00000446197 15/15 87 82 5 95 95 0 strelka-varscan DCAF11,synonymous_variant,p.=,ENST00000446197,NM_025230.4;DCAF11,synonymous_variant,p.=,ENST00000559115,NM_001163484.1;DCAF11,synonymous_variant,p.=,ENST00000396936,;DCAF11,synonymous_variant,p.=,ENST00000396941,NM_181357.2;DCAF11,3_prime_UTR_variant,,ENST00000559144,;RP11-468E2.6,intron_variant,,ENST00000558325,;DCAF11,downstream_gene_variant,,ENST00000561375,;DCAF11,downstream_gene_variant,,ENST00000560171,;DCAF11,3_prime_UTR_variant,,ENST00000557802,;DCAF11,3_prime_UTR_variant,,ENST00000326009,;DCAF11,3_prime_UTR_variant,,ENST00000558914,;DCAF11,non_coding_transcript_exon_variant,,ENST00000558624,;DCAF11,downstream_gene_variant,,ENST00000559472,;DCAF11,downstream_gene_variant,,ENST00000560046,; A ENST00000446197 Transcript synonymous_variant 2242/4299 1515/1641 505/546 G ggG/ggA 1 1 DCAF11 HGNC HGNC:20258 protein_coding YES CCDS9610.1 ENSP00000415556 Q8TEB1 UPI0000073AB2 NM_025230.4 15/15 PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19847,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF038135,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -10.91982 1 1 1 1 0 A 2 1 99 24123183 24123183 G A 1 0 0 0 0 0 0 0 1 4063 1161 41 3 3 DCAF11 14 24123183 Silent SNP G C3N-02423_T 3899101 24123183 82920535 294 29424 NPAS3 0 . GRCh38 14 33800636 33800636 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.2329G>T p.Gly777Cys p.G777C ENST00000356141 12/12 102 92 10 113 113 0 strelka-varscan-mutect NPAS3,missense_variant,p.Gly745Cys,ENST00000346562,NM_022123.2;NPAS3,missense_variant,p.Gly747Cys,ENST00000548645,NM_001165893.1;NPAS3,missense_variant,p.Gly782Cys,ENST00000551492,;NPAS3,missense_variant,p.Gly777Cys,ENST00000356141,NM_001164749.1;NPAS3,missense_variant,p.Gly764Cys,ENST00000357798,NM_173159.2;NPAS3,missense_variant,p.Gly751Cys,ENST00000551634,; T ENST00000356141 Transcript missense_variant 2329/2802 2329/2802 777/933 G/C Ggc/Tgc 1 1 NPAS3 HGNC HGNC:19311 protein_coding YES CCDS53891.1 ENSP00000348460 Q8IXF0 X5D2Q4 UPI00000743C2 NM_001164749.1 deleterious_low_confidence(0) 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR23043:SF30,hmmpanther:PTHR23043 MODERATE 1 SNV 1 1 PASS rs1168372419 . 0 201 9 0 0 0 0 0 -19.7482 0.9999848 1 1 1 0 T 3 4 99 33800636 33800636 G T 1 0 0 0 0 1 0 0 0 10612 1116 39 1 1 NPAS3 14 33800636 Missense_Mutation SNP G C3N-02423_T 9677453 33800636 73243082 295 29425 GCH1 0 . GRCh38 14 54843870 54843870 + Splice_Site SNP C C T novel C3N-02423_T C3N-02423_N C C c.627-1G>A p.X209_splice ENST00000543643 253 238 15 258 258 0 strelka-varscan-mutect GCH1,splice_acceptor_variant,,ENST00000543643,NM_001024070.1;GCH1,3_prime_UTR_variant,,ENST00000491895,;GCH1,3_prime_UTR_variant,,ENST00000622544,NM_000161.2;GCH1,intron_variant,,ENST00000395514,NM_001024024.1;GCH1,intron_variant,,ENST00000536224,NM_001024071.1;GCH1,non_coding_transcript_exon_variant,,ENST00000254299,;GCH1,intron_variant,,ENST00000395521,; T ENST00000543643 Transcript splice_acceptor_variant -/1897 627/702 209/233 1 -1 GCH1 HGNC HGNC:4193 protein_coding CCDS41954.1 ENSP00000444011 P30793 UPI000002AA51 NM_001024070.1 5/6 HIGH SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 99 54843870 54843870 C T 1 0 0 0 0 0 0 1 0 6161 695 24 3 3 GCH1 14 54843870 Splice_Site SNP C C3N-02423_T 21043234 54843870 52199848 296 29426 MAX 0 . GRCh38 14 65084269 65084269 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.202C>T p.Pro68Ser p.P68S ENST00000246163 4/4 473 444 29 451 450 1 strelka-varscan-mutect MAX,missense_variant,p.Pro68Ser,ENST00000246163,NM_145114.2;MAX,intron_variant,,ENST00000284165,;MAX,intron_variant,,ENST00000618858,NM_001320415.1,NM_145113.2;MAX,intron_variant,,ENST00000358402,NM_145112.2;MAX,intron_variant,,ENST00000555932,;MAX,intron_variant,,ENST00000358664,NM_002382.4;MAX,intron_variant,,ENST00000555419,;MAX,intron_variant,,ENST00000557277,;MAX,intron_variant,,ENST00000556979,;MAX,intron_variant,,ENST00000556443,;MAX,intron_variant,,ENST00000555667,;MAX,intron_variant,,ENST00000557746,;MAX,intron_variant,,ENST00000556892,;MAX,intron_variant,,ENST00000341653,NM_197957.3;RP11-840I19.3,intron_variant,,ENST00000556127,;MAX,intron_variant,,ENST00000394606,;MAX,intron_variant,,ENST00000553951,;MAX,intron_variant,,ENST00000553928,; A ENST00000246163 Transcript missense_variant 372/897 202/291 68/96 P/S Cct/Tct 1 -1 MAX HGNC HGNC:6913 protein_coding CCDS9774.1 ENSP00000246163 P61244 UPI000006D02E NM_145114.2 tolerated_low_confidence(0.23) 4/4 PROSITE_profiles:PS50888 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 65084269 65084269 G A 1 0 0 0 0 1 0 0 0 9266 1174 41 3 3 MAX 14 65084269 Missense_Mutation SNP G C3N-02423_T 10240399 65084269 41959449 297 29427 EXD2 0 . GRCh38 14 69228954 69228954 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.472G>C p.Asp158His p.D158H ENST00000312994 3/9 387 362 25 413 413 0 strelka-varscan-mutect EXD2,missense_variant,p.Asp158His,ENST00000312994,NM_001193362.1,NM_001193363.1;EXD2,missense_variant,p.Asp33His,ENST00000409014,;EXD2,missense_variant,p.Asp158His,ENST00000409018,NM_001193361.1,NM_001193360.1;EXD2,missense_variant,p.Asp33His,ENST00000409675,NM_018199.3;EXD2,missense_variant,p.Asp33His,ENST00000409949,;EXD2,missense_variant,p.Asp33His,ENST00000409242,;EXD2,missense_variant,p.Asp33His,ENST00000413191,;EXD2,non_coding_transcript_exon_variant,,ENST00000492815,;EXD2,non_coding_transcript_exon_variant,,ENST00000489133,;EXD2,non_coding_transcript_exon_variant,,ENST00000494629,; C ENST00000312994 Transcript missense_variant 793/5107 472/1866 158/621 D/H Gat/Cat 1 1 EXD2 HGNC HGNC:20217 protein_coding YES CCDS53902.1 ENSP00000313140 Q9NVH0 UPI0000577ED7 NM_001193362.1,NM_001193363.1 deleterious(0) 3/9 Gene3D:3.30.420.10,Pfam_domain:PF01612,hmmpanther:PTHR13620,hmmpanther:PTHR13620:SF0,SMART_domains:SM00474,Superfamily_domains:SSF53098 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 69228954 69228954 G C 1 0 0 0 0 1 0 0 0 5165 942 33 4 4 EXD2 14 69228954 Missense_Mutation SNP G C3N-02423_T 4144685 69228954 37814764 298 29428 MAP3K9 0 . GRCh38 14 70738273 70738273 + Nonsense_Mutation SNP G G A rs374508438 C3N-02423_T C3N-02423_N G G c.1816C>T p.Gln606Ter p.Q606* ENST00000555993 8/13 123 113 10 132 132 0 strelka-mutect MAP3K9,stop_gained,p.Gln606Ter,ENST00000554752,NM_001284230.1;MAP3K9,stop_gained,p.Gln391Ter,ENST00000611979,NM_001284231.1;MAP3K9,stop_gained,p.Gln606Ter,ENST00000555993,NM_033141.3;MAP3K9,stop_gained,p.Gln606Ter,ENST00000381250,;MAP3K9,stop_gained,p.Gln348Ter,ENST00000553414,NM_001284232.1;MAP3K9,stop_gained,p.Gln343Ter,ENST00000554146,; A ENST00000555993 Transcript stop_gained 2179/4449 1816/3357 606/1118 Q/* Cag/Tag rs374508438 1 -1 MAP3K9 HGNC HGNC:6861 protein_coding YES CCDS32112.1 ENSP00000451263 P80192 UPI00001D7B5C NM_033141.3 8/13 hmmpanther:PTHR23257:SF401,hmmpanther:PTHR23257,PIRSF_domain:PIRSF000556 HIGH 1 SNV 1 1 PASS rs374508438 . 0 207 0 2 0 0 0 0 -14.67968 0.9999997 1 1 1 0 A 4 1 99 70738273 70738273 G A 1 0 0 0 0 0 1 0 0 9181 1299 45 3 3 MAP3K9 14 70738273 Nonsense_Mutation SNP G C3N-02423_T 1509319 70738273 36305445 299 29429 PCNX1 0 . GRCh38 14 71103470 71103470 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.5896G>C p.Glu1966Gln p.E1966Q ENST00000304743 32/36 397 368 29 405 405 0 strelka-mutect PCNX1,missense_variant,p.Glu1966Gln,ENST00000304743,NM_014982.2;PCNX1,missense_variant,p.Glu1855Gln,ENST00000439984,NM_001308160.1;PCNX1,missense_variant,p.Glu953Gln,ENST00000554691,;PCNX1,non_coding_transcript_exon_variant,,ENST00000556272,;PCNX1,downstream_gene_variant,,ENST00000557428,; C ENST00000304743 Transcript missense_variant 6342/12919 5896/7026 1966/2341 E/Q Gag/Cag 1 1 PCNX1 HGNC HGNC:19740 protein_coding YES CCDS9806.1 ENSP00000304192 Q96RV3 UPI000013E9BB NM_014982.2 deleterious(0) 32/36 hmmpanther:PTHR12372:SF2,hmmpanther:PTHR12372,Pfam_domain:PF05041 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 71103470 71103470 G C 1 0 0 0 0 1 0 0 0 11679 943 33 4 4 PCNX1 14 71103470 Missense_Mutation SNP G C3N-02423_T 365197 71103470 35940248 300 29430 HEATR4 0 . GRCh38 14 73522533 73522533 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.620T>C p.Leu207Pro p.L207P ENST00000553558 3/18 272 246 26 251 251 0 strelka-varscan-mutect HEATR4,missense_variant,p.Leu207Pro,ENST00000553558,NM_001220484.1;HEATR4,missense_variant,p.Leu207Pro,ENST00000334988,NM_203309.2;HEATR4,downstream_gene_variant,,ENST00000556455,;HEATR4,downstream_gene_variant,,ENST00000563329,;HEATR4,downstream_gene_variant,,ENST00000557603,;RP3-414A15.11,upstream_gene_variant,,ENST00000553394,;RP3-414A15.2,upstream_gene_variant,,ENST00000555972,; G ENST00000553558 Transcript missense_variant 942/3523 620/3081 207/1026 L/P cTg/cCg 1 -1 HEATR4 HGNC HGNC:16761 protein_coding YES CCDS9815.2 ENSP00000450444 Q86WZ0 UPI00001FD7FD NM_001220484.1 deleterious(0) 3/18 hmmpanther:PTHR12697,hmmpanther:PTHR12697:SF20 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 73522533 73522533 A G 1 0 0 0 0 1 0 0 0 6912 188 7 5 5 HEATR4 14 73522533 Missense_Mutation SNP A C3N-02423_T 2419063 73522533 33521185 301 29431 ISM2 0 . GRCh38 14 77478267 77478267 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1173C>T p.= p.R391R ENST00000342219 6/7 184 170 14 163 163 0 strelka-varscan-mutect ISM2,missense_variant,p.Ala276Val,ENST00000493585,NM_182509.3;ISM2,synonymous_variant,p.=,ENST00000342219,NM_199296.2;ISM2,downstream_gene_variant,,ENST00000554801,;ISM2,3_prime_UTR_variant,,ENST00000216481,;ISM2,non_coding_transcript_exon_variant,,ENST00000487738,;ISM2,downstream_gene_variant,,ENST00000471734,; A ENST00000342219 Transcript synonymous_variant 1230/2971 1173/1716 391/571 R cgC/cgT 1 -1 ISM2 HGNC HGNC:23176 protein_coding YES CCDS9864.1 ENSP00000341490 Q6H9L7 UPI000019950C NM_199296.2 6/7 hmmpanther:PTHR10239:SF28,hmmpanther:PTHR10239 LOW 1 SNV 1 1 PASS rs1192446145 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 77478267 77478267 G A 1 0 0 0 0 0 0 0 1 7768 1319 46 3 3 ISM2 14 77478267 Silent SNP G C3N-02423_T 3955734 77478267 29565451 302 29432 NRXN3 0 . GRCh38 14 78988128 78988128 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.2130C>A p.Asn710Lys p.N710K ENST00000554719 12/17 420 341 79 391 391 0 strelka-varscan-mutect NRXN3,missense_variant,p.Asn1072Lys,ENST00000634499,;NRXN3,missense_variant,p.Asn1083Lys,ENST00000635466,;NRXN3,missense_variant,p.Asn710Lys,ENST00000554719,NM_004796.5;NRXN3,missense_variant,p.Asn844Lys,ENST00000335750,;NRXN3,non_coding_transcript_exon_variant,,ENST00000634266,;NRXN3,missense_variant,p.Asn1072Lys,ENST00000554738,;NRXN3,non_coding_transcript_exon_variant,,ENST00000556496,; A ENST00000554719 Transcript missense_variant 2621/4156 2130/3186 710/1061 N/K aaC/aaA 1 1 NRXN3 HGNC HGNC:8010 protein_coding YES CCDS9870.1 ENSP00000451648 Q9Y4C0 UPI0000167BBA NM_004796.5 deleterious(0.02) 12/17 Gene3D:2.10.25.10,PROSITE_profiles:PS50026,SMART_domains:SM00181,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 78988128 78988128 C A 1 0 0 0 0 1 0 0 0 10726 506 18 2 2 NRXN3 14 78988128 Missense_Mutation SNP C C3N-02423_T 1509861 78988128 28055590 303 29433 KCNK13 0 . GRCh38 14 90184151 90184151 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.375C>G p.Ile125Met p.I125M ENST00000282146 2/2 113 107 6 112 112 0 strelka-varscan-mutect KCNK13,missense_variant,p.Ile125Met,ENST00000282146,NM_022054.3; G ENST00000282146 Transcript missense_variant 816/2522 375/1227 125/408 I/M atC/atG 1 1 KCNK13 HGNC HGNC:6275 protein_coding YES CCDS9889.1 ENSP00000282146 Q9HB14 UPI0000127A55 NM_022054.3 deleterious(0.01) 2/2 Transmembrane_helices:TMhelix,hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF57,Pfam_domain:PF07885,Gene3D:1.10.287.70,Superfamily_domains:SSF81324,Prints_domain:PR01333 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -12.14647 1 1 1 1 0 G 3 3 99 90184151 90184151 C G 1 0 0 0 0 1 0 0 0 7978 903 32 4 4 KCNK13 14 90184151 Missense_Mutation SNP C C3N-02423_T 11196023 90184151 16859567 304 29434 RPS6KA5 0 . GRCh38 14 90875324 90875324 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1873C>G p.His625Asp p.H625D ENST00000614987 15/17 217 198 19 173 173 0 strelka-varscan-mutect RPS6KA5,missense_variant,p.His625Asp,ENST00000614987,NM_004755.2;RPS6KA5,missense_variant,p.His546Asp,ENST00000536315,;RPS6KA5,3_prime_UTR_variant,,ENST00000556178,; C ENST00000614987 Transcript missense_variant 2047/26795 1873/2409 625/802 H/D Cat/Gat 1 -1 RPS6KA5 HGNC HGNC:10434 protein_coding YES CCDS9893.1 ENSP00000479667 O75582 UPI0000031C30 NM_004755.2 tolerated(0.62) 15/17 Gene3D:1.10.510.10,Pfam_domain:PF00069,PIRSF_domain:PIRSF000606,PROSITE_profiles:PS50011,SMART_domains:SM00220,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 90875324 90875324 G C 1 0 0 0 0 1 0 0 0 13909 1290 45 4 4 RPS6KA5 14 90875324 Missense_Mutation SNP G C3N-02423_T 691173 90875324 16168394 305 29435 UNC79 0 . GRCh38 14 93686591 93686591 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.6425A>T p.Glu2142Val p.E2142V ENST00000256339 44/50 184 153 31 179 179 0 strelka-mutect UNC79,missense_variant,p.Glu2341Val,ENST00000553484,;UNC79,missense_variant,p.Glu2280Val,ENST00000555664,;UNC79,missense_variant,p.Glu2142Val,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Glu2319Val,ENST00000393151,;UNC79,missense_variant,p.Glu2142Val,ENST00000621021,;UNC79,upstream_gene_variant,,ENST00000554549,; T ENST00000256339 Transcript missense_variant 7080/8400 6425/7377 2142/2458 E/V gAg/gTg 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 deleterious(0) 44/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 93686591 93686591 A T 1 0 0 0 0 1 0 0 0 17520 304 11 4 4 UNC79 14 93686591 Missense_Mutation SNP A C3N-02423_T 2811267 93686591 13357127 306 29436 CCNK 0 . GRCh38 14 99502247 99502247 + Missense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.616A>T p.Ile206Leu p.I206L ENST00000389879 7/11 271 233 38 193 193 0 strelka-varscan-mutect CCNK,missense_variant,p.Ile206Leu,ENST00000389879,NM_001099402.1;CCNK,missense_variant,p.Ile206Leu,ENST00000555049,;CCNK,missense_variant,p.Ile206Leu,ENST00000557441,;CCDC85C,3_prime_UTR_variant,,ENST00000380243,NM_001144995.1;CCNK,non_coding_transcript_exon_variant,,ENST00000557165,;CCNK,non_coding_transcript_exon_variant,,ENST00000553865,;CCNK,downstream_gene_variant,,ENST00000556641,; T ENST00000389879 Transcript missense_variant 739/3524 616/1743 206/580 I/L Ata/Tta 1 1 CCNK HGNC HGNC:1596 protein_coding YES CCDS45160.1 ENSP00000374529 O75909 A0A024R6K1 UPI00001FDB50 NM_001099402.1 deleterious(0) 7/11 hmmpanther:PTHR10026:SF71,hmmpanther:PTHR10026,Pfam_domain:PF02984,SMART_domains:SM01332,SMART_domains:SM00385,Superfamily_domains:SSF47954 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 99502247 99502247 A T 1 0 0 0 0 1 0 0 0 2629 217 8 4 4 CCNK 14 99502247 Missense_Mutation SNP A C3N-02423_T 5815656 99502247 7541471 307 29437 ZNF839 0 . GRCh38 14 102331661 102331661 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1231G>A p.Glu411Lys p.E411K ENST00000442396 3/8 259 236 23 263 263 0 strelka-varscan-mutect ZNF839,missense_variant,p.Glu411Lys,ENST00000442396,NM_018335.4;ZNF839,missense_variant,p.Glu295Lys,ENST00000558850,NM_001267827.1;ZNF839,missense_variant,p.Glu295Lys,ENST00000559185,NM_001267828.1;ZNF839,missense_variant,p.Glu9Lys,ENST00000559155,;ZNF839,5_prime_UTR_variant,,ENST00000560568,;ZNF839,intron_variant,,ENST00000561251,;ZNF839,upstream_gene_variant,,ENST00000558490,;ZNF839,upstream_gene_variant,,ENST00000560112,;ZNF839,upstream_gene_variant,,ENST00000558462,;ZNF839,missense_variant,p.Glu347Lys,ENST00000559098,;ZNF839,upstream_gene_variant,,ENST00000557803,; A ENST00000442396 Transcript missense_variant 1246/2987 1231/2784 411/927 E/K Gaa/Aaa 1 1 ZNF839 HGNC HGNC:20345 protein_coding YES CCDS45164.1 ENSP00000399863 A8K0R7 UPI0001596890 NM_018335.4 deleterious(0.02) 3/8 hmmpanther:PTHR16116,Pfam_domain:PF15961 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 102331661 102331661 G A 1 0 0 0 0 1 0 0 0 18774 1291 45 3 3 ZNF839 14 102331661 Missense_Mutation SNP G C3N-02423_T 2829414 102331661 4712057 308 29438 TDRD9 0 . GRCh38 14 104004248 104004248 + Silent SNP A A G C3N-02423_T C3N-02423_N A A c.1494A>G p.= p.G498G ENST00000409874 14/36 117 104 13 114 114 0 strelka-mutect TDRD9,synonymous_variant,p.=,ENST00000409874,NM_153046.2;TDRD9,synonymous_variant,p.=,ENST00000339063,;TDRD9,synonymous_variant,p.=,ENST00000557332,;TDRD9,upstream_gene_variant,,ENST00000466378,; G ENST00000409874 Transcript synonymous_variant 1542/4782 1494/4149 498/1382 G ggA/ggG COSM4917409,COSM4917410 1 1 TDRD9 HGNC HGNC:20122 protein_coding YES CCDS9987.2 ENSP00000387303 Q8NDG6 UPI0001642306 NM_153046.2 14/36 PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF113,Pfam_domain:PF00271,Gene3D:3.40.50.300,SMART_domains:SM00490,Superfamily_domains:SSF52540 1,1 LOW 1 SNV 5 1,1 1 PASS rs1028920764 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 104004248 104004248 A G 1 0 0 0 0 0 0 0 1 16146 262 10 5 5 TDRD9 14 104004248 Silent SNP A C3N-02423_T 1672587 104004248 3039470 309 29439 CYFIP1 0 . GRCh38 15 22882892 22882892 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.2796G>A p.= p.E932E ENST00000617928 24/31 75 71 4 96 96 0 varscan-mutect CYFIP1,synonymous_variant,p.=,ENST00000617928,NM_014608.3;CYFIP1,synonymous_variant,p.=,ENST00000617556,NM_001033028.1;CYFIP1,synonymous_variant,p.=,ENST00000610365,NM_001287810.1;CYFIP1,non_coding_transcript_exon_variant,,ENST00000619348,; T ENST00000617928 Transcript synonymous_variant 2851/6793 2796/3762 932/1253 E gaG/gaA 1 -1 CYFIP1 HGNC HGNC:13759 protein_coding YES CCDS73696.1 ENSP00000481038 Q7L576 UPI0000163A89 NM_014608.3 24/31 hmmpanther:PTHR12195,hmmpanther:PTHR12195:SF2,PIRSF_domain:PIRSF008153,Pfam_domain:PF05994 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -9.780294 1 1 1 1 0 T 2 4 99 22882892 22882892 C T 1 0 0 0 0 0 0 0 1 3940 796 28 3 3 CYFIP1 15 22882892 Silent SNP C C3N-02423_T 22882892 79108297 310 29440 NDN 0 . GRCh38 15 23687173 23687173 + Silent SNP G G T novel C3N-02423_T C3N-02423_N G G c.45C>A p.= p.A15A ENST00000331837 1/1 43 36 7 64 64 0 strelka-varscan-mutect NDN,synonymous_variant,p.=,ENST00000331837,NM_002487.2; T ENST00000331837 Transcript synonymous_variant 158/1931 45/966 15/321 A gcC/gcA 1 -1 NDN HGNC HGNC:7675 protein_coding YES CCDS10014.1 ENSP00000332643 Q99608 X5D982 UPI000012FEF1 NM_002487.2 1/1 hmmpanther:PTHR11736,hmmpanther:PTHR11736:SF10 LOW 1 SNV 1 PASS . . 0 203 6 0 0 0 0 0 -17.30854 0.9999999 1 1 1 0 T 2 4 99 23687173 23687173 G T 1 0 0 0 0 0 0 0 1 10268 1103 39 1 1 NDN 15 23687173 Silent SNP G C3N-02423_T 804281 23687173 78304016 311 29441 HERC2 0 . GRCh38 15 28143979 28143979 + Missense_Mutation SNP C C G C3N-02423_T C3N-02423_N C C c.11312G>C p.Arg3771Thr p.R3771T ENST00000261609 74/93 233 184 49 265 265 0 strelka-varscan-mutect HERC2,missense_variant,p.Arg3771Thr,ENST00000261609,NM_004667.5;HERC2,upstream_gene_variant,,ENST00000564519,; G ENST00000261609 Transcript missense_variant 11421/15337 11312/14505 3771/4834 R/T aGa/aCa COSM1678314 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 deleterious(0) 74/93 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 28143979 28143979 C G 1 0 0 0 0 1 0 0 0 6942 913 32 4 4 HERC2 15 28143979 Missense_Mutation SNP C C3N-02423_T 4456806 28143979 73847210 312 29442 GOLGA8M 0 . GRCh38 15 28708405 28708405 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.318G>A p.= p.Q106Q ENST00000563027 5/19 150 137 13 170 170 0 varscan-mutect GOLGA8M,synonymous_variant,p.=,ENST00000563027,NM_001282468.1;RN7SL719P,upstream_gene_variant,,ENST00000620196,;GOLGA8M,downstream_gene_variant,,ENST00000563213,; T ENST00000563027 Transcript synonymous_variant 318/1899 318/1899 106/632 Q caG/caA 1 -1 GOLGA8M HGNC HGNC:44404 protein_coding YES CCDS61572.1 ENSP00000456927 H3BSY2 UPI0001A5E7A0 NM_001282468.1 5/19 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 28708405 28708405 C T 1 0 0 0 0 0 0 0 1 6454 912 32 3 3 GOLGA8M 15 28708405 Silent SNP C C3N-02423_T 564426 28708405 73282784 313 29443 GOLGA6L7P 0 . GRCh38 15 28845776 28845776 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.297G>C p.Gln99His p.Q99H ENST00000567390 5/9 231 214 17 277 277 0 varscan-mutect GOLGA6L7P,missense_variant,p.Gln99His,ENST00000567390,;PDCD6IPP2,intron_variant,,ENST00000566178,;PDCD6IPP2,intron_variant,,ENST00000564604,;GOLGA6L7P,non_coding_transcript_exon_variant,,ENST00000569815,; G ENST00000567390 Transcript missense_variant 423/2397 297/1869 99/622 Q/H caG/caC 1 -1 GOLGA6L7P HGNC HGNC:37442 protein_coding YES ENSP00000490318 deleterious(0) 5/9 hmmpanther:PTHR23143,hmmpanther:PTHR23143:SF11 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 28845776 28845776 C G 1 0 0 0 0 1 0 0 0 6443 912 32 4 4 GOLGA6L7P 15 28845776 Missense_Mutation SNP C C3N-02423_T 137371 28845776 73145413 314 29444 APBA2 0 . GRCh38 15 29076086 29076086 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.1064T>A p.Val355Glu p.V355E ENST00000558402 7/16 387 343 44 369 369 0 strelka-varscan-mutect APBA2,missense_variant,p.Val355Glu,ENST00000558402,;APBA2,missense_variant,p.Val355Glu,ENST00000558259,NM_005503.3;APBA2,missense_variant,p.Val355Glu,ENST00000411764,NM_001130414.1;APBA2,missense_variant,p.Val355Glu,ENST00000558330,;APBA2,missense_variant,p.Val355Glu,ENST00000561069,;APBA2,non_coding_transcript_exon_variant,,ENST00000559814,;APBA2,non_coding_transcript_exon_variant,,ENST00000382938,; A ENST00000558402 Transcript missense_variant 1663/4031 1064/2250 355/749 V/E gTg/gAg 1 1 APBA2 HGNC HGNC:579 protein_coding YES CCDS10022.1 ENSP00000453293 Q99767 UPI0000046798 deleterious(0.04) 7/16 hmmpanther:PTHR12345,hmmpanther:PTHR12345:SF12 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 29076086 29076086 T A 1 0 0 0 0 1 0 0 0 877 1710 59 4 4 APBA2 15 29076086 Missense_Mutation SNP T C3N-02423_T 230310 29076086 72915103 315 29445 GOLGA8K 0 . GRCh38 15 32398624 32398624 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.527G>T p.Arg176Leu p.R176L ENST00000512626 8/19 88 82 6 139 139 0 varscan-mutect GOLGA8K,missense_variant,p.Arg176Leu,ENST00000512626,NM_001282493.1;RN7SL185P,upstream_gene_variant,,ENST00000615150,;RP13-395E19.3,downstream_gene_variant,,ENST00000562108,;GOLGA8K,downstream_gene_variant,,ENST00000435655,; A ENST00000512626 Transcript missense_variant 528/1894 527/1893 176/630 R/L cGt/cTt 1 -1 GOLGA8K HGNC HGNC:38652 protein_coding YES CCDS61577.1 ENSP00000426691 D6RF30 UPI0001A5E7CC NM_001282493.1 deleterious(0.03) 8/19 hmmpanther:PTHR10881,hmmpanther:PTHR10881:SF48 MODERATE SNV 5 1 PASS rs1369300791 . 4 196 10 0 0 0 0 0 -12.51514 0.9998982 1 1 1 0 A 3 1 99 32398624 32398624 C A 1 0 0 0 0 1 0 0 0 6453 536 19 1 1 GOLGA8K 15 32398624 Missense_Mutation SNP C C3N-02423_T 3322538 32398624 69592565 316 29446 TMCO5A 0 . GRCh38 15 37951047 37951047 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.680G>T p.Cys227Phe p.C227F ENST00000319669 11/11 123 102 21 167 167 0 strelka-varscan-mutect TMCO5A,missense_variant,p.Cys227Phe,ENST00000319669,NM_152453.3;TMCO5A,intron_variant,,ENST00000559502,;TMCO5A,3_prime_UTR_variant,,ENST00000560653,; T ENST00000319669 Transcript missense_variant 782/1274 680/867 227/288 C/F tGt/tTt 1 1 TMCO5A HGNC HGNC:28558 protein_coding YES CCDS10046.1 ENSP00000327234 Q8N6Q1 A0A024R9I9 UPI00001BBFD2 NM_152453.3 tolerated(0.5) 11/11 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR22422:SF7,hmmpanther:PTHR22422,Pfam_domain:PF14992 MODERATE 1 SNV 1 1 PASS rs759657395 . 0 179 3 23 5 0 0 0 -12.26817 0.08504132 0 1 0 0 T 3 4 99 37951047 37951047 G T 1 0 0 0 0 1 0 0 0 16445 1377 48 2 2 TMCO5A 15 37951047 Missense_Mutation SNP G C3N-02423_T 5552423 37951047 64040142 317 29447 UBR1 0 . GRCh38 15 43002676 43002676 + Nonsense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.3538C>T p.Gln1180Ter p.Q1180* ENST00000290650 32/47 349 320 29 450 449 1 strelka-varscan-mutect UBR1,stop_gained,p.Gln1180Ter,ENST00000290650,NM_174916.2;UBR1,downstream_gene_variant,,ENST00000568782,;UBR1,upstream_gene_variant,,ENST00000566493,; A ENST00000290650 Transcript stop_gained 3617/7761 3538/5250 1180/1749 Q/* Cag/Tag 1 -1 UBR1 HGNC HGNC:16808 protein_coding YES CCDS10091.1 ENSP00000290650 Q8IWV7 UPI0000074467 NM_174916.2 32/47 hmmpanther:PTHR21497,hmmpanther:PTHR21497:SF27,Gene3D:3.30.40.10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 43002676 43002676 G A 1 0 0 0 0 0 1 0 0 17425 1299 45 3 3 UBR1 15 43002676 Nonsense_Mutation SNP G C3N-02423_T 5051629 43002676 58988513 318 29448 CTXN2 0 . GRCh38 15 48201376 48201376 + Nonsense_Mutation SNP G G T rs866505882 C3N-02423_T C3N-02423_N G G c.76G>T p.Glu26Ter p.E26* ENST00000417307 2/2 313 264 49 394 394 0 strelka-varscan-mutect CTXN2,stop_gained,p.Glu26Ter,ENST00000417307,NM_001145668.1;SLC12A1,intron_variant,,ENST00000559641,;SLC12A1,intron_variant,,ENST00000561127,;SLC12A1,upstream_gene_variant,,ENST00000396577,NM_001184832.1;SLC12A1,upstream_gene_variant,,ENST00000380993,NM_000338.2;RP11-605F22.1,non_coding_transcript_exon_variant,,ENST00000559875,; T ENST00000417307 Transcript stop_gained 448/2828 76/246 26/81 E/* Gag/Tag rs866505882 1 1 CTXN2 HGNC HGNC:31109 protein_coding YES CCDS45254.1 ENSP00000406145 P0C2S0 UPI00005A8DAF NM_001145668.1 2/2 hmmpanther:PTHR16736,hmmpanther:PTHR16736:SF2,Pfam_domain:PF11057,PD054489 HIGH 1 SNV 1 1 PASS rs866505882 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 48201376 48201376 G T 1 0 0 0 0 0 1 0 0 3859 1175 41 2 2 CTXN2 15 48201376 Nonsense_Mutation SNP G C3N-02423_T 5198700 48201376 53789813 319 29449 SLC27A2 0 . GRCh38 15 50182571 50182571 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.144G>A p.= p.K48K ENST00000267842 1/10 282 256 26 280 280 0 strelka-varscan-mutect SLC27A2,synonymous_variant,p.=,ENST00000267842,NM_003645.3;SLC27A2,synonymous_variant,p.=,ENST00000380902,NM_001159629.1;ATP8B4,5_prime_UTR_variant,,ENST00000558829,; A ENST00000267842 Transcript synonymous_variant 376/2394 144/1863 48/620 K aaG/aaA 1 1 SLC27A2 HGNC HGNC:10996 protein_coding YES CCDS10133.1 ENSP00000267842 O14975 UPI000013D776 NM_003645.3 1/10 hmmpanther:PTHR24096:SF127,hmmpanther:PTHR24096 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 50182571 50182571 G A 1 0 0 0 0 0 0 0 1 14796 962 34 3 3 SLC27A2 15 50182571 Silent SNP G C3N-02423_T 1981195 50182571 51808618 320 29450 NEO1 0 . GRCh38 15 73273855 73273855 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.3010G>A p.Asp1004Asn p.D1004N ENST00000339362 21/30 165 153 12 167 166 1 strelka-varscan-mutect NEO1,missense_variant,p.Asp1004Asn,ENST00000339362,;NEO1,missense_variant,p.Asp1004Asn,ENST00000261908,NM_002499.3;NEO1,missense_variant,p.Asp684Asn,ENST00000560328,;NEO1,missense_variant,p.Asp1004Asn,ENST00000558964,NM_001172624.1;NEO1,missense_variant,p.Asp1004Asn,ENST00000560262,NM_001172623.1; A ENST00000339362 Transcript missense_variant 3457/7342 3010/4386 1004/1461 D/N Gac/Aac 1 1 NEO1 HGNC HGNC:7754 protein_coding YES CCDS10247.1 ENSP00000341198 Q92859 UPI000013D221 deleterious(0.04) 21/30 PROSITE_profiles:PS50853,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF55,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 73273855 73273855 G A 1 0 0 0 0 1 0 0 0 10370 1290 45 3 3 NEO1 15 73273855 Missense_Mutation SNP G C3N-02423_T 23091284 73273855 28717334 321 29451 LMAN1L 0 . GRCh38 15 74821865 74821865 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1096G>T p.Gly366Trp p.G366W ENST00000309664 10/14 85 78 7 92 91 1 strelka-varscan-mutect LMAN1L,missense_variant,p.Gly366Trp,ENST00000309664,NM_021819.2;LMAN1L,missense_variant,p.Gly354Trp,ENST00000379709,;LMAN1L,missense_variant,p.Gly47Trp,ENST00000567848,;CPLX3,upstream_gene_variant,,ENST00000395018,NM_001030005.2;RP11-414J4.2,non_coding_transcript_exon_variant,,ENST00000564823,;RP11-414J4.2,non_coding_transcript_exon_variant,,ENST00000488000,;LMAN1L,non_coding_transcript_exon_variant,,ENST00000565585,;LMAN1L,downstream_gene_variant,,ENST00000470711,;LMAN1L,downstream_gene_variant,,ENST00000456603,;LMAN1L,upstream_gene_variant,,ENST00000566046,; T ENST00000309664 Transcript missense_variant 1235/1873 1096/1581 366/526 G/W Ggg/Tgg 1 1 LMAN1L HGNC HGNC:6632 protein_coding YES CCDS10270.1 ENSP00000310431 Q9HAT1 UPI00001AEF1F NM_021819.2 deleterious(0) 10/14 hmmpanther:PTHR12223,hmmpanther:PTHR12223:SF31 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -15.32652 1 1 1 1 0 T 3 4 99 74821865 74821865 G T 1 0 0 0 0 1 0 0 0 8761 1000 35 2 2 LMAN1L 15 74821865 Missense_Mutation SNP G C3N-02423_T 1548010 74821865 27169324 322 29452 C15orf39 0 . GRCh38 15 75210832 75210832 + Nonsense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.2860C>T p.Gln954Ter p.Q954* ENST00000360639 3/3 205 182 23 191 191 0 strelka-mutect C15orf39,stop_gained,p.Gln954Ter,ENST00000360639,;C15orf39,stop_gained,p.Gln954Ter,ENST00000394987,NM_015492.4;C15orf39,3_prime_UTR_variant,,ENST00000567617,;C15orf39,downstream_gene_variant,,ENST00000565074,;C15orf39,downstream_gene_variant,,ENST00000563905,;C15orf39,downstream_gene_variant,,ENST00000562637,;C15orf39,downstream_gene_variant,,ENST00000564848,;RP11-69H7.3,downstream_gene_variant,,ENST00000563568,; T ENST00000360639 Transcript stop_gained 3180/4517 2860/3144 954/1047 Q/* Cag/Tag 1 1 C15orf39 HGNC HGNC:24497 protein_coding YES CCDS10276.1 ENSP00000353854 Q6ZRI6 UPI000004F079 3/3 hmmpanther:PTHR28422 HIGH 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 75210832 75210832 C T 1 0 0 0 0 0 1 0 0 1843 827 29 3 3 C15orf39 15 75210832 Nonsense_Mutation SNP C C3N-02423_T 388967 75210832 26780357 323 29453 FSD2 0 . GRCh38 15 82762117 82762117 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1982C>A p.Thr661Lys p.T661K ENST00000334574 12/13 111 97 14 148 148 0 strelka-varscan-mutect FSD2,missense_variant,p.Thr661Lys,ENST00000334574,NM_001007122.3;FSD2,missense_variant,p.Thr616Lys,ENST00000541889,NM_001281806.1,NM_001281805.1;SNHG21,downstream_gene_variant,,ENST00000561107,;SNHG21,downstream_gene_variant,,ENST00000558174,;SNHG21,downstream_gene_variant,,ENST00000559366,;SCARNA15,downstream_gene_variant,,ENST00000607520,; T ENST00000334574 Transcript missense_variant 2164/6418 1982/2250 661/749 T/K aCa/aAa 1 -1 FSD2 HGNC HGNC:18024 protein_coding YES CCDS45332.1 ENSP00000335651 A1L4K1 UPI0000161097 NM_001007122.3 tolerated(0.21) 12/13 PROSITE_profiles:PS50188,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF6,Pfam_domain:PF00622,SMART_domains:SM00449,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 82762117 82762117 G T 1 0 0 0 0 1 0 0 0 5945 1377 48 2 2 FSD2 15 82762117 Missense_Mutation SNP G C3N-02423_T 7551285 82762117 19229072 324 29454 ACAN 0 . GRCh38 15 88838685 88838685 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.93C>A p.= p.V31V ENST00000439576 3/18 25 19 6 43 43 0 strelka-varscan-mutect ACAN,synonymous_variant,p.=,ENST00000439576,NM_013227.3;ACAN,synonymous_variant,p.=,ENST00000617301,;ACAN,synonymous_variant,p.=,ENST00000559004,;ACAN,synonymous_variant,p.=,ENST00000561243,;ACAN,synonymous_variant,p.=,ENST00000352105,NM_001135.3;ACAN,synonymous_variant,p.=,ENST00000558207,; A ENST00000439576 Transcript synonymous_variant 467/8840 93/7593 31/2530 V gtC/gtA 1 1 ACAN HGNC HGNC:319 protein_coding YES CCDS53970.1 ENSP00000387356 E7EX88 UPI0001B23381 NM_013227.3 3/18 hmmpanther:PTHR22804:SF42,hmmpanther:PTHR22804 LOW 1 SNV 5 1 PASS rs1457808102 . 0 206 4 0 0 0 0 0 -16.90894 1 1 1 1 0 A 2 1 99 88838685 88838685 C A 1 0 0 0 0 0 0 0 1 160 813 29 2 2 ACAN 15 88838685 Silent SNP C C3N-02423_T 6076568 88838685 13152504 325 29455 TICRR 0 . GRCh38 15 89625525 89625525 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.5215G>C p.Glu1739Gln p.E1739Q ENST00000268138 20/22 286 269 17 337 337 0 strelka-varscan-mutect TICRR,missense_variant,p.Glu1739Gln,ENST00000268138,NM_152259.3;TICRR,missense_variant,p.Glu1738Gln,ENST00000560985,NM_001308025.1;KIF7,downstream_gene_variant,,ENST00000394412,NM_198525.2;KIF7,intron_variant,,ENST00000558928,;TICRR,missense_variant,p.Glu43Gln,ENST00000561095,; C ENST00000268138 Transcript missense_variant 5320/6775 5215/5733 1739/1910 E/Q Gag/Cag 1 1 TICRR HGNC HGNC:28704 protein_coding YES CCDS10352.2 ENSP00000268138 Q7Z2Z1 UPI0000D61399 NM_152259.3 deleterious(0) 20/22 hmmpanther:PTHR21556 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 89625525 89625525 G C 1 0 0 0 0 1 0 0 0 16328 1291 45 4 4 TICRR 15 89625525 Missense_Mutation SNP G C3N-02423_T 786840 89625525 12365664 326 29456 AC004754.3 0 . GRCh38 16 254659 254659 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.246G>T p.Trp82Cys p.W82C ENST00000399932 3/13 196 181 15 178 178 0 strelka-varscan-mutect FAM234A,missense_variant,p.Trp82Cys,ENST00000399932,NM_001284497.1,NM_032039.3;FAM234A,missense_variant,p.Trp82Cys,ENST00000301678,;AC004754.3,missense_variant,p.Trp82Cys,ENST00000600536,;FAM234A,missense_variant,p.Trp82Cys,ENST00000301679,;FAM234A,missense_variant,p.Trp82Cys,ENST00000420046,;FAM234A,missense_variant,p.Trp82Cys,ENST00000453430,;FAM234A,missense_variant,p.Trp82Cys,ENST00000449945,;FAM234A,missense_variant,p.Trp11Cys,ENST00000421000,;FAM234A,missense_variant,p.Trp82Cys,ENST00000419173,;FAM234A,missense_variant,p.Trp82Cys,ENST00000438220,;FAM234A,missense_variant,p.Trp82Cys,ENST00000420500,;FAM234A,missense_variant,p.Trp82Cys,ENST00000447499,;FAM234A,downstream_gene_variant,,ENST00000417499,;FAM234A,downstream_gene_variant,,ENST00000426695,;FAM234A,non_coding_transcript_exon_variant,,ENST00000496874,; T ENST00000399932 Transcript missense_variant 697/3213 246/1659 82/552 W/C tgG/tgT 1 1 FAM234A HGNC HGNC:14163 protein_coding YES CCDS10402.1 ENSP00000382814 Q9H0X4 UPI000006DF0D NM_001284497.1,NM_032039.3 deleterious(0) 3/13 hmmpanther:PTHR21419,hmmpanther:PTHR21419:SF7,Superfamily_domains:SSF50998 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 254659 254659 G T 1 0 0 0 0 1 0 0 0 115 1183 41 2 2 AC004754.3 16 254659 Missense_Mutation SNP G C3N-02423_T 254659 90083686 327 29457 AXIN1 0 . GRCh38 16 297138 297138 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1873G>T p.Asp625Tyr p.D625Y ENST00000262320 7/11 330 308 22 305 305 0 strelka-varscan-mutect AXIN1,missense_variant,p.Asp625Tyr,ENST00000262320,NM_003502.3;AXIN1,missense_variant,p.Asp625Tyr,ENST00000354866,NM_181050.2;AXIN1,upstream_gene_variant,,ENST00000457798,;AXIN1,downstream_gene_variant,,ENST00000481769,;AXIN1,non_coding_transcript_exon_variant,,ENST00000461023,; A ENST00000262320 Transcript missense_variant 2245/3643 1873/2589 625/862 D/Y Gat/Tat 1 -1 AXIN1 HGNC HGNC:903 protein_coding YES CCDS10405.1 ENSP00000262320 O15169 A0A0S2Z4R0 UPI000012669E NM_003502.3 deleterious(0) 7/11 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 297138 297138 C A 1 0 0 0 0 1 0 0 0 1393 855 30 2 2 AXIN1 16 297138 Missense_Mutation SNP C C3N-02423_T 42479 297138 90041207 328 29458 JMJD8 0 . GRCh38 16 684306 684306 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.77C>T p.Ser26Leu p.S26L ENST00000412368 1/9 175 164 11 111 110 1 strelka-varscan-mutect JMJD8,missense_variant,p.Ser26Leu,ENST00000412368,NM_001323918.1,NM_001005920.2;JMJD8,missense_variant,p.Ser5Leu,ENST00000609261,;JMJD8,missense_variant,p.Ser5Leu,ENST00000562824,;JMJD8,missense_variant,p.Ser5Leu,ENST00000562111,;WDR24,downstream_gene_variant,,ENST00000293883,NM_032259.3;WDR24,downstream_gene_variant,,ENST00000248142,;STUB1,downstream_gene_variant,,ENST00000565677,NM_001293197.1;STUB1,downstream_gene_variant,,ENST00000219548,NM_005861.3;STUB1,downstream_gene_variant,,ENST00000564370,;STUB1,downstream_gene_variant,,ENST00000567173,;STUB1,downstream_gene_variant,,ENST00000564316,;STUB1,downstream_gene_variant,,ENST00000566408,;LA16c-313D11.9,upstream_gene_variant,,ENST00000571933,;LA16c-313D11.9,upstream_gene_variant,,ENST00000567091,;STUB1,downstream_gene_variant,,ENST00000566181,;JMJD8,non_coding_transcript_exon_variant,,ENST00000567120,;JMJD8,non_coding_transcript_exon_variant,,ENST00000568689,;JMJD8,non_coding_transcript_exon_variant,,ENST00000565302,;JMJD8,non_coding_transcript_exon_variant,,ENST00000569441,;JMJD8,non_coding_transcript_exon_variant,,ENST00000569396,;JMJD8,non_coding_transcript_exon_variant,,ENST00000566199,;LA16c-313D11.12,upstream_gene_variant,,ENST00000575305,;STUB1,downstream_gene_variant,,ENST00000569248,;JMJD8,upstream_gene_variant,,ENST00000563088,;JMJD8,upstream_gene_variant,,ENST00000568313,;STUB1,downstream_gene_variant,,ENST00000563505,;JMJD8,upstream_gene_variant,,ENST00000570037,;JMJD8,upstream_gene_variant,,ENST00000567901,;WDR24,downstream_gene_variant,,ENST00000567014,;JMJD8,upstream_gene_variant,,ENST00000564436,;JMJD8,upstream_gene_variant,,ENST00000565258,;STUB1,downstream_gene_variant,,ENST00000567790,;STUB1,downstream_gene_variant,,ENST00000565813,; A ENST00000412368 Transcript missense_variant 134/2038 77/858 26/285 S/L tCg/tTg 1 -1 JMJD8 HGNC HGNC:14148 protein_coding YES CCDS45369.1 ENSP00000399475 Q96S16 UPI0000471011 NM_001323918.1,NM_001005920.2 tolerated_low_confidence(0.12) 1/9 Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM,hmmpanther:PTHR12480:SF18,hmmpanther:PTHR12480 MODERATE 1 SNV 1 1 PASS rs1244807531 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 684306 684306 G A 1 0 0 0 0 1 0 0 0 7868 1059 37 1 1 JMJD8 16 684306 Missense_Mutation SNP G C3N-02423_T 387168 684306 89654039 329 29459 WDR24 0 . GRCh38 16 686180 686180 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1339C>G p.Gln447Glu p.Q447E ENST00000293883 4/9 128 121 7 99 99 0 strelka-varscan-mutect WDR24,missense_variant,p.Gln447Glu,ENST00000293883,NM_032259.3;WDR24,missense_variant,p.Gln577Glu,ENST00000248142,;JMJD8,upstream_gene_variant,,ENST00000412368,NM_001323918.1,NM_001005920.2;JMJD8,upstream_gene_variant,,ENST00000609261,;STUB1,downstream_gene_variant,,ENST00000565677,NM_001293197.1;STUB1,downstream_gene_variant,,ENST00000219548,NM_005861.3;JMJD8,upstream_gene_variant,,ENST00000562824,;STUB1,downstream_gene_variant,,ENST00000564370,;JMJD8,upstream_gene_variant,,ENST00000562111,;STUB1,downstream_gene_variant,,ENST00000567173,;STUB1,downstream_gene_variant,,ENST00000564316,;STUB1,downstream_gene_variant,,ENST00000566408,;LA16c-313D11.12,upstream_gene_variant,,ENST00000566927,;STUB1,downstream_gene_variant,,ENST00000566181,;WDR24,non_coding_transcript_exon_variant,,ENST00000567014,;LA16c-313D11.12,upstream_gene_variant,,ENST00000575305,;JMJD8,upstream_gene_variant,,ENST00000567120,;JMJD8,upstream_gene_variant,,ENST00000568689,;JMJD8,upstream_gene_variant,,ENST00000565302,;STUB1,downstream_gene_variant,,ENST00000569248,;JMJD8,upstream_gene_variant,,ENST00000569441,;JMJD8,upstream_gene_variant,,ENST00000563088,;JMJD8,upstream_gene_variant,,ENST00000568313,;STUB1,downstream_gene_variant,,ENST00000563505,;JMJD8,upstream_gene_variant,,ENST00000570037,;JMJD8,upstream_gene_variant,,ENST00000567901,;JMJD8,upstream_gene_variant,,ENST00000569396,;JMJD8,upstream_gene_variant,,ENST00000566199,;JMJD8,upstream_gene_variant,,ENST00000564436,;JMJD8,upstream_gene_variant,,ENST00000565258,;STUB1,downstream_gene_variant,,ENST00000567790,;STUB1,downstream_gene_variant,,ENST00000565813,; C ENST00000293883 Transcript missense_variant 2099/3245 1339/2373 447/790 Q/E Caa/Gaa 1 -1 WDR24 HGNC HGNC:20852 protein_coding YES CCDS10420.1 ENSP00000293883 Q96S15 UPI0000037D32 NM_032259.3 tolerated(0.28) 4/9 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 686180 686180 G C 1 0 0 0 0 1 0 0 0 17841 1328 46 4 4 WDR24 16 686180 Missense_Mutation SNP G C3N-02423_T 1874 686180 89652165 330 29460 NARFL 0 . GRCh38 16 732358 732358 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.839T>C p.Leu280Ser p.L280S ENST00000251588 8/11 180 158 22 188 188 0 strelka-varscan-mutect NARFL,missense_variant,p.Leu178Ser,ENST00000540986,NM_001304799.1;NARFL,missense_variant,p.Leu178Ser,ENST00000568545,;NARFL,missense_variant,p.Leu280Ser,ENST00000251588,NM_022493.2;NARFL,missense_variant,p.Leu178Ser,ENST00000562421,;HAGHL,downstream_gene_variant,,ENST00000549114,;HAGHL,downstream_gene_variant,,ENST00000341413,;HAGHL,downstream_gene_variant,,ENST00000564537,;HAGHL,downstream_gene_variant,,ENST00000389703,NM_001290137.1,NM_001290139.1,NM_032304.3;HAGHL,downstream_gene_variant,,ENST00000561546,;HAGHL,downstream_gene_variant,,ENST00000568141,;HAGHL,downstream_gene_variant,,ENST00000567414,;HAGHL,downstream_gene_variant,,ENST00000564545,;HAGHL,downstream_gene_variant,,ENST00000562141,;NARFL,downstream_gene_variant,,ENST00000567403,;NARFL,downstream_gene_variant,,ENST00000566614,;HAGHL,downstream_gene_variant,,ENST00000563792,;HAGHL,downstream_gene_variant,,ENST00000562187,;NARFL,non_coding_transcript_exon_variant,,ENST00000562862,;HAGHL,intron_variant,,ENST00000563156,;HAGHL,upstream_gene_variant,,ENST00000569604,;NARFL,downstream_gene_variant,,ENST00000563534,;NARFL,downstream_gene_variant,,ENST00000567455,;NARFL,downstream_gene_variant,,ENST00000569759,;NARFL,3_prime_UTR_variant,,ENST00000565425,;NARFL,non_coding_transcript_exon_variant,,ENST00000563051,;NARFL,non_coding_transcript_exon_variant,,ENST00000566650,;NARFL,non_coding_transcript_exon_variant,,ENST00000564285,;HAGHL,downstream_gene_variant,,ENST00000567696,;NARFL,downstream_gene_variant,,ENST00000565341,;HAGHL,downstream_gene_variant,,ENST00000389701,;NARFL,downstream_gene_variant,,ENST00000562752,;HAGHL,downstream_gene_variant,,ENST00000561750,;NARFL,downstream_gene_variant,,ENST00000565065,;NARFL,downstream_gene_variant,,ENST00000570066,;HAGHL,downstream_gene_variant,,ENST00000569143,;NARFL,downstream_gene_variant,,ENST00000570289,;HAGHL,downstream_gene_variant,,ENST00000569385,;HAGHL,downstream_gene_variant,,ENST00000561561,; G ENST00000251588 Transcript missense_variant 856/2112 839/1431 280/476 L/S tTg/tCg 1 -1 NARFL HGNC HGNC:14179 protein_coding YES CCDS10425.1 ENSP00000251588 Q9H6Q4 UPI0000070186 NM_022493.2 deleterious(0) 8/11 Gene3D:1hfeL01,Pfam_domain:PF02906,hmmpanther:PTHR11615,hmmpanther:PTHR11615:SF103,Superfamily_domains:SSF53920 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 732358 732358 A G 1 0 0 0 0 1 0 0 0 10178 131 5 5 5 NARFL 16 732358 Missense_Mutation SNP A C3N-02423_T 46178 732358 89605987 331 29461 CRAMP1 0 . GRCh38 16 1659953 1659953 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.2303C>T p.Pro768Leu p.P768L ENST00000397412 11/21 292 265 27 263 263 0 strelka-varscan-mutect CRAMP1,missense_variant,p.Pro768Leu,ENST00000397412,;CRAMP1,missense_variant,p.Pro768Leu,ENST00000293925,NM_020825.3;CRAMP1,upstream_gene_variant,,ENST00000415022,;LA16c-431H6.6,3_prime_UTR_variant,,ENST00000454337,;CRAMP1,upstream_gene_variant,,ENST00000492778,;CRAMP1,upstream_gene_variant,,ENST00000498594,;CRAMP1,upstream_gene_variant,,ENST00000466562,; T ENST00000397412 Transcript missense_variant 2402/7772 2303/3810 768/1269 P/L cCc/cTc 1 1 CRAMP1 HGNC HGNC:14122 protein_coding YES CCDS10440.2 ENSP00000380559 Q96RY5 UPI000066D946 deleterious(0.01) 11/21 hmmpanther:PTHR21677:SF1,hmmpanther:PTHR21677 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 1659953 1659953 C T 1 0 0 0 0 1 0 0 0 3646 623 22 3 3 CRAMP1 16 1659953 Missense_Mutation SNP C C3N-02423_T 927595 1659953 88678392 332 29462 SRRM2 0 . GRCh38 16 2761908 2761908 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.1380G>T p.Lys460Asn p.K460N ENST00000301740 11/15 147 123 24 152 152 0 strelka-varscan-mutect SRRM2,missense_variant,p.Lys460Asn,ENST00000301740,NM_016333.3;SRRM2,missense_variant,p.Lys460Asn,ENST00000576924,;SRRM2,missense_variant,p.Lys364Asn,ENST00000571378,;SRRM2,intron_variant,,ENST00000630499,;SRRM2,downstream_gene_variant,,ENST00000575009,;SRRM2,downstream_gene_variant,,ENST00000570971,;SRRM2,downstream_gene_variant,,ENST00000574340,;SRRM2,downstream_gene_variant,,ENST00000576415,;SRRM2,downstream_gene_variant,,ENST00000572278,;SRRM2,downstream_gene_variant,,ENST00000575870,;SRRM2,upstream_gene_variant,,ENST00000576674,;SRRM2,non_coding_transcript_exon_variant,,ENST00000572952,;SRRM2,downstream_gene_variant,,ENST00000576894,;SRRM2,downstream_gene_variant,,ENST00000573498,;SRRM2,downstream_gene_variant,,ENST00000576076,;SRRM2,downstream_gene_variant,,ENST00000575701,;SRRM2,downstream_gene_variant,,ENST00000570655,;SRRM2,downstream_gene_variant,,ENST00000571372,;SRRM2,downstream_gene_variant,,ENST00000573451,; T ENST00000301740 Transcript missense_variant 1929/9353 1380/8259 460/2752 K/N aaG/aaT 1 1 SRRM2 HGNC HGNC:16639 protein_coding YES CCDS32373.1 ENSP00000301740 Q9UQ35 A0A140VK53 UPI000049DDFC NM_016333.3 deleterious_low_confidence(0) 11/15 hmmpanther:PTHR32093:SF13,hmmpanther:PTHR32093 MODERATE 1 SNV 1 1 PASS rs1212729544 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 2761908 2761908 G T 1 0 0 0 0 1 0 0 0 15530 933 33 2 2 SRRM2 16 2761908 Missense_Mutation SNP G C3N-02423_T 1101955 2761908 87576437 333 29463 SLX4 0 . GRCh38 16 3583176 3583176 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.5074G>C p.Asp1692His p.D1692H ENST00000294008 14/15 384 363 21 410 409 1 strelka-varscan-mutect SLX4,missense_variant,p.Asp1692His,ENST00000294008,NM_032444.2;RP11-461A8.1,non_coding_transcript_exon_variant,,ENST00000573982,; G ENST00000294008 Transcript missense_variant 5715/7307 5074/5505 1692/1834 D/H Gat/Cat 1 -1 SLX4 HGNC HGNC:23845 protein_coding YES CCDS10506.2 ENSP00000294008 Q8IY92 UPI000050D2C5 NM_032444.2 deleterious(0.03) 14/15 hmmpanther:PTHR21541,hmmpanther:PTHR21541:SF3 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 3583176 3583176 C G 1 0 0 0 0 1 0 0 0 15048 826 29 4 4 SLX4 16 3583176 Missense_Mutation SNP C C3N-02423_T 821268 3583176 86755169 334 29464 ERCC4 0 . GRCh38 16 13932236 13932236 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1053G>A p.Met351Ile p.M351I ENST00000311895 6/11 181 168 13 209 208 1 strelka-varscan-mutect ERCC4,missense_variant,p.Met351Ile,ENST00000311895,NM_005236.2;ERCC4,missense_variant,p.Met351Ile,ENST00000575156,;CTD-2135D7.2,non_coding_transcript_exon_variant,,ENST00000575137,;CTD-2135D7.2,intron_variant,,ENST00000570663,;ERCC4,downstream_gene_variant,,ENST00000574781,;ERCC4,3_prime_UTR_variant,,ENST00000574194,;ERCC4,non_coding_transcript_exon_variant,,ENST00000389138,;ERCC4,upstream_gene_variant,,ENST00000573018,; A ENST00000311895 Transcript missense_variant 1062/6758 1053/2751 351/916 M/I atG/atA 1 1 ERCC4 HGNC HGNC:3436 protein_coding YES CCDS32390.1 ENSP00000310520 Q92889 UPI0000161BBF NM_005236.2 tolerated_low_confidence(0.3) 6/11 hmmpanther:PTHR10150,Low_complexity_(Seg):seg,TIGRFAM_domain:TIGR00596 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.89156 0.9999707 1 1 1 0 A 3 1 99 13932236 13932236 G A 1 0 0 0 0 1 0 0 0 5064 1290 45 3 3 ERCC4 16 13932236 Missense_Mutation SNP G C3N-02423_T 10349060 13932236 76406109 335 29465 NOMO1 0 . GRCh38 16 14880136 14880136 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.2879C>A p.Ala960Asp p.A960D ENST00000287667 24/31 124 108 16 118 118 0 varscan-mutect NOMO1,missense_variant,p.Ala960Asp,ENST00000287667,NM_014287.3;NOMO1,missense_variant,p.Ala960Asp,ENST00000620755,;NOMO1,missense_variant,p.Ala793Asp,ENST00000610363,; A ENST00000287667 Transcript missense_variant 3050/4355 2879/3669 960/1222 A/D gCt/gAt 1 1 NOMO1 HGNC HGNC:30060 protein_coding YES CCDS10556.1 ENSP00000287667 Q15155 UPI000013D37E NM_014287.3 deleterious(0) 24/31 hmmpanther:PTHR23303 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 14880136 14880136 C A 1 0 0 0 0 1 0 0 0 10575 797 28 2 2 NOMO1 16 14880136 Missense_Mutation SNP C C3N-02423_T 947900 14880136 75458209 336 29466 100 2 NOMO1 0 . GRCh38 16 14880138 14880138 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.2881T>A p.Tyr961Asn p.Y961N ENST00000287667 24/31 122 107 15 120 120 0 varscan-mutect NOMO1,missense_variant,p.Tyr961Asn,ENST00000287667,NM_014287.3;NOMO1,missense_variant,p.Tyr961Asn,ENST00000620755,;NOMO1,missense_variant,p.Tyr794Asn,ENST00000610363,; A ENST00000287667 Transcript missense_variant 3052/4355 2881/3669 961/1222 Y/N Tac/Aac 1 1 NOMO1 HGNC HGNC:30060 protein_coding YES CCDS10556.1 ENSP00000287667 Q15155 UPI000013D37E NM_014287.3 deleterious(0) 24/31 hmmpanther:PTHR23303 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 14880138 14880138 T A 1 0 0 0 0 1 0 0 0 10575 1768 61 4 4 NOMO1 16 14880138 Missense_Mutation SNP T C3N-02423_T 2 14880138 75458207 337 29467 100 2 PDXDC1 0 . GRCh38 16 15004240 15004240 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.296G>A p.Gly99Glu p.G99E ENST00000396410 5/23 293 276 17 287 287 0 strelka-varscan-mutect PDXDC1,missense_variant,p.Gly99Glu,ENST00000396410,NM_001324019.1,NM_015027.3;PDXDC1,missense_variant,p.Gly72Glu,ENST00000569715,NM_001285444.1;PDXDC1,missense_variant,p.Gly117Glu,ENST00000563679,NM_001285447.1;PDXDC1,missense_variant,p.Gly71Glu,ENST00000627450,NM_001285445.1;PDXDC1,missense_variant,p.Gly99Glu,ENST00000455313,NM_001285450.1;PDXDC1,missense_variant,p.Gly99Glu,ENST00000535621,NM_001324020.1,NM_001285449.1;PDXDC1,missense_variant,p.Gly99Glu,ENST00000325823,;PDXDC1,missense_variant,p.Gly84Glu,ENST00000567306,;PDXDC1,missense_variant,p.Gly84Glu,ENST00000563522,;PDXDC1,missense_variant,p.Gly144Glu,ENST00000563667,;PDXDC1,intron_variant,,ENST00000450288,NM_001285448.1;PDXDC1,3_prime_UTR_variant,,ENST00000565362,;PDXDC1,non_coding_transcript_exon_variant,,ENST00000570001,;PDXDC1,intron_variant,,ENST00000562119,; A ENST00000396410 Transcript missense_variant 393/4521 296/2367 99/788 G/E gGa/gAa 1 1 PDXDC1 HGNC HGNC:28995 protein_coding YES CCDS32393.1 ENSP00000379691 Q6P996 UPI000004A864 NM_001324019.1,NM_015027.3 deleterious(0) 5/23 hmmpanther:PTHR11999:SF108,hmmpanther:PTHR11999,Superfamily_domains:SSF53383 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 15004240 15004240 G A 1 0 0 0 0 1 0 0 0 11784 1174 41 3 3 PDXDC1 16 15004240 Missense_Mutation SNP G C3N-02423_T 124102 15004240 75334105 338 29468 SMG1 0 . GRCh38 16 18869128 18869128 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2809C>G p.Gln937Glu p.Q937E ENST00000446231 20/63 250 233 17 254 254 0 varscan-mutect SMG1,missense_variant,p.Gln937Glu,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Gln827Glu,ENST00000565324,;SMG1,missense_variant,p.Gln368Glu,ENST00000563235,;SMG1,upstream_gene_variant,,ENST00000566328,;SMG1,missense_variant,p.Gln283Glu,ENST00000568038,; C ENST00000446231 Transcript missense_variant 3222/16115 2809/10986 937/3661 Q/E Caa/Gaa 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 deleterious(0.01) 20/63 Pfam_domain:PF15785,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF71 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 18869128 18869128 G C 1 0 0 0 0 1 0 0 0 15089 1299 45 4 4 SMG1 16 18869128 Missense_Mutation SNP G C3N-02423_T 3864888 18869128 71469217 339 29469 SMG1 0 . GRCh38 16 18870862 18870862 + Missense_Mutation SNP G G C rs138302613 C3N-02423_T C3N-02423_N G G c.2329C>G p.Leu777Val p.L777V ENST00000446231 17/63 149 141 8 140 140 0 varscan-mutect SMG1,missense_variant,p.Leu777Val,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Leu667Val,ENST00000565324,;SMG1,missense_variant,p.Leu208Val,ENST00000563235,;SMG1,downstream_gene_variant,,ENST00000561947,;SMG1,downstream_gene_variant,,ENST00000565224,;SMG1,upstream_gene_variant,,ENST00000566328,;SMG1,missense_variant,p.Leu123Val,ENST00000568038,; C ENST00000446231 Transcript missense_variant 2742/16115 2329/10986 777/3661 L/V Ctg/Gtg rs138302613 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 deleterious(0.04) 17/63 Pfam_domain:PF15785,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF71,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs138302613 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 18870862 18870862 G C 1 0 0 0 0 1 0 0 0 15089 933 33 4 4 SMG1 16 18870862 Missense_Mutation SNP G C3N-02423_T 1734 18870862 71467483 340 29470 KIAA0556 0 . GRCh38 16 27777745 27777745 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.4687C>T p.His1563Tyr p.H1563Y ENST00000261588 26/28 96 77 19 112 112 0 strelka-varscan-mutect KIAA0556,missense_variant,p.His1563Tyr,ENST00000261588,NM_015202.2;KIAA0556,non_coding_transcript_exon_variant,,ENST00000568622,; T ENST00000261588 Transcript missense_variant 4706/6616 4687/4857 1563/1618 H/Y Cac/Tac 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 tolerated(0.16) 26/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 27777745 27777745 C T 1 0 0 0 0 1 0 0 0 8088 594 21 3 3 KIAA0556 16 27777745 Missense_Mutation SNP C C3N-02423_T 8906883 27777745 62560600 341 29471 CD2BP2 0 . GRCh38 16 30353452 30353452 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.724C>G p.Pro242Ala p.P242A ENST00000305596 5/7 313 295 18 306 306 0 strelka-varscan-mutect CD2BP2,missense_variant,p.Pro242Ala,ENST00000305596,NM_006110.2;CD2BP2,missense_variant,p.Pro242Ala,ENST00000569466,NM_001243646.1;TBC1D10B,downstream_gene_variant,,ENST00000409939,NM_015527.3;TBC1D10B,downstream_gene_variant,,ENST00000490703,;RP11-347C12.10,upstream_gene_variant,,ENST00000563252,;TBC1D10B,downstream_gene_variant,,ENST00000478158,;TBC1D10B,downstream_gene_variant,,ENST00000475650,;CD2BP2,downstream_gene_variant,,ENST00000564525,; C ENST00000305596 Transcript missense_variant 900/3421 724/1026 242/341 P/A Ccc/Gcc 1 -1 CD2BP2 HGNC HGNC:1656 protein_coding YES CCDS10675.1 ENSP00000304903 O95400 A0A024QZC1 UPI000006D625 NM_006110.2 tolerated(0.67) 5/7 hmmpanther:PTHR13138,hmmpanther:PTHR13138:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 30353452 30353452 G C 1 0 0 0 0 1 0 0 0 2699 1174 41 4 4 CD2BP2 16 30353452 Missense_Mutation SNP G C3N-02423_T 2575707 30353452 59984893 342 29472 SETD1A 0 . GRCh38 16 30961350 30961350 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.330G>A p.= p.L110L ENST00000262519 4/19 399 377 22 370 370 0 strelka-varscan-mutect SETD1A,synonymous_variant,p.=,ENST00000262519,NM_014712.2;SETD1A,synonymous_variant,p.=,ENST00000452917,;ORAI3,downstream_gene_variant,,ENST00000562699,;RP11-1072A3.4,upstream_gene_variant,,ENST00000614997,;AC135048.13,downstream_gene_variant,,ENST00000562642,; A ENST00000262519 Transcript synonymous_variant 1016/6903 330/5124 110/1707 L ctG/ctA 1 1 SETD1A HGNC HGNC:29010 protein_coding YES CCDS32435.1 ENSP00000262519 O15047 UPI00001C1FA9 NM_014712.2 4/19 Gene3D:3.30.70.330,Pfam_domain:PF00076,PROSITE_profiles:PS50102,SMART_domains:SM00360,Superfamily_domains:SSF54928 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 30961350 30961350 G A 1 0 0 0 0 0 0 0 1 14407 1277 45 3 3 SETD1A 16 30961350 Silent SNP G C3N-02423_T 607898 30961350 59376995 343 29473 ITGAX 0 . GRCh38 16 31362961 31362961 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.1386C>G p.= p.L462L ENST00000562522 13/31 159 149 10 198 198 0 strelka-varscan-mutect ITGAX,synonymous_variant,p.=,ENST00000268296,NM_000887.4;ITGAX,synonymous_variant,p.=,ENST00000562522,NM_001286375.1;ITGAX,downstream_gene_variant,,ENST00000562918,;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,;RP11-120K18.3,upstream_gene_variant,,ENST00000561830,; G ENST00000562522 Transcript synonymous_variant 1419/3990 1386/3510 462/1169 L ctC/ctG 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 13/31 Gene3D:3nigC00,Pfam_domain:PF01839,Prints_domain:PR01185,PROSITE_profiles:PS51470,hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,SMART_domains:SM00191,Superfamily_domains:SSF69318 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 31362961 31362961 C G 1 0 0 0 0 0 0 0 1 7796 900 32 4 4 ITGAX 16 31362961 Silent SNP C C3N-02423_T 401611 31362961 58975384 344 29474 ITGAX 0 . GRCh38 16 31379994 31379994 + Missense_Mutation SNP C C G rs143932593 C3N-02423_T C3N-02423_N C C c.2989C>G p.Arg997Gly p.R997G ENST00000562522 26/31 274 243 31 238 238 0 strelka-varscan-mutect ITGAX,missense_variant,p.Arg997Gly,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Arg997Gly,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,; G ENST00000562522 Transcript missense_variant 3022/3990 2989/3510 997/1169 R/G Cgg/Ggg rs143932593 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 tolerated(0.28) 26/31 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69179 MODERATE 1 SNV 1 1 PASS rs143932593 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 31379994 31379994 C G 1 0 0 0 0 1 0 0 0 7796 875 31 4 4 ITGAX 16 31379994 Missense_Mutation SNP C C3N-02423_T 17033 31379994 58958351 345 29475 C16orf58 0 . GRCh38 16 31493619 31493619 + Missense_Mutation SNP C C A rs759045764 C3N-02423_T C3N-02423_N C C c.942G>T p.Met314Ile p.M314I ENST00000327237 8/13 415 390 25 366 366 0 strelka-varscan-mutect C16orf58,missense_variant,p.Met314Ile,ENST00000327237,NM_022744.3;C16orf58,missense_variant,p.Met312Ile,ENST00000570164,;C16orf58,missense_variant,p.Met314Ile,ENST00000430477,;C16orf58,missense_variant,p.Met269Ile,ENST00000567994,;SLC5A2,downstream_gene_variant,,ENST00000330498,NM_003041.3;C16orf58,downstream_gene_variant,,ENST00000564807,;SLC5A2,downstream_gene_variant,,ENST00000564197,;SLC5A2,downstream_gene_variant,,ENST00000567051,;C16orf58,non_coding_transcript_exon_variant,,ENST00000568491,;C16orf58,non_coding_transcript_exon_variant,,ENST00000541442,;C16orf58,non_coding_transcript_exon_variant,,ENST00000567673,;SLC5A2,downstream_gene_variant,,ENST00000568188,;SLC5A2,downstream_gene_variant,,ENST00000419665,;SLC5A2,downstream_gene_variant,,ENST00000568891,;C16orf58,downstream_gene_variant,,ENST00000567578,;C16orf58,downstream_gene_variant,,ENST00000565128,; A ENST00000327237 Transcript missense_variant 982/2793 942/1407 314/468 M/I atG/atT rs759045764 1 -1 C16orf58 HGNC HGNC:25848 protein_coding YES CCDS10715.1 ENSP00000317579 Q96GQ5 A0A024QZE6 UPI0000141B4B NM_022744.3 tolerated(0.1) 8/13 hmmpanther:PTHR12770,hmmpanther:PTHR12770:SF22 MODERATE 1 SNV 1 1 PASS rs759045764 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 31493619 31493619 C A 1 0 0 0 0 1 0 0 0 1859 594 21 2 2 C16orf58 16 31493619 Missense_Mutation SNP C C3N-02423_T 113625 31493619 58844726 346 29476 NETO2 0 . GRCh38 16 47083709 47083709 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.1090A>T p.Ile364Phe p.I364F ENST00000562435 9/9 259 224 35 226 226 0 strelka-varscan-mutect NETO2,missense_variant,p.Ile364Phe,ENST00000562435,NM_018092.4;NETO2,missense_variant,p.Ile357Phe,ENST00000303155,NM_001201477.1;NETO2,missense_variant,p.Ile204Phe,ENST00000562559,;NETO2,missense_variant,p.Ile67Phe,ENST00000564667,;NETO2,missense_variant,p.Ile163Phe,ENST00000563078,; A ENST00000562435 Transcript missense_variant 1475/7481 1090/1578 364/525 I/F Att/Ttt 1 -1 NETO2 HGNC HGNC:14644 protein_coding YES CCDS10727.1 ENSP00000455169 Q8NC67 UPI000003C718 NM_018092.4 deleterious(0.04) 9/9 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10127:SF314,hmmpanther:PTHR10127 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 47083709 47083709 T A 1 0 0 0 0 1 0 0 0 10375 1406 49 4 4 NETO2 16 47083709 Missense_Mutation SNP T C3N-02423_T 15590090 47083709 43254636 347 29477 ABCC11 0 . GRCh38 16 48198231 48198231 + Silent SNP T T C novel C3N-02423_T C3N-02423_N T T c.2127A>G p.= p.K709K ENST00000394747 15/29 321 303 18 305 305 0 strelka-varscan-mutect ABCC11,synonymous_variant,p.=,ENST00000394747,NM_033151.3;ABCC11,synonymous_variant,p.=,ENST00000356608,;ABCC11,synonymous_variant,p.=,ENST00000394748,NM_032583.3;ABCC11,synonymous_variant,p.=,ENST00000353782,NM_145186.2;ABCC11,non_coding_transcript_exon_variant,,ENST00000569172,; C ENST00000394747 Transcript synonymous_variant 2477/4862 2127/4149 709/1382 K aaA/aaG 1 -1 ABCC11 HGNC HGNC:14639 protein_coding YES CCDS10732.1 ENSP00000378230 Q96J66 A0A024R6Q6 UPI0000052711 NM_033151.3 15/29 PROSITE_profiles:PS50893,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF168,Gene3D:3.40.50.300,SMART_domains:SM00382,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 48198231 48198231 T C 1 0 0 0 0 0 0 0 1 55 1838 64 5 5 ABCC11 16 48198231 Silent SNP T C3N-02423_T 1114522 48198231 42140114 348 29478 IRX5 0 . GRCh38 16 54933310 54933310 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.889G>T p.Ala297Ser p.A297S ENST00000394636 3/3 110 95 15 85 85 0 strelka-varscan-mutect IRX5,missense_variant,p.Ala297Ser,ENST00000394636,NM_005853.5;IRX5,missense_variant,p.Ala296Ser,ENST00000320990,NM_001252197.1;IRX5,intron_variant,,ENST00000620085,;IRX5,intron_variant,,ENST00000560154,;CRNDE,upstream_gene_variant,,ENST00000560208,;CRNDE,upstream_gene_variant,,ENST00000559598,;CRNDE,upstream_gene_variant,,ENST00000502066,;CRNDE,upstream_gene_variant,,ENST00000501177,;CRNDE,upstream_gene_variant,,ENST00000558952,;CRNDE,upstream_gene_variant,,ENST00000559432,;CTD-3032H12.1,downstream_gene_variant,,ENST00000559802,;CTD-3032H12.1,downstream_gene_variant,,ENST00000558156,;CRNDE,upstream_gene_variant,,ENST00000557792,;CRNDE,upstream_gene_variant,,ENST00000560912,;CTD-3032H12.2,upstream_gene_variant,,ENST00000560487,;IRX5,non_coding_transcript_exon_variant,,ENST00000558597,; T ENST00000394636 Transcript missense_variant 1226/2401 889/1452 297/483 A/S Gcg/Tcg 1 1 IRX5 HGNC HGNC:14361 protein_coding YES CCDS10751.1 ENSP00000378132 P78411 UPI00001FF1CD NM_005853.5 tolerated(0.59) 3/3 hmmpanther:PTHR11211,hmmpanther:PTHR11211:SF17,Low_complexity_(Seg):seg MODERATE 1 SNV 3 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 54933310 54933310 G T 1 0 0 0 0 1 0 0 0 7755 1203 42 2 2 IRX5 16 54933310 Missense_Mutation SNP G C3N-02423_T 6735079 54933310 35405035 349 29479 GNAO1 0 . GRCh38 16 56340899 56340899 + Silent SNP G G T rs773592961 C3N-02423_T C3N-02423_N G G c.789G>T p.= p.T263T ENST00000262494 7/8 205 187 18 224 224 0 strelka-varscan-mutect GNAO1,synonymous_variant,p.=,ENST00000262494,NM_138736.2;GNAO1,intron_variant,,ENST00000262493,NM_020988.2;GNAO1,intron_variant,,ENST00000568375,;GNAO1,non_coding_transcript_exon_variant,,ENST00000564798,; T ENST00000262494 Transcript synonymous_variant 1049/5574 789/1065 263/354 T acG/acT rs773592961 1 1 GNAO1 HGNC HGNC:4389 protein_coding YES CCDS10757.1 ENSP00000262494 P09471 UPI000007349C NM_138736.2 7/8 Gene3D:3.40.50.300,Pfam_domain:PF00503,hmmpanther:PTHR10218,hmmpanther:PTHR10218:SF203,SMART_domains:SM00275,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs773592961 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 56340899 56340899 G T 1 0 0 0 0 0 0 0 1 6388 1132 40 1 1 GNAO1 16 56340899 Silent SNP G C3N-02423_T 1407589 56340899 33997446 350 29480 SLC12A3 0 . GRCh38 16 56904457 56904457 + Missense_Mutation SNP C C G rs779473697 C3N-02423_T C3N-02423_N C C c.2946C>G p.Ile982Met p.I982M ENST00000438926 25/26 414 358 56 423 423 0 strelka-varscan-mutect SLC12A3,missense_variant,p.Ile982Met,ENST00000438926,NM_000339.2;SLC12A3,missense_variant,p.Ile972Met,ENST00000262502,;SLC12A3,missense_variant,p.Ile973Met,ENST00000563236,NM_001126108.1;SLC12A3,missense_variant,p.Ile981Met,ENST00000566786,NM_001126107.1;MIR6863,downstream_gene_variant,,ENST00000636112,;SLC12A3,upstream_gene_variant,,ENST00000563352,;SLC12A3,non_coding_transcript_exon_variant,,ENST00000569002,;RPS24P17,upstream_gene_variant,,ENST00000479895,; G ENST00000438926 Transcript missense_variant 2975/5567 2946/3093 982/1030 I/M atC/atG rs779473697 1 1 SLC12A3 HGNC HGNC:10912 protein_coding YES CCDS10770.1 ENSP00000402152 P55017 UPI00001FF243 NM_000339.2 deleterious(0) 25/26 hmmpanther:PTHR11827:SF9,hmmpanther:PTHR11827,TIGRFAM_domain:TIGR00930,Pfam_domain:PF03522 MODERATE 1 SNV 1 1 PASS rs779473697 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 56904457 56904457 C G 1 0 0 0 0 1 0 0 0 14649 898 31 4 4 SLC12A3 16 56904457 Missense_Mutation SNP C C3N-02423_T 563558 56904457 33433888 351 29481 NLRC5 0 . GRCh38 16 57028136 57028136 + Missense_Mutation SNP G G T rs748383955 C3N-02423_T C3N-02423_N G G c.2140G>T p.Gly714Trp p.G714W ENST00000262510 7/49 76 68 8 76 76 0 strelka-varscan-mutect NLRC5,missense_variant,p.Gly714Trp,ENST00000262510,;NLRC5,missense_variant,p.Gly714Trp,ENST00000436936,NM_032206.4;NLRC5,missense_variant,p.Gly714Trp,ENST00000539144,;NLRC5,missense_variant,p.Gly467Trp,ENST00000538805,;NLRC5,missense_variant,p.Gly221Trp,ENST00000538110,;NLRC5,missense_variant,p.Gly69Trp,ENST00000543030,;NLRC5,missense_variant,p.Gly442Trp,ENST00000545081,;NLRC5,missense_variant,p.Gly714Trp,ENST00000539881,;NLRC5,non_coding_transcript_exon_variant,,ENST00000536231,; T ENST00000262510 Transcript missense_variant 2365/6822 2140/5601 714/1866 G/W Ggg/Tgg rs748383955 1 1 NLRC5 HGNC HGNC:29933 protein_coding YES CCDS10773.1 ENSP00000262510 Q86WI3 UPI00001AEE94 deleterious(0) 7/49 Gene3D:3.80.10.10,SMART_domains:SM00367,SMART_domains:SM00368,Superfamily_domains:SSF52047 MODERATE 1 SNV 5 1 PASS rs748383955 . 0 207 0 2 0 0 0 0 -13.5992 0.9999999 1 1 1 0 T 3 4 99 57028136 57028136 G T 1 0 0 0 0 1 0 0 0 10507 1232 43 2 2 NLRC5 16 57028136 Missense_Mutation SNP G C3N-02423_T 123679 57028136 33310209 352 29482 CNOT1 0 . GRCh38 16 58543737 58543737 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.4304C>G p.Ser1435Cys p.S1435C ENST00000317147 31/49 167 157 10 189 189 0 strelka-varscan-mutect CNOT1,missense_variant,p.Ser1435Cys,ENST00000317147,NM_016284.4;CNOT1,missense_variant,p.Ser1430Cys,ENST00000569240,NM_001265612.1;CNOT1,missense_variant,p.Ser1435Cys,ENST00000441024,NM_206999.2;CNOT1,missense_variant,p.Ser142Cys,ENST00000567133,;CNOT1,upstream_gene_variant,,ENST00000568917,;CNOT1,downstream_gene_variant,,ENST00000567285,;SNORA46,downstream_gene_variant,,ENST00000384762,;CNOT1,missense_variant,p.Ser1430Cys,ENST00000567188,;CNOT1,missense_variant,p.Ser23Cys,ENST00000566240,;CNOT1,upstream_gene_variant,,ENST00000563283,; C ENST00000317147 Transcript missense_variant 4637/8471 4304/7131 1435/2376 S/C tCt/tGt 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 tolerated(0.11) 31/49 hmmpanther:PTHR13162,Pfam_domain:PF12842 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 58543737 58543737 G C 1 0 0 0 0 1 0 0 0 3396 942 33 4 4 CNOT1 16 58543737 Missense_Mutation SNP G C3N-02423_T 1515601 58543737 31794608 353 29483 101 2 CNOT1 0 . GRCh38 16 58543746 58543746 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.4295C>T p.Ser1432Leu p.S1432L ENST00000317147 31/49 192 175 17 208 207 1 strelka-varscan-mutect CNOT1,missense_variant,p.Ser1432Leu,ENST00000317147,NM_016284.4;CNOT1,missense_variant,p.Ser1427Leu,ENST00000569240,NM_001265612.1;CNOT1,missense_variant,p.Ser1432Leu,ENST00000441024,NM_206999.2;CNOT1,missense_variant,p.Ser139Leu,ENST00000567133,;CNOT1,upstream_gene_variant,,ENST00000568917,;CNOT1,downstream_gene_variant,,ENST00000567285,;SNORA46,downstream_gene_variant,,ENST00000384762,;CNOT1,missense_variant,p.Ser1427Leu,ENST00000567188,;CNOT1,missense_variant,p.Ser20Leu,ENST00000566240,;CNOT1,upstream_gene_variant,,ENST00000563283,; A ENST00000317147 Transcript missense_variant 4628/8471 4295/7131 1432/2376 S/L tCg/tTg 1 -1 CNOT1 HGNC HGNC:7877 protein_coding YES CCDS10799.1 ENSP00000320949 A5YKK6 UPI00001FF2F6 NM_016284.4 deleterious(0) 31/49 hmmpanther:PTHR13162,Pfam_domain:PF12842 MODERATE 1 SNV 1 1 PASS . . 0 207 0 0 2 0 0 0 -6.62733 0.9914209 1 1 1 0 A 3 1 99 58543746 58543746 G A 1 0 0 0 0 1 0 0 0 3396 1059 37 1 1 CNOT1 16 58543746 Missense_Mutation SNP G C3N-02423_T 9 58543746 31794599 354 29484 101 2 CARMIL2 0 . GRCh38 16 67645605 67645605 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.106G>A p.Glu36Lys p.E36K ENST00000334583 2/38 306 284 22 292 292 0 strelka-varscan-mutect CARMIL2,missense_variant,p.Glu36Lys,ENST00000334583,NM_001013838.1;CARMIL2,missense_variant,p.Glu36Lys,ENST00000545661,NM_001317026.1;CARMIL2,non_coding_transcript_exon_variant,,ENST00000602467,;CARMIL2,intron_variant,,ENST00000602563,;CARMIL2,upstream_gene_variant,,ENST00000602321,;CARMIL2,upstream_gene_variant,,ENST00000602562,;CARMIL2,upstream_gene_variant,,ENST00000602633,;CARMIL2,upstream_gene_variant,,ENST00000602742,; A ENST00000334583 Transcript missense_variant 434/4687 106/4308 36/1435 E/K Gag/Aag 1 1 CARMIL2 HGNC HGNC:27089 protein_coding YES CCDS45513.1 ENSP00000334958 Q6F5E8 UPI00005194F2 NM_001013838.1 tolerated(0.86) 2/38 hmmpanther:PTHR24112:SF32,hmmpanther:PTHR24112 MODERATE 1 SNV 1 1 PASS rs1206066185 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 67645605 67645605 G A 1 0 0 0 0 1 0 0 0 2352 1175 41 3 3 CARMIL2 16 67645605 Missense_Mutation SNP G C3N-02423_T 9101859 67645605 22692740 355 29485 FA2H 0 . GRCh38 16 74774603 74774603 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.153G>T p.= p.R51R ENST00000219368 1/7 146 128 18 172 172 0 strelka-varscan-mutect FA2H,synonymous_variant,p.=,ENST00000219368,NM_024306.4;FA2H,synonymous_variant,p.=,ENST00000567683,; A ENST00000219368 Transcript synonymous_variant 223/2424 153/1119 51/372 R cgG/cgT 1 -1 FA2H HGNC HGNC:21197 protein_coding YES CCDS10911.1 ENSP00000219368 Q7L5A8 UPI000013C77C NM_024306.4 1/7 PROSITE_profiles:PS50255,hmmpanther:PTHR12863,Pfam_domain:PF00173,PIRSF_domain:PIRSF005149,Gene3D:3.10.120.10,SMART_domains:SM01117,Superfamily_domains:SSF55856,Prints_domain:PR00363 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 74774603 74774603 C A 1 0 0 0 0 0 0 0 1 5221 610 22 2 2 FA2H 16 74774603 Silent SNP C C3N-02423_T 7128998 74774603 15563742 356 29486 ZNF469 0 . GRCh38 16 88436012 88436012 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.8458G>A p.Asp2820Asn p.D2820N ENST00000437464 2/2 539 494 45 610 610 0 strelka-varscan-mutect ZNF469,missense_variant,p.Asp2848Asn,ENST00000565624,;ZNF469,missense_variant,p.Asp2820Asn,ENST00000437464,NM_001127464.2; A ENST00000437464 Transcript missense_variant 8458/13203 8458/11778 2820/3925 D/N Gat/Aat 1 1 ZNF469 HGNC HGNC:23216 protein_coding YES CCDS45544.1 ENSP00000402343 Q96JG9 UPI0004E4C937 NM_001127464.2 tolerated(0.05) 2/2 hmmpanther:PTHR21465:SF2,hmmpanther:PTHR21465 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 88436012 88436012 G A 1 0 0 0 0 1 0 0 0 18500 1174 41 3 3 ZNF469 16 88436012 Missense_Mutation SNP G C3N-02423_T 13661409 88436012 1902333 357 29487 POLR2A 0 . GRCh38 17 7502020 7502020 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.2470G>C p.Glu824Gln p.E824Q ENST00000617998 15/29 172 143 29 190 190 0 strelka-varscan-mutect POLR2A,missense_variant,p.Glu824Gln,ENST00000617998,NM_000937.4;POLR2A,downstream_gene_variant,,ENST00000572844,;POLR2A,downstream_gene_variant,,ENST00000575547,;POLR2A,upstream_gene_variant,,ENST00000576718,;POLR2A,downstream_gene_variant,,ENST00000576952,;POLR2A,upstream_gene_variant,,ENST00000574158,;POLR2A,upstream_gene_variant,,ENST00000576114,; C ENST00000617998 Transcript missense_variant 2869/6751 2470/5943 824/1980 E/Q Gag/Cag 1 1 POLR2A HGNC HGNC:9187 protein_coding YES ENSP00000480158 A0A087WWE2 UPI0004620E89 NM_000937.4 deleterious(0.01) 15/29 hmmpanther:PTHR19376,hmmpanther:PTHR19376:SF37,Superfamily_domains:SSF64484 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 7502020 7502020 G C 1 0 0 0 0 1 0 0 0 12324 1175 41 4 4 POLR2A 17 7502020 Missense_Mutation SNP G C3N-02423_T 7502020 75755421 358 29488 TP53 0 . GRCh38 17 7673579 7673579 + Nonsense_Mutation SNP G G A rs764735889 C3N-02423_T C3N-02423_N G G c.949C>T p.Gln317Ter p.Q317* ENST00000269305 9/11 273 223 50 333 332 1 strelka-varscan-mutect TP53,stop_gained,p.Gln317Ter,ENST00000617185,NM_001126114.2;TP53,stop_gained,p.Gln317Ter,ENST00000420246,;TP53,stop_gained,p.Gln278Ter,ENST00000622645,NM_001276696.1;TP53,stop_gained,p.Gln278Ter,ENST00000610292,NM_001126118.1;TP53,stop_gained,p.Gln317Ter,ENST00000455263,NM_001126113.2;TP53,stop_gained,p.Gln278Ter,ENST00000610538,NM_001276695.1;TP53,stop_gained,p.Gln317Ter,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,stop_gained,p.Gln278Ter,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,stop_gained,p.Gln317Ter,ENST00000445888,;TP53,stop_gained,p.Gln278Ter,ENST00000619485,;TP53,stop_gained,p.Gln185Ter,ENST00000510385,NM_001126116.1;TP53,stop_gained,p.Gln158Ter,ENST00000618944,NM_001276698.1;TP53,stop_gained,p.Gln185Ter,ENST00000504290,NM_001126117.1;TP53,stop_gained,p.Gln158Ter,ENST00000610623,NM_001276699.1;TP53,stop_gained,p.Gln185Ter,ENST00000504937,NM_001126115.1;TP53,stop_gained,p.Gln158Ter,ENST00000619186,NM_001276697.1;TP53,stop_gained,p.Gln317Ter,ENST00000359597,;TP53,stop_gained,p.Gln306Ter,ENST00000615910,;TP53,stop_gained,p.Gln185Ter,ENST00000509690,;TP53,stop_gained,p.Gln4Ter,ENST00000576024,;TP53,intron_variant,,ENST00000413465,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,stop_gained,p.Gln278Ter,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript stop_gained 1139/2579 949/1182 317/393 Q/* Cag/Tag rs764735889,TP53_g.14021del,TP53_g.14021C>T,TP53_g.14021C>A,COSM10786,COSM1630410,COSM165085,COSM1709728,COSM1735382,COSM3388166,COSM43573,COSM43769 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 9/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6 0,0,0,0,1,1,1,1,1,1,1,1 HIGH 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1 1 PASS rs764735889 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 7673579 7673579 G A 1 0 0 0 0 0 1 0 0 16859 1357 47 3 3 TP53 17 7673579 Nonsense_Mutation SNP G C3N-02423_T 171559 7673579 75583862 359 29489 MYH2 0 . GRCh38 17 10543111 10543111 + Silent SNP A A T novel C3N-02423_T C3N-02423_N A A c.792T>A p.= p.A264A ENST00000245503 9/40 192 170 22 261 261 0 strelka-varscan-mutect MYH2,synonymous_variant,p.=,ENST00000245503,NM_017534.5;MYH2,synonymous_variant,p.=,ENST00000397183,NM_001100112.1;MYH2,synonymous_variant,p.=,ENST00000532183,;MYH2,synonymous_variant,p.=,ENST00000622564,;MYH2,downstream_gene_variant,,ENST00000420805,;MYH2,downstream_gene_variant,,ENST00000578017,;MYHAS,intron_variant,,ENST00000587182,; T ENST00000245503 Transcript synonymous_variant 1177/6339 792/5826 264/1941 A gcT/gcA 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 9/40 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,SMART_domains:SM00242,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 10543111 10543111 A T 1 0 0 0 0 0 0 0 1 10035 175 7 4 4 MYH2 17 10543111 Silent SNP A C3N-02423_T 2869532 10543111 72714330 360 29490 MYH3 0 . GRCh38 17 10642551 10642551 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1754G>T p.Gly585Val p.G585V ENST00000583535 16/41 337 278 59 458 458 0 strelka-varscan-mutect MYH3,missense_variant,p.Gly585Val,ENST00000583535,NM_002470.3; A ENST00000583535 Transcript missense_variant 1842/6037 1754/5823 585/1940 G/V gGc/gTc 1 -1 MYH3 HGNC HGNC:7573 protein_coding YES CCDS11157.1 ENSP00000464317 P11055 UPI000013C892 NM_002470.3 deleterious(0) 16/41 PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF427,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 10642551 10642551 C A 1 0 0 0 0 1 0 0 0 10036 739 26 2 2 MYH3 17 10642551 Missense_Mutation SNP C C3N-02423_T 99440 10642551 72614890 361 29491 FBXW10 0 . GRCh38 17 18775194 18775194 + Splice_Site SNP T T A novel C3N-02423_T C3N-02423_N T T c.2335+2T>A p.X779_splice ENST00000395665 219 199 20 164 164 0 strelka-varscan-mutect FBXW10,splice_donor_variant,,ENST00000395665,NM_001267585.1;FBXW10,splice_donor_variant,,ENST00000301938,NM_001267586.1;FBXW10,intron_variant,,ENST00000308799,;FBXW10,downstream_gene_variant,,ENST00000573605,;FBXW10,splice_donor_variant,,ENST00000574478,; A ENST00000395665 Transcript splice_donor_variant -/3431 2335/3159 779/1052 1 1 FBXW10 HGNC HGNC:1211 protein_coding YES CCDS11199.3 ENSP00000379025 Q5XX13 UPI0000200B30 NM_001267585.1 13/13 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 99 18775194 18775194 T A 1 0 0 0 0 0 0 1 0 5626 1652 57 4 4 FBXW10 17 18775194 Splice_Site SNP T C3N-02423_T 8132643 18775194 64482247 362 29492 LGALS9 0 . GRCh38 17 27647054 27647054 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.694C>T p.= p.L232L ENST00000395473 9/11 328 304 24 366 365 1 strelka-varscan-mutect LGALS9,synonymous_variant,p.=,ENST00000395473,NM_009587.2;LGALS9,synonymous_variant,p.=,ENST00000302228,NM_002308.3;LGALS9,synonymous_variant,p.=,ENST00000313648,;LGALS9,synonymous_variant,p.=,ENST00000581710,;LGALS9,synonymous_variant,p.=,ENST00000577392,;LGALS9,synonymous_variant,p.=,ENST00000578944,;LGALS9,downstream_gene_variant,,ENST00000584661,;LGALS9,3_prime_UTR_variant,,ENST00000467111,;LGALS9,3_prime_UTR_variant,,ENST00000580779,;LGALS9,non_coding_transcript_exon_variant,,ENST00000486774,;LGALS9,non_coding_transcript_exon_variant,,ENST00000481514,;LGALS9,non_coding_transcript_exon_variant,,ENST00000584386,;LGALS9,downstream_gene_variant,,ENST00000579930,;LGALS9,downstream_gene_variant,,ENST00000583671,;NOS2P1,downstream_gene_variant,,ENST00000580780,; T ENST00000395473 Transcript synonymous_variant 2162/3114 694/1068 232/355 L Ctg/Ttg 1 1 LGALS9 HGNC HGNC:6570 protein_coding YES CCDS11222.1 ENSP00000378856 O00182 A0A024QZ55 UPI000012E437 NM_009587.2 9/11 Gene3D:2.60.120.200,Pfam_domain:PF00337,PROSITE_profiles:PS51304,hmmpanther:PTHR11346,hmmpanther:PTHR11346:SF91,SMART_domains:SM00276,SMART_domains:SM00908,Superfamily_domains:SSF49899 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 27647054 27647054 C T 1 0 0 0 0 0 0 0 1 8657 912 32 3 3 LGALS9 17 27647054 Silent SNP C C3N-02423_T 8871860 27647054 55610387 363 29493 LIG3 0 . GRCh38 17 34999856 34999856 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.2331G>T p.Lys777Asn p.K777N ENST00000378526 16/20 164 136 28 167 167 0 strelka-varscan-mutect LIG3,missense_variant,p.Lys777Asn,ENST00000378526,NM_013975.3;LIG3,missense_variant,p.Lys777Asn,ENST00000262327,NM_002311.4;LIG3,splice_region_variant,,ENST00000593099,;LIG3,splice_region_variant,,ENST00000586119,;LIG3,downstream_gene_variant,,ENST00000590630,;LIG3,downstream_gene_variant,,ENST00000586058,;LIG3,downstream_gene_variant,,ENST00000588713,;LIG3,upstream_gene_variant,,ENST00000592244,;LIG3,downstream_gene_variant,,ENST00000585370,; T ENST00000378526 Transcript missense_variant,splice_region_variant 2464/8400 2331/3030 777/1009 K/N aaG/aaT 1 1 LIG3 HGNC HGNC:6600 protein_coding YES CCDS11284.2 ENSP00000367787 P49916 UPI0000350B71 NM_013975.3 tolerated(0.07) 16/20 Gene3D:2.40.50.140,Pfam_domain:PF04679,hmmpanther:PTHR10459,hmmpanther:PTHR10459:SF11,Superfamily_domains:SSF50249,TIGRFAM_domain:TIGR00574 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 34999856 34999856 G T 1 0 0 0 0 1 0 0 0 8691 1014 35 2 2 LIG3 17 34999856 Missense_Mutation SNP G C3N-02423_T 7352802 34999856 48257585 364 29494 C17orf50 0 . GRCh38 17 35764166 35764166 + Missense_Mutation SNP A A C novel C3N-02423_T C3N-02423_N A A c.173A>C p.Glu58Ala p.E58A ENST00000605587 2/3 437 414 23 367 366 1 strelka-varscan-mutect C17orf50,missense_variant,p.Glu58Ala,ENST00000605587,NM_145272.3;C17orf50,missense_variant,p.Glu58Ala,ENST00000604830,;C17orf50,synonymous_variant,p.=,ENST00000603305,;MMP28,intron_variant,,ENST00000615317,;MMP28,downstream_gene_variant,,ENST00000615136,NM_032950.3;MMP28,downstream_gene_variant,,ENST00000605424,NM_024302.4;MMP28,downstream_gene_variant,,ENST00000612292,;MMP28,intron_variant,,ENST00000619655,;TAF15,intron_variant,,ENST00000603067,; C ENST00000605587 Transcript missense_variant 205/1018 173/525 58/174 E/A gAg/gCg 1 1 C17orf50 HGNC HGNC:29581 protein_coding YES CCDS42298.1 ENSP00000475146 Q8WW18 UPI00002016EC NM_145272.3 tolerated(0.26) 2/3 Low_complexity_(Seg):seg,hmmpanther:PTHR37878:SF1,hmmpanther:PTHR37878,Pfam_domain:PF15470 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 35764166 35764166 A C 1 0 0 0 0 1 0 0 0 1881 304 11 5 5 C17orf50 17 35764166 Missense_Mutation SNP A C3N-02423_T 764310 35764166 47493275 365 29495 CWC25 0 . GRCh38 17 38806876 38806876 + Missense_Mutation SNP G G C rs777251017 C3N-02423_T C3N-02423_N G G c.791C>G p.Ser264Cys p.S264C ENST00000614790 7/10 189 175 14 151 150 1 strelka-varscan-mutect CWC25,missense_variant,p.Ser264Cys,ENST00000614790,NM_017748.4;CWC25,non_coding_transcript_exon_variant,,ENST00000619818,;CWC25,3_prime_UTR_variant,,ENST00000619299,;CWC25,3_prime_UTR_variant,,ENST00000618122,;CWC25,3_prime_UTR_variant,,ENST00000619462,;CWC25,non_coding_transcript_exon_variant,,ENST00000611845,;CWC25,downstream_gene_variant,,ENST00000622665,; C ENST00000614790 Transcript missense_variant 1089/3234 791/1278 264/425 S/C tCc/tGc rs777251017 1 -1 CWC25 HGNC HGNC:25989 protein_coding YES CCDS45663.1 ENSP00000478070 Q9NXE8 UPI000007081D NM_017748.4 tolerated(0.06) 7/10 Low_complexity_(Seg):seg,hmmpanther:PTHR16196 MODERATE 1 SNV 1 1 PASS rs777251017 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 38806876 38806876 G C 1 0 0 0 0 1 0 0 0 3879 1174 41 4 4 CWC25 17 38806876 Missense_Mutation SNP G C3N-02423_T 3042710 38806876 44450565 366 29496 MED1 0 . GRCh38 17 39415300 39415300 + Nonsense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1337C>G p.Ser446Ter p.S446* ENST00000300651 15/17 304 283 21 309 309 0 strelka-varscan-mutect MED1,stop_gained,p.Ser446Ter,ENST00000300651,NM_004774.3;MED1,stop_gained,p.Ser446Ter,ENST00000394287,;MED1,3_prime_UTR_variant,,ENST00000577831,; C ENST00000300651 Transcript stop_gained 1561/5844 1337/4746 446/1581 S/* tCa/tGa 1 -1 MED1 HGNC HGNC:9234 protein_coding YES CCDS11336.1 ENSP00000300651 Q15648 UPI0000167F57 NM_004774.3 15/17 hmmpanther:PTHR12881 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 99 39415300 39415300 G C 1 0 0 0 0 0 1 0 0 9364 1294 45 4 4 MED1 17 39415300 Nonsense_Mutation SNP G C3N-02423_T 608424 39415300 43842141 367 29497 KRTAP4-7 0 . GRCh38 17 41084449 41084449 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.243C>G p.Ile81Met p.I81M ENST00000391417 1/1 392 368 24 436 436 0 varscan-mutect KRTAP4-7,missense_variant,p.Ile81Met,ENST00000391417,NM_033061.3;KRTAP4-7,missense_variant,p.Ile81Met,ENST00000612231,;KRTAP4-7,missense_variant,p.Ile81Met,ENST00000621138,; G ENST00000391417 Transcript missense_variant 300/992 243/468 81/155 I/M atC/atG 1 1 KRTAP4-7 HGNC HGNC:18898 protein_coding YES CCDS45673.1 ENSP00000375236 Q9BYR0 UPI00001B0238 NM_033061.3 tolerated(0.08) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR23262,hmmpanther:PTHR23262:SF60,Pfam_domain:PF13885 MODERATE 1 SNV 1 PASS rs1315835532 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 41084449 41084449 C G 1 0 0 0 0 1 0 0 0 8450 903 32 4 4 KRTAP4-7 17 41084449 Missense_Mutation SNP C C3N-02423_T 1669149 41084449 42172992 368 29498 STAT3 0 . GRCh38 17 42329771 42329771 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1115C>T p.Ser372Phe p.S372F ENST00000264657 12/24 588 553 35 514 514 0 strelka-varscan-mutect STAT3,missense_variant,p.Ser372Phe,ENST00000264657,NM_139276.2;STAT3,missense_variant,p.Ser372Phe,ENST00000585517,NM_213662.1;STAT3,missense_variant,p.Ser372Phe,ENST00000588969,;STAT3,missense_variant,p.Ser372Phe,ENST00000404395,NM_003150.3;STAT3,missense_variant,p.Ser274Phe,ENST00000389272,;STAT3,non_coding_transcript_exon_variant,,ENST00000478276,;STAT3,upstream_gene_variant,,ENST00000471989,;STAT3,upstream_gene_variant,,ENST00000498330,; A ENST00000264657 Transcript missense_variant 1428/5047 1115/2313 372/770 S/F tCt/tTt 1 -1 STAT3 HGNC HGNC:11364 protein_coding YES CCDS32656.1 ENSP00000264657 P40763 UPI0000031047 NM_139276.2 tolerated(0.1) 12/24 hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF2,Pfam_domain:PF02864,Gene3D:2.60.40.630,Superfamily_domains:SSF49417 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 42329771 42329771 G A 1 0 0 0 0 1 0 0 0 15642 956 33 3 3 STAT3 17 42329771 Missense_Mutation SNP G C3N-02423_T 1245322 42329771 40927670 369 29499 PTGES3L 0 . GRCh38 17 42980139 42980139 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.44G>C p.Arg15Thr p.R15T ENST00000421990 1/17 178 168 10 129 129 0 strelka-varscan-mutect PTGES3L-AARSD1,missense_variant,p.Arg15Thr,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,missense_variant,p.Arg15Thr,ENST00000409399,;PTGES3L,missense_variant,p.Arg15Thr,ENST00000409446,NM_001142654.1;RUNDC1,upstream_gene_variant,,ENST00000361677,NM_001321381.1,NM_173079.2;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000360221,NM_025267.3;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000409103,;PTGES3L,upstream_gene_variant,,ENST00000424284,;RUNDC1,upstream_gene_variant,,ENST00000589705,;PTGES3L,upstream_gene_variant,,ENST00000591916,NM_001261430.1;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000454303,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000452752,;PTGES3L,upstream_gene_variant,,ENST00000451885,NM_001142653.1;PTGES3L,non_coding_transcript_exon_variant,,ENST00000462157,;RUNDC1,upstream_gene_variant,,ENST00000590836,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000423601,; G ENST00000421990 Transcript missense_variant 390/2150 44/1761 15/586 R/T aGa/aCa 1 -1 PTGES3L-AARSD1 HGNC HGNC:43946 protein_coding YES CCDS45691.1 ENSP00000409924 Q9BTE6 UPI0000D4E5DF NM_001136042.2 deleterious_low_confidence(0.03) 1/17 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 42980139 42980139 C G 1 0 0 0 0 1 0 0 0 12904 913 32 4 4 PTGES3L 17 42980139 Missense_Mutation SNP C C3N-02423_T 650368 42980139 40277302 370 29500 RUNDC1 0 . GRCh38 17 42981024 42981024 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.448G>A p.Glu150Lys p.E150K ENST00000361677 1/5 180 168 12 170 170 0 strelka-varscan-mutect RUNDC1,missense_variant,p.Glu150Lys,ENST00000361677,NM_001321381.1,NM_173079.2;RUNDC1,missense_variant,p.Glu149Lys,ENST00000589705,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000421990,NM_001136042.2;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000409399,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000360221,NM_025267.3;PTGES3L,upstream_gene_variant,,ENST00000409446,NM_001142654.1;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000409103,;PTGES3L,upstream_gene_variant,,ENST00000424284,;PTGES3L,upstream_gene_variant,,ENST00000591916,NM_001261430.1;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000454303,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000452752,;PTGES3L,upstream_gene_variant,,ENST00000451885,NM_001142653.1;RUNDC1,non_coding_transcript_exon_variant,,ENST00000590836,;PTGES3L,upstream_gene_variant,,ENST00000462157,;PTGES3L-AARSD1,upstream_gene_variant,,ENST00000423601,; A ENST00000361677 Transcript missense_variant 460/3828 448/1842 150/613 E/K Gag/Aag 1 1 RUNDC1 HGNC HGNC:25418 protein_coding YES CCDS11448.1 ENSP00000354622 Q96C34 UPI00001AED0E NM_001321381.1,NM_173079.2 tolerated(0.68) 1/5 hmmpanther:PTHR22957,hmmpanther:PTHR22957:SF2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 42981024 42981024 G A 1 0 0 0 0 1 0 0 0 14004 1291 45 3 3 RUNDC1 17 42981024 Missense_Mutation SNP G C3N-02423_T 885 42981024 40276417 371 29501 RUNDC3A 0 . GRCh38 17 44313126 44313126 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.246G>A p.= p.V82V ENST00000426726 3/11 112 105 7 109 109 0 strelka-varscan-mutect RUNDC3A,synonymous_variant,p.=,ENST00000426726,NM_001144825.1;RUNDC3A,synonymous_variant,p.=,ENST00000225441,NM_006695.4;RUNDC3A,synonymous_variant,p.=,ENST00000590941,NM_001144826.1;RUNDC3A,synonymous_variant,p.=,ENST00000612735,;RUNDC3A-AS1,intron_variant,,ENST00000588097,;RUNDC3A-AS1,upstream_gene_variant,,ENST00000586388,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000587483,;RUNDC3A,non_coding_transcript_exon_variant,,ENST00000590834,;RUNDC3A,upstream_gene_variant,,ENST00000588564,;RUNDC3A,upstream_gene_variant,,ENST00000593079,; A ENST00000426726 Transcript synonymous_variant 520/2048 246/1341 82/446 V gtG/gtA 1 1 RUNDC3A HGNC HGNC:16984 protein_coding YES CCDS45698.1 ENSP00000410862 Q59EK9 UPI0000EE7B82 NM_001144825.1 3/11 Superfamily_domains:0052343,Pfam_domain:PF02759,PROSITE_profiles:PS50826,hmmpanther:PTHR22835,hmmpanther:PTHR22835:SF38 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 44313126 44313126 G A 1 0 0 0 0 0 0 0 1 14005 1277 45 3 3 RUNDC3A 17 44313126 Silent SNP G C3N-02423_T 1332102 44313126 38944315 372 29502 CSHL1 0 . GRCh38 17 63910477 63910477 + Silent SNP G G A rs61762509 C3N-02423_T C3N-02423_N G G c.249C>T p.= p.F83F ENST00000309894 3/5 446 416 30 429 429 0 varscan-mutect CSHL1,synonymous_variant,p.=,ENST00000392824,;CSHL1,synonymous_variant,p.=,ENST00000611417,;CSHL1,synonymous_variant,p.=,ENST00000309894,NM_022581.1,NM_022579.1;CSHL1,5_prime_UTR_variant,,ENST00000450719,;CSHL1,5_prime_UTR_variant,,ENST00000346606,NM_001318.2;CSHL1,intron_variant,,ENST00000561003,;CSHL1,intron_variant,,ENST00000259003,NM_001321068.1;CSHL1,intron_variant,,ENST00000438387,NM_022580.1;CSHL1,non_coding_transcript_exon_variant,,ENST00000558099,;CSHL1,non_coding_transcript_exon_variant,,ENST00000560999,;CSHL1,non_coding_transcript_exon_variant,,ENST00000558609,; A ENST00000309894 Transcript synonymous_variant 249/669 249/669 83/222 F ttC/ttT rs61762509 1 -1 CSHL1 HGNC HGNC:2442 protein_coding YES CCDS11652.1 ENSP00000309524 Q14406 UPI00001602B9 NM_022581.1,NM_022579.1 3/5 Gene3D:1.20.1250.10,Pfam_domain:PF00103,hmmpanther:PTHR11417,hmmpanther:PTHR11417:SF40,Superfamily_domains:SSF47266 LOW 1 SNV 5 1 PASS rs61762509 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 63910477 63910477 G A 1 0 0 0 0 0 0 0 1 3743 933 33 3 3 CSHL1 17 63910477 Silent SNP G C3N-02423_T 19597351 63910477 19346964 373 29503 MGAT5B 0 . GRCh38 17 76904351 76904351 + Missense_Mutation SNP T T C novel C3N-02423_T C3N-02423_N T T c.652T>C p.Phe218Leu p.F218L ENST00000428789 5/16 300 247 53 247 247 0 strelka-varscan-mutect MGAT5B,missense_variant,p.Phe207Leu,ENST00000569840,NM_001199172.1;MGAT5B,missense_variant,p.Phe207Leu,ENST00000301618,NM_144677.2;MGAT5B,missense_variant,p.Phe218Leu,ENST00000428789,NM_198955.1;MGAT5B,non_coding_transcript_exon_variant,,ENST00000374998,;MGAT5B,missense_variant,p.Phe218Leu,ENST00000565043,; C ENST00000428789 Transcript missense_variant 755/4053 652/2406 218/801 F/L Ttc/Ctc 1 1 MGAT5B HGNC HGNC:24140 protein_coding YES CCDS45788.1 ENSP00000391227 Q3V5L5 UPI0000231C88 NM_198955.1 deleterious(0.01) 5/16 Pfam_domain:PF15024,hmmpanther:PTHR15075,hmmpanther:PTHR15075:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 76904351 76904351 T C 1 0 0 0 0 1 0 0 0 9510 1725 60 5 5 MGAT5B 17 76904351 Missense_Mutation SNP T C3N-02423_T 12993874 76904351 6353090 374 29504 SEPT9 0 . GRCh38 17 77307156 77307156 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.35C>G p.Ser12Cys p.S12C ENST00000427177 2/12 572 533 39 505 505 0 strelka-varscan-mutect SEPT9,missense_variant,p.Ser12Cys,ENST00000427177,NM_001113491.1;SEPT9,5_prime_UTR_variant,,ENST00000431235,;SEPT9,5_prime_UTR_variant,,ENST00000449803,NM_001113492.1;SEPT9,intron_variant,,ENST00000591198,NM_001293695.1;SEPT9,intron_variant,,ENST00000589070,;SEPT9,non_coding_transcript_exon_variant,,ENST00000587237,;SEPT9,3_prime_UTR_variant,,ENST00000590576,;SEPT9,3_prime_UTR_variant,,ENST00000591833,; G ENST00000427177 Transcript missense_variant 161/3821 35/1761 12/586 S/C tCc/tGc 1 1 SEPT9 HGNC HGNC:7323 protein_coding YES CCDS45790.1 ENSP00000391249 Q9UHD8 UPI00001AF955 NM_001113491.1 deleterious_low_confidence(0.03) 2/12 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 77307156 77307156 C G 1 0 0 0 0 1 0 0 0 14347 855 30 4 4 SEPT9 17 77307156 Missense_Mutation SNP C C3N-02423_T 402805 77307156 5950285 375 29505 USP36 0 . GRCh38 17 78803955 78803955 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.2240C>T p.Ser747Leu p.S747L ENST00000542802 16/21 68 63 5 64 64 0 strelka-varscan-mutect USP36,missense_variant,p.Ser747Leu,ENST00000542802,NM_001321291.1;USP36,missense_variant,p.Ser747Leu,ENST00000312010,NM_025090.3;USP36,upstream_gene_variant,,ENST00000592231,;USP36,downstream_gene_variant,,ENST00000449938,;USP36,upstream_gene_variant,,ENST00000588130,;USP36,downstream_gene_variant,,ENST00000588467,;USP36,missense_variant,p.Ser747Leu,ENST00000589225,;USP36,missense_variant,p.Ser747Leu,ENST00000588086,;USP36,upstream_gene_variant,,ENST00000587010,; A ENST00000542802 Transcript missense_variant 2684/6063 2240/3372 747/1123 S/L tCa/tTa COSM3523102,COSM3523103 1 -1 USP36 HGNC HGNC:20062 protein_coding YES CCDS32755.1 ENSP00000441214 Q9P275 A0A024R8V6 UPI00000398BB NM_001321291.1 tolerated(0.13) 16/21 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 205 5 0 0 0 0 0 -11.56796 1 1 1 1 0 A 3 1 99 78803955 78803955 G A 1 0 0 0 0 1 0 0 0 17609 1294 45 3 3 USP36 17 78803955 Missense_Mutation SNP G C3N-02423_T 1496799 78803955 4453486 376 29506 RNF213 0 . GRCh38 17 80339590 80339590 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.5223C>G p.= p.V1741V ENST00000582970 26/68 212 198 14 208 208 0 strelka-varscan-mutect RNF213,synonymous_variant,p.=,ENST00000582970,NM_001256071.2;RNF213,synonymous_variant,p.=,ENST00000508628,;CTD-2047H16.3,upstream_gene_variant,,ENST00000622931,;RNF213,downstream_gene_variant,,ENST00000559070,;RNF213,downstream_gene_variant,,ENST00000571908,; G ENST00000582970 Transcript synonymous_variant 5366/21055 5223/15624 1741/5207 V gtC/gtG 1 1 RNF213 HGNC HGNC:14539 protein_coding YES CCDS58606.1 ENSP00000464087 A0A0A0MTR7 UPI00043788D6 NM_001256071.2 26/68 hmmpanther:PTHR22605:SF5,hmmpanther:PTHR22605 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 80339590 80339590 C G 1 0 0 0 0 0 0 0 1 13656 900 32 4 4 RNF213 17 80339590 Silent SNP C C3N-02423_T 1535635 80339590 2917851 377 29507 FASN 0 . GRCh38 17 82079223 82079223 + Missense_Mutation SNP C C G rs779013746 C3N-02423_T C3N-02423_N C C c.7456G>C p.Glu2486Gln p.E2486Q ENST00000306749 43/43 601 565 36 523 523 0 strelka-varscan-mutect FASN,missense_variant,p.Glu2486Gln,ENST00000306749,NM_004104.4;FASN,missense_variant,p.Glu2484Gln,ENST00000634990,;FASN,3_prime_UTR_variant,,ENST00000636628,;FASN,3_prime_UTR_variant,,ENST00000580382,;FASN,non_coding_transcript_exon_variant,,ENST00000578424,;FASN,non_coding_transcript_exon_variant,,ENST00000584610,; G ENST00000306749 Transcript missense_variant 7675/8565 7456/7536 2486/2511 E/Q Gag/Cag rs779013746 1 -1 FASN HGNC HGNC:3594 protein_coding YES CCDS11801.1 ENSP00000304592 P49327 UPI000013EB82 NM_004104.4 tolerated(0.37) 43/43 Gene3D:3.40.50.1820,Pfam_domain:PF00975,hmmpanther:PTHR11712,hmmpanther:PTHR11712:SF280,Low_complexity_(Seg):seg,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS rs779013746 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 82079223 82079223 C G 1 0 0 0 0 1 0 0 0 5543 864 30 4 4 FASN 17 82079223 Missense_Mutation SNP C C3N-02423_T 1739633 82079223 1178218 378 29508 ANKRD30B 0 . GRCh38 18 14851580 14851580 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.3279G>T p.Met1093Ile p.M1093I ENST00000358984 36/36 69 63 6 114 114 0 varscan-mutect ANKRD30B,missense_variant,p.Met1093Ile,ENST00000358984,NM_001145029.1;ANKRD30B,non_coding_transcript_exon_variant,,ENST00000320584,; T ENST00000358984 Transcript missense_variant 3459/4359 3279/4179 1093/1392 M/I atG/atT 1 1 ANKRD30B HGNC HGNC:24165 protein_coding YES CCDS54182.1 ENSP00000351875 Q9BXX2 UPI0000425FF7 NM_001145029.1 tolerated(0.16) 36/36 Pfam_domain:PF14915,hmmpanther:PTHR24147,hmmpanther:PTHR24147:SF20 MODERATE 1 SNV 1 1 PASS rs755113891 . 0 203 5 2 0 0 0 0 -10.67409 0.9998816 1 1 1 0 T 3 4 99 14851580 14851580 G T 1 0 0 0 0 1 0 0 0 762 1319 46 2 2 ANKRD30B 18 14851580 Missense_Mutation SNP G C3N-02423_T 14851580 65521705 379 29509 TTC39C 0 . GRCh38 18 24080633 24080633 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.509A>G p.Asn170Ser p.N170S ENST00000317571 5/14 147 119 28 158 158 0 strelka-varscan-mutect TTC39C,missense_variant,p.Asn170Ser,ENST00000317571,NM_001135993.1;TTC39C,missense_variant,p.Asn109Ser,ENST00000304621,NM_153211.3;RP11-403A21.3,intron_variant,,ENST00000578443,;TTC39C,non_coding_transcript_exon_variant,,ENST00000578150,; G ENST00000317571 Transcript missense_variant 745/2442 509/1752 170/583 N/S aAt/aGt 1 1 TTC39C HGNC HGNC:26595 protein_coding YES CCDS45839.1 ENSP00000323645 Q8N584 UPI0000EF8875 NM_001135993.1 tolerated(0.07) 5/14 Pfam_domain:PF10300,hmmpanther:PTHR31859,hmmpanther:PTHR31859:SF1 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 24080633 24080633 A G 1 0 0 0 0 1 0 0 0 17218 101 4 5 5 TTC39C 18 24080633 Missense_Mutation SNP A C3N-02423_T 9229053 24080633 56292652 380 29510 ZNF521 0 . GRCh38 18 25224924 25224924 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.2994G>A p.= p.Q998Q ENST00000361524 4/8 248 232 16 272 272 0 strelka-varscan-mutect ZNF521,synonymous_variant,p.=,ENST00000361524,NM_015461.2;ZNF521,synonymous_variant,p.=,ENST00000584787,NM_001308225.1;ZNF521,synonymous_variant,p.=,ENST00000538137,;ZNF521,downstream_gene_variant,,ENST00000577801,;ZNF521,upstream_gene_variant,,ENST00000577775,;ZNF521,downstream_gene_variant,,ENST00000580488,;ZNF521,downstream_gene_variant,,ENST00000579111,;ZNF521,downstream_gene_variant,,ENST00000577720,;ZNF521,downstream_gene_variant,,ENST00000583005,;ZNF521,downstream_gene_variant,,ENST00000581869,;ZNF521,synonymous_variant,p.=,ENST00000399425,;ZNF521,downstream_gene_variant,,ENST00000583398,; T ENST00000361524 Transcript synonymous_variant 3143/4871 2994/3936 998/1311 Q caG/caA 1 -1 ZNF521 HGNC HGNC:24605 protein_coding YES CCDS32806.1 ENSP00000354794 Q96K83 UPI000006F982 NM_015461.2 4/8 hmmpanther:PTHR24402:SF222,hmmpanther:PTHR24402,PROSITE_patterns:PS00028,SMART_domains:SM00355 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 25224924 25224924 C T 1 0 0 0 0 0 0 0 1 18537 912 32 3 3 ZNF521 18 25224924 Silent SNP C C3N-02423_T 1144291 25224924 55148361 381 29511 EPG5 0 . GRCh38 18 45916525 45916525 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.3297C>T p.= p.V1099V ENST00000282041 18/44 119 110 9 113 113 0 strelka-varscan-mutect EPG5,synonymous_variant,p.=,ENST00000282041,NM_020964.2;EPG5,non_coding_transcript_exon_variant,,ENST00000585906,;EPG5,non_coding_transcript_exon_variant,,ENST00000586655,;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,;EPG5,upstream_gene_variant,,ENST00000587884,;EPG5,upstream_gene_variant,,ENST00000592272,;EPG5,upstream_gene_variant,,ENST00000590884,; A ENST00000282041 Transcript synonymous_variant 3332/12633 3297/7740 1099/2579 V gtC/gtT 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 18/44 hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 LOW 1 SNV 2 1 PASS . . 0 207 2 0 0 0 0 0 -17.99559 1 1 1 1 0 A 2 1 99 45916525 45916525 G A 1 0 0 0 0 0 0 0 1 5010 1277 45 3 3 EPG5 18 45916525 Silent SNP G C3N-02423_T 20691601 45916525 34456760 382 29512 EPG5 0 . GRCh38 18 45922532 45922532 + Nonsense_Mutation SNP C C T C3N-02423_T C3N-02423_N C C c.2907G>A p.Trp969Ter p.W969* ENST00000282041 16/44 383 313 70 430 430 0 strelka-varscan-mutect EPG5,stop_gained,p.Trp969Ter,ENST00000282041,NM_020964.2;EPG5,upstream_gene_variant,,ENST00000585906,;EPG5,non_coding_transcript_exon_variant,,ENST00000587974,; T ENST00000282041 Transcript stop_gained 2942/12633 2907/7740 969/2579 W/* tgG/tgA COSM1480334 1 -1 EPG5 HGNC HGNC:29331 protein_coding YES CCDS11926.2 ENSP00000282041 Q9HCE0 UPI00004F6F8A NM_020964.2 16/44 hmmpanther:PTHR31139,hmmpanther:PTHR31139:SF4 1 HIGH 1 SNV 2 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 45922532 45922532 C T 1 0 0 0 0 0 1 0 0 5010 856 30 3 3 EPG5 18 45922532 Nonsense_Mutation SNP C C3N-02423_T 6007 45922532 34450753 383 29513 CTIF 0 . GRCh38 18 48859435 48859435 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1679C>A p.Ser560Ter p.S560* ENST00000382998 13/13 457 416 41 407 406 1 strelka-varscan-mutect CTIF,stop_gained,p.Ser558Ter,ENST00000256413,NM_014772.2;CTIF,stop_gained,p.Ser560Ter,ENST00000382998,NM_001142397.1;CTIF,upstream_gene_variant,,ENST00000592658,;CTIF,upstream_gene_variant,,ENST00000590422,;CTIF,non_coding_transcript_exon_variant,,ENST00000587860,; A ENST00000382998 Transcript stop_gained 1936/4407 1679/1803 560/600 S/* tCg/tAg 1 1 CTIF HGNC HGNC:23925 protein_coding YES CCDS45864.1 ENSP00000372459 O43310 UPI0000074650 NM_001142397.1 13/13 hmmpanther:PTHR23254,Gene3D:1.25.40.180,Pfam_domain:PF02854,SMART_domains:SM00543,Superfamily_domains:SSF48371 HIGH 1 SNV 1 1 PASS rs1428809381 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 48859435 48859435 C A 1 0 0 0 0 0 1 0 0 3819 893 31 1 1 CTIF 18 48859435 Nonsense_Mutation SNP C C3N-02423_T 2936903 48859435 31513850 384 29514 ZADH2 0 . GRCh38 18 75201679 75201679 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.871G>A p.Ala291Thr p.A291T ENST00000322342 2/2 189 172 17 202 202 0 strelka-varscan-mutect ZADH2,missense_variant,p.Ala291Thr,ENST00000322342,NM_175907.4;ZADH2,missense_variant,p.Ala168Thr,ENST00000537114,NM_001306093.1;ZADH2,downstream_gene_variant,,ENST00000582437,;ZADH2,downstream_gene_variant,,ENST00000581620,; T ENST00000322342 Transcript missense_variant 1161/7732 871/1134 291/377 A/T Gcc/Acc 1 -1 ZADH2 HGNC HGNC:28697 protein_coding YES CCDS12008.1 ENSP00000323678 Q8N4Q0 UPI00000350AF NM_175907.4 tolerated(0.5) 2/2 hmmpanther:PTHR11695:SF264,hmmpanther:PTHR11695,Pfam_domain:PF00107,Gene3D:3.40.50.720,SMART_domains:SM00829,Superfamily_domains:SSF51735 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -6.718708 0.9919125 1 1 1 0 T 3 4 99 75201679 75201679 C T 1 0 0 0 0 1 0 0 0 18073 797 28 3 3 ZADH2 18 75201679 Missense_Mutation SNP C C3N-02423_T 26342244 75201679 5171606 385 29515 C2CD4C 0 . GRCh38 19 407549 407549 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.813C>T p.= p.D271D ENST00000332235 2/2 28 23 5 38 38 0 strelka-varscan-mutect C2CD4C,synonymous_variant,p.=,ENST00000332235,NM_001136263.1; A ENST00000332235 Transcript synonymous_variant 1018/3129 813/1266 271/421 D gaC/gaT 1 -1 C2CD4C HGNC HGNC:29417 protein_coding YES CCDS45890.1 ENSP00000328677 Q8TF44 UPI00001C2016 NM_001136263.1 2/2 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF116 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 407549 407549 G A 1 0 0 0 0 0 0 0 1 2028 1136 40 1 1 C2CD4C 19 407549 Silent SNP G C3N-02423_T 407549 58210067 386 29516 SLC39A3 0 . GRCh38 19 2733113 2733113 + Missense_Mutation SNP C C T C3N-02423_T C3N-02423_N C C c.583G>A p.Glu195Lys p.E195K ENST00000269740 3/3 169 152 17 160 160 0 strelka-varscan-mutect SLC39A3,missense_variant,p.Glu195Lys,ENST00000269740,NM_144564.4;SLC39A3,missense_variant,p.Glu195Lys,ENST00000545664,;AC006538.4,intron_variant,,ENST00000586572,;SLC39A3,downstream_gene_variant,,ENST00000455372,NM_213568.1;SLC39A3,downstream_gene_variant,,ENST00000589363,;SLC39A3,downstream_gene_variant,,ENST00000589166,;AC006538.1,upstream_gene_variant,,ENST00000567905,;SLC39A3,downstream_gene_variant,,ENST00000590875,; T ENST00000269740 Transcript missense_variant 913/1502 583/945 195/314 E/K Gag/Aag COSM4727328 1 -1 SLC39A3 HGNC HGNC:17128 protein_coding YES CCDS12093.1 ENSP00000269740 Q9BRY0 UPI00001B216E NM_144564.4 tolerated(0.83) 3/3 Low_complexity_(Seg):seg,hmmpanther:PTHR11040:SF64,hmmpanther:PTHR11040,Pfam_domain:PF02535 1 MODERATE 1 SNV 1 1 1 PASS . . 0 206 0 4 0 0 0 0 -19.99982 0.9998197 1 1 1 0 T 3 4 99 2733113 2733113 C T 1 0 0 0 0 1 0 0 0 14897 864 30 3 3 SLC39A3 19 2733113 Missense_Mutation SNP C C3N-02423_T 2325564 2733113 55884503 387 29517 DAPK3 0 . GRCh38 19 3964772 3964772 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.282G>A p.= p.E94E ENST00000545797 3/9 265 245 20 259 259 0 strelka-varscan-mutect DAPK3,synonymous_variant,p.=,ENST00000545797,NM_001348.2;DAPK3,synonymous_variant,p.=,ENST00000301264,;DAPK3,synonymous_variant,p.=,ENST00000596311,;DAPK3,synonymous_variant,p.=,ENST00000593844,;DAPK3,synonymous_variant,p.=,ENST00000601824,;DAPK3,upstream_gene_variant,,ENST00000594894,;DAPK3,upstream_gene_variant,,ENST00000385000,;DAPK3,upstream_gene_variant,,ENST00000595279,; T ENST00000545797 Transcript synonymous_variant 526/2257 282/1365 94/454 E gaG/gaA 1 -1 DAPK3 HGNC HGNC:2676 protein_coding YES CCDS12116.1 ENSP00000442973 O43293 UPI000006F7FA NM_001348.2 3/9 PROSITE_profiles:PS50011,hmmpanther:PTHR24347,Pfam_domain:PF00069,Gene3D:3.30.200.20,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 3964772 3964772 C T 1 0 0 0 0 0 0 0 1 4038 796 28 3 3 DAPK3 19 3964772 Silent SNP C C3N-02423_T 1231659 3964772 54652844 388 29518 FUT5 0 . GRCh38 19 5867683 5867683 + Missense_Mutation SNP G G A rs561364366 C3N-02423_T C3N-02423_N G G c.43C>T p.Arg15Cys p.R15C ENST00000588525 2/2 321 297 24 322 321 1 strelka-varscan-mutect FUT5,missense_variant,p.Arg15Cys,ENST00000588525,NM_002034.2;FUT5,missense_variant,p.Arg15Cys,ENST00000252675,;AC024592.12,missense_variant,p.Pro147Leu,ENST00000586349,;AC024592.12,missense_variant,p.Pro122Leu,ENST00000585661,;AC024592.12,3_prime_UTR_variant,,ENST00000592091,; A ENST00000588525 Transcript missense_variant 131/1988 43/1125 15/374 R/C Cgc/Tgc rs561364366 1 -1 FUT5 HGNC HGNC:4016 protein_coding YES CCDS12154.1 ENSP00000466880 K7ENC0 UPI000013CD7B NM_002034.2 tolerated(0.18) 2/2 hmmpanther:PTHR11929,hmmpanther:PTHR11929:SF150,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs561364366 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 5867683 5867683 G A 1 0 0 0 0 1 0 0 0 5979 1116 39 1 1 FUT5 19 5867683 Missense_Mutation SNP G C3N-02423_T 1902911 5867683 52749933 389 29519 MUC16 0 . GRCh38 19 8898986 8898986 + Missense_Mutation SNP G G C rs747610660 C3N-02423_T C3N-02423_N G G c.39064C>G p.Leu13022Val p.L13022V ENST00000397910 39/84 173 164 9 210 210 0 varscan-mutect MUC16,missense_variant,p.Leu13022Val,ENST00000397910,NM_024690.2;MUC16,upstream_gene_variant,,ENST00000599436,;MUC16,upstream_gene_variant,,ENST00000601404,; C ENST00000397910 Transcript missense_variant 39268/43816 39064/43524 13022/14507 L/V Ctg/Gtg rs747610660,COSM715537,COSM715538 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 39/84 PROSITE_profiles:PS50024,hmmpanther:PTHR14672,Gene3D:1ivzA00,Pfam_domain:PF01390,SMART_domains:SM00200,Superfamily_domains:0047452 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs747610660 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 8898986 8898986 G C 1 0 0 0 0 1 0 0 0 9972 933 33 4 4 MUC16 19 8898986 Missense_Mutation SNP G C3N-02423_T 3031303 8898986 49718630 390 29520 MUC16 0 . GRCh38 19 8935939 8935939 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.35016C>T p.= p.F11672F ENST00000397910 5/84 232 210 22 248 248 0 strelka-varscan-mutect MUC16,synonymous_variant,p.=,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript synonymous_variant 35220/43816 35016/43524 11672/14507 F ttC/ttT 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 8935939 8935939 G A 1 0 0 0 0 0 0 0 1 9972 1281 45 3 3 MUC16 19 8935939 Silent SNP G C3N-02423_T 36953 8935939 49681677 391 29521 MUC16 0 . GRCh38 19 8936789 8936789 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.34166C>T p.Ser11389Leu p.S11389L ENST00000397910 5/84 162 146 16 219 219 0 strelka-varscan-mutect MUC16,missense_variant,p.Ser11389Leu,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 34370/43816 34166/43524 11389/14507 S/L tCa/tTa COSM4768342,COSM4768343 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 8936789 8936789 G A 1 0 0 0 0 1 0 0 0 9972 1294 45 3 3 MUC16 19 8936789 Missense_Mutation SNP G C3N-02423_T 850 8936789 49680827 392 29522 MUC16 0 . GRCh38 19 8938586 8938586 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.32369C>T p.Ser10790Leu p.S10790L ENST00000397910 5/84 137 124 13 197 197 0 strelka-mutect MUC16,missense_variant,p.Ser10790Leu,ENST00000397910,NM_024690.2; A ENST00000397910 Transcript missense_variant 32573/43816 32369/43524 10790/14507 S/L tCa/tTa COSM4849067,COSM4849068 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 5/84 1,1 MODERATE 1 SNV 5 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 8938586 8938586 G A 1 0 0 0 0 1 0 0 0 9972 1294 45 3 3 MUC16 19 8938586 Missense_Mutation SNP G C3N-02423_T 1797 8938586 49679030 393 29523 COL5A3 0 . GRCh38 19 9996230 9996230 + Frame_Shift_Del DEL C C - novel C3N-02423_T C3N-02423_N C C c.1455delG p.Leu486SerfsTer16 p.L486Sfs*16 ENST00000264828 14/67 21 16 5 43 43 0 sindel-pindel COL5A3,frameshift_variant,p.Leu486SerfsTer16,ENST00000264828,NM_015719.3;CTD-2553C6.1,non_coding_transcript_exon_variant,,ENST00000592332,; - ENST00000264828 Transcript frameshift_variant 1541/6174 1455/5238 485/1745 G/X ggG/gg 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 14/67 Pfam_domain:PF01391 HIGH 1 deletion 1 1 PASS . . 1 203 5 0 0 0 0 0 -14.75639 1 1 1 1 0 - 7 5 99 9996230 9996230 C - 1 0 1 0 1 0 0 0 0 3487 726 26 0 0 COL5A3 19 9996230 Frame_Shift_Del DEL C C3N-02423_T 1057644 9996230 48621386 394 29524 CDC37 0 . GRCh38 19 10403431 10403431 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.49G>C p.Asp17His p.D17H ENST00000222005 1/8 285 269 16 232 232 0 strelka-mutect CDC37,missense_variant,p.Asp17His,ENST00000222005,NM_007065.3;CDC37,missense_variant,p.Asp17His,ENST00000593124,;CDC37,missense_variant,p.Asp17His,ENST00000589629,;CDC37,downstream_gene_variant,,ENST00000408639,;CDC37,missense_variant,p.Asp17His,ENST00000588869,;CDC37,non_coding_transcript_exon_variant,,ENST00000591248,; G ENST00000222005 Transcript missense_variant 103/1608 49/1137 17/378 D/H Gac/Cac 1 -1 CDC37 HGNC HGNC:1735 protein_coding YES CCDS12237.1 ENSP00000222005 Q16543 A0A024R7B7 UPI000012723D NM_007065.3 deleterious(0) 1/8 hmmpanther:PTHR12800:SF3,hmmpanther:PTHR12800,Pfam_domain:PF03234,SMART_domains:SM01071 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 10403431 10403431 C G 1 0 0 0 0 1 0 0 0 2771 913 32 4 4 CDC37 19 10403431 Missense_Mutation SNP C C3N-02423_T 407201 10403431 48214185 395 29525 C19orf43 0 . GRCh38 19 12734343 12734343 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.315G>T p.Arg105Ser p.R105S ENST00000242784 1/3 30 26 4 39 39 0 strelka-mutect C19orf43,missense_variant,p.Arg105Ser,ENST00000242784,NM_024038.2;C19orf43,missense_variant,p.Arg105Ser,ENST00000588213,;C19orf43,missense_variant,p.Arg105Ser,ENST00000592273,;ASNA1,upstream_gene_variant,,ENST00000591090,;ASNA1,upstream_gene_variant,,ENST00000357332,NM_004317.2;ASNA1,upstream_gene_variant,,ENST00000611688,;ASNA1,upstream_gene_variant,,ENST00000586561,;C19orf43,missense_variant,p.Arg105Ser,ENST00000591254,;C19orf43,upstream_gene_variant,,ENST00000589590,;ASNA1,upstream_gene_variant,,ENST00000590633,; A ENST00000242784 Transcript missense_variant 433/970 315/531 105/176 R/S agG/agT 1 -1 C19orf43 HGNC HGNC:28424 protein_coding YES CCDS12279.1 ENSP00000242784 Q9BQ61 UPI00000701FA NM_024038.2 tolerated(0.6) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR34753:SF1,hmmpanther:PTHR34753 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -11.80038 1 1 1 1 0 A 3 1 99 12734343 12734343 C A 1 0 0 0 0 1 0 0 0 1910 854 30 2 2 C19orf43 19 12734343 Missense_Mutation SNP C C3N-02423_T 2330912 12734343 45883273 396 29526 C19orf43 0 . GRCh38 19 12734633 12734633 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.25G>A p.Glu9Lys p.E9K ENST00000242784 1/3 162 152 10 142 142 0 strelka-varscan-mutect C19orf43,missense_variant,p.Glu9Lys,ENST00000242784,NM_024038.2;C19orf43,missense_variant,p.Glu9Lys,ENST00000588213,;C19orf43,missense_variant,p.Glu9Lys,ENST00000592273,;ASNA1,upstream_gene_variant,,ENST00000591090,;ASNA1,upstream_gene_variant,,ENST00000357332,NM_004317.2;ASNA1,upstream_gene_variant,,ENST00000611688,;ASNA1,upstream_gene_variant,,ENST00000586561,;C19orf43,missense_variant,p.Glu9Lys,ENST00000591254,;C19orf43,upstream_gene_variant,,ENST00000589590,;ASNA1,upstream_gene_variant,,ENST00000590633,; T ENST00000242784 Transcript missense_variant 143/970 25/531 9/176 E/K Gag/Aag 1 -1 C19orf43 HGNC HGNC:28424 protein_coding YES CCDS12279.1 ENSP00000242784 Q9BQ61 UPI00000701FA NM_024038.2 deleterious_low_confidence(0) 1/3 Low_complexity_(Seg):seg,hmmpanther:PTHR34753:SF1,hmmpanther:PTHR34753 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 12734633 12734633 C T 1 0 0 0 0 1 0 0 0 1910 864 30 3 3 C19orf43 19 12734633 Missense_Mutation SNP C C3N-02423_T 290 12734633 45882983 397 29527 DDX39A 0 . GRCh38 19 14413119 14413119 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.102C>T p.= p.I34I ENST00000242776 2/11 379 354 25 370 370 0 strelka-varscan-mutect DDX39A,synonymous_variant,p.=,ENST00000242776,NM_005804.3;DDX39A,synonymous_variant,p.=,ENST00000454233,;DDX39A,synonymous_variant,p.=,ENST00000589675,;DDX39A,synonymous_variant,p.=,ENST00000586993,;DDX39A,synonymous_variant,p.=,ENST00000590315,;DDX39A,synonymous_variant,p.=,ENST00000590239,;DDX39A,synonymous_variant,p.=,ENST00000590696,;DDX39A,synonymous_variant,p.=,ENST00000591275,;ADGRE5,downstream_gene_variant,,ENST00000242786,NM_078481.3;ADGRE5,downstream_gene_variant,,ENST00000357355,NM_001025160.2;ADGRE5,downstream_gene_variant,,ENST00000358600,NM_001784.4;CTC-548K16.5,upstream_gene_variant,,ENST00000590626,;DDX39A,non_coding_transcript_exon_variant,,ENST00000593008,;DDX39A,synonymous_variant,p.=,ENST00000588692,;DDX39A,synonymous_variant,p.=,ENST00000324340,;DDX39A,non_coding_transcript_exon_variant,,ENST00000589318,;DDX39A,non_coding_transcript_exon_variant,,ENST00000588542,;DDX39A,non_coding_transcript_exon_variant,,ENST00000586558,;DDX39A,non_coding_transcript_exon_variant,,ENST00000590260,;DDX39A,non_coding_transcript_exon_variant,,ENST00000592632,;DDX39A,upstream_gene_variant,,ENST00000587730,;DDX39A,upstream_gene_variant,,ENST00000592391,;DDX39A,upstream_gene_variant,,ENST00000592927,;DDX39A,upstream_gene_variant,,ENST00000593026,;DDX39A,upstream_gene_variant,,ENST00000590556,; A ENST00000242776 Transcript synonymous_variant 204/1471 102/1284 34/427 I atC/atT 1 -1 DDX39A HGNC HGNC:17821 protein_coding YES CCDS12308.1 ENSP00000242776 O00148 UPI00000713A1 NM_005804.3 2/11 Gene3D:3.40.50.300,hmmpanther:PTHR24031,hmmpanther:PTHR24031:SF212 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 14413119 14413119 G A 1 0 0 0 0 0 0 0 1 4159 1280 45 3 3 DDX39A 19 14413119 Silent SNP G C3N-02423_T 1678486 14413119 44204497 398 29528 OR7A10 0 . GRCh38 19 14841838 14841838 + Missense_Mutation SNP G G A C3N-02423_T C3N-02423_N G G c.40C>T p.Leu14Phe p.L14F ENST00000248058 1/1 120 111 9 126 126 0 strelka-varscan-mutect OR7A10,missense_variant,p.Leu14Phe,ENST00000248058,NM_001005190.1; A ENST00000248058 Transcript missense_variant 40/930 40/930 14/309 L/F Ctc/Ttc COSM3822140 1 -1 OR7A10 HGNC HGNC:8356 protein_coding YES CCDS32936.1 ENSP00000248058 O76100 A0A126GVC8 UPI0000130B4B NM_001005190.1 deleterious_low_confidence(0.01) 1/1 hmmpanther:PTHR26451,hmmpanther:PTHR26451:SF408,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -17.7841 1 1 1 1 0 A 3 1 99 14841838 14841838 G A 1 0 0 0 0 1 0 0 0 11284 942 33 3 3 OR7A10 19 14841838 Missense_Mutation SNP G C3N-02423_T 428719 14841838 43775778 399 29529 UNC13A 0 . GRCh38 19 17627567 17627567 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.3862G>C p.Glu1288Gln p.E1288Q ENST00000519716 33/44 168 159 9 167 167 0 strelka-varscan-mutect UNC13A,missense_variant,p.Glu1288Gln,ENST00000519716,NM_001080421.2;UNC13A,missense_variant,p.Glu1288Gln,ENST00000551649,;UNC13A,missense_variant,p.Glu1288Gln,ENST00000552293,;UNC13A,missense_variant,p.Glu1286Gln,ENST00000550896,;CTD-3149D2.2,downstream_gene_variant,,ENST00000624803,;UNC13A,non_coding_transcript_exon_variant,,ENST00000601528,; G ENST00000519716 Transcript missense_variant 3862/9838 3862/5112 1288/1703 E/Q Gag/Cag 1 -1 UNC13A HGNC HGNC:23150 protein_coding YES CCDS46013.2 ENSP00000429562 Q9UPW8 UPI00006C19A7 NM_001080421.2 deleterious(0.03) 33/44 hmmpanther:PTHR10480 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 17627567 17627567 C G 1 0 0 0 0 1 0 0 0 17508 864 30 4 4 UNC13A 19 17627567 Missense_Mutation SNP C C3N-02423_T 2785729 17627567 40990049 400 29530 ZNF730 0 . GRCh38 19 23145701 23145701 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.657T>A p.His219Gln p.H219Q ENST00000597761 4/4 161 132 29 201 201 0 strelka-varscan-mutect ZNF730,missense_variant,p.His219Gln,ENST00000597761,NM_001277403.1;ZNF730,downstream_gene_variant,,ENST00000599195,; A ENST00000597761 Transcript missense_variant 856/2374 657/1512 219/503 H/Q caT/caA 1 1 ZNF730 HGNC HGNC:32470 protein_coding YES CCDS59371.1 ENSP00000472959 Q6ZMV8 UPI000035E7F4 NM_001277403.1 deleterious(0) 4/4 Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 23145701 23145701 T A 1 0 0 0 0 1 0 0 0 18704 1403 49 4 4 ZNF730 19 23145701 Missense_Mutation SNP T C3N-02423_T 5518134 23145701 35471915 401 29531 FFAR3 0 . GRCh38 19 35359812 35359812 + Nonsense_Mutation SNP G G T C3N-02423_T C3N-02423_N G G c.922G>T p.Glu308Ter p.E308* ENST00000327809 2/2 229 215 14 266 265 1 varscan-mutect FFAR3,stop_gained,p.Glu308Ter,ENST00000327809,NM_005304.3;FFAR3,stop_gained,p.Glu308Ter,ENST00000594310,; T ENST00000327809 Transcript stop_gained 1123/1796 922/1041 308/346 E/* Gag/Tag COSM994972 1 1 FFAR3 HGNC HGNC:4499 protein_coding YES CCDS12459.1 ENSP00000328230 O14843 A0A0K0PUW7 UPI0000001C3F NM_005304.3 2/2 hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF40 1 HIGH 1 SNV 1 1 1 PASS rs1414980010 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 35359812 35359812 G T 1 0 0 0 0 0 1 0 0 5692 1175 41 2 2 FFAR3 19 35359812 Nonsense_Mutation SNP G C3N-02423_T 12214111 35359812 23257804 402 29532 PSENEN 0 . GRCh38 19 35746741 35746741 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.200G>T p.Trp67Leu p.W67L ENST00000587708 4/4 471 442 29 514 513 1 strelka-varscan-mutect PSENEN,missense_variant,p.Trp67Leu,ENST00000587708,;PSENEN,missense_variant,p.Trp67Leu,ENST00000222266,NM_001281532.1,NM_172341.2;PSENEN,3_prime_UTR_variant,,ENST00000591949,;IGFLR1,upstream_gene_variant,,ENST00000246532,;IGFLR1,upstream_gene_variant,,ENST00000592537,NM_024660.2;LIN37,upstream_gene_variant,,ENST00000301159,NM_019104.2;U2AF1L4,upstream_gene_variant,,ENST00000412391,;U2AF1L4,upstream_gene_variant,,ENST00000378975,NM_001040425.2;IGFLR1,upstream_gene_variant,,ENST00000588992,;U2AF1L4,upstream_gene_variant,,ENST00000292879,NM_144987.3;LIN37,upstream_gene_variant,,ENST00000587751,;U2AF1L4,upstream_gene_variant,,ENST00000587886,;AC002398.11,downstream_gene_variant,,ENST00000591091,;AC002398.11,downstream_gene_variant,,ENST00000585365,;U2AF1L4,upstream_gene_variant,,ENST00000588100,;LIN37,upstream_gene_variant,,ENST00000591076,;AC002398.9,intron_variant,,ENST00000591613,;U2AF1L4,upstream_gene_variant,,ENST00000588892,;U2AF1L4,upstream_gene_variant,,ENST00000588980,;U2AF1L4,upstream_gene_variant,,ENST00000586476,;AD000671.6,upstream_gene_variant,,ENST00000589807,;U2AF1L4,upstream_gene_variant,,ENST00000590135,;LIN37,upstream_gene_variant,,ENST00000595455,;LIN37,upstream_gene_variant,,ENST00000587108,;LIN37,upstream_gene_variant,,ENST00000590706,;U2AF1L4,upstream_gene_variant,,ENST00000585554,;IGFLR1,upstream_gene_variant,,ENST00000588018,;U2AF1L4,upstream_gene_variant,,ENST00000587987,;U2AF1L4,upstream_gene_variant,,ENST00000592913,;U2AF1L4,upstream_gene_variant,,ENST00000591855,;U2AF1L4,upstream_gene_variant,,ENST00000591084,;U2AF1L4,upstream_gene_variant,,ENST00000594792,;U2AF1L4,upstream_gene_variant,,ENST00000585771,;U2AF1L4,upstream_gene_variant,,ENST00000591057,;LIN37,upstream_gene_variant,,ENST00000592871,;IGFLR1,upstream_gene_variant,,ENST00000589175,;U2AF1L4,upstream_gene_variant,,ENST00000589429,;U2AF1L4,upstream_gene_variant,,ENST00000600296,;U2AF1L4,upstream_gene_variant,,ENST00000601236,;U2AF1L4,upstream_gene_variant,,ENST00000590650,; T ENST00000587708 Transcript missense_variant 883/1661 200/306 67/101 W/L tGg/tTg 1 1 PSENEN HGNC HGNC:30100 protein_coding YES CCDS12474.1 ENSP00000468411 Q9NZ42 UPI000006FFC1 deleterious(0) 4/4 Pfam_domain:PF10251,hmmpanther:PTHR16318,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 35746741 35746741 G T 1 0 0 0 0 1 0 0 0 12803 1357 47 2 2 PSENEN 19 35746741 Missense_Mutation SNP G C3N-02423_T 386929 35746741 22870875 403 29533 APLP1 0 . GRCh38 19 35874660 35874660 + Nonsense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1213C>T p.Gln405Ter p.Q405* ENST00000221891 9/17 124 109 15 119 119 0 strelka-varscan-mutect APLP1,stop_gained,p.Gln405Ter,ENST00000221891,NM_005166.3,NM_001024807.1;APLP1,stop_gained,p.Gln366Ter,ENST00000537454,;APLP1,stop_gained,p.Gln399Ter,ENST00000586861,;APLP1,stop_gained,p.Gln52Ter,ENST00000587274,;APLP1,intron_variant,,ENST00000588808,;APLP1,downstream_gene_variant,,ENST00000592316,;APLP1,downstream_gene_variant,,ENST00000589743,;APLP1,splice_region_variant,,ENST00000589298,;APLP1,upstream_gene_variant,,ENST00000591165,;APLP1,splice_region_variant,,ENST00000590561,;APLP1,upstream_gene_variant,,ENST00000590926,; T ENST00000221891 Transcript stop_gained,splice_region_variant 1405/2495 1213/1956 405/651 Q/* Cag/Tag 1 1 APLP1 HGNC HGNC:597 protein_coding YES CCDS32997.1 ENSP00000221891 P51693 UPI000020215E NM_005166.3,NM_001024807.1 9/17 hmmpanther:PTHR23103,Pfam_domain:PF12925,Superfamily_domains:0043391 HIGH 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 35874660 35874660 C T 1 0 0 0 0 0 1 0 0 900 840 29 3 3 APLP1 19 35874660 Nonsense_Mutation SNP C C3N-02423_T 127919 35874660 22742956 404 29534 ZNF565 0 . GRCh38 19 36183168 36183168 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.798G>T p.= p.L266L ENST00000304116 5/5 217 199 18 236 236 0 strelka-varscan-mutect ZNF565,synonymous_variant,p.=,ENST00000355114,;ZNF565,synonymous_variant,p.=,ENST00000304116,NM_152477.4;ZNF565,synonymous_variant,p.=,ENST00000392173,NM_001042474.2;ZNF565,synonymous_variant,p.=,ENST00000591473,; A ENST00000304116 Transcript synonymous_variant 915/2023 798/1500 266/499 L ctG/ctT 1 -1 ZNF565 HGNC HGNC:26726 protein_coding YES CCDS12491.1 ENSP00000306869 Q8N9K5 UPI000006E728 NM_152477.4 5/5 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF70,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 36183168 36183168 C A 1 0 0 0 0 0 0 0 1 18570 813 29 2 2 ZNF565 19 36183168 Silent SNP C C3N-02423_T 308508 36183168 22434448 405 29535 MAP4K1 0 . GRCh38 19 38609940 38609940 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.896C>T p.Ser299Phe p.S299F ENST00000591517 12/32 164 148 16 176 176 0 strelka-mutect MAP4K1,missense_variant,p.Ser299Phe,ENST00000591517,NM_007181.5;MAP4K1,missense_variant,p.Ser295Phe,ENST00000589130,;MAP4K1,missense_variant,p.Ser299Phe,ENST00000396857,NM_001042600.2;MAP4K1,missense_variant,p.Ser299Phe,ENST00000586296,;MAP4K1,upstream_gene_variant,,ENST00000591921,;MAP4K1,non_coding_transcript_exon_variant,,ENST00000589002,;MAP4K1,3_prime_UTR_variant,,ENST00000585583,;MAP4K1,downstream_gene_variant,,ENST00000591707,;MAP4K1,downstream_gene_variant,,ENST00000592888,;MAP4K1,downstream_gene_variant,,ENST00000592225,;MAP4K1,downstream_gene_variant,,ENST00000588083,; A ENST00000591517 Transcript missense_variant 925/2700 896/2502 299/833 S/F tCc/tTc 1 -1 MAP4K1 HGNC HGNC:6863 protein_coding YES CCDS59385.1 ENSP00000465039 Q92918 UPI00000747ED NM_007181.5 tolerated(0.7) 12/32 hmmpanther:PTHR24361:SF88,hmmpanther:PTHR24361,PIRSF_domain:PIRSF038172 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 38609940 38609940 G A 1 0 0 0 0 1 0 0 0 9183 1174 41 3 3 MAP4K1 19 38609940 Missense_Mutation SNP G C3N-02423_T 2426772 38609940 20007676 406 29536 PLEKHG2 0 . GRCh38 19 39425067 39425067 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.3934C>A p.Pro1312Thr p.P1312T ENST00000425673 19/19 41 29 12 60 60 0 strelka-varscan-mutect PLEKHG2,missense_variant,p.Pro1312Thr,ENST00000425673,NM_022835.2;PLEKHG2,missense_variant,p.Pro1180Thr,ENST00000205135,;PLEKHG2,intron_variant,,ENST00000458508,;PLEKHG2,intron_variant,,ENST00000409797,;PLEKHG2,intron_variant,,ENST00000596339,;PLEKHG2,intron_variant,,ENST00000600210,;PLEKHG2,intron_variant,,ENST00000596443,;PLEKHG2,intron_variant,,ENST00000598238,;PLEKHG2,intron_variant,,ENST00000594124,;PLEKHG2,intron_variant,,ENST00000594161,;PLEKHG2,downstream_gene_variant,,ENST00000474449,;PLEKHG2,downstream_gene_variant,,ENST00000478523,;PLEKHG2,downstream_gene_variant,,ENST00000594307,; A ENST00000425673 Transcript missense_variant 4784/8132 3934/4161 1312/1386 P/T Ccc/Acc 1 1 PLEKHG2 HGNC HGNC:29515 protein_coding YES CCDS33022.2 ENSP00000392906 Q9H7P9 UPI00001C2028 NM_022835.2 deleterious_low_confidence(0) 19/19 hmmpanther:PTHR22826,hmmpanther:PTHR22826:SF135,Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 39425067 39425067 C A 1 0 0 0 0 1 0 0 0 12162 855 30 2 2 PLEKHG2 19 39425067 Missense_Mutation SNP C C3N-02423_T 815127 39425067 19192549 407 29537 FCGBP 0 . GRCh38 19 39879843 39879843 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.8580G>T p.Gln2860His p.Q2860H ENST00000616721 19/28 190 178 12 208 208 0 varscan-mutect FCGBP,missense_variant,p.Gln2860His,ENST00000616721,NM_003890.2; A ENST00000616721 Transcript missense_variant 8588/12787 8580/12615 2860/4204 Q/H caG/caT 1 -1 FCGBP HGNC HGNC:13572 protein_coding YES ENSP00000481056 A0A087WXI2 UPI0004620B9E NM_003890.2 tolerated(0.11) 19/28 SMART_domains:SM00274 MODERATE 1 SNV 1 1 PASS rs1303575880 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 39879843 39879843 C A 1 0 0 0 0 1 0 0 0 5641 680 24 2 2 FCGBP 19 39879843 Missense_Mutation SNP C C3N-02423_T 454776 39879843 18737773 408 29538 NUMBL 0 . GRCh38 19 40669948 40669948 + Missense_Mutation SNP G G C novel C3N-02423_T C3N-02423_N G G c.1109C>G p.Ser370Cys p.S370C ENST00000252891 9/10 155 139 16 179 179 0 strelka-varscan-mutect NUMBL,missense_variant,p.Ser370Cys,ENST00000252891,NM_004756.4;NUMBL,missense_variant,p.Ser329Cys,ENST00000598779,NM_001289979.1;NUMBL,missense_variant,p.Ser329Cys,ENST00000540131,NM_001289980.1;NUMBL,downstream_gene_variant,,ENST00000598773,;NUMBL,downstream_gene_variant,,ENST00000600967,;NUMBL,downstream_gene_variant,,ENST00000593367,; C ENST00000252891 Transcript missense_variant 1277/3561 1109/1830 370/609 S/C tCt/tGt 1 -1 NUMBL HGNC HGNC:8061 protein_coding YES CCDS12561.1 ENSP00000252891 Q9Y6R0 UPI000003032B NM_004756.4 deleterious(0.01) 9/10 Pfam_domain:PF06311,PIRSF_domain:PIRSF017607,hmmpanther:PTHR11232,hmmpanther:PTHR11232:SF32,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99921 0.9999999 1 1 1 0 C 3 2 99 40669948 40669948 G C 1 0 0 0 0 1 0 0 0 10817 942 33 4 4 NUMBL 19 40669948 Missense_Mutation SNP G C3N-02423_T 790105 40669948 17947668 409 29539 CEACAM20 0 . GRCh38 19 44513274 44513274 + Missense_Mutation SNP G G A rs779003662 C3N-02423_T C3N-02423_N G G c.1325C>T p.Ser442Phe p.S442F ENST00000614924 7/12 90 82 8 95 95 0 strelka-varscan-mutect CEACAM20,missense_variant,p.Ser442Phe,ENST00000621342,;CEACAM20,missense_variant,p.Ser442Phe,ENST00000617951,;CEACAM20,missense_variant,p.Ser442Phe,ENST00000614924,NM_001102597.2;CEACAM20,missense_variant,p.Ser442Phe,ENST00000611497,NM_001102600.2;CEACAM20,missense_variant,p.Ser349Phe,ENST00000614577,NM_001102599.2;CEACAM20,missense_variant,p.Ser349Phe,ENST00000620096,NM_001102598.2; A ENST00000614924 Transcript missense_variant 1341/1809 1325/1791 442/596 S/F tCc/tTc rs779003662,COSM4464260 1 -1 CEACAM20 HGNC HGNC:24879 protein_coding YES CCDS74393.1 ENSP00000481937 A0A087WYM6 UPI0003EC04B5 NM_001102597.2 deleterious(0) 7/12 Low_complexity_(Seg):seg 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs779003662 . 0 207 3 0 0 0 0 0 -16.98255 1 1 1 1 0 A 3 1 99 44513274 44513274 G A 1 0 0 0 0 1 0 0 0 2897 1174 41 3 3 CEACAM20 19 44513274 Missense_Mutation SNP G C3N-02423_T 3843326 44513274 14104342 410 29540 CD3EAP 0 . GRCh38 19 45407145 45407145 + Nonsense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.80C>A p.Ser27Ter p.S27* ENST00000589804 2/3 130 122 8 170 170 0 varscan-mutect CD3EAP,stop_gained,p.Ser25Ter,ENST00000309424,NM_012099.1;CD3EAP,stop_gained,p.Ser27Ter,ENST00000589804,NM_001297590.1;CD3EAP,5_prime_UTR_variant,,ENST00000592852,;CD3EAP,intron_variant,,ENST00000590794,;ERCC1,downstream_gene_variant,,ENST00000300853,NM_001983.3;ERCC1,downstream_gene_variant,,ENST00000423698,;PPP1R13L,upstream_gene_variant,,ENST00000418234,NM_001142502.1;PPP1R13L,upstream_gene_variant,,ENST00000360957,NM_006663.3;ERCC1,downstream_gene_variant,,ENST00000589165,;ERCC1,downstream_gene_variant,,ENST00000340192,NM_001166049.1;ERCC1,downstream_gene_variant,,ENST00000591636,;PPP1R13L,upstream_gene_variant,,ENST00000593226,;PPP1R13L,upstream_gene_variant,,ENST00000592134,;ERCC1,downstream_gene_variant,,ENST00000590701,;ERCC1,downstream_gene_variant,,ENST00000588738,;PPP1R13L,upstream_gene_variant,,ENST00000585905,; A ENST00000589804 Transcript stop_gained 86/1830 80/1539 27/512 S/* tCa/tAa 1 1 CD3EAP HGNC HGNC:24219 protein_coding YES CCDS74397.1 ENSP00000465099 O15446 UPI000006DE66 NM_001297590.1 2/3 hmmpanther:PTHR15484,hmmpanther:PTHR15484:SF8 HIGH 1 SNV 1 1 PASS rs771308001 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 99 45407145 45407145 C A 1 0 0 0 0 0 1 0 0 2716 838 29 2 2 CD3EAP 19 45407145 Nonsense_Mutation SNP C C3N-02423_T 893871 45407145 13210471 411 29541 VASP 0 . GRCh38 19 45525966 45525966 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1068G>A p.= p.K356K ENST00000245932 12/13 178 161 17 167 167 0 strelka-mutect VASP,synonymous_variant,p.=,ENST00000245932,NM_003370.3;OPA3,downstream_gene_variant,,ENST00000323060,NM_001017989.2;VASP,downstream_gene_variant,,ENST00000592139,;VASP,downstream_gene_variant,,ENST00000590603,;VASP,downstream_gene_variant,,ENST00000586619,;VASP,3_prime_UTR_variant,,ENST00000586014,;VASP,3_prime_UTR_variant,,ENST00000588482,;VASP,non_coding_transcript_exon_variant,,ENST00000588273,;VASP,non_coding_transcript_exon_variant,,ENST00000587444,;VASP,downstream_gene_variant,,ENST00000588463,;VASP,downstream_gene_variant,,ENST00000590459,; A ENST00000245932 Transcript synonymous_variant 1424/2305 1068/1143 356/380 K aaG/aaA 1 1 VASP HGNC HGNC:12652 protein_coding YES CCDS33051.1 ENSP00000245932 P50552 A0A024R0V4 UPI0000001C69 NM_003370.3 12/13 Superfamily_domains:0053530,Coiled-coils_(Ncoils):Coil,Pfam_domain:PF08776,PIRSF_domain:PIRSF038010,hmmpanther:PTHR11202,hmmpanther:PTHR11202:SF12,Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99977 0.9999998 1 1 1 0 A 2 1 99 45525966 45525966 G A 1 0 0 0 0 0 0 0 1 17673 933 33 3 3 VASP 19 45525966 Silent SNP G C3N-02423_T 118821 45525966 13091650 412 29542 HIF3A 0 . GRCh38 19 46329272 46329272 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.1506C>T p.= p.L502L ENST00000377670 12/15 136 128 8 132 132 0 strelka-varscan-mutect HIF3A,synonymous_variant,p.=,ENST00000377670,NM_152795.3;HIF3A,synonymous_variant,p.=,ENST00000300862,NM_152794.3;HIF3A,synonymous_variant,p.=,ENST00000244303,NM_022462.4;HIF3A,synonymous_variant,p.=,ENST00000600383,;HIF3A,intron_variant,,ENST00000472815,NM_152796.2;AC007193.10,intron_variant,,ENST00000596807,;HIF3A,non_coding_transcript_exon_variant,,ENST00000244302,;HIF3A,non_coding_transcript_exon_variant,,ENST00000291300,;HIF3A,non_coding_transcript_exon_variant,,ENST00000529542,;HIF3A,downstream_gene_variant,,ENST00000528563,; T ENST00000377670 Transcript synonymous_variant 1537/5852 1506/2010 502/669 L ctC/ctT 1 1 HIF3A HGNC HGNC:15825 protein_coding YES CCDS12681.2 ENSP00000366898 Q9Y2N7 UPI00002026E2 NM_152795.3 12/15 hmmpanther:PTHR23043:SF18,hmmpanther:PTHR23043,Pfam_domain:PF11413 LOW 1 SNV 1 1 PASS . . 0 205 2 3 0 0 0 0 -11.14688 0.9997347 1 1 1 0 T 2 4 99 46329272 46329272 C T 1 0 0 0 0 0 0 0 1 6990 813 29 3 3 HIF3A 19 46329272 Silent SNP C C3N-02423_T 803306 46329272 12288344 413 29543 NKG7 0 . GRCh38 19 51371815 51371815 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.460C>T p.His154Tyr p.H154Y ENST00000221978 4/4 56 52 4 72 72 0 varscan-mutect NKG7,missense_variant,p.His154Tyr,ENST00000221978,NM_005601.3;NKG7,missense_variant,p.His74Tyr,ENST00000600427,;NKG7,missense_variant,p.His61Tyr,ENST00000593572,;NKG7,missense_variant,p.His78Tyr,ENST00000595157,;NKG7,3_prime_UTR_variant,,ENST00000595217,;CLDND2,upstream_gene_variant,,ENST00000291715,NM_152353.2;CLDND2,upstream_gene_variant,,ENST00000601435,;CLDND2,upstream_gene_variant,,ENST00000593841,;CTD-2616J11.11,upstream_gene_variant,,ENST00000600067,; A ENST00000221978 Transcript missense_variant 640/843 460/498 154/165 H/Y Cac/Tac 1 -1 NKG7 HGNC HGNC:7830 protein_coding YES CCDS12830.1 ENSP00000221978 Q16617 UPI00001301FE NM_005601.3 tolerated(0.26) 4/4 hmmpanther:PTHR10671,hmmpanther:PTHR10671:SF34 MODERATE 1 SNV 1 1 PASS rs1190666154 . 0 203 6 0 0 0 0 0 -9.94097 0.9999997 1 1 1 0 A 3 1 99 51371815 51371815 G A 1 0 0 0 0 1 0 0 0 10478 1290 45 3 3 NKG7 19 51371815 Missense_Mutation SNP G C3N-02423_T 5042543 51371815 7245801 414 29544 NLRP2 0 . GRCh38 19 54982616 54982616 + Silent SNP G G A C3N-02423_T C3N-02423_N G G c.918G>A p.= p.G306G ENST00000543010 6/13 207 170 37 258 258 0 strelka-varscan-mutect NLRP2,synonymous_variant,p.=,ENST00000543010,NM_001174081.1;NLRP2,synonymous_variant,p.=,ENST00000448584,NM_017852.3;NLRP2,synonymous_variant,p.=,ENST00000537859,NM_001174082.1;NLRP2,synonymous_variant,p.=,ENST00000263437,;NLRP2,synonymous_variant,p.=,ENST00000339757,;NLRP2,synonymous_variant,p.=,ENST00000391721,;NLRP2,synonymous_variant,p.=,ENST00000427260,NM_001174083.1;NLRP2,upstream_gene_variant,,ENST00000540005,;NLRP2,downstream_gene_variant,,ENST00000588619,;NLRP2,downstream_gene_variant,,ENST00000588107,;NLRP2,downstream_gene_variant,,ENST00000585500,;NLRP2,downstream_gene_variant,,ENST00000397169,;NLRP2,downstream_gene_variant,,ENST00000433772,;NLRP2,non_coding_transcript_exon_variant,,ENST00000540597,;NLRP2,upstream_gene_variant,,ENST00000543277,;NLRP2,downstream_gene_variant,,ENST00000539848,;NLRP2,upstream_gene_variant,,ENST00000381637,; A ENST00000543010 Transcript synonymous_variant 1061/3576 918/3189 306/1062 G ggG/ggA COSM3893504 1 1 NLRP2 HGNC HGNC:22948 protein_coding YES CCDS12913.1 ENSP00000445135 Q9NX02 UPI000004C0CC NM_001174081.1 6/13 PROSITE_profiles:PS50837,hmmpanther:PTHR24106:SF129,hmmpanther:PTHR24106,Gene3D:3.40.50.300,Pfam_domain:PF05729 1 LOW 1 SNV 1 1 1 PASS rs1161320383 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 54982616 54982616 G A 1 0 0 0 0 0 0 0 1 10514 1219 43 3 3 NLRP2 19 54982616 Silent SNP G C3N-02423_T 3610801 54982616 3635000 415 29545 FIZ1 0 . GRCh38 19 55592721 55592721 + Missense_Mutation SNP G G C rs753074266 C3N-02423_T C3N-02423_N G G c.1220C>G p.Ser407Cys p.S407C ENST00000221665 3/3 247 229 18 217 217 0 strelka-varscan-mutect FIZ1,missense_variant,p.Ser407Cys,ENST00000221665,NM_032836.2;FIZ1,downstream_gene_variant,,ENST00000590714,;FIZ1,downstream_gene_variant,,ENST00000587678,;FIZ1,downstream_gene_variant,,ENST00000592585,; C ENST00000221665 Transcript missense_variant 1310/2660 1220/1491 407/496 S/C tCc/tGc rs753074266 1 -1 FIZ1 HGNC HGNC:25917 protein_coding YES CCDS12928.1 ENSP00000221665 Q96SL8 UPI000013C7D7 NM_032836.2 deleterious(0.04) 3/3 hmmpanther:PTHR24383,hmmpanther:PTHR24383:SF13 MODERATE 1 SNV 1 1 PASS rs753074266 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 55592721 55592721 G C 1 0 0 0 0 1 0 0 0 5763 1174 41 4 4 FIZ1 19 55592721 Missense_Mutation SNP G C3N-02423_T 610105 55592721 3024895 416 29546 ZNF784 0 . GRCh38 19 55622013 55622013 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.710C>A p.Ser237Ter p.S237* ENST00000325351 2/2 238 224 14 219 219 0 strelka-varscan-mutect ZNF784,stop_gained,p.Ser237Ter,ENST00000325351,NM_203374.1;ZNF784,3_prime_UTR_variant,,ENST00000591479,;ZNF865,downstream_gene_variant,,ENST00000568956,NM_001195605.1; T ENST00000325351 Transcript stop_gained 750/2021 710/972 237/323 S/* tCg/tAg 1 -1 ZNF784 HGNC HGNC:33111 protein_coding YES CCDS12930.1 ENSP00000320096 Q8NCA9 UPI000006D6D0 NM_203374.1 2/2 PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF36,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 HIGH 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 55622013 55622013 G T 1 0 0 0 0 0 1 0 0 18740 1059 37 1 1 ZNF784 19 55622013 Nonsense_Mutation SNP G C3N-02423_T 29292 55622013 2995603 417 29547 ZNF256 0 . GRCh38 19 57941418 57941418 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1390G>C p.Glu464Gln p.E464Q ENST00000282308 3/3 236 215 21 252 252 0 strelka-varscan-mutect ZNF256,missense_variant,p.Glu464Gln,ENST00000282308,NM_005773.2;ZNF256,3_prime_UTR_variant,,ENST00000598928,; G ENST00000282308 Transcript missense_variant 1587/2172 1390/1884 464/627 E/Q Gag/Cag 1 -1 ZNF256 HGNC HGNC:13049 protein_coding YES CCDS12966.1 ENSP00000282308 Q9Y2P7 UPI00001D69EC NM_005773.2 deleterious(0.02) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF214,hmmpanther:PTHR24387,Gene3D:3.30.160.60,Pfam_domain:PF13912,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 57941418 57941418 C G 1 0 0 0 0 1 0 0 0 18375 835 29 4 4 ZNF256 19 57941418 Missense_Mutation SNP C C3N-02423_T 2319405 57941418 676198 418 29548 1 27 4 4 1072 C 6.538179e-07 ZNF256 0 . GRCh38 19 57941866 57941866 + Missense_Mutation SNP C C G C3N-02423_T C3N-02423_N C C c.942G>C p.Gln314His p.Q314H ENST00000282308 3/3 238 224 14 252 252 0 strelka-varscan-mutect ZNF256,missense_variant,p.Gln314His,ENST00000282308,NM_005773.2;ZNF256,3_prime_UTR_variant,,ENST00000598928,; G ENST00000282308 Transcript missense_variant 1139/2172 942/1884 314/627 Q/H caG/caC COSM3540599,COSM3540600 1 -1 ZNF256 HGNC HGNC:13049 protein_coding YES CCDS12966.1 ENSP00000282308 Q9Y2P7 UPI00001D69EC NM_005773.2 tolerated(0.11) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24387:SF214,hmmpanther:PTHR24387,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 57941866 57941866 C G 1 0 0 0 0 1 0 0 0 18375 912 32 4 4 ZNF256 19 57941866 Missense_Mutation SNP C C3N-02423_T 448 57941866 675750 419 29549 1 27 4 4 1072 C 6.538179e-07 ZNF256 0 . GRCh38 19 57942269 57942269 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.539G>C p.Arg180Thr p.R180T ENST00000282308 3/3 281 260 21 299 298 1 strelka-varscan-mutect ZNF256,missense_variant,p.Arg180Thr,ENST00000282308,NM_005773.2;ZNF256,3_prime_UTR_variant,,ENST00000598928,; G ENST00000282308 Transcript missense_variant 736/2172 539/1884 180/627 R/T aGa/aCa 1 -1 ZNF256 HGNC HGNC:13049 protein_coding YES CCDS12966.1 ENSP00000282308 Q9Y2P7 UPI00001D69EC NM_005773.2 tolerated(0.99) 3/3 hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF214 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 57942269 57942269 C G 1 0 0 0 0 1 0 0 0 18375 913 32 4 4 ZNF256 19 57942269 Missense_Mutation SNP C C3N-02423_T 403 57942269 675347 420 29550 1 27 4 4 1072 C 6.538179e-07 ZNF256 0 . GRCh38 19 57942489 57942489 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.319G>C p.Glu107Gln p.E107Q ENST00000282308 3/3 338 300 38 329 329 0 strelka-varscan-mutect ZNF256,missense_variant,p.Glu107Gln,ENST00000282308,NM_005773.2;ZNF256,3_prime_UTR_variant,,ENST00000598928,; G ENST00000282308 Transcript missense_variant 516/2172 319/1884 107/627 E/Q Gaa/Caa 1 -1 ZNF256 HGNC HGNC:13049 protein_coding YES CCDS12966.1 ENSP00000282308 Q9Y2P7 UPI00001D69EC NM_005773.2 deleterious(0.02) 3/3 PROSITE_profiles:PS50157,hmmpanther:PTHR24387,hmmpanther:PTHR24387:SF214,PROSITE_patterns:PS00028,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 57942489 57942489 C G 1 0 0 0 0 1 0 0 0 18375 835 29 4 4 ZNF256 19 57942489 Missense_Mutation SNP C C3N-02423_T 220 57942489 675127 421 29551 1 27 4 4 1072 C 6.538179e-07 PLCB4 0 . GRCh38 20 9421456 9421456 + Missense_Mutation SNP C C T rs148851937 C3N-02423_T C3N-02423_N C C c.2278C>T p.Arg760Trp p.R760W ENST00000378501 23/36 64 40 24 71 71 0 strelka-varscan-mutect PLCB4,missense_variant,p.Arg760Trp,ENST00000378501,NM_000933.3;PLCB4,missense_variant,p.Arg760Trp,ENST00000378493,;PLCB4,missense_variant,p.Arg772Trp,ENST00000378473,NM_001172646.1;PLCB4,missense_variant,p.Arg760Trp,ENST00000278655,NM_182797.2;PLCB4,missense_variant,p.Arg772Trp,ENST00000414679,;PLCB4,non_coding_transcript_exon_variant,,ENST00000492632,;PLCB4,non_coding_transcript_exon_variant,,ENST00000464199,;PLCB4,non_coding_transcript_exon_variant,,ENST00000482123,;PLCB4,non_coding_transcript_exon_variant,,ENST00000473151,; T ENST00000378501 Transcript missense_variant 2293/5833 2278/3585 760/1194 R/W Cgg/Tgg rs148851937,COSM107902,COSM4100742 1 1 PLCB4 HGNC HGNC:9059 protein_coding YES CCDS13104.1 ENSP00000367762 Q15147 UPI00002069DF NM_000933.3 deleterious(0) 23/36 Gene3D:2.60.40.150,Pfam_domain:PF00168,PIRSF_domain:PIRSF000956,PROSITE_profiles:PS50004,hmmpanther:PTHR10336,hmmpanther:PTHR10336:SF106,SMART_domains:SM00239,Superfamily_domains:SSF49562 1,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs148851937 . 0 201 8 0 0 0 0 0 -20 0.9999997 1 1 1 0 T 3 4 99 9421456 9421456 C T 1 0 0 0 0 1 0 0 0 12124 898 31 1 1 PLCB4 20 9421456 Missense_Mutation SNP C C3N-02423_T 9421456 55022711 422 29552 ZNF133 0 . GRCh38 20 18316295 18316295 + Missense_Mutation SNP A A G novel C3N-02423_T C3N-02423_N A A c.1483A>G p.Ile495Val p.I495V ENST00000535822 3/3 87 60 27 109 109 0 strelka-varscan-mutect ZNF133,missense_variant,p.Ile481Val,ENST00000396026,NM_001282995.1,NM_001083330.2;ZNF133,missense_variant,p.Ile481Val,ENST00000377671,NM_003434.5;ZNF133,missense_variant,p.Ile482Val,ENST00000622607,NM_001283001.1,NM_001283000.1,NM_001282999.1;ZNF133,missense_variant,p.Ile482Val,ENST00000401790,NM_001282997.1,NM_001282998.1;ZNF133,missense_variant,p.Ile419Val,ENST00000402618,NM_001283003.1,NM_001283004.1;ZNF133,missense_variant,p.Ile495Val,ENST00000535822,NM_001283006.1,NM_001283007.1;ZNF133,missense_variant,p.Ile485Val,ENST00000628216,NM_001283002.1;ZNF133,missense_variant,p.Ile463Val,ENST00000538547,NM_001283005.1;ZNF133,missense_variant,p.Ile482Val,ENST00000316358,;ZNF133,missense_variant,p.Ile387Val,ENST00000630056,NM_001283008.1;ZNF133,downstream_gene_variant,,ENST00000425686,;ZNF133,downstream_gene_variant,,ENST00000434018,;ZNF133,downstream_gene_variant,,ENST00000360010,;RP4-568F9.3,upstream_gene_variant,,ENST00000436848,;ZNF133,non_coding_transcript_exon_variant,,ENST00000462170,;ZNF133,downstream_gene_variant,,ENST00000626025,; G ENST00000535822 Transcript missense_variant 1642/2341 1483/2004 495/667 I/V Atc/Gtc 1 1 ZNF133 HGNC HGNC:12917 protein_coding YES CCDS74703.1 ENSP00000439427 A0A0A0MTH2 UPI0004E4C963 NM_001283006.1,NM_001283007.1 tolerated(0.13) 3/3 Gene3D:3.30.160.60,Pfam_domain:PF00096,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24381,hmmpanther:PTHR24381:SF119,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE SNV 3 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 99 18316295 18316295 A G 1 0 0 0 0 1 0 0 0 18304 217 8 5 5 ZNF133 20 18316295 Missense_Mutation SNP A C3N-02423_T 8894839 18316295 46127872 423 29553 SYNDIG1 0 . GRCh38 20 24543289 24543289 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.192C>A p.Ser64Arg p.S64R ENST00000376862 2/4 166 117 49 197 197 0 strelka-varscan-mutect SYNDIG1,missense_variant,p.Ser64Arg,ENST00000376862,NM_024893.2; A ENST00000376862 Transcript missense_variant 825/2522 192/777 64/258 S/R agC/agA 1 1 SYNDIG1 HGNC HGNC:15885 protein_coding YES CCDS13164.1 ENSP00000366058 Q9H7V2 UPI00001285DC NM_024893.2 tolerated(0.48) 2/4 hmmpanther:PTHR14768,hmmpanther:PTHR14768:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 24543289 24543289 C A 1 0 0 0 0 1 0 0 0 15835 709 25 2 2 SYNDIG1 20 24543289 Missense_Mutation SNP C C3N-02423_T 6226994 24543289 39900878 424 29554 NINL 0 . GRCh38 20 25476213 25476213 + Silent SNP G G C C3N-02423_T C3N-02423_N G G c.3078C>G p.= p.L1026L ENST00000278886 17/24 208 197 11 224 224 0 strelka-varscan-mutect NINL,synonymous_variant,p.=,ENST00000278886,NM_025176.4;NINL,intron_variant,,ENST00000422516,NM_001318226.1;NINL,intron_variant,,ENST00000336104,; C ENST00000278886 Transcript synonymous_variant 3152/4969 3078/4149 1026/1382 L ctC/ctG COSM5535408 1 -1 NINL HGNC HGNC:29163 protein_coding YES CCDS33452.1 ENSP00000278886 Q9Y2I6 UPI0000206B64 NM_025176.4 17/24 hmmpanther:PTHR18905:SF12,hmmpanther:PTHR18905 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 25476213 25476213 G C 1 0 0 0 0 0 0 0 1 10455 1161 41 4 4 NINL 20 25476213 Silent SNP G C3N-02423_T 932924 25476213 38967954 425 29555 REM1 0 . GRCh38 20 31476658 31476658 + Silent SNP C C T rs759705636 C3N-02423_T C3N-02423_N C C c.213C>T p.= p.S71S ENST00000201979 2/5 287 271 16 344 344 0 strelka-varscan-mutect REM1,synonymous_variant,p.=,ENST00000201979,NM_014012.5;DEFB124,upstream_gene_variant,,ENST00000317676,NM_001037500.1;DEFB124,non_coding_transcript_exon_variant,,ENST00000481595,; T ENST00000201979 Transcript synonymous_variant 506/1665 213/897 71/298 S agC/agT rs759705636,COSM121730,COSM5694772 1 1 REM1 HGNC HGNC:15922 protein_coding YES CCDS13181.1 ENSP00000201979 O75628 UPI0000073CEB NM_014012.5 2/5 PIRSF_domain:PIRSF038017,PROSITE_profiles:PS51421,hmmpanther:PTHR24070,hmmpanther:PTHR24070:SF260,Low_complexity_(Seg):seg 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs759705636 . 0 207 0 2 0 0 0 0 -18.18743 0.9999994 1 1 1 0 T 2 4 99 31476658 31476658 C T 1 0 0 0 0 0 0 0 1 13392 767 27 1 1 REM1 20 31476658 Silent SNP C C3N-02423_T 6000445 31476658 32967509 426 29556 SPAG4 0 . GRCh38 20 35616232 35616232 + Nonsense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.229C>T p.Gln77Ter p.Q77* ENST00000374273 1/12 80 71 9 57 57 0 strelka-varscan-mutect SPAG4,stop_gained,p.Gln77Ter,ENST00000374273,NM_001317931.1,NM_003116.1;SPAG4,upstream_gene_variant,,ENST00000454819,;SPAG4,upstream_gene_variant,,ENST00000430878,;SPAG4,upstream_gene_variant,,ENST00000462896,;SPAG4,upstream_gene_variant,,ENST00000468248,;SPAG4,upstream_gene_variant,,ENST00000463973,;SPAG4,upstream_gene_variant,,ENST00000498203,; T ENST00000374273 Transcript stop_gained 341/1453 229/1314 77/437 Q/* Cag/Tag 1 1 SPAG4 HGNC HGNC:11214 protein_coding YES CCDS13259.1 ENSP00000363391 Q9NPE6 UPI0000135D8F NM_001317931.1,NM_003116.1 1/12 hmmpanther:PTHR12911,hmmpanther:PTHR12911:SF16 HIGH 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -19.2846 1 1 1 1 0 T 4 4 99 35616232 35616232 C T 1 0 0 0 0 0 1 0 0 15311 827 29 3 3 SPAG4 20 35616232 Nonsense_Mutation SNP C C3N-02423_T 4139574 35616232 28827935 427 29557 RPRD1B 0 . GRCh38 20 38057554 38057554 + Silent SNP G G C novel C3N-02423_T C3N-02423_N G G c.438G>C p.= p.L146L ENST00000373433 4/7 160 147 13 173 173 0 strelka-varscan-mutect RPRD1B,synonymous_variant,p.=,ENST00000373433,NM_021215.3;RPRD1B,synonymous_variant,p.=,ENST00000449186,;RPRD1B,missense_variant,p.Glu102Gln,ENST00000495457,;RPRD1B,3_prime_UTR_variant,,ENST00000462548,; C ENST00000373433 Transcript synonymous_variant 840/3874 438/981 146/326 L ctG/ctC 1 1 RPRD1B HGNC HGNC:16209 protein_coding YES CCDS13301.1 ENSP00000362532 Q9NQG5 UPI00001285EB NM_021215.3 4/7 hmmpanther:PTHR12460,hmmpanther:PTHR12460:SF3 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 99 38057554 38057554 G C 1 0 0 0 0 0 0 0 1 13870 1277 45 4 4 RPRD1B 20 38057554 Silent SNP G C3N-02423_T 2441322 38057554 26386613 428 29558 KCNK15 0 . GRCh38 20 44750619 44750619 + Silent SNP C C A novel C3N-02423_T C3N-02423_N C C c.774C>A p.= p.A258A ENST00000372861 2/2 115 78 37 178 177 1 strelka-varscan-mutect KCNK15,synonymous_variant,p.=,ENST00000372861,NM_022358.3;RIMS4,downstream_gene_variant,,ENST00000372851,NM_182970.3;RP4-781B1.5,downstream_gene_variant,,ENST00000611368,;KCNK15-AS1,upstream_gene_variant,,ENST00000427303,;KCNK15-AS1,upstream_gene_variant,,ENST00000445420,; A ENST00000372861 Transcript synonymous_variant 905/2599 774/993 258/330 A gcC/gcA 1 1 KCNK15 HGNC HGNC:13814 protein_coding YES CCDS13337.1 ENSP00000361952 Q9H427 UPI000003EA1C NM_022358.3 2/2 hmmpanther:PTHR11003,hmmpanther:PTHR11003:SF18,PIRSF_domain:PIRSF038061,Prints_domain:PR01690 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 44750619 44750619 C A 1 0 0 0 0 0 0 0 1 7979 610 22 2 2 KCNK15 20 44750619 Silent SNP C C3N-02423_T 6693065 44750619 19693548 429 29559 PTGIS 0 . GRCh38 20 49539620 49539620 + Missense_Mutation SNP C C A rs145802460 C3N-02423_T C3N-02423_N C C c.623G>T p.Arg208Leu p.R208L ENST00000244043 5/10 236 216 20 255 254 1 strelka-varscan-mutect PTGIS,missense_variant,p.Arg208Leu,ENST00000244043,NM_000961.3;PTGIS,non_coding_transcript_exon_variant,,ENST00000478971,; A ENST00000244043 Transcript missense_variant 653/5579 623/1503 208/500 R/L cGc/cTc rs145802460,COSM189985 1 -1 PTGIS HGNC HGNC:9603 protein_coding YES CCDS13419.1 ENSP00000244043 Q16647 UPI00001328DF NM_000961.3 deleterious(0.03) 5/10 hmmpanther:PTHR24306,hmmpanther:PTHR24306:SF4,PIRSF_domain:PIRSF500628,PIRSF_domain:PIRSF000047,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs145802460 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 49539620 49539620 C A 1 0 0 0 0 1 0 0 0 12908 768 27 1 1 PTGIS 20 49539620 Missense_Mutation SNP C C3N-02423_T 4789001 49539620 14904547 430 29560 BMP7 0 . GRCh38 20 57174993 57174993 + Missense_Mutation SNP C C A rs200825690 C3N-02423_T C3N-02423_N C C c.973G>T p.Asp325Tyr p.D325Y ENST00000395863 5/7 634 455 179 606 605 1 strelka-varscan-mutect BMP7,missense_variant,p.Asp325Tyr,ENST00000395863,NM_001719.2;BMP7,missense_variant,p.Asp325Tyr,ENST00000450594,;BMP7,missense_variant,p.Asp259Tyr,ENST00000395864,;BMP7,missense_variant,p.Asp247Tyr,ENST00000433911,;BMP7,non_coding_transcript_exon_variant,,ENST00000460817,;BMP7,downstream_gene_variant,,ENST00000463939,;BMP7,upstream_gene_variant,,ENST00000476877,; A ENST00000395863 Transcript missense_variant 1479/4013 973/1296 325/431 D/Y Gac/Tac rs200825690,COSM1713710 1 -1 BMP7 HGNC HGNC:1074 protein_coding YES CCDS13455.1 ENSP00000379204 P18075 A8K571 UPI00000349AD NM_001719.2 deleterious(0.01) 5/7 Gene3D:2.10.90.10,PROSITE_profiles:PS51362,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF135,Superfamily_domains:SSF57501 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs200825690 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 57174993 57174993 C A 1 0 0 0 0 1 0 0 0 1620 884 31 1 1 BMP7 20 57174993 Missense_Mutation SNP C C3N-02423_T 7635373 57174993 7269174 431 29561 RBBP8NL 0 . GRCh38 20 62416808 62416808 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.265G>A p.Glu89Lys p.E89K ENST00000252998 5/14 156 147 9 156 156 0 strelka-varscan-mutect RBBP8NL,missense_variant,p.Glu89Lys,ENST00000252998,NM_080833.2; T ENST00000252998 Transcript missense_variant 422/2793 265/1995 89/664 E/K Gag/Aag 1 -1 RBBP8NL HGNC HGNC:16144 protein_coding YES CCDS13498.1 ENSP00000252998 Q8NC74 UPI000013CDA2 NM_080833.2 deleterious(0) 5/14 Pfam_domain:PF10482,hmmpanther:PTHR15107,hmmpanther:PTHR15107:SF3 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 62416808 62416808 C T 1 0 0 0 0 1 0 0 0 13267 864 30 3 3 RBBP8NL 20 62416808 Missense_Mutation SNP C C3N-02423_T 5241815 62416808 2027359 432 29562 YTHDF1 0 . GRCh38 20 63202579 63202579 + Missense_Mutation SNP G G A novel C3N-02423_T C3N-02423_N G G c.1361C>T p.Ser454Phe p.S454F ENST00000370339 4/5 226 208 18 282 282 0 strelka-varscan-mutect YTHDF1,missense_variant,p.Ser454Phe,ENST00000370339,NM_017798.3;YTHDF1,intron_variant,,ENST00000370334,; A ENST00000370339 Transcript missense_variant 1703/3301 1361/1680 454/559 S/F tCc/tTc 1 -1 YTHDF1 HGNC HGNC:15867 protein_coding YES CCDS13511.1 ENSP00000359364 Q9BYJ9 UPI0000128DD9 NM_017798.3 deleterious(0) 4/5 PROSITE_profiles:PS50882,hmmpanther:PTHR12357,hmmpanther:PTHR12357:SF20,Pfam_domain:PF04146 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 63202579 63202579 G A 1 0 0 0 0 1 0 0 0 18059 1174 41 3 3 YTHDF1 20 63202579 Missense_Mutation SNP G C3N-02423_T 785771 63202579 1241588 433 29563 HELZ2 0 . GRCh38 20 63567187 63567187 + Missense_Mutation SNP T T C novel C3N-02423_T C3N-02423_N T T c.2171A>G p.Tyr724Cys p.Y724C ENST00000467148 6/19 394 297 97 361 360 1 strelka-varscan-mutect HELZ2,missense_variant,p.Tyr724Cys,ENST00000467148,NM_001037335.2;HELZ2,missense_variant,p.Tyr155Cys,ENST00000427522,NM_033405.3;HELZ2,downstream_gene_variant,,ENST00000479540,;HELZ2,downstream_gene_variant,,ENST00000454223,;HELZ2,downstream_gene_variant,,ENST00000370082,; C ENST00000467148 Transcript missense_variant 2241/8064 2171/7950 724/2649 Y/C tAc/tGc 1 -1 HELZ2 HGNC HGNC:30021 protein_coding YES CCDS33508.1 ENSP00000417401 Q9BYK8 UPI0000246BF7 NM_001037335.2 deleterious(0) 6/19 Gene3D:3.40.50.300,Pfam_domain:PF13087,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 63567187 63567187 T C 1 0 0 0 0 1 0 0 0 6932 1638 57 5 5 HELZ2 20 63567187 Missense_Mutation SNP T C3N-02423_T 364608 63567187 876980 434 29564 C21orf91 0 . GRCh38 21 17795236 17795236 + Silent SNP C C G novel C3N-02423_T C3N-02423_N C C c.699G>C p.= p.L233L ENST00000284881 4/5 279 261 18 350 350 0 strelka-varscan-mutect C21orf91,synonymous_variant,p.=,ENST00000284881,NM_001100420.1;C21orf91,synonymous_variant,p.=,ENST00000400559,NM_017447.3;C21orf91,synonymous_variant,p.=,ENST00000405964,;C21orf91,intron_variant,,ENST00000400558,NM_001100421.1;C21orf91-OT1,upstream_gene_variant,,ENST00000430815,;C21orf91-OT1,upstream_gene_variant,,ENST00000439392,;C21orf91-OT1,upstream_gene_variant,,ENST00000430401,;AL109761.5,intron_variant,,ENST00000428689,;C21orf91,downstream_gene_variant,,ENST00000493464,; G ENST00000284881 Transcript synonymous_variant 790/5433 699/894 233/297 L ctG/ctC 1 -1 C21orf91 HGNC HGNC:16459 protein_coding YES CCDS42907.1 ENSP00000284881 Q9NYK6 UPI000004A0E1 NM_001100420.1 4/5 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF06937,hmmpanther:PTHR15961 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 99 17795236 17795236 C G 1 0 0 0 0 0 0 0 1 2016 813 29 4 4 C21orf91 21 17795236 Silent SNP C C3N-02423_T 17795236 28914747 435 29565 SCAF4 0 . GRCh38 21 31671751 31671751 + Missense_Mutation SNP C C T C3N-02423_T C3N-02423_N C C c.3092G>A p.Arg1031Lys p.R1031K ENST00000286835 20/20 200 187 13 243 243 0 strelka-varscan-mutect SCAF4,missense_variant,p.Arg1031Lys,ENST00000286835,NM_020706.2;SCAF4,missense_variant,p.Arg1009Lys,ENST00000399804,NM_001145445.1;SCAF4,missense_variant,p.Arg1016Lys,ENST00000434667,NM_001145444.1;SOD1,downstream_gene_variant,,ENST00000270142,NM_000454.4;SOD1,downstream_gene_variant,,ENST00000389995,;AP000254.8,upstream_gene_variant,,ENST00000609934,;SOD1,downstream_gene_variant,,ENST00000470944,;SOD1,downstream_gene_variant,,ENST00000476106,; T ENST00000286835 Transcript missense_variant 3475/4193 3092/3444 1031/1147 R/K aGa/aAa COSM4101209 1 -1 SCAF4 HGNC HGNC:19304 protein_coding YES CCDS33537.1 ENSP00000286835 O95104 UPI0000206D66 NM_020706.2 deleterious_low_confidence(0.01) 20/20 Low_complexity_(Seg):seg 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 31671751 31671751 C T 1 0 0 0 0 1 0 0 0 14134 913 32 3 3 SCAF4 21 31671751 Missense_Mutation SNP C C3N-02423_T 13876515 31671751 15038232 436 29566 TTC3 0 . GRCh38 21 37091414 37091414 + Splice_Site SNP G G T rs762013648 C3N-02423_T C3N-02423_N G G c.601+1G>T p.X201_splice ENST00000399017 121 114 7 170 170 0 varscan-mutect TTC3,splice_donor_variant,,ENST00000399017,NM_003316.3;TTC3,splice_donor_variant,,ENST00000354749,;TTC3,splice_donor_variant,,ENST00000355666,NM_001001894.1;TTC3,splice_donor_variant,,ENST00000418766,;TTC3,splice_donor_variant,,ENST00000438055,;TTC3,splice_donor_variant,,ENST00000450533,;TTC3,splice_donor_variant,,ENST00000399010,;TTC3,intron_variant,,ENST00000540756,;TTC3,splice_donor_variant,,ENST00000479930,;TTC3,splice_donor_variant,,ENST00000485402,;TTC3,splice_donor_variant,,ENST00000491952,;TTC3,non_coding_transcript_exon_variant,,ENST00000484047,;TTC3,intron_variant,,ENST00000481605,;TTC3,intron_variant,,ENST00000494243,;TTC3,intron_variant,,ENST00000463216,;TTC3,intron_variant,,ENST00000492275,;TTC3,splice_donor_variant,,ENST00000460328,; T ENST00000399017 Transcript splice_donor_variant -/10363 601/6078 201/2025 rs762013648 1 1 TTC3 HGNC HGNC:12393 protein_coding YES CCDS13651.1 ENSP00000381981 P53804 UPI00001B043E NM_003316.3 7/45 HIGH 1 SNV 1 1 PASS rs762013648 . 0 207 2 0 0 0 0 0 -14.08161 1 1 1 1 0 T 5 4 99 37091414 37091414 G T 1 0 0 0 0 0 0 1 0 17206 1391 48 2 2 TTC3 21 37091414 Splice_Site SNP G C3N-02423_T 5419663 37091414 9618569 437 29567 COL6A2 0 . GRCh38 21 46116669 46116669 + Missense_Mutation SNP G G T rs762882543 C3N-02423_T C3N-02423_N G G c.946G>T p.Gly316Cys p.G316C ENST00000300527 9/28 410 381 29 494 494 0 strelka-varscan-mutect COL6A2,missense_variant,p.Gly316Cys,ENST00000300527,NM_001849.3;COL6A2,missense_variant,p.Gly316Cys,ENST00000310645,NM_058175.2;COL6A2,missense_variant,p.Gly316Cys,ENST00000409416,;COL6A2,missense_variant,p.Gly316Cys,ENST00000397763,NM_058174.2;COL6A2,downstream_gene_variant,,ENST00000436769,;COL6A2,upstream_gene_variant,,ENST00000413758,;COL6A2,downstream_gene_variant,,ENST00000460886,;COL6A2,non_coding_transcript_exon_variant,,ENST00000485591,; T ENST00000300527 Transcript missense_variant 1050/3461 946/3060 316/1019 G/C Ggt/Tgt rs762882543 1 1 COL6A2 HGNC HGNC:2212 protein_coding YES CCDS13728.1 ENSP00000300527 P12110 UPI00001AECE0 NM_001849.3 deleterious(0) 9/28 hmmpanther:PTHR24023:SF119,hmmpanther:PTHR24023,Pfam_domain:PF01391,Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs762882543 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 46116669 46116669 G T 1 0 0 0 0 1 0 0 0 3489 1116 39 1 1 COL6A2 21 46116669 Missense_Mutation SNP G C3N-02423_T 9025255 46116669 593314 438 29568 OR11H1 0 . GRCh38 22 15528574 15528574 + Missense_Mutation SNP T T A novel C3N-02423_T C3N-02423_N T T c.416T>A p.Leu139His p.L139H ENST00000252835 1/1 107 98 9 131 131 0 varscan-mutect OR11H1,missense_variant,p.Leu139His,ENST00000252835,NM_001005239.1; A ENST00000252835 Transcript missense_variant 417/982 416/981 139/326 L/H cTt/cAt 1 1 OR11H1 HGNC HGNC:15404 protein_coding YES CCDS74807.1 ENSP00000252835 Q8NG94 UPI000004B1CF NM_001005239.1 deleterious(0) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR24242:SF201,hmmpanther:PTHR24242,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 208 2 0 0 0 0 0 -18.45923 1 1 1 1 0 A 3 1 99 15528574 15528574 T A 1 0 0 0 0 1 0 0 0 11002 1609 56 4 4 OR11H1 22 15528574 Missense_Mutation SNP T C3N-02423_T 15528574 35289894 439 29569 IL17RA 0 . GRCh38 22 17108527 17108546 + Frame_Shift_Del DEL GGTGGAGAGCAACTCTAAGA GGTGGAGAGCAACTCTAAGA - novel C3N-02423_T C3N-02423_N GGTGGAGAGCAACTCTAAGA GGTGGAGAGCAACTCTAAGA c.1308_1327delGGTGGAGAGCAACTCTAAGA p.Met436IlefsTer68 p.M436Ifs*68 ENST00000319363 13/13 463 436 27 577 577 0 sindel-pindel IL17RA,frameshift_variant,p.Met436IlefsTer68,ENST00000319363,NM_014339.6;IL17RA,frameshift_variant,p.Met402IlefsTer68,ENST00000612619,NM_001289905.1; - ENST00000319363 Transcript frameshift_variant 1441-1460/8607 1308-1327/2601 436-443/866 MVESNSKI/IX atGGTGGAGAGCAACTCTAAGAtc/attc 1 1 IL17RA HGNC HGNC:5985 protein_coding YES CCDS13739.1 ENSP00000320936 Q96F46 UPI000005031F NM_014339.6 13/13 Pfam_domain:PF08357,PROSITE_profiles:PS51534,hmmpanther:PTHR15583,hmmpanther:PTHR15583:SF13 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 99 17108527 17108527 GGTGGAGAGCAACTCTAAGA - 1 0 1 0 1 0 0 0 0 7547 1348 47 0 0 IL17RA 22 17108527 Frame_Shift_Del DEL GGTGGAGAGCAACTCTAAGA C3N-02423_T 1579953 17108527 33709941 440 29570 TXNRD2 0 . GRCh38 22 19895545 19895545 + Missense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.811C>A p.His271Asn p.H271N ENST00000400521 11/18 289 258 31 315 315 0 strelka-varscan-mutect TXNRD2,missense_variant,p.His270Asn,ENST00000400519,;TXNRD2,missense_variant,p.His239Asn,ENST00000491939,;TXNRD2,missense_variant,p.His271Asn,ENST00000400521,NM_006440.4;TXNRD2,missense_variant,p.His241Asn,ENST00000400518,;TXNRD2,missense_variant,p.His175Asn,ENST00000542719,;TXNRD2,missense_variant,p.His271Asn,ENST00000334363,NM_001282512.1;TXNRD2,missense_variant,p.His248Asn,ENST00000400525,;TXNRD2,missense_variant,p.His104Asn,ENST00000475995,;TXNRD2,non_coding_transcript_exon_variant,,ENST00000635155,;TXNRD2,missense_variant,p.His252Asn,ENST00000474308,;TXNRD2,missense_variant,p.His14Asn,ENST00000634537,;TXNRD2,non_coding_transcript_exon_variant,,ENST00000494454,; T ENST00000400521 Transcript missense_variant 1000/2115 811/1575 271/524 H/N Cat/Aat 1 -1 TXNRD2 HGNC HGNC:18155 protein_coding YES CCDS42981.1 ENSP00000383365 Q9NNW7 UPI0000167BDD NM_006440.4 deleterious(0.04) 11/18 Gene3D:3.50.50.60,Pfam_domain:PF07992,PIRSF_domain:PIRSF000350,hmmpanther:PTHR22912,hmmpanther:PTHR22912:SF182,Superfamily_domains:SSF51905,TIGRFAM_domain:TIGR01438 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 19895545 19895545 G T 1 0 0 0 0 1 0 0 0 17322 1290 45 2 2 TXNRD2 22 19895545 Missense_Mutation SNP G C3N-02423_T 2787018 19895545 30922923 441 29571 SPECC1L 0 . GRCh38 22 24334453 24334453 + Missense_Mutation SNP G G T rs139167350 C3N-02423_T C3N-02423_N G G c.2440G>T p.Val814Phe p.V814F ENST00000314328 9/17 447 415 32 483 483 0 strelka-varscan-mutect SPECC1L,missense_variant,p.Val814Phe,ENST00000314328,NM_015330.4;SPECC1L,missense_variant,p.Val814Phe,ENST00000437398,NM_001145468.3;SPECC1L,missense_variant,p.Val814Phe,ENST00000541492,NM_001254732.2;SPECC1L,downstream_gene_variant,,ENST00000421374,;SPECC1L-ADORA2A,missense_variant,p.Val814Phe,ENST00000358654,; T ENST00000314328 Transcript missense_variant 2725/6756 2440/3354 814/1117 V/F Gtt/Ttt rs139167350 1 1 SPECC1L HGNC HGNC:29022 protein_coding YES CCDS33619.1 ENSP00000325785 Q69YQ0 UPI0004620B3B NM_015330.4 deleterious(0.01) 9/17 hmmpanther:PTHR23167,hmmpanther:PTHR23167:SF18 MODERATE 1 SNV 1 1 PASS rs139167350 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 99 24334453 24334453 G T 1 0 0 0 0 1 0 0 0 15384 1145 40 1 1 SPECC1L 22 24334453 Missense_Mutation SNP G C3N-02423_T 4438908 24334453 26484015 442 29572 MYO18B 0 . GRCh38 22 25785488 25785488 + Silent SNP C C A C3N-02423_T C3N-02423_N C C c.2373C>A p.= p.S791S ENST00000335473 11/44 207 196 11 224 223 1 strelka-varscan-mutect MYO18B,synonymous_variant,p.=,ENST00000335473,NM_001318245.1,NM_032608.5;MYO18B,synonymous_variant,p.=,ENST00000407587,;MYO18B,synonymous_variant,p.=,ENST00000536101,;MYO18B,synonymous_variant,p.=,ENST00000539302,;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,; A ENST00000335473 Transcript synonymous_variant 2623/8565 2373/7704 791/2567 S tcC/tcA COSM5393303 1 1 MYO18B HGNC HGNC:18150 protein_coding YES CCDS54507.1 ENSP00000334563 A0A075B6F5 UPI0000207402 NM_001318245.1,NM_032608.5 11/44 Pfam_domain:PF00063,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF372,SMART_domains:SM00242,Superfamily_domains:SSF52540 1 LOW 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 25785488 25785488 C A 1 0 0 0 0 0 0 0 1 10067 608 21 2 2 MYO18B 22 25785488 Silent SNP C C3N-02423_T 1451035 25785488 25032980 443 29573 POLR2F 0 . GRCh38 22 37986177 37986177 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.317C>T p.Pro106Leu p.P106L ENST00000407936 5/6 93 82 11 126 126 0 strelka-varscan-mutect POLR2F,missense_variant,p.Pro106Leu,ENST00000407936,NM_001301130.1,NM_001301131.1;SOX10,intron_variant,,ENST00000360880,;POLR2F,intron_variant,,ENST00000405557,;SOX10,upstream_gene_variant,,ENST00000396884,NM_006941.3;SOX10,upstream_gene_variant,,ENST00000446929,;POLR2F,upstream_gene_variant,,ENST00000427034,;SOX10,upstream_gene_variant,,ENST00000427770,;POLR2F,upstream_gene_variant,,ENST00000333418,;MIR6820,upstream_gene_variant,,ENST00000578108,;MIR6820,non_coding_transcript_exon_variant,,ENST00000623111,;SOX10,upstream_gene_variant,,ENST00000470555,;POLR2F,3_prime_UTR_variant,,ENST00000443002,; T ENST00000407936 Transcript missense_variant 408/582 317/477 106/158 P/L cCc/cTc 1 1 POLR2F HGNC HGNC:9193 protein_coding YES CCDS77673.1 ENSP00000385725 B0QYL9 UPI000161112B NM_001301130.1,NM_001301131.1 deleterious_low_confidence(0) 5/6 MODERATE SNV 3 1 PASS . . 0 204 3 3 0 0 0 0 -17.53782 0.9998695 1 1 1 0 T 3 4 99 37986177 37986177 C T 1 0 0 0 0 1 0 0 0 12329 623 22 3 3 POLR2F 22 37986177 Missense_Mutation SNP C C3N-02423_T 12200689 37986177 12832291 444 29574 EP300 0 . GRCh38 22 41158415 41158415 + Nonsense_Mutation SNP G G T novel C3N-02423_T C3N-02423_N G G c.3505G>T p.Glu1169Ter p.E1169* ENST00000263253 19/31 451 427 24 475 475 0 strelka-varscan-mutect EP300,stop_gained,p.Glu1169Ter,ENST00000263253,NM_001429.3;EP300,upstream_gene_variant,,ENST00000635584,;EP300,non_coding_transcript_exon_variant,,ENST00000635691,;EP300,upstream_gene_variant,,ENST00000635552,; T ENST00000263253 Transcript stop_gained 4724/9587 3505/7245 1169/2414 E/* Gag/Tag 1 1 EP300 HGNC HGNC:3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 UPI00001AE876 NM_001429.3 19/31 hmmpanther:PTHR13808:SF4,hmmpanther:PTHR13808,Pfam_domain:PF06001 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 41158415 41158415 G T 1 0 0 0 0 0 1 0 0 4994 1188 41 2 2 EP300 22 41158415 Nonsense_Mutation SNP G C3N-02423_T 3172238 41158415 9660053 445 29575 GTSE1 0 . GRCh38 22 46326587 46326587 + Missense_Mutation SNP G G T rs147391974 C3N-02423_T C3N-02423_N G G c.1657G>T p.Val553Leu p.V553L ENST00000454366 9/12 210 194 16 191 191 0 strelka-varscan-mutect GTSE1,missense_variant,p.Val553Leu,ENST00000454366,NM_016426.6;TRMU,upstream_gene_variant,,ENST00000476901,;TRMU,upstream_gene_variant,,ENST00000486620,;GTSE1,non_coding_transcript_exon_variant,,ENST00000466510,;GTSE1,non_coding_transcript_exon_variant,,ENST00000479645,;GTSE1,upstream_gene_variant,,ENST00000491863,; T ENST00000454366 Transcript missense_variant 1869/3112 1657/2220 553/739 V/L Gtg/Ttg rs147391974 1 1 GTSE1 HGNC HGNC:13698 protein_coding YES CCDS14074.2 ENSP00000415430 Q9NYZ3 UPI000021D19B NM_016426.6 tolerated(1) 9/12 hmmpanther:PTHR21584,hmmpanther:PTHR21584:SF10 MODERATE 1 SNV 1 1 PASS rs147391974 . 0 206 0 4 0 0 0 0 -19.77721 0.9996841 1 1 1 0 T 3 4 99 46326587 46326587 G T 1 0 0 0 0 1 0 0 0 6766 1145 40 1 1 GTSE1 22 46326587 Missense_Mutation SNP G C3N-02423_T 5168172 46326587 4491881 446 29576 ARSD 0 . GRCh38 X 2925730 2925730 + Missense_Mutation SNP A A C novel C3N-02423_T C3N-02423_N A A c.80T>G p.Leu27Arg p.L27R ENST00000381154 2/10 112 71 41 127 127 0 strelka-varscan-mutect ARSD,missense_variant,p.Leu27Arg,ENST00000381154,NM_001669.3;ARSD,non_coding_transcript_exon_variant,,ENST00000217890,;ARSD,intron_variant,,ENST00000495294,;ARSD,missense_variant,p.Leu27Arg,ENST00000559324,;ARSD,non_coding_transcript_exon_variant,,ENST00000494870,; C ENST00000381154 Transcript missense_variant 156/5159 80/1782 27/593 L/R cTt/cGt 1 -1 ARSD HGNC HGNC:717 protein_coding YES CCDS35196.1 ENSP00000370546 P51689 A0A140VK06 UPI0000070902 NM_001669.3 tolerated(0.07) 2/10 hmmpanther:PTHR10342,hmmpanther:PTHR10342:SF216,Low_complexity_(Seg):seg,Cleavage_site_(Signalp):SignalP-noTM MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 99 2925730 2925730 A C 1 0 0 0 0 1 0 0 0 1132 72 3 5 5 ARSD 23 2925730 Missense_Mutation SNP A C3N-02423_T 2925730 153115165 447 29577 NLGN4X 0 . GRCh38 X 5893167 5893167 + Missense_Mutation SNP C C A rs766889075 C3N-02423_T C3N-02423_N C C c.2101G>T p.Asp701Tyr p.D701Y ENST00000381095 6/6 220 157 63 221 220 1 strelka-varscan-mutect NLGN4X,missense_variant,p.Asp701Tyr,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Asp701Tyr,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Asp701Tyr,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Asp701Tyr,ENST00000381092,;NLGN4X,missense_variant,p.Asp702Tyr,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,; A ENST00000381095 Transcript missense_variant 2729/5870 2101/2451 701/816 D/Y Gac/Tac rs766889075,COSM4861124,COSM757941 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0) 6/6 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs766889075 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 5893167 5893167 C A 1 0 0 0 0 1 0 0 0 10501 855 30 2 2 NLGN4X 23 5893167 Missense_Mutation SNP C C3N-02423_T 2967437 5893167 150147728 448 29578 NLGN4X 0 . GRCh38 X 5893290 5893290 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1978G>T p.Asp660Tyr p.D660Y ENST00000381095 6/6 362 251 111 356 356 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Asp660Tyr,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Asp660Tyr,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Asp660Tyr,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Asp660Tyr,ENST00000381092,;NLGN4X,missense_variant,p.Asp661Tyr,ENST00000538097,;NLGN4X,intron_variant,,ENST00000477079,; A ENST00000381095 Transcript missense_variant 2606/5870 1978/2451 660/816 D/Y Gac/Tac 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0.01) 6/6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 5893290 5893290 C A 1 0 0 0 0 1 0 0 0 10501 855 30 2 2 NLGN4X 23 5893290 Missense_Mutation SNP C C3N-02423_T 123 5893290 150147605 449 29579 NLGN4X 0 . GRCh38 X 5903557 5903557 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.1121G>T p.Gly374Val p.G374V ENST00000381095 5/6 141 100 41 140 140 0 strelka-varscan-mutect NLGN4X,missense_variant,p.Gly374Val,ENST00000381095,NM_181332.2,NM_001282145.1;NLGN4X,missense_variant,p.Gly374Val,ENST00000381093,NM_001282146.1;NLGN4X,missense_variant,p.Gly374Val,ENST00000275857,NM_020742.3;NLGN4X,missense_variant,p.Gly374Val,ENST00000381092,;NLGN4X,missense_variant,p.Gly375Val,ENST00000538097,;NLGN4X,upstream_gene_variant,,ENST00000477079,; A ENST00000381095 Transcript missense_variant 1749/5870 1121/2451 374/816 G/V gGg/gTg 1 -1 NLGN4X HGNC HGNC:14287 protein_coding YES CCDS14126.1 ENSP00000370485 Q8N0W4 A0A024RBV0 UPI0000072EC5 NM_181332.2,NM_001282145.1 deleterious(0) 5/6 Gene3D:3.40.50.1820,Pfam_domain:PF00135,hmmpanther:PTHR11559,hmmpanther:PTHR11559:SF260,Superfamily_domains:SSF53474 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 99 5903557 5903557 C A 1 0 0 0 0 1 0 0 0 10501 623 22 2 2 NLGN4X 23 5903557 Missense_Mutation SNP C C3N-02423_T 10267 5903557 150137338 450 29580 REPS2 0 . GRCh38 X 17022137 17022137 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.412C>T p.Arg138Cys p.R138C ENST00000357277 3/18 75 65 10 77 77 0 strelka-varscan-mutect REPS2,missense_variant,p.Arg138Cys,ENST00000357277,NM_004726.2;REPS2,missense_variant,p.Arg138Cys,ENST00000303843,NM_001080975.1;REPS2,non_coding_transcript_exon_variant,,ENST00000481792,; T ENST00000357277 Transcript missense_variant 583/7953 412/1983 138/660 R/C Cgc/Tgc 1 1 REPS2 HGNC HGNC:9963 protein_coding YES CCDS14180.2 ENSP00000349824 Q8NFH8 UPI00001BBB18 NM_004726.2 deleterious(0) 3/18 hmmpanther:PTHR11216:SF64,hmmpanther:PTHR11216,Gene3D:1.10.238.10 MODERATE 1 SNV 1 1 PASS rs949060639 . 0 207 2 0 0 0 0 0 -19.99777 1 1 1 1 0 T 3 4 99 17022137 17022137 C T 1 0 0 0 0 1 0 0 0 13399 884 31 1 1 REPS2 23 17022137 Missense_Mutation SNP C C3N-02423_T 11118580 17022137 139018758 451 29581 PDK3 0 . GRCh38 X 24533983 24533983 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.1132C>T p.Arg378Cys p.R378C ENST00000441463 11/12 97 83 14 84 84 0 strelka-varscan-mutect PDK3,missense_variant,p.Arg378Cys,ENST00000441463,NM_001142386.2;PDK3,missense_variant,p.Arg378Cys,ENST00000379162,NM_005391.4; T ENST00000441463 Transcript missense_variant 1132/1921 1132/1248 378/415 R/C Cgc/Tgc 1 1 PDK3 HGNC HGNC:8811 protein_coding YES CCDS48088.1 ENSP00000387536 Q15120 UPI00002124D4 NM_001142386.2 deleterious(0) 11/12 hmmpanther:PTHR11947,hmmpanther:PTHR11947:SF21 MODERATE 1 SNV 2 1 PASS rs1356075616 . 0 204 4 2 0 0 0 0 -19.99914 0.9999816 1 1 1 0 T 3 4 99 24533983 24533983 C T 1 0 0 0 0 1 0 0 0 11765 768 27 1 1 PDK3 23 24533983 Missense_Mutation SNP C C3N-02423_T 7511846 24533983 131506912 452 29582 MAGEB3 0 . GRCh38 X 30236965 30236965 + Silent SNP G G A novel C3N-02423_T C3N-02423_N G G c.1041G>A p.= p.*347* ENST00000361644 5/5 37 20 17 39 39 0 strelka-varscan-mutect MAGEB3,stop_retained_variant,p.=,ENST00000361644,NM_002365.4;MAGEB3,stop_retained_variant,p.=,ENST00000620842,; A ENST00000361644 Transcript stop_retained_variant 1778/2305 1041/1041 347/346 * taG/taA 1 1 MAGEB3 HGNC HGNC:6810 protein_coding YES CCDS14220.1 ENSP00000355198 O15480 UPI000013E79F NM_002365.4 5/5 LOW 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 99 30236965 30236965 G A 1 0 0 0 0 0 0 0 1 9093 1024 36 3 3 MAGEB3 23 30236965 Silent SNP G C3N-02423_T 5702982 30236965 125803930 453 29583 CYBB 0 . GRCh38 X 37803894 37803894 + Silent SNP C C T C3N-02423_T C3N-02423_N C C c.915C>T p.= p.F305F ENST00000378588 9/13 180 170 10 183 183 0 strelka-varscan-mutect CYBB,synonymous_variant,p.=,ENST00000378588,NM_000397.3;RP5-972B16.2,intron_variant,,ENST00000465127,;CYBB,non_coding_transcript_exon_variant,,ENST00000492288,; T ENST00000378588 Transcript synonymous_variant 982/4324 915/1713 305/570 F ttC/ttT CD044781,CYBBbase_D0025:g.24831delC 1 1 CYBB HGNC HGNC:2578 protein_coding YES CCDS14242.1 ENSP00000367851 P04839 A0A0S2Z3S6 UPI0000001628 NM_000397.3 9/13 Gene3D:2.40.30.10,Pfam_domain:PF08022,PROSITE_profiles:PS51384,hmmpanther:PTHR11972,hmmpanther:PTHR11972:SF60,Superfamily_domains:SSF63380 LOW 1 SNV 1 1,0 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 99 37803894 37803894 C T 1 0 0 0 0 0 0 0 1 3936 825 29 3 3 CYBB 23 37803894 Silent SNP C C3N-02423_T 7566929 37803894 118237001 454 29584 SSX2 0 . GRCh38 X 52698089 52698089 + Splice_Site SNP C C A novel C3N-02423_T C3N-02423_N C C c.613-1G>T p.X205_splice ENST00000336777 215 166 49 263 262 1 strelka-varscan-mutect SSX2,splice_acceptor_variant,,ENST00000336777,NM_003147.5,NM_001278697.1;SSX2,splice_acceptor_variant,,ENST00000337502,NM_175698.2;SSX2,splice_acceptor_variant,,ENST00000476392,; A ENST00000336777 Transcript splice_acceptor_variant -/1410 613/672 205/223 1 -1 SSX2 HGNC HGNC:11336 protein_coding YES CCDS14345.2 ENSP00000338796 Q16385 UPI000006D209 NM_003147.5,NM_001278697.1 7/8 HIGH 1 SNV 1 1 PASS rs1418130412 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 99 52698089 52698089 C A 1 0 0 0 0 0 0 1 0 15582 695 24 2 2 SSX2 23 52698089 Splice_Site SNP C C3N-02423_T 14894195 52698089 103342806 455 29585 IQSEC2 0 . GRCh38 X 53254829 53254829 + Missense_Mutation SNP C C G novel C3N-02423_T C3N-02423_N C C c.1102G>C p.Glu368Gln p.E368Q ENST00000396435 4/15 114 102 12 123 123 0 strelka-varscan-mutect IQSEC2,missense_variant,p.Glu368Gln,ENST00000396435,NM_001111125.2;IQSEC2,missense_variant,p.Glu163Gln,ENST00000375365,NM_015075.1; G ENST00000396435 Transcript missense_variant 1303/6011 1102/4467 368/1488 E/Q Gag/Cag 1 -1 IQSEC2 HGNC HGNC:29059 protein_coding YES CCDS48130.1 ENSP00000379712 Q5JU85 UPI00001C207D NM_001111125.2 tolerated(0.1) 4/15 PROSITE_profiles:PS50096,hmmpanther:PTHR10663:SF61,hmmpanther:PTHR10663 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99998 1 1 1 1 0 G 3 3 99 53254829 53254829 C G 1 0 0 0 0 1 0 0 0 7724 835 29 4 4 IQSEC2 23 53254829 Missense_Mutation SNP C C3N-02423_T 556740 53254829 102786066 456 29586 WNK3 0 . GRCh38 X 54238980 54238980 + Nonsense_Mutation SNP A A T novel C3N-02423_T C3N-02423_N A A c.3771T>A p.Cys1257Ter p.C1257* ENST00000354646 18/24 109 86 23 116 116 0 strelka-varscan-mutect WNK3,stop_gained,p.Cys1257Ter,ENST00000354646,NM_020922.4;WNK3,stop_gained,p.Cys1257Ter,ENST00000375159,;WNK3,stop_gained,p.Cys1257Ter,ENST00000620763,;WNK3,intron_variant,,ENST00000375169,NM_001002838.3; T ENST00000354646 Transcript stop_gained 4210/11341 3771/5403 1257/1800 C/* tgT/tgA 1 -1 WNK3 HGNC HGNC:14543 protein_coding YES CCDS14357.1 ENSP00000346667 Q9BYP7 UPI00001AF003 NM_020922.4 18/24 hmmpanther:PTHR13902,hmmpanther:PTHR13902:SF47 HIGH 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 99 54238980 54238980 A T 1 0 0 0 0 0 1 0 0 17935 273 10 4 4 WNK3 23 54238980 Nonsense_Mutation SNP A C3N-02423_T 984151 54238980 101801915 457 29587 USP51 0 . GRCh38 X 55488512 55488512 + Missense_Mutation SNP C C A novel C3N-02423_T C3N-02423_N C C c.428G>T p.Arg143Leu p.R143L ENST00000500968 2/2 41 33 8 46 46 0 strelka-varscan-mutect USP51,missense_variant,p.Arg143Leu,ENST00000500968,NM_201286.3;USP51,intron_variant,,ENST00000586165,; A ENST00000500968 Transcript missense_variant 511/4407 428/2136 143/711 R/L cGg/cTg 1 -1 USP51 HGNC HGNC:23086 protein_coding YES CCDS14370.1 ENSP00000423333 Q70EK9 UPI0000232F07 NM_201286.3 tolerated_low_confidence(0.12) 2/2 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1423659906 . 0 204 6 0 0 0 0 0 -19.6504 1 1 1 1 0 A 3 1 99 55488512 55488512 C A 1 0 0 0 0 1 0 0 0 17626 652 23 1 1 USP51 23 55488512 Missense_Mutation SNP C C3N-02423_T 1249532 55488512 100552383 458 29588 KIAA1210 0 . GRCh38 X 119081496 119081496 + Missense_Mutation SNP C C T novel C3N-02423_T C3N-02423_N C C c.4963G>A p.Glu1655Lys p.E1655K ENST00000402510 14/14 53 44 9 39 39 0 strelka-varscan-mutect KIAA1210,missense_variant,p.Glu1655Lys,ENST00000402510,NM_020721.1; T ENST00000402510 Transcript missense_variant 4963/7824 4963/5130 1655/1709 E/K Gaa/Aaa 1 -1 KIAA1210 HGNC HGNC:29218 protein_coding YES CCDS48156.1 ENSP00000384670 Q9ULL0 UPI0001596C4C NM_020721.1 deleterious(0.01) 14/14 hmmpanther:PTHR22118:SF15,hmmpanther:PTHR22118 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -19.98596 1 1 1 1 0 T 3 4 99 119081496 119081496 C T 1 0 0 0 0 1 0 0 0 8106 835 29 3 3 KIAA1210 23 119081496 Missense_Mutation SNP C C3N-02423_T 63592984 119081496 36959399 459 29589 FAM50A 0 . GRCh38 X 154444256 154444256 + Silent SNP C C T novel C3N-02423_T C3N-02423_N C C c.21C>T p.= p.A7A ENST00000393600 1/13 88 79 9 92 92 0 strelka-varscan-mutect FAM50A,synonymous_variant,p.=,ENST00000393600,NM_004699.3;GDI1,downstream_gene_variant,,ENST00000447750,NM_001493.2;FAM50A,upstream_gene_variant,,ENST00000158526,;GDI1,downstream_gene_variant,,ENST00000630693,;GDI1,downstream_gene_variant,,ENST00000465640,;GDI1,downstream_gene_variant,,ENST00000471972,;FAM50A,non_coding_transcript_exon_variant,,ENST00000464419,;FAM50A,non_coding_transcript_exon_variant,,ENST00000481619,;GDI1,downstream_gene_variant,,ENST00000491154,;GDI1,downstream_gene_variant,,ENST00000468483,;GDI1,downstream_gene_variant,,ENST00000476540,;GDI1,downstream_gene_variant,,ENST00000481304,;GDI1,downstream_gene_variant,,ENST00000489589,;GDI1,downstream_gene_variant,,ENST00000434049,;FAM50A,upstream_gene_variant,,ENST00000478509,;GDI1,downstream_gene_variant,,ENST00000445564,;GDI1,downstream_gene_variant,,ENST00000460984,;FAM50A,upstream_gene_variant,,ENST00000490480,; T ENST00000393600 Transcript synonymous_variant 131/1352 21/1020 7/339 A gcC/gcT 1 1 FAM50A HGNC HGNC:18786 protein_coding YES CCDS14751.1 ENSP00000377225 Q14320 UPI0000138FCD NM_004699.3 1/13 hmmpanther:PTHR12722,hmmpanther:PTHR12722:SF2 LOW 1 SNV 1 1 PASS . . 0 204 5 0 0 0 0 0 -18.91123 1 1 1 1 0 T 2 4 99 154444256 154444256 C T 1 0 0 0 0 0 0 0 1 5453 639 23 1 1 FAM50A 23 154444256 Silent SNP C C3N-02423_T 35362760 154444256 1596639 460 29590 ARHGEF16 0 . GRCh38 1 3463205 3463205 + Missense_Mutation SNP T T A novel C3N-02424_T C3N-02424_N T T c.121T>A p.Ser41Thr p.S41T ENST00000378378 2/15 63 52 11 75 75 0 strelka-varscan-mutect ARHGEF16,missense_variant,p.Ser41Thr,ENST00000378378,NM_014448.3;ARHGEF16,upstream_gene_variant,,ENST00000378371,;ARHGEF16,upstream_gene_variant,,ENST00000378373,; A ENST00000378378 Transcript missense_variant 526/3061 121/2130 41/709 S/T Tcc/Acc 1 1 ARHGEF16 HGNC HGNC:15515 protein_coding YES CCDS46.2 ENSP00000367629 Q5VV41 UPI00002039A3 NM_014448.3 tolerated(0.25) 2/15 hmmpanther:PTHR12845:SF3,hmmpanther:PTHR12845 MODERATE 1 SNV 2 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 3463205 3463205 T A 1 0 0 0 0 1 0 0 0 1029 1551 54 4 4 ARHGEF16 1 3463205 Missense_Mutation SNP T C3N-02424_T 3463205 245493217 1 29591 USP24 0 . GRCh38 1 55079546 55079546 + Missense_Mutation SNP G G C novel C3N-02424_T C3N-02424_N G G c.7192C>G p.Leu2398Val p.L2398V ENST00000294383 60/68 201 190 11 425 424 1 strelka-varscan-mutect USP24,missense_variant,p.Leu2398Val,ENST00000294383,NM_015306.2;USP24,upstream_gene_variant,,ENST00000484447,;USP24,downstream_gene_variant,,ENST00000472566,;USP24,downstream_gene_variant,,ENST00000512504,; C ENST00000294383 Transcript missense_variant 7192/10549 7192/7863 2398/2620 L/V Ctg/Gtg 1 -1 USP24 HGNC HGNC:12623 protein_coding YES CCDS44154.2 ENSP00000294383 Q9UPU5 UPI000059CFDE NM_015306.2 tolerated(0.19) 60/68 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 55079546 55079546 G C 1 0 0 0 0 1 0 0 0 17596 991 35 4 4 USP24 1 55079546 Missense_Mutation SNP G C3N-02424_T 51616341 55079546 193876876 2 29592 LHX8 0 . GRCh38 1 75143261 75143262 + Frame_Shift_Ins INS - - T novel C3N-02424_T C3N-02424_N - - c.536dupT p.Leu179PhefsTer13 p.L179Ffs*13 ENST00000294638 6/10 165 144 21 312 312 0 sindel-varindel-pindel LHX8,frameshift_variant,p.Leu179PhefsTer13,ENST00000294638,NM_001001933.1;LHX8,frameshift_variant,p.Leu169PhefsTer13,ENST00000356261,NM_001256114.1; T ENST00000294638 Transcript frameshift_variant 1197-1198/2373 533-534/1071 178/356 A/AX gct/gcTt 1 1 LHX8 HGNC HGNC:28838 protein_coding YES CCDS30756.1 ENSP00000294638 Q68G74 UPI00001972E8 NM_001001933.1 6/10 Gene3D:2.10.110.10,Pfam_domain:PF00412,PROSITE_profiles:PS50023,hmmpanther:PTHR24208,SMART_domains:SM00132 HIGH 1 insertion 1 3 1 PASS . . 0 208 0 2 0 0 0 0 -20 0.9999999 1 1 1 0 T 7 5 100 75143261 75143261 - T 1 0 1 1 0 0 0 0 0 8685 797 28 0 0 LHX8 1 75143261 Frame_Shift_Ins INS - C3N-02424_T 20063715 75143261 173813161 3 29593 BRDT 0 . GRCh38 1 91991240 91991240 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.2071G>T p.Val691Leu p.V691L ENST00000399546 13/19 22 19 3 93 93 0 strelka-mutect BRDT,missense_variant,p.Val614Leu,ENST00000370389,NM_001242810.2;BRDT,missense_variant,p.Val687Leu,ENST00000362005,NM_001242805.2,NM_207189.3;BRDT,missense_variant,p.Val691Leu,ENST00000399546,NM_001242806.2;BRDT,missense_variant,p.Val641Leu,ENST00000394530,NM_001242808.2,NM_001242807.2;BRDT,missense_variant,p.Val687Leu,ENST00000402388,NM_001726.4; T ENST00000399546 Transcript missense_variant 2420/3357 2071/2856 691/951 V/L Gta/Tta 1 1 BRDT HGNC HGNC:1105 protein_coding YES CCDS72820.1 ENSP00000387822 Q58F21 UPI000292A27D NM_001242806.2 tolerated(0.31) 13/19 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -9.779573 1 1 1 1 0 T 3 4 100 91991240 91991240 G T 1 0 0 0 0 1 0 0 0 1678 1391 48 2 2 BRDT 1 91991240 Missense_Mutation SNP G C3N-02424_T 16847979 91991240 156965182 4 29594 FLG 0 . GRCh38 1 152308784 152308784 + Missense_Mutation SNP A A T rs766524788 C3N-02424_T C3N-02424_N A A c.6102T>A p.Ser2034Arg p.S2034R ENST00000368799 3/3 737 664 73 1142 1142 0 strelka-varscan-mutect FLG,missense_variant,p.Ser2034Arg,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript missense_variant 6138/12747 6102/12186 2034/4061 S/R agT/agA rs766524788 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 tolerated(0.5) 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 MODERATE 1 SNV 1 1 PASS rs766524788 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 152308784 152308784 A T 1 0 0 0 0 1 0 0 0 5784 156 6 4 4 FLG 1 152308784 Missense_Mutation SNP A C3N-02424_T 60317544 152308784 96647638 5 29595 ARHGAP30 0 . GRCh38 1 161048173 161048173 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.2848C>A p.Pro950Thr p.P950T ENST00000368013 12/12 196 178 18 280 279 1 strelka-varscan-mutect ARHGAP30,missense_variant,p.Pro950Thr,ENST00000368013,NM_001287600.1,NM_001025598.1;ARHGAP30,missense_variant,p.Pro773Thr,ENST00000368015,NM_001287602.1;ARHGAP30,missense_variant,p.Pro739Thr,ENST00000368016,NM_181720.2;USF1,upstream_gene_variant,,ENST00000368021,NM_007122.4,NM_207005.2;USF1,upstream_gene_variant,,ENST00000368020,NM_001276373.1;USF1,upstream_gene_variant,,ENST00000368019,;USF1,upstream_gene_variant,,ENST00000531842,;USF1,upstream_gene_variant,,ENST00000534633,;ARHGAP30,non_coding_transcript_exon_variant,,ENST00000461003,;ARHGAP30,downstream_gene_variant,,ENST00000490279,;USF1,upstream_gene_variant,,ENST00000473969,;USF1,upstream_gene_variant,,ENST00000496363,;USF1,upstream_gene_variant,,ENST00000491629,;USF1,upstream_gene_variant,,ENST00000529476,; T ENST00000368013 Transcript missense_variant 3169/4394 2848/3306 950/1101 P/T Ccc/Acc 1 -1 ARHGAP30 HGNC HGNC:27414 protein_coding YES CCDS30918.1 ENSP00000356992 Q7Z6I6 UPI0000160677 NM_001287600.1,NM_001025598.1 deleterious(0) 12/12 hmmpanther:PTHR15729:SF12,hmmpanther:PTHR15729 MODERATE SNV 2 1 PASS . . 0 207 0 2 0 0 0 0 -19.99996 0.9999998 1 1 1 0 T 3 4 100 161048173 161048173 G T 1 0 0 0 0 1 0 0 0 1004 1203 42 2 2 ARHGAP30 1 161048173 Missense_Mutation SNP G C3N-02424_T 8739389 161048173 87908249 6 29596 CR1L 0 . GRCh38 1 207677448 207677448 + Missense_Mutation SNP T T A rs747900861 C3N-02424_T C3N-02424_N T T c.157T>A p.Phe53Ile p.F53I ENST00000508064 2/12 134 127 7 170 170 0 varscan-mutect CR1L,missense_variant,p.Phe53Ile,ENST00000508064,NM_175710.1;CR1L,non_coding_transcript_exon_variant,,ENST00000530905,;CR1L,non_coding_transcript_exon_variant,,ENST00000430248,;CR1L,non_coding_transcript_exon_variant,,ENST00000531844,;CR1L,upstream_gene_variant,,ENST00000294997,; A ENST00000508064 Transcript missense_variant 217/1788 157/1710 53/569 F/I Ttt/Att rs747900861 1 1 CR1L HGNC HGNC:2335 protein_coding YES CCDS44310.1 ENSP00000421736 Q2VPA4 UPI0000DD792A NM_175710.1 deleterious(0.03) 2/12 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF354,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 2 1 PASS rs747900861 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 207677448 207677448 T A 1 0 0 0 0 1 0 0 0 3639 1609 56 4 4 CR1L 1 207677448 Missense_Mutation SNP T C3N-02424_T 46629275 207677448 41278974 7 29597 MYT1L 0 . GRCh38 2 1943229 1943229 + Frame_Shift_Del DEL T T - novel C3N-02424_T C3N-02424_N T T c.258delA p.Val87TrpfsTer87 p.V87Wfs*87 ENST00000399161 9/25 285 250 35 394 394 0 sindel-varindel-pindel MYT1L,frameshift_variant,p.Val87TrpfsTer87,ENST00000399161,NM_001303052.1;MYT1L,frameshift_variant,p.Val87TrpfsTer87,ENST00000428368,NM_015025.3; - ENST00000399161 Transcript frameshift_variant 1006/7063 258/3561 86/1186 S/X tcA/tc 1 -1 MYT1L HGNC HGNC:7623 protein_coding YES CCDS77378.1 ENSP00000382114 Q9UL68 UPI0000140B19 NM_001303052.1 9/25 Low_complexity_(Seg):seg,hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF11 HIGH 1 deletion 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 100 1943229 1943229 T - 1 0 1 0 1 0 0 0 0 10106 1567 55 0 0 MYT1L 2 1943229 Frame_Shift_Del DEL T C3N-02424_T 1943229 240250300 8 29598 ADAMTS9 0 . GRCh38 3 64686782 64686782 + Missense_Mutation SNP C C T novel C3N-02424_T C3N-02424_N C C c.302G>A p.Arg101His p.R101H ENST00000498707 2/40 254 221 33 373 373 0 strelka-varscan-mutect ADAMTS9,missense_variant,p.Arg101His,ENST00000498707,NM_182920.1;ADAMTS9,missense_variant,p.Arg101His,ENST00000295903,NM_001318781.1;ADAMTS9,missense_variant,p.Arg101His,ENST00000459780,;ADAMTS9-AS2,intron_variant,,ENST00000460833,;ADAMTS9-AS2,intron_variant,,ENST00000474768,;ADAMTS9-AS2,intron_variant,,ENST00000481312,;ADAMTS9-AS2,intron_variant,,ENST00000485174,;ADAMTS9,non_coding_transcript_exon_variant,,ENST00000475557,;ADAMTS9,upstream_gene_variant,,ENST00000482490,; T ENST00000498707 Transcript missense_variant 645/7624 302/5808 101/1935 R/H cGc/cAc 1 -1 ADAMTS9 HGNC HGNC:13202 protein_coding YES CCDS2903.1 ENSP00000418735 Q9P2N4 UPI00000463F0 NM_182920.1 deleterious(0) 2/40 Pfam_domain:PF01562 MODERATE 1 SNV 1 1 PASS rs1175785790 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 64686782 64686782 C T 1 0 0 0 0 1 0 0 0 317 768 27 1 1 ADAMTS9 3 64686782 Missense_Mutation SNP C C3N-02424_T 64686782 133608777 9 29599 EVC 0 . GRCh38 4 5798723 5798723 + Silent SNP G G A novel C3N-02424_T C3N-02424_N G G c.2235G>A p.= p.G745G ENST00000264956 15/21 235 215 20 341 340 1 strelka-varscan-mutect EVC,synonymous_variant,p.=,ENST00000264956,NM_001306090.1,NM_153717.2;EVC,non_coding_transcript_exon_variant,,ENST00000515113,;CRMP1,intron_variant,,ENST00000506216,;EVC,downstream_gene_variant,,ENST00000506240,; A ENST00000264956 Transcript synonymous_variant 2419/6431 2235/2979 745/992 G ggG/ggA 1 1 EVC HGNC HGNC:3497 protein_coding YES CCDS3383.1 ENSP00000264956 P57679 UPI000012A2A5 NM_001306090.1,NM_153717.2 15/21 hmmpanther:PTHR16795,hmmpanther:PTHR16795:SF13 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 100 5798723 5798723 G A 1 0 0 0 0 0 0 0 1 5152 1190 42 3 3 EVC 4 5798723 Silent SNP G C3N-02424_T 5798723 184415832 10 29600 ADGRL3 0 . GRCh38 4 61983414 61983414 + Missense_Mutation SNP A A G novel C3N-02424_T C3N-02424_N A A c.2843A>G p.His948Arg p.H948R ENST00000514591 18/25 119 99 20 187 187 0 strelka-varscan ADGRL3,missense_variant,p.His948Arg,ENST00000512091,NM_001322246.1;ADGRL3,missense_variant,p.His948Arg,ENST00000514591,NM_015236.4;ADGRL3,missense_variant,p.His1016Arg,ENST00000509896,;ADGRL3,missense_variant,p.His1016Arg,ENST00000511324,;ADGRL3,missense_variant,p.His1016Arg,ENST00000508693,;ADGRL3,missense_variant,p.His1016Arg,ENST00000507164,;ADGRL3,missense_variant,p.His1016Arg,ENST00000506720,;ADGRL3,missense_variant,p.His1016Arg,ENST00000506746,;ADGRL3,missense_variant,p.His1016Arg,ENST00000507625,;ADGRL3,missense_variant,p.His948Arg,ENST00000506700,;ADGRL3,missense_variant,p.His948Arg,ENST00000504896,;ADGRL3,missense_variant,p.His948Arg,ENST00000514157,;ADGRL3,missense_variant,p.His948Arg,ENST00000508946,;ADGRL3,missense_variant,p.His948Arg,ENST00000514996,;ADGRL3,missense_variant,p.His406Arg,ENST00000502815,; G ENST00000514591 Transcript missense_variant 3172/6297 2843/4410 948/1469 H/R cAt/cGt 1 1 ADGRL3 HGNC HGNC:20974 protein_coding YES CCDS54768.1 ENSP00000422533 Q9HAR2 UPI00016278EF NM_015236.4 deleterious(0) 18/25 Low_complexity_(Seg):seg,PROSITE_profiles:PS50261,hmmpanther:PTHR12011:SF60,hmmpanther:PTHR12011,Pfam_domain:PF00002,Superfamily_domains:SSF81321,Prints_domain:PR00249,Transmembrane_helices:TMhelix MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 100 61983414 61983414 A G 1 0 0 0 0 1 0 0 0 377 217 8 5 5 ADGRL3 4 61983414 Missense_Mutation SNP A C3N-02424_T 56184691 61983414 128231141 11 29601 UGT2A1 0 . GRCh38 4 69589521 69589521 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.1933C>A p.His645Asn p.H645N ENST00000514019 7/7 232 201 31 408 407 1 strelka-varscan UGT2A1,missense_variant,p.His479Asn,ENST00000503640,NM_006798.4;UGT2A1,missense_variant,p.His435Asn,ENST00000512704,NM_001301239.1;UGT2A1,missense_variant,p.His645Asn,ENST00000514019,NM_001252274.2;UGT2A1,missense_variant,p.His479Asn,ENST00000286604,NM_001252275.2;UGT2A2,missense_variant,p.His488Asn,ENST00000604629,NM_001105677.2;UGT2A2,missense_variant,p.His444Asn,ENST00000604021,NM_001301233.1;UGT2A1,downstream_gene_variant,,ENST00000502343,;RP11-401E5.2,upstream_gene_variant,,ENST00000506662,; T ENST00000514019 Transcript missense_variant 2049/2376 1933/2082 645/693 H/N Cat/Aat 1 -1 UGT2A1 HGNC HGNC:12542 protein_coding YES CCDS58902.1 ENSP00000425497 A0A140T9Z0 UPI0004620AF5 NM_001252274.2 deleterious(0.01) 7/7 Pfam_domain:PF00201,hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF229 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 69589521 69589521 G T 1 0 0 0 0 1 0 0 0 17478 1348 47 2 2 UGT2A1 4 69589521 Missense_Mutation SNP G C3N-02424_T 7606107 69589521 120625034 12 29602 SHROOM3 0 . GRCh38 4 76754309 76754309 + Splice_Site SNP A A T novel C3N-02424_T C3N-02424_N A A c.3828-2A>T p.X1276_splice ENST00000296043 222 201 21 302 302 0 strelka-varscan SHROOM3,splice_acceptor_variant,,ENST00000296043,NM_020859.3;RP11-359D14.2,downstream_gene_variant,,ENST00000452412,;RP11-359D14.3,downstream_gene_variant,,ENST00000449007,;SHROOM3,splice_acceptor_variant,,ENST00000469923,; T ENST00000296043 Transcript splice_acceptor_variant -/11020 3828/5991 1276/1996 1 1 SHROOM3 HGNC HGNC:30422 protein_coding YES CCDS3579.2 ENSP00000296043 Q8TF72 UPI0000E5AC1C NM_020859.3 6/10 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 100 76754309 76754309 A T 1 0 0 0 0 0 0 1 0 14558 202 7 4 4 SHROOM3 4 76754309 Splice_Site SNP A C3N-02424_T 7164788 76754309 113460246 13 29603 FGB 0 . GRCh38 4 154570481 154570481 + Missense_Mutation SNP G G A novel C3N-02424_T C3N-02424_N G G c.1307G>A p.Arg436Lys p.R436K ENST00000302068 8/8 356 337 19 522 522 0 strelka-varscan FGB,missense_variant,p.Arg436Lys,ENST00000302068,NM_005141.4,NM_001184741.1;FGB,missense_variant,p.Arg217Lys,ENST00000509493,;FGB,non_coding_transcript_exon_variant,,ENST00000502545,;FGB,downstream_gene_variant,,ENST00000498375,;FGB,downstream_gene_variant,,ENST00000473984,;FGB,downstream_gene_variant,,ENST00000497097,;FGB,downstream_gene_variant,,ENST00000425838,; A ENST00000302068 Transcript missense_variant 1370/1975 1307/1476 436/491 R/K aGa/aAa 1 1 FGB HGNC HGNC:3662 protein_coding YES CCDS3786.1 ENSP00000306099 P02675 V9HVY1 UPI000012A778 NM_005141.4,NM_001184741.1 tolerated(0.3) 8/8 Gene3D:4.10.530.10,Pfam_domain:PF00147,PROSITE_patterns:PS00514,PROSITE_profiles:PS51406,hmmpanther:PTHR19143,hmmpanther:PTHR19143:SF203,SMART_domains:SM00186,Superfamily_domains:SSF56496 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 154570481 154570481 G A 1 0 0 0 0 1 0 0 0 5695 942 33 3 3 FGB 4 154570481 Missense_Mutation SNP G C3N-02424_T 77816172 154570481 35644074 14 29604 UBE2QL1 0 . GRCh38 5 6448902 6448902 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.9G>T p.Glu3Asp p.E3D ENST00000399816 1/2 110 100 10 81 81 0 strelka-varscan-mutect UBE2QL1,missense_variant,p.Glu3Asp,ENST00000399816,NM_001145161.2; T ENST00000399816 Transcript missense_variant 280/4317 9/486 3/161 E/D gaG/gaT 1 1 UBE2QL1 HGNC HGNC:37269 protein_coding YES CCDS47189.1 ENSP00000382713 A1L167 UPI000020BF29 NM_001145161.2 deleterious(0) 1/2 PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF72,hmmpanther:PTHR24068,Pfam_domain:PF00179,Gene3D:3.10.110.10,SMART_domains:SM00212,Superfamily_domains:SSF54495 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -19.73935 1 1 1 1 0 T 3 4 100 6448902 6448902 G T 1 0 0 0 0 1 0 0 0 17393 962 34 2 2 UBE2QL1 5 6448902 Missense_Mutation SNP G C3N-02424_T 6448902 175089357 15 29605 UBE2QL1 0 . GRCh38 5 6449161 6449161 + Nonsense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.268G>T p.Glu90Ter p.E90* ENST00000399816 1/2 102 96 6 73 73 0 strelka-mutect UBE2QL1,stop_gained,p.Glu90Ter,ENST00000399816,NM_001145161.2; T ENST00000399816 Transcript stop_gained 539/4317 268/486 90/161 E/* Gag/Tag 1 1 UBE2QL1 HGNC HGNC:37269 protein_coding YES CCDS47189.1 ENSP00000382713 A1L167 UPI000020BF29 NM_001145161.2 1/2 PROSITE_profiles:PS50127,hmmpanther:PTHR24068:SF72,hmmpanther:PTHR24068,Pfam_domain:PF00179,Gene3D:3.10.110.10,SMART_domains:SM00212,Superfamily_domains:SSF54495 HIGH 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -12.58461 1 1 1 1 0 T 4 4 100 6449161 6449161 G T 1 0 0 0 0 0 1 0 0 17393 1175 41 2 2 UBE2QL1 5 6449161 Nonsense_Mutation SNP G C3N-02424_T 259 6449161 175089098 16 29606 PDE6A 0 . GRCh38 5 149944651 149944651 + Missense_Mutation SNP T T A novel C3N-02424_T C3N-02424_N T T c.23A>T p.Glu8Val p.E8V ENST00000255266 1/22 252 221 31 364 364 0 strelka-varscan-mutect PDE6A,missense_variant,p.Glu8Val,ENST00000255266,NM_000440.2;PDE6A,missense_variant,p.Glu8Val,ENST00000613228,;PDE6A,missense_variant,p.Glu8Val,ENST00000617647,;Y_RNA,upstream_gene_variant,,ENST00000363464,;PDE6A,non_coding_transcript_exon_variant,,ENST00000508173,; A ENST00000255266 Transcript missense_variant 143/5642 23/2583 8/860 E/V gAg/gTg 1 -1 PDE6A HGNC HGNC:8785 protein_coding YES CCDS4299.1 ENSP00000255266 P16499 UPI000013CE9F NM_000440.2 tolerated(0.33) 1/22 hmmpanther:PTHR11347:SF115,hmmpanther:PTHR11347 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 149944651 149944651 T A 1 0 0 0 0 1 0 0 0 11733 1551 54 4 4 PDE6A 5 149944651 Missense_Mutation SNP T C3N-02424_T 143495490 149944651 31593608 17 29607 TNXB 0 . GRCh38 6 32095831 32095831 + Silent SNP G G T rs553907333 C3N-02424_T C3N-02424_N G G c.2022C>A p.= p.G674G ENST00000375244 3/44 294 231 63 387 386 1 strelka-varscan TNXB,synonymous_variant,p.=,ENST00000375244,NM_019105.6;TNXB,synonymous_variant,p.=,ENST00000613214,;TNXB,synonymous_variant,p.=,ENST00000479795,;TNXB,downstream_gene_variant,,ENST00000442721,;ATF6B,downstream_gene_variant,,ENST00000494022,;TNXB,non_coding_transcript_exon_variant,,ENST00000486148,; T ENST00000375244 Transcript synonymous_variant 2224/13132 2022/12735 674/4244 G ggC/ggA rs553907333 1 -1 TNXB HGNC HGNC:11976 protein_coding ENSP00000364393 P22105 E7EPZ9 UPI0001B798E9 NM_019105.6 3/44 PROSITE_patterns:PS00022,PROSITE_patterns:PS01186,Gene3D:2gy5A03,SMART_domains:SM00181 LOW SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 100 32095831 32095831 G T 1 0 0 0 0 0 0 0 1 16820 1074 38 1 1 TNXB 6 32095831 Silent SNP G C3N-02424_T 32095831 138710148 18 29608 MDN1 0 . GRCh38 6 89793953 89793953 + Missense_Mutation SNP A A C novel C3N-02424_T C3N-02424_N A A c.664T>G p.Leu222Val p.L222V ENST00000369393 5/102 69 53 16 64 63 1 strelka-mutect MDN1,missense_variant,p.Leu222Val,ENST00000369393,NM_014611.2;MDN1,missense_variant,p.Leu222Val,ENST00000629399,;MDN1,missense_variant,p.Leu222Val,ENST00000439638,;DNAJC19P6,upstream_gene_variant,,ENST00000401853,; C ENST00000369393 Transcript missense_variant,splice_region_variant 780/18413 664/16791 222/5596 L/V Tta/Gta 1 -1 MDN1 HGNC HGNC:18302 protein_coding YES CCDS5024.1 ENSP00000358400 Q9NU22 UPI000013C4B8 NM_014611.2 tolerated(0.1) 5/102 hmmpanther:PTHR22908,hmmpanther:PTHR22908:SF64 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 89793953 89793953 A C 1 0 0 0 0 1 0 0 0 9353 57 2 5 5 MDN1 6 89793953 Missense_Mutation SNP A C3N-02424_T 57698122 89793953 81012026 19 29609 RSPH4A 0 . GRCh38 6 116628150 116628152 + In_Frame_Del DEL TAA TAA - novel C3N-02424_T C3N-02424_N TAA TAA c.1444_1446delAAT p.Asn482del p.N482del ENST00000229554 3/6 191 180 11 277 277 0 varindel-pindel RSPH4A,inframe_deletion,p.Asn482del,ENST00000229554,NM_001010892.2;RSPH4A,inframe_deletion,p.Asn482del,ENST00000368581,NM_001161664.1;RSPH4A,intron_variant,,ENST00000368580,; - ENST00000229554 Transcript inframe_deletion 1580-1582/2825 1443-1445/2151 481-482/716 SN/S agTAAt/agt 1 1 RSPH4A HGNC HGNC:21558 protein_coding YES CCDS34521.1 ENSP00000229554 Q5TD94 UPI00001D80C4 NM_001010892.2 3/6 hmmpanther:PTHR13159:SF4,hmmpanther:PTHR13159,Pfam_domain:PF04712 MODERATE 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 100 116628150 116628150 TAA - 1 0 1 0 1 0 0 0 0 13964 1635 57 0 0 RSPH4A 6 116628150 In_Frame_Del DEL TAA C3N-02424_T 26834197 116628150 54177829 20 29610 SCIN 0 . GRCh38 7 12644203 12644203 + Missense_Mutation SNP T T G novel C3N-02424_T C3N-02424_N T T c.1647T>G p.Ser549Arg p.S549R ENST00000297029 12/16 175 141 34 254 254 0 strelka-varscan-mutect SCIN,missense_variant,p.Ser549Arg,ENST00000297029,NM_001112706.2;SCIN,missense_variant,p.Ser302Arg,ENST00000519209,NM_033128.3;SCIN,intron_variant,,ENST00000341757,; G ENST00000297029 Transcript missense_variant 1748/9713 1647/2148 549/715 S/R agT/agG 1 1 SCIN HGNC HGNC:21695 protein_coding YES CCDS47545.1 ENSP00000297029 Q9Y6U3 UPI000013C4DF NM_001112706.2 tolerated(0.42) 12/16 Gene3D:3.40.20.10,Pfam_domain:PF00626,hmmpanther:PTHR11977,hmmpanther:PTHR11977:SF14,SMART_domains:SM00262,Superfamily_domains:SSF55753 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 100 12644203 12644203 T G 1 0 0 0 0 1 0 0 0 14174 1693 59 5 5 SCIN 7 12644203 Missense_Mutation SNP T C3N-02424_T 12644203 146701770 21 29611 DNAH11 0 . GRCh38 7 21816686 21816686 + Missense_Mutation SNP C C T novel C3N-02424_T C3N-02424_N C C c.10552C>T p.His3518Tyr p.H3518Y ENST00000409508 64/82 135 117 18 183 183 0 strelka-varscan-mutect DNAH11,missense_variant,p.His3518Tyr,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.His3525Tyr,ENST00000328843,;DNAH11,missense_variant,p.His3525Tyr,ENST00000620169,; T ENST00000409508 Transcript missense_variant 10583/14167 10552/13551 3518/4516 H/Y Cat/Tat 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 deleterious(0) 64/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676,Pfam_domain:PF12781 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 21816686 21816686 C T 1 0 0 0 0 1 0 0 0 4413 478 17 3 3 DNAH11 7 21816686 Missense_Mutation SNP C C3N-02424_T 9172483 21816686 137529287 22 29612 EVX1 0 . GRCh38 7 27243453 27243453 + Missense_Mutation SNP C C G C3N-02424_T C3N-02424_N C C c.423C>G p.Ser141Arg p.S141R ENST00000496902 1/3 65 60 5 79 79 0 strelka-varscan EVX1,missense_variant,p.Ser141Arg,ENST00000496902,NM_001989.4,NM_001304519.1;EVX1,intron_variant,,ENST00000580535,;EVX1,intron_variant,,ENST00000222761,;RP1-170O19.17,upstream_gene_variant,,ENST00000523608,;EVX1-AS,intron_variant,,ENST00000519218,;EVX1-AS,intron_variant,,ENST00000517726,;EVX1-AS,upstream_gene_variant,,ENST00000519050,;EVX1,upstream_gene_variant,,ENST00000518886,; G ENST00000496902 Transcript missense_variant 754/2955 423/1224 141/407 S/R agC/agG COSM746298 1 1 EVX1 HGNC HGNC:3506 protein_coding YES CCDS5413.1 ENSP00000419266 P49640 UPI000012A2AD NM_001989.4,NM_001304519.1 tolerated(0.11) 1/3 hmmpanther:PTHR24329:SF246,hmmpanther:PTHR24329 1 MODERATE 1 SNV 1 1 1 PASS . . 0 205 5 0 0 0 0 0 -11.68722 1 1 1 1 0 G 3 3 100 27243453 27243453 C G 1 0 0 0 0 1 0 0 0 5161 724 25 4 4 EVX1 7 27243453 Missense_Mutation SNP C C3N-02424_T 5426767 27243453 132102520 23 29613 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02424_T C3N-02424_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 503 472 31 583 581 2 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 100 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02424_T 27948369 55191822 104154151 24 29614 ZNF716 0 . GRCh38 7 57462532 57462532 + Missense_Mutation SNP C C A novel C3N-02424_T C3N-02424_N C C c.112C>A p.Gln38Lys p.Q38K ENST00000420713 2/4 149 133 16 308 307 1 strelka-varscan-mutect ZNF716,missense_variant,p.Gln38Lys,ENST00000420713,NM_001159279.1; A ENST00000420713 Transcript missense_variant 224/5197 112/1488 38/495 Q/K Cag/Aag 1 1 ZNF716 HGNC HGNC:32458 protein_coding YES CCDS55112.1 ENSP00000394248 A6NP11 UPI00004192FD NM_001159279.1 deleterious(0.05) 2/4 Superfamily_domains:0044637,Pfam_domain:PF01352,PROSITE_profiles:PS50805,hmmpanther:PTHR24384,hmmpanther:PTHR24384:SF100,SMART_domains:SM00349 MODERATE 1 SNV 4 1 PASS rs1242623812 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 57462532 57462532 C A 1 0 0 0 0 1 0 0 0 18694 711 25 2 2 ZNF716 7 57462532 Missense_Mutation SNP C C3N-02424_T 2270710 57462532 101883441 25 29615 SEMA3A 0 . GRCh38 7 83977191 83977191 + Missense_Mutation SNP G G C novel C3N-02424_T C3N-02424_N G G c.1658C>G p.Thr553Arg p.T553R ENST00000265362 15/17 84 79 5 165 165 0 strelka-varscan SEMA3A,missense_variant,p.Thr553Arg,ENST00000265362,NM_006080.2;SEMA3A,missense_variant,p.Thr553Arg,ENST00000436949,; C ENST00000265362 Transcript missense_variant 1973/8225 1658/2316 553/771 T/R aCa/aGa 1 -1 SEMA3A HGNC HGNC:10723 protein_coding YES CCDS5599.1 ENSP00000265362 Q14563 UPI0000135A60 NM_006080.2 tolerated(0.05) 15/17 Gene3D:3.30.1680.10,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF23,SMART_domains:SM00423,Superfamily_domains:SSF103575 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 83977191 83977191 G C 1 0 0 0 0 1 0 0 0 14300 1391 48 4 4 SEMA3A 7 83977191 Missense_Mutation SNP G C3N-02424_T 26514659 83977191 75368782 26 29616 DLX6 0 . GRCh38 7 97006010 97006010 + Missense_Mutation SNP G G C novel C3N-02424_T C3N-02424_N G G c.33G>C p.Leu11Phe p.L11F ENST00000518156 1/3 125 106 19 201 201 0 strelka-varscan DLX6,missense_variant,p.Leu11Phe,ENST00000518156,NM_005222.3;DLX6,upstream_gene_variant,,ENST00000555308,;DLX6-AS1,intron_variant,,ENST00000430027,;DLX6-AS1,intron_variant,,ENST00000605417,;DLX6-AS1,intron_variant,,ENST00000437331,;DLX6-AS1,intron_variant,,ENST00000452769,;DLX6-AS1,intron_variant,,ENST00000458352,;DLX6-AS1,intron_variant,,ENST00000430404,;DLX6-AS1,intron_variant,,ENST00000437541,;DLX6-AS1,upstream_gene_variant,,ENST00000431497,;DLX6,upstream_gene_variant,,ENST00000493273,; C ENST00000518156 Transcript missense_variant 463/2304 33/882 11/293 L/F ttG/ttC 1 1 DLX6 HGNC HGNC:2919 protein_coding YES CCDS47647.2 ENSP00000428480 P56179 UPI0000EE57E0 NM_005222.3 deleterious(0) 1/3 hmmpanther:PTHR24327,hmmpanther:PTHR24327:SF26 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 97006010 97006010 G C 1 0 0 0 0 1 0 0 0 4382 1339 47 4 4 DLX6 7 97006010 Missense_Mutation SNP G C3N-02424_T 13028819 97006010 62339963 27 29617 RELN 0 . GRCh38 7 103651667 103651667 + Missense_Mutation SNP T T A novel C3N-02424_T C3N-02424_N T T c.1886A>T p.Tyr629Phe p.Y629F ENST00000428762 15/65 270 243 27 345 345 0 strelka-varscan-mutect RELN,missense_variant,p.Tyr629Phe,ENST00000424685,;RELN,missense_variant,p.Tyr629Phe,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Tyr629Phe,ENST00000343529,NM_173054.2; A ENST00000428762 Transcript missense_variant 2046/11571 1886/10383 629/3460 Y/F tAc/tTc 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.4) 15/65 hmmpanther:PTHR11841,Superfamily_domains:SSF50939 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 103651667 103651667 T A 1 0 0 0 0 1 0 0 0 13390 1638 57 4 4 RELN 7 103651667 Missense_Mutation SNP T C3N-02424_T 6645657 103651667 55694306 28 29618 NEFM 0 . GRCh38 8 24918383 24918384 + Frame_Shift_Ins INS - - G novel C3N-02424_T C3N-02424_N - - c.2534dupG p.Asp846Ter p.D846* ENST00000221166 3/3 325 304 21 534 532 2 varindel-pindel NEFM,frameshift_variant,p.Asp846Ter,ENST00000221166,NM_005382.2;NEFM,frameshift_variant,p.Asp807Ter,ENST00000437366,;NEFM,frameshift_variant,p.Asp470Ter,ENST00000433454,NM_001105541.1;NEFM,frameshift_variant,p.Asp628Ter,ENST00000518131,;GS1-72M22.1,upstream_gene_variant,,ENST00000607058,;NEFM,non_coding_transcript_exon_variant,,ENST00000521540,;NEFM,downstream_gene_variant,,ENST00000523467,; G ENST00000221166 Transcript frameshift_variant 3310-3311/4020 2528-2529/2751 843/916 K/KX aag/aaGg 1 1 NEFM HGNC HGNC:7734 protein_coding YES CCDS6046.1 ENSP00000221166 P07197 UPI000013C7A9 NM_005382.2 3/3 Low_complexity_(Seg):seg HIGH 1 insertion 1 6 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 7 5 100 24918383 24918383 - G 1 0 1 1 0 0 0 0 0 10344 72 3 0 0 NEFM 8 24918383 Frame_Shift_Ins INS - C3N-02424_T 24918383 120220253 29 29619 PKIA 0 . GRCh38 8 78598389 78598389 + Missense_Mutation SNP C C T C3N-02424_T C3N-02424_N C C c.5C>T p.Thr2Ile p.T2I ENST00000396418 3/4 62 58 4 98 98 0 strelka-varscan-mutect PKIA,missense_variant,p.Thr2Ile,ENST00000396418,NM_006823.3,NM_181839.2;PKIA,missense_variant,p.Thr2Ile,ENST00000352966,;PKIA,missense_variant,p.Thr2Ile,ENST00000518467,; T ENST00000396418 Transcript missense_variant 491/4163 5/231 2/76 T/I aCt/aTt COSM1101870 1 1 PKIA HGNC HGNC:9017 protein_coding YES CCDS6222.1 ENSP00000379696 P61925 A0A024R7Y9 UPI0000000298 NM_006823.3,NM_181839.2 deleterious(0) 3/4 PD010366,Pfam_domain:PF02827,PIRSF_domain:PIRSF001667,hmmpanther:PTHR15416,hmmpanther:PTHR15416:SF2 1 MODERATE 1 SNV 2 1 1 PASS . . 0 197 12 0 0 0 0 0 -9.417139 0.9995391 1 1 1 0 T 3 4 100 78598389 78598389 C T 1 0 0 0 0 1 0 0 0 12069 565 20 3 3 PKIA 8 78598389 Missense_Mutation SNP C C3N-02424_T 53680006 78598389 66540247 30 29620 PMP2 0 . GRCh38 8 81444989 81444989 + Missense_Mutation SNP C C G rs376781525 C3N-02424_T C3N-02424_N C C c.74G>C p.Gly25Ala p.G25A ENST00000256103 2/4 76 71 5 80 80 0 varscan-mutect PMP2,missense_variant,p.Gly25Ala,ENST00000256103,NM_002677.3;PMP2,intron_variant,,ENST00000519260,;RP11-157I4.4,intron_variant,,ENST00000524085,; G ENST00000256103 Transcript missense_variant,splice_region_variant 211/3608 74/399 25/132 G/A gGt/gCt rs376781525 1 -1 PMP2 HGNC HGNC:9117 protein_coding YES CCDS6229.1 ENSP00000256103 P02689 UPI000013CEEB NM_002677.3 deleterious(0) 2/4 hmmpanther:PTHR11955:SF64,hmmpanther:PTHR11955,Gene3D:2.40.128.20,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR00178 MODERATE 1 SNV 1 1 PASS rs376781525 . 0 177 27 6 0 0 0 0 -8.383313 0.4903049 0 1 0 0 G 3 3 100 81444989 81444989 C G 1 0 0 0 0 1 0 0 0 12245 521 18 4 4 PMP2 8 81444989 Missense_Mutation SNP C C3N-02424_T 2846600 81444989 63693647 31 29621 STOML2 0 . GRCh38 9 35100643 35100643 + Missense_Mutation SNP G G C novel C3N-02424_T C3N-02424_N G G c.888C>G p.Ile296Met p.I296M ENST00000356493 9/10 300 280 20 371 371 0 strelka-varscan-mutect STOML2,missense_variant,p.Ile251Met,ENST00000452248,NM_001287031.1;STOML2,missense_variant,p.Ile250Met,ENST00000619795,NM_001287033.1;STOML2,missense_variant,p.Ile296Met,ENST00000356493,NM_013442.2,NM_001287032.1;FAM214B,downstream_gene_variant,,ENST00000378561,;PIGO,upstream_gene_variant,,ENST00000378617,NM_032634.3;FAM214B,downstream_gene_variant,,ENST00000603301,NM_001317991.1;FAM214B,downstream_gene_variant,,ENST00000378557,;FAM214B,downstream_gene_variant,,ENST00000322813,NM_025182.2;FAM214B,downstream_gene_variant,,ENST00000605244,;FAM214B,downstream_gene_variant,,ENST00000488109,;PIGO,upstream_gene_variant,,ENST00000298004,NM_001201484.1;FAM214B,downstream_gene_variant,,ENST00000378566,;PIGO,upstream_gene_variant,,ENST00000361778,NM_152850.3;RP11-182N22.8,downstream_gene_variant,,ENST00000431804,;PIGO,upstream_gene_variant,,ENST00000492770,;PIGO,upstream_gene_variant,,ENST00000472208,;STOML2,downstream_gene_variant,,ENST00000487490,;STOML2,3_prime_UTR_variant,,ENST00000488050,;PIGO,upstream_gene_variant,,ENST00000474436,;PIGO,upstream_gene_variant,,ENST00000465745,; C ENST00000356493 Transcript missense_variant 951/1278 888/1071 296/356 I/M atC/atG 1 -1 STOML2 HGNC HGNC:14559 protein_coding YES CCDS6577.1 ENSP00000348886 Q9UJZ1 UPI000006E47E NM_013442.2,NM_001287032.1 tolerated(0.37) 9/10 hmmpanther:PTHR10264:SF27,hmmpanther:PTHR10264,Pfam_domain:PF16200 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 35100643 35100643 G C 1 0 0 0 0 1 0 0 0 15693 1164 41 4 4 STOML2 9 35100643 Missense_Mutation SNP G C3N-02424_T 35100643 103294074 32 29622 GLIPR2 0 . GRCh38 9 36162481 36162481 + Nonsense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.424G>T p.Glu142Ter p.E142* ENST00000377960 5/5 311 251 60 415 415 0 strelka-varscan-mutect GLIPR2,stop_gained,p.Glu142Ter,ENST00000377960,NM_001287013.1,NM_022343.3,NM_001287011.1;GLIPR2,stop_gained,p.Glu60Ter,ENST00000619700,NM_001287014.1;GLIPR2,stop_gained,p.Glu116Ter,ENST00000377959,NM_001287010.1;GLIPR2,3_prime_UTR_variant,,ENST00000396613,NM_001287012.1;GLIPR2,non_coding_transcript_exon_variant,,ENST00000474050,; T ENST00000377960 Transcript stop_gained 458/1890 424/465 142/154 E/* Gag/Tag 1 1 GLIPR2 HGNC HGNC:18007 protein_coding YES CCDS6598.1 ENSP00000367196 Q9H4G4 UPI000006DF50 NM_001287013.1,NM_022343.3,NM_001287011.1 5/5 Gene3D:3.40.33.10,hmmpanther:PTHR10334,Superfamily_domains:SSF55797 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 100 36162481 36162481 G T 1 0 0 0 0 0 1 0 0 6322 1291 45 2 2 GLIPR2 9 36162481 Nonsense_Mutation SNP G C3N-02424_T 1061838 36162481 102232236 33 29623 INPP5E 0 . GRCh38 9 136429709 136429709 + Missense_Mutation SNP C C A novel C3N-02424_T C3N-02424_N C C c.1901G>T p.Ser634Ile p.S634I ENST00000371712 10/10 385 332 53 547 547 0 strelka-varscan-mutect INPP5E,missense_variant,p.Ser634Ile,ENST00000371712,NM_001318502.1,NM_019892.4; A ENST00000371712 Transcript missense_variant 2304/3394 1901/1935 634/644 S/I aGt/aTt 1 -1 INPP5E HGNC HGNC:21474 protein_coding YES CCDS7000.1 ENSP00000360777 Q9NRR6 UPI000014053C NM_001318502.1,NM_019892.4 deleterious(0.05) 10/10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 136429709 136429709 C A 1 0 0 0 0 1 0 0 0 7660 565 20 2 2 INPP5E 9 136429709 Missense_Mutation SNP C C3N-02424_T 100267228 136429709 1965008 34 29624 MALRD1 0 . GRCh38 10 19531325 19531325 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.5452G>T p.Asp1818Tyr p.D1818Y ENST00000454679 32/40 66 54 12 104 104 0 strelka-mutect MALRD1,missense_variant,p.Asp1818Tyr,ENST00000454679,NM_001142308.2;MALRD1,missense_variant,p.Asp1197Tyr,ENST00000377266,;MALRD1,missense_variant,p.Asp169Tyr,ENST00000377265,;MALRD1,downstream_gene_variant,,ENST00000492202,; T ENST00000454679 Transcript missense_variant 5620/6880 5452/6471 1818/2156 D/Y Gat/Tat 1 1 MALRD1 HGNC HGNC:24331 protein_coding YES CCDS73071.1 ENSP00000412763 Q5VYJ5 UPI000387C99A NM_001142308.2 deleterious(0.01) 32/40 PROSITE_profiles:PS50060,hmmpanther:PTHR23282,hmmpanther:PTHR23282:SF86,Pfam_domain:PF00629,SMART_domains:SM00137,Superfamily_domains:SSF49899 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -19.98584 0.9999884 1 1 1 0 T 3 4 100 19531325 19531325 G T 1 0 0 0 0 1 0 0 0 9121 1290 45 2 2 MALRD1 10 19531325 Missense_Mutation SNP G C3N-02424_T 19531325 114266097 35 29625 CRTAC1 0 . GRCh38 10 97936338 97936338 + Missense_Mutation SNP A A T novel C3N-02424_T C3N-02424_N A A c.253T>A p.Tyr85Asn p.Y85N ENST00000370597 3/15 75 62 13 89 89 0 strelka-varscan-mutect CRTAC1,missense_variant,p.Tyr85Asn,ENST00000370597,NM_018058.6;CRTAC1,missense_variant,p.Tyr85Asn,ENST00000370591,NM_001206528.2;CRTAC1,missense_variant,p.Tyr77Asn,ENST00000309155,;CRTAC1,upstream_gene_variant,,ENST00000413387,; T ENST00000370597 Transcript missense_variant 609/2890 253/1986 85/661 Y/N Tat/Aat 1 -1 CRTAC1 HGNC HGNC:14882 protein_coding YES CCDS31266.1 ENSP00000359629 Q9NQ79 UPI000006D454 NM_018058.6 deleterious(0) 3/15 Pfam_domain:PF13517,hmmpanther:PTHR16026,hmmpanther:PTHR16026:SF4,Superfamily_domains:SSF69318 MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 97936338 97936338 A T 1 0 0 0 0 1 0 0 0 3698 391 14 4 4 CRTAC1 10 97936338 Missense_Mutation SNP A C3N-02424_T 78405013 97936338 35861084 36 29626 OTOG 0 . GRCh38 11 17642200 17642200 + Missense_Mutation SNP G G T rs117315845 C3N-02424_T C3N-02424_N G G c.8405G>T p.Arg2802Leu p.R2802L ENST00000399391 52/55 97 91 6 138 138 0 strelka-varscan-mutect OTOG,missense_variant,p.Arg2790Leu,ENST00000399397,NM_001292063.1;OTOG,missense_variant,p.Arg2802Leu,ENST00000399391,NM_001277269.1;OTOG,downstream_gene_variant,,ENST00000342528,; T ENST00000399391 Transcript missense_variant 8405/8778 8405/8778 2802/2925 R/L cGc/cTc rs117315845 1 1 OTOG HGNC HGNC:8516 protein_coding YES CCDS76390.1 ENSP00000382323 Q6ZRI0 UPI0001662628 NM_001277269.1 tolerated(0.26) 52/55 hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF228 MODERATE 1 SNV 5 1 PASS rs117315845 . 0 202 6 2 0 0 0 0 -9.643595 0.999516 1 1 1 0 T 3 4 100 17642200 17642200 G T 1 0 0 0 0 1 0 0 0 11370 1087 38 1 1 OTOG 11 17642200 Missense_Mutation SNP G C3N-02424_T 17642200 117444422 37 29627 FERMT3 0 . GRCh38 11 64207430 64207430 + Silent SNP G G A novel C3N-02424_T C3N-02424_N G G c.66G>A p.= p.V22V ENST00000279227 2/15 155 133 22 170 169 1 strelka-varscan-mutect FERMT3,synonymous_variant,p.=,ENST00000279227,NM_178443.2;FERMT3,synonymous_variant,p.=,ENST00000345728,NM_031471.5;FERMT3,synonymous_variant,p.=,ENST00000544997,;STIP1,downstream_gene_variant,,ENST00000358794,NM_001282652.1;STIP1,downstream_gene_variant,,ENST00000305218,NM_006819.2;STIP1,downstream_gene_variant,,ENST00000538945,NM_001282653.1;STIP1,downstream_gene_variant,,ENST00000540887,;FERMT3,upstream_gene_variant,,ENST00000541252,;FERMT3,upstream_gene_variant,,ENST00000541326,;STIP1,downstream_gene_variant,,ENST00000536973,;FERMT3,upstream_gene_variant,,ENST00000546255,;STIP1,downstream_gene_variant,,ENST00000355603,; A ENST00000279227 Transcript synonymous_variant 161/2489 66/2004 22/667 V gtG/gtA 1 1 FERMT3 HGNC HGNC:23151 protein_coding YES CCDS8060.1 ENSP00000279227 Q86UX7 UPI000019270B NM_178443.2 2/15 hmmpanther:PTHR16160,hmmpanther:PTHR16160:SF1 LOW 1 SNV 1 1 PASS . . 0 205 0 5 0 0 0 0 -20 0.9994995 1 1 1 0 A 2 1 100 64207430 64207430 G A 1 0 0 0 0 0 0 0 1 5682 1335 47 3 3 FERMT3 11 64207430 Silent SNP G C3N-02424_T 46565230 64207430 70879192 38 29628 PLCB3 0 . GRCh38 11 64259223 64259223 + Missense_Mutation SNP G G A rs370491975 C3N-02424_T C3N-02424_N G G c.1504G>A p.Glu502Lys p.E502K ENST00000540288 13/32 41 37 4 56 56 0 strelka-varscan-mutect PLCB3,missense_variant,p.Glu502Lys,ENST00000540288,NM_001316314.1,NM_000932.2;PLCB3,missense_variant,p.Glu502Lys,ENST00000279230,;PLCB3,missense_variant,p.Glu435Lys,ENST00000325234,NM_001184883.1;PLCB3,upstream_gene_variant,,ENST00000536243,; A ENST00000540288 Transcript missense_variant 1607/4469 1504/3705 502/1234 E/K Gag/Aag rs370491975 1 1 PLCB3 HGNC HGNC:9056 protein_coding YES CCDS8064.1 ENSP00000443631 Q01970 UPI0000131AFF NM_001316314.1,NM_000932.2 tolerated(0.1) 13/32 Low_complexity_(Seg):seg,hmmpanther:PTHR10336:SF11,hmmpanther:PTHR10336,PIRSF_domain:PIRSF000956 MODERATE 1 SNV 1 1 PASS rs370491975 . 0 207 3 0 0 0 0 0 -10.92873 1 1 1 1 0 A 3 1 100 64259223 64259223 G A 1 0 0 0 0 1 0 0 0 12123 1059 37 1 1 PLCB3 11 64259223 Missense_Mutation SNP G C3N-02424_T 51793 64259223 70827399 39 29629 MMP10 0 . GRCh38 11 102779240 102779240 + Missense_Mutation SNP C C T novel C3N-02424_T C3N-02424_N C C c.469G>A p.Asp157Asn p.D157N ENST00000279441 3/10 208 170 38 203 203 0 strelka-varscan-mutect MMP10,missense_variant,p.Asp157Asn,ENST00000279441,NM_002425.2;MMP10,missense_variant,p.Asp157Asn,ENST00000539681,;WTAPP1,intron_variant,,ENST00000371455,;WTAPP1,upstream_gene_variant,,ENST00000525739,;WTAPP1,upstream_gene_variant,,ENST00000544704,; T ENST00000279441 Transcript missense_variant 506/1758 469/1431 157/476 D/N Gat/Aat 1 -1 MMP10 HGNC HGNC:7156 protein_coding YES CCDS8321.1 ENSP00000279441 P09238 UPI00000422C0 NM_002425.2 deleterious(0) 3/10 Gene3D:3.40.390.10,Pfam_domain:PF00413,PIRSF_domain:PIRSF001191,Prints_domain:PR00138,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF153,SMART_domains:SM00235,Superfamily_domains:SSF55486 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 102779240 102779240 C T 1 0 0 0 0 1 0 0 0 9612 826 29 3 3 MMP10 11 102779240 Missense_Mutation SNP C C3N-02424_T 38520017 102779240 32307382 40 29630 MMP3 0 . GRCh38 11 102842529 102842529 + Missense_Mutation SNP A A G novel C3N-02424_T C3N-02424_N A A c.401T>C p.Val134Ala p.V134A ENST00000299855 3/10 283 125 158 246 246 0 strelka-varscan-mutect MMP3,missense_variant,p.Val134Ala,ENST00000299855,NM_002422.3;MMP3,upstream_gene_variant,,ENST00000434103,;MMP3,3_prime_UTR_variant,,ENST00000524478,; G ENST00000299855 Transcript missense_variant 658/2016 401/1434 134/477 V/A gTt/gCt 1 -1 MMP3 HGNC HGNC:7173 protein_coding YES CCDS8323.1 ENSP00000299855 P08254 UPI00000422BF NM_002422.3 deleterious(0) 3/10 hmmpanther:PTHR10201:SF164,hmmpanther:PTHR10201,PIRSF_domain:PIRSF001191,Pfam_domain:PF00413,Gene3D:3.40.390.10,SMART_domains:SM00235,Superfamily_domains:SSF55486,Prints_domain:PR00138 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 100 102842529 102842529 A G 1 0 0 0 0 1 0 0 0 9629 43 2 5 5 MMP3 11 102842529 Missense_Mutation SNP A C3N-02424_T 63289 102842529 32244093 41 29631 PDE3A 0 . GRCh38 12 20369551 20369551 + Silent SNP G G A novel C3N-02424_T C3N-02424_N G G c.267G>A p.= p.L89L ENST00000359062 1/16 68 53 15 103 103 0 strelka-varscan-mutect PDE3A,synonymous_variant,p.=,ENST00000359062,NM_000921.4,NM_001244683.1;RP11-284H19.1,intron_variant,,ENST00000535755,;PDE3A,upstream_gene_variant,,ENST00000542675,; A ENST00000359062 Transcript synonymous_variant 307/7576 267/3426 89/1141 L ctG/ctA 1 1 PDE3A HGNC HGNC:8778 protein_coding YES CCDS31754.1 ENSP00000351957 Q14432 UPI000014175F NM_000921.4,NM_001244683.1 1/16 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 100 20369551 20369551 G A 1 0 0 0 0 0 0 0 1 11725 1335 47 3 3 PDE3A 12 20369551 Silent SNP G C3N-02424_T 20369551 112905758 42 29632 DDX11 0 . GRCh38 12 31085103 31085103 + Silent SNP T T C rs778843332 C3N-02424_T C3N-02424_N T T c.615T>C p.= p.D205D ENST00000545668 5/27 384 332 52 521 521 0 varscan-mutect DDX11,synonymous_variant,p.=,ENST00000545668,NM_152438.1,NM_001257144.1;DDX11,synonymous_variant,p.=,ENST00000350437,NM_004399.2;DDX11,synonymous_variant,p.=,ENST00000228264,NM_001257145.1;DDX11,synonymous_variant,p.=,ENST00000542838,NM_030653.3;DDX11,synonymous_variant,p.=,ENST00000438391,;DDX11,synonymous_variant,p.=,ENST00000415475,;DDX11,intron_variant,,ENST00000544652,;DDX11,downstream_gene_variant,,ENST00000535317,;DDX11,upstream_gene_variant,,ENST00000545717,;DDX11,synonymous_variant,p.=,ENST00000435753,;DDX11,synonymous_variant,p.=,ENST00000539049,;DDX11,synonymous_variant,p.=,ENST00000542129,;DDX11,synonymous_variant,p.=,ENST00000540935,;DDX11,3_prime_UTR_variant,,ENST00000542244,;DDX11,non_coding_transcript_exon_variant,,ENST00000536265,;DDX11,non_coding_transcript_exon_variant,,ENST00000535158,;DDX11,intron_variant,,ENST00000538345,;DDX11,upstream_gene_variant,,ENST00000543026,;DDX11,upstream_gene_variant,,ENST00000542242,;DDX11,downstream_gene_variant,,ENST00000543756,; C ENST00000545668 Transcript synonymous_variant 695/3751 615/2913 205/970 D gaT/gaC rs778843332 1 1 DDX11 HGNC HGNC:2736 protein_coding YES CCDS44856.1 ENSP00000440402 Q96FC9 UPI000006F88F NM_152438.1,NM_001257144.1 5/27 PROSITE_profiles:PS51193,hmmpanther:PTHR11472,hmmpanther:PTHR11472:SF36,SMART_domains:SM00488,TIGRFAM_domain:TIGR00604 LOW 1 SNV 1 1 PASS rs778843332 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 100 31085103 31085103 T C 1 0 0 0 0 0 0 0 1 4147 1461 51 5 5 DDX11 12 31085103 Silent SNP T C3N-02424_T 10715552 31085103 102190206 43 29633 KRT85 0 . GRCh38 12 52364160 52364160 + Missense_Mutation SNP C C A rs764225566 C3N-02424_T C3N-02424_N C C c.694G>T p.Val232Leu p.V232L ENST00000257901 4/9 564 482 82 656 656 0 strelka-varscan-mutect KRT85,missense_variant,p.Val232Leu,ENST00000257901,NM_002283.3;KRT85,missense_variant,p.Val20Leu,ENST00000544265,NM_001300810.1;KRT85,non_coding_transcript_exon_variant,,ENST00000552537,; A ENST00000257901 Transcript missense_variant 770/2447 694/1524 232/507 V/L Gtg/Ttg rs764225566 1 -1 KRT85 HGNC HGNC:6462 protein_coding YES CCDS8824.1 ENSP00000257901 P78386 UPI000006EB3B NM_002283.3 deleterious(0) 4/9 Pfam_domain:PF00038,hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF113,SMART_domains:SM01391 MODERATE 1 SNV 1 1 PASS rs764225566 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 52364160 52364160 C A 1 0 0 0 0 1 0 0 0 8381 550 19 1 1 KRT85 12 52364160 Missense_Mutation SNP C C3N-02424_T 21279057 52364160 80911149 44 29634 KIAA1033 0 . GRCh38 12 105127195 105127195 + Frame_Shift_Del DEL C C - rs371244423 C3N-02424_T C3N-02424_N C C c.1106delC p.Pro369GlnfsTer7 p.P369Qfs*7 ENST00000620430 13/33 158 145 13 311 311 0 varindel-pindel KIAA1033,frameshift_variant,p.Pro369GlnfsTer7,ENST00000332180,NM_015275.2;KIAA1033,frameshift_variant,p.Pro369GlnfsTer7,ENST00000620430,NM_001293640.1;KIAA1033,3_prime_UTR_variant,,ENST00000550053,;KIAA1033,non_coding_transcript_exon_variant,,ENST00000311317,;KIAA1033,downstream_gene_variant,,ENST00000547404,; - ENST00000620430 Transcript frameshift_variant 1192/5807 1105/3525 369/1174 P/X Cca/ca rs371244423 1 1 KIAA1033 HGNC HGNC:29174 protein_coding YES CCDS73514.1 ENSP00000484713 A0A087X256 UPI000387C216 NM_001293640.1 13/33 Pfam_domain:PF14745,hmmpanther:PTHR31409,hmmpanther:PTHR31409:SF0 HIGH 1 deletion 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 100 105127195 105127195 C - 1 0 1 0 1 0 0 0 0 8099 507 18 0 0 KIAA1033 12 105127195 Frame_Shift_Del DEL C C3N-02424_T 52763035 105127195 28148114 45 29635 TBX3 0 . GRCh38 12 114674667 114674667 + Missense_Mutation SNP C C A rs145432134 C3N-02424_T C3N-02424_N C C c.1268G>T p.Arg423Leu p.R423L ENST00000257566 7/8 183 151 32 219 219 0 strelka-varscan-mutect TBX3,missense_variant,p.Arg403Leu,ENST00000349155,NM_005996.3;TBX3,missense_variant,p.Arg423Leu,ENST00000257566,NM_016569.3;TBX3,downstream_gene_variant,,ENST00000548503,; A ENST00000257566 Transcript missense_variant 1658/4208 1268/2232 423/743 R/L cGg/cTg rs145432134 1 -1 TBX3 HGNC HGNC:11602 protein_coding YES CCDS9176.1 ENSP00000257566 O15119 A0A024RBL6 UPI0000136AA0 NM_016569.3 deleterious(0.02) 7/8 hmmpanther:PTHR11267,hmmpanther:PTHR11267:SF91 MODERATE 1 SNV 1 1 PASS rs145432134 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 114674667 114674667 C A 1 0 0 0 0 1 0 0 0 16064 652 23 1 1 TBX3 12 114674667 Missense_Mutation SNP C C3N-02424_T 9547472 114674667 18600642 46 29636 HPD 0 . GRCh38 12 121854704 121854704 + Missense_Mutation SNP G G A rs762065329 C3N-02424_T C3N-02424_N G G c.413C>T p.Thr138Met p.T138M ENST00000289004 7/14 326 285 41 371 371 0 strelka-varscan-mutect HPD,missense_variant,p.Thr99Met,ENST00000543163,NM_001171993.1;HPD,missense_variant,p.Thr138Met,ENST00000289004,NM_002150.2;RP11-7M8.2,upstream_gene_variant,,ENST00000543848,;HPD,splice_region_variant,,ENST00000542159,;HPD,downstream_gene_variant,,ENST00000535114,; A ENST00000289004 Transcript missense_variant,splice_region_variant 449/1419 413/1182 138/393 T/M aCg/aTg rs762065329,COSM1359524 1 -1 HPD HGNC HGNC:5147 protein_coding YES CCDS9224.1 ENSP00000289004 A0A0B4J1R4 UPI0000366920 NM_002150.2 deleterious(0) 7/14 Gene3D:3.10.180.10,PIRSF_domain:PIRSF009283,hmmpanther:PTHR11959,hmmpanther:PTHR11959:SF9,Superfamily_domains:SSF54593,TIGRFAM_domain:TIGR01263 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs762065329 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 100 121854704 121854704 G A 1 0 0 0 0 1 0 0 0 7226 1159 40 1 1 HPD 12 121854704 Missense_Mutation SNP G C3N-02424_T 7180037 121854704 11420605 47 29637 TSHR 0 . GRCh38 14 81143146 81143146 + Missense_Mutation SNP T T C rs777555037 C3N-02424_T C3N-02424_N T T c.1088T>C p.Ile363Thr p.I363T ENST00000541158 11/11 420 379 41 811 810 1 strelka-varscan-mutect TSHR,missense_variant,p.Ile363Thr,ENST00000541158,;TSHR,missense_variant,p.Ile363Thr,ENST00000298171,NM_000369.2;RP11-114N19.3,intron_variant,,ENST00000557775,;TSHR,non_coding_transcript_exon_variant,,ENST00000636454,;TSHR,upstream_gene_variant,,ENST00000637447,; C ENST00000541158 Transcript missense_variant 1410/4566 1088/2295 363/764 I/T aTc/aCc rs777555037 1 1 TSHR HGNC HGNC:12373 protein_coding YES CCDS9872.1 ENSP00000441235 A0A0A0MTJ0 UPI000013E4A2 tolerated(0.68) 11/11 Prints_domain:PR01145,hmmpanther:PTHR24372,hmmpanther:PTHR24372:SF0 MODERATE SNV 5 1 PASS rs777555037 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 81143146 81143146 T C 1 0 0 0 0 1 0 0 0 17127 1435 50 5 5 TSHR 14 81143146 Missense_Mutation SNP T C3N-02424_T 81143146 25900572 48 29638 TLN2 0 . GRCh38 15 62657870 62657870 + Missense_Mutation SNP G G C novel C3N-02424_T C3N-02424_N G G c.760G>C p.Glu254Gln p.E254Q ENST00000561311 8/58 159 149 10 251 251 0 strelka-varscan-mutect TLN2,missense_variant,p.Glu254Gln,ENST00000561311,NM_015059.2;TLN2,intron_variant,,ENST00000636159,;TLN2,non_coding_transcript_exon_variant,,ENST00000474847,; C ENST00000561311 Transcript missense_variant 990/11880 760/7629 254/2542 E/Q Gaa/Caa 1 1 TLN2 HGNC HGNC:15447 protein_coding YES CCDS32261.1 ENSP00000453508 Q9Y4G6 UPI00001FE5FC NM_015059.2 deleterious(0) 8/58 PROSITE_profiles:PS50057,hmmpanther:PTHR19981,hmmpanther:PTHR19981:SF15,Gene3D:1.20.80.10,Pfam_domain:PF00373,SMART_domains:SM00295,Superfamily_domains:SSF47031 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 100 62657870 62657870 G C 1 0 0 0 0 1 0 0 0 16394 1175 41 4 4 TLN2 15 62657870 Missense_Mutation SNP G C3N-02424_T 62657870 39333319 49 29639 NPTN 0 . GRCh38 15 73573734 73573734 + Silent SNP A A G novel C3N-02424_T C3N-02424_N A A c.768T>C p.= p.T256T ENST00000345330 5/9 100 88 12 119 119 0 strelka-mutect NPTN,synonymous_variant,p.=,ENST00000351217,NM_017455.3;NPTN,synonymous_variant,p.=,ENST00000345330,NM_012428.3;NPTN,synonymous_variant,p.=,ENST00000565282,;NPTN,synonymous_variant,p.=,ENST00000563691,NM_001161363.1;NPTN,synonymous_variant,p.=,ENST00000562924,NM_001161364.1;NPTN,synonymous_variant,p.=,ENST00000565325,;NPTN-IT1,upstream_gene_variant,,ENST00000628401,;NPTN,non_coding_transcript_exon_variant,,ENST00000564551,; G ENST00000345330 Transcript synonymous_variant 966/2444 768/1197 256/398 T acT/acC 1 -1 NPTN HGNC HGNC:17867 protein_coding YES CCDS10249.1 ENSP00000290401 Q9Y639 UPI0000072D5C NM_012428.3 5/9 PROSITE_profiles:PS50835,hmmpanther:PTHR10075:SF5,hmmpanther:PTHR10075,PIRSF_domain:PIRSF000615,Pfam_domain:PF13927,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 100 73573734 73573734 A G 1 0 0 0 0 0 0 0 1 10657 407 15 5 5 NPTN 15 73573734 Silent SNP A C3N-02424_T 10915864 73573734 28417455 50 29640 SALL1 0 . GRCh38 16 51140468 51140468 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.1754C>A p.Thr585Asn p.T585N ENST00000251020 2/3 85 69 16 132 132 0 strelka-varscan-mutect SALL1,missense_variant,p.Thr488Asn,ENST00000440970,NM_001127892.1;SALL1,missense_variant,p.Thr585Asn,ENST00000251020,NM_002968.2;SALL1,missense_variant,p.Thr488Asn,ENST00000570206,;SALL1,intron_variant,,ENST00000566102,;SALL1,downstream_gene_variant,,ENST00000562674,; T ENST00000251020 Transcript missense_variant 1788/5146 1754/3975 585/1324 T/N aCc/aAc 1 -1 SALL1 HGNC HGNC:10524 protein_coding YES CCDS10747.1 ENSP00000251020 Q9NSC2 UPI000013CCD8 NM_002968.2 tolerated(0.52) 2/3 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF51 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 51140468 51140468 G T 1 0 0 0 0 1 0 0 0 14069 1261 44 2 2 SALL1 16 51140468 Missense_Mutation SNP G C3N-02424_T 51140468 39197877 51 29641 CLEC18B 0 . GRCh38 16 74413639 74413639 + Missense_Mutation SNP C C T rs58016779 C3N-02424_T C3N-02424_N C C c.494G>A p.Arg165Gln p.R165Q ENST00000339953 4/13 510 439 71 627 627 0 strelka-varscan-mutect CLEC18B,missense_variant,p.Arg165Gln,ENST00000617101,;CLEC18B,missense_variant,p.Arg165Gln,ENST00000619275,;CLEC18B,missense_variant,p.Arg165Gln,ENST00000339953,NM_001011880.2;CLEC18B,missense_variant,p.Arg165Gln,ENST00000620745,;CLEC18B,non_coding_transcript_exon_variant,,ENST00000425714,;CLEC18B,upstream_gene_variant,,ENST00000564842,; T ENST00000339953 Transcript missense_variant 616/1865 494/1368 165/455 R/Q cGg/cAg rs58016779,COSM116727 1 -1 CLEC18B HGNC HGNC:33849 protein_coding YES CCDS32484.1 ENSP00000341051 Q6UXF7 UPI000025210E NM_001011880.2 tolerated(0.37) 4/13 Gene3D:3.40.33.10,Pfam_domain:PF00188,hmmpanther:PTHR10334,hmmpanther:PTHR10334:SF245,SMART_domains:SM00198,Superfamily_domains:SSF55797 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs58016779 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 74413639 74413639 C T 1 0 0 0 0 1 0 0 0 3269 652 23 1 1 CLEC18B 16 74413639 Missense_Mutation SNP C C3N-02424_T 23273171 74413639 15924706 52 29642 TP53 0 . GRCh38 17 7674899 7674900 + Frame_Shift_Del DEL GT GT - C3N-02424_T C3N-02424_N GT GT c.631_632delAC p.Thr211PhefsTer4 p.T211Ffs*4 ENST00000269305 6/11 406 370 36 564 564 0 sindel-varindel-pindel TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000617185,NM_001126114.2;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000420246,;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000622645,NM_001276696.1;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000610292,NM_001126118.1;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000455263,NM_001126113.2;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000610538,NM_001276695.1;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000445888,;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000619485,;TP53,frameshift_variant,p.Thr79PhefsTer4,ENST00000510385,NM_001126116.1;TP53,frameshift_variant,p.Thr52PhefsTer4,ENST00000618944,NM_001276698.1;TP53,frameshift_variant,p.Thr79PhefsTer4,ENST00000504290,NM_001126117.1;TP53,frameshift_variant,p.Thr52PhefsTer4,ENST00000610623,NM_001276699.1;TP53,frameshift_variant,p.Thr79PhefsTer4,ENST00000504937,NM_001126115.1;TP53,frameshift_variant,p.Thr52PhefsTer4,ENST00000619186,NM_001276697.1;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000359597,;TP53,frameshift_variant,p.Thr200PhefsTer4,ENST00000615910,;TP53,frameshift_variant,p.Thr211PhefsTer4,ENST00000413465,;TP53,frameshift_variant,p.Thr79PhefsTer4,ENST00000509690,;TP53,frameshift_variant,p.Thr118PhefsTer4,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,frameshift_variant,p.Thr172PhefsTer4,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; - ENST00000269305 Transcript frameshift_variant 821-822/2579 631-632/1182 211/393 T/X ACt/t TP53_g.12700_12701del,COSM45222,COSM46301,COSM5080077,COSM5080078,COSM5080079,COSM5080080,COSM5080081,COSM5080082 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,1,1,1,1,1,1,1,1 HIGH 1 deletion 1 0,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 100 7674899 7674899 GT - 1 0 1 0 1 0 0 0 0 16859 1029 36 0 0 TP53 17 7674899 Frame_Shift_Del DEL GT C3N-02424_T 7674899 75582542 53 29643 DRG2 0 . GRCh38 17 18101533 18101533 + Silent SNP C C G rs770979886 C3N-02424_T C3N-02424_N C C c.672C>G p.= p.S224S ENST00000225729 8/13 236 219 17 243 242 1 strelka-varscan-mutect DRG2,synonymous_variant,p.=,ENST00000225729,NM_001388.4;DRG2,synonymous_variant,p.=,ENST00000395726,;DRG2,intron_variant,,ENST00000583355,;DRG2,downstream_gene_variant,,ENST00000579601,;DRG2,downstream_gene_variant,,ENST00000580929,;DRG2,missense_variant,p.Pro224Ala,ENST00000580055,;DRG2,3_prime_UTR_variant,,ENST00000467099,;DRG2,3_prime_UTR_variant,,ENST00000582314,;DRG2,non_coding_transcript_exon_variant,,ENST00000582528,;DRG2,upstream_gene_variant,,ENST00000482564,;DRG2,downstream_gene_variant,,ENST00000583162,;DRG2,upstream_gene_variant,,ENST00000497744,;DRG2,downstream_gene_variant,,ENST00000496428,;DRG2,downstream_gene_variant,,ENST00000579224,;DRG2,downstream_gene_variant,,ENST00000577771,;DRG2,downstream_gene_variant,,ENST00000578767,;DRG2,downstream_gene_variant,,ENST00000577450,;DRG2,downstream_gene_variant,,ENST00000582419,;DRG2,downstream_gene_variant,,ENST00000578173,;DRG2,downstream_gene_variant,,ENST00000584212,; G ENST00000225729 Transcript synonymous_variant 810/1964 672/1095 224/364 S tcC/tcG rs770979886 1 1 DRG2 HGNC HGNC:3030 protein_coding YES CCDS11191.1 ENSP00000225729 P55039 UPI000012987D NM_001388.4 8/13 Pfam_domain:PF16897,PROSITE_profiles:PS51710,hmmpanther:PTHR11702,hmmpanther:PTHR11702:SF26,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs770979886 . 0 207 0 3 0 0 0 0 -19.94573 0.9999709 1 1 1 0 G 2 3 100 18101533 18101533 C G 1 0 0 0 0 0 0 0 1 4581 610 22 4 4 DRG2 17 18101533 Silent SNP C C3N-02424_T 10426634 18101533 65155908 54 29644 CFAP53 0 . GRCh38 18 50262108 50262108 + Missense_Mutation SNP G G T rs550993731 C3N-02424_T C3N-02424_N G G c.181C>A p.Arg61Ser p.R61S ENST00000398545 2/8 221 209 12 320 320 0 strelka-varscan-mutect CFAP53,missense_variant,p.Arg61Ser,ENST00000398545,NM_145020.3;MBD1,downstream_gene_variant,,ENST00000585672,NM_001204141.1;MBD1,downstream_gene_variant,,ENST00000592060,; T ENST00000398545 Transcript missense_variant 299/1851 181/1545 61/514 R/S Cgc/Agc rs550993731,COSM3422217 1 -1 CFAP53 HGNC HGNC:26530 protein_coding YES CCDS11940.2 ENSP00000381553 Q96M91 UPI000014C50D NM_145020.3 tolerated(0.09) 2/8 hmmpanther:PTHR31183,hmmpanther:PTHR31183:SF1 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs550993731 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 50262108 50262108 G T 1 0 0 0 0 1 0 0 0 3024 1058 37 1 1 CFAP53 18 50262108 Missense_Mutation SNP G C3N-02424_T 50262108 30111177 55 29645 BMP2 0 . GRCh38 20 6770299 6770299 + Missense_Mutation SNP T T G novel C3N-02424_T C3N-02424_N T T c.173T>G p.Leu58Arg p.L58R ENST00000378827 2/3 232 205 27 298 297 1 strelka-varscan-mutect BMP2,missense_variant,p.Leu58Arg,ENST00000378827,NM_001200.2; G ENST00000378827 Transcript missense_variant 1392/3601 173/1191 58/396 L/R cTc/cGc 1 1 BMP2 HGNC HGNC:1069 protein_coding YES CCDS13099.1 ENSP00000368104 P12643 C8C060 UPI0000126A21 NM_001200.2 deleterious(0) 2/3 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF143 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 100 6770299 6770299 T G 1 0 0 0 0 1 0 0 0 1614 1551 54 5 5 BMP2 20 6770299 Missense_Mutation SNP T C3N-02424_T 6770299 57673868 56 29646 BMP2 0 . GRCh38 20 6770385 6770385 + Missense_Mutation SNP T T C novel C3N-02424_T C3N-02424_N T T c.259T>C p.Ser87Pro p.S87P ENST00000378827 2/3 135 122 13 156 156 0 strelka-varscan-mutect BMP2,missense_variant,p.Ser87Pro,ENST00000378827,NM_001200.2; C ENST00000378827 Transcript missense_variant 1478/3601 259/1191 87/396 S/P Tca/Cca 1 1 BMP2 HGNC HGNC:1069 protein_coding YES CCDS13099.1 ENSP00000368104 P12643 C8C060 UPI0000126A21 NM_001200.2 deleterious(0.02) 2/3 Pfam_domain:PF00688,hmmpanther:PTHR11848,hmmpanther:PTHR11848:SF143 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -18.66488 0.9999842 1 1 1 0 C 3 2 100 6770385 6770385 T C 1 0 0 0 0 1 0 0 0 1614 1551 54 5 5 BMP2 20 6770385 Missense_Mutation SNP T C3N-02424_T 86 6770385 57673782 57 29647 KLHDC7B 0 . GRCh38 22 50549887 50549887 + Missense_Mutation SNP C C A rs774373269 C3N-02424_T C3N-02424_N C C c.1721C>A p.Thr574Asn p.T574N ENST00000395676 1/1 75 69 6 71 71 0 strelka-varscan-mutect KLHDC7B,missense_variant,p.Thr574Asn,ENST00000395676,NM_138433.3;SYCE3,downstream_gene_variant,,ENST00000406915,NM_001123225.1;SYCE3,downstream_gene_variant,,ENST00000402753,;CTA-384D8.31,downstream_gene_variant,,ENST00000434237,; A ENST00000395676 Transcript missense_variant 1855/2991 1721/1785 574/594 T/N aCc/aAc rs774373269 1 1 KLHDC7B HGNC HGNC:25145 protein_coding YES CCDS14097.2 ENSP00000379034 Q96G42 UPI00005A75D4 NM_138433.3 deleterious(0) 1/1 hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF206 MODERATE SNV 1 PASS rs774373269 . 0 206 4 0 0 0 0 0 -13.40669 1 1 1 1 0 A 3 1 100 50549887 50549887 C A 1 0 0 0 0 1 0 0 0 8225 507 18 2 2 KLHDC7B 22 50549887 Missense_Mutation SNP C C3N-02424_T 50549887 268581 58 29648 SLC9A6 0 . GRCh38 X 136040154 136040154 + Missense_Mutation SNP G G T novel C3N-02424_T C3N-02424_N G G c.1806G>T p.Arg602Ser p.R602S ENST00000370695 15/16 109 86 23 119 119 0 strelka-varscan-mutect SLC9A6,missense_variant,p.Arg550Ser,ENST00000637581,;SLC9A6,missense_variant,p.Arg550Ser,ENST00000636347,;SLC9A6,missense_variant,p.Arg518Ser,ENST00000637195,;SLC9A6,missense_variant,p.Arg550Ser,ENST00000370701,NM_001177651.1;SLC9A6,missense_variant,p.Arg602Ser,ENST00000370695,NM_001042537.1;SLC9A6,missense_variant,p.Arg71Ser,ENST00000636206,;SLC9A6,missense_variant,p.Arg550Ser,ENST00000636092,;SLC9A6,missense_variant,p.Arg550Ser,ENST00000637234,;SLC9A6,missense_variant,p.Arg570Ser,ENST00000370698,NM_006359.2;SLC9A6,missense_variant,p.Arg129Ser,ENST00000630721,;SLC9A6,downstream_gene_variant,,ENST00000638078,;SLC9A6,non_coding_transcript_exon_variant,,ENST00000636798,;SLC9A6,non_coding_transcript_exon_variant,,ENST00000636625,;SLC9A6,non_coding_transcript_exon_variant,,ENST00000626147,; T ENST00000370695 Transcript missense_variant 1882/4725 1806/2106 602/701 R/S agG/agT 1 1 SLC9A6 HGNC HGNC:11079 protein_coding YES CCDS44003.1 ENSP00000359729 Q92581 UPI0000062320 NM_001042537.1 tolerated(0.11) 15/16 Prints_domain:PR01088,hmmpanther:PTHR10110,hmmpanther:PTHR10110:SF94 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 100 136040154 136040154 G T 1 0 0 0 0 1 0 0 0 15000 1252 44 2 2 SLC9A6 23 136040154 Missense_Mutation SNP G C3N-02424_T 136040154 20000741 59 29649 MAGEA4 0 . GRCh38 X 151923703 151923703 + Frame_Shift_Del DEL G G - C3N-02424_T C3N-02424_N G G c.40delG p.Glu14LysfsTer137 p.E14Kfs*137 ENST00000360243 3/3 91 69 22 135 135 0 sindel-varindel-pindel MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000360243,NM_001011550.1;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000370335,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000370340,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000393921,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000276344,NM_001011548.1;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000393920,NM_002362.4,NM_001011549.1;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000416020,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000431971,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000441865,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000457310,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000430273,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000425182,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000448295,;MAGEA4,frameshift_variant,p.Glu14LysfsTer137,ENST00000431963,; - ENST00000360243 Transcript frameshift_variant 306/1773 39/954 13/317 E/X gaG/ga COSM3559190 1 1 MAGEA4 HGNC HGNC:6802 protein_coding YES CCDS14702.1 ENSP00000353379 P43358 A0A024RC12 UPI000013EA1F NM_001011550.1 3/3 hmmpanther:PTHR11736:SF48,hmmpanther:PTHR11736,Pfam_domain:PF12440,SMART_domains:SM01392 1 HIGH 1 deletion 1 1 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 100 151923703 151923703 G - 1 0 1 0 1 0 0 0 0 9084 991 35 0 0 MAGEA4 23 151923703 Frame_Shift_Del DEL G C3N-02424_T 15883549 151923703 4117192 60 29650 ADAMTS4 0 . GRCh38 1 161196280 161196280 + Silent SNP G G A rs770033830 C3N-02433_T C3N-02433_N G G c.981C>T p.= p.C327C ENST00000367996 3/9 101 93 8 53 53 0 strelka-varscan-mutect ADAMTS4,synonymous_variant,p.=,ENST00000367996,NM_005099.4;ADAMTS4,3_prime_UTR_variant,,ENST00000367995,;NDUFS2,upstream_gene_variant,,ENST00000367993,NM_004550.4;NDUFS2,upstream_gene_variant,,ENST00000496133,;NDUFS2,upstream_gene_variant,,ENST00000479948,;ADAMTS4,upstream_gene_variant,,ENST00000478394,; A ENST00000367996 Transcript synonymous_variant 1410/9773 981/2514 327/837 C tgC/tgT rs770033830,COSM1582209,COSM1582210,COSM1583662,COSM898519 1 -1 ADAMTS4 HGNC HGNC:220 protein_coding YES CCDS1223.1 ENSP00000356975 O75173 UPI000014194C NM_005099.4 3/9 PROSITE_profiles:PS50215,hmmpanther:PTHR13723:SF38,hmmpanther:PTHR13723,Pfam_domain:PF01421,Gene3D:3.40.390.10,Superfamily_domains:SSF55486 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS rs770033830 . 0 194 14 2 0 0 0 0 -12.47609 0.9897106 1 1 1 0 A 2 1 101 161196280 161196280 G A 1 0 0 0 0 0 0 0 1 312 1079 38 1 1 ADAMTS4 1 161196280 Silent SNP G C3N-02433_T 161196280 87760142 1 29651 TOR3A 0 . GRCh38 1 179094218 179094218 + Splice_Site SNP G G T novel C3N-02433_T C3N-02433_N G G c.943+1G>T p.X315_splice ENST00000367627 112 90 22 79 79 0 strelka-varscan-mutect TOR3A,splice_donor_variant,,ENST00000367627,NM_022371.3;TOR3A,splice_donor_variant,,ENST00000352445,;TOR3A,downstream_gene_variant,,ENST00000447595,;TOR3A,downstream_gene_variant,,ENST00000472001,; T ENST00000367627 Transcript splice_donor_variant -/2724 943/1194 315/397 1 1 TOR3A HGNC HGNC:11997 protein_coding YES CCDS1329.1 ENSP00000356599 Q9H497 UPI000006F204 NM_022371.3 5/5 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 101 179094218 179094218 G T 1 0 0 0 0 0 0 1 0 16853 1275 44 2 2 TOR3A 1 179094218 Splice_Site SNP G C3N-02433_T 17897938 179094218 69862204 2 29652 ZNF648 0 . GRCh38 1 182057611 182057611 + Missense_Mutation SNP A A T rs747432726 C3N-02433_T C3N-02433_N A A c.400T>A p.Leu134Met p.L134M ENST00000339948 2/2 700 577 123 439 438 1 strelka-varscan-mutect ZNF648,missense_variant,p.Leu134Met,ENST00000339948,NM_001009992.1; T ENST00000339948 Transcript missense_variant 608/3649 400/1707 134/568 L/M Ttg/Atg rs747432726 1 -1 ZNF648 HGNC HGNC:18190 protein_coding YES CCDS30952.1 ENSP00000344129 Q5T619 UPI0000161414 NM_001009992.1 tolerated(0.13) 2/2 hmmpanther:PTHR24376:SF1,hmmpanther:PTHR24376 MODERATE 1 SNV 1 1 PASS rs747432726 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 182057611 182057611 A T 1 0 0 0 0 1 0 0 0 18636 98 4 4 4 ZNF648 1 182057611 Missense_Mutation SNP A C3N-02433_T 2963393 182057611 66898811 3 29653 CRB1 0 . GRCh38 1 197435247 197435247 + Silent SNP C C T novel C3N-02433_T C3N-02433_N C C c.3384C>T p.= p.I1128I ENST00000367400 9/12 303 286 17 296 296 0 strelka-varscan-mutect CRB1,synonymous_variant,p.=,ENST00000367397,;CRB1,synonymous_variant,p.=,ENST00000535699,NM_001257965.1;CRB1,synonymous_variant,p.=,ENST00000367400,NM_201253.2;CRB1,synonymous_variant,p.=,ENST00000367399,NM_001193640.1;CRB1,intron_variant,,ENST00000538660,NM_001257966.1;RP11-75C23.1,downstream_gene_variant,,ENST00000422250,;CRB1,synonymous_variant,p.=,ENST00000484075,; T ENST00000367400 Transcript synonymous_variant 3519/4932 3384/4221 1128/1406 I atC/atT 1 1 CRB1 HGNC HGNC:2343 protein_coding YES CCDS1390.1 ENSP00000356370 P82279 UPI0000073345 NM_201253.2 9/12 Gene3D:2.60.120.200,PROSITE_profiles:PS50025,hmmpanther:PTHR24049 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 101 197435247 197435247 C T 1 0 0 0 0 0 0 0 1 3648 903 32 3 3 CRB1 1 197435247 Silent SNP C C3N-02433_T 15377636 197435247 51521175 4 29654 C1orf116 0 . GRCh38 1 207021964 207021966 + In_Frame_Del DEL CTT CTT - novel C3N-02433_T C3N-02433_N CTT CTT c.1798_1800delAAG p.Lys600del p.K600del ENST00000359470 4/4 19 16 3 18 18 0 sindel-pindel C1orf116,inframe_deletion,p.Lys600del,ENST00000359470,NM_023938.5;C1orf116,inframe_deletion,p.Lys354del,ENST00000461135,NM_001083924.1; - ENST00000359470 Transcript inframe_deletion 2048-2050/5493 1798-1800/1806 600/601 K/- AAG/- 1 -1 C1orf116 HGNC HGNC:28667 protein_coding YES CCDS1475.1 ENSP00000352447 Q9BW04 UPI000013E1EF NM_023938.5 4/4 Pfam_domain:PF15385,hmmpanther:PTHR21555,hmmpanther:PTHR21555:SF0 MODERATE 1 deletion 1 1 PASS . . 13 196 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 101 207021964 207021964 CTT - 1 0 1 0 1 0 0 0 0 1961 680 24 0 0 C1orf116 1 207021964 In_Frame_Del DEL CTT C3N-02433_T 9586717 207021964 41934458 5 29655 OR2M7 0 . GRCh38 1 248324233 248324233 + Silent SNP G G A novel C3N-02433_T C3N-02433_N G G c.336C>T p.= p.C112C ENST00000317965 1/1 336 291 45 278 278 0 strelka-varscan OR2M7,synonymous_variant,p.=,ENST00000317965,NM_001004691.1; A ENST00000317965 Transcript synonymous_variant 336/939 336/939 112/312 C tgC/tgT 1 -1 OR2M7 HGNC HGNC:19594 protein_coding YES CCDS31111.1 ENSP00000324557 Q8NG81 A0A126GVZ1 UPI000004B236 NM_001004691.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF28,PROSITE_patterns:PS00237,Pfam_domain:PF13853,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 248324233 248324233 G A 1 0 0 0 0 0 0 0 1 11092 963 34 3 3 OR2M7 1 248324233 Silent SNP G C3N-02433_T 41302269 248324233 632189 6 29656 PFN4 0 . GRCh38 2 24121251 24121251 + Missense_Mutation SNP G G C novel C3N-02433_T C3N-02433_N G G c.167C>G p.Pro56Arg p.P56R ENST00000313213 3/5 128 104 24 155 154 1 strelka-varscan PFN4,missense_variant,p.Pro56Arg,ENST00000313213,NM_199346.2;FAM228B,intron_variant,,ENST00000613899,NM_001291328.1;FAM228B,upstream_gene_variant,,ENST00000615575,NM_001145710.1;FAM228B,upstream_gene_variant,,ENST00000611127,;PFN4,downstream_gene_variant,,ENST00000436622,;PFN4,non_coding_transcript_exon_variant,,ENST00000465360,;FAM228B,intron_variant,,ENST00000486967,;RP11-507M3.1,upstream_gene_variant,,ENST00000610442,;FAM228B,upstream_gene_variant,,ENST00000615135,; C ENST00000313213 Transcript missense_variant 539/974 167/390 56/129 P/R cCt/cGt 1 -1 PFN4 HGNC HGNC:31103 protein_coding YES CCDS1709.1 ENSP00000322170 Q8NHR9 UPI000006CFF1 NM_199346.2 tolerated(0.08) 3/5 Gene3D:3.30.450.30,Pfam_domain:PF00235,hmmpanther:PTHR11604,hmmpanther:PTHR11604:SF2,SMART_domains:SM00392,Superfamily_domains:SSF55770 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 24121251 24121251 G C 1 0 0 0 0 1 0 0 0 11860 1000 35 4 4 PFN4 2 24121251 Missense_Mutation SNP G C3N-02433_T 24121251 218072278 7 29657 CCDC88A 0 . GRCh38 2 55318926 55318926 + Missense_Mutation SNP C C A C3N-02433_T C3N-02433_N C C c.3238G>T p.Ala1080Ser p.A1080S ENST00000336838 19/33 148 122 26 187 186 1 strelka-varscan CCDC88A,missense_variant,p.Ala1081Ser,ENST00000436346,;CCDC88A,missense_variant,p.Ala1081Ser,ENST00000263630,NM_018084.4;CCDC88A,missense_variant,p.Ala1080Ser,ENST00000413716,NM_001254943.1;CCDC88A,missense_variant,p.Ala1080Ser,ENST00000336838,NM_001135597.1;CCDC88A,missense_variant,p.Ala256Ser,ENST00000426576,;CCDC88A,missense_variant,p.Ala126Ser,ENST00000412148,;CCDC88A,missense_variant,p.Ala62Ser,ENST00000456975,;AC012358.8,intron_variant,,ENST00000630025,;AC012358.8,intron_variant,,ENST00000599475,;AC012358.8,intron_variant,,ENST00000625679,;AC012358.8,intron_variant,,ENST00000626674,;AC012358.8,intron_variant,,ENST00000600219,;AC012358.8,intron_variant,,ENST00000599352,;AC012358.8,intron_variant,,ENST00000594078,;AC012358.8,intron_variant,,ENST00000626053,;AC012358.8,intron_variant,,ENST00000608103,;AC012358.8,intron_variant,,ENST00000628820,;AC012358.8,intron_variant,,ENST00000629788,;AC012358.8,intron_variant,,ENST00000629546,;AC012358.8,intron_variant,,ENST00000625264,;AC012358.8,intron_variant,,ENST00000628048,;AC012358.8,intron_variant,,ENST00000626036,;AC012358.8,intron_variant,,ENST00000629859,;AC012358.8,intron_variant,,ENST00000629819,;AC012358.8,intron_variant,,ENST00000626359,;AC012358.8,intron_variant,,ENST00000627989,;AC012358.8,intron_variant,,ENST00000628537,;AC012358.8,downstream_gene_variant,,ENST00000366287,;AC012358.8,downstream_gene_variant,,ENST00000613806,;AC012358.8,downstream_gene_variant,,ENST00000625718,;AC012358.8,downstream_gene_variant,,ENST00000626226,;AC012358.8,downstream_gene_variant,,ENST00000625841,;AC012358.8,downstream_gene_variant,,ENST00000625627,;CCDC88A,upstream_gene_variant,,ENST00000474059,;CCDC88A,upstream_gene_variant,,ENST00000476903,; A ENST00000336838 Transcript missense_variant 3772/9505 3238/5613 1080/1870 A/S Gct/Tct COSM4618248,COSM4618249 1 -1 CCDC88A HGNC HGNC:25523 protein_coding YES CCDS46288.1 ENSP00000338728 Q3V6T2 UPI00005B7220 NM_001135597.1 tolerated(0.87) 19/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR18947:SF30,hmmpanther:PTHR18947 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 101 55318926 55318926 C A 1 0 0 0 0 1 0 0 0 2562 739 26 2 2 CCDC88A 2 55318926 Missense_Mutation SNP C C3N-02433_T 31197675 55318926 186874603 8 29658 BCL11A 0 . GRCh38 2 60461077 60461077 + Nonsense_Mutation SNP G G T C3N-02433_T C3N-02433_N G G c.1835C>A p.Ser612Ter p.S612* ENST00000335712 4/4 57 51 6 44 44 0 strelka-varscan BCL11A,stop_gained,p.Ser612Ter,ENST00000335712,NM_022893.3;BCL11A,stop_gained,p.Ser612Ter,ENST00000356842,NM_018014.3;BCL11A,stop_gained,p.Ser578Ter,ENST00000358510,;BCL11A,intron_variant,,ENST00000359629,NM_138559.1;BCL11A,intron_variant,,ENST00000489516,;BCL11A,upstream_gene_variant,,ENST00000479026,;BCL11A,non_coding_transcript_exon_variant,,ENST00000477659,;BCL11A,intron_variant,,ENST00000492272,;BCL11A,3_prime_UTR_variant,,ENST00000631857,; T ENST00000335712 Transcript stop_gained 2063/5942 1835/2508 612/835 S/* tCg/tAg COSM3053783,COSM3053784 1 -1 BCL11A HGNC HGNC:13221 protein_coding YES CCDS1862.1 ENSP00000338774 Q9H165 D6W5D9 UPI000013DC00 NM_022893.3 4/4 hmmpanther:PTHR23233,hmmpanther:PTHR23233:SF43 1,1 HIGH 1 SNV 1 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -14.26144 1 1 1 1 0 T 4 4 101 60461077 60461077 G T 1 0 0 0 0 0 1 0 0 1510 1059 37 1 1 BCL11A 2 60461077 Nonsense_Mutation SNP G C3N-02433_T 5142151 60461077 181732452 9 29659 CCT4 0 . GRCh38 2 61888437 61888437 + Missense_Mutation SNP T T G rs749405108 C3N-02433_T C3N-02433_N T T c.71A>C p.Tyr24Ser p.Y24S ENST00000394440 1/14 194 169 25 123 123 0 strelka-varscan CCT4,missense_variant,p.Tyr24Ser,ENST00000394440,NM_006430.3;CCT4,missense_variant,p.Tyr24Ser,ENST00000544079,NM_001256721.1;AC107081.5,downstream_gene_variant,,ENST00000425779,;CCT4,non_coding_transcript_exon_variant,,ENST00000461370,;COMMD1,upstream_gene_variant,,ENST00000472729,; G ENST00000394440 Transcript missense_variant 368/2520 71/1620 24/539 Y/S tAt/tCt rs749405108 1 -1 CCT4 HGNC HGNC:1617 protein_coding YES CCDS33206.1 ENSP00000377958 P50991 UPI00000362DF NM_006430.3 tolerated(0.08) 1/14 hmmpanther:PTHR11353,TIGRFAM_domain:TIGR02342 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 61888437 61888437 T G 1 0 0 0 0 1 0 0 0 2656 1406 49 5 5 CCT4 2 61888437 Missense_Mutation SNP T C3N-02433_T 1427360 61888437 180305092 10 29660 EXOC3 0 . GRCh38 5 459392 459392 + Missense_Mutation SNP A A G novel C3N-02433_T C3N-02433_N A A c.1324A>G p.Ile442Val p.I442V ENST00000512944 7/13 59 51 8 104 104 0 strelka-varscan-mutect EXOC3,missense_variant,p.Ile442Val,ENST00000512944,NM_007277.4;EXOC3,missense_variant,p.Ile442Val,ENST00000315013,;EXOC3,missense_variant,p.Ile312Val,ENST00000503889,;EXOC3,non_coding_transcript_exon_variant,,ENST00000510028,;EXOC3,intron_variant,,ENST00000515601,;EXOC3,upstream_gene_variant,,ENST00000511015,; G ENST00000512944 Transcript missense_variant 1513/2825 1324/2238 442/745 I/V Ata/Gta 1 1 EXOC3 HGNC HGNC:30378 protein_coding YES CCDS54830.1 ENSP00000425587 O60645 A0A024QYZ6 UPI000004A021 NM_007277.4 tolerated(0.25) 7/13 hmmpanther:PTHR21292:SF13,hmmpanther:PTHR21292,Pfam_domain:PF06046 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 459392 459392 A G 1 0 0 0 0 1 0 0 0 5170 333 12 5 5 EXOC3 5 459392 Missense_Mutation SNP A C3N-02433_T 459392 181078867 11 29661 CDH18 0 . GRCh38 5 19746980 19746980 + Missense_Mutation SNP C C A C3N-02433_T C3N-02433_N C C c.485G>T p.Gly162Val p.G162V ENST00000507958 6/15 161 124 37 163 163 0 strelka-varscan-mutect CDH18,missense_variant,p.Gly162Val,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Gly162Val,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Gly162Val,ENST00000274170,;CDH18,missense_variant,p.Gly162Val,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Gly162Val,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Gly162Val,ENST00000511273,;CDH18,missense_variant,p.Gly108Val,ENST00000515257,;CDH18,non_coding_transcript_exon_variant,,ENST00000508350,; A ENST00000507958 Transcript missense_variant 1476/3542 485/2373 162/790 G/V gGa/gTa COSM737348,COSM737349 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 deleterious(0) 6/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Gene3D:2.60.40.60,Superfamily_domains:SSF49313,Prints_domain:PR00205 1,1 MODERATE 1 SNV 2 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 101 19746980 19746980 C A 1 0 0 0 0 1 0 0 0 2806 855 30 2 2 CDH18 5 19746980 Missense_Mutation SNP C C3N-02433_T 19287588 19746980 161791279 12 29662 PDE4D 0 . GRCh38 5 58976412 58976412 + Missense_Mutation SNP C C T C3N-02433_T C3N-02433_N C C c.1768G>A p.Glu590Lys p.E590K ENST00000340635 13/15 154 103 51 188 188 0 strelka-varscan-mutect PDE4D,missense_variant,p.Glu590Lys,ENST00000340635,NM_001104631.1;PDE4D,missense_variant,p.Glu459Lys,ENST00000546160,;PDE4D,missense_variant,p.Glu480Lys,ENST00000636120,;PDE4D,missense_variant,p.Glu526Lys,ENST00000507116,NM_001197218.1;PDE4D,missense_variant,p.Glu454Lys,ENST00000360047,NM_006203.4;PDE4D,missense_variant,p.Glu288Lys,ENST00000358923,NM_001197221.1,NM_001197222.1;PDE4D,missense_variant,p.Glu460Lys,ENST00000503258,NM_001197220.1;PDE4D,missense_variant,p.Glu299Lys,ENST00000317118,NM_001197223.1;PDE4D,missense_variant,p.Glu529Lys,ENST00000502484,NM_001165899.1;PDE4D,missense_variant,p.Glu468Lys,ENST00000405755,NM_001197219.1;PDE4D,missense_variant,p.Glu288Lys,ENST00000505453,;PDE4D,3_prime_UTR_variant,,ENST00000309641,;PDE4D,non_coding_transcript_exon_variant,,ENST00000515011,; T ENST00000340635 Transcript missense_variant 1944/8232 1768/2430 590/809 E/K Gaa/Aaa COSM1150113,COSM1150114,COSM4860577,COSM738451,COSM738452,COSM738453,COSM738454,COSM738455 1 -1 PDE4D HGNC HGNC:8783 protein_coding YES CCDS47213.1 ENSP00000345502 Q08499 A0A140VJR0 UPI0000050EB1 NM_001104631.1 deleterious_low_confidence(0) 13/15 hmmpanther:PTHR11347,hmmpanther:PTHR11347:SF91,Pfam_domain:PF00233,Gene3D:1.10.1300.10,Superfamily_domains:SSF109604 1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 58976412 58976412 C T 1 0 0 0 0 1 0 0 0 11730 835 29 3 3 PDE4D 5 58976412 Missense_Mutation SNP C C3N-02433_T 39229432 58976412 122561847 13 29663 SPZ1 0 . GRCh38 5 80321115 80321115 + Missense_Mutation SNP G G T novel C3N-02433_T C3N-02433_N G G c.900G>T p.Lys300Asn p.K300N ENST00000296739 1/1 123 81 42 114 114 0 strelka-varscan-mutect SPZ1,missense_variant,p.Lys300Asn,ENST00000296739,NM_032567.3;SPZ1,downstream_gene_variant,,ENST00000511881,; T ENST00000296739 Transcript missense_variant 1141/1868 900/1293 300/430 K/N aaG/aaT 1 1 SPZ1 HGNC HGNC:30721 protein_coding YES CCDS43336.1 ENSP00000369611 Q9BXG8 A0A140VKA5 UPI000020CBA6 NM_032567.3 tolerated(0.33) 1/1 hmmpanther:PTHR23158:SF40,hmmpanther:PTHR23158 MODERATE 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 80321115 80321115 G T 1 0 0 0 0 1 0 0 0 15486 962 34 2 2 SPZ1 5 80321115 Missense_Mutation SNP G C3N-02433_T 21344703 80321115 101217144 14 29664 PRR16 0 . GRCh38 5 120464585 120464585 + Silent SNP C C T novel C3N-02433_T C3N-02433_N C C c.99C>T p.= p.I33I ENST00000407149 1/2 162 126 36 176 176 0 strelka-varscan-mutect PRR16,synonymous_variant,p.=,ENST00000407149,NM_001300783.1;PRR16,5_prime_UTR_variant,,ENST00000379551,NM_016644.2;PRR16,upstream_gene_variant,,ENST00000509923,; T ENST00000407149 Transcript synonymous_variant 308/1747 99/915 33/304 I atC/atT 1 1 PRR16 HGNC HGNC:29654 protein_coding YES CCDS75290.1 ENSP00000385118 Q569H4 UPI00004F9C36 NM_001300783.1 1/2 hmmpanther:PTHR15917,hmmpanther:PTHR15917:SF0 LOW 1 SNV 1 1 PASS rs1325026375 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 101 120464585 120464585 C T 1 0 0 0 0 0 0 0 1 12725 874 31 1 1 PRR16 5 120464585 Silent SNP C C3N-02433_T 40143470 120464585 61073674 15 29665 C6orf89 0 . GRCh38 6 36899594 36899595 + Frame_Shift_Ins INS - - C rs777115998 C3N-02433_T C3N-02433_N - - c.179dupC p.Gln61AlafsTer10 p.Q61Afs*10 ENST00000355190 2/8 267 212 55 220 220 0 sindel-varindel C6orf89,frameshift_variant,p.Gln54AlafsTer10,ENST00000480824,NM_001286635.1;C6orf89,frameshift_variant,p.Gln54AlafsTer10,ENST00000373685,;C6orf89,frameshift_variant,p.Gln61AlafsTer10,ENST00000355190,NM_152734.3;C6orf89,5_prime_UTR_variant,,ENST00000359359,NM_001286636.1,NM_001286637.1; C ENST00000355190 Transcript frameshift_variant 334-335/1309 171-172/1065 57-58/354 -/X -/C rs777115998 1 1 C6orf89 HGNC HGNC:21114 protein_coding YES CCDS4827.1 ENSP00000347322 Q6UWU4 UPI000035E870 NM_152734.3 2/8 hmmpanther:PTHR35259,hmmpanther:PTHR35259:SF1 HIGH 1 insertion 1 8 1 PASS . . 0 114 0 0 96 0 0 0 -20 0 0 1 0 0 C 7 5 101 36899594 36899594 - C 1 0 1 1 0 0 0 0 0 2133 272 10 0 0 C6orf89 6 36899594 Frame_Shift_Ins INS - C3N-02433_T 36899594 133906385 16 29666 BYSL 0 . GRCh38 6 41932654 41932654 + Missense_Mutation SNP T T G novel C3N-02433_T C3N-02433_N T T c.1262T>G p.Leu421Arg p.L421R ENST00000230340 7/7 128 95 33 104 103 1 strelka-varscan BYSL,missense_variant,p.Leu421Arg,ENST00000230340,NM_004053.3;CCND3,downstream_gene_variant,,ENST00000511642,;CCND3,downstream_gene_variant,,ENST00000372987,NM_001287427.1;CCND3,downstream_gene_variant,,ENST00000372988,NM_001136017.3;CCND3,downstream_gene_variant,,ENST00000372991,NM_001760.4;CCND3,downstream_gene_variant,,ENST00000616010,NM_001287434.1;CCND3,downstream_gene_variant,,ENST00000415497,NM_001136126.2;CCND3,downstream_gene_variant,,ENST00000414200,NM_001136125.2;CCND3,downstream_gene_variant,,ENST00000510503,;CCND3,downstream_gene_variant,,ENST00000512426,;CCND3,downstream_gene_variant,,ENST00000508143,;CCND3,downstream_gene_variant,,ENST00000505064,;CCND3,downstream_gene_variant,,ENST00000511686,;CCND3,downstream_gene_variant,,ENST00000513956,;CCND3,downstream_gene_variant,,ENST00000506555,;BYSL,3_prime_UTR_variant,,ENST00000372996,;BYSL,3_prime_UTR_variant,,ENST00000489290,;CCND3,downstream_gene_variant,,ENST00000505672,;CCND3,downstream_gene_variant,,ENST00000510058,;BYSL,downstream_gene_variant,,ENST00000475702,;CCND3,downstream_gene_variant,,ENST00000505884,;CCND3,downstream_gene_variant,,ENST00000511161,; G ENST00000230340 Transcript missense_variant 1637/2029 1262/1314 421/437 L/R cTt/cGt 1 1 BYSL HGNC HGNC:1157 protein_coding YES CCDS34450.1 ENSP00000230340 Q13895 UPI0000034CC4 NM_004053.3 deleterious(0) 7/7 hmmpanther:PTHR12821,hmmpanther:PTHR12821:SF0,Pfam_domain:PF05291 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 41932654 41932654 T G 1 0 0 0 0 1 0 0 0 1752 1609 56 5 5 BYSL 6 41932654 Missense_Mutation SNP T C3N-02433_T 5033060 41932654 128873325 17 29667 RPL7L1 0 . GRCh38 6 42880948 42880948 + Silent SNP A A T novel C3N-02433_T C3N-02433_N A A c.102A>T p.= p.A34A ENST00000493763 2/6 304 243 61 280 280 0 strelka-varscan RPL7L1,synonymous_variant,p.=,ENST00000493763,NM_198486.2;RPL7L1,synonymous_variant,p.=,ENST00000304734,;RPL7L1,synonymous_variant,p.=,ENST00000602561,;RPL7L1,non_coding_transcript_exon_variant,,ENST00000397415,;RPL7L1,non_coding_transcript_exon_variant,,ENST00000462348,;RPL7L1,non_coding_transcript_exon_variant,,ENST00000492836,;RPL7L1,intron_variant,,ENST00000483998,;RPL7L1,intron_variant,,ENST00000487619,;RPL7L1,non_coding_transcript_exon_variant,,ENST00000497417,;RPL7L1,upstream_gene_variant,,ENST00000459829,; T ENST00000493763 Transcript synonymous_variant 405/4476 102/741 34/246 A gcA/gcT 1 1 RPL7L1 HGNC HGNC:21370 protein_coding YES CCDS4873.1 ENSP00000418221 Q6DKI1 UPI00001D81E1 NM_198486.2 2/6 Low_complexity_(Seg):seg,hmmpanther:PTHR11524,hmmpanther:PTHR11524:SF13,Pfam_domain:PF08079,TIGRFAM_domain:TIGR01310 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 101 42880948 42880948 A T 1 0 0 0 0 0 0 0 1 13854 146 6 4 4 RPL7L1 6 42880948 Silent SNP A C3N-02433_T 948294 42880948 127925031 18 29668 CD109 0 . GRCh38 6 73730539 73730539 + Missense_Mutation SNP A A C rs760918169 C3N-02433_T C3N-02433_N A A c.472A>C p.Lys158Gln p.K158Q ENST00000287097 4/33 152 114 38 155 155 0 strelka-varscan CD109,missense_variant,p.Lys158Gln,ENST00000437994,NM_001159587.2;CD109,missense_variant,p.Lys158Gln,ENST00000287097,NM_133493.4;CD109,intron_variant,,ENST00000422508,NM_001159588.2; C ENST00000287097 Transcript missense_variant 584/9130 472/4338 158/1445 K/Q Aag/Cag rs760918169 1 1 CD109 HGNC HGNC:21685 protein_coding YES CCDS4982.1 ENSP00000287097 Q6YHK3 UPI000013DE92 NM_133493.4 deleterious(0) 4/33 hmmpanther:PTHR11412,hmmpanther:PTHR11412:SF80,Pfam_domain:PF01835 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 73730539 73730539 A C 1 0 0 0 0 1 0 0 0 2666 363 13 5 5 CD109 6 73730539 Missense_Mutation SNP A C3N-02433_T 30849591 73730539 97075440 19 29669 ARID1B 0 . GRCh38 6 156778329 156778329 + Missense_Mutation SNP A A G novel C3N-02433_T C3N-02433_N A A c.400A>G p.Ile134Val p.I134V ENST00000346085 1/20 232 186 46 212 212 0 strelka-varscan ARID1B,missense_variant,p.Ile134Val,ENST00000346085,NM_020732.3;ARID1B,missense_variant,p.Ile134Val,ENST00000636930,;ARID1B,missense_variant,p.Ile134Val,ENST00000350026,NM_017519.2;ARID1B,upstream_gene_variant,,ENST00000636748,;ARID1B,upstream_gene_variant,,ENST00000414678,;ARID1B,upstream_gene_variant,,ENST00000638000,;ARID1B,upstream_gene_variant,,ENST00000494260,;ARID1B,upstream_gene_variant,,ENST00000636607,;RP11-230C9.4,upstream_gene_variant,,ENST00000604082,;MIR4466,downstream_gene_variant,,ENST00000606121,;RP11-230C9.2,non_coding_transcript_exon_variant,,ENST00000603191,;RP11-230C9.3,downstream_gene_variant,,ENST00000604792,;ARID1B,upstream_gene_variant,,ENST00000637910,; G ENST00000346085 Transcript missense_variant 956/10194 400/6750 134/2249 I/V Att/Gtt 1 1 ARID1B HGNC HGNC:18040 protein_coding YES CCDS55072.1 ENSP00000344546 Q8NFD5 UPI000058E4B2 NM_020732.3 tolerated_low_confidence(0.07) 1/20 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 156778329 156778329 A G 1 0 0 0 0 1 0 0 0 1050 217 8 5 5 ARID1B 6 156778329 Missense_Mutation SNP A C3N-02433_T 83047790 156778329 14027650 20 29670 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02433_T C3N-02433_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 679 437 242 403 403 0 strelka-varscan EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02433_T 55191822 104154151 21 29671 ZNF800 0 . GRCh38 7 127391545 127391545 + Missense_Mutation SNP C C T novel C3N-02433_T C3N-02433_N C C c.13G>A p.Asp5Asn p.D5N ENST00000393313 2/6 293 261 32 224 224 0 strelka-varscan ZNF800,missense_variant,p.Asp5Asn,ENST00000393313,;ZNF800,missense_variant,p.Asp5Asn,ENST00000265827,NM_176814.4;ZNF800,missense_variant,p.Asp5Asn,ENST00000393312,;ZNF800,missense_variant,p.Asp5Asn,ENST00000619291,;ZNF800,missense_variant,p.Asp5Asn,ENST00000434602,;ZNF800,missense_variant,p.Asp5Asn,ENST00000436992,;ZNF800,missense_variant,p.Asp5Asn,ENST00000439506,; T ENST00000393313 Transcript missense_variant 605/4358 13/1995 5/664 D/N Gac/Aac 1 -1 ZNF800 HGNC HGNC:27267 protein_coding YES CCDS5795.1 ENSP00000376989 Q2TB10 UPI000020FA03 tolerated(0.12) 2/6 hmmpanther:PTHR21020 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 127391545 127391545 C T 1 0 0 0 0 1 0 0 0 18754 855 30 3 3 ZNF800 7 127391545 Missense_Mutation SNP C C3N-02433_T 72199723 127391545 31954428 22 29672 ENY2 0 . GRCh38 8 109342708 109342709 + Frame_Shift_Ins INS - - G novel C3N-02433_T C3N-02433_N - - c.234dupG p.Pro79AlafsTer38 p.P79Afs*38 ENST00000520147 5/6 160 116 44 118 118 0 sindel-varindel-pindel ENY2,frameshift_variant,p.Pro79AlafsTer38,ENST00000520147,;ENY2,intron_variant,,ENST00000521688,NM_020189.5;ENY2,intron_variant,,ENST00000521662,NM_001193557.1;ENY2,intron_variant,,ENST00000522407,;ENY2,intron_variant,,ENST00000517756,;ENY2,intron_variant,,ENST00000517311,;ENY2,intron_variant,,ENST00000518118,;ENY2,intron_variant,,ENST00000517350,;ENY2,intron_variant,,ENST00000523335,;ENY2,intron_variant,,ENST00000521619,;ENY2,intron_variant,,ENST00000523707,;ENY2,intron_variant,,ENST00000522766,;ENY2,intron_variant,,ENST00000339942,;ENY2,downstream_gene_variant,,ENST00000518584,;ENY2,downstream_gene_variant,,ENST00000519754,; G ENST00000520147 Transcript frameshift_variant 305-306/857 233-234/303 78/100 L/LX ttg/ttGg 1 1 ENY2 HGNC HGNC:24449 protein_coding ENSP00000429588 E5RHX8 UPI0001E8F67C 5/6 HAMAP:MF_03046 HIGH insertion 4 1 1 PASS . . 0 206 0 3 0 0 0 0 -20 0.999998 1 1 1 0 G 7 5 101 109342708 109342708 - G 1 0 1 1 0 0 0 0 0 4991 1821 63 0 0 ENY2 8 109342708 Frame_Shift_Ins INS - C3N-02433_T 109342708 35795928 23 29673 ARC 0 . GRCh38 8 142613285 142613285 + Silent SNP C C T novel C3N-02433_T C3N-02433_N C C c.987G>A p.= p.L329L ENST00000356613 1/3 244 176 68 138 138 0 strelka-varscan-mutect ARC,synonymous_variant,p.=,ENST00000356613,NM_015193.4;ARC,upstream_gene_variant,,ENST00000581404,; T ENST00000356613 Transcript synonymous_variant 1188/2948 987/1191 329/396 L ctG/ctA 1 -1 ARC HGNC HGNC:648 protein_coding YES CCDS34950.1 ENSP00000349022 Q7LC44 UPI0000163B0F NM_015193.4 1/3 hmmpanther:PTHR15962 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 101 142613285 142613285 C T 1 0 0 0 0 0 0 0 1 963 697 25 3 3 ARC 8 142613285 Silent SNP C C3N-02433_T 33270577 142613285 2525351 24 29674 ZBTB5 0 . GRCh38 9 37441873 37441873 + Missense_Mutation SNP G G A novel C3N-02433_T C3N-02433_N G G c.679C>T p.His227Tyr p.H227Y ENST00000307750 2/2 195 129 66 174 174 0 strelka-varscan-mutect ZBTB5,missense_variant,p.His227Tyr,ENST00000307750,NM_014872.2;GRHPR,downstream_gene_variant,,ENST00000318158,NM_012203.1;GRHPR,downstream_gene_variant,,ENST00000497693,;GRHPR,downstream_gene_variant,,ENST00000480596,;GRHPR,downstream_gene_variant,,ENST00000494290,; A ENST00000307750 Transcript missense_variant 868/4627 679/2034 227/677 H/Y Cat/Tat 1 -1 ZBTB5 HGNC HGNC:23836 protein_coding YES CCDS6610.1 ENSP00000307604 O15062 Q5T942 UPI000006FAE2 NM_014872.2 deleterious(0) 2/2 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 101 37441873 37441873 G A 1 0 0 0 0 1 0 0 0 18121 1290 45 3 3 ZBTB5 9 37441873 Missense_Mutation SNP G C3N-02433_T 37441873 100952844 25 29675 SHB 0 . GRCh38 9 37974793 37974793 + Nonsense_Mutation SNP G G A novel C3N-02433_T C3N-02433_N G G c.883C>T p.Gln295Ter p.Q295* ENST00000377707 3/6 190 176 14 208 208 0 strelka-varscan-mutect SHB,stop_gained,p.Gln295Ter,ENST00000377707,NM_003028.2;RP11-613M10.9,3_prime_UTR_variant,,ENST00000540557,; A ENST00000377707 Transcript stop_gained 1449/2783 883/1530 295/509 Q/* Cag/Tag 1 -1 SHB HGNC HGNC:10838 protein_coding YES CCDS43806.1 ENSP00000366936 Q15464 UPI000021143B NM_003028.2 3/6 hmmpanther:PTHR15127:SF31,hmmpanther:PTHR15127 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 101 37974793 37974793 G A 1 0 0 0 0 0 1 0 0 14527 1357 47 3 3 SHB 9 37974793 Nonsense_Mutation SNP G C3N-02433_T 532920 37974793 100419924 26 29676 CNNM2 0 . GRCh38 10 102919321 102919321 + Missense_Mutation SNP G G T novel C3N-02433_T C3N-02433_N G G c.841G>T p.Ala281Ser p.A281S ENST00000369878 1/8 794 645 149 643 643 0 strelka-varscan-mutect CNNM2,missense_variant,p.Ala281Ser,ENST00000369878,NM_017649.4;CNNM2,missense_variant,p.Ala281Ser,ENST00000433628,NM_199076.2;CNNM2,missense_variant,p.Ala281Ser,ENST00000369875,NM_199077.2;RP11-724N1.1,downstream_gene_variant,,ENST00000610034,; T ENST00000369878 Transcript missense_variant 1029/15857 841/2628 281/875 A/S Gcc/Tcc 1 1 CNNM2 HGNC HGNC:103 protein_coding YES CCDS44474.1 ENSP00000358894 Q9H8M5 UPI0000231CA6 NM_017649.4 tolerated(0.16) 1/8 hmmpanther:PTHR12064:SF22,hmmpanther:PTHR12064,Pfam_domain:PF01595 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 102919321 102919321 G T 1 0 0 0 0 1 0 0 0 3393 1203 42 2 2 CNNM2 10 102919321 Missense_Mutation SNP G C3N-02433_T 102919321 30878101 27 29677 MUC5B 0 . GRCh38 11 1250061 1250061 + Missense_Mutation SNP A A G novel C3N-02433_T C3N-02433_N A A c.13181A>G p.Glu4394Gly p.E4394G ENST00000529681 31/49 531 442 89 464 464 0 strelka-varscan-mutect MUC5B,missense_variant,p.Glu4394Gly,ENST00000529681,NM_002458.2;RP11-532E4.2,upstream_gene_variant,,ENST00000532061,; G ENST00000529681 Transcript missense_variant 13239/17911 13181/17289 4394/5762 E/G gAg/gGg 1 1 MUC5B HGNC HGNC:7516 protein_coding YES CCDS44515.2 ENSP00000436812 Q9HC84 UPI0001DD21C7 NM_002458.2 tolerated_low_confidence(0.27) 31/49 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 1250061 1250061 A G 1 0 0 0 0 1 0 0 0 9979 304 11 5 5 MUC5B 11 1250061 Missense_Mutation SNP A C3N-02433_T 1250061 133836561 28 29678 CLCF1 0 . GRCh38 11 67367481 67367481 + Silent SNP G G A novel C3N-02433_T C3N-02433_N G G c.162C>T p.= p.L54L ENST00000312438 2/3 251 184 67 187 187 0 strelka-varscan-mutect CLCF1,synonymous_variant,p.=,ENST00000312438,NM_013246.2;CLCF1,synonymous_variant,p.=,ENST00000533438,NM_001166212.1;AP003419.11,intron_variant,,ENST00000543494,;RN7SKP239,downstream_gene_variant,,ENST00000364814,;RAD9A,intron_variant,,ENST00000622583,; A ENST00000312438 Transcript synonymous_variant 360/1844 162/678 54/225 L ctC/ctT 1 -1 CLCF1 HGNC HGNC:17412 protein_coding YES CCDS31617.1 ENSP00000309338 Q9UBD9 UPI000003F7F1 NM_013246.2 2/3 Gene3D:1.20.1250.10,Pfam_domain:PF06875,hmmpanther:PTHR21353,hmmpanther:PTHR21353:SF7,Superfamily_domains:SSF47266 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 67367481 67367481 G A 1 0 0 0 0 0 0 0 1 3225 1161 41 3 3 CLCF1 11 67367481 Silent SNP G C3N-02433_T 66117420 67367481 67719141 29 29679 ELMOD1 0 . GRCh38 11 107630491 107630491 + Missense_Mutation SNP T T C novel C3N-02433_T C3N-02433_N T T c.92T>C p.Leu31Pro p.L31P ENST00000265840 3/12 145 124 21 187 187 0 strelka-varscan-mutect ELMOD1,missense_variant,p.Leu31Pro,ENST00000265840,NM_018712.3;ELMOD1,missense_variant,p.Leu31Pro,ENST00000443271,NM_001130037.1;ELMOD1,missense_variant,p.Leu25Pro,ENST00000531234,NM_001308018.1; C ENST00000265840 Transcript missense_variant 357/2852 92/1005 31/334 L/P cTa/cCa 1 1 ELMOD1 HGNC HGNC:25334 protein_coding YES CCDS44723.1 ENSP00000265840 Q8N336 UPI000006DF30 NM_018712.3 deleterious(0.05) 3/12 hmmpanther:PTHR12771:SF18,hmmpanther:PTHR12771 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 107630491 107630491 T C 1 0 0 0 0 1 0 0 0 4902 1522 53 5 5 ELMOD1 11 107630491 Missense_Mutation SNP T C3N-02433_T 40263010 107630491 27456131 30 29680 OR8B12 0 . GRCh38 11 124542839 124542839 + Silent SNP C C A novel C3N-02433_T C3N-02433_N C C c.816G>T p.= p.V272V ENST00000306842 1/1 189 168 21 177 177 0 strelka-varscan-mutect OR8B12,synonymous_variant,p.=,ENST00000306842,NM_001005195.1;RP11-728D14.6,upstream_gene_variant,,ENST00000533869,; A ENST00000306842 Transcript synonymous_variant 841/998 816/933 272/310 V gtG/gtT 1 -1 OR8B12 HGNC HGNC:15307 protein_coding YES CCDS31711.1 ENSP00000307159 Q8NGG6 A0A126GWS7 UPI0000041E25 NM_001005195.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF267,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 124542839 124542839 C A 1 0 0 0 0 0 0 0 1 11296 465 17 2 2 OR8B12 11 124542839 Silent SNP C C3N-02433_T 16912348 124542839 10543783 31 29681 AEBP2 0 . GRCh38 12 19439907 19439907 + Frame_Shift_Del DEL G G - novel C3N-02433_T C3N-02433_N G G c.209delG p.Gly70AlafsTer71 p.G70Afs*71 ENST00000398864 1/9 86 51 35 79 79 0 sindel-varindel-pindel AEBP2,frameshift_variant,p.Gly70AlafsTer71,ENST00000398864,NM_001114176.1;AEBP2,frameshift_variant,p.Gly70AlafsTer71,ENST00000266508,NM_153207.4;AEBP2,intron_variant,,ENST00000541908,;AEBP2,intron_variant,,ENST00000538425,;AEBP2,upstream_gene_variant,,ENST00000360995,NM_001267043.1; - ENST00000398864 Transcript frameshift_variant 234/5099 208/1554 70/517 G/X Ggc/gc 1 1 AEBP2 HGNC HGNC:24051 protein_coding YES CCDS44841.1 ENSP00000381840 Q6ZN18 UPI00002290BB NM_001114176.1 1/9 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF80,Low_complexity_(Seg):seg HIGH 1 deletion 1 1 1 PASS . . 0 194 13 3 0 0 0 0 -20 0.9990604 1 1 1 0 - 7 5 101 19439907 19439907 G - 1 0 1 0 1 0 0 0 0 425 1116 39 0 0 AEBP2 12 19439907 Frame_Shift_Del DEL G C3N-02433_T 19439907 113835402 32 29682 MON2 0 . GRCh38 12 62565369 62565369 + Nonsense_Mutation SNP A A T novel C3N-02433_T C3N-02433_N A A c.4165A>T p.Lys1389Ter p.K1389* ENST00000393630 27/35 72 68 4 86 86 0 varscan-mutect MON2,stop_gained,p.Lys1389Ter,ENST00000393630,NM_015026.2,NM_001278472.1;MON2,stop_gained,p.Lys1389Ter,ENST00000546600,NM_001278469.1;MON2,stop_gained,p.Lys1389Ter,ENST00000393629,NM_001278470.1;MON2,stop_gained,p.Lys1366Ter,ENST00000552738,NM_001278471.1;MON2,3_prime_UTR_variant,,ENST00000547095,;MON2,non_coding_transcript_exon_variant,,ENST00000551307,;MON2,non_coding_transcript_exon_variant,,ENST00000547287,;MON2,upstream_gene_variant,,ENST00000549539,; T ENST00000393630 Transcript stop_gained 4556/13275 4165/5154 1389/1717 K/* Aaa/Taa 1 1 MON2 HGNC HGNC:29177 protein_coding YES CCDS31849.1 ENSP00000377250 Q7Z3U7 UPI00001AEA4C NM_015026.2,NM_001278472.1 27/35 Pfam_domain:PF16206,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF138 HIGH 1 SNV 1 1 PASS . . 0 194 7 6 3 0 0 0 -3.009688 0.2283077 1 1 0 0 T 4 4 101 62565369 62565369 A T 1 0 0 0 0 0 1 0 0 9664 15 1 4 4 MON2 12 62565369 Nonsense_Mutation SNP A C3N-02433_T 43125462 62565369 70709940 33 29683 ANKS1B 0 . GRCh38 12 99246808 99246808 + Missense_Mutation SNP A A G rs758891412 C3N-02433_T C3N-02433_N A A c.1813T>C p.Phe605Leu p.F605L ENST00000547776 13/26 131 71 60 102 102 0 strelka-varscan-mutect ANKS1B,missense_variant,p.Phe605Leu,ENST00000547776,NM_152788.4;ANKS1B,missense_variant,p.Phe185Leu,ENST00000547010,;ANKS1B,downstream_gene_variant,,ENST00000549866,;ANKS1B,upstream_gene_variant,,ENST00000550778,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000550833,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000546631,;ANKS1B,non_coding_transcript_exon_variant,,ENST00000550157,; G ENST00000547776 Transcript missense_variant 1813/3885 1813/3747 605/1248 F/L Ttt/Ctt rs758891412 1 -1 ANKS1B HGNC HGNC:24600 protein_coding YES CCDS55872.1 ENSP00000449629 Q7Z6G8 UPI00003FE521 NM_152788.4 deleterious(0) 13/26 hmmpanther:PTHR24174,hmmpanther:PTHR24174:SF3 MODERATE 1 SNV 1 1 PASS rs758891412 . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 99246808 99246808 A G 1 0 0 0 0 1 0 0 0 795 101 4 5 5 ANKS1B 12 99246808 Missense_Mutation SNP A C3N-02433_T 36681439 99246808 34028501 34 29684 MYCBP2 0 . GRCh38 13 77180211 77180211 + Silent SNP G G C rs574817467 C3N-02433_T C3N-02433_N G G c.4935C>G p.= p.L1645L ENST00000544440 34/83 231 215 16 231 231 0 strelka-varscan-mutect MYCBP2,synonymous_variant,p.=,ENST00000357337,NM_015057.4;MYCBP2,synonymous_variant,p.=,ENST00000544440,; C ENST00000544440 Transcript synonymous_variant 4953/14664 4935/13923 1645/4640 L ctC/ctG rs574817467 1 -1 MYCBP2 HGNC HGNC:23386 protein_coding YES ENSP00000444596 O75592 UPI0000212757 34/83 LOW 1 SNV 1 1 PASS rs574817467 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 101 77180211 77180211 G C 1 0 0 0 0 0 0 0 1 10018 929 33 4 4 MYCBP2 13 77180211 Silent SNP G C3N-02433_T 77180211 37184117 35 29685 MYO1E 0 . GRCh38 15 59223116 59223116 + Missense_Mutation SNP G G C novel C3N-02433_T C3N-02433_N G G c.853C>G p.Leu285Val p.L285V ENST00000288235 9/28 295 195 100 257 257 0 strelka-varscan-mutect MYO1E,missense_variant,p.Leu285Val,ENST00000288235,NM_004998.3;MYO1E,missense_variant,p.Leu115Val,ENST00000559269,;MYO1E,upstream_gene_variant,,ENST00000559489,;MYO1E,non_coding_transcript_exon_variant,,ENST00000558814,;MYO1E,downstream_gene_variant,,ENST00000558571,; C ENST00000288235 Transcript missense_variant 1253/8673 853/3327 285/1108 L/V Ctg/Gtg 1 -1 MYO1E HGNC HGNC:7599 protein_coding YES CCDS32254.1 ENSP00000288235 Q12965 Q4KMR3 UPI00001FE590 NM_004998.3 deleterious(0.03) 9/28 PROSITE_profiles:PS51456,hmmpanther:PTHR13140:SF288,hmmpanther:PTHR13140,Pfam_domain:PF00063,SMART_domains:SM00242,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 59223116 59223116 G C 1 0 0 0 0 1 0 0 0 10073 991 35 4 4 MYO1E 15 59223116 Missense_Mutation SNP G C3N-02433_T 59223116 42768073 36 29686 CYP1A2 0 . GRCh38 15 74750275 74750275 + Silent SNP G G A novel C3N-02433_T C3N-02433_N G G c.537G>A p.= p.L179L ENST00000343932 2/7 240 223 17 223 223 0 strelka-varscan-mutect CYP1A2,synonymous_variant,p.=,ENST00000343932,NM_000761.4; A ENST00000343932 Transcript synonymous_variant 600/2728 537/1551 179/516 L ctG/ctA 1 1 CYP1A2 HGNC HGNC:2596 protein_coding YES CCDS32293.1 ENSP00000342007 P05177 UPI0000073775 NM_000761.4 2/7 hmmpanther:PTHR24299:SF7,hmmpanther:PTHR24299,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 74750275 74750275 G A 1 0 0 0 0 0 0 0 1 3953 1277 45 3 3 CYP1A2 15 74750275 Silent SNP G C3N-02433_T 15527159 74750275 27240914 37 29687 RHCG 0 . GRCh38 15 89483090 89483090 + Missense_Mutation SNP A A C novel C3N-02433_T C3N-02433_N A A c.499T>G p.Phe167Val p.F167V ENST00000268122 3/11 52 37 15 44 44 0 strelka-mutect RHCG,missense_variant,p.Phe167Val,ENST00000268122,NM_001321041.1,NM_016321.2;RHCG,upstream_gene_variant,,ENST00000558360,;RHCG,missense_variant,p.Phe167Val,ENST00000560081,;RHCG,3_prime_UTR_variant,,ENST00000558184,;RHCG,intron_variant,,ENST00000558030,;RHCG,upstream_gene_variant,,ENST00000559638,; C ENST00000268122 Transcript missense_variant 568/1982 499/1440 167/479 F/V Ttc/Gtc 1 -1 RHCG HGNC HGNC:18140 protein_coding YES CCDS10351.1 ENSP00000268122 Q9UBD6 UPI00000343FD NM_001321041.1,NM_016321.2 deleterious(0.03) 3/11 Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,Prints_domain:PR00342,hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF30,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 89483090 89483090 A C 1 0 0 0 0 1 0 0 0 13498 43 2 5 5 RHCG 15 89483090 Missense_Mutation SNP A C3N-02433_T 14732815 89483090 12508099 38 29688 RHCG 0 . GRCh38 15 89483215 89483215 + Missense_Mutation SNP A A G novel C3N-02433_T C3N-02433_N A A c.374T>C p.Leu125Pro p.L125P ENST00000268122 3/11 43 31 12 26 26 0 strelka-varscan-mutect RHCG,missense_variant,p.Leu125Pro,ENST00000268122,NM_001321041.1,NM_016321.2;RHCG,upstream_gene_variant,,ENST00000558360,;RHCG,missense_variant,p.Leu125Pro,ENST00000560081,;RHCG,missense_variant,p.Leu125Pro,ENST00000558030,;RHCG,splice_region_variant,,ENST00000558184,;RHCG,upstream_gene_variant,,ENST00000559638,; G ENST00000268122 Transcript missense_variant,splice_region_variant 443/1982 374/1440 125/479 L/P cTc/cCc 1 -1 RHCG HGNC HGNC:18140 protein_coding YES CCDS10351.1 ENSP00000268122 Q9UBD6 UPI00000343FD NM_001321041.1,NM_016321.2 deleterious(0.01) 3/11 Superfamily_domains:0044218,Gene3D:1.10.3430.10,Pfam_domain:PF00909,hmmpanther:PTHR11730,hmmpanther:PTHR11730:SF30,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS rs1409127242 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 89483215 89483215 A G 1 0 0 0 0 1 0 0 0 13498 318 11 5 5 RHCG 15 89483215 Missense_Mutation SNP A C3N-02433_T 125 89483215 12507974 39 29689 CDH5 0 . GRCh38 16 66402844 66402844 + Missense_Mutation SNP C C T novel C3N-02433_T C3N-02433_N C C c.2030C>T p.Ala677Val p.A677V ENST00000341529 12/12 269 255 14 167 167 0 strelka-varscan-mutect CDH5,missense_variant,p.Ala677Val,ENST00000341529,NM_001795.3;CDH5,missense_variant,p.Ala562Val,ENST00000614547,;CDH5,missense_variant,p.Ala116Val,ENST00000539168,;CDH5,3_prime_UTR_variant,,ENST00000565334,; T ENST00000341529 Transcript missense_variant 2178/4120 2030/2355 677/784 A/V gCg/gTg 1 1 CDH5 HGNC HGNC:1764 protein_coding YES CCDS10804.1 ENSP00000344115 P33151 UPI000016B272 NM_001795.3 tolerated(0.26) 12/12 hmmpanther:PTHR24027:SF89,hmmpanther:PTHR24027,Pfam_domain:PF01049 MODERATE 1 SNV 1 1 PASS rs1201962235 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 66402844 66402844 C T 1 0 0 0 0 1 0 0 0 2816 768 27 1 1 CDH5 16 66402844 Missense_Mutation SNP C C3N-02433_T 66402844 23935501 40 29690 ZNF23 0 . GRCh38 16 71448842 71448842 + Missense_Mutation SNP T T C novel C3N-02433_T C3N-02433_N T T c.1183A>G p.Thr395Ala p.T395A ENST00000393539 6/6 208 177 31 170 170 0 strelka-varscan-mutect ZNF23,missense_variant,p.Thr395Ala,ENST00000393539,NM_145911.2;ZNF23,missense_variant,p.Thr395Ala,ENST00000357254,NM_001304492.1;ZNF23,missense_variant,p.Thr337Ala,ENST00000564528,NM_001304493.1,NM_001304494.1;ZNF23,missense_variant,p.Thr395Ala,ENST00000428724,;ZNF23,3_prime_UTR_variant,,ENST00000497160,;ZNF23,3_prime_UTR_variant,,ENST00000358700,;ZNF23,downstream_gene_variant,,ENST00000567340,;ZNF23,downstream_gene_variant,,ENST00000565718,;ZNF23,non_coding_transcript_exon_variant,,ENST00000539742,;AC010547.9,3_prime_UTR_variant,,ENST00000561908,;ZNF23,non_coding_transcript_exon_variant,,ENST00000576258,;RP11-510M2.8,upstream_gene_variant,,ENST00000571789,; C ENST00000393539 Transcript missense_variant 1997/3242 1183/1932 395/643 T/A Act/Gct 1 -1 ZNF23 HGNC HGNC:13023 protein_coding YES CCDS10900.1 ENSP00000377171 P17027 UPI000013C406 NM_145911.2 tolerated(0.3) 6/6 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF180,hmmpanther:PTHR24377,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 71448842 71448842 T C 1 0 0 0 0 1 0 0 0 18360 1696 59 5 5 ZNF23 16 71448842 Missense_Mutation SNP T C3N-02433_T 5045998 71448842 18889503 41 29691 NCOR1 0 . GRCh38 17 16048970 16048970 + Silent SNP T T G C3N-02433_T C3N-02433_N T T c.6411A>C p.= p.P2137P ENST00000268712 41/46 105 77 28 67 67 0 strelka-varscan-mutect NCOR1,synonymous_variant,p.=,ENST00000268712,NM_006311.3;NCOR1,synonymous_variant,p.=,ENST00000395857,;NCOR1,synonymous_variant,p.=,ENST00000395851,NM_001190440.1;NCOR1,synonymous_variant,p.=,ENST00000395849,;NCOR1,synonymous_variant,p.=,ENST00000580554,;NCOR1,synonymous_variant,p.=,ENST00000579606,;TTC19,downstream_gene_variant,,ENST00000470649,;NCOR1,upstream_gene_variant,,ENST00000579573,;NCOR1,non_coding_transcript_exon_variant,,ENST00000470782,;NCOR1,non_coding_transcript_exon_variant,,ENST00000458113,;NCOR1,non_coding_transcript_exon_variant,,ENST00000464381,;NCOR1,non_coding_transcript_exon_variant,,ENST00000583234,;RPLP1P11,downstream_gene_variant,,ENST00000453002,; G ENST00000268712 Transcript synonymous_variant 6669/10720 6411/7323 2137/2440 P ccA/ccC COSM472342,COSM4857479 1 -1 NCOR1 HGNC HGNC:7672 protein_coding YES CCDS11175.1 ENSP00000268712 O75376 A0A024RD47 UPI000013D7D5 NM_006311.3 41/46 hmmpanther:PTHR13992:SF5,hmmpanther:PTHR13992 1,1 LOW 1 SNV 1 1,1 1 PASS rs927584857 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 101 16048970 16048970 T G 1 0 0 0 0 0 0 0 1 10254 1567 55 5 5 NCOR1 17 16048970 Silent SNP T C3N-02433_T 16048970 67208471 42 29692 GNA13 0 . GRCh38 17 65014285 65014285 + Missense_Mutation SNP T T C novel C3N-02433_T C3N-02433_N T T c.1106A>G p.Asp369Gly p.D369G ENST00000439174 4/4 179 168 11 97 97 0 strelka-varscan-mutect GNA13,missense_variant,p.Asp369Gly,ENST00000439174,NM_006572.5;GNA13,missense_variant,p.Asp274Gly,ENST00000541118,NM_001282425.1; C ENST00000439174 Transcript missense_variant 1352/4922 1106/1134 369/377 D/G gAc/gGc 1 -1 GNA13 HGNC HGNC:4381 protein_coding YES CCDS11661.1 ENSP00000400717 Q14344 A0A024R8M0 UPI0000073EBA NM_006572.5 tolerated(0.32) 4/4 hmmpanther:PTHR10218:SF85,hmmpanther:PTHR10218,Gene3D:3.40.50.300,SMART_domains:SM00275,Superfamily_domains:SSF52540,Prints_domain:PR00440 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 101 65014285 65014285 T C 1 0 0 0 0 1 0 0 0 6381 1667 58 5 5 GNA13 17 65014285 Missense_Mutation SNP T C3N-02433_T 48965315 65014285 18243156 43 29693 B3GNTL1 0 . GRCh38 17 82965735 82965735 + Silent SNP T T A novel C3N-02433_T C3N-02433_N T T c.516A>T p.= p.S172S ENST00000320865 7/13 309 244 65 223 223 0 strelka-varscan-mutect B3GNTL1,synonymous_variant,p.=,ENST00000576599,;B3GNTL1,synonymous_variant,p.=,ENST00000320865,NM_001009905.1;B3GNTL1,non_coding_transcript_exon_variant,,ENST00000571954,;B3GNTL1,intron_variant,,ENST00000570947,;B3GNTL1,5_prime_UTR_variant,,ENST00000572977,;B3GNTL1,upstream_gene_variant,,ENST00000571394,; A ENST00000320865 Transcript synonymous_variant 530/1383 516/1086 172/361 S tcA/tcT 1 -1 B3GNTL1 HGNC HGNC:21727 protein_coding YES CCDS32778.1 ENSP00000319979 Q67FW5 A0A024R8X6 UPI00003B5C5A NM_001009905.1 7/13 Gene3D:3.90.550.10,Pfam_domain:PF00535,hmmpanther:PTHR22916,hmmpanther:PTHR22916:SF3,Superfamily_domains:SSF53448 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 82965735 82965735 T A 1 0 0 0 0 0 0 0 1 1421 1799 63 4 4 B3GNTL1 17 82965735 Silent SNP T C3N-02433_T 17951450 82965735 291706 44 29694 VAPA 0 . GRCh38 18 9954190 9954190 + Silent SNP T T C novel C3N-02433_T C3N-02433_N T T c.864T>C p.= p.F288F ENST00000340541 7/7 94 70 24 146 146 0 strelka-varscan-mutect VAPA,synonymous_variant,p.=,ENST00000400000,NM_194434.2;VAPA,synonymous_variant,p.=,ENST00000340541,NM_003574.5;VAPA,downstream_gene_variant,,ENST00000584796,;VAPA,non_coding_transcript_exon_variant,,ENST00000583475,;VAPA,non_coding_transcript_exon_variant,,ENST00000583879,;VAPA,downstream_gene_variant,,ENST00000577539,; C ENST00000340541 Transcript synonymous_variant 1059/1227 864/885 288/294 F ttT/ttC 1 1 VAPA HGNC HGNC:12648 protein_coding YES CCDS11847.2 ENSP00000345656 Q9P0L0 UPI000059D45E NM_003574.5 7/7 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR10809,hmmpanther:PTHR10809:SF40,PIRSF_domain:PIRSF019693 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 101 9954190 9954190 T C 1 0 0 0 0 0 0 0 1 17666 1780 62 5 5 VAPA 18 9954190 Silent SNP T C3N-02433_T 9954190 70419095 45 29695 EIF3G 0 . GRCh38 19 10117166 10117166 + Nonsense_Mutation SNP G G C novel C3N-02433_T C3N-02433_N G G c.323C>G p.Ser108Ter p.S108* ENST00000253108 6/11 93 72 21 52 52 0 strelka-varscan-mutect EIF3G,stop_gained,p.Ser108Ter,ENST00000253108,NM_003755.3;EIF3G,stop_gained,p.Ser108Ter,ENST00000589454,;EIF3G,stop_gained,p.Ser110Ter,ENST00000588709,;EIF3G,intron_variant,,ENST00000587146,;PPAN-P2RY11,downstream_gene_variant,,ENST00000428358,NM_001198690.1;PPAN-P2RY11,downstream_gene_variant,,ENST00000393796,NM_001040664.2;P2RY11,downstream_gene_variant,,ENST00000321826,NM_002566.4;EIF3G,upstream_gene_variant,,ENST00000593054,;P2RY11,downstream_gene_variant,,ENST00000471843,;EIF3G,downstream_gene_variant,,ENST00000587168,;EIF3G,synonymous_variant,p.=,ENST00000593095,;EIF3G,3_prime_UTR_variant,,ENST00000593066,;EIF3G,3_prime_UTR_variant,,ENST00000587993,;EIF3G,non_coding_transcript_exon_variant,,ENST00000589009,;EIF3G,non_coding_transcript_exon_variant,,ENST00000589674,;EIF3G,upstream_gene_variant,,ENST00000590158,;EIF3G,downstream_gene_variant,,ENST00000592485,;EIF3G,downstream_gene_variant,,ENST00000590940,;EIF3G,downstream_gene_variant,,ENST00000587681,; C ENST00000253108 Transcript stop_gained 366/1103 323/963 108/320 S/* tCa/tGa 1 -1 EIF3G HGNC HGNC:3274 protein_coding YES CCDS12227.1 ENSP00000253108 O75821 UPI000012D2FE NM_003755.3 6/11 HAMAP:MF_03006,Pfam_domain:PF12353,PIRSF_domain:PIRSF037949,hmmpanther:PTHR10352 HIGH 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 C 4 2 101 10117166 10117166 G C 1 0 0 0 0 0 1 0 0 4851 1294 45 4 4 EIF3G 19 10117166 Nonsense_Mutation SNP G C3N-02433_T 10117166 48500450 46 29696 MBOAT7 0 . GRCh38 19 54188455 54188455 + Silent SNP G G A novel C3N-02433_T C3N-02433_N G G c.54C>T p.= p.I18I ENST00000245615 2/8 176 165 11 128 128 0 strelka-varscan-mutect MBOAT7,synonymous_variant,p.=,ENST00000245615,NM_024298.4;MBOAT7,synonymous_variant,p.=,ENST00000391754,NM_001146082.2;MBOAT7,synonymous_variant,p.=,ENST00000414665,;MBOAT7,synonymous_variant,p.=,ENST00000453320,;MBOAT7,5_prime_UTR_variant,,ENST00000431666,NM_001146083.2;MBOAT7,intron_variant,,ENST00000338624,NM_001146056.2;TSEN34,upstream_gene_variant,,ENST00000302937,NM_024075.4;TSEN34,upstream_gene_variant,,ENST00000429671,NM_001282333.1;MBOAT7,upstream_gene_variant,,ENST00000495279,;TSEN34,upstream_gene_variant,,ENST00000396383,NM_001282332.1;TSEN34,upstream_gene_variant,,ENST00000396388,NM_001077446.3;TSEN34,upstream_gene_variant,,ENST00000455798,;TSEN34,upstream_gene_variant,,ENST00000456872,;MBOAT7,upstream_gene_variant,,ENST00000449249,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000495968,;MBOAT7,intron_variant,,ENST00000474910,;MBOAT7,synonymous_variant,p.=,ENST00000437868,;MBOAT7,non_coding_transcript_exon_variant,,ENST00000491216,;TSEN34,upstream_gene_variant,,ENST00000496583,;MBOAT7,upstream_gene_variant,,ENST00000464098,; A ENST00000245615 Transcript synonymous_variant 535/2529 54/1419 18/472 I atC/atT 1 -1 MBOAT7 HGNC HGNC:15505 protein_coding YES CCDS12883.1 ENSP00000245615 Q96N66 UPI000013CBAC NM_024298.4 2/8 Transmembrane_helices:TMhelix,hmmpanther:PTHR13906:SF16,hmmpanther:PTHR13906 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -14.3644 0.9999996 1 1 1 0 A 2 1 101 54188455 54188455 G A 1 0 0 0 0 0 0 0 1 9291 1048 37 1 1 MBOAT7 19 54188455 Silent SNP G C3N-02433_T 44071289 54188455 4429161 47 29697 RSPO4 0 . GRCh38 20 968088 968088 + Nonsense_Mutation SNP C C A rs753113241 C3N-02433_T C3N-02433_N C C c.130G>T p.Glu44Ter p.E44* ENST00000217260 2/5 379 352 27 282 282 0 strelka-varscan-mutect RSPO4,stop_gained,p.Glu44Ter,ENST00000217260,NM_001029871.3;RSPO4,stop_gained,p.Glu44Ter,ENST00000400634,NM_001040007.2; A ENST00000217260 Transcript stop_gained 227/2707 130/705 44/234 E/* Gag/Tag rs753113241 1 -1 RSPO4 HGNC HGNC:16175 protein_coding YES CCDS42846.1 ENSP00000217260 Q2I0M5 UPI00001D8320 NM_001029871.3 2/5 hmmpanther:PTHR23275,hmmpanther:PTHR23275:SF51,Pfam_domain:PF15913,Gene3D:2.10.220.10,SMART_domains:SM00261,Superfamily_domains:SSF57184 HIGH 1 SNV 2 1 PASS rs753113241 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 101 968088 968088 C A 1 0 0 0 0 0 1 0 0 13970 864 30 2 2 RSPO4 20 968088 Nonsense_Mutation SNP C C3N-02433_T 968088 63476079 48 29698 RABL2B 0 . GRCh38 22 50768787 50768787 + Missense_Mutation SNP G G A novel C3N-02433_T C3N-02433_N G G c.706C>T p.Pro236Ser p.P236S ENST00000395593 10/10 324 283 41 219 218 1 varscan-mutect RABL2B,missense_variant,p.Pro227Ser,ENST00000395595,NM_001130921.1;RABL2B,missense_variant,p.Pro236Ser,ENST00000395593,NM_001130923.1;RABL2B,missense_variant,p.Pro226Ser,ENST00000395598,NM_001130922.1,NM_007081.2;RABL2B,missense_variant,p.Pro227Ser,ENST00000354869,NM_001130920.1,NM_001130919.1,NM_001003789.1;RABL2B,missense_variant,p.Pro163Ser,ENST00000395591,;RABL2B,missense_variant,p.Pro226Ser,ENST00000435118,;RABL2B,downstream_gene_variant,,ENST00000395590,;RABL2B,non_coding_transcript_exon_variant,,ENST00000465063,;RPL23AP82,intron_variant,,ENST00000496652,;RABL2B,3_prime_UTR_variant,,ENST00000436958,;RABL2B,3_prime_UTR_variant,,ENST00000425098,;RABL2B,downstream_gene_variant,,ENST00000464678,;RABL2B,downstream_gene_variant,,ENST00000482308,; A ENST00000395593 Transcript missense_variant 1060/2341 706/717 236/238 P/S Ccc/Tcc 1 -1 RABL2B HGNC HGNC:9800 protein_coding YES CCDS46738.1 ENSP00000378958 Q9UNT1 UPI00004214D6 NM_001130923.1 tolerated_low_confidence(0.14) 10/10 PROSITE_profiles:PS51419 MODERATE 1 SNV 1 1 PASS rs1185359244 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 101 50768787 50768787 G A 1 0 0 0 0 1 0 0 0 13130 1174 41 3 3 RABL2B 22 50768787 Missense_Mutation SNP G C3N-02433_T 50768787 49681 49 29699 1 28 3 3 83 G 1.053228e-08 RABL2B 0 . GRCh38 22 50768804 50768804 + Missense_Mutation SNP G G A novel C3N-02433_T C3N-02433_N G G c.689C>T p.Ser230Leu p.S230L ENST00000395593 10/10 364 310 54 253 253 0 strelka-varscan-mutect RABL2B,missense_variant,p.Ser221Leu,ENST00000395595,NM_001130921.1;RABL2B,missense_variant,p.Ser230Leu,ENST00000395593,NM_001130923.1;RABL2B,missense_variant,p.Ser220Leu,ENST00000395598,NM_001130922.1,NM_007081.2;RABL2B,missense_variant,p.Ser221Leu,ENST00000354869,NM_001130920.1,NM_001130919.1,NM_001003789.1;RABL2B,missense_variant,p.Ser157Leu,ENST00000395591,;RABL2B,missense_variant,p.Ser220Leu,ENST00000435118,;RABL2B,downstream_gene_variant,,ENST00000395590,;RABL2B,non_coding_transcript_exon_variant,,ENST00000465063,;RPL23AP82,intron_variant,,ENST00000496652,;RABL2B,3_prime_UTR_variant,,ENST00000436958,;RABL2B,3_prime_UTR_variant,,ENST00000425098,;RABL2B,downstream_gene_variant,,ENST00000464678,;RABL2B,downstream_gene_variant,,ENST00000482308,; A ENST00000395593 Transcript missense_variant 1043/2341 689/717 230/238 S/L tCa/tTa 1 -1 RABL2B HGNC HGNC:9800 protein_coding YES CCDS46738.1 ENSP00000378958 Q9UNT1 UPI00004214D6 NM_001130923.1 deleterious_low_confidence(0.02) 10/10 PROSITE_profiles:PS51419 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 101 50768804 50768804 G A 1 0 0 0 0 1 0 0 0 13130 1294 45 3 3 RABL2B 22 50768804 Missense_Mutation SNP G C3N-02433_T 17 50768804 49664 50 29700 1 28 3 3 83 G 1.053228e-08 RABL2B 0 . GRCh38 22 50768869 50768869 + Silent SNP G G A novel C3N-02433_T C3N-02433_N G G c.624C>T p.= p.F208F ENST00000395593 10/10 182 157 25 116 116 0 varscan-mutect RABL2B,synonymous_variant,p.=,ENST00000395595,NM_001130921.1;RABL2B,synonymous_variant,p.=,ENST00000395593,NM_001130923.1;RABL2B,synonymous_variant,p.=,ENST00000395598,NM_001130922.1,NM_007081.2;RABL2B,synonymous_variant,p.=,ENST00000354869,NM_001130920.1,NM_001130919.1,NM_001003789.1;RABL2B,synonymous_variant,p.=,ENST00000395591,;RABL2B,synonymous_variant,p.=,ENST00000435118,;RABL2B,downstream_gene_variant,,ENST00000395590,;RABL2B,non_coding_transcript_exon_variant,,ENST00000465063,;RPL23AP82,intron_variant,,ENST00000496652,;RABL2B,3_prime_UTR_variant,,ENST00000436958,;RABL2B,3_prime_UTR_variant,,ENST00000425098,;RABL2B,downstream_gene_variant,,ENST00000464678,;RABL2B,downstream_gene_variant,,ENST00000482308,; A ENST00000395593 Transcript synonymous_variant 978/2341 624/717 208/238 F ttC/ttT 1 -1 RABL2B HGNC HGNC:9800 protein_coding YES CCDS46738.1 ENSP00000378958 Q9UNT1 UPI00004214D6 NM_001130923.1 10/10 PROSITE_profiles:PS51419,hmmpanther:PTHR24073,hmmpanther:PTHR24073:SF263,Low_complexity_(Seg):seg,SMART_domains:SM00176 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 101 50768869 50768869 G A 1 0 0 0 0 0 0 0 1 13130 1304 45 3 3 RABL2B 22 50768869 Silent SNP G C3N-02433_T 65 50768869 49599 51 29701 1 28 3 3 83 G 1.053228e-08 CLCN4 0 . GRCh38 X 10206431 10206431 + Missense_Mutation SNP C C T novel C3N-02433_T C3N-02433_N C C c.629C>T p.Thr210Met p.T210M ENST00000380833 7/13 410 328 82 301 301 0 strelka-varscan-mutect CLCN4,missense_variant,p.Thr210Met,ENST00000380833,NM_001830.3;CLCN4,missense_variant,p.Thr116Met,ENST00000421085,NM_001256944.1;CLCN4,missense_variant,p.Thr210Met,ENST00000380829,;CLCN4,intron_variant,,ENST00000454850,; T ENST00000380833 Transcript missense_variant 1020/6750 629/2283 210/760 T/M aCg/aTg 1 1 CLCN4 HGNC HGNC:2022 protein_coding YES CCDS14137.1 ENSP00000370213 P51793 UPI0000127A99 NM_001830.3 deleterious(0.01) 7/13 Gene3D:1otsB00,Pfam_domain:PF00654,Prints_domain:PR00762,hmmpanther:PTHR11689,hmmpanther:PTHR11689:SF18,Low_complexity_(Seg):seg,Superfamily_domains:SSF81340,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 10206431 10206431 C T 1 0 0 0 0 1 0 0 0 3229 536 19 1 1 CLCN4 23 10206431 Missense_Mutation SNP C C3N-02433_T 10206431 145834464 52 29702 GSPT2 0 . GRCh38 X 51743838 51743838 + Missense_Mutation SNP C C G novel C3N-02433_T C3N-02433_N C C c.212C>G p.Ser71Cys p.S71C ENST00000340438 1/1 109 88 21 99 99 0 strelka-varscan-mutect GSPT2,missense_variant,p.Ser71Cys,ENST00000340438,NM_018094.4; G ENST00000340438 Transcript missense_variant 408/2802 212/1887 71/628 S/C tCc/tGc 1 1 GSPT2 HGNC HGNC:4622 protein_coding YES CCDS14336.1 ENSP00000341247 Q8IYD1 UPI0000073899 NM_018094.4 deleterious_low_confidence(0.02) 1/1 MODERATE 1 SNV 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 101 51743838 51743838 C G 1 0 0 0 0 1 0 0 0 6711 855 30 4 4 GSPT2 23 51743838 Missense_Mutation SNP C C3N-02433_T 41537407 51743838 104297057 53 29703 TCEAL5 0 . GRCh38 X 103274115 103274115 + Missense_Mutation SNP C C T novel C3N-02433_T C3N-02433_N C C c.449G>A p.Gly150Glu p.G150E ENST00000372680 3/3 384 363 21 324 323 1 varscan-mutect TCEAL5,missense_variant,p.Gly150Glu,ENST00000372680,NM_001012979.2; T ENST00000372680 Transcript missense_variant 744/1168 449/621 150/206 G/E gGa/gAa 1 -1 TCEAL5 HGNC HGNC:22282 protein_coding YES CCDS35356.1 ENSP00000361765 Q5H9L2 UPI00001998F8 NM_001012979.2 tolerated(0.13) 3/3 hmmpanther:PTHR14754,hmmpanther:PTHR14754:SF17,Pfam_domain:PF04538 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 103274115 103274115 C T 1 0 0 0 0 1 0 0 0 16081 855 30 3 3 TCEAL5 23 103274115 Missense_Mutation SNP C C3N-02433_T 51530277 103274115 52766780 54 29704 MAP7D3 0 . GRCh38 X 136231695 136231695 + Missense_Mutation SNP C C T novel C3N-02433_T C3N-02433_N C C c.1262G>A p.Ser421Asn p.S421N ENST00000316077 8/19 240 210 30 210 210 0 strelka-varscan-mutect MAP7D3,missense_variant,p.Ser421Asn,ENST00000316077,NM_024597.3;MAP7D3,missense_variant,p.Ser403Asn,ENST00000370663,NM_001173516.1;MAP7D3,missense_variant,p.Ser386Asn,ENST00000370661,NM_001173517.1;MAP7D3,missense_variant,p.Ser380Asn,ENST00000370660,;MAP7D3,upstream_gene_variant,,ENST00000495432,;MAP7D3,upstream_gene_variant,,ENST00000477124,;MAP7D3,upstream_gene_variant,,ENST00000489788,; T ENST00000316077 Transcript missense_variant 1483/4567 1262/2631 421/876 S/N aGc/aAc 1 -1 MAP7D3 HGNC HGNC:25742 protein_coding YES CCDS44004.1 ENSP00000318086 Q8IWC1 UPI00001C207C NM_024597.3 tolerated(0.3) 8/19 hmmpanther:PTHR15073,hmmpanther:PTHR15073:SF5 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 101 136231695 136231695 C T 1 0 0 0 0 1 0 0 0 9193 797 28 3 3 MAP7D3 23 136231695 Missense_Mutation SNP C C3N-02433_T 32957580 136231695 19809200 55 29705 USP1 0 . GRCh38 1 62450308 62450308 + Missense_Mutation SNP T T G novel C3N-02529_T C3N-02529_N T T c.1685T>G p.Leu562Trp p.L562W ENST00000339950 9/9 120 108 12 159 159 0 strelka-varscan-mutect USP1,missense_variant,p.Leu562Trp,ENST00000339950,NM_003368.4;USP1,missense_variant,p.Leu562Trp,ENST00000371146,NM_001017415.1,NM_001017416.1;DOCK7,downstream_gene_variant,,ENST00000251157,;DOCK7,downstream_gene_variant,,ENST00000454575,NM_001271999.1;DOCK7,downstream_gene_variant,,ENST00000340370,NM_033407.3;DOCK7,downstream_gene_variant,,ENST00000637255,;DOCK7,downstream_gene_variant,,ENST00000634495,;DOCK7,downstream_gene_variant,,ENST00000635983,;DOCK7,downstream_gene_variant,,ENST00000635348,; G ENST00000339950 Transcript missense_variant 2500/3996 1685/2358 562/785 L/W tTg/tGg 1 1 USP1 HGNC HGNC:12607 protein_coding YES CCDS621.1 ENSP00000343526 O94782 UPI00001379D4 NM_003368.4 deleterious(0) 9/9 Pfam_domain:PF00443,PROSITE_profiles:PS50235,hmmpanther:PTHR24006,Superfamily_domains:SSF54001 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 62450308 62450308 T G 1 0 0 0 0 1 0 0 0 17574 1821 63 5 5 USP1 1 62450308 Missense_Mutation SNP T C3N-02529_T 62450308 186506114 1 29706 TYW3 0 . GRCh38 1 74733304 74733304 + Silent SNP C C T C3N-02529_T C3N-02529_N C C c.60C>T p.= p.L20L ENST00000370867 1/6 296 271 25 250 250 0 strelka-varscan-mutect TYW3,synonymous_variant,p.=,ENST00000370867,NM_138467.2;TYW3,synonymous_variant,p.=,ENST00000457880,NM_001162916.1;CRYZ,5_prime_UTR_variant,,ENST00000417775,NM_001130042.1;TYW3,5_prime_UTR_variant,,ENST00000479111,;CRYZ,upstream_gene_variant,,ENST00000340866,NM_001889.3;CRYZ,upstream_gene_variant,,ENST00000370872,NM_001134759.1;CRYZ,upstream_gene_variant,,ENST00000370871,NM_001130043.1;CRYZ,upstream_gene_variant,,ENST00000370870,;TYW3,upstream_gene_variant,,ENST00000483990,;CRYZ,upstream_gene_variant,,ENST00000441120,; T ENST00000370867 Transcript synonymous_variant 149/3430 60/780 20/259 L ctC/ctT COSM3790256 1 1 TYW3 HGNC HGNC:24757 protein_coding YES CCDS666.1 ENSP00000359904 Q6IPR3 UPI000006EC9D NM_138467.2 1/6 Superfamily_domains:0044041,Gene3D:1tljA00,Pfam_domain:PF02676,hmmpanther:PTHR23245 1 LOW 1 SNV 1 1 1 PASS rs1293025026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 74733304 74733304 C T 1 0 0 0 0 0 0 0 1 17335 813 29 3 3 TYW3 1 74733304 Silent SNP C C3N-02529_T 12282996 74733304 174223118 2 29707 C1orf226 0 . GRCh38 1 162383520 162383520 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.785G>A p.Arg262Lys p.R262K ENST00000426197 3/3 398 363 35 301 301 0 strelka-varscan-mutect C1orf226,missense_variant,p.Arg219Lys,ENST00000458626,NM_001085375.1;C1orf226,missense_variant,p.Arg262Lys,ENST00000426197,NM_001135240.1;C1orf226,downstream_gene_variant,,ENST00000420220,;RP11-565P22.6,downstream_gene_variant,,ENST00000431696,;RP11-565P22.6,3_prime_UTR_variant,,ENST00000367932,; A ENST00000426197 Transcript missense_variant 858/1049 785/948 262/315 R/K aGa/aAa 1 1 C1orf226 HGNC HGNC:34351 protein_coding YES CCDS44268.1 ENSP00000413150 A1L170 UPI00006C02B3 NM_001135240.1 tolerated(0.08) 3/3 Pfam_domain:PF15429 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 162383520 162383520 G A 1 0 0 0 0 1 0 0 0 1984 942 33 3 3 C1orf226 1 162383520 Missense_Mutation SNP G C3N-02529_T 87650216 162383520 86572902 3 29708 HMCN1 0 . GRCh38 1 186015982 186015982 + Nonsense_Mutation SNP T T A novel C3N-02529_T C3N-02529_N T T c.4934T>A p.Leu1645Ter p.L1645* ENST00000271588 32/107 216 201 15 213 213 0 strelka-varscan-mutect HMCN1,stop_gained,p.Leu1645Ter,ENST00000271588,NM_031935.2; A ENST00000271588 Transcript stop_gained 5163/18208 4934/16908 1645/5635 L/* tTg/tAg 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 32/107 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,Superfamily_domains:SSF48726 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 102 186015982 186015982 T A 1 0 0 0 0 0 1 0 0 7111 1821 63 4 4 HMCN1 1 186015982 Nonsense_Mutation SNP T C3N-02529_T 23632462 186015982 62940440 4 29709 PKP1 0 . GRCh38 1 201323094 201323094 + Missense_Mutation SNP C C A rs747503125 C3N-02529_T C3N-02529_N C C c.1648C>A p.Arg550Ser p.R550S ENST00000263946 10/15 376 310 66 262 261 1 strelka-varscan-mutect PKP1,missense_variant,p.Arg550Ser,ENST00000263946,NM_000299.3;PKP1,missense_variant,p.Arg529Ser,ENST00000367324,NM_001005337.2;PKP1,missense_variant,p.Arg550Ser,ENST00000352845,;PKP1,downstream_gene_variant,,ENST00000475988,; A ENST00000263946 Transcript missense_variant 1899/5447 1648/2244 550/747 R/S Cgc/Agc rs747503125 1 1 PKP1 HGNC HGNC:9023 protein_coding YES CCDS30966.1 ENSP00000263946 Q13835 UPI0000131B86 NM_000299.3 deleterious(0.01) 10/15 Gene3D:1.25.10.10,hmmpanther:PTHR10372,hmmpanther:PTHR10372:SF3,SMART_domains:SM00185,Superfamily_domains:SSF48371 MODERATE 1 SNV 5 1 PASS rs747503125 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 201323094 201323094 C A 1 0 0 0 0 1 0 0 0 12080 652 23 1 1 PKP1 1 201323094 Missense_Mutation SNP C C3N-02529_T 15307112 201323094 47633328 5 29710 PM20D1 0 . GRCh38 1 205830290 205830290 + Missense_Mutation SNP C C G C3N-02529_T C3N-02529_N C C c.1375G>C p.Asp459His p.D459H ENST00000367136 12/13 325 294 31 227 227 0 strelka-varscan-mutect PM20D1,missense_variant,p.Asp459His,ENST00000367136,NM_152491.4;PM20D1,non_coding_transcript_exon_variant,,ENST00000460624,;PM20D1,non_coding_transcript_exon_variant,,ENST00000461807,;PM20D1,upstream_gene_variant,,ENST00000469861,; G ENST00000367136 Transcript missense_variant 1420/2152 1375/1509 459/502 D/H Gac/Cac COSM902838,COSM902839 1 -1 PM20D1 HGNC HGNC:26518 protein_coding YES CCDS1460.1 ENSP00000356104 Q6GTS8 UPI00003665FD NM_152491.4 deleterious(0) 12/13 hmmpanther:PTHR11014:SF16,hmmpanther:PTHR11014,Pfam_domain:PF01546,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1408330500 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 205830290 205830290 C G 1 0 0 0 0 1 0 0 0 12234 913 32 4 4 PM20D1 1 205830290 Missense_Mutation SNP C C3N-02529_T 4507196 205830290 43126132 6 29711 POMC 0 . GRCh38 2 25161086 25161086 + Missense_Mutation SNP C C T C3N-02529_T C3N-02529_N C C c.799G>A p.Glu267Lys p.E267K ENST00000405623 3/3 231 203 28 177 177 0 strelka-varscan-mutect POMC,missense_variant,p.Glu267Lys,ENST00000405623,NM_001319205.1;POMC,missense_variant,p.Glu267Lys,ENST00000380794,NM_001035256.1;POMC,missense_variant,p.Glu267Lys,ENST00000264708,;POMC,missense_variant,p.Glu267Lys,ENST00000395826,NM_000939.2;EFR3B,downstream_gene_variant,,ENST00000403714,NM_001319099.1,NM_014971.1;POMC,downstream_gene_variant,,ENST00000449220,; T ENST00000405623 Transcript missense_variant 1255/1426 799/804 267/267 E/K Gag/Aag COSM5035397,COSM5553172 1 -1 POMC HGNC HGNC:9201 protein_coding YES CCDS1717.1 ENSP00000384092 P01189 UPI0000127E5B NM_001319205.1 deleterious(0.01) 3/3 hmmpanther:PTHR11416 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs948316373 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 25161086 25161086 C T 1 0 0 0 0 1 0 0 0 12354 893 31 1 1 POMC 2 25161086 Missense_Mutation SNP C C3N-02529_T 25161086 217032443 7 29712 BIRC6 0 . GRCh38 2 32416044 32416044 + Nonsense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.2753C>G p.Ser918Ter p.S918* ENST00000421745 10/74 183 162 21 190 190 0 strelka-varscan-mutect BIRC6,stop_gained,p.Ser918Ter,ENST00000421745,NM_016252.3; G ENST00000421745 Transcript stop_gained 2887/15703 2753/14574 918/4857 S/* tCa/tGa 1 1 BIRC6 HGNC HGNC:13516 protein_coding YES CCDS33175.2 ENSP00000393596 Q9NR09 UPI000159689D NM_016252.3 10/74 Gene3D:2.130.10.10 HIGH 1 SNV 1 1 PASS rs1021660118 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 4 3 102 32416044 32416044 C G 1 0 0 0 0 0 1 0 0 1589 838 29 4 4 BIRC6 2 32416044 Nonsense_Mutation SNP C C3N-02529_T 7254958 32416044 209777485 8 29713 ASTL 0 . GRCh38 2 96133455 96133455 + Missense_Mutation SNP C C G C3N-02529_T C3N-02529_N C C c.425G>C p.Arg142Thr p.R142T ENST00000342380 5/9 286 262 24 211 210 1 strelka-varscan-mutect ASTL,missense_variant,p.Arg142Thr,ENST00000342380,NM_001002036.3;ASTL,downstream_gene_variant,,ENST00000470582,; G ENST00000342380 Transcript missense_variant 425/1296 425/1296 142/431 R/T aGa/aCa COSM198879 1 -1 ASTL HGNC HGNC:31704 protein_coding YES CCDS33249.1 ENSP00000343674 Q6HA08 UPI0000161978 NM_001002036.3 tolerated(0.09) 5/9 Gene3D:3.40.390.10,Pfam_domain:PF01400,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF649,SMART_domains:SM00235,Superfamily_domains:SSF55486 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 96133455 96133455 C G 1 0 0 0 0 1 0 0 0 1210 913 32 4 4 ASTL 2 96133455 Missense_Mutation SNP C C3N-02529_T 63717411 96133455 146060074 9 29714 ZAP70 0 . GRCh38 2 97733160 97733160 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.738C>T p.= p.L246L ENST00000264972 6/14 456 415 41 330 330 0 strelka-varscan-mutect ZAP70,synonymous_variant,p.=,ENST00000264972,NM_001079.3;ZAP70,upstream_gene_variant,,ENST00000451498,NM_207519.1;ZAP70,non_coding_transcript_exon_variant,,ENST00000463643,;ZAP70,non_coding_transcript_exon_variant,,ENST00000487283,;ZAP70,non_coding_transcript_exon_variant,,ENST00000483781,;ZAP70,non_coding_transcript_exon_variant,,ENST00000498836,;ZAP70,upstream_gene_variant,,ENST00000495754,;ZAP70,upstream_gene_variant,,ENST00000489250,; T ENST00000264972 Transcript synonymous_variant 953/2437 738/1860 246/619 L ctC/ctT 1 1 ZAP70 HGNC HGNC:12858 protein_coding YES CCDS33254.1 ENSP00000264972 P43403 UPI000013C370 NM_001079.3 6/14 Gene3D:3.30.505.10,PIRSF_domain:PIRSF000604,PROSITE_profiles:PS50001,hmmpanther:PTHR24418,hmmpanther:PTHR24418:SF262,Superfamily_domains:SSF55550 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 97733160 97733160 C T 1 0 0 0 0 0 0 0 1 18075 813 29 3 3 ZAP70 2 97733160 Silent SNP C C3N-02529_T 1599705 97733160 144460369 10 29715 KCNH7 0 . GRCh38 2 162423446 162423446 + Silent SNP G G T rs374177414 C3N-02529_T C3N-02529_N G G c.2044C>A p.= p.R682R ENST00000332142 9/16 253 237 16 252 251 1 strelka-varscan-mutect KCNH7,synonymous_variant,p.=,ENST00000332142,NM_033272.3;KCNH7,synonymous_variant,p.=,ENST00000618399,;KCNH7,synonymous_variant,p.=,ENST00000328032,NM_173162.2;KCNH7,synonymous_variant,p.=,ENST00000621889,; T ENST00000332142 Transcript synonymous_variant 2144/4113 2044/3591 682/1196 R Cga/Aga rs374177414,COSM312183,COSM4086035,COSM4086036,COSM5657801 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 9/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Gene3D:3bpzA01,Superfamily_domains:SSF51206 0,1,1,1,1 LOW 1 SNV 1 0,1,1,1,1 1 PASS rs374177414 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 162423446 162423446 G T 1 0 0 0 0 0 0 0 1 7953 1095 38 1 1 KCNH7 2 162423446 Silent SNP G C3N-02529_T 64690286 162423446 79770083 11 29716 102 2 KCNH7 0 . GRCh38 2 162423448 162423448 + Missense_Mutation SNP A A G novel C3N-02529_T C3N-02529_N A A c.2042T>C p.Leu681Pro p.L681P ENST00000332142 9/16 250 235 15 247 247 0 strelka-varscan-mutect KCNH7,missense_variant,p.Leu681Pro,ENST00000332142,NM_033272.3;KCNH7,missense_variant,p.Leu581Pro,ENST00000618399,;KCNH7,missense_variant,p.Leu674Pro,ENST00000328032,NM_173162.2;KCNH7,missense_variant,p.Leu572Pro,ENST00000621889,; G ENST00000332142 Transcript missense_variant 2142/4113 2042/3591 681/1196 L/P cTg/cCg 1 -1 KCNH7 HGNC HGNC:18863 protein_coding YES CCDS2219.1 ENSP00000331727 Q9NS40 UPI0000167D11 NM_033272.3 deleterious(0) 9/16 hmmpanther:PTHR10217:SF466,hmmpanther:PTHR10217,Gene3D:3bpzA01,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 162423448 162423448 A G 1 0 0 0 0 1 0 0 0 7953 188 7 5 5 KCNH7 2 162423448 Missense_Mutation SNP A C3N-02529_T 2 162423448 79770081 12 29717 102 2 TTC30B 0 . GRCh38 2 177552313 177552313 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.451G>A p.Glu151Lys p.E151K ENST00000408939 1/1 306 277 29 338 338 0 strelka-varscan-mutect TTC30B,missense_variant,p.Glu151Lys,ENST00000408939,NM_152517.2;AGPS,intron_variant,,ENST00000637633,; T ENST00000408939 Transcript missense_variant 702/4017 451/1998 151/665 E/K Gag/Aag 1 -1 TTC30B HGNC HGNC:26425 protein_coding YES CCDS42784.1 ENSP00000386181 Q8N4P2 UPI000013DE25 NM_152517.2 tolerated(0.42) 1/1 Low_complexity_(Seg):seg,hmmpanther:PTHR20931:SF2,hmmpanther:PTHR20931,Superfamily_domains:SSF48452 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 177552313 177552313 C T 1 0 0 0 0 1 0 0 0 17208 893 31 1 1 TTC30B 2 177552313 Missense_Mutation SNP C C3N-02529_T 15128865 177552313 64641216 13 29718 DNAH7 0 . GRCh38 2 195888427 195888427 + Missense_Mutation SNP C C G C3N-02529_T C3N-02529_N C C c.5237G>C p.Arg1746Thr p.R1746T ENST00000312428 33/65 143 134 9 131 131 0 strelka-varscan-mutect DNAH7,missense_variant,p.Arg1746Thr,ENST00000312428,NM_018897.2;DNAH7,downstream_gene_variant,,ENST00000475293,; G ENST00000312428 Transcript missense_variant 5338/12394 5237/12075 1746/4024 R/T aGa/aCa COSM4551239 1 -1 DNAH7 HGNC HGNC:18661 protein_coding YES CCDS42794.1 ENSP00000311273 Q8WXX0 UPI0000141B95 NM_018897.2 deleterious(0) 33/65 hmmpanther:PTHR10676:SF138,hmmpanther:PTHR10676,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 195888427 195888427 C G 1 0 0 0 0 1 0 0 0 4421 913 32 4 4 DNAH7 2 195888427 Missense_Mutation SNP C C3N-02529_T 18336114 195888427 46305102 14 29719 LHFPL4 0 . GRCh38 3 9552669 9552669 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.11C>G p.Ser4Trp p.S4W ENST00000287585 2/4 98 92 6 109 109 0 strelka-varscan-mutect LHFPL4,missense_variant,p.Ser4Trp,ENST00000287585,NM_198560.2;LHFPL4,non_coding_transcript_exon_variant,,ENST00000498277,;LHFPL4,upstream_gene_variant,,ENST00000495730,; C ENST00000287585 Transcript missense_variant 297/4880 11/744 4/247 S/W tCg/tGg 1 -1 LHFPL4 HGNC HGNC:29568 protein_coding YES CCDS33691.1 ENSP00000287585 Q7Z7J7 UPI000019B16A NM_198560.2 deleterious(0) 2/4 hmmpanther:PTHR12489,hmmpanther:PTHR12489:SF14 MODERATE 1 SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -12.70724 1 1 1 1 0 C 3 2 102 9552669 9552669 G C 1 0 0 0 0 1 0 0 0 8676 1059 37 4 4 LHFPL4 3 9552669 Missense_Mutation SNP G C3N-02529_T 9552669 188742890 15 29720 CTNNB1 0 . GRCh38 3 41224622 41224622 + Missense_Mutation SNP C C T rs121913403 C3N-02529_T C3N-02529_N C C c.110C>T p.Ser37Phe p.S37F ENST00000349496 3/15 513 483 30 454 454 0 strelka-varscan-mutect CTNNB1,missense_variant,p.Ser37Phe,ENST00000349496,NM_001904.3;CTNNB1,missense_variant,p.Ser37Phe,ENST00000396185,NM_001098209.1;CTNNB1,missense_variant,p.Ser37Phe,ENST00000396183,NM_001098210.1;CTNNB1,missense_variant,p.Ser30Phe,ENST00000453024,;CTNNB1,missense_variant,p.Ser37Phe,ENST00000405570,;CTNNB1,missense_variant,p.Ser37Phe,ENST00000450969,;CTNNB1,missense_variant,p.Ser37Phe,ENST00000431914,;CTNNB1,missense_variant,p.Ser37Phe,ENST00000441708,;CTNNB1,missense_variant,p.Ser30Phe,ENST00000426215,;CTNNB1,downstream_gene_variant,,ENST00000433400,;CTNNB1,non_coding_transcript_exon_variant,,ENST00000488914,; T ENST00000349496 Transcript missense_variant 390/3737 110/2346 37/781 S/F tCt/tTt rs121913403,COSM5662,COSM5666,COSM5679 1 1 CTNNB1 HGNC HGNC:2514 protein_coding YES CCDS2694.1 ENSP00000344456 P35222 A0A024R2Q3 UPI000012862F NM_001904.3 deleterious(0) 3/15 hmmpanther:PTHR23315,hmmpanther:PTHR23315:SF53 likely_pathogenic,pathogenic 0,1,1,1 MODERATE 1 SNV 1 1,1,1,1 1 PASS rs121913403 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 41224622 41224622 C T 1 0 0 0 0 1 0 0 0 3825 913 32 3 3 CTNNB1 3 41224622 Missense_Mutation SNP C C3N-02529_T 31671953 41224622 157070937 16 29721 EPHA6 0 . GRCh38 3 97448574 97448574 + Missense_Mutation SNP G G A C3N-02529_T C3N-02529_N G G c.1738G>A p.Glu580Lys p.E580K ENST00000389672 7/18 185 170 15 177 176 1 strelka-varscan-mutect EPHA6,missense_variant,p.Glu580Lys,ENST00000389672,NM_001080448.2;EPHA6,5_prime_UTR_variant,,ENST00000514100,NM_001278300.1;EPHA6,5_prime_UTR_variant,,ENST00000502694,NM_173655.3;EPHA6,5_prime_UTR_variant,,ENST00000477384,;EPHA6,5_prime_UTR_variant,,ENST00000503760,;EPHA6,5_prime_UTR_variant,,ENST00000508345,; A ENST00000389672 Transcript missense_variant 1776/3971 1738/3393 580/1130 E/K Gag/Aag COSM1538558,COSM1538559,COSM1538560 1 1 EPHA6 HGNC HGNC:19296 protein_coding YES CCDS46876.1 ENSP00000374323 A0A0B4J1T8 UPI000004BB12 NM_001080448.2 tolerated(0.27) 7/18 Gene3D:2.60.40.10,Pfam_domain:PF00041,PROSITE_profiles:PS50853,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF364,SMART_domains:SM00060,Superfamily_domains:SSF49265 1,1,1 MODERATE 1 SNV 2 1,1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 97448574 97448574 G A 1 0 0 0 0 1 0 0 0 5018 1291 45 3 3 EPHA6 3 97448574 Missense_Mutation SNP G C3N-02529_T 56223952 97448574 100846985 17 29722 UPK1B 0 . GRCh38 3 119187814 119187814 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.109G>A p.Val37Ile p.V37I ENST00000264234 3/8 484 438 46 420 420 0 strelka-varscan-mutect UPK1B,missense_variant,p.Val37Ile,ENST00000264234,NM_006952.3;UPK1B,missense_variant,p.Val37Ile,ENST00000460625,;UPK1B,missense_variant,p.Val37Ile,ENST00000479520,;UPK1B,missense_variant,p.Val37Ile,ENST00000494855,;UPK1B,5_prime_UTR_variant,,ENST00000497685,;RP11-484M3.5,downstream_gene_variant,,ENST00000490594,; A ENST00000264234 Transcript missense_variant 258/2118 109/783 37/260 V/I Gta/Ata 1 1 UPK1B HGNC HGNC:12578 protein_coding YES CCDS2985.1 ENSP00000264234 O75841 UPI000013D4E8 NM_006952.3 tolerated(0.19) 3/8 hmmpanther:PTHR19282:SF24,hmmpanther:PTHR19282,Pfam_domain:PF00335 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 119187814 119187814 G A 1 0 0 0 0 1 0 0 0 17534 1377 48 3 3 UPK1B 3 119187814 Missense_Mutation SNP G C3N-02529_T 21739240 119187814 79107745 18 29723 ZNF148 0 . GRCh38 3 125277760 125277760 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.633G>A p.= p.K211K ENST00000360647 7/9 216 178 38 238 238 0 strelka-varscan-mutect ZNF148,synonymous_variant,p.=,ENST00000360647,NM_021964.2;ZNF148,synonymous_variant,p.=,ENST00000485866,;ZNF148,synonymous_variant,p.=,ENST00000484491,;ZNF148,synonymous_variant,p.=,ENST00000492394,;ZNF148,synonymous_variant,p.=,ENST00000468369,;ZNF148,non_coding_transcript_exon_variant,,ENST00000497929,; T ENST00000360647 Transcript synonymous_variant 1119/9651 633/2385 211/794 K aaG/aaA 1 -1 ZNF148 HGNC HGNC:12933 protein_coding YES CCDS3031.1 ENSP00000353863 Q9UQR1 UPI000013C2FF NM_021964.2 7/9 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24409,hmmpanther:PTHR24409:SF65,SMART_domains:SM00355,Superfamily_domains:SSF57667 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 125277760 125277760 C T 1 0 0 0 0 0 0 0 1 18315 564 20 3 3 ZNF148 3 125277760 Silent SNP C C3N-02529_T 6089946 125277760 73017799 19 29724 ZBTB38 0 . GRCh38 3 141445963 141445963 + Missense_Mutation SNP A A T novel C3N-02529_T C3N-02529_N A A c.3575A>T p.Asn1192Ile p.N1192I ENST00000514251 4/4 98 85 13 75 75 0 strelka-varscan-mutect ZBTB38,missense_variant,p.Asn1192Ile,ENST00000514251,;ZBTB38,missense_variant,p.Asn1192Ile,ENST00000637056,NM_001080412.2;ZBTB38,missense_variant,p.Asn1192Ile,ENST00000441582,;ZBTB38,missense_variant,p.Asn1192Ile,ENST00000321464,;ZBTB38,downstream_gene_variant,,ENST00000636289,;ZBTB38,downstream_gene_variant,,ENST00000509883,;ZBTB38,downstream_gene_variant,,ENST00000509842,;ZBTB38,downstream_gene_variant,,ENST00000510726,;ZBTB38,downstream_gene_variant,,ENST00000509813,;ZBTB38,downstream_gene_variant,,ENST00000513570,;ZBTB38,downstream_gene_variant,,ENST00000510338,;ZBTB38,downstream_gene_variant,,ENST00000507722,;ZBTB38,downstream_gene_variant,,ENST00000513258,;ZBTB38,downstream_gene_variant,,ENST00000504673,;ZBTB38,downstream_gene_variant,,ENST00000503809,;ZBTB38,upstream_gene_variant,,ENST00000512769,; T ENST00000514251 Transcript missense_variant 3854/7683 3575/3588 1192/1195 N/I aAt/aTt 1 1 ZBTB38 HGNC HGNC:26636 protein_coding YES CCDS43157.1 ENSP00000426387 Q8NAP3 UPI000020A364 deleterious_low_confidence(0.01) 4/4 MODERATE 1 SNV 2 1 PASS rs1377321099 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 141445963 141445963 A T 1 0 0 0 0 1 0 0 0 18108 101 4 4 4 ZBTB38 3 141445963 Missense_Mutation SNP A C3N-02529_T 16168203 141445963 56849596 20 29725 TSC22D2 0 . GRCh38 3 150458454 150458454 + Missense_Mutation SNP G G A C3N-02529_T C3N-02529_N G G c.2161G>A p.Glu721Lys p.E721K ENST00000361875 4/4 247 228 19 216 216 0 strelka-varscan-mutect TSC22D2,missense_variant,p.Glu721Lys,ENST00000361875,NM_014779.3;TSC22D2,missense_variant,p.Glu145Lys,ENST00000466814,;TSC22D2,3_prime_UTR_variant,,ENST00000480589,;TSC22D2,3_prime_UTR_variant,,ENST00000485421,;TSC22D2,non_coding_transcript_exon_variant,,ENST00000460316,; A ENST00000361875 Transcript missense_variant 3177/11154 2161/2343 721/780 E/K Gaa/Aaa COSM5328712 1 1 TSC22D2 HGNC HGNC:29095 protein_coding YES CCDS3149.1 ENSP00000354543 O75157 UPI00000722E0 NM_014779.3 deleterious(0) 4/4 Superfamily_domains:0053404,Gene3D:1.20.5.490,Coiled-coils_(Ncoils):Coil,PD007152,Pfam_domain:PF01166,hmmpanther:PTHR12348,hmmpanther:PTHR12348:SF17 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 150458454 150458454 G A 1 0 0 0 0 1 0 0 0 17114 1291 45 3 3 TSC22D2 3 150458454 Missense_Mutation SNP G C3N-02529_T 9012491 150458454 47837105 21 29726 TNIP2 0 . GRCh38 4 2747698 2747698 + Missense_Mutation SNP C C T rs539733626 C3N-02529_T C3N-02529_N C C c.524G>A p.Arg175Gln p.R175Q ENST00000315423 2/6 174 158 16 173 173 0 strelka-varscan-mutect TNIP2,missense_variant,p.Arg68Gln,ENST00000510267,NM_001161527.1;TNIP2,missense_variant,p.Arg175Gln,ENST00000315423,NM_024309.3;TNIP2,missense_variant,p.Arg175Gln,ENST00000503235,NM_001292016.1;TNIP2,upstream_gene_variant,,ENST00000505186,;TNIP2,non_coding_transcript_exon_variant,,ENST00000511352,;TNIP2,non_coding_transcript_exon_variant,,ENST00000507686,;TNIP2,upstream_gene_variant,,ENST00000502256,; T ENST00000315423 Transcript missense_variant 611/1974 524/1290 175/429 R/Q cGa/cAa rs539733626,COSM277750 1 -1 TNIP2 HGNC HGNC:19118 protein_coding YES CCDS3362.1 ENSP00000321203 Q8NFZ5 UPI00000702D2 NM_024309.3 tolerated(0.21) 2/6 hmmpanther:PTHR31882 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs539733626 . 0 208 0 2 0 0 0 0 -19.99422 0.9999998 1 1 1 0 T 3 4 102 2747698 2747698 C T 1 0 0 0 0 1 0 0 0 16788 884 31 1 1 TNIP2 4 2747698 Missense_Mutation SNP C C3N-02529_T 2747698 187466857 22 29727 KIAA1211 0 . GRCh38 4 56315387 56315387 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.1885C>T p.His629Tyr p.H629Y ENST00000504228 6/9 199 164 35 164 164 0 strelka-varscan-mutect KIAA1211,missense_variant,p.His629Tyr,ENST00000504228,;KIAA1211,missense_variant,p.His622Tyr,ENST00000541073,;KIAA1211,missense_variant,p.His629Tyr,ENST00000264229,NM_020722.1;KIAA1211,downstream_gene_variant,,ENST00000636006,;KIAA1211,upstream_gene_variant,,ENST00000514330,;KIAA1211,downstream_gene_variant,,ENST00000505410,; T ENST00000504228 Transcript missense_variant 1990/4628 1885/3702 629/1233 H/Y Cac/Tac 1 1 KIAA1211 HGNC HGNC:29219 protein_coding YES CCDS43230.1 ENSP00000423366 Q6ZU35 UPI0000237309 tolerated(0.54) 6/9 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 56315387 56315387 C T 1 0 0 0 0 1 0 0 0 8107 710 25 3 3 KIAA1211 4 56315387 Missense_Mutation SNP C C3N-02529_T 53567689 56315387 133899168 23 29728 CCDC158 0 . GRCh38 4 76382642 76382642 + Silent SNP G G T novel C3N-02529_T C3N-02529_N G G c.882C>A p.= p.A294A ENST00000388914 7/24 234 187 47 201 201 0 strelka-varscan-mutect CCDC158,synonymous_variant,p.=,ENST00000388914,NM_001042784.1;CCDC158,synonymous_variant,p.=,ENST00000434846,;CCDC158,downstream_gene_variant,,ENST00000509851,; T ENST00000388914 Transcript synonymous_variant 1035/3663 882/3342 294/1113 A gcC/gcA 1 -1 CCDC158 HGNC HGNC:26374 protein_coding YES CCDS43242.1 ENSP00000373566 Q5M9N0 UPI00004DF23B NM_001042784.1 7/24 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15921,hmmpanther:PTHR13140 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 76382642 76382642 G T 1 0 0 0 0 0 0 0 1 2478 1335 47 2 2 CCDC158 4 76382642 Silent SNP G C3N-02529_T 20067255 76382642 113831913 24 29729 LIN54 0 . GRCh38 4 82946273 82946273 + Nonsense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.1153C>T p.Gln385Ter p.Q385* ENST00000340417 5/13 252 227 25 226 226 0 strelka-varscan-mutect LIN54,stop_gained,p.Gln385Ter,ENST00000340417,NM_194282.3;LIN54,stop_gained,p.Gln164Ter,ENST00000442461,NM_001115008.2;LIN54,stop_gained,p.Gln164Ter,ENST00000446851,NM_001288997.1;LIN54,stop_gained,p.Gln296Ter,ENST00000506560,NM_001288996.1;LIN54,stop_gained,p.Gln385Ter,ENST00000505397,;LIN54,stop_gained,p.Gln164Ter,ENST00000510557,NM_001115007.2;Y_RNA,upstream_gene_variant,,ENST00000362660,;LIN54,3_prime_UTR_variant,,ENST00000510877,;LIN54,intron_variant,,ENST00000508171,; A ENST00000340417 Transcript stop_gained 1531/6127 1153/2250 385/749 Q/* Cag/Tag 1 -1 LIN54 HGNC HGNC:25397 protein_coding YES CCDS3599.1 ENSP00000341947 Q6MZP7 A0A024RDD8 UPI00001D75DE NM_194282.3 5/13 hmmpanther:PTHR12446,hmmpanther:PTHR12446:SF14 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 102 82946273 82946273 G A 1 0 0 0 0 0 1 0 0 8717 1299 45 3 3 LIN54 4 82946273 Nonsense_Mutation SNP G C3N-02529_T 6563631 82946273 107268282 25 29730 SLC12A7 0 . GRCh38 5 1083787 1083787 + Missense_Mutation SNP C C T rs199733676 C3N-02529_T C3N-02529_N C C c.1087G>A p.Glu363Lys p.E363K ENST00000264930 8/24 172 151 21 129 129 0 strelka-varscan-mutect SLC12A7,missense_variant,p.Glu363Lys,ENST00000264930,NM_006598.2;SLC12A7,missense_variant,p.Glu264Lys,ENST00000634447,;SLC12A7,upstream_gene_variant,,ENST00000510943,; T ENST00000264930 Transcript missense_variant 1131/5280 1087/3252 363/1083 E/K Gaa/Aaa rs199733676,COSM1059400 1 -1 SLC12A7 HGNC HGNC:10915 protein_coding YES CCDS34129.1 ENSP00000264930 Q9Y666 UPI0000141815 NM_006598.2 tolerated(0.19) 8/24 TIGRFAM_domain:TIGR00930 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs199733676 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 1083787 1083787 C T 1 0 0 0 0 1 0 0 0 14653 893 31 1 1 SLC12A7 5 1083787 Missense_Mutation SNP C C3N-02529_T 1083787 180454472 26 29731 DNAJC21 0 . GRCh38 5 34938990 34938990 + Missense_Mutation SNP A A C novel C3N-02529_T C3N-02529_N A A c.876A>C p.Glu292Asp p.E292D ENST00000382021 6/13 232 174 58 145 144 1 strelka-varscan-mutect DNAJC21,missense_variant,p.Glu292Asp,ENST00000382021,NM_194283.3;DNAJC21,missense_variant,p.Glu292Asp,ENST00000342382,NM_001012339.2;DNAJC21,non_coding_transcript_exon_variant,,ENST00000514237,; C ENST00000382021 Transcript missense_variant 1103/6208 876/1731 292/576 E/D gaA/gaC 1 1 DNAJC21 HGNC HGNC:27030 protein_coding YES CCDS3907.2 ENSP00000371451 Q5F1R6 UPI000053E489 NM_194283.3 tolerated(0.15) 6/13 Low_complexity_(Seg):seg MODERATE 1 SNV 2 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 34938990 34938990 A C 1 0 0 0 0 1 0 0 0 4454 40 2 5 5 DNAJC21 5 34938990 Missense_Mutation SNP A C3N-02529_T 33855203 34938990 146599269 27 29732 PCDHB4 0 . GRCh38 5 141122093 141122093 + Missense_Mutation SNP A A T rs782318038 C3N-02529_T C3N-02529_N A A c.95A>T p.Tyr32Phe p.Y32F ENST00000194152 1/1 180 149 31 161 161 0 strelka-varscan-mutect PCDHB4,missense_variant,p.Tyr32Phe,ENST00000194152,NM_018938.3;AC005754.8,downstream_gene_variant,,ENST00000606030,;AC005754.7,intron_variant,,ENST00000625128,;AC005754.7,intron_variant,,ENST00000625066,;AC005754.7,intron_variant,,ENST00000624802,;PCDHB4,intron_variant,,ENST00000623478,; T ENST00000194152 Transcript missense_variant 295/3825 95/2388 32/795 Y/F tAt/tTt rs782318038,COSM1434186 1 1 PCDHB4 HGNC HGNC:8689 protein_coding YES CCDS4246.1 ENSP00000194152 Q9Y5E5 UPI00001273DF NM_018938.3 tolerated_low_confidence(0.16) 1/1 Gene3D:2.60.40.60,Pfam_domain:PF08266,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF55,Superfamily_domains:SSF49313 0,1 MODERATE 1 SNV 0,1 1 PASS rs782318038 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 141122093 141122093 A T 1 0 0 0 0 1 0 0 0 11631 449 16 4 4 PCDHB4 5 141122093 Missense_Mutation SNP A C3N-02529_T 106183103 141122093 40416166 28 29733 PCDHB11 0 . GRCh38 5 141201838 141201838 + Silent SNP C C G rs150158596 C3N-02529_T C3N-02529_N C C c.2064C>G p.= p.V688V ENST00000354757 1/1 489 418 71 578 576 2 strelka-varscan-mutect PCDHB11,synonymous_variant,p.=,ENST00000354757,NM_018931.2;PCDHB11,synonymous_variant,p.=,ENST00000624887,;CH17-140K24.2,intron_variant,,ENST00000624192,;CH17-140K24.7,upstream_gene_variant,,ENST00000624549,; G ENST00000354757 Transcript synonymous_variant 2257/4198 2064/2394 688/797 V gtC/gtG rs150158596 1 1 PCDHB11 HGNC HGNC:8682 protein_coding YES CCDS4253.1 ENSP00000346802 Q9Y5F2 UPI00001273E6 NM_018931.2 1/1 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF91 LOW SNV 1 PASS rs150158596 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 102 141201838 141201838 C G 1 0 0 0 0 0 0 0 1 11623 900 32 4 4 PCDHB11 5 141201838 Silent SNP C C3N-02529_T 79745 141201838 40336421 29 29734 CSF1R 0 . GRCh38 5 150056134 150056134 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.2446C>T p.Arg816Cys p.R816C ENST00000286301 19/22 139 117 22 120 120 0 strelka-varscan-mutect CSF1R,missense_variant,p.Arg816Cys,ENST00000286301,NM_001288705.1,NM_005211.3;HMGXB3,downstream_gene_variant,,ENST00000613459,;HMGXB3,downstream_gene_variant,,ENST00000503427,;HMGXB3,downstream_gene_variant,,ENST00000502717,NM_014983.2;CSF1R,downstream_gene_variant,,ENST00000515239,;CSF1R,3_prime_UTR_variant,,ENST00000504875,;CSF1R,3_prime_UTR_variant,,ENST00000515068,;CSF1R,upstream_gene_variant,,ENST00000509861,;CSF1R,downstream_gene_variant,,ENST00000513609,; A ENST00000286301 Transcript missense_variant 2738/3989 2446/2919 816/972 R/C Cgc/Tgc 1 -1 CSF1R HGNC HGNC:2433 protein_coding YES CCDS4302.1 ENSP00000286301 P07333 UPI000004984A NM_001288705.1,NM_005211.3 deleterious(0) 19/22 PROSITE_profiles:PS50011,hmmpanther:PTHR24416:SF47,hmmpanther:PTHR24416,Pfam_domain:PF07714,PIRSF_domain:PIRSF000615,Gene3D:1.10.510.10,PIRSF_domain:PIRSF500947,SMART_domains:SM00219,Superfamily_domains:SSF56112 MODERATE 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 150056134 150056134 G A 1 0 0 0 0 1 0 0 0 3733 1130 39 1 1 CSF1R 5 150056134 Missense_Mutation SNP G C3N-02529_T 8854296 150056134 31482125 30 29735 HRH2 0 . GRCh38 5 175684041 175684041 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.808G>C p.Glu270Gln p.E270Q ENST00000377291 2/3 508 463 45 431 430 1 strelka-varscan-mutect HRH2,missense_variant,p.Glu270Gln,ENST00000636584,;HRH2,missense_variant,p.Glu270Gln,ENST00000377291,NM_001131055.1;HRH2,missense_variant,p.Glu270Gln,ENST00000231683,NM_022304.2;HRH2,missense_variant,p.Glu270Gln,ENST00000624694,; C ENST00000377291 Transcript missense_variant 1459/2561 808/1194 270/397 E/Q Gaa/Caa 1 1 HRH2 HGNC HGNC:5183 protein_coding YES CCDS47344.1 ENSP00000366506 P25021 UPI00001B2326 NM_001131055.1 tolerated(0.29) 2/3 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24249:SF280,hmmpanther:PTHR24249,Pfam_domain:PF00001,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR00531 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 175684041 175684041 G C 1 0 0 0 0 1 0 0 0 7251 943 33 4 4 HRH2 5 175684041 Missense_Mutation SNP G C3N-02529_T 25627907 175684041 5854218 31 29736 SUPT3H 0 . GRCh38 6 45322889 45322889 + Missense_Mutation SNP T T C novel C3N-02529_T C3N-02529_N T T c.28A>G p.Asn10Asp p.N10D ENST00000371460 3/13 235 214 21 220 220 0 strelka-varscan-mutect SUPT3H,missense_variant,p.Asn10Asp,ENST00000371460,NM_181356.2;SUPT3H,intron_variant,,ENST00000371459,NM_003599.3;SUPT3H,intron_variant,,ENST00000459689,;SUPT3H,intron_variant,,ENST00000475057,; C ENST00000371460 Transcript missense_variant 346/2389 28/987 10/328 N/D Aac/Gac 1 -1 SUPT3H HGNC HGNC:11466 protein_coding YES CCDS34466.1 ENSP00000360515 O75486 UPI000018CE7C NM_181356.2 tolerated_low_confidence(0.06) 3/13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 45322889 45322889 T C 1 0 0 0 0 1 0 0 0 15784 1812 63 5 5 SUPT3H 6 45322889 Missense_Mutation SNP T C3N-02529_T 45322889 125483090 32 29737 MEP1A 0 . GRCh38 6 46825480 46825480 + Silent SNP A A C novel C3N-02529_T C3N-02529_N A A c.765A>C p.= p.R255R ENST00000230588 8/14 132 121 11 122 122 0 strelka-varscan-mutect MEP1A,synonymous_variant,p.=,ENST00000611727,;MEP1A,synonymous_variant,p.=,ENST00000230588,NM_005588.2; C ENST00000230588 Transcript synonymous_variant 774/2892 765/2241 255/746 R cgA/cgC 1 1 MEP1A HGNC HGNC:7015 protein_coding YES CCDS4918.1 ENSP00000230588 Q16819 UPI000006E4E9 NM_005588.2 8/14 Gene3D:3.40.390.10,Pfam_domain:PF01400,PIRSF_domain:PIRSF001196,Prints_domain:PR00480,hmmpanther:PTHR10127,hmmpanther:PTHR10127:SF311,Superfamily_domains:SSF55486 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 102 46825480 46825480 A C 1 0 0 0 0 0 0 0 1 9420 233 9 5 5 MEP1A 6 46825480 Silent SNP A C3N-02529_T 1502591 46825480 123980499 33 29738 PHF3 0 . GRCh38 6 63706171 63706171 + Missense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.3510C>G p.Phe1170Leu p.F1170L ENST00000262043 12/16 168 155 13 118 118 0 strelka-varscan-mutect PHF3,missense_variant,p.Phe1170Leu,ENST00000262043,NM_001290259.1;PHF3,missense_variant,p.Phe1170Leu,ENST00000393387,NM_015153.3;PHF3,missense_variant,p.Phe984Leu,ENST00000506783,;PHF3,missense_variant,p.Phe439Leu,ENST00000515594,;PHF3,upstream_gene_variant,,ENST00000505138,;PHF3,downstream_gene_variant,,ENST00000503248,;PHF3,3_prime_UTR_variant,,ENST00000509876,; G ENST00000262043 Transcript missense_variant 3850/8233 3510/6120 1170/2039 F/L ttC/ttG 1 1 PHF3 HGNC HGNC:8921 protein_coding YES CCDS4966.1 ENSP00000262043 Q92576 UPI000007154D NM_001290259.1 tolerated(1) 12/16 hmmpanther:PTHR11477,hmmpanther:PTHR11477:SF10 MODERATE 1 SNV 5 1 PASS . . 0 206 2 0 0 0 0 0 -19.99996 1 1 1 1 0 G 3 3 102 63706171 63706171 C G 1 0 0 0 0 1 0 0 0 11923 912 32 4 4 PHF3 6 63706171 Missense_Mutation SNP C C3N-02529_T 16880691 63706171 107099808 34 29739 SYTL3 0 . GRCh38 6 158757234 158757234 + Frame_Shift_Del DEL G G - novel C3N-02529_T C3N-02529_N G G c.1162delG p.Val388Ter p.V388* ENST00000611299 14/18 125 91 34 123 123 0 sindel-varindel-pindel SYTL3,frameshift_variant,p.Val388Ter,ENST00000611299,NM_001242394.1;SYTL3,frameshift_variant,p.Val320Ter,ENST00000367081,NM_001242395.1,NM_001009991.3;SYTL3,frameshift_variant,p.Val388Ter,ENST00000360448,NM_001242384.1;SYTL3,frameshift_variant,p.Val388Ter,ENST00000297239,; - ENST00000611299 Transcript frameshift_variant 1952/2896 1161/1833 387/610 L/X ctG/ct 1 1 SYTL3 HGNC HGNC:15587 protein_coding YES CCDS56458.1 ENSP00000483936 Q4VX76 UPI000015FE68 NM_001242394.1 14/18 Gene3D:2.60.40.150,Pfam_domain:PF00168,PROSITE_profiles:PS50004,hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF222,SMART_domains:SM00239,Superfamily_domains:SSF49562 HIGH 1 deletion 5 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 102 158757234 158757234 G - 1 0 1 0 1 0 0 0 0 15878 1335 47 0 0 SYTL3 6 158757234 Frame_Shift_Del DEL G C3N-02529_T 95051063 158757234 12048745 35 29740 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02529_T C3N-02529_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 647 458 189 531 530 1 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02529_T 55191822 104154151 36 29741 CLIP2 0 . GRCh38 7 74403838 74403838 + Missense_Mutation SNP A A G C3N-02529_T C3N-02529_N A A c.3131A>G p.Asp1044Gly p.D1044G ENST00000223398 17/17 500 461 39 344 344 0 strelka-varscan-mutect CLIP2,missense_variant,p.Asp1044Gly,ENST00000223398,NM_003388.4;CLIP2,missense_variant,p.Asp1009Gly,ENST00000361545,NM_032421.2;CLIP2,missense_variant,p.Asp1044Gly,ENST00000395060,;CLIP2,missense_variant,p.Asp26Gly,ENST00000487447,; G ENST00000223398 Transcript missense_variant,splice_region_variant 3458/5563 3131/3141 1044/1046 D/G gAc/gGc COSM1091661,COSM1597126 1 1 CLIP2 HGNC HGNC:2586 protein_coding YES CCDS5569.1 ENSP00000223398 Q9UDT6 UPI000007061E NM_003388.4 tolerated_low_confidence(0.08) 17/17 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1178852228 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 74403838 74403838 A G 1 0 0 0 0 1 0 0 0 3302 289 10 5 5 CLIP2 7 74403838 Missense_Mutation SNP A C3N-02529_T 19212016 74403838 84942135 37 29742 MUC17 0 . GRCh38 7 101043721 101043721 + Missense_Mutation SNP C C A novel C3N-02529_T C3N-02529_N C C c.12305C>A p.Thr4102Asn p.T4102N ENST00000306151 3/13 292 273 19 168 167 1 strelka-varscan-mutect MUC17,missense_variant,p.Thr4102Asn,ENST00000306151,NM_001040105.1;MUC17,missense_variant,p.Thr4102Asn,ENST00000379439,;MUC17,non_coding_transcript_exon_variant,,ENST00000470303,; A ENST00000306151 Transcript missense_variant 12369/14247 12305/13482 4102/4493 T/N aCc/aAc 1 1 MUC17 HGNC HGNC:16800 protein_coding YES CCDS34711.1 ENSP00000302716 Q685J3 UPI0000D5BB56 NM_001040105.1 deleterious(0) 3/13 Low_complexity_(Seg):seg,hmmpanther:PTHR37999:SF1,hmmpanther:PTHR37999 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -19.99697 0.9999996 1 1 1 0 A 3 1 102 101043721 101043721 C A 1 0 0 0 0 1 0 0 0 9973 507 18 2 2 MUC17 7 101043721 Missense_Mutation SNP C C3N-02529_T 26639883 101043721 58302252 38 29743 LRRC17 0 . GRCh38 7 102934084 102934084 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.171C>T p.= p.Y57Y ENST00000339431 2/4 243 197 46 180 180 0 strelka-varscan-mutect LRRC17,synonymous_variant,p.=,ENST00000249377,NM_005824.2;LRRC17,synonymous_variant,p.=,ENST00000339431,NM_001031692.2;LRRC17,synonymous_variant,p.=,ENST00000455453,;FBXL13,intron_variant,,ENST00000313221,NM_145032.3;FBXL13,intron_variant,,ENST00000379308,;FBXL13,intron_variant,,ENST00000436908,;FBXL13,intron_variant,,ENST00000379305,NM_001287150.1;FBXL13,intron_variant,,ENST00000455112,NM_001111038.1;FBXL13,intron_variant,,ENST00000456695,;FBXL13,intron_variant,,ENST00000477915,;LRRC17,upstream_gene_variant,,ENST00000485478,;FBXL13,upstream_gene_variant,,ENST00000468216,;LRRC17,downstream_gene_variant,,ENST00000498487,;FBXL13,intron_variant,,ENST00000448002,; T ENST00000339431 Transcript synonymous_variant 466/1963 171/1326 57/441 Y taC/taT 1 1 LRRC17 HGNC HGNC:16895 protein_coding YES CCDS34721.1 ENSP00000344242 Q8N6Y2 UPI00000719CD NM_001031692.2 2/4 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF323,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 102934084 102934084 C T 1 0 0 0 0 0 0 0 1 8868 489 17 3 3 LRRC17 7 102934084 Silent SNP C C3N-02529_T 1890363 102934084 56411889 39 29744 SND1 0 . GRCh38 7 128091998 128091998 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.2673C>T p.= p.N891N ENST00000354725 24/24 236 219 17 158 158 0 strelka-varscan-mutect SND1,synonymous_variant,p.=,ENST00000354725,NM_014390.2;SND1,non_coding_transcript_exon_variant,,ENST00000485871,;SND1,non_coding_transcript_exon_variant,,ENST00000489417,; T ENST00000354725 Transcript synonymous_variant 2867/3476 2673/2733 891/910 N aaC/aaT 1 1 SND1 HGNC HGNC:30646 protein_coding YES CCDS34747.1 ENSP00000346762 Q7KZF4 A0A140VK49 UPI00000727E5 NM_014390.2 24/24 Superfamily_domains:0047647,Gene3D:2.40.50.90,Pfam_domain:PF00565,PIRSF_domain:PIRSF017179,hmmpanther:PTHR12302,hmmpanther:PTHR12302:SF5 LOW 1 SNV 1 1 PASS . . 0 206 0 3 0 0 0 0 -19.94573 0.9999696 1 1 1 0 T 2 4 102 128091998 128091998 C T 1 0 0 0 0 0 0 0 1 15165 521 18 3 3 SND1 7 128091998 Silent SNP C C3N-02529_T 25157914 128091998 31253975 40 29745 OR2F2 0 . GRCh38 7 143935381 143935381 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.149G>A p.Arg50Lys p.R50K ENST00000408955 1/1 233 218 15 206 206 0 varscan-mutect OR2F2,missense_variant,p.Arg50Lys,ENST00000408955,NM_001004685.1; A ENST00000408955 Transcript missense_variant 216/1114 149/954 50/317 R/K aGa/aAa 1 1 OR2F2 HGNC HGNC:8247 protein_coding YES CCDS43666.1 ENSP00000386222 O95006 UPI0000041C25 NM_001004685.1 tolerated(0.21) 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF63,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 143935381 143935381 G A 1 0 0 0 0 1 0 0 0 11075 942 33 3 3 OR2F2 7 143935381 Missense_Mutation SNP G C3N-02529_T 15843383 143935381 15410592 41 29746 GIMAP8 0 . GRCh38 7 150477727 150477727 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.1945G>A p.Glu649Lys p.E649K ENST00000307271 5/5 222 201 21 184 184 0 strelka-varscan-mutect GIMAP8,missense_variant,p.Glu649Lys,ENST00000307271,NM_175571.3; A ENST00000307271 Transcript missense_variant 2519/4184 1945/1998 649/665 E/K Gaa/Aaa 1 1 GIMAP8 HGNC HGNC:21792 protein_coding YES CCDS34777.1 ENSP00000305107 Q8ND71 A0A090N8H2 UPI0000168646 NM_175571.3 tolerated(0.28) 5/5 hmmpanther:PTHR10903:SF73,hmmpanther:PTHR10903,Pfam_domain:PF04548 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 150477727 150477727 G A 1 0 0 0 0 1 0 0 0 6265 1175 41 3 3 GIMAP8 7 150477727 Missense_Mutation SNP G C3N-02529_T 6542346 150477727 8868246 42 29747 CSMD1 0 . GRCh38 8 3087194 3087194 + Nonsense_Mutation SNP G G T novel C3N-02529_T C3N-02529_N G G c.7380C>A p.Cys2460Ter p.C2460* ENST00000520002 50/71 383 352 31 252 252 0 strelka-varscan-mutect CSMD1,stop_gained,p.Cys2321Ter,ENST00000537824,;CSMD1,stop_gained,p.Cys1877Ter,ENST00000335551,;CSMD1,stop_gained,p.Cys2460Ter,ENST00000520002,;CSMD1,stop_gained,p.Cys2460Ter,ENST00000602557,;CSMD1,stop_gained,p.Cys2459Ter,ENST00000635120,NM_033225.5;CSMD1,stop_gained,p.Cys2460Ter,ENST00000400186,;CSMD1,stop_gained,p.Cys2460Ter,ENST00000602723,; T ENST00000520002 Transcript stop_gained 7936/11740 7380/10698 2460/3565 C/* tgC/tgA 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 50/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 102 3087194 3087194 G T 1 0 0 0 0 0 1 0 0 3745 1311 46 2 2 CSMD1 8 3087194 Nonsense_Mutation SNP G C3N-02529_T 3087194 142051442 43 29748 PRDM14 0 . GRCh38 8 70069839 70069839 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.22G>A p.Glu8Lys p.E8K ENST00000276594 2/8 148 133 15 108 108 0 strelka-varscan-mutect PRDM14,missense_variant,p.Glu8Lys,ENST00000276594,NM_024504.3;PRDM14,missense_variant,p.Glu8Lys,ENST00000426346,; T ENST00000276594 Transcript missense_variant 224/2344 22/1716 8/571 E/K Gag/Aag 1 -1 PRDM14 HGNC HGNC:14001 protein_coding YES CCDS6206.1 ENSP00000276594 Q9GZV8 UPI0000132186 NM_024504.3 tolerated(0.09) 2/8 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 70069839 70069839 C T 1 0 0 0 0 1 0 0 0 12586 835 29 3 3 PRDM14 8 70069839 Missense_Mutation SNP C C3N-02529_T 66982645 70069839 75068797 44 29749 FABP12 0 . GRCh38 8 81525082 81525082 + Nonsense_Mutation SNP G G C rs781709156 C3N-02529_T C3N-02529_N G G c.387C>G p.Tyr129Ter p.Y129* ENST00000360464 4/4 280 221 59 177 177 0 strelka-varscan-mutect FABP12,stop_gained,p.Tyr129Ter,ENST00000360464,NM_001105281.1;RP11-257P3.3,intron_variant,,ENST00000523380,;RP11-257P3.3,intron_variant,,ENST00000518637,;RP11-157I4.4,downstream_gene_variant,,ENST00000524085,;FABP12,3_prime_UTR_variant,,ENST00000519696,;FTH1P11,upstream_gene_variant,,ENST00000517577,; C ENST00000360464 Transcript stop_gained 450/551 387/423 129/140 Y/* taC/taG rs781709156,COSM299934,COSM3835064 1 -1 FABP12 HGNC HGNC:34524 protein_coding YES CCDS47882.1 ENSP00000353650 A6NFH5 UPI00001B2E3D NM_001105281.1 4/4 hmmpanther:PTHR11955,hmmpanther:PTHR11955:SF76,Gene3D:2.40.128.20,Pfam_domain:PF00061,Superfamily_domains:SSF50814,Prints_domain:PR00178 0,1,1 HIGH 1 SNV 1 0,1,1 1 PASS rs765561681 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 4 2 102 81525082 81525082 G C 1 0 0 0 0 0 1 0 0 5228 1140 40 4 4 FABP12 8 81525082 Nonsense_Mutation SNP G C3N-02529_T 11455243 81525082 63613554 45 29750 MROH6 0 . GRCh38 8 143569819 143569819 + Missense_Mutation SNP C C A novel C3N-02529_T C3N-02529_N C C c.1180G>T p.Ala394Ser p.A394S ENST00000398882 8/14 264 247 17 137 137 0 strelka-varscan-mutect MROH6,missense_variant,p.Ala394Ser,ENST00000398882,NM_001100878.1;MROH6,missense_variant,p.Arg406Leu,ENST00000529971,;NAPRT,downstream_gene_variant,,ENST00000449291,NM_145201.5;MROH6,upstream_gene_variant,,ENST00000533679,;NAPRT,downstream_gene_variant,,ENST00000435154,;MROH6,upstream_gene_variant,,ENST00000524906,;MROH6,upstream_gene_variant,,ENST00000534459,;NAPRT,downstream_gene_variant,,ENST00000426292,NM_001286829.1;MROH6,upstream_gene_variant,,ENST00000532862,;RP11-661A12.9,upstream_gene_variant,,ENST00000531730,;MROH6,upstream_gene_variant,,ENST00000532704,;MROH6,upstream_gene_variant,,ENST00000533582,;MROH6,upstream_gene_variant,,ENST00000533210,;NAPRT,downstream_gene_variant,,ENST00000340490,;NAPRT,downstream_gene_variant,,ENST00000464332,;MROH6,upstream_gene_variant,,ENST00000533120,;NAPRT,downstream_gene_variant,,ENST00000460623,;MROH6,upstream_gene_variant,,ENST00000533083,;NAPRT,downstream_gene_variant,,ENST00000529179,;NAPRT,downstream_gene_variant,,ENST00000498076,; A ENST00000398882 Transcript missense_variant 1437/3469 1180/2160 394/719 A/S Gca/Tca 1 -1 MROH6 HGNC HGNC:27814 protein_coding YES CCDS47928.1 ENSP00000381857 A6NGR9 UPI0000DD7EFB NM_001100878.1 tolerated(0.32) 8/14 hmmpanther:PTHR23120:SF7,hmmpanther:PTHR23120,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 143569819 143569819 C A 1 0 0 0 0 1 0 0 0 9746 768 27 1 1 MROH6 8 143569819 Missense_Mutation SNP C C3N-02529_T 62044737 143569819 1568817 46 29751 LRRC24 0 . GRCh38 8 144522953 144522953 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.1064G>A p.Arg355His p.R355H ENST00000529415 5/5 234 217 17 116 116 0 strelka-mutect LRRC24,missense_variant,p.Arg355His,ENST00000529415,NM_001024678.3;LRRC24,missense_variant,p.Arg352His,ENST00000533758,;LRRC14,3_prime_UTR_variant,,ENST00000292524,NM_014665.3;C8orf82,downstream_gene_variant,,ENST00000524821,NM_001001795.1;LRRC14,downstream_gene_variant,,ENST00000529022,NM_001272036.1;C8orf82,downstream_gene_variant,,ENST00000313465,;LRRC14,downstream_gene_variant,,ENST00000527730,;C8orf82,downstream_gene_variant,,ENST00000532827,;LRRC14,downstream_gene_variant,,ENST00000530854,;LRRC14,downstream_gene_variant,,ENST00000525766,;LRRC14,non_coding_transcript_exon_variant,,ENST00000528528,;LRRC14,upstream_gene_variant,,ENST00000529995,;LRRC14,upstream_gene_variant,,ENST00000530242,;C8orf82,downstream_gene_variant,,ENST00000534680,;LRRC14,downstream_gene_variant,,ENST00000531310,; T ENST00000529415 Transcript missense_variant 1182/1758 1064/1542 355/513 R/H cGc/cAc 1 -1 LRRC24 HGNC HGNC:28947 protein_coding YES CCDS34969.1 ENSP00000434849 Q50LG9 UPI0000419443 NM_001024678.3 deleterious(0.02) 5/5 Gene3D:2.60.40.10,PROSITE_profiles:PS50835,hmmpanther:PTHR24367,hmmpanther:PTHR24367:SF255,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 144522953 144522953 C T 1 0 0 0 0 1 0 0 0 8874 768 27 1 1 LRRC24 8 144522953 Missense_Mutation SNP C C3N-02529_T 953134 144522953 615683 47 29752 MPDZ 0 . GRCh38 9 13222411 13222411 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.569C>T p.Ala190Val p.A190V ENST00000541718 6/46 163 142 21 170 170 0 strelka-varscan-mutect MPDZ,missense_variant,p.Ala190Val,ENST00000319217,;MPDZ,missense_variant,p.Ala190Val,ENST00000541718,NM_003829.4;MPDZ,missense_variant,p.Ala190Val,ENST00000381022,NM_001261406.1;MPDZ,missense_variant,p.Ala190Val,ENST00000546205,;MPDZ,missense_variant,p.Ala190Val,ENST00000447879,;MPDZ,missense_variant,p.Ala190Val,ENST00000536827,NM_001261407.1;MPDZ,upstream_gene_variant,,ENST00000494251,; A ENST00000541718 Transcript missense_variant 791/7603 569/6126 190/2041 A/V gCt/gTt 1 -1 MPDZ HGNC HGNC:7208 protein_coding YES CCDS47951.1 ENSP00000439807 O75970 UPI00015367D3 NM_003829.4 tolerated(0.07) 6/46 Gene3D:2.30.42.10,Pfam_domain:PF00595,PROSITE_profiles:PS50106,hmmpanther:PTHR19964,hmmpanther:PTHR19964:SF10,SMART_domains:SM00228,Superfamily_domains:SSF50156 MODERATE 1 SNV 1 1 PASS rs1031665272 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 13222411 13222411 G A 1 0 0 0 0 1 0 0 0 9687 971 34 3 3 MPDZ 9 13222411 Missense_Mutation SNP G C3N-02529_T 13222411 125172306 48 29753 ACER2 0 . GRCh38 9 19435032 19435032 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.451C>T p.= p.L151L ENST00000340967 4/6 271 241 30 256 256 0 strelka-varscan-mutect ACER2,synonymous_variant,p.=,ENST00000340967,NM_001010887.2; T ENST00000340967 Transcript synonymous_variant 477/2238 451/828 151/275 L Ctg/Ttg 1 1 ACER2 HGNC HGNC:23675 protein_coding YES CCDS34992.1 ENSP00000342609 Q5QJU3 UPI000014042D NM_001010887.2 4/6 hmmpanther:PTHR12956,hmmpanther:PTHR12956:SF21,Pfam_domain:PF05875 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 19435032 19435032 C T 1 0 0 0 0 0 0 0 1 177 912 32 3 3 ACER2 9 19435032 Silent SNP C C3N-02529_T 6212621 19435032 118959685 49 29754 IZUMO3 0 . GRCh38 9 24545047 24545047 + Missense_Mutation SNP G G T novel C3N-02529_T C3N-02529_N G G c.316C>A p.Gln106Lys p.Q106K ENST00000604921 3/6 174 157 17 237 237 0 strelka-varscan-mutect IZUMO3,missense_variant,p.Gln106Lys,ENST00000543880,;IZUMO3,missense_variant,p.Gln106Lys,ENST00000604921,NM_001271706.1;IZUMO3,missense_variant,p.Gln25Lys,ENST00000418122,;RP11-20A20.2,upstream_gene_variant,,ENST00000602851,;RP11-20A20.2,upstream_gene_variant,,ENST00000602614,; T ENST00000604921 Transcript missense_variant 343/743 316/702 106/233 Q/K Caa/Aaa 1 -1 IZUMO3 HGNC HGNC:31421 protein_coding YES CCDS65020.1 ENSP00000474246 S4R3E6 UPI0002742D6C NM_001271706.1 deleterious(0.01) 3/6 hmmpanther:PTHR36470,Pfam_domain:PF15005 MODERATE 1 SNV 5 1 PASS rs1424807148 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 24545047 24545047 G T 1 0 0 0 0 1 0 0 0 7842 1299 45 2 2 IZUMO3 9 24545047 Missense_Mutation SNP G C3N-02529_T 5110015 24545047 113849670 50 29755 TRPM3 0 . GRCh38 9 70536094 70536094 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.4983C>G p.Asp1661Glu p.D1661E ENST00000377110 25/25 236 221 15 196 196 0 strelka-varscan-mutect TRPM3,missense_variant,p.Asp1661Glu,ENST00000377110,NM_001007471.2;TRPM3,missense_variant,p.Asp1523Glu,ENST00000360823,NM_206944.3,NM_206947.3;TRPM3,missense_variant,p.Asp1520Glu,ENST00000377105,NM_024971.5;TRPM3,missense_variant,p.Asp1665Glu,ENST00000357533,;TRPM3,missense_variant,p.Asp1533Glu,ENST00000396292,NM_206946.3;TRPM3,missense_variant,p.Asp1523Glu,ENST00000358082,;TRPM3,missense_variant,p.Asp1520Glu,ENST00000396285,NM_020952.4;TRPM3,missense_variant,p.Asp1520Glu,ENST00000408909,;TRPM3,missense_variant,p.Asp1510Glu,ENST00000396280,NM_206945.3;TRPM3,intron_variant,,ENST00000377111,; C ENST00000377110 Transcript missense_variant 5227/12258 4983/5124 1661/1707 D/E gaC/gaG 1 -1 TRPM3 HGNC HGNC:17992 protein_coding YES CCDS43835.1 ENSP00000366314 Q9HCF6 UPI0001596895 NM_001007471.2 tolerated_low_confidence(0.25) 25/25 hmmpanther:PTHR13800,hmmpanther:PTHR13800:SF7 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 70536094 70536094 G C 1 0 0 0 0 1 0 0 0 17093 1368 48 4 4 TRPM3 9 70536094 Missense_Mutation SNP G C3N-02529_T 45991047 70536094 67858623 51 29756 TRIM14 0 . GRCh38 9 98100015 98100015 + Nonsense_Mutation SNP G G T novel C3N-02529_T C3N-02529_N G G c.453C>A p.Cys151Ter p.C151* ENST00000341469 3/6 463 418 45 299 299 0 strelka-varscan-mutect TRIM14,stop_gained,p.Cys151Ter,ENST00000341469,NM_014788.3;TRIM14,stop_gained,p.Cys151Ter,ENST00000375098,;TRIM14,stop_gained,p.Cys151Ter,ENST00000342043,NM_033219.2;TRIM14,non_coding_transcript_exon_variant,,ENST00000478401,;TRIM14,intron_variant,,ENST00000475147,; T ENST00000341469 Transcript stop_gained 463/4454 453/1329 151/442 C/* tgC/tgA 1 -1 TRIM14 HGNC HGNC:16283 protein_coding YES CCDS6734.1 ENSP00000344208 Q14142 A0A024R165 UPI0000137065 NM_014788.3 3/6 hmmpanther:PTHR24103:SF35,hmmpanther:PTHR24103 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 102 98100015 98100015 G T 1 0 0 0 0 0 1 0 0 16978 1311 46 2 2 TRIM14 9 98100015 Nonsense_Mutation SNP G C3N-02529_T 27563921 98100015 40294702 52 29757 MURC 0 . GRCh38 9 100578213 100578213 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.70G>A p.Asp24Asn p.D24N ENST00000307584 1/2 140 122 18 104 104 0 strelka-varscan-mutect MURC,missense_variant,p.Asp24Asn,ENST00000307584,NM_001018116.2;TMEFF1,downstream_gene_variant,,ENST00000374879,NM_003692.4;MSANTD3-TMEFF1,downstream_gene_variant,,ENST00000502978,NM_001198812.1;RN7SKP87,downstream_gene_variant,,ENST00000364096,; A ENST00000307584 Transcript missense_variant 135/2615 70/1095 24/364 D/N Gat/Aat 1 1 MURC HGNC HGNC:33742 protein_coding YES CCDS35083.1 ENSP00000418668 Q5BKX8 UPI000004CC0D NM_001018116.2 deleterious(0.01) 1/2 hmmpanther:PTHR15240,hmmpanther:PTHR15240:SF4 MODERATE 1 SNV 1 1 PASS rs1234079781 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 100578213 100578213 G A 1 0 0 0 0 1 0 0 0 9985 942 33 3 3 MURC 9 100578213 Missense_Mutation SNP G C3N-02529_T 2478198 100578213 37816504 53 29758 SVEP1 0 . GRCh38 9 110429958 110429958 + Missense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.5577G>C p.Glu1859Asp p.E1859D ENST00000374469 34/48 291 267 24 259 259 0 strelka-varscan-mutect SVEP1,missense_variant,p.Glu1862Asp,ENST00000401783,;SVEP1,missense_variant,p.Glu1859Asp,ENST00000374469,NM_153366.3; G ENST00000374469 Transcript missense_variant 5772/12194 5577/10716 1859/3571 E/D gaG/gaC 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 tolerated(0.92) 34/48 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF43,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 110429958 110429958 C G 1 0 0 0 0 1 0 0 0 15805 680 24 4 4 SVEP1 9 110429958 Missense_Mutation SNP C C3N-02529_T 9851745 110429958 27964759 54 29759 CNTRL 0 . GRCh38 9 121125863 121125863 + Missense_Mutation SNP A A C rs774635839 C3N-02529_T C3N-02529_N A A c.1952A>C p.Gln651Pro p.Q651P ENST00000373855 14/44 585 542 43 498 498 0 strelka-varscan-mutect CNTRL,missense_variant,p.Gln651Pro,ENST00000373855,;CNTRL,missense_variant,p.Gln651Pro,ENST00000238341,NM_007018.4;CNTRL,missense_variant,p.Gln99Pro,ENST00000373850,;CNTRL,missense_variant,p.Gln99Pro,ENST00000373847,;CNTRL,non_coding_transcript_exon_variant,,ENST00000373851,; C ENST00000373855 Transcript missense_variant 2212/7660 1952/6978 651/2325 Q/P cAg/cCg rs774635839 1 1 CNTRL HGNC HGNC:1858 protein_coding YES CCDS35118.1 ENSP00000362962 Q7Z7A1 UPI0000211718 deleterious(0.01) 14/44 Coiled-coils_(Ncoils):Coil MODERATE 1 SNV 5 1 PASS rs774635839 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 121125863 121125863 A C 1 0 0 0 0 1 0 0 0 3433 188 7 5 5 CNTRL 9 121125863 Missense_Mutation SNP A C3N-02529_T 10695905 121125863 17268854 55 29760 FNBP1 0 . GRCh38 9 129900041 129900041 + Silent SNP C C A rs377247806 C3N-02529_T C3N-02529_N C C c.1611G>T p.= p.T537T ENST00000446176 15/17 122 100 22 90 90 0 strelka-varscan-mutect FNBP1,synonymous_variant,p.=,ENST00000420781,;FNBP1,synonymous_variant,p.=,ENST00000446176,NM_015033.2;FNBP1,synonymous_variant,p.=,ENST00000443566,;FNBP1,synonymous_variant,p.=,ENST00000449089,;FNBP1,synonymous_variant,p.=,ENST00000355681,;FNBP1,non_coding_transcript_exon_variant,,ENST00000478129,;FNBP1,non_coding_transcript_exon_variant,,ENST00000462766,; A ENST00000446176 Transcript synonymous_variant 1798/5393 1611/1854 537/617 T acG/acT rs377247806 1 -1 FNBP1 HGNC HGNC:17069 protein_coding YES CCDS48040.1 ENSP00000413625 Q96RU3 UPI000022408C NM_015033.2 15/17 hmmpanther:PTHR10663:SF157,hmmpanther:PTHR10663 LOW 1 SNV 1 1 PASS rs377247806 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 102 129900041 129900041 C A 1 0 0 0 0 0 0 0 1 5821 639 23 1 1 FNBP1 9 129900041 Silent SNP C C3N-02529_T 8774178 129900041 8494676 56 29761 NUP214 0 . GRCh38 9 131174267 131174267 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.3106G>A p.Ala1036Thr p.A1036T ENST00000359428 22/36 460 430 30 325 325 0 strelka-varscan-mutect NUP214,missense_variant,p.Ala1036Thr,ENST00000359428,NM_005085.3;NUP214,missense_variant,p.Ala1026Thr,ENST00000411637,NM_001318324.1;NUP214,missense_variant,p.Ala465Thr,ENST00000451030,;NUP214,upstream_gene_variant,,ENST00000531929,;NUP214,missense_variant,p.Ala34Thr,ENST00000526346,;NUP214,non_coding_transcript_exon_variant,,ENST00000525980,; A ENST00000359428 Transcript missense_variant 3250/7600 3106/6273 1036/2090 A/T Gct/Act 1 1 NUP214 HGNC HGNC:8064 protein_coding YES CCDS6940.1 ENSP00000352400 P35658 UPI00001BBB2F NM_005085.3 tolerated(0.26) 22/36 hmmpanther:PTHR23193,hmmpanther:PTHR23193:SF21 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 131174267 131174267 G A 1 0 0 0 0 1 0 0 0 10827 1319 46 3 3 NUP214 9 131174267 Missense_Mutation SNP G C3N-02529_T 1274226 131174267 7220450 57 29762 SEC16A 0 . GRCh38 9 136445700 136445700 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.6812C>T p.Ser2271Leu p.S2271L ENST00000313050 27/30 329 309 20 214 214 0 strelka-varscan-mutect SEC16A,missense_variant,p.Ser2271Leu,ENST00000313050,NM_014866.1;SEC16A,missense_variant,p.Ser993Leu,ENST00000453963,;SEC16A,missense_variant,p.Ser665Leu,ENST00000277537,;SEC16A,missense_variant,p.Ser299Leu,ENST00000313084,;SEC16A,intron_variant,,ENST00000290037,NM_001276418.1;SEC16A,intron_variant,,ENST00000371706,;SEC16A,intron_variant,,ENST00000431893,;SEC16A,upstream_gene_variant,,ENST00000467838,; A ENST00000313050 Transcript missense_variant 6886/8806 6812/7074 2271/2357 S/L tCa/tTa 1 -1 SEC16A HGNC HGNC:29006 protein_coding YES CCDS55351.1 ENSP00000325827 J3KNL6 UPI0000F0888B NM_014866.1 tolerated(1) 27/30 hmmpanther:PTHR13402,hmmpanther:PTHR13402:SF13 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 136445700 136445700 G A 1 0 0 0 0 1 0 0 0 14263 1294 45 3 3 SEC16A 9 136445700 Missense_Mutation SNP G C3N-02529_T 5271433 136445700 1949017 58 29763 GDI2 0 . GRCh38 10 5794898 5794898 + Silent SNP T T C novel C3N-02529_T C3N-02529_N T T c.375A>G p.= p.E125E ENST00000380191 4/11 146 119 27 160 160 0 strelka-varscan-mutect GDI2,synonymous_variant,p.=,ENST00000380191,NM_001494.3;GDI2,synonymous_variant,p.=,ENST00000456041,;GDI2,synonymous_variant,p.=,ENST00000418688,;GDI2,synonymous_variant,p.=,ENST00000608581,;GDI2,synonymous_variant,p.=,ENST00000380127,;GDI2,intron_variant,,ENST00000380181,NM_001115156.1;GDI2,downstream_gene_variant,,ENST00000609712,; C ENST00000380191 Transcript synonymous_variant 666/2412 375/1338 125/445 E gaA/gaG 1 -1 GDI2 HGNC HGNC:4227 protein_coding YES CCDS7071.1 ENSP00000369538 P50395 Q6IAT1 UPI000012B39E NM_001494.3 4/11 hmmpanther:PTHR11787:SF1,hmmpanther:PTHR11787,Pfam_domain:PF00996,Gene3D:1.10.405.10,Superfamily_domains:SSF51905 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 102 5794898 5794898 T C 1 0 0 0 0 0 0 0 1 6194 1606 56 5 5 GDI2 10 5794898 Silent SNP T C3N-02529_T 5794898 128002524 59 29764 ANKRD30A 0 . GRCh38 10 37219392 37219392 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.3512G>A p.Gly1171Glu p.G1171E ENST00000361713 34/36 162 151 11 263 263 0 strelka-varscan-mutect ANKRD30A,missense_variant,p.Gly1290Glu,ENST00000374660,;ANKRD30A,missense_variant,p.Gly1227Glu,ENST00000611781,;ANKRD30A,missense_variant,p.Gly1171Glu,ENST00000602533,;ANKRD30A,missense_variant,p.Gly1171Glu,ENST00000361713,NM_052997.2; A ENST00000361713 Transcript missense_variant 3611/4405 3512/4026 1171/1341 G/E gGa/gAa 1 1 ANKRD30A HGNC HGNC:17234 protein_coding YES CCDS7193.1 ENSP00000354432 R4GNA2 UPI0000458879 NM_052997.2 tolerated(0.16) 34/36 hmmpanther:PTHR24147:SF20,hmmpanther:PTHR24147,Pfam_domain:PF14915 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 37219392 37219392 G A 1 0 0 0 0 1 0 0 0 761 1174 41 3 3 ANKRD30A 10 37219392 Missense_Mutation SNP G C3N-02529_T 31424494 37219392 96578030 60 29765 C10orf62 0 . GRCh38 10 97590181 97590181 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.284C>T p.Thr95Ile p.T95I ENST00000370640 1/1 354 321 33 329 329 0 strelka-varscan-mutect C10orf62,missense_variant,p.Thr95Ile,ENST00000370640,NM_001009997.2;HOGA1,intron_variant,,ENST00000370646,NM_138413.3;HOGA1,intron_variant,,ENST00000370647,NM_001134670.1;RP11-548K23.11,intron_variant,,ENST00000370649,;HOGA1,intron_variant,,ENST00000465608,; T ENST00000370640 Transcript missense_variant 455/1208 284/672 95/223 T/I aCc/aTc 1 1 C10orf62 HGNC HGNC:23294 protein_coding YES CCDS31261.1 ENSP00000359674 Q5T681 UPI000046FEE3 NM_001009997.2 tolerated(0.11) 1/1 hmmpanther:PTHR23008:SF0,hmmpanther:PTHR23008 MODERATE SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 97590181 97590181 C T 1 0 0 0 0 1 0 0 0 1767 507 18 3 3 C10orf62 10 97590181 Missense_Mutation SNP C C3N-02529_T 60370789 97590181 36207241 61 29766 OR5M1 0 . GRCh38 11 56613282 56613282 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.221C>G p.Ser74Cys p.S74C ENST00000526538 1/1 393 356 37 535 534 1 varscan-mutect OR5M1,missense_variant,p.Ser74Cys,ENST00000526538,NM_001004740.1; C ENST00000526538 Transcript missense_variant 221/948 221/948 74/315 S/C tCt/tGt 1 -1 OR5M1 HGNC HGNC:8352 protein_coding YES CCDS53631.1 ENSP00000435416 Q8NGP8 UPI0000041C9B NM_001004740.1 deleterious(0) 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF98,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 56613282 56613282 G C 1 0 0 0 0 1 0 0 0 11241 942 33 4 4 OR5M1 11 56613282 Missense_Mutation SNP G C3N-02529_T 56613282 78473340 62 29767 RAB3IL1 0 . GRCh38 11 61899360 61899360 + Missense_Mutation SNP G G T rs745743430 C3N-02529_T C3N-02529_N G G c.1020C>A p.Phe340Leu p.F340L ENST00000394836 9/10 207 185 22 179 179 0 strelka-varscan-mutect RAB3IL1,missense_variant,p.Phe340Leu,ENST00000394836,NM_013401.3;RAB3IL1,missense_variant,p.Phe314Leu,ENST00000301773,NM_001271686.1;RAB3IL1,upstream_gene_variant,,ENST00000526200,;RAB3IL1,non_coding_transcript_exon_variant,,ENST00000533136,;RAB3IL1,downstream_gene_variant,,ENST00000530888,; T ENST00000394836 Transcript missense_variant 1178/2284 1020/1149 340/382 F/L ttC/ttA rs745743430 1 -1 RAB3IL1 HGNC HGNC:9780 protein_coding YES CCDS8014.1 ENSP00000378313 Q8TBN0 UPI000007260E NM_013401.3 tolerated(0.07) 9/10 hmmpanther:PTHR14430:SF1,hmmpanther:PTHR14430 MODERATE 1 SNV 1 1 PASS rs745743430 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 61899360 61899360 G T 1 0 0 0 0 1 0 0 0 13096 933 33 2 2 RAB3IL1 11 61899360 Missense_Mutation SNP G C3N-02529_T 5286078 61899360 73187262 63 29768 KDM2A 0 . GRCh38 11 67250208 67250208 + Missense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.2178C>G p.Ile726Met p.I726M ENST00000529006 17/21 211 166 45 219 219 0 strelka-varscan-mutect KDM2A,missense_variant,p.Ile726Met,ENST00000529006,NM_012308.2;KDM2A,missense_variant,p.Ile726Met,ENST00000398645,;KDM2A,missense_variant,p.Ile709Met,ENST00000308783,;KDM2A,missense_variant,p.Ile287Met,ENST00000530342,NM_001256405.1;KDM2A,non_coding_transcript_exon_variant,,ENST00000526258,;KDM2A,non_coding_transcript_exon_variant,,ENST00000531696,;KDM2A,upstream_gene_variant,,ENST00000524657,;KDM2A,downstream_gene_variant,,ENST00000525041,;KDM2A,downstream_gene_variant,,ENST00000534486,;KDM2A,downstream_gene_variant,,ENST00000529124,; G ENST00000529006 Transcript missense_variant 2624/6967 2178/3489 726/1162 I/M atC/atG 1 1 KDM2A HGNC HGNC:13606 protein_coding YES CCDS44657.1 ENSP00000432786 Q9Y2K7 I3VM53 UPI00001678A9 NM_012308.2 tolerated(0.07) 17/21 hmmpanther:PTHR23123,hmmpanther:PTHR23123:SF3 MODERATE 1 SNV 1 1 PASS rs1391692151 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 67250208 67250208 C G 1 0 0 0 0 1 0 0 0 8042 845 30 4 4 KDM2A 11 67250208 Missense_Mutation SNP C C3N-02529_T 5350848 67250208 67836414 64 29769 FCHSD2 0 . GRCh38 11 73083739 73083739 + Missense_Mutation SNP T T A novel C3N-02529_T C3N-02529_N T T c.121A>T p.Thr41Ser p.T41S ENST00000409418 3/20 157 145 12 191 191 0 strelka-mutect FCHSD2,missense_variant,p.Thr41Ser,ENST00000409314,;FCHSD2,missense_variant,p.Thr41Ser,ENST00000409418,NM_014824.2;FCHSD2,missense_variant,p.Thr20Ser,ENST00000422375,;FCHSD2,splice_region_variant,,ENST00000311172,;FCHSD2,splice_region_variant,,ENST00000458644,;FCHSD2,splice_region_variant,,ENST00000409853,; A ENST00000409418 Transcript missense_variant,splice_region_variant 505/3154 121/2223 41/740 T/S Aca/Tca 1 -1 FCHSD2 HGNC HGNC:29114 protein_coding YES CCDS8218.2 ENSP00000386722 O94868 UPI0000251F08 NM_014824.2 tolerated(1) 3/20 PROSITE_profiles:PS51741,hmmpanther:PTHR15735:SF11,hmmpanther:PTHR15735,Pfam_domain:PF00611,SMART_domains:SM00055,Superfamily_domains:SSF103657 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 73083739 73083739 T A 1 0 0 0 0 1 0 0 0 5652 1681 58 4 4 FCHSD2 11 73083739 Missense_Mutation SNP T C3N-02529_T 5833531 73083739 62002883 65 29770 ANO2 0 . GRCh38 12 5575839 5575839 + Silent SNP G G A C3N-02529_T C3N-02529_N G G c.2619C>T p.= p.F873F ENST00000356134 25/27 77 72 5 92 92 0 strelka-varscan-mutect ANO2,synonymous_variant,p.=,ENST00000327087,;ANO2,synonymous_variant,p.=,ENST00000356134,NM_001278597.1,NM_001278596.1;ANO2,synonymous_variant,p.=,ENST00000546188,; A ENST00000356134 Transcript synonymous_variant 2691/3717 2619/3000 873/999 F ttC/ttT COSM4482509,COSM4482510,COSM4482511 1 -1 ANO2 HGNC HGNC:1183 protein_coding YES CCDS44807.2 ENSP00000348453 Q9NQ90 UPI00000715DF NM_001278597.1,NM_001278596.1 25/27 hmmpanther:PTHR12308:SF20,hmmpanther:PTHR12308,Pfam_domain:PF04547 1,1,1 LOW 1 SNV 5 1,1,1 1 PASS . . 0 204 6 0 0 0 0 0 -11.16118 0.9999996 1 1 1 0 A 2 1 102 5575839 5575839 G A 1 0 0 0 0 0 0 0 1 804 956 33 3 3 ANO2 12 5575839 Silent SNP G C3N-02529_T 5575839 127699470 66 29771 ABCC9 0 . GRCh38 12 21845605 21845605 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.3094C>G p.Gln1032Glu p.Q1032E ENST00000261200 24/38 356 314 42 385 385 0 strelka-varscan-mutect ABCC9,missense_variant,p.Gln1032Glu,ENST00000261200,NM_020297.3;ABCC9,missense_variant,p.Gln1032Glu,ENST00000261201,NM_005691.3;ABCC9,missense_variant,p.Gln659Glu,ENST00000544039,;RP11-729I10.2,intron_variant,,ENST00000539874,; C ENST00000261200 Transcript missense_variant,splice_region_variant 3094/8293 3094/4650 1032/1549 Q/E Cag/Gag 1 -1 ABCC9 HGNC HGNC:60 protein_coding YES CCDS8693.1 ENSP00000261200 O60706 UPI000013D13F NM_020297.3 tolerated(0.44) 24/38 PROSITE_profiles:PS50929,hmmpanther:PTHR24223,hmmpanther:PTHR24223:SF173,Gene3D:2hydA01,Pfam_domain:PF00664,Superfamily_domains:SSF90123 MODERATE SNV 5 1 PASS rs1269392352 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 21845605 21845605 G C 1 0 0 0 0 1 0 0 0 63 1304 45 4 4 ABCC9 12 21845605 Missense_Mutation SNP G C3N-02529_T 16269766 21845605 111429704 67 29772 DDN 0 . GRCh38 12 48998547 48998547 + Missense_Mutation SNP T T C novel C3N-02529_T C3N-02529_N T T c.329A>G p.Gln110Arg p.Q110R ENST00000421952 2/2 113 91 22 88 88 0 strelka-varscan-mutect DDN,missense_variant,p.Gln110Arg,ENST00000421952,NM_015086.1;PRKAG1,downstream_gene_variant,,ENST00000548065,NM_002733.4;PRKAG1,downstream_gene_variant,,ENST00000316299,NM_001206709.1;PRKAG1,downstream_gene_variant,,ENST00000547306,;PRKAG1,downstream_gene_variant,,ENST00000552212,NM_001206710.1;PRKAG1,downstream_gene_variant,,ENST00000551770,;PRKAG1,downstream_gene_variant,,ENST00000548362,;PRKAG1,downstream_gene_variant,,ENST00000551696,;RP11-386G11.5,non_coding_transcript_exon_variant,,ENST00000547866,;RP11-386G11.5,non_coding_transcript_exon_variant,,ENST00000552933,;RP11-386G11.5,non_coding_transcript_exon_variant,,ENST00000552284,;RP11-386G11.5,non_coding_transcript_exon_variant,,ENST00000547395,;RP11-386G11.3,downstream_gene_variant,,ENST00000549516,;PRKAG1,downstream_gene_variant,,ENST00000546531,; C ENST00000421952 Transcript missense_variant 351/3749 329/2136 110/711 Q/R cAa/cGa 1 -1 DDN HGNC HGNC:24458 protein_coding YES CCDS31791.2 ENSP00000390590 O94850 UPI000019821C NM_015086.1 deleterious_low_confidence(0) 2/2 Coiled-coils_(Ncoils):Coil,Pfam_domain:PF15498,hmmpanther:PTHR16757 MODERATE 1 SNV 1 1 PASS rs1216085971 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 48998547 48998547 T C 1 0 0 0 0 1 0 0 0 4137 1812 63 5 5 DDN 12 48998547 Missense_Mutation SNP T C3N-02529_T 27152942 48998547 84276762 68 29773 SCARB1 0 . GRCh38 12 124807831 124807831 + Silent SNP G G A rs763936290 C3N-02529_T C3N-02529_N G G c.939C>T p.= p.I313I ENST00000261693 7/13 316 278 38 235 235 0 strelka-varscan-mutect SCARB1,synonymous_variant,p.=,ENST00000339570,NM_001082959.1;SCARB1,synonymous_variant,p.=,ENST00000415380,;SCARB1,synonymous_variant,p.=,ENST00000261693,NM_005505.4;SCARB1,synonymous_variant,p.=,ENST00000544327,;SCARB1,synonymous_variant,p.=,ENST00000546215,;SCARB1,non_coding_transcript_exon_variant,,ENST00000535005,;SCARB1,non_coding_transcript_exon_variant,,ENST00000538291,; A ENST00000261693 Transcript synonymous_variant 1066/2611 939/1530 313/509 I atC/atT rs763936290 1 -1 SCARB1 HGNC HGNC:1664 protein_coding YES CCDS9259.1 ENSP00000261693 Q8WTV0 A0A024RBS4 UPI000014CE1C NM_005505.4 7/13 Pfam_domain:PF01130,hmmpanther:PTHR11923,hmmpanther:PTHR11923:SF62 LOW 1 SNV 1 1 PASS rs763936290 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 102 124807831 124807831 G A 1 0 0 0 0 0 0 0 1 14147 932 33 3 3 SCARB1 12 124807831 Silent SNP G C3N-02529_T 75809284 124807831 8467478 69 29774 TMEM132C 0 . GRCh38 12 128697402 128697402 + Missense_Mutation SNP G G T C3N-02529_T C3N-02529_N G G c.2108G>T p.Arg703Leu p.R703L ENST00000435159 8/9 61 52 9 46 46 0 strelka-varscan-mutect TMEM132C,missense_variant,p.Arg703Leu,ENST00000435159,NM_001136103.2; T ENST00000435159 Transcript missense_variant 2108/4947 2108/3327 703/1108 R/L cGg/cTg COSM2227798,COSM2227799 1 1 TMEM132C HGNC HGNC:25436 protein_coding YES ENSP00000410852 Q8N3T6 UPI0001C0B37C NM_001136103.2 deleterious(0.01) 8/9 hmmpanther:PTHR13388,hmmpanther:PTHR13388:SF4,Pfam_domain:PF16070 1,1 MODERATE 1 SNV 5 1,1 1 PASS rs1006445144 . 0 199 10 0 0 0 0 0 -19.8273 0.9999816 1 1 1 0 T 3 4 102 128697402 128697402 G T 1 0 0 0 0 1 0 0 0 16491 1116 39 1 1 TMEM132C 12 128697402 Missense_Mutation SNP G C3N-02529_T 3889571 128697402 4577907 70 29775 CCDC168 0 . GRCh38 13 102747354 102747354 + Missense_Mutation SNP T T C novel C3N-02529_T C3N-02529_N T T c.3343A>G p.Lys1115Glu p.K1115E ENST00000322527 4/4 79 71 8 171 171 0 strelka-varscan-mutect CCDC168,missense_variant,p.Lys1115Glu,ENST00000322527,NM_001146197.1;LINC00283,downstream_gene_variant,,ENST00000430111,; C ENST00000322527 Transcript missense_variant 3481/21466 3343/21246 1115/7081 K/E Aaa/Gaa 1 -1 CCDC168 HGNC HGNC:26851 protein_coding YES CCDS73596.1 ENSP00000320232 Q8NDH2 UPI0001991308 NM_001146197.1 deleterious(0.02) 4/4 MODERATE 1 SNV 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 102747354 102747354 T C 1 0 0 0 0 1 0 0 0 2484 1850 64 5 5 CCDC168 13 102747354 Missense_Mutation SNP T C3N-02529_T 102747354 11616974 71 29776 SPTB 0 . GRCh38 14 64797779 64797779 + Nonsense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.1132C>T p.Gln378Ter p.Q378* ENST00000556626 10/36 576 532 44 537 537 0 strelka-varscan-mutect SPTB,stop_gained,p.Gln378Ter,ENST00000556626,;SPTB,stop_gained,p.Gln378Ter,ENST00000389722,NM_001024858.2;SPTB,stop_gained,p.Gln378Ter,ENST00000389721,NM_000347.5;SPTB,stop_gained,p.Gln378Ter,ENST00000389720,; A ENST00000556626 Transcript stop_gained 1275/10153 1132/6987 378/2328 Q/* Cag/Tag 1 -1 SPTB HGNC HGNC:11274 protein_coding YES CCDS32099.1 ENSP00000451752 P11277 UPI000053030D 10/36 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF248,PIRSF_domain:PIRSF002297,Gene3D:1.20.58.60,Pfam_domain:PF00435,SMART_domains:SM00150,Superfamily_domains:SSF46966 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 102 64797779 64797779 G A 1 0 0 0 0 0 1 0 0 15474 1299 45 3 3 SPTB 14 64797779 Nonsense_Mutation SNP G C3N-02529_T 64797779 42245939 72 29777 RYR3 0 . GRCh38 15 33788387 33788387 + Silent SNP C C T rs55650127 C3N-02529_T C3N-02529_N C C c.9759C>T p.= p.D3253D ENST00000634891 67/104 294 251 43 287 287 0 strelka-varscan-mutect RYR3,synonymous_variant,p.=,ENST00000634891,NM_001036.4;RYR3,synonymous_variant,p.=,ENST00000622037,;RYR3,synonymous_variant,p.=,ENST00000415757,NM_001243996.2;RYR3,synonymous_variant,p.=,ENST00000389232,;RYR3,synonymous_variant,p.=,ENST00000634418,;RYR3,synonymous_variant,p.=,ENST00000635790,; T ENST00000634891 Transcript synonymous_variant 9860/15591 9759/14613 3253/4870 D gaC/gaT rs55650127,COSM1243582,COSM3981455 1 1 RYR3 HGNC HGNC:10485 protein_coding YES CCDS45210.1 ENSP00000489262 Q15413 UPI0000E5B01A NM_001036.4 67/104 hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF16 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs55650127 . 0 208 0 0 0 0 0 2 -4.019944 0 0 1 0 0 T 2 4 102 33788387 33788387 C T 1 0 0 0 0 0 0 0 1 14030 535 19 1 1 RYR3 15 33788387 Silent SNP C C3N-02529_T 33788387 68202802 73 29778 CASC5 0 . GRCh38 15 40625472 40625472 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.5286G>C p.Lys1762Asn p.K1762N ENST00000346991 11/27 200 181 19 222 222 0 strelka-varscan-mutect CASC5,missense_variant,p.Lys1762Asn,ENST00000346991,NM_170589.4;CASC5,missense_variant,p.Lys1736Asn,ENST00000399668,NM_144508.4;CASC5,splice_region_variant,,ENST00000527044,;CASC5,upstream_gene_variant,,ENST00000532406,;CASC5,downstream_gene_variant,,ENST00000614337,;CASC5,missense_variant,p.Lys781Asn,ENST00000526913,;CASC5,non_coding_transcript_exon_variant,,ENST00000533001,;CASC5,intron_variant,,ENST00000534204,; C ENST00000346991 Transcript missense_variant 5676/9573 5286/7029 1762/2342 K/N aaG/aaC 1 1 CASC5 HGNC HGNC:24054 protein_coding YES CCDS42023.1 ENSP00000335463 Q8NG31 UPI0000E59BD3 NM_170589.4 tolerated(0.13) 11/27 hmmpanther:PTHR16520,hmmpanther:PTHR16520:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 40625472 40625472 G C 1 0 0 0 0 1 0 0 0 2363 991 35 4 4 CASC5 15 40625472 Missense_Mutation SNP G C3N-02529_T 6837085 40625472 61365717 74 29779 MAPKBP1 0 . GRCh38 15 41819352 41819352 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.2416C>T p.Leu806Phe p.L806F ENST00000456763 22/32 130 121 9 142 141 1 strelka-varscan-mutect MAPKBP1,missense_variant,p.Leu800Phe,ENST00000457542,NM_014994.2;MAPKBP1,missense_variant,p.Leu806Phe,ENST00000456763,NM_001128608.1;MAPKBP1,missense_variant,p.Leu800Phe,ENST00000514566,NM_001265611.1;MAPKBP1,3_prime_UTR_variant,,ENST00000512970,;MAPKBP1,3_prime_UTR_variant,,ENST00000505373,;MAPKBP1,non_coding_transcript_exon_variant,,ENST00000505061,;MAPKBP1,downstream_gene_variant,,ENST00000502292,;MAPKBP1,upstream_gene_variant,,ENST00000508050,;MAPKBP1,upstream_gene_variant,,ENST00000512433,;MAPKBP1,upstream_gene_variant,,ENST00000502695,;MAPKBP1,upstream_gene_variant,,ENST00000506301,;MAPKBP1,downstream_gene_variant,,ENST00000503526,; T ENST00000456763 Transcript missense_variant 2612/7158 2416/4545 806/1514 L/F Ctt/Ttt 1 1 MAPKBP1 HGNC HGNC:29536 protein_coding YES CCDS45239.1 ENSP00000393099 O60336 UPI00002375CB NM_001128608.1 tolerated(0.51) 22/32 hmmpanther:PTHR22847,hmmpanther:PTHR22847:SF432 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -12.93328 0.9999997 1 1 1 0 T 3 4 102 41819352 41819352 C T 1 0 0 0 0 1 0 0 0 9216 681 24 3 3 MAPKBP1 15 41819352 Missense_Mutation SNP C C3N-02529_T 1193880 41819352 60171837 75 29780 NEO1 0 . GRCh38 15 73178314 73178314 + Missense_Mutation SNP A A G novel C3N-02529_T C3N-02529_N A A c.1178A>G p.His393Arg p.H393R ENST00000339362 8/30 157 138 19 180 180 0 strelka-varscan-mutect NEO1,missense_variant,p.His393Arg,ENST00000339362,;NEO1,missense_variant,p.His393Arg,ENST00000261908,NM_002499.3;NEO1,missense_variant,p.His69Arg,ENST00000560328,;NEO1,missense_variant,p.His393Arg,ENST00000558964,NM_001172624.1;NEO1,missense_variant,p.His393Arg,ENST00000560262,NM_001172623.1; G ENST00000339362 Transcript missense_variant 1625/7342 1178/4386 393/1461 H/R cAt/cGt 1 1 NEO1 HGNC HGNC:7754 protein_coding YES CCDS10247.1 ENSP00000341198 Q92859 UPI000013D221 tolerated(0.18) 8/30 PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF55,Pfam_domain:PF07679,Gene3D:2.60.40.10,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 73178314 73178314 A G 1 0 0 0 0 1 0 0 0 10370 217 8 5 5 NEO1 15 73178314 Missense_Mutation SNP A C3N-02529_T 31358962 73178314 28812875 76 29781 FAM219B 0 . GRCh38 15 74902750 74902750 + Missense_Mutation SNP C C A novel C3N-02529_T C3N-02529_N C C c.466G>T p.Asp156Tyr p.D156Y ENST00000357635 5/5 93 77 16 115 115 0 strelka-varscan-mutect FAM219B,missense_variant,p.Asp156Tyr,ENST00000357635,NM_001321922.1,NM_020447.3;FAM219B,missense_variant,p.Asp156Tyr,ENST00000563119,NM_001321920.1,NM_001321923.1;FAM219B,missense_variant,p.Asp70Tyr,ENST00000565772,;FAM219B,missense_variant,p.Asp155Tyr,ENST00000562698,;MPI,downstream_gene_variant,,ENST00000352410,NM_002435.2;MPI,downstream_gene_variant,,ENST00000566377,NM_001289155.1;MPI,downstream_gene_variant,,ENST00000563786,;MPI,downstream_gene_variant,,ENST00000323744,NM_001289157.1;MPI,downstream_gene_variant,,ENST00000535694,NM_001289156.1;MPI,downstream_gene_variant,,ENST00000567177,;FAM219B,non_coding_transcript_exon_variant,,ENST00000563706,;MPI,downstream_gene_variant,,ENST00000564692,;FAM219B,upstream_gene_variant,,ENST00000564723,;FAM219B,missense_variant,p.Asp154Tyr,ENST00000563671,;FAM219B,3_prime_UTR_variant,,ENST00000569524,;FAM219B,3_prime_UTR_variant,,ENST00000563069,;FAM219B,3_prime_UTR_variant,,ENST00000570143,;FAM219B,3_prime_UTR_variant,,ENST00000563877,;FAM219B,3_prime_UTR_variant,,ENST00000566194,;FAM219B,3_prime_UTR_variant,,ENST00000563413,;FAM219B,3_prime_UTR_variant,,ENST00000566132,;FAM219B,3_prime_UTR_variant,,ENST00000564019,;FAM219B,3_prime_UTR_variant,,ENST00000569761,;FAM219B,3_prime_UTR_variant,,ENST00000567388,;FAM219B,non_coding_transcript_exon_variant,,ENST00000566894,;FAM219B,non_coding_transcript_exon_variant,,ENST00000564857,;MPI,downstream_gene_variant,,ENST00000566556,; A ENST00000357635 Transcript missense_variant 787/3550 466/597 156/198 D/Y Gat/Tat 1 -1 FAM219B HGNC HGNC:24695 protein_coding YES CCDS32295.1 ENSP00000350260 Q5XKK7 UPI0000073A99 NM_001321922.1,NM_020447.3 deleterious(0) 5/5 Pfam_domain:PF15260,hmmpanther:PTHR31281,hmmpanther:PTHR31281:SF2 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 74902750 74902750 C A 1 0 0 0 0 1 0 0 0 5410 855 30 2 2 FAM219B 15 74902750 Missense_Mutation SNP C C3N-02529_T 1724436 74902750 27088439 77 29782 RHOT2 0 . GRCh38 16 670300 670300 + Silent SNP C C A rs774343527 C3N-02529_T C3N-02529_N C C c.381C>A p.= p.S127S ENST00000315082 7/19 286 221 65 205 205 0 strelka-varscan-mutect RHOT2,synonymous_variant,p.=,ENST00000315082,NM_138769.2;RHOT2,synonymous_variant,p.=,ENST00000563134,;RHOT2,synonymous_variant,p.=,ENST00000561929,;WDR90,downstream_gene_variant,,ENST00000549091,;WDR90,downstream_gene_variant,,ENST00000293879,NM_145294.4;WDR90,downstream_gene_variant,,ENST00000547944,;WDR90,downstream_gene_variant,,ENST00000315764,;WDR90,downstream_gene_variant,,ENST00000551100,;RHOT2,upstream_gene_variant,,ENST00000569197,;WDR90,downstream_gene_variant,,ENST00000546896,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569943,;WDR90,downstream_gene_variant,,ENST00000547543,;RHOT2,missense_variant,p.His122Asn,ENST00000562333,;RHOT2,missense_variant,p.His122Asn,ENST00000561983,;RHOT2,3_prime_UTR_variant,,ENST00000563637,;RHOT2,3_prime_UTR_variant,,ENST00000570280,;RHOT2,3_prime_UTR_variant,,ENST00000566214,;RHOT2,non_coding_transcript_exon_variant,,ENST00000602564,;RHOT2,non_coding_transcript_exon_variant,,ENST00000568636,;RHOT2,non_coding_transcript_exon_variant,,ENST00000569675,;RHOT2,non_coding_transcript_exon_variant,,ENST00000568950,;RHOT2,non_coding_transcript_exon_variant,,ENST00000567017,;RHOT2,non_coding_transcript_exon_variant,,ENST00000563776,;RHOT2,non_coding_transcript_exon_variant,,ENST00000566965,;RHOT2,non_coding_transcript_exon_variant,,ENST00000570092,;RHOT2,non_coding_transcript_exon_variant,,ENST00000562708,;RHOT2,non_coding_transcript_exon_variant,,ENST00000562598,;WDR90,downstream_gene_variant,,ENST00000547407,;WDR90,downstream_gene_variant,,ENST00000552728,;WDR90,downstream_gene_variant,,ENST00000549024,;WDR90,downstream_gene_variant,,ENST00000553080,;RHOT2,upstream_gene_variant,,ENST00000569358,;RHOT2,upstream_gene_variant,,ENST00000565004,;RHOT2,upstream_gene_variant,,ENST00000564659,;RHOT2,upstream_gene_variant,,ENST00000561711,;RHOT2,downstream_gene_variant,,ENST00000569706,;RHOT2,upstream_gene_variant,,ENST00000567589,;RHOT2,upstream_gene_variant,,ENST00000562957,;WDR90,downstream_gene_variant,,ENST00000548448,; A ENST00000315082 Transcript synonymous_variant 495/2539 381/1857 127/618 S tcC/tcA rs774343527 1 1 RHOT2 HGNC HGNC:21169 protein_coding YES CCDS10417.1 ENSP00000321971 Q8IXI1 UPI000007310B NM_138769.2 7/19 Gene3D:3.40.50.300,Pfam_domain:PF00071,PIRSF_domain:PIRSF037488,PROSITE_profiles:PS51423,hmmpanther:PTHR24072,hmmpanther:PTHR24072:SF70,SMART_domains:SM00173,SMART_domains:SM00174,SMART_domains:SM00175,Superfamily_domains:SSF52540 LOW 1 SNV 1 1 PASS rs774343527 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 102 670300 670300 C A 1 0 0 0 0 0 0 0 1 13517 581 21 2 2 RHOT2 16 670300 Silent SNP C C3N-02529_T 670300 89668045 78 29783 VASN 0 . GRCh38 16 4381898 4381898 + Nonsense_Mutation SNP G G T novel C3N-02529_T C3N-02529_N G G c.1021G>T p.Glu341Ter p.E341* ENST00000304735 2/2 368 335 33 286 285 1 strelka-varscan-mutect VASN,stop_gained,p.Glu341Ter,ENST00000304735,NM_138440.2;CORO7,intron_variant,,ENST00000251166,NM_024535.4;CORO7,intron_variant,,ENST00000537233,NM_001201472.1;CORO7-PAM16,intron_variant,,ENST00000572467,NM_001201479.1;CORO7,intron_variant,,ENST00000574025,NM_001201473.1;CORO7,intron_variant,,ENST00000572549,;CORO7,intron_variant,,ENST00000572044,;CORO7-PAM16,intron_variant,,ENST00000575334,;CORO7,intron_variant,,ENST00000571227,;CORO7,intron_variant,,ENST00000575714,;CORO7,intron_variant,,ENST00000571756,;CORO7,intron_variant,,ENST00000574311,;CORO7,intron_variant,,ENST00000576437,; T ENST00000304735 Transcript stop_gained 1176/2806 1021/2022 341/673 E/* Gag/Tag 1 1 VASN HGNC HGNC:18517 protein_coding YES CCDS10514.1 ENSP00000306864 Q6EMK4 UPI000003E779 NM_138440.2 2/2 hmmpanther:PTHR24365,hmmpanther:PTHR24365:SF367,Gene3D:3.80.10.10,SMART_domains:SM00082 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 102 4381898 4381898 G T 1 0 0 0 0 0 1 0 0 17672 1175 41 2 2 VASN 16 4381898 Nonsense_Mutation SNP G C3N-02529_T 3711598 4381898 85956447 79 29784 KIAA0556 0 . GRCh38 16 27628733 27628733 + Silent SNP C C T rs762842250 C3N-02529_T C3N-02529_N C C c.213C>T p.= p.V71V ENST00000261588 4/28 348 305 43 326 326 0 strelka-varscan-mutect KIAA0556,synonymous_variant,p.=,ENST00000261588,NM_015202.2;KIAA0556,synonymous_variant,p.=,ENST00000568258,;KIAA0556,synonymous_variant,p.=,ENST00000618117,;KIAA0556,upstream_gene_variant,,ENST00000567894,;KIAA0556,synonymous_variant,p.=,ENST00000565672,;KIAA0556,non_coding_transcript_exon_variant,,ENST00000564749,; T ENST00000261588 Transcript synonymous_variant 232/6616 213/4857 71/1618 V gtC/gtT rs762842250 1 1 KIAA0556 HGNC HGNC:29068 protein_coding YES CCDS32415.1 ENSP00000261588 O60303 UPI000045693C NM_015202.2 4/28 hmmpanther:PTHR21534:SF0,hmmpanther:PTHR21534 LOW 1 SNV 1 1 PASS rs762842250 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 27628733 27628733 C T 1 0 0 0 0 0 0 0 1 8088 900 32 3 3 KIAA0556 16 27628733 Silent SNP C C3N-02529_T 23246835 27628733 62709612 80 29785 ZFHX3 0 . GRCh38 16 72960105 72960105 + Missense_Mutation SNP T T C novel C3N-02529_T C3N-02529_N T T c.41A>G p.Asn14Ser p.N14S ENST00000268489 2/10 53 49 4 41 41 0 strelka-mutect ZFHX3,missense_variant,p.Asn14Ser,ENST00000268489,NM_006885.3;ZFHX3,intron_variant,,ENST00000397992,NM_001164766.1; C ENST00000268489 Transcript missense_variant 714/16064 41/11112 14/3703 N/S aAt/aGt 1 -1 ZFHX3 HGNC HGNC:777 protein_coding YES CCDS10908.1 ENSP00000268489 Q15911 UPI00001AE937 NM_006885.3 deleterious_low_confidence(0) 2/10 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -10.53889 1 1 1 1 0 C 3 2 102 72960105 72960105 T C 1 0 0 0 0 1 0 0 0 18212 1493 52 5 5 ZFHX3 16 72960105 Missense_Mutation SNP T C3N-02529_T 45331372 72960105 17378240 81 29786 TP53 0 . GRCh38 17 7674935 7674935 + Missense_Mutation SNP C C A C3N-02529_T C3N-02529_N C C c.596G>T p.Gly199Val p.G199V ENST00000269305 6/11 452 346 106 503 503 0 strelka-varscan-mutect TP53,missense_variant,p.Gly199Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Gly199Val,ENST00000420246,;TP53,missense_variant,p.Gly160Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Gly160Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Gly199Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Gly160Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Gly199Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Gly160Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Gly199Val,ENST00000445888,;TP53,missense_variant,p.Gly160Val,ENST00000619485,;TP53,missense_variant,p.Gly67Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Gly40Val,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Gly67Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Gly40Val,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Gly67Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Gly40Val,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Gly199Val,ENST00000359597,;TP53,missense_variant,p.Gly188Val,ENST00000615910,;TP53,missense_variant,p.Gly199Val,ENST00000413465,;TP53,missense_variant,p.Gly67Val,ENST00000509690,;TP53,missense_variant,p.Gly106Val,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Gly160Val,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 786/2579 596/1182 199/393 G/V gGa/gTa TP53_g.12665G>T,TP53_g.12665G>C,TP53_g.12665G>A,TP53_g.12665del,COSM1610848,COSM1610849,COSM1610850,COSM1610851,COSM255787,COSM255788,COSM255789,COSM255790,COSM3675524,COSM3675525,COSM43989,COSM44140,COSM45199,COSM45387,COSM4776916,COSM4776917,COSM4776918,COSM4776919,COSM4776920,COSM4776921 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 7674935 7674935 C A 1 0 0 0 0 1 0 0 0 16859 855 30 2 2 TP53 17 7674935 Missense_Mutation SNP C C3N-02529_T 7674935 75582506 82 29787 SOCS7 0 . GRCh38 17 38364853 38364853 + Missense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.955C>G p.Leu319Val p.L319V ENST00000612932 3/10 217 190 27 140 140 0 strelka-varscan-mutect SOCS7,missense_variant,p.Leu319Val,ENST00000612932,NM_014598.3;SOCS7,missense_variant,p.Leu319Val,ENST00000613678,;SOCS7,intron_variant,,ENST00000617765,;SOCS7,non_coding_transcript_exon_variant,,ENST00000617360,; G ENST00000612932 Transcript missense_variant 955/7857 955/1746 319/581 L/V Cta/Gta 1 1 SOCS7 HGNC HGNC:29846 protein_coding YES CCDS32637.1 ENSP00000482229 O14512 UPI00001AFDEB NM_014598.3 deleterious_low_confidence(0.02) 3/10 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF82,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 38364853 38364853 C G 1 0 0 0 0 1 0 0 0 15240 695 24 4 4 SOCS7 17 38364853 Missense_Mutation SNP C C3N-02529_T 30689918 38364853 44892588 83 29788 MED1 0 . GRCh38 17 39405303 39405314 + Splice_Site DEL TTTGATCTGGGA TTTGATCTGGGA - novel C3N-02529_T C3N-02529_N TTTGATCTGGGA TTTGATCTGGGA c.1641-6_1646delTCCCAGATCAAA p.X547_splice ENST00000394287 18/18 190 124 66 159 159 0 sindel-varindel MED1,splice_acceptor_variant,,ENST00000394287,;FBXL20,upstream_gene_variant,,ENST00000264658,NM_032875.2;MED1,downstream_gene_variant,,ENST00000300651,NM_004774.3;FBXL20,upstream_gene_variant,,ENST00000394294,NM_001184906.1;FBXL20,upstream_gene_variant,,ENST00000583610,;FBXL20,upstream_gene_variant,,ENST00000577399,;CTB-131K11.1,intron_variant,,ENST00000582842,;MED1,downstream_gene_variant,,ENST00000577831,; - ENST00000394287 Transcript splice_acceptor_variant,coding_sequence_variant,intron_variant ?-1852/2870 ?-1646/1671 ?-549/556 1 -1 MED1 HGNC HGNC:9234 protein_coding ENSP00000377828 Q15648 UPI00002132C2 18/18 17/17 HIGH deletion 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999988 1 1 1 0 - 8 5 102 39405303 39405303 TTTGATCTGGGA - 1 0 1 0 1 0 0 1 0 9364 1623 56 0 0 MED1 17 39405303 Splice_Site DEL TTTGATCTGGGA C3N-02529_T 1040450 39405303 43852138 84 29789 KRT28 0 . GRCh38 17 40797234 40797234 + Silent SNP C C T rs745779688 C3N-02529_T C3N-02529_N C C c.738G>A p.= p.E246E ENST00000306658 4/8 307 278 29 176 176 0 strelka-varscan-mutect KRT28,synonymous_variant,p.=,ENST00000306658,NM_181535.3; T ENST00000306658 Transcript synonymous_variant 804/1685 738/1395 246/464 E gaG/gaA rs745779688 1 -1 KRT28 HGNC HGNC:30842 protein_coding YES CCDS11376.1 ENSP00000305263 Q7Z3Y7 UPI0000246D70 NM_181535.3 4/8 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF215,Pfam_domain:PF00038,SMART_domains:SM01391,Prints_domain:PR01248 LOW 1 SNV 1 1 PASS rs745779688 . 0 208 0 2 0 0 0 0 -20 0.9999998 1 1 1 0 T 2 4 102 40797234 40797234 C T 1 0 0 0 0 0 0 0 1 8347 912 32 3 3 KRT28 17 40797234 Silent SNP C C3N-02529_T 1391931 40797234 42460207 85 29790 NPEPPS 0 . GRCh38 17 47531375 47531375 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.75C>T p.= p.L25L ENST00000322157 1/23 144 125 19 144 143 1 varscan-mutect NPEPPS,synonymous_variant,p.=,ENST00000322157,NM_006310.3;NPEPPS,intron_variant,,ENST00000530173,;NPEPPS,intron_variant,,ENST00000525007,;NPEPPS,non_coding_transcript_exon_variant,,ENST00000533573,;NPEPPS,intron_variant,,ENST00000525037,;NPEPPS,intron_variant,,ENST00000528751,;NPEPPS,synonymous_variant,p.=,ENST00000527298,;NPEPPS,intron_variant,,ENST00000532729,;NPEPPS,intron_variant,,ENST00000526247,;NPEPPS,upstream_gene_variant,,ENST00000534691,; T ENST00000322157 Transcript synonymous_variant 312/4353 75/2760 25/919 L ctC/ctT 1 1 NPEPPS HGNC HGNC:7900 protein_coding YES CCDS45721.1 ENSP00000320324 P55786 UPI0000140D51 NM_006310.3 1/23 Low_complexity_(Seg):seg,hmmpanther:PTHR11533:SF187,hmmpanther:PTHR11533 LOW 1 SNV 1 1 PASS rs1380876042 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 47531375 47531375 C T 1 0 0 0 0 0 0 0 1 10623 842 30 3 3 NPEPPS 17 47531375 Silent SNP C C3N-02529_T 6734141 47531375 35726066 86 29791 SEPT4 0 . GRCh38 17 58521829 58521829 + Missense_Mutation SNP G G T novel C3N-02529_T C3N-02529_N G G c.867C>A p.Phe289Leu p.F289L ENST00000457347 8/13 353 319 34 309 308 1 strelka-varscan-mutect SEPT4,missense_variant,p.Phe289Leu,ENST00000457347,NM_001256782.1;SEPT4,missense_variant,p.Phe274Leu,ENST00000317268,NM_004574.4;SEPT4,missense_variant,p.Phe127Leu,ENST00000583114,NM_001256822.1;SEPT4,missense_variant,p.Phe266Leu,ENST00000412945,NM_001198713.1;SEPT4,missense_variant,p.Phe255Leu,ENST00000393086,;SEPT4,missense_variant,p.Phe255Leu,ENST00000317256,NM_080416.3;SEPT4,missense_variant,p.Phe175Leu,ENST00000580844,;SEPT4,missense_variant,p.Phe175Leu,ENST00000579371,;SEPT4,missense_variant,p.Phe180Leu,ENST00000577729,;SEPT4,3_prime_UTR_variant,,ENST00000426861,NM_080415.3;SEPT4,3_prime_UTR_variant,,ENST00000580809,;MTMR4,upstream_gene_variant,,ENST00000323456,NM_004687.4;MTMR4,upstream_gene_variant,,ENST00000579925,;SEPT4,downstream_gene_variant,,ENST00000583291,;SEPT4,downstream_gene_variant,,ENST00000581607,;MTMR4,upstream_gene_variant,,ENST00000579921,;SEPT4-AS1,intron_variant,,ENST00000580589,;SEPT4-AS1,upstream_gene_variant,,ENST00000580769,;SEPT4-AS1,upstream_gene_variant,,ENST00000578022,;SEPT4,downstream_gene_variant,,ENST00000580791,;SEPT4,downstream_gene_variant,,ENST00000584528,;SEPT4,downstream_gene_variant,,ENST00000580740,;SEPT4,downstream_gene_variant,,ENST00000581921,;SEPT4,non_coding_transcript_exon_variant,,ENST00000580796,;SEPT4,non_coding_transcript_exon_variant,,ENST00000582270,;SEPT4,non_coding_transcript_exon_variant,,ENST00000583273,;SEPT4,non_coding_transcript_exon_variant,,ENST00000577440,;SEPT4,non_coding_transcript_exon_variant,,ENST00000584488,;SEPT4,downstream_gene_variant,,ENST00000585170,;SEPT4,downstream_gene_variant,,ENST00000584789,;SEPT4,downstream_gene_variant,,ENST00000581615,;SEPT4,downstream_gene_variant,,ENST00000582248,;MTMR4,upstream_gene_variant,,ENST00000582663,;SEPT4,downstream_gene_variant,,ENST00000578747,;SEPT4,downstream_gene_variant,,ENST00000578131,; T ENST00000457347 Transcript missense_variant 1012/1795 867/1482 289/493 F/L ttC/ttA 1 -1 SEPT4 HGNC HGNC:9165 protein_coding YES CCDS58582.1 ENSP00000402000 O43236 UPI00017A809C NM_001256782.1 deleterious(0.03) 8/13 Gene3D:3.40.50.300,Pfam_domain:PF00735,PROSITE_profiles:PS51719,hmmpanther:PTHR18884,hmmpanther:PTHR18884:SF71,Superfamily_domains:SSF52540 MODERATE SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 58521829 58521829 G T 1 0 0 0 0 1 0 0 0 14342 1281 45 2 2 SEPT4 17 58521829 Missense_Mutation SNP G C3N-02529_T 10990454 58521829 24735612 87 29792 COG1 0 . GRCh38 17 73201526 73201526 + Nonsense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.1699C>T p.Gln567Ter p.Q567* ENST00000299886 7/14 437 413 24 449 447 2 strelka-varscan-mutect COG1,stop_gained,p.Gln567Ter,ENST00000438720,;COG1,stop_gained,p.Gln567Ter,ENST00000618996,;COG1,stop_gained,p.Gln567Ter,ENST00000299886,NM_018714.2;COG1,upstream_gene_variant,,ENST00000582672,;COG1,upstream_gene_variant,,ENST00000582512,;RP11-143K11.7,downstream_gene_variant,,ENST00000613523,;RP11-143K11.5,downstream_gene_variant,,ENST00000580671,;COG1,downstream_gene_variant,,ENST00000582587,;COG1,upstream_gene_variant,,ENST00000577238,;COG1,upstream_gene_variant,,ENST00000580271,;COG1,upstream_gene_variant,,ENST00000577844,; T ENST00000299886 Transcript stop_gained 1779/3079 1699/2943 567/980 Q/* Cag/Tag 1 1 COG1 HGNC HGNC:6545 protein_coding YES CCDS11692.1 ENSP00000299886 Q8WTW3 UPI0000127E34 NM_018714.2 7/14 hmmpanther:PTHR31658,hmmpanther:PTHR31658:SF0 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 102 73201526 73201526 C T 1 0 0 0 0 0 1 0 0 3445 711 25 3 3 COG1 17 73201526 Nonsense_Mutation SNP C C3N-02529_T 14679697 73201526 10055915 88 29793 FAAP100 0 . GRCh38 17 81551149 81551149 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.345G>A p.= p.V115V ENST00000327787 3/9 113 106 7 79 79 0 strelka-varscan-mutect FAAP100,synonymous_variant,p.=,ENST00000327787,NM_025161.5;FAAP100,synonymous_variant,p.=,ENST00000536161,;FAAP100,5_prime_UTR_variant,,ENST00000541246,;FAAP100,5_prime_UTR_variant,,ENST00000544302,;FAAP100,upstream_gene_variant,,ENST00000425898,;FAAP100,3_prime_UTR_variant,,ENST00000443656,;FAAP100,upstream_gene_variant,,ENST00000545865,; T ENST00000327787 Transcript synonymous_variant 392/3627 345/2646 115/881 V gtG/gtA 1 -1 FAAP100 HGNC HGNC:26171 protein_coding YES CCDS32765.2 ENSP00000333283 Q0VG06 UPI0001C53D21 NM_025161.5 3/9 hmmpanther:PTHR14890,hmmpanther:PTHR14890:SF1 LOW 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -13.92353 1 1 1 1 0 T 2 4 102 81551149 81551149 C T 1 0 0 0 0 0 0 0 1 5224 813 29 3 3 FAAP100 17 81551149 Silent SNP C C3N-02529_T 8349623 81551149 1706292 89 29794 CCDC57 0 . GRCh38 17 82157845 82157845 + Missense_Mutation SNP T T A novel C3N-02529_T C3N-02529_N T T c.2144A>T p.Glu715Val p.E715V ENST00000389641 14/18 323 303 20 244 243 1 strelka-varscan-mutect CCDC57,missense_variant,p.Glu715Val,ENST00000389641,;CCDC57,missense_variant,p.Glu715Val,ENST00000392347,NM_198082.2;CCDC57,missense_variant,p.Glu715Val,ENST00000392343,;CCDC57,missense_variant,p.Glu99Val,ENST00000419322,;RP11-1376P16.2,downstream_gene_variant,,ENST00000579979,;RP11-1376P16.1,upstream_gene_variant,,ENST00000582774,;CCDC57,non_coding_transcript_exon_variant,,ENST00000327026,;CCDC57,upstream_gene_variant,,ENST00000475635,; A ENST00000389641 Transcript missense_variant 2181/3000 2144/2751 715/916 E/V gAg/gTg 1 -1 CCDC57 HGNC HGNC:27564 protein_coding YES ENSP00000374292 Q2TAC2 UPI000155D557 deleterious(0) 14/18 hmmpanther:PTHR23161,hmmpanther:PTHR23161:SF1 MODERATE SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 82157845 82157845 T A 1 0 0 0 0 1 0 0 0 2529 1551 54 4 4 CCDC57 17 82157845 Missense_Mutation SNP T C3N-02529_T 606696 82157845 1099596 90 29795 DCC 0 . GRCh38 18 53467979 53467979 + Missense_Mutation SNP G G T C3N-02529_T C3N-02529_N G G c.3705G>T p.Met1235Ile p.M1235I ENST00000442544 25/29 334 274 60 315 315 0 strelka-varscan-mutect DCC,missense_variant,p.Met1235Ile,ENST00000442544,NM_005215.3;DCC,missense_variant,p.Met1212Ile,ENST00000412726,;DCC,missense_variant,p.Met870Ile,ENST00000581580,; T ENST00000442544 Transcript missense_variant 4321/10206 3705/4344 1235/1447 M/I atG/atT COSM1711373 1 1 DCC HGNC HGNC:2701 protein_coding YES CCDS11952.1 ENSP00000389140 P43146 UPI00001AEDC6 NM_005215.3 deleterious(0.01) 25/29 Pfam_domain:PF06583,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF68 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 53467979 53467979 G T 1 0 0 0 0 1 0 0 0 4084 1290 45 2 2 DCC 18 53467979 Missense_Mutation SNP G C3N-02529_T 53467979 26905306 91 29796 ALPK2 0 . GRCh38 18 58536262 58536262 + Missense_Mutation SNP C C T C3N-02529_T C3N-02529_N C C c.3925G>A p.Asp1309Asn p.D1309N ENST00000361673 5/13 159 127 32 186 186 0 strelka-varscan-mutect ALPK2,missense_variant,p.Asp1309Asn,ENST00000361673,NM_052947.3;RP11-1151B14.4,non_coding_transcript_exon_variant,,ENST00000591360,;ALPK2,downstream_gene_variant,,ENST00000587842,;ALPK2,non_coding_transcript_exon_variant,,ENST00000589204,; T ENST00000361673 Transcript missense_variant 4139/7303 3925/6513 1309/2170 D/N Gat/Aat COSM1660504,COSM1660505 1 -1 ALPK2 HGNC HGNC:20565 protein_coding YES CCDS11966.2 ENSP00000354991 Q86TB3 UPI000022A768 NM_052947.3 tolerated(1) 5/13 hmmpanther:PTHR14187,hmmpanther:PTHR14187:SF6 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs966215600 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 58536262 58536262 C T 1 0 0 0 0 1 0 0 0 645 826 29 3 3 ALPK2 18 58536262 Missense_Mutation SNP C C3N-02529_T 5068283 58536262 21837023 92 29797 C2CD4C 0 . GRCh38 19 407451 407451 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.911G>A p.Gly304Asp p.G304D ENST00000332235 2/2 47 42 5 71 71 0 strelka-varscan-mutect C2CD4C,missense_variant,p.Gly304Asp,ENST00000332235,NM_001136263.1; T ENST00000332235 Transcript missense_variant 1116/3129 911/1266 304/421 G/D gGc/gAc 1 -1 C2CD4C HGNC HGNC:29417 protein_coding YES CCDS45890.1 ENSP00000328677 Q8TF44 UPI00001C2016 NM_001136263.1 tolerated(0.17) 2/2 hmmpanther:PTHR10024,hmmpanther:PTHR10024:SF116,Superfamily_domains:SSF49562 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -12.94793 1 1 1 1 0 T 3 4 102 407451 407451 C T 1 0 0 0 0 1 0 0 0 2028 739 26 3 3 C2CD4C 19 407451 Missense_Mutation SNP C C3N-02529_T 407451 58210165 93 29798 ZNF675 0 . GRCh38 19 23654213 23654213 + Missense_Mutation SNP G G C rs146787061 C3N-02529_T C3N-02529_N G G c.720C>G p.Phe240Leu p.F240L ENST00000359788 4/4 176 158 18 277 277 0 strelka-varscan-mutect ZNF675,missense_variant,p.Phe240Leu,ENST00000359788,NM_138330.2;ZNF675,intron_variant,,ENST00000601935,;ZNF675,intron_variant,,ENST00000596211,;ZNF675,intron_variant,,ENST00000600313,;ZNF675,downstream_gene_variant,,ENST00000599535,;ZNF675,downstream_gene_variant,,ENST00000601010,;ZNF675,non_coding_transcript_exon_variant,,ENST00000600299,;ZNF675,downstream_gene_variant,,ENST00000597074,; C ENST00000359788 Transcript missense_variant 889/2301 720/1707 240/568 F/L ttC/ttG rs146787061 1 -1 ZNF675 HGNC HGNC:30768 protein_coding YES CCDS32981.1 ENSP00000352836 Q8TD23 UPI0000203902 NM_138330.2 tolerated(0.39) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,Superfamily_domains:SSF57667 MODERATE 1 SNV 1 1 PASS rs146787061 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 23654213 23654213 G C 1 0 0 0 0 1 0 0 0 18655 933 33 4 4 ZNF675 19 23654213 Missense_Mutation SNP G C3N-02529_T 23246762 23654213 34963403 94 29799 LYPD5 0 . GRCh38 19 43798588 43798588 + Silent SNP C C A rs371523113 C3N-02529_T C3N-02529_N C C c.384G>T p.= p.P128P ENST00000377950 4/5 172 149 23 170 170 0 strelka-varscan-mutect LYPD5,synonymous_variant,p.=,ENST00000377950,NM_001031749.2;LYPD5,synonymous_variant,p.=,ENST00000414615,NM_182573.2;LYPD5,synonymous_variant,p.=,ENST00000594013,NM_001288763.1;LYPD5,synonymous_variant,p.=,ENST00000602179,;LYPD5,synonymous_variant,p.=,ENST00000594049,;AC115522.3,upstream_gene_variant,,ENST00000595680,;LYPD5,non_coding_transcript_exon_variant,,ENST00000595666,;LYPD5,non_coding_transcript_exon_variant,,ENST00000601224,; A ENST00000377950 Transcript synonymous_variant 465/2499 384/756 128/251 P ccG/ccT rs371523113,COSM1304713,COSM1304714 1 -1 LYPD5 HGNC HGNC:26397 protein_coding YES CCDS46096.1 ENSP00000367185 Q6UWN5 UPI00006A77F6 NM_001031749.2 4/5 hmmpanther:PTHR10624 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS rs371523113 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 102 43798588 43798588 C A 1 0 0 0 0 0 0 0 1 9024 871 31 1 1 LYPD5 19 43798588 Silent SNP C C3N-02529_T 20144375 43798588 14819028 95 29800 PLEKHA4 0 . GRCh38 19 48837419 48837419 + Missense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.2210G>A p.Arg737Gln p.R737Q ENST00000263265 20/20 183 170 13 190 190 0 strelka-varscan-mutect PLEKHA4,missense_variant,p.Arg737Gln,ENST00000263265,NM_020904.2;PLEKHA4,3_prime_UTR_variant,,ENST00000355496,NM_001161354.1;PLEKHA4,3_prime_UTR_variant,,ENST00000597129,;HSD17B14,upstream_gene_variant,,ENST00000263278,NM_016246.2;HSD17B14,upstream_gene_variant,,ENST00000599157,;HSD17B14,upstream_gene_variant,,ENST00000595764,;PLEKHA4,non_coding_transcript_exon_variant,,ENST00000601146,; T ENST00000263265 Transcript missense_variant 2766/3088 2210/2340 737/779 R/Q cGa/cAa 1 -1 PLEKHA4 HGNC HGNC:14339 protein_coding YES CCDS12737.1 ENSP00000263265 Q9H4M7 UPI00000721A6 NM_020904.2 tolerated_low_confidence(0.48) 20/20 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 102 48837419 48837419 C T 1 0 0 0 0 1 0 0 0 12151 884 31 1 1 PLEKHA4 19 48837419 Missense_Mutation SNP C C3N-02529_T 5038831 48837419 9780197 96 29801 SLC6A16 0 . GRCh38 19 49290171 49290171 + Silent SNP T T C novel C3N-02529_T C3N-02529_N T T c.2163A>G p.= p.L721L ENST00000335875 12/12 237 156 81 169 169 0 strelka-varscan-mutect SLC6A16,synonymous_variant,p.=,ENST00000335875,NM_014037.2;SLC6A16,3_prime_UTR_variant,,ENST00000454748,;SLC6A16,downstream_gene_variant,,ENST00000598828,;SLC6A16,downstream_gene_variant,,ENST00000598221,; C ENST00000335875 Transcript synonymous_variant 2405/2938 2163/2211 721/736 L ctA/ctG 1 -1 SLC6A16 HGNC HGNC:13622 protein_coding YES CCDS42590.1 ENSP00000338627 Q9GZN6 UPI00001305CE NM_014037.2 12/12 hmmpanther:PTHR11616,hmmpanther:PTHR11616:SF113 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 102 49290171 49290171 T C 1 0 0 0 0 0 0 0 1 14962 1625 57 5 5 SLC6A16 19 49290171 Silent SNP T C3N-02529_T 452752 49290171 9327445 97 29802 NR1H2 0 . GRCh38 19 50377837 50377837 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.148G>C p.Asp50His p.D50H ENST00000253727 4/10 55 48 7 44 44 0 strelka-varscan-mutect NR1H2,missense_variant,p.Asp50His,ENST00000253727,NM_007121.5;NR1H2,missense_variant,p.Asp50His,ENST00000598168,;NR1H2,missense_variant,p.Asp50His,ENST00000599105,;NR1H2,missense_variant,p.Asp50His,ENST00000593926,;NR1H2,missense_variant,p.Asp50His,ENST00000411902,NM_001256647.1;NR1H2,missense_variant,p.Asp50His,ENST00000597130,;NR1H2,missense_variant,p.Asp50His,ENST00000597157,;NR1H2,missense_variant,p.Asp50His,ENST00000597790,;NR1H2,downstream_gene_variant,,ENST00000600355,;NR1H2,missense_variant,p.Asp50His,ENST00000593532,;NR1H2,non_coding_transcript_exon_variant,,ENST00000595730,;NR1H2,upstream_gene_variant,,ENST00000597085,; C ENST00000253727 Transcript missense_variant 383/1998 148/1383 50/460 D/H Gat/Cat 1 1 NR1H2 HGNC HGNC:7965 protein_coding YES CCDS42593.1 ENSP00000253727 P55055 UPI000013CDEE NM_007121.5 deleterious(0.01) 4/10 Low_complexity_(Seg):seg,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF316 MODERATE 1 SNV 1 1 PASS . . 0 203 7 0 0 0 0 0 -16.34312 0.9999994 1 1 1 0 C 3 2 102 50377837 50377837 G C 1 0 0 0 0 1 0 0 0 10673 1290 45 4 4 NR1H2 19 50377837 Missense_Mutation SNP G C3N-02529_T 1087666 50377837 8239779 98 29803 GPR32 0 . GRCh38 19 50771555 50771555 + Missense_Mutation SNP G G A C3N-02529_T C3N-02529_N G G c.955G>A p.Val319Ile p.V319I ENST00000270590 1/1 288 217 71 261 261 0 strelka-varscan-mutect GPR32,missense_variant,p.Val319Ile,ENST00000270590,NM_001506.2;CTD-2568A17.1,downstream_gene_variant,,ENST00000563228,; A ENST00000270590 Transcript missense_variant 1092/1269 955/1071 319/356 V/I Gtt/Att COSM1395558 1 1 GPR32 HGNC HGNC:4487 protein_coding YES CCDS12801.1 ENSP00000270590 O75388 H9NIL6 UPI000005045C NM_001506.2 tolerated(1) 1/1 Gene3D:1.20.1070.10,Prints_domain:PR00237,hmmpanther:PTHR24225,hmmpanther:PTHR24225:SF27,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 PASS rs879062227 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 50771555 50771555 G A 1 0 0 0 0 1 0 0 0 6572 1145 40 1 1 GPR32 19 50771555 Missense_Mutation SNP G C3N-02529_T 393718 50771555 7846061 99 29804 ZNF320 0 . GRCh38 19 52880998 52880998 + Missense_Mutation SNP C C G novel C3N-02529_T C3N-02529_N C C c.1128G>C p.Gln376His p.Q376H ENST00000595635 8/8 251 232 19 287 287 0 strelka-varscan-mutect ZNF320,missense_variant,p.Gln376His,ENST00000595635,;ZNF320,missense_variant,p.Gln376His,ENST00000391781,NM_207333.2;CTD-2331H12.8,missense_variant,p.Gln376His,ENST00000634278,;ZNF320,downstream_gene_variant,,ENST00000597091,;ZNF320,downstream_gene_variant,,ENST00000593618,;ZNF320,downstream_gene_variant,,ENST00000594741,;ZNF320,downstream_gene_variant,,ENST00000597265,;ZNF320,intron_variant,,ENST00000597909,;ZNF320,intron_variant,,ENST00000600930,;ZNF320,upstream_gene_variant,,ENST00000598199,; G ENST00000595635 Transcript missense_variant 1630/6448 1128/1530 376/509 Q/H caG/caC 1 -1 ZNF320 HGNC HGNC:13842 protein_coding YES CCDS33095.1 ENSP00000473091 A2RRD8 UPI00004EC06C tolerated(0.25) 8/8 PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF197,PROSITE_patterns:PS00028,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 102 52880998 52880998 C G 1 0 0 0 0 1 0 0 0 18414 912 32 4 4 ZNF320 19 52880998 Missense_Mutation SNP C C3N-02529_T 2109443 52880998 5736618 100 29805 CFAP61 0 . GRCh38 20 20164197 20164197 + Missense_Mutation SNP C C A novel C3N-02529_T C3N-02529_N C C c.1174C>A p.Leu392Met p.L392M ENST00000245957 11/27 172 159 13 114 114 0 strelka-mutect CFAP61,missense_variant,p.Leu392Met,ENST00000245957,NM_015585.3;CFAP61,missense_variant,p.Leu392Met,ENST00000377306,;CFAP61,missense_variant,p.Leu392Met,ENST00000451767,NM_001167816.1;CFAP61,missense_variant,p.Leu346Met,ENST00000340348,;CFAP61,intron_variant,,ENST00000442372,; A ENST00000245957 Transcript missense_variant 1250/4082 1174/3714 392/1237 L/M Ctg/Atg 1 1 CFAP61 HGNC HGNC:15872 protein_coding YES CCDS33447.1 ENSP00000245957 Q8NHU2 UPI0000206AE4 NM_015585.3 deleterious(0) 11/27 hmmpanther:PTHR21178,hmmpanther:PTHR21178:SF8 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -19.99995 1 1 1 1 0 A 3 1 102 20164197 20164197 C A 1 0 0 0 0 1 0 0 0 3028 796 28 2 2 CFAP61 20 20164197 Missense_Mutation SNP C C3N-02529_T 20164197 44279970 101 29806 MYH9 0 . GRCh38 22 36293864 36293864 + Splice_Site SNP C C T novel C3N-02529_T C3N-02529_N C C c.3838-1G>A p.X1280_splice ENST00000216181 253 226 27 223 223 0 strelka-varscan-mutect MYH9,splice_acceptor_variant,,ENST00000216181,NM_002473.5;MYH9,downstream_gene_variant,,ENST00000459960,; T ENST00000216181 Transcript splice_acceptor_variant -/7501 3838/5883 1280/1960 1 -1 MYH9 HGNC HGNC:7579 protein_coding YES CCDS13927.1 ENSP00000216181 P35579 A0A024R1N1 UPI000012FB80 NM_002473.5 28/40 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 5 4 102 36293864 36293864 C T 1 0 0 0 0 0 0 1 0 10042 695 24 3 3 MYH9 22 36293864 Splice_Site SNP C C3N-02529_T 36293864 14524604 102 29807 EP300 0 . GRCh38 22 41177007 41177007 + Nonsense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.5296C>T p.Gln1766Ter p.Q1766* ENST00000263253 31/31 470 419 51 453 453 0 strelka-varscan-mutect EP300,stop_gained,p.Gln1766Ter,ENST00000263253,NM_001429.3;EP300-AS1,intron_variant,,ENST00000420537,;RP1-85F18.6,intron_variant,,ENST00000415054,;EP300,downstream_gene_variant,,ENST00000635083,; T ENST00000263253 Transcript stop_gained 6515/9587 5296/7245 1766/2414 Q/* Cag/Tag 1 1 EP300 HGNC HGNC:3373 protein_coding YES CCDS14010.1 ENSP00000263253 Q09472 UPI00001AE876 NM_001429.3 31/31 PROSITE_profiles:PS50134,hmmpanther:PTHR13808:SF4,hmmpanther:PTHR13808,Pfam_domain:PF02135,Gene3D:1.20.1020.10,SMART_domains:SM00551,Superfamily_domains:SSF57933 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 102 41177007 41177007 C T 1 0 0 0 0 0 1 0 0 4994 711 25 3 3 EP300 22 41177007 Nonsense_Mutation SNP C C3N-02529_T 4883143 41177007 9641461 103 29808 TYMP 0 . GRCh38 22 50526460 50526460 + Nonsense_Mutation SNP C C T novel C3N-02529_T C3N-02529_N C C c.945G>A p.Trp315Ter p.W315* ENST00000395681 8/10 96 81 15 112 112 0 strelka-varscan-mutect TYMP,stop_gained,p.Trp315Ter,ENST00000252029,NM_001113756.2,NM_001257988.1,NM_001953.4,NM_001113755.2;TYMP,stop_gained,p.Trp315Ter,ENST00000395678,;TYMP,stop_gained,p.Trp315Ter,ENST00000395680,;TYMP,stop_gained,p.Trp315Ter,ENST00000395681,NM_001257989.1;TYMP,stop_gained,p.Trp282Ter,ENST00000425169,;NCAPH2,downstream_gene_variant,,ENST00000395701,;NCAPH2,downstream_gene_variant,,ENST00000420993,NM_152299.3;NCAPH2,downstream_gene_variant,,ENST00000299821,NM_001185011.1;SCO2,upstream_gene_variant,,ENST00000543927,NM_001169109.1;SCO2,upstream_gene_variant,,ENST00000535425,NM_001169110.1;SCO2,upstream_gene_variant,,ENST00000252785,NM_001169111.1;SCO2,upstream_gene_variant,,ENST00000395693,NM_005138.2;ODF3B,downstream_gene_variant,,ENST00000329363,NM_001014440.3;NCAPH2,downstream_gene_variant,,ENST00000523045,;ODF3B,downstream_gene_variant,,ENST00000405135,;ODF3B,downstream_gene_variant,,ENST00000401779,;ODF3B,downstream_gene_variant,,ENST00000428989,;ODF3B,downstream_gene_variant,,ENST00000403326,;NCAPH2,downstream_gene_variant,,ENST00000522304,;CTA-384D8.36,downstream_gene_variant,,ENST00000608319,;NCAPH2,downstream_gene_variant,,ENST00000520297,;TYMP,non_coding_transcript_exon_variant,,ENST00000487577,;TYMP,non_coding_transcript_exon_variant,,ENST00000476284,;TYMP,downstream_gene_variant,,ENST00000487162,;ODF3B,downstream_gene_variant,,ENST00000468249,;NCAPH2,downstream_gene_variant,,ENST00000522048,;ODF3B,downstream_gene_variant,,ENST00000463472,;ODF3B,downstream_gene_variant,,ENST00000469660,; T ENST00000395681 Transcript stop_gained 1067/1604 945/1464 315/487 W/* tgG/tgA 1 -1 TYMP HGNC HGNC:3148 protein_coding YES CCDS58811.1 ENSP00000379038 P19971 UPI000155D5D9 NM_001257989.1 8/10 Gene3D:3.40.1030.10,Pfam_domain:PF00591,PIRSF_domain:PIRSF000478,hmmpanther:PTHR10515,hmmpanther:PTHR10515:SF1,Superfamily_domains:SSF52418,TIGRFAM_domain:TIGR02644 HIGH 1 SNV 1 1 PASS rs1052593047 . 0 204 6 0 0 0 0 0 -20 0.9999999 1 1 1 0 T 4 4 102 50526460 50526460 C T 1 0 0 0 0 0 1 0 0 17326 740 26 3 3 TYMP 22 50526460 Nonsense_Mutation SNP C C3N-02529_T 9349453 50526460 292008 104 29809 SHANK3 0 . GRCh38 22 50730727 50730727 + Silent SNP C C T novel C3N-02529_T C3N-02529_N C C c.4608C>T p.= p.F1536F ENST00000262795 25/25 155 144 11 143 142 1 strelka-varscan-mutect SHANK3,synonymous_variant,p.=,ENST00000262795,;SHANK3,synonymous_variant,p.=,ENST00000445220,NM_033517.1;SHANK3,non_coding_transcript_exon_variant,,ENST00000414786,; T ENST00000262795 Transcript synonymous_variant 4608/7091 4608/5193 1536/1730 F ttC/ttT 1 1 SHANK3 HGNC HGNC:14294 protein_coding YES ENSP00000489147 A0A0U1RQS4 UPI00071AFB18 25/25 hmmpanther:PTHR24135:SF4,hmmpanther:PTHR24135 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 102 50730727 50730727 C T 1 0 0 0 0 0 0 0 1 14525 825 29 3 3 SHANK3 22 50730727 Silent SNP C C3N-02529_T 204267 50730727 87741 105 29810 P2RY8 0 . GRCh38 X 1465674 1465674 + Missense_Mutation SNP A A C novel C3N-02529_T C3N-02529_N A A c.885T>G p.Phe295Leu p.F295L ENST00000381297 2/2 421 399 22 416 416 0 strelka-varscan-mutect P2RY8,missense_variant,p.Phe295Leu,ENST00000381297,NM_178129.4;P2RY8,downstream_gene_variant,,ENST00000460672,; C ENST00000381297 Transcript missense_variant 1096/4198 885/1080 295/359 F/L ttT/ttG 1 -1 P2RY8 HGNC HGNC:15524 protein_coding YES CCDS14115.1 ENSP00000370697 Q86VZ1 UPI000000DA6D NM_178129.4 tolerated(0.09) 2/2 hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF25,Gene3D:1.20.1070.10,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 1465674 1465674 A C 1 0 0 0 0 1 0 0 0 11428 127 5 5 5 P2RY8 23 1465674 Missense_Mutation SNP A C3N-02529_T 1465674 154575221 106 29811 PPP4R3CP 0 . GRCh38 X 27462264 27462264 + Nonsense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.1033C>T p.Gln345Ter p.Q345* ENST00000412172 1/1 165 154 11 175 175 0 strelka-varscan-mutect PPP4R3CP,stop_gained,p.Gln345Ter,ENST00000412172,; A ENST00000412172 Transcript stop_gained 1078/3131 1033/2499 345/832 Q/* Cag/Tag 1 -1 PPP4R3CP HGNC HGNC:33146 protein_coding YES ENSP00000489770 UPI0000D61D3F 1/1 Pfam_domain:PF04802,hmmpanther:PTHR23318,hmmpanther:PTHR23318:SF5,Superfamily_domains:SSF48371 HIGH 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 102 27462264 27462264 G A 1 0 0 0 0 0 1 0 0 12529 1299 45 3 3 PPP4R3CP 23 27462264 Nonsense_Mutation SNP G C3N-02529_T 25996590 27462264 128578631 107 29812 ATP6AP2 0 . GRCh38 X 40599704 40599704 + Missense_Mutation SNP G G C novel C3N-02529_T C3N-02529_N G G c.701G>C p.Arg234Thr p.R234T ENST00000636580 7/9 564 510 54 555 555 0 strelka-varscan-mutect ATP6AP2,missense_variant,p.Arg234Thr,ENST00000636580,NM_005765.2;ATP6AP2,missense_variant,p.Arg234Thr,ENST00000378438,;ATP6AP2,missense_variant,p.Arg202Thr,ENST00000636409,;ATP6AP2,missense_variant,p.Arg158Thr,ENST00000637327,;ATP6AP2,missense_variant,p.Arg202Thr,ENST00000636287,;ATP6AP2,missense_variant,p.Arg158Thr,ENST00000636251,;ATP6AP2,missense_variant,p.Arg185Thr,ENST00000637526,;ATP6AP2,missense_variant,p.Arg80Thr,ENST00000637482,;ATP6AP2,missense_variant,p.Arg229Thr,ENST00000636196,;ATP6AP2,missense_variant,p.Arg215Thr,ENST00000638153,;ATP6AP2,missense_variant,p.Arg234Thr,ENST00000447485,;ATP6AP2,missense_variant,p.Arg126Thr,ENST00000636970,;ATP6AP2,missense_variant,p.Arg156Thr,ENST00000423649,;ATP6AP2,missense_variant,p.Arg218Thr,ENST00000637955,;ATP6AP2,missense_variant,p.Arg70Thr,ENST00000637614,;ATP6AP2,downstream_gene_variant,,ENST00000436783,;ATP6AP2,upstream_gene_variant,,ENST00000637165,;ATP6AP2,downstream_gene_variant,,ENST00000637930,;ATP6AP2,missense_variant,p.Arg234Thr,ENST00000636787,;ATP6AP2,3_prime_UTR_variant,,ENST00000636639,;ATP6AP2,3_prime_UTR_variant,,ENST00000636574,;ATP6AP2,3_prime_UTR_variant,,ENST00000635774,;ATP6AP2,3_prime_UTR_variant,,ENST00000635734,;ATP6AP2,3_prime_UTR_variant,,ENST00000486558,;ATP6AP2,non_coding_transcript_exon_variant,,ENST00000635829,;ATP6AP2,non_coding_transcript_exon_variant,,ENST00000637140,;ATP6AP2,non_coding_transcript_exon_variant,,ENST00000638046,;ATP6AP2,downstream_gene_variant,,ENST00000637793,;ATP6AP2,downstream_gene_variant,,ENST00000637019,;ATP6AP2,downstream_gene_variant,,ENST00000479120,; C ENST00000636580 Transcript missense_variant 892/2337 701/1053 234/350 R/T aGa/aCa 1 1 ATP6AP2 HGNC HGNC:18305 protein_coding YES CCDS14252.1 ENSP00000490083 UPI000006EC3F NM_005765.2 tolerated(0.24) 7/9 hmmpanther:PTHR13351 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 40599704 40599704 G C 1 0 0 0 0 1 0 0 0 1320 942 33 4 4 ATP6AP2 23 40599704 Missense_Mutation SNP G C3N-02529_T 13137440 40599704 115441191 108 29813 FAM120C 0 . GRCh38 X 54116725 54116725 + Missense_Mutation SNP G G C C3N-02529_T C3N-02529_N G G c.2132C>G p.Ser711Cys p.S711C ENST00000375180 10/16 392 372 20 306 306 0 strelka-mutect FAM120C,missense_variant,p.Ser711Cys,ENST00000375180,NM_017848.5;FAM120C,missense_variant,p.Ser711Cys,ENST00000328235,NM_001300788.1; C ENST00000375180 Transcript missense_variant 2189/8057 2132/3291 711/1096 S/C tCt/tGt COSM5587760 1 -1 FAM120C HGNC HGNC:16949 protein_coding YES CCDS14356.1 ENSP00000364324 Q9NX05 UPI00001D68ED NM_017848.5 deleterious(0.03) 10/16 hmmpanther:PTHR15976,hmmpanther:PTHR15976:SF15 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 102 54116725 54116725 G C 1 0 0 0 0 1 0 0 0 5275 942 33 4 4 FAM120C 23 54116725 Missense_Mutation SNP G C3N-02529_T 13517021 54116725 101924170 109 29814 ATP7A 0 . GRCh38 X 78040659 78040659 + Missense_Mutation SNP C C A novel C3N-02529_T C3N-02529_N C C c.3727C>A p.Leu1243Met p.L1243M ENST00000341514 19/23 307 289 18 351 351 0 strelka-varscan-mutect ATP7A,missense_variant,p.Leu1243Met,ENST00000341514,NM_000052.6;ATP7A,missense_variant,p.Leu1165Met,ENST00000343533,NM_001282224.1; A ENST00000341514 Transcript missense_variant 3882/8483 3727/4503 1243/1500 L/M Ctg/Atg 1 1 ATP7A HGNC HGNC:869 protein_coding YES CCDS35339.1 ENSP00000345728 Q04656 UPI000044D414 NM_000052.6 deleterious(0) 19/23 Gene3D:3.40.50.1000,Pfam_domain:PF00702,hmmpanther:PTHR24093,hmmpanther:PTHR24093:SF326,Superfamily_domains:SSF56784,TIGRFAM_domain:TIGR01494,TIGRFAM_domain:TIGR01525 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 78040659 78040659 C A 1 0 0 0 0 1 0 0 0 1343 912 32 2 2 ATP7A 23 78040659 Missense_Mutation SNP C C3N-02529_T 23923934 78040659 78000236 110 29815 LHFPL1 0 . GRCh38 X 112671040 112671040 + Silent SNP T T A novel C3N-02529_T C3N-02529_N T T c.351A>T p.= p.G117G ENST00000371968 2/4 106 81 25 121 121 0 strelka-varscan-mutect LHFPL1,synonymous_variant,p.=,ENST00000371968,NM_178175.3;LHFPL1,intron_variant,,ENST00000478229,; A ENST00000371968 Transcript synonymous_variant 591/1675 351/663 117/220 G ggA/ggT 1 -1 LHFPL1 HGNC HGNC:6587 protein_coding YES CCDS14562.1 ENSP00000361036 Q86WI0 UPI00000622AD NM_178175.3 2/4 hmmpanther:PTHR12489:SF15,hmmpanther:PTHR12489,Pfam_domain:PF10242 LOW 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 102 112671040 112671040 T A 1 0 0 0 0 0 0 0 1 8673 1654 58 4 4 LHFPL1 23 112671040 Silent SNP T C3N-02529_T 34630381 112671040 43369855 111 29816 FAM127B 0 . GRCh38 X 135052099 135052099 + Missense_Mutation SNP G G A rs374739071 C3N-02529_T C3N-02529_N G G c.10C>T p.Arg4Trp p.R4W ENST00000370775 1/1 72 62 10 102 102 0 strelka-varscan-mutect FAM127B,missense_variant,p.Arg4Trp,ENST00000370775,NM_001078172.1;FAM127B,non_coding_transcript_exon_variant,,ENST00000520964,;FAM127B,non_coding_transcript_exon_variant,,ENST00000522309,;FAM127B,upstream_gene_variant,,ENST00000518153,; A ENST00000370775 Transcript missense_variant 77/1244 10/342 4/113 R/W Cgg/Tgg rs374739071 1 -1 FAM127B HGNC HGNC:24514 protein_coding YES CCDS43998.1 ENSP00000375267 Q9BWD3 UPI0000140B18 NM_001078172.1 deleterious(0) 1/1 hmmpanther:PTHR15503:SF6,hmmpanther:PTHR15503,Pfam_domain:PF16297 MODERATE 1 SNV 1 PASS rs374739071 . 0 208 2 0 0 0 0 0 -19.99861 1 1 1 1 0 A 3 1 102 135052099 135052099 G A 1 0 0 0 0 1 0 0 0 5284 1057 37 1 1 FAM127B 23 135052099 Missense_Mutation SNP G C3N-02529_T 22381059 135052099 20988796 112 29817 PLXNB3 0 . GRCh38 X 153767621 153767621 + Missense_Mutation SNP G G A novel C3N-02529_T C3N-02529_N G G c.863G>A p.Arg288His p.R288H ENST00000538966 4/37 155 136 19 109 108 1 strelka-varscan-mutect PLXNB3,missense_variant,p.Arg288His,ENST00000538966,NM_001163257.1;PLXNB3,missense_variant,p.Arg265His,ENST00000361971,NM_005393.2;U52111.14,upstream_gene_variant,,ENST00000434284,;U52111.14,upstream_gene_variant,,ENST00000416854,; A ENST00000538966 Transcript missense_variant 1134/6377 863/5799 288/1932 R/H cGc/cAc 1 1 PLXNB3 HGNC HGNC:9105 protein_coding YES CCDS55536.1 ENSP00000442736 Q9ULL4 UPI0001AFF680 NM_001163257.1 deleterious(0) 4/37 Gene3D:2.130.10.10,Pfam_domain:PF01403,PROSITE_profiles:PS51004,hmmpanther:PTHR22625,hmmpanther:PTHR22625:SF33,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 102 153767621 153767621 G A 1 0 0 0 0 1 0 0 0 12231 1087 38 1 1 PLXNB3 23 153767621 Missense_Mutation SNP G C3N-02529_T 18715522 153767621 2273274 113 29818 SLC35E2B 0 . GRCh38 1 1675522 1675522 + Missense_Mutation SNP T T C novel C3N-02572_T C3N-02572_N T T c.527A>G p.Lys176Arg p.K176R ENST00000617444 5/10 79 74 5 68 68 0 varscan-mutect SLC35E2B,missense_variant,p.Lys176Arg,ENST00000617444,NM_001290264.1;SLC35E2B,missense_variant,p.Lys176Arg,ENST00000611123,NM_001110781.2;SLC35E2B,missense_variant,p.Lys176Arg,ENST00000614300,;RP11-345P4.6,downstream_gene_variant,,ENST00000596308,;SLC35E2B,non_coding_transcript_exon_variant,,ENST00000481276,;RP11-345P4.6,downstream_gene_variant,,ENST00000597891,; C ENST00000617444 Transcript missense_variant 1288/6283 527/1218 176/405 K/R aAg/aGg 1 -1 SLC35E2B HGNC HGNC:33941 protein_coding YES CCDS44041.1 ENSP00000481694 P0CK96 UPI00001B6AFE NM_001290264.1 deleterious(0.04) 5/10 Pfam_domain:PF03151,hmmpanther:PTHR11132,hmmpanther:PTHR11132:SF43 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -11.09376 0.9999996 1 1 1 0 C 3 2 103 1675522 1675522 T C 1 0 0 0 0 1 0 0 0 14856 1609 56 5 5 SLC35E2B 1 1675522 Missense_Mutation SNP T C3N-02572_T 1675522 247280900 1 29819 ERICH3 0 . GRCh38 1 74646685 74646685 + Missense_Mutation SNP A A C novel C3N-02572_T C3N-02572_N A A c.225T>G p.His75Gln p.H75Q ENST00000326665 3/15 71 66 5 149 149 0 varscan-mutect ERICH3,missense_variant,p.His75Gln,ENST00000326665,NM_001002912.4; C ENST00000326665 Transcript missense_variant 444/7159 225/4593 75/1530 H/Q caT/caG 1 -1 ERICH3 HGNC HGNC:25346 protein_coding YES CCDS30755.1 ENSP00000322609 Q5RHP9 UPI0000237200 NM_001002912.4 deleterious(0.04) 3/15 hmmpanther:PTHR23034 MODERATE 1 SNV 5 1 PASS . . 0 181 0 3 24 0 0 0 -2.617176 0 0 1 0 0 C 3 2 103 74646685 74646685 A C 1 0 0 0 0 1 0 0 0 5083 446 16 5 5 ERICH3 1 74646685 Missense_Mutation SNP A C3N-02572_T 72971163 74646685 174309737 2 29820 HMCN1 0 . GRCh38 1 186144221 186144221 + Missense_Mutation SNP G G C novel C3N-02572_T C3N-02572_N G G c.13973G>C p.Ser4658Thr p.S4658T ENST00000271588 90/107 53 33 20 62 62 0 strelka-varscan-mutect HMCN1,missense_variant,p.Ser4658Thr,ENST00000271588,NM_031935.2; C ENST00000271588 Transcript missense_variant 14202/18208 13973/16908 4658/5635 S/T aGt/aCt 1 1 HMCN1 HGNC HGNC:19194 protein_coding YES CCDS30956.1 ENSP00000271588 Q96RW7 UPI0000458C0E NM_031935.2 tolerated(1) 90/107 Gene3D:2.20.100.10,Pfam_domain:PF00090,PROSITE_profiles:PS50092,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF678,SMART_domains:SM00209,Superfamily_domains:SSF82895 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 103 186144221 186144221 G C 1 0 0 0 0 1 0 0 0 7111 1029 36 4 4 HMCN1 1 186144221 Missense_Mutation SNP G C3N-02572_T 111497536 186144221 62812201 3 29821 CHRM3 0 . GRCh38 1 239908426 239908426 + Missense_Mutation SNP G G T novel C3N-02572_T C3N-02572_N G G c.975G>T p.Glu325Asp p.E325D ENST00000255380 5/5 127 119 8 89 89 0 strelka-varscan CHRM3,missense_variant,p.Glu325Asp,ENST00000255380,NM_000740.2;CHRM3,missense_variant,p.Glu325Asp,ENST00000615928,;CHRM3,downstream_gene_variant,,ENST00000448020,; T ENST00000255380 Transcript missense_variant 1754/8780 975/1773 325/590 E/D gaG/gaT 1 1 CHRM3 HGNC HGNC:1952 protein_coding YES CCDS1616.1 ENSP00000255380 P20309 A0A024R3S2 UPI0000050453 NM_000740.2 tolerated(0.61) 5/5 Pfam_domain:PF00001,PROSITE_profiles:PS50262,SMART_domains:SM01381 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 103 239908426 239908426 G T 1 0 0 0 0 1 0 0 0 3138 962 34 2 2 CHRM3 1 239908426 Missense_Mutation SNP G C3N-02572_T 53764205 239908426 9047996 4 29822 ROCK2 0 . GRCh38 2 11215528 11215528 + Nonsense_Mutation SNP G G A novel C3N-02572_T C3N-02572_N G G c.1579C>T p.Arg527Ter p.R527* ENST00000315872 14/33 55 51 4 94 94 0 varscan-mutect ROCK2,stop_gained,p.Arg527Ter,ENST00000315872,NM_001321643.1,NM_004850.3;ROCK2,stop_gained,p.Arg284Ter,ENST00000401753,;ROCK2,5_prime_UTR_variant,,ENST00000616279,;ROCK2,3_prime_UTR_variant,,ENST00000261535,;ROCK2,downstream_gene_variant,,ENST00000484951,; A ENST00000315872 Transcript stop_gained 2028/8292 1579/4167 527/1388 R/* Cga/Tga 1 -1 ROCK2 HGNC HGNC:10252 protein_coding YES CCDS42654.1 ENSP00000317985 O75116 UPI000034ECB0 NM_001321643.1,NM_004850.3 14/33 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR22988,hmmpanther:PTHR22988:SF28,PIRSF_domain:PIRSF037568 HIGH 1 SNV 1 1 PASS . . 0 195 3 5 7 0 0 0 -3.058936 0.06904941 1 1 0 0 A 4 1 103 11215528 11215528 G A 1 0 0 0 0 0 1 0 0 13696 1153 40 1 1 ROCK2 2 11215528 Nonsense_Mutation SNP G C3N-02572_T 11215528 230978001 5 29823 ESPNL 0 . GRCh38 2 238107805 238107805 + Missense_Mutation SNP C C A novel C3N-02572_T C3N-02572_N C C c.687C>A p.Asp229Glu p.D229E ENST00000343063 4/9 118 111 7 65 65 0 strelka-varscan ESPNL,missense_variant,p.Asp229Glu,ENST00000343063,NM_194312.2;ESPNL,missense_variant,p.Asp229Glu,ENST00000409169,;ESPNL,upstream_gene_variant,,ENST00000612395,; A ENST00000343063 Transcript missense_variant 950/4836 687/3018 229/1005 D/E gaC/gaA 1 1 ESPNL HGNC HGNC:27937 protein_coding YES CCDS2525.1 ENSP00000339115 Q6ZVH7 UPI000022BC90 NM_194312.2 deleterious(0.02) 4/9 PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24153:SF0,hmmpanther:PTHR24153,Pfam_domain:PF12796,Gene3D:1.25.40.20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -13.86855 1 1 1 1 0 A 3 1 103 238107805 238107805 C A 1 0 0 0 0 1 0 0 0 5117 477 17 2 2 ESPNL 2 238107805 Missense_Mutation SNP C C3N-02572_T 226892277 238107805 4085724 6 29824 LRRIQ4 0 . GRCh38 3 169822327 169822327 + Missense_Mutation SNP G G A rs747187885,rs758532964 C3N-02572_T C3N-02572_N G G c.406G>A p.Val136Ile p.V136I ENST00000340806 1/5 106 93 13 97 97 0 strelka-varscan-mutect LRRIQ4,missense_variant,p.Val136Ile,ENST00000340806,NM_001080460.1; A ENST00000340806 Transcript missense_variant 406/1827 406/1683 136/560 V/I Gtc/Atc rs747187885,rs758532964,COSM5570702 1 1 LRRIQ4 HGNC HGNC:34298 protein_coding YES CCDS46951.1 ENSP00000342188 A6NIV6 UPI0000197671 NM_001080460.1 tolerated(0.18) 1/5 Gene3D:3.80.10.10,Pfam_domain:PF13855,PROSITE_profiles:PS51450,SMART_domains:SM00369,Superfamily_domains:SSF52058 0,0,1 MODERATE 1 SNV 5 0,0,1 1 PASS rs747187885 . 0 204 3 3 0 0 0 0 -19.78506 0.9998785 1 1 1 0 A 3 1 103 169822327 169822327 G A 1 0 0 0 0 1 0 0 0 8937 1145 40 1 1 LRRIQ4 3 169822327 Missense_Mutation SNP G C3N-02572_T 169822327 28473232 7 29825 C4orf50 0 . GRCh38 4 5988823 5988823 + Missense_Mutation SNP C C T rs537996369 C3N-02572_T C3N-02572_N C C c.3223G>A p.Val1075Met p.V1075M ENST00000531445 6/12 332 315 17 265 265 0 strelka-varscan-mutect C4orf50,missense_variant,p.Val1075Met,ENST00000531445,;C4orf50,5_prime_UTR_variant,,ENST00000324058,; T ENST00000531445 Transcript missense_variant 3299/6860 3223/4527 1075/1508 V/M Gtg/Atg rs537996369 1 -1 C4orf50 HGNC HGNC:33766 protein_coding YES ENSP00000437121 E9PNW5 deleterious(0.01) 6/12 hmmpanther:PTHR36866 MODERATE 1 SNV 1 1 PASS rs537996369 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 103 5988823 5988823 C T 1 0 0 0 0 1 0 0 0 2089 536 19 1 1 C4orf50 4 5988823 Missense_Mutation SNP C C3N-02572_T 5988823 184225732 8 29826 TMPRSS11B 0 . GRCh38 4 68234477 68234477 + Missense_Mutation SNP G G A C3N-02572_T C3N-02572_N G G c.455C>T p.Ser152Phe p.S152F ENST00000332644 5/10 87 69 18 113 113 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Ser152Phe,ENST00000332644,NM_182502.3;TMPRSS11B,non_coding_transcript_exon_variant,,ENST00000502365,;TMPRSS11B,upstream_gene_variant,,ENST00000510856,; A ENST00000332644 Transcript missense_variant 617/2671 455/1251 152/416 S/F tCc/tTc COSM734949 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 deleterious(0) 5/10 PROSITE_profiles:PS50024,PIRSF_domain:PIRSF037941,Superfamily_domains:0047452 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 68234477 68234477 G A 1 0 0 0 0 1 0 0 0 16716 1174 41 3 3 TMPRSS11B 4 68234477 Missense_Mutation SNP G C3N-02572_T 62245654 68234477 121980078 9 29827 103 2 1 29 3 2 63 N G 9.033783e-05 TMPRSS11B 0 . GRCh38 4 68234484 68234484 + Missense_Mutation SNP G G A novel C3N-02572_T C3N-02572_N G G c.448C>T p.Pro150Ser p.P150S ENST00000332644 5/10 101 79 22 128 128 0 strelka-varscan-mutect TMPRSS11B,missense_variant,p.Pro150Ser,ENST00000332644,NM_182502.3;TMPRSS11B,non_coding_transcript_exon_variant,,ENST00000502365,;TMPRSS11B,upstream_gene_variant,,ENST00000510856,; A ENST00000332644 Transcript missense_variant 610/2671 448/1251 150/416 P/S Cct/Tct 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 tolerated(0.28) 5/10 PROSITE_profiles:PS50024,PIRSF_domain:PIRSF037941,Superfamily_domains:0047452 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 68234484 68234484 G A 1 0 0 0 0 1 0 0 0 16716 1174 41 3 3 TMPRSS11B 4 68234484 Missense_Mutation SNP G C3N-02572_T 7 68234484 121980071 10 29828 103 2 1 29 3 2 63 N G 9.033783e-05 TMPRSS11B 0 . GRCh38 4 68234539 68234539 + Silent SNP G G A novel C3N-02572_T C3N-02572_N G G c.393C>T p.= p.I131I ENST00000332644 5/10 167 130 37 260 260 0 strelka-varscan-mutect TMPRSS11B,synonymous_variant,p.=,ENST00000332644,NM_182502.3;TMPRSS11B,non_coding_transcript_exon_variant,,ENST00000502365,;TMPRSS11B,upstream_gene_variant,,ENST00000510856,; A ENST00000332644 Transcript synonymous_variant 555/2671 393/1251 131/416 I atC/atT 1 -1 TMPRSS11B HGNC HGNC:25398 protein_coding YES CCDS3521.1 ENSP00000330475 Q86T26 UPI000013E249 NM_182502.3 5/10 PROSITE_profiles:PS50024,Pfam_domain:PF01390,PIRSF_domain:PIRSF037941,Gene3D:1ivzA00,Superfamily_domains:0047452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 103 68234539 68234539 G A 1 0 0 0 0 0 0 0 1 16716 1280 45 3 3 TMPRSS11B 4 68234539 Silent SNP G C3N-02572_T 55 68234539 121980016 11 29829 1 29 3 2 63 N G 9.033783e-05 UGT2B4 0 . GRCh38 4 69495234 69495234 + Frame_Shift_Del DEL T T - novel C3N-02572_T C3N-02572_N T T c.628delA p.Arg210GlyfsTer2 p.R210Gfs*2 ENST00000305107 1/6 25 19 6 65 65 0 sindel-varindel-pindel UGT2B4,frameshift_variant,p.Arg210GlyfsTer2,ENST00000305107,NM_021139.2;UGT2B4,frameshift_variant,p.Arg210GlyfsTer2,ENST00000512583,NM_001297615.1;UGT2B4,downstream_gene_variant,,ENST00000510114,;UGT2B4,non_coding_transcript_exon_variant,,ENST00000502655,;UGT2B4,intron_variant,,ENST00000506580,;UGT2B4,intron_variant,,ENST00000503836,; - ENST00000305107 Transcript frameshift_variant 675/2103 628/1587 210/528 R/X Agg/gg 1 -1 UGT2B4 HGNC HGNC:12553 protein_coding YES CCDS43234.1 ENSP00000305221 P06133 UPI000000087F NM_021139.2 1/6 hmmpanther:PTHR11926,hmmpanther:PTHR11926:SF198,Pfam_domain:PF00201,Superfamily_domains:SSF53756 HIGH 1 deletion 1 1 PASS . . 0 190 19 0 0 0 0 0 -16.23252 0.9990224 1 1 1 0 - 7 5 103 69495234 69495234 T - 1 0 1 0 1 0 0 0 0 17485 1550 54 0 0 UGT2B4 4 69495234 Frame_Shift_Del DEL T C3N-02572_T 1260695 69495234 120719321 12 29830 FNDC1 0 . GRCh38 6 159233306 159233306 + Missense_Mutation SNP A A T novel C3N-02572_T C3N-02572_N A A c.2794A>T p.Thr932Ser p.T932S ENST00000297267 11/23 373 338 35 230 230 0 strelka-varscan-mutect FNDC1,missense_variant,p.Thr932Ser,ENST00000297267,NM_032532.2;FNDC1,missense_variant,p.Thr828Ser,ENST00000329629,; T ENST00000297267 Transcript missense_variant 2994/6552 2794/5685 932/1894 T/S Aca/Tca 1 1 FNDC1 HGNC HGNC:21184 protein_coding YES CCDS47512.1 ENSP00000297267 Q4ZHG4 UPI0000579B80 NM_032532.2 tolerated_low_confidence(0.33) 11/23 hmmpanther:PTHR23197,hmmpanther:PTHR23197:SF8 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 103 159233306 159233306 A T 1 0 0 0 0 1 0 0 0 5824 159 6 4 4 FNDC1 6 159233306 Missense_Mutation SNP A C3N-02572_T 159233306 11572673 13 29831 ETV1 0 . GRCh38 7 13909636 13909636 + Silent SNP G G A rs765227604 C3N-02572_T C3N-02572_N G G c.936C>T p.= p.F312F ENST00000430479 11/14 121 111 10 158 158 0 strelka-varscan ETV1,synonymous_variant,p.=,ENST00000430479,NM_004956.4;ETV1,synonymous_variant,p.=,ENST00000242066,NM_001163148.1;ETV1,synonymous_variant,p.=,ENST00000420159,NM_001163151.1;ETV1,synonymous_variant,p.=,ENST00000399357,NM_001163152.1;ETV1,synonymous_variant,p.=,ENST00000405192,NM_001163147.1;ETV1,synonymous_variant,p.=,ENST00000405358,;ETV1,synonymous_variant,p.=,ENST00000405218,;ETV1,synonymous_variant,p.=,ENST00000403527,NM_001163150.1;ETV1,synonymous_variant,p.=,ENST00000403685,NM_001163149.1;ETV1,synonymous_variant,p.=,ENST00000438956,;ETV1,downstream_gene_variant,,ENST00000443608,;ETV1,downstream_gene_variant,,ENST00000476720,;ETV1,synonymous_variant,p.=,ENST00000443137,;ETV1,non_coding_transcript_exon_variant,,ENST00000472931,;ETV1,upstream_gene_variant,,ENST00000493831,; A ENST00000430479 Transcript synonymous_variant 1604/6740 936/1434 312/477 F ttC/ttT rs765227604,COSM1086161,COSM1596796 1 -1 ETV1 HGNC HGNC:3490 protein_coding YES CCDS55088.1 ENSP00000405327 P50549 UPI000012A26E NM_004956.4 11/14 Gene3D:1.10.10.10,Pfam_domain:PF04621,hmmpanther:PTHR11849,hmmpanther:PTHR11849:SF210 0,1,1 LOW 1 SNV 1 0,1,1 1 PASS . . 0 205 0 3 0 0 0 0 -14.58223 0.9999762 1 1 1 0 A 2 1 103 13909636 13909636 G A 1 0 0 0 0 0 0 0 1 5141 1072 37 1 1 ETV1 7 13909636 Silent SNP G C3N-02572_T 13909636 145436337 14 29832 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02572_T C3N-02572_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 618 390 228 380 380 0 strelka-varscan EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 103 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02572_T 41282186 55191822 104154151 15 29833 TRRAP 0 . GRCh38 7 98933379 98933379 + Nonsense_Mutation SNP G G T novel C3N-02572_T C3N-02572_N G G c.3991G>T p.Glu1331Ter p.E1331* ENST00000359863 27/72 151 143 8 92 92 0 strelka-varscan TRRAP,stop_gained,p.Glu1331Ter,ENST00000359863,NM_001244580.1;TRRAP,stop_gained,p.Glu1330Ter,ENST00000628380,;TRRAP,stop_gained,p.Glu1331Ter,ENST00000355540,NM_003496.3;TRRAP,stop_gained,p.Glu1330Ter,ENST00000446306,;TRRAP,stop_gained,p.Glu1046Ter,ENST00000456197,; T ENST00000359863 Transcript stop_gained 4200/12677 3991/11580 1331/3859 E/* Gag/Tag 1 1 TRRAP HGNC HGNC:12347 protein_coding YES CCDS59066.1 ENSP00000352925 Q9Y4A5 UPI00004575B4 NM_001244580.1 27/72 hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF1 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 103 98933379 98933379 G T 1 0 0 0 0 0 1 0 0 17107 1175 41 2 2 TRRAP 7 98933379 Nonsense_Mutation SNP G C3N-02572_T 43741557 98933379 60412594 16 29834 TJP2 0 . GRCh38 9 69205220 69205220 + Missense_Mutation SNP G G C novel C3N-02572_T C3N-02572_N G G c.59G>C p.Arg20Thr p.R20T ENST00000539225 1/23 201 190 11 197 197 0 strelka-mutect TJP2,missense_variant,p.Arg20Thr,ENST00000535702,NM_001170415.1;TJP2,missense_variant,p.Arg20Thr,ENST00000539225,NM_001170416.1;TJP2,intron_variant,,ENST00000636438,;TJP2,intron_variant,,ENST00000377245,NM_004817.3;TJP2,intron_variant,,ENST00000453658,NM_001170414.2;TJP2,intron_variant,,ENST00000348208,NM_201629.3;AL358113.1,intron_variant,,ENST00000265384,NM_001170630.1;TJP2,intron_variant,,ENST00000423935,;TJP2,intron_variant,,ENST00000606364,;TJP2,intron_variant,,ENST00000636247,;TJP2,intron_variant,,ENST00000377259,; C ENST00000539225 Transcript missense_variant 59/3838 59/3666 20/1221 R/T aGa/aCa 1 1 TJP2 HGNC HGNC:11828 protein_coding YES CCDS55316.1 ENSP00000438262 Q9UDY2 UPI0001C0B37F NM_001170416.1 tolerated_low_confidence(0.68) 1/23 MODERATE SNV 2 1 PASS rs1200954763 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 103 69205220 69205220 G C 1 0 0 0 0 1 0 0 0 16372 942 33 4 4 TJP2 9 69205220 Missense_Mutation SNP G C3N-02572_T 69205220 69189497 17 29835 ABHD17B 0 . GRCh38 9 71866990 71866991 + Frame_Shift_Ins INS - - A novel C3N-02572_T C3N-02572_N - - c.663dupT p.Lys222Ter p.K222* ENST00000377041 4/5 90 70 20 139 139 0 sindel-varindel-pindel ABHD17B,frameshift_variant,p.Lys222Ter,ENST00000333421,NM_001025780.1;ABHD17B,frameshift_variant,p.Lys222Ter,ENST00000377041,NM_016014.2; A ENST00000377041 Transcript frameshift_variant 964-965/1312 663-664/882 221-222/293 -/X -/T 1 -1 ABHD17B HGNC HGNC:24278 protein_coding YES CCDS35042.1 ENSP00000366240 Q5VST6 UPI0000210B1F NM_016014.2 4/5 Gene3D:3.40.50.1820,hmmpanther:PTHR12277,hmmpanther:PTHR12277:SF48,Superfamily_domains:SSF53474 HIGH 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 103 71866990 71866990 - A 1 0 1 1 0 0 0 0 0 89 1763 61 0 0 ABHD17B 9 71866990 Frame_Shift_Ins INS - C3N-02572_T 2661770 71866990 66527727 18 29836 SECISBP2 0 . GRCh38 9 89358012 89358012 + Missense_Mutation SNP A A G novel C3N-02572_T C3N-02572_N A A c.2282A>G p.Lys761Arg p.K761R ENST00000375807 16/17 687 603 84 410 409 1 strelka-varscan-mutect SECISBP2,missense_variant,p.Lys693Arg,ENST00000534113,NM_001282690.1;SECISBP2,missense_variant,p.Lys761Arg,ENST00000375807,NM_001282688.1,NM_024077.4;SECISBP2,missense_variant,p.Lys688Arg,ENST00000339901,NM_001282689.1;SEMA4D,downstream_gene_variant,,ENST00000420987,NM_001142287.1;SEMA4D,downstream_gene_variant,,ENST00000339861,;SEMA4D,downstream_gene_variant,,ENST00000455551,;SEMA4D,downstream_gene_variant,,ENST00000420101,;SECISBP2,non_coding_transcript_exon_variant,,ENST00000496597,;SECISBP2,non_coding_transcript_exon_variant,,ENST00000498819,;SEMA4D,downstream_gene_variant,,ENST00000469653,;SEMA4D,downstream_gene_variant,,ENST00000475255,;SEMA4D,downstream_gene_variant,,ENST00000429836,;SEMA4D,downstream_gene_variant,,ENST00000537934,;SEMA4D,downstream_gene_variant,,ENST00000492386,; G ENST00000375807 Transcript missense_variant 2353/3462 2282/2565 761/854 K/R aAg/aGg 1 1 SECISBP2 HGNC HGNC:30972 protein_coding YES CCDS6683.1 ENSP00000364965 Q96T21 UPI00001AEA0A NM_001282688.1,NM_024077.4 tolerated(0.63) 16/17 hmmpanther:PTHR13284,hmmpanther:PTHR13284:SF9,Gene3D:3.30.1330.30,Superfamily_domains:SSF55315 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 103 89358012 89358012 A G 1 0 0 0 0 1 0 0 0 14283 72 3 5 5 SECISBP2 9 89358012 Missense_Mutation SNP A C3N-02572_T 17491022 89358012 49036705 19 29837 CCDC183 0 . GRCh38 9 136799217 136799217 + Silent SNP C C T novel C3N-02572_T C3N-02572_N C C c.186C>T p.= p.A62A ENST00000338005 2/14 84 79 5 55 55 0 strelka-mutect CCDC183,synonymous_variant,p.=,ENST00000338005,NM_001039374.4;CCDC183-AS1,downstream_gene_variant,,ENST00000414656,;CCDC183,non_coding_transcript_exon_variant,,ENST00000371682,;CCDC183,synonymous_variant,p.=,ENST00000479371,;RP11-216L13.17,3_prime_UTR_variant,,ENST00000456614,;RP11-216L13.19,upstream_gene_variant,,ENST00000415992,;CCDC183,upstream_gene_variant,,ENST00000430612,;CCDC183,upstream_gene_variant,,ENST00000481601,;CCDC183,upstream_gene_variant,,ENST00000609471,;RP11-216L13.18,upstream_gene_variant,,ENST00000471502,; T ENST00000338005 Transcript synonymous_variant 221/1671 186/1605 62/534 A gcC/gcT 1 1 CCDC183 HGNC HGNC:28236 protein_coding YES CCDS43906.1 ENSP00000338013 Q5T5S1 UPI00015E02CD NM_001039374.4 2/14 hmmpanther:PTHR21694,hmmpanther:PTHR21694:SF16 LOW 1 SNV 1 1 PASS rs776454199 . 0 204 6 0 0 0 0 0 -10.93264 0.9999995 1 1 1 0 T 2 4 103 136799217 136799217 C T 1 0 0 0 0 0 0 0 1 2499 581 21 3 3 CCDC183 9 136799217 Silent SNP C C3N-02572_T 47441205 136799217 1595500 20 29838 CACNA1B 0 . GRCh38 9 138118755 138118755 + Missense_Mutation SNP C C T rs202011106 C3N-02572_T C3N-02572_N C C c.6017C>T p.Ala2006Val p.A2006V ENST00000371372 44/47 185 167 18 120 120 0 strelka-varscan-mutect CACNA1B,missense_variant,p.Ala2006Val,ENST00000371372,NM_000718.3;CACNA1B,missense_variant,p.Ala2004Val,ENST00000371363,;CACNA1B,missense_variant,p.Ala2007Val,ENST00000371355,;CACNA1B,missense_variant,p.Ala2005Val,ENST00000371357,;CACNA1B,missense_variant,p.Ala2006Val,ENST00000277549,;CACNA1B,missense_variant,p.Ala2006Val,ENST00000277551,NM_001243812.1; T ENST00000371372 Transcript missense_variant 6162/9790 6017/7020 2006/2339 A/V gCg/gTg rs202011106,COSM3089979,COSM4372840 1 1 CACNA1B HGNC HGNC:1389 protein_coding YES CCDS59522.1 ENSP00000360423 Q00975 UPI0000127267 NM_000718.3 tolerated(0.11) 44/47 hmmpanther:PTHR10037,hmmpanther:PTHR10037:SF161 0,1,1 MODERATE 1 SNV 5 0,1,1 1 PASS rs202011106 . 0 207 0 3 0 0 0 0 -19.99998 0.9999845 1 1 1 0 T 3 4 103 138118755 138118755 C T 1 0 0 0 0 1 0 0 0 2227 768 27 1 1 CACNA1B 9 138118755 Missense_Mutation SNP C C3N-02572_T 1319538 138118755 275962 21 29839 EBLN1 0 . GRCh38 10 22208993 22208993 + Missense_Mutation SNP T T A novel C3N-02572_T C3N-02572_N T T c.991A>T p.Thr331Ser p.T331S ENST00000422359 1/1 104 93 11 186 186 0 strelka-varscan-mutect EBLN1,missense_variant,p.Thr331Ser,ENST00000422359,NM_001199938.1; A ENST00000422359 Transcript missense_variant 1029/1208 991/1101 331/366 T/S Aca/Tca 1 -1 EBLN1 HGNC HGNC:39430 protein_coding YES CCDS60498.1 ENSP00000473842 P0CF75 UPI0000199CEF NM_001199938.1 tolerated_low_confidence(0.56) 1/1 Gene3D:1n93X02,Pfam_domain:PF06407,Superfamily_domains:0041272 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 22208993 22208993 T A 1 0 0 0 0 1 0 0 0 4709 1638 57 4 4 EBLN1 10 22208993 Missense_Mutation SNP T C3N-02572_T 22208993 111588429 22 29840 OR5T3 0 . GRCh38 11 56252751 56252751 + Silent SNP A A G C3N-02572_T C3N-02572_N A A c.552A>G p.= p.L184L ENST00000303059 1/1 78 69 9 189 189 0 strelka-varscan-mutect OR5T3,synonymous_variant,p.=,ENST00000303059,NM_001004747.1; G ENST00000303059 Transcript synonymous_variant 552/1023 552/1023 184/340 L ttA/ttG COSM5144313 1 1 OR5T3 HGNC HGNC:15297 protein_coding YES CCDS31524.1 ENSP00000305403 Q8NGG3 UPI0000061E96 NM_001004747.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,PROSITE_profiles:PS50262,hmmpanther:PTHR24247,hmmpanther:PTHR24247:SF87,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 1 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 103 56252751 56252751 A G 1 0 0 0 0 0 0 0 1 11251 388 14 5 5 OR5T3 11 56252751 Silent SNP A C3N-02572_T 56252751 78833871 23 29841 ACY3 0 . GRCh38 11 67645758 67645758 + Missense_Mutation SNP C C G novel C3N-02572_T C3N-02572_N C C c.366G>C p.Met122Ile p.M122I ENST00000255082 4/8 188 171 17 112 112 0 strelka-varscan-mutect ACY3,start_lost,p.Met1?,ENST00000529256,;ACY3,missense_variant,p.Met122Ile,ENST00000255082,NM_080658.1; G ENST00000255082 Transcript missense_variant 537/1300 366/960 122/319 M/I atG/atC 1 -1 ACY3 HGNC HGNC:24104 protein_coding YES CCDS8175.1 ENSP00000255082 Q96HD9 A0A024R5L2 UPI0000073C5C NM_080658.1 deleterious(0.01) 4/8 HAMAP:MF_00704,hmmpanther:PTHR15162:SF5,hmmpanther:PTHR15162,Pfam_domain:PF04952,PIRSF_domain:PIRSF018001,Gene3D:3.40.630.10,Superfamily_domains:SSF53187 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 103 67645758 67645758 C G 1 0 0 0 0 1 0 0 0 271 594 21 4 4 ACY3 11 67645758 Missense_Mutation SNP C C3N-02572_T 11393007 67645758 67440864 24 29842 CRACR2A 0 . GRCh38 12 3696985 3696985 + Missense_Mutation SNP G G T rs148897271 C3N-02572_T C3N-02572_N G G c.15C>A p.Asp5Glu p.D5E ENST00000440314 4/20 180 168 12 111 111 0 strelka-varscan-mutect CRACR2A,missense_variant,p.Asp5Glu,ENST00000440314,NM_001144958.1;CRACR2A,missense_variant,p.Asp5Glu,ENST00000252322,NM_032680.3; T ENST00000440314 Transcript missense_variant 489/2697 15/2196 5/731 D/E gaC/gaA rs148897271 1 -1 CRACR2A HGNC HGNC:28657 protein_coding YES CCDS44803.1 ENSP00000409382 Q9BSW2 UPI00017A8807 NM_001144958.1 tolerated_low_confidence(0.24) 4/20 hmmpanther:PTHR22621:SF2,hmmpanther:PTHR22621 MODERATE 1 SNV 2 1 PASS rs148897271 . 0 208 0 2 0 0 0 0 -15.65796 0.9999996 1 1 1 0 T 3 4 103 3696985 3696985 G T 1 0 0 0 0 1 0 0 0 3643 1136 40 1 1 CRACR2A 12 3696985 Missense_Mutation SNP G C3N-02572_T 3696985 129578324 25 29843 RB1 0 . GRCh38 13 48476728 48476728 + Nonsense_Mutation SNP C C T C3N-02572_T C3N-02572_N C C c.2548C>T p.Gln850Ter p.Q850* ENST00000267163 25/27 80 71 9 230 227 3 strelka-varscan-mutect RB1,stop_gained,p.Gln850Ter,ENST00000267163,NM_000321.2;RB1,non_coding_transcript_exon_variant,,ENST00000484879,;RB1,non_coding_transcript_exon_variant,,ENST00000531171,; T ENST00000267163 Transcript stop_gained 2686/4840 2548/2787 850/928 Q/* Cag/Tag COSM1300235,COSM13404 1 1 RB1 HGNC HGNC:9884 protein_coding YES CCDS31973.1 ENSP00000267163 P06400 A0A024RDV3 UPI0000001C79 NM_000321.2 25/27 Pfam_domain:PF08934,hmmpanther:PTHR13742,hmmpanther:PTHR13742:SF21,SMART_domains:SM01369 1,1 HIGH 1 SNV 1 1,1 1 PASS rs886042935 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 103 48476728 48476728 C T 1 0 0 0 0 0 1 0 0 13259 827 29 3 3 RB1 13 48476728 Nonsense_Mutation SNP C C3N-02572_T 48476728 65887600 26 29844 DCT 0 . GRCh38 13 94478978 94478978 + Missense_Mutation SNP C C A rs151208955 C3N-02572_T C3N-02572_N C C c.278G>T p.Arg93Leu p.R93L ENST00000446125 1/10 142 132 10 62 62 0 strelka-varscan-mutect DCT,missense_variant,p.Arg93Leu,ENST00000377028,NM_001922.3;DCT,missense_variant,p.Arg93Leu,ENST00000446125,NM_001129889.1;DCT,non_coding_transcript_exon_variant,,ENST00000472871,; A ENST00000446125 Transcript missense_variant 705/2395 278/1659 93/552 R/L cGg/cTg rs151208955 1 -1 DCT HGNC HGNC:2709 protein_coding YES CCDS45060.1 ENSP00000392762 P40126 UPI0000E13F02 NM_001129889.1 deleterious(0) 1/10 Gene3D:1.10.1280.10,hmmpanther:PTHR11474,hmmpanther:PTHR11474:SF4,Superfamily_domains:SSF48056 MODERATE 1 SNV 1 1 PASS rs151208955 . 0 199 8 0 0 0 0 2 -6.899546 0 0 1 0 0 A 3 1 103 94478978 94478978 C A 1 0 0 0 0 1 0 0 0 4107 652 23 1 1 DCT 13 94478978 Missense_Mutation SNP C C3N-02572_T 46002250 94478978 19885350 27 29845 TUBGCP3 0 . GRCh38 13 112527377 112527377 + Silent SNP C C T novel C3N-02572_T C3N-02572_N C C c.1443G>A p.= p.R481R ENST00000261965 12/22 37 32 5 35 35 0 varscan-mutect TUBGCP3,synonymous_variant,p.=,ENST00000261965,NM_006322.5,NM_001286277.1;TUBGCP3,synonymous_variant,p.=,ENST00000375669,NM_001286278.1;TUBGCP3,non_coding_transcript_exon_variant,,ENST00000462580,; T ENST00000261965 Transcript synonymous_variant 1630/3899 1443/2724 481/907 R agG/agA 1 -1 TUBGCP3 HGNC HGNC:18598 protein_coding YES CCDS9525.1 ENSP00000261965 Q96CW5 UPI000000DB88 NM_006322.5,NM_001286277.1 12/22 Pfam_domain:PF04130,hmmpanther:PTHR19302,hmmpanther:PTHR19302:SF14 LOW 1 SNV 1 1 PASS . . 0 201 9 0 0 0 0 0 -12.93887 0.9999922 1 1 1 0 T 2 4 103 112527377 112527377 C T 1 0 0 0 0 0 0 0 1 17277 869 30 3 3 TUBGCP3 13 112527377 Silent SNP C C3N-02572_T 18048399 112527377 1836951 28 29846 UNC13C 0 . GRCh38 15 54015624 54015624 + Silent SNP C C T novel C3N-02572_T C3N-02572_N C C c.2721C>T p.= p.H907H ENST00000260323 1/32 38 27 11 99 99 0 strelka-varscan-mutect UNC13C,synonymous_variant,p.=,ENST00000260323,NM_001080534.1; T ENST00000260323 Transcript synonymous_variant 2721/12946 2721/6645 907/2214 H caC/caT 1 1 UNC13C HGNC HGNC:23149 protein_coding YES CCDS45264.1 ENSP00000260323 Q8NB66 UPI0000DD82AB NM_001080534.1 1/32 hmmpanther:PTHR10480,hmmpanther:PTHR10480:SF2 LOW 1 SNV 5 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 103 54015624 54015624 C T 1 0 0 0 0 0 0 0 1 17510 506 18 3 3 UNC13C 15 54015624 Silent SNP C C3N-02572_T 54015624 47975565 29 29847 FSD2 0 . GRCh38 15 82782944 82782944 + Missense_Mutation SNP T T C novel C3N-02572_T C3N-02572_N T T c.817A>G p.Lys273Glu p.K273E ENST00000334574 4/13 150 118 32 254 253 1 strelka-varscan-mutect FSD2,missense_variant,p.Lys273Glu,ENST00000334574,NM_001007122.3;FSD2,missense_variant,p.Lys273Glu,ENST00000541889,NM_001281806.1,NM_001281805.1;FSD2,downstream_gene_variant,,ENST00000561368,; C ENST00000334574 Transcript missense_variant 999/6418 817/2250 273/749 K/E Aaa/Gaa 1 -1 FSD2 HGNC HGNC:18024 protein_coding YES CCDS45332.1 ENSP00000335651 A1L4K1 UPI0000161097 NM_001007122.3 deleterious(0) 4/13 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24099,hmmpanther:PTHR24099:SF6 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 103 82782944 82782944 T C 1 0 0 0 0 1 0 0 0 5945 1850 64 5 5 FSD2 15 82782944 Missense_Mutation SNP T C3N-02572_T 28767320 82782944 19208245 30 29848 ABCA3 0 . GRCh38 16 2308543 2308544 + In_Frame_Ins INS - - GTT novel C3N-02572_T C3N-02572_N - - c.1189_1191dupAAC p.Asn397dup p.N397dup ENST00000301732 11/33 452 253 199 350 350 0 sindel-varindel-pindel ABCA3,inframe_insertion,p.Asn397dup,ENST00000301732,NM_001089.2;ABCA3,intron_variant,,ENST00000382381,;ABCA3,non_coding_transcript_exon_variant,,ENST00000563623,; GTT ENST00000301732 Transcript inframe_insertion 1892-1893/6609 1191-1192/5115 397-398/1704 -/N -/AAC 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 11/33 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98 MODERATE 1 insertion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 GTT 7 5 103 2308543 2308543 - GTT 1 0 1 1 0 0 0 0 0 37 188 7 0 0 ABCA3 16 2308543 In_Frame_Ins INS - C3N-02572_T 2308543 88029802 31 29849 2 30 2 2 26 N GTAGGGGAT_- 3.642753e-05 ABCA3 0 . GRCh38 16 2308568 2308576 + In_Frame_Del DEL GTAGGGGAT GTAGGGGAT - novel C3N-02572_T C3N-02572_N GTAGGGGAT GTAGGGGAT c.1159_1167delATCCCCTAC p.Ile387_Tyr389del p.I387_Y389del ENST00000301732 11/33 464 291 173 380 380 0 sindel-varindel-pindel ABCA3,inframe_deletion,p.Ile387_Tyr389del,ENST00000301732,NM_001089.2;ABCA3,intron_variant,,ENST00000382381,;ABCA3,non_coding_transcript_exon_variant,,ENST00000563623,; - ENST00000301732 Transcript inframe_deletion 1860-1868/6609 1159-1167/5115 387-389/1704 IPY/- ATCCCCTAC/- 1 -1 ABCA3 HGNC HGNC:33 protein_coding YES CCDS10466.1 ENSP00000301732 Q99758 UPI0000001232 NM_001089.2 11/33 Pfam_domain:PF12698,hmmpanther:PTHR19229,hmmpanther:PTHR19229:SF98,Transmembrane_helices:TMhelix MODERATE 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 103 2308568 2308568 GTAGGGGAT - 1 0 1 0 1 0 0 0 0 37 1024 36 0 0 ABCA3 16 2308568 In_Frame_Del DEL GTAGGGGAT C3N-02572_T 25 2308568 88029777 32 29850 2 30 2 2 26 N GTAGGGGAT_- 3.642753e-05 TP53 0 . GRCh38 17 7674241 7674241 + Missense_Mutation SNP G G A rs28934573 C3N-02572_T C3N-02572_N G G c.722C>T p.Ser241Phe p.S241F ENST00000269305 7/11 315 211 104 297 297 0 strelka-varscan-mutect TP53,missense_variant,p.Ser241Phe,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Ser241Phe,ENST00000420246,;TP53,missense_variant,p.Ser202Phe,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Ser202Phe,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Ser241Phe,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Ser202Phe,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Ser241Phe,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Ser202Phe,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Ser241Phe,ENST00000445888,;TP53,missense_variant,p.Ser202Phe,ENST00000619485,;TP53,missense_variant,p.Ser109Phe,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Ser82Phe,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Ser109Phe,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Ser82Phe,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Ser109Phe,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Ser82Phe,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Ser241Phe,ENST00000359597,;TP53,missense_variant,p.Ser230Phe,ENST00000615910,;TP53,missense_variant,p.Ser241Phe,ENST00000413465,;TP53,missense_variant,p.Ser109Phe,ENST00000509690,;TP53,missense_variant,p.Ser148Phe,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Ser202Phe,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 912/2579 722/1182 241/393 S/F tCc/tTc rs28934573,CM920673,TP53_g.13359C>A,TP53_g.13359del,TP53_g.13359C>T,TP53_g.13359C>G,COSM10709,COSM10812,COSM10935,COSM1230110,COSM1230111,COSM1230112,COSM1649402,COSM214170,COSM214171,COSM214172,COSM2744619,COSM2744620,COSM3362448,COSM3522695,COSM3712577,COSM437501,COSM437502,COSM437503,COSM44657 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 likely_pathogenic,pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 2510566021264207 MODERATE 1 SNV 1 1,1,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs28934573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 7674241 7674241 G A 1 0 0 0 0 1 0 0 0 16859 1174 41 3 3 TP53 17 7674241 Missense_Mutation SNP G C3N-02572_T 7674241 75583200 33 29851 TRIM37 0 . GRCh38 17 59056968 59056968 + Missense_Mutation SNP A A G novel C3N-02572_T C3N-02572_N A A c.1106T>C p.Val369Ala p.V369A ENST00000262294 13/24 125 118 7 189 189 0 strelka-varscan-mutect TRIM37,missense_variant,p.Val369Ala,ENST00000262294,NM_015294.3;TRIM37,missense_variant,p.Val369Ala,ENST00000393066,NM_001005207.2;TRIM37,missense_variant,p.Val335Ala,ENST00000393065,;TRIM37,downstream_gene_variant,,ENST00000581468,;RN7SL716P,upstream_gene_variant,,ENST00000580539,;TRIM37,3_prime_UTR_variant,,ENST00000577554,NM_001320990.1; G ENST00000262294 Transcript missense_variant 1366/4330 1106/2895 369/964 V/A gTt/gCt 1 -1 TRIM37 HGNC HGNC:7523 protein_coding YES CCDS32694.1 ENSP00000262294 O94972 UPI0000167B57 NM_015294.3 tolerated(0.09) 13/24 Gene3D:2.60.210.10,Pfam_domain:PF00917,PROSITE_profiles:PS50144,hmmpanther:PTHR24103,hmmpanther:PTHR24103:SF301,SMART_domains:SM00061,Superfamily_domains:SSF49599 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 103 59056968 59056968 A G 1 0 0 0 0 1 0 0 0 17000 43 2 5 5 TRIM37 17 59056968 Missense_Mutation SNP A C3N-02572_T 51382727 59056968 24200473 34 29852 SPHK1 0 . GRCh38 17 76387288 76387288 + Missense_Mutation SNP A A C novel C3N-02572_T C3N-02572_N A A c.1115A>C p.His372Pro p.H372P ENST00000323374 6/6 249 185 64 132 132 0 strelka-varscan-mutect SPHK1,missense_variant,p.His286Pro,ENST00000545180,;SPHK1,missense_variant,p.His372Pro,ENST00000323374,NM_182965.2;SPHK1,missense_variant,p.His300Pro,ENST00000590959,NM_021972.3;SPHK1,missense_variant,p.His286Pro,ENST00000592299,NM_001142601.1;SPHK1,missense_variant,p.His286Pro,ENST00000392496,NM_001142602.1;UBE2O,downstream_gene_variant,,ENST00000319380,NM_022066.3;UBE2O,downstream_gene_variant,,ENST00000587127,;PRPSAP1,upstream_gene_variant,,ENST00000442767,;SPHK1,downstream_gene_variant,,ENST00000588682,;SPHK1,downstream_gene_variant,,ENST00000590379,;PRPSAP1,upstream_gene_variant,,ENST00000423915,;SPHK1,downstream_gene_variant,,ENST00000591651,;SPHK1,non_coding_transcript_exon_variant,,ENST00000591762,;SPHK1,downstream_gene_variant,,ENST00000587167,; C ENST00000323374 Transcript missense_variant 1571/2138 1115/1413 372/470 H/P cAt/cCt 1 1 SPHK1 HGNC HGNC:11240 protein_coding YES CCDS11744.1 ENSP00000313681 Q9NYA1 UPI00001AF3B5 NM_182965.2 deleterious(0) 6/6 hmmpanther:PTHR12358:SF47,hmmpanther:PTHR12358,Superfamily_domains:SSF111331 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 103 76387288 76387288 A C 1 0 0 0 0 1 0 0 0 15397 217 8 5 5 SPHK1 17 76387288 Missense_Mutation SNP A C3N-02572_T 17330320 76387288 6870153 35 29853 CELF4 0 . GRCh38 18 37259223 37259223 + Missense_Mutation SNP C C T novel C3N-02572_T C3N-02572_N C C c.1291G>A p.Glu431Lys p.E431K ENST00000420428 11/13 145 119 26 125 125 0 strelka-varscan-mutect CELF4,missense_variant,p.Glu431Lys,ENST00000420428,NM_020180.3;CELF4,missense_variant,p.Glu429Lys,ENST00000591287,;CELF4,missense_variant,p.Glu430Lys,ENST00000603232,NM_001025087.1;CELF4,missense_variant,p.Glu429Lys,ENST00000361795,NM_001025088.1;CELF4,missense_variant,p.Glu429Lys,ENST00000601019,;CELF4,missense_variant,p.Glu431Lys,ENST00000591282,;CELF4,missense_variant,p.Glu419Lys,ENST00000588597,;CELF4,missense_variant,p.Glu120Lys,ENST00000589386,;CELF4,missense_variant,p.Glu119Lys,ENST00000587657,;CELF4,intron_variant,,ENST00000334919,NM_001025089.1;CELF4,intron_variant,,ENST00000588591,;CELF4,intron_variant,,ENST00000586009,;CELF4,intron_variant,,ENST00000587911,;CELF4,intron_variant,,ENST00000593271,;CELF4,3_prime_UTR_variant,,ENST00000590112,; T ENST00000420428 Transcript missense_variant 1687/4052 1291/1461 431/486 E/K Gag/Aag 1 -1 CELF4 HGNC HGNC:14015 protein_coding YES CCDS32818.1 ENSP00000410584 Q9BZC1 UPI00000726FC NM_020180.3 deleterious(0) 11/13 PROSITE_profiles:PS50102,hmmpanther:PTHR24012:SF462,hmmpanther:PTHR24012,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 103 37259223 37259223 C T 1 0 0 0 0 1 0 0 0 2925 864 30 3 3 CELF4 18 37259223 Missense_Mutation SNP C C3N-02572_T 37259223 43114062 36 29854 AMH 0 . GRCh38 19 2251144 2251144 + Missense_Mutation SNP C C A rs765937994 C3N-02572_T C3N-02572_N C C c.870C>A p.Phe290Leu p.F290L ENST00000221496 5/5 435 391 44 310 309 1 strelka-varscan-mutect AMH,missense_variant,p.Phe290Leu,ENST00000221496,NM_000479.3;SF3A2,downstream_gene_variant,,ENST00000221494,NM_007165.4;JSRP1,downstream_gene_variant,,ENST00000300961,NM_144616.3;JSRP1,downstream_gene_variant,,ENST00000593238,;SF3A2,downstream_gene_variant,,ENST00000586396,;AMH,downstream_gene_variant,,ENST00000592276,;AMH,downstream_gene_variant,,ENST00000592877,;AMH,non_coding_transcript_exon_variant,,ENST00000589313,;SF3A2,downstream_gene_variant,,ENST00000592314,;SF3A2,downstream_gene_variant,,ENST00000587637,; A ENST00000221496 Transcript missense_variant 892/1821 870/1683 290/560 F/L ttC/ttA rs765937994 1 1 AMH HGNC HGNC:464 protein_coding YES CCDS12085.1 ENSP00000221496 P03971 UPI000013C7D0 NM_000479.3 deleterious(0.05) 5/5 hmmpanther:PTHR15009,Pfam_domain:PF04709,PIRSF_domain:PIRSF037270 MODERATE 1 SNV 1 1 PASS rs765937994 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 2251144 2251144 C A 1 0 0 0 0 1 0 0 0 671 854 30 2 2 AMH 19 2251144 Missense_Mutation SNP C C3N-02572_T 2251144 56366472 37 29855 FBN3 0 . GRCh38 19 8111074 8111074 + Missense_Mutation SNP G G C novel C3N-02572_T C3N-02572_N G G c.4194C>G p.Asp1398Glu p.D1398E ENST00000600128 33/64 102 96 6 82 82 0 strelka-varscan-mutect FBN3,missense_variant,p.Asp1398Glu,ENST00000600128,;FBN3,missense_variant,p.Asp1398Glu,ENST00000270509,NM_032447.3;FBN3,missense_variant,p.Asp1398Glu,ENST00000601739,NM_001321431.1;FBN3,non_coding_transcript_exon_variant,,ENST00000594331,; C ENST00000600128 Transcript missense_variant 4609/9362 4194/8430 1398/2809 D/E gaC/gaG 1 -1 FBN3 HGNC HGNC:18794 protein_coding YES CCDS12196.1 ENSP00000470498 Q75N90 UPI000013D88F deleterious(0.01) 33/64 PROSITE_profiles:PS50026,hmmpanther:PTHR24039:SF0,hmmpanther:PTHR24039,PROSITE_patterns:PS01186,PIRSF_domain:PIRSF036312,Pfam_domain:PF07645,Gene3D:2.10.25.10,SMART_domains:SM00179,SMART_domains:SM00181,Superfamily_domains:SSF57184 MODERATE 1 SNV 1 1 PASS . . 0 203 6 0 0 0 0 0 -12.28358 0.9999995 1 1 1 0 C 3 2 103 8111074 8111074 G C 1 0 0 0 0 1 0 0 0 5567 1252 44 4 4 FBN3 19 8111074 Missense_Mutation SNP G C3N-02572_T 5859930 8111074 50506542 38 29856 MUC16 0 . GRCh38 19 8956755 8956755 + Missense_Mutation SNP G G T rs188615098 C3N-02572_T C3N-02572_N G G c.20015C>A p.Thr6672Lys p.T6672K ENST00000397910 3/84 72 63 9 110 110 0 strelka-varscan-mutect MUC16,missense_variant,p.Thr6672Lys,ENST00000397910,NM_024690.2; T ENST00000397910 Transcript missense_variant 20219/43816 20015/43524 6672/14507 T/K aCa/aAa rs188615098 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 3/84 MODERATE 1 SNV 5 1 PASS rs188615098 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 103 8956755 8956755 G T 1 0 0 0 0 1 0 0 0 9972 1377 48 2 2 MUC16 19 8956755 Missense_Mutation SNP G C3N-02572_T 845681 8956755 49660861 39 29857 TRMT1 0 . GRCh38 19 13105009 13105009 + Missense_Mutation SNP C C A novel C3N-02572_T C3N-02572_N C C c.1906G>T p.Ala636Ser p.A636S ENST00000592062 18/18 155 147 8 83 83 0 strelka-varscan-mutect TRMT1,missense_variant,p.Ala636Ser,ENST00000592062,;TRMT1,missense_variant,p.Ala636Ser,ENST00000437766,NM_017722.3;TRMT1,missense_variant,p.Ala607Ser,ENST00000221504,NM_001142554.1;TRMT1,missense_variant,p.Ala636Ser,ENST00000357720,NM_001136035.2;LYL1,upstream_gene_variant,,ENST00000264824,NM_005583.4;LYL1,upstream_gene_variant,,ENST00000590974,;TRMT1,downstream_gene_variant,,ENST00000587487,;TRMT1,non_coding_transcript_exon_variant,,ENST00000588511,;TRMT1,non_coding_transcript_exon_variant,,ENST00000593157,;LYL1,upstream_gene_variant,,ENST00000590120,;TRMT1,downstream_gene_variant,,ENST00000585435,;TRMT1,downstream_gene_variant,,ENST00000586830,; A ENST00000592062 Transcript missense_variant 2477/2579 1906/1980 636/659 A/S Gcc/Tcc 1 -1 TRMT1 HGNC HGNC:25980 protein_coding YES CCDS12293.1 ENSP00000466967 Q9NXH9 A0A024R7I5 UPI0000000A02 tolerated_low_confidence(0.81) 18/18 MODERATE SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -14.82627 1 1 1 1 0 A 3 1 103 13105009 13105009 C A 1 0 0 0 0 1 0 0 0 17060 710 25 2 2 TRMT1 19 13105009 Missense_Mutation SNP C C3N-02572_T 4148254 13105009 45512607 40 29858 ACTN4 0 . GRCh38 19 38708159 38708159 + Silent SNP C C T novel C3N-02572_T C3N-02572_N C C c.615C>T p.= p.H205H ENST00000252699 6/21 577 507 70 441 441 0 strelka-varscan-mutect ACTN4,synonymous_variant,p.=,ENST00000252699,NM_004924.4;ACTN4,synonymous_variant,p.=,ENST00000586538,;ACTN4,intron_variant,,ENST00000390009,;ACTN4,intron_variant,,ENST00000424234,;ACTN4,intron_variant,,ENST00000589528,;ACTN4,non_coding_transcript_exon_variant,,ENST00000495553,;ACTN4,non_coding_transcript_exon_variant,,ENST00000588618,;ACTN4,upstream_gene_variant,,ENST00000489451,; T ENST00000252699 Transcript synonymous_variant 691/4963 615/2736 205/911 H caC/caT 1 1 ACTN4 HGNC HGNC:166 protein_coding YES CCDS12518.1 ENSP00000252699 O43707 A0A0S2Z3G9 UPI0000125093 NM_004924.4 6/21 PROSITE_profiles:PS50021,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF271,Pfam_domain:PF00307,Gene3D:1.10.418.10,SMART_domains:SM00033,Superfamily_domains:SSF47576 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 103 38708159 38708159 C T 1 0 0 0 0 0 0 0 1 251 477 17 3 3 ACTN4 19 38708159 Silent SNP C C3N-02572_T 25603150 38708159 19909457 41 29859 PPP1R16B 0 . GRCh38 20 38902690 38902690 + Silent SNP C C T rs200868467 C3N-02572_T C3N-02572_N C C c.594C>T p.= p.N198N ENST00000299824 6/11 223 198 25 141 141 0 strelka-mutect PPP1R16B,synonymous_variant,p.=,ENST00000299824,NM_015568.2;PPP1R16B,synonymous_variant,p.=,ENST00000373331,NM_001172735.1; T ENST00000299824 Transcript synonymous_variant 783/6251 594/1704 198/567 N aaC/aaT rs200868467,COSM284183 1 1 PPP1R16B HGNC HGNC:15850 protein_coding YES CCDS13309.1 ENSP00000299824 Q96T49 UPI0000132059 NM_015568.2 6/11 PROSITE_profiles:PS50297,hmmpanther:PTHR24186,hmmpanther:PTHR24186:SF6,Gene3D:1.25.40.20,PIRSF_domain:PIRSF038159,Superfamily_domains:SSF48403 0,1 LOW 1 SNV 1 0,1 1 PASS rs200868467 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 103 38902690 38902690 C T 1 0 0 0 0 0 0 0 1 12476 535 19 1 1 PPP1R16B 20 38902690 Silent SNP C C3N-02572_T 38902690 25541477 42 29860 KCNQ2 0 . GRCh38 20 63407042 63407042 + Missense_Mutation SNP G G A C3N-02572_T C3N-02572_N G G c.2221C>T p.Arg741Cys p.R741C ENST00000359125 17/17 75 66 9 53 53 0 strelka-varscan-mutect KCNQ2,missense_variant,p.Arg723Cys,ENST00000626839,NM_172106.1;KCNQ2,missense_variant,p.Arg741Cys,ENST00000359125,NM_172107.2;KCNQ2,missense_variant,p.Arg540Cys,ENST00000637193,;KCNQ2,missense_variant,p.Arg713Cys,ENST00000360480,NM_004518.4;KCNQ2,missense_variant,p.Arg710Cys,ENST00000344462,NM_172108.3;KCNQ2,missense_variant,p.Arg597Cys,ENST00000357249,;KCNQ2,splice_region_variant,,ENST00000370224,;KCNQ2,splice_region_variant,,ENST00000625514,;KCNQ2,splice_region_variant,,ENST00000629241,;KCNQ2,intron_variant,,ENST00000629676,;KCNQ2,downstream_gene_variant,,ENST00000636614,;KCNQ2,downstream_gene_variant,,ENST00000637063,;KCNQ2,downstream_gene_variant,,ENST00000637338,;KCNQ2,downstream_gene_variant,,ENST00000637656,; A ENST00000359125 Transcript missense_variant 2348/3253 2221/2619 741/872 R/C Cgc/Tgc COSM5176407,COSM5176408,COSM5176409 1 -1 KCNQ2 HGNC HGNC:6296 protein_coding YES CCDS13520.1 ENSP00000352035 O43526 UPI00001279ED NM_172107.2 deleterious_low_confidence(0) 17/17 Pfam_domain:PF16642 1,1,1 MODERATE 1 SNV 1 1,1,1 1 PASS . . 0 199 11 0 0 0 0 0 -19.24346 0.9999383 1 1 1 0 A 3 1 103 63407042 63407042 G A 1 0 0 0 0 1 0 0 0 7999 1101 38 1 1 KCNQ2 20 63407042 Missense_Mutation SNP G C3N-02572_T 24504352 63407042 1037125 43 29861 GRAP2 0 . GRCh38 22 39971059 39971059 + Missense_Mutation SNP A A C rs752554043 C3N-02572_T C3N-02572_N A A c.968A>C p.Asn323Thr p.N323T ENST00000344138 8/8 224 206 18 158 157 1 strelka-varscan-mutect GRAP2,missense_variant,p.Asn323Thr,ENST00000344138,NM_004810.3,NM_001291824.1;GRAP2,missense_variant,p.Asn323Thr,ENST00000407075,NM_001291825.1;GRAP2,downstream_gene_variant,,ENST00000478445,;GRAP2,non_coding_transcript_exon_variant,,ENST00000460449,;GRAP2,downstream_gene_variant,,ENST00000481263,; C ENST00000344138 Transcript missense_variant 1231/3893 968/993 323/330 N/T aAc/aCc rs752554043 1 1 GRAP2 HGNC HGNC:4563 protein_coding YES CCDS13999.1 ENSP00000339186 O75791 Q6FI14 UPI000012BB02 NM_004810.3,NM_001291824.1 deleterious(0) 8/8 Gene3D:2.30.30.40,Prints_domain:PR00452,PROSITE_profiles:PS50002,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS rs752554043 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 103 39971059 39971059 A C 1 0 0 0 0 1 0 0 0 6633 43 2 5 5 GRAP2 22 39971059 Missense_Mutation SNP A C3N-02572_T 39971059 10847409 44 29862 EFCAB6 0 . GRCh38 22 43711506 43711506 + Missense_Mutation SNP G G A novel C3N-02572_T C3N-02572_N G G c.1000C>T p.Pro334Ser p.P334S ENST00000262726 10/32 50 46 4 91 91 0 varscan-mutect EFCAB6,missense_variant,p.Pro334Ser,ENST00000262726,NM_022785.3;EFCAB6,missense_variant,p.Pro182Ser,ENST00000396231,NM_198856.2;EFCAB6,non_coding_transcript_exon_variant,,ENST00000404038,; A ENST00000262726 Transcript missense_variant 1254/4869 1000/4506 334/1501 P/S Cca/Tca 1 -1 EFCAB6 HGNC HGNC:24204 protein_coding YES CCDS14049.1 ENSP00000262726 Q5THR3 UPI0000225CD7 NM_022785.3 deleterious(0.04) 10/32 Gene3D:1.10.238.10,Superfamily_domains:SSF47473 MODERATE 1 SNV 2 1 PASS . . 0 201 5 4 0 0 0 0 -8.013102 0.9964096 1 1 1 0 A 3 1 103 43711506 43711506 G A 1 0 0 0 0 1 0 0 0 4773 1261 44 3 3 EFCAB6 22 43711506 Missense_Mutation SNP G C3N-02572_T 3740447 43711506 7106962 45 29863 FAM47C 0 . GRCh38 X 37009461 37009461 + Missense_Mutation SNP G G A C3N-02572_T C3N-02572_N G G c.1051G>A p.Val351Met p.V351M ENST00000358047 1/1 198 183 15 138 138 0 varscan-mutect FAM47C,missense_variant,p.Val351Met,ENST00000358047,NM_001013736.2; A ENST00000358047 Transcript missense_variant 1065/3270 1051/3108 351/1035 V/M Gtg/Atg COSM311058,COSM311059 1 1 FAM47C HGNC HGNC:25301 protein_coding YES CCDS35227.1 ENSP00000367913 Q5HY64 UPI000041ABF8 NM_001013736.2 deleterious(0.01) 1/1 hmmpanther:PTHR23213:SF203,hmmpanther:PTHR23213,Pfam_domain:PF14642 1,1 MODERATE 1 SNV 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 103 37009461 37009461 G A 1 0 0 0 0 1 0 0 0 5449 1029 36 3 3 FAM47C 23 37009461 Missense_Mutation SNP G C3N-02572_T 37009461 119031434 46 29864 ESPN 0 . GRCh38 1 6457241 6457241 + Missense_Mutation SNP C C T novel C3N-02582_T C3N-02582_N C C c.2383C>T p.Arg795Trp p.R795W ENST00000377828 11/13 266 247 19 338 338 0 varscan-mutect ESPN,missense_variant,p.Arg795Trp,ENST00000377828,NM_031475.2;ESPN,missense_variant,p.Arg229Trp,ENST00000461727,;ESPN,missense_variant,p.Arg178Trp,ENST00000633239,;ESPN,missense_variant,p.Arg229Trp,ENST00000416731,;ESPN,missense_variant,p.Arg150Trp,ENST00000475228,;ESPN,missense_variant,p.Arg139Trp,ENST00000434576,;ESPN,missense_variant,p.Arg170Trp,ENST00000636644,;ESPN,downstream_gene_variant,,ENST00000636330,;TNFRSF25,downstream_gene_variant,,ENST00000377782,NM_148965.1;TNFRSF25,downstream_gene_variant,,ENST00000356876,NM_003790.2;TNFRSF25,downstream_gene_variant,,ENST00000351959,NM_148966.1;TNFRSF25,downstream_gene_variant,,ENST00000348333,NM_148967.1;TNFRSF25,downstream_gene_variant,,ENST00000351748,NM_148970.1;ESPN,upstream_gene_variant,,ENST00000468561,;TNFRSF25,downstream_gene_variant,,ENST00000475730,;ESPN,non_coding_transcript_exon_variant,,ENST00000477679,;TNFRSF25,downstream_gene_variant,,ENST00000513135,;TNFRSF25,downstream_gene_variant,,ENST00000485036,;TNFRSF25,downstream_gene_variant,,ENST00000480393,;TNFRSF25,downstream_gene_variant,,ENST00000473343,;TNFRSF25,downstream_gene_variant,,ENST00000414040,;TNFRSF25,downstream_gene_variant,,ENST00000510563,;TNFRSF25,downstream_gene_variant,,ENST00000453260,;TNFRSF25,downstream_gene_variant,,ENST00000502588,;TNFRSF25,downstream_gene_variant,,ENST00000502730,;TNFRSF25,downstream_gene_variant,,ENST00000469691,; T ENST00000377828 Transcript missense_variant 2551/3531 2383/2565 795/854 R/W Cgg/Tgg 1 1 ESPN HGNC HGNC:13281 protein_coding YES CCDS70.1 ENSP00000367059 B1AK53 UPI000013D2B6 NM_031475.2 deleterious(0) 11/13 Low_complexity_(Seg):seg,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR24153:SF14,hmmpanther:PTHR24153 MODERATE 1 SNV 1 1 PASS rs1436366629 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 6457241 6457241 C T 1 0 0 0 0 1 0 0 0 5116 759 27 1 1 ESPN 1 6457241 Missense_Mutation SNP C C3N-02582_T 6457241 242499181 1 29865 UBR4 0 . GRCh38 1 19141362 19141362 + Nonsense_Mutation SNP G G A novel C3N-02582_T C3N-02582_N G G c.8473C>T p.Gln2825Ter p.Q2825* ENST00000375254 57/106 286 243 43 386 386 0 strelka-varscan-mutect UBR4,stop_gained,p.Gln2825Ter,ENST00000375254,NM_020765.2;UBR4,stop_gained,p.Gln1546Ter,ENST00000417040,;UBR4,stop_gained,p.Gln468Ter,ENST00000425413,;UBR4,downstream_gene_variant,,ENST00000465036,; A ENST00000375254 Transcript stop_gained 8501/15906 8473/15552 2825/5183 Q/* Cag/Tag 1 -1 UBR4 HGNC HGNC:30313 protein_coding YES CCDS189.1 ENSP00000364403 Q5T4S7 UPI000021276F NM_020765.2 57/106 Low_complexity_(Seg):seg,hmmpanther:PTHR21725 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 104 19141362 19141362 G A 1 0 0 0 0 0 1 0 0 17428 1328 46 3 3 UBR4 1 19141362 Nonsense_Mutation SNP G C3N-02582_T 12684121 19141362 229815060 2 29866 ZNF362 0 . GRCh38 1 33299012 33299012 + Missense_Mutation SNP C C T novel C3N-02582_T C3N-02582_N C C c.1229C>T p.Ser410Phe p.S410F ENST00000539719 9/9 136 125 11 187 187 0 strelka-varscan-mutect ZNF362,missense_variant,p.Ser410Phe,ENST00000539719,NM_152493.2;ZNF362,missense_variant,p.Ser410Phe,ENST00000373428,; T ENST00000539719 Transcript missense_variant 1399/3106 1229/1263 410/420 S/F tCc/tTc 1 1 ZNF362 HGNC HGNC:18079 protein_coding YES CCDS377.1 ENSP00000446335 Q5T0B9 UPI000013E046 NM_152493.2 deleterious_low_confidence(0) 9/9 MODERATE 1 SNV 5 1 PASS . . 0 205 0 4 0 0 0 0 -15.4001 0.9997093 1 1 1 0 T 3 4 104 33299012 33299012 C T 1 0 0 0 0 1 0 0 0 18440 855 30 3 3 ZNF362 1 33299012 Missense_Mutation SNP C C3N-02582_T 14157650 33299012 215657410 3 29867 AGO1 0 . GRCh38 1 35894096 35894096 + Missense_Mutation SNP G G A novel C3N-02582_T C3N-02582_N G G c.709G>A p.Asp237Asn p.D237N ENST00000373204 6/19 32 24 8 43 43 0 strelka-varscan-mutect AGO1,missense_variant,p.Asp237Asn,ENST00000373204,NM_012199.2;AGO1,missense_variant,p.Asp162Asn,ENST00000373206,;AGO1,3_prime_UTR_variant,,ENST00000635259,; A ENST00000373204 Transcript missense_variant 922/13708 709/2574 237/857 D/N Gac/Aac 1 1 AGO1 HGNC HGNC:3262 protein_coding YES CCDS398.1 ENSP00000362300 Q9UL18 UPI000012D07D NM_012199.2 tolerated(0.21) 6/19 PROSITE_profiles:PS50821,hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891,Gene3D:2.170.260.10,Pfam_domain:PF02170,SMART_domains:SM00949,Superfamily_domains:SSF101690 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 35894096 35894096 G A 1 0 0 0 0 1 0 0 0 464 1174 41 3 3 AGO1 1 35894096 Missense_Mutation SNP G C3N-02582_T 2595084 35894096 213062326 4 29868 TIE1 0 . GRCh38 1 43304995 43304995 + Missense_Mutation SNP G G A rs774803318 C3N-02582_T C3N-02582_N G G c.203G>A p.Arg68His p.R68H ENST00000372476 2/23 50 45 5 53 53 0 strelka-mutect TIE1,missense_variant,p.Arg68His,ENST00000372476,NM_005424.4,NM_001253357.1;TIE1,missense_variant,p.Arg68His,ENST00000538015,;TIE1,non_coding_transcript_exon_variant,,ENST00000485125,;TIE1,upstream_gene_variant,,ENST00000488437,;TIE1,upstream_gene_variant,,ENST00000480269,; A ENST00000372476 Transcript missense_variant 282/3882 203/3417 68/1138 R/H cGt/cAt rs774803318,COSM1229279 1 1 TIE1 HGNC HGNC:11809 protein_coding YES CCDS482.1 ENSP00000361554 P35590 UPI0000032E59 NM_005424.4,NM_001253357.1 deleterious(0.02) 2/23 hmmpanther:PTHR24416:SF341,hmmpanther:PTHR24416 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs774803318 . 0 202 8 0 0 0 0 0 -12.18038 0.9999955 1 1 1 0 A 3 1 104 43304995 43304995 G A 1 0 0 0 0 1 0 0 0 16329 1145 40 1 1 TIE1 1 43304995 Missense_Mutation SNP G C3N-02582_T 7410899 43304995 205651427 5 29869 SCP2 0 . GRCh38 1 53028000 53028000 + Frame_Shift_Del DEL C C - novel C3N-02582_T C3N-02582_N C C c.1268delC p.Pro423GlnfsTer30 p.P423Qfs*30 ENST00000371514 13/16 249 180 69 385 385 0 sindel-varindel-pindel SCP2,frameshift_variant,p.Pro19GlnfsTer25,ENST00000488965,;SCP2,frameshift_variant,p.Pro423GlnfsTer30,ENST00000371514,NM_002979.4;SCP2,frameshift_variant,p.Pro399GlnfsTer30,ENST00000407246,NM_001193599.1;SCP2,frameshift_variant,p.Pro342GlnfsTer30,ENST00000528311,NM_001193617.1;SCP2,frameshift_variant,p.Pro379GlnfsTer30,ENST00000371509,NM_001193600.1;SCP2,frameshift_variant,p.Pro19GlnfsTer25,ENST00000408941,NM_001007250.2;SCP2,frameshift_variant,p.Pro38GlnfsTer30,ENST00000478274,;SCP2,frameshift_variant,p.Pro16GlnfsTer30,ENST00000430330,NM_001007100.2;SCP2,frameshift_variant,p.Pro19GlnfsTer30,ENST00000435345,NM_001007099.2;SCP2,frameshift_variant,p.Pro38GlnfsTer25,ENST00000484100,;SCP2,3_prime_UTR_variant,,ENST00000478631,;SCP2,intron_variant,,ENST00000533119,; - ENST00000371514 Transcript frameshift_variant 1435/2811 1267/1644 423/547 P/X Cca/ca 1 1 SCP2 HGNC HGNC:10606 protein_coding YES CCDS572.1 ENSP00000360569 P22307 UPI0000130258 NM_002979.4 13/16 HIGH 1 deletion 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 53028000 53028000 C - 1 0 1 0 1 0 0 0 0 14203 855 30 0 0 SCP2 1 53028000 Frame_Shift_Del DEL C C3N-02582_T 9723005 53028000 195928422 6 29870 NBPF9 0 . GRCh38 1 149075691 149075700 + Frame_Shift_Del DEL GTTGAGTTAG GTTGAGTTAG - novel C3N-02582_T C3N-02582_N GTTGAGTTAG GTTGAGTTAG c.943_952delCTAACTCAAC p.Leu315TrpfsTer21 p.L315Wfs*21 ENST00000615421 11/29 412 365 47 677 677 0 sindel-varindel-pindel NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000615421,;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000621645,;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000584027,NM_001277444.1;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000613969,NM_001037501.2;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000613595,NM_001037675.3;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000621074,;NBPF9,frameshift_variant,p.Leu315TrpfsTer21,ENST00000610300,;NBPF9,frameshift_variant,p.Leu44TrpfsTer21,ENST00000483630,; - ENST00000615421 Transcript frameshift_variant 1813-1822/5835 943-952/3336 315-318/1111 LTQL/X CTAACTCAACtg/tg 1 -1 NBPF9 HGNC HGNC:31991 protein_coding YES CCDS72896.1 ENSP00000477979 A0A075B761 UPI000292EE30 11/29 hmmpanther:PTHR14199:SF20,hmmpanther:PTHR14199 HIGH 1 deletion 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 149075691 149075691 GTTGAGTTAG - 1 0 1 0 1 0 0 0 0 10215 1020 36 0 0 NBPF9 1 149075691 Frame_Shift_Del DEL GTTGAGTTAG C3N-02582_T 96047691 149075691 99880731 7 29871 ATP8B2 0 . GRCh38 1 154343958 154343958 + Silent SNP C C T rs2274988 C3N-02582_T C3N-02582_N C C c.1923C>T p.= p.Y641Y ENST00000368489 18/28 114 107 7 143 143 0 strelka-varscan-mutect ATP8B2,synonymous_variant,p.=,ENST00000368489,NM_020452.3;ATP8B2,downstream_gene_variant,,ENST00000426445,;ATP8B2,upstream_gene_variant,,ENST00000505882,; T ENST00000368489 Transcript synonymous_variant 1923/5861 1923/3672 641/1223 Y taC/taT rs2274988 1 1 ATP8B2 HGNC HGNC:13534 protein_coding YES CCDS1066.1 ENSP00000357475 P98198 UPI00001B92AB NM_020452.3 18/28 Gene3D:3.40.1110.10,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF46,Superfamily_domains:SSF56784,Superfamily_domains:SSF81660,TIGRFAM_domain:TIGR01652 LOW 1 SNV 1 1 PASS rs2274988 . 0 143 0 0 0 0 0 64 -5.111404 0 0 1 0 0 T 2 4 104 154343958 154343958 C T 1 0 0 0 0 0 0 0 1 1348 547 19 1 1 ATP8B2 1 154343958 Silent SNP C C3N-02582_T 5268267 154343958 94612464 8 29872 ASH1L 0 . GRCh38 1 155354616 155354616 + Missense_Mutation SNP T T C novel C3N-02582_T C3N-02582_N T T c.7070A>G p.Lys2357Arg p.K2357R ENST00000392403 16/28 124 114 10 155 155 0 varscan-mutect ASH1L,missense_variant,p.Lys2362Arg,ENST00000368346,;ASH1L,missense_variant,p.Lys2357Arg,ENST00000392403,NM_018489.2;RNU6-106P,downstream_gene_variant,,ENST00000384405,; C ENST00000392403 Transcript missense_variant 7549/10979 7070/8895 2357/2964 K/R aAg/aGg 1 -1 ASH1L HGNC HGNC:19088 protein_coding YES CCDS1113.2 ENSP00000376204 Q9NR48 UPI0000DACAC8 NM_018489.2 deleterious_low_confidence(0.04) 16/28 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 155354616 155354616 T C 1 0 0 0 0 1 0 0 0 1183 1609 56 5 5 ASH1L 1 155354616 Missense_Mutation SNP T C3N-02582_T 1010658 155354616 93601806 9 29873 SCYL3 0 . GRCh38 1 169854307 169854307 + Missense_Mutation SNP T T C novel C3N-02582_T C3N-02582_N T T c.2132A>G p.Gln711Arg p.Q711R ENST00000367772 13/14 84 76 8 110 110 0 strelka-varscan-mutect SCYL3,missense_variant,p.Gln657Arg,ENST00000367771,NM_020423.6;SCYL3,missense_variant,p.Gln711Arg,ENST00000367772,NM_181093.3;SCYL3,missense_variant,p.Gln711Arg,ENST00000367770,;C1orf112,downstream_gene_variant,,ENST00000286031,NM_018186.2;C1orf112,downstream_gene_variant,,ENST00000359326,;C1orf112,downstream_gene_variant,,ENST00000413811,;SCYL3,downstream_gene_variant,,ENST00000423670,;C1orf112,downstream_gene_variant,,ENST00000498289,;SCYL3,downstream_gene_variant,,ENST00000470238,;C1orf112,downstream_gene_variant,,ENST00000459772,; C ENST00000367772 Transcript missense_variant 2354/3090 2132/2229 711/742 Q/R cAg/cGg 1 -1 SCYL3 HGNC HGNC:19285 protein_coding YES CCDS1287.1 ENSP00000356746 Q8IZE3 UPI00001AE580 NM_181093.3 tolerated(0.29) 13/14 hmmpanther:PTHR12984,hmmpanther:PTHR12984:SF15 MODERATE SNV 2 1 PASS . . 0 206 4 0 0 0 0 0 -17.13466 1 1 1 1 0 C 3 2 104 169854307 169854307 T C 1 0 0 0 0 1 0 0 0 14221 1580 55 5 5 SCYL3 1 169854307 Missense_Mutation SNP T C3N-02582_T 14499691 169854307 79102115 10 29874 CAMSAP2 0 . GRCh38 1 200848941 200848941 + Silent SNP G G A novel C3N-02582_T C3N-02582_N G G c.2205G>A p.= p.V735V ENST00000236925 12/18 371 337 34 405 405 0 strelka-varscan-mutect CAMSAP2,synonymous_variant,p.=,ENST00000358823,NM_203459.2;CAMSAP2,synonymous_variant,p.=,ENST00000236925,NM_001297707.1;CAMSAP2,synonymous_variant,p.=,ENST00000413307,NM_001297708.1;CAMSAP2,intron_variant,,ENST00000447701,; A ENST00000236925 Transcript synonymous_variant 2254/7161 2205/4470 735/1489 V gtG/gtA 1 1 CAMSAP2 HGNC HGNC:29188 protein_coding YES CCDS72998.1 ENSP00000236925 Q08AD1 UPI0000160246 NM_001297707.1 12/18 hmmpanther:PTHR21595,hmmpanther:PTHR21595:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 104 200848941 200848941 G A 1 0 0 0 0 0 0 0 1 2304 1335 47 3 3 CAMSAP2 1 200848941 Silent SNP G C3N-02582_T 30994634 200848941 48107481 11 29875 ITPKB 0 . GRCh38 1 226737178 226737178 + Missense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.281G>T p.Gly94Val p.G94V ENST00000429204 2/8 89 84 5 107 107 0 varscan-mutect ITPKB,missense_variant,p.Gly94Val,ENST00000429204,NM_002221.3;ITPKB,missense_variant,p.Gly94Val,ENST00000272117,;ITPKB,missense_variant,p.Gly94Val,ENST00000366784,; A ENST00000429204 Transcript missense_variant 621/6162 281/2841 94/946 G/V gGc/gTc 1 -1 ITPKB HGNC HGNC:6179 protein_coding YES CCDS1555.1 ENSP00000411152 P27987 UPI000013D92B NM_002221.3 tolerated_low_confidence(0.13) 2/8 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 109 0 2 0 0 0 98 -4.312423 0 0 1 0 0 A 3 1 104 226737178 226737178 C A 1 0 0 0 0 1 0 0 0 7824 739 26 2 2 ITPKB 1 226737178 Missense_Mutation SNP C C3N-02582_T 25888237 226737178 22219244 12 29876 TTC13 0 . GRCh38 1 230940476 230940476 + Silent SNP C C T novel C3N-02582_T C3N-02582_N C C c.753G>A p.= p.L251L ENST00000366661 7/23 296 236 60 283 283 0 strelka-varscan-mutect TTC13,synonymous_variant,p.=,ENST00000366661,NM_024525.4;TTC13,synonymous_variant,p.=,ENST00000366662,NM_001122835.2;TTC13,synonymous_variant,p.=,ENST00000522399,;TTC13,intron_variant,,ENST00000522821,;TTC13,synonymous_variant,p.=,ENST00000481976,;TTC13,downstream_gene_variant,,ENST00000466507,;TTC13,upstream_gene_variant,,ENST00000519379,; T ENST00000366661 Transcript synonymous_variant 761/3253 753/2583 251/860 L ctG/ctA 1 -1 TTC13 HGNC HGNC:26204 protein_coding YES CCDS1588.1 ENSP00000355621 Q8NBP0 UPI000013D91C NM_024525.4 7/23 PROSITE_profiles:PS50005,PROSITE_profiles:PS50293,hmmpanther:PTHR23083,hmmpanther:PTHR23083:SF448,Gene3D:1.25.40.10,SMART_domains:SM00028,Superfamily_domains:SSF48452,Superfamily_domains:SSF48452 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 230940476 230940476 C T 1 0 0 0 0 0 0 0 1 17190 465 17 3 3 TTC13 1 230940476 Silent SNP C C3N-02582_T 4203298 230940476 18015946 13 29877 DDX1 0 . GRCh38 2 15621105 15621105 + Missense_Mutation SNP C C G novel C3N-02582_T C3N-02582_N C C c.1436C>G p.Ala479Gly p.A479G ENST00000381341 19/27 96 87 9 181 181 0 strelka-varscan-mutect DDX1,missense_variant,p.Ala479Gly,ENST00000381341,;DDX1,missense_variant,p.Ala479Gly,ENST00000233084,NM_004939.2;DDX1,missense_variant,p.Ala398Gly,ENST00000617198,;DDX1,missense_variant,p.Ala398Gly,ENST00000621973,;DDX1,non_coding_transcript_exon_variant,,ENST00000459706,;DDX1,non_coding_transcript_exon_variant,,ENST00000470674,;DDX1,upstream_gene_variant,,ENST00000478695,; G ENST00000381341 Transcript missense_variant 1825/2817 1436/2223 479/740 A/G gCt/gGt 1 1 DDX1 HGNC HGNC:2734 protein_coding YES CCDS1686.1 ENSP00000370745 Q92499 A3RJH1 UPI00001290D1 tolerated(0.39) 19/27 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 15621105 15621105 C G 1 0 0 0 0 1 0 0 0 4145 797 28 4 4 DDX1 2 15621105 Missense_Mutation SNP C C3N-02582_T 15621105 226572424 14 29878 EIF2AK2 0 . GRCh38 2 37141654 37141654 + Silent SNP T T C rs765847525 C3N-02582_T C3N-02582_N T T c.288A>G p.= p.L96L ENST00000233057 5/17 195 180 15 256 256 0 strelka-varscan-mutect EIF2AK2,synonymous_variant,p.=,ENST00000233057,;EIF2AK2,synonymous_variant,p.=,ENST00000395127,NM_001135651.2,NM_002759.3;EIF2AK2,synonymous_variant,p.=,ENST00000405334,NM_001135652.2;EIF2AK2,synonymous_variant,p.=,ENST00000411537,;EIF2AK2,synonymous_variant,p.=,ENST00000390013,;EIF2AK2,non_coding_transcript_exon_variant,,ENST00000496059,; C ENST00000233057 Transcript synonymous_variant 611/10042 288/1656 96/551 L ttA/ttG rs765847525 1 -1 EIF2AK2 HGNC HGNC:9437 protein_coding YES CCDS1786.1 ENSP00000233057 P19525 UPI000000D925 5/17 hmmpanther:PTHR11042,hmmpanther:PTHR11042:SF102,Superfamily_domains:SSF54768 LOW 1 SNV 2 1 PASS rs765847525 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 104 37141654 37141654 T C 1 0 0 0 0 0 0 0 1 4833 1403 49 5 5 EIF2AK2 2 37141654 Silent SNP T C3N-02582_T 21520549 37141654 205051875 15 29879 APLF 0 . GRCh38 2 68646077 68646077 + Missense_Mutation SNP G G T novel C3N-02582_T C3N-02582_N G G c.256G>T p.Ala86Ser p.A86S ENST00000303786 2/3 115 109 6 162 161 1 strelka-mutect PROKR1,missense_variant,p.Ala86Ser,ENST00000303786,;APLF,missense_variant,p.Ala86Ser,ENST00000394342,NM_138964.2;APLF,non_coding_transcript_exon_variant,,ENST00000627740,; T ENST00000303786 Transcript missense_variant 676/4273 256/1182 86/393 A/S Gcc/Tcc 1 1 PROKR1 HGNC HGNC:4524 protein_coding YES CCDS1889.1 ENSP00000303775 Q8TCW9 UPI000003EAA7 tolerated(0.33) 2/3 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24242,hmmpanther:PTHR24242:SF229,Superfamily_domains:SSF81321 MODERATE 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 68646077 68646077 G T 1 0 0 0 0 1 0 0 0 897 1319 46 2 2 APLF 2 68646077 Missense_Mutation SNP G C3N-02582_T 31504423 68646077 173547452 16 29880 AAK1 0 . GRCh38 2 69520961 69520961 + Silent SNP C C T novel C3N-02582_T C3N-02582_N C C c.1083G>A p.= p.E361E ENST00000409085 11/22 206 192 14 289 289 0 strelka-varscan-mutect AAK1,synonymous_variant,p.=,ENST00000409085,NM_014911.3;AAK1,synonymous_variant,p.=,ENST00000406297,;AAK1,synonymous_variant,p.=,ENST00000409068,;SNORA36C,upstream_gene_variant,,ENST00000384289,;RN7SL604P,downstream_gene_variant,,ENST00000492589,; T ENST00000409085 Transcript synonymous_variant 1460/11345 1083/2886 361/961 E gaG/gaA 1 -1 AAK1 HGNC HGNC:19679 protein_coding YES CCDS1893.2 ENSP00000386456 Q2M2I8 UPI0001881663 NM_014911.3 11/22 hmmpanther:PTHR22967:SF57,hmmpanther:PTHR22967 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 69520961 69520961 C T 1 0 0 0 0 0 0 0 1 17 912 32 3 3 AAK1 2 69520961 Silent SNP C C3N-02582_T 874884 69520961 172672568 17 29881 IL17RE 0 . GRCh38 3 9915612 9915612 + Frame_Shift_Del DEL C C - novel C3N-02582_T C3N-02582_N C C c.1814delC p.Pro605ArgfsTer46 p.P605Rfs*46 ENST00000383814 16/16 51 47 4 92 92 0 sindel-pindel IL17RE,frameshift_variant,p.Pro605ArgfsTer46,ENST00000383814,NM_153480.1,NM_153481.1;IL17RE,frameshift_variant,p.Pro638ArgfsTer46,ENST00000421412,NM_153483.2;IL17RE,3_prime_UTR_variant,,ENST00000454190,NM_001193380.1;IL17RC,upstream_gene_variant,,ENST00000295981,NM_153461.3;IL17RC,upstream_gene_variant,,ENST00000403601,NM_153460.3;IL17RC,upstream_gene_variant,,ENST00000383812,NM_032732.5;IL17RC,upstream_gene_variant,,ENST00000416074,NM_001203264.1;IL17RC,upstream_gene_variant,,ENST00000455057,NM_001203265.1;IL17RC,upstream_gene_variant,,ENST00000413608,NM_001203263.1;IL17RC,upstream_gene_variant,,ENST00000436503,;IL17RC,upstream_gene_variant,,ENST00000438091,;RNU6-882P,downstream_gene_variant,,ENST00000391025,;IL17RC,upstream_gene_variant,,ENST00000498214,;IL17RE,3_prime_UTR_variant,,ENST00000383815,;IL17RE,3_prime_UTR_variant,,ENST00000434065,;IL17RC,upstream_gene_variant,,ENST00000466046,;IL17RC,upstream_gene_variant,,ENST00000494365,;IL17RC,upstream_gene_variant,,ENST00000483582,;IL17RC,upstream_gene_variant,,ENST00000451271,;IL17RC,upstream_gene_variant,,ENST00000451231,;IL17RC,upstream_gene_variant,,ENST00000412901,;IL17RC,upstream_gene_variant,,ENST00000490512,;IL17RC,upstream_gene_variant,,ENST00000451165,;IL17RC,upstream_gene_variant,,ENST00000476810,;IL17RE,downstream_gene_variant,,ENST00000444427,;IL17RC,upstream_gene_variant,,ENST00000424206,;IL17RC,upstream_gene_variant,,ENST00000434756,;IL17RC,upstream_gene_variant,,ENST00000440502,;IL17RC,upstream_gene_variant,,ENST00000478206,;IL17RC,upstream_gene_variant,,ENST00000469686,;IL17RC,upstream_gene_variant,,ENST00000481032,;IL17RC,upstream_gene_variant,,ENST00000497102,;IL17RE,downstream_gene_variant,,ENST00000480244,;IL17RE,downstream_gene_variant,,ENST00000483258,; - ENST00000383814 Transcript frameshift_variant 1914/2704 1809/2004 603/667 I/X atC/at 1 1 IL17RE HGNC HGNC:18439 protein_coding YES CCDS2589.1 ENSP00000373325 Q8NFR9 UPI000003E87E NM_153480.1,NM_153481.1 16/16 PROSITE_profiles:PS51534,hmmpanther:PTHR15583:SF5,hmmpanther:PTHR15583,Pfam_domain:PF08357 HIGH 1 deletion 1 5 1 PASS . . 0 197 10 2 0 0 0 0 -8.264129 0.9974354 1 1 1 0 - 7 5 104 9915612 9915612 C - 1 0 1 0 1 0 0 0 0 7551 845 30 0 0 IL17RE 3 9915612 Frame_Shift_Del DEL C C3N-02582_T 9915612 188379947 18 29882 ALS2CL 0 . GRCh38 3 46687684 46687684 + Missense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.303G>T p.Glu101Asp p.E101D ENST00000318962 4/26 77 71 6 107 107 0 strelka-varscan-mutect ALS2CL,missense_variant,p.Glu101Asp,ENST00000318962,NM_147129.3;ALS2CL,missense_variant,p.Glu101Asp,ENST00000415953,NM_001190707.1;ALS2CL,missense_variant,p.Glu32Asp,ENST00000423707,;ALS2CL,missense_variant,p.Glu101Asp,ENST00000434140,;ALS2CL,splice_region_variant,,ENST00000450172,;ALS2CL,splice_region_variant,,ENST00000431015,; A ENST00000318962 Transcript missense_variant,splice_region_variant 387/4741 303/2862 101/953 E/D gaG/gaT 1 -1 ALS2CL HGNC HGNC:20605 protein_coding YES CCDS2743.1 ENSP00000313670 Q60I27 A0A024R2U1 UPI00001B5641 NM_147129.3 tolerated(0.13) 4/26 Gene3D:1.20.900.10,Superfamily_domains:SSF48065 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 46687684 46687684 C A 1 0 0 0 0 1 0 0 0 651 521 18 2 2 ALS2CL 3 46687684 Missense_Mutation SNP C C3N-02582_T 36772072 46687684 151607875 19 29883 DNAH1 0 . GRCh38 3 52359988 52359988 + Missense_Mutation SNP G G A rs369984253 C3N-02582_T C3N-02582_N G G c.4480G>A p.Val1494Ile p.V1494I ENST00000420323 27/78 229 197 32 370 370 0 strelka-varscan-mutect DNAH1,missense_variant,p.Val1494Ile,ENST00000420323,NM_015512.4;DNAH1,upstream_gene_variant,,ENST00000466628,;DNAH1,non_coding_transcript_exon_variant,,ENST00000486752,; A ENST00000420323 Transcript missense_variant 4741/13104 4480/12798 1494/4265 V/I Gtc/Atc rs369984253,COSM86463 1 1 DNAH1 HGNC HGNC:2940 protein_coding YES CCDS46842.1 ENSP00000401514 Q9P2D7 A0A140VJI6 UPI00017EE9F6 NM_015512.4 deleterious(0) 27/78 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF137 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs369984253 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 52359988 52359988 G A 1 0 0 0 0 1 0 0 0 4410 1145 40 1 1 DNAH1 3 52359988 Missense_Mutation SNP G C3N-02582_T 5672304 52359988 145935571 20 29884 SHQ1 0 . GRCh38 3 72750749 72750749 + Missense_Mutation SNP T T A novel C3N-02582_T C3N-02582_N T T c.1269A>T p.Glu423Asp p.E423D ENST00000325599 11/11 133 109 24 219 219 0 strelka-varscan-mutect SHQ1,missense_variant,p.Glu423Asp,ENST00000325599,NM_018130.2;SHQ1,missense_variant,p.Glu395Asp,ENST00000463369,;SHQ1,non_coding_transcript_exon_variant,,ENST00000468371,;SHQ1,3_prime_UTR_variant,,ENST00000444040,; A ENST00000325599 Transcript missense_variant 1409/2879 1269/1734 423/577 E/D gaA/gaT 1 -1 SHQ1 HGNC HGNC:25543 protein_coding YES CCDS33788.1 ENSP00000315182 Q6PI26 UPI00001416C5 NM_018130.2 deleterious(0) 11/11 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR12967,hmmpanther:PTHR12967:SF0,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 72750749 72750749 T A 1 0 0 0 0 1 0 0 0 14555 1606 56 4 4 SHQ1 3 72750749 Missense_Mutation SNP T C3N-02582_T 20390761 72750749 125544810 21 29885 DCBLD2 0 . GRCh38 3 98800636 98800636 + Missense_Mutation SNP C C T rs749511785 C3N-02582_T C3N-02582_N C C c.1801G>A p.Glu601Lys p.E601K ENST00000326840 15/16 193 153 40 269 269 0 strelka-varscan-mutect DCBLD2,missense_variant,p.Glu601Lys,ENST00000326840,NM_080927.3;DCBLD2,missense_variant,p.Glu615Lys,ENST00000326857,;ST3GAL6,downstream_gene_variant,,ENST00000394162,NM_001323352.1,NM_001323365.1,NM_006100.3;ST3GAL6,downstream_gene_variant,,ENST00000613264,NM_001271145.1;ST3GAL6,downstream_gene_variant,,ENST00000265261,NM_001271147.1,NM_001271142.1;RNU6-26P,downstream_gene_variant,,ENST00000383985,;ST3GAL6,intron_variant,,ENST00000491912,;ST3GAL6,upstream_gene_variant,,ENST00000495502,;DCBLD2,non_coding_transcript_exon_variant,,ENST00000496736,;ST3GAL6,downstream_gene_variant,,ENST00000486249,;DCBLD2,downstream_gene_variant,,ENST00000494614,; T ENST00000326840 Transcript missense_variant 2164/6122 1801/2328 601/775 E/K Gaa/Aaa rs749511785 1 -1 DCBLD2 HGNC HGNC:24627 protein_coding YES CCDS46878.1 ENSP00000321573 Q96PD2 UPI0000072ABB NM_080927.3 tolerated(0.13) 15/16 hmmpanther:PTHR10127 MODERATE 1 SNV 1 1 PASS rs749511785 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 98800636 98800636 C T 1 0 0 0 0 1 0 0 0 4083 893 31 1 1 DCBLD2 3 98800636 Missense_Mutation SNP C C3N-02582_T 26049887 98800636 99494923 22 29886 ALB 0 . GRCh38 4 73418181 73418181 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.1522A>T p.Arg508Trp p.R508W ENST00000295897 12/15 260 226 34 414 414 0 strelka-varscan-mutect ALB,missense_variant,p.Arg508Trp,ENST00000295897,NM_000477.5;ALB,missense_variant,p.Arg508Trp,ENST00000509063,;ALB,missense_variant,p.Arg358Trp,ENST00000503124,;ALB,missense_variant,p.Arg393Trp,ENST00000401494,;ALB,missense_variant,p.Arg295Trp,ENST00000621628,;ALB,missense_variant,p.Arg353Trp,ENST00000511370,;ALB,missense_variant,p.Arg316Trp,ENST00000415165,;ALB,missense_variant,p.Arg295Trp,ENST00000621085,;ALB,non_coding_transcript_exon_variant,,ENST00000505649,;ALB,upstream_gene_variant,,ENST00000495173,;ALB,3_prime_UTR_variant,,ENST00000476441,;ALB,non_coding_transcript_exon_variant,,ENST00000486939,;ALB,downstream_gene_variant,,ENST00000484992,;ALB,downstream_gene_variant,,ENST00000504043,;ALB,upstream_gene_variant,,ENST00000508932,; T ENST00000295897 Transcript missense_variant 1611/2263 1522/1830 508/609 R/W Agg/Tgg 1 1 ALB HGNC HGNC:399 protein_coding YES CCDS3555.1 ENSP00000295897 P02768 UPI000002C1AC NM_000477.5 deleterious(0) 12/15 Gene3D:1.10.246.10,Pfam_domain:PF00273,PIRSF_domain:PIRSF002520,SMART_domains:SM00103,Superfamily_domains:SSF48552,PROSITE_profiles:PS51438,hmmpanther:PTHR11385:SF13,hmmpanther:PTHR11385 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 73418181 73418181 A T 1 0 0 0 0 1 0 0 0 586 179 7 4 4 ALB 4 73418181 Missense_Mutation SNP A C3N-02582_T 73418181 116796374 23 29887 ADH1A 0 . GRCh38 4 99282509 99282509 + Missense_Mutation SNP G G A rs781090973 C3N-02582_T C3N-02582_N G G c.665C>T p.Ala222Val p.A222V ENST00000209668 6/9 288 263 25 398 397 1 varscan-mutect ADH1A,missense_variant,p.Ala222Val,ENST00000209668,NM_000667.3;RP11-696N14.1,intron_variant,,ENST00000500358,;RP11-696N14.1,downstream_gene_variant,,ENST00000506160,;ADH1A,downstream_gene_variant,,ENST00000511656,;ADH1A,non_coding_transcript_exon_variant,,ENST00000503461,; A ENST00000209668 Transcript missense_variant 779/1499 665/1128 222/375 A/V gCg/gTg rs781090973,COSM1049401 1 -1 ADH1A HGNC HGNC:249 protein_coding YES CCDS3648.1 ENSP00000209668 P07327 UPI0000062219 NM_000667.3 deleterious(0.03) 6/9 hmmpanther:PTHR11695:SF527,hmmpanther:PTHR11695,Pfam_domain:PF00107,Gene3D:3.40.50.720,SMART_domains:SM00829,Superfamily_domains:SSF51735 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs781090973 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 99282509 99282509 G A 1 0 0 0 0 1 0 0 0 380 1087 38 1 1 ADH1A 4 99282509 Missense_Mutation SNP G C3N-02582_T 25864328 99282509 90932046 24 29888 PLK4 0 . GRCh38 4 127887454 127887454 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.1417A>G p.Thr473Ala p.T473A ENST00000270861 6/16 205 194 11 241 241 0 strelka-varscan-mutect PLK4,missense_variant,p.Thr473Ala,ENST00000270861,NM_014264.4;PLK4,missense_variant,p.Thr473Ala,ENST00000515069,;PLK4,missense_variant,p.Thr439Ala,ENST00000507249,;PLK4,missense_variant,p.Thr441Ala,ENST00000513090,NM_001190799.1;PLK4,missense_variant,p.Thr432Ala,ENST00000514379,NM_001190801.1;PLK4,upstream_gene_variant,,ENST00000508113,;RNU6-583P,upstream_gene_variant,,ENST00000516012,;PLK4,downstream_gene_variant,,ENST00000511942,;PLK4,non_coding_transcript_exon_variant,,ENST00000510605,;PLK4,upstream_gene_variant,,ENST00000507454,;PLK4,downstream_gene_variant,,ENST00000503914,; G ENST00000270861 Transcript missense_variant 1691/3841 1417/2913 473/970 T/A Act/Gct 1 1 PLK4 HGNC HGNC:11397 protein_coding YES CCDS3735.1 ENSP00000270861 O00444 UPI000007426E NM_014264.4 tolerated(0.66) 6/16 hmmpanther:PTHR24345,hmmpanther:PTHR24345:SF50 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 127887454 127887454 A G 1 0 0 0 0 1 0 0 0 12193 275 10 5 5 PLK4 4 127887454 Missense_Mutation SNP A C3N-02582_T 28604945 127887454 62327101 25 29889 PCDH10 0 . GRCh38 4 133152283 133152283 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.2143A>T p.Thr715Ser p.T715S ENST00000264360 1/5 113 103 10 164 164 0 strelka-varscan-mutect PCDH10,missense_variant,p.Thr715Ser,ENST00000264360,NM_032961.2;PCDH10,missense_variant,p.Thr715Ser,ENST00000618019,NM_020815.2;RP11-9G1.3,upstream_gene_variant,,ENST00000505289,;RP11-9G1.3,upstream_gene_variant,,ENST00000509715,;PCDH10,upstream_gene_variant,,ENST00000511112,; T ENST00000264360 Transcript missense_variant 2969/8489 2143/3123 715/1040 T/S Acc/Tcc 1 1 PCDH10 HGNC HGNC:13404 protein_coding YES CCDS34063.1 ENSP00000264360 Q9P2E7 X5D999 UPI0000161C61 NM_032961.2 tolerated(0.27) 1/5 Pfam_domain:PF16492,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF0 MODERATE 1 SNV 1 1 PASS . . 0 207 3 0 0 0 0 0 -19.73603 1 1 1 1 0 T 3 4 104 133152283 133152283 A T 1 0 0 0 0 1 0 0 0 11594 159 6 4 4 PCDH10 4 133152283 Missense_Mutation SNP A C3N-02582_T 5264829 133152283 57062272 26 29890 DNAH5 0 . GRCh38 5 13844951 13844951 + Silent SNP G G A rs749688197 C3N-02582_T C3N-02582_N G G c.5157C>T p.= p.F1719F ENST00000265104 32/79 286 254 32 278 278 0 strelka-varscan-mutect DNAH5,synonymous_variant,p.=,ENST00000265104,NM_001369.2; A ENST00000265104 Transcript synonymous_variant 5262/15633 5157/13875 1719/4624 F ttC/ttT rs749688197,COSM3609121 1 -1 DNAH5 HGNC HGNC:2950 protein_coding YES CCDS3882.1 ENSP00000265104 Q8TE73 UPI0000110101 NM_001369.2 32/79 hmmpanther:PTHR10676:SF240,hmmpanther:PTHR10676,Pfam_domain:PF08393 0,1 LOW 1 SNV 1 0,1 1 PASS rs749688197 . 0 208 0 0 2 0 0 0 -12.18284 0.9946344 1 1 1 0 A 2 1 104 13844951 13844951 G A 1 0 0 0 0 0 0 0 1 4419 1049 37 1 1 DNAH5 5 13844951 Silent SNP G C3N-02582_T 13844951 167693308 27 29891 NIPBL 0 . GRCh38 5 37027373 37027373 + Silent SNP A A G novel C3N-02582_T C3N-02582_N A A c.5823A>G p.= p.R1941R ENST00000282516 32/47 385 312 73 433 432 1 strelka-varscan-mutect NIPBL,synonymous_variant,p.=,ENST00000282516,NM_133433.3;NIPBL,synonymous_variant,p.=,ENST00000448238,NM_015384.4;NIPBL,intron_variant,,ENST00000621733,; G ENST00000282516 Transcript synonymous_variant 6322/10435 5823/8415 1941/2804 R agA/agG 1 1 NIPBL HGNC HGNC:28862 protein_coding YES CCDS3920.1 ENSP00000282516 Q6KC79 UPI00003761B5 NM_133433.3 32/47 hmmpanther:PTHR21704,hmmpanther:PTHR21704:SF18,Superfamily_domains:SSF48371 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 104 37027373 37027373 A G 1 0 0 0 0 0 0 0 1 10463 301 11 5 5 NIPBL 5 37027373 Silent SNP A C3N-02582_T 23182422 37027373 144510886 28 29892 C5orf42 0 . GRCh38 5 37184995 37184995 + Missense_Mutation SNP T T C novel C3N-02582_T C3N-02582_N T T c.4274A>G p.Asn1425Ser p.N1425S ENST00000425232 25/52 272 218 54 309 309 0 strelka-varscan-mutect C5orf42,missense_variant,p.Asn1425Ser,ENST00000425232,NM_023073.3;C5orf42,missense_variant,p.Asn1425Ser,ENST00000508244,;C5orf42,missense_variant,p.Asn473Ser,ENST00000514429,;C5orf42,missense_variant,p.Asn430Ser,ENST00000509849,; C ENST00000425232 Transcript missense_variant 4505/11199 4274/9594 1425/3197 N/S aAt/aGt 1 -1 C5orf42 HGNC HGNC:25801 protein_coding YES CCDS34146.2 ENSP00000389014 Q9H799 UPI0001AAB3EA NM_023073.3 deleterious(0) 25/52 hmmpanther:PTHR14492,hmmpanther:PTHR14492:SF3 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 37184995 37184995 T C 1 0 0 0 0 1 0 0 0 2100 1493 52 5 5 C5orf42 5 37184995 Missense_Mutation SNP T C3N-02582_T 157622 37184995 144353264 29 29893 DHX29 0 . GRCh38 5 55273374 55273374 + Nonsense_Mutation SNP A A C rs779785381 C3N-02582_T C3N-02582_N A A c.2694T>G p.Tyr898Ter p.Y898* ENST00000251636 17/27 41 33 8 54 54 0 strelka-varscan-mutect DHX29,stop_gained,p.Tyr898Ter,ENST00000251636,NM_019030.2;DHX29,stop_gained,p.Tyr898Ter,ENST00000621106,;RP11-506H20.1,intron_variant,,ENST00000506435,;DHX29,non_coding_transcript_exon_variant,,ENST00000504778,;DHX29,non_coding_transcript_exon_variant,,ENST00000513447,; C ENST00000251636 Transcript stop_gained 2843/4502 2694/4110 898/1369 Y/* taT/taG rs779785381 1 -1 DHX29 HGNC HGNC:15815 protein_coding YES CCDS34158.1 ENSP00000251636 Q7Z478 UPI00001AE72C NM_019030.2 17/27 PROSITE_profiles:PS51194,hmmpanther:PTHR18934,hmmpanther:PTHR18934:SF139,Gene3D:3.40.50.300,Pfam_domain:PF00271,SMART_domains:SM00490,Superfamily_domains:SSF52540 HIGH 1 SNV 1 1 PASS rs779785381 . 0 206 4 0 0 0 0 0 -19.73887 1 1 1 1 0 C 4 2 104 55273374 55273374 A C 1 0 0 0 0 0 1 0 0 4307 463 16 5 5 DHX29 5 55273374 Nonsense_Mutation SNP A C3N-02582_T 18088379 55273374 126264885 30 29894 ADGRV1 0 . GRCh38 5 90685822 90685822 + Missense_Mutation SNP C C T rs186999408 C3N-02582_T C3N-02582_N C C c.6317C>T p.Ala2106Val p.A2106V ENST00000405460 29/90 307 287 20 261 261 0 strelka-varscan-mutect ADGRV1,missense_variant,p.Ala2106Val,ENST00000405460,NM_032119.3; T ENST00000405460 Transcript missense_variant 6413/19338 6317/18921 2106/6306 A/V gCg/gTg rs186999408,COSM39595 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 deleterious(0) 29/90 hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,Superfamily_domains:SSF141072 benign 0,1 MODERATE 1 SNV 1 1,1 1 PASS rs186999408 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 90685822 90685822 C T 1 0 0 0 0 1 0 0 0 379 768 27 1 1 ADGRV1 5 90685822 Missense_Mutation SNP C C3N-02582_T 35412448 90685822 90852437 31 29895 LOX 0 . GRCh38 5 122070585 122070585 + Frame_Shift_Del DEL A A - novel C3N-02582_T C3N-02582_N A A c.1040delT p.Leu347Ter p.L347* ENST00000231004 5/7 55 48 7 127 127 0 sindel-varindel-pindel LOX,frameshift_variant,p.Leu347Ter,ENST00000231004,NM_002317.5;LOX,non_coding_transcript_exon_variant,,ENST00000513319,;LOX,non_coding_transcript_exon_variant,,ENST00000505593,;SRFBP1,intron_variant,,ENST00000504881,;LOX,3_prime_UTR_variant,,ENST00000508067,;LOX,non_coding_transcript_exon_variant,,ENST00000503759,; - ENST00000231004 Transcript frameshift_variant 1340/5102 1040/1254 347/417 L/X tTg/tg 1 -1 LOX HGNC HGNC:6664 protein_coding YES CCDS4129.1 ENSP00000231004 P28300 D0PNI2 UPI000012EA87 NM_002317.5 5/7 hmmpanther:PTHR19331:SF3,hmmpanther:PTHR19331,Pfam_domain:PF01186,Prints_domain:PR00074 HIGH 1 deletion 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 122070585 122070585 A - 1 0 1 0 1 0 0 0 0 8800 144 5 0 0 LOX 5 122070585 Frame_Shift_Del DEL A C3N-02582_T 31384763 122070585 59467674 32 29896 SH3RF2 0 . GRCh38 5 146000161 146000161 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.482A>G p.Asn161Ser p.N161S ENST00000511217 2/10 267 187 80 376 376 0 strelka-varscan-mutect SH3RF2,missense_variant,p.Asn161Ser,ENST00000511217,;SH3RF2,missense_variant,p.Asn161Ser,ENST00000359120,NM_152550.3;AC005351.1,downstream_gene_variant,,ENST00000511152,; G ENST00000511217 Transcript missense_variant 534/5607 482/2190 161/729 N/S aAt/aGt 1 1 SH3RF2 HGNC HGNC:26299 protein_coding YES CCDS4280.1 ENSP00000424497 Q8TEC5 UPI0000457366 deleterious(0) 2/10 PROSITE_profiles:PS50002,hmmpanther:PTHR10663,hmmpanther:PTHR10663:SF151,Gene3D:2.30.30.40,Pfam_domain:PF07653,SMART_domains:SM00326,Superfamily_domains:SSF50044 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 146000161 146000161 A G 1 0 0 0 0 1 0 0 0 14518 101 4 5 5 SH3RF2 5 146000161 Missense_Mutation SNP A C3N-02582_T 23929576 146000161 35538098 33 29897 NSD1 0 . GRCh38 5 177135801 177135801 + Missense_Mutation SNP C C G novel C3N-02582_T C3N-02582_N C C c.698C>G p.Thr233Ser p.T233S ENST00000439151 2/23 91 80 11 102 102 0 strelka-varscan-mutect NSD1,missense_variant,p.Thr233Ser,ENST00000439151,NM_022455.4;NSD1,intron_variant,,ENST00000354179,NM_172349.2;NSD1,intron_variant,,ENST00000347982,;NSD1,intron_variant,,ENST00000511258,;NSD1,intron_variant,,ENST00000508896,;NSD1,intron_variant,,ENST00000510954,;NSD1,non_coding_transcript_exon_variant,,ENST00000602285,;NSD1,downstream_gene_variant,,ENST00000512992,; G ENST00000439151 Transcript missense_variant 743/12892 698/8091 233/2696 T/S aCt/aGt 1 1 NSD1 HGNC HGNC:14234 protein_coding YES CCDS4412.1 ENSP00000395929 Q96L73 UPI000006F9C6 NM_022455.4 tolerated_low_confidence(0.11) 2/23 MODERATE 1 SNV 1 1 PASS . . 0 204 6 0 0 0 0 0 -19.99958 0.9999999 1 1 1 0 G 3 3 104 177135801 177135801 C G 1 0 0 0 0 1 0 0 0 10728 565 20 4 4 NSD1 5 177135801 Missense_Mutation SNP C C3N-02582_T 31135640 177135801 4402458 34 29898 FLT4 0 . GRCh38 5 180631748 180631748 + Frame_Shift_Del DEL G G - C3N-02582_T C3N-02582_N G G c.89delC p.Pro30ArgfsTer3 p.P30Rfs*3 ENST00000261937 2/30 219 147 72 295 294 1 sindel-varindel-pindel FLT4,frameshift_variant,p.Pro30ArgfsTer3,ENST00000261937,NM_182925.4;FLT4,frameshift_variant,p.Pro30ArgfsTer3,ENST00000393347,NM_002020.4;FLT4,frameshift_variant,p.Pro30ArgfsTer3,ENST00000502649,;FLT4,frameshift_variant,p.Pro30ArgfsTer3,ENST00000619105,;FLT4,non_coding_transcript_exon_variant,,ENST00000424276,;FLT4,non_coding_transcript_exon_variant,,ENST00000502293,;FLT4,non_coding_transcript_exon_variant,,ENST00000513527,;FLT4,upstream_gene_variant,,ENST00000507059,; - ENST00000261937 Transcript frameshift_variant 168/5857 89/4092 30/1363 P/X cCg/cg COSM296843,COSM296844,COSM4685088,COSM4685089 1 -1 FLT4 HGNC HGNC:3767 protein_coding YES CCDS4457.1 ENSP00000261937 P35916 UPI00001488E7 NM_182925.4 2/30 PROSITE_profiles:PS50835,Gene3D:2.60.40.10,Superfamily_domains:SSF48726 1,1,1,1 HIGH 1 deletion 1 1,1,1,1 1 PASS . . 0 196 0 0 14 0 0 0 -20 0.1370237 1 1 0 0 - 7 5 104 180631748 180631748 G - 1 0 1 0 1 0 0 0 0 5800 1116 39 0 0 FLT4 5 180631748 Frame_Shift_Del DEL G C3N-02582_T 3495947 180631748 906511 35 29899 RNF182 0 . GRCh38 6 13977553 13977553 + Missense_Mutation SNP G G C novel C3N-02582_T C3N-02582_N G G c.434G>C p.Ser145Thr p.S145T ENST00000488300 3/3 174 160 14 239 239 0 strelka-varscan-mutect RNF182,missense_variant,p.Ser145Thr,ENST00000488300,NM_152737.3;RNF182,missense_variant,p.Ser145Thr,ENST00000544682,NM_001165032.1;RNF182,missense_variant,p.Ser145Thr,ENST00000537663,NM_001165034.1;RNF182,missense_variant,p.Ser145Thr,ENST00000537388,NM_001165033.1;RNF182,missense_variant,p.Ser145Thr,ENST00000420478,;RNF182,downstream_gene_variant,,ENST00000488763,;RNF182,downstream_gene_variant,,ENST00000423553,;RNF182,downstream_gene_variant,,ENST00000471906,; C ENST00000488300 Transcript missense_variant 957/3706 434/744 145/247 S/T aGc/aCc 1 1 RNF182 HGNC HGNC:28522 protein_coding YES CCDS4531.1 ENSP00000420465 Q8N6D2 A0A024QZW5 UPI000006E1CA NM_152737.3 tolerated(0.08) 3/3 hmmpanther:PTHR13139,hmmpanther:PTHR13139:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 13977553 13977553 G C 1 0 0 0 0 1 0 0 0 13643 971 34 4 4 RNF182 6 13977553 Missense_Mutation SNP G C3N-02582_T 13977553 156828426 36 29900 ZFP57 0 . GRCh38 6 29672900 29672900 + Missense_Mutation SNP T T C C3N-02582_T C3N-02582_N T T c.1211A>G p.Lys404Arg p.K404R ENST00000488757 4/4 665 618 47 845 845 0 strelka-varscan-mutect ZFP57,missense_variant,p.Lys384Arg,ENST00000376883,;ZFP57,missense_variant,p.Lys404Arg,ENST00000488757,NM_001109809.2;ZFP57,missense_variant,p.Lys320Arg,ENST00000376881,;MOG,downstream_gene_variant,,ENST00000376894,;MOG,downstream_gene_variant,,ENST00000376917,NM_206809.3;MOG,downstream_gene_variant,,ENST00000431798,NM_206812.3;MOG,downstream_gene_variant,,ENST00000376888,NM_206814.5;MOG,downstream_gene_variant,,ENST00000376898,NM_002433.4;MOG,downstream_gene_variant,,ENST00000494692,NM_206811.3;MOG,downstream_gene_variant,,ENST00000396701,NM_206810.3;MOG,downstream_gene_variant,,ENST00000376891,NM_001008229.2;MOG,downstream_gene_variant,,ENST00000396704,NM_001008228.2;MOG,downstream_gene_variant,,ENST00000416766,;MOG,downstream_gene_variant,,ENST00000490427,NM_001170418.1;MOG,downstream_gene_variant,,ENST00000483013,;MOG,downstream_gene_variant,,ENST00000376889,;MOG,downstream_gene_variant,,ENST00000485211,;MOG,downstream_gene_variant,,ENST00000485885,; C ENST00000488757 Transcript missense_variant 1362/1870 1211/1611 404/536 K/R aAg/aGg COSM5441985 1 -1 ZFP57 HGNC HGNC:18791 protein_coding YES CCDS43436.2 ENSP00000418259 Q9NU63 UPI0001951170 NM_001109809.2 tolerated(0.09) 4/4 Gene3D:3.30.160.60,PROSITE_patterns:PS00028,PROSITE_profiles:PS50157,hmmpanther:PTHR24402,hmmpanther:PTHR24402:SF179,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 29672900 29672900 T C 1 0 0 0 0 1 0 0 0 18226 1609 56 5 5 ZFP57 6 29672900 Missense_Mutation SNP T C3N-02582_T 15695347 29672900 141133079 37 29901 BRD2 0 . GRCh38 6 32980693 32980693 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.2486A>T p.Asp829Val p.D829V ENST00000395287 13/13 219 206 13 220 220 0 strelka-varscan-mutect BRD2,missense_variant,p.Asp794Val,ENST00000374825,NM_005104.3;BRD2,missense_variant,p.Asp794Val,ENST00000374831,NM_001113182.2;BRD2,missense_variant,p.Asp829Val,ENST00000395287,NM_001199455.1;BRD2,missense_variant,p.Asp800Val,ENST00000449025,;BRD2,missense_variant,p.Asp747Val,ENST00000449085,NM_001291986.1,NM_001199456.1;BRD2,downstream_gene_variant,,ENST00000607833,;BRD2,downstream_gene_variant,,ENST00000456339,;BRD2,downstream_gene_variant,,ENST00000606059,;BRD2,3_prime_UTR_variant,,ENST00000482914,;BRD2,non_coding_transcript_exon_variant,,ENST00000469132,;BRD2,non_coding_transcript_exon_variant,,ENST00000482838,;BRD2,downstream_gene_variant,,ENST00000495733,;BRD2,downstream_gene_variant,,ENST00000464592,;BRD2,downstream_gene_variant,,ENST00000463639,;BRD2,downstream_gene_variant,,ENST00000481259,; T ENST00000395287 Transcript missense_variant 2655/3467 2486/2511 829/836 D/V gAc/gTc 1 1 BRD2 HGNC HGNC:1103 protein_coding YES CCDS56420.1 ENSP00000378702 P25440 UPI0000227E6A NM_001199455.1 deleterious_low_confidence(0.01) 13/13 hmmpanther:PTHR22880,hmmpanther:PTHR22880:SF126,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1184085354 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 32980693 32980693 A T 1 0 0 0 0 1 0 0 0 1672 275 10 4 4 BRD2 6 32980693 Missense_Mutation SNP A C3N-02582_T 3307793 32980693 137825286 38 29902 RFX6 0 . GRCh38 6 116919143 116919143 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.1029A>T p.Leu343Phe p.L343F ENST00000332958 11/19 175 164 11 257 257 0 strelka-varscan-mutect RFX6,missense_variant,p.Leu343Phe,ENST00000332958,NM_173560.3;RFX6,downstream_gene_variant,,ENST00000471966,;RFX6,non_coding_transcript_exon_variant,,ENST00000487683,; T ENST00000332958 Transcript missense_variant 1045/3460 1029/2787 343/928 L/F ttA/ttT 1 1 RFX6 HGNC HGNC:21478 protein_coding YES CCDS5113.1 ENSP00000332208 Q8HWS3 UPI00001609BE NM_173560.3 deleterious(0.01) 11/19 hmmpanther:PTHR12619,hmmpanther:PTHR12619:SF28 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 116919143 116919143 A T 1 0 0 0 0 1 0 0 0 13441 417 15 4 4 RFX6 6 116919143 Missense_Mutation SNP A C3N-02582_T 83938450 116919143 53886836 39 29903 ARHGAP18 0 . GRCh38 6 129600775 129600775 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.1439T>A p.Met480Lys p.M480K ENST00000368149 11/15 238 204 34 340 340 0 strelka-varscan-mutect ARHGAP18,missense_variant,p.Met480Lys,ENST00000368149,NM_033515.2;ARHGAP18,upstream_gene_variant,,ENST00000463225,;ARHGAP18,upstream_gene_variant,,ENST00000483367,; T ENST00000368149 Transcript missense_variant 1528/4462 1439/1992 480/663 M/K aTg/aAg 1 -1 ARHGAP18 HGNC HGNC:21035 protein_coding YES CCDS34535.1 ENSP00000357131 Q8N392 UPI000020E208 NM_033515.2 deleterious(0.01) 11/15 Gene3D:1.10.555.10,Pfam_domain:PF00620,PROSITE_profiles:PS50238,hmmpanther:PTHR14963,hmmpanther:PTHR14963:SF6,SMART_domains:SM00324,Superfamily_domains:SSF48350 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 129600775 129600775 A T 1 0 0 0 0 1 0 0 0 992 217 8 4 4 ARHGAP18 6 129600775 Missense_Mutation SNP A C3N-02582_T 12681632 129600775 41205204 40 29904 MED23 0 . GRCh38 6 131620701 131620701 + Missense_Mutation SNP G G A novel C3N-02582_T C3N-02582_N G G c.524C>T p.Ala175Val p.A175V ENST00000368068 7/29 317 279 38 318 317 1 strelka-varscan-mutect MED23,missense_variant,p.Ala175Val,ENST00000368068,NM_004830.3;MED23,missense_variant,p.Ala175Val,ENST00000354577,NM_015979.3,NM_001270521.1;MED23,missense_variant,p.Ala175Val,ENST00000368058,;MED23,missense_variant,p.Ala175Val,ENST00000368060,NM_001270522.1;MED23,missense_variant,p.Ala175Val,ENST00000368053,;MED23,missense_variant,p.Ala175Val,ENST00000539158,; A ENST00000368068 Transcript missense_variant 704/5233 524/4107 175/1368 A/V gCc/gTc 1 -1 MED23 HGNC HGNC:2372 protein_coding YES CCDS5147.1 ENSP00000357047 Q9ULK4 UPI000012855F NM_004830.3 tolerated(0.29) 7/29 Pfam_domain:PF11573,hmmpanther:PTHR12691,hmmpanther:PTHR12691:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 131620701 131620701 G A 1 0 0 0 0 1 0 0 0 9380 1203 42 3 3 MED23 6 131620701 Missense_Mutation SNP G C3N-02582_T 2019926 131620701 39185278 41 29905 VNN1 0 . GRCh38 6 132683225 132683225 + Missense_Mutation SNP G G A C3N-02582_T C3N-02582_N G G c.1457C>T p.Ser486Leu p.S486L ENST00000367928 7/7 279 262 17 282 282 0 strelka-varscan-mutect VNN1,missense_variant,p.Ser486Leu,ENST00000367928,NM_004666.2; A ENST00000367928 Transcript missense_variant 1471/3106 1457/1542 486/513 S/L tCa/tTa COSM79316 1 -1 VNN1 HGNC HGNC:12705 protein_coding YES CCDS5159.1 ENSP00000356905 O95497 UPI000013C91E NM_004666.2 tolerated(0.76) 7/7 hmmpanther:PTHR10609,hmmpanther:PTHR10609:SF16,PIRSF_domain:PIRSF011861 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 132683225 132683225 G A 1 0 0 0 0 1 0 0 0 17729 1294 45 3 3 VNN1 6 132683225 Missense_Mutation SNP G C3N-02582_T 1062524 132683225 38122754 42 29906 HBS1L 0 . GRCh38 6 135050636 135050636 + Missense_Mutation SNP C C T rs772534723 C3N-02582_T C3N-02582_N C C c.55G>A p.Asp19Asn p.D19N ENST00000367837 2/18 213 201 12 164 164 0 strelka-varscan-mutect HBS1L,missense_variant,p.Asp19Asn,ENST00000367837,NM_006620.3;HBS1L,missense_variant,p.Asp19Asn,ENST00000367822,NM_001145207.1;HBS1L,missense_variant,p.Asp19Asn,ENST00000367826,NM_001145158.1;HBS1L,missense_variant,p.Asp19Asn,ENST00000415177,;HBS1L,missense_variant,p.Asp19Asn,ENST00000314674,;HBS1L,missense_variant,p.Asp19Asn,ENST00000367820,;HBS1L,missense_variant,p.Asp34Asn,ENST00000529882,;HBS1L,intron_variant,,ENST00000525067,;HBS1L,intron_variant,,ENST00000524715,;HBS1L,upstream_gene_variant,,ENST00000533274,;CTA-212D2.2,upstream_gene_variant,,ENST00000447508,;HBS1L,missense_variant,p.Asp4Asn,ENST00000526100,; T ENST00000367837 Transcript missense_variant 262/7163 55/2055 19/684 D/N Gat/Aat rs772534723 1 -1 HBS1L HGNC HGNC:4834 protein_coding YES CCDS5173.1 ENSP00000356811 Q9Y450 D9YZV0 UPI00000372EA NM_006620.3 tolerated(0.06) 2/18 PD278081 MODERATE 1 SNV 1 1 PASS rs772534723 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 135050636 135050636 C T 1 0 0 0 0 1 0 0 0 6873 826 29 3 3 HBS1L 6 135050636 Missense_Mutation SNP C C3N-02582_T 2367411 135050636 35755343 43 29907 UTRN 0 . GRCh38 6 144840784 144840784 + Missense_Mutation SNP C C T novel C3N-02582_T C3N-02582_N C C c.10222C>T p.Leu3408Phe p.L3408F ENST00000367545 72/74 439 370 69 329 329 0 strelka-varscan-mutect UTRN,missense_variant,p.Leu3408Phe,ENST00000367545,NM_007124.2;UTRN,missense_variant,p.Leu963Phe,ENST00000367526,;UTRN,downstream_gene_variant,,ENST00000417142,;UTRN,downstream_gene_variant,,ENST00000455022,;UTRN,non_coding_transcript_exon_variant,,ENST00000460618,;UTRN,downstream_gene_variant,,ENST00000465299,; T ENST00000367545 Transcript missense_variant 10222/12339 10222/10302 3408/3433 L/F Ctc/Ttc 1 1 UTRN HGNC HGNC:12635 protein_coding YES CCDS34547.1 ENSP00000356515 P46939 UPI00003673F1 NM_007124.2 deleterious(0) 72/74 hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF225 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 144840784 144840784 C T 1 0 0 0 0 1 0 0 0 17647 913 32 3 3 UTRN 6 144840784 Missense_Mutation SNP C C3N-02582_T 9790148 144840784 25965195 44 29908 OGDH 0 . GRCh38 7 44697626 44697626 + Missense_Mutation SNP G G A novel C3N-02582_T C3N-02582_N G G c.2202G>A p.Met734Ile p.M734I ENST00000222673 17/23 204 157 47 232 232 0 strelka-varscan-mutect OGDH,missense_variant,p.Met734Ile,ENST00000222673,NM_002541.3;OGDH,missense_variant,p.Met733Ile,ENST00000631326,;OGDH,missense_variant,p.Met730Ile,ENST00000449767,NM_001165036.1;OGDH,missense_variant,p.Met745Ile,ENST00000447398,;OGDH,missense_variant,p.Met749Ile,ENST00000444676,;OGDH,missense_variant,p.Met584Ile,ENST00000439616,; A ENST00000222673 Transcript missense_variant 2244/4181 2202/3072 734/1023 M/I atG/atA 1 1 OGDH HGNC HGNC:8124 protein_coding YES CCDS34627.1 ENSP00000222673 Q02218 UPI000006D5FE NM_002541.3 tolerated(0.06) 17/23 Gene3D:3.40.50.970,Pfam_domain:PF02779,PIRSF_domain:PIRSF000157,hmmpanther:PTHR23152,hmmpanther:PTHR23152:SF7,SMART_domains:SM00861,Superfamily_domains:SSF52518,TIGRFAM_domain:TIGR00239 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 44697626 44697626 G A 1 0 0 0 0 1 0 0 0 10913 1362 47 3 3 OGDH 7 44697626 Missense_Mutation SNP G C3N-02582_T 44697626 114648347 45 29909 EGFR 0 . GRCh38 7 55174773 55174787 + In_Frame_Del DEL GAATTAAGAGAAGCA GAATTAAGAGAAGCA - rs727504233 C3N-02582_T C3N-02582_N GAATTAAGAGAAGCA GAATTAAGAGAAGCA c.2236_2250delGAATTAAGAGAAGCA p.Glu746_Ala750del p.E746_A750del ENST00000275493 19/28 721 287 434 599 599 0 sindel-varindel-pindel EGFR,inframe_deletion,p.Glu746_Ala750del,ENST00000275493,NM_005228.3;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000454757,;EGFR,inframe_deletion,p.Glu701_Ala705del,ENST00000455089,;EGFR,downstream_gene_variant,,ENST00000344576,NM_201284.1;EGFR-AS1,downstream_gene_variant,,ENST00000442411,; - ENST00000275493 Transcript inframe_deletion 2413-2427/9821 2236-2250/3633 746-750/1210 ELREA/- GAATTAAGAGAAGCA/- rs727504233,COSM6225 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 19/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,Gene3D:3.30.200.20,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1 MODERATE 1 deletion 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 55174773 55174773 GAATTAAGAGAAGCA - 1 0 1 0 1 0 0 0 0 4803 1175 41 0 0 EGFR 7 55174773 In_Frame_Del DEL GAATTAAGAGAAGCA C3N-02582_T 10477147 55174773 104171200 46 29910 ZNF655 0 . GRCh38 7 99572370 99572371 + Frame_Shift_Ins INS - - TA novel C3N-02582_T C3N-02582_N - - c.367_368insTA p.Glu123ValfsTer10 p.E123Vfs*10 ENST00000424881 4/4 154 127 27 237 237 0 sindel-varindel-pindel ZNF655,frameshift_variant,p.Glu123ValfsTer10,ENST00000424881,NM_001085368.1;ZNF655,frameshift_variant,p.Glu88ValfsTer10,ENST00000394163,NM_001009960.1;ZNF655,frameshift_variant,p.Glu88ValfsTer10,ENST00000252713,NM_138494.2;ZNF655,frameshift_variant,p.Glu123ValfsTer10,ENST00000493277,NM_001083956.1;ZNF655,frameshift_variant,p.Glu123ValfsTer10,ENST00000422164,;ZNF655,3_prime_UTR_variant,,ENST00000425063,;ZNF655,downstream_gene_variant,,ENST00000626122,;ZNF655,downstream_gene_variant,,ENST00000422647,;ZNF655,downstream_gene_variant,,ENST00000454654,;ZNF655,downstream_gene_variant,,ENST00000427931,;ZNF655,downstream_gene_variant,,ENST00000449244,;ZNF655,non_coding_transcript_exon_variant,,ENST00000419215,;GS1-259H13.13,intron_variant,,ENST00000486324,;ZNF655,non_coding_transcript_exon_variant,,ENST00000494357,;GS1-259H13.13,intron_variant,,ENST00000455905,;ZNF655,downstream_gene_variant,,ENST00000412636,;ZNF655,downstream_gene_variant,,ENST00000493947,; TA ENST00000424881 Transcript frameshift_variant 587-588/4666 367-368/1581 123/526 E/VX gaa/gTAaa 1 1 ZNF655 HGNC HGNC:30899 protein_coding YES CCDS47655.1 ENSP00000393876 Q8N720 UPI000020F66D NM_001085368.1 4/4 hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF284 HIGH 1 insertion 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 TA 7 5 104 99572370 99572370 - TA 1 0 1 1 0 0 0 0 0 18641 943 33 0 0 ZNF655 7 99572370 Frame_Shift_Ins INS - C3N-02582_T 44397597 99572370 59773603 47 29911 ORC5 0 . GRCh38 7 104200876 104200876 + Missense_Mutation SNP A A C novel C3N-02582_T C3N-02582_N A A c.248T>G p.Leu83Arg p.L83R ENST00000297431 3/14 182 167 15 284 283 1 strelka-varscan-mutect ORC5,missense_variant,p.Leu83Arg,ENST00000297431,NM_002553.3;ORC5,missense_variant,p.Leu83Arg,ENST00000447452,NM_181747.3;ORC5,downstream_gene_variant,,ENST00000626700,;ORC5,non_coding_transcript_exon_variant,,ENST00000485726,;ORC5,upstream_gene_variant,,ENST00000463152,;ORC5,3_prime_UTR_variant,,ENST00000422497,;ORC5,3_prime_UTR_variant,,ENST00000448563,; C ENST00000297431 Transcript missense_variant 391/1958 248/1308 83/435 L/R cTt/cGt 1 -1 ORC5 HGNC HGNC:8491 protein_coding YES CCDS5734.1 ENSP00000297431 O43913 A4D0P7 UPI0000001C1C NM_002553.3 tolerated(0.36) 3/14 hmmpanther:PTHR12705,Pfam_domain:PF13191,Gene3D:3.40.50.300,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 104200876 104200876 A C 1 0 0 0 0 1 0 0 0 11331 72 3 5 5 ORC5 7 104200876 Missense_Mutation SNP A C3N-02582_T 4628506 104200876 55145097 48 29912 THAP5 0 . GRCh38 7 108564978 108564978 + Missense_Mutation SNP T T A C3N-02582_T C3N-02582_N T T c.401A>T p.Asp134Val p.D134V ENST00000415914 3/3 159 129 30 262 262 0 strelka-varscan-mutect THAP5,missense_variant,p.Asp134Val,ENST00000415914,NM_001130475.2;THAP5,missense_variant,p.Asp92Val,ENST00000313516,NM_182529.3;THAP5,3_prime_UTR_variant,,ENST00000438865,;DNAJB9,upstream_gene_variant,,ENST00000249356,NM_012328.2;THAP5,non_coding_transcript_exon_variant,,ENST00000493722,;PNPLA8,intron_variant,,ENST00000489738,;THAP5,intron_variant,,ENST00000468884,;THAP5,downstream_gene_variant,,ENST00000412935,;THAP5,downstream_gene_variant,,ENST00000446771,;THAP5,downstream_gene_variant,,ENST00000484452,;DNAJB9,upstream_gene_variant,,ENST00000491582,; A ENST00000415914 Transcript missense_variant 555/3306 401/1188 134/395 D/V gAt/gTt COSM3941957 1 -1 THAP5 HGNC HGNC:23188 protein_coding YES CCDS47687.1 ENSP00000400500 Q7Z6K1 UPI00003E4106 NM_001130475.2 tolerated(0.14) 3/3 hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF77 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 108564978 108564978 T A 1 0 0 0 0 1 0 0 0 16280 1435 50 4 4 THAP5 7 108564978 Missense_Mutation SNP T C3N-02582_T 4364102 108564978 50780995 49 29913 FOXP2 0 . GRCh38 7 114570816 114570816 + Missense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.268C>A p.Pro90Thr p.P90T ENST00000408937 4/18 270 254 16 316 315 1 strelka-varscan-mutect FOXP2,missense_variant,p.Pro90Thr,ENST00000408937,NM_148898.3;FOXP2,missense_variant,p.Pro89Thr,ENST00000390668,NM_001172767.2;FOXP2,intron_variant,,ENST00000403559,NM_148900.3;FOXP2,intron_variant,,ENST00000393491,;FOXP2,intron_variant,,ENST00000635534,;FOXP2,intron_variant,,ENST00000634411,;FOXP2,intron_variant,,ENST00000393494,;FOXP2,intron_variant,,ENST00000350908,NM_001172766.2,NM_014491.3;FOXP2,intron_variant,,ENST00000393498,;FOXP2,intron_variant,,ENST00000635638,;FOXP2,intron_variant,,ENST00000393489,;FOXP2,intron_variant,,ENST00000378237,;FOXP2,intron_variant,,ENST00000634623,;FOXP2,intron_variant,,ENST00000360232,NM_148899.3;FOXP2,intron_variant,,ENST00000393495,;FOXP2,intron_variant,,ENST00000452963,;FOXP2,non_coding_transcript_exon_variant,,ENST00000459666,;FOXP2,3_prime_UTR_variant,,ENST00000412402,;FOXP2,intron_variant,,ENST00000441290,;FOXP2,intron_variant,,ENST00000635109,;FOXP2,intron_variant,,ENST00000440349,; A ENST00000408937 Transcript missense_variant 642/6443 268/2223 90/740 P/T Cca/Aca 1 1 FOXP2 HGNC HGNC:13875 protein_coding YES CCDS43635.1 ENSP00000386200 O15409 X5D2H2 UPI000007412B NM_148898.3 tolerated_low_confidence(0.23) 4/18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 114570816 114570816 C A 1 0 0 0 0 1 0 0 0 5892 855 30 2 2 FOXP2 7 114570816 Missense_Mutation SNP C C3N-02582_T 6005838 114570816 44775157 50 29914 CADPS2 0 . GRCh38 7 122320230 122320230 + Missense_Mutation SNP C C G rs779920720 C3N-02582_T C3N-02582_N C C c.3826G>C p.Val1276Leu p.V1276L ENST00000449022 30/30 155 145 10 160 160 0 strelka-varscan-mutect CADPS2,missense_variant,p.Val1281Leu,ENST00000615869,;CADPS2,missense_variant,p.Val1174Leu,ENST00000313070,NM_001167940.1;CADPS2,missense_variant,p.Val1274Leu,ENST00000334010,;CADPS2,missense_variant,p.Val1235Leu,ENST00000412584,NM_001009571.3;CADPS2,missense_variant,p.Val1276Leu,ENST00000449022,NM_017954.10;CADPS2,missense_variant,p.Val879Leu,ENST00000397721,;CADPS2,missense_variant,p.Val470Leu,ENST00000462699,; G ENST00000449022 Transcript missense_variant 3846/4073 3826/3891 1276/1296 V/L Gtt/Ctt rs779920720 1 -1 CADPS2 HGNC HGNC:16018 protein_coding YES CCDS55158.1 ENSP00000398481 Q86UW7 UPI0000668808 NM_017954.10 tolerated(0.3) 30/30 hmmpanther:PTHR12166,hmmpanther:PTHR12166:SF7 MODERATE 1 SNV 5 1 PASS rs779920720 . 0 207 0 2 0 0 0 0 -13.57948 0.9999996 1 1 1 0 G 3 3 104 122320230 122320230 C G 1 0 0 0 0 1 0 0 0 2261 478 17 4 4 CADPS2 7 122320230 Missense_Mutation SNP C C3N-02582_T 7749414 122320230 37025743 51 29915 BRAF 0 . GRCh38 7 140924686 140924686 + Silent SNP A A G novel C3N-02582_T C3N-02582_N A A c.18T>C p.= p.G6G ENST00000288602 1/18 206 194 12 213 213 0 strelka-varscan-mutect BRAF,synonymous_variant,p.=,ENST00000288602,NM_004333.4;BRAF,non_coding_transcript_exon_variant,,ENST00000469930,;BRAF,upstream_gene_variant,,ENST00000497784,; G ENST00000288602 Transcript synonymous_variant 79/2480 18/2301 6/766 G ggT/ggC 1 -1 BRAF HGNC HGNC:1097 protein_coding YES CCDS5863.1 ENSP00000288602 P15056 UPI000013DF26 NM_004333.4 1/18 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 104 140924686 140924686 A G 1 0 0 0 0 0 0 0 1 1665 146 6 5 5 BRAF 7 140924686 Silent SNP A C3N-02582_T 18604456 140924686 18421287 52 29916 CNTNAP2 0 . GRCh38 7 146839863 146839863 + Missense_Mutation SNP G G T C3N-02582_T C3N-02582_N G G c.361G>T p.Gly121Trp p.G121W ENST00000361727 3/24 288 269 19 339 339 0 strelka-varscan-mutect CNTNAP2,missense_variant,p.Gly121Trp,ENST00000361727,NM_014141.5;CNTNAP2,downstream_gene_variant,,ENST00000625365,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637694,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000638117,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000636561,;CNTNAP2,non_coding_transcript_exon_variant,,ENST00000637150,; T ENST00000361727 Transcript missense_variant 879/9896 361/3996 121/1331 G/W Ggg/Tgg COSM122241 1 1 CNTNAP2 HGNC HGNC:13830 protein_coding YES CCDS5889.1 ENSP00000354778 Q9UHC6 A0A090N7T7 UPI00001285FA NM_014141.5 deleterious(0) 3/24 Gene3D:2.60.120.260,Pfam_domain:PF00754,PROSITE_profiles:PS50022,SMART_domains:SM00231,Superfamily_domains:SSF49785 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 146839863 146839863 G T 1 0 0 0 0 1 0 0 0 3428 1000 35 2 2 CNTNAP2 7 146839863 Missense_Mutation SNP G C3N-02582_T 5915177 146839863 12506110 53 29917 C8orf46 0 . GRCh38 8 66516028 66516028 + Missense_Mutation SNP G G C novel C3N-02582_T C3N-02582_N G G c.576G>C p.Lys192Asn p.K192N ENST00000305454 6/6 196 170 26 143 143 0 strelka-varscan-mutect C8orf46,missense_variant,p.Lys192Asn,ENST00000305454,NM_152765.3;C8orf46,3_prime_UTR_variant,,ENST00000522977,;C8orf46,downstream_gene_variant,,ENST00000480005,;C8orf46,downstream_gene_variant,,ENST00000521495,;C8orf46,downstream_gene_variant,,ENST00000482608,;C8orf46,downstream_gene_variant,,ENST00000519702,;C8orf46,downstream_gene_variant,,ENST00000485639,;C8orf46,3_prime_UTR_variant,,ENST00000460144,;C8orf46,3_prime_UTR_variant,,ENST00000450307,; C ENST00000305454 Transcript missense_variant 1017/3513 576/624 192/207 K/N aaG/aaC 1 1 C8orf46 HGNC HGNC:28498 protein_coding YES CCDS6191.2 ENSP00000302260 Q8TAG6 UPI00003750A4 NM_152765.3 deleterious(0) 6/6 Pfam_domain:PF15505,hmmpanther:PTHR31520 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 66516028 66516028 G C 1 0 0 0 0 1 0 0 0 2159 933 33 4 4 C8orf46 8 66516028 Missense_Mutation SNP G C3N-02582_T 66516028 78622608 54 29918 PEX2 0 . GRCh38 8 76984109 76984109 + Missense_Mutation SNP C C G novel C3N-02582_T C3N-02582_N C C c.70G>C p.Glu24Gln p.E24Q ENST00000357039 4/4 113 76 37 130 130 0 strelka-varscan-mutect PEX2,missense_variant,p.Glu24Gln,ENST00000357039,NM_000318.2,NM_001172086.1;PEX2,missense_variant,p.Glu24Gln,ENST00000522527,NM_001079867.1;PEX2,missense_variant,p.Glu24Gln,ENST00000520103,NM_001172087.1;PEX2,missense_variant,p.Glu24Gln,ENST00000518986,;PEX2,downstream_gene_variant,,ENST00000519956,;PEX2,downstream_gene_variant,,ENST00000520203,; G ENST00000357039 Transcript missense_variant 466/4317 70/918 24/305 E/Q Gaa/Caa 1 -1 PEX2 HGNC HGNC:9717 protein_coding YES CCDS6221.1 ENSP00000349543 P28328 UPI000013E3FB NM_000318.2,NM_001172086.1 deleterious(0.05) 4/4 PD124462 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 76984109 76984109 C G 1 0 0 0 0 1 0 0 0 11835 835 29 4 4 PEX2 8 76984109 Missense_Mutation SNP C C3N-02582_T 10468081 76984109 68154527 55 29919 ESRP1 0 . GRCh38 8 94671651 94671651 + Missense_Mutation SNP C C T novel C3N-02582_T C3N-02582_N C C c.1432C>T p.His478Tyr p.H478Y ENST00000433389 11/16 270 220 50 189 189 0 strelka-varscan-mutect ESRP1,missense_variant,p.His478Tyr,ENST00000433389,NM_017697.3;ESRP1,missense_variant,p.His478Tyr,ENST00000358397,NM_001034915.2;ESRP1,missense_variant,p.His478Tyr,ENST00000423620,NM_001122826.1;ESRP1,missense_variant,p.His478Tyr,ENST00000454170,NM_001122825.1,NM_001122827.1;ESRP1,missense_variant,p.His344Tyr,ENST00000519505,;ESRP1,missense_variant,p.His337Tyr,ENST00000517610,;ESRP1,downstream_gene_variant,,ENST00000517556,; T ENST00000433389 Transcript missense_variant 1622/3770 1432/2046 478/681 H/Y Cac/Tac 1 1 ESRP1 HGNC HGNC:25966 protein_coding YES CCDS47897.1 ENSP00000405738 Q6NXG1 UPI0000210327 NM_017697.3 deleterious(0) 11/16 hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF37,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 94671651 94671651 C T 1 0 0 0 0 1 0 0 0 5120 826 29 3 3 ESRP1 8 94671651 Missense_Mutation SNP C C3N-02582_T 17687542 94671651 50466985 56 29920 1 31 2 2 16 C 5.051253e-05 ESRP1 0 . GRCh38 8 94671666 94671666 + Missense_Mutation SNP C C T C3N-02582_T C3N-02582_N C C c.1447C>T p.His483Tyr p.H483Y ENST00000433389 11/16 227 185 42 153 153 0 strelka-varscan-mutect ESRP1,missense_variant,p.His483Tyr,ENST00000433389,NM_017697.3;ESRP1,missense_variant,p.His483Tyr,ENST00000358397,NM_001034915.2;ESRP1,missense_variant,p.His483Tyr,ENST00000423620,NM_001122826.1;ESRP1,missense_variant,p.His483Tyr,ENST00000454170,NM_001122825.1,NM_001122827.1;ESRP1,missense_variant,p.His349Tyr,ENST00000519505,;ESRP1,missense_variant,p.His342Tyr,ENST00000517610,;ESRP1,downstream_gene_variant,,ENST00000517556,; T ENST00000433389 Transcript missense_variant 1637/3770 1447/2046 483/681 H/Y Cac/Tac COSM4466667,COSM4466668 1 1 ESRP1 HGNC HGNC:25966 protein_coding YES CCDS47897.1 ENSP00000405738 Q6NXG1 UPI0000210327 NM_017697.3 deleterious(0.03) 11/16 hmmpanther:PTHR13976,hmmpanther:PTHR13976:SF37,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs1427069577 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 94671666 94671666 C T 1 0 0 0 0 1 0 0 0 5120 840 29 3 3 ESRP1 8 94671666 Missense_Mutation SNP C C3N-02582_T 15 94671666 50466970 57 29921 1 31 2 2 16 C 5.051253e-05 ATP6V1C1 0 . GRCh38 8 103040964 103040965 + Frame_Shift_Ins INS - - A novel C3N-02582_T C3N-02582_N - - c.131dupA p.Val45GlyfsTer13 p.V45Gfs*13 ENST00000395862 2/13 147 67 80 158 158 0 sindel-varindel-pindel ATP6V1C1,frameshift_variant,p.Val45GlyfsTer13,ENST00000395862,NM_001695.4;ATP6V1C1,frameshift_variant,p.Val45GlyfsTer13,ENST00000518738,;ATP6V1C1,intron_variant,,ENST00000518857,;ATP6V1C1,intron_variant,,ENST00000521514,; A ENST00000395862 Transcript frameshift_variant 287-288/5612 128-129/1149 43/382 L/LX tta/ttAa 1 1 ATP6V1C1 HGNC HGNC:856 protein_coding YES CCDS6296.1 ENSP00000379203 P21283 A0A024R9I0 UPI0000049C2A NM_001695.4 2/13 hmmpanther:PTHR10137:SF5,hmmpanther:PTHR10137,Pfam_domain:PF03223,Gene3D:1u7lA02,Superfamily_domains:0049812 HIGH 1 insertion 1 3 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 7 5 104 103040964 103040964 - A 1 0 1 1 0 0 0 0 0 1333 1768 61 0 0 ATP6V1C1 8 103040964 Frame_Shift_Ins INS - C3N-02582_T 8369298 103040964 42097672 58 29922 TMEM249 0 . GRCh38 8 144354697 144354697 + Missense_Mutation SNP C C T novel C3N-02582_T C3N-02582_N C C c.71G>A p.Gly24Glu p.G24E ENST00000565365 1/5 389 367 22 261 261 0 strelka-varscan-mutect TMEM249,missense_variant,p.Gly24Glu,ENST00000565365,NM_001252402.2,NM_001280561.1;TMEM249,missense_variant,p.Gly24Glu,ENST00000562477,NM_001252404.2;SLC52A2,intron_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532887,;SLC52A2,upstream_gene_variant,,ENST00000329994,NM_024531.4;SLC52A2,upstream_gene_variant,,ENST00000527078,;FBXL6,downstream_gene_variant,,ENST00000331890,NM_012162.3;SLC52A2,upstream_gene_variant,,ENST00000402965,NM_001253815.1;SLC52A2,upstream_gene_variant,,ENST00000530047,NM_001253816.1;FBXL6,downstream_gene_variant,,ENST00000455319,NM_024555.5;SLC52A2,upstream_gene_variant,,ENST00000534725,;SLC52A2,upstream_gene_variant,,ENST00000526752,;SLC52A2,upstream_gene_variant,,ENST00000526338,;SLC52A2,splice_region_variant,,ENST00000532815,;FBXL6,downstream_gene_variant,,ENST00000526524,;FBXL6,downstream_gene_variant,,ENST00000527000,;SLC52A2,upstream_gene_variant,,ENST00000526891,;FBXL6,downstream_gene_variant,,ENST00000530687,;FBXL6,downstream_gene_variant,,ENST00000524909,;GS1-393G12.13,3_prime_UTR_variant,,ENST00000531225,;FBXL6,downstream_gene_variant,,ENST00000530142,;FBXL6,downstream_gene_variant,,ENST00000524492,;TMEM249,upstream_gene_variant,,ENST00000561638,;SLC52A2,upstream_gene_variant,,ENST00000533662,;SLC52A2,upstream_gene_variant,,ENST00000526779,;FBXL6,downstream_gene_variant,,ENST00000529279,; T ENST00000565365 Transcript missense_variant 218/975 71/708 24/235 G/E gGa/gAa 1 -1 TMEM249 HGNC HGNC:44155 protein_coding YES CCDS59117.1 ENSP00000454468 Q2WGJ8 UPI000019984E NM_001252402.2,NM_001280561.1 deleterious(0.01) 1/5 hmmpanther:PTHR35442 MODERATE SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 144354697 144354697 C T 1 0 0 0 0 1 0 0 0 16608 855 30 3 3 TMEM249 8 144354697 Missense_Mutation SNP C C3N-02582_T 41313733 144354697 783939 59 29923 FBXL6 0 . GRCh38 8 144355564 144355564 + Silent SNP C C T novel C3N-02582_T C3N-02582_N C C c.1587G>A p.= p.L529L ENST00000331890 9/9 261 244 17 132 132 0 strelka-varscan-mutect FBXL6,synonymous_variant,p.=,ENST00000331890,NM_012162.3;FBXL6,synonymous_variant,p.=,ENST00000455319,NM_024555.5;SLC52A2,intron_variant,,ENST00000524541,;SLC52A2,upstream_gene_variant,,ENST00000532887,;SLC52A2,upstream_gene_variant,,ENST00000329994,NM_024531.4;SLC52A2,upstream_gene_variant,,ENST00000527078,;SLC52A2,upstream_gene_variant,,ENST00000402965,NM_001253815.1;SLC52A2,upstream_gene_variant,,ENST00000530047,NM_001253816.1;TMEM249,upstream_gene_variant,,ENST00000565365,NM_001252402.2,NM_001280561.1;SLC52A2,upstream_gene_variant,,ENST00000534725,;TMEM249,upstream_gene_variant,,ENST00000562477,NM_001252404.2;SLC52A2,upstream_gene_variant,,ENST00000526752,;SLC52A2,upstream_gene_variant,,ENST00000526338,;FBXL6,non_coding_transcript_exon_variant,,ENST00000526524,;SLC52A2,intron_variant,,ENST00000532815,;FBXL6,downstream_gene_variant,,ENST00000527000,;SLC52A2,upstream_gene_variant,,ENST00000526891,;FBXL6,downstream_gene_variant,,ENST00000530687,;FBXL6,downstream_gene_variant,,ENST00000524909,;GS1-393G12.13,synonymous_variant,p.=,ENST00000531225,;FBXL6,non_coding_transcript_exon_variant,,ENST00000530142,;FBXL6,non_coding_transcript_exon_variant,,ENST00000524492,;TMEM249,upstream_gene_variant,,ENST00000561638,;SLC52A2,upstream_gene_variant,,ENST00000533662,;SLC52A2,upstream_gene_variant,,ENST00000526779,;FBXL6,downstream_gene_variant,,ENST00000529279,; T ENST00000331890 Transcript synonymous_variant 1652/1785 1587/1620 529/539 L ctG/ctA 1 -1 FBXL6 HGNC HGNC:13603 protein_coding YES CCDS6422.1 ENSP00000330098 Q8N531 UPI0002064E15 NM_012162.3 9/9 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 144355564 144355564 C T 1 0 0 0 0 0 0 0 1 5586 581 21 3 3 FBXL6 8 144355564 Silent SNP C C3N-02582_T 867 144355564 783072 60 29924 ADCK5 0 . GRCh38 8 144391152 144391152 + Missense_Mutation SNP G G A C3N-02582_T C3N-02582_N G G c.562G>A p.Glu188Lys p.E188K ENST00000308860 6/15 430 395 35 230 230 0 strelka-varscan-mutect ADCK5,missense_variant,p.Glu188Lys,ENST00000308860,NM_174922.4;CPSF1,downstream_gene_variant,,ENST00000616140,NM_013291.2;CPSF1,downstream_gene_variant,,ENST00000620219,;CPSF1,downstream_gene_variant,,ENST00000531727,;CPSF1,downstream_gene_variant,,ENST00000532935,;CPSF1,downstream_gene_variant,,ENST00000401314,;ADCK5,non_coding_transcript_exon_variant,,ENST00000526231,;ADCK5,downstream_gene_variant,,ENST00000534714,;ADCK5,3_prime_UTR_variant,,ENST00000529654,;ADCK5,3_prime_UTR_variant,,ENST00000533715,;CPSF1,downstream_gene_variant,,ENST00000531480,;CPSF1,downstream_gene_variant,,ENST00000526271,;ADCK5,downstream_gene_variant,,ENST00000526833,;CPSF1,downstream_gene_variant,,ENST00000527827,;CPSF1,downstream_gene_variant,,ENST00000532725,;ADCK5,downstream_gene_variant,,ENST00000532190,;CPSF1,downstream_gene_variant,,ENST00000529288,;CPSF1,downstream_gene_variant,,ENST00000531042,; A ENST00000308860 Transcript missense_variant 606/1949 562/1743 188/580 E/K Gag/Aag COSM4831050 1 1 ADCK5 HGNC HGNC:21738 protein_coding YES CCDS34965.2 ENSP00000310547 Q3MIX3 UPI00005B7249 NM_174922.4 deleterious(0.02) 6/15 hmmpanther:PTHR10566,hmmpanther:PTHR10566:SF59 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 144391152 144391152 G A 1 0 0 0 0 1 0 0 0 335 1291 45 3 3 ADCK5 8 144391152 Missense_Mutation SNP G C3N-02582_T 35588 144391152 747484 61 29925 RGS3 0 . GRCh38 9 113595721 113595721 + Missense_Mutation SNP A A C novel C3N-02582_T C3N-02582_N A A c.3367A>C p.Lys1123Gln p.K1123Q ENST00000374140 25/26 113 102 11 191 191 0 strelka-varscan-mutect RGS3,missense_variant,p.Lys1123Gln,ENST00000374140,NM_144488.5;RGS3,missense_variant,p.Lys1123Gln,ENST00000350696,NM_001282923.1;RGS3,missense_variant,p.Lys842Gln,ENST00000343817,NM_130795.3;RGS3,missense_variant,p.Lys444Gln,ENST00000374134,NM_001282922.1;RGS3,missense_variant,p.Lys444Gln,ENST00000462143,NM_001276260.1;RGS3,missense_variant,p.Lys516Gln,ENST00000394646,NM_001276261.1;RGS3,missense_variant,p.Lys236Gln,ENST00000462403,;RGS3,missense_variant,p.Lys236Gln,ENST00000613049,NM_144489.3;RGS3,missense_variant,p.Lys93Gln,ENST00000342620,NM_134427.2,NM_001276262.1;RGS3,missense_variant,p.Lys117Gln,ENST00000620489,;RGS3,downstream_gene_variant,,ENST00000467805,;RGS3,non_coding_transcript_exon_variant,,ENST00000496275,;RGS3,non_coding_transcript_exon_variant,,ENST00000478599,;RGS3,non_coding_transcript_exon_variant,,ENST00000487344,;RGS3,non_coding_transcript_exon_variant,,ENST00000490241,;RGS3,downstream_gene_variant,,ENST00000485822,;RGS3,downstream_gene_variant,,ENST00000488620,;RGS3,downstream_gene_variant,,ENST00000497435,; C ENST00000374140 Transcript missense_variant 3576/4591 3367/3597 1123/1198 K/Q Aag/Cag 1 1 RGS3 HGNC HGNC:9999 protein_coding YES CCDS43869.1 ENSP00000363255 P49796 UPI00001C0F58 NM_144488.5 tolerated(0.06) 25/26 Gene3D:1.10.167.10,Pfam_domain:PF00615,Prints_domain:PR01301,PROSITE_profiles:PS50132,hmmpanther:PTHR10845,hmmpanther:PTHR10845:SF4,Low_complexity_(Seg):seg,SMART_domains:SM00315,Superfamily_domains:SSF48097 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 113595721 113595721 A C 1 0 0 0 0 1 0 0 0 13477 131 5 5 5 RGS3 9 113595721 Missense_Mutation SNP A C3N-02582_T 113595721 24798996 62 29926 RALGPS1 0 . GRCh38 9 127184002 127184002 + Missense_Mutation SNP C C G rs758344268 C3N-02582_T C3N-02582_N C C c.1046C>G p.Pro349Arg p.P349R ENST00000394022 12/12 249 201 48 411 411 0 strelka-varscan-mutect RALGPS1,missense_variant,p.Pro349Arg,ENST00000394022,;RALGPS1,intron_variant,,ENST00000259351,NM_014636.2;RALGPS1,intron_variant,,ENST00000373434,NM_001190728.1;RALGPS1,intron_variant,,ENST00000424082,NM_001322320.1,NM_001190729.1; G ENST00000394022 Transcript missense_variant 1338/1672 1046/1155 349/384 P/R cCg/cGg rs758344268 1 1 RALGPS1 HGNC HGNC:16851 protein_coding ENSP00000377590 Q5JS13 UPI000006E36A deleterious_low_confidence(0.05) 12/12 hmmpanther:PTHR23113,hmmpanther:PTHR23113:SF167,Low_complexity_(Seg):seg MODERATE SNV 1 1 PASS rs758344268 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 127184002 127184002 C G 1 0 0 0 0 1 0 0 0 13176 652 23 4 4 RALGPS1 9 127184002 Missense_Mutation SNP C C3N-02582_T 13588281 127184002 11210715 63 29927 SARDH 0 . GRCh38 9 133708375 133708375 + Missense_Mutation SNP T T A novel C3N-02582_T C3N-02582_N T T c.1382A>T p.His461Leu p.H461L ENST00000371872 11/21 100 87 13 149 149 0 strelka-varscan-mutect SARDH,missense_variant,p.His461Leu,ENST00000371872,NM_007101.3;SARDH,missense_variant,p.His461Leu,ENST00000439388,NM_001134707.1;SARDH,missense_variant,p.His181Leu,ENST00000422262,;SARDH,missense_variant,p.His461Leu,ENST00000427237,;SARDH,upstream_gene_variant,,ENST00000371868,; A ENST00000371872 Transcript missense_variant 1640/3344 1382/2757 461/918 H/L cAt/cTt 1 -1 SARDH HGNC HGNC:10536 protein_coding YES CCDS6978.1 ENSP00000360938 Q9UL12 UPI000006F076 NM_007101.3 deleterious(0) 11/21 hmmpanther:PTHR13847:SF200,hmmpanther:PTHR13847,Pfam_domain:PF16350,Superfamily_domains:SSF51905 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 133708375 133708375 T A 1 0 0 0 0 1 0 0 0 14102 1464 51 4 4 SARDH 9 133708375 Missense_Mutation SNP T C3N-02582_T 6524373 133708375 4686342 64 29928 MLLT10 0 . GRCh38 10 21726316 21726316 + Missense_Mutation SNP A A G rs137946053 C3N-02582_T C3N-02582_N A A c.1951A>G p.Met651Val p.M651V ENST00000307729 15/23 164 151 13 214 214 0 strelka-varscan-mutect MLLT10,missense_variant,p.Met667Val,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Met651Val,ENST00000307729,;MLLT10,missense_variant,p.Met651Val,ENST00000631589,;MLLT10,missense_variant,p.Met651Val,ENST00000377059,NM_001195626.1;MLLT10,missense_variant,p.Met310Val,ENST00000438473,; G ENST00000307729 Transcript missense_variant 2129/5032 1951/3207 651/1068 M/V Atg/Gtg rs137946053 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 tolerated(0.19) 15/23 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93 MODERATE 1 SNV 1 1 PASS rs137946053 . 0 206 0 2 0 0 0 2 -6.843847 0 0 1 0 0 G 3 3 104 21726316 21726316 A G 1 0 0 0 0 1 0 0 0 9589 101 4 5 5 MLLT10 10 21726316 Missense_Mutation SNP A C3N-02582_T 21726316 112071106 65 29929 OR10W1 0 . GRCh38 11 58266985 58266985 + Missense_Mutation SNP C C T rs140648233 C3N-02582_T C3N-02582_N C C c.874G>A p.Val292Ile p.V292I ENST00000395079 1/1 30 24 6 56 56 0 strelka-varscan-mutect OR10W1,missense_variant,p.Val292Ile,ENST00000395079,NM_207374.3; T ENST00000395079 Transcript missense_variant 1276/1469 874/918 292/305 V/I Gta/Ata rs140648233,COSM1737484 1 -1 OR10W1 HGNC HGNC:15139 protein_coding YES CCDS7968.1 ENSP00000378516 Q8NGF6 UPI000004B229 NM_207374.3 tolerated(0.17) 1/1 hmmpanther:PTHR26452:SF165,hmmpanther:PTHR26452,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 0,1 MODERATE 1 SNV 0,1 1 PASS rs140648233 . 0 203 7 0 0 0 0 0 -16.06631 0.9999998 1 1 1 0 T 3 4 104 58266985 58266985 C T 1 0 0 0 0 1 0 0 0 10998 536 19 1 1 OR10W1 11 58266985 Missense_Mutation SNP C C3N-02582_T 58266985 76819637 66 29930 FLRT1 0 . GRCh38 11 64116341 64116341 + Missense_Mutation SNP C C G novel C3N-02582_T C3N-02582_N C C c.74C>G p.Thr25Ser p.T25S ENST00000246841 2/2 142 107 35 176 176 0 strelka-varscan-mutect FLRT1,missense_variant,p.Thr25Ser,ENST00000246841,NM_013280.4;MACROD1,intron_variant,,ENST00000255681,NM_014067.3;RP11-21A7A.3,downstream_gene_variant,,ENST00000543817,;MACROD1,intron_variant,,ENST00000542359,;MACROD1,intron_variant,,ENST00000543422,;MACROD1,intron_variant,,ENST00000545464,; G ENST00000246841 Transcript missense_variant 1117/3949 74/2025 25/674 T/S aCc/aGc 1 1 FLRT1 HGNC HGNC:3760 protein_coding YES CCDS8057.1 ENSP00000246841 Q9NZU1 UPI0000039F94 NM_013280.4 tolerated_low_confidence(0.65) 2/2 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF30,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1425516751 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 64116341 64116341 C G 1 0 0 0 0 1 0 0 0 5794 507 18 4 4 FLRT1 11 64116341 Missense_Mutation SNP C C3N-02582_T 5849356 64116341 70970281 67 29931 KDM5A 0 . GRCh38 12 307499 307499 + Silent SNP G G A novel C3N-02582_T C3N-02582_N G G c.3885C>T p.= p.I1295I ENST00000399788 23/28 337 300 37 222 222 0 strelka-varscan-mutect KDM5A,synonymous_variant,p.=,ENST00000399788,NM_001042603.2;KDM5A,downstream_gene_variant,,ENST00000544760,;KDM5A,non_coding_transcript_exon_variant,,ENST00000540156,;KDM5A,downstream_gene_variant,,ENST00000535269,; A ENST00000399788 Transcript synonymous_variant 4248/10763 3885/5073 1295/1690 I atC/atT 1 -1 KDM5A HGNC HGNC:9886 protein_coding YES CCDS41736.1 ENSP00000382688 P29375 UPI0000DB2E73 NM_001042603.2 23/28 hmmpanther:PTHR10694,hmmpanther:PTHR10694:SF17 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 104 307499 307499 G A 1 0 0 0 0 0 0 0 1 8051 1280 45 3 3 KDM5A 12 307499 Silent SNP G C3N-02582_T 307499 132967810 68 29932 SDSL 0 . GRCh38 12 113435429 113435429 + Missense_Mutation SNP G G T novel C3N-02582_T C3N-02582_N G G c.544G>T p.Val182Leu p.V182L ENST00000403593 6/8 131 121 10 147 147 0 strelka-mutect SDSL,missense_variant,p.Val182Leu,ENST00000403593,NM_001304993.1;SDSL,missense_variant,p.Val182Leu,ENST00000345635,NM_138432.3;SDSL,missense_variant,p.Val78Leu,ENST00000546672,;SDSL,missense_variant,p.Val124Leu,ENST00000553248,;SDSL,upstream_gene_variant,,ENST00000551760,; T ENST00000403593 Transcript missense_variant 806/1449 544/990 182/329 V/L Gtg/Ttg 1 1 SDSL HGNC HGNC:30404 protein_coding YES CCDS9170.1 ENSP00000385790 Q96GA7 A0A024RBL2 UPI0000072263 NM_001304993.1 deleterious(0.02) 6/8 Low_complexity_(Seg):seg,hmmpanther:PTHR10314,hmmpanther:PTHR10314:SF99,Gene3D:3.40.50.1100,Pfam_domain:PF00291,Superfamily_domains:SSF53686 MODERATE 1 SNV 1 1 PASS rs1483880517 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 113435429 113435429 G T 1 0 0 0 0 1 0 0 0 14252 1261 44 2 2 SDSL 12 113435429 Missense_Mutation SNP G C3N-02582_T 113127930 113435429 19839880 69 29933 HCAR2 0 . GRCh38 12 122702576 122702576 + Silent SNP C C T novel C3N-02582_T C3N-02582_N C C c.708G>A p.= p.V236V ENST00000328880 1/1 380 292 88 456 456 0 strelka-varscan-mutect HCAR2,synonymous_variant,p.=,ENST00000328880,NM_177551.3;RP11-324E6.6,intron_variant,,ENST00000543611,; T ENST00000328880 Transcript synonymous_variant 768/2051 708/1092 236/363 V gtG/gtA 1 -1 HCAR2 HGNC HGNC:24827 protein_coding YES CCDS9235.1 ENSP00000375066 Q8TDS4 UPI000003BCD5 NM_177551.3 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24231,hmmpanther:PTHR24231:SF0,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 122702576 122702576 C T 1 0 0 0 0 0 0 0 1 6876 581 21 3 3 HCAR2 12 122702576 Silent SNP C C3N-02582_T 9267147 122702576 10572733 70 29934 ZFYVE19 0 . GRCh38 15 40807297 40807297 + Silent SNP A A C novel C3N-02582_T C3N-02582_N A A c.9A>C p.= p.A3A ENST00000336455 1/12 96 88 8 158 157 1 strelka-varscan-mutect ZFYVE19,synonymous_variant,p.=,ENST00000336455,NM_032850.4;ZFYVE19,synonymous_variant,p.=,ENST00000570108,;ZFYVE19,5_prime_UTR_variant,,ENST00000355341,NM_001077268.1;ZFYVE19,5_prime_UTR_variant,,ENST00000564258,NM_001258421.1;DNAJC17,intron_variant,,ENST00000220496,NM_018163.2;DNAJC17,intron_variant,,ENST00000627802,;ZFYVE19,upstream_gene_variant,,ENST00000299173,NM_001258420.1;ZFYVE19,upstream_gene_variant,,ENST00000566407,;ZFYVE19,upstream_gene_variant,,ENST00000561617,;ZFYVE19,upstream_gene_variant,,ENST00000566767,;ZFYVE19,upstream_gene_variant,,ENST00000563530,;DNAJC17,intron_variant,,ENST00000559238,;DNAJC17,intron_variant,,ENST00000560301,;DNAJC17,intron_variant,,ENST00000560645,;DNAJC17,intron_variant,,ENST00000561018,;DNAJC17,intron_variant,,ENST00000559310,;DNAJC17,intron_variant,,ENST00000560065,;ZFYVE19,upstream_gene_variant,,ENST00000560078,;ZFYVE19,upstream_gene_variant,,ENST00000561768,;ZFYVE19,upstream_gene_variant,,ENST00000569057,;ZFYVE19,upstream_gene_variant,,ENST00000568062,;ZFYVE19,upstream_gene_variant,,ENST00000567756,;ZFYVE19,upstream_gene_variant,,ENST00000570162,; C ENST00000336455 Transcript synonymous_variant 64/1784 9/1386 3/461 A gcA/gcC 1 1 ZFYVE19 HGNC HGNC:20758 protein_coding CCDS58353.1 ENSP00000337824 Q96K21 UPI0000D48D6C NM_032850.4 1/12 LOW SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 104 40807297 40807297 A C 1 0 0 0 0 0 0 0 1 18243 175 7 5 5 ZFYVE19 15 40807297 Silent SNP A C3N-02582_T 40807297 61183892 71 29935 FBN1 0 . GRCh38 15 48456636 48456636 + Splice_Site SNP C C A novel C3N-02582_T C3N-02582_N C C c.5422+1G>T p.X1808_splice ENST00000316623 330 296 34 596 595 1 strelka-varscan-mutect FBN1,splice_donor_variant,,ENST00000316623,NM_000138.4;FBN1,splice_donor_variant,,ENST00000559133,;FBN1,splice_donor_variant,,ENST00000537463,; A ENST00000316623 Transcript splice_donor_variant -/11756 5422/8616 1808/2871 1 -1 FBN1 HGNC HGNC:3603 protein_coding YES CCDS32232.1 ENSP00000325527 P35555 UPI0000EE4EBC NM_000138.4 44/65 HIGH 1 SNV 1 1 PASS rs1064793116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 104 48456636 48456636 C A 1 0 0 0 0 0 0 1 0 5565 521 18 2 2 FBN1 15 48456636 Splice_Site SNP C C3N-02582_T 7649339 48456636 53534553 72 29936 ZNF280D 0 . GRCh38 15 56701236 56701236 + Missense_Mutation SNP T T C novel C3N-02582_T C3N-02582_N T T c.178A>G p.Ile60Val p.I60V ENST00000267807 5/22 75 61 14 129 128 1 strelka-varscan-mutect ZNF280D,missense_variant,p.Ile47Val,ENST00000559237,NM_001002843.2;ZNF280D,missense_variant,p.Ile47Val,ENST00000559000,;ZNF280D,missense_variant,p.Ile60Val,ENST00000267807,NM_001288588.1,NM_017661.3;ZNF280D,missense_variant,p.Ile60Val,ENST00000558320,NM_001288589.1,NM_001002844.2;ZNF280D,missense_variant,p.Ile60Val,ENST00000559352,;ZNF280D,missense_variant,p.Ile60Val,ENST00000560002,;ZNF280D,missense_variant,p.Ile60Val,ENST00000558002,; C ENST00000267807 Transcript missense_variant,splice_region_variant 395/4328 178/2940 60/979 I/V Att/Gtt 1 -1 ZNF280D HGNC HGNC:25953 protein_coding YES CCDS32245.1 ENSP00000267807 Q6N043 UPI00003FF962 NM_001288588.1,NM_017661.3 tolerated(0.08) 5/22 Pfam_domain:PF13836,hmmpanther:PTHR19303,hmmpanther:PTHR19303:SF276 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 56701236 56701236 T C 1 0 0 0 0 1 0 0 0 18393 1420 49 5 5 ZNF280D 15 56701236 Missense_Mutation SNP T C3N-02582_T 8244600 56701236 45289953 73 29937 BAIAP3 0 . GRCh38 16 1347306 1347306 + Silent SNP C C T novel C3N-02582_T C3N-02582_N C C c.2865C>T p.= p.V955V ENST00000324385 29/34 199 189 10 195 195 0 strelka-varscan-mutect BAIAP3,synonymous_variant,p.=,ENST00000628027,;BAIAP3,synonymous_variant,p.=,ENST00000324385,NM_003933.4;BAIAP3,synonymous_variant,p.=,ENST00000397488,NM_001286464.1;BAIAP3,synonymous_variant,p.=,ENST00000426824,NM_001199097.1;BAIAP3,synonymous_variant,p.=,ENST00000421665,NM_001199096.1;BAIAP3,synonymous_variant,p.=,ENST00000568887,NM_001199099.1;BAIAP3,synonymous_variant,p.=,ENST00000562208,NM_001199098.1;BAIAP3,synonymous_variant,p.=,ENST00000561793,;BAIAP3,intron_variant,,ENST00000566162,;GNPTG,upstream_gene_variant,,ENST00000204679,NM_032520.4;TSR3,downstream_gene_variant,,ENST00000007390,NM_001001410.2;GNPTG,upstream_gene_variant,,ENST00000529110,;GNPTG,upstream_gene_variant,,ENST00000527137,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000564213,;BAIAP3,non_coding_transcript_exon_variant,,ENST00000566389,;BAIAP3,downstream_gene_variant,,ENST00000567825,;GNPTG,upstream_gene_variant,,ENST00000527168,;GNPTG,upstream_gene_variant,,ENST00000529957,;BAIAP3,downstream_gene_variant,,ENST00000568198,;TSR3,downstream_gene_variant,,ENST00000566296,;BAIAP3,downstream_gene_variant,,ENST00000561602,;GNPTG,upstream_gene_variant,,ENST00000526820,;GNPTG,upstream_gene_variant,,ENST00000527876,;BAIAP3,downstream_gene_variant,,ENST00000567203,;GNPTG,upstream_gene_variant,,ENST00000534197,; T ENST00000324385 Transcript synonymous_variant 3023/4678 2865/3564 955/1187 V gtC/gtT 1 1 BAIAP3 HGNC HGNC:948 protein_coding YES CCDS10434.1 ENSP00000324510 O94812 UPI0000071E58 NM_003933.4 29/34 Pfam_domain:PF10540,PROSITE_profiles:PS51259,hmmpanther:PTHR10774,hmmpanther:PTHR10774:SF65 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 1347306 1347306 C T 1 0 0 0 0 0 0 0 1 1456 813 29 3 3 BAIAP3 16 1347306 Silent SNP C C3N-02582_T 1347306 88991039 74 29938 SMG1 0 . GRCh38 16 18836059 18836059 + Missense_Mutation SNP T T C rs372184477 C3N-02582_T C3N-02582_N T T c.7931A>G p.Tyr2644Cys p.Y2644C ENST00000446231 48/63 365 313 52 439 439 0 strelka-varscan-mutect SMG1,missense_variant,p.Tyr2644Cys,ENST00000446231,NM_015092.4;SMG1,missense_variant,p.Tyr2534Cys,ENST00000565324,;SMG1,downstream_gene_variant,,ENST00000563448,; C ENST00000446231 Transcript missense_variant 8344/16115 7931/10986 2644/3661 Y/C tAt/tGt rs372184477 1 -1 SMG1 HGNC HGNC:30045 protein_coding YES CCDS45430.1 ENSP00000402515 Q96Q15 UPI00004F8E22 NM_015092.4 deleterious(0) 48/63 MODERATE 1 SNV 1 1 PASS rs372184477 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 18836059 18836059 T C 1 0 0 0 0 1 0 0 0 15089 1406 49 5 5 SMG1 16 18836059 Missense_Mutation SNP T C3N-02582_T 17488753 18836059 71502286 75 29939 DNAH3 0 . GRCh38 16 20935432 20935432 + Silent SNP G G A novel C3N-02582_T C3N-02582_N G G c.11913C>T p.= p.F3971F ENST00000261383 61/62 325 281 44 360 360 0 strelka-varscan-mutect DNAH3,synonymous_variant,p.=,ENST00000261383,NM_017539.2; A ENST00000261383 Transcript synonymous_variant 11913/12394 11913/12351 3971/4116 F ttC/ttT 1 -1 DNAH3 HGNC HGNC:2949 protein_coding YES CCDS10594.1 ENSP00000261383 Q8TD57 UPI00001100F2 NM_017539.2 61/62 hmmpanther:PTHR10676:SF242,hmmpanther:PTHR10676,Pfam_domain:PF03028 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 104 20935432 20935432 G A 1 0 0 0 0 0 0 0 1 4418 1281 45 3 3 DNAH3 16 20935432 Silent SNP G C3N-02582_T 2099373 20935432 69402913 76 29940 PHKB 0 . GRCh38 16 47580322 47580322 + Silent SNP A A G novel C3N-02582_T C3N-02582_N A A c.738A>G p.= p.L246L ENST00000323584 8/31 267 226 41 428 427 1 strelka-varscan-mutect PHKB,synonymous_variant,p.=,ENST00000299167,;PHKB,synonymous_variant,p.=,ENST00000323584,NM_000293.2;PHKB,synonymous_variant,p.=,ENST00000566044,NM_001031835.2;PHKB,non_coding_transcript_exon_variant,,ENST00000567402,;PHKB,3_prime_UTR_variant,,ENST00000570047,; G ENST00000323584 Transcript synonymous_variant 762/4283 738/3282 246/1093 L ctA/ctG 1 1 PHKB HGNC HGNC:8927 protein_coding YES CCDS10729.1 ENSP00000313504 Q93100 UPI0000141140 NM_000293.2 8/31 Pfam_domain:PF00723,hmmpanther:PTHR10749,Superfamily_domains:SSF48208 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 104 47580322 47580322 A G 1 0 0 0 0 0 0 0 1 11933 407 15 5 5 PHKB 16 47580322 Silent SNP A C3N-02582_T 26644890 47580322 42758023 77 29941 LCAT 0 . GRCh38 16 67943098 67943098 + Missense_Mutation SNP A A C novel C3N-02582_T C3N-02582_N A A c.269T>G p.Met90Arg p.M90R ENST00000264005 2/6 232 159 73 291 290 1 strelka-varscan-mutect LCAT,missense_variant,p.Met90Arg,ENST00000264005,NM_000229.1;LCAT,missense_variant,p.Met18Arg,ENST00000570980,;SLC12A4,downstream_gene_variant,,ENST00000316341,NM_001145961.1,NM_005072.4;SLC12A4,downstream_gene_variant,,ENST00000422611,NM_001145962.1;SLC12A4,downstream_gene_variant,,ENST00000576616,;SLC12A4,downstream_gene_variant,,ENST00000541864,NM_001145964.1;SLC12A4,downstream_gene_variant,,ENST00000572037,;SLC12A4,downstream_gene_variant,,ENST00000537830,NM_001145963.1;LCAT,upstream_gene_variant,,ENST00000576450,;LCAT,upstream_gene_variant,,ENST00000570369,;LCAT,upstream_gene_variant,,ENST00000570396,;LCAT,missense_variant,p.His82Gln,ENST00000575467,;LCAT,non_coding_transcript_exon_variant,,ENST00000575277,;SLC12A4,downstream_gene_variant,,ENST00000570802,;SLC12A4,downstream_gene_variant,,ENST00000573023,;LCAT,upstream_gene_variant,,ENST00000573538,;SLC12A4,downstream_gene_variant,,ENST00000575857,;LCAT,upstream_gene_variant,,ENST00000573846,;SLC12A4,downstream_gene_variant,,ENST00000576513,;SLC12A4,downstream_gene_variant,,ENST00000570616,; C ENST00000264005 Transcript missense_variant 299/1507 269/1323 90/440 M/R aTg/aGg 1 -1 LCAT HGNC HGNC:6522 protein_coding YES CCDS10854.1 ENSP00000264005 P04180 A0A140VK24 UPI0000000DE7 NM_000229.1 deleterious(0.01) 2/6 Pfam_domain:PF02450,hmmpanther:PTHR11440,hmmpanther:PTHR11440:SF18 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 67943098 67943098 A C 1 0 0 0 0 1 0 0 0 8563 217 8 5 5 LCAT 16 67943098 Missense_Mutation SNP A C3N-02582_T 20362776 67943098 22395247 78 29942 TP53 0 . GRCh38 17 7674256 7674256 + Missense_Mutation SNP T T C rs730882026 C3N-02582_T C3N-02582_N T T c.707A>G p.Tyr236Cys p.Y236C ENST00000269305 7/11 254 241 13 449 449 0 strelka-varscan-mutect TP53,missense_variant,p.Tyr236Cys,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Tyr236Cys,ENST00000420246,;TP53,missense_variant,p.Tyr197Cys,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Tyr197Cys,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Tyr236Cys,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Tyr197Cys,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Tyr236Cys,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Tyr197Cys,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Tyr236Cys,ENST00000445888,;TP53,missense_variant,p.Tyr197Cys,ENST00000619485,;TP53,missense_variant,p.Tyr104Cys,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Tyr77Cys,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Tyr104Cys,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Tyr77Cys,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Tyr104Cys,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Tyr77Cys,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Tyr236Cys,ENST00000359597,;TP53,missense_variant,p.Tyr225Cys,ENST00000615910,;TP53,missense_variant,p.Tyr236Cys,ENST00000413465,;TP53,missense_variant,p.Tyr104Cys,ENST00000509690,;TP53,missense_variant,p.Tyr143Cys,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,non_coding_transcript_exon_variant,,ENST00000574684,;TP53,missense_variant,p.Tyr197Cys,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 897/2579 707/1182 236/393 Y/C tAc/tGc rs730882026,CM004907,TP53_g.13344A>C,TP53_g.13344A>G,TP53_g.13344A>T,COSM10731,COSM116672,COSM116673,COSM116674,COSM1172470,COSM1172471,COSM1172472,COSM1646851,COSM3773303,COSM3958809,COSM3958810,COSM3958811,COSM3958812,COSM3958813,COSM3958814,COSM44693,COSM4766269,COSM4766270 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 uncertain_significance 0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 MODERATE 1 SNV 1 1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs730882026 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 7674256 7674256 T C 1 0 0 0 0 1 0 0 0 16859 1638 57 5 5 TP53 17 7674256 Missense_Mutation SNP T C3N-02582_T 7674256 75583185 79 29943 DHRS7B 0 . GRCh38 17 21172198 21172198 + Splice_Site SNP T T A novel C3N-02582_T C3N-02582_N T T c.199+2T>A p.X67_splice ENST00000395511 139 131 8 136 136 0 strelka-varscan-mutect DHRS7B,splice_donor_variant,,ENST00000395511,NM_015510.4;DHRS7B,splice_donor_variant,,ENST00000579303,;DHRS7B,splice_donor_variant,,ENST00000582161,;DHRS7B,splice_donor_variant,,ENST00000346603,;DHRS7B,splice_donor_variant,,ENST00000578426,;DHRS7B,non_coding_transcript_exon_variant,,ENST00000577350,;DHRS7B,non_coding_transcript_exon_variant,,ENST00000579099,; A ENST00000395511 Transcript splice_donor_variant -/2175 199/978 67/325 1 1 DHRS7B HGNC HGNC:24547 protein_coding YES CCDS11215.1 ENSP00000378887 Q6IAN0 UPI00000739CB NM_015510.4 2/6 HIGH 1 SNV 1 1 PASS rs1272828699 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 104 21172198 21172198 T A 1 0 0 0 0 0 0 1 0 4300 1710 59 4 4 DHRS7B 17 21172198 Splice_Site SNP T C3N-02582_T 13497942 21172198 62085243 80 29944 NF1 0 . GRCh38 17 31232729 31232729 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.3344A>G p.Asn1115Ser p.N1115S ENST00000358273 26/58 348 326 22 433 433 0 strelka-varscan-mutect NF1,missense_variant,p.Asn1115Ser,ENST00000358273,NM_001042492.2;NF1,missense_variant,p.Asn1115Ser,ENST00000356175,NM_000267.3;NF1,missense_variant,p.Asn781Ser,ENST00000456735,;NF1,missense_variant,p.Asn1149Ser,ENST00000579081,;NF1,3_prime_UTR_variant,,ENST00000495910,;NF1,non_coding_transcript_exon_variant,,ENST00000493220,;NF1,upstream_gene_variant,,ENST00000466819,;NF1,upstream_gene_variant,,ENST00000479614,; G ENST00000358273 Transcript missense_variant 3727/12425 3344/8520 1115/2839 N/S aAt/aGt 1 1 NF1 HGNC HGNC:7765 protein_coding YES CCDS42292.1 ENSP00000351015 P21359 UPI000012FFAE NM_001042492.2 deleterious(0.01) 26/58 hmmpanther:PTHR10194,hmmpanther:PTHR10194:SF90 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 31232729 31232729 A G 1 0 0 0 0 1 0 0 0 10393 101 4 5 5 NF1 17 31232729 Missense_Mutation SNP A C3N-02582_T 10060531 31232729 52024712 81 29945 EVI2A 0 . GRCh38 17 31318998 31318998 + Missense_Mutation SNP C C T rs759341310 C3N-02582_T C3N-02582_N C C c.85G>A p.Glu29Lys p.E29K ENST00000247270 3/3 99 93 6 113 113 0 strelka-varscan-mutect EVI2A,missense_variant,p.Glu29Lys,ENST00000247270,NM_001003927.2;EVI2A,missense_variant,p.Glu6Lys,ENST00000462804,NM_014210.3;EVI2A,missense_variant,p.Glu6Lys,ENST00000461237,;NF1,intron_variant,,ENST00000358273,NM_001042492.2;NF1,intron_variant,,ENST00000356175,NM_000267.3;NF1,intron_variant,,ENST00000456735,;EVI2B,upstream_gene_variant,,ENST00000330927,NM_006495.3;EVI2B,upstream_gene_variant,,ENST00000577894,;CTD-2370N5.3,upstream_gene_variant,,ENST00000578584,;CTD-2370N5.3,upstream_gene_variant,,ENST00000584948,;NF1,intron_variant,,ENST00000581113,;NF1,intron_variant,,ENST00000579081,;NF1,intron_variant,,ENST00000493220,;CTD-2370N5.3,upstream_gene_variant,,ENST00000581884,;CTD-2370N5.3,upstream_gene_variant,,ENST00000578021,; T ENST00000247270 Transcript missense_variant 422/1860 85/780 29/259 E/K Gaa/Aaa rs759341310,COSM4065344 1 -1 EVI2A HGNC HGNC:3499 protein_coding YES CCDS32608.1 ENSP00000247270 P22794 UPI000042B0AE NM_001003927.2 tolerated(0.1) 3/3 PD037847,Pfam_domain:PF05399,PIRSF_domain:PIRSF019625,hmmpanther:PTHR15568 0,1 MODERATE SNV 2 0,1 1 PASS rs759341310 . 0 203 7 0 0 0 0 0 -12.30813 0.9999969 1 1 1 0 T 3 4 104 31318998 31318998 C T 1 0 0 0 0 1 0 0 0 5154 864 30 3 3 EVI2A 17 31318998 Missense_Mutation SNP C C3N-02582_T 86269 31318998 51938443 82 29946 LRRC37B 0 . GRCh38 17 32045767 32045785 + Frame_Shift_Del DEL ACAGTCAAGCTGCATTGCA ACAGTCAAGCTGCATTGCA - novel C3N-02582_T C3N-02582_N ACAGTCAAGCTGCATTGCA ACAGTCAAGCTGCATTGCA c.2194_2212delGTCAAGCTGCATTGCAACA p.Val732LeufsTer4 p.V732Lfs*4 ENST00000341671 8/12 254 237 17 370 370 0 sindel-pindel LRRC37B,frameshift_variant,p.Val759LeufsTer4,ENST00000327564,;LRRC37B,frameshift_variant,p.Val650LeufsTer4,ENST00000543378,NM_001321350.1;LRRC37B,frameshift_variant,p.Val732LeufsTer4,ENST00000341671,;LRRC37B,frameshift_variant,p.Val732LeufsTer4,ENST00000394713,NM_052888.2;LRRC37B,frameshift_variant,p.Val693LeufsTer4,ENST00000584368,;LRRC37B,upstream_gene_variant,,ENST00000582117,;SH3GL1P1,downstream_gene_variant,,ENST00000579186,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000583758,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000581086,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000582815,;LRRC37B,non_coding_transcript_exon_variant,,ENST00000578118,;LRRC37B,intron_variant,,ENST00000578674,;LRRC37B,upstream_gene_variant,,ENST00000579094,;LRRC37B,upstream_gene_variant,,ENST00000579766,;SH3GL1P1,downstream_gene_variant,,ENST00000583601,; - ENST00000341671 Transcript frameshift_variant 2196-2214/3025 2191-2209/2844 731-737/947 TVKLHCN/X ACAGTCAAGCTGCATTGCAac/ac 1 1 LRRC37B HGNC HGNC:29070 protein_coding YES CCDS32609.1 ENSP00000340519 Q96QE4 UPI000044D37B 8/12 hmmpanther:PTHR23045 HIGH 1 deletion 1 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 32045767 32045767 ACAGTCAAGCTGCATTGCA - 1 0 1 0 1 0 0 0 0 8888 275 10 0 0 LRRC37B 17 32045767 Frame_Shift_Del DEL ACAGTCAAGCTGCATTGCA C3N-02582_T 726769 32045767 51211674 83 29947 ACLY 0 . GRCh38 17 41869067 41869067 + Missense_Mutation SNP A A C novel C3N-02582_T C3N-02582_N A A c.3110T>G p.Leu1037Arg p.L1037R ENST00000352035 27/29 229 209 20 268 267 1 strelka-varscan-mutect ACLY,missense_variant,p.Leu1037Arg,ENST00000352035,NM_001303274.1,NM_001096.2;ACLY,missense_variant,p.Leu1027Arg,ENST00000353196,NM_001303275.1,NM_198830.1;ACLY,missense_variant,p.Leu1037Arg,ENST00000590151,;ACLY,missense_variant,p.Leu1027Arg,ENST00000393896,;ACLY,missense_variant,p.Leu766Arg,ENST00000537919,;KLHL11,upstream_gene_variant,,ENST00000319121,NM_018143.2;RP11-229E13.4,downstream_gene_variant,,ENST00000619176,;ACLY,non_coding_transcript_exon_variant,,ENST00000588779,; C ENST00000352035 Transcript missense_variant 3241/4339 3110/3306 1037/1101 L/R cTt/cGt 1 -1 ACLY HGNC HGNC:115 protein_coding YES CCDS11412.1 ENSP00000253792 P53396 A0A024R1T9 UPI000013CDF3 NM_001303274.1,NM_001096.2 deleterious(0) 27/29 Pfam_domain:PF00285,PIRSF_domain:PIRSF036511,hmmpanther:PTHR23118,Superfamily_domains:SSF48256 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 41869067 41869067 A C 1 0 0 0 0 1 0 0 0 185 72 3 5 5 ACLY 17 41869067 Missense_Mutation SNP A C3N-02582_T 9823300 41869067 41388374 84 29948 ATP6V0A1 0 . GRCh38 17 42501285 42501285 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.2006A>G p.Tyr669Cys p.Y669C ENST00000264649 17/21 127 112 15 134 134 0 strelka-varscan-mutect ATP6V0A1,missense_variant,p.Tyr662Cys,ENST00000343619,NM_001130021.1;ATP6V0A1,missense_variant,p.Tyr669Cys,ENST00000264649,NM_001130020.1;ATP6V0A1,missense_variant,p.Tyr308Cys,ENST00000544137,;ATP6V0A1,missense_variant,p.Tyr662Cys,ENST00000393829,NM_005177.3;ATP6V0A1,missense_variant,p.Tyr619Cys,ENST00000537728,;ATP6V0A1,missense_variant,p.Tyr619Cys,ENST00000585525,;ATP6V0A1,missense_variant,p.Tyr67Cys,ENST00000586201,;ATP6V0A1,missense_variant,p.Tyr15Cys,ENST00000588138,;RP11-194N12.2,downstream_gene_variant,,ENST00000591343,;ATP6V0A1,missense_variant,p.Tyr78Cys,ENST00000587510,; G ENST00000264649 Transcript missense_variant 2137/4110 2006/2517 669/838 Y/C tAt/tGt 1 1 ATP6V0A1 HGNC HGNC:865 protein_coding YES CCDS45683.1 ENSP00000264649 Q93050 UPI0000E59F9E NM_001130020.1 deleterious(0.04) 17/21 hmmpanther:PTHR11629:SF68,hmmpanther:PTHR11629,PIRSF_domain:PIRSF001293,Pfam_domain:PF01496 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 42501285 42501285 A G 1 0 0 0 0 1 0 0 0 1321 449 16 5 5 ATP6V0A1 17 42501285 Missense_Mutation SNP A C3N-02582_T 632218 42501285 40756156 85 29949 MRC2 0 . GRCh38 17 62667403 62667403 + Missense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.987C>A p.Asn329Lys p.N329K ENST00000303375 6/30 85 72 13 97 97 0 strelka-varscan-mutect MRC2,missense_variant,p.Asn329Lys,ENST00000303375,NM_006039.4;MRC2,non_coding_transcript_exon_variant,,ENST00000584265,; A ENST00000303375 Transcript missense_variant 1389/5988 987/4440 329/1479 N/K aaC/aaA 1 1 MRC2 HGNC HGNC:16875 protein_coding YES CCDS11634.1 ENSP00000307513 Q9UBG0 UPI000013E895 NM_006039.4 deleterious(0.05) 6/30 Gene3D:3.10.100.10,Pfam_domain:PF00059,PROSITE_profiles:PS50041,hmmpanther:PTHR22803,hmmpanther:PTHR22803:SF69,SMART_domains:SM00034,Superfamily_domains:SSF56436 MODERATE 1 SNV 1 1 PASS rs1481220158 . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 62667403 62667403 C A 1 0 0 0 0 1 0 0 0 9723 506 18 2 2 MRC2 17 62667403 Missense_Mutation SNP C C3N-02582_T 20166118 62667403 20590038 86 29950 TMC6 0 . GRCh38 17 78120696 78120696 + Missense_Mutation SNP C C T rs199724291 C3N-02582_T C3N-02582_N C C c.1672G>A p.Val558Ile p.V558I ENST00000590602 13/20 354 304 50 566 566 0 strelka-varscan-mutect TMC6,missense_variant,p.Val558Ile,ENST00000590602,NM_001127198.1;TMC6,missense_variant,p.Val558Ile,ENST00000392467,;TMC6,missense_variant,p.Val558Ile,ENST00000322914,NM_007267.6;TMC6,3_prime_UTR_variant,,ENST00000589553,;TMC6,intron_variant,,ENST00000306591,;TMC6,intron_variant,,ENST00000591436,;TMC6,downstream_gene_variant,,ENST00000589271,;TMC6,downstream_gene_variant,,ENST00000592063,;TMC6,non_coding_transcript_exon_variant,,ENST00000590934,;TMC6,intron_variant,,ENST00000592076,;TMC6,non_coding_transcript_exon_variant,,ENST00000593044,;TMC6,non_coding_transcript_exon_variant,,ENST00000588087,;TMC6,non_coding_transcript_exon_variant,,ENST00000591756,;TMC6,downstream_gene_variant,,ENST00000586271,;TMC6,downstream_gene_variant,,ENST00000591594,;TMC6,upstream_gene_variant,,ENST00000589933,;TMC6,downstream_gene_variant,,ENST00000585849,; T ENST00000590602 Transcript missense_variant 1832/5268 1672/2418 558/805 V/I Gtc/Atc rs199724291,COSM3970396 1 -1 TMC6 HGNC HGNC:18021 protein_coding YES CCDS32748.1 ENSP00000465261 Q7Z403 A0A024R8V2 UPI000013D819 NM_001127198.1 tolerated(1) 13/20 Transmembrane_helices:TMhelix,hmmpanther:PTHR23302:SF4,hmmpanther:PTHR23302,Pfam_domain:PF07810 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs199724291 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 78120696 78120696 C T 1 0 0 0 0 1 0 0 0 16435 536 19 1 1 TMC6 17 78120696 Missense_Mutation SNP C C3N-02582_T 15453293 78120696 5136745 87 29951 LAMA1 0 . GRCh38 18 7016561 7016561 + Silent SNP T T A novel C3N-02582_T C3N-02582_N T T c.2919A>T p.= p.P973P ENST00000389658 21/63 295 280 15 451 451 0 strelka-varscan-mutect LAMA1,synonymous_variant,p.=,ENST00000389658,NM_005559.3;LAMA1,non_coding_transcript_exon_variant,,ENST00000579014,; A ENST00000389658 Transcript synonymous_variant 3013/9657 2919/9228 973/3075 P ccA/ccT 1 -1 LAMA1 HGNC HGNC:6481 protein_coding YES CCDS32787.1 ENSP00000374309 P25391 UPI00001C1FF9 NM_005559.3 21/63 Gene3D:2.10.25.10,Pfam_domain:PF00053,PROSITE_patterns:PS01248,PROSITE_profiles:PS50027,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF299,SMART_domains:SM00180,SMART_domains:SM00181,Superfamily_domains:SSF57196 LOW 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 104 7016561 7016561 T A 1 0 0 0 0 0 0 0 1 8509 1567 55 4 4 LAMA1 18 7016561 Silent SNP T C3N-02582_T 7016561 73356724 88 29952 ZNF407 0 . GRCh38 18 74633353 74633353 + Silent SNP A A T novel C3N-02582_T C3N-02582_N A A c.2334A>T p.= p.V778V ENST00000299687 1/8 87 82 5 200 200 0 strelka-varscan-mutect ZNF407,synonymous_variant,p.=,ENST00000299687,NM_017757.2;ZNF407,synonymous_variant,p.=,ENST00000577538,NM_001146189.1;ZNF407,synonymous_variant,p.=,ENST00000582337,;ZNF407,synonymous_variant,p.=,ENST00000309902,NM_001146190.1; T ENST00000299687 Transcript synonymous_variant 2334/7948 2334/6747 778/2248 V gtA/gtT 1 1 ZNF407 HGNC HGNC:19904 protein_coding YES CCDS45885.1 ENSP00000299687 Q9C0G0 UPI0000F58ED1 NM_017757.2 1/8 LOW 1 SNV 1 1 PASS rs901490398 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 104 74633353 74633353 A T 1 0 0 0 0 0 0 0 1 18459 436 16 4 4 ZNF407 18 74633353 Silent SNP A C3N-02582_T 67616792 74633353 5739932 89 29953 PQLC1 0 . GRCh38 18 79904180 79904180 + Missense_Mutation SNP G G C novel C3N-02582_T C3N-02582_N G G c.612C>G p.Ile204Met p.I204M ENST00000397778 6/6 169 160 9 299 298 1 strelka-varscan-mutect PQLC1,stop_gained,p.Ser114Ter,ENST00000590381,NM_001146343.1;PQLC1,missense_variant,p.Ile204Met,ENST00000397778,NM_025078.4;PQLC1,missense_variant,p.Ile186Met,ENST00000357575,NM_001146345.1;KCNG2,downstream_gene_variant,,ENST00000316249,NM_012283.1;RP11-248M19.1,upstream_gene_variant,,ENST00000618070,;PQLC1,non_coding_transcript_exon_variant,,ENST00000590895,;PQLC1,non_coding_transcript_exon_variant,,ENST00000469369,;PQLC1,non_coding_transcript_exon_variant,,ENST00000589000,;KCNG2,downstream_gene_variant,,ENST00000590307,;PQLC1,3_prime_UTR_variant,,ENST00000351365,;PQLC1,3_prime_UTR_variant,,ENST00000474967,;PQLC1,non_coding_transcript_exon_variant,,ENST00000466449,; C ENST00000397778 Transcript missense_variant 795/2555 612/816 204/271 I/M atC/atG 1 -1 PQLC1 HGNC HGNC:26188 protein_coding YES CCDS12020.1 ENSP00000380880 Q8N2U9 UPI0000073855 NM_025078.4 deleterious(0.01) 6/6 Pfam_domain:PF04193,hmmpanther:PTHR14856,hmmpanther:PTHR14856:SF10,SMART_domains:SM00679 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 79904180 79904180 G C 1 0 0 0 0 1 0 0 0 12544 1304 45 4 4 PQLC1 18 79904180 Missense_Mutation SNP G C3N-02582_T 5270827 79904180 469105 90 29954 PLPPR3 0 . GRCh38 19 814600 814600 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.749T>C p.Phe250Ser p.F250S ENST00000359894 6/7 161 66 95 234 234 0 strelka-varscan-mutect PLPPR3,missense_variant,p.Phe250Ser,ENST00000359894,NM_024888.2;PLPPR3,missense_variant,p.Phe222Ser,ENST00000520876,NM_001270366.1;PLPPR3,intron_variant,,ENST00000517665,;PTBP1,downstream_gene_variant,,ENST00000635647,;PTBP1,downstream_gene_variant,,ENST00000356948,NM_002819.4;PTBP1,downstream_gene_variant,,ENST00000394601,NM_031990.3;PTBP1,downstream_gene_variant,,ENST00000349038,NM_031991.3;PTBP1,downstream_gene_variant,,ENST00000350092,;PTBP1,downstream_gene_variant,,ENST00000627714,;PLPPR3,downstream_gene_variant,,ENST00000519502,;MIR3187,downstream_gene_variant,,ENST00000583431,;PTBP1,downstream_gene_variant,,ENST00000586944,;PTBP1,downstream_gene_variant,,ENST00000585856,;PTBP1,downstream_gene_variant,,ENST00000621737,;PTBP1,downstream_gene_variant,,ENST00000585932,; G ENST00000359894 Transcript missense_variant 813/2387 749/2241 250/746 F/S tTc/tCc 1 -1 PLPPR3 HGNC HGNC:23497 protein_coding YES CCDS12043.1 ENSP00000352962 Q6T4P5 UPI00000730B6 NM_024888.2 deleterious(0.03) 6/7 Pfam_domain:PF01569,SMART_domains:SM00014 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 2 0 0 0 -20 0.9997326 1 1 1 0 G 3 3 104 814600 814600 A G 1 0 0 0 0 1 0 0 0 12211 246 9 5 5 PLPPR3 19 814600 Missense_Mutation SNP A C3N-02582_T 814600 57803016 91 29955 EEF2 0 . GRCh38 19 3981423 3981424 + Frame_Shift_Del DEL TT TT - novel C3N-02582_T C3N-02582_N TT TT c.926_927delAA p.Lys309ArgfsTer77 p.K309Rfs*77 ENST00000309311 7/15 133 105 28 303 303 0 sindel-varindel-pindel EEF2,frameshift_variant,p.Lys309ArgfsTer77,ENST00000309311,NM_001961.3;EEF2,upstream_gene_variant,,ENST00000600794,;SNORD37,downstream_gene_variant,,ENST00000384048,;EEF2,downstream_gene_variant,,ENST00000600720,;EEF2,non_coding_transcript_exon_variant,,ENST00000598182,;EEF2,non_coding_transcript_exon_variant,,ENST00000598436,;EEF2,downstream_gene_variant,,ENST00000594885,;EEF2,upstream_gene_variant,,ENST00000596417,; - ENST00000309311 Transcript frameshift_variant 1015-1016/3164 926-927/2577 309/858 K/X aAA/a 1 -1 EEF2 HGNC HGNC:3214 protein_coding YES CCDS12117.1 ENSP00000307940 P13639 UPI00001649F3 NM_001961.3 7/15 Gene3D:1n0uA03,Pfam_domain:PF00009,PROSITE_profiles:PS51722,Superfamily_domains:SSF52540 HIGH 1 deletion 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 104 3981423 3981423 TT - 1 0 1 0 1 0 0 0 0 4759 1606 56 0 0 EEF2 19 3981423 Frame_Shift_Del DEL TT C3N-02582_T 3166823 3981423 54636193 92 29956 MUC16 0 . GRCh38 19 8848946 8848946 + Nonsense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.43510G>T p.Glu14504Ter p.E14504* ENST00000397910 84/84 162 151 11 249 249 0 strelka-varscan-mutect MUC16,stop_gained,p.Glu14504Ter,ENST00000397910,NM_024690.2;MUC16,stop_gained,p.Glu1327Ter,ENST00000599436,;MUC16,3_prime_UTR_variant,,ENST00000601404,;MUC16,3_prime_UTR_variant,,ENST00000596768,; A ENST00000397910 Transcript stop_gained 43714/43816 43510/43524 14504/14507 E/* Gag/Tag 1 -1 MUC16 HGNC HGNC:15582 protein_coding YES CCDS54212.1 ENSP00000381008 Q8WXI7 UPI000065CA24 NM_024690.2 84/84 hmmpanther:PTHR14672 HIGH 1 SNV 5 1 PASS . . 0 208 0 2 0 0 0 0 -14.79158 0.9999996 1 1 1 0 A 4 1 104 8848946 8848946 C A 1 0 0 0 0 0 1 0 0 9972 864 30 2 2 MUC16 19 8848946 Nonsense_Mutation SNP C C3N-02582_T 4867523 8848946 49768670 93 29957 AP1M1 0 . GRCh38 19 16206376 16206376 + Missense_Mutation SNP C C A novel C3N-02582_T C3N-02582_N C C c.235C>A p.Leu79Met p.L79M ENST00000444449 3/13 195 174 21 288 288 0 strelka-varscan-mutect AP1M1,missense_variant,p.Leu79Met,ENST00000291439,NM_032493.3;AP1M1,missense_variant,p.Leu79Met,ENST00000444449,NM_001130524.1;AP1M1,missense_variant,p.Leu79Met,ENST00000429941,;AP1M1,missense_variant,p.Leu53Met,ENST00000591775,;AP1M1,missense_variant,p.Leu53Met,ENST00000589822,;AP1M1,missense_variant,p.Leu53Met,ENST00000590945,;AP1M1,missense_variant,p.Leu79Met,ENST00000590263,;AP1M1,missense_variant,p.Leu16Met,ENST00000589782,;AP1M1,intron_variant,,ENST00000590756,;AP1M1,non_coding_transcript_exon_variant,,ENST00000589991,;AP1M1,non_coding_transcript_exon_variant,,ENST00000586957,;AP1M1,upstream_gene_variant,,ENST00000586461,;AP1M1,upstream_gene_variant,,ENST00000591966,; A ENST00000444449 Transcript missense_variant 328/2311 235/1308 79/435 L/M Ctg/Atg 1 1 AP1M1 HGNC HGNC:13667 protein_coding YES CCDS46008.1 ENSP00000388996 Q9BXS5 UPI000051DDEE NM_001130524.1 tolerated(0.37) 3/13 hmmpanther:PTHR10529:SF257,hmmpanther:PTHR10529,Gene3D:3.30.450.60,Pfam_domain:PF01217,Superfamily_domains:SSF64356 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 16206376 16206376 C A 1 0 0 0 0 1 0 0 0 850 796 28 2 2 AP1M1 19 16206376 Missense_Mutation SNP C C3N-02582_T 7357430 16206376 42411240 94 29958 ZNF429 0 . GRCh38 19 21537738 21537738 + Missense_Mutation SNP A A G novel C3N-02582_T C3N-02582_N A A c.1685A>G p.Glu562Gly p.E562G ENST00000358491 4/4 128 85 43 365 365 0 strelka-varscan-mutect ZNF429,missense_variant,p.Glu562Gly,ENST00000358491,NM_001001415.2;ZNF429,missense_variant,p.Glu531Gly,ENST00000618549,;ZNF429,intron_variant,,ENST00000597078,;ZNF429,upstream_gene_variant,,ENST00000594385,;ZNF429,downstream_gene_variant,,ENST00000594022,; G ENST00000358491 Transcript missense_variant 1893/2233 1685/2025 562/674 E/G gAg/gGg 1 1 ZNF429 HGNC HGNC:20817 protein_coding YES CCDS42537.1 ENSP00000351280 Q86V71 UPI000022ABC2 NM_001001415.2 deleterious(0.01) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24377,hmmpanther:PTHR24377:SF367,Superfamily_domains:SSF57667 MODERATE 1 SNV 3 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 21537738 21537738 A G 1 0 0 0 0 1 0 0 0 18474 304 11 5 5 ZNF429 19 21537738 Missense_Mutation SNP A C3N-02582_T 5331362 21537738 37079878 95 29959 GRIK5 0 . GRCh38 19 41999156 41999156 + Missense_Mutation SNP G G C C3N-02582_T C3N-02582_N G G c.2658C>G p.Ser886Arg p.S886R ENST00000262895 19/19 183 158 25 276 276 0 strelka-varscan-mutect GRIK5,missense_variant,p.Ser886Arg,ENST00000262895,NM_002088.4;GRIK5,missense_variant,p.Ser886Arg,ENST00000593562,;ATP1A3,upstream_gene_variant,,ENST00000545399,NM_001256214.1;ATP1A3,upstream_gene_variant,,ENST00000302102,NM_152296.4;GRIK5,downstream_gene_variant,,ENST00000301218,NM_001301030.1;ATP1A3,upstream_gene_variant,,ENST00000473086,;GRIK5,non_coding_transcript_exon_variant,,ENST00000454993,;ATP1A3,upstream_gene_variant,,ENST00000441343,;GRIK5,downstream_gene_variant,,ENST00000602210,; C ENST00000262895 Transcript missense_variant 2658/3493 2658/2943 886/980 S/R agC/agG COSM5446277 1 -1 GRIK5 HGNC HGNC:4583 protein_coding CCDS12595.1 ENSP00000262895 Q16478 UPI000013D353 NM_002088.4 deleterious(0) 19/19 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF34 1 MODERATE SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 104 41999156 41999156 G C 1 0 0 0 0 1 0 0 0 6659 1310 46 4 4 GRIK5 19 41999156 Missense_Mutation SNP G C3N-02582_T 20461418 41999156 16618460 96 29960 ZNF766 0 . GRCh38 19 52290353 52290353 + Missense_Mutation SNP G G A C3N-02582_T C3N-02582_N G G c.562G>A p.Glu188Lys p.E188K ENST00000439461 4/4 80 71 9 186 186 0 strelka-varscan-mutect ZNF766,missense_variant,p.Glu188Lys,ENST00000439461,NM_001010851.2;ZNF766,missense_variant,p.Glu203Lys,ENST00000593612,;ZNF766,missense_variant,p.Glu129Lys,ENST00000593703,;ZNF766,3_prime_UTR_variant,,ENST00000599581,;ZNF766,downstream_gene_variant,,ENST00000600821,;ZNF766,downstream_gene_variant,,ENST00000595000,;ZNF766,downstream_gene_variant,,ENST00000595149,;CTD-2525I3.5,intron_variant,,ENST00000594865,; A ENST00000439461 Transcript missense_variant 605/6298 562/1407 188/468 E/K Gaa/Aaa COSM1000461 1 1 ZNF766 HGNC HGNC:28063 protein_coding YES CCDS46163.1 ENSP00000409652 Q5HY98 UPI0000202AF7 NM_001010851.2 tolerated(1) 4/4 Gene3D:3.30.160.60,PROSITE_profiles:PS50157,hmmpanther:PTHR24407,hmmpanther:PTHR24407:SF5,SMART_domains:SM00355,Superfamily_domains:SSF57667 1 MODERATE 1 SNV 1 1 1 PASS rs1337492997 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 52290353 52290353 G A 1 0 0 0 0 1 0 0 0 18723 1059 37 1 1 ZNF766 19 52290353 Missense_Mutation SNP G C3N-02582_T 10291197 52290353 6327263 97 29961 B4GALT5 0 . GRCh38 20 49656638 49656638 + Silent SNP G G A C3N-02582_T C3N-02582_N G G c.180C>T p.= p.I60I ENST00000371711 2/9 325 308 17 424 423 1 strelka-varscan-mutect B4GALT5,synonymous_variant,p.=,ENST00000371711,NM_004776.3; A ENST00000371711 Transcript synonymous_variant 368/4722 180/1167 60/388 I atC/atT COSM1136802 1 -1 B4GALT5 HGNC HGNC:928 protein_coding YES CCDS13420.1 ENSP00000360776 O43286 UPI0000126720 NM_004776.3 2/9 hmmpanther:PTHR19300:SF45,hmmpanther:PTHR19300 1 LOW 1 SNV 1 1 1 PASS rs1347088909 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 104 49656638 49656638 G A 1 0 0 0 0 0 0 0 1 1430 1048 37 1 1 B4GALT5 20 49656638 Silent SNP G C3N-02582_T 49656638 14787529 98 29962 TCF20 0 . GRCh38 22 42213733 42213733 + Missense_Mutation SNP T T A novel C3N-02582_T C3N-02582_N T T c.1573A>T p.Ser525Cys p.S525C ENST00000359486 1/5 163 153 10 301 300 1 strelka-varscan-mutect TCF20,missense_variant,p.Ser525Cys,ENST00000359486,NM_005650.2;TCF20,missense_variant,p.Ser525Cys,ENST00000335626,NM_181492.2;TCF20,upstream_gene_variant,,ENST00000404876,;TCF20,downstream_gene_variant,,ENST00000515426,; A ENST00000359486 Transcript missense_variant 1710/7410 1573/5883 525/1960 S/C Agc/Tgc 1 -1 TCF20 HGNC HGNC:11631 protein_coding YES CCDS14033.1 ENSP00000352463 Q9UGU0 W5ZR30 UPI00001A95D9 NM_005650.2 deleterious(0) 1/5 hmmpanther:PTHR14955:SF7,hmmpanther:PTHR14955 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 42213733 42213733 T A 1 0 0 0 0 1 0 0 0 16097 1580 55 4 4 TCF20 22 42213733 Missense_Mutation SNP T C3N-02582_T 42213733 8604735 99 29963 PPARA 0 . GRCh38 22 46231835 46231835 + Missense_Mutation SNP A A T novel C3N-02582_T C3N-02582_N A A c.755A>T p.Lys252Met p.K252M ENST00000407236 7/8 145 124 21 270 270 0 strelka-varscan-mutect PPARA,missense_variant,p.Lys252Met,ENST00000407236,;PPARA,missense_variant,p.Lys252Met,ENST00000262735,NM_005036.4,NM_001001928.2;PPARA,missense_variant,p.Lys252Met,ENST00000402126,; T ENST00000407236 Transcript missense_variant 968/9995 755/1407 252/468 K/M aAg/aTg 1 1 PPARA HGNC HGNC:9232 protein_coding YES CCDS33669.1 ENSP00000385523 Q07869 F1D8S4 UPI000000D8E0 deleterious(0.03) 7/8 Gene3D:1.10.565.10,Prints_domain:PR01289,hmmpanther:PTHR24082,hmmpanther:PTHR24082:SF197,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 104 46231835 46231835 A T 1 0 0 0 0 1 0 0 0 12406 72 3 4 4 PPARA 22 46231835 Missense_Mutation SNP A C3N-02582_T 4018102 46231835 4586633 100 29964 GRPR 0 . GRCh38 X 16124107 16124107 + Missense_Mutation SNP C C A rs74381274 C3N-02582_T C3N-02582_N C C c.154C>A p.Leu52Met p.L52M ENST00000380289 1/3 151 135 16 196 196 0 strelka-varscan-mutect GRPR,missense_variant,p.Leu52Met,ENST00000380289,NM_005314.2; A ENST00000380289 Transcript missense_variant 552/1929 154/1155 52/384 L/M Ctg/Atg rs74381274 1 1 GRPR HGNC HGNC:4609 protein_coding YES CCDS14174.1 ENSP00000369643 P30550 X5D7H2 UPI00000503FE NM_005314.2 tolerated(0.1) 1/3 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR24243,hmmpanther:PTHR24243:SF116,Gene3D:1.20.1070.10,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237 MODERATE 1 SNV 1 1 PASS rs74381274 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 104 16124107 16124107 C A 1 0 0 0 0 1 0 0 0 6690 912 32 2 2 GRPR 23 16124107 Missense_Mutation SNP C C3N-02582_T 16124107 139916788 101 29965 BCOR 0 . GRCh38 X 40074909 40074909 + Missense_Mutation SNP C C G novel C3N-02582_T C3N-02582_N C C c.437G>C p.Ser146Thr p.S146T ENST00000378444 4/15 158 150 8 196 196 0 strelka-mutect BCOR,missense_variant,p.Ser146Thr,ENST00000342274,NM_001123383.1;BCOR,missense_variant,p.Ser146Thr,ENST00000378444,NM_001123385.1;BCOR,missense_variant,p.Ser146Thr,ENST00000378455,NM_001123384.1;BCOR,missense_variant,p.Ser146Thr,ENST00000397354,NM_017745.5;BCOR,missense_variant,p.Ser146Thr,ENST00000406200,;BCOR,intron_variant,,ENST00000615339,;BCOR,downstream_gene_variant,,ENST00000412952,;BCOR,non_coding_transcript_exon_variant,,ENST00000490976,; G ENST00000378444 Transcript missense_variant 666/6358 437/5268 146/1755 S/T aGt/aCt 1 -1 BCOR HGNC HGNC:20893 protein_coding YES CCDS48093.1 ENSP00000367705 Q6W2J9 UPI00002318CF NM_001123385.1 tolerated(0.29) 4/15 hmmpanther:PTHR24117:SF8,hmmpanther:PTHR24117 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 104 40074909 40074909 C G 1 0 0 0 0 1 0 0 0 1533 565 20 4 4 BCOR 23 40074909 Missense_Mutation SNP C C3N-02582_T 23950802 40074909 115965986 102 29966 RGAG4 0 . GRCh38 X 72130380 72130380 + Missense_Mutation SNP C C A C3N-02582_T C3N-02582_N C C c.1161G>T p.Met387Ile p.M387I ENST00000609883 1/1 84 77 7 123 123 0 strelka-varscan-mutect RGAG4,missense_variant,p.Met387Ile,ENST00000609883,NM_001024455.3;NHSL2,intron_variant,,ENST00000633930,NM_001013627.2;NHSL2,intron_variant,,ENST00000631375,;NHSL2,intron_variant,,ENST00000632230,;NHSL2,upstream_gene_variant,,ENST00000510661,;NHSL2,intron_variant,,ENST00000631833,;RGAG4,missense_variant,p.Met387Ile,ENST00000479991,;NHSL2,upstream_gene_variant,,ENST00000373677,; A ENST00000609883 Transcript missense_variant 1449/4105 1161/1710 387/569 M/I atG/atT COSM5538146 1 -1 RGAG4 HGNC HGNC:29430 protein_coding YES CCDS55446.1 ENSP00000476792 Q5HYW3 UPI00001C2079 NM_001024455.3 tolerated_low_confidence(0.06) 1/1 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15503,hmmpanther:PTHR15503:SF2,Low_complexity_(Seg):seg 1 MODERATE SNV 1 1 PASS . . 0 206 3 0 0 0 0 0 -15.19245 1 1 1 1 0 A 3 1 104 72130380 72130380 C A 1 0 0 0 0 1 0 0 0 13447 826 29 2 2 RGAG4 23 72130380 Missense_Mutation SNP C C3N-02582_T 32055471 72130380 83910515 103 29967 AGTR2 0 . GRCh38 X 116173329 116173329 + Missense_Mutation SNP G G A C3N-02582_T C3N-02582_N G G c.1049G>A p.Arg350Gln p.R350Q ENST00000371906 3/3 177 164 13 163 163 0 strelka-varscan-mutect AGTR2,missense_variant,p.Arg350Gln,ENST00000371906,NM_000686.4; A ENST00000371906 Transcript missense_variant 1239/2882 1049/1092 350/363 R/Q cGg/cAg COSM77238 1 1 AGTR2 HGNC HGNC:338 protein_coding YES CCDS14569.1 ENSP00000360973 P50052 UPI0000125687 NM_000686.4 deleterious(0.01) 3/3 Prints_domain:PR00636,hmmpanther:PTHR24228,hmmpanther:PTHR24228:SF8,Superfamily_domains:SSF81321 1 MODERATE 1 SNV 1 1 1 PASS rs1468172864 . 0 203 4 3 0 0 0 0 -17.02683 0.9993657 1 1 1 0 A 3 1 104 116173329 116173329 G A 1 0 0 0 0 1 0 0 0 481 1116 39 1 1 AGTR2 23 116173329 Missense_Mutation SNP G C3N-02582_T 44042949 116173329 39867566 104 29968 DISP3 0 . GRCh38 1 11520812 11520812 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.2326C>A p.Leu776Met p.L776M ENST00000294484 10/21 150 70 80 343 342 1 strelka-varscan-mutect DISP3,missense_variant,p.Leu776Met,ENST00000294484,NM_020780.1; A ENST00000294484 Transcript missense_variant 2464/5215 2326/4179 776/1392 L/M Ctg/Atg 1 1 DISP3 HGNC HGNC:29251 protein_coding YES CCDS41247.1 ENSP00000294484 Q9P2K9 UPI00001C1D7A NM_020780.1 tolerated(0.07) 10/21 hmmpanther:PTHR10796,hmmpanther:PTHR10796:SF125 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 11520812 11520812 C A 1 0 0 0 0 1 0 0 0 4347 680 24 2 2 DISP3 1 11520812 Missense_Mutation SNP C C3N-02586_T 11520812 237435610 1 29969 IL23R 0 . GRCh38 1 67200810 67200810 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.565G>T p.Gly189Cys p.G189C ENST00000347310 5/11 287 153 134 625 625 0 strelka-varscan-mutect IL23R,missense_variant,p.Gly189Cys,ENST00000347310,NM_144701.2;IL23R,5_prime_UTR_variant,,ENST00000637002,;C1orf141,intron_variant,,ENST00000371007,NM_001276351.1;C1orf141,intron_variant,,ENST00000448166,;RNU6-586P,downstream_gene_variant,,ENST00000517265,; T ENST00000347310 Transcript missense_variant 736/2912 565/1890 189/629 G/C Ggc/Tgc 1 1 IL23R HGNC HGNC:19100 protein_coding YES CCDS637.1 ENSP00000321345 Q5VWK5 UPI000004CACD NM_144701.2 deleterious(0) 5/11 Gene3D:2.60.40.10,PROSITE_profiles:PS50853,hmmpanther:PTHR23036,hmmpanther:PTHR23036:SF112,Superfamily_domains:SSF49265 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 67200810 67200810 G T 1 0 0 0 0 1 0 0 0 7579 1348 47 2 2 IL23R 1 67200810 Missense_Mutation SNP G C3N-02586_T 55679998 67200810 181755612 2 29970 CLCA4 0 . GRCh38 1 86563674 86563674 + Silent SNP C C T novel C3N-02586_T C3N-02586_N C C c.462C>T p.= p.V154V ENST00000370563 4/14 150 69 81 280 280 0 strelka-varscan-mutect CLCA4,synonymous_variant,p.=,ENST00000370563,NM_012128.3; T ENST00000370563 Transcript synonymous_variant 504/3211 462/2760 154/919 V gtC/gtT 1 1 CLCA4 HGNC HGNC:2018 protein_coding YES CCDS41355.1 ENSP00000359594 Q14CN2 UPI00000389E8 NM_012128.3 4/14 hmmpanther:PTHR10579:SF2,hmmpanther:PTHR10579,TIGRFAM_domain:TIGR00868,Pfam_domain:PF08434 LOW 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 86563674 86563674 C T 1 0 0 0 0 0 0 0 1 3223 842 30 3 3 CLCA4 1 86563674 Silent SNP C C3N-02586_T 19362864 86563674 162392748 3 29971 FLG 0 . GRCh38 1 152309802 152309802 + Nonsense_Mutation SNP G G T rs772851618 C3N-02586_T C3N-02586_N G G c.5084C>A p.Ser1695Ter p.S1695* ENST00000368799 3/3 389 195 194 731 731 0 strelka-varscan-mutect FLG,stop_gained,p.Ser1695Ter,ENST00000368799,NM_002016.1;FLG-AS1,intron_variant,,ENST00000420707,;FLG-AS1,intron_variant,,ENST00000593011,;FLG-AS1,upstream_gene_variant,,ENST00000392688,; T ENST00000368799 Transcript stop_gained 5120/12747 5084/12186 1695/4061 S/* tCa/tAa rs772851618,CM092260 1 -1 FLG HGNC HGNC:3748 protein_coding YES CCDS30860.1 ENSP00000357789 P20930 UPI0000470CB3 NM_002016.1 3/3 hmmpanther:PTHR22571:SF21,hmmpanther:PTHR22571,Pfam_domain:PF03516 HIGH 1 SNV 1 0,1 1 PASS rs772851618 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 105 152309802 152309802 G T 1 0 0 0 0 0 1 0 0 5784 1294 45 2 2 FLG 1 152309802 Nonsense_Mutation SNP G C3N-02586_T 65746128 152309802 96646620 4 29972 SDHC 0 . GRCh38 1 161356690 161356690 + Silent SNP T T C novel C3N-02586_T C3N-02586_N T T c.255T>C p.= p.F85F ENST00000367975 5/6 358 198 160 695 695 0 strelka-varscan-mutect SDHC,synonymous_variant,p.=,ENST00000367975,NM_003001.3;SDHC,synonymous_variant,p.=,ENST00000432287,NM_001035512.1;SDHC,synonymous_variant,p.=,ENST00000392169,NM_001035513.1;SDHC,intron_variant,,ENST00000342751,NM_001035511.1;SDHC,intron_variant,,ENST00000513009,NM_001278172.1;SDHC,3_prime_UTR_variant,,ENST00000470743,;SDHC,3_prime_UTR_variant,,ENST00000504963,; C ENST00000367975 Transcript synonymous_variant 404/13566 255/510 85/169 F ttT/ttC 1 1 SDHC HGNC HGNC:10682 protein_coding YES CCDS1230.1 ENSP00000356953 Q99643 A0A0S2Z4B7 UPI0000001636 NM_003001.3 5/6 hmmpanther:PTHR10978:SF3,hmmpanther:PTHR10978,TIGRFAM_domain:TIGR02970,Gene3D:1.20.1300.10,Pfam_domain:PF01127,Superfamily_domains:SSF81343,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 105 161356690 161356690 T C 1 0 0 0 0 0 0 0 1 14241 1809 63 5 5 SDHC 1 161356690 Silent SNP T C3N-02586_T 9046888 161356690 87599732 5 29973 LMX1A 0 . GRCh38 1 165353259 165353259 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.80G>T p.Arg27Ile p.R27I ENST00000342310 3/9 117 53 64 181 181 0 strelka-varscan-mutect LMX1A,missense_variant,p.Arg27Ile,ENST00000342310,NM_177398.3;LMX1A,missense_variant,p.Arg27Ile,ENST00000294816,NM_001174069.1;LMX1A,missense_variant,p.Arg27Ile,ENST00000367893,; A ENST00000342310 Transcript missense_variant 463/3545 80/1149 27/382 R/I aGa/aTa 1 -1 LMX1A HGNC HGNC:6653 protein_coding YES CCDS1247.1 ENSP00000340226 Q8TE12 UPI000012E793 NM_177398.3 tolerated_low_confidence(0.18) 3/9 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF88 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 165353259 165353259 C A 1 0 0 0 0 1 0 0 0 8788 927 32 2 2 LMX1A 1 165353259 Missense_Mutation SNP C C3N-02586_T 3996569 165353259 83603163 6 29974 TNN 0 . GRCh38 1 175118725 175118725 + Missense_Mutation SNP G G C novel C3N-02586_T C3N-02586_N G G c.2551G>C p.Val851Leu p.V851L ENST00000239462 11/19 364 222 142 731 731 0 strelka-varscan TNN,missense_variant,p.Val851Leu,ENST00000239462,NM_022093.1;TNN,missense_variant,p.Val674Leu,ENST00000621086,;TNN,missense_variant,p.Val674Leu,ENST00000622870,; C ENST00000239462 Transcript missense_variant 2664/5008 2551/3900 851/1299 V/L Gtc/Ctc 1 1 TNN HGNC HGNC:22942 protein_coding YES CCDS30943.1 ENSP00000239462 Q9UQP3 UPI00001D7DA9 NM_022093.1 tolerated(0.2) 11/19 PROSITE_profiles:PS50853,hmmpanther:PTHR19143:SF252,hmmpanther:PTHR19143,Gene3D:2.60.40.10,Pfam_domain:PF00041,SMART_domains:SM00060,Superfamily_domains:SSF49265 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 175118725 175118725 G C 1 0 0 0 0 1 0 0 0 16796 1377 48 4 4 TNN 1 175118725 Missense_Mutation SNP G C3N-02586_T 9765466 175118725 73837697 7 29975 DNAH14 0 . GRCh38 1 225264256 225264256 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.7199G>T p.Ser2400Ile p.S2400I ENST00000430092 47/84 71 35 36 298 298 0 strelka-varscan DNAH14,missense_variant,p.Ser2400Ile,ENST00000430092,NM_001373.1;DNAH14,missense_variant,p.Ser2400Ile,ENST00000439375,;DNAH14,missense_variant,p.Ser172Ile,ENST00000450490,;DNAH14,intron_variant,,ENST00000445597,;DNAH14,missense_variant,p.Ser167Ile,ENST00000327794,; T ENST00000430092 Transcript missense_variant 7414/13763 7199/13548 2400/4515 S/I aGt/aTt 1 1 DNAH14 HGNC HGNC:2945 protein_coding ENSP00000414402 Q0VDD8 UPI000192C36D NM_001373.1 tolerated(0.22) 47/84 SMART_domains:SM00382 MODERATE SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 225264256 225264256 G T 1 0 0 0 0 1 0 0 0 4415 1043 36 2 2 DNAH14 1 225264256 Missense_Mutation SNP G C3N-02586_T 50145531 225264256 23692166 8 29976 RYR2 0 . GRCh38 1 237784821 237784821 + Missense_Mutation SNP C C G novel C3N-02586_T C3N-02586_N C C c.13109C>G p.Thr4370Arg p.T4370R ENST00000366574 90/105 99 52 47 159 159 0 strelka-varscan RYR2,missense_variant,p.Thr4370Arg,ENST00000366574,NM_001035.2;RYR2,missense_variant,p.Thr4354Arg,ENST00000360064,;RYR2,non_coding_transcript_exon_variant,,ENST00000609119,; G ENST00000366574 Transcript missense_variant 13426/16562 13109/14904 4370/4967 T/R aCa/aGa 1 1 RYR2 HGNC HGNC:10484 protein_coding YES CCDS55691.1 ENSP00000355533 Q92736 UPI0000DD0308 NM_001035.2 tolerated(0.5) 90/105 Pfam_domain:PF06459,hmmpanther:PTHR13715,hmmpanther:PTHR13715:SF75,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 237784821 237784821 C G 1 0 0 0 0 1 0 0 0 14029 478 17 4 4 RYR2 1 237784821 Missense_Mutation SNP C C3N-02586_T 12520565 237784821 11171601 9 29977 TDRD15 0 . GRCh38 2 21141353 21141353 + Frame_Shift_Del DEL A A - novel C3N-02586_T C3N-02586_N A A c.3888delA p.Val1297LeufsTer24 p.V1297Lfs*24 ENST00000405799 4/4 98 49 49 315 315 0 sindel-varindel-pindel TDRD15,frameshift_variant,p.Val1297LeufsTer24,ENST00000405799,;TDRD15,frameshift_variant,p.Val1297LeufsTer24,ENST00000622654,; - ENST00000405799 Transcript frameshift_variant 4216/6135 3886/5805 1296/1934 K/X Aaa/aa 1 1 TDRD15 HGNC HGNC:45037 protein_coding YES CCDS77385.1 ENSP00000384376 B5MCY1 UPI000173A3F5 4/4 Pfam_domain:PF00567,hmmpanther:PTHR22948,hmmpanther:PTHR22948:SF7 HIGH 1 deletion 2 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 105 21141353 21141353 A - 1 0 1 0 1 0 0 0 0 16141 131 5 0 0 TDRD15 2 21141353 Frame_Shift_Del DEL A C3N-02586_T 21141353 221052176 10 29978 LRRTM4 0 . GRCh38 2 77519664 77519664 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.205A>T p.Arg69Trp p.R69W ENST00000409093 3/4 317 154 163 610 610 0 strelka-varscan LRRTM4,missense_variant,p.Arg69Trp,ENST00000409088,NM_024993.4;LRRTM4,missense_variant,p.Arg70Trp,ENST00000409911,;LRRTM4,missense_variant,p.Arg70Trp,ENST00000409282,NM_001282928.1;LRRTM4,missense_variant,p.Arg69Trp,ENST00000409093,NM_001282924.1;LRRTM4,missense_variant,p.Arg69Trp,ENST00000409884,NM_001134745.1;LRRTM4,downstream_gene_variant,,ENST00000456154,; A ENST00000409093 Transcript missense_variant 542/2247 205/1773 69/590 R/W Agg/Tgg 1 -1 LRRTM4 HGNC HGNC:19411 protein_coding YES CCDS46346.1 ENSP00000386357 Q86VH4 UPI0000047808 NM_001282924.1 deleterious(0) 3/4 hmmpanther:PTHR24369,hmmpanther:PTHR24369:SF1,Gene3D:3.80.10.10,Pfam_domain:PF13855,Superfamily_domains:SSF52058 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 77519664 77519664 T A 1 0 0 0 0 1 0 0 0 8948 1608 56 4 4 LRRTM4 2 77519664 Missense_Mutation SNP T C3N-02586_T 56378311 77519664 164673865 11 29979 LYPD6B 0 . GRCh38 2 149212992 149212992 + Missense_Mutation SNP A A G novel C3N-02586_T C3N-02586_N A A c.329A>G p.Asn110Ser p.N110S ENST00000409642 6/7 137 68 69 251 251 0 strelka-varscan-mutect LYPD6B,missense_variant,p.Asn110Ser,ENST00000409642,NM_177964.3;LYPD6B,missense_variant,p.Asn86Ser,ENST00000409029,NM_001317004.1;LYPD6B,missense_variant,p.Asn86Ser,ENST00000409876,;LYPD6B,missense_variant,p.Asn86Ser,ENST00000280115,;LYPD6B,splice_region_variant,,ENST00000498249,;LYPD6B,downstream_gene_variant,,ENST00000442722,; G ENST00000409642 Transcript missense_variant,splice_region_variant 730/1577 329/624 110/207 N/S aAt/aGt 1 1 LYPD6B HGNC HGNC:27018 protein_coding YES CCDS46423.1 ENSP00000387077 Q8NI32 UPI00001BDB14 NM_177964.3 6/7 Pfam_domain:PF16975,hmmpanther:PTHR31171,hmmpanther:PTHR31171:SF3,Superfamily_domains:SSF57302 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 149212992 149212992 A G 1 0 0 0 0 1 0 0 0 9026 347 12 5 5 LYPD6B 2 149212992 Missense_Mutation SNP A C3N-02586_T 71693328 149212992 92980537 12 29980 CYP20A1 0 . GRCh38 2 203251976 203251976 + Missense_Mutation SNP T T G novel C3N-02586_T C3N-02586_N T T c.299T>G p.Phe100Cys p.F100C ENST00000356079 4/13 83 45 38 228 228 0 strelka-varscan-mutect CYP20A1,missense_variant,p.Phe100Cys,ENST00000356079,NM_177538.2;CYP20A1,missense_variant,p.Phe100Cys,ENST00000429815,;CYP20A1,missense_variant,p.Phe100Cys,ENST00000443941,;CYP20A1,5_prime_UTR_variant,,ENST00000613925,;CYP20A1,non_coding_transcript_exon_variant,,ENST00000461371,;CYP20A1,non_coding_transcript_exon_variant,,ENST00000463131,;CYP20A1,non_coding_transcript_exon_variant,,ENST00000489360,;CYP20A1,missense_variant,p.Phe44Leu,ENST00000431118,;CYP20A1,missense_variant,p.Phe100Cys,ENST00000449301,;CYP20A1,missense_variant,p.Phe44Leu,ENST00000428265,; G ENST00000356079 Transcript missense_variant 422/1949 299/1389 100/462 F/C tTt/tGt 1 1 CYP20A1 HGNC HGNC:20576 protein_coding YES CCDS2357.1 ENSP00000348380 Q6UW02 UPI0000048EFF NM_177538.2 deleterious(0) 4/13 hmmpanther:PTHR24280,Pfam_domain:PF00067,Gene3D:1.10.630.10,Superfamily_domains:SSF48264 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 203251976 203251976 T G 1 0 0 0 0 1 0 0 0 3955 1841 64 5 5 CYP20A1 2 203251976 Missense_Mutation SNP T C3N-02586_T 54038984 203251976 38941553 13 29981 EAF2 0 . GRCh38 3 121872663 121872663 + Missense_Mutation SNP C C A C3N-02586_T C3N-02586_N C C c.611C>A p.Ser204Tyr p.S204Y ENST00000273668 5/6 123 72 51 416 416 0 strelka-varscan EAF2,missense_variant,p.Ser204Tyr,ENST00000273668,NM_018456.4;EAF2,missense_variant,p.Ser204Tyr,ENST00000451944,;EAF2,3_prime_UTR_variant,,ENST00000490434,NM_001320041.1; A ENST00000273668 Transcript missense_variant 682/992 611/783 204/260 S/Y tCc/tAc COSM3586053 1 1 EAF2 HGNC HGNC:23115 protein_coding YES CCDS3006.1 ENSP00000273668 Q96CJ1 UPI000000D7DA NM_018456.4 tolerated(0.08) 5/6 Low_complexity_(Seg):seg,hmmpanther:PTHR15970:SF7,hmmpanther:PTHR15970 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 121872663 121872663 C A 1 0 0 0 0 1 0 0 0 4700 855 30 2 2 EAF2 3 121872663 Missense_Mutation SNP C C3N-02586_T 121872663 76422896 14 29982 SLITRK3 0 . GRCh38 3 165189091 165189091 + Silent SNP G G T rs569158591 C3N-02586_T C3N-02586_N G G c.1740C>A p.= p.I580I ENST00000475390 2/2 303 238 65 575 575 0 strelka-varscan SLITRK3,synonymous_variant,p.=,ENST00000475390,NM_001318811.1,NM_001318810.1;SLITRK3,synonymous_variant,p.=,ENST00000241274,NM_014926.2;SLITRK3,downstream_gene_variant,,ENST00000497724,; T ENST00000475390 Transcript synonymous_variant 2184/4555 1740/2934 580/977 I atC/atA rs569158591 1 -1 SLITRK3 HGNC HGNC:23501 protein_coding YES CCDS3197.1 ENSP00000420091 O94933 UPI000004F259 NM_001318811.1,NM_001318810.1 2/2 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF14,Gene3D:3.80.10.10,SMART_domains:SM00082,Superfamily_domains:SSF52058 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 165189091 165189091 G T 1 0 0 0 0 0 0 0 1 15035 1280 45 2 2 SLITRK3 3 165189091 Silent SNP G C3N-02586_T 43316428 165189091 33106468 15 29983 IDUA 0 . GRCh38 4 987163 987163 + Missense_Mutation SNP G G A novel C3N-02586_T C3N-02586_N G G c.79G>A p.Glu27Lys p.E27K ENST00000247933 1/14 116 66 50 227 227 0 strelka-varscan-mutect IDUA,missense_variant,p.Glu27Lys,ENST00000247933,NM_000203.4;IDUA,missense_variant,p.Glu27Lys,ENST00000502910,;IDUA,synonymous_variant,p.=,ENST00000504568,;SLC26A1,intron_variant,,ENST00000398520,NM_134425.2;SLC26A1,intron_variant,,ENST00000622731,;SLC26A1,downstream_gene_variant,,ENST00000361661,NM_213613.3;SLC26A1,downstream_gene_variant,,ENST00000398516,NM_022042.3;IDUA,upstream_gene_variant,,ENST00000509948,;IDUA,upstream_gene_variant,,ENST00000514192,;DGKQ,upstream_gene_variant,,ENST00000510286,;IDUA,upstream_gene_variant,,ENST00000509744,;SLC26A1,downstream_gene_variant,,ENST00000513138,;IDUA,non_coding_transcript_exon_variant,,ENST00000514698,;IDUA,non_coding_transcript_exon_variant,,ENST00000506561,;IDUA,non_coding_transcript_exon_variant,,ENST00000508168,; A ENST00000247933 Transcript missense_variant 167/2163 79/1962 27/653 E/K Gag/Aag 1 1 IDUA HGNC HGNC:5391 protein_coding YES CCDS3343.1 ENSP00000247933 P35475 UPI00004571D0 NM_000203.4 tolerated_low_confidence(0.13) 1/14 Pfam_domain:PF01229,hmmpanther:PTHR12631,hmmpanther:PTHR12631:SF8,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1297418198 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 987163 987163 G A 1 0 0 0 0 1 0 0 0 7405 1059 37 1 1 IDUA 4 987163 Missense_Mutation SNP G C3N-02586_T 987163 189227392 16 29984 FAM193A 0 . GRCh38 4 2662969 2662969 + Frame_Shift_Del DEL A A - novel C3N-02586_T C3N-02586_N A A c.1007delA p.Asn336ThrfsTer4 p.N336Tfs*4 ENST00000324666 9/20 78 38 40 140 140 0 sindel-varindel-pindel FAM193A,frameshift_variant,p.Asn627ThrfsTer4,ENST00000637812,;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000324666,NM_001256666.1;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000382839,NM_003704.3;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000505311,NM_001256668.1;FAM193A,frameshift_variant,p.Asn358ThrfsTer4,ENST00000502458,NM_001256667.1;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000545951,;FAM193A,frameshift_variant,p.Asn190ThrfsTer4,ENST00000513350,;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000512465,;FAM193A,frameshift_variant,p.Asn336ThrfsTer4,ENST00000513898,;FAM193A,non_coding_transcript_exon_variant,,ENST00000506904,; - ENST00000324666 Transcript frameshift_variant 1355/4846 1004/3798 335/1265 E/X gAa/ga 1 1 FAM193A HGNC HGNC:16822 protein_coding YES CCDS58875.1 ENSP00000324587 P78312 UPI0000551BCA NM_001256666.1 9/20 hmmpanther:PTHR15109:SF2,hmmpanther:PTHR15109 HIGH 1 deletion 1 3 1 PASS . . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 105 2662969 2662969 A - 1 0 1 0 1 0 0 0 0 5371 246 9 0 0 FAM193A 4 2662969 Frame_Shift_Del DEL A C3N-02586_T 1675806 2662969 187551586 17 29985 WDR19 0 . GRCh38 4 39224930 39224930 + Missense_Mutation SNP A A G novel C3N-02586_T C3N-02586_N A A c.1526A>G p.Asn509Ser p.N509S ENST00000399820 15/37 88 45 43 304 304 0 strelka-varscan-mutect WDR19,missense_variant,p.Asn509Ser,ENST00000399820,NM_025132.3;WDR19,intron_variant,,ENST00000511729,;WDR19,upstream_gene_variant,,ENST00000515631,;WDR19,3_prime_UTR_variant,,ENST00000506869,NM_001317924.1;WDR19,non_coding_transcript_exon_variant,,ENST00000512095,;WDR19,upstream_gene_variant,,ENST00000507228,; G ENST00000399820 Transcript missense_variant 1680/4520 1526/4029 509/1342 N/S aAt/aGt 1 1 WDR19 HGNC HGNC:18340 protein_coding YES CCDS47042.1 ENSP00000382717 Q8NEZ3 UPI000004CC24 NM_025132.3 tolerated(0.4) 15/37 Pfam_domain:PF15911,hmmpanther:PTHR14920,hmmpanther:PTHR14920:SF0,Superfamily_domains:SSF82171 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 39224930 39224930 A G 1 0 0 0 0 1 0 0 0 17839 101 4 5 5 WDR19 4 39224930 Missense_Mutation SNP A C3N-02586_T 36561961 39224930 150989625 18 29986 FAM149A 0 . GRCh38 4 186153670 186153670 + Missense_Mutation SNP C C G novel C3N-02586_T C3N-02586_N C C c.112C>G p.Pro38Ala p.P38A ENST00000227065 5/14 133 70 63 214 214 0 strelka-varscan-mutect FAM149A,missense_variant,p.Pro329Ala,ENST00000356371,;FAM149A,missense_variant,p.Pro38Ala,ENST00000227065,NM_015398.2,NM_001006655.2;FAM149A,missense_variant,p.Pro38Ala,ENST00000514153,;FAM149A,missense_variant,p.Pro38Ala,ENST00000503432,;FAM149A,missense_variant,p.Pro38Ala,ENST00000502970,;FAM149A,missense_variant,p.Pro38Ala,ENST00000389354,;FAM149A,missense_variant,p.Pro38Ala,ENST00000504330,;FAM149A,missense_variant,p.Pro38Ala,ENST00000510790,;FAM149A,downstream_gene_variant,,ENST00000509574,;FAM149A,non_coding_transcript_exon_variant,,ENST00000514829,;FAM149A,non_coding_transcript_exon_variant,,ENST00000513030,;FAM149A,downstream_gene_variant,,ENST00000513212,;FAM149A,downstream_gene_variant,,ENST00000508379,;FAM149A,non_coding_transcript_exon_variant,,ENST00000515078,;RPSAP70,upstream_gene_variant,,ENST00000504462,; G ENST00000227065 Transcript missense_variant 691/2708 112/1449 38/482 P/A Ccc/Gcc 1 1 FAM149A HGNC HGNC:24527 protein_coding YES CCDS34117.1 ENSP00000227065 A5PLN7 UPI00001C1E1F NM_015398.2,NM_001006655.2 deleterious(0) 5/14 Pfam_domain:PF12516,hmmpanther:PTHR31997,hmmpanther:PTHR31997:SF2 MODERATE 1 SNV 1 1 PASS . . 0 204 4 2 0 0 0 0 -20 0.9999982 1 1 1 0 G 3 3 105 186153670 186153670 C G 1 0 0 0 0 1 0 0 0 5304 739 26 4 4 FAM149A 4 186153670 Missense_Mutation SNP C C3N-02586_T 146928740 186153670 4060885 19 29987 FAM105A 0 . GRCh38 5 14607341 14607341 + Silent SNP A A G novel C3N-02586_T C3N-02586_N A A c.510A>G p.= p.K170K ENST00000274217 6/8 215 159 56 271 269 2 strelka-varscan FAM105A,synonymous_variant,p.=,ENST00000274217,NM_019018.2;FAM105A,non_coding_transcript_exon_variant,,ENST00000513825,;FAM105A,upstream_gene_variant,,ENST00000506258,; G ENST00000274217 Transcript synonymous_variant 630/3597 510/1071 170/356 K aaA/aaG 1 1 FAM105A HGNC HGNC:25629 protein_coding YES CCDS3884.1 ENSP00000274217 Q9NUU6 UPI000004A036 NM_019018.2 6/8 Pfam_domain:PF16218,Prints_domain:PR02056,hmmpanther:PTHR33662,hmmpanther:PTHR33662:SF1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 14607341 14607341 A G 1 0 0 0 0 0 0 0 1 5255 40 2 5 5 FAM105A 5 14607341 Silent SNP A C3N-02586_T 14607341 166930918 20 29988 ADAMTS12 0 . GRCh38 5 33576988 33576988 + Missense_Mutation SNP C C A C3N-02586_T C3N-02586_N C C c.3038G>T p.Gly1013Val p.G1013V ENST00000504830 19/24 765 606 159 730 730 0 strelka-varscan-mutect ADAMTS12,missense_variant,p.Gly1013Val,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Gly928Val,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,; A ENST00000504830 Transcript missense_variant 3374/8774 3038/4785 1013/1594 G/V gGa/gTa COSM5589545 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 tolerated(0.2) 19/24 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 33576988 33576988 C A 1 0 0 0 0 1 0 0 0 301 855 30 2 2 ADAMTS12 5 33576988 Missense_Mutation SNP C C3N-02586_T 18969647 33576988 147961271 21 29989 ADAMTS12 0 . GRCh38 5 33614354 33614354 + Missense_Mutation SNP G G T rs773052280 C3N-02586_T C3N-02586_N G G c.2411C>A p.Pro804His p.P804H ENST00000504830 16/24 253 197 56 225 224 1 strelka-varscan-mutect ADAMTS12,missense_variant,p.Pro804His,ENST00000504830,NM_030955.2;ADAMTS12,missense_variant,p.Pro719His,ENST00000352040,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000504582,;ADAMTS12,non_coding_transcript_exon_variant,,ENST00000506952,; T ENST00000504830 Transcript missense_variant 2747/8774 2411/4785 804/1594 P/H cCt/cAt rs773052280 1 -1 ADAMTS12 HGNC HGNC:14605 protein_coding YES CCDS34140.1 ENSP00000422554 P58397 UPI000013DC51 NM_030955.2 deleterious(0) 16/24 Pfam_domain:PF05986,hmmpanther:PTHR13723,hmmpanther:PTHR13723:SF189 MODERATE 1 SNV 1 1 PASS rs773052280 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 33614354 33614354 G T 1 0 0 0 0 1 0 0 0 301 1000 35 2 2 ADAMTS12 5 33614354 Missense_Mutation SNP G C3N-02586_T 37366 33614354 147923905 22 29990 RANBP3L 0 . GRCh38 5 36261951 36261951 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.647C>A p.Ala216Glu p.A216E ENST00000502994 8/15 141 96 45 260 260 0 strelka-varscan-mutect RANBP3L,missense_variant,p.Ala191Glu,ENST00000296604,NM_145000.3;RANBP3L,missense_variant,p.Ala216Glu,ENST00000502994,NM_001161429.1;RANBP3L,missense_variant,p.Ala191Glu,ENST00000515759,;RANBP3L,downstream_gene_variant,,ENST00000505865,; T ENST00000502994 Transcript missense_variant 1131/2278 647/1473 216/490 A/E gCa/gAa 1 -1 RANBP3L HGNC HGNC:26353 protein_coding YES CCDS54843.1 ENSP00000421853 Q86VV4 UPI0001A5C4B2 NM_001161429.1 tolerated(0.26) 8/15 hmmpanther:PTHR23138:SF88,hmmpanther:PTHR23138 MODERATE 1 SNV 2 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 36261951 36261951 G T 1 0 0 0 0 1 0 0 0 13189 1319 46 2 2 RANBP3L 5 36261951 Missense_Mutation SNP G C3N-02586_T 2647597 36261951 145276308 23 29991 SEPP1 0 . GRCh38 5 42800750 42800750 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.1116G>T p.Gln372His p.Q372H ENST00000514985 5/5 136 98 38 152 152 0 strelka-varscan-mutect SEPP1,missense_variant,p.Gln372His,ENST00000514985,NM_005410.2;SEPP1,missense_variant,p.Gln372His,ENST00000506577,;SEPP1,missense_variant,p.Gln372His,ENST00000511224,NM_001085486.1;CCDC152,3_prime_UTR_variant,,ENST00000361970,NM_001134848.1;CCDC152,downstream_gene_variant,,ENST00000388827,;SEPP1,downstream_gene_variant,,ENST00000514218,;SEPP1,downstream_gene_variant,,ENST00000510965,;SEPP1,downstream_gene_variant,,ENST00000507920,;SEPP1,downstream_gene_variant,,ENST00000509276,;SEPP1,downstream_gene_variant,,ENST00000513303,;SEPP1,non_coding_transcript_exon_variant,,ENST00000512980,;SEPP1,downstream_gene_variant,,ENST00000514403,;SEPP1,downstream_gene_variant,,ENST00000505309,; A ENST00000514985 Transcript missense_variant 1373/2243 1116/1146 372/381 Q/H caG/caT 1 -1 SEPP1 HGNC HGNC:10751 protein_coding YES CCDS43311.1 ENSP00000420939 P49908 UPI00001C1D4A NM_005410.2 deleterious_low_confidence(0.01) 5/5 Pfam_domain:PF04593 MODERATE 1 SNV 1 1 PASS rs1348743808 . 0 89 40 43 8 30 0 0 -2.802414 0 0 1 0 0 A 3 1 105 42800750 42800750 C A 1 0 0 0 0 1 0 0 0 14333 680 24 2 2 SEPP1 5 42800750 Missense_Mutation SNP C C3N-02586_T 6538799 42800750 138737509 24 29992 ADGRV1 0 . GRCh38 5 90711290 90711290 + Nonsense_Mutation SNP C C T novel C3N-02586_T C3N-02586_N C C c.9010C>T p.Gln3004Ter p.Q3004* ENST00000405460 41/90 119 66 53 240 240 0 strelka-varscan-mutect ADGRV1,stop_gained,p.Gln3004Ter,ENST00000405460,NM_032119.3;ADGRV1,stop_gained,p.Gln570Ter,ENST00000509621,; T ENST00000405460 Transcript stop_gained 9106/19338 9010/18921 3004/6306 Q/* Caa/Taa 1 1 ADGRV1 HGNC HGNC:17416 protein_coding YES CCDS47246.1 ENSP00000384582 Q8WXG9 UPI00002127A7 NM_032119.3 41/90 Pfam_domain:PF03160,hmmpanther:PTHR11878,hmmpanther:PTHR11878:SF20,SMART_domains:SM00237,Superfamily_domains:SSF141072 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 105 90711290 90711290 C T 1 0 0 0 0 0 1 0 0 379 479 17 3 3 ADGRV1 5 90711290 Nonsense_Mutation SNP C C3N-02586_T 47910540 90711290 90826969 25 29993 CAMK4 0 . GRCh38 5 111394761 111394761 + Silent SNP A A G novel C3N-02586_T C3N-02586_N A A c.438A>G p.= p.K146K ENST00000282356 5/11 157 90 67 348 346 2 strelka-varscan-mutect CAMK4,synonymous_variant,p.=,ENST00000282356,NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4;CAMK4,synonymous_variant,p.=,ENST00000512453,;CAMK4,downstream_gene_variant,,ENST00000508074,;CAMK4,non_coding_transcript_exon_variant,,ENST00000505763,;CAMK4,non_coding_transcript_exon_variant,,ENST00000509408,;CAMK4,non_coding_transcript_exon_variant,,ENST00000502916,;CAMK4,3_prime_UTR_variant,,ENST00000515231,;CAMK4,3_prime_UTR_variant,,ENST00000514007,;CAMK4,3_prime_UTR_variant,,ENST00000504544,; G ENST00000282356 Transcript synonymous_variant 836/12240 438/1422 146/473 K aaA/aaG 1 1 CAMK4 HGNC HGNC:1464 protein_coding YES CCDS4103.1 ENSP00000282356 Q16566 UPI000000128E NM_001323377.1,NM_001323376.1,NM_001323374.1,NM_001323375.1,NM_001744.4 5/11 PROSITE_profiles:PS50011,hmmpanther:PTHR24349,hmmpanther:PTHR24349:SF152,Pfam_domain:PF00069,Gene3D:1.10.510.10,SMART_domains:SM00220,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 111394761 111394761 A G 1 0 0 0 0 0 0 0 1 2296 40 2 5 5 CAMK4 5 111394761 Silent SNP A C3N-02586_T 20683471 111394761 70143498 26 29994 SEMA6A 0 . GRCh38 5 116504869 116504869 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.76C>A p.Pro26Thr p.P26T ENST00000257414 2/20 219 121 98 489 489 0 strelka-varscan SEMA6A,missense_variant,p.Pro26Thr,ENST00000343348,NM_020796.4;SEMA6A,missense_variant,p.Pro26Thr,ENST00000257414,NM_001300780.1;SEMA6A,missense_variant,p.Pro26Thr,ENST00000510263,;SEMA6A,missense_variant,p.Pro26Thr,ENST00000515009,;SEMA6A,missense_variant,p.Pro26Thr,ENST00000509665,;SEMA6A-AS1,intron_variant,,ENST00000510682,;SEMA6A,upstream_gene_variant,,ENST00000503962,; T ENST00000257414 Transcript missense_variant 325/4256 76/3144 26/1047 P/T Cca/Aca 1 -1 SEMA6A HGNC HGNC:10738 protein_coding YES CCDS75288.1 ENSP00000257414 A0A0A0MQU6 UPI000018DB92 NM_001300780.1 deleterious(0) 2/20 PROSITE_profiles:PS51004,hmmpanther:PTHR11036,hmmpanther:PTHR11036:SF12 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 116504869 116504869 G T 1 0 0 0 0 1 0 0 0 14315 1203 42 2 2 SEMA6A 5 116504869 Missense_Mutation SNP G C3N-02586_T 5110108 116504869 65033390 27 29995 PCDHGA10 0 . GRCh38 5 141414897 141414897 + Silent SNP C C T novel C3N-02586_T C3N-02586_N C C c.1722C>T p.= p.D574D ENST00000398610 1/4 401 367 34 742 742 0 varscan-mutect PCDHGA10,synonymous_variant,p.=,ENST00000398610,NM_018913.2;PCDHGA10,synonymous_variant,p.=,ENST00000612503,NM_032090.1;PCDHGA4,intron_variant,,ENST00000571252,NM_018917.3;PCDHGA6,intron_variant,,ENST00000517434,NM_018919.2;PCDHGA3,intron_variant,,ENST00000253812,NM_018916.3;PCDHGB3,intron_variant,,ENST00000576222,NM_018924.4;PCDHGA2,intron_variant,,ENST00000394576,NM_018915.3;PCDHGA8,intron_variant,,ENST00000398604,NM_032088.1;PCDHGA7,intron_variant,,ENST00000518325,NM_018920.3;PCDHGA9,intron_variant,,ENST00000573521,NM_018921.2;PCDHGA1,intron_variant,,ENST00000517417,NM_018912.2;PCDHGA5,intron_variant,,ENST00000518069,NM_018918.2;PCDHGB2,intron_variant,,ENST00000522605,NM_018923.2;PCDHGB6,intron_variant,,ENST00000520790,NM_018926.2;PCDHGB1,intron_variant,,ENST00000523390,NM_018922.2;PCDHGB4,intron_variant,,ENST00000519479,NM_003736.2;PCDHGB5,intron_variant,,ENST00000617380,NM_018925.2;PCDHGB7,upstream_gene_variant,,ENST00000398594,NM_018927.3;PCDHGB6,downstream_gene_variant,,ENST00000616430,NM_032100.1;PCDHGB7,upstream_gene_variant,,ENST00000612073,NM_032101.2;PCDHGA3,intron_variant,,ENST00000612467,; T ENST00000398610 Transcript synonymous_variant 1722/4617 1722/2811 574/936 D gaC/gaT 1 1 PCDHGA10 HGNC HGNC:8697 protein_coding YES CCDS47292.1 ENSP00000381611 Q9Y5H3 UPI00000726C3 NM_018913.2 1/4 hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF110,Superfamily_domains:SSF49313 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 141414897 141414897 C T 1 0 0 0 0 0 0 0 1 11638 535 19 1 1 PCDHGA10 5 141414897 Silent SNP C C3N-02586_T 24910028 141414897 40123362 28 29996 HMGXB3 0 . GRCh38 5 150047660 150047660 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.2987G>T p.Gly996Val p.G996V ENST00000502717 17/20 265 143 122 458 457 1 strelka-varscan-mutect HMGXB3,missense_variant,p.Gly1242Val,ENST00000613459,;HMGXB3,missense_variant,p.Gly964Val,ENST00000503427,;HMGXB3,missense_variant,p.Gly996Val,ENST00000502717,NM_014983.2;HMGXB3,3_prime_UTR_variant,,ENST00000514469,;HMGXB3,non_coding_transcript_exon_variant,,ENST00000510472,; T ENST00000502717 Transcript missense_variant 3451/4974 2987/3879 996/1292 G/V gGc/gTc 1 1 HMGXB3 HGNC HGNC:28982 protein_coding YES CCDS54935.1 ENSP00000421917 Q12766 UPI00001C1E29 NM_014983.2 deleterious(0.01) 17/20 hmmpanther:PTHR17609:SF2,hmmpanther:PTHR17609 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 150047660 150047660 G T 1 0 0 0 0 1 0 0 0 7131 1203 42 2 2 HMGXB3 5 150047660 Missense_Mutation SNP G C3N-02586_T 8632763 150047660 31490599 29 29997 EBF1 0 . GRCh38 5 159095645 159095645 + Missense_Mutation SNP C C A C3N-02586_T C3N-02586_N C C c.386G>T p.Arg129Leu p.R129L ENST00000313708 4/16 189 122 67 339 339 0 strelka-varscan EBF1,missense_variant,p.Arg129Leu,ENST00000313708,NM_001324107.1,NM_024007.3,NM_001290360.1;EBF1,missense_variant,p.Arg129Leu,ENST00000380654,NM_182708.1;EBF1,missense_variant,p.Arg129Leu,ENST00000517373,;RP11-175K6.1,upstream_gene_variant,,ENST00000517335,;RP11-175K6.1,upstream_gene_variant,,ENST00000523301,;EBF1,non_coding_transcript_exon_variant,,ENST00000518836,;EBF1,non_coding_transcript_exon_variant,,ENST00000523315,;EBF1,non_coding_transcript_exon_variant,,ENST00000519739,;EBF1,non_coding_transcript_exon_variant,,ENST00000522192,; A ENST00000313708 Transcript missense_variant 669/5250 386/1776 129/591 R/L cGc/cTc COSM160629 1 -1 EBF1 HGNC HGNC:3126 protein_coding YES CCDS4343.1 ENSP00000322898 Q9UH73 UPI000000D95E NM_001324107.1,NM_024007.3,NM_001290360.1 deleterious(0) 4/16 hmmpanther:PTHR10747,Pfam_domain:PF16422 1 MODERATE 1 SNV 1 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 159095645 159095645 C A 1 0 0 0 0 1 0 0 0 4704 768 27 1 1 EBF1 5 159095645 Missense_Mutation SNP C C3N-02586_T 9047985 159095645 22442614 30 29998 PRSS16 0 . GRCh38 6 27247989 27247989 + Missense_Mutation SNP G G C novel C3N-02586_T C3N-02586_N G G c.178G>C p.Gly60Arg p.G60R ENST00000230582 2/12 138 75 63 266 266 0 strelka-varscan-mutect PRSS16,missense_variant,p.Gly60Arg,ENST00000230582,NM_005865.3;PRSS16,missense_variant,p.Gly60Arg,ENST00000421826,;PRSS16,upstream_gene_variant,,ENST00000475106,;PRSS16,upstream_gene_variant,,ENST00000485993,;PRSS16,upstream_gene_variant,,ENST00000377456,;PRSS16,upstream_gene_variant,,ENST00000484493,;PRSS16,upstream_gene_variant,,ENST00000468138,;PRSS16,upstream_gene_variant,,ENST00000471463,;PRSS16,upstream_gene_variant,,ENST00000478690,;PRSS16,upstream_gene_variant,,ENST00000459736,;PRSS16,missense_variant,p.Gly60Arg,ENST00000454665,;PRSS16,missense_variant,p.Gly60Arg,ENST00000470870,;PRSS16,missense_variant,p.Gly60Arg,ENST00000468930,;PRSS16,missense_variant,p.Gly60Arg,ENST00000466364,;PRSS16,upstream_gene_variant,,ENST00000485603,;PRSS16,upstream_gene_variant,,ENST00000492575,;PRSS16,upstream_gene_variant,,ENST00000488649,;PRSS16,upstream_gene_variant,,ENST00000495683,;PRSS16,upstream_gene_variant,,ENST00000481125,;PRSS16,upstream_gene_variant,,ENST00000462664,; C ENST00000230582 Transcript missense_variant 193/2716 178/1545 60/514 G/R Ggg/Cgg 1 1 PRSS16 HGNC HGNC:9480 protein_coding YES CCDS4623.1 ENSP00000230582 Q9NQE7 UPI0000137773 NM_005865.3 tolerated(0.06) 2/12 hmmpanther:PTHR11010,hmmpanther:PTHR11010:SF22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 27247989 27247989 G C 1 0 0 0 0 1 0 0 0 12763 1232 43 4 4 PRSS16 6 27247989 Missense_Mutation SNP G C3N-02586_T 27247989 143557990 31 29999 KIF6 0 . GRCh38 6 39596143 39596143 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.757G>T p.Gly253Cys p.G253C ENST00000287152 7/23 395 208 187 785 785 0 strelka-varscan-mutect KIF6,missense_variant,p.Gly253Cys,ENST00000287152,NM_145027.4,NM_001289021.1,NM_001289020.1;KIF6,missense_variant,p.Gly145Cys,ENST00000458470,;KIF6,missense_variant,p.Gly40Cys,ENST00000441975,;KIF6,5_prime_UTR_variant,,ENST00000538893,; A ENST00000287152 Transcript missense_variant 852/9082 757/2445 253/814 G/C Ggt/Tgt 1 -1 KIF6 HGNC HGNC:21202 protein_coding YES CCDS4844.1 ENSP00000287152 Q6ZMV9 UPI0000457436 NM_145027.4,NM_001289021.1,NM_001289020.1 deleterious(0) 7/23 Gene3D:3.40.850.10,Pfam_domain:PF00225,Prints_domain:PR00380,PROSITE_patterns:PS00411,PROSITE_profiles:PS50067,hmmpanther:PTHR24115,hmmpanther:PTHR24115:SF194,SMART_domains:SM00129,Superfamily_domains:SSF52540 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 39596143 39596143 C A 1 0 0 0 0 1 0 0 0 8173 594 21 2 2 KIF6 6 39596143 Missense_Mutation SNP C C3N-02586_T 12348154 39596143 131209836 32 30000 TFAP2B 0 . GRCh38 6 50843132 50843132 + Silent SNP C C A novel C3N-02586_T C3N-02586_N C C c.1123C>A p.= p.R375R ENST00000393655 7/7 403 190 213 604 604 0 strelka-varscan-mutect TFAP2B,synonymous_variant,p.=,ENST00000393655,NM_003221.3; A ENST00000393655 Transcript synonymous_variant 1292/5773 1123/1383 375/460 R Cgg/Agg 1 1 TFAP2B HGNC HGNC:11743 protein_coding YES CCDS4934.2 ENSP00000377265 Q92481 UPI000020DE90 NM_003221.3 7/7 Pfam_domain:PF03299,hmmpanther:PTHR10812,hmmpanther:PTHR10812:SF14 LOW 1 SNV 1 1 PASS rs1311113453 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 50843132 50843132 C A 1 0 0 0 0 0 0 0 1 16221 643 23 1 1 TFAP2B 6 50843132 Silent SNP C C3N-02586_T 11246989 50843132 119962847 33 30001 CNR1 0 . GRCh38 6 88144686 88144686 + Missense_Mutation SNP T T C novel C3N-02586_T C3N-02586_N T T c.589A>G p.Thr197Ala p.T197A ENST00000369501 2/2 230 208 22 490 489 1 strelka-varscan-mutect CNR1,missense_variant,p.Thr197Ala,ENST00000369501,NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1;CNR1,missense_variant,p.Thr197Ala,ENST00000369499,;CNR1,missense_variant,p.Thr197Ala,ENST00000549890,;CNR1,missense_variant,p.Thr197Ala,ENST00000428600,;CNR1,missense_variant,p.Thr164Ala,ENST00000468898,NM_033181.3;CNR1,3_prime_UTR_variant,,ENST00000362094,;CNR1,downstream_gene_variant,,ENST00000551417,; C ENST00000369501 Transcript missense_variant 1209/6031 589/1419 197/472 T/A Acg/Gcg 1 -1 CNR1 HGNC HGNC:2159 protein_coding YES CCDS5015.1 ENSP00000358513 P21554 S5TLS4 UPI00000008AA NM_016083.4,NM_001160226.1,NM_001160258.1,NM_001160259.1 deleterious(0.04) 2/2 PROSITE_profiles:PS50262,hmmpanther:PTHR22750:SF47,hmmpanther:PTHR22750,Pfam_domain:PF00001,Gene3D:1.20.1070.10,PIRSF_domain:PIRSF037995,SMART_domains:SM01381,Superfamily_domains:SSF81321,Prints_domain:PR00237,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 88144686 88144686 T C 1 0 0 0 0 1 0 0 0 3413 1696 59 5 5 CNR1 6 88144686 Missense_Mutation SNP T C3N-02586_T 37301554 88144686 82661293 34 30002 AKAP12 0 . GRCh38 6 151350311 151350311 + Missense_Mutation SNP C C A rs186475520 C3N-02586_T C3N-02586_N C C c.1920C>A p.Ser640Arg p.S640R ENST00000402676 4/5 256 132 124 338 337 1 strelka-varscan-mutect AKAP12,missense_variant,p.Ser640Arg,ENST00000402676,NM_005100.3;AKAP12,missense_variant,p.Ser640Arg,ENST00000253332,;AKAP12,missense_variant,p.Ser542Arg,ENST00000354675,NM_144497.2;AKAP12,missense_variant,p.Ser535Arg,ENST00000359755,;AKAP12,downstream_gene_variant,,ENST00000490177,; A ENST00000402676 Transcript missense_variant 2160/8432 1920/5349 640/1782 S/R agC/agA rs186475520 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 deleterious(0) 4/5 Low_complexity_(Seg):seg,hmmpanther:PTHR23209 MODERATE 1 SNV 5 1 PASS rs186475520 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 151350311 151350311 C A 1 0 0 0 0 1 0 0 0 531 767 27 1 1 AKAP12 6 151350311 Missense_Mutation SNP C C3N-02586_T 63205625 151350311 19455668 35 30003 SYNE1 0 . GRCh38 6 152206214 152206214 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.22973G>T p.Ser7658Ile p.S7658I ENST00000367255 126/146 299 148 151 629 628 1 strelka-varscan-mutect SYNE1,missense_variant,p.Ser7658Ile,ENST00000367255,NM_182961.3;SYNE1,missense_variant,p.Ser7587Ile,ENST00000423061,NM_033071.3;SYNE1,missense_variant,p.Ser7253Ile,ENST00000341594,;SYNE1,missense_variant,p.Ser580Ile,ENST00000367251,;SYNE1,missense_variant,p.Ser304Ile,ENST00000367257,;SYNE1,non_coding_transcript_exon_variant,,ENST00000367256,;SYNE1,non_coding_transcript_exon_variant,,ENST00000409694,; A ENST00000367255 Transcript missense_variant 23575/27748 22973/26394 7658/8797 S/I aGc/aTc 1 -1 SYNE1 HGNC HGNC:17089 protein_coding YES CCDS5236.2 ENSP00000356224 Q8NF91 UPI000204AF58 NM_182961.3 126/146 Gene3D:1.20.58.60,Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR11915,hmmpanther:PTHR11915:SF267,SMART_domains:SM00150,Superfamily_domains:SSF46966 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 152206214 152206214 C A 1 0 0 0 0 1 0 0 0 15837 797 28 2 2 SYNE1 6 152206214 Missense_Mutation SNP C C3N-02586_T 855903 152206214 18599765 36 30004 ITGB8 0 . GRCh38 7 20394896 20394896 + Missense_Mutation SNP G G T C3N-02586_T C3N-02586_N G G c.1057G>T p.Asp353Tyr p.D353Y ENST00000222573 8/14 237 163 74 255 255 0 strelka-varscan-mutect ITGB8,missense_variant,p.Asp353Tyr,ENST00000222573,NM_002214.2;ITGB8,missense_variant,p.Asp218Tyr,ENST00000537992,;ITGB8,splice_region_variant,,ENST00000478974,; T ENST00000222573 Transcript missense_variant,splice_region_variant 1741/8751 1057/2310 353/769 D/Y Gat/Tat COSM3637168,COSM3637169 1 1 ITGB8 HGNC HGNC:6163 protein_coding YES CCDS5370.1 ENSP00000222573 P26012 UPI000012DA14 NM_002214.2 deleterious(0) 8/14 hmmpanther:PTHR10082:SF9,hmmpanther:PTHR10082,Gene3D:3.40.50.410,Pfam_domain:PF00362,PIRSF_domain:PIRSF002512,SMART_domains:SM00187,Superfamily_domains:SSF53300 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 20394896 20394896 G T 1 0 0 0 0 1 0 0 0 7807 1188 41 2 2 ITGB8 7 20394896 Missense_Mutation SNP G C3N-02586_T 20394896 138951077 37 30005 GLI3 0 . GRCh38 7 42048647 42048647 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.523A>T p.Arg175Trp p.R175W ENST00000395925 5/15 622 465 157 556 556 0 strelka-varscan-mutect GLI3,missense_variant,p.Arg175Trp,ENST00000395925,NM_000168.5;GLI3,missense_variant,p.Arg175Trp,ENST00000448703,;GLI3,non_coding_transcript_exon_variant,,ENST00000479210,; A ENST00000395925 Transcript missense_variant 608/8208 523/4743 175/1580 R/W Agg/Tgg 1 -1 GLI3 HGNC HGNC:4319 protein_coding YES CCDS5465.1 ENSP00000379258 P10071 UPI000020EE4C NM_000168.5 deleterious(0) 5/15 hmmpanther:PTHR19818,hmmpanther:PTHR19818:SF5 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 42048647 42048647 T A 1 0 0 0 0 1 0 0 0 6317 1521 53 4 4 GLI3 7 42048647 Missense_Mutation SNP T C3N-02586_T 21653751 42048647 117297326 38 30006 TYW1B 0 . GRCh38 7 72815470 72815470 + Silent SNP T T C novel C3N-02586_T C3N-02586_N T T c.147A>G p.= p.T49T ENST00000620995 3/14 174 89 85 361 361 0 strelka-varscan-mutect TYW1B,synonymous_variant,p.=,ENST00000620995,NM_001145440.2;TYW1B,synonymous_variant,p.=,ENST00000612372,;TYW1B,synonymous_variant,p.=,ENST00000610600,; C ENST00000620995 Transcript synonymous_variant 270/3113 147/2007 49/668 T acA/acG 1 -1 TYW1B HGNC HGNC:33908 protein_coding YES CCDS69309.1 ENSP00000482502 A0A087WZB2 UPI000178DF1B NM_001145440.2 3/14 Gene3D:3.40.50.360,Pfam_domain:PF00258,PROSITE_profiles:PS50902,hmmpanther:PTHR13930,Superfamily_domains:SSF52218 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 105 72815470 72815470 T C 1 0 0 0 0 0 0 0 1 17334 1567 55 5 5 TYW1B 7 72815470 Silent SNP T C3N-02586_T 30766823 72815470 86530503 39 30007 CACNA2D1 0 . GRCh38 7 81961947 81961947 + Missense_Mutation SNP G G C rs761648569 C3N-02586_T C3N-02586_N G G c.2913C>G p.Phe971Leu p.F971L ENST00000356860 36/39 141 89 52 384 384 0 strelka-varscan-mutect CACNA2D1,missense_variant,p.Phe971Leu,ENST00000356860,NM_000722.3;CACNA2D1,missense_variant,p.Phe983Leu,ENST00000356253,;CACNA2D1,non_coding_transcript_exon_variant,,ENST00000469297,; C ENST00000356860 Transcript missense_variant 3252/7563 2913/3276 971/1091 F/L ttC/ttG rs761648569,COSM299100,COSM3698554 1 -1 CACNA2D1 HGNC HGNC:1399 protein_coding YES CCDS5598.1 ENSP00000349320 P54289 UPI00003674CD NM_000722.3 deleterious(0.03) 36/39 Pfam_domain:PF08473,hmmpanther:PTHR10166,hmmpanther:PTHR10166:SF6 0,1,1 MODERATE 1 SNV 1 0,1,1 1 PASS rs761648569 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 81961947 81961947 G C 1 0 0 0 0 1 0 0 0 2236 1049 37 4 4 CACNA2D1 7 81961947 Missense_Mutation SNP G C3N-02586_T 9146477 81961947 77384026 40 30008 RELN 0 . GRCh38 7 103630059 103630059 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.2583G>T p.Met861Ile p.M861I ENST00000428762 20/65 319 175 144 702 701 1 strelka-varscan-mutect RELN,missense_variant,p.Met861Ile,ENST00000424685,;RELN,missense_variant,p.Met861Ile,ENST00000428762,NM_005045.3;RELN,missense_variant,p.Met861Ile,ENST00000343529,NM_173054.2;RELN,non_coding_transcript_exon_variant,,ENST00000473457,; A ENST00000428762 Transcript missense_variant 2743/11571 2583/10383 861/3460 M/I atG/atT 1 -1 RELN HGNC HGNC:9957 protein_coding YES CCDS47680.1 ENSP00000392423 P78509 UPI00001678BC NM_005045.3 tolerated(0.83) 20/65 hmmpanther:PTHR11841 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 103630059 103630059 C A 1 0 0 0 0 1 0 0 0 13390 826 29 2 2 RELN 7 103630059 Missense_Mutation SNP C C3N-02586_T 21668112 103630059 55715914 41 30009 KCP 0 . GRCh38 7 128881718 128881718 + Missense_Mutation SNP G G A novel C3N-02586_T C3N-02586_N G G c.3332C>T p.Thr1111Ile p.T1111I ENST00000610776 31/40 116 65 51 243 243 0 strelka-varscan-mutect KCP,missense_variant,p.Thr1111Ile,ENST00000610776,;KCP,missense_variant,p.Thr1115Ile,ENST00000613019,;KCP,missense_variant,p.Thr1051Ile,ENST00000620378,NM_001135914.1;KCP,missense_variant,p.Thr1115Ile,ENST00000611280,;KCP,upstream_gene_variant,,ENST00000492679,;KCP,upstream_gene_variant,,ENST00000460528,; A ENST00000610776 Transcript missense_variant 3375/5108 3332/4887 1111/1628 T/I aCa/aTa 1 -1 KCP HGNC HGNC:17585 protein_coding YES ENSP00000479679 A0A087WVT8 UPI0004620CE8 deleterious(0) 31/40 PROSITE_profiles:PS50184,PROSITE_patterns:PS01208,SMART_domains:SM00214,Superfamily_domains:SSF57603 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 128881718 128881718 G A 1 0 0 0 0 1 0 0 0 8012 1377 48 3 3 KCP 7 128881718 Missense_Mutation SNP G C3N-02586_T 25251659 128881718 30464255 42 30010 SSPO 0 . GRCh38 7 149791693 149791693 + Silent SNP G G T novel C3N-02586_T C3N-02586_N G G c.5235G>T p.= p.T1745T ENST00000378016 33/107 27 14 13 50 50 0 strelka-varscan-mutect SSPO,synonymous_variant,p.=,ENST00000378016,NM_198455.2;SSPO,non_coding_transcript_exon_variant,,ENST00000623373,;SSPO,non_coding_transcript_exon_variant,,ENST00000475488,; T ENST00000378016 Transcript synonymous_variant 5235/15589 5235/15453 1745/5150 T acG/acT 1 1 SSPO HGNC HGNC:21998 protein_coding YES ENSP00000485256 A0A096LNW2 UPI000514C5D0 NM_198455.2 33/107 Pfam_domain:PF00090,Gene3D:2.20.100.10,SMART_domains:SM00209,PROSITE_profiles:PS50092,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF294 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 149791693 149791693 G T 1 0 0 0 0 0 0 0 1 15566 1103 39 1 1 SSPO 7 149791693 Silent SNP G C3N-02586_T 20909975 149791693 9554280 43 30011 CSMD1 0 . GRCh38 8 2938714 2938714 + Silent SNP A A G novel C3N-02586_T C3N-02586_N A A c.10569T>C p.= p.Y3523Y ENST00000520002 71/71 188 88 100 313 313 0 strelka-varscan-mutect CSMD1,synonymous_variant,p.=,ENST00000537824,;CSMD1,synonymous_variant,p.=,ENST00000335551,;CSMD1,synonymous_variant,p.=,ENST00000520002,;CSMD1,synonymous_variant,p.=,ENST00000602557,;CSMD1,synonymous_variant,p.=,ENST00000635120,NM_033225.5;CSMD1,synonymous_variant,p.=,ENST00000400186,;CSMD1,synonymous_variant,p.=,ENST00000602723,; G ENST00000520002 Transcript synonymous_variant 11125/11740 10569/10698 3523/3565 Y taT/taC 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB 71/71 hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 2938714 2938714 A G 1 0 0 0 0 0 0 0 1 3745 224 8 5 5 CSMD1 8 2938714 Silent SNP A C3N-02586_T 2938714 142199922 44 30012 CSMD1 0 . GRCh38 8 2998113 2998113 + Missense_Mutation SNP C C A rs757594371 C3N-02586_T C3N-02586_N C C c.8278G>T p.Val2760Phe p.V2760F ENST00000520002 55/71 237 154 83 464 464 0 strelka-varscan-mutect CSMD1,missense_variant,p.Val2621Phe,ENST00000537824,;CSMD1,missense_variant,p.Val2177Phe,ENST00000335551,;CSMD1,missense_variant,p.Val2760Phe,ENST00000520002,;CSMD1,missense_variant,p.Val2760Phe,ENST00000602557,;CSMD1,missense_variant,p.Val2759Phe,ENST00000635120,NM_033225.5;CSMD1,missense_variant,p.Val2702Phe,ENST00000400186,;CSMD1,missense_variant,p.Val2702Phe,ENST00000602723,;CSMD1,downstream_gene_variant,,ENST00000519623,; A ENST00000520002 Transcript missense_variant 8834/11740 8278/10698 2760/3565 V/F Gtc/Ttc rs757594371 1 -1 CSMD1 HGNC HGNC:14026 protein_coding YES ENSP00000430733 E5RIG2 UPI00015D46BB deleterious(0) 55/71 Gene3D:2.10.70.10,Pfam_domain:PF00084,PROSITE_profiles:PS50923,hmmpanther:PTHR19325,hmmpanther:PTHR19325:SF350,SMART_domains:SM00032,Superfamily_domains:SSF57535 MODERATE 1 SNV 5 1 PASS rs757594371 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 2998113 2998113 C A 1 0 0 0 0 1 0 0 0 3745 478 17 2 2 CSMD1 8 2998113 Missense_Mutation SNP C C3N-02586_T 59399 2998113 142140523 45 30013 TNFRSF10B 0 . GRCh38 8 23030776 23030776 + Missense_Mutation SNP C C T novel C3N-02586_T C3N-02586_N C C c.347G>A p.Cys116Tyr p.C116Y ENST00000276431 3/9 455 254 201 840 840 0 strelka-varscan-mutect TNFRSF10B,missense_variant,p.Cys116Tyr,ENST00000276431,NM_003842.4;TNFRSF10B,missense_variant,p.Cys116Tyr,ENST00000347739,NM_147187.2;TNFRSF10B,non_coding_transcript_exon_variant,,ENST00000519910,;TNFRSF10B,missense_variant,p.Ala81Thr,ENST00000523504,;TNFRSF10B,non_coding_transcript_exon_variant,,ENST00000518531,;TNFRSF10B,upstream_gene_variant,,ENST00000523752,;TNFRSF10B,upstream_gene_variant,,ENST00000520109,; T ENST00000276431 Transcript missense_variant 632/4146 347/1323 116/440 C/Y tGc/tAc 1 -1 TNFRSF10B HGNC HGNC:11905 protein_coding YES CCDS6035.1 ENSP00000276431 O14763 UPI000013DAC6 NM_003842.4 deleterious(0) 3/9 PROSITE_profiles:PS50050,hmmpanther:PTHR23097:SF88,hmmpanther:PTHR23097,PROSITE_patterns:PS00652,Pfam_domain:PF00020,PIRSF_domain:PIRSF037867,Gene3D:2.10.50.10,SMART_domains:SM00208,Superfamily_domains:SSF57586 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 23030776 23030776 C T 1 0 0 0 0 1 0 0 0 16755 710 25 3 3 TNFRSF10B 8 23030776 Missense_Mutation SNP C C3N-02586_T 20032663 23030776 122107860 46 30014 IDO2 0 . GRCh38 8 39987964 39987964 + Silent SNP G G T novel C3N-02586_T C3N-02586_N G G c.582G>T p.= p.G194G ENST00000502986 7/11 107 56 51 195 195 0 strelka-varscan-mutect IDO2,synonymous_variant,p.=,ENST00000502986,NM_194294.2;IDO2,synonymous_variant,p.=,ENST00000389060,;RP11-44K6.3,intron_variant,,ENST00000517623,;IDO2,non_coding_transcript_exon_variant,,ENST00000343295,;IDO2,non_coding_transcript_exon_variant,,ENST00000418094,; T ENST00000502986 Transcript synonymous_variant 824/2294 582/1263 194/420 G ggG/ggT 1 1 IDO2 HGNC HGNC:27269 protein_coding YES ENSP00000443432 Q6ZQW0 UPI000152B4F4 NM_194294.2 7/11 hmmpanther:PTHR28657,hmmpanther:PTHR28657:SF4,Pfam_domain:PF01231,Superfamily_domains:SSF140959 LOW SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 39987964 39987964 G T 1 0 0 0 0 0 0 0 1 7403 1161 41 2 2 IDO2 8 39987964 Silent SNP G C3N-02586_T 16957188 39987964 105150672 47 30015 HNF4G 0 . GRCh38 8 75551446 75551446 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.411C>A p.Asn137Lys p.N137K ENST00000396423 4/10 345 257 88 497 497 0 strelka-varscan-mutect HNF4G,missense_variant,p.Asn137Lys,ENST00000396423,NM_004133.4;HNF4G,missense_variant,p.Asn100Lys,ENST00000354370,;HNF4G,non_coding_transcript_exon_variant,,ENST00000396419,; A ENST00000396423 Transcript missense_variant 535/4209 411/1338 137/445 N/K aaC/aaA 1 1 HNF4G HGNC HGNC:5026 protein_coding YES CCDS6220.2 ENSP00000379701 Q14541 F1D8Q4 UPI0000D47E07 NM_004133.4 tolerated(0.12) 4/10 hmmpanther:PTHR24083:SF42,hmmpanther:PTHR24083,Gene3D:1.10.565.10,Superfamily_domains:SSF48508 MODERATE 1 SNV 1 1 PASS rs1182646505 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 75551446 75551446 C A 1 0 0 0 0 1 0 0 0 7145 477 17 2 2 HNF4G 8 75551446 Missense_Mutation SNP C C3N-02586_T 35563482 75551446 69587190 48 30016 RIMS2 0 . GRCh38 8 103961065 103961065 + Missense_Mutation SNP G G A novel C3N-02586_T C3N-02586_N G G c.2702G>A p.Arg901Lys p.R901K ENST00000504942 15/24 163 125 38 401 401 0 strelka-varscan-mutect RIMS2,missense_variant,p.Arg693Lys,ENST00000507740,NM_014677.4;RIMS2,missense_variant,p.Arg679Lys,ENST00000436393,;RIMS2,missense_variant,p.Arg901Lys,ENST00000504942,NM_001100117.2;RIMS2,missense_variant,p.Arg843Lys,ENST00000626043,;RIMS2,missense_variant,p.Arg693Lys,ENST00000408894,;RIMS2,missense_variant,p.Arg740Lys,ENST00000262231,NM_001282881.1;RIMS2,missense_variant,p.Arg889Lys,ENST00000632716,;RIMS2,missense_variant,p.Arg295Lys,ENST00000507677,; A ENST00000504942 Transcript missense_variant,splice_region_variant 2841/4228 2702/4050 901/1349 R/K aGg/aAg 1 1 RIMS2 HGNC HGNC:17283 protein_coding YES CCDS55269.1 ENSP00000427018 Q9UQ26 UPI0001597063 NM_001100117.2 deleterious_low_confidence(0) 15/24 hmmpanther:PTHR12157,hmmpanther:PTHR12157:SF15 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 103961065 103961065 G A 1 0 0 0 0 1 0 0 0 13543 1246 43 3 3 RIMS2 8 103961065 Missense_Mutation SNP G C3N-02586_T 28409619 103961065 41177571 49 30017 PKHD1L1 0 . GRCh38 8 109400115 109400115 + Missense_Mutation SNP G G A rs200182716 C3N-02586_T C3N-02586_N G G c.1052G>A p.Arg351His p.R351H ENST00000378402 13/78 239 171 68 282 282 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Arg351His,ENST00000378402,NM_177531.4; A ENST00000378402 Transcript missense_variant 1156/13076 1052/12732 351/4243 R/H cGt/cAt rs200182716 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0.02) 13/78 Gene3D:1accA01,SMART_domains:SM00429,SMART_domains:SM00758 MODERATE 1 SNV 1 1 PASS rs200182716 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 109400115 109400115 G A 1 0 0 0 0 1 0 0 0 12068 1145 40 1 1 PKHD1L1 8 109400115 Missense_Mutation SNP G C3N-02586_T 5439050 109400115 35738521 50 30018 PKHD1L1 0 . GRCh38 8 109445186 109445186 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.5317G>T p.Gly1773Trp p.G1773W ENST00000378402 38/78 255 171 84 389 389 0 strelka-varscan-mutect PKHD1L1,missense_variant,p.Gly1773Trp,ENST00000378402,NM_177531.4; T ENST00000378402 Transcript missense_variant 5421/13076 5317/12732 1773/4243 G/W Ggg/Tgg 1 1 PKHD1L1 HGNC HGNC:20313 protein_coding YES CCDS47911.1 ENSP00000367655 Q86WI1 UPI0000E5B020 NM_177531.4 deleterious(0) 38/78 Gene3D:2.60.40.10,Pfam_domain:PF01833,SMART_domains:SM00429,Superfamily_domains:SSF81296 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 109445186 109445186 G T 1 0 0 0 0 1 0 0 0 12068 1232 43 2 2 PKHD1L1 8 109445186 Missense_Mutation SNP G C3N-02586_T 45071 109445186 35693450 51 30019 TRPS1 0 . GRCh38 8 115414391 115414391 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.3517A>T p.Asn1173Tyr p.N1173Y ENST00000395715 7/7 490 329 161 608 608 0 strelka-varscan-mutect TRPS1,missense_variant,p.Asn1173Tyr,ENST00000395715,NM_014112.4,NM_001282903.2;TRPS1,missense_variant,p.Asn1160Tyr,ENST00000220888,;TRPS1,missense_variant,p.Asn1164Tyr,ENST00000520276,NM_001282902.2;TRPS1,missense_variant,p.Asn914Tyr,ENST00000519076,;TRPS1,downstream_gene_variant,,ENST00000518018,; A ENST00000395715 Transcript missense_variant 4095/9990 3517/3885 1173/1294 N/Y Aat/Tat 1 -1 TRPS1 HGNC HGNC:12340 protein_coding YES CCDS6318.2 ENSP00000379065 Q9UHF7 UPI00002104B8 NM_014112.4,NM_001282903.2 deleterious_low_confidence(0) 7/7 hmmpanther:PTHR10071,hmmpanther:PTHR10071:SF176 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 115414391 115414391 T A 1 0 0 0 0 1 0 0 0 17099 1812 63 4 4 TRPS1 8 115414391 Missense_Mutation SNP T C3N-02586_T 5969205 115414391 29724245 52 30020 MROH6 0 . GRCh38 8 143568153 143568154 + Frame_Shift_Del DEL AG AG - novel C3N-02586_T C3N-02586_N AG AG c.1752_1753delCT p.Cys585LeufsTer154 p.C585Lfs*154 ENST00000398882 11/14 180 102 78 204 204 0 sindel-varindel MROH6,frameshift_variant,p.Cys585LeufsTer154,ENST00000398882,NM_001100878.1;MROH6,5_prime_UTR_variant,,ENST00000524906,;MROH6,5_prime_UTR_variant,,ENST00000534459,;MROH6,intron_variant,,ENST00000533679,;MROH6,intron_variant,,ENST00000532862,;MROH6,downstream_gene_variant,,ENST00000529971,;MROH6,non_coding_transcript_exon_variant,,ENST00000533582,;MROH6,upstream_gene_variant,,ENST00000532704,;MROH6,non_coding_transcript_exon_variant,,ENST00000533210,;MROH6,intron_variant,,ENST00000533083,;MROH6,upstream_gene_variant,,ENST00000533120,; - ENST00000398882 Transcript frameshift_variant 2009-2010/3469 1752-1753/2160 584-585/719 LC/LX ctCTgc/ctgc 1 -1 MROH6 HGNC HGNC:27814 protein_coding YES CCDS47928.1 ENSP00000381857 A6NGR9 UPI0000DD7EFB NM_001100878.1 11/14 hmmpanther:PTHR23120:SF7,hmmpanther:PTHR23120,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 HIGH 1 deletion 5 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999998 1 1 1 0 - 7 5 105 143568153 143568153 AG - 1 0 1 0 1 0 0 0 0 9746 188 7 0 0 MROH6 8 143568153 Frame_Shift_Del DEL AG C3N-02586_T 28153762 143568153 1570483 53 30021 SMARCA2 0 . GRCh38 9 2084086 2084086 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.2416G>T p.Gly806Cys p.G806C ENST00000382203 17/34 135 103 32 219 219 0 strelka-varscan-mutect SMARCA2,missense_variant,p.Gly806Cys,ENST00000382203,NM_001289396.1;SMARCA2,missense_variant,p.Gly806Cys,ENST00000357248,NM_139045.3;SMARCA2,missense_variant,p.Gly806Cys,ENST00000349721,NM_003070.4;SMARCA2,missense_variant,p.Gly806Cys,ENST00000382194,;SMARCA2,missense_variant,p.Gly806Cys,ENST00000450198,NM_001289397.1;SMARCA2,missense_variant,p.Gly143Cys,ENST00000635185,;SMARCA2,splice_region_variant,,ENST00000635739,;SMARCA2,upstream_gene_variant,,ENST00000636157,;SMARCA2,upstream_gene_variant,,ENST00000634925,;SMARCA2,upstream_gene_variant,,ENST00000636969,;SMARCA2,missense_variant,p.Gly806Cys,ENST00000634760,;SMARCA2,downstream_gene_variant,,ENST00000635129,; T ENST00000382203 Transcript missense_variant,splice_region_variant 2625/5867 2416/4773 806/1590 G/C Ggt/Tgt 1 1 SMARCA2 HGNC HGNC:11098 protein_coding YES CCDS34977.1 ENSP00000371638 P51531 UPI00001AE8EB NM_001289396.1 deleterious(0) 17/34 Gene3D:3.40.50.300,Pfam_domain:PF00176,PROSITE_profiles:PS51192,hmmpanther:PTHR10799,hmmpanther:PTHR10799:SF541,SMART_domains:SM00487,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 2084086 2084086 G T 1 0 0 0 0 1 0 0 0 15062 1246 43 2 2 SMARCA2 9 2084086 Missense_Mutation SNP G C3N-02586_T 2084086 136310631 54 30022 HRCT1 0 . GRCh38 9 35906356 35906356 + Silent SNP G G C novel C3N-02586_T C3N-02586_N G G c.69G>C p.= p.L23L ENST00000354323 1/1 43 37 6 99 98 1 varscan-mutect HRCT1,synonymous_variant,p.=,ENST00000354323,NM_001039792.1;LINC00961,upstream_gene_variant,,ENST00000443779,;LINC00961,upstream_gene_variant,,ENST00000636776,;LINC00961,upstream_gene_variant,,ENST00000638062,; C ENST00000354323 Transcript synonymous_variant 165/950 69/348 23/115 L ctG/ctC 1 1 HRCT1 HGNC HGNC:33872 protein_coding YES CCDS35012.1 ENSP00000346283 Q6UXD1 UPI0000048EC9 NM_001039792.1 1/1 hmmpanther:PTHR23009,hmmpanther:PTHR23009:SF2,Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix LOW SNV 1 PASS rs1475836520 . 0 166 9 27 5 0 0 2 -2.728108 0 0 1 0 0 C 2 2 105 35906356 35906356 G C 1 0 0 0 0 0 0 0 1 7248 1306 46 4 4 HRCT1 9 35906356 Silent SNP G C3N-02586_T 33822270 35906356 102488361 55 30023 FOXB2 0 . GRCh38 9 77020921 77020921 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.1267G>T p.Gly423Cys p.G423C ENST00000376708 1/1 152 85 67 276 276 0 strelka-varscan-mutect FOXB2,missense_variant,p.Gly423Cys,ENST00000376708,NM_001013735.1; T ENST00000376708 Transcript missense_variant 1267/1299 1267/1299 423/432 G/C Ggc/Tgc 1 1 FOXB2 HGNC HGNC:23315 protein_coding YES CCDS35045.1 ENSP00000365898 Q5VYV0 UPI00004588EE NM_001013735.1 deleterious_low_confidence(0) 1/1 MODERATE 1 SNV 1 PASS rs1411715116 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 77020921 77020921 G T 1 0 0 0 0 1 0 0 0 5853 1116 39 1 1 FOXB2 9 77020921 Missense_Mutation SNP G C3N-02586_T 41114565 77020921 61373796 56 30024 SVEP1 0 . GRCh38 9 110472219 110472219 + Silent SNP G G T rs763911828 C3N-02586_T C3N-02586_N G G c.2704C>A p.= p.R902R ENST00000374469 15/48 207 124 83 341 341 0 strelka-varscan-mutect SVEP1,synonymous_variant,p.=,ENST00000401783,;SVEP1,synonymous_variant,p.=,ENST00000374469,NM_153366.3;SVEP1,downstream_gene_variant,,ENST00000374461,;SVEP1,non_coding_transcript_exon_variant,,ENST00000467821,; T ENST00000374469 Transcript synonymous_variant 2899/12194 2704/10716 902/3571 R Cgg/Agg rs763911828,COSM1103938,COSM5233972,COSM606851 1 -1 SVEP1 HGNC HGNC:15985 protein_coding YES CCDS48004.1 ENSP00000363593 Q4LDE5 UPI000153DA74 NM_153366.3 15/48 0,1,1,1 LOW 1 SNV 5 0,1,1,1 1 PASS rs763911828 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 110472219 110472219 G T 1 0 0 0 0 0 0 0 1 15805 1144 40 1 1 SVEP1 9 110472219 Silent SNP G C3N-02586_T 33451298 110472219 27922498 57 30025 HMCN2 0 . GRCh38 9 130396304 130396304 + Missense_Mutation SNP G G C novel C3N-02586_T C3N-02586_N G G c.11186G>C p.Arg3729Thr p.R3729T ENST00000624552 73/98 42 22 20 84 84 0 strelka-varscan-mutect HMCN2,missense_variant,p.Arg3729Thr,ENST00000624552,NM_001291815.1;RN7SL665P,upstream_gene_variant,,ENST00000578793,;HMCN2,3_prime_UTR_variant,,ENST00000487727,;HMCN2,upstream_gene_variant,,ENST00000480829,; C ENST00000624552 Transcript missense_variant 11186/15610 11186/15180 3729/5059 R/T aGg/aCg 1 1 HMCN2 HGNC HGNC:21293 protein_coding YES ENSP00000485357 Q8NDA2 UPI0004F23675 NM_001291815.1 tolerated(0.11) 73/98 Gene3D:2.60.40.10,Pfam_domain:PF07679,PROSITE_profiles:PS50835,hmmpanther:PTHR10489,hmmpanther:PTHR10489:SF25,SMART_domains:SM00408,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 5 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 130396304 130396304 G C 1 0 0 0 0 1 0 0 0 7112 1000 35 4 4 HMCN2 9 130396304 Missense_Mutation SNP G C3N-02586_T 19924085 130396304 7998413 58 30026 MLLT10 0 . GRCh38 10 21670602 21670602 + Missense_Mutation SNP G G T rs780160506 C3N-02586_T C3N-02586_N G G c.949G>T p.Gly317Trp p.G317W ENST00000307729 10/23 342 158 184 680 680 0 strelka-varscan-mutect MLLT10,missense_variant,p.Gly317Trp,ENST00000377072,NM_004641.3;MLLT10,missense_variant,p.Gly317Trp,ENST00000307729,;MLLT10,missense_variant,p.Gly317Trp,ENST00000631589,;MLLT10,missense_variant,p.Gly317Trp,ENST00000377059,NM_001195626.1;MLLT10,missense_variant,p.Gly57Trp,ENST00000438473,;MLLT10,upstream_gene_variant,,ENST00000420525,;MLLT10,non_coding_transcript_exon_variant,,ENST00000468309,; T ENST00000307729 Transcript missense_variant 1127/5032 949/3207 317/1068 G/W Ggg/Tgg rs780160506 1 1 MLLT10 HGNC HGNC:16063 protein_coding YES CCDS55708.1 ENSP00000307411 P55197 UPI00001F8FF7 deleterious(0) 10/23 hmmpanther:PTHR13793,hmmpanther:PTHR13793:SF93,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs780160506 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 21670602 21670602 G T 1 0 0 0 0 1 0 0 0 9589 1000 35 2 2 MLLT10 10 21670602 Missense_Mutation SNP G C3N-02586_T 21670602 112126820 59 30027 ANKRD1 0 . GRCh38 10 90915793 90915793 + Missense_Mutation SNP C C A rs752017996 C3N-02586_T C3N-02586_N C C c.739G>T p.Ala247Ser p.A247S ENST00000371697 7/9 429 270 159 800 799 1 strelka-varscan-mutect ANKRD1,missense_variant,p.Ala247Ser,ENST00000371697,NM_014391.2; A ENST00000371697 Transcript missense_variant 988/1979 739/960 247/319 A/S Gcc/Tcc rs752017996 1 -1 ANKRD1 HGNC HGNC:15819 protein_coding YES CCDS7412.1 ENSP00000360762 Q15327 UPI00000735C1 NM_014391.2 deleterious(0.03) 7/9 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24126,hmmpanther:PTHR24126:SF7,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS rs752017996 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 90915793 90915793 C A 1 0 0 0 0 1 0 0 0 738 768 27 1 1 ANKRD1 10 90915793 Missense_Mutation SNP C C3N-02586_T 69245191 90915793 42881629 60 30028 TACC2 0 . GRCh38 10 122216743 122216743 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.7461C>A p.Asp2487Glu p.D2487E ENST00000369005 11/23 458 271 187 1010 1009 1 strelka-varscan-mutect TACC2,missense_variant,p.Asp2487Glu,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Asp2487Glu,ENST00000334433,;TACC2,missense_variant,p.Asp2491Glu,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Asp2491Glu,ENST00000453444,;TACC2,missense_variant,p.Asp2442Glu,ENST00000515603,NM_001291876.1;TACC2,missense_variant,p.Asp633Glu,ENST00000513429,NM_206861.2;TACC2,missense_variant,p.Asp565Glu,ENST00000360561,NM_206860.2;TACC2,missense_variant,p.Asp577Glu,ENST00000368999,;TACC2,missense_variant,p.Asp633Glu,ENST00000358010,;TACC2,missense_variant,p.Asp187Glu,ENST00000369000,;TACC2,missense_variant,p.Asp191Glu,ENST00000369001,NM_001291879.1;TACC2,missense_variant,p.Asp577Glu,ENST00000369004,NM_001291878.1;TACC2,missense_variant,p.Asp565Glu,ENST00000260733,NM_006997.3;TACC2,missense_variant,p.Asp582Glu,ENST00000514539,;TACC2,missense_variant,p.Asp222Glu,ENST00000496913,;TACC2,missense_variant,p.Asp67Glu,ENST00000508411,;TACC2,downstream_gene_variant,,ENST00000505639,;TACC2,3_prime_UTR_variant,,ENST00000440764,;TACC2,non_coding_transcript_exon_variant,,ENST00000368997,; A ENST00000369005 Transcript missense_variant 7801/9673 7461/8847 2487/2948 D/E gaC/gaA 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 tolerated(0.14) 11/23 hmmpanther:PTHR13924,hmmpanther:PTHR13924:SF11 MODERATE 1 SNV 1 1 PASS rs1453396717 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 122216743 122216743 C A 1 0 0 0 0 1 0 0 0 15898 506 18 2 2 TACC2 10 122216743 Missense_Mutation SNP C C3N-02586_T 31300950 122216743 11580679 61 30029 MUC5AC 0 . GRCh38 11 1198946 1198946 + Missense_Mutation SNP G G T rs756871136 C3N-02586_T C3N-02586_N G G c.16246G>T p.Ala5416Ser p.A5416S ENST00000621226 44/49 482 347 135 496 496 0 strelka-varscan-mutect MUC5AC,missense_variant,p.Ala5416Ser,ENST00000621226,NM_001304359.1; T ENST00000621226 Transcript missense_variant 16293/17448 16246/16965 5416/5654 A/S Gcg/Tcg rs756871136 1 1 MUC5AC HGNC HGNC:7515 protein_coding YES CCDS76369.1 ENSP00000485659 P98088 UPI0004F23658 NM_001304359.1 tolerated(1) 44/49 PROSITE_patterns:PS01208,PROSITE_profiles:PS50184,hmmpanther:PTHR11339,hmmpanther:PTHR11339:SF291,SMART_domains:SM00214 MODERATE 1 SNV 5 1 PASS rs756871136 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 1198946 1198946 G T 1 0 0 0 0 1 0 0 0 9978 1087 38 1 1 MUC5AC 11 1198946 Missense_Mutation SNP G C3N-02586_T 1198946 133887676 62 30030 ARL14EP 0 . GRCh38 11 30331153 30331153 + Nonsense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.205G>T p.Glu69Ter p.E69* ENST00000282032 2/4 120 90 30 322 322 0 strelka-varscan-mutect ARL14EP,stop_gained,p.Glu69Ter,ENST00000530909,;ARL14EP,stop_gained,p.Glu69Ter,ENST00000282032,NM_152316.2;ARL14EP,upstream_gene_variant,,ENST00000533457,;ARL14EP,non_coding_transcript_exon_variant,,ENST00000532047,; T ENST00000282032 Transcript stop_gained 420/2430 205/783 69/260 E/* Gag/Tag 1 1 ARL14EP HGNC HGNC:26798 protein_coding YES CCDS7869.1 ENSP00000282032 Q8N8R7 UPI000000DC5B NM_152316.2 2/4 hmmpanther:PTHR23080,hmmpanther:PTHR23080:SF72 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 105 30331153 30331153 G T 1 0 0 0 0 0 1 0 0 1068 1291 45 2 2 ARL14EP 11 30331153 Nonsense_Mutation SNP G C3N-02586_T 29132207 30331153 104755469 63 30031 FNBP4 0 . GRCh38 11 47767117 47767117 + Missense_Mutation SNP T T C novel C3N-02586_T C3N-02586_N T T c.172A>G p.Thr58Ala p.T58A ENST00000263773 1/17 95 89 6 233 231 2 varscan-mutect FNBP4,missense_variant,p.Thr58Ala,ENST00000263773,NM_001318339.1,NM_015308.2;FNBP4,missense_variant,p.Thr58Ala,ENST00000540172,;FNBP4,non_coding_transcript_exon_variant,,ENST00000534003,;FNBP4,non_coding_transcript_exon_variant,,ENST00000542975,; C ENST00000263773 Transcript missense_variant 185/3972 172/3054 58/1017 T/A Acc/Gcc 1 -1 FNBP4 HGNC HGNC:19752 protein_coding YES CCDS41644.1 ENSP00000263773 Q8N3X1 UPI0000DBEF37 NM_001318339.1,NM_015308.2 tolerated(0.82) 1/17 Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS rs1338130809 . 0 60 0 0 0 0 0 150 -3.970144 0 0 1 0 0 C 3 2 105 47767117 47767117 T C 1 0 0 0 0 1 0 0 0 5823 1696 59 5 5 FNBP4 11 47767117 Missense_Mutation SNP T C3N-02586_T 17435964 47767117 87319505 64 30032 OR5L2 0 . GRCh38 11 55827653 55827653 + Silent SNP C C A novel C3N-02586_T C3N-02586_N C C c.435C>A p.= p.T145T ENST00000378397 1/1 238 104 134 496 496 0 strelka-varscan-mutect OR5L2,synonymous_variant,p.=,ENST00000378397,NM_001004739.1; A ENST00000378397 Transcript synonymous_variant 435/936 435/936 145/311 T acC/acA 1 1 OR5L2 HGNC HGNC:8351 protein_coding YES CCDS31511.1 ENSP00000367650 Q8NGL0 UPI0000041C49 NM_001004739.1 1/1 PROSITE_profiles:PS50262,hmmpanther:PTHR26452,hmmpanther:PTHR26452:SF368,Gene3D:1.20.1070.10,Pfam_domain:PF13853,Superfamily_domains:SSF81321 LOW 1 SNV 1 PASS rs1393697802 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 55827653 55827653 C A 1 0 0 0 0 0 0 0 1 11240 668 24 2 2 OR5L2 11 55827653 Silent SNP C C3N-02586_T 8060536 55827653 79258969 65 30033 MS4A14 0 . GRCh38 11 60416775 60416775 + Missense_Mutation SNP G G A novel C3N-02586_T C3N-02586_N G G c.1906G>A p.Asp636Asn p.D636N ENST00000531783 6/6 298 148 150 542 542 0 strelka-varscan-mutect MS4A14,missense_variant,p.Asp619Asn,ENST00000395001,NM_001261827.1;MS4A14,missense_variant,p.Asp603Asn,ENST00000300187,NM_032597.4;MS4A14,missense_variant,p.Asp636Asn,ENST00000531783,NM_001261828.1;MS4A14,missense_variant,p.Asp586Asn,ENST00000395005,NM_001079692.2;MS4A14,missense_variant,p.Asp491Asn,ENST00000531787,;MS4A14,3_prime_UTR_variant,,ENST00000530662,;MS4A14,3_prime_UTR_variant,,ENST00000527841,;MS4A14,3_prime_UTR_variant,,ENST00000525397,; A ENST00000531783 Transcript missense_variant 1997/2910 1906/2139 636/712 D/N Gat/Aat 1 1 MS4A14 HGNC HGNC:30706 protein_coding YES CCDS58136.1 ENSP00000433761 Q96JA4 UPI0001F77AC2 NM_001261828.1 tolerated(0.27) 6/6 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 60416775 60416775 G A 1 0 0 0 0 1 0 0 0 9835 1174 41 3 3 MS4A14 11 60416775 Missense_Mutation SNP G C3N-02586_T 4589122 60416775 74669847 66 30034 STX5 0 . GRCh38 11 62825091 62825091 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.624A>T p.Arg208Ser p.R208S ENST00000294179 8/11 248 145 103 441 441 0 strelka-varscan-mutect STX5,missense_variant,p.Arg208Ser,ENST00000294179,NM_003164.4;STX5,missense_variant,p.Arg208Ser,ENST00000377897,NM_001244666.1;STX5,missense_variant,p.Arg154Ser,ENST00000394690,;STX5,missense_variant,p.Arg63Ser,ENST00000431400,;STX5,missense_variant,p.Arg208Ser,ENST00000491231,;STX5,3_prime_UTR_variant,,ENST00000492066,;STX5,downstream_gene_variant,,ENST00000488303,;STX5,downstream_gene_variant,,ENST00000486437,; A ENST00000294179 Transcript missense_variant 778/1794 624/1068 208/355 R/S agA/agT 1 -1 STX5 HGNC HGNC:11440 protein_coding YES CCDS8038.2 ENSP00000294179 Q13190 UPI00001FA9B0 NM_003164.4 deleterious(0.02) 8/11 hmmpanther:PTHR19957,hmmpanther:PTHR19957:SF3,Gene3D:1.20.58.70,Superfamily_domains:SSF47661 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 62825091 62825091 T A 1 0 0 0 0 1 0 0 0 15732 1548 54 4 4 STX5 11 62825091 Missense_Mutation SNP T C3N-02586_T 2408316 62825091 72261531 67 30035 CCDC82 0 . GRCh38 11 96384511 96384511 + Silent SNP T T G rs139035220 C3N-02586_T C3N-02586_N T T c.237A>C p.= p.P79P ENST00000278520 3/9 162 82 80 457 457 0 strelka-varscan-mutect CCDC82,synonymous_variant,p.=,ENST00000278520,NM_001318736.1,NM_024725.3;CCDC82,synonymous_variant,p.=,ENST00000423339,;CCDC82,synonymous_variant,p.=,ENST00000538597,;CCDC82,downstream_gene_variant,,ENST00000530203,;CCDC82,downstream_gene_variant,,ENST00000525786,;CCDC82,downstream_gene_variant,,ENST00000524836,;CCDC82,non_coding_transcript_exon_variant,,ENST00000530106,; G ENST00000278520 Transcript synonymous_variant 666/2941 237/1635 79/544 P ccA/ccC rs139035220 1 -1 CCDC82 HGNC HGNC:26282 protein_coding YES CCDS8307.1 ENSP00000278520 Q8N4S0 A0A024R3B3 UPI000007367A NM_001318736.1,NM_024725.3 3/9 hmmpanther:PTHR14689 LOW 1 SNV 5 1 PASS rs139035220 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 96384511 96384511 T G 1 0 0 0 0 0 0 0 1 2554 1567 55 5 5 CCDC82 11 96384511 Silent SNP T C3N-02586_T 33559420 96384511 38702111 68 30036 GRIA4 0 . GRCh38 11 105971934 105971934 + Frame_Shift_Del DEL T T - novel C3N-02586_T C3N-02586_N T T c.2318delT p.Leu773Ter p.L773* ENST00000282499 15/17 205 104 101 412 412 0 sindel-varindel-pindel GRIA4,frameshift_variant,p.Leu773Ter,ENST00000282499,NM_000829.3;GRIA4,frameshift_variant,p.Leu773Ter,ENST00000530497,;GRIA4,intron_variant,,ENST00000393127,NM_001077243.2;GRIA4,intron_variant,,ENST00000525187,;RNU6-277P,downstream_gene_variant,,ENST00000516272,;GRIA4,intron_variant,,ENST00000533094,;GRIA4,frameshift_variant,p.Phe101LeufsTer?,ENST00000525942,; - ENST00000282499 Transcript frameshift_variant 2761/5508 2315/2709 772/902 V/X gTt/gt 1 1 GRIA4 HGNC HGNC:4574 protein_coding YES CCDS8333.1 ENSP00000282499 P48058 UPI000013DCE6 NM_000829.3 15/17 hmmpanther:PTHR18966,hmmpanther:PTHR18966:SF100,Pfam_domain:PF00060,SMART_domains:SM00079,Superfamily_domains:SSF53850 HIGH 1 deletion 5 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 105 105971934 105971934 T - 1 0 1 0 1 0 0 0 0 6650 1725 60 0 0 GRIA4 11 105971934 Frame_Shift_Del DEL T C3N-02586_T 9587423 105971934 29114688 69 30037 IGSF9B 0 . GRCh38 11 133909114 133909114 + Silent SNP G G A novel C3N-02586_T C3N-02586_N G G c.4269C>T p.= p.L1423L ENST00000533871 20/20 243 190 53 411 411 0 strelka-varscan-mutect IGSF9B,synonymous_variant,p.=,ENST00000533871,NM_001277285.1;IGSF9B,non_coding_transcript_exon_variant,,ENST00000564347,;IGSF9B,downstream_gene_variant,,ENST00000530957,; A ENST00000533871 Transcript synonymous_variant 4500/5050 4269/4314 1423/1437 L ctC/ctT 1 -1 IGSF9B HGNC HGNC:32326 protein_coding YES CCDS61010.1 ENSP00000436552 Q9UPX0 UPI0002C439DB NM_001277285.1 20/20 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 133909114 133909114 G A 1 0 0 0 0 0 0 0 1 7514 1277 45 3 3 IGSF9B 11 133909114 Silent SNP G C3N-02586_T 27937180 133909114 1177508 70 30038 WNK1 0 . GRCh38 12 868994 868997 + Frame_Shift_Del DEL CAGA CAGA - novel C3N-02586_T C3N-02586_N CAGA CAGA c.3526_3529delACAG p.Thr1176CysfsTer21 p.T1176Cfs*21 ENST00000340908 10/28 64 34 30 113 113 0 sindel-varindel-pindel WNK1,frameshift_variant,p.Thr1091CysfsTer21,ENST00000530271,;WNK1,frameshift_variant,p.Thr1091CysfsTer21,ENST00000537687,NM_001184985.1;WNK1,frameshift_variant,p.Thr1176CysfsTer21,ENST00000340908,NM_213655.4;WNK1,frameshift_variant,p.Thr390CysfsTer21,ENST00000574564,;WNK1,frameshift_variant,p.Thr144CysfsTer21,ENST00000574679,;WNK1,intron_variant,,ENST00000315939,NM_018979.3;WNK1,intron_variant,,ENST00000535572,NM_014823.2;WNK1,intron_variant,,ENST00000535698,;WNK1,intron_variant,,ENST00000544965,;WNK1,intron_variant,,ENST00000545285,; - ENST00000340908 Transcript frameshift_variant 4166-4169/11208 3523-3526/7905 1175-1176/2634 QT/X CAGAca/ca 1 1 WNK1 HGNC HGNC:14540 protein_coding YES CCDS73419.1 ENSP00000341292 Q9H4A3 UPI0001DD21C4 NM_213655.4 10/28 HIGH 1 deletion 5 3 1 PASS . . 0 202 8 0 0 0 0 0 -20 0.9999998 1 1 1 0 - 7 5 105 868994 868994 CAGA - 1 0 1 0 1 0 0 0 0 17933 827 29 0 0 WNK1 12 868994 Frame_Shift_Del DEL CAGA C3N-02586_T 868994 132406315 71 30039 CHD4 0 . GRCh38 12 6598389 6598389 + Missense_Mutation SNP T T C novel C3N-02586_T C3N-02586_N T T c.1519A>G p.Ile507Val p.I507V ENST00000357008 11/40 69 39 30 128 128 0 strelka-varscan-mutect CHD4,missense_variant,p.Ile504Val,ENST00000544484,;CHD4,missense_variant,p.Ile500Val,ENST00000544040,NM_001297553.1;CHD4,missense_variant,p.Ile507Val,ENST00000357008,NM_001273.3;CHD4,downstream_gene_variant,,ENST00000545942,;CHD4,downstream_gene_variant,,ENST00000545584,;CHD4,downstream_gene_variant,,ENST00000535810,;CHD4,upstream_gene_variant,,ENST00000536999,;CHD4,downstream_gene_variant,,ENST00000430771,; C ENST00000357008 Transcript missense_variant 1683/6496 1519/5739 507/1912 I/V Atc/Gtc 1 -1 CHD4 HGNC HGNC:1919 protein_coding YES CCDS8552.1 ENSP00000349508 Q14839 UPI000013C8EF NM_001273.3 tolerated(0.51) 11/40 Gene3D:2.40.50.40,SMART_domains:SM00298,Superfamily_domains:SSF54160 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 6598389 6598389 T C 1 0 0 0 0 1 0 0 0 3086 1493 52 5 5 CHD4 12 6598389 Missense_Mutation SNP T C3N-02586_T 5729395 6598389 126676920 72 30040 GSG1 0 . GRCh38 12 13087185 13087185 + Missense_Mutation SNP C C T novel C3N-02586_T C3N-02586_N C C c.644G>A p.Arg215Lys p.R215K ENST00000432710 5/6 151 81 70 275 275 0 strelka-varscan-mutect GSG1,missense_variant,p.Arg202Lys,ENST00000337630,NM_153823.3;GSG1,missense_variant,p.Arg215Lys,ENST00000432710,NM_001206842.1,NM_001080555.2;GSG1,missense_variant,p.Arg151Lys,ENST00000457134,NM_001206845.1;GSG1,missense_variant,p.Arg174Lys,ENST00000537302,NM_001206843.1;GSG1,synonymous_variant,p.=,ENST00000396302,NM_031289.3;GSG1,synonymous_variant,p.=,ENST00000351606,NM_001080554.2;FAM234B,intron_variant,,ENST00000537625,;FAM234B,downstream_gene_variant,,ENST00000197268,NM_020853.1;GSG1,downstream_gene_variant,,ENST00000545401,;GSG1,downstream_gene_variant,,ENST00000542415,;GSG1,downstream_gene_variant,,ENST00000545699,;FAM234B,downstream_gene_variant,,ENST00000416494,; T ENST00000432710 Transcript missense_variant 777/1231 644/1020 215/339 R/K aGa/aAa 1 -1 GSG1 HGNC HGNC:19716 protein_coding YES CCDS55808.1 ENSP00000405032 Q2KHT4 UPI00001413B2 NM_001206842.1,NM_001080555.2 tolerated(0.15) 5/6 hmmpanther:PTHR10671:SF43,hmmpanther:PTHR10671 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 13087185 13087185 C T 1 0 0 0 0 1 0 0 0 6703 913 32 3 3 GSG1 12 13087185 Missense_Mutation SNP C C3N-02586_T 6488796 13087185 120188124 73 30041 KRT73 0 . GRCh38 12 52616376 52616376 + Missense_Mutation SNP C C G rs758072157 C3N-02586_T C3N-02586_N C C c.452G>C p.Arg151Pro p.R151P ENST00000305748 2/9 171 89 82 358 358 0 strelka-varscan-mutect KRT73,missense_variant,p.Arg151Pro,ENST00000305748,NM_175068.2;KRT73,upstream_gene_variant,,ENST00000552855,;KRT73-AS1,downstream_gene_variant,,ENST00000552364,;KRT73-AS1,downstream_gene_variant,,ENST00000549180,;KRT73-AS1,downstream_gene_variant,,ENST00000551089,;KRT73,non_coding_transcript_exon_variant,,ENST00000546934,; G ENST00000305748 Transcript missense_variant 487/2284 452/1623 151/540 R/P cGg/cCg rs758072157 1 -1 KRT73 HGNC HGNC:28928 protein_coding YES CCDS8834.1 ENSP00000307014 Q86Y46 UPI000000DCB8 NM_175068.2 deleterious(0) 2/9 hmmpanther:PTHR23239,hmmpanther:PTHR23239:SF85,Pfam_domain:PF00038,SMART_domains:SM01391,Superfamily_domains:SSF64593 MODERATE 1 SNV 1 1 PASS rs758072157 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 52616376 52616376 C G 1 0 0 0 0 1 0 0 0 8368 666 23 4 4 KRT73 12 52616376 Missense_Mutation SNP C C3N-02586_T 39529191 52616376 80658933 74 30042 RASSF9 0 . GRCh38 12 85804769 85804769 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.1241G>T p.Gly414Val p.G414V ENST00000361228 2/2 104 57 47 178 177 1 strelka-varscan-mutect RASSF9,missense_variant,p.Gly414Val,ENST00000361228,NM_005447.3; A ENST00000361228 Transcript missense_variant 1610/5682 1241/1308 414/435 G/V gGt/gTt 1 -1 RASSF9 HGNC HGNC:15739 protein_coding YES CCDS44950.1 ENSP00000354884 O75901 UPI000003E7E4 NM_005447.3 deleterious(0) 2/2 hmmpanther:PTHR15286,hmmpanther:PTHR15286:SF10 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 85804769 85804769 C A 1 0 0 0 0 1 0 0 0 13254 507 18 2 2 RASSF9 12 85804769 Missense_Mutation SNP C C3N-02586_T 33188393 85804769 47470540 75 30043 ANO4 0 . GRCh38 12 101110484 101110484 + Missense_Mutation SNP G G A novel C3N-02586_T C3N-02586_N G G c.2230G>A p.Glu744Lys p.E744K ENST00000392977 23/28 134 83 51 336 336 0 strelka-varscan-mutect ANO4,missense_variant,p.Glu709Lys,ENST00000392979,NM_178826.3;ANO4,missense_variant,p.Glu744Lys,ENST00000392977,NM_001286615.1,NM_001286616.1;ANO4,missense_variant,p.Glu264Lys,ENST00000550015,; A ENST00000392977 Transcript missense_variant 2440/3509 2230/2868 744/955 E/K Gaa/Aaa 1 1 ANO4 HGNC HGNC:23837 protein_coding YES CCDS66445.1 ENSP00000376703 Q32M45 UPI0000577AB6 NM_001286615.1,NM_001286616.1 deleterious(0) 23/28 hmmpanther:PTHR12308,hmmpanther:PTHR12308:SF28,Pfam_domain:PF04547 MODERATE 1 SNV 2 1 PASS rs1337641247 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 101110484 101110484 G A 1 0 0 0 0 1 0 0 0 806 1291 45 3 3 ANO4 12 101110484 Missense_Mutation SNP G C3N-02586_T 15305715 101110484 32164825 76 30044 WSCD2 0 . GRCh38 12 108232748 108232748 + Missense_Mutation SNP A A G novel C3N-02586_T C3N-02586_N A A c.997A>G p.Arg333Gly p.R333G ENST00000332082 8/10 111 50 61 204 204 0 strelka-varscan-mutect WSCD2,missense_variant,p.Arg333Gly,ENST00000332082,NM_001304447.1;WSCD2,missense_variant,p.Arg333Gly,ENST00000547525,NM_014653.3;WSCD2,missense_variant,p.Arg333Gly,ENST00000549903,;WSCD2,non_coding_transcript_exon_variant,,ENST00000546629,; G ENST00000332082 Transcript missense_variant 1815/4710 997/1698 333/565 R/G Aga/Gga 1 1 WSCD2 HGNC HGNC:29117 protein_coding YES CCDS41828.1 ENSP00000331933 Q2TBF2 UPI00001C1F3A NM_001304447.1 deleterious(0.01) 8/10 hmmpanther:PTHR19297,hmmpanther:PTHR19297:SF5,Superfamily_domains:SSF52540 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 108232748 108232748 A G 1 0 0 0 0 1 0 0 0 17964 180 7 5 5 WSCD2 12 108232748 Missense_Mutation SNP A C3N-02586_T 7122264 108232748 25042561 77 30045 ZNF268 0 . GRCh38 12 133191995 133191995 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.449C>A p.Thr150Asn p.T150N ENST00000536435 5/6 78 45 33 203 203 0 strelka-varscan-mutect ZNF268,missense_variant,p.Thr150Asn,ENST00000536435,NM_003415.2;ZNF268,missense_variant,p.Thr150Asn,ENST00000541009,NM_152943.2;ZNF268,missense_variant,p.Thr135Asn,ENST00000542986,;ZNF268,missense_variant,p.Thr150Asn,ENST00000228289,NM_001165881.2;CTD-2140B24.4,missense_variant,p.Thr315Asn,ENST00000540096,;ZNF268,missense_variant,p.Thr150Asn,ENST00000416488,;ZNF268,missense_variant,p.Pro41Thr,ENST00000542711,NM_001165886.1;ZNF268,missense_variant,p.Pro108Thr,ENST00000541211,NM_001165885.1;ZNF268,missense_variant,p.Thr67Asn,ENST00000500625,NM_001165882.2;ZNF268,missense_variant,p.Thr83Asn,ENST00000592241,NM_001165887.1;ZNF268,missense_variant,p.Thr70Asn,ENST00000591951,;ZNF268,missense_variant,p.Thr83Asn,ENST00000611984,;ZNF268,intron_variant,,ENST00000536899,NM_001165884.2;ZNF268,intron_variant,,ENST00000539248,NM_001165883.1;ZNF268,downstream_gene_variant,,ENST00000541975,;ZNF268,missense_variant,p.Pro41Thr,ENST00000588312,;ZNF268,non_coding_transcript_exon_variant,,ENST00000585488,;ZNF268,non_coding_transcript_exon_variant,,ENST00000534953,;ZNF268,downstream_gene_variant,,ENST00000546126,;ZNF268,downstream_gene_variant,,ENST00000537973,; A ENST00000536435 Transcript missense_variant 779/13475 449/2844 150/947 T/N aCc/aAc 1 1 ZNF268 HGNC HGNC:13061 protein_coding YES CCDS45012.1 ENSP00000444412 Q14587 UPI000013C33E NM_003415.2 tolerated(0.34) 5/6 PROSITE_profiles:PS50805,hmmpanther:PTHR24377:SF255,hmmpanther:PTHR24377 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 133191995 133191995 C A 1 0 0 0 0 1 0 0 0 18383 507 18 2 2 ZNF268 12 133191995 Missense_Mutation SNP C C3N-02586_T 24959247 133191995 83314 78 30046 COL4A2 0 . GRCh38 13 110495378 110495378 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.3671C>A p.Pro1224His p.P1224H ENST00000360467 40/48 355 181 174 595 595 0 strelka-varscan-mutect COL4A2,missense_variant,p.Pro1224His,ENST00000360467,NM_001846.2; A ENST00000360467 Transcript missense_variant 3977/6281 3671/5139 1224/1712 P/H cCt/cAt 1 1 COL4A2 HGNC HGNC:2203 protein_coding YES CCDS41907.1 ENSP00000353654 P08572 A0A024RDW8 UPI000041C713 NM_001846.2 tolerated(0.1) 40/48 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 110495378 110495378 C A 1 0 0 0 0 1 0 0 0 3479 681 24 2 2 COL4A2 13 110495378 Missense_Mutation SNP C C3N-02586_T 110495378 3868950 79 30047 TMEM255B 0 . GRCh38 13 113801722 113801722 + Silent SNP C C T novel C3N-02586_T C3N-02586_N C C c.579C>T p.= p.Y193Y ENST00000375353 7/9 109 78 31 248 248 0 strelka-varscan-mutect TMEM255B,synonymous_variant,p.=,ENST00000375353,NM_182614.2;TMEM255B,downstream_gene_variant,,ENST00000488362,;TMEM255B,non_coding_transcript_exon_variant,,ENST00000498692,;TMEM255B,upstream_gene_variant,,ENST00000467169,;TMEM255B,downstream_gene_variant,,ENST00000375348,; T ENST00000375353 Transcript synonymous_variant 606/6100 579/981 193/326 Y taC/taT 1 1 TMEM255B HGNC HGNC:28297 protein_coding YES CCDS45071.1 ENSP00000364502 Q8WV15 UPI0000071C2C NM_182614.2 7/9 hmmpanther:PTHR33721:SF3,hmmpanther:PTHR33721,Pfam_domain:PF14967 LOW 1 SNV 1 1 PASS . . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 113801722 113801722 C T 1 0 0 0 0 0 0 0 1 16615 518 18 3 3 TMEM255B 13 113801722 Silent SNP C C3N-02586_T 3306344 113801722 562606 80 30048 LRRC9 0 . GRCh38 14 59960982 59960982 + Missense_Mutation SNP T T C novel C3N-02586_T C3N-02586_N T T c.1148T>C p.Leu383Ser p.L383S ENST00000445360 10/32 63 39 24 281 281 0 strelka-varscan-mutect LRRC9,missense_variant,p.Leu383Ser,ENST00000445360,;LRRC9,downstream_gene_variant,,ENST00000454474,;LRRC9,missense_variant,p.Leu383Ser,ENST00000254271,; C ENST00000445360 Transcript missense_variant 1352/4717 1148/4362 383/1453 L/S tTg/tCg 1 1 LRRC9 HGNC HGNC:19848 protein_coding YES ENSP00000454748 Q6ZRR7 UPI000173AA0B deleterious(0) 10/32 Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 59960982 59960982 T C 1 0 0 0 0 1 0 0 0 8930 1821 63 5 5 LRRC9 14 59960982 Missense_Mutation SNP T C3N-02586_T 59960982 47082736 81 30049 IRF2BPL 0 . GRCh38 14 77026386 77026386 + Silent SNP C C A novel C3N-02586_T C3N-02586_N C C c.1407G>T p.= p.G469G ENST00000238647 1/1 183 91 92 316 316 0 strelka-varscan-mutect IRF2BPL,synonymous_variant,p.=,ENST00000238647,NM_024496.3;RP11-7F17.8,upstream_gene_variant,,ENST00000619017,; A ENST00000238647 Transcript synonymous_variant 2314/4157 1407/2391 469/796 G ggG/ggT 1 -1 IRF2BPL HGNC HGNC:14282 protein_coding YES CCDS9854.1 ENSP00000238647 Q9H1B7 UPI00000738BA NM_024496.3 1/1 hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF14 LOW 1 SNV 1 PASS rs1207735151 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 77026386 77026386 C A 1 0 0 0 0 0 0 0 1 7737 610 22 2 2 IRF2BPL 14 77026386 Silent SNP C C3N-02586_T 17065404 77026386 30017332 82 30050 UNC79 0 . GRCh38 14 93659223 93659223 + Missense_Mutation SNP A A G novel C3N-02586_T C3N-02586_N A A c.6073A>G p.Ile2025Val p.I2025V ENST00000256339 40/50 81 46 35 325 325 0 strelka-varscan-mutect UNC79,missense_variant,p.Ile2224Val,ENST00000553484,;UNC79,missense_variant,p.Ile2163Val,ENST00000555664,;UNC79,missense_variant,p.Ile2025Val,ENST00000256339,NM_020818.3;UNC79,missense_variant,p.Ile2202Val,ENST00000393151,;UNC79,missense_variant,p.Ile2025Val,ENST00000621021,; G ENST00000256339 Transcript missense_variant 6728/8400 6073/7377 2025/2458 I/V Att/Gtt 1 1 UNC79 HGNC HGNC:19966 protein_coding YES CCDS9911.2 ENSP00000256339 Q9P2D8 UPI0000D62441 NM_020818.3 tolerated(0.13) 40/50 hmmpanther:PTHR21696:SF2,hmmpanther:PTHR21696 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 105 93659223 93659223 A G 1 0 0 0 0 1 0 0 0 17520 333 12 5 5 UNC79 14 93659223 Missense_Mutation SNP A C3N-02586_T 16632837 93659223 13384495 83 30051 IL16 0 . GRCh38 15 81297046 81297046 + Missense_Mutation SNP A A T novel C3N-02586_T C3N-02586_N A A c.2021A>T p.Glu674Val p.E674V ENST00000302987 12/18 110 56 54 187 187 0 strelka-varscan-mutect IL16,missense_variant,p.Glu674Val,ENST00000394660,NM_001172128.1;IL16,missense_variant,p.Glu674Val,ENST00000302987,NM_172217.3;IL16,5_prime_UTR_variant,,ENST00000394652,NM_004513.5;IL16,downstream_gene_variant,,ENST00000559383,;IL16,upstream_gene_variant,,ENST00000558332,;IL16,non_coding_transcript_exon_variant,,ENST00000560230,;IL16,missense_variant,p.Glu20Val,ENST00000558857,;IL16,3_prime_UTR_variant,,ENST00000360547,;IL16,3_prime_UTR_variant,,ENST00000560115,;IL16,downstream_gene_variant,,ENST00000560241,; T ENST00000302987 Transcript missense_variant 2021/3999 2021/3999 674/1332 E/V gAg/gTg 1 1 IL16 HGNC HGNC:5980 protein_coding YES CCDS42069.1 ENSP00000302935 Q14005 UPI0000229CE7 NM_172217.3 tolerated(0.28) 12/18 hmmpanther:PTHR11324:SF2,hmmpanther:PTHR11324 MODERATE 1 SNV 1 1 PASS rs1038053856 . 0 207 2 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 81297046 81297046 A T 1 0 0 0 0 1 0 0 0 7541 304 11 4 4 IL16 15 81297046 Missense_Mutation SNP A C3N-02586_T 81297046 20694143 84 30052 ITGAX 0 . GRCh38 16 31380578 31380578 + Missense_Mutation SNP C C T C3N-02586_T C3N-02586_N C C c.3230C>T p.Ser1077Phe p.S1077F ENST00000562522 28/31 402 235 167 854 854 0 strelka-varscan-mutect ITGAX,missense_variant,p.Ser1077Phe,ENST00000268296,NM_000887.4;ITGAX,missense_variant,p.Ser1077Phe,ENST00000562522,NM_001286375.1;ITGAX,non_coding_transcript_exon_variant,,ENST00000571644,; T ENST00000562522 Transcript missense_variant 3263/3990 3230/3510 1077/1169 S/F tCc/tTc COSM3509191 1 1 ITGAX HGNC HGNC:6152 protein_coding YES CCDS67014.1 ENSP00000454623 H3BN02 UPI000041E001 NM_001286375.1 deleterious(0) 28/31 hmmpanther:PTHR23220,hmmpanther:PTHR23220:SF17,Superfamily_domains:SSF69179 1 MODERATE 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 31380578 31380578 C T 1 0 0 0 0 1 0 0 0 7796 855 30 3 3 ITGAX 16 31380578 Missense_Mutation SNP C C3N-02586_T 31380578 58957767 85 30053 TRPV3 0 . GRCh38 17 3514652 3514652 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.2219C>A p.Thr740Asn p.T740N ENST00000301365 17/18 192 109 83 375 375 0 strelka-varscan-mutect TRPV3,missense_variant,p.Thr724Asn,ENST00000616411,;TRPV3,missense_variant,p.Thr740Asn,ENST00000301365,NM_001258205.1;TRPV3,missense_variant,p.Thr740Asn,ENST00000572519,;TRPV3,missense_variant,p.Thr740Asn,ENST00000576742,NM_145068.3;SPATA22,upstream_gene_variant,,ENST00000541913,NM_001321336.1;SPATA22,upstream_gene_variant,,ENST00000570318,;TRPV3,3_prime_UTR_variant,,ENST00000381913,;TRPV3,3_prime_UTR_variant,,ENST00000573539,;TRPV3,3_prime_UTR_variant,,ENST00000571139,;TRPV3,3_prime_UTR_variant,,ENST00000577016,; T ENST00000301365 Transcript missense_variant 2351/3235 2219/2376 740/791 T/N aCt/aAt 1 -1 TRPV3 HGNC HGNC:18084 protein_coding YES CCDS58500.1 ENSP00000301365 Q8NET8 UPI0000200627 NM_001258205.1 tolerated(0.21) 17/18 hmmpanther:PTHR10582:SF6,hmmpanther:PTHR10582,Prints_domain:PR01768 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 3514652 3514652 G T 1 0 0 0 0 1 0 0 0 17103 1029 36 2 2 TRPV3 17 3514652 Missense_Mutation SNP G C3N-02586_T 3514652 79742789 86 30054 TP53 0 . GRCh38 17 7674187 7674187 + Missense_Mutation SNP T T A rs745425759 C3N-02586_T C3N-02586_N T T c.776A>T p.Asp259Val p.D259V ENST00000269305 7/11 243 126 117 441 439 2 strelka-varscan-mutect TP53,missense_variant,p.Asp259Val,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Asp259Val,ENST00000420246,;TP53,missense_variant,p.Asp220Val,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Asp220Val,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Asp259Val,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Asp220Val,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Asp259Val,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Asp220Val,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Asp259Val,ENST00000445888,;TP53,missense_variant,p.Asp220Val,ENST00000619485,;TP53,missense_variant,p.Asp127Val,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Asp100Val,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Asp127Val,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Asp100Val,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Asp127Val,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Asp100Val,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Asp259Val,ENST00000359597,;TP53,missense_variant,p.Asp248Val,ENST00000615910,;TP53,missense_variant,p.Asp259Val,ENST00000413465,;TP53,missense_variant,p.Asp127Val,ENST00000509690,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,downstream_gene_variant,,ENST00000514944,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,downstream_gene_variant,,ENST00000574684,;TP53,missense_variant,p.Asp220Val,ENST00000635293,;TP53,downstream_gene_variant,,ENST00000505014,; A ENST00000269305 Transcript missense_variant 966/2579 776/1182 259/393 D/V gAc/gTc rs745425759,TP53_g.13413A>G,TP53_g.13413A>T,TP53_g.13413A>C,TP53_g.13413del,COSM1646864,COSM3378342,COSM43724,COSM45615,COSM707907,COSM707908 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0.01) 7/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417 uncertain_significance 0,0,0,0,0,1,1,1,1,1,1 MODERATE 1 SNV 1 1,0,0,0,0,1,1,1,1,1,1 1 PASS rs745425759 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 7674187 7674187 T A 1 0 0 0 0 1 0 0 0 16859 1667 58 4 4 TP53 17 7674187 Missense_Mutation SNP T C3N-02586_T 4159535 7674187 75583254 87 30055 MYH2 0 . GRCh38 17 10543737 10543737 + Missense_Mutation SNP C C A rs775289093 C3N-02586_T C3N-02586_N C C c.715G>T p.Val239Leu p.V239L ENST00000245503 8/40 332 167 165 686 686 0 strelka-varscan-mutect MYH2,missense_variant,p.Val239Leu,ENST00000245503,NM_017534.5;MYH2,missense_variant,p.Val239Leu,ENST00000397183,NM_001100112.1;MYH2,missense_variant,p.Val239Leu,ENST00000532183,;MYH2,missense_variant,p.Val239Leu,ENST00000622564,;MYH2,downstream_gene_variant,,ENST00000420805,;MYH2,downstream_gene_variant,,ENST00000578017,;MYHAS,intron_variant,,ENST00000587182,; A ENST00000245503 Transcript missense_variant 1100/6339 715/5826 239/1941 V/L Gtg/Ttg rs775289093,COSM4063876 1 -1 MYH2 HGNC HGNC:7572 protein_coding YES CCDS11156.1 ENSP00000245503 Q9UKX2 UPI000012FB6C NM_017534.5 tolerated(0.38) 8/40 Pfam_domain:PF00063,Prints_domain:PR00193,PROSITE_profiles:PS51456,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF385,SMART_domains:SM00242,Superfamily_domains:SSF52540 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs775289093 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 10543737 10543737 C A 1 0 0 0 0 1 0 0 0 10035 536 19 1 1 MYH2 17 10543737 Missense_Mutation SNP C C3N-02586_T 2869550 10543737 72713704 88 30056 SHISA6 0 . GRCh38 17 11263501 11263501 + Silent SNP T T A novel C3N-02586_T C3N-02586_N T T c.774T>A p.= p.P258P ENST00000441885 2/6 182 87 95 251 251 0 strelka-varscan-mutect SHISA6,synonymous_variant,p.=,ENST00000441885,NM_207386.3;SHISA6,synonymous_variant,p.=,ENST00000432116,NM_001173462.1;SHISA6,synonymous_variant,p.=,ENST00000409168,NM_001173461.1;SHISA6,synonymous_variant,p.=,ENST00000343478,; A ENST00000441885 Transcript synonymous_variant 934/7575 774/1656 258/551 P ccT/ccA 1 1 SHISA6 HGNC HGNC:34491 protein_coding YES CCDS45615.1 ENSP00000390084 Q6ZSJ9 UPI000183CBD8 NM_207386.3 2/6 hmmpanther:PTHR31774,hmmpanther:PTHR31774:SF0,Pfam_domain:PF13908 LOW 1 SNV 5 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 11263501 11263501 T A 1 0 0 0 0 0 0 0 1 14544 1567 55 4 4 SHISA6 17 11263501 Silent SNP T C3N-02586_T 719764 11263501 71993940 89 30057 ANKRD40 0 . GRCh38 17 50699648 50699648 + Missense_Mutation SNP G G A C3N-02586_T C3N-02586_N G G c.529C>T p.Arg177Trp p.R177W ENST00000285243 3/5 256 128 128 410 409 1 strelka-varscan-mutect ANKRD40,missense_variant,p.Arg177Trp,ENST00000285243,NM_052855.3;ANKRD40,missense_variant,p.Arg99Trp,ENST00000513072,;RP11-294J22.6,downstream_gene_variant,,ENST00000574246,;Y_RNA,downstream_gene_variant,,ENST00000364470,;ANKRD40,downstream_gene_variant,,ENST00000507114,; A ENST00000285243 Transcript missense_variant 799/4184 529/1107 177/368 R/W Cgg/Tgg COSM145097 1 -1 ANKRD40 HGNC HGNC:28233 protein_coding YES CCDS11572.1 ENSP00000285243 Q6AI12 A8IK34 UPI000006F76F NM_052855.3 tolerated(0.18) 3/5 hmmpanther:PTHR24192 1 MODERATE 1 SNV 1 1 1 PASS rs1358649196 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 50699648 50699648 G A 1 0 0 0 0 1 0 0 0 775 1115 39 1 1 ANKRD40 17 50699648 Missense_Mutation SNP G C3N-02586_T 39436147 50699648 32557793 90 30058 TOB1 0 . GRCh38 17 50863913 50863913 + Silent SNP A A T rs371095924 C3N-02586_T C3N-02586_N A A c.105T>A p.= p.L35L ENST00000499247 2/2 188 173 15 440 440 0 strelka-varscan-mutect TOB1,synonymous_variant,p.=,ENST00000499247,NM_005749.3,NM_001243885.1;TOB1,synonymous_variant,p.=,ENST00000268957,NM_001243877.1;TOB1-AS1,upstream_gene_variant,,ENST00000416263,;TOB1-AS1,upstream_gene_variant,,ENST00000514358,;TOB1-AS1,upstream_gene_variant,,ENST00000523470,;TOB1,non_coding_transcript_exon_variant,,ENST00000509385,; T ENST00000499247 Transcript synonymous_variant 539/2229 105/1038 35/345 L ctT/ctA rs371095924 1 -1 TOB1 HGNC HGNC:11979 protein_coding YES CCDS11576.1 ENSP00000427695 P50616 UPI00001370FB NM_005749.3,NM_001243885.1 2/2 Low_complexity_(Seg):seg,hmmpanther:PTHR17537:SF6,hmmpanther:PTHR17537,Pfam_domain:PF07742,SMART_domains:SM00099,Superfamily_domains:SSF160696,Prints_domain:PR00310 LOW 1 SNV 1 1 PASS rs371095924 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 50863913 50863913 A T 1 0 0 0 0 0 0 0 1 16821 233 9 4 4 TOB1 17 50863913 Silent SNP A C3N-02586_T 164265 50863913 32393528 91 30059 KLHL14 0 . GRCh38 18 32769950 32769950 + Silent SNP C C G novel C3N-02586_T C3N-02586_N C C c.642G>C p.= p.L214L ENST00000359358 2/9 370 213 157 869 869 0 strelka-varscan-mutect KLHL14,synonymous_variant,p.=,ENST00000359358,NM_020805.1;KLHL14,synonymous_variant,p.=,ENST00000358095,;KLHL14,downstream_gene_variant,,ENST00000583263,;AC012123.1,non_coding_transcript_exon_variant,,ENST00000426194,; G ENST00000359358 Transcript synonymous_variant 1081/4312 642/1887 214/628 L ctG/ctC 1 -1 KLHL14 HGNC HGNC:29266 protein_coding YES CCDS32813.1 ENSP00000352314 Q9P2G3 UPI00001C1FF2 NM_020805.1 2/9 Pfam_domain:PF07707,hmmpanther:PTHR24412,hmmpanther:PTHR24412:SF60,SMART_domains:SM00875 LOW 1 SNV 1 1 PASS rs1285674467 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 32769950 32769950 C G 1 0 0 0 0 0 0 0 1 8234 697 25 4 4 KLHL14 18 32769950 Silent SNP C C3N-02586_T 32769950 47603335 92 30060 COL5A3 0 . GRCh38 19 9995611 9995611 + Missense_Mutation SNP G G C novel C3N-02586_T C3N-02586_N G G c.1540C>G p.Arg514Gly p.R514G ENST00000264828 16/67 63 36 27 108 108 0 strelka-varscan-mutect COL5A3,missense_variant,p.Arg514Gly,ENST00000264828,NM_015719.3;CTD-2553C6.1,upstream_gene_variant,,ENST00000592332,; C ENST00000264828 Transcript missense_variant 1626/6174 1540/5238 514/1745 R/G Cga/Gga 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 deleterious(0) 16/67 Pfam_domain:PF01391 MODERATE 1 SNV 1 1 PASS rs1229439408 . 0 198 10 2 0 0 0 0 -20 0.9998981 1 1 1 0 C 3 2 105 9995611 9995611 G C 1 0 0 0 0 1 0 0 0 3487 1124 39 4 4 COL5A3 19 9995611 Missense_Mutation SNP G C3N-02586_T 9995611 48622005 93 30061 SLC1A6 0 . GRCh38 19 14954270 14954270 + Missense_Mutation SNP C C T C3N-02586_T C3N-02586_N C C c.1229G>A p.Arg410His p.R410H ENST00000221742 7/9 377 226 151 751 751 0 strelka-varscan-mutect SLC1A6,missense_variant,p.Arg346His,ENST00000430939,;SLC1A6,missense_variant,p.Arg332His,ENST00000600144,;SLC1A6,missense_variant,p.Arg410His,ENST00000221742,NM_005071.2; T ENST00000221742 Transcript missense_variant 1237/1719 1229/1695 410/564 R/H cGc/cAc COSM4074896 1 -1 SLC1A6 HGNC HGNC:10944 protein_coding YES CCDS12321.1 ENSP00000221742 P48664 UPI0000129B1A NM_005071.2 deleterious(0) 7/9 hmmpanther:PTHR11958:SF67,hmmpanther:PTHR11958,Pfam_domain:PF00375,Gene3D:2nwlC00,Superfamily_domains:0053221 1 MODERATE 1 SNV 1 1 1 PASS rs1320404699 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 14954270 14954270 C T 1 0 0 0 0 1 0 0 0 14702 768 27 1 1 SLC1A6 19 14954270 Missense_Mutation SNP C C3N-02586_T 4958659 14954270 43663346 94 30062 TSHZ3 0 . GRCh38 19 31279133 31279133 + Missense_Mutation SNP G G C rs779306559 C3N-02586_T C3N-02586_N G G c.660C>G p.Ser220Arg p.S220R ENST00000240587 2/2 109 48 61 149 149 0 strelka-varscan-mutect TSHZ3,missense_variant,p.Ser220Arg,ENST00000240587,NM_020856.2;TSHZ3,downstream_gene_variant,,ENST00000560707,; C ENST00000240587 Transcript missense_variant 988/5176 660/3246 220/1081 S/R agC/agG rs779306559 1 -1 TSHZ3 HGNC HGNC:30700 protein_coding YES CCDS12421.2 ENSP00000240587 Q63HK5 UPI0000202000 NM_020856.2 deleterious(0) 2/2 PROSITE_patterns:PS00028,hmmpanther:PTHR12487,hmmpanther:PTHR12487:SF5,SMART_domains:SM00355 MODERATE 1 SNV 1 1 PASS rs779306559 . 0 203 7 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 31279133 31279133 G C 1 0 0 0 0 1 0 0 0 17130 1078 38 4 4 TSHZ3 19 31279133 Missense_Mutation SNP G C3N-02586_T 16324863 31279133 27338483 95 30063 PSG2 0 . GRCh38 19 43081073 43081073 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.238A>T p.Thr80Ser p.T80S ENST00000406487 2/6 252 143 109 556 556 0 strelka-varscan-mutect PSG2,missense_variant,p.Thr80Ser,ENST00000406487,NM_031246.3;CTC-490G23.6,intron_variant,,ENST00000635495,;PSG2,intron_variant,,ENST00000593482,;PSG2,downstream_gene_variant,,ENST00000491995,; A ENST00000406487 Transcript missense_variant 337/1538 238/1008 80/335 T/S Aca/Tca 1 -1 PSG2 HGNC HGNC:9519 protein_coding YES CCDS12616.1 ENSP00000385706 P11465 A0A024R0M4 UPI000013CCF5 NM_031246.3 deleterious(0.02) 2/6 Pfam_domain:PF07686,Gene3D:2.60.40.10,SMART_domains:SM00409,Superfamily_domains:SSF48726 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 43081073 43081073 T A 1 0 0 0 0 1 0 0 0 12806 1638 57 4 4 PSG2 19 43081073 Missense_Mutation SNP T C3N-02586_T 11801940 43081073 15536543 96 30064 ZNF45 0 . GRCh38 19 43914705 43914705 + Missense_Mutation SNP C C A novel C3N-02586_T C3N-02586_N C C c.731G>T p.Gly244Val p.G244V ENST00000269973 10/10 101 57 44 265 264 1 strelka-varscan-mutect ZNF45,missense_variant,p.Gly244Val,ENST00000269973,NM_003425.3;ZNF45,missense_variant,p.Gly244Val,ENST00000615985,;ZNF45,missense_variant,p.Gly244Val,ENST00000589703,;ZNF45,downstream_gene_variant,,ENST00000588140,;RP11-15A1.2,intron_variant,,ENST00000586247,; A ENST00000269973 Transcript missense_variant 1822/3898 731/2049 244/682 G/V gGa/gTa 1 -1 ZNF45 HGNC HGNC:13111 protein_coding YES CCDS12632.1 ENSP00000269973 Q02386 UPI0000001C64 NM_003425.3 tolerated(0.1) 10/10 PROSITE_profiles:PS50157,hmmpanther:PTHR24377:SF174,hmmpanther:PTHR24377,Gene3D:3.30.160.60,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 43914705 43914705 C A 1 0 0 0 0 1 0 0 0 18492 855 30 2 2 ZNF45 19 43914705 Missense_Mutation SNP C C3N-02586_T 833632 43914705 14702911 97 30065 SYMPK 0 . GRCh38 19 45816154 45816154 + Silent SNP C C A rs563199567 C3N-02586_T C3N-02586_N C C c.3384G>T p.= p.P1128P ENST00000245934 26/27 54 37 17 79 79 0 strelka-varscan-mutect SYMPK,synonymous_variant,p.=,ENST00000245934,NM_004819.2;SYMPK,downstream_gene_variant,,ENST00000599814,;SYMPK,downstream_gene_variant,,ENST00000599460,;RSPH6A,upstream_gene_variant,,ENST00000221538,NM_030785.3;RSPH6A,upstream_gene_variant,,ENST00000597055,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598155,;SYMPK,3_prime_UTR_variant,,ENST00000600237,;SYMPK,3_prime_UTR_variant,,ENST00000596824,;SYMPK,non_coding_transcript_exon_variant,,ENST00000593504,;SYMPK,non_coding_transcript_exon_variant,,ENST00000598364,;SYMPK,downstream_gene_variant,,ENST00000598329,; A ENST00000245934 Transcript synonymous_variant 3629/4195 3384/3825 1128/1274 P ccG/ccT rs563199567 1 -1 SYMPK HGNC HGNC:22935 protein_coding YES CCDS12676.2 ENSP00000245934 Q92797 A0A024R0R6 UPI00002026C0 NM_004819.2 26/27 Low_complexity_(Seg):seg LOW 1 SNV 1 1 PASS rs563199567 . 0 204 6 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 45816154 45816154 C A 1 0 0 0 0 0 0 0 1 15829 639 23 1 1 SYMPK 19 45816154 Silent SNP C C3N-02586_T 1901449 45816154 12801462 98 30066 ZNF808 0 . GRCh38 19 52553309 52553309 + Silent SNP A A G novel C3N-02586_T C3N-02586_N A A c.393A>G p.= p.K131K ENST00000359798 5/5 137 103 34 269 269 0 strelka-varscan-mutect ZNF808,synonymous_variant,p.=,ENST00000359798,NM_001321424.1,NM_001039886.3;ZNF808,synonymous_variant,p.=,ENST00000465448,;ZNF808,synonymous_variant,p.=,ENST00000461321,;ZNF808,synonymous_variant,p.=,ENST00000486474,;ZNF808,upstream_gene_variant,,ENST00000611267,;ZNF808,downstream_gene_variant,,ENST00000461779,;ZNF701,upstream_gene_variant,,ENST00000478039,;ZNF808,synonymous_variant,p.=,ENST00000487863,; G ENST00000359798 Transcript synonymous_variant 573/3600 393/2712 131/903 K aaA/aaG 1 1 ZNF808 HGNC HGNC:33230 protein_coding YES CCDS46167.1 ENSP00000352846 Q8N4W9 UPI000041AA80 NM_001321424.1,NM_001039886.3 5/5 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 2 3 105 52553309 52553309 A G 1 0 0 0 0 0 0 0 1 18758 11 1 5 5 ZNF808 19 52553309 Silent SNP A C3N-02586_T 6737155 52553309 6064307 99 30067 NLRP13 0 . GRCh38 19 55898895 55898895 + Silent SNP C C A rs749721321 C3N-02586_T C3N-02586_N C C c.2832G>T p.= p.L944L ENST00000342929 10/11 94 61 33 218 218 0 strelka-varscan-mutect NLRP13,synonymous_variant,p.=,ENST00000588751,NM_001321057.1;NLRP13,synonymous_variant,p.=,ENST00000342929,NM_176810.2; A ENST00000342929 Transcript synonymous_variant 2832/3132 2832/3132 944/1043 L ctG/ctT rs749721321 1 -1 NLRP13 HGNC HGNC:22937 protein_coding YES CCDS33119.1 ENSP00000343891 Q86W25 UPI00001AEEC8 NM_176810.2 10/11 Gene3D:3.80.10.10,hmmpanther:PTHR24106,hmmpanther:PTHR24106:SF10,SMART_domains:SM00368,Superfamily_domains:SSF52047 LOW 1 SNV 1 1 PASS rs749721321 . 0 203 5 2 0 0 0 0 -20 0.9999925 1 1 1 0 A 2 1 105 55898895 55898895 C A 1 0 0 0 0 0 0 0 1 10512 581 21 2 2 NLRP13 19 55898895 Silent SNP C C3N-02586_T 3345586 55898895 2718721 100 30068 EPB41L1 0 . GRCh38 20 36190291 36190291 + Missense_Mutation SNP G G C novel C3N-02586_T C3N-02586_N G G c.1041G>C p.Glu347Asp p.E347D ENST00000338074 10/22 343 288 55 626 626 0 strelka-varscan-mutect EPB41L1,missense_variant,p.Glu347Asp,ENST00000373946,NM_001258329.1;EPB41L1,missense_variant,p.Glu347Asp,ENST00000338074,NM_012156.2;EPB41L1,missense_variant,p.Glu285Asp,ENST00000441639,NM_177996.2;EPB41L1,missense_variant,p.Glu250Asp,ENST00000373950,;EPB41L1,missense_variant,p.Glu285Asp,ENST00000202028,NM_001258331.1;EPB41L1,missense_variant,p.Glu316Asp,ENST00000628415,NM_001258330.1;EPB41L1,missense_variant,p.Glu347Asp,ENST00000373941,;EPB41L1,downstream_gene_variant,,ENST00000430276,;EPB41L1,upstream_gene_variant,,ENST00000451082,;EPB41L1,downstream_gene_variant,,ENST00000373945,; C ENST00000338074 Transcript missense_variant 1202/6266 1041/2646 347/881 E/D gaG/gaC 1 1 EPB41L1 HGNC HGNC:3378 protein_coding YES CCDS13271.1 ENSP00000337168 Q9H4G0 UPI0000129AF8 NM_012156.2 deleterious(0) 10/22 PROSITE_profiles:PS50057,hmmpanther:PTHR23280,hmmpanther:PTHR23280:SF24,PIRSF_domain:PIRSF002304,Gene3D:2.30.29.30,Pfam_domain:PF09380,SMART_domains:SM01196,Superfamily_domains:SSF50729 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 105 36190291 36190291 G C 1 0 0 0 0 1 0 0 0 4999 933 33 4 4 EPB41L1 20 36190291 Missense_Mutation SNP G C3N-02586_T 36190291 28253876 101 30069 SLC12A5 0 . GRCh38 20 46043214 46043214 + Silent SNP G G C rs6073997 C3N-02586_T C3N-02586_N G G c.1197G>C p.= p.S399S ENST00000454036 9/26 208 122 86 365 365 0 strelka-varscan-mutect SLC12A5,synonymous_variant,p.=,ENST00000243964,NM_020708.4;SLC12A5,synonymous_variant,p.=,ENST00000454036,NM_001134771.1;SLC12A5,synonymous_variant,p.=,ENST00000616201,;SLC12A5,3_prime_UTR_variant,,ENST00000616933,;SLC12A5,intron_variant,,ENST00000616202,;SLC12A5,intron_variant,,ENST00000626937,;SLC12A5,non_coding_transcript_exon_variant,,ENST00000608594,;SLC12A5,intron_variant,,ENST00000539566,;SLC12A5,downstream_gene_variant,,ENST00000629054,;SLC12A5,downstream_gene_variant,,ENST00000625683,;SLC12A5,downstream_gene_variant,,ENST00000372315,;SLC12A5,downstream_gene_variant,,ENST00000622711,;SLC12A5,upstream_gene_variant,,ENST00000626144,; C ENST00000454036 Transcript synonymous_variant 1273/3593 1197/3420 399/1139 S tcG/tcC rs6073997,COSM3294258 1 1 SLC12A5 HGNC HGNC:13818 protein_coding YES CCDS46610.1 ENSP00000387694 Q9H2X9 UPI00015F4605 NM_001134771.1 9/26 TIGRFAM_domain:TIGR00930 0,1 LOW 1 SNV 5 0,1 1 PASS rs6073997 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 105 46043214 46043214 G C 1 0 0 0 0 0 0 0 1 14651 1103 39 4 4 SLC12A5 20 46043214 Silent SNP G C3N-02586_T 9852923 46043214 18400953 102 30070 KRTAP26-1 0 . GRCh38 21 30319925 30319925 + Silent SNP T T A C3N-02586_T C3N-02586_N T T c.111A>T p.= p.G37G ENST00000360542 1/1 148 88 60 276 276 0 strelka-varscan-mutect KRTAP26-1,synonymous_variant,p.=,ENST00000360542,NM_203405.1; A ENST00000360542 Transcript synonymous_variant 392/1193 111/633 37/210 G ggA/ggT COSM3389963 1 -1 KRTAP26-1 HGNC HGNC:33760 protein_coding YES CCDS13588.1 ENSP00000353742 Q6PEX3 UPI00001CE052 NM_203405.1 1/1 hmmpanther:PTHR19051,hmmpanther:PTHR19051:SF6,Pfam_domain:PF05287 1 LOW 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 30319925 30319925 T A 1 0 0 0 0 0 0 0 1 8435 1538 54 4 4 KRTAP26-1 21 30319925 Silent SNP T C3N-02586_T 30319925 16390058 103 30071 POTEH 0 . GRCh38 22 15698707 15698707 + Missense_Mutation SNP C C A rs775983930 C3N-02586_T C3N-02586_N C C c.967C>A p.Gln323Lys p.Q323K ENST00000343518 4/11 960 908 52 2733 2732 1 varscan-mutect POTEH,missense_variant,p.Gln323Lys,ENST00000343518,NM_001136213.1;POTEH,missense_variant,p.Gln286Lys,ENST00000621704,;RNU6-816P,upstream_gene_variant,,ENST00000390914,;POTEH-AS1,downstream_gene_variant,,ENST00000422014,;POTEH,3_prime_UTR_variant,,ENST00000452800,; A ENST00000343518 Transcript missense_variant 1019/1928 967/1638 323/545 Q/K Caa/Aaa rs775983930 1 1 POTEH HGNC HGNC:133 protein_coding YES CCDS74808.1 ENSP00000340610 Q6S545 UPI0000E5A425 NM_001136213.1 tolerated(0.33) 4/11 Gene3D:1.25.40.20,Pfam_domain:PF12796,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24118,hmmpanther:PTHR24118:SF43,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE SNV 5 1 PASS rs775983930 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 15698707 15698707 C A 1 0 0 0 0 1 0 0 0 12381 711 25 2 2 POTEH 22 15698707 Missense_Mutation SNP C C3N-02586_T 15698707 35119761 104 30072 SGSM1 0 . GRCh38 22 24867160 24867160 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.994G>T p.Val332Phe p.V332F ENST00000400359 10/26 366 137 229 540 540 0 strelka-varscan-mutect SGSM1,missense_variant,p.Val332Phe,ENST00000400358,NM_001098497.2;SGSM1,missense_variant,p.Val332Phe,ENST00000610372,NM_133454.3,NM_001098498.2;SGSM1,missense_variant,p.Val332Phe,ENST00000400359,NM_001039948.3;SGSM1,splice_region_variant,,ENST00000473458,;SGSM1,splice_region_variant,,ENST00000480523,; T ENST00000400359 Transcript missense_variant,splice_region_variant 1001/4317 994/3447 332/1148 V/F Gtt/Ttt 1 1 SGSM1 HGNC HGNC:29410 protein_coding YES CCDS46674.1 ENSP00000383212 Q2NKQ1 UPI00006EB130 NM_001039948.3 tolerated(0.21) 10/26 hmmpanther:PTHR22957:SF187,hmmpanther:PTHR22957 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 24867160 24867160 G T 1 0 0 0 0 1 0 0 0 14480 1014 35 2 2 SGSM1 22 24867160 Missense_Mutation SNP G C3N-02586_T 9168453 24867160 25951308 105 30073 SMC1B 0 . GRCh38 22 45372230 45372230 + Silent SNP T T C novel C3N-02586_T C3N-02586_N T T c.2121A>G p.= p.G707G ENST00000357450 13/25 105 43 62 303 303 0 strelka-varscan-mutect SMC1B,synonymous_variant,p.=,ENST00000357450,NM_148674.4;SMC1B,synonymous_variant,p.=,ENST00000404354,NM_001291501.1; C ENST00000357450 Transcript synonymous_variant 2121/4201 2121/3708 707/1235 G ggA/ggG 1 -1 SMC1B HGNC HGNC:11112 protein_coding YES CCDS43027.1 ENSP00000350036 Q8NDV3 UPI0004438059 NM_148674.4 13/25 Pfam_domain:PF02463,PIRSF_domain:PIRSF005719,hmmpanther:PTHR18937,hmmpanther:PTHR18937:SF147 LOW 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 2 2 105 45372230 45372230 T C 1 0 0 0 0 0 0 0 1 15075 1770 62 5 5 SMC1B 22 45372230 Silent SNP T C3N-02586_T 20505070 45372230 5446238 106 30074 DCAF8L2 0 . GRCh38 X 27748500 27748500 + Missense_Mutation SNP T T A C3N-02586_T C3N-02586_N T T c.1605T>A p.His535Gln p.H535Q ENST00000451261 5/5 150 85 65 307 307 0 strelka-varscan-mutect DCAF8L2,missense_variant,p.His535Gln,ENST00000451261,;DCAF8L2,missense_variant,p.His535Gln,ENST00000545306,NM_001136533.1;DCAF8L2,downstream_gene_variant,,ENST00000431122,;DCAF8L2,downstream_gene_variant,,ENST00000583068,; A ENST00000451261 Transcript missense_variant 2004/2295 1605/1896 535/631 H/Q caT/caA COSM4966667,COSM4966668 1 1 DCAF8L2 HGNC HGNC:31811 protein_coding YES CCDS59162.1 ENSP00000462745 P0C7V8 UPI000183CBD9 tolerated(0.06) 5/5 Gene3D:2.130.10.10,Pfam_domain:PF00400,PROSITE_profiles:PS50294,hmmpanther:PTHR15574,hmmpanther:PTHR15574:SF42,SMART_domains:SM00320,Superfamily_domains:SSF50978 1,1 MODERATE 1 SNV 4 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 27748500 27748500 T A 1 0 0 0 0 1 0 0 0 4079 1461 51 4 4 DCAF8L2 23 27748500 Missense_Mutation SNP T C3N-02586_T 27748500 128292395 107 30075 FAM47A 0 . GRCh38 X 34132015 34132015 + Silent SNP A A T novel C3N-02586_T C3N-02586_N A A c.264T>A p.= p.A88A ENST00000346193 1/1 76 43 33 162 162 0 strelka-varscan-mutect FAM47A,synonymous_variant,p.=,ENST00000346193,NM_203408.3;FAM47A,synonymous_variant,p.=,ENST00000613251,; T ENST00000346193 Transcript synonymous_variant 297/2556 264/2376 88/791 A gcT/gcA 1 -1 FAM47A HGNC HGNC:29962 protein_coding YES CCDS43926.1 ENSP00000345029 Q5JRC9 UPI000013F1F4 NM_203408.3 1/1 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF200,Pfam_domain:PF14642 LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 105 34132015 34132015 A T 1 0 0 0 0 0 0 0 1 5447 175 7 4 4 FAM47A 23 34132015 Silent SNP A C3N-02586_T 6383515 34132015 121908880 108 30076 GAGE2A 0 . GRCh38 X 49591306 49591306 + Missense_Mutation SNP C C A rs782136866 C3N-02586_T C3N-02586_N C C c.191C>A p.Ser64Tyr p.S64Y ENST00000362097 3/5 643 547 96 1144 1143 1 varscan-mutect GAGE2A,missense_variant,p.Ser64Tyr,ENST00000362097,NM_001472.2,NM_012196.1,NM_001127212.1;GAGE1,intron_variant,,ENST00000610680,NM_001098405.2,NM_001127200.2;GAGE12H,downstream_gene_variant,,ENST00000381722,NM_001098410.1; A ENST00000362097 Transcript missense_variant 274/528 191/351 64/116 S/Y tCt/tAt rs782136866 1 1 GAGE2A HGNC HGNC:4099 protein_coding YES CCDS48114.1 ENSP00000355421 Q6NT46 UPI00001AF5C0 NM_001472.2,NM_012196.1,NM_001127212.1 deleterious(0) 3/5 Pfam_domain:PF05831,hmmpanther:PTHR14047,hmmpanther:PTHR14047:SF6,SMART_domains:SM01379 MODERATE 1 SNV 1 1 PASS rs782136866 . 68 142 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 49591306 49591306 C A 1 0 0 0 0 1 0 0 0 6062 913 32 2 2 GAGE2A 23 49591306 Missense_Mutation SNP C C3N-02586_T 15459291 49591306 106449589 109 30077 LPAR4 0 . GRCh38 X 78755767 78755767 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.898G>T p.Ala300Ser p.A300S ENST00000435339 2/2 168 91 77 346 346 0 strelka-varscan-mutect LPAR4,missense_variant,p.Ala300Ser,ENST00000435339,NM_005296.2;LPAR4,missense_variant,p.Ala300Ser,ENST00000614823,NM_001278000.1;LPAR4,downstream_gene_variant,,ENST00000514744,;LPAR4,downstream_gene_variant,,ENST00000610214,;LPAR4,downstream_gene_variant,,ENST00000607964,; T ENST00000435339 Transcript missense_variant 1284/2611 898/1113 300/370 A/S Gca/Tca 1 1 LPAR4 HGNC HGNC:4478 protein_coding YES CCDS14441.1 ENSP00000408205 Q99677 UPI000005041D NM_005296.2 deleterious(0.01) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,PROSITE_profiles:PS50262,hmmpanther:PTHR24232,hmmpanther:PTHR24232:SF41,SMART_domains:SM01381,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 78755767 78755767 G T 1 0 0 0 0 1 0 0 0 8810 1319 46 2 2 LPAR4 23 78755767 Missense_Mutation SNP G C3N-02586_T 29164461 78755767 77285128 110 30078 P2RY10 0 . GRCh38 X 78960784 78960784 + Silent SNP C C A C3N-02586_T C3N-02586_N C C c.264C>A p.= p.P88P ENST00000171757 4/4 193 95 98 290 290 0 strelka-varscan-mutect P2RY10,synonymous_variant,p.=,ENST00000171757,NM_014499.2;P2RY10,synonymous_variant,p.=,ENST00000544091,NM_198333.1;P2RY10,non_coding_transcript_exon_variant,,ENST00000475374,;P2RY10,non_coding_transcript_exon_variant,,ENST00000461541,; A ENST00000171757 Transcript synonymous_variant 544/1714 264/1020 88/339 P ccC/ccA COSM3563623 1 1 P2RY10 HGNC HGNC:19906 protein_coding YES CCDS14442.1 ENSP00000171757 O00398 UPI0000050471 NM_014499.2 4/4 Transmembrane_helices:TMhelix,PROSITE_profiles:PS50262,hmmpanther:PTHR24232:SF47,hmmpanther:PTHR24232,Gene3D:1.20.1070.10,Pfam_domain:PF00001,Superfamily_domains:SSF81321,Prints_domain:PR00237,Prints_domain:PR01157 1 LOW 1 SNV 1 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 105 78960784 78960784 C A 1 0 0 0 0 0 0 0 1 11420 610 22 2 2 P2RY10 23 78960784 Silent SNP C C3N-02586_T 205017 78960784 77080111 111 30079 PAK3 0 . GRCh38 X 111163568 111163568 + Missense_Mutation SNP A A T C3N-02586_T C3N-02586_N A A c.715A>T p.Thr239Ser p.T239S ENST00000360648 8/16 197 113 84 253 252 1 strelka-varscan-mutect PAK3,missense_variant,p.Thr203Ser,ENST00000372007,NM_001324327.1,NM_001324326.1,NM_001324331.1,NM_001324333.1,NM_001324332.1,NM_001324334.1,NM_001324328.1,NM_001324330.1,NM_001324325.1,NM_002578.3;PAK3,missense_variant,p.Thr224Ser,ENST00000519681,;PAK3,missense_variant,p.Thr218Ser,ENST00000372010,;PAK3,missense_variant,p.Thr203Ser,ENST00000446737,NM_001128166.1;PAK3,missense_variant,p.Thr203Ser,ENST00000425146,NM_001128167.1;PAK3,missense_variant,p.Thr239Ser,ENST00000360648,NM_001128168.1;PAK3,missense_variant,p.Thr224Ser,ENST00000417227,NM_001128172.1;PAK3,missense_variant,p.Thr218Ser,ENST00000262836,NM_001128173.1;PAK3,missense_variant,p.Thr202Ser,ENST00000620137,;PAK3,missense_variant,p.Thr239Ser,ENST00000518291,; T ENST00000360648 Transcript missense_variant 742/2241 715/1743 239/580 T/S Act/Tct COSM1740779,COSM1740780 1 1 PAK3 HGNC HGNC:8592 protein_coding YES CCDS48151.1 ENSP00000353864 O75914 UPI0000D61DBC NM_001128168.1 tolerated(0.07) 8/16 hmmpanther:PTHR24361,hmmpanther:PTHR24361:SF250 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 111163568 111163568 A T 1 0 0 0 0 1 0 0 0 11482 391 14 4 4 PAK3 23 111163568 Missense_Mutation SNP A C3N-02586_T 32202784 111163568 44877327 112 30080 NKRF 0 . GRCh38 X 119589411 119589411 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.2059C>A p.Gln687Lys p.Q687K ENST00000542113 4/4 98 48 50 91 91 0 strelka-varscan-mutect NKRF,missense_variant,p.Gln672Lys,ENST00000371527,NM_001173488.1;NKRF,missense_variant,p.Gln687Lys,ENST00000542113,NM_001173487.1;NKRF,missense_variant,p.Gln672Lys,ENST00000304449,NM_017544.3;UBE2A,intron_variant,,ENST00000631185,;UBE2A,downstream_gene_variant,,ENST00000371558,NM_003336.3;UBE2A,downstream_gene_variant,,ENST00000630695,;NKRF,intron_variant,,ENST00000487600,;UBE2A,downstream_gene_variant,,ENST00000371569,; T ENST00000542113 Transcript missense_variant 2281/3351 2059/2118 687/705 Q/K Cag/Aag 1 -1 NKRF HGNC HGNC:19374 protein_coding YES CCDS55486.1 ENSP00000442308 O15226 UPI0000211E22 NM_001173487.1 deleterious(0.01) 4/4 hmmpanther:PTHR16148,hmmpanther:PTHR16148:SF6 MODERATE SNV 3 1 PASS . . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 119589411 119589411 G T 1 0 0 0 0 1 0 0 0 10482 1299 45 2 2 NKRF 23 119589411 Missense_Mutation SNP G C3N-02586_T 8425843 119589411 36451484 113 30081 SPANXN3 0 . GRCh38 X 143508874 143508874 + Missense_Mutation SNP G G T novel C3N-02586_T C3N-02586_N G G c.367C>A p.Gln123Lys p.Q123K ENST00000370503 2/2 143 107 36 147 147 0 strelka-varscan-mutect SPANXN3,missense_variant,p.Gln123Lys,ENST00000370503,NM_001009609.3;GS1-256O22.5,intron_variant,,ENST00000431432,; T ENST00000370503 Transcript missense_variant 451/590 367/426 123/141 Q/K Cag/Aag 1 -1 SPANXN3 HGNC HGNC:33176 protein_coding YES CCDS35418.1 ENSP00000359534 Q5MJ09 UPI0000DA7993 NM_001009609.3 tolerated_low_confidence(0.06) 2/2 hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF6,Low_complexity_(Seg):seg MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 105 143508874 143508874 G T 1 0 0 0 0 1 0 0 0 15323 1386 48 2 2 SPANXN3 23 143508874 Missense_Mutation SNP G C3N-02586_T 23919463 143508874 12532021 114 30082 SPANXN1 0 . GRCh38 X 145247635 145247635 + Missense_Mutation SNP T T A novel C3N-02586_T C3N-02586_N T T c.49T>A p.Cys17Ser p.C17S ENST00000370493 1/2 294 152 142 322 322 0 strelka-varscan-mutect SPANXN1,missense_variant,p.Cys17Ser,ENST00000370493,NM_001009614.2; A ENST00000370493 Transcript missense_variant 808/1276 49/219 17/72 C/S Tgt/Agt 1 1 SPANXN1 HGNC HGNC:33174 protein_coding YES CCDS35421.1 ENSP00000359524 Q5VSR9 UPI0000458AF7 NM_001009614.2 tolerated(0.09) 1/2 Pfam_domain:PF07458,hmmpanther:PTHR23425,hmmpanther:PTHR23425:SF7 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 105 145247635 145247635 T A 1 0 0 0 0 1 0 0 0 15321 1580 55 4 4 SPANXN1 23 145247635 Missense_Mutation SNP T C3N-02586_T 1738761 145247635 10793260 115 30083 MPV17 0 . GRCh38 2 27313072 27313072 + Missense_Mutation SNP C C A C3N-02587_T C3N-02587_N C C c.108G>T p.Gln36His p.Q36H ENST00000380044 3/8 591 501 90 804 803 1 strelka-varscan MPV17,missense_variant,p.Gln36His,ENST00000380044,NM_002437.4;MPV17,missense_variant,p.Gln36His,ENST00000233545,;MPV17,missense_variant,p.Gln36His,ENST00000402310,;MPV17,missense_variant,p.Gln51His,ENST00000405983,;MPV17,missense_variant,p.Ala25Ser,ENST00000402722,;MPV17,missense_variant,p.Gln36His,ENST00000403262,;MPV17,missense_variant,p.Gln36His,ENST00000405076,;MPV17,missense_variant,p.Gln10His,ENST00000428910,;MPV17,missense_variant,p.Gln13His,ENST00000430991,;MPV17,intron_variant,,ENST00000357186,;UCN,upstream_gene_variant,,ENST00000296099,NM_003353.2;MPV17,downstream_gene_variant,,ENST00000399052,;MPV17,upstream_gene_variant,,ENST00000620797,;MPV17,missense_variant,p.Ala25Ser,ENST00000426513,;MPV17,splice_region_variant,,ENST00000621470,;MPV17,non_coding_transcript_exon_variant,,ENST00000616707,;MPV17,non_coding_transcript_exon_variant,,ENST00000617583,;MPV17,non_coding_transcript_exon_variant,,ENST00000621183,;MPV17,non_coding_transcript_exon_variant,,ENST00000622003,;MPV17,non_coding_transcript_exon_variant,,ENST00000616446,;MPV17,intron_variant,,ENST00000415514,;MPV17,downstream_gene_variant,,ENST00000486898,;MPV17,upstream_gene_variant,,ENST00000475085,; A ENST00000380044 Transcript missense_variant 164/1005 108/531 36/176 Q/H caG/caT COSM4392706,COSM4392707 1 -1 MPV17 HGNC HGNC:7224 protein_coding YES CCDS1748.1 ENSP00000369383 P39210 A0A0S2Z3Z9 UPI000012F4BD NM_002437.4 deleterious(0.03) 3/8 hmmpanther:PTHR11266 1,1 MODERATE 1 SNV 1 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 106 27313072 27313072 C A 1 0 0 0 0 1 0 0 0 9711 811 28 2 2 MPV17 2 27313072 Missense_Mutation SNP C C3N-02587_T 27313072 214880457 1 30084 EML6 0 . GRCh38 2 54928690 54928690 + Missense_Mutation SNP A A T rs574788707 C3N-02587_T C3N-02587_N A A c.3943A>T p.Ile1315Phe p.I1315F ENST00000356458 27/41 375 311 64 495 495 0 strelka-varscan EML6,missense_variant,p.Ile1315Phe,ENST00000356458,NM_001039753.2; T ENST00000356458 Transcript missense_variant 4463/8320 3943/5877 1315/1958 I/F Atc/Ttc rs574788707 1 1 EML6 HGNC HGNC:35412 protein_coding YES CCDS46286.1 ENSP00000348842 Q6ZMW3 UPI00006C0432 NM_001039753.2 deleterious(0.03) 27/41 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 106 54928690 54928690 A T 1 0 0 0 0 1 0 0 0 4944 217 8 4 4 EML6 2 54928690 Missense_Mutation SNP A C3N-02587_T 27615618 54928690 187264839 2 30085 MST1R 0 . GRCh38 3 49899247 49899247 + Missense_Mutation SNP A A C novel C3N-02587_T C3N-02587_N A A c.1247T>G p.Leu416Arg p.L416R ENST00000296474 2/20 194 160 34 264 264 0 strelka-varscan-mutect MST1R,missense_variant,p.Leu416Arg,ENST00000296474,NM_002447.2;MST1R,missense_variant,p.Leu416Arg,ENST00000344206,NM_001244937.1;MST1R,intron_variant,,ENST00000621387,NM_001318913.1;MST1R,intron_variant,,ENST00000613534,;MST1R,intron_variant,,ENST00000612032,;MST1R,upstream_gene_variant,,ENST00000434765,;MST1R,upstream_gene_variant,,ENST00000440292,;CTD-2330K9.3,upstream_gene_variant,,ENST00000419183,;CTD-2330K9.2,upstream_gene_variant,,ENST00000435478,;CTD-2330K9.3,upstream_gene_variant,,ENST00000424174,;CTD-2330K9.3,upstream_gene_variant,,ENST00000412015,;MST1R,missense_variant,p.Leu416Arg,ENST00000411578,;MST1R,non_coding_transcript_exon_variant,,ENST00000468525,;MST1R,non_coding_transcript_exon_variant,,ENST00000485044,;MST1R,non_coding_transcript_exon_variant,,ENST00000497001,;MST1R,intron_variant,,ENST00000493535,;MST1R,upstream_gene_variant,,ENST00000467110,;MST1R,upstream_gene_variant,,ENST00000490053,; C ENST00000296474 Transcript missense_variant 1275/4536 1247/4203 416/1400 L/R cTc/cGc 1 -1 MST1R HGNC HGNC:7381 protein_coding YES CCDS2807.1 ENSP00000296474 Q04912 UPI000159688A NM_002447.2 tolerated(0.2) 2/20 Gene3D:2.130.10.10,Pfam_domain:PF01403,PIRSF_domain:PIRSF000617,PROSITE_profiles:PS51004,SMART_domains:SM00630,Superfamily_domains:SSF101912 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 106 49899247 49899247 A C 1 0 0 0 0 1 0 0 0 9876 304 11 5 5 MST1R 3 49899247 Missense_Mutation SNP A C3N-02587_T 49899247 148396312 3 30086 NSUN3 0 . GRCh38 3 94084329 94084329 + Silent SNP C C A novel C3N-02587_T C3N-02587_N C C c.345C>A p.= p.L115L ENST00000314622 3/6 322 275 47 544 544 0 strelka-varscan NSUN3,synonymous_variant,p.=,ENST00000314622,NM_022072.3;NSUN3,downstream_gene_variant,,ENST00000485793,;NSUN3,downstream_gene_variant,,ENST00000468555,;NSUN3,downstream_gene_variant,,ENST00000494128,;NSUN3,non_coding_transcript_exon_variant,,ENST00000476588,;NSUN3,intron_variant,,ENST00000483378,; A ENST00000314622 Transcript synonymous_variant 556/3289 345/1023 115/340 L ctC/ctA 1 1 NSUN3 HGNC HGNC:26208 protein_coding YES CCDS2927.1 ENSP00000318986 Q9H649 UPI00000373B2 NM_022072.3 3/6 PROSITE_profiles:PS51686,hmmpanther:PTHR22808,hmmpanther:PTHR22808:SF8,Superfamily_domains:SSF53335 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 106 94084329 94084329 C A 1 0 0 0 0 0 0 0 1 10742 842 30 2 2 NSUN3 3 94084329 Silent SNP C C3N-02587_T 44185082 94084329 104211230 4 30087 CDH18 0 . GRCh38 5 19721362 19721362 + Missense_Mutation SNP C C T rs750768779 C3N-02587_T C3N-02587_N C C c.628G>A p.Val210Ile p.V210I ENST00000507958 7/15 140 130 10 152 152 0 strelka-varscan CDH18,missense_variant,p.Val210Ile,ENST00000507958,NM_001291956.1;CDH18,missense_variant,p.Val210Ile,ENST00000382275,NM_004934.3;CDH18,missense_variant,p.Val210Ile,ENST00000274170,;CDH18,missense_variant,p.Val210Ile,ENST00000506372,NM_001291957.1;CDH18,missense_variant,p.Val210Ile,ENST00000502796,NM_001167667.1;CDH18,missense_variant,p.Val210Ile,ENST00000511273,;CDH18,missense_variant,p.Val156Ile,ENST00000515257,;CDH18,downstream_gene_variant,,ENST00000508350,; T ENST00000507958 Transcript missense_variant 1619/3542 628/2373 210/790 V/I Gtc/Atc rs750768779,COSM182561,COSM3854517 1 -1 CDH18 HGNC HGNC:1757 protein_coding YES CCDS3889.1 ENSP00000425093 Q13634 UPI0000126DBD NM_001291956.1 tolerated(0.1) 7/15 PROSITE_profiles:PS50268,hmmpanther:PTHR24027:SF106,hmmpanther:PTHR24027,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 0,1,1 MODERATE 1 SNV 2 0,1,1 1 PASS . . 0 198 12 0 0 0 0 0 -18.41682 0.9996397 1 1 1 0 T 3 4 106 19721362 19721362 C T 1 0 0 0 0 1 0 0 0 2806 536 19 1 1 CDH18 5 19721362 Missense_Mutation SNP C C3N-02587_T 19721362 161816897 5 30088 AKAP12 0 . GRCh38 6 151305801 151305801 + Nonsense_Mutation SNP G G T novel C3N-02587_T C3N-02587_N G G c.217G>T p.Glu73Ter p.E73* ENST00000402676 3/5 150 114 36 296 296 0 strelka-varscan-mutect AKAP12,stop_gained,p.Glu73Ter,ENST00000402676,NM_005100.3;AKAP12,stop_gained,p.Glu73Ter,ENST00000253332,; T ENST00000402676 Transcript stop_gained 457/8432 217/5349 73/1782 E/* Gag/Tag 1 1 AKAP12 HGNC HGNC:370 protein_coding YES CCDS5229.1 ENSP00000384537 Q02952 UPI000013CDC7 NM_005100.3 3/5 hmmpanther:PTHR23209 HIGH 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 106 151305801 151305801 G T 1 0 0 0 0 0 1 0 0 531 1291 45 2 2 AKAP12 6 151305801 Nonsense_Mutation SNP G C3N-02587_T 151305801 19500178 6 30089 SFTPC 0 . GRCh38 8 22164393 22164393 + Missense_Mutation SNP G G A novel C3N-02587_T C3N-02587_N G G c.404G>A p.Gly135Glu p.G135E ENST00000520605 4/4 89 63 26 122 122 0 strelka-varscan-mutect SFTPC,missense_variant,p.Gly135Glu,ENST00000520605,;SFTPC,3_prime_UTR_variant,,ENST00000521315,NM_001172357.1;SFTPC,3_prime_UTR_variant,,ENST00000318561,NM_001317778.1,NM_001317780.1,NM_003018.3,NM_001172410.1;SFTPC,3_prime_UTR_variant,,ENST00000524255,;BMP1,upstream_gene_variant,,ENST00000306385,NM_006129.4;BMP1,upstream_gene_variant,,ENST00000354870,;BMP1,upstream_gene_variant,,ENST00000306349,NM_001199.3;SFTPC,downstream_gene_variant,,ENST00000522109,;BMP1,upstream_gene_variant,,ENST00000397814,;SFTPC,downstream_gene_variant,,ENST00000437090,;SFTPC,downstream_gene_variant,,ENST00000523296,;CTD-2530N21.5,upstream_gene_variant,,ENST00000619681,;SFTPC,downstream_gene_variant,,ENST00000522880,;SFTPC,downstream_gene_variant,,ENST00000524318,;SFTPC,downstream_gene_variant,,ENST00000524350,;BMP1,upstream_gene_variant,,ENST00000520970,;BMP1,upstream_gene_variant,,ENST00000520626,;BMP1,upstream_gene_variant,,ENST00000520982,;BMP1,upstream_gene_variant,,ENST00000471755,;BMP1,upstream_gene_variant,,ENST00000518913,;BMP1,upstream_gene_variant,,ENST00000483364,;BMP1,upstream_gene_variant,,ENST00000521385,;BMP1,upstream_gene_variant,,ENST00000518656,;SFTPC,downstream_gene_variant,,ENST00000518615,;SFTPC,downstream_gene_variant,,ENST00000522630,;CTD-2530N21.5,upstream_gene_variant,,ENST00000314927,; A ENST00000520605 Transcript missense_variant 433/519 404/468 135/155 G/E gGg/gAg 1 1 SFTPC HGNC HGNC:10802 protein_coding ENSP00000430266 E5RG20 UPI0000E5AE48 deleterious_low_confidence(0) 4/4 PROSITE_profiles:PS50869 MODERATE SNV 3 1 PASS . . 0 203 7 0 0 0 0 0 -20 0.9999999 1 1 1 0 A 3 1 106 22164393 22164393 G A 1 0 0 0 0 1 0 0 0 14452 1232 43 3 3 SFTPC 8 22164393 Missense_Mutation SNP G C3N-02587_T 22164393 122974243 7 30090 SPATA31D1 0 . GRCh38 9 81992303 81992303 + Silent SNP C C T rs201473485 C3N-02587_T C3N-02587_N C C c.1833C>T p.= p.N611N ENST00000344803 4/4 587 485 102 912 912 0 strelka-varscan-mutect SPATA31D1,synonymous_variant,p.=,ENST00000344803,NM_001001670.2;RP11-15B24.5,intron_variant,,ENST00000637606,;SPATA31D1,downstream_gene_variant,,ENST00000603921,; T ENST00000344803 Transcript synonymous_variant 1880/4833 1833/4731 611/1576 N aaC/aaT rs201473485,COSM1463220,COSM1463221 1 1 SPATA31D1 HGNC HGNC:37283 protein_coding YES CCDS47986.1 ENSP00000341988 Q6ZQQ2 UPI00001C10A6 NM_001001670.2 4/4 hmmpanther:PTHR21859,hmmpanther:PTHR21859:SF12,Pfam_domain:PF14650 0,1,1 LOW 1 SNV 2 0,1,1 1 PASS rs201473485 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 106 81992303 81992303 C T 1 0 0 0 0 0 0 0 1 15347 535 19 1 1 SPATA31D1 9 81992303 Silent SNP C C3N-02587_T 81992303 56402414 8 30091 AKNA 0 . GRCh38 9 114357991 114357991 + Missense_Mutation SNP A A G novel C3N-02587_T C3N-02587_N A A c.2669T>C p.Leu890Pro p.L890P ENST00000307564 12/22 76 58 18 97 97 0 strelka-varscan-mutect AKNA,missense_variant,p.Leu890Pro,ENST00000307564,NM_030767.4;AKNA,missense_variant,p.Leu890Pro,ENST00000374088,NM_001317950.1,NM_001317952.1;AKNA,missense_variant,p.Leu809Pro,ENST00000374075,;AKNA,missense_variant,p.Leu350Pro,ENST00000223791,;AKNA,downstream_gene_variant,,ENST00000312033,;AKNA,non_coding_transcript_exon_variant,,ENST00000490767,; G ENST00000307564 Transcript missense_variant 2831/7380 2669/4320 890/1439 L/P cTg/cCg 1 -1 AKNA HGNC HGNC:24108 protein_coding YES CCDS6805.1 ENSP00000303769 Q7Z591 UPI000021168C NM_030767.4 deleterious(0.02) 12/22 hmmpanther:PTHR21510:SF15,hmmpanther:PTHR21510 MODERATE 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 106 114357991 114357991 A G 1 0 0 0 0 1 0 0 0 547 188 7 5 5 AKNA 9 114357991 Missense_Mutation SNP A C3N-02587_T 32365688 114357991 24036726 9 30092 MRGPRX2 0 . GRCh38 11 19056012 19056012 + Missense_Mutation SNP C C T rs200815634 C3N-02587_T C3N-02587_N C C c.391G>A p.Val131Ile p.V131I ENST00000329773 2/2 277 255 22 346 346 0 strelka-varscan-mutect MRGPRX2,missense_variant,p.Val131Ile,ENST00000329773,NM_001303615.1,NM_054030.3; T ENST00000329773 Transcript missense_variant 479/2036 391/993 131/330 V/I Gtc/Atc rs200815634 1 -1 MRGPRX2 HGNC HGNC:17983 protein_coding YES CCDS7847.1 ENSP00000333800 Q96LB1 UPI0000038C81 NM_001303615.1,NM_054030.3 tolerated(0.18) 2/2 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR00237,Prints_domain:PR02108,PROSITE_patterns:PS00237,PROSITE_profiles:PS50262,hmmpanther:PTHR11334,hmmpanther:PTHR11334:SF35,Superfamily_domains:SSF81321 MODERATE 1 SNV 1 1 PASS rs200815634 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 106 19056012 19056012 C T 1 0 0 0 0 1 0 0 0 9734 536 19 1 1 MRGPRX2 11 19056012 Missense_Mutation SNP C C3N-02587_T 19056012 116030610 10 30093 ETS1 0 . GRCh38 11 128486084 128486084 + Missense_Mutation SNP A A C novel C3N-02587_T C3N-02587_N A A c.598T>G p.Ser200Ala p.S200A ENST00000392668 6/10 213 139 74 271 270 1 strelka-varscan-mutect ETS1,missense_variant,p.Ser200Ala,ENST00000392668,NM_001143820.1;ETS1,missense_variant,p.Ser156Ala,ENST00000526145,;ETS1,missense_variant,p.Ser156Ala,ENST00000319397,NM_005238.3;ETS1,missense_variant,p.Ser156Ala,ENST00000531611,;ETS1,intron_variant,,ENST00000535549,NM_001162422.1;ETS1,downstream_gene_variant,,ENST00000608978,; C ENST00000392668 Transcript missense_variant 683/5139 598/1458 200/485 S/A Tcg/Gcg 1 -1 ETS1 HGNC HGNC:3488 protein_coding YES CCDS44767.1 ENSP00000376436 P14921 UPI00001BDB62 NM_001143820.1 tolerated(0.05) 6/10 hmmpanther:PTHR11849:SF209,hmmpanther:PTHR11849,PIRSF_domain:PIRSF001698 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 C 3 2 106 128486084 128486084 A C 1 0 0 0 0 1 0 0 0 5139 304 11 5 5 ETS1 11 128486084 Missense_Mutation SNP A C3N-02587_T 109430072 128486084 6600538 11 30094 STAT2 0 . GRCh38 12 56348548 56348548 + Nonsense_Mutation SNP T T A novel C3N-02587_T C3N-02587_N T T c.1705A>T p.Lys569Ter p.K569* ENST00000314128 19/24 324 231 93 490 490 0 strelka-varscan-mutect STAT2,stop_gained,p.Lys569Ter,ENST00000314128,NM_005419.3;STAT2,stop_gained,p.Lys565Ter,ENST00000557235,NM_198332.1;STAT2,downstream_gene_variant,,ENST00000418572,;RNU7-40P,downstream_gene_variant,,ENST00000516397,;STAT2,non_coding_transcript_exon_variant,,ENST00000556539,;STAT2,downstream_gene_variant,,ENST00000557252,;STAT2,downstream_gene_variant,,ENST00000557156,;STAT2,non_coding_transcript_exon_variant,,ENST00000557199,;STAT2,downstream_gene_variant,,ENST00000556140,;STAT2,downstream_gene_variant,,ENST00000555519,;STAT2,upstream_gene_variant,,ENST00000555488,; A ENST00000314128 Transcript stop_gained 1729/3259 1705/2556 569/851 K/* Aag/Tag 1 -1 STAT2 HGNC HGNC:11363 protein_coding YES CCDS8917.1 ENSP00000315768 P52630 R9QE65 UPI00000473FC NM_005419.3 19/24 Gene3D:1.10.238.10,hmmpanther:PTHR11801,hmmpanther:PTHR11801:SF41,Superfamily_domains:SSF55550 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 106 56348548 56348548 T A 1 0 0 0 0 0 1 0 0 15641 1792 62 4 4 STAT2 12 56348548 Nonsense_Mutation SNP T C3N-02587_T 56348548 76926761 12 30095 GPR137C 0 . GRCh38 14 52632298 52632298 + Missense_Mutation SNP C C G novel C3N-02587_T C3N-02587_N C C c.856C>G p.Leu286Val p.L286V ENST00000321662 4/7 160 129 31 196 195 1 strelka-varscan-mutect GPR137C,missense_variant,p.Leu286Val,ENST00000321662,NM_001099652.1;GPR137C,missense_variant,p.Leu256Val,ENST00000542169,;GPR137C,downstream_gene_variant,,ENST00000555622,;GPR137C,non_coding_transcript_exon_variant,,ENST00000555369,; G ENST00000321662 Transcript missense_variant 856/3888 856/1290 286/429 L/V Ctt/Gtt 1 1 GPR137C HGNC HGNC:25445 protein_coding YES CCDS45106.1 ENSP00000315106 Q8N3F9 UPI0000043F5A NM_001099652.1 tolerated(1) 4/7 hmmpanther:PTHR15146,hmmpanther:PTHR15146:SF1 MODERATE 1 SNV 2 1 PASS rs1471947612 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 106 52632298 52632298 C G 1 0 0 0 0 1 0 0 0 6533 913 32 4 4 GPR137C 14 52632298 Missense_Mutation SNP C C3N-02587_T 52632298 54411420 13 30096 AP4E1 0 . GRCh38 15 50929161 50929161 + Missense_Mutation SNP T T A novel C3N-02587_T C3N-02587_N T T c.695T>A p.Met232Lys p.M232K ENST00000261842 6/21 278 232 46 440 440 0 strelka-varscan-mutect AP4E1,missense_variant,p.Met232Lys,ENST00000261842,NM_007347.4;AP4E1,missense_variant,p.Met157Lys,ENST00000560508,NM_001252127.1;AP4E1,missense_variant,p.Met232Lys,ENST00000558439,;AP4E1,missense_variant,p.Met157Lys,ENST00000561393,;AP4E1,missense_variant,p.Met232Lys,ENST00000561441,; A ENST00000261842 Transcript missense_variant 801/6758 695/3414 232/1137 M/K aTg/aAg 1 1 AP4E1 HGNC HGNC:573 protein_coding YES CCDS32240.1 ENSP00000261842 Q9UPM8 UPI00001D89D8 NM_007347.4 deleterious(0) 6/21 hmmpanther:PTHR22780,hmmpanther:PTHR22780:SF13,Pfam_domain:PF01602,PIRSF_domain:PIRSF037097,Gene3D:1.25.10.10,Superfamily_domains:SSF48371 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 106 50929161 50929161 T A 1 0 0 0 0 1 0 0 0 868 1464 51 4 4 AP4E1 15 50929161 Missense_Mutation SNP T C3N-02587_T 50929161 51062028 14 30097 BRCA1 0 . GRCh38 17 43091337 43091337 + Nonsense_Mutation SNP A A T novel C3N-02587_T C3N-02587_N A A c.4194T>A p.Tyr1398Ter p.Y1398* ENST00000354071 10/10 44 40 4 91 90 1 varscan-mutect BRCA1,stop_gained,p.Tyr1398Ter,ENST00000354071,;BRCA1,intron_variant,,ENST00000357654,NM_007294.3;BRCA1,intron_variant,,ENST00000471181,NM_007300.3;BRCA1,intron_variant,,ENST00000493795,NM_007297.3;BRCA1,intron_variant,,ENST00000352993,;BRCA1,intron_variant,,ENST00000468300,NM_007299.3;BRCA1,intron_variant,,ENST00000491747,NM_007298.3;BRCA1,intron_variant,,ENST00000478531,;BRCA1,intron_variant,,ENST00000493919,;BRCA1,intron_variant,,ENST00000484087,;BRCA1,intron_variant,,ENST00000591534,;BRCA1,intron_variant,,ENST00000487825,;BRCA1,intron_variant,,ENST00000586385,;BRCA1,intron_variant,,ENST00000461574,;BRCA1,intron_variant,,ENST00000591849,;BRCA1,downstream_gene_variant,,ENST00000634433,;BRCA1,downstream_gene_variant,,ENST00000470026,;BRCA1,downstream_gene_variant,,ENST00000477152,;BRCA1,downstream_gene_variant,,ENST00000494123,;BRCA1,downstream_gene_variant,,ENST00000473961,;BRCA1,downstream_gene_variant,,ENST00000497488,;BRCA1,downstream_gene_variant,,ENST00000476777,;BRCA1,intron_variant,,ENST00000461221,;BRCA1,downstream_gene_variant,,ENST00000492859,;BRCA1,downstream_gene_variant,,ENST00000412061,; T ENST00000354071 Transcript stop_gained 4258/4497 4194/4200 1398/1399 Y/* taT/taA 1 -1 BRCA1 HGNC HGNC:1100 protein_coding ENSP00000326002 Q5YLB2 UPI000044D375 10/10 HIGH SNV 1 1 PASS . . 0 204 3 0 0 0 0 2 -3.438717 0 0 1 0 0 T 4 4 106 43091337 43091337 A T 1 0 0 0 0 0 1 0 0 1668 456 16 4 4 BRCA1 17 43091337 Nonsense_Mutation SNP A C3N-02587_T 43091337 40166104 15 30098 SRSF1 0 . GRCh38 17 58006482 58006483 + Frame_Shift_Ins INS - - T novel C3N-02587_T C3N-02587_N - - c.239dupA p.Asp80GlufsTer41 p.D80Efs*41 ENST00000258962 2/4 127 96 31 232 232 0 sindel-varindel-pindel SRSF1,frameshift_variant,p.Asp80GlufsTer41,ENST00000582730,NM_001078166.1;SRSF1,frameshift_variant,p.Asp80GlufsTer41,ENST00000258962,NM_006924.4;SRSF1,frameshift_variant,p.Asp80GlufsTer41,ENST00000584773,;SRSF1,intron_variant,,ENST00000585096,;RP11-159D12.5,upstream_gene_variant,,ENST00000578794,;RP11-159D12.6,upstream_gene_variant,,ENST00000624641,;SRSF1,upstream_gene_variant,,ENST00000581497,;SRSF1,frameshift_variant,p.Asp80GlufsTer41,ENST00000581979,;SRSF1,3_prime_UTR_variant,,ENST00000583741,;SRSF1,non_coding_transcript_exon_variant,,ENST00000578430,;SRSF1,upstream_gene_variant,,ENST00000584668,; T ENST00000258962 Transcript frameshift_variant 448-449/1513 239-240/747 80/248 D/EX gat/gaAt 1 -1 SRSF1 HGNC HGNC:10780 protein_coding YES CCDS11600.1 ENSP00000258962 Q07955 UPI0000001220 NM_006924.4 2/4 Low_complexity_(Seg):seg,PROSITE_profiles:PS50102,hmmpanther:PTHR24012,hmmpanther:PTHR24012:SF487,Pfam_domain:PF00076,Gene3D:3.30.70.330,SMART_domains:SM00360,Superfamily_domains:SSF54928 HIGH 1 insertion 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999993 1 1 1 0 T 7 5 106 58006482 58006482 - T 1 0 1 1 0 0 0 0 0 15535 214 8 0 0 SRSF1 17 58006482 Frame_Shift_Ins INS - C3N-02587_T 14915145 58006482 25250959 16 30099 MYO5B 0 . GRCh38 18 49837734 49837734 + Missense_Mutation SNP G G T rs780999931 C3N-02587_T C3N-02587_N G G c.4921C>A p.Arg1641Ser p.R1641S ENST00000285039 37/40 418 310 108 542 542 0 strelka-varscan-mutect MYO5B,missense_variant,p.Arg1641Ser,ENST00000285039,NM_001080467.2;MYO5B,missense_variant,p.Arg758Ser,ENST00000324581,;MYO5B,missense_variant,p.Arg211Ser,ENST00000592688,;SNHG22,intron_variant,,ENST00000589499,;SNHG22,upstream_gene_variant,,ENST00000617833,;RP11-886H22.1,upstream_gene_variant,,ENST00000590532,; T ENST00000285039 Transcript missense_variant 5221/9505 4921/5547 1641/1848 R/S Cgc/Agc rs780999931 1 -1 MYO5B HGNC HGNC:7603 protein_coding YES CCDS42436.1 ENSP00000285039 Q9ULV0 UPI00001D7B21 NM_001080467.2 deleterious(0.02) 37/40 PROSITE_profiles:PS51126,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF356 MODERATE 1 SNV 1 1 PASS rs780999931 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 106 49837734 49837734 G T 1 0 0 0 0 1 0 0 0 10080 1087 38 1 1 MYO5B 18 49837734 Missense_Mutation SNP G C3N-02587_T 49837734 30535551 17 30100 COL5A3 0 . GRCh38 19 9968418 9968418 + Silent SNP G G A rs768598683 C3N-02587_T C3N-02587_N G G c.4281C>T p.= p.G1427G ENST00000264828 59/67 153 127 26 209 209 0 strelka-varscan-mutect COL5A3,synonymous_variant,p.=,ENST00000264828,NM_015719.3;COL5A3,non_coding_transcript_exon_variant,,ENST00000461214,; A ENST00000264828 Transcript synonymous_variant 4367/6174 4281/5238 1427/1745 G ggC/ggT rs768598683,COSM1757000 1 -1 COL5A3 HGNC HGNC:14864 protein_coding YES CCDS12222.1 ENSP00000264828 P25940 UPI00002032A3 NM_015719.3 59/67 Low_complexity_(Seg):seg,hmmpanther:PTHR24023,hmmpanther:PTHR24023:SF516 0,1 LOW 1 SNV 1 0,1 1 PASS rs768598683 . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 106 9968418 9968418 G A 1 0 0 0 0 0 0 0 1 3487 1074 38 1 1 COL5A3 19 9968418 Silent SNP G C3N-02587_T 9968418 48649198 18 30101 ZNF729 0 . GRCh38 19 22316367 22316367 + Missense_Mutation SNP G G T novel C3N-02587_T C3N-02587_N G G c.2950G>T p.Ala984Ser p.A984S ENST00000601693 4/4 126 101 25 387 387 0 strelka-varscan-mutect ZNF729,missense_variant,p.Ala984Ser,ENST00000601693,NM_001242680.1; T ENST00000601693 Transcript missense_variant 3068/3877 2950/3759 984/1252 A/S Gca/Tca 1 1 ZNF729 HGNC HGNC:32464 protein_coding YES CCDS59368.1 ENSP00000469582 A6NN14 UPI000042600C NM_001242680.1 tolerated(0.34) 4/4 PROSITE_profiles:PS50157,hmmpanther:PTHR24375,hmmpanther:PTHR24375:SF187,PROSITE_patterns:PS00028,Pfam_domain:PF00096,Gene3D:3.30.160.60,SMART_domains:SM00355,Superfamily_domains:SSF57667 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 106 22316367 22316367 G T 1 0 0 0 0 1 0 0 0 18703 971 34 2 2 ZNF729 19 22316367 Missense_Mutation SNP G C3N-02587_T 12347949 22316367 36301249 19 30102 CACNG6 0 . GRCh38 19 53993204 53993204 + Silent SNP C C T rs750723015 C3N-02587_T C3N-02587_N C C c.327C>T p.= p.P109P ENST00000252729 1/4 202 150 52 312 312 0 strelka-mutect CACNG6,synonymous_variant,p.=,ENST00000252729,NM_145814.1;CACNG6,synonymous_variant,p.=,ENST00000352529,NM_031897.2;CACNG6,synonymous_variant,p.=,ENST00000346968,NM_145815.1;CACNG8,downstream_gene_variant,,ENST00000270458,NM_031895.5; T ENST00000252729 Transcript synonymous_variant 917/1853 327/783 109/260 P ccC/ccT rs750723015 1 1 CACNG6 HGNC HGNC:13625 protein_coding YES CCDS12870.1 ENSP00000252729 Q9BXT2 UPI0000001276 NM_145814.1 1/4 Pfam_domain:PF13903,Prints_domain:PR01794,hmmpanther:PTHR15025,hmmpanther:PTHR15025:SF6 LOW 1 SNV 1 1 PASS rs750723015 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 106 53993204 53993204 C T 1 0 0 0 0 0 0 0 1 2249 666 23 1 1 CACNG6 19 53993204 Silent SNP C C3N-02587_T 31676837 53993204 4624412 20 30103 SH3BGR 0 . GRCh38 21 39452069 39452069 + Frame_Shift_Del DEL G G - C3N-02587_T C3N-02587_N G G c.167delG p.Gly56GlufsTer22 p.G56Efs*22 ENST00000333634 1/7 258 244 14 343 343 0 varindel-pindel SH3BGR,frameshift_variant,p.Gly56GlufsTer22,ENST00000333634,NM_007341.2;SH3BGR,intron_variant,,ENST00000380637,NM_001317742.1,NM_001001713.1;SH3BGR,intron_variant,,ENST00000380634,;SH3BGR,intron_variant,,ENST00000458295,;SH3BGR,intron_variant,,ENST00000380631,;SH3BGR,intron_variant,,ENST00000440288,;SH3BGR,upstream_gene_variant,,ENST00000452550,;MIR6508,downstream_gene_variant,,ENST00000611656,; - ENST00000333634 Transcript frameshift_variant 240/1251 162/720 54/239 L/X ttG/tt COSM5274884 1 1 SH3BGR HGNC HGNC:10822 protein_coding YES CCDS13666.1 ENSP00000332513 P55822 UPI00001B03C6 NM_007341.2 1/7 1 HIGH 1 deletion 1 5 1 1 PASS . . 0 207 0 3 0 0 0 0 -16.08272 0.9999467 1 1 1 0 - 7 5 106 39452069 39452069 G - 1 0 1 0 1 0 0 0 0 14498 1339 47 0 0 SH3BGR 21 39452069 Frame_Shift_Del DEL G C3N-02587_T 39452069 7257914 21 30104 TP73 0 . GRCh38 1 3727187 3727187 + Missense_Mutation SNP C C T novel C3N-02588_T C3N-02588_N C C c.805C>T p.Arg269Trp p.R269W ENST00000378295 7/14 287 212 75 152 152 0 strelka-varscan-mutect TP73,missense_variant,p.Arg269Trp,ENST00000378295,NM_005427.3,NM_001204185.1;TP73,missense_variant,p.Arg220Trp,ENST00000378288,NM_001204191.1,NM_001126240.2,NM_001204190.1;TP73,missense_variant,p.Arg269Trp,ENST00000357733,NM_001204187.1;TP73,missense_variant,p.Arg269Trp,ENST00000346387,NM_001204188.1;TP73,missense_variant,p.Arg269Trp,ENST00000604074,NM_001204189.1,NM_001204186.1;TP73,missense_variant,p.Arg269Trp,ENST00000354437,NM_001204184.1;TP73,missense_variant,p.Arg220Trp,ENST00000378285,NM_001126241.2;TP73,missense_variant,p.Arg220Trp,ENST00000378280,NM_001126242.2;TP73,missense_variant,p.Arg198Trp,ENST00000378290,NM_001204192.1;TP73,missense_variant,p.Arg269Trp,ENST00000603362,;TP73,missense_variant,p.Arg269Trp,ENST00000604479,;TP73,non_coding_transcript_exon_variant,,ENST00000603364,;TP73,upstream_gene_variant,,ENST00000604566,; T ENST00000378295 Transcript missense_variant 960/5188 805/1911 269/636 R/W Cgg/Tgg 1 1 TP73 HGNC HGNC:12003 protein_coding YES CCDS49.1 ENSP00000367545 O15350 A0A024R4C3 UPI000002E988 NM_005427.3,NM_001204185.1 deleterious(0) 7/14 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF21,PROSITE_patterns:PS00348,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 MODERATE 1 SNV 1 1 PASS . . 0 207 0 3 0 0 0 0 -20 0.9999979 1 1 1 0 T 3 4 107 3727187 3727187 C T 1 0 0 0 0 1 0 0 0 16872 759 27 1 1 TP73 1 3727187 Missense_Mutation SNP C C3N-02588_T 3727187 245229235 1 30105 RNF186 0 . GRCh38 1 19814559 19814559 + Silent SNP C C T novel C3N-02588_T C3N-02588_N C C c.543G>A p.= p.V181V ENST00000375121 1/1 616 501 115 322 322 0 strelka-varscan-mutect RNF186,synonymous_variant,p.=,ENST00000375121,NM_019062.1;RP11-91K11.2,splice_region_variant,,ENST00000454736,; T ENST00000375121 Transcript synonymous_variant 720/1250 543/684 181/227 V gtG/gtA 1 -1 RNF186 HGNC HGNC:25978 protein_coding YES CCDS199.1 ENSP00000364263 Q9NXI6 UPI0000073BA5 NM_019062.1 1/1 Transmembrane_helices:TMhelix,hmmpanther:PTHR16450 LOW SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 107 19814559 19814559 C T 1 0 0 0 0 0 0 0 1 13646 697 25 3 3 RNF186 1 19814559 Silent SNP C C3N-02588_T 16087372 19814559 229141863 2 30106 LRRC40 0 . GRCh38 1 70148656 70148656 + Nonsense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1534G>T p.Glu512Ter p.E512* ENST00000370952 14/15 53 49 4 71 71 0 varscan-mutect LRRC40,stop_gained,p.Glu512Ter,ENST00000370952,NM_017768.4;LRRC7,intron_variant,,ENST00000441830,;LRRC7,downstream_gene_variant,,ENST00000565615,;LRRC7,downstream_gene_variant,,ENST00000609072,;LRRC7,downstream_gene_variant,,ENST00000607936,;LRRC7,downstream_gene_variant,,ENST00000608744,;LRRC7,downstream_gene_variant,,ENST00000588515,; A ENST00000370952 Transcript stop_gained 1614/2884 1534/1809 512/602 E/* Gaa/Taa 1 -1 LRRC40 HGNC HGNC:26004 protein_coding YES CCDS646.1 ENSP00000359990 Q9H9A6 A0A140VJN3 UPI000004A0A0 NM_017768.4 14/15 PROSITE_profiles:PS51450,hmmpanther:PTHR23155,hmmpanther:PTHR23155:SF424,Gene3D:3.80.10.10,SMART_domains:SM00369,SMART_domains:SM00364,Superfamily_domains:SSF52058 HIGH 1 SNV 1 1 PASS . . 0 192 16 0 0 0 0 0 -9.635798 0.9971429 1 1 1 0 A 4 1 107 70148656 70148656 C A 1 0 0 0 0 0 1 0 0 8894 835 29 2 2 LRRC40 1 70148656 Nonsense_Mutation SNP C C3N-02588_T 50334097 70148656 178807766 3 30107 DENND2D 0 . GRCh38 1 111187658 111187658 + Nonsense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1363G>T p.Glu455Ter p.E455* ENST00000357640 12/12 222 206 16 204 204 0 strelka-varscan-mutect DENND2D,stop_gained,p.Glu455Ter,ENST00000357640,NM_024901.4;DENND2D,stop_gained,p.Glu452Ter,ENST00000369752,NM_001271833.1;CEPT1,downstream_gene_variant,,ENST00000545121,NM_001007794.1;CEPT1,downstream_gene_variant,,ENST00000357172,NM_006090.3;CEPT1,downstream_gene_variant,,ENST00000615636,;RP5-1180E21.5,upstream_gene_variant,,ENST00000610049,;DENND2D,non_coding_transcript_exon_variant,,ENST00000468692,;CEPT1,downstream_gene_variant,,ENST00000467362,;CEPT1,downstream_gene_variant,,ENST00000478042,;CEPT1,downstream_gene_variant,,ENST00000498239,;CEPT1,downstream_gene_variant,,ENST00000473474,;CEPT1,downstream_gene_variant,,ENST00000483427,; A ENST00000357640 Transcript stop_gained 1593/2077 1363/1416 455/471 E/* Gaa/Taa 1 -1 DENND2D HGNC HGNC:26192 protein_coding YES CCDS831.1 ENSP00000350266 Q9H6A0 A0A024R0G2 UPI000006E1E1 NM_024901.4 12/12 Low_complexity_(Seg):seg,hmmpanther:PTHR15288:SF2,hmmpanther:PTHR15288 HIGH 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 107 111187658 111187658 C A 1 0 0 0 0 0 1 0 0 4235 835 29 2 2 DENND2D 1 111187658 Nonsense_Mutation SNP C C3N-02588_T 41039002 111187658 137768764 4 30108 FLAD1 0 . GRCh38 1 154990250 154990250 + Missense_Mutation SNP A A G rs761846561 C3N-02588_T C3N-02588_N A A c.1357A>G p.Ile453Val p.I453V ENST00000292180 4/7 438 344 94 173 173 0 strelka-varscan-mutect FLAD1,missense_variant,p.Ile453Val,ENST00000368433,;FLAD1,missense_variant,p.Ile453Val,ENST00000292180,NM_025207.4;FLAD1,missense_variant,p.Ile356Val,ENST00000368432,NM_001184891.1;FLAD1,missense_variant,p.Ile356Val,ENST00000315144,NM_201398.2;FLAD1,synonymous_variant,p.=,ENST00000295530,;FLAD1,5_prime_UTR_variant,,ENST00000368428,;FLAD1,downstream_gene_variant,,ENST00000368431,NM_001184892.1;LENEP,upstream_gene_variant,,ENST00000392487,NM_018655.2;FLAD1,non_coding_transcript_exon_variant,,ENST00000489992,;FLAD1,non_coding_transcript_exon_variant,,ENST00000477609,;FLAD1,downstream_gene_variant,,ENST00000487371,;FLAD1,downstream_gene_variant,,ENST00000492620,;FLAD1,upstream_gene_variant,,ENST00000481758,;LENEP,upstream_gene_variant,,ENST00000368427,; G ENST00000292180 Transcript missense_variant 1679/2160 1357/1764 453/587 I/V Atc/Gtc rs761846561 1 1 FLAD1 HGNC HGNC:24671 protein_coding YES CCDS1078.1 ENSP00000292180 Q8NFF5 UPI00000735B2 NM_025207.4 tolerated(1) 4/7 hmmpanther:PTHR23293,hmmpanther:PTHR23293:SF9,Pfam_domain:PF01507,PIRSF_domain:PIRSF036620,Gene3D:3.40.50.620,Superfamily_domains:SSF52402 MODERATE 1 SNV 1 1 PASS rs761846561 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 107 154990250 154990250 A G 1 0 0 0 0 1 0 0 0 5782 449 16 5 5 FLAD1 1 154990250 Missense_Mutation SNP A C3N-02588_T 43802592 154990250 93966172 5 30109 PTPN7 0 . GRCh38 1 202148617 202148617 + Missense_Mutation SNP G G T rs201036614 C3N-02588_T C3N-02588_N G G c.1387C>A p.Pro463Thr p.P463T ENST00000309017 10/10 339 308 31 142 142 0 strelka-varscan PTPN7,missense_variant,p.Pro463Thr,ENST00000309017,NM_002832.3;PTPN7,missense_variant,p.Pro397Thr,ENST00000367279,NM_080588.2;PTPN7,missense_variant,p.Pro439Thr,ENST00000477554,NM_001199797.1;ARL8A,upstream_gene_variant,,ENST00000272217,NM_138795.3;ARL8A,upstream_gene_variant,,ENST00000614750,NM_001256129.1;PTPN7,downstream_gene_variant,,ENST00000477625,;PTPN7,downstream_gene_variant,,ENST00000492977,;PTPN7,missense_variant,p.Pro358Thr,ENST00000495688,;PTPN7,3_prime_UTR_variant,,ENST00000496197,;PTPN7,3_prime_UTR_variant,,ENST00000480836,;PTPN7,3_prime_UTR_variant,,ENST00000462815,; T ENST00000309017 Transcript missense_variant 2161/3765 1387/1398 463/465 P/T Ccc/Acc rs201036614 1 -1 PTPN7 HGNC HGNC:9659 protein_coding YES CCDS1423.2 ENSP00000309116 P35236 UPI00004701F6 NM_002832.3 tolerated_low_confidence(0.12) 10/10 hmmpanther:PTHR19134:SF41,hmmpanther:PTHR19134 MODERATE 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 202148617 202148617 G T 1 0 0 0 0 1 0 0 0 12947 1261 44 2 2 PTPN7 1 202148617 Missense_Mutation SNP G C3N-02588_T 47158367 202148617 46807805 6 30110 ALK 0 . GRCh38 2 29328365 29328365 + Nonsense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1399G>T p.Glu467Ter p.E467* ENST00000389048 6/29 717 573 144 284 284 0 strelka-varscan ALK,stop_gained,p.Glu467Ter,ENST00000389048,NM_004304.4;ALK,stop_gained,p.Glu90Ter,ENST00000618119,; A ENST00000389048 Transcript stop_gained 2306/6220 1399/4863 467/1620 E/* Gag/Tag 1 -1 ALK HGNC HGNC:427 protein_coding YES CCDS33172.1 ENSP00000373700 Q9UM73 UPI00001684DA NM_004304.4 6/29 Gene3D:4.10.400.10,SMART_domains:SM00192,Superfamily_domains:SSF57424 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 4 1 107 29328365 29328365 C A 1 0 0 0 0 0 1 0 0 625 835 29 2 2 ALK 2 29328365 Nonsense_Mutation SNP C C3N-02588_T 29328365 212865164 7 30111 PPP1R21 0 . GRCh38 2 48458196 48458199 + Frame_Shift_Del DEL AGAT AGAT - novel C3N-02588_T C3N-02588_N AGAT AGAT c.347_350delTAGA p.Ile116LysfsTer24 p.I116Kfs*24 ENST00000294952 4/22 97 81 16 148 148 0 sindel-varindel-pindel PPP1R21,frameshift_variant,p.Ile116LysfsTer24,ENST00000294952,NM_001135629.2;PPP1R21,frameshift_variant,p.Ile116LysfsTer24,ENST00000281394,NM_152994.4;PPP1R21,frameshift_variant,p.Ile116LysfsTer24,ENST00000449090,NM_001193475.1;PPP1R21,downstream_gene_variant,,ENST00000421486,;PPP1R21,3_prime_UTR_variant,,ENST00000416913,;PPP1R21,3_prime_UTR_variant,,ENST00000431614,; - ENST00000294952 Transcript frameshift_variant 501-504/3142 344-347/2343 115-116/780 KI/X aAGATa/aa 1 1 PPP1R21 HGNC HGNC:30595 protein_coding YES CCDS46278.1 ENSP00000294952 Q6ZMI0 UPI000015C523 NM_001135629.2 4/22 hmmpanther:PTHR21448 HIGH 1 deletion 1 3 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 107 48458196 48458196 AGAT - 1 0 1 0 1 0 0 0 0 12483 72 3 0 0 PPP1R21 2 48458196 Frame_Shift_Del DEL AGAT C3N-02588_T 19129831 48458196 193735333 8 30112 SULT1C2 0 . GRCh38 2 108294246 108294246 + Missense_Mutation SNP G G A C3N-02588_T C3N-02588_N G G c.169G>A p.Glu57Lys p.E57K ENST00000326853 3/9 341 322 19 169 169 0 strelka-varscan-mutect SULT1C2,missense_variant,p.Glu57Lys,ENST00000326853,NM_176825.2;SULT1C2,missense_variant,p.Glu57Lys,ENST00000251481,NM_001056.3;SULT1C2,missense_variant,p.Glu57Lys,ENST00000437390,;SULT1C2,missense_variant,p.Glu57Lys,ENST00000409880,;SULT1C2,missense_variant,p.Glu54Lys,ENST00000409067,;SULT1C2,missense_variant,p.Glu57Lys,ENST00000438339,;SULT1C2,non_coding_transcript_exon_variant,,ENST00000492554,;SULT1C2,missense_variant,p.Glu55Lys,ENST00000442801,;SULT1C2,upstream_gene_variant,,ENST00000495441,; A ENST00000326853 Transcript missense_variant 622/2828 169/924 57/307 E/K Gaa/Aaa COSM4900296,COSM4900297 1 1 SULT1C2 HGNC HGNC:11456 protein_coding YES CCDS2076.1 ENSP00000319622 O00338 UPI000002B313 NM_176825.2 deleterious(0.01) 3/9 hmmpanther:PTHR11783:SF73,hmmpanther:PTHR11783,Gene3D:3.40.50.300,Pfam_domain:PF00685,Superfamily_domains:SSF52540 1,1 MODERATE 1 SNV 1 1,1 1 PASS rs969530695 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 108294246 108294246 G A 1 0 0 0 0 1 0 0 0 15763 1175 41 3 3 SULT1C2 2 108294246 Missense_Mutation SNP G C3N-02588_T 59836050 108294246 133899283 9 30113 ZEB2 0 . GRCh38 2 144398544 144398544 + Missense_Mutation SNP G G T novel C3N-02588_T C3N-02588_N G G c.2643C>A p.Asn881Lys p.N881K ENST00000637267 9/11 375 305 70 324 324 0 strelka-varscan-mutect ZEB2,missense_variant,p.Asn881Lys,ENST00000637267,;ZEB2,missense_variant,p.Asn906Lys,ENST00000636471,;ZEB2,missense_variant,p.Asn881Lys,ENST00000627532,NM_014795.3;ZEB2,missense_variant,p.Asn881Lys,ENST00000636026,;ZEB2,missense_variant,p.Asn769Lys,ENST00000638087,;ZEB2,missense_variant,p.Asn769Lys,ENST00000637304,;ZEB2,missense_variant,p.Asn769Lys,ENST00000638007,;ZEB2,missense_variant,p.Asn769Lys,ENST00000637045,;ZEB2,missense_variant,p.Asn769Lys,ENST00000636413,;ZEB2,missense_variant,p.Asn622Lys,ENST00000638128,;ZEB2,missense_variant,p.Asn881Lys,ENST00000409487,;ZEB2,missense_variant,p.Asn857Lys,ENST00000539609,NM_001171653.1;ZEB2,missense_variant,p.Asn881Lys,ENST00000558170,;ZEB2,missense_variant,p.Asn880Lys,ENST00000303660,;ZEB2,intron_variant,,ENST00000440875,;ZEB2,intron_variant,,ENST00000419938,;ZEB2,downstream_gene_variant,,ENST00000427902,;ZEB2,downstream_gene_variant,,ENST00000392861,;ZEB2,upstream_gene_variant,,ENST00000637873,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636820,;ZEB2,non_coding_transcript_exon_variant,,ENST00000636179,;ZEB2,3_prime_UTR_variant,,ENST00000636732,; T ENST00000637267 Transcript missense_variant 3484/9856 2643/3645 881/1214 N/K aaC/aaA 1 -1 ZEB2 HGNC HGNC:14881 protein_coding YES CCDS2186.1 ENSP00000490293 UPI00001359A2 tolerated(0.17) 9/11 hmmpanther:PTHR24391,hmmpanther:PTHR24391:SF11 MODERATE 1 SNV 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 144398544 144398544 G T 1 0 0 0 0 1 0 0 0 18200 1252 44 2 2 ZEB2 2 144398544 Missense_Mutation SNP G C3N-02588_T 36104298 144398544 97794985 10 30114 CIR1 0 . GRCh38 2 174395585 174395585 + Missense_Mutation SNP T T A novel C3N-02588_T C3N-02588_N T T c.38A>T p.Asp13Val p.D13V ENST00000342016 1/10 466 424 42 277 277 0 strelka-varscan-mutect CIR1,missense_variant,p.Asp13Val,ENST00000342016,NM_004882.3;SCRN3,upstream_gene_variant,,ENST00000272732,NM_024583.4;SCRN3,upstream_gene_variant,,ENST00000409673,NM_001193528.1;SCRN3,upstream_gene_variant,,ENST00000427038,;SCRN3,upstream_gene_variant,,ENST00000458563,;SCRN3,upstream_gene_variant,,ENST00000548031,;SCRN3,upstream_gene_variant,,ENST00000435964,;SCRN3,upstream_gene_variant,,ENST00000424069,;SCRN3,upstream_gene_variant,,ENST00000490927,;SCRN3,upstream_gene_variant,,ENST00000488349,;CIR1,non_coding_transcript_exon_variant,,ENST00000461454,;CIR1,non_coding_transcript_exon_variant,,ENST00000472169,;SCRN3,upstream_gene_variant,,ENST00000548868,;SCRN3,upstream_gene_variant,,ENST00000437944,; A ENST00000342016 Transcript missense_variant 131/1921 38/1353 13/450 D/V gAc/gTc 1 -1 CIR1 HGNC HGNC:24217 protein_coding YES CCDS2256.1 ENSP00000339723 Q86X95 UPI000000DB2A NM_004882.3 deleterious(0.02) 1/10 hmmpanther:PTHR13151,Pfam_domain:PF10197,SMART_domains:SM01083 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 174395585 174395585 T A 1 0 0 0 0 1 0 0 0 3195 1667 58 4 4 CIR1 2 174395585 Missense_Mutation SNP T C3N-02588_T 29997041 174395585 67797944 11 30115 SLC40A1 0 . GRCh38 2 189575207 189575207 + Silent SNP C C T novel C3N-02588_T C3N-02588_N C C c.225G>A p.= p.L75L ENST00000261024 3/8 577 488 89 308 308 0 strelka-varscan-mutect SLC40A1,synonymous_variant,p.=,ENST00000261024,NM_014585.5;SLC40A1,synonymous_variant,p.=,ENST00000427241,;SLC40A1,downstream_gene_variant,,ENST00000455320,;SLC40A1,downstream_gene_variant,,ENST00000427419,;SLC40A1,downstream_gene_variant,,ENST00000440626,;SLC40A1,non_coding_transcript_exon_variant,,ENST00000418714,;SLC40A1,non_coding_transcript_exon_variant,,ENST00000479598,; T ENST00000261024 Transcript synonymous_variant 652/3442 225/1716 75/571 L ctG/ctA 1 -1 SLC40A1 HGNC HGNC:10909 protein_coding YES CCDS2299.1 ENSP00000261024 Q9NP59 UPI0000034CC2 NM_014585.5 3/8 Low_complexity_(Seg):seg,Transmembrane_helices:TMhelix,hmmpanther:PTHR11660,hmmpanther:PTHR11660:SF47,Pfam_domain:PF06963,Superfamily_domains:SSF103473 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 107 189575207 189575207 C T 1 0 0 0 0 0 0 0 1 14906 581 21 3 3 SLC40A1 2 189575207 Silent SNP C C3N-02588_T 15179622 189575207 52618322 12 30116 GRM7 0 . GRCh38 3 7461648 7461648 + Nonsense_Mutation SNP C C T C3N-02588_T C3N-02588_N C C c.1441C>T p.Gln481Ter p.Q481* ENST00000357716 7/10 401 321 80 237 237 0 strelka-varscan-mutect GRM7,stop_gained,p.Gln481Ter,ENST00000486284,NM_181874.2;GRM7,stop_gained,p.Gln481Ter,ENST00000357716,NM_000844.3;GRM7,stop_gained,p.Gln481Ter,ENST00000389336,;GRM7,stop_gained,p.Gln236Ter,ENST00000402647,;GRM7,stop_gained,p.Gln138Ter,ENST00000445087,;GRM7,non_coding_transcript_exon_variant,,ENST00000458641,;GRM7,stop_gained,p.Gln481Ter,ENST00000467425,;GRM7,stop_gained,p.Gln481Ter,ENST00000440923,;GRM7,stop_gained,p.Gln481Ter,ENST00000389335,;GRM7,non_coding_transcript_exon_variant,,ENST00000463676,; T ENST00000357716 Transcript stop_gained 1715/4127 1441/2748 481/915 Q/* Cag/Tag COSM5469031,COSM5469032,COSM5469033 1 1 GRM7 HGNC HGNC:4599 protein_coding YES CCDS43042.1 ENSP00000350348 Q14831 UPI000004A7E3 NM_000844.3 7/10 hmmpanther:PTHR24060:SF98,hmmpanther:PTHR24060,Gene3D:3.40.50.2300,Pfam_domain:PF01094,Superfamily_domains:SSF53822,Prints_domain:PR01057 1,1,1 HIGH 1 SNV 1 1,1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 107 7461648 7461648 C T 1 0 0 0 0 0 1 0 0 6684 827 29 3 3 GRM7 3 7461648 Nonsense_Mutation SNP C C3N-02588_T 7461648 190833911 13 30117 ANO10 0 . GRCh38 3 43605728 43605728 + Missense_Mutation SNP T T A novel C3N-02588_T C3N-02588_N T T c.125A>T p.Lys42Ile p.K42I ENST00000292246 2/13 314 284 30 278 278 0 strelka-varscan-mutect ANO10,missense_variant,p.Lys42Ile,ENST00000292246,NM_018075.3;ANO10,missense_variant,p.Lys42Ile,ENST00000414522,NM_001204831.1;ANO10,missense_variant,p.Lys42Ile,ENST00000396091,NM_001204832.1;ANO10,missense_variant,p.Lys42Ile,ENST00000350459,NM_001204834.1;ANO10,missense_variant,p.Lys42Ile,ENST00000451430,NM_001204833.1;ANO10,missense_variant,p.Lys42Ile,ENST00000427171,;ANO10,missense_variant,p.Lys42Ile,ENST00000428831,;ANO10,missense_variant,p.Lys42Ile,ENST00000428472,;ANO10,missense_variant,p.Lys42Ile,ENST00000444344,;ANO10,missense_variant,p.Lys42Ile,ENST00000439141,;ANO10,missense_variant,p.Lys42Ile,ENST00000456438,;ANO10,missense_variant,p.Lys42Ile,ENST00000413397,;ANO10,downstream_gene_variant,,ENST00000436073,; A ENST00000292246 Transcript missense_variant 296/3212 125/1983 42/660 K/I aAa/aTa 1 -1 ANO10 HGNC HGNC:25519 protein_coding YES CCDS2710.2 ENSP00000292246 Q9NW15 A0A024R2S0 UPI000020A59A NM_018075.3 tolerated(0.06) 2/13 hmmpanther:PTHR12308:SF40,hmmpanther:PTHR12308 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 43605728 43605728 T A 1 0 0 0 0 1 0 0 0 803 1841 64 4 4 ANO10 3 43605728 Missense_Mutation SNP T C3N-02588_T 36144080 43605728 154689831 14 30118 CLSTN2 0 . GRCh38 3 140562922 140562922 + Missense_Mutation SNP A A G novel C3N-02588_T C3N-02588_N A A c.2324A>G p.Asn775Ser p.N775S ENST00000458420 14/17 501 266 235 188 188 0 strelka-varscan CLSTN2,missense_variant,p.Asn775Ser,ENST00000458420,NM_022131.2; G ENST00000458420 Transcript missense_variant 2514/14202 2324/2868 775/955 N/S aAt/aGt 1 1 CLSTN2 HGNC HGNC:17448 protein_coding YES CCDS3112.1 ENSP00000402460 Q9H4D0 UPI00001B0051 NM_022131.2 deleterious(0.05) 14/17 hmmpanther:PTHR14139,hmmpanther:PTHR14139:SF3 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 107 140562922 140562922 A G 1 0 0 0 0 1 0 0 0 3334 101 4 5 5 CLSTN2 3 140562922 Missense_Mutation SNP A C3N-02588_T 96957194 140562922 57732637 15 30119 ARHGEF26 0 . GRCh38 3 154122950 154122950 + Missense_Mutation SNP G G T C3N-02588_T C3N-02588_N G G c.958G>T p.Ala320Ser p.A320S ENST00000356448 2/15 1193 889 304 404 403 1 strelka-varscan ARHGEF26,missense_variant,p.Ala320Ser,ENST00000356448,NM_001251962.1;ARHGEF26,missense_variant,p.Ala320Ser,ENST00000465093,NM_015595.3;ARHGEF26,missense_variant,p.Ala320Ser,ENST00000496710,NM_001251963.1;ARHGEF26,missense_variant,p.Ala320Ser,ENST00000465817,;ARHGEF26-AS1,upstream_gene_variant,,ENST00000491862,;ARHGEF26-AS1,upstream_gene_variant,,ENST00000467912,;ARHGEF26-AS1,upstream_gene_variant,,ENST00000479270,;ARHGEF26-AS1,upstream_gene_variant,,ENST00000480639,; T ENST00000356448 Transcript missense_variant 1242/5254 958/2616 320/871 A/S Gca/Tca COSM1040127,COSM1040128 1 1 ARHGEF26 HGNC HGNC:24490 protein_coding YES CCDS46938.1 ENSP00000348828 Q96DR7 A0A140VJU4 UPI00001410D0 NM_001251962.1 deleterious(0) 2/15 hmmpanther:PTHR12845:SF4,hmmpanther:PTHR12845 1,1 MODERATE SNV 2 1,1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 154122950 154122950 G T 1 0 0 0 0 1 0 0 0 1035 1203 42 2 2 ARHGEF26 3 154122950 Missense_Mutation SNP G C3N-02588_T 13560028 154122950 44172609 16 30120 ARHGAP24 0 . GRCh38 4 85995618 85995618 + Missense_Mutation SNP T T G novel C3N-02588_T C3N-02588_N T T c.1964T>G p.Met655Arg p.M655R ENST00000395184 9/10 284 226 58 188 188 0 strelka-varscan-mutect ARHGAP24,missense_variant,p.Met655Arg,ENST00000395184,NM_001025616.2;ARHGAP24,missense_variant,p.Met562Arg,ENST00000264343,NM_031305.2;ARHGAP24,missense_variant,p.Met560Arg,ENST00000395183,NM_001042669.1;ARHGAP24,missense_variant,p.Met570Arg,ENST00000514229,NM_001287805.1;RP13-514E23.2,downstream_gene_variant,,ENST00000610225,; G ENST00000395184 Transcript missense_variant 2430/4661 1964/2247 655/748 M/R aTg/aGg 1 1 ARHGAP24 HGNC HGNC:25361 protein_coding YES CCDS34025.1 ENSP00000378611 Q8N264 UPI00001AF1D9 NM_001025616.2 deleterious(0) 9/10 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR15228,hmmpanther:PTHR15228:SF19 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 107 85995618 85995618 T G 1 0 0 0 0 1 0 0 0 998 1464 51 5 5 ARHGAP24 4 85995618 Missense_Mutation SNP T C3N-02588_T 85995618 104218937 17 30121 GABRA1 0 . GRCh38 5 161873268 161873268 + Frame_Shift_Del DEL C C - novel C3N-02588_T C3N-02588_N C C c.409delC p.His137ThrfsTer3 p.H137Tfs*3 ENST00000393943 5/10 603 495 108 310 310 0 sindel-varindel-pindel GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000393943,NM_001127644.1,NM_001127648.1;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000428797,NM_001127643.1;GABRA1,frameshift_variant,p.His152ThrfsTer3,ENST00000638159,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000437025,NM_001127645.1;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000638112,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000636573,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000023897,NM_000806.5;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000637827,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000635880,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000634335,;GABRA1,frameshift_variant,p.His137ThrfsTer3,ENST00000519621,;GABRA1,downstream_gene_variant,,ENST00000522651,;GABRA1,non_coding_transcript_exon_variant,,ENST00000636408,;GABRA1,non_coding_transcript_exon_variant,,ENST00000635916,;GABRA1,3_prime_UTR_variant,,ENST00000637044,;GABRA1,3_prime_UTR_variant,,ENST00000636340,;GABRA1,non_coding_transcript_exon_variant,,ENST00000519542,; - ENST00000393943 Transcript frameshift_variant 1190/4686 407/1371 136/456 A/X gCc/gc 1 1 GABRA1 HGNC HGNC:4075 protein_coding YES CCDS4357.1 ENSP00000377517 P14867 UPI000012AF95 NM_001127644.1,NM_001127648.1 5/10 Superfamily_domains:0038932,Gene3D:2.70.170.10,Pfam_domain:PF02931,hmmpanther:PTHR18945,hmmpanther:PTHR18945:SF514,TIGRFAM_domain:TIGR00860 HIGH 1 deletion 1 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 107 161873268 161873268 C - 1 0 1 0 1 0 0 0 0 6031 739 26 0 0 GABRA1 5 161873268 Frame_Shift_Del DEL C C3N-02588_T 161873268 19664991 18 30122 DNAH8 0 . GRCh38 6 38734582 38734582 + Missense_Mutation SNP G G C rs188018051 C3N-02588_T C3N-02588_N G G c.719G>C p.Arg240Pro p.R240P ENST00000327475 5/93 210 157 53 224 224 0 strelka-varscan DNAH8,missense_variant,p.Arg240Pro,ENST00000327475,NM_001206927.1;DNAH8,missense_variant,p.Arg23Pro,ENST00000359357,;DNAH8,missense_variant,p.Arg240Pro,ENST00000449981,;DNAH8,downstream_gene_variant,,ENST00000373278,; C ENST00000327475 Transcript missense_variant 828/14360 719/14124 240/4707 R/P cGt/cCt rs188018051 1 1 DNAH8 HGNC HGNC:2952 protein_coding YES CCDS75447.1 ENSP00000333363 A0A075B6F3 UPI000179A984 NM_001206927.1 deleterious(0) 5/93 hmmpanther:PTHR10676:SF280,hmmpanther:PTHR10676 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 38734582 38734582 G C 1 0 0 0 0 1 0 0 0 4422 1145 40 4 4 DNAH8 6 38734582 Missense_Mutation SNP G C3N-02588_T 38734582 132071397 19 30123 EYS 0 . GRCh38 6 65332415 65332415 + Missense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1769G>T p.Arg590Ile p.R590I ENST00000393380 12/12 129 120 9 211 210 1 strelka-varscan-mutect EYS,missense_variant,p.Arg590Ile,ENST00000393380,NM_001142801.1;EYS,intron_variant,,ENST00000503581,NM_001142800.1;EYS,intron_variant,,ENST00000370621,NM_001292009.1;EYS,downstream_gene_variant,,ENST00000342421,NM_198283.1; A ENST00000393380 Transcript missense_variant,splice_region_variant 2307/5450 1769/1860 590/619 R/I aGa/aTa 1 -1 EYS HGNC HGNC:21555 protein_coding CCDS47446.1 ENSP00000377042 Q5T1H1 UPI00001D812F NM_001142801.1 tolerated_low_confidence(0.41) 12/12 MODERATE SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 65332415 65332415 C A 1 0 0 0 0 1 0 0 0 5200 927 32 2 2 EYS 6 65332415 Missense_Mutation SNP C C3N-02588_T 26597833 65332415 105473564 20 30124 SCAF8 0 . GRCh38 6 154802024 154802024 + Silent SNP C C T novel C3N-02588_T C3N-02588_N C C c.894C>T p.= p.S298S ENST00000417268 8/21 337 257 80 148 148 0 strelka-varscan-mutect SCAF8,synonymous_variant,p.=,ENST00000367178,NM_001286199.1,NM_014892.4;SCAF8,synonymous_variant,p.=,ENST00000417268,NM_001286188.1,NM_001286194.1;SCAF8,synonymous_variant,p.=,ENST00000367186,NM_001286189.1; T ENST00000417268 Transcript synonymous_variant 939/4944 894/4050 298/1349 S tcC/tcT 1 1 SCAF8 HGNC HGNC:20959 protein_coding YES CCDS75541.1 ENSP00000413098 A0A0A0MT33 UPI0003BD245C NM_001286188.1,NM_001286194.1 8/21 Low_complexity_(Seg):seg LOW 1 SNV 2 1 PASS rs1309831606 . 0 207 0 3 0 0 0 0 -20 0.9999975 1 1 1 0 T 2 4 107 154802024 154802024 C T 1 0 0 0 0 0 0 0 1 14135 581 21 3 3 SCAF8 6 154802024 Silent SNP C C3N-02588_T 89469609 154802024 16003955 21 30125 SERAC1 0 . GRCh38 6 158113470 158113470 + Missense_Mutation SNP C C T C3N-02588_T C3N-02588_N C C c.1807G>A p.Val603Met p.V603M ENST00000367104 16/17 148 102 46 93 93 0 strelka-varscan-mutect SERAC1,missense_variant,p.Val603Met,ENST00000367104,NM_032861.3;SERAC1,downstream_gene_variant,,ENST00000367101,;SERAC1,downstream_gene_variant,,ENST00000435180,;SERAC1,3_prime_UTR_variant,,ENST00000607742,;SERAC1,3_prime_UTR_variant,,ENST00000607071,;SERAC1,downstream_gene_variant,,ENST00000606965,; T ENST00000367104 Transcript missense_variant 1939/3948 1807/1965 603/654 V/M Gtg/Atg COSM4160325 1 -1 SERAC1 HGNC HGNC:21061 protein_coding YES CCDS5255.1 ENSP00000356071 Q96JX3 UPI0000070959 NM_032861.3 deleterious(0) 16/17 hmmpanther:PTHR22731,Superfamily_domains:SSF53474 1 MODERATE 1 SNV 1 1 1 PASS rs1033568259 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 158113470 158113470 C T 1 0 0 0 0 1 0 0 0 14349 478 17 3 3 SERAC1 6 158113470 Missense_Mutation SNP C C3N-02588_T 3311446 158113470 12692509 22 30126 GRID2IP 0 . GRCh38 7 6520735 6520735 + Missense_Mutation SNP G G A novel C3N-02588_T C3N-02588_N G G c.1111C>T p.Pro371Ser p.P371S ENST00000457091 7/22 183 154 29 86 86 0 strelka-varscan-mutect GRID2IP,missense_variant,p.Pro371Ser,ENST00000457091,NM_001145118.1;GRID2IP,missense_variant,p.Pro181Ser,ENST00000452113,;GRID2IP,missense_variant,p.Pro188Ser,ENST00000435185,; A ENST00000457091 Transcript missense_variant 1111/3636 1111/3636 371/1211 P/S Ccg/Tcg 1 -1 GRID2IP HGNC HGNC:18464 protein_coding YES CCDS47537.1 ENSP00000397351 A4D2P6 UPI0001722D0B NM_001145118.1 tolerated(0.51) 7/22 hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF242,Low_complexity_(Seg):seg MODERATE 1 SNV 5 1 PASS rs977409588 . 0 205 5 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 6520735 6520735 G A 1 0 0 0 0 1 0 0 0 6653 1232 43 3 3 GRID2IP 7 6520735 Missense_Mutation SNP G C3N-02588_T 6520735 152825238 23 30127 MET 0 . GRCh38 7 116731716 116731716 + Nonsense_Mutation SNP C C T rs369705803 C3N-02588_T C3N-02588_N C C c.1249C>T p.Arg417Ter p.R417* ENST00000318493 3/21 431 357 74 264 264 0 strelka-varscan-mutect MET,stop_gained,p.Arg417Ter,ENST00000397752,NM_000245.2;MET,stop_gained,p.Arg417Ter,ENST00000318493,NM_001127500.1;MET,stop_gained,p.Arg417Ter,ENST00000436117,;MET,non_coding_transcript_exon_variant,,ENST00000495962,; T ENST00000318493 Transcript stop_gained 1436/4632 1249/4227 417/1408 R/* Cga/Tga rs369705803,COSM3632204 1 1 MET HGNC HGNC:7029 protein_coding YES CCDS47689.1 ENSP00000317272 P08581 A0A024R728 UPI000014033E NM_001127500.1 3/21 PROSITE_profiles:PS51004,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF332,Pfam_domain:PF01403,PIRSF_domain:PIRSF000617,Gene3D:2.130.10.10,SMART_domains:SM00630,Superfamily_domains:SSF101912 0,1 HIGH 1 SNV 1 0,1 1 PASS rs369705803 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 107 116731716 116731716 C T 1 0 0 0 0 0 1 0 0 9430 876 31 1 1 MET 7 116731716 Nonsense_Mutation SNP C C3N-02588_T 110210981 116731716 42614257 24 30128 PRKDC 0 . GRCh38 8 47782494 47782494 + Silent SNP C C T novel C3N-02588_T C3N-02588_N C C c.11280G>A p.= p.Q3760Q ENST00000314191 79/86 621 573 48 276 276 0 strelka-varscan-mutect PRKDC,synonymous_variant,p.=,ENST00000314191,NM_006904.6;PRKDC,synonymous_variant,p.=,ENST00000338368,NM_001081640.1;PRKDC,upstream_gene_variant,,ENST00000536429,;PRKDC,non_coding_transcript_exon_variant,,ENST00000521331,;PRKDC,non_coding_transcript_exon_variant,,ENST00000432581,;PRKDC,upstream_gene_variant,,ENST00000536483,;PRKDC,upstream_gene_variant,,ENST00000536710,; T ENST00000314191 Transcript synonymous_variant 11337/13509 11280/12387 3760/4128 Q caG/caA 1 -1 PRKDC HGNC HGNC:9413 protein_coding YES CCDS75735.1 ENSP00000313420 P78527 UPI0000013593 NM_006904.6 79/86 PROSITE_profiles:PS50290,hmmpanther:PTHR11139,hmmpanther:PTHR11139:SF68,PROSITE_patterns:PS00915,Pfam_domain:PF00454,Gene3D:3.30.1010.10,SMART_domains:SM00146,Superfamily_domains:SSF56112 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 107 47782494 47782494 C T 1 0 0 0 0 0 0 0 1 12654 680 24 3 3 PRKDC 8 47782494 Silent SNP C C3N-02588_T 47782494 97356142 25 30129 AGO2 0 . GRCh38 8 140551368 140551368 + Silent SNP G G T rs142051728 C3N-02588_T C3N-02588_N G G c.1338C>A p.= p.I446I ENST00000220592 11/19 116 106 10 47 47 0 strelka-mutect AGO2,synonymous_variant,p.=,ENST00000220592,NM_012154.3;AGO2,synonymous_variant,p.=,ENST00000519980,NM_001164623.1;AGO2,3_prime_UTR_variant,,ENST00000523609,;AGO2,downstream_gene_variant,,ENST00000521325,; T ENST00000220592 Transcript synonymous_variant 1451/14581 1338/2580 446/859 I atC/atA rs142051728 1 -1 AGO2 HGNC HGNC:3263 protein_coding YES CCDS6380.1 ENSP00000220592 Q9UKV8 UPI0000168652 NM_012154.3 11/19 HAMAP:MF_03031,hmmpanther:PTHR22891:SF17,hmmpanther:PTHR22891,Gene3D:3.40.50.2300,Pfam_domain:PF16487 LOW 1 SNV 2 1 PASS rs142051728 . 0 206 3 0 0 0 0 0 -19.6727 1 1 1 1 0 T 2 4 107 140551368 140551368 G T 1 0 0 0 0 0 0 0 1 465 1048 37 1 1 AGO2 8 140551368 Silent SNP G C3N-02588_T 92768874 140551368 4587268 26 30130 CCDC171 0 . GRCh38 9 15678768 15678768 + Nonsense_Mutation SNP G G T novel C3N-02588_T C3N-02588_N G G c.1087G>T p.Glu363Ter p.E363* ENST00000380701 10/26 81 47 34 109 109 0 strelka-varscan-mutect CCDC171,stop_gained,p.Glu363Ter,ENST00000380701,NM_173550.2; T ENST00000380701 Transcript stop_gained 1415/6512 1087/3981 363/1326 E/* Gag/Tag 1 1 CCDC171 HGNC HGNC:29828 protein_coding YES CCDS6481.1 ENSP00000370077 Q6TFL3 UPI000021C44B NM_173550.2 10/26 Coiled-coils_(Ncoils):Coil,hmmpanther:PTHR13140,hmmpanther:PTHR13140:SF388 HIGH 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 107 15678768 15678768 G T 1 0 0 0 0 0 1 0 0 2488 943 33 2 2 CCDC171 9 15678768 Nonsense_Mutation SNP G C3N-02588_T 15678768 122715949 27 30131 STIM1 0 . GRCh38 11 4023911 4023911 + Silent SNP G G A novel C3N-02588_T C3N-02588_N G G c.309G>A p.= p.V103V ENST00000616714 3/12 647 502 145 389 389 0 strelka-varscan-mutect STIM1,synonymous_variant,p.=,ENST00000616714,NM_001277961.1;STIM1,synonymous_variant,p.=,ENST00000300737,NM_003156.3;STIM1,synonymous_variant,p.=,ENST00000527651,NM_001277962.1;STIM1,synonymous_variant,p.=,ENST00000532990,;STIM1,synonymous_variant,p.=,ENST00000525403,;STIM1,synonymous_variant,p.=,ENST00000525055,;STIM1,synonymous_variant,p.=,ENST00000528656,;STIM1,synonymous_variant,p.=,ENST00000532919,;STIM1,synonymous_variant,p.=,ENST00000530554,;STIM1,synonymous_variant,p.=,ENST00000532610,;STIM1,synonymous_variant,p.=,ENST00000524822,;STIM1,non_coding_transcript_exon_variant,,ENST00000527484,;STIM1,non_coding_transcript_exon_variant,,ENST00000526771,;RPS29P20,downstream_gene_variant,,ENST00000489592,; A ENST00000616714 Transcript synonymous_variant 877/4356 309/2376 103/791 V gtG/gtA 1 1 STIM1 HGNC HGNC:11386 protein_coding YES CCDS73247.1 ENSP00000478059 G0XQ39 UPI000217FCDA NM_001277961.1 3/12 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF9 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 107 4023911 4023911 G A 1 0 0 0 0 0 0 0 1 15660 1277 45 3 3 STIM1 11 4023911 Silent SNP G C3N-02588_T 4023911 131062711 28 30132 1 32 3 3 74 G 8.640396e-09 STIM1 0 . GRCh38 11 4023941 4023941 + Missense_Mutation SNP G G C rs777644508 C3N-02588_T C3N-02588_N G G c.339G>C p.Lys113Asn p.K113N ENST00000616714 3/12 661 523 138 430 429 1 strelka-varscan-mutect STIM1,missense_variant,p.Lys113Asn,ENST00000616714,NM_001277961.1;STIM1,missense_variant,p.Lys113Asn,ENST00000300737,NM_003156.3;STIM1,missense_variant,p.Lys113Asn,ENST00000527651,NM_001277962.1;STIM1,missense_variant,p.Lys39Asn,ENST00000532990,;STIM1,missense_variant,p.Lys39Asn,ENST00000525403,;STIM1,missense_variant,p.Lys39Asn,ENST00000525055,;STIM1,missense_variant,p.Lys39Asn,ENST00000528656,;STIM1,missense_variant,p.Lys39Asn,ENST00000532919,;STIM1,missense_variant,p.Lys39Asn,ENST00000530554,;STIM1,missense_variant,p.Lys39Asn,ENST00000532610,;STIM1,missense_variant,p.Lys39Asn,ENST00000524822,;STIM1,non_coding_transcript_exon_variant,,ENST00000527484,;STIM1,non_coding_transcript_exon_variant,,ENST00000526771,;RPS29P20,downstream_gene_variant,,ENST00000489592,; C ENST00000616714 Transcript missense_variant 907/4356 339/2376 113/791 K/N aaG/aaC rs777644508 1 1 STIM1 HGNC HGNC:11386 protein_coding YES CCDS73247.1 ENSP00000478059 G0XQ39 UPI000217FCDA NM_001277961.1 tolerated(0.09) 3/12 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF9 MODERATE 1 SNV 1 1 PASS rs777644508 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 4023941 4023941 G C 1 0 0 0 0 1 0 0 0 15660 962 34 4 4 STIM1 11 4023941 Missense_Mutation SNP G C3N-02588_T 30 4023941 131062681 29 30133 1 32 3 3 74 G 8.640396e-09 STIM1 0 . GRCh38 11 4023984 4023984 + Missense_Mutation SNP G G C novel C3N-02588_T C3N-02588_N G G c.382G>C p.Glu128Gln p.E128Q ENST00000616714 3/12 647 511 136 467 467 0 strelka-varscan-mutect STIM1,missense_variant,p.Glu128Gln,ENST00000616714,NM_001277961.1;STIM1,missense_variant,p.Glu128Gln,ENST00000300737,NM_003156.3;STIM1,missense_variant,p.Glu128Gln,ENST00000527651,NM_001277962.1;STIM1,missense_variant,p.Glu54Gln,ENST00000532990,;STIM1,missense_variant,p.Glu54Gln,ENST00000525403,;STIM1,missense_variant,p.Glu54Gln,ENST00000525055,;STIM1,missense_variant,p.Glu54Gln,ENST00000528656,;STIM1,missense_variant,p.Glu54Gln,ENST00000532919,;STIM1,missense_variant,p.Glu54Gln,ENST00000530554,;STIM1,missense_variant,p.Glu54Gln,ENST00000532610,;STIM1,missense_variant,p.Glu54Gln,ENST00000524822,;STIM1,non_coding_transcript_exon_variant,,ENST00000527484,;STIM1,non_coding_transcript_exon_variant,,ENST00000526771,;RPS29P20,downstream_gene_variant,,ENST00000489592,; C ENST00000616714 Transcript missense_variant 950/4356 382/2376 128/791 E/Q Gaa/Caa 1 1 STIM1 HGNC HGNC:11386 protein_coding YES CCDS73247.1 ENSP00000478059 G0XQ39 UPI000217FCDA NM_001277961.1 deleterious(0.03) 3/12 hmmpanther:PTHR15136,hmmpanther:PTHR15136:SF9,Gene3D:1.10.150.50,Superfamily_domains:SSF47769 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 4023984 4023984 G C 1 0 0 0 0 1 0 0 0 15660 956 33 4 4 STIM1 11 4023984 Missense_Mutation SNP G C3N-02588_T 43 4023984 131062638 30 30134 1 32 3 3 74 G 8.640396e-09 MRVI1 0 . GRCh38 11 10604415 10604415 + Missense_Mutation SNP G G A novel C3N-02588_T C3N-02588_N G G c.1733C>T p.Ala578Val p.A578V ENST00000423302 13/21 225 201 24 119 119 0 varscan-mutect MRVI1,missense_variant,p.Ala263Val,ENST00000547195,NM_001206881.1;MRVI1,missense_variant,p.Ala578Val,ENST00000423302,NM_130385.3;MRVI1,missense_variant,p.Ala263Val,ENST00000424001,;MRVI1,missense_variant,p.Ala263Val,ENST00000558540,NM_001100167.2;MRVI1,missense_variant,p.Ala570Val,ENST00000531107,NM_001098579.2;MRVI1,missense_variant,p.Ala263Val,ENST00000534266,;MRVI1,missense_variant,p.Ala487Val,ENST00000527509,NM_001100163.2;MRVI1,missense_variant,p.Ala372Val,ENST00000541483,NM_001206880.1;MRVI1-AS1,downstream_gene_variant,,ENST00000525578,;MRVI1-AS1,downstream_gene_variant,,ENST00000529979,;MRVI1-AS1,downstream_gene_variant,,ENST00000529829,;LYVE1,intron_variant,,ENST00000531706,;MRVI1,missense_variant,p.Ala321Val,ENST00000526414,;MRVI1,3_prime_UTR_variant,,ENST00000529448,; A ENST00000423302 Transcript missense_variant 1883/6126 1733/2739 578/912 A/V gCt/gTt 1 -1 MRVI1 HGNC HGNC:7237 protein_coding YES CCDS55746.1 ENSP00000412130 Q9Y6F6 UPI0001F78343 NM_130385.3 tolerated(0.05) 13/21 Pfam_domain:PF05781,hmmpanther:PTHR15352,hmmpanther:PTHR15352:SF2 MODERATE 1 SNV 2 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 10604415 10604415 G A 1 0 0 0 0 1 0 0 0 9830 971 34 3 3 MRVI1 11 10604415 Missense_Mutation SNP G C3N-02588_T 6580431 10604415 124482207 31 30135 AHNAK 0 . GRCh38 11 62529364 62529364 + Missense_Mutation SNP G G A novel C3N-02588_T C3N-02588_N G G c.5053C>T p.Pro1685Ser p.P1685S ENST00000378024 5/5 764 639 125 432 432 0 strelka-varscan-mutect AHNAK,missense_variant,p.Pro1685Ser,ENST00000378024,NM_001620.2;AHNAK,intron_variant,,ENST00000257247,NM_024060.3;AHNAK,intron_variant,,ENST00000530124,;AHNAK,intron_variant,,ENST00000533365,;AHNAK,downstream_gene_variant,,ENST00000530285,;AHNAK,downstream_gene_variant,,ENST00000528508,; A ENST00000378024 Transcript missense_variant 5328/18787 5053/17673 1685/5890 P/S Cca/Tca 1 -1 AHNAK HGNC HGNC:347 protein_coding YES CCDS31584.1 ENSP00000367263 Q09666 UPI00004EC29C NM_001620.2 deleterious(0.02) 5/5 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 62529364 62529364 G A 1 0 0 0 0 1 0 0 0 491 1203 42 3 3 AHNAK 11 62529364 Missense_Mutation SNP G C3N-02588_T 51924949 62529364 72557258 32 30136 MMP12 0 . GRCh38 11 102872932 102872945 + Frame_Shift_Del DEL GGACTCCACATCGA GGACTCCACATCGA - novel C3N-02588_T C3N-02588_N GGACTCCACATCGA GGACTCCACATCGA c.270_283delTCGATGTGGAGTCC p.Gly93ProfsTer23 p.G93Pfs*23 ENST00000571244 2/10 677 580 97 366 366 0 sindel-varindel-pindel MMP12,frameshift_variant,p.Gly93ProfsTer23,ENST00000571244,NM_002426.4; - ENST00000571244 Transcript frameshift_variant 367-380/1874 270-283/1413 90-95/470 PRCGVP/PX ccTCGATGTGGAGTCCcc/cccc 1 -1 MMP12 HGNC HGNC:7158 protein_coding YES CCDS73375.1 ENSP00000458585 P39900 UPI00000422BE NM_002426.4 2/10 Gene3D:3.40.390.10,PIRSF_domain:PIRSF001191,Prints_domain:PR00138,PROSITE_patterns:PS00546,hmmpanther:PTHR10201,hmmpanther:PTHR10201:SF32,Superfamily_domains:SSF47090 HIGH 1 deletion 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 - 7 5 107 102872932 102872932 GGACTCCACATCGA - 1 0 1 0 1 0 0 0 0 9614 1232 43 0 0 MMP12 11 102872932 Frame_Shift_Del DEL GGACTCCACATCGA C3N-02588_T 40343568 102872932 32213690 33 30137 NFRKB 0 . GRCh38 11 129865902 129865902 + Missense_Mutation SNP T T C rs371917436 C3N-02588_T C3N-02588_N T T c.3688A>G p.Ile1230Val p.I1230V ENST00000524794 23/25 386 304 82 139 138 1 strelka-varscan-mutect NFRKB,missense_variant,p.Ile1205Val,ENST00000446488,NM_001143835.1;NFRKB,missense_variant,p.Ile1230Val,ENST00000524794,NM_006165.3;NFRKB,missense_variant,p.Ile1205Val,ENST00000524746,;NFRKB,downstream_gene_variant,,ENST00000531755,; C ENST00000524794 Transcript missense_variant 3809/4351 3688/3975 1230/1324 I/V Atc/Gtc rs371917436 1 -1 NFRKB HGNC HGNC:7802 protein_coding YES CCDS8483.1 ENSP00000436926 Q6P4R8 UPI000006E542 NM_006165.3 deleterious_low_confidence(0) 23/25 MODERATE 1 SNV 1 1 PASS rs371917436 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 129865902 129865902 T C 1 0 0 0 0 1 0 0 0 10420 1464 51 5 5 NFRKB 11 129865902 Missense_Mutation SNP T C3N-02588_T 26992970 129865902 5220720 34 30138 INF2 0 . GRCh38 14 104708434 104708435 + Splice_Site DEL AG AG - novel C3N-02588_T C3N-02588_N AG AG c.1736_1737delAG p.Glu579AlafsTer70 p.X579_splice ENST00000392634 166 131 35 99 99 0 sindel-varindel-pindel INF2,splice_acceptor_variant,p.Glu579AlafsTer70,ENST00000330634,NM_001031714.3;INF2,splice_acceptor_variant,p.Glu579AlafsTer70,ENST00000392634,NM_022489.3;INF2,splice_acceptor_variant,p.Glu47AlafsTer70,ENST00000252527,;INF2,splice_acceptor_variant,,ENST00000617571,;INF2,downstream_gene_variant,,ENST00000398337,NM_032714.2;INF2,non_coding_transcript_exon_variant,,ENST00000474229,;INF2,upstream_gene_variant,,ENST00000480763,;INF2,upstream_gene_variant,,ENST00000477497,; - ENST00000392634 Transcript splice_acceptor_variant -/4672 1736/3750 579/1249 1 1 INF2 HGNC HGNC:23791 protein_coding YES CCDS9989.2 ENSP00000376410 Q27J81 UPI000156D0FB NM_022489.3 8/22 HIGH 1 deletion 5 2 1 PASS . . 0 202 7 0 0 0 0 0 -20 0.9999998 1 1 1 0 - 8 5 107 104708434 104708434 AG - 1 0 1 0 1 0 0 1 0 7636 202 7 0 0 INF2 14 104708434 Splice_Site DEL AG C3N-02588_T 104708434 2335284 35 30139 INF2 0 . GRCh38 14 104709679 104709679 + Missense_Mutation SNP C C G novel C3N-02588_T C3N-02588_N C C c.2112C>G p.Phe704Leu p.F704L ENST00000392634 12/23 398 319 79 169 169 0 strelka-varscan-mutect INF2,missense_variant,p.Phe704Leu,ENST00000330634,NM_001031714.3;INF2,missense_variant,p.Phe704Leu,ENST00000392634,NM_022489.3;INF2,missense_variant,p.Phe172Leu,ENST00000252527,;INF2,5_prime_UTR_variant,,ENST00000617571,;INF2,downstream_gene_variant,,ENST00000398337,NM_032714.2;INF2,non_coding_transcript_exon_variant,,ENST00000474229,;INF2,upstream_gene_variant,,ENST00000480763,;INF2,upstream_gene_variant,,ENST00000477497,; G ENST00000392634 Transcript missense_variant 2224/4672 2112/3750 704/1249 F/L ttC/ttG 1 1 INF2 HGNC HGNC:23791 protein_coding YES CCDS9989.2 ENSP00000376410 Q27J81 UPI000156D0FB NM_022489.3 deleterious(0.01) 12/23 PROSITE_profiles:PS51444,hmmpanther:PTHR23213,hmmpanther:PTHR23213:SF5,Pfam_domain:PF02181,SMART_domains:SM00498,Superfamily_domains:SSF101447 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 107 104709679 104709679 C G 1 0 0 0 0 1 0 0 0 7636 912 32 4 4 INF2 14 104709679 Missense_Mutation SNP C C3N-02588_T 1245 104709679 2334039 36 30140 NTN3 0 . GRCh38 16 2471990 2471990 + Missense_Mutation SNP T T A novel C3N-02588_T C3N-02588_N T T c.289T>A p.Ser97Thr p.S97T ENST00000293973 1/6 195 175 20 79 79 0 strelka-varscan-mutect NTN3,missense_variant,p.Ser97Thr,ENST00000293973,NM_006181.2;TBC1D24,upstream_gene_variant,,ENST00000567020,NM_020705.2;TBC1D24,upstream_gene_variant,,ENST00000293970,NM_001199107.1;RP11-715J22.6,upstream_gene_variant,,ENST00000561847,;RP11-715J22.2,upstream_gene_variant,,ENST00000563775,;TBC1D24,upstream_gene_variant,,ENST00000630263,;TBC1D24,upstream_gene_variant,,ENST00000569874,; A ENST00000293973 Transcript missense_variant 492/1986 289/1743 97/580 S/T Tcc/Acc 1 1 NTN3 HGNC HGNC:8030 protein_coding YES CCDS10469.1 ENSP00000293973 O00634 UPI000006ED30 NM_006181.2 tolerated(0.75) 1/6 PROSITE_profiles:PS51117,hmmpanther:PTHR10574,hmmpanther:PTHR10574:SF292,Pfam_domain:PF00055,SMART_domains:SM00136 MODERATE 1 SNV 1 1 PASS . . 0 201 6 3 0 0 0 0 -20 0.9990628 1 1 1 0 A 3 1 107 2471990 2471990 T A 1 0 0 0 0 1 0 0 0 10766 1667 58 4 4 NTN3 16 2471990 Missense_Mutation SNP T C3N-02588_T 2471990 87866355 37 30141 IL32 0 . GRCh38 16 3069048 3069048 + Missense_Mutation SNP C C T rs768089141 C3N-02588_T C3N-02588_N C C c.398C>T p.Ser133Phe p.S133F ENST00000534507 6/6 222 200 22 134 134 0 varscan-mutect IL32,missense_variant,p.Ser87Phe,ENST00000525643,;IL32,missense_variant,p.Ser87Phe,ENST00000526464,;IL32,missense_variant,p.Ser133Phe,ENST00000534507,;IL32,missense_variant,p.Ser87Phe,ENST00000325568,NM_001012718.1,NM_004221.4;IL32,missense_variant,p.Ser133Phe,ENST00000396890,;IL32,missense_variant,p.Ser67Phe,ENST00000008180,NM_001012634.1;IL32,missense_variant,p.Ser67Phe,ENST00000613483,;IL32,missense_variant,p.Ser133Phe,ENST00000548476,;IL32,missense_variant,p.Ser87Phe,ENST00000528163,NM_001012631.1;IL32,missense_variant,p.Ser87Phe,ENST00000440815,;IL32,missense_variant,p.Ser87Phe,ENST00000444393,;IL32,missense_variant,p.Ser78Phe,ENST00000382213,NM_001012636.1;IL32,missense_variant,p.Ser87Phe,ENST00000533097,;IL32,missense_variant,p.Ser78Phe,ENST00000548652,;IL32,missense_variant,p.Ser133Phe,ENST00000548807,;IL32,missense_variant,p.Ser124Phe,ENST00000551513,;IL32,missense_variant,p.Ser87Phe,ENST00000396887,NM_001012633.1;IL32,missense_variant,p.Ser67Phe,ENST00000530890,NM_001012635.1;IL32,missense_variant,p.Ser87Phe,ENST00000529550,;IL32,missense_variant,p.Ser77Phe,ENST00000531965,;IL32,missense_variant,p.Ser87Phe,ENST00000551122,;IL32,missense_variant,p.Ser87Phe,ENST00000552664,NM_001012632.1;IL32,missense_variant,p.Ser111Phe,ENST00000552936,;IL32,missense_variant,p.Ser87Phe,ENST00000530538,;IL32,missense_variant,p.Ser67Phe,ENST00000529699,;IL32,missense_variant,p.Ser87Phe,ENST00000549213,;IL32,missense_variant,p.Ser67Phe,ENST00000552356,;IL32,missense_variant,p.Ser58Phe,ENST00000525228,;IL32,missense_variant,p.Ser47Phe,ENST00000548246,;IL32,intron_variant,,ENST00000525377,;RNU1-125P,upstream_gene_variant,,ENST00000516752,;IL32,non_coding_transcript_exon_variant,,ENST00000525003,;IL32,non_coding_transcript_exon_variant,,ENST00000528652,;IL32,downstream_gene_variant,,ENST00000532247,;IL32,downstream_gene_variant,,ENST00000532086,;IL32,downstream_gene_variant,,ENST00000534748,; T ENST00000534507 Transcript missense_variant 609/1112 398/705 133/234 S/F tCc/tTc rs768089141,COSM3888434 1 1 IL32 HGNC HGNC:16830 protein_coding YES CCDS76811.1 ENSP00000431775 P24001 UPI0000070836 tolerated(0.08) 6/6 Pfam_domain:PF15225 0,1 MODERATE 1 SNV 2 0,1 1 PASS rs768089141 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 3069048 3069048 C T 1 0 0 0 0 1 0 0 0 7591 855 30 3 3 IL32 16 3069048 Missense_Mutation SNP C C3N-02588_T 597058 3069048 87269297 38 30142 GDE1 0 . GRCh38 16 19503513 19503513 + Missense_Mutation SNP T T C C3N-02588_T C3N-02588_N T T c.953A>G p.Tyr318Cys p.Y318C ENST00000353258 6/6 296 253 43 136 136 0 strelka-varscan-mutect GDE1,missense_variant,p.Tyr318Cys,ENST00000353258,NM_001324066.1,NM_016641.3;TMC5,downstream_gene_variant,,ENST00000396229,NM_001105248.1;TMC5,downstream_gene_variant,,ENST00000542583,NM_001261841.1;TMC5,downstream_gene_variant,,ENST00000381414,NM_001105249.1;TMC5,downstream_gene_variant,,ENST00000219821,NM_024780.4;GDE1,downstream_gene_variant,,ENST00000569899,;GDE1,downstream_gene_variant,,ENST00000569773,;RNU4-46P,downstream_gene_variant,,ENST00000410818,;CTA-363E6.7,downstream_gene_variant,,ENST00000569345,;CTA-363E6.8,upstream_gene_variant,,ENST00000623745,;GDE1,3_prime_UTR_variant,,ENST00000564172,;GDE1,non_coding_transcript_exon_variant,,ENST00000563645,; C ENST00000353258 Transcript missense_variant 1134/2958 953/996 318/331 Y/C tAt/tGt COSM1518482 1 -1 GDE1 HGNC HGNC:29644 protein_coding YES CCDS10578.1 ENSP00000261386 Q9NZC3 UPI000003776E NM_001324066.1,NM_016641.3 deleterious(0) 6/6 Gene3D:3.20.20.190,PROSITE_profiles:PS51704,hmmpanther:PTHR23344,hmmpanther:PTHR23344:SF28 1 MODERATE 1 SNV 1 1 1 PASS rs1436465969 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 19503513 19503513 T C 1 0 0 0 0 1 0 0 0 6182 1406 49 5 5 GDE1 16 19503513 Missense_Mutation SNP T C3N-02588_T 16434465 19503513 70834832 39 30143 PRSS36 0 . GRCh38 16 31143776 31143776 + Missense_Mutation SNP G G C novel C3N-02588_T C3N-02588_N G G c.782C>G p.Thr261Ser p.T261S ENST00000268281 7/15 831 684 147 348 348 0 strelka-varscan-mutect PRSS36,missense_variant,p.Thr261Ser,ENST00000268281,NM_173502.4;PRSS36,missense_variant,p.Thr261Ser,ENST00000569305,NM_001258290.1;PRSS36,missense_variant,p.Thr261Ser,ENST00000418068,NM_001258291.1;PRSS36,non_coding_transcript_exon_variant,,ENST00000562368,;PRSS36,upstream_gene_variant,,ENST00000563693,;PRSS36,downstream_gene_variant,,ENST00000569614,;PRSS36,upstream_gene_variant,,ENST00000571878,; C ENST00000268281 Transcript missense_variant 841/2840 782/2568 261/855 T/S aCc/aGc 1 -1 PRSS36 HGNC HGNC:26906 protein_coding YES CCDS32436.1 ENSP00000268281 Q5K4E3 UPI00001FFF6A NM_173502.4 deleterious(0.01) 7/15 PROSITE_profiles:PS50240,hmmpanther:PTHR24276,hmmpanther:PTHR24276:SF62,PIRSF_domain:PIRSF037933,Pfam_domain:PF00089,Gene3D:2.40.10.10,SMART_domains:SM00020,Superfamily_domains:SSF50494 MODERATE 1 SNV 1 1 PASS rs746814248 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 31143776 31143776 G C 1 0 0 0 0 1 0 0 0 12772 1261 44 4 4 PRSS36 16 31143776 Missense_Mutation SNP G C3N-02588_T 11640263 31143776 59194569 40 30144 CCDC102A 0 . GRCh38 16 57528592 57528592 + Splice_Site SNP C C A novel C3N-02588_T C3N-02588_N C C c.585+1G>T p.X195_splice ENST00000258214 87 63 24 34 34 0 strelka-varscan-mutect CCDC102A,splice_donor_variant,,ENST00000258214,NM_033212.3; A ENST00000258214 Transcript splice_donor_variant -/2463 585/1653 195/550 1 -1 CCDC102A HGNC HGNC:28097 protein_coding YES CCDS10784.1 ENSP00000258214 Q96A19 UPI000013CFBA NM_033212.3 2/8 HIGH 1 SNV 1 1 PASS . . 0 206 4 0 0 0 0 0 -20 1 1 1 1 0 A 5 1 107 57528592 57528592 C A 1 0 0 0 0 0 0 1 0 2434 521 18 2 2 CCDC102A 16 57528592 Splice_Site SNP C C3N-02588_T 26384816 57528592 32809753 41 30145 CHTF8 0 . GRCh38 16 69120144 69120144 + Nonsense_Mutation SNP C C T novel C3N-02588_T C3N-02588_N C C c.206G>A p.Trp69Ter p.W69* ENST00000523421 4/5 185 129 56 113 113 0 strelka-varscan-mutect CHTF8,stop_gained,p.Trp69Ter,ENST00000523421,;CHTF8,missense_variant,p.Met95Ile,ENST00000306585,;CHTF8,3_prime_UTR_variant,,ENST00000448552,NM_001039690.3;CHTF8,3_prime_UTR_variant,,ENST00000398235,NM_001040146.3;CHTF8,3_prime_UTR_variant,,ENST00000519520,;CHTF8,3_prime_UTR_variant,,ENST00000522497,;CHTF8,3_prime_UTR_variant,,ENST00000567763,;CHTF8,intron_variant,,ENST00000518041,;HAS3,downstream_gene_variant,,ENST00000306560,NM_005329.2;HAS3,downstream_gene_variant,,ENST00000569188,NM_001199280.1;HAS3,downstream_gene_variant,,ENST00000219322,NM_138612.2;CHTF8,downstream_gene_variant,,ENST00000522091,;CHTF8,downstream_gene_variant,,ENST00000520529,;CHTF8,3_prime_UTR_variant,,ENST00000519534,; T ENST00000523421 Transcript stop_gained 325/766 206/228 69/75 W/* tGg/tAg 1 -1 CHTF8 HGNC HGNC:24353 protein_coding ENSP00000430899 E5RHL4 UPI0000489694 4/5 HIGH SNV 3 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 T 4 4 107 69120144 69120144 C T 1 0 0 0 0 0 1 0 0 3175 595 21 3 3 CHTF8 16 69120144 Nonsense_Mutation SNP C C3N-02588_T 11591552 69120144 21218201 42 30146 TP53 0 . GRCh38 17 7674872 7674872 + Missense_Mutation SNP T T C rs121912666 C3N-02588_T C3N-02588_N T T c.659A>G p.Tyr220Cys p.Y220C ENST00000269305 6/11 806 615 191 383 383 0 strelka-varscan-mutect TP53,missense_variant,p.Tyr220Cys,ENST00000617185,NM_001126114.2;TP53,missense_variant,p.Tyr220Cys,ENST00000420246,;TP53,missense_variant,p.Tyr181Cys,ENST00000622645,NM_001276696.1;TP53,missense_variant,p.Tyr181Cys,ENST00000610292,NM_001126118.1;TP53,missense_variant,p.Tyr220Cys,ENST00000455263,NM_001126113.2;TP53,missense_variant,p.Tyr181Cys,ENST00000610538,NM_001276695.1;TP53,missense_variant,p.Tyr220Cys,ENST00000269305,NM_001126112.2,NM_000546.5;TP53,missense_variant,p.Tyr181Cys,ENST00000620739,NM_001276760.1,NM_001276761.1;TP53,missense_variant,p.Tyr220Cys,ENST00000445888,;TP53,missense_variant,p.Tyr181Cys,ENST00000619485,;TP53,missense_variant,p.Tyr88Cys,ENST00000510385,NM_001126116.1;TP53,missense_variant,p.Tyr61Cys,ENST00000618944,NM_001276698.1;TP53,missense_variant,p.Tyr88Cys,ENST00000504290,NM_001126117.1;TP53,missense_variant,p.Tyr61Cys,ENST00000610623,NM_001276699.1;TP53,missense_variant,p.Tyr88Cys,ENST00000504937,NM_001126115.1;TP53,missense_variant,p.Tyr61Cys,ENST00000619186,NM_001276697.1;TP53,missense_variant,p.Tyr220Cys,ENST00000359597,;TP53,missense_variant,p.Tyr209Cys,ENST00000615910,;TP53,missense_variant,p.Tyr220Cys,ENST00000413465,;TP53,missense_variant,p.Tyr88Cys,ENST00000509690,;TP53,missense_variant,p.Tyr127Cys,ENST00000514944,;TP53,downstream_gene_variant,,ENST00000508793,;TP53,downstream_gene_variant,,ENST00000604348,;TP53,downstream_gene_variant,,ENST00000503591,;TP53,upstream_gene_variant,,ENST00000576024,;TP53,intron_variant,,ENST00000574684,;TP53,missense_variant,p.Tyr181Cys,ENST00000635293,;TP53,non_coding_transcript_exon_variant,,ENST00000505014,; C ENST00000269305 Transcript missense_variant 849/2579 659/1182 220/393 Y/C tAt/tGt rs121912666,CM015378,CM951227,TP53_g.12728A>T,TP53_g.12728A>C,TP53_g.12728A>G,COSM10758,COSM1644277,COSM251426,COSM251427,COSM251428,COSM3355993,COSM3675522,COSM3675523,COSM43850,COSM99718,COSM99719,COSM99720 1 -1 TP53 HGNC HGNC:11998 protein_coding YES CCDS11118.1 ENSP00000269305 P04637 K7PPA8 UPI000002ED67 NM_001126112.2,NM_000546.5 deleterious(0) 6/11 hmmpanther:PTHR11447,hmmpanther:PTHR11447:SF6,Gene3D:2.60.40.720,Pfam_domain:PF00870,Superfamily_domains:SSF49417,Prints_domain:PR00386 pathogenic 0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 25404506 MODERATE 1 SNV 1 1,1,1,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1 1 PASS rs121912666 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 7674872 7674872 T C 1 0 0 0 0 1 0 0 0 16859 1406 49 5 5 TP53 17 7674872 Missense_Mutation SNP T C3N-02588_T 7674872 75582569 43 30147 DNAH2 0 . GRCh38 17 7770844 7770844 + Missense_Mutation SNP G G T novel C3N-02588_T C3N-02588_N G G c.4273G>T p.Asp1425Tyr p.D1425Y ENST00000572933 27/86 447 346 101 262 262 0 strelka-varscan-mutect DNAH2,missense_variant,p.Asp1425Tyr,ENST00000572933,NM_020877.3;DNAH2,missense_variant,p.Asp1425Tyr,ENST00000389173,;DNAH2,3_prime_UTR_variant,,ENST00000574518,; T ENST00000572933 Transcript missense_variant 5733/14955 4273/13284 1425/4427 D/Y Gat/Tat 1 1 DNAH2 HGNC HGNC:2948 protein_coding YES CCDS32551.1 ENSP00000458355 Q9P225 UPI00005B2F0D NM_020877.3 deleterious(0.01) 27/86 hmmpanther:PTHR10676,hmmpanther:PTHR10676:SF183,Pfam_domain:PF08393 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 7770844 7770844 G T 1 0 0 0 0 1 0 0 0 4417 1174 41 2 2 DNAH2 17 7770844 Missense_Mutation SNP G C3N-02588_T 95972 7770844 75486597 44 30148 SLC4A1 0 . GRCh38 17 44260744 44260744 + Silent SNP G G T novel C3N-02588_T C3N-02588_N G G c.240C>A p.= p.R80R ENST00000262418 5/20 972 802 170 351 351 0 strelka-varscan-mutect SLC4A1,synonymous_variant,p.=,ENST00000262418,NM_000342.3;SLC4A1,synonymous_variant,p.=,ENST00000399246,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000471005,;SLC4A1,non_coding_transcript_exon_variant,,ENST00000497360,;SLC4A1,downstream_gene_variant,,ENST00000498270,; T ENST00000262418 Transcript synonymous_variant 396/4965 240/2736 80/911 R cgC/cgA 1 -1 SLC4A1 HGNC HGNC:11027 protein_coding YES CCDS11481.1 ENSP00000262418 P02730 UPI00000375B8 NM_000342.3 5/20 Gene3D:1hynR00,hmmpanther:PTHR11453,hmmpanther:PTHR11453:SF12,Superfamily_domains:SSF55804,TIGRFAM_domain:TIGR00834 LOW 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 107 44260744 44260744 G T 1 0 0 0 0 0 0 0 1 14927 958 34 2 2 SLC4A1 17 44260744 Silent SNP G C3N-02588_T 36489900 44260744 38996697 45 30149 MED13 0 . GRCh38 17 61955452 61955452 + Silent SNP A A G novel C3N-02588_T C3N-02588_N A A c.5898T>C p.= p.S1966S ENST00000397786 26/30 68 49 19 75 75 0 strelka-varscan-mutect MED13,synonymous_variant,p.=,ENST00000397786,NM_005121.2;MED13,non_coding_transcript_exon_variant,,ENST00000582786,; G ENST00000397786 Transcript synonymous_variant 5975/10465 5898/6525 1966/2174 S tcT/tcC 1 -1 MED13 HGNC HGNC:22474 protein_coding YES CCDS42366.1 ENSP00000380888 Q9UHV7 A0A024QZ75 UPI0000D7D6F6 NM_005121.2 26/30 hmmpanther:PTHR10791:SF51,hmmpanther:PTHR10791,Pfam_domain:PF06333 LOW 1 SNV 1 1 PASS . . 0 206 2 2 0 0 0 0 -20 0.9999995 1 1 1 0 G 2 3 107 61955452 61955452 A G 1 0 0 0 0 0 0 0 1 9369 175 7 5 5 MED13 17 61955452 Silent SNP A C3N-02588_T 17694708 61955452 21301989 46 30150 CD79B 0 . GRCh38 17 63930076 63930076 + Missense_Mutation SNP A A C rs755181653 C3N-02588_T C3N-02588_N A A c.431T>G p.Met144Arg p.M144R ENST00000392795 3/6 931 772 159 388 388 0 strelka-varscan-mutect CD79B,missense_variant,p.Met143Arg,ENST00000006750,NM_000626.2;CD79B,missense_variant,p.Met144Arg,ENST00000392795,NM_001039933.1;CD79B,intron_variant,,ENST00000349817,NM_021602.2;CD79B,splice_region_variant,,ENST00000559358,;CD79B,downstream_gene_variant,,ENST00000558969,;CD79B,downstream_gene_variant,,ENST00000583260,; C ENST00000392795 Transcript missense_variant,splice_region_variant 506/1254 431/693 144/230 M/R aTg/aGg rs755181653 1 -1 CD79B HGNC HGNC:1699 protein_coding YES CCDS42372.1 ENSP00000376544 P40259 UPI00001B2490 NM_001039933.1 deleterious(0) 3/6 hmmpanther:PTHR14334:SF2,hmmpanther:PTHR14334,SMART_domains:SM00409 MODERATE 1 SNV 1 1 PASS rs755181653 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 107 63930076 63930076 A C 1 0 0 0 0 1 0 0 0 2741 231 8 5 5 CD79B 17 63930076 Missense_Mutation SNP A C3N-02588_T 1974624 63930076 19327365 47 30151 UNK 0 . GRCh38 17 75784921 75784921 + Missense_Mutation SNP C C T rs75277629 C3N-02588_T C3N-02588_N C C c.41C>T p.Ser14Leu p.S14L ENST00000589666 1/16 350 275 75 116 116 0 strelka-varscan-mutect UNK,missense_variant,p.Ser14Leu,ENST00000589666,NM_001080419.2;H3F3B,intron_variant,,ENST00000586607,;H3F3B,upstream_gene_variant,,ENST00000579134,;UNK,missense_variant,p.Ser14Leu,ENST00000586527,;UNK,missense_variant,p.Ser14Leu,ENST00000587501,;UNK,missense_variant,p.Ser14Leu,ENST00000592629,;H3F3B,non_coding_transcript_exon_variant,,ENST00000591893,;UNK,non_coding_transcript_exon_variant,,ENST00000589790,; T ENST00000589666 Transcript missense_variant 151/3925 41/2433 14/810 S/L tCg/tTg rs75277629,COSM396981 1 1 UNK HGNC HGNC:29369 protein_coding YES CCDS45778.2 ENSP00000464893 Q9C0B0 A0A024R8N4 UPI00001C1FC3 NM_001080419.2 tolerated_low_confidence(0.39) 1/16 Low_complexity_(Seg):seg,hmmpanther:PTHR14493:SF36,hmmpanther:PTHR14493 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs75277629 . 0 205 2 2 0 0 0 0 -20 0.999999 1 1 1 0 T 3 4 107 75784921 75784921 C T 1 0 0 0 0 1 0 0 0 17526 893 31 1 1 UNK 17 75784921 Missense_Mutation SNP C C3N-02588_T 11854845 75784921 7472520 48 30152 MPPE1 0 . GRCh38 18 11886515 11886515 + Missense_Mutation SNP C C T rs145870573 C3N-02588_T C3N-02588_N C C c.851G>A p.Arg284Gln p.R284Q ENST00000588072 9/11 633 514 119 259 259 0 strelka-varscan-mutect MPPE1,missense_variant,p.Arg284Gln,ENST00000588072,NM_023075.5;MPPE1,missense_variant,p.Arg262Gln,ENST00000344987,;MPPE1,missense_variant,p.Arg284Gln,ENST00000592977,;MPPE1,missense_variant,p.Arg105Gln,ENST00000587724,;MPPE1,intron_variant,,ENST00000317235,;MPPE1,intron_variant,,ENST00000309976,NM_001242904.1;GNAL,downstream_gene_variant,,ENST00000334049,NM_182978.3;GNAL,downstream_gene_variant,,ENST00000423027,;MPPE1,downstream_gene_variant,,ENST00000588191,;MPPE1,downstream_gene_variant,,ENST00000588186,;MPPE1,downstream_gene_variant,,ENST00000589267,;MPPE1,downstream_gene_variant,,ENST00000592331,;MPPE1,upstream_gene_variant,,ENST00000592755,;MPPE1,downstream_gene_variant,,ENST00000586364,;MPPE1,missense_variant,p.Arg284Gln,ENST00000496196,;MPPE1,missense_variant,p.Arg187Gln,ENST00000317251,;MPPE1,missense_variant,p.Arg64Gln,ENST00000592306,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592447,;MPPE1,non_coding_transcript_exon_variant,,ENST00000589731,;MPPE1,non_coding_transcript_exon_variant,,ENST00000592894,; T ENST00000588072 Transcript missense_variant 2073/4236 851/1191 284/396 R/Q cGg/cAg rs145870573 1 -1 MPPE1 HGNC HGNC:15988 protein_coding YES CCDS11853.1 ENSP00000465894 Q53F39 UPI000013DDD8 NM_023075.5 tolerated(0.92) 9/11 hmmpanther:PTHR13315:SF0,hmmpanther:PTHR13315,Gene3D:3.60.21.10,Pfam_domain:PF00149,Superfamily_domains:SSF56300 MODERATE 1 SNV 1 1 PASS rs145870573 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 11886515 11886515 C T 1 0 0 0 0 1 0 0 0 9706 652 23 1 1 MPPE1 18 11886515 Missense_Mutation SNP C C3N-02588_T 11886515 68486770 49 30153 NCOA6 0 . GRCh38 20 34757533 34757533 + Missense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1215G>T p.Lys405Asn p.K405N ENST00000374796 8/16 233 180 53 140 140 0 strelka-varscan-mutect NCOA6,missense_variant,p.Lys405Asn,ENST00000374796,NM_001318240.1;NCOA6,missense_variant,p.Lys405Asn,ENST00000359003,NM_014071.3;NCOA6,missense_variant,p.Lys405Asn,ENST00000612493,NM_001242539.1;NCOA6,missense_variant,p.Lys405Asn,ENST00000616167,; A ENST00000374796 Transcript missense_variant 3786/9311 1215/6192 405/2063 K/N aaG/aaT 1 -1 NCOA6 HGNC HGNC:15936 protein_coding YES CCDS13241.1 ENSP00000363929 Q14686 UPI000013C634 NM_001318240.1 deleterious(0) 8/16 hmmpanther:PTHR15690,hmmpanther:PTHR15690:SF0 MODERATE 1 SNV 1 1 PASS rs1320282322 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 34757533 34757533 C A 1 0 0 0 0 1 0 0 0 10252 912 32 2 2 NCOA6 20 34757533 Missense_Mutation SNP C C3N-02588_T 34757533 29686634 50 30154 CDH22 0 . GRCh38 20 46216892 46216892 + Missense_Mutation SNP A A G novel C3N-02588_T C3N-02588_N A A c.772T>C p.Ser258Pro p.S258P ENST00000537909 5/12 228 202 26 104 104 0 strelka-varscan-mutect CDH22,missense_variant,p.Ser258Pro,ENST00000537909,NM_021248.2;CDH22,missense_variant,p.Ser258Pro,ENST00000372262,;CDH22,non_coding_transcript_exon_variant,,ENST00000474438,; G ENST00000537909 Transcript missense_variant 1415/3902 772/2487 258/828 S/P Tcg/Ccg 1 -1 CDH22 HGNC HGNC:13251 protein_coding YES CCDS13395.1 ENSP00000437790 Q9UJ99 UPI0000126DC0 NM_021248.2 deleterious(0) 5/12 PROSITE_profiles:PS50268,hmmpanther:PTHR24027,hmmpanther:PTHR24027:SF311,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313,Prints_domain:PR00205 MODERATE 1 SNV 2 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 107 46216892 46216892 A G 1 0 0 0 0 1 0 0 0 2810 304 11 5 5 CDH22 20 46216892 Missense_Mutation SNP A C3N-02588_T 11459359 46216892 18227275 51 30155 MYT1 0 . GRCh38 20 64213578 64213578 + Missense_Mutation SNP C C T novel C3N-02588_T C3N-02588_N C C c.1562C>T p.Ser521Phe p.S521F ENST00000328439 10/23 483 424 59 243 243 0 strelka-varscan-mutect MYT1,missense_variant,p.Ser521Phe,ENST00000536311,;MYT1,missense_variant,p.Ser521Phe,ENST00000328439,NM_004535.2;MYT1,missense_variant,p.Ser223Phe,ENST00000622439,;MYT1,missense_variant,p.Ser223Phe,ENST00000360149,; T ENST00000328439 Transcript missense_variant 1926/5535 1562/3366 521/1121 S/F tCc/tTc 1 1 MYT1 HGNC HGNC:7622 protein_coding YES CCDS13558.1 ENSP00000327465 Q01538 UPI000012FBFA NM_004535.2 deleterious(0.02) 10/23 Superfamily_domains:0042508,hmmpanther:PTHR10816,hmmpanther:PTHR10816:SF10 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 64213578 64213578 C T 1 0 0 0 0 1 0 0 0 10105 855 30 3 3 MYT1 20 64213578 Missense_Mutation SNP C C3N-02588_T 17996686 64213578 230589 52 30156 ATP6V1E1 0 . GRCh38 22 17613287 17613287 + Missense_Mutation SNP G G A novel C3N-02588_T C3N-02588_N G G c.133C>T p.Leu45Phe p.L45F ENST00000253413 3/9 268 243 25 245 245 0 varscan-mutect ATP6V1E1,missense_variant,p.Leu45Phe,ENST00000253413,NM_001696.3;ATP6V1E1,missense_variant,p.Leu45Phe,ENST00000399796,NM_001039367.1;ATP6V1E1,missense_variant,p.Leu23Phe,ENST00000399798,NM_001039366.1;ATP6V1E1,missense_variant,p.Leu46Phe,ENST00000413576,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000478963,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000460085,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000484653,;ATP6V1E1,non_coding_transcript_exon_variant,,ENST00000481365,; A ENST00000253413 Transcript missense_variant 316/1402 133/681 45/226 L/F Ctt/Ttt 1 -1 ATP6V1E1 HGNC HGNC:857 protein_coding YES CCDS13745.1 ENSP00000253413 P36543 Q53Y06 UPI0000000C60 NM_001696.3 deleterious(0.02) 3/9 HAMAP:MF_00311,hmmpanther:PTHR12317:SF20,hmmpanther:PTHR12317,Pfam_domain:PF01991 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 17613287 17613287 G A 1 0 0 0 0 1 0 0 0 1336 971 34 3 3 ATP6V1E1 22 17613287 Missense_Mutation SNP G C3N-02588_T 17613287 33205181 53 30157 CDKL5 0 . GRCh38 X 18650560 18650560 + Missense_Mutation SNP C C T novel C3N-02588_T C3N-02588_N C C c.2948C>T p.Thr983Ile p.T983I ENST00000379989 21/22 366 300 66 161 161 0 strelka-varscan-mutect CDKL5,missense_variant,p.Thr983Ile,ENST00000379989,NM_001037343.1;CDKL5,missense_variant,p.Thr983Ile,ENST00000379996,NM_003159.2;RS1,intron_variant,,ENST00000379984,NM_000330.3;RS1,upstream_gene_variant,,ENST00000476595,; T ENST00000379989 Transcript missense_variant 3233/3463 2948/3093 983/1030 T/I aCt/aTt 1 1 CDKL5 HGNC HGNC:11411 protein_coding YES CCDS14186.1 ENSP00000369325 O76039 UPI0000136103 NM_001037343.1 deleterious_low_confidence(0) 21/22 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 107 18650560 18650560 C T 1 0 0 0 0 1 0 0 0 2861 565 20 3 3 CDKL5 23 18650560 Missense_Mutation SNP C C3N-02588_T 18650560 137390335 54 30158 RBM3 0 . GRCh38 X 48576241 48576242 + Frame_Shift_Ins INS - - CCTT novel C3N-02588_T C3N-02588_N - - c.57_60dupCCTT p.Ala21ProfsTer12 p.A21Pfs*12 ENST00000354480 1/3 403 324 79 174 174 0 sindel-varindel-pindel RBM3,frameshift_variant,p.Ala21ProfsTer12,ENST00000354480,;RBM3,intron_variant,,ENST00000376759,NM_006743.4;RBM3,intron_variant,,ENST00000376755,;RP11-1148L6.9,upstream_gene_variant,,ENST00000376775,;RP11-1148L6.5,downstream_gene_variant,,ENST00000453810,;RBM3,non_coding_transcript_exon_variant,,ENST00000485213,;RBM3,intron_variant,,ENST00000466764,;RBM3,intron_variant,,ENST00000488216,;RBM3,intron_variant,,ENST00000489344,;RBM3,intron_variant,,ENST00000490127,;RBM3,intron_variant,,ENST00000472897,;RBM3,downstream_gene_variant,,ENST00000491240,;RBM3,downstream_gene_variant,,ENST00000491236,;RP11-1148L6.8,upstream_gene_variant,,ENST00000623114,; CCTT ENST00000354480 Transcript frameshift_variant 343-344/1884 56-57/468 19/155 T/TLX acc/acCCTTc 1 1 RBM3 HGNC HGNC:9900 protein_coding ENSP00000346473 Q9H5V0 UPI0000073995 1/3 Transmembrane_helices:TMhelix,Cleavage_site_(Signalp):SignalP-TM,PROSITE_profiles:PS51257,hmmpanther:PTHR13284 HIGH insertion 2 4 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 CCTT 7 5 107 48576241 48576241 - CCTT 1 0 1 1 0 0 0 0 0 13295 507 18 0 0 RBM3 23 48576241 Frame_Shift_Ins INS - C3N-02588_T 29925681 48576241 107464654 55 30159 CNGA2 0 . GRCh38 X 151743692 151743692 + Missense_Mutation SNP C C A novel C3N-02588_T C3N-02588_N C C c.1189C>A p.Gln397Lys p.Q397K ENST00000329903 6/6 329 218 111 155 155 0 strelka-varscan-mutect CNGA2,missense_variant,p.Gln397Lys,ENST00000329903,NM_005140.1; A ENST00000329903 Transcript missense_variant 1222/2834 1189/1995 397/664 Q/K Cag/Aag 1 1 CNGA2 HGNC HGNC:2149 protein_coding YES CCDS14701.1 ENSP00000328478 Q16280 UPI000003E7AE NM_005140.1 tolerated(0.24) 6/6 hmmpanther:PTHR10217:SF389,hmmpanther:PTHR10217,Gene3D:3bpzA01,Superfamily_domains:SSF51206 MODERATE 1 SNV 1 1 PASS . . 0 207 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 107 151743692 151743692 C A 1 0 0 0 0 1 0 0 0 3377 711 25 2 2 CNGA2 23 151743692 Missense_Mutation SNP C C3N-02588_T 103167451 151743692 4297203 56 30160 GPR153 0 . GRCh38 1 6253942 6253942 + Missense_Mutation SNP C C T rs769601920 C3N-02729_T C3N-02729_N C C c.562G>A p.Val188Met p.V188M ENST00000377893 3/6 296 274 22 260 260 0 strelka-varscan-mutect GPR153,missense_variant,p.Val188Met,ENST00000377893,NM_207370.2; T ENST00000377893 Transcript missense_variant 822/4082 562/1830 188/609 V/M Gtg/Atg rs769601920,COSM5516124 1 -1 GPR153 HGNC HGNC:23618 protein_coding YES CCDS64.1 ENSP00000367125 Q6NV75 A0A0I9QQ03 UPI000040E9D7 NM_207370.2 deleterious(0.04) 3/6 Gene3D:1.20.1070.10,Pfam_domain:PF00001,Prints_domain:PR01991,PROSITE_profiles:PS50262,hmmpanther:PTHR16518,hmmpanther:PTHR16518:SF5,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix 0,1 MODERATE 1 SNV 1 0,1 1 PASS rs769601920 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 6253942 6253942 C T 1 0 0 0 0 1 0 0 0 6545 536 19 1 1 GPR153 1 6253942 Missense_Mutation SNP C C3N-02729_T 6253942 242702480 1 30161 MIER1 0 . GRCh38 1 66958146 66958151 + In_Frame_Del DEL GAAGAG GAAGAG - novel C3N-02729_T C3N-02729_N GAAGAG GAAGAG c.432_437delGGAAGA p.Glu146_Glu147del p.E146_E147del ENST00000401041 5/14 72 64 8 249 249 0 sindel-varindel-pindel MIER1,inframe_deletion,p.Glu110_Glu111del,ENST00000357692,NM_001146112.1,NM_020948.3,NM_001146110.1;MIER1,inframe_deletion,p.Glu93_Glu94del,ENST00000355356,NM_001077701.2;MIER1,inframe_deletion,p.Glu110_Glu111del,ENST00000371018,NM_001146111.1;MIER1,inframe_deletion,p.Glu30_Glu31del,ENST00000355977,NM_001146113.1;MIER1,inframe_deletion,p.Glu146_Glu147del,ENST00000401041,NM_001077700.2;MIER1,inframe_deletion,p.Glu110_Glu111del,ENST00000371016,NM_001077702.2;MIER1,inframe_deletion,p.Glu146_Glu147del,ENST00000371014,NM_001077703.2;MIER1,inframe_deletion,p.Glu93_Glu94del,ENST00000401042,NM_001077704.2;MIER1,non_coding_transcript_exon_variant,,ENST00000479067,;MIER1,upstream_gene_variant,,ENST00000493357,; - ENST00000401041 Transcript inframe_deletion 497-502/2552 427-432/1698 143-144/565 EE/- GAAGAG/- 1 1 MIER1 HGNC HGNC:29657 protein_coding YES CCDS53326.1 ENSP00000383820 Q8N108 UPI0000204526 NM_001077700.2 5/14 Low_complexity_(Seg):seg,hmmpanther:PTHR10865,hmmpanther:PTHR10865:SF24 MODERATE 1 deletion 2 5 1 PASS . . 0 204 0 3 0 0 0 2 -3.53191 0 0 1 0 0 - 7 5 108 66958146 66958146 GAAGAG - 1 0 1 0 1 0 0 0 0 9543 943 33 0 0 MIER1 1 66958146 In_Frame_Del DEL GAAGAG C3N-02729_T 60704204 66958146 181998276 2 30162 OR2T2 0 . GRCh38 1 248453517 248453517 + Silent SNP T T A novel C3N-02729_T C3N-02729_N T T c.720T>A p.= p.A240A ENST00000342927 1/1 568 470 98 518 517 1 strelka-varscan OR2T2,synonymous_variant,p.=,ENST00000342927,NM_001004136.1; A ENST00000342927 Transcript synonymous_variant 720/975 720/975 240/324 A gcT/gcA 1 1 OR2T2 HGNC HGNC:14725 protein_coding YES CCDS31116.1 ENSP00000343062 Q6IF00 UPI0000048DB0 NM_001004136.1 1/1 Gene3D:1.20.1070.10,Pfam_domain:PF13853,Prints_domain:PR00245,PROSITE_profiles:PS50262,hmmpanther:PTHR26453,hmmpanther:PTHR26453:SF18,Superfamily_domains:SSF81321,Transmembrane_helices:TMhelix LOW 1 SNV 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 108 248453517 248453517 T A 1 0 0 0 0 0 0 0 1 11097 1509 53 4 4 OR2T2 1 248453517 Silent SNP T C3N-02729_T 181495371 248453517 502905 3 30163 COPS9 0 . GRCh38 2 240136263 240136263 + Missense_Mutation SNP T T G novel C3N-02729_T C3N-02729_N T T c.85A>C p.Met29Leu p.M29L ENST00000307266 1/5 149 126 23 162 162 0 strelka-varscan-mutect COPS9,missense_variant,p.Met29Leu,ENST00000307266,NM_138336.1;COPS9,missense_variant,p.Met29Leu,ENST00000403160,;COPS9,missense_variant,p.Met8Leu,ENST00000607357,NM_001163424.1;OTOS,downstream_gene_variant,,ENST00000391989,;OTOS,downstream_gene_variant,,ENST00000319460,NM_148961.3;COPS9,upstream_gene_variant,,ENST00000489698,;COPS9,upstream_gene_variant,,ENST00000491765,; G ENST00000307266 Transcript missense_variant 85/759 85/759 29/252 M/L Atg/Ctg 1 -1 COPS9 HGNC HGNC:21314 protein_coding YES CCDS2532.1 ENSP00000304147 Q8WXC6 UPI0000071F75 NM_138336.1 deleterious_low_confidence(0.02) 1/5 hmmpanther:PTHR28562,hmmpanther:PTHR28562:SF1,Pfam_domain:PF15004 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 108 240136263 240136263 T G 1 0 0 0 0 1 0 0 0 3534 1435 50 5 5 COPS9 2 240136263 Missense_Mutation SNP T C3N-02729_T 240136263 2057266 4 30164 WHSC1 0 . GRCh38 4 1952206 1952206 + Silent SNP G G A novel C3N-02729_T C3N-02729_N G G c.2112G>A p.= p.R704R ENST00000382895 13/24 172 133 39 169 168 1 strelka-varscan-mutect WHSC1,synonymous_variant,p.=,ENST00000382895,NM_133330.2;WHSC1,synonymous_variant,p.=,ENST00000382892,NM_133331.2;WHSC1,synonymous_variant,p.=,ENST00000382891,NM_133335.3;WHSC1,synonymous_variant,p.=,ENST00000508803,NM_001042424.2;WHSC1,synonymous_variant,p.=,ENST00000514329,;WHSC1,5_prime_UTR_variant,,ENST00000382888,;WHSC1,downstream_gene_variant,,ENST00000503128,;WHSC1,downstream_gene_variant,,ENST00000398261,NM_133334.2;WHSC1,non_coding_transcript_exon_variant,,ENST00000482415,;WHSC1,non_coding_transcript_exon_variant,,ENST00000505643,;WHSC1,non_coding_transcript_exon_variant,,ENST00000513726,;WHSC1,intron_variant,,ENST00000502425,;WHSC1,upstream_gene_variant,,ENST00000503207,;WHSC1,3_prime_UTR_variant,,ENST00000312087,;WHSC1,3_prime_UTR_variant,,ENST00000353275,;WHSC1,downstream_gene_variant,,ENST00000511904,;WHSC1,upstream_gene_variant,,ENST00000507094,; A ENST00000382895 Transcript synonymous_variant 2543/7827 2112/4098 704/1365 R agG/agA 1 1 WHSC1 HGNC HGNC:12766 protein_coding YES CCDS33940.1 ENSP00000372351 O96028 UPI0000073F57 NM_133330.2 13/24 PROSITE_profiles:PS50016,hmmpanther:PTHR22884:SF293,hmmpanther:PTHR22884,PROSITE_patterns:PS01359,Gene3D:3.30.40.10,SMART_domains:SM00184,SMART_domains:SM00249,Superfamily_domains:SSF57903 LOW 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 2 1 108 1952206 1952206 G A 1 0 0 0 0 0 0 0 1 17920 1252 44 3 3 WHSC1 4 1952206 Silent SNP G C3N-02729_T 1952206 188262349 5 30165 ADD1 0 . GRCh38 4 2884661 2884661 + Missense_Mutation SNP A A T novel C3N-02729_T C3N-02729_N A A c.505A>T p.Ile169Phe p.I169F ENST00000264758 4/15 35 18 17 67 67 0 strelka-mutect ADD1,missense_variant,p.Ile169Phe,ENST00000355842,NM_001286645.1;ADD1,missense_variant,p.Ile169Phe,ENST00000398125,NM_176801.2;ADD1,missense_variant,p.Ile169Phe,ENST00000264758,NM_014189.3;ADD1,missense_variant,p.Ile169Phe,ENST00000398129,NM_001119.4;ADD1,missense_variant,p.Ile169Phe,ENST00000446856,;ADD1,missense_variant,p.Ile169Phe,ENST00000503455,;ADD1,missense_variant,p.Ile169Phe,ENST00000513328,NM_014190.3;ADD1,missense_variant,p.Ile169Phe,ENST00000398123,;ADD1,intron_variant,,ENST00000508277,;ADD1,downstream_gene_variant,,ENST00000511797,;ADD1,3_prime_UTR_variant,,ENST00000510101,;ADD1,non_coding_transcript_exon_variant,,ENST00000508684,;ADD1,non_coding_transcript_exon_variant,,ENST00000503169,;ADD1,non_coding_transcript_exon_variant,,ENST00000509039,;ADD1,non_coding_transcript_exon_variant,,ENST00000534870,;ADD1,upstream_gene_variant,,ENST00000506157,; T ENST00000264758 Transcript missense_variant 693/4045 505/2307 169/768 I/F Atc/Ttc 1 1 ADD1 HGNC HGNC:243 protein_coding YES CCDS3363.1 ENSP00000264758 P35611 UPI000002A35E NM_014189.3 deleterious(0.01) 4/15 hmmpanther:PTHR10672:SF4,hmmpanther:PTHR10672,Pfam_domain:PF00596,Gene3D:3.40.225.10,SMART_domains:SM01007,Superfamily_domains:SSF53639 MODERATE 1 SNV 5 1 PASS . . 0 207 3 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 2884661 2884661 A T 1 0 0 0 0 1 0 0 0 348 463 16 4 4 ADD1 4 2884661 Missense_Mutation SNP A C3N-02729_T 932455 2884661 187329894 6 30166 JAKMIP1 0 . GRCh38 4 6050663 6050663 + Missense_Mutation SNP G G A novel C3N-02729_T C3N-02729_N G G c.1823C>T p.Ser608Leu p.S608L ENST00000409021 14/21 194 156 38 260 260 0 strelka-varscan-mutect JAKMIP1,missense_variant,p.Ser608Leu,ENST00000409021,NM_001099433.1;JAKMIP1,missense_variant,p.Ser423Leu,ENST00000409371,;JAKMIP1,missense_variant,p.Ser176Leu,ENST00000637373,;JAKMIP1,downstream_gene_variant,,ENST00000282924,NM_144720.3;JAKMIP1,downstream_gene_variant,,ENST00000409831,NM_001306133.1;JAKMIP1,downstream_gene_variant,,ENST00000410077,NM_001306134.1;JAKMIP1,downstream_gene_variant,,ENST00000473053,; A ENST00000409021 Transcript missense_variant 2273/2975 1823/2496 608/831 S/L tCg/tTg 1 -1 JAKMIP1 HGNC HGNC:26460 protein_coding YES CCDS47005.1 ENSP00000386711 Q96N16 UPI00015734C1 NM_001099433.1 deleterious(0.03) 14/21 hmmpanther:PTHR18935,hmmpanther:PTHR18935:SF6,Pfam_domain:PF16034 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 6050663 6050663 G A 1 0 0 0 0 1 0 0 0 7853 1059 37 1 1 JAKMIP1 4 6050663 Missense_Mutation SNP G C3N-02729_T 3166002 6050663 184163892 7 30167 TAPT1 0 . GRCh38 4 16188239 16188239 + Silent SNP G G A novel C3N-02729_T C3N-02729_N G G c.729C>T p.= p.F243F ENST00000405303 5/14 57 45 12 169 169 0 strelka-varscan TAPT1,synonymous_variant,p.=,ENST00000405303,NM_153365.2;TAPT1,non_coding_transcript_exon_variant,,ENST00000508888,;TAPT1,non_coding_transcript_exon_variant,,ENST00000513359,;TAPT1,non_coding_transcript_exon_variant,,ENST00000505152,;TAPT1,non_coding_transcript_exon_variant,,ENST00000510868,;TAPT1,non_coding_transcript_exon_variant,,ENST00000511866,;TAPT1,3_prime_UTR_variant,,ENST00000505603,;TAPT1,non_coding_transcript_exon_variant,,ENST00000507425,;TAPT1,intron_variant,,ENST00000513782,;TAPT1,downstream_gene_variant,,ENST00000505317,;TAPT1,upstream_gene_variant,,ENST00000504281,;TAPT1,downstream_gene_variant,,ENST00000513833,; A ENST00000405303 Transcript synonymous_variant 813/4591 729/1704 243/567 F ttC/ttT 1 -1 TAPT1 HGNC HGNC:26887 protein_coding YES CCDS47030.1 ENSP00000385347 Q6NXT6 UPI0000253B29 NM_153365.2 5/14 Transmembrane_helices:TMhelix,hmmpanther:PTHR13317,hmmpanther:PTHR13317:SF4,Pfam_domain:PF05346 LOW 1 SNV 1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 2 1 108 16188239 16188239 G A 1 0 0 0 0 0 0 0 1 15953 1281 45 3 3 TAPT1 4 16188239 Silent SNP G C3N-02729_T 10137576 16188239 174026316 8 30168 ATP10D 0 . GRCh38 4 47512764 47512764 + Missense_Mutation SNP G G A rs750138858 C3N-02729_T C3N-02729_N G G c.224G>A p.Arg75Gln p.R75Q ENST00000273859 2/23 123 98 25 154 154 0 strelka-varscan ATP10D,missense_variant,p.Arg75Gln,ENST00000273859,NM_020453.3;ATP10D,missense_variant,p.Arg75Gln,ENST00000504445,;ATP10D,non_coding_transcript_exon_variant,,ENST00000507889,; A ENST00000273859 Transcript missense_variant 493/6655 224/4281 75/1426 R/Q cGa/cAa rs750138858,COSM256370 1 1 ATP10D HGNC HGNC:13549 protein_coding YES CCDS3476.1 ENSP00000273859 Q9P241 UPI00001AE9B7 NM_020453.3 tolerated(0.12) 2/23 Superfamily_domains:0049473,Pfam_domain:PF16209,hmmpanther:PTHR24092,hmmpanther:PTHR24092:SF84,TIGRFAM_domain:TIGR01652 0,1 MODERATE 1 SNV 1 0,1 1 PASS . . 0 208 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 47512764 47512764 G A 1 0 0 0 0 1 0 0 0 1270 1058 37 1 1 ATP10D 4 47512764 Missense_Mutation SNP G C3N-02729_T 31324525 47512764 142701791 9 30169 MRPL1 0 . GRCh38 4 77885259 77885259 + Missense_Mutation SNP A A T novel C3N-02729_T C3N-02729_N A A c.406A>T p.Asn136Tyr p.N136Y ENST00000315567 4/9 138 91 47 269 269 0 strelka-varscan MRPL1,missense_variant,p.Asn136Tyr,ENST00000315567,NM_020236.3;MRPL1,missense_variant,p.Asn90Tyr,ENST00000502384,;MRPL1,non_coding_transcript_exon_variant,,ENST00000506674,;MRPL1,non_coding_transcript_exon_variant,,ENST00000511521,;MRPL1,downstream_gene_variant,,ENST00000515625,; T ENST00000315567 Transcript missense_variant 735/1490 406/978 136/325 N/Y Aac/Tac 1 1 MRPL1 HGNC HGNC:14275 protein_coding YES CCDS3583.2 ENSP00000315017 Q9BYD6 UPI000020B07E NM_020236.3 deleterious(0) 4/9 hmmpanther:PTHR23105:SF5,hmmpanther:PTHR23105,Pfam_domain:PF00687,TIGRFAM_domain:TIGR01170,Gene3D:3.30.190.20,Superfamily_domains:SSF56808 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 77885259 77885259 A T 1 0 0 0 0 1 0 0 0 9749 28 1 4 4 MRPL1 4 77885259 Missense_Mutation SNP A C3N-02729_T 30372495 77885259 112329296 10 30170 MAST4 0 . GRCh38 5 67166235 67166235 + Missense_Mutation SNP A A T novel C3N-02729_T C3N-02729_N A A c.7056A>T p.Arg2352Ser p.R2352S ENST00000403625 29/29 193 132 61 331 331 0 strelka-varscan-mutect MAST4,missense_variant,p.Arg2352Ser,ENST00000403625,NM_001164664.1;MAST4,missense_variant,p.Arg2173Ser,ENST00000405643,NM_001290226.1;MAST4,missense_variant,p.Arg2158Ser,ENST00000261569,NM_001290227.1,NM_001297651.1;MAST4,missense_variant,p.Arg2163Ser,ENST00000403666,NM_015183.2;MAST4,missense_variant,p.Arg1409Ser,ENST00000443808,; T ENST00000403625 Transcript missense_variant 7351/10711 7056/7872 2352/2623 R/S agA/agT 1 1 MAST4 HGNC HGNC:19037 protein_coding YES CCDS54861.1 ENSP00000385727 J3QT34 UPI000173A2B0 NM_001164664.1 deleterious_low_confidence(0.04) 29/29 MODERATE 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 67166235 67166235 A T 1 0 0 0 0 1 0 0 0 9253 272 10 4 4 MAST4 5 67166235 Missense_Mutation SNP A C3N-02729_T 67166235 114372024 11 30171 PCDHA3 0 . GRCh38 5 140802047 140802047 + Missense_Mutation SNP G G A novel C3N-02729_T C3N-02729_N G G c.850G>A p.Asp284Asn p.D284N ENST00000522353 1/4 174 111 63 393 393 0 strelka-varscan-mutect PCDHA3,missense_variant,p.Asp284Asn,ENST00000522353,NM_018906.2;PCDHA3,missense_variant,p.Asp284Asn,ENST00000532566,NM_031497.1;PCDHA1,intron_variant,,ENST00000504120,NM_018900.3;PCDHA2,intron_variant,,ENST00000526136,NM_018905.2;PCDHA2,intron_variant,,ENST00000520672,NM_031496.1;PCDHA1,intron_variant,,ENST00000394633,NM_031411.2;PCDHA4,upstream_gene_variant,,ENST00000618834,NM_031500.2;PCDHA2,downstream_gene_variant,,ENST00000378132,NM_031495.1;PCDHA4,upstream_gene_variant,,ENST00000378125,;AC005609.16,intron_variant,,ENST00000624712,;AC005609.16,upstream_gene_variant,,ENST00000624176,; A ENST00000522353 Transcript missense_variant 850/5260 850/2853 284/950 D/N Gac/Aac 1 1 PCDHA3 HGNC HGNC:8669 protein_coding YES CCDS54915.1 ENSP00000429808 Q9Y5H8 UPI00001273CB NM_018906.2 tolerated_low_confidence(0.35) 1/4 PROSITE_profiles:PS50268,hmmpanther:PTHR24028,hmmpanther:PTHR24028:SF93,Pfam_domain:PF00028,Gene3D:2.60.40.60,SMART_domains:SM00112,Superfamily_domains:SSF49313 MODERATE 1 SNV 1 1 PASS rs1361472766 . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 140802047 140802047 G A 1 0 0 0 0 1 0 0 0 11612 1174 41 3 3 PCDHA3 5 140802047 Missense_Mutation SNP G C3N-02729_T 73635812 140802047 40736212 12 30172 ADAM19 0 . GRCh38 5 157570965 157570965 + Missense_Mutation SNP C C A novel C3N-02729_T C3N-02729_N C C c.110G>T p.Gly37Val p.G37V ENST00000257527 2/23 156 92 64 221 221 0 strelka-varscan-mutect ADAM19,missense_variant,p.Gly37Val,ENST00000257527,NM_033274.4;ADAM19,missense_variant,p.Gly37Val,ENST00000517905,;AC106801.1,downstream_gene_variant,,ENST00000518054,;ADAM19,missense_variant,p.Gly37Val,ENST00000517951,;ADAM19,non_coding_transcript_exon_variant,,ENST00000519752,; A ENST00000257527 Transcript missense_variant 189/6481 110/2757 37/918 G/V gGc/gTc 1 -1 ADAM19 HGNC HGNC:197 protein_coding YES CCDS4338.1 ENSP00000257527 Q9H013 UPI000013CF6A NM_033274.4 tolerated(0.14) 2/23 hmmpanther:PTHR11905:SF19,hmmpanther:PTHR11905 MODERATE 1 SNV 1 1 PASS rs1327017962 . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 157570965 157570965 C A 1 0 0 0 0 1 0 0 0 284 739 26 2 2 ADAM19 5 157570965 Missense_Mutation SNP C C3N-02729_T 16768918 157570965 23967294 13 30173 DNAH11 0 . GRCh38 7 21717878 21717878 + Missense_Mutation SNP A A G novel C3N-02729_T C3N-02729_N A A c.7087A>G p.Thr2363Ala p.T2363A ENST00000409508 43/82 89 59 30 149 149 0 strelka-varscan DNAH11,missense_variant,p.Thr2363Ala,ENST00000409508,NM_001277115.1;DNAH11,missense_variant,p.Thr2370Ala,ENST00000328843,;DNAH11,missense_variant,p.Thr2370Ala,ENST00000620169,; G ENST00000409508 Transcript missense_variant 7118/14167 7087/13551 2363/4516 T/A Aca/Gca 1 1 DNAH11 HGNC HGNC:2942 protein_coding YES CCDS64602.1 ENSP00000475939 Q96DT5 UPI0002B8CE70 NM_001277115.1 tolerated(0.18) 43/82 hmmpanther:PTHR10676:SF263,hmmpanther:PTHR10676 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 108 21717878 21717878 A G 1 0 0 0 0 1 0 0 0 4413 43 2 5 5 DNAH11 7 21717878 Missense_Mutation SNP A C3N-02729_T 21717878 137628095 14 30174 EGFR 0 . GRCh38 7 55191822 55191822 + Missense_Mutation SNP T T G rs121434568 C3N-02729_T C3N-02729_N T T c.2573T>G p.Leu858Arg p.L858R ENST00000275493 21/28 627 434 193 530 529 1 strelka-varscan-mutect EGFR,missense_variant,p.Leu858Arg,ENST00000275493,NM_005228.3;EGFR,missense_variant,p.Leu813Arg,ENST00000454757,;EGFR,missense_variant,p.Leu813Arg,ENST00000455089,;EGFR-AS1,upstream_gene_variant,,ENST00000442411,;EGFR,upstream_gene_variant,,ENST00000485503,; G ENST00000275493 Transcript missense_variant 2750/9821 2573/3633 858/1210 L/R cTg/cGg rs121434568,COSM29578,COSM6224 1 1 EGFR HGNC HGNC:3236 protein_coding YES CCDS5514.1 ENSP00000275493 P00533 UPI000003E750 NM_005228.3 deleterious(0) 21/28 PROSITE_profiles:PS50011,hmmpanther:PTHR24416,hmmpanther:PTHR24416:SF91,PIRSF_domain:PIRSF000619,Pfam_domain:PF07714,Gene3D:1.10.510.10,SMART_domains:SM00219,Superfamily_domains:SSF56112 drug_response 0,1,1 26053404 MODERATE 1 SNV 1 1,1,1 1 PASS rs121434568 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 G 3 3 108 55191822 55191822 T G 1 0 0 0 0 1 0 0 0 4803 1580 55 5 5 EGFR 7 55191822 Missense_Mutation SNP T C3N-02729_T 33473944 55191822 104154151 15 30175 PEG10 0 . GRCh38 7 94664017 94664017 + Missense_Mutation SNP T T A novel C3N-02729_T C3N-02729_N T T c.689T>A p.Met230Lys p.M230K ENST00000488574 2/2 397 252 145 367 367 0 strelka-varscan PEG10,missense_variant,p.Met154Lys,ENST00000482108,NM_015068.3,NM_001184961.1,NM_001172437.2,NM_001040152.1;PEG10,missense_variant,p.Met188Lys,ENST00000615790,NM_001184962.1;PEG10,missense_variant,p.Met188Lys,ENST00000612941,;PEG10,missense_variant,p.Met154Lys,ENST00000617526,;PEG10,missense_variant,p.Met230Lys,ENST00000488574,NM_001172438.2;PEG10,missense_variant,p.Met230Lys,ENST00000612748,;PEG10,downstream_gene_variant,,ENST00000613043,;PEG10,intron_variant,,ENST00000493935,;PEG10,upstream_gene_variant,,ENST00000465184,; A ENST00000488574 Transcript missense_variant 906/2587 689/1206 230/401 M/K aTg/aAg 1 1 PEG10 HGNC HGNC:14005 protein_coding YES CCDS75636.1 ENSP00000418944 B4DSP0 UPI0000037665 NM_001172438.2 deleterious(0) 2/2 hmmpanther:PTHR15503:SF10,hmmpanther:PTHR15503,Pfam_domain:PF16297 MODERATE 1 SNV 2 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 94664017 94664017 T A 1 0 0 0 0 1 0 0 0 11807 1464 51 4 4 PEG10 7 94664017 Missense_Mutation SNP T C3N-02729_T 39472195 94664017 64681956 16 30176 ANK1 0 . GRCh38 8 41715678 41715678 + Missense_Mutation SNP C C T novel C3N-02729_T C3N-02729_N C C c.1675G>A p.Glu559Lys p.E559K ENST00000265709 14/43 237 167 70 402 402 0 strelka-varscan-mutect ANK1,missense_variant,p.Glu526Lys,ENST00000289734,NM_000037.3;ANK1,missense_variant,p.Glu526Lys,ENST00000347528,NM_020476.2,NM_020475.2,NM_020477.2;ANK1,missense_variant,p.Glu559Lys,ENST00000265709,NM_001142446.1; T ENST00000265709 Transcript missense_variant 1957/6379 1675/5694 559/1897 E/K Gaa/Aaa 1 -1 ANK1 HGNC HGNC:492 protein_coding YES CCDS47849.1 ENSP00000265709 P16157 UPI0000E4453A NM_001142446.1 tolerated(0.08) 14/43 Gene3D:1.25.40.20,PROSITE_profiles:PS50088,PROSITE_profiles:PS50297,hmmpanther:PTHR24123,hmmpanther:PTHR24123:SF20,SMART_domains:SM00248,Superfamily_domains:SSF48403 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 41715678 41715678 C T 1 0 0 0 0 1 0 0 0 720 864 30 3 3 ANK1 8 41715678 Missense_Mutation SNP C C3N-02729_T 41715678 103422958 17 30177 ZFHX4 0 . GRCh38 8 76851428 76851428 + Missense_Mutation SNP G G A novel C3N-02729_T C3N-02729_N G G c.4507G>A p.Gly1503Arg p.G1503R ENST00000521891 10/11 201 126 75 224 224 0 strelka-varscan-mutect ZFHX4,missense_variant,p.Gly1503Arg,ENST00000521891,NM_024721.4;ZFHX4,missense_variant,p.Gly1477Arg,ENST00000518282,;ZFHX4,downstream_gene_variant,,ENST00000523625,;ZFHX4,downstream_gene_variant,,ENST00000522409,;ZFHX4,downstream_gene_variant,,ENST00000519536,; A ENST00000521891 Transcript missense_variant 4955/14019 4507/10851 1503/3616 G/R Gga/Aga 1 1 ZFHX4 HGNC HGNC:30939 protein_coding YES CCDS47878.2 ENSP00000430497 Q86UP3 UPI0000424CC7 NM_024721.4 deleterious(0.01) 10/11 hmmpanther:PTHR24208,hmmpanther:PTHR24208:SF40 MODERATE 1 SNV 5 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 76851428 76851428 G A 1 0 0 0 0 1 0 0 0 18213 1001 35 3 3 ZFHX4 8 76851428 Missense_Mutation SNP G C3N-02729_T 35135750 76851428 68287208 18 30178 UAP1L1 0 . GRCh38 9 137080748 137080748 + Missense_Mutation SNP A A C novel C3N-02729_T C3N-02729_N A A c.1238A>C p.Glu413Ala p.E413A ENST00000409858 7/9 176 119 57 154 154 0 strelka-varscan-mutect UAP1L1,missense_variant,p.Glu413Ala,ENST00000409858,NM_207309.2;UAP1L1,missense_variant,p.Glu290Ala,ENST00000360271,;MAN1B1-AS1,downstream_gene_variant,,ENST00000596585,;UAP1L1,non_coding_transcript_exon_variant,,ENST00000474787,;UAP1L1,downstream_gene_variant,,ENST00000476184,; C ENST00000409858 Transcript missense_variant 1270/3365 1238/1524 413/507 E/A gAg/gCg 1 1 UAP1L1 HGNC HGNC:28082 protein_coding YES CCDS7028.2 ENSP00000386935 Q3KQV9 UPI000016047B NM_207309.2 deleterious(0.05) 7/9 Gene3D:3.90.550.10,Pfam_domain:PF01704,hmmpanther:PTHR11952,hmmpanther:PTHR11952:SF6,Superfamily_domains:SSF53448 MODERATE 1 SNV 1 1 PASS . . 0 209 0 0 0 0 0 0 -20 1 1 1 1 0 C 3 2 108 137080748 137080748 A C 1 0 0 0 0 1 0 0 0 17345 304 11 5 5 UAP1L1 9 137080748 Missense_Mutation SNP A C3N-02729_T 137080748 1313969 19 30179 TACC2 0 . GRCh38 10 122083805 122083805 + Missense_Mutation SNP A A T novel C3N-02729_T C3N-02729_N A A c.1305A>T p.Glu435Asp p.E435D ENST00000369005 4/23 139 69 70 194 194 0 strelka-varscan-mutect TACC2,missense_variant,p.Glu435Asp,ENST00000369005,NM_206862.3;TACC2,missense_variant,p.Glu435Asp,ENST00000334433,;TACC2,missense_variant,p.Glu435Asp,ENST00000515273,NM_001291877.1;TACC2,missense_variant,p.Glu435Asp,ENST00000453444,;TACC2,missense_variant,p.Glu435Asp,ENST00000515603,NM_001291876.1;TACC2,intron_variant,,ENST00000513429,NM_206861.2;TACC2,intron_variant,,ENST00000358010,;TACC2,downstream_gene_variant,,ENST00000491540,;TACC2,downstream_gene_variant,,ENST00000498721,; T ENST00000369005 Transcript missense_variant 1645/9673 1305/8847 435/2948 E/D gaA/gaT 1 1 TACC2 HGNC HGNC:11523 protein_coding YES CCDS7626.1 ENSP00000358001 O95359 UPI0000246F6B NM_206862.3 deleterious_low_confidence(0) 4/23 hmmpanther:PTHR13924:SF11,hmmpanther:PTHR13924 MODERATE 1 SNV 1 1 PASS . . 0 208 0 2 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 122083805 122083805 A T 1 0 0 0 0 1 0 0 0 15898 69 3 4 4 TACC2 10 122083805 Missense_Mutation SNP A C3N-02729_T 122083805 11713617 20 30180 DCDC1 0 . GRCh38 11 30908976 30908976 + Silent SNP A A T novel C3N-02729_T C3N-02729_N A A c.1209T>A p.= p.S403S ENST00000406071 10/20 61 42 19 168 168 0 strelka-varscan-mutect DCDC1,synonymous_variant,p.=,ENST00000597505,;DCDC1,synonymous_variant,p.=,ENST00000406071,NM_020869.3;DCDC1,synonymous_variant,p.=,ENST00000444572,;DCDC1,non_coding_transcript_exon_variant,,ENST00000483396,;DCDC1,non_coding_transcript_exon_variant,,ENST00000429306,;DCDC1,upstream_gene_variant,,ENST00000303697,; T ENST00000406071 Transcript synonymous_variant 1525/4758 1209/2673 403/890 S tcT/tcA 1 -1 DCDC1 HGNC HGNC:20625 protein_coding YES CCDS73270.1 ENSP00000385936 B6ZDN3 UPI0001FB41A5 NM_020869.3 10/20 hmmpanther:PTHR14958:SF27,hmmpanther:PTHR14958 LOW 1 SNV 5 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 108 30908976 30908976 A T 1 0 0 0 0 0 0 0 1 4086 175 7 4 4 DCDC1 11 30908976 Silent SNP A C3N-02729_T 30908976 104177646 21 30181 LRFN5 0 . GRCh38 14 41891763 41891763 + Missense_Mutation SNP G G T novel C3N-02729_T C3N-02729_N G G c.1899G>T p.Trp633Cys p.W633C ENST00000298119 4/6 406 268 138 583 583 0 strelka-varscan-mutect LRFN5,missense_variant,p.Trp633Cys,ENST00000298119,NM_152447.3;LRFN5,intron_variant,,ENST00000554171,;LRFN5,intron_variant,,ENST00000554120,; T ENST00000298119 Transcript missense_variant 3088/3723 1899/2160 633/719 W/C tgG/tgT 1 1 LRFN5 HGNC HGNC:20360 protein_coding YES CCDS9678.1 ENSP00000298119 Q96NI6 UPI000000DA1E NM_152447.3 tolerated_low_confidence(0.09) 4/6 hmmpanther:PTHR24373,hmmpanther:PTHR24373:SF3 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 41891763 41891763 G T 1 0 0 0 0 1 0 0 0 8835 1183 41 2 2 LRFN5 14 41891763 Missense_Mutation SNP G C3N-02729_T 41891763 65151955 22 30182 PSMC6 0 . GRCh38 14 52708483 52708483 + Missense_Mutation SNP A A T novel C3N-02729_T C3N-02729_N A A c.208A>T p.Ile70Phe p.I70F ENST00000445930 3/14 111 74 37 263 263 0 strelka-varscan-mutect PSMC6,missense_variant,p.Ile70Phe,ENST00000445930,;PSMC6,missense_variant,p.Ile70Phe,ENST00000612399,NM_002806.3;PSMC6,missense_variant,p.Ile56Phe,ENST00000606149,;PSMC6,missense_variant,p.Ile56Phe,ENST00000556813,;PSMC6,intron_variant,,ENST00000555339,;PSMC6,splice_region_variant,,ENST00000554952,;PSMC6,missense_variant,p.Ile56Phe,ENST00000554044,;PSMC6,missense_variant,p.Ile56Phe,ENST00000557240,;PSMC6,splice_region_variant,,ENST00000458604,;PSMC6,splice_region_variant,,ENST00000553899,;PSMC6,splice_region_variant,,ENST00000557517,;PSMC6,splice_region_variant,,ENST00000555887,;PSMC6,splice_region_variant,,ENST00000553798,;PSMC6,splice_region_variant,,ENST00000554956,;PSMC6,upstream_gene_variant,,ENST00000557085,; T ENST00000445930 Transcript missense_variant,splice_region_variant 214/2188 208/1212 70/403 I/F Atc/Ttc 1 1 PSMC6 HGNC HGNC:9553 protein_coding YES CCDS9710.2 ENSP00000401802 A0A087X2I1 UPI00001FD556 tolerated(0.08) 3/14 hmmpanther:PTHR23073:SF33,hmmpanther:PTHR23073,TIGRFAM_domain:TIGR01242 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 3 4 108 52708483 52708483 A T 1 0 0 0 0 1 0 0 0 12842 347 12 4 4 PSMC6 14 52708483 Missense_Mutation SNP A C3N-02729_T 10816720 52708483 54335235 23 30183 HERC2 0 . GRCh38 15 28146264 28146264 + Missense_Mutation SNP C C T rs368367299 C3N-02729_T C3N-02729_N C C c.10981G>A p.Val3661Ile p.V3661I ENST00000261609 71/93 199 186 13 245 245 0 strelka-varscan-mutect HERC2,missense_variant,p.Val3661Ile,ENST00000261609,NM_004667.5;HERC2,upstream_gene_variant,,ENST00000564519,; T ENST00000261609 Transcript missense_variant 11090/15337 10981/14505 3661/4834 V/I Gtc/Atc rs368367299 1 -1 HERC2 HGNC HGNC:4868 protein_coding YES CCDS10021.1 ENSP00000261609 O95714 UPI00004578F7 NM_004667.5 tolerated(0.06) 71/93 MODERATE 1 SNV 1 1 PASS rs368367299 . 0 208 0 2 0 0 0 0 -16.49578 0.9999996 1 1 1 0 T 3 4 108 28146264 28146264 C T 1 0 0 0 0 1 0 0 0 6942 536 19 1 1 HERC2 15 28146264 Missense_Mutation SNP C C3N-02729_T 28146264 73844925 24 30184 PITPNM3 0 . GRCh38 17 6478060 6478060 + Missense_Mutation SNP G G A novel C3N-02729_T C3N-02729_N G G c.815C>T p.Ala272Val p.A272V ENST00000262483 8/20 246 121 125 302 302 0 strelka-varscan-mutect PITPNM3,missense_variant,p.Ala272Val,ENST00000262483,NM_031220.3;PITPNM3,missense_variant,p.Ala236Val,ENST00000421306,NM_001165966.1;PITPNM3,upstream_gene_variant,,ENST00000576664,;PITPNM3,non_coding_transcript_exon_variant,,ENST00000572795,; A ENST00000262483 Transcript missense_variant 903/7086 815/2925 272/974 A/V gCc/gTc 1 -1 PITPNM3 HGNC HGNC:21043 protein_coding YES CCDS11076.1 ENSP00000262483 Q9BZ71 UPI000022A281 NM_031220.3 deleterious(0.04) 8/20 hmmpanther:PTHR10658 MODERATE 1 SNV 1 1 PASS . . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 6478060 6478060 G A 1 0 0 0 0 1 0 0 0 12048 1203 42 3 3 PITPNM3 17 6478060 Missense_Mutation SNP G C3N-02729_T 6478060 76779381 25 30185 H3F3B 0 . GRCh38 17 75779122 75779123 + Frame_Shift_Ins INS - - G rs779064600 C3N-02729_T C3N-02729_N - - c.52dupC p.Arg18ProfsTer80 p.R18Pfs*80 ENST00000254810 2/4 92 75 17 73 73 0 sindel-varindel-pindel H3F3B,frameshift_variant,p.Arg18ProfsTer80,ENST00000254810,NM_005324.4;H3F3B,frameshift_variant,p.Arg18ProfsTer96,ENST00000592643,;H3F3B,frameshift_variant,p.Arg18ProfsTer118,ENST00000591890,;H3F3B,frameshift_variant,p.Arg18ProfsTer98,ENST00000587171,;H3F3B,frameshift_variant,p.Arg18ProfsTer80,ENST00000589599,;H3F3B,frameshift_variant,p.Arg18ProfsTer80,ENST00000586607,;H3F3B,frameshift_variant,p.Arg18ProfsTer80,ENST00000587560,;H3F3B,frameshift_variant,p.Arg18ProfsTer80,ENST00000586270,;H3F3B,intron_variant,,ENST00000593254,;H3F3B,non_coding_transcript_exon_variant,,ENST00000586518,;H3F3B,non_coding_transcript_exon_variant,,ENST00000589949,;H3F3B,non_coding_transcript_exon_variant,,ENST00000589417,;H3F3B,downstream_gene_variant,,ENST00000591893,; G ENST00000254810 Transcript frameshift_variant 185-186/2705 52-53/411 18/136 R/PX cgc/cCgc rs779064600 1 -1 H3F3B HGNC HGNC:4765 protein_coding YES CCDS11729.1 ENSP00000254810 P84243 B2R4P9 UPI00000007B0 NM_005324.4 2/4 Gene3D:1.10.20.10,Pfam_domain:PF00125,Prints_domain:PR00622,PROSITE_patterns:PS00322,hmmpanther:PTHR11426,Superfamily_domains:SSF47113 HIGH 1 insertion 1 1 PASS . . 0 191 17 2 0 0 0 0 -20 0.9950088 1 1 1 0 G 7 5 108 75779122 75779122 - G 1 0 1 1 0 0 0 0 0 6816 768 27 0 0 H3F3B 17 75779122 Frame_Shift_Ins INS - C3N-02729_T 69301062 75779122 7478319 26 30186 TOMM40 0 . GRCh38 19 44903152 44903152 + Missense_Mutation SNP G G A novel C3N-02729_T C3N-02729_N G G c.1069G>A p.Gly357Ser p.G357S ENST00000426677 9/9 282 215 67 130 130 0 strelka-varscan-mutect TOMM40,missense_variant,p.Gly357Ser,ENST00000426677,NM_001128917.1;TOMM40,missense_variant,p.Gly357Ser,ENST00000405636,NM_001128916.1;TOMM40,missense_variant,p.Gly357Ser,ENST00000252487,NM_006114.2;TOMM40,3_prime_UTR_variant,,ENST00000592434,;APOE,upstream_gene_variant,,ENST00000252486,NM_000041.3,NM_001302691.1,NM_001302689.1,NM_001302690.1;APOE,upstream_gene_variant,,ENST00000425718,;APOE,upstream_gene_variant,,ENST00000434152,NM_001302688.1;APOE,upstream_gene_variant,,ENST00000446996,;APOE,upstream_gene_variant,,ENST00000485628,;TOMM40,downstream_gene_variant,,ENST00000592041,; A ENST00000426677 Transcript missense_variant 1249/1725 1069/1086 357/361 G/S Ggc/Agc 1 1 TOMM40 HGNC HGNC:18001 protein_coding YES CCDS12646.1 ENSP00000410339 O96008 A0A024R0P9 UPI0000130CBB NM_001128917.1 tolerated(0.11) 9/9 Gene3D:2.40.160.10,hmmpanther:PTHR10802,hmmpanther:PTHR10802:SF1 MODERATE 1 SNV 1 1 PASS . . 0 208 2 0 0 0 0 0 -20 1 1 1 1 0 A 3 1 108 44903152 44903152 G A 1 0 0 0 0 1 0 0 0 16832 1348 47 3 3 TOMM40 19 44903152 Missense_Mutation SNP G C3N-02729_T 44903152 13714464 27 30187 SLC32A1 0 . GRCh38 20 38727718 38727718 + Silent SNP C C T rs150170740 C3N-02729_T C3N-02729_N C C c.657C>T p.= p.I219I ENST00000217420 2/2 564 372 192 435 434 1 strelka-varscan-mutect SLC32A1,synonymous_variant,p.=,ENST00000217420,NM_080552.2; T ENST00000217420 Transcript synonymous_variant 920/2574 657/1578 219/525 I atC/atT rs150170740 1 1 SLC32A1 HGNC HGNC:11018 protein_coding YES CCDS13307.1 ENSP00000217420 Q9H598 UPI0000043423 NM_080552.2 2/2 Pfam_domain:PF01490,hmmpanther:PTHR22950,hmmpanther:PTHR22950:SF221,Transmembrane_helices:TMhelix LOW 1 SNV 1 1 PASS rs150170740 . 0 210 0 0 0 0 0 0 -20 1 1 1 1 0 T 2 4 108 38727718 38727718 C T 1 0 0 0 0 0 0 0 1 14835 845 30 3 3 SLC32A1 20 38727718 Silent SNP C C3N-02729_T 38727718 25716449 28 30188